#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
OR13C5	138799	hgsc.bcm.edu	37	9	107360769	107360769	+	Frame_Shift_Del	DEL	T	T	-	rs78341003|rs11314210	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107360769delT	ENST00000374779.2	-	1	1019	c.926delA	c.(925-927)cacfs	p.H309fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						TCTCAGTAGGTGTTTTACTGC	0.323													T|T|-|deletion	2184	0.436102	0.6475	0.2277	5008	,	,		19983	0.5754		0.1789	False		,,,				2504	0.4192				p.H309fs		Pindel,Atlas-Indel	.											.	OR13C5	60	.	0			c.927delC						PASS	.			2496,1768		742,1012,378	57.0	85.0	77.0			-8.0	0.0	9	dbSNP_120	94	1603,6651		175,1253,2699	no	frameshift	OR13C5	NM_001004482.1		917,2265,3077	A1A1,A1R,RR		19.4209,41.4634,32.7448			107360769	4099,8419	1566	4154	5720	SO:0001589	frameshift_variant	138799	exon1			.		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.926delA	9.37:g.107360769delT	ENSP00000363911:p.His309fs	Somatic	156	.	.		WXS	Illumina HiSeq	Phase_I	145	44	0.303	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	CCDS35091.1																																																																																			T|0.620;-|0.380	0.380	strong		0.323	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
IGSF3	3321	hgsc.bcm.edu	37	1	117122288	117122289	+	In_Frame_Ins	INS	-	-	TCCTCC	rs56982445|rs647711	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:117122288_117122289insTCCTCC	ENST00000369486.3	-	10	3824_3825	c.3059_3060insGGAGGA	c.(3058-3060)gac>gaGGAGGAc	p.1019_1020insEE	IGSF3_ENST00000369483.1_In_Frame_Ins_p.1039_1040insEE|IGSF3_ENST00000318837.6_In_Frame_Ins_p.1039_1040insEE	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1019	Ig-like C2-type 8.		D -> E (in dbSNP:rs647711). {ECO:0000269|PubMed:9790749}.		lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)				NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		cgtcgtcgtcgtcctcctcctc	0.634																																					p.D1040delinsEED		Atlas-Indel	.											IGSF3_ENST00000369483,caecum,carcinoma,0,2	IGSF3	294	2	0			c.3120_3121insGGAGGA						PASS	.																																			SO:0001652	inframe_insertion	3321	exon11			.	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3054_3059dupGGAGGA	1.37:g.117122289_117122294dupTCCTCC	ENSP00000358498:p.Glu1018_Glu1019dup	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	105	30	0.285714	NM_001542	A6NJZ6|A6NMC7	In_Frame_Ins	INS	ENST00000369486.3	37	CCDS30813.1																																																																																			.	.	none		0.634	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
EPSTI1	94240	hgsc.bcm.edu	37	13	43462434	43462435	+	IGR	INS	-	-	TCAGG	rs397971974|rs61389340|rs76888419|rs375469696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:43462434_43462435insTCAGG	ENST00000398762.3	-	0	957				EPSTI1_ENST00000313640.7_Frame_Shift_Ins_p.E395fs|EPSTI1_ENST00000313624.7_3'UTR			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)									p.E395D(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|skin(1)	17		Lung NSC(96;3.6e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000528)|BRCA - Breast invasive adenocarcinoma(63;0.0858)		TAAATATGAGTTCAGGAATCAG	0.406														631	0.125998	0.1914	0.0605	5008	,	,		17089	0.1597		0.0348	False		,,,				2504	0.1431				p.E395fs		Pindel,Atlas-Indel	.											EPSTI1,NS,carcinoma,0,1	EPSTI1	47	1	1	Substitution - Missense(1)	kidney(1)	c.1185_1186insCCTGA						PASS	.		,	657,3605		44,569,1518					,	-0.9	0.0		dbSNP_132	43	215,8037		4,207,3915	no	utr-3,frameshift	EPSTI1	NM_033255.2,NM_001002264.1	,	48,776,5433	A1A1,A1R,RR		2.6054,15.4153,6.9682	,	,		872,11642				SO:0001628	intergenic_variant	94240	exon13			.	AF396928	CCDS9387.1, CCDS31964.1	13q13.3	2011-06-27			ENSG00000133106	ENSG00000133106			16465	protein-coding gene	gene with protein product	"""epithelial stromal interaction protein 1"""	607441				11991720	Standard	NM_033255		Approved	BRESI1, MGC29634	uc001uyw.2	Q96J88	OTTHUMG00000016814		13.37:g.43462435_43462439dupTCAGG		Somatic	172	.	.		WXS	Illumina HiSeq	Phase_I	205	63	0.307	NM_001002264	Q8IVC7|Q8NDQ7	Frame_Shift_Ins	INS	ENST00000398762.3	37	CCDS9387.1																																																																																			-|0.890;TCAGG|0.110	0.110	strong		0.406	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264	
OR2B11	127623	hgsc.bcm.edu	37	1	247615262	247615262	+	Frame_Shift_Del	DEL	A	A	-	rs35305980|rs397733455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:247615262delA	ENST00000318749.6	-	1	46	c.23delT	c.(22-24)ttcfs	p.F8fs		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(13)|large_intestine(7)|lung(31)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	60	all_cancers(71;4.51e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.241)	OV - Ovarian serous cystadenocarcinoma(106;0.0188)			GTCCCCTAAGAAGCTATGGTT	0.473													AA|AA|A|deletion	2249	0.449081	0.2852	0.5274	5008	,	,		21865	0.4762		0.4563	False		,,,				2504	0.5798				p.F8fs		Pindel,Atlas-Indel	.											.	OR2B11	102	.	0			c.24delC						PASS	.			1318,2948		196,926,1011	74.0	72.0	73.0			0.0	0.0	1	dbSNP_131	112	3624,4628		809,2006,1311	no	frameshift	OR2B11	NM_001004492.1		1005,2932,2322	A1A1,A1R,RR		43.9166,30.8955,39.4792			247615262	4942,7576	2167	4183	6350	SO:0001589	frameshift_variant	127623	exon1			.		CCDS31090.1	1q44	2012-08-09			ENSG00000177535	ENSG00000177535		"""GPCR / Class A : Olfactory receptors"""	31249	protein-coding gene	gene with protein product							Standard	NM_001004492		Approved		uc010pyx.2	Q5JQS5	OTTHUMG00000040572	ENST00000318749.6:c.23delT	1.37:g.247615262delA	ENSP00000325682:p.Phe8fs	Somatic	99	.	.		WXS	Illumina HiSeq	Phase_I	96	26	0.271	NM_001004492	B2RP03	Frame_Shift_Del	DEL	ENST00000318749.6	37	CCDS31090.1																																																																																			A|0.570;-|0.430	0.430	strong		0.473	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388504	1388505	+	Frame_Shift_Del	DEL	CG	CG	-	rs568118449|rs528384190|rs115485610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388504_1388505delCG	ENST00000324803.4	+	1	3165_3166	c.205_206delCG	c.(205-207)cgtfs	p.R69fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	69					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGCTCACACACGTGTCCATGTG	0.629														54	0.0107827	0.0174	0.0043	5008	,	,		20699	0.002		0.0169	False		,,,				2504	0.0092				p.68_69del		Atlas-Indel	.											.	CRIPAK	185	.	0			c.204_205del						PASS	.																																			SO:0001589	frameshift_variant	285464	exon1			.	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.205_206delCG	4.37:g.1388504_1388505delCG	ENSP00000323978:p.Arg69fs	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	182	14	0.0769231	NM_175918	Q8NB03	Frame_Shift_Del	DEL	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.629	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
TP53TG5	27296	hgsc.bcm.edu	37	20	44004156	44004158	+	In_Frame_Del	DEL	ATT	ATT	-	rs562359566|rs76663890|rs10546815	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ATT	ATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:44004156_44004158delATT	ENST00000372726.3	-	4	445_447	c.289_291delAAT	c.(289-291)aatdel	p.N97del	TP53TG5_ENST00000537995.1_In_Frame_Del_p.N81del|SYS1-DBNDD2_ENST00000452133.1_Intron|SYS1-DBNDD2_ENST00000475242.1_Intron|TP53TG5_ENST00000494455.1_5'UTR|SYS1_ENST00000426004.1_3'UTR	NM_014477.2	NP_055292.1	Q9Y2B4	T53G5_HUMAN	TP53 target 5	97					intracellular signal transduction (GO:0035556)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	12						GGAACTCTTCATTATTTTGTTTT	0.493														1936	0.386581	0.1914	0.4452	5008	,	,		18977	0.255		0.659	False		,,,				2504	0.4642				p.97_98del		Pindel,Atlas-Indel	.											.	TP53TG5	36	.	0			c.290_292del						PASS	.		,	1076,3182		141,794,1194					,	-3.1	0.0		dbSNP_119	93	5309,2943		1723,1863,540	no	coding,utr-3	TP53TG5,SYS1	NM_014477.2,NM_001099791.2	,	1864,2657,1734	A1A1,A1R,RR		35.6641,25.2701,48.9608	,	,		6385,6125				SO:0001651	inframe_deletion	27296	exon4			.	AB017802	CCDS13352.1	20q13.12	2008-09-18	2008-09-18	2008-09-18	ENSG00000124251	ENSG00000124251			15856	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 10"""	C20orf10			Standard	NM_014477		Approved	CLG01, dJ453C12.5	uc002xny.3	Q9Y2B4	OTTHUMG00000032582	ENST00000372726.3:c.289_291delAAT	20.37:g.44004159_44004161delATT	ENSP00000361811:p.Asn97del	Somatic	65	.	.		WXS	Illumina HiSeq	Phase_I	55	20	0.364	NM_014477		In_Frame_Del	DEL	ENST00000372726.3	37	CCDS13352.1																																																																																			ATT|0.574;-|0.426	0.426	strong		0.493	TP53TG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079460.1	NM_014477	
ANP32E	81611	hgsc.bcm.edu	37	1	150199040	150199045	+	In_Frame_Del	DEL	TCCTCT	TCCTCT	-	rs56692627|rs28594165|rs68136184|rs28460085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TCCTCT	TCCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:150199040_150199045delTCCTCT	ENST00000314136.8	-	5	945_950	c.576_581delAGAGGA	c.(574-582)gaagaggag>gag	p.192_194EEE>E	ANP32E_ENST00000436748.2_In_Frame_Del_p.151_153EEE>E|ANP32E_ENST00000369119.3_In_Frame_Del_p.144_146EEE>E|ANP32E_ENST00000369116.4_In_Frame_Del_p.60_62EEE>E|ANP32E_ENST00000533654.1_In_Frame_Del_p.KR137del|ANP32E_ENST00000369114.5_Intron|ANP32E_ENST00000369115.2_In_Frame_Del_p.60_62EEE>E	NM_001136478.2|NM_001280559.1|NM_030920.3	NP_001129950.1|NP_001267488.1|NP_112182.1	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	192	Asp/Glu-rich (highly acidic).				histone exchange (GO:0043486)|negative regulation of catalytic activity (GO:0043086)	cytoplasmic membrane-bounded vesicle (GO:0016023)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	histone binding (GO:0042393)|phosphatase inhibitor activity (GO:0019212)			breast(3)|endometrium(3)|lung(7)|skin(1)|urinary_tract(1)	15	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			atcctcatcctcctcttcctcttcct	0.437														1756	0.350639	0.1596	0.3559	5008	,	,		19419	0.5446		0.2753	False		,,,				2504	0.4826				p.193_194del		Pindel,Atlas-Indel	.											.	ANP32E	28	.	0			c.577_582del						PASS	.		,,	627,3639		79,469,1585					,,	-6.5	0.0		dbSNP_130	261	1908,6340		294,1320,2510	no	coding,coding,coding	ANP32E	NM_030920.3,NM_001136479.1,NM_001136478.2	,,	373,1789,4095	A1A1,A1R,RR		23.1329,14.6976,20.2573	,,	,,		2535,9979				SO:0001651	inframe_deletion	81611	exon5			.	AK092672	CCDS946.1, CCDS44214.1, CCDS44215.1, CCDS60245.1	1q22	2008-02-05			ENSG00000143401	ENSG00000143401		"""ANP32 acidic nuclear phosphoproteins"""	16673	protein-coding gene	gene with protein product		609611				12438741	Standard	NM_030920		Approved	LANPL, MGC5350, LANP-L	uc001etw.3	Q9BTT0	OTTHUMG00000012547	ENST00000314136.8:c.576_581delAGAGGA	1.37:g.150199046_150199051delTCCTCT	ENSP00000324074:p.Glu192_Glu193del	Somatic	118	.	.		WXS	Illumina HiSeq	Phase_I	107	45	0.421	NM_030920	B4E0I6|E9PEA6|Q5TB18|Q5TB20|Q8N1S4|Q8WWW9	In_Frame_Del	DEL	ENST00000314136.8	37	CCDS946.1																																																																																			TCCTCT|0.685;-|0.315	0.315	strong		0.437	ANP32E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035056.1	NM_030920	
ATG2B	55102	hgsc.bcm.edu	37	14	96790337	96790338	+	Splice_Site	INS	-	-	A	rs74857333|rs34296665|rs397948209	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:96790337_96790338insA	ENST00000359933.4	-	16	3331		c.e16-2		snoU13_ENST00000458931.1_RNA	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B						autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GGAACGATCCTAAAAAAAAAGA	0.386													AAAAAAAAAA|AAAAAAAAA|AAAAAAAAAA|deletion	1785	0.35643	0.4902	0.2291	5008	,	,		17409	0.3472		0.3002	False		,,,				2504	0.3333				.		Pindel,Atlas-Indel	.											.	ATG2B	169	.	0			c.2438-2->T						PASS	.			1613,1945		375,863,541						5.3	1.0		dbSNP_126	66	2130,5696		281,1568,2064	no	splice-3	ATG2B	NM_018036.5		656,2431,2605	A1A1,A1R,RR		27.217,45.3345,32.8795				3743,7641				SO:0001630	splice_region_variant	55102	exon17			.	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.2438-2->T	14.37:g.96790346_96790346dupA		Somatic	24	.	.		WXS	Illumina HiSeq	Phase_I	27	10	0.370	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Splice_Site	INS	ENST00000359933.4	37	CCDS9944.2																																																																																			-|0.648;A|0.352	0.352	strong		0.386	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	Intron
CDR1	1038	hgsc.bcm.edu	37	X	139866424	139866441	+	In_Frame_Del	DEL	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:139866424_139866441delGTCTTCCAACAAAGGTAC	ENST00000370532.2	-	1	282_299	c.91_108delGTACCTTTGTTGGAAGAC	c.(91-108)gtacctttgttggaagacdel	p.VPLLED31del		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	31	23 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				GCCTACTTGTGTCTTCCAACAAAGGTACGTCTTCCAAC	0.44																																					p.31_37del		Atlas-Indel	.											.	CDR1	58	.	0			c.92_109del						PASS	.			205,3516		5,155,40,1432,497						-2.7	0.0			152	40,6440		8,5,19,2342,1751	no	coding	CDR1	NM_004065.2		13,160,59,3774,2248	A1A1,A1R,A1,RR,R		0.6173,5.5093,2.4017				245,9956				SO:0001651	inframe_deletion	1038	exon1			.		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"""Cerebellar degeneration-related protein-1 (34kD)"""	302650	"""cerebellar degeneration-related protein (34kD)"""	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.91_108delGTACCTTTGTTGGAAGAC	X.37:g.139866424_139866441delGTCTTCCAACAAAGGTAC	ENSP00000359563:p.Val31_Asp36del	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	195	104	0.533333	NM_004065	Q5JXH6	In_Frame_Del	DEL	ENST00000370532.2	37	CCDS14670.1																																																																																			.	.	none		0.440	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065	
SLC22A1	6580	hgsc.bcm.edu	37	6	160560898	160560905	+	Splice_Site	DEL	TGGTAAGT	TGGTAAGT	-	rs36056065|rs35854239|rs200234072|rs77297078|rs113569197	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGGTAAGT	TGGTAAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:160560898_160560905delTGGTAAGT	ENST00000366963.4	+	7	1422_1423	c.1275_1276delTGGTAAGT	c.(1273-1278)cctggt>ccgt	p.G426fs	SLC22A1_ENST00000324965.4_Splice_Site_p.G426fs|SLC22A1_ENST00000457470.2_Splice_Site_p.G426fs	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	426					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	TTATCTCACCTGGTAAGTTGGTAAGTTG	0.495														3453	0.689497	0.7413	0.7839	5008	,	,		15006	0.7411		0.5825	False		,,,				2504	0.6094				p.425_426del		Pindel,Atlas-Indel	.											.	SLC22A1	69	.	0			c.1274_1276del						PASS	.																																			SO:0001630	splice_region_variant	6580	exon7			.	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"""Solute carriers"""	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.1276+1TGGTAAGT>-	6.37:g.160560906_160560913delTGGTAAGT		Somatic	52	.	.		WXS	Illumina HiSeq	Phase_I	23	17	0.739	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	In_Frame_Del	DEL	ENST00000366963.4	37	CCDS5274.1																																																																																			TGGTAAGT|0.311;-|0.689	0.689	strong		0.495	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		Frame_Shift_Del
KIAA0040	9674	hgsc.bcm.edu	37	1	175129946	175129946	+	Frame_Shift_Del	DEL	C	C	-	rs386636937|rs542219168|rs71563271|rs2072035	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:175129946delC	ENST00000423313.1	-	4	740	c.204delG	c.(202-204)aagfs	p.K75fs	KIAA0040_ENST00000444639.1_Frame_Shift_Del_p.K75fs|KIAA0040_ENST00000545251.2_Frame_Shift_Del_p.K75fs|KIAA0040_ENST00000567124.1_5'Flank	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tcttcttcttcttcttcttgt	0.498																																					p.K69fs		Atlas-Indel	.											.	KIAA0040	2	.	0			c.205delA						PASS	.						82.0	69.0	73.0					1																	175129946		692	1591	2283	SO:0001589	frameshift_variant	9674	exon5			.	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.204delG	1.37:g.175129946delC	ENSP00000462172:p.Lys75fs	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	96	14	0.145833	NM_001162893	A8K9H6|Q2NKQ0	Frame_Shift_Del	DEL	ENST00000423313.1	37																																																																																				-|1.000	.	weak		0.498	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361452	+	Frame_Shift_Del	DEL	GC	GC	-	rs376107801|rs201540433|rs377523807|rs199665292	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107361451_107361452delGC	ENST00000374779.2	-	1	336_337	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAGCTCACTAGCGTGGAGGGAA	0.51																																					p.82_82del		Atlas-Indel	.											.	OR13C5	60	.	0			c.244_245del						PASS	.																																			SO:0001589	frameshift_variant	138799	exon1			.		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243_244delGC	9.37:g.107361451_107361452delGC	ENSP00000363911:p.Leu82fs	Somatic	600	0	0		WXS	Illumina HiSeq	Phase_I	455	70	0.153846	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Frame_Shift_Del	DEL	ENST00000374779.2	37	CCDS35091.1																																																																																			GC|0.500;-|0.500	0.500	strong		0.510	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
GNRH2	2797	hgsc.bcm.edu	37	20	3026345	3026346	+	Frame_Shift_Ins	INS	-	-	GCCCC	rs544846287|rs67749149|rs16996832|rs377041343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3026345_3026346insGCCCC	ENST00000245983.2	+	4	377_378	c.326_327insGCCCC	c.(325-330)gagcccfs	p.-111fs	MRPS26_ENST00000380325.3_5'Flank|GNRH2_ENST00000359100.2_Frame_Shift_Ins_p.-104fs|GNRH2_ENST00000380346.2_Frame_Shift_Ins_p.-103fs|GNRH2_ENST00000359987.1_Frame_Shift_Ins_p.-103fs|GNRH2_ENST00000380347.2_Frame_Shift_Ins_p.-104fs	NM_001501.1	NP_001492.1	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2						multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			ovary(1)|upper_aerodigestive_tract(1)	2						GCAGCCCGAGAGCCCCGCCCCG	0.634														729	0.145567	0.0295	0.1571	5008	,	,		10164	0.2391		0.1014	False		,,,				2504	0.2434				p.E109fs		Pindel,Atlas-Indel	.											.	GNRH2	15	.	0			c.326_327insGCCCC						PASS	.																																			SO:0001589	frameshift_variant	2797	exon4			.	AF036329	CCDS13040.1, CCDS13041.1, CCDS13042.1	20p13	2013-02-26			ENSG00000125787	ENSG00000125787		"""Endogenous ligands"""	4420	protein-coding gene	gene with protein product		602352				9419371, 12447356	Standard	NM_178331		Approved		uc002whr.1	O43555	OTTHUMG00000031723	ENST00000245983.2:c.337_341dupGCCCC	20.37:g.3026351_3026355dupGCCCC	ENSP00000245983:p.Arg111fs	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	77	23	0.299	NM_001501	Q14C68|Q14C69|Q9BYN9|Q9BYP0	Frame_Shift_Ins	INS	ENST00000245983.2	37	CCDS13040.1																																																																																			-|0.814;GCCCC|0.186	0.186	strong		0.634	GNRH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077694.2	NM_001501	
HERC4	26091	hgsc.bcm.edu	37	10	69785435	69785436	+	Splice_Site	INS	-	-	A	rs397840935|rs3834396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:69785435_69785436insA	ENST00000395198.3	-	8	1025		c.e8-2		HERC4_ENST00000395187.2_Splice_Site|HERC4_ENST00000373700.4_Splice_Site|HERC4_ENST00000412272.2_Splice_Site|HERC4_ENST00000277817.6_Splice_Site	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4						cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.?(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						TCCACCTTCCTAAAAAAAGACA	0.342													?|AAAAAAA|AAAAAAAA|unsure	984	0.196486	0.1876	0.1744	5008	,	,		18753	0.3889		0.0855	False		,,,				2504	0.1401				.		Pindel,Atlas-Indel	.											.	HERC4	78	.	1	Unknown(1)	pancreas(1)	c.778-2->T						PASS	.		,	756,3508		72,612,1448					,	5.2	1.0		dbSNP_130	89	542,7712		17,508,3602	no	splice-3,splice-3	HERC4	NM_022079.2,NM_015601.3	,	89,1120,5050	A1A1,A1R,RR		6.5665,17.7298,10.3691	,	,		1298,11220				SO:0001630	splice_region_variant	26091	exon9			.	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.778-2->T	10.37:g.69785442_69785442dupA		Somatic	71	.	.		WXS	Illumina HiSeq	Phase_I	67	20	0.299	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Splice_Site	INS	ENST00000395198.3	37	CCDS41533.1																																																																																			-|0.798;A|0.202	0.202	strong		0.342	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	Intron
VEZF1	7716	hgsc.bcm.edu	37	17	56056604	56056605	+	In_Frame_Ins	INS	-	-	TGC	rs61731354|rs57786397|rs138088904|rs369163670	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56056604_56056605insTGC	ENST00000581208.1	-	5	1086_1087	c.1046_1047insGCA	c.(1045-1047)caa>caGCAa	p.349_349Q>QQ	VEZF1_ENST00000584396.1_In_Frame_Ins_p.340_340Q>QQ	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	349	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						gttgttgttgttgctgctgctg	0.465																																					p.Q349delinsQQ		Atlas-Indel	.											VEZF1,colon,carcinoma,0,2	VEZF1	50	2	0			c.1047_1048insGCA						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.1044_1046dupGCA	17.37:g.56056611_56056613dupTGC	ENSP00000462337:p.Gln354dup	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	171	25	0.146199	NM_007146		In_Frame_Ins	INS	ENST00000581208.1	37	CCDS32687.1																																																																																			.	.	weak		0.465	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
FOXD4L2	100036519	hgsc.bcm.edu	37	9	42719280	42719280	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:42719280delC	ENST00000377590.1	+	1	2047	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_001099279.1	NP_001092749.1	Q6VB85	FX4L2_HUMAN	forkhead box D4-like 2	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.W406fs*>11(1)		haematopoietic_and_lymphoid_tissue(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		GGGCGCGGTGCTGGGCGGGCA	0.677																																					p.C405fs		Atlas-Indel	.											.	FOXD4L4	5	.	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.1214delG						PASS	.																																			SO:0001589	frameshift_variant	349334	exon1			.			9p12	2008-07-21			ENSG00000204828				24813	protein-coding gene	gene with protein product						12421752	Standard			Approved	OTTHUMG00000066752	uc004acn.3	Q6VB85	OTTHUMG00000066752	ENST00000377590.1:c.1215delC	9.37:g.42719280delC	ENSP00000366814:p.Cys405fs	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	286	55	0.192308	NM_199244		Frame_Shift_Del	DEL	ENST00000377590.1	37	CCDS43817.1																																																																																			.	.	weak		0.677	FOXD4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143077.1	NM_001099279	
MIR509-1	574514	hgsc.bcm.edu	37	X	146340339	146340339	+	RNA	DEL	T	T	-	rs36092315		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:146340339delT	ENST00000385265.1	-	0	94				MIR509-3_ENST00000390725.1_RNA|MIR509-2_ENST00000390724.1_RNA	NR_030236.1|NR_030586.1				microRNA 509-1																		TGATTGCCACTGTCTGCAGTA	0.438																																					.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.						82.0	78.0	79.0					X																	146340339		1403	3211	4614			574514	.			.			Xq27.3	2011-09-12	2007-10-23	2008-12-18	ENSG00000208000	ENSG00000208000		"""ncRNAs / Micro RNAs"""	32146	non-coding RNA	RNA, micro		300875	"""microRNA 509"""	MIRN509, MIRN509-1			Standard	NR_030236		Approved	hsa-mir-509, hsa-mir-509-1	uc022cfy.1				X.37:g.146340339delT		Somatic	395	.	.		WXS	Illumina HiSeq	Phase_I	105	52	0.495	.		RNA	DEL	ENST00000385265.1	37																																																																																				T|0.937;-|0.063	0.063	strong		0.438	MIR509-1-201	KNOWN	basic	miRNA	miRNA		NR_030236	
GNLY	10578	hgsc.bcm.edu	37	2	85922121	85922122	+	Intron	INS	-	-	A	rs113717357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:85922121_85922122insA	ENST00000263863.4	+	2	180				GNLY_ENST00000533041.1_Splice_Site|GNLY_ENST00000524600.1_Splice_Site|GNLY_ENST00000409696.3_Splice_Site	NM_006433.3	NP_006424.2	P22749	GNLY_HUMAN	granulysin						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						GGATGGAAGGTAAAAAAAGAAA	0.52													AAAAAAA|AAAAAAA|AAAAAAAA|insertion	1149	0.229433	0.6172	0.098	5008	,	,		20731	0.0337		0.0765	False		,,,				2504	0.1575				.		Atlas-Indel	.											.	GNLY	29	.	0			c.7+2->A						PASS	.		,	2025,1655		575,875,390					,	-1.7	0.0		dbSNP_132	60	669,7245		29,611,3317	no	splice-5,intron	GNLY	NM_012483.2,NM_006433.3	,	604,1486,3707	A1A1,A1R,RR		8.4534,44.9728,23.2362	,	,		2694,8900				SO:0001627	intron_variant	10578	exon2			.	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.53-321->A	2.37:g.85922128_85922128dupA		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_012483	P09325|Q6GU08	Splice_Site	INS	ENST00000263863.4	37	CCDS1984.1																																																																																			-|0.808;A|0.192	0.192	strong		0.520	GNLY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252497.1	NM_006433	
NINL	22981	hgsc.bcm.edu	37	20	25457050	25457055	+	In_Frame_Del	DEL	CTCCCA	CTCCCA	-	rs68078266|rs146288604|rs200097181|rs34410422|rs201074890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTCCCA	CTCCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25457050_25457055delCTCCCA	ENST00000278886.6	-	17	2945_2950	c.2872_2877delTGGGAG	c.(2872-2877)tgggagdel	p.WE958del	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	958				Missing (in Ref. 4; AAH36380). {ECO:0000305}.	G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						TCAGGGGTGGCTCCCACATCCGTGGC	0.689														2791	0.557308	0.5356	0.3559	5008	,	,		14584	0.9067		0.4304	False		,,,				2504	0.5				p.958_960del		Pindel,Atlas-Indel	.											.	NINL	148	.	0			c.2873_2878del						PASS	.			1921,2191		513,895,648						0.3	0.0		dbSNP_130	17	3184,4816		750,1684,1566	no	coding	NINL	NM_025176.4		1263,2579,2214	A1A1,A1R,RR		39.8,46.7169,42.1483				5105,7007				SO:0001651	inframe_deletion	22981	exon17			.		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2872_2877delTGGGAG	20.37:g.25457050_25457055delCTCCCA	ENSP00000278886:p.Trp958_Glu959del	Somatic	73	.	.		WXS	Illumina HiSeq	Phase_I	73	16	0.219	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	In_Frame_Del	DEL	ENST00000278886.6	37	CCDS33452.1																																																																																			CTCCCA|0.450;-|0.550	0.550	strong		0.689	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
FOXD4L5	653427	hgsc.bcm.edu	37	9	70176769	70176769	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:70176769delG	ENST00000377420.1	-	1	2046	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_001126334.1	NP_001119806.1	Q5VV16	FX4L5_HUMAN	forkhead box D4-like 5	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|lung(2)	7						TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W406fs		Pindel,Atlas-Indel	.											.	FOXD4L5	27	.	0			c.1216delT						PASS	.			10,4		5,0,2	0.0	1.0	1.0			1.1	0.1	9		1	16,8		8,0,4	no	frameshift	FOXD4L5	NM_001126334.1		13,0,6	A1A1,A1R,RR		33.3333,28.5714,31.5789			70176769	26,12	0	3	3	SO:0001589	frameshift_variant	653427	exon1			.		CCDS47977.1	9q13	2008-07-21			ENSG00000204779	ENSG00000204779			18522	protein-coding gene	gene with protein product						12234674	Standard	NM_001126334		Approved	bA15J10.2, OTTHUMG00000013332	uc010moc.3	Q5VV16	OTTHUMG00000013332	ENST00000377420.1:c.1215delC	9.37:g.70176769delG	ENSP00000366637:p.Cys405fs	Somatic	206	.	.		WXS	Illumina HiSeq	Phase_I	339	58	0.171	NM_001126334		Frame_Shift_Del	DEL	ENST00000377420.1	37	CCDS47977.1																																																																																			.	.	weak		0.677	FOXD4L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037122.1	NM_001126334	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140772899	140772899	+	Frame_Shift_Del	DEL	C	C	-	rs397780331|rs3214276	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140772899delC	ENST00000398604.2	+	1	519	c.519delC	c.(517-519)agcfs	p.S173fs	PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	173	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCAGCTCAGCCCCAATCACC	0.572													|||unknown(NO_COVERAGE)	639	0.127596	0.1747	0.1513	5008	,	,		17007	0.1181		0.0586	False		,,,				2504	0.1278				p.S173fs		Pindel,Atlas-Indel	.											.	PCDHGA8	146	.	0			c.518delG						PASS	.		,,,,,,,,,,,,	743,3289		100,543,1373	50.0	60.0	56.0		,,,,,,,,,,,,	2.5	1.0	5	dbSNP_106	62	639,7495		39,561,3467	yes	frameshift,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,frameshift,intron	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_032088.1,NM_018924.2,NM_018923.2,NM_018922.2,NM_018920.2,NM_018919.2,NM_018918.2,NM_018917.2,NM_018916.3,NM_018915.2,NM_018912.2,NM_014004.2,NM_003736.2	,,,,,,,,,,,,	139,1104,4840	A1A1,A1R,RR		7.8559,18.4276,11.3595	,,,,,,,,,,,,	,,,,,,,,,,,,	140772899	1382,10784	2064	4239	6303	SO:0001589	frameshift_variant	9708	exon1			.	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.519delC	5.37:g.140772899delC	ENSP00000381605:p.Ser173fs	Somatic	111	.	.		WXS	Illumina HiSeq	Phase_I	118	77	0.653	NM_014004	A7MCZ4|O15039	Frame_Shift_Del	DEL	ENST00000398604.2	37	CCDS47291.1																																																																																			C|0.882;-|0.118	0.118	strong		0.572	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803308	43803309	+	Splice_Site	INS	-	-	TA	rs34966432|rs56283966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43803308_43803309insTA	ENST00000291532.3	-	8	1572		c.e8-1		TMPRSS3_ENST00000474596.1_Splice_Site|TMPRSS3_ENST00000398397.3_Splice_Site|TMPRSS3_ENST00000398405.1_Splice_Site|TMPRSS3_ENST00000380399.1_Splice_Site|TMPRSS3_ENST00000433957.2_Splice_Site	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3						cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)	p.?(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TGACCACAGGCTATGGAGGGGA	0.599														870	0.173722	0.118	0.0865	5008	,	,		22290	0.3145		0.0865	False		,,,				2504	0.2556				.		Pindel,Atlas-Indel	.											TMPRSS3,NS,carcinoma,0,2	TMPRSS3	40	2	2	Unknown(2)	ovary(2)	c.617-1->TA						PASS	.		,	532,3732		34,464,1634				http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,	4.8	0.9		dbSNP_129	68	605,7649		19,567,3541	no	splice-3,splice-3	TMPRSS3	NM_032405.1,NM_024022.2	,	53,1031,5175	A1A1,A1R,RR		7.3298,12.4765,9.0829	,	,		1137,11381				SO:0001630	splice_region_variant	64699	exon9			.	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.617-1->TA	21.37:g.43803309_43803310dupTA		Somatic	45	.	.		WXS	Illumina HiSeq	Phase_I	64	15	0.234	NM_024022	D3DSJ6|Q5USC7|Q6ZMC3	Splice_Site	INS	ENST00000291532.3	37	CCDS13686.1																																																																																			-|0.840;TA|0.160	0.160	strong		0.599	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		Intron
FAM83G	644815	hgsc.bcm.edu	37	17	18874685	18874686	+	In_Frame_Ins	INS	-	-	GGT	rs3071666|rs75294421|rs538676818|rs36060906	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18874685_18874686insGGT	ENST00000388995.6	-	6	2681_2682	c.2458_2459insACC	c.(2458-2460)cgc>cACCgc	p.819_820insH	SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000585154.2_In_Frame_Ins_p.819_820insH|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_In_Frame_Ins_p.819_820insH|SLC5A10_ENST00000395643.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	819					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						GGGGTCTTTGCGGTCCCGGGGG	0.634														3264	0.651757	0.674	0.6801	5008	,	,		17224	0.6349		0.5865	False		,,,				2504	0.6861				p.R820delinsHR		Pindel,Atlas-Indel	.											.	FAM83G	51	.	0			c.2459_2460insACC						PASS	.		,,	2729,1459		927,875,292					,,	-11.1	0.0		dbSNP_102	49	4619,3535		1344,1931,802	no	intron,intron,coding	SLC5A10,FAM83G	NM_152351.3,NM_001042450.1,NM_001039999.2	,,	2271,2806,1094	A1A1,A1R,RR		43.353,34.8376,40.4635	,,	,,		7348,4994				SO:0001652	inframe_insertion	644815	exon6			.	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.2456_2458dupACC	17.37:g.18874686_18874688dupGGT	ENSP00000373647:p.Asp819_Arg820insHis	Somatic	66	.	.		WXS	Illumina HiSeq	Phase_I	54	33	0.611	NM_001039999	Q3KQZ4|Q6ZW60	In_Frame_Ins	INS	ENST00000388995.6	37	CCDS42276.1																																																																																			-|0.250;GGT|0.750	0.750	strong		0.634	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970760	45970774	+	In_Frame_Del	DEL	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	-	rs113146284|rs371219783|rs200215960|rs67692969|rs76536096|rs76021731|rs71199610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTTGCAGCAGACAGG	CTTGCAGCAGACAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45970760_45970774delCTTGCAGCAGACAGG	ENST00000391621.1	-	1	614_628	c.568_582delCCTGTCTGCTGCAAG	c.(568-582)cctgtctgctgcaagdel	p.PVCCK190del	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						AGCAGATGGACTTGCAGCAGACAGGCTTGCAGCAG	0.609														1066	0.212859	0.1664	0.1513	5008	,	,		23256	0.3661		0.2058	False		,,,				2504	0.1687				p.190_195del		Pindel,Atlas-Indel	.											.	KRTAP10-2	21	.	0			c.569_583del						PASS	.		,	649,3615		35,579,1518					,	0.6	0.0		dbSNP_130	134	1460,6792		93,1274,2759	no	coding,intron	TSPEAR,KRTAP10-2	NM_198693.2,NM_144991.2	,	128,1853,4277	A1A1,A1R,RR		17.6927,15.2205,16.8504	,	,		2109,10407				SO:0001651	inframe_deletion	386679	exon1			.	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.568_582delCCTGTCTGCTGCAAG	21.37:g.45970760_45970774delCTTGCAGCAGACAGG	ENSP00000375479:p.Pro190_Lys194del	Somatic	155	.	.		WXS	Illumina HiSeq	Phase_I	98	15	0.153	NM_198693	Q70LJ5	In_Frame_Del	DEL	ENST00000391621.1	37	CCDS42955.1																																																																																			CTTGCAGCAGACAGG|0.758;-|0.242	0.242	strong		0.609	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
KMT2D	8085	hgsc.bcm.edu	37	12	49444214	49444214	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49444214delA	ENST00000301067.7	-	11	3156	c.3157delT	c.(3157-3159)tccfs	p.S1053fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1053	Pro-rich.				chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CTCAACGGGGAGGGAACGGAC	0.572																																					p.S1053fs		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.3158delC						PASS	.						49.0	55.0	53.0					12																	49444214		2068	4208	6276	SO:0001589	frameshift_variant	8085	exon11			.	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.3157delT	12.37:g.49444214delA	ENSP00000301067:p.Ser1053fs	Somatic	214	.	.		WXS	Illumina HiSeq	Phase_I	193	47	0.244	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.572	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
FERD3L	222894	hgsc.bcm.edu	37	7	19184746	19184747	+	In_Frame_Ins	INS	-	-	TCT	rs34966908|rs199985178|rs71017023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:19184746_19184747insTCT	ENST00000275461.3	-	1	297_298	c.239_240insAGA	c.(238-240)gag>gaAGAg	p.80_80E>EE	AC003986.5_ENST00000452700.1_RNA	NM_152898.2	NP_690862.1	Q96RJ6	FER3L_HUMAN	Fer3-like bHLH transcription factor	80	Poly-Glu.				cell development (GO:0048468)|floor plate development (GO:0033504)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurogenesis (GO:0050767)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E81_R82insE(1)		breast(1)|endometrium(4)|large_intestine(8)|lung(16)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	35						ttccgcgctcctcttcctcctc	0.624														836	0.166933	0.0446	0.1643	5008	,	,		17679	0.1587		0.2654	False		,,,				2504	0.2413				p.E80delinsEE		Pindel,Atlas-Indel	.											.	FERD3L	63	.	1	Insertion - In frame(1)	ovary(1)	c.240_241insAGA						PASS	.			307,0,3957		13,0,281,0,0,1838						0.6	0.7		dbSNP_134	60	2211,1,6042		291,0,1629,0,1,2206	no	codingComplex	FERD3L	NM_152898.2		304,0,1910,0,1,4044	A1A1,A1A2,A1R,A2A2,A2R,RR		26.7991,7.1998,20.123				2518,1,9999				SO:0001652	inframe_insertion	222894	exon1			.	AF369897	CCDS5368.1	7p21.3	2013-10-17	2013-10-17		ENSG00000146618	ENSG00000146618		"""Basic helix-loop-helix proteins"""	16660	protein-coding gene	gene with protein product			"""Fer3-like (Drosophila)"""			11472856, 12217327	Standard	NM_152898		Approved	NATO3, N-TWIST, bHLHa31	uc003suo.1	Q96RJ6	OTTHUMG00000090823	ENST00000275461.3:c.237_239dupAGA	7.37:g.19184747_19184749dupTCT	ENSP00000275461:p.Glu81dup	Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	53	18	0.340	NM_152898	Q495K0	In_Frame_Ins	INS	ENST00000275461.3	37	CCDS5368.1																																																																																			-|0.500;TCT|0.500	0.500	strong		0.624	FERD3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207627.1		
RBMX	27316	hgsc.bcm.edu	37	X	135960146	135960147	+	Frame_Shift_Ins	INS	-	-	AA			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135960146_135960147insAA	ENST00000320676.7	-	4	469_470	c.315_316insTT	c.(313-318)cctccafs	p.P106fs	RBMX_ENST00000562646.1_Frame_Shift_Ins_p.P106fs|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_5'UTR|RBMX_ENST00000570135.1_Intron|SNORD61_ENST00000384252.1_RNA	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	106					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.P106fs*32(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					AGACCTCTTGGAGGGCCTCTAC	0.535																																					p.P106fs		Atlas-Indel	.											.	RBMX	149	.	1	Insertion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	c.316_317insTT						PASS	.																																			SO:0001589	frameshift_variant	27316	exon4			.		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.315_316insTT	X.37:g.135960146_135960147insAA	ENSP00000359645:p.Pro106fs	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	280	60	0.214286	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Frame_Shift_Ins	INS	ENST00000320676.7	37	CCDS14661.1																																																																																			.	.	none		0.535	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
EPB41L4A	64097	hgsc.bcm.edu	37	5	111500816	111500817	+	Splice_Site	INS	-	-	TAAAA	rs145708081|rs369027426		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:111500816_111500817insTAAAA	ENST00000261486.5	-	23	2209		c.e23-1		EPB41L4A_ENST00000507810.1_Intron|EPB41L4A-AS1_ENST00000413221.2_lincRNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A							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)		CATTTCTTCTCTAAAATATATT	0.317																																					.		Atlas-Indel	.											.	EPB41L4A	130	.	0			c.1933-1->TTTTA						PASS	.			3408,36		1689,30,3						5.3	1.0		dbSNP_134	59	7446,316		3600,246,35	no	splice-3	EPB41L4A	NM_022140.3		5289,276,38	A1A1,A1R,RR		4.0711,1.0453,3.1412				10854,352				SO:0001630	splice_region_variant	64097	exon24			.	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.1933-1->TTTTA	5.37:g.111500817_111500821dupTAAAA		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	112	38	0.339286	NM_022140	A4FUI6	Splice_Site	INS	ENST00000261486.5	37	CCDS43350.1																																																																																			-|0.025;TAAAA|0.975	0.975	strong		0.317	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		Intron
DDX12P	440081	hgsc.bcm.edu	37	12	9590651	9590652	+	IGR	INS	-	-	CTGAGTAAC	rs376958229		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9590651_9590652insCTGAGTAAC								RP13-735L24.1 (40438 upstream) : SNORA75 (7001 downstream)														p.Q116_F117insVTQ(1)									TTCTGCACAAACTGAGTAACCC	0.564														1256	0.250799	0.2231	0.1988	5008	,	,		14239	0.2847		0.2237	False		,,,				2504	0.318				.		Pindel,Atlas-Indel	.											.	.	.	.	1	Insertion - In frame(1)	ovary(1)	.						PASS	.			705,2671		132,441,1115						2.4	1.0			56	1273,5605		63,1147,2229	no	intergenic				195,1588,3344	A1A1,A1R,RR		18.5083,20.8827,19.29				1978,8276				SO:0001628	intergenic_variant	440081	.			.																													12.37:g.9590652_9590660dupCTGAGTAAC		Somatic	281	.	.		WXS	Illumina HiSeq	Phase_I	238	54	0.227	.		RNA	INS		37																																																																																				.	.	weak	0	0.564								
APEH	327	hgsc.bcm.edu	37	3	49722525	49722525	+	IGR	DEL	A	A	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49722525delA	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000449682.2_Intron	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)		GGCCCTGCCTAGAGGAGTGGG	0.582																																					.		Atlas-Indel	.											.	MST1	84	.	0			c.1545-2T>-						PASS	.						11.0	12.0	12.0					3																	49722525		2187	4289	6476	SO:0001628	intergenic_variant	4485	exon15			.	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.49722525delA		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	151	11	0.0728477	NM_020998	Q9BQ33|Q9P0Y2	Splice_Site	DEL	ENST00000296456.5	37	CCDS2801.1																																																																																			.	.	none		0.582	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
HTR3E	285242	hgsc.bcm.edu	37	3	183818222	183818222	+	Intron	DEL	G	G	-	rs5855015|rs397897677	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183818222delG	ENST00000415389.2	+	2	533				HTR3E_ENST00000425359.2_Intron|HTR3E_ENST00000335304.2_Frame_Shift_Del_p.R21fs|HTR3E-AS1_ENST00000431427.1_RNA|HTR3E_ENST00000440596.2_Frame_Shift_Del_p.R21fs|HTR3E_ENST00000436361.2_Frame_Shift_Del_p.R21fs	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	40	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	CTCTCATATAGGGAGCACAGG	0.527													GGG|GGG|GG|deletion	178	0.0355431	0.0023	0.0764	5008	,	,		17512	0.0		0.1113	False		,,,				2504	0.0102				p.R21fs	Melanoma(7;227 727 6634 44770)	Pindel,Atlas-Indel	.											.	HTR3E	65	.	0			c.61delA						PASS	.			99,4167		3,93,2037	157.0	143.0	147.0			2.5	0.0	3	dbSNP_114	156	829,7423		36,757,3333	yes	frameshift	HTR3E	NM_182589.2		39,850,5370	A1A1,A1R,RR		10.046,2.3207,7.4133			183818222	928,11590	2202	4293	6495	SO:0001627	intron_variant	285242	exon1			.	AY159813	CCDS3251.1, CCDS58868.1, CCDS58869.1, CCDS58870.1, CCDS58871.1	3q27	2012-05-22	2012-02-03		ENSG00000186038	ENSG00000186038		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24005	protein-coding gene	gene with protein product		610123	"""5-hydroxytryptamine (serotonin) receptor 3, family member E"""			12801637, 15157181	Standard	NM_001256613		Approved		uc010hxr.3	A5X5Y0	OTTHUMG00000156857	ENST00000415389.2:c.68-51G>-	3.37:g.183818222delG		Somatic	92	.	.		WXS	Illumina HiSeq	Phase_I	106	32	0.302	NM_001256614	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Frame_Shift_Del	DEL	ENST00000415389.2	37	CCDS58868.1																																																																																			G|0.951;-|0.049	0.049	strong		0.527	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589	
CFTR	1080	hgsc.bcm.edu	37	7	117144306	117144307	+	Splice_Site	INS	-	-	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:117144306_117144307insC	ENST00000003084.6	+	2	185_186		c.e2-1		CFTR_ENST00000454343.1_Splice_Site	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)						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)	CTTTATTTTAGCTGGACCAGAC	0.381									Cystic Fibrosis																												.		Pindel,Atlas-Indel	.											.	CFTR	171	.	0			c.54-1->C						PASS	.																																			SO:0001630	splice_region_variant	1080	exon2	Familial Cancer Database	CF	.	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.54-1->C	7.37:g.117144307_117144307dupC		Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	87	20	0.230	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Splice_Site	INS	ENST00000003084.6	37	CCDS5773.1																																																																																			.	.	none		0.381	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	Intron
MGAM	8972	hgsc.bcm.edu	37	7	141708306	141708329	+	Splice_Site	DEL	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	-	rs199885071	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141708306_141708329delCCCCAGATCCTGGGACAACTGGTA	ENST00000549489.2	+	3	223_246	c.128_151delCCCCAGATCCTGGGACAACTGGTA	c.(127-153)gccccagatcctgggacaactggtacc>gcc	p.PDPGTTGT60del	MGAM_ENST00000475668.2_Splice_Site_p.PDPGTTGT60del	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	60	Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTTGGTATAGCCCCAGATCCTGGGACAACTGGTACCCCAGATCC	0.469																																					p.43_50del		Atlas-Indel	.											.	MGAM	767	.	0			c.128_150del						PASS	.			10,3480		0,10,1735						0.4	0.0			57	7,7801		1,5,3898	no	coding-near-splice	MGAM	NM_004668.2		1,15,5633	A1A1,A1R,RR		0.0897,0.2865,0.1505				17,11281				SO:0001630	splice_region_variant	8972	exon3			.	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.128-1CCCCAGATCCTGGGACAACTGGTA>-	7.37:g.141708306_141708329delCCCCAGATCCTGGGACAACTGGTA		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	135	40	0.296296	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	none		0.469	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		In_Frame_Del
DSPP	1834	hgsc.bcm.edu	37	4	88536317	88536319	+	In_Frame_Del	DEL	AGC	AGC	-	rs143008261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88536317_88536319delAGC	ENST00000282478.7	+	4	2536_2538	c.2503_2505delAGC	c.(2503-2505)agcdel	p.S836del	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Del_p.S836del			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	836	Asp/Ser-rich.			S -> C (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)		cagcagcgatagcagcaacagca	0.498														418	0.0834665	0.0537	0.1023	5008	,	,		37195	0.0942		0.1213	False		,,,				2504	0.0603				p.834_835del		Pindel,Atlas-Indel	.											.	DSPP	174	.	0			c.2502_2504del						PASS	.			179,2961		27,125,1418						-0.4	0.0		dbSNP_134	106	716,4848		92,532,2158	no	coding	DSPP	NM_014208.3		119,657,3576	A1A1,A1R,RR		12.8684,5.7006,10.2826				895,7809				SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2503_2505delAGC	4.37:g.88536320_88536322delAGC	ENSP00000282478:p.Ser836del	Somatic	216	.	.		WXS	Illumina HiSeq	Phase_I	221	34	0.154	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	37	CCDS43248.1																																																																																			AGC|0.917;-|0.083	0.083	strong		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
CYP3A5	1577	hgsc.bcm.edu	37	7	99273810	99273811	+	Frame_Shift_Ins	INS	-	-	C	rs200579169|rs28383469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99273810_99273811insC	ENST00000222982.4	-	2	191_192	c.92_93insG	c.(91-93)ggafs	p.G31fs	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000439761.1_Frame_Shift_Ins_p.G31fs|CYP3A5_ENST00000343703.5_Frame_Shift_Ins_p.G21fs|CYP3A5_ENST00000480723.1_5'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	31					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TCTTAAAAAGTCCATGTGTACG	0.46													CC|CC|CCC|insertion	17	0.00339457	0.0	0.0014	5008	,	,		20943	0.0		0.0119	False		,,,				2504	0.0041				p.G31fs		Pindel,Atlas-Indel	.											.	CYP3A5	46	.	0			c.93_94insG	GRCh37	CI067571	CYP3A5	I		PASS	.		,	6,4258		0,6,2126					,	-4.4	0.0		dbSNP_125	108	77,8175		0,77,4049	no	frameshift,frameshift	CYP3A5	NM_001190484.1,NM_000777.3	,	0,83,6175	A1A1,A1R,RR		0.9331,0.1407,0.6632	,	,		83,12433				SO:0001589	frameshift_variant	1577	exon2			.	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.93dupG	7.37:g.99273812_99273812dupC	ENSP00000222982:p.Gly31fs	Somatic	92	.	.		WXS	Illumina HiSeq	Phase_I	127	38	0.299	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Frame_Shift_Ins	INS	ENST00000222982.4	37	CCDS5672.1																																																																																			-|0.994;C|0.006	0.006	strong		0.460	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
GPRIN1	114787	hgsc.bcm.edu	37	5	176026136	176026146	+	Frame_Shift_Del	DEL	CCTCCTTCCTC	CCTCCTTCCTC	-	rs79403503|rs386695335|rs550332435|rs77245696|rs142779818|rs371149640|rs201635586	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTCCTTCCTC	CCTCCTTCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176026136_176026146delCCTCCTTCCTC	ENST00000303991.4	-	2	867_877	c.690_700delGAGGAAGGAGG	c.(688-702)ccgaggaaggaggatfs	p.RKED231fs		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	231				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GACCCAGGATCCTCCTTCCTCGGTGACACTG	0.498																																					p.231_234del		Atlas-Indel	.											.	GPRIN1	77	.	0			c.691_701del						PASS	.			563,3699		9,545,1577						-2.4	0.0		dbSNP_134	89	851,7393		18,815,3289	no	frameshift	GPRIN1	NM_052899.2		27,1360,4866	A1A1,A1R,RR		10.3227,13.2098,11.3066				1414,11092				SO:0001589	frameshift_variant	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.690_700delGAGGAAGGAGG	5.37:g.176026136_176026146delCCTCCTTCCTC	ENSP00000305839:p.Arg231fs	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	124	19	0.153226	NM_052899	C9JM70|Q8ND74|Q96PZ4	Frame_Shift_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	none		0.498	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
CFAP74	85452	hgsc.bcm.edu	37	1	1900106	1900107	+	IGR	INS	-	-	CTC	rs61233860|rs145742571|rs72634902	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1900106_1900107insCTC								TMEM52 (49394 upstream) : C1orf222 (19455 downstream)																							ACTGTGGTCTTCTTGCAAAAGT	0.569														997	0.199081	0.1324	0.1945	5008	,	,		21168	0.3284		0.2376	False		,,,				2504	0.1196				p.K405delinsEK		Pindel,Atlas-Indel	.											.	KIAA1751	92	.	0			c.1213_1214insGAG						PASS	.			643,3311		79,485,1413						-3.9	0.0		dbSNP_129	188	1999,6033		265,1469,2282	no	coding	KIAA1751	NM_001080484.1		344,1954,3695	A1A1,A1R,RR		24.8879,16.262,22.0424				2642,9344				SO:0001628	intergenic_variant	85452	exon11			.																													1.37:g.1900106_1900107insCTC		Somatic	168	.	.		WXS	Illumina HiSeq	Phase_I	122	62	0.508	NM_001080484		In_Frame_Ins	INS		37																																																																																				.	.	strong	0	0.569								
OR13C2	392376	hgsc.bcm.edu	37	9	107367665	107367666	+	Frame_Shift_Del	DEL	GC	GC	-	rs377668801|rs143760725|rs144815315|rs140970710	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107367665_107367666delGC	ENST00000542196.1	-	1	285_286	c.243_244delGC	c.(241-246)acgctafs	p.L82fs		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						AAGCTCACTAGCGTGGAGGGAA	0.515														1574	0.314297	0.4138	0.2003	5008	,	,		20880	0.4097		0.16	False		,,,				2504	0.3211				p.82_82del		Pindel,Atlas-Indel	.											.	OR13C2	46	.	0			c.244_245del						PASS	.			2387,1861		730,927,467						2.2	0.0		dbSNP_134	35	1565,6681		171,1223,2729	no	frameshift	OR13C2	NM_001004481.1		901,2150,3196	A1A1,A1R,RR		18.9789,43.8089,31.6312				3952,8542				SO:0001589	frameshift_variant	392376	exon1			.		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.243_244delGC	9.37:g.107367665_107367666delGC	ENSP00000438815:p.Leu82fs	Somatic	568	.	.		WXS	Illumina HiSeq	Phase_I	566	100	0.177	NM_001004481	B9EGV8|Q6IF54	Frame_Shift_Del	DEL	ENST00000542196.1	37	CCDS35092.1																																																																																			.	.	strong		0.515	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
SLC39A14	23516	hgsc.bcm.edu	37	8	22262229	22262234	+	In_Frame_Del	DEL	GCTGCT	GCTGCT	-	rs145380823|rs111662782|rs3052256|rs150063686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCTGCT	GCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22262229_22262234delGCTGCT	ENST00000381237.1	+	2	125_130	c.6_11delGCTGCT	c.(4-12)aagctgctg>aag	p.LL5del	SLC39A14_ENST00000289952.5_In_Frame_Del_p.LL5del|SLC39A14_ENST00000240095.6_In_Frame_Del_p.LL5del|SLC39A14_ENST00000359741.5_In_Frame_Del_p.LL5del	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	5					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		TCACCATGAAGCTGCTGCTGCTGCAC	0.617														1591	0.317692	0.6929	0.1571	5008	,	,		16427	0.1806		0.2078	False		,,,				2504	0.1789				p.2_4del		Pindel,Atlas-Indel	.											.	SLC39A14	59	.	0			c.5_10del						PASS	.		,,,	2454,1772		745,964,404					,,,	3.4	1.0		dbSNP_132	80	1420,6814		142,1136,2839	no	coding,coding,coding,coding	SLC39A14	NM_015359.4,NM_001135154.1,NM_001135153.1,NM_001128431.2	,,,	887,2100,3243	A1A1,A1R,RR		17.2456,41.9309,31.0915	,,,	,,,		3874,8586				SO:0001651	inframe_deletion	23516	exon2			.	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.6_11delGCTGCT	8.37:g.22262235_22262240delGCTGCT	ENSP00000370635:p.Leu5_Leu6del	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	83	59	0.711	NM_001135154	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	In_Frame_Del	DEL	ENST00000381237.1	37	CCDS47823.1																																																																																			GCTGCT|0.701;-|0.299	0.299	strong		0.617	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
RBM12	10137	hgsc.bcm.edu	37	20	34240740	34240741	+	In_Frame_Ins	INS	-	-	GGGCCG	rs376657170|rs201181145		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:34240740_34240741insGGGCCG	ENST00000374114.3	-	3	2767_2768	c.2504_2505insCGGCCC	c.(2503-2505)cct>ccCGGCCCt	p.835_835P>PGP	CPNE1_ENST00000317677.5_Intron|RBM12_ENST00000374104.3_In_Frame_Ins_p.835_835P>PGP|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000397443.1_Intron|RBM12_ENST00000359646.1_In_Frame_Ins_p.835_835P>PGP|RP1-309K20.6_ENST00000541176.2_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	835	Gly-rich.|Pro-rich.					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)			GGATTgggccagggccggggcc	0.599																																					p.P835delinsPGP		Pindel,Atlas-Indel	.											RBM12,rectum,carcinoma,0,1	RBM12	93	1	0			c.2505_2506insCGGCCC						PASS	.																																			SO:0001652	inframe_insertion	10137	exon2			.	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.2499_2504dupCGGCCC	20.37:g.34240741_34240746dupGGGCCG	ENSP00000363228:p.GlyPro837dup	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	55	12	0.218	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	In_Frame_Ins	INS	ENST00000374114.3	37	CCDS13261.1																																																																																			-|0.961;GGGCCG|0.039	0.039	strong		0.599	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
SLC3A1	6519	hgsc.bcm.edu	37	2	44528268	44528268	+	Splice_Site	DEL	T	T	-	rs556841667|rs61179824	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:44528268delT	ENST00000260649.6	+	6	1212		c.e6+2		SLC3A1_ENST00000409741.1_Splice_Site|SLC3A1_ENST00000409294.1_Intron|SLC3A1_ENST00000409229.3_Splice_Site|SLC3A1_ENST00000409380.1_Splice_Site|SLC3A1_ENST00000410056.3_Frame_Shift_Del_p.L380fs|SLC3A1_ENST00000409740.3_5'Flank|SLC3A1_ENST00000409387.1_Splice_Site	NM_000341.3	NP_000332.2	Q07837	SLC31_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 1						amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|basic amino acid transport (GO:0015802)|carbohydrate metabolic process (GO:0005975)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)|vacuolar membrane (GO:0005774)	amino acid transmembrane transporter activity (GO:0015171)|basic amino acid transmembrane transporter activity (GO:0015174)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|L-cystine transmembrane transporter activity (GO:0015184)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(3)	26		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)			L-Cystine(DB00138)	CAGATACAGGTTGACCACGGC	0.507													T|TT|T|insertion	560	0.111821	0.2708	0.0821	5008	,	,		20412	0.001		0.1243	False		,,,				2504	0.0194				.		Pindel,Atlas-Indel	.											.	SLC3A1	62	.	0			c.1136+1T>-	GRCh37	CS013629	SLC3A1	S	rs146125507	PASS	.			1011,3255		126,759,1248	78.0	75.0	76.0			5.3	1.0	2	dbSNP_134	89	935,7319		49,837,3241	no	splice-5	SLC3A1	NM_000341.3		175,1596,4489	A1A1,A1R,RR		11.3278,23.699,15.5431			44528268	1946,10574	2170	4288	6458	SO:0001630	splice_region_variant	6519	exon6			.		CCDS1819.1	2p16.3	2013-07-19	2013-07-19		ENSG00000138079	ENSG00000138079		"""Solute carriers"""	11025	protein-coding gene	gene with protein product		104614	"""solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1"""			8486766, 9186880	Standard	NM_000341		Approved	CSNU1, D2H, RBAT, ATR1, NBAT	uc002ruc.4	Q07837	OTTHUMG00000128759	ENST00000260649.6:c.1136+2T>-	2.37:g.44528268delT		Somatic	89	.	.		WXS	Illumina HiSeq	Phase_I	90	31	0.344	NM_000341	A8K0S1|O00658|Q15295|Q4J6B4|Q4J6B5|Q4J6B6|Q4J6B7|Q4J6B8|Q4J6B9|Q52M92|Q52M94	Splice_Site	DEL	ENST00000260649.6	37	CCDS1819.1																																																																																			T|0.888;-|0.112	0.112	strong		0.507	SLC3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250676.1	NM_000341	Intron
LCE4A	199834	hgsc.bcm.edu	37	1	152681680	152681681	+	In_Frame_Ins	INS	-	-	AGCTCTGGGGGCTGCTGT	rs6143428|rs11269814|rs200890315|rs33921874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152681680_152681681insAGCTCTGGGGGCTGCTGT	ENST00000368777.1	+	2	385_386	c.129_130insAGCTCTGGGGGCTGCTGT	c.(130-132)agc>AGCTCTGGGGGCTGCTGTagc	p.44_44S>SSGGCCS	LCE4A_ENST00000335535.3_In_Frame_Ins_p.44_44S>SSGGCCS			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	44	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			GCTGTGGCTCCAGCTCTGGGGG	0.599														4009	0.800519	0.9758	0.853	5008	,	,		18534	0.6855		0.7177	False		,,,				2504	0.7301				p.S43delinsSSSGGCC		Pindel,Atlas-Indel	.											LCE4A,rectum,carcinoma,+1,3	LCE4A	37	3	0			c.129_130insAGCTCTGGGGGCTGCTGT						PASS	.																																			SO:0001652	inframe_insertion	199834	exon1			.	BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"""Late cornified envelopes"""	16613	protein-coding gene	gene with protein product		612618	"""small proline rich-like (epidermal differentiation complex) 4A"""	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	Exception_encountered	1.37:g.152681680_152681681insAGCTCTGGGGGCTGCTGT	Exception_encountered	Somatic	195	.	.		WXS	Illumina HiSeq	Phase_I	135	62	0.459	NM_178356	Q14D97	In_Frame_Ins	INS	ENST00000368777.1	37	CCDS1022.1																																																																																			.	.	strong		0.599	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356	
ZNF408	79797	hgsc.bcm.edu	37	11	46724717	46724728	+	In_Frame_Del	DEL	AGTGGTGACAGA	AGTGGTGACAGA	-	rs376220307|rs77373752|rs148055528|rs145722187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGTGGTGACAGA	AGTGGTGACAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:46724717_46724728delAGTGGTGACAGA	ENST00000311764.2	+	4	806_817	c.576_587delAGTGGTGACAGA	c.(574-588)gcagtggtgacagaa>gca	p.VVTE193del	ARHGAP1_ENST00000311956.4_5'Flank	NM_001184751.1|NM_024741.2	NP_001171680.1|NP_079017.1	Q9H9D4	ZN408_HUMAN	zinc finger protein 408	193					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CAGCTGTAGCAGTGGTGACAGAAGTGGAGTCT	0.571														1092	0.218051	0.0061	0.2795	5008	,	,		22078	0.5942		0.1223	False		,,,				2504	0.1718				p.192_196del	Pancreas(79;698 1390 6545 18745 34127)|Esophageal Squamous(120;1014 1625 12837 24601 49525)	Pindel,Atlas-Indel	.											.	ZNF408	70	.	0			c.575_586del						PASS	.		,	216,4046		40,136,1955					,	1.0	0.0		dbSNP_134	42	1150,7104		149,852,3126	no	coding,coding	ZNF408	NM_024741.2,NM_001184751.1	,	189,988,5081	A1A1,A1R,RR		13.9326,5.068,10.914	,	,		1366,11150				SO:0001651	inframe_deletion	79797	exon4			.	AF346626	CCDS7923.1	11p11.2	2008-02-05			ENSG00000175213	ENSG00000175213		"""Zinc fingers, C2H2-type"""	20041	protein-coding gene	gene with protein product						15231747	Standard	NM_024741		Approved	FLJ12827	uc010rgw.2	Q9H9D4	OTTHUMG00000166568	ENST00000311764.2:c.576_587delAGTGGTGACAGA	11.37:g.46724717_46724728delAGTGGTGACAGA	ENSP00000309606:p.Val193_Glu196del	Somatic	143	.	.		WXS	Illumina HiSeq	Phase_I	78	23	0.295	NM_024741		In_Frame_Del	DEL	ENST00000311764.2	37	CCDS7923.1																																																																																			AGTGGTGACAGA|0.755;-|0.245	0.245	strong		0.571	ZNF408-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390485.2	NM_024741	
TMEM87B	84910	hgsc.bcm.edu	37	2	112832536	112832538	+	Splice_Site	DEL	AAT	AAT	-	rs201146763|rs71385858	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:112832536_112832538delAAT	ENST00000283206.4	+	5	867_869	c.498_500delAAT	c.(496-501)tcaatg>tcg	p.M167del		NM_032824.2	NP_116213.1	Q96K49	TM87B_HUMAN	transmembrane protein 87B	167						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)	19						AGGAAAGATCAATGGTAAGCAGT	0.3														1297	0.258986	0.2118	0.2954	5008	,	,		17959	0.1835		0.3976	False		,,,				2504	0.2321				p.166_167del		Pindel,Atlas-Indel	.											.	TMEM87B	52	.	0			c.497_499del						PASS	.			915,3343		103,709,1317						3.6	0.8		dbSNP_130	41	3245,4989		636,1973,1508	no	coding-near-splice	TMEM87B	NM_032824.2		739,2682,2825	A1A1,A1R,RR		39.4098,21.489,33.3013				4160,8332				SO:0001630	splice_region_variant	84910	exon5			.	AC092645	CCDS33275.1	2q13	2008-02-05			ENSG00000153214	ENSG00000153214			25913	protein-coding gene	gene with protein product							Standard	NM_032824		Approved	FLJ14681	uc002thm.2	Q96K49	OTTHUMG00000153266	ENST00000283206.4:c.501+1AAT>-	2.37:g.112832536_112832538delAAT		Somatic	261	.	.		WXS	Illumina HiSeq	Phase_I	222	71	0.320	NM_032824	A8K2M9|Q1RLN2|Q53R54	In_Frame_Del	DEL	ENST00000283206.4	37	CCDS33275.1																																																																																			AAT|0.722;-|0.278	0.278	strong		0.300	TMEM87B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330500.1	NM_032824	In_Frame_Del
OR13C2	392376	hgsc.bcm.edu	37	9	107367393	107367396	+	Frame_Shift_Del	DEL	GTTA	GTTA	-	rs112364120|rs143198170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GTTA	GTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107367393_107367396delGTTA	ENST00000542196.1	-	1	555_558	c.513_516delTAAC	c.(511-516)aataacfs	p.NN171fs		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	171						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GATTGATGATGTTATTCCTGCAGA	0.451														1868	0.373003	0.4304	0.2161	5008	,	,		20908	0.5665		0.1789	False		,,,				2504	0.407				p.172_173del		Atlas-Indel	.											.	OR13C2	46	.	0			c.514_517del						PASS	.			1624,2632		344,936,848						1.3	0.3		dbSNP_129	138	1571,6681		165,1241,2720	no	frameshift	OR13C2	NM_001004481.1		509,2177,3568	A1A1,A1R,RR		19.0378,38.1579,25.5437				3195,9313				SO:0001589	frameshift_variant	392376	exon1			.		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.513_516delTAAC	9.37:g.107367393_107367396delGTTA	ENSP00000438815:p.Asn171fs	Somatic	366	0	0		WXS	Illumina HiSeq	Phase_I	376	130	0.345745	NM_001004481	B9EGV8|Q6IF54	Frame_Shift_Del	DEL	ENST00000542196.1	37	CCDS35092.1																																																																																			.	.	strong		0.451	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
GFM2	84340	hgsc.bcm.edu	37	5	74021847	74021852	+	In_Frame_Del	DEL	ACTCAA	ACTCAA	-	rs5868753|rs76339998	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ACTCAA	ACTCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:74021847_74021852delACTCAA	ENST00000296805.3	-	18	2283_2288	c.1826_1831delTTGAGT	c.(1825-1833)tttgagtat>tat	p.FE609del	RNU6-658P_ENST00000384606.1_RNA|GFM2_ENST00000345239.2_In_Frame_Del_p.FE562del|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000509430.1_In_Frame_Del_p.FE609del	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2									p.F609Y(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		CTTTCAGCATACTCAAACTCAATCAC	0.413														1915	0.382388	0.7572	0.3372	5008	,	,		20860	0.1974		0.2425	False		,,,				2504	0.2423				p.609_611del		Pindel,Atlas-Indel	.											.	GFM2	38	.	1	Substitution - Missense(1)	lung(1)	c.1827_1832del						PASS	.																																			SO:0001651	inframe_deletion	84340	exon18			.	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.1826_1831delTTGAGT	5.37:g.74021853_74021858delACTCAA	ENSP00000296805:p.Phe609_Glu610del	Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	109	32	0.294	NM_032380		In_Frame_Del	DEL	ENST00000296805.3	37	CCDS4023.1																																																																																			ACTCAA|0.643;-|0.357	0.357	strong		0.413	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
HAVCR1	26762	hgsc.bcm.edu	37	5	156479568	156479569	+	In_Frame_Ins	INS	-	-	GTT	rs386693994|rs139041445|rs6149307|rs10068551|rs141023871|rs77147640|rs376729615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:156479568_156479569insGTT	ENST00000339252.3	-	3	1008_1009	c.476_477insAAC	c.(475-477)acg>acAACg	p.159_159T>TT	HAVCR1_ENST00000544197.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000425854.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000522693.1_In_Frame_Ins_p.159_159T>TT|HAVCR1_ENST00000523175.1_In_Frame_Ins_p.159_159T>TT	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)	p.T160_V161insT(1)		endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TTGGAACAGTCGTCATTGGAAC	0.49														1655	0.330471	0.6165	0.2363	5008	,	,		22483	0.2232		0.2097	False		,,,				2504	0.2454				p.T159delinsTT		Pindel,Atlas-Indel	.											.	HAVCR1	84	.	1	Insertion - In frame(1)	ovary(1)	c.477_478insAAC						PASS	.																																			SO:0001652	inframe_insertion	26762	exon4			.	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.476_477insAAC	5.37:g.156479568_156479569insGTT	ENSP00000344844:p.Thr160dup	Somatic	383	.	.		WXS	Illumina HiSeq	Phase_I	572	100	0.175	NM_001099414	O43656	In_Frame_Ins	INS	ENST00000339252.3	37	CCDS43392.1																																																																																			.	.	strong		0.490	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
AGAP6	414189	hgsc.bcm.edu	37	10	51768675	51768676	+	Frame_Shift_Del	DEL	AA	AA	-	rs141217862|rs200646112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:51768675_51768676delAA	ENST00000374056.4	+	7	1119_1120	c.721_722delAA	c.(721-723)aaafs	p.K241fs	AGAP6_ENST00000412531.3_Frame_Shift_Del_p.K264fs			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	241					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						TGACCCAGACAAAGAGAGGAAA	0.55														591	0.118011	0.0356	0.1542	5008	,	,		18267	0.0327		0.2694	False		,,,				2504	0.136				p.263_264del		Pindel,Atlas-Indel	.											.	AGAP6	53	.	0			c.789_790del						PASS	.																																			SO:0001589	frameshift_variant	414189	exon8			.		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.721_722delAA	10.37:g.51768675_51768676delAA	ENSP00000363168:p.Lys241fs	Somatic	110	.	.		WXS	Illumina HiSeq	Phase_I	90	14	0.156	NM_001077665		Frame_Shift_Del	DEL	ENST00000374056.4	37																																																																																				AA|0.500;-|0.500	0.500	weak		0.550	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388375	1388376	+	Frame_Shift_Ins	INS	-	-	CA	rs533172496|rs530731346|rs373032956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388375_1388376insCA	ENST00000324803.4	+	1	3036_3037	c.76_77insCA	c.(76-78)tcafs	p.S26fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	26					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCCCGCCTGCTCATGTGCCCAT	0.639														782	0.15615	0.1952	0.1412	5008	,	,		17889	0.0278		0.2286	False		,,,				2504	0.1718				p.S26fs		Atlas-Indel	.											.	CRIPAK	185	.	0			c.76_77insCA						PASS	.																																			SO:0001589	frameshift_variant	285464	exon1			.	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.77_78dupCA	4.37:g.1388376_1388377dupCA	ENSP00000323978:p.Ser26fs	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	174	14	0.0804598	NM_175918	Q8NB03	Frame_Shift_Ins	INS	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.639	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964409	37964429	+	In_Frame_Del	DEL	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	-	rs13056859|rs13055845|rs77417880|rs62235033|rs62235034|rs187761157|rs66468174|rs200195385	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCGCCTGCTGCAAACCCCT	CAGCGCCTGCTGCAAACCCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37964409_37964429delCAGCGCCTGCTGCAAACCCCT	ENST00000249014.4	+	3	1178_1198	c.758_778delCAGCGCCTGCTGCAAACCCCT	c.(757-780)ccagcgcctgctgcaaacccctca>cca	p.APAANPS254del		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	254	8 X 7 AA tandem repeats of [PT]-[AT]-A- [ENT]-[PT]-[PTS]-[AG].				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)		p.N258_A264delNPSAPAA(3)		endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					GCAAACCCCCCAGCGCCTGCTGCAAACCCCTCAGCACCTGC	0.665																																					p.253_259del		Atlas-Indel	.											.	CDC42EP1	53	.	3	Deletion - In frame(3)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(1)	c.757_777del						PASS	.			868,3338		98,672,1333						1.5	0.0		dbSNP_130	10	4310,3696		1298,1714,991	no	coding	CDC42EP1	NM_152243.2		1396,2386,2324	A1A1,A1R,RR		46.1654,20.6372,42.4009				5178,7034				SO:0001651	inframe_deletion	11135	exon3			.	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.758_778delCAGCGCCTGCTGCAAACCCCT	22.37:g.37964409_37964429delCAGCGCCTGCTGCAAACCCCT	ENSP00000249014:p.Ala254_Ser260del	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	175	63	0.36	NM_152243	A8K825|Q96GN1	In_Frame_Del	DEL	ENST00000249014.4	37	CCDS13949.1																																																																																			CAGCGCCTGCTGCAAACCCCT|0.610;-|0.390	0.390	strong		0.665	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
RBBP6	5930	hgsc.bcm.edu	37	16	24583713	24583718	+	In_Frame_Del	DEL	AAAGAG	AAAGAG	-	rs148143334|rs199567078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAAGAG	AAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:24583713_24583718delAAAGAG	ENST00000319715.4	+	18	5758_5763	c.5326_5331delAAAGAG	c.(5326-5331)aaagagdel	p.KE1780del	RBBP6_ENST00000381039.3_In_Frame_Del_p.KE940del|RBBP6_ENST00000348022.2_In_Frame_Del_p.KE1746del	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	1780					embryonic organ development (GO:0048568)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|somite development (GO:0061053)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(4)|pancreas(1)|prostate(2)|urinary_tract(1)	46				GBM - Glioblastoma multiforme(48;0.0518)		gaacaaagataaagagaaggagaagg	0.311														121	0.0241613	0.0045	0.0375	5008	,	,		24421	0.0		0.0726	False		,,,				2504	0.0164				p.1775_1777del		Atlas-Indel	.											.	RBBP6	158	.	0			c.5325_5330del						PASS	.		,	75,3587		6,63,1762					,	0.7	1.0		dbSNP_134	25	547,6527		74,399,3064	no	coding,coding	RBBP6	NM_018703.3,NM_006910.4	,	80,462,4826	A1A1,A1R,RR		7.7325,2.0481,5.7936	,	,		622,10114				SO:0001651	inframe_deletion	5930	exon18			.		CCDS10621.1, CCDS10622.1, CCDS45444.1	16p12.2	2008-08-04	2001-11-28		ENSG00000122257	ENSG00000122257			9889	protein-coding gene	gene with protein product	"""proliferation potential-related protein"""	600938	"""retinoblastoma-binding protein 6"""			8595913, 16396680	Standard	NM_006910		Approved	P2P-R, PACT, SNAMA	uc002dmh.3	Q7Z6E9	OTTHUMG00000096991	ENST00000319715.4:c.5326_5331delAAAGAG	16.37:g.24583713_24583718delAAAGAG	ENSP00000317872:p.Lys1780_Glu1781del	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	32	13	0.40625	NM_006910	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	In_Frame_Del	DEL	ENST00000319715.4	37	CCDS10621.1																																																																																			AAAGAG|0.968;-|0.032	0.032	strong		0.311	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910	
KMT2D	8085	hgsc.bcm.edu	37	12	49422949	49422950	+	Frame_Shift_Ins	INS	-	-	CA	rs376628232		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49422949_49422950insCA	ENST00000301067.7	-	44	14144_14145	c.14145_14146insTG	c.(14143-14148)ttggggfs	p.G4716fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4716					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)										GCCTCCTCCCCCAAGATGCTCT	0.589																																					p.G4716fs		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.14146_14147insTG						PASS	.																																			SO:0001589	frameshift_variant	8085	exon44			.	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.14144_14145dupTG	12.37:g.49422950_49422951dupCA	ENSP00000301067:p.Gly4716fs	Somatic	71	.	.		WXS	Illumina HiSeq	Phase_I	94	29	0.309	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.589	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
CFAP74	85452	hgsc.bcm.edu	37	1	1887112	1887112	+	IGR	DEL	C	C	-	rs3838975	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1887112delC								TMEM52 (36400 upstream) : C1orf222 (32450 downstream)																							CCTGGCTTGGCCTGGCAGCCT	0.667													CC|CC|C|deletion	936	0.186901	0.1059	0.232	5008	,	,		12880	0.2292		0.2475	False		,,,				2504	0.1585				p.A732fs		Atlas-Indel	.											.	KIAA1751	92	.	0			c.2195delC						PASS	.			512,3372		50,412,1480	42.0	43.0	43.0			1.2	0.1	1	dbSNP_107	46	2092,5888		286,1520,2184	no	frameshift	KIAA1751	NM_001080484.1		336,1932,3664	A1A1,A1R,RR		26.2155,13.1823,21.9488			1887112	2604,9260	2027	4130	6157	SO:0001628	intergenic_variant	85452	exon18			.																													1.37:g.1887112delC		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	85	69	0.811765	NM_001080484		Frame_Shift_Del	DEL		37																																																																																				C|0.783;-|0.217	0.217	strong	0	0.667								
NUCB2	4925	hgsc.bcm.edu	37	11	17352478	17352480	+	In_Frame_Del	DEL	ACA	ACA	-	rs189362726|rs535406012|rs3842269	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:17352478_17352480delACA	ENST00000529010.1	+	13	1422_1424	c.1203_1205delACA	c.(1201-1206)ttacaa>tta	p.Q403del	NUCB2_ENST00000458064.2_In_Frame_Del_p.Q373del|NUCB2_ENST00000323688.6_In_Frame_Del_p.Q403del	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	403	Binds to necdin. {ECO:0000250}.					cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AAAAAAAATTACAACAAGGAATT	0.32														1270	0.253594	0.1127	0.1484	5008	,	,		15929	0.5139		0.2992	False		,,,				2504	0.2035				p.401_402del		Pindel,Atlas-Indel	.											.	NUCB2	31	.	0			c.1202_1204del						PASS	.			466,3024		27,412,1306						5.5	1.0		dbSNP_107	44	2131,5673		291,1549,2062	no	coding	NUCB2	NM_005013.2		318,1961,3368	A1A1,A1R,RR		27.3065,13.3524,22.9945				2597,8697				SO:0001651	inframe_deletion	4925	exon13			.	AF052642	CCDS41623.1	11p15.1	2013-01-10						"""EF-hand domain containing"""	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.1203_1205delACA	11.37:g.17352481_17352483delACA	ENSP00000436455:p.Gln403del	Somatic	154	.	.		WXS	Illumina HiSeq	Phase_I	127	28	0.220	NM_005013	A8K642|D3DQX5|Q8NFT5	In_Frame_Del	DEL	ENST00000529010.1	37	CCDS41623.1																																																																																			ACA|0.718;-|0.282	0.282	strong		0.320	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388622	1388623	+	Frame_Shift_Ins	INS	-	-	CA	rs79704405|rs540461234|rs558358960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388622_1388623insCA	ENST00000324803.4	+	1	3283_3284	c.323_324insCA	c.(322-327)ctcacgfs	p.LT108fs		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	108					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.L108H(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCCCGCCTGCTCACGTGCCCAT	0.668														506	0.101038	0.0567	0.1427	5008	,	,		19207	0.0169		0.1759	False		,,,				2504	0.1411				p.L108fs		Atlas-Indel	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	1	Substitution - Missense(1)	pancreas(1)	c.323_324insCA						PASS	.																																			SO:0001589	frameshift_variant	285464	exon1			.	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.324_325dupCA	4.37:g.1388623_1388624dupCA	ENSP00000323978:p.Leu108fs	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	131	38	0.290076	NM_175918	Q8NB03	Frame_Shift_Ins	INS	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.668	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586676	+	Frame_Shift_Del	DEL	TTTTA	TTTTA	-	rs201063949|rs199927874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTTTA	TTTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145586672_145586676delTTTTA	ENST00000334513.5	-	8	911_915	c.900_904delTAAAA	c.(898-906)tgtaaaagtfs	p.CKS300fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	300							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TAAGCTGCACTTTTACACGGTGGGG	0.532														72	0.014377	0.0015	0.0303	5008	,	,		19363	0.0		0.0398	False		,,,				2504	0.0092				p.301_302del		Atlas-Indel	.											.	NUDT17	25	.	0			c.901_905del						PASS	.			14,4252		0,14,2119						-1.1	0.0			111	162,8092		2,158,3967	no	frameshift	NUDT17	NM_001012758.2		2,172,6086	A1A1,A1R,RR		1.9627,0.3282,1.4058				176,12344				SO:0001589	frameshift_variant	200035	exon8			.	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"""Nudix motif containing"""	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.900_904delTAAAA	1.37:g.145586672_145586676delTTTTA	ENSP00000334437:p.Cys300fs	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	129	32	0.248062	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			TTTTA|0.983;-|0.017	0.017	strong		0.532	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
SYT14	255928	hgsc.bcm.edu	37	1	210267894	210267896	+	In_Frame_Del	DEL	GAA	GAA	-	rs144713062|rs200839898|rs2307890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:210267894_210267896delGAA	ENST00000472886.1	+	5	684_686	c.670_672delGAA	c.(670-672)gaadel	p.E225del	SYT14_ENST00000367019.1_In_Frame_Del_p.E225del|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000537238.1_In_Frame_Del_p.E187del|SYT14_ENST00000367015.1_In_Frame_Del_p.E187del|SYT14_ENST00000534859.1_In_Frame_Del_p.E225del|SYT14_ENST00000422431.1_In_Frame_Del_p.E270del|SYT14_ENST00000399639.2_In_Frame_Del_p.E225del			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	225					cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		TAAAGGATATGAAGAAGATGTTC	0.384														399	0.0796725	0.0098	0.0677	5008	,	,		16957	0.0655		0.1421	False		,,,				2504	0.1329				p.268_269del		Pindel,Atlas-Indel	.											.	SYT14	89	.	0			c.804_806del						PASS	.		,,,	107,4159		4,99,2030					,,,	2.2	1.0		dbSNP_134	76	1145,7109		84,977,3066	no	coding,coding,coding,coding	SYT14	NM_153262.2,NM_001146264.1,NM_001146262.1,NM_001146261.1	,,,	88,1076,5096	A1A1,A1R,RR		13.8721,2.5082,10.0	,,,	,,,		1252,11268				SO:0001651	inframe_deletion	255928	exon6			.	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"""Synaptotagmins"""	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.670_672delGAA	1.37:g.210267897_210267899delGAA	ENSP00000418901:p.Glu225del	Somatic	165	.	.		WXS	Illumina HiSeq	Phase_I	132	46	0.348	NM_001146264	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	In_Frame_Del	DEL	ENST00000472886.1	37	CCDS31014.1																																																																																			GAA|0.912;-|0.088	0.088	strong		0.384	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161021121	161021122	+	In_Frame_Ins	INS	-	-	GGCCAG	rs201733366		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161021121_161021122insGGCCAG	ENST00000368013.3	-	10	1722_1723	c.1402_1403insCTGGCC	c.(1402-1404)ctt>cCTGGCCtt	p.467_468insPG	ARHGAP30_ENST00000368016.3_In_Frame_Ins_p.467_468insPG|ARHGAP30_ENST00000368015.1_In_Frame_Ins_p.290_291insPG	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	467					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			gccagggccaaggccagggcca	0.619																																					p.L468delinsPGL		Atlas-Indel	.											.	ARHGAP30	105	.	0			c.1403_1404insCTGGCC						PASS	.																																			SO:0001652	inframe_insertion	257106	exon10			.	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1397_1402dupCTGGCC	1.37:g.161021122_161021127dupGGCCAG	ENSP00000356992:p.Pro466_Gly467dup	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	50	16	0.32	NM_181720	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	In_Frame_Ins	INS	ENST00000368013.3	37	CCDS30918.1																																																																																			.	.	none		0.619	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
HCLS1	3059	hgsc.bcm.edu	37	3	121351315	121351316	+	In_Frame_Ins	INS	-	-	GGCTCAGGCTCA	rs150627065|rs372720825|rs80289672	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:121351315_121351316insGGCTCAGGCTCA	ENST00000314583.3	-	12	1194_1195	c.1103_1104insTGAGCCTGAGCC	c.(1102-1104)ccc>ccTGAGCCTGAGCCc	p.368_368P>PEPEP	HCLS1_ENST00000473883.1_5'UTR|HCLS1_ENST00000428394.2_In_Frame_Ins_p.331_331P>PEPEP	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	368					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		gctcaggctcgggctcaggctc	0.604														1208	0.241214	0.1573	0.1599	5008	,	,		14710	0.4563		0.2485	False		,,,				2504	0.183				p.P368delinsPEPEP		Pindel,Atlas-Indel	.											HCLS1,caecum,carcinoma,0,1	HCLS1	78	1	0			c.1104_1105insTGAGCCTGAGCC	GRCh37	CI045897	HCLS1	I	rs80289672	PASS	.																																			SO:0001652	inframe_insertion	3059	exon12			.		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.1092_1103dupTGAGCCTGAGCC	3.37:g.121351315_121351316insGGCTCAGGCTCA	ENSP00000320176:p.GluProGluPro372dup	Somatic	106	.	.		WXS	Illumina HiSeq	Phase_I	131	21	0.160	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	In_Frame_Ins	INS	ENST00000314583.3	37	CCDS3003.1																																																																																			-|0.731;GGCTCAGGCTCA|0.269	0.269	strong		0.604	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	
ZNF844	284391	hgsc.bcm.edu	37	19	12187316	12187317	+	Frame_Shift_Del	DEL	CA	CA	-	rs201088213|rs61471402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187316_12187317delCA	ENST00000439326.3	+	4	1556_1557	c.1381_1382delCA	c.(1381-1383)cacfs	p.H461fs	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	461					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AGATCTGCCTCACACCTTCAAA	0.431														57	0.0113818	0.0371	0.0029	5008	,	,		24663	0.0		0.006	False		,,,				2504	0.0				p.460_461del		Atlas-Indel	.											.	ZNF844	69	.	0			c.1380_1381del						PASS	.			196,4068		7,182,1943						-5.0	0.0		dbSNP_129	63	24,8228		1,22,4103	no	frameshift	ZNF844	NM_001136501.1		8,204,6046	A1A1,A1R,RR		0.2908,4.5966,1.7578				220,12296				SO:0001589	frameshift_variant	284391	exon4			.	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1381_1382delCA	19.37:g.12187318_12187319delCA	ENSP00000392024:p.His461fs	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_001136501	Q5JPI8	Frame_Shift_Del	DEL	ENST00000439326.3	37	CCDS45985.1																																																																																			CA|0.987;-|0.013	0.013	strong		0.431	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
TDRD3	81550	hgsc.bcm.edu	37	13	61102576	61102578	+	In_Frame_Del	DEL	ATA	ATA	-	rs148917045|rs75684327	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:61102576_61102578delATA	ENST00000196169.3	+	11	1726_1728	c.938_940delATA	c.(937-942)gataat>gat	p.N315del	TDRD3_ENST00000377881.2_In_Frame_Del_p.N315del|TDRD3_ENST00000377894.2_In_Frame_Del_p.N315del|TDRD3_ENST00000535286.1_In_Frame_Del_p.N408del	NM_001146071.1|NM_030794.2	NP_001139543.1|NP_110421.1	Q9H7E2	TDRD3_HUMAN	tudor domain containing 3	315					chromatin modification (GO:0016568)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	40		Prostate(109;0.173)|Breast(118;0.174)		GBM - Glioblastoma multiforme(99;0.000291)		GGAGTAAAAGATAATAATCATCT	0.384														604	0.120607	0.0325	0.1153	5008	,	,		16312	0.0129		0.1889	False		,,,				2504	0.2843				p.406_406del	Colon(36;164 906 35820 50723)	Pindel,Atlas-Indel	.											TDRD3_ENST00000535286,NS,carcinoma,0,4	TDRD3	123	4	0			c.1216_1218del						PASS	.		,,	224,4040		12,200,1920					,,	6.1	1.0		dbSNP_134	101	1585,6669		152,1281,2694	no	coding,coding,coding	TDRD3	NM_030794.2,NM_001146071.1,NM_001146070.1	,,	164,1481,4614	A1A1,A1R,RR		19.2028,5.2533,14.4512	,,	,,		1809,10709				SO:0001651	inframe_deletion	81550	exon11			.	AK023578	CCDS9441.1, CCDS53872.1	13q14.3	2013-01-23			ENSG00000083544	ENSG00000083544		"""Tudor domain containing"""	20612	protein-coding gene	gene with protein product		614392					Standard	NM_030794		Approved	FLJ21007	uc010aeg.3	Q9H7E2	OTTHUMG00000017007	ENST00000196169.3:c.938_940delATA	13.37:g.61102579_61102581delATA	ENSP00000196169:p.Asn315del	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	67	50	0.746	NM_001146070	B2MWP9|Q53XA6|Q6P992	In_Frame_Del	DEL	ENST00000196169.3	37	CCDS9441.1																																																																																			ATA|0.894;-|0.106	0.106	strong		0.384	TDRD3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045175.2	NM_030794	
ASXL3	80816	hgsc.bcm.edu	37	18	31323500	31323500	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:31323500delC	ENST00000269197.5	+	12	3688	c.3688delC	c.(3688-3690)cttfs	p.L1230fs		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1230	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						TGTGCCCATGCTTTTTAATAA	0.368																																					p.M1229fs		Atlas-Indel	.											ASXL3_ENST00000269197,NS,carcinoma,+2,2	ASXL3	405	2	0			c.3687delG						PASS	.						82.0	74.0	76.0					18																	31323500		1835	4083	5918	SO:0001589	frameshift_variant	80816	exon12			.	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.3688delC	18.37:g.31323500delC	ENSP00000269197:p.Leu1230fs	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Frame_Shift_Del	DEL	ENST00000269197.5	37	CCDS45847.1																																																																																			.	.	none		0.368	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
KIAA0040	9674	hgsc.bcm.edu	37	1	175129948	175129955	+	Frame_Shift_Del	DEL	TCTTCTTG	TCTTCTTG	-	rs3208835|rs542219168|rs71563271|rs202239690|rs386636937|rs57794404		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TCTTCTTG	TCTTCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:175129948_175129955delTCTTCTTG	ENST00000423313.1	-	4	731_738	c.195_202delCAAGAAGA	c.(193-204)aacaagaagaagfs	p.NKK65fs	KIAA0040_ENST00000444639.1_Frame_Shift_Del_p.NKK65fs|KIAA0040_ENST00000545251.2_Frame_Shift_Del_p.NKK65fs|KIAA0040_ENST00000567124.1_5'Flank	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	ttcttcttcttcttcttgttcttctCTG	0.51																																					p.66_68del		Atlas-Indel	.											.	KIAA0040	2	.	0			c.196_203del						PASS	.																																			SO:0001589	frameshift_variant	9674	exon5			.	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.195_202delCAAGAAGA	1.37:g.175129948_175129955delTCTTCTTG	ENSP00000462172:p.Asn65fs	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	97	14	0.14433	NM_001162893	A8K9H6|Q2NKQ0	Frame_Shift_Del	DEL	ENST00000423313.1	37																																																																																				.	.	none		0.510	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
TICAM1	148022	hgsc.bcm.edu	37	19	4817288	4817289	+	In_Frame_Ins	INS	-	-	AGG	rs144100421|rs11466722|rs368322317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4817288_4817289insAGG	ENST00000248244.5	-	2	1330_1331	c.1101_1102insCCT	c.(1099-1104)ccttca>cctCCTtca	p.367_368insP		NM_182919.3	NP_891549.1	Q8IUC6	TCAM1_HUMAN	toll-like receptor adaptor molecule 1	367	Pro-rich.				apoptotic signaling pathway (GO:0097190)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of protein homodimerization activity (GO:0043496)|response to exogenous dsRNA (GO:0043330)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|ripoptosome (GO:0097342)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0139)		GGAGTAGATGAaggaggaggag	0.52														798	0.159345	0.2761	0.1311	5008	,	,		14915	0.0665		0.1491	False		,,,				2504	0.1278				p.S368delinsPS		Pindel,Atlas-Indel	.											.	TICAM1	69	.	0			c.1102_1103insCCT						PASS	.																																			SO:0001652	inframe_insertion	148022	exon2			.	AB086380	CCDS12136.1	19p13.3	2014-09-17				ENSG00000127666			18348	protein-coding gene	gene with protein product		607601				12539043, 12471095	Standard	NM_182919		Approved	TRIF, TICAM-1, MGC35334, PRVTIRB	uc002mbi.4	Q8IUC6		ENST00000248244.5:c.1099_1101dupCCT	19.37:g.4817295_4817297dupAGG	ENSP00000248244:p.Pro367_Pro367dup	Somatic	205	.	.		WXS	Illumina HiSeq	Phase_I	204	73	0.358	NM_182919	B3Y691|O75532|Q86XP8|Q96GA0	In_Frame_Ins	INS	ENST00000248244.5	37	CCDS12136.1																																																																																			.	.	strong		0.520	TICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450435.1	NM_014261	
OR5B3	441608	hgsc.bcm.edu	37	11	58170793	58170793	+	Frame_Shift_Del	DEL	G	G	-	rs200799158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58170793delG	ENST00000309403.2	-	1	89	c.90delC	c.(88-90)cccfs	p.P30fs		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	30			P -> L (in dbSNP:rs17152661).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TATAGATGAAGGGGAACGTTA	0.393													GgAG|GGGG|GGG|complex_deletion	68	0.0135783	0.0008	0.0245	5008	,	,		18777	0.0		0.0447	False		,,,				2504	0.0051				p.F31fs		Pindel,Atlas-Indel	.											.	OR5B3	65	.	0			c.91delT						PASS	.			53,4211		8,37,2087	120.0	113.0	115.0			-3.2	0.0	11		118	416,7838		23,370,3734	no	frameshift	OR5B3	NM_001005469.1		31,407,5821	A1A1,A1R,RR		5.04,1.243,3.7466			58170793	469,12049	2201	4293	6494	SO:0001589	frameshift_variant	441608	exon1			.	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"""GPCR / Class A : Olfactory receptors"""	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.90delC	11.37:g.58170793delG	ENSP00000308270:p.Pro30fs	Somatic	83	.	.		WXS	Illumina HiSeq	Phase_I	65	18	0.277	NM_001005469	Q6IEV6	Frame_Shift_Del	DEL	ENST00000309403.2	37	CCDS31549.1																																																																																			G|0.982;-|0.018	0.018	strong		0.393	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469	
APLF	200558	hgsc.bcm.edu	37	2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-	rs149897324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:68805143delA	ENST00000303795.4	+	10	1696	c.1525delA	c.(1525-1527)aaafs	p.K509fs	APLF_ENST00000471727.1_Intron	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	509					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AAGGTTTATGAAAAGAAAATA	0.358													AAAA|AAAA|AAA|deletion	23	0.00459265	0.0008	0.0058	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0061				p.M508fs		Pindel,Atlas-Indel	.											.	APLF	69	.	0			c.1524delG						PASS	.			15,4251		0,15,2118	68.0	74.0	72.0			2.8	1.0	2	dbSNP_134	73	121,8127		3,115,4006	no	frameshift	APLF	NM_173545.2		3,130,6124	A1A1,A1R,RR		1.467,0.3516,1.0868			68805143	136,12378	2203	4299	6502	SO:0001589	frameshift_variant	200558	exon10			.	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1525delA	2.37:g.68805143delA	ENSP00000307004:p.Lys509fs	Somatic	58	.	.		WXS	Illumina HiSeq	Phase_I	64	26	0.406	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Frame_Shift_Del	DEL	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.991;-|0.009	0.009	strong		0.358	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
CLCA4	22802	hgsc.bcm.edu	37	1	87045902	87045903	+	In_Frame_Ins	INS	-	-	CCTACT	rs1932809|rs4001061|rs77067122|rs56040873|rs574759485|rs368263974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:87045902_87045903insCCTACT	ENST00000370563.3	+	14	2676_2677	c.2634_2635insCCTACT	c.(2635-2637)cct>CCTACTcct	p.879_879P>PTP	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	879					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)		TTGAtcctacacctactcctac	0.347														18	0.00359425	0.0023	0.0101	5008	,	,		16699	0.0		0.007	False		,,,				2504	0.001				p.T878delinsTPT		Pindel,Atlas-Indel	.											.	CLCA4	131	.	0			c.2634_2635insCCTACT						PASS	.																																			SO:0001652	inframe_insertion	22802	exon14			.	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2653_2658dupCCTACT	1.37:g.87045903_87045908dupCCTACT	ENSP00000359594:p.ThrPro887dup	Somatic	160	.	.		WXS	Illumina HiSeq	Phase_I	139	30	0.216	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	In_Frame_Ins	INS	ENST00000370563.3	37	CCDS41355.1																																																																																			.	.	weak		0.347	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
BTBD10	84280	hgsc.bcm.edu	37	11	13410691	13410694	+	Intron	DEL	GAAA	GAAA	-	rs375824034|rs3833472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAAA	GAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:13410691_13410694delGAAA	ENST00000278174.5	-	9	1363				BTBD10_ENST00000528120.1_Intron|BTBD10_ENST00000530907.1_Intron	NM_032320.5	NP_115696.2	Q9BSF8	BTBDA_HUMAN	BTB (POZ) domain containing 10							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)		AGGATAACCTGAAAGAAAGAAAGA	0.392														407	0.08127	0.0772	0.0764	5008	,	,		19335	0.0675		0.1233	False		,,,				2504	0.0613				.		Pindel,Atlas-Indel	.											.	BTBD10	43	.	0			.						PASS	.			358,3904		23,312,1796						4.1	1.0		dbSNP_107	46	1001,7253		58,885,3184	no	intron	BTBD10	NM_032320.5		81,1197,4980	A1A1,A1R,RR		12.1275,8.3998,10.8581				1359,11157				SO:0001627	intron_variant	84280	.			.	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.1118-3TTTC>-	11.37:g.13410699_13410702delGAAA		Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	56	35	0.625	.	B7Z228|Q86WG1	Splice_Site	DEL	ENST00000278174.5	37	CCDS7811.1																																																																																			GAAA|0.908;-|0.092	0.092	strong		0.392	BTBD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386200.1	NM_032320	
PI4KAP2	375133	hgsc.bcm.edu	37	22	21829514	21829517	+	RNA	DEL	TGTC	TGTC	-	rs113567369|rs57294418	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGTC	TGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:21829514_21829517delTGTC	ENST00000450651.1	-	0	1821_1824							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						AGAGCTTGATTGTCTGGCCGCGAA	0.564														3270	0.652955	0.8162	0.5865	5008	,	,		11476	0.4454		0.8708	False		,,,				2504	0.4693				.		Atlas-Indel	.											.	PI4KAP2	11	.	0			.						PASS	.			3028,976		1236,556,210						2.4	1.0		dbSNP_132	21	6139,1303		2723,693,305	no	intergenic				3959,1249,515	A1A1,A1R,RR		17.5087,24.3756,19.9109				9167,2279						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.21829514_21829517delTGTC		Somatic	380	0	0		WXS	Illumina HiSeq	Phase_I	456	47	0.10307	.	Q6ICJ0|Q6ZT68|Q8WUK7	RNA	DEL	ENST00000450651.1	37																																																																																				TGTC|0.500;-|0.500	0.500	strong		0.564	PI4KAP2-005	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000334908.1		
A2ML1	144568	hgsc.bcm.edu	37	12	9016563	9016564	+	Frame_Shift_Del	DEL	GC	GC	-	rs144686314		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9016563_9016564delGC	ENST00000299698.7	+	29	3856_3857	c.3676_3677delGC	c.(3676-3678)gccfs	p.A1226fs	A2ML1_ENST00000539547.1_Frame_Shift_Del_p.A735fs	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						GGCTTGGTTGGCCAAGCAACAC	0.485														135	0.0269569	0.0023	0.0432	5008	,	,		15031	0.002		0.0447	False		,,,				2504	0.0562				p.1225_1226del		Pindel,Atlas-Indel	.											.	A2ML1	199	.	0			c.3675_3676del						PASS	.			39,3661		1,37,1812						1.6	0.3		dbSNP_134	52	418,7468		17,384,3542	no	frameshift	A2ML1	NM_144670.3		18,421,5354	A1A1,A1R,RR		5.3005,1.0541,3.9444				457,11129				SO:0001589	frameshift_variant	144568	exon29			.	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.3676_3677delGC	12.37:g.9016563_9016564delGC	ENSP00000299698:p.Ala1226fs	Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	59	21	0.356	NM_144670		Frame_Shift_Del	DEL	ENST00000299698.7	37	CCDS8596.2																																																																																			GC|0.979;-|0.021	0.021	strong		0.485	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
HNRNPA0	10949	hgsc.bcm.edu	37	5	137088945	137088946	+	In_Frame_Ins	INS	-	-	GCT	rs78232709|rs201570235|rs548286503	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:137088945_137088946insGCT	ENST00000314940.4	-	1	1093_1094	c.810_811insAGC	c.(808-813)agcggc>agcAGCggc	p.270_271insS		NM_006805.3	NP_006796.1	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	270	Gly-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|response to lipopolysaccharide (GO:0032496)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			large_intestine(1)|lung(2)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ccgccgccgccgcTCTTCATGG	0.673														38	0.00758786	0.0015	0.013	5008	,	,		9196	0.0		0.0209	False		,,,				2504	0.0061				p.G271delinsSG		Pindel,Atlas-Indel	.											.	HNRNPA0	17	.	0			c.811_812insAGC						PASS	.			20,3804		3,14,1895						2.6	0.0		dbSNP_131	9	196,7418		14,168,3625	no	coding	HNRNPA0	NM_006805.3		17,182,5520	A1A1,A1R,RR		2.5742,0.523,1.8884				216,11222				SO:0001652	inframe_insertion	10949	exon1			.	U23803	CCDS4193.1	5q31	2013-02-12		2007-08-16	ENSG00000177733	ENSG00000177733		"""RNA binding motif (RRM) containing"""	5030	protein-coding gene	gene with protein product		609409		HNRPA0		7585247	Standard	NM_006805		Approved	hnRNPA0	uc003lbt.3	Q13151	OTTHUMG00000129156	ENST00000314940.4:c.808_810dupAGC	5.37:g.137088946_137088948dupGCT	ENSP00000316042:p.Ser270_Ser270dup	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	91	22	0.242	NM_006805	Q6IB18	In_Frame_Ins	INS	ENST00000314940.4	37	CCDS4193.1																																																																																			.	.	none		0.673	HNRNPA0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251221.1	NM_006805	
RBMX	27316	hgsc.bcm.edu	37	X	135956571	135956572	+	Frame_Shift_Ins	INS	-	-	GG	rs369155856		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135956571_135956572insGG	ENST00000320676.7	-	9	1059_1060	c.905_906insCC	c.(904-906)ccafs	p.P302fs	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Frame_Shift_Ins_p.P174fs|RBMX_ENST00000570135.1_Frame_Shift_Ins_p.P167fs|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	302					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CACCATAAGATGGCGGGGGCCC	0.465																																					p.P302fs		Atlas-Indel	.											.	RBMX	149	.	0			c.906_907insCC						PASS	.																																			SO:0001589	frameshift_variant	27316	exon9			.		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.904_905dupCC	X.37:g.135956572_135956573dupGG	ENSP00000359645:p.Pro302fs	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	160	35	0.21875	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Frame_Shift_Ins	INS	ENST00000320676.7	37	CCDS14661.1																																																																																			.	.	weak		0.465	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7661048	7661050	+	In_Frame_Del	DEL	CTC	CTC	-	rs375552735|rs143023559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7661048_7661050delCTC	ENST00000299492.4	+	15	1710_1712	c.1322_1324delCTC	c.(1321-1326)tctcct>tct	p.P443del	PPFIBP2_ENST00000528883.1_In_Frame_Del_p.P331del|PPFIBP2_ENST00000533792.1_In_Frame_Del_p.P285del|PPFIBP2_ENST00000530181.1_In_Frame_Del_p.P300del|PPFIBP2_ENST00000530582.1_3'UTR	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	443					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.P442S(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		GCTGCCAAATCTCCTCCCACCAT	0.596														226	0.0451278	0.0129	0.0576	5008	,	,		18604	0.0933		0.0477	False		,,,				2504	0.0276				p.441_441del		Pindel,Atlas-Indel	.											.	PPFIBP2	87	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.1321_1323del						PASS	.			85,4179		1,83,2048						1.4	0.0		dbSNP_134	94	316,7928		9,298,3815	no	coding	PPFIBP2	NM_003621.2		10,381,5863	A1A1,A1R,RR		3.8331,1.9934,3.2059				401,12107				SO:0001651	inframe_deletion	8495	exon15			.	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1322_1324delCTC	11.37:g.7661051_7661053delCTC	ENSP00000299492:p.Pro443del	Somatic	111	.	.		WXS	Illumina HiSeq	Phase_I	137	47	0.343	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	In_Frame_Del	DEL	ENST00000299492.4	37	CCDS31419.1																																																																																			CTC|0.944;-|0.056	0.056	strong		0.596	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
HSP90B1	7184	hgsc.bcm.edu	37	12	104341188	104341190	+	In_Frame_Del	DEL	GAA	GAA	-	rs5800607|rs201427769	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:104341188_104341190delGAA	ENST00000299767.5	+	17	2544_2546	c.2362_2364delGAA	c.(2362-2364)gaadel	p.E791del	C12orf73_ENST00000543740.2_5'Flank	NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	791					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)			central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	gggaacagatgaagaagaagaaA	0.424														600	0.119808	0.0053	0.111	5008	,	,		20608	0.3254		0.0954	False		,,,				2504	0.0941				p.787_788del		Pindel,Atlas-Indel	.											.	HSP90B1	72	.	0			c.2361_2363del						PASS	.			250,4012		72,106,1953						-7.4	0.4		dbSNP_114	222	1075,7179		156,763,3208	no	coding	HSP90B1	NM_003299.1		228,869,5161	A1A1,A1R,RR		13.024,5.8658,10.5864				1325,11191				SO:0001651	inframe_deletion	7184	exon17			.	AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.2362_2364delGAA	12.37:g.104341197_104341199delGAA	ENSP00000299767:p.Glu791del	Somatic	150	.	.		WXS	Illumina HiSeq	Phase_I	168	54	0.321	NM_003299	Q96A97	In_Frame_Del	DEL	ENST00000299767.5	37	CCDS9094.1																																																																																			GAA|0.865;-|0.135	0.135	strong		0.424	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
IFNE	338376	hgsc.bcm.edu	37	9	21482125	21482126	+	5'UTR	INS	-	-	A	rs397819775|rs34814436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:21482125_21482126insA	ENST00000448696.3	-	0	186_187				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						GAGTAAAACTTACCAAAGGCTT	0.292													?|A|AA|unsure	958	0.191294	0.1498	0.2147	5008	,	,		15147	0.0417		0.331	False		,,,				2504	0.2413				.		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.-433->T	9.37:g.21482126_21482126dupA		Somatic	102	.	.		WXS	Illumina HiSeq	Phase_I	74	25	0.338	.		RNA	INS	ENST00000448696.3	37	CCDS34997.1																																																																																			-|0.806;A|0.194	0.194	strong		0.292	IFNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051901.2	NM_176891	
DMKN	93099	hgsc.bcm.edu	37	19	36002419	36002421	+	In_Frame_Del	DEL	CCA	CCA	-	rs72334573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36002419_36002421delCCA	ENST00000339686.3	-	5	986_988	c.810_812delTGG	c.(808-813)ggtggc>ggc	p.270_271GG>G	DMKN_ENST00000440396.1_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000418261.1_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000451297.2_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000424570.2_In_Frame_Del_p.270_271GG>G|DMKN_ENST00000436012.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	270	Gly-rich.			Missing (in Ref. 3; ABN11273/ABN11274). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			actgctgctgccaccactgctgc	0.655														1022	0.204073	0.2405	0.1369	5008	,	,		13814	0.3403		0.172	False		,,,				2504	0.0951				p.271_271del		Atlas-Indel	.											DMKN,colon,carcinoma,-2,1	DMKN	116	1	0			c.811_813del						PASS	.		,,,,,,	945,3305		85,775,1265					,,,,,,	-1.4	0.0		dbSNP_132	28	1553,6687		146,1261,2713	no	coding,coding,coding,intron,coding,coding,intron	DMKN	NM_033317.4,NM_001190349.1,NM_001190348.1,NM_001190347.1,NM_001126058.2,NM_001126057.2,NM_001126056.2	,,,,,,	231,2036,3978	A1A1,A1R,RR		18.8471,22.2353,20.0	,,,,,,	,,,,,,		2498,9992				SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.810_812delTGG	19.37:g.36002422_36002424delCCA	ENSP00000342012:p.Gly271del	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	61	35	0.57377	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			CCA|0.786;-|0.214	0.214	strong		0.655	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
PHF14	9678	hgsc.bcm.edu	37	7	11091329	11091330	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:11091329_11091330insA	ENST00000403050.3	+	14	2855_2856	c.2403_2404insA	c.(2404-2406)aggfs	p.R802fs	PHF14_ENST00000445996.2_Frame_Shift_Ins_p.R517fs	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	802					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		AACGATCAAGGAGGCAGATTAA	0.446																																					p.R801fs		Atlas-Indel	.											.	PHF14	90	.	0			c.2403_2404insA						PASS	.																																			SO:0001589	frameshift_variant	9678	exon14			.	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"""Zinc fingers, PHD-type"""	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.2404dupA	7.37:g.11091330_11091330dupA	ENSP00000385795:p.Arg802fs	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	76	16	0.210526	NM_014660	A7MCZ3|B4DI82	Frame_Shift_Ins	INS	ENST00000403050.3	37	CCDS47542.1																																																																																			.	.	none		0.446	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660	
KIAA0586	9786	hgsc.bcm.edu	37	14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-	rs534542684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:58899157delG	ENST00000556134.1	+	5	621	c.347delG	c.(346-348)agafs	p.R116fs	KIAA0586_ENST00000261244.5_Frame_Shift_Del_p.R131fs|KIAA0586_ENST00000423743.3_Frame_Shift_Del_p.R46fs|KIAA0586_ENST00000354386.6_Frame_Shift_Del_p.R143fs	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	116					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						GATGCTCTAAGAACAGTTTTA	0.279													G|G|-|deletion	12	0.00239617	0.0	0.0058	5008	,	,		15268	0.0		0.007	False		,,,				2504	0.001				p.R143fs		Pindel,Atlas-Indel	.											.	KIAA0586	180	.	0			c.427delA						PASS	.			3,3511		0,3,1754	44.0	43.0	43.0			5.2	1.0	14		43	25,7757		0,25,3866	no	frameshift	KIAA0586	NM_014749.3		0,28,5620	A1A1,A1R,RR		0.3213,0.0854,0.2479			58899157	28,11268	1814	4055	5869	SO:0001589	frameshift_variant	9786	exon5			.	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.347delG	14.37:g.58899157delG	ENSP00000452351:p.Arg116fs	Somatic	154	.	.		WXS	Illumina HiSeq	Phase_I	171	61	0.357	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Frame_Shift_Del	DEL	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	none		0.279	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749	
OR8B3	390271	hgsc.bcm.edu	37	11	124266697	124266698	+	Frame_Shift_Ins	INS	-	-	G	rs201661436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124266697_124266698insG	ENST00000354597.3	-	1	566_567	c.550_551insC	c.(550-552)ctcfs	p.L184fs		NM_001005467.1	NP_001005467.1	Q8NGG8	OR8B3_HUMAN	olfactory receptor, family 8, subfamily B, member 3	184						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AAGCTGGAGGAGGGGGAGTATG	0.49													ggggg|GGGGG|GGGGGG|insertion	176	0.0351438	0.0008	0.0288	5008	,	,		20997	0.0079		0.0477	False		,,,				2504	0.1012				p.L184fs		Atlas-Indel	.											.	OR8B3	36	.	0			c.551_552insC						PASS	.			41,4223		0,41,2091						3.6	1.0			43	431,7821		14,403,3709	no	frameshift	OR8B3	NM_001005467.1		14,444,5800	A1A1,A1R,RR		5.223,0.9615,3.7712				472,12044				SO:0001589	frameshift_variant	390271	exon1			.	AB065827	CCDS31709.1	11q24.1	2012-08-09			ENSG00000196661	ENSG00000196661		"""GPCR / Class A : Olfactory receptors"""	8472	protein-coding gene	gene with protein product							Standard	NM_001005467		Approved		uc010saj.2	Q8NGG8	OTTHUMG00000165983	ENST00000354597.3:c.551dupC	11.37:g.124266702_124266702dupG	ENSP00000346611:p.Leu184fs	Somatic	422	0	0		WXS	Illumina HiSeq	Phase_I	442	156	0.352941	NM_001005467	Q6IFQ8|Q8NGH1	Frame_Shift_Ins	INS	ENST00000354597.3	37	CCDS31709.1																																																																																			-|0.977;G|0.023	0.023	strong		0.490	OR8B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387291.1	NM_001005467	
HLA-B	3106	hgsc.bcm.edu	37	6	31324737	31324737	+	Intron	DEL	G	G	-	rs151341085|rs371250843	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31324737delG	ENST00000412585.2	-	2	102					NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B						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						GTGGGAGCCTGGGGGTGAGGA	0.721									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				|||unknown(NO_COVERAGE)	130	0.0259585	0.0318	0.0389	5008	,	,		10733	0.004		0.0378	False		,,,				2504	0.0194				.		Pindel,Atlas-Indel	.											.	HLA-B	54	.	0			c.74-2C>-						PASS	.						8.0	7.0	8.0					6																	31324737		2008	3903	5911	SO:0001627	intron_variant	3106	exon3	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.74-3C>-	6.37:g.31324737delG		Somatic	13	.	.		WXS	Illumina HiSeq	Phase_I	33	13	0.394	NM_005514	Q29764	Splice_Site	DEL	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	weak		0.721	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026122	176026134	+	Frame_Shift_Del	DEL	CAAAGACCCAGGA	CAAAGACCCAGGA	-	rs3797464|rs200519605|rs386695335|rs550332435|rs142779818|rs371149640|rs199714570|rs373697082	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAAAGACCCAGGA	CAAAGACCCAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176026122_176026134delCAAAGACCCAGGA	ENST00000303991.4	-	2	879_891	c.702_714delTCCTGGGTCTTTG	c.(700-714)gatcctgggtctttgfs	p.DPGSL234fs		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	234				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)		p.L238L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCACCTTTCTCAAAGACCCAGGATCCTCCTTCC	0.488																																					p.235_239del		Atlas-Indel	.											.	GPRIN1	77	.	1	Substitution - coding silent(1)	lung(1)	c.703_715del						PASS	.			721,3495		76,569,1463						-0.3	0.0		dbSNP_107	106	1092,7070		103,886,3092	no	frameshift	GPRIN1	NM_052899.2		179,1455,4555	A1A1,A1R,RR		13.3791,17.1015,14.647				1813,10565				SO:0001589	frameshift_variant	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.702_714delTCCTGGGTCTTTG	5.37:g.176026122_176026134delCAAAGACCCAGGA	ENSP00000305839:p.Asp234fs	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	108	19	0.175926	NM_052899	C9JM70|Q8ND74|Q96PZ4	Frame_Shift_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	none		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382373	24382374	+	IGR	INS	-	-	TGC	rs371342199|rs35206911|rs201827126		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:24382373_24382374insTGC								AC004552.1 (15350 upstream) : PDK3 (100963 downstream)																							gctgctgctattgctgctgctg	0.574																																					p.I499delinsIA		Atlas-Indel	.											.	.	.	.	0			c.1496_1497insTGC						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382380_24382382dupTGC		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	167	34	0.203593	NM_001136234		In_Frame_Ins	INS		37																																																																																				.	.	weak	0	0.574								
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75816814	75816815	+	Intron	INS	-	-	ACA	rs199738162|rs397750292|rs144850646|rs59277111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:75816814_75816815insACA	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000320460.4_In_Frame_Ins_p.239_240insN|GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000378692.3_Intron	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2							integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						TAATGGATTGGACAAGAAAAAT	0.312														1714	0.342252	0.2511	0.2622	5008	,	,		17045	0.4683		0.3767	False		,,,				2504	0.3569				p.D239delinsDN		Pindel,Atlas-Indel	.											.	GLIPR1L2	54	.	0			c.715_716insACA						PASS	.			1181,3083		163,855,1114						0.0	0.0		dbSNP_130	117	3246,5006		650,1946,1530	no	coding	GLIPR1L2	NM_152436.1		813,2801,2644	A1A1,A1R,RR		39.3359,27.697,35.3707				4427,8089				SO:0001627	intron_variant	144321	exon4			.	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.670+45->ACA	12.37:g.75816815_75816817dupACA		Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	64	26	0.406	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	In_Frame_Ins	INS	ENST00000550916.1	37	CCDS58258.1																																																																																			.	.	strong		0.312	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33801989	33801990	+	Frame_Shift_Ins	INS	-	-	AAAA	rs532206571		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33801989_33801990insAAAA	ENST00000260908.7	-	4	1836_1837	c.1719_1720insTTTT	c.(1717-1722)tttcgtfs	p.R574fs	SLFN12L_ENST00000361112.4_Frame_Shift_Ins_p.R603fs|SLFN12L_ENST00000449046.1_Frame_Shift_Ins_p.R605fs	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	574						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						aaacaaaaacgaaacaaacaaa	0.381																																					p.R574fs		Pindel,Atlas-Indel	.											.	SLFN12L	140	.	0			c.1720_1721insTTTT						PASS	.																																			SO:0001589	frameshift_variant	100506736	exon4			.	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.1719_1720insTTTT	17.37:g.33801989_33801990insAAAA	ENSP00000437635:p.Arg574fs	Somatic	86	.	.		WXS	Illumina HiSeq	Phase_I	61	25	0.410	NM_001195790	F5H6G3	Frame_Shift_Ins	INS	ENST00000260908.7	37	CCDS56026.1																																																																																			.	.	none		0.381	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
HDGFRP2	84717	hgsc.bcm.edu	37	19	4498017	4498019	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4498017_4498019delAGA	ENST00000301284.4	+	11	1455_1457	c.1391_1393delAGA	c.(1390-1395)gagaag>gag	p.K467del	HDGFRP2_ENST00000586684.1_In_Frame_Del_p.K467del	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		467					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGGAAGGTAGAGAAGAAGAAAGG	0.66																																					p.464_464del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1390_1392del						PASS	.																																			SO:0001651	inframe_deletion	0	exon11			.																												ENST00000301284.4:c.1391_1393delAGA	19.37:g.4498023_4498025delAGA	ENSP00000301284:p.Lys467del	Somatic	78	.	.		WXS	Illumina HiSeq	Phase_I	79	32	0.405	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	In_Frame_Del	DEL	ENST00000301284.4	37	CCDS42472.1																																																																																			.	.	none		0.660	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
CPS1	1373	hgsc.bcm.edu	37	2	211421452	211421453	+	5'UTR	INS	-	-	TCT	rs61509952|rs3835047|rs34778124|rs201874641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211421452_211421453insTCT	ENST00000233072.5	+	0	191_192				CPS1_ENST00000430249.2_In_Frame_Ins_p.5_6insF	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial						anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	GCCACAAATCATCAAAATGACG	0.347														2389	0.477037	0.5968	0.5086	5008	,	,		19934	0.3492		0.4175	False		,,,				2504	0.4857				p.I5delinsIF		Pindel,Atlas-Indel	.											.	CPS1	485	.	0			c.13_14insTCT						PASS	.		,	2464,1802		707,1050,376					,	3.0	1.0		dbSNP_107	63	3312,4938		646,2020,1459	no	utr-5,coding	CPS1	NM_001875.4,NM_001122633.2	,	1353,3070,1835	A1A1,A1R,RR		40.1455,42.241,46.1489	,	,		5776,6740				SO:0001623	5_prime_UTR_variant	1373	exon2			.	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.-5->TCT	2.37:g.211421452_211421453insTCT		Somatic	150	.	.		WXS	Illumina HiSeq	Phase_I	118	34	0.288	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	In_Frame_Ins	INS	ENST00000233072.5	37	CCDS2393.1																																																																																			-|0.556;TCT|0.444	0.444	strong		0.347	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
BTN2A3P	54718	hgsc.bcm.edu	37	6	26422387	26422388	+	RNA	INS	-	-	CTTCCTCCTCCT	rs141260282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26422387_26422388insCTTCCTCCTCCT	ENST00000466808.2	+	0	41_42							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)											CGGCCAGCCTCCCTCCTCCTCC	0.589														503	0.100439	0.1188	0.1427	5008	,	,		16333	0.0258		0.1083	False		,,,				2504	0.1145				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.																																					54718	.			.	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422387_26422388insCTTCCTCCTCCT		Somatic	95	.	.		WXS	Illumina HiSeq	Phase_I	64	19	0.297	.	A6NEF4	RNA	INS	ENST00000466808.2	37																																																																																				.	.	strong		0.589	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000040118.4	NR_027795	
ASPHD1	253982	hgsc.bcm.edu	37	16	29912802	29912803	+	In_Frame_Ins	INS	-	-	GGT	rs35784618|rs140411458|rs375867010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:29912802_29912803insGGT	ENST00000308748.5	+	1	762_763	c.510_511insGGT	c.(511-513)ggt>GGTggt	p.171_171G>GG	SEZ6L2_ENST00000537485.1_5'Flank|SEZ6L2_ENST00000350527.3_5'Flank|ASPHD1_ENST00000483405.1_Intron|SEZ6L2_ENST00000308713.5_5'Flank|SEZ6L2_ENST00000346932.5_5'Flank	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	171	Gly-rich.				peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)	dioxygenase activity (GO:0051213)			endometrium(4)|large_intestine(2)|lung(1)|prostate(1)	8						GGGCAGCTCAGGGTGGCCCAGG	0.673														1013	0.202276	0.1104	0.2925	5008	,	,		13741	0.0804		0.4563	False		,,,				2504	0.1268				p.Q170delinsQG		Pindel,Atlas-Indel	.											.	ASPHD1	28	.	0			c.510_511insGGT						PASS	.			673,3567		66,541,1513						3.2	1.0		dbSNP_126	30	3768,4432		929,1910,1261	no	coding	ASPHD1	NM_181718.3		995,2451,2774	A1A1,A1R,RR		45.9512,15.8726,35.6994				4441,7999				SO:0001652	inframe_insertion	253982	exon1			.	AF070642	CCDS10660.1	16p11.2	2008-02-05			ENSG00000174939	ENSG00000174939			27380	protein-coding gene	gene with protein product							Standard	NM_181718		Approved		uc002dut.3	Q5U4P2	OTTHUMG00000132121	ENST00000308748.5:c.511_513dupGGT	16.37:g.29912803_29912805dupGGT	ENSP00000311447:p.Gly172dup	Somatic	14	.	.		WXS	Illumina HiSeq	Phase_I	39	18	0.462	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	In_Frame_Ins	INS	ENST00000308748.5	37	CCDS10660.1																																																																																			-|0.756;GGT|0.244	0.244	strong		0.673	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718	
FKBP15	23307	hgsc.bcm.edu	37	9	115932150	115932151	+	In_Frame_Ins	INS	-	-	TTC	rs370557763|rs113480096|rs62620695	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115932150_115932151insTTC	ENST00000238256.3	-	26	2955_2956	c.2838_2839insGAA	c.(2836-2841)gaaaaa>gaaGAAaaa	p.946_947insE		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	946					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						tcttctgctttttcttcttctt	0.525																																					p.K947delinsEK		Pindel,Atlas-Indel	.											.	FKBP15	128	.	0			c.2839_2840insGAA						PASS	.																																			SO:0001652	inframe_insertion	23307	exon26			.	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2836_2838dupGAA	9.37:g.115932157_115932159dupTTC	ENSP00000238256:p.Glu946_Glu946dup	Somatic	44	.	.		WXS	Illumina HiSeq	Phase_I	44	11	0.250	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	In_Frame_Ins	INS	ENST00000238256.3	37	CCDS48007.1																																																																																			-|0.943;TTC|0.057	0.057	strong		0.525	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
TLX1NB	100038246	hgsc.bcm.edu	37	10	102849370	102849370	+	Frame_Shift_Del	DEL	T	T	-	rs200664029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:102849370delT	ENST00000445873.1	-	3	1569	c.293delA	c.(292-294)cagfs	p.Q98fs	TLX1NB_ENST00000425505.1_5'Flank	NM_001085398.1	NP_001078867.1	P0CAT3	TLXNB_HUMAN	TLX1 neighbor	98																	TTTCTCCAGCTGAGGTGACCT	0.572													T|T|-|deletion	7	0.00139776	0.0008	0.0014	5008	,	,		15955	0.0		0.005	False		,,,				2504	0.0				p.Q98fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.294delG						PASS	.			8,3620		0,8,1806	33.0	33.0	33.0			1.1	0.0	10		33	75,7807		1,73,3867	no	frameshift	TLX1NB	NM_001085398.1		1,81,5673	A1A1,A1R,RR		0.9515,0.2205,0.7211			102849370	83,11427	1881	4116	5997	SO:0001589	frameshift_variant	100038246	exon3			.	BC019674	CCDS60615.1	10q24	2014-04-01			ENSG00000236311	ENSG00000236311			37183	protein-coding gene	gene with protein product		612734				17303350	Standard	NM_001085398		Approved	TD1, TDI, APT-B7	uc001ksv.3	P0CAT3	OTTHUMG00000018925	ENST00000445873.1:c.293delA	10.37:g.102849370delT	ENSP00000475001:p.Gln98fs	Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	97	33	0.340	NM_001085398		Frame_Shift_Del	DEL	ENST00000445873.1	37																																																																																				T|0.996;-|0.004	0.004	strong		0.572	TLX1NB-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000049925.2	NM_001085398	
HOXD9	3235	hgsc.bcm.edu	37	2	176988290	176988291	+	In_Frame_Ins	INS	-	-	GCA	rs529626130|rs35578003|rs200417886|rs397814627|rs559323002|rs56007470	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:176988290_176988291insGCA	ENST00000249499.6	+	1	1203_1204	c.794_795insGCA	c.(793-798)ccgcag>ccGCAgcag	p.269_270insQ	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	269			Missing. {ECO:0000269|PubMed:11857506}.		adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		CATTCGCAGCCGCAGCAGCAGC	0.554																																					p.P265delinsPQ	GBM(47;924 952 7959 9248 12176)	Pindel,Atlas-Indel	.											.	HOXD9	49	.	0			c.794_795insGCA						PASS	.																																			SO:0001652	inframe_insertion	3235	exon1			.		CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"""Homeoboxes / ANTP class : HOXL subclass"""	5140	protein-coding gene	gene with protein product		142982	"""homeo box D9"""	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.804_806dupGCA	2.37:g.176988297_176988299dupGCA	ENSP00000249499:p.Gln269_Gln269dup	Somatic	24	.	.		WXS	Illumina HiSeq	Phase_I	33	13	0.394	NM_014213	Q86ST1	In_Frame_Ins	INS	ENST00000249499.6	37	CCDS2267.2																																																																																			-|0.685;GCA|0.315	0.315	strong		0.554	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4		
TBP	6908	hgsc.bcm.edu	37	6	170871038	170871040	+	In_Frame_Del	DEL	CAA	CAA	-	rs71815788|rs55736770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	62	0	0		WXS	Illumina HiSeq	Phase_I	44	36	0.818182	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	
E2F4	1874	hgsc.bcm.edu	37	16	67229794	67229811	+	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAG	-	rs544893537|rs562856782|rs557254925|rs577742150|rs3830472|rs575614504	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67229794_67229811delCAGCAGCAGCAGCAGCAG	ENST00000379378.3	+	7	977_994	c.918_935delCAGCAGCAGCAGCAGCAG	c.(916-936)gacagcagcagcagcagcagc>gac	p.SSSSSS313del		NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	313	Poly-Ser.				blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.S319_N320insS(1)		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)		CCCTGCTGGAcagcagcagcagcagcagcagcagcagc	0.606																																					p.306_312del		Pindel,Atlas-Indel	.											.	E2F4	25	.	1	Insertion - In frame(1)	breast(1)	c.917_934del						PASS	.			119,95,114,24,205,410,3265		18,0,2,1,4,4,72,33,0,0,1,3,25,17,1,6,2,69,2,2,3,13,37,6,112,34,324,1325						4.1	0.9		dbSNP_132	47	48,74,119,62,17,1047,6793		16,0,0,2,0,3,11,16,0,0,0,1,41,6,2,0,1,104,4,0,2,48,1,0,15,34,972,2801	no	codingComplex	E2F4	NM_001950.3		34,0,2,3,4,7,83,49,0,0,1,4,66,23,3,6,3,173,6,2,5,61,38,6,127,68,1296,4126	A1A1,A1A2,A1A3,A1A4,A1A5,A1A6,A1R,A2A2,A2A3,A2A4,A2A5,A2A6,A2R,A3A3,A3A4,A3A5,A3A6,A3R,A4A4,A4A5,A4A6,A4R,A5A5,A5A6,A5R,A6A6,A6R,RR		16.7525,22.8497,18.8347				167,169,233,86,222,1457,10058				SO:0001651	inframe_deletion	1874	exon7			.	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.918_935delCAGCAGCAGCAGCAGCAG	16.37:g.67229794_67229811delCAGCAGCAGCAGCAGCAG	ENSP00000368686:p.Ser313_Ser318del	Somatic	77	.	.		WXS	Illumina HiSeq	Phase_I	87	26	0.299	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	In_Frame_Del	DEL	ENST00000379378.3	37	CCDS32464.1																																																																																			-|1.000;|0.000	1.000	alt		0.606	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
FOXD4L4	349334	hgsc.bcm.edu	37	9	70427685	70427685	+	Frame_Shift_Del	DEL	G	G	-	rs59364037		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:70427685delG	ENST00000377413.1	-	1	2046	c.1215delC	c.(1213-1215)tgcfs	p.C405fs		NM_199244.2	NP_954714.2	Q8WXT5	FX4L4_HUMAN	forkhead box D4-like 4	405					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)								GBM - Glioblastoma multiforme(29;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W406fs		Pindel,Atlas-Indel	.											.	FOXD4L4	5	.	0			c.1216delT						PASS	.																																			SO:0001589	frameshift_variant	349334	exon1			.		CCDS75845.1	9q13	2007-03-19			ENSG00000184659	ENSG00000184659			23762	protein-coding gene	gene with protein product		611085					Standard	NM_199244		Approved	bA460E7.2, OTTHUMG00000013337		Q8WXT5	OTTHUMG00000013337	ENST00000377413.1:c.1215delC	9.37:g.70427685delG	ENSP00000366630:p.Cys405fs	Somatic	208	.	.		WXS	Illumina HiSeq	Phase_I	293	45	0.154	NM_199244	Q5RIB4	Frame_Shift_Del	DEL	ENST00000377413.1	37	CCDS6621.1																																																																																			.	.	weak		0.677	FOXD4L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037143.2		
MICA	100507436	hgsc.bcm.edu	37	6	31380158	31380161	+	Frame_Shift_Del	DEL	GCTG	GCTG	-	rs41293539|rs547446871|rs138201170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCTG	GCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31380158_31380161delGCTG	ENST00000449934.2	+	5	1003_1006	c.949_952delGCTG	c.(949-954)gctggcfs	p.AG317fs	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TGCTGTTGCTGCTGGCTGCTGCTA	0.456														480	0.0958466	0.0976	0.0692	5008	,	,		20271	0.121		0.1203	False		,,,				2504	0.0613				p.316_317del		Pindel,Atlas-Indel	.											.	MICA	21	.	0			c.948_951del						PASS	.			1009,2901		76,857,1022						0.3	0.0		dbSNP_127	255	1985,6023		143,1699,2162	no	frameshift	MICA	NM_001177519.1		219,2556,3184	A1A1,A1R,RR		24.7877,25.8056,25.1217				2994,8924				SO:0001589	frameshift_variant	100507436	exon5			.	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.949_952delGCTG	6.37:g.31380162_31380165delGCTG	ENSP00000413079:p.Ala317fs	Somatic	176	.	.		WXS	Illumina HiSeq	Phase_I	121	39	0.322	NM_001177519		Frame_Shift_Del	DEL	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	strong		0.456	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CHRNA7	1139	hgsc.bcm.edu	37	15	32449875	32449876	+	Frame_Shift_Del	DEL	TG	TG	-	rs374603734		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:32449875_32449876delTG	ENST00000306901.3	+	6	594_595	c.497_498delTG	c.(496-498)ctgfs	p.L166fs	CHRNA7_ENST00000454250.3_Frame_Shift_Del_p.L195fs|CHRNA7_ENST00000455693.2_5'UTR	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	166					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)			endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	CACTGCAAACTGAAGTTTGGGT	0.505																																					p.195_195del	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-Indel	.											.	CHRNA7	57	.	0			c.583_584del						PASS	.		,	3,2221		1,1,1110					,	5.0	0.8			13	19,4303		2,15,2144	no	frameshift,frameshift	CHRNA7	NM_001190455.1,NM_000746.4	,	3,16,3254	A1A1,A1R,RR		0.4396,0.1349,0.3361	,	,		22,6524				SO:0001589	frameshift_variant	1139	exon6			.	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1960	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 7 (neuronal)"""	118511	"""cholinergic receptor, nicotinic, alpha polypeptide 7"""			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.497_498delTG	15.37:g.32449875_32449876delTG	ENSP00000303727:p.Leu166fs	Somatic	830	0	0		WXS	Illumina HiSeq	Phase_I	1120	202	0.180357	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Frame_Shift_Del	DEL	ENST00000306901.3	37	CCDS10027.1																																																																																			.	.	weak		0.505	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2		
PRSS48	345062	hgsc.bcm.edu	37	4	152201018	152201019	+	Frame_Shift_Ins	INS	-	-	CAGGT	rs148861921|rs71901196|rs77216366	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:152201018_152201019insCAGGT	ENST00000455694.2	+	2	125_126	c.123_124insCAGGT	c.(124-126)cagfs	p.-43fs	SH3D19_ENST00000604030.1_Intron|PRSS48_ENST00000441586.2_Intron	NM_183375.2	NP_899231.2	Q7RTY5	PRS48_HUMAN	protease, serine, 48							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8						GCTGGCCTTGGCAGGTCAGCCT	0.53														1064	0.21246	0.0787	0.2464	5008	,	,		20396	0.1766		0.4205	False		,,,				2504	0.1922				p.W41fs		Pindel,Atlas-Indel	.											.	PRSS48	91	.	0			c.123_124insCAGGT						PASS	.			524,3274		60,404,1435						5.0	1.0		dbSNP_130	113	3418,4526		764,1890,1318	no	frameshift	PRSS48	NM_183375.2		824,2294,2753	A1A1,A1R,RR		43.0262,13.7967,33.5718				3942,7800				SO:0001589	frameshift_variant	345062	exon2			.	BN000134	CCDS47145.1	4q31.3	2010-05-07			ENSG00000189099	ENSG00000189099		"""Serine peptidases / Serine peptidases"""	24635	protein-coding gene	gene with protein product						12838346	Standard	NM_183375		Approved	ESSPL	uc011cif.2	Q7RTY5	OTTHUMG00000161673	ENST00000455694.2:c.124_128dupCAGGT	4.37:g.152201019_152201023dupCAGGT	ENSP00000401328:p.Val43fs	Somatic	147	.	.		WXS	Illumina HiSeq	Phase_I	104	32	0.308	NM_183375	Q08E82|Q0VAD4	Frame_Shift_Ins	INS	ENST00000455694.2	37	CCDS47145.1																																																																																			.	.	strong		0.530	PRSS48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365685.3	NM_183375	
NR1H2	7376	hgsc.bcm.edu	37	19	50881820	50881821	+	In_Frame_Ins	INS	-	-	AAC	rs57917904|rs397738863|rs78398331|rs55652650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50881820_50881821insAAC	ENST00000253727.5	+	6	749_750	c.514_515insAAC	c.(514-516)aaa>aAACaa	p.175_176insQ	NR1H2_ENST00000411902.2_In_Frame_Ins_p.78_79insQ|NR1H2_ENST00000598168.1_In_Frame_Ins_p.175_176insQ|NR1H2_ENST00000593926.1_In_Frame_Ins_p.175_176insQ|NR1H2_ENST00000542413.1_5'UTR|NR1H2_ENST00000599105.1_In_Frame_Ins_p.175_176insQ	NM_007121.5	NP_009052	P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2	175				Q -> QQ (in Ref. 1; AAA61783, 2; BAF83544/BAG60288, 4; AAH07790/AAH33500/ AAH47750/AAH74500 and 5; AAA58594). {ECO:0000305}.	cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|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 transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|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)|sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		GAAGATTCGGAAACAGCAGCAG	0.639														2745	0.548123	0.3434	0.5259	5008	,	,		18006	0.7857		0.5994	False		,,,				2504	0.5429				p.K172delinsKQ		Pindel,Atlas-Indel	.											.	NR1H2	47	.	0			c.514_515insAAC						PASS	.			3058,1042		1021,1016,13						3.4	0.8		dbSNP_129	42	6607,1515		2573,1461,27	no	coding	NR1H2	NM_007121.4		3594,2477,40	A1A1,A1R,RR		18.653,25.4146,20.9213				9665,2557				SO:0001652	inframe_insertion	7376	exon6			.	U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"""Nuclear hormone receptors"""	7965	protein-coding gene	gene with protein product	"""liver X receptor-beta"""	600380	"""ubiquitously-expressed nuclear receptor"""	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000253727.5:c.515_517dupAAC	19.37:g.50881821_50881823dupAAC	ENSP00000253727:p.Gln175_Gln175dup	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	79	23	0.291	NM_007121	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	In_Frame_Ins	INS	ENST00000253727.5	37	CCDS42593.1																																																																																			-|0.132;AAC|0.868	0.868	strong		0.639	NR1H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464724.2		
HAVCR1	26762	hgsc.bcm.edu	37	5	156479444	156479446	+	In_Frame_Del	DEL	TTG	TTG	-	rs45439103|rs74944471|rs398065342|rs386693990	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTG	TTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:156479444_156479446delTTG	ENST00000339252.3	-	3	1131_1133	c.599_601delCAA	c.(598-603)acaagt>agt	p.T200del	HAVCR1_ENST00000544197.1_In_Frame_Del_p.T200del|HAVCR1_ENST00000425854.1_In_Frame_Del_p.T200del|HAVCR1_ENST00000522693.1_In_Frame_Del_p.T200del|HAVCR1_ENST00000523175.1_In_Frame_Del_p.T200del	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	11 X 6 AA approximate tandem repeats of V-P-T-T-T-T].|Thr-rich.				viral process (GO:0016032)	integral component of membrane (GO:0016021)	virus receptor activity (GO:0001618)			endometrium(3)|large_intestine(2)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACTGGAACACTTGTTGTTGTTGG	0.463														1221	0.24381	0.385	0.1873	5008	,	,		28364	0.2034		0.1869	False		,,,				2504	0.1933				p.200_201del		Pindel,Atlas-Indel	.											HAVCR1,NS,carcinoma,-1,1	HAVCR1	84	1	0			c.600_602del						PASS	.		,,	1271,2705		243,785,960					,,	-1.7	0.0		dbSNP_131	374	1639,6415		165,1309,2553	no	coding,coding,coding	HAVCR1	NM_012206.2,NM_001173393.1,NM_001099414.1	,,	408,2094,3513	A1A1,A1R,RR		20.3501,31.9668,24.1895	,,	,,		2910,9120				SO:0001651	inframe_deletion	26762	exon4			.	AF043724	CCDS43392.1	5q33.2	2014-01-14			ENSG00000113249	ENSG00000113249		"""Immunoglobulin superfamily / V-set domain containing"""	17866	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 1"""	606518				9658108, 11725301	Standard	NM_012206		Approved	HAVCR-1, TIM-1, TIM1, HAVCR, TIMD1	uc021ygj.1	Q96D42	OTTHUMG00000163466	ENST00000339252.3:c.599_601delCAA	5.37:g.156479453_156479455delTTG	ENSP00000344844:p.Thr200del	Somatic	325	.	.		WXS	Illumina HiSeq	Phase_I	361	126	0.349	NM_001099414	O43656	In_Frame_Del	DEL	ENST00000339252.3	37	CCDS43392.1																																																																																			TTG|0.766;-|0.234	0.234	strong		0.463	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1		
CFAP74	85452	hgsc.bcm.edu	37	1	1887092	1887092	+	IGR	DEL	G	G	-	rs3838976|rs139735565	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1887092delG								TMEM52 (36380 upstream) : C1orf222 (32470 downstream)																							GGCCCTCACCGCCCGCCCACC	0.632													G|G|-|deletion	942	0.188099	0.1089	0.2334	5008	,	,		13367	0.2292		0.2485	False		,,,				2504	0.1585				p.G739fs		Atlas-Indel	.											.	KIAA1751	92	.	0			c.2215delG						PASS	.						45.0	46.0	46.0					1																	1887092		1963	4068	6031	SO:0001628	intergenic_variant	85452	exon18			.																													1.37:g.1887092delG		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	77	65	0.844156	NM_001080484		Frame_Shift_Del	DEL		37																																																																																				G|0.777;-|0.223	0.223	strong	0	0.632								
ZNF816	125893	hgsc.bcm.edu	37	19	53454475	53454476	+	In_Frame_Ins	INS	-	-	ACT	rs33949217|rs79186164|rs139421374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53454475_53454476insACT	ENST00000357666.4	-	5	852_853	c.552_553insAGT	c.(550-555)atcggt>atcAGTggt	p.184_185IG>ISG	ZNF816_ENST00000444460.2_In_Frame_Ins_p.184_185IG>ISG|ZNF321P_ENST00000391777.3_Intron|ZNF816_ENST00000434371.2_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	184				I -> IS (in Ref. 4; AAI05741). {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)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(10)|lung(9)|stomach(1)|urinary_tract(2)	27						GAGGAAGCACCGATAGACTTGT	0.376														2329	0.465056	0.8699	0.2954	5008	,	,		19549	0.252		0.3052	False		,,,				2504	0.4223				p.G185delinsSG		Pindel,Atlas-Indel	.											.	ZNF816	73	.	0			c.553_554insAGT						PASS	.		,,,	3536,726		1466,604,61					,,,	-1.0	0.0		dbSNP_126	107	3279,4975		634,2011,1482	no	intron,coding,coding,coding	ZNF816,ZNF816-ZNF321P	NM_001202473.1,NM_001202457.1,NM_001202456.1,NM_001031665.2	,,,	2100,2615,1543	A1A1,A1R,RR		39.7262,17.0343,45.5497	,,,	,,,		6815,5701				SO:0001652	inframe_insertion	125893	exon4			.	BC063805	CCDS33096.1	19q13.41	2013-01-08	2010-07-23	2010-07-23		ENSG00000180257		"""Zinc fingers, C2H2-type"", ""-"""	26995	protein-coding gene	gene with protein product			"""zinc finger protein 816A"""	ZNF816A			Standard	NM_001031665		Approved		uc002qam.2	Q0VGE8		ENST00000357666.4:c.552_553insAGT	19.37:g.53454475_53454476insACT	ENSP00000350295:p.Ile184_Gly185insSer	Somatic	122	.	.		WXS	Illumina HiSeq	Phase_I	102	24	0.235	NM_001202457	A8K7H5|Q3KR39|Q659B3	In_Frame_Ins	INS	ENST00000357666.4	37	CCDS33096.1																																																																																			ACT|1.000;|0.000	1.000	weak		0.376	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665	
CELA1	1990	hgsc.bcm.edu	37	12	51723598	51723599	+	Frame_Shift_Ins	INS	-	-	G	rs398102298|rs76813052|rs17860363|rs75442020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51723598_51723599insG	ENST00000293636.1	-	7	668_669	c.628_629insC	c.(628-630)ctcfs	p.L210fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	210	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.L210fs*24(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						CAAGCAATGGAGGGGGCCCCCA	0.564													GGGGG|GGGGG|GGGGGG|insertion	729	0.145567	0.084	0.1772	5008	,	,		16900	0.0407		0.2863	False		,,,				2504	0.1697				p.L210fs		Pindel,Atlas-Indel	.											.	CELA1	39	.	1	Insertion - Frameshift(1)	ovary(1)	c.629_630insC						PASS	.			562,3700		35,492,1604						5.4	0.2		dbSNP_123	63	2566,5688		406,1754,1967	no	frameshift	CELA1	NM_001971.5		441,2246,3571	A1A1,A1R,RR		31.088,13.1863,24.992				3128,9388				SO:0001589	frameshift_variant	1990	exon7			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.629dupC	12.37:g.51723603_51723603dupG	ENSP00000293636:p.Leu210fs	Somatic	74	.	.		WXS	Illumina HiSeq	Phase_I	48	20	0.417	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Frame_Shift_Ins	INS	ENST00000293636.1	37	CCDS8812.1																																																																																			-|0.851;G|0.149	0.149	strong		0.564	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
GNAI2	2771	hgsc.bcm.edu	37	3	50294456	50294458	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50294456_50294458delAAG	ENST00000313601.6	+	7	1195_1197	c.811_813delAAG	c.(811-813)aagdel	p.K272del	GNAI2_ENST00000422163.1_In_Frame_Del_p.K256del|GNAI2_ENST00000491100.1_3'UTR|GNAI2_ENST00000451956.1_In_Frame_Del_p.K235del|GNAI2_ENST00000536647.1_In_Frame_Del_p.K191del|GNAI2_ENST00000266027.5_In_Frame_Del_p.K256del|GNAI2_ENST00000440628.1_In_Frame_Del_p.K220del	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	272					activation of MAPKK activity (GO:0000186)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of synaptic transmission (GO:0050805)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|regulation of calcium ion transport (GO:0051924)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|liver(2)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		CTTCCTCAACAAGAAGGACCTGT	0.517											OREG0015582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.270_271del		Atlas-Indel	.											.	GNAI2	42	.	0			c.810_812del						PASS	.																																			SO:0001651	inframe_deletion	2771	exon7			.	X04828	CCDS2813.1, CCDS54587.1, CCDS63642.1, CCDS63644.1	3p21.31	2010-08-27			ENSG00000114353	ENSG00000114353			4385	protein-coding gene	gene with protein product	"""GTP-binding regulatory protein Gi alpha-2 chain"""	139360		GNAI2B		3100330, 1733849	Standard	NM_001166425		Approved	GIP	uc003cyq.1	P04899	OTTHUMG00000156940	ENST00000313601.6:c.811_813delAAG	3.37:g.50294459_50294461delAAG	ENSP00000312999:p.Lys272del	Somatic	160	0	0	968	WXS	Illumina HiSeq	Phase_I	174	18	0.103448	NM_002070	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	In_Frame_Del	DEL	ENST00000313601.6	37	CCDS2813.1																																																																																			.	.	none		0.517	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070	
PTCHD3	374308	hgsc.bcm.edu	37	10	27702256	27702257	+	Frame_Shift_Ins	INS	-	-	C	rs369926016|rs112067123|rs75297921|rs377312318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:27702256_27702257insC	ENST00000438700.3	-	1	1040_1041	c.923_924insG	c.(922-924)ggcfs	p.G308fs		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	308					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TTCCTAGGCTGCCCCCCAAGAT	0.589													CCCCCC|CCCCCC|CCCCCCC|insertion	1387	0.276957	0.2693	0.304	5008	,	,		18563	0.1806		0.3449	False		,,,				2504	0.2975				p.G308fs		Pindel,Atlas-Indel	.											.	PTCHD3	140	.	0			c.924_925insG						PASS	.																																			SO:0001589	frameshift_variant	374308	exon1			.	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.924dupG	10.37:g.27702262_27702262dupC	ENSP00000417658:p.Gly308fs	Somatic	94	.	.		WXS	Illumina HiSeq	Phase_I	101	62	0.614	NM_001034842	I3L499|Q6ZU28	Frame_Shift_Ins	INS	ENST00000438700.3	37	CCDS31173.1																																																																																			-|0.732;C|0.268	0.268	strong		0.589	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
C14orf177	283598	hgsc.bcm.edu	37	14	99182527	99182535	+	Start_Codon_Del	DEL	GGATGCATC	GGATGCATC	-	rs17097718|rs373583218|rs139827156	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GGATGCATC	GGATGCATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:99182527_99182535delGGATGCATC	ENST00000325812.2	+	0	418_426					NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177											endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CAGTACGACTGGATGCATCGGAAAGAGCC	0.569														134	0.0267572	0.0356	0.0245	5008	,	,		21205	0.004		0.0567	False		,,,				2504	0.0092				.		Pindel,Atlas-Indel	.											.	C14orf177	37	.	0			.						PASS	.			127,4135		2,123,2006						1.8	0.0		dbSNP_134	53	465,7787		31,403,3692	no	coding	C14orf177	NM_182560.2		33,526,5698	A1A1,A1R,RR		5.635,2.9798,4.7307				592,11922				SO:0001582	initiator_codon_variant	283598	wholegene			.	AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745		14.37:g.99182527_99182535delGGATGCATC		Somatic	53	.	.		WXS	Illumina HiSeq	Phase_I	52	18	0.346	NM_182560	Q8N7D2	Frame_Shift_Del	DEL	ENST00000325812.2	37	CCDS9948.1																																																																																			GGATGCATC|0.963;-|0.037	0.037	strong		0.569	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1	NM_182560	
KIAA1841	84542	hgsc.bcm.edu	37	2	61361326	61361326	+	Frame_Shift_Del	DEL	G	G	-	rs142269591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:61361326delG	ENST00000295031.5	+	21	2460	c.2083delG	c.(2083-2085)ggtfs	p.G695fs		NM_032506.2	NP_115895.2	Q6NSI8	K1841_HUMAN	KIAA1841	0										breast(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	25			Epithelial(17;0.193)			cagaaaaagtggTTTGAGCAG	0.393													GG|GG|G|deletion	119	0.023762	0.0038	0.036	5008	,	,		21790	0.001		0.0736	False		,,,				2504	0.0143				p.S694fs		Pindel,Atlas-Indel	.											.	KIAA1841	95	.	0			c.2082delT						PASS	.			74,4190		0,74,2058	171.0	143.0	152.0			0.8	0.1	2	dbSNP_134	161	685,7569		38,609,3480	no	frameshift	KIAA1841	NM_032506.2		38,683,5538	A1A1,A1R,RR		8.299,1.7355,6.0633			61361326	759,11759	2203	4286	6489	SO:0001589	frameshift_variant	84542	exon21			.	BC070104	CCDS1867.1, CCDS46296.1	2p15	2010-06-22			ENSG00000162929	ENSG00000162929			29387	protein-coding gene	gene with protein product						11347906	Standard	NM_032506		Approved		uc002saw.4	Q6NSI8	OTTHUMG00000129421	ENST00000295031.5:c.2083delG	2.37:g.61361326delG	ENSP00000295031:p.Gly695fs	Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	139	45	0.324	NM_032506	Q49AF0|Q6ZND0|Q96JI6	Frame_Shift_Del	DEL	ENST00000295031.5	37	CCDS1867.1																																																																																			G|0.962;-|0.038	0.038	strong		0.393	KIAA1841-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251580.1	NM_032506	
IRF8	3394	hgsc.bcm.edu	37	16	85954879	85954879	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954879delC	ENST00000268638.5	+	9	1694	c.1272delC	c.(1270-1272)atcfs	p.I424fs	IRF8_ENST00000562492.1_Frame_Shift_Del_p.I220fs	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	424					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				ACCAACAGATCACCGTCTAAG	0.557																																					p.I424fs		Atlas-Indel	.											IRF8,NS,lymphoid_neoplasm,0,1	IRF8	65	1	0			c.1271delT						PASS	.						71.0	77.0	75.0					16																	85954879		2198	4300	6498	SO:0001589	frameshift_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.1272delC	16.37:g.85954879delC	ENSP00000268638:p.Ile424fs	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	36	10	0.277778	NM_002163	A0AV82	Frame_Shift_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.557	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
SIRPA	140885	hgsc.bcm.edu	37	20	1896052	1896054	+	In_Frame_Del	DEL	CGA	CGA	-	rs139878822|rs202172737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CGA	CGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1896052_1896054delCGA	ENST00000358771.4	+	2	539_541	c.387_389delCGA	c.(385-390)cccgat>cct	p.D131del	SIRPA_ENST00000356025.3_In_Frame_Del_p.D131del|SIRPA_ENST00000400068.3_In_Frame_Del_p.D131del	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	131	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.D131delD(2)|p.D130A(1)|p.P129P(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		AAGGGAGCCCCGATGACGTGGAG	0.527														1950	0.389377	0.264	0.4063	5008	,	,		16040	0.5933		0.2932	False		,,,				2504	0.4356				p.129_130del	GBM(155;1668 1920 5945 42733 48121)	Atlas-Indel	.											SIRPA,NS,carcinoma,-1,1	SIRPA	83	1	4	Deletion - In frame(2)|Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)|upper_aerodigestive_tract(1)|large_intestine(1)	c.386_388del						PASS	.		,,	1147,3105		167,813,1146					,,	2.0	0.0		dbSNP_134	106	2654,5494		452,1750,1872	no	coding,coding,coding	SIRPA	NM_080792.2,NM_001040023.1,NM_001040022.1	,,	619,2563,3018	A1A1,A1R,RR		32.5724,26.9755,30.6532	,,	,,		3801,8599				SO:0001651	inframe_deletion	140885	exon3			.	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.387_389delCGA	20.37:g.1896052_1896054delCGA	ENSP00000351621:p.Asp131del	Somatic	393	0	0		WXS	Illumina HiSeq	Phase_I	223	30	0.134529	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	In_Frame_Del	DEL	ENST00000358771.4	37	CCDS13022.1																																																																																			.	.	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
MN1	4330	hgsc.bcm.edu	37	22	28194933	28194934	+	In_Frame_Ins	INS	-	-	TGC	rs572936881|rs34890218|rs373314940|rs71194738	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:28194933_28194934insTGC	ENST00000302326.4	-	1	2552_2553	c.1598_1599insGCA	c.(1597-1599)caa>caGCAa	p.533_533Q>QQ		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	533	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						gctgctgctgttgctgctgctg	0.653			T	ETV6	"""AML, meningioma"""									447	0.0892572	0.0393	0.1196	5008	,	,		12327	0.0774		0.1789	False		,,,				2504	0.0552				p.Q533delinsQQ		Atlas-Indel	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	MN1,caecum,carcinoma,0,2	MN1	122	2	0			c.1599_1600insGCA						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.1596_1598dupGCA	22.37:g.28194940_28194942dupTGC	ENSP00000304956:p.Gln550dup	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	61	20	0.327869	NM_002430	A9Z1V9	In_Frame_Ins	INS	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	weak		0.653	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119755	38119757	+	In_Frame_Del	DEL	CAA	CAA	-	rs201160789|rs71322688|rs55745992|rs67890459|rs77530465|rs199535040	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38119755_38119757delCAA	ENST00000406386.3	+	7	1447_1449	c.1192_1194delCAA	c.(1192-1194)caadel	p.Q398del		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	398					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.Q398R(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGAACCACTCAACGAGAGAATT	0.552														1684	0.336262	0.1536	0.2853	5008	,	,		18750	0.5863		0.3877	False		,,,				2504	0.3088				p.397_398del		Pindel,Atlas-Indel	.											.	TRIOBP	262	.	1	Substitution - Missense(1)	lung(1)	c.1191_1193del						PASS	.			658,3014		76,506,1254						-4.9	0.1		dbSNP_132	129	3439,4489		755,1929,1280	no	coding	TRIOBP	NM_001039141.2		831,2435,2534	A1A1,A1R,RR		43.3779,17.9194,35.319				4097,7503				SO:0001651	inframe_deletion	11078	exon7			.	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.1192_1194delCAA	22.37:g.38119755_38119757delCAA	ENSP00000384312:p.Gln398del	Somatic	167	.	.		WXS	Illumina HiSeq	Phase_I	146	83	0.568	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	In_Frame_Del	DEL	ENST00000406386.3	37	CCDS43015.1																																																																																			-|0.368;CAA|0.632	0.368	strong		0.552	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
OR8B2	26595	hgsc.bcm.edu	37	11	124252689	124252690	+	Frame_Shift_Ins	INS	-	-	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124252689_124252690insG	ENST00000375013.2	-	1	568_569	c.550_551insC	c.(550-552)ctcfs	p.L184fs		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	184						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0277)		AAGCTGGAGGAGGGGGAGTATG	0.5																																					p.L184fs		Atlas-Indel	.											.	OR8B2	42	.	0			c.551_552insC						PASS	.																																			SO:0001589	frameshift_variant	26595	exon1			.	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.551dupC	11.37:g.124252694_124252694dupG	ENSP00000364152:p.Leu184fs	Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	481	47	0.0977131	NM_001005468	Q8NGH2	Frame_Shift_Ins	INS	ENST00000375013.2	37	CCDS31708.1																																																																																			.	.	none		0.500	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
GOLIM4	27333	hgsc.bcm.edu	37	3	167742354	167742356	+	In_Frame_Del	DEL	TCC	TCC	-	rs144680891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:167742354_167742356delTCC	ENST00000470487.1	-	14	2507_2509	c.1818_1820delGGA	c.(1816-1821)gaggac>gac	p.E606del	GOLIM4_ENST00000309027.4_In_Frame_Del_p.E578del	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	606	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						ATCAACATTGTCCTCCTGCTGGT	0.453														33	0.00658946	0.0008	0.0043	5008	,	,		21615	0.0		0.0109	False		,,,				2504	0.0184				p.607_607del		Pindel,Atlas-Indel	.											.	GOLIM4	71	.	0			c.1819_1821del						PASS	.			17,4249		0,17,2116						-4.6	0.0		dbSNP_134	247	157,8097		1,155,3971	no	coding	GOLIM4	NM_014498.3		1,172,6087	A1A1,A1R,RR		1.9021,0.3985,1.3898				174,12346				SO:0001651	inframe_deletion	27333	exon14			.	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.1818_1820delGGA	3.37:g.167742357_167742359delTCC	ENSP00000417354:p.Glu606del	Somatic	155	.	.		WXS	Illumina HiSeq	Phase_I	180	54	0.300	NM_014498		In_Frame_Del	DEL	ENST00000470487.1	37	CCDS3204.1																																																																																			.	.	strong		0.453	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2		
ZFPM1	161882	hgsc.bcm.edu	37	16	88594540	88594542	+	In_Frame_Del	DEL	GAA	GAA	-	rs10606433|rs57580812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88594540_88594542delGAA	ENST00000319555.3	+	6	928_930	c.606_608delGAA	c.(604-609)gtgaag>gtg	p.K204del	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	204					atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GCCACCCTGTGAAGAAGGAGCCA	0.7														269	0.0537141	0.1694	0.0259	5008	,	,		15149	0.001		0.0229	False		,,,				2504	0.0031				p.202_203del	Pancreas(49;850 1106 29641 32847 38344)	Pindel,Atlas-Indel	.											.	ZFPM1	32	.	0			c.605_607del						PASS	.			581,3623		50,481,1571						3.3	0.9		dbSNP_119	19	205,8003		33,139,3932	no	coding	ZFPM1	NM_153813.2		83,620,5503	A1A1,A1R,RR		2.4976,13.8202,6.3326				786,11626				SO:0001651	inframe_deletion	161882	exon6			.	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.606_608delGAA	16.37:g.88594543_88594545delGAA	ENSP00000326630:p.Lys204del	Somatic	70	.	.		WXS	Illumina HiSeq	Phase_I	43	30	0.698	NM_153813		In_Frame_Del	DEL	ENST00000319555.3	37	CCDS32502.1																																																																																			GAA|0.940;-|0.060	0.060	strong		0.700	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
INHBE	83729	hgsc.bcm.edu	37	12	57850304	57850319	+	Frame_Shift_Del	DEL	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	-	rs536111730		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57850304_57850319delTGCGACCCCCTTATGT	ENST00000266646.2	+	2	942_957	c.726_741delTGCGACCCCCTTATGT	c.(724-741)cctgcgacccccttatgtfs	p.PATPLC242fs	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	242					growth (GO:0040007)	extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						CCTGTGAGCCTGCGACCCCCTTATGTTGCAGGCGAG	0.611											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.242_247del	GBM(191;1808 2166 15720 36624 50371)	Pindel,Atlas-Indel	.											.	INHBE	38	.	0			c.725_740del						PASS	.																																			SO:0001589	frameshift_variant	83729	exon2			.		CCDS8939.1	12q13.2	2008-02-05				ENSG00000139269			24029	protein-coding gene	gene with protein product		612031				12242034	Standard	NM_031479		Approved	activin, MGC4638	uc001snw.3	P58166		ENST00000266646.2:c.726_741delTGCGACCCCCTTATGT	12.37:g.57850304_57850319delTGCGACCCCCTTATGT	ENSP00000266646:p.Pro242fs	Somatic	105	.	.	1026	WXS	Illumina HiSeq	Phase_I	73	20	0.274	NM_031479		Frame_Shift_Del	DEL	ENST00000266646.2	37	CCDS8939.1																																																																																			.	.	none		0.611	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479	
DST	667	hgsc.bcm.edu	37	6	56510983	56510983	+	Intron	DEL	A	A	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56510983delA	ENST00000361203.3	-	10	929				DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370788.2_Intron			Q03001	DYST_HUMAN	dystonin						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)			TAAAGTGCCTAAAATAAAAAG	0.299																																					.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.						18.0	17.0	17.0					6																	56510983		1782	4017	5799	SO:0001627	intron_variant	100873774	.			.	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.922-3T>-	6.37:g.56510983delA		Somatic	41	.	.		WXS	Illumina HiSeq	Phase_I	37	11	0.297	.	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	RNA	DEL	ENST00000361203.3	37																																																																																				.	.	none		0.299	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
PSORS1C2	170680	hgsc.bcm.edu	37	6	31105858	31105858	+	Frame_Shift_Del	DEL	G	G	-	rs373592714|rs79153019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31105858delG	ENST00000259845.4	-	2	604	c.281delC	c.(280-282)cctfs	p.P95fs	PSORS1C1_ENST00000547221.1_Intron|PSORS1C1_ENST00000481450.2_5'Flank|PSORS1C1_ENST00000259881.9_Intron	NM_014069.2	NP_054788.2	Q9UIG4	PS1C2_HUMAN	psoriasis susceptibility 1 candidate 2	95						extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						AGGCCGGGGAGGTTGAGGAGG	0.652													GG|GG|G|deletion	266	0.053115	0.0272	0.0562	5008	,	,		13538	0.0079		0.1014	False		,,,				2504	0.0828				p.P94fs		Pindel,Atlas-Indel	.											.	PSORS1C2	11	.	0			c.282delT						PASS	.		,	150,3062		13,124,1469	40.0	48.0	45.0		,	4.7	1.0	6	dbSNP_131	48	571,5421		61,449,2486	yes	frameshift,intron	PSORS1C1,PSORS1C2	NM_014069.2,NM_014068.2	,	74,573,3955	A1A1,A1R,RR		9.5294,4.67,7.8336	,	,	31105858	721,8483	1500	2684	4184	SO:0001589	frameshift_variant	170680	exon2			.	AB031480	CCDS4694.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204538	ENSG00000204538			17199	protein-coding gene	gene with protein product		613526	"""chromosome 6 open reading frame 17"""	C6orf17			Standard	NM_014069		Approved	SPR1	uc003nso.4	Q9UIG4	OTTHUMG00000031081	ENST00000259845.4:c.281delC	6.37:g.31105858delG	ENSP00000259845:p.Pro95fs	Somatic	63	.	.		WXS	Illumina HiSeq	Phase_I	55	21	0.382	NM_014069	Q5STD0	Frame_Shift_Del	DEL	ENST00000259845.4	37	CCDS4694.1																																																																																			G|0.946;-|0.054	0.054	strong		0.652	PSORS1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076115.3		
BPNT1	10380	hgsc.bcm.edu	37	1	220231181	220231181	+	3'UTR	DEL	T	T	-	rs34887640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:220231181delT	ENST00000469520.2	-	0	2381				BPNT1_ENST00000354807.3_3'UTR|BPNT1_ENST00000322067.7_3'UTR			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1						3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)			breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		TTAAAATTACTGTGAAAAACA	0.318													T|T|-|deletion	1037	0.207069	0.0197	0.2305	5008	,	,		15564	0.2093		0.3588	False		,,,				2504	0.2853				.		Pindel,Atlas-Indel	.											.	BPNT1	29	.	0			.						PASS	.			49,665		19,11,327	1.0	1.0	1.0			1.2	0.0	1	dbSNP_126	1	439,805		197,45,380	no	utr-3	BPNT1	NM_006085.4		216,56,707	A1A1,A1R,RR		35.2894,6.8627,24.9234			220231181	488,1470	244	349	593	SO:0001624	3_prime_UTR_variant	10380	.			.	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.*1005A>-	1.37:g.220231181delT		Somatic	133	.	.		WXS	Illumina HiSeq	Phase_I	102	58	0.569	.	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	RNA	DEL	ENST00000469520.2	37	CCDS41469.1																																																																																			T|0.776;-|0.224	0.224	strong		0.318	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085	
ZNRF2	223082	hgsc.bcm.edu	37	7	30329454	30329456	+	Intron	DEL	TGT	TGT	-	rs373052300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:30329454_30329456delTGT	ENST00000323037.4	+	1	1520				MIR550A1_ENST00000385037.1_RNA	NM_147128.3	NP_667339.1	Q8NHG8	ZNRF2_HUMAN	zinc and ring finger 2							cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(2)|prostate(1)	5						GTAAGAGCCCTGTTGTTGTAAGA	0.493														60	0.0119808	0.0197	0.0159	5008	,	,		16444	0.0		0.0139	False		,,,				2504	0.0092				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			257,3721		19,219,1751						-0.5	0.0			141	846,6652		32,782,2935	no	intron	ZNRF2	NM_147128.3		51,1001,4686	A1A1,A1R,RR		11.283,6.4605,9.6114				1103,10373				SO:0001627	intron_variant	693133	.			.	AF513707	CCDS5426.1	7p15.1	2013-01-09			ENSG00000180233	ENSG00000180233		"""RING-type (C3HC4) zinc fingers"""	22316	protein-coding gene	gene with protein product		612061					Standard	NM_147128		Approved	RNF202	uc003tat.3	Q8NHG8	OTTHUMG00000097759	ENST00000323037.4:c.469+4012TGT>-	7.37:g.30329460_30329462delTGT		Somatic	129	.	.		WXS	Illumina HiSeq	Phase_I	144	23	0.160	.		RNA	DEL	ENST00000323037.4	37	CCDS5426.1																																																																																			.	.	weak		0.493	ZNRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214992.1	NM_147128	
RP1L1	94137	hgsc.bcm.edu	37	8	10467629	10467630	+	In_Frame_Ins	INS	-	-	TTC	rs386722178|rs146656804|rs367656981|rs374529674|rs139405108		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10467629_10467630insTTC	ENST00000382483.3	-	4	4201_4202	c.3978_3979insGAA	c.(3976-3981)aaaaca>aaaGAAaca	p.1326_1327KT>KET		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1342	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		Missing (in allele RP1L1-1).|TE -> VI (in allele RP1L1-3).		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)		ccttcttctgttttagtttcct	0.455																																					p.T1327delinsET		Atlas-Indel	.											.	RP1L1	453	.	0			c.3979_3980insGAA						PASS	.																																			SO:0001652	inframe_insertion	94137	exon4			.	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.3978_3979insGAA	8.37:g.10467629_10467630insTTC	ENSP00000371923:p.Lys1326_Thr1327insGlu	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	141	23	0.163121	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	In_Frame_Ins	INS	ENST00000382483.3	37	CCDS43708.1																																																																																			.	.	strong		0.455	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
NUDT17	200035	hgsc.bcm.edu	37	1	145586679	145586679	+	Frame_Shift_Del	DEL	C	C	-	rs199513201|rs150364859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145586679delC	ENST00000334513.5	-	8	908	c.897delG	c.(895-897)ccgfs	p.P299fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	299							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CACTTTTACACGGTGGGGGTG	0.522													C|C|-|deletion	72	0.014377	0.0015	0.0303	5008	,	,		18793	0.0		0.0398	False		,,,				2504	0.0092				p.C300fs		Atlas-Indel	.											.	NUDT17	25	.	0			c.898delT						PASS	.			11,4255		0,11,2122	106.0	107.0	107.0			-8.2	0.0	1		106	142,8112		2,138,3987	no	frameshift	NUDT17	NM_001012758.2		2,149,6109	A1A1,A1R,RR		1.7204,0.2579,1.222			145586679	153,12367	2203	4300	6503	SO:0001589	frameshift_variant	200035	exon8			.	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"""Nudix motif containing"""	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.897delG	1.37:g.145586679delC	ENSP00000334437:p.Pro299fs	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	127	32	0.251969	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			C|0.983;-|0.017	0.017	strong		0.522	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
SAA2	6289	hgsc.bcm.edu	37	11	18267597	18267598	+	Splice_Site	INS	-	-	GGAAA	rs370424188|rs202167679|rs201840682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18267597_18267598insGGAAA	ENST00000526900.1	-	3	275		c.e3-2		SAA2-SAA4_ENST00000524555.1_RNA|SAA2_ENST00000414546.2_Splice_Site|SAA2_ENST00000528349.1_Splice_Site|SAA2_ENST00000530400.1_Splice_Site|SAA2_ENST00000256733.4_Splice_Site|SAA2_ENST00000529528.1_Splice_Site|RNA5SP333_ENST00000363466.1_RNA			P0DJI9	SAA2_HUMAN	serum amyloid A2						acute-phase response (GO:0006953)	extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)				central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(1)	6						CCCGAGCCCCTGGAAAGGAAAG	0.48														316	0.063099	0.0575	0.1239	5008	,	,		28174	0.0843		0.0517	False		,,,				2504	0.0174				.		Atlas-Indel	.											.	SAA2	22	.	0			c.92-2->TTTCC						PASS	.		,,	187,4053		4,179,1937					,,	4.1	0.8		dbSNP_119	29	347,7847		4,339,3754	no	splice-3,splice-3,splice-3	SAA2,SAA2-SAA4	NM_030754.4,NM_001199744.1,NM_001127380.2	,,	8,518,5691	A1A1,A1R,RR		4.2348,4.4104,4.2947	,,	,,		534,11900				SO:0001630	splice_region_variant	6289	exon4			.	M26152	CCDS7833.1, CCDS44548.1	11p15.1-p14	2008-07-21			ENSG00000134339	ENSG00000134339			10514	protein-coding gene	gene with protein product		104751				7686132	Standard	NM_030754		Approved			P0DJI9	OTTHUMG00000166484	ENST00000526900.1:c.92-2->TTTCC	11.37:g.18267603_18267607dupGGAAA		Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	314	39	0.124204	NM_001127380	G3XAK9|P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Splice_Site	INS	ENST00000526900.1	37	CCDS7833.1																																																																																			-|0.929;GGAAA|0.071	0.071	strong		0.480	SAA2-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389983.1	NM_030754	Intron
NUP54	53371	hgsc.bcm.edu	37	4	77065318	77065319	+	In_Frame_Ins	INS	-	-	TGT	rs76406406|rs57577548|rs36024409|rs67608403	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77065318_77065319insTGT	ENST00000264883.3	-	3	418_419	c.278_279insACA	c.(277-279)cag>caACAg	p.93_93Q>QQ	NUP54_ENST00000514987.1_Intron|NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	93	9 X 2 AA repeats of F-G.|Poly-Gln.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.Q93>HK(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						GCTGCTGCTGCTGTGTATTAAA	0.411														776	0.154952	0.0567	0.1282	5008	,	,		16499	0.3512		0.1312	False		,,,				2504	0.1288				p.Q93delinsQQ		Pindel,Atlas-Indel	.											NUP54,NS,carcinoma,0,1	NUP54	48	1	1	Complex - insertion inframe(1)	kidney(1)	c.279_280insACA						PASS	.			300,3966		14,272,1847						5.2	1.0		dbSNP_126	211	1244,7010		96,1052,2979	no	coding	NUP54	NM_017426.2		110,1324,4826	A1A1,A1R,RR		15.0715,7.0323,12.3323				1544,10976				SO:0001652	inframe_insertion	53371	exon3			.	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.276_278dupACA	4.37:g.77065319_77065321dupTGT	ENSP00000264883:p.Gln97dup	Somatic	138	.	.		WXS	Illumina HiSeq	Phase_I	117	38	0.325	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	In_Frame_Ins	INS	ENST00000264883.3	37	CCDS3576.1																																																																																			-|0.827;TGT|0.173	0.173	strong		0.411	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
PNPLA7	375775	hgsc.bcm.edu	37	9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T	rs372921391|rs372038516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140444627_140444628insT	ENST00000277531.4	-	1	208_209	c.22_23insA	c.(22-24)agcfs	p.S8fs	PNPLA7_ENST00000406427.1_Frame_Shift_Ins_p.S8fs|MRPL41_ENST00000371443.5_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	8					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TACCTGTGGGCTGTCATCTTTC	0.559													C|T|TT|complex_insertion	13	0.00259585	0.0	0.0043	5008	,	,		18178	0.0		0.0099	False		,,,				2504	0.0				p.S8fs		Pindel,Atlas-Indel	.											.	PNPLA7	124	.	0			c.23_24insA						PASS	.		,	12,4252		0,12,2120					,	0.2	0.0			114	100,8154		0,100,4027	no	frameshift,frameshift	PNPLA7	NM_152286.3,NM_001098537.1	,	0,112,6147	A1A1,A1R,RR		1.2115,0.2814,0.8947	,	,		112,12406				SO:0001589	frameshift_variant	375775	exon1			.	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.23dupA	9.37:g.140444628_140444628dupT	ENSP00000277531:p.Ser8fs	Somatic	49	.	.		WXS	Illumina HiSeq	Phase_I	67	22	0.328	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Ins	INS	ENST00000277531.4	37	CCDS7045.1																																																																																			.	.	weak		0.559	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
OR9K2	441639	hgsc.bcm.edu	37	12	55523587	55523587	+	Frame_Shift_Del	DEL	T	T	-	rs398102299|rs58036029|rs200050297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55523587delT	ENST00000305377.5	+	1	123	c.35delT	c.(34-36)attfs	p.I12fs		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	12						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CATTTGTATATTTTGCCCTGT	0.363													|||unknown(ALL_OTHER_Ns)	1523	0.304113	0.4085	0.2421	5008	,	,		18883	0.1141		0.334	False		,,,				2504	0.3722				p.I12fs		Pindel,Atlas-Indel	.											.	OR9K2	63	.	0			c.34delA						PASS	.			1650,2614		298,1054,780	93.0	101.0	98.0			2.5	0.8	12	dbSNP_132	145	2679,5575		443,1793,1891	no	frameshift	OR9K2	NM_001005243.1		741,2847,2671	A1A1,A1R,RR		32.457,38.6961,34.5822			55523587	4329,8189	2195	4296	6491	SO:0001589	frameshift_variant	441639	exon1			.	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.35delT	12.37:g.55523587delT	ENSP00000307598:p.Ile12fs	Somatic	124	.	.		WXS	Illumina HiSeq	Phase_I	112	36	0.321	NM_001005243	B9EH19|Q6IFD6	Frame_Shift_Del	DEL	ENST00000305377.5	37	CCDS31814.1																																																																																			T|0.711;-|0.289	0.289	strong		0.363	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
OR7G3	390883	hgsc.bcm.edu	37	19	9236698	9236699	+	Frame_Shift_Ins	INS	-	-	ATGGT	rs111867493|rs3029651|rs111279560|rs138680298	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9236698_9236699insATGGT	ENST00000305444.2	-	1	927_928	c.928_929insACCAT	c.(928-930)tctfs	p.S310fs		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	310						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						TCAATGGAAAGATGGTATCCTA	0.446														2122	0.423722	0.711	0.245	5008	,	,		19331	0.3651		0.3141	False		,,,				2504	0.3354				p.S310fs		Pindel,Atlas-Indel	.											.	OR7G3	41	.	0			c.929_930insACCAT						PASS	.			2730,1532		902,926,303						-1.2	0.0		dbSNP_132	66	2459,5795		353,1753,2021	no	frameshift	OR7G3	NM_001001958.1		1255,2679,2324	A1A1,A1R,RR		29.7916,35.9456,41.4589				5189,7327				SO:0001589	frameshift_variant	390883	exon1			.		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"""GPCR / Class A : Olfactory receptors"""	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.924_928dupACCAT	19.37:g.9236699_9236703dupATGGT	ENSP00000302867:p.Ser310fs	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	127	50	0.394	NM_001001958	Q6IFJ6|Q96R99	Frame_Shift_Ins	INS	ENST00000305444.2	37	CCDS32899.1																																																																																			-|0.601;ATGGT|0.399	0.399	strong		0.446	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1		
NUTM2F	54754	hgsc.bcm.edu	37	9	97080945	97080947	+	In_Frame_Del	DEL	AGA	AGA	-	rs150455117|rs112857574	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:97080945_97080947delAGA	ENST00000253262.4	-	7	2091_2093	c.2071_2073delTCT	c.(2071-2073)tctdel	p.S691del	NUTM2F_ENST00000341207.4_In_Frame_Del_p.S676del|NUTM2F_ENST00000335456.7_Intron	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	691				Missing (in Ref. 2; AAI30391 and 3; CAB61394). {ECO:0000305}.				p.S557delS(1)									TGCTGGCAGGAGAAGGTGATGGG	0.611														3777	0.754193	0.6051	0.8084	5008	,	,		15297	0.8869		0.7227	False		,,,				2504	0.8129				p.691_692del		Atlas-Indel	.											.	FAM22F	72	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.2072_2074del						PASS	.			2288,1260		619,1050,105						-3.0	0.0		dbSNP_134	20	5646,2060		2048,1550,255	no	coding	FAM22F	NM_017561.1		2667,2600,360	A1A1,A1R,RR		26.7324,35.513,29.5006				7934,3320				SO:0001651	inframe_deletion	54754	exon7			.		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.2071_2073delTCT	9.37:g.97080945_97080947delAGA	ENSP00000253262:p.Ser691del	Somatic	469	0	0		WXS	Illumina HiSeq	Phase_I	423	142	0.335697	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	In_Frame_Del	DEL	ENST00000253262.4	37	CCDS47994.1																																																																																			.	.	strong		0.611	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
IRF8	3394	hgsc.bcm.edu	37	16	85954881	85954886	+	Stop_Codon_Del	DEL	CCGTCT	CCGTCT	-	rs147057451|rs146135491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCGTCT	CCGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954881_85954886delCCGTCT	ENST00000268638.5	+	0	1696_1701				IRF8_ENST00000562492.1_Stop_Codon_Del	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8						cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CAACAGATCACCGTCTAAGTGCGTCG	0.558																																					p.425_426del		Atlas-Indel	.											.	IRF8	65	.	0			c.1273_1278del						PASS	.																																			SO:0001567	stop_retained_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	Exception_encountered	16.37:g.85954881_85954886delCCGTCT	ENSP00000268638:p.*427Tyrext*22	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	38	10	0.263158	NM_002163	A0AV82	In_Frame_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.558	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
LINC00482	284185	hgsc.bcm.edu	37	17	79279019	79279020	+	lincRNA	INS	-	-	C	rs185100858|rs3215153	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79279019_79279020insC	ENST00000332012.5	-	0	573_574					NR_038080.1		Q8N8I6	CQ055_HUMAN	long intergenic non-protein coding RNA 482																		CCCAGGCACAGCCCCTGAGGCA	0.673													CCCC|CCCC|CCCCC|insertion	348	0.0694888	0.0091	0.0389	5008	,	,		17826	0.1379		0.0944	False		,,,				2504	0.0767				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			70,3778		6,58,1860						1.4	0.0		dbSNP_106	9	743,7211		62,619,3296	no	intergenic				68,677,5156	A1A1,A1R,RR		9.3412,1.8191,6.8887				813,10989						284185	.			.	AK096740		17q25.3	2012-10-12	2011-09-01	2011-09-01	ENSG00000185168	ENSG00000185168		"""Long non-coding RNAs"""	26816	non-coding RNA	RNA, long non-coding			"""chromosome 17 open reading frame 55"""	C17orf55			Standard	NR_038080		Approved	FLJ39421	uc002kac.1	Q8N8I6			17.37:g.79279023_79279023dupC		Somatic	42	.	.		WXS	Illumina HiSeq	Phase_I	54	18	0.333	.		RNA	INS	ENST00000332012.5	37																																																																																				-|0.924;C|0.076	0.076	strong		0.673	LINC00482-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000439605.1	NM_178519	
SNAPC4	6621	hgsc.bcm.edu	37	9	139277995	139277997	+	In_Frame_Del	DEL	GCT	GCT	-	rs147271628|rs34427285|rs35266724|rs34222232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139277995_139277997delGCT	ENST00000298532.2	-	15	1992_1994	c.1624_1626delAGC	c.(1624-1626)agcdel	p.S542del		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa									p.S542delS(2)		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)		CGTCCTCCTCgctgctgctgctg	0.69														955	0.190695	0.1808	0.3184	5008	,	,		11493	0.0565		0.2356	False		,,,				2504	0.2055				p.542_543del		Pindel,Atlas-Indel	.											.	SNAPC4	82	.	2	Deletion - In frame(2)	prostate(1)|central_nervous_system(1)	c.1625_1627del						PASS	.																																			SO:0001651	inframe_deletion	6621	exon15			.	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.1624_1626delAGC	9.37:g.139278004_139278006delGCT	ENSP00000298532:p.Ser542del	Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	41	10	0.244	NM_003086		In_Frame_Del	DEL	ENST00000298532.2	37	CCDS6998.1																																																																																			.	.	strong		0.690	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
SLC38A10	124565	hgsc.bcm.edu	37	17	79219501	79219503	+	In_Frame_Del	DEL	ATG	ATG	-	rs10569617|rs3833102|rs201518560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ATG	ATG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79219501_79219503delATG	ENST00000374759.3	-	16	3596_3598	c.3213_3215delCAT	c.(3211-3216)atcatt>att	p.1071_1072II>I		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	1071				Missing (in Ref. 5; AAG17235). {ECO:0000305}.	amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GTTAAGGCCAATGATGACCCCAT	0.685														2114	0.422125	0.025	0.4712	5008	,	,		16375	0.6776		0.4364	False		,,,				2504	0.6462				p.1072_1072del		Pindel,Atlas-Indel	.											.	SLC38A10	133	.	0			c.3214_3216del						PASS	.			353,3595		37,279,1658						-2.8	0.0		dbSNP_119	35	3598,4380		853,1892,1244	no	coding	SLC38A10	NM_001037984.1		890,2171,2902	A1A1,A1R,RR		45.099,8.9412,33.1293				3951,7975				SO:0001651	inframe_deletion	124565	exon16			.	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.3213_3215delCAT	17.37:g.79219504_79219506delATG	ENSP00000363891:p.Ile1072del	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	197	61	0.310	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	In_Frame_Del	DEL	ENST00000374759.3	37	CCDS42397.1																																																																																			ATG|0.576;-|0.424	0.424	strong		0.685	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
CCDC63	160762	hgsc.bcm.edu	37	12	111342460	111342460	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:111342460delG	ENST00000308208.5	+	11	1653	c.1411delG	c.(1411-1413)gggfs	p.G471fs	CCDC63_ENST00000545036.1_Frame_Shift_Del_p.G431fs|CCDC63_ENST00000552694.1_Frame_Shift_Del_p.G392fs	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	471										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						GGAAGTGGAAGGGGCAGAGGC	0.572																																					p.E470fs		Pindel,Atlas-Indel	.											.	CCDC63	89	.	0			c.1410delA						PASS	.			1,4263		0,1,2131	82.0	78.0	79.0			-5.0	0.0	12		79	6,8248		0,6,4121	no	frameshift	CCDC63	NM_152591.1		0,7,6252	A1A1,A1R,RR		0.0727,0.0235,0.0559			111342460	7,12511	2203	4300	6503	SO:0001589	frameshift_variant	160762	exon11			.	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"""outer row dynein assembly 5 homolog (Chlamydomonas)"""						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1411delG	12.37:g.111342460delG	ENSP00000312399:p.Gly471fs	Somatic	107	.	.		WXS	Illumina HiSeq	Phase_I	164	52	0.317	NM_152591	B4DY03|Q0P603|Q6P2E1	Frame_Shift_Del	DEL	ENST00000308208.5	37	CCDS9151.1																																																																																			.	.	none		0.572	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591	
IRF8	3394	hgsc.bcm.edu	37	16	85954879	85954886	+	Stop_Codon_Del	DEL	CACCGTCT	CACCGTCT	-	rs147057451|rs146135491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CACCGTCT	CACCGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954879_85954886delCACCGTCT	ENST00000268638.5	+	0	1694_1701				IRF8_ENST00000562492.1_Stop_Codon_Del	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8						cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				ACCAACAGATCACCGTCTAAGTGCGTCG	0.558																																					p.424_426del		Pindel	.											IRF8,NS,lymphoid_neoplasm,0,1	IRF8	65	1	0			c.1271_1278del						PASS	.																																			SO:0001567	stop_retained_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	Exception_encountered	16.37:g.85954879_85954886delCACCGTCT		Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	37	10	0.270	NM_002163	A0AV82	Frame_Shift_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.558	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789313	117789327	+	In_Frame_Del	DEL	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	-	rs577467360|rs201746372|rs200205086|rs61900346|rs371814093|rs58754377|rs201983451|rs368164118|rs201369736	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:117789313_117789327delGGGCTGGAGATGCCT	ENST00000430170.2	-	2	335_349	c.248_262delAGGCATCTCCAGCCC	c.(247-264)caggcatctccagcccgg>cgg	p.QASPA83del	TMPRSS13_ENST00000524993.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000445164.2_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000526090.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000528626.1_In_Frame_Del_p.QASPA83del	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	83	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGAGATGCCCGGGCTGGAGATGCCTGGGCTGGAGA	0.66																																					p.83_88del		Pindel	.											TMPRSS13_ENST00000445164,NS,NS,0,3	TMPRSS13	75	3	1	Deletion - In frame(1)	urinary_tract(1)	c.249_263del						PASS	.		,,	2974,624		1262,450,87					,,	0.0	0.0		dbSNP_126	58	5904,1944		2214,1476,234	no	coding,coding,coding	TMPRSS13	NM_001206790.1,NM_001206789.1,NM_001077263.2	,,	3476,1926,321	A1A1,A1R,RR		24.7706,17.343,22.4358	,,	,,		8878,2568				SO:0001651	inframe_deletion	84000	exon2			.	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.248_262delAGGCATCTCCAGCCC	11.37:g.117789313_117789327delGGGCTGGAGATGCCT	ENSP00000387702:p.Gln83_Ala87del	Somatic	125	.	.		WXS	Illumina HiSeq	Phase_I	109	18	0.165	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	In_Frame_Del	DEL	ENST00000430170.2	37	CCDS58185.1																																																																																			GGGCTGGAGATGCCT|0.257;-|0.743	0.743	strong		0.660	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
MUC4	4585	hgsc.bcm.edu	37	3	195506713	195506760	+	In_Frame_Del	DEL	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	-	rs62282473|rs550221890|rs62282471|rs200597845|rs201121891|rs9882363|rs192522651|rs62282470|rs554841787|rs201914190|rs200055147|rs181895767|rs374267078|rs199635197|rs201530419|rs200381819|rs201961213	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	GCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENST00000463781.3	-	2	12150_12197	c.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	c.(11689-11739)gcatccacacgtcacgccacccctcttcctgtcaccgacacttcctcagct>gct	p.3897_3913ASTRHATPLPVTDTSSA>A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.3897_3913ASTRHATPLPVTDTSSA>A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3902V(2)|p.P3904S(2)|p.A3902T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ATCTGTGGAAGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGATGCTGAGGAAG	0.593																																					p.3898_3913del		Pindel	.											.	MUC4	1505	.	5	Substitution - Missense(5)	kidney(2)|skin(2)|endometrium(1)	c.11692_11739del						PASS	.		,,	327,1561		144,39,761					,,		0.0			8	1397,2107		610,177,965	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	754,216,1726	A1A1,A1R,RR		39.8687,17.3199,31.9733	,,	,,		1724,3668				SO:0001651	inframe_deletion	4585	exon2			.	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11691_11738delATCCACACGTCACGCCACCCCTCTTCCTGTCACCGACACTTCCTCAGC	3.37:g.195506713_195506760delGCTGAGGAAGTGTCGGTGACAGGAAGAGGGGTGGCGTGACGTGTGGAT	ENSP00000417498:p.Ala3897_Ser3912del	Somatic	17	.	.		WXS	Illumina HiSeq	Phase_I	89	23	0.258	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.593	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106501	31106501	+	Frame_Shift_Del	DEL	C	C	-	rs9278990|rs386698869	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31106501delC	ENST00000259881.9	+	5	401	c.112delC	c.(112-114)cccfs	p.P39fs	PSORS1C1_ENST00000547221.1_5'UTR|PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000481450.2_Intron	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	39								p.H40fs*3(2)		kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGAAACTCGTCCCCCCCACGT	0.562														560	0.111821	0.1626	0.1196	5008	,	,		17255	0.0625		0.1491	False		,,,				2504	0.0501				p.R37fs		Pindel	.											.	PSORS1C1	11	.	2	Insertion - Frameshift(2)	ovary(1)|kidney(1)	c.111delT						PASS	.						125.0	129.0	127.0					6																	31106501		1511	2709	4220	SO:0001589	frameshift_variant	170679	exon5			.	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.112delC	6.37:g.31106501delC	ENSP00000259881:p.Pro39fs	Somatic	92	.	.		WXS	Illumina HiSeq	Phase_I	141	76	0.539	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Frame_Shift_Del	DEL	ENST00000259881.9	37	CCDS34390.1																																																																																			.	.	strong		0.562	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026115	176026138	+	In_Frame_Del	DEL	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	-	rs3797464|rs200519605|rs386695335|rs550332435|rs142779818|rs371149640|rs199714570|rs373697082|rs201635586	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTTTCTCAAAGACCCAGGATCCT	CCTTTCTCAAAGACCCAGGATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176026115_176026138delCCTTTCTCAAAGACCCAGGATCCT	ENST00000303991.4	-	2	875_898	c.698_721delAGGATCCTGGGTCTTTGAGAAAGG	c.(697-723)gaggatcctgggtctttgagaaaggtg>gtg	p.EDPGSLRK233del		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	233				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)		p.L238L(1)		NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ACAGGATCCACCTTTCTCAAAGACCCAGGATCCTCCTTCCTCGG	0.496																																					p.233_241del		Pindel	.											.	GPRIN1	77	.	1	Substitution - coding silent(1)	lung(1)	c.699_722del						PASS	.																																			SO:0001651	inframe_deletion	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.698_721delAGGATCCTGGGTCTTTGAGAAAGG	5.37:g.176026115_176026138delCCTTTCTCAAAGACCCAGGATCCT	ENSP00000305839:p.Glu233_Lys240del	Somatic	159	.	.		WXS	Illumina HiSeq	Phase_I	125	36	0.288	NM_052899	C9JM70|Q8ND74|Q96PZ4	In_Frame_Del	DEL	ENST00000303991.4	37	CCDS4405.1																																																																																			.	.	none		0.496	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129925	175129933	+	In_Frame_Del	DEL	CTTCTTCTT	CTTCTTCTT	-	rs567102553|rs150137790|rs374766108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTTCTTCTT	CTTCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:175129925_175129933delCTTCTTCTT	ENST00000423313.1	-	4	753_761	c.217_225delAAGAAGAAG	c.(217-225)aagaagaagdel	p.KKK73del	KIAA0040_ENST00000444639.1_In_Frame_Del_p.KKK73del|KIAA0040_ENST00000545251.2_In_Frame_Del_p.KKK73del|KIAA0040_ENST00000567124.1_5'Flank	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	cttcttcatccttcttcttcttcttcttc	0.502																																					p.73_76del		Pindel	.											.	KIAA0040	2	.	0			c.218_226del						PASS	.																																			SO:0001651	inframe_deletion	9674	exon5			.	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.217_225delAAGAAGAAG	1.37:g.175129934_175129942delCTTCTTCTT	ENSP00000462172:p.Lys73_Lys75del	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	100	21	0.210	NM_001162893	A8K9H6|Q2NKQ0	In_Frame_Del	DEL	ENST00000423313.1	37																																																																																				.	.	strong		0.502	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
ARHGEF35	445328	hgsc.bcm.edu	37	7	143885448	143885449	+	Frame_Shift_Ins	INS	-	-	CTCCACGCTGGGCCTCCTCAGC			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:143885448_143885449insCTCCACGCTGGGCCTCCTCAGC	ENST00000378115.2	-	2	157_158	c.28_29insGCTGAGGAGGCCCAGCGTGGAG	c.(28-30)gccfs	p.A10fs	ARHGEF35_ENST00000543357.1_Frame_Shift_Ins_p.A10fs	NM_001003702.2	NP_001003702.2	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF) 35	10										kidney(1)|large_intestine(1)|lung(3)|stomach(1)	6						GGGAGGAGAGGCTCCATGCTGG	0.51																																					p.A10_S11delinsGX		Pindel	.											.	ARHGEF35	11	.	0			c.29_30insGCTGAGGAGGCCCAGCGTGGAG						PASS	.																																			SO:0001589	frameshift_variant	445328	exon2			.	AK125680	CCDS34770.1	7q35	2012-07-24	2010-04-13	2010-04-13	ENSG00000213214	ENSG00000213214		"""Rho guanine nucleotide exchange factors"""	33846	protein-coding gene	gene with protein product			"""Rho guanine nucleotide exchange factor (GEF) 5-like"""	ARHGEF5L			Standard	NM_001003702		Approved	FLJ43692, CTAGE4	uc003wdz.2	A5YM69	OTTHUMG00000158010	ENST00000378115.2:c.28_29insGCTGAGGAGGCCCAGCGTGGAG	7.37:g.143885448_143885449insCTCCACGCTGGGCCTCCTCAGC	ENSP00000367355:p.Ala10fs	Somatic	40	.	.		WXS	Illumina HiSeq	Phase_I	311	54	0.174	NM_001003702	Q6ZUI2	Frame_Shift_Ins	INS	ENST00000378115.2	37	CCDS34770.1																																																																																			.	.	none		0.510	ARHGEF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349997.1	NM_001003702	
KRT1	3848	hgsc.bcm.edu	37	12	53069223	53069243	+	In_Frame_Del	DEL	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	-	rs77846840|rs540699806|rs11170232|rs370799361|rs267607656	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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		Pindel	.											.	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	7	.	.		WXS	Illumina HiSeq	Phase_I	18	11	0.611	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	
SELPLG	6404	hgsc.bcm.edu	37	12	109017651	109017680	+	In_Frame_Del	DEL	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	-	rs200527674|rs540144714|rs368721402|rs63748999|rs372173288|rs201851784|rs377406736|rs200694582|rs200732108|rs199985195|rs558357966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	GAGTGGTCTGTGCCTCCGTGGGCACTGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENST00000550948.1	-	2	628_657	c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	c.(403-435)caaccagtgcccacggaggcacagaccactcca>cca	p.QPVPTEAQTT135del	SELPLG_ENST00000388962.3_Splice_Site_p.NQCPR131del|SELPLG_ENST00000228463.6_In_Frame_Del_p.QPVPTEAQTT151del			Q14242	SELPL_HUMAN	selectin P ligand	135	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.Q135P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCTGCCAGTGGAGTGGTCTGTGCCTCCGTGGGCACTGGTTGAGTGGTCTG	0.617														558	0.111422	0.0817	0.0879	5008	,	,		27757	0.13		0.0835	False		,,,				2504	0.1779				p.151_161del		Pindel	.											.	SELPLG	138	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.453_482del						PASS	.		,	500,3762		33,434,1664					,	-2.0	0.0		dbSNP_129	146	1398,6854		132,1134,2860	no	coding,coding	SELPLG	NM_003006.4,NM_001206609.1	,	165,1568,4524	A1A1,A1R,RR		16.9413,11.7316,15.167	,	,		1898,10616				SO:0001651	inframe_deletion	6404	exon2			.		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.404_433delAACCAGTGCCCACGGAGGCACAGACCACTC	12.37:g.109017651_109017680delGAGTGGTCTGTGCCTCCGTGGGCACTGGTT	ENSP00000447752:p.Gln135_Thr144del	Somatic	182	.	.		WXS	Illumina HiSeq	Phase_I	167	36	0.216	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	In_Frame_Del	DEL	ENST00000550948.1	37	CCDS31895.2																																																																																			.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
NFKB1	4790	hgsc.bcm.edu	37	4	103534740	103534741	+	Splice_Site	INS	-	-	A	rs386357216|rs148268461	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:103534740_103534741insA	ENST00000505458.1	+	23	3023		c.e23+2		NFKB1_ENST00000600343.1_Splice_Site|NFKB1_ENST00000394820.4_Splice_Site|NFKB1_ENST00000226574.4_Splice_Site			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1						apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	AGCAAATAGGTAAAAAAAAAGA	0.5													?|AAAAAAAAA|AAAAAAAAAA|unsure	422	0.0842652	0.1641	0.0389	5008	,	,		18742	0.0605		0.0696	False		,,,				2504	0.0481				.		Pindel	.											.	NFKB1	78	.	0			c.2746+2->A						PASS	.		,	509,3757		21,467,1645					,	4.8	1.0		dbSNP_126	29	537,7717		10,517,3600	no	splice-5,splice-5	NFKB1	NM_003998.3,NM_001165412.1	,	31,984,5245	A1A1,A1R,RR		6.5059,11.9316,8.3546	,	,		1046,11474				SO:0001630	splice_region_variant	4790	exon23			.	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.2746+2->A	4.37:g.103534749_103534749dupA		Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	77	18	0.234	NM_001165412	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Splice_Site	INS	ENST00000505458.1	37	CCDS54783.1																																																																																			-|0.899;A|0.101	0.101	strong		0.500	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		Intron
RBM43	375287	hgsc.bcm.edu	37	2	152108088	152108088	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:152108088delT	ENST00000331426.5	-	4	557	c.406delA	c.(406-408)atcfs	p.I136fs		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	136							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.I136fs*4(1)		endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		AAACTCGGGATTTTTTTTTTC	0.388																																					p.I136fs		Pindel	.											.	RBM43	35	.	1	Deletion - Frameshift(1)	ovary(1)	c.407delT						PASS	.			67,49,4116		3,1,60,6,36,2010	81.0	90.0	87.0			4.3	0.8	2	dbSNP_134	89	115,71,8038		0,1,114,8,54,3935	no	codingComplex	RBM43	NM_198557.2		3,2,174,14,90,5945	A1A1,A1A2,A1R,A2A2,A2R,RR		2.2617,2.741,2.4245			152108088	182,120,12154	2198	4292	6490	SO:0001589	frameshift_variant	375287	exon4			.	AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"""RNA binding motif (RRM) containing"""	24790	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 38"""	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.406delA	2.37:g.152108088delT	ENSP00000331211:p.Ile136fs	Somatic	83	.	.		WXS	Illumina HiSeq	Phase_I	78	12	0.154	NM_198557	B2RMT5	Frame_Shift_Del	DEL	ENST00000331426.5	37	CCDS2191.1																																																																																			.	.	strong		0.388	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557	
SKA3	221150	hgsc.bcm.edu	37	13	21729952	21729953	+	Splice_Site	INS	-	-	AA	rs538865299|rs200184849|rs550091625|rs11446085|rs58481196|rs531482037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:21729952_21729953insAA	ENST00000314759.5	-	8	1244		c.e8-2		SKA3_ENST00000400018.3_Intron	NM_145061.5	NP_659498.4	Q8IX90	SKA3_HUMAN	spindle and kinetochore associated complex subunit 3						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.?(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						TGATAAAAGCTAAAAAAAAAAA	0.342																																					.		Pindel	.											.	SKA3	76	.	1	Unknown(1)	lung(1)	c.1120-2->TT						PASS	.																																			SO:0001630	splice_region_variant	221150	exon9			.	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.1120-2->TT	13.37:g.21729961_21729962dupAA		Somatic	39	.	.		WXS	Illumina HiSeq	Phase_I	54	11	0.204	NM_145061	A2A330|A2A331|B2RBY2|Q5VZV5|Q86WR2|Q8NBG1|Q96D22	Splice_Site	INS	ENST00000314759.5	37	CCDS31946.1																																																																																			-|0.500;A|0.500	.	strong		0.342	SKA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000272912.1	NM_145061	Intron
MICA	100507436	hgsc.bcm.edu	37	6	31380099	31380161	+	Splice_Site	DEL	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	-	rs547446871|rs193153971|rs41293539|rs201198334|rs553060235|rs138201170|rs535905110|rs199843678|rs41558418|rs372677694	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31380099_31380161delCAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	ENST00000449934.2	+	5	946_1006	c.892_952delCAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG	c.(892-954)cagggaaagtgctggtgcttcagagtcattggcagacattccatgtttctgctgttgctgctg>tg	p.QGKCWCFRVIGRHSMFLLLLL298del	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CCCTTTTTTTCAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTGGCTGCTGCTA	0.498																																					p.298_317del		Pindel	.											.	MICA	21	.	0			c.893_951del						PASS	.																																			SO:0001630	splice_region_variant	100507436	exon5			.	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.893-1CAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG>-	6.37:g.31380099_31380161delCAGGGAAAGTGCTGGTGCTTCAGAGTCATTGGCAGACATTCCATGTTTCTGCTGTTGCTGCTG		Somatic	191	.	.		WXS	Illumina HiSeq	Phase_I	145	31	0.214	NM_001177519		Frame_Shift_Del	DEL	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	none		0.498	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	In_Frame_Del
VWDE	221806	hgsc.bcm.edu	37	7	12391268	12391269	+	Frame_Shift_Ins	INS	-	-	A	rs11454536|rs398094831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:12391268_12391269insA	ENST00000275358.3	-	19	4004_4005	c.3816_3817insT	c.(3814-3819)aataaafs	p.K1273fs		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1273						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TCCTCTTCTTTATTTACACTTT	0.337													A|A|AA|insertion	697	0.139177	0.1505	0.0937	5008	,	,		16921	0.1905		0.1014	False		,,,				2504	0.1421				p.K1273_E1274delinsX		Pindel	.											.	VWDE	123	.	0			c.3817_3818insT						PASS	.			310,1762		51,208,777						1.9	0.0		dbSNP_120	217	402,3750		45,312,1719	no	frameshift	VWDE	NM_001135924.1		96,520,2496	A1A1,A1R,RR		9.6821,14.9614,11.4396				712,5512				SO:0001589	frameshift_variant	221806	exon19			.		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.3817dupT	7.37:g.12391269_12391269dupA	ENSP00000275358:p.Lys1273fs	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	141	35	0.248	NM_001135924	B7ZM77|Q96SQ3	Frame_Shift_Ins	INS	ENST00000275358.3	37	CCDS47544.1																																																																																			-|0.844;A|0.156	0.156	strong		0.337	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
ACKR4	51554	hgsc.bcm.edu	37	3	132320802	132320803	+	3'UTR	INS	-	-	A	rs546634560|rs201720609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132320802_132320803insA	ENST00000249887.2	+	0	1657_1658				ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000264990.6_Intron|ACAD11_ENST00000355458.3_Intron	NM_016557.2|NM_178445.2	NP_057641.1|NP_848540.1	Q9NPB9	ACKR4_HUMAN	atypical chemokine receptor 4						chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										taaaacaagttaaaaaaaAACC	0.307													?|AAAAAAAAA|AAAAAAAAAA|unsure	2186	0.436502	0.5182	0.2133	5008	,	,		15883	0.6806		0.2435	False		,,,				2504	0.4315				.		Pindel	.											.	CCRL1	30	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	51554	.			.	AF110640	CCDS3075.1	3q22	2013-07-17	2013-07-16	2013-07-16	ENSG00000129048	ENSG00000129048		"""GPCR / Class A : Chemokine receptors : Atypical"""	1611	protein-coding gene	gene with protein product		606065	"""chemokine (C-C motif) receptor-like 1"""	CCRL1		10767544, 16148	Standard	NM_016557		Approved	CCR11, CCBP2, VSHK1, CCX-CKR, PPR1	uc003eow.3	Q9NPB9	OTTHUMG00000159768	ENST00000249887.2:c.*509->A	3.37:g.132320811_132320811dupA		Somatic	130	.	.		WXS	Illumina HiSeq	Phase_I	117	30	0.256	.	B2R9U7	RNA	INS	ENST00000249887.2	37	CCDS3075.1																																																																																			.	.	weak		0.307	ACKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357238.2	NM_016557	
ASXL3	80816	hgsc.bcm.edu	37	18	31323501	31323501	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:31323501delT	ENST00000269197.5	+	12	3689	c.3689delT	c.(3688-3690)cttfs	p.L1230fs		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1230	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GTGCCCATGCTTTTTAATAAA	0.373																																					p.L1230fs		Pindel	.											.	ASXL3	405	.	0			c.3688delC						PASS	.						81.0	73.0	76.0					18																	31323501		1834	4083	5917	SO:0001589	frameshift_variant	80816	exon12			.	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.3689delT	18.37:g.31323501delT	ENSP00000269197:p.Leu1230fs	Somatic	76	.	.		WXS	Illumina HiSeq	Phase_I	68	25	0.368	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Frame_Shift_Del	DEL	ENST00000269197.5	37	CCDS45847.1																																																																																			.	.	none		0.373	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
NOTCH4	4855	hgsc.bcm.edu	37	6	32191659	32191661	+	In_Frame_Del	DEL	AGC	AGC	-	rs534749933|rs72110219|rs150280230|rs35795312|rs543450919|rs148340623	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32191659_32191661delAGC	ENST00000375023.3	-	1	183_185	c.45_47delGCT	c.(43-48)ctgcta>cta	p.15_16LL>L		NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	15					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						TGAGACACATagcagcagcagca	0.635														2380	0.47524	0.6293	0.3977	5008	,	,		25118	0.4921		0.331	False		,,,				2504	0.453				p.16_16del		Pindel	.											.	NOTCH4	201	.	0			c.46_48del						PASS	.																																			SO:0001651	inframe_deletion	4855	exon1			.		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.45_47delGCT	6.37:g.32191668_32191670delAGC	ENSP00000364163:p.Leu16del	Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	80	12	0.150	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	In_Frame_Del	DEL	ENST00000375023.3	37	CCDS34420.1																																																																																			.	.	alt		0.635	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
KRTAP17-1	83902	hgsc.bcm.edu	37	17	39471753	39471767	+	In_Frame_Del	DEL	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	-	rs373758570|rs74252500|rs572148015|rs386797077|rs577925182	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCCCCCGCAGCCAGA	GCCCCCGCAGCCAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	.											.	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	30	.	.		WXS	Illumina HiSeq	Phase_I	53	18	0.340	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		
TNRC6B	23112	hgsc.bcm.edu	37	22	40697177	40697179	+	In_Frame_Del	DEL	GCA	GCA	-	rs66700157|rs10617561|rs139908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:40697177_40697179delGCA	ENST00000454349.2	+	15	4171_4173	c.3960_3962delGCA	c.(3958-3963)ctgcag>ctg	p.Q1328del	TNRC6B_ENST00000301923.9_In_Frame_Del_p.Q524del|TNRC6B_ENST00000402203.1_In_Frame_Del_p.Q524del|TNRC6B_ENST00000335727.9_In_Frame_Del_p.Q1218del	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	1328	Silencing domain; interaction with CNOT1 and PAN3.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)	1						TGAGTGCACTgcagcagcagcag	0.596														1289	0.257388	0.4622	0.1499	5008	,	,		20853	0.0179		0.2396	False		,,,				2504	0.3221				p.1320_1321del		Pindel	.											.	TNRC6B	195	.	0			c.3959_3961del						PASS	.																																			SO:0001651	inframe_deletion	23112	exon15			.	AB029016	CCDS46712.1, CCDS46713.1, CCDS54533.1	22q13	2006-08-22			ENSG00000100354	ENSG00000100354		"""Trinucleotide (CAG) repeat containing"""	29190	protein-coding gene	gene with protein product		610740					Standard	NM_015088		Approved	KIAA1093	uc011aor.2	Q9UPQ9	OTTHUMG00000151114	ENST00000454349.2:c.3960_3962delGCA	22.37:g.40697186_40697188delGCA	ENSP00000401946:p.Gln1328del	Somatic	39	.	.		WXS	Illumina HiSeq	Phase_I	53	14	0.264	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	In_Frame_Del	DEL	ENST00000454349.2	37	CCDS54533.1																																																																																			GCA|0.779;-|0.221	0.221	strong		0.596	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
UBXN11	91544	hgsc.bcm.edu	37	1	26608883	26608884	+	In_Frame_Ins	INS	-	-	CCGGGACCGGGACAGGGACTGGGG	rs1134580|rs140364749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608883_26608884insCCGGGACCGGGACAGGGACTGGGG	ENST00000374222.1	-	16	1933_1934	c.1469_1470insCCCCAGTCCCTGTCCCGGTCCCGG	c.(1468-1470)ggt>ggCCCCAGTCCCTGTCCCGGTCCCGGt	p.490_490G>GPSPCPGPG	UBXN11_ENST00000314675.7_In_Frame_Ins_p.370_370G>GPSPCPGPG|UBXN11_ENST00000374217.2_In_Frame_Ins_p.457_457G>GPSPCPGPG|UBXN11_ENST00000357089.4_In_Frame_Ins_p.457_457G>GPSPCPGPG|UBXN11_ENST00000374223.1_In_Frame_Ins_p.247_247G>GPSPCPGPG|UBXN11_ENST00000374221.3_In_Frame_Ins_p.490_490G>GPSPCPGPG			Q5T124	UBX11_HUMAN	UBX domain protein 11	490	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						tggggccgggaccgggaccggg	0.713																																					p.G490delinsGPSPCPGPG		Pindel	.											UBXN11,NS,carcinoma,-2,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.1470_1471insCCCCAGTCCCTGTCCCGGTCCCGG						PASS	.																																			SO:0001652	inframe_insertion	91544	exon16			.	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.1469_1470insCCCCAGTCCCTGTCCCGGTCCCGG	1.37:g.26608883_26608884insCCGGGACCGGGACAGGGACTGGGG	Exception_encountered	Somatic	39	.	.		WXS	Illumina HiSeq	Phase_I	53	11	0.208	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	In_Frame_Ins	INS	ENST00000374222.1	37	CCDS41288.1																																																																																			.	.	alt		0.713	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
ODF1	4956	hgsc.bcm.edu	37	8	103573011	103573037	+	In_Frame_Del	DEL	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	-	rs143802899|rs111689913|rs568456031|rs372688769|rs369192995|rs377699584|rs62523271|rs62523272|rs62523273|rs386728348|rs58232162|rs386728346|rs150771034	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGCAACCCCTGCAGCCCCTGCAACCCG	TGCAACCCCTGCAGCCCCTGCAACCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:103573011_103573037delTGCAACCCCTGCAGCCCCTGCAACCCG	ENST00000285402.3	+	2	808_834	c.652_678delTGCAACCCCTGCAGCCCCTGCAACCCG	c.(652-678)tgcaacccctgcagcccctgcaacccgdel	p.CNPCSPCNP218del	ODF1_ENST00000518835.1_In_Frame_Del_p.CNPCSPCNP11del	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	218	C-X-P repeat region.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			ctgcagcccctgcaacccctgcagcccctgcaacccgtgcagcccAT	0.542														1567	0.312899	0.2731	0.4193	5008	,	,		21683	0.3244		0.2614	False		,,,				2504	0.3323				p.217_226del		Pindel	.											.	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.651_677del						PASS	.																																			SO:0001651	inframe_deletion	4956	exon2			.	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.652_678delTGCAACCCCTGCAGCCCCTGCAACCCG	8.37:g.103573011_103573037delTGCAACCCCTGCAGCCCCTGCAACCCG	ENSP00000285402:p.Cys218_Pro226del	Somatic	109	.	.		WXS	Illumina HiSeq	Phase_I	111	36	0.324	NM_024410	Q3SX72	In_Frame_Del	DEL	ENST00000285402.3	37	CCDS6293.1																																																																																			.	.	none		0.542	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
DNAH5	1767	hgsc.bcm.edu	37	5	13868104	13868104	+	Intron	DEL	A	A	-	rs397769827|rs35398031|rs376631255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13868104delA	ENST00000265104.4	-	25	3939				CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5						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)					TAAGATTCCTAAAAAAAAATA	0.363									Kartagener syndrome					1744	0.348243	0.2731	0.3184	5008	,	,		19615	0.2659		0.4433	False		,,,				2504	0.4581				.		Pindel	.											.	DNAH5	868	.	0			c.3835-2T>-						PASS	.			3,1314,2949		0,0,3,214,886,1030	35.0	28.0	30.0			5.1	0.9	5	dbSNP_134	46	5,3668,4581		0,1,4,858,1951,1313	no	intron	DNAH5	NM_001369.2		0,1,7,1072,2837,2343	A1A1,A1A2,A1R,A2A2,A2R,RR		44.4996,30.872,39.8562			13868104	8,4982,7530	2203	4296	6499	SO:0001627	intron_variant	1767	exon26	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	.	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.3835-3T>-	5.37:g.13868104delA		Somatic	83	.	.		WXS	Illumina HiSeq	Phase_I	69	21	0.304	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Splice_Site	DEL	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.250;-|0.750	0.750	strong		0.363	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
CTSA	5476	hgsc.bcm.edu	37	20	44520238	44520240	+	In_Frame_Del	DEL	CTG	CTG	-	rs3080212|rs11468075|rs10582052|rs397784956|rs397839006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:44520238_44520240delCTG	ENST00000372459.2	+	1	224_226	c.31_33delCTG	c.(31-33)ctgdel	p.L19del	NEURL2_ENST00000372518.4_5'Flank|CTSA_ENST00000354880.5_In_Frame_Del_p.L37del|RP3-337O18.9_ENST00000607703.1_RNA|CTSA_ENST00000191018.5_In_Frame_Del_p.L19del|CTSA_ENST00000372484.3_In_Frame_Del_p.L37del			P10619	PPGB_HUMAN	cathepsin A	19				Missing (in Ref. 4; AAH00597). {ECO:0000305}.	glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)	p.L29delL(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				gccgctgttcctgctgctgctgc	0.709														3252	0.649361	0.6868	0.7248	5008	,	,		16739	0.5784		0.6173	False		,,,				2504	0.6513				p.28_29del		Pindel	.											.	CTSA	52	.	1	Deletion - In frame(1)	breast(1)	c.84_86del						PASS	.																																			SO:0001651	inframe_deletion	5476	exon2			.	M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"""Cathepsins"""	9251	protein-coding gene	gene with protein product	"""carboxypeptidase C"", ""lysosomal protective protein"", ""carboxypeptidase-L"", ""carboxypeptidase Y-like kininase"", ""deamidase"", ""lysosomal carboxypeptidase A"", ""urinary kininase"""	613111	"""protective protein for beta-galactosidase (galactosialidosis)"""	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.31_33delCTG	20.37:g.44520247_44520249delCTG	ENSP00000361537:p.Leu19del	Somatic	12	.	.		WXS	Illumina HiSeq	Phase_I	26	16	0.615	NM_000308	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	In_Frame_Del	DEL	ENST00000372459.2	37	CCDS46609.1																																																																																			CTG|0.332;-|0.668	0.668	strong		0.709	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2	NM_000308	
SAMD11	148398	hgsc.bcm.edu	37	1	874779	874826	+	In_Frame_Del	DEL	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	-	rs200584816|rs568340123|rs201898716|rs141207077|rs200996316|rs201782804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	CCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:874779_874826delCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	ENST00000342066.3	+	7	728_775	c.645_692delCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	c.(643-693)ggcctccccagccacggtgaggacccaccctggcatgatccccctcatcac>ggc	p.LPSHGEDPPWHDPPHH216del		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	216					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		ACCACCTGGGCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCACCTCCCCAGC	0.657																																					p.215_231del		Pindel	.											.	SAMD11	34	.	0			c.644_691del						PASS	.																																			SO:0001651	inframe_deletion	148398	exon7			.	BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.645_692delCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	1.37:g.874779_874826delCCTCCCCAGCCACGGTGAGGACCCACCCTGGCATGATCCCCCTCATCA	ENSP00000342313:p.Leu216_His231del	Somatic	183	.	.		WXS	Illumina HiSeq	Phase_I	85	38	0.447	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	In_Frame_Del	DEL	ENST00000342066.3	37	CCDS2.2																																																																																			.	.	none		0.657	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
SPATA3	130560	hgsc.bcm.edu	37	2	231861033	231861059	+	In_Frame_Del	DEL	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	-	rs13005918|rs72362780	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENST00000452881.1	+	1	193_219	c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	c.(85-111)cagcagcctagccctgaatccacaccadel	p.QQPSPESTP47del	AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000455816.1_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000433428.2_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000424440.1_In_Frame_Del_p.QQPSPESTP47del			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	47			Missing.							endometrium(2)|lung(1)	3						TTCCACCTCTCAGCAGCCTAGCCCTGAATCCACACCACAGCAGCCTA	0.564																																					p.28_37del		Pindel	.											.	SPATA3	52	.	0			c.84_110del						PASS	.			924,1842		222,480,681						-8.0	0.0		dbSNP_130	187	2754,2350		871,1012,669	no	coding	SPATA3	NM_139073.3		1093,1492,1350	A1A1,A1R,RR		46.0423,33.4056,46.7344				3678,4192				SO:0001651	inframe_deletion	130560	exon1			.	AY032925	CCDS2481.1	2q37.1	2008-02-05			ENSG00000173699	ENSG00000173699			17884	protein-coding gene	gene with protein product							Standard	NM_139073		Approved	TSARG1	uc010zmd.2	Q8NHX4	OTTHUMG00000133221	ENST00000452881.1:c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	2.37:g.231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENSP00000388895:p.Gln47_Pro55del	Somatic	82	.	.		WXS	Illumina HiSeq	Phase_I	86	32	0.372	NM_139073	Q86WX5|Q8N9Y6	In_Frame_Del	DEL	ENST00000452881.1	37	CCDS2481.1																																																																																			.	.	strong		0.564	SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
WDR60	55112	hgsc.bcm.edu	37	7	158664075	158664077	+	In_Frame_Del	DEL	GAA	GAA	-	rs3833679|rs145233696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158664075_158664077delGAA	ENST00000407559.3	+	3	470_472	c.312_314delGAA	c.(310-315)ctgaag>ctg	p.K105del		NM_018051.4	NP_060521.4	Q8WVS4	WDR60_HUMAN	WD repeat domain 60	105					cell projection organization (GO:0030030)	cilium (GO:0005929)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.K105delK(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(4)|lung(16)|ovary(2)	35	Ovarian(565;0.152)	all_cancers(7;1.25e-09)|all_epithelial(9;0.000894)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00174)	UCEC - Uterine corpus endometrioid carcinoma (81;0.19)|STAD - Stomach adenocarcinoma(7;0.18)		aagaaaagctgaaggagaaacat	0.542														583	0.116414	0.0908	0.0965	5008	,	,		19368	0.0556		0.1889	False		,,,				2504	0.1534				p.104_105del		Pindel	.											.	WDR60	94	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.311_313del						PASS	.			346,3112		52,242,1435						-8.3	0.0		dbSNP_107	66	1313,5999		217,879,2560	no	coding	WDR60	NM_018051.4		269,1121,3995	A1A1,A1R,RR		17.9568,10.0058,15.4039				1659,9111				SO:0001651	inframe_deletion	55112	exon3			.		CCDS47757.1	7q36.3	2013-11-15			ENSG00000126870	ENSG00000126870		"""WD repeat domain containing"""	21862	protein-coding gene	gene with protein product		615462				23910462	Standard	NM_018051		Approved	FLJ10300, FAP163	uc003woe.4	Q8WVS4	OTTHUMG00000151443	ENST00000407559.3:c.312_314delGAA	7.37:g.158664075_158664077delGAA	ENSP00000384290:p.Lys105del	Somatic	54	.	.		WXS	Illumina HiSeq	Phase_I	40	28	0.700	NM_018051	Q9NW58	In_Frame_Del	DEL	ENST00000407559.3	37	CCDS47757.1																																																																																			GAA|0.880;-|0.120	0.120	strong		0.542	WDR60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322668.1	NM_018051	
RIMBP3	85376	hgsc.bcm.edu	37	22	20460113	20460115	+	In_Frame_Del	DEL	CCG	CCG	-	rs201820173		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20460113_20460115delCCG	ENST00000426804.1	-	1	1671_1673	c.1187_1189delCGG	c.(1186-1191)gcggag>gag	p.A396del		NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	396				A -> E (in Ref. 2; BAB33336). {ECO:0000305}.						breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			TGCTTGTTCTCCGCTTGCAGGGT	0.675																																					p.396_397del		Pindel	.											.	RIMBP3	42	.	0			c.1188_1190del						PASS	.																																			SO:0001651	inframe_deletion	85376	exon1			.	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.1187_1189delCGG	22.37:g.20460113_20460115delCCG	ENSP00000391564:p.Ala396del	Somatic	114	.	.		WXS	Illumina HiSeq	Phase_I	28	28	1.000	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	In_Frame_Del	DEL	ENST00000426804.1	37	CCDS46665.1																																																																																			.	.	alt		0.675	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
CFAP74	85452	hgsc.bcm.edu	37	1	1887092	1887112	+	IGR	DEL	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	-	rs3838976|rs199780644|rs3838975|rs562842260|rs139735565	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCCCGCCCACCCTGGCTTGGC	GCCCGCCCACCCTGGCTTGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1887092_1887112delGCCCGCCCACCCTGGCTTGGC								TMEM52 (36380 upstream) : C1orf222 (32450 downstream)														p.W736R(1)|p.K733N(1)									GGCCCTCACCGCCCGCCCACCCTGGCTTGGCCTGGCAGCCT	0.643																																					p.732_739del		Pindel	.											.	KIAA1751	92	.	2	Substitution - Missense(2)	lung(1)|endometrium(1)	c.2195_2215del						PASS	.																																			SO:0001628	intergenic_variant	85452	exon18			.																													1.37:g.1887092_1887112delGCCCGCCCACCCTGGCTTGGC		Somatic	98	.	.		WXS	Illumina HiSeq	Phase_I	83	33	0.398	NM_001080484		In_Frame_Del	DEL		37																																																																																				-|0.223;G|0.777	0.223	alt	0	0.643								
COL6A3	1293	hgsc.bcm.edu	37	2	238244864	238244866	+	In_Frame_Del	DEL	GCA	GCA	-	rs35879189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238244864_238244866delGCA	ENST00000295550.4	-	40	9329_9331	c.8877_8879delTGC	c.(8875-8880)gctgca>gca	p.2959_2960AA>A	COL6A3_ENST00000353578.4_In_Frame_Del_p.2753_2754AA>A|COL6A3_ENST00000346358.4_In_Frame_Del_p.2759_2760AA>A|COL6A3_ENST00000347401.3_In_Frame_Del_p.2758_2759AA>A|COL6A3_ENST00000409809.1_In_Frame_Del_p.2753_2754AA>A|COL6A3_ENST00000472056.1_In_Frame_Del_p.2352_2353AA>A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2959	Ala-rich.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CACTGGTTTTGCAGCAGCAGCAG	0.611														256	0.0511182	0.003	0.0591	5008	,	,		19560	0.0089		0.1302	False		,,,				2504	0.0726				p.2960_2960del		Pindel	.											.	COL6A3	608	.	0			c.8878_8880del						PASS	.		,,	96,4160		2,92,2034					,,	2.1	0.0		dbSNP_126	40	977,7259		76,825,3217	no	coding,coding,coding	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	,,	78,917,5251	A1A1,A1R,RR		11.8626,2.2556,8.5895	,,	,,		1073,11419				SO:0001651	inframe_deletion	1293	exon40			.	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.8877_8879delTGC	2.37:g.238244873_238244875delGCA	ENSP00000295550:p.Ala2960del	Somatic	60	.	.		WXS	Illumina HiSeq	Phase_I	58	39	0.672	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	In_Frame_Del	DEL	ENST00000295550.4	37	CCDS33412.1																																																																																			GCA|0.935;-|0.065	0.065	strong		0.611	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
TRAK1	22906	hgsc.bcm.edu	37	3	42251578	42251580	+	Intron	DEL	GGA	GGA	-	rs35624871		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:42251578_42251580delGGA	ENST00000327628.5	+	14	2363				TRAK1_ENST00000341421.3_In_Frame_Del_p.E640del|TRAK1_ENST00000487159.1_Intron|TRAK1_ENST00000396175.1_Intron	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1						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)		p.E640delE(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						CAGCGGCCACggaggaggaggag	0.621																																					p.688_689del	GBM(44;195 884 22595 31865 41850)	Pindel	.											TRAK1,caecum,carcinoma,0,1	TRAK1	188	1	1	Deletion - In frame(1)	kidney(1)	c.2063_2065del						PASS	.																																			SO:0001627	intron_variant	22906	exon14			.		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.1963+101GGA>-	3.37:g.42251587_42251589delGGA		Somatic	69	.	.		WXS	Illumina HiSeq	Phase_I	88	28	0.318	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	In_Frame_Del	DEL	ENST00000327628.5	37	CCDS43072.1																																																																																			.	.	strong		0.621	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
TMEM255B	348013	hgsc.bcm.edu	37	13	114503876	114503957	+	Splice_Site	DEL	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	-	rs9577890|rs76163514|rs111667140|rs41284484|rs41284485|rs144347748|rs9577889|rs79620376|rs114746443|rs41284483|rs66696122|rs371072437|rs553476183|rs148763547|rs371342802|rs115620789|rs550352190|rs575880631|rs386775130|rs372249488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:114503876_114503957delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	ENST00000375353.3	+	6	527_536	c.500_509delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA	c.(499-510)gcctgcgggagg>gg	p.ACGR167fs		NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	167						integral component of membrane (GO:0016021)											GACCTCTATGCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACACCTGCGGGAG	0.652																																					p.167_170del		Pindel	.											.	.	.	.	0			c.499_509del						PASS	.			409,860,2993		20,66,303,99,596,1047						-3.0	0.0		dbSNP_130	62	1222,24,7006		90,3,1039,0,21,2973	no	codingComplex	FAM70B	NM_182614.2		110,69,1342,99,617,4020	A1A1,A1A2,A1R,A2A2,A2R,RR		15.0994,29.7748,20.0975				1631,884,9999				SO:0001630	splice_region_variant	348013	exon6			.	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.509+1CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA>-	13.37:g.114503876_114503957delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAGGTGAGGGGCGCTGGGGACCCCCGTATCTACA		Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	78	19	0.244	NM_182614		Frame_Shift_Del	DEL	ENST00000375353.3	37	CCDS45071.1																																																																																			.	.	none		0.652	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614	Frame_Shift_Del
KBTBD12	166348	hgsc.bcm.edu	37	3	127646660	127646661	+	Frame_Shift_Ins	INS	-	-	AGAA			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:127646660_127646661insAGAA	ENST00000405109.1	+	3	1591_1592	c.1124_1125insAGAA	c.(1123-1128)cgagaafs	p.-376fs	KBTBD12_ENST00000405256.1_Frame_Shift_Ins_p.-376fs|KBTBD12_ENST00000343941.4_Frame_Shift_Ins_p.-17fs|KBTBD12_ENST00000492025.1_Intron|KBTBD12_ENST00000407609.3_5'UTR			Q3ZCT8	KBTBC_HUMAN	kelch repeat and BTB (POZ) domain containing 12											endometrium(1)|large_intestine(6)|lung(5)|ovary(1)	13						GCTGAATTTCGAGAACTCTATG	0.366																																					p.R375fs		Pindel	.											KBTBD12,NS,malignant_melanoma,+1,2	KBTBD12	41	2	0			c.1124_1125insAGAA						PASS	.																																			SO:0001589	frameshift_variant	166348	exon2			.		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.1125_1128dupAGAA	3.37:g.127646661_127646664dupAGAA	ENSP00000385957:p.Glu376fs	Somatic	183	.	.		WXS	Illumina HiSeq	Phase_I	151	46	0.305	NM_207335	B5MCC6|Q6ZRK1	Frame_Shift_Ins	INS	ENST00000405109.1	37	CCDS33848.2																																																																																			.	.	none		0.366	KBTBD12-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318682.1	NM_207335	
DRICH1	51233	hgsc.bcm.edu	37	22	23964283	23964285	+	In_Frame_Del	DEL	CAT	CAT	-	rs66974032|rs142649853|rs10564183|rs200087148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAT	CAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:23964283_23964285delCAT	ENST00000317749.5	-	4	674_676	c.377_379delATG	c.(376-381)gatgcc>gcc	p.D126del		NM_016449.3	NP_057533.2	Q6PGQ1	DRIC1_HUMAN		126	Asp-rich.							p.D126delD(1)		endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)	11						CTTACCTGGGcatcatcatcatc	0.429														621	0.124002	0.1036	0.0937	5008	,	,		21629	0.1895		0.1133	False		,,,				2504	0.1166				p.126_127del		Pindel	.											.	C22orf43	18	.	1	Deletion - In frame(1)	pancreas(1)	c.378_380del						PASS	.																																			SO:0001651	inframe_deletion	51233	exon4			.																												ENST00000317749.5:c.377_379delATG	22.37:g.23964292_23964294delCAT	ENSP00000316137:p.Asp126del	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	47	14	0.298	NM_016449	Q6ICJ8|Q6P4I3|Q9NU31	In_Frame_Del	DEL	ENST00000317749.5	37	CCDS42985.1																																																																																			.	.	weak		0.429	C22orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319708.2		
SYNGR1	9145	hgsc.bcm.edu	37	22	39777822	39777823	+	In_Frame_Ins	INS	-	-	CAA	rs57910921|rs149306472|rs72417605	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39777822_39777823insCAA	ENST00000328933.5	+	4	620_621	c.605_606insCAA	c.(604-609)cccact>ccCAAcact	p.202_203PT>PNT		NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	202			P -> PN. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:17049558, ECO:0000269|PubMed:9760194}.		protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					TACGTGGAGCCCACTGGGCCGG	0.668														4311	0.860823	0.9228	0.7925	5008	,	,		12298	0.999		0.6541	False		,,,				2504	0.8957				p.P202delinsPN		Pindel	.											.	SYNGR1	19	.	0			c.605_606insCAA						PASS	.			3794,444		1706,382,31						4.3	1.0		dbSNP_130	29	5453,2791		1805,1843,474	no	coding	SYNGR1	NM_004711.4		3511,2225,505	A1A1,A1R,RR		33.8549,10.4766,25.9173				9247,3235				SO:0001652	inframe_insertion	9145	exon4			.	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	Exception_encountered	22.37:g.39777822_39777823insCAA	ENSP00000332287:p.Pro202_Thr203insAsn	Somatic	119	.	.		WXS	Illumina HiSeq	Phase_I	128	52	0.406	NM_004711	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	In_Frame_Ins	INS	ENST00000328933.5	37	CCDS13989.1																																																																																			.	.	strong		0.668	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711	
DEFB132	400830	hgsc.bcm.edu	37	20	238436	238441	+	In_Frame_Del	DEL	TGGTCT	TGGTCT	-	rs66489228|rs398088193|rs371825938|rs79204234|rs74636637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGGTCT	TGGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:238436_238441delTGGTCT	ENST00000382376.3	+	1	60_65	c.17_22delTGGTCT	c.(16-24)ctggtcttg>ctg	p.6_8LVL>L		NM_207469.2	NP_997352.1	Q7Z7B7	DB132_HUMAN	defensin, beta 132	6					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				breast(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	4						TTCCTGCTCCTGGTCTTGGCAGCCCT	0.515																																					p.6_7del		Pindel	.											.	DEFB132	17	.	0			c.16_21del						PASS	.			2698,1566		848,1002,282						2.2	0.7		dbSNP_130	87	4920,3332		1500,1920,706	no	coding	DEFB132	NM_207469.2		2348,2922,988	A1A1,A1R,RR		40.3781,36.7261,39.1339				7618,4898				SO:0001651	inframe_deletion	400830	exon1			.	AF525932	CCDS12993.1	20p13	2009-12-04	2008-10-23		ENSG00000186458	ENSG00000186458		"""Defensins, beta"""	33806	protein-coding gene	gene with protein product						18416833	Standard	NM_207469		Approved	RP5-1103G7.6, DEFB32	uc002wdb.3	Q7Z7B7	OTTHUMG00000043061	ENST00000382376.3:c.17_22delTGGTCT	20.37:g.238436_238441delTGGTCT	ENSP00000371813:p.Leu6_Val7del	Somatic	50	.	.		WXS	Illumina HiSeq	Phase_I	32	24	0.750	NM_207469	B2RP72|Q4QY40	In_Frame_Del	DEL	ENST00000382376.3	37	CCDS12993.1																																																																																			TGGTCT|0.380;-|0.620	0.620	strong		0.515	DEFB132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101365.1	NM_207469	
C14orf23	387978	hgsc.bcm.edu	37	14	29261309	29261310	+	In_Frame_Ins	INS	-	-	AAC	rs79677598|rs71101677|rs56025822|rs151028783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:29261309_29261310insAAC	ENST00000399387.4	+	3	450_451	c.346_347insAAC	c.(346-348)aaa>aAACaa	p.116_117insQ	C14orf23_ENST00000548213.1_Intron|C14orf23_ENST00000550266.1_Intron					chromosome 14 open reading frame 23											central_nervous_system(1)	1						AGCACTAAAAAAAACAAACAAA	0.381														2112	0.421725	0.3949	0.4683	5008	,	,		16071	0.3998		0.3241	False		,,,				2504	0.5481				.		Pindel	.											.	C14orf23	5	.	0			.						PASS	.																																			SO:0001652	inframe_insertion	387978	.			.			14q11.2	2013-01-15			ENSG00000186960	ENSG00000186960			19828	other	unknown							Standard	NR_026731		Approved		uc001wqf.3	Q86U37	OTTHUMG00000029410	Exception_encountered	14.37:g.29261309_29261310insAAC	ENSP00000382318:p.Lys116_Thr117insGln	Somatic	116	.	.		WXS	Illumina HiSeq	Phase_I	113	21	0.186	.		RNA	INS	ENST00000399387.4	37																																																																																				AAC|1.000	.	strong		0.381	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000134019.2	NR_026731	
LUZP4	51213	hgsc.bcm.edu	37	X	114541251	114541252	+	In_Frame_Ins	INS	-	-	CACTCAGAGAGATCTCGTGGC	rs146034702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:114541251_114541252insCACTCAGAGAGATCTCGTGGC	ENST00000371920.3	+	4	831_832	c.824_825insCACTCAGAGAGATCTCGTGGC	c.(823-828)gtcact>gtCACTCAGAGAGATCTCGTGGCcact	p.283_284insQRDLVAT	LUZP4_ENST00000451986.2_In_Frame_Ins_p.201_202insQRDLVAT	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	283						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						GATCTCATAGTCACTCAGAGAG	0.45																																					p.V275delinsVTQRDLVA		Pindel	.											.	LUZP4	51	.	0			c.824_825insCACTCAGAGAGATCTCGTGGC						PASS	.																																			SO:0001652	inframe_insertion	51213	exon4			.	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"""cancer/testis antigen 28"""	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.825_845dupCACTCAGAGAGATCTCGTGGC	X.37:g.114541251_114541252insCACTCAGAGAGATCTCGTGGC	ENSP00000360988:p.Gln277_Thr283dup	Somatic	220	.	.		WXS	Illumina HiSeq	Phase_I	216	56	0.259	NM_016383	B3KSD6	In_Frame_Ins	INS	ENST00000371920.3	37	CCDS14567.1																																																																																			.	.	none		0.450	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383	
PRKCSH	5589	hgsc.bcm.edu	37	19	11558341	11558343	+	In_Frame_Del	DEL	GAG	GAG	-	rs397840350|rs71166603|rs3217229	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11558341_11558343delGAG	ENST00000589838.1	+	10	937_939	c.937_939delGAG	c.(937-939)gagdel	p.E325del	PRKCSH_ENST00000592741.1_In_Frame_Del_p.E325del|PRKCSH_ENST00000591462.1_In_Frame_Del_p.E325del|PRKCSH_ENST00000412601.1_In_Frame_Del_p.E325del|PRKCSH_ENST00000252455.2_In_Frame_Del_p.E325del|PRKCSH_ENST00000587327.1_In_Frame_Del_p.E325del			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	325	Glu-rich (acidic).			Missing (in Ref. 1; AAA52493, 2; AAA98668, 4; AAP88860 and 6; AAH13586). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						GTCGCCCACAgaggaggaggagg	0.65														2250	0.449281	0.559	0.4323	5008	,	,		15796	0.3661		0.4245	False		,,,				2504	0.4243				p.312_313del		Pindel	.											.	PRKCSH	55	.	0			c.936_938del						PASS	.																																			SO:0001651	inframe_deletion	5589	exon11			.		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.937_939delGAG	19.37:g.11558350_11558352delGAG	ENSP00000465461:p.Glu325del	Somatic	108	.	.		WXS	Illumina HiSeq	Phase_I	132	25	0.189	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	In_Frame_Del	DEL	ENST00000589838.1	37	CCDS32911.1																																																																																			GAG|0.500;-|0.500	0.500	strong		0.650	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-	rs201063949|rs199513201|rs199927874|rs150364859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145586672_145586679delTTTTACAC	ENST00000334513.5	-	8	908_915	c.897_904delGTGTAAAA	c.(895-906)ccgtgtaaaagtfs	p.CKS300fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	300							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TAAGCTGCACTTTTACACGGTGGGGGTG	0.534																																					p.300_302del		Pindel	.											.	NUDT17	25	.	0			c.898_905del						PASS	.																																			SO:0001589	frameshift_variant	200035	exon8			.	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"""Nudix motif containing"""	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.897_904delGTGTAAAA	1.37:g.145586672_145586679delTTTTACAC	ENSP00000334437:p.Cys300fs	Somatic	137	.	.		WXS	Illumina HiSeq	Phase_I	133	27	0.203	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			-|0.017;TTTTA|0.983	0.017	alt		0.534	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
CELA1	1990	hgsc.bcm.edu	37	12	51740388	51740416	+	Splice_Site	DEL	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	-	rs150350903|rs573952082|rs532961697|rs141305161|rs117443541|rs377599213|rs143199509|rs61761206|rs3059200|rs148235680|rs370927847|rs907354|rs148270827|rs116944010|rs57614420|rs386762976|rs55827519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTGGACCATATCCACTTACCATAAAGGAC	CTGGACCATATCCACTTACCATAAAGGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51740388_51740416delCTGGACCATATCCACTTACCATAAAGGAC	ENST00000293636.1	-	1	47_57	c.7_17delGTCCTTTATGGTAAGTGGATATGGTCCAG	c.(7-18)gtcctttatggt>t	p.VLYG3fs		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	3					exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.V3fs*21(1)|p.L4P(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						AGGGTTGCGACTGGACCATATCCACTTACCATAAAGGACCAGCATGTTG	0.511																																					p.3_6del		Pindel	.											.	CELA1	39	.	2	Substitution - Missense(1)|Deletion - Frameshift(1)	large_intestine(1)|lung(1)	c.8_16del						PASS	.																																			SO:0001630	splice_region_variant	1990	exon1			.		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.16+1GTCCTTTATGGTAAGTGGATATGGTCCAG>-	12.37:g.51740388_51740416delCTGGACCATATCCACTTACCATAAAGGAC		Somatic	142	.	.		WXS	Illumina HiSeq	Phase_I	92	15	0.163	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	In_Frame_Del	DEL	ENST00000293636.1	37	CCDS8812.1																																																																																			-|0.574;CACCAGGAAGCG|0.426	0.574	alt		0.511	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	Frame_Shift_Del
NCOA3	8202	hgsc.bcm.edu	37	20	46279815	46279823	+	In_Frame_Del	DEL	GCAGCAGCA	GCAGCAGCA	-	rs3830810		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GCAGCAGCA	GCAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:46279815_46279823delGCAGCAGCA	ENST00000371998.3	+	20	3932_3940	c.3741_3749delGCAGCAGCA	c.(3739-3750)atgcagcagcag>atg	p.QQQ1272del	NCOA3_ENST00000371997.3_In_Frame_Del_p.QQQ1263del|NCOA3_ENST00000341724.6_In_Frame_Del_p.QQQ1198del|NCOA3_ENST00000372004.3_In_Frame_Del_p.QQQ1268del			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1272	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CTATGATGATgcagcagcagcagcagcag	0.545																																					p.1247_1250del		Pindel	.											.	NCOA3	156	.	0			c.3740_3748del						PASS	.																																			SO:0001651	inframe_deletion	8202	exon20			.	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3741_3749delGCAGCAGCA	20.37:g.46279824_46279832delGCAGCAGCA	ENSP00000361066:p.Gln1272_Gln1274del	Somatic	88	.	.		WXS	Illumina HiSeq	Phase_I	82	14	0.171	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	In_Frame_Del	DEL	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	none		0.545	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
HOXB1	3211	hgsc.bcm.edu	37	17	46608184	46608185	+	In_Frame_Ins	INS	-	-	GGGCGCTGT	rs534792734|rs145570960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:46608184_46608185insGGGCGCTGT	ENST00000239174.6	-	1	174_175	c.82_83insACAGCGCCC	c.(82-84)cca>cACAGCGCCCca	p.27_28insHSA	HOXB1_ENST00000577092.1_In_Frame_Ins_p.27_28insHSA	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	27			A -> AHSA (in allele HOXB1*B). {ECO:0000269|PubMed:10671062, ECO:0000269|PubMed:11091361}.		anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)	p.A27_P28insHSA(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAAGGAGGTTGGGGCGCTGTGG	0.619														667	0.133187	0.1157	0.1225	5008	,	,		17469	0.0982		0.2008	False		,,,				2504	0.1309				p.P28delinsHSAP		Pindel	.											.	HOXB1	67	.	1	Insertion - In frame(1)	lung(1)	c.83_84insACAGCGCCC						PASS	.			528,3732		33,462,1635						4.2	1.0		dbSNP_134	66	1685,6565		171,1343,2611	no	coding	HOXB1	NM_002144.3		204,1805,4246	A1A1,A1R,RR		20.4242,12.3944,17.6898				2213,10297				SO:0001652	inframe_insertion	3211	exon1			.		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.74_82dupACAGCGCCC	17.37:g.46608185_46608193dupGGGCGCTGT	ENSP00000355140:p.His25_Ala27dup	Somatic	46	.	.		WXS	Illumina HiSeq	Phase_I	39	11	0.282	NM_002144	Q4VB03	In_Frame_Ins	INS	ENST00000239174.6	37	CCDS32675.1																																																																																			.	.	strong		0.619	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
ATN1	1822	hgsc.bcm.edu	37	12	7045892	7045912	+	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAGCAG	-	rs377147612|rs144280633|rs60216939	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7045892_7045912delCAGCAGCAGCAGCAGCAGCAG	ENST00000356654.4	+	5	1699_1719	c.1462_1482delCAGCAGCAGCAGCAGCAGCAG	c.(1462-1482)cagcagcagcagcagcagcagdel	p.QQQQQQQ495del	ATN1_ENST00000396684.2_In_Frame_Del_p.QQQQQQQ495del	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	495	Poly-Gln.				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						gcaacagcaacagcagcagcagcagcagcagcagcagcagc	0.643																																					p.487_494del		Pindel	.											ATN1,NS,carcinoma,0,3	ATN1	95	3	2	Insertion - In frame(1)|Deletion - In frame(1)	breast(2)	c.1461_1481del						PASS	.																																			SO:0001651	inframe_deletion	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.1462_1482delCAGCAGCAGCAGCAGCAGCAG	12.37:g.7045892_7045912delCAGCAGCAGCAGCAGCAGCAG	ENSP00000349076:p.Gln495_Gln501del	Somatic	101	.	.		WXS	Illumina HiSeq	Phase_I	127	30	0.236	NM_001007026	Q99495|Q99621|Q9UEK7	In_Frame_Del	DEL	ENST00000356654.4	37	CCDS31734.1																																																																																			.	.	alt		0.643	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
OR52B4	143496	hgsc.bcm.edu	37	11	4389405	4389405	+	Frame_Shift_Del	DEL	G	G	-	rs398075683|rs397699893|rs201331071|rs11310407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4389405delG	ENST00000408920.2	-	1	211	c.121delC	c.(121-123)cttfs	p.L42fs		NM_001005161.3	NP_001005161.2	Q8NGK2	O52B4_HUMAN	olfactory receptor, family 52, subfamily B, member 4	42					cognition (GO:0050890)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(3)|large_intestine(7)|lung(15)|skin(2)	31		Medulloblastoma(188;0.0075)|Breast(177;0.0249)|all_neural(188;0.0577)		Epithelial(150;1.57e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0826)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTCCCAAGAAGGGCGGTGACA	0.522													GGG|GGG|GG|deletion	1601	0.319688	0.1422	0.4193	5008	,	,		24468	0.4157		0.3499	False		,,,				2504	0.3589				p.L41fs		Pindel	.											.	OR52B4	56	.	0			c.122delT	GRCh37	CD035871	OR52B4	D	rs80193749	PASS	.			717,3355		101,515,1420	55.0	47.0	50.0			4.9	0.0	11	dbSNP_131	68	2865,5269		532,1801,1734	no	frameshift	OR52B4	NM_001005161.3		633,2316,3154	A1A1,A1R,RR		35.2225,17.6081,29.3462			4389405	3582,8624	2066	4141	6207	SO:0001589	frameshift_variant	143496	exon1			.	AB065792	CCDS41609.1	11p15.4	2012-08-09			ENSG00000221996	ENSG00000221996		"""GPCR / Class A : Olfactory receptors"""	15209	protein-coding gene	gene with protein product							Standard	NM_001005161		Approved		uc010qye.2	Q8NGK2	OTTHUMG00000154222	ENST00000408920.2:c.121delC	11.37:g.4389405delG	ENSP00000386160:p.Leu42fs	Somatic	113	.	.		WXS	Illumina HiSeq	Phase_I	115	43	0.374	NM_001005161	A6NP68|Q6IFK6	Frame_Shift_Del	DEL	ENST00000408920.2	37	CCDS41609.1																																																																																			G|0.671;-|0.329	0.329	strong		0.522	OR52B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334449.3	NM_001005161	
POC1B	282809	hgsc.bcm.edu	37	12	89866055	89866064	+	Intron	DEL	AGAAAGAAGA	AGAAAGAAGA	-	rs59139895|rs71082492|rs147832668|rs147021755|rs398055805|rs191378952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGAAAGAAGA	AGAAAGAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:89866055_89866064delAGAAAGAAGA	ENST00000313546.3	-	5	581				POC1B_ENST00000541909.1_Intron|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000378528.2_Intron|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000549504.1_Intron	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B						cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						GTGAAAATCTAGAAAGAAGAAGAAAGAAGA	0.367														2704	0.539936	0.6823	0.4784	5008	,	,		11890	0.5456		0.499	False		,,,				2504	0.4274				.		Pindel	.											.	POC1B	41	.	0			.						PASS	.																																			SO:0001627	intron_variant	282809	.			.	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"""WD repeat domain containing"""	30836	protein-coding gene	gene with protein product		614784	"""WD repeat domain 51B"", ""POC1 centriolar protein homolog B (Chlamydomonas)"""	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.453-3TCTTCTTTCT>-	12.37:g.89866065_89866074delAGAAAGAAGA		Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	37	11	0.297	.	G3V1X0	Splice_Site	DEL	ENST00000313546.3	37	CCDS31869.1																																																																																			-|1.000;|0.000	1.000	strong		0.367	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240	
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535833	+	In_Frame_Ins	INS	-	-	TAGCAGTGACAGCAGCAG	rs201553143|rs142316753		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88535832_88535833insTAGCAGTGACAGCAGCAG	ENST00000282478.7	+	4	2051_2052	c.2018_2019insTAGCAGTGACAGCAGCAG	c.(2017-2022)gatagc>gaTAGCAGTGACAGCAGCAGtagc	p.680_681insSDSSSS	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_In_Frame_Ins_p.680_681insSDSSSS			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	680	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgatagcagtgaca	0.485																																					p.D673delinsDSSDSSS		Pindel	.											.	DSPP	174	.	0			c.2018_2019insTAGCAGTGACAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2019_2036dupTAGCAGTGACAGCAGCAG	4.37:g.88535832_88535833insTAGCAGTGACAGCAGCAG	ENSP00000282478:p.Ser675_Ser680dup	Somatic	168	.	.		WXS	Illumina HiSeq	Phase_I	194	36	0.186	NM_014208	A8MUI0|O95815	In_Frame_Ins	INS	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	alt		0.485	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
RNH1	6050	hgsc.bcm.edu	37	11	502130	502144	+	In_Frame_Del	DEL	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	-	rs71462090|rs71022920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CTGGATGTCCAGGCT	CTGGATGTCCAGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:502130_502144delCTGGATGTCCAGGCT	ENST00000534797.1	-	1	1426_1440	c.19_33delAGCCTGGACATCCAG	c.(19-33)agcctggacatccagdel	p.SLDIQ7del	RNH1_ENST00000354420.2_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000438658.2_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000397615.2_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000533410.1_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000397614.1_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000533592.1_5'UTR|RNH1_ENST00000397604.3_In_Frame_Del_p.SLDIQ7del|RNH1_ENST00000356187.5_In_Frame_Del_p.SLDIQ7del			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0					mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCTCCTCACACTGGATGTCCAGGCTCTGGATGTCC	0.633														278	0.0555112	0.0061	0.2118	5008	,	,		19876	0.002		0.0974	False		,,,				2504	0.0235				p.7_12del		Pindel	.											.	RNH1	24	.	0			c.20_34del						PASS	.		,,,,,,,	104,4158		3,98,2030					,,,,,,,	2.4	0.7		dbSNP_130	66	994,7260		61,872,3194	no	coding,coding,coding,coding,coding,coding,coding,coding	RNH1	NM_203389.1,NM_203388.1,NM_203387.1,NM_203386.1,NM_203385.1,NM_203384.1,NM_203383.1,NM_002939.3	,,,,,,,	64,970,5224	A1A1,A1R,RR		12.0426,2.4402,8.7728	,,,,,,,	,,,,,,,		1098,11418				SO:0001651	inframe_deletion	6050	exon3			.		CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.19_33delAGCCTGGACATCCAG	11.37:g.502130_502144delCTGGATGTCCAGGCT	ENSP00000433999:p.Ser7_Gln11del	Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	48	12	0.250	NM_203386	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	In_Frame_Del	DEL	ENST00000534797.1	37	CCDS7697.1																																																																																			CTGGATGTCCAGGCT|0.938;-|0.062	0.062	strong		0.633	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389	
C17orf82	388407	hgsc.bcm.edu	37	17	59489893	59489893	+	Missense_Mutation	SNP	T	T	C	rs200497494|rs9907379	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:59489893T>C	ENST00000335108.2	+	1	782	c.557T>C	c.(556-558)cTc>cCc	p.L186P	RP11-332H18.4_ENST00000592009.1_RNA	NM_203425.1	NP_982249	Q86X59	CQ082_HUMAN	chromosome 17 open reading frame 82	186			L -> P (in dbSNP:rs9907379). {ECO:0000269|PubMed:15489334}.							cervix(1)|lung(1)	2						CGGCAACTCCTCACAGGTCCA	0.731													C|||	3623	0.723442	0.7769	0.6571	5008	,	,		12512	0.7004		0.8002	False		,,,				2504	0.6431				p.L186P		Atlas-SNP	.											C17orf82_ENST00000335108,NS,carcinoma,0,2	C17orf82	16	2	0			c.T557C						scavenged	.	C	PRO/LEU	3143,775		1281,581,97	4.0	6.0	5.0		557	0.9	0.1	17	dbSNP_119	5	6355,1647		2560,1235,206	no	missense	C17orf82	NM_203425.1	98	3841,1816,303	CC,CT,TT		20.5824,19.7805,20.3188	benign	186/252	59489893	9498,2422	1959	4001	5960	SO:0001583	missense	388407	exon1			AACTCCTCACAGG	BC046200	CCDS11628.1	17q23.2	2012-10-23			ENSG00000187013	ENSG00000187013			32699	protein-coding gene	gene with protein product							Standard	NM_203425		Approved		uc002izh.1	Q86X59	OTTHUMG00000180077	ENST00000335108.2:c.557T>C	17.37:g.59489893T>C	ENSP00000335229:p.Leu186Pro	Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	6	6	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	
ENPP2	5168	hgsc.bcm.edu	37	8	120575184	120575184	+	Silent	SNP	G	G	A	rs1058913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:120575184G>A	ENST00000075322.6	-	24	2392	c.2334C>T	c.(2332-2334)ttC>ttT	p.F778F	ENPP2_ENST00000427067.2_Silent_p.F799F|ENPP2_ENST00000522167.1_Silent_p.F413F|ENPP2_ENST00000522826.1_Silent_p.F803F|ENPP2_ENST00000259486.6_Silent_p.F830F	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	778					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CAGGCTGAGTGAAATCCAGAC	0.517													G|||	479	0.095647	0.0234	0.1326	5008	,	,		17700	0.0387		0.1948	False		,,,				2504	0.1237				p.F830F	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.C2490T						PASS	.	G	,,	292,4114	160.7+/-193.0	15,262,1926	134.0	113.0	120.0		2334,2409,2490	4.9	1.0	8	dbSNP_86	120	1996,6604	350.8+/-328.0	243,1510,2547	no	coding-synonymous,coding-synonymous,coding-synonymous	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	,,	258,1772,4473	AA,AG,GG		23.2093,6.6273,17.5919	,,	778/864,803/889,830/916	120575184	2288,10718	2203	4300	6503	SO:0001819	synonymous_variant	5168	exon25			CTGAGTGAAATCC	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2334C>T	8.37:g.120575184G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			G|0.859;A|0.141	0.141	strong		0.517	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
PCDHB16	57717	hgsc.bcm.edu	37	5	140564088	140564088	+	Missense_Mutation	SNP	C	C	T	rs13176519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140564088C>T	ENST00000361016.2	+	1	3109	c.1954C>T	c.(1954-1956)Cgc>Tgc	p.R652C		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	652	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.			R -> C (in Ref. 3; BAB13447). {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)			CGAGCCTCCGCGCTCGGCCAC	0.716													C|||	1355	0.270567	0.0484	0.3055	5008	,	,		12564	0.5298		0.2306	False		,,,				2504	0.32				p.R652C		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C1954T						PASS	.						17.0	20.0	19.0					5																	140564088		2102	4146	6248	SO:0001583	missense	57717	exon1			CCTCCGCGCTCGG	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.1954C>T	5.37:g.140564088C>T	ENSP00000354293:p.Arg652Cys	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	571	0.26144688644688646	15	0.03048780487804878	86	0.23756906077348067	302	0.527972027972028	168	0.22163588390501318	c	14.06	2.422182	0.43020	.	.	ENSG00000196963	ENST00000361016	T	0.55234	0.53	3.75	1.8	0.24995	Cadherin (4);Cadherin-like (1);	1.580290	0.04823	N	0.437375	T	0.00012	0.0000	M	0.71581	2.175	0.26867	P	0.9678304	B	0.22683	0.073	B	0.27715	0.082	T	0.45498	-0.9257	9	0.62326	D	0.03	.	7.6146	0.28150	0.1683:0.7384:0.0:0.0934	rs13176519;rs17844665	652	Q9NRJ7	PCDBG_HUMAN	C	652	ENSP00000354293:R652C	ENSP00000354293:R652C	R	+	1	0	PCDHB16	140544272	0.002000	0.14202	0.884000	0.34674	0.827000	0.46813	1.911000	0.39937	0.511000	0.28236	0.298000	0.19748	CGC	.	.	weak		0.716	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
PRR22	163154	hgsc.bcm.edu	37	19	5783712	5783712	+	Silent	SNP	C	C	T	rs2446211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5783712C>T	ENST00000419421.2	-	3	650	c.546G>A	c.(544-546)ccG>ccA	p.P182P		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	182	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGGGTGGCAGCGGGGCCGGGC	0.716													c|||	1687	0.336861	0.4228	0.1931	5008	,	,		8488	0.5456		0.165	False		,,,				2504	0.2843				p.P182P		Atlas-SNP	.											PRR22_ENST00000419421,NS,carcinoma,0,2	PRR22	25	2	0			c.G546A						PASS	.	T		1038,2702		151,736,983	3.0	5.0	4.0		546	-5.2	0.0	19	dbSNP_100	4	1020,6676		80,860,2908	no	coding-synonymous	PRR22	NM_001134316.1		231,1596,3891	TT,TC,CC		13.2536,27.754,17.9958		182/423	5783712	2058,9378	1870	3848	5718	SO:0001819	synonymous_variant	163154	exon3			TGGCAGCGGGGCC	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.546G>A	19.37:g.5783712C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	36	12	0.333333	NM_001134316	E9PB31	Silent	SNP	ENST00000419421.2	37	CCDS45933.1																																																																																			C|0.689;T|0.311	0.311	strong		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
LCE2D	353141	hgsc.bcm.edu	37	1	152636843	152636843	+	Missense_Mutation	SNP	A	A	T	rs9793541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152636843A>T	ENST00000368784.1	+	2	317	c.262A>T	c.(262-264)Agc>Tgc	p.S88C		NM_178430.2	NP_848517.1	Q5TA82	LCE2D_HUMAN	late cornified envelope 2D	88	Cys-rich.				keratinization (GO:0031424)					large_intestine(1)|lung(7)|prostate(2)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGGCACCAGAGCCCCGATTG	0.672													A|||	624	0.124601	0.0159	0.1585	5008	,	,		12797	0.0298		0.3032	False		,,,				2504	0.1616				p.S88C		Atlas-SNP	.											LCE2D,NS,carcinoma,-1,1	LCE2D	26	1	0			c.A262T						scavenged	.	A	CYS/SER	289,4099		24,241,1929	40.0	52.0	48.0		262	0.3	0.0	1	dbSNP_119	48	2484,6092		395,1694,2199	no	missense	LCE2D	NM_178430.2	112	419,1935,4128	TT,TA,AA		28.9646,6.5861,21.39	possibly-damaging	88/111	152636843	2773,10191	2194	4288	6482	SO:0001583	missense	353141	exon2			CACCAGAGCCCCG	BI670513	CCDS1018.1	1q21.3	2008-02-05	2004-10-11	2004-10-15	ENSG00000187223	ENSG00000187223		"""Late cornified envelopes"""	16518	protein-coding gene	gene with protein product		612612	"""small proline rich-like (epidermal differentiation complex) 1A"""	SPRL1A		11698679	Standard	NM_178430		Approved	LEP12	uc001fag.4	Q5TA82	OTTHUMG00000014400	ENST00000368784.1:c.262A>T	1.37:g.152636843A>T	ENSP00000357773:p.Ser88Cys	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_178430	A1L4M8	Missense_Mutation	SNP	ENST00000368784.1	37	CCDS1018.1	314	0.14377289377289376	4	0.008130081300813009	67	0.1850828729281768	17	0.02972027972027972	226	0.29815303430079154	a	4.613	0.113868	0.08831	0.065861	0.289646	ENSG00000187223	ENST00000368784	T	0.06068	3.35	2.75	0.291	0.15732	.	.	.	.	.	T	0.02193	0.0068	M	0.76328	2.33	0.80722	P	0.0	P	0.43392	0.805	B	0.31016	0.123	T	0.37888	-0.9686	8	0.87932	D	0	.	4.6936	0.12793	0.6844:0.0:0.3156:0.0	rs9793541	88	Q5TA82	LCE2D_HUMAN	C	88	ENSP00000357773:S88C	ENSP00000357773:S88C	S	+	1	0	LCE2D	150903467	0.001000	0.12720	0.003000	0.11579	0.074000	0.17049	0.682000	0.25335	-0.181000	0.10619	-0.756000	0.03474	AGC	A|0.803;T|0.197	0.197	strong		0.672	LCE2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040058.1	NM_178430	
CERS6	253782	hgsc.bcm.edu	37	2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	rs4496303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:169312974G>A	ENST00000305747.6	+	1	603	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	CERS6_ENST00000392687.4_Missense_Mutation_p.A6T	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	6					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGGGATCTTAGCCTGGTTCTG	0.657													G|||	39	0.00778754	0.0061	0.0101	5008	,	,		8564	0.0		0.0209	False		,,,				2504	0.0031				p.A6T		Atlas-SNP	.											.	.	.	.	0			c.G16A						PASS	.	G	THR/ALA	35,4371	40.0+/-72.8	2,31,2170	162.0	130.0	141.0		16	4.3	1.0	2	dbSNP_111	141	101,8499	56.4+/-117.6	0,101,4199	yes	missense	CERS6	NM_203463.1	58	2,132,6369	AA,AG,GG		1.1744,0.7944,1.0457	benign	6/385	169312974	136,12870	2203	4300	6503	SO:0001583	missense	253782	exon1			ATCTTAGCCTGGT	BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"""Homeoboxes / CERS class"""	23826	protein-coding gene	gene with protein product		615336	"""LAG1 longevity assurance homolog 6 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 6"""	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.16G>A	2.37:g.169312974G>A	ENSP00000306579:p.Ala6Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001256126	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	24	0.01098901098901099	4	0.008130081300813009	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	21.6	4.173118	0.78452	0.007944	0.011744	ENSG00000172292	ENST00000305747;ENST00000392687	T;T	0.21734	1.99;1.99	5.22	4.34	0.51931	.	0.105238	0.64402	N	0.000004	T	0.08358	0.0208	L	0.40543	1.245	0.58432	D	0.999999	B;B	0.32203	0.209;0.36	B;B	0.28465	0.045;0.09	T	0.04165	-1.0972	10	0.22706	T	0.39	-18.0462	13.4206	0.60996	0.0755:0.0:0.9245:0.0	.	6;6	Q32M63;Q6ZMG9	.;CERS6_HUMAN	T	6	ENSP00000306579:A6T;ENSP00000376453:A6T	ENSP00000306579:A6T	A	+	1	0	CERS6	169021220	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.346000	0.97056	1.188000	0.43014	0.467000	0.42956	GCC	A|0.008;G|0.990;T|0.002	0.008	strong		0.657	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463	
FAM131C	348487	hgsc.bcm.edu	37	1	16384986	16384986	+	Silent	SNP	G	G	T	rs28496958	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16384986G>T	ENST00000375662.4	-	7	972	c.789C>A	c.(787-789)ctC>ctA	p.L263L	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	263	Pro-rich.									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)		CCATGGAGGGGAGGGAGCCCG	0.711																																					p.L263L		Atlas-SNP	.											FAM131C,colon,carcinoma,0,1	FAM131C	21	1	0			c.C789A						PASS	.						2.0	2.0	2.0					1																	16384986		1272	2832	4104	SO:0001819	synonymous_variant	348487	exon7			GGAGGGGAGGGAG		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.789C>A	1.37:g.16384986G>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.704;T|0.296	0.296	strong		0.711	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
SERPINC1	462	hgsc.bcm.edu	37	1	173878862	173878862	+	Silent	SNP	T	T	C	rs5877	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:173878862T>C	ENST00000367698.3	-	5	1099	c.981A>G	c.(979-981)gtA>gtG	p.V327V	SERPINC1_ENST00000494024.1_5'Flank	NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	327					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	GTTCCTTCTCTACCTTGGCCA	0.572													C|||	2731	0.545327	0.8366	0.4251	5008	,	,		20145	0.619		0.34	False		,,,				2504	0.3722				p.V327V		Atlas-SNP	.											.	SERPINC1	57	.	0			c.A981G	GRCh37	CD930906	SERPINC1	D	rs5877	PASS	.	C		3326,1080	391.4+/-328.1	1257,812,134	146.0	140.0	142.0		981	3.6	1.0	1	dbSNP_52	142	2964,5636	668.0+/-402.5	505,1954,1841	no	coding-synonymous	SERPINC1	NM_000488.3		1762,2766,1975	CC,CT,TT		34.4651,24.512,48.3623		327/465	173878862	6290,6716	2203	4300	6503	SO:0001819	synonymous_variant	462	exon5			CTTCTCTACCTTG	X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"""Serine (or cysteine) peptidase inhibitors"""	775	protein-coding gene	gene with protein product	"""antithrombin III"", ""signal peptide antithrombin part 1"", ""coding sequence signal peptide antithrombin part 1"", ""antithrombin (aa 375-432)"""	107300	"""serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"""	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.981A>G	1.37:g.173878862T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_000488	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Silent	SNP	ENST00000367698.3	37	CCDS1313.1																																																																																			T|0.474;C|0.526	0.526	strong		0.572	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912406	45912406	+	Missense_Mutation	SNP	G	G	A	rs2336219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45912406G>A	ENST00000309424.3	+	3	1668	c.1180G>A	c.(1180-1182)Gat>Aat	p.D394N	ERCC1_ENST00000588738.1_5'Flank|PPP1R13L_ENST00000418234.2_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.D396N|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	394			D -> N (in dbSNP:rs2336219).		rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		AAAACAGCAAGATGCCACAGT	0.577													A|||	1415	0.282548	0.298	0.219	5008	,	,		17482	0.4613		0.1322	False		,,,				2504	0.2771				p.D394N		Atlas-SNP	.											.	CD3EAP	27	.	0			c.G1180A						PASS	.	A	,,ASN/ASP	1113,3281		150,813,1234	57.0	70.0	65.0		,,1180	-2.1	0.0	19	dbSNP_100	65	1133,7443		77,979,3232	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,23	227,1792,4466	AA,AG,GG		13.2113,25.33,17.3169	,,benign	,,394/511	45912406	2246,10724	2197	4288	6485	SO:0001583	missense	10849	exon3			CAGCAAGATGCCA	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.1180G>A	19.37:g.45912406G>A	ENSP00000310966:p.Asp394Asn	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	562	0.2573260073260073	125	0.2540650406504065	70	0.19337016574585636	259	0.4527972027972028	108	0.1424802110817942	A	2.513	-0.312418	0.05422	0.2533	0.132113	ENSG00000117877	ENST00000309424	T	0.11712	2.75	5.46	-2.07	0.07276	.	1.771500	0.03042	N	0.153457	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45716	-0.9242	9	0.02654	T	1	0.0578	10.4878	0.44733	0.1931:0.1532:0.6537:0.0	rs2336219;rs61002808;rs2336219	396;394	O15446-2;O15446	.;RPA34_HUMAN	N	394	ENSP00000310966:D394N	ENSP00000310966:D394N	D	+	1	0	CD3EAP	50604246	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.647000	0.05397	-0.620000	0.05641	-0.361000	0.07541	GAT	G|0.767;A|0.233	0.233	strong		0.577	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
DST	667	hgsc.bcm.edu	37	6	56463410	56463410	+	Missense_Mutation	SNP	T	T	C	rs4712138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56463410T>C	ENST00000361203.3	-	42	11166	c.11159A>G	c.(11158-11160)cAg>cGg	p.Q3720R	DST_ENST00000446842.2_Missense_Mutation_p.Q3396R|DST_ENST00000421834.2_Missense_Mutation_p.Q1634R|DST_ENST00000370769.4_Missense_Mutation_p.Q3722R|DST_ENST00000370754.5_Missense_Mutation_p.Q3900R|DST_ENST00000312431.6_Missense_Mutation_p.Q3720R|DST_ENST00000244364.6_Missense_Mutation_p.Q1308R|DST_ENST00000370788.2_Missense_Mutation_p.Q1634R			Q03001	DYST_HUMAN	dystonin	3720			Q -> R (in dbSNP:rs4712138).		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)			CTTATCTTCCTGTGACAGCTT	0.358													C|||	1644	0.328275	0.351	0.3804	5008	,	,		16060	0.254		0.3837	False		,,,				2504	0.2802				p.Q1308R		Atlas-SNP	.											.	DST	1427	.	0			c.A3923G						PASS	.	C	ARG/GLN	1330,2366		226,878,744	160.0	150.0	153.0		3923	-11.8	0.0	6	dbSNP_111	153	3193,4981		645,1903,1539	yes	missense	DST	NM_015548.4	43	871,2781,2283	CC,CT,TT		39.0629,35.9848,38.1045	benign	1308/5172	56463410	4523,7347	1848	4087	5935	SO:0001583	missense	667	exon27			TCTTCCTGTGACA	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.11159A>G	6.37:g.56463410T>C	ENSP00000354508:p.Gln3720Arg	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	156	72	0.461538	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		745	0.3411172161172161	182	0.3699186991869919	144	0.39779005524861877	141	0.2465034965034965	278	0.36675461741424803	C	10.74	1.435997	0.25813	0.359848	0.390629	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.9	-11.8	0.00035	.	0.981666	0.08301	N	0.966933	T	0.12646	0.0307	M	0.63428	1.95	0.09310	P	0.999998	B;B;B;B;B	0.10296	0.0;0.003;0.002;0.0;0.001	B;B;B;B;B	0.13407	0.001;0.009;0.005;0.0;0.003	T	0.03384	-1.1042	9	0.17369	T	0.5	.	6.5803	0.22589	0.0679:0.074:0.2054:0.6527	rs4712138;rs52826808;rs59623485;rs4712138	1634;3722;3900;3720;1308	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	R	1308;3900;3722;1634;3396;3720;1634;3720	ENSP00000244364:Q1308R;ENSP00000359790:Q3900R;ENSP00000359805:Q3722R;ENSP00000400883:Q1634R;ENSP00000393645:Q3396R;ENSP00000307959:Q3720R;ENSP00000359824:Q1634R;ENSP00000354508:Q3720R	ENSP00000244364:Q1308R	Q	-	2	0	DST	56571369	0.449000	0.25689	0.000000	0.03702	0.802000	0.45316	-0.337000	0.07852	-3.140000	0.00233	-0.790000	0.03334	CAG	C|0.341;N|0.000	0.341	strong		0.358	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
CPZ	8532	hgsc.bcm.edu	37	4	8621172	8621172	+	Missense_Mutation	SNP	G	G	A	rs61734020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:8621172G>A	ENST00000360986.4	+	11	1961	c.1787G>A	c.(1786-1788)cGg>cAg	p.R596Q	CPZ_ENST00000429646.2_Missense_Mutation_p.R204Q|CPZ_ENST00000382480.2_Missense_Mutation_p.R459Q|CPZ_ENST00000315782.6_Missense_Mutation_p.R585Q	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	596					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						CATGGGCTGCGGAGGACTGGG	0.662													G|||	108	0.0215655	0.0424	0.0086	5008	,	,		14106	0.0238		0.0179	False		,,,				2504	0.0041				p.R596Q		Atlas-SNP	.											.	CPZ	95	.	0			c.G1787A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	203,4203	126.6+/-163.6	7,189,2007	46.0	48.0	47.0		1787,1376,1754	-5.9	0.0	4	dbSNP_129	47	153,8447	74.2+/-136.8	3,147,4150	yes	missense,missense,missense	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	43,43,43	10,336,6157	AA,AG,GG		1.7791,4.6074,2.7372	benign,benign,benign	596/653,459/516,585/642	8621172	356,12650	2203	4300	6503	SO:0001583	missense	8532	exon11			GGCTGCGGAGGAC	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.1787G>A	4.37:g.8621172G>A	ENSP00000354255:p.Arg596Gln	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	169	89	0.526627	NM_001014447	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	39	0.017857142857142856	14	0.028455284552845527	3	0.008287292817679558	9	0.015734265734265736	13	0.017150395778364115	G	12.40	1.928003	0.34002	0.046074	0.017791	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782;ENST00000429646	T;T;T;T	0.57273	0.73;2.12;0.41;1.98	4.77	-5.92	0.02261	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);	15.730500	0.00397	N	0.000041	T	0.08403	0.0209	L	0.54323	1.7	0.09310	N	1	B;B	0.19073	0.033;0.019	B;B	0.08055	0.003;0.001	T	0.07616	-1.0763	10	0.13470	T	0.59	-14.8336	2.4645	0.04549	0.4359:0.0929:0.3216:0.1496	rs61734020	585;596	Q66K79-2;Q66K79	.;CBPZ_HUMAN	Q	596;459;585;204	ENSP00000354255:R596Q;ENSP00000371920:R459Q;ENSP00000315074:R585Q;ENSP00000403981:R204Q	ENSP00000315074:R585Q	R	+	2	0	CPZ	8672072	0.014000	0.17966	0.000000	0.03702	0.021000	0.10359	-0.088000	0.11198	-1.323000	0.02275	-2.030000	0.00424	CGG	G|0.977;A|0.023	0.023	strong		0.662	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
ATP2B2	491	hgsc.bcm.edu	37	3	10420087	10420087	+	Silent	SNP	T	T	C	rs751122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:10420087T>C	ENST00000352432.4	-	9	1119	c.1050A>G	c.(1048-1050)caA>caG	p.Q350Q	ATP2B2_ENST00000397077.1_Silent_p.Q305Q|ATP2B2_ENST00000383800.4_Silent_p.Q305Q|ATP2B2_ENST00000343816.4_Silent_p.Q336Q|ATP2B2_ENST00000360273.2_Silent_p.Q350Q			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	350					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						CCCCGTCCTGTTGTTTGGCTG	0.617													C|||	2470	0.493211	0.4418	0.317	5008	,	,		20457	0.6994		0.3708	False		,,,				2504	0.6012				p.Q350Q	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A1050G						PASS	.	C	,	1731,2675	643.1+/-397.8	338,1055,810	55.0	53.0	54.0		1050,915	3.9	1.0	3	dbSNP_86	54	2964,5636	658.6+/-401.6	506,1952,1842	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	844,3007,2652	CC,CT,TT		34.4651,39.2873,36.0987	,	350/1244,305/1199	10420087	4695,8311	2203	4300	6503	SO:0001819	synonymous_variant	491	exon10			GTCCTGTTGTTTG	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1050A>G	3.37:g.10420087T>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	29	10	0.344828	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			T|0.596;C|0.404	0.404	strong		0.617	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
OR6B3	150681	hgsc.bcm.edu	37	2	240984833	240984833	+	Silent	SNP	C	C	G	rs13389099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:240984833C>G	ENST00000319423.4	-	1	656	c.657G>C	c.(655-657)gcG>gcC	p.A219A	PRR21_ENST00000408934.1_5'Flank	NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(10)|lung(4)|ovary(2)|prostate(1)	18		all_epithelial(40;1.64e-11)|Breast(86;0.000327)|Renal(207;0.00571)|Ovarian(221;0.104)|all_hematologic(139;0.182)|all_lung(227;0.229)|Melanoma(123;0.238)		Epithelial(121;1.05e-29)|all cancers(36;3.52e-28)|OV - Ovarian serous cystadenocarcinoma(60;4.63e-14)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.56e-05)|Lung(119;0.00344)|LUSC - Lung squamous cell carcinoma(224;0.0148)|Colorectal(34;0.019)|COAD - Colon adenocarcinoma(134;0.141)		GGGTGATGTGCGCATATGACA	0.592													t|||	1218	0.243211	0.2912	0.1744	5008	,	,		20769	0.2054		0.2614	False		,,,				2504	0.2474				p.A219A		Atlas-SNP	.											.	OR6B3	37	.	0			c.G657C						PASS	.	T		1287,3011		197,893,1059	62.0	67.0	65.0		657	-8.2	0.0	2	dbSNP_121	65	2297,6203		310,1677,2263	no	coding-synonymous	OR6B3	NM_173351.1		507,2570,3322	GG,GC,CC		27.0235,29.9442,28.0044		219/332	240984833	3584,9214	2149	4250	6399	SO:0001819	synonymous_variant	150681	exon1			GATGTGCGCATAT		CCDS42837.1	2q37.3	2013-09-23	2002-11-13	2002-11-15	ENSG00000178586	ENSG00000178586		"""GPCR / Class A : Olfactory receptors"""	15042	protein-coding gene	gene with protein product			"""olfactory receptor, family 6, subfamily B, member 3 pseudogene"""	OR6B3P			Standard	NM_173351		Approved	OR6B3Q	uc010zoe.2	Q8NGW1	OTTHUMG00000152399	ENST00000319423.4:c.657G>C	2.37:g.240984833C>G		Somatic	264	2	0.00757576		WXS	Illumina HiSeq	Phase_I	298	295	0.989933	NM_173351	Q6IFH3	Silent	SNP	ENST00000319423.4	37	CCDS42837.1																																																																																			C|0.751;G|0.249	0.249	strong		0.592	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1		
MBD1	4152	hgsc.bcm.edu	37	18	47801800	47801800	+	Intron	SNP	G	G	A	rs140690	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:47801800G>A	ENST00000591416.1	-	8	1224				MBD1_ENST00000590208.1_Intron|MBD1_ENST00000588937.1_Intron|MBD1_ENST00000585672.1_Intron|MBD1_ENST00000591535.1_Intron|MBD1_ENST00000349085.2_Intron|MBD1_ENST00000353909.3_Intron|MBD1_ENST00000339998.6_Intron|MBD1_ENST00000382948.5_Intron|MBD1_ENST00000587605.1_Intron|MBD1_ENST00000269468.5_Intron|MBD1_ENST00000269471.5_Intron|MBD1_ENST00000398495.2_Silent_p.R269R|MBD1_ENST00000398493.1_Intron|MBD1_ENST00000436910.1_Intron|MBD1_ENST00000398488.1_Intron|MBD1_ENST00000347968.3_Intron|MBD1_ENST00000585595.1_Silent_p.R269R|MBD1_ENST00000457839.2_Silent_p.R269R|MBD1_ENST00000424334.2_Silent_p.R295R			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1						negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36						GGCGACGCAGGCGGTGAGCAA	0.622													G|||	1019	0.203474	0.1051	0.1873	5008	,	,		17450	0.123		0.3956	False		,,,				2504	0.2331				p.R269R		Atlas-SNP	.											MBD1_ENST00000457839,NS,carcinoma,0,1	MBD1	228	1	0			c.C807T						PASS	.	G	,,,,,,,,,,,,,	286,1460		21,244,608	14.0	14.0	14.0		,807,807,,807,,,,,,,,,	-1.5	0.9	18	dbSNP_78	14	1479,2495		281,917,789	no	intron,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron	MBD1	NM_001204136.1,NM_001204137.1,NM_001204138.1,NM_001204139.1,NM_001204140.1,NM_001204141.1,NM_001204142.1,NM_001204143.1,NM_001204151.1,NM_002384.2,NM_015844.2,NM_015845.3,NM_015846.3,NM_015847.3	,,,,,,,,,,,,,	302,1161,1397	AA,AG,GG		37.2169,16.3803,30.8566	,,,,,,,,,,,,,	,269/631,269/630,,269/575,,,,,,,,,	47801800	1765,3955	873	1987	2860	SO:0001627	intron_variant	4152	exon9			ACGCAGGCGGTGA	Y10746	CCDS11941.1, CCDS11942.1, CCDS11943.1, CCDS11944.1, CCDS32832.1, CCDS56071.1, CCDS56072.1, CCDS56073.1, CCDS59318.1, CCDS59319.1, CCDS59320.1	18q21	2014-02-18			ENSG00000141644	ENSG00000141644			6916	protein-coding gene	gene with protein product		156535				9207790, 10441743	Standard	NM_015844		Approved	PCM1, CXXC3	uc002lem.4	Q9UIS9	OTTHUMG00000132669	ENST00000591416.1:c.792+169C>T	18.37:g.47801800G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	37	CCDS11943.1																																																																																			G|0.782;A|0.218	0.218	strong		0.622	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846	
ESPNL	339768	hgsc.bcm.edu	37	2	239039075	239039075	+	Missense_Mutation	SNP	G	G	T	rs13006204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:239039075G>T	ENST00000343063.3	+	9	1983	c.1720G>T	c.(1720-1722)Gca>Tca	p.A574S	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.A206S|ESPNL_ENST00000409169.1_Missense_Mutation_p.A530S	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	574			A -> S (in dbSNP:rs13006204). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGCTGAGCCCGCAGGGTCTGC	0.706													G|||	1954	0.390176	0.3411	0.3876	5008	,	,		13997	0.4415		0.3827	False		,,,				2504	0.4131				p.A574S		Atlas-SNP	.											.	ESPNL	63	.	0			c.G1720T						PASS	.	G	SER/ALA	1547,2753		314,919,917	7.0	10.0	9.0		1720	-5.0	0.0	2	dbSNP_121	9	3307,5193		687,1933,1630	no	missense	ESPNL	NM_194312.2	99	1001,2852,2547	TT,TG,GG		38.9059,35.9767,37.9219	benign	574/1006	239039075	4854,7946	2150	4250	6400	SO:0001583	missense	339768	exon9			GAGCCCGCAGGGT	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1720G>T	2.37:g.239039075G>T	ENSP00000339115:p.Ala574Ser	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	846	0.3873626373626374	177	0.3597560975609756	150	0.4143646408839779	236	0.4125874125874126	283	0.3733509234828496	G	0.019	-1.458749	0.01062	0.359767	0.389059	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.62105	0.05;1.15;0.74	2.52	-5.03	0.02973	.	8.367350	0.00721	N	0.000888	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.16603	0.001;0.018	B;B	0.06405	0.001;0.002	T	0.16867	-1.0388	9	0.13853	T	0.58	-0.9182	1.4149	0.02299	0.3048:0.148:0.3979:0.1493	rs13006204	530;574	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	S	574;530;206	ENSP00000339115:A574S;ENSP00000386577:A530S;ENSP00000386579:A206S	ENSP00000339115:A574S	A	+	1	0	ESPNL	238703814	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-3.396000	0.00485	-1.405000	0.02048	-1.763000	0.00667	GCA	G|0.611;T|0.389	0.389	strong		0.706	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
TDRD5	163589	hgsc.bcm.edu	37	1	179631242	179631242	+	Missense_Mutation	SNP	G	G	A	rs35448215	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:179631242G>A	ENST00000367614.1	+	14	2523	c.2164G>A	c.(2164-2166)Gag>Aag	p.E722K	TDRD5_ENST00000444136.1_Missense_Mutation_p.E776K|TDRD5_ENST00000294848.8_Missense_Mutation_p.E722K	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	722			E -> K (in dbSNP:rs35448215). {ECO:0000269|PubMed:15489334}.		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)		p.E722K(1)		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						ATTTTAGGATGAGATCCCCAC	0.388													G|||	510	0.101837	0.0129	0.098	5008	,	,		18653	0.0456		0.2117	False		,,,				2504	0.1697				p.E776K		Atlas-SNP	.											TDRD5,NS,carcinoma,0,1	TDRD5	149	1	1	Substitution - Missense(1)	stomach(1)	c.G2326A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	194,4212	121.7+/-159.2	6,182,2015	138.0	121.0	127.0		2326,2326,2164,829,2164	4.5	1.0	1	dbSNP_126	127	2030,6570	353.7+/-329.2	249,1532,2519	yes	missense,missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_001199092.1,NM_173533.3	56,56,56,56,56	255,1714,4534	AA,AG,GG		23.6047,4.4031,17.0998	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	776/1036,776/1036,722/982,277/537,722/982	179631242	2224,10782	2203	4300	6503	SO:0001583	missense	163589	exon15			TAGGATGAGATCC	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.2164G>A	1.37:g.179631242G>A	ENSP00000356586:p.Glu722Lys	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	264	0.12087912087912088	17	0.034552845528455285	45	0.12430939226519337	30	0.05244755244755245	172	0.22691292875989447	G	19.32	3.805193	0.70682	0.044031	0.236047	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.38887	2.22;2.22;2.63;1.11	5.41	4.49	0.54785	.	0.533866	0.18452	N	0.140811	T	0.00012	0.0000	M	0.68952	2.095	0.39673	P	0.02921700000000005	B;D	0.55800	0.374;0.973	B;P	0.48704	0.094;0.587	T	0.12889	-1.0530	9	0.15066	T	0.55	-19.9607	9.3963	0.38404	0.0958:0.0:0.9042:0.0	rs35448215;rs61826423	776;722	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	K	722;722;776;232	ENSP00000356586:E722K;ENSP00000294848:E722K;ENSP00000406052:E776K;ENSP00000410744:E232K	ENSP00000294848:E722K	E	+	1	0	TDRD5	177897865	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	3.036000	0.49767	2.699000	0.92147	0.650000	0.86243	GAG	G|0.839;A|0.161	0.161	strong		0.388	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
DIS3L	115752	hgsc.bcm.edu	37	15	66618342	66618342	+	Missense_Mutation	SNP	A	A	G	rs3803412	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:66618342A>G	ENST00000319212.4	+	12	1891	c.1841A>G	c.(1840-1842)gAt>gGt	p.D614G	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Missense_Mutation_p.D531G	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	614			D -> G (in dbSNP:rs3803412). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA catabolic process (GO:0016075)	cytoplasmic exosome (RNase complex) (GO:0000177)	3'-5'-exoribonuclease activity (GO:0000175)|enzyme binding (GO:0019899)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AAAGACTTGGATGAGAAGAGC	0.453													A|||	1258	0.251198	0.0953	0.3199	5008	,	,		19288	0.3165		0.2952	False		,,,				2504	0.3006				p.D614G		Atlas-SNP	.											.	DIS3L	175	.	0			c.A1841G						PASS	.	A	GLY/ASP,GLY/ASP	608,3794	264.7+/-266.2	35,538,1628	121.0	113.0	116.0		1841,1592	5.3	0.7	15	dbSNP_107	116	2617,5981	423.7+/-354.4	397,1823,2079	yes	missense,missense	DIS3L	NM_001143688.1,NM_133375.3	94,94	432,2361,3707	GG,GA,AA		30.4373,13.8119,24.8077	benign,benign	614/1055,531/972	66618342	3225,9775	2201	4299	6500	SO:0001583	missense	115752	exon12			ACTTGGATGAGAA		CCDS10214.1, CCDS45286.1	15q22.31	2014-03-05	2014-03-05		ENSG00000166938	ENSG00000166938			28698	protein-coding gene	gene with protein product		614183	"""DIS3 mitotic control homolog (S. cerevisiae)-like"""			20531386	Standard	NM_001143688		Approved	MGC4562, FLJ38088, KIAA1955, DIS3L1	uc010ujm.2	Q8TF46	OTTHUMG00000133181	ENST00000319212.4:c.1841A>G	15.37:g.66618342A>G	ENSP00000321711:p.Asp614Gly	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	40	0.366972	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Missense_Mutation	SNP	ENST00000319212.4	37	CCDS45286.1	551	0.2522893772893773	46	0.09349593495934959	106	0.292817679558011	172	0.3006993006993007	227	0.2994722955145119	A	9.152	1.016533	0.19355	0.138119	0.304373	ENSG00000166938	ENST00000319194;ENST00000319212	T;T	0.25250	1.81;1.81	5.31	5.31	0.75309	Ribonuclease II/R (2);	0.391663	0.30999	N	0.008458	T	0.00012	0.0000	N	0.04043	-0.29	0.09310	P	1.0	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.11329	0.006;0.003;0.003	T	0.41088	-0.9528	9	0.36615	T	0.2	-17.8793	14.4288	0.67236	1.0:0.0:0.0:0.0	rs3803412;rs52810111;rs3803412	614;480;614	Q8TF46;Q8TF46-2;Q8TF46-3	DI3L1_HUMAN;.;.	G	531;614	ENSP00000321583:D531G;ENSP00000321711:D614G	ENSP00000321583:D531G	D	+	2	0	DIS3L	64405396	1.000000	0.71417	0.712000	0.30502	0.337000	0.28794	4.706000	0.61845	1.991000	0.58162	0.379000	0.24179	GAT	A|0.760;G|0.240	0.240	strong		0.453	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
COL3A1	1281	hgsc.bcm.edu	37	2	189862097	189862097	+	Silent	SNP	G	G	A	rs7579903	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:189862097G>A	ENST00000304636.3	+	26	2021	c.1851G>A	c.(1849-1851)caG>caA	p.Q617Q	COL3A1_ENST00000317840.5_Silent_p.Q617Q	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	617	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)	CTGGACCTCAGGGACCCCCAG	0.423													G|||	646	0.128994	0.23	0.0793	5008	,	,		17160	0.0		0.16	False		,,,				2504	0.1288				p.Q617Q		Atlas-SNP	.											.	COL3A1	292	.	0			c.G1851A						PASS	.	G		877,3529	322.3+/-297.6	79,719,1405	75.0	79.0	78.0		1851	0.6	1.0	2	dbSNP_116	78	1263,7337	245.0+/-274.0	96,1071,3133	no	coding-synonymous	COL3A1	NM_000090.3		175,1790,4538	AA,AG,GG		14.686,19.9047,16.4539		617/1467	189862097	2140,10866	2203	4300	6503	SO:0001819	synonymous_variant	1281	exon26			ACCTCAGGGACCC	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.1851G>A	2.37:g.189862097G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	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																																																																																			G|0.844;A|0.156	0.156	strong		0.423	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
C12orf49	79794	hgsc.bcm.edu	37	12	117160976	117160976	+	Missense_Mutation	SNP	T	T	C	rs10507274	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117160976T>C	ENST00000261318.3	-	2	324	c.164A>G	c.(163-165)cAg>cGg	p.Q55R	C12orf49_ENST00000536380.1_Intron	NM_024738.1	NP_079014.1	Q9H741	CL049_HUMAN	chromosome 12 open reading frame 49	55			Q -> R (in dbSNP:rs10507274).			extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)|skin(1)	4	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0281)		CGGGATGGGCTGATTATGGTC	0.483													T|||	121	0.0241613	0.0023	0.049	5008	,	,		19917	0.001		0.0746	False		,,,				2504	0.0082				p.Q55R		Atlas-SNP	.											.	C12orf49	17	.	0			c.A164G						PASS	.	T	ARG/GLN	46,4360	47.5+/-82.1	0,46,2157	162.0	118.0	133.0		164	3.9	1.0	12	dbSNP_119	133	601,7999	158.9+/-212.3	25,551,3724	yes	missense	C12orf49	NM_024738.1	43	25,597,5881	CC,CT,TT		6.9884,1.044,4.9746	benign	55/206	117160976	647,12359	2203	4300	6503	SO:0001583	missense	79794	exon2			ATGGGCTGATTAT	AK025068	CCDS9179.1	12q24.22	2012-05-30			ENSG00000111412	ENSG00000111412			26128	protein-coding gene	gene with protein product						12477932	Standard	NM_024738		Approved	FLJ21415	uc001tvz.1	Q9H741	OTTHUMG00000169392	ENST00000261318.3:c.164A>G	12.37:g.117160976T>C	ENSP00000261318:p.Gln55Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_024738	Q53GE8	Missense_Mutation	SNP	ENST00000261318.3	37	CCDS9179.1	83	0.038003663003663	1	0.0020325203252032522	24	0.06629834254143646	0	0.0	58	0.07651715039577836	T	13.62	2.292853	0.40594	0.01044	0.069884	ENSG00000111412	ENST00000261318	T	0.41400	1.0	3.89	3.89	0.44902	.	0.111999	0.64402	D	0.000007	T	0.01489	0.0048	L	0.34521	1.04	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.02683	-1.1124	10	0.05833	T	0.94	-12.3152	13.7774	0.63062	0.0:0.0:0.0:1.0	rs10507274;rs17428938;rs52811228;rs10507274	55	Q9H741	CL049_HUMAN	R	55	ENSP00000261318:Q55R	ENSP00000261318:Q55R	Q	-	2	0	C12orf49	115645359	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	5.512000	0.67030	1.998000	0.58463	0.533000	0.62120	CAG	T|0.954;C|0.046	0.046	strong		0.483	C12orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403847.1	NM_024738	
TRIML1	339976	hgsc.bcm.edu	37	4	189060803	189060803	+	Missense_Mutation	SNP	T	T	A	rs62618670	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:189060803T>A	ENST00000332517.3	+	1	231	c.91T>A	c.(91-93)Tgt>Agt	p.C31S	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	31					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GACCACCGAGTGTGGGCACAG	0.527													T|||	15	0.00299521	0.0	0.0043	5008	,	,		21199	0.0		0.0109	False		,,,				2504	0.001				p.C31S	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.T91A						PASS	.	T	SER/CYS	12,4394	19.1+/-41.9	0,12,2191	180.0	178.0	179.0		91	5.6	1.0	4	dbSNP_129	179	96,8504	53.6+/-114.3	2,92,4206	yes	missense	TRIML1	NM_178556.3	112	2,104,6397	AA,AT,TT		1.1163,0.2724,0.8304	possibly-damaging	31/469	189060803	108,12898	2203	4300	6503	SO:0001583	missense	339976	exon1			ACCGAGTGTGGGC	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.91T>A	4.37:g.189060803T>A	ENSP00000327738:p.Cys31Ser	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	237	127	0.535865	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	T	26.0	4.691634	0.88735	0.002724	0.011163	ENSG00000184108	ENST00000332517	T	0.54479	0.57	5.59	5.59	0.84812	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type, conserved site (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.000000	0.56097	D	0.000027	T	0.78394	0.4276	H	0.98388	4.22	0.49915	D	0.999839	D	0.89917	1.0	D	0.91635	0.999	D	0.87710	0.2566	10	0.87932	D	0	-15.1966	14.037	0.64651	0.0:0.0:0.0:1.0	rs62618670	31	Q8N9V2	TRIML_HUMAN	S	31	ENSP00000327738:C31S	ENSP00000327738:C31S	C	+	1	0	TRIML1	189297797	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.353000	0.79414	2.263000	0.75096	0.533000	0.62120	TGT	T|0.993;A|0.007	0.007	strong		0.527	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
NBEAL2	23218	hgsc.bcm.edu	37	3	47043622	47043622	+	Silent	SNP	G	G	A	rs2305635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:47043622G>A	ENST00000450053.3	+	31	5174	c.4995G>A	c.(4993-4995)gtG>gtA	p.V1665V	NBEAL2_ENST00000292309.5_Silent_p.V1481V|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1665					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)		CCTGGCTGGTGCCACTGGTGC	0.647													G|||	1603	0.320088	0.2163	0.317	5008	,	,		16773	0.3373		0.3926	False		,,,				2504	0.3701				p.V1665V		Atlas-SNP	.											.	NBEAL2	267	.	0			c.G4995A						PASS	.	G		906,3076		135,636,1220	7.0	8.0	8.0		4995	1.7	1.0	3	dbSNP_100	8	3067,4923		683,1701,1611	no	coding-synonymous	NBEAL2	NM_015175.1		818,2337,2831	AA,AG,GG		38.3855,22.7524,33.1858		1665/2755	47043622	3973,7999	1991	3995	5986	SO:0001819	synonymous_variant	23218	exon31			GCTGGTGCCACTG	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.4995G>A	3.37:g.47043622G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	689|689	0.31547619047619047|0.31547619047619047	101|101	0.20528455284552846|0.20528455284552846	105|105	0.2900552486187845|0.2900552486187845	186|186	0.32517482517482516|0.32517482517482516	297|297	0.391820580474934|0.391820580474934	G|G	6.501|6.501	0.460666|0.460666	0.12342|0.12342	0.227524|0.227524	0.383855|0.383855	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.49|4.49	1.71|1.71	0.24356|0.24356	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43972|0.43972	-0.9358|-0.9358	3|3	.|.	.|.	.|.	.|.	4.6581|4.6581	0.12628|0.12628	0.2533:0.0:0.5966:0.1501|0.2533:0.0:0.5966:0.1501	rs2305635;rs17223759;rs2305635|rs2305635;rs17223759;rs2305635	.|.	.|.	.|.	T|Y	34|953	.|.	.|.	A|C	+|+	1|2	0|0	NBEAL2|NBEAL2	47018626|47018626	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.750000|0.750000	0.42670|0.42670	0.763000|0.763000	0.26517|0.26517	0.168000|0.168000	0.19655|0.19655	-0.263000|-0.263000	0.10527|0.10527	GCC|TGC	G|0.685;A|0.315	0.315	strong		0.647	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
C10orf90	118611	hgsc.bcm.edu	37	10	128192985	128192985	+	Missense_Mutation	SNP	C	C	T	rs11245007	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:128192985C>T	ENST00000284694.7	-	3	904	c.784G>A	c.(784-786)Gat>Aat	p.D262N	C10orf90_ENST00000544758.1_Missense_Mutation_p.D359N|C10orf90_ENST00000454341.1_Missense_Mutation_p.D262N|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000356858.3_Missense_Mutation_p.D215N|C10orf90_ENST00000392694.1_Missense_Mutation_p.D215N	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	262			D -> N (in dbSNP:rs11245007). {ECO:0000269|PubMed:15489334}.		mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		TAGATTGAATCTGGACACTGC	0.522											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2507	0.500599	0.6876	0.4121	5008	,	,		17270	0.5099		0.3082	False		,,,				2504	0.499				p.D262N		Atlas-SNP	.											.	C10orf90	121	.	0			c.G784A						PASS	.	T	ASN/ASP	2620,1786	525.9+/-371.7	780,1060,363	107.0	114.0	112.0		784	1.6	0.0	10	dbSNP_120	112	2596,6004	688.7+/-404.3	388,1820,2092	yes	missense	C10orf90	NM_001004298.2	23	1168,2880,2455	TT,TC,CC		30.186,40.5356,40.1046	benign	262/700	128192985	5216,7790	2203	4300	6503	SO:0001583	missense	118611	exon3			TTGAATCTGGACA	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.784G>A	10.37:g.128192985C>T	ENSP00000284694:p.Asp262Asn	Somatic	117	0	0	1563	WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	973	0.44551282051282054	330	0.6707317073170732	140	0.3867403314917127	273	0.4772727272727273	230	0.3034300791556728	T	2.249	-0.371988	0.05034	0.594644	0.30186	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.14516	2.82;2.83;2.74;2.81;2.5	5.38	1.59	0.23543	.	0.558322	0.17356	N	0.177212	T	0.00012	0.0000	N	0.00268	-1.735	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.34650	-0.9820	9	0.02654	T	1	-6.3276	5.2208	0.15368	0.0:0.1499:0.286:0.5641	rs11245007;rs52797966;rs56501299;rs60291468;rs11245007	359;359;215;262;262	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	N	215;262;262;359;262;215;215	ENSP00000284694:D262N;ENSP00000398786:D262N;ENSP00000444369:D359N;ENSP00000405995:D262N;ENSP00000376459:D215N	ENSP00000284694:D262N	D	-	1	0	C10orf90	128182975	0.005000	0.15991	0.000000	0.03702	0.011000	0.07611	1.599000	0.36751	-0.113000	0.11958	-1.062000	0.02293	GAT	C|0.557;T|0.443	0.443	strong		0.522	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12942961	12942961	+	Missense_Mutation	SNP	A	A	C	rs4625290	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12942961A>C	ENST00000235349.5	-	2	325	c.255T>G	c.(253-255)gaT>gaG	p.D85E		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	85			D -> E (in dbSNP:rs4625290).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CATCCAGCCCATCGAGCACAG	0.627													a|||	524	0.104633	0.0946	0.1009	5008	,	,		18029	0.1399		0.1133	False		,,,				2504	0.0757				p.D85E		Atlas-SNP	.											.	PRAMEF4	62	.	0			c.T255G						PASS	.	A	GLU/ASP	507,3873		62,383,1745	52.0	53.0	53.0		255	-1.3	0.0	1	dbSNP_111	53	999,7571		105,789,3391	no	missense	PRAMEF4	NM_001009611.2	45	167,1172,5136	CC,CA,AA		11.6569,11.5753,11.6293	benign	85/479	12942961	1506,11444	2190	4285	6475	SO:0001583	missense	400735	exon2			CAGCCCATCGAGC		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"""-"""	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.255T>G	1.37:g.12942961A>C	ENSP00000235349:p.Asp85Glu	Somatic	296	0	0		WXS	Illumina HiSeq	Phase_I	370	15	0.0405405	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	217	0.09935897435897435	38	0.07723577235772358	32	0.08839779005524862	62	0.10839160839160839	85	0.11213720316622691	a	1.703	-0.501150	0.04261	0.115753	0.116569	ENSG00000243073	ENST00000235349	T	0.05199	3.48	1.48	-1.32	0.09201	.	0.744226	0.12606	N	0.454302	T	0.00073	0.0002	N	0.24115	0.695	0.09310	N	1	B	0.15930	0.015	B	0.18871	0.023	T	0.46789	-0.9166	10	0.14656	T	0.56	.	1.5274	0.02528	0.4816:0.0:0.213:0.3054	rs4625290	85	O60810	PRAM4_HUMAN	E	85	ENSP00000235349:D85E	ENSP00000235349:D85E	D	-	3	2	PRAMEF4	12865548	0.000000	0.05858	0.004000	0.12327	0.005000	0.04900	-0.665000	0.05286	-0.377000	0.07930	0.329000	0.21502	GAT	A|0.894;C|0.106	0.106	strong		0.627	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
DNAH14	127602	hgsc.bcm.edu	37	1	225270409	225270409	+	Intron	SNP	A	A	T	rs3128655	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:225270409A>T	ENST00000445597.2	+	15	2938				DNAH14_ENST00000439375.2_Missense_Mutation_p.N1099Y|DNAH14_ENST00000430092.1_Missense_Mutation_p.N1099Y			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						GCTTGATAAAAACTGTAAAGT	0.393													A|||	3316	0.662141	0.3366	0.7277	5008	,	,		14483	0.7133		0.8817	False		,,,				2504	0.7771				p.N1099Y		Atlas-SNP	.											.	DNAH14	300	.	0			c.A3295T						PASS	.	A	TYR/ASN	649,735		152,345,195	79.0	71.0	74.0		3295	0.9	0.0	1	dbSNP_103	74	2829,353		1257,315,19	yes	missense	DNAH14	NM_001373.1	143	1409,660,214	TT,TA,AA		11.0937,46.8931,23.8283	possibly-damaging	1099/4516	225270409	3478,1088	692	1591	2283	SO:0001627	intron_variant	127602	exon20			GATAAAAACTGTA	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.2938+1959A>T	1.37:g.225270409A>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		1514	0.6932234432234432	166	0.33739837398373984	263	0.7265193370165746	417	0.7290209790209791	668	0.8812664907651715	A	11.61	1.690826	0.29962	0.468931	0.889063	ENSG00000185842	ENST00000430092;ENST00000439375;ENST00000328556	T;T;T	0.61742	0.08;0.08;0.08	5.12	0.889	0.19212	.	.	.	.	.	T	0.00012	0.0000	N	0.11255	0.115	0.54753	P	1.7000000000044757E-5	D	0.54207	0.965	P	0.51135	0.66	T	0.32640	-0.9899	8	0.51188	T	0.08	.	7.0226	0.24922	0.6953:0.1339:0.1708:0.0	rs3128655;rs52801862;rs57743079;rs3128655	1099	Q0VDD8-4	.	Y	1099;1099;177	ENSP00000414402:N1099Y;ENSP00000392061:N1099Y;ENSP00000332424:N177Y	ENSP00000332424:N177Y	N	+	1	0	DNAH14	223337032	0.997000	0.39634	0.015000	0.15790	0.359000	0.29487	1.599000	0.36751	0.240000	0.21263	0.491000	0.48974	AAC	A|0.283;T|0.717	0.717	strong		0.393	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
TUBB6	84617	hgsc.bcm.edu	37	18	12308793	12308793	+	Splice_Site	SNP	G	G	C	rs11267036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:12308793G>C	ENST00000317702.5	+	2	399	c.165G>C	c.(163-165)tcG>tcC	p.S55S	TUBB6_ENST00000586653.1_Splice_Site_p.S55S|TUBB6_ENST00000590967.1_Splice_Site_p.S55S|TUBB6_ENST00000591208.1_Splice_Site_p.S55S|TUBB6_ENST00000592683.1_Splice_Site_p.S55S|TUBB6_ENST00000591909.1_Splice_Site_p.S55S			Q9BUF5	TBB6_HUMAN	tubulin, beta 6 class V	55					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)	14				READ - Rectum adenocarcinoma(1;0.0649)		ATGAGTCATCGTGTGAGTAGC	0.642													G|||	648	0.129393	0.084	0.1801	5008	,	,		10583	0.1478		0.1322	False		,,,				2504	0.1329				p.S55S		Atlas-SNP	.											.	TUBB6	35	.	0			c.G165C						PASS	.	G		356,4050	181.2+/-209.3	12,332,1859	46.0	47.0	46.0		165	-7.4	0.8	18	dbSNP_120	46	968,7632	207.9+/-249.5	49,870,3381	yes	coding-synonymous-near-splice	TUBB6	NM_032525.1		61,1202,5240	CC,CG,GG		11.2558,8.0799,10.1799		55/447	12308793	1324,11682	2203	4300	6503	SO:0001630	splice_region_variant	84617	exon2			GTCATCGTGTGAG	AK001295	CCDS11858.1	18p11.21	2011-10-10	2011-10-10		ENSG00000176014	ENSG00000176014		"""Tubulins"""	20776	protein-coding gene	gene with protein product	"""tubulin beta MGC4083"", ""class V beta-tubulin"""	615103	"""tubulin, beta 6"""			12477932	Standard	NM_032525		Approved	MGC4083, HsT1601	uc002kqw.3	Q9BUF5	OTTHUMG00000131692	ENST00000317702.5:c.166+1G>C	18.37:g.12308793G>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_032525	B3KM76|Q9HA42	Silent	SNP	ENST00000317702.5	37	CCDS11858.1																																																																																			G|0.887;C|0.113	0.113	strong		0.642	TUBB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254600.2	NM_032525	Silent
MED16	10025	hgsc.bcm.edu	37	19	871222	871222	+	Silent	SNP	G	G	A	rs8100258	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:871222G>A	ENST00000589119.1	-	12	2129	c.2130C>T	c.(2128-2130)gaC>gaT	p.D710D	MED16_ENST00000269814.4_Missense_Mutation_p.T646M|MED16_ENST00000312090.6_Silent_p.D729D|MED16_ENST00000395808.3_Silent_p.D710D|MED16_ENST00000325464.1_Silent_p.D710D|MED16_ENST00000606828.1_5'Flank			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	710					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)		CCAGCGCCTCGTCCGGCTCGC	0.706													g|||	640	0.127796	0.084	0.1225	5008	,	,		13479	0.0089		0.2505	False		,,,				2504	0.1871				p.D710D		Atlas-SNP	.											.	MED16	61	.	0			c.C2130T						PASS	.			508,3672		53,402,1635	9.0	9.0	9.0		2130	-5.0	0.1	19	dbSNP_116	9	1957,6373		272,1413,2480	no	coding-synonymous	MED16	NM_005481.2		325,1815,4115	AA,AG,GG		23.4934,12.1531,19.7042		710/878	871222	2465,10045	2090	4165	6255	SO:0001819	synonymous_variant	10025	exon13			CGCCTCGTCCGGC	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.2130C>T	19.37:g.871222G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	56	37	0.660714	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1	302	0.1382783882783883	51	0.10365853658536585	55	0.15193370165745856	7	0.012237762237762238	189	0.24934036939313983	g	9.363	1.068497	0.20067	0.121531	0.234934	ENSG00000175221	ENST00000269814	.	.	.	4.13	-5.03	0.02973	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.44500	P	0.002557999999999949	B	0.14438	0.01	B	0.15052	0.012	T	0.21759	-1.0236	6	0.39692	T	0.17	-22.4712	11.7769	0.51991	0.7109:0.0:0.2891:0.0	rs8100258	646	Q9Y2X0-4	.	M	646	.	ENSP00000269814:T646M	T	-	2	0	MED16	822222	0.003000	0.15002	0.126000	0.21872	0.229000	0.25112	-1.383000	0.02544	-0.752000	0.04728	-0.244000	0.11960	ACG	G|0.860;A|0.140	0.140	strong		0.706	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
RALGAPB	57148	hgsc.bcm.edu	37	20	37168469	37168469	+	Silent	SNP	G	G	T	rs6070521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37168469G>T	ENST00000262879.6	+	17	2714	c.2430G>T	c.(2428-2430)gtG>gtT	p.V810V	RALGAPB_ENST00000397042.3_Silent_p.V806V|RALGAPB_ENST00000397038.1_Silent_p.V588V|RALGAPB_ENST00000397040.1_Silent_p.V810V			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	810					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TCAGTTCTGTGTGCACCTACA	0.468													G|||	177	0.0353435	0.0923	0.0216	5008	,	,		16795	0.006		0.0179	False		,,,				2504	0.0164				p.V810V		Atlas-SNP	.											.	RALGAPB	134	.	0			c.G2430T						PASS	.	G		393,4013	197.7+/-221.8	21,351,1831	155.0	127.0	137.0		2430	2.6	1.0	20	dbSNP_114	137	175,8425	81.5+/-144.1	1,173,4126	no	coding-synonymous	RALGAPB	NM_020336.2		22,524,5957	TT,TG,GG		2.0349,8.9197,4.3672		810/1495	37168469	568,12438	2203	4300	6503	SO:0001819	synonymous_variant	57148	exon17			TTCTGTGTGCACC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.2430G>T	20.37:g.37168469G>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	37	CCDS13305.1																																																																																			G|0.954;T|0.046	0.046	strong		0.468	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
ANKS1B	56899	hgsc.bcm.edu	37	12	99640557	99640557	+	Silent	SNP	T	T	C	rs1552759	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:99640557T>C	ENST00000547776.2	-	13	1841	c.1842A>G	c.(1840-1842)ccA>ccG	p.P614P	ANKS1B_ENST00000550833.1_5'UTR|ANKS1B_ENST00000547010.1_Silent_p.P194P|ANKS1B_ENST00000329257.7_Silent_p.P614P	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	614						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)		ACTCACAGGCTGGAGAGGATC	0.463													t|||	3166	0.632188	0.3003	0.647	5008	,	,		18945	0.9087		0.6083	False		,,,				2504	0.8098				p.P614P		Atlas-SNP	.											.	ANKS1B	180	.	0			c.A1842G						PASS	.	C		1357,2387		237,883,752	151.0	141.0	144.0		1842	4.5	1.0	12	dbSNP_88	144	5392,2814		1768,1856,479	no	coding-synonymous	ANKS1B	NM_152788.4		2005,2739,1231	CC,CT,TT		34.292,36.2447,43.523		614/1249	99640557	6749,5201	1872	4103	5975	SO:0001819	synonymous_variant	56899	exon13			ACAGGCTGGAGAG	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.1842A>G	12.37:g.99640557T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1																																																																																			T|0.381;C|0.619	0.619	strong		0.463	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
GPR111	222611	hgsc.bcm.edu	37	6	47646748	47646748	+	Missense_Mutation	SNP	T	T	C	rs13212023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:47646748T>C	ENST00000296862.1	+	4	349	c.349T>C	c.(349-351)Tcc>Ccc	p.S117P	GPR111_ENST00000398742.2_Missense_Mutation_p.S49P|GPR111_ENST00000507065.1_Missense_Mutation_p.S49P			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	117					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TACAGACTACTCCCAGTGTAC	0.517													T|||	333	0.0664936	0.0106	0.1167	5008	,	,		19519	0.0		0.2217	False		,,,				2504	0.0153				p.S49P		Atlas-SNP	.											.	GPR111	123	.	0			c.T145C						PASS	.	T	PRO/SER	159,3767		3,153,1807	141.0	134.0	137.0		145	2.1	0.0	6	dbSNP_121	137	1697,6641		164,1369,2636	yes	missense	GPR111	NM_153839.6	74	167,1522,4443	CC,CT,TT		20.3526,4.0499,15.1337	probably-damaging	49/643	47646748	1856,10408	1963	4169	6132	SO:0001583	missense	222611	exon5			GACTACTCCCAGT	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.349T>C	6.37:g.47646748T>C	ENSP00000296862:p.Ser117Pro	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	185	89	0.481081	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		220	0.10073260073260074	6	0.012195121951219513	41	0.1132596685082873	0	0.0	173	0.22823218997361477	T	14.90	2.674804	0.47781	0.040499	0.203526	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.39787	1.83;1.79;1.06	4.69	2.12	0.27331	.	0.690450	0.12542	N	0.459788	T	0.29389	0.0732	L	0.32530	0.975	0.80722	P	0.0	D;D	0.67145	0.993;0.996	P;P	0.62089	0.898;0.871	T	0.08953	-1.0697	9	0.59425	D	0.04	.	5.1443	0.14977	0.3152:0.0:0.1633:0.5214	rs13212023;rs52822010;rs57009416;rs13212023	49;117	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	P	49;117;49	ENSP00000422934:S49P;ENSP00000296862:S117P;ENSP00000381727:S49P	ENSP00000296862:S117P	S	+	1	0	GPR111	47754707	0.052000	0.20516	0.007000	0.13788	0.037000	0.13140	0.961000	0.29267	0.334000	0.23590	0.524000	0.50904	TCC	T|0.874;C|0.126	0.126	strong		0.517	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
MYOM2	9172	hgsc.bcm.edu	37	8	2054066	2054066	+	Silent	SNP	A	A	G	rs17684416	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:2054066A>G	ENST00000262113.4	+	22	2910	c.2769A>G	c.(2767-2769)caA>caG	p.Q923Q	MYOM2_ENST00000523438.1_Silent_p.Q348Q	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	923	Ig-like C2-type 3.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TCGATGAACAAGGCAACATCT	0.483													A|||	871	0.173922	0.0855	0.2046	5008	,	,		17443	0.2857		0.1799	False		,,,				2504	0.1503				p.Q923Q		Atlas-SNP	.											.	MYOM2	251	.	0			c.A2769G						PASS	.	A		415,3991	203.8+/-226.2	21,373,1809	149.0	134.0	139.0		2769	-10.1	0.0	8	dbSNP_123	139	1368,7232	266.0+/-286.5	127,1114,3059	no	coding-synonymous	MYOM2	NM_003970.2		148,1487,4868	GG,GA,AA		15.907,9.419,13.7091		923/1466	2054066	1783,11223	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon22			TGAACAAGGCAAC		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.2769A>G	8.37:g.2054066A>G		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			A|0.843;G|0.157	0.157	strong		0.483	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
PTK2B	2185	hgsc.bcm.edu	37	8	27255128	27255128	+	Silent	SNP	T	T	C	rs1045510	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27255128T>C	ENST00000397501.1	+	7	835	c.27T>C	c.(25-27)agT>agC	p.S9S	PTK2B_ENST00000420218.2_Silent_p.S9S|PTK2B_ENST00000346049.5_Silent_p.S9S|PTK2B_ENST00000517339.1_Silent_p.S9S|PTK2B_ENST00000544172.1_Silent_p.S9S|PTK2B_ENST00000338238.4_Silent_p.S9S	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	9					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)	AGCCCCTGAGTCGAGTAAAGT	0.592													C|||	1593	0.318091	0.2057	0.3818	5008	,	,		18715	0.2748		0.4324	False		,,,				2504	0.3517				p.S9S		Atlas-SNP	.											.	PTK2B	304	.	0			c.T27C						PASS	.	C	,,,	1024,3382	728.0+/-409.9	128,768,1307	121.0	104.0	110.0		27,27,27,27	2.9	1.0	8	dbSNP_86	110	3841,4759	610.6+/-395.7	868,2105,1327	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	996,2873,2634	CC,CT,TT		44.6628,23.241,37.4058	,,,	9/1010,9/1010,9/968,9/1010	27255128	4865,8141	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon7			CCTGAGTCGAGTA	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.27T>C	8.37:g.27255128T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	84	46	0.547619	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			T|0.642;C|0.358	0.358	strong		0.592	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
DNAH12	201625	hgsc.bcm.edu	37	3	57335876	57335876	+	Missense_Mutation	SNP	C	C	T	rs4060726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:57335876C>T	ENST00000351747.2	-	55	8857	c.8677G>A	c.(8677-8679)Ggt>Agt	p.G2893S	DNAH12_ENST00000344804.4_Missense_Mutation_p.G480S	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	2893	AAA 5. {ECO:0000250}.		G -> S (in dbSNP:rs4060726). {ECO:0000269|PubMed:14702039}.		microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						AGTAAGCTACCGGAGAGTGCC	0.443													C|||	3331	0.665136	0.4932	0.7233	5008	,	,		15834	0.9157		0.6233	False		,,,				2504	0.6411				p.G2893S		Atlas-SNP	.											DNAH12,colon,carcinoma,0,1	DNAH12	182	1	0			c.G8677A						scavenged	.	C	SER/GLY	691,693		171,349,172	133.0	116.0	121.0		8677	2.3	1.0	3	dbSNP_108	121	1943,1239		596,751,244	yes	missense	DNAH12	NM_178504.4	56	767,1100,416	TT,TC,CC		38.9378,49.9277,42.3127	benign	2893/3093	57335876	2634,1932	692	1591	2283	SO:0001583	missense	201625	exon55			AGCTACCGGAGAG	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.8677G>A	3.37:g.57335876C>T	ENSP00000295937:p.Gly2893Ser	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Missense_Mutation	SNP	ENST00000351747.2	37		1473|1473	0.6744505494505495|0.6744505494505495	228|228	0.4634146341463415|0.4634146341463415	248|248	0.6850828729281768|0.6850828729281768	526|526	0.9195804195804196|0.9195804195804196	471|471	0.6213720316622692|0.6213720316622692	C|C	0.291|0.291	-0.979871|-0.979871	0.02197|0.02197	0.499277|0.499277	0.610622|0.610622	ENSG00000174844|ENSG00000174844	ENST00000351747;ENST00000466540;ENST00000344804|ENST00000462199	T;T;T|.	0.07216|.	3.21;3.21;3.21|.	5.53|5.53	2.34|2.34	0.29019|0.29019	Dynein heavy chain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.03000|0.03000	-0.44|-0.44	0.42046|0.42046	P|P	0.008909999999999973|0.008909999999999973	B;B|.	0.25206|.	0.0;0.12|.	B;B|.	0.31686|.	0.001;0.134|.	T|T	0.24977|0.24977	-1.0145|-1.0145	9|4	0.02654|.	T|.	1|.	.|.	12.0331|12.0331	0.53410|0.53410	0.0:0.7798:0.0:0.2202|0.0:0.7798:0.0:0.2202	rs4060726;rs17057982;rs52819112;rs56457745;rs56934802;rs4060726|rs4060726;rs17057982;rs52819112;rs56457745;rs56934802;rs4060726	480;2893|.	Q6ZR08-2;Q6ZR08|.	.;DYH12_HUMAN|.	S|Q	2893;538;480|583	ENSP00000295937:G2893S;ENSP00000420359:G538S;ENSP00000340464:G480S|.	ENSP00000340464:G480S|.	G|R	-|-	1|2	0|0	DNAH12|DNAH12	57310916|57310916	0.000000|0.000000	0.05858|0.05858	0.988000|0.988000	0.46212|0.46212	0.071000|0.071000	0.16799|0.16799	-0.355000|-0.355000	0.07671|0.07671	0.717000|0.717000	0.32145|0.32145	-0.128000|-0.128000	0.14901|0.14901	GGT|CGG	C|0.352;T|0.648	0.648	strong		0.443	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
TFIP11	24144	hgsc.bcm.edu	37	22	26897989	26897989	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26897989C>T	ENST00000407690.1	-	8	961	c.678G>A	c.(676-678)agG>agA	p.R226R	TFIP11_ENST00000405938.1_Silent_p.R226R|TFIP11_ENST00000496523.1_5'UTR|TFIP11_ENST00000407431.1_Silent_p.R226R|TFIP11_ENST00000407148.1_Silent_p.R226R	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	226					biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						TTGGGTCTTTCCTCCACTGGC	0.498																																					p.R226R		Atlas-SNP	.											TFIP11,caecum,carcinoma,-1,1	TFIP11	72	1	0			c.G678A						scavenged	.						189.0	167.0	174.0					22																	26897989		2203	4300	6503	SO:0001819	synonymous_variant	24144	exon9			GTCTTTCCTCCAC	AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"""G patch domain containing"""	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.678G>A	22.37:g.26897989C>T		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	185	3	0.0162162	NM_001008697	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Silent	SNP	ENST00000407690.1	37	CCDS13838.1	.	.	.	.	.	.	.	.	.	.	C	10.42	1.343946	0.24339	.	.	ENSG00000100109	ENST00000450493	.	.	.	5.42	2.19	0.27852	.	.	.	.	.	T	0.52175	0.1718	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40098	-0.9581	4	.	.	.	-56.857	5.2353	0.15443	0.1425:0.6335:0.0:0.224	.	.	.	.	E	77	.	.	G	-	2	0	TFIP11	25227989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.808000	0.27154	0.409000	0.25649	0.650000	0.86243	GGA	.	.	none		0.498	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697	
DNHD1	144132	hgsc.bcm.edu	37	11	6578004	6578004	+	Silent	SNP	G	G	A	rs11600179	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6578004G>A	ENST00000527990.2	+	23	7479	c.7479G>A	c.(7477-7479)acG>acA	p.T2493T	DNHD1_ENST00000254579.6_Silent_p.T2493T			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2493					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AACTGCAGACGCTGCAGCCTA	0.587													A|||	923	0.184305	0.4448	0.1484	5008	,	,		21654	0.0169		0.0915	False		,,,				2504	0.1258				p.T2493T		Atlas-SNP	.											.	DNHD1	198	.	0			c.G7479A						PASS	.	A		605,779		128,349,215	68.0	64.0	65.0		7479	-11.8	0.1	11	dbSNP_120	65	354,2828		18,318,1255	yes	coding-synonymous	DNHD1	NM_144666.2		146,667,1470	AA,AG,GG		11.1251,43.7139,21.0031		2493/4754	6578004	959,3607	692	1591	2283	SO:0001819	synonymous_variant	144132	exon25			GCAGACGCTGCAG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.7479G>A	11.37:g.6578004G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	107	103	0.962617	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.842;A|0.158	0.158	strong		0.587	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
SLC39A13	91252	hgsc.bcm.edu	37	11	47431703	47431703	+	Missense_Mutation	SNP	A	A	G	rs61897432	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:47431703A>G	ENST00000362021.4	+	2	100	c.58A>G	c.(58-60)Act>Gct	p.T20A	SLC39A13_ENST00000533076.1_Missense_Mutation_p.T20A|RP11-750H9.5_ENST00000532943.1_RNA|SLC39A13_ENST00000524928.1_Missense_Mutation_p.T20A|RP11-750H9.5_ENST00000532340.1_RNA|SLC39A13_ENST00000354884.4_Missense_Mutation_p.T20A|SLC39A13_ENST00000531974.1_Missense_Mutation_p.T20A	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	20					cellular zinc ion homeostasis (GO:0006882)|connective tissue development (GO:0061448)|zinc ion transmembrane transport (GO:0071577)	Golgi apparatus (GO:0005794)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	protein homodimerization activity (GO:0042803)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|kidney(1)|lung(1)|prostate(1)	4				Lung(87;0.0936)		CCTCTTCCTCACTGCCCTTGC	0.627													A|||	383	0.0764776	0.0628	0.098	5008	,	,		3883	0.0466		0.1491	False		,,,				2504	0.0358				p.T20A		Atlas-SNP	.											.	SLC39A13	18	.	0			c.A58G						PASS	.	A	ALA/THR,ALA/THR	370,4020		15,340,1840	53.0	60.0	58.0		58,58	-1.2	0.1	11	dbSNP_129	58	1191,7375		97,997,3189	yes	missense,missense	SLC39A13	NM_001128225.2,NM_152264.4	58,58	112,1337,5029	GG,GA,AA		13.9038,8.4282,12.0485	benign,benign	20/372,20/365	47431703	1561,11395	2195	4283	6478	SO:0001583	missense	91252	exon2			TTCCTCACTGCCC		CCDS7934.1, CCDS44592.1	11p11.2	2013-05-22			ENSG00000165915	ENSG00000165915		"""Solute carriers"""	20859	protein-coding gene	gene with protein product		608735	"""solute carrier family 39 (metal ion transporter), member 13"""			12659941	Standard	NM_001128225		Approved	FLJ25785	uc009ylq.3	Q96H72	OTTHUMG00000166890	ENST00000362021.4:c.58A>G	11.37:g.47431703A>G	ENSP00000354689:p.Thr20Ala	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_152264	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Missense_Mutation	SNP	ENST00000362021.4	37	CCDS44592.1	212	0.09706959706959707	42	0.08536585365853659	40	0.11049723756906077	18	0.03146853146853147	112	0.14775725593667546	A	10.11	1.260164	0.23051	0.084282	0.139038	ENSG00000165915	ENST00000533076;ENST00000531974;ENST00000531419;ENST00000531865;ENST00000362021;ENST00000354884;ENST00000526614;ENST00000527091;ENST00000524928	T;T;T;T;T;T;T;T;T	0.70282	-0.47;1.01;1.03;-0.44;-0.33;-0.13;0.02;1.01;0.96	5.4	-1.24	0.09435	.	0.820829	0.10843	N	0.627968	T	0.00241	0.0007	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.09022	0.0;0.001;0.002	B;B;B	0.12156	0.002;0.001;0.007	T	0.06862	-1.0803	9	0.08381	T	0.77	-2.3508	5.0379	0.14443	0.3836:0.0:0.4545:0.1619	rs61897432	20;20;20	Q96H72;Q96H72-2;E9PNE7	S39AD_HUMAN;.;.	A	20	ENSP00000434290:T20A;ENSP00000435845:T20A;ENSP00000432302:T20A;ENSP00000434684:T20A;ENSP00000354689:T20A;ENSP00000346956:T20A;ENSP00000432499:T20A;ENSP00000435076:T20A;ENSP00000437186:T20A	ENSP00000346956:T20A	T	+	1	0	SLC39A13	47388279	0.000000	0.05858	0.100000	0.21137	0.592000	0.36648	-0.111000	0.10807	0.052000	0.16007	0.459000	0.35465	ACT	A|0.882;G|0.118	0.118	strong		0.627	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264	
CCDC86	79080	hgsc.bcm.edu	37	11	60609972	60609972	+	Silent	SNP	A	A	G	rs2074422	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60609972A>G	ENST00000227520.5	+	1	429	c.375A>G	c.(373-375)ccA>ccG	p.P125P	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	125	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						AGGAGGCACCAAAGTGTTCTC	0.617													A|||	848	0.169329	0.1596	0.1297	5008	,	,		16754	0.128		0.2117	False		,,,				2504	0.2096				p.P125P		Atlas-SNP	.											.	CCDC86	24	.	0			c.A375G						PASS	.	A		783,3623	302.7+/-287.5	56,671,1476	67.0	65.0	66.0		375	-7.9	0.0	11	dbSNP_96	66	1922,6674	319.7+/-314.3	196,1530,2572	no	coding-synonymous	CCDC86	NM_024098.3		252,2201,4048	GG,GA,AA		22.3592,17.7712,20.8045		125/361	60609972	2705,10297	2203	4298	6501	SO:0001819	synonymous_variant	79080	exon1			GGCACCAAAGTGT	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.375A>G	11.37:g.60609972A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_024098	B4DY99	Silent	SNP	ENST00000227520.5	37	CCDS7993.1																																																																																			A|0.807;G|0.193	0.193	strong		0.617	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
ZNF844	284391	hgsc.bcm.edu	37	19	12186761	12186761	+	Missense_Mutation	SNP	A	A	G	rs7259845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12186761A>G	ENST00000439326.3	+	4	1001	c.826A>G	c.(826-828)Act>Gct	p.T276A	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	276			T -> A (in dbSNP:rs7259845).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AAGAACTCACACTGGAGAGAA	0.408													.|||	1455	0.290535	0.73	0.1455	5008	,	,		20627	0.0853		0.161	False		,,,				2504	0.1442				p.T276A		Atlas-SNP	.											.	ZNF844	69	.	0			c.A826G						PASS	.	A	ALA/THR	887,497		287,313,92	42.0	40.0	40.0		826	1.5	0.0	19	dbSNP_116	40	416,2766		25,366,1200	yes	missense	ZNF844	NM_001136501.1	58	312,679,1292	GG,GA,AA		13.0735,35.9104,28.537	benign	276/667	12186761	1303,3263	692	1591	2283	SO:0001583	missense	284391	exon4			ACTCACACTGGAG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.826A>G	19.37:g.12186761A>G	ENSP00000392024:p.Thr276Ala	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	573	0.2623626373626374	339	0.6890243902439024	53	0.1464088397790055	53	0.09265734265734266	128	0.16886543535620052	A	14.28	2.487242	0.44249	0.640896	0.130735	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505	T	0.26518	1.73	2.5	1.45	0.22620	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.62266	1.93	0.09310	P	0.999999999404092	B	0.32302	0.363	B	0.30316	0.114	T	0.25779	-1.0122	8	0.59425	D	0.04	.	6.394	0.21603	0.8647:0.0:0.1353:0.0	rs7259845;rs52791364;rs59360268;rs7259845	276	Q08AG5	ZN844_HUMAN	A	276;276;251	ENSP00000392024:T276A	ENSP00000392024:T276A	T	+	1	0	ZNF844	12047761	0.076000	0.21285	0.014000	0.15608	0.565000	0.35776	1.389000	0.34453	0.202000	0.20498	0.172000	0.16884	ACT	A|0.715;G|0.285	0.285	strong		0.408	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
PPIB	5479	hgsc.bcm.edu	37	15	64455123	64455123	+	Silent	SNP	G	G	T	rs4904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:64455123G>T	ENST00000300026.3	-	1	281	c.63C>A	c.(61-63)tcC>tcA	p.S21S	PPIB_ENST00000558492.1_5'UTR	NM_000942.4	NP_000933.1	P23284	PPIB_HUMAN	peptidylprolyl isomerase B (cyclophilin B)	21					bone development (GO:0060348)|chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|positive regulation of multicellular organism growth (GO:0040018)|protein peptidyl-prolyl isomerization (GO:0000413)|protein stabilization (GO:0050821)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(6)	10					L-Proline(DB00172)	GGAAGAAGACGGACCCCGCGA	0.647													G|||	243	0.0485224	0.0212	0.1916	5008	,	,		10062	0.0357		0.0229	False		,,,				2504	0.0235				p.S21S	GBM(105;399 1481 32889 33051 36637)	Atlas-SNP	.											.	PPIB	20	.	0			c.C63A						PASS	.	G		96,4310	73.6+/-111.7	1,94,2108	25.0	29.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	63	0.8	1.0	15	dbSNP_52	28	166,8432	72.6+/-135.2	1,164,4134	no	coding-synonymous	PPIB	NM_000942.4		2,258,6242	TT,TG,GG		1.9307,2.1788,2.0148		21/217	64455123	262,12742	2203	4299	6502	SO:0001819	synonymous_variant	5479	exon1			GAAGACGGACCCC		CCDS10191.1	15q21-q22	2014-09-17			ENSG00000166794	ENSG00000166794	5.2.1.8		9255	protein-coding gene	gene with protein product		123841				2000394, 20089953	Standard	NM_000942		Approved	CYPB, OI9	uc002and.3	P23284	OTTHUMG00000133018	ENST00000300026.3:c.63C>A	15.37:g.64455123G>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	147	61	0.414966	NM_000942	A8K534|Q6IBH5|Q9BVK5	Silent	SNP	ENST00000300026.3	37	CCDS10191.1																																																																																			G|0.969;T|0.031	0.031	strong		0.647	PPIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256604.1		
TM6SF2	53345	hgsc.bcm.edu	37	19	19379549	19379549	+	Missense_Mutation	SNP	C	C	T	rs58542926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19379549C>T	ENST00000389363.4	-	6	571	c.499G>A	c.(499-501)Gag>Aag	p.E167K	TM6SF2_ENST00000586107.1_5'UTR|AC138430.4_ENST00000586064.2_RNA	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	167			E -> K (in dbSNP:rs58542926).			integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			GGCCTGATCTCGGAGCTGTAT	0.577													C|||	334	0.0666933	0.0227	0.0634	5008	,	,		19607	0.0863		0.0676	False		,,,				2504	0.1074				p.E167K		Atlas-SNP	.											.	TM6SF2	39	.	0			c.G499A						PASS	.	C	LYS/GLU	126,3970		3,120,1925	76.0	79.0	78.0		499	5.0	1.0	19	dbSNP_129	78	599,7793		20,559,3617	yes	missense	TM6SF2	NM_001001524.2	56	23,679,5542	TT,TC,CC		7.1378,3.0762,5.8056	probably-damaging	167/378	19379549	725,11763	2048	4196	6244	SO:0001583	missense	53345	exon6			TGATCTCGGAGCT	AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.499G>A	19.37:g.19379549C>T	ENSP00000374014:p.Glu167Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	82	31	0.378049	NM_001001524	Q0IJ64	Missense_Mutation	SNP	ENST00000389363.4	37	CCDS42528.1	139	0.06364468864468864	18	0.036585365853658534	26	0.0718232044198895	42	0.07342657342657342	53	0.06992084432717678	C	17.03	3.283643	0.59867	0.030762	0.071378	ENSG00000213996	ENST00000389363;ENST00000269990	T	0.41065	1.01	5.01	5.01	0.66863	.	0.000000	0.47093	U	0.000242	T	0.05364	0.0142	L	0.61036	1.89	0.24096	P	0.99589286	D	0.67145	0.996	P	0.47402	0.546	T	0.24621	-1.0155	9	0.18276	T	0.48	-13.7739	15.8064	0.78517	0.0:1.0:0.0:0.0	rs58542926	167	Q9BZW4	TM6S2_HUMAN	K	167	ENSP00000374014:E167K	ENSP00000269990:E167K	E	-	1	0	TM6SF2	19240549	0.981000	0.34729	0.999000	0.59377	0.657000	0.38888	2.542000	0.45744	2.340000	0.79590	0.650000	0.86243	GAG	C|0.939;T|0.061	0.061	strong		0.577	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510	
ALPK2	115701	hgsc.bcm.edu	37	18	56204768	56204768	+	Missense_Mutation	SNP	G	G	A	rs3809974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:56204768G>A	ENST00000361673.3	-	5	2864	c.2651C>T	c.(2650-2652)tCa>tTa	p.S884L	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	884			S -> L (in dbSNP:rs3809974).			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						GGACATGACTGAGTTGCCGTC	0.438													G|||	275	0.0549121	0.1286	0.0288	5008	,	,		22818	0.0268		0.0268	False		,,,				2504	0.0317				p.S884L		Atlas-SNP	.											.	ALPK2	487	.	0			c.C2651T						PASS	.	G	LEU/SER	443,3963	213.8+/-233.3	22,399,1782	72.0	67.0	68.0		2651	1.2	0.0	18	dbSNP_107	68	189,8411	84.5+/-147.0	3,183,4114	yes	missense	ALPK2	NM_052947.3	145	25,582,5896	AA,AG,GG		2.1977,10.0545,4.8593	probably-damaging	884/2171	56204768	632,12374	2203	4300	6503	SO:0001583	missense	115701	exon5			ATGACTGAGTTGC	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.2651C>T	18.37:g.56204768G>A	ENSP00000354991:p.Ser884Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	139	65	0.467626	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	98	0.04487179487179487	53	0.10772357723577236	8	0.022099447513812154	19	0.033216783216783216	18	0.023746701846965697	G	15.42	2.827320	0.50739	0.100545	0.021977	ENSG00000198796	ENST00000361673	T	0.56611	0.45	5.16	1.21	0.21127	.	1.269890	0.05449	N	0.549077	T	0.01061	0.0035	L	0.54323	1.7	0.09310	N	1	B;B	0.23650	0.089;0.006	B;B	0.24974	0.057;0.008	T	0.07214	-1.0784	10	0.38643	T	0.18	0.6541	1.9122	0.03290	0.1789:0.1588:0.4985:0.1638	rs3809974;rs17065150;rs3809974	884;884	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	L	884	ENSP00000354991:S884L	ENSP00000354991:S884L	S	-	2	0	ALPK2	54355748	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.911000	0.28584	-0.057000	0.13199	-0.274000	0.10170	TCA	G|0.949;A|0.051	0.051	strong		0.438	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
LMAN1	3998	hgsc.bcm.edu	37	18	57026450	57026450	+	Silent	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:57026450G>C	ENST00000251047.5	-	1	744	c.27C>G	c.(25-27)ctC>ctG	p.L9L	RP11-27G24.1_ENST00000591331.1_lincRNA	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	9					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	CTCTGGCCCGGAGACCCCTTT	0.701																																					p.L9L		Atlas-SNP	.											.	LMAN1	57	.	0			c.C27G						PASS	.						41.0	49.0	46.0					18																	57026450		2203	4300	6503	SO:0001819	synonymous_variant	3998	exon1			GGCCCGGAGACCC	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"""endoplasmic reticulum-golgi intermediate compartment protein 53"""	601567	"""coagulation factor V-factor VIII combined deficiency"""	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.27C>G	18.37:g.57026450G>C		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	51	0.443478	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Silent	SNP	ENST00000251047.5	37	CCDS11974.1																																																																																			.	.	none		0.701	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570	
BAIAP2	10458	hgsc.bcm.edu	37	17	79009061	79009061	+	Silent	SNP	C	C	T	rs8068528	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79009061C>T	ENST00000321300.6	+	1	100	c.7C>T	c.(7-9)Ctg>Ttg	p.L3L	BAIAP2_ENST00000435091.3_Silent_p.L3L|BAIAP2_ENST00000575712.1_Silent_p.L3L|BAIAP2_ENST00000321280.7_Silent_p.L3L|BAIAP2_ENST00000573894.1_3'UTR|BAIAP2-AS1_ENST00000577066.1_lincRNA|BAIAP2_ENST00000392411.3_5'UTR|BAIAP2_ENST00000575245.1_Silent_p.L3L|BAIAP2_ENST00000428708.2_Silent_p.L3L	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	3	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				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)			GACCATGTCTCTGTCTCGCTC	0.687													C|||	691	0.137979	0.0946	0.0865	5008	,	,		4463	0.253		0.0855	False		,,,				2504	0.1687				p.L3L		Atlas-SNP	.											BAIAP2_ENST00000321300,NS,carcinoma,0,2	BAIAP2	74	2	0			c.C7T						PASS	.	C	,,,	419,3971		25,369,1801	19.0	17.0	17.0		7,7,7,7	2.6	1.0	17	dbSNP_116	17	769,7817		33,703,3557	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP2	NM_001144888.1,NM_006340.2,NM_017450.2,NM_017451.2	,,,	58,1072,5358	TT,TC,CC		8.9564,9.5444,9.1554	,,,	3/535,3/521,3/522,3/553	79009061	1188,11788	2195	4293	6488	SO:0001819	synonymous_variant	10458	exon1			ATGTCTCTGTCTC	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.7C>T	17.37:g.79009061C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Silent	SNP	ENST00000321300.6	37	CCDS11775.1																																																																																			C|0.889;T|0.111	0.111	strong		0.687	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
TUBA8	51807	hgsc.bcm.edu	37	22	18609128	18609128	+	Missense_Mutation	SNP	C	C	T	rs2234331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18609128C>T	ENST00000330423.3	+	4	456	c.383C>T	c.(382-384)gCt>gTt	p.A128V	TUBA8_ENST00000316027.6_Missense_Mutation_p.A62V	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	128			A -> V (in dbSNP:rs2234331).		microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						TAGACAGATGCTTGCTCTGGC	0.532													C|||	15	0.00299521	0.0	0.0014	5008	,	,		17837	0.0		0.0089	False		,,,				2504	0.0051				p.A128V		Atlas-SNP	.											.	TUBA8	36	.	0			c.C383T						PASS	.	C	VAL/ALA,VAL/ALA	14,4392	19.1+/-41.9	0,14,2189	86.0	90.0	88.0		185,383	5.5	1.0	22	dbSNP_98	88	97,8503	51.9+/-112.3	0,97,4203	yes	missense,missense	TUBA8	NM_001193414.1,NM_018943.2	64,64	0,111,6392	TT,TC,CC		1.1279,0.3177,0.8535	benign,benign	62/384,128/450	18609128	111,12895	2203	4300	6503	SO:0001583	missense	51807	exon4			CAGATGCTTGCTC	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"""Tubulins"""	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.383C>T	22.37:g.18609128C>T	ENSP00000333326:p.Ala128Val	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	13.23	2.174373	0.38413	0.003177	0.011279	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	T;T;T	0.68765	-0.35;-0.35;-0.35	5.49	5.49	0.81192	Tubulin/FtsZ, GTPase domain (4);	0.257566	0.40385	N	0.001118	T	0.57636	0.2067	L	0.55017	1.72	0.48040	D	0.999573	B;B	0.28783	0.222;0.039	B;B	0.34489	0.184;0.102	T	0.64659	-0.6355	10	0.87932	D	0	.	13.6603	0.62363	0.1545:0.8455:0.0:0.0	rs2234331;rs52811979;rs2234331	152;128	C9J2C0;Q9NY65	.;TBA8_HUMAN	V	62;128;152	ENSP00000318575:A62V;ENSP00000333326:A128V;ENSP00000412646:A152V	ENSP00000318575:A62V	A	+	2	0	TUBA8	16989128	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.833000	0.48159	2.735000	0.93741	0.655000	0.94253	GCT	C|0.993;T|0.007	0.007	strong		0.532	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943	
POC1B	282809	hgsc.bcm.edu	37	12	89865394	89865394	+	Missense_Mutation	SNP	G	G	C	rs145981936		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:89865394G>C	ENST00000313546.3	-	6	801	c.673C>G	c.(673-675)Caa>Gaa	p.Q225E	POC1B_ENST00000541909.1_Missense_Mutation_p.Q95E|POC1B_ENST00000549035.1_Missense_Mutation_p.Q183E|POC1B_ENST00000378528.2_Intron|POC1B_ENST00000393179.4_Missense_Mutation_p.Q95E|POC1B_ENST00000549504.1_Intron	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	225					cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						TTGTTACCTTGGTAATGCTGT	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		17728	0.0		0.001	False		,,,				2504	0.0				p.Q225E		Atlas-SNP	.											.	POC1B	41	.	0			c.C673G						PASS	.	G	GLU/GLN,GLU/GLN	0,4406		0,0,2203	147.0	137.0	140.0		547,673	6.0	1.0	12	dbSNP_134	140	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	POC1B	NM_001199777.1,NM_172240.2	29,29	0,5,6498	CC,CG,GG		0.0581,0.0,0.0384	,	183/437,225/479	89865394	5,13001	2203	4300	6503	SO:0001583	missense	282809	exon6			TACCTTGGTAATG	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"""WD repeat domain containing"""	30836	protein-coding gene	gene with protein product		614784	"""WD repeat domain 51B"", ""POC1 centriolar protein homolog B (Chlamydomonas)"""	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.673C>G	12.37:g.89865394G>C	ENSP00000323302:p.Gln225Glu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	34	0.336634	NM_172240	G3V1X0	Missense_Mutation	SNP	ENST00000313546.3	37	CCDS31869.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471636	0.43942	0.0	5.81E-4	ENSG00000139323	ENST00000393179;ENST00000313546;ENST00000549035;ENST00000541909	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	6.02	6.02	0.97574	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.155036	0.64402	D	0.000014	T	0.40719	0.1128	N	0.10972	0.075	0.80722	D	1	B	0.31655	0.334	B	0.35182	0.197	T	0.31308	-0.9948	10	0.13853	T	0.58	.	16.1501	0.81611	0.0:0.0:0.8588:0.1412	.	225	Q8TC44	POC1B_HUMAN	E	95;225;183;95	ENSP00000376877:Q95E;ENSP00000323302:Q225E;ENSP00000447916:Q183E;ENSP00000440301:Q95E	ENSP00000323302:Q225E	Q	-	1	0	POC1B	88389525	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.072000	0.64389	2.857000	0.98124	0.650000	0.86243	CAA	G|0.999;C|0.001	0.001	strong		0.413	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751274	19751274	+	Silent	SNP	G	G	A	rs143115179	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19751274G>A	ENST00000400113.3	-	4	953	c.849C>T	c.(847-849)caC>caT	p.H283H		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	283					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		ACAGCTGCTCGTGGTAGGCCT	0.607																																					p.H283H		Atlas-SNP	.											.	TUBA3C	166	.	0			c.C849T						PASS	.						143.0	128.0	133.0					13																	19751274		2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			CTGCTCGTGGTAG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.849C>T	13.37:g.19751274G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	218	16	0.0733945	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			G|0.992;A|0.008	0.008	strong		0.607	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
HABP2	3026	hgsc.bcm.edu	37	10	115341846	115341846	+	Silent	SNP	G	G	A	rs2245058	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115341846G>A	ENST00000351270.3	+	9	1146	c.1050G>A	c.(1048-1050)gcG>gcA	p.A350A	HABP2_ENST00000542051.1_Silent_p.A324A|HABP2_ENST00000541666.1_Intron	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	350	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	GTGGTGGGGCGCTGATCCACC	0.672													G|||	1884	0.376198	0.4145	0.4914	5008	,	,		17348	0.2986		0.3917	False		,,,				2504	0.3067				p.A350A		Atlas-SNP	.											.	HABP2	52	.	0			c.G1050A						PASS	.	G	,	1826,2580	504.4+/-365.8	355,1116,732	25.0	28.0	27.0		972,1050	-9.9	0.0	10	dbSNP_100	27	3615,4985	502.0+/-375.6	720,2175,1405	no	coding-synonymous,coding-synonymous	HABP2	NM_001177660.1,NM_004132.3	,	1075,3291,2137	AA,AG,GG		42.0349,41.4435,41.8345	,	324/535,350/561	115341846	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	3026	exon9			TGGGGCGCTGATC		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.1050G>A	10.37:g.115341846G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Silent	SNP	ENST00000351270.3	37	CCDS7577.1																																																																																			G|0.599;A|0.401	0.401	strong		0.672	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
KLHL30	377007	hgsc.bcm.edu	37	2	239049540	239049540	+	Missense_Mutation	SNP	G	G	A	rs2241985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:239049540G>A	ENST00000409223.1	+	2	252	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	KLHL30_ENST00000305959.4_Missense_Mutation_p.G31S			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.			G -> S (in Ref. 4; AAI05697). {ECO:0000305}.						lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		ATGCCACCGCGGCCTCCTGGC	0.697													G|||	1935	0.386382	0.3812	0.4006	5008	,	,		17698	0.3938		0.3847	False		,,,				2504	0.3773				p.G49S		Atlas-SNP	.											.	KLHL30	79	.	0			c.G145A						PASS	.	G	SER/GLY	1662,2602		333,996,803	40.0	48.0	46.0		145	1.3	1.0	2	dbSNP_98	46	3261,5177		633,1995,1591	yes	missense	KLHL30	NM_198582.3	56	966,2991,2394	AA,AG,GG		38.6466,38.9775,38.7577	benign	49/579	239049540	4923,7779	2132	4219	6351	SO:0001583	missense	377007	exon2			CACCGCGGCCTCC		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.145G>A	2.37:g.239049540G>A	ENSP00000386389:p.Gly49Ser	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	848	0.3882783882783883	194	0.3943089430894309	150	0.4143646408839779	213	0.3723776223776224	291	0.3839050131926121	G	6.300	0.423477	0.11928	0.389775	0.386466	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.66280	-0.2;-0.2	5.66	1.26	0.21427	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.378699	0.28958	N	0.013586	T	0.00012	0.0000	N	0.01529	-0.815	0.80722	P	0.0	B	0.23937	0.094	B	0.23018	0.043	T	0.42682	-0.9437	9	0.46703	T	0.11	.	7.8189	0.29276	0.485:0.0:0.515:0.0	rs2241985;rs2241985	49	Q0D2K2	KLH30_HUMAN	S	49;31	ENSP00000386389:G49S;ENSP00000302386:G31S	ENSP00000302386:G31S	G	+	1	0	KLHL30	238714279	0.319000	0.24607	0.963000	0.40424	0.927000	0.56198	0.962000	0.29280	0.329000	0.23460	-0.218000	0.12543	GGC	G|0.618;A|0.382	0.382	strong		0.697	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
ADAD2	161931	hgsc.bcm.edu	37	16	84229580	84229580	+	Silent	SNP	C	C	T	rs2303239	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84229580C>T	ENST00000315906.5	+	7	1264	c.1212C>T	c.(1210-1212)gcC>gcT	p.A404A	ADAD2_ENST00000268624.3_Silent_p.A486A|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	404	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CACGCTGGGCCGTGCTGGGGC	0.677													C|||	1453	0.290136	0.1793	0.4352	5008	,	,		15982	0.2421		0.325	False		,,,				2504	0.3507				p.A486A		Atlas-SNP	.											.	ADAD2	46	.	0			c.C1458T						PASS	.	C	,	928,3466		111,706,1380	20.0	24.0	23.0		1212,1458	-11.0	0.0	16	dbSNP_100	23	2702,5880		455,1792,2044	no	coding-synonymous,coding-synonymous	ADAD2	NM_001145400.1,NM_139174.3	,	566,2498,3424	TT,TC,CC		31.4845,21.1197,27.9747	,	404/584,486/666	84229580	3630,9346	2197	4291	6488	SO:0001819	synonymous_variant	161931	exon8			CTGGGCCGTGCTG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1212C>T	16.37:g.84229580C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	28	10	0.357143	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																			C|0.720;T|0.280	0.280	strong		0.677	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
IGDCC4	57722	hgsc.bcm.edu	37	15	65703625	65703625	+	Missense_Mutation	SNP	C	C	G	rs34355056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:65703625C>G	ENST00000352385.2	-	2	363	c.154G>C	c.(154-156)Gct>Cct	p.A52P		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	52	Ig-like C2-type 1.		A -> P (in dbSNP:rs34355056).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						AGCACTGCAGCCTGCTCTGGG	0.647													C|||	723	0.144369	0.233	0.196	5008	,	,		18791	0.0417		0.1471	False		,,,				2504	0.091				p.A52P		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G154C						PASS	.	C	PRO/ALA	935,3467	350.8+/-311.0	96,743,1362	39.0	37.0	38.0		154	3.0	0.4	15	dbSNP_126	38	1263,7335	245.1+/-274.1	89,1085,3125	yes	missense	IGDCC4	NM_020962.1	27	185,1828,4487	GG,GC,CC		14.6895,21.2403,16.9077	benign	52/1251	65703625	2198,10802	2201	4299	6500	SO:0001583	missense	57722	exon2			CTGCAGCCTGCTC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.154G>C	15.37:g.65703625C>G	ENSP00000319623:p.Ala52Pro	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	295	0.13507326007326007	103	0.20934959349593496	50	0.13812154696132597	32	0.055944055944055944	110	0.14511873350923482	C	1.856	-0.463746	0.04476	0.212403	0.146895	ENSG00000103742	ENST00000352385	T	0.76448	-1.02	5.07	3.0	0.34707	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.528595	0.18896	N	0.128174	T	0.00073	0.0002	N	0.16037	0.36	0.40067	P	0.024035999999999946	B	0.14805	0.011	B	0.16722	0.016	T	0.03086	-1.1074	9	0.16896	T	0.51	-2.9139	6.3413	0.21324	0.3286:0.585:0.0:0.0864	rs34355056	52	Q8TDY8	IGDC4_HUMAN	P	52	ENSP00000319623:A52P	ENSP00000319623:A52P	A	-	1	0	IGDCC4	63490678	0.414000	0.25408	0.448000	0.26945	0.113000	0.19764	0.420000	0.21263	1.088000	0.41272	0.563000	0.77884	GCT	C|0.845;G|0.155	0.155	strong		0.647	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
TNFRSF4	7293	hgsc.bcm.edu	37	1	1147422	1147422	+	Silent	SNP	C	C	T	rs17568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1147422C>T	ENST00000379236.3	-	5	538	c.534G>A	c.(532-534)gaG>gaA	p.E178E	TNFRSF4_ENST00000453580.1_5'UTR	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	178					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCCCTGGGTCTCCTGGGGCT	0.701													c|||	2496	0.498403	0.4297	0.5043	5008	,	,		13575	0.7837		0.2117	False		,,,				2504	0.5879				p.E178E		Atlas-SNP	.											.	TNFRSF4	12	.	0			c.G534A						PASS	.	C		1662,2718		306,1050,834	16.0	20.0	18.0		534	0.3	0.9	1	dbSNP_63	18	1756,6800		195,1366,2717	no	coding-synonymous	TNFRSF4	NM_003327.3		501,2416,3551	TT,TC,CC		20.5236,37.9452,26.4224		178/278	1147422	3418,9518	2190	4278	6468	SO:0001819	synonymous_variant	7293	exon5			CTGGGTCTCCTGG	X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.534G>A	1.37:g.1147422C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_003327	Q13663|Q2M312|Q5T7M0	Silent	SNP	ENST00000379236.3	37	CCDS11.1	993	0.45467032967032966	231	0.4695121951219512	172	0.47513812154696133	433	0.756993006993007	157	0.20712401055408972	C	5.772	0.326856	0.10900	0.379452	0.205236	ENSG00000186827	ENST00000453580	.	.	.	3.47	0.346	0.16017	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20764	P	0.999857777	.	.	.	.	.	.	T	0.25152	-1.0140	3	.	.	.	-12.4998	2.9742	0.05932	0.1675:0.5134:0.2059:0.1132	rs17568;rs62648068	.	.	.	N	124	.	.	D	-	1	0	TNFRSF4	1137285	0.461000	0.25783	0.890000	0.34922	0.026000	0.11368	0.431000	0.21444	0.250000	0.21479	0.491000	0.48974	GAC	C|0.674;T|0.326	0.326	strong		0.701	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1		
TPR	7175	hgsc.bcm.edu	37	1	186301447	186301447	+	Silent	SNP	T	T	C	rs7526540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186301447T>C	ENST00000367478.4	-	38	5780	c.5484A>G	c.(5482-5484)ccA>ccG	p.P1828P		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1828	Sufficient and essential for mediating its nuclear import.				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)		GTGTACGCTTTGGCAAAGAAG	0.373			T	NTRK1	papillary thyroid								T|||	151	0.0301518	0.0446	0.013	5008	,	,		17549	0.001		0.0388	False		,,,				2504	0.044				p.P1828P		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A5484G						PASS	.	T		170,3568		1,168,1700	92.0	85.0	87.0		5484	-7.3	1.0	1	dbSNP_116	87	367,7811		11,345,3733	no	coding-synonymous	TPR	NM_003292.2		12,513,5433	CC,CT,TT		4.4876,4.5479,4.5065		1828/2364	186301447	537,11379	1869	4089	5958	SO:0001819	synonymous_variant	7175	exon38			ACGCTTTGGCAAA	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.5484A>G	1.37:g.186301447T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																			T|0.958;C|0.042	0.042	strong		0.373	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
OR2W1	26692	hgsc.bcm.edu	37	6	29012116	29012116	+	Silent	SNP	G	G	A	rs7341218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29012116G>A	ENST00000377175.1	-	1	901	c.837C>T	c.(835-837)acC>acT	p.T279T		NM_030903.3	NP_112165.1	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W, member 1	279						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|skin(1)	23						GAGTGATGACGGTGTAAAAGA	0.433													G|||	1444	0.288339	0.354	0.2839	5008	,	,		18806	0.3929		0.1889	False		,,,				2504	0.1973				p.T279T		Atlas-SNP	.											.	OR2W1	36	.	0			c.C837T						PASS	.	G	,	961,2061		143,675,693	108.0	84.0	93.0		,837	-1.5	1.0	6	dbSNP_116	93	907,4511		78,751,1880	no	utr-5,coding-synonymous	OR2W1,LOC100129636	NM_001195202.1,NM_030903.3	,	221,1426,2573	AA,AG,GG		16.7405,31.8001,22.1327	,	,279/321	29012116	1868,6572	1511	2709	4220	SO:0001819	synonymous_variant	26692	exon1			GATGACGGTGTAA	AL035402	CCDS4656.1	6p22.1	2012-08-09			ENSG00000204704	ENSG00000204704		"""GPCR / Class A : Olfactory receptors"""	8281	protein-coding gene	gene with protein product							Standard	NM_030903		Approved	hs6M1-15	uc003nlw.2	Q9Y3N9	OTTHUMG00000031048	ENST00000377175.1:c.837C>T	6.37:g.29012116G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	212	105	0.495283	NM_030903	B0S7Y5|Q5JNZ1|Q6IEU0|Q96R17|Q9GZL0|Q9GZL1	Silent	SNP	ENST00000377175.1	37	CCDS4656.1																																																																																			G|0.748;A|0.252	0.252	strong		0.433	OR2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076053.2		
CKAP2	26586	hgsc.bcm.edu	37	13	53039547	53039547	+	Missense_Mutation	SNP	C	C	T	rs143514154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:53039547C>T	ENST00000378037.5	+	6	1516	c.1426C>T	c.(1426-1428)Cct>Tct	p.P476S	CKAP2_ENST00000490903.1_Missense_Mutation_p.P427S|CKAP2_ENST00000258607.5_Missense_Mutation_p.P475S|CKAP2_ENST00000378034.3_Missense_Mutation_p.P475S	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2											breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.6e-08)		AATCACAAGTCCTATTGAAAA	0.338													c|||	17	0.00339457	0.0	0.0101	5008	,	,		16813	0.0		0.0099	False		,,,				2504	0.0				p.P476S		Atlas-SNP	.											.	CKAP2	51	.	0			c.C1426T						PASS	.	C	SER/PRO,SER/PRO	12,4394		0,12,2191	86.0	91.0	89.0		1426,1423	2.9	1.0	13	dbSNP_134	89	88,8504		0,88,4208	yes	missense,missense	CKAP2	NM_001098525.1,NM_018204.3	74,74	0,100,6399	TT,TC,CC		1.0242,0.2724,0.7693	probably-damaging,probably-damaging	476/684,475/683	53039547	100,12898	2203	4296	6499	SO:0001583	missense	26586	exon6			ACAAGTCCTATTG	AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.1426C>T	13.37:g.53039547C>T	ENSP00000367276:p.Pro476Ser	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	182	78	0.428571	NM_001098525		Missense_Mutation	SNP	ENST00000378037.5	37	CCDS41893.1	11	0.005036630036630037	0	0.0	6	0.016574585635359115	0	0.0	5	0.006596306068601583	.	14.37	2.516023	0.44763	0.002724	0.010242	ENSG00000136108	ENST00000398044;ENST00000258607;ENST00000378034;ENST00000378037;ENST00000490903	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.63	2.94	0.34122	.	0.512341	0.20916	N	0.083379	T	0.11922	0.0290	M	0.82056	2.57	0.36976	D	0.894063	P;P;P;P	0.40211	0.513;0.513;0.513;0.707	B;B;B;B	0.38655	0.147;0.147;0.147;0.278	T	0.08086	-1.0739	10	0.56958	D	0.05	-1.6008	3.444	0.07474	0.1396:0.5775:0.135:0.148	.	427;476;475;476	E9PD90;Q8WWK9;B2RMQ4;A8MYU4	.;CKAP2_HUMAN;.;.	S	476;475;475;476;427	ENSP00000258607:P475S;ENSP00000367273:P475S;ENSP00000367276:P476S;ENSP00000417830:P427S	ENSP00000258607:P475S	P	+	1	0	CKAP2	51937548	0.976000	0.34144	1.000000	0.80357	0.993000	0.82548	0.547000	0.23299	0.390000	0.25115	0.655000	0.94253	CCT	C|0.994;T|0.006	0.006	strong		0.338	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2		
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41811706	41811706	+	Silent	SNP	C	C	T	rs372346124		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41811706C>T	ENST00000392006.3	+	14	2561	c.2388C>T	c.(2386-2388)ccC>ccT	p.P796P	HNRNPUL1_ENST00000595018.1_Silent_p.P696P|HNRNPUL1_ENST00000352456.3_Silent_p.P706P|HNRNPUL1_ENST00000602130.1_Intron|HNRNPUL1_ENST00000378215.4_Silent_p.P692P|HNRNPUL1_ENST00000593587.1_Silent_p.P696P|HNRNPUL1_ENST00000263367.3_Silent_p.P707P	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	796	Necessary for interaction with TP53.|Pro-rich.|Tyr-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						ACCCGGCCCCCTATACCCCAC	0.627																																					p.P796P		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.C2388T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	57.0	57.0	57.0		2388,2088	-2.8	1.0	19		57	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,coding-synonymous	HNRNPUL1	NM_007040.3,NM_144732.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	796/857,696/757	41811706	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11100	exon14			GGCCCCCTATACC	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.2388C>T	19.37:g.41811706C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Silent	SNP	ENST00000392006.3	37	CCDS12576.1																																																																																			.	.	weak		0.627	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
SLC27A5	10998	hgsc.bcm.edu	37	19	59023166	59023166	+	Missense_Mutation	SNP	G	G	A	rs34415062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:59023166G>A	ENST00000263093.2	-	1	266	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W	SLC27A5_ENST00000601355.1_Missense_Mutation_p.R53W	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	53			R -> W (in dbSNP:rs34415062).		bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		AGCCAGGGCCGTGCTAACATG	0.697													g|||	810	0.161741	0.1823	0.1715	5008	,	,		16961	0.0565		0.2187	False		,,,				2504	0.1769				p.R53W		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C157T						PASS	.	A	TRP/ARG	758,3572		76,606,1483	9.0	10.0	10.0		157	-8.6	0.0	19	dbSNP_126	10	1437,7025		126,1185,2920	yes	missense	SLC27A5	NM_012254.2	101	202,1791,4403	AA,AG,GG		16.9818,17.5058,17.1592	benign	53/691	59023166	2195,10597	2165	4231	6396	SO:0001583	missense	10998	exon1			AGGGCCGTGCTAA	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.157C>T	19.37:g.59023166G>A	ENSP00000263093:p.Arg53Trp	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	354	0.1620879120879121	103	0.20934959349593496	64	0.17679558011049723	34	0.05944055944055944	153	0.20184696569920843	g	10.06	1.248102	0.22880	0.175058	0.169818	ENSG00000083807	ENST00000263093	T	0.55760	0.5	4.31	-8.62	0.00881	.	3.204120	0.01052	N	0.004491	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03394	-1.1041	9	0.37606	T	0.19	0.0155	6.2565	0.20877	0.2565:0.0993:0.5413:0.103	rs34415062;rs34415062	53	Q9Y2P5	S27A5_HUMAN	W	53	ENSP00000263093:R53W	ENSP00000263093:R53W	R	-	1	2	SLC27A5	63714978	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.165000	0.01274	-3.044000	0.00262	-0.372000	0.07161	CGG	G|0.817;A|0.183	0.183	strong		0.697	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
APOH	350	hgsc.bcm.edu	37	17	64216854	64216854	+	Missense_Mutation	SNP	A	A	G	rs52797880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:64216854A>G	ENST00000205948.6	-	5	459	c.422T>C	c.(421-423)aTc>aCc	p.I141T		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	141	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			TGGAGGGCAGATGATGGCTGG	0.368													G|||	352	0.0702875	0.115	0.0418	5008	,	,		18261	0.0516		0.0696	False		,,,				2504	0.0501				p.I141T	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.T422C						PASS	.	G	THR/ILE	397,4009		17,363,1823	85.0	85.0	85.0		422	3.4	0.1	17	dbSNP_128	85	560,8040		17,526,3757	yes	missense	APOH	NM_000042.2	89	34,889,5580	GG,GA,AA		6.5116,9.0104,7.3581	benign	141/346	64216854	957,12049	2203	4300	6503	SO:0001583	missense	350	exon5			GGGCAGATGATGG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.422T>C	17.37:g.64216854A>G	ENSP00000205948:p.Ile141Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	167	0.07646520146520147	62	0.12601626016260162	16	0.04419889502762431	35	0.06118881118881119	54	0.0712401055408971	N	1.071	-0.670004	0.03403	0.090104	0.065116	ENSG00000091583	ENST00000205948	T	0.22743	1.94	5.4	3.37	0.38596	Complement control module (1);Sushi/SCR/CCP (1);	0.221461	0.46145	N	0.000314	T	0.00039	0.0001	N	0.00223	-1.815	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34179	-0.9839	9	0.02654	T	1	.	5.9326	0.19148	0.1474:0.0:0.5803:0.2723	rs52797880	141	P02749	APOH_HUMAN	T	141	ENSP00000205948:I141T	ENSP00000205948:I141T	I	-	2	0	APOH	61647316	1.000000	0.71417	0.060000	0.19600	0.045000	0.14185	1.743000	0.38258	0.253000	0.21552	-0.229000	0.12294	ATC	A|0.927;G|0.073	0.073	strong		0.368	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
KLK3	354	hgsc.bcm.edu	37	19	51359503	51359503	+	Silent	SNP	A	A	G	rs1135766	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51359503A>G	ENST00000326003.2	+	2	95	c.54A>G	c.(52-54)gcA>gcG	p.A18A	KLK3_ENST00000593997.1_Silent_p.A18A|KLK3_ENST00000360617.3_Silent_p.A18A|KLK3_ENST00000597483.1_Silent_p.A18A|KLK3_ENST00000595952.1_Silent_p.A18A	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	18					cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CAGGTGCTGCACCCCTCATCC	0.592													a|||	1702	0.339856	0.1921	0.4914	5008	,	,		19322	0.4851		0.4195	False		,,,				2504	0.2004				p.A18A	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											KLK3_ENST00000360617,colon,carcinoma,0,2	KLK3	76	2	0			c.A54G						scavenged	.	G	,,,	1071,3335	391.4+/-328.1	140,791,1272	96.0	86.0	89.0		54,54,54,54	-4.2	0.0	19	dbSNP_86	89	3585,5015	518.6+/-379.3	765,2055,1480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KLK3	NM_001030047.1,NM_001030048.1,NM_001030050.1,NM_001648.2	,,,	905,2846,2752	GG,GA,AA		41.686,24.3078,35.7989	,,,	18/239,18/219,18/70,18/262	51359503	4656,8350	2203	4300	6503	SO:0001819	synonymous_variant	354	exon2			TGCTGCACCCCTC	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.54A>G	19.37:g.51359503A>G		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	115	64	0.556522	NM_001030050	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			A|0.599;C|0.019	.	strong		0.592	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
LRP2	4036	hgsc.bcm.edu	37	2	170103336	170103336	+	Silent	SNP	T	T	C	rs831043	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:170103336T>C	ENST00000263816.3	-	21	3354	c.3069A>G	c.(3067-3069)acA>acG	p.T1023T	LRP2_ENST00000443831.1_Silent_p.T886T	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1023					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CACACTGCTCTGTGGGTGGTT	0.493													C|||	3098	0.61861	0.7201	0.6369	5008	,	,		17744	0.4792		0.4622	False		,,,				2504	0.773				p.T1023T		Atlas-SNP	.											.	LRP2	751	.	0			c.A3069G						PASS	.	C		3047,1359	452.6+/-350.1	1064,919,220	143.0	131.0	135.0		3069	-1.9	0.0	2	dbSNP_86	135	3921,4679	604.9+/-394.9	890,2141,1269	no	coding-synonymous	LRP2	NM_004525.2		1954,3060,1489	CC,CT,TT		45.593,30.8443,46.4247		1023/4656	170103336	6968,6038	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon21			CTGCTCTGTGGGT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.3069A>G	2.37:g.170103336T>C		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	223	117	0.524664	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.456;C|0.544	0.544	strong		0.493	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
IL17REL	400935	hgsc.bcm.edu	37	22	50435480	50435480	+	Missense_Mutation	SNP	A	A	G	rs5771069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50435480A>G	ENST00000389983.2	-	14	1262	c.998T>C	c.(997-999)cTt>cCt	p.L333P	IL17REL_ENST00000341280.5_Missense_Mutation_p.L333P	NM_001001694.2	NP_001001694.2	Q6ZVW7	I17EL_HUMAN	interleukin 17 receptor E-like	333			L -> P (in dbSNP:rs5771069).							endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6		all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		GGAAGGCAAAAGCAGGGGCGG	0.637													G|||	3040	0.607029	0.6505	0.4755	5008	,	,		18704	0.5536		0.5209	False		,,,				2504	0.7853				p.L333P		Atlas-SNP	.											.	IL17REL	21	.	0			c.T998C						PASS	.	G	PRO/LEU	2651,1721		832,987,367	34.0	36.0	35.0	http://omim.org/entry/266600|http://www.ncbi.nlm.nih.gov/pubmed?term	998	-4.3	0.0	22	dbSNP_114	35	4311,4279		1079,2153,1063	yes	missense	IL17REL	NM_001001694.2	98	1911,3140,1430	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	49.8137,39.3641,46.2892	benign	333/337	50435480	6962,6000	2186	4295	6481	SO:0001583	missense	400935	exon14			GGCAAAAGCAGGG	AK123987	CCDS33679.1	22q13.33	2009-01-13			ENSG00000188263	ENSG00000188263			33808	protein-coding gene	gene with protein product		613414					Standard	NM_001001694		Approved	FLJ41993	uc003bje.1	Q6ZVW7	OTTHUMG00000150242	ENST00000389983.2:c.998T>C	22.37:g.50435480A>G	ENSP00000374633:p.Leu333Pro	Somatic	343	2	0.0058309		WXS	Illumina HiSeq	Phase_I	345	340	0.985507	NM_001001694	A6NCN4|A6PVC1	Missense_Mutation	SNP	ENST00000389983.2	37	CCDS33679.1	1213	0.5554029304029304	327	0.6646341463414634	177	0.4889502762430939	307	0.5367132867132867	402	0.5303430079155673	G	6.947	0.544605	0.13312	0.606359	0.501863	ENSG00000188263	ENST00000389983;ENST00000341280	T;T	0.27402	1.67;1.67	2.79	-4.33	0.03677	.	.	.	.	.	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	0.41858	-0.9485	8	0.31617	T	0.26	.	1.356	0.02182	0.1398:0.2964:0.3237:0.2401	rs5771069;rs8135877;rs17780586;rs59525470;rs5771069	333	Q6ZVW7	I17EL_HUMAN	P	333	ENSP00000374633:L333P;ENSP00000342520:L333P	ENSP00000342520:L333P	L	-	2	0	IL17REL	48777607	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-3.930000	0.00332	-1.041000	0.03266	-0.355000	0.07637	CTT	A|0.431;G|0.569	0.569	strong		0.637	IL17REL-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317011.1	NM_001001694	
MDN1	23195	hgsc.bcm.edu	37	6	90371202	90371202	+	Silent	SNP	G	G	A	rs9444701	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90371202G>A	ENST00000369393.3	-	88	14776	c.14661C>T	c.(14659-14661)ctC>ctT	p.L4887L	MDN1_ENST00000428876.1_Silent_p.L4887L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4887					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTTCACTGTCGAGGTTCAAGT	0.473													G|||	3633	0.725439	0.7163	0.7824	5008	,	,		17383	0.9167		0.6501	False		,,,				2504	0.5777				p.L4887L		Atlas-SNP	.											.	MDN1	478	.	0			c.C14661T						PASS	.	G		3139,1267	701.9+/-406.8	1130,879,194	182.0	172.0	176.0		14661	-8.6	0.8	6	dbSNP_119	176	5601,2999	665.5+/-402.3	1879,1843,578	no	coding-synonymous	MDN1	NM_014611.1		3009,2722,772	AA,AG,GG		34.8721,28.7562,32.8002		4887/5597	90371202	8740,4266	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon88			ACTGTCGAGGTTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14661C>T	6.37:g.90371202G>A		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	120	119	0.991667	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			G|0.286;A|0.714	0.714	strong		0.473	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
PDE4DIP	9659	hgsc.bcm.edu	37	1	145015976	145015976	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145015976C>T	ENST00000530740.1	-	3	363	c.325G>A	c.(325-327)Gtg>Atg	p.V109M	RP11-326G21.1_ENST00000610119.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.V109M|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.V109M|PDE4DIP_ENST00000493130.2_Missense_Mutation_p.V38M|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.V38M|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.V38M			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0				I -> M (in Ref. 1; BAB17759/BAB17760/ BAB17761/BAB17762 and 6; AAH25406/ AAI10295). {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)		TGTGACTGCACTGGAGGGCCT	0.423			T	PDGFRB	MPD																																p.V109M		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G325A						PASS	.																																			SO:0001583	missense	9659	exon3			ACTGCACTGGAGG	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.325G>A	1.37:g.145015976C>T	ENSP00000435654:p.Val109Met	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	214	30	0.140187	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		.	.	.	.	.	.	.	.	.	.	C	9.285	1.049170	0.19827	.	.	ENSG00000178104	ENST00000313382;ENST00000530740;ENST00000369359;ENST00000532801;ENST00000530078;ENST00000369348;ENST00000531369;ENST00000493130;ENST00000478649	T;T;T;T;T;T	0.49139	4.55;4.67;4.67;0.79;2.96;1.88	5.26	-0.476	0.12100	.	.	.	.	.	T	0.09905	0.0243	N	0.14661	0.345	0.09310	N	1	B;B;B	0.18863	0.007;0.004;0.031	B;B;B	0.14023	0.003;0.002;0.01	T	0.29610	-1.0006	9	0.36615	T	0.2	.	4.6702	0.12685	0.1441:0.2711:0.4924:0.0925	.	38;109;38	Q5VU43-3;E9PJ64;E9PQH9	.;.;.	M	38;109;109;38;38;109;39;38;38	ENSP00000327209:V38M;ENSP00000435654:V109M;ENSP00000358366:V109M;ENSP00000436751:V38M;ENSP00000358354:V109M;ENSP00000435616:V39M	ENSP00000327209:V38M	V	-	1	0	PDE4DIP	143727333	0.000000	0.05858	0.002000	0.10522	0.350000	0.29205	0.037000	0.13840	0.046000	0.15833	0.655000	0.94253	GTG	.	.	none		0.423	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
PSD4	23550	hgsc.bcm.edu	37	2	113940839	113940839	+	Missense_Mutation	SNP	G	G	C	rs4849167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113940839G>C	ENST00000245796.6	+	2	1001	c.806G>C	c.(805-807)gGg>gCg	p.G269A	PSD4_ENST00000441564.3_Missense_Mutation_p.G269A	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	269			G -> A (in dbSNP:rs4849167). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.		neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TTTTCCTGGGGGGCTTCAGAC	0.592													G|||	2589	0.516973	0.5272	0.5	5008	,	,		18291	0.6012		0.4423	False		,,,				2504	0.5051				p.G269A		Atlas-SNP	.											.	PSD4	74	.	0			c.G806C						PASS	.	G	ALA/GLY	2223,2183	591.5+/-387.6	561,1101,541	71.0	73.0	73.0		806	0.9	0.1	2	dbSNP_111	73	3507,5093	512.2+/-377.9	730,2047,1523	yes	missense	PSD4	NM_012455.2	60	1291,3148,2064	CC,CG,GG		40.7791,49.5461,44.0566	possibly-damaging	269/1057	113940839	5730,7276	2203	4300	6503	SO:0001583	missense	23550	exon2			CCTGGGGGGCTTC	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.806G>C	2.37:g.113940839G>C	ENSP00000245796:p.Gly269Ala	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	37	CCDS33276.1	1171	0.5361721611721612	283	0.5752032520325203	185	0.511049723756906	353	0.6171328671328671	350	0.46174142480211083	G	15.48	2.844789	0.51164	0.504539	0.407791	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.12255	2.76;2.7	5.83	0.861	0.19048	.	0.493472	0.20113	N	0.098974	T	0.00012	0.0000	L	0.27053	0.805	0.36052	P	0.159169	P;P	0.41524	0.753;0.639	B;B	0.37091	0.241;0.122	T	0.25082	-1.0142	8	.	.	.	.	5.1622	0.15068	0.3159:0.1389:0.5452:0.0	rs4849167;rs17846131;rs17859138;rs4849167	269;269	Q8NDX1-2;Q8NDX1	.;PSD4_HUMAN	A	269	ENSP00000245796:G269A;ENSP00000413997:G269A	.	G	+	2	0	PSD4	113657310	0.007000	0.16637	0.054000	0.19295	0.733000	0.41908	-0.260000	0.08708	-0.120000	0.11809	0.655000	0.94253	GGG	G|0.507;C|0.493	0.493	strong		0.592	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
CDHR5	53841	hgsc.bcm.edu	37	11	619322	619322	+	Silent	SNP	C	C	T	rs61732115	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:619322C>T	ENST00000358353.3	-	13	1684	c.1362G>A	c.(1360-1362)caG>caA	p.Q454Q	CDHR5_ENST00000349570.7_Silent_p.Q454Q|CDHR5_ENST00000397542.2_Silent_p.Q454Q			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	454	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043, ECO:0000305}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						AGGGGGGCTCCTGTTCGGAAA	0.612													C|||	61	0.0121805	0.0	0.0086	5008	,	,		15768	0.0		0.0179	False		,,,				2504	0.0378				p.Q454Q		Atlas-SNP	.											.	CDHR5	77	.	0			c.G1362A						PASS	.	C	,,	14,4390	22.3+/-47.3	0,14,2188	47.0	49.0	48.0		1362,1362,1362	1.9	0.0	11	dbSNP_129	48	179,8419	79.8+/-142.4	3,173,4123	no	coding-synonymous,coding-synonymous,coding-synonymous	CDHR5	NM_001171968.1,NM_021924.4,NM_031264.3	,,	3,187,6311	TT,TC,CC		2.0819,0.3179,1.4844	,,	454/840,454/846,454/652	619322	193,12809	2202	4299	6501	SO:0001819	synonymous_variant	53841	exon12			GGGCTCCTGTTCG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1362G>A	11.37:g.619322C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_031264	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Silent	SNP	ENST00000358353.3	37	CCDS7707.1																																																																																			C|0.986;T|0.014	0.014	strong		0.612	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
YWHAB	7529	hgsc.bcm.edu	37	20	43530234	43530234	+	Silent	SNP	A	A	C	rs4931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43530234A>C	ENST00000372839.3	+	3	334	c.60A>C	c.(58-60)cgA>cgC	p.R20R	YWHAB_ENST00000353703.4_Silent_p.R20R|YWHAB_ENST00000479421.1_3'UTR	NM_003404.3	NP_003395.1	P31946	1433B_HUMAN	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta	20					activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cytoplasmic sequestering of protein (GO:0051220)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|hippo signaling (GO:0035329)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|MAPK cascade (GO:0000165)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of protein dephosphorylation (GO:0035308)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of catalytic activity (GO:0043085)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein heterooligomerization (GO:0051291)|protein targeting (GO:0006605)|Ras protein signal transduction (GO:0007265)|RNA metabolic process (GO:0016070)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|phosphoprotein binding (GO:0051219)|phosphoserine binding (GO:0050815)|protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(1)	12		Myeloproliferative disorder(115;0.0122)				AGGCTGAGCGATATGATGATA	0.463													C|||	1505	0.300519	0.5514	0.1916	5008	,	,		19591	0.1409		0.2903	False		,,,				2504	0.2137				p.R20R		Atlas-SNP	.											.	YWHAB	24	.	0			c.A60C						PASS	.	C	,	2198,2208	582.3+/-385.5	563,1072,568	69.0	68.0	68.0		60,60	3.7	1.0	20	dbSNP_52	68	2573,6027	679.4+/-403.5	410,1753,2137	no	coding-synonymous,coding-synonymous	YWHAB	NM_003404.3,NM_139323.2	,	973,2825,2705	CC,CA,AA		29.9186,49.8865,36.6831	,	20/247,20/247	43530234	4771,8235	2203	4300	6503	SO:0001819	synonymous_variant	7529	exon3			TGAGCGATATGAT	X57346	CCDS13339.1	20q13.1	2013-12-03	2013-12-03		ENSG00000166913	ENSG00000166913			12849	protein-coding gene	gene with protein product	"""14-3-3 beta"", ""14-3-3 alpha"""	601289	"""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, alpha polypeptide"", ""tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide"""	YWHAA		8617504, 7890696	Standard	NM_003404		Approved		uc002xmu.3	P31946	OTTHUMG00000032549	ENST00000372839.3:c.60A>C	20.37:g.43530234A>C		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_003404	A8K9K2|E1P616	Silent	SNP	ENST00000372839.3	37	CCDS13339.1																																																																																			A|0.659;C|0.340;G|0.000;T|0.000	0.340	strong		0.463	YWHAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079386.3	NM_003404	
ZNF844	284391	hgsc.bcm.edu	37	19	12186148	12186148	+	Silent	SNP	T	T	C	rs10424893	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12186148T>C	ENST00000439326.3	+	4	388	c.213T>C	c.(211-213)gtT>gtC	p.V71V	ZNF844_ENST00000441304.2_Missense_Mutation_p.L51S	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	71	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GAGAGAGAGTTGATGAAAATA	0.333													.|||	1421	0.283746	0.7035	0.1455	5008	,	,		15619	0.0863		0.161	False		,,,				2504	0.1442				p.V71V		Atlas-SNP	.											ZNF844,NS,NS,+2,1	ZNF844	69	1	0			c.T213C						PASS	.	C		839,545		256,327,109	64.0	61.0	62.0		213	-0.9	0.0	19	dbSNP_119	62	416,2766		25,366,1200	no	coding-synonymous	ZNF844	NM_001136501.1		281,693,1309	CC,CT,TT		13.0735,39.3786,27.4858		71/667	12186148	1255,3311	692	1591	2283	SO:0001819	synonymous_variant	284391	exon4			GAGAGTTGATGAA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.213T>C	19.37:g.12186148T>C		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	29	19	0.655172	NM_001136501	Q5JPI8	Silent	SNP	ENST00000439326.3	37	CCDS45985.1	553	0.2532051282051282	319	0.6483739837398373	53	0.1464088397790055	54	0.0944055944055944	127	0.16754617414248021	t	0.777	-0.763841	0.02996	0.606214	0.130735	ENSG00000223547	ENST00000441304	T	0.01821	4.62	1.56	-0.936	0.10419	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.04551	-1.0943	5	0.45353	T	0.12	.	3.1725	0.06558	0.3397:0.4089:0.0:0.2514	rs10424893;rs10424893	.	.	.	S	51	ENSP00000402097:L51S	ENSP00000402097:L51S	L	+	2	0	ZNF844	12047148	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.757000	0.04772	-0.637000	0.05516	-1.222000	0.01597	TTG	T|0.725;C|0.275	0.275	strong		0.333	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
IL12RB1	3594	hgsc.bcm.edu	37	19	18188408	18188408	+	Missense_Mutation	SNP	C	C	T	rs11575926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18188408C>T	ENST00000600835.2	-	6	765	c.467G>A	c.(466-468)cGt>cAt	p.R156H	IL12RB1_ENST00000322153.7_Missense_Mutation_p.R156H|IL12RB1_ENST00000593993.2_Missense_Mutation_p.R156H			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	156	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H (in dbSNP:rs11575926). {ECO:0000269|Ref.3}.		cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						CCACTCCATACGCAGCTGCCC	0.582													C|||	280	0.0559105	0.0068	0.0692	5008	,	,		16517	0.001		0.1551	False		,,,				2504	0.0675				p.R156H		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G467A						PASS	.	C	HIS/ARG,HIS/ARG	158,4248	107.8+/-146.2	3,152,2048	65.0	54.0	58.0		467,467	-7.8	0.0	19	dbSNP_120	58	1494,7106	283.3+/-296.1	127,1240,2933	no	missense,missense	IL12RB1	NM_005535.1,NM_153701.1	29,29	130,1392,4981	TT,TC,CC		17.3721,3.586,12.7018	benign,benign	156/663,156/382	18188408	1652,11354	2203	4300	6503	SO:0001583	missense	3594	exon5			TCCATACGCAGCT	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.467G>A	19.37:g.18188408C>T	ENSP00000470788:p.Arg156His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	146	0.06684981684981685	2	0.0040650406504065045	26	0.0718232044198895	1	0.0017482517482517483	117	0.15435356200527706	C	9.619	1.133424	0.21041	0.03586	0.173721	ENSG00000096996	ENST00000430026;ENST00000322153	T;D	0.85955	-1.49;-2.05	3.9	-7.79	0.01218	Immunoglobulin-like fold (1);	1.817980	0.03453	N	0.210996	T	0.00440	0.0014	L	0.29908	0.895	0.09310	N	1	B;B;B	0.29862	0.025;0.259;0.014	B;B;B	0.17433	0.007;0.018;0.003	T	0.18023	-1.0350	10	0.30854	T	0.27	-1.1907	6.7248	0.23350	0.6568:0.1478:0.0:0.1953	rs11575926;rs17884715	156;156;156	P42701-2;P42701-3;P42701	.;.;I12R1_HUMAN	H	156	ENSP00000403103:R156H;ENSP00000314425:R156H	ENSP00000314425:R156H	R	-	2	0	IL12RB1	18049408	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	-1.507000	0.02268	-1.510000	0.01796	-0.302000	0.09304	CGT	C|0.900;T|0.100	0.100	strong		0.582	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
RFX7	64864	hgsc.bcm.edu	37	15	56387859	56387859	+	Silent	SNP	T	T	C	rs3803459	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:56387859T>C	ENST00000559447.2	-	9	2047	c.1776A>G	c.(1774-1776)aaA>aaG	p.K592K	RFX7_ENST00000422057.1_Silent_p.K592K|RFX7_ENST00000423270.1_Silent_p.K689K|RFX7_ENST00000317318.6_Silent_p.K689K			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	592					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CACTGCCTTGTTTCTGCCCTT	0.453													T|||	1140	0.227636	0.0635	0.1513	5008	,	,		22128	0.494		0.1123	False		,,,				2504	0.3476				p.K689K		Atlas-SNP	.											.	RFX7	170	.	0			c.A2067G						PASS	.	T		330,3478		13,304,1587	121.0	112.0	115.0		2067	2.1	1.0	15	dbSNP_107	115	1063,7185		72,919,3133	no	coding-synonymous	RFX7	NM_022841.5		85,1223,4720	CC,CT,TT		12.888,8.666,11.5544		689/1461	56387859	1393,10663	1904	4124	6028	SO:0001819	synonymous_variant	64864	exon9			GCCTTGTTTCTGC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1776A>G	15.37:g.56387859T>C		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	172	88	0.511628	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				T|0.799;C|0.201	0.201	strong		0.453	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
UNC5B	219699	hgsc.bcm.edu	37	10	73051388	73051388	+	Silent	SNP	T	T	C	rs3740460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:73051388T>C	ENST00000335350.6	+	10	1910	c.1494T>C	c.(1492-1494)gaT>gaC	p.D498D	UNC5B_ENST00000373192.4_Silent_p.D487D	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	498					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						GCCTGGCAGATGGGGCTGACC	0.642													t|||	972	0.194089	0.2088	0.1657	5008	,	,		17689	0.2014		0.1272	False		,,,				2504	0.2556				p.D498D		Atlas-SNP	.											.	UNC5B	123	.	0			c.T1494C						PASS	.			794,3612	318.8+/-295.8	78,638,1487	53.0	54.0	54.0		1494	-8.5	0.4	10	dbSNP_107	54	1056,7544	223.7+/-260.4	62,932,3306	no	coding-synonymous	UNC5B	NM_170744.4		140,1570,4793	CC,CT,TT		12.2791,18.0209,14.2242		498/946	73051388	1850,11156	2203	4300	6503	SO:0001819	synonymous_variant	219699	exon10			GGCAGATGGGGCT	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.1494T>C	10.37:g.73051388T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			T|0.845;C|0.155	0.155	strong		0.642	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
SPECC1	92521	hgsc.bcm.edu	37	17	20107773	20107773	+	Silent	SNP	T	T	C	rs2703805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:20107773T>C	ENST00000261503.5	+	4	462	c.411T>C	c.(409-411)tcT>tcC	p.S137S	AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395529.3_Silent_p.S137S|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395525.3_Silent_p.S56S|SPECC1_ENST00000395522.2_Silent_p.S56S|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395530.2_Silent_p.S56S|SPECC1_ENST00000584527.1_5'Flank|SPECC1_ENST00000395527.4_Silent_p.S137S	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	137					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)		GTCCAACTTCTTCCAACACTC	0.532													T|||	2704	0.539936	0.4062	0.4741	5008	,	,		16850	0.7937		0.3996	False		,,,				2504	0.6503				p.S137S		Atlas-SNP	.											.	SPECC1	100	.	0			c.T411C						PASS	.	T	,,,	1757,2649	522.7+/-370.9	350,1057,796	155.0	156.0	156.0		411,168,168,411	-4.4	0.4	17	dbSNP_100	156	3422,5178	505.0+/-376.3	687,2048,1565	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPECC1	NM_001033553.2,NM_001033554.2,NM_001033555.2,NM_152904.4	,,,	1037,3105,2361	CC,CT,TT		39.7907,39.8774,39.8201	,,,	137/1069,56/710,56/988,137/791	20107773	5179,7827	2203	4300	6503	SO:0001819	synonymous_variant	92521	exon4			AACTTCTTCCAAC	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.411T>C	17.37:g.20107773T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	117	62	0.529915	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																			T|0.550;C|0.450	0.450	strong		0.532	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
SPAG11A	653423	hgsc.bcm.edu	37	8	7718187	7718187	+	Nonstop_Mutation	SNP	T	T	G	rs3177011	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:7718187T>G	ENST00000434307.2	+	4	477	c.310T>G	c.(310-312)Tag>Gag	p.*104E	SPAG11A_ENST00000351436.4_Intron|SPAG11A_ENST00000326558.5_Missense_Mutation_p.I78M|SPAG11A_ENST00000326625.5_Missense_Mutation_p.I25M|SPAG11A_ENST00000454911.2_Nonstop_Mutation_p.*51E			Q6PDA7	SG11A_HUMAN	sperm associated antigen 11A	0						extracellular region (GO:0005576)				central_nervous_system(1)|lung(2)	3				COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.236)		CACTGGGAATTAGAAATACCA	0.448													T|||	2010	0.401358	0.1846	0.5865	5008	,	,		22837	0.4673		0.4394	False		,,,				2504	0.456				p.I78M		Atlas-SNP	.											.	SPAG11A	6	.	0			c.T234G						PASS	.	T	MET/ILE	919,3453		90,739,1357	149.0	114.0	126.0		234	-1.5	0.4	8	dbSNP_105	126	3796,4782		881,2034,1374	no	missense	SPAG11A	NM_001081552.2	10	971,2773,2731	GG,GT,TT		44.2527,21.0201,36.4093		78/109	7718187	4715,8235	2186	4289	6475	SO:0001578	stop_lost	653423	exon3			GGGAATTAGAAAT		CCDS43700.1	8p23.1	2009-09-12	2007-03-15		ENSG00000178287	ENSG00000178287			33342	protein-coding gene	gene with protein product	"""epididymal protein 2A"""						Standard	NM_001081552		Approved	HE2, EDDM2A		Q6PDA7	OTTHUMG00000162440	ENST00000434307.2:c.310T>G	8.37:g.7718187T>G	ENSP00000416991:p.*104Gluext*20	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	58	51	0.87931	NM_001081552	A6NIY0|E9PAK7	Missense_Mutation	SNP	ENST00000434307.2	37		793|793	0.3630952380952381|0.3630952380952381	85|85	0.17276422764227642|0.17276422764227642	189|189	0.5220994475138122|0.5220994475138122	224|224	0.3916083916083916|0.3916083916083916	295|295	0.3891820580474934|0.3891820580474934	T|T	0.003|0.003	-2.536925|-2.536925	0.00143|0.00143	0.210201|0.210201	0.442527|0.442527	ENSG00000178287|ENSG00000178287	ENST00000326558;ENST00000326625|ENST00000434307;ENST00000454911	.|.	.|.	.|.	2.28|2.28	-1.48|-1.48	0.08745|0.08745	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.58432|0.58432	P|P	2.9999999999752447E-6|2.9999999999752447E-6	P;D|.	0.64830|.	0.815;0.994|.	B;D|.	0.79784|.	0.316;0.993|.	T|.	0.47761|.	-0.9092|.	6|.	0.52906|.	T|.	0.07|.	-18.7851|-18.7851	5.8795|5.8795	0.18848|0.18848	0.0:0.5425:0.0:0.4575|0.0:0.5425:0.0:0.4575	rs3177011;rs11555590;rs17846564;rs17859642;rs3177011|rs3177011;rs11555590;rs17846564;rs17859642;rs3177011	78;78|.	Q6PDA7-2;C9JN37|.	.;.|.	M|E	78;25|104;51	.|.	ENSP00000316012:I78M|.	I|X	+|+	3|1	3|0	SPAG11A|SPAG11A	7755597|7755597	0.978000|0.978000	0.34361|0.34361	0.406000|0.406000	0.26421|0.26421	0.075000|0.075000	0.17131|0.17131	-0.344000|-0.344000	0.07780|0.07780	-0.359000|-0.359000	0.08150|0.08150	0.329000|0.329000	0.21502|0.21502	ATT|TAG	T|0.650;G|0.350	0.350	strong		0.448	SPAG11A-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000383798.1	NM_001081552	
ZNF33A	7581	hgsc.bcm.edu	37	10	38344895	38344895	+	Missense_Mutation	SNP	G	G	A	rs12256916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38344895G>A	ENST00000458705.2	+	5	1998	c.1840G>A	c.(1840-1842)Gga>Aga	p.G614R	ZNF33A_ENST00000307441.9_Missense_Mutation_p.G614R|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Missense_Mutation_p.G621R|ZNF33A_ENST00000374618.3_Missense_Mutation_p.G615R			Q06730	ZN33A_HUMAN	zinc finger protein 33A	614			G -> R (in dbSNP:rs12256916).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						TAATGAATGTGGAAAAGCCTT	0.368													G|||	140	0.0279553	0.0915	0.013	5008	,	,		20194	0.0		0.0099	False		,,,				2504	0.0				p.G615R		Atlas-SNP	.											.	ZNF33A	103	.	0			c.G1843A						PASS	.	G	ARG/GLY,ARG/GLY	363,4043	184.7+/-212.0	19,325,1859	75.0	74.0	74.0		1843,1840	1.7	1.0	10	dbSNP_120	74	54,8546	34.3+/-88.2	0,54,4246	no	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	125,125	19,379,6105	AA,AG,GG		0.6279,8.2388,3.2062	probably-damaging,probably-damaging	615/812,614/811	38344895	417,12589	2203	4300	6503	SO:0001583	missense	7581	exon5			GAATGTGGAAAAG	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1840G>A	10.37:g.38344895G>A	ENSP00000387713:p.Gly614Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	50	0.022893772893772892	35	0.07113821138211382	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	14.71	2.615327	0.46631	0.082388	0.006279	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.01484	4.84;4.84;4.84;4.84	1.69	1.69	0.24217	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34386	N	0.004010	T	0.00468	0.0015	M	0.85373	2.75	0.31075	N	0.712553	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.77004	0.981;0.989;0.859	T	0.00756	-1.1579	10	0.56958	D	0.05	.	8.8982	0.35479	0.0:0.0:1.0:0.0	rs12256916;rs52814973;rs12256916	621;614;615	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	R	615;621;614;614	ENSP00000363747:G615R;ENSP00000402467:G621R;ENSP00000387713:G614R;ENSP00000304268:G614R	ENSP00000304268:G614R	G	+	1	0	ZNF33A	38384901	1.000000	0.71417	0.998000	0.56505	0.725000	0.41563	4.320000	0.59203	0.902000	0.36520	0.313000	0.20887	GGA	G|0.970;A|0.030	0.030	strong		0.368	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
ZSCAN32	54925	hgsc.bcm.edu	37	16	3434699	3434699	+	Missense_Mutation	SNP	A	A	G	rs27230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3434699A>G	ENST00000396852.4	-	6	1301	c.994T>C	c.(994-996)Tat>Cat	p.Y332H	ZSCAN32_ENST00000573830.1_Missense_Mutation_p.Y43H|ZSCAN32_ENST00000396846.3_Missense_Mutation_p.Y332H|ZSCAN32_ENST00000439568.2_Missense_Mutation_p.Y43H|ZSCAN32_ENST00000304926.3_Missense_Mutation_p.Y120H|NAA60_ENST00000576906.1_3'UTR|ZSCAN32_ENST00000574940.1_Missense_Mutation_p.Y332H|ZSCAN32_ENST00000422427.2_Missense_Mutation_p.Y120H	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	332			Y -> H (in dbSNP:rs27230).		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)										ATTTCCTCATAAAAGATACAA	0.512													A|||	329	0.0656949	0.0091	0.1196	5008	,	,		21176	0.0		0.1779	False		,,,				2504	0.0562				p.Y120H		Atlas-SNP	.											.	.	.	.	0			c.T358C						PASS	.	A	HIS/TYR	162,4232	106.9+/-145.3	5,152,2040	131.0	134.0	133.0		358	0.6	0.0	16	dbSNP_76	133	1605,6995	299.7+/-304.6	159,1287,2854	yes	missense	ZNF434	NM_017810.2	83	164,1439,4894	GG,GA,AA		18.6628,3.6868,13.5986	possibly-damaging	120/486	3434699	1767,11227	2197	4300	6497	SO:0001583	missense	54925	exon5			CCTCATAAAAGAT	AK000424	CCDS10503.1, CCDS66920.1, CCDS66921.1	16p13.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000140987	ENSG00000140987		"""-"", ""Zinc fingers, C2H2-type"""	20812	protein-coding gene	gene with protein product			"""zinc finger protein 434"""	ZNF434			Standard	XM_005255402		Approved	FLJ20417	uc002cux.4	Q9NX65	OTTHUMG00000129357	ENST00000396852.4:c.994T>C	16.37:g.3434699A>G	ENSP00000380061:p.Tyr332His	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	205	107	0.521951	NM_017810	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Missense_Mutation	SNP	ENST00000396852.4	37		189	0.08653846153846154	5	0.01016260162601626	44	0.12154696132596685	0	0.0	140	0.18469656992084432	A	13.81	2.346838	0.41599	0.036868	0.186628	ENSG00000140987	ENST00000304926;ENST00000396852;ENST00000396846;ENST00000439568;ENST00000422427	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	3.02	0.563	0.17296	.	0.630262	0.11876	N	0.521018	T	0.00178	0.0005	M	0.86651	2.83	0.80722	P	0.0	P;B;B	0.44776	0.843;0.001;0.001	P;B;B	0.58391	0.838;0.008;0.008	T	0.06972	-1.0797	9	0.30854	T	0.27	.	3.4475	0.07486	0.6302:0.233:0.1368:0.0	rs27230;rs17691164;rs57730795;rs27230	120;120;332	B4DR24;Q9NX65;Q6WMU8	.;ZN434_HUMAN;.	H	120;332;332;43;120	ENSP00000302502:Y120H;ENSP00000380061:Y332H;ENSP00000380057:Y332H;ENSP00000391787:Y43H;ENSP00000407312:Y120H	ENSP00000302502:Y120H	Y	-	1	0	ZNF434	3374700	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.419000	0.07071	-0.156000	0.11079	0.533000	0.62120	TAT	A|0.885;G|0.115	0.115	strong		0.512	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2	NM_017810	
SYCE3	644186	hgsc.bcm.edu	37	22	50989742	50989742	+	Missense_Mutation	SNP	C	C	T	rs55829948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50989742C>T	ENST00000406915.3	-	3	246	c.199G>A	c.(199-201)Gtc>Atc	p.V67I	SYCE3_ENST00000402753.1_Missense_Mutation_p.V67I	NM_001123225.1	NP_001116697.1	A1L190	SYCE3_HUMAN	synaptonemal complex central element protein 3	67					positive regulation of apoptotic process (GO:0043065)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|chromosome (GO:0005694)|nucleus (GO:0005634)				endometrium(1)|kidney(1)	2						TTGCAGTTGACGAAGGCATCC	0.602													C|||	9	0.00179712	0.0	0.0	5008	,	,		20192	0.0		0.008	False		,,,				2504	0.001				p.V67I		Atlas-SNP	.											.	SYCE3	10	.	0			c.G199A						PASS	.	C	ILE/VAL	4,1380		0,4,688	50.0	50.0	50.0		199	2.4	1.0	22	dbSNP_129	50	21,3161		0,21,1570	yes	missense	C22orf41	NM_001123225.1	29	0,25,2258	TT,TC,CC		0.66,0.289,0.5475	benign	67/89	50989742	25,4541	692	1591	2283	SO:0001583	missense	644186	exon3			AGTTGACGAAGGC		CCDS46733.1	22q13.33	2011-10-05	2011-10-05	2011-10-05	ENSG00000217442	ENSG00000217442			35245	protein-coding gene	gene with protein product	"""testis highly expressed protein 2"""	615775	"""chromosome 22 open reading frame 41"""	C22orf41		21637789	Standard	NM_001123225		Approved		uc010hbe.3	A1L190	OTTHUMG00000150273	ENST00000406915.3:c.199G>A	22.37:g.50989742C>T	ENSP00000385480:p.Val67Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_001123225		Missense_Mutation	SNP	ENST00000406915.3	37	CCDS46733.1	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	C	11.45	1.643125	0.29246	0.00289	0.0066	ENSG00000217442	ENST00000406915;ENST00000402753	T;T	0.42900	0.96;0.96	6.04	2.36	0.29203	.	.	.	.	.	T	0.19485	0.0468	.	.	.	0.20638	N	0.999879	B	0.23058	0.079	B	0.11329	0.006	T	0.12630	-1.0540	8	0.38643	T	0.18	-0.1893	6.0115	0.19578	0.2341:0.1521:0.6138:0.0	rs55829948	67	A1L190	SYCE3_HUMAN	I	67	ENSP00000385480:V67I;ENSP00000385122:V67I	ENSP00000385122:V67I	V	-	1	0	C22orf41	49336608	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	2.037000	0.41174	0.892000	0.36259	-0.270000	0.10280	GTC	C|0.995;T|0.005	0.005	strong		0.602	SYCE3-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317660.1	NM_001123225	
ATR	545	hgsc.bcm.edu	37	3	142277575	142277575	+	Silent	SNP	A	A	T	rs2227930	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142277575A>T	ENST00000350721.4	-	8	1897	c.1776T>A	c.(1774-1776)ggT>ggA	p.G592G	ATR_ENST00000383101.3_Silent_p.G528G	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	592					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G592G(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GTGAGAGCATACCACATAAAT	0.333								Other conserved DNA damage response genes					T|||	2995	0.598043	0.8533	0.5058	5008	,	,		12509	0.4732		0.5865	False		,,,				2504	0.4591				p.G592G		Atlas-SNP	.											ATR,NS,carcinoma,0,1	ATR	285	1	1	Substitution - coding silent(1)	stomach(1)	c.T1776A						scavenged	.	T		3506,900	347.2+/-309.4	1397,712,94	205.0	217.0	213.0		1776	1.8	1.0	3	dbSNP_98	213	5117,3483	510.5+/-377.5	1497,2123,680	no	coding-synonymous	ATR	NM_001184.3		2894,2835,774	TT,TA,AA		40.5,20.4267,33.6998		592/2645	142277575	8623,4383	2203	4300	6503	SO:0001819	synonymous_variant	545	exon8			GAGCATACCACAT	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.1776T>A	3.37:g.142277575A>T		Somatic	181	2	0.0110497		WXS	Illumina HiSeq	Phase_I	190	101	0.531579	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Silent	SNP	ENST00000350721.4	37	CCDS3124.1																																																																																			A|0.359;T|0.641	0.641	strong		0.333	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
EIF2A	83939	hgsc.bcm.edu	37	3	150285520	150285520	+	Silent	SNP	T	T	C	rs2293151	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:150285520T>C	ENST00000460851.1	+	7	625	c.516T>C	c.(514-516)gaT>gaC	p.D172D	SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000383043.3_5'Flank|EIF2A_ENST00000406576.3_Silent_p.D111D|EIF2A_ENST00000487799.1_Silent_p.D147D|SERP1_ENST00000479209.1_Intron|EIF2A_ENST00000273435.5_Silent_p.D167D			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	172					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			AAATTAATGATTTTGTATTAT	0.279													T|||	597	0.119209	0.1619	0.1441	5008	,	,		20121	0.0208		0.1581	False		,,,				2504	0.1053				p.D172D		Atlas-SNP	.											.	EIF2A	59	.	0			c.T516C						PASS	.	T		531,3049		33,465,1292	72.0	63.0	65.0		516	3.6	1.0	3	dbSNP_100	65	1227,6867		110,1007,2930	no	coding-synonymous	EIF2A	NM_032025.3		143,1472,4222	CC,CT,TT		15.1594,14.8324,15.0591		172/586	150285520	1758,9916	1790	4047	5837	SO:0001819	synonymous_variant	83939	exon7			TAATGATTTTGTA	AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.516T>C	3.37:g.150285520T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	206	103	0.5	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	37	CCDS46935.1																																																																																			T|0.885;C|0.115	0.115	strong		0.279	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
EGFLAM	133584	hgsc.bcm.edu	37	5	38370537	38370537	+	Missense_Mutation	SNP	T	T	C	rs1465567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:38370537T>C	ENST00000354891.3	+	6	1031	c.685T>C	c.(685-687)Tgg>Cgg	p.W229R	EGFLAM_ENST00000322350.5_Missense_Mutation_p.W229R	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	229	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		W -> R (in dbSNP:rs1465567).		extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)	p.W229R(1)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					CCCCCGCAGCTGGCCCAGTGA	0.567													T|||	1288	0.257188	0.4372	0.1354	5008	,	,		17182	0.1796		0.2038	False		,,,				2504	0.2352				p.W229R	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											EGFLAM,NS,carcinoma,0,1	EGFLAM	302	1	1	Substitution - Missense(1)	stomach(1)	c.T685C						PASS	.	T	ARG/TRP,ARG/TRP	1746,2660	520.6+/-370.3	349,1048,806	43.0	42.0	42.0		685,685	-2.0	0.0	5	dbSNP_88	42	1663,6937	305.6+/-307.5	175,1313,2812	yes	missense,missense	EGFLAM	NM_001205301.1,NM_152403.3	101,101	524,2361,3618	CC,CT,TT		19.3372,39.6278,26.211	benign,benign	229/1018,229/1010	38370537	3409,9597	2203	4300	6503	SO:0001583	missense	133584	exon6			CGCAGCTGGCCCA	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.685T>C	5.37:g.38370537T>C	ENSP00000346964:p.Trp229Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	565	0.2586996336996337	239	0.48577235772357724	58	0.16022099447513813	118	0.2062937062937063	150	0.19788918205804748	T	7.093	0.572574	0.13623	0.396278	0.193372	ENSG00000164318	ENST00000354891;ENST00000322350	T;T	0.52057	0.68;0.68	5.82	-2.02	0.07388	Fibronectin, type III (2);Immunoglobulin-like fold (1);	2.059790	0.01504	N	0.017616	T	0.00012	0.0000	N	0.01761	-0.735	0.53688	P	2.6999999999999247E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.35847	-0.9772	9	0.06625	T	0.88	-0.0747	5.516	0.16906	0.0841:0.6017:0.2313:0.083	rs1465567;rs1465567	229;229	Q63HQ2;Q63HQ2-2	EGFLA_HUMAN;.	R	229	ENSP00000346964:W229R;ENSP00000313084:W229R	ENSP00000313084:W229R	W	+	1	0	EGFLAM	38406294	0.000000	0.05858	0.016000	0.15963	0.941000	0.58515	-0.353000	0.07691	-0.389000	0.07786	-0.379000	0.06801	TGG	T|0.741;C|0.259	0.259	strong		0.567	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
AGBL1	123624	hgsc.bcm.edu	37	15	86702241	86702241	+	Missense_Mutation	SNP	C	C	T	rs79814209	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:86702241C>T	ENST00000441037.2	+	4	429	c.334C>T	c.(334-336)Cgc>Tgc	p.R112C	AGBL1_ENST00000421325.2_Missense_Mutation_p.R112C	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	112					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						CACCCGAAAGCGCACCCAAGC	0.438													C|||	73	0.0145767	0.0	0.0086	5008	,	,		20806	0.0		0.0408	False		,,,				2504	0.0266				p.R112C		Atlas-SNP	.											.	AGBL1	151	.	0			c.C334T						PASS	.	C	CYS/ARG	35,3831		0,35,1898	126.0	116.0	119.0		334	4.1	0.0	15	dbSNP_131	119	347,7925		5,337,3794	yes	missense	AGBL1	NM_152336.2	180	5,372,5692	TT,TC,CC		4.1949,0.9053,3.1471	probably-damaging	112/1067	86702241	382,11756	1933	4136	6069	SO:0001583	missense	123624	exon4			CGAAAGCGCACCC	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.334C>T	15.37:g.86702241C>T	ENSP00000413001:p.Arg112Cys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	31	0.014194139194139194	0	0.0	1	0.0027624309392265192	0	0.0	30	0.0395778364116095	C	8.492	0.862235	0.17178	0.009053	0.041949	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.35236	1.32	5.01	4.08	0.47627	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.11879	0.0289	L	0.47716	1.5	0.23070	N	0.998347	D	0.64830	0.994	P	0.47744	0.556	T	0.02774	-1.1112	9	0.54805	T	0.06	-2.3402	11.7532	0.51859	0.0:0.8222:0.1778:0.0	.	112	Q96MI9	CBPC4_HUMAN	C	141;112	ENSP00000397173:R112C	ENSP00000397173:R112C	R	+	1	0	AGBL1	84503245	0.718000	0.27976	0.019000	0.16419	0.054000	0.15201	1.328000	0.33758	1.218000	0.43458	0.655000	0.94253	CGC	C|0.980;T|0.020	0.020	strong		0.438	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
OR8B4	283162	hgsc.bcm.edu	37	11	124294127	124294127	+	Missense_Mutation	SNP	A	A	G	rs370187249		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124294127A>G	ENST00000356130.3	-	1	662	c.641T>C	c.(640-642)gTc>gCc	p.V214A		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GTAAGAGATGACGATGCTTAT	0.483																																					p.V214A		Atlas-SNP	.											OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	0			c.T641C						PASS	.	A	ALA/VAL	0,4402		0,0,2201	89.0	75.0	80.0		641	1.8	0.4	11		80	1,8597		0,1,4298	no	missense	OR8B4	NM_001005196.1	64	0,1,6499	GG,GA,AA		0.0116,0.0,0.0077	benign	214/310	124294127	1,12999	2201	4299	6500	SO:0001583	missense	283162	exon1			GAGATGACGATGC	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.641T>C	11.37:g.124294127A>G	ENSP00000348449:p.Val214Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	5.431	0.264595	0.10294	0.0	1.16E-4	ENSG00000198657	ENST00000356130	T	0.00272	8.36	4.14	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	0.367346	0.23494	N	0.047561	T	0.00178	0.0005	L	0.33792	1.035	0.09310	N	1	B	0.16603	0.018	B	0.22601	0.04	T	0.40213	-0.9575	10	0.87932	D	0	.	6.2461	0.20818	0.7765:0.0:0.0809:0.1426	.	214	Q96RC9	OR8B4_HUMAN	A	214	ENSP00000348449:V214A	ENSP00000348449:V214A	V	-	2	0	OR8B4	123799337	0.019000	0.18553	0.397000	0.26308	0.088000	0.18126	2.931000	0.48932	0.389000	0.25086	0.533000	0.62120	GTC	.	.	weak		0.483	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
PLCG2	5336	hgsc.bcm.edu	37	16	81888152	81888152	+	Silent	SNP	A	A	G	rs1143686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81888152A>G	ENST00000359376.3	+	3	511	c.297A>G	c.(295-297)ctA>ctG	p.L99L	PLCG2_ENST00000565400.1_3'UTR	NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	99	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						TCACCATCCTATATGGCACTC	0.483													G|||	1062	0.212061	0.1415	0.2853	5008	,	,		21919	0.0625		0.3111	False		,,,				2504	0.3078				p.L99L		Atlas-SNP	.											.	PLCG2	276	.	0			c.A297G						PASS	.	G		656,3564		55,546,1509	166.0	174.0	171.0		297	-11.3	0.1	16	dbSNP_86	171	2588,5878		414,1760,2059	no	coding-synonymous	PLCG2	NM_002661.3		469,2306,3568	GG,GA,AA		30.5693,15.545,25.5715		99/1266	81888152	3244,9442	2110	4233	6343	SO:0001819	synonymous_variant	5336	exon3			CATCCTATATGGC		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.297A>G	16.37:g.81888152A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			A|0.791;G|0.209	0.209	strong		0.483	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
RASAL1	8437	hgsc.bcm.edu	37	12	113542098	113542098	+	Silent	SNP	A	A	G	rs12423570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113542098A>G	ENST00000261729.5	-	18	2148	c.1833T>C	c.(1831-1833)tgT>tgC	p.C611C	RASAL1_ENST00000548055.1_Silent_p.C612C|RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000546530.1_Silent_p.C613C|RASAL1_ENST00000446861.3_Intron			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	611	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						GGATGGAGTGACACATCTGGG	0.652													g|||	316	0.063099	0.0348	0.0879	5008	,	,		12690	0.0		0.1521	False		,,,				2504	0.0573				p.C613C		Atlas-SNP	.											.	RASAL1	89	.	0			c.T1839C						PASS	.	T	,,	252,4136		8,236,1950	12.0	10.0	11.0		1839,,1833	-3.1	0.0	12	dbSNP_120	11	1205,7375		92,1021,3177	no	coding-synonymous,intron,coding-synonymous	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	,,	100,1257,5127	GG,GA,AA		14.0443,5.7429,11.2353	,,	613/807,,611/805	113542098	1457,11511	2194	4290	6484	SO:0001819	synonymous_variant	8437	exon18			GGAGTGACACATC	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.1833T>C	12.37:g.113542098A>G		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	188	84	0.446809	NM_001193520	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Silent	SNP	ENST00000261729.5	37	CCDS9165.1																																																																																			A|0.911;G|0.089	0.089	strong		0.652	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
CDH20	28316	hgsc.bcm.edu	37	18	59174759	59174759	+	Missense_Mutation	SNP	C	C	A	rs1943330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:59174759C>A	ENST00000262717.4	+	6	1381	c.983C>A	c.(982-984)cCc>cAc	p.P328H	CDH20_ENST00000538374.1_Missense_Mutation_p.P328H|CDH20_ENST00000536675.2_Missense_Mutation_p.P328H			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	328	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> H (in dbSNP:rs1943330).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				AGCACAGATCCCAATTTCCAA	0.393													C|||	297	0.0593051	0.0121	0.0793	5008	,	,		17704	0.0317		0.1461	False		,,,				2504	0.0481				p.P328H		Atlas-SNP	.											CDH20,right_upper_lobe,carcinoma,-1,1	CDH20	117	1	0			c.C983A						PASS	.	C	HIS/PRO	124,4282	92.0+/-130.7	1,122,2080	167.0	141.0	150.0		983	4.9	1.0	18	dbSNP_92	150	1220,7380	246.1+/-274.7	87,1046,3167	yes	missense	CDH20	NM_031891.2	77	88,1168,5247	AA,AC,CC		14.186,2.8143,10.3337	probably-damaging	328/802	59174759	1344,11662	2203	4300	6503	SO:0001583	missense	28316	exon5			CAGATCCCAATTT	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.983C>A	18.37:g.59174759C>A	ENSP00000262717:p.Pro328His	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	165	0.07554945054945054	10	0.02032520325203252	33	0.09116022099447514	18	0.03146853146853147	104	0.13720316622691292	C	16.95	3.263748	0.59431	0.028143	0.14186	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.53640	0.61;0.61;0.61	5.76	4.89	0.63831	Cadherin (4);Cadherin-like (1);	0.053678	0.85682	D	0.000000	T	0.01156	0.0038	M	0.81341	2.54	0.22581	P	0.99896011	D	0.76494	0.999	D	0.73708	0.981	T	0.14504	-1.0470	9	0.52906	T	0.07	.	16.4267	0.83816	0.132:0.868:0.0:0.0	rs1943330;rs17749069;rs52809328;rs57072012;rs1943330	328	Q9HBT6	CAD20_HUMAN	H	328	ENSP00000444767:P328H;ENSP00000442226:P328H;ENSP00000262717:P328H	ENSP00000262717:P328H	P	+	2	0	CDH20	57325739	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.904000	0.56325	1.411000	0.46957	0.555000	0.69702	CCC	C|0.911;A|0.089	0.089	strong		0.393	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592312	1592312	+	Intron	SNP	T	T	C	rs72484087	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1592312T>C	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Missense_Mutation_p.I42V|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Missense_Mutation_p.I42V|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GCAACTGATATGGACTTGTCA	0.557													N|||	3317	0.66234	0.7352	0.5245	5008	,	,		6786	0.7639		0.5149	False		,,,				2504	0.7086				p.I42V		Atlas-SNP	.											.	SIRPB1	83	.	0			c.A124G						PASS	.						42.0	52.0	50.0					20																	1592312		444	1336	1780	SO:0001627	intron_variant	10326	exon2			CTGATATGGACTT	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8202A>G	20.37:g.1592312T>C		Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	23	21	0.913043	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	1213	0.5554029304029304	332	0.6747967479674797	169	0.46685082872928174	390	0.6818181818181818	322	0.42480211081794195	.	0.004	-2.307917	0.00240	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.61510	0.1	2.61	0.574	0.17368	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00972	-1.085	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.42632	-0.9440	8	0.02654	T	1	.	5.5118	0.16884	0.0:0.5769:0.0:0.4231	.	42	Q5TFQ8	SIRBL_HUMAN	V	42	ENSP00000279477:I42V	ENSP00000279477:I42V	I	-	1	0	SIRPB1	1540312	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.670000	0.25157	-0.280000	0.09154	-2.568000	0.00172	ATA	T|0.465;C|0.535	0.535	strong		0.557	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
KTN1	3895	hgsc.bcm.edu	37	14	56146357	56146357	+	Silent	SNP	G	G	A	rs11546	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:56146357G>A	ENST00000395314.3	+	43	4091	c.4023G>A	c.(4021-4023)gcG>gcA	p.A1341A	KTN1_ENST00000554507.1_Silent_p.A579A|KTN1_ENST00000438792.2_Silent_p.A1284A|KTN1_ENST00000395309.3_Silent_p.A1341A|KTN1_ENST00000395311.1_Silent_p.A1290A|KTN1_ENST00000413890.2_Silent_p.A1290A|KTN1_ENST00000555573.1_Silent_p.A318A|KTN1_ENST00000395308.1_Silent_p.A1290A|KTN1_ENST00000416613.1_Silent_p.A1341A	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1341					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTTCAGGCGGTAAACCAAC	0.408			T	RET	papillary thryoid								A|||	313	0.0625	0.053	0.0749	5008	,	,		20007	0.0159		0.0626	False		,,,				2504	0.1145				p.A1341A		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.G4023A						PASS	.	A	,,,	277,4129	800.7+/-415.6	8,261,1934	133.0	132.0	133.0		4023,3870,3852,4023	-2.3	0.0	14	dbSNP_52	133	845,7755	781.1+/-407.6	43,759,3498	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	51,1020,5432	AA,AG,GG		9.8256,6.2869,8.6268	,,,	1341/1358,1290/1307,1284/1301,1341/1358	56146357	1122,11884	2203	4300	6503	SO:0001819	synonymous_variant	3895	exon43			TCAGGCGGTAAAC		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.4023G>A	14.37:g.56146357G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_001079521	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1	113	0.051739926739926737	28	0.056910569105691054	27	0.07458563535911603	7	0.012237762237762238	51	0.06728232189973615	A	6.153	0.396415	0.11638	0.062869	0.098256	ENSG00000126777	ENST00000554294	.	.	.	6.17	-2.35	0.06684	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17258	-1.0375	4	.	.	.	3.4215	0.509	0.00592	0.3443:0.2056:0.2497:0.2004	rs11546;rs1051114;rs3191495;rs10147720;rs17354479;rs17685568	.	.	.	Q	112	.	.	R	+	2	0	KTN1	55216110	0.139000	0.22563	0.010000	0.14722	0.691000	0.40173	-0.219000	0.09228	-0.584000	0.05913	-0.254000	0.11334	CGG	G|0.923;A|0.077	0.077	strong		0.408	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
TMEM2	23670	hgsc.bcm.edu	37	9	74360209	74360209	+	Silent	SNP	G	G	C	rs3739783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:74360209G>C	ENST00000377044.4	-	4	1298	c.759C>G	c.(757-759)ccC>ccG	p.P253P	TMEM2_ENST00000377066.5_Silent_p.P253P	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	253					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.P253P(1)		central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		AGGACCCAAAGGGCAAGCCTG	0.502													G|||	629	0.125599	0.0348	0.2046	5008	,	,		18189	0.1577		0.1421	False		,,,				2504	0.1421				p.P253P		Atlas-SNP	.											TMEM2,NS,carcinoma,0,1	TMEM2	112	1	1	Substitution - coding silent(1)	stomach(1)	c.C759G						PASS	.	G	,	208,4198	128.2+/-165.1	8,192,2003	78.0	72.0	74.0		759,759	-0.6	0.0	9	dbSNP_107	74	1140,7460	235.1+/-267.8	71,998,3231	no	coding-synonymous,coding-synonymous	TMEM2	NM_001135820.1,NM_013390.2	,	79,1190,5234	CC,CG,GG		13.2558,4.7208,10.3644	,	253/1321,253/1384	74360209	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	23670	exon4			CCCAAAGGGCAAG		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.759C>G	9.37:g.74360209G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	55	21	0.381818	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Silent	SNP	ENST00000377044.4	37	CCDS6638.1																																																																																			G|0.890;C|0.110	0.110	strong		0.502	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
DDX42	11325	hgsc.bcm.edu	37	17	61898928	61898928	+	IGR	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61898928G>A	ENST00000578681.1	+	0	4337				FTSJ3_ENST00000427159.2_Missense_Mutation_p.R558W	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42						protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						CCCTTCCGCCGGTTCTCAAAT	0.567																																					p.R558W		Atlas-SNP	.											FTSJ3,NS,carcinoma,0,1	FTSJ3	63	1	0			c.C1672T						PASS	.						56.0	59.0	58.0					17																	61898928		2203	4300	6503	SO:0001628	intergenic_variant	117246	exon16			TCCGCCGGTTCTC	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3			17.37:g.61898928G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	41	26	0.634146	NM_017647	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	37	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994511	0.74703	.	.	ENSG00000108592	ENST00000427159	T	0.34275	1.37	5.17	5.17	0.71159	.	0.410282	0.25651	N	0.029207	T	0.37652	0.1011	N	0.22421	0.69	0.39415	D	0.966828	D	0.69078	0.997	P	0.53490	0.727	T	0.29941	-0.9995	10	0.72032	D	0.01	-4.4553	14.0344	0.64636	0.0:0.0:1.0:0.0	.	558	Q8IY81	RRMJ3_HUMAN	W	558	ENSP00000396673:R558W	ENSP00000396673:R558W	R	-	1	2	FTSJ3	59252660	0.045000	0.20229	0.773000	0.31616	0.045000	0.14185	2.138000	0.42140	2.688000	0.91661	0.563000	0.77884	CGG	.	.	none		0.567	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
MED16	10025	hgsc.bcm.edu	37	19	872089	872089	+	Silent	SNP	A	A	G	rs72984031	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:872089A>G	ENST00000589119.1	-	11	1934	c.1935T>C	c.(1933-1935)ttT>ttC	p.F645F	MED16_ENST00000269814.4_Intron|MED16_ENST00000312090.6_Silent_p.F645F|MED16_ENST00000395808.3_Silent_p.F645F|MED16_ENST00000325464.1_Silent_p.F645F|MED16_ENST00000606828.1_5'Flank			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	645					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)		CGTCCCGCAGAAAGCTGTGGC	0.657													-|||	885	0.176717	0.2133	0.1412	5008	,	,		9195	0.0089		0.2793	False		,,,				2504	0.2198				p.F645F		Atlas-SNP	.											.	MED16	61	.	0			c.T1935C						PASS	.			1029,3309	361.4+/-315.7	131,767,1271	35.0	33.0	33.0		1935	-0.2	1.0	19	dbSNP_130	33	2337,6219	368.3+/-335.0	331,1675,2272	no	coding-synonymous	MED16	NM_005481.2		462,2442,3543	GG,GA,AA		27.3142,23.7206,26.1052		645/878	872089	3366,9528	2169	4278	6447	SO:0001819	synonymous_variant	10025	exon12			CCGCAGAAAGCTG	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.1935T>C	19.37:g.872089A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Silent	SNP	ENST00000589119.1	37	CCDS12047.1																																																																																			A|0.775;G|0.225	0.225	strong		0.657	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481	
WDR87	83889	hgsc.bcm.edu	37	19	38379446	38379446	+	Missense_Mutation	SNP	C	C	T	rs6508750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38379446C>T	ENST00000303868.5	-	6	4972	c.4748G>A	c.(4747-4749)cGa>cAa	p.R1583Q	WDR87_ENST00000447313.2_Missense_Mutation_p.R1622Q	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	1583	Glu-rich.		R -> Q (in dbSNP:rs6508750).							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						TTTTTCAGCTCGGGCTCGTTT	0.473																																					p.R1583Q		Atlas-SNP	.											.	WDR87	191	.	0			c.G4748A						PASS	.	C	GLN/ARG	1011,373		371,269,52	204.0	144.0	162.0		4748	-3.5	0.0	19	dbSNP_116	162	1247,1935		254,739,598	yes	missense	WDR87	NM_031951.3	43	625,1008,650	TT,TC,CC		39.1892,26.9509,49.4525	benign	1583/2874	38379446	2258,2308	692	1591	2283	SO:0001583	missense	83889	exon6			TCAGCTCGGGCTC	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.4748G>A	19.37:g.38379446C>T	ENSP00000368025:p.Arg1583Gln	Somatic	444	0	0		WXS	Illumina HiSeq	Phase_I	494	493	0.997976	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	1354	0.61996336996337	397	0.806910569105691	183	0.505524861878453	462	0.8076923076923077	312	0.41160949868073876	C	11.75	1.730380	0.30684	0.730491	0.391892	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.41758	0.99;0.99	3.34	-3.53	0.04667	.	.	.	.	.	T	0.00012	0.0000	N	0.05124	-0.11	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.36696	-0.9737	8	0.10902	T	0.67	.	1.9676	0.03399	0.1621:0.4302:0.1644:0.2433	rs6508750;rs17664031;rs52828250;rs61040067;rs6508750	1583;1622	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	Q	1622;1583	ENSP00000405012:R1622Q;ENSP00000368025:R1583Q	ENSP00000368025:R1583Q	R	-	2	0	WDR87	43071286	0.000000	0.05858	0.000000	0.03702	0.673000	0.39480	-1.560000	0.02160	-0.583000	0.05921	-0.734000	0.03567	CGA	C|0.387;T|0.613	0.613	strong		0.473	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
PPP2R5A	5525	hgsc.bcm.edu	37	1	212459615	212459615	+	Missense_Mutation	SNP	C	C	G	rs75232123	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:212459615C>G	ENST00000261461.2	+	1	737	c.163C>G	c.(163-165)Ccg>Gcg	p.P55A		NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	55					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of lipid kinase activity (GO:0090219)|positive regulation of protein dephosphorylation (GO:0035307)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|M band (GO:0031430)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)|Z disc (GO:0030018)	kinase binding (GO:0019900)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		AGAGCTGCACCCGCTGCCCCA	0.682													C|||	47	0.00938498	0.0008	0.0144	5008	,	,		15457	0.001		0.0348	False		,,,				2504	0.0				p.P55A		Atlas-SNP	.											.	PPP2R5A	48	.	0			c.C163G						PASS	.	C	ALA/PRO	13,4307		0,13,2147	9.0	9.0	9.0		163	3.4	1.0	1	dbSNP_132	9	156,8332		0,156,4088	yes	missense	PPP2R5A	NM_006243.3	27	0,169,6235	GG,GC,CC		1.8379,0.3009,1.3195	benign	55/487	212459615	169,12639	2160	4244	6404	SO:0001583	missense	5525	exon1			CTGCACCCGCTGC	BC022474	CCDS1503.1, CCDS55686.1	1q32.2-q32.3	2010-06-18	2010-04-14		ENSG00000066027	ENSG00000066027		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9309	protein-coding gene	gene with protein product		601643	"""protein phosphatase 2, regulatory subunit B (B56), alpha isoform"", ""protein phosphatase 2, regulatory subunit B', alpha isoform"""			7592815	Standard	NM_006243		Approved	PR61A, B56A	uc001hjb.3	Q15172	OTTHUMG00000036750	ENST00000261461.2:c.163C>G	1.37:g.212459615C>G	ENSP00000261461:p.Pro55Ala	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_006243	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Missense_Mutation	SNP	ENST00000261461.2	37	CCDS1503.1	39	0.017857142857142856	3	0.006097560975609756	7	0.019337016574585635	1	0.0017482517482517483	28	0.036939313984168866	C	12.36	1.915605	0.33815	0.003009	0.018379	ENSG00000066027	ENST00000542178;ENST00000261461	.	.	.	4.32	3.4	0.38934	.	0.169049	0.53938	D	0.000060	T	0.13628	0.0330	L	0.35593	1.075	0.80722	D	1	B	0.10296	0.003	B	0.17979	0.02	T	0.04781	-1.0927	9	0.10111	T	0.7	-0.9103	11.3432	0.49546	0.0:0.9098:0.0:0.0902	.	55	Q15172	2A5A_HUMAN	A	55	.	ENSP00000261461:P55A	P	+	1	0	PPP2R5A	210526238	1.000000	0.71417	0.997000	0.53966	0.851000	0.48451	4.944000	0.63561	0.803000	0.34113	0.467000	0.42956	CCG	C|0.980;G|0.020	0.020	strong		0.682	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243	
PRR22	163154	hgsc.bcm.edu	37	19	5783713	5783713	+	Missense_Mutation	SNP	G	G	A	rs141874203	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5783713G>A	ENST00000419421.2	-	3	649	c.545C>T	c.(544-546)cCg>cTg	p.P182L		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	182	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGGTGGCAGCGGGGCCGGGCC	0.716													G|||	51	0.0101837	0.0	0.0202	5008	,	,		8447	0.0		0.0258	False		,,,				2504	0.0112				p.P182L		Atlas-SNP	.											PRR22_ENST00000419421,NS,carcinoma,+1,2	PRR22	25	2	0			c.C545T						PASS	.	G	LEU/PRO	23,3621		0,23,1799	3.0	5.0	4.0		545	2.6	0.0	19	dbSNP_134	4	224,7348		0,224,3562	no	missense	PRR22	NM_001134316.1	98	0,247,5361	AA,AG,GG		2.9583,0.6312,2.2022	possibly-damaging	182/423	5783713	247,10969	1822	3786	5608	SO:0001583	missense	163154	exon3			GGCAGCGGGGCCG	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.545C>T	19.37:g.5783713G>A	ENSP00000407653:p.Pro182Leu	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	35	0.016025641025641024	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	26	0.03430079155672823	G	13.85	2.360615	0.41801	0.006312	0.029583	ENSG00000212123	ENST00000419421	T	0.20200	2.09	2.58	2.58	0.30949	.	.	.	.	.	T	0.04588	0.0125	L	0.32530	0.975	0.09310	N	1	P;P	0.42161	0.772;0.772	B;B	0.34779	0.189;0.189	T	0.10800	-1.0614	9	0.62326	D	0.03	.	8.7627	0.34685	0.0:0.0:1.0:0.0	.	182;180	E9PB31;Q8IZ63	.;PRR22_HUMAN	L	182	ENSP00000407653:P182L	ENSP00000407653:P182L	P	-	2	0	PRR22	5734713	0.123000	0.22298	0.002000	0.10522	0.003000	0.03518	2.157000	0.42320	1.759000	0.51996	0.491000	0.48974	CCG	G|0.984;A|0.016	0.016	strong		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
OR10S1	219873	hgsc.bcm.edu	37	11	123847473	123847473	+	Missense_Mutation	SNP	A	A	G	rs55944888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:123847473A>G	ENST00000531945.1	-	1	1015	c.926T>C	c.(925-927)gTg>gCg	p.V309A		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		AGCATGCTTCACCTCCTTGTT	0.527													A|||	577	0.115216	0.0552	0.1585	5008	,	,		21721	0.1081		0.1829	False		,,,				2504	0.1033				p.V309A		Atlas-SNP	.											.	OR10S1	78	.	0			c.T926C						PASS	.	A	ALA/VAL	332,4072	174.8+/-204.3	17,298,1887	81.0	78.0	79.0		926	4.8	0.9	11	dbSNP_129	79	1454,7144	277.4+/-292.8	120,1214,2965	yes	missense	OR10S1	NM_001004474.1	64	137,1512,4852	GG,GA,AA		16.9109,7.5386,13.7363	possibly-damaging	309/332	123847473	1786,11216	2202	4299	6501	SO:0001583	missense	219873	exon1			TGCTTCACCTCCT	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.926T>C	11.37:g.123847473A>G	ENSP00000431914:p.Val309Ala	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	69	42	0.608696	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	274	0.12545787545787546	16	0.032520325203252036	65	0.17955801104972377	68	0.11888111888111888	125	0.16490765171503957	A	9.610	1.131046	0.21041	0.075386	0.169109	ENSG00000196248	ENST00000531945	T	0.39592	1.07	4.82	4.82	0.62117	.	0.000000	0.31989	U	0.006759	T	0.00109	0.0003	M	0.67569	2.06	0.80722	P	0.0	B	0.20368	0.044	B	0.15870	0.014	T	0.07366	-1.0776	9	0.87932	D	0	-20.1912	14.1878	0.65617	1.0:0.0:0.0:0.0	rs55944888	309	Q8NGN2	O10S1_HUMAN	A	309	ENSP00000431914:V309A	ENSP00000431914:V309A	V	-	2	0	OR10S1	123352683	0.440000	0.25618	0.900000	0.35374	0.282000	0.26991	5.304000	0.65744	2.004000	0.58718	0.460000	0.39030	GTG	A|0.862;G|0.138	0.138	strong		0.527	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
HLA-A	3105	hgsc.bcm.edu	37	6	29910622	29910622	+	Silent	SNP	C	C	T	rs199501996	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910622C>T	ENST00000396634.1	+	4	503	c.162C>T	c.(160-162)gaC>gaT	p.D54D	HLA-A_ENST00000376809.5_Silent_p.D54D|HLA-A_ENST00000376806.5_Silent_p.D54D|HLA-A_ENST00000376802.2_Silent_p.D54D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	54	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.D54D(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ACGTGGACGACACGCAGTTCG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.D54D		Atlas-SNP	.											HLA-A,NS,carcinoma,0,4	HLA-A	89	4	2	Substitution - coding silent(2)	prostate(2)	c.C162T						PASS	.						47.0	40.0	42.0					6																	29910622		2202	4299	6501	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGACGACACGCAG	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.162C>T	6.37:g.29910622C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	105	19	0.180952	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.998;T|0.002	0.002	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90565242	90565242	+	RNA	SNP	A	A	G	rs369328	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90565242A>G	ENST00000551025.1	+	0	1716									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		TGATGAAAAAATTTAAAGAAA	0.289													G|||	2118	0.422923	0.3502	0.3314	5008	,	,		16871	0.3006		0.5417	False		,,,				2504	0.59				p.K93K	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.A279G						PASS	.	G	,,	1207,2167		264,679,744	14.0	13.0	14.0		279,279,279	-0.1	1.0	6	dbSNP_80	14	3785,3857		1039,1707,1075	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	,,	1303,2386,1819	GG,GA,AA		49.5289,35.7736,45.3159	,,	93/1967,93/1967,93/1967	90565242	4992,6024	1687	3821	5508			9994	exon5			GAAAAAATTTAAA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90565242A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	51	45	0.882353	NM_001137667		Silent	SNP	ENST00000551025.1	37																																																																																				G|0.396;N|0.000	0.396	strong		0.289	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
NRP1	8829	hgsc.bcm.edu	37	10	33469181	33469181	+	Silent	SNP	A	A	G	rs1048804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:33469181A>G	ENST00000265371.4	-	18	3120	c.2595T>C	c.(2593-2595)agT>agC	p.S865S	NRP1_ENST00000395995.1_Silent_p.S848S|NRP1_ENST00000374875.1_Silent_p.S677S|NRP1_ENST00000374867.2_Silent_p.S865S			O14786	NRP1_HUMAN	neuropilin 1	865					angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.S865S(1)		NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	CCCCCAGGGCACTCATGGCTA	0.532													G|||	2125	0.424321	0.5666	0.2061	5008	,	,		18341	0.622		0.2455	False		,,,				2504	0.3671				p.S865S	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											NRP1,NS,carcinoma,0,1	NRP1	126	1	1	Substitution - coding silent(1)	stomach(1)	c.T2595C						PASS	.	G		2210,2196	585.1+/-386.2	574,1062,567	187.0	177.0	181.0		2595	-4.9	0.8	10	dbSNP_86	181	2024,6576	721.1+/-406.3	223,1578,2499	no	coding-synonymous	NRP1	NM_003873.5		797,2640,3066	GG,GA,AA		23.5349,49.8411,32.5542		865/924	33469181	4234,8772	2203	4300	6503	SO:0001819	synonymous_variant	8829	exon17			CAGGGCACTCATG	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.2595T>C	10.37:g.33469181A>G		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	210	207	0.985714	NM_003873	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Silent	SNP	ENST00000265371.4	37	CCDS7177.1																																																																																			A|0.634;G|0.366	0.366	strong		0.532	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
KCNS1	3787	hgsc.bcm.edu	37	20	43727155	43727155	+	Silent	SNP	C	C	T	rs13043825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43727155C>T	ENST00000306117.1	-	4	654	c.258G>A	c.(256-258)gaG>gaA	p.E86E	KCNS1_ENST00000537075.1_Silent_p.E86E	NM_002251.3	NP_002242.2	Q96KK3	KCNS1_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 1	86					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(1)|lung(3)|ovary(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				GCCGCGCCTGCTCCTCCGACG	0.741													C|||	658	0.13139	0.0113	0.1729	5008	,	,		8507	0.131		0.2893	False		,,,				2504	0.1022				p.E86E		Atlas-SNP	.											.	KCNS1	30	.	0			c.G258A						PASS	.	C		198,3818		14,170,1824	8.0	10.0	9.0		258	3.8	1.0	20	dbSNP_121	9	1830,5974		196,1438,2268	no	coding-synonymous	KCNS1	NM_002251.3		210,1608,4092	TT,TC,CC		23.4495,4.9303,17.1574		86/527	43727155	2028,9792	2008	3902	5910	SO:0001819	synonymous_variant	3787	exon4			CGCCTGCTCCTCC	AF043473	CCDS13342.1	20q12	2011-07-05			ENSG00000124134	ENSG00000124134		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6300	protein-coding gene	gene with protein product		602905				9305895, 16382104	Standard	NM_002251		Approved	Kv9.1	uc002xnc.3	Q96KK3	OTTHUMG00000033079	ENST00000306117.1:c.258G>A	20.37:g.43727155C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_002251	A2RUL9|B7ZM31|O43652|Q6DJU6	Silent	SNP	ENST00000306117.1	37	CCDS13342.1																																																																																			C|0.838;T|0.162	0.162	strong		0.741	KCNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080507.3	NM_002251	
SPPL2C	162540	hgsc.bcm.edu	37	17	43922640	43922640	+	Missense_Mutation	SNP	G	G	A	rs17763658	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:43922640G>A	ENST00000329196.5	+	1	385	c.368G>A	c.(367-369)cGg>cAg	p.R123Q	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	123	PA.		R -> Q (in dbSNP:rs17763658).			endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										ATCGTGAGCCGGGTCAGTGAC	0.637													G|||	454	0.090655	0.0734	0.0663	5008	,	,		17382	0.1181		0.0805	False		,,,				2504	0.1135				p.R123Q		Atlas-SNP	.											.	.	.	.	0			c.G368A						PASS	.	G	GLN/ARG	344,4062	178.0+/-206.8	15,314,1874	53.0	53.0	53.0		368	0.5	0.1	17	dbSNP_123	53	589,8011	155.8+/-209.8	23,543,3734	yes	missense	IMP5	NM_175882.2	43	38,857,5608	AA,AG,GG		6.8488,7.8075,7.1736	probably-damaging	123/685	43922640	933,12073	2203	4300	6503	SO:0001583	missense	162540	exon1			TGAGCCGGGTCAG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.368G>A	17.37:g.43922640G>A	ENSP00000332488:p.Arg123Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	191	0.08745421245421245	39	0.07926829268292683	29	0.08011049723756906	63	0.11013986013986014	60	0.079155672823219	G	8.681	0.905052	0.17760	0.078075	0.068488	ENSG00000185294	ENST00000329196	T	0.07688	3.17	4.64	0.472	0.16758	Protease-associated domain, PA (1);	0.368339	0.19781	N	0.106216	T	0.00241	0.0007	L	0.49350	1.555	0.26367	P	0.9769541	P	0.52842	0.956	P	0.51453	0.67	T	0.19943	-1.0290	9	0.37606	T	0.19	-3.1037	6.8244	0.23874	0.3859:0.0:0.6141:0.0	rs17763658;rs52794767;rs17763658	123	Q8IUH8	IMP5_HUMAN	Q	123	ENSP00000332488:R123Q	ENSP00000332488:R123Q	R	+	2	0	AC217771.1	41278420	1.000000	0.71417	0.141000	0.22245	0.005000	0.04900	1.345000	0.33953	-0.018000	0.14079	-0.808000	0.03180	CGG	G|0.922;A|0.078	0.078	strong		0.637	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
HIST1H4D	8360	hgsc.bcm.edu	37	6	26189010	26189010	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26189010A>C	ENST00000340756.2	-	1	294	c.295T>G	c.(295-297)Tat>Gat	p.Y99D		NM_003539.3	NP_003530.1	P62805	H4_HUMAN	histone cluster 1, H4d	99					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)			breast(2)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)	8		all_hematologic(11;0.196)				CCGAAGCCATAAAGAGTGCGT	0.552																																					p.Y99D		Atlas-SNP	.											HIST1H4D,colon,carcinoma,0,1	HIST1H4D	28	1	0			c.T295G						PASS	.						119.0	102.0	108.0					6																	26189010		2203	4300	6503	SO:0001583	missense	8360	exon1			AGCCATAAAGAGT	X60482	CCDS4589.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000188987	ENSG00000277157		"""Histones / Replication-dependent"""	4782	protein-coding gene	gene with protein product		602823	"""H4 histone family, member B"", ""histone 1, H4d"""	H4FB		9119399, 12408966	Standard	NM_003539		Approved	H4/b	uc003ngu.3	P62805	OTTHUMG00000014423	ENST00000340756.2:c.295T>G	6.37:g.26189010A>C	ENSP00000343282:p.Tyr99Asp	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_003539	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000340756.2	37	CCDS4589.1	.	.	.	.	.	.	.	.	.	.	.	17.92	3.506691	0.64410	.	.	ENSG00000188987	ENST00000340756	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	.	.	.	0.46499	D	0.999071	.	.	.	.	.	.	T	0.74708	-0.3574	6	0.87932	D	0	.	14.4576	0.67428	1.0:0.0:0.0:0.0	.	.	.	.	D	99	.	ENSP00000343282:Y99D	Y	-	1	0	HIST1H4D	26296989	1.000000	0.71417	0.740000	0.30986	0.041000	0.13682	8.784000	0.91818	2.017000	0.59298	0.528000	0.53228	TAT	.	.	none		0.552	HIST1H4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040085.1	NM_003539	
LILRB1	10859	hgsc.bcm.edu	37	19	55142739	55142739	+	Silent	SNP	A	A	C	rs1985501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55142739A>C	ENST00000396331.1	+	4	409	c.52A>C	c.(52-54)Agg>Cgg	p.R18R	LILRB1_ENST00000434867.2_Silent_p.R18R|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000396315.1_Silent_p.R18R|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000427581.2_Silent_p.R54R|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Silent_p.R18R|LILRB1_ENST00000396317.1_Silent_p.R18R|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000396327.3_Silent_p.R18R|LILRB1_ENST00000324602.7_Silent_p.R18R	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	18					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)		TCTGGGCCCCAGGACCCACGT	0.667										HNSCC(37;0.09)			a|||	2257	0.450679	0.5537	0.4841	5008	,	,		15896	0.5982		0.3032	False		,,,				2504	0.2873				p.R18R		Atlas-SNP	.											.	LILRB1	140	.	0			c.A52C						PASS	.	A	,,,	2264,2142	571.7+/-383.1	584,1096,523	54.0	65.0	61.0		52,52,52,52	1.5	0.0	19	dbSNP_92	61	2749,5849	425.4+/-354.9	429,1891,1979	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	,,,	1013,2987,2502	CC,CA,AA		31.9726,48.6155,38.5497	,,,	18/653,18/652,18/652,18/651	55142739	5013,7991	2203	4299	6502	SO:0001819	synonymous_variant	10859	exon3			GGCCCCAGGACCC	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.52A>C	19.37:g.55142739A>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	68	0.53125	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			A|0.588;C|0.412	0.412	strong		0.667	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
BTN1A1	696	hgsc.bcm.edu	37	6	26505403	26505403	+	Silent	SNP	C	C	A	rs3736782	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26505403C>A	ENST00000244513.6	+	3	744	c.678C>A	c.(676-678)ggC>ggA	p.G226G		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	226	Ig-like V-type 2.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						TCCTTCTTGGCCAGGAGAAGA	0.468													C|||	2843	0.567692	0.5121	0.5879	5008	,	,		19737	0.745		0.4423	False		,,,				2504	0.5746				p.G226G		Atlas-SNP	.											.	BTN1A1	68	.	0			c.C678A						PASS	.	C		2288,2118	600.5+/-389.5	588,1112,503	89.0	92.0	91.0		678	3.6	1.0	6	dbSNP_107	91	4045,4555	557.2+/-387.0	984,2077,1239	no	coding-synonymous	BTN1A1	NM_001732.2		1572,3189,1742	AA,AC,CC		47.0349,48.0708,48.6929		226/527	26505403	6333,6673	2203	4300	6503	SO:0001819	synonymous_variant	696	exon3			TCTTGGCCAGGAG	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.678C>A	6.37:g.26505403C>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Silent	SNP	ENST00000244513.6	37	CCDS4614.1																																																																																			C|0.487;A|0.513	0.513	strong		0.468	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
PNPLA1	285848	hgsc.bcm.edu	37	6	36274153	36274153	+	Splice_Site	SNP	C	C	T	rs12197079	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36274153C>T	ENST00000394571.2	+	7	1469	c.1469C>T	c.(1468-1470)aCg>aTg	p.T490M	PNPLA1_ENST00000388715.3_Splice_Site_p.T395M|PNPLA1_ENST00000312917.5_Splice_Site_p.T404M	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	490			T -> M (in dbSNP:rs12197079). {ECO:0000269|PubMed:15489334}.		lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						CCTTATGTAACGTAAGTTTCC	0.488													T|||	1204	0.240415	0.3238	0.1859	5008	,	,		19609	0.1032		0.2565	False		,,,				2504	0.2914				p.T490M		Atlas-SNP	.											.	PNPLA1	92	.	0			c.C1469T						PASS	.	T	MET/THR,MET/THR,MET/THR	1401,3005	687.2+/-404.8	225,951,1027	157.0	148.0	151.0		1211,1469,1184	-3.4	0.0	6	dbSNP_120	151	2464,6136	695.8+/-404.8	376,1712,2212	yes	missense-near-splice,missense-near-splice,missense-near-splice	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	81,81,81	601,2663,3239	TT,TC,CC		28.6512,31.7975,29.7171	benign,benign,benign	404/447,490/533,395/438	36274153	3865,9141	2203	4300	6503	SO:0001630	splice_region_variant	285848	exon7			ATGTAACGTAAGT		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1469+1C>T	6.37:g.36274153C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	468	0.21428571428571427	148	0.3008130081300813	73	0.20165745856353592	54	0.0944055944055944	193	0.2546174142480211	T	9.014	0.983174	0.18889	0.317975	0.286512	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.27557	1.89;1.89;1.66;1.66	4.25	-3.36	0.04913	.	1.943300	0.02601	N	0.101010	T	0.03871	0.0109	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	0.23762	-1.0179	9	0.30078	T	0.28	0.6036	6.6281	0.22841	0.1679:0.5507:0.0:0.2814	rs12197079;rs52834844;rs60801136;rs12197079	490;404	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	M	395;404;491;490	ENSP00000373367:T395M;ENSP00000321116:T404M;ENSP00000391868:T491M;ENSP00000378072:T490M	ENSP00000321116:T404M	T	+	2	0	PNPLA1	36382131	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.405000	0.00482	-0.715000	0.04968	-0.361000	0.07541	ACG	C|0.747;N|0.000	.	strong		0.488	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	Missense_Mutation
AK7	122481	hgsc.bcm.edu	37	14	96871104	96871104	+	Missense_Mutation	SNP	G	G	A	rs2275554	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:96871104G>A	ENST00000267584.4	+	3	349	c.305G>A	c.(304-306)cGa>cAa	p.R102Q	AK7_ENST00000554313.1_3'UTR	NM_152327.3	NP_689540.2	Q96M32	KAD7_HUMAN	adenylate kinase 7	102			R -> Q (in dbSNP:rs2275554). {ECO:0000269|PubMed:14702039}.		axoneme assembly (GO:0035082)|brain development (GO:0007420)|epithelial cilium movement (GO:0003351)|inflammatory response to antigenic stimulus (GO:0002437)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			breast(2)|cervix(2)|endometrium(3)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31		all_cancers(154;0.0482)|all_epithelial(191;0.128)|Melanoma(154;0.155)		Epithelial(152;0.134)|COAD - Colon adenocarcinoma(157;0.228)		GCCATCTCTCGAGAAGACCTT	0.403													G|||	1069	0.213458	0.2269	0.1657	5008	,	,		18454	0.1944		0.2684	False		,,,				2504	0.1922				p.R102Q		Atlas-SNP	.											.	AK7	69	.	0			c.G305A						PASS	.	G	GLN/ARG	1009,3397	376.1+/-321.9	127,755,1321	94.0	87.0	89.0		305	4.5	0.2	14	dbSNP_100	89	2191,6409	372.7+/-336.7	309,1573,2418	yes	missense	AK7	NM_152327.2	43	436,2328,3739	AA,AG,GG		25.4767,22.9006,24.604	benign	102/724	96871104	3200,9806	2203	4300	6503	SO:0001583	missense	122481	exon3			TCTCTCGAGAAGA	AK057426	CCDS9945.1	14q32.31	2012-08-15			ENSG00000140057	ENSG00000140057		"""Adenylate kinases"""	20091	protein-coding gene	gene with protein product		615364					Standard	NM_152327		Approved	FLJ32864	uc001yfn.3	Q96M32	OTTHUMG00000171421	ENST00000267584.4:c.305G>A	14.37:g.96871104G>A	ENSP00000267584:p.Arg102Gln	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_152327	Q8IYP6	Missense_Mutation	SNP	ENST00000267584.4	37	CCDS9945.1	427	0.1955128205128205	87	0.17682926829268292	55	0.15193370165745856	104	0.18181818181818182	181	0.23878627968337732	G	10.47	1.360434	0.24598	0.229006	0.254767	ENSG00000140057	ENST00000267584	T	0.41065	1.01	5.35	4.47	0.54385	.	0.200218	0.41097	N	0.000951	T	0.00012	0.0000	L	0.31476	0.935	0.09310	P	0.9999999999999996	B	0.26547	0.152	B	0.21917	0.037	T	0.18681	-1.0329	9	0.33940	T	0.23	-6.7224	12.998	0.58660	0.0794:0.0:0.9206:0.0	rs2275554;rs59019715;rs2275554	102	Q96M32	KAD7_HUMAN	Q	102	ENSP00000267584:R102Q	ENSP00000267584:R102Q	R	+	2	0	AK7	95940857	1.000000	0.71417	0.190000	0.23270	0.094000	0.18550	3.268000	0.51585	1.270000	0.44297	0.467000	0.42956	CGA	G|0.770;A|0.230	0.230	strong		0.403	AK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413340.1		
RFPL3	10738	hgsc.bcm.edu	37	22	32754232	32754232	+	Silent	SNP	C	C	T	rs57606003|rs386820741	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:32754232C>T	ENST00000249007.4	+	1	379	c.174C>T	c.(172-174)acC>acT	p.T58T	RFPL3_ENST00000397468.1_Silent_p.T29T|RFPL3_ENST00000382088.3_Silent_p.T29T|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	58							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GTGGATGCACCGTCTGCCTCA	0.542													c|||	724	0.144569	0.0265	0.0893	5008	,	,		19377	0.4583		0.0408	False		,,,				2504	0.1268				p.T58T		Atlas-SNP	.											.	RFPL3	91	.	0			c.C174T						PASS	.	C	,	165,4241	98.0+/-136.7	6,153,2044	119.0	113.0	115.0		174,87	-0.3	0.0	22	dbSNP_129	115	453,8147	130.0+/-188.0	11,431,3858	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	17,584,5902	TT,TC,CC		5.2674,3.7449,4.7517	,	58/318,29/289	32754232	618,12388	2203	4300	6503	SO:0001819	synonymous_variant	10738	exon1			ATGCACCGTCTGC	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.174C>T	22.37:g.32754232C>T		Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	278	149	0.535971	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			C|0.923;T|0.077	0.077	strong		0.542	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
OR6Q1	219952	hgsc.bcm.edu	37	11	57799371	57799371	+	Missense_Mutation	SNP	G	G	C	rs1374570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57799371G>C	ENST00000302622.3	+	1	970	c.947G>C	c.(946-948)gGa>gCa	p.G316A	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	316			G -> A (in dbSNP:rs1374570).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				TTTTGGAAGGGACAGTGAGGA	0.448													G|||	2094	0.418131	0.4871	0.5418	5008	,	,		21163	0.244		0.5417	False		,,,				2504	0.2894				p.G316A		Atlas-SNP	.											OR6Q1,NS,carcinoma,-1,1	OR6Q1	58	1	0			c.G947C						PASS	.	G	ALA/GLY	2168,2114		585,998,558	39.0	41.0	40.0		947	2.4	0.0	11	dbSNP_88	40	4542,3790		1282,1978,906	yes	missense	OR6Q1	NM_001005186.2	60	1867,2976,1464	CC,CG,GG		45.4873,49.3695,46.8051	benign	316/318	57799371	6710,5904	2141	4166	6307	SO:0001583	missense	219952	exon1			GGAAGGGACAGTG	AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"""GPCR / Class A : Olfactory receptors"""	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.947G>C	11.37:g.57799371G>C	ENSP00000307734:p.Gly316Ala	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	57	34	0.596491	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	37	CCDS31541.1	1028	0.4706959706959707	247	0.5020325203252033	210	0.580110497237569	159	0.27797202797202797	412	0.5435356200527705	G	10.01	1.234500	0.22626	0.506305	0.545127	ENSG00000172381	ENST00000302622	T	0.02103	4.45	4.29	2.38	0.29361	.	0.640127	0.12873	N	0.432114	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.24258	0.1	B	0.21708	0.036	T	0.09378	-1.0677	9	0.56958	D	0.05	.	11.799	0.52116	0.0:0.3418:0.6582:0.0	rs1374570;rs52838041;rs1374570	316	Q8NGQ2	OR6Q1_HUMAN	A	316	ENSP00000307734:G316A	ENSP00000307734:G316A	G	+	2	0	OR6Q1	57555947	0.000000	0.05858	0.001000	0.08648	0.164000	0.22412	0.146000	0.16180	0.443000	0.26582	-0.122000	0.15005	GGA	G|0.500;C|0.500	0.500	strong		0.448	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553856	140553856	+	Silent	SNP	G	G	A	rs2907330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140553856G>A	ENST00000231137.3	+	1	1614	c.1440G>A	c.(1438-1440)tcG>tcA	p.S480S		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	480	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAGAGACTCGGGCACCAACG	0.652													A|||	3143	0.627596	0.6891	0.6369	5008	,	,		16633	0.6607		0.5487	False		,,,				2504	0.5849				p.S480S		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G1440A						PASS	.	A		2931,1475		969,993,241	104.0	102.0	103.0		1440	-5.5	0.2	5	dbSNP_101	103	4898,3702		1416,2066,818	no	coding-synonymous	PCDHB7	NM_018940.2		2385,3059,1059	AA,AG,GG		43.0465,33.4771,39.8047		480/794	140553856	7829,5177	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			AGACTCGGGCACC	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1440G>A	5.37:g.140553856G>A		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			G|0.395;A|0.605	0.605	strong		0.652	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
IL37	27178	hgsc.bcm.edu	37	2	113676381	113676381	+	Missense_Mutation	SNP	G	G	A	rs2723192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113676381G>A	ENST00000263326.3	+	5	694	c.652G>A	c.(652-654)Gat>Aat	p.D218N	IL37_ENST00000353225.3_Missense_Mutation_p.D178N|IL37_ENST00000352179.3_Missense_Mutation_p.D197N|IL37_ENST00000311328.2_Missense_Mutation_p.D192N|IL37_ENST00000349806.3_Missense_Mutation_p.D157N	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	218			D -> N (in dbSNP:rs2723192). {ECO:0000269|Ref.6}.		immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						TGAGGTCAGCGATTAGGAAAC	0.408													g|||	380	0.0758786	0.174	0.0591	5008	,	,		20093	0.001		0.0795	False		,,,				2504	0.0286				p.D218N		Atlas-SNP	.											.	IL37	56	.	0			c.G652A						PASS	.		ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	730,3676	302.1+/-287.2	51,628,1524	58.0	62.0	60.0		652,589,469,532,574	1.2	0.0	2	dbSNP_100	60	690,7910	171.3+/-222.3	37,616,3647	yes	missense,missense,missense,missense,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1,NM_173205.1	23,23,23,23,23	88,1244,5171	AA,AG,GG		8.0233,16.5683,10.918	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	218/219,197/198,157/158,178/179,192/193	113676381	1420,11586	2203	4300	6503	SO:0001583	missense	27178	exon5			GTCAGCGATTAGG	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.652G>A	2.37:g.113676381G>A	ENSP00000263326:p.Asp218Asn	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	164	0.07509157509157509	81	0.16463414634146342	26	0.0718232044198895	1	0.0017482517482517483	56	0.07387862796833773	g	12.07	1.826524	0.32329	0.165683	0.080233	ENSG00000125571	ENST00000263326;ENST00000352179;ENST00000349806;ENST00000353225;ENST00000311328	T;T;T;T;T	0.21031	2.48;2.63;2.03;2.14;2.37	3.05	1.2	0.21068	.	1.620940	0.04261	N	0.340419	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	P;B;P;D;P	0.54047	0.759;0.305;0.938;0.964;0.94	B;B;B;P;B	0.46452	0.162;0.078;0.29;0.517;0.318	T	0.14090	-1.0485	9	0.46703	T	0.11	-27.877	5.0763	0.14632	0.2853:0.0:0.7147:0.0	rs2723192;rs56516427;rs59312925;rs2723192	192;157;178;197;218	Q9NZH6-2;Q9NZH6-5;Q9NZH6-3;Q9NZH6-4;Q9NZH6	.;.;.;.;IL37_HUMAN	N	218;197;157;178;192	ENSP00000263326:D218N;ENSP00000263327:D197N;ENSP00000263328:D157N;ENSP00000309208:D178N;ENSP00000309883:D192N	ENSP00000263326:D218N	D	+	1	0	IL37	113392852	0.000000	0.05858	0.000000	0.03702	0.257000	0.26127	0.043000	0.13971	0.322000	0.23283	0.486000	0.48141	GAT	G|0.903;A|0.097	0.097	strong		0.408	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
C2orf80	389073	hgsc.bcm.edu	37	2	209036712	209036712	+	Splice_Site	SNP	T	T	C	rs10804166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:209036712T>C	ENST00000341287.4	-	7	649	c.454A>G	c.(454-456)Agt>Ggt	p.S152G	C2orf80_ENST00000451346.1_Splice_Site_p.S133G|C2orf80_ENST00000453017.1_Intron	NM_001099334.2	NP_001092804	Q0P641	CB080_HUMAN	chromosome 2 open reading frame 80	152			S -> G (in dbSNP:rs10804166).							endometrium(2)|large_intestine(3)|lung(6)|skin(2)	13						CCAGGCTTACTCTGTTTGCGG	0.463													T|||	4291	0.856829	0.7943	0.9352	5008	,	,		20312	0.8542		0.9274	False		,,,				2504	0.816				p.S152G		Atlas-SNP	.											.	C2orf80	19	.	0			c.A454G						PASS	.	T	GLY/SER	3171,687		1309,553,67	225.0	225.0	225.0		454	1.5	1.0	2	dbSNP_120	225	7628,646		3512,604,21	yes	missense-near-splice	C2orf80	NM_001099334.2	56	4821,1157,88	CC,CT,TT		7.8076,17.8072,10.9875	possibly-damaging	152/194	209036712	10799,1333	1929	4137	6066	SO:0001630	splice_region_variant	389073	exon7			GCTTACTCTGTTT	AC016697, AW136505, BC035737	CCDS42809.1	2q33.3	2013-10-31			ENSG00000188674	ENSG00000188674			34352	protein-coding gene	gene with protein product	"""gonad development associated 1"""	615536				22080834, 24055526	Standard	NM_001099334		Approved	LOC389073, GONDA1	uc002vcr.3	Q0P641	OTTHUMG00000154751	ENST00000341287.4:c.454+1A>G	2.37:g.209036712T>C		Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	168	94	0.559524	NM_001099334	A6NKZ3	Missense_Mutation	SNP	ENST00000341287.4	37	CCDS42809.1	1906|1906|1906	0.8727106227106227|0.8727106227106227|0.8727106227106227	383|383|383	0.7784552845528455|0.7784552845528455|0.7784552845528455	338|338|338	0.9337016574585635|0.9337016574585635|0.9337016574585635	485|485|485	0.8479020979020979|0.8479020979020979|0.8479020979020979	700|700|700	0.9234828496042217|0.9234828496042217|0.9234828496042217	T|T|T	13.01|13.01|13.01	2.109816|2.109816|2.109816	0.37242|0.37242|0.37242	0.821928|0.821928|0.821928	0.921924|0.921924|0.921924	ENSG00000188674|ENSG00000188674|ENSG00000188674	ENST00000428015|ENST00000451342|ENST00000341287;ENST00000451346;ENST00000423952	.|T|T;T;T	.|0.29142|0.40756	.|1.58|1.55;1.48;1.02	5.25|5.25|5.25	1.54|1.54|1.54	0.23209|0.23209|0.23209	.|.|.	.|.|0.093570	.|.|0.47852	.|.|N	.|.|0.000220	T|T|T	0.00012|0.00012|0.00012	0.0000|0.0000|0.0000	L|L|L	0.32530|0.32530|0.32530	0.975|0.975|0.975	0.09310|0.09310|0.09310	P|P|P	0.999999999998778|0.999999999998778|0.999999999998778	.|.|B	.|.|0.09022	.|.|0.002	.|.|B	.|.|0.12156	.|.|0.007	T|T|T	0.15150|0.15150|0.15150	-1.0447|-1.0447|-1.0447	4|5|8	.|.|.	.|.|.	.|.|.	-15.7651|-15.7651|-15.7651	3.8963|3.8963|3.8963	0.09141|0.09141|0.09141	0.1471:0.2378:0.0:0.6151|0.1471:0.2378:0.0:0.6151|0.1471:0.2378:0.0:0.6151	rs10804166;rs52833089;rs56708342;rs10804166|rs10804166;rs52833089;rs56708342;rs10804166|rs10804166;rs52833089;rs56708342;rs10804166	.|.|152	.|.|Q0P641	.|.|CB080_HUMAN	G|V|G	103|77|152;133;65	.|ENSP00000389385:I77V|ENSP00000343171:S152G;ENSP00000405393:S133G;ENSP00000413016:S65G	.|.|.	E|I|S	-|-|-	2|1|1	0|0|0	C2orf80|C2orf80|C2orf80	208744957|208744957|208744957	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.999000|0.999000|0.999000	0.59377|0.59377|0.59377	0.045000|0.045000|0.045000	0.14185|0.14185|0.14185	1.553000|1.553000|1.553000	0.36255|0.36255|0.36255	0.177000|0.177000|0.177000	0.19895|0.19895|0.19895	-0.297000|-0.297000|-0.297000	0.09499|0.09499|0.09499	GAG|ATA|AGT	T|0.134;C|0.866	0.866	strong		0.463	C2orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336931.1	NM_001099334	Missense_Mutation
GFM2	84340	hgsc.bcm.edu	37	5	74037386	74037386	+	Missense_Mutation	SNP	T	T	A	rs16872235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:74037386T>A	ENST00000296805.3	-	11	1355	c.898A>T	c.(898-900)Agt>Tgt	p.S300C	GFM2_ENST00000345239.2_Missense_Mutation_p.S300C|GFM2_ENST00000427854.2_Missense_Mutation_p.S300C|GFM2_ENST00000509430.1_Missense_Mutation_p.S300C	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		AAATTCTCACTAAATTCTTCT	0.289													T|||	543	0.108427	0.1732	0.1066	5008	,	,		15709	0.0208		0.1382	False		,,,				2504	0.0818				p.S300C		Atlas-SNP	.											.	GFM2	38	.	0			c.A898T						PASS	.	T	CYS/SER,CYS/SER,CYS/SER	798,3594	289.8+/-280.6	65,668,1463	44.0	46.0	46.0		898,898,898	5.9	1.0	5	dbSNP_123	46	1051,7519	206.1+/-248.3	63,925,3297	yes	missense,missense,missense	GFM2	NM_032380.3,NM_170681.1,NM_170691.1	112,112,112	128,1593,4760	AA,AT,TT		12.2637,18.1694,14.2648	possibly-damaging,possibly-damaging,possibly-damaging	300/780,300/514,300/733	74037386	1849,11113	2196	4285	6481	SO:0001583	missense	84340	exon11			TCTCACTAAATTC	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.898A>T	5.37:g.74037386T>A	ENSP00000296805:p.Ser300Cys	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	283	145	0.512367	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	233	0.10668498168498168	87	0.17682926829268292	45	0.12430939226519337	14	0.024475524475524476	87	0.11477572559366754	T	18.66	3.671118	0.67814	0.181694	0.122637	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430;ENST00000427854;ENST00000509097	T;T;T;T;T	0.74421	-0.02;0.11;-0.02;-0.84;-0.14	5.88	5.88	0.94601	Protein synthesis factor, GTP-binding (1);	0.074495	0.85682	D	0.000000	T	0.00552	0.0018	L	0.39898	1.24	0.18873	P	0.9999851399	D;D;D;D;D	0.71674	0.998;0.99;0.996;0.997;0.992	P;P;P;D;P	0.64144	0.893;0.849;0.849;0.922;0.907	T	0.14282	-1.0478	9	0.87932	D	0	-20.6679	16.2868	0.82725	0.0:0.0:0.0:1.0	rs16872235;rs16872235	300;300;300;300;300	F5H687;Q969S9-3;Q969S9-5;Q969S9-2;Q969S9	.;.;.;.;RRF2M_HUMAN	C	300;300;300;300;300;258	ENSP00000296805:S300C;ENSP00000296804:S300C;ENSP00000427004:S300C;ENSP00000405808:S300C;ENSP00000421717:S258C	ENSP00000296805:S300C	S	-	1	0	GFM2	74073142	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.039000	0.57325	2.244000	0.73946	0.460000	0.39030	AGT	T|0.878;A|0.122	0.122	strong		0.289	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
MUC4	4585	hgsc.bcm.edu	37	3	195513365	195513365	+	Missense_Mutation	SNP	G	G	A	rs62282501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195513365G>A	ENST00000463781.3	-	2	5545	c.5086C>T	c.(5086-5088)Cgt>Tgt	p.R1696C	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.R1696C	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGACGGGTGGTGTCA	0.602													.|||	681	0.135982	0.118	0.1758	5008	,	,		25005	0.0476		0.2127	False		,,,				2504	0.1442				p.R1696C		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5086T						PASS	.						40.0	43.0	42.0					3																	195513365		689	1582	2271	SO:0001583	missense	4585	exon2			GAAGACGGGTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5086C>T	3.37:g.195513365G>A	ENSP00000417498:p.Arg1696Cys	Somatic	416	0	0		WXS	Illumina HiSeq	Phase_I	346	121	0.349711	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	273	0.125	36	0.07317073170731707	56	0.15469613259668508	36	0.06293706293706294	145	0.19129287598944592	-	4.772	0.143509	0.09134	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32988	1.43;1.43	.	.	.	.	.	.	.	.	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B	0.12013	0.005	B	0.01281	0.0	T	0.35674	-0.9779	6	.	.	.	.	2.8509	0.05558	3.0E-4:2.0E-4:0.5024:0.497	.	1696	E7ESK3	.	C	1696	ENSP00000417498:R1696C;ENSP00000420243:R1696C	.	R	-	1	0	MUC4	196997760	0.002000	0.14202	0.006000	0.13384	0.006000	0.05464	0.009000	0.13219	0.088000	0.17205	0.089000	0.15464	CGT	G|0.863;A|0.137	0.137	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RGPD8	727851	hgsc.bcm.edu	37	2	113127773	113127773	+	Silent	SNP	A	A	G	rs186330915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113127773A>G	ENST00000302558.3	-	23	5471	c.5280T>C	c.(5278-5280)ccT>ccC	p.P1760P	RGPD8_ENST00000409750.1_Silent_p.P1620P	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	1760				P -> A (in Ref. 3; CAI56757). {ECO:0000305}.	protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						AAGAACGGGAAGGATTTTCTT	0.308													.|||	8	0.00159744	0.0	0.0029	5008	,	,		13164	0.0		0.0	False		,,,				2504	0.0061				p.P1760P		Atlas-SNP	.											RGPD8_ENST00000302558,NS,carcinoma,-2,18	RGPD8	81	18	0			c.T5280C						PASS	.	A		2,1372		0,2,685	231.0	167.0	186.0		5280	0.7	0.9	2		186	4,3110		0,4,1553	no	coding-synonymous	RGPD8	NM_001164463.1		0,6,2238	GG,GA,AA		0.1285,0.1456,0.1337		1760/1766	113127773	6,4482	687	1557	2244	SO:0001819	synonymous_variant	727851	exon23			ACGGGAAGGATTT	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.5280T>C	2.37:g.113127773A>G		Somatic	621	0	0		WXS	Illumina HiSeq	Phase_I	568	264	0.464789	NM_001164463	Q5CZA8	Silent	SNP	ENST00000302558.3	37	CCDS46394.1																																																																																			A|0.999;G|0.001	0.001	strong		0.308	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386176	7386176	+	Silent	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:7386176G>C	ENST00000412468.2	+	2	988	c.873G>C	c.(871-873)gtG>gtC	p.V291V	POLR2A_ENST00000572844.1_5'Flank|POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	291	EamA 2.					integral component of membrane (GO:0016021)											CCGAGGTGGTGGTGGCCCTTA	0.582																																					p.V291V		Atlas-SNP	.											POLR2A_ENST00000412468,NS,haematopoietic_neoplasm,0,1	.	.	1	0			c.G873C						scavenged	.						197.0	182.0	187.0					17																	7386176		2203	4300	6503	SO:0001819	synonymous_variant	643664	exon2			GGTGGTGGTGGCC		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.873G>C	17.37:g.7386176G>C		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	358	23	0.0642458	NM_001102614		Silent	SNP	ENST00000412468.2	37	CCDS45603.1																																																																																			.	.	alt		0.582	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
ZNF146	7705	hgsc.bcm.edu	37	19	36727365	36727365	+	Missense_Mutation	SNP	G	G	A	rs2070132	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36727365G>A	ENST00000443387.2	+	4	1015	c.23G>A	c.(22-24)aGa>aAa	p.R8K	ZNF146_ENST00000456324.1_Missense_Mutation_p.R8K|ZNF565_ENST00000355114.5_Intron	NM_007145.2	NP_009076.2	Q15072	OZF_HUMAN	zinc finger protein 146	8			R -> K (in dbSNP:rs2070132). {ECO:0000269|PubMed:11306801, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8107129}.		regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11	Esophageal squamous(110;0.162)					AGCCAGCAGAGAATTTACAGT	0.433													G|||	1938	0.386981	0.3041	0.33	5008	,	,		18898	0.4683		0.3807	False		,,,				2504	0.4622				p.R8K		Atlas-SNP	.											.	ZNF146	32	.	0			c.G23A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	1500,2906	472.2+/-356.3	272,956,975	44.0	46.0	46.0		23,23,23	-1.9	0.3	19	dbSNP_96	46	3401,5199	499.6+/-375.0	697,2007,1596	yes	missense,missense,missense	ZNF146	NM_001099638.1,NM_001099639.1,NM_007145.2	26,26,26	969,2963,2571	AA,AG,GG		39.5465,34.0445,37.6826	benign,benign,benign	8/293,8/293,8/293	36727365	4901,8105	2203	4300	6503	SO:0001583	missense	7705	exon3			AGCAGAGAATTTA	X70394	CCDS12492.1	19q13.1	2013-01-08				ENSG00000167635		"""Zinc fingers, C2H2-type"""	12931	protein-coding gene	gene with protein product		601505				10449921, 8641144	Standard	NM_001099639		Approved	OZF	uc010eeu.3	Q15072		ENST00000443387.2:c.23G>A	19.37:g.36727365G>A	ENSP00000392095:p.Arg8Lys	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_001099638	Q2TB94	Missense_Mutation	SNP	ENST00000443387.2	37	CCDS12492.1	815	0.3731684981684982	154	0.3130081300813008	134	0.3701657458563536	243	0.42482517482517484	284	0.37467018469656993	G	11.56	1.675475	0.29783	0.340445	0.395465	ENSG00000167635	ENST00000443387;ENST00000456324	T;T	0.17054	2.3;2.3	4.46	-1.92	0.07618	.	0.499069	0.17087	N	0.187536	T	0.00012	0.0000	L	0.31578	0.945	0.39327	P	0.03465399999999996	B	0.06786	0.001	B	0.08055	0.003	T	0.48559	-0.9025	9	0.52906	T	0.07	-9.1357	9.9012	0.41348	0.5376:0.0:0.4624:0.0	rs2070132;rs17639642;rs52831725;rs59509631;rs2070132	8	Q15072	OZF_HUMAN	K	8	ENSP00000392095:R8K;ENSP00000400391:R8K	ENSP00000392095:R8K	R	+	2	0	ZNF146	41419205	0.000000	0.05858	0.294000	0.24946	0.816000	0.46133	-0.758000	0.04766	-0.180000	0.10637	-0.806000	0.03193	AGA	G|0.622;A|0.378	0.378	strong		0.433	ZNF146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451706.1	NM_007145	
MAK16	84549	hgsc.bcm.edu	37	8	33356074	33356074	+	Missense_Mutation	SNP	A	A	G	rs6468171	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:33356074A>G	ENST00000360128.6	+	10	1287	c.830A>G	c.(829-831)cAg>cGg	p.Q277R	TTI2_ENST00000519356.1_Intron	NM_032509.3	NP_115898.2	Q9BXY0	MAK16_HUMAN	MAK16 homolog (S. cerevisiae)	277			Q -> R (in dbSNP:rs6468171). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	8						GGACCACTGCAGAGAAAACGA	0.483													A|||	2771	0.553315	0.6762	0.4914	5008	,	,		15259	0.4851		0.6322	False		,,,				2504	0.4202				p.Q277R		Atlas-SNP	.											.	MAK16	25	.	0			c.A830G						PASS	.	A	ARG/GLN	3005,1401	687.6+/-404.9	1028,949,226	77.0	78.0	78.0		830	-7.7	0.0	8	dbSNP_116	78	5362,3238	650.8+/-400.8	1667,2028,605	yes	missense	MAK16	NM_032509.3	43	2695,2977,831	GG,GA,AA		37.6512,31.7975,35.6682	benign	277/301	33356074	8367,4639	2203	4300	6503	SO:0001583	missense	84549	exon10			CACTGCAGAGAAA	AF251062	CCDS6089.1	8p12	2011-10-13	2008-06-04	2008-06-04	ENSG00000198042	ENSG00000198042		"""RNA binding motif (RRM) containing"""	13703	protein-coding gene	gene with protein product			"""RNA binding motif protein 13"""	RBM13			Standard	NM_032509		Approved	MAK16L	uc003xjj.3	Q9BXY0	OTTHUMG00000163957	ENST00000360128.6:c.830A>G	8.37:g.33356074A>G	ENSP00000353246:p.Gln277Arg	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	127	69	0.543307	NM_032509	B2RB44|Q5U5T1|Q86UC4|Q96SY6	Missense_Mutation	SNP	ENST00000360128.6	37	CCDS6089.1	1275	0.5837912087912088	338	0.6869918699186992	181	0.5	283	0.49475524475524474	473	0.6240105540897097	A	0.008	-1.880408	0.00537	0.682025	0.623488	ENSG00000198042	ENST00000360128	T	0.40225	1.04	5.5	-7.74	0.01241	.	0.671566	0.14962	N	0.288291	T	0.00012	0.0000	N	0.00642	-1.3	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27262	-1.0079	9	0.02654	T	1	1.1579	11.6164	0.51092	0.5923:0.0:0.3273:0.0804	rs6468171;rs56555602;rs60555743;rs6468171	277	Q9BXY0	MAK16_HUMAN	R	277	ENSP00000353246:Q277R	ENSP00000353246:Q277R	Q	+	2	0	MAK16	33475616	0.012000	0.17670	0.026000	0.17262	0.024000	0.10985	0.068000	0.14531	-1.724000	0.01373	-2.367000	0.00236	CAG	A|0.389;G|0.611	0.611	strong		0.483	MAK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376559.3	NM_032509	
C6orf15	29113	hgsc.bcm.edu	37	6	31079889	31079889	+	Missense_Mutation	SNP	C	C	G	rs1265053	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31079889C>G	ENST00000259870.3	-	2	250	c.247G>C	c.(247-249)Gca>Cca	p.A83P	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	83			A -> P (in dbSNP:rs1265053). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15217361}.		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CCATCTGATGCAGGCACGCTG	0.607													G|||	2653	0.529752	0.5469	0.562	5008	,	,		16906	0.4861		0.5119	False		,,,				2504	0.547				p.A83P		Atlas-SNP	.											.	C6orf15	29	.	0			c.G247C						PASS	.	G	PRO/ALA	2434,1972	540.4+/-375.5	663,1108,432	57.0	63.0	61.0		247	2.8	0.0	6	dbSNP_87	61	4513,4087	555.0+/-386.6	1176,2161,963	yes	missense	C6orf15	NM_014070.2	27	1839,3269,1395	GG,GC,CC		47.5233,44.7571,46.5862	benign	83/326	31079889	6947,6059	2203	4300	6503	SO:0001583	missense	29113	exon2			CTGATGCAGGCAC	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.247G>C	6.37:g.31079889C>G	ENSP00000259870:p.Ala83Pro	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	1132	0.5183150183150184	277	0.5630081300813008	206	0.569060773480663	268	0.46853146853146854	381	0.5026385224274407	G	0.037	-1.301149	0.01364	0.552429	0.524767	ENSG00000204542	ENST00000259870	T	0.04454	3.62	4.61	2.79	0.32731	.	0.757705	0.11265	N	0.582147	T	0.00300	0.0009	N	0.00119	-2.075	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44097	-0.9350	9	0.02654	T	1	-13.4484	8.0239	0.30425	0.0:0.3333:0.4943:0.1724	rs1265053;rs61694373;rs1265053	83	Q6UXA7	CF015_HUMAN	P	83	ENSP00000259870:A83P	ENSP00000259870:A83P	A	-	1	0	C6orf15	31187868	0.010000	0.17322	0.000000	0.03702	0.000000	0.00434	1.057000	0.30492	0.181000	0.19994	-2.303000	0.00259	GCA	C|0.471;G|0.529	0.529	strong		0.607	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
ZNF443	10224	hgsc.bcm.edu	37	19	12542653	12542653	+	Missense_Mutation	SNP	T	T	G	rs369138475|rs4239550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12542653T>G	ENST00000301547.5	-	4	530	c.333A>C	c.(331-333)aaA>aaC	p.K111N	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	111			K -> I (in dbSNP:rs28599549).|K -> N (in dbSNP:rs4239550).		apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						GACCCATGACTTTTTCTCCTC	0.428													.|||	1954	0.390176	0.4773	0.3084	5008	,	,		20733	0.3452		0.2793	False		,,,				2504	0.4908				p.K111N		Atlas-SNP	.											.	ZNF443	63	.	0			c.A333C						PASS	.	G	ASN/LYS	1938,2468		413,1112,678	138.0	118.0	125.0		333	-0.0	0.0	19	dbSNP_111	125	2442,6158		371,1700,2229	no	missense	ZNF443	NM_005815.4	94	784,2812,2907	GG,GT,TT		28.3953,43.9855,33.6768	benign	111/672	12542653	4380,8626	2203	4300	6503	SO:0001583	missense	10224	exon4			CATGACTTTTTCT	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.333A>C	19.37:g.12542653T>G	ENSP00000301547:p.Lys111Asn	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	199	97	0.487437	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	599	0.2742673992673993	171	0.3475609756097561	96	0.26519337016574585	174	0.3041958041958042	158	0.20844327176781002	t	1.150	-0.646905	0.03506	0.439855	0.283953	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.08102	3.13	1.19	-0.0065	0.14013	.	.	.	.	.	T	0.00012	0.0000	N	0.11756	0.17	0.80722	P	0.0	B	0.14012	0.009	B	0.09377	0.004	T	0.44221	-0.9342	8	0.38643	T	0.18	.	3.8601	0.08991	0.153:0.0:0.2394:0.6075	rs4239550;rs4804690;rs6423443;rs7408558;rs58660924	111	Q9Y2A4	ZN443_HUMAN	N	111	ENSP00000301547:K111N	ENSP00000301547:K111N	K	-	3	2	ZNF443	12403653	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.345000	0.07770	-0.356000	0.08187	-0.363000	0.07495	AAA	G|0.323;T|0.677	0.323	strong		0.428	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
TMEM173	340061	hgsc.bcm.edu	37	5	138861078	138861078	+	Missense_Mutation	SNP	C	C	T	rs11554776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:138861078C>T	ENST00000330794.4	-	3	545	c.212G>A	c.(211-213)cGc>cAc	p.R71H	TMEM173_ENST00000511850.1_5'UTR	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	71			R -> H (in dbSNP:rs11554776).		activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			GTGGATGTGGCGCAGCTCCTC	0.617													C|||	1017	0.203075	0.0121	0.2781	5008	,	,		18966	0.4008		0.1471	False		,,,				2504	0.2618				p.R71H		Atlas-SNP	.											TMEM173,NS,carcinoma,0,1	TMEM173	19	1	0			c.G212A						PASS	.	C	HIS/ARG	163,4243	103.8+/-142.4	5,153,2045	53.0	53.0	53.0		212	1.8	0.0	5	dbSNP_120	53	1200,7400	236.4+/-268.6	89,1022,3189	yes	missense	TMEM173	NM_198282.2	29	94,1175,5234	TT,TC,CC		13.9535,3.6995,10.4798	possibly-damaging	71/380	138861078	1363,11643	2203	4300	6503	SO:0001583	missense	340061	exon3			ATGTGGCGCAGCT		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.212G>A	5.37:g.138861078C>T	ENSP00000331288:p.Arg71His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	135	47	0.348148	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	438	0.20054945054945056	11	0.022357723577235773	82	0.2265193370165746	232	0.40559440559440557	113	0.14907651715039577	C	4.677	0.125829	0.08931	0.036995	0.139535	ENSG00000184584	ENST00000330794;ENST00000510817	T;T	0.41758	0.99;0.99	5.58	1.84	0.25277	.	0.590726	0.19132	N	0.121905	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.13594	0.008	B	0.06405	0.002	T	0.43278	-0.9401	9	0.40728	T	0.16	-1.9834	3.65	0.08199	0.2713:0.4307:0.0:0.2979	rs11554776;rs11742049;rs52823365;rs57564432;rs11554776	71	Q86WV6	TM173_HUMAN	H	71	ENSP00000331288:R71H;ENSP00000427455:R71H	ENSP00000331288:R71H	R	-	2	0	TMEM173	138841262	0.000000	0.05858	0.028000	0.17463	0.331000	0.28603	-0.120000	0.10660	0.053000	0.16036	0.561000	0.74099	CGC	C|0.867;T|0.133	0.133	strong		0.617	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
PTK2B	2185	hgsc.bcm.edu	37	8	27255263	27255263	+	Silent	SNP	A	A	G	rs1045512	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27255263A>G	ENST00000397501.1	+	7	970	c.162A>G	c.(160-162)aaA>aaG	p.K54K	PTK2B_ENST00000420218.2_Silent_p.K54K|PTK2B_ENST00000346049.5_Silent_p.K54K|PTK2B_ENST00000517339.1_Silent_p.K54K|PTK2B_ENST00000544172.1_Silent_p.K54K|PTK2B_ENST00000338238.4_Silent_p.K54K	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	54	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)	p.K54K(1)		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)	ATCCTGGGAAAAACTTCAAAC	0.522													G|||	1591	0.317692	0.2057	0.3818	5008	,	,		21011	0.2748		0.4304	False		,,,				2504	0.3517				p.K54K		Atlas-SNP	.											PTK2B_ENST00000544172,NS,carcinoma,0,1	PTK2B	304	1	1	Substitution - coding silent(1)	stomach(1)	c.A162G						PASS	.	G	,,,	1024,3382	727.9+/-409.9	128,768,1307	155.0	142.0	146.0		162,162,162,162	3.9	1.0	8	dbSNP_86	146	3840,4760	610.7+/-395.7	868,2104,1328	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	996,2872,2635	GG,GA,AA		44.6512,23.241,37.3981	,,,	54/1010,54/1010,54/968,54/1010	27255263	4864,8142	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon7			TGGGAAAAACTTC	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.162A>G	8.37:g.27255263A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	140	60	0.428571	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			A|0.641;G|0.359	0.359	strong		0.522	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
TTC24	164118	hgsc.bcm.edu	37	1	156551848	156551848	+	Missense_Mutation	SNP	A	A	G	rs6682716	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156551848A>G	ENST00000368237.3	+	1	692	c.692A>G	c.(691-693)gAg>gGg	p.E231G	TTC24_ENST00000368236.3_Missense_Mutation_p.E231G			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	231			E -> G (in dbSNP:rs6682716).							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)					AGGAGCACTGAGAGGCGACTG	0.627													A|||	1753	0.35004	0.0825	0.4553	5008	,	,		17940	0.2877		0.7018	False		,,,				2504	0.3395				p.E231G		Atlas-SNP	.											TTC24,NS,carcinoma,0,1	TTC24	46	1	0			c.A692G						PASS	.	A	GLY/GLU	267,1113		36,195,459	9.0	10.0	10.0		692	3.4	0.0	1	dbSNP_116	10	2284,898		832,620,139	yes	missense	TTC24	NM_001105669.2	98	868,815,598	GG,GA,AA		28.2212,19.3478,44.0815		231/583	156551848	2551,2011	690	1591	2281	SO:0001583	missense	164118	exon2			GCACTGAGAGGCG		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.692A>G	1.37:g.156551848A>G	ENSP00000357220:p.Glu231Gly	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	116	116	1	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	922|922	0.42216117216117216|0.42216117216117216	47|47	0.09552845528455285|0.09552845528455285	178|178	0.49171270718232046|0.49171270718232046	166|166	0.2902097902097902|0.2902097902097902	531|531	0.7005277044854882|0.7005277044854882	A|A	13.36|13.36	2.213651|2.213651	0.39102|0.39102	0.193478|0.193478	0.717788|0.717788	ENSG00000187862|ENSG00000187862	ENST00000368236;ENST00000368237|ENST00000340086	T;T|.	0.76060|.	-0.99;-0.99|.	4.58|4.58	3.41|3.41	0.39046|0.39046	.|.	0.524885|.	0.16286|.	N|.	0.221131|.	T|T	0.17238|0.17238	0.0414|0.0414	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.07121|0.07121	-1.0789|-1.0789	6|4	.|.	.|.	.|.	-8.3235|-8.3235	9.4528|9.4528	0.38736|0.38736	0.9114:0.0:0.0886:0.0|0.9114:0.0:0.0886:0.0	rs6682716;rs52791705;rs58971631;rs6682716|rs6682716;rs52791705;rs58971631;rs6682716	.|.	.|.	.|.	G|G	231|4	ENSP00000357219:E231G;ENSP00000357220:E231G|.	.|.	E|R	+|+	2|1	0|2	TTC24|TTC24	154818472|154818472	0.024000|0.024000	0.19004|0.19004	0.019000|0.019000	0.16419|0.16419	0.077000|0.077000	0.17291|0.17291	2.290000|2.290000	0.43531|0.43531	1.933000|1.933000	0.56026|0.56026	0.374000|0.374000	0.22700|0.22700	GAG|AGA	A|0.624;G|0.376	0.376	strong		0.627	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
ANKIB1	54467	hgsc.bcm.edu	37	7	92027064	92027064	+	Missense_Mutation	SNP	G	G	T	rs200132000		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92027064G>T	ENST00000265742.3	+	19	2799	c.2423G>T	c.(2422-2424)cGc>cTc	p.R808L		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	808							zinc ion binding (GO:0008270)	p.R808L(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGCAGCAGCCGCAGGCCTGGC	0.473																																					p.R808L		Atlas-SNP	.											ANKIB1,NS,carcinoma,0,1	ANKIB1	92	1	1	Substitution - Missense(1)	lung(1)	c.G2423T						PASS	.						153.0	164.0	161.0					7																	92027064		1949	4164	6113	SO:0001583	missense	54467	exon19			GCAGCCGCAGGCC	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2423G>T	7.37:g.92027064G>T	ENSP00000265742:p.Arg808Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	37	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271294	0.59649	.	.	ENSG00000001629	ENST00000265742	T	0.10763	2.84	5.87	3.91	0.45181	.	0.335987	0.35615	N	0.003097	T	0.11367	0.0277	L	0.29908	0.895	0.46823	D	0.999216	P;P	0.35551	0.509;0.465	B;B	0.40165	0.321;0.069	T	0.07028	-1.0794	10	0.87932	D	0	.	12.8561	0.57886	0.1408:0.0:0.8592:0.0	.	160;808	Q4VBX8;Q9P2G1	.;AKIB1_HUMAN	L	808	ENSP00000265742:R808L	ENSP00000265742:R808L	R	+	2	0	ANKIB1	91865000	1.000000	0.71417	0.999000	0.59377	0.817000	0.46193	1.255000	0.32909	0.816000	0.34421	0.655000	0.94253	CGC	.	.	alt		0.473	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
PHKB	5257	hgsc.bcm.edu	37	16	47533770	47533770	+	Silent	SNP	C	C	T	rs139431568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:47533770C>T	ENST00000323584.5	+	3	294	c.270C>T	c.(268-270)tgC>tgT	p.C90C	PHKB_ENST00000566044.1_Silent_p.C83C|PHKB_ENST00000455779.1_Silent_p.C83C|PHKB_ENST00000299167.8_Silent_p.C90C|PHKB_ENST00000567402.1_3'UTR	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	90					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.C90C(2)|p.C83C(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GCCTATACTGCGCTGCTGGGG	0.507													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19579	0.0		0.002	False		,,,				2504	0.0				p.C90C		Atlas-SNP	.											PHKB_ENST00000323584,colon,carcinoma,0,3	PHKB	298	3	3	Substitution - coding silent(3)	large_intestine(3)	c.C270T						PASS	.	C	,	0,4402		0,0,2201	137.0	124.0	128.0		270,249	0.2	1.0	16	dbSNP_134	128	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	PHKB	NM_000293.2,NM_001031835.2	,	0,12,6489	TT,TC,CC		0.1395,0.0,0.0923	,	90/1094,83/1087	47533770	12,12990	2201	4300	6501	SO:0001819	synonymous_variant	5257	exon3			ATACTGCGCTGCT		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.270C>T	16.37:g.47533770C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	135	55	0.407407	NM_000293	Q8N4T5	Silent	SNP	ENST00000323584.5	37	CCDS10729.1																																																																																			C|0.999;T|0.001	0.001	strong		0.507	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		
IGF2R	3482	hgsc.bcm.edu	37	6	160464289	160464289	+	Silent	SNP	G	G	A	rs894817	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:160464289G>A	ENST00000356956.1	+	12	1738	c.1590G>A	c.(1588-1590)ggG>ggA	p.G530G		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	530					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	AGGCACGAGGGTGTCCCGAGG	0.493													G|||	2122	0.423722	0.2784	0.3516	5008	,	,		18930	0.748		0.3181	False		,,,				2504	0.4458				p.G530G		Atlas-SNP	.											.	IGF2R	251	.	0			c.G1590A						PASS	.	G		1232,3174	425.7+/-340.9	159,914,1130	137.0	127.0	130.0		1590	3.6	0.5	6	dbSNP_86	130	2632,5968	426.4+/-355.3	416,1800,2084	no	coding-synonymous	IGF2R	NM_000876.2		575,2714,3214	AA,AG,GG		30.6047,27.9619,29.7094		530/2492	160464289	3864,9142	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon12			ACGAGGGTGTCCC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1590G>A	6.37:g.160464289G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	36	28	0.777778	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			G|0.650;A|0.350	0.350	strong		0.493	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
FHAD1	114827	hgsc.bcm.edu	37	1	15723833	15723833	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15723833G>A	ENST00000375998.4	+	30	4163	c.4163G>A	c.(4162-4164)aGa>aAa	p.R1388K	FHAD1_ENST00000314740.8_Missense_Mutation_p.R659K|FHAD1_ENST00000358897.4_Missense_Mutation_p.R1388K|FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000417793.1_Missense_Mutation_p.R1352K			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1388										skin(1)|stomach(1)	2						GACCAAGAAAGAGAGATGCTG	0.473																																					p.R1388K		Atlas-SNP	.											.	FHAD1	78	.	0			c.G4163A						PASS	.						120.0	113.0	115.0					1																	15723833		692	1591	2283	SO:0001583	missense	114827	exon31			AAGAAAGAGAGAT	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.4163G>A	1.37:g.15723833G>A	ENSP00000365166:p.Arg1388Lys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	74	4	0.0540541	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		.	.	.	.	.	.	.	.	.	.	G	3.840	-0.033936	0.07543	.	.	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668	T;T;T;T;T;T	0.61510	0.83;0.83;0.83;0.1;0.11;0.86	4.54	2.69	0.31865	.	.	.	.	.	T	0.43700	0.1259	L	0.44542	1.39	0.24039	N	0.996089	B;B	0.15930	0.015;0.005	B;B	0.23419	0.046;0.004	T	0.33369	-0.9871	9	0.08599	T	0.76	.	6.7927	0.23709	0.2048:0.0:0.7952:0.0	.	659;1388	B7WPP2;B1AJZ9	.;FHAD1_HUMAN	K	1388;1352;1388;677;659;623	ENSP00000351770:R1388K;ENSP00000407615:R1352K;ENSP00000365166:R1388K;ENSP00000434909:R677K;ENSP00000322979:R659K;ENSP00000318812:R623K	ENSP00000318812:R623K	R	+	2	0	FHAD1	15596420	0.999000	0.42202	0.965000	0.40720	0.041000	0.13682	0.887000	0.28254	0.850000	0.35239	0.655000	0.94253	AGA	.	.	none		0.473	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
PROC	5624	hgsc.bcm.edu	37	2	128184770	128184770	+	Silent	SNP	T	T	C	rs5937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:128184770T>C	ENST00000234071.3	+	8	855	c.768T>C	c.(766-768)gaT>gaC	p.D256D	PROC_ENST00000409048.1_Silent_p.D290D|PROC_ENST00000422777.3_Silent_p.D256D|PROC_ENST00000453608.2_Silent_p.D311D	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	256	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	ACTGCATGGATGAGTCCAAGA	0.632													T|||	1151	0.229832	0.3472	0.2104	5008	,	,		14990	0.001		0.3052	False		,,,				2504	0.2434				p.D256D		Atlas-SNP	.											.	PROC	31	.	0			c.T768C						PASS	.	T		1389,3017	455.1+/-350.9	232,925,1046	56.0	57.0	57.0		768	-2.8	0.0	2	dbSNP_52	57	2826,5774	442.6+/-360.1	495,1836,1969	no	coding-synonymous	PROC	NM_000312.3		727,2761,3015	CC,CT,TT		32.8605,31.5252,32.4081		256/462	128184770	4215,8791	2203	4300	6503	SO:0001819	synonymous_variant	5624	exon8			CATGGATGAGTCC	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.768T>C	2.37:g.128184770T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	41	23	0.560976	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Silent	SNP	ENST00000234071.3	37	CCDS2145.1																																																																																			T|0.718;C|0.282	0.282	strong		0.632	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312	
STK31	56164	hgsc.bcm.edu	37	7	23775454	23775454	+	Missense_Mutation	SNP	G	G	A	rs10264952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:23775454G>A	ENST00000355870.3	+	7	900	c.781G>A	c.(781-783)Gag>Aag	p.E261K	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.E238K|STK31_ENST00000428484.1_Missense_Mutation_p.E238K|STK31_ENST00000433467.2_Missense_Mutation_p.E261K	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	261			E -> K (in dbSNP:rs10264952). {ECO:0000269|PubMed:17344846}.			acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GCACTTAAGTGAGAAAATGAC	0.413													g|||	423	0.0844649	0.0582	0.1196	5008	,	,		18454	0.0308		0.173	False		,,,				2504	0.0593				p.E261K		Atlas-SNP	.											.	STK31	175	.	0			c.G781A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	353,4053	181.9+/-209.8	14,325,1864	72.0	74.0	73.0		712,781,712	5.2	0.9	7	dbSNP_119	73	1622,6978	300.4+/-304.9	133,1356,2811	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	56,56,56	147,1681,4675	AA,AG,GG		18.8605,8.0118,15.1853	benign,benign,benign	238/997,261/1020,238/997	23775454	1975,11031	2203	4300	6503	SO:0001583	missense	56164	exon7			TTAAGTGAGAAAA	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.781G>A	7.37:g.23775454G>A	ENSP00000348132:p.Glu261Lys	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	232	0.10622710622710622	32	0.06504065040650407	55	0.15193370165745856	15	0.026223776223776224	130	0.17150395778364116	g	9.806	1.181881	0.21787	0.080118	0.188605	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	5.16	5.16	0.70880	.	0.412070	0.25302	N	0.031648	T	0.00012	0.0000	N	0.08118	0	0.38838	P	0.044008999999999965	B;B	0.21520	0.002;0.057	B;B	0.20767	0.001;0.031	T	0.23297	-1.0192	9	0.36615	T	0.2	-3.9172	10.0315	0.42103	0.0927:0.0:0.9073:0.0	rs10264952;rs52803859;rs57441640;rs10264952	261;261	B4DZ06;Q9BXU1	.;STK31_HUMAN	K	261;261;238;238	ENSP00000348132:E261K;ENSP00000411852:E261K;ENSP00000346660:E238K;ENSP00000406146:E238K	ENSP00000346660:E238K	E	+	1	0	STK31	23741979	1.000000	0.71417	0.933000	0.37362	0.064000	0.16182	4.713000	0.61895	2.557000	0.86248	0.467000	0.42956	GAG	G|0.873;A|0.127	0.127	strong		0.413	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
IL12RB1	3594	hgsc.bcm.edu	37	19	18180413	18180413	+	Missense_Mutation	SNP	C	C	G	rs401502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18180413C>G	ENST00000600835.2	-	11	1430	c.1132G>C	c.(1132-1134)Ggg>Cgg	p.G378R	IL12RB1_ENST00000593993.2_Missense_Mutation_p.G378R			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	378	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> R (in dbSNP:rs401502). {ECO:0000269|Ref.3}.		cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GCAAGGCCCCCGTCCTGGCCC	0.627													C|||	1260	0.251597	0.1747	0.1729	5008	,	,		18697	0.376		0.3121	False		,,,				2504	0.2209				p.G378R		Atlas-SNP	.											.	IL12RB1	92	.	0			c.G1132C	GRCh37	CM030471	IL12RB1	M	rs401502	PASS	.	C	ARG/GLY	796,3248		76,644,1302	54.0	62.0	59.0		1132	-4.1	0.0	19	dbSNP_80	59	2582,5764		396,1790,1987	yes	missense	IL12RB1	NM_005535.1	125	472,2434,3289	GG,GC,CC		30.937,19.6835,27.2639	benign	378/663	18180413	3378,9012	2022	4173	6195	SO:0001583	missense	3594	exon10			GGCCCCCGTCCTG	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.1132G>C	19.37:g.18180413C>G	ENSP00000470788:p.Gly378Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	598	0.27380952380952384	84	0.17073170731707318	72	0.19889502762430938	206	0.36013986013986016	236	0.3113456464379947	C	5.700	0.313642	0.10789	0.196835	0.30937	ENSG00000096996	ENST00000430026	T	0.79454	-1.27	4.2	-4.14	0.03892	.	1.317880	0.04893	N	0.449891	T	0.00012	0.0000	N	0.10874	0.06	0.80722	P	0.0	B;B	0.12013	0.005;0.003	B;B	0.12837	0.008;0.003	T	0.04128	-1.0975	9	0.12766	T	0.61	-1.3151	5.1974	0.15245	0.1609:0.2116:0.0:0.6276	rs401502;rs2230367;rs17885175;rs401502	378;378	P42701-2;P42701	.;I12R1_HUMAN	R	378	ENSP00000403103:G378R	ENSP00000403103:G378R	G	-	1	0	IL12RB1	18041413	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.856000	0.01662	-0.371000	0.08004	0.430000	0.28490	GGG	C|0.703;G|0.297	0.297	strong		0.627	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
SCCPDH	51097	hgsc.bcm.edu	37	1	246930564	246930564	+	Missense_Mutation	SNP	G	G	C	rs7779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:246930564G>C	ENST00000366510.3	+	12	1628	c.1252G>C	c.(1252-1254)Ggt>Cgt	p.G418R		NM_016002.2	NP_057086.2	Q8NBX0	SCPDL_HUMAN	saccharopine dehydrogenase (putative)	418			G -> R (in dbSNP:rs7779).			lipid particle (GO:0005811)|membrane (GO:0016020)|midbody (GO:0030496)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(9)|ovary(1)	17	all_cancers(71;6.8e-05)|all_epithelial(71;7.93e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0545)|Lung NSC(105;0.0618)	all_cancers(173;0.0343)	OV - Ovarian serous cystadenocarcinoma(106;0.00323)	GBM - Glioblastoma multiforme(49;0.0896)		CAACAAACACGGTATTGAGTT	0.383													G|||	119	0.023762	0.0015	0.0562	5008	,	,		16912	0.0		0.0666	False		,,,				2504	0.0112				p.G418R		Atlas-SNP	.											.	SCCPDH	37	.	0			c.G1252C						PASS	.	G	ARG/GLY	59,4347	58.7+/-95.3	0,59,2144	102.0	99.0	100.0		1252	5.9	1.0	1	dbSNP_52	100	637,7963	164.5+/-216.8	42,553,3705	yes	missense	SCCPDH	NM_016002.2	125	42,612,5849	CC,CG,GG		7.407,1.3391,5.3514	probably-damaging	418/430	246930564	696,12310	2203	4300	6503	SO:0001583	missense	51097	exon12			AAACACGGTATTG		CCDS31084.1	1q44	2009-11-06			ENSG00000143653	ENSG00000143653			24275	protein-coding gene	gene with protein product						10810093	Standard	NM_016002		Approved	CGI-49, NET11	uc001ibr.3	Q8NBX0	OTTHUMG00000040221	ENST00000366510.3:c.1252G>C	1.37:g.246930564G>C	ENSP00000355467:p.Gly418Arg	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	165	79	0.478788	NM_016002	Q8TAR0|Q9Y363	Missense_Mutation	SNP	ENST00000366510.3	37	CCDS31084.1	74	0.03388278388278388	1	0.0020325203252032522	25	0.06906077348066299	0	0.0	48	0.0633245382585752	G	32	5.148460	0.94603	0.013391	0.07407	ENSG00000143653	ENST00000366510;ENST00000366509	T	0.75589	-0.95	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54983	0.1892	H	0.95816	3.725	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81217	-0.1033	10	0.87932	D	0	.	20.2985	0.98592	0.0:0.0:1.0:0.0	rs7779;rs1127113;rs3182666;rs7779	418	Q8NBX0	SCPDL_HUMAN	R	418;230	ENSP00000355467:G418R	ENSP00000355466:G230R	G	+	1	0	SCCPDH	244997187	1.000000	0.71417	0.951000	0.38953	0.934000	0.57294	9.010000	0.93611	2.793000	0.96121	0.655000	0.94253	GGT	G|0.954;C|0.046	0.046	strong		0.383	SCCPDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096902.2	NM_016002	
GM2A	2760	hgsc.bcm.edu	37	5	150646888	150646888	+	Missense_Mutation	SNP	T	T	C	rs61740602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:150646888T>C	ENST00000357164.3	+	4	783	c.458T>C	c.(457-459)gTt>gCt	p.V153A		NM_000405.4|NM_001167607.1	NP_000396.2|NP_001161079.1	P17900	SAP3_HUMAN	GM2 ganglioside activator	153					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|learning or memory (GO:0007611)|lipid storage (GO:0019915)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|positive regulation of hydrolase activity (GO:0051345)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	apical cortex (GO:0045179)|cytoplasmic side of plasma membrane (GO:0009898)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|mitochondrion (GO:0005739)	beta-N-acetylhexosaminidase activity (GO:0004563)|lipid transporter activity (GO:0005319)|phospholipase activator activity (GO:0016004)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|upper_aerodigestive_tract(2)	8		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCGAATTCGTTGTGCCTGAC	0.597													T|||	282	0.0563099	0.0159	0.0533	5008	,	,		19066	0.0169		0.0944	False		,,,				2504	0.1145				p.V153A		Atlas-SNP	.											GM2A,colon,carcinoma,0,2	GM2A	24	2	0			c.T458C						PASS	.	T	ALA/VAL,	120,4286	89.7+/-128.4	0,120,2083	80.0	69.0	73.0		458,	-4.4	0.0	5	dbSNP_129	73	794,7806	186.2+/-233.7	26,742,3532	yes	missense,intron	GM2A	NM_000405.4,NM_001167607.1	64,	26,862,5615	CC,CT,TT		9.2326,2.7236,7.0275	benign,	153/194,	150646888	914,12092	2203	4300	6503	SO:0001583	missense	2760	exon4			AATTCGTTGTGCC		CCDS4313.1	5q33.1	2010-03-17	2004-05-20		ENSG00000196743	ENSG00000196743			4367	protein-coding gene	gene with protein product	"""cerebroside sulfate activator protein"", ""sphingolipid activator protein 3"""	613109	"""GM2 ganglioside activator protein"""			115863, 1915857	Standard	NM_000405		Approved	SAP-3	uc003ltr.4	P17900	OTTHUMG00000130124	ENST00000357164.3:c.458T>C	5.37:g.150646888T>C	ENSP00000349687:p.Val153Ala	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	205	98	0.478049	NM_000405	B2R699|D3DQH6|Q14426|Q14428|Q6LBL5	Missense_Mutation	SNP	ENST00000357164.3	37	CCDS4313.1	105	0.04807692307692308	8	0.016260162601626018	17	0.04696132596685083	9	0.015734265734265736	71	0.09366754617414248	T	5.743	0.321444	0.10845	0.027236	0.092326	ENSG00000196743	ENST00000357164	T	0.70749	-0.51	5.15	-4.36	0.03645	MD-2-related lipid-recognition (1);	1.302560	0.04420	N	0.367500	T	0.02119	0.0066	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.02860	-1.1101	9	0.16896	T	0.51	-18.9983	5.2528	0.15531	0.2971:0.2831:0.0:0.4198	rs61740602	153	P17900	SAP3_HUMAN	A	153	ENSP00000349687:V153A	ENSP00000349687:V153A	V	+	2	0	GM2A	150627081	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.486000	0.06513	-0.679000	0.05217	-0.475000	0.04921	GTT	T|0.934;C|0.066	0.066	strong		0.597	GM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252432.1	NM_000405	
ABCC6	368	hgsc.bcm.edu	37	16	16278869	16278869	+	Silent	SNP	G	G	C	rs8058696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:16278869G>C	ENST00000205557.7	-	15	1919	c.1890C>G	c.(1888-1890)acC>acG	p.T630T	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	630	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CACTGTGTATGGTGATGCAAT	0.597													G|||	1666	0.332668	0.3245	0.4769	5008	,	,		17287	0.1627		0.4861	False		,,,				2504	0.2587				p.T630T		Atlas-SNP	.											.	ABCC6	110	.	0			c.C1890G						PASS	.	G		1574,2820	492.2+/-362.3	287,1000,910	164.0	125.0	138.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1890	-10.3	0.0	16	dbSNP_116	138	4313,4287	578.8+/-390.8	1084,2145,1071	no	coding-synonymous	ABCC6	NM_001171.5		1371,3145,1981	CC,CG,GG		49.8488,35.8216,45.3055		630/1504	16278869	5887,7107	2197	4300	6497	SO:0001819	synonymous_variant	368	exon15			GTGTATGGTGATG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1890C>G	16.37:g.16278869G>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Silent	SNP	ENST00000205557.7	37	CCDS10568.1																																																																																			G|0.598;C|0.402	0.402	strong		0.597	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
SAMM50	25813	hgsc.bcm.edu	37	22	44372632	44372632	+	Silent	SNP	C	C	T	rs14315	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:44372632C>T	ENST00000350028.4	+	9	937	c.780C>T	c.(778-780)caC>caT	p.H260H	SAMM50_ENST00000396202.3_Silent_p.H50H	NM_015380.4	NP_056195.3	Q9Y512	SAM50_HUMAN	SAMM50 sorting and assembly machinery component	260					cellular protein metabolic process (GO:0044267)|protein import into mitochondrial outer membrane (GO:0045040)|protein targeting to mitochondrion (GO:0006626)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrial sorting and assembly machinery complex (GO:0001401)|mitochondrion (GO:0005739)		p.H260H(1)		endometrium(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_neural(38;0.0966)|Ovarian(80;0.105)|Glioma(61;0.222)				TCTTTCAGCACGCCATGGTCA	0.458													C|||	2358	0.470847	0.615	0.3876	5008	,	,		20257	0.4613		0.326	False		,,,				2504	0.4939				p.H260H		Atlas-SNP	.											SAMM50,NS,carcinoma,0,1	SAMM50	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C780T						PASS	.	C		2472,1934	622.5+/-394.0	699,1074,430	117.0	99.0	106.0		780	-5.6	0.9	22	dbSNP_52	106	2330,6270	388.2+/-342.5	329,1672,2299	no	coding-synonymous	SAMM50	NM_015380.4		1028,2746,2729	TT,TC,CC		27.093,43.8947,36.9214		260/470	44372632	4802,8204	2203	4300	6503	SO:0001819	synonymous_variant	25813	exon9			TCAGCACGCCATG	AK001087	CCDS14055.1	22q13.31	2013-08-21	2013-08-21	2005-11-20	ENSG00000100347	ENSG00000100347			24276	protein-coding gene	gene with protein product		612058	"""sorting and assembly machinery component 50 homolog (S. cerevisiae)"""			15644312	Standard	NM_015380		Approved	CGI-51, TRG-3, YNL026W, OMP85, TOB55	uc003bej.3	Q9Y512	OTTHUMG00000150557	ENST00000350028.4:c.780C>T	22.37:g.44372632C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	102	59	0.578431	NM_015380	Q53HC4|Q56VW7|Q969Y9|Q96I46|Q9NW85|Q9UQM9	Silent	SNP	ENST00000350028.4	37	CCDS14055.1																																																																																			.	.	weak		0.458	SAMM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318898.2	NM_015380	
KRT6B	3854	hgsc.bcm.edu	37	12	52844246	52844246	+	Silent	SNP	A	A	G	rs28542657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52844246A>G	ENST00000252252.3	-	2	746	c.699T>C	c.(697-699)ggT>ggC	p.G233G		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	233	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)	p.G233G(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		AGTCCAGACGACCCCGTTCCC	0.557													G|||	394	0.0786741	0.0061	0.0821	5008	,	,		23280	0.1875		0.0875	False		,,,				2504	0.0532				p.G233G		Atlas-SNP	.											KRT6B,NS,carcinoma,0,1	KRT6B	90	1	1	Substitution - coding silent(1)	ovary(1)	c.T699C						scavenged	.						210.0	184.0	193.0					12																	52844246		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon2			CAGACGACCCCGT	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.699T>C	12.37:g.52844246A>G		Somatic	281	2	0.00711744		WXS	Illumina HiSeq	Phase_I	386	64	0.165803	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			.	.	weak		0.557	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
OR5H6	79295	hgsc.bcm.edu	37	3	97983374	97983374	+	Silent	SNP	A	A	G	rs4857358	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:97983374A>G	ENST00000383696.2	+	1	287	c.246A>G	c.(244-246)ttA>ttG	p.L82L	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TTGGGAGTTTAGCCTTTGTGG	0.408													A|||	1469	0.293331	0.3132	0.2695	5008	,	,		21749	0.4891		0.1233	False		,,,				2504	0.2566				p.L82L		Atlas-SNP	.											.	OR5H6	89	.	0			c.A246G						PASS	.	A		1375,3031		220,935,1048	200.0	208.0	205.0		246	-4.4	0.0	3	dbSNP_111	205	1031,7569		56,919,3325	no	coding-synonymous	OR5H6	NM_001005479.1		276,1854,4373	GG,GA,AA		11.9884,31.2074,18.4992		82/326	97983374	2406,10600	2203	4300	6503	SO:0001819	synonymous_variant	79295	exon1			GAGTTTAGCCTTT	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.246A>G	3.37:g.97983374A>G		Somatic	473	0	0		WXS	Illumina HiSeq	Phase_I	494	251	0.508097	NM_001005479	Q6IF88	Silent	SNP	ENST00000383696.2	37	CCDS33800.1																																																																																			A|0.785;G|0.215	0.215	strong		0.408	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2		
GPR157	80045	hgsc.bcm.edu	37	1	9165669	9165669	+	Missense_Mutation	SNP	G	G	A	rs12075362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:9165669G>A	ENST00000377411.4	-	3	810	c.668C>T	c.(667-669)gCg>gTg	p.A223V	GPR157_ENST00000414642.2_Intron	NM_024980.4	NP_079256.4	Q5UAW9	GP157_HUMAN	G protein-coupled receptor 157	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(4)|prostate(1)	5	all_lung(157;0.185)	all_epithelial(116;5.02e-20)|all_lung(118;3.6e-06)|Lung NSC(185;7.93e-06)|Renal(390;0.000147)|Breast(348;0.000688)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.16e-07)|COAD - Colon adenocarcinoma(227;7.73e-05)|Kidney(185;0.000252)|KIRC - Kidney renal clear cell carcinoma(229;0.000917)|STAD - Stomach adenocarcinoma(132;0.00178)|BRCA - Breast invasive adenocarcinoma(304;0.00186)|READ - Rectum adenocarcinoma(331;0.0642)		CTTCTTGTCCGCCATGGAGGA	0.657													G|||	214	0.0427316	0.0923	0.0231	5008	,	,		20009	0.001		0.0278	False		,,,				2504	0.0481				p.A223V		Atlas-SNP	.											.	GPR157	14	.	0			c.C668T						PASS	.	G	VAL/ALA	387,4019	191.2+/-216.9	16,355,1832	66.0	61.0	63.0		668	3.9	0.3	1	dbSNP_120	63	379,8221	123.1+/-182.0	3,373,3924	no	missense	GPR157	NM_024980.4	64	19,728,5756	AA,AG,GG		4.407,8.7835,5.8896	probably-damaging	223/336	9165669	766,12240	2203	4300	6503	SO:0001583	missense	80045	exon3			TTGTCCGCCATGG	AK022194	CCDS100.2	1p36.22	2012-08-21			ENSG00000180758	ENSG00000180758		"""GPCR / Class B : Orphans"""	23687	protein-coding gene	gene with protein product						10574461	Standard	XM_005263496		Approved	FLJ12132	uc001apq.1	Q5UAW9	OTTHUMG00000001758	ENST00000377411.4:c.668C>T	1.37:g.9165669G>A	ENSP00000366628:p.Ala223Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	191	183	0.958115	NM_024980	A2A334|Q8WWB8|Q9HA73	Missense_Mutation	SNP	ENST00000377411.4	37	CCDS100.2	67	0.030677655677655676	36	0.07317073170731707	9	0.024861878453038673	2	0.0034965034965034965	20	0.026385224274406333	G	17.41	3.382146	0.61845	0.087835	0.04407	ENSG00000180758	ENST00000377411	T	0.37752	1.18	4.82	3.91	0.45181	GPCR, family 2-like (1);	0.099178	0.64402	D	0.000002	T	0.02119	0.0066	L	0.48986	1.54	0.80722	D	1	D	0.63046	0.992	P	0.53313	0.723	T	0.00270	-1.1860	10	0.66056	D	0.02	-9.6716	12.4347	0.55593	0.082:0.0:0.918:0.0	rs12075362	223	Q5UAW9	GP157_HUMAN	V	223	ENSP00000366628:A223V	ENSP00000366628:A223V	A	-	2	0	GPR157	9088256	1.000000	0.71417	0.310000	0.25168	0.138000	0.21146	6.935000	0.75886	1.180000	0.42898	0.549000	0.68633	GCG	G|0.949;A|0.051	0.051	strong		0.657	GPR157-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127658.2	NM_024980	
IGFBP1	3484	hgsc.bcm.edu	37	7	45932669	45932669	+	Missense_Mutation	SNP	A	A	G	rs4619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45932669A>G	ENST00000275525.3	+	4	1055	c.759A>G	c.(757-759)atA>atG	p.I253M	IGFBP1_ENST00000468955.1_Missense_Mutation_p.I210M|IGFBP1_ENST00000457280.1_Missense_Mutation_p.I251M	NM_000596.2	NP_000587.1	P08833	IBP1_HUMAN	insulin-like growth factor binding protein 1	253			I -> M (in dbSNP:rs4619). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.10}.		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)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)|tissue regeneration (GO:0042246)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	insulin-like growth factor binding (GO:0005520)			large_intestine(2)|lung(4)	6						ACTGCCAGATATATTTTAATG	0.418													G|||	1883	0.375998	0.444	0.3588	5008	,	,		15297	0.5268		0.334	False		,,,				2504	0.184				p.I253M		Atlas-SNP	.											.	IGFBP1	19	.	0			c.A759G	GRCh37	CM055287	IGFBP1	M	rs4619	PASS	.	G	MET/ILE	1998,2408	613.7+/-392.2	469,1060,674	53.0	54.0	54.0		759	1.5	0.0	7	dbSNP_52	54	3041,5559	662.6+/-402.0	526,1989,1785	yes	missense	IGFBP1	NM_000596.2	10	995,3049,2459	GG,GA,AA		35.3605,45.3473,38.7437	benign	253/260	45932669	5039,7967	2203	4300	6503	SO:0001583	missense	3484	exon4			CCAGATATATTTT		CCDS5504.1	7p12.3	2014-09-16			ENSG00000146678	ENSG00000146678			5469	protein-coding gene	gene with protein product	"""placental protein 12"", ""amniotic fluid binding protein"", ""alpha-pregnancy-associated endometrial globulin"", ""growth hormone independent-binding protein"", ""binding protein-28"", ""binding protein-26"", ""binding protein-25"", ""IGF-binding protein 1"""	146730		IBP1		2461294	Standard	NM_000596		Approved	IGF-BP25, AFBP, hIGFBP-1, PP12	uc003tnp.3	P08833	OTTHUMG00000152343	ENST00000275525.3:c.759A>G	7.37:g.45932669A>G	ENSP00000275525:p.Ile253Met	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	29	29	1	NM_000596	A4D2F4|D3DVL9|Q8IYP5	Missense_Mutation	SNP	ENST00000275525.3	37	CCDS5504.1	882	0.40384615384615385	242	0.491869918699187	102	0.281767955801105	280	0.48951048951048953	258	0.3403693931398417	G	1.240	-0.621478	0.03636	0.453473	0.353605	ENSG00000146678	ENST00000275525;ENST00000457280;ENST00000468955	T;T;T	0.62941	-0.01;-0.01;-0.01	5.44	1.51	0.23008	Thyroglobulin type-1 (2);	0.547615	0.20243	N	0.096243	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.10450	0.0;0.005;0.005	T	0.43410	-0.9393	9	0.59425	D	0.04	-20.5084	6.1715	0.20421	0.2899:0.1242:0.5859:0.0	rs4619;rs3173754;rs9658226;rs10464236;rs11539263;rs17846130;rs17859136;rs58707225;rs4619	210;253;251	C9J6H2;P08833;C9JXF9	.;IBP1_HUMAN;.	M	253;251;210	ENSP00000275525:I253M;ENSP00000413511:I251M;ENSP00000417069:I210M	ENSP00000275525:I253M	I	+	3	3	IGFBP1	45899194	0.934000	0.31675	0.004000	0.12327	0.000000	0.00434	1.012000	0.29924	0.045000	0.15804	-1.889000	0.00537	ATA	A|0.602;G|0.397	0.397	strong		0.418	IGFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251355.2	NM_000596	
TBC1D20	128637	hgsc.bcm.edu	37	20	428553	428553	+	Missense_Mutation	SNP	T	T	C	rs36088178	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:428553T>C	ENST00000354200.4	-	2	383	c.236A>G	c.(235-237)aAt>aGt	p.N79S	Y_RNA_ENST00000384070.1_RNA	NM_144628.2	NP_653229.1	Q96BZ9	TBC20_HUMAN	TBC1 domain family, member 20	79	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		N -> S (in dbSNP:rs36088178).		acrosome assembly (GO:0001675)|cargo loading into COPII-coated vesicle (GO:0090110)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|lens fiber cell morphogenesis (GO:0070309)|lipid particle organization (GO:0034389)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|seminiferous tubule development (GO:0072520)|virion assembly (GO:0019068)	endoplasmic reticulum membrane (GO:0005789)|integral component of Golgi membrane (GO:0030173)|nuclear membrane (GO:0031965)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	12		all_epithelial(17;0.228)|Breast(17;0.231)				AGGTGGGTCATTGGCATTGAC	0.502													T|||	360	0.071885	0.0847	0.0591	5008	,	,		16481	0.1002		0.0229	False		,,,				2504	0.0849				p.N79S		Atlas-SNP	.											.	TBC1D20	34	.	0			c.A236G						PASS	.	T	SER/ASN	313,4093	166.9+/-198.0	13,287,1903	98.0	78.0	85.0		236	-4.2	0.8	20	dbSNP_126	85	228,8372	93.8+/-155.7	4,220,4076	yes	missense	TBC1D20	NM_144628.2	46	17,507,5979	CC,CT,TT		2.6512,7.1039,4.1596	benign	79/404	428553	541,12465	2203	4300	6503	SO:0001583	missense	128637	exon2			GGGTCATTGGCAT	AK055573	CCDS13002.1	20p13	2013-07-10	2005-01-05	2005-01-05	ENSG00000125875	ENSG00000125875			16133	protein-coding gene	gene with protein product		611663	"""chromosome 20 open reading frame 140"""	C20orf140		17901050	Standard	XM_005260661		Approved	dJ852M4.2	uc002wds.3	Q96BZ9	OTTHUMG00000031637	ENST00000354200.4:c.236A>G	20.37:g.428553T>C	ENSP00000346139:p.Asn79Ser	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	49	0.644737	NM_144628	A8K6I3|B9A6M1|Q5JWQ7|Q6ZSY8|Q96NE1|Q9BYM7|Q9H140	Missense_Mutation	SNP	ENST00000354200.4	37	CCDS13002.1	122	0.055860805860805864	41	0.08333333333333333	17	0.04696132596685083	46	0.08041958041958042	18	0.023746701846965697	T	0.372	-0.933372	0.02359	0.071039	0.026512	ENSG00000125875	ENST00000354200;ENST00000246077	T	0.10860	2.83	5.24	-4.21	0.03812	Rab-GAP/TBC domain (4);	0.854074	0.11047	N	0.605462	T	0.00271	0.0008	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48387	-0.9040	9	0.09843	T	0.71	-0.2232	12.4606	0.55729	0.0:0.2936:0.0:0.7064	rs36088178	79	Q96BZ9	TBC20_HUMAN	S	79;104	ENSP00000346139:N79S	ENSP00000246077:N104S	N	-	2	0	TBC1D20	376553	0.000000	0.05858	0.821000	0.32701	0.093000	0.18481	-0.413000	0.07123	-0.653000	0.05401	-0.248000	0.11899	AAT	T|0.953;C|0.047	0.047	strong		0.502	TBC1D20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251397.2	NM_144628	
PRDM6	93166	hgsc.bcm.edu	37	5	122435627	122435627	+	Missense_Mutation	SNP	G	G	A	rs1008058	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:122435627G>A	ENST00000407847.4	+	3	1285	c.871G>A	c.(871-873)Gcc>Acc	p.A291T	PRDM6_ENST00000464424.1_3'UTR	NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6	291	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						GCAGGCAGGCGCCGTGAGGAA	0.672													G|||	927	0.185104	0.0643	0.2334	5008	,	,		16270	0.3859		0.1054	False		,,,				2504	0.1892				p.A291T		Atlas-SNP	.											.	PRDM6	26	.	0			c.G871A						PASS	.	G	THR/ALA	84,1298		0,84,607	17.0	19.0	18.0		871	5.1	1.0	5	dbSNP_86	18	356,2826		17,322,1252	yes	missense	PRDM6	NM_001136239.1	58	17,406,1859	AA,AG,GG		11.1879,6.0781,9.6407	possibly-damaging	291/596	122435627	440,4124	691	1591	2282	SO:0001583	missense	93166	exon3			GCAGGCGCCGTGA	AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469	ENST00000407847.4:c.871G>A	5.37:g.122435627G>A	ENSP00000384725:p.Ala291Thr	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	181	76	0.41989	NM_001136239	B5MCJ4|Q9NQW9	Missense_Mutation	SNP	ENST00000407847.4	37	CCDS47259.1	435	0.19917582417582416	42	0.08536585365853659	64	0.17679558011049723	254	0.44405594405594406	75	0.09894459102902374	G	20.4	3.989064	0.74589	0.060781	0.111879	ENSG00000061455	ENST00000407847	T	0.72615	-0.67	5.91	5.05	0.67936	SET domain (3);	0.188519	0.44483	N	0.000459	T	0.00012	0.0000	L	0.39514	1.22	0.24453	P	0.99447099	B	0.29862	0.259	B	0.19946	0.027	T	0.33497	-0.9866	9	0.31617	T	0.26	-5.1987	14.9405	0.70989	0.0682:0.0:0.9318:0.0	rs1008058;rs1008058	291	Q9NQX0	PRDM6_HUMAN	T	291	ENSP00000384725:A291T	ENSP00000384725:A291T	A	+	1	0	PRDM6	122463526	0.906000	0.30813	1.000000	0.80357	0.997000	0.91878	2.842000	0.48230	1.518000	0.48934	0.655000	0.94253	GCC	G|0.784;A|0.216	0.216	strong		0.672	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2	XM_049619	
GPR179	440435	hgsc.bcm.edu	37	17	36493598	36493598	+	Silent	SNP	A	A	G	rs9894059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36493598A>G	ENST00000342292.4	-	3	929	c.909T>C	c.(907-909)gtT>gtC	p.V303V		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	303					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TCTCCAGGGGAACACACTATG	0.562													G|||	1295	0.258586	0.5968	0.1326	5008	,	,		18903	0.119		0.1481	False		,,,				2504	0.1483				p.V303V		Atlas-SNP	.											.	GPR179	170	.	0			c.T909C						PASS	.	G		1898,2078		474,950,564	46.0	55.0	52.0		909	0.6	1.0	17	dbSNP_119	52	925,7381		58,809,3286	no	coding-synonymous	GPR179	NM_001004334.2		532,1759,3850	GG,GA,AA		11.1365,47.7364,22.9849		303/2368	36493598	2823,9459	1988	4153	6141	SO:0001819	synonymous_variant	440435	exon3			CAGGGGAACACAC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.909T>C	17.37:g.36493598A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			A|0.762;G|0.238	0.238	strong		0.562	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
STARD6	147323	hgsc.bcm.edu	37	18	51855721	51855721	+	Missense_Mutation	SNP	C	C	T	rs2917782	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:51855721C>T	ENST00000581310.1	-	8	848	c.475G>A	c.(475-477)Gaa>Aaa	p.E159K	STARD6_ENST00000580990.2_Intron|STARD6_ENST00000307844.3_Missense_Mutation_p.E159K			P59095	STAR6_HUMAN	StAR-related lipid transfer (START) domain containing 6	159	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.		E -> K (in dbSNP:rs2917782).		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)		ACTTACTCTTCCATTGGTGAA	0.338													T|||	315	0.0628994	0.0983	0.0432	5008	,	,		15472	0.0069		0.0656	False		,,,				2504	0.0838				p.E159K		Atlas-SNP	.											.	STARD6	19	.	0			c.G475A						PASS	.	T	LYS/GLU	407,3999	788.1+/-414.9	20,367,1816	136.0	149.0	145.0		475	1.2	0.5	18	dbSNP_101	145	524,8070	793.7+/-407.5	16,492,3789	yes	missense	STARD6	NM_139171.1	56	36,859,5605	TT,TC,CC		6.0973,9.2374,7.1615	benign	159/221	51855721	931,12069	2203	4297	6500	SO:0001583	missense	147323	exon5			ACTCTTCCATTGG	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.475G>A	18.37:g.51855721C>T	ENSP00000462349:p.Glu159Lys	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	16	0.275862	NM_139171		Missense_Mutation	SNP	ENST00000581310.1	37	CCDS11955.1	121	0.0554029304029304	51	0.10365853658536585	19	0.052486187845303865	5	0.008741258741258742	46	0.06068601583113457	T	0.046	-1.264821	0.01433	0.092374	0.060973	ENSG00000174448	ENST00000307844	T	0.42900	0.96	5.53	1.23	0.21249	Lipid-binding START (3);START-like domain (1);	0.846769	0.10274	N	0.694452	T	0.00300	0.0009	N	0.00583	-1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18650	-1.0330	10	0.07644	T	0.81	.	7.7078	0.28661	0.0:0.2048:0.2427:0.5524	rs2917782;rs59947446;rs2917782	159	P59095	STAR6_HUMAN	K	159	ENSP00000310814:E159K	ENSP00000310814:E159K	E	-	1	0	STARD6	50109719	0.980000	0.34600	0.510000	0.27712	0.053000	0.15095	0.104000	0.15313	-0.328000	0.08539	-0.439000	0.05793	GAA	C|0.931;T|0.069	0.069	strong		0.338	STARD6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256000.3	NM_139171	
DNHD1	144132	hgsc.bcm.edu	37	11	6541225	6541225	+	Missense_Mutation	SNP	C	C	G	rs11603869	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6541225C>G	ENST00000527990.2	+	7	1678	c.1678C>G	c.(1678-1680)Cag>Gag	p.Q560E	DNHD1_ENST00000354685.3_Missense_Mutation_p.Q560E|DNHD1_ENST00000254579.6_Missense_Mutation_p.Q560E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	560			Q -> E (in dbSNP:rs11603869).		microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TCTCTCATCACAGCTGGTCTT	0.488													C|||	714	0.142572	0.1233	0.1628	5008	,	,		20440	0.0327		0.1909	False		,,,				2504	0.2178				p.Q560E		Atlas-SNP	.											.	DNHD1	198	.	0			c.C1678G						PASS	.	C	GLU/GLN,GLU/GLN	545,3857	247.2+/-255.5	36,473,1692	161.0	149.0	153.0		1678,1678	3.6	0.2	11	dbSNP_120	153	1840,6752	328.8+/-318.4	201,1438,2657	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	29,29	237,1911,4349	GG,GC,CC		21.4153,12.3807,18.3546	possibly-damaging,possibly-damaging	560/4754,560/598	6541225	2385,10609	2201	4296	6497	SO:0001583	missense	144132	exon8			TCATCACAGCTGG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.1678C>G	11.37:g.6541225C>G	ENSP00000436180:p.Gln560Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	291	0.13324175824175824	65	0.13211382113821138	52	0.143646408839779	25	0.043706293706293704	149	0.19656992084432717	C	10.69	1.420306	0.25552	0.123807	0.214153	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.25579	1.79;2.79;1.79	5.7	3.63	0.41609	.	0.813344	0.10962	N	0.614855	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B;B	0.32467	0.001;0.372	B;B	0.27796	0.002;0.083	T	0.13019	-1.0525	9	0.02654	T	1	.	9.8502	0.41053	0.1636:0.695:0.1414:0.0	rs11603869;rs11603869	560;560	Q96M86;Q96M86-4	DNHD1_HUMAN;.	E	560	ENSP00000254579:Q560E;ENSP00000346716:Q560E;ENSP00000436180:Q560E	ENSP00000254579:Q560E	Q	+	1	0	DNHD1	6497801	0.348000	0.24861	0.198000	0.23420	0.556000	0.35491	1.531000	0.36018	1.401000	0.46761	0.561000	0.74099	CAG	C|0.836;G|0.164	0.164	strong		0.488	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
ZNF98	148198	hgsc.bcm.edu	37	19	22585674	22585674	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:22585674G>A	ENST00000357774.5	-	3	291	c.170C>T	c.(169-171)tCt>tTt	p.S57F	ZNF98_ENST00000601553.1_Missense_Mutation_p.S57F	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	57	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S57Y(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)				GTCTGGCTTAGAGGCAGCAAT	0.393																																					p.S57F		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,0,2	ZNF98	230	2	2	Substitution - Missense(2)	prostate(2)	c.C170T						PASS	.																																			SO:0001583	missense	148198	exon3			GGCTTAGAGGCAG		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.170C>T	19.37:g.22585674G>A	ENSP00000350418:p.Ser57Phe	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	13.75	2.330284	0.41297	.	.	ENSG00000197360	ENST00000357774	T	0.00848	5.62	0.476	0.476	0.16779	Krueppel-associated box (3);	.	.	.	.	T	0.01029	0.0034	L	0.35793	1.09	0.22389	N	0.999141	P	0.37525	0.598	B	0.37888	0.26	T	0.50923	-0.8770	8	0.45353	T	0.12	.	.	.	.	.	57	A6NK75	ZNF98_HUMAN	F	57	ENSP00000350418:S57F	ENSP00000350418:S57F	S	-	2	0	ZNF98	22377514	0.164000	0.22935	0.816000	0.32577	0.950000	0.60333	0.418000	0.21230	0.532000	0.28657	0.298000	0.19748	TCT	.	.	none		0.393	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
TMPRSS2	7113	hgsc.bcm.edu	37	21	42866296	42866296	+	Silent	SNP	T	T	C	rs3787950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:42866296T>C	ENST00000332149.5	-	3	359	c.225A>G	c.(223-225)acA>acG	p.T75T	TMPRSS2_ENST00000398585.3_Silent_p.T112T|TMPRSS2_ENST00000458356.1_Silent_p.T75T|TMPRSS2_ENST00000497881.1_Intron	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	75					positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.T75T(1)	TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				AGGTGCACACTGTCCCGGATG	0.602			T	"""ERG, ETV1, ETV4, ETV5"""	prostate								T|||	816	0.162939	0.2179	0.0605	5008	,	,		18021	0.1548		0.0785	False		,,,				2504	0.2566				p.T112T		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"""transmembrane protease, serine 2"""		E	TMPRSS2_ENST00000332149,NS,carcinoma,0,1	TMPRSS2	148	1	1	Substitution - coding silent(1)	stomach(1)	c.A336G						PASS	.	T	,	831,3575	325.6+/-299.2	91,649,1463	47.0	46.0	46.0		336,225	-9.0	0.0	21	dbSNP_107	46	700,7900	167.4+/-219.2	38,624,3638	no	coding-synonymous,coding-synonymous	TMPRSS2	NM_001135099.1,NM_005656.3	,	129,1273,5101	CC,CT,TT		8.1395,18.8606,11.7715	,	112/530,75/493	42866296	1531,11475	2203	4300	6503	SO:0001819	synonymous_variant	7113	exon3			GCACACTGTCCCG	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"""Serine peptidases / Transmembrane"""	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.225A>G	21.37:g.42866296T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Silent	SNP	ENST00000332149.5	37	CCDS33564.1																																																																																			C|0.135;N|0.001	0.135	strong		0.602	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1		
ATG4B	23192	hgsc.bcm.edu	37	2	242610738	242610738	+	Silent	SNP	T	T	C	rs11538896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:242610738T>C	ENST00000404914.3	+	12	1129	c.1026T>C	c.(1024-1026)ctT>ctC	p.L342L	ATG4B_ENST00000474739.2_Silent_p.L328L|ATG4B_ENST00000402096.1_Silent_p.L268L|ATG4B_ENST00000396411.3_Silent_p.L268L|ATG4B_ENST00000405546.3_Silent_p.L342L	NM_013325.4|NM_178326.2	NP_037457.3|NP_847896.1	Q9Y4P1	ATG4B_HUMAN	autophagy related 4B, cysteine peptidase	342					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|positive regulation of autophagy (GO:0010508)|positive regulation of protein catabolic process (GO:0045732)|protein transport (GO:0015031)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)			breast(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;2.44e-33)|all cancers(36;5.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.75e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0848)		TGTCTCTGCTTGGAGGTGCCC	0.627													C|||	1027	0.205072	0.0787	0.2089	5008	,	,		19333	0.2966		0.2336	False		,,,				2504	0.2495				p.L342L	Melanoma(78;458 1323 6342 12171 39523)	Atlas-SNP	.											.	ATG4B	35	.	0			c.T1026C						PASS	.	C	,	413,3859		23,367,1746	65.0	71.0	69.0		1026,1026	-9.1	0.0	2	dbSNP_120	69	1876,6578		229,1418,2580	no	coding-synonymous,coding-synonymous	ATG4B	NM_013325.4,NM_178326.2	,	252,1785,4326	CC,CT,TT		22.1907,9.6676,17.9868	,	342/394,342/381	242610738	2289,10437	2136	4227	6363	SO:0001819	synonymous_variant	23192	exon12			TCTGCTTGGAGGT	AB023160	CCDS46564.1, CCDS46565.1	2q37.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000168397	ENSG00000168397			20790	protein-coding gene	gene with protein product		611338	"""APG4 autophagy 4 homolog B (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog B (S. cerevisiae)"""	APG4B		12446702	Standard	NM_013325		Approved	Apg4B, KIAA0943, DKFZp586D1822, AUTL1	uc002wbv.3	Q9Y4P1	OTTHUMG00000151514	ENST00000404914.3:c.1026T>C	2.37:g.242610738T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	44	0.4	NM_178326	B7WNK2|Q53NU4|Q6ZUV8|Q8WYM9|Q96K07|Q96K96|Q96SZ1|Q9Y2F2	Silent	SNP	ENST00000404914.3	37	CCDS46564.1																																																																																			T|0.776;C|0.224	0.224	strong		0.627	ATG4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322967.3	NM_013325	
TRPC4	7223	hgsc.bcm.edu	37	13	38211046	38211046	+	Silent	SNP	T	T	C	rs731860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:38211046T>C	ENST00000379705.3	-	11	3785	c.2928A>G	c.(2926-2928)agA>agG	p.R976R	TRPC4_ENST00000355779.2_Silent_p.R835R|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000338947.5_Silent_p.R803R|TRPC4_ENST00000358477.2_Silent_p.R892R|TRPC4_ENST00000379681.3_Silent_p.R981R|TRPC4_ENST00000447043.1_Silent_p.R835R|TRPC4_ENST00000379679.1_Silent_p.R803R|TRPC4_ENST00000379673.2_Silent_p.R827R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	976	Binds to ITPR1, ITPR2 and ITPR3.|PDZ-binding domain.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		AGTATCACAATCTTGTGGTCA	0.403													T|||	154	0.0307508	0.1112	0.0086	5008	,	,		19821	0.0		0.001	False		,,,				2504	0.0				p.R981R		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2943G						PASS	.	T	,,,,,	428,3978	208.5+/-229.5	24,380,1799	118.0	111.0	114.0		2676,2481,2505,2409,2943,2928	-1.3	0.2	13	dbSNP_86	114	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	24,387,6092	CC,CT,TT		0.0814,9.714,3.3446	,,,,,	892/894,827/829,835/837,803/805,981/983,976/978	38211046	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon11			TCACAATCTTGTG	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2928A>G	13.37:g.38211046T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			T|0.959;C|0.041	0.041	strong		0.403	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
CAST	831	hgsc.bcm.edu	37	5	96031569	96031569	+	5'UTR	SNP	A	A	G	rs9667	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96031569A>G	ENST00000341926.3	+	0	81				CAST_ENST00000510756.1_Silent_p.Q56Q|CAST_ENST00000325674.7_Silent_p.Q56Q|CAST_ENST00000395812.2_Silent_p.Q56Q|CAST_ENST00000508830.1_Silent_p.Q56Q|CAST_ENST00000359176.4_Silent_p.Q56Q|CAST_ENST00000395813.1_Silent_p.Q56Q|CAST_ENST00000508608.1_Silent_p.Q41Q|AC020900.2_ENST00000580431.1_RNA|CAST_ENST00000338252.3_5'UTR			P20810	ICAL_HUMAN	calpastatin						negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		GCAGCAGTCAATCCTCCAGAA	0.428													A|||	1014	0.202476	0.1225	0.2305	5008	,	,		16879	0.253		0.1889	False		,,,				2504	0.2526				p.Q56Q		Atlas-SNP	.											.	CAST	58	.	0			c.A168G						PASS	.	A	,	500,3220		38,424,1398	42.0	40.0	41.0		168,	-8.6	0.0	5	dbSNP_52	41	1564,6620		154,1256,2682	no	coding-synonymous,utr-5	CAST	NM_001042440.2,NM_001190442.1	,	192,1680,4080	GG,GA,AA		19.1105,13.4409,17.3387	,	56/751,	96031569	2064,9840	1860	4092	5952	SO:0001623	5_prime_UTR_variant	831	exon3			CAGTCAATCCTCC	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.-82A>G	5.37:g.96031569A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Silent	SNP	ENST00000341926.3	37		408	0.18681318681318682	50	0.1016260162601626	73	0.20165745856353592	143	0.25	142	0.18733509234828497	A	1.723	-0.496032	0.04291	0.134409	0.191105	ENSG00000153113	ENST00000512620	.	.	.	5.18	-8.58	0.00897	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.37307	P	0.091028	.	.	.	.	.	.	T	0.16600	-1.0397	3	.	.	.	-0.5219	8.4796	0.33034	0.6194:0.2114:0.1693:0.0	rs9667;rs27894;rs1135385;rs3198018;rs9667	.	.	.	S	39	.	.	N	+	2	0	CAST	96057325	0.000000	0.05858	0.002000	0.10522	0.226000	0.24999	-1.032000	0.03574	-1.388000	0.02092	0.459000	0.35465	AAT	A|0.818;G|0.182	0.182	strong		0.428	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	
TFAM	7019	hgsc.bcm.edu	37	10	60145342	60145342	+	Missense_Mutation	SNP	G	G	C	rs1937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:60145342G>C	ENST00000487519.1	+	1	561	c.35G>C	c.(34-36)aGt>aCt	p.S12T	TFAM_ENST00000373899.3_3'UTR|TFAM_ENST00000373895.3_Missense_Mutation_p.S12T	NM_001270782.1|NM_003201.2	NP_001257711.1|NP_003192.1	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial	12			S -> T (in dbSNP:rs1937). {ECO:0000269|PubMed:1610904, ECO:0000269|PubMed:19054851, ECO:0000269|PubMed:19096125}.		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						GGCGTGCTGAGTGCCCTGGGA	0.642											OREG0020196	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	443	0.0884585	0.0068	0.0908	5008	,	,		15287	0.1716		0.0875	False		,,,				2504	0.1125				p.S12T		Atlas-SNP	.											.	TFAM	52	.	0			c.G35C	GRCh37	CM086330	TFAM	M	rs1937	PASS	.	G	THR/SER	93,4305		0,93,2106	77.0	64.0	68.0		35	0.6	0.1	10	dbSNP_36	68	812,7778		32,748,3515	yes	missense	TFAM	NM_003201.1	58	32,841,5621	CC,CG,GG		9.4529,2.1146,6.968	benign	12/247	60145342	905,12083	2199	4295	6494	SO:0001583	missense	7019	exon1			TGCTGAGTGCCCT	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.35G>C	10.37:g.60145342G>C	ENSP00000420588:p.Ser12Thr	Somatic	97	0	0	1043	WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_003201	A8MRB2|A9QXC6|B5BU05|Q5U0C6	Missense_Mutation	SNP	ENST00000487519.1	37	CCDS7253.1	205	0.09386446886446886	4	0.008130081300813009	33	0.09116022099447514	98	0.17132867132867133	70	0.09234828496042216	G	2.997	-0.206794	0.06180	0.021146	0.094529	ENSG00000108064	ENST00000487519;ENST00000373895	T;T	0.14766	2.49;2.48	4.97	0.598	0.17512	.	0.437414	0.25025	N	0.033729	T	0.00039	0.0001	L	0.36672	1.1	0.80722	P	0.0	B;B	0.13594	0.008;0.008	B;B	0.09377	0.004;0.002	T	0.31052	-0.9957	9	0.39692	T	0.17	.	6.523	0.22285	0.2509:0.1335:0.6156:0.0	rs1937;rs1049400;rs2228267;rs3189561;rs11006128;rs17149816;rs17847534;rs61037439;rs1937	12;12	A8MRB2;Q00059	.;TFAM_HUMAN	T	12	ENSP00000420588:S12T;ENSP00000363002:S12T	ENSP00000363002:S12T	S	+	2	0	TFAM	59815348	0.583000	0.26757	0.096000	0.21009	0.296000	0.27459	0.553000	0.23391	0.066000	0.16515	-0.797000	0.03246	AGT	G|0.919;C|0.081	0.081	strong		0.642	TFAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048146.1	NM_003201	
RPLP0	6175	hgsc.bcm.edu	37	12	120636498	120636498	+	Silent	SNP	G	G	A	rs138718343		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:120636498G>A	ENST00000551150.1	-	5	825	c.510C>T	c.(508-510)agC>agT	p.S170S	PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000539446.1_RNA|RPLP0_ENST00000550296.1_5'Flank|PXN-AS1_ENST00000542265.1_RNA|PXN-AS1_ENST00000542314.1_RNA|PXN-AS1_ENST00000538804.1_RNA|RPLP0_ENST00000313104.5_Intron|RPLP0_ENST00000552292.1_5'Flank|RPLP0_ENST00000546989.1_Intron|RPLP0_ENST00000392514.4_Silent_p.S170S|RPLP0_ENST00000228306.4_Silent_p.S170S			P05388	RLA0_HUMAN	ribosomal protein, large, P0	170					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)					GCGTGGCTTCGCTGGCTCCCA	0.527																																					p.S170S		Atlas-SNP	.											.	RPLP0	27	.	0			c.C510T						PASS	.	G	,	0,4406		0,0,2203	72.0	69.0	70.0		510,510	-0.5	1.0	12	dbSNP_134	70	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	RPLP0	NM_001002.3,NM_053275.3	,	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	,	170/318,170/318	120636498	3,12999	2203	4298	6501	SO:0001819	synonymous_variant	6175	exon6			GGCTTCGCTGGCT	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.510C>T	12.37:g.120636498G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	201	86	0.427861	NM_053275	Q3B7A4|Q9BVK4	Silent	SNP	ENST00000551150.1	37	CCDS9193.1																																																																																			G|1.000;A|0.000	0.000	weak		0.527	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275	
SIRPA	140885	hgsc.bcm.edu	37	20	1895889	1895889	+	Missense_Mutation	SNP	G	G	C	rs72620874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1895889G>C	ENST00000358771.4	+	2	376	c.224G>C	c.(223-225)gGc>gCc	p.G75A	SIRPA_ENST00000356025.3_Missense_Mutation_p.G75A|SIRPA_ENST00000400068.3_Missense_Mutation_p.G75A	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	75	Ig-like V-type.		G -> A (in dbSNP:rs1057114). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.G75A(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		GCTGGACCAGGCCGGGAATTA	0.537													G|||	2164	0.432109	0.298	0.4553	5008	,	,		14136	0.6369		0.3588	False		,,,				2504	0.4611				p.G75A	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,right_upper_lobe,carcinoma,+1,3	SIRPA	83	3	1	Substitution - Missense(1)	pancreas(1)	c.G224C						PASS	.						68.0	62.0	64.0					20																	1895889		2203	4297	6500	SO:0001583	missense	140885	exon3			GACCAGGCCGGGA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.224G>C	20.37:g.1895889G>C	ENSP00000351621:p.Gly75Ala	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	163	20	0.122699	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	952	0.4358974358974359	153	0.31097560975609756	151	0.4171270718232044	373	0.6520979020979021	275	0.3627968337730871	G	8.882	0.951948	0.18431	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.66995	-0.24;-0.24;-0.24	5.11	-1.44	0.08856	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.281220	0.04967	N	0.463081	T	0.00012	0.0000	L	0.60957	1.885	0.80722	P	0.0	B;B;B	0.22851	0.0;0.076;0.001	B;B;B	0.26416	0.02;0.069;0.012	T	0.48514	-0.9029	9	0.37606	T	0.19	.	8.9336	0.35686	0.7056:0.0:0.2944:0.0	.	55;75;75	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	A	75	ENSP00000382941:G75A;ENSP00000348307:G75A;ENSP00000351621:G75A	ENSP00000348307:G75A	G	+	2	0	SIRPA	1843889	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.791000	0.04599	-0.225000	0.09913	-0.266000	0.10368	GGC	G|0.689;C|0.311	0.311	strong		0.537	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
SLC7A7	9056	hgsc.bcm.edu	37	14	23282449	23282449	+	Silent	SNP	C	C	T	rs1805059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23282449C>T	ENST00000397532.3	-	2	684	c.159G>A	c.(157-159)tcG>tcA	p.S53S	SLC7A7_ENST00000555702.1_Silent_p.S53S|SLC7A7_ENST00000285850.7_Silent_p.S53S|SLC7A7_ENST00000397528.4_Silent_p.S53S|SLC7A7_ENST00000554517.1_Intron|SLC7A7_ENST00000397529.2_Silent_p.S53S			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7	53			S -> L (in LPI). {ECO:0000269|PubMed:17764084}.		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)		CAAAGATGCCCGAGCCGATCA	0.587													C|||	3035	0.60603	0.4947	0.7104	5008	,	,		17088	0.7857		0.5964	False		,,,				2504	0.5072				p.S53S		Atlas-SNP	.											.	SLC7A7	36	.	0			c.G159A						PASS	.	C	,,	2126,2280	578.8+/-384.8	501,1124,578	111.0	108.0	109.0		159,159,159	-10.4	0.8	14	dbSNP_89	109	5189,3411	638.6+/-399.4	1537,2115,648	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC7A7	NM_001126105.2,NM_001126106.2,NM_003982.3	,,	2038,3239,1226	TT,TC,CC		39.6628,48.2524,43.7567	,,	53/512,53/512,53/512	23282449	7315,5691	2203	4300	6503	SO:0001819	synonymous_variant	9056	exon3			GATGCCCGAGCCG	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"""Solute carriers"""	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692	ENST00000397532.3:c.159G>A	14.37:g.23282449C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_001126105	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Silent	SNP	ENST00000397532.3	37	CCDS9574.1																																																																																			C|0.412;T|0.588	0.588	strong		0.587	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3		
CACNA1G	8913	hgsc.bcm.edu	37	17	48703752	48703752	+	Silent	SNP	T	T	C	rs739925	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48703752T>C	ENST00000359106.5	+	38	6774	c.6774T>C	c.(6772-6774)ccT>ccC	p.P2258P	CACNA1G_ENST00000514717.1_Silent_p.P2108P|CACNA1G_ENST00000442258.2_Silent_p.P2124P|CACNA1G_ENST00000512389.1_Silent_p.P2154P|CACNA1G_ENST00000513964.1_Silent_p.P2120P|CACNA1G_ENST00000507609.1_Silent_p.P2158P|CACNA1G_ENST00000503485.1_Silent_p.P2131P|CACNA1G_ENST00000513689.2_Silent_p.P2168P|CACNA1G_ENST00000505165.1_Silent_p.P2086P|CACNA1G_ENST00000507336.1_Silent_p.P2247P|CACNA1G_ENST00000515765.1_Silent_p.P2202P|CACNA1G_ENST00000502264.1_Silent_p.P2187P|CACNA1G_ENST00000510115.1_Silent_p.P2179P|CACNA1G_ENST00000360761.4_Silent_p.P2142P|CACNA1G_ENST00000354983.4_Silent_p.P2224P|CACNA1G_ENST00000507896.1_Silent_p.P2075P|CACNA1G_ENST00000358244.5_Silent_p.P2052P|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000515165.1_Silent_p.P2165P|CACNA1G_ENST00000510366.1_Silent_p.P2113P|CACNA1G_ENST00000515411.1_Silent_p.P2195P|CACNA1G_ENST00000352832.5_Silent_p.P2131P|CACNA1G_ENST00000514181.1_Silent_p.P2140P|CACNA1G_ENST00000514079.1_Silent_p.P2172P|CACNA1G_ENST00000507510.2_Silent_p.P2213P|CACNA1G_ENST00000429973.2_Silent_p.P2147P	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2258					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGCGCCGGCCTACGTCCTGGC	0.677											OREG0024569	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1839	0.367212	0.5393	0.2651	5008	,	,		14167	0.1786		0.4433	False		,,,				2504	0.3231				p.P2258P		Atlas-SNP	.											.	CACNA1G	659	.	0			c.T6774C						PASS	.	C	,,,,,,,,,,,,,	2057,2001		538,981,510	16.0	21.0	19.0		6774,6156,6705,6462,6537,6606,6426,6561,6495,6639,6441,6393,6372,6672	-10.9	0.0	17	dbSNP_86	19	3608,4724		780,2048,1338	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1	,,,,,,,,,,,,,	1318,3029,1848	CC,CT,TT		43.3029,49.31,45.7224	,,,,,,,,,,,,,	2258/2378,2052/2172,2235/2355,2154/2274,2179/2299,2202/2322,2142/2262,2187/2307,2165/2285,2213/2333,2147/2267,2131/2251,2124/2244,2224/2344	48703752	5665,6725	2029	4166	6195	SO:0001819	synonymous_variant	8913	exon38			CCGGCCTACGTCC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.6774T>C	17.37:g.48703752T>C		Somatic	123	1	0.00813008	956	WXS	Illumina HiSeq	Phase_I	122	119	0.97541	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			T|0.603;G|0.006	.	strong		0.677	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209816	84209816	+	Missense_Mutation	SNP	T	T	C	rs2288022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84209816T>C	ENST00000378553.5	+	11	2100	c.1976T>C	c.(1975-1977)cTa>cCa	p.L659P	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	659			L -> P (in dbSNP:rs2288022). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.|L -> V (in dbSNP:rs2288021).		axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						TCTGGCCAGCTACTGATGCCC	0.562													C|||	1339	0.267372	0.0613	0.4049	5008	,	,		17071	0.375		0.3439	False		,,,				2504	0.2587				p.L659P		Atlas-SNP	.											.	DNAAF1	81	.	0			c.T1976C						PASS	.	C	PRO/LEU	480,3920	773.9+/-414.0	32,416,1752	36.0	33.0	34.0		1976	2.3	0.0	16	dbSNP_100	34	3017,5583	653.0+/-401.0	558,1901,1841	yes	missense	DNAAF1	NM_178452.4	98	590,2317,3593	CC,CT,TT		35.0814,10.9091,26.9	benign	659/726	84209816	3497,9503	2200	4300	6500	SO:0001583	missense	123872	exon11			GCCAGCTACTGAT	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1976T>C	16.37:g.84209816T>C	ENSP00000367815:p.Leu659Pro	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	658	0.30128205128205127	36	0.07317073170731707	124	0.3425414364640884	237	0.4143356643356643	261	0.34432717678100266	C	0.017	-1.499376	0.01001	0.109091	0.350814	ENSG00000154099	ENST00000378553	T	0.19394	2.15	4.67	2.33	0.28932	.	1.269100	0.05886	N	0.627428	T	0.00012	0.0000	N	0.00583	-1.355	0.58432	P	1.999999999946489E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45745	-0.9240	9	0.02654	T	1	1.8768	6.3052	0.21135	0.0:0.594:0.0:0.406	rs2288022;rs17845737;rs17858687	423;659	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	P	659	ENSP00000367815:L659P	ENSP00000367815:L659P	L	+	2	0	DNAAF1	82767317	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.001000	0.13038	0.156000	0.19299	-0.355000	0.07637	CTA	A|0.000;C|0.285;T|0.715	0.285	strong		0.562	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
MROH9	80133	hgsc.bcm.edu	37	1	170959088	170959088	+	Silent	SNP	C	C	T	rs28634500	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:170959088C>T	ENST00000367758.3	+	11	1071	c.972C>T	c.(970-972)tgC>tgT	p.C324C	MROH9_ENST00000367759.4_Silent_p.C324C	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	324																	TGTTGACATGCACTTCACCCA	0.458													T|||	1109	0.221446	0.4614	0.1902	5008	,	,		20280	0.001		0.2227	False		,,,				2504	0.1452				p.C324C		Atlas-SNP	.											.	.	.	.	0			c.C972T						PASS	.	T	,	1558,2326		317,924,701	141.0	135.0	136.0		972,972	-10.4	0.0	1	dbSNP_125	136	1712,6574		185,1342,2616	no	coding-synonymous,coding-synonymous	C1orf129	NM_001163629.1,NM_025063.2	,	502,2266,3317	TT,TC,CC		20.6614,40.1133,26.8694	,	324/862,324/574	170959088	3270,8900	1942	4143	6085	SO:0001819	synonymous_variant	80133	exon11			GACATGCACTTCA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.972C>T	1.37:g.170959088C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	145	75	0.517241	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1																																																																																			C|0.791;T|0.209	0.209	strong		0.458	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
ADD2	119	hgsc.bcm.edu	37	2	70900403	70900403	+	Intron	SNP	G	G	A	rs4984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:70900403G>A	ENST00000264436.4	-	15	2186				ADD2_ENST00000355733.3_Silent_p.S599S|ADD2_ENST00000407644.2_Intron	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)						actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						GGAGGGCAACGCTGAAGAACT	0.542													A|||	633	0.126398	0.2428	0.134	5008	,	,		16056	0.004		0.1203	False		,,,				2504	0.0961				p.S599S		Atlas-SNP	.											.	ADD2	261	.	0			c.C1797T						PASS	.	A	,,	953,3453	735.5+/-410.7	97,759,1347	86.0	81.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,1797	-4.8	0.0	2	dbSNP_52	83	1121,7479	767.4+/-407.6	77,967,3256	no	intron,intron,coding-synonymous	ADD2	NM_001185054.1,NM_001617.3,NM_017488.3	,,	174,1726,4603	AA,AG,GG		13.0349,21.6296,15.9465	,,	,,599/644	70900403	2074,10932	2203	4300	6503	SO:0001627	intron_variant	119	exon15			GGCAACGCTGAAG	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.1742-265C>T	2.37:g.70900403G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	45	0.608108	NM_017488	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Silent	SNP	ENST00000264436.4	37	CCDS1906.1																																																																																			G|0.855;A|0.145	0.145	strong		0.542	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
MMP20	9313	hgsc.bcm.edu	37	11	102495998	102495998	+	Missense_Mutation	SNP	T	T	G	rs2245803	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102495998T>G	ENST00000260228.2	-	1	65	c.53A>C	c.(52-54)aAg>aCg	p.K18T	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	0					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	AGTGGAAAACTTCAAAGCCAT	0.537													T|||	3388	0.676518	0.6036	0.6816	5008	,	,		16935	0.8016		0.6262	False		,,,				2504	0.6943				p.K18T		Atlas-SNP	.											.	MMP20	52	.	0			c.A53C						PASS	.	T	THR/LYS	2751,1655	657.1+/-400.2	857,1037,309	129.0	103.0	112.0		53	4.1	0.7	11	dbSNP_100	112	5538,3060	660.5+/-401.8	1773,1992,534	yes	missense	MMP20	NM_004771.3	78	2630,3029,843	GG,GT,TT		35.5897,37.5624,36.2581	benign	18/484	102495998	8289,4715	2203	4299	6502	SO:0001583	missense	9313	exon1			GAAAACTTCAAAG	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.53A>C	11.37:g.102495998T>G	ENSP00000260228:p.Lys18Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	1483	0.6790293040293041	301	0.6117886178861789	247	0.6823204419889503	462	0.8076923076923077	473	0.6240105540897097	T	5.964	0.361845	0.11296	0.624376	0.644103	ENSG00000137674	ENST00000260228	T	0.12774	2.65	5.26	4.12	0.48240	.	1.072100	0.07112	N	0.842373	T	0.00012	0.0000	N	0.08118	0	0.36335	P	0.14090899999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.25984	-1.0116	9	0.12766	T	0.61	.	11.56	0.50772	0.0:0.0:0.1499:0.8501	rs2245803;rs11565201;rs17099166;rs58085681;rs2245803	18	O60882	MMP20_HUMAN	T	18	ENSP00000260228:K18T	ENSP00000260228:K18T	K	-	2	0	MMP20	102001208	0.997000	0.39634	0.727000	0.30756	0.562000	0.35680	2.004000	0.40854	0.999000	0.39023	0.460000	0.39030	AAG	T|0.342;G|0.658	0.658	strong		0.537	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
CLEC10A	10462	hgsc.bcm.edu	37	17	6980105	6980105	+	Missense_Mutation	SNP	G	G	A	rs35318160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6980105G>A	ENST00000254868.4	-	5	627	c.299C>T	c.(298-300)aCg>aTg	p.T100M	CLEC10A_ENST00000416562.2_Missense_Mutation_p.T100M|CLEC10A_ENST00000571664.1_Missense_Mutation_p.T100M|CLEC10A_ENST00000576617.1_Missense_Mutation_p.T100M	NM_182906.2	NP_878910.1	Q8IUN9	CLC10_HUMAN	C-type lectin domain family 10, member A	100			T -> M (in dbSNP:rs35318160).		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						AGATGCTATCGTTTCTTCCAA	0.602													g|||	90	0.0179712	0.0121	0.0159	5008	,	,		18296	0.0218		0.0278	False		,,,				2504	0.0133				p.T100M		Atlas-SNP	.											.	CLEC10A	40	.	0			c.C299T						PASS	.	G	MET/THR,MET/THR	70,4336	64.1+/-101.4	1,68,2134	217.0	196.0	203.0		299,299	-9.7	0.0	17	dbSNP_126	203	221,8379	90.9+/-153.0	2,217,4081	yes	missense,missense	CLEC10A	NM_006344.2,NM_182906.2	81,81	3,285,6215	AA,AG,GG		2.5698,1.5887,2.2374	benign,benign	100/293,100/317	6980105	291,12715	2203	4300	6503	SO:0001583	missense	10462	exon5			GCTATCGTTTCTT	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.299C>T	17.37:g.6980105G>A	ENSP00000254868:p.Thr100Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_182906	A8K8J8|Q14538|Q6PIW3	Missense_Mutation	SNP	ENST00000254868.4	37	CCDS11087.1	41	0.018772893772893772	7	0.014227642276422764	6	0.016574585635359115	9	0.015734265734265736	19	0.025065963060686015	G	2.887	-0.230615	0.05983	0.015887	0.025698	ENSG00000132514	ENST00000254868;ENST00000416562	T;T	0.17370	2.28;2.28	4.86	-9.71	0.00518	Hepatic lectin, N-terminal (1);	1.412210	0.04392	N	0.362625	T	0.01489	0.0048	N	0.04043	-0.29	0.09310	N	1	B;B;B;B	0.31383	0.274;0.321;0.037;0.013	B;B;B;B	0.16289	0.004;0.007;0.015;0.01	T	0.18116	-1.0347	10	0.44086	T	0.13	.	2.5245	0.04688	0.4485:0.0745:0.1875:0.2895	rs35318160	100;100;100;100	Q8IUN9-3;A8K7G0;Q8IUN9;Q8IUN9-2	.;.;CLC10_HUMAN;.	M	100	ENSP00000254868:T100M;ENSP00000414938:T100M	ENSP00000254868:T100M	T	-	2	0	CLEC10A	6920829	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.637000	0.00205	-4.070000	0.00076	-1.761000	0.00669	ACG	G|0.978;A|0.022	0.022	strong		0.602	CLEC10A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439837.2	NM_006344	
TG	7038	hgsc.bcm.edu	37	8	134145885	134145885	+	Silent	SNP	G	G	A	rs111563366		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:134145885G>A	ENST00000220616.4	+	47	8209	c.8169G>A	c.(8167-8169)tcG>tcA	p.S2723S	TG_ENST00000542445.1_Silent_p.S1093S|TG_ENST00000377869.1_Silent_p.S2666S|TG_ENST00000519543.1_Silent_p.S856S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2723					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)		AGTACATCTCGTCTCTGAAGA	0.562																																					p.S2723S		Atlas-SNP	.											.	TG	416	.	0			c.G8169A						PASS	.	G		1,4405	4.2+/-10.8	0,1,2202	55.0	51.0	53.0		8169	-1.1	0.2	8	dbSNP_132	53	0,8600		0,0,4300	no	coding-synonymous	TG	NM_003235.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2723/2769	134145885	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon47			CATCTCGTCTCTG	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.8169G>A	8.37:g.134145885G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	152	52	0.342105	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	0.026	-1.372534	0.01214	2.27E-4	0.0	ENSG00000042832	ENST00000519178	.	.	.	4.84	-1.12	0.09808	.	.	.	.	.	T	0.23171	0.0560	.	.	.	0.20403	N	0.999907	.	.	.	.	.	.	T	0.28554	-1.0040	4	.	.	.	.	4.4635	0.11678	0.3929:0.0:0.4574:0.1498	.	.	.	.	I	1179	.	.	V	+	1	0	TG	134215067	0.002000	0.14202	0.191000	0.23289	0.059000	0.15707	0.558000	0.23469	-0.078000	0.12730	-1.332000	0.01269	GTC	G|0.500;A|0.500	0.500	weak		0.562	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
RDH13	112724	hgsc.bcm.edu	37	19	55559715	55559715	+	Silent	SNP	G	G	A	rs2305543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55559715G>A	ENST00000415061.3	-	5	783	c.640C>T	c.(640-642)Ctg>Ttg	p.L214L	RDH13_ENST00000396247.3_Silent_p.L143L|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.6_ENST00000585492.1_RNA	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	214					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	CGCCGGCTCAGCTCCTTGGTG	0.582													.|||	1574	0.314297	0.2799	0.2219	5008	,	,		19412	0.4593		0.2485	False		,,,				2504	0.3446				p.L214L		Atlas-SNP	.											.	RDH13	43	.	0			c.C640T						PASS	.	G	,	1016,2940		127,762,1089	49.0	51.0	50.0		640,427	3.2	1.0	19	dbSNP_100	50	2065,6275		234,1597,2339	no	coding-synonymous,coding-synonymous	RDH13	NM_001145971.1,NM_138412.3	,	361,2359,3428	AA,AG,GG		24.7602,25.6825,25.0569	,	214/332,143/261	55559715	3081,9215	1978	4170	6148	SO:0001819	synonymous_variant	112724	exon5			GGCTCAGCTCCTT		CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19978	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 3"""		"""retinol dehydrogenase 13 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.640C>T	19.37:g.55559715G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_001145971	Q6UX79|Q96G88	Silent	SNP	ENST00000415061.3	37	CCDS54320.1																																																																																			G|0.701;A|0.299	0.299	strong		0.582	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451470.1	NM_138412	
CDRT15	146822	hgsc.bcm.edu	37	17	14139888	14139888	+	Splice_Site	SNP	C	C	T	rs11650811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:14139888C>T	ENST00000420162.2	-	1	278		c.e1+1		CDRT15_ENST00000431716.2_Intron	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15									p.?(1)		endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		GGCCACCTCACCAAGTGTCTG	0.552													C|||	278	0.0555112	0.0749	0.0259	5008	,	,		19503	0.0784		0.0398	False		,,,				2504	0.0429				.		Atlas-SNP	.											CDRT15,NS,carcinoma,0,1	CDRT15	20	1	1	Unknown(1)	prostate(1)	c.262+1G>A						scavenged	.						6.0	6.0	6.0					17																	14139888		2170	4243	6413	SO:0001630	splice_region_variant	146822	exon2			ACCTCACCAAGTG	AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.262+1G>A	17.37:g.14139888C>T		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	240	25	0.104167	NM_001007530	B2RUU5	Splice_Site	SNP	ENST00000420162.2	37	CCDS32569.1	220	0.10073260073260074	29	0.05894308943089431	25	0.06906077348066299	97	0.16958041958041958	69	0.09102902374670185	C	0.056	-1.236753	0.01493	.	.	ENSG00000223510	ENST00000420162	.	.	.	0.128	-0.256	0.12984	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	rs11650811	.	.	.	.	-1	.	.	.	-	.	.	CDRT15	14080613	0.037000	0.19845	0.058000	0.19502	0.061000	0.15899	0.124000	0.15728	-1.023000	0.03342	-1.036000	0.02392	.	C|0.917;T|0.083	0.083	strong		0.552	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	Intron
CFAP57	149465	hgsc.bcm.edu	37	1	43675539	43675539	+	Silent	SNP	G	G	A	rs148341430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43675539G>A	ENST00000372492.4	+	11	2205	c.1881G>A	c.(1879-1881)ctG>ctA	p.L627L	WDR65_ENST00000528956.1_Silent_p.L627L	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		627										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTCTGCCTCTGCAGAAGGAAT	0.572													g|||	2	0.000399361	0.0	0.0014	5008	,	,		18599	0.0		0.001	False		,,,				2504	0.0				p.L627L		Atlas-SNP	.											.	WDR65	76	.	0			c.G1881A						PASS	.	G	,,	0,4406		0,0,2203	176.0	149.0	158.0		1881,1881,1881	1.7	1.0	1	dbSNP_134	158	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,,	627/699,627/699,627/699	43675539	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon11			GCCTCTGCAGAAG																												ENST00000372492.4:c.1881G>A	1.37:g.43675539G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.999;A|0.001	0.001	strong		0.572	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29910538	29910538	+	Silent	SNP	C	C	T	rs1136657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910538C>T	ENST00000396634.1	+	4	419	c.78C>T	c.(76-78)tcC>tcT	p.S26S	HLA-A_ENST00000376809.5_Silent_p.S26S|HLA-A_ENST00000376806.5_Silent_p.S26S|HLA-A_ENST00000376802.2_Silent_p.S26S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	26	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCCCAGGCTCCCACTCCATGA	0.721									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.S26S		Atlas-SNP	.											HLA-A,caecum,carcinoma,0,1	HLA-A	89	1	0			c.C78T						PASS	.						13.0	12.0	12.0					6																	29910538		2164	4231	6395	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGCTCCCACTCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.78C>T	6.37:g.29910538C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.821;T|0.179	0.179	strong		0.721	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
NSUN5	55695	hgsc.bcm.edu	37	7	72717933	72717933	+	Silent	SNP	C	C	T	rs11544043	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:72717933C>T	ENST00000252594.6	-	8	1050	c.1035G>A	c.(1033-1035)gcG>gcA	p.A345A	NSUN5_ENST00000310326.8_Silent_p.A345A|NSUN5_ENST00000428206.1_Silent_p.A307A|NSUN5_ENST00000438747.2_Silent_p.A345A			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	345					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GGAAAGTGAGCGCGTGGCACA	0.662													.|||	1253	0.2502	0.2595	0.3228	5008	,	,		16894	0.2381		0.2197	False		,,,				2504	0.2301				p.A345A		Atlas-SNP	.											NSUN5_ENST00000438747,NS,carcinoma,0,2	NSUN5	47	2	0			c.G1035A						PASS	.	C	,,,	1103,3303		141,821,1241	36.0	39.0	38.0		1035,921,1035,1035	-4.2	0.0	7	dbSNP_120	38	2086,6512		247,1592,2460	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	,,,	388,2413,3701	TT,TC,CC		24.2615,25.034,24.5232	,,,	345/471,307/392,345/430,345/467	72717933	3189,9815	2203	4299	6502	SO:0001819	synonymous_variant	55695	exon8			AGTGAGCGCGTGG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.1035G>A	7.37:g.72717933C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	181	98	0.541436	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	CCDS5547.1																																																																																			C|0.714;T|0.286	0.286	strong		0.662	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
PTPN22	26191	hgsc.bcm.edu	37	1	114394689	114394689	+	Missense_Mutation	SNP	C	C	T	rs33996649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:114394689C>T	ENST00000359785.5	-	10	923	c.788G>A	c.(787-789)cGg>cAg	p.R263Q	PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Missense_Mutation_p.R263Q|PTPN22_ENST00000538253.1_Missense_Mutation_p.R19Q|PTPN22_ENST00000525799.1_Missense_Mutation_p.R136Q|PTPN22_ENST00000528414.1_Intron	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)	263	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		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)		CCGCATTTCCCGGATCAAACT	0.348													c|||	55	0.0109824	0.0023	0.0202	5008	,	,		19125	0.0		0.0258	False		,,,				2504	0.0123				p.R263Q		Atlas-SNP	.											.	PTPN22	90	.	0			c.G788A	GRCh37	CM090201	PTPN22	M	rs33996649	PASS	.	T	GLN/ARG,,GLN/ARG	28,4378	34.3+/-65.2	0,28,2175	76.0	73.0	74.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	788,,788	3.4	1.0	1	dbSNP_126	74	181,8419	81.8+/-144.4	3,175,4122	yes	missense,intron,missense	PTPN22	NM_001193431.1,NM_012411.4,NM_015967.5	43,,43	3,203,6297	TT,TC,CC		2.1047,0.6355,1.607	benign,,benign	263/780,,263/808	114394689	209,12797	2203	4300	6503	SO:0001583	missense	26191	exon10			ATTTCCCGGATCA	AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9652	protein-coding gene	gene with protein product		600716	"""protein tyrosine phosphatase, non-receptor type 8"""	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.788G>A	1.37:g.114394689C>T	ENSP00000352833:p.Arg263Gln	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_015967	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Missense_Mutation	SNP	ENST00000359785.5	37	CCDS863.1	27	0.012362637362637362	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	17	0.022427440633245383	c	6.840	0.524195	0.13066	0.006355	0.021047	ENSG00000134242	ENST00000359785;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69	5.73	3.43	0.39272	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.225050	0.39687	N	0.001294	T	0.31513	0.0799	N	0.01640	-0.785	0.19300	N	0.999979	B;B;B;B;B	0.14805	0.0;0.011;0.001;0.001;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.001;0.001	T	0.37798	-0.9690	10	0.02654	T	1	.	13.0449	0.58920	0.0:0.0702:0.0:0.9298	rs33996649	19;136;263;263;263	F5H2S8;E9PPI1;E9PMT0;G5E984;Q9Y2R2	.;.;.;.;PTN22_HUMAN	Q	263;19;263;136;263	ENSP00000352833:R263Q;ENSP00000439372:R19Q;ENSP00000388229:R263Q;ENSP00000432674:R136Q	ENSP00000346621:R263Q	R	-	2	0	PTPN22	114196212	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.684000	0.54671	0.460000	0.27045	-1.193000	0.01689	CGG	C|0.985;T|0.015	0.015	strong		0.348	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1	NM_015967	
C12orf43	64897	hgsc.bcm.edu	37	12	121442241	121442241	+	Silent	SNP	C	C	T	rs73214128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121442241C>T	ENST00000288757.3	-	6	526	c.504G>A	c.(502-504)gcG>gcA	p.A168A	C12orf43_ENST00000539736.1_Silent_p.A158A|C12orf43_ENST00000445832.3_Silent_p.A138A|C12orf43_ENST00000366211.2_Silent_p.A127A|C12orf43_ENST00000537817.1_Silent_p.A169A|C12orf43_ENST00000536407.2_Intron	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	168										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GGATGTCGGACGCCGACACAG	0.582													.|||	200	0.0399361	0.0045	0.0461	5008	,	,		16552	0.0079		0.0616	False		,,,				2504	0.0941				p.A168A		Atlas-SNP	.											.	C12orf43	30	.	0			c.G504A						PASS	.	C		54,4352	52.9+/-88.7	2,50,2151	87.0	102.0	97.0		504	-4.5	0.0	12	dbSNP_130	97	481,8119	139.5+/-196.2	15,451,3834	no	coding-synonymous	C12orf43	NM_022895.1		17,501,5985	TT,TC,CC		5.593,1.2256,4.1135		168/263	121442241	535,12471	2203	4300	6503	SO:0001819	synonymous_variant	64897	exon6			GTCGGACGCCGAC	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.504G>A	12.37:g.121442241C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_022895	Q53HF0|Q9H9Z7	Silent	SNP	ENST00000288757.3	37	CCDS9210.1	75	0.034340659340659344	5	0.01016260162601626	19	0.052486187845303865	2	0.0034965034965034965	49	0.06464379947229551	C	1.352	-0.591095	0.03799	0.012256	0.05593	ENSG00000157895	ENST00000546272	.	.	.	5.73	-4.49	0.03504	.	.	.	.	.	T	0.01627	0.0052	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22977	-1.0201	4	.	.	.	-6.4613	0.8027	0.01078	0.3201:0.2727:0.2234:0.1838	.	.	.	.	H	122	.	.	R	-	2	0	C12orf43	119926624	0.001000	0.12720	0.012000	0.15200	0.137000	0.21094	-0.285000	0.08410	-0.458000	0.07023	-0.302000	0.09304	CGT	C|0.960;T|0.040	0.040	strong		0.582	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
CFAP74	85452	hgsc.bcm.edu	37	1	1887245	1887245	+	IGR	SNP	G	G	A	rs28575980	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1887245G>A								TMEM52 (36533 upstream) : C1orf222 (32317 downstream)																							AGCTGGTGGCGGCTTTGTCAT	0.562													G|||	908	0.18131	0.1044	0.219	5008	,	,		17542	0.2292		0.2316	False		,,,				2504	0.1575				p.A687A		Atlas-SNP	.											KIAA1751,NS,carcinoma,0,1	KIAA1751	92	1	0			c.C2061T						PASS	.	G		517,3601		38,441,1580	44.0	48.0	47.0		2061	-1.6	0.0	1	dbSNP_125	47	2075,6339		258,1559,2390	no	coding-synonymous	KIAA1751	NM_001080484.1		296,2000,3970	AA,AG,GG		24.6613,12.5546,20.6831		687/763	1887245	2592,9940	2059	4207	6266	SO:0001628	intergenic_variant	85452	exon18			GGTGGCGGCTTTG																													1.37:g.1887245G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	68	0.918919	NM_001080484		Silent	SNP		37		480	0.21978021978021978	59	0.11991869918699187	82	0.2265193370165746	159	0.27797202797202797	180	0.23746701846965698	G	3.005	-0.205185	0.06180	0.125546	0.246613	ENSG00000142609	ENST00000493316	.	.	.	2.8	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.35724	-0.9777	3	.	.	.	-1.4405	5.1203	0.14856	0.3205:0.1589:0.5206:0.0	rs28575980;rs61496843	.	.	.	L	93	.	.	P	-	2	0	C1orf222	1877105	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.129000	0.15830	-0.723000	0.04915	-1.119000	0.02030	CCG	G|0.777;A|0.223	0.223	strong	0	0.562								
TRIP11	9321	hgsc.bcm.edu	37	14	92441066	92441066	+	Missense_Mutation	SNP	C	C	T	rs1051340	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92441066C>T	ENST00000267622.4	-	19	5852	c.5479G>A	c.(5479-5481)Ggt>Agt	p.G1827S		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1827			G -> S (in dbSNP:rs1051340). {ECO:0000269|PubMed:10189370, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7776974, ECO:0000269|PubMed:9373237}.		protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		CTGGTAACACCGCCCTGATCG	0.368			T	PDGFRB	AML								C|||	1359	0.271366	0.2095	0.1643	5008	,	,		15466	0.3065		0.3131	False		,,,				2504	0.3517				p.G1827S	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G5479A						PASS	.	C	SER/GLY	983,3423	368.6+/-318.7	100,783,1320	67.0	60.0	63.0		5479	3.9	0.6	14	dbSNP_86	63	2832,5768	445.8+/-361.1	497,1838,1965	yes	missense	TRIP11	NM_004239.3	56	597,2621,3285	TT,TC,CC		32.9302,22.3105,29.3326	probably-damaging	1827/1980	92441066	3815,9191	2203	4300	6503	SO:0001583	missense	9321	exon19			TAACACCGCCCTG	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.5479G>A	14.37:g.92441066C>T	ENSP00000267622:p.Gly1827Ser	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	600|600	0.27472527472527475|0.27472527472527475	98|98	0.1991869918699187|0.1991869918699187	63|63	0.17403314917127072|0.17403314917127072	193|193	0.3374125874125874|0.3374125874125874	246|246	0.3245382585751979|0.3245382585751979	C|C	17.62|17.62	3.433947|3.433947	0.62955|0.62955	0.223105|0.223105	0.329302|0.329302	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.04970|.	3.52|.	5.71|5.71	3.9|3.9	0.45041|0.45041	.|.	0.050236|.	0.85682|.	D|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.27053|0.27053	0.805|0.805	0.21915|0.21915	P|P	0.999473102|0.999473102	D;P|.	0.55800|.	0.973;0.903|.	B;B|.	0.41236|.	0.322;0.351|.	T|T	0.36939|0.36939	-0.9727|-0.9727	9|4	0.56958|.	D|.	0.05|.	.|.	12.3669|12.3669	0.55234|0.55234	0.0:0.8639:0.0:0.1361|0.0:0.8639:0.0:0.1361	rs1051340;rs3191717;rs8014538;rs11554399;rs17806291;rs61645330;rs1051340|rs1051340;rs3191717;rs8014538;rs11554399;rs17806291;rs61645330;rs1051340	1563;1827|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	S|Q	1827;1563|1542	ENSP00000267622:G1827S|.	ENSP00000267622:G1827S|.	G|R	-|-	1|2	0|0	TRIP11|TRIP11	91510819|91510819	0.962000|0.962000	0.33011|0.33011	0.632000|0.632000	0.29296|0.29296	0.597000|0.597000	0.36814|0.36814	2.209000|2.209000	0.42806|0.42806	0.770000|0.770000	0.33336|0.33336	-0.136000|-0.136000	0.14681|0.14681	GGT|CGG	C|0.709;T|0.291	0.291	strong		0.368	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
MCC	4163	hgsc.bcm.edu	37	5	112379289	112379289	+	Silent	SNP	G	G	A	rs2227948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:112379289G>A	ENST00000302475.4	-	15	2687	c.2124C>T	c.(2122-2124)gcC>gcT	p.A708A	MCC_ENST00000515367.2_Silent_p.A645A|MCC_ENST00000408903.3_Silent_p.A898A|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	708					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)		TCCTGAGTTCGGCTAGGGACA	0.577											OREG0016728	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A898A		Atlas-SNP	.											.	MCC	234	.	0			c.C2694T						PASS	.	G	,	1917,2487	547.5+/-377.3	434,1049,719	115.0	77.0	90.0		2694,2124	-10.3	0.0	5	dbSNP_98	90	4424,4176	584.8+/-391.8	1139,2146,1015	no	coding-synonymous,coding-synonymous	MCC	NM_001085377.1,NM_002387.2	,	1573,3195,1734	AA,AG,GG		48.5581,43.5286,48.7619	,	898/1020,708/830	112379289	6341,6663	2202	4300	6502	SO:0001819	synonymous_variant	4163	exon17			GAGTTCGGCTAGG		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.2124C>T	5.37:g.112379289G>A		Somatic	50	0	0	1442	WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			G|0.493;A|0.507	0.507	strong		0.577	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
KLB	152831	hgsc.bcm.edu	37	4	39450229	39450229	+	Missense_Mutation	SNP	C	C	A	rs4975017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:39450229C>A	ENST00000257408.4	+	5	3155	c.3058C>A	c.(3058-3060)Cag>Aag	p.Q1020K		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	1020			Q -> K (in dbSNP:rs4975017).		carbohydrate metabolic process (GO:0005975)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor binding (GO:0017134)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(11)|skin(6)	29						TTTTCAAAGGCAGAAGAGAAG	0.388													C|||	1644	0.328275	0.118	0.402	5008	,	,		22119	0.3819		0.3201	False		,,,				2504	0.5133				p.Q1020K		Atlas-SNP	.											.	KLB	95	.	0			c.C3058A						PASS	.	C	LYS/GLN	684,3722	285.7+/-278.4	54,576,1573	107.0	102.0	104.0		3058	2.8	0.0	4	dbSNP_111	104	2792,5808	436.5+/-358.3	441,1910,1949	yes	missense	KLB	NM_175737.3	53	495,2486,3522	AA,AC,CC		32.4651,15.5243,26.7261	benign	1020/1045	39450229	3476,9530	2203	4300	6503	SO:0001583	missense	152831	exon5			CAAAGGCAGAAGA	AB079373	CCDS3451.1	4p14	2008-02-05			ENSG00000134962	ENSG00000134962			15527	protein-coding gene	gene with protein product		611135					Standard	NM_175737		Approved		uc003gua.3	Q86Z14	OTTHUMG00000128577	ENST00000257408.4:c.3058C>A	4.37:g.39450229C>A	ENSP00000257408:p.Gln1020Lys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	713	0.32646520146520147	57	0.11585365853658537	150	0.4143646408839779	243	0.42482517482517484	263	0.3469656992084433	C	0.005	-2.212627	0.00289	0.155243	0.324651	ENSG00000134962	ENST00000257408	T	0.25250	1.81	5.78	2.81	0.32909	.	0.900332	0.09745	N	0.761361	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.20887	0.049;0.049	B;B	0.14023	0.01;0.01	T	0.46816	-0.9164	9	0.02654	T	1	-0.5786	5.2329	0.15432	0.4452:0.385:0.0:0.1697	rs4975017;rs17584864;rs52837022;rs60465305;rs4975017	1011;1020	B7ZL50;Q86Z14	.;KLOTB_HUMAN	K	1020	ENSP00000257408:Q1020K	ENSP00000257408:Q1020K	Q	+	1	0	KLB	39126624	1.000000	0.71417	0.015000	0.15790	0.104000	0.19210	1.848000	0.39309	0.786000	0.33708	0.313000	0.20887	CAG	C|0.717;A|0.282	0.282	strong		0.388	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737	
TNFRSF8	943	hgsc.bcm.edu	37	1	12164437	12164437	+	Splice_Site	SNP	C	C	T	rs2230622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12164437C>T	ENST00000263932.2	+	4	492	c.270C>T	c.(268-270)gaC>gaT	p.D90D	TNFRSF8_ENST00000417814.2_5'UTR	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	90					cellular response to mechanical stimulus (GO:0071260)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of TRAIL biosynthetic process (GO:0045556)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	27	Ovarian(185;0.249)	Lung NSC(185;8.71e-05)|all_lung(284;9.89e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.66e-06)|COAD - Colon adenocarcinoma(227;0.000261)|BRCA - Breast invasive adenocarcinoma(304;0.000304)|Kidney(185;0.000777)|KIRC - Kidney renal clear cell carcinoma(229;0.00261)|STAD - Stomach adenocarcinoma(313;0.0073)|READ - Rectum adenocarcinoma(331;0.0649)	Brentuximab vedotin(DB08870)	GTCCCTTAGACGACCTCGTGG	0.597													C|||	1466	0.292732	0.2118	0.379	5008	,	,		16676	0.3264		0.2296	False		,,,				2504	0.3712				p.D90D		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.C270T						PASS	.	C		956,3450		101,754,1348	109.0	89.0	96.0		270	-8.1	0.0	1	dbSNP_98	96	2082,6518		247,1588,2465	yes	coding-synonymous-near-splice	TNFRSF8	NM_001243.3		348,2342,3813	TT,TC,CC		24.2093,21.6977,23.3584		90/596	12164437	3038,9968	2203	4300	6503	SO:0001630	splice_region_variant	943	exon4			CTTAGACGACCTC	M83554	CCDS144.1, CCDS59989.1	1p36	2008-02-05			ENSG00000120949	ENSG00000120949		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11923	protein-coding gene	gene with protein product		153243		CD30, D1S166E		1330892, 1310894	Standard	XM_006711049		Approved	KI-1	uc001atq.3	P28908	OTTHUMG00000001827	ENST00000263932.2:c.269-1C>T	1.37:g.12164437C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	118	104	0.881356	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Silent	SNP	ENST00000263932.2	37	CCDS144.1																																																																																			C|0.611;A|0.050	.	strong		0.597	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1		Silent
KIR3DL1	3811	hgsc.bcm.edu	37	19	55341575	55341575	+	Missense_Mutation	SNP	G	G	C	rs1130513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55341575G>C	ENST00000391728.4	+	9	1213	c.1180G>C	c.(1180-1182)Gag>Cag	p.E394Q	KIR2DS4_ENST00000339924.8_RNA|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.E377Q|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.E377Q|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.E299Q|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.E394Q	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	394			E -> Q (in dbSNP:rs1130513).		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ACAAGACCCTGAGGAGGTGAC	0.522													c|||	884	0.176518	0.1815	0.1758	5008	,	,		15583	0.1111		0.2942	False		,,,				2504	0.1166				p.E394Q		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.G1180C						PASS	.	C	GLN/GLU	897,3447		194,509,1469	237.0	218.0	225.0		1180	0.7	0.0	19	dbSNP_86	225	2044,6284		538,968,2658	no	missense	KIR3DL1	NM_013289.2	29	732,1477,4127	CC,CG,GG		24.5437,20.6492,23.2086		394/445	55341575	2941,9731	2172	4164	6336	SO:0001583	missense	3811	exon9			GACCCTGAGGAGG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1180G>C	19.37:g.55341575G>C	ENSP00000375608:p.Glu394Gln	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	71	43	0.605634	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	376	0.17216117216117216	65	0.13211382113821138	58	0.16022099447513813	54	0.0944055944055944	199	0.262532981530343	-	0.003	-2.458893	0.00173	0.206492	0.245437	ENSG00000167633	ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T	0.00475	7.26;7.37;7.26;7.37;7.17	0.719	0.719	0.18208	.	.	.	.	.	T	0.00012	0.0000	N	0.00085	-2.2	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.26155	-1.0111	7	0.02654	T	1	.	.	.	.	rs1130513;rs3189435;rs16986003	377;299;394	Q15702;Q14946;P43629	.;.;KI3L1_HUMAN	Q	394;377;372;394;377;299	ENSP00000443350:E394Q;ENSP00000442355:E377Q;ENSP00000375608:E394Q;ENSP00000326868:E377Q;ENSP00000350901:E299Q	ENSP00000326868:E377Q	E	+	1	0	KIR3DL1	60033387	0.139000	0.22563	0.002000	0.10522	0.006000	0.05464	0.000000	0.12993	-0.105000	0.12132	-1.123000	0.02005	GAG	G|0.828;C|0.172	0.172	strong		0.522	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
PNN	5411	hgsc.bcm.edu	37	14	39644498	39644498	+	Silent	SNP	G	G	A	rs11558738|rs1061583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:39644498G>A	ENST00000216832.4	+	1	82	c.15G>A	c.(13-15)gtG>gtA	p.V5V	PNN_ENST00000556530.1_Silent_p.V5V|RP11-407N17.4_ENST00000556537.1_lincRNA|PNN_ENST00000553331.1_Silent_p.V5V	NM_002687.3	NP_002678	Q9H307	PININ_HUMAN	pinin, desmosome associated protein	5	Necessary for interaction with RNPS1.|Necessary for interactions with KRT8, KRT18 and KRT19.|Necessary for mediating alternative 5' splicing.				cell adhesion (GO:0007155)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(2)|stomach(1)	27	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0119)		CGGTCGCCGTGAGAACTTTGC	0.602													G|||	935	0.186701	0.0091	0.2017	5008	,	,		14330	0.2321		0.2783	False		,,,				2504	0.2751				p.V5V		Atlas-SNP	.											PNN,right_upper_lobe,carcinoma,+2,1	PNN	67	1	0			c.G15A						PASS	.	G		228,4178	133.7+/-170.0	6,216,1981	53.0	45.0	48.0		15	5.2	1.0	14	dbSNP_86	48	2255,6345	377.2+/-338.5	290,1675,2335	no	coding-synonymous	PNN	NM_002687.3		296,1891,4316	AA,AG,GG		26.2209,5.1748,19.0912		5/718	39644498	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	5411	exon1			CGCCGTGAGAACT	U77718	CCDS9671.1	14q21.1	2010-07-02			ENSG00000100941	ENSG00000100941			9162	protein-coding gene	gene with protein product		603154				8922384	Standard	NM_002687		Approved	memA	uc001wuw.4	Q9H307	OTTHUMG00000028821	ENST00000216832.4:c.15G>A	14.37:g.39644498G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	62	60	0.967742	NM_002687	B4DZX8|O60899|Q53EM7|Q6P5X4|Q7KYL1|Q99738|Q9UHZ9|Q9UQR9	Silent	SNP	ENST00000216832.4	37	CCDS9671.1																																																																																			G|0.804;A|0.196	0.196	strong		0.602	PNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276776.2	NM_002687	
SSFA2	6744	hgsc.bcm.edu	37	2	182766660	182766660	+	Missense_Mutation	SNP	C	C	T	rs576974564		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:182766660C>T	ENST00000431877.2	+	8	1059	c.880C>T	c.(880-882)Cgt>Tgt	p.R294C	SSFA2_ENST00000409001.1_Missense_Mutation_p.R294C|SSFA2_ENST00000320370.7_Missense_Mutation_p.R294C|SSFA2_ENST00000428267.2_Missense_Mutation_p.R141C	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	294						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R294C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			CACTGCAAATCGTTTAATGAA	0.423													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16148	0.0		0.0	False		,,,				2504	0.0				p.R294C		Atlas-SNP	.											SSFA2,NS,carcinoma,0,1	SSFA2	130	1	1	Substitution - Missense(1)	prostate(1)	c.C880T						scavenged	.						61.0	61.0	61.0					2																	182766660		2203	4300	6503	SO:0001583	missense	6744	exon8			GCAAATCGTTTAA	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.880C>T	2.37:g.182766660C>T	ENSP00000388731:p.Arg294Cys	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	111	4	0.036036	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218127	0.79464	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267	T;T;T;T	0.25414	2.04;1.8;2.03;2.08	5.66	5.66	0.87406	.	0.399158	0.26010	N	0.026887	T	0.51839	0.1698	M	0.74881	2.28	0.58432	D	0.999992	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.998;0.998	T	0.51988	-0.8635	10	0.87932	D	0	-12.7913	14.9079	0.70733	0.1432:0.8568:0.0:0.0	.	141;294;294;294	E7END2;E9PHV5;P28290;P28290-3	.;.;SSFA2_HUMAN;.	C	294;294;294;141	ENSP00000388731:R294C;ENSP00000314669:R294C;ENSP00000387319:R294C;ENSP00000409867:R141C	ENSP00000314669:R294C	R	+	1	0	SSFA2	182474905	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	2.985000	0.49362	2.831000	0.97527	0.650000	0.86243	CGT	.	.	none		0.423	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
OR4K15	81127	hgsc.bcm.edu	37	14	20443872	20443872	+	Silent	SNP	C	C	G	rs4499148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20443872C>G	ENST00000305051.5	+	1	270	c.195C>G	c.(193-195)ggC>ggG	p.G65G		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	65						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTCTGTTGGGCAACTTTCTCA	0.443													C|||	1880	0.375399	0.7451	0.2017	5008	,	,		21174	0.1498		0.2435	False		,,,				2504	0.3671				p.G65G		Atlas-SNP	.											OR4K15,NS,carcinoma,+1,1	OR4K15	82	1	0			c.C195G						scavenged	.	C		3038,1368		1038,962,203	100.0	115.0	109.0		195	-4.4	0.7	14	dbSNP_111	109	2426,6172		333,1760,2206	no	coding-synonymous	OR4K15	NM_001005486.1		1371,2722,2409	GG,GC,CC		28.2159,31.0486,42.0178		65/349	20443872	5464,7540	2203	4299	6502	SO:0001819	synonymous_variant	81127	exon1			GTTGGGCAACTTT		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.195C>G	14.37:g.20443872C>G		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	178	64	0.359551	NM_001005486	B9EIL3|Q6IEZ4	Silent	SNP	ENST00000305051.5	37	CCDS32026.1																																																																																			.	.	weak		0.443	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
MADD	8567	hgsc.bcm.edu	37	11	47306628	47306628	+	Missense_Mutation	SNP	G	G	A	rs3736101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:47306628G>A	ENST00000311027.5	+	13	2459	c.2294G>A	c.(2293-2295)cGg>cAg	p.R765Q	MADD_ENST00000395344.3_Intron|MADD_ENST00000402799.1_Intron|MADD_ENST00000342922.4_Missense_Mutation_p.R765Q|MADD_ENST00000402192.2_Missense_Mutation_p.R765Q|MADD_ENST00000406482.1_Intron|MADD_ENST00000407859.3_Intron|MADD_ENST00000349238.3_Missense_Mutation_p.R765Q|MADD_ENST00000395336.3_Missense_Mutation_p.R765Q	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)		TCAGTGCGCCGGCGAATCTAT	0.562													G|||	370	0.0738818	0.025	0.0677	5008	,	,		19379	0.0516		0.1163	False		,,,				2504	0.1237				p.R765Q		Atlas-SNP	.											.	MADD	172	.	0			c.G2294A						PASS	.	G	,,GLN/ARG,GLN/ARG,,,GLN/ARG,,GLN/ARG,GLN/ARG	176,4226	115.0+/-153.0	2,172,2027	98.0	92.0	94.0		,,2294,2294,,,2294,,2294,2294	0.7	0.9	11	dbSNP_107	94	900,7696	200.9+/-244.5	43,814,3441	yes	intron,intron,missense,missense,intron,intron,missense,intron,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	,,43,43,,,43,,43,43	45,986,5468	AA,AG,GG		10.47,3.9982,8.2782	,,benign,benign,,,benign,,benign,benign	,,765/1648,765/1589,,,765/1609,,765/1582,765/1588	47306628	1076,11922	2201	4298	6499	SO:0001583	missense	8567	exon13			TGCGCCGGCGAAT	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.2294G>A	11.37:g.47306628G>A	ENSP00000310933:p.Arg765Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_130470		Missense_Mutation	SNP	ENST00000311027.5	37	CCDS7930.1	158	0.07234432234432235	13	0.026422764227642278	30	0.08287292817679558	33	0.057692307692307696	82	0.10817941952506596	G	11.01	1.511868	0.27036	0.039982	0.1047	ENSG00000110514	ENST00000342922;ENST00000349238;ENST00000311027;ENST00000395336;ENST00000402192	T;T;T;T;T	0.05382	3.45;3.5;3.5;3.5;3.45	5.99	0.696	0.18075	.	0.309294	0.34002	N	0.004345	T	0.00109	0.0003	N	0.24115	0.695	0.80722	P	0.0	B;B;B;B	0.12013	0.001;0.001;0.0;0.005	B;B;B;B	0.08055	0.003;0.002;0.001;0.003	T	0.43556	-0.9384	9	0.24483	T	0.36	-0.2463	10.2559	0.43397	0.5124:0.0:0.4875:0.0	rs3736101;rs3736101	765;765;765;765	Q8WXG6-7;Q8WXG6-2;Q8WXG6;Q8WXG6-3	.;.;MADD_HUMAN;.	Q	765	ENSP00000343902:R765Q;ENSP00000304505:R765Q;ENSP00000310933:R765Q;ENSP00000378745:R765Q;ENSP00000384287:R765Q	ENSP00000310933:R765Q	R	+	2	0	MADD	47263204	0.028000	0.19301	0.890000	0.34922	0.952000	0.60782	0.100000	0.15231	-0.117000	0.11872	0.655000	0.94253	CGG	G|0.922;A|0.078	0.078	strong		0.562	MADD-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317746.1		
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821576	100821576	+	Missense_Mutation	SNP	G	G	A	rs7496668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:100821576G>A	ENST00000268070.4	-	4	752	c.647C>T	c.(646-648)tCg>tTg	p.S216L		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	216			S -> L (in dbSNP:rs7496668). {ECO:0000269|PubMed:19836009}.			proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		CCAGTCCCGCGAAGGCCTGCC	0.597													G|||	2427	0.484625	0.447	0.5504	5008	,	,		16139	0.505		0.3489	False		,,,				2504	0.6074				p.S216L		Atlas-SNP	.											ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	0			c.C647T						PASS	.	G	LEU/SER	1873,2497		409,1055,721	29.0	27.0	28.0		647	3.6	0.0	15	dbSNP_116	28	2807,5731		446,1915,1908	yes	missense	ADAMTS17	NM_139057.2	145	855,2970,2629	AA,AG,GG		32.8766,42.8604,36.2566	benign	216/1096	100821576	4680,8228	2185	4269	6454	SO:0001583	missense	170691	exon4			TCCCGCGAAGGCC	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.647C>T	15.37:g.100821576G>A	ENSP00000268070:p.Ser216Leu	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	958	0.43864468864468864	236	0.4796747967479675	184	0.5082872928176796	280	0.48951048951048953	258	0.3403693931398417	G	14.09	2.430321	0.43122	0.428604	0.328766	ENSG00000140470	ENST00000268070	T	0.61980	0.06	4.51	3.57	0.40892	.	0.752556	0.12004	N	0.508584	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.14012	0.009	B	0.06405	0.002	T	0.45101	-0.9284	9	0.25106	T	0.35	.	12.6923	0.56982	0.0:0.166:0.834:0.0	rs7496668;rs60305285;rs7496668	216	Q8TE56	ATS17_HUMAN	L	216	ENSP00000268070:S216L	ENSP00000268070:S216L	S	-	2	0	ADAMTS17	98639099	0.000000	0.05858	0.002000	0.10522	0.107000	0.19398	0.272000	0.18644	0.852000	0.35287	0.462000	0.41574	TCG	G|0.589;A|0.411	0.411	strong		0.597	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
HLA-B	3106	hgsc.bcm.edu	37	6	31324516	31324516	+	Missense_Mutation	SNP	C	C	A	rs1131215	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31324516C>A	ENST00000412585.2	-	2	320	c.292G>T	c.(292-294)Gac>Tac	p.D98Y		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	98	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CTCTCTCGGTCAGTCTGTGCC	0.682									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	3525	0.703874	0.7163	0.7507	5008	,	,		6748	0.6419		0.5954	False		,,,				2504	0.8292				p.D98Y		Atlas-SNP	.											HLA-B,colon,carcinoma,0,1	HLA-B	54	1	0			c.G292T						scavenged	.	A	TYR/ASP	2329,1909		891,547,681	50.0	52.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	292	-6.4	0.0	6	dbSNP_86	52	3737,4619		1270,1197,1711	no	missense	HLA-B	NM_005514.6	160	2161,1744,2392	AA,AC,CC		44.7224,45.0448,48.1658		98/363	31324516	6066,6528	2119	4178	6297	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CTCGGTCAGTCTG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.292G>T	6.37:g.31324516C>A	ENSP00000399168:p.Asp98Tyr	Somatic	13	13	1		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1363	0.6240842490842491	310	0.6300813008130082	257	0.7099447513812155	374	0.6538461538461539	422	0.5567282321899736	N	3.390	-0.124570	0.06795	0.549552	0.447224	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00009	9.52;9.52	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	6.155240	0.01158	U	0.006566	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;D	0.89917	0.354;0.057;1.0	B;B;D	0.97110	0.291;0.083;1.0	T	0.62120	-0.6921	9	0.02654	T	1	.	2.0223	0.03512	0.3366:0.364:0.0893:0.21	rs1131215;rs3177922;rs3190915;rs9266166;rs17413622	98;98;73	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	Y	98;109	ENSP00000399168:D98Y;ENSP00000405931:D109Y	ENSP00000399168:D98Y	D	-	1	0	HLA-B	31432495	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.850000	0.01670	-2.027000	0.00932	-6.206000	0.00000	GAC	C|0.415;A|0.585	0.585	strong		0.682	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
TMEM173	340061	hgsc.bcm.edu	37	5	138857925	138857925	+	Missense_Mutation	SNP	C	C	G	rs78233829	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:138857925C>G	ENST00000330794.4	-	6	1022	c.689G>C	c.(688-690)gGt>gCt	p.G230A	TMEM173_ENST00000511850.1_5'Flank	NM_198282.2	NP_938023.1	Q86WV6	STING_HUMAN	transmembrane protein 173	230	c-di-GMP-binding domain (CBD).				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|interferon-beta production (GO:0032608)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of protein binding (GO:0032092)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	cyclic-di-GMP binding (GO:0035438)|cyclic-GMP-AMP binding (GO:0061507)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|transcription factor binding (GO:0008134)			endometrium(1)|kidney(1)|lung(6)|upper_aerodigestive_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGCATGGTCACCGGTCTGCTG	0.557													G|||	1342	0.267971	0.2368	0.2983	5008	,	,		19260	0.4058		0.1541	False		,,,				2504	0.2638				p.G230A		Atlas-SNP	.											.	TMEM173	19	.	0			c.G689C						PASS	.	G	ALA/GLY	1046,3360	725.9+/-409.7	118,810,1275	114.0	106.0	109.0		689	1.0	0.0	5	dbSNP_131	109	1218,7382	762.7+/-407.6	91,1036,3173	yes	missense	TMEM173	NM_198282.2	60	209,1846,4448	GG,GC,CC		14.1628,23.7404,17.4074	benign	230/380	138857925	2264,10742	2203	4300	6503	SO:0001583	missense	340061	exon6			TGGTCACCGGTCT		CCDS4215.1	5q31.2	2009-11-06			ENSG00000184584	ENSG00000184584			27962	protein-coding gene	gene with protein product		612374				12477932	Standard	XM_005268445		Approved	FLJ38577, NET23	uc003lep.3	Q86WV6	OTTHUMG00000129239	ENST00000330794.4:c.689G>C	5.37:g.138857925C>G	ENSP00000331288:p.Gly230Ala	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_198282	A8K3P6|B6EB35|D6RBX0|D6RE01|D6RID9	Missense_Mutation	SNP	ENST00000330794.4	37	CCDS4215.1	551	0.2522893772893773	108	0.21951219512195122	91	0.2513812154696133	238	0.4160839160839161	114	0.1503957783641161	G	5.562	0.288555	0.10513	0.237404	0.141628	ENSG00000184584	ENST00000330794;ENST00000510817	T;T	0.20598	2.06;2.06	5.79	0.964	0.19655	.	1.017410	0.07828	N	0.960847	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	0.45731	-0.9241	9	0.22109	T	0.4	0.8351	5.5191	0.16923	0.4359:0.1359:0.4282:0.0	.	230	Q86WV6	TM173_HUMAN	A	230	ENSP00000331288:G230A;ENSP00000427455:G230A	ENSP00000331288:G230A	G	-	2	0	TMEM173	138838109	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.501000	0.22578	-0.103000	0.12175	-0.998000	0.02512	GGT	C|0.807;G|0.193	0.193	strong		0.557	TMEM173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251338.1	NM_198282	
EPHA3	2042	hgsc.bcm.edu	37	3	89448530	89448530	+	Missense_Mutation	SNP	C	C	A	rs144696297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:89448530C>A	ENST00000336596.2	+	7	1719	c.1494C>A	c.(1492-1494)agC>agA	p.S498R	EPHA3_ENST00000494014.1_Missense_Mutation_p.S498R|EPHA3_ENST00000452448.2_Missense_Mutation_p.S498R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	498	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CCATCAGTAGCCTCAAGCCTG	0.423										TSP Lung(6;0.00050)			C|||	2	0.000399361	0.0	0.0	5008	,	,		15456	0.0		0.002	False		,,,				2504	0.0				p.S498R		Atlas-SNP	.											.	EPHA3	501	.	0			c.C1494A						PASS	.						93.0	90.0	91.0					3																	89448530		2203	4300	6503	SO:0001583	missense	2042	exon7			CAGTAGCCTCAAG	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.1494C>A	3.37:g.89448530C>A	ENSP00000337451:p.Ser498Arg	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.56	3.420551	0.62622	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.57595	0.39;0.39;0.39	5.35	5.35	0.76521	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.045473	0.85682	D	0.000000	T	0.38612	0.1047	N	0.20845	0.615	0.41304	D	0.987066	B;B	0.32101	0.106;0.356	B;B	0.37422	0.249;0.212	T	0.25984	-1.0116	9	.	.	.	.	10.524	0.44936	0.0:0.7909:0.1352:0.0739	.	498;498	P29320;P29320-2	EPHA3_HUMAN;.	R	498	ENSP00000337451:S498R;ENSP00000399926:S498R;ENSP00000419190:S498R	.	S	+	3	2	EPHA3	89531220	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	0.799000	0.27028	2.505000	0.84491	0.563000	0.77884	AGC	C|0.999;A|0.001	0.001	strong		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
ABCC3	8714	hgsc.bcm.edu	37	17	48768486	48768486	+	Silent	SNP	A	A	G	rs1051640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48768486A>G	ENST00000285238.8	+	31	4589	c.4509A>G	c.(4507-4509)gaA>gaG	p.E1503E	RP11-294J22.6_ENST00000574246.1_RNA	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1503	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)	TAGTAGCTGAATTTGATTCTC	0.483													A|||	521	0.104034	0.09	0.1095	5008	,	,		21371	0.0417		0.1829	False		,,,				2504	0.1022				p.E1503E		Atlas-SNP	.											.	ABCC3	138	.	0			c.A4509G						PASS	.	A		371,4035	189.9+/-215.9	17,337,1849	120.0	106.0	111.0		4509	0.6	1.0	17	dbSNP_86	111	1533,7067	290.7+/-299.9	149,1235,2916	no	coding-synonymous	ABCC3	NM_003786.3		166,1572,4765	GG,GA,AA		17.8256,8.4203,14.6394		1503/1528	48768486	1904,11102	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon31			AGCTGAATTTGAT	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.4509A>G	17.37:g.48768486A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			A|0.876;G|0.124	0.124	strong		0.483	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
KALRN	8997	hgsc.bcm.edu	37	3	124044859	124044859	+	Silent	SNP	C	C	T	rs16835275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124044859C>T	ENST00000240874.3	+	7	1276	c.1119C>T	c.(1117-1119)tcC>tcT	p.S373S	KALRN_ENST00000460856.1_Silent_p.S373S|KALRN_ENST00000360013.3_Silent_p.S373S	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	373					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						GCATCATGTCCGTGGCTTCCC	0.547													C|||	29	0.00579073	0.0061	0.0058	5008	,	,		16950	0.0099		0.005	False		,,,				2504	0.002				p.S373S		Atlas-SNP	.											KALRN_ENST00000360013,NS,malignant_melanoma,+1,2	KALRN	556	2	0			c.C1119T						PASS	.	C	,	27,4379	32.6+/-62.9	0,27,2176	102.0	93.0	97.0		1119,1119	-9.3	0.0	3	dbSNP_123	97	73,8525	42.2+/-99.7	1,71,4227	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	1,98,6403	TT,TC,CC		0.849,0.6128,0.769	,	373/2987,373/1664	124044859	100,12904	2203	4299	6502	SO:0001819	synonymous_variant	8997	exon7			CATGTCCGTGGCT	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.1119C>T	3.37:g.124044859C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	191	86	0.450262	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	16	0.007326007326007326	1	0.0020325203252032522	5	0.013812154696132596	7	0.012237762237762238	3	0.00395778364116095	C	6.705	0.498764	0.12762	0.006128	0.00849	ENSG00000160145	ENST00000354186	.	.	.	4.64	-9.28	0.00656	.	.	.	.	.	T	0.49830	0.1580	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74463	-0.3657	4	.	.	.	.	12.8333	0.57759	0.0:0.4623:0.2765:0.2612	rs16835275;rs16835275	.	.	.	L	351	.	.	P	+	2	0	KALRN	125527549	0.000000	0.05858	0.012000	0.15200	0.920000	0.55202	-5.264000	0.00136	-4.734000	0.00034	-1.876000	0.00548	CCG	C|0.992;T|0.008	0.008	strong		0.547	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
CCDC39	339829	hgsc.bcm.edu	37	3	180365956	180365956	+	Silent	SNP	G	G	A	rs6769457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:180365956G>A	ENST00000442201.2	-	10	1478	c.1359C>T	c.(1357-1359)agC>agT	p.S453S	CCDC39_ENST00000273654.4_Silent_p.S537S	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	453					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CATCTACCTGGCTGTACATAA	0.343													A|||	1597	0.31889	0.7375	0.2911	5008	,	,		18222	0.004		0.2515	False		,,,				2504	0.1667				p.S453S		Atlas-SNP	.											.	CCDC39	242	.	0			c.C1359T						PASS	.	A		2333,1391		731,871,260	74.0	72.0	72.0		1359	1.5	1.0	3	dbSNP_116	72	1803,6395		198,1407,2494	no	coding-synonymous	CCDC39	NM_181426.1		929,2278,2754	AA,AG,GG		21.9932,37.3523,34.6922		453/942	180365956	4136,7786	1862	4099	5961	SO:0001819	synonymous_variant	339829	exon10			TACCTGGCTGTAC	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.1359C>T	3.37:g.180365956G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	37	CCDS46964.1																																																																																			G|0.678;A|0.322	0.322	strong		0.343	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
CFAP70	118491	hgsc.bcm.edu	37	10	75037999	75037999	+	Missense_Mutation	SNP	C	C	A	rs12256262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75037999C>A	ENST00000310715.3	-	21	2666	c.2546G>T	c.(2545-2547)tGg>tTg	p.W849L	TTC18_ENST00000493787.1_Intron|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000401621.2_Missense_Mutation_p.W849L|RNU6-833P_ENST00000363486.1_RNA|TTC18_ENST00000355577.3_Missense_Mutation_p.W318L|TTC18_ENST00000394865.1_Missense_Mutation_p.W849L|DNAJC9-AS1_ENST00000440197.2_RNA	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		849			W -> L (in dbSNP:rs12256262).			extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					ACTTGGATCCCAAGTTTGTGT	0.378													C|||	121	0.0241613	0.0847	0.013	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.W849L		Atlas-SNP	.											.	TTC18	106	.	0			c.G2546T						PASS	.	C	LEU/TRP	294,4112	161.4+/-193.6	9,276,1918	184.0	180.0	181.0		2546	0.2	0.7	10	dbSNP_120	181	20,8580	14.6+/-50.1	0,20,4280	yes	missense	TTC18	NM_145170.3	61	9,296,6198	AA,AC,CC		0.2326,6.6727,2.4143	benign	849/1122	75037999	314,12692	2203	4300	6503	SO:0001583	missense	118491	exon21			GGATCCCAAGTTT																												ENST00000310715.3:c.2546G>T	10.37:g.75037999C>A	ENSP00000310829:p.Trp849Leu	Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	251	120	0.478088	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	49	0.022435897435897436	36	0.07317073170731707	6	0.016574585635359115	2	0.0034965034965034965	5	0.006596306068601583	C	2.654	-0.281206	0.05642	0.066727	0.002326	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	T;T;T;T	0.28666	2.03;2.03;1.6;1.63	4.56	0.152	0.14893	.	0.762705	0.11325	N	0.575616	T	0.00695	0.0023	N	0.03115	-0.41	0.25123	N	0.990622	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	10	0.11485	T	0.65	-0.0236	3.4795	0.07597	0.4634:0.1102:0.0:0.4264	rs12256262;rs52797721;rs57681861;rs12256262	849	Q5T0N1	TTC18_HUMAN	L	849;849;849;256;849	ENSP00000310829:W849L;ENSP00000384479:W849L;ENSP00000409527:W256L;ENSP00000378334:W849L	ENSP00000310829:W849L	W	-	2	0	TTC18	74708005	0.691000	0.27709	0.746000	0.31095	0.029000	0.11900	0.181000	0.16880	-0.081000	0.12662	-0.312000	0.09012	TGG	C|0.973;A|0.027	0.027	strong		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
ZNF587	84914	hgsc.bcm.edu	37	19	58371259	58371259	+	Silent	SNP	A	A	G	rs75951435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58371259A>G	ENST00000339656.5	+	3	1661	c.1479A>G	c.(1477-1479)gaA>gaG	p.E493E	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF587_ENST00000419854.1_Silent_p.E450E|ZNF587_ENST00000423137.1_Silent_p.E492E|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	493					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.E493E(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GGCCGTATGAATGCAGTGAAT	0.423																																					p.E493E	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											ZNF587,NS,carcinoma,0,1	ZNF587	53	1	1	Substitution - coding silent(1)	stomach(1)	c.A1479G						PASS	.						145.0	149.0	148.0					19																	58371259		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			GTATGAATGCAGT	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1479A>G	19.37:g.58371259A>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	356	75	0.210674	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			A|0.963;G|0.037	0.037	strong		0.423	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
ZNF584	201514	hgsc.bcm.edu	37	19	58929136	58929136	+	Silent	SNP	G	G	A	rs3764534	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58929136G>A	ENST00000306910.4	+	4	1774	c.1251G>A	c.(1249-1251)aaG>aaA	p.K417K	ZNF584_ENST00000593920.1_Silent_p.K372K|ZNF584_ENST00000599238.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	417					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(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		CACATGGGAAGGTCGTTAGCT	0.512													A|||	2507	0.500599	0.7882	0.379	5008	,	,		23025	0.3254		0.497	False		,,,				2504	0.3824				p.K417K		Atlas-SNP	.											ZNF584,caecum,carcinoma,0,1	ZNF584	31	1	0			c.G1251A						scavenged	.	A		3377,1029	371.5+/-320.0	1306,765,132	80.0	81.0	81.0		1251	-0.2	0.0	19	dbSNP_107	81	4147,4453	578.0+/-390.7	1007,2133,1160	no	coding-synonymous	ZNF584	NM_173548.1		2313,2898,1292	AA,AG,GG		48.2209,23.3545,42.1498		417/422	58929136	7524,5482	2203	4300	6503	SO:0001819	synonymous_variant	201514	exon4			TGGGAAGGTCGTT	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"""Zinc fingers, C2H2-type"", ""-"""	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.1251G>A	19.37:g.58929136G>A		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	105	35	0.333333	NM_173548	A8K203	Silent	SNP	ENST00000306910.4	37	CCDS12979.1																																																																																			G|0.453;A|0.547	0.547	strong		0.512	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548	
ZNF516	9658	hgsc.bcm.edu	37	18	74154296	74154296	+	Missense_Mutation	SNP	C	C	T	rs12961584		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:74154296C>T	ENST00000443185.2	-	3	1032	c.715G>A	c.(715-717)Ggc>Agc	p.G239S	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	239			G -> S (in dbSNP:rs12961584).		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)		TCGGGCTTGCCGTTCTCCACG	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		15391	0.0		0.001	False		,,,				2504	0.0				p.G239S		Atlas-SNP	.											.	ZNF516	102	.	0			c.G715A						PASS	.	C	SER/GLY	2,4128		0,2,2063	12.0	14.0	14.0		715	3.5	1.0	18	dbSNP_121	14	33,8345		0,33,4156	no	missense	ZNF516	NM_014643.3	56	0,35,6219	TT,TC,CC		0.3939,0.0484,0.2798	probably-damaging	239/1164	74154296	35,12473	2065	4189	6254	SO:0001583	missense	9658	exon3			GCTTGCCGTTCTC	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.715G>A	18.37:g.74154296C>T	ENSP00000394757:p.Gly239Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	39	26	0.666667	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		.	.	.	.	.	.	.	.	.	.	C	16.18	3.050132	0.55218	4.84E-4	0.003939	ENSG00000101493	ENST00000443185	T	0.11063	2.81	4.39	3.5	0.40072	.	0.497156	0.19611	N	0.110146	T	0.16854	0.0405	.	.	.	0.30781	N	0.741935	D	0.69078	0.997	P	0.53760	0.734	T	0.04509	-1.0946	9	0.22109	T	0.4	-22.5334	12.8858	0.58042	0.3101:0.6899:0.0:0.0	rs12961584	239	Q92618	ZN516_HUMAN	S	239	ENSP00000394757:G239S	ENSP00000394757:G239S	G	-	1	0	ZNF516	72283284	0.628000	0.27138	0.994000	0.49952	0.971000	0.66376	1.269000	0.33074	1.187000	0.43000	0.557000	0.71058	GGC	C|0.667;T|0.333	0.333	strong		0.692	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
CD22	933	hgsc.bcm.edu	37	19	35832468	35832468	+	Missense_Mutation	SNP	T	T	C	rs369129095		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35832468T>C	ENST00000085219.5	+	8	1796	c.1730T>C	c.(1729-1731)aTa>aCa	p.I577T	CD22_ENST00000544992.2_Missense_Mutation_p.I577T|CD22_ENST00000419549.2_Missense_Mutation_p.I405T|CD22_ENST00000536635.2_Missense_Mutation_p.I489T|CD22_ENST00000341773.6_Missense_Mutation_p.I400T|CD22_ENST00000270311.6_Missense_Mutation_p.I457T|CD22_ENST00000594250.1_Missense_Mutation_p.I400T	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	577	Ig-like C2-type 5.				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)			AACAACTCCATAGGACAGACA	0.557																																					p.I577T	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.T1730C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	0,4406		0,0,2203	73.0	72.0	72.0		1466,1730,1199,1730	3.5	0.0	19		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	89,89,89,89	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	489/760,577/752,400/671,577/848	35832468	1,13005	2203	4300	6503	SO:0001583	missense	933	exon8			ACTCCATAGGACA	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.1730T>C	19.37:g.35832468T>C	ENSP00000085219:p.Ile577Thr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	37	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420287	0.42918	0.0	1.16E-4	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;2.76	5.73	3.54	0.40534	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.679676	0.13703	N	0.368667	T	0.18882	0.0453	L	0.56124	1.755	0.09310	N	1	P;P;D;B;D	0.54964	0.931;0.9;0.969;0.223;0.96	P;P;P;B;P	0.59357	0.765;0.653;0.856;0.129;0.755	T	0.11397	-1.0589	10	0.22706	T	0.39	.	5.5235	0.16945	0.0:0.0879:0.1731:0.739	.	405;577;489;577;400	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	T	577;489;400;577;457;405	ENSP00000085219:I577T;ENSP00000442279:I489T;ENSP00000339349:I400T;ENSP00000441237:I577T;ENSP00000270311:I457T;ENSP00000403822:I405T	ENSP00000085219:I577T	I	+	2	0	CD22	40524308	0.002000	0.14202	0.013000	0.15412	0.133000	0.20885	1.081000	0.30791	1.001000	0.39076	-0.411000	0.06167	ATA	.	.	weak		0.557	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
C6orf222	389384	hgsc.bcm.edu	37	6	36287312	36287312	+	Missense_Mutation	SNP	G	G	C	rs743852	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36287312G>C	ENST00000437635.2	-	11	1921	c.1744C>G	c.(1744-1746)Ctg>Gtg	p.L582V		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	582			L -> V (in dbSNP:rs743852).							breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						TGGCTGCGCAGGGTGGCTACC	0.532													G|||	1945	0.388379	0.3737	0.3689	5008	,	,		20115	0.2183		0.5596	False		,,,				2504	0.4213				p.L582V		Atlas-SNP	.											.	C6orf222	72	.	0			c.C1744G						PASS	.	G	VAL/LEU	1750,2656	521.5+/-370.6	363,1024,816	73.0	72.0	72.0		1744	3.6	0.7	6	dbSNP_86	72	4783,3817	613.1+/-396.1	1368,2047,885	yes	missense	C6orf222	NM_001010903.4	32	1731,3071,1701	CC,CG,GG		44.3837,39.7186,49.7693	probably-damaging	582/653	36287312	6533,6473	2203	4300	6503	SO:0001583	missense	389384	exon11			TGCGCAGGGTGGC		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.1744C>G	6.37:g.36287312G>C	ENSP00000418983:p.Leu582Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_001010903	B2RTY8	Missense_Mutation	SNP	ENST00000437635.2	37	CCDS34439.1	851	0.38965201465201466	191	0.3882113821138211	136	0.3756906077348066	108	0.1888111888111888	416	0.5488126649076517	G	18.82	3.704316	0.68615	0.397186	0.556163	ENSG00000189325	ENST00000437635	T	0.62498	0.02	5.43	3.6	0.41247	.	0.000000	0.37178	N	0.002217	T	0.67449	0.2894	M	0.78637	2.42	0.42422	P	0.007353999999999972	D	0.89917	1.0	D	0.79784	0.993	T	0.71606	-0.4542	9	0.66056	D	0.02	-36.1032	7.0432	0.25031	0.2052:0.0:0.7948:0.0	rs743852;rs743852	582	P0C671	CF222_HUMAN	V	582	ENSP00000418983:L582V	ENSP00000418983:L582V	L	-	1	2	C6orf222	36395290	0.600000	0.26899	0.704000	0.30370	0.973000	0.67179	0.853000	0.27777	1.398000	0.46701	0.563000	0.77884	CTG	G|0.540;C|0.460	0.460	strong		0.532	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903	
CLIC5	53405	hgsc.bcm.edu	37	6	46047458	46047458	+	Silent	SNP	C	C	T	rs3734207	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46047458C>T	ENST00000185206.6	-	1	674	c.522G>A	c.(520-522)gaG>gaA	p.E174E		NM_001114086.1	NP_001107558.1	Q9NZA1	CLIC5_HUMAN	chloride intracellular channel 5	174					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						AGAGGTAAATCTCAGGGTTCA	0.453													C|||	983	0.196286	0.0303	0.1196	5008	,	,		23723	0.3343		0.174	False		,,,				2504	0.3558				p.E174E		Atlas-SNP	.											.	CLIC5	48	.	0			c.G522A						PASS	.						75.0	70.0	71.0					6																	46047458		692	1591	2283	SO:0001819	synonymous_variant	53405	exon1			GTAAATCTCAGGG	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.522G>A	6.37:g.46047458C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	54	0.412214	NM_001114086	B3KUF1|Q5T4Z0|Q8NBY3|Q96JT5|Q9BWZ0	Silent	SNP	ENST00000185206.6	37	CCDS47438.1																																																																																			C|0.815;T|0.185	0.185	strong		0.453	CLIC5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040761.1		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305956	39305956	+	Missense_Mutation	SNP	G	G	A	rs1497383	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39305956G>A	ENST00000343246.4	-	1	98	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	22	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		R -> C (in dbSNP:rs1497383). {ECO:0000269|PubMed:11279113}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CAGCTGGGGCGGCAGCAGTTC	0.632													G|||	2209	0.441094	0.3699	0.5144	5008	,	,		16738	0.3532		0.4861	False		,,,				2504	0.5297				p.R22C		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.C64T						PASS	.	G	CYS/ARG	1658,2746		319,1020,863	30.0	34.0	33.0		64	1.5	0.5	17	dbSNP_88	33	4137,4449		994,2149,1150	yes	missense	KRTAP4-5	NM_033188.3	180	1313,3169,2013	AA,AG,GG		48.1831,37.6476,44.6112	benign	22/182	39305956	5795,7195	2202	4293	6495	SO:0001583	missense	85289	exon1			TGGGGCGGCAGCA	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.64C>T	17.37:g.39305956G>A	ENSP00000340546:p.Arg22Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	142	69	0.485915	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	954	0.4368131868131868	186	0.3780487804878049	187	0.5165745856353591	216	0.3776223776223776	365	0.4815303430079156	.	4.323	0.059209	0.08339	0.376476	0.481831	ENSG00000198271	ENST00000343246	T	0.01446	4.88	3.52	1.46	0.22682	.	0.915314	0.08847	U	0.884953	T	0.00012	0.0000	M	0.72576	2.205	0.41445	P	0.012055999999999956	B	0.21753	0.06	B	0.15484	0.013	T	0.35624	-0.9781	9	0.49607	T	0.09	.	2.1325	0.03754	0.1118:0.1821:0.4821:0.224	rs1497383;rs6503605;rs1497383	22	Q9BYR2	KRA45_HUMAN	C	22	ENSP00000340546:R22C	ENSP00000340546:R22C	R	-	1	0	KRTAP4-5	36559482	0.022000	0.18835	0.504000	0.27639	0.011000	0.07611	-0.126000	0.10563	0.421000	0.25980	-0.254000	0.11334	CGC	G|0.556;A|0.444	0.444	strong		0.632	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
ITPR2	3709	hgsc.bcm.edu	37	12	26732987	26732987	+	Silent	SNP	G	G	A	rs2230376	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:26732987G>A	ENST00000381340.3	-	33	4898	c.4482C>T	c.(4480-4482)ccC>ccT	p.P1494P		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1494					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TGTCTGAAAAGGGAGAATTAA	0.363													G|||	935	0.186701	0.0923	0.2248	5008	,	,		16444	0.0744		0.332	False		,,,				2504	0.2536				p.P1494P		Atlas-SNP	.											.	ITPR2	270	.	0			c.C4482T						PASS	.	G		475,3141		30,415,1363	116.0	104.0	108.0		4482	-10.1	0.0	12	dbSNP_98	108	2587,5565		428,1731,1917	no	coding-synonymous	ITPR2	NM_002223.2		458,2146,3280	AA,AG,GG		31.7345,13.1361,26.0197		1494/2702	26732987	3062,8706	1808	4076	5884	SO:0001819	synonymous_variant	3709	exon33			TGAAAAGGGAGAA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4482C>T	12.37:g.26732987G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.794;A|0.206	0.206	strong		0.363	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296600	39296600	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39296600C>T	ENST00000345847.4	-	1	139	c.140G>A	c.(139-141)aGa>aAa	p.R47K		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	47	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)		p.R47K(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GCACTGGGGTCTGCAGCAGCT	0.682																																					p.R47K		Atlas-SNP	.											KRTAP4-6,NS,carcinoma,0,2	KRTAP4-6	46	2	1	Substitution - Missense(1)	prostate(1)	c.G140A						scavenged	.																																			SO:0001583	missense	81871	exon1			TGGGGTCTGCAGC	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.140G>A	17.37:g.39296600C>T	ENSP00000328270:p.Arg47Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	4	0.0493827	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	.	.	.	.	.	.	.	.	.	.	.	6.616	0.482131	0.12581	.	.	ENSG00000198090	ENST00000345847	T	0.00590	6.36	5.01	2.62	0.31277	.	2.335370	0.02364	N	0.077186	T	0.00875	0.0029	M	0.67625	2.065	0.09310	N	1	.	.	.	.	.	.	T	0.62435	-0.6855	8	0.05959	T	0.93	.	4.9322	0.13923	0.1734:0.6205:0.0:0.2061	.	.	.	.	K	47	ENSP00000328270:R47K	ENSP00000328270:R47K	R	-	2	0	KRTAP4-6	36550126	0.019000	0.18553	0.192000	0.23308	0.098000	0.18820	1.906000	0.39887	1.096000	0.41439	0.650000	0.86243	AGA	.	.	none		0.682	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
CD82	3732	hgsc.bcm.edu	37	11	44636839	44636839	+	Silent	SNP	C	C	T	rs883752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:44636839C>T	ENST00000227155.4	+	7	602	c.354C>T	c.(352-354)ggC>ggT	p.G118G	CD82_ENST00000342935.3_Silent_p.G93G|CD82_ENST00000530931.1_3'UTR	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	118						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						AGGAGATGGGCGGCATCGTGA	0.612													C|||	1143	0.228235	0.1014	0.17	5008	,	,		19655	0.2748		0.34	False		,,,				2504	0.2781				p.G118G		Atlas-SNP	.											.	CD82	27	.	0			c.C354T						PASS	.	C	,	619,3787	269.5+/-269.1	45,529,1629	73.0	60.0	64.0		279,354	-3.8	0.0	11	dbSNP_86	64	2968,5630	459.1+/-364.8	521,1926,1852	no	coding-synonymous,coding-synonymous	CD82	NM_001024844.1,NM_002231.3	,	566,2455,3481	TT,TC,CC		34.5197,14.049,27.5838	,	93/243,118/268	44636839	3587,9417	2203	4299	6502	SO:0001819	synonymous_variant	3732	exon7			GATGGGCGGCATC	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.354C>T	11.37:g.44636839C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	184	100	0.543478	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Silent	SNP	ENST00000227155.4	37	CCDS7909.1																																																																																			C|0.739;N|0.000	.	strong		0.612	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1		
JMJD1C	221037	hgsc.bcm.edu	37	10	64927823	64927823	+	Missense_Mutation	SNP	C	C	G	rs1935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:64927823C>G	ENST00000399262.2	-	26	7823	c.7605G>C	c.(7603-7605)gaG>gaC	p.E2535D	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000402544.1_Missense_Mutation_p.E2298D|JMJD1C_ENST00000542921.1_Missense_Mutation_p.E2353D	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2535			E -> D (in dbSNP:rs1935). {ECO:0000269|PubMed:17974005}.		blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)	p.E2298D(2)|p.E2535D(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTTCCATATCCTCTACTTCAT	0.333													C|||	1964	0.392173	0.2859	0.3112	5008	,	,		17437	0.3601		0.4901	False		,,,				2504	0.5256				p.E2535D		Atlas-SNP	.											JMJD1C_ENST00000399262,NS,carcinoma,0,2	JMJD1C	347	2	3	Substitution - Missense(3)	prostate(3)	c.G7605C						PASS	.	C	ASP/GLU,ASP/GLU	1271,2471		208,855,808	174.0	159.0	164.0		6894,7605	3.6	1.0	10	dbSNP_36	164	3919,4275		952,2015,1130	yes	missense,missense	JMJD1C	NM_004241.2,NM_032776.1	45,45	1160,2870,1938	GG,GC,CC		47.8277,33.9658,43.4819	probably-damaging,probably-damaging	2298/2304,2535/2541	64927823	5190,6746	1871	4097	5968	SO:0001583	missense	221037	exon26			CATATCCTCTACT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7605G>C	10.37:g.64927823C>G	ENSP00000382204:p.Glu2535Asp	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	852	0.3901098901098901	135	0.27439024390243905	134	0.3701657458563536	225	0.39335664335664333	358	0.47229551451187335	C	15.29	2.788518	0.49997	0.339658	0.478277	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.55930	0.83;0.49;0.83	5.42	3.57	0.40892	.	0.117118	0.56097	D	0.000029	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.9999999999965508	B;B	0.32071	0.355;0.152	B;B	0.24974	0.057;0.021	T	0.47674	-0.9099	9	0.42905	T	0.14	-14.8807	5.1962	0.15239	0.0:0.6035:0.0:0.3965	rs1935;rs17574273;rs52815148;rs1935	2535;2353	Q15652;A0T124	JHD2C_HUMAN;.	D	2535;2298;2353	ENSP00000382204:E2535D;ENSP00000384990:E2298D;ENSP00000444682:E2353D	ENSP00000382204:E2535D	E	-	3	2	JMJD1C	64597829	0.484000	0.25964	1.000000	0.80357	0.998000	0.95712	-0.006000	0.12833	1.279000	0.44446	0.591000	0.81541	GAG	C|0.570;G|0.430	0.430	strong		0.333	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
ANXA11	311	hgsc.bcm.edu	37	10	81927059	81927059	+	Missense_Mutation	SNP	C	C	T	rs2229554	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:81927059C>T	ENST00000438331.1	-	7	1054	c.572G>A	c.(571-573)cGa>cAa	p.R191Q	ANXA11_ENST00000422982.3_Missense_Mutation_p.R191Q|ANXA11_ENST00000372231.3_Missense_Mutation_p.R191Q|ANXA11_ENST00000537102.1_Missense_Mutation_p.R158Q|ANXA11_ENST00000360615.4_Missense_Mutation_p.R191Q|ANXA11_ENST00000265447.4_Missense_Mutation_p.R191Q|ANXA11_ENST00000535999.1_Missense_Mutation_p.R191Q	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	191			R -> Q (in dbSNP:rs2229554).		cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			GATGGTGCCTCGGCTTCCAAA	0.587													.|||	110	0.0219649	0.0023	0.0274	5008	,	,		18018	0.0		0.0606	False		,,,				2504	0.0276				p.R191Q		Atlas-SNP	.											.	ANXA11	32	.	0			c.G572A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	42,4364		0,42,2161	61.0	59.0	59.0		572,572,572	5.3	1.0	10	dbSNP_98	59	577,8023		15,547,3738	yes	missense,missense,missense	ANXA11	NM_001157.2,NM_145868.1,NM_145869.1	43,43,43	15,589,5899	TT,TC,CC		6.7093,0.9532,4.7593	probably-damaging,probably-damaging,probably-damaging	191/506,191/506,191/506	81927059	619,12387	2203	4300	6503	SO:0001583	missense	311	exon6			GTGCCTCGGCTTC	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"""Annexins"""	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.572G>A	10.37:g.81927059C>T	ENSP00000398610:p.Arg191Gln	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	58	0.026556776556776556	0	0.0	11	0.03038674033149171	0	0.0	47	0.06200527704485488	.	24.3	4.519196	0.85495	0.009532	0.067093	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102;ENST00000445524	T;T;T;T;T;T;T	0.04706	3.57;3.57;3.57;3.57;3.57;3.57;3.57	5.31	5.31	0.75309	.	0.170416	0.50627	D	0.000119	T	0.00875	0.0029	L	0.39898	1.24	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.66351	0.922;0.943;0.943	T	0.43032	-0.9416	10	0.18276	T	0.48	.	16.8441	0.85976	0.0:1.0:0.0:0.0	rs2229554;rs17100686;rs52835600;rs17100686	291;191;191	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	Q	191;191;191;191;191;191;191;98;158;191	ENSP00000361305:R191Q;ENSP00000404412:R191Q;ENSP00000398610:R191Q;ENSP00000353827:R191Q;ENSP00000265447:R191Q;ENSP00000441748:R191Q;ENSP00000441400:R158Q	ENSP00000265447:R191Q	R	-	2	0	ANXA11	81917039	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	7.347000	0.79356	2.663000	0.90544	0.561000	0.74099	CGA	T|0.035;G|0.159	0.035	strong		0.587	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869	
OR2L2	26246	hgsc.bcm.edu	37	1	248202344	248202344	+	Missense_Mutation	SNP	G	G	C	rs6658141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248202344G>C	ENST00000366479.2	+	1	871	c.775G>C	c.(775-777)Gta>Cta	p.V259L	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	259			V -> L (in dbSNP:rs6658141).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(28)|ovary(1)|skin(4)|urinary_tract(1)	42	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TTATACCTATGTACGTCCAAG	0.507													N|||	1728	0.345048	0.7799	0.1484	5008	,	,		20898	0.3036		0.1551	False		,,,				2504	0.135				p.V259L		Atlas-SNP	.											.	OR2L2	115	.	0			c.G775C						PASS	.	C	LEU/VAL,	3005,1401		1027,951,225	157.0	141.0	146.0		775,	1.9	0.0	1	dbSNP_116	146	1249,7351		91,1067,3142	no	missense,intron	OR2L2,OR2L13	NM_001004686.2,NM_175911.2	32,	1118,2018,3367	CC,CG,GG		14.5233,31.7975,32.708	benign,	259/313,	248202344	4254,8752	2203	4300	6503	SO:0001583	missense	26246	exon1			ACCTATGTACGTC	X64978	CCDS31103.1	1q44	2012-08-09			ENSG00000203663	ENSG00000203663		"""GPCR / Class A : Olfactory receptors"""	8266	protein-coding gene	gene with protein product				OR2L4P, OR2L12		1370859	Standard	NM_001004686		Approved	HTPCRH07, HSHTPCRH07	uc001idw.3	Q8NH16	OTTHUMG00000040214	ENST00000366479.2:c.775G>C	1.37:g.248202344G>C	ENSP00000355435:p.Val259Leu	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	751	0.34386446886446886	381	0.774390243902439	58	0.16022099447513813	201	0.3513986013986014	111	0.14643799472295516	.	0.161	-1.081535	0.01888	0.682025	0.145233	ENSG00000203663	ENST00000366479	T	0.33654	1.4	1.9	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.000000	0.26055	N	0.026610	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32771	-0.9894	8	0.12103	T	0.63	.	3.3465	0.07137	0.0:0.5:0.2296:0.2703	rs6658141;rs6658141	259	Q8NH16	OR2L2_HUMAN	L	259	ENSP00000355435:V259L	ENSP00000355435:V259L	V	+	1	0	OR2L2	246268967	0.000000	0.05858	0.007000	0.13788	0.132000	0.20833	-3.472000	0.00459	0.046000	0.15833	-1.041000	0.02371	GTA	G|0.650;C|0.350	0.350	strong		0.507	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887394	9887394	+	Silent	SNP	C	C	T	rs2240910	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9887394C>T	ENST00000306084.6	+	2	1117	c.918C>T	c.(916-918)gcC>gcT	p.A306A	TXNDC2_ENST00000357775.5_Silent_p.A239A|TXNDC2_ENST00000536353.2_Intron	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	306	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						TAGAGGAAGCCATCCAGCCCA	0.602													-|||	2596	0.518371	0.3623	0.5331	5008	,	,		20966	0.8155		0.4761	False		,,,				2504	0.456				p.A306A		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	0			c.C918T						PASS	.	C	,	1751,2655		357,1037,809	132.0	127.0	128.0		918,717	-0.1	0.0	18	dbSNP_98	128	4210,4390		1043,2124,1133	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	1400,3161,1942	TT,TC,CC		48.9535,39.7413,45.8327	,	306/554,239/487	9887394	5961,7045	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			GGAAGCCATCCAG	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.918C>T	18.37:g.9887394C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			C|0.531;T|0.469	0.469	strong		0.602	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
DENND3	22898	hgsc.bcm.edu	37	8	142200467	142200467	+	Silent	SNP	G	G	A	rs1045303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:142200467G>A	ENST00000262585.2	+	20	3368	c.3090G>A	c.(3088-3090)ccG>ccA	p.P1030P	DENND3_ENST00000523308.1_Silent_p.P80P|DENND3_ENST00000424248.1_Silent_p.P978P|DENND3_ENST00000519811.1_Silent_p.P1110P	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	1030					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)			TCCAGCTGCCGCGAGGTGGCC	0.647													G|||	1882	0.375799	0.2035	0.3256	5008	,	,		16360	0.6171		0.2644	False		,,,				2504	0.5102				p.P1030P		Atlas-SNP	.											.	DENND3	127	.	0			c.G3090A						PASS	.	G		1034,3372	357.4+/-313.9	127,780,1296	51.0	48.0	49.0		3090	-10.6	0.0	8	dbSNP_86	49	2217,6383	357.4+/-330.7	286,1645,2369	no	coding-synonymous	DENND3	NM_014957.2		413,2425,3665	AA,AG,GG		25.7791,23.468,24.9962		1030/1199	142200467	3251,9755	2203	4300	6503	SO:0001819	synonymous_variant	22898	exon20			GCTGCCGCGAGGT	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.3090G>A	8.37:g.142200467G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	119	65	0.546219	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	37	CCDS34947.1	779	0.3566849816849817	100	0.2032520325203252	126	0.34806629834254144	353	0.6171328671328671	200	0.2638522427440633	G	0.218	-1.031100	0.02029	0.23468	0.257791	ENSG00000105339	ENST00000518668	.	.	.	5.31	-10.6	0.00265	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.34903	P	0.25326899999999997	.	.	.	.	.	.	T	0.16808	-1.0390	3	.	.	.	-30.1385	15.5131	0.75798	0.175:0.6549:0.1108:0.0593	rs1045303;rs3185194;rs17407339;rs56738741;rs1045303	.	.	.	T	1035	.	.	A	+	1	0	DENND3	142269649	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.815000	0.01722	-4.470000	0.00047	-0.657000	0.03884	GCG	A|0.299;C|0.000;G|0.700	0.299	strong		0.647	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
ATP10B	23120	hgsc.bcm.edu	37	5	159992751	159992751	+	Silent	SNP	A	A	G	rs4921150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:159992751A>G	ENST00000327245.5	-	26	4941	c.4095T>C	c.(4093-4095)acT>acC	p.T1365T		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1365					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTGGGTGGTGAGTTGGTCGAG	0.532													G|||	719	0.14357	0.2935	0.1023	5008	,	,		14517	0.0119		0.0954	False		,,,				2504	0.1554				p.T1365T		Atlas-SNP	.											ATP10B,colon,carcinoma,0,1	ATP10B	201	1	0			c.T4095C						scavenged	.	G		935,2933		114,707,1113	103.0	114.0	111.0		4095	3.8	0.0	5	dbSNP_111	111	982,7304		62,858,3223	no	coding-synonymous	ATP10B	NM_025153.2		176,1565,4336	GG,GA,AA		11.8513,24.1727,15.7726		1365/1462	159992751	1917,10237	1934	4143	6077	SO:0001819	synonymous_variant	23120	exon26			GTGGTGAGTTGGT	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.4095T>C	5.37:g.159992751A>G		Somatic	114	3	0.0263158		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	37	CCDS43394.1																																																																																			A|0.867;G|0.133	0.133	strong		0.532	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
OTOF	9381	hgsc.bcm.edu	37	2	26697480	26697480	+	Silent	SNP	C	C	T	rs80356573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26697480C>T	ENST00000272371.2	-	26	3315	c.3189G>A	c.(3187-3189)gcG>gcA	p.A1063A	OTOF_ENST00000339598.3_Silent_p.A316A|OTOF_ENST00000403946.3_Silent_p.A1063A|OTOF_ENST00000338581.6_Silent_p.A316A|OTOF_ENST00000402415.3_Silent_p.A373A	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1063					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GTGGGCAGTACGCCTCGTCTG	0.617													c|||	35	0.00698882	0.0061	0.013	5008	,	,		13284	0.0		0.0159	False		,,,				2504	0.002				p.A1063A	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000402415,NS,carcinoma,0,3	OTOF	524	3	0			c.G3189A						PASS	.		,,,	48,4358	50.2+/-85.5	0,48,2155	95.0	81.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	948,3189,1119,948	-11.2	0.0	2	dbSNP_131	85	200,8398	86.1+/-148.5	3,194,4102	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	3,242,6257	TT,TC,CC		2.3261,1.0894,1.9071	,,,	316/1231,1063/1998,373/1308,316/1231	26697480	248,12756	2203	4299	6502	SO:0001819	synonymous_variant	9381	exon26			GCAGTACGCCTCG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3189G>A	2.37:g.26697480C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			C|0.983;T|0.017	0.017	strong		0.617	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
TATDN3	128387	hgsc.bcm.edu	37	1	212985592	212985592	+	Silent	SNP	G	G	A	rs78095001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:212985592G>A	ENST00000366974.4	+	9	697	c.603G>A	c.(601-603)aaG>aaA	p.K201K	TATDN3_ENST00000532324.1_Silent_p.K208K|TATDN3_ENST00000526641.1_Silent_p.K180K|TATDN3_ENST00000525569.1_Splice_Site|TATDN3_ENST00000526997.1_Splice_Site|TATDN3_ENST00000366973.4_Splice_Site|TATDN3_ENST00000531963.1_Silent_p.K208K	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	201					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)		TCTCTAAGAAGCAGAAACTTG	0.303													G|||	101	0.0201677	0.0008	0.0202	5008	,	,		18323	0.0119		0.0368	False		,,,				2504	0.0378				p.K208K		Atlas-SNP	.											.	TATDN3	23	.	0			c.G624A						PASS	.	G	,,,,	30,4372	33.5+/-64.1	0,30,2171	45.0	47.0	46.0		603,,624,540,624	5.3	1.0	1	dbSNP_132	46	288,8310	104.4+/-165.4	3,282,4014	yes	coding-synonymous,splice-3,coding-synonymous,coding-synonymous,coding-synonymous	TATDN3	NM_001042552.2,NM_001042553.2,NM_001146169.1,NM_001146170.1,NM_001146171.1	,,,,	3,312,6185	AA,AG,GG		3.3496,0.6815,2.4462	,,,,	201/275,,208/241,180/254,208/282	212985592	318,12682	2201	4299	6500	SO:0001819	synonymous_variant	128387	exon9			TAAGAAGCAGAAA	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.603G>A	1.37:g.212985592G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_001146169	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Silent	SNP	ENST00000366974.4	37	CCDS31019.1	43	0.019688644688644688	2	0.0040650406504065045	6	0.016574585635359115	9	0.015734265734265736	26	0.03430079155672823	G	21.4	4.148633	0.78001	0.006815	0.033496	ENSG00000203705	ENST00000366973;ENST00000526997	.	.	.	5.28	5.28	0.74379	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.524	0.90965	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TATDN3	211052215	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.834000	0.69361	2.476000	0.83614	0.650000	0.86243	.	G|0.975;A|0.025	0.025	strong		0.303	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838	
KRT27	342574	hgsc.bcm.edu	37	17	38938591	38938591	+	Missense_Mutation	SNP	C	C	G	rs2469826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38938591C>G	ENST00000301656.3	-	1	195	c.155G>C	c.(154-156)aGc>aCc	p.S52T		NM_181537.3	NP_853515.2			keratin 27									p.S52T(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TGCAGATGAGCTGCCCCCAAA	0.602													C|||	1543	0.308107	0.3737	0.3977	5008	,	,		16787	0.2361		0.2773	False		,,,				2504	0.2618				p.S52T		Atlas-SNP	.											KRT27,NS,carcinoma,0,1	KRT27	41	1	1	Substitution - Missense(1)	stomach(1)	c.G155C						scavenged	.	C	THR/SER	1594,2812	492.7+/-362.5	300,994,909	65.0	59.0	61.0		155	3.4	1.0	17	dbSNP_100	61	2244,6356	377.8+/-338.7	305,1634,2361	yes	missense	KRT27	NM_181537.3	58	605,2628,3270	GG,GC,CC		26.093,36.1779,29.5095	possibly-damaging	52/460	38938591	3838,9168	2203	4300	6503	SO:0001583	missense	342574	exon1			GATGAGCTGCCCC	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.155G>C	17.37:g.38938591C>G	ENSP00000301656:p.Ser52Thr	Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	78	76	0.974359	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	677	0.309981684981685	190	0.3861788617886179	134	0.3701657458563536	152	0.26573426573426573	201	0.26517150395778366	C	10.22	1.291162	0.23564	0.361779	0.26093	ENSG00000171446	ENST00000301656	D	0.83591	-1.74	5.43	3.41	0.39046	.	0.089857	0.49305	D	0.000147	T	0.00012	0.0000	L	0.60455	1.87	0.36333	P	0.14099700000000004	B	0.31485	0.325	B	0.32677	0.15	T	0.09862	-1.0655	9	0.27082	T	0.32	.	10.227	0.43231	0.0:0.788:0.1368:0.0752	rs2469826;rs56419417;rs2469826	52	Q7Z3Y8	K1C27_HUMAN	T	52	ENSP00000301656:S52T	ENSP00000301656:S52T	S	-	2	0	KRT27	36192117	0.000000	0.05858	0.972000	0.41901	0.401000	0.30781	1.215000	0.32431	0.749000	0.32854	0.655000	0.94253	AGC	C|0.685;G|0.315	0.315	strong		0.602	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
HLA-B	3106	hgsc.bcm.edu	37	6	31322911	31322911	+	Missense_Mutation	SNP	C	C	T	rs1051488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31322911C>T	ENST00000412585.2	-	5	1013	c.985G>A	c.(985-987)Gct>Act	p.A329T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	329			A -> T (in dbSNP:rs1051488).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.A329T(3)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CACATCACAGCAGCGACCACA	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				C|||	2689	0.536941	0.6573	0.4971	5008	,	,		20334	0.5556		0.3827	False		,,,				2504	0.5419				p.A329T		Atlas-SNP	.											HLA-B,NS,carcinoma,0,7	HLA-B	54	7	3	Substitution - Missense(3)	kidney(3)	c.G985A						PASS	.	C	THR/ALA	1738,1284		487,764,260	102.0	101.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	985	1.7	0.1	6	dbSNP_86	101	1925,3493		353,1219,1137	yes	missense	HLA-B	NM_005514.6	58	840,1983,1397	TT,TC,CC		35.5297,42.4884,43.4005		329/363	31322911	3663,4777	1511	2709	4220	SO:0001583	missense	3106	exon5	Familial Cancer Database	;Lichen Sclerosis, Familial	TCACAGCAGCGAC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.985G>A	6.37:g.31322911C>T	ENSP00000399168:p.Ala329Thr	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	172	170	0.988372	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1030	0.4716117216117216	286	0.5813008130081301	179	0.494475138121547	297	0.5192307692307693	268	0.35356200527704484	N	8.411	0.844238	0.16963	0.575116	0.355297	ENSG00000234745	ENST00000412585;ENST00000428231	T	0.00631	6.09	3.73	1.67	0.24075	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.32481	-0.9905	7	0.48119	T	0.1	.	8.1384	0.31069	0.43:0.57:0.0:0.0	rs1051488;rs2308519;rs3178024;rs3191873;rs3819280;rs3873389;rs3957102;rs7768625;rs9266122;rs17199390;rs17417354;rs17840057;rs17845375;rs17858229;rs52797228;rs61195158	329	P01889	1B07_HUMAN	T	329;208	ENSP00000399168:A329T	ENSP00000399168:A329T	A	-	1	0	HLA-B	31430890	0.000000	0.05858	0.111000	0.21465	0.015000	0.08874	-0.118000	0.10692	0.660000	0.30964	0.448000	0.29417	GCT	T|0.451;G|0.000;C|0.549	0.451	strong		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ESRP2	80004	hgsc.bcm.edu	37	16	68269820	68269820	+	Silent	SNP	C	C	T	rs150603076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68269820C>T	ENST00000565858.1	-	1	215	c.129G>A	c.(127-129)cgG>cgA	p.R43R	ESRP2_ENST00000473183.2_Silent_p.R43R|RP11-96D1.6_ENST00000564147.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	43					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						AGCCCAGGTCCCGTCCCAGCG	0.711													C|||	15	0.00299521	0.0	0.0029	5008	,	,		7867	0.0		0.007	False		,,,				2504	0.0061				p.R43R		Atlas-SNP	.											.	ESRP2	118	.	0			c.G129A						PASS	.	C		3,4377		0,3,2187	18.0	14.0	15.0		129	-6.1	0.7	16	dbSNP_134	15	38,8532		0,38,4247	no	coding-synonymous	ESRP2	NM_024939.2		0,41,6434	TT,TC,CC		0.4434,0.0685,0.3166		43/718	68269820	41,12909	2190	4285	6475	SO:0001819	synonymous_variant	80004	exon1			CAGGTCCCGTCCC	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"""RNA binding motif (RRM) containing"""	26152	protein-coding gene	gene with protein product		612960	"""RNA binding motif protein 35B"""	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.129G>A	16.37:g.68269820C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	34	18	0.529412	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Silent	SNP	ENST00000565858.1	37																																																																																				C|0.997;T|0.003	0.003	strong		0.711	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939	
FCRL1	115350	hgsc.bcm.edu	37	1	157768000	157768000	+	Silent	SNP	G	G	C	rs3811024	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:157768000G>C	ENST00000368176.3	-	8	1132	c.1065C>G	c.(1063-1065)acC>acG	p.T355T	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000358292.3_Silent_p.T316T|FCRL1_ENST00000491942.1_Silent_p.T355T	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	355						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGTTGAGGTAGGTGAACTCTT	0.493													G|||	1158	0.23123	0.3434	0.2032	5008	,	,		20568	0.1855		0.2406	False		,,,				2504	0.137				p.T355T	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.C1065G						PASS	.	G	,,	1381,3025	456.3+/-351.3	216,949,1038	116.0	111.0	112.0		948,1065,1065	-0.7	0.0	1	dbSNP_107	112	2098,6502	362.6+/-332.8	252,1594,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	468,2543,3492	CC,CG,GG		24.3953,31.3436,26.7492	,,	316/367,355/429,355/430	157768000	3479,9527	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon8			GAGGTAGGTGAAC	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.1065C>G	1.37:g.157768000G>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	92	54	0.586957	NM_001159398	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			G|0.747;C|0.253	0.253	strong		0.493	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	
ZNF347	84671	hgsc.bcm.edu	37	19	53644443	53644443	+	Silent	SNP	G	G	A	rs1661935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53644443G>A	ENST00000334197.7	-	5	1706	c.1638C>T	c.(1636-1638)tgC>tgT	p.C546C	ZNF347_ENST00000601804.1_Intron|ZNF347_ENST00000601469.2_Silent_p.C547C|ZNF347_ENST00000452676.2_Silent_p.C547C	NM_032584.2	NP_115973.2	Q96SE7	ZN347_HUMAN	zinc finger protein 347	546					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)		AGGCTTTGCCGCACTCATTAC	0.403													G|||	277	0.0553115	0.1165	0.049	5008	,	,		22458	0.0		0.0795	False		,,,				2504	0.0092				p.C547C	Melanoma(64;205 1597 17324 45721)	Atlas-SNP	.											.	ZNF347	87	.	0			c.C1641T						PASS	.	G	,,	421,3985	206.2+/-227.9	18,385,1800	159.0	153.0	155.0		1641,1641,1638	-0.4	0.0	19	dbSNP_89	155	609,7991	160.3+/-213.4	34,541,3725	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF347	NM_001172674.1,NM_001172675.1,NM_032584.2	,,	52,926,5525	AA,AG,GG		7.0814,9.5552,7.9194	,,	547/841,547/841,546/840	53644443	1030,11976	2203	4300	6503	SO:0001819	synonymous_variant	84671	exon5			TTTGCCGCACTCA	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.1638C>T	19.37:g.53644443G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	101	37	0.366337	NM_001172675	B3KU77|B9EG59|G5E9N4|Q8TCN1	Silent	SNP	ENST00000334197.7	37	CCDS33097.1																																																																																			G|0.924;A|0.076	0.076	strong		0.403	ZNF347-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464170.1	NM_032584	
FARP2	9855	hgsc.bcm.edu	37	2	242350466	242350466	+	Silent	SNP	A	A	G	rs2240479	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:242350466A>G	ENST00000264042.3	+	6	599	c.429A>G	c.(427-429)caA>caG	p.Q143Q	FARP2_ENST00000545004.1_Silent_p.Q143Q|FARP2_ENST00000373287.4_Silent_p.Q143Q	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	143	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)		TTGCCTTGCAACTTAAGAGAG	0.478													A|||	424	0.0846645	0.0877	0.0548	5008	,	,		20810	0.0744		0.0924	False		,,,				2504	0.1043				p.Q143Q		Atlas-SNP	.											.	FARP2	92	.	0			c.A429G						PASS	.	A		406,4000	194.7+/-219.5	19,368,1816	111.0	97.0	102.0		429	-5.9	0.5	2	dbSNP_98	102	871,7729	193.7+/-239.3	45,781,3474	yes	coding-synonymous	FARP2	NM_014808.2		64,1149,5290	GG,GA,AA		10.1279,9.2147,9.8185		143/1055	242350466	1277,11729	2203	4300	6503	SO:0001819	synonymous_variant	9855	exon6			CTTGCAACTTAAG	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.429A>G	2.37:g.242350466A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	52	0.422764	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Silent	SNP	ENST00000264042.3	37	CCDS33424.1																																																																																			A|0.904;G|0.096	0.096	strong		0.478	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228486404	228486404	+	Intron	SNP	C	C	T	rs56021350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228486404C>T	ENST00000422127.1	+	43	11703				OBSCN_ENST00000359599.6_3'UTR|OBSCN_ENST00000366707.4_Missense_Mutation_p.T1089M|RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000284548.11_Intron|OBSCN_ENST00000570156.2_Missense_Mutation_p.T4399M	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACCTCGGCCACGCTCACTGTC	0.547													C|||	831	0.165935	0.1982	0.2378	5008	,	,		21966	0.1518		0.1581	False		,,,				2504	0.0941				p.T4399M		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	0			c.C13196T						PASS	.	C	,	402,1350		37,328,511	99.0	84.0	89.0		,	-4.7	0.0	1	dbSNP_129	89	712,3270		62,588,1341	no	intron,intron	OBSCN	NM_001098623.1,NM_052843.2	,	99,916,1852	TT,TC,CC		17.8805,22.9452,19.428	,	,	228486404	1114,4620	876	1991	2867	SO:0001627	intron_variant	84033	exon49			CGGCCACGCTCAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11659+3660C>T	1.37:g.228486404C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	380	0.17399267399267399	86	0.17479674796747968	85	0.23480662983425415	87	0.1520979020979021	122	0.16094986807387862	C	8.711	0.911956	0.17907	0.229452	0.178805	ENSG00000154358	ENST00000366707	T	0.68903	-0.36	4.68	-4.67	0.03319	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.24119	-1.0169	5	0.33940	T	0.23	.	12.6558	0.56786	0.0:0.3898:0.0:0.6102	rs56021350;rs61825284	.	.	.	M	1089	ENSP00000355668:T1089M	ENSP00000355668:T1089M	T	+	2	0	OBSCN	226553027	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.459000	0.01000	-1.387000	0.02095	-0.254000	0.11334	ACG	C|0.825;T|0.175	0.175	strong		0.547	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
P2RX7	5027	hgsc.bcm.edu	37	12	121615103	121615103	+	Missense_Mutation	SNP	G	G	A	rs1718119	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121615103G>A	ENST00000546057.1	+	11	1185	c.1042G>A	c.(1042-1044)Gct>Act	p.A348T	P2RX7_ENST00000328963.5_Missense_Mutation_p.A178T|P2RX7_ENST00000541446.1_Missense_Mutation_p.A59T|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_Missense_Mutation_p.A258T	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	348			A -> T (in dbSNP:rs1718119). {ECO:0000269|PubMed:9826911}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCCCCAGGCCGCTGTGTTCAT	0.498													A|||	1615	0.322484	0.4599	0.2003	5008	,	,		20159	0.1419		0.3827	False		,,,				2504	0.3476				p.A348T		Atlas-SNP	.											P2RX7,NS,carcinoma,0,1	P2RX7	53	1	0			c.G1042A						PASS	.	A	THR/ALA	2007,2399	614.4+/-392.4	454,1099,650	138.0	121.0	127.0		1042	5.6	1.0	12	dbSNP_89	127	3418,5182	639.4+/-399.5	723,1972,1605	yes	missense	P2RX7	NM_002562.5	58	1177,3071,2255	AA,AG,GG		39.7442,45.5515,41.7115	benign	348/596	121615103	5425,7581	2203	4300	6503	SO:0001583	missense	5027	exon11			CAGGCCGCTGTGT	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1042G>A	12.37:g.121615103G>A	ENSP00000442349:p.Ala348Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	137	136	0.992701	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	673	0.30815018315018317	231	0.4695121951219512	76	0.20994475138121546	73	0.12762237762237763	293	0.3865435356200528	A	6.616	0.482145	0.12581	0.455515	0.397442	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.03580	3.88;3.88;3.88;3.88	5.62	5.62	0.85841	.	0.382952	0.23821	N	0.044240	T	0.00012	0.0000	N	0.00112	-2.095	0.52501	P	4.199999999998649E-5	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.38887	-0.9640	9	0.02654	T	1	.	7.4513	0.27240	0.8325:0.0:0.1675:0.0	rs1718119;rs2230910;rs17525154;rs52812840;rs58430687;rs1718119	178;59;258;348	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	T	348;178;258;59	ENSP00000442349:A348T;ENSP00000330696:A178T;ENSP00000442572:A258T;ENSP00000437471:A59T	ENSP00000330696:A178T	A	+	1	0	P2RX7	120099486	0.976000	0.34144	0.978000	0.43139	0.854000	0.48673	0.672000	0.25187	0.980000	0.38523	-0.332000	0.08345	GCT	G|0.628;N|0.001	.	strong		0.498	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
AKAP12	9590	hgsc.bcm.edu	37	6	151670172	151670172	+	Missense_Mutation	SNP	A	A	C	rs3734799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151670172A>C	ENST00000253332.1	+	3	835	c.646A>C	c.(646-648)Aag>Cag	p.K216Q	AKAP12_ENST00000490177.1_3'UTR|AKAP12_ENST00000402676.2_Missense_Mutation_p.K216Q|AKAP12_ENST00000354675.6_Missense_Mutation_p.K118Q|AKAP12_ENST00000359755.5_Missense_Mutation_p.K111Q|snoU13_ENST00000458767.1_RNA			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	216			K -> Q (in dbSNP:rs3734799). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:9000000, ECO:0000269|Ref.3, ECO:0000269|Ref.6}.		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)		TGGCGACCACAAGGACCCCAG	0.527													C|||	2724	0.54393	0.3638	0.6254	5008	,	,		13794	0.4593		0.7614	False		,,,				2504	0.593				p.K216Q	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.A646C						PASS	.	C	GLN/LYS,GLN/LYS	1880,2526	618.7+/-393.2	418,1044,741	55.0	60.0	59.0		646,352	4.5	0.9	6	dbSNP_107	59	6524,2076	351.0+/-328.1	2500,1524,276	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	53,53	2918,2568,1017	CC,CA,AA		24.1395,42.6691,35.3837	benign,benign	216/1783,118/1685	151670172	8404,4602	2203	4300	6503	SO:0001583	missense	9590	exon4			GACCACAAGGACC	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.646A>C	6.37:g.151670172A>C	ENSP00000253332:p.Lys216Gln	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	18	17	0.944444	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	1268	0.5805860805860806	166	0.33739837398373984	231	0.638121546961326	294	0.513986013986014	577	0.7612137203166227	C	0.041	-1.286511	0.01387	0.426691	0.758605	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07688	3.17;3.17;3.17;3.18	5.41	4.49	0.54785	.	0.723850	0.11488	N	0.559024	T	0.00580	0.0019	N	0.00237	-1.79	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.45991	-0.9223	9	0.08381	T	0.77	.	8.2812	0.31902	0.3357:0.4395:0.2249:0.0	rs3734799;rs57478243;rs3734799	111;118;216	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	Q	216;216;118;111	ENSP00000384537:K216Q;ENSP00000253332:K216Q;ENSP00000346702:K118Q;ENSP00000352794:K111Q	ENSP00000253332:K216Q	K	+	1	0	AKAP12	151711865	0.012000	0.17670	0.874000	0.34290	0.010000	0.07245	0.834000	0.27518	1.443000	0.47586	-0.224000	0.12420	AAG	A|0.400;C|0.600	0.600	strong		0.527	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
KRT82	3888	hgsc.bcm.edu	37	12	52788928	52788928	+	Missense_Mutation	SNP	G	G	A	rs2658658	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52788928G>A	ENST00000257974.2	-	9	1450	c.1373C>T	c.(1372-1374)aCg>aTg	p.T458M	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	458	Tail.		T -> M (in dbSNP:rs2658658).			keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		GAGGACAGGCGTGCTGACCCC	0.642													G|||	1696	0.338658	0.3374	0.3746	5008	,	,		20091	0.0645		0.4702	False		,,,				2504	0.4622				p.T458M		Atlas-SNP	.											.	KRT82	45	.	0			c.C1373T						PASS	.	G	MET/THR	1604,2802	494.1+/-362.9	305,994,904	52.0	45.0	47.0		1373	3.8	0.7	12	dbSNP_100	47	4105,4495	557.3+/-387.0	979,2147,1174	yes	missense	KRT82	NM_033033.3	81	1284,3141,2078	AA,AG,GG		47.7326,36.4049,43.8951	probably-damaging	458/514	52788928	5709,7297	2203	4300	6503	SO:0001583	missense	3888	exon9			ACAGGCGTGCTGA	Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.1373C>T	12.37:g.52788928G>A	ENSP00000257974:p.Thr458Met	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	697	0.3191391941391941	170	0.34552845528455284	142	0.39226519337016574	32	0.055944055944055944	353	0.4656992084432718	G	10.42	1.344757	0.24426	0.364049	0.477326	ENSG00000161850	ENST00000257974	D	0.82711	-1.64	4.73	3.84	0.44239	.	0.181657	0.26967	N	0.021583	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	D	0.76494	0.999	P	0.59221	0.854	T	0.36962	-0.9726	9	0.72032	D	0.01	.	7.9321	0.29907	0.191:0.0:0.809:0.0	rs2658658;rs3741733;rs17715642;rs52836177;rs57500516;rs2658658	458	Q9NSB4	KRT82_HUMAN	M	458	ENSP00000257974:T458M	ENSP00000257974:T458M	T	-	2	0	KRT82	51075195	0.030000	0.19436	0.696000	0.30242	0.028000	0.11728	2.017000	0.40981	1.137000	0.42214	-0.215000	0.12644	ACG	G|0.611;A|0.389	0.389	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033	
MOV10L1	54456	hgsc.bcm.edu	37	22	50555686	50555686	+	Missense_Mutation	SNP	A	A	C	rs760749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50555686A>C	ENST00000262794.5	+	9	1443	c.1360A>C	c.(1360-1362)Att>Ctt	p.I454L	MOV10L1_ENST00000540615.1_Missense_Mutation_p.I434L|MOV10L1_ENST00000545383.1_Missense_Mutation_p.I454L|MOV10L1_ENST00000395843.1_5'UTR|MOV10L1_ENST00000395858.3_Missense_Mutation_p.I454L	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	454			I -> L (in dbSNP:rs760749). {ECO:0000269|PubMed:15489334, 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)		GGAGTCACTAATTGCTGCGCG	0.443													A|||	741	0.147963	0.0212	0.1182	5008	,	,		17252	0.2391		0.1849	False		,,,				2504	0.2086				p.I454L		Atlas-SNP	.											.	MOV10L1	238	.	0			c.A1360C						PASS	.	A	LEU/ILE,LEU/ILE,LEU/ILE	175,4231	114.6+/-152.6	0,175,2028	89.0	85.0	86.0		1360,1300,1360	5.8	0.0	22	dbSNP_86	86	1389,7211	268.5+/-287.9	110,1169,3021	yes	missense,missense,missense	MOV10L1	NM_001164104.1,NM_001164105.1,NM_018995.2	5,5,5	110,1344,5049	CC,CA,AA		16.1512,3.9719,12.0252	benign,benign,benign	454/1166,434/1166,454/1212	50555686	1564,11442	2203	4300	6503	SO:0001583	missense	54456	exon9			TCACTAATTGCTG	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.1360A>C	22.37:g.50555686A>C	ENSP00000262794:p.Ile454Leu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	342	0.1565934065934066	12	0.024390243902439025	62	0.1712707182320442	126	0.2202797202797203	142	0.18733509234828497	A	6.800	0.516669	0.12944	0.039719	0.161512	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;T;D	0.84730	-1.7;-1.7;-1.28;-1.89	5.76	5.76	0.90799	.	0.107622	0.64402	D	0.000007	T	0.00109	0.0003	L	0.32530	0.975	0.54753	P	1.399999999995849E-5	P;B;B;B	0.34837	0.472;0.097;0.059;0.059	B;B;B;B	0.27715	0.082;0.026;0.012;0.012	T	0.40997	-0.9533	9	0.05525	T	0.97	-17.816	10.326	0.43793	0.853:0.0:0.0:0.147	rs760749;rs5771173;rs17836613;rs59634867;rs760749	215;434;454;454	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	L	454;454;454;434	ENSP00000438978:I454L;ENSP00000262794:I454L;ENSP00000379199:I454L;ENSP00000438542:I434L	ENSP00000262794:I454L	I	+	1	0	MOV10L1	48897813	0.291000	0.24352	0.048000	0.18961	0.040000	0.13550	0.754000	0.26390	2.193000	0.70182	0.528000	0.53228	ATT	A|0.868;C|0.132	0.132	strong		0.443	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
CDH19	28513	hgsc.bcm.edu	37	18	64176365	64176365	+	Silent	SNP	G	G	T	rs1055335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:64176365G>T	ENST00000262150.2	-	11	1987	c.1695C>A	c.(1693-1695)acC>acA	p.T565T	CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	1840	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				GGATGGTAAGGGTGTTTGTAC	0.453													G|||	1264	0.252396	0.0651	0.2795	5008	,	,		16004	0.2331		0.3529	False		,,,				2504	0.4029				p.T565T		Atlas-SNP	.											.	CDH19	141	.	0			c.C1695A						PASS	.	G		529,3877	240.3+/-251.1	34,461,1708	212.0	179.0	190.0		1695	-0.1	1.0	18	dbSNP_86	190	3261,5339	489.9+/-372.7	632,1997,1671	no	coding-synonymous	CDH19	NM_021153.2		666,2458,3379	TT,TG,GG		37.9186,12.0064,29.1404		565/773	64176365	3790,9216	2203	4300	6503	SO:0001819	synonymous_variant	28513	exon11			GGTAAGGGTGTTT	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.1695C>A	18.37:g.64176365G>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	208	201	0.966346	NM_021153	O15098	Silent	SNP	ENST00000262150.2	37	CCDS11994.1																																																																																			G|0.731;T|0.269	0.269	strong		0.453	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
NEFL	4747	hgsc.bcm.edu	37	8	24813798	24813798	+	RNA	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:24813798C>T	ENST00000221169.5	-	0	826				CTD-2168K21.2_ENST00000607735.1_RNA			P07196	NFL_HUMAN	neurofilament, light polypeptide						anterograde axon cargo transport (GO:0008089)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|intermediate filament organization (GO:0045109)|locomotion (GO:0040011)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron apoptotic process (GO:0043524)|neurofilament bundle assembly (GO:0033693)|neuromuscular process controlling balance (GO:0050885)|neuron projection morphogenesis (GO:0048812)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of axonogenesis (GO:0050772)|protein polymerization (GO:0051258)|regulation of axon diameter (GO:0031133)|response to corticosterone (GO:0051412)|response to peptide hormone (GO:0043434)|response to toxic substance (GO:0009636)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|neurofilament (GO:0005883)	identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|protein C-terminus binding (GO:0008022)|structural constituent of cytoskeleton (GO:0005200)	p.A78T(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)	21		Ovarian(32;0.00965)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		TTGCTGATGGCGGCTACCTGG	0.637																																					p.A78T		Atlas-SNP	.											NEFL,colon,carcinoma,0,1	NEFL	47	1	1	Substitution - Missense(1)	large_intestine(1)	c.G232A						scavenged	.						30.0	34.0	32.0					8																	24813798		2173	4274	6447			4747	exon1			TGATGGCGGCTAC		CCDS75712.1	8p21.2	2014-09-17	2008-09-19		ENSG00000104725	ENSG00000277586		"""Intermediate filaments type IV"""	7739	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 110"""	162280	"""neurofilament, light polypeptide 68kDa"""			17620486, 3145240	Standard	NM_006158		Approved	NFL, CMT1F, CMT2E, NF68, PPP1R110	uc003xee.4	P07196	OTTHUMG00000134284		8.37:g.24813798C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	178	3	0.0168539	NM_006158	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	37																																																																																				.	.	none		0.637	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158	
ESPL1	9700	hgsc.bcm.edu	37	12	53662624	53662624	+	Missense_Mutation	SNP	C	C	A	rs6580942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:53662624C>A	ENST00000257934.4	+	2	165	c.74C>A	c.(73-75)gCc>gAc	p.A25D	ESPL1_ENST00000552462.1_Missense_Mutation_p.A25D	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	25				A -> D (in Ref. 1; AAR18247). {ECO:0000305}.	apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TTGCTGCCCGCCTTGAAGGTG	0.527													A|||	4449	0.888379	0.9841	0.7954	5008	,	,		17314	0.999		0.673	False		,,,				2504	0.9325				p.A25D	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C74A						PASS	.	A	ASP/ALA	4135,271	151.0+/-185.0	1946,243,14	35.0	34.0	34.0	http://omim.org/entry/606257	74	4.8	0.1	12	dbSNP_116	34	5835,2765	433.7+/-357.5	1997,1841,462	yes	missense	ESPL1	NM_012291.4	126	3943,2084,476	AA,AC,CC		32.1512,6.1507,23.3431	benign	25/2121	53662624	9970,3036	2203	4300	6503	SO:0001583	missense	9700	exon2			TGCCCGCCTTGAA	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.74C>A	12.37:g.53662624C>A	ENSP00000257934:p.Ala25Asp	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	1822	0.8342490842490843	475	0.9654471544715447	281	0.7762430939226519	572	1.0	494	0.6517150395778364	A	1.127	-0.653471	0.03480	0.938493	0.678488	ENSG00000135476	ENST00000257934;ENST00000552462	T;T	0.10668	2.85;2.85	5.95	4.79	0.61399	.	0.227922	0.36519	N	0.002552	T	0.00012	0.0000	N	0.00116	-2.08	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37753	-0.9692	9	0.02654	T	1	.	11.3037	0.49323	0.7081:0.2919:0.0:0.0	rs6580942;rs17750752;rs52806931;rs60259413;rs6580942	25	Q14674	ESPL1_HUMAN	D	25	ENSP00000257934:A25D;ENSP00000449831:A25D	ENSP00000257934:A25D	A	+	2	0	ESPL1	51948891	0.995000	0.38212	0.137000	0.22149	0.354000	0.29330	3.448000	0.52943	0.492000	0.27815	-0.256000	0.11100	GCC	C|0.192;A|0.808	0.808	strong		0.527	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94343023	94343023	+	Silent	SNP	A	A	G	rs2391322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:94343023A>G	ENST00000436063.2	-	2	525	c.468T>C	c.(466-468)ccT>ccC	p.P156P	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	156					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TTTTTTCTGTAGGAAGCACAA	0.393													G|||	2188	0.436901	0.3782	0.3718	5008	,	,		20363	0.5585		0.3499	False		,,,				2504	0.5266				p.P156P		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.T468C						PASS	.	G		1395,2271		250,895,688	112.0	104.0	106.0		468	-0.4	0.0	1	dbSNP_100	106	2925,5263		505,1915,1674	no	coding-synonymous	DNTTIP2	NM_014597.4		755,2810,2362	GG,GA,AA		35.723,38.0524,36.4434		156/757	94343023	4320,7534	1833	4094	5927	SO:0001819	synonymous_variant	30836	exon2			TTCTGTAGGAAGC	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.468T>C	1.37:g.94343023A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Silent	SNP	ENST00000436063.2	37	CCDS44174.1																																																																																			A|0.587;G|0.413	0.413	strong		0.393	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
ADAM19	8728	hgsc.bcm.edu	37	5	156917340	156917340	+	Missense_Mutation	SNP	A	A	C	rs10067096	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:156917340A>C	ENST00000517905.1	-	19	2262	c.2218T>G	c.(2218-2220)Tcc>Gcc	p.S740A	ADAM19_ENST00000257527.4_Missense_Mutation_p.S740A|ADAM19_ENST00000430702.2_Missense_Mutation_p.S473A|ADAM19_ENST00000394020.1_Missense_Mutation_p.S742A			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	740					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTCAGCTTGGAAGGGAGAGCT	0.493													A|||	603	0.120407	0.205	0.1124	5008	,	,		18142	0.005		0.1968	False		,,,				2504	0.0521				p.S740A		Atlas-SNP	.											.	ADAM19	216	.	0			c.T2218G						PASS	.	A	ALA/SER	852,3554	334.4+/-303.4	79,694,1430	180.0	156.0	164.0		2218	4.2	1.0	5	dbSNP_119	164	1705,6895	312.3+/-310.8	186,1333,2781	yes	missense	ADAM19	NM_033274.3	99	265,2027,4211	CC,CA,AA		19.8256,19.3373,19.6602	benign	740/919	156917340	2557,10449	2203	4300	6503	SO:0001583	missense	8728	exon19			GCTTGGAAGGGAG	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.2218T>G	5.37:g.156917340A>C	ENSP00000428654:p.Ser740Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		300	0.13736263736263737	94	0.1910569105691057	42	0.11602209944751381	4	0.006993006993006993	160	0.21108179419525067	A	12.44	1.939797	0.34189	0.193373	0.198256	ENSG00000135074	ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	T;T;T;T	0.01685	4.69;4.83;4.85;4.82	5.41	4.24	0.50183	.	0.207319	0.34700	N	0.003743	T	0.00012	0.0000	L	0.56769	1.78	0.43073	P	0.005283999999999955	B;B;B	0.34015	0.417;0.435;0.149	B;B;B	0.30495	0.116;0.078;0.098	T	0.28933	-1.0028	9	0.07325	T	0.83	.	4.8818	0.13683	0.7489:0.0:0.0864:0.1647	rs10067096;rs61143303;rs10067096	740;740;473	Q9H013-2;Q9H013;E9PD32	.;ADA19_HUMAN;.	A	473;740;742;740	ENSP00000414088:S473A;ENSP00000257527:S740A;ENSP00000377588:S742A;ENSP00000428654:S740A	ENSP00000257527:S740A	S	-	1	0	ADAM19	156849918	0.980000	0.34600	0.974000	0.42286	0.617000	0.37484	2.373000	0.44266	0.866000	0.35629	0.533000	0.62120	TCC	A|0.827;C|0.173	0.173	strong		0.493	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
NUP54	53371	hgsc.bcm.edu	37	4	77057501	77057501	+	Silent	SNP	A	A	G	rs11558468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77057501A>G	ENST00000264883.3	-	4	500	c.360T>C	c.(358-360)acT>acC	p.T120T	NUP54_ENST00000514987.1_Silent_p.T72T|NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_Intron|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	120	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						GAGCACTCGCAGTATTTATCA	0.433													A|||	776	0.154952	0.0567	0.1282	5008	,	,		16678	0.3512		0.1312	False		,,,				2504	0.1288				p.T120T		Atlas-SNP	.											.	NUP54	48	.	0			c.T360C						PASS	.	A		308,4098	166.2+/-197.5	15,278,1910	92.0	94.0	93.0		360	3.2	1.0	4	dbSNP_120	93	1299,7301	257.3+/-281.4	101,1097,3102	no	coding-synonymous	NUP54	NM_017426.2		116,1375,5012	GG,GA,AA		15.1047,6.9905,12.3558		120/508	77057501	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon4			ACTCGCAGTATTT	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.360T>C	4.37:g.77057501A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			A|0.865;G|0.135	0.135	strong		0.433	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
FAM205A	259308	hgsc.bcm.edu	37	9	34724786	34724786	+	Silent	SNP	G	G	A	rs72617336	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34724786G>A	ENST00000378788.3	-	4	2490	c.2451C>T	c.(2449-2451)ccC>ccT	p.P817P		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	817						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GGATTTCCACGGGACTAGGCT	0.542													G|||	2001	0.399561	0.0666	0.3991	5008	,	,		19790	0.6171		0.4791	False		,,,				2504	0.544				p.P817P		Atlas-SNP	.											.	FAM205A	45	.	0			c.C2451T						PASS	.	G		168,1216		7,154,531	30.0	26.0	27.0		2451	1.0	0.0	9	dbSNP_130	27	1526,1656		355,816,420	no	coding-synonymous	FAM205A	NM_001141917.1		362,970,951	AA,AG,GG		47.9573,12.1387,37.1003		817/1336	34724786	1694,2872	692	1591	2283	SO:0001819	synonymous_variant	259308	exon4			TTCCACGGGACTA		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.2451C>T	9.37:g.34724786G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	235	115	0.489362	NM_001141917	A8MVW7	Silent	SNP	ENST00000378788.3	37	CCDS55305.1																																																																																			G|0.580;A|0.420	0.420	strong		0.542	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
LAMB4	22798	hgsc.bcm.edu	37	7	107677984	107677984	+	Missense_Mutation	SNP	G	G	A	rs1627354	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:107677984G>A	ENST00000388781.3	-	30	4611	c.4528C>T	c.(4528-4530)Cac>Tac	p.H1510Y	AC005048.1_ENST00000401266.1_RNA|LAMB4_ENST00000388780.3_Missense_Mutation_p.H1510Y|LAMB4_ENST00000483484.1_5'Flank|LAMB4_ENST00000205386.4_Missense_Mutation_p.H1510Y	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1510	Domain I.		H -> Y (in dbSNP:rs1627354).		cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						ATTGGTAGGTGAATGTCAAGC	0.398													G|||	1032	0.20607	0.612	0.0879	5008	,	,		21557	0.0268		0.0845	False		,,,				2504	0.0511				p.H1510Y		Atlas-SNP	.											.	LAMB4	253	.	0			c.C4528T						PASS	.	G	TYR/HIS	2419,1987	617.3+/-392.9	652,1115,436	226.0	213.0	217.0		4528	2.7	0.0	7	dbSNP_89	217	531,8069	147.1+/-202.6	18,495,3787	yes	missense	LAMB4	NM_007356.2	83	670,1610,4223	AA,AG,GG		6.1744,45.0976,22.6818	benign	1510/1762	107677984	2950,10056	2203	4300	6503	SO:0001583	missense	22798	exon30			GTAGGTGAATGTC	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.4528C>T	7.37:g.107677984G>A	ENSP00000373433:p.His1510Tyr	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	213	108	0.507042	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	417	0.19093406593406592	291	0.5914634146341463	41	0.1132596685082873	13	0.022727272727272728	72	0.09498680738786279	G	6.127	0.391582	0.11581	0.549024	0.061744	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.31510	1.49;1.49;1.91;1.52	4.48	2.66	0.31614	.	0.264049	0.26654	N	0.023195	T	0.00012	0.0000	N	0.19112	0.55	0.51482	P	7.500000000004725E-5	P;P	0.50528	0.917;0.936	B;B	0.42462	0.388;0.25	T	0.39035	-0.9633	9	0.66056	D	0.02	.	4.0874	0.09953	0.1976:0.0:0.618:0.1844	rs1627354;rs3735592;rs10341067;rs52793585;rs59660148;rs1627354	1510;1510	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	Y	1510;1510;536;1510	ENSP00000205386:H1510Y;ENSP00000373433:H1510Y;ENSP00000416562:H536Y;ENSP00000373432:H1510Y	ENSP00000205386:H1510Y	H	-	1	0	LAMB4	107465220	0.977000	0.34250	0.014000	0.15608	0.028000	0.11728	1.051000	0.30417	0.620000	0.30215	0.655000	0.94253	CAC	G|0.784;A|0.216	0.216	strong		0.398	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
RPTOR	57521	hgsc.bcm.edu	37	17	78519519	78519519	+	Silent	SNP	T	T	C	rs61750765	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:78519519T>C	ENST00000306801.3	+	1	452	c.90T>C	c.(88-90)ttT>ttC	p.F30F	RPTOR_ENST00000537330.1_5'UTR|RPTOR_ENST00000570891.1_Silent_p.F30F|RPTOR_ENST00000544334.2_Silent_p.F30F	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	30					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						CTTTGGCTTTTATGAAAAAGA	0.507													T|||	249	0.0497204	0.0393	0.0807	5008	,	,		16873	0.001		0.1173	False		,,,				2504	0.0225				p.F30F		Atlas-SNP	.											.	RPTOR	122	.	0			c.T90C						PASS	.	T	,	250,4156	146.9+/-181.5	11,228,1964	83.0	86.0	85.0		90,90	-1.4	1.0	17	dbSNP_129	85	1144,7456	235.3+/-267.9	85,974,3241	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	96,1202,5205	CC,CT,TT		13.3023,5.6741,10.7181	,	30/1178,30/1336	78519519	1394,11612	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon1			GGCTTTTATGAAA		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.90T>C	17.37:g.78519519T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			T|0.903;C|0.097	0.097	strong		0.507	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
OR51F1	256892	hgsc.bcm.edu	37	11	4790482	4790482	+	Silent	SNP	T	T	C	rs12792898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4790482T>C	ENST00000380383.1	-	1	686	c.687A>G	c.(685-687)ttA>ttG	p.L229L	OR51F1_ENST00000343430.3_Silent_p.L222L|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	229						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)		AGTGAATAATTAAGATATATG	0.443													T|||	230	0.0459265	0.0061	0.0951	5008	,	,		22294	0.0		0.1412	False		,,,				2504	0.0143				p.L222L		Atlas-SNP	.											OR51F1,NS,carcinoma,-2,1	OR51F1	60	1	0			c.A666G						PASS	.	T		140,4262	98.0+/-136.7	1,138,2062	127.0	125.0	126.0		666	1.1	0.1	11	dbSNP_121	126	1159,7437	238.5+/-269.9	94,971,3233	no	coding-synonymous	OR51F1	NM_001004752.1		95,1109,5295	CC,CT,TT		13.483,3.1804,9.9938		222/313	4790482	1299,11699	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			AATAATTAAGATA	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.687A>G	11.37:g.4790482T>C		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				T|0.909;C|0.091	0.091	strong		0.443	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
UPF2	26019	hgsc.bcm.edu	37	10	12043790	12043790	+	Silent	SNP	T	T	G	rs11595168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:12043790T>G	ENST00000356352.2	-	5	2012	c.1539A>C	c.(1537-1539)tcA>tcC	p.S513S	UPF2_ENST00000397053.2_Silent_p.S513S|UPF2_ENST00000357604.5_Silent_p.S513S			Q9HAU5	RENT2_HUMAN	UPF2 regulator of nonsense transcripts homolog (yeast)	513					gene expression (GO:0010467)|liver development (GO:0001889)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|organ regeneration (GO:0031100)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(14)|lung(17)|ovary(2)|skin(3)|urinary_tract(2)	56		Renal(717;0.228)				CATCGGGACTTGATACCTCCT	0.358													T|||	158	0.0315495	0.003	0.0274	5008	,	,		16786	0.001		0.0855	False		,,,				2504	0.0491				p.S513S		Atlas-SNP	.											.	UPF2	111	.	0			c.A1539C						PASS	.	T	,	79,4325	66.4+/-103.9	0,79,2123	99.0	93.0	95.0		1539,1539	3.1	1.0	10	dbSNP_120	95	688,7912	168.3+/-219.8	27,634,3639	no	coding-synonymous,coding-synonymous	UPF2	NM_015542.2,NM_080599.1	,	27,713,5762	GG,GT,TT		8.0,1.7938,5.8982	,	513/1273,513/1273	12043790	767,12237	2202	4300	6502	SO:0001819	synonymous_variant	26019	exon6			GGGACTTGATACC	AB037829	CCDS7086.1	10p14-p13	2011-06-21			ENSG00000151461	ENSG00000151461			17854	protein-coding gene	gene with protein product	"""smg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	605529				11073994, 11113196	Standard	NM_080599		Approved	RENT2, DKFZP434D222, KIAA1408, smg-3	uc001ilb.3	Q9HAU5	OTTHUMG00000017678	ENST00000356352.2:c.1539A>C	10.37:g.12043790T>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	111	43	0.387387	NM_080599	A6NLJ5|D3DRS0|Q14BM1|Q5W0J4|Q8N8U1|Q9H1J2|Q9NWL1|Q9P2D9|Q9Y4M9	Silent	SNP	ENST00000356352.2	37	CCDS7086.1																																																																																			T|0.947;G|0.053	0.053	strong		0.358	UPF2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046783.1		
CFAP46	54777	hgsc.bcm.edu	37	10	134735672	134735672	+	Silent	SNP	A	A	G	rs7915371	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134735672A>G	ENST00000368586.5	-	13	1642	c.1542T>C	c.(1540-1542)aaT>aaC	p.N514N	TTC40_ENST00000368582.2_Silent_p.N514N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CCAGGCCTGCATTCACCAGGA	0.572													G|||	2678	0.534744	0.6558	0.6081	5008	,	,		18661	0.3542		0.4712	False		,,,				2504	0.5706				p.N514N		Atlas-SNP	.											.	TTC40	100	.	0			c.T1542C						PASS	.																																			SO:0001819	synonymous_variant	54777	exon13			GCCTGCATTCACC																												ENST00000368586.5:c.1542T>C	10.37:g.134735672A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	143	61	0.426573	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			A|0.515;G|0.485	0.485	strong		0.572	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
CDK5R2	8941	hgsc.bcm.edu	37	2	219824731	219824731	+	Silent	SNP	G	G	C	rs78141300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219824731G>C	ENST00000302625.4	+	1	355	c.189G>C	c.(187-189)gcG>gcC	p.A63A	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	63					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATCTCGGCGCTCACCTGGA	0.716													G|||	163	0.0325479	0.0061	0.0375	5008	,	,		7620	0.0179		0.0398	False		,,,				2504	0.0726				p.A63A		Atlas-SNP	.											.	CDK5R2	17	.	0			c.G189C						PASS	.	G		22,4302		2,18,2142	10.0	14.0	13.0		189	2.5	1.0	2	dbSNP_131	13	213,8313		1,211,4051	no	coding-synonymous	CDK5R2	NM_003936.3		3,229,6193	CC,CG,GG		2.4982,0.5088,1.8288		63/368	219824731	235,12615	2162	4263	6425	SO:0001819	synonymous_variant	8941	exon1			CTCGGCGCTCACC	U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"""neuronal CDK5 activator isoform"""	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.189G>C	2.37:g.219824731G>C		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_003936	Q4ZFW6	Silent	SNP	ENST00000302625.4	37	CCDS2427.1																																																																																			G|0.972;C|0.028	0.028	strong		0.716	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936	
PRTN3	5657	hgsc.bcm.edu	37	19	844020	844020	+	Missense_Mutation	SNP	G	G	A	rs351111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:844020G>A	ENST00000234347.5	+	3	401	c.355G>A	c.(355-357)Gtt>Att	p.V119I	PRTN3_ENST00000544537.2_Missense_Mutation_p.V78I	NM_002777.3	NP_002768.3	P24158	PRTN3_HUMAN	proteinase 3	119	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		V -> I (in dbSNP:rs351111). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1681549, ECO:0000269|PubMed:2377228, ECO:0000269|PubMed:2598267, ECO:0000269|PubMed:7539799, ECO:0000269|PubMed:9924693, ECO:0000269|Ref.3}.		collagen catabolic process (GO:0030574)|mature dendritic cell differentiation (GO:0097029)|negative regulation of phagocytosis (GO:0050765)|positive regulation of cell proliferation (GO:0008284)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			lung(1)|ovary(2)|urinary_tract(1)	4		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACTGAACGACGTTCTCCTCAT	0.647													g|||	2223	0.44389	0.5333	0.4971	5008	,	,		9006	0.3512		0.4006	False		,,,				2504	0.4254				p.V119I		Atlas-SNP	.											.	PRTN3	9	.	0			c.G355A						PASS	.		ILE/VAL	2319,2083		616,1087,498	33.0	34.0	34.0		355	-3.6	0.0	19	dbSNP_79	34	3531,5067		711,2109,1479	yes	missense	PRTN3	NM_002777.3	29	1327,3196,1977	AA,AG,GG		41.0677,47.3194,45.0	benign	119/257	844020	5850,7150	2201	4299	6500	SO:0001583	missense	5657	exon3			AACGACGTTCTCC		CCDS32860.1	19p13.3	2008-07-31	2008-07-31			ENSG00000196415			9495	protein-coding gene	gene with protein product	"""myeloblastin"", ""serine proteinase, neutrophil"", ""Wegener granulomatosis autoantigen"""	177020				2258701	Standard	NM_002777		Approved	PR-3, ACPA, C-ANCA, AGP7, MBT, P29	uc002lqa.1	P24158		ENST00000234347.5:c.355G>A	19.37:g.844020G>A	ENSP00000234347:p.Val119Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_002777	P15637|P18078|Q4VB08|Q4VB09|Q6LBM7|Q6LBN2|Q9UD25|Q9UQD8	Missense_Mutation	SNP	ENST00000234347.5	37	CCDS32860.1	964	0.4413919413919414	250	0.508130081300813	185	0.511049723756906	213	0.3723776223776224	316	0.41688654353562005	g	0.118	-1.128857	0.01756	0.526806	0.410677	ENSG00000196415	ENST00000234347;ENST00000544537	T	0.49139	0.79	2.73	-3.59	0.04583	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.00473	-1.45	0.80722	P	0.0	B	0.30406	0.278	B	0.28139	0.086	T	0.31475	-0.9942	8	0.02654	T	1	.	7.6584	0.28389	0.6738:0.0:0.3262:0.0	rs351111;rs600071;rs1126597;rs3181721;rs17366042;rs17400579;rs58626854;rs351111	119	P24158	PRTN3_HUMAN	I	119;78	ENSP00000234347:V119I	ENSP00000234347:V119I	V	+	1	0	PRTN3	795020	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.066000	0.03454	-0.588000	0.05882	-0.348000	0.07805	GTT	G|0.546;A|0.454	0.454	strong		0.647	PRTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457888.2	NM_002777	
RGS6	9628	hgsc.bcm.edu	37	14	72945012	72945012	+	Silent	SNP	T	T	C	rs2302143	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:72945012T>C	ENST00000553530.1	+	12	1036	c.829T>C	c.(829-831)Ttg>Ctg	p.L277L	RGS6_ENST00000406236.4_Silent_p.L277L|RGS6_ENST00000407322.4_Silent_p.L277L|RGS6_ENST00000553525.1_Silent_p.L277L|RGS6_ENST00000554782.1_Silent_p.L138L|RGS6_ENST00000434263.2_Silent_p.L208L|RGS6_ENST00000404301.2_Silent_p.L277L|RGS6_ENST00000556437.1_Silent_p.L277L|RGS6_ENST00000343854.6_Silent_p.L277L|RGS6_ENST00000555571.1_Silent_p.L277L|RGS6_ENST00000355512.6_Silent_p.L277L|RGS6_ENST00000402788.2_Silent_p.L277L	NM_001204417.1|NM_001204418.1|NM_001204420.1|NM_001204421.1|NM_001204422.1|NM_004296.5	NP_001191346.1|NP_001191347.1|NP_001191349.1|NP_001191350.1|NP_001191351.1|NP_004287.3	P49758	RGS6_HUMAN	regulator of G-protein signaling 6	277	G protein gamma.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neuron differentiation (GO:0045666)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33				all cancers(60;0.00309)|BRCA - Breast invasive adenocarcinoma(234;0.0281)|STAD - Stomach adenocarcinoma(64;0.0302)|OV - Ovarian serous cystadenocarcinoma(108;0.0476)		CAGACATTGTTTGAAAATGTC	0.338													T|||	630	0.125799	0.0567	0.2219	5008	,	,		21617	0.0675		0.1262	False		,,,				2504	0.2106				p.L277L	Ovarian(143;1926 2468 21071 48641)	Atlas-SNP	.											RGS6_ENST00000553525,NS,carcinoma,-2,2	RGS6	92	2	0			c.T829C						PASS	.	T	,,,,,,,,,	321,4085	171.2+/-201.5	12,297,1894	123.0	120.0	121.0		829,829,829,829,829,829,829,724,829,829	5.6	1.0	14	dbSNP_100	121	1037,7561	219.0+/-257.2	65,907,3327	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGS6	NM_001204416.1,NM_001204417.1,NM_001204418.1,NM_001204419.1,NM_001204420.1,NM_001204421.1,NM_001204422.1,NM_001204423.1,NM_001204424.1,NM_004296.5	,,,,,,,,,	77,1204,5221	CC,CT,TT		12.0609,7.2855,10.4429	,,,,,,,,,	277/491,277/486,277/468,277/454,277/436,277/449,277/431,242/438,277/491,277/473	72945012	1358,11646	2203	4299	6502	SO:0001819	synonymous_variant	9628	exon12			CATTGTTTGAAAA	AF073920	CCDS9808.1, CCDS55924.1, CCDS73655.1	14q24.3	2008-07-28	2007-08-14			ENSG00000182732		"""Regulators of G-protein signaling"""	10002	protein-coding gene	gene with protein product		603894	"""regulator of G-protein signalling 6"""			10083744, 14734556	Standard	NM_004296		Approved		uc010ttn.2	P49758		ENST00000553530.1:c.829T>C	14.37:g.72945012T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001204424	C9JE95|F8W7W5|O75576|O75577|Q7Z4K3|Q7Z4K4|Q7Z4K5|Q7Z4K6|Q8TE13|Q8TE14|Q8TE15|Q8TE16|Q8TE17|Q8TE18|Q8TE19|Q8TE20|Q8TE21|Q8TE22|Q9UDS8|Q9UDT0|Q9Y245|Q9Y647	Silent	SNP	ENST00000553530.1	37	CCDS9808.1																																																																																			T|0.889;C|0.111	0.111	strong		0.338	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2		
RASSF5	83593	hgsc.bcm.edu	37	1	206680983	206680983	+	Silent	SNP	A	A	C	rs2095124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:206680983A>C	ENST00000355294.4	+	1	105	c.48A>C	c.(46-48)ctA>ctC	p.L16L	RASSF5_ENST00000367117.3_Silent_p.L16L	NM_182663.2	NP_872604.1	Q8WWW0	RASF5_HUMAN	Ras association (RalGDS/AF-6) domain family member 5	16					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|positive regulation of protein ubiquitination (GO:0031398)|regulation of protein localization to nucleus (GO:1900180)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	8	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.166)			ACCCGCTACTATTGGACCCCG	0.736													C|||	4776	0.953674	0.9955	0.9323	5008	,	,		9108	1.0		0.8519	False		,,,				2504	0.9693				p.L16L	GBM(162;656 1984 11916 22872 31529)	Atlas-SNP	.											RASSF5,caecum,carcinoma,0,1	RASSF5	54	1	0			c.A48C						PASS	.	C	,	2879,81		1400,79,1	2.0	3.0	3.0		48,48	0.6	0.5	1	dbSNP_96	3	5574,982		2366,842,70	no	coding-synonymous,coding-synonymous	RASSF5	NM_182663.2,NM_182664.2	,	3766,921,71	CC,CA,AA		14.9786,2.7365,11.1707	,	16/419,16/337	206680983	8453,1063	1480	3278	4758	SO:0001819	synonymous_variant	83593	exon1			GCTACTATTGGAC	BC004270	CCDS1463.1, CCDS1464.1, CCDS30998.1	1q31	2014-04-10	2008-02-22		ENSG00000136653	ENSG00000266094			17609	protein-coding gene	gene with protein product		607020				11978988, 11965544	Standard	NM_182663		Approved	Maxp1, NORE1, RAPL	uc001hed.3	Q8WWW0	OTTHUMG00000184616	ENST00000355294.4:c.48A>C	1.37:g.206680983A>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_182663	A8K1E6|Q5SY32|Q8WWV9|Q8WXF4|Q9BT99	Silent	SNP	ENST00000355294.4	37	CCDS30998.1																																																																																			A|0.080;C|0.920	0.920	strong		0.736	RASSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088469.1	NM_031437	
MMP8	4317	hgsc.bcm.edu	37	11	102595492	102595492	+	Missense_Mutation	SNP	G	G	A	rs3765620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102595492G>A	ENST00000236826.3	-	1	193	c.95C>T	c.(94-96)aCt>aTt	p.T32I		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	32			T -> I (in dbSNP:rs3765620). {ECO:0000269|PubMed:2159879, ECO:0000269|Ref.2}.		collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	TACCTGAACAGTTTTTGTATT	0.363													A|||	3277	0.654353	0.8147	0.5605	5008	,	,		19429	0.5774		0.5885	False		,,,				2504	0.6513				p.T32I		Atlas-SNP	.											.	MMP8	68	.	0			c.C95T						PASS	.	A	ILE/THR	3309,1097	393.7+/-329.0	1232,845,126	126.0	149.0	142.0		95	1.0	0.0	11	dbSNP_107	142	4788,3810	538.7+/-383.5	1326,2136,837	yes	missense	MMP8	NM_002424.2	89	2558,2981,963	AA,AG,GG		44.3126,24.8979,37.7345	benign	32/468	102595492	8097,4907	2203	4299	6502	SO:0001583	missense	4317	exon1			TGAACAGTTTTTG	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.95C>T	11.37:g.102595492G>A	ENSP00000236826:p.Thr32Ile	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	169	78	0.461538	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	1384	0.6336996336996337	399	0.8109756097560976	213	0.5883977900552486	343	0.5996503496503497	429	0.5659630606860159	A	10.71	1.428057	0.25726	0.751021	0.556874	ENSG00000118113	ENST00000236826	T	0.35789	1.29	5.09	0.964	0.19655	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	1.716080	0.03198	N	0.174354	T	0.00012	0.0000	N	0.03029	-0.43	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42699	-0.9436	9	0.31617	T	0.26	.	8.3601	0.32353	0.5761:0.0:0.4239:0.0	rs3765620;rs52832345;rs59665335;rs3765620	32	P22894	MMP8_HUMAN	I	32	ENSP00000236826:T32I	ENSP00000236826:T32I	T	-	2	0	MMP8	102100702	0.010000	0.17322	0.001000	0.08648	0.006000	0.05464	0.819000	0.27308	-0.276000	0.09206	-0.269000	0.10298	ACT	G|0.357;A|0.643	0.643	strong		0.363	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
DSG3	1830	hgsc.bcm.edu	37	18	29049138	29049138	+	Missense_Mutation	SNP	C	C	T	rs61730311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:29049138C>T	ENST00000257189.4	+	12	1806	c.1723C>T	c.(1723-1725)Cgg>Tgg	p.R575W		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	575					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)			TCAGAACAATCGGTGTGAGAT	0.527													C|||	23	0.00459265	0.0	0.0029	5008	,	,		20150	0.0		0.0099	False		,,,				2504	0.0112				p.R575W		Atlas-SNP	.											.	DSG3	172	.	0			c.C1723T						PASS	.	C	TRP/ARG	14,4392	21.2+/-45.6	0,14,2189	151.0	136.0	141.0		1723	0.5	0.0	18	dbSNP_129	141	98,8502	54.0+/-114.7	1,96,4203	yes	missense	DSG3	NM_001944.2	101	1,110,6392	TT,TC,CC		1.1395,0.3177,0.8611	possibly-damaging	575/1000	29049138	112,12894	2203	4300	6503	SO:0001583	missense	1830	exon12			AACAATCGGTGTG	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.1723C>T	18.37:g.29049138C>T	ENSP00000257189:p.Arg575Trp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	14.16	2.451113	0.43531	0.003177	0.011395	ENSG00000134757	ENST00000257189	T	0.59502	0.26	5.95	0.463	0.16700	.	1.487420	0.04727	N	0.420484	T	0.34019	0.0883	N	0.22421	0.69	0.09310	N	1	P	0.52316	0.952	B	0.40741	0.339	T	0.35822	-0.9773	10	0.66056	D	0.02	.	5.6006	0.17351	0.5361:0.3006:0.0:0.1633	rs61730311	575	P32926	DSG3_HUMAN	W	575	ENSP00000257189:R575W	ENSP00000257189:R575W	R	+	1	2	DSG3	27303136	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.080000	0.11339	0.118000	0.18165	-0.181000	0.13052	CGG	C|0.993;T|0.007	0.007	strong		0.527	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
SLC38A6	145389	hgsc.bcm.edu	37	14	61448049	61448049	+	Silent	SNP	C	C	G	rs17097938	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:61448049C>G	ENST00000267488.4	+	1	170	c.54C>G	c.(52-54)gtC>gtG	p.V18V	RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000554304.1_3'UTR|TRMT5_ENST00000261249.6_5'UTR|SLC38A6_ENST00000354886.2_Silent_p.V18V|SLC38A6_ENST00000456840.2_5'Flank	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6	18					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		ATGTCTCTGTCCAGCAGCCTG	0.612											OREG0007220	type=TRANSCRIPTION FACTOR BINDING SITE|Gene=TRMT5|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	C|||	176	0.0351438	0.0023	0.0231	5008	,	,		18153	0.0813		0.0517	False		,,,				2504	0.0235				p.V18V		Atlas-SNP	.											.	SLC38A6	87	.	0			c.C54G						PASS	.	C	,	43,4363	45.3+/-79.5	0,43,2160	70.0	67.0	68.0		54,54	0.9	0.0	14	dbSNP_123	68	279,8319	101.0+/-162.3	3,273,4023	no	coding-synonymous,coding-synonymous	SLC38A6	NM_001172702.1,NM_153811.2	,	3,316,6183	GG,GC,CC		3.2449,0.9759,2.4762	,	18/522,18/457	61448049	322,12682	2203	4299	6502	SO:0001819	synonymous_variant	145389	exon1			CTCTGTCCAGCAG	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335	ENST00000267488.4:c.54C>G	14.37:g.61448049C>G		Somatic	63	0	0	1053	WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_153811	C9JWA6|Q86SY5	Silent	SNP	ENST00000267488.4	37	CCDS9751.1																																																																																			C|0.968;G|0.032	0.032	strong		0.612	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		
MICA	100507436	hgsc.bcm.edu	37	6	31382882	31382882	+	3'UTR	SNP	C	C	A	rs9266825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31382882C>A	ENST00000449934.2	+	0	1176				HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CTGATGTCAGCTCTTGGGTCC	0.572													t|||	1717	0.342851	0.4372	0.3516	5008	,	,		14470	0.2996		0.2992	False		,,,				2504	0.2986				p.A373D		Atlas-SNP	.											.	MICA	21	.	0			c.C1118A						PASS	.	C		524,860		108,308,276	173.0	157.0	162.0			-1.5	0.0	6	dbSNP_118	162	821,2361		97,627,867	yes	utr-3	MICA	NM_001177519.1		205,935,1143	AA,AC,CC		25.8014,37.8613,29.4569			31382882	1345,3221	692	1591	2283	SO:0001624	3_prime_UTR_variant	100507436	exon7			TGTCAGCTCTTGG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.*123C>A	6.37:g.31382882C>A		Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_000247		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.666;A|0.334	0.334	strong		0.572	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
WDR62	284403	hgsc.bcm.edu	37	19	36583651	36583651	+	Silent	SNP	G	G	A	rs61494900	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36583651G>A	ENST00000270301.7	+	19	2271	c.2271G>A	c.(2269-2271)ctG>ctA	p.L757L	WDR62_ENST00000401500.2_Silent_p.L757L			O43379	WDR62_HUMAN	WD repeat domain 62	757					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			AGCACTTGCTGGAGATTGACC	0.597													G|||	615	0.122804	0.2617	0.0735	5008	,	,		19094	0.0		0.1342	False		,,,				2504	0.0849				p.L757L		Atlas-SNP	.											.	WDR62	102	.	0			c.G2271A						PASS	.	G	,	1005,3401	374.4+/-321.2	111,783,1309	93.0	94.0	93.0		2271,2271	2.9	1.0	19	dbSNP_129	93	890,7710	199.7+/-243.7	54,782,3464	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	165,1565,4773	AA,AG,GG		10.3488,22.8098,14.5702	,	757/1524,757/1519	36583651	1895,11111	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon19			CTTGCTGGAGATT	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2271G>A	19.37:g.36583651G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	177	94	0.531073	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			G|0.864;A|0.136	0.136	strong		0.597	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
HERC1	8925	hgsc.bcm.edu	37	15	63967170	63967170	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:63967170A>G	ENST00000443617.2	-	38	7304	c.7217T>C	c.(7216-7218)aTg>aCg	p.M2406T	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	2406					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						CTGTTTGCCCATGTCTTCATG	0.502																																					p.M2406T		Atlas-SNP	.											.	HERC1	624	.	0			c.T7217C						PASS	.						152.0	144.0	146.0					15																	63967170		2042	4201	6243	SO:0001583	missense	8925	exon38			TTGCCCATGTCTT	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.7217T>C	15.37:g.63967170A>G	ENSP00000390158:p.Met2406Thr	Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	243	106	0.436214	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	A	7.518	0.656022	0.14580	.	.	ENSG00000103657	ENST00000443617	T	0.22743	1.94	5.51	4.39	0.52855	.	0.515835	0.20490	N	0.091313	T	0.09379	0.0231	N	0.08118	0	0.19575	N	0.999966	B	0.02656	0.0	B	0.01281	0.0	T	0.35699	-0.9778	10	0.13470	T	0.59	.	7.9035	0.29748	0.7169:0.0:0.2831:0.0	.	2406	Q15751	HERC1_HUMAN	T	2406	ENSP00000390158:M2406T	ENSP00000390158:M2406T	M	-	2	0	HERC1	61754223	0.091000	0.21658	1.000000	0.80357	0.964000	0.63967	0.681000	0.25320	0.931000	0.37242	0.528000	0.53228	ATG	.	.	none		0.502	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
STK11	6794	hgsc.bcm.edu	37	19	1207176	1207176	+	Silent	SNP	C	C	A	rs56354945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1207176C>A	ENST00000326873.7	+	1	1437	c.264C>A	c.(262-264)atC>atA	p.I88I	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with SIRT1.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|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)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCGAAGGATCCCCAACGGGG	0.597		14	"""D, Mis, N, F, S"""		"""NSCLC, pancreatic"""	"""jejunal harmartoma, ovarian, testicular, pancreatic"""			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)			C|||	119	0.023762	0.0832	0.0086	5008	,	,		18552	0.0		0.003	False		,,,				2504	0.0				p.I88I		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"""E, M, O"""	STK11,brain,glioma,0,2	STK11	410	2	23	Whole gene deletion(20)|Unknown(2)|Deletion - Frameshift(1)	cervix(15)|lung(3)|skin(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C264A						PASS	.	C		255,3773		6,243,1765	29.0	32.0	31.0		264	3.9	1.0	19	dbSNP_129	31	2,8300		0,2,4149	no	coding-synonymous	STK11	NM_000455.4		6,245,5914	AA,AC,CC		0.0241,6.3307,2.0843		88/434	1207176	257,12073	2014	4151	6165	SO:0001819	synonymous_variant	6794	exon1	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	AAGGATCCCCAAC	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"""polarization-related protein LKB1"""	602216	"""serine/threonine kinase 11 (Peutz-Jeghers syndrome)"""			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.264C>A	19.37:g.1207176C>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_000455	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																			C|0.980;A|0.020	0.020	strong		0.597	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455	
LRRC8E	80131	hgsc.bcm.edu	37	19	7963949	7963949	+	Missense_Mutation	SNP	A	A	G	rs386806520|rs2042919	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7963949A>G	ENST00000306708.6	+	3	643	c.542A>G	c.(541-543)gAa>gGa	p.E181G	AC010336.1_ENST00000539278.1_3'UTR	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	181			E -> G (in dbSNP:rs2042919).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						GCAGCCACCGAACGGGCTGCG	0.642													G|||	1166	0.232827	0.323	0.183	5008	,	,		17165	0.2292		0.2425	False		,,,				2504	0.1401				p.E181G		Atlas-SNP	.											.	LRRC8E	67	.	0			c.A542G						PASS	.	G	GLY/GLU	1068,3336		204,660,1338	30.0	38.0	36.0		542	4.1	0.0	19	dbSNP_94	36	2087,6509		274,1539,2485	no	missense	LRRC8E	NM_025061.3	98	478,2199,3823	GG,GA,AA		24.2787,24.2507,24.2692	benign	181/797	7963949	3155,9845	2202	4298	6500	SO:0001583	missense	80131	exon4			CCACCGAACGGGC		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.542A>G	19.37:g.7963949A>G	ENSP00000306524:p.Glu181Gly	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	37	CCDS12189.1	546	0.25	173	0.3516260162601626	63	0.17403314917127072	132	0.23076923076923078	178	0.23482849604221637	G	0.069	-1.206104	0.01568	0.242507	0.242787	ENSG00000171017	ENST00000306708	T	0.27890	1.64	5.19	4.14	0.48551	.	0.468333	0.23620	N	0.046258	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.40875	0.731	B	0.36464	0.225	T	0.46638	-0.9177	9	0.22109	T	0.4	.	5.5225	0.16941	0.171:0.1642:0.6648:0.0	rs2042919;rs3745380;rs60626324	181	Q6NSJ5	LRC8E_HUMAN	G	181	ENSP00000306524:E181G	ENSP00000306524:E181G	E	+	2	0	LRRC8E	7869949	0.001000	0.12720	0.009000	0.14445	0.002000	0.02628	1.315000	0.33608	0.785000	0.33685	-0.802000	0.03209	GAA	A|0.759;G|0.241	0.241	strong		0.642	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
MAP3K6	9064	hgsc.bcm.edu	37	1	27682530	27682530	+	Missense_Mutation	SNP	C	C	G	rs17162549	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:27682530C>G	ENST00000493901.1	-	28	3937	c.3698G>C	c.(3697-3699)gGc>gCc	p.G1233A	MAP3K6_ENST00000374040.3_Missense_Mutation_p.G1225A|MAP3K6_ENST00000357582.2_Missense_Mutation_p.G1233A	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	1233			G -> A (in dbSNP:rs17162549).		activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)			breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		TTGGATGGTGCCTGAATCCAC	0.557													C|||	447	0.0892572	0.2451	0.049	5008	,	,		20136	0.001		0.0547	False		,,,				2504	0.0337				p.G1233A		Atlas-SNP	.											.	MAP3K6	134	.	0			c.G3698C						PASS	.	C	ALA/GLY	881,3525	337.3+/-304.8	91,699,1413	87.0	81.0	83.0		3698	0.8	1.0	1	dbSNP_123	83	320,8280	113.7+/-173.7	7,306,3987	yes	missense	MAP3K6	NM_004672.3	60	98,1005,5400	GG,GC,CC		3.7209,19.9955,9.2342	benign	1233/1289	27682530	1201,11805	2203	4300	6503	SO:0001583	missense	9064	exon27			ATGGTGCCTGAAT	AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.3698G>C	1.37:g.27682530C>G	ENSP00000419591:p.Gly1233Ala	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	188	173	0.920213	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	171|171	0.0782967032967033|0.0782967032967033	113|113	0.22967479674796748|0.22967479674796748	19|19	0.052486187845303865|0.052486187845303865	1|1	0.0017482517482517483|0.0017482517482517483	38|38	0.05013192612137203|0.05013192612137203	C|C	6.967|6.967	0.548397|0.548397	0.13312|0.13312	0.199955|0.199955	0.037209|0.037209	ENSG00000142733|ENSG00000142733	ENST00000486046|ENST00000374040;ENST00000493901;ENST00000374036;ENST00000357582	.|T;T;T	.|0.64085	.|-0.08;-0.08;-0.08	4.92|4.92	0.768|0.768	0.18487|0.18487	.|Sterile alpha motif/pointed domain (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.28274|0.28274	0.84|0.84	0.45307|0.45307	P|P	0.001699000000000006|0.001699000000000006	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.10636|0.10636	-1.0621|-1.0621	4|8	.|0.07990	.|T	.|0.79	.|.	3.6693|3.6693	0.08268|0.08268	0.1516:0.4011:0.3552:0.0921|0.1516:0.4011:0.3552:0.0921	rs17162549;rs17162549|rs17162549;rs17162549	.|1225;1233	.|O95382-3;O95382	.|.;M3K6_HUMAN	P|A	49|1225;1233;71;1233	.|ENSP00000363152:G1225A;ENSP00000419591:G1233A;ENSP00000350195:G1233A	.|ENSP00000350195:G1233A	A|G	-|-	1|2	0|0	MAP3K6|MAP3K6	27555117|27555117	0.975000|0.975000	0.34042|0.34042	0.990000|0.990000	0.47175|0.47175	0.974000|0.974000	0.67602|0.67602	-0.082000|-0.082000	0.11304|0.11304	-0.016000|-0.016000	0.14127|0.14127	-0.211000|-0.211000	0.12701|0.12701	GCA|GGC	C|0.919;G|0.081	0.081	strong		0.557	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
CR1L	1379	hgsc.bcm.edu	37	1	207872595	207872595	+	Missense_Mutation	SNP	A	A	G	rs12729569	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:207872595A>G	ENST00000508064.2	+	8	1264	c.1204A>G	c.(1204-1206)Aat>Gat	p.N402D	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	402	Sushi 6. {ECO:0000255|PROSITE- ProRule:PRU00302}.		N -> D (in dbSNP:rs12729569). {ECO:0000269|PubMed:15489334}.			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						AAGCCTTTGGAATAGCAGTGT	0.418											OREG0014195	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	559	0.111621	0.053	0.1441	5008	,	,		19328	0.0317		0.2535	False		,,,				2504	0.1043				p.N402D		Atlas-SNP	.											.	CR1L	97	.	0			c.A1204G						PASS	.	A	ASP/ASN	337,3427		18,301,1563	243.0	220.0	227.0		1204	1.6	0.8	1	dbSNP_121	227	2159,6055		278,1603,2226	no	missense	CR1L	NM_175710.1	23	296,1904,3789	GG,GA,AA		26.2844,8.9532,20.8382	probably-damaging	402/570	207872595	2496,9482	1882	4107	5989	SO:0001583	missense	1379	exon8			CTTTGGAATAGCA	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.1204A>G	1.37:g.207872595A>G	ENSP00000421736:p.Asn402Asp	Somatic	426	0	0	2170	WXS	Illumina HiSeq	Phase_I	459	230	0.501089	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	309	0.14148351648351648	24	0.04878048780487805	66	0.18232044198895028	24	0.04195804195804196	195	0.25725593667546176	.	14.04	2.416352	0.42918	0.089532	0.262844	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.63255	-0.03	1.65	1.65	0.23941	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	L	0.41027	1.25	0.58432	P	2.9999999999752447E-6	D	0.64830	0.994	D	0.70227	0.968	T	0.06409	-1.0828	8	0.28530	T	0.3	.	5.4429	0.16519	1.0:0.0:0.0:0.0	rs12729569	402	Q2VPA4	CR1L_HUMAN	D	402	ENSP00000421736:N402D	ENSP00000434864:N346D	N	+	1	0	CR1L	205939218	1.000000	0.71417	0.843000	0.33291	0.860000	0.49131	3.166000	0.50785	1.027000	0.39758	0.242000	0.17961	AAT	A|0.831;G|0.169	0.169	strong		0.418	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
UTP20	27340	hgsc.bcm.edu	37	12	101685852	101685852	+	Silent	SNP	G	G	A	rs11110737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101685852G>A	ENST00000261637.4	+	10	1317	c.1143G>A	c.(1141-1143)ccG>ccA	p.P381P		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	381					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						TTTCCTTGCCGGAGACCCTCA	0.383													G|||	441	0.0880591	0.0219	0.111	5008	,	,		16923	0.0278		0.165	False		,,,				2504	0.1442				p.P381P		Atlas-SNP	.											.	UTP20	222	.	0			c.G1143A						PASS	.	G		187,4219	118.4+/-156.1	5,177,2021	149.0	143.0	145.0		1143	-2.9	0.9	12	dbSNP_120	145	1422,7178	274.5+/-291.2	121,1180,2999	no	coding-synonymous	UTP20	NM_014503.2		126,1357,5020	AA,AG,GG		16.5349,4.2442,12.3712		381/2786	101685852	1609,11397	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon10			CTTGCCGGAGACC	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.1143G>A	12.37:g.101685852G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			G|0.888;A|0.112	0.112	strong		0.383	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21792811	21792811	+	Silent	SNP	G	G	A	rs9322965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21792811G>A	ENST00000400017.2	+	14	1797	c.1797G>A	c.(1795-1797)ccG>ccA	p.P599P	RPGRIP1_ENST00000556336.1_Intron|RPGRIP1_ENST00000206660.6_Silent_p.P599P|RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000382933.4_Intron|RPGRIP1_ENST00000557771.1_Silent_p.P561P|RPGRIP1_ENST00000307974.4_Missense_Mutation_p.R8H	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	599					eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GCACCCGACCGTTGTCGTTAT	0.478													G|||	925	0.184704	0.2421	0.1427	5008	,	,		21117	0.0188		0.2336	False		,,,				2504	0.2577				p.P599P		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G1797A						PASS	.	G		835,3111		96,643,1234	125.0	117.0	120.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1797	3.2	0.1	14	dbSNP_119	120	1996,6294		228,1540,2377	no	coding-synonymous	RPGRIP1	NM_020366.3		324,2183,3611	AA,AG,GG		24.0772,21.1607,23.1366		599/1287	21792811	2831,9405	1973	4145	6118	SO:0001819	synonymous_variant	57096	exon14			CCGACCGTTGTCG	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.1797G>A	14.37:g.21792811G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Silent	SNP	ENST00000400017.2	37	CCDS45080.1	357	0.16346153846153846	115	0.23373983739837398	56	0.15469613259668508	6	0.01048951048951049	180	0.23746701846965698	G	8.657	0.899673	0.17686	0.211607	0.240772	ENSG00000092200	ENST00000307974	T	0.79454	-1.27	5.28	3.17	0.36434	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.04320	-1.0960	7	0.37606	T	0.19	-0.1041	2.6329	0.04950	0.2604:0.0:0.3544:0.3852	rs9322965;rs59052867;rs9322965	8	Q96KN7-3	.	H	8	ENSP00000309721:R8H	ENSP00000309721:R8H	R	+	2	0	RPGRIP1	20862651	0.000000	0.05858	0.052000	0.19188	0.972000	0.66771	-0.363000	0.07593	0.534000	0.28695	0.655000	0.94253	CGT	G|0.856;A|0.144	0.144	strong		0.478	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
ZMYM5	9205	hgsc.bcm.edu	37	13	20411701	20411701	+	Intron	SNP	C	C	T	rs7988277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:20411701C>T	ENST00000337963.4	-	6	1303				ZMYM5_ENST00000382907.4_3'UTR|ZMYM5_ENST00000382905.4_Missense_Mutation_p.R378H	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5							nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		ATCCAGAACACGTGCATTATG	0.313													T|||	587	0.117212	0.211	0.0836	5008	,	,		18615	0.0813		0.0984	False		,,,				2504	0.0706				p.R378H		Atlas-SNP	.											.	ZMYM5	73	.	0			c.G1133A						PASS	.	T	,HIS/ARG,	864,3534	709.0+/-407.7	86,692,1421	59.0	68.0	65.0		,1133,	-2.1	0.0	13	dbSNP_116	65	628,7952	773.5+/-407.7	20,588,3682	yes	utr-3,missense,intron	ZMYM5	NM_001039649.2,NM_001039650.2,NM_001142684.1	,29,	106,1280,5103	TT,TC,CC		7.3193,19.6453,11.4964	,,	,378/383,	20411701	1492,11486	2199	4290	6489	SO:0001627	intron_variant	9205	exon6			AGAACACGTGCAT	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"""Zinc fingers, MYM type"""	13029	protein-coding gene	gene with protein product			"""zinc finger protein 237"""	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.1038+94G>A	13.37:g.20411701C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		212	0.09706959706959707	82	0.16666666666666666	30	0.08287292817679558	35	0.06118881118881119	65	0.08575197889182058	T	9.174	1.021882	0.19433	0.196453	0.073193	ENSG00000132950	ENST00000382905	T	0.25749	1.78	3.91	-2.1	0.07210	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25710	-1.0124	7	0.87932	D	0	.	5.7512	0.18148	0.0:0.4715:0.1707:0.3579	rs7988277;rs52824363;rs60203785;rs7988277	378	Q9UJ78-1	.	H	378	ENSP00000372361:R378H	ENSP00000372361:R378H	R	-	2	0	ZMYM5	19309701	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.438000	0.06905	-0.881000	0.03992	-0.521000	0.04368	CGT	C|0.887;T|0.113	0.113	strong		0.313	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242	
LTBP1	4052	hgsc.bcm.edu	37	2	33488419	33488419	+	Silent	SNP	G	G	A	rs12468099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:33488419G>A	ENST00000404816.2	+	15	2930	c.2577G>A	c.(2575-2577)acG>acA	p.T859T	LTBP1_ENST00000404525.1_Silent_p.T480T|LTBP1_ENST00000407925.1_Silent_p.T533T|LTBP1_ENST00000390003.4_Silent_p.T534T|LTBP1_ENST00000402934.1_Silent_p.T480T|LTBP1_ENST00000418533.2_Silent_p.T533T|LTBP1_ENST00000354476.3_Silent_p.T860T			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	859					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)				AAGCTTCTACGTCTAGTGCCA	0.428													G|||	839	0.167532	0.0166	0.1844	5008	,	,		17578	0.2371		0.2863	False		,,,				2504	0.1656				p.T859T		Atlas-SNP	.											.	LTBP1	317	.	0			c.G2577A						PASS	.	G	,,,,	277,4129	153.7+/-187.2	8,261,1934	143.0	138.0	139.0		1599,1599,1440,1440,2577	-4.5	0.9	2	dbSNP_120	139	2489,6111	409.6+/-349.9	373,1743,2184	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	381,2004,4118	AA,AG,GG		28.9419,6.2869,21.2671	,,,,	533/1396,533/1354,480/1343,480/1301,859/1722	33488419	2766,10240	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon15			TTCTACGTCTAGT		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.2577G>A	2.37:g.33488419G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			G|0.797;A|0.203	0.203	strong		0.428	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
CENPM	79019	hgsc.bcm.edu	37	22	42336172	42336172	+	Intron	SNP	G	G	A	rs5758511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:42336172G>A	ENST00000215980.5	-	6	490				CENPM_ENST00000402420.1_Intron|CENPM_ENST00000404067.1_Intron|CENPM_ENST00000407253.3_Intron|CENPM_ENST00000472374.2_Nonsense_Mutation_p.R3*|CENPM_ENST00000402338.1_Intron	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M						mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						tcccacactcggcccatgcac	0.562													G|||	1198	0.239217	0.0265	0.2147	5008	,	,		17200	0.5575		0.2664	False		,,,				2504	0.1881				p.R3X		Atlas-SNP	.											.	CENPM	8	.	0			c.C7T						PASS	.	G	,stop/ARG,	182,2954		5,172,1391	58.0	52.0	54.0		,7,	0.8	0.0	22	dbSNP_114	54	2020,5138		291,1438,1850	yes	intron,stop-gained,intron	CENPM	NM_001002876.1,NM_001110215.1,NM_024053.3	,,	296,1610,3241	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	28.2202,5.8036,21.3911	,,	,3/59,	42336172	2202,8092	1568	3579	5147	SO:0001627	intron_variant	79019	exon1			ACACTCGGCCCAT	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"""chromosome 22 open reading frame 18"""	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.403-972C>T	22.37:g.42336172G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_001110215	A7LM22|B1AHQ9|Q6I9W3	Nonsense_Mutation	SNP	ENST00000215980.5	37	CCDS14025.1	582	0.2664835164835165	16	0.032520325203252036	73	0.20165745856353592	289	0.5052447552447552	204	0.2691292875989446	G	11.61	1.690609	0.29962	0.058036	0.282202	ENSG00000100162	ENST00000472374	.	.	.	1.82	0.783	0.18572	.	.	.	.	.	.	.	.	.	.	.	0.52099	P	5.500000000002725E-5	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.15	0.10234	0.2157:0.0:0.7843:0.0	rs5758511;rs61341024;rs5758511	.	.	.	X	3	.	ENSP00000430624:R3X	R	-	1	2	CENPM	40666118	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	-0.136000	0.10405	0.337000	0.23665	0.407000	0.27541	CGA	G|0.752;A|0.248	0.248	strong		0.562	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053	
MDN1	23195	hgsc.bcm.edu	37	6	90455084	90455084	+	Silent	SNP	A	A	G	rs9359861	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90455084A>G	ENST00000369393.3	-	29	4201	c.4086T>C	c.(4084-4086)caT>caC	p.H1362H	MDN1_ENST00000428876.1_Silent_p.H1362H			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1362					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TCCACACGATATGGCCAAAGT	0.423													G|||	4669	0.932308	0.9834	0.928	5008	,	,		17611	0.997		0.837	False		,,,				2504	0.8978				p.H1362H		Atlas-SNP	.											.	MDN1	478	.	0			c.T4086C						PASS	.	G		4244,162	108.6+/-147.0	2045,154,4	122.0	108.0	113.0		4086	1.8	0.0	6	dbSNP_119	113	7149,1451	277.5+/-292.9	2980,1189,131	no	coding-synonymous	MDN1	NM_014611.1		5025,1343,135	GG,GA,AA		16.8721,3.6768,12.402		1362/5597	90455084	11393,1613	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon29			CACGATATGGCCA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.4086T>C	6.37:g.90455084A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			A|0.100;G|0.900	0.900	strong		0.423	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
FMO2	2327	hgsc.bcm.edu	37	1	171154959	171154959	+	Missense_Mutation	SNP	A	A	G	rs2020870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:171154959A>G	ENST00000209929.7	+	2	265	c.107A>G	c.(106-108)gAt>gGt	p.D36G	FMO2_ENST00000529935.1_Intron|FMO2_ENST00000441535.1_Missense_Mutation_p.D36G			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	36					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AGAACTGAAGATATTGGAGGA	0.453													A|||	461	0.0920527	0.0628	0.0447	5008	,	,		18771	0.1508		0.0586	False		,,,				2504	0.1391				p.D36G		Atlas-SNP	.											.	FMO2	66	.	0			c.A107G	GRCh37	CM033897	FMO2	M	rs2020870	PASS	.	A	GLY/ASP	290,4116	160.0+/-192.4	12,266,1925	254.0	244.0	248.0		107	5.7	1.0	1	dbSNP_98	248	583,8017	156.4+/-210.3	32,519,3749	yes	missense	FMO2	NM_001460.2	94	44,785,5674	GG,GA,AA		6.7791,6.5819,6.7123	benign	36/472	171154959	873,12133	2203	4300	6503	SO:0001583	missense	2327	exon2			CTGAAGATATTGG	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.107A>G	1.37:g.171154959A>G	ENSP00000209929:p.Asp36Gly	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	178	0.0815018315018315	39	0.07926829268292683	16	0.04419889502762431	76	0.13286713286713286	47	0.06200527704485488	A	28.8	4.948795	0.92660	0.065819	0.067791	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.64085	-0.08;-0.08	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.64527	0.2606	M	0.78223	2.4	0.09310	P	0.99999530272	B	0.33212	0.402	P	0.44772	0.46	T	0.71896	-0.4454	9	0.72032	D	0.01	-28.1586	14.8692	0.70444	1.0:0.0:0.0:0.0	rs2020870;rs2266712;rs52821140;rs58458262;rs2020870	36	Q99518	FMO2_HUMAN	G	36	ENSP00000209929:D36G;ENSP00000405905:D36G	ENSP00000209929:D36G	D	+	2	0	FMO2	169421583	1.000000	0.71417	0.971000	0.41717	0.938000	0.57974	8.869000	0.92326	2.145000	0.66743	0.533000	0.62120	GAT	A|0.919;G|0.081	0.081	strong		0.453	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
PRG4	10216	hgsc.bcm.edu	37	1	186281400	186281400	+	Missense_Mutation	SNP	C	C	T	rs12134934	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186281400C>T	ENST00000445192.2	+	11	3932	c.3887C>T	c.(3886-3888)aCg>aTg	p.T1296M	PRG4_ENST00000367484.3_Missense_Mutation_p.T825M|PRG4_ENST00000367483.4_Missense_Mutation_p.T1255M|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367485.4_Missense_Mutation_p.T1203M|PRG4_ENST00000367486.3_Missense_Mutation_p.T1253M|TPR_ENST00000367478.4_3'UTR	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1296			T -> M (in dbSNP:rs12134934). {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						TATGGAGAAACGACACAGGTT	0.443													C|||	153	0.0305511	0.0454	0.013	5008	,	,		15416	0.002		0.0388	False		,,,				2504	0.044				p.T1296M		Atlas-SNP	.											.	PRG4	259	.	0			c.C3887T						PASS	.	C	MET/THR,MET/THR,MET/THR,,MET/THR	203,4203	124.5+/-161.8	2,199,2002	131.0	128.0	129.0		3764,3608,3485,,3887	-1.6	0.0	1	dbSNP_120	129	388,8212	125.3+/-183.9	12,364,3924	yes	missense,missense,missense,utr-3,missense	TPR,PRG4	NM_001127708.1,NM_001127709.1,NM_001127710.1,NM_003292.2,NM_005807.3	81,81,81,,81	14,563,5926	TT,TC,CC		4.5116,4.6074,4.5441	probably-damaging,probably-damaging,probably-damaging,,probably-damaging	1255/1364,1203/1312,1162/1271,,1296/1405	186281400	591,12415	2203	4300	6503	SO:0001583	missense	10216	exon11			GAGAAACGACACA	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.3887C>T	1.37:g.186281400C>T	ENSP00000399679:p.Thr1296Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	68	0.031135531135531136	30	0.06097560975609756	4	0.011049723756906077	1	0.0017482517482517483	33	0.04353562005277045	C	10.40	1.339292	0.24339	0.046074	0.045116	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.05447	3.45;3.56;3.56;3.44;3.56	5.38	-1.59	0.08453	Hemopexin/matrixin (1);	0.526053	0.15728	N	0.247589	T	0.00815	0.0027	L	0.47716	1.5	0.09310	N	1	D;D;P;D	0.53312	0.959;0.959;0.931;0.959	P;P;B;P	0.48189	0.57;0.483;0.366;0.57	T	0.17198	-1.0377	10	0.72032	D	0.01	0.1886	9.3509	0.38138	0.0:0.4603:0.0:0.5397	rs12134934;rs52836796;rs58324543;rs12134934	1162;1203;1296;1255	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	M	1253;825;1255;1203;1296	ENSP00000356456:T1253M;ENSP00000356454:T825M;ENSP00000356453:T1255M;ENSP00000356455:T1203M;ENSP00000399679:T1296M	ENSP00000356453:T1255M	T	+	2	0	PRG4	184548023	0.000000	0.05858	0.000000	0.03702	0.960000	0.62799	-0.888000	0.04148	-0.516000	0.06470	0.585000	0.79938	ACG	C|0.958;T|0.042	0.042	strong		0.443	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
CPS1	1373	hgsc.bcm.edu	37	2	211456639	211456639	+	Silent	SNP	C	C	T	rs386654705|rs2229589	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211456639C>T	ENST00000233072.5	+	10	1228	c.1032C>T	c.(1030-1032)acC>acT	p.T344T	CPS1_ENST00000430249.2_Silent_p.T350T|CPS1_ENST00000451903.2_5'Flank	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	344	Glutamine amidotransferase type-1.		T -> A (in dbSNP:rs1047883). {ECO:0000269|PubMed:12853138, ECO:0000269|PubMed:9711878, ECO:0000269|Ref.11}.|T -> S (in dbSNP:rs1047883).		anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	TGGACAACACCCTCCCTGCTG	0.433													C|||	2961	0.591254	0.6679	0.4914	5008	,	,		16517	0.5585		0.5646	False		,,,				2504	0.6196				p.T350T		Atlas-SNP	.											.	CPS1	485	.	0			c.C1050T						PASS	.	C	,	2891,1515	671.6+/-402.5	962,967,274	83.0	77.0	79.0		1050,1032	3.0	1.0	2	dbSNP_98	79	4881,3719	617.7+/-396.7	1361,2159,780	no	coding-synonymous,coding-synonymous	CPS1	NM_001122633.2,NM_001875.4	,	2323,3126,1054	TT,TC,CC		43.2442,34.3849,40.243	,	350/1507,344/1501	211456639	7772,5234	2203	4300	6503	SO:0001819	synonymous_variant	1373	exon11			CAACACCCTCCCT	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.1032C>T	2.37:g.211456639C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	69	28	0.405797	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	37	CCDS2393.1																																																																																			C|0.408;T|0.592	0.592	strong		0.433	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
OR12D2	26529	hgsc.bcm.edu	37	6	29364685	29364685	+	Missense_Mutation	SNP	G	G	T	rs36210740	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29364685G>T	ENST00000383555.2	+	1	270	c.209G>T	c.(208-210)tGt>tTt	p.C70F	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	31						CTGGATATCTGTTACTCTACG	0.448													G|||	24	0.00479233	0.0015	0.0072	5008	,	,		22627	0.001		0.006	False		,,,				2504	0.0102				p.C70F		Atlas-SNP	.											.	OR12D2	42	.	0			c.G209T						PASS	.	G	PHE/CYS	5,3011		0,5,1503	106.0	106.0	106.0		209	2.2	0.0	6	dbSNP_126	106	40,5378		0,40,2669	yes	missense	OR12D2	NM_013936.3	205	0,45,4172	TT,TG,GG		0.7383,0.1658,0.5336	benign	70/308	29364685	45,8389	1508	2709	4217	SO:0001583	missense	26529	exon1			ATATCTGTTACTC		CCDS4659.1	6p22.2-p21.31	2013-10-10	2013-10-10		ENSG00000168787	ENSG00000168787		"""GPCR / Class A : Olfactory receptors"""	8178	protein-coding gene	gene with protein product			"""olfactory receptor, family 12, subfamily D, member 2"""				Standard	NM_013936		Approved	hs6M1-20	uc003nmf.4	P58182	OTTHUMG00000031049	ENST00000383555.2:c.209G>T	6.37:g.29364685G>T	ENSP00000373047:p.Cys70Phe	Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	302	137	0.453642	NM_013936	B0S862|Q5SUN9|Q6IET9	Missense_Mutation	SNP	ENST00000383555.2	37	CCDS4659.1	.	.	.	.	.	.	.	.	.	.	G	0.833	-0.744453	0.03065	0.001658	0.007383	ENSG00000168787	ENST00000383555	T	0.79033	-1.23	4.07	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.093597	0.47852	D	0.000217	T	0.60702	0.2289	M	0.76328	2.33	0.09310	N	1	B	0.12013	0.005	B	0.12837	0.008	T	0.61247	-0.7101	10	0.66056	D	0.02	.	10.202	0.43089	0.0:0.1475:0.6996:0.1529	.	70	P58182	O12D2_HUMAN	F	70	ENSP00000373047:C70F	ENSP00000373047:C70F	C	+	2	0	OR12D2	29472664	0.000000	0.05858	0.014000	0.15608	0.001000	0.01503	0.409000	0.21082	0.335000	0.23614	0.411000	0.27672	TGT	A|0.001;G|0.994;T|0.005	0.005	strong		0.448	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2		
CUBN	8029	hgsc.bcm.edu	37	10	16877110	16877110	+	Missense_Mutation	SNP	G	G	A	rs1801230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:16877110G>A	ENST00000377833.4	-	64	10330	c.10265C>T	c.(10264-10266)aCc>aTc	p.T3422I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3422	CUB 26. {ECO:0000255|PROSITE- ProRule:PRU00059}.		T -> I (in dbSNP:rs1801230). {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)	GAGAGTAACGGTGCAATCCTT	0.458													G|||	41	0.0081869	0.0038	0.0144	5008	,	,		17717	0.0		0.0229	False		,,,				2504	0.0031				p.T3422I		Atlas-SNP	.											.	CUBN	515	.	0			c.C10265T						PASS	.	G	ILE/THR	29,4377	35.2+/-66.4	0,29,2174	178.0	151.0	160.0		10265	3.9	0.7	10	dbSNP_89	160	248,8352	98.6+/-160.1	4,240,4056	yes	missense	CUBN	NM_001081.3	89	4,269,6230	AA,AG,GG		2.8837,0.6582,2.1298	benign	3422/3624	16877110	277,12729	2203	4300	6503	SO:0001583	missense	8029	exon64			GTAACGGTGCAAT	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.10265C>T	10.37:g.16877110G>A	ENSP00000367064:p.Thr3422Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	138	55	0.398551	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	30	0.013736263736263736	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	14.17	2.455908	0.43634	0.006582	0.028837	ENSG00000107611	ENST00000377833;ENST00000545090	T	0.35421	1.31	4.84	3.94	0.45596	CUB (5);	0.538075	0.15554	N	0.256250	T	0.13243	0.0321	L	0.33753	1.03	0.80722	D	1	P	0.40000	0.698	B	0.42798	0.398	T	0.01596	-1.1316	10	0.38643	T	0.18	.	13.2177	0.59869	0.0768:0.0:0.9232:0.0	rs1801230;rs52825510	3422	O60494	CUBN_HUMAN	I	3422;263	ENSP00000367064:T3422I	ENSP00000367064:T3422I	T	-	2	0	CUBN	16917116	0.983000	0.35010	0.712000	0.30502	0.003000	0.03518	1.834000	0.39171	1.262000	0.44165	-0.258000	0.10820	ACC	G|0.982;A|0.018	0.018	strong		0.458	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MUC4	4585	hgsc.bcm.edu	37	3	195512242	195512242	+	Missense_Mutation	SNP	G	G	A	rs566214772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195512242G>A	ENST00000463781.3	-	2	6668	c.6209C>T	c.(6208-6210)cCt>cTt	p.P2070L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2070L	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)		TGCTGAGGAAGGGTTAGTGAC	0.562													.|||	31	0.0061901	0.0061	0.0058	5008	,	,		13554	0.003		0.0099	False		,,,				2504	0.0061				p.P2070L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6209T						PASS	.																																			SO:0001583	missense	4585	exon2			GAGGAAGGGTTAG	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.6209C>T	3.37:g.195512242G>A	ENSP00000417498:p.Pro2070Leu	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	176	29	0.164773	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	2.744	-0.261597	0.05791	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28069	1.63;1.67	.	.	.	.	.	.	.	.	T	0.11495	0.0280	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.28964	-1.0027	6	.	.	.	.	.	.	.	.	2070	E7ESK3	.	L	2070	ENSP00000417498:P2070L;ENSP00000420243:P2070L	.	P	-	2	0	MUC4	196996637	0.004000	0.15560	0.004000	0.12327	0.011000	0.07611	-0.008000	0.12788	-0.833000	0.04245	0.064000	0.15345	CCT	G|0.500;A|0.500	0.500	weak		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ABCG8	64241	hgsc.bcm.edu	37	2	44078913	44078913	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:44078913C>A	ENST00000272286.2	+	4	603	c.513C>A	c.(511-513)gcC>gcA	p.A171A		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	171	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CCTTCATTGCCCAGATGCGGC	0.612																																					p.A171A		Atlas-SNP	.											.	ABCG8	98	.	0			c.C513A						PASS	.						113.0	116.0	115.0					2																	44078913		2203	4300	6503	SO:0001819	synonymous_variant	64241	exon4			CATTGCCCAGATG	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.513C>A	2.37:g.44078913C>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	105	38	0.361905	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	37	CCDS1815.1																																																																																			.	.	none		0.612	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
PDZRN3	23024	hgsc.bcm.edu	37	3	73453325	73453325	+	Silent	SNP	C	C	T	rs2291463	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:73453325C>T	ENST00000263666.4	-	4	1254	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V	PDZRN3_ENST00000466780.1_Silent_p.V37V|PDZRN3_ENST00000479530.1_Silent_p.V97V|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Silent_p.V37V|PDZRN3_ENST00000535920.1_Silent_p.V102V	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	380					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		AGGGATCCAGCACGGGTGGGC	0.478													C|||	3013	0.601637	0.4811	0.6297	5008	,	,		18193	0.8353		0.5567	False		,,,				2504	0.5501				p.V380V		Atlas-SNP	.											.	PDZRN3	196	.	0			c.G1140A						PASS	.	C		2203,2203	589.8+/-387.2	538,1127,538	126.0	110.0	116.0		1140	-0.8	0.0	3	dbSNP_100	116	4751,3849	610.4+/-395.7	1332,2087,881	no	coding-synonymous	PDZRN3	NM_015009.1		1870,3214,1419	TT,TC,CC		44.7558,50.0,46.5324		380/1067	73453325	6954,6052	2203	4300	6503	SO:0001819	synonymous_variant	23024	exon4			ATCCAGCACGGGT	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.1140G>A	3.37:g.73453325C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	129	126	0.976744	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																			C|0.427;T|0.573	0.573	strong		0.478	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
KRT40	125115	hgsc.bcm.edu	37	17	39135205	39135205	+	Silent	SNP	A	A	G	rs386797018|rs8064910	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39135205A>G	ENST00000398486.2	-	8	1207	c.1047T>C	c.(1045-1047)tgT>tgC	p.C349C	KRT40_ENST00000377755.4_Silent_p.C349C	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	349	Coil 2.|Rod.			C -> R (in Ref. 1; CAH10353). {ECO:0000305}.		intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.C349C(1)		endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				TATCGATCAGACACTGAATTT	0.592													G|||	3501	0.699081	0.9365	0.6787	5008	,	,		16186	0.5863		0.5378	False		,,,				2504	0.6748				p.C349C		Atlas-SNP	.											KRT40,NS,carcinoma,0,1	KRT40	27	1	1	Substitution - coding silent(1)	prostate(1)	c.T1047C						PASS	.	G		3751,651	263.1+/-265.3	1591,569,41	89.0	99.0	96.0		1047	1.4	1.0	17	dbSNP_116	96	4509,4081	545.5+/-384.8	1163,2183,949	no	coding-synonymous	KRT40	NM_182497.3		2754,2752,990	GG,GA,AA		47.5087,14.7887,36.4224		349/432	39135205	8260,4732	2201	4295	6496	SO:0001819	synonymous_variant	125115	exon8			GATCAGACACTGA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1047T>C	17.37:g.39135205A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	37	CCDS42320.1																																																																																			A|0.340;G|0.660	0.660	strong		0.592	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
LRRCC1	85444	hgsc.bcm.edu	37	8	86057707	86057707	+	Silent	SNP	A	A	G	rs62525428	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:86057707A>G	ENST00000360375.3	+	19	3209	c.3060A>G	c.(3058-3060)caA>caG	p.Q1020Q	LRRCC1_ENST00000414626.2_Silent_p.Q1000Q	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	1020					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AAATTAAGCAACTTGCTTTTG	0.299													A|||	286	0.0571086	0.0083	0.0389	5008	,	,		12994	0.0159		0.0905	False		,,,				2504	0.1442				p.Q1020Q		Atlas-SNP	.											.	LRRCC1	212	.	0			c.A3060G						PASS	.	A		71,3547		0,71,1738	55.0	52.0	53.0		3060	4.0	1.0	8	dbSNP_129	53	898,7228		42,814,3207	no	coding-synonymous	LRRCC1	NM_033402.4		42,885,4945	GG,GA,AA		11.0509,1.9624,8.251		1020/1033	86057707	969,10775	1809	4063	5872	SO:0001819	synonymous_variant	85444	exon19			TAAGCAACTTGCT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.3060A>G	8.37:g.86057707A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	236	112	0.474576	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Silent	SNP	ENST00000360375.3	37	CCDS43750.1																																																																																			A|0.926;G|0.074	0.074	strong		0.299	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
TOPBP1	11073	hgsc.bcm.edu	37	3	133368362	133368362	+	Missense_Mutation	SNP	T	T	G	rs3192149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:133368362T>G	ENST00000260810.5	-	10	1500	c.1369A>C	c.(1369-1371)Aag>Cag	p.K457Q	TOPBP1_ENST00000511439.1_5'UTR	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	457				K -> Q (in Ref. 1; BAA34202 and 2; BAA13389). {ECO:0000305}.	cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						CTTTCAGGCTTATGTGAAACT	0.383								Other conserved DNA damage response genes					G|||	3485	0.695887	0.7905	0.6398	5008	,	,		18413	0.625		0.7724	False		,,,				2504	0.6022				p.K457Q	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A1369C						PASS	.	G	GLN/LYS	2902,788		1141,620,84	165.0	155.0	158.0		1369	4.8	0.9	3	dbSNP_105	158	6273,1909		2416,1441,234	yes	missense	TOPBP1	NM_007027.3	53	3557,2061,318	GG,GT,TT		23.3317,21.355,22.7173	benign	457/1523	133368362	9175,2697	1845	4091	5936	SO:0001583	missense	11073	exon10			CAGGCTTATGTGA	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.1369A>C	3.37:g.133368362T>G	ENSP00000260810:p.Lys457Gln	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	1558	0.7133699633699634	384	0.7804878048780488	226	0.6243093922651933	364	0.6363636363636364	584	0.7704485488126649	G	2.916	-0.224167	0.06061	0.78645	0.766683	ENSG00000163781	ENST00000260810	T	0.11712	2.75	5.72	4.84	0.62591	.	0.483083	0.23775	N	0.044697	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.19943	-1.0290	9	0.09843	T	0.71	.	15.3445	0.74324	0.0:0.0:0.7446:0.2554	rs3192149;rs16840574;rs52800635;rs58841240;rs3192149	457	Q92547	TOPB1_HUMAN	Q	457	ENSP00000260810:K457Q	ENSP00000260810:K457Q	K	-	1	0	TOPBP1	134851052	0.993000	0.37304	0.921000	0.36526	0.784000	0.44337	3.153000	0.50685	0.777000	0.33496	-0.127000	0.14921	AAG	T|0.283;G|0.717	0.717	strong		0.383	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
FAT2	2196	hgsc.bcm.edu	37	5	150948016	150948016	+	Silent	SNP	C	C	T	rs3734062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:150948016C>T	ENST00000261800.5	-	1	489	c.477G>A	c.(475-477)gaG>gaA	p.E159E		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	159	Cadherin 2. {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)			GGGGCATGTCCTCAGAGATGG	0.517													C|||	256	0.0511182	0.003	0.062	5008	,	,		23257	0.0774		0.0865	False		,,,				2504	0.045				p.E159E		Atlas-SNP	.											.	FAT2	465	.	0			c.G477A						PASS	.	C		66,4340	62.3+/-99.4	0,66,2137	138.0	126.0	130.0		477	2.5	1.0	5	dbSNP_107	130	571,8029	154.2+/-208.4	15,541,3744	no	coding-synonymous	FAT2	NM_001447.2		15,607,5881	TT,TC,CC		6.6395,1.498,4.8977		159/4350	150948016	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			CATGTCCTCAGAG	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.477G>A	5.37:g.150948016C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	242	107	0.442149	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.944;T|0.056	0.056	strong		0.517	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
XIRP2	129446	hgsc.bcm.edu	37	2	168104627	168104627	+	Missense_Mutation	SNP	G	G	A	rs61750760	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168104627G>A	ENST00000409195.1	+	9	6814	c.6725G>A	c.(6724-6726)cGg>cAg	p.R2242Q	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R2020Q|XIRP2_ENST00000295237.9_Missense_Mutation_p.R2242Q|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2067					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACAAAAAGCGGGAGACTGAT	0.388													A|||	993	0.198283	0.3268	0.1326	5008	,	,		16388	0.12		0.1233	False		,,,				2504	0.229				p.R2242Q		Atlas-SNP	.											XIRP2,NS,carcinoma,+1,1	XIRP2	914	1	0			c.G6725A						PASS	.	A	,,,GLN/ARG,GLN/ARG	1051,2617		157,737,940	69.0	63.0	65.0		,,,6725,6059	5.3	1.0	2	dbSNP_129	65	919,7261		56,807,3227	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,43,43	213,1544,4167	AA,AG,GG		11.2347,28.6532,16.6273	,,,benign,benign	,,,2242/3550,2020/3328	168104627	1970,9878	1834	4090	5924	SO:0001583	missense	129446	exon9			AAAAGCGGGAGAC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6725G>A	2.37:g.168104627G>A	ENSP00000386840:p.Arg2242Gln	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	195	91	0.466667	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	386	0.17673992673992675	172	0.34959349593495936	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	A	0.882	-0.728533	0.03135	0.286532	0.112347	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02197	4.4;4.4;4.41	5.34	5.34	0.76211	.	0.706038	0.13958	N	0.351060	T	0.00012	0.0000	N	0.00138	-2.015	0.58432	P	2.9999999999752447E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.37663	-0.9696	9	0.02654	T	1	-0.1717	10.4051	0.44252	0.9212:0.0:0.0788:0.0	rs61750760	2067;2067;2020	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	2242;2242;2020	ENSP00000386840:R2242Q;ENSP00000295237:R2242Q;ENSP00000387255:R2020Q	ENSP00000295237:R2242Q	R	+	2	0	XIRP2	167812873	1.000000	0.71417	0.969000	0.41365	0.100000	0.18952	4.128000	0.57951	0.868000	0.35678	-0.254000	0.11334	CGG	G|0.842;A|0.158	0.158	strong		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
GABBR1	2550	hgsc.bcm.edu	37	6	29576393	29576393	+	Silent	SNP	A	A	G	rs29230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29576393A>G	ENST00000377034.4	-	16	2312	c.1977T>C	c.(1975-1977)ttT>ttC	p.F659F	GABBR1_ENST00000355973.3_Silent_p.F542F|GABBR1_ENST00000377012.4_Silent_p.F542F|GABBR1_ENST00000377016.4_Silent_p.F597F|GABBR1_ENST00000376977.3_3'UTR	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	659					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	AGACGAAAGGAAACTGGTTCC	0.547													G|||	1068	0.213259	0.1467	0.2017	5008	,	,		19957	0.252		0.1531	False		,,,				2504	0.3333				p.F659F		Atlas-SNP	.											GABBR1,NS,carcinoma,0,1	GABBR1	95	1	0			c.T1977C						PASS	.	G	,,	486,2536		38,410,1063	100.0	85.0	90.0		1977,1626,1791	2.7	1.0	6	dbSNP_76	90	935,4481		88,759,1861	no	coding-synonymous,coding-synonymous,coding-synonymous	GABBR1	NM_001470.2,NM_021903.2,NM_021904.2	,,	126,1169,2924	GG,GA,AA		17.2637,16.0821,16.8405	,,	659/962,542/845,597/900	29576393	1421,7017	1511	2708	4219	SO:0001819	synonymous_variant	2550	exon16			GAAAGGAAACTGG	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4070	protein-coding gene	gene with protein product	"""GABA-B receptor"""	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1977T>C	6.37:g.29576393A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	100	40	0.4	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1	373	0.1707875457875458	71	0.1443089430894309	56	0.15469613259668508	137	0.2395104895104895	109	0.1437994722955145	G	9.044	0.990308	0.18966	0.160821	0.172637	ENSG00000204681	ENST00000485026	.	.	.	4.49	2.66	0.31614	.	.	.	.	.	T	0.24851	0.0603	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.08411	-1.0723	3	.	.	.	-24.184	6.8441	0.23979	0.3854:0.0:0.6146:0.0	rs29230;rs17854215;rs17854637;rs57003227;rs29230	.	.	.	P	40	.	.	S	-	1	0	GABBR1	29684372	1.000000	0.71417	0.997000	0.53966	0.849000	0.48306	2.255000	0.43222	0.541000	0.28827	-0.226000	0.12346	TCC	A|0.820;G|0.180	0.180	strong		0.547	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3		
CLIP4	79745	hgsc.bcm.edu	37	2	29366646	29366646	+	Silent	SNP	C	C	T	rs35024908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29366646C>T	ENST00000320081.5	+	7	975	c.720C>T	c.(718-720)gcC>gcT	p.A240A	CLIP4_ENST00000401617.2_Silent_p.A133A|CLIP4_ENST00000404424.1_Silent_p.A240A|CLIP4_ENST00000401605.1_Silent_p.A240A	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	240										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TGGCTGACGCCGCAGCCACTG	0.448													C|||	151	0.0301518	0.0318	0.0303	5008	,	,		20421	0.0		0.0765	False		,,,				2504	0.0112				p.A240A		Atlas-SNP	.											CLIP4,NS,carcinoma,+2,1	CLIP4	69	1	0			c.C720T						PASS	.	C		157,4249	106.5+/-144.9	2,153,2048	111.0	106.0	108.0		720	-11.0	0.0	2	dbSNP_126	108	592,8008	157.0+/-210.8	24,544,3732	no	coding-synonymous	CLIP4	NM_024692.4		26,697,5780	TT,TC,CC		6.8837,3.5633,5.7589		240/706	29366646	749,12257	2203	4300	6503	SO:0001819	synonymous_variant	79745	exon7			TGACGCCGCAGCC	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.720C>T	2.37:g.29366646C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	196	88	0.44898	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	37	CCDS1770.1																																																																																			C|0.949;T|0.051	0.051	strong		0.448	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
CCBL2	56267	hgsc.bcm.edu	37	1	89426902	89426902	+	Silent	SNP	G	G	A	rs3738055	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89426902G>A	ENST00000260508.4	-	8	1072	c.735C>T	c.(733-735)agC>agT	p.S245S	CCBL2_ENST00000370485.2_3'UTR|CCBL2_ENST00000370491.3_Silent_p.S211S|CCBL2_ENST00000446900.2_5'UTR	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	245					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)	p.S211S(1)		endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		AAACCTCATCGCTGATGCAGA	0.373													G|||	1850	0.369409	0.2307	0.5043	5008	,	,		20966	0.4633		0.4771	False		,,,				2504	0.2536				p.S245S		Atlas-SNP	.											CCBL2_ENST00000370491,NS,carcinoma,0,1	CCBL2	138	1	1	Substitution - coding silent(1)	stomach(1)	c.C735T						PASS	.	G	,	1257,3149	432.4+/-343.3	188,881,1134	158.0	153.0	154.0		735,633	1.2	1.0	1	dbSNP_107	154	4220,4380	571.1+/-389.5	1042,2136,1122	no	coding-synonymous,coding-synonymous	CCBL2	NM_001008661.2,NM_001008662.2	,	1230,3017,2256	AA,AG,GG		49.0698,28.5293,42.1113	,	245/455,211/421	89426902	5477,7529	2203	4300	6503	SO:0001819	synonymous_variant	56267	exon8			CTCATCGCTGATG	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.735C>T	1.37:g.89426902G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Silent	SNP	ENST00000260508.4	37	CCDS30766.1																																																																																			G|0.584;A|0.416	0.416	strong		0.373	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661	
TBX4	9496	hgsc.bcm.edu	37	17	59557600	59557600	+	Missense_Mutation	SNP	C	C	T	rs3744438	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:59557600C>T	ENST00000240335.1	+	7	986	c.941C>T	c.(940-942)gCg>gTg	p.A314V	TBX4_ENST00000589449.1_3'UTR|TBX4_ENST00000393853.4_Missense_Mutation_p.A314V	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	314			A -> V (in dbSNP:rs3744438).		angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						TCACAGCTCGCGGAGCCGCAG	0.647													C|||	1068	0.213259	0.4402	0.134	5008	,	,		13484	0.1111		0.1213	False		,,,				2504	0.1626				p.A314V		Atlas-SNP	.											TBX4,mouth,carcinoma,-1,1	TBX4	69	1	0			c.C941T						PASS	.	C	VAL/ALA	1822,2584	528.6+/-372.4	381,1060,762	61.0	55.0	57.0		941	5.8	0.0	17	dbSNP_107	57	1070,7530	222.2+/-259.3	66,938,3296	yes	missense	TBX4	NM_018488.2	64	447,1998,4058	TT,TC,CC		12.4419,41.3527,22.2359	possibly-damaging	314/546	59557600	2892,10114	2203	4300	6503	SO:0001583	missense	9496	exon7			AGCTCGCGGAGCC	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.941C>T	17.37:g.59557600C>T	ENSP00000240335:p.Ala314Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	102	43	0.421569	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Missense_Mutation	SNP	ENST00000240335.1	37	CCDS11629.1	374	0.17124542124542125	190	0.3861788617886179	43	0.11878453038674033	63	0.11013986013986014	78	0.10290237467018469	C	14.31	2.496648	0.44352	0.413527	0.124419	ENSG00000121075	ENST00000393853;ENST00000240335	D;D	0.81499	-1.5;-1.5	5.84	5.84	0.93424	.	0.374762	0.29876	N	0.010974	T	0.00012	0.0000	L	0.36672	1.1	0.45979	P	0.0012090000000000156	P;P	0.46020	0.871;0.85	B;B	0.35240	0.198;0.041	T	0.25152	-1.0140	8	.	.	.	.	19.1261	0.93384	0.0:1.0:0.0:0.0	rs3744438;rs57055977;rs3744438	314;314	A5PKU7;P57082	.;TBX4_HUMAN	V	314	ENSP00000377435:A314V;ENSP00000240335:A314V	.	A	+	2	0	TBX4	56912382	0.289000	0.24334	0.011000	0.14972	0.022000	0.10575	4.496000	0.60360	2.779000	0.95612	0.655000	0.94253	GCG	C|0.789;T|0.211	0.211	strong		0.647	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
NOP58	51602	hgsc.bcm.edu	37	2	203157538	203157538	+	Silent	SNP	A	A	G	rs16839032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:203157538A>G	ENST00000264279.5	+	9	1045	c.819A>G	c.(817-819)gaA>gaG	p.E273E	SNORD11_ENST00000459124.1_RNA|SNORD11B_ENST00000607707.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	273					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.E273E(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						AGCTCTATGAATATCTACAAA	0.368													A|||	31	0.0061901	0.0	0.0187	5008	,	,		18977	0.0		0.0159	False		,,,				2504	0.002				p.E273E		Atlas-SNP	.											NOP58,NS,carcinoma,0,1	NOP58	41	1	1	Substitution - coding silent(1)	prostate(1)	c.A819G						PASS	.	A		12,4394	19.1+/-41.9	0,12,2191	159.0	160.0	160.0		819	0.3	1.0	2	dbSNP_123	160	133,8467	67.0+/-129.4	3,127,4170	no	coding-synonymous	NOP58	NM_015934.3		3,139,6361	GG,GA,AA		1.5465,0.2724,1.1149		273/530	203157538	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	51602	exon9			CTATGAATATCTA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"""NOP58 ribonucleoprotein homolog (yeast)"""			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.819A>G	2.37:g.203157538A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			A|0.989;G|0.011	0.011	strong		0.368	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934	
MEFV	4210	hgsc.bcm.edu	37	16	3299749	3299749	+	Silent	SNP	G	G	A	rs224213	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3299749G>A	ENST00000219596.1	-	3	981	c.942C>T	c.(940-942)cgC>cgT	p.R314R	MEFV_ENST00000339854.4_Silent_p.R134R|MEFV_ENST00000536379.1_Silent_p.R103R|MEFV_ENST00000541159.1_Silent_p.R103R	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	314					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GGGCGTGGCAGCGGGGACTCG	0.607													A|||	3459	0.690695	0.7322	0.6412	5008	,	,		19762	0.7083		0.5606	False		,,,				2504	0.7853				p.R314R		Atlas-SNP	.											.	MEFV	170	.	0			c.C942T						PASS	.	A	,	3101,1293	431.4+/-342.9	1092,917,188	35.0	39.0	38.0		942,309	-5.9	0.0	16	dbSNP_79	38	4639,3961	544.1+/-384.5	1289,2061,950	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2381,2978,1138	AA,AG,GG		46.0581,29.4265,40.434	,	314/782,103/446	3299749	7740,5254	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon3			GTGGCAGCGGGGA	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.942C>T	16.37:g.3299749G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	126	67	0.531746	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			G|0.373;A|0.627	0.627	strong		0.607	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
N4BP1	9683	hgsc.bcm.edu	37	16	48595110	48595110	+	Missense_Mutation	SNP	T	T	C	rs371090316		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:48595110T>C	ENST00000262384.3	-	2	1680	c.1444A>G	c.(1444-1446)Att>Gtt	p.I482V	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	482					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				GTGTTACAAATGTAGTTCTGG	0.413																																					p.I482V		Atlas-SNP	.											.	N4BP1	121	.	0			c.A1444G						PASS	.	T	VAL/ILE	1,3799		0,1,1899	139.0	141.0	141.0		1444	-12.2	0.0	16		141	0,8216		0,0,4108	no	missense	N4BP1	NM_153029.3	29	0,1,6007	CC,CT,TT		0.0,0.0263,0.0083	benign	482/897	48595110	1,12015	1900	4108	6008	SO:0001583	missense	9683	exon2			TACAAATGTAGTT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.1444A>G	16.37:g.48595110T>C	ENSP00000262384:p.Ile482Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	118	64	0.542373	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	37	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.369847	0.00209	2.63E-4	0.0	ENSG00000102921	ENST00000262384	T	0.39787	1.06	6.08	-12.2	0.00006	.	2.515080	0.01180	N	0.007078	T	0.17492	0.0420	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10823	-1.0613	10	0.25751	T	0.34	5.5903	9.9679	0.41736	0.061:0.0984:0.1832:0.6574	.	482	O75113	N4BP1_HUMAN	V	482	ENSP00000262384:I482V	ENSP00000262384:I482V	I	-	1	0	N4BP1	47152611	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.256000	0.02869	-3.027000	0.00267	-1.021000	0.02439	ATT	.	.	weak		0.413	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664	
IMPACT	55364	hgsc.bcm.edu	37	18	22008842	22008842	+	Missense_Mutation	SNP	C	C	T	rs187130387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:22008842C>T	ENST00000284202.4	+	3	316	c.175C>T	c.(175-177)Ccg>Tcg	p.P59S	Y_RNA_ENST00000362766.1_RNA	NM_018439.3	NP_060909	Q9P2X3	IMPCT_HUMAN	impact RWD domain protein	59	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				negative regulation of protein phosphorylation (GO:0001933)|regulation of translational initiation (GO:0006446)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(2)	16	all_cancers(21;0.00018)|all_epithelial(16;1.5e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)					GGTGATGCTGCCGAATGAATA	0.358													C|||	2	0.000399361	0.0	0.0029	5008	,	,		16432	0.0		0.0	False		,,,				2504	0.0				p.P59S		Atlas-SNP	.											IMPACT,pharynx,carcinoma,-2,1	IMPACT	37	1	0			c.C175T						PASS	.						122.0	109.0	113.0					18																	22008842		2203	4300	6503	SO:0001583	missense	55364	exon3			ATGCTGCCGAATG	AB026264	CCDS11886.1	18q11.2-q12.1	2012-12-07	2012-12-07		ENSG00000154059	ENSG00000154059			20387	protein-coding gene	gene with protein product	"""RWD domain containing 5"""	615319	"""Impact homolog (mouse)"""			11116084	Standard	NM_018439		Approved	RWDD5	uc002kvh.4	Q9P2X3	OTTHUMG00000131943	ENST00000284202.4:c.175C>T	18.37:g.22008842C>T	ENSP00000284202:p.Pro59Ser	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_018439	A8MXG0|Q49AM0|Q9H2X4	Missense_Mutation	SNP	ENST00000284202.4	37	CCDS11886.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	11.82	1.753700	0.31046	.	.	ENSG00000154059	ENST00000284202	T	0.29142	1.58	4.95	4.95	0.65309	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.000000	0.85682	D	0.000000	T	0.58119	0.2100	M	0.92122	3.275	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.73251	-0.4042	10	0.66056	D	0.02	.	17.304	0.87190	0.0:1.0:0.0:0.0	.	59	Q9P2X3	IMPCT_HUMAN	S	59	ENSP00000284202:P59S	ENSP00000284202:P59S	P	+	1	0	IMPACT	20262840	0.999000	0.42202	0.320000	0.25306	0.704000	0.40688	5.856000	0.69518	2.434000	0.82447	0.561000	0.74099	CCG	C|0.999;T|0.001	0.001	strong		0.358	IMPACT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254901.1	NM_018439	
LRRC18	474354	hgsc.bcm.edu	37	10	50121760	50121760	+	Silent	SNP	G	G	A	rs41283291	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50121760G>A	ENST00000374160.3	-	1	517	c.441C>T	c.(439-441)caC>caT	p.H147H	LRRC18_ENST00000298124.3_Silent_p.H147H|RP11-523O18.7_ENST00000430438.1_RNA|WDFY4_ENST00000325239.5_Intron|WDFY4_ENST00000413659.2_Intron	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	147						cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						GCCCTACCTCGTGGAGCTCCT	0.562													G|||	570	0.113818	0.1475	0.0937	5008	,	,		20355	0.002		0.1451	False		,,,				2504	0.1656				p.H147H		Atlas-SNP	.											.	LRRC18	52	.	0			c.C441T						PASS	.	G	,	632,3774	269.8+/-269.2	42,548,1613	80.0	79.0	79.0		441,	-3.9	0.9	10	dbSNP_127	79	1205,7395	242.9+/-272.7	106,993,3201	yes	coding-synonymous,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	,	148,1541,4814	AA,AG,GG		14.0116,14.3441,14.1243	,	147/262,	50121760	1837,11169	2203	4300	6503	SO:0001819	synonymous_variant	474354	exon1			TACCTCGTGGAGC	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.441C>T	10.37:g.50121760G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_001006939	Q6UY02	Silent	SNP	ENST00000374160.3	37	CCDS31197.1																																																																																			G|0.863;A|0.137	0.137	strong		0.562	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
KIF24	347240	hgsc.bcm.edu	37	9	34256539	34256539	+	Silent	SNP	A	A	G	rs36025573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34256539A>G	ENST00000402558.2	-	10	3090	c.3066T>C	c.(3064-3066)acT>acC	p.T1022T	KIF24_ENST00000379174.3_Silent_p.T888T|KIF24_ENST00000345050.2_Silent_p.T888T|KIF24_ENST00000379166.2_Silent_p.T1022T			Q5T7B8	KIF24_HUMAN	kinesin family member 24	1022					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)			CGTTTTTCACAGTGCTGGTCA	0.557													A|||	116	0.0231629	0.003	0.0908	5008	,	,		21711	0.0		0.0348	False		,,,				2504	0.0143				p.T1022T		Atlas-SNP	.											.	KIF24	64	.	0			c.T3066C						PASS	.	A		69,4337	63.5+/-100.7	0,69,2134	148.0	132.0	137.0		3066	-0.9	0.0	9	dbSNP_126	137	532,8068	148.9+/-204.1	22,488,3790	no	coding-synonymous	KIF24	NM_194313.2		22,557,5924	GG,GA,AA		6.186,1.566,4.6209		1022/1369	34256539	601,12405	2203	4300	6503	SO:0001819	synonymous_variant	347240	exon11			TTTCACAGTGCTG	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.3066T>C	9.37:g.34256539A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Silent	SNP	ENST00000402558.2	37	CCDS6551.2	58	0.026556776556776556	3	0.006097560975609756	23	0.06353591160220995	0	0.0	32	0.04221635883905013	A	3.872	-0.027771	0.07589	0.01566	0.06186	ENSG00000186638	ENST00000443226	.	.	.	4.78	-0.853	0.10709	.	.	.	.	.	T	0.02119	0.0066	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.17167	-1.0378	4	.	.	.	.	2.0153	0.03497	0.4915:0.0867:0.1266:0.2952	rs36025573	.	.	.	R	68	.	.	C	-	1	0	KIF24	34246539	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.531000	0.02219	-0.011000	0.14247	-0.624000	0.04008	TGT	A|0.960;G|0.040	0.040	strong		0.557	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
DCAF13	25879	hgsc.bcm.edu	37	8	104432545	104432545	+	Missense_Mutation	SNP	A	A	G	rs3134253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:104432545A>G	ENST00000297579.5	+	2	857	c.580A>G	c.(580-582)Ata>Gta	p.I194V	DCAF13_ENST00000521716.1_Missense_Mutation_p.I38V|DCAF13_ENST00000521971.1_Missense_Mutation_p.I38V|DCAF13_ENST00000519682.1_Missense_Mutation_p.I38V|DCAF13_ENST00000521999.1_Intron	NM_015420.6	NP_056235.4	Q9NV06	DCA13_HUMAN	DDB1 and CUL4 associated factor 13	42					protein ubiquitination (GO:0016567)|rRNA processing (GO:0006364)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ACGAGAATATATAAGAGCTTT	0.383													G|||	1269	0.253395	0.202	0.268	5008	,	,		19647	0.3313		0.2316	False		,,,				2504	0.2546				p.I194V		Atlas-SNP	.											.	DCAF13	66	.	0			c.A580G						PASS	.	G	VAL/ILE	964,3442	734.4+/-410.6	104,756,1343	98.0	92.0	94.0		580	-0.4	0.3	8	dbSNP_103	94	1830,6770	731.0+/-406.8	191,1448,2661	no	missense	DCAF13	NM_015420.6	29	295,2204,4004	GG,GA,AA		21.2791,21.8793,21.4824	benign	194/598	104432545	2794,10212	2203	4300	6503	SO:0001583	missense	25879	exon2			GAATATATAAGAG	AK074725	CCDS34934.1	8q22.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000164934	ENSG00000164934		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	24535	protein-coding gene	gene with protein product			"""WD repeats and SOF1 domain containing"""	WDSOF1		11042152	Standard	NM_015420		Approved	DKFZP564O0463, Gm83, HSPC064	uc003yln.3	Q9NV06	OTTHUMG00000164888	ENST00000297579.5:c.580A>G	8.37:g.104432545A>G	ENSP00000297579:p.Ile194Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_015420	Q3MII9|Q8NCH8|Q8TC51|Q96JY7|Q9NZX3	Missense_Mutation	SNP	ENST00000297579.5	37	CCDS34934.1	577	0.2641941391941392	106	0.21544715447154472	93	0.2569060773480663	196	0.34265734265734266	182	0.24010554089709762	G	7.825	0.718601	0.15372	0.218793	0.212791	ENSG00000164934	ENST00000297579;ENST00000521716;ENST00000521971;ENST00000388778;ENST00000519682	T;T;T;T	0.01252	5.1;5.1;5.1;5.1	5.26	-0.374	0.12512	.	0.522492	0.21591	N	0.072093	T	0.00012	0.0000	N	0.00046	-2.44	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21211	-1.0252	9	0.10902	T	0.67	-5.3123	11.2365	0.48944	0.6324:0.0:0.3676:0.0	rs3134253;rs52822106;rs3134253	42	B3KME9	.	V	194;38;38;42;38	ENSP00000297579:I194V;ENSP00000430645:I38V;ENSP00000430883:I38V;ENSP00000430411:I38V	ENSP00000297579:I194V	I	+	1	0	DCAF13	104501721	0.000000	0.05858	0.294000	0.24946	0.994000	0.84299	0.477000	0.22196	-0.208000	0.10171	-0.119000	0.15052	ATA	A|0.768;G|0.232	0.232	strong		0.383	DCAF13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380797.2	NM_015420	
C7orf62	219557	hgsc.bcm.edu	37	7	88424115	88424115	+	Missense_Mutation	SNP	C	C	G	rs2373396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:88424115C>G	ENST00000297203.2	-	2	327	c.142G>C	c.(142-144)Gat>Cat	p.D48H	ZNF804B_ENST00000333190.4_Intron	NM_152706.3	NP_689919.1	Q8TBZ9	CG062_HUMAN	chromosome 7 open reading frame 62	48			D -> H (in dbSNP:rs2373396).							NS(1)|breast(1)|endometrium(3)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	30						AACATCCTATCAAGAAGGAAT	0.383													G|||	769	0.153554	0.2216	0.1556	5008	,	,		19269	0.1171		0.175	False		,,,				2504	0.0757				p.D48H		Atlas-SNP	.											.	C7orf62	63	.	0			c.G142C						PASS	.	G	HIS/ASP,	938,3468	737.0+/-410.8	98,742,1363	125.0	133.0	130.0		142,	-2.0	0.0	7	dbSNP_100	130	1274,7326	759.9+/-407.6	92,1090,3118	yes	missense,intron	C7orf62,ZNF804B	NM_152706.2,NM_181646.2	81,	190,1832,4481	GG,GC,CC		14.814,21.2892,17.0075	benign,	48/254,	88424115	2212,10794	2203	4300	6503	SO:0001583	missense	219557	exon2			TCCTATCAAGAAG	BC028365	CCDS34678.1	7q21.13	2013-10-11			ENSG00000164645	ENSG00000164645			22402	protein-coding gene	gene with protein product						12690205	Standard	NM_152706		Approved	MGC26647	uc003ujv.3	Q8TBZ9	OTTHUMG00000153859	ENST00000297203.2:c.142G>C	7.37:g.88424115C>G	ENSP00000297203:p.Asp48His	Somatic	295	0	0		WXS	Illumina HiSeq	Phase_I	300	141	0.47	NM_152706		Missense_Mutation	SNP	ENST00000297203.2	37	CCDS34678.1	351	0.16071428571428573	113	0.22967479674796748	59	0.16298342541436464	60	0.1048951048951049	119	0.15699208443271767	G	0.012	-1.689031	0.00738	0.212892	0.14814	ENSG00000164645	ENST00000297203	T	0.10860	2.83	6.16	-1.99	0.07457	.	0.369134	0.30667	N	0.009140	T	0.00012	0.0000	N	0.00052	-2.395	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36866	-0.9730	9	0.02654	T	1	-9.2818	11.3375	0.49513	0.0:0.4201:0.1876:0.3923	rs2373396;rs10371464;rs2373396	48	Q8TBZ9	CG062_HUMAN	H	48	ENSP00000297203:D48H	ENSP00000297203:D48H	D	-	1	0	C7orf62	88262051	0.245000	0.23899	0.001000	0.08648	0.488000	0.33401	0.090000	0.15025	-1.099000	0.03034	-0.843000	0.03049	GAT	C|0.824;G|0.176	0.176	strong		0.383	C7orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332714.1	NM_152706	
SDHA	6389	hgsc.bcm.edu	37	5	228362	228362	+	Silent	SNP	T	T	C	rs2115272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:228362T>C	ENST00000264932.6	+	6	799	c.684T>C	c.(682-684)aaT>aaC	p.N228N	SDHA_ENST00000510361.1_Silent_p.N180N|SDHA_ENST00000504309.1_Silent_p.N228N	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	228					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)	TGATGGAGAATGGGGAGTGCC	0.453									Familial Paragangliomas				C|||	1239	0.247404	0.6233	0.2406	5008	,	,		18495	0.0585		0.1113	False		,,,				2504	0.0787				p.N228N		Atlas-SNP	.											.	SDHA	80	.	0			c.T684C						PASS	.	C		2363,2043	565.7+/-381.7	637,1089,477	91.0	86.0	88.0		684	-5.3	0.0	5	dbSNP_96	88	1170,7430	765.6+/-407.6	75,1020,3205	yes	coding-synonymous	SDHA	NM_004168.2		712,2109,3682	CC,CT,TT		13.6047,46.3686,27.1644		228/665	228362	3533,9473	2203	4300	6503	SO:0001819	synonymous_variant	6389	exon6	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	GGAGAATGGGGAG	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.684T>C	5.37:g.228362T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			T|0.754;C|0.246	0.246	strong		0.453	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
FMR1	2332	hgsc.bcm.edu	37	X	146993715	146993715	+	Silent	SNP	G	G	T	rs111485627	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:146993715G>T	ENST00000370475.4	+	1	146	c.18G>T	c.(16-18)gtG>gtT	p.V6V	FMR1_ENST00000334557.6_Silent_p.V6V|FMR1_ENST00000370470.1_Silent_p.V6V|FMR1-AS1_ENST00000598667.1_RNA|FMR1-AS1_ENST00000596112.1_RNA|FMR1_ENST00000439526.2_Silent_p.V6V|FMR1_ENST00000370471.3_Silent_p.V6V|FMR1_ENST00000370477.1_Silent_p.V6V|FMR1-AS1_ENST00000594922.1_RNA|FMR1_ENST00000218200.8_Silent_p.V6V	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	6	Agenet-like 1.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					AGCTGGTGGTGGAAGTGCGGG	0.677									Fragile X syndrome				G|||	15	0.00397351	0.0	0.0029	3775	,	,		5155	0.0		0.0129	False		,,,				2504	0.0				p.V6V		Atlas-SNP	.											.	FMR1	93	.	0			c.G18T						PASS	.	G	,,,,	6,3525		0,6,0,1538,443	76.0	50.0	59.0		18,18,18,18,18	4.0	1.0	X	dbSNP_132	59	79,6026		0,62,17,2208,1548	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FMR1	NM_001185075.1,NM_001185076.1,NM_001185081.1,NM_001185082.1,NM_002024.5	,,,,	0,68,17,3746,1991	TT,TG,T,GG,G		1.294,0.1699,0.8821	,,,,	6/538,6/612,6/517,6/587,6/633	146993715	85,9551	1987	3835	5822	SO:0001819	synonymous_variant	2332	exon1	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	GGTGGTGGAAGTG	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"""premature ovarian failure 1"""	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.18G>T	X.37:g.146993715G>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	114	113	0.991228	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1																																																																																			C|0.000;G|0.987;T|0.013	0.013	strong		0.677	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	
MAN2B2	23324	hgsc.bcm.edu	37	4	6610889	6610889	+	Missense_Mutation	SNP	G	G	A	rs61733402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:6610889G>A	ENST00000285599.3	+	12	1906	c.1870G>A	c.(1870-1872)Ggg>Agg	p.G624R	MAN2B2_ENST00000504248.1_Missense_Mutation_p.G573R|MAN2B2_ENST00000504960.1_3'UTR	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	624					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CCACGTCAACGGGGATGTGAA	0.572													G|||	181	0.0361422	0.0061	0.0389	5008	,	,		21881	0.001		0.0885	False		,,,				2504	0.0573				p.G624R		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G1870A						PASS	.	G	ARG/GLY	79,4327	69.2+/-107.0	0,79,2124	102.0	90.0	94.0		1870	0.3	0.0	4	dbSNP_129	94	818,7782	190.0+/-236.6	46,726,3528	yes	missense	MAN2B2	NM_015274.1	125	46,805,5652	AA,AG,GG		9.5116,1.793,6.8968	probably-damaging	624/1010	6610889	897,12109	2203	4300	6503	SO:0001583	missense	23324	exon12			GTCAACGGGGATG	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1870G>A	4.37:g.6610889G>A	ENSP00000285599:p.Gly624Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	92	0.04212454212454213	6	0.012195121951219513	15	0.04143646408839779	0	0.0	71	0.09366754617414248	G	23.1	4.376100	0.82682	0.01793	0.095116	ENSG00000013288	ENST00000285599;ENST00000504248	T;T	0.79141	-1.24;-1.24	4.36	0.289	0.15723	Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	0.520725	0.20150	N	0.098165	T	0.11580	0.0282	L	0.60455	1.87	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.991	D;D;P	0.68353	0.957;0.936;0.763	T	0.48502	-0.9030	10	0.62326	D	0.03	-0.1459	5.3779	0.16176	0.1494:0.0:0.579:0.2715	rs61733402	573;624;624	E9PCD7;Q9Y2E5;Q9Y2E5-2	.;MA2B2_HUMAN;.	R	624;573	ENSP00000285599:G624R;ENSP00000423129:G573R	ENSP00000285599:G624R	G	+	1	0	MAN2B2	6661790	0.985000	0.35326	0.000000	0.03702	0.904000	0.53231	2.922000	0.48860	-0.356000	0.08187	0.313000	0.20887	GGG	G|0.936;A|0.064	0.064	strong		0.572	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
DZANK1	55184	hgsc.bcm.edu	37	20	18395988	18395988	+	Missense_Mutation	SNP	C	C	T	rs6035037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:18395988C>T	ENST00000358866.6	-	10	1082	c.1060G>A	c.(1060-1062)Ggc>Agc	p.G354S	DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000357236.4_Missense_Mutation_p.G240S|DZANK1_ENST00000262547.5_Missense_Mutation_p.G354S|DZANK1_ENST00000329494.5_Missense_Mutation_p.G356S			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	354							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						CCACACCAGCCGCAGAAGGAC	0.562													C|||	1251	0.2498	0.1573	0.2983	5008	,	,		15727	0.1696		0.3151	False		,,,				2504	0.3558				p.G354S		Atlas-SNP	.											DZANK1,NS,carcinoma,0,2	DZANK1	65	2	0			c.G1060A						PASS	.	C	SER/GLY	643,3185		54,535,1325	77.0	87.0	84.0		1060	3.5	1.0	20	dbSNP_114	84	2529,5711		368,1793,1959	yes	missense	DZANK1	NM_001099407.1	56	422,2328,3284	TT,TC,CC		30.6917,16.7973,26.2844	benign	354/753	18395988	3172,8896	1914	4120	6034	SO:0001583	missense	55184	exon11			ACCAGCCGCAGAA	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"""Ankyrin repeat domain containing"""	15858	protein-coding gene	gene with protein product	"""ankyrin repeat domain 64"""		"""chromosome 20 open reading frame 12"""	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.1060G>A	20.37:g.18395988C>T	ENSP00000351734:p.Gly354Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Missense_Mutation	SNP	ENST00000358866.6	37	CCDS46582.1	515	0.2358058608058608	77	0.1565040650406504	98	0.27071823204419887	104	0.18181818181818182	236	0.3113456464379947	C	14.53	2.562631	0.45694	0.167973	0.306917	ENSG00000089091	ENST00000377630;ENST00000262547;ENST00000329494;ENST00000414623;ENST00000357236	T;T;T;T	0.61627	0.26;0.09;0.76;0.21	5.57	3.54	0.40534	.	0.634496	0.17261	N	0.180784	T	0.00012	0.0000	N	0.10972	0.075	0.50467	P	1.2199999999995548E-4	B;B;B	0.32031	0.267;0.352;0.063	B;B;B	0.24848	0.056;0.048;0.004	T	0.25467	-1.0131	9	0.46703	T	0.11	-6.1428	8.6331	0.33930	0.0:0.7597:0.1522:0.0881	rs6035037;rs17204022;rs52820643;rs61438457;rs6035037	373;240;354	B7Z631;Q9NVP4-4;Q9NVP4	.;.;DZAN1_HUMAN	S	181;354;356;180;240	ENSP00000366857:G181S;ENSP00000262547:G354S;ENSP00000328866:G356S;ENSP00000349774:G240S	ENSP00000262547:G354S	G	-	1	0	C20orf12	18343988	0.998000	0.40836	0.980000	0.43619	0.858000	0.48976	3.120000	0.50430	0.619000	0.30197	0.313000	0.20887	GGC	C|0.764;T|0.236	0.236	strong		0.562	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407	
SART3	9733	hgsc.bcm.edu	37	12	108954862	108954862	+	Missense_Mutation	SNP	G	G	C	rs2072579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:108954862G>C	ENST00000228284.3	-	1	303	c.69C>G	c.(67-69)gaC>gaG	p.D23E	ISCU_ENST00000539593.1_5'Flank|ISCU_ENST00000311893.9_5'Flank|ISCU_ENST00000547005.1_5'Flank|ISCU_ENST00000392807.4_5'Flank|ISCU_ENST00000431221.2_5'Flank|ISCU_ENST00000535729.1_5'Flank|SART3_ENST00000431469.2_Missense_Mutation_p.D23E|SART3_ENST00000552221.1_5'UTR|SART3_ENST00000546611.1_Missense_Mutation_p.D23E|ISCU_ENST00000338291.4_5'Flank	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	23			D -> E (in dbSNP:rs2072579). {ECO:0000269|PubMed:14702039}.		cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						CCTCCTCTCCGTCAGCCTTGG	0.617									Porokeratosis				G|||	1254	0.250399	0.1445	0.389	5008	,	,		17805	0.3819		0.161	False		,,,				2504	0.2515				p.D23E		Atlas-SNP	.											.	SART3	64	.	0			c.C69G						PASS	.	G	GLU/ASP	790,3616	312.7+/-292.7	72,646,1485	69.0	63.0	65.0		69	3.2	1.0	12	dbSNP_96	65	1531,7069	286.6+/-297.8	134,1263,2903	yes	missense	SART3	NM_014706.3	45	206,1909,4388	CC,CG,GG		17.8023,17.9301,17.8456	benign	23/964	108954862	2321,10685	2203	4300	6503	SO:0001583	missense	9733	exon1	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	CTCTCCGTCAGCC	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"""RNA binding motif (RRM) containing"""	16860	protein-coding gene	gene with protein product		611684	"""squamous cell carcinoma antigen recognised by T cells 3"""			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.69C>G	12.37:g.108954862G>C	ENSP00000228284:p.Asp23Glu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_014706	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Missense_Mutation	SNP	ENST00000228284.3	37	CCDS9117.1	530	0.24267399267399267	80	0.16260162601626016	128	0.35359116022099446	212	0.3706293706293706	110	0.14511873350923482	G	1.090	-0.664443	0.03428	0.179301	0.178023	ENSG00000075856	ENST00000228284;ENST00000431469;ENST00000546815;ENST00000546611	T;T;T;T	0.51574	2.69;2.59;0.7;1.16	4.99	3.15	0.36227	.	0.130292	0.35525	N	0.003147	T	0.00012	0.0000	N	0.01048	-1.04	0.51012	P	9.599999999998499E-5	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.13407	0.0;0.009;0.0	T	0.41645	-0.9497	9	0.02654	T	1	-24.3203	6.7605	0.23538	0.0:0.684:0.2185:0.0975	rs2072579;rs17040769;rs52813194;rs2072579	23;23;23	B7ZKM0;Q15020-3;Q15020	.;.;SART3_HUMAN	E	23	ENSP00000228284:D23E;ENSP00000414453:D23E;ENSP00000449386:D23E;ENSP00000448554:D23E	ENSP00000228284:D23E	D	-	3	2	SART3	107478992	0.826000	0.29277	0.991000	0.47740	0.377000	0.30045	-0.048000	0.11944	0.789000	0.33779	-0.211000	0.12701	GAC	G|0.800;C|0.200	0.200	strong		0.617	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1		
NPNT	255743	hgsc.bcm.edu	37	4	106861730	106861730	+	Missense_Mutation	SNP	A	A	G	rs4340795	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:106861730A>G	ENST00000379987.2	+	7	916	c.700A>G	c.(700-702)Ata>Gta	p.I234V	NPNT_ENST00000514622.1_Missense_Mutation_p.I234V|NPNT_ENST00000453617.2_Missense_Mutation_p.I251V|NPNT_ENST00000305572.8_Missense_Mutation_p.I234V|NPNT_ENST00000427316.2_Missense_Mutation_p.I264V|NPNT_ENST00000506666.1_Missense_Mutation_p.I264V	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	234	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		I -> V (in dbSNP:rs4340795). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		ATGTTATAACATACGTGGGTC	0.423													A|||	4454	0.889377	0.7171	0.9179	5008	,	,		18908	1.0		0.9175	False		,,,				2504	0.9591				p.I264V		Atlas-SNP	.											.	NPNT	69	.	0			c.A790G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	3227,1179	711.1+/-408.0	1173,881,149	189.0	167.0	175.0		700,751,790,700,790	-9.7	0.0	4	dbSNP_111	175	7822,778	784.4+/-407.6	3555,712,33	yes	missense,missense,missense,missense,missense	NPNT	NM_001033047.2,NM_001184690.1,NM_001184691.1,NM_001184692.1,NM_001184693.1	29,29,29,29,29	4728,1593,182	GG,GA,AA		9.0465,26.759,15.0469	benign,benign,benign,benign,benign	234/566,251/583,264/596,234/537,264/567	106861730	11049,1957	2203	4300	6503	SO:0001583	missense	255743	exon8			TATAACATACGTG		CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.700A>G	4.37:g.106861730A>G	ENSP00000369323:p.Ile234Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001184691	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Missense_Mutation	SNP	ENST00000379987.2	37	CCDS34046.1	1953|1953	0.8942307692307693|0.8942307692307693	354|354	0.7195121951219512|0.7195121951219512	327|327	0.9033149171270718|0.9033149171270718	572|572	1.0|1.0	700|700	0.9234828496042217|0.9234828496042217	A|A	4.888|4.888	0.165030|0.165030	0.09339|0.09339	0.73241|0.73241	0.909535|0.909535	ENSG00000168743|ENSG00000168743	ENST00000514837|ENST00000379987;ENST00000453617;ENST00000427316;ENST00000514622;ENST00000305572;ENST00000506666;ENST00000503451	.|D;D;D;D;D;D;D	.|0.91996	.|-2.95;-2.95;-2.95;-2.95;-2.95;-2.95;-2.95	5.29|5.29	-9.72|-9.72	0.00515|0.00515	.|EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|0.505405	.|0.21166	.|N	.|0.079061	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.26092|0.26092	0.79|0.79	0.58432|0.58432	P|P	5.000000000032756E-6|5.000000000032756E-6	.|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	.|0.002;0.001;0.001;0.001;0.001;0.001;0.001	T|T	0.40496|0.40496	-0.9560|-0.9560	4|9	.|0.33940	.|T	.|0.23	.|.	10.1038|10.1038	0.42521|0.42521	0.7246:0.0859:0.1034:0.0861|0.7246:0.0859:0.1034:0.0861	rs4340795;rs52818641;rs60755410;rs4340795|rs4340795;rs52818641;rs60755410;rs4340795	.|234;264;264;251;281;234;234	.|E9PF04;E9PE64;E9PCQ1;E9PCK8;D6RH31;Q6UXI9-2;Q6UXI9	.|.;.;.;.;.;.;NPNT_HUMAN	R|V	210|234;251;264;234;234;264;281	.|ENSP00000369323:I234V;ENSP00000402884:I251V;ENSP00000389252:I264V;ENSP00000422044:I234V;ENSP00000302557:I234V;ENSP00000422474:I264V;ENSP00000426146:I281V	.|ENSP00000302557:I234V	H|I	+|+	2|1	0|0	NPNT|NPNT	107081179|107081179	0.925000|0.925000	0.31364|0.31364	0.000000|0.000000	0.03702|0.03702	0.123000|0.123000	0.20343|0.20343	0.593000|0.593000	0.23999|0.23999	-2.809000|-2.809000	0.00348|0.00348	-0.408000|-0.408000	0.06270|0.06270	CAT|ATA	A|0.136;G|0.864	0.864	strong		0.423	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278	
CD33	945	hgsc.bcm.edu	37	19	51728477	51728477	+	Missense_Mutation	SNP	C	C	T	rs12459419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51728477C>T	ENST00000262262.4	+	2	62	c.41C>T	c.(40-42)gCc>gTc	p.A14V	CD33_ENST00000436584.2_Intron|CD33_ENST00000391796.3_Missense_Mutation_p.A14V|CD33_ENST00000421133.2_Intron	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	14			A -> V (in dbSNP:rs12459419). {ECO:0000269|PubMed:14702039}.		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	CCCACAGGGGCCCTGGCTATG	0.622													c|||	1055	0.210663	0.0514	0.4841	5008	,	,		18557	0.1855		0.3101	False		,,,				2504	0.1554				p.A14V		Atlas-SNP	.											.	CD33	55	.	0			c.C41T						PASS	.	C	,VAL/ALA,VAL/ALA	411,3995		17,377,1809	39.0	43.0	41.0		,41,41	0.9	0.0	19	dbSNP_120	41	2585,6015		399,1787,2114	no	intron,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	,64,64	416,2164,3923	TT,TC,CC		30.0581,9.3282,23.0355	,benign,benign	,14/311,14/365	51728477	2996,10010	2203	4300	6503	SO:0001583	missense	945	exon2			CAGGGGCCCTGGC	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.41C>T	19.37:g.51728477C>T	ENSP00000262262:p.Ala14Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	521	0.23855311355311357	34	0.06910569105691057	152	0.4198895027624309	101	0.17657342657342656	234	0.3087071240105541	.	12.28	1.889446	0.33348	0.093282	0.300581	ENSG00000105383	ENST00000262262;ENST00000391796	T;T	0.16743	2.45;2.32	3.32	0.919	0.19392	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.54753	P	1.399999999995849E-5	P;P	0.41947	0.766;0.478	B;B	0.38842	0.283;0.109	T	0.49916	-0.8888	8	0.45353	T	0.12	.	9.354	0.38155	0.0:0.5882:0.4118:0.0	rs12459419	14;14	F8WAL2;P20138	.;CD33_HUMAN	V	14	ENSP00000262262:A14V;ENSP00000375673:A14V	ENSP00000262262:A14V	A	+	2	0	CD33	56420289	0.003000	0.15002	0.001000	0.08648	0.016000	0.09150	0.120000	0.15647	0.184000	0.20083	0.467000	0.42956	GCC	C|0.765;T|0.235	0.235	strong		0.622	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
SNED1	25992	hgsc.bcm.edu	37	2	242004866	242004866	+	Silent	SNP	A	A	G	rs2286321	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:242004866A>G	ENST00000310397.8	+	21	2865	c.2865A>G	c.(2863-2865)acA>acG	p.T955T	AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.T955T|SNED1_ENST00000401884.1_Silent_p.T955T|SNED1_ENST00000405547.3_Silent_p.T955T	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	955	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		ACCGCCGCACAGACTTTGTGG	0.622													G|||	1910	0.38139	0.6596	0.2795	5008	,	,		16152	0.4097		0.2008	False		,,,				2504	0.2342				p.T955T		Atlas-SNP	.											.	SNED1	76	.	0			c.A2865G						PASS	.	G		2180,1854		610,960,447	46.0	58.0	54.0		2865	-9.6	0.1	2	dbSNP_100	54	1446,6904		135,1176,2864	no	coding-synonymous	SNED1	NM_001080437.1		745,2136,3311	GG,GA,AA		17.3174,45.9593,29.2797		955/1414	242004866	3626,8758	2017	4175	6192	SO:0001819	synonymous_variant	25992	exon21			CCGCACAGACTTT	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.2865A>G	2.37:g.242004866A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			A|0.630;G|0.370	0.370	strong		0.622	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
LANCL3	347404	hgsc.bcm.edu	37	X	37527659	37527659	+	Intron	SNP	T	T	C	rs28503960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:37527659T>C	ENST00000378619.3	+	4	1322				LANCL3_ENST00000378621.3_Missense_Mutation_p.L381P|TM4SF2_ENST00000465127.1_Intron	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)								catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						gaacatctgctgtataccaga	0.294													T|||	568	0.150464	0.1256	0.0994	3775	,	,		9346	0.0496		0.1123	False		,,,				2504	0.1738				p.L381P		Atlas-SNP	.											.	LANCL3	42	.	0			c.T1142C						PASS	.	T	,PRO/LEU	697,3136		55,490,97,1086,474	54.0	49.0	51.0		,1142	2.2	0.0	X	dbSNP_125	51	1168,5558		84,695,305,1648,1567	yes	intron,missense	LANCL3	NM_001170331.1,NM_198511.2	,98	139,1185,402,2734,2041	CC,CT,C,TT,T		17.3654,18.1842,17.6627	,benign	,381/389	37527659	1865,8694	2202	4299	6501	SO:0001627	intron_variant	347404	exon5			ATCTGCTGTATAC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.1103+917T>C	X.37:g.37527659T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_198511	A6NHE3	Missense_Mutation	SNP	ENST00000378619.3	37	CCDS55398.1	214	0.1289933694996986	46	0.10222222222222223	20	0.060240963855421686	16	0.02877697841726619	63	0.08898305084745763	T	4.137	0.023659	0.08006	0.181842	0.173654	ENSG00000147036	ENST00000378621	.	.	.	2.17	2.17	0.27698	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.32968	0.392	B	0.27500	0.08	T	0.13872	-1.0493	6	0.30078	T	0.28	.	5.629	0.17499	0.0:0.0:0.0:1.0	rs28503960	381	Q6ZV70-2	.	P	381	.	ENSP00000367885:L381P	L	+	2	0	LANCL3	37412578	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.193000	0.17116	1.111000	0.41721	0.430000	0.28490	CTG	T|0.847;C|0.153	0.153	strong		0.294	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511	
DSTYK	25778	hgsc.bcm.edu	37	1	205129319	205129319	+	Silent	SNP	G	G	A	rs1062715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:205129319G>A	ENST00000367162.3	-	8	2058	c.2028C>T	c.(2026-2028)ttC>ttT	p.F676F	DSTYK_ENST00000367160.4_Intron|DSTYK_ENST00000367161.3_Silent_p.F676F	NM_015375.2	NP_056190.1	Q6XUX3	DUSTY_HUMAN	dual serine/threonine and tyrosine protein kinase	676	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to fibroblast growth factor stimulus (GO:0044344)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of kinase activity (GO:0033674)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)	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)			breast(2)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)|skin(2)	14						GGGCACAAGGGAAGTGTCCTC	0.502													G|||	1860	0.371406	0.4175	0.3184	5008	,	,		18020	0.4008		0.2565	False		,,,				2504	0.4346				p.F676F		Atlas-SNP	.											.	DSTYK	87	.	0			c.C2028T						PASS	.	G	,	1684,2722	510.3+/-367.5	302,1080,821	155.0	146.0	149.0		2028,2028	5.2	1.0	1	dbSNP_86	149	2031,6569	355.5+/-329.9	220,1591,2489	no	coding-synonymous,coding-synonymous	DSTYK	NM_015375.2,NM_199462.2	,	522,2671,3310	AA,AG,GG		23.6163,38.2206,28.5637	,	676/930,676/885	205129319	3715,9291	2203	4300	6503	SO:0001819	synonymous_variant	25778	exon8			ACAAGGGAAGTGT	AF068286	CCDS1451.1, CCDS1452.1	1q32	2008-12-18	2008-12-18	2008-12-18	ENSG00000133059	ENSG00000133059			29043	protein-coding gene	gene with protein product		612666	"""receptor interacting protein kinase 5"""	RIPK5		15178406	Standard	NM_015375		Approved	KIAA0472, DustyPK, RIP5	uc001hbw.3	Q6XUX3	OTTHUMG00000037102	ENST00000367162.3:c.2028C>T	1.37:g.205129319G>A		Somatic	248	1	0.00403226		WXS	Illumina HiSeq	Phase_I	255	132	0.517647	NM_199462	B7ZL64|O75060|Q17R94|Q5RKT0|Q6IN87|Q6P997|Q86Y03|Q9P1S5	Silent	SNP	ENST00000367162.3	37	CCDS1451.1																																																																																			G|0.705;A|0.295	0.295	strong		0.502	DSTYK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090345.1	NM_015375	
TENM4	26011	hgsc.bcm.edu	37	11	78437182	78437182	+	Silent	SNP	G	G	A	rs689369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:78437182G>A	ENST00000278550.7	-	23	3954	c.3492C>T	c.(3490-3492)gaC>gaT	p.D1164D		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1164					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										GCTTGGACGCGTCAATTTCAT	0.453													A|||	903	0.180312	0.2398	0.2277	5008	,	,		20862	0.1438		0.161	False		,,,				2504	0.1237				p.D1164D		Atlas-SNP	.											.	.	.	.	0			c.C3492T						PASS	.	A		810,3066		100,610,1228	317.0	307.0	310.0		3492	-1.0	1.0	11	dbSNP_83	310	1377,6895		121,1135,2880	yes	coding-synonymous	ODZ4	NM_001098816.2		221,1745,4108	AA,AG,GG		16.6465,20.8978,18.003		1164/2770	78437182	2187,9961	1938	4136	6074	SO:0001819	synonymous_variant	26011	exon23			GGACGCGTCAATT	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.3492C>T	11.37:g.78437182G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	187	85	0.454545	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			G|0.814;A|0.186	0.186	strong		0.453	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
LRRC23	10233	hgsc.bcm.edu	37	12	7023123	7023123	+	3'UTR	SNP	A	A	G	rs710415	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7023123A>G	ENST00000007969.8	+	0	1345				ENO2_ENST00000535366.1_5'Flank|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000541477.1_5'Flank|ENO2_ENST00000538763.1_5'Flank|ENO2_ENST00000229277.1_5'Flank|ENO2_ENST00000544774.1_5'Flank|LRRC23_ENST00000429740.1_Missense_Mutation_p.N187D|LRRC23_ENST00000436789.1_3'UTR|LRRC23_ENST00000443597.2_3'UTR|LRRC23_ENST00000323702.5_Missense_Mutation_p.E276G	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23											NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						TATGACAGAGAACAGAGGATG	0.542													G|||	2393	0.477835	0.8169	0.2896	5008	,	,		-128	0.4732		0.2972	False		,,,				2504	0.3436				p.E276G		Atlas-SNP	.											.	LRRC23	46	.	0			c.A827G						PASS	.	G	,GLY/GLU,	3115,1291	437.8+/-345.1	1117,881,205	137.0	129.0	132.0		,827,	-0.8	0.0	12	dbSNP_86	132	2441,6159	698.0+/-405.0	363,1715,2222	yes	utr-3,missense,utr-3	LRRC23	NM_001135217.1,NM_006992.3,NM_201650.2	,98,	1480,2596,2427	GG,GA,AA		28.3837,29.301,42.7187	,,	,276/313,	7023123	5556,7450	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10233	exon7			ACAGAGAACAGAG	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.*93A>G	12.37:g.7023123A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_006992	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	989|989	0.45283882783882784|0.45283882783882784	384|384	0.7804878048780488|0.7804878048780488	128|128	0.35359116022099446|0.35359116022099446	254|254	0.44405594405594406|0.44405594405594406	223|223	0.2941952506596306|0.2941952506596306	G|G	10.42|10.42	1.346628|1.346628	0.24426|0.24426	0.70699|0.70699	0.283837|0.283837	ENSG00000010626|ENSG00000010626	ENST00000323702|ENST00000429740	T|T	0.67865|0.37915	-0.29|1.17	2.86|2.86	-0.778|-0.778	0.10977|0.10977	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	4.000000000004E-6|4.000000000004E-6	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.21655|0.21655	-1.0239|-1.0239	7|7	0.35671|0.72032	T|D	0.21|0.01	.|.	3.6922|3.6922	0.08350|0.08350	0.4899:0.2031:0.307:0.0|0.4899:0.2031:0.307:0.0	rs710415;rs3168597;rs17788615;rs52833239;rs56597060;rs60356840;rs710415|rs710415;rs3168597;rs17788615;rs52833239;rs56597060;rs60356840;rs710415	276|187	Q53EV4-2|E9PDZ4	.|.	G|D	276|187	ENSP00000317464:E276G|ENSP00000397192:N187D	ENSP00000317464:E276G|ENSP00000397192:N187D	E|N	+|+	2|1	0|0	LRRC23|LRRC23	6893384|6893384	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-0.005000|-0.005000	0.12855|0.12855	-0.503000|-0.503000	0.06586|0.06586	-0.355000|-0.355000	0.07637|0.07637	GAA|AAC	A|0.551;G|0.449	0.449	strong		0.542	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
OR4K15	81127	hgsc.bcm.edu	37	14	20444012	20444012	+	Missense_Mutation	SNP	A	A	T	rs3861512	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20444012A>T	ENST00000305051.5	+	1	410	c.335A>T	c.(334-336)gAg>gTg	p.E112V		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	112			E -> V (in dbSNP:rs3861512). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCTGGTTGAGCGCAAGACT	0.448													A|||	1093	0.218251	0.2141	0.1715	5008	,	,		22012	0.123		0.2227	False		,,,				2504	0.3507				p.E112V		Atlas-SNP	.											OR4K15,colon,carcinoma,0,2	OR4K15	82	2	0			c.A335T						PASS	.	A	VAL/GLU	1058,3348		122,814,1267	126.0	132.0	130.0		335	-0.3	0.0	14	dbSNP_108	130	2282,6312		290,1702,2305	yes	missense	OR4K15	NM_001005486.1	121	412,2516,3572	TT,TA,AA		26.5534,24.0127,25.6923	benign	112/349	20444012	3340,9660	2203	4297	6500	SO:0001583	missense	81127	exon1			TGGTTGAGCGCAA		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.335A>T	14.37:g.20444012A>T	ENSP00000304077:p.Glu112Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	180	76	0.422222	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	400	0.18315018315018314	95	0.19308943089430894	65	0.17955801104972377	66	0.11538461538461539	174	0.22955145118733508	.	6.499	0.460280	0.12342	0.240127	0.265534	ENSG00000169488	ENST00000305051	T	0.01572	4.76	3.6	-0.288	0.12855	GPCR, rhodopsin-like superfamily (1);	0.388604	0.21610	N	0.071810	T	0.00012	0.0000	M	0.71036	2.16	0.80722	P	0.0	P	0.37781	0.608	B	0.38428	0.273	T	0.48007	-0.9072	9	0.66056	D	0.02	.	7.2471	0.26127	0.5441:0.0:0.4559:0.0	rs3861512;rs17210948;rs52792471;rs61025663;rs3861512	112	Q8NH41	OR4KF_HUMAN	V	112	ENSP00000304077:E112V	ENSP00000304077:E112V	E	+	2	0	OR4K15	19513852	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	0.973000	0.29422	-0.252000	0.09528	-0.361000	0.07541	GAG	A|0.772;T|0.228	0.228	strong		0.448	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
TMEM79	84283	hgsc.bcm.edu	37	1	156255560	156255560	+	Silent	SNP	G	G	A	rs140033065	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156255560G>A	ENST00000405535.2	+	2	714	c.543G>A	c.(541-543)ccG>ccA	p.P181P	TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000357501.2_Intron|SMG5_ENST00000361813.5_5'Flank|SMG5_ENST00000368267.5_5'Flank|TMEM79_ENST00000295694.5_Silent_p.P181P	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	181					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					TGGTGAGGCCGCCTGGCTGTT	0.682													G|||	5	0.000998403	0.0	0.0	5008	,	,		12551	0.0		0.004	False		,,,				2504	0.001				p.P181P		Atlas-SNP	.											.	TMEM79	43	.	0			c.G543A						PASS	.	G		5,4395		0,5,2195	39.0	45.0	43.0		543	-11.3	0.0	1	dbSNP_134	43	29,8569		1,27,4271	no	coding-synonymous	TMEM79	NM_032323.2		1,32,6466	AA,AG,GG		0.3373,0.1136,0.2616		181/395	156255560	34,12964	2200	4299	6499	SO:0001819	synonymous_variant	84283	exon2			GAGGCCGCCTGGC	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"""mattrin"""	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.543G>A	1.37:g.156255560G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_032323	B2RE22|D3DVB8	Silent	SNP	ENST00000405535.2	37	CCDS1138.1																																																																																			G|0.997;A|0.003	0.003	strong		0.682	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323	
EGFLAM	133584	hgsc.bcm.edu	37	5	38409147	38409147	+	Silent	SNP	C	C	T	rs16903964	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:38409147C>T	ENST00000354891.3	+	10	1636	c.1290C>T	c.(1288-1290)aaC>aaT	p.N430N	EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000322350.5_Silent_p.N430N|EGFLAM_ENST00000336740.6_Silent_p.N196N	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	430	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)					GTGGGGAGAACGAACACGGGA	0.502													C|||	235	0.0469249	0.1717	0.0101	5008	,	,		15939	0.001		0.0	False		,,,				2504	0.0				p.N430N	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1290T						PASS	.	C	,,	599,3807		33,533,1637	83.0	80.0	81.0		1290,1290,588	-9.4	0.0	5	dbSNP_123	81	12,8588		0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	,,	33,545,5925	TT,TC,CC		0.1395,13.5951,4.6978	,,	430/1018,430/1010,196/776	38409147	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	133584	exon10			GGAGAACGAACAC	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.1290C>T	5.37:g.38409147C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	37	CCDS56363.1																																																																																			C|0.949;T|0.051	0.051	strong		0.502	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
CSTF2T	23283	hgsc.bcm.edu	37	10	53458167	53458167	+	Silent	SNP	C	C	T	rs3824686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:53458167C>T	ENST00000331173.4	-	1	1188	c.1143G>A	c.(1141-1143)agG>agA	p.R381R	PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	381	Gly-rich.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		ATGGCCCTCCCCTCATCTCAT	0.552													C|||	455	0.0908546	0.0764	0.0461	5008	,	,		16290	0.1369		0.0736	False		,,,				2504	0.1125				p.R381R		Atlas-SNP	.											.	CSTF2T	64	.	0			c.G1143A						PASS	.	C	,,	300,4106	163.6+/-195.4	10,280,1913	84.0	89.0	87.0		,,1143	0.8	1.0	10	dbSNP_107	87	513,8087	143.3+/-199.3	16,481,3803	no	intron,intron,coding-synonymous	PRKG1,CSTF2T	NM_001098512.2,NM_006258.3,NM_015235.2	,,	26,761,5716	TT,TC,CC		5.9651,6.8089,6.251	,,	,,381/617	53458167	813,12193	2203	4300	6503	SO:0001819	synonymous_variant	23283	exon1			CCCTCCCCTCATC	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"""RNA binding motif (RRM) containing"""	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.1143G>A	10.37:g.53458167C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	61	36	0.590164	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Silent	SNP	ENST00000331173.4	37	CCDS7245.1																																																																																			C|0.920;T|0.080	0.080	strong		0.552	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235	
OAS3	4940	hgsc.bcm.edu	37	12	113400593	113400593	+	Missense_Mutation	SNP	C	C	T	rs200778728		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113400593C>T	ENST00000228928.7	+	9	2149	c.1970C>T	c.(1969-1971)aCg>aTg	p.T657M	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	657	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						GGCTTCCGGACGGTGCTGGGG	0.597																																					p.T657M		Atlas-SNP	.											OAS3,NS,carcinoma,-1,1	OAS3	63	1	0			c.C1970T						PASS	.	C	MET/THR	1,4099		0,1,2049	119.0	128.0	125.0		1970	3.2	0.0	12		125	2,8408		0,2,4203	yes	missense	OAS3	NM_006187.2	81	0,3,6252	TT,TC,CC		0.0238,0.0244,0.024	probably-damaging	657/1088	113400593	3,12507	2050	4205	6255	SO:0001583	missense	4940	exon9			TCCGGACGGTGCT	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.1970C>T	12.37:g.113400593C>T	ENSP00000228928:p.Thr657Met	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476130	0.44044	2.44E-4	2.38E-4	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.59224	0.28	4.1	3.19	0.36642	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.	.	.	.	T	0.76271	0.3964	M	0.87900	2.915	0.18873	N	0.999981	D	0.89917	1.0	D	0.77557	0.99	T	0.64415	-0.6413	9	0.87932	D	0	.	8.9438	0.35747	0.2222:0.7778:0.0:0.0	.	657	Q9Y6K5	OAS3_HUMAN	M	657;656	ENSP00000228928:T657M	ENSP00000228928:T657M	T	+	2	0	OAS3	111884976	0.568000	0.26635	0.002000	0.10522	0.012000	0.07955	2.416000	0.44644	0.917000	0.36895	0.655000	0.94253	ACG	.	.	weak		0.597	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057720	46057720	+	Missense_Mutation	SNP	A	A	C	rs4818949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057720A>C	ENST00000380095.1	+	1	448	c.386A>C	c.(385-387)cAg>cCg	p.Q129P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	129	15 X 5 AA repeats of C-C-X(3).		Q -> P (in dbSNP:rs4818949).			keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TGCTGCCAGCAGTCTAGCTGC	0.607													A|||	1395	0.278554	0.4773	0.2233	5008	,	,		23323	0.0526		0.2425	False		,,,				2504	0.319				p.Q129P		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.A386C						PASS	.	A	,PRO/GLN	1971,2435	556.5+/-379.5	445,1081,677	259.0	234.0	243.0		,386	-0.1	1.0	21	dbSNP_111	243	2165,6435	369.3+/-335.4	281,1603,2416	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,76	726,2684,3093	CC,CA,AA		25.1744,44.7345,31.8007	,benign	,129/252	46057720	4136,8870	2203	4300	6503	SO:0001583	missense	353333	exon1			GCCAGCAGTCTAG	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.386A>C	21.37:g.46057720A>C	ENSP00000369438:p.Gln129Pro	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	541	0.24771062271062272	232	0.4715447154471545	88	0.2430939226519337	31	0.05419580419580419	190	0.25065963060686014	a	6.718	0.501193	0.12822	0.447345	0.251744	ENSG00000221859	ENST00000380095	T	0.01165	5.24	3.04	-0.0501	0.13832	.	.	.	.	.	T	0.00012	0.0000	L	0.52364	1.645	0.37030	P	0.10338099999999995	B	0.15141	0.012	B	0.14023	0.01	T	0.17167	-1.0378	8	0.16896	T	0.51	.	4.4006	0.11385	0.4554:0.3648:0.0:0.1798	rs4818949;rs56858729	129	P60014	KR10A_HUMAN	P	129	ENSP00000369438:Q129P	ENSP00000369438:Q129P	Q	+	2	0	KRTAP10-10	44882148	0.000000	0.05858	0.998000	0.56505	0.378000	0.30076	0.029000	0.13666	0.190000	0.20209	0.378000	0.23410	CAG	A|0.711;C|0.289	0.289	strong		0.607	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
KIF1B	23095	hgsc.bcm.edu	37	1	10435324	10435324	+	Silent	SNP	C	C	A	rs11121552	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:10435324C>A	ENST00000377086.1	+	48	5503	c.5301C>A	c.(5299-5301)acC>acA	p.T1767T	KIF1B_ENST00000263934.6_Silent_p.T1721T|KIF1B_ENST00000377081.1_Silent_p.T1767T			O60333	KIF1B_HUMAN	kinesin family member 1B	1767	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)	p.T1721T(1)		breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CACCAAACACCTTTGCTGTCT	0.478													C|||	1160	0.231629	0.0575	0.3199	5008	,	,		21284	0.2827		0.3091	False		,,,				2504	0.272				p.T1721T		Atlas-SNP	.											KIF1B,NS,carcinoma,0,1	KIF1B	242	1	1	Substitution - coding silent(1)	stomach(1)	c.C5163A						PASS	.	C		413,3993	200.8+/-224.0	28,357,1818	97.0	93.0	94.0		5163	0.1	1.0	1	dbSNP_120	94	2585,6015	419.1+/-353.0	409,1767,2124	no	coding-synonymous	KIF1B	NM_015074.3		437,2124,3942	AA,AC,CC		30.0581,9.3736,23.0509		1721/1771	10435324	2998,10008	2203	4300	6503	SO:0001819	synonymous_variant	23095	exon46			AAACACCTTTGCT	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.5301C>A	1.37:g.10435324C>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	120	9	0.075	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				C|0.759;A|0.241	0.241	strong		0.478	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
C11orf21	29125	hgsc.bcm.edu	37	11	2320884	2320884	+	Silent	SNP	A	A	G	rs1501466	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2320884A>G	ENST00000381153.3	-	3	452	c.201T>C	c.(199-201)ggT>ggC	p.G67G	TSPAN32_ENST00000381121.3_5'Flank|C11orf21_ENST00000470369.1_5'UTR|TSPAN32_ENST00000182290.4_5'Flank			Q9P2W6	CK021_HUMAN	chromosome 11 open reading frame 21	67						cytoplasm (GO:0005737)											GAACAAGGGCACCATGGGCGG	0.627													G|||	1056	0.210863	0.3865	0.2262	5008	,	,		15372	0.0704		0.164	False		,,,				2504	0.1554				p.G113G		Atlas-SNP	.											C11orf21,NS,carcinoma,-2,1	C11orf21	11	1	0			c.T339C						PASS	.	G		494,890		82,330,280	119.0	127.0	125.0		339	-0.2	0.0	11	dbSNP_88	125	538,2644		49,440,1102	no	coding-synonymous	C11orf21	NM_001142946.1		131,770,1382	GG,GA,AA		16.9076,35.6936,22.6018		113/179	2320884	1032,3534	692	1591	2283	SO:0001819	synonymous_variant	29125	exon4			AAGGGCACCATGG	AB029488	CCDS44518.1	11p15.5	2012-08-09			ENSG00000110665	ENSG00000110665			13231	protein-coding gene	gene with protein product		611033				11054561	Standard	NM_001142946		Approved		uc009ydj.2	Q9P2W6	OTTHUMG00000009759	ENST00000381153.3:c.201T>C	11.37:g.2320884A>G		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_001142946		Silent	SNP	ENST00000381153.3	37																																																																																				A|0.799;G|0.201	0.201	strong		0.627	C11orf21-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000026908.2	NM_001142946	
EIF2S3	1968	hgsc.bcm.edu	37	X	24075862	24075862	+	Missense_Mutation	SNP	A	A	G	rs16997659	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:24075862A>G	ENST00000253039.4	+	4	627	c.374A>G	c.(373-375)aAa>aGa	p.K125R		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	125	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.		K -> R (in dbSNP:rs16997659).		cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						GGGAACTTCAAATTAGTCAGG	0.423													A|||	386	0.102252	0.0219	0.1023	3775	,	,		11437	0.006		0.1123	False		,,,				2504	0.1708				p.K125R		Atlas-SNP	.											.	EIF2S3	31	.	0			c.A374G						PASS	.	A	ARG/LYS	146,3689		3,125,15,1504,556	62.0	59.0	60.0		374	3.8	1.0	X	dbSNP_123	60	1077,5651		59,671,288,1698,1584	yes	missense	EIF2S3	NM_001415.3	26	62,796,303,3202,2140	GG,GA,G,AA,A		16.0077,3.807,11.5782	benign	125/473	24075862	1223,9340	2203	4300	6503	SO:0001583	missense	1968	exon4			ACTTCAAATTAGT	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"""eukaryotic translation initiation factor 2G"""	300161	"""eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"""	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.374A>G	X.37:g.24075862A>G	ENSP00000253039:p.Lys125Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001415	B5BTZ4	Missense_Mutation	SNP	ENST00000253039.4	37	CCDS14210.1	142	0.08559373116335142	7	0.014644351464435146	27	0.07758620689655173	2	0.0035087719298245615	61	0.08739255014326648	A	10.25	1.297530	0.23650	0.03807	0.160077	ENSG00000130741	ENST00000253039	T	0.70986	-0.53	5.02	3.85	0.44370	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	T	0.00300	0.0009	.	.	.	0.21950	P	0.999451154	B	0.02656	0.0	B	0.10450	0.005	T	0.06570	-1.0819	8	0.18276	T	0.48	.	10.0729	0.42343	0.9192:0.0:0.0808:0.0	rs16997659;rs16997659	125	P41091	IF2G_HUMAN	R	125	ENSP00000253039:K125R	ENSP00000253039:K125R	K	+	2	0	EIF2S3	23985783	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	6.988000	0.76212	0.675000	0.31264	0.412000	0.27726	AAA	A|0.888;0|0.013	.	strong		0.423	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415	
SETX	23064	hgsc.bcm.edu	37	9	135139901	135139901	+	Missense_Mutation	SNP	T	T	C	rs1056899	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135139901T>C	ENST00000224140.5	-	26	7941	c.7759A>G	c.(7759-7761)Ata>Gta	p.I2587V	SETX_ENST00000477049.1_5'UTR|SETX_ENST00000372169.2_Missense_Mutation_p.I2616V|SETX_ENST00000393220.1_Missense_Mutation_p.I2554V	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin	2587			I -> V (in dbSNP:rs1056899). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		cell death (GO:0008219)|circadian rhythm (GO:0007623)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|RNA processing (GO:0006396)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			breast(7)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(1)|lung(36)|ovary(2)|prostate(2)|skin(1)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	97		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000171)		GGCTGCTGTATATGGCTCAGG	0.632													C|||	2698	0.538738	0.8094	0.3487	5008	,	,		15929	0.6835		0.2694	False		,,,				2504	0.4356				p.I2587V		Atlas-SNP	.											.	SETX	234	.	0			c.A7759G						PASS	.	C	VAL/ILE	3227,1179	410.0+/-335.2	1199,829,175	65.0	76.0	72.0		7759	-3.8	0.0	9	dbSNP_86	72	2550,6050	690.4+/-404.4	374,1802,2124	yes	missense	SETX	NM_015046.5	29	1573,2631,2299	CC,CT,TT		29.6512,26.759,44.418	benign	2587/2678	135139901	5777,7229	2203	4300	6503	SO:0001583	missense	23064	exon26			GCTGTATATGGCT	AB014525	CCDS6947.1	9q34	2014-09-17	2005-11-29	2005-11-29	ENSG00000107290	ENSG00000107290			445	protein-coding gene	gene with protein product		608465	"""amyotrophic lateral sclerosis 4"", ""spinocerebellar ataxia, recessive, non-Friedreich type 1"""	ALS4, SCAR1		9497266, 11022012	Standard	NM_015046		Approved	KIAA0625, AOA2	uc004cbk.3	Q7Z333	OTTHUMG00000020834	ENST00000224140.5:c.7759A>G	9.37:g.135139901T>C	ENSP00000224140:p.Ile2587Val	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Missense_Mutation	SNP	ENST00000224140.5	37	CCDS6947.1	1114	0.51007326007326	380	0.7723577235772358	137	0.3784530386740331	395	0.6905594405594405	202	0.26649076517150394	C	0.692	-0.794242	0.02862	0.73241	0.296512	ENSG00000107290	ENST00000224140;ENST00000436441;ENST00000372169;ENST00000393220	D;D;D;D	0.89681	-1.95;-2.55;-2.03;-1.66	5.0	-3.8	0.04307	.	1.973910	0.02590	N	0.099880	T	0.00012	0.0000	N	0.04880	-0.145	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	0.48581	-0.9023	9	0.02654	T	1	.	0.0833	0.00033	0.3191:0.1632:0.2101:0.3076	rs1056899;rs3197515;rs3739926;rs59785171;rs1056899	2554;2587;2616	Q7Z333-3;Q7Z333;Q7Z333-4	.;SETX_HUMAN;.	V	2587;858;2616;2554	ENSP00000224140:I2587V;ENSP00000409143:I858V;ENSP00000361242:I2616V;ENSP00000376913:I2554V	ENSP00000224140:I2587V	I	-	1	0	SETX	134129722	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.111000	0.03303	-0.616000	0.05671	-1.383000	0.01170	ATA	T|0.505;C|0.495	0.495	strong		0.632	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046	
RASSF7	8045	hgsc.bcm.edu	37	11	562219	562219	+	Missense_Mutation	SNP	C	C	G	rs2242183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:562219C>G	ENST00000397583.3	+	3	698	c.265C>G	c.(265-267)Ccc>Gcc	p.P89A	RASSF7_ENST00000524468.1_3'UTR|RP11-496I9.1_ENST00000527620.1_RNA|RP11-496I9.1_ENST00000527113.1_RNA|RASSF7_ENST00000431809.1_Missense_Mutation_p.P89A|C11orf35_ENST00000329451.3_5'Flank|RASSF7_ENST00000344375.4_Missense_Mutation_p.P89A|RASSF7_ENST00000397582.3_Missense_Mutation_p.P89A|RASSF7_ENST00000454668.2_Missense_Mutation_p.P89A	NM_003475.3	NP_003466.1	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	89	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.		P -> A (in dbSNP:rs2242183). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(3)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCGCACAGGGCCCAGCCTAGC	0.657													C|||	537	0.107228	0.0053	0.0648	5008	,	,		17268	0.3016		0.0656	False		,,,				2504	0.1176				p.P89A	Pancreas(184;1170 3913 7268)	Atlas-SNP	.											.	RASSF7	22	.	0			c.C265G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	64,4342	57.4+/-93.9	0,64,2139	47.0	46.0	47.0		265,265,265	3.8	1.0	11	dbSNP_98	47	465,8135	128.5+/-186.7	7,451,3842	yes	missense,missense,missense	RASSF7	NM_001143993.1,NM_001143994.1,NM_003475.3	27,27,27	7,515,5981	GG,GC,CC		5.407,1.4526,4.0674	probably-damaging,probably-damaging,probably-damaging	89/338,89/321,89/374	562219	529,12477	2203	4300	6503	SO:0001583	missense	8045	exon3			ACAGGGCCCAGCC	M91083	CCDS7702.1, CCDS44505.1, CCDS44506.1	11p15.5	2008-02-22	2008-02-22	2005-09-14	ENSG00000099849	ENSG00000099849			1166	protein-coding gene	gene with protein product		143023	"""chromosome 11 open reading frame 13"""	C11orf13		1339391	Standard	NM_001143993		Approved	HRC1, HRAS1	uc001lqc.3	Q02833	OTTHUMG00000132004	ENST00000397583.3:c.265C>G	11.37:g.562219C>G	ENSP00000380713:p.Pro89Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001143994	G5E9N9|Q3KP41|Q3KP42	Missense_Mutation	SNP	ENST00000397583.3	37	CCDS7702.1	264	0.12087912087912088	4	0.008130081300813009	23	0.06353591160220995	183	0.31993006993006995	54	0.0712401055408971	C	22.7	4.318867	0.81469	0.014526	0.05407	ENSG00000099849	ENST00000431809;ENST00000397582;ENST00000344375;ENST00000397583;ENST00000454668	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	3.81	3.81	0.43845	Ras-association (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.72894	2.215	0.09310	P	0.99999999876555	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.997	T	0.11792	-1.0573	9	0.30078	T	0.28	-3.5329	15.8892	0.79279	0.0:1.0:0.0:0.0	rs2242183;rs2242183	89;89;89	G5E9N9;Q02833;Q02833-2	.;RASF7_HUMAN;.	A	89	ENSP00000403068:P89A;ENSP00000380712:P89A;ENSP00000344226:P89A;ENSP00000380713:P89A;ENSP00000405606:P89A	ENSP00000344226:P89A	P	+	1	0	RASSF7	552219	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	4.717000	0.61923	1.975000	0.57531	0.561000	0.74099	CCC	C|0.930;G|0.070	0.070	strong		0.657	RASSF7-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254972.2	NM_003475	
ZNF30	90075	hgsc.bcm.edu	37	19	35422808	35422808	+	Missense_Mutation	SNP	C	C	T	rs10422961	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35422808C>T	ENST00000601142.1	+	3	308	c.71C>T	c.(70-72)tCc>tTc	p.S24F	ZNF30_ENST00000439785.1_Missense_Mutation_p.S24F|ZNF30_ENST00000601957.1_Missense_Mutation_p.S24F|ZNF30_ENST00000426813.2_5'UTR|ZNF30_ENST00000303586.7_Missense_Mutation_p.S24F			P17039	ZNF30_HUMAN	zinc finger protein 30	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.			S -> F (in Ref. 1; BAG58432). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)	16	all_lung(56;8.38e-08)|Lung NSC(56;1.31e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)	GBM - Glioblastoma multiforme(1328;0.0265)		ATAGCCTTCTCCCAGCAGGAG	0.463													C|||	1443	0.288139	0.2693	0.232	5008	,	,		20449	0.2202		0.3618	False		,,,				2504	0.3476				p.S24F		Atlas-SNP	.											ZNF30,colon,carcinoma,0,1	ZNF30	44	1	0			c.C71T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	1094,3212		155,784,1214	79.0	85.0	83.0		71,71,71	1.5	1.0	19	dbSNP_119	83	2777,5777		466,1845,1966	yes	missense,missense,missense	ZNF30	NM_001099437.1,NM_001099438.1,NM_194325.2	155,155,155	621,2629,3180	TT,TC,CC		32.4643,25.4064,30.1011	benign,benign,benign	24/625,24/625,24/624	35422808	3871,8989	2153	4277	6430	SO:0001583	missense	90075	exon3			CCTTCTCCCAGCA	X52359	CCDS46044.1, CCDS46045.1	19q13.13	2013-01-08	2006-05-10			ENSG00000168661		"""Zinc fingers, C2H2-type"", ""-"""	13090	protein-coding gene	gene with protein product			"""zinc finger protein 30 (KOX 28)"""				Standard	NM_001099437		Approved	KOX28, DKFZp686N19164, FLJ20562	uc010edq.1	P17039		ENST00000601142.1:c.71C>T	19.37:g.35422808C>T	ENSP00000469954:p.Ser24Phe	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	90	0.978261	NM_001099438	A5PLP1|A8K320|B4DIC0|Q6N068	Missense_Mutation	SNP	ENST00000601142.1	37	CCDS46045.1	637	0.2916666666666667	128	0.2601626016260163	93	0.2569060773480663	136	0.23776223776223776	280	0.36939313984168864	C	11.43	1.637390	0.29157	0.254064	0.324643	ENSG00000168661	ENST00000439785;ENST00000303586	T;T	0.02944	4.1;4.1	1.55	1.55	0.23275	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	H	0.98701	4.305	0.09310	P	0.999999999831031	P;B	0.39903	0.694;0.031	B;B	0.41236	0.351;0.021	T	0.15235	-1.0444	8	0.72032	D	0.01	.	6.5714	0.22541	0.0:1.0:0.0:0.0	rs10422961;rs10422961	24;24	P17039-2;P17039	.;ZNF30_HUMAN	F	24	ENSP00000403441:S24F;ENSP00000303889:S24F	ENSP00000303889:S24F	S	+	2	0	ZNF30	40114648	0.676000	0.27567	0.991000	0.47740	0.971000	0.66376	1.149000	0.31626	1.167000	0.42706	0.514000	0.50259	TCC	C|0.700;T|0.300	0.300	strong		0.463	ZNF30-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464432.1	NM_194325	
PTCRA	171558	hgsc.bcm.edu	37	6	42891022	42891022	+	Missense_Mutation	SNP	G	G	A	rs9471966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42891022G>A	ENST00000304672.1	+	2	397	c.316G>A	c.(316-318)Gtc>Atc	p.V106I	PTCRA_ENST00000441198.1_Missense_Mutation_p.V81I|PTCRA_ENST00000446507.1_Intron	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	106			V -> I (in dbSNP:rs9471966). {ECO:0000269|PubMed:15489334}.		negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			GGAGCCTTTGGTCTGCCACAC	0.632													G|||	1204	0.240415	0.3994	0.2133	5008	,	,		21832	0.0238		0.2893	False		,,,				2504	0.2178				p.V106I		Atlas-SNP	.											.	PTCRA	24	.	0			c.G316A						PASS	.	G	ILE/VAL	1522,2884	483.3+/-359.7	264,994,945	82.0	68.0	73.0		316	4.8	1.0	6	dbSNP_119	73	2278,6322	383.5+/-340.8	285,1708,2307	yes	missense	PTCRA	NM_138296.2	29	549,2702,3252	AA,AG,GG		26.4884,34.5438,29.2173	benign	106/282	42891022	3800,9206	2203	4300	6503	SO:0001583	missense	171558	exon2			CCTTTGGTCTGCC	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.316G>A	6.37:g.42891022G>A	ENSP00000304447:p.Val106Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	181	82	0.453039	NM_138296	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	511	0.23397435897435898	201	0.40853658536585363	83	0.2292817679558011	15	0.026223776223776224	212	0.2796833773087071	G	23.0	4.362653	0.82353	0.345438	0.264884	ENSG00000171611	ENST00000304672;ENST00000441198	T;T	0.54279	0.58;0.58	5.69	4.82	0.62117	Immunoglobulin-like fold (1);	0.000000	0.42682	D	0.000670	T	0.46698	0.1406	L	0.36672	1.1	0.09310	P	0.9999999999999986	D;D	0.65815	0.995;0.98	P;P	0.61800	0.894;0.691	T	0.51919	-0.8644	9	0.52906	T	0.07	-35.6978	9.6018	0.39609	0.0925:0.0:0.9075:0.0	rs9471966;rs52795622;rs58242015;rs9471966	81;106	Q6ISU1-3;Q6ISU1	.;PTCRA_HUMAN	I	106;81	ENSP00000304447:V106I;ENSP00000409550:V81I	ENSP00000304447:V106I	V	+	1	0	PTCRA	42999000	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	3.635000	0.54309	2.668000	0.90789	0.650000	0.86243	GTC	G|0.729;A|0.271	0.271	strong		0.632	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
VEPH1	79674	hgsc.bcm.edu	37	3	157081324	157081324	+	Missense_Mutation	SNP	A	A	G	rs11918974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:157081324A>G	ENST00000362010.2	-	9	1871	c.1564T>C	c.(1564-1566)Tca>Cca	p.S522P	VEPH1_ENST00000392832.2_Missense_Mutation_p.S522P|RP11-550I24.2_ENST00000487238.1_RNA|VEPH1_ENST00000392833.2_Missense_Mutation_p.S522P|VEPH1_ENST00000543418.1_Missense_Mutation_p.S522P	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	522			S -> P (in dbSNP:rs11918974). {ECO:0000269|PubMed:15489334}.			plasma membrane (GO:0005886)		p.S522P(1)		autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ACAGTTTCTGACAAATTCTCT	0.383													G|||	1255	0.250599	0.093	0.4971	5008	,	,		17050	0.3512		0.2694	False		,,,				2504	0.1656				p.S522P		Atlas-SNP	.											VEPH1,colon,carcinoma,0,2	VEPH1	129	2	1	Substitution - Missense(1)	stomach(1)	c.T1564C						PASS	.	G	PRO/SER,PRO/SER,PRO/SER	507,3899	773.6+/-414.0	34,439,1730	114.0	123.0	120.0		1564,1564,1564	4.6	0.8	3	dbSNP_120	120	2176,6424	711.4+/-405.8	285,1606,2409	yes	missense,missense,missense	VEPH1	NM_001167911.1,NM_001167912.1,NM_024621.2	74,74,74	319,2045,4139	GG,GA,AA		25.3023,11.507,20.6289	benign,benign,benign	522/789,522/834,522/834	157081324	2683,10323	2203	4300	6503	SO:0001583	missense	79674	exon9			TTTCTGACAAATT	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1564T>C	3.37:g.157081324A>G	ENSP00000354919:p.Ser522Pro	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_001167911	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	37	CCDS3179.1	613	0.2806776556776557	48	0.0975609756097561	157	0.43370165745856354	211	0.3688811188811189	197	0.2598944591029024	G	2.489	-0.317941	0.05386	0.11507	0.253023	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.12569	2.67;2.8;2.67;2.8	5.5	4.6	0.57074	.	0.224833	0.47093	N	0.000255	T	0.00012	0.0000	N	0.00926	-1.1	0.09310	P	0.999999999691026	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46992	-0.9151	9	0.02654	T	1	-0.3419	7.5867	0.27998	0.1423:0.1362:0.7215:0.0	rs11918974;rs60788773;rs11918974	522;522	Q14D04-2;Q14D04	.;MELT_HUMAN	P	522	ENSP00000376578:S522P;ENSP00000354919:S522P;ENSP00000446258:S522P;ENSP00000376577:S522P	ENSP00000354919:S522P	S	-	1	0	VEPH1	158564018	0.990000	0.36364	0.766000	0.31476	0.726000	0.41606	0.919000	0.28692	0.671000	0.31185	-0.119000	0.15052	TCA	A|0.767;G|0.233	0.233	strong		0.383	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296521	39296521	+	Silent	SNP	G	G	A	rs201084737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39296521G>A	ENST00000345847.4	-	1	218	c.219C>T	c.(217-219)acC>acT	p.T73T		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	73	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						TCCTGCAGCAGGTGGTCTgac	0.657																																					p.T73T		Atlas-SNP	.											.	KRTAP4-6	46	.	0			c.C219T						PASS	.																																			SO:0001819	synonymous_variant	81871	exon1			GCAGCAGGTGGTC	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.219C>T	17.37:g.39296521G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			G|0.996;A|0.004	0.004	strong		0.657	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
SLC12A7	10723	hgsc.bcm.edu	37	5	1063998	1063998	+	Silent	SNP	G	G	A	rs7722287	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:1063998G>A	ENST00000264930.5	-	20	2743	c.2700C>T	c.(2698-2700)taC>taT	p.Y900Y	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	900					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	TGCGCAAGTGGTACAAGAACA	0.637													G|||	1486	0.296725	0.0295	0.3588	5008	,	,		9752	0.3175		0.4523	False		,,,				2504	0.4325				p.Y900Y		Atlas-SNP	.											SLC12A7,NS,carcinoma,0,1	SLC12A7	97	1	0			c.C2700T						PASS	.	G		450,3954	214.5+/-233.7	19,412,1771	137.0	103.0	114.0		2700	3.4	1.0	5	dbSNP_116	114	4044,4556	557.1+/-387.0	935,2174,1191	no	coding-synonymous	SLC12A7	NM_006598.2		954,2586,2962	AA,AG,GG		47.0233,10.218,34.5586		900/1084	1063998	4494,8510	2202	4300	6502	SO:0001819	synonymous_variant	10723	exon20			CAAGTGGTACAAG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2700C>T	5.37:g.1063998G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	249	130	0.522088	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1	695	0.3182234432234432	20	0.04065040650406504	136	0.3756906077348066	180	0.3146853146853147	359	0.4736147757255937	G	6.481	0.456993	0.12283	0.10218	0.470233	ENSG00000113504	ENST00000513223	.	.	.	4.25	3.37	0.38596	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.49244	-0.8960	3	.	.	.	.	7.5063	0.27547	0.206:0.0:0.794:0.0	rs7722287;rs35783179;rs57920515;rs7722287	.	.	.	S	258	.	.	P	-	1	0	SLC12A7	1116998	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	2.387000	0.44389	0.773000	0.33404	0.305000	0.20034	CCA	G|0.675;A|0.325	0.325	strong		0.637	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
RAB3D	9545	hgsc.bcm.edu	37	19	11436221	11436221	+	Silent	SNP	A	A	G	rs12981706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11436221A>G	ENST00000222120.3	-	5	773	c.513T>C	c.(511-513)aaT>aaC	p.N171N	RAB3D_ENST00000589655.1_Silent_p.N171N|CTC-510F12.4_ENST00000586356.1_RNA|CTC-510F12.6_ENST00000586051.1_RNA|TSPAN16_ENST00000316737.1_Intron	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	171					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						CCTGCTTCACATTGATGTTCT	0.557													A|||	286	0.0571086	0.1762	0.0187	5008	,	,		14659	0.0		0.0318	False		,,,				2504	0.0082				p.N171N		Atlas-SNP	.											.	RAB3D	24	.	0			c.T513C						PASS	.	A	,	617,3789	268.6+/-268.5	43,531,1629	146.0	132.0	136.0		513,	-6.2	1.0	19	dbSNP_121	136	293,8307	108.0+/-168.7	3,287,4010	no	coding-synonymous,intron	RAB3D,TSPAN16	NM_004283.3,NM_012466.2	,	46,818,5639	GG,GA,AA		3.407,14.0036,6.9968	,	171/220,	11436221	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	9545	exon5			CTTCACATTGATG	AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"""RAB, member RAS oncogene"""	9779	protein-coding gene	gene with protein product	"""Rab3D upregulated with myeloid differentiation"", ""glioblastoma overexpressed"""	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.513T>C	19.37:g.11436221A>G		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_004283		Silent	SNP	ENST00000222120.3	37	CCDS12257.1																																																																																			A|0.939;G|0.061;T|0.000	0.061	strong		0.557	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283	
SLX4	84464	hgsc.bcm.edu	37	16	3656645	3656645	+	Missense_Mutation	SNP	A	A	G	rs147826749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3656645A>G	ENST00000294008.3	-	3	1230	c.590T>C	c.(589-591)gTg>gCg	p.V197A		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	197	Interaction with SLX4IP, ERCC4 and MSH2.		V -> A (in dbSNP:rs147826749). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GGGACTTGGCACTGCTGTTGT	0.527								Direct reversal of damage					A|||	2	0.000399361	0.0	0.0029	5008	,	,		19478	0.0		0.0	False		,,,				2504	0.0				p.V197A		Atlas-SNP	.											.	SLX4	173	.	0			c.T590C						PASS	.	A	ALA/VAL	1,4393	2.1+/-5.4	0,1,2196	167.0	166.0	167.0		590	-3.5	0.0	16	dbSNP_134	167	26,8574	18.5+/-59.3	0,26,4274	yes	missense	SLX4	NM_032444.2	64	0,27,6470	GG,GA,AA		0.3023,0.0228,0.2078	benign	197/1835	3656645	27,12967	2197	4300	6497	SO:0001583	missense	84464	exon3			CTTGGCACTGCTG	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.590T>C	16.37:g.3656645A>G	ENSP00000294008:p.Val197Ala	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	186	90	0.483871	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	A	10.77	1.443209	0.25987	2.28E-4	0.003023	ENSG00000188827	ENST00000294008	T	0.01369	4.97	5.03	-3.52	0.04682	.	2.372270	0.01586	N	0.021329	T	0.00815	0.0027	N	0.17474	0.49	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.48068	-0.9067	10	0.18276	T	0.48	.	6.9022	0.24288	0.4116:0.1398:0.4486:0.0	.	197	Q8IY92	SLX4_HUMAN	A	197	ENSP00000294008:V197A	ENSP00000294008:V197A	V	-	2	0	SLX4	3596646	0.000000	0.05858	0.002000	0.10522	0.452000	0.32318	-0.831000	0.04405	-0.925000	0.03775	-0.441000	0.05720	GTG	A|0.997;G|0.003	0.003	strong		0.527	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
ZNF333	84449	hgsc.bcm.edu	37	19	14829345	14829345	+	Silent	SNP	C	C	T	rs147332855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14829345C>T	ENST00000292530.6	+	12	1297	c.1206C>T	c.(1204-1206)gcC>gcT	p.A402A	ZNF333_ENST00000536363.1_Silent_p.A293A|ZNF333_ENST00000540689.2_Intron	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	402					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						GTGGGCAAGCCTTCAAATATT	0.443													C|||	5	0.000998403	0.0	0.0043	5008	,	,		20841	0.0		0.001	False		,,,				2504	0.001				p.A402A	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.C1206T						PASS	.	C		0,4406		0,0,2203	58.0	56.0	57.0		1206	1.1	0.9	19	dbSNP_134	57	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	ZNF333	NM_032433.2		0,13,6490	TT,TC,CC		0.1512,0.0,0.1		402/666	14829345	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	84449	exon12			GCAAGCCTTCAAA		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"""Zinc fingers, C2H2-type"", ""-"""	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.1206C>T	19.37:g.14829345C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Silent	SNP	ENST00000292530.6	37	CCDS12316.1																																																																																			C|0.999;T|0.001	0.001	strong		0.443	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433	
CRNN	49860	hgsc.bcm.edu	37	1	152383373	152383373	+	Missense_Mutation	SNP	T	T	A	rs571572587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152383373T>A	ENST00000271835.3	-	3	247	c.185A>T	c.(184-186)gAt>gTt	p.D62V	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	62	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)			GTGGTCTTCATCCAGCAGACG	0.537													T|||	4	0.000798722	0.0	0.0	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0041				p.D62V		Atlas-SNP	.											.	CRNN	78	.	0			c.A185T						PASS	.						45.0	47.0	47.0					1																	152383373		2196	4287	6483	SO:0001583	missense	49860	exon3			TCTTCATCCAGCA	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.185A>T	1.37:g.152383373T>A	ENSP00000271835:p.Asp62Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.321521	0.60634	.	.	ENSG00000143536	ENST00000271835;ENST00000451038	T	0.55234	0.53	4.73	4.73	0.59995	EF-hand-like domain (1);	0.000000	0.48286	D	0.000186	T	0.77458	0.4133	H	0.97940	4.11	0.58432	D	0.999995	D	0.89917	1.0	D	0.85130	0.997	D	0.84507	0.0620	10	0.87932	D	0	.	10.5413	0.45035	0.0:0.0:0.0:1.0	.	62	Q9UBG3	CRNN_HUMAN	V	62	ENSP00000271835:D62V	ENSP00000271835:D62V	D	-	2	0	CRNN	150649997	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	3.886000	0.56190	1.983000	0.57843	0.254000	0.18369	GAT	.	.	none		0.537	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190	
MTG2	26164	hgsc.bcm.edu	37	20	60768497	60768497	+	Silent	SNP	C	C	T	rs2236527	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60768497C>T	ENST00000370823.3	+	2	39	c.21C>T	c.(19-21)ttC>ttT	p.F7F	MTG2_ENST00000536470.1_Intron|MTG2_ENST00000436421.2_Silent_p.F7F	NM_015666.3	NP_056481.1	Q9H4K7	MTG2_HUMAN	mitochondrial ribosome-associated GTPase 2	7					GTP catabolic process (GO:0006184)|regulation of mitochondrial translation (GO:0070129)|regulation of respiratory system process (GO:0044065)|ribosome biogenesis (GO:0042254)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial ribosome (GO:0005761)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)										CAAGGTGTTTCTCAGCAAGAT	0.547													C|||	1094	0.21845	0.174	0.1282	5008	,	,		20152	0.4881		0.1173	False		,,,				2504	0.1687				p.F7F		Atlas-SNP	.											.	GTPBP5	43	.	0			c.C21T						PASS	.	C		591,3815	262.8+/-265.1	36,519,1648	101.0	103.0	102.0		21	4.1	0.0	20	dbSNP_98	102	1032,7568	219.1+/-257.3	64,904,3332	no	coding-synonymous	GTPBP5	NM_015666.3		100,1423,4980	TT,TC,CC		12.0,13.4135,12.4789		7/407	60768497	1623,11383	2203	4300	6503	SO:0001819	synonymous_variant	26164	exon2			GTGTTTCTCAGCA	AK001603	CCDS13492.1	20q13.33	2013-05-24	2013-05-24	2013-05-24	ENSG00000101181	ENSG00000101181			16239	protein-coding gene	gene with protein product		610919	"""GTP-binding protein 5 (putative)"", ""GTP binding protein 5 (putative)"""	GTPBP5		17054726, 23396448	Standard	NM_015666		Approved	FLJ10741, dJ1005F21.2, ObgH1		Q9H4K7	OTTHUMG00000032897	ENST00000370823.3:c.21C>T	20.37:g.60768497C>T		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	209	98	0.4689	NM_015666	A6NDR3|B4DR85|Q96I17|Q9NVG9|Q9UFR4	Silent	SNP	ENST00000370823.3	37	CCDS13492.1																																																																																			C|0.827;T|0.173	0.173	strong		0.547	MTG2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079989.1	NM_015666	
HYI	81888	hgsc.bcm.edu	37	1	43917888	43917888	+	Silent	SNP	C	C	G	rs41270373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43917888C>G	ENST00000372425.4	-	3	609	c.414G>C	c.(412-414)ggG>ggC	p.G138G	HYI-AS1_ENST00000444386.1_RNA|HYI_ENST00000583037.1_Silent_p.G65G|SZT2_ENST00000372442.1_3'UTR|HYI_ENST00000372432.1_Silent_p.G138G|HYI_ENST00000486909.1_Silent_p.G138G|HYI_ENST00000372426.1_Silent_p.G90G|SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372434.1_Silent_p.G163G			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	138							hydroxypyruvate isomerase activity (GO:0008903)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGCCAAAACCCCAGCTGCAT	0.572													C|||	49	0.00978435	0.0	0.0231	5008	,	,		22722	0.0		0.0308	False		,,,				2504	0.002				p.G163G		Atlas-SNP	.											.	HYI	23	.	0			c.G489C						PASS	.	C	,,	26,4380	31.7+/-61.6	1,24,2178	174.0	153.0	160.0		414,,414	-1.0	1.0	1	dbSNP_127	160	243,8357	95.0+/-156.8	3,237,4060	no	coding-synonymous,utr-3,coding-synonymous	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	,,	4,261,6238	GG,GC,CC		2.8256,0.5901,2.0683	,,	138/278,,138/248	43917888	269,12737	2203	4300	6503	SO:0001819	synonymous_variant	81888	exon4			CAAAACCCCAGCT		CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"""hydroxypyruvate isomerase homolog (E. coli)"""			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502	ENST00000372425.4:c.414G>C	1.37:g.43917888C>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	94	51	0.542553	NM_001243526	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Silent	SNP	ENST00000372425.4	37	CCDS53309.1	33	0.01510989010989011	0	0.0	9	0.024861878453038673	0	0.0	24	0.0316622691292876	C	8.031	0.761814	0.15914	0.005901	0.028256	ENSG00000178922	ENST00000470662;ENST00000487366	T;T	0.40476	1.03;1.03	5.38	-1.03	0.10102	.	0.308735	0.38111	N	0.001809	T	0.11879	0.0289	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02654	-1.1128	7	0.18710	T	0.47	.	6.2682	0.20939	0.1866:0.2033:0.5363:0.0739	rs41270373	.	.	.	A	57;62	ENSP00000428803:G57A;ENSP00000428501:G62A	ENSP00000428803:G57A	G	-	2	0	HYI	43690475	0.752000	0.28338	0.967000	0.41034	0.766000	0.43426	0.384000	0.20668	0.028000	0.15324	0.462000	0.41574	GGG	C|0.981;G|0.019	0.019	strong		0.572	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207	
C2orf74	339804	hgsc.bcm.edu	37	2	61389737	61389737	+	Missense_Mutation	SNP	T	T	G	rs1729674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:61389737T>G	ENST00000432605.1	+	1	109	c.109T>G	c.(109-111)Tat>Gat	p.Y37D	RP11-493E12.1_ENST00000605902.1_lincRNA|C2orf74_ENST00000426997.1_Intron	NM_001143959.1	NP_001137431.1	A8MZ97	CB074_HUMAN	chromosome 2 open reading frame 74	37						integral component of membrane (GO:0016021)				endometrium(1)	1						GGTTTTTTTATATAAATGGTA	0.318													T|||	1972	0.39377	0.4455	0.389	5008	,	,		20712	0.3968		0.4533	False		,,,				2504	0.2628				p.Y37D		Atlas-SNP	.											.	C2orf74	22	.	0			c.T109G						PASS	.						218.0	173.0	187.0					2																	61389737		692	1591	2283	SO:0001583	missense	339804	exon1			TTTTTATATAAAT			2p15	2012-08-06			ENSG00000237651	ENSG00000237651			34439	protein-coding gene	gene with protein product							Standard	NM_001143959		Approved	LOC339804	uc010ypm.1	A8MZ97		ENST00000432605.1:c.109T>G	2.37:g.61389737T>G	ENSP00000402915:p.Tyr37Asp	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	NM_001143959	C9JP62	Missense_Mutation	SNP	ENST00000432605.1	37		938	0.42948717948717946	210	0.4268292682926829	158	0.43646408839779005	223	0.38986013986013984	347	0.4577836411609499	T	12.42	1.933117	0.34096	.	.	ENSG00000237651	ENST00000432605	.	.	.	4.9	2.31	0.28768	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	1.0000000000287557E-6	D	0.54207	0.965	P	0.54312	0.748	T	0.45190	-0.9278	7	0.87932	D	0	.	1.6236	0.02719	0.1687:0.0969:0.1747:0.5597	rs1729674;rs52790424;rs56837693;rs1729674	37	A8MZ97	CB074_HUMAN	D	37	.	ENSP00000402915:Y37D	Y	+	1	0	C2orf74	61243241	0.829000	0.29322	0.939000	0.37840	0.582000	0.36321	1.552000	0.36244	0.831000	0.34780	0.254000	0.18369	TAT	T|0.583;G|0.417	0.417	strong		0.318	C2orf74-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001143959	
BTN2A1	11120	hgsc.bcm.edu	37	6	26458872	26458872	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26458872C>T	ENST00000312541.5	+	2	256	c.8C>T	c.(7-9)tCa>tTa	p.S3L	BTN2A1_ENST00000541522.1_Intron|BTN2A1_ENST00000469185.1_Missense_Mutation_p.S3L|BTN2A1_ENST00000429381.1_Missense_Mutation_p.S3L	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	3					lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CTCATGGAATCAGCTGCTGCC	0.622																																					p.S3L		Atlas-SNP	.											.	BTN2A1	118	.	0			c.C8T						PASS	.						232.0	171.0	191.0					6																	26458872		2203	4300	6503	SO:0001583	missense	11120	exon2			TGGAATCAGCTGC	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.8C>T	6.37:g.26458872C>T	ENSP00000312158:p.Ser3Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	6	0.0540541	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.510906	0.27036	.	.	ENSG00000112763	ENST00000312541;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T	0.77098	-0.48;-1.07;-1.06	3.03	0.102	0.14522	.	0.876207	0.09516	N	0.791659	T	0.41581	0.1165	L	0.27053	0.805	0.09310	N	0.999998	B;B	0.12013	0.005;0.005	B;B	0.11329	0.004;0.006	T	0.31806	-0.9930	10	0.44086	T	0.13	.	5.0586	0.14546	0.0:0.4487:0.4235:0.1277	.	3;3	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	L	3	ENSP00000312158:S3L;ENSP00000416945:S3L;ENSP00000419043:S3L	ENSP00000265424:S3L	S	+	2	0	BTN2A1	26566851	0.020000	0.18652	0.003000	0.11579	0.023000	0.10783	0.059000	0.14322	-0.006000	0.14370	0.484000	0.47621	TCA	.	.	none		0.622	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
C6orf223	221416	hgsc.bcm.edu	37	6	43970602	43970602	+	Silent	SNP	G	G	C	rs117880737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43970602G>C	ENST00000336600.5	+	4	488	c.468G>C	c.(466-468)ccG>ccC	p.P156P	C6orf223_ENST00000439969.2_3'UTR|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000448947.2_3'UTR|C6orf223_ENST00000442114.2_Silent_p.P136P|RP5-1120P11.1_ENST00000607590.1_RNA	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	156										central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			CGAGGAGCCCGGGACAGGTGA	0.791													G|||	208	0.0415335	0.053	0.0303	5008	,	,		8130	0.0466		0.0427	False		,,,				2504	0.0276				p.P156P		Atlas-SNP	.											.	C6orf223	14	.	0			c.G468C						PASS	.	G	,	100,3698		0,100,1799	4.0	5.0	5.0		,468	-7.6	0.0	6	dbSNP_132	5	119,7499		2,115,3692	no	utr-3,coding-synonymous	C6orf223	NM_001171992.1,NM_153246.4	,	2,215,5491	CC,CG,GG		1.5621,2.633,1.9184	,	,156/243	43970602	219,11197	1899	3809	5708	SO:0001819	synonymous_variant	221416	exon4			GAGCCCGGGACAG	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.468G>C	6.37:g.43970602G>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	13	9	0.692308	NM_153246	E9PB59|Q8N575	Silent	SNP	ENST00000336600.5	37	CCDS34459.1																																																																																			G|0.957;C|0.043	0.043	strong		0.791	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246	
DGCR14	8220	hgsc.bcm.edu	37	22	19132061	19132061	+	Silent	SNP	C	C	T	rs2298274	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19132061C>T	ENST00000252137.6	-	1	136	c.93G>A	c.(91-93)gcG>gcA	p.A31A		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	31			A -> V (in dbSNP:rs113904207). {ECO:0000269|PubMed:9063747}.		mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					GCTTGCTCGTCGCAGCCCCAG	0.672													C|||	406	0.0810703	0.0726	0.0634	5008	,	,		13321	0.1468		0.0676	False		,,,				2504	0.0511				p.A31A		Atlas-SNP	.											.	DGCR14	43	.	0			c.G93A						PASS	.	C		338,4060		8,322,1869	21.0	21.0	21.0		93	1.4	0.0	22	dbSNP_100	21	498,8092		15,468,3812	no	coding-synonymous	DGCR14	NM_022719.2		23,790,5681	TT,TC,CC		5.7974,7.6853,6.4367		31/477	19132061	836,12152	2199	4295	6494	SO:0001819	synonymous_variant	8220	exon1			GCTCGTCGCAGCC	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"""DiGeorge syndrome critical region gene 13"""	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.93G>A	22.37:g.19132061C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	130	81	0.623077	NM_022719	Q49AH7|Q9BTZ4	Silent	SNP	ENST00000252137.6	37	CCDS13756.1																																																																																			C|0.926;T|0.074	0.074	strong		0.672	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2		
XIRP2	129446	hgsc.bcm.edu	37	2	168099796	168099796	+	Missense_Mutation	SNP	T	T	C	rs16853306	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168099796T>C	ENST00000409195.1	+	9	1983	c.1894T>C	c.(1894-1896)Tat>Cat	p.Y632H	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.Y410H|XIRP2_ENST00000295237.9_Missense_Mutation_p.Y632H|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	457					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ACTTGGGGCTTATTCTTCTGA	0.453													C|||	1211	0.241813	0.3858	0.17	5008	,	,		20293	0.2163		0.1282	False		,,,				2504	0.2413				p.Y632H		Atlas-SNP	.											.	XIRP2	914	.	0			c.T1894C						PASS	.	C	,,,HIS/TYR,HIS/TYR	1269,2611		212,845,883	70.0	74.0	73.0		,,,1894,1228	5.0	0.6	2	dbSNP_123	73	931,7327		55,821,3253	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,83,83	267,1666,4136	CC,CT,TT		11.2739,32.7062,18.1249	,,,benign,benign	,,,632/3550,410/3328	168099796	2200,9938	1940	4129	6069	SO:0001583	missense	129446	exon9			GGGGCTTATTCTT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.1894T>C	2.37:g.168099796T>C	ENSP00000386840:p.Tyr632His	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	248	111	0.447581	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	488	0.22344322344322345	200	0.4065040650406504	53	0.1464088397790055	135	0.23601398601398602	100	0.13192612137203166	C	0.018	-1.480157	0.01027	0.327062	0.112739	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02323	4.34;4.34;4.34	5.93	5.0	0.66597	.	0.552719	0.19301	N	0.117625	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.31806	-0.9930	9	0.09084	T	0.74	-1.6335	9.997	0.41905	0.0:0.6817:0.2482:0.0701	rs16853306;rs52838025;rs58003618;rs16853306	457;457;410	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	H	632;632;410	ENSP00000386840:Y632H;ENSP00000295237:Y632H;ENSP00000387255:Y410H	ENSP00000295237:Y632H	Y	+	1	0	XIRP2	167808042	0.000000	0.05858	0.574000	0.28523	0.446000	0.32137	-0.707000	0.05041	1.535000	0.49220	-0.119000	0.15052	TAT	T|0.774;C|0.226	0.226	strong		0.453	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
LGALS12	85329	hgsc.bcm.edu	37	11	63277334	63277334	+	Missense_Mutation	SNP	A	A	G	rs117587231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:63277334A>G	ENST00000394618.3	+	4	814	c.523A>G	c.(523-525)Atc>Gtc	p.I175V	LGALS12_ENST00000425950.2_Missense_Mutation_p.I114V|LGALS12_ENST00000340246.5_Missense_Mutation_p.I176V|LGALS12_ENST00000415491.2_Missense_Mutation_p.I114V|LGALS12_ENST00000255684.5_Missense_Mutation_p.I175V	NM_001142535.1|NM_033101.3	NP_001136007.1|NP_149092.2	Q96DT0	LEG12_HUMAN	lectin, galactoside-binding, soluble, 12	175	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	16						ATTTGGTGACATCCTGGTAGA	0.537													A|||	27	0.00539137	0.0	0.0115	5008	,	,		18345	0.0		0.0169	False		,,,				2504	0.002				p.I176V		Atlas-SNP	.											.	LGALS12	35	.	0			c.A526G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	16,4386	23.3+/-48.9	0,16,2185	147.0	125.0	132.0		526,523,340,340,523	4.4	0.8	11	dbSNP_132	132	100,8496	54.8+/-115.7	1,98,4199	yes	missense,missense,missense,missense,missense	LGALS12	NM_001142535.1,NM_001142536.1,NM_001142537.1,NM_001142538.1,NM_033101.3	29,29,29,29,29	1,114,6384	GG,GA,AA		1.1633,0.3635,0.8924	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	176/338,175/328,114/276,114/267,175/337	63277334	116,12882	2201	4298	6499	SO:0001583	missense	85329	exon4			GGTGACATCCTGG	AF222695	CCDS8045.1, CCDS44633.1, CCDS44634.1, CCDS44635.1, CCDS53648.1	11q13	2011-08-04	2008-07-25		ENSG00000133317	ENSG00000133317		"""Lectins, galactoside-binding"""	15788	protein-coding gene	gene with protein product	"""galectin 12"""	606096				11283015, 11435439	Standard	NM_033101		Approved	GRIP1	uc001nxc.2	Q96DT0	OTTHUMG00000167807	ENST00000394618.3:c.523A>G	11.37:g.63277334A>G	ENSP00000378116:p.Ile175Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	173	70	0.404624	NM_001142535	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000394618.3	37	CCDS8045.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	A	0.187	-1.056612	0.01965	0.003635	0.011633	ENSG00000133317	ENST00000255684;ENST00000394618;ENST00000340246;ENST00000415491;ENST00000425950	T;T;T;T;T	0.04194	3.68;3.68;3.68;3.68;3.68	5.55	4.42	0.53409	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.102234	0.42821	N	0.000645	T	0.01320	0.0043	N	0.21097	0.63	0.32137	N	0.585991	B;B;B;B	0.12013	0.005;0.004;0.002;0.005	B;B;B;B	0.15052	0.012;0.004;0.006;0.007	T	0.34551	-0.9824	10	0.02654	T	1	-31.0467	7.0738	0.25193	0.8252:0.0:0.1748:0.0	.	135;176;175;175	Q9NZ03;G5E970;Q96DT0-3;Q96DT0	.;.;.;LEG12_HUMAN	V	175;175;176;114;114	ENSP00000255684:I175V;ENSP00000378116:I175V;ENSP00000339374:I176V;ENSP00000394659:I114V;ENSP00000399093:I114V	ENSP00000255684:I175V	I	+	1	0	LGALS12	63033910	0.896000	0.30565	0.791000	0.31998	0.494000	0.33585	1.071000	0.30666	0.939000	0.37446	0.418000	0.28097	ATC	A|0.992;G|0.008	0.008	strong		0.537	LGALS12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396378.1	NM_033101	
TET3	200424	hgsc.bcm.edu	37	2	74274329	74274329	+	Missense_Mutation	SNP	C	C	T	rs61741171	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:74274329C>T	ENST00000409262.3	+	1	880	c.880C>T	c.(880-882)Cct>Tct	p.P294S		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	294					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCCAGCAACTCCTAGAACTGA	0.612													C|||	122	0.024361	0.0015	0.049	5008	,	,		15708	0.0		0.0755	False		,,,				2504	0.0102				p.P294S		Atlas-SNP	.											.	TET3	101	.	0			c.C880T						PASS	.	C	SER/PRO	43,3991		1,41,1975	58.0	63.0	61.0		880	5.8	0.5	2	dbSNP_129	61	478,7884		12,454,3715	yes	missense	TET3	NM_144993.1	74	13,495,5690	TT,TC,CC		5.7163,1.0659,4.203	probably-damaging	294/1661	74274329	521,11875	2017	4181	6198	SO:0001583	missense	200424	exon1			GCAACTCCTAGAA		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.880C>T	2.37:g.74274329C>T	ENSP00000386869:p.Pro294Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Missense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	75	0.034340659340659344	0	0.0	19	0.052486187845303865	0	0.0	56	0.07387862796833773	C	12.63	1.995278	0.35226	0.010659	0.057163	ENSG00000187605	ENST00000305799;ENST00000409262;ENST00000233310	T;T	0.27557	1.66;2.56	5.84	5.84	0.93424	.	.	.	.	.	T	0.02888	0.0086	N	0.14661	0.345	0.44871	D	0.99788	D	0.56521	0.976	P	0.54815	0.761	T	0.00802	-1.1560	9	0.38643	T	0.18	.	18.8993	0.92435	0.0:1.0:0.0:0.0	rs61741171	294	O43151	TET3_HUMAN	S	336;294;294	ENSP00000307803:P336S;ENSP00000386869:P294S	ENSP00000233310:P294S	P	+	1	0	TET3	74127837	0.445000	0.25657	0.477000	0.27303	0.639000	0.38242	2.996000	0.49449	2.768000	0.95171	0.561000	0.74099	CCT	C|0.963;T|0.037	0.037	strong		0.612	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4		
COL15A1	1306	hgsc.bcm.edu	37	9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	rs35901514	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:101804366T>C	ENST00000375001.3	+	24	2974	c.2551T>C	c.(2551-2553)Ttt>Ctt	p.F851L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	851	Collagen-like 3.|Triple-helical region 4 (COL4).				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)				TTTACCTGGCTTTCCAGGACT	0.423													T|||	16	0.00319489	0.0015	0.0058	5008	,	,		17702	0.0		0.008	False		,,,				2504	0.002				p.F851L		Atlas-SNP	.											.	COL15A1	211	.	0			c.T2551C						PASS	.	T	LEU/PHE	11,4395	17.9+/-39.9	0,11,2192	95.0	103.0	100.0		2551	5.9	1.0	9	dbSNP_126	100	108,8492	57.2+/-118.5	0,108,4192	yes	missense	COL15A1	NM_001855.3	22	0,119,6384	CC,CT,TT		1.2558,0.2497,0.915	probably-damaging	851/1389	101804366	119,12887	2203	4300	6503	SO:0001583	missense	1306	exon24			CCTGGCTTTCCAG	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.2551T>C	9.37:g.101804366T>C	ENSP00000364140:p.Phe851Leu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	11	0.005036630036630037	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	19.54	3.846980	0.71603	0.002497	0.012558	ENSG00000204291	ENST00000375001	D	0.93133	-3.17	5.92	5.92	0.95590	.	0.251977	0.40818	N	0.001007	D	0.88815	0.6539	N	0.10760	0.04	0.40583	D	0.981411	D	0.69078	0.997	D	0.77004	0.989	D	0.88409	0.3020	10	0.20046	T	0.44	-12.7642	12.7552	0.57331	0.0:0.0:0.0:1.0	rs35901514	851	P39059	COFA1_HUMAN	L	851	ENSP00000364140:F851L	ENSP00000364140:F851L	F	+	1	0	COL15A1	100844187	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	2.145000	0.42207	2.270000	0.75569	0.459000	0.35465	TTT	T|0.993;C|0.007	0.007	strong		0.423	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
NLRC3	197358	hgsc.bcm.edu	37	16	3613207	3613207	+	RNA	SNP	G	G	T	rs9940099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3613207G>T	ENST00000301749.7	-	0	2136				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000359128.5_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGGCCAGCTCGGTGTGCTGCA	0.706													T|||	236	0.0471246	0.0197	0.072	5008	,	,		16044	0.0546		0.0636	False		,,,				2504	0.0419				p.T577T		Atlas-SNP	.											.	NLRC3	103	.	0			c.C1731A						PASS	.						9.0	12.0	11.0					16																	3613207		2120	4214	6334			197358	exon5			CAGCTCGGTGTGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613207G>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				A|0.074;G|0.926	.	strong		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
KPRP	448834	hgsc.bcm.edu	37	1	152733301	152733301	+	Missense_Mutation	SNP	T	T	A	rs4329520	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152733301T>A	ENST00000606109.1	+	1	1265	c.1237T>A	c.(1237-1239)Tgc>Agc	p.C413S	KPRP_ENST00000368773.1_Missense_Mutation_p.C413S			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	413	Pro-rich.		C -> S (in dbSNP:rs4329520).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCAGAACCATGCATAAGTCT	0.577													T|||	2455	0.490216	0.5787	0.4914	5008	,	,		19481	0.4177		0.5159	False		,,,				2504	0.4182				p.C413S		Atlas-SNP	.											.	KPRP	152	.	0			c.T1237A						PASS	.	T	SER/CYS	2439,1967	620.2+/-393.5	676,1087,440	166.0	170.0	168.0		1237	-0.3	0.0	1	dbSNP_111	168	4323,4277	579.2+/-390.9	1097,2129,1074	yes	missense	KPRP	NM_001025231.1	112	1773,3216,1514	AA,AT,TT		49.7326,44.6437,48.0086	benign	413/580	152733301	6762,6244	2203	4300	6503	SO:0001583	missense	448834	exon2			GAACCATGCATAA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.1237T>A	1.37:g.152733301T>A	ENSP00000475216:p.Cys413Ser	Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	1120	0.5128205128205128	294	0.5975609756097561	196	0.5414364640883977	248	0.43356643356643354	382	0.503957783641161	T	13.38	2.220864	0.39201	0.553563	0.502674	ENSG00000203786	ENST00000368773	T	0.24908	1.83	4.88	-0.312	0.12758	.	0.277746	0.26359	N	0.024827	T	0.04452	0.0122	L	0.52573	1.65	0.80722	P	0.0	B	0.16396	0.017	B	0.15484	0.013	T	0.38023	-0.9680	9	0.09590	T	0.72	-8.4552	0.3401	0.00332	0.2846:0.1651:0.1471:0.4032	rs4329520;rs60534699;rs4329520	413	Q5T749	KPRP_HUMAN	S	413	ENSP00000357762:C413S	ENSP00000357762:C413S	C	+	1	0	KPRP	150999925	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.196000	0.09532	-0.142000	0.11354	0.379000	0.24179	TGC	T|0.489;A|0.511	0.511	strong		0.577	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
SNAP29	9342	hgsc.bcm.edu	37	22	21213416	21213416	+	Silent	SNP	A	A	G	rs1061064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:21213416A>G	ENST00000215730.7	+	1	146	c.18A>G	c.(16-18)aaA>aaG	p.K6K	PI4KA_ENST00000255882.6_5'Flank|PI4KA_ENST00000572273.1_5'Flank	NM_004782.3	NP_004773.1	O95721	SNP29_HUMAN	synaptosomal-associated protein, 29kDa	6					autophagic vacuole fusion (GO:0000046)|exocytosis (GO:0006887)|membrane fusion (GO:0061025)|protein transport (GO:0015031)|vesicle targeting (GO:0006903)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|SNARE complex (GO:0031201)|synapse (GO:0045202)	SNAP receptor activity (GO:0005484)			breast(1)|endometrium(1)|large_intestine(5)|lung(1)|upper_aerodigestive_tract(1)	9	all_cancers(11;2.77e-25)|all_epithelial(7;8.92e-24)|Lung NSC(8;1.49e-15)|all_lung(8;2.54e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000592)|Lung(15;0.0117)			CTTACCCTAAAAGCTACAATC	0.731													A|||	2021	0.403554	0.1604	0.4323	5008	,	,		12279	0.372		0.5249	False		,,,				2504	0.6196				p.K6K		Atlas-SNP	.											SNAP29,NS,carcinoma,0,1	SNAP29	22	1	0			c.A18G						PASS	.	A		909,3459		120,669,1395	10.0	12.0	12.0		18	-2.2	0.2	22	dbSNP_86	12	4457,4057		1243,1971,1043	no	coding-synonymous	SNAP29	NM_004782.3		1363,2640,2438	GG,GA,AA		47.6509,20.8104,41.655		6/259	21213416	5366,7516	2184	4257	6441	SO:0001819	synonymous_variant	9342	exon1			CCCTAAAAGCTAC	AF115436	CCDS13784.1	22q11.21	2008-06-10	2002-08-29		ENSG00000099940	ENSG00000099940			11133	protein-coding gene	gene with protein product	"""soluble 29 kDa NSF attachment protein"""	604202	"""synaptosomal-associated protein, 29kD"""			9852078, 10591208	Standard	NM_004782		Approved	SNAP-29, CEDNIK	uc011ahw.2	O95721	OTTHUMG00000150765	ENST00000215730.7:c.18A>G	22.37:g.21213416A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_004782		Silent	SNP	ENST00000215730.7	37	CCDS13784.1																																																																																			A|0.600;G|0.400	0.400	strong		0.731	SNAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320000.4	NM_004782	
SLC12A4	6560	hgsc.bcm.edu	37	16	67997920	67997920	+	Intron	SNP	T	T	C	rs3785100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67997920T>C	ENST00000316341.3	-	2	256				SLC12A4_ENST00000338335.3_Intron|SLC12A4_ENST00000572010.1_Intron|SLC12A4_ENST00000572037.1_Intron|SLC12A4_ENST00000541864.2_Intron|SLC12A4_ENST00000576616.1_Intron|SLC12A4_ENST00000422611.2_Intron|SLC12A4_ENST00000537830.2_Missense_Mutation_p.E4G	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4						cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CACAGCACCTTCGGCTGCCAT	0.677													T|||	842	0.168131	0.2466	0.1643	5008	,	,		14956	0.0893		0.1382	False		,,,				2504	0.1769				p.E4G		Atlas-SNP	.											.	SLC12A4	81	.	0			c.A11G						PASS	.	T	,,GLY/GLU,,	295,1089		40,215,437	23.0	28.0	26.0		,,11,,	4.1	0.0	16	dbSNP_107	26	412,2770		35,342,1214	yes	intron,intron,missense,intron,intron	SLC12A4	NM_001145961.1,NM_001145962.1,NM_001145963.1,NM_001145964.1,NM_005072.4	,,98,,	75,557,1651	CC,CT,TT		12.9478,21.315,15.484	,,,,	,,4/1080,,	67997920	707,3859	692	1591	2283	SO:0001627	intron_variant	6560	exon1			GCACCTTCGGCTG		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.116-458A>G	16.37:g.67997920T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001145963	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Missense_Mutation	SNP	ENST00000316341.3	37	CCDS10855.1	343	0.15705128205128205	112	0.22764227642276422	59	0.16298342541436464	65	0.11363636363636363	107	0.14116094986807387	T	17.05	3.289942	0.59976	0.21315	0.129478	ENSG00000124067	ENST00000537830	D	0.84660	-1.88	4.12	4.12	0.48240	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.27632	P	0.9480008	B	0.12630	0.006	B	0.16289	0.015	T	0.07927	-1.0747	8	0.59425	D	0.04	.	9.8187	0.40869	0.0:0.0:0.0:1.0	rs3785100;rs3785100	4	F5H0S9	.	G	4	ENSP00000445962:E4G	ENSP00000445962:E4G	E	-	2	0	SLC12A4	66555421	0.002000	0.14202	0.004000	0.12327	0.026000	0.11368	0.768000	0.26590	2.098000	0.63641	0.459000	0.35465	GAA	T|0.841;C|0.159	0.159	strong		0.677	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072	
MPPE1	65258	hgsc.bcm.edu	37	18	11893554	11893554	+	Silent	SNP	C	C	G	rs34932177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:11893554C>G	ENST00000588072.1	-	4	1524	c.303G>C	c.(301-303)gcG>gcC	p.A101A	MPPE1_ENST00000344987.7_Silent_p.A101A|MPPE1_ENST00000399978.2_Silent_p.A101A|MPPE1_ENST00000317235.7_Silent_p.A101A|MPPE1_ENST00000309976.9_Silent_p.A101A	NM_023075.5	NP_075563.3	Q53F39	MPPE1_HUMAN	metallophosphoesterase 1	101					ER to Golgi vesicle-mediated transport (GO:0006888)|GPI anchor biosynthetic process (GO:0006506)	cis-Golgi network (GO:0005801)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	GPI anchor binding (GO:0034235)|manganese ion binding (GO:0030145)|phosphoric diester hydrolase activity (GO:0008081)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	5						CTGTCTGGAACGCTCTCTCCA	0.498													G|||	319	0.0636981	0.149	0.0274	5008	,	,		21421	0.0774		0.0139	False		,,,				2504	0.0112				p.A101A		Atlas-SNP	.											.	MPPE1	21	.	0			c.G303C						PASS	.	G	,	590,3816	772.1+/-413.9	54,482,1667	73.0	64.0	67.0		303,303	-0.1	1.0	18	dbSNP_126	67	148,8452	812.9+/-407.0	2,144,4154	no	coding-synonymous,coding-synonymous	MPPE1	NM_001242904.1,NM_023075.5	,	56,626,5821	GG,GC,CC		1.7209,13.3908,5.6743	,	101/334,101/397	11893554	738,12268	2203	4300	6503	SO:0001819	synonymous_variant	65258	exon3			CTGGAACGCTCTC	BC002877	CCDS11853.1, CCDS56054.1	18p11.21	2004-04-30			ENSG00000154889	ENSG00000154889			15988	protein-coding gene	gene with protein product		611900				11978971	Standard	NM_001242904		Approved		uc002kqf.3	Q53F39	OTTHUMG00000131661	ENST00000588072.1:c.303G>C	18.37:g.11893554C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	51	0.6	NM_001242904	B0YJ39|B0YJ40|B0YJ41|B5ME53|B7WNJ3|D3DUI5|D3DUI7|Q6GMP1|Q8TAD6|Q8TE26|Q8WZ32|Q9BU58|Q9H958|Q9HAI4	Silent	SNP	ENST00000588072.1	37	CCDS11853.1																																																																																			C|0.939;G|0.061	0.061	strong		0.498	MPPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254562.2	NM_023075	
APOL3	80833	hgsc.bcm.edu	37	22	36537893	36537893	+	Silent	SNP	A	A	G	rs3827346	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:36537893A>G	ENST00000349314.2	-	3	601	c.564T>C	c.(562-564)aaT>aaC	p.N188N	APOL3_ENST00000424878.2_5'UTR|APOL3_ENST00000487423.1_5'UTR|APOL3_ENST00000397287.2_5'UTR|APOL3_ENST00000361710.2_5'UTR|APOL3_ENST00000397293.2_Silent_p.N117N	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	188					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						TGGACACCACATTGGAGATGG	0.532													A|||	1298	0.259185	0.0144	0.402	5008	,	,		21061	0.623		0.1998	False		,,,				2504	0.1748				p.N188N		Atlas-SNP	.											.	APOL3	60	.	0			c.T564C						PASS	.	A	,,	196,4210	123.7+/-161.0	3,190,2010	105.0	98.0	100.0		564,,	-8.6	0.0	22	dbSNP_107	100	1617,6983	299.5+/-304.5	163,1291,2846	no	coding-synonymous,utr-5,utr-5	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	,,	166,1481,4856	GG,GA,AA		18.8023,4.4485,13.9397	,,	188/403,,	36537893	1813,11193	2203	4300	6503	SO:0001819	synonymous_variant	80833	exon3			CACCACATTGGAG	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.564T>C	22.37:g.36537893A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Silent	SNP	ENST00000349314.2	37	CCDS13922.1																																																																																			A|0.793;G|0.207	0.207	strong		0.532	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
MFGE8	4240	hgsc.bcm.edu	37	15	89450587	89450587	+	Missense_Mutation	SNP	G	G	T	rs1878326	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89450587G>T	ENST00000566497.1	-	3	287	c.226C>A	c.(226-228)Ctg>Atg	p.L76M	MFGE8_ENST00000559997.1_5'UTR|MFGE8_ENST00000268151.7_Missense_Mutation_p.L76M|MFGE8_ENST00000539437.1_Missense_Mutation_p.L68M|MFGE8_ENST00000268150.8_Missense_Mutation_p.L76M|MFGE8_ENST00000542878.1_Missense_Mutation_p.L32M			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	76	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.		M -> L (in dbSNP:rs1878326). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16572171, ECO:0000269|Ref.5}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)	p.L76M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					CCATTCTCCAGGCCCAGTGGC	0.612													T|||	3197	0.638379	0.8011	0.6167	5008	,	,		18586	0.4554		0.6372	False		,,,				2504	0.6237				p.L76M		Atlas-SNP	.											MFGE8,NS,carcinoma,0,2	MFGE8	60	2	1	Substitution - Missense(1)	stomach(1)	c.C226A						PASS	.	T	MET/LEU,MET/LEU	3453,947	359.9+/-315.0	1351,751,98	107.0	78.0	88.0		226,226	4.2	1.0	15	dbSNP_92	88	5609,2989	463.0+/-365.8	1812,1985,502	yes	missense,missense	MFGE8	NM_001114614.1,NM_005928.2	15,15	3163,2736,600	TT,TG,GG		34.7639,21.5227,30.2816	benign,benign	76/336,76/388	89450587	9062,3936	2200	4299	6499	SO:0001583	missense	4240	exon3			TCTCCAGGCCCAG	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.226C>A	15.37:g.89450587G>T	ENSP00000456281:p.Leu76Met	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	174	76	0.436782	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Missense_Mutation	SNP	ENST00000566497.1	37	CCDS10347.1	1336	0.6117216117216118	376	0.7642276422764228	220	0.6077348066298343	260	0.45454545454545453	480	0.633245382585752	T	0.010	-1.772135	0.00645	0.784773	0.652361	ENSG00000140545	ENST00000268150;ENST00000268151;ENST00000539437;ENST00000542878	D;D;D;D	0.97209	-4.29;-4.29;-4.29;-1.62	5.32	4.18	0.49190	.	0.036199	0.85682	N	0.000000	T	0.00012	0.0000	.	.	.	0.50813	P	1.0100000000001774E-4	B;B	0.14438	0.01;0.0	B;B	0.16722	0.016;0.005	T	0.46498	-0.9187	8	0.02654	T	1	-48.0241	8.268	0.31827	0.1319:0.0:0.1384:0.7297	rs1878326;rs11557314;rs17202746;rs17856089;rs60806175;rs1878326	32;68	F5GZN3;F5H7N9	.;.	M	76;76;68;32	ENSP00000268150:L76M;ENSP00000268151:L76M;ENSP00000442386:L68M;ENSP00000444332:L32M	ENSP00000268150:L76M	L	-	1	2	MFGE8	87251591	1.000000	0.71417	1.000000	0.80357	0.029000	0.11900	2.742000	0.47434	0.319000	0.23209	-0.525000	0.04345	CTG	G|0.336;T|0.658	0.658	strong		0.612	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
C20orf194	25943	hgsc.bcm.edu	37	20	3356878	3356878	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3356878G>A	ENST00000252032.9	-	4	422	c.355C>T	c.(355-357)Cct>Tct	p.P119S		NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	119										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						GCCACATAAGGTAAGAGATAG	0.368																																					p.P119S		Atlas-SNP	.											.	C20orf194	83	.	0			c.C355T						PASS	.						148.0	134.0	138.0					20																	3356878		1869	4112	5981	SO:0001583	missense	25943	exon4			CATAAGGTAAGAG	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.355C>T	20.37:g.3356878G>A	ENSP00000252032:p.Pro119Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	197	90	0.456853	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.822991	0.90873	.	.	ENSG00000088854	ENST00000252032	T	0.27890	1.64	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62421	-0.6858	10	0.87932	D	0	.	18.4941	0.90858	0.0:0.0:1.0:0.0	.	119	Q5TEA3	CT194_HUMAN	S	119	ENSP00000252032:P119S	ENSP00000252032:P119S	P	-	1	0	C20orf194	3304878	1.000000	0.71417	0.981000	0.43875	0.981000	0.71138	7.298000	0.78815	2.740000	0.93945	0.561000	0.74099	CCT	.	.	none		0.368	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
EPHB1	2047	hgsc.bcm.edu	37	3	134670524	134670524	+	Silent	SNP	C	C	T	rs7644369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:134670524C>T	ENST00000398015.3	+	3	805	c.435C>T	c.(433-435)agC>agT	p.S145S	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	145	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|camera-type eye morphogenesis (GO:0048593)|cell chemotaxis (GO:0060326)|cell-substrate adhesion (GO:0031589)|central nervous system projection neuron axonogenesis (GO:0021952)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|neural precursor cell proliferation (GO:0061351)|neurogenesis (GO:0022008)|optic nerve morphogenesis (GO:0021631)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of JNK cascade (GO:0046328)|retinal ganglion cell axon guidance (GO:0031290)	axon (GO:0030424)|early endosome membrane (GO:0031901)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(63)|ovary(8)|pancreas(2)|prostate(8)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	130						CAGATGAGAGCTTCTCCCAGG	0.498													C|||	2411	0.48143	0.6377	0.5692	5008	,	,		19990	0.2123		0.4394	False		,,,				2504	0.5286				p.S145S		Atlas-SNP	.											.	EPHB1	519	.	0			c.C435T						PASS	.	C		2277,1677		699,879,399	154.0	152.0	153.0		435	4.6	1.0	3	dbSNP_116	153	3757,4657		844,2069,1294	no	coding-synonymous	EPHB1	NM_004441.4		1543,2948,1693	TT,TC,CC		44.6518,42.4127,48.7872		145/985	134670524	6034,6334	1977	4207	6184	SO:0001819	synonymous_variant	2047	exon3			TGAGAGCTTCTCC	L40636	CCDS46921.1	3q21-q23	2013-02-11	2004-10-28			ENSG00000154928		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3392	protein-coding gene	gene with protein product		600600	"""EphB1"""	EPHT2		8666391	Standard	NM_004441		Approved	Hek6	uc003eqt.3	P54762		ENST00000398015.3:c.435C>T	3.37:g.134670524C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	191	191	1	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Silent	SNP	ENST00000398015.3	37	CCDS46921.1																																																																																			C|0.559;T|0.441	0.441	strong		0.498	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441	
GYG1	2992	hgsc.bcm.edu	37	3	148727133	148727133	+	Silent	SNP	G	G	A	rs4938	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148727133G>A	ENST00000345003.4	+	5	852	c.552G>A	c.(550-552)ccG>ccA	p.P184P	GYG1_ENST00000484197.1_Silent_p.P184P|GYG1_ENST00000483267.1_Intron|GYG1_ENST00000296048.6_Silent_p.P184P|GYG1_ENST00000479119.1_3'UTR	NM_004130.3	NP_004121.2	P46976	GLYG_HUMAN	glycogenin 1	184					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogenin glucosyltransferase activity (GO:0008466)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(3)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AACACCTGCCGTTTATTTATA	0.378													G|||	1509	0.301318	0.2844	0.3055	5008	,	,		16635	0.3284		0.335	False		,,,				2504	0.2587				p.P184P		Atlas-SNP	.											.	GYG1	29	.	0			c.G552A						PASS	.	G	,,	1211,3195	422.1+/-339.6	177,857,1169	109.0	115.0	113.0		552,552,552	0.2	1.0	3	dbSNP_52	113	2617,5983	424.5+/-354.7	399,1819,2082	no	coding-synonymous,coding-synonymous,coding-synonymous	GYG1	NM_001184720.1,NM_001184721.1,NM_004130.3	,,	576,2676,3251	AA,AG,GG		30.4302,27.4852,29.4326	,,	184/334,184/280,184/351	148727133	3828,9178	2203	4300	6503	SO:0001819	synonymous_variant	2992	exon5			CCTGCCGTTTATT	AF087942	CCDS3139.1, CCDS54654.1, CCDS54655.1	3q24-q25.1	2013-02-22	2005-11-04	2005-11-04	ENSG00000163754	ENSG00000163754	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4699	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	603942	"""glycogenin"""	GYG		8602861	Standard	NM_004130		Approved		uc003ewn.3	P46976	OTTHUMG00000159533	ENST00000345003.4:c.552G>A	3.37:g.148727133G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_004130	D3DNH0|D3DNH1|D3DNH2|Q6FHZ1|Q9UNV0	Silent	SNP	ENST00000345003.4	37	CCDS3139.1																																																																																			G|0.703;A|0.297	0.297	strong		0.378	GYG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356046.1	NM_004130	
MRPL45	84311	hgsc.bcm.edu	37	17	36474601	36474601	+	Silent	SNP	A	A	G	rs59939216	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36474601A>G	ENST00000312513.5	+	5	638	c.477A>G	c.(475-477)cgA>cgG	p.R159R		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	159						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				ACCATGACCGACTTCATACCT	0.408													A|||	619	0.123602	0.2579	0.0576	5008	,	,		11874	0.0962		0.0825	False		,,,				2504	0.0593				p.R159R		Atlas-SNP	.											.	MRPL45	27	.	0			c.A477G						PASS	.	A		1007,3399	375.4+/-321.6	113,781,1309	197.0	182.0	187.0		477	-5.5	0.9	17	dbSNP_129	187	641,7959	164.5+/-216.8	25,591,3684	no	coding-synonymous	MRPL45	NM_032351.4		138,1372,4993	GG,GA,AA		7.4535,22.8552,12.6711		159/307	36474601	1648,11358	2203	4300	6503	SO:0001819	synonymous_variant	84311	exon5			TGACCGACTTCAT	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.477A>G	17.37:g.36474601A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	197	100	0.507614	NM_032351	A1L436|Q6ZMJ5	Silent	SNP	ENST00000312513.5	37	CCDS11326.1																																																																																			A|0.873;G|0.127	0.127	strong		0.408	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
GAB4	128954	hgsc.bcm.edu	37	22	17469049	17469049	+	Nonsense_Mutation	SNP	C	C	A	rs28502153	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:17469049C>A	ENST00000400588.1	-	3	594	c.487G>T	c.(487-489)Gga>Tga	p.G163*	GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	163										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)				GAAATGTTTCCCAGGAAGCCT	0.552													c|||	1771	0.353634	0.1982	0.4265	5008	,	,		19665	0.3938		0.3698	False		,,,				2504	0.454				p.G163X		Atlas-SNP	.											.	GAB4	95	.	0			c.G487T						PASS	.	-	stop/GLY	994,3258		126,742,1258	37.0	47.0	44.0		487	-0.5	0.1	22	dbSNP_125	44	3334,5200		694,1946,1627	yes	stop-gained	GAB4	NM_001037814.1		820,2688,2885	AA,AC,CC		39.0673,23.3772,33.8495		163/575	17469049	4328,8458	2126	4267	6393	SO:0001587	stop_gained	128954	exon3			TGTTTCCCAGGAA	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.487G>T	22.37:g.17469049C>A	ENSP00000383431:p.Gly163*	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001037814		Nonsense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	734	0.3360805860805861	92	0.18699186991869918	140	0.3867403314917127	227	0.3968531468531469	275	0.3627968337730871	C	11.48	1.650227	0.29336	0.233772	0.390673	ENSG00000215568	ENST00000400588	.	.	.	1.9	-0.505	0.11993	.	238.900000	0.00166	U	0.000000	.	.	.	.	.	.	0.09310	P	0.9999999999999991	.	.	.	.	.	.	.	.	.	.	0.09338	T	0.73	.	2.2739	0.04097	0.0:0.2171:0.3125:0.4705	rs28502153	.	.	.	X	163	.	ENSP00000383431:G163X	G	-	1	0	GAB4	15849049	1.000000	0.71417	0.141000	0.22245	0.007000	0.05969	1.798000	0.38814	-0.183000	0.10585	0.313000	0.20887	GGA	C|0.664;A|0.336	0.336	strong		0.552	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
ATP9A	10079	hgsc.bcm.edu	37	20	50235577	50235577	+	Silent	SNP	G	G	A	rs2295004	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:50235577G>A	ENST00000338821.5	-	20	2385	c.2121C>T	c.(2119-2121)acC>acT	p.T707T	ATP9A_ENST00000311637.5_Silent_p.T571T|ATP9A_ENST00000402822.1_Silent_p.T586T	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	707					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CCCCGCGGTTGGTCACCTGGA	0.592													G|||	556	0.111022	0.0287	0.1945	5008	,	,		18078	0.1349		0.1083	False		,,,				2504	0.1411				p.T707T		Atlas-SNP	.											.	ATP9A	135	.	0			c.C2121T						PASS	.	G		160,4246	106.9+/-145.3	2,156,2045	50.0	47.0	48.0		2121	2.9	1.0	20	dbSNP_100	48	923,7677	203.7+/-246.6	53,817,3430	no	coding-synonymous	ATP9A	NM_006045.1		55,973,5475	AA,AG,GG		10.7326,3.6314,8.3269		707/1048	50235577	1083,11923	2203	4300	6503	SO:0001819	synonymous_variant	10079	exon20			GCGGTTGGTCACC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.2121C>T	20.37:g.50235577G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			G|0.904;A|0.096	0.096	strong		0.592	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
CCDC185	164127	hgsc.bcm.edu	37	1	223567803	223567803	+	Missense_Mutation	SNP	G	G	A	rs10907376	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:223567803G>A	ENST00000366875.3	+	1	1089	c.986G>A	c.(985-987)gGc>gAc	p.G329D		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		329			G -> D (in dbSNP:rs10907376). {ECO:0000269|PubMed:15489334}.							breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		GAGCAGCGCGGCCTGCGGCGG	0.697													G|||	881	0.175919	0.1831	0.1916	5008	,	,		14025	0.1101		0.2734	False		,,,				2504	0.1227				p.G329D		Atlas-SNP	.											C1orf65,NS,carcinoma,0,4	C1orf65	71	4	0			c.G986A						PASS	.	G	ASP/GLY	834,3424		100,634,1395	11.0	10.0	11.0		986	-0.7	0.0	1	dbSNP_120	11	2191,6245		296,1599,2323	no	missense	C1orf65	NM_152610.2	94	396,2233,3718	AA,AG,GG		25.972,19.5867,23.8302	probably-damaging	329/624	223567803	3025,9669	2129	4218	6347	SO:0001583	missense	164127	exon1			AGCGCGGCCTGCG																												ENST00000366875.3:c.986G>A	1.37:g.223567803G>A	ENSP00000355840:p.Gly329Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	448	0.20512820512820512	88	0.17886178861788618	86	0.23756906077348067	72	0.1258741258741259	202	0.26649076517150394	G	5.552	0.286677	0.10513	0.195867	0.25972	ENSG00000178395	ENST00000366875	T	0.23147	1.92	4.71	-0.728	0.11162	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.29432	0.244	B	0.24848	0.056	T	0.42292	-0.9460	8	0.17369	T	0.5	.	1.5099	0.02494	0.1275:0.3469:0.209:0.3166	rs10907376;rs17481328;rs17852895;rs17858889;rs58442298;rs10907376	329	Q8N715	CA065_HUMAN	D	329	ENSP00000355840:G329D	ENSP00000355840:G329D	G	+	2	0	C1orf65	221634426	0.000000	0.05858	0.001000	0.08648	0.032000	0.12392	-0.021000	0.12504	-0.055000	0.13244	0.650000	0.86243	GGC	G|0.814;A|0.186	0.186	strong		0.697	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
BTNL2	56244	hgsc.bcm.edu	37	6	32362669	32362669	+	Silent	SNP	T	T	G	rs41449245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32362669T>G	ENST00000374993.1	-	6	1211	c.1212A>C	c.(1210-1212)tcA>tcC	p.S404S	BTNL2_ENST00000414363.1_Silent_p.S194S|BTNL2_ENST00000544175.1_Silent_p.S127S|BTNL2_ENST00000540315.1_Silent_p.S194S|BTNL2_ENST00000429232.2_3'UTR|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Silent_p.S310S|BTNL2_ENST00000454136.3_Silent_p.S404S	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	404						integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CCTGGGAAGATGATGGTATCG	0.552													t|||	821	0.163938	0.1422	0.1599	5008	,	,		20290	0.1587		0.163	False		,,,				2504	0.2025				p.S404S		Atlas-SNP	.											.	BTNL2	50	.	0			c.A1212C						PASS	.			551,3855	248.1+/-256.1	28,495,1680	233.0	221.0	225.0		1212	-10.2	0.0	6	dbSNP_127	225	1241,7359	248.3+/-276.0	92,1057,3151	no	coding-synonymous	BTNL2	NM_019602.1		120,1552,4831	GG,GT,TT		14.4302,12.5057,13.7783		404/456	32362669	1792,11214	2203	4300	6503	SO:0001819	synonymous_variant	56244	exon6			GGAAGATGATGGT	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1212A>C	6.37:g.32362669T>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				T|0.859;G|0.141	0.141	strong		0.552	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
FRMD1	79981	hgsc.bcm.edu	37	6	168479568	168479568	+	Silent	SNP	G	G	A	rs78152017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:168479568G>A	ENST00000283309.6	-	1	271	c.207C>T	c.(205-207)gcC>gcT	p.A69A		NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	69	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					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)		TCACCCCCACGGCCAGCCGCA	0.706													G|||	506	0.101038	0.1051	0.0807	5008	,	,		13489	0.1181		0.0676	False		,,,				2504	0.1268				p.A69A	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C207T						PASS	.	G		389,4015		15,359,1828	47.0	55.0	52.0		207	-5.8	0.1	6	dbSNP_131	52	685,7905		29,627,3639	no	coding-synonymous	FRMD1	NM_024919.3		44,986,5467	AA,AG,GG		7.9744,8.8329,8.2654		69/550	168479568	1074,11920	2202	4295	6497	SO:0001819	synonymous_variant	79981	exon1			CCCCACGGCCAGC		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.207C>T	6.37:g.168479568G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	24	4	0.166667	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Silent	SNP	ENST00000283309.6	37	CCDS5306.1																																																																																			G|0.913;A|0.087	0.087	strong		0.706	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
DNHD1	144132	hgsc.bcm.edu	37	11	6569896	6569896	+	Missense_Mutation	SNP	G	G	A	rs11606889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6569896G>A	ENST00000527990.2	+	22	7120	c.7120G>A	c.(7120-7122)Gtg>Atg	p.V2374M	DNHD1_ENST00000254579.6_Missense_Mutation_p.V2374M			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2374					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CTTGTATGTGGTGGACCTGCT	0.522													G|||	636	0.126997	0.0832	0.1729	5008	,	,		19672	0.0228		0.1829	False		,,,				2504	0.2035				p.V2374M		Atlas-SNP	.											.	DNHD1	198	.	0			c.G7120A						PASS	.	G	MET/VAL	136,1248		8,120,564	59.0	52.0	54.0		7120	4.9	1.0	11	dbSNP_120	54	619,2563		51,517,1023	yes	missense	DNHD1	NM_144666.2	21	59,637,1587	AA,AG,GG		19.4532,9.8266,16.5353	probably-damaging	2374/4754	6569896	755,3811	692	1591	2283	SO:0001583	missense	144132	exon24			TATGTGGTGGACC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.7120G>A	11.37:g.6569896G>A	ENSP00000436180:p.Val2374Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	253	0.11584249084249085	47	0.09552845528455285	50	0.13812154696132597	18	0.03146853146853147	138	0.1820580474934037	G	15.97	2.988476	0.53934	0.098266	0.194532	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.29397	1.57;1.57	5.96	4.95	0.65309	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.39708	P	0.028714000000000017	D	0.63046	0.992	P	0.58077	0.832	T	0.06006	-1.0851	8	0.22706	T	0.39	.	9.6269	0.39757	0.1245:0.0:0.8755:0.0	rs11606889;rs58131910;rs11606889	2374	Q96M86	DNHD1_HUMAN	M	2374	ENSP00000254579:V2374M;ENSP00000436180:V2374M	ENSP00000254579:V2374M	V	+	1	0	DNHD1	6526472	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.820000	0.39032	2.813000	0.96785	0.655000	0.94253	GTG	G|0.887;A|0.113	0.113	strong		0.522	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
OTUD4	54726	hgsc.bcm.edu	37	4	146062553	146062553	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:146062553C>T	ENST00000447906.2	-	19	2248	c.2061G>A	c.(2059-2061)caG>caA	p.Q687Q	OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Silent_p.Q622Q			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	687					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					CCTCCCCAGTCTGACACAGTG	0.428																																					p.Q622Q		Atlas-SNP	.											OTUD4,NS,carcinoma,-2,1	OTUD4	120	1	0			c.G1866A						scavenged	.						72.0	71.0	72.0					4																	146062553		2203	4300	6503	SO:0001819	synonymous_variant	54726	exon19			CCCAGTCTGACAC		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2061G>A	4.37:g.146062553C>T		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	194	2	0.0103093	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Silent	SNP	ENST00000447906.2	37																																																																																				.	.	none		0.428	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493	
SGOL2	151246	hgsc.bcm.edu	37	2	201437334	201437334	+	Silent	SNP	T	T	C	rs12052989	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:201437334T>C	ENST00000357799.4	+	7	2363	c.2265T>C	c.(2263-2265)ccT>ccC	p.P755P		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	755					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						AAATCATCCCTGGAAACCTAG	0.348													T|||	3636	0.726038	0.7027	0.6614	5008	,	,		17738	0.8135		0.7982	False		,,,				2504	0.6391				p.P755P		Atlas-SNP	.											.	SGOL2	126	.	0			c.T2265C						PASS	.	T	,,	2530,1106		873,784,161	56.0	53.0	54.0		2265,2265,2265	-2.3	0.0	2	dbSNP_120	54	6424,1702		2551,1322,190	yes	coding-synonymous,coding-synonymous,coding-synonymous	SGOL2	NM_001160033.1,NM_001160046.1,NM_152524.5	,,	3424,2106,351	CC,CT,TT		20.9451,30.418,23.8735	,,	755/1261,755/1262,755/1266	201437334	8954,2808	1818	4063	5881	SO:0001819	synonymous_variant	151246	exon7			CATCCCTGGAAAC	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2265T>C	2.37:g.201437334T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	37	CCDS42796.1																																																																																			T|0.238;C|0.762	0.762	strong		0.348	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
ITGB1	3688	hgsc.bcm.edu	37	10	33214802	33214802	+	Silent	SNP	A	A	G	rs2298141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:33214802A>G	ENST00000396033.2	-	6	918	c.783T>C	c.(781-783)tgT>tgC	p.C261C	ITGB1_ENST00000423113.1_Silent_p.C261C|ITGB1_ENST00000484088.1_5'Flank|ITGB1_ENST00000374956.4_Silent_p.C261C|ITGB1_ENST00000302278.3_Silent_p.C261C	NM_133376.2	NP_596867.1	P05556	ITB1_HUMAN	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	261	VWFA.			CGSLI -> VWMLL (in Ref. 6; AAI13902). {ECO:0000305}.	axon extension (GO:0048675)|axon guidance (GO:0007411)|B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cardiac muscle cell differentiation (GO:0055007)|cell fate specification (GO:0001708)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular response to ionizing radiation (GO:0071479)|cellular response to mechanical stimulus (GO:0071260)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|formation of radial glial scaffolds (GO:0021943)|G1/S transition of mitotic cell cycle (GO:0000082)|germ cell migration (GO:0008354)|heterotypic cell-cell adhesion (GO:0034113)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|maternal process involved in female pregnancy (GO:0060135)|mesodermal cell differentiation (GO:0048333)|negative regulation of anoikis (GO:2000811)|negative regulation of cell projection organization (GO:0031345)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein transport within lipid bilayer (GO:0032594)|regulation of cell cycle (GO:0051726)|regulation of collagen catabolic process (GO:0010710)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of immune response (GO:0050776)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|response to transforming growth factor beta (GO:0071559)|sarcomere organization (GO:0045214)|tight junction assembly (GO:0070830)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	acrosomal vesicle (GO:0001669)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha1-beta1 complex (GO:0034665)|integrin alpha10-beta1 complex (GO:0034680)|integrin alpha11-beta1 complex (GO:0034681)|integrin alpha2-beta1 complex (GO:0034666)|integrin alpha3-beta1 complex (GO:0034667)|integrin alpha7-beta1 complex (GO:0034677)|integrin alpha8-beta1 complex (GO:0034678)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|intercalated disc (GO:0014704)|invadopodium membrane (GO:0071438)|membrane (GO:0016020)|membrane raft (GO:0045121)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|cell adhesion molecule binding (GO:0050839)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)|peptide binding (GO:0042277)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|virus receptor activity (GO:0001618)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Ovarian(717;1.34e-05)|Breast(68;0.0634)			Antithymocyte globulin(DB00098)	CGCTTACTCCACAAACTGCAA	0.348													A|||	784	0.15655	0.0401	0.1859	5008	,	,		18818	0.245		0.172	False		,,,				2504	0.1861				p.C261C		Atlas-SNP	.											.	ITGB1	156	.	0			c.T783C						PASS	.	A	,,	250,4156	143.8+/-178.8	9,232,1962	96.0	89.0	92.0		783,783,783	4.6	1.0	10	dbSNP_100	92	1510,7090	285.7+/-297.3	139,1232,2929	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB1	NM_002211.3,NM_033668.2,NM_133376.2	,,	148,1464,4891	GG,GA,AA		17.5581,5.6741,13.5322	,,	261/799,261/802,261/799	33214802	1760,11246	2203	4300	6503	SO:0001819	synonymous_variant	3688	exon6			TACTCCACAAACT	BC020057	CCDS7174.1	10p11.2	2010-10-13			ENSG00000150093	ENSG00000150093		"""CD molecules"", ""Integrins"""	6153	protein-coding gene	gene with protein product		135630		FNRB, MSK12, MDF2		2524991	Standard	NM_033668		Approved	CD29, GPIIA	uc001iwt.4	P05556	OTTHUMG00000017928	ENST00000396033.2:c.783T>C	10.37:g.33214802A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_002211	A8K6N2|D3DRX9|D3DRY3|D3DRY4|D3DRY5|P78466|P78467|Q13089|Q13090|Q13091|Q13212|Q14622|Q14647|Q29RW2|Q7Z3V1|Q8WUM6	Silent	SNP	ENST00000396033.2	37	CCDS7174.1																																																																																			A|0.852;G|0.148	0.148	strong		0.348	ITGB1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047496.1	NM_002211	
OR4C11	219429	hgsc.bcm.edu	37	11	55371381	55371381	+	Nonsense_Mutation	SNP	G	G	A	rs75423534	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55371381G>A	ENST00000302231.4	-	1	493	c.469C>T	c.(469-471)Cag>Tag	p.Q157*		NM_001004700.2	NP_001004700.2	Q6IEV9	OR4CB_HUMAN	olfactory receptor, family 4, subfamily C, member 11	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q157K(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|prostate(1)|skin(1)	33						AGGATAATCTGAGCTGTAGAG	0.458													g|||	346	0.0690895	0.003	0.1225	5008	,	,		14125	0.005		0.1322	False		,,,				2504	0.1217				p.Q157X		Atlas-SNP	.											OR4C11,rectum,carcinoma,0,1	OR4C11	73	1	1	Substitution - Missense(1)	large_intestine(1)	c.C469T						PASS	.	G	stop/GLN	126,4232		19,88,2072	69.0	60.0	63.0		469	4.3	0.2	11	dbSNP_131	63	1094,6920		260,574,3173	yes	stop-gained	OR4C11	NM_001004700.2		279,662,5245	AA,AG,GG		13.6511,2.8912,9.861		157/311	55371381	1220,11152	2179	4007	6186	SO:0001587	stop_gained	219429	exon1			TAATCTGAGCTGT	AB065774	CCDS31503.1	11q11	2012-08-09		2004-03-10	ENSG00000172188	ENSG00000172188		"""GPCR / Class A : Olfactory receptors"""	15167	protein-coding gene	gene with protein product				OR4C11P			Standard	NM_001004700		Approved		uc010rii.2	Q6IEV9	OTTHUMG00000165290	ENST00000302231.4:c.469C>T	11.37:g.55371381G>A	ENSP00000306651:p.Gln157*	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001004700	B9EIL4|Q8NGL8	Nonsense_Mutation	SNP	ENST00000302231.4	37	CCDS31503.1	161	0.07371794871794872	1	0.0020325203252032522	41	0.1132596685082873	4	0.006993006993006993	115	0.1517150395778364	G	9.320	1.057753	0.19907	0.028912	0.136511	ENSG00000172188	ENST00000302231	.	.	.	4.34	4.34	0.51931	.	0.000000	0.46442	U	0.000300	.	.	.	.	.	.	0.09310	P	0.9999999999999756	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	15.9533	0.79861	0.0:0.0:1.0:0.0	.	.	.	.	X	157	.	ENSP00000306651:Q157X	Q	-	1	0	OR4C11	55127957	0.001000	0.12720	0.213000	0.23690	0.004000	0.04260	0.160000	0.16462	2.425000	0.82216	0.478000	0.44815	CAG	G|0.926;A|0.074	0.074	strong		0.458	OR4C11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383268.1	NM_001004700	
ATP13A3	79572	hgsc.bcm.edu	37	3	194157937	194157937	+	Silent	SNP	G	G	A	rs369809078		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194157937G>A	ENST00000439040.1	-	20	2798	c.2007C>T	c.(2005-2007)gtC>gtT	p.V669V	ATP13A3_ENST00000256031.4_Silent_p.V669V			Q9H7F0	AT133_HUMAN	ATPase type 13A3	669						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		TTTGAAAATCGACAGGAACTT	0.348																																					p.V669V		Atlas-SNP	.											.	ATP13A3	94	.	0			c.C2007T						PASS	.	G		0,3612		0,0,1806	98.0	93.0	94.0		2007	-1.1	0.8	3		94	1,8175		0,1,4087	no	coding-synonymous	ATP13A3	NM_024524.3		0,1,5893	AA,AG,GG		0.0122,0.0,0.0085		669/1227	194157937	1,11787	1806	4088	5894	SO:0001819	synonymous_variant	79572	exon19			AAAATCGACAGGA	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"""ATPases / P-type"""	24113	protein-coding gene	gene with protein product	"""ATPase family homolog up regulated in senescence cells"""	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.2007C>T	3.37:g.194157937G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_024524	Q8NC11|Q96KS1	Silent	SNP	ENST00000439040.1	37	CCDS43187.1																																																																																			.	.	weak		0.348	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524	
APOB	338	hgsc.bcm.edu	37	2	21232804	21232804	+	Silent	SNP	G	G	A	rs386643884|rs1041968	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:21232804G>A	ENST00000233242.1	-	26	7063	c.6936C>T	c.(6934-6936)gaC>gaT	p.D2312D		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2312					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTCAAGAATGTCATTTATTC	0.348													G|||	1248	0.249201	0.2095	0.3775	5008	,	,		20035	0.0615		0.4423	False		,,,				2504	0.2065				p.D2312D		Atlas-SNP	.											APOB,NS,malignant_melanoma,-2,1	APOB	761	1	0			c.C6936T						PASS	.	G		1032,3374		139,754,1310	116.0	119.0	118.0		6936	-2.2	0.0	2	dbSNP_86	118	4118,4482		1092,1934,1274	no	coding-synonymous	APOB	NM_000384.2		1231,2688,2584	AA,AG,GG		47.8837,23.4226,39.5971		2312/4564	21232804	5150,7856	2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			AAGAATGTCATTT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.6936C>T	2.37:g.21232804G>A		Somatic	183	1	0.00546448		WXS	Illumina HiSeq	Phase_I	146	143	0.979452	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.640;A|0.360	0.360	strong		0.348	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
STRIP2	57464	hgsc.bcm.edu	37	7	129093179	129093179	+	Missense_Mutation	SNP	T	T	C	rs201255678		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129093179T>C	ENST00000249344.2	+	5	561	c.521T>C	c.(520-522)aTg>aCg	p.M174T	STRIP2_ENST00000435494.2_Missense_Mutation_p.M174T	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	174					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											CTACTCCACATGGAAATTGAG	0.512													T|||	1	0.000199681	0.0	0.0014	5008	,	,		20828	0.0		0.0	False		,,,				2504	0.0				p.M174T		Atlas-SNP	.											.	.	.	.	0			c.T521C						PASS	.						142.0	114.0	124.0					7																	129093179		2203	4300	6503	SO:0001583	missense	57464	exon5			TCCACATGGAAAT	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.521T>C	7.37:g.129093179T>C	ENSP00000249344:p.Met174Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.467920	0.43839	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.47177	0.86;0.85	5.68	5.68	0.88126	.	0.041546	0.85682	D	0.000000	T	0.56202	0.1969	M	0.62723	1.935	0.80722	D	1	B;P	0.46395	0.071;0.877	B;P	0.53861	0.062;0.736	T	0.51772	-0.8663	10	0.13108	T	0.6	-20.1919	13.8875	0.63717	0.0:0.0:0.0:1.0	.	174;174	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	T	174	ENSP00000249344:M174T;ENSP00000392393:M174T	ENSP00000249344:M174T	M	+	2	0	FAM40B	128880415	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.179000	0.69175	0.459000	0.35465	ATG	T|0.999;C|0.001	0.001	weak		0.512	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336	
NBEAL2	23218	hgsc.bcm.edu	37	3	47036756	47036756	+	Missense_Mutation	SNP	C	C	G	rs11720139	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:47036756C>G	ENST00000450053.3	+	13	1710	c.1531C>G	c.(1531-1533)Cgc>Ggc	p.R511G	NBEAL2_ENST00000292309.5_Missense_Mutation_p.R511G|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	511			R -> G (in dbSNP:rs11720139).		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)		CCTGGAGGCCCGCTGCCAAGA	0.657													C|||	1586	0.316693	0.2027	0.3141	5008	,	,		19464	0.3383		0.3936	False		,,,				2504	0.3712				p.R511G		Atlas-SNP	.											NBEAL2_ENST00000450053,NS,carcinoma,0,4	NBEAL2	267	4	0			c.C1531G						scavenged	.	C	GLY/ARG	789,3121		86,617,1252	8.0	10.0	9.0		1531	4.5	0.9	3	dbSNP_120	9	2983,5223		583,1817,1703	yes	missense	NBEAL2	NM_015175.1	125	669,2434,2955	GG,GC,CC		36.3515,20.179,31.1324	possibly-damaging	511/2755	47036756	3772,8344	1955	4103	6058	SO:0001583	missense	23218	exon13			GAGGCCCGCTGCC	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.1531C>G	3.37:g.47036756C>G	ENSP00000415034:p.Arg511Gly	Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	680	0.31135531135531136	91	0.18495934959349594	105	0.2900552486187845	186	0.32517482517482516	298	0.39313984168865435	C	5.007	0.187024	0.09547	0.20179	0.363515	ENSG00000160796	ENST00000292309;ENST00000450053;ENST00000296147	T;T	0.33438	1.41;1.41	4.54	4.54	0.55810	Armadillo-like helical (1);Armadillo-type fold (1);	0.311770	0.31685	N	0.007232	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	1.0	B;B	0.31383	0.321;0.094	B;B	0.26094	0.066;0.041	T	0.47636	-0.9102	9	0.27082	T	0.32	.	11.5906	0.50943	0.1783:0.8216:0.0:0.0	rs11720139;rs58658507;rs11720139	477;511	Q6ZNJ1-4;Q6ZNJ1	.;NBEL2_HUMAN	G	511;511;477	ENSP00000292309:R511G;ENSP00000415034:R511G	ENSP00000292309:R511G	R	+	1	0	NBEAL2	47011760	0.414000	0.25408	0.870000	0.34147	0.094000	0.18550	1.491000	0.35583	2.506000	0.84524	0.655000	0.94253	CGC	C|0.687;G|0.313	0.313	strong		0.657	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
ANKRD50	57182	hgsc.bcm.edu	37	4	125590478	125590478	+	Silent	SNP	T	T	C	rs1874748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:125590478T>C	ENST00000504087.1	-	4	4991	c.3954A>G	c.(3952-3954)ccA>ccG	p.P1318P	ANKRD50_ENST00000515641.1_Silent_p.P1139P	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1318										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						TTTGTTTAGGTGGTGCAGCAG	0.398													T|||	1070	0.213658	0.2292	0.1816	5008	,	,		19308	0.2421		0.16	False		,,,				2504	0.2413				p.P1318P		Atlas-SNP	.											.	ANKRD50	136	.	0			c.A3954G						PASS	.	T	,	969,3437	363.1+/-316.4	99,771,1333	145.0	146.0	146.0		3417,3954	-10.4	0.0	4	dbSNP_92	146	1303,7297	257.5+/-281.5	107,1089,3104	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	206,1860,4437	CC,CT,TT		15.1512,21.9927,17.4689	,	1139/1251,1318/1430	125590478	2272,10734	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			TTTAGGTGGTGCA	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.3954A>G	4.37:g.125590478T>C		Somatic	278	1	0.00359712		WXS	Illumina HiSeq	Phase_I	267	128	0.479401	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			T|0.820;C|0.180	0.180	strong		0.398	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
E2F4	1874	hgsc.bcm.edu	37	16	67234134	67234134	+	IGR	SNP	A	A	G	rs8058861	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67234134A>G	ENST00000379378.3	+	0	2096				ELMO3_ENST00000360833.1_Missense_Mutation_p.N131D|ELMO3_ENST00000571638.1_3'UTR|ELMO3_ENST00000393997.2_Missense_Mutation_p.N148D|ELMO3_ENST00000477898.1_5'UTR|MIR328_ENST00000385213.1_RNA	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		GCTGCAGAGTAACAGTCCTGA	0.622													G|||	1010	0.201677	0.5182	0.0735	5008	,	,		13259	0.0238		0.0696	False		,,,				2504	0.184				p.N148D		Atlas-SNP	.											.	ELMO3	41	.	0			c.A442G						PASS	.	G	ASP/ASN	1657,2387		342,973,707	36.0	38.0	37.0		442	0.7	0.0	16	dbSNP_116	37	583,7741		29,525,3608	yes	missense	ELMO3	NM_024712.3	23	371,1498,4315	GG,GA,AA		7.0038,40.9743,18.1113	benign	148/774	67234134	2240,10128	2022	4162	6184	SO:0001628	intergenic_variant	79767	exon5			CAGAGTAACAGTC	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975		16.37:g.67234134A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	333	0.15247252747252749	239	0.48577235772357724	33	0.09116022099447514	12	0.02097902097902098	49	0.06464379947229551	G	10.23	1.291660	0.23564	0.409743	0.070038	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.46819	0.86;0.86	5.16	0.709	0.18150	.	1.206870	0.05741	N	0.601429	T	0.00012	0.0000	N	0.12182	0.205	0.36902	P	0.109541	B;B	0.18166	0.011;0.026	B;B	0.17722	0.019;0.019	T	0.45160	-0.9280	9	0.25106	T	0.35	-1.8862	1.3437	0.02159	0.2925:0.242:0.3415:0.124	rs8058861;rs8058861	131;148	F8W9E7;Q96BJ8-3	.;.	D	131;148	ENSP00000354077:N131D;ENSP00000377566:N148D	ENSP00000354077:N131D	N	+	1	0	ELMO3	65791635	0.001000	0.12720	0.035000	0.18076	0.556000	0.35491	-0.293000	0.08320	-0.315000	0.08703	-0.366000	0.07423	AAC	A|0.847;G|0.153	0.153	strong		0.622	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
POPDC2	64091	hgsc.bcm.edu	37	3	119378977	119378977	+	Silent	SNP	G	G	A	rs2873788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:119378977G>A	ENST00000264231.3	-	1	460	c.294C>T	c.(292-294)cgC>cgT	p.R98R	POPDC2_ENST00000493094.1_Silent_p.R98R|POPDC2_ENST00000538678.1_Silent_p.R98R|POPDC2_ENST00000468801.1_Silent_p.R98R|POPDC2_ENST00000474523.1_Intron	NM_022135.2	NP_071418.2	Q9HBU9	POPD2_HUMAN	popeye domain containing 2	98					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)		CCTCACGCAGGCGGTATACCA	0.582													G|||	419	0.0836661	0.0166	0.0951	5008	,	,		19865	0.001		0.164	False		,,,				2504	0.1687				p.R98R		Atlas-SNP	.											POPDC2,NS,carcinoma,-1,1	POPDC2	36	1	0			c.C294T						PASS	.	G		164,4242	109.1+/-147.4	3,158,2042	134.0	117.0	123.0		294	0.3	1.0	3	dbSNP_101	123	1667,6933	308.2+/-308.8	161,1345,2794	no	coding-synonymous	POPDC2	NM_022135.2		164,1503,4836	AA,AG,GG		19.3837,3.7222,14.0781		98/365	119378977	1831,11175	2203	4300	6503	SO:0001819	synonymous_variant	64091	exon1			ACGCAGGCGGTAT	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.294C>T	3.37:g.119378977G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_022135	Q86UE7	Silent	SNP	ENST00000264231.3	37	CCDS2992.1																																																																																			G|0.887;A|0.113	0.113	strong		0.582	POPDC2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355378.1	NM_022135	
COPG1	22820	hgsc.bcm.edu	37	3	128971751	128971751	+	Silent	SNP	C	C	T	rs73202214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:128971751C>T	ENST00000314797.6	+	5	380	c.276C>T	c.(274-276)atC>atT	p.I92I		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	92					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										ACTTGACCATCAAGGAGATGT	0.542													C|||	4	0.000798722	0.0	0.0043	5008	,	,		21362	0.0		0.001	False		,,,				2504	0.0				p.I92I		Atlas-SNP	.											.	.	.	.	0			c.C276T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	186.0	160.0	169.0		276	5.1	1.0	3	dbSNP_130	169	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	COPG	NM_016128.3		0,17,6486	TT,TC,CC		0.1628,0.0681,0.1307		92/875	128971751	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	22820	exon5			GACCATCAAGGAG	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"""coat protein gamma-cop"""	615525	"""coatomer protein complex, subunit gamma"""	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.276C>T	3.37:g.128971751C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																			C|0.998;T|0.002	0.002	strong		0.542	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	
RFX7	64864	hgsc.bcm.edu	37	15	56388033	56388033	+	Silent	SNP	T	T	C	rs12439907	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:56388033T>C	ENST00000559447.2	-	9	1873	c.1602A>G	c.(1600-1602)ttA>ttG	p.L534L	RFX7_ENST00000422057.1_Silent_p.L534L|RFX7_ENST00000423270.1_Silent_p.L631L|RFX7_ENST00000317318.6_Silent_p.L631L			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	534					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGGTGAAAGTTAAGTTCTGAG	0.418													T|||	1364	0.272364	0.0794	0.2767	5008	,	,		23220	0.5		0.1968	False		,,,				2504	0.3732				p.L631L		Atlas-SNP	.											.	RFX7	170	.	0			c.A1893G						PASS	.	T		459,3521		27,405,1558	81.0	79.0	79.0		1893	0.1	1.0	15	dbSNP_120	79	1733,6607		179,1375,2616	no	coding-synonymous	RFX7	NM_022841.5		206,1780,4174	CC,CT,TT		20.7794,11.5327,17.7922		631/1461	56388033	2192,10128	1990	4170	6160	SO:0001819	synonymous_variant	64864	exon9			GAAAGTTAAGTTC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.1602A>G	15.37:g.56388033T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				T|0.747;C|0.253	0.253	strong		0.418	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
BCLAF1	9774	hgsc.bcm.edu	37	6	136589448	136589448	+	Missense_Mutation	SNP	C	C	A	rs78267720	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:136589448C>A	ENST00000531224.1	-	10	2501	c.2249G>T	c.(2248-2250)cGa>cTa	p.R750L	BCLAF1_ENST00000353331.4_Missense_Mutation_p.R748L|BCLAF1_ENST00000530767.1_Missense_Mutation_p.R577L|BCLAF1_ENST00000392348.2_Missense_Mutation_p.R748L|BCLAF1_ENST00000529917.1_5'UTR|BCLAF1_ENST00000031135.9_5'UTR|BCLAF1_ENST00000527759.1_Missense_Mutation_p.R748L|BCLAF1_ENST00000527536.1_Missense_Mutation_p.R750L	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	750	Poly-Ser.				apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		GGATGAAGATCGAGAATGATC	0.343																																					p.R750L	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,bladder,carcinoma,-1,1	BCLAF1	203	1	0			c.G2249T						PASS	.						106.0	91.0	97.0					6																	136589448		2203	4300	6503	SO:0001583	missense	9774	exon10			GAAGATCGAGAAT	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.2249G>T	6.37:g.136589448C>A	ENSP00000435210:p.Arg750Leu	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	109	30	0.275229	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529872	0.64860	.	.	ENSG00000029363	ENST00000531224;ENST00000353331;ENST00000527536;ENST00000530767;ENST00000527759;ENST00000392348	T;T;T;T;T;T	0.14022	2.54;2.54;2.54;2.54;2.54;2.54	4.97	4.97	0.65823	.	0.000000	0.47852	D	0.000213	T	0.20455	0.0492	L	0.47190	1.495	0.80722	D	1	D;D;D;D;D	0.71674	0.991;0.998;0.991;0.991;0.991	P;D;P;P;P	0.69654	0.771;0.965;0.771;0.771;0.771	T	0.00752	-1.1581	10	0.35671	T	0.21	-3.7893	16.7666	0.85525	0.0:1.0:0.0:0.0	.	748;78;748;750;577	Q9NYF8-2;B7Z8J9;Q9NYF8-3;Q9NYF8;Q9NYF8-4	.;.;.;BCLF1_HUMAN;.	L	750;748;750;577;748;748	ENSP00000435210:R750L;ENSP00000229446:R748L;ENSP00000435441:R750L;ENSP00000436501:R577L;ENSP00000434826:R748L;ENSP00000376159:R748L	ENSP00000229446:R748L	R	-	2	0	BCLAF1	136631141	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.587000	0.60991	2.478000	0.83669	0.484000	0.47621	CGA	C|0.811;A|0.190	0.190	strong		0.343	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
CRMP1	1400	hgsc.bcm.edu	37	4	5841350	5841350	+	Silent	SNP	A	A	G	rs16837723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5841350A>G	ENST00000397890.2	-	9	1081	c.867T>C	c.(865-867)caT>caC	p.H289H	CRMP1_ENST00000324989.7_Silent_p.H403H|CRMP1_ENST00000512574.1_Silent_p.H287H|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	289					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		TGCTCCAGTAATGGGTGCCAT	0.587													A|||	1494	0.298323	0.4531	0.1628	5008	,	,		17453	0.4762		0.1163	False		,,,				2504	0.1892				p.H403H		Atlas-SNP	.											.	CRMP1	118	.	0			c.T1209C						PASS	.	A	,	1797,2609	512.4+/-368.1	352,1093,758	32.0	34.0	34.0		1209,867	0.6	1.0	4	dbSNP_123	34	1133,7467	226.9+/-262.5	69,995,3236	no	coding-synonymous,coding-synonymous	CRMP1	NM_001014809.1,NM_001313.3	,	421,2088,3994	GG,GA,AA		13.1744,40.7853,22.5281	,	403/687,289/573	5841350	2930,10076	2203	4300	6503	SO:0001819	synonymous_variant	1400	exon9			CCAGTAATGGGTG	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.867T>C	4.37:g.5841350A>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	24	0.387097	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																			A|0.731;G|0.269	0.269	strong		0.587	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
GALNTL6	442117	hgsc.bcm.edu	37	4	172735851	172735851	+	Silent	SNP	G	G	A	rs111570068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:172735851G>A	ENST00000506823.1	+	2	777	c.120G>A	c.(118-120)gcG>gcA	p.A40A	GALNTL6_ENST00000511251.1_Silent_p.A40A	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	40					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.A40A(1)		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						TGAAGTCAGCGGAGCCCGGGG	0.537													G|||	52	0.0103834	0.0174	0.0086	5008	,	,		17897	0.0129		0.007	False		,,,				2504	0.0031				p.A40A		Atlas-SNP	.											GALNTL6,NS,carcinoma,0,1	GALNTL6	102	1	1	Substitution - coding silent(1)	pancreas(1)	c.G120A						PASS	.	G		69,4337	61.7+/-98.7	0,69,2134	79.0	77.0	78.0		120	-10.2	0.0	4	dbSNP_132	78	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	GALNTL6	NM_001034845.2		0,93,6410	AA,AG,GG		0.2791,1.566,0.7151		40/602	172735851	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	442117	exon2			GTCAGCGGAGCCC		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.120G>A	4.37:g.172735851G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	37	CCDS34104.1																																																																																			G|0.991;A|0.009	0.009	strong		0.537	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	
USHBP1	83878	hgsc.bcm.edu	37	19	17367354	17367354	+	Silent	SNP	G	G	A	rs141680124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17367354G>A	ENST00000252597.3	-	9	1569	c.1396C>T	c.(1396-1398)Ctg>Ttg	p.L466L	AC010646.3_ENST00000594059.1_5'Flank|USHBP1_ENST00000431146.2_Silent_p.L402L	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TGGGTCCCCAGAATGGCCTGC	0.612													G|||	21	0.00419329	0.0	0.013	5008	,	,		18612	0.0		0.007	False		,,,				2504	0.0051				p.L466L		Atlas-SNP	.											.	USHBP1	85	.	0			c.C1396T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	74.0	77.0	76.0		1396	3.8	1.0	19	dbSNP_134	76	96,8504	51.9+/-112.3	0,96,4204	no	coding-synonymous	USHBP1	NM_031941.3		0,107,6396	AA,AG,GG		1.1163,0.2497,0.8227		466/704	17367354	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon9			TCCCCAGAATGGC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1396C>T	19.37:g.17367354G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605271	32605271	+	Silent	SNP	C	C	T	rs1047993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32605271C>T	ENST00000343139.5	+	1	138	c.36C>T	c.(34-36)ctC>ctT	p.L12L	HLA-DQA1_ENST00000374949.2_Silent_p.L12L|HLA-DQA1_ENST00000395363.1_Silent_p.L12L	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	12					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						TGGGGGCCCTCGCTCTGACCA	0.522													.|||	1368	0.273163	0.323	0.3285	5008	,	,		15613	0.2282		0.2883	False		,,,				2504	0.1973				p.L12L		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C36T						PASS	.	C		1199,3207		229,741,1233	74.0	67.0	69.0		36	-6.0	0.0	6	dbSNP_86	69	1968,6632		313,1342,2645	no	coding-synonymous	HLA-DQA1	NM_002122.3		542,2083,3878	TT,TC,CC		22.8837,27.2129,24.3503		12/256	32605271	3167,9839	2203	4300	6503	SO:0001819	synonymous_variant	3117	exon1			GGCCCTCGCTCTG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.36C>T	6.37:g.32605271C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	101	23	0.227723	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1																																																																																			C|0.717;T|0.283	0.283	strong		0.522	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20131115	20131115	+	Silent	SNP	C	C	T	rs9605069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20131115C>T	ENST00000334554.7	+	10	2103	c.1962C>T	c.(1960-1962)aaC>aaT	p.N654N	ZDHHC8_ENST00000320602.7_Silent_p.N562N|ZDHHC8_ENST00000405930.3_Silent_p.N654N	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	654					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					CCAGCAGCAACGCCCCGGGGC	0.721													C|||	416	0.0830671	0.0045	0.1037	5008	,	,		14342	0.004		0.168	False		,,,				2504	0.1687				p.N654N		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.C1962T						PASS	.	C	,	132,4234		3,126,2054	18.0	19.0	19.0		1962,1962	0.9	0.8	22	dbSNP_119	19	1514,7072		129,1256,2908	no	coding-synonymous,coding-synonymous	ZDHHC8	NM_001185024.1,NM_013373.3	,	132,1382,4962	TT,TC,CC		17.6334,3.0234,12.7085	,	654/779,654/766	20131115	1646,11306	2183	4293	6476	SO:0001819	synonymous_variant	29801	exon10			CAGCAACGCCCCG	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1962C>T	22.37:g.20131115C>T		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																			C|0.905;T|0.095	0.095	strong		0.721	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
C6	729	hgsc.bcm.edu	37	5	41161898	41161898	+	Missense_Mutation	SNP	C	C	T	rs142896559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:41161898C>T	ENST00000263413.3	-	10	1619	c.1355G>A	c.(1354-1356)gGa>gAa	p.G452E	C6_ENST00000337836.5_Missense_Mutation_p.G452E|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	452	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|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)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				CAAAGCTGCTCCATATTCACT	0.423													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		18136	0.0		0.004	False		,,,				2504	0.0051				p.G452E		Atlas-SNP	.											.	C6	197	.	0			c.G1355A						PASS	.	C	GLU/GLY,GLU/GLY	5,4401	9.9+/-24.2	0,5,2198	127.0	124.0	125.0		1355,1355	4.5	0.4	5	dbSNP_134	125	54,8546	34.3+/-88.2	0,54,4246	yes	missense,missense	C6	NM_000065.2,NM_001115131.1	98,98	0,59,6444	TT,TC,CC		0.6279,0.1135,0.4536	benign,benign	452/935,452/935	41161898	59,12947	2203	4300	6503	SO:0001583	missense	729	exon10			GCTGCTCCATATT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1355G>A	5.37:g.41161898C>T	ENSP00000263413:p.Gly452Glu	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	137	74	0.540146	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	16.72	3.202704	0.58234	0.001135	0.006279	ENSG00000039537	ENST00000337836;ENST00000263413	D;D	0.83335	-1.71;-1.71	5.35	4.48	0.54585	Membrane attack complex component/perforin (MACPF) domain (3);	0.311897	0.38778	N	0.001563	T	0.70090	0.3184	L	0.29908	0.895	0.30383	N	0.78175	B	0.09022	0.002	B	0.06405	0.002	T	0.72811	-0.4180	10	0.72032	D	0.01	-7.7633	16.7694	0.85533	0.0:0.1292:0.8708:0.0	.	452	P13671	CO6_HUMAN	E	452	ENSP00000338861:G452E;ENSP00000263413:G452E	ENSP00000263413:G452E	G	-	2	0	C6	41197655	0.998000	0.40836	0.415000	0.26534	0.970000	0.65996	5.677000	0.68142	1.638000	0.50547	-0.128000	0.14901	GGA	C|0.996;T|0.004	0.004	strong		0.423	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
TUBA3E	112714	hgsc.bcm.edu	37	2	130952038	130952038	+	Splice_Site	SNP	G	G	A	rs13000721	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130952038G>A	ENST00000312988.7	-	4	477	c.377C>T	c.(376-378)gCg>gTg	p.A126V		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	126			A -> V (in dbSNP:rs13000721).		microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A126V(7)		endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GCACAGATCCGCCTGAGAGAA	0.577																																					p.A126V		Atlas-SNP	.											TUBA3E,NS,carcinoma,0,8	TUBA3E	73	8	7	Substitution - Missense(7)	kidney(7)	c.C377T						scavenged	.						31.0	26.0	28.0					2																	130952038		2195	4267	6462	SO:0001630	splice_region_variant	112714	exon4			AGATCCGCCTGAG	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.376-1C>T	2.37:g.130952038G>A		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	227	69	0.303965	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	729	0.33379120879120877	99	0.20121951219512196	146	0.40331491712707185	247	0.4318181818181818	237	0.31266490765171506	g	9.044	0.990487	0.18966	.	.	ENSG00000152086	ENST00000312988	T	0.66638	-0.22	2.71	1.82	0.25136	Tubulin/FtsZ, GTPase domain (4);	0.305164	0.22723	U	0.056440	T	0.00012	0.0000	L	0.54323	1.7	0.23023	P	0.9984105	B	0.33299	0.407	B	0.40659	0.336	T	0.37663	-0.9696	9	0.87932	D	0	.	7.5288	0.27671	0.1401:0.0:0.8599:0.0	rs13000721;rs52833426;rs13000721	126	Q6PEY2	TBA3E_HUMAN	V	126	ENSP00000318197:A126V	ENSP00000318197:A126V	A	-	2	0	TUBA3E	130668508	1.000000	0.71417	0.941000	0.38009	0.623000	0.37688	6.296000	0.72751	0.488000	0.27723	0.449000	0.29647	GCG	G|0.676;A|0.324	0.324	strong		0.577	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	Missense_Mutation
ANKRD27	84079	hgsc.bcm.edu	37	19	33098632	33098632	+	Missense_Mutation	SNP	G	G	C	rs2302970	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33098632G>C	ENST00000306065.4	-	23	2440	c.2282C>G	c.(2281-2283)cCc>cGc	p.P761R	SNORA68_ENST00000364518.1_RNA	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	761			P -> R (in dbSNP:rs2302970). {ECO:0000269|PubMed:11230166}.		early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					CAGCAGGAGGGGGATGAGGTC	0.692													G|||	1328	0.265176	0.0537	0.3329	5008	,	,		15307	0.0923		0.5517	False		,,,				2504	0.3865				p.P761R		Atlas-SNP	.											.	ANKRD27	86	.	0			c.C2282G						PASS	.	G	ARG/PRO	593,3813	246.5+/-255.1	38,517,1648	38.0	34.0	35.0		2282	-0.6	0.2	19	dbSNP_100	35	4820,3780	578.0+/-390.6	1337,2146,817	yes	missense	ANKRD27	NM_032139.2	103	1375,2663,2465	CC,CG,GG		43.9535,13.4589,41.6193	benign	761/1051	33098632	5413,7593	2203	4300	6503	SO:0001583	missense	84079	exon23			AGGAGGGGGATGA	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2282C>G	19.37:g.33098632G>C	ENSP00000304292:p.Pro761Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	37	CCDS32986.1	644	0.2948717948717949	26	0.052845528455284556	138	0.3812154696132597	51	0.08916083916083917	429	0.5659630606860159	G	1.489	-0.555202	0.03967	0.134589	0.560465	ENSG00000105186	ENST00000306065	T	0.61627	0.09	5.7	-0.569	0.11756	Ankyrin repeat-containing domain (4);	0.316688	0.27379	N	0.019638	T	0.00012	0.0000	N	0.00453	-1.485	0.80722	P	0.0	B	0.11235	0.004	B	0.10450	0.005	T	0.48007	-0.9072	9	0.33141	T	0.24	-5.4917	2.458	0.04534	0.202:0.2284:0.4524:0.1172	rs2302970;rs2302970	761	Q96NW4	ANR27_HUMAN	R	761	ENSP00000304292:P761R	ENSP00000304292:P761R	P	-	2	0	ANKRD27	37790472	0.929000	0.31497	0.233000	0.24025	0.396000	0.30629	0.470000	0.22084	0.350000	0.24002	0.655000	0.94253	CCC	G|0.651;C|0.349	0.349	strong		0.692	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
ISLR	3671	hgsc.bcm.edu	37	15	74467856	74467856	+	Silent	SNP	G	G	A	rs1052622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:74467856G>A	ENST00000249842.3	+	2	1014	c.657G>A	c.(655-657)acG>acA	p.T219T	ISLR_ENST00000395118.1_Silent_p.T219T|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	219	LRRCT.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						TCAAGGGTACGCCGCTGAGCC	0.667													G|||	2933	0.585663	0.407	0.7104	5008	,	,		15910	0.5615		0.6988	False		,,,				2504	0.6472				p.T219T		Atlas-SNP	.											ISLR,NS,carcinoma,0,1	ISLR	49	1	0			c.G657A						scavenged	.	G	,	2058,2338	542.2+/-376.0	503,1052,643	39.0	36.0	37.0		657,657	-8.4	0.1	15	dbSNP_86	37	5860,2734	654.2+/-401.1	2005,1850,442	no	coding-synonymous,coding-synonymous	ISLR	NM_005545.3,NM_201526.1	,	2508,2902,1085	AA,AG,GG		31.8129,46.8153,39.0454	,	219/429,219/429	74467856	7918,5072	2198	4297	6495	SO:0001819	synonymous_variant	3671	exon2			GGGTACGCCGCTG	AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.657G>A	15.37:g.74467856G>A		Somatic	59	1	0.0169492		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_201526		Silent	SNP	ENST00000249842.3	37	CCDS10260.1																																																																																			G|0.400;A|0.600	0.600	strong		0.667	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545	
PLIN5	440503	hgsc.bcm.edu	37	19	4525046	4525046	+	Missense_Mutation	SNP	A	A	G	rs1610090	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4525046A>G	ENST00000381848.3	-	7	843	c.763T>C	c.(763-765)Tgc>Cgc	p.C255R		NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	255	Interaction with PNPLA2 and ABHD5. {ECO:0000250}.		C -> R (in dbSNP:rs1610090). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17234449}.		lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						TTCCCAGGGCAGGCCGGGGCG	0.692													G|||	4243	0.847244	0.9713	0.9121	5008	,	,		8784	0.6706		0.8588	False		,,,				2504	0.8037				p.C255R		Atlas-SNP	.											.	PLIN5	27	.	0			c.T763C						PASS	.	G	ARG/CYS	3507,115		1699,109,3	4.0	5.0	5.0		763	-4.3	0.0	19	dbSNP_88	5	6981,789		3128,725,32	yes	missense	PLIN5	NM_001013706.2	180	4827,834,35	GG,GA,AA		10.1544,3.175,7.9354	benign	255/464	4525046	10488,904	1811	3885	5696	SO:0001583	missense	440503	exon7			CAGGGCAGGCCGG	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"""Perilipins"""	33196	protein-coding gene	gene with protein product	"""lipid storage droplet protein 5"""	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.763T>C	19.37:g.4525046A>G	ENSP00000371272:p.Cys255Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	127	124	0.976378	NM_001013706	A2RRC1|Q6ZS68	Missense_Mutation	SNP	ENST00000381848.3	37	CCDS42473.1	1843	0.8438644688644689	475	0.9654471544715447	334	0.9226519337016574	381	0.666083916083916	653	0.8614775725593667	.	4.884	0.164221	0.09287	0.96825	0.898456	ENSG00000214456	ENST00000381848	T	0.04809	3.55	4.06	-4.28	0.03732	.	1.624090	0.08080	U	1.000000	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14811	-1.0459	9	0.19590	T	0.45	-2.0517	1.9256	0.03316	0.4788:0.1371:0.2448:0.1393	rs1610090;rs2288923;rs12979629;rs59173256;rs1610090	255	Q00G26	PLIN5_HUMAN	R	255	ENSP00000371272:C255R	ENSP00000371272:C255R	C	-	1	0	PLIN5	4476046	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.354000	0.07681	-0.553000	0.06158	-1.977000	0.00459	TGC	A|0.154;G|0.846	0.846	strong		0.692	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706	
IQUB	154865	hgsc.bcm.edu	37	7	123152157	123152157	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:123152157C>G	ENST00000466202.1	-	2	814	c.238G>C	c.(238-240)Gaa>Caa	p.E80Q	IQUB_ENST00000434450.1_Missense_Mutation_p.E80Q|IQUB_ENST00000324698.6_Missense_Mutation_p.E80Q|IQUB_ENST00000488987.1_Intron	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	80					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						ATAACCTCTTCCATGAGTTGT	0.408																																					p.E80Q		Atlas-SNP	.											.	IQUB	117	.	0			c.G238C						PASS	.						245.0	205.0	218.0					7																	123152157		2203	4300	6503	SO:0001583	missense	154865	exon2			CCTCTTCCATGAG	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.238G>C	7.37:g.123152157C>G	ENSP00000417769:p.Glu80Gln	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	293	139	0.474403	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656291	0.29425	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.48201	1.84;1.84;0.82	5.1	2.24	0.28232	.	0.791632	0.10762	N	0.637086	T	0.40546	0.1121	L	0.29908	0.895	0.09310	N	1	B;P;P	0.48016	0.244;0.904;0.718	B;P;B	0.48227	0.084;0.571;0.203	T	0.17198	-1.0377	10	0.45353	T	0.12	.	6.4052	0.21660	0.1487:0.6816:0.0:0.1697	.	80;80;80	A1A4Z1;Q8NA54-2;Q8NA54	.;.;IQUB_HUMAN	Q	80	ENSP00000417769:E80Q;ENSP00000324882:E80Q;ENSP00000388498:E80Q	ENSP00000324882:E80Q	E	-	1	0	IQUB	122939393	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.554000	0.23407	0.404000	0.25506	-0.813000	0.03139	GAA	.	.	none		0.408	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
KL	9365	hgsc.bcm.edu	37	13	33628138	33628138	+	Missense_Mutation	SNP	T	T	G	rs9536314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:33628138T>G	ENST00000380099.3	+	2	1062	c.1054T>G	c.(1054-1056)Ttt>Gtt	p.F352V	KL_ENST00000426690.2_Missense_Mutation_p.F45V|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	352	Glycosyl hydrolase-1 1.		F -> V (in allele KL-VS; associated with S-370; dbSNP:rs9536314). {ECO:0000269|PubMed:11792841, ECO:0000269|PubMed:15677572}.		acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TCTGCCTGATTTTACTGAATC	0.398													T|||	651	0.129992	0.2005	0.0821	5008	,	,		19946	0.0		0.1938	False		,,,				2504	0.137				p.F352V		Atlas-SNP	.											.	KL	106	.	0			c.T1054G	GRCh37	CM020378	KL	M	rs9536314	PASS	.	T	VAL/PHE	816,3590	325.6+/-299.2	74,668,1461	172.0	175.0	174.0		1054	5.9	0.9	13	dbSNP_119	174	1411,7189	273.9+/-290.9	116,1179,3005	yes	missense	KL	NM_004795.3	50	190,1847,4466	GG,GT,TT		16.407,18.5202,17.1229	probably-damaging	352/1013	33628138	2227,10779	2203	4300	6503	SO:0001583	missense	9365	exon2			CCTGATTTTACTG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1054T>G	13.37:g.33628138T>G	ENSP00000369442:p.Phe352Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	287	0.13141025641025642	93	0.18902439024390244	41	0.1132596685082873	0	0.0	153	0.20184696569920843	T	24.2	4.501579	0.85176	0.185202	0.16407	ENSG00000133116	ENST00000426690;ENST00000380099	T;T	0.32753	1.44;1.44	5.9	5.9	0.94986	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.74467	2.265	0.09310	P	0.9999999999726445	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.00202	-1.1925	9	0.87932	D	0	-24.0951	16.3317	0.83023	0.0:0.0:0.0:1.0	rs9536314;rs52816323;rs58038499;rs9536314	352;45	Q9UEF7;B3KUJ4	KLOT_HUMAN;.	V	45;352	ENSP00000399513:F45V;ENSP00000369442:F352V	ENSP00000369442:F352V	F	+	1	0	KL	32526138	1.000000	0.71417	0.944000	0.38274	0.853000	0.48598	7.914000	0.87478	2.264000	0.75181	0.533000	0.62120	TTT	T|0.846;G|0.154	0.154	strong		0.398	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
ABTB2	25841	hgsc.bcm.edu	37	11	34378381	34378381	+	Missense_Mutation	SNP	G	G	C	rs1925368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:34378381G>C	ENST00000435224.2	-	1	1174	c.750C>G	c.(748-750)caC>caG	p.H250Q	ABTB2_ENST00000298992.2_Missense_Mutation_p.H64Q	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	250			H -> Q (in dbSNP:rs1925368). {ECO:0000269|PubMed:14702039}.		cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				CATCAGGGCTGTGGCTGGCCA	0.667													C|||	896	0.178914	0.2859	0.0879	5008	,	,		16857	0.373		0.0626	False		,,,				2504	0.0184				p.H250Q		Atlas-SNP	.											.	ABTB2	101	.	0			c.C750G						PASS	.	C	GLN/HIS	1058,3346		127,804,1271	24.0	21.0	22.0		750	3.8	1.0	11	dbSNP_92	22	575,8019		12,551,3734	yes	missense	ABTB2	NM_145804.2	24	139,1355,5005	CC,CG,GG		6.6907,24.0236,12.5635	benign	250/1026	34378381	1633,11365	2202	4297	6499	SO:0001583	missense	25841	exon1			AGGGCTGTGGCTG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.750C>G	11.37:g.34378381G>C	ENSP00000410157:p.His250Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	37	CCDS7890.2	438	0.20054945054945056	137	0.2784552845528455	36	0.09944751381215469	225	0.39335664335664333	40	0.052770448548812667	C	2.321	-0.355532	0.05138	0.240236	0.066907	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.57907	0.37;0.37	4.72	3.81	0.43845	Histone-fold (2);	0.145459	0.47093	N	0.000255	T	0.00012	0.0000	N	0.00436	-1.5	0.51233	P	8.60000000000305E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.40794	-0.9544	9	0.11485	T	0.65	-9.1489	9.2476	0.37536	0.0:0.7737:0.1463:0.08	rs1925368;rs3740794;rs1925368	64	Q8N961	ABTB2_HUMAN	Q	250;64	ENSP00000410157:H250Q;ENSP00000298992:H64Q	ENSP00000298992:H64Q	H	-	3	2	ABTB2	34334957	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	2.560000	0.45896	0.437000	0.26423	-0.371000	0.07208	CAC	G|0.844;C|0.156	0.156	strong		0.667	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
TOX3	27324	hgsc.bcm.edu	37	16	52473263	52473263	+	Silent	SNP	A	A	G	rs9925256	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:52473263A>G	ENST00000219746.9	-	7	1889	c.1605T>C	c.(1603-1605)ccT>ccC	p.P535P	TOX3_ENST00000407228.3_Silent_p.P530P	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	535	Gln-rich.				apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)	p.P535P(1)		NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						GAGAGGCGACAGGGGAGTGCT	0.607													G|||	2452	0.489617	0.7648	0.3977	5008	,	,		16094	0.2679		0.4473	False		,,,				2504	0.455				p.P535P		Atlas-SNP	.											TOX3,NS,carcinoma,0,1	TOX3	121	1	1	Substitution - coding silent(1)	stomach(1)	c.T1605C						PASS	.	G	,	3033,1091		1138,757,167	20.0	22.0	21.0		1605,1590	-12.0	0.0	16	dbSNP_119	21	3986,4480		920,2146,1167	no	coding-synonymous,coding-synonymous	TOX3	NM_001080430.2,NM_001146188.1	,	2058,2903,1334	GG,GA,AA		47.0824,26.4549,44.2494	,	535/577,530/572	52473263	7019,5571	2062	4233	6295	SO:0001819	synonymous_variant	27324	exon7			GGCGACAGGGGAG	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.1605T>C	16.37:g.52473263A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	41	0.383178	NM_001080430	B4DRD0|B5MCW4	Silent	SNP	ENST00000219746.9	37	CCDS54009.1																																																																																			A|0.542;G|0.458	0.458	strong		0.607	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
PRAM1	84106	hgsc.bcm.edu	37	19	8564474	8564474	+	Missense_Mutation	SNP	G	G	T	rs371461475|rs4239541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8564474G>T	ENST00000423345.4	-	2	738	c.218C>A	c.(217-219)cCg>cAg	p.P73Q	PRAM1_ENST00000255612.3_Missense_Mutation_p.P73Q			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	121	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.		Q -> P (in dbSNP:rs4239541).		integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						GACCTCAGGCGGCGGGGGCTT	0.627													-|||	2119	0.423123	0.7973	0.3415	5008	,	,		11587	0.1677		0.335	False		,,,				2504	0.3292				p.P73Q		Atlas-SNP	.											.	PRAM1	53	.	0			c.C218A						PASS	.						46.0	59.0	55.0					19																	8564474		1861	4089	5950	SO:0001583	missense	84106	exon2			TCAGGCGGCGGGG	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.218C>A	19.37:g.8564474G>T	ENSP00000408342:p.Pro73Gln	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	835	0.3823260073260073	393	0.7987804878048781	112	0.30939226519337015	82	0.14335664335664336	248	0.32717678100263853	g	0.011	-1.711669	0.00712	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.12147	2.71;2.71	3.91	-1.47	0.08772	.	0.765173	0.10313	N	0.689739	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.13145	0.002;0.007	B;B	0.04013	0.001;0.001	T	0.32508	-0.9904	9	0.02654	T	1	.	6.8516	0.24018	0.1315:0.0:0.4151:0.4534	rs4239541	73;121	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	Q	73	ENSP00000255612:P73Q;ENSP00000408342:P73Q	ENSP00000255612:P73Q	P	-	2	0	PRAM1	8470474	0.000000	0.05858	0.006000	0.13384	0.011000	0.07611	-0.213000	0.09305	-0.121000	0.11787	-1.496000	0.00964	CCG	G|0.653;T|0.347	0.347	strong		0.627	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
KCNV1	27012	hgsc.bcm.edu	37	8	110986480	110986480	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110986480G>A	ENST00000524391.1	-	2	1170	c.138C>T	c.(136-138)ggC>ggT	p.G46G	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Silent_p.G46G			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	46					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			AGCGGCTGCCGCCCACGTTGA	0.692																																					p.G46G		Atlas-SNP	.											.	KCNV1	101	.	0			c.C138T						PASS	.						8.0	7.0	8.0					8																	110986480		2140	4178	6318	SO:0001819	synonymous_variant	27012	exon1			GCTGCCGCCCACG	AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.138C>T	8.37:g.110986480G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_014379	Q9UHJ4	Silent	SNP	ENST00000524391.1	37	CCDS6314.1																																																																																			.	.	none		0.692	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379	
TAS2R8	50836	hgsc.bcm.edu	37	12	10959031	10959031	+	Silent	SNP	C	C	T	rs1548803	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:10959031C>T	ENST00000240615.2	-	1	861	c.549G>A	c.(547-549)ttG>ttA	p.L183L		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	183					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TAAAGAGAGTCAAGGGTTCAA	0.323													C|||	2524	0.503994	0.1641	0.5692	5008	,	,		19896	0.6448		0.6789	False		,,,				2504	0.592				p.L183L		Atlas-SNP	.											.	TAS2R8	42	.	0			c.G549A						PASS	.	C		1026,3380	377.8+/-322.6	124,778,1301	149.0	133.0	138.0		549	-3.5	0.0	12	dbSNP_88	138	5190,3410	636.6+/-399.1	1578,2034,688	no	coding-synonymous	TAS2R8	NM_023918.1		1702,2812,1989	TT,TC,CC		39.6512,23.2864,47.7933		183/310	10959031	6216,6790	2203	4300	6503	SO:0001819	synonymous_variant	50836	exon1			GAGAGTCAAGGGT	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.549G>A	12.37:g.10959031C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	147	146	0.993197	NM_023918	Q4KN29|Q645Y2	Silent	SNP	ENST00000240615.2	37	CCDS8632.1																																																																																			C|0.498;T|0.502	0.502	strong		0.323	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
CAMKK2	10645	hgsc.bcm.edu	37	12	121712077	121712077	+	Missense_Mutation	SNP	T	T	A	rs3817190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121712077T>A	ENST00000324774.5	-	2	1081	c.253A>T	c.(253-255)Acc>Tcc	p.T85S	CAMKK2_ENST00000404169.3_Missense_Mutation_p.T85S|CAMKK2_ENST00000402834.4_Missense_Mutation_p.T85S|CAMKK2_ENST00000337174.3_Missense_Mutation_p.T85S|CAMKK2_ENST00000347034.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000446440.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000392474.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000392473.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000538733.1_Missense_Mutation_p.T85S|CAMKK2_ENST00000412367.2_Missense_Mutation_p.T85S|CAMKK2_ENST00000535524.1_5'UTR	NM_006549.3	NP_006540.3	Q96RR4	KKCC2_HUMAN	calcium/calmodulin-dependent protein kinase kinase 2, beta	85			T -> S (in dbSNP:rs3817190). {ECO:0000269|PubMed:11395482, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872452}.		calcium-mediated signaling (GO:0019722)|MAPK cascade (GO:0000165)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of protein kinase activity (GO:0045859)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GACCCGGAGGTGTCAAGGGGG	0.692													T|||	2062	0.411741	0.6225	0.3084	5008	,	,		13569	0.2976		0.4076	False		,,,				2504	0.3221				p.T85S		Atlas-SNP	.											CAMKK2_ENST00000392473,NS,carcinoma,0,2	CAMKK2	87	2	0			c.A253T						PASS	.	T	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	2469,1931		700,1069,431	20.0	24.0	23.0		253,253,253,253,253,253,253	-0.6	0.0	12	dbSNP_107	23	3539,5057		752,2035,1511	no	missense,missense,missense,missense,missense,missense,missense	CAMKK2	NM_006549.3,NM_153499.2,NM_153500.1,NM_172214.2,NM_172215.2,NM_172216.1,NM_172226.2	58,58,58,58,58,58,58	1452,3104,1942	AA,AT,TT		41.1703,43.8864,46.2296	benign,benign,benign,benign,benign,benign,benign	85/589,85/542,85/499,85/534,85/491,85/546,85/542	121712077	6008,6988	2200	4298	6498	SO:0001583	missense	10645	exon2			CGGAGGTGTCAAG	AF101264	CCDS9216.1, CCDS9217.1, CCDS9218.1, CCDS9219.1, CCDS44999.1, CCDS53837.1, CCDS58283.1	12q24.2	2002-08-13				ENSG00000110931			1470	protein-coding gene	gene with protein product		615002				9662074	Standard	NM_172226		Approved	CAMKK, KIAA0787, CAMKKB, MGC15254	uc001tzu.3	Q96RR4		ENST00000324774.5:c.253A>T	12.37:g.121712077T>A	ENSP00000312741:p.Thr85Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_153500	A8K7Q7|O94883|Q8IUG2|Q8IUG3|Q8N3I4|Q8WY03|Q8WY04|Q8WY05|Q8WY06|Q96RP1|Q96RP2|Q96RR3|Q9BWE9|Q9UER3|Q9UES2|Q9Y5N2	Missense_Mutation	SNP	ENST00000324774.5	37	CCDS9216.1	936	0.42857142857142855	318	0.6463414634146342	121	0.3342541436464088	186	0.32517482517482516	311	0.4102902374670185	T	0.231	-1.020843	0.02061	0.561136	0.411703	ENSG00000110931	ENST00000392474;ENST00000347034;ENST00000538733;ENST00000337174;ENST00000324774;ENST00000412367;ENST00000404169;ENST00000360452;ENST00000446440;ENST00000392473;ENST00000543477;ENST00000544485	T;T;T;T;T;T;T;T;T;T;T	0.72167	-0.63;-0.6;-0.61;-0.63;-0.63;-0.63;-0.63;-0.63;-0.63;2.03;1.56	4.17	-0.591	0.11675	.	1.005170	0.08018	N	0.991504	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0;0.0;0.001	T	0.43734	-0.9373	9	0.10902	T	0.67	-0.6485	2.7347	0.05237	0.3091:0.4379:0.152:0.101	rs3817190;rs17852337;rs3817190	85;85;85;85;85;85;85	Q96RR4-6;Q96RR4-2;Q96RR4-7;Q96RR4-5;Q96RR4-4;Q96RR4;Q96RR4-3	.;.;.;.;.;KKCC2_HUMAN;.	S	85;85;85;85;85;85;85;68;85;85;85;85	ENSP00000376266:T85S;ENSP00000321230:T85S;ENSP00000445944:T85S;ENSP00000336634:T85S;ENSP00000312741:T85S;ENSP00000388368:T85S;ENSP00000384600:T85S;ENSP00000388273:T85S;ENSP00000376265:T85S;ENSP00000444894:T85S;ENSP00000445400:T85S	ENSP00000312741:T85S	T	-	1	0	CAMKK2	120196460	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	-0.775000	0.04679	0.061000	0.16311	-0.464000	0.05259	ACC	T|0.543;A|0.457	0.457	strong		0.692	CAMKK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402563.1	NM_172226	
RSPH9	221421	hgsc.bcm.edu	37	6	43638636	43638636	+	Missense_Mutation	SNP	G	G	A	rs16896629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43638636G>A	ENST00000372163.4	+	5	834	c.781G>A	c.(781-783)Gtc>Atc	p.V261I	RSPH9_ENST00000372165.4_Missense_Mutation_p.R278H	NM_152732.4	NP_689945.2	Q9H1X1	RSPH9_HUMAN	radial spoke head 9 homolog (Chlamydomonas)	261			V -> I (in dbSNP:rs16896629). {ECO:0000269|PubMed:14702039}.		axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)				NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CTATGGCTACGTCTACGTGGG	0.542									Kartagener syndrome				A|||	652	0.130192	0.0908	0.0432	5008	,	,		21458	0.2421		0.0577	False		,,,				2504	0.2045				p.R278H		Atlas-SNP	.											RSPH9,NS,NS,-2,1	RSPH9	60	1	0			c.G833A						scavenged	.	A	HIS/ARG,ILE/VAL	356,4050	793.6+/-415.2	19,318,1866	96.0	75.0	82.0		833,781	3.4	1.0	6	dbSNP_123	82	466,8134	798.3+/-407.4	13,440,3847	yes	missense,missense	RSPH9	NM_001193341.1,NM_152732.4	29,29	32,758,5713	AA,AG,GG		5.4186,8.0799,6.3202	benign,benign	278/307,261/277	43638636	822,12184	2203	4300	6503	SO:0001583	missense	221421	exon6	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGCTACGTCTACG	AK055407	CCDS4905.1, CCDS55005.1	6p21.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000172426	ENSG00000172426			21057	protein-coding gene	gene with protein product		612648	"""mitochondrial ribosomal protein S18A-like 1"", ""chromosome 6 open reading frame 206"""	MRPS18AL1, C6orf206		19200523	Standard	NM_152732		Approved	FLJ30845, CILD12	uc003ovx.2	Q9H1X1	OTTHUMG00000014746	ENST00000372163.4:c.781G>A	6.37:g.43638636G>A	ENSP00000361236:p.Val261Ile	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	141	78	0.553191	NM_001193341	A8K5T4|Q96NH9	Missense_Mutation	SNP	ENST00000372163.4	37	CCDS4905.1	238|238	0.10897435897435898|0.10897435897435898	49|49	0.09959349593495935|0.09959349593495935	13|13	0.03591160220994475|0.03591160220994475	131|131	0.229020979020979|0.229020979020979	45|45	0.059366754617414245|0.059366754617414245	A|A	5.962|5.962	0.361504|0.361504	0.11296|0.11296	0.080799|0.080799	0.054186|0.054186	ENSG00000172426|ENSG00000172426	ENST00000372165|ENST00000372163	.|T	.|0.16196	.|2.36	5.97|5.97	3.4|3.4	0.38934|0.38934	.|.	0.811907|.	0.11951|.	N|.	0.513688|.	T|T	0.01353|0.01353	0.0044|0.0044	.|.	.|.	.|.	0.47905|0.47905	P|P	4.5200000000000795E-4|4.5200000000000795E-4	B|B	0.02656|0.06786	0.0|0.001	B|B	0.01281|0.06405	0.0|0.002	T|T	0.45673|0.45673	-0.9245|-0.9245	7|7	0.18276|0.06099	T|T	0.48|0.92	-35.1298|-35.1298	1.491|1.491	0.02456|0.02456	0.56:0.1446:0.1562:0.1392|0.56:0.1446:0.1562:0.1392	rs16896629;rs56470353;rs16896629|rs16896629;rs56470353;rs16896629	278|261	Q96NH9|Q9H1X1	.|RSPH9_HUMAN	H|I	278|261	.|ENSP00000361236:V261I	ENSP00000361238:R278H|ENSP00000361236:V261I	R|V	+|+	2|1	0|0	RSPH9|RSPH9	43746614|43746614	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.824000|0.824000	0.46624|0.46624	0.818000|0.818000	0.27295|0.27295	0.488000|0.488000	0.27723|0.27723	-0.254000|-0.254000	0.11334|0.11334	CGT|GTC	G|0.908;A|0.092	0.092	strong		0.542	RSPH9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040690.1	NM_152732	
ZNF474	133923	hgsc.bcm.edu	37	5	121488506	121488506	+	Missense_Mutation	SNP	C	C	G	rs35262183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:121488506C>G	ENST00000296600.4	+	2	1204	c.821C>G	c.(820-822)tCc>tGc	p.S274C	CTC-441N14.1_ENST00000505209.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.2_ENST00000504829.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	274							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		AATGCACAGTCCAGCCAAGCG	0.537													C|||	1249	0.249401	0.09	0.2406	5008	,	,		17701	0.3909		0.2724	False		,,,				2504	0.3016				p.S274C		Atlas-SNP	.											.	ZNF474	43	.	0			c.C821G						PASS	.	C	CYS/SER	512,3894	235.8+/-248.2	25,462,1716	80.0	74.0	76.0		821	2.5	0.0	5	dbSNP_126	76	2424,6176	402.2+/-347.4	356,1712,2232	yes	missense	ZNF474	NM_207317.1	112	381,2174,3948	GG,GC,CC		28.186,11.6205,22.5742	possibly-damaging	274/365	121488506	2936,10070	2203	4300	6503	SO:0001583	missense	133923	exon2			CACAGTCCAGCCA	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.821C>G	5.37:g.121488506C>G	ENSP00000296600:p.Ser274Cys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	597	0.2733516483516483	45	0.09146341463414634	108	0.2983425414364641	237	0.4143356643356643	207	0.27308707124010556	C	5.333	0.246830	0.10130	0.116205	0.28186	ENSG00000164185	ENST00000296600	T	0.49432	0.78	5.29	2.52	0.30459	.	0.691718	0.11714	U	0.536586	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	D	0.59357	0.985	B	0.43103	0.408	T	0.40270	-0.9572	9	0.46703	T	0.11	-1.2244	7.6208	0.28183	0.2916:0.6297:0.0:0.0787	rs35262183	274	Q6S9Z5	ZN474_HUMAN	C	274	ENSP00000296600:S274C	ENSP00000296600:S274C	S	+	2	0	ZNF474	121516405	0.001000	0.12720	0.005000	0.12908	0.002000	0.02628	0.799000	0.27028	0.216000	0.20781	-0.897000	0.02905	TCC	C|0.753;G|0.247	0.247	strong		0.537	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
UBAP2	55833	hgsc.bcm.edu	37	9	33941759	33941759	+	Missense_Mutation	SNP	T	T	C	rs307658	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:33941759T>C	ENST00000379238.1	-	16	1934	c.1817A>G	c.(1816-1818)aAt>aGt	p.N606S	UBAP2_ENST00000379239.4_Missense_Mutation_p.N339S|UBAP2_ENST00000449054.1_Missense_Mutation_p.N606S|UBAP2_ENST00000418786.2_Missense_Mutation_p.N553S|UBAP2_ENST00000539807.1_Missense_Mutation_p.N361S|UBAP2_ENST00000360802.1_Missense_Mutation_p.N606S|UBAP2_ENST00000379225.1_Missense_Mutation_p.N239S					ubiquitin associated protein 2									p.N606S(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		ACTAGCAGAATTCAGTGATGA	0.448													C|||	1857	0.370807	0.5083	0.268	5008	,	,		18167	0.1726		0.3837	False		,,,				2504	0.4489				p.N606S		Atlas-SNP	.											UBAP2,NS,carcinoma,0,1	UBAP2	82	1	1	Substitution - Missense(1)	stomach(1)	c.A1817G						PASS	.	C	SER/ASN	2060,2346	607.3+/-390.9	478,1104,621	174.0	159.0	164.0		1817	5.8	1.0	9	dbSNP_79	164	3291,5309	646.8+/-400.3	648,1995,1657	yes	missense	UBAP2	NM_018449.2	46	1126,3099,2278	CC,CT,TT		38.2674,46.7544,41.1425	benign	606/1120	33941759	5351,7655	2203	4300	6503	SO:0001583	missense	55833	exon16			GCAGAATTCAGTG	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.1817A>G	9.37:g.33941759T>C	ENSP00000368540:p.Asn606Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	173	66	0.381503	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	778	0.35622710622710624	248	0.5040650406504065	106	0.292817679558011	114	0.1993006993006993	310	0.40897097625329815	C	1.094	-0.663234	0.03428	0.467544	0.382674	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379239;ENST00000539807;ENST00000418786;ENST00000379225	T;T;T;T;T;T;T	0.20738	2.79;2.79;2.79;2.58;2.59;2.28;2.05	5.76	5.76	0.90799	.	0.521330	0.23587	N	0.046596	T	0.00012	0.0000	N	0.01015	-1.05	0.58432	P	4.000000000004E-6	B;B;B;B;B;B;B;B	0.17038	0.0;0.006;0.0;0.0;0.0;0.001;0.003;0.02	B;B;B;B;B;B;B;B	0.06405	0.001;0.0;0.0;0.0;0.0;0.0;0.0;0.002	T	0.41124	-0.9526	9	0.02654	T	1	-4.2248	12.9291	0.58276	0.0:0.866:0.0:0.134	rs307658;rs601694;rs1626808;rs52833981;rs60695207;rs307658	553;531;361;339;515;239;531;606	E7EWG4;F5H4D5;F5H2U4;A6NCA8;F5H2C8;A2A306;B4DH66;Q5T6F2	.;.;.;.;.;.;.;UBAP2_HUMAN	S	606;606;606;515;339;361;553;239	ENSP00000368540:N606S;ENSP00000416932:N606S;ENSP00000354039:N606S;ENSP00000368541:N339S;ENSP00000439329:N361S;ENSP00000404436:N553S;ENSP00000368527:N239S	ENSP00000354039:N606S	N	-	2	0	UBAP2	33931759	1.000000	0.71417	1.000000	0.80357	0.356000	0.29392	2.117000	0.41939	1.449000	0.47699	-0.119000	0.15052	AAT	T|0.617;C|0.383	0.383	strong		0.448	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
TFB2M	64216	hgsc.bcm.edu	37	1	246707858	246707858	+	Silent	SNP	A	A	G	rs3129568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:246707858A>G	ENST00000366514.4	-	7	1169	c.984T>C	c.(982-984)ttT>ttC	p.F328F		NM_022366.2	NP_071761.1	Q9H5Q4	TFB2M_HUMAN	transcription factor B2, mitochondrial	328					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)			TGCGCCTCCCAAAACAGTGCT	0.338													G|||	767	0.153155	0.1732	0.219	5008	,	,		17523	0.003		0.2803	False		,,,				2504	0.1033				p.F328F		Atlas-SNP	.											.	TFB2M	46	.	0			c.T984C						PASS	.	G		824,3582	743.6+/-411.5	88,648,1467	85.0	91.0	89.0		984	4.0	1.0	1	dbSNP_103	89	2307,6293	705.2+/-405.5	337,1633,2330	no	coding-synonymous	TFB2M	NM_022366.2		425,2281,3797	GG,GA,AA		26.8256,18.7018,24.0735		328/397	246707858	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	64216	exon7			CCTCCCAAAACAG	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.984T>C	1.37:g.246707858A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	113	67	0.59292	NM_022366	Q9H626	Silent	SNP	ENST00000366514.4	37	CCDS1627.1																																																																																			A|0.783;G|0.217	0.217	strong		0.338	TFB2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096673.1	NM_022366	
VARS2	57176	hgsc.bcm.edu	37	6	30882781	30882781	+	Silent	SNP	G	G	T	rs1264301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30882781G>T	ENST00000321897.5	+	1	800	c.168G>T	c.(166-168)gcG>gcT	p.A56A	VARS2_ENST00000541562.1_Silent_p.A86A|VARS2_ENST00000542001.1_Intron|VARS2_ENST00000416670.2_Silent_p.A56A			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	56					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						AGAAGCAGGCGACTCTGGAGG	0.582													G|||	1112	0.222045	0.0983	0.2075	5008	,	,		17920	0.247		0.3559	False		,,,				2504	0.2362				p.A86A		Atlas-SNP	.											.	VARS2	60	.	0			c.G258T						PASS	.	G	,,	442,2578		35,372,1103	50.0	61.0	57.0		,258,168	-1.4	0.2	6	dbSNP_87	57	2042,3376		366,1310,1033	no	intron,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	401,1682,2136	TT,TG,GG		37.6892,14.6358,29.4383	,,	,86/1094,56/1064	30882781	2484,5954	1510	2709	4219	SO:0001819	synonymous_variant	57176	exon2			GCAGGCGACTCTG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.168G>T	6.37:g.30882781G>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			G|0.731;T|0.269	0.269	strong		0.582	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
KLHL30	377007	hgsc.bcm.edu	37	2	239050033	239050033	+	Missense_Mutation	SNP	C	C	T	rs12692216	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:239050033C>T	ENST00000409223.1	+	2	745	c.638C>T	c.(637-639)gCc>gTc	p.A213V	KLHL30_ENST00000305959.4_Missense_Mutation_p.A195V			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	213	BACK.			A -> V (in Ref. 3; BAC86148 and 4; AAI05697). {ECO:0000305}.						lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GCCCGGGCCGCCCACCTGCCC	0.697													c|||	3648	0.728435	0.7307	0.7176	5008	,	,		17390	0.872		0.6103	False		,,,				2504	0.7065				p.A213V		Atlas-SNP	.											.	KLHL30	79	.	0			c.C638T						PASS	.		VAL/ALA	3105,979		1211,683,148	7.0	9.0	8.0		638	2.7	0.5	2	dbSNP_121	8	5215,3071		1727,1761,655	no	missense	KLHL30	NM_198582.3	64	2938,2444,803	TT,TC,CC		37.0625,23.9716,32.7405	benign	213/579	239050033	8320,4050	2042	4143	6185	SO:0001583	missense	377007	exon2			GGGCCGCCCACCT		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.638C>T	2.37:g.239050033C>T	ENSP00000386389:p.Ala213Val	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	13	10	0.769231	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	1574	0.7206959706959707	368	0.7479674796747967	261	0.7209944751381215	484	0.8461538461538461	461	0.6081794195250659	C	0.433	-0.902470	0.02453	0.760284	0.629375	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.69175	-0.38;-0.38	5.6	2.65	0.31530	BTB/Kelch-associated (2);	1.632010	0.03019	N	0.150437	T	0.00012	0.0000	N	0.21508	0.67	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.44050	-0.9353	9	0.28530	T	0.3	.	4.2475	0.10679	0.2322:0.5259:0.1582:0.0837	rs12692216;rs61492542	213	Q0D2K2	KLH30_HUMAN	V	213;195	ENSP00000386389:A213V;ENSP00000302386:A195V	ENSP00000302386:A195V	A	+	2	0	KLHL30	238714772	0.000000	0.05858	0.532000	0.27989	0.005000	0.04900	-0.175000	0.09825	0.672000	0.31204	0.655000	0.94253	GCC	C|0.280;T|0.720	0.720	strong		0.697	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
OXNAD1	92106	hgsc.bcm.edu	37	3	16327909	16327909	+	Missense_Mutation	SNP	C	C	T	rs6777976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:16327909C>T	ENST00000285083.5	+	5	709	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	OXNAD1_ENST00000544043.1_Missense_Mutation_p.R100C|OXNAD1_ENST00000605932.1_Missense_Mutation_p.R82C|OXNAD1_ENST00000606098.1_Missense_Mutation_p.R82C|OXNAD1_ENST00000435829.2_Missense_Mutation_p.R100C	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	82	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		R -> C (in dbSNP:rs6777976). {ECO:0000269|Ref.3}.			mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						GAAGAGCCTCCGCTTGCTTGT	0.463													C|||	888	0.177316	0.2663	0.1081	5008	,	,		19351	0.1696		0.162	False		,,,				2504	0.1299				p.R82C		Atlas-SNP	.											OXNAD1,NS,carcinoma,-1,1	OXNAD1	31	1	0			c.C244T						PASS	.	C	CYS/ARG	1023,3383	378.0+/-322.7	105,813,1285	239.0	200.0	214.0		244	4.4	0.8	3	dbSNP_116	214	1220,7380	245.4+/-274.3	91,1038,3171	yes	missense	OXNAD1	NM_138381.3	180	196,1851,4456	TT,TC,CC		14.186,23.2183,17.2459	benign	82/313	16327909	2243,10763	2203	4300	6503	SO:0001583	missense	92106	exon5			AGCCTCCGCTTGC	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.244C>T	3.37:g.16327909C>T	ENSP00000285083:p.Arg82Cys	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	232	109	0.469828	NM_138381	Q2HYC7|Q59FA4	Missense_Mutation	SNP	ENST00000285083.5	37	CCDS2630.1	401	0.18360805860805862	133	0.2703252032520325	40	0.11049723756906077	110	0.19230769230769232	118	0.15567282321899736	C	13.27	2.185915	0.38609	0.232183	0.14186	ENSG00000154814	ENST00000285083;ENST00000435829;ENST00000544043	T;T;T	0.15834	2.39;2.39;2.39	5.26	4.38	0.52667	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);	0.144057	0.64402	N	0.000009	T	0.00012	0.0000	M	0.83384	2.64	0.09310	P	0.999999804086	B;B	0.17038	0.02;0.006	B;B	0.14578	0.011;0.003	T	0.15378	-1.0439	9	0.39692	T	0.17	-8.4499	13.8797	0.63676	0.0:0.9255:0.0:0.0745	rs6777976;rs61694623;rs6777976	100;82	F5H620;Q96HP4	.;OXND1_HUMAN	C	82;82;100	ENSP00000285083:R82C;ENSP00000389872:R82C;ENSP00000437967:R100C	ENSP00000285083:R82C	R	+	1	0	OXNAD1	16302913	0.001000	0.12720	0.824000	0.32777	0.610000	0.37248	0.332000	0.19751	1.204000	0.43247	0.655000	0.94253	CGC	C|0.824;T|0.176	0.176	strong		0.463	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381	
CCPG1	9236	hgsc.bcm.edu	37	15	55664110	55664110	+	Missense_Mutation	SNP	G	G	C	rs117236526	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:55664110G>C	ENST00000310958.6	-	6	885	c.587C>G	c.(586-588)gCt>gGt	p.A196G	CCPG1_ENST00000569205.1_Missense_Mutation_p.A196G|MIR628_ENST00000385229.1_RNA|CCPG1_ENST00000442196.3_Missense_Mutation_p.A196G|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000425574.3_Missense_Mutation_p.A196G	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	196	Interaction with MCF2L and SRC. {ECO:0000250}.			A -> G (in Ref. 1; BAA86568). {ECO:0000305}.	cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TTCTTGTTCAGCAACTAGCCG	0.448													G|||	182	0.0363419	0.0015	0.0389	5008	,	,		17926	0.001		0.0696	False		,,,				2504	0.0838				p.A196G		Atlas-SNP	.											.	CCPG1	74	.	0			c.C587G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	67,3689		0,67,1811	96.0	90.0	92.0		587,587,587,587	1.4	0.0	15	dbSNP_132	92	607,7603		18,571,3516	yes	missense,missense,missense,missense	CCPG1	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_020739.3	60,60,60,60	18,638,5327	CC,CG,GG		7.3934,1.7838,5.6326	benign,benign,benign,benign	196/808,196/425,196/758,196/758	55664110	674,11292	1878	4105	5983	SO:0001583	missense	9236	exon6			TGTTCAGCAACTA	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.587C>G	15.37:g.55664110G>C	ENSP00000311656:p.Ala196Gly	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	163	68	0.417178	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	37	CCDS42039.1	73	0.033424908424908424	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	56	0.07387862796833773	G	6.652	0.488778	0.12641	0.017838	0.073934	ENSG00000256061	ENST00000310958;ENST00000442196;ENST00000425574	T;T;T	0.32515	3.78;3.78;1.45	5.74	1.42	0.22433	.	1.328530	0.04456	N	0.373577	T	0.01905	0.0060	L	0.51422	1.61	0.09310	N	1	B;B;B;B	0.16166	0.002;0.016;0.002;0.001	B;B;B;B	0.16289	0.004;0.015;0.006;0.004	T	0.13980	-1.0489	10	0.19590	T	0.45	.	3.2974	0.06971	0.1161:0.1212:0.4335:0.3291	.	196;196;196;52	A8K9T0;Q9ULG6-3;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	G	196	ENSP00000311656:A196G;ENSP00000403400:A196G;ENSP00000415128:A196G	ENSP00000311656:A196G	A	-	2	0	DYX1C1	53451402	0.000000	0.05858	0.021000	0.16686	0.364000	0.29643	-0.006000	0.12833	0.719000	0.32188	0.655000	0.94253	GCT	G|0.947;C|0.053	0.053	strong		0.448	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
TYW3	127253	hgsc.bcm.edu	37	1	75214441	75214441	+	Missense_Mutation	SNP	A	A	G	rs1133891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:75214441A>G	ENST00000370867.3	+	4	450	c.361A>G	c.(361-363)Atg>Gtg	p.M121V	TYW3_ENST00000457880.2_Missense_Mutation_p.M88V|TYW3_ENST00000479111.1_Start_Codon_SNP_p.M1V|TYW3_ENST00000421739.2_Intron	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	121			M -> V (in dbSNP:rs1133891). {ECO:0000269|PubMed:14702039}.		tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						ACAGCATTCCATGGCAATAGA	0.348													A|||	1799	0.359225	0.2496	0.317	5008	,	,		18562	0.7063		0.1262	False		,,,				2504	0.4192				p.M121V		Atlas-SNP	.											.	TYW3	36	.	0			c.A361G						PASS	.	A	VAL/MET,VAL/MET	987,3419	369.8+/-319.3	108,771,1324	109.0	110.0	110.0		262,361	5.0	1.0	1	dbSNP_86	110	962,7638	209.0+/-250.3	49,864,3387	yes	missense,missense	TYW3	NM_001162916.1,NM_138467.2	21,21	157,1635,4711	GG,GA,AA		11.186,22.4013,14.9854	benign,benign	88/227,121/260	75214441	1949,11057	2203	4300	6503	SO:0001583	missense	127253	exon4			CATTCCATGGCAA	BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"""chromosome 1 open reading frame 171"""	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.361A>G	1.37:g.75214441A>G	ENSP00000359904:p.Met121Val	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	236	109	0.461864	NM_138467	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Missense_Mutation	SNP	ENST00000370867.3	37	CCDS666.1	717	0.3282967032967033	110	0.22357723577235772	99	0.27348066298342544	402	0.7027972027972028	106	0.13984168865435356	A	0.319	-0.962859	0.02249	0.224013	0.11186	ENSG00000162623	ENST00000457880;ENST00000370867	T;T	0.24723	1.84;1.84	5.94	5.03	0.67393	tRNA wybutosine-synthesizing protein (2);	0.105878	0.64402	N	0.000005	T	0.01421	0.0046	N	0.00086	-2.195	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40117	-0.9580	9	0.02654	T	1	-5.3508	14.4234	0.67200	0.072:0.0:0.928:0.0	rs11538280	88;121	E9PGR7;Q6IPR3	.;TYW3_HUMAN	V	88;121	ENSP00000407025:M88V;ENSP00000359904:M121V	ENSP00000359904:M121V	M	+	1	0	TYW3	74987029	1.000000	0.71417	0.997000	0.53966	0.248000	0.25809	5.631000	0.67812	1.528000	0.49103	-0.252000	0.11476	ATG	A|0.763;G|0.237	0.237	strong		0.348	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467	
OR2AE1	81392	hgsc.bcm.edu	37	7	99474438	99474438	+	Silent	SNP	A	A	G	rs139077767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99474438A>G	ENST00000316368.2	-	1	242	c.219T>C	c.(217-219)caT>caC	p.H73H		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	73						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)					TTGTGGAGACATGCATCAGAT	0.488													A|||	19	0.00379393	0.0008	0.0029	5008	,	,		23330	0.001		0.007	False		,,,				2504	0.0082				p.H73H		Atlas-SNP	.											.	OR2AE1	32	.	0			c.T219C						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	113.0	96.0	102.0		219	-7.2	0.0	7	dbSNP_134	102	68,8532	42.2+/-99.7	0,68,4232	no	coding-synonymous	OR2AE1	NM_001005276.1		0,77,6426	GG,GA,AA		0.7907,0.2043,0.592		73/324	99474438	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	81392	exon1			GGAGACATGCATC	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.219T>C	7.37:g.99474438A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_001005276	B2RPD2	Silent	SNP	ENST00000316368.2	37	CCDS34696.1																																																																																			A|0.994;G|0.006	0.006	strong		0.488	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
MT1E	4493	hgsc.bcm.edu	37	16	56660841	56660841	+	Silent	SNP	C	C	T	rs72818418	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:56660841C>T	ENST00000306061.6	+	3	521	c.144C>T	c.(142-144)tgC>tgT	p.C48C	MT1E_ENST00000568293.1_Silent_p.C26C|MT1E_ENST00000330439.6_3'UTR	NM_175617.3	NP_783316.2	P04732	MT1E_HUMAN	metallothionein 1E	48	Alpha.				cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)										CCCAGGGCTGCGTCTGCAAAG	0.577													.|||	557	0.111222	0.1346	0.1124	5008	,	,		17608	0.0139		0.1262	False		,,,				2504	0.1636				p.C48C		Atlas-SNP	.											.	MT1E	7	.	0			c.C144T						PASS	.	C		593,3803	261.9+/-264.6	38,517,1643	136.0	128.0	131.0		144	-5.4	0.2	16	dbSNP_130	131	1154,7446	236.7+/-268.8	67,1020,3213	no	coding-synonymous	MT1E	NM_175617.3		105,1537,4856	TT,TC,CC		13.4186,13.4895,13.4426		48/62	56660841	1747,11249	2198	4300	6498	SO:0001819	synonymous_variant	4493	exon3			GGGCTGCGTCTGC	BC009699	CCDS10764.2	16q13	2008-08-11	2007-03-02		ENSG00000169715	ENSG00000169715		"""Metallothioneins"""	7397	protein-coding gene	gene with protein product		156351		MT1		6089206, 2581970	Standard	XM_005255956		Approved	MTD	uc002ejl.3	P04732	OTTHUMG00000133014	ENST00000306061.6:c.144C>T	16.37:g.56660841C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_175617	A2RRF7|Q86YX4|Q8TD51	Silent	SNP	ENST00000306061.6	37	CCDS10764.2																																																																																			C|0.877;T|0.123	0.123	strong		0.577	MT1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256600.1	NM_175617	
ARMC10	83787	hgsc.bcm.edu	37	7	102738862	102738862	+	Silent	SNP	T	T	C	rs14029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:102738862T>C	ENST00000323716.3	+	7	1286	c.894T>C	c.(892-894)gcT>gcC	p.A298A	ARMC10_ENST00000428183.2_Silent_p.A239A|ARMC10_ENST00000425331.1_Silent_p.A239A|ARMC10_ENST00000441711.2_Silent_p.A263A|ARMC10_ENST00000541300.1_Silent_p.A180A|ARMC10_ENST00000454559.1_Silent_p.A204A	NM_031905.4	NP_114111.2	Q8N2F6	ARM10_HUMAN	armadillo repeat containing 10	298					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						GCCATTTAGCTGTGCAGCCTA	0.403																																					p.A298A		Atlas-SNP	.											.	ARMC10	25	.	0			c.T894C						PASS	.	T	,,,,,	384,4022	175.5+/-204.9	5,374,1824	83.0	78.0	80.0		789,717,717,612,540,894	3.1	0.0	7	dbSNP_52	80	608,7992	152.4+/-207.0	5,598,3697	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARMC10	NM_001161009.2,NM_001161010.2,NM_001161011.2,NM_001161012.2,NM_001161013.2,NM_031905.4	,,,,,	10,972,5521	CC,CT,TT		7.0698,8.7154,7.6272	,,,,,	263/309,239/285,239/285,204/250,180/226,298/344	102738862	992,12014	2203	4300	6503	SO:0001819	synonymous_variant	83787	exon7			TTTAGCTGTGCAG	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.894T>C	7.37:g.102738862T>C		Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	587	198	0.337308	NM_031905	A8K703|B4DWJ8|F5GX65|Q75K91|Q75MG6|Q75ML8|Q8IZC1|Q8IZC2|Q8IZC3|Q9BTM6	Silent	SNP	ENST00000323716.3	37	CCDS5728.1																																																																																			.	.	weak		0.403	ARMC10-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347882.1	NM_031905	
SOX21	11166	hgsc.bcm.edu	37	13	95364046	95364046	+	Silent	SNP	C	C	G	rs1060474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:95364046C>G	ENST00000376945.2	-	1	343	c.258G>C	c.(256-258)ctG>ctC	p.L86L	SOX21-AS1_ENST00000438290.2_lincRNA	NM_007084.2	NP_009015.1	Q9Y651	SOX21_HUMAN	SRY (sex determining region Y)-box 21	86					hair follicle development (GO:0001942)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(3)|lung(1)|prostate(1)|skin(1)	6	all_neural(89;0.0646)|Medulloblastoma(90;0.163)					CCTTCTTGAGCAGCGTCTTGG	0.692													c|||	1905	0.380391	0.267	0.428	5008	,	,		8078	0.4692		0.4692	False		,,,				2504	0.317				p.L86L		Atlas-SNP	.											.	SOX21	21	.	0			c.G258C						PASS	.	C		1334,3072	442.5+/-346.7	205,924,1074	67.0	60.0	62.0		258	3.0	1.0	13	dbSNP_86	62	3639,4961	522.1+/-380.0	760,2119,1421	no	coding-synonymous	SOX21	NM_007084.2		965,3043,2495	GG,GC,CC		42.314,30.2769,38.2362		86/277	95364046	4973,8033	2203	4300	6503	SO:0001819	synonymous_variant	11166	exon1			CTTGAGCAGCGTC	AF107044	CCDS9473.1	13q31-q32	2008-07-18			ENSG00000125285	ENSG00000125285		"""SRY (sex determining region Y)-boxes"""	11197	protein-coding gene	gene with protein product	"""SRY-box 21"""	604974				10441749	Standard	NM_007084		Approved	SOX25	uc001vma.3	Q9Y651	OTTHUMG00000017209	ENST00000376945.2:c.258G>C	13.37:g.95364046C>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	94	43	0.457447	NM_007084	P35715|Q15504|Q5TBS1	Silent	SNP	ENST00000376945.2	37	CCDS9473.1																																																																																			C|0.605;G|0.395	0.395	strong		0.692	SOX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045467.4	NM_007084	
POLR1E	64425	hgsc.bcm.edu	37	9	37498215	37498215	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37498215C>T	ENST00000377798.4	+	9	993	c.880C>T	c.(880-882)Cgg>Tgg	p.R294W	POLR1E_ENST00000442009.2_Missense_Mutation_p.R224W|POLR1E_ENST00000377792.3_Missense_Mutation_p.R356W	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)		GGTAGTTAAGCGGAAAAGTAA	0.388																																					p.R294W	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.C880T						PASS	.						96.0	93.0	94.0					9																	37498215		2203	4300	6503	SO:0001583	missense	64425	exon9			GTTAAGCGGAAAA	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.880C>T	9.37:g.37498215C>T	ENSP00000367029:p.Arg294Trp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_022490	O75395|Q5JTE3	Missense_Mutation	SNP	ENST00000377798.4	37	CCDS6611.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.783965	0.49891	.	.	ENSG00000137054	ENST00000377798;ENST00000442009;ENST00000377792	T;T;T	0.24723	1.84;1.84;1.84	5.76	3.78	0.43462	.	0.538678	0.19258	N	0.118753	T	0.43612	0.1255	L	0.59436	1.845	0.35039	D	0.75957	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.69479	0.939;0.964;0.862	T	0.56619	-0.7949	10	0.56958	D	0.05	-12.8494	11.1968	0.48717	0.1376:0.7205:0.1419:0.0	.	224;356;294	E7EX70;Q9GZS1;Q9GZS1-2	.;RPA49_HUMAN;.	W	294;224;356	ENSP00000367029:R294W;ENSP00000399887:R224W;ENSP00000367023:R356W	ENSP00000367023:R356W	R	+	1	2	POLR1E	37488215	1.000000	0.71417	1.000000	0.80357	0.155000	0.21991	2.300000	0.43620	1.534000	0.49203	0.655000	0.94253	CGG	.	.	none		0.388	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
NCAPD2	9918	hgsc.bcm.edu	37	12	6634817	6634817	+	Silent	SNP	C	C	T	rs71579347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:6634817C>T	ENST00000315579.5	+	18	3082	c.2283C>T	c.(2281-2283)acC>acT	p.T761T	NCAPD2_ENST00000542492.1_3'UTR|NCAPD2_ENST00000545962.1_Silent_p.T716T	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	761					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						AGCGGGCCACCGAGAAGGTCG	0.547													C|||	8	0.00159744	0.0	0.0	5008	,	,		18865	0.0		0.0	False		,,,				2504	0.0082				p.T761T		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C2283T						PASS	.	C		0,4406		0,0,2203	78.0	70.0	73.0		2283	-11.7	0.0	12	dbSNP_130	73	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NCAPD2	NM_014865.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		761/1402	6634817	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9918	exon18			GGCCACCGAGAAG	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.2283C>T	12.37:g.6634817C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	87	51	0.586207	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
GEMIN4	50628	hgsc.bcm.edu	37	17	649505	649505	+	Missense_Mutation	SNP	T	T	A	rs4968104	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:649505T>A	ENST00000319004.5	-	2	1896	c.1778A>T	c.(1777-1779)gAg>gTg	p.E593V	GEMIN4_ENST00000576778.1_Missense_Mutation_p.E582V	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	593				E -> V (in Ref. 1; AAF35283 and 3; CAB45743). {ECO:0000305}.	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)		GGGACCCTGCTCTTCCACAAA	0.498													T|||	795	0.158746	0.0545	0.1772	5008	,	,		19029	0.122		0.2465	False		,,,				2504	0.2342				p.E593V		Atlas-SNP	.											GEMIN4_ENST00000319004,NS,carcinoma,0,4	GEMIN4	116	4	0			c.A1778T						PASS	.	T	VAL/GLU	361,3573		17,327,1623	98.0	102.0	101.0		1778	5.5	0.9	17	dbSNP_111	101	2103,6257		286,1531,2363	yes	missense	GEMIN4	NM_015721.2	121	303,1858,3986	AA,AT,TT		25.1555,9.1764,20.0423	possibly-damaging	593/1059	649505	2464,9830	1967	4180	6147	SO:0001583	missense	50628	exon2			CCCTGCTCTTCCA	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.1778A>T	17.37:g.649505T>A	ENSP00000321706:p.Glu593Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	358	0.16391941391941392	26	0.052845528455284556	72	0.19889502762430938	75	0.13111888111888112	185	0.24406332453825857	T	2.280	-0.364930	0.05103	0.091764	0.251555	ENSG00000179409	ENST00000319004	T	0.16597	2.33	5.46	5.46	0.80206	.	0.885835	0.09880	N	0.743765	T	0.00012	0.0000	L	0.57536	1.79	0.09310	P	0.9999999547019	B	0.30439	0.279	B	0.28139	0.086	T	0.34850	-0.9812	9	0.36615	T	0.2	-13.2991	5.9152	0.19052	0.0:0.0844:0.168:0.7476	rs4968104;rs52822209;rs4968104	593	P57678	GEMI4_HUMAN	V	593	ENSP00000321706:E593V	ENSP00000321706:E593V	E	-	2	0	GEMIN4	596255	0.000000	0.05858	0.900000	0.35374	0.022000	0.10575	0.530000	0.23036	2.079000	0.62486	0.482000	0.46254	GAG	T|0.816;A|0.184	0.184	strong		0.498	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
ANXA10	11199	hgsc.bcm.edu	37	4	169083757	169083757	+	Silent	SNP	C	C	T	rs114905136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169083757C>T	ENST00000359299.3	+	4	460	c.274C>T	c.(274-276)Ctg>Ttg	p.L92L		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	92						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)			endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		CCCACCACCACTGTATGATGC	0.468													C|||	21	0.00419329	0.0015	0.0086	5008	,	,		19237	0.0		0.0119	False		,,,				2504	0.001				p.L92L		Atlas-SNP	.											.	ANXA10	44	.	0			c.C274T						PASS	.	C		13,4393	20.2+/-43.8	0,13,2190	111.0	96.0	101.0		274	1.0	0.1	4	dbSNP_132	101	148,8452	72.0+/-134.6	2,144,4154	no	coding-synonymous	ANXA10	NM_007193.4		2,157,6344	TT,TC,CC		1.7209,0.2951,1.2379		92/325	169083757	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	11199	exon4			CCACCACTGTATG	AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"""Annexins"""	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.274C>T	4.37:g.169083757C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	239	112	0.468619	NM_007193	Q96IQ5|Q9UJV4	Silent	SNP	ENST00000359299.3	37	CCDS34096.1																																																																																			C|0.990;T|0.010	0.010	strong		0.468	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193	
SH2D4A	63898	hgsc.bcm.edu	37	8	19192332	19192332	+	Silent	SNP	G	G	T	rs56005620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:19192332G>T	ENST00000265807.3	+	4	888	c.477G>T	c.(475-477)tcG>tcT	p.S159S	SH2D4A_ENST00000518040.1_Silent_p.S114S|SH2D4A_ENST00000519207.1_Silent_p.S159S	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	159					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AGCAAGGATCGAGGCCAGCAC	0.483													T|||	1531	0.305711	0.5809	0.1945	5008	,	,		17983	0.2073		0.167	False		,,,				2504	0.2566				p.S159S		Atlas-SNP	.											SH2D4A,NS,carcinoma,+1,3	SH2D4A	49	3	0			c.G477T						PASS	.	T	,,	2229,2177	585.4+/-386.2	560,1109,534	98.0	94.0	95.0		477,342,477	-10.8	0.0	8	dbSNP_129	95	1608,6992	742.3+/-407.2	155,1298,2847	no	coding-synonymous,coding-synonymous,coding-synonymous	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	,,	715,2407,3381	TT,TG,GG		18.6977,49.4099,29.5018	,,	159/455,114/410,159/455	19192332	3837,9169	2203	4300	6503	SO:0001819	synonymous_variant	63898	exon4			AGGATCGAGGCCA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.477G>T	8.37:g.19192332G>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	67	26	0.38806	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Silent	SNP	ENST00000265807.3	37	CCDS6009.1																																																																																			G|0.718;T|0.282	0.282	strong		0.483	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
PRKCZ	5590	hgsc.bcm.edu	37	1	2105427	2105427	+	Silent	SNP	C	C	T	rs142352833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2105427C>T	ENST00000400921.2	+	11	1511	c.828C>T	c.(826-828)gaC>gaT	p.D276D	PRKCZ_ENST00000400920.1_Silent_p.D276D|PRKCZ_ENST00000479263.1_3'UTR	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	459	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|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 excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	ACAACCCGGACATGAACACAG	0.597											OREG0013007	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D459D		Atlas-SNP	.											.	PRKCZ	84	.	0			c.C1377T						PASS	.	C	,,,	0,4406	2.1+/-5.4	0,0,2203	136.0	116.0	122.0		828,828,1065,1377	3.0	1.0	1	dbSNP_134	122	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKCZ	NM_001033581.1,NM_001033582.1,NM_001242874.1,NM_002744.4	,,,	0,15,6488	TT,TC,CC		0.1744,0.0,0.1153	,,,	276/410,276/410,355/489,459/593	2105427	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5590	exon14			CCCGGACATGAAC	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.828C>T	1.37:g.2105427C>T		Somatic	134	0	0	601	WXS	Illumina HiSeq	Phase_I	98	89	0.908163	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	37	CCDS41229.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744	
KIAA2026	158358	hgsc.bcm.edu	37	9	6007500	6007500	+	Silent	SNP	G	G	A	rs1061767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:6007500G>A	ENST00000399933.3	-	1	287	c.288C>T	c.(286-288)ggC>ggT	p.G96G	KIAA2026_ENST00000381461.2_Silent_p.G96G|MIR4665_ENST00000581132.1_RNA	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	96										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GGGCGGTGAGGCCCCGGTGCT	0.711													G|||	855	0.170727	0.0998	0.1744	5008	,	,		14281	0.3194		0.1849	False		,,,				2504	0.0961				p.G96G		Atlas-SNP	.											.	KIAA2026	231	.	0			c.C288T						PASS	.	G		449,3521		27,395,1563	19.0	24.0	22.0		288	3.2	1.0	9	dbSNP_86	22	1636,6640		161,1314,2663	no	coding-synonymous	KIAA2026	NM_001017969.2		188,1709,4226	AA,AG,GG		19.768,11.3098,17.026		96/2104	6007500	2085,10161	1985	4138	6123	SO:0001819	synonymous_variant	158358	exon1			GGTGAGGCCCCGG	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.288C>T	9.37:g.6007500G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	30	0.461538	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	37																																																																																				G|0.786;A|0.214	0.214	strong		0.711	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
GRID2	2895	hgsc.bcm.edu	37	4	93511396	93511396	+	Missense_Mutation	SNP	C	C	T	rs34144324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:93511396C>T	ENST00000282020.4	+	2	461	c.203C>T	c.(202-204)aCg>aTg	p.T68M	GRID2_ENST00000510992.1_Missense_Mutation_p.T68M|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	68			T -> M (in dbSNP:rs34144324). {ECO:0000269|Ref.2}.		cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)	p.T68M(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		TTTTCAGTGACGTTTGTTGAT	0.388													C|||	114	0.0227636	0.0121	0.0533	5008	,	,		16950	0.002		0.0447	False		,,,				2504	0.0143				p.T68M		Atlas-SNP	.											GRID2,NS,carcinoma,0,1	GRID2	233	1	1	Substitution - Missense(1)	prostate(1)	c.C203T						PASS	.	C	MET/THR	92,4314	76.8+/-115.0	2,88,2113	160.0	155.0	157.0		203	6.0	1.0	4	dbSNP_126	157	435,8165	133.5+/-191.0	11,413,3876	yes	missense	GRID2	NM_001510.2	81	13,501,5989	TT,TC,CC		5.0581,2.0881,4.052	possibly-damaging	68/1008	93511396	527,12479	2203	4300	6503	SO:0001583	missense	2895	exon2			CAGTGACGTTTGT	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.203C>T	4.37:g.93511396C>T	ENSP00000282020:p.Thr68Met	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	65	0.02976190476190476	7	0.014227642276422764	21	0.058011049723756904	1	0.0017482517482517483	36	0.047493403693931395	C	19.44	3.828449	0.71143	0.020881	0.050581	ENSG00000152208	ENST00000282020;ENST00000510992	D;T	0.83250	-1.7;2.38	5.96	5.96	0.96718	Extracellular ligand-binding receptor (1);	0.087100	0.45867	D	0.000333	T	0.29850	0.0746	N	0.08118	0	0.25800	N	0.984527	P;D	0.53885	0.923;0.963	B;P	0.48921	0.379;0.595	T	0.60905	-0.7170	10	0.87932	D	0	.	15.9476	0.79806	0.1355:0.8645:0.0:0.0	rs34144324	68;68	E9PH24;O43424	.;GRID2_HUMAN	M	68	ENSP00000282020:T68M;ENSP00000421257:T68M	ENSP00000282020:T68M	T	+	2	0	GRID2	93730419	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.085000	0.64468	2.826000	0.97356	0.655000	0.94253	ACG	C|0.961;T|0.039	0.039	strong		0.388	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2		
OR4K2	390431	hgsc.bcm.edu	37	14	20345346	20345346	+	Missense_Mutation	SNP	A	A	T	rs12883767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20345346A>T	ENST00000298642.2	+	1	956	c.920A>T	c.(919-921)aAt>aTt	p.N307I		NM_001005501.1	NP_001005501.1	Q8NGD2	OR4K2_HUMAN	olfactory receptor, family 4, subfamily K, member 2	307			N -> I (in dbSNP:rs12883767).			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(6)|lung(16)|ovary(2)|skin(9)|upper_aerodigestive_tract(2)	43	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		AGGTTTCTAAATTTTAATAAG	0.333													A|||	1397	0.278954	0.2239	0.2839	5008	,	,		26910	0.122		0.4742	False		,,,				2504	0.3108				p.N307I		Atlas-SNP	.											.	OR4K2	97	.	0			c.A920T						PASS	.	A	ILE/ASN	988,3416		92,804,1306	49.0	53.0	52.0		920	2.9	0.9	14	dbSNP_121	52	3250,5346		584,2082,1632	yes	missense	OR4K2	NM_001005501.1	149	676,2886,2938	TT,TA,AA		37.8083,22.4342,32.6	benign	307/315	20345346	4238,8762	2202	4298	6500	SO:0001583	missense	390431	exon1			TTCTAAATTTTAA		CCDS32023.1	14q11.2	2013-09-23			ENSG00000165762	ENSG00000165762		"""GPCR / Class A : Olfactory receptors"""	14728	protein-coding gene	gene with protein product							Standard	NM_001005501		Approved		uc001vwh.1	Q8NGD2	OTTHUMG00000170624	ENST00000298642.2:c.920A>T	14.37:g.20345346A>T	ENSP00000298642:p.Asn307Ile	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	19	12	0.631579	NM_001005501	B2RNK8|Q6IFA5	Missense_Mutation	SNP	ENST00000298642.2	37	CCDS32023.1	642	0.29395604395604397	116	0.23577235772357724	118	0.3259668508287293	57	0.09965034965034965	351	0.4630606860158311	.	6.549	0.469523	0.12461	0.224342	0.378083	ENSG00000165762	ENST00000298642	T	0.06608	3.28	5.25	2.87	0.33458	.	0.241065	0.29321	N	0.012499	T	0.00012	0.0000	N	0.08118	0	0.35665	P	0.18711500000000003	B	0.28605	0.217	B	0.32090	0.14	T	0.39583	-0.9607	9	0.27785	T	0.31	.	6.7463	0.23462	0.8119:0.0:0.1881:0.0	rs12883767;rs52825198;rs12883767	307	Q8NGD2	OR4K2_HUMAN	I	307	ENSP00000298642:N307I	ENSP00000298642:N307I	N	+	2	0	OR4K2	19415186	0.116000	0.22171	0.874000	0.34290	0.025000	0.11179	1.415000	0.34748	1.021000	0.39600	0.482000	0.46254	AAT	A|0.666;T|0.334	0.334	strong		0.333	OR4K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409864.1		
OR6C68	403284	hgsc.bcm.edu	37	12	55886489	55886489	+	Missense_Mutation	SNP	T	T	A	rs7304753	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55886489T>A	ENST00000548615.1	+	1	328	c.328T>A	c.(328-330)Ttt>Att	p.F110I	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|OR6C68_ENST00000379662.1_Missense_Mutation_p.F115I	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						GGTAACTGAATTTTTTCTTTT	0.373													T|||	1321	0.263778	0.2156	0.1945	5008	,	,		20662	0.4931		0.1918	False		,,,				2504	0.2157				p.F110I		Atlas-SNP	.											.	OR6C68	36	.	0			c.T328A						PASS	.	T	ILE/PHE	962,3444	362.1+/-316.0	107,748,1348	163.0	153.0	156.0		328	4.8	1.0	12	dbSNP_116	156	1794,6806	323.2+/-315.9	198,1398,2704	yes	missense	OR6C68	NM_001005519.2	21	305,2146,4052	AA,AT,TT		20.8605,21.8339,21.1902	probably-damaging	110/313	55886489	2756,10250	2203	4300	6503	SO:0001583	missense	403284	exon1			ACTGAATTTTTTC		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"""GPCR / Class A : Olfactory receptors"""	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.328T>A	12.37:g.55886489T>A	ENSP00000448811:p.Phe110Ile	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_001005519		Missense_Mutation	SNP	ENST00000548615.1	37	CCDS31826.2	602	0.27564102564102566	102	0.2073170731707317	71	0.19613259668508287	279	0.48776223776223776	150	0.19788918205804748	T	14.60	2.583592	0.46006	0.218339	0.208605	ENSG00000205327	ENST00000379662;ENST00000548615	T;T	0.00824	5.65;5.65	4.77	4.77	0.60923	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000085	T	0.00012	0.0000	L	0.36672	1.1	0.39285	P	0.03537000000000001	D	0.76494	0.999	D	0.69479	0.964	T	0.54833	-0.8234	9	0.87932	D	0	.	14.4463	0.67352	0.0:0.0:0.0:1.0	rs7304753;rs7304753	110	A6NDL8	O6C68_HUMAN	I	115;110	ENSP00000368983:F115I;ENSP00000448811:F110I	ENSP00000368983:F115I	F	+	1	0	OR6C68	54172756	0.000000	0.05858	1.000000	0.80357	0.057000	0.15508	0.026000	0.13599	2.138000	0.66242	0.491000	0.48974	TTT	T|0.768;A|0.232	0.232	strong		0.373	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1		
SLC2A9	56606	hgsc.bcm.edu	37	4	9922167	9922167	+	Missense_Mutation	SNP	C	C	T	rs16890979	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:9922167C>T	ENST00000264784.3	-	7	897	c.844G>A	c.(844-846)Gtt>Att	p.V282I	SLC2A9_ENST00000309065.3_Missense_Mutation_p.V253I|SLC2A9_ENST00000506583.1_Missense_Mutation_p.V253I|RP13-560N11.1_ENST00000504249.1_RNA	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	282			V -> I (in dbSNP:rs16890979). {ECO:0000269|PubMed:18327256}.		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)	TCTTGGGAAACGTCTGCTTTA	0.577													C|||	1321	0.263778	0.4803	0.3818	5008	,	,		21107	0.0129		0.2137	False		,,,				2504	0.1973				p.V282I		Atlas-SNP	.											.	SLC2A9	158	.	0			c.G844A	GRCh37	CM086145	SLC2A9	M	rs16890979	PASS	.	C	ILE/VAL,ILE/VAL	1826,2580	527.1+/-372.1	389,1048,766	55.0	49.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	757,844	1.6	0.0	4	dbSNP_123	51	1898,6702	333.8+/-320.7	220,1458,2622	yes	missense,missense	SLC2A9	NM_001001290.1,NM_020041.2	29,29	609,2506,3388	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	22.0698,41.4435,28.6329	benign,benign	253/512,282/541	9922167	3724,9282	2203	4300	6503	SO:0001583	missense	56606	exon7			GGGAAACGTCTGC	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.844G>A	4.37:g.9922167C>T	ENSP00000264784:p.Val282Ile	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	155	87	0.56129	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	487	0.222985347985348	212	0.43089430894308944	120	0.3314917127071823	3	0.005244755244755245	152	0.20052770448548812	C	8.913	0.959077	0.18507	0.414435	0.220698	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065	T;T;T	0.75367	-0.93;-0.93;-0.93	5.2	1.61	0.23674	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.127893	0.52532	N	0.000078	T	0.00012	0.0000	L	0.49455	1.56	0.37213	P	0.09511800000000004	P;P	0.39883	0.693;0.613	B;B	0.35607	0.114;0.206	T	0.35076	-0.9803	8	.	.	.	.	9.6932	0.40141	0.0:0.7308:0.0:0.2692	rs16890979;rs52793226;rs16890979	253;282	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	I	253;282;253	ENSP00000422209:V253I;ENSP00000264784:V282I;ENSP00000311383:V253I	.	V	-	1	0	SLC2A9	9531265	0.855000	0.29742	0.001000	0.08648	0.002000	0.02628	1.648000	0.37271	-0.007000	0.14345	-0.145000	0.13849	GTT	C|0.737;T|0.263	0.263	strong		0.577	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
OVGP1	5016	hgsc.bcm.edu	37	1	111957311	111957311	+	Missense_Mutation	SNP	G	G	C	rs10067	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:111957311G>C	ENST00000369732.3	-	11	1867	c.1812C>G	c.(1810-1812)caC>caG	p.H604Q		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	604			H -> Q (in dbSNP:rs10067).		binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)	p.H604Q(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		CCATCCTGGGGTGAGTGCCCA	0.522													G|||	1477	0.294928	0.4539	0.1628	5008	,	,		18670	0.3919		0.1103	False		,,,				2504	0.2638				p.H604Q		Atlas-SNP	.											OVGP1_ENST00000369728,NS,carcinoma,-1,3	OVGP1	177	3	1	Substitution - Missense(1)	stomach(1)	c.C1812G	GRCh37	CM066158	OVGP1	M	rs10067	scavenged	.	G	GLN/HIS	1700,2706	512.9+/-368.2	328,1044,831	79.0	78.0	78.0		1812	0.2	0.0	1	dbSNP_52	78	709,7891	174.6+/-224.8	31,647,3622	yes	missense	OVGP1	NM_002557.3	24	359,1691,4453	CC,CG,GG		8.2442,38.5837,18.5222	benign	604/679	111957311	2409,10597	2203	4300	6503	SO:0001583	missense	5016	exon11			CCTGGGGTGAGTG	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1812C>G	1.37:g.111957311G>C	ENSP00000358747:p.His604Gln	Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	137	71	0.518248	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	568	0.2600732600732601	186	0.3780487804878049	59	0.16298342541436464	240	0.4195804195804196	83	0.10949868073878628	G	6.288	0.421200	0.11928	0.385837	0.082442	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04119	3.7	3.3	0.215	0.15253	.	32.642700	0.00166	N	0.000000	T	0.01061	0.0035	N	0.14661	0.345	0.80722	P	0.0	B;B	0.12013	0.005;0.005	B;B	0.10450	0.005;0.005	T	0.46582	-0.9181	9	0.66056	D	0.02	2.2789	4.0053	0.09598	0.1197:0.0:0.4665:0.4138	rs10067;rs3767611;rs17027624;rs52822661;rs10067	604;668	Q12889;Q59HH5	OVGP1_HUMAN;.	Q	604;668;412	ENSP00000358747:H604Q	ENSP00000358743:H668Q	H	-	3	2	OVGP1	111758834	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.609000	0.05635	0.059000	0.16252	0.585000	0.79938	CAC	G|0.785;C|0.214	0.214	strong		0.522	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
SDC4	6385	hgsc.bcm.edu	37	20	43976991	43976991	+	Missense_Mutation	SNP	A	A	G	rs2228384	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43976991A>G	ENST00000372733.3	-	1	73	c.34T>C	c.(34-36)Ttc>Ctc	p.F12L	SDC4_ENST00000537976.1_5'UTR	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	12			F -> L (in dbSNP:rs4458268). {ECO:0000269|PubMed:1500433, ECO:0000269|Ref.6}.		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				CCTACGAAGAACAGCAGCAGC	0.736			T	ROS1	NSCLC								G|||	1564	0.3123	0.1324	0.3012	5008	,	,		7892	0.4216		0.3807	False		,,,				2504	0.3804				p.F12L		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	SDC4,NS,carcinoma,0,1	SDC4	16	1	0			c.T34C						PASS	.	G	LEU/PHE	704,3632		68,568,1532	14.0	16.0	16.0		34	1.9	0.7	20	dbSNP_111	16	2893,5617		542,1809,1904	yes	missense	SDC4	NM_002999.3	22	610,2377,3436	GG,GA,AA		33.9953,16.2362,28.0009	benign	12/199	43976991	3597,9249	2168	4255	6423	SO:0001583	missense	6385	exon1			CGAAGAACAGCAG	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"""Proteoglycans / Cell Surface : Syndecans"""	10661	protein-coding gene	gene with protein product	"""syndecan proteoglycan 4"""	600017	"""syndecan 4 (amphiglycan, ryudocan)"""			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.34T>C	20.37:g.43976991A>G	ENSP00000361818:p.Phe12Leu	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	45	20	0.444444	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	735	0.33653846153846156	49	0.09959349593495935	128	0.35359116022099446	262	0.458041958041958	296	0.39050131926121373	G	11.74	1.727977	0.30593	0.162362	0.339953	ENSG00000124145	ENST00000372733	T	0.26660	1.72	3.88	1.9	0.25705	.	1.457070	0.04340	N	0.353868	T	0.00012	0.0000	N	0.00210	-1.845	0.09310	P	0.99999838508	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.09590	T	0.72	-1.4689	5.8347	0.18601	0.3534:0.0:0.6466:0.0	rs4458268;rs17173359;rs60954343;rs4458268	12	P31431	SDC4_HUMAN	L	12	ENSP00000361818:F12L	ENSP00000361818:F12L	F	-	1	0	SDC4	43410405	0.991000	0.36638	0.736000	0.30914	0.806000	0.45545	0.205000	0.17356	0.091000	0.17302	-0.186000	0.12905	TTC	A|0.686;G|0.314	0.314	strong		0.736	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999	
SP140L	93349	hgsc.bcm.edu	37	2	231222655	231222655	+	Silent	SNP	G	G	T	rs10498250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231222655G>T	ENST00000415673.2	+	3	329	c.243G>T	c.(241-243)cgG>cgT	p.R81R	SP140L_ENST00000243810.6_Silent_p.R81R|SP140L_ENST00000458341.1_5'UTR|SP140_ENST00000486687.2_3'UTR|SP140L_ENST00000396563.4_Silent_p.R81R|SP140L_ENST00000444636.1_Silent_p.R81R	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	81	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.					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						TCCGCGATCGGGAACTCATCA	0.358													T|||	579	0.115615	0.1293	0.1311	5008	,	,		21124	0.1042		0.1252	False		,,,				2504	0.0879				p.R81R		Atlas-SNP	.											SP140L_ENST00000415673,NS,carcinoma,+2,2	SP140L	68	2	0			c.G243T						PASS	.	T		529,3791		39,451,1670	136.0	146.0	143.0		243	-0.9	0.0	2	dbSNP_119	143	1033,7547		67,899,3324	no	coding-synonymous	SP140L	NM_138402.4		106,1350,4994	TT,TG,GG		12.0396,12.2454,12.1085		81/581	231222655	1562,11338	2160	4290	6450	SO:0001819	synonymous_variant	93349	exon3			CGATCGGGAACTC	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.243G>T	2.37:g.231222655G>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Silent	SNP	ENST00000415673.2	37	CCDS46538.1																																																																																			G|0.883;T|0.117	0.117	strong		0.358	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
ZNF705G	100131980	hgsc.bcm.edu	37	8	7215694	7215694	+	Missense_Mutation	SNP	A	A	G	rs9693671	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:7215694A>G	ENST00000400156.4	-	7	988	c.707T>C	c.(706-708)gTc>gCc	p.V236A	ZNF705G_ENST00000400078.2_Missense_Mutation_p.V236A|FAM66B_ENST00000606573.1_lincRNA			A8MUZ8	Z705G_HUMAN	zinc finger protein 705G	236					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(9)	9						TTGAATAAAGACTTTCCCATA	0.383																																					p.V236A		Atlas-SNP	.											.	ZNF705G	24	.	0			c.T707C						PASS	.						130.0	176.0	162.0					8																	7215694		671	1591	2262	SO:0001583	missense	100131980	exon5			ATAAAGACTTTCC		CCDS47773.1	8p23.1	2013-01-08			ENSG00000215372	ENSG00000215372		"""Zinc fingers, C2H2-type"", ""-"""	37134	protein-coding gene	gene with protein product							Standard	NM_001164457		Approved		uc022are.1	A8MUZ8	OTTHUMG00000165384	ENST00000400156.4:c.707T>C	8.37:g.7215694A>G	ENSP00000383020:p.Val236Ala	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	282	126	0.446809	NM_001164457		Missense_Mutation	SNP	ENST00000400156.4	37		.	.	.	.	.	.	.	.	.	.	G	0.003	-2.447359	0.00178	.	.	ENSG00000215372	ENST00000400156;ENST00000400078	T;T	0.16324	2.35;2.35	1.0	0.0489	0.14287	.	.	.	.	.	T	0.05410	0.0143	N	0.04787	-0.16	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.44190	-0.9344	6	0.02654	T	1	.	4.1841	0.10390	0.1795:0.4491:0.3714:0.0	rs9693671;rs61387799	.	.	.	A	236	ENSP00000383020:V236A;ENSP00000445477:V236A	ENSP00000445477:V236A	V	-	2	0	ZNF705G	7203104	0.000000	0.05858	0.071000	0.20095	0.016000	0.09150	0.108000	0.15396	-0.499000	0.06623	-3.359000	0.00041	GTC	A|0.500;G|0.500	0.500	strong		0.383	ZNF705G-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383776.1	XM_001720517	
SACM1L	22908	hgsc.bcm.edu	37	3	45779136	45779136	+	Missense_Mutation	SNP	A	A	T	rs1468542	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:45779136A>T	ENST00000389061.5	+	15	1505	c.1301A>T	c.(1300-1302)tAc>tTc	p.Y434F	SACM1L_ENST00000541314.1_Missense_Mutation_p.Y373F|SACM1L_ENST00000418611.1_Missense_Mutation_p.Y331F	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	434	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.		Y -> F (in dbSNP:rs1468542). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)	p.Y434F(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		GAGAAGATTTACAAAAATGGT	0.294													A|||	2746	0.548323	0.6505	0.5706	5008	,	,		17482	0.3958		0.6849	False		,,,				2504	0.411				p.Y434F		Atlas-SNP	.											SACM1L,NS,carcinoma,0,1	SACM1L	38	1	1	Substitution - Missense(1)	stomach(1)	c.A1301T						PASS	.	A	PHE/TYR	2769,1637	636.4+/-396.6	857,1055,291	97.0	104.0	102.0		1301	6.1	1.0	3	dbSNP_88	102	5708,2892	667.5+/-402.5	1883,1942,475	yes	missense	SACM1L	NM_014016.3	22	2740,2997,766	TT,TA,AA		33.6279,37.1539,34.8224	benign	434/588	45779136	8477,4529	2203	4300	6503	SO:0001583	missense	22908	exon15			AGATTTACAAAAA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.1301A>T	3.37:g.45779136A>T	ENSP00000373713:p.Tyr434Phe	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	NM_014016	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	37	CCDS33745.1	1247	0.5709706959706959	307	0.6239837398373984	211	0.5828729281767956	199	0.3479020979020979	530	0.6992084432717678	A	6.322	0.427520	0.11987	0.628461	0.663721	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000541314;ENST00000433336	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	6.06	6.06	0.98353	Synaptojanin, N-terminal (1);	0.056921	0.64402	D	0.000001	T	0.00012	0.0000	N	0.02842	-0.48	0.19575	P	0.9999684212	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.33929	-0.9849	9	0.02654	T	1	-3.1835	16.6127	0.84892	1.0:0.0:0.0:0.0	rs1468542;rs17851402;rs56496861;rs1468542	373;434	B4DK71;Q9NTJ5	.;SAC1_HUMAN	F	331;434;373;111	ENSP00000396387:Y331F;ENSP00000373713:Y434F;ENSP00000443373:Y373F;ENSP00000412883:Y111F	ENSP00000373713:Y434F	Y	+	2	0	SACM1L	45754140	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.805000	0.69143	2.322000	0.78497	0.528000	0.53228	TAC	A|0.405;T|0.595	0.595	strong		0.294	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016	
PRR21	643905	hgsc.bcm.edu	37	2	240981668	240981668	+	Silent	SNP	C	C	A	rs199598022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:240981668C>A	ENST00000408934.1	-	1	731	c.732G>T	c.(730-732)acG>acT	p.T244T		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	244	Pro-rich.							p.T244T(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						GACGAAGGGCCGTGGGTGAAG	0.642													c|||	752	0.15016	0.1861	0.1138	5008	,	,		9753	0.1012		0.1431	False		,,,				2504	0.1851				p.T244T		Atlas-SNP	.											PRR21,caecum,carcinoma,0,2	PRR21	53	2	2	Substitution - coding silent(2)	large_intestine(2)	c.G732T						scavenged	.						1.0	1.0	1.0					2																	240981668		446	864	1310	SO:0001819	synonymous_variant	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.732G>T	2.37:g.240981668C>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	7	6	0.857143	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			C|0.678;A|0.322	0.322	strong		0.642	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
SIRPD	128646	hgsc.bcm.edu	37	20	1538249	1538249	+	Silent	SNP	C	C	T	rs2250055	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1538249C>T	ENST00000381623.3	-	1	1240	c.51G>A	c.(49-51)ctG>ctA	p.L17L	SIRPD_ENST00000381621.1_Silent_p.L17L|RP4-576H24.4_ENST00000564763.1_Intron			Q9H106	SIRPD_HUMAN	signal-regulatory protein delta	17						extracellular region (GO:0005576)				breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(2)|skin(1)	15						GCAGCAGATACAGCAGTAAGG	0.572													C|||	536	0.107029	0.0219	0.1153	5008	,	,		17762	0.0188		0.2306	False		,,,				2504	0.18				p.L17L		Atlas-SNP	.											.	SIRPD	34	.	0			c.G51A						PASS	.	C		252,4154		10,232,1961	238.0	176.0	197.0		51	-0.0	0.2	20	dbSNP_100	197	2055,6545		254,1547,2499	yes	coding-synonymous	SIRPD	NM_178460.2		264,1779,4460	TT,TC,CC		23.8953,5.7195,17.738		17/198	1538249	2307,10699	2203	4300	6503	SO:0001819	synonymous_variant	128646	exon1			CAGATACAGCAGT	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.51G>A	20.37:g.1538249C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_178460	B3KS88|Q5TFQ6	Silent	SNP	ENST00000381623.3	37	CCDS13018.1																																																																																			C|0.856;T|0.144	0.144	strong		0.572	SIRPD-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077552.1	NM_178460	
LRP2	4036	hgsc.bcm.edu	37	2	170092395	170092395	+	Silent	SNP	A	A	G	rs2229267	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:170092395A>G	ENST00000263816.3	-	29	5160	c.4875T>C	c.(4873-4875)tgT>tgC	p.C1625C		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1625					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CATTATAATCACAAAAGTCCA	0.433													A|||	2310	0.461262	0.7088	0.4697	5008	,	,		18625	0.4058		0.2634	False		,,,				2504	0.3814				p.C1625C		Atlas-SNP	.											.	LRP2	751	.	0			c.T4875C						PASS	.	A		2843,1563	668.4+/-402.0	933,977,293	133.0	122.0	126.0		4875	3.0	1.0	2	dbSNP_98	126	2073,6527	359.4+/-331.5	261,1551,2488	no	coding-synonymous	LRP2	NM_004525.2		1194,2528,2781	GG,GA,AA		24.1047,35.4744,37.7979		1625/4656	170092395	4916,8090	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon29			ATAATCACAAAAG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.4875T>C	2.37:g.170092395A>G		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.095;G|0.314	0.314	strong		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
PER3	8863	hgsc.bcm.edu	37	1	7890026	7890026	+	Missense_Mutation	SNP	A	A	G	rs199947375|rs57875989		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:7890026A>G	ENST00000361923.2	+	18	3167	c.2992A>G	c.(2992-2994)Aag>Gag	p.K998E	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.K1007E	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	998	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)	p.K998E(1)		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)		GCCTCCCATGAAGAATCCATC	0.587																																					p.K998E		Atlas-SNP	.											PER3,NS,carcinoma,0,4	PER3	95	4	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2992G						scavenged	.						84.0	69.0	74.0					1																	7890026		1999	3897	5896	SO:0001583	missense	8863	exon18			CCCATGAAGAATC	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.2992A>G	1.37:g.7890026A>G	ENSP00000355031:p.Lys998Glu	Somatic	134	4	0.0298507		WXS	Illumina HiSeq	Phase_I	86	15	0.174419	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.434686	0.00182	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.13538	2.58;2.58	.	.	.	Period circadian-like, C-terminal (1);	5.912170	0.01354	N	0.012011	T	0.04724	0.0128	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.26503	-1.0101	8	0.02654	T	1	.	.	.	.	.	998;1007;1007;998	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	E	1007;998	ENSP00000366755:K1007E;ENSP00000355031:K998E	ENSP00000355031:K998E	K	+	1	0	PER3	7812613	0.002000	0.14202	0.013000	0.15412	0.014000	0.08584	-0.844000	0.04345	-0.911000	0.03843	-0.891000	0.02926	AAG	.	.	weak		0.587	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
UBE4A	9354	hgsc.bcm.edu	37	11	118242324	118242324	+	Silent	SNP	A	A	G	rs145949976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118242324A>G	ENST00000431736.2	+	5	576	c.504A>G	c.(502-504)gcA>gcG	p.A168A	UBE4A_ENST00000252108.3_Silent_p.A168A					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	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;3.28e-05)		ATCGAGATGCAGGAGAGAGGC	0.433													A|||	6	0.00119808	0.0038	0.0014	5008	,	,		16924	0.0		0.0	False		,,,				2504	0.0				p.A168A		Atlas-SNP	.											.	UBE4A	97	.	0			c.A504G						PASS	.	A	,	11,4389	17.9+/-39.9	0,11,2189	138.0	128.0	131.0		504,504	0.3	1.0	11	dbSNP_134	131	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous	UBE4A	NM_001204077.1,NM_004788.3	,	0,12,6484	GG,GA,AA		0.0116,0.25,0.0924	,	168/1067,168/1074	118242324	12,12980	2200	4296	6496	SO:0001819	synonymous_variant	9354	exon5			AGATGCAGGAGAG	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"""U-box domain containing"""	12499	protein-coding gene	gene with protein product		603753	"""ubiquitination factor E4A (homologous to yeast UFD2)"", ""ubiquitination factor E4A (UFD2 homolog, yeast)"""			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.504A>G	11.37:g.118242324A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	48	0.6	NM_004788		Silent	SNP	ENST00000431736.2	37	CCDS8396.1																																																																																			A|0.999;G|0.001	0.001	strong		0.433	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788	
TMEM45B	120224	hgsc.bcm.edu	37	11	129722553	129722553	+	Missense_Mutation	SNP	C	C	T	rs558813	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:129722553C>T	ENST00000524567.1	+	2	457	c.176C>T	c.(175-177)aCt>aTt	p.T59I	TMEM45B_ENST00000281441.3_Missense_Mutation_p.T59I			Q96B21	TM45B_HUMAN	transmembrane protein 45B	59			T -> I (in dbSNP:rs558813).			integral component of membrane (GO:0016021)		p.T59I(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		TTTTCCGTCACTGGTAAGAGC	0.478													c|||	1129	0.225439	0.4539	0.1974	5008	,	,		20778	0.0952		0.165	False		,,,				2504	0.1329				p.T59I		Atlas-SNP	.											TMEM45B,NS,carcinoma,0,1	TMEM45B	25	1	1	Substitution - Missense(1)	stomach(1)	c.C176T						scavenged	.	C	ILE/THR	1888,2514	544.5+/-376.5	397,1094,710	110.0	104.0	106.0		176	3.3	0.1	11	dbSNP_83	106	1571,7023	294.6+/-302.0	143,1285,2869	yes	missense	TMEM45B	NM_138788.3	89	540,2379,3579	TT,TC,CC		18.2802,42.8896,26.6159	benign	59/276	129722553	3459,9537	2201	4297	6498	SO:0001583	missense	120224	exon2			CCGTCACTGGTAA	AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.176C>T	11.37:g.129722553C>T	ENSP00000436293:p.Thr59Ile	Somatic	194	1	0.00515464		WXS	Illumina HiSeq	Phase_I	183	84	0.459016	NM_138788	A8K2L8	Missense_Mutation	SNP	ENST00000524567.1	37	CCDS8482.1	471	0.21565934065934067	219	0.4451219512195122	65	0.17955801104972377	61	0.10664335664335664	126	0.1662269129287599	c	0.672	-0.801700	0.02841	0.428896	0.182802	ENSG00000151715	ENST00000281441;ENST00000524567	T;T	0.26810	1.71;1.71	5.64	3.34	0.38264	.	0.201259	0.51477	N	0.000099	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48547	-0.9026	9	0.02654	T	1	-15.493	9.4769	0.38878	0.0:0.146:0.0:0.854	rs558813;rs3205706;rs11552100;rs17401429;rs52814728;rs57773245;rs558813	59	Q96B21	TM45B_HUMAN	I	59	ENSP00000281441:T59I;ENSP00000436293:T59I	ENSP00000281441:T59I	T	+	2	0	TMEM45B	129227763	0.311000	0.24536	0.103000	0.21229	0.003000	0.03518	2.306000	0.43673	0.411000	0.25702	-1.137000	0.01932	ACT	C|0.754;T|0.246	0.246	strong		0.478	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788	
KLRG1	10219	hgsc.bcm.edu	37	12	9142297	9142297	+	Silent	SNP	T	T	C	rs1805723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9142297T>C	ENST00000266551.4	+	1	81	c.66T>C	c.(64-66)taT>taC	p.Y22Y	RP11-259O18.4_ENST00000545706.1_RNA|KLRG1_ENST00000538029.1_Intron|KLRG1_ENST00000356986.3_Silent_p.Y22Y	NM_005810.3	NP_005801.3	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	22					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						AGAATGACTATGGACCACAGC	0.428													t|||	1731	0.345647	0.1377	0.3775	5008	,	,		-128	0.3998		0.4334	False		,,,				2504	0.4581				p.Y22Y		Atlas-SNP	.											.	KLRG1	16	.	0			c.T66C						PASS	.	C		761,3645	310.5+/-291.6	63,635,1505	92.0	88.0	89.0		66	-0.1	0.0	12	dbSNP_92	89	3836,4764	541.4+/-384.0	852,2132,1316	no	coding-synonymous	KLRG1	NM_005810.3		915,2767,2821	CC,CT,TT		44.6047,17.2719,35.3452		22/190	9142297	4597,8409	2203	4300	6503	SO:0001819	synonymous_variant	10219	exon1			TGACTATGGACCA	AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	6380	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member A"""	604874				9862378, 9842918, 16461340, 16140789	Standard	NM_005810		Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000266551.4:c.66T>C	12.37:g.9142297T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_005810	B7ZAM2|O43198|O75613	Silent	SNP	ENST00000266551.4	37																																																																																				T|0.639;C|0.361	0.361	strong		0.428	KLRG1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399145.1	NM_005810	
CROCC	9696	hgsc.bcm.edu	37	1	17264920	17264920	+	Missense_Mutation	SNP	C	C	T	rs4463721	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17264920C>T	ENST00000375541.5	+	11	1385	c.1316C>T	c.(1315-1317)gCg>gTg	p.A439V	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.A439V(3)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGGAGCAGGCGGCCCTGGAG	0.617																																					p.A439V		Atlas-SNP	.											CROCC,NS,carcinoma,0,3	CROCC	185	3	3	Substitution - Missense(3)	prostate(3)	c.C1316T						PASS	.						19.0	16.0	17.0					1																	17264920		2174	4263	6437	SO:0001583	missense	9696	exon11			AGCAGGCGGCCCT	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1316C>T	1.37:g.17264920C>T	ENSP00000364691:p.Ala439Val	Somatic	249	0	0		WXS	Illumina HiSeq	Phase_I	498	227	0.455823	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	628	0.2875457875457875	134	0.27235772357723576	93	0.2569060773480663	201	0.3513986013986014	200	0.2638522427440633	C	12.64	1.997905	0.35226	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.12465	2.68	4.81	4.81	0.61882	.	.	.	.	.	T	0.00012	0.0000	L	0.41573	1.285	0.24969	N	0.991679	B;B;P	0.39022	0.003;0.017;0.655	B;B;B	0.31751	0.002;0.003;0.135	T	0.48525	-0.9028	9	0.12103	T	0.63	.	10.9447	0.47294	0.187:0.813:0.0:0.0	rs4463721;rs59602954	302;302;439	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	V	439;320	ENSP00000364691:A439V	ENSP00000364691:A439V	A	+	2	0	CROCC	17137507	0.006000	0.16342	0.535000	0.28026	0.666000	0.39218	-0.113000	0.10774	2.374000	0.81015	0.561000	0.74099	GCG	C|0.713;T|0.287	0.287	strong		0.617	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
AKNAD1	254268	hgsc.bcm.edu	37	1	109369915	109369915	+	Missense_Mutation	SNP	G	G	T	rs7551421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:109369915G>T	ENST00000370001.3	-	11	2116	c.1848C>A	c.(1846-1848)aaC>aaA	p.N616K	AKNAD1_ENST00000369994.1_Missense_Mutation_p.N586K|AKNAD1_ENST00000357393.4_Missense_Mutation_p.N323K|AKNAD1_ENST00000369995.3_Missense_Mutation_p.N616K	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	616			N -> K (in dbSNP:rs7551421). {ECO:0000269|PubMed:17974005}.			cytoplasm (GO:0005737)		p.N616K(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						TTTTCTCCACGTTTTGCTTCC	0.378													T|||	2520	0.503195	0.6331	0.5288	5008	,	,		16967	0.2649		0.5805	False		,,,				2504	0.4755				p.N616K		Atlas-SNP	.											AKNAD1,NS,carcinoma,-2,2	AKNAD1	83	2	1	Substitution - Missense(1)	stomach(1)	c.C1848A						PASS	.	T	LYS/ASN	2802,1604	495.1+/-363.2	896,1010,297	152.0	158.0	156.0		1848	-7.4	0.0	1	dbSNP_116	156	5195,3403	501.8+/-375.5	1582,2031,686	yes	missense	AKNAD1	NM_152763.3	94	2478,3041,983	TT,TG,GG		39.579,36.4049,38.5035	benign	616/837	109369915	7997,5007	2203	4299	6502	SO:0001583	missense	254268	exon11			CTCCACGTTTTGC	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.1848C>A	1.37:g.109369915G>T	ENSP00000359018:p.Asn616Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Missense_Mutation	SNP	ENST00000370001.3	37	CCDS791.2	1112	0.5091575091575091	316	0.6422764227642277	205	0.5662983425414365	152	0.26573426573426573	439	0.579155672823219	T	0.038	-1.296348	0.01364	0.635951	0.60421	ENSG00000162641	ENST00000370001;ENST00000357393;ENST00000369994;ENST00000369995	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.0	-7.42	0.01388	.	0.949771	0.08698	N	0.906845	T	0.00552	0.0018	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36792	-0.9733	9	0.02654	T	1	-0.0014	2.3068	0.04176	0.2031:0.2145:0.4134:0.169	rs7551421;rs52829264;rs58082587;rs7551421	323;616	B4DET8;Q5T1N1	.;AKND1_HUMAN	K	616;323;586;616	ENSP00000359018:N616K;ENSP00000349968:N323K;ENSP00000359011:N586K;ENSP00000359012:N616K	ENSP00000349968:N323K	N	-	3	2	AKNAD1	109171438	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.357000	0.02607	-2.161000	0.00785	-1.554000	0.00893	AAC	G|0.440;N|0.001	.	strong		0.378	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
ZNF417	147687	hgsc.bcm.edu	37	19	58420162	58420162	+	Missense_Mutation	SNP	T	T	C	rs10416584	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58420162T>C	ENST00000312026.5	-	3	1648	c.1484A>G	c.(1483-1485)aAt>aGt	p.N495S	ZNF417_ENST00000536263.1_Missense_Mutation_p.N296S|ZNF417_ENST00000595559.1_Missense_Mutation_p.N494S|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	495			N -> S (in dbSNP:rs10416584). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		CCCACATTCATTGCATTCATA	0.408													C|||	1576	0.314696	0.2943	0.2882	5008	,	,		21501	0.2996		0.3698	False		,,,				2504	0.32				p.N495S		Atlas-SNP	.											.	ZNF417	44	.	0			c.A1484G						PASS	.	C	SER/ASN	951,3455		164,623,1416	111.0	91.0	98.0		1484	-4.8	0.0	19	dbSNP_119	98	2498,6098		564,1370,2364	no	missense	ZNF417	NM_152475.2	46	728,1993,3780	CC,CT,TT		29.06,21.5842,26.5267	benign	495/576	58420162	3449,9553	2203	4298	6501	SO:0001583	missense	147687	exon3			CATTCATTGCATT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1484A>G	19.37:g.58420162T>C	ENSP00000311319:p.Asn495Ser	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	607	0.27793040293040294	110	0.22357723577235772	110	0.30386740331491713	141	0.2465034965034965	246	0.3245382585751979	.	0.125	-1.120845	0.01785	0.215842	0.2906	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.07216	3.21;3.21	2.38	-4.76	0.03229	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12611	0.24	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.42413	-0.9453	8	0.02654	T	1	.	1.0708	0.01621	0.205:0.1385:0.2171:0.4394	rs10416584;rs17856733	495	Q8TAU3	ZN417_HUMAN	S	495;296	ENSP00000311319:N495S;ENSP00000442760:N296S	ENSP00000311319:N495S	N	-	2	0	ZNF417	63111974	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-8.711000	0.00017	-3.048000	0.00261	-0.665000	0.03846	AAT	T|0.053;C|0.947	0.947	strong		0.408	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
STAB1	23166	hgsc.bcm.edu	37	3	52556890	52556890	+	Missense_Mutation	SNP	A	A	G	rs4434138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52556890A>G	ENST00000321725.6	+	62	6920	c.6844A>G	c.(6844-6846)Ata>Gta	p.I2282V		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2282	Link. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.		I -> V (in dbSNP:rs4434138). {ECO:0000269|PubMed:11829752}.		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)		TCGGGTGGGCATAGTCAGCCT	0.627													A|||	1709	0.341254	0.1528	0.4957	5008	,	,		16846	0.4385		0.4732	False		,,,				2504	0.2505				p.I2282V		Atlas-SNP	.											.	STAB1	178	.	0			c.A6844G						PASS	.	A	VAL/ILE	827,3579	328.3+/-300.5	76,675,1452	88.0	91.0	90.0		6844	-0.5	0.2	3	dbSNP_111	90	4070,4530	557.6+/-387.1	1002,2066,1232	yes	missense	STAB1	NM_015136.2	29	1078,2741,2684	GG,GA,AA		47.3256,18.7699,37.6519	benign	2282/2571	52556890	4897,8109	2203	4300	6503	SO:0001583	missense	23166	exon62			GTGGGCATAGTCA	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.6844A>G	3.37:g.52556890A>G	ENSP00000312946:p.Ile2282Val	Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	180	84	0.466667	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	916	0.4194139194139194	87	0.17682926829268292	182	0.5027624309392266	288	0.5034965034965035	359	0.4736147757255937	a	11.31	1.602172	0.28534	0.187699	0.473256	ENSG00000010327	ENST00000321725	T	0.04275	3.66	5.73	-0.467	0.12150	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.477047	0.20847	N	0.084583	T	0.00012	0.0000	N	0.05510	-0.035	0.45554	P	0.001495000000000024	B	0.10296	0.003	B	0.13407	0.009	T	0.32929	-0.9888	9	0.22109	T	0.4	.	9.8647	0.41136	0.7551:0.0:0.2449:0.0	rs4434138	2282	Q9NY15	STAB1_HUMAN	V	2282	ENSP00000312946:I2282V	ENSP00000312946:I2282V	I	+	1	0	STAB1	52531930	0.993000	0.37304	0.151000	0.22473	0.838000	0.47535	1.215000	0.32431	-0.043000	0.13513	0.454000	0.30748	ATA	A|0.608;G|0.392	0.392	strong		0.627	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
ADAP1	11033	hgsc.bcm.edu	37	7	940181	940181	+	Missense_Mutation	SNP	C	C	T	rs10256887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:940181C>T	ENST00000265846.5	-	7	940	c.721G>A	c.(721-723)Ggc>Agc	p.G241S	ADAP1_ENST00000539900.1_Missense_Mutation_p.G252S|ADAP1_ENST00000449296.2_Missense_Mutation_p.G169S	NM_001284308.1|NM_001284309.1|NM_001284311.1|NM_006869.2	NP_001271237.1|NP_001271238.1|NP_001271240.1|NP_006860	O75689	ADAP1_HUMAN	ArfGAP with dual PH domains 1	241			G -> S (in dbSNP:rs10256887). {ECO:0000269|PubMed:10333475, ECO:0000269|PubMed:12761501, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell surface receptor signaling pathway (GO:0007166)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF GTPase activity (GO:0032312)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	6						TCTGCGTCGCCGGCCCCTGGG	0.662													T|||	4342	0.867013	0.9539	0.8069	5008	,	,		15523	0.8988		0.828	False		,,,				2504	0.7996				p.G241S		Atlas-SNP	.											.	ADAP1	23	.	0			c.G721A						PASS	.	T	SER/GLY	4094,296	152.2+/-185.9	1911,272,12	42.0	34.0	37.0		721	4.5	0.9	7	dbSNP_119	37	7274,1314	246.0+/-274.6	3078,1118,98	yes	missense	ADAP1	NM_006869.2	56	4989,1390,110	TT,TC,CC		15.3004,6.7426,12.4056	benign	241/375	940181	11368,1610	2195	4294	6489	SO:0001583	missense	11033	exon7			CGTCGCCGGCCCC	AJ006422	CCDS5318.1, CCDS64576.1, CCDS64577.1, CCDS75558.1	7p22.3	2013-01-10	2008-09-22	2008-09-22	ENSG00000105963	ENSG00000105963		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	16486	protein-coding gene	gene with protein product		608114	"""centaurin, alpha 1"""	CENTA1		10333475	Standard	NM_006869		Approved	GCS1L	uc003sjo.4	O75689	OTTHUMG00000023380	ENST00000265846.5:c.721G>A	7.37:g.940181C>T	ENSP00000265846:p.Gly241Ser	Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	159	155	0.974843	NM_006869	A4D2Q2|B3KRZ4|B4DVA6|F6XZ68|H7C2Q4	Missense_Mutation	SNP	ENST00000265846.5	37	CCDS5318.1	1908|1908	0.8736263736263736|0.8736263736263736	474|474	0.9634146341463414|0.9634146341463414	302|302	0.8342541436464088|0.8342541436464088	499|499	0.8723776223776224|0.8723776223776224	633|633	0.8350923482849604|0.8350923482849604	t|t	0.012|0.012	-1.689529|-1.689529	0.00738|0.00738	0.932574|0.932574	0.846996|0.846996	ENSG00000105963|ENSG00000105963	ENST00000265846;ENST00000449296;ENST00000449929;ENST00000538188;ENST00000539900;ENST00000453175|ENST00000454383	T;T;T|.	0.21543|.	2.0;2.0;2.0|.	4.47|4.47	4.47|4.47	0.54385|0.54385	.|.	0.257271|.	0.36815|.	N|.	0.002400|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00075|0.00075	-2.25|-2.25	0.52099|0.52099	P|P	5.999999999994898E-5|5.999999999994898E-5	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.32693|0.32693	-0.9897|-0.9897	9|4	0.02654|.	T|.	1|.	-6.6935|-6.6935	5.2829|5.2829	0.15686|0.15686	0.0:0.1644:0.149:0.6866|0.0:0.1644:0.149:0.6866	rs10256887;rs17856983;rs36170344;rs60689133;rs10256887|rs10256887;rs17856983;rs36170344;rs60689133;rs10256887	241|.	O75689|.	ADAP1_HUMAN|.	S|Q	241;169;67;127;252;106|181	ENSP00000265846:G241S;ENSP00000407267:G169S;ENSP00000442682:G252S|.	ENSP00000265846:G241S|.	G|R	-|-	1|2	0|0	ADAP1|ADAP1	906707|906707	0.026000|0.026000	0.19158|0.19158	0.929000|0.929000	0.37066|0.37066	0.025000|0.025000	0.11179|0.11179	0.460000|0.460000	0.21924|0.21924	0.564000|0.564000	0.29238|0.29238	-0.376000|-0.376000	0.06991|0.06991	GGC|CGG	C|0.114;T|0.886	0.886	strong		0.662	ADAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059701.2	NM_006869	
FAM170B	170370	hgsc.bcm.edu	37	10	50339962	50339962	+	Missense_Mutation	SNP	A	A	T	rs75297145	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50339962A>T	ENST00000311787.5	-	2	637	c.548T>A	c.(547-549)cTg>cAg	p.L183Q	FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	183										central_nervous_system(1)|endometrium(1)|skin(1)	3						GCAGCACTCCAGCAGGTCTAT	0.652													A|||	442	0.0882588	0.0144	0.1095	5008	,	,		16806	0.003		0.1938	False		,,,				2504	0.1524				p.L183Q		Atlas-SNP	.											.	FAM170B	20	.	0			c.T548A						PASS	.	A	GLN/LEU	55,1329		1,53,638	21.0	23.0	23.0		548	1.9	0.8	10	dbSNP_132	23	662,2520		71,520,1000	no	missense	FAM170B	NM_001164484.1	113	72,573,1638	TT,TA,AA		20.8045,3.974,15.703	benign	183/284	50339962	717,3849	692	1591	2283	SO:0001583	missense	170370	exon2			CACTCCAGCAGGT		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.548T>A	10.37:g.50339962A>T	ENSP00000308292:p.Leu183Gln	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	199	0.09111721611721611	9	0.018292682926829267	35	0.09668508287292818	0	0.0	155	0.20448548812664907	A	8.876	0.950364	0.18431	0.03974	0.208045	ENSG00000172538	ENST00000311787	T	0.32515	1.45	5.73	1.93	0.25924	.	0.862135	0.09814	N	0.752387	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B	0.25955	0.138	B	0.21708	0.036	T	0.22103	-1.0226	9	0.51188	T	0.08	-13.7362	2.8237	0.05479	0.6126:0.0:0.2004:0.1869	.	183	A6NMN3	F170B_HUMAN	Q	183	ENSP00000308292:L183Q	ENSP00000308292:L183Q	L	-	2	0	FAM170B	50009968	0.000000	0.05858	0.768000	0.31515	0.115000	0.19883	-0.175000	0.09825	1.011000	0.39340	0.491000	0.48974	CTG	A|0.908;T|0.092	0.092	strong		0.652	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
ANKRD2	26287	hgsc.bcm.edu	37	10	99332488	99332488	+	Silent	SNP	A	A	C	rs12221474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99332488A>C	ENST00000307518.5	+	1	291	c.24A>C	c.(22-24)gcA>gcC	p.A8A	ANKRD2_ENST00000298808.5_Silent_p.A8A|ANKRD2_ENST00000455090.1_5'Flank|ANKRD2_ENST00000370655.1_5'UTR			Q9GZV1	ANKR2_HUMAN	ankyrin repeat domain 2 (stretch responsive muscle)	8	May mediate interaction with PML, p53/TP53 and YBX1.				muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|euchromatin (GO:0000791)|I band (GO:0031674)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	protein kinase B binding (GO:0043422)|structural constituent of muscle (GO:0008307)			breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	7		all_hematologic(284;1.95e-06)|Colorectal(252;0.0163)		Epithelial(162;1.18e-94)|all cancers(201;9.31e-86)|BRCA - Breast invasive adenocarcinoma(275;0.0233)|STAD - Stomach adenocarcinoma(243;0.181)|KIRC - Kidney renal clear cell carcinoma(50;0.206)|Kidney(138;0.241)		CCAGCTGGGCAGGGGTGGGTG	0.677											OREG0020418	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1770	0.353435	0.2557	0.2666	5008	,	,		16027	0.5288		0.2724	False		,,,				2504	0.4499				p.A8A		Atlas-SNP	.											.	ANKRD2	27	.	0			c.A24C						PASS	.	A	,	1027,3379		125,777,1301	25.0	23.0	24.0		24,24	2.8	0.6	10	dbSNP_120	24	2202,6394		276,1650,2372	no	coding-synonymous,coding-synonymous	ANKRD2	NM_001129981.1,NM_020349.2	,	401,2427,3673	CC,CA,AA		25.6166,23.3091,24.8346	,	8/328,8/361	99332488	3229,9773	2203	4298	6501	SO:0001819	synonymous_variant	26287	exon1			CTGGGCAGGGGTG	AJ304805	CCDS7466.1, CCDS44468.1	10q23	2013-01-10			ENSG00000165887	ENSG00000165887		"""Ankyrin repeat domain containing"""	495	protein-coding gene	gene with protein product		610734				10873377, 15136035, 15677738	Standard	NM_001129981		Approved	ARPP	uc001knw.3	Q9GZV1	OTTHUMG00000018860	ENST00000307518.5:c.24A>C	10.37:g.99332488A>C		Somatic	189	0	0	1342	WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_001129981	Q3B778|Q5T456|Q70EZ9|Q8WUD7|Q96MG0|Q9NQC9	Silent	SNP	ENST00000307518.5	37	CCDS7466.1																																																																																			A|0.721;C|0.279	0.279	strong		0.677	ANKRD2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
HEATR5A	25938	hgsc.bcm.edu	37	14	31856407	31856407	+	Missense_Mutation	SNP	C	C	T	rs73259359	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:31856407C>T	ENST00000389961.3	-	7	1089	c.1090G>A	c.(1090-1092)Ggt>Agt	p.G364S	HEATR5A_ENST00000439727.1_Missense_Mutation_p.G77S|HEATR5A_ENST00000439348.1_Missense_Mutation_p.G364S|HEATR5A_ENST00000543095.2_Missense_Mutation_p.G370S|HEATR5A_ENST00000404677.3_Missense_Mutation_p.G370S			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	364										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		AGAAGACCACCTATAGTAGTT	0.468													C|||	145	0.0289537	0.0968	0.0187	5008	,	,		16103	0.0		0.003	False		,,,				2504	0.001				p.G370S		Atlas-SNP	.											.	HEATR5A	181	.	0			c.G1108A						PASS	.	C	SER/GLY	239,3561		9,221,1670	126.0	119.0	121.0		1108	4.7	1.0	14	dbSNP_130	121	15,8239		0,15,4112	yes	missense	HEATR5A	NM_015473.3	56	9,236,5782	TT,TC,CC		0.1817,6.2895,2.1072	probably-damaging	370/2047	31856407	254,11800	1900	4127	6027	SO:0001583	missense	25938	exon8			GACCACCTATAGT	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.1090G>A	14.37:g.31856407C>T	ENSP00000374611:p.Gly364Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	178	91	0.511236	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		60|60	0.027472527472527472|0.027472527472527472	53|53	0.10772357723577236|0.10772357723577236	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	29.3|29.3	4.991400|4.991400	0.93106|0.93106	0.062895|0.062895	0.001817|0.001817	ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677|ENST00000550366	T;T;T;T;T|.	0.07567|.	3.18;3.18;3.18;3.18;3.18|.	5.53|5.53	4.65|4.65	0.58169|0.58169	.|.	0.124234|.	0.53938|.	D|.	0.000055|.	T|T	0.04907|0.04907	0.0132|0.0132	M|M	0.77313|0.77313	2.365|2.365	0.09310|0.09310	P|P	0.9999999539453|0.9999999539453	D|.	0.58970|.	0.984|.	P|.	0.59643|.	0.861|.	T|T	0.51911|0.51911	-0.8645|-0.8645	9|4	0.72032|.	D|.	0.01|.	.|.	14.2073|14.2073	0.65741|0.65741	0.0:0.9281:0.0:0.0719|0.0:0.9281:0.0:0.0719	.|.	370|.	B5MC49|.	.|.	S|K	364;364;77;370;370|28	ENSP00000374611:G364S;ENSP00000405407:G364S;ENSP00000408681:G77S;ENSP00000437968:G370S;ENSP00000384646:G370S|.	ENSP00000374611:G364S|.	G|R	-|-	1|2	0|0	HEATR5A|HEATR5A	30926158|30926158	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	7.632000|7.632000	0.83247|0.83247	1.339000|1.339000	0.45563|0.45563	0.491000|0.491000	0.48974|0.48974	GGT|AGG	C|0.977;T|0.023	0.023	strong		0.468	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	
AVPI1	60370	hgsc.bcm.edu	37	10	99439541	99439541	+	Missense_Mutation	SNP	G	G	C	rs2275047	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99439541G>C	ENST00000370626.3	-	2	689	c.122C>G	c.(121-123)gCc>gGc	p.A41G		NM_021732.2	NP_068378.2	Q5T686	AVPI1_HUMAN	arginine vasopressin-induced 1	41			A -> G (in dbSNP:rs2275047). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874, ECO:0000269|Ref.3}.		activation of MAPK activity (GO:0000187)|cell cycle (GO:0007049)					breast(1)|endometrium(1)|large_intestine(2)|skin(1)	5		Colorectal(252;0.162)		Epithelial(162;8.37e-11)|all cancers(201;7.94e-09)		TTGAAACAGGGCTTGGATCTG	0.662													C|||	2545	0.508187	0.6982	0.438	5008	,	,		17525	0.4742		0.3579	False		,,,				2504	0.4908				p.A41G		Atlas-SNP	.											AVPI1,NS,carcinoma,0,2	AVPI1	16	2	0			c.C122G						PASS	.	C	GLY/ALA	2846,1560		944,958,301	38.0	29.0	32.0		122	5.1	1.0	10	dbSNP_100	32	3408,5192		678,2052,1570	yes	missense	AVPI1	NM_021732.2	60	1622,3010,1871	CC,CG,GG		39.6279,35.4063,48.0855	benign	41/148	99439541	6254,6752	2203	4300	6503	SO:0001583	missense	60370	exon2			AACAGGGCTTGGA	AF131791	CCDS7470.1	10q24.2	2004-04-05			ENSG00000119986	ENSG00000119986			30898	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_021732		Approved	VIP32, PP5395, VIT32	uc001koi.2	Q5T686	OTTHUMG00000018864	ENST00000370626.3:c.122C>G	10.37:g.99439541G>C	ENSP00000359660:p.Ala41Gly	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	174	91	0.522988	NM_021732	Q53G32|Q9H2R9|Q9HBN9	Missense_Mutation	SNP	ENST00000370626.3	37	CCDS7470.1	1018	0.4661172161172161	339	0.6890243902439024	149	0.4116022099447514	261	0.4562937062937063	269	0.3548812664907652	C	4.439	0.081327	0.08533	0.645937	0.396279	ENSG00000119986	ENST00000370626	T	0.28895	1.59	5.09	5.09	0.68999	.	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.24870	-1.0148	8	0.32370	T	0.25	0.0051	13.3971	0.60861	0.0:0.6982:0.3018:0.0	rs2275047;rs17856022;rs52810646;rs57044806;rs2275047	41	Q5T686	AVPI1_HUMAN	G	41	ENSP00000359660:A41G	ENSP00000359660:A41G	A	-	2	0	AVPI1	99429531	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	1.539000	0.36104	1.383000	0.46405	-0.216000	0.12614	GCC	G|0.524;C|0.476	0.476	strong		0.662	AVPI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049736.1	NM_021732	
LMTK3	114783	hgsc.bcm.edu	37	19	49001600	49001600	+	Missense_Mutation	SNP	A	A	G	rs61745738	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49001600A>G	ENST00000600059.1	-	11	2953	c.2726T>C	c.(2725-2727)gTc>gCc	p.V909A	LMTK3_ENST00000270238.3_Missense_Mutation_p.V938A			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	909	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GTTGCCCAGGACTGTCGGGTC	0.667													G|||	503	0.100439	0.2398	0.0634	5008	,	,		13447	0.0079		0.0527	False		,,,				2504	0.0828				p.V938A		Atlas-SNP	.											.	LMTK3	125	.	0			c.T2813C						PASS	.	G	ALA/VAL	764,3070		85,594,1238	27.0	31.0	30.0		2813	-0.0	0.2	19	dbSNP_129	30	354,7868		9,336,3766	yes	missense	LMTK3	NM_001080434.1	64	94,930,5004	GG,GA,AA		4.3055,19.927,9.2734	benign	938/1490	49001600	1118,10938	1917	4111	6028	SO:0001583	missense	114783	exon12			CCCAGGACTGTCG	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.2726T>C	19.37:g.49001600A>G	ENSP00000472020:p.Val909Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	71	41	0.577465	NM_001080434	Q4G0U1	Missense_Mutation	SNP	ENST00000600059.1	37		185	0.08470695970695971	110	0.22357723577235772	28	0.07734806629834254	6	0.01048951048951049	41	0.05408970976253298	a	0	-2.762715	0.00082	0.19927	0.043055	ENSG00000142235	ENST00000270238	T	0.79033	-1.23	3.89	-0.00579	0.14016	.	1.029000	0.07801	N	0.956498	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.02721	-1.1119	9	0.02654	T	1	.	7.0955	0.25307	0.5615:0.0:0.4385:0.0	.	909	Q96Q04	LMTK3_HUMAN	A	938	ENSP00000270238:V938A	ENSP00000270238:V938A	V	-	2	0	LMTK3	53693412	0.045000	0.20229	0.186000	0.23195	0.001000	0.01503	0.353000	0.20130	-0.400000	0.07656	-0.386000	0.06593	GTC	A|0.922;G|0.078	0.078	strong		0.667	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	
TRPC1	7220	hgsc.bcm.edu	37	3	142523349	142523349	+	Silent	SNP	G	G	A	rs3821647	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142523349G>A	ENST00000476941.1	+	12	2517	c.2031G>A	c.(2029-2031)acG>acA	p.T677T	TRPC1_ENST00000273482.6_Silent_p.T643T	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	677					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.T643T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						ACAAATGTACGTTACCTCCAC	0.368													G|||	972	0.194089	0.2186	0.1354	5008	,	,		16060	0.2391		0.2038	False		,,,				2504	0.1462				p.T677T		Atlas-SNP	.											TRPC1,NS,carcinoma,0,1	TRPC1	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G2031A						PASS	.	G		928,3478	352.6+/-311.8	97,734,1372	100.0	95.0	97.0		1929	-3.1	1.0	3	dbSNP_107	97	1578,7022	294.8+/-302.1	163,1252,2885	no	coding-synonymous	TRPC1	NM_003304.4		260,1986,4257	AA,AG,GG		18.3488,21.0622,19.268		643/760	142523349	2506,10500	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon12			ATGTACGTTACCT	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2031G>A	3.37:g.142523349G>A		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	194	99	0.510309	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			G|0.806;A|0.194	0.194	strong		0.368	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
SLC26A1	10861	hgsc.bcm.edu	37	4	983809	983809	+	Silent	SNP	C	C	T	rs4690221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:983809C>T	ENST00000361661.2	-	4	1295	c.918G>A	c.(916-918)tcG>tcA	p.S306S	SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398520.2_Intron|SLC26A1_ENST00000398516.2_Silent_p.S306S	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	306					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)	p.S306S(1)		central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GCCCGAAGTGCGACACGAGTG	0.667													C|||	1948	0.388978	0.3419	0.5418	5008	,	,		16919	0.3482		0.4145	False		,,,				2504	0.3599				p.S306S		Atlas-SNP	.											SLC26A1,NS,carcinoma,0,2	SLC26A1	44	2	1	Substitution - coding silent(1)	prostate(1)	c.G918A						PASS	.	C	,,,	1467,2883		260,947,968	31.0	24.0	26.0		,918,,918	1.8	1.0	4	dbSNP_111	26	3527,5047		740,2047,1500	no	intron,coding-synonymous,intron,coding-synonymous	IDUA,SLC26A1	NM_000203.3,NM_022042.2,NM_134425.1,NM_213613.2	,,,	1000,2994,2468	TT,TC,CC		41.136,33.7241,38.6413	,,,	,306/702,,306/702	983809	4994,7930	2175	4287	6462	SO:0001819	synonymous_variant	10861	exon3			GAAGTGCGACACG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"""Solute carriers"""	10993	protein-coding gene	gene with protein product		610130	"""solute carrier family 26 (sulfate transporter), member 1"""				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.918G>A	4.37:g.983809C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Silent	SNP	ENST00000361661.2	37	CCDS33934.1																																																																																			C|0.606;T|0.394	0.394	strong		0.667	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425	
PALLD	23022	hgsc.bcm.edu	37	4	169433444	169433444	+	Silent	SNP	C	C	T	rs72695199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169433444C>T	ENST00000505667.1	+	2	962	c.789C>T	c.(787-789)agC>agT	p.S263S	PALLD_ENST00000261509.6_Silent_p.S263S|PALLD_ENST00000333488.4_Silent_p.S140S|PALLD_ENST00000335742.7_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	263					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		AGCCCCACAGCGCCCTCCACT	0.567									Pancreatic Cancer, Familial Clustering of				C|||	287	0.0573083	0.0189	0.0778	5008	,	,		17753	0.0		0.1173	False		,,,				2504	0.092				p.S263S	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C789T						PASS	.	C	,	189,4217	118.4+/-156.1	9,171,2023	65.0	59.0	61.0		789,789	-10.4	0.0	4	dbSNP_130	61	1168,7432	238.9+/-270.2	76,1016,3208	no	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	85,1187,5231	TT,TC,CC		13.5814,4.2896,10.4336	,	263/1124,263/1107	169433444	1357,11649	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CCACAGCGCCCTC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.789C>T	4.37:g.169433444C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.907;T|0.093	0.093	strong		0.567	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
USP34	9736	hgsc.bcm.edu	37	2	61415492	61415492	+	Silent	SNP	A	A	G	rs14170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:61415492A>G	ENST00000398571.2	-	80	10462	c.10386T>C	c.(10384-10386)gcT>gcC	p.A3462A	AHSA2_ENST00000394457.3_3'UTR	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3462					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ATTCTTCCTCAGCTAGGGTAG	0.453													A|||	2062	0.411741	0.4781	0.4164	5008	,	,		21759	0.3929		0.4901	False		,,,				2504	0.2577				p.A3462A		Atlas-SNP	.											.	USP34	334	.	0			c.T10386C						PASS	.	A		1798,1958		455,888,535	85.0	79.0	80.0		10386	-0.6	1.0	2	dbSNP_52	80	4028,4222		984,2060,1081	no	coding-synonymous	USP34	NM_014709.3		1439,2948,1616	GG,GA,AA		48.8242,47.8701,48.5257		3462/3547	61415492	5826,6180	1878	4125	6003	SO:0001819	synonymous_variant	9736	exon80			TTCCTCAGCTAGG	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.10386T>C	2.37:g.61415492A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1	1003	0.4592490842490842	240	0.4878048780487805	165	0.4558011049723757	217	0.3793706293706294	381	0.5026385224274407	.	4.254	0.046111	0.08243	0.478701	0.488242	ENSG00000115464	ENST00000411912	.	.	.	5.52	-0.572	0.11745	.	.	.	.	.	.	.	.	.	.	.	0.18873	P	0.999985041	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.133	0.06430	0.3824:0.1165:0.3872:0.1138	rs14170;rs3205597;rs3814034;rs11548862;rs17540386;rs17846593;rs17859675;rs61060947	.	.	.	R	1139	.	.	X	-	1	0	USP34	61268996	0.078000	0.21339	0.957000	0.39632	0.987000	0.75469	-0.555000	0.05999	0.049000	0.15920	0.482000	0.46254	TGA	A|0.525;G|0.475	0.475	strong		0.453	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
SKIDA1	387640	hgsc.bcm.edu	37	10	21804487	21804487	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:21804487C>T	ENST00000449193.2	-	4	4517	c.2265G>A	c.(2263-2265)caG>caA	p.Q755Q	SKIDA1_ENST00000444772.3_Silent_p.Q676Q	NM_207371.3	NP_997254.3	Q1XH10	SKDA1_HUMAN	SKI/DACH domain containing 1	674						nucleus (GO:0005634)											ATGAAAGGCCCTGACTTTGAG	0.458																																					p.Q755Q		Atlas-SNP	.											C10orf140_ENST00000449193,rectum,carcinoma,-2,2	.	.	2	0			c.G2265A						scavenged	.						156.0	149.0	151.0					10																	21804487		1857	4093	5950	SO:0001819	synonymous_variant	387640	exon4			AAGGCCCTGACTT	AK131456	CCDS44363.1	10p12.31	2012-06-13	2012-06-13	2012-06-13	ENSG00000180592	ENSG00000180592			32697	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 140"""	C10orf140			Standard	NM_207371		Approved	FLJ45187	uc021pnx.1	Q1XH10	OTTHUMG00000017797	ENST00000449193.2:c.2265G>A	10.37:g.21804487C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	123	2	0.0162602	NM_207371	B1ANA5|Q6ZMX4|Q8N3C3	Silent	SNP	ENST00000449193.2	37	CCDS44363.1																																																																																			.	.	none		0.458	SKIDA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286950.2	NM_207371	
MRPS27	23107	hgsc.bcm.edu	37	5	71524163	71524163	+	Silent	SNP	A	A	T	rs10942927	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:71524163A>T	ENST00000261413.5	-	8	663	c.624T>A	c.(622-624)ctT>ctA	p.L208L	MRPS27_ENST00000457646.4_Silent_p.L152L|MRPS27_ENST00000513900.1_Silent_p.L222L|MRPS27_ENST00000522562.1_5'UTR|MRPS27_ENST00000515404.1_Silent_p.L152L	NM_015084.2	NP_055899.2	Q92552	RT27_HUMAN	mitochondrial ribosomal protein S27	208						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.46e-53)		CTGGAAGCAAAAGGGATGCAC	0.398													T|||	955	0.190695	0.1256	0.17	5008	,	,		18027	0.0218		0.3688	False		,,,				2504	0.2843				p.L208L		Atlas-SNP	.											.	MRPS27	23	.	0			c.T624A						PASS	.	T		680,3726	763.4+/-413.2	53,574,1576	156.0	152.0	153.0		624	-1.9	0.1	5	dbSNP_120	153	2944,5656	669.0+/-402.6	520,1904,1876	no	coding-synonymous	MRPS27	NM_015084.2		573,2478,3452	TT,TA,AA		34.2326,15.4335,27.8641		208/415	71524163	3624,9382	2203	4300	6503	SO:0001819	synonymous_variant	23107	exon8			AAGCAAAAGGGAT	D87453	CCDS4013.1, CCDS68890.1, CCDS75257.1	5q13.2	2012-09-13			ENSG00000113048	ENSG00000113048		"""Mitochondrial ribosomal proteins / small subunits"""	14512	protein-coding gene	gene with protein product		611989					Standard	NM_015084		Approved	KIAA0264	uc003kbz.4	Q92552	OTTHUMG00000100951	ENST00000261413.5:c.624T>A	5.37:g.71524163A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_015084	B4DRT2|Q6P1S1	Silent	SNP	ENST00000261413.5	37	CCDS4013.1																																																																																			A|0.768;T|0.232	0.232	strong		0.398	MRPS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218560.2	NM_015084	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377242	49377242	+	Missense_Mutation	SNP	G	G	C	rs557806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49377242G>C	ENST00000200453.5	+	2	1021	c.752G>C	c.(751-753)cGa>cCa	p.R251P		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	251	Glu-rich.		R -> P (in dbSNP:rs557806).		apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		GTGTCCCCCCGATCTTCAGGC	0.547													C|||	1742	0.347843	0.736	0.255	5008	,	,		18967	0.1091		0.1471	False		,,,				2504	0.3415				p.R251P		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.G752C						PASS	.	C	PRO/ARG	2894,1512	468.7+/-355.2	955,984,264	56.0	67.0	63.0		752	1.2	0.0	19	dbSNP_83	63	1142,7458	759.5+/-407.6	67,1008,3225	yes	missense	PPP1R15A	NM_014330.3	103	1022,1992,3489	CC,CG,GG		13.2791,34.3168,31.0318	benign	251/675	49377242	4036,8970	2203	4300	6503	SO:0001583	missense	23645	exon2			CCCCCCGATCTTC	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.752G>C	19.37:g.49377242G>C	ENSP00000200453:p.Arg251Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Missense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	620	0.2838827838827839	348	0.7073170731707317	93	0.2569060773480663	63	0.11013986013986014	116	0.15303430079155672	C	4.357	0.065741	0.08388	0.656832	0.132791	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	T	0.05139	3.49	3.46	1.24	0.21308	.	2.791140	0.01408	N	0.013878	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	0.43426	-0.9392	9	0.21540	T	0.41	-8.0E-4	11.3067	0.49340	0.0:0.4399:0.5601:0.0	rs557806;rs3745702;rs60558988;rs557806	251	O75807	PR15A_HUMAN	P	251;91;209	ENSP00000200453:R251P	ENSP00000200453:R251P	R	+	2	0	PPP1R15A	54069054	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.162000	0.10012	0.113000	0.18004	-0.929000	0.02709	CGA	G|0.699;C|0.301	0.301	strong		0.547	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058090	79058090	+	Missense_Mutation	SNP	A	A	G	rs2929158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79058090A>G	ENST00000388820.4	-	19	4373	c.4163T>C	c.(4162-4164)gTc>gCc	p.V1388A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1388					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						GGTCTCAGGGACTCTGTGGCT	0.687																																					p.V1388A		Atlas-SNP	.											ADAMTS7,rectum,carcinoma,0,1	ADAMTS7	142	1	0			c.T4163C						scavenged	.						22.0	29.0	26.0					15																	79058090		2166	4248	6414	SO:0001583	missense	11173	exon19			TCAGGGACTCTGT	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.4163T>C	15.37:g.79058090A>G	ENSP00000373472:p.Val1388Ala	Somatic	78	3	0.0384615		WXS	Illumina HiSeq	Phase_I	88	13	0.147727	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	249	0.11401098901098901	2	0.0040650406504065045	43	0.11878453038674033	198	0.34615384615384615	6	0.0079155672823219	a	0.637	-0.814774	0.02776	.	.	ENSG00000136378	ENST00000388820	T	0.58506	0.33	3.65	-3.31	0.04988	.	0.591257	0.16562	N	0.209003	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35724	-0.9777	9	0.15066	T	0.55	.	0.8256	0.01120	0.1904:0.2419:0.3106:0.2571	rs2929158	1388	Q9UKP4	ATS7_HUMAN	A	1388	ENSP00000373472:V1388A	ENSP00000373472:V1388A	V	-	2	0	ADAMTS7	76845145	0.000000	0.05858	0.052000	0.19188	0.008000	0.06430	-1.706000	0.01895	-0.534000	0.06315	-2.103000	0.00360	GTC	A|0.897;G|0.103	0.103	strong		0.687	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580931	140580931	+	Missense_Mutation	SNP	C	C	G	rs34415020|rs799834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140580931C>G	ENST00000354757.3	+	1	1584	c.1584C>G	c.(1582-1584)gaC>gaG	p.D528E	PCDHB11_ENST00000536699.1_Missense_Mutation_p.D163E	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		D -> E (in dbSNP:rs799834).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGCTTTCGACTTCCGCGTGG	0.677													G|||	2793	0.557708	0.7648	0.5576	5008	,	,		16257	0.5694		0.4105	False		,,,				2504	0.4172				p.D528E		Atlas-SNP	.											PCDHB11,NS,carcinoma,+2,1	PCDHB11	162	1	0			c.C1584G						PASS	.	G	GLU/ASP	3038,1366		1027,984,191	58.0	76.0	70.0		1584	1.6	0.0	5	dbSNP_86	70	3520,5080		757,2006,1537	no	missense	PCDHB11	NM_018931.2	45	1784,2990,1728	GG,GC,CC		40.9302,31.0173,49.5694	benign	528/798	140580931	6558,6446	2202	4300	6502	SO:0001583	missense	56125	exon1			TTTCGACTTCCGC	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1584C>G	5.37:g.140580931C>G	ENSP00000346802:p.Asp528Glu	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	274	273	0.99635	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	1096	0.5018315018315018	329	0.6686991869918699	165	0.4558011049723757	320	0.5594405594405595	282	0.3720316622691293	N	0.046	-1.265433	0.01433	0.689827	0.409302	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.01705	4.68;4.68	2.51	1.61	0.23674	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.18461	-1.0336	8	0.02654	T	1	.	3.8674	0.09022	0.3311:0.1861:0.4828:0.0	rs799834;rs61497114	528	Q9Y5F2	PCDBB_HUMAN	E	163;528	ENSP00000440344:D163E;ENSP00000346802:D528E	ENSP00000346802:D528E	D	+	3	2	PCDHB11	140561115	0.001000	0.12720	0.010000	0.14722	0.076000	0.17211	0.179000	0.16840	0.005000	0.14708	-0.702000	0.03669	GAC	C|0.497;G|0.503	0.503	strong		0.677	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
FOLH1	2346	hgsc.bcm.edu	37	11	49204779	49204779	+	Missense_Mutation	SNP	C	C	T	rs116795343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:49204779C>T	ENST00000256999.2	-	7	1102	c.842G>A	c.(841-843)cGt>cAt	p.R281H	FOLH1_ENST00000356696.3_Missense_Mutation_p.R281H|FOLH1_ENST00000533034.1_Missense_Mutation_p.R266H|FOLH1_ENST00000343844.4_De_novo_Start_OutOfFrame|FOLH1_ENST00000340334.7_Missense_Mutation_p.R266H	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	281	NAALADase.				folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.R281L(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGCAATTCCACGCCTATAAGC	0.348																																					p.R281H		Atlas-SNP	.											FOLH1,NS,carcinoma,-1,2	FOLH1	141	2	1	Substitution - Missense(1)	lung(1)	c.G842A						scavenged	.						72.0	73.0	73.0					11																	49204779		2201	4298	6499	SO:0001583	missense	2346	exon7			ATTCCACGCCTAT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.842G>A	11.37:g.49204779C>T	ENSP00000256999:p.Arg281His	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	179	6	0.0335196	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	2.929	-0.221410	0.06061	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	2.76	-1.12	0.09808	.	0.978445	0.08346	N	0.960084	T	0.21427	0.0516	N	0.14661	0.345	0.80722	D	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.0	B;B;B;B	0.06405	0.001;0.0;0.002;0.0	T	0.23655	-1.0182	10	0.14656	T	0.56	.	6.6038	0.22714	0.0:0.3193:0.0:0.6807	.	266;266;281;281	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	H	281;281;266;266;281	ENSP00000256999:R281H;ENSP00000349129:R281H;ENSP00000344131:R266H;ENSP00000431463:R266H	ENSP00000256999:R281H	R	-	2	0	FOLH1	49161355	0.002000	0.14202	0.792000	0.32020	0.272000	0.26649	-0.922000	0.04004	-0.085000	0.12573	0.194000	0.17425	CGT	C|0.974;T|0.026	0.026	strong		0.348	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
PTGIS	5740	hgsc.bcm.edu	37	20	48129706	48129706	+	Silent	SNP	G	G	T	rs5629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:48129706G>T	ENST00000244043.4	-	8	1146	c.1117C>A	c.(1117-1119)Cga>Aga	p.R373R	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	373					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	TTGAATTCTCGCCCGTCTGCC	0.602													G|||	1103	0.220248	0.1248	0.2723	5008	,	,		16672	0.2321		0.2604	False		,,,				2504	0.2587				p.R373R		Atlas-SNP	.											PTGIS,colon,carcinoma,+1,2	PTGIS	60	2	0			c.C1117A						PASS	.	G		582,3824	257.4+/-261.8	38,506,1659	101.0	90.0	94.0		1117	2.6	1.0	20	dbSNP_52	94	2247,6353	380.0+/-339.5	285,1677,2338	no	coding-synonymous	PTGIS	NM_000961.3		323,2183,3997	TT,TG,GG		26.1279,13.2093,21.7515		373/501	48129706	2829,10177	2203	4300	6503	SO:0001819	synonymous_variant	5740	exon8			ATTCTCGCCCGTC		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.1117C>A	20.37:g.48129706G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																			G|0.782;T|0.218	0.218	strong		0.602	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
MXRA5	25878	hgsc.bcm.edu	37	X	3238733	3238733	+	Missense_Mutation	SNP	G	G	A	rs1974522	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3238733G>A	ENST00000217939.6	-	5	5147	c.4993C>T	c.(4993-4995)Cca>Tca	p.P1665S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1665			P -> S (in dbSNP:rs1974522).			extracellular vesicular exosome (GO:0070062)		p.P1665S(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GATAATCTTGGAGTTGTAAAC	0.423													G|||	1629	0.431523	0.2118	0.3905	3775	,	,		16126	0.2728		0.4573	False		,,,				2504	0.3507				p.P1665S		Atlas-SNP	.											.	MXRA5	815	.	2	Substitution - Missense(2)	stomach(2)	c.C4993T						PASS	.	G	SER/PRO	1167,2668		139,714,175,779,396	166.0	158.0	161.0		4993	2.3	0.0	X	dbSNP_92	161	3839,2889		793,1187,1066,448,806	yes	missense	MXRA5	NM_015419.3	74	932,1901,1241,1227,1202	AA,AG,A,GG,G		42.94,30.4302,47.3918	probably-damaging	1665/2829	3238733	5006,5557	2203	4300	6503	SO:0001583	missense	25878	exon5			ATCTTGGAGTTGT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.4993C>T	X.37:g.3238733G>A	ENSP00000217939:p.Pro1665Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	743	0.4478601567209162	70	0.16203703703703703	89	0.31338028169014087	105	0.23863636363636365	240	0.43636363636363634	g	9.833	1.188977	0.21954	0.304302	0.5706	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.63096	-0.02	3.2	2.3	0.28687	.	0.184807	0.26149	U	0.026059	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.39809	0.689	B	0.31547	0.132	T	0.46965	-0.9153	9	0.51188	T	0.08	.	11.4118	0.49929	0.0:0.0:0.8176:0.1824	rs1974522;rs3752335;rs17335205;rs57959586;rs1974522	1665	Q9NR99	MXRA5_HUMAN	S	1665	ENSP00000217939:P1665S	ENSP00000217939:P1665S	P	-	1	0	MXRA5	3248733	0.091000	0.21658	0.004000	0.12327	0.040000	0.13550	1.291000	0.33330	0.345000	0.23873	0.431000	0.28591	CCA	0|0.015;A|0.441;C|0.000;G|0.544;N|0.000	0.441	strong		0.423	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
NLRP14	338323	hgsc.bcm.edu	37	11	7064560	7064560	+	Missense_Mutation	SNP	A	A	T	rs200574634		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7064560A>T	ENST00000299481.4	+	4	1649	c.1303A>T	c.(1303-1305)Ata>Tta	p.I435L		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	435	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TGCCAAAGGAATATGGACTAT	0.428													A|||	1	0.000199681	0.0	0.0	5008	,	,		20937	0.0		0.001	False		,,,				2504	0.0				p.I435L		Atlas-SNP	.											.	NLRP14	187	.	0			c.A1303T						PASS	.						128.0	131.0	130.0					11																	7064560		2201	4296	6497	SO:0001583	missense	338323	exon4			AAAGGAATATGGA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1303A>T	11.37:g.7064560A>T	ENSP00000299481:p.Ile435Leu	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	5.302	0.241082	0.10077	.	.	ENSG00000158077	ENST00000299481	T	0.74421	-0.84	4.48	-0.234	0.13074	.	0.513668	0.17972	N	0.155815	T	0.49389	0.1554	N	0.12637	0.245	0.23542	N	0.997459	B	0.22800	0.075	B	0.21151	0.033	T	0.30736	-0.9968	10	0.17369	T	0.5	.	7.7052	0.28646	0.5723:0.0:0.4277:0.0	.	435	Q86W24	NAL14_HUMAN	L	435	ENSP00000299481:I435L	ENSP00000299481:I435L	I	+	1	0	NLRP14	7021136	0.888000	0.30383	0.733000	0.30861	0.937000	0.57800	0.803000	0.27083	-0.106000	0.12110	-0.256000	0.11100	ATA	A|1.000;T|0.000	0.000	strong		0.428	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
HIST1H4F	8361	hgsc.bcm.edu	37	6	26240752	26240752	+	Silent	SNP	C	C	T	rs16891477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26240752C>T	ENST00000377745.2	+	1	192	c.99C>T	c.(97-99)ccC>ccT	p.P33P		NM_003540.3	NP_003531.1	P62805	H4_HUMAN	histone cluster 1, H4f	33					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)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				TCACGAAGCCCGCCATCCGTC	0.567													C|||	302	0.0603035	0.0726	0.0461	5008	,	,		14971	0.0675		0.0427	False		,,,				2504	0.0644				p.P33P		Atlas-SNP	.											.	HIST1H4F	9	.	0			c.C99T						PASS	.	C		266,4140		6,254,1943	48.0	46.0	47.0		99	-0.6	1.0	6	dbSNP_123	47	384,8216		12,360,3928	no	coding-synonymous	HIST1H4F	NM_003540.3		18,614,5871	TT,TC,CC		4.4651,6.0372,4.9977		33/104	26240752	650,12356	2203	4300	6503	SO:0001819	synonymous_variant	8361	exon1			GAAGCCCGCCATC	M60749	CCDS4598.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198327			"""Histones / Replication-dependent"""	4783	protein-coding gene	gene with protein product		602824	"""H4 histone family, member C"", ""histone 1, H4f"""	H4FC		1916825, 9119399, 12408966	Standard	NM_003540		Approved	H4/c, H4	uc003nhe.1	P62805	OTTHUMG00000014443	ENST00000377745.2:c.99C>T	6.37:g.26240752C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_003540	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377745.2	37	CCDS4598.1																																																																																			C|0.952;T|0.048	0.048	strong		0.567	HIST1H4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040106.1	NM_003540	
PON3	5446	hgsc.bcm.edu	37	7	95001555	95001555	+	Silent	SNP	C	C	T	rs1053275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:95001555C>T	ENST00000265627.5	-	4	307	c.297G>A	c.(295-297)gcG>gcA	p.A99A	PON3_ENST00000451904.1_Silent_p.A99A|PON1_ENST00000542556.1_Intron|PON3_ENST00000427422.1_Silent_p.A99A	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	99					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	TGATTTCTAGCGCTTGTGCCC	0.398													T|||	3308	0.660543	0.6422	0.6772	5008	,	,		17161	0.7788		0.501	False		,,,				2504	0.7157				p.A99A		Atlas-SNP	.											.	PON3	59	.	0			c.G297A						PASS	.	T		2501,1905	544.8+/-376.6	708,1085,410	156.0	147.0	150.0		297	-0.6	0.0	7	dbSNP_86	150	3933,4667	604.0+/-394.7	906,2121,1273	no	coding-synonymous	PON3	NM_000940.2		1614,3206,1683	TT,TC,CC		45.7326,43.2365,49.4695		99/355	95001555	6434,6572	2203	4300	6503	SO:0001819	synonymous_variant	5446	exon4			TTCTAGCGCTTGT	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.297G>A	7.37:g.95001555C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	200	199	0.995	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																			C|0.417;T|0.583	0.583	strong		0.398	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
SLC45A3	85414	hgsc.bcm.edu	37	1	205633713	205633713	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:205633713T>C	ENST00000367145.3	-	2	367	c.72A>G	c.(70-72)ctA>ctG	p.L24L	SLC45A3_ENST00000460934.1_5'Flank	NM_033102.2	NP_149093.1	Q96JT2	S45A3_HUMAN	solute carrier family 45, member 3	24					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)			GGCCAAAGGTTAGCAGGTTGA	0.632			T	"""ETV1, ETV5, ELK4, ERG"""	prostate																																p.L24L		Atlas-SNP	.		Dom	yes		1	1q32	85414	"""solute carrier family 45, member 3"""		E	SLC45A3,right_lower_lobe,carcinoma,-1,1	SLC45A3	54	1	0			c.A72G						scavenged	.						113.0	111.0	112.0					1																	205633713		2203	4300	6503	SO:0001819	synonymous_variant	85414	exon2			AAAGGTTAGCAGG	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.72A>G	1.37:g.205633713T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	188	3	0.0159574	NM_033102	A8K2U9	Silent	SNP	ENST00000367145.3	37	CCDS1458.1																																																																																			.	.	none		0.632	SLC45A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090619.1	NM_033102	
TBL2	26608	hgsc.bcm.edu	37	7	72985148	72985148	+	Missense_Mutation	SNP	C	C	T	rs35607697	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:72985148C>T	ENST00000305632.5	-	7	1274	c.1033G>A	c.(1033-1035)Gtc>Atc	p.V345I	TBL2_ENST00000432538.1_Missense_Mutation_p.V309I|TBL2_ENST00000459913.1_5'UTR	NM_012453.2	NP_036585.1	Q9Y4P3	TBL2_HUMAN	transducin (beta)-like 2	345			V -> I (in dbSNP:rs35607697).				poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	19		Lung NSC(55;0.0659)|all_lung(88;0.152)				AAGGCCAAGACCTGGGCGTTG	0.617													C|||	79	0.0157748	0.0015	0.0216	5008	,	,		16763	0.0		0.0567	False		,,,				2504	0.0051				p.V345I		Atlas-SNP	.											.	TBL2	47	.	0			c.G1033A						PASS	.	C	ILE/VAL	41,4365	44.6+/-78.6	1,39,2163	66.0	70.0	69.0		1033	5.1	1.0	7	dbSNP_126	69	448,8152	133.8+/-191.2	9,430,3861	yes	missense	TBL2	NM_012453.2	29	10,469,6024	TT,TC,CC		5.2093,0.9305,3.7598	possibly-damaging	345/448	72985148	489,12517	2203	4300	6503	SO:0001583	missense	26608	exon7			CCAAGACCTGGGC	AF056183	CCDS5551.1	7q11.23	2013-01-10			ENSG00000106638	ENSG00000106638		"""WD repeat domain containing"""	11586	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 13"""	605842				9860302, 10575226	Standard	XM_006715923		Approved	WS-betaTRP, WBSCR13, DKFZP43N024	uc003tyh.3	Q9Y4P3	OTTHUMG00000023427	ENST00000305632.5:c.1033G>A	7.37:g.72985148C>T	ENSP00000307260:p.Val345Ile	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	73	42	0.575342	NM_012453	Q9UQE2	Missense_Mutation	SNP	ENST00000305632.5	37	CCDS5551.1	49	0.022435897435897436	0	0.0	10	0.027624309392265192	0	0.0	39	0.051451187335092345	C	19.07	3.755919	0.69648	0.009305	0.052093	ENSG00000106638	ENST00000305632;ENST00000541783;ENST00000432538	T;T	0.28666	1.6;1.6	5.98	5.1	0.69264	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.05456	0.0144	L	0.35542	1.07	0.80722	D	1	P;D	0.54964	0.917;0.969	B;P	0.48654	0.37;0.585	T	0.00527	-1.1688	10	0.29301	T	0.29	-29.6221	12.9725	0.58520	0.0:0.9219:0.0:0.0781	rs35607697;rs35607697	309;345	E9PF19;Q9Y4P3	.;TBL2_HUMAN	I	345;345;309	ENSP00000307260:V345I;ENSP00000413979:V309I	ENSP00000307260:V345I	V	-	1	0	TBL2	72623084	1.000000	0.71417	0.996000	0.52242	0.698000	0.40448	5.786000	0.69006	1.538000	0.49270	0.655000	0.94253	GTC	C|0.966;T|0.034	0.034	strong		0.617	TBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252233.3	NM_012453	
KRTAP9-4	85280	hgsc.bcm.edu	37	17	39406409	39406409	+	Missense_Mutation	SNP	C	C	A	rs2191379	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39406409C>A	ENST00000334109.2	+	1	471	c.437C>A	c.(436-438)tCc>tAc	p.S146Y		NM_033191.2	NP_149461.2	Q9BYQ2	KRA94_HUMAN	keratin associated protein 9-4	146	15 X 5 AA repeats of C-C-[RQVGE]-[SPTN]- [TASPF].		S -> Y (in dbSNP:rs62065349). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				breast(1)|large_intestine(1)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACCTGTGTGTCCAGCTGCTGT	0.552													.|||	3385	0.675919	0.5053	0.8012	5008	,	,		21709	0.631		0.7336	False		,,,				2504	0.8047				p.S146Y		Atlas-SNP	.											.	KRTAP9-4	30	.	0			c.C437A						PASS	.	C	TYR/SER	2292,2114		611,1070,522	169.0	170.0	170.0		437	1.4	0.0	17	dbSNP_96	170	6228,2372		2222,1784,294	no	missense	KRTAP9-4	NM_033191.2	144	2833,2854,816	AA,AC,CC		27.5814,47.98,34.4918	benign	146/155	39406409	8520,4486	2203	4300	6503	SO:0001583	missense	85280	exon1			GTGTGTCCAGCTG	AJ406948	CCDS11386.1	17q21.2	2013-06-25			ENSG00000241595	ENSG00000241595		"""Keratin associated proteins"""	18902	protein-coding gene	gene with protein product						11279113	Standard	NM_033191		Approved	KAP9.4	uc002hwi.3	Q9BYQ2	OTTHUMG00000133438	ENST00000334109.2:c.437C>A	17.37:g.39406409C>A	ENSP00000334922:p.Ser146Tyr	Somatic	320	0	0		WXS	Illumina HiSeq	Phase_I	344	172	0.5	NM_033191	Q0VAE3	Missense_Mutation	SNP	ENST00000334109.2	37	CCDS11386.1	1460	0.6684981684981685	257	0.5223577235772358	282	0.7790055248618785	368	0.6433566433566433	553	0.7295514511873351	.	10.72	1.429114	0.25726	0.5202	0.724186	ENSG00000241595	ENST00000334109	T	0.01126	5.3	2.38	1.38	0.22167	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.31769	0.339	B	0.28709	0.093	T	0.01382	-1.1369	8	0.39692	T	0.17	.	4.3378	0.11095	0.0:0.7905:0.0:0.2095	rs62065349	146	Q9BYQ2	KRA94_HUMAN	Y	146	ENSP00000334922:S146Y	ENSP00000334922:S146Y	S	+	2	0	KRTAP9-4	36659935	0.947000	0.32204	0.008000	0.14137	0.507000	0.33981	-0.100000	0.10990	0.535000	0.28714	0.393000	0.25936	TCC	C|0.336;A|0.664	0.664	strong		0.552	KRTAP9-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257306.1		
CEP135	9662	hgsc.bcm.edu	37	4	56883987	56883987	+	Silent	SNP	C	C	G	rs35143702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:56883987C>G	ENST00000257287.4	+	22	3100	c.2976C>G	c.(2974-2976)acC>acG	p.T992T		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	992					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					ATATTATGACCCAGCAATTGA	0.333													C|||	111	0.0221645	0.003	0.0793	5008	,	,		18200	0.002		0.0318	False		,,,				2504	0.0184				p.T992T		Atlas-SNP	.											CEP135,NS,carcinoma,0,1	CEP135	115	1	0			c.C2976G						PASS	.	C		34,4372	37.6+/-69.7	0,34,2169	50.0	53.0	52.0		2976	-1.8	0.9	4	dbSNP_126	52	237,8363	93.5+/-155.5	5,227,4068	no	coding-synonymous	CEP135	NM_025009.3		5,261,6237	GG,GC,CC		2.7558,0.7717,2.0837		992/1141	56883987	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	9662	exon22			TATGACCCAGCAA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.2976C>G	4.37:g.56883987C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	128	51	0.398438	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Silent	SNP	ENST00000257287.4	37	CCDS33986.1																																																																																			C|0.978;G|0.022	0.022	strong		0.333	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
LRRC15	131578	hgsc.bcm.edu	37	3	194081392	194081392	+	Silent	SNP	G	G	A	rs923936	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194081392G>A	ENST00000347624.3	-	2	466	c.381C>T	c.(379-381)ctC>ctT	p.L127L	LRRC15_ENST00000428839.1_Silent_p.L133L|LRRC15_ENST00000439944.2_Silent_p.L133L	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	127					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GGAGAGACTCGAGGCTGTCCA	0.617													G|||	583	0.116414	0.093	0.1052	5008	,	,		19110	0.0685		0.2097	False		,,,				2504	0.1094				p.L133L		Atlas-SNP	.											.	LRRC15	137	.	0			c.C399T						PASS	.	G	,	430,3976	207.5+/-228.8	16,398,1789	50.0	54.0	53.0		399,381	-9.6	0.1	3	dbSNP_86	53	1997,6603	349.3+/-327.4	235,1527,2538	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	251,1925,4327	AA,AG,GG		23.2209,9.7594,18.6606	,	133/588,127/582	194081392	2427,10579	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			AGACTCGAGGCTG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.381C>T	3.37:g.194081392G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	121	65	0.53719	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			G|0.832;A|0.168	0.168	strong		0.617	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32833766	32833766	+	Missense_Mutation	SNP	A	A	C	rs61731888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:32833766A>C	ENST00000420878.3	-	5	1588	c.1133T>G	c.(1132-1134)aTc>aGc	p.I378S	ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000261333.6_Intron|ZNF397_ENST00000355632.4_Intron|ZSCAN30_ENST00000333206.5_Missense_Mutation_p.I378S|ZNF397_ENST00000589420.1_Intron	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	378					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(3)|urinary_tract(1)	9						TCCAGTGTGGATTCTCCGATG	0.453													A|||	114	0.0227636	0.0522	0.0202	5008	,	,		20229	0.001		0.0209	False		,,,				2504	0.0092				p.I378S		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.T1133G						PASS	.	A	SER/ILE,SER/ILE,	147,2989		5,137,1426	96.0	90.0	92.0		1133,1133,	2.4	1.0	18	dbSNP_129	92	153,7011		2,149,3431	yes	missense,missense,intron	ZNF397,ZSCAN30	NM_001112734.2,NM_001166012.1,NM_032347.2	142,142,	7,286,4857	CC,CA,AA		2.1357,4.6875,2.9126	probably-damaging,probably-damaging,	378/495,378/495,	32833766	300,10000	1568	3582	5150	SO:0001583	missense	100101467	exon5			GTGTGGATTCTCC	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"""-"", ""Zinc fingers, C2H2-type"""	33517	protein-coding gene	gene with protein product			"""zinc finger protein 397 opposite strand"", ""ZNF397 opposite strand"""	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.1133T>G	18.37:g.32833766A>C	ENSP00000392371:p.Ile378Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	37	CCDS42427.1	63	0.028846153846153848	34	0.06910569105691057	12	0.03314917127071823	1	0.0017482517482517483	16	0.021108179419525065	A	17.36	3.370099	0.61624	0.046875	0.021357	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932	T;T	0.06933	3.24;3.24	4.7	2.37	0.29283	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.217388	0.23491	N	0.047605	T	0.00815	0.0027	N	0.20685	0.6	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.19095	-1.0316	10	0.59425	D	0.04	.	5.4094	0.16341	0.6984:0.0:0.3016:0.0	rs61731888	378	Q86W11	ZSC30_HUMAN	S	378;378;313	ENSP00000392371:I378S;ENSP00000329738:I378S	ENSP00000329738:I378S	I	-	2	0	ZSCAN30	31087764	0.024000	0.19004	1.000000	0.80357	0.996000	0.88848	0.796000	0.26986	0.933000	0.37291	0.533000	0.62120	ATC	A|0.975;C|0.025	0.025	strong		0.453	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734	
LEPREL1	55214	hgsc.bcm.edu	37	3	189713205	189713205	+	Silent	SNP	T	T	C	rs9821880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:189713205T>C	ENST00000319332.5	-	2	704	c.507A>G	c.(505-507)gaA>gaG	p.E169E	LEPREL1_ENST00000427335.2_5'UTR	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	169					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)	TGTGAGCTGCTTCCACTGCTT	0.408													T|||	1607	0.320887	0.2035	0.3069	5008	,	,		15965	0.4881		0.3002	False		,,,				2504	0.3384				p.E169E		Atlas-SNP	.											.	LEPREL1	95	.	0			c.A507G						PASS	.	T	,	942,3464	342.5+/-307.2	94,754,1355	105.0	91.0	96.0		,507	4.1	1.0	3	dbSNP_119	96	2669,5931	416.4+/-352.1	435,1799,2066	no	utr-5,coding-synonymous	LEPREL1	NM_001134418.1,NM_018192.3	,	529,2553,3421	CC,CT,TT		31.0349,21.3799,27.7641	,	,169/709	189713205	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	55214	exon2			AGCTGCTTCCACT		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.507A>G	3.37:g.189713205T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_018192	B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Silent	SNP	ENST00000319332.5	37	CCDS3294.1																																																																																			C|0.302;N|0.001	0.302	strong		0.408	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1	NM_018192	
EHMT2	10919	hgsc.bcm.edu	37	6	31864547	31864547	+	Missense_Mutation	SNP	G	G	T	rs7887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31864547G>T	ENST00000375537.4	-	3	170	c.164C>A	c.(163-165)aCc>aAc	p.T55N	C2_ENST00000469372.1_5'Flank|EHMT2_ENST00000375528.4_Missense_Mutation_p.T112N|EHMT2_ENST00000375530.4_Missense_Mutation_p.T55N|EHMT2_ENST00000395728.3_Missense_Mutation_p.T112N|EHMT2_ENST00000480912.1_5'Flank	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	55			T -> N (in dbSNP:rs7887). {ECO:0000269|PubMed:11707778, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		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						GGAGTCGGGGGTGGCCTTGGG	0.587													g|||	1648	0.329073	0.0348	0.4813	5008	,	,		15899	0.5476		0.3638	False		,,,				2504	0.3579				p.T55N		Atlas-SNP	.											.	EHMT2	45	.	0			c.C164A						PASS	.		ASN/THR,ASN/THR	280,2740		18,244,1248	58.0	67.0	64.0		164,164	-6.0	0.2	6	dbSNP_52	64	1888,3530		326,1236,1147	yes	missense,missense	EHMT2	NM_006709.3,NM_025256.5	65,65	344,1480,2395	TT,TG,GG		34.8468,9.2715,25.6933	benign,benign	55/1211,55/1177	31864547	2168,6270	1510	2709	4219	SO:0001583	missense	10919	exon3			TCGGGGGTGGCCT	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.164C>A	6.37:g.31864547G>T	ENSP00000364687:p.Thr55Asn	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	113	43	0.380531	NM_025256	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	800	0.3663003663003663	25	0.0508130081300813	176	0.4861878453038674	335	0.5856643356643356	264	0.3482849604221636	g	0.003	-2.455217	0.00173	0.092715	0.348468	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	2.98	-5.96	0.02234	.	1.636390	0.03613	N	0.235192	T	0.03220	0.0094	N	0.08118	0	0.48395	P	3.5399999999996545E-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	0.17137	-1.0379	9	0.10377	T	0.69	.	6.8694	0.24113	0.0:0.5466:0.1547:0.2987	rs7887;rs1047697;rs3173327;rs3763301;rs58258725;rs7887	112;55;55;55	A2ABF8;Q96KQ7-3;Q96KQ7-2;Q96KQ7	.;.;.;EHMT2_HUMAN	N	112;112;55;55	ENSP00000379078:T112N;ENSP00000364678:T112N;ENSP00000364680:T55N;ENSP00000364687:T55N	ENSP00000364678:T112N	T	-	2	0	EHMT2	31972526	0.461000	0.25783	0.192000	0.23308	0.032000	0.12392	-0.433000	0.06948	-1.497000	0.01826	-1.102000	0.02115	ACC	G|0.694;T|0.306	0.306	strong		0.587	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709	
C8B	732	hgsc.bcm.edu	37	1	57422511	57422511	+	Missense_Mutation	SNP	C	C	T	rs12067507	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:57422511C>T	ENST00000371237.4	-	3	388	c.322G>A	c.(322-324)Gaa>Aaa	p.E108K	C8B_ENST00000543257.1_Missense_Mutation_p.E56K|C8B_ENST00000535057.1_Missense_Mutation_p.E46K	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	108	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		E -> K (in dbSNP:rs12067507).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)		p.E108K(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ACACAGTCTTCGACTTCCTTG	0.498													C|||	208	0.0415335	0.0575	0.0331	5008	,	,		20252	0.0		0.0547	False		,,,				2504	0.0552				p.E108K		Atlas-SNP	.											C8B,caecum,carcinoma,0,1	C8B	107	1	1	Substitution - Missense(1)	large_intestine(1)	c.G322A						PASS	.	C	LYS/GLU	288,4118	159.2+/-191.8	8,272,1923	257.0	237.0	244.0		322	4.5	0.9	1	dbSNP_120	244	479,8121	140.5+/-197.0	14,451,3835	yes	missense	C8B	NM_000066.2	56	22,723,5758	TT,TC,CC		5.5698,6.5365,5.8973	probably-damaging	108/592	57422511	767,12239	2203	4300	6503	SO:0001583	missense	732	exon3			AGTCTTCGACTTC	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.322G>A	1.37:g.57422511C>T	ENSP00000360281:p.Glu108Lys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	32	0.367816	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	90	0.04120879120879121	34	0.06910569105691057	16	0.04419889502762431	0	0.0	40	0.052770448548812667	C	24.7	4.557566	0.86231	0.065365	0.055698	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.27557	2.16;2.16;1.66	5.41	4.47	0.54385	.	0.101764	0.64402	D	0.000002	T	0.05181	0.0138	L	0.37697	1.125	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.987;0.997;0.97	T	0.00918	-1.1515	10	0.35671	T	0.21	-27.0469	15.8821	0.79211	0.0:0.864:0.136:0.0	rs12067507;rs52799290;rs56715593;rs12067507	56;46;108	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	K	108;56;46	ENSP00000360281:E108K;ENSP00000442548:E56K;ENSP00000440113:E46K	ENSP00000360281:E108K	E	-	1	0	C8B	57195099	0.990000	0.36364	0.911000	0.35937	0.704000	0.40688	2.981000	0.49329	1.370000	0.46153	0.650000	0.86243	GAA	C|0.944;T|0.056	0.056	strong		0.498	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
NACAD	23148	hgsc.bcm.edu	37	7	45122324	45122324	+	Missense_Mutation	SNP	C	C	A	rs3735493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45122324C>A	ENST00000490531.2	-	2	3474	c.3455G>T	c.(3454-3456)tGc>tTc	p.C1152F		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1152			C -> F (in dbSNP:rs3735493).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						AGACTCTGGGCAGGAGTCCAG	0.662													C|||	553	0.110423	0.0166	0.1657	5008	,	,		15349	0.121		0.174	False		,,,				2504	0.1217				p.C1152F		Atlas-SNP	.											.	NACAD	44	.	0			c.G3455T						PASS	.						19.0	28.0	25.0					7																	45122324		692	1590	2282	SO:0001583	missense	23148	exon2			TCTGGGCAGGAGT	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.3455G>T	7.37:g.45122324C>A	ENSP00000420477:p.Cys1152Phe	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	262	0.11996336996336997	8	0.016260162601626018	64	0.17679558011049723	59	0.10314685314685315	131	0.17282321899736147	c	14.82	2.649534	0.47362	.	.	ENSG00000136274	ENST00000490531	T	0.12984	2.63	3.08	2.16	0.27623	.	.	.	.	.	T	0.00039	0.0001	L	0.32530	0.975	0.80722	P	0.0	D	0.65815	0.995	P	0.57911	0.829	T	0.24333	-1.0163	8	0.42905	T	0.14	-2.9206	9.0995	0.36660	0.0:0.557:0.443:0.0	rs3735493;rs10377947;rs3735493	1152	O15069	NACAD_HUMAN	F	1152	ENSP00000420477:C1152F	ENSP00000420477:C1152F	C	-	2	0	NACAD	45088849	0.000000	0.05858	0.319000	0.25293	0.438000	0.31896	-0.135000	0.10420	0.576000	0.29452	0.290000	0.19541	TGC	C|0.891;A|0.109	0.109	strong		0.662	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
GOT2	2806	hgsc.bcm.edu	37	16	58757668	58757668	+	Silent	SNP	A	A	C	rs14221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58757668A>C	ENST00000245206.5	-	2	356	c.228T>G	c.(226-228)gtT>gtG	p.V76V	GOT2_ENST00000434819.2_Silent_p.V76V|GOT2_ENST00000564400.1_5'UTR	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	76					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	CGCTAGGCAGAACGTAAGGCT	0.493													C|||	3547	0.708267	0.8676	0.7608	5008	,	,		20232	0.6339		0.662	False		,,,				2504	0.5798				p.V76V		Atlas-SNP	.											.	GOT2	42	.	0			c.T228G						PASS	.	C		3631,765	310.5+/-291.6	1493,645,60	201.0	205.0	203.0		228	3.2	1.0	16	dbSNP_52	203	5581,3019	465.9+/-366.6	1809,1963,528	no	coding-synonymous	GOT2	NM_002080.2		3302,2608,588	CC,CA,AA		35.1047,17.4022,29.1167		76/431	58757668	9212,3784	2198	4300	6498	SO:0001819	synonymous_variant	2806	exon2			AGGCAGAACGTAA		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.228T>G	16.37:g.58757668A>C		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	172	171	0.994186	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1																																																																																			A|0.293;C|0.707;G|0.000	0.707	strong		0.493	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
OXCT2	64064	hgsc.bcm.edu	37	1	40236145	40236145	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:40236145A>G	ENST00000327582.5	-	1	875	c.783T>C	c.(781-783)gtT>gtC	p.V261V	BMP8B_ENST00000372827.3_Intron|BMP8B_ENST00000397360.2_Intron	NM_022120.1	NP_071403.1	Q9BYC2	SCOT2_HUMAN	3-oxoacid CoA transferase 2	261					ketone body catabolic process (GO:0046952)	mitochondrion (GO:0005739)|motile cilium (GO:0031514)	3-oxoacid CoA-transferase activity (GO:0008260)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|pancreas(1)|upper_aerodigestive_tract(1)	6	all_cancers(7;5.56e-14)|all_lung(5;3.88e-17)|all_epithelial(6;3.78e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;1.92e-17)|all cancers(16;4.03e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		Succinic acid(DB00139)	AAATGTTAGGAACGTGGATGT	0.517											OREG0013400	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V261V		Atlas-SNP	.											OXCT2,colon,carcinoma,-2,1	OXCT2	12	1	0			c.T783C						scavenged	.						81.0	98.0	92.0					1																	40236145		2195	4295	6490	SO:0001819	synonymous_variant	64064	exon1			GTTAGGAACGTGG	AB050193	CCDS445.1	1p34	2008-02-05			ENSG00000198754	ENSG00000198754			18606	protein-coding gene	gene with protein product		610289				11214971, 11756565	Standard	NM_022120		Approved	FKSG25, FLJ00030, SCOT-T	uc001ceb.1	Q9BYC2	OTTHUMG00000009249	ENST00000327582.5:c.783T>C	1.37:g.40236145A>G		Somatic	98	0	0	891	WXS	Illumina HiSeq	Phase_I	114	2	0.0175439	NM_022120	B2RBB4|Q5QPK4|Q8NHR1|Q9H1I4	Silent	SNP	ENST00000327582.5	37	CCDS445.1	.	.	.	.	.	.	.	.	.	.	a	6.289	0.421510	0.11928	.	.	ENSG00000198754	ENST00000542949	.	.	.	2.58	-3.13	0.05266	.	.	.	.	.	T	0.56001	0.1956	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57106	-0.7868	5	0.66056	D	0.02	.	5.531	0.16985	0.2295:0.5145:0.256:0.0	.	.	.	.	S	261	.	ENSP00000438055:F261S	F	-	2	0	OXCT2	40008732	0.771000	0.28555	0.009000	0.14445	0.004000	0.04260	-0.323000	0.07997	-0.777000	0.04572	-0.370000	0.07254	TTC	.	.	none		0.517	OXCT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025656.1	NM_022120	
CENPF	1063	hgsc.bcm.edu	37	1	214814571	214814571	+	Silent	SNP	C	C	T	rs3795521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:214814571C>T	ENST00000366955.3	+	12	3058	c.2890C>T	c.(2890-2892)Cta>Tta	p.L964L		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		CATCATTTCTCTAAATAAAAG	0.358													C|||	1197	0.239018	0.0522	0.317	5008	,	,		18098	0.122		0.499	False		,,,				2504	0.2894				p.L964L	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,2	CENPF	321	2	0			c.C2890T						PASS	.	C		506,3842		51,404,1719	50.0	56.0	54.0		2890	2.2	0.0	1	dbSNP_107	54	4412,4166		1141,2130,1018	no	coding-synonymous	CENPF	NM_016343.3		1192,2534,2737	TT,TC,CC		48.5661,11.6375,38.0473		964/3115	214814571	4918,8008	2174	4289	6463	SO:0001819	synonymous_variant	1063	exon12			ATTTCTCTAAATA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.2890C>T	1.37:g.214814571C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			C|0.681;T|0.319	0.319	strong		0.358	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
CXorf22	170063	hgsc.bcm.edu	37	X	35969297	35969297	+	Missense_Mutation	SNP	G	G	A	rs2336029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:35969297G>A	ENST00000297866.5	+	5	772	c.706G>A	c.(706-708)Gtg>Atg	p.V236M		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	236			V -> M (in dbSNP:rs2336029). {ECO:0000269|PubMed:14702039}.							breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						CAAAGCTCATGTGGTTGAGCA	0.343													G|||	709	0.187815	0.0537	0.2104	3775	,	,		13657	0.1855		0.1083	False		,,,				2504	0.2004				p.V236M		Atlas-SNP	.											.	CXorf22	272	.	0			c.G706A						PASS	.	G	MET/VAL	302,3531		10,237,45,1384,526	116.0	102.0	107.0		706	4.0	0.3	X	dbSNP_100	107	761,5967		29,488,215,1911,1657	yes	missense	CXorf22	NM_152632.3	21	39,725,260,3295,2183	AA,AG,A,GG,G		11.3109,7.8789,10.0653	probably-damaging	236/977	35969297	1063,9498	2202	4300	6502	SO:0001583	missense	170063	exon5			GCTCATGTGGTTG	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.706G>A	X.37:g.35969297G>A	ENSP00000297866:p.Val236Met	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	295	0.17781796262808922	14	0.029535864978902954	48	0.147239263803681	79	0.16188524590163936	62	0.08707865168539326	G	16.56	3.156172	0.57259	0.078789	0.113109	ENSG00000165164	ENST00000297866	T	0.21031	2.03	5.75	3.95	0.45737	.	0.059759	0.64402	D	0.000003	T	0.00210	0.0006	M	0.77103	2.36	0.80722	P	0.0	D	0.89917	1.0	D	0.80764	0.994	T	0.04467	-1.0949	9	0.40728	T	0.16	-16.3494	9.575	0.39452	0.0764:0.0:0.7835:0.1401	rs2336029;rs17272944;rs59162540;rs2336029	236	Q6ZTR5	CX022_HUMAN	M	236	ENSP00000297866:V236M	ENSP00000297866:V236M	V	+	1	0	CXorf22	35879218	1.000000	0.71417	0.281000	0.24762	0.934000	0.57294	3.335000	0.52105	1.159000	0.42565	0.506000	0.49869	GTG	0|0.015;A|0.136	0.136	strong		0.343	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	
HKDC1	80201	hgsc.bcm.edu	37	10	71026510	71026510	+	Missense_Mutation	SNP	C	C	A	rs906219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:71026510C>A	ENST00000354624.5	+	18	2884	c.2751C>A	c.(2749-2751)aaC>aaA	p.N917K	RP11-227H15.5_ENST00000413220.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	917			N -> K (in dbSNP:rs906219).		carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						AGAAGGAGAACTAGGAACCCC	0.522													C|||	1684	0.336262	0.1104	0.4914	5008	,	,		18300	0.5942		0.3559	False		,,,				2504	0.2454				p.N917K		Atlas-SNP	.											.	HKDC1	98	.	0			c.C2751A						PASS	.	C	LYS/ASN	687,3719	288.4+/-279.8	61,565,1577	127.0	107.0	114.0		2751	0.7	0.0	10	dbSNP_86	114	3039,5561	469.0+/-367.5	513,2013,1774	yes	missense	HKDC1	NM_025130.3	94	574,2578,3351	AA,AC,CC		35.3372,15.5924,28.6483	benign	917/918	71026510	3726,9280	2203	4300	6503	SO:0001583	missense	80201	exon18			GGAGAACTAGGAA		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.2751C>A	10.37:g.71026510C>A	ENSP00000346643:p.Asn917Lys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	790	0.3617216117216117	47	0.09552845528455285	156	0.430939226519337	316	0.5524475524475524	271	0.3575197889182058	C	13.21	2.169602	0.38315	0.155924	0.353372	ENSG00000156510	ENST00000354624	D	0.97041	-4.22	4.81	0.702	0.18110	.	0.780610	0.11363	N	0.571730	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	9	0.66056	D	0.02	.	4.5356	0.12026	0.3945:0.4123:0.1186:0.0746	rs906219;rs52823840;rs61560703;rs906219	917	Q2TB90	HKDC1_HUMAN	K	917	ENSP00000346643:N917K	ENSP00000346643:N917K	N	+	3	2	HKDC1	70696516	0.998000	0.40836	0.034000	0.17996	0.482000	0.33219	0.590000	0.23954	0.029000	0.15352	0.655000	0.94253	AAC	C|0.688;A|0.312	0.312	strong		0.522	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
GTPBP10	85865	hgsc.bcm.edu	37	7	89984409	89984409	+	Missense_Mutation	SNP	A	A	G	rs42664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:89984409A>G	ENST00000222511.6	+	4	395	c.329A>G	c.(328-330)aAt>aGt	p.N110S	GTPBP10_ENST00000257659.8_Intron	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	110			N -> S (in dbSNP:rs42664). {ECO:0000269|PubMed:15489334}.		ribosome biogenesis (GO:0042254)	chromosome (GO:0005694)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)	10						GGAGAACTCAATAAAGAAAAT	0.318													A|||	2567	0.51258	0.3109	0.5317	5008	,	,		16010	0.6468		0.5517	False		,,,				2504	0.593				p.N110S		Atlas-SNP	.											.	GTPBP10	31	.	0			c.A329G						PASS	.	A	,SER/ASN	1591,2815	484.9+/-360.2	299,993,911	81.0	86.0	85.0		,329	5.9	1.0	7	dbSNP_76	85	4939,3659	618.9+/-396.8	1435,2069,795	yes	intron,missense	GTPBP10	NM_001042717.2,NM_033107.3	,46	1734,3062,1706	GG,GA,AA		42.5564,36.1099,49.7847	,benign	,110/388	89984409	6530,6474	2203	4299	6502	SO:0001583	missense	85865	exon4			AACTCAATAAAGA		CCDS5617.1, CCDS43614.1	7q21.13	2006-08-15			ENSG00000105793	ENSG00000105793			25106	protein-coding gene	gene with protein product		610920				12477932	Standard	NM_001042717		Approved	DKFZP686A10121, FLJ38242	uc003ukm.2	A4D1E9	OTTHUMG00000023655	ENST00000222511.6:c.329A>G	7.37:g.89984409A>G	ENSP00000222511:p.Asn110Ser	Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	191	190	0.994764	NM_033107	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Missense_Mutation	SNP	ENST00000222511.6	37	CCDS5617.1	1135	0.5196886446886447	155	0.3150406504065041	195	0.5386740331491713	357	0.6241258741258742	428	0.5646437994722955	A	15.16	2.750984	0.49257	0.361099	0.574436	ENSG00000105793	ENST00000426366;ENST00000450619;ENST00000222511	T;T;T	0.20881	2.04;2.04;2.04	5.93	5.93	0.95920	GTP1/OBG subdomain (3);	0.046736	0.85682	D	0.000000	T	0.00012	0.0000	N	0.17564	0.495	0.19575	P	0.999969057	B;B;B	0.30361	0.01;0.163;0.277	B;B;B	0.36378	0.04;0.068;0.223	T	0.34775	-0.9815	8	.	.	.	-1.3969	16.3839	0.83495	1.0:0.0:0.0:0.0	rs42664;rs10359194;rs10394250;rs11555363;rs11563900;rs17621860;rs57705979;rs42664	110;101;127	A4D1E9;C9J8R7;C9JNI1	GTPBA_HUMAN;.;.	S	101;127;110	ENSP00000405697:N101S;ENSP00000389510:N127S;ENSP00000222511:N110S	.	N	+	2	0	GTPBP10	89822345	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	6.499000	0.73683	2.258000	0.74832	0.533000	0.62120	AAT	A|0.499;G|0.501	0.501	strong		0.318	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107	
MORN4	118812	hgsc.bcm.edu	37	10	99376092	99376092	+	Silent	SNP	T	T	C	rs3814555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99376092T>C	ENST00000307450.6	-	5	532	c.369A>G	c.(367-369)cgA>cgG	p.R123R	PI4K2A_ENST00000555577.1_Intron|MORN4_ENST00000335628.3_Silent_p.R181R|MORN4_ENST00000478953.1_3'UTR|PI4K2A_ENST00000370649.3_Intron	NM_001098831.1|NM_178832.3	NP_001092301.1|NP_849154.1	Q8NDC4	MORN4_HUMAN	MORN repeat containing 4	123								p.R123R(2)		large_intestine(1)|lung(1)|stomach(2)	4						ACTTCTCACGTCGCAGCAGCT	0.532													C|||	1497	0.298922	0.4864	0.2507	5008	,	,		19837	0.2817		0.1978	False		,,,				2504	0.2014				p.R123R		Atlas-SNP	.											MORN4_ENST00000307450,NS,carcinoma,0,4	MORN4	24	4	2	Substitution - coding silent(2)	stomach(2)	c.A369G						scavenged	.	C	,	1921,2485	625.6+/-394.6	423,1075,705	61.0	58.0	59.0		369,369	-1.8	0.5	10	dbSNP_107	59	1886,6714	728.0+/-406.7	195,1496,2609	no	coding-synonymous,coding-synonymous	MORN4	NM_001098831.1,NM_178832.3	,	618,2571,3314	CC,CT,TT		21.9302,43.5996,29.2711	,	123/147,123/147	99376092	3807,9199	2203	4300	6503	SO:0001819	synonymous_variant	118812	exon5			CTCACGTCGCAGC	AJ431726	CCDS7468.1	10q24.2	2008-06-23	2008-06-23	2008-06-23	ENSG00000171160	ENSG00000171160			24001	protein-coding gene	gene with protein product	"""44050 protein"""		"""chromosome 10 open reading frame 83"""	C10orf83		12477932	Standard	NM_178832		Approved	bA548K23.4, FLJ25925	uc001koe.3	Q8NDC4	OTTHUMG00000018861	ENST00000307450.6:c.369A>G	10.37:g.99376092T>C		Somatic	67	2	0.0298507		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_001098831	Q86Y54	Silent	SNP	ENST00000307450.6	37	CCDS7468.1																																																																																			T|0.703;C|0.297	0.297	strong		0.532	MORN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049730.1	NM_178832	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254361	30254361	+	Missense_Mutation	SNP	G	G	A	rs2071308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:30254361G>A	ENST00000361644.2	+	5	1057	c.320G>A	c.(319-321)cGc>cAc	p.R107H		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	107			R -> H (in dbSNP:rs2071308). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9441743}.					p.R107H(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						GTGCAGTCTCGCACAGACCCT	0.393													G|||	1761	0.46649	0.2474	0.3746	3775	,	,		15649	0.4008		0.3648	False		,,,				2504	0.4121				p.R107H		Atlas-SNP	.											.	MAGEB3	54	.	1	Substitution - Missense(1)	prostate(1)	c.G320A						PASS	.	G	HIS/ARG	1296,2537		173,752,198,706,373	53.0	46.0	48.0		320	-8.2	0.0	X	dbSNP_96	48	3005,3723		470,1214,851,744,1021	yes	missense	MAGEB3	NM_002365.4	29	643,1966,1049,1450,1394	AA,AG,A,GG,G		44.6641,33.8116,40.7253	benign	107/347	30254361	4301,6260	2202	4300	6502	SO:0001583	missense	4114	exon5			AGTCTCGCACAGA	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.320G>A	X.37:g.30254361G>A	ENSP00000355198:p.Arg107His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_002365	A0AVE4|B3KQ52|O75861	Missense_Mutation	SNP	ENST00000361644.2	37	CCDS14220.1	778	0.4689572031344183	91	0.21064814814814814	97	0.3592592592592593	142	0.355	200	0.3412969283276451	G	0.013	-1.639962	0.00799	0.338116	0.446641	ENSG00000198798	ENST00000378986;ENST00000361644	T;T	0.01804	4.63;4.63	4.1	-8.21	0.01041	.	1.050360	0.07707	U	0.941400	T	0.00012	0.0000	N	0.21324	0.655	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	9	0.13108	T	0.6	.	14.2771	0.66187	0.0972:0.4816:0.4211:0.0	rs2071308;rs2071308	107	O15480	MAGB3_HUMAN	H	107	ENSP00000368271:R107H;ENSP00000355198:R107H	ENSP00000355198:R107H	R	+	2	0	MAGEB3	30164282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.470000	0.00460	-6.183000	0.00006	-1.991000	0.00449	CGC	G|0.569;A|0.431	0.431	strong		0.393	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
LAMA5	3911	hgsc.bcm.edu	37	20	60909316	60909316	+	Missense_Mutation	SNP	C	C	T	rs6062223	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60909316C>T	ENST00000252999.3	-	22	2731	c.2665G>A	c.(2665-2667)Gtg>Atg	p.V889M	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	889	Domain IV 1 (domain IV B).		V -> M (in dbSNP:rs6062223). {ECO:0000269|PubMed:11572484}.		angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CCAAAGCGCACGGCGTGACCC	0.682													c|||	545	0.108826	0.2693	0.1369	5008	,	,		16259	0.0427		0.0209	False		,,,				2504	0.0307				p.V889M		Atlas-SNP	.											.	LAMA5	268	.	0			c.G2665A						PASS	.		MET/VAL	1016,3388	360.6+/-315.3	119,778,1305	35.0	37.0	36.0		2665	1.4	0.0	20	dbSNP_114	36	195,8403	82.9+/-145.4	5,185,4109	yes	missense	LAMA5	NM_005560.3	21	124,963,5414	TT,TC,CC		2.268,23.0699,9.314	probably-damaging	889/3696	60909316	1211,11791	2202	4299	6501	SO:0001583	missense	3911	exon22			AGCGCACGGCGTG	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.2665G>A	20.37:g.60909316C>T	ENSP00000252999:p.Val889Met	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	180	88	0.488889	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	192	0.08791208791208792	113	0.22967479674796748	48	0.13259668508287292	16	0.027972027972027972	15	0.01978891820580475	c	9.983	1.228672	0.22542	0.230699	0.02268	ENSG00000130702	ENST00000252999	T	0.23754	1.89	4.47	1.42	0.22433	.	0.134600	0.49916	U	0.000125	T	0.00012	0.0000	M	0.70595	2.14	0.09310	P	0.9999999999975331	D	0.63880	0.993	P	0.52554	0.702	T	0.07046	-1.0793	9	0.54805	T	0.06	.	6.1753	0.20441	0.1383:0.6535:0.1333:0.0749	rs6062223;rs59553737;rs6062223	889	O15230	LAMA5_HUMAN	M	889	ENSP00000252999:V889M	ENSP00000252999:V889M	V	-	1	0	LAMA5	60342711	0.993000	0.37304	0.048000	0.18961	0.012000	0.07955	3.085000	0.50151	0.105000	0.17753	-1.153000	0.01818	GTG	C|0.902;T|0.098	0.098	strong		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
RPP38	10557	hgsc.bcm.edu	37	10	15145855	15145855	+	Missense_Mutation	SNP	C	C	G	rs15772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:15145855C>G	ENST00000378197.4	+	3	1056	c.542C>G	c.(541-543)gCg>gGg	p.A181G	RPP38_ENST00000378202.5_Missense_Mutation_p.A181G|RPP38_ENST00000451677.1_Intron|NMT2_ENST00000466201.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	181			A -> G (in dbSNP:rs15772). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						CTAGCCTTGGCGTTCAAAAAG	0.488													G|||	1813	0.362021	0.8699	0.2118	5008	,	,		19539	0.1131		0.2346	False		,,,				2504	0.1697				p.A181G	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.C542G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	3327,1079	390.3+/-327.6	1253,821,129	67.0	67.0	67.0		542,542,542	5.7	1.0	10	dbSNP_52	67	2031,6569	720.8+/-406.3	239,1553,2508	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	60,60,60	1492,2374,2637	GG,GC,CC		23.6163,24.4893,41.1964	benign,benign,benign	181/284,181/284,181/284	15145855	5358,7648	2203	4300	6503	SO:0001583	missense	10557	exon2			CCTTGGCGTTCAA	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.542C>G	10.37:g.15145855C>G	ENSP00000367439:p.Ala181Gly	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	760	0.34798534798534797	430	0.8739837398373984	89	0.24585635359116023	63	0.11013986013986014	178	0.23482849604221637	G	3.216	-0.160663	0.06502	0.755107	0.236163	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.53206	0.63;0.63;0.63	5.68	5.68	0.88126	Ribosomal protein L7Ae/L30e/S12e/Gadd45 (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00808	-1.17	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41822	-0.9487	9	0.02654	T	1	-20.1945	16.8756	0.86051	0.0:0.1285:0.8715:0.0	rs15772;rs1132102;rs3192597;rs52820525;rs58876686;rs15772	181	P78345	RPP38_HUMAN	G	181	ENSP00000367445:A181G;ENSP00000367444:A181G;ENSP00000367439:A181G	ENSP00000367439:A181G	A	+	2	0	RPP38	15185861	1.000000	0.71417	0.961000	0.40146	0.003000	0.03518	7.662000	0.83803	1.415000	0.47037	-0.187000	0.12897	GCG	C|0.612;G|0.388	0.388	strong		0.488	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
RP1L1	94137	hgsc.bcm.edu	37	8	10474042	10474042	+	Missense_Mutation	SNP	T	T	G	rs4388421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10474042T>G	ENST00000382483.3	-	3	888	c.665A>C	c.(664-666)cAt>cCt	p.H222P		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	222	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.		H -> P (in dbSNP:rs4388421).		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)		GAAGGCCTCATGCCCGGCACA	0.582													T|||	1085	0.216653	0.1573	0.2392	5008	,	,		17626	0.4573		0.1382	False		,,,				2504	0.1135				p.H222P		Atlas-SNP	.											RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	0			c.A665C						PASS	.	T	PRO/HIS	618,3232		56,506,1363	47.0	49.0	49.0		665	3.2	0.0	8	dbSNP_111	49	1268,7008		106,1056,2976	yes	missense	RP1L1	NM_178857.5	77	162,1562,4339	GG,GT,TT		15.3214,16.0519,15.5534	possibly-damaging	222/2401	10474042	1886,10240	1925	4138	6063	SO:0001583	missense	94137	exon3			GCCTCATGCCCGG	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.665A>C	8.37:g.10474042T>G	ENSP00000371923:p.His222Pro	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	542	0.24816849816849818	81	0.16463414634146342	88	0.2430939226519337	271	0.4737762237762238	102	0.1345646437994723	T	10.43	1.348313	0.24426	0.160519	0.153214	ENSG00000183638	ENST00000382483	D	0.92048	-2.96	4.42	3.24	0.37175	.	1.072000	0.07446	N	0.898278	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	D	0.56035	0.974	P	0.54026	0.74	T	0.13980	-1.0489	9	0.48119	T	0.1	-2.2994	3.2303	0.06746	0.2065:0.113:0.0:0.6805	rs4388421;rs4388421	222	A6NKC6	.	P	222	ENSP00000371923:H222P	ENSP00000371923:H222P	H	-	2	0	RP1L1	10511452	0.944000	0.32072	0.003000	0.11579	0.151000	0.21798	3.784000	0.55416	0.716000	0.32124	0.379000	0.24179	CAT	T|0.771;G|0.229	0.229	strong		0.582	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
LILRB4	11006	hgsc.bcm.edu	37	19	55179145	55179145	+	Missense_Mutation	SNP	A	A	T	rs61738946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55179145A>T	ENST00000391736.1	+	13	1416	c.1101A>T	c.(1099-1101)agA>agT	p.R367S	LILRB4_ENST00000391733.3_Missense_Mutation_p.R368S|LILRB4_ENST00000270452.2_Missense_Mutation_p.R367S|LILRB4_ENST00000391734.3_Intron|LILRB4_ENST00000430952.2_Missense_Mutation_p.R366S	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	367					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		AACACTCCAGACCTAGGAGAG	0.567																																					p.R367S		Atlas-SNP	.											LILRB4,NS,carcinoma,+2,1	LILRB4	86	1	0			c.A1101T						scavenged	.						116.0	118.0	117.0					19																	55179145		2203	4300	6503	SO:0001583	missense	11006	exon11			CTCCAGACCTAGG	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1101A>T	19.37:g.55179145A>T	ENSP00000375616:p.Arg367Ser	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	347	12	0.0345821	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	23	0.010531135531135532	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	6.892	0.534167	0.13188	.	.	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391733;ENST00000434286	T;T;T;T;T	0.00505	6.93;6.93;7.0;6.94;6.93	1.73	1.73	0.24493	.	.	.	.	.	T	0.00144	0.0004	L	0.41710	1.295	0.09310	N	1	B;B;B;B	0.23490	0.002;0.086;0.086;0.043	B;B;B;B	0.12837	0.0;0.008;0.008;0.007	T	0.40627	-0.9553	9	0.27785	T	0.31	.	5.5252	0.16955	1.0:0.0:0.0:0.0	rs61738946	366;368;366;367	C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;LIRB4_HUMAN	S	367;367;366;368;366	ENSP00000375616:R367S;ENSP00000270452:R367S;ENSP00000408995:R366S;ENSP00000375613:R368S;ENSP00000401962:R366S	ENSP00000270452:R367S	R	+	3	2	LILRB4	59870957	0.002000	0.14202	0.018000	0.16275	0.021000	0.10359	0.274000	0.18680	1.054000	0.40438	0.459000	0.35465	AGA	A|0.990;T|0.010	0.010	strong		0.567	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
DCAF12	25853	hgsc.bcm.edu	37	9	34107505	34107505	+	Missense_Mutation	SNP	C	C	T	rs11557154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34107505C>T	ENST00000361264.4	-	3	733	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	DCAF12_ENST00000463286.1_5'UTR	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	131			R -> Q (in dbSNP:rs11557154). {ECO:0000269|PubMed:15489334}.		protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						TCCAGGCTCCCGGTCTTTCAG	0.483													C|||	1137	0.227037	0.0106	0.2147	5008	,	,		19495	0.6012		0.1372	False		,,,				2504	0.2352				p.R131Q		Atlas-SNP	.											DCAF12,colon,carcinoma,+1,1	DCAF12	37	1	0			c.G392A						PASS	.	C	GLN/ARG	151,4255	103.8+/-142.4	3,145,2055	104.0	100.0	102.0		392	4.2	1.0	9	dbSNP_120	102	1064,7536	222.9+/-259.8	78,908,3314	yes	missense	DCAF12	NM_015397.3	43	81,1053,5369	TT,TC,CC		12.3721,3.4271,9.3418	probably-damaging	131/454	34107505	1215,11791	2203	4300	6503	SO:0001583	missense	25853	exon3			GGCTCCCGGTCTT	AB067479	CCDS6549.1	9p11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000198876	ENSG00000198876		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	19911	protein-coding gene	gene with protein product	"""cancer/testis antigen 102"""		"""KIAA1892"", ""WD repeat domain 40A"""	KIAA1892, WDR40A		11572484, 9110174	Standard	NM_015397		Approved	DKFZP434O125, MGC1058, CT102, TCC52	uc003ztt.2	Q5T6F0	OTTHUMG00000019806	ENST00000361264.4:c.392G>A	9.37:g.34107505C>T	ENSP00000355114:p.Arg131Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_015397	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Missense_Mutation	SNP	ENST00000361264.4	37	CCDS6549.1	532	0.24358974358974358	10	0.02032520325203252	76	0.20994475138121546	335	0.5856643356643356	111	0.14643799472295516	C	22.7	4.325631	0.81580	0.034271	0.123721	ENSG00000198876	ENST00000361264;ENST00000396990;ENST00000450964	T;T;T	0.30182	1.54;1.54;1.54	5.07	4.17	0.49024	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.58101	1.795	0.20489	P	0.999890017	D	0.64830	0.994	P	0.47376	0.545	T	0.46735	-0.9170	9	0.31617	T	0.26	-22.0702	11.837	0.52330	0.0:0.9192:0.0:0.0808	rs11557154;rs17855881;rs11557154	131	Q5T6F0	DCA12_HUMAN	Q	131;113;110	ENSP00000355114:R131Q;ENSP00000380187:R113Q;ENSP00000415833:R110Q	ENSP00000355114:R131Q	R	-	2	0	DCAF12	34097505	1.000000	0.71417	0.976000	0.42696	0.769000	0.43574	7.287000	0.78681	1.368000	0.46115	0.655000	0.94253	CGG	C|0.846;T|0.154	0.154	strong		0.483	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397	
DENND6B	414918	hgsc.bcm.edu	37	22	50752150	50752150	+	Missense_Mutation	SNP	C	C	T	rs68178377	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50752150C>T	ENST00000413817.3	-	15	1278	c.1207G>A	c.(1207-1209)Gtg>Atg	p.V403M	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	403					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										TTCTTCTGCACGCCCTGCAGG	0.672													C|||	1407	0.28095	0.1982	0.3199	5008	,	,		9059	0.1994		0.2922	False		,,,				2504	0.4376				p.V403M		Atlas-SNP	.											.	.	.	.	0			c.G1207A						PASS	.	C	MET/VAL	834,3260		89,656,1302	19.0	22.0	21.0		1207	-2.6	0.0	22	dbSNP_130	21	2487,5839		382,1723,2058	yes	missense	FAM116B	NM_001001794.3	21	471,2379,3360	TT,TC,CC		29.8703,20.3713,26.7391	benign	403/586	50752150	3321,9099	2047	4163	6210	SO:0001583	missense	414918	exon15			TCTGCACGCCCTG	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.1207G>A	22.37:g.50752150C>T	ENSP00000391524:p.Val403Met	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	72	42	0.583333	NM_001001794	A6X8I5	Missense_Mutation	SNP	ENST00000413817.3	37	CCDS46732.1	548	0.2509157509157509	105	0.21341463414634146	101	0.27900552486187846	113	0.19755244755244755	229	0.3021108179419525	C	9.702	1.154751	0.21371	0.203713	0.298703	ENSG00000205593	ENST00000413817	.	.	.	4.82	-2.63	0.06133	.	0.554792	0.18959	N	0.126460	T	0.00012	0.0000	N	0.16266	0.395	0.54753	P	1.0999999999983245E-5	B;B	0.24317	0.101;0.101	B;B	0.11329	0.004;0.006	T	0.39292	-0.9621	8	0.27785	T	0.31	-3.5588	6.125	0.20174	0.0:0.2459:0.3228:0.4313	.	403;403	Q8NEG7;C9JIV6	F116B_HUMAN;.	M	403	.	ENSP00000391524:V403M	V	-	1	0	FAM116B	49094722	0.041000	0.20044	0.032000	0.17829	0.733000	0.41908	0.249000	0.18216	-0.577000	0.05967	0.462000	0.41574	GTG	C|0.747;T|0.253	0.253	strong		0.672	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
DSCAML1	57453	hgsc.bcm.edu	37	11	117403235	117403235	+	Missense_Mutation	SNP	G	G	T	rs3741280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:117403235G>T	ENST00000321322.6	-	4	695	c.694C>A	c.(694-696)Cac>Aac	p.H232N	DSCAML1_ENST00000527706.1_Intron	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	172	Ig-like C2-type 3.				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)	p.H232N(1)		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)		AAAAACCTGTGTTCTGGAGAC	0.498													T|||	2267	0.452676	0.4796	0.3732	5008	,	,		19258	0.5417		0.2654	False		,,,				2504	0.5736				p.H232N		Atlas-SNP	.											DSCAML1,NS,carcinoma,0,1	DSCAML1	286	1	1	Substitution - Missense(1)	stomach(1)	c.C694A						PASS	.	T	ASN/HIS	1928,2474	624.5+/-394.3	425,1078,698	88.0	81.0	84.0		694	4.9	1.0	11	dbSNP_107	84	2265,6327	707.5+/-405.6	309,1647,2340	yes	missense	DSCAML1	NM_020693.2	68	734,2725,3038	TT,TG,GG		26.3617,43.7983,32.2687	benign	232/2114	117403235	4193,8801	2201	4296	6497	SO:0001583	missense	57453	exon4			ACCTGTGTTCTGG		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.694C>A	11.37:g.117403235G>T	ENSP00000315465:p.His232Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	823	0.3768315018315018	215	0.4369918699186992	118	0.3259668508287293	297	0.5192307692307693	193	0.2546174142480211	T	5.290	0.238934	0.10023	0.437983	0.263617	ENSG00000177103	ENST00000321322	T	0.76316	-1.01	4.88	4.88	0.63580	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	0.47737	P	4.92000000000048E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.44620	-0.9316	8	0.23302	T	0.38	.	6.9151	0.24355	0.0:0.0752:0.1524:0.7724	rs3741280;rs52818394;rs60670777;rs3741280	172	Q8TD84	DSCL1_HUMAN	N	232	ENSP00000315465:H232N	ENSP00000315465:H232N	H	-	1	0	DSCAML1	116908445	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.341000	0.52151	0.993000	0.38866	-0.256000	0.11100	CAC	G|0.640;T|0.360	0.360	strong		0.498	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
ALPK2	115701	hgsc.bcm.edu	37	18	56202231	56202231	+	Missense_Mutation	SNP	T	T	C	rs17065127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:56202231T>C	ENST00000361673.3	-	5	5401	c.5188A>G	c.(5188-5190)Aaa>Gaa	p.K1730E	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1730			K -> E (in dbSNP:rs17065127).			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						GACAAAATTTTCTTCTTTACT	0.488													T|||	288	0.057508	0.1354	0.0303	5008	,	,		18954	0.0268		0.0268	False		,,,				2504	0.0348				p.K1730E		Atlas-SNP	.											.	ALPK2	487	.	0			c.A5188G						PASS	.	T	GLU/LYS	460,3946	219.4+/-237.2	22,416,1765	116.0	111.0	113.0		5188	5.7	1.0	18	dbSNP_123	113	188,8412	84.2+/-146.7	3,182,4115	yes	missense	ALPK2	NM_052947.3	56	25,598,5880	CC,CT,TT		2.186,10.4403,4.9823	probably-damaging	1730/2171	56202231	648,12358	2203	4300	6503	SO:0001583	missense	115701	exon5			AAATTTTCTTCTT	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.5188A>G	18.37:g.56202231T>C	ENSP00000354991:p.Lys1730Glu	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	214	120	0.560748	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	98	0.04487179487179487	53	0.10772357723577236	8	0.022099447513812154	19	0.033216783216783216	18	0.023746701846965697	T	15.69	2.907108	0.52333	0.104403	0.02186	ENSG00000198796	ENST00000361673	T	0.58060	0.36	5.65	5.65	0.86999	.	0.000000	0.64402	D	0.000007	T	0.03220	0.0094	L	0.57536	1.79	0.35142	D	0.76891	D;D	0.71674	0.998;0.996	D;D	0.72625	0.978;0.951	T	0.53236	-0.8467	10	0.66056	D	0.02	-28.9861	13.4006	0.60881	0.0:0.0:0.0:1.0	rs17065127;rs52806198;rs17065127	1725;1730	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	E	1730	ENSP00000354991:K1730E	ENSP00000354991:K1730E	K	-	1	0	ALPK2	54353211	1.000000	0.71417	1.000000	0.80357	0.106000	0.19336	4.529000	0.60588	2.149000	0.67028	0.533000	0.62120	AAA	T|0.948;C|0.052	0.052	strong		0.488	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
PTX4	390667	hgsc.bcm.edu	37	16	1536380	1536380	+	Missense_Mutation	SNP	G	G	T	rs2667672	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1536380G>T	ENST00000447419.2	-	3	1022	c.997C>A	c.(997-999)Ctg>Atg	p.L333M	PTX4_ENST00000440447.2_Silent_p.P184P|PTX4_ENST00000293922.1_Missense_Mutation_p.L328M			Q96A99	PTX4_HUMAN	pentraxin 4, long	333	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CCGGGCAGCAGGGAGTCTCGG	0.667													G|||	1552	0.309904	0.705	0.1916	5008	,	,		16773	0.0665		0.2306	False		,,,				2504	0.1922				p.L328M		Atlas-SNP	.											.	PTX4	46	.	0			c.C982A						PASS	.	G	MET/LEU	2767,1631	649.8+/-398.9	855,1057,287	50.0	60.0	57.0		982	4.5	0.6	16	dbSNP_100	57	1838,6762	326.9+/-317.6	192,1454,2654	yes	missense	PTX4	NM_001013658.1	15	1047,2511,2941	TT,TG,GG		21.3721,37.085,35.4285	probably-damaging	328/474	1536380	4605,8393	2199	4300	6499	SO:0001583	missense	390667	exon3			GCAGCAGGGAGTC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.997C>A	16.37:g.1536380G>T	ENSP00000445277:p.Leu333Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		632	0.2893772893772894	336	0.6829268292682927	75	0.20718232044198895	34	0.05944055944055944	187	0.24670184696569922	G	4.294	0.053733	0.08291	0.62915	0.213721	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06294	3.47;3.32	5.5	4.54	0.55810	.	0.426092	0.21261	N	0.077474	T	0.00012	0.0000	M	0.86268	2.805	0.80722	P	0.0	P	0.43826	0.818	B	0.35770	0.21	T	0.06250	-1.0837	9	0.40728	T	0.16	.	9.391	0.38372	0.0:0.1572:0.6798:0.163	rs2667672;rs60531683;rs2667672	328	Q96A99-2	.	M	333;328	ENSP00000445277:L333M;ENSP00000293922:L328M	ENSP00000293922:L328M	L	-	1	2	PTX4	1476381	0.000000	0.05858	0.573000	0.28510	0.006000	0.05464	0.479000	0.22228	1.328000	0.45358	-0.152000	0.13540	CTG	G|0.655;T|0.345	0.345	strong		0.667	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
HDAC7	51564	hgsc.bcm.edu	37	12	48177906	48177906	+	Silent	SNP	C	C	T	rs7306788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48177906C>T	ENST00000427332.2	-	25	2925	c.2769G>A	c.(2767-2769)gtG>gtA	p.V923V	HDAC7_ENST00000552960.1_Silent_p.V945V|HDAC7_ENST00000080059.7_Silent_p.V962V|AC004466.1_ENST00000599515.1_5'Flank|HDAC7_ENST00000354334.3_Silent_p.V925V|HDAC7_ENST00000380610.4_Silent_p.*1015*			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	923	Interaction with SIN3A. {ECO:0000250}.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		CCAGTGCGGTCACTGCCTCCA	0.627													C|||	358	0.0714856	0.0197	0.0951	5008	,	,		17928	0.002		0.1769	False		,,,				2504	0.0879				p.V962V		Atlas-SNP	.											.	HDAC7	71	.	0			c.G2886A						PASS	.	C	,	184,4222	118.4+/-156.1	4,176,2023	55.0	51.0	52.0		2775,2886	2.4	1.0	12	dbSNP_116	52	1624,6976	299.5+/-304.5	130,1364,2806	no	coding-synonymous,coding-synonymous	HDAC7	NM_001098416.2,NM_015401.3	,	134,1540,4829	TT,TC,CC		18.8837,4.1761,13.9013	,	925/955,962/992	48177906	1808,11198	2203	4300	6503	SO:0001819	synonymous_variant	51564	exon25			TGCGGTCACTGCC	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.2769G>A	12.37:g.48177906C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	106	57	0.537736	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Silent	SNP	ENST00000427332.2	37																																																																																				C|0.879;G|0.000;T|0.121	0.121	strong		0.627	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
NARFL	64428	hgsc.bcm.edu	37	16	781633	781633	+	Silent	SNP	G	G	A	rs3829492	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:781633G>A	ENST00000251588.2	-	9	982	c.966C>T	c.(964-966)caC>caT	p.H322H	NARFL_ENST00000301694.5_3'UTR|NARFL_ENST00000568545.1_Silent_p.H220H|NARFL_ENST00000540986.1_Silent_p.H220H|NARFL_ENST00000562862.1_5'UTR	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	322					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				GCCGGAACACGTGCTCCAGGT	0.657													G|||	1908	0.38099	0.1271	0.4539	5008	,	,		18429	0.7599		0.2147	False		,,,				2504	0.453				p.H322H		Atlas-SNP	.											NARFL,NS,adenoma,0,1	NARFL	31	1	0			c.C966T						PASS	.	G		476,3844		18,440,1702	32.0	27.0	29.0		966	-4.5	0.9	16	dbSNP_107	29	1536,7010		136,1264,2873	no	coding-synonymous	NARFL	NM_022493.1		154,1704,4575	AA,AG,GG		17.9733,11.0185,15.6381		322/477	781633	2012,10854	2160	4273	6433	SO:0001819	synonymous_variant	64428	exon9			GAACACGTGCTCC	AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 1"""	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.966C>T	16.37:g.781633G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	16	0.421053	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Silent	SNP	ENST00000251588.2	37	CCDS10425.1																																																																																			G|0.714;A|0.286	0.286	strong		0.657	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493	
MAP4K1	11184	hgsc.bcm.edu	37	19	39092142	39092142	+	Silent	SNP	C	C	T	rs35423612	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39092142C>T	ENST00000591517.1	-	20	1498	c.1470G>A	c.(1468-1470)ttG>ttA	p.L490L	MAP4K1_ENST00000423454.2_Silent_p.L152L|MAP4K1_ENST00000586296.1_Intron|MAP4K1_ENST00000589130.1_Silent_p.L486L|MAP4K1_ENST00000396857.2_Silent_p.L490L|CTB-186G2.1_ENST00000589557.1_RNA	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	490					activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGCCATTGAACAACTTTACGA	0.617													C|||	45	0.00898562	0.0008	0.0058	5008	,	,		15542	0.0		0.0199	False		,,,				2504	0.0204				p.L490L		Atlas-SNP	.											.	MAP4K1	165	.	0			c.G1470A						PASS	.	C	,	18,4112		0,18,2047	29.0	33.0	32.0		1470,1470	-1.3	0.7	19	dbSNP_126	32	268,8106		5,258,3924	no	coding-synonymous,coding-synonymous	MAP4K1	NM_001042600.1,NM_007181.4	,	5,276,5971	TT,TC,CC		3.2004,0.4358,2.2873	,	490/822,490/834	39092142	286,12218	2065	4187	6252	SO:0001819	synonymous_variant	11184	exon20			ATTGAACAACTTT	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6863	protein-coding gene	gene with protein product	"""hematopoietic progenitor kinase 1"""	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.1470G>A	19.37:g.39092142C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_007181		Silent	SNP	ENST00000591517.1	37	CCDS59385.1																																																																																			C|0.990;T|0.010	0.010	strong		0.617	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600	
CENPE	1062	hgsc.bcm.edu	37	4	104062223	104062223	+	Silent	SNP	C	C	T	rs1381658	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:104062223C>T	ENST00000265148.3	-	36	5591	c.5502G>A	c.(5500-5502)acG>acA	p.T1834T	CENPE_ENST00000380026.3_Silent_p.T1809T	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1834					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		CTTTTTTTAACGTAATAAGTT	0.284													C|||	847	0.169129	0.0431	0.1916	5008	,	,		19051	0.1548		0.1779	False		,,,				2504	0.3292				p.T1834T		Atlas-SNP	.											.	CENPE	253	.	0			c.G5502A						PASS	.	C		277,4125	140.0+/-175.5	8,261,1932	64.0	64.0	64.0		5502	2.9	1.0	4	dbSNP_88	64	1538,7052	281.3+/-295.0	141,1256,2898	no	coding-synonymous	CENPE	NM_001813.2		149,1517,4830	TT,TC,CC		17.9045,6.2926,13.9701		1834/2702	104062223	1815,11177	2201	4295	6496	SO:0001819	synonymous_variant	1062	exon36			TTTTAACGTAATA	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.5502G>A	4.37:g.104062223C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_001813	A6NKY9|A8K2U7|Q4LE75	Silent	SNP	ENST00000265148.3	37	CCDS34042.1																																																																																			C|0.861;T|0.139	0.139	strong		0.284	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TLE3	7090	hgsc.bcm.edu	37	15	70347482	70347482	+	Missense_Mutation	SNP	G	G	A	rs200508723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:70347482G>A	ENST00000558939.1	-	15	2870	c.1493C>T	c.(1492-1494)aCg>aTg	p.T498M	TLE3_ENST00000317509.8_Missense_Mutation_p.T486M|TLE3_ENST00000558201.1_Missense_Mutation_p.T504M|TLE3_ENST00000539550.1_Missense_Mutation_p.T425M|TLE3_ENST00000557907.1_Missense_Mutation_p.T490M|TLE3_ENST00000557997.1_Missense_Mutation_p.T490M|TLE3_ENST00000560589.1_Missense_Mutation_p.T442M|TLE3_ENST00000560939.1_Missense_Mutation_p.T500M|TLE3_ENST00000559191.1_Missense_Mutation_p.T79M|TLE3_ENST00000559929.1_Missense_Mutation_p.T508M|TLE3_ENST00000559048.1_Missense_Mutation_p.T498M|TLE3_ENST00000440567.3_Missense_Mutation_p.T488M|TLE3_ENST00000451782.2_Missense_Mutation_p.T495M|TLE3_ENST00000558379.1_Missense_Mutation_p.T493M|TLE3_ENST00000442299.2_Missense_Mutation_p.T490M	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	498				T -> S (in Ref. 1; AAA61194). {ECO:0000305}.	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						GACGTGCCTCGTGGGGTTGCT	0.657													G|||	2	0.000399361	0.0	0.0	5008	,	,		18004	0.0		0.002	False		,,,				2504	0.0				p.T498M		Atlas-SNP	.											.	TLE3	104	.	0			c.C1493T						PASS	.	G	MET/THR,MET/THR,MET/THR	4,4394	6.2+/-15.9	0,4,2195	66.0	70.0	69.0		1484,1493,1457	4.5	1.0	15		69	32,8564	22.2+/-67.0	0,32,4266	yes	missense,missense,missense	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	81,81,81	0,36,6461	AA,AG,GG		0.3723,0.091,0.2771	probably-damaging,probably-damaging,probably-damaging	495/770,498/773,486/761	70347482	36,12958	2199	4298	6497	SO:0001583	missense	7090	exon15			TGCCTCGTGGGGT	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.1493C>T	15.37:g.70347482G>A	ENSP00000452871:p.Thr498Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.436998	0.83885	9.1E-4	0.003723	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550;ENST00000542329	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	4.54	4.54	0.55810	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.33673	0.0871	M	0.76170	2.325	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.80764	0.978;0.987;0.935;0.987;0.989;0.994;0.985;0.965	T	0.12372	-1.0550	10	0.87932	D	0	-9.2287	16.2284	0.82315	0.0:0.0:1.0:0.0	.	488;495;490;493;486;498;498;425	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	M	490;495;498;488;425;165	ENSP00000390007:T490M;ENSP00000394717:T495M;ENSP00000415057:T488M;ENSP00000442594:T425M	ENSP00000319233:T498M	T	-	2	0	TLE3	68134536	1.000000	0.71417	0.968000	0.41197	0.975000	0.68041	9.530000	0.98051	2.352000	0.79861	0.462000	0.41574	ACG	G|0.999;A|0.001	0.001	weak		0.657	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
EPB41	2035	hgsc.bcm.edu	37	1	29379679	29379679	+	Missense_Mutation	SNP	G	G	A	rs138888144		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:29379679G>A	ENST00000343067.4	+	12	1827	c.1700G>A	c.(1699-1701)gGt>gAt	p.G567D	EPB41_ENST00000356093.2_Missense_Mutation_p.G567D|EPB41_ENST00000347529.3_Missense_Mutation_p.G532D|EPB41_ENST00000373798.1_Missense_Mutation_p.G567D|EPB41_ENST00000373797.1_Missense_Mutation_p.G567D|EPB41_ENST00000373800.3_Missense_Mutation_p.G358D|EPB41_ENST00000398863.2_Missense_Mutation_p.G567D|EPB41_ENST00000349460.4_Missense_Mutation_p.G358D	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	567	Hydrophilic.				actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		ATTACTCAGGGTCAGGTTGCA	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		19582	0.0		0.0	False		,,,				2504	0.001				p.G567D		Atlas-SNP	.											EPB41_ENST00000343067,NS,carcinoma,+1,2	EPB41	118	2	0			c.G1700A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	5,4401	9.9+/-24.2	0,5,2198	56.0	59.0	58.0		1700,1700,1073,1073,1073,1595	5.9	1.0	1	dbSNP_134	58	74,8526	44.0+/-102.2	1,72,4227	yes	missense,missense,missense,missense,missense,missense	EPB41	NM_001166005.1,NM_001166006.1,NM_001166007.1,NM_004437.3,NM_203342.2,NM_203343.2	94,94,94,94,94,94	1,77,6425	AA,AG,GG		0.8605,0.1135,0.6074	benign,benign,benign,benign,benign,benign	567/865,567/721,358/602,358/589,358/642,532/776	29379679	79,12927	2203	4300	6503	SO:0001583	missense	2035	exon12			CTCAGGGTCAGGT	BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"""elliptocytosis 1, RH-linked"""	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.1700G>A	1.37:g.29379679G>A	ENSP00000345259:p.Gly567Asp	Somatic	260	1	0.00384615		WXS	Illumina HiSeq	Phase_I	242	228	0.942149	NM_001166006	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Missense_Mutation	SNP	ENST00000343067.4	37	CCDS53288.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.690291	0.48097	0.001135	0.008605	ENSG00000159023	ENST00000358989;ENST00000343067;ENST00000356093;ENST00000398863;ENST00000398861;ENST00000398865;ENST00000349460;ENST00000373800;ENST00000347529;ENST00000373798;ENST00000373797	D;D;D;D;D;D;D;D	0.84370	-1.77;-1.84;-1.65;-1.76;-1.76;-1.5;-1.77;-1.75	5.91	5.91	0.95273	.	1.534880	0.03353	N	0.196448	T	0.69242	0.3089	N	0.03608	-0.345	0.30658	N	0.754682	B;B;B;B;B;B;B;B;B;B	0.25441	0.003;0.005;0.005;0.001;0.004;0.009;0.019;0.005;0.126;0.004	B;B;B;B;B;B;B;B;B;B	0.27380	0.01;0.017;0.017;0.003;0.023;0.038;0.017;0.023;0.079;0.029	T	0.60141	-0.7321	10	0.48119	T	0.1	.	12.7211	0.57142	0.0771:0.0:0.9229:0.0	.	461;567;567;567;567;567;584;532;358;358	E9PEX0;E9PEW9;C9JTS2;P11171;P11171-2;P11171-7;Q59F12;P11171-5;P11171-4;P11171-3	.;.;.;41_HUMAN;.;.;.;.;.;.	D	584;567;567;567;461;567;358;358;532;567;567	ENSP00000345259:G567D;ENSP00000348397:G567D;ENSP00000381839:G567D;ENSP00000317597:G358D;ENSP00000362906:G358D;ENSP00000290100:G532D;ENSP00000362904:G567D;ENSP00000362903:G567D	ENSP00000345259:G567D	G	+	2	0	EPB41	29252266	1.000000	0.71417	0.999000	0.59377	0.876000	0.50452	3.356000	0.52269	2.793000	0.96121	0.655000	0.94253	GGT	G|0.995;A|0.005	0.005	strong		0.502	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	NM_203342	
LANCL3	347404	hgsc.bcm.edu	37	X	37518806	37518806	+	Silent	SNP	C	C	T	rs12009345	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:37518806C>T	ENST00000378619.3	+	3	1008	c.789C>T	c.(787-789)agC>agT	p.S263S	LANCL3_ENST00000378621.3_Silent_p.S263S|TM4SF2_ENST00000465127.1_Intron	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	263							catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						TATGGCAGAGCGTGGACTTTC	0.522													C|||	1121	0.296954	0.5197	0.147	3775	,	,		12831	0.0496		0.1113	False		,,,				2504	0.1738				p.S263S		Atlas-SNP	.											.	LANCL3	42	.	0			c.C789T						PASS	.	C	,	2413,1420		652,750,359,229,212	79.0	67.0	71.0		789,789	-0.3	1.0	X	dbSNP_120	71	1158,5570		84,684,306,1660,1566	no	coding-synonymous,coding-synonymous	LANCL3	NM_001170331.1,NM_198511.2	,	736,1434,665,1889,1778	TT,TC,T,CC,C		17.2117,37.0467,33.8131	,	263/421,263/389	37518806	3571,6990	2202	4300	6502	SO:0001819	synonymous_variant	347404	exon3			GCAGAGCGTGGAC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.789C>T	X.37:g.37518806C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001170331	A6NHE3	Silent	SNP	ENST00000378619.3	37	CCDS55398.1																																																																																			C|0.681;0|0.003	.	strong		0.522	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511	
CFAP46	54777	hgsc.bcm.edu	37	10	134738232	134738232	+	Silent	SNP	A	A	G	rs4075501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134738232A>G	ENST00000368586.5	-	11	1324	c.1224T>C	c.(1222-1224)gcT>gcC	p.A408A	TTC40_ENST00000368582.2_Silent_p.A408A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CCGCAACGCCAGCCAGGGGCT	0.677													G|||	2670	0.533147	0.7035	0.6153	5008	,	,		16344	0.3512		0.4722	False		,,,				2504	0.4949				p.A408A		Atlas-SNP	.											.	TTC40	100	.	0			c.T1224C						PASS	.																																			SO:0001819	synonymous_variant	54777	exon11			AACGCCAGCCAGG																												ENST00000368586.5:c.1224T>C	10.37:g.134738232A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	63	23	0.365079	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			A|0.499;G|0.501	0.501	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
AP1S3	130340	hgsc.bcm.edu	37	2	224642579	224642579	+	Missense_Mutation	SNP	A	A	C	rs116107386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:224642579A>C	ENST00000446015.2	-	2	44	c.11T>G	c.(10-12)tTc>tGc	p.F4C	AP1S3_ENST00000443700.1_Missense_Mutation_p.F4C|AP1S3_ENST00000396653.2_Missense_Mutation_p.F4C|AP1S3_ENST00000423110.1_Missense_Mutation_p.F4C|AP1S3_ENST00000396654.2_Missense_Mutation_p.F4C|AP1S3_ENST00000409375.1_Missense_Mutation_p.F4C			Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3 subunit	4					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|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)	coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane coat (GO:0030117)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			NS(1)|breast(1)|lung(2)	4		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GAGCAATATGAAATGTATCTA	0.408													A|||	15	0.00299521	0.0015	0.0029	5008	,	,		16772	0.0		0.0099	False		,,,				2504	0.001				p.F4C		Atlas-SNP	.											.	AP1S3	10	.	0			c.T11G						PASS	.	A	CYS/PHE	10,3754		0,10,1872	60.0	55.0	56.0		11	5.8	1.0	2	dbSNP_132	56	105,8127		0,105,4011	yes	missense	AP1S3	NM_001039569.1	205	0,115,5883	CC,CA,AA		1.2755,0.2657,0.9587	probably-damaging	4/155	224642579	115,11881	1882	4116	5998	SO:0001583	missense	130340	exon2			AATATGAAATGTA	AF393369	CCDS42827.1	2q36.3	2008-02-05			ENSG00000152056	ENSG00000152056			18971	protein-coding gene	gene with protein product		615781					Standard	NR_110905		Approved		uc002vnn.3	Q96PC3	OTTHUMG00000133165	ENST00000446015.2:c.11T>G	2.37:g.224642579A>C	ENSP00000388738:p.Phe4Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_001039569	B4DQZ1|Q8WTY1|Q96DD1	Missense_Mutation	SNP	ENST00000446015.2	37		11	0.005036630036630037	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	A	22.0	4.226842	0.79576	0.002657	0.012755	ENSG00000152056	ENST00000443700;ENST00000396654;ENST00000396653;ENST00000446015;ENST00000409375;ENST00000423110	.	.	.	5.81	5.81	0.92471	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.82747	0.5104	M	0.93594	3.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.88388	0.3006	9	0.87932	D	0	.	16.1652	0.81750	1.0:0.0:0.0:0.0	.	4;4	Q96PC3;Q96PC3-4	AP1S3_HUMAN;.	C	4	.	ENSP00000333888:F4C	F	-	2	0	AP1S3	224350823	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.940000	0.92958	2.230000	0.72887	0.528000	0.53228	TTC	A|0.993;C|0.007	0.007	strong		0.408	AP1S3-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383293.1		
KLK3	354	hgsc.bcm.edu	37	19	51361757	51361757	+	Missense_Mutation	SNP	T	T	C	rs17632542	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51361757T>C	ENST00000326003.2	+	4	577	c.536T>C	c.(535-537)aTt>aCt	p.I179T	KLK3_ENST00000593997.1_Missense_Mutation_p.I179T|KLK3_ENST00000360617.3_Missense_Mutation_p.I179T|KLK3_ENST00000597483.1_Missense_Mutation_p.I136T|KLK3_ENST00000595952.1_Missense_Mutation_p.I136T	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	179	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		I -> T (in dbSNP:rs17632542).		cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CTCCATGTTATTTCCAATGAC	0.552													T|||	141	0.028155	0.0008	0.0274	5008	,	,		22287	0.001		0.0706	False		,,,				2504	0.0501				p.I179T	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.T536C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE	60,4346	55.5+/-91.7	1,58,2144	211.0	183.0	193.0	http://www.ncbi.nlm.nih.gov/pubmed?term	536,407,536	1.9	0.0	19	dbSNP_123	193	648,7952	166.2+/-218.2	21,606,3673	yes	missense,missense,missense	KLK3	NM_001030047.1,NM_001030048.1,NM_001648.2	89,89,89	22,664,5817	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	7.5349,1.3618,5.4436	benign,benign,benign	179/239,136/219,179/262	51361757	708,12298	2203	4300	6503	SO:0001583	missense	354	exon4			ATGTTATTTCCAA	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.536T>C	19.37:g.51361757T>C	ENSP00000314151:p.Ile179Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	81	51	0.62963	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Missense_Mutation	SNP	ENST00000326003.2	37	CCDS12807.1	69	0.03159340659340659	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	57	0.07519788918205805	T	9.050	0.991951	0.18966	0.013618	0.075349	ENSG00000142515	ENST00000326003;ENST00000422986;ENST00000360617;ENST00000326052	D;D	0.88818	-2.43;-2.43	2.95	1.85	0.25348	.	1.165310	0.06828	N	0.793430	T	0.31857	0.0810	L	0.53780	1.695	0.20307	N	0.999919	P;B;B	0.37141	0.584;0.335;0.171	B;B;B	0.37346	0.247;0.131;0.087	T	0.59637	-0.7417	10	0.87932	D	0	.	5.4924	0.16783	0.2479:0.0:0.0:0.7521	rs17632542;rs52818115;rs56537636;rs17632542	138;179;136	Q8NCW4;G3XAE3;G3V0H4	.;.;.	T	179;136;179;138	ENSP00000314151:I179T;ENSP00000353829:I179T	ENSP00000314151:I179T	I	+	2	0	KLK3	56053569	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	0.302000	0.19192	0.278000	0.22164	0.329000	0.21502	ATT	T|0.952;C|0.048	0.048	strong		0.552	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
CSTF2T	23283	hgsc.bcm.edu	37	10	53458998	53458998	+	Silent	SNP	A	A	G	rs2292828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:53458998A>G	ENST00000331173.4	-	1	357	c.312T>C	c.(310-312)ctT>ctC	p.L104L	PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	104					mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L104L(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		CTGCAGGCCCAAGGCTCTTTA	0.557													G|||	1581	0.315695	0.6831	0.1455	5008	,	,		16978	0.2123		0.1571	False		,,,				2504	0.2096				p.L104L		Atlas-SNP	.											CSTF2T,NS,carcinoma,0,1	CSTF2T	64	1	1	Substitution - coding silent(1)	stomach(1)	c.T312C						PASS	.	G	,,	2493,1913	546.6+/-377.1	713,1067,423	96.0	109.0	104.0		,,312	-7.8	0.3	10	dbSNP_100	104	1204,7396	763.8+/-407.6	85,1034,3181	no	intron,intron,coding-synonymous	PRKG1,CSTF2T	NM_001098512.2,NM_006258.3,NM_015235.2	,,	798,2101,3604	GG,GA,AA		14.0,43.4181,28.4253	,,	,,104/617	53458998	3697,9309	2203	4300	6503	SO:0001819	synonymous_variant	23283	exon1			AGGCCCAAGGCTC	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"""RNA binding motif (RRM) containing"""	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.312T>C	10.37:g.53458998A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Silent	SNP	ENST00000331173.4	37	CCDS7245.1																																																																																			A|0.710;C|0.003;G|0.282;T|0.006	0.282	strong		0.557	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235	
PCNT	5116	hgsc.bcm.edu	37	21	47831618	47831618	+	Silent	SNP	C	C	T	rs16979162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47831618C>T	ENST00000359568.5	+	28	5738	c.5631C>T	c.(5629-5631)atC>atT	p.I1877I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1877					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)					ATTTAGAAATCGACGCTCTGA	0.637													T|||	892	0.178115	0.4879	0.0937	5008	,	,		16231	0.004		0.0895	False		,,,				2504	0.09				p.I1877I		Atlas-SNP	.											.	PCNT	283	.	0			c.C5631T						PASS	.	T		1837,2559		391,1055,752	27.0	30.0	29.0		5631	-11.6	0.0	21	dbSNP_123	29	632,7952		19,594,3679	no	coding-synonymous	PCNT	NM_006031.5		410,1649,4431	TT,TC,CC		7.3625,41.788,19.0216		1877/3337	47831618	2469,10511	2198	4292	6490	SO:0001819	synonymous_variant	5116	exon28			AGAAATCGACGCT	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.5631C>T	21.37:g.47831618C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.812;T|0.188	0.188	strong		0.637	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
SSX2IP	117178	hgsc.bcm.edu	37	1	85113229	85113229	+	Missense_Mutation	SNP	A	A	G	rs1057746	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:85113229A>G	ENST00000342203.3	-	14	1995	c.1732T>C	c.(1732-1734)Tgt>Cgt	p.C578R	SSX2IP_ENST00000605755.1_Missense_Mutation_p.C551R|SSX2IP_ENST00000437941.2_Missense_Mutation_p.C551R	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	578			C -> R (in dbSNP:rs1057746). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.		cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TGATTTGTACATTCTCCTCCA	0.388													A|||	2567	0.51258	0.2458	0.5346	5008	,	,		17943	0.7034		0.6521	False		,,,				2504	0.5174				p.C578R		Atlas-SNP	.											.	SSX2IP	53	.	0			c.T1732C						PASS	.	A	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	1297,3109	439.2+/-345.6	195,907,1101	247.0	199.0	215.0		1732,1651,1651,1732,1732	2.2	0.9	1	dbSNP_86	215	5425,3175	653.7+/-401.1	1728,1969,603	yes	missense,missense,missense,missense,missense	SSX2IP	NM_001166293.1,NM_001166294.1,NM_001166295.1,NM_001166417.1,NM_014021.3	180,180,180,180,180	1923,2876,1704	GG,GA,AA		36.9186,29.4371,48.3162	benign,benign,benign,benign,benign	578/615,551/588,551/588,578/615,578/615	85113229	6722,6284	2203	4300	6503	SO:0001583	missense	117178	exon15			TTGTACATTCTCC		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1732T>C	1.37:g.85113229A>G	ENSP00000340279:p.Cys578Arg	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_001166417	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	37	CCDS699.1	1215	0.5563186813186813	116	0.23577235772357724	200	0.5524861878453039	399	0.6975524475524476	500	0.6596306068601583	A	10.57	1.387185	0.25031	0.294371	0.630814	ENSG00000117155	ENST00000342203;ENST00000437941	T;T	0.48836	0.81;0.8	5.86	2.16	0.27623	.	0.378812	0.26248	N	0.025466	T	0.11965	0.0291	N	0.22421	0.69	0.09310	P	0.99999999713442	B	0.14438	0.01	B	0.14023	0.01	T	0.09250	-1.0683	9	0.46703	T	0.11	-2.7955	3.5408	0.07811	0.6564:0.1353:0.0712:0.1371	rs1057746;rs3198288;rs17838125;rs1057746	578	Q9Y2D8	ADIP_HUMAN	R	578;551	ENSP00000340279:C578R;ENSP00000412781:C551R	ENSP00000340279:C578R	C	-	1	0	SSX2IP	84885817	0.750000	0.28316	0.925000	0.36789	0.616000	0.37450	1.041000	0.30291	0.103000	0.17682	0.533000	0.62120	TGT	A|0.476;G|0.524	0.524	strong		0.388	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021	
CCDC137	339230	hgsc.bcm.edu	37	17	79634813	79634813	+	Silent	SNP	T	T	C	rs11546632	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79634813T>C	ENST00000329214.8	+	2	592	c.189T>C	c.(187-189)atT>atC	p.I63I	OXLD1_ENST00000571503.1_5'Flank|OXLD1_ENST00000374741.3_5'Flank|OXLD1_ENST00000573786.1_5'Flank	NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	63							poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			AACAGGAGATTCCTTTCCGGC	0.517													C|||	537	0.107228	0.1467	0.0951	5008	,	,		16061	0.002		0.1928	False		,,,				2504	0.0828				p.I63I		Atlas-SNP	.											.	CCDC137	27	.	0			c.T189C						PASS	.	C		714,3016		71,572,1222	50.0	53.0	52.0		189	-0.3	1.0	17	dbSNP_120	52	1366,6824		126,1114,2855	no	coding-synonymous	CCDC137	NM_199287.2		197,1686,4077	CC,CT,TT		16.6789,19.1421,17.4497		63/290	79634813	2080,9840	1865	4095	5960	SO:0001819	synonymous_variant	339230	exon2			GGAGATTCCTTTC	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.189T>C	17.37:g.79634813T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	26	15	0.576923	NM_199287		Silent	SNP	ENST00000329214.8	37	CCDS42400.1																																																																																			T|0.868;C|0.132	0.132	strong		0.517	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
STK31	56164	hgsc.bcm.edu	37	7	23811795	23811795	+	Missense_Mutation	SNP	T	T	G	rs10263079	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:23811795T>G	ENST00000355870.3	+	15	1982	c.1863T>G	c.(1861-1863)aaT>aaG	p.N621K	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.N598K|STK31_ENST00000428484.1_Missense_Mutation_p.N598K|STK31_ENST00000433467.2_Missense_Mutation_p.N621K	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	621			N -> K (in dbSNP:rs10263079). {ECO:0000269|PubMed:17344846}.	NKS -> KKI (in Ref. 1; AAK31978). {ECO:0000305}.		acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						AATATTTAAATAAGAGTCCCA	0.289													T|||	484	0.0966454	0.0454	0.1297	5008	,	,		16803	0.0575		0.2117	False		,,,				2504	0.0644				p.N621K		Atlas-SNP	.											.	STK31	175	.	0			c.T1863G						PASS	.	T	LYS/ASN,LYS/ASN,LYS/ASN	305,4097	154.4+/-187.8	14,277,1910	42.0	44.0	43.0		1794,1863,1794	1.5	1.0	7	dbSNP_119	43	1823,6755	318.2+/-313.6	179,1465,2645	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	94,94,94	193,1742,4555	GG,GT,TT		21.252,6.9287,16.3945	possibly-damaging,possibly-damaging,possibly-damaging	598/997,621/1020,598/997	23811795	2128,10852	2201	4289	6490	SO:0001583	missense	56164	exon15			TTTAAATAAGAGT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1863T>G	7.37:g.23811795T>G	ENSP00000348132:p.Asn621Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	284	0.13003663003663005	28	0.056910569105691054	61	0.1685082872928177	31	0.05419580419580419	164	0.21635883905013192	T	17.51	3.408289	0.62399	0.069287	0.21252	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.70045	-0.45;1.29;-0.44;-0.44	5.19	1.51	0.23008	.	0.121725	0.53938	D	0.000050	T	0.00073	0.0002	M	0.64997	1.995	0.29422	P	0.860491	P;P	0.52842	0.956;0.956	P;P	0.45071	0.468;0.468	T	0.03259	-1.1055	9	0.51188	T	0.08	-16.6838	8.6987	0.34312	0.0:0.2245:0.0:0.7755	rs10263079;rs10263079	621;621	B4DZ06;Q9BXU1	.;STK31_HUMAN	K	621;621;598;598	ENSP00000348132:N621K;ENSP00000411852:N621K;ENSP00000346660:N598K;ENSP00000406146:N598K	ENSP00000346660:N598K	N	+	3	2	STK31	23778320	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	1.330000	0.33781	0.024000	0.15214	-0.379000	0.06801	AAT	T|0.843;G|0.157	0.157	strong		0.289	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
IRS2	8660	hgsc.bcm.edu	37	13	110435914	110435914	+	Silent	SNP	G	G	A	rs12853546	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:110435914G>A	ENST00000375856.3	-	1	3001	c.2487C>T	c.(2485-2487)ccC>ccT	p.P829P		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	829					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TGCGCCCCACGGGGGAGCTCA	0.731													.|||	1127	0.22504	0.2027	0.1542	5008	,	,		8938	0.2173		0.2565	False		,,,				2504	0.2812				p.P829P	Melanoma(100;613 2409 40847)	Atlas-SNP	.											IRS2,NS,carcinoma,0,1	IRS2	44	1	0			c.C2487T						PASS	.	G		757,3251		86,585,1333	4.0	6.0	5.0		2487	-10.3	0.3	13	dbSNP_121	5	1742,6278		224,1294,2492	no	coding-synonymous	IRS2	NM_003749.2		310,1879,3825	AA,AG,GG		21.7207,18.8872,20.7765		829/1339	110435914	2499,9529	2004	4010	6014	SO:0001819	synonymous_variant	8660	exon1			CCCCACGGGGGAG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2487C>T	13.37:g.110435914G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Silent	SNP	ENST00000375856.3	37	CCDS9510.1																																																																																			G|0.788;A|0.212	0.212	strong		0.731	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749	
FUT10	84750	hgsc.bcm.edu	37	8	33318913	33318913	+	Missense_Mutation	SNP	C	C	T	rs77009471	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:33318913C>T	ENST00000327671.5	-	2	689	c.58G>A	c.(58-60)Gtc>Atc	p.V20I	FUT10_ENST00000335589.3_5'UTR|FUT10_ENST00000524021.1_Intron|FUT10_ENST00000518672.1_Intron	NM_032664.3	NP_116053.3	Q6P4F1	FUT10_HUMAN	fucosyltransferase 10 (alpha (1,3) fucosyltransferase)	20					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)			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)		AGCAGAAAGACGGTGGCTGTG	0.537													C|||	101	0.0201677	0.0628	0.0072	5008	,	,		14895	0.0		0.007	False		,,,				2504	0.0061				p.V20I		Atlas-SNP	.											.	FUT10	62	.	0			c.G58A						PASS	.	C	ILE/VAL	188,4218	120.0+/-157.7	5,178,2020	178.0	134.0	149.0		58	-4.9	0.0	8	dbSNP_131	149	50,8550	32.3+/-84.9	0,50,4250	yes	missense	FUT10	NM_032664.3	29	5,228,6270	TT,TC,CC		0.5814,4.2669,1.8299	benign	20/480	33318913	238,12768	2203	4300	6503	SO:0001583	missense	84750	exon2			GAAAGACGGTGGC	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.58G>A	8.37:g.33318913C>T	ENSP00000332757:p.Val20Ile	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	58	42	0.724138	NM_032664	A8KAC8|Q70GG3|Q8IVI6|Q8IVI7|Q8IVJ3|Q8TE43|Q9BSR3	Missense_Mutation	SNP	ENST00000327671.5	37	CCDS6088.1	39	0.017857142857142856	29	0.05894308943089431	4	0.011049723756906077	0	0.0	6	0.0079155672823219	C	8.788	0.929937	0.18131	0.042669	0.005814	ENSG00000172728	ENST00000327671;ENST00000380081	T	0.23950	1.88	5.79	-4.9	0.03094	.	3.760300	0.00682	N	0.000682	T	0.01835	0.0058	L	0.38531	1.155	0.09310	N	0.999997	B;B;B	0.13594	0.003;0.008;0.004	B;B;B	0.10450	0.001;0.003;0.005	T	0.13899	-1.0492	10	0.28530	T	0.3	1.7437	5.3164	0.15858	0.2807:0.2081:0.0:0.5112	.	20;20;20	B4DLS4;Q6P4F1-5;Q6P4F1	.;.;FUT10_HUMAN	I	20	ENSP00000332757:V20I	ENSP00000332757:V20I	V	-	1	0	FUT10	33438455	0.016000	0.18221	0.002000	0.10522	0.925000	0.55904	0.067000	0.14510	-0.725000	0.04901	-0.147000	0.13772	GTC	C|0.980;T|0.020	0.020	strong		0.537	FUT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376540.1	NM_032664	
MAML2	84441	hgsc.bcm.edu	37	11	95826485	95826485	+	Missense_Mutation	SNP	T	T	C	rs61749253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:95826485T>C	ENST00000524717.1	-	2	1994	c.710A>G	c.(709-711)cAa>cGa	p.Q237R		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	237					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CAGGGGTGCTTGGCTCATAGG	0.478			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid								T|||	27	0.00539137	0.0015	0.0043	5008	,	,		19485	0.0		0.0209	False		,,,				2504	0.001				p.Q237R		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.A710G						PASS	.	T	ARG/GLN	12,3878		0,12,1933	122.0	118.0	119.0		710	5.4	0.7	11	dbSNP_129	119	166,8120		2,162,3979	yes	missense	MAML2	NM_032427.1	43	2,174,5912	CC,CT,TT		2.0034,0.3085,1.4619	probably-damaging	237/1157	95826485	178,11998	1945	4143	6088	SO:0001583	missense	84441	exon2			GGTGCTTGGCTCA	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.710A>G	11.37:g.95826485T>C	ENSP00000434552:p.Gln237Arg	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	286	171	0.597902	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	T	8.969	0.972374	0.18736	0.003085	0.020034	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.47869	0.83;0.83	5.42	5.42	0.78866	.	0.109437	0.42682	D	0.000666	T	0.33847	0.0877	L	0.54323	1.7	0.31335	N	0.684305	D	0.58268	0.982	P	0.52554	0.702	T	0.49283	-0.8956	10	0.17832	T	0.49	-9.134	10.6675	0.45739	0.1428:0.0:0.0:0.8572	rs61749253	237	Q8IZL2	MAML2_HUMAN	R	237	ENSP00000434552:Q237R;ENSP00000412394:Q237R	ENSP00000412394:Q237R	Q	-	2	0	MAML2	95466133	1.000000	0.71417	0.692000	0.30179	0.890000	0.51754	4.231000	0.58639	2.050000	0.60909	0.374000	0.22700	CAA	T|0.990;C|0.010	0.010	strong		0.478	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
CEP68	23177	hgsc.bcm.edu	37	2	65299330	65299330	+	Missense_Mutation	SNP	T	T	A	rs141499084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:65299330T>A	ENST00000377990.2	+	3	1303	c.1100T>A	c.(1099-1101)tTt>tAt	p.F367Y	CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000497039.1_3'UTR|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000546106.1_Missense_Mutation_p.F367Y|CEP68_ENST00000260569.4_Missense_Mutation_p.F367Y	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	367					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						GCCCTGCCATTTTCTGGGCCC	0.567													T|||	21	0.00419329	0.0	0.0086	5008	,	,		18965	0.0		0.0139	False		,,,				2504	0.001				p.F367Y		Atlas-SNP	.											.	CEP68	69	.	0			c.T1100A						PASS	.	T	TYR/PHE	16,4390	22.3+/-47.3	0,16,2187	90.0	95.0	93.0		1100	2.9	0.1	2	dbSNP_134	93	169,8431	76.9+/-139.5	0,169,4131	yes	missense	CEP68	NM_015147.2	22	0,185,6318	AA,AT,TT		1.9651,0.3631,1.4224	possibly-damaging	367/758	65299330	185,12821	2203	4300	6503	SO:0001583	missense	23177	exon3			TGCCATTTTCTGG	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.1100T>A	2.37:g.65299330T>A	ENSP00000367229:p.Phe367Tyr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	77	39	0.506494	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	17	0.007783882783882784	0	0.0	6	0.016574585635359115	0	0.0	11	0.014511873350923483	T	23.4	4.415682	0.83449	0.003631	0.019651	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.16196	2.37;2.36;2.37	5.66	2.91	0.33838	.	0.460130	0.22130	N	0.064202	T	0.16854	0.0405	M	0.63428	1.95	0.09310	N	1	D;D;D;P;D	0.71674	0.995;0.987;0.983;0.933;0.998	P;P;P;P;P	0.62649	0.836;0.775;0.67;0.597;0.905	T	0.01863	-1.1258	10	0.62326	D	0.03	-11.404	6.9502	0.24540	0.0:0.0893:0.1532:0.7575	.	355;367;367;367;367	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	Y	367;367;367;355	ENSP00000367229:F367Y;ENSP00000438306:F367Y;ENSP00000260569:F367Y	ENSP00000260569:F367Y	F	+	2	0	CEP68	65152834	0.001000	0.12720	0.112000	0.21494	0.810000	0.45777	0.594000	0.24014	0.951000	0.37770	0.402000	0.26972	TTT	T|0.987;A|0.013	0.013	strong		0.567	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
KNG1	3827	hgsc.bcm.edu	37	3	186435370	186435370	+	Silent	SNP	G	G	A	rs1050274	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:186435370G>A	ENST00000265023.4	+	1	251	c.39G>A	c.(37-39)ctG>ctA	p.L13L	RP11-573D15.8_ENST00000599314.1_RNA|KNG1_ENST00000287611.2_Silent_p.L13L|KNG1_ENST00000447445.1_Silent_p.L13L	NM_001102416.2	NP_001095886.1	P01042	KNG1_HUMAN	kininogen 1	13					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)		GCTCCAGGCTGCTACTAAGTT	0.428													G|||	1953	0.389976	0.4728	0.3098	5008	,	,		15579	0.3393		0.3241	False		,,,				2504	0.455				p.L13L		Atlas-SNP	.											KNG1_ENST00000265023,NS,adenoma,0,2	KNG1	129	2	0			c.G39A						PASS	.	G	,,	2047,2359	565.1+/-381.6	473,1101,629	112.0	115.0	114.0		39,39,39	3.3	1.0	3	dbSNP_86	114	2755,5845	437.2+/-358.5	444,1867,1989	no	coding-synonymous,coding-synonymous,coding-synonymous	KNG1	NM_000893.3,NM_001102416.2,NM_001166451.1	,,	917,2968,2618	AA,AG,GG		32.0349,46.4594,36.9214	,,	13/428,13/645,13/392	186435370	4802,8204	2203	4300	6503	SO:0001819	synonymous_variant	3827	exon1			CAGGCTGCTACTA		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.39G>A	3.37:g.186435370G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_000893	A8K474|B2RCR2|C9JEX1|P01043|Q53EQ0|Q6PAU9|Q7M4P1	Silent	SNP	ENST00000265023.4	37	CCDS43183.1																																																																																			G|0.637;A|0.363	0.363	strong		0.428	KNG1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317738.1	NM_001102416	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957832	152957832	+	Missense_Mutation	SNP	C	C	A	rs1611762|rs17882377|rs372951479	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152957832C>A	ENST00000368762.1	+	1	126	c.126C>A	c.(124-126)caC>caA	p.H42Q	SPRR1A_ENST00000307122.2_Missense_Mutation_p.H42Q			P35321	SPR1A_HUMAN	small proline-rich protein 1A	42	6 X 8 AA approximate tandem repeats.		H -> Q (in dbSNP:rs1611762). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8325635, ECO:0000269|Ref.3}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCCCTGCCACCCCAAGGTGC	0.647													C|||	2531	0.505391	0.4523	0.4395	5008	,	,		14293	0.5972		0.5348	False		,,,				2504	0.499				p.H42Q		Atlas-SNP	.											.	SPRR1A	17	.	0			c.C126A						PASS	.						122.0	126.0	125.0					1																	152957832		2203	4300	6503	SO:0001583	missense	6698	exon2			CTGCCACCCCAAG	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.126C>A	1.37:g.152957832C>A	ENSP00000357751:p.His42Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	124	51	0.41129	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	1174	0.5375457875457875	234	0.47560975609756095	180	0.4972375690607735	358	0.6258741258741258	402	0.5303430079155673	C	9.564	1.119172	0.20877	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.13657	2.57;2.57	4.77	1.54	0.23209	.	0.648090	0.12758	N	0.441596	T	0.03136	0.0092	.	.	.	0.52099	P	5.3999999999998494E-5	B	0.27013	0.166	B	0.24848	0.056	T	0.40850	-0.9541	8	0.36615	T	0.2	-2.9027	7.3544	0.26711	0.3386:0.4971:0.1643:0.0	rs1611762;rs17884470;rs58509799;rs1611762	42	P35321	SPR1A_HUMAN	Q	42	ENSP00000307340:H42Q;ENSP00000357751:H42Q	ENSP00000307340:H42Q	H	+	3	2	SPRR1A	151224456	0.620000	0.27068	0.970000	0.41538	0.731000	0.41821	0.156000	0.16382	0.397000	0.25310	0.549000	0.68633	CAC	C|0.457;A|0.543	0.543	strong		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
SELPLG	6404	hgsc.bcm.edu	37	12	109017674	109017674	+	Missense_Mutation	SNP	A	A	G	rs63748999|rs372173288|rs201851784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109017674A>G	ENST00000550948.1	-	2	634	c.410T>C	c.(409-411)gTg>gCg	p.V137A	SELPLG_ENST00000388962.3_Intron|SELPLG_ENST00000228463.6_Missense_Mutation_p.V153A			Q14242	SELPL_HUMAN	selectin P ligand	137	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CTCCGTGGGCACTGGTTGAGT	0.612													G|||	1010	0.201677	0.1097	0.1412	5008	,	,		19840	0.3413		0.171	False		,,,				2504	0.2566				p.V153A		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,0,7	SELPLG	138	7	0			c.T458C						scavenged	.						159.0	124.0	136.0					12																	109017674		2199	4273	6472	SO:0001583	missense	6404	exon2			GTGGGCACTGGTT		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.410T>C	12.37:g.109017674A>G	ENSP00000447752:p.Val137Ala	Somatic	178	2	0.011236		WXS	Illumina HiSeq	Phase_I	147	35	0.238095	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	G	0.025	-1.376284	0.01214	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.12984	2.63;2.63	3.42	-5.49	0.02584	.	.	.	.	.	T	0.03390	0.0098	N	0.04880	-0.145	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.39251	-0.9623	9	0.02654	T	1	0.1678	0.7612	0.01007	0.3376:0.1925:0.2876:0.1824	.	153;137	B7Z5C7;Q14242	.;SELPL_HUMAN	A	137;153	ENSP00000447752:V137A;ENSP00000228463:V153A	ENSP00000228463:V153A	V	-	2	0	SELPLG	107541803	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.356000	0.02609	-1.321000	0.02281	-1.471000	0.01009	GTG	A|0.896;G|0.104	0.104	strong		0.612	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
CEP97	79598	hgsc.bcm.edu	37	3	101477214	101477214	+	Silent	SNP	C	C	A	rs368609945		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:101477214C>A	ENST00000341893.3	+	9	2516	c.1764C>A	c.(1762-1764)atC>atA	p.I588I	CEP97_ENST00000494050.1_Silent_p.I529I|CEP97_ENST00000327230.4_Silent_p.I588I			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	588	CCP110-binding.				cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						GTTACGAAATCCGGCTACGCA	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		21512	0.0		0.0	False		,,,				2504	0.001				p.I588I		Atlas-SNP	.											.	CEP97	122	.	0			c.C1764A						PASS	.	C		0,4406		0,0,2203	62.0	66.0	65.0		1764	-0.3	1.0	3		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEP97	NM_024548.2		0,1,6502	AA,AC,CC		0.0116,0.0,0.0077		588/866	101477214	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79598	exon9			CGAAATCCGGCTA	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"""leucine-rich repeats and IQ motif containing 2"""	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.1764C>A	3.37:g.101477214C>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	21	0.323077	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Silent	SNP	ENST00000341893.3	37	CCDS2944.1																																																																																			.	.	weak		0.463	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548	
EML1	2009	hgsc.bcm.edu	37	14	100331876	100331876	+	Silent	SNP	T	T	C	rs11160553	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:100331876T>C	ENST00000262233.6	+	3	415	c.276T>C	c.(274-276)ccT>ccC	p.P92P	EML1_ENST00000327921.9_Silent_p.P61P|EML1_ENST00000334192.4_Silent_p.P92P|EML1_ENST00000556758.1_3'UTR	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	92					brain development (GO:0007420)|hematopoietic progenitor cell differentiation (GO:0002244)|microtubule cytoskeleton organization (GO:0000226)|mitotic spindle organization (GO:0007052)|neuroblast proliferation (GO:0007405)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	calcium ion binding (GO:0005509)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Melanoma(154;0.0879)|all_epithelial(191;0.216)				AGACCCTGCCTTTAAGAACCA	0.478													T|||	917	0.183107	0.143	0.196	5008	,	,		20476	0.1369		0.3082	False		,,,				2504	0.1472				p.P92P		Atlas-SNP	.											.	EML1	97	.	0			c.T276C						PASS	.	T	,	871,3535	338.1+/-305.1	78,715,1410	97.0	89.0	91.0		276,276	2.9	1.0	14	dbSNP_120	91	2692,5908	428.1+/-355.8	435,1822,2043	no	coding-synonymous,coding-synonymous	EML1	NM_001008707.1,NM_004434.2	,	513,2537,3453	CC,CT,TT		31.3023,19.7685,27.395	,	92/835,92/816	100331876	3563,9443	2203	4300	6503	SO:0001819	synonymous_variant	2009	exon3			CCTGCCTTTAAGA	AK023861	CCDS32154.1, CCDS32155.1	14q32	2013-01-10		2002-02-15		ENSG00000066629		"""WD repeat domain containing"""	3330	protein-coding gene	gene with protein product		602033		EMAPL		9226380, 10521658	Standard	XM_005267397		Approved	EMAP, HuEMAP, ELP79	uc001ygr.3	O00423		ENST00000262233.6:c.276T>C	14.37:g.100331876T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Silent	SNP	ENST00000262233.6	37	CCDS32155.1																																																																																			T|0.760;C|0.240	0.240	strong		0.478	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707	
CCDC38	120935	hgsc.bcm.edu	37	12	96260947	96260947	+	Silent	SNP	A	A	G	rs7960706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:96260947A>G	ENST00000344280.3	-	16	2156	c.1599T>C	c.(1597-1599)ttT>ttC	p.F533F	SNRPF_ENST00000553192.1_Intron|SNRPF_ENST00000552085.1_Intron	NM_182496.2	NP_872302.2	Q502W7	CCD38_HUMAN	coiled-coil domain containing 38	533										breast(1)|endometrium(2)|large_intestine(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GTTTTGAATGAAAGACAAGTC	0.289													A|||	1574	0.314297	0.2231	0.3112	5008	,	,		18523	0.2014		0.3767	False		,,,				2504	0.4918				p.F533F		Atlas-SNP	.											.	CCDC38	45	.	0			c.T1599C						PASS	.	A		1211,3193	389.1+/-327.2	172,867,1163	60.0	58.0	59.0		1599	-4.4	0.0	12	dbSNP_116	59	3520,5074	496.3+/-374.3	766,1988,1543	no	coding-synonymous	CCDC38	NM_182496.2		938,2855,2706	GG,GA,AA		40.9588,27.4977,36.3979		533/564	96260947	4731,8267	2202	4297	6499	SO:0001819	synonymous_variant	120935	exon16			TGAATGAAAGACA	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.1599T>C	12.37:g.96260947A>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	159	62	0.389937	NM_182496	Q8N835	Silent	SNP	ENST00000344280.3	37	CCDS9056.1																																																																																			A|0.677;G|0.323	0.323	strong		0.289	CCDC38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408634.1	NM_182496	
SSPO	23145	hgsc.bcm.edu	37	7	149529970	149529970	+	RNA	SNP	G	G	T	rs55976638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149529970G>T	ENST00000378016.2	+	0	15387							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCGTGGTGCTGCCGGTCATCC	0.662													G|||	403	0.0804712	0.0061	0.085	5008	,	,		15106	0.0387		0.0994	False		,,,				2504	0.2014				p.L5128L		Atlas-SNP	.											.	.	.	.	0			c.G15384T						PASS	.	G		69,3955		1,67,1944	16.0	22.0	20.0		15403	1.3	1.0	7	dbSNP_129	20	617,7739		26,565,3587	yes	coding-synonymous	SSPO	NM_198455.2		27,632,5531	TT,TG,GG		7.3839,1.7147,5.5412		5128/5148	149529970	686,11694	2012	4178	6190			23145	exon109			GGTGCTGCCGGTC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149529970G>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				G|0.938;T|0.062	0.062	strong		0.662	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SPATA6	54558	hgsc.bcm.edu	37	1	48825355	48825355	+	Missense_Mutation	SNP	G	G	A	rs1338314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:48825355G>A	ENST00000371847.3	-	10	1161	c.997C>T	c.(997-999)Cgg>Tgg	p.R333W	SPATA6_ENST00000396199.3_Missense_Mutation_p.R261W|SPATA6_ENST00000371843.3_Missense_Mutation_p.R333W	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	333			R -> W (in dbSNP:rs1338314).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						GCTGAATGCCGGGGCTTACTA	0.458													G|||	70	0.0139776	0.0008	0.0331	5008	,	,		14053	0.0		0.0408	False		,,,				2504	0.0051				p.R333W		Atlas-SNP	.											.	SPATA6	45	.	0			c.C997T						PASS	.	G	TRP/ARG	53,4353	52.3+/-87.9	0,53,2150	102.0	97.0	99.0		997	4.1	1.0	1	dbSNP_88	99	307,8293	109.8+/-170.3	4,299,3997	yes	missense	SPATA6	NM_019073.2	101	4,352,6147	AA,AG,GG		3.5698,1.2029,2.768	possibly-damaging	333/489	48825355	360,12646	2203	4300	6503	SO:0001583	missense	54558	exon10			AATGCCGGGGCTT	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.997C>T	1.37:g.48825355G>A	ENSP00000360913:p.Arg333Trp	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	38	0.0173992673992674	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	25	0.032981530343007916	G	10.35	1.324952	0.24080	0.012029	0.035698	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.46063	2.71;2.71;2.71;0.88	4.99	4.05	0.47172	.	1.098750	0.06782	N	0.785446	T	0.06462	0.0166	N	0.08118	0	0.19945	N	0.999948	P;P;P	0.44281	0.61;0.831;0.831	B;B;B	0.39152	0.292;0.219;0.219	T	0.06092	-1.0846	10	0.51188	T	0.08	.	8.7171	0.34419	0.0803:0.2907:0.6291:0.0	rs1338314;rs17429088;rs52805877;rs59077352;rs1338314	261;333;333	B4DX17;Q9NWH7-2;Q9NWH7	.;.;SPAT6_HUMAN	W	333;333;261;174	ENSP00000360913:R333W;ENSP00000360909:R333W;ENSP00000379502:R261W;ENSP00000360907:R174W	ENSP00000360907:R174W	R	-	1	2	SPATA6	48597942	0.971000	0.33674	1.000000	0.80357	0.015000	0.08874	1.086000	0.30853	1.278000	0.44430	0.655000	0.94253	CGG	G|0.975;A|0.025	0.025	strong		0.458	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120343	38120343	+	Missense_Mutation	SNP	A	A	G	rs71317067		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38120343A>G	ENST00000406386.3	+	7	2035	c.1780A>G	c.(1780-1782)Aca>Gca	p.T594A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	594					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T594A(5)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAATAGAGCTACACGAGACAA	0.572																																					p.T594A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,5	TRIOBP	262	5	5	Substitution - Missense(5)	skin(2)|large_intestine(1)|NS(1)|prostate(1)	c.A1780G						scavenged	.						112.0	164.0	147.0					22																	38120343		1955	4165	6120	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1780A>G	22.37:g.38120343A>G	ENSP00000384312:p.Thr594Ala	Somatic	411	11	0.026764		WXS	Illumina HiSeq	Phase_I	444	14	0.0315315	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	-	7.079	0.569772	0.13560	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.20738	2.05	2.6	0.164	0.14990	.	.	.	.	.	T	0.11879	0.0289	L	0.28115	0.83	0.09310	N	0.999998	B	0.21381	0.055	B	0.12837	0.008	T	0.32745	-0.9895	9	0.26408	T	0.33	.	5.3198	0.15876	0.5376:0.0:0.0:0.4624	.	594	Q9H2D6	TARA_HUMAN	A	594	ENSP00000384312:T594A	ENSP00000384312:T594A	T	+	1	0	TRIOBP	36450289	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.521000	0.06245	-0.162000	0.10964	-1.765000	0.00666	ACA	A|0.500;G|0.500	0.500	weak		0.572	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
NOM1	64434	hgsc.bcm.edu	37	7	156761818	156761818	+	Missense_Mutation	SNP	G	G	A	rs2302445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:156761818G>A	ENST00000275820.3	+	10	2351	c.2336G>A	c.(2335-2337)cGt>cAt	p.R779H		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	779			R -> H (in dbSNP:rs2302445).			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)		CCCAGAGTCCGTTTTTTACGA	0.368													A|||	2240	0.447284	0.4334	0.5231	5008	,	,		15269	0.2778		0.5706	False		,,,				2504	0.4601				p.R779H		Atlas-SNP	.											.	NOM1	73	.	0			c.G2336A						PASS	.	A	HIS/ARG	1930,2476	621.6+/-393.8	435,1060,708	77.0	79.0	78.0		2336	2.7	1.0	7	dbSNP_100	78	4903,3697	529.1+/-381.5	1387,2129,784	yes	missense	NOM1	NM_138400.1	29	1822,3189,1492	AA,AG,GG		42.9884,43.8039,47.4627	benign	779/861	156761818	6833,6173	2203	4300	6503	SO:0001583	missense	64434	exon10			GAGTCCGTTTTTT	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.2336G>A	7.37:g.156761818G>A	ENSP00000275820:p.Arg779His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	1002	0.45879120879120877	230	0.46747967479674796	198	0.5469613259668509	154	0.2692307692307692	420	0.554089709762533	A	5.608	0.296935	0.10622	0.438039	0.570116	ENSG00000146909	ENST00000275820	T	0.12774	2.65	5.14	2.73	0.32206	.	0.453294	0.25944	N	0.027293	T	0.00012	0.0000	N	0.11789	0.175	0.44871	P	0.0021170000000000355	B	0.18461	0.028	B	0.14023	0.01	T	0.44406	-0.9330	9	0.06365	T	0.9	-13.4943	1.4392	0.02350	0.4974:0.1363:0.2347:0.1316	rs2302445;rs12698008;rs52802201;rs56649293;rs58095136;rs2302445	779	Q5C9Z4	NOM1_HUMAN	H	779	ENSP00000275820:R779H	ENSP00000275820:R779H	R	+	2	0	NOM1	156454579	0.429000	0.25530	0.960000	0.40013	0.912000	0.54170	1.128000	0.31369	0.002000	0.14630	-0.332000	0.08345	CGT	G|0.508;A|0.492	0.492	strong		0.368	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
CROCC	9696	hgsc.bcm.edu	37	1	17263290	17263290	+	Missense_Mutation	SNP	G	G	A	rs57442576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17263290G>A	ENST00000375541.5	+	9	1184	c.1115G>A	c.(1114-1116)cGg>cAg	p.R372Q	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GAGCAGCTGCGGGACAAGGTG	0.682													g|||	464	0.0926518	0.152	0.0677	5008	,	,		25223	0.0377		0.1024	False		,,,				2504	0.0767				p.R372Q		Atlas-SNP	.											.	CROCC	185	.	0			c.G1115A						PASS	.	G	GLN/ARG	659,3745		4,651,1547	37.0	34.0	35.0		1115	-2.8	0.1	1	dbSNP_129	35	749,7845		2,745,3550	no	missense	CROCC	NM_014675.3	43	6,1396,5097	AA,AG,GG		8.7154,14.9637,10.8324	benign	372/2018	17263290	1408,11590	2202	4297	6499	SO:0001583	missense	9696	exon9			AGCTGCGGGACAA	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1115G>A	1.37:g.17263290G>A	ENSP00000364691:p.Arg372Gln	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	145	8	0.0551724	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	182	0.08333333333333333	71	0.1443089430894309	23	0.06353591160220995	18	0.03146853146853147	70	0.09234828496042216	G	12.85	2.062876	0.36373	0.149637	0.087154	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.11169	2.8	4.1	-2.84	0.05751	.	.	.	.	.	T	0.00039	0.0001	L	0.28458	0.855	0.46317	P	0.0010109999999999841	B;B;B	0.25809	0.135;0.068;0.002	B;B;B	0.14023	0.01;0.005;0.002	T	0.45629	-0.9248	8	0.15499	T	0.54	.	10.356	0.43964	0.5601:0.0:0.4399:0.0	rs57442576	235;235;372	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	Q	372;253	ENSP00000364691:R372Q	ENSP00000364691:R372Q	R	+	2	0	CROCC	17135877	1.000000	0.71417	0.053000	0.19242	0.481000	0.33189	0.626000	0.24492	-0.699000	0.05077	-0.362000	0.07510	CGG	G|0.924;A|0.076	0.076	strong		0.682	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
TRAPPC11	60684	hgsc.bcm.edu	37	4	184614874	184614874	+	Silent	SNP	C	C	T	rs4862234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:184614874C>T	ENST00000334690.6	+	21	2572	c.2370C>T	c.(2368-2370)acC>acT	p.T790T	TRAPPC11_ENST00000357207.4_Silent_p.T790T|TRAPPC11_ENST00000512476.1_Silent_p.T396T	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	790					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											TGAAGCTCACCGCTGGCTTAA	0.388													C|||	1117	0.223043	0.3268	0.1974	5008	,	,		17881	0.1776		0.2177	False		,,,				2504	0.1534				p.T790T		Atlas-SNP	.											.	.	.	.	0			c.C2370T						PASS	.	C	,	1417,2989	462.3+/-353.2	223,971,1009	112.0	112.0	112.0		2370,2370	-0.9	1.0	4	dbSNP_111	112	1932,6668	341.4+/-324.0	221,1490,2589	no	coding-synonymous,coding-synonymous	C4orf41	NM_021942.4,NM_199053.1	,	444,2461,3598	TT,TC,CC		22.4651,32.1607,25.7497	,	790/1134,790/1087	184614874	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	60684	exon21			GCTCACCGCTGGC		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.2370C>T	4.37:g.184614874C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	37	CCDS34112.1																																																																																			C|0.756;T|0.244	0.244	strong		0.388	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
SNX2	6643	hgsc.bcm.edu	37	5	122165317	122165317	+	Silent	SNP	C	C	T	rs13662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:122165317C>T	ENST00000379516.2	+	15	1642	c.1534C>T	c.(1534-1536)Cta>Tta	p.L512L	SNX2_ENST00000510372.1_3'UTR|CTB-36H16.2_ENST00000565823.1_RNA|SNX2_ENST00000514949.1_Silent_p.L395L	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	512					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		GGAAGCATTCCTACCTGAAGC	0.348													C|||	193	0.0385383	0.0091	0.0187	5008	,	,		19035	0.1002		0.0398	False		,,,				2504	0.0276				p.L512L		Atlas-SNP	.											.	SNX2	42	.	0			c.C1534T						PASS	.	C		57,4349	53.6+/-89.4	1,55,2147	111.0	114.0	113.0		1534	3.0	0.6	5	dbSNP_52	113	327,8273	113.7+/-173.7	5,317,3978	no	coding-synonymous	SNX2	NM_003100.2		6,372,6125	TT,TC,CC		3.8023,1.2937,2.9525		512/520	122165317	384,12622	2203	4300	6503	SO:0001819	synonymous_variant	6643	exon15			GCATTCCTACCTG	AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"""Sorting nexins"""	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1534C>T	5.37:g.122165317C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_003100	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Silent	SNP	ENST00000379516.2	37	CCDS34217.1																																																																																			C|0.964;T|0.036	0.036	strong		0.348	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346468	140346468	+	Silent	SNP	T	T	A	rs155364	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140346468T>A	ENST00000289269.5	+	1	649	c.117T>A	c.(115-117)ccT>ccA	p.P39P	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	39					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			tACCTGGCCCTGCGGCCTCCC	0.706													A|||	2918	0.582668	0.7352	0.5994	5008	,	,		15939	0.6111		0.5209	False		,,,				2504	0.3988				p.P39P	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											PCDHAC2,NS,carcinoma,0,1	PCDHAC2	142	1	0			c.T117A						PASS	.	A	,,,,,,,,,,,,,,,,,,	3069,1221		1139,791,215	9.0	8.0	8.0		,117,,,,,,,,,,,,,,,,,117	-1.1	1.0	5	dbSNP_79	8	4360,4002		1212,1936,1033	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	2351,2727,1248	AA,AT,TT		47.8594,28.4615,41.282	,,,,,,,,,,,,,,,,,,	,39/1008,,,,,,,,,,,,,,,,,39/885	140346468	7429,5223	2145	4181	6326	SO:0001819	synonymous_variant	56134	exon1			TGGCCCTGCGGCC	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.117T>A	5.37:g.140346468T>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			T|0.409;A|0.591	0.591	strong		0.706	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
PRPF18	8559	hgsc.bcm.edu	37	10	13653653	13653653	+	Silent	SNP	A	A	G	rs1135102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13653653A>G	ENST00000378572.3	+	6	709	c.549A>G	c.(547-549)aaA>aaG	p.K183K		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	183					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						ATGATCATAAAGACATGGACA	0.393													A|||	1835	0.366414	0.4644	0.487	5008	,	,		18703	0.0615		0.4632	False		,,,				2504	0.363				p.K183K		Atlas-SNP	.											.	PRPF18	32	.	0			c.A549G						PASS	.	A		2101,2305	575.3+/-384.0	524,1053,626	138.0	128.0	131.0		549	0.9	1.0	10	dbSNP_86	131	4057,4543	558.4+/-387.2	941,2175,1184	no	coding-synonymous	PRPF18	NM_003675.3		1465,3228,1810	GG,GA,AA		47.1744,47.685,47.3474		183/343	13653653	6158,6848	2203	4300	6503	SO:0001819	synonymous_variant	8559	exon6			TCATAAAGACATG	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"""PRP18 pre-mRNA processing factor 18 homolog (yeast)"", ""PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"""			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.549A>G	10.37:g.13653653A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_003675	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																			A|0.659;G|0.341	0.341	strong		0.393	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
C6orf222	389384	hgsc.bcm.edu	37	6	36294864	36294864	+	Silent	SNP	A	A	G	rs41270098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36294864A>G	ENST00000437635.2	-	4	912	c.735T>C	c.(733-735)gcT>gcC	p.A245A		NM_001010903.4	NP_001010903.3	P0C671	CF222_HUMAN	chromosome 6 open reading frame 222	245										breast(4)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(4)|urinary_tract(4)	26						TCTGAATGATAGCATCCTCTG	0.433													A|||	166	0.033147	0.0053	0.0591	5008	,	,		22631	0.004		0.0954	False		,,,				2504	0.0184				p.A245A		Atlas-SNP	.											.	C6orf222	72	.	0			c.T735C						PASS	.	A		129,4277	93.4+/-132.2	1,127,2075	176.0	160.0	165.0		735	-9.0	0.0	6	dbSNP_127	165	992,7608	214.9+/-254.4	63,866,3371	no	coding-synonymous	C6orf222	NM_001010903.4		64,993,5446	GG,GA,AA		11.5349,2.9278,8.6191		245/653	36294864	1121,11885	2203	4300	6503	SO:0001819	synonymous_variant	389384	exon4			AATGATAGCATCC		CCDS34439.1	6p21.31	2012-02-22			ENSG00000189325	ENSG00000189325			33769	protein-coding gene	gene with protein product							Standard	NM_001010903		Approved	DKFZp779B1540	uc003oly.3	P0C671	OTTHUMG00000014591	ENST00000437635.2:c.735T>C	6.37:g.36294864A>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	NM_001010903	B2RTY8	Silent	SNP	ENST00000437635.2	37	CCDS34439.1																																																																																			A|0.926;G|0.074	0.074	strong		0.433	C6orf222-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040338.2	NM_001010903	
ZNF17	7565	hgsc.bcm.edu	37	19	57931553	57931553	+	Silent	SNP	C	C	T	rs10417533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57931553C>T	ENST00000601808.1	+	3	906	c.693C>T	c.(691-693)tcC>tcT	p.S231S	ZNF17_ENST00000307658.7_Silent_p.S233S|AC004076.7_ENST00000597410.1_Intron	NM_006959.2	NP_008890.2	P17021	ZNF17_HUMAN	zinc finger protein 17	231					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.0234)|GBM - Glioblastoma multiforme(193;0.000426)|Lung(386;0.176)		GGTACAACTCCGACCTTATTA	0.413													C|||	1133	0.226238	0.3449	0.2176	5008	,	,		23816	0.0794		0.2694	False		,,,				2504	0.1789				p.S231S	Melanoma(149;1637 1853 29914 42869 44988)	Atlas-SNP	.											.	ZNF17	49	.	0			c.C693T						PASS	.	C		1306,3092	411.3+/-335.7	195,916,1088	87.0	89.0	89.0		693	-3.5	0.0	19	dbSNP_119	89	2171,6427	363.7+/-333.3	274,1623,2402	no	coding-synonymous	ZNF17	NM_006959.2		469,2539,3490	TT,TC,CC		25.2501,29.6953,26.7544		231/663	57931553	3477,9519	2199	4299	6498	SO:0001819	synonymous_variant	7565	exon3			CAACTCCGACCTT	X52341	CCDS42636.1	19q13.43	2013-01-08	2006-05-10			ENSG00000186272		"""Zinc fingers, C2H2-type"", ""-"""	12958	protein-coding gene	gene with protein product			"""zinc finger protein 17 (HPF3, KOX 10)"""			2115127, 2014798	Standard	NM_006959		Approved	HPF3, KOX10, KIAA1947, FLJ40864, FLJ46058, FLJ46615	uc002qoo.1	P17021		ENST00000601808.1:c.693C>T	19.37:g.57931553C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_006959	B3KXU2|B3KY20|Q8N7M1|Q8N893|Q8TF54	Silent	SNP	ENST00000601808.1	37	CCDS42636.1																																																																																			C|0.772;T|0.228	0.228	strong		0.413	ZNF17-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466384.1	NM_006959	
TMEM132A	54972	hgsc.bcm.edu	37	11	60704213	60704213	+	Missense_Mutation	SNP	C	C	T	rs2469887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60704213C>T	ENST00000453848.2	+	11	3064	c.2906C>T	c.(2905-2907)gCg>gTg	p.A969V	TMEM132A_ENST00000005286.4_Missense_Mutation_p.A970V			Q24JP5	T132A_HUMAN	transmembrane protein 132A	969	Confers cellular localization similar to full-length form. {ECO:0000250}.		A -> V (in dbSNP:rs2469887). {ECO:0000269|PubMed:14702039}.			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						GTGACATTTGCGCCAGCCCCT	0.672													C|||	2113	0.421925	0.4735	0.4467	5008	,	,		16318	0.3165		0.4225	False		,,,				2504	0.4427				p.A970V		Atlas-SNP	.											.	TMEM132A	135	.	0			c.C2909T						PASS	.	C	VAL/ALA,VAL/ALA	2057,2349	530.1+/-372.8	469,1119,615	23.0	28.0	27.0		2909,2906	3.7	0.2	11	dbSNP_100	27	3702,4896	503.5+/-375.9	801,2100,1398	yes	missense,missense	TMEM132A	NM_017870.3,NM_178031.2	64,64	1270,3219,2013	TT,TC,CC		43.0565,46.6863,44.2864	probably-damaging,probably-damaging	970/1025,969/1024	60704213	5759,7245	2203	4299	6502	SO:0001583	missense	54972	exon11			CATTTGCGCCAGC	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.2906C>T	11.37:g.60704213C>T	ENSP00000405823:p.Ala969Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	901	0.4125457875457875	232	0.4715447154471545	164	0.4530386740331492	185	0.32342657342657344	320	0.42216358839050133	C	13.07	2.127516	0.37533	0.466863	0.430565	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	T;T	0.06608	3.28;3.28	4.61	3.7	0.42460	.	0.312828	0.26149	N	0.026050	T	0.00012	0.0000	L	0.59436	1.845	0.36902	P	0.10954900000000001	B;B	0.24132	0.098;0.098	B;B	0.12837	0.008;0.008	T	0.45775	-0.9238	9	0.87932	D	0	-17.4679	5.1482	0.14996	0.1462:0.6297:0.1422:0.0819	rs2469887;rs56748518;rs2469887	969;970	Q24JP5;Q24JP5-2	T132A_HUMAN;.	V	720;969;970	ENSP00000405823:A969V;ENSP00000005286:A970V	ENSP00000005286:A970V	A	+	2	0	TMEM132A	60460789	0.939000	0.31865	0.222000	0.23844	0.691000	0.40173	4.120000	0.57897	1.312000	0.45043	0.655000	0.94253	GCG	C|0.570;T|0.430	0.430	strong		0.672	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
SP110	3431	hgsc.bcm.edu	37	2	231042276	231042276	+	Missense_Mutation	SNP	A	A	G	rs1135791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231042276A>G	ENST00000358662.4	-	14	1646	c.1568T>C	c.(1567-1569)aTg>aCg	p.M523T	SP110_ENST00000392048.3_Missense_Mutation_p.M521T|SP110_ENST00000258382.5_Missense_Mutation_p.M523T|SP110_ENST00000540870.1_Missense_Mutation_p.M529T|SP110_ENST00000338556.3_Missense_Mutation_p.M225T|SP110_ENST00000258381.6_Missense_Mutation_p.M523T	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	523	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.		M -> T (in dbSNP:rs1135791). {ECO:0000269|PubMed:10913195, ECO:0000269|PubMed:16803959}.		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)		TCCTAGGGTCATTCCTTCACA	0.423													G|||	1627	0.32488	0.208	0.3545	5008	,	,		20126	0.1677		0.496	False		,,,				2504	0.4479				p.M529T		Atlas-SNP	.											.	SP110	105	.	0			c.T1586C						PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET	1124,3282	717.8+/-408.8	128,868,1207	370.0	347.0	355.0		1586,1568,1568,1568	-0.8	0.0	2	dbSNP_86	355	4306,4294	577.4+/-390.5	1110,2086,1104	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	81,81,81,81	1238,2954,2311	GG,GA,AA		49.9302,25.5107,41.75	benign,benign,benign,benign	529/556,523/690,523/550,523/714	231042276	5430,7576	2203	4300	6503	SO:0001583	missense	3431	exon15			AGGGTCATTCCTT	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.1568T>C	2.37:g.231042276A>G	ENSP00000351488:p.Met523Thr	Somatic	317	1	0.00315457		WXS	Illumina HiSeq	Phase_I	351	171	0.487179	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	738	0.33791208791208793	120	0.24390243902439024	146	0.40331491712707185	97	0.16958041958041958	375	0.4947229551451187	G	3.063	-0.192867	0.06259	0.255107	0.500698	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	4.61	-0.782	0.10961	SAND domain-like (2);SAND domain (3);	0.977573	0.08310	N	0.965581	T	0.00012	0.0000	N	0.02247	-0.625	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	0.41928	-0.9481	9	0.21014	T	0.42	.	0.2939	0.00262	0.2799:0.1726:0.15:0.3975	rs1135791;rs1804027;rs3198703;rs11556889;rs17327944;rs59171471;rs1135791	521;225;529;523;523	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	T	523;523;521;523;529;225	ENSP00000258381:M523T;ENSP00000351488:M523T;ENSP00000375902:M521T;ENSP00000258382:M523T;ENSP00000439558:M529T;ENSP00000344049:M225T	ENSP00000258381:M523T	M	-	2	0	SP110	230750520	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.527000	0.06200	-0.498000	0.06632	-1.974000	0.00461	ATG	A|0.640;G|0.360	0.360	strong		0.423	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
OR13C5	138799	hgsc.bcm.edu	37	9	107360826	107360826	+	Missense_Mutation	SNP	A	A	G	rs1851725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107360826A>G	ENST00000374779.2	-	1	962	c.869T>C	c.(868-870)aTg>aCg	p.M290T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	290			M -> T (in dbSNP:rs1851725).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AGGATTCATCATGGGAGTCAT	0.373													G|||	2184	0.436102	0.6475	0.2277	5008	,	,		20206	0.5754		0.1789	False		,,,				2504	0.4192				p.M290T		Atlas-SNP	.											.	OR13C5	60	.	0			c.T869C						PASS	.	G	THR/MET	2577,1829	532.5+/-373.5	762,1053,388	112.0	114.0	113.0		869	-0.1	0.0	9	dbSNP_92	113	1669,6931	739.5+/-407.1	183,1303,2814	yes	missense	OR13C5	NM_001004482.1	81	945,2356,3202	GG,GA,AA		19.407,41.5116,32.6465	benign	290/319	107360826	4246,8760	2203	4300	6503	SO:0001583	missense	138799	exon1			TTCATCATGGGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.869T>C	9.37:g.107360826A>G	ENSP00000363911:p.Met290Thr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	154	67	0.435065	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	839	0.3841575091575092	297	0.6036585365853658	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	G	9.506	1.104528	0.20632	0.584884	0.19407	ENSG00000255800	ENST00000374779	T	0.37411	1.2	4.03	-0.0854	0.13686	GPCR, rhodopsin-like superfamily (1);	0.153284	0.29660	N	0.011536	T	0.00012	0.0000	M	0.80508	2.5	0.49687	P	1.8499999999999073E-4	B	0.17268	0.021	B	0.20577	0.03	T	0.34675	-0.9819	9	0.45353	T	0.12	.	4.7671	0.13137	0.6686:0.0:0.191:0.1404	rs1851725;rs58161788;rs1851725	290	Q8NGS8	O13C5_HUMAN	T	290	ENSP00000363911:M290T	ENSP00000363911:M290T	M	-	2	0	OR13C5	106400647	0.002000	0.14202	0.005000	0.12908	0.202000	0.24057	1.919000	0.40015	-0.437000	0.07243	-2.339000	0.00246	ATG	A|0.634;G|0.366	0.366	strong		0.373	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
MRPS10	55173	hgsc.bcm.edu	37	6	42185564	42185564	+	Silent	SNP	A	A	C	rs9471809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42185564A>C	ENST00000053468.3	-	1	39	c.24T>G	c.(22-24)ggT>ggG	p.G8G		NM_018141.3	NP_060611.2	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	8						mitochondrion (GO:0005739)|ribosome (GO:0005840)				endometrium(1)|lung(1)	2	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			GGCACACAGCACCGAACGCTG	0.607													C|||	1485	0.296526	0.6906	0.2579	5008	,	,		14949	0.1141		0.2038	False		,,,				2504	0.0746				p.G8G		Atlas-SNP	.											.	MRPS10	9	.	0			c.T24G						PASS	.	C		2567,1839		765,1037,401	24.0	28.0	27.0		24	-10.5	0.0	6	dbSNP_119	27	1825,6775		202,1421,2677	no	coding-synonymous	MRPS10	NM_018141.3		967,2458,3078	CC,CA,AA		21.2209,41.7385,33.769		8/202	42185564	4392,8614	2203	4300	6503	SO:0001819	synonymous_variant	55173	exon1			CACAGCACCGAAC		CCDS4866.1	6p21.1	2012-09-13			ENSG00000048544	ENSG00000048544		"""Mitochondrial ribosomal proteins / small subunits"""	14502	protein-coding gene	gene with protein product		611976				11279123	Standard	NM_018141		Approved	FLJ10567	uc003osa.4	P82664	OTTHUMG00000014694	ENST00000053468.3:c.24T>G	6.37:g.42185564A>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_018141	B2RE89|Q9H3E5|Q9NVR3	Silent	SNP	ENST00000053468.3	37	CCDS4866.1																																																																																			A|0.679;C|0.321	0.321	strong		0.607	MRPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040547.1		
ATL2	64225	hgsc.bcm.edu	37	2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	rs34873284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:38537579T>C	ENST00000378954.4	-	8	816	c.815A>G	c.(814-816)aAt>aGt	p.N272S	ATL2_ENST00000539122.1_Missense_Mutation_p.N101S|ATL2_ENST00000452935.2_Missense_Mutation_p.N254S|ATL2_ENST00000406122.1_Missense_Mutation_p.N101S|ATL2_ENST00000332337.4_Missense_Mutation_p.N254S|ATL2_ENST00000546051.1_Missense_Mutation_p.N101S|ATL2_ENST00000402054.1_Missense_Mutation_p.N101S|ATL2_ENST00000419554.2_Missense_Mutation_p.N272S	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	272	GB1/RHD3-type G.		N -> S (in dbSNP:rs34873284).		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						TTCATGTTGATTTTGTTTTAC	0.383													T|||	72	0.014377	0.0045	0.0216	5008	,	,		17843	0.0		0.0398	False		,,,				2504	0.0112				p.N272S		Atlas-SNP	.											.	ATL2	49	.	0			c.A815G						PASS	.	T	SER/ASN,SER/ASN	48,4358	48.9+/-83.8	1,46,2156	133.0	118.0	123.0		815,815	5.1	1.0	2	dbSNP_126	123	420,8180	130.8+/-188.7	10,400,3890	yes	missense,missense	ATL2	NM_001135673.1,NM_022374.2	46,46	11,446,6046	CC,CT,TT		4.8837,1.0894,3.5983	benign,benign	272/584,272/580	38537579	468,12538	2203	4300	6503	SO:0001583	missense	64225	exon8			TGTTGATTTTGTT		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.815A>G	2.37:g.38537579T>C	ENSP00000368237:p.Asn272Ser	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	40|40	0.018315018315018316|0.018315018315018316	4|4	0.008130081300813009|0.008130081300813009	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	31|31	0.040897097625329816|0.040897097625329816	T|T	15.82|15.82	2.945674|2.945674	0.53079|0.53079	0.010894|0.010894	0.048837|0.048837	ENSG00000119787|ENSG00000119787	ENST00000443098|ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051;ENST00000449130	.|T;T;T;T;T;T;T;T;T	.|0.74421	.|-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	5.11|5.11	5.11|5.11	0.69529|0.69529	.|Guanylate-binding protein, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.28764|0.28764	0.0713|0.0713	L|L	0.47078|0.47078	1.49|1.49	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B	.|0.17268	.|0.021;0.001;0.003;0.005;0.001	.|B;B;B;B;B	.|0.11329	.|0.006;0.001;0.001;0.002;0.002	T|T	0.53542|0.53542	-0.8424|-0.8424	5|10	.|0.44086	.|T	.|0.13	-21.5939|-21.5939	14.0983|14.0983	0.65037|0.65037	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34873284;rs61754250|rs34873284;rs61754250	.|101;254;254;272;272	.|B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.|.;.;.;.;ATLA2_HUMAN	V|S	191|272;101;101;101;254;272;254;101;90	.|ENSP00000368237:N272S;ENSP00000385446:N101S;ENSP00000384062:N101S;ENSP00000446192:N101S;ENSP00000333393:N254S;ENSP00000415336:N272S;ENSP00000390743:N254S;ENSP00000438938:N101S;ENSP00000409811:N90S	.|ENSP00000333393:N254S	I|N	-|-	1|2	0|0	ATL2|ATL2	38391083|38391083	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.982000|0.982000	0.71751|0.71751	6.134000|6.134000	0.71689|0.71689	1.917000|1.917000	0.55516|0.55516	0.455000|0.455000	0.32223|0.32223	ATC|AAT	T|0.967;C|0.033	0.033	strong		0.383	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374	
MAP4	4134	hgsc.bcm.edu	37	3	48040283	48040283	+	Missense_Mutation	SNP	C	C	T	rs11711953	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:48040283C>T	ENST00000360240.6	-	2	586	c.68G>A	c.(67-69)cGg>cAg	p.R23Q	MAP4_ENST00000439356.1_Missense_Mutation_p.R23Q|MAP4_ENST00000383737.4_Missense_Mutation_p.R23Q|MAP4_ENST00000395734.3_Missense_Mutation_p.R23Q|MAP4_ENST00000434267.1_Missense_Mutation_p.R23Q|MAP4_ENST00000426837.2_Missense_Mutation_p.R23Q	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	23			R -> Q (in dbSNP:rs11711953).		cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	AATGAAGTCCCGCTTTATCTC	0.468													C|||	146	0.0291534	0.0008	0.0346	5008	,	,		19003	0.0		0.0726	False		,,,				2504	0.0491				p.R23Q		Atlas-SNP	.											.	MAP4	176	.	0			c.G68A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	74,4332	65.8+/-103.3	0,74,2129	187.0	168.0	175.0		68,68,68	4.6	1.0	3	dbSNP_120	175	672,7928	168.7+/-220.2	21,630,3649	yes	missense,missense,missense	MAP4	NM_001134364.1,NM_002375.4,NM_030885.3	43,43,43	21,704,5778	TT,TC,CC		7.814,1.6795,5.7358	probably-damaging,probably-damaging,probably-damaging	23/1136,23/1153,23/100	48040283	746,12260	2203	4300	6503	SO:0001583	missense	4134	exon2			AAGTCCCGCTTTA		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.68G>A	3.37:g.48040283C>T	ENSP00000353375:p.Arg23Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	165	84	0.509091	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	75|75	0.034340659340659344|0.034340659340659344	1|1	0.0020325203252032522|0.0020325203252032522	14|14	0.03867403314917127|0.03867403314917127	0|0	0.0|0.0	60|60	0.079155672823219|0.079155672823219	C|C	18.82|18.82	3.704374|3.704374	0.68615|0.68615	0.016795|0.016795	0.07814|0.07814	ENSG00000047849|ENSG00000047849	ENST00000423088|ENST00000383737;ENST00000395734;ENST00000426837;ENST00000360240;ENST00000434267;ENST00000439356	.|T;T;T;T;T;T	.|0.52295	.|0.67;0.67;0.67;0.67;0.67;0.67	4.56|4.56	4.56|4.56	0.56223|0.56223	.|.	.|.	.|.	.|.	.|.	T|T	0.08537|0.08537	0.0212|0.0212	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.999;1.0;1.0	.|D;D;D;D	.|0.85130	.|0.994;0.99;0.997;0.996	T|T	0.11372|0.11372	-1.0590|-1.0590	5|9	.|0.39692	.|T	.|0.17	-7.7369|-7.7369	13.0269|13.0269	0.58821|0.58821	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs11711953;rs52793755;rs61530442;rs11711953|rs11711953;rs52793755;rs61530442;rs11711953	.|23;23;23;23	.|C9JFC3;Q86V26;P27816-6;P27816	.|.;.;.;MAP4_HUMAN	R|Q	30|23	.|ENSP00000373243:R23Q;ENSP00000379083:R23Q;ENSP00000407602:R23Q;ENSP00000353375:R23Q;ENSP00000402767:R23Q;ENSP00000397414:R23Q	.|ENSP00000353375:R23Q	G|R	-|-	1|2	0|0	MAP4|MAP4	48015287|48015287	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.939000|0.939000	0.58152|0.58152	2.639000|2.639000	0.46570|0.46570	2.535000|2.535000	0.85469|0.85469	0.467000|0.467000	0.42956|0.42956	GGG|CGG	C|0.948;T|0.052	0.052	strong		0.468	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
BAG6	7917	hgsc.bcm.edu	37	6	31606977	31606977	+	Silent	SNP	C	C	T	rs34745996	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31606977C>T	ENST00000375964.6	-	25	3643	c.3330G>A	c.(3328-3330)ctG>ctA	p.L1110L	BAG6_ENST00000375976.4_Silent_p.L1104L|BAG6_ENST00000404765.2_Silent_p.L1140L|BAG6_ENST00000211379.5_Silent_p.L1104L|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000362049.6_Silent_p.L1055L|BAG6_ENST00000439687.2_Silent_p.L881L	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	1110					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						GGTCTTCCTGCAGTCGTTTTT	0.532													C|||	111	0.0221645	0.0023	0.0043	5008	,	,		15490	0.0119		0.002	False		,,,				2504	0.093				p.L1110L		Atlas-SNP	.											.	BAG6	73	.	0			c.G3330A						PASS	.	C	,,,,,	19,4387	26.2+/-53.5	0,19,2184	51.0	48.0	49.0		3312,2643,3165,3330,3312,3312	3.4	1.0	6	dbSNP_126	49	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAG6	NM_001098534.1,NM_001199697.1,NM_001199698.1,NM_004639.3,NM_080702.2,NM_080703.2	,,,,,	0,41,6462	TT,TC,CC		0.2558,0.4312,0.3152	,,,,,	1104/1127,881/904,1055/1078,1110/1133,1104/1127,1104/1127	31606977	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	7917	exon25			TTCCTGCAGTCGT	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.3330G>A	6.37:g.31606977C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_004639	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Silent	SNP	ENST00000375964.6	37	CCDS47403.1	5	0.0022893772893772895	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	C	7.007	0.555995	0.13436	0.004312	0.002558	ENSG00000204463	ENST00000422948;ENST00000441793	.	.	.	5.38	3.4	0.38934	.	.	.	.	.	T	0.31827	0.0809	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32295	-0.9912	4	.	.	.	.	3.0714	0.06231	0.3594:0.4148:0.1377:0.088	rs34745996	.	.	.	Y	114;204	.	.	C	-	2	0	BAG6	31714956	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.653000	0.24902	1.445000	0.47624	0.655000	0.94253	TGC	C|0.997;T|0.003	0.003	strong		0.532	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_080703	
TPCN2	219931	hgsc.bcm.edu	37	11	68840160	68840160	+	Missense_Mutation	SNP	A	A	G	rs3750965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68840160A>G	ENST00000294309.3	+	12	1228	c.1127A>G	c.(1126-1128)aAa>aGa	p.K376R	TPCN2_ENST00000542467.1_Missense_Mutation_p.K376R|TPCN2_ENST00000442692.2_Intron	NM_139075.3	NP_620714.2	Q8NHX9	TPC2_HUMAN	two pore segment channel 2	376			K -> R (in dbSNP:rs3750965).		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)			AGCTCCCACAAACAGGCCATG	0.632													A|||	1456	0.290735	0.2322	0.1945	5008	,	,		15326	0.2063		0.3032	False		,,,				2504	0.5123				p.K376R		Atlas-SNP	.											TPCN2,colon,carcinoma,0,1	TPCN2	63	1	0			c.A1127G						PASS	.	A	ARG/LYS	1078,3322	387.7+/-326.6	133,812,1255	51.0	49.0	50.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1127	2.6	0.0	11	dbSNP_107	50	2710,5878	429.7+/-356.3	408,1894,1992	yes	missense	TPCN2	NM_139075.3	26	541,2706,3247	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	31.5557,24.5,29.1654	benign	376/753	68840160	3788,9200	2200	4294	6494	SO:0001583	missense	219931	exon12			CCCACAAACAGGC	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.1127A>G	11.37:g.68840160A>G	ENSP00000294309:p.Lys376Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_139075	Q9NT82	Missense_Mutation	SNP	ENST00000294309.3	37	CCDS8189.1	558	0.2554945054945055	104	0.21138211382113822	83	0.2292817679558011	135	0.23601398601398602	236	0.3113456464379947	A	0.628	-0.818239	0.02776	0.245	0.315557	ENSG00000162341	ENST00000294309;ENST00000535009;ENST00000542467	D;D	0.96913	-4.16;-4.17	4.94	2.61	0.31194	.	0.188884	0.44688	N	0.000427	T	0.00039	0.0001	M	0.64997	1.995	0.33812	P	0.37205200000000005	B;B;B	0.33379	0.287;0.287;0.41	B;B;B	0.29524	0.048;0.048;0.103	T	0.00862	-1.1536	9	0.25106	T	0.35	-5.9663	6.5291	0.22316	0.8026:0.0:0.1974:0.0	rs3750965;rs57180849;rs3750965	376;376;291	E7ETX0;Q8NHX9;F5H1G5	.;TPC2_HUMAN;.	R	376;291;376	ENSP00000294309:K376R;ENSP00000445551:K376R	ENSP00000294309:K376R	K	+	2	0	TPCN2	68596736	0.057000	0.20700	0.030000	0.17652	0.117000	0.20001	0.272000	0.18644	0.327000	0.23409	0.459000	0.35465	AAA	A|0.718;G|0.282	0.282	strong		0.632	TPCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396878.2	NM_139075	
ANKRD13C	81573	hgsc.bcm.edu	37	1	70820008	70820008	+	Silent	SNP	C	C	T	rs61782675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:70820008C>T	ENST00000370944.4	-	1	397	c.84G>A	c.(82-84)gaG>gaA	p.E28E	HHLA3_ENST00000359875.5_5'Flank|HHLA3_ENST00000432224.1_5'Flank|ANKRD13C_ENST00000262346.6_Silent_p.E28E|HHLA3_ENST00000370940.5_5'Flank|HHLA3_ENST00000361764.4_5'Flank|HHLA3_ENST00000531950.1_5'Flank	NM_030816.4	NP_110443.3	Q8N6S4	AN13C_HUMAN	ankyrin repeat domain 13C	28					protein retention in ER lumen (GO:0006621)|regulation of anoikis (GO:2000209)|regulation of receptor biosynthetic process (GO:0010869)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	19						CCGCCGCTTCCTCATCCCCGG	0.622													C|||	471	0.0940495	0.0325	0.0908	5008	,	,		16430	0.0645		0.1054	False		,,,				2504	0.1984				p.E28E		Atlas-SNP	.											.	ANKRD13C	36	.	0			c.G84A						PASS	.	C		171,4235		5,161,2037	34.0	41.0	39.0		84	1.8	1.0	1	dbSNP_129	39	763,7833		28,707,3563	no	coding-synonymous	ANKRD13C	NM_030816.4		33,868,5600	TT,TC,CC		8.8762,3.8811,7.1835		28/542	70820008	934,12068	2203	4298	6501	SO:0001819	synonymous_variant	81573	exon1			CGCTTCCTCATCC		CCDS648.2	1p32.3-p31.3	2013-01-10			ENSG00000118454	ENSG00000118454		"""Ankyrin repeat domain containing"""	25374	protein-coding gene	gene with protein product		615125				11230166	Standard	NM_030816		Approved	DKFZP566D1346, dJ677H15.3	uc001dex.4	Q8N6S4	OTTHUMG00000009343	ENST00000370944.4:c.84G>A	1.37:g.70820008C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_030816	B3KQ97|Q5VYH4|Q5VYH5|Q6PJE4|Q9H0N9	Silent	SNP	ENST00000370944.4	37	CCDS648.2																																																																																			C|0.928;T|0.072	0.072	strong		0.622	ANKRD13C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025903.1	NM_030816	
GPR78	27201	hgsc.bcm.edu	37	4	8589023	8589023	+	Missense_Mutation	SNP	G	G	A	rs9685931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:8589023G>A	ENST00000382487.4	+	3	1442	c.1025G>A	c.(1024-1026)cGc>cAc	p.R342H	GPR78_ENST00000509216.1_3'UTR	NM_080819.4	NP_543009.2	Q96P69	GPR78_HUMAN	G protein-coupled receptor 78	342			R -> H (in dbSNP:rs9685931).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(4)|kidney(4)|large_intestine(1)|lung(8)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	26						AGAACCCCGCGCCCAGCGTCC	0.637													G|||	585	0.116813	0.2035	0.0548	5008	,	,		16899	0.0427		0.1143	False		,,,				2504	0.1227				p.R342H		Atlas-SNP	.											GPR78,NS,carcinoma,0,3	GPR78	58	3	0			c.G1025A						PASS	.	G	HIS/ARG	863,3539		83,697,1421	42.0	47.0	45.0		1025	-4.0	0.0	4	dbSNP_119	45	941,7645		51,839,3403	yes	missense	GPR78	NM_080819.2	29	134,1536,4824	AA,AG,GG		10.9597,19.6047,13.8897	benign	342/364	8589023	1804,11184	2201	4293	6494	SO:0001583	missense	27201	exon3			CCCCGCGCCCAGC	AF411107	CCDS3403.1	4p16.1	2012-08-21			ENSG00000155269	ENSG00000155269		"""GPCR / Class A : Orphans"""	4528	protein-coding gene	gene with protein product		606921				11574155	Standard	NM_080819		Approved		uc003glk.4	Q96P69	OTTHUMG00000128483	ENST00000382487.4:c.1025G>A	4.37:g.8589023G>A	ENSP00000371927:p.Arg342His	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	221	122	0.552036	NM_080819	Q8NGV3	Missense_Mutation	SNP	ENST00000382487.4	37	CCDS3403.1	249	0.11401098901098901	112	0.22764227642276422	24	0.06629834254143646	25	0.043706293706293704	88	0.11609498680738786	G	0.040	-1.286694	0.01387	0.196047	0.109597	ENSG00000155269	ENST00000382487	T	0.61742	0.08	2.02	-4.03	0.04021	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06734	-1.0810	8	0.25106	T	0.35	.	3.3539	0.07162	0.1861:0.1529:0.509:0.152	rs9685931;rs17857471;rs52825020;rs9685931	342	Q96P69	GPR78_HUMAN	H	342	ENSP00000371927:R342H	ENSP00000371927:R342H	R	+	2	0	GPR78	8639923	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-2.614000	0.00443	-2.912000	0.00091	CGC	G|0.871;A|0.129	0.129	strong		0.637	GPR78-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359201.1		
CD3EAP	10849	hgsc.bcm.edu	37	19	45912750	45912750	+	Silent	SNP	G	G	A	rs118178942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45912750G>A	ENST00000309424.3	+	3	2012	c.1524G>A	c.(1522-1524)caG>caA	p.Q508Q	ERCC1_ENST00000588738.1_5'Flank|CD3EAP_ENST00000589804.1_Silent_p.Q510Q|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	508	Poly-Gln.				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)		AGCAGCAGCAGCCTGTGTAGT	0.617													G|||	36	0.0071885	0.0	0.0144	5008	,	,		14483	0.0		0.0189	False		,,,				2504	0.0072				p.Q508Q		Atlas-SNP	.											.	CD3EAP	27	.	0			c.G1524A						PASS	.	G	,,	17,4341		0,17,2162	12.0	14.0	13.0		,,1524	-0.8	0.0	19	dbSNP_132	13	137,8421		1,135,4143	no	utr-3,utr-3,coding-synonymous	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,	1,152,6305	AA,AG,GG		1.6008,0.3901,1.1923	,,	,,508/511	45912750	154,12762	2179	4279	6458	SO:0001819	synonymous_variant	10849	exon3			GCAGCAGCCTGTG	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.1524G>A	19.37:g.45912750G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Silent	SNP	ENST00000309424.3	37	CCDS12661.1																																																																																			G|0.990;A|0.010	0.010	strong		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
KTN1	3895	hgsc.bcm.edu	37	14	56105908	56105908	+	Silent	SNP	C	C	T	rs80214241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:56105908C>T	ENST00000395314.3	+	13	1859	c.1791C>T	c.(1789-1791)tcC>tcT	p.S597S	KTN1_ENST00000438792.2_Silent_p.S597S|KTN1_ENST00000395309.3_Silent_p.S597S|KTN1_ENST00000395311.1_Silent_p.S597S|KTN1_ENST00000413890.2_Silent_p.S597S|KTN1_ENST00000395308.1_Silent_p.S597S|KTN1_ENST00000416613.1_Silent_p.S597S	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	597					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						CTTAGACCTCCGCTTCAGTTC	0.313			T	RET	papillary thryoid								C|||	73	0.0145767	0.0219	0.0014	5008	,	,		17209	0.003		0.002	False		,,,				2504	0.0389				p.S597S		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.C1791T						PASS	.	C	,,,	73,4331	65.8+/-103.3	2,69,2131	91.0	90.0	90.0		1791,1791,1791,1791	-6.3	0.9	14	dbSNP_132	90	31,8567	22.2+/-67.0	0,31,4268	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	2,100,6399	TT,TC,CC		0.3605,1.6576,0.7999	,,,	597/1358,597/1307,597/1301,597/1358	56105908	104,12898	2202	4299	6501	SO:0001819	synonymous_variant	3895	exon13			GACCTCCGCTTCA		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.1791C>T	14.37:g.56105908C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	174	78	0.448276	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																			C|0.991;T|0.009	0.009	strong		0.313	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
PLA2G4A	5321	hgsc.bcm.edu	37	1	186946869	186946869	+	Missense_Mutation	SNP	A	A	G	rs28395831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186946869A>G	ENST00000367466.3	+	16	2061	c.1909A>G	c.(1909-1911)Atc>Gtc	p.I637V	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.I577V	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	637	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		I -> V (in dbSNP:rs28395831).		arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TTGCCCAACCATCATCCACTT	0.418													A|||	33	0.00658946	0.0015	0.0014	5008	,	,		19824	0.0		0.0189	False		,,,				2504	0.0112				p.I637V		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.A1909G						PASS	.	A	VAL/ILE	6,4400	11.4+/-27.6	0,6,2197	121.0	112.0	115.0		1909	3.7	0.6	1	dbSNP_126	115	94,8506	53.6+/-114.3	0,94,4206	yes	missense	PLA2G4A	NM_024420.2	29	0,100,6403	GG,GA,AA		1.093,0.1362,0.7689	benign	637/750	186946869	100,12906	2203	4300	6503	SO:0001583	missense	5321	exon16			CCAACCATCATCC	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.1909A>G	1.37:g.186946869A>G	ENSP00000356436:p.Ile637Val	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	219	97	0.442922	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	37	CCDS1372.1	15	0.006868131868131868	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	A	7.587	0.670036	0.14776	0.001362	0.01093	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.03124	4.04;4.04	5.98	3.68	0.42216	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.250277	0.47093	N	0.000250	T	0.00784	0.0026	N	0.03177	-0.4	0.36550	D	0.871822	B;B	0.11235	0.004;0.003	B;B	0.21708	0.036;0.026	T	0.42849	-0.9427	10	0.02654	T	1	-15.1412	8.1494	0.31132	0.7827:0.0:0.2173:0.0	rs28395831;rs45544833	577;637	E7EU42;P47712	.;PA24A_HUMAN	V	637;577	ENSP00000356436:I637V;ENSP00000406892:I577V	ENSP00000356436:I637V	I	+	1	0	PLA2G4A	185213492	0.996000	0.38824	0.615000	0.29064	0.985000	0.73830	3.247000	0.51422	0.516000	0.28340	0.533000	0.62120	ATC	A|0.992;G|0.008	0.008	strong		0.418	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420	
PRR22	163154	hgsc.bcm.edu	37	19	5783634	5783634	+	Silent	SNP	T	T	C	rs2446210	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5783634T>C	ENST00000419421.2	-	3	728	c.624A>G	c.(622-624)ccA>ccG	p.P208P		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	208	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						TGTAGGCGTCTGGGGGCAGTG	0.706													C|||	2259	0.451078	0.7769	0.2334	5008	,	,		11349	0.5496		0.1928	False		,,,				2504	0.3292				p.P208P		Atlas-SNP	.											.	PRR22	25	.	0			c.A624G						PASS	.	C		2924,1454		1004,916,269	13.0	16.0	15.0		624	-7.8	0.0	19	dbSNP_100	15	1601,6985		129,1343,2821	no	coding-synonymous	PRR22	NM_001134316.1		1133,2259,3090	CC,CT,TT		18.6466,33.2115,34.9044		208/423	5783634	4525,8439	2189	4293	6482	SO:0001819	synonymous_variant	163154	exon3			GGCGTCTGGGGGC	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.624A>G	19.37:g.5783634T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_001134316	E9PB31	Silent	SNP	ENST00000419421.2	37	CCDS45933.1																																																																																			T|0.612;C|0.388	0.388	strong		0.706	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
FOXK2	3607	hgsc.bcm.edu	37	17	80545021	80545021	+	Silent	SNP	G	G	A	rs139592674		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80545021G>A	ENST00000335255.5	+	8	1833	c.1659G>A	c.(1657-1659)ccG>ccA	p.P553P	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	553					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			AGACCACCCCGGTCCAGACGG	0.532																																					p.P553P		Atlas-SNP	.											.	FOXK2	46	.	0			c.G1659A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	100.0	83.0	89.0		1659	-4.4	0.7	17	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FOXK2	NM_004514.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		553/661	80545021	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3607	exon8			CACCCCGGTCCAG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1659G>A	17.37:g.80545021G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			G|1.000;A|0.000	0.000	weak		0.532	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
CLASP2	23122	hgsc.bcm.edu	37	3	33728610	33728610	+	Missense_Mutation	SNP	A	A	G	rs61738888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:33728610A>G	ENST00000468888.2	-	5	534	c.488T>C	c.(487-489)cTa>cCa	p.L163P	CLASP2_ENST00000359576.5_Missense_Mutation_p.L163P|CLASP2_ENST00000399362.4_Missense_Mutation_p.L163P|CLASP2_ENST00000307312.7_5'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1216					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						GCTGATGACTAGTGGCTGAGC	0.303													A|||	250	0.0499201	0.0303	0.0778	5008	,	,		15933	0.0288		0.0984	False		,,,				2504	0.0286				p.L163P		Atlas-SNP	.											.	CLASP2	138	.	0			c.T488C						PASS	.	A	PRO/LEU	119,3491		6,107,1692	36.0	33.0	34.0		488	5.1	0.9	3	dbSNP_129	34	854,7290		54,746,3272	yes	missense	CLASP2	NM_015097.2	98	60,853,4964	GG,GA,AA		10.4862,3.2964,8.278	probably-damaging	163/1516	33728610	973,10781	1805	4072	5877	SO:0001583	missense	23122	exon5			ATGACTAGTGGCT	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.488T>C	3.37:g.33728610A>G	ENSP00000419974:p.Leu163Pro	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		123	0.05631868131868132	11	0.022357723577235773	36	0.09944751381215469	15	0.026223776223776224	61	0.08047493403693931	A	19.69	3.874747	0.72180	0.032964	0.104862	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576	T;T;T	0.66280	-0.2;-0.2;-0.2	5.11	5.11	0.69529	.	0.000000	0.64402	D	0.000009	T	0.09423	0.0232	M	0.76838	2.35	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.54377	-0.8303	10	0.87932	D	0	-12.1512	12.7394	0.57243	1.0:0.0:0.0:0.0	.	163	F5H604	.	P	163	ENSP00000419974:L163P;ENSP00000382297:L163P;ENSP00000352581:L163P	ENSP00000352581:L163P	L	-	2	0	CLASP2	33703614	1.000000	0.71417	0.896000	0.35187	0.977000	0.68977	7.387000	0.79785	2.072000	0.62099	0.477000	0.44152	CTA	A|0.934;G|0.066	0.066	strong		0.303	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
MRGPRE	116534	hgsc.bcm.edu	37	11	3249829	3249829	+	Silent	SNP	G	G	A	rs11026040	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:3249829G>A	ENST00000389832.5	-	2	507	c.201C>T	c.(199-201)tgC>tgT	p.C67C	MRGPRE_ENST00000436689.2_Silent_p.C66C|AC109309.4_ENST00000418995.2_RNA			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	67						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)		TGAGATCCGCGCAGGCCACGT	0.637													G|||	1131	0.225839	0.2776	0.3213	5008	,	,		18071	0.13		0.1431	False		,,,				2504	0.272				p.C67C		Atlas-SNP	.											.	MRGPRE	35	.	0			c.C201T						PASS	.	G		1085,3169		138,809,1180	79.0	97.0	91.0		198	-7.0	0.0	11	dbSNP_120	91	1029,7463		57,915,3274	no	coding-synonymous	MRGPRE	NM_001039165.2		195,1724,4454	AA,AG,GG		12.1173,25.5054,16.5856		66/312	3249829	2114,10632	2127	4246	6373	SO:0001819	synonymous_variant	116534	exon2			ATCCGCGCAGGCC	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.201C>T	11.37:g.3249829G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	73	41	0.561644	NM_001039165	Q2M1V7	Silent	SNP	ENST00000389832.5	37																																																																																				A|0.172;G|0.828	0.172	strong		0.637	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
NXPE4	54827	hgsc.bcm.edu	37	11	114441943	114441943	+	Missense_Mutation	SNP	G	G	A	rs10891705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:114441943G>A	ENST00000375478.3	-	6	1532	c.1352C>T	c.(1351-1353)gCc>gTc	p.A451V	NXPE4_ENST00000424261.2_Missense_Mutation_p.A167V	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	451			A -> V (in dbSNP:rs10891705). {ECO:0000269|PubMed:15375555}.			extracellular vesicular exosome (GO:0070062)											GACATTGAGGGCCCTTCGGAT	0.438													G|||	1803	0.360024	0.2118	0.2968	5008	,	,		17837	0.6746		0.332	False		,,,				2504	0.3098				p.A451V		Atlas-SNP	.											.	.	.	.	0			c.C1352T						PASS	.	G	VAL/ALA,VAL/ALA	889,2877		91,707,1085	136.0	125.0	129.0		1352,500	-0.9	1.0	11	dbSNP_120	129	2795,5417		460,1875,1771	yes	missense,missense	FAM55D	NM_001077639.1,NM_017678.2	64,64	551,2582,2856	AA,AG,GG		34.0356,23.6059,30.7564	benign,benign	451/545,167/261	114441943	3684,8294	1883	4106	5989	SO:0001583	missense	54827	exon6			TTGAGGGCCCTTC	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1352C>T	11.37:g.114441943G>A	ENSP00000364627:p.Ala451Val	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	182	179	0.983516	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	844	0.38644688644688646	110	0.22357723577235772	105	0.2900552486187845	381	0.666083916083916	248	0.32717678100263853	G	11.30	1.599017	0.28534	0.236059	0.340356	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.20598	2.06;2.06	5.51	-0.856	0.10697	.	0.586195	0.16084	N	0.230369	T	0.00012	0.0000	L	0.45285	1.41	0.40129	P	0.023301000000000016	B	0.27316	0.175	B	0.37304	0.246	T	0.30851	-0.9964	9	0.14656	T	0.56	.	6.3911	0.21587	0.5261:0.0:0.3512:0.1227	rs10891705;rs61407553;rs10891705	451	Q6UWF7	FA55D_HUMAN	V	167;451	ENSP00000401503:A167V;ENSP00000364627:A451V	ENSP00000364627:A451V	A	-	2	0	FAM55D	113947153	0.038000	0.19896	0.967000	0.41034	0.984000	0.73092	0.241000	0.18065	-0.347000	0.08299	-1.074000	0.02243	GCC	G|0.639;A|0.361	0.361	strong		0.438	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
MUC16	94025	hgsc.bcm.edu	37	19	9072221	9072221	+	Silent	SNP	G	G	A	rs66498329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9072221G>A	ENST00000397910.4	-	3	15428	c.15225C>T	c.(15223-15225)ggC>ggT	p.G5075G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5077	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						TCTTCACTAGGCCAGAGGTGA	0.468													G|||	1007	0.201078	0.0946	0.2824	5008	,	,		21007	0.3254		0.167	False		,,,				2504	0.1943				p.G5075G		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	0			c.C15225T						scavenged	.			401,3443		18,365,1539	153.0	138.0	143.0		15225	-3.4	0.0	19	dbSNP_130	143	1503,6757		136,1231,2763	no	coding-synonymous	MUC16	NM_024690.2		154,1596,4302	AA,AG,GG		18.1961,10.4318,15.7303		5075/14508	9072221	1904,10200	1922	4130	6052	SO:0001819	synonymous_variant	94025	exon3			CACTAGGCCAGAG	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.15225C>T	19.37:g.9072221G>A		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.787;A|0.213	0.213	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SLC1A5	6510	hgsc.bcm.edu	37	19	47278859	47278859	+	Missense_Mutation	SNP	C	C	G	rs3027961	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:47278859C>G	ENST00000542575.2	-	8	2162	c.1534G>C	c.(1534-1536)Gtc>Ctc	p.V512L	FKRP_ENST00000600646.1_Intron|SLC1A5_ENST00000434726.2_Missense_Mutation_p.V310L|SLC1A5_ENST00000412532.2_Missense_Mutation_p.V284L|SLC1A5_ENST00000594991.1_Missense_Mutation_p.V336L	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	512			V -> L (in dbSNP:rs3027961). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:19690332}.		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)	TCAGTGGGGACTGGCAGCGGA	0.587													-|||	660	0.131789	0.146	0.1254	5008	,	,		14789	0.001		0.2306	False		,,,				2504	0.1503				p.V512L		Atlas-SNP	.											.	SLC1A5	31	.	0			c.G1534C						PASS	.		LEU/VAL,LEU/VAL,LEU/VAL	768,3638		60,648,1495	146.0	145.0	146.0		850,928,1534	-2.1	0.0	19	dbSNP_102	146	2255,6345		302,1651,2347	yes	missense,missense,missense	SLC1A5	NM_001145144.1,NM_001145145.1,NM_005628.2	32,32,32	362,2299,3842	GG,GC,CC		26.2209,17.4308,23.2431	benign,benign,benign	284/314,310/340,512/542	47278859	3023,9983	2203	4300	6503	SO:0001583	missense	6510	exon8			TGGGGACTGGCAG	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.1534G>C	19.37:g.47278859C>G	ENSP00000444408:p.Val512Leu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Missense_Mutation	SNP	ENST00000542575.2	37	CCDS12692.1	303	0.13873626373626374	68	0.13821138211382114	53	0.1464088397790055	2	0.0034965034965034965	180	0.23746701846965698	-	11.76	1.734189	0.30684	0.174308	0.262209	ENSG00000105281	ENST00000542575;ENST00000434726;ENST00000412532;ENST00000306894	T;T;T	0.63096	0.81;-0.02;-0.01	4.58	-2.11	0.07187	.	1.994340	0.02456	N	0.086045	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.09185	-1.0686	9	0.02654	T	1	-3.983	6.1016	0.20051	0.0:0.373:0.3862:0.2408	rs3027961;rs17855343;rs52803135;rs3027961	310;512;512	E9PC01;Q15758;Q71UA6	.;AAAT_HUMAN;.	L	512;310;284;519	ENSP00000444408:V512L;ENSP00000406532:V310L;ENSP00000397924:V284L	ENSP00000303623:V519L	V	-	1	0	SLC1A5	51970699	0.000000	0.05858	0.000000	0.03702	0.339000	0.28857	-0.180000	0.09754	-0.280000	0.09154	0.550000	0.68814	GTC	C|0.796;G|0.204	0.204	strong		0.587	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29911092	29911092	+	Missense_Mutation	SNP	G	G	T	rs1136702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911092G>T	ENST00000396634.1	+	5	732	c.391G>T	c.(391-393)Ggg>Tgg	p.G131W	HLA-A_ENST00000376809.5_Missense_Mutation_p.G131W|HLA-A_ENST00000376806.5_Missense_Mutation_p.G131W|HLA-A_ENST00000376802.2_Missense_Mutation_p.G131W			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	131	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|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						GGGGTCGGACGGGCGCTTCCT	0.697									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|||	1224	0.244409	0.1747	0.3357	5008	,	,		11611	0.2887		0.3181	False		,,,				2504	0.1524				p.G131W		Atlas-SNP	.											.	HLA-A	89	.	0			c.G391T						PASS	.						29.0	23.0	25.0					6																	29911092		1501	2696	4197	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TCGGACGGGCGCT	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.391G>T	6.37:g.29911092G>T	ENSP00000379873:p.Gly131Trp	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	540	0.24725274725274726	87	0.17682926829268292	87	0.24033149171270718	144	0.2517482517482518	222	0.2928759894459103	.	5.810	0.333674	0.11013	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00020	9.05;9.05;9.05;9.05	3.78	-0.575	0.11734	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	0.208432	0.22974	U	0.053390	T	0.00109	0.0003	.	.	.	0.80722	P	0.0	D;B;D;B;D;P;B	0.89917	1.0;0.24;1.0;0.24;1.0;0.533;0.24	D;B;D;B;D;B;B	0.97110	1.0;0.066;1.0;0.111;1.0;0.111;0.06	T	0.56823	-0.7915	8	0.28530	T	0.3	.	8.255	0.31751	0.0935:0.45:0.4565:0.0	rs1136702;rs2231023;rs3179191;rs3200181;rs17433779;rs28749150;rs41563214	10;131;131;131;131;131;131	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	W	131	ENSP00000379873:G131W;ENSP00000366002:G131W;ENSP00000366005:G131W;ENSP00000365998:G131W	ENSP00000348012:G131W	G	+	1	0	HLA-A	30019071	0.004000	0.15560	0.164000	0.22755	0.596000	0.36781	0.228000	0.17814	-0.248000	0.09583	-0.494000	0.04653	GGG	G|0.749;T|0.251	0.251	strong		0.697	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
HAPLN3	145864	hgsc.bcm.edu	37	15	89430506	89430506	+	Silent	SNP	C	C	T	rs3743395	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89430506C>T	ENST00000359595.3	-	2	238	c.24G>A	c.(22-24)ccG>ccA	p.P8P	HAPLN3_ENST00000562889.1_Silent_p.P70P	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	8					cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	GCAGGAGCAACGGGACCAGGA	0.612													C|||	1020	0.203674	0.1755	0.2248	5008	,	,		18625	0.2222		0.2505	False		,,,				2504	0.1595				p.P8P		Atlas-SNP	.											.	HAPLN3	43	.	0			c.G24A						PASS	.	C		815,3585	322.6+/-297.7	86,643,1471	107.0	95.0	99.0		24	-0.2	0.0	15	dbSNP_107	99	2267,6331	382.7+/-340.5	277,1713,2309	no	coding-synonymous	HAPLN3	NM_178232.2		363,2356,3780	TT,TC,CC		26.3666,18.5227,23.7113		8/361	89430506	3082,9916	2200	4299	6499	SO:0001819	synonymous_variant	145864	exon2			GAGCAACGGGACC	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.24G>A	15.37:g.89430506C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	149	71	0.47651	NM_178232	A8K7P0	Silent	SNP	ENST00000359595.3	37	CCDS10346.1																																																																																			C|0.770;T|0.230	0.230	strong		0.612	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
PLOD1	5351	hgsc.bcm.edu	37	1	12024235	12024235	+	Silent	SNP	C	C	T	rs1130529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12024235C>T	ENST00000196061.4	+	12	1233	c.1206C>T	c.(1204-1206)aaC>aaT	p.N402N	PLOD1_ENST00000376369.3_Silent_p.N449N	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	402					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	CCCTCAGGAACGTCATTGCCC	0.622													C|||	1745	0.348442	0.2693	0.3545	5008	,	,		15315	0.3839		0.3151	False		,,,				2504	0.4489				p.N402N		Atlas-SNP	.											.	PLOD1	75	.	0			c.C1206T						PASS	.	C		1281,3125	435.9+/-344.5	182,917,1104	150.0	144.0	146.0		1206	-5.4	1.0	1	dbSNP_86	146	2761,5839	439.9+/-359.4	458,1845,1997	no	coding-synonymous	PLOD1	NM_000302.3		640,2762,3101	TT,TC,CC		32.1047,29.074,31.078		402/728	12024235	4042,8964	2203	4300	6503	SO:0001819	synonymous_variant	5351	exon12			CAGGAACGTCATT	BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"""lysyl hydroxlase 1"""	153454	"""procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"""	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.1206C>T	1.37:g.12024235C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_000302	B4DR87|Q96AV9|Q9H132	Silent	SNP	ENST00000196061.4	37	CCDS142.1																																																																																			C|0.687;N|0.001	.	strong		0.622	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
OTOF	9381	hgsc.bcm.edu	37	2	26702508	26702508	+	Silent	SNP	G	G	A	rs72853741	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26702508G>A	ENST00000272371.2	-	17	2052	c.1926C>T	c.(1924-1926)aaC>aaT	p.N642N	OTOF_ENST00000339598.3_5'Flank|OTOF_ENST00000403946.3_Silent_p.N642N|OTOF_ENST00000338581.6_5'Flank|OTOF_ENST00000402415.3_5'Flank	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	642					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CATCAACTTCGTTCCCATAGT	0.627													G|||	99	0.0197684	0.0454	0.0245	5008	,	,		19127	0.0		0.0199	False		,,,				2504	0.002				p.N642N	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C1926T						PASS	.	G		210,4192	124.5+/-161.8	6,198,1997	31.0	35.0	33.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1926	-3.4	0.8	2	dbSNP_130	33	215,8379	85.3+/-147.7	3,209,4085	no	coding-synonymous	OTOF	NM_194248.2		9,407,6082	AA,AG,GG		2.5017,4.7706,3.2702		642/1998	26702508	425,12571	2201	4297	6498	SO:0001819	synonymous_variant	9381	exon17			AACTTCGTTCCCA	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.1926C>T	2.37:g.26702508G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.970;A|0.030	0.030	strong		0.627	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
COL27A1	85301	hgsc.bcm.edu	37	9	116967405	116967405	+	Silent	SNP	G	G	T	rs13290696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:116967405G>T	ENST00000356083.3	+	8	2539	c.2148G>T	c.(2146-2148)ccG>ccT	p.P716P		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	716	Collagen-like 2.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						ATCCTGGACCGGCAGGGCACC	0.667													G|||	399	0.0796725	0.0416	0.0331	5008	,	,		17714	0.0208		0.0785	False		,,,				2504	0.226				p.P716P		Atlas-SNP	.											.	COL27A1	200	.	0			c.G2148T						PASS	.	G		222,4184	132.5+/-169.0	5,212,1986	66.0	53.0	57.0		2148	-10.1	0.0	9	dbSNP_121	57	821,7779	189.3+/-236.1	34,753,3513	no	coding-synonymous	COL27A1	NM_032888.2		39,965,5499	TT,TG,GG		9.5465,5.0386,8.0194		716/1861	116967405	1043,11963	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon8			TGGACCGGCAGGG	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.2148G>T	9.37:g.116967405G>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.932;T|0.068	0.068	strong		0.667	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388508	1388508	+	Missense_Mutation	SNP	T	T	C	rs55703801		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388508T>C	ENST00000324803.4	+	1	3169	c.209T>C	c.(208-210)gTc>gCc	p.V70A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	70					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACACGTGTCCATGTGGAG	0.632																																					p.V70A		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,1	CRIPAK	185	1	0			c.T209C						scavenged	.						283.0	245.0	257.0					4																	1388508		2203	4300	6503	SO:0001583	missense	285464	exon1			CACGTGTCCATGT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.209T>C	4.37:g.1388508T>C	ENSP00000323978:p.Val70Ala	Somatic	152	3	0.0197368		WXS	Illumina HiSeq	Phase_I	185	20	0.108108	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	8.717	0.913380	0.17907	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.24350	1.86	1.09	-2.19	0.07015	.	.	.	.	.	T	0.08714	0.0216	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.25257	-1.0137	9	0.16896	T	0.51	.	0.4342	0.00476	0.19:0.3247:0.1898:0.2955	rs55703801	70	Q8N1N5	CRPAK_HUMAN	A	70;63	ENSP00000323978:V70A	ENSP00000323978:V70A	V	+	2	0	CRIPAK	1378508	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	-1.991000	0.01478	-2.302000	0.00657	-1.823000	0.00598	GTC	.	.	weak		0.632	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
LRPAP1	4043	hgsc.bcm.edu	37	4	3534042	3534042	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3534042C>A	ENST00000500728.2	-	1	244	c.98G>T	c.(97-99)gGc>gTc	p.G33V	LRPAP1_ENST00000296325.5_5'Flank	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	33					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)		CGAGTACTTGCCGCCGTGGCT	0.672																																					p.G33V		Atlas-SNP	.											.	LRPAP1	29	.	0			c.G98T						PASS	.						20.0	20.0	20.0					4																	3534042		2170	4270	6440	SO:0001583	missense	4043	exon1			TACTTGCCGCCGT		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.98G>T	4.37:g.3534042C>A	ENSP00000421922:p.Gly33Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Missense_Mutation	SNP	ENST00000500728.2	37	CCDS3371.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740844	0.89573	.	.	ENSG00000163956	ENST00000500728	T	0.46451	0.87	3.8	3.8	0.43715	Alpha-2-macroglobulin receptor-associated protein, domain 1 (1);	0.120269	0.56097	D	0.000032	T	0.58395	0.2119	M	0.68317	2.08	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.60459	-0.7259	10	0.52906	T	0.07	-30.362	11.0418	0.47835	0.0:1.0:0.0:0.0	.	33	P30533	AMRP_HUMAN	V	33	ENSP00000421922:G33V	ENSP00000421922:G33V	G	-	2	0	LRPAP1	3503840	0.998000	0.40836	1.000000	0.80357	0.924000	0.55760	4.856000	0.62932	1.937000	0.56155	0.591000	0.81541	GGC	.	.	none		0.672	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
PTX3	5806	hgsc.bcm.edu	37	3	157155314	157155314	+	Missense_Mutation	SNP	C	C	A	rs3816527	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:157155314C>A	ENST00000295927.3	+	2	288	c.143C>A	c.(142-144)gCc>gAc	p.A48D	VEPH1_ENST00000392832.2_Intron|VEPH1_ENST00000392833.2_Intron|VEPH1_ENST00000362010.2_Intron|VEPH1_ENST00000543418.1_Intron	NM_002852.3	NP_002843.2	P26022	PTX3_HUMAN	pentraxin 3, long	48			A -> D (in dbSNP:rs3816527). {ECO:0000269|PubMed:1429570, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7679696, ECO:0000269|PubMed:8131794}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of viral entry into host cell (GO:0046597)|opsonization (GO:0008228)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phagocytosis (GO:0050766)|response to yeast (GO:0001878)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	(1->3)-beta-D-glucan binding (GO:0001872)|complement component C1q binding (GO:0001849)|virion binding (GO:0046790)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)	10			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ACGCCGTGCGCCTGCGGTCAG	0.602													A|||	3579	0.714657	0.7436	0.7176	5008	,	,		17859	0.7569		0.6024	False		,,,				2504	0.7454				p.A48D		Atlas-SNP	.											.	PTX3	27	.	0			c.C143A						PASS	.	A	,,ASP/ALA,	3146,1122		1188,770,176	12.0	11.0	11.0		,,143,	3.5	1.0	3	dbSNP_107	11	4869,3543		1514,1841,851	yes	intron,intron,missense,intron	PTX3,VEPH1	NM_001167911.1,NM_001167912.1,NM_002852.3,NM_024621.2	,,126,	2702,2611,1027	AA,AC,CC		42.1184,26.2887,36.7902	,,benign,	,,48/382,	157155314	8015,4665	2134	4206	6340	SO:0001583	missense	5806	exon2			CGTGCGCCTGCGG	X63613	CCDS3180.1	3q25	2010-03-11	2010-03-11		ENSG00000163661	ENSG00000163661			9692	protein-coding gene	gene with protein product		602492	"""pentaxin-related gene, rapidly induced by IL-1 beta"", ""tumor necrosis factor, alpha-induced protein 5"", ""pentraxin-related gene, rapidly induced by IL-1 beta"""	TNFAIP5		1429570	Standard	NM_002852		Approved	TSG-14	uc003fbl.4	P26022	OTTHUMG00000158750	ENST00000295927.3:c.143C>A	3.37:g.157155314C>A	ENSP00000295927:p.Ala48Asp	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_002852	B2R6T6|Q38M82	Missense_Mutation	SNP	ENST00000295927.3	37	CCDS3180.1	1515	0.6936813186813187	364	0.7398373983739838	245	0.6767955801104972	456	0.7972027972027972	450	0.5936675461741425	A	0.566	-0.843373	0.02671	0.737113	0.578816	ENSG00000163661	ENST00000295927	T	0.06768	3.26	4.66	3.48	0.39840	.	0.693410	0.13134	N	0.411169	T	0.00012	0.0000	N	0.00170	-1.935	0.48830	P	2.8399999999995096E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33033	-0.9884	9	0.02654	T	1	-8.9853	11.4409	0.50096	0.7121:0.2879:0.0:0.0	rs3816527;rs17857200;rs61677924	48	P26022	PTX3_HUMAN	D	48	ENSP00000295927:A48D	ENSP00000295927:A48D	A	+	2	0	PTX3	158638008	1.000000	0.71417	0.998000	0.56505	0.330000	0.28571	3.669000	0.54561	0.166000	0.19597	-0.363000	0.07495	GCC	C|0.346;A|0.654	0.654	strong		0.602	PTX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352028.1	NM_002852	
ABCC5	10057	hgsc.bcm.edu	37	3	183696402	183696402	+	Silent	SNP	A	A	G	rs1132776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183696402A>G	ENST00000334444.6	-	9	1425	c.1185T>C	c.(1183-1185)gcT>gcC	p.A395A	ABCC5_ENST00000492216.1_5'UTR|ABCC5_ENST00000265586.6_Silent_p.A395A	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	395	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	GGAAGTACCCAGCTTTTTCCA	0.483													G|||	3388	0.676518	0.7489	0.5879	5008	,	,		19155	0.8522		0.5746	False		,,,				2504	0.5654				p.A395A		Atlas-SNP	.											.	ABCC5	142	.	0			c.T1185C						PASS	.	G		2986,1084		1113,760,162	90.0	105.0	100.0		1185	-11.4	0.1	3	dbSNP_86	100	4731,3647		1333,2065,791	no	coding-synonymous	ABCC5	NM_005688.2		2446,2825,953	GG,GA,AA		43.5307,26.6339,38.0061		395/1438	183696402	7717,4731	2035	4189	6224	SO:0001819	synonymous_variant	10057	exon9			GTACCCAGCTTTT	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.1185T>C	3.37:g.183696402A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			A|0.339;G|0.661	0.661	strong		0.483	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
C10orf120	399814	hgsc.bcm.edu	37	10	124457480	124457480	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124457480A>G	ENST00000329446.4	-	3	808	c.777T>C	c.(775-777)caT>caC	p.H259H		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	259										endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				GATCATTTCCATGGTATGTTA	0.388																																					p.H259H		Atlas-SNP	.											.	C10orf120	55	.	0			c.T777C						PASS	.						140.0	136.0	137.0					10																	124457480		2203	4300	6503	SO:0001819	synonymous_variant	399814	exon3			ATTTCCATGGTAT		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.777T>C	10.37:g.124457480A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	124	55	0.443548	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1																																																																																			.	.	none		0.388	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
CPA5	93979	hgsc.bcm.edu	37	7	129986338	129986338	+	Silent	SNP	C	C	T	rs6973851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129986338C>T	ENST00000485477.1	+	2	1141	c.12C>T	c.(10-12)acC>acT	p.T4T	CPA5_ENST00000461828.1_Silent_p.T4T|CPA5_ENST00000355388.3_Silent_p.T4T|CPA5_ENST00000431780.2_Silent_p.T4T|CPA5_ENST00000466363.2_Silent_p.T4T|CPA5_ENST00000393213.3_Silent_p.T4T|CPA5_ENST00000474905.1_Silent_p.T4T|snoU13_ENST00000459205.1_RNA			Q8WXQ8	CBPA5_HUMAN	carboxypeptidase A5	4						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(2)|large_intestine(7)|lung(4)|ovary(3)|pancreas(1)|skin(2)	23	Melanoma(18;0.0435)					TGCAGGGCACCCCTGGAGGCG	0.622													C|||	2972	0.59345	0.6467	0.6484	5008	,	,		18970	0.5347		0.5845	False		,,,				2504	0.5521				p.T4T		Atlas-SNP	.											.	CPA5	61	.	0			c.C12T						PASS	.	C	,,	2812,1594	662.3+/-401.0	900,1012,291	66.0	72.0	70.0		12,12,12	1.6	0.0	7	dbSNP_116	70	4989,3611	624.1+/-397.5	1444,2101,755	no	coding-synonymous,coding-synonymous,coding-synonymous	CPA5	NM_001127441.1,NM_001127442.1,NM_080385.4	,,	2344,3113,1046	TT,TC,CC		41.9884,36.1779,40.02	,,	4/437,4/404,4/437	129986338	7801,5205	2203	4300	6503	SO:0001819	synonymous_variant	93979	exon3			GGGCACCCCTGGA	AF384667	CCDS5819.1, CCDS47713.1	7q32	2008-07-18			ENSG00000158525	ENSG00000158525			15722	protein-coding gene	gene with protein product		609561				11836249	Standard	NM_080385		Approved		uc003vps.2	Q8WXQ8	OTTHUMG00000157824	ENST00000485477.1:c.12C>T	7.37:g.129986338C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_080385	G3V0G8|Q6ZNI6|Q86SE2|Q86XM3|Q8NA08	Silent	SNP	ENST00000485477.1	37	CCDS5819.1																																																																																			C|0.418;T|0.582	0.582	strong		0.622	CPA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349712.1	NM_001127441	
AVPR2	554	hgsc.bcm.edu	37	X	153171993	153171993	+	Silent	SNP	A	A	G	rs5201	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153171993A>G	ENST00000358927.2	+	4	1136	c.927A>G	c.(925-927)ctA>ctG	p.L309L	AVPR2_ENST00000337474.5_Silent_p.L309L|AVPR2_ENST00000370049.1_3'UTR|ARHGAP4_ENST00000467421.1_5'Flank			P30518	V2R_HUMAN	arginine vasopressin receptor 2	309			L -> P (in XNDI). {ECO:0000269|PubMed:9452109}.|L -> R (in XNDI).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|excretion (GO:0007588)|hemostasis (GO:0007599)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|interferon-gamma production (GO:0032609)|negative regulation of renal sodium excretion (GO:0035814)|negative regulation of urine volume (GO:0035811)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of systemic arterial blood pressure (GO:0003084)|response to cytokine (GO:0034097)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	vasopressin receptor activity (GO:0005000)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	26	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)				Conivaptan(DB00872)|Desmopressin(DB00035)|Terlipressin(DB02638)|Tolvaptan(DB06212)|Vasopressin(DB00067)	CCTTTGTGCTACTCATGTTGC	0.612													G|||	2599	0.688477	0.711	0.487	3775	,	,		14121	0.5446		0.2425	False		,,,				2504	0.5399				p.L309L		Atlas-SNP	.											.	AVPR2	43	.	0			c.A927G						PASS	.	G	,	3287,548		1199,389,500,44,71	160.0	139.0	146.0		927,	3.4	1.0	X	dbSNP_52	146	2018,4710		209,998,602,1221,1270	no	coding-synonymous,utr-3	AVPR2	NM_000054.4,NM_001146151.1	,	1408,1387,1102,1265,1341	GG,GA,G,AA,A		29.9941,14.2894,49.7775	,	309/372,	153171993	5305,5258	2203	4300	6503	SO:0001819	synonymous_variant	554	exon3			TGTGCTACTCATG	Z11687	CCDS14735.1, CCDS55539.1	Xq28	2014-09-17	2008-08-01		ENSG00000126895	ENSG00000126895		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	897	protein-coding gene	gene with protein product	"""nephrogenic diabetes insipidus"""	300538		DIR3, DIR		1324225	Standard	NM_000054		Approved	V2R	uc004fjh.4	P30518	OTTHUMG00000024227	ENST00000358927.2:c.927A>G	X.37:g.153171993A>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	95	95	1	NM_000054	C5HF20|O43192|Q3MJD3|Q9UCV9	Silent	SNP	ENST00000358927.2	37	CCDS14735.1	993	0.5985533453887885	242	0.8120805369127517	123	0.45555555555555555	212	0.572972972972973	130	0.2006172839506173	g	4.708	0.131710	0.08981	0.857106	0.299941	ENSG00000126895	ENST00000430697	T	0.41758	0.99	4.3	3.44	0.39384	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09885	-1.0654	5	0.66056	D	0.02	-19.7909	5.1929	0.15218	0.1993:0.284:0.5167:0.0	rs5201;rs2228584;rs5201	.	.	.	C	280	ENSP00000393513:Y280C	ENSP00000393513:Y280C	Y	+	2	0	AVPR2	152825187	0.974000	0.33945	1.000000	0.80357	0.185000	0.23345	0.989000	0.29629	0.258000	0.21686	-1.480000	0.00990	TAC	A|0.412;0|0.001	.	strong		0.612	AVPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061127.2		
MICAL3	57553	hgsc.bcm.edu	37	22	18310439	18310439	+	Missense_Mutation	SNP	G	G	A	rs61744286	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18310439G>A	ENST00000441493.2	-	22	3516	c.3164C>T	c.(3163-3165)gCg>gTg	p.A1055V		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1055	Glu-rich.				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)		AGAGGCCGGCGCCATCCTCTC	0.652													G|||	335	0.066893	0.0998	0.036	5008	,	,		16545	0.0804		0.0646	False		,,,				2504	0.0327				p.A1055V		Atlas-SNP	.											.	MICAL3	53	.	0			c.C3164T						PASS	.	G	VAL/ALA	389,3593		16,357,1618	19.0	23.0	22.0		3164	-1.5	0.0	22	dbSNP_129	22	489,7805		15,459,3673	yes	missense	MICAL3	NM_015241.2	64	31,816,5291	AA,AG,GG		5.8958,9.769,7.1522	benign	1055/2003	18310439	878,11398	1991	4147	6138	SO:0001583	missense	57553	exon22			GCCGGCGCCATCC	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.3164C>T	22.37:g.18310439G>A	ENSP00000416015:p.Ala1055Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	181|181	0.08287545787545787|0.08287545787545787	59|59	0.11991869918699187|0.11991869918699187	16|16	0.04419889502762431|0.04419889502762431	50|50	0.08741258741258741|0.08741258741258741	56|56	0.07387862796833773|0.07387862796833773	G|G	4.543|4.543	0.100866|0.100866	0.08731|0.08731	0.09769|0.09769	0.058958|0.058958	ENSG00000093100|ENSG00000093100	ENST00000441493|ENST00000252134	T|.	0.61040|.	0.14|.	4.95|4.95	-1.52|-1.52	0.08637|0.08637	.|.	.|.	.|.	.|.	.|.	T|T	0.00144|0.00144	0.0004|0.0004	N|N	0.02916|0.02916	-0.46|-0.46	0.49798|0.49798	P|P	1.7800000000001148E-4|1.7800000000001148E-4	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|T	0.30822|0.30822	-0.9965|-0.9965	8|4	0.16420|.	T|.	0.52|.	.|.	1.7269|1.7269	0.02924|0.02924	0.3318:0.2422:0.306:0.12|0.3318:0.2422:0.306:0.12	.|.	1055|.	Q7RTP6|.	MICA3_HUMAN|.	V|C	1055|37	ENSP00000416015:A1055V|.	ENSP00000416015:A1055V|.	A|R	-|-	2|1	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16690439|16690439	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.437000|0.437000	0.31866|0.31866	-0.007000|-0.007000	0.12810|0.12810	-0.239000|-0.239000	0.09710|0.09710	-0.490000|-0.490000	0.04691|0.04691	GCG|CGC	G|0.917;A|0.083	0.083	strong		0.652	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629129	32629129	+	Missense_Mutation	SNP	T	T	C	rs1130432	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629129T>C	ENST00000399084.1	-	5	945	c.767A>G	c.(766-768)cAg>cGg	p.Q256R	HLA-DQB1_ENST00000399079.3_Intron|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.Q256R|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.Q256R|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	256			Q -> R (in allele DQB1*05:01, allele DQB1*05:02 and allele DQB1*05:03; dbSNP:rs1130432).		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)"""	CTCACCTTTCTGACTCCTTTG	0.557									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1335	0.266573	0.2723	0.1902	5008	,	,		12932	0.3204		0.2445	False		,,,				2504	0.2802				p.Q256R	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.A767G						PASS	.	T	ARG/GLN	946,3042		238,470,1286	28.0	25.0	26.0		767	3.6	0.9	6	dbSNP_86	26	1711,6421		446,819,2801	yes	missense	HLA-DQB1	NM_002123.4	43	684,1289,4087	CC,CT,TT		21.0403,23.7212,21.9224	benign	256/262	32629129	2657,9463	1994	4066	6060	SO:0001583	missense	3119	exon4	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CCTTTCTGACTCC		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.767A>G	6.37:g.32629129T>C	ENSP00000382034:p.Gln256Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	46	0.901961	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	417	0.19093406593406592	113	0.22967479674796748	63	0.17403314917127072	86	0.15034965034965034	155	0.20448548812664907	.	13.83	2.354500	0.41700	0.237212	0.210403	ENSG00000179344	ENST00000374943;ENST00000434651;ENST00000399084	T;T;T	0.00637	6.13;6.05;6.05	4.75	3.6	0.41247	.	0.567063	0.16716	N	0.202474	T	0.00384	0.0012	L	0.54965	1.715	0.39169	P	0.03744599999999998	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.10450	0.003;0.004;0.005	T	0.39702	-0.9601	9	0.87932	D	0	.	7.8247	0.29307	0.0:0.1:0.0:0.9	rs1130432;rs3189265;rs9273619;rs9273620;rs12722395;rs35107830	221;256;256	A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.	R	256	ENSP00000364080:Q256R;ENSP00000407332:Q256R;ENSP00000382034:Q256R	ENSP00000364080:Q256R	Q	-	2	0	HLA-DQB1	32737107	0.999000	0.42202	0.933000	0.37362	0.910000	0.53928	1.001000	0.29783	1.776000	0.52262	0.528000	0.53228	CAG	T|0.827;C|0.173	0.173	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	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751657	19751657	+	Silent	SNP	G	G	T	rs9507566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19751657G>T	ENST00000400113.3	-	4	570	c.466C>A	c.(466-468)Cgg>Agg	p.R156R		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	156					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		ACTGAGAGCCGCTCCATGAGC	0.582													G|||	153	0.0305511	0.0038	0.0461	5008	,	,		17318	0.0129		0.0596	False		,,,				2504	0.044				p.R156R		Atlas-SNP	.											TUBA3C,NS,carcinoma,+1,1	TUBA3C	166	1	0			c.C466A						PASS	.	G		73,4333	65.8+/-103.3	1,71,2131	85.0	88.0	87.0		466	1.2	1.0	13	dbSNP_119	87	506,8094	144.7+/-200.5	20,466,3814	no	coding-synonymous	TUBA3C	NM_006001.2		21,537,5945	TT,TG,GG		5.8837,1.6568,4.4518		156/451	19751657	579,12427	2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			AGAGCCGCTCCAT	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.466C>A	13.37:g.19751657G>T		Somatic	323	0	0		WXS	Illumina HiSeq	Phase_I	362	189	0.522099	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			G|0.957;T|0.043	0.043	strong		0.582	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
MUC4	4585	hgsc.bcm.edu	37	3	195506579	195506579	+	Missense_Mutation	SNP	T	T	C	rs200317787|rs71291866	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506579T>C	ENST00000463781.3	-	2	12331	c.11872A>G	c.(11872-11874)Act>Gct	p.T3958A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3958A	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)		ACTGAGGAAGTGTCGGTGACA	0.597																																					p.T3958A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.A11872G						scavenged	.						17.0	11.0	13.0					3																	195506579		678	1521	2199	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11872A>G	3.37:g.195506579T>C	ENSP00000417498:p.Thr3958Ala	Somatic	34	2	0.0588235		WXS	Illumina HiSeq	Phase_I	63	7	0.111111	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.312	-0.967054	0.02232	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.41;1.5	.	.	.	.	.	.	.	.	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	1	B	0.17465	0.022	B	0.15870	0.014	T	0.20240	-1.0281	7	.	.	.	.	4.0904	0.09967	0.0:1.0E-4:0.3498:0.6501	.	3830	E7ESK3	.	A	3958	ENSP00000417498:T3958A;ENSP00000420243:T3958A	.	T	-	1	0	MUC4	196991358	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.372000	0.07504	-2.418000	0.00566	-2.418000	0.00219	ACT	CGTC|0.500;TGTT|0.500	.	alt		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ASXL2	55252	hgsc.bcm.edu	37	2	25991689	25991689	+	Missense_Mutation	SNP	T	T	C	rs147191545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:25991689T>C	ENST00000435504.4	-	7	846	c.553A>G	c.(553-555)Agc>Ggc	p.S185G	ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000404843.1_5'UTR|ASXL2_ENST00000336112.4_Missense_Mutation_p.S157G|ASXL2_ENST00000497092.1_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	185	Ser-rich.				adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGGATATGCTTGGCCTGCAT	0.438													T|||	3	0.000599042	0.0	0.0	5008	,	,		13298	0.0		0.003	False		,,,				2504	0.0				p.S185G		Atlas-SNP	.											.	ASXL2	217	.	0			c.A553G						PASS	.	T	GLY/SER	1,4041		0,1,2020	170.0	173.0	172.0		553	3.7	0.8	2	dbSNP_134	172	29,8385		0,29,4178	yes	missense	ASXL2	NM_018263.4	56	0,30,6198	CC,CT,TT		0.3447,0.0247,0.2408	probably-damaging	185/1436	25991689	30,12426	2021	4207	6228	SO:0001583	missense	55252	exon6			ATATGCTTGGCCT			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.553A>G	2.37:g.25991689T>C	ENSP00000391447:p.Ser185Gly	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	5.976	0.364036	0.11296	2.47E-4	0.003447	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.16897	2.31;2.31	6.03	3.67	0.42095	.	0.312422	0.39544	N	0.001327	T	0.07908	0.0198	N	0.04508	-0.205	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.16217	-1.0410	10	0.87932	D	0	-5.0436	7.3591	0.26735	0.0:0.2424:0.0:0.7576	.	185	Q76L83	ASXL2_HUMAN	G	185;157	ENSP00000391447:S185G;ENSP00000337250:S157G	ENSP00000337250:S157G	S	-	1	0	ASXL2	25845193	0.966000	0.33281	0.772000	0.31596	0.755000	0.42902	1.653000	0.37323	0.530000	0.28619	0.533000	0.62120	AGC	T|0.998;C|0.002	0.002	strong		0.438	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
BRCA2	675	hgsc.bcm.edu	37	13	32968840	32968840	+	Missense_Mutation	SNP	G	G	A	rs80359194		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32968840G>A	ENST00000380152.3	+	25	9504	c.9271G>A	c.(9271-9273)Gtc>Atc	p.V3091I	BRCA2_ENST00000544455.1_Missense_Mutation_p.V3091I			P51587	BRCA2_HUMAN	breast cancer 2, early onset	3091					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)		TGCCCCTTTCGTCTATTTGTC	0.323			"""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)																											p.V3091I	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.G9271A						PASS	.						60.0	60.0	60.0					13																	32968840		2203	4300	6503	SO:0001583	missense	675	exon25	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)	CCTTTCGTCTATT	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.9271G>A	13.37:g.32968840G>A	ENSP00000369497:p.Val3091Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	7.433	0.639093	0.14386	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.85702	-2.02;-2.02	5.9	4.16	0.48862	Nucleic acid-binding, OB-fold-like (1);BRCA2, oligonucleotide/oligosaccharide-binding 3 (1);	0.182235	0.48767	N	0.000170	D	0.84529	0.5492	M	0.70903	2.155	0.34869	D	0.74338	B	0.24043	0.096	B	0.26202	0.067	T	0.83263	-0.0047	10	0.52906	T	0.07	.	13.938	0.64036	0.1334:0.0:0.8666:0.0	.	3091	P51587	BRCA2_HUMAN	I	3091	ENSP00000369497:V3091I;ENSP00000439902:V3091I	ENSP00000369497:V3091I	V	+	1	0	BRCA2	31866840	1.000000	0.71417	0.998000	0.56505	0.025000	0.11179	2.306000	0.43673	0.409000	0.25649	-1.119000	0.02030	GTC	.	.	weak		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
LUZP4	51213	hgsc.bcm.edu	37	X	114541277	114541277	+	Missense_Mutation	SNP	G	G	C	rs141415241		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:114541277G>C	ENST00000371920.3	+	4	857	c.850G>C	c.(850-852)Gag>Cag	p.E284Q	LUZP4_ENST00000451986.2_Missense_Mutation_p.E202Q	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	284						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						CGTGGCCACTGAGAGAGATCT	0.418																																					p.E284Q		Atlas-SNP	.											.	LUZP4	51	.	0			c.G850C						PASS	.						80.0	72.0	74.0					X																	114541277		2203	4300	6503	SO:0001583	missense	51213	exon4			GCCACTGAGAGAG	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"""cancer/testis antigen 28"""	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.850G>C	X.37:g.114541277G>C	ENSP00000360988:p.Glu284Gln	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	206	41	0.199029	NM_016383	B3KSD6	Missense_Mutation	SNP	ENST00000371920.3	37	CCDS14567.1	.	.	.	.	.	.	.	.	.	.	g	8.590	0.884248	0.17467	.	.	ENSG00000102021	ENST00000451986;ENST00000371920	D;D	0.82619	-1.63;-1.63	3.18	-0.0432	0.13860	.	0.524458	0.14377	N	0.323399	T	0.57740	0.2074	N	0.08118	0	0.09310	N	1	B;B	0.14438	0.005;0.01	B;B	0.06405	0.001;0.002	T	0.45833	-0.9234	10	0.06365	T	0.9	.	5.9519	0.19250	0.0:0.5051:0.3674:0.1274	.	202;284	B3KSD6;Q9P127	.;LUZP4_HUMAN	Q	202;284	ENSP00000411212:E202Q;ENSP00000360988:E284Q	ENSP00000360988:E284Q	E	+	1	0	LUZP4	114447533	0.000000	0.05858	0.000000	0.03702	0.147000	0.21601	-0.842000	0.04354	0.104000	0.17725	0.171000	0.16805	GAG	.	.	weak		0.418	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383	
RTTN	25914	hgsc.bcm.edu	37	18	67802449	67802449	+	Silent	SNP	T	T	C	rs35139926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:67802449T>C	ENST00000255674.6	-	22	3142	c.2856A>G	c.(2854-2856)ttA>ttG	p.L952L	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000437017.1_Silent_p.L952L	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	952					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)				CTTCATCAAATAATAGAAGAC	0.289													T|||	27	0.00539137	0.0	0.0029	5008	,	,		16957	0.0		0.0249	False		,,,				2504	0.0				p.L952L		Atlas-SNP	.											.	RTTN	184	.	0			c.A2856G						PASS	.	T		17,3579		1,15,1782	89.0	77.0	81.0		2856	-3.0	0.8	18	dbSNP_126	81	195,7941		1,193,3874	no	coding-synonymous	RTTN	NM_173630.3		2,208,5656	CC,CT,TT		2.3968,0.4727,1.807		952/2227	67802449	212,11520	1798	4068	5866	SO:0001819	synonymous_variant	25914	exon22			ATCAAATAATAGA	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.2856A>G	18.37:g.67802449T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	143	82	0.573427	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Silent	SNP	ENST00000255674.6	37	CCDS42443.1																																																																																			T|0.986;C|0.014	0.014	strong		0.289	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
ZNF781	163115	hgsc.bcm.edu	37	19	38160742	38160742	+	Missense_Mutation	SNP	T	T	C	rs149500211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38160742T>C	ENST00000590008.1	-	5	1160	c.308A>G	c.(307-309)cAt>cGt	p.H103R	ZNF781_ENST00000358582.4_Missense_Mutation_p.H103R|ZNF781_ENST00000593040.1_5'Flank|ZFP30_ENST00000586732.1_Intron			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						TCGAATAAGATGTGCACTCCG	0.368																																					p.H103R		Atlas-SNP	.											.	ZNF781	66	.	0			c.A308G						PASS	.	T	ARG/HIS	3,4403	6.2+/-15.9	0,3,2200	122.0	119.0	120.0		308	1.2	0.0	19	dbSNP_134	120	7,8593	7.1+/-27.0	0,7,4293	yes	missense	ZNF781	NM_152605.3	29	0,10,6493	CC,CT,TT		0.0814,0.0681,0.0769	possibly-damaging	103/328	38160742	10,12996	2203	4300	6503	SO:0001583	missense	163115	exon4			ATAAGATGTGCAC	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"""Zinc fingers, C2H2-type"""	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.308A>G	19.37:g.38160742T>C	ENSP00000466370:p.His103Arg	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	29	0.659091	NM_152605	Q2VPJ8	Missense_Mutation	SNP	ENST00000590008.1	37	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	T	5.903	0.350770	0.11182	6.81E-4	8.14E-4	ENSG00000196381	ENST00000358582;ENST00000545586	T	0.18174	2.23	2.23	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13030	0.0316	N	0.25789	0.76	0.09310	N	1	B	0.29862	0.259	B	0.37601	0.254	T	0.37314	-0.9711	9	0.35671	T	0.21	.	6.1414	0.20261	0.0:0.1428:0.0:0.8572	.	103	Q8N8C0	ZN781_HUMAN	R	103	ENSP00000351391:H103R	ENSP00000351391:H103R	H	-	2	0	ZNF781	42852582	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.032000	0.12266	0.114000	0.18032	-0.410000	0.06199	CAT	T|0.999;C|0.001	0.001	strong		0.368	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605	
TBPL2	387332	hgsc.bcm.edu	37	14	55907172	55907172	+	Missense_Mutation	SNP	C	C	G	rs8019270	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:55907172C>G	ENST00000247219.5	-	1	162	c.92G>C	c.(91-93)cGg>cCg	p.R31P		NM_199047.2	NP_950248.1			TATA box binding protein like 2											endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8						CTCCATGGACCGTAATCCCAC	0.662													G|||	3429	0.684704	0.8079	0.7291	5008	,	,		14117	0.6349		0.5984	False		,,,				2504	0.6268				p.R31P		Atlas-SNP	.											TBPL2,NS,carcinoma,0,2	TBPL2	27	2	0			c.G92C						PASS	.	G	PRO/ARG	3369,971		1333,703,134	38.0	40.0	40.0		92	-4.0	0.0	14	dbSNP_116	40	4943,3589		1495,1953,818	yes	missense	TBPL2	NM_199047.2	103	2828,2656,952	GG,GC,CC		42.0652,22.3733,35.4257	benign	31/376	55907172	8312,4560	2170	4266	6436	SO:0001583	missense	387332	exon1			ATGGACCGTAATC	AY457923	CCDS9724.1	14q22.2	2004-06-03			ENSG00000182521	ENSG00000182521			19841	protein-coding gene	gene with protein product		608964				14634207	Standard	NM_199047		Approved	TRF3, TBP2	uc001xby.3	Q6SJ96	OTTHUMG00000140313	ENST00000247219.5:c.92G>C	14.37:g.55907172C>G	ENSP00000247219:p.Arg31Pro	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_199047		Missense_Mutation	SNP	ENST00000247219.5	37	CCDS9724.1	1477	0.6762820512820513	387	0.7865853658536586	272	0.7513812154696132	366	0.6398601398601399	452	0.5963060686015831	G	5.876	0.345715	0.11126	0.776267	0.579348	ENSG00000182521	ENST00000247219	T	0.45276	0.9	3.12	-3.98	0.04082	.	1.197560	0.06202	N	0.683464	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	0.33523	-0.9865	9	0.38643	T	0.18	8.6782	6.0453	0.19755	0.2829:0.2463:0.4707:0.0	rs8019270;rs52821151;rs8019270	31	Q6SJ96	TBPL2_HUMAN	P	31	ENSP00000247219:R31P	ENSP00000247219:R31P	R	-	2	0	TBPL2	54976925	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.407000	0.07178	-1.351000	0.02197	-1.567000	0.00876	CGG	C|0.350;G|0.650	0.650	strong		0.662	TBPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276916.1	NM_199047	
STX17	55014	hgsc.bcm.edu	37	9	102677589	102677589	+	Missense_Mutation	SNP	T	T	C	rs41305451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:102677589T>C	ENST00000259400.6	+	2	204	c.68T>C	c.(67-69)aTa>aCa	p.I23T	STX17_ENST00000525640.1_Missense_Mutation_p.I23T|RP11-60I3.4_ENST00000524512.1_RNA|STX17_ENST00000534052.1_Missense_Mutation_p.I23T	NM_017919.2	NP_060389.2	P56962	STX17_HUMAN	syntaxin 17	23					autophagic vacuole fusion (GO:0000046)|endoplasmic reticulum-Golgi intermediate compartment organization (GO:0097111)|ER to Golgi vesicle-mediated transport (GO:0006888)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|protein localization to pre-autophagosomal structure (GO:0034497)	autophagic vacuole membrane (GO:0000421)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle (GO:0030134)|ER-mitochondrion membrane contact site (GO:0044233)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|smooth endoplasmic reticulum membrane (GO:0030868)|SNARE complex (GO:0031201)	protein phosphatase binding (GO:0019903)|SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				TTCATTAAGATAGTAATCCCA	0.363													T|||	153	0.0305511	0.0038	0.036	5008	,	,		16231	0.001		0.0924	False		,,,				2504	0.0297				p.I23T		Atlas-SNP	.											.	STX17	17	.	0			c.T68C						PASS	.	T	THR/ILE	63,4343	59.3+/-96.0	1,61,2141	99.0	102.0	101.0		68	5.3	1.0	9	dbSNP_127	101	770,7830	182.2+/-230.7	35,700,3565	yes	missense	STX17	NM_017919.2	89	36,761,5706	CC,CT,TT		8.9535,1.4299,6.4047	benign	23/303	102677589	833,12173	2203	4300	6503	SO:0001583	missense	55014	exon2			TTAAGATAGTAAT	AL834371	CCDS6745.1	9q31.1	2008-02-05			ENSG00000136874	ENSG00000136874			11432	protein-coding gene	gene with protein product		604204				9852078	Standard	NM_017919		Approved	FLJ20651	uc004bal.4	P56962	OTTHUMG00000020359	ENST00000259400.6:c.68T>C	9.37:g.102677589T>C	ENSP00000259400:p.Ile23Thr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_017919	Q4VXC2	Missense_Mutation	SNP	ENST00000259400.6	37	CCDS6745.1	94	0.04304029304029304	4	0.008130081300813009	13	0.03591160220994475	1	0.0017482517482517483	76	0.10026385224274406	T	16.64	3.180517	0.57800	0.014299	0.089535	ENSG00000136874	ENST00000259400;ENST00000531035;ENST00000525640;ENST00000534052;ENST00000526607	T;T;T	0.21734	1.99;1.99;1.99	5.32	5.32	0.75619	t-SNARE (1);	0.108846	0.64402	D	0.000007	T	0.00356	0.0011	N	0.19112	0.55	0.35359	D	0.78806	B;P	0.38504	0.309;0.634	B;B	0.34242	0.039;0.178	T	0.17653	-1.0362	10	0.66056	D	0.02	-5.6625	12.974	0.58527	0.0:0.0:0.0:1.0	rs41305451	23;23	P56962;B4DJ69	STX17_HUMAN;.	T	23	ENSP00000259400:I23T;ENSP00000435981:I23T;ENSP00000433484:I23T	ENSP00000259400:I23T	I	+	2	0	STX17	101717410	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.766000	0.68843	2.150000	0.67090	0.533000	0.62120	ATA	T|0.945;C|0.055	0.055	strong		0.363	STX17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053398.3	NM_017919	
PALLD	23022	hgsc.bcm.edu	37	4	169432673	169432673	+	Silent	SNP	C	C	T	rs61051061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169432673C>T	ENST00000505667.1	+	2	191	c.18C>T	c.(16-18)tcC>tcT	p.S6S	PALLD_ENST00000261509.6_Silent_p.S6S|PALLD_ENST00000333488.4_5'Flank|PALLD_ENST00000335742.7_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	6					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		GGACCTCCTCCCATGAGTCCT	0.483									Pancreatic Cancer, Familial Clustering of				C|||	926	0.184904	0.2292	0.1441	5008	,	,		17777	0.1925		0.1958	False		,,,				2504	0.135				p.S6S	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C18T						PASS	.	C	,	1033,3373	373.0+/-320.6	129,775,1299	67.0	67.0	67.0		18,18	2.9	0.9	4	dbSNP_129	67	1775,6825	309.3+/-309.3	184,1407,2709	yes	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	313,2182,4008	TT,TC,CC		20.6395,23.4453,21.59	,	6/1124,6/1107	169432673	2808,10198	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CTCCTCCCATGAG	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.18C>T	4.37:g.169432673C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.791;T|0.209	0.209	strong		0.483	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
ALOX5	240	hgsc.bcm.edu	37	10	45869748	45869748	+	Silent	SNP	C	C	T	rs4987105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45869748C>T	ENST00000374391.2	+	1	74	c.21C>T	c.(19-21)acC>acT	p.T7T	ALOX5_ENST00000542434.1_Silent_p.T7T	NM_000698.3|NM_001256153.1	NP_000689.1|NP_001243082.1	P09917	LOX5_HUMAN	arachidonate 5-lipoxygenase	7	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				arachidonic acid metabolic process (GO:0019369)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|nuclear envelope (GO:0005635)|nuclear envelope lumen (GO:0005641)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)	arachidonate 5-lipoxygenase activity (GO:0004051)|iron ion binding (GO:0005506)			breast(1)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Lung SC(717;0.0257)			Aminosalicylic Acid(DB00233)|Balsalazide(DB01014)|Diclofenac(DB00586)|Diethylcarbamazine(DB00711)|Masoprocol(DB00179)|Meclofenamic acid(DB00939)|Mesalazine(DB00244)|Minocycline(DB01017)|Montelukast(DB00471)|Sulfasalazine(DB00795)|Vitamin E(DB00163)|Zileuton(DB00744)	ACACGGTCACCGTGGCCACTG	0.711													C|||	856	0.170927	0.1626	0.1326	5008	,	,		8346	0.1855		0.1759	False		,,,				2504	0.1892				p.T7T		Atlas-SNP	.											.	ALOX5	88	.	0			c.C21T						PASS	.	C		498,3684		27,444,1620	18.0	12.0	14.0		21	-2.2	1.0	10	dbSNP_113	14	1033,7217		64,905,3156	no	coding-synonymous	ALOX5	NM_000698.2		91,1349,4776	TT,TC,CC		12.5212,11.9082,12.315		7/675	45869748	1531,10901	2091	4125	6216	SO:0001819	synonymous_variant	240	exon1			GGTCACCGTGGCC	J03571	CCDS7212.1, CCDS58078.1	10q11.2	2008-03-18			ENSG00000012779	ENSG00000012779	1.13.11.34	"""Arachidonate lipoxygenases"""	435	protein-coding gene	gene with protein product		152390				2565035	Standard	NM_001256153		Approved	5-LOX	uc001jce.4	P09917	OTTHUMG00000018081	ENST00000374391.2:c.21C>T	10.37:g.45869748C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_000698	B7ZLS0|E5FPY5|E5FPY7|E5FPY8|Q5JQ14	Silent	SNP	ENST00000374391.2	37	CCDS7212.1																																																																																			C|0.852;T|0.148	0.148	strong		0.711	ALOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047780.1		
FAM129A	116496	hgsc.bcm.edu	37	1	184764824	184764824	+	Missense_Mutation	SNP	C	C	T	rs35704242	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:184764824C>T	ENST00000367511.3	-	14	2267	c.2074G>A	c.(2074-2076)Gat>Aat	p.D692N	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	692	Glu-rich.		D -> N (in dbSNP:rs35704242). {ECO:0000269|Ref.7}.		negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						GGTTCTTCATCCTCAAGGGTC	0.572													C|||	188	0.0375399	0.0371	0.0418	5008	,	,		17643	0.001		0.0676	False		,,,				2504	0.0419				p.D692N		Atlas-SNP	.											.	FAM129A	98	.	0			c.G2074A						PASS	.	C	ASN/ASP	209,4197	129.4+/-166.1	2,205,1996	60.0	52.0	55.0		2074	-0.2	0.0	1	dbSNP_126	55	546,8054	149.2+/-204.3	17,512,3771	yes	missense	FAM129A	NM_052966.2	23	19,717,5767	TT,TC,CC		6.3488,4.7435,5.805	possibly-damaging	692/929	184764824	755,12251	2203	4300	6503	SO:0001583	missense	116496	exon14			CTTCATCCTCAAG	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.2074G>A	1.37:g.184764824C>T	ENSP00000356481:p.Asp692Asn	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	90	0.04120879120879121	21	0.042682926829268296	15	0.04143646408839779	1	0.0017482517482517483	53	0.06992084432717678	C	9.724	1.160370	0.21454	0.047435	0.063488	ENSG00000135842	ENST00000367511	T	0.10573	2.86	5.58	-0.151	0.13411	.	0.847425	0.10520	N	0.665133	T	0.00440	0.0014	L	0.34521	1.04	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.43782	-0.9370	10	0.07482	T	0.82	-1.1787	3.9377	0.09313	0.0:0.2839:0.3578:0.3583	rs35704242	692	Q9BZQ8	NIBAN_HUMAN	N	692	ENSP00000356481:D692N	ENSP00000356481:D692N	D	-	1	0	FAM129A	183031447	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.098000	0.11024	0.306000	0.22856	0.491000	0.48974	GAT	C|0.954;T|0.046	0.046	strong		0.572	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
SPINK5	11005	hgsc.bcm.edu	37	5	147475386	147475386	+	Missense_Mutation	SNP	A	A	G	rs6892205	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:147475386A>G	ENST00000256084.7	+	10	842	c.800A>G	c.(799-801)cAg>cGg	p.Q267R	SPINK5_ENST00000398454.1_Missense_Mutation_p.Q267R|SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Missense_Mutation_p.Q267R	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	267	Kazal-like 4. {ECO:0000255|PROSITE- ProRule:PRU00798}.		Q -> R (in dbSNP:rs6892205). {ECO:0000269|PubMed:10419450, ECO:0000269|PubMed:10835624, ECO:0000269|PubMed:16374478}.		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGCAAGCAGCGTTTTTCA	0.328													G|||	2549	0.508986	0.4682	0.6513	5008	,	,		16973	0.4812		0.4911	False		,,,				2504	0.5102				p.Q267R		Atlas-SNP	.											.	SPINK5	245	.	0			c.A800G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN	1667,1953		395,877,538	62.0	59.0	60.0		800,800,800	-7.6	0.0	5	dbSNP_116	60	4132,4000		1035,2062,969	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	43,43,43	1430,2939,1507	GG,GA,AA		49.1884,46.0497,49.3448	benign,benign,benign	267/1095,267/917,267/1065	147475386	5799,5953	1810	4066	5876	SO:0001583	missense	11005	exon10			GCAAGCAGCGTTT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.800A>G	5.37:g.147475386A>G	ENSP00000256084:p.Gln267Arg	Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	285	283	0.992982	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	1066	0.4880952380952381	234	0.47560975609756095	225	0.6215469613259669	261	0.4562937062937063	346	0.45646437994722955	G	0.001	-2.903181	0.00058	0.460497	0.508116	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.03982	3.74;3.74;3.74;3.74	3.82	-7.64	0.01286	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	1.769670	0.03657	N	0.241988	T	0.00012	0.0000	N	0.03324	-0.35	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.38090	-0.9677	9	0.10636	T	0.68	4.561	16.3779	0.83412	0.2944:0.0:0.7056:0.0	rs6892205;rs58932860;rs6892205	267;267;267	Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;ISK5_HUMAN;.	R	267;267;248;267	ENSP00000381472:Q267R;ENSP00000352936:Q267R;ENSP00000421519:Q248R;ENSP00000256084:Q267R	ENSP00000256084:Q267R	Q	+	2	0	SPINK5	147455579	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-4.017000	0.00312	-2.626000	0.00437	-2.194000	0.00310	CAG	A|0.517;G|0.483	0.483	strong		0.328	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
EHMT1	79813	hgsc.bcm.edu	37	9	140638416	140638416	+	Silent	SNP	G	G	A	rs1129767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140638416G>A	ENST00000460843.1	+	6	1071	c.1044G>A	c.(1042-1044)tcG>tcA	p.S348S	EHMT1_ENST00000334856.6_Silent_p.S317S|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.S348S	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	348					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		AGATGGACTCGGATGAGGACG	0.632													G|||	763	0.152356	0.0068	0.3862	5008	,	,		18222	0.1012		0.167	False		,,,				2504	0.2209				p.S348S		Atlas-SNP	.											EHMT1_ENST00000460843,colon,carcinoma,+1,2	EHMT1	196	2	0			c.G1044A						PASS	.	G	,	169,4237	109.9+/-148.2	2,165,2036	56.0	50.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1044,1044	-10.8	0.0	9	dbSNP_86	52	1537,7063	288.9+/-299.0	144,1249,2907	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	146,1414,4943	AA,AG,GG		17.8721,3.8357,13.117	,	348/809,348/1299	140638416	1706,11300	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon6			GGACTCGGATGAG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1044G>A	9.37:g.140638416G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			G|0.862;A|0.138	0.138	strong		0.632	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
WDR5B	54554	hgsc.bcm.edu	37	3	122133830	122133830	+	Silent	SNP	T	T	G	rs3749213	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:122133830T>G	ENST00000330689.4	-	1	1052	c.546A>C	c.(544-546)atA>atC	p.I182I	RP11-299J3.8_ENST00000608346.1_RNA|RP11-299J3.8_ENST00000608756.1_RNA|RP11-299J3.8_ENST00000608465.1_RNA|RP11-299J3.8_ENST00000608015.1_RNA|RP11-299J3.8_ENST00000609469.1_RNA	NM_019069.3	NP_061942.2	Q86VZ2	WDR5B_HUMAN	WD repeat domain 5B	182										kidney(2)|large_intestine(4)|lung(2)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	13				GBM - Glioblastoma multiforme(114;0.0704)		TACCTGACACTATCAAGGACC	0.428													T|||	983	0.196286	0.1089	0.2118	5008	,	,		20763	0.2192		0.2584	False		,,,				2504	0.2157				p.I182I		Atlas-SNP	.											.	WDR5B	36	.	0			c.A546C						PASS	.	T		542,3864	244.3+/-253.7	26,490,1687	81.0	80.0	80.0		546	0.8	1.0	3	dbSNP_107	80	2239,6361	376.6+/-338.2	295,1649,2356	no	coding-synonymous	WDR5B	NM_019069.3		321,2139,4043	GG,GT,TT		26.0349,12.3014,21.3824		182/331	122133830	2781,10225	2203	4300	6503	SO:0001819	synonymous_variant	54554	exon1			TGACACTATCAAG	AK002149	CCDS3012.1	3q21.1	2013-01-09			ENSG00000196981	ENSG00000196981		"""WD repeat domain containing"""	17826	protein-coding gene	gene with protein product						10369878	Standard	NM_019069		Approved	FLJ11287	uc003efa.1	Q86VZ2	OTTHUMG00000159489	ENST00000330689.4:c.546A>C	3.37:g.122133830T>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	136	58	0.426471	NM_019069	B2RCM9|Q9NUL4	Silent	SNP	ENST00000330689.4	37	CCDS3012.1																																																																																			T|0.790;G|0.210	0.210	strong		0.428	WDR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355753.1	NM_019069	
OPLAH	26873	hgsc.bcm.edu	37	8	145108191	145108191	+	Missense_Mutation	SNP	T	T	C	rs200702041	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145108191T>C	ENST00000426825.1	-	20	2873	c.2792A>G	c.(2791-2793)cAg>cGg	p.Q931R	CTD-3065J16.6_ENST00000561181.1_RNA|OPLAH_ENST00000534424.1_5'UTR|CTD-3065J16.6_ENST00000528912.1_RNA	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	931					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)			GATGCCCTTCTGGTTGGCTGC	0.657													T|||	2	0.000399361	0.0	0.0	5008	,	,		19625	0.0		0.002	False		,,,				2504	0.0				p.Q931R		Atlas-SNP	.											.	OPLAH	78	.	0			c.A2792G						PASS	.	T	ARG/GLN	2,4156		0,2,2077	50.0	56.0	54.0		2792	4.6	1.0	8		54	46,8358		0,46,4156	yes	missense	OPLAH	NM_017570.3	43	0,48,6233	CC,CT,TT		0.5474,0.0481,0.3821	benign	931/1289	145108191	48,12514	2079	4202	6281	SO:0001583	missense	26873	exon20			CCCTTCTGGTTGG	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.2792A>G	8.37:g.145108191T>C	ENSP00000475943:p.Gln931Arg	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	152	63	0.414474	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	T	15.78	2.934711	0.52866	4.81E-4	0.005474	ENSG00000178814	ENST00000426825	.	.	.	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	.	.	.	0.42144	D	0.991525	B	0.21225	0.053	B	0.25759	0.063	T	0.57039	-0.7879	7	0.42905	T	0.14	.	11.8502	0.52407	0.0:0.0:0.0:1.0	.	931	O14841	OPLA_HUMAN	R	931	.	ENSP00000412071:Q931R	Q	-	2	0	OPLAH	145180179	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.215000	0.42862	1.681000	0.50988	0.368000	0.22195	CAG	T|0.996;C|0.004	0.004	weak		0.657	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
ACVR1	90	hgsc.bcm.edu	37	2	158636910	158636910	+	Silent	SNP	G	G	A	rs2227861	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:158636910G>A	ENST00000263640.3	-	4	699	c.270C>T	c.(268-270)gcC>gcT	p.A90A	ACVR1_ENST00000409283.2_Silent_p.A90A|ACVR1_ENST00000487456.1_5'UTR|ACVR1_ENST00000434821.1_Silent_p.A90A|ACVR1_ENST00000410057.2_Silent_p.A90A	NM_001105.4	NP_001096.1	Q04771	ACVR1_HUMAN	activin A receptor, type I	90					activin receptor signaling pathway (GO:0032924)|acute inflammatory response (GO:0002526)|atrial septum primum morphogenesis (GO:0003289)|BMP signaling pathway (GO:0030509)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to glucocorticoid stimulus (GO:0071385)|determination of left/right symmetry (GO:0007368)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cushion cell fate commitment (GO:0061445)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation with mouth forming second (GO:0001702)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|mesoderm formation (GO:0001707)|mitral valve morphogenesis (GO:0003183)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of signal transduction (GO:0009968)|neural crest cell migration (GO:0001755)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|patterning of blood vessels (GO:0001569)|peptidyl-threonine phosphorylation (GO:0018107)|pharyngeal system development (GO:0060037)|positive regulation of bone mineralization (GO:0030501)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of ossification (GO:0030278)|regulation of skeletal muscle tissue development (GO:0048641)|smooth muscle cell differentiation (GO:0051145)|transforming growth factor beta receptor signaling pathway (GO:0007179)|urogenital system development (GO:0001655)	activin receptor complex (GO:0048179)|apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|peptide hormone binding (GO:0017046)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	19				BRCA - Breast invasive adenocarcinoma(221;0.104)	Adenosine triphosphate(DB00171)	AGCACTCCACGGCTTGGCCAG	0.537													G|||	3260	0.650958	0.1838	0.7666	5008	,	,		19153	0.9067		0.7793	False		,,,				2504	0.8047				p.A90A		Atlas-SNP	.											.	ACVR1	52	.	0			c.C270T						PASS	.	G	,	1220,3186	422.3+/-339.7	178,864,1161	64.0	67.0	66.0		270,270	-7.7	0.8	2	dbSNP_98	66	6645,1955	723.8+/-406.5	2563,1519,218	no	coding-synonymous,coding-synonymous	ACVR1	NM_001105.4,NM_001111067.2	,	2741,2383,1379	AA,AG,GG		22.7326,27.6895,39.5279	,	90/510,90/510	158636910	7865,5141	2203	4300	6503	SO:0001819	synonymous_variant	90	exon4			CTCCACGGCTTGG		CCDS2206.1	2q23-q24	2008-06-13			ENSG00000115170	ENSG00000115170			171	protein-coding gene	gene with protein product		102576		ACVRLK2		8397373	Standard	NM_001105		Approved	SKR1, ALK2, ACVR1A	uc010fog.2	Q04771	OTTHUMG00000131967	ENST00000263640.3:c.270C>T	2.37:g.158636910G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	91	87	0.956044	NM_001105		Silent	SNP	ENST00000263640.3	37	CCDS2206.1																																																																																			G|0.366;A|0.634	0.634	strong		0.537	ACVR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254927.1	NM_001105	
ABCA13	154664	hgsc.bcm.edu	37	7	48314279	48314279	+	Silent	SNP	G	G	A	rs6955212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48314279G>A	ENST00000435803.1	+	17	5040	c.5016G>A	c.(5014-5016)aaG>aaA	p.K1672K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1672					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						CCCTTAAGAAGGCAGACATAG	0.393													G|||	968	0.193291	0.1498	0.2709	5008	,	,		22975	0.2153		0.1322	False		,,,				2504	0.2372				p.K1672K		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,+1,2	ABCA13	1192	2	0			c.G5016A						PASS	.	G		585,3223		48,489,1367	153.0	145.0	148.0		5016	2.3	0.3	7	dbSNP_116	148	1164,7050		92,980,3035	no	coding-synonymous	ABCA13	NM_152701.3		140,1469,4402	AA,AG,GG		14.1709,15.3624,14.5483		1672/5059	48314279	1749,10273	1904	4107	6011	SO:0001819	synonymous_variant	154664	exon17			TAAGAAGGCAGAC	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.5016G>A	7.37:g.48314279G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			G|0.816;A|0.184	0.184	strong		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
KIAA0020	9933	hgsc.bcm.edu	37	9	2804393	2804393	+	Silent	SNP	A	A	G	rs12171	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:2804393A>G	ENST00000397885.2	-	18	2091	c.1885T>C	c.(1885-1887)Ttg>Ctg	p.L629L		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	629						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		GTTTTTTCCAATGTAGGAATC	0.368													A|||	525	0.104832	0.2103	0.0922	5008	,	,		18240	0.0506		0.0378	False		,,,				2504	0.0961				p.L629L		Atlas-SNP	.											.	KIAA0020	56	.	0			c.T1885C						PASS	.	A		832,3574	330.4+/-301.5	78,676,1449	113.0	103.0	106.0		1885	-3.4	0.0	9	dbSNP_52	106	394,8206	126.0+/-184.5	8,378,3914	no	coding-synonymous	KIAA0020	NM_014878.4		86,1054,5363	GG,GA,AA		4.5814,18.8833,9.4264		629/649	2804393	1226,11780	2203	4300	6503	SO:0001819	synonymous_variant	9933	exon18			TTTCCAATGTAGG	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1885T>C	9.37:g.2804393A>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	199	95	0.477387	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Silent	SNP	ENST00000397885.2	37	CCDS6448.2																																																																																			A|0.909;G|0.091	0.091	strong		0.368	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
OR51A7	119687	hgsc.bcm.edu	37	11	4928841	4928841	+	Missense_Mutation	SNP	T	T	C	rs7108225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4928841T>C	ENST00000359350.4	+	1	242	c.242T>C	c.(241-243)aTg>aCg	p.M81T	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	81			M -> T (in dbSNP:rs7108225).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTTCCTACCATGTTGAGGGTC	0.458													T|||	287	0.0573083	0.0295	0.0663	5008	,	,		22110	0.002		0.1193	False		,,,				2504	0.0818				p.M81T		Atlas-SNP	.											OR51A7,colon,carcinoma,0,4	OR51A7	86	4	0			c.T242C						scavenged	.	T	THR/MET	231,4171	136.1+/-172.1	5,221,1975	155.0	133.0	141.0		242	3.9	1.0	11	dbSNP_116	141	1037,7559	221.5+/-258.9	63,911,3324	yes	missense	OR51A7	NM_001004749.1	81	68,1132,5299	CC,CT,TT		12.0638,5.2476,9.7553	benign	81/313	4928841	1268,11730	2201	4298	6499	SO:0001583	missense	119687	exon1			CTACCATGTTGAG	AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.242T>C	11.37:g.4928841T>C	ENSP00000352305:p.Met81Thr	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_001004749	Q6IFH8	Missense_Mutation	SNP	ENST00000359350.4	37	CCDS31364.1	126	0.057692307692307696	12	0.024390243902439025	27	0.07458563535911603	1	0.0017482517482517483	86	0.11345646437994723	T	12.31	1.899731	0.33535	0.052476	0.120638	ENSG00000176895	ENST00000359350;ENST00000545959;ENST00000544684	T	0.05996	3.36	5.02	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000020	T	0.00144	0.0004	L	0.58354	1.805	0.26250	N	0.978736	B	0.24920	0.114	B	0.31869	0.137	T	0.25745	-1.0123	10	0.31617	T	0.26	.	9.9807	0.41811	0.0:0.0826:0.0:0.9173	rs7108225;rs17252300;rs52835214;rs61049276;rs7108225	81	Q8NH64	O51A7_HUMAN	T	81;81;70	ENSP00000352305:M81T	ENSP00000352305:M81T	M	+	2	0	OR51A7	4885417	0.003000	0.15002	0.998000	0.56505	0.856000	0.48823	1.307000	0.33516	2.098000	0.63641	0.533000	0.62120	ATG	T|0.918;C|0.082	0.082	strong		0.458	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
FAM120B	84498	hgsc.bcm.edu	37	6	170627761	170627761	+	Missense_Mutation	SNP	A	A	G	rs6900199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:170627761A>G	ENST00000476287.1	+	2	1391	c.1283A>G	c.(1282-1284)tAt>tGt	p.Y428C	FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000540480.1_Missense_Mutation_p.Y440C|FAM120B_ENST00000537664.1_Missense_Mutation_p.Y451C	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	428			Y -> C (in dbSNP:rs6900199).		cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GTTCCCATGTATACAGACTCT	0.507													G|||	820	0.163738	0.0885	0.2075	5008	,	,		20552	0.2817		0.1262	False		,,,				2504	0.1513				p.Y428C		Atlas-SNP	.											.	FAM120B	108	.	0			c.A1283G						PASS	.	A	CYS/TYR	520,3886	777.7+/-414.2	33,454,1716	183.0	199.0	194.0		1283	-2.0	0.0	6	dbSNP_116	194	1214,7386	762.3+/-407.6	95,1024,3181	no	missense	FAM120B	NM_032448.1	194	128,1478,4897	GG,GA,AA		14.1163,11.8021,13.3323	benign	428/911	170627761	1734,11272	2203	4300	6503	SO:0001583	missense	84498	exon2			CCATGTATACAGA	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.1283A>G	6.37:g.170627761A>G	ENSP00000417970:p.Tyr428Cys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	60	6	0.1	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	388	0.17765567765567766	64	0.13008130081300814	61	0.1685082872928177	164	0.2867132867132867	99	0.13060686015831136	G	3.367	-0.129275	0.06753	0.118021	0.141163	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.08102	3.13;3.13;3.13	3.07	-2.02	0.07388	.	1.085760	0.06844	N	0.796216	T	0.00524	0.0017	N	0.00159	-1.955	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47573	-0.9107	9	0.54805	T	0.06	1.1396	4.8427	0.13498	0.4009:0.0:0.4558:0.1433	rs6900199;rs17860762;rs6900199	428;428	Q96EK7;F2Z2E1	F120B_HUMAN;.	C	440;451;428	ENSP00000444125:Y440C;ENSP00000440125:Y451C;ENSP00000417970:Y428C	ENSP00000436640:Y428C	Y	+	2	0	FAM120B	170469686	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.638000	0.02013	-0.544000	0.06232	-0.734000	0.03567	TAT	A|0.862;G|0.138	0.138	strong		0.507	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
INSR	3643	hgsc.bcm.edu	37	19	7184518	7184518	+	Silent	SNP	G	G	A	rs891087	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7184518G>A	ENST00000302850.5	-	3	925	c.783C>T	c.(781-783)gaC>gaT	p.D261D	INSR_ENST00000341500.5_Silent_p.D261D	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	261	Cys-rich.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CACACCTGCCGTCCAGGTAGA	0.627													G|||	694	0.138578	0.2262	0.085	5008	,	,		12759	0.0486		0.0726	False		,,,				2504	0.2188				p.D261D		Atlas-SNP	.											.	INSR	265	.	0			c.C783T						PASS	.	G	,	885,3521	334.7+/-303.5	91,703,1409	43.0	38.0	39.0		783,783	-8.6	0.5	19	dbSNP_86	39	747,7853	176.2+/-226.1	28,691,3581	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	119,1394,4990	AA,AG,GG		8.686,20.0862,12.5481	,	261/1383,261/1371	7184518	1632,11374	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon3			CCTGCCGTCCAGG	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.783C>T	19.37:g.7184518G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			A|0.117;C|0.000;G|0.883;T|0.000	0.117	strong		0.627	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
NASP	4678	hgsc.bcm.edu	37	1	46073697	46073697	+	Missense_Mutation	SNP	C	C	A	rs200497808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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_ENST00000372052.4_Intron|NASP_ENST00000351223.3_Intron|NASP_ENST00000537798.1_Missense_Mutation_p.P308T	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	322	6	0.0186335		WXS	Illumina HiSeq	Phase_I	351	15	0.042735	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	
PZP	5858	hgsc.bcm.edu	37	12	9303296	9303296	+	Missense_Mutation	SNP	A	A	T	rs10842971	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9303296A>T	ENST00000261336.2	-	34	4356	c.4328T>A	c.(4327-4329)aTc>aAc	p.I1443N	PZP_ENST00000381997.2_Missense_Mutation_p.I1229N	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1443			I -> N (in dbSNP:rs10842971).		female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.I1229N(1)|p.I1443N(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						TCCTACTGGGATGTCTTGCAG	0.398													A|||	954	0.190495	0.1172	0.3458	5008	,	,		-128	0.0655		0.2823	False		,,,				2504	0.2137				p.I1443N	Melanoma(125;1402 1695 4685 34487 38571)	Atlas-SNP	.											PZP_ENST00000381997,NS,carcinoma,0,2	PZP	422	2	2	Substitution - Missense(2)	stomach(2)	c.T4328A						PASS	.	A	ASN/ILE	625,3781	270.4+/-269.6	40,545,1618	130.0	123.0	125.0		4328	4.2	0.0	12	dbSNP_120	125	2559,6041	416.9+/-352.3	388,1783,2129	yes	missense	PZP	NM_002864.2	149	428,2328,3747	TT,TA,AA		29.7558,14.1852,24.481	probably-damaging	1443/1483	9303296	3184,9822	2203	4300	6503	SO:0001583	missense	5858	exon34			ACTGGGATGTCTT	X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.4328T>A	12.37:g.9303296A>T	ENSP00000261336:p.Ile1443Asn	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_002864	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	435	0.19917582417582416	53	0.10772357723577236	117	0.32320441988950277	34	0.05944055944055944	231	0.30474934036939316	A	9.854	1.194413	0.22037	0.141852	0.297558	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.23950	1.88;1.88	4.18	4.18	0.49190	Alpha-macroglobulin, receptor-binding (3);	0.289408	0.27311	U	0.019954	T	0.00012	0.0000	L	0.57536	1.79	0.52099	P	5.100000000002325E-5	P;D	0.76494	0.899;0.999	P;D	0.69824	0.491;0.966	T	0.30297	-0.9983	9	0.40728	T	0.16	.	12.7098	0.57083	1.0:0.0:0.0:0.0	rs10842971;rs17803568;rs10842971	1229;1443	P20742-2;P20742	.;PZP_HUMAN	N	1443;1229	ENSP00000261336:I1443N;ENSP00000371427:I1229N	ENSP00000261336:I1443N	I	-	2	0	PZP	9194563	0.334000	0.24739	0.040000	0.18447	0.161000	0.22273	4.995000	0.63908	1.817000	0.53016	0.460000	0.39030	ATC	A|0.782;T|0.218	0.218	strong		0.398	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1	NM_002864	
ALPK2	115701	hgsc.bcm.edu	37	18	56204644	56204644	+	Silent	SNP	T	T	G	rs12963422	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:56204644T>G	ENST00000361673.3	-	5	2988	c.2775A>C	c.(2773-2775)gtA>gtC	p.V925V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	925						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						GGCCAGCATGTACTGTGGAGG	0.488													T|||	1690	0.33746	0.0696	0.3184	5008	,	,		19240	0.5734		0.3221	False		,,,				2504	0.4857				p.V925V		Atlas-SNP	.											.	ALPK2	487	.	0			c.A2775C						PASS	.	T		551,3855	246.8+/-255.3	46,459,1698	49.0	52.0	51.0		2775	-8.2	0.0	18	dbSNP_121	51	3187,5413	482.5+/-370.9	600,1987,1713	no	coding-synonymous	ALPK2	NM_052947.3		646,2446,3411	GG,GT,TT		37.0581,12.5057,28.7406		925/2171	56204644	3738,9268	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			AGCATGTACTGTG	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.2775A>C	18.37:g.56204644T>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	89	55	0.617977	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			G|0.303;N|0.000	0.303	strong		0.488	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
CDKN1A	1026	hgsc.bcm.edu	37	6	36651971	36651971	+	Missense_Mutation	SNP	C	C	A	rs1801270	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36651971C>A	ENST00000405375.1	+	2	328	c.93C>A	c.(91-93)agC>agA	p.S31R	CDKN1A_ENST00000448526.2_Missense_Mutation_p.S65R|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000373711.2_Missense_Mutation_p.S31R|CDKN1A_ENST00000244741.5_Missense_Mutation_p.S31R	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	31			S -> R (in dbSNP:rs1801270). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7655464, ECO:0000269|Ref.8}.		cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						AGCAGCTGAGCCGCGACTGTG	0.647													C|||	1283	0.25619	0.3094	0.2493	5008	,	,		18195	0.4881		0.0666	False		,,,				2504	0.1452				p.S31R		Atlas-SNP	.											.	CDKN1A	27	.	0			c.C93A	GRCh37	CM940226	CDKN1A	M	rs1801270	PASS	.	C	ARG/SER,ARG/SER,ARG/SER,ARG/SER	1057,3349	376.1+/-321.9	130,797,1276	40.0	37.0	38.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	93,93,93,93	-3.6	0.3	6	dbSNP_89	38	602,7998	157.3+/-211.0	21,560,3719	yes	missense,missense,missense,missense	CDKN1A	NM_000389.4,NM_001220777.1,NM_001220778.1,NM_078467.2	110,110,110,110	151,1357,4995	AA,AC,CC		7.0,23.99,12.7557	benign,benign,benign,benign	31/165,31/165,31/165,31/165	36651971	1659,11347	2203	4300	6503	SO:0001583	missense	1026	exon2			GCTGAGCCGCGAC	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.93C>A	6.37:g.36651971C>A	ENSP00000384849:p.Ser31Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	539	0.2467948717948718	147	0.29878048780487804	80	0.22099447513812154	262	0.458041958041958	50	0.06596306068601583	C	0.006	-2.057394	0.00390	0.2399	0.07	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	5.06	-3.6	0.04570	.	0.965863	0.08530	N	0.932136	T	0.30759	0.0775	N	0.05012	-0.13	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.07809	-1.0753	9	0.05351	T	0.99	-7.2889	5.3115	0.15833	0.2314:0.199:0.4908:0.0788	rs1801270;rs3176351;rs17849556;rs17851079;rs1801270	65;31;31	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	R	65;31;31;31	ENSP00000409259:S65R;ENSP00000244741:S31R;ENSP00000384849:S31R;ENSP00000362815:S31R	ENSP00000244741:S31R	S	+	3	2	CDKN1A	36759949	0.925000	0.31364	0.288000	0.24862	0.068000	0.16541	0.270000	0.18607	-0.519000	0.06444	-1.383000	0.01170	AGC	C|0.812;A|0.188	0.188	strong		0.647	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	
MXRA5	25878	hgsc.bcm.edu	37	X	3228411	3228411	+	Silent	SNP	G	G	A	rs1635233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3228411G>A	ENST00000217939.6	-	7	7987	c.7833C>T	c.(7831-7833)gcC>gcT	p.A2611A		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2611	Ig-like C2-type 10.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGTAGGCCCCGGCGTCCACCG	0.607													g|||	2802	0.742252	0.6672	0.5202	3775	,	,		10932	0.5565		0.5209	False		,,,				2504	0.4847				p.A2611A		Atlas-SNP	.											.	MXRA5	815	.	0			c.C7833T						PASS	.	A		3229,558		1206,350,467,58,92	17.0	18.0	18.0		7833	-8.5	0.0	X	dbSNP_89	18	4289,2368		1029,1084,1147,301,682	no	coding-synonymous	MXRA5	NM_015419.3		2235,1434,1614,359,774	AA,AG,A,GG,G		35.5716,14.7346,28.0161		2611/2829	3228411	7518,2926	2173	4243	6416	SO:0001819	synonymous_variant	25878	exon7			GGCCCCGGCGTCC	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.7833C>T	X.37:g.3228411G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	223	211	0.946188	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			A|1.000;|0.000	1.000	weak		0.607	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
C17orf107	100130311	hgsc.bcm.edu	37	17	4803711	4803711	+	Nonsense_Mutation	SNP	G	G	A	rs35400274	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4803711G>A	ENST00000381365.3	+	3	683	c.456G>A	c.(454-456)tgG>tgA	p.W152*	C17orf107_ENST00000521575.1_3'UTR|CHRNE_ENST00000575637.1_5'Flank|CHRNE_ENST00000293780.4_Intron	NM_001145536.1	NP_001139008.1	Q6ZR85	CQ107_HUMAN	chromosome 17 open reading frame 107	152										endometrium(2)	2						AGGGAGCATGGCTATGCCTGT	0.687													G|||	1110	0.221645	0.4145	0.2378	5008	,	,		15004	0.0863		0.1511	False		,,,				2504	0.1616				p.W152X		Atlas-SNP	.											.	C17orf107	8	.	0			c.G456A						PASS	.	G	,stop/TRP	494,890		84,326,282	22.0	30.0	28.0		,456	4.6	1.0	17	dbSNP_126	28	444,2738		34,376,1181	yes	intron,stop-gained	CHRNE,C17orf107	NM_000080.3,NM_001145536.1	,	118,702,1463	AA,AG,GG		13.9535,35.6936,20.5431	,	,152/191	4803711	938,3628	692	1591	2283	SO:0001587	stop_gained	100130311	exon3			AGCATGGCTATGC	AK128415	CCDS45591.1	17p13.2	2009-09-30			ENSG00000205710	ENSG00000205710			37238	protein-coding gene	gene with protein product							Standard	NM_001145536		Approved		uc002fzl.3	Q6ZR85	OTTHUMG00000164838	ENST00000381365.3:c.456G>A	17.37:g.4803711G>A	ENSP00000370770:p.Trp152*	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001145536		Nonsense_Mutation	SNP	ENST00000381365.3	37	CCDS45591.1	452	0.20695970695970695	219	0.4451219512195122	84	0.23204419889502761	49	0.08566433566433566	100	0.13192612137203166	G	19.87	3.907762	0.72868	0.356936	0.139535	ENSG00000205710	ENST00000381365	.	.	.	4.62	4.62	0.57501	.	0.786555	0.10471	N	0.670805	.	.	.	.	.	.	0.09310	P	0.99999863135	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.5576	12.8268	0.57725	0.0:0.0:1.0:0.0	rs35400274;rs56837916	.	.	.	X	152	.	ENSP00000370770:W152X	W	+	3	0	C17orf107	4744490	0.793000	0.28825	0.994000	0.49952	0.119000	0.20118	1.993000	0.40747	2.411000	0.81874	0.561000	0.74099	TGG	G|0.791;A|0.209	0.209	strong		0.687	C17orf107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380556.1	NM_001145536	
ENTPD3	956	hgsc.bcm.edu	37	3	40468896	40468896	+	Missense_Mutation	SNP	C	C	T	rs1047855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:40468896C>T	ENST00000301825.3	+	11	1605	c.1487C>T	c.(1486-1488)gCg>gTg	p.A496V	ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3_ENST00000456402.1_Missense_Mutation_p.A496V|ENTPD3-AS1_ENST00000452768.1_RNA	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	496			A -> V (in dbSNP:rs1047855). {ECO:0000269|PubMed:9676430}.		nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		TTCTTCACAGCGGCAGCCTTG	0.537													C|||	1392	0.277955	0.0378	0.2867	5008	,	,		21086	0.4881		0.2883	False		,,,				2504	0.3691				p.A496V		Atlas-SNP	.											ENTPD3,NS,carcinoma,-1,1	ENTPD3	48	1	0			c.C1487T						PASS	.	C	VAL/ALA	376,4030	191.9+/-217.4	23,330,1850	118.0	102.0	107.0		1487	-1.6	0.0	3	dbSNP_86	107	2551,6049	416.3+/-352.1	397,1757,2146	yes	missense	ENTPD3	NM_001248.2	64	420,2087,3996	TT,TC,CC		29.6628,8.5338,22.505	benign	496/530	40468896	2927,10079	2203	4300	6503	SO:0001583	missense	956	exon11			TCACAGCGGCAGC	AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.1487C>T	3.37:g.40468896C>T	ENSP00000301825:p.Ala496Val	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	172	171	0.994186	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Missense_Mutation	SNP	ENST00000301825.3	37	CCDS2691.1	622	0.2847985347985348	30	0.06097560975609756	117	0.32320441988950277	255	0.4458041958041958	220	0.29023746701846964	C	3.599	-0.081966	0.07141	0.085338	0.296628	ENSG00000168032	ENST00000301825;ENST00000456402	T;T	0.09817	2.94;2.94	5.18	-1.64	0.08318	.	0.634926	0.15141	N	0.278298	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.11235	0.004	B	0.06405	0.002	T	0.43877	-0.9364	9	0.16896	T	0.51	-0.097	5.6082	0.17391	0.0:0.403:0.266:0.331	rs1047855;rs3733166;rs52835170;rs58911447;rs1047855	496	O75355	ENTP3_HUMAN	V	496	ENSP00000301825:A496V;ENSP00000401565:A496V	ENSP00000301825:A496V	A	+	2	0	ENTPD3	40443900	0.014000	0.17966	0.000000	0.03702	0.167000	0.22549	0.238000	0.18004	-0.395000	0.07715	-0.140000	0.14226	GCG	C|0.754;T|0.246	0.246	strong		0.537	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248	
OR5R1	219479	hgsc.bcm.edu	37	11	56184888	56184888	+	Missense_Mutation	SNP	G	G	A	rs998544	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56184888G>A	ENST00000312253.1	-	1	820	c.821C>T	c.(820-822)gCt>gTt	p.A274V		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	274			A -> V (in dbSNP:rs998544).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					AAATACAGAAGCCATCTTGTC	0.413													G|||	2238	0.446885	0.1838	0.5922	5008	,	,		17733	0.6429		0.3708	False		,,,				2504	0.5757				p.A274V		Atlas-SNP	.											.	OR5R1	83	.	0			c.C821T						PASS	.	G	VAL/ALA	950,3452	361.4+/-315.7	113,724,1364	174.0	164.0	168.0		821	1.5	0.6	11	dbSNP_86	168	3189,5403	483.4+/-371.1	617,1955,1724	yes	missense	OR5R1	NM_001004744.1	64	730,2679,3088	AA,AG,GG		37.1159,21.5811,31.8532	probably-damaging	274/325	56184888	4139,8855	2201	4296	6497	SO:0001583	missense	219479	exon1			ACAGAAGCCATCT	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.821C>T	11.37:g.56184888G>A	ENSP00000308595:p.Ala274Val	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	933	0.4271978021978022	85	0.17276422764227642	211	0.5828729281767956	368	0.6433566433566433	269	0.3548812664907652	G	10.26	1.300901	0.23650	0.215811	0.371159	ENSG00000174942	ENST00000312253	T	0.34275	1.37	5.52	1.53	0.23141	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32593	U	0.005885	T	0.00012	0.0000	L	0.33668	1.02	0.80722	P	0.0	D	0.76494	0.999	D	0.75484	0.986	T	0.40079	-0.9582	9	0.26408	T	0.33	-11.0225	4.9356	0.13939	0.359:0.2515:0.3895:0.0	rs998544;rs52811598;rs61607512;rs998544	274	Q8NH85	OR5R1_HUMAN	V	274	ENSP00000308595:A274V	ENSP00000308595:A274V	A	-	2	0	OR5R1	55941464	0.000000	0.05858	0.634000	0.29324	0.078000	0.17371	0.518000	0.22847	0.691000	0.31592	-0.152000	0.13540	GCT	G|0.630;N|0.000	.	strong		0.413	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744	
IL15RA	3601	hgsc.bcm.edu	37	10	6008172	6008172	+	Silent	SNP	C	C	T	rs2296139	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:6008172C>T	ENST00000379977.3	-	2	316	c.219G>A	c.(217-219)acG>acA	p.T73T	IL15RA_ENST00000534292.1_5'UTR|IL15RA_ENST00000397250.2_Intron|IL15RA_ENST00000530685.1_Silent_p.T73T|IL15RA_ENST00000397251.3_Intron|IL15RA_ENST00000397255.3_Silent_p.T73T|IL15RA_ENST00000397248.2_Silent_p.T37T|IL15RA_ENST00000528354.1_Silent_p.T73T|IL15RA_ENST00000525219.2_Silent_p.T37T|IL15RA_ENST00000379971.1_Intron			Q13261	I15RA_HUMAN	interleukin 15 receptor, alpha	73	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|JAK-STAT cascade (GO:0007259)|negative regulation of neuron projection development (GO:0010977)|positive regulation of natural killer cell differentiation (GO:0032825)|response to nutrient levels (GO:0031667)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|signal transducer activity (GO:0004871)			cervix(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5						ACACGCACTCCGTCAGGCTGG	0.557													C|||	906	0.180911	0.1528	0.2363	5008	,	,		19718	0.2728		0.1372	False		,,,				2504	0.1299				p.T159T		Atlas-SNP	.											.	IL15RA	17	.	0			c.G477A						PASS	.	C	,	710,3696	295.3+/-283.6	69,572,1562	91.0	78.0	82.0		219,219	-9.6	0.0	10	dbSNP_100	82	1168,7432	238.5+/-269.9	78,1012,3210	no	coding-synonymous,coding-synonymous	IL15RA	NM_002189.3,NM_172200.2	,	147,1584,4772	TT,TC,CC		13.5814,16.1144,14.4395	,	73/268,73/235	6008172	1878,11128	2203	4300	6503	SO:0001819	synonymous_variant	3601	exon3			GCACTCCGTCAGG	U31628	CCDS7074.1, CCDS7075.1, CCDS7075.2, CCDS58069.1, CCDS73065.1	10p15.1	2012-02-27			ENSG00000134470	ENSG00000134470		"""Interleukins and interleukin receptors"", ""CD molecules"""	5978	protein-coding gene	gene with protein product		601070				8530383	Standard	NM_002189		Approved	CD215, IL-15RA	uc021pmo.1	Q13261	OTTHUMG00000017612	ENST00000379977.3:c.219G>A	10.37:g.6008172C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	154	75	0.487013	NM_001256765	B4E2C2|Q3B769|Q5JVA1|Q5JVA2|Q5JVA4|Q6B0J2|Q7LDR4|Q7Z609	Silent	SNP	ENST00000379977.3	37	CCDS7074.1	435	0.19917582417582416	75	0.1524390243902439	89	0.24585635359116023	161	0.28146853146853146	110	0.14511873350923482	C	0.281	-0.986178	0.02180	0.161144	0.135814	ENSG00000134470	ENST00000532039	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	6.999999999979245E-6	.	.	.	.	.	.	T	0.16247	-1.0409	3	.	.	.	-16.2672	4.7489	0.13050	0.1859:0.2269:0.4771:0.1101	rs2296139;rs3181146;rs59321592;rs2296139	.	.	.	Q	44	.	.	R	-	2	0	IL15RA	6048178	0.000000	0.05858	0.012000	0.15200	0.048000	0.14542	-4.151000	0.00285	-2.394000	0.00583	-1.393000	0.01150	CGG	C|0.832;T|0.168	0.168	strong		0.557	IL15RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046615.2	NM_172200, NM_002189	
AVL9	23080	hgsc.bcm.edu	37	7	32598630	32598630	+	Missense_Mutation	SNP	T	T	A	rs2290213	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:32598630T>A	ENST00000318709.4	+	10	990	c.769T>A	c.(769-771)Tgt>Agt	p.C257S	AVL9_ENST00000409301.1_Missense_Mutation_p.C257S|AVL9_ENST00000404479.1_Missense_Mutation_p.C257S	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	257			C -> S (in dbSNP:rs2290213).		cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AAGTAACCCATGTGCAGATGA	0.443													T|||	780	0.155751	0.1793	0.1066	5008	,	,		18083	0.129		0.1243	False		,,,				2504	0.2188				p.C257S		Atlas-SNP	.											.	AVL9	66	.	0			c.T769A						PASS	.	T	SER/CYS	794,3612	314.7+/-293.7	89,616,1498	97.0	94.0	95.0		769	-1.3	0.0	7	dbSNP_100	95	1098,7502	228.0+/-263.2	64,970,3266	yes	missense	AVL9	NM_015060.1	112	153,1586,4764	AA,AT,TT		12.7674,18.0209,14.5471	benign	257/649	32598630	1892,11114	2203	4300	6503	SO:0001583	missense	23080	exon10			AACCCATGTGCAG	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.769T>A	7.37:g.32598630T>A	ENSP00000315568:p.Cys257Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	37	CCDS34613.1	327	0.14972527472527472	98	0.1991869918699187	39	0.10773480662983426	91	0.1590909090909091	99	0.13060686015831136	T	0.014	-1.585371	0.00872	0.180209	0.127674	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714;ENST00000404479;ENST00000446718	T;T;T;T	0.39787	1.11;1.11;1.07;1.06	5.31	-1.29	0.09288	.	0.871343	0.10468	N	0.671197	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.31916	-0.9926	9	0.08381	T	0.77	-28.4598	6.015	0.19598	0.1203:0.42:0.0:0.4597	rs2290213;rs52798277;rs2290213	257;257;257	Q8N6Z3;Q8NBF6-2;Q8NBF6	.;.;AVL9_HUMAN	S	257;257;257;257;188	ENSP00000315568:C257S;ENSP00000387011:C257S;ENSP00000385242:C257S;ENSP00000395134:C188S	ENSP00000315568:C257S	C	+	1	0	AVL9	32565155	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-0.114000	0.10757	-0.455000	0.07054	-0.326000	0.08463	TGT	A|0.150;C|0.000;T|0.850	0.150	strong		0.443	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
DNAH17	8632	hgsc.bcm.edu	37	17	76475574	76475574	+	Silent	SNP	C	C	A	rs78514572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76475574C>A	ENST00000585328.1	-	50	8002	c.7878G>T	c.(7876-7878)gcG>gcT	p.A2626A	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.A2617A	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2617	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(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)			TACCCAGGGCCGCGGCCACCA	0.552													C|||	72	0.014377	0.0144	0.0202	5008	,	,		15817	0.001		0.0318	False		,,,				2504	0.0061				p.A2631A		Atlas-SNP	.											.	DNAH17	347	.	0			c.G7893T						PASS	.	C		65,3825		0,65,1880	46.0	49.0	48.0		7893	-8.4	0.0	17	dbSNP_133	48	225,8033		5,215,3909	no	coding-synonymous	DNAH17	NM_173628.3		5,280,5789	AA,AC,CC		2.7246,1.671,2.3872		2631/4463	76475574	290,11858	1945	4129	6074	SO:0001819	synonymous_variant	8632	exon50			CAGGGCCGCGGCC	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.7878G>T	17.37:g.76475574C>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	34	20	0.588235	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				C|0.973;A|0.027	0.027	strong		0.552	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
OR5H14	403273	hgsc.bcm.edu	37	3	97869072	97869072	+	Silent	SNP	A	A	C	rs558065491		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:97869072A>C	ENST00000437310.1	+	1	903	c.843A>C	c.(841-843)atA>atC	p.I281I	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	281						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ACACTGTCATAGTTCCTTTAT	0.378																																					p.I281I		Atlas-SNP	.											OR5H14,colon,carcinoma,+1,1	OR5H14	56	1	0			c.A843C						PASS	.						50.0	48.0	48.0					3																	97869072		2203	4297	6500	SO:0001819	synonymous_variant	403273	exon1			TGTCATAGTTCCT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.843A>C	3.37:g.97869072A>C		Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	228	106	0.464912	NM_001005514	B9EH15	Silent	SNP	ENST00000437310.1	37	CCDS33798.1																																																																																			.	.	none		0.378	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
PON1	5444	hgsc.bcm.edu	37	7	94940880	94940880	+	Missense_Mutation	SNP	A	A	C	rs144390653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:94940880A>C	ENST00000222381.3	-	5	611	c.380T>G	c.(379-381)aTg>aGg	p.M127R	PON1_ENST00000542556.1_Missense_Mutation_p.M127R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	127					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)	p.M127R(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	CAGGAGGTACATGGCATTATC	0.403													A|||	13	0.00259585	0.0	0.0072	5008	,	,		18834	0.0		0.002	False		,,,				2504	0.0061				p.M127R	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											PON1,NS,carcinoma,0,1	PON1	55	1	1	Substitution - Missense(1)	pancreas(1)	c.T380G						PASS	.	A	ARG/MET	1,4405	2.1+/-5.4	0,1,2202	115.0	108.0	111.0		380	4.9	0.6	7	dbSNP_134	111	12,8588	8.4+/-32.0	0,12,4288	yes	missense	PON1	NM_000446.5	91	0,13,6490	CC,CA,AA		0.1395,0.0227,0.1	benign	127/356	94940880	13,12993	2203	4300	6503	SO:0001583	missense	5444	exon5			AGGTACATGGCAT	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.380T>G	7.37:g.94940880A>C	ENSP00000222381:p.Met127Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	7	0.003205128205128205	0	0.0	5	0.013812154696132596	0	0.0	2	0.002638522427440633	A	10.59	1.391561	0.25118	2.27E-4	0.001395	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.39406	1.08;1.08	4.88	4.88	0.63580	Six-bladed beta-propeller, TolB-like (1);	0.186666	0.47093	D	0.000258	T	0.20536	0.0494	N	0.08118	0	0.33135	D	0.543587	B;B	0.18741	0.03;0.005	B;B	0.25614	0.062;0.017	T	0.36065	-0.9763	10	0.87932	D	0	-9.4635	14.9578	0.71131	1.0:0.0:0.0:0.0	.	127;127	F5H4W9;P27169	.;PON1_HUMAN	R	127	ENSP00000222381:M127R;ENSP00000444854:M127R	ENSP00000222381:M127R	M	-	2	0	PON1	94778816	0.997000	0.39634	0.588000	0.28705	0.083000	0.17756	8.294000	0.89934	2.187000	0.69744	0.533000	0.62120	ATG	A|0.998;C|0.002	0.002	strong		0.403	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
ALPP	250	hgsc.bcm.edu	37	2	233245026	233245026	+	Missense_Mutation	SNP	G	G	A	rs2853378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233245026G>A	ENST00000392027.2	+	6	1057	c.788G>A	c.(787-789)cGc>cAc	p.R263H	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	263			R -> H (in dbSNP:rs2853378). {ECO:0000269|PubMed:3461452}.		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)		CTGGCGAAGCGCCAGGTGATG	0.662													A|||	501	0.10004	0.0507	0.0605	5008	,	,		10859	0.2242		0.1004	False		,,,				2504	0.0665				p.R263H		Atlas-SNP	.											ALPP,NS,carcinoma,+1,1	ALPP	53	1	0			c.G788A						PASS	.						69.0	73.0	71.0					2																	233245026		2203	4300	6503	SO:0001583	missense	250	exon6			CGAAGCGCCAGGT	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.788G>A	2.37:g.233245026G>A	ENSP00000375881:p.Arg263His	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	251	121	0.482072	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	224	0.10256410256410256	21	0.042682926829268296	22	0.06077348066298342	111	0.19405594405594406	70	0.09234828496042216	.	0.012	-1.655324	0.00779	.	.	ENSG00000163283	ENST00000392027	D	0.96522	-4.04	2.31	-0.177	0.13307	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	1.003840	0.08014	N	0.990937	T	0.00608	0.0020	N	0.02685	-0.53	0.80722	P	0.0	B	0.13145	0.007	B	0.04013	0.001	T	0.54549	-0.8277	9	0.05959	T	0.93	.	7.1392	0.25546	0.6554:0.0:0.3446:0.0	rs2853378;rs12617638;rs17838624	263	P05187	PPB1_HUMAN	H	263	ENSP00000375881:R263H	ENSP00000375881:R263H	R	+	2	0	ALPP	232953270	0.000000	0.05858	0.964000	0.40570	0.162000	0.22319	0.146000	0.16180	0.135000	0.18707	-1.054000	0.02325	CGC	G|0.500;A|0.500	0.500	weak		0.662	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
MYBPC3	4607	hgsc.bcm.edu	37	11	47370041	47370041	+	Missense_Mutation	SNP	T	T	C	rs3729989	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:47370041T>C	ENST00000545968.1	-	6	760	c.706A>G	c.(706-708)Agc>Ggc	p.S236G	MYBPC3_ENST00000256993.4_Missense_Mutation_p.S236G|MYBPC3_ENST00000399249.2_Missense_Mutation_p.S236G	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	236	Ig-like C2-type 1.		S -> G (in dbSNP:rs3729989). {ECO:0000269|PubMed:12379228, ECO:0000269|PubMed:12974739, ECO:0000269|PubMed:15519027, ECO:0000269|PubMed:15582318, ECO:0000269|PubMed:18403758, ECO:0000269|Ref.4}.		cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|heart morphogenesis (GO:0003007)|muscle filament sliding (GO:0030049)|myosin filament assembly (GO:0031034)|positive regulation of ATPase activity (GO:0032781)|regulation of heart rate (GO:0002027)|regulation of muscle filament sliding (GO:0032971)|regulation of striated muscle contraction (GO:0006942)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	A band (GO:0031672)|C zone (GO:0014705)|cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle myosin thick filament (GO:0005863)	ATPase activator activity (GO:0001671)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|myosin binding (GO:0017022)|myosin heavy chain binding (GO:0032036)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(3)|urinary_tract(2)	42				Lung(87;0.176)		CAGCGGTAGCTGCCAGTGAAG	0.617													C|||	336	0.0670927	0.0431	0.0836	5008	,	,		18193	0.0268		0.1412	False		,,,				2504	0.0532				p.S236G		Atlas-SNP	.											.	MYBPC3	102	.	0			c.A706G	GRCh37	CM043536	MYBPC3	M	rs3729989	PASS	.	C	GLY/SER	239,3925		8,223,1851	46.0	57.0	53.0		706	5.1	0.9	11	dbSNP_107	53	1060,7334		69,922,3206	yes	missense	MYBPC3	NM_000256.3	56	77,1145,5057	CC,CT,TT		12.6281,5.7397,10.344	benign	236/1275	47370041	1299,11259	2082	4197	6279	SO:0001583	missense	4607	exon6			GGTAGCTGCCAGT	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.706A>G	11.37:g.47370041T>C	ENSP00000442795:p.Ser236Gly	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	126	73	0.579365	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	189	0.08653846153846154	32	0.06504065040650407	38	0.10497237569060773	14	0.024475524475524476	105	0.13852242744063326	C	4.342	0.062968	0.08388	0.057397	0.126281	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.68025	-0.3;-0.3;-0.3	5.12	5.12	0.69794	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00210	0.0006	N	0.00317	-1.655	0.47659	P	5.169999999999897E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.12319	-1.0552	8	0.02654	T	1	.	13.8315	0.63384	0.0:0.9259:0.0:0.0741	rs3729989;rs57344110;rs3729989	236	Q14896	MYPC3_HUMAN	G	236	ENSP00000442795:S236G;ENSP00000382193:S236G;ENSP00000256993:S236G	ENSP00000256993:S236G	S	-	1	0	MYBPC3	47326617	0.252000	0.23972	0.859000	0.33776	0.579000	0.36224	2.559000	0.45888	1.170000	0.42753	-0.215000	0.12644	AGC	T|0.916;C|0.084	0.084	strong		0.617	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
RYR1	6261	hgsc.bcm.edu	37	19	38991543	38991543	+	Silent	SNP	G	G	A	rs2071088	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38991543G>A	ENST00000359596.3	+	47	7527	c.7527G>A	c.(7525-7527)gtG>gtA	p.V2509V	RYR1_ENST00000355481.4_Silent_p.V2509V|RYR1_ENST00000360985.3_Silent_p.V2509V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2509	6 X approximate repeats.		V -> I (in dbSNP:rs2071088).		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)	TGGACCGTGTGTATGGCATCG	0.627													G|||	681	0.135982	0.0794	0.1095	5008	,	,		17827	0.1776		0.0845	False		,,,				2504	0.2413				p.V2509V		Atlas-SNP	.											.	RYR1	708	.	0			c.G7527A						PASS	.	G	,	406,4000	202.5+/-225.2	18,370,1815	105.0	72.0	83.0		7527,7527	-2.6	0.6	19	dbSNP_96	83	741,7859	178.9+/-228.2	33,675,3592	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	51,1045,5407	AA,AG,GG		8.6163,9.2147,8.819	,	2509/5039,2509/5034	38991543	1147,11859	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon47			CCGTGTGTATGGC	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.7527G>A	19.37:g.38991543G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	156	60	0.384615	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			G|0.904;A|0.096	0.096	strong		0.627	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
C1orf177	163747	hgsc.bcm.edu	37	1	55273580	55273580	+	Missense_Mutation	SNP	G	G	T	rs9782980	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:55273580G>T	ENST00000371273.3	+	4	391	c.376G>T	c.(376-378)Ggc>Tgc	p.G126C	C1orf177_ENST00000358193.3_Missense_Mutation_p.G126C	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	126			G -> C (in dbSNP:rs9782980). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GCTGGGCCCCGGCTCCTACAA	0.547													G|||	2494	0.498003	0.5023	0.4568	5008	,	,		18603	0.2708		0.5905	False		,,,				2504	0.6605				p.G126C		Atlas-SNP	.											.	C1orf177	36	.	0			c.G376T						PASS	.	G	CYS/GLY,CYS/GLY	2245,2161	593.5+/-388.0	582,1081,540	72.0	83.0	79.0		376,376	4.4	1.0	1	dbSNP_119	79	5145,3455	636.4+/-399.1	1550,2045,705	yes	missense,missense	C1orf177	NM_001110533.1,NM_152607.2	159,159	2132,3126,1245	TT,TG,GG		40.1744,49.0468,43.1801	probably-damaging,probably-damaging	126/419,126/415	55273580	7390,5616	2203	4300	6503	SO:0001583	missense	163747	exon4			GGCCCCGGCTCCT	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.376G>T	1.37:g.55273580G>T	ENSP00000360320:p.Gly126Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_001110533	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	1040	0.47619047619047616	257	0.5223577235772358	175	0.48342541436464087	159	0.27797202797202797	449	0.5923482849604221	G	14.62	2.589442	0.46214	0.509532	0.598256	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26067	1.76;1.76	5.37	4.45	0.53987	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	M	0.70275	2.135	0.21147	P	0.99977731	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.48525	-0.9028	9	0.87932	D	0	-6.5581	9.0072	0.36120	0.0986:0.0:0.9014:0.0	rs9782980;rs17855891;rs60697485;rs9782980	126;126	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	C	126	ENSP00000350924:G126C;ENSP00000360320:G126C	ENSP00000350924:G126C	G	+	1	0	C1orf177	55046168	0.998000	0.40836	0.987000	0.45799	0.343000	0.28985	3.474000	0.53129	2.531000	0.85337	0.561000	0.74099	GGC	G|0.474;T|0.526	0.526	strong		0.547	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
DCHS1	8642	hgsc.bcm.edu	37	11	6647596	6647596	+	Missense_Mutation	SNP	C	C	T	rs142577975		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6647596C>T	ENST00000299441.3	-	16	6791	c.6380G>A	c.(6379-6381)cGc>cAc	p.R2127H		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2127	Cadherin 20. {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)		CTCTGCTGAGCGAACTGTGAT	0.587													c|||	1	0.000199681	0.0	0.0	5008	,	,		20274	0.0		0.001	False		,,,				2504	0.0				p.R2127H		Atlas-SNP	.											.	DCHS1	277	.	0			c.G6380A						PASS	.	T	HIS/ARG	0,4402		0,0,2201	58.0	57.0	57.0		6380	-1.9	0.2	11	dbSNP_134	57	1,8591	1.2+/-3.3	0,1,4295	yes	missense	DCHS1	NM_003737.2	29	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	benign	2127/3299	6647596	1,12993	2201	4296	6497	SO:0001583	missense	8642	exon16			GCTGAGCGAACTG	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.6380G>A	11.37:g.6647596C>T	ENSP00000299441:p.Arg2127His	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	67	40	0.597015	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	10.48	1.362070	0.24684	0.0	1.16E-4	ENSG00000166341	ENST00000299441	T	0.53206	0.63	4.92	-1.87	0.07737	Cadherin (4);Cadherin-like (1);	1.016160	0.07896	N	0.971952	T	0.35307	0.0927	L	0.41824	1.3	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35500	-0.9786	10	0.52906	T	0.07	.	6.5512	0.22436	0.0:0.2635:0.1437:0.5928	.	2127	Q96JQ0	PCD16_HUMAN	H	2127	ENSP00000299441:R2127H	ENSP00000299441:R2127H	R	-	2	0	DCHS1	6604172	0.115000	0.22152	0.189000	0.23252	0.888000	0.51559	0.617000	0.24359	-0.190000	0.10465	-0.224000	0.12420	CGC	C|1.000;T|0.000	0.000	strong		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
KIF4B	285643	hgsc.bcm.edu	37	5	154395470	154395470	+	Missense_Mutation	SNP	A	A	G	rs10056252	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:154395470A>G	ENST00000435029.4	+	1	2211	c.2051A>G	c.(2050-2052)tAt>tGt	p.Y684C		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	684	Interaction with PRC1. {ECO:0000250}.		Y -> C (in dbSNP:rs10056252).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AAGAGGCAATATGAGCTGCTC	0.428													A|||	237	0.0473243	0.1263	0.0274	5008	,	,		22143	0.0089		0.0139	False		,,,				2504	0.0286				p.Y684C		Atlas-SNP	.											.	KIF4B	307	.	0			c.A2051G						PASS	.	A	CYS/TYR	566,3840	251.2+/-258.0	30,506,1667	123.0	126.0	125.0		2051	2.9	1.0	5	dbSNP_119	125	193,8407	85.0+/-147.5	2,189,4109	yes	missense	KIF4B	NM_001099293.1	194	32,695,5776	GG,GA,AA		2.2442,12.8461,5.8358	probably-damaging	684/1235	154395470	759,12247	2203	4300	6503	SO:0001583	missense	285643	exon1			GGCAATATGAGCT	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2051A>G	5.37:g.154395470A>G	ENSP00000387875:p.Tyr684Cys	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	216	112	0.518519	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	79	0.036172161172161175	49	0.09959349593495935	13	0.03591160220994475	4	0.006993006993006993	13	0.017150395778364115	a	14.19	2.460003	0.43736	0.128461	0.022442	ENSG00000226650	ENST00000435029	T	0.17213	2.29	2.86	2.86	0.33363	.	.	.	.	.	T	0.00210	0.0006	M	0.62154	1.92	0.58432	D	0.999995	P	0.41393	0.748	B	0.43680	0.427	T	0.03193	-1.1062	9	0.42905	T	0.14	.	9.0994	0.36658	1.0:0.0:0.0:0.0	rs10056252	684	Q2VIQ3	KIF4B_HUMAN	C	684	ENSP00000387875:Y684C	ENSP00000387875:Y684C	Y	+	2	0	KIF4B	154375663	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	5.304000	0.65744	1.091000	0.41335	0.460000	0.39030	TAT	A|0.965;G|0.035	0.035	strong		0.428	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
ADAMTS2	9509	hgsc.bcm.edu	37	5	178562967	178562967	+	Silent	SNP	G	G	A	rs1972715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:178562967G>A	ENST00000251582.7	-	13	2129	c.2028C>T	c.(2026-2028)gaC>gaT	p.D676D		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	676	Cys-rich.				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)		AGCGCGTCCCGTCATGCACCA	0.647													G|||	984	0.196486	0.2481	0.2291	5008	,	,		17005	0.0992		0.2594	False		,,,				2504	0.1391				p.D676D		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C2028T						PASS	.	G		1086,3320	390.3+/-327.6	124,838,1241	110.0	102.0	105.0		2028	-5.2	0.8	5	dbSNP_92	105	2035,6565	353.7+/-329.2	251,1533,2516	no	coding-synonymous	ADAMTS2	NM_014244.4		375,2371,3757	AA,AG,GG		23.6628,24.6482,23.9966		676/1212	178562967	3121,9885	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon13			CGTCCCGTCATGC	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.2028C>T	5.37:g.178562967G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	151	69	0.456954	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			G|0.775;A|0.225	0.225	strong		0.647	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
WDHD1	11169	hgsc.bcm.edu	37	14	55408294	55408294	+	Missense_Mutation	SNP	C	C	T	rs41309252	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:55408294C>T	ENST00000360586.3	-	26	3369	c.3304G>A	c.(3304-3306)Gag>Aag	p.E1102K	WDHD1_ENST00000359167.4_Missense_Mutation_p.E620K|WDHD1_ENST00000420358.2_Missense_Mutation_p.E979K|WDHD1_ENST00000421192.1_Missense_Mutation_p.E979K	NM_007086.3	NP_009017.1	O75717	WDHD1_HUMAN	WD repeat and HMG-box DNA binding protein 1	1102			E -> K (in dbSNP:rs41309252).		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						TTCAGGTTCTCTTTTGCTTTT	0.373													C|||	145	0.0289537	0.0287	0.0173	5008	,	,		14879	0.0546		0.0189	False		,,,				2504	0.0215				p.E1102K		Atlas-SNP	.											.	WDHD1	82	.	0			c.G3304A						PASS	.	C	LYS/GLU,LYS/GLU	79,4323	68.1+/-105.8	1,77,2123	156.0	157.0	157.0		2935,3304	5.7	0.9	14	dbSNP_127	157	128,8470	65.6+/-127.9	0,128,4171	yes	missense,missense	WDHD1	NM_001008396.2,NM_007086.3	56,56	1,205,6294	TT,TC,CC		1.4887,1.7946,1.5923	possibly-damaging,possibly-damaging	979/1007,1102/1130	55408294	207,12793	2201	4299	6500	SO:0001583	missense	11169	exon26			GGTTCTCTTTTGC	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.3304G>A	14.37:g.55408294C>T	ENSP00000353793:p.Glu1102Lys	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	178	82	0.460674	NM_007086	C9JW18|F6W0U7	Missense_Mutation	SNP	ENST00000360586.3	37	CCDS9721.1	62	0.028388278388278388	12	0.024390243902439025	6	0.016574585635359115	30	0.05244755244755245	14	0.018469656992084433	C	13.24	2.177625	0.38413	0.017946	0.014887	ENSG00000198554	ENST00000360586;ENST00000359167;ENST00000421192	T;T;T	0.63096	0.35;0.83;-0.02	5.65	5.65	0.86999	.	0.263863	0.33005	N	0.005397	T	0.22781	0.0550	L	0.56769	1.78	0.46437	D	0.999043	P;P	0.50617	0.921;0.937	P;B	0.47430	0.547;0.328	T	0.50541	-0.8816	10	0.07325	T	0.83	.	17.5045	0.87741	0.0:1.0:0.0:0.0	rs41309252	620;1102	F8W7P7;O75717	.;WDHD1_HUMAN	K	1102;620;979	ENSP00000353793:E1102K;ENSP00000352085:E620K;ENSP00000391049:E979K	ENSP00000352085:E620K	E	-	1	0	WDHD1	54478044	1.000000	0.71417	0.927000	0.36925	0.002000	0.02628	3.243000	0.51392	2.677000	0.91161	0.655000	0.94253	GAG	C|0.980;T|0.020	0.020	strong		0.373	WDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276897.2	NM_007086	
ISX	91464	hgsc.bcm.edu	37	22	35463179	35463179	+	Silent	SNP	T	T	C	rs361668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:35463179T>C	ENST00000308700.6	+	1	1051	c.99T>C	c.(97-99)atT>atC	p.I33I	RP1-272J12.1_ENST00000448318.4_RNA|ISX_ENST00000404699.2_Silent_p.I33I	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	33					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						CCTTCTCCATTGAGGCGATCC	0.607													C|||	4005	0.79972	0.8752	0.6441	5008	,	,		18421	0.8552		0.671	False		,,,				2504	0.8834				p.I33I		Atlas-SNP	.											.	ISX	62	.	0			c.T99C						PASS	.	C		3773,633	270.7+/-269.8	1618,537,48	40.0	41.0	41.0		99	-4.2	0.9	22	dbSNP_79	41	5667,2933	456.2+/-364.0	1859,1949,492	no	coding-synonymous	ISX	NM_001008494.1		3477,2486,540	CC,CT,TT		34.1047,14.3668,27.4181		33/246	35463179	9440,3566	2203	4300	6503	SO:0001819	synonymous_variant	91464	exon1			CTCCATTGAGGCG	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.99T>C	22.37:g.35463179T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001008494	Q68DJ5	Silent	SNP	ENST00000308700.6	37	CCDS33640.1																																																																																			T|0.246;C|0.754	0.754	strong		0.607	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
FPGS	2356	hgsc.bcm.edu	37	9	130569258	130569258	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130569258C>T	ENST00000373247.2	+	5	443	c.393C>T	c.(391-393)ccC>ccT	p.P131P	FPGS_ENST00000373245.1_Silent_p.P131P|FPGS_ENST00000373225.3_Silent_p.P81P|FPGS_ENST00000460181.1_Intron|FPGS_ENST00000393706.2_Silent_p.P131P	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	131					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GCAGCTCTCCCCACCTGGTGC	0.652																																					p.P131P		Atlas-SNP	.											.	FPGS	30	.	0			c.C393T						PASS	.						58.0	59.0	59.0					9																	130569258		2203	4300	6503	SO:0001819	synonymous_variant	2356	exon5			CTCTCCCCACCTG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.393C>T	9.37:g.130569258C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Silent	SNP	ENST00000373247.2	37	CCDS35148.1																																																																																			.	.	none		0.652	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1		
SPTA1	6708	hgsc.bcm.edu	37	1	158597507	158597507	+	Missense_Mutation	SNP	G	G	C	rs3737515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158597507G>C	ENST00000368147.4	-	40	5752	c.5572C>G	c.(5572-5574)Cta>Gta	p.L1858V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1858			L -> V (in dbSNP:rs3737515). {ECO:0000269|PubMed:8486776}.		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)					TGCTTCATTAGCAAGCTCTGC	0.403													G|||	1141	0.227835	0.1906	0.2133	5008	,	,		19212	0.2054		0.2863	False		,,,				2504	0.2515				p.L1858V		Atlas-SNP	.											.	SPTA1	720	.	0			c.C5572G						PASS	.	G	VAL/LEU	710,2988		63,584,1202	143.0	127.0	132.0		5572	2.7	0.7	1	dbSNP_107	132	2255,5929		309,1637,2146	yes	missense	SPTA1	NM_003126.2	32	372,2221,3348	CC,CG,GG		27.5538,19.1996,24.9537	benign	1858/2420	158597507	2965,8917	1849	4092	5941	SO:0001583	missense	6708	exon40			TCATTAGCAAGCT	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.5572C>G	1.37:g.158597507G>C	ENSP00000357129:p.Leu1858Val	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	538	0.24633699633699635	104	0.21138211382113822	83	0.2292817679558011	124	0.21678321678321677	227	0.2994722955145119	G	13.00	2.107732	0.37242	0.191996	0.275538	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48201	0.82;0.82	5.55	2.68	0.31781	.	0.398187	0.14832	N	0.295829	T	0.37320	0.0999	M	0.75447	2.3	0.26869	P	0.9677948	P	0.37594	0.601	B	0.42692	0.395	T	0.28427	-1.0044	9	0.56958	D	0.05	.	10.2495	0.43360	0.2184:0.0:0.7816:0.0	rs3737515;rs52827684;rs56522116;rs59553946;rs3737515	1858	P02549	SPTA1_HUMAN	V	1858	ENSP00000357130:L1858V;ENSP00000357129:L1858V	ENSP00000357129:L1858V	L	-	1	2	SPTA1	156864131	1.000000	0.71417	0.678000	0.29963	0.560000	0.35617	2.457000	0.45005	0.451000	0.26802	-0.136000	0.14681	CTA	G|0.758;C|0.242	0.242	strong		0.403	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
APBA3	9546	hgsc.bcm.edu	37	19	3753769	3753769	+	Silent	SNP	C	C	T	rs3746120	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:3753769C>T	ENST00000316757.3	-	6	1205	c.1005G>A	c.(1003-1005)gcG>gcA	p.A335A	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	335	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)		TCACGTCCTCCGCGTAGAATA	0.692													C|||	1703	0.340056	0.2405	0.4179	5008	,	,		13758	0.4474		0.3797	False		,,,				2504	0.2679				p.A335A		Atlas-SNP	.											APBA3,NS,carcinoma,0,1	APBA3	28	1	0			c.G1005A						PASS	.	C		1070,3286		139,792,1247	9.0	9.0	9.0		1005	-7.9	0.2	19	dbSNP_107	9	3082,5446		560,1962,1742	no	coding-synonymous	APBA3	NM_004886.3		699,2754,2989	TT,TC,CC		36.1398,24.5638,32.226		335/576	3753769	4152,8732	2178	4264	6442	SO:0001819	synonymous_variant	9546	exon6			GTCCTCCGCGTAG	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.1005G>A	19.37:g.3753769C>T		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	18	7	0.388889	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			C|0.654;T|0.346	0.346	strong		0.692	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
NLRP1	22861	hgsc.bcm.edu	37	17	5425077	5425077	+	Missense_Mutation	SNP	T	T	C	rs11651270	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5425077T>C	ENST00000572272.1	-	13	3549	c.3550A>G	c.(3550-3552)Atg>Gtg	p.M1184V	NLRP1_ENST00000354411.3_Missense_Mutation_p.M1154V|NLRP1_ENST00000269280.4_Missense_Mutation_p.M1184V|NLRP1_ENST00000262467.5_Missense_Mutation_p.M1188V|NLRP1_ENST00000345221.3_Missense_Mutation_p.M1184V|NLRP1_ENST00000577119.1_Missense_Mutation_p.M1154V			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1184			M -> V (in dbSNP:rs11651270). {ECO:0000269|PubMed:11270363, ECO:0000269|PubMed:17974005}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				AAGTGGGCCATTTGGAACAGG	0.478													C|||	2093	0.417931	0.4841	0.4294	5008	,	,		17171	0.2768		0.4612	False		,,,				2504	0.4213				p.M1188V		Atlas-SNP	.											.	NLRP1	358	.	0			c.A3562G						PASS	.	C	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	2249,2157	566.0+/-381.8	582,1085,536	53.0	58.0	56.0		3562,3550,3550,3460,3460	2.3	0.2	17	dbSNP_120	56	4028,4572	591.8+/-392.9	934,2160,1206	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	1516,3245,1742	CC,CT,TT		46.8372,48.956,48.2623	benign,benign,benign,benign,benign	1188/1376,1184/1430,1184/1474,1154/1444,1154/1400	5425077	6277,6729	2203	4300	6503	SO:0001583	missense	22861	exon13			GGGCCATTTGGAA	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3550A>G	17.37:g.5425077T>C	ENSP00000460475:p.Met1184Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001033053	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	886	0.4056776556776557	253	0.5142276422764228	140	0.3867403314917127	152	0.26573426573426573	341	0.449868073878628	C	0.051	-1.251336	0.01469	0.51044	0.468372	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82	4.3	2.26	0.28386	.	0.226772	0.22584	N	0.058166	T	0.00012	0.0000	N	0.00041	-2.485	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.43310	-0.9399	9	0.02654	T	1	.	6.0509	0.19785	0.0:0.6519:0.1609:0.1872	rs11651270;rs57152836;rs11651270	1154;1154;1184;1184;1188	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	V	1188;1188;1184;1154;1184;450	ENSP00000442029:M1188V;ENSP00000262467:M1188V;ENSP00000269280:M1184V;ENSP00000346390:M1154V;ENSP00000324366:M1184V	ENSP00000262467:M1188V	M	-	1	0	NLRP1	5365801	0.004000	0.15560	0.153000	0.22517	0.983000	0.72400	0.439000	0.21575	0.565000	0.29255	-0.124000	0.14976	ATG	T|0.542;C|0.458	0.458	strong		0.478	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
NBAS	51594	hgsc.bcm.edu	37	2	15470848	15470848	+	Silent	SNP	C	C	T	rs34395824	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:15470848C>T	ENST00000281513.5	-	36	4246	c.4221G>A	c.(4219-4221)ttG>ttA	p.L1407L	NBAS_ENST00000441750.1_Silent_p.L1287L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	1407					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						TGGTCCAGCGCAATAGGTCAG	0.473													T|||	102	0.0203674	0.0151	0.0202	5008	,	,		17453	0.0099		0.0388	False		,,,				2504	0.0194				p.L1407L		Atlas-SNP	.											.	NBAS	246	.	0			c.G4221A						PASS	.	T		86,4320	818.6+/-416.3	3,80,2120	175.0	150.0	158.0		4221	-9.9	0.0	2	dbSNP_126	158	278,8322	807.2+/-407.2	5,268,4027	no	coding-synonymous	NBAS	NM_015909.2		8,348,6147	TT,TC,CC		3.2326,1.9519,2.7987		1407/2372	15470848	364,12642	2203	4300	6503	SO:0001819	synonymous_variant	51594	exon36			CCAGCGCAATAGG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.4221G>A	2.37:g.15470848C>T		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	226	125	0.553097	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1	58	0.026556776556776556	9	0.018292682926829267	13	0.03591160220994475	6	0.01048951048951049	30	0.0395778364116095	T	4.067	0.010176	0.07912	0.019519	0.032326	ENSG00000151779	ENST00000442506	.	.	.	5.61	-9.9	0.00461	.	.	.	.	.	T	0.28995	0.0720	.	.	.	0.45995	D	0.998808	.	.	.	.	.	.	T	0.71971	-0.4431	4	.	.	.	.	16.5801	0.84712	0.0:0.6635:0.0819:0.2545	rs34395824	.	.	.	Y	455	.	.	C	-	2	0	NBAS	15388299	0.000000	0.05858	0.001000	0.08648	0.584000	0.36387	-1.942000	0.01541	-2.788000	0.00357	-1.103000	0.02113	TGC	C|0.972;T|0.028	0.028	strong		0.473	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
ADGB	79747	hgsc.bcm.edu	37	6	146993445	146993445	+	Missense_Mutation	SNP	T	T	C	rs9497606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:146993445T>C	ENST00000397944.3	+	8	1005	c.929T>C	c.(928-930)aTa>aCa	p.I310T	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	310	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		I -> T (in dbSNP:rs9497606). {ECO:0000269|PubMed:14702039}.		oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						GAAAGCAAAATAGCAGTGTTA	0.393													T|||	1423	0.284145	0.416	0.3372	5008	,	,		17282	0.124		0.2127	False		,,,				2504	0.3067				p.I310T		Atlas-SNP	.											.	ADGB	93	.	0			c.T929C						PASS	.	T	THR/ILE	537,847		101,335,256	71.0	62.0	65.0		929	-4.2	0.0	6	dbSNP_119	65	649,2533		71,507,1013	yes	missense	C6orf103	NM_024694.3	89	172,842,1269	CC,CT,TT		20.396,38.8006,25.9746	probably-damaging	310/1668	146993445	1186,3380	692	1591	2283	SO:0001583	missense	79747	exon8			GCAAAATAGCAGT	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.929T>C	6.37:g.146993445T>C	ENSP00000381036:p.Ile310Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	71	68	0.957747	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		528	0.24175824175824176	196	0.3983739837398374	107	0.2955801104972376	62	0.10839160839160839	163	0.21503957783641162	T	10.40	1.340751	0.24339	0.388006	0.20396	ENSG00000118492	ENST00000397944	D	0.87256	-2.23	5.01	-4.19	0.03835	Peptidase C2, calpain, catalytic domain (3);	1.559840	0.03266	N	0.184008	T	0.67040	0.2851	L	0.54323	1.7	0.80722	P	0.0	B	0.23735	0.09	B	0.23150	0.044	T	0.52586	-0.8556	9	0.13108	T	0.6	-2.3532	8.9248	0.35634	0.0:0.512:0.126:0.362	rs9497606;rs52829379;rs56454038;rs56826710;rs9497606	310	Q8N7X0	CAN7L_HUMAN	T	310	ENSP00000381036:I310T	ENSP00000381036:I310T	I	+	2	0	C6orf103	147035138	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.390000	0.07332	-0.492000	0.06687	-0.462000	0.05337	ATA	T|0.734;C|0.266	0.266	strong		0.393	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
OR11H6	122748	hgsc.bcm.edu	37	14	20692453	20692453	+	Missense_Mutation	SNP	G	G	T	rs17211285	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20692453G>T	ENST00000315519.2	+	1	663	c.585G>T	c.(583-585)ttG>ttT	p.L195F		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	195			L -> F (in dbSNP:rs17211285).			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)		TTGACCACTTGGTGTGTGACC	0.502													N|||	1950	0.389377	0.4735	0.3516	5008	,	,		21345	0.2361		0.4781	False		,,,				2504	0.3691				p.L195F		Atlas-SNP	.											.	OR11H6	60	.	0			c.G585T						PASS	.	T	PHE/LEU	2256,2150	581.8+/-385.5	610,1036,557	99.0	93.0	95.0		585	-5.7	0.0	14	dbSNP_123	95	4155,4445	587.9+/-392.3	997,2161,1142	yes	missense	OR11H6	NM_001004480.1	22	1607,3197,1699	TT,TG,GG		48.314,48.7971,49.2926	benign	195/331	20692453	6411,6595	2203	4300	6503	SO:0001583	missense	122748	exon1			CCACTTGGTGTGT		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.585G>T	14.37:g.20692453G>T	ENSP00000319071:p.Leu195Phe	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	869	0.39789377289377287	237	0.4817073170731707	135	0.3729281767955801	122	0.21328671328671328	375	0.4947229551451187	T	0.008	-1.904680	0.00512	0.512029	0.48314	ENSG00000176219	ENST00000315519	T	0.00009	9.48	4.62	-5.69	0.02428	GPCR, rhodopsin-like superfamily (1);	0.425679	0.19588	N	0.110693	T	0.00012	0.0000	N	0.00022	-2.735	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48536	-0.9027	9	0.02654	T	1	.	6.6385	0.22897	0.1202:0.5514:0.123:0.2054	rs17211285;rs52820270;rs58685861;rs17211285	195	Q8NGC7	O11H6_HUMAN	F	195	ENSP00000319071:L195F	ENSP00000319071:L195F	L	+	3	2	OR11H6	19762293	0.000000	0.05858	0.005000	0.12908	0.612000	0.37316	-2.544000	0.00933	-1.967000	0.01008	-1.079000	0.02226	TTG	G|0.540;N|0.001	.	strong		0.502	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
GOLGA5	9950	hgsc.bcm.edu	37	14	93263982	93263982	+	Missense_Mutation	SNP	C	C	G	rs17128572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93263982C>G	ENST00000163416.2	+	2	456	c.200C>G	c.(199-201)gCt>gGt	p.A67G	GOLGA5_ENST00000355976.2_Missense_Mutation_p.A67G	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	67			A -> G (in dbSNP:rs17128572). {ECO:0000269|PubMed:15489334}.		Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		TCATCAGCAGCTGATAACATT	0.378			T	RET	papillary thyroid								C|||	598	0.119409	0.0363	0.1585	5008	,	,		22044	0.1548		0.0895	False		,,,				2504	0.1984				p.A67G		Atlas-SNP	.		Dom	yes		14	14q	9950	"""golgi autoantigen, golgin subfamily a, 5  (PTC5)"""		E	.	GOLGA5	84	.	0			c.C200G	GRCh37	CM065242	GOLGA5	M	rs17128572	PASS	.	C	GLY/ALA	204,4202	126.6+/-163.6	2,200,2001	94.0	91.0	92.0		200	5.7	1.0	14	dbSNP_123	92	532,8068	148.9+/-204.1	14,504,3782	yes	missense	GOLGA5	NM_005113.2	60	16,704,5783	GG,GC,CC		6.186,4.63,5.6589	probably-damaging	67/732	93263982	736,12270	2203	4300	6503	SO:0001583	missense	9950	exon2			CAGCAGCTGATAA	AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"""golgi integral membrane protein 5"""	606918	"""golgi autoantigen, golgin subfamily a, 5"""			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.200C>G	14.37:g.93263982C>G	ENSP00000163416:p.Ala67Gly	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	52	0.45614	NM_005113	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Missense_Mutation	SNP	ENST00000163416.2	37	CCDS9905.1	230	0.10531135531135531	22	0.044715447154471545	53	0.1464088397790055	89	0.1555944055944056	66	0.0870712401055409	C	24.9	4.578405	0.86645	0.0463	0.06186	ENSG00000066455	ENST00000163416;ENST00000355976;ENST00000439315	T;T	0.42513	0.98;0.97	5.65	5.65	0.86999	.	0.000000	0.48767	D	0.000170	T	0.00328	0.0010	M	0.69823	2.125	0.09310	P	0.99999999523114	D	0.58620	0.983	P	0.50791	0.65	T	0.00028	-1.2301	9	0.33940	T	0.23	-19.5535	20.0965	0.97849	0.0:1.0:0.0:0.0	rs17128572;rs17852131;rs52799990;rs59264365;rs17128572	67	Q8TBA6	GOGA5_HUMAN	G	67	ENSP00000163416:A67G;ENSP00000348252:A67G	ENSP00000163416:A67G	A	+	2	0	GOLGA5	92333735	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	6.765000	0.74965	2.824000	0.97209	0.655000	0.94253	GCT	C|0.926;G|0.074	0.074	strong		0.378	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1		
USH2A	7399	hgsc.bcm.edu	37	1	215901492	215901492	+	Silent	SNP	C	C	T	rs2820718	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:215901492C>T	ENST00000307340.3	-	61	12332	c.11946G>A	c.(11944-11946)ctG>ctA	p.L3982L	USH2A_ENST00000366943.2_Silent_p.L3982L	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3982	Fibronectin type-III 25. {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)		TCCAATTCAACAGAACTGAAT	0.493										HNSCC(13;0.011)			C|||	595	0.11881	0.1687	0.0965	5008	,	,		17267	0.003		0.1879	False		,,,				2504	0.1155				p.L3982L		Atlas-SNP	.											.	USH2A	1168	.	0			c.G11946A						PASS	.	C		755,3651	308.6+/-290.6	75,605,1523	112.0	108.0	110.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	11946	3.6	0.5	1	dbSNP_100	110	1587,7013	296.9+/-303.1	138,1311,2851	no	coding-synonymous	USH2A	NM_206933.2		213,1916,4374	TT,TC,CC		18.4535,17.1357,18.0071		3982/5203	215901492	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon61			ATTCAACAGAACT	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.11946G>A	1.37:g.215901492C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	153	75	0.490196	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			C|0.836;T|0.164	0.164	strong		0.493	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
FKBP15	23307	hgsc.bcm.edu	37	9	115933978	115933978	+	Silent	SNP	G	G	A	rs1128117|rs386737766	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115933978G>A	ENST00000238256.3	-	24	2658	c.2541C>T	c.(2539-2541)gcC>gcT	p.A847A		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	847			A -> S (in dbSNP:rs1128116).		endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GGGCCTGGAGGGCTAAACACT	0.502													G|||	399	0.0796725	0.0991	0.0389	5008	,	,		11897	0.0387		0.0477	False		,,,				2504	0.1575				p.A847A		Atlas-SNP	.											.	FKBP15	128	.	0			c.C2541T						PASS	.	G		382,3380		14,354,1513	83.0	84.0	84.0		2541	-1.9	0.8	9	dbSNP_86	84	505,7723		15,475,3624	no	coding-synonymous	FKBP15	NM_015258.1		29,829,5137	AA,AG,GG		6.1376,10.1542,7.3978		847/1220	115933978	887,11103	1881	4114	5995	SO:0001819	synonymous_variant	23307	exon24			CTGGAGGGCTAAA	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2541C>T	9.37:g.115933978G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.940;A|0.060	0.060	strong		0.502	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
COLQ	8292	hgsc.bcm.edu	37	3	15495386	15495386	+	Silent	SNP	G	G	A	rs55866379	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:15495386G>A	ENST00000383788.5	-	16	1373	c.1248C>T	c.(1246-1248)gaC>gaT	p.D416D	COLQ_ENST00000383785.2_3'UTR|COLQ_ENST00000435459.2_Silent_p.D406D|COLQ_ENST00000383781.4_Silent_p.D406D|COLQ_ENST00000383787.2_Silent_p.D407D|EAF1-AS1_ENST00000608408.1_RNA|COLQ_ENST00000603808.1_Silent_p.D417D|COLQ_ENST00000383786.5_Silent_p.D382D|COLQ_ENST00000603752.1_5'Flank	NM_005677.3	NP_005668.2	Q9Y215	COLQ_HUMAN	collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase	416					acetylcholine catabolic process in synaptic cleft (GO:0001507)|asymmetric protein localization (GO:0008105)	basal lamina (GO:0005605)|cell junction (GO:0030054)|collagen trimer (GO:0005581)|extracellular space (GO:0005615)|synapse (GO:0045202)				endometrium(2)|large_intestine(4)|lung(10)|skin(3)	19						AGCCGTCACAGTCCTCCACAC	0.592													G|||	76	0.0151757	0.0038	0.0259	5008	,	,		20005	0.0		0.0328	False		,,,				2504	0.0204				p.D416D		Atlas-SNP	.											.	COLQ	82	.	0			c.C1248T						PASS	.	G	,,	44,4362	47.5+/-82.1	1,42,2160	182.0	144.0	157.0		1248,1218,1146	3.4	1.0	3	dbSNP_129	157	308,8292	108.4+/-169.1	2,304,3994	no	coding-synonymous,coding-synonymous,coding-synonymous	COLQ	NM_005677.3,NM_080538.2,NM_080539.3	,,	3,346,6154	AA,AG,GG		3.5814,0.9986,2.7064	,,	416/456,406/446,382/422	15495386	352,12654	2203	4300	6503	SO:0001819	synonymous_variant	8292	exon16			GTCACAGTCCTCC	AF057036	CCDS33709.1, CCDS43057.1, CCDS46768.1	3p	2008-07-18			ENSG00000206561	ENSG00000206561			2226	protein-coding gene	gene with protein product	"""single strand of homotrimeric collagen-like tail subunit of asymmetric acetylcholinesterase"", ""collagenic tail of endplate acetylcholinesterase"", ""AChE Q subunit"", ""acetylcholinesterase-associated collagen"""	603033				9689136	Standard	NM_005677		Approved	EAD	uc003bzx.3	Q9Y215	OTTHUMG00000156233	ENST00000383788.5:c.1248C>T	3.37:g.15495386G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_005677	B3KY09|Q6DK18|Q6YH18|Q6YH19|Q6YH20|Q6YH21|Q9NP18|Q9NP19|Q9NP20|Q9NP21|Q9NP22|Q9NP23|Q9NP24|Q9UP88	Silent	SNP	ENST00000383788.5	37	CCDS33709.1																																																																																			G|0.975;A|0.025	0.025	strong		0.592	COLQ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000343575.1	NM_005677	
LEPRE1	64175	hgsc.bcm.edu	37	1	43215930	43215930	+	Missense_Mutation	SNP	C	C	T	rs11581921	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43215930C>T	ENST00000296388.5	-	11	1698	c.1647G>A	c.(1645-1647)atG>atA	p.M549I	LEPRE1_ENST00000462474.1_5'Flank|LEPRE1_ENST00000236040.4_Missense_Mutation_p.M549I|LEPRE1_ENST00000397054.3_Missense_Mutation_p.M549I			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	549			M -> I (in dbSNP:rs11581921).		bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	AGTAGGACTCCATGATGCGCC	0.582													C|||	288	0.057508	0.0106	0.0504	5008	,	,		16643	0.0407		0.0845	False		,,,				2504	0.1155				p.M549I		Atlas-SNP	.											.	LEPRE1	130	.	0			c.G1647A						PASS	.	C	ILE/MET,ILE/MET	145,4261	101.2+/-139.8	1,143,2059	144.0	116.0	126.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1647,1647	4.2	1.0	1	dbSNP_120	126	665,7935	167.3+/-219.0	22,621,3657	yes	missense,missense	LEPRE1	NM_001146289.1,NM_022356.3	10,10	23,764,5716	TT,TC,CC		7.7326,3.291,6.2279	benign,benign	549/698,549/737	43215930	810,12196	2203	4300	6503	SO:0001583	missense	64175	exon11			GGACTCCATGATG	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.1647G>A	1.37:g.43215930C>T	ENSP00000296388:p.Met549Ile	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	103	0.04716117216117216	7	0.014227642276422764	16	0.04419889502762431	13	0.022727272727272728	67	0.08839050131926121	C	11.57	1.679490	0.29783	0.03291	0.077326	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.39229	1.09;1.09;1.09	5.13	4.22	0.49857	Prolyl 4-hydroxylase, alpha subunit (1);	0.244651	0.42964	N	0.000622	T	0.00906	0.0030	N	0.19112	0.55	0.29014	N	0.886722	B;B;B	0.14438	0.008;0.0;0.01	B;B;B	0.14023	0.01;0.001;0.002	T	0.03259	-1.1055	10	0.32370	T	0.25	-17.0103	7.6341	0.28257	0.0:0.8093:0.0:0.1907	rs11581921;rs61014852;rs11581921	549;414;549	Q32P28-3;B4DNM8;Q32P28	.;.;P3H1_HUMAN	I	549;549;549;414	ENSP00000380245:M549I;ENSP00000236040:M549I;ENSP00000296388:M549I	ENSP00000236040:M549I	M	-	3	0	LEPRE1	42988517	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.864000	0.27926	1.167000	0.42706	0.467000	0.42956	ATG	C|0.948;T|0.052	0.052	strong		0.582	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
LAMA5	3911	hgsc.bcm.edu	37	20	60885978	60885978	+	Silent	SNP	G	G	T	rs201094237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60885978G>T	ENST00000252999.3	-	74	10327	c.10261C>A	c.(10261-10263)Cgg>Agg	p.R3421R	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3421	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CGGCCAGGCCGGGAGCGCTGG	0.697													.|||	3	0.000599042	0.0	0.0	5008	,	,		12759	0.0		0.001	False		,,,				2504	0.002				p.R3421R		Atlas-SNP	.											.	LAMA5	268	.	0			c.C10261A						PASS	.			0,4154		0,0,2077	12.0	16.0	14.0		10261	0.8	0.0	20		14	4,8320		0,4,4158	no	coding-synonymous	LAMA5	NM_005560.3		0,4,6235	TT,TG,GG		0.0481,0.0,0.0321		3421/3696	60885978	4,12474	2077	4162	6239	SO:0001819	synonymous_variant	3911	exon74			CAGGCCGGGAGCG	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.10261C>A	20.37:g.60885978G>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	42	30	0.714286	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			.	.	weak		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
OR51B6	390058	hgsc.bcm.edu	37	11	5372751	5372751	+	Missense_Mutation	SNP	A	A	C	rs4910755	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5372751A>C	ENST00000380219.1	+	1	14	c.14A>C	c.(13-15)aAg>aCg	p.K5T	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	5			K -> T (in dbSNP:rs4910755). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGCTCAATAAGTCTGCTTCC	0.433													A|||	1178	0.235224	0.3283	0.2349	5008	,	,		21631	0.0863		0.2644	False		,,,				2504	0.2331				p.K5T		Atlas-SNP	.											.	OR51B6	53	.	0			c.A14C						PASS	.	A	THR/LYS	1298,3104	441.0+/-346.2	177,944,1080	78.0	67.0	71.0		14	-4.6	0.0	11	dbSNP_111	71	2268,6326	381.2+/-339.9	310,1648,2339	yes	missense	OR51B6	NM_001004750.1	78	487,2592,3419	CC,CA,AA		26.3905,29.4866,27.4392	benign	5/313	5372751	3566,9430	2201	4297	6498	SO:0001583	missense	390058	exon1			TCAATAAGTCTGC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.14A>C	11.37:g.5372751A>C	ENSP00000369568:p.Lys5Thr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	177	80	0.451977	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	160	0.3252032520325203	90	0.24861878453038674	30	0.05244755244755245	192	0.2532981530343008	A	5.628	0.300519	0.10678	0.294866	0.263905	ENSG00000176239	ENST00000380219	T	0.00316	8.13	4.63	-4.64	0.03349	.	2.386480	0.01623	N	0.023135	T	0.00012	0.0000	N	0.03294	-0.36	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.11446	-1.0587	9	0.10377	T	0.69	.	0.8917	0.01255	0.3948:0.1828:0.2435:0.1789	rs4910755;rs59085266;rs4910755	5	Q9H340	O51B6_HUMAN	T	5	ENSP00000369568:K5T	ENSP00000369568:K5T	K	+	2	0	OR51B6	5329327	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.699000	0.05087	-0.615000	0.05679	-0.460000	0.05396	AAG	A|0.770;C|0.230	0.230	strong		0.433	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
ACSS1	84532	hgsc.bcm.edu	37	20	24994289	24994289	+	Missense_Mutation	SNP	C	C	T	rs6050249	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:24994289C>T	ENST00000323482.4	-	10	1541	c.1462G>A	c.(1462-1464)Gtg>Atg	p.V488M	ACSS1_ENST00000542618.1_Missense_Mutation_p.V367M|ACSS1_ENST00000484396.1_5'Flank|ACSS1_ENST00000537502.1_Missense_Mutation_p.V405M|ACSS1_ENST00000432802.2_Missense_Mutation_p.V488M	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	488			V -> M (in dbSNP:rs6050249). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)	CTGCCCTCCACGACGCTGCCC	0.627													C|||	821	0.163938	0.3064	0.1513	5008	,	,		19085	0.0595		0.167	False		,,,				2504	0.0849				p.V488M		Atlas-SNP	.											ACSS1,colon,carcinoma,0,2	ACSS1	46	2	0			c.G1462A						PASS	.	C	MET/VAL	1378,3028	440.6+/-346.1	210,958,1035	35.0	34.0	34.0		1462	-10.6	0.0	20	dbSNP_114	34	1562,7038	286.3+/-297.7	137,1288,2875	no	missense	ACSS1	NM_032501.2	21	347,2246,3910	TT,TC,CC		18.1628,31.2755,22.605	benign	488/690	24994289	2940,10066	2203	4300	6503	SO:0001583	missense	84532	exon10			CCTCCACGACGCT		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.1462G>A	20.37:g.24994289C>T	ENSP00000316924:p.Val488Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	66	27	0.409091	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Missense_Mutation	SNP	ENST00000323482.4	37	CCDS13167.1	397	0.18177655677655677	165	0.3353658536585366	74	0.20441988950276244	42	0.07342657342657342	116	0.15303430079155672	C	12.75	2.031940	0.35893	0.312755	0.181628	ENSG00000154930	ENST00000323482;ENST00000376727;ENST00000537502;ENST00000432802;ENST00000542618	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.28	-10.6	0.00265	AMP-dependent synthetase/ligase (1);	0.931963	0.09151	N	0.841609	T	0.00012	0.0000	L	0.52266	1.64	0.53688	P	2.5000000000052758E-5	B;B;B;B	0.27823	0.095;0.158;0.19;0.153	B;B;B;B	0.27715	0.009;0.049;0.082;0.056	T	0.16988	-1.0384	9	0.62326	D	0.03	-35.3763	2.2329	0.04001	0.182:0.1005:0.2864:0.431	rs6050249;rs8115396;rs17853908;rs17854324;rs17854886;rs52790525;rs6050249	283;486;488;405	E9PC79;Q9NUB1-2;Q9NUB1;Q6ZV30	.;.;ACS2L_HUMAN;.	M	488;283;405;488;367	ENSP00000316924:V488M;ENSP00000439304:V405M;ENSP00000388793:V488M;ENSP00000437657:V367M	ENSP00000316924:V488M	V	-	1	0	ACSS1	24942289	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.494000	0.00972	-1.951000	0.01029	-0.137000	0.14449	GTG	C|0.785;T|0.215	0.215	strong		0.627	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
ZNF132	7691	hgsc.bcm.edu	37	19	58946203	58946203	+	Missense_Mutation	SNP	C	C	T	rs1122955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58946203C>T	ENST00000254166.3	-	3	1008	c.608G>A	c.(607-609)gGc>gAc	p.G203D		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	203			G -> D (in dbSNP:rs1122955).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_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;0.0171)|Lung(386;0.182)		GTCACAGCTGCCCAGGATGAC	0.512													C|||	732	0.146166	0.1059	0.1772	5008	,	,		19564	0.0546		0.2445	False		,,,				2504	0.1718				p.G203D		Atlas-SNP	.											ZNF132,extremity,malignant_melanoma,-1,1	ZNF132	56	1	0			c.G608A						PASS	.	C	ASP/GLY	477,3929	223.0+/-239.6	31,415,1757	99.0	85.0	90.0		608	0.2	0.0	19	dbSNP_86	90	1761,6839	319.5+/-314.2	184,1393,2723	yes	missense	ZNF132	NM_003433.3	94	215,1808,4480	TT,TC,CC		20.4767,10.8261,17.2074	benign	203/707	58946203	2238,10768	2203	4300	6503	SO:0001583	missense	7691	exon3			CAGCTGCCCAGGA	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"""Zinc fingers, C2H2-type"", ""-"""	12916	protein-coding gene	gene with protein product		604074	"""zinc finger protein 132 (clone pHZ-12)"""			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.608G>A	19.37:g.58946203C>T	ENSP00000254166:p.Gly203Asp	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	140	70	0.5	NM_003433	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	37	CCDS12980.1	332	0.152014652014652	60	0.12195121951219512	66	0.18232044198895028	32	0.055944055944055944	174	0.22955145118733508	C	0.033	-1.324593	0.01309	0.108261	0.204767	ENSG00000131849	ENST00000254166	T	0.14640	2.49	2.49	0.23	0.15372	.	.	.	.	.	T	0.00012	0.0000	N	0.04260	-0.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48258	-0.9051	8	0.17832	T	0.49	.	3.7817	0.08683	0.0:0.1322:0.2207:0.6471	rs1122955;rs2229374;rs17747821;rs52819540;rs60515011;rs1122955	203	P52740	ZN132_HUMAN	D	203	ENSP00000254166:G203D	ENSP00000254166:G203D	G	-	2	0	ZNF132	63638015	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.269000	0.08596	-0.007000	0.14345	-0.290000	0.09829	GGC	C|0.842;T|0.158	0.158	strong		0.512	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433	
ATOH7	220202	hgsc.bcm.edu	37	10	69991099	69991099	+	Silent	SNP	G	G	A	rs201955526		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:69991099G>A	ENST00000373673.3	-	1	772	c.336C>T	c.(334-336)caC>caT	p.H112H	RP11-153K11.3_ENST00000444086.1_lincRNA	NM_145178.3	NP_660161.1	Q8N100	ATOH7_HUMAN	atonal homolog 7 (Drosophila)	112					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|neural retina development (GO:0003407)|optic nerve development (GO:0021554)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)										AGTGCTCACAGTGGAGACCCA	0.672																																					p.H112H		Atlas-SNP	.											.	ATOH7	4	.	0			c.C336T						PASS	.	G		0,4406		0,0,2203	33.0	34.0	34.0		336	4.1	1.0	10		34	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATOH7	NM_145178.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		112/153	69991099	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	220202	exon1			CTCACAGTGGAGA	AF418922	CCDS7276.1	10q22.2	2013-05-21			ENSG00000179774	ENSG00000179774		"""Basic helix-loop-helix proteins"""	13907	protein-coding gene	gene with protein product		609875				11889557	Standard	NM_145178		Approved	Math5, bHLHa13	uc001jnq.3	Q8N100	OTTHUMG00000018346	ENST00000373673.3:c.336C>T	10.37:g.69991099G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_145178		Silent	SNP	ENST00000373673.3	37	CCDS7276.1																																																																																			G|0.999;A|0.001	0.001	weak		0.672	ATOH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048312.1		
PODXL	5420	hgsc.bcm.edu	37	7	131195712	131195712	+	Missense_Mutation	SNP	G	G	A	rs12670788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:131195712G>A	ENST00000378555.3	-	2	828	c.581C>T	c.(580-582)tCg>tTg	p.S194L	PODXL_ENST00000322985.9_Missense_Mutation_p.S194L|PODXL_ENST00000537928.1_Missense_Mutation_p.S194L|PODXL_ENST00000465001.1_5'Flank|PODXL_ENST00000541194.1_Missense_Mutation_p.S196L			O00592	PODXL_HUMAN	podocalyxin-like	194	Thr-rich.		S -> L (in dbSNP:rs12670788). {ECO:0000269|PubMed:9188463}.		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)					AGGATGCGTCGAAGTGGGTTG	0.527													G|||	1820	0.363419	0.0363	0.3948	5008	,	,		19195	0.6518		0.4324	False		,,,				2504	0.4151				p.S194L		Atlas-SNP	.											.	PODXL	53	.	0			c.C581T						PASS	.	G	LEU/SER,LEU/SER	472,3934	220.4+/-237.8	27,418,1758	207.0	180.0	189.0		581,581	-2.0	0.0	7	dbSNP_120	189	4077,4523	560.3+/-387.6	972,2133,1195	yes	missense,missense	PODXL	NM_001018111.2,NM_005397.3	145,145	999,2551,2953	AA,AG,GG		47.407,10.7127,34.9762	benign,benign	194/559,194/527	131195712	4549,8457	2203	4300	6503	SO:0001583	missense	5420	exon2			TGCGTCGAAGTGG		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.581C>T	7.37:g.131195712G>A	ENSP00000367817:p.Ser194Leu	Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	308	142	0.461039	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	856	0.39194139194139194	30	0.06097560975609756	130	0.35911602209944754	351	0.6136363636363636	345	0.4551451187335092	g	4.782	0.145408	0.09134	0.107127	0.47407	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.14391	2.51;2.6;2.51;2.81	3.08	-2.05	0.07321	.	28.627400	0.00166	N	0.000001	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.33022	0.394;0.273	B;B	0.22880	0.042;0.019	T	0.44019	-0.9355	9	0.21014	T	0.42	.	1.1922	0.01867	0.2085:0.3236:0.3025:0.1654	rs12670788;rs17823063;rs60946866;rs12670788	194;194	O00592-2;O00592	.;PODXL_HUMAN	L	196;194;184;194;194	ENSP00000440518:S196L;ENSP00000442655:S194L;ENSP00000367817:S194L;ENSP00000319782:S194L	ENSP00000319782:S194L	S	-	2	0	PODXL	130846252	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.157000	0.10085	-0.524000	0.06400	-4.755000	0.00003	TCG	G|0.634;A|0.366	0.366	strong		0.527	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
VIPR2	7434	hgsc.bcm.edu	37	7	158896517	158896517	+	Silent	SNP	G	G	A	rs2270313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158896517G>A	ENST00000262178.2	-	4	473	c.288C>T	c.(286-288)gaC>gaT	p.D96D	VIPR2_ENST00000402066.1_Silent_p.D237D	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	96					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CTGACCATCCGTCACTCGTAC	0.507													G|||	1206	0.240815	0.3185	0.1873	5008	,	,		20770	0.1974		0.2485	False		,,,				2504	0.2106				p.D96D	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.C288T						PASS	.	G		1334,3072	447.9+/-348.5	214,906,1083	235.0	192.0	206.0		288	-7.6	0.2	7	dbSNP_100	206	1995,6605	350.5+/-327.9	225,1545,2530	no	coding-synonymous	VIPR2	NM_003382.4		439,2451,3613	AA,AG,GG		23.1977,30.2769,25.5959		96/439	158896517	3329,9677	2203	4300	6503	SO:0001819	synonymous_variant	7434	exon4			CCATCCGTCACTC	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12695	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 2"""	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.288C>T	7.37:g.158896517G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1	560	0.2564102564102564	169	0.3434959349593496	76	0.20994475138121546	127	0.22202797202797203	188	0.24802110817941952	G	0.289	-0.981342	0.02197	0.302769	0.231977	ENSG00000106018	ENST00000418475	.	.	.	5.0	-7.55	0.01327	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.21841	P	0.999511805	.	.	.	.	.	.	T	0.24621	-1.0155	3	.	.	.	.	9.5043	0.39037	0.7778:0.0:0.1167:0.1054	rs2270313;rs2270313	.	.	.	W	92	.	.	R	-	1	2	VIPR2	158589278	0.647000	0.27304	0.188000	0.23233	0.014000	0.08584	-0.332000	0.07904	-1.063000	0.03177	-1.012000	0.02466	CGG	G|0.750;A|0.250	0.250	strong		0.507	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
SEMA6A	57556	hgsc.bcm.edu	37	5	115811273	115811273	+	Missense_Mutation	SNP	C	C	T	rs17432496	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:115811273C>T	ENST00000343348.6	-	16	2463	c.1676G>A	c.(1675-1677)cGt>cAt	p.R559H	SEMA6A_ENST00000282394.6_Missense_Mutation_p.R91H|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.R559H|CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000507558.1_RNA|SEMA6A_ENST00000257414.8_Missense_Mutation_p.R559H|CTB-118N6.3_ENST00000514214.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	559			R -> H (in dbSNP:rs17432496).		apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		TGTATTGCCACGCTCTATGTC	0.398													C|||	53	0.0105831	0.0008	0.0187	5008	,	,		19995	0.0		0.0378	False		,,,				2504	0.001				p.R559H		Atlas-SNP	.											.	SEMA6A	93	.	0			c.G1676A						PASS	.	C	HIS/ARG	31,3791		0,31,1880	70.0	64.0	66.0		1676	4.2	1.0	5	dbSNP_123	66	293,7947		3,287,3830	yes	missense	SEMA6A	NM_020796.3	29	3,318,5710	TT,TC,CC		3.5558,0.8111,2.6861	benign	559/1031	115811273	324,11738	1911	4120	6031	SO:0001583	missense	57556	exon16			TTGCCACGCTCTA	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.1676G>A	5.37:g.115811273C>T	ENSP00000345512:p.Arg559His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	37	CCDS47256.1	41|41	0.018772893772893772|0.018772893772893772	1|1	0.0020325203252032522|0.0020325203252032522	10|10	0.027624309392265192|0.027624309392265192	0|0	0.0|0.0	30|30	0.0395778364116095|0.0395778364116095	C|C	11.87|11.87	1.767837|1.767837	0.31320|0.31320	0.008111|0.008111	0.035558|0.035558	ENSG00000092421|ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000282394;ENST00000510263|ENST00000515129	T;T;T;T|.	0.22134|.	1.97;1.97;1.97;1.97|.	6.17|6.17	4.19|4.19	0.49359|0.49359	.|.	3.298410|.	0.01352|.	N|.	0.011951|.	T|T	0.03477|0.03477	0.0100|0.0100	N|N	0.04724|0.04724	-0.175|-0.175	0.28162|0.28162	N|N	0.928926|0.928926	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|T	0.11372|0.11372	-1.0590|-1.0590	10|5	0.21540|.	T|.	0.41|.	.|.	4.536|4.536	0.12032|0.12032	0.0:0.5977:0.0:0.4023|0.0:0.5977:0.0:0.4023	rs17432496;rs56555803;rs17432496|rs17432496;rs56555803;rs17432496	559;103;559;91|.	Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3|.	SEM6A_HUMAN;.;.;.|.	H|M	559;559;91;559|129	ENSP00000345512:R559H;ENSP00000257414:R559H;ENSP00000282394:R91H;ENSP00000424388:R559H|.	ENSP00000257414:R559H|.	R|V	-|-	2|1	0|0	SEMA6A|SEMA6A	115839172|115839172	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.936000|1.936000	0.40183|0.40183	1.633000|1.633000	0.50488|0.50488	0.655000|0.655000	0.94253|0.94253	CGT|GTG	C|0.976;T|0.024	0.024	strong		0.398	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
SLC16A4	9122	hgsc.bcm.edu	37	1	110924316	110924316	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110924316T>C	ENST00000369779.4	-	4	571	c.322A>G	c.(322-324)Aca>Gca	p.T108A	SLC16A4_ENST00000472422.2_Intron|SLC16A4_ENST00000497687.1_Intron|SLC16A4_ENST00000437429.2_Intron|SLC16A4_ENST00000541986.1_Missense_Mutation_p.T46A|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Missense_Mutation_p.T108A	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	108					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	GGAATACTTGTGGCCCAGCTG	0.458																																					p.T108A		Atlas-SNP	.											.	SLC16A4	47	.	0			c.A322G						PASS	.						102.0	94.0	96.0					1																	110924316		2203	4300	6503	SO:0001583	missense	9122	exon4			TACTTGTGGCCCA	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.322A>G	1.37:g.110924316T>C	ENSP00000358794:p.Thr108Ala	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	228	110	0.482456	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Missense_Mutation	SNP	ENST00000369779.4	37	CCDS823.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.129800	0.77549	.	.	ENSG00000168679	ENST00000369779;ENST00000369781;ENST00000541986	T;T;T	0.55760	0.5;0.5;0.5	4.86	3.73	0.42828	Major facilitator superfamily domain, general substrate transporter (1);	0.253587	0.45867	N	0.000340	T	0.61602	0.2360	M	0.87971	2.92	0.80722	D	1	D;D;P;D	0.65815	0.995;0.994;0.947;0.992	D;D;P;D	0.68621	0.91;0.959;0.823;0.91	T	0.63633	-0.6593	10	0.30854	T	0.27	.	9.0678	0.36473	0.0:0.0848:0.0:0.9152	.	46;108;108;108	B4DJ67;Q53FH9;Q8WU09;O15374	.;.;.;MOT5_HUMAN	A	108;108;46	ENSP00000358794:T108A;ENSP00000358796:T108A;ENSP00000446087:T46A	ENSP00000358794:T108A	T	-	1	0	SLC16A4	110725839	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	5.203000	0.65174	0.994000	0.38892	0.533000	0.62120	ACA	.	.	none		0.458	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
GPR144	347088	hgsc.bcm.edu	37	9	127228596	127228596	+	Silent	SNP	A	A	G	rs4838184	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:127228596A>G	ENST00000334810.1	+	11	1851	c.1851A>G	c.(1849-1851)acA>acG	p.T617T				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	617	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						GGGCCACCACAGGCTGCTCCG	0.602													G|||	3757	0.7502	0.7322	0.7954	5008	,	,		15815	0.8135		0.6451	False		,,,				2504	0.7853				p.T617T		Atlas-SNP	.											.	GPR144	33	.	0			c.A1851G						PASS	.						29.0	32.0	31.0					9																	127228596		692	1591	2283	SO:0001819	synonymous_variant	347088	exon11			CACCACAGGCTGC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.1851A>G	9.37:g.127228596A>G		Somatic	318	1	0.00314465		WXS	Illumina HiSeq	Phase_I	287	285	0.993031	NM_001161808	Q86SL4|Q8NH12	Silent	SNP	ENST00000334810.1	37	CCDS48016.1	1603	0.7339743589743589	358	0.7276422764227642	270	0.7458563535911602	483	0.8444055944055944	492	0.6490765171503958	G	0.499	-0.871711	0.02570	.	.	ENSG00000180264	ENST00000439837	.	.	.	5.46	-10.9	0.00192	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999595964	.	.	.	.	.	.	T	0.30563	-0.9974	4	0.46703	T	0.11	.	0.9339	0.01340	0.3033:0.233:0.2847:0.179	rs4838184;rs60375364	.	.	.	G	339	.	ENSP00000405734:R339G	R	+	1	2	GPR144	126268417	0.000000	0.05858	0.001000	0.08648	0.119000	0.20118	-3.960000	0.00325	-3.361000	0.00179	-2.497000	0.00192	AGG	A|0.273;G|0.727	0.727	strong		0.602	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
COL4A3	1285	hgsc.bcm.edu	37	2	228121101	228121101	+	Missense_Mutation	SNP	G	G	T	rs55703767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:228121101G>T	ENST00000396578.3	+	17	1138	c.976G>T	c.(976-978)Gat>Tat	p.D326Y	AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000396588.2_RNA|AC097662.2_ENST00000606119.1_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	326	Triple-helical region.		D -> Y (in dbSNP:rs55703767). {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)		AATGGGTGAAGATGGCATTAA	0.448													G|||	580	0.115815	0.0189	0.1542	5008	,	,		19808	0.129		0.2117	False		,,,				2504	0.1074				p.D326Y		Atlas-SNP	.											.	COL4A3	293	.	0			c.G976T						PASS	.	G	TYR/ASP	159,3543		0,159,1692	126.0	113.0	117.0		976	3.0	0.8	2	dbSNP_129	117	1814,6386		207,1400,2493	yes	missense	COL4A3	NM_000091.4	160	207,1559,4185	TT,TG,GG		22.122,4.295,16.577	probably-damaging	326/1671	228121101	1973,9929	1851	4100	5951	SO:0001583	missense	1285	exon17			GGTGAAGATGGCA		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.976G>T	2.37:g.228121101G>T	ENSP00000379823:p.Asp326Tyr	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	309	0.14148351648351648	8	0.016260162601626018	62	0.1712707182320442	65	0.11363636363636363	174	0.22955145118733508	G	9.616	1.132535	0.21041	0.04295	0.22122	ENSG00000169031	ENST00000396578;ENST00000328380;ENST00000335583;ENST00000396574;ENST00000315699	D	0.93859	-3.3	5.87	3.01	0.34805	.	0.946366	0.08846	N	0.885103	T	0.00300	0.0009	L	0.56340	1.77	0.40599	P	0.01843499999999998	B;B;B;B	0.30634	0.244;0.244;0.244;0.288	B;B;B;B	0.33042	0.026;0.06;0.097;0.157	T	0.37798	-0.9690	9	0.59425	D	0.04	.	5.6832	0.17788	0.172:0.0:0.6504:0.1776	rs55703767;rs62277854	326;326;326;326	Q01955-5;Q01955-4;Q01955-2;Q01955	.;.;.;CO4A3_HUMAN	Y	326	ENSP00000379823:D326Y	ENSP00000323334:D326Y	D	+	1	0	COL4A3	227829345	0.695000	0.27747	0.788000	0.31933	0.349000	0.29174	0.499000	0.22546	0.898000	0.36418	-0.136000	0.14681	GAT	G|0.828;T|0.172	0.172	strong		0.448	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
ZMYM5	9205	hgsc.bcm.edu	37	13	20425911	20425911	+	Missense_Mutation	SNP	C	C	A	rs9579717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:20425911C>A	ENST00000337963.4	-	3	674	c.410G>T	c.(409-411)tGt>tTt	p.C137F	ZMYM5_ENST00000382907.4_Missense_Mutation_p.C137F|ZMYM5_ENST00000382905.4_Missense_Mutation_p.C137F	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	137			C -> F (in dbSNP:rs9579717). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		TTCGATAAAACAGGAAGACTT	0.378													C|||	485	0.096845	0.1672	0.0735	5008	,	,		18768	0.0813		0.0924	False		,,,				2504	0.0389				p.C137F		Atlas-SNP	.											.	ZMYM5	73	.	0			c.G410T						PASS	.	C	PHE/CYS,PHE/CYS,PHE/CYS	701,3705	284.3+/-277.5	61,579,1563	78.0	83.0	81.0		410,410,410	-2.2	0.0	13	dbSNP_119	81	587,8013	155.1+/-209.2	15,557,3728	yes	missense,missense,missense	ZMYM5	NM_001039649.2,NM_001039650.2,NM_001142684.1	205,205,205	76,1136,5291	AA,AC,CC		6.8256,15.9101,9.9031	benign,benign,benign	137/209,137/383,137/670	20425911	1288,11718	2203	4300	6503	SO:0001583	missense	9205	exon3			ATAAAACAGGAAG	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"""Zinc fingers, MYM type"""	13029	protein-coding gene	gene with protein product			"""zinc finger protein 237"""	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.410G>T	13.37:g.20425911C>A	ENSP00000337034:p.Cys137Phe	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	151	62	0.410596	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		191	0.08745421245421245	69	0.1402439024390244	26	0.0718232044198895	35	0.06118881118881119	61	0.08047493403693931	C	6.095	0.385875	0.11524	0.159101	0.068256	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382907;ENST00000382905	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.31	-2.22	0.06952	.	.	.	.	.	T	0.00073	0.0002	N	0.22421	0.69	0.48571	P	3.250000000000197E-4	B;B;B	0.24882	0.038;0.113;0.113	B;B;B	0.28638	0.029;0.011;0.092	T	0.26155	-1.0111	8	0.54805	T	0.06	0.3923	5.8782	0.18840	0.0:0.5084:0.2643:0.2273	rs9579717;rs17850148;rs52804480;rs9579717	137;137;137	Q9UJ78;Q9UJ78-2;Q9UJ78-1	ZMYM5_HUMAN;.;.	F	137;127;137;137	ENSP00000337034:C137F;ENSP00000445779:C127F;ENSP00000372364:C137F;ENSP00000372361:C137F	ENSP00000337034:C137F	C	-	2	0	ZMYM5	19323911	0.998000	0.40836	0.006000	0.13384	0.395000	0.30598	0.643000	0.24750	-0.623000	0.05618	0.491000	0.48974	TGT	C|0.902;A|0.098	0.098	strong		0.378	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242	
LILRB3	11025	hgsc.bcm.edu	37	19	54722250	54722250	+	Missense_Mutation	SNP	T	T	C	rs1132610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54722250T>C	ENST00000391750.1	-	12	1709	c.1573A>G	c.(1573-1575)Agg>Ggg	p.R525G	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Missense_Mutation_p.R525G|LILRB3_ENST00000407860.2_Missense_Mutation_p.R542G|LILRB3_ENST00000424807.1_Missense_Mutation_p.R525G|LILRB3_ENST00000346401.6_Missense_Mutation_p.R537G|LILRA6_ENST00000419410.2_Missense_Mutation_p.R525G|LILRB3_ENST00000245620.9_Missense_Mutation_p.R525G|LILRA6_ENST00000270464.5_Missense_Mutation_p.R525G			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	525				R -> G (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGCTCCACCCTGTCCTCAGAC	0.617													.|||	740	0.147764	0.3525	0.1354	5008	,	,		18421	0.002		0.1103	False		,,,				2504	0.0685				p.R525G		Atlas-SNP	.											LILRB3,colon,carcinoma,+2,1	LILRB3	67	1	0			c.A1573G						PASS	.	G	GLY/ARG,GLY/ARG	1383,3023		239,905,1059	119.0	102.0	108.0		1573,1573	-0.3	0.0	19	dbSNP_86	108	1039,7561		58,923,3319	yes	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	125,125	297,1828,4378	CC,CT,TT		12.0814,31.389,18.6222	benign,benign	525/633,525/632	54722250	2422,10584	2203	4300	6503	SO:0001583	missense	11025	exon11			CCACCCTGTCCTC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1573A>G	19.37:g.54722250T>C	ENSP00000375630:p.Arg525Gly	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	214	104	0.485981	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	294	0.1346153846153846	176	0.35772357723577236	42	0.11602209944751381	2	0.0034965034965034965	74	0.09762532981530343	G	0.006	-2.043597	0.00398	0.31389	0.120814	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00454	7.49;7.49;7.36;7.47;7.32;7.48;7.49;7.49	3.11	-0.331	0.12679	.	.	.	.	.	T	0.00012	0.0000	N	0.00221	-1.82	0.80722	P	0.0	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B;B	0.12156	0.0;0.001;0.0;0.007;0.003;0.001;0.001	T	0.25047	-1.0143	8	0.02654	T	1	.	4.2725	0.10794	0.0:0.4068:0.3677:0.2255	rs1132610;rs3193489;rs52834610;rs58789613	542;525;525;537;542;525;525	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	G	525;525;537;525;542;525;525;525	ENSP00000375630:R525G;ENSP00000412771:R525G;ENSP00000345184:R537G;ENSP00000245620:R525G;ENSP00000384274:R542G;ENSP00000390120:R525G;ENSP00000270464:R525G;ENSP00000411227:R525G	ENSP00000270464:R525G	R	-	1	2	LILRB3;LILRA6	59414062	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.023000	0.01438	-0.189000	0.10482	-3.810000	0.00019	AGG	T|0.826;C|0.174	0.174	strong		0.617	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
MCF2L	23263	hgsc.bcm.edu	37	13	113720476	113720476	+	Silent	SNP	C	C	T	rs2297192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113720476C>T	ENST00000375608.3	+	9	1021	c.963C>T	c.(961-963)acC>acT	p.T321T	MCF2L_ENST00000423482.2_Silent_p.T289T|MCF2L_ENST00000442652.2_Silent_p.T321T|MCF2L_ENST00000535094.2_Silent_p.T291T|MCF2L_ENST00000434480.2_Silent_p.T297T|MCF2L_ENST00000375604.2_Silent_p.T348T|MCF2L_ENST00000375601.3_Silent_p.T295T|MCF2L_ENST00000375597.4_Silent_p.T289T|MCF2L_ENST00000397030.1_Silent_p.T324T|MCF2L_ENST00000421756.1_Silent_p.T295T			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	321					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				ACCAGGCCACCGTGCAGAGGT	0.617													C|||	944	0.188498	0.025	0.2478	5008	,	,		18249	0.4573		0.1571	False		,,,				2504	0.1227				p.T291T		Atlas-SNP	.											.	MCF2L	182	.	0			c.C873T						PASS	.	C	,	235,4171	137.3+/-173.1	8,219,1976	86.0	72.0	77.0		873,867	-10.0	0.4	13	dbSNP_100	77	1400,7198	269.3+/-288.3	107,1186,3006	yes	coding-synonymous,coding-synonymous	MCF2L	NM_001112732.2,NM_024979.4	,	115,1405,4982	TT,TC,CC		16.2829,5.3336,12.5731	,	291/1126,289/1124	113720476	1635,11369	2203	4299	6502	SO:0001819	synonymous_variant	23263	exon8			GGCCACCGTGCAG	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.963C>T	13.37:g.113720476C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	11	0.297297	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Silent	SNP	ENST00000375608.3	37																																																																																				C|0.846;T|0.154	0.154	strong		0.617	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
RGR	5995	hgsc.bcm.edu	37	10	86004865	86004865	+	Silent	SNP	C	C	T	rs11200938	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:86004865C>T	ENST00000359452.4	+	1	57	c.19C>T	c.(19-21)Ctg>Ttg	p.L7L	RGR_ENST00000372092.3_Silent_p.L7L|RGR_ENST00000358110.5_Silent_p.L7L	NM_001012720.1|NM_002921.3	NP_001012738.1|NP_002912.2	P47804	RGR_HUMAN	retinal G protein coupled receptor	7					chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	17						GACCAGTGCCCTGCCCACTGG	0.652													C|||	198	0.0395367	0.0038	0.098	5008	,	,		17526	0.0218		0.0746	False		,,,				2504	0.0286				p.L7L	NSCLC(15;204 545 5889 6385 32445)	Atlas-SNP	.											RGR,right_upper_lobe,carcinoma,-2,1	RGR	42	1	0			c.C19T						PASS	.	C	,,	79,4327	68.1+/-105.8	2,75,2126	107.0	92.0	97.0		19,19,19	3.0	1.0	10	dbSNP_120	97	674,7926	168.3+/-219.8	23,628,3649	no	coding-synonymous,coding-synonymous,coding-synonymous	RGR	NM_001012720.1,NM_001012722.1,NM_002921.3	,,	25,703,5775	TT,TC,CC		7.8372,1.793,5.7896	,,	7/292,7/254,7/296	86004865	753,12253	2203	4300	6503	SO:0001819	synonymous_variant	5995	exon1			AGTGCCCTGCCCA	BC011349	CCDS7374.1, CCDS41543.1	10q23	2013-02-14			ENSG00000148604	ENSG00000148604		"""GPCR / Class A : Opsin receptors"""	9990	protein-coding gene	gene with protein product	"""RGR-opsin"""	600342				8641686	Standard	NM_002921		Approved	RP44	uc001kdd.1	P47804	OTTHUMG00000018636	ENST00000359452.4:c.19C>T	10.37:g.86004865C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_001012722	A6NKK7|Q96FC5	Silent	SNP	ENST00000359452.4	37	CCDS7374.1																																																																																			C|0.948;T|0.052	0.052	strong		0.652	RGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049116.1	NM_002921	
ERAP1	51752	hgsc.bcm.edu	37	5	96126308	96126308	+	Silent	SNP	A	A	G	rs27529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96126308A>G	ENST00000443439.2	-	9	1425	c.1359T>C	c.(1357-1359)agT>agC	p.S453S	ERAP1_ENST00000296754.3_Silent_p.S453S	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	453					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)		ATGCGTCAGCACTAAGATACT	0.353													A|||	2985	0.596046	0.5976	0.5951	5008	,	,		19952	0.5456		0.6501	False		,,,				2504	0.591				p.S453S		Atlas-SNP	.											.	ERAP1	59	.	0			c.T1359C						PASS	.	A	,,	2629,1777	642.4+/-397.6	784,1061,358	111.0	112.0	112.0		1359,1359,1359	4.4	0.8	5	dbSNP_76	112	5536,3064	660.3+/-401.8	1770,1996,534	no	coding-synonymous,coding-synonymous,coding-synonymous	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	,,	2554,3057,892	GG,GA,AA		35.6279,40.3314,37.2213	,,	453/942,453/942,453/949	96126308	8165,4841	2203	4300	6503	SO:0001819	synonymous_variant	51752	exon9			GTCAGCACTAAGA	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.1359T>C	5.37:g.96126308A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			A|0.393;G|0.607	0.607	strong		0.353	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
FBN3	84467	hgsc.bcm.edu	37	19	8197983	8197983	+	Silent	SNP	G	G	A	rs35202360	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8197983G>A	ENST00000600128.1	-	14	2013	c.1599C>T	c.(1597-1599)aaC>aaT	p.N533N	FBN3_ENST00000601739.1_Silent_p.N533N|FBN3_ENST00000270509.2_Silent_p.N533N			Q75N90	FBN3_HUMAN	fibrillin 3	533	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGGCACACTCGTTGTGGTCTG	0.652													g|||	238	0.047524	0.0295	0.1009	5008	,	,		18439	0.001		0.0765	False		,,,				2504	0.0521				p.N533N		Atlas-SNP	.											.	FBN3	300	.	0			c.C1599T						PASS	.			171,4225		1,169,2028	48.0	30.0	36.0		1599	-0.2	0.9	19	dbSNP_126	36	796,7798		39,718,3540	no	coding-synonymous	FBN3	NM_032447.3		40,887,5568	AA,AG,GG		9.2623,3.8899,7.4442		533/2810	8197983	967,12023	2198	4297	6495	SO:0001819	synonymous_variant	84467	exon13			ACACTCGTTGTGG		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.1599C>T	19.37:g.8197983G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.929;A|0.071	0.071	strong		0.652	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
PCNT	5116	hgsc.bcm.edu	37	21	47850107	47850107	+	Missense_Mutation	SNP	G	G	A	rs8131693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47850107G>A	ENST00000359568.5	+	36	7981	c.7874G>A	c.(7873-7875)cGg>cAg	p.R2625Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2625			R -> Q (in dbSNP:rs8131693).		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)					CAGCTGTCCCGGTCCCTCTGC	0.622													G|||	319	0.0636981	0.2269	0.0245	5008	,	,		17998	0.0		0.002	False		,,,				2504	0.0				p.R2625Q		Atlas-SNP	.											.	PCNT	283	.	0			c.G7874A						PASS	.	G	GLN/ARG	879,3527	340.2+/-306.1	96,687,1420	67.0	65.0	66.0		7874	0.3	0.0	21	dbSNP_116	66	14,8586	8.4+/-32.0	0,14,4286	yes	missense	PCNT	NM_006031.5	43	96,701,5706	AA,AG,GG		0.1628,19.9501,6.8661	benign	2625/3337	47850107	893,12113	2203	4300	6503	SO:0001583	missense	5116	exon36			TGTCCCGGTCCCT	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.7874G>A	21.37:g.47850107G>A	ENSP00000352572:p.Arg2625Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	95	0.043498168498168496	88	0.17886178861788618	7	0.019337016574585635	0	0.0	0	0.0	G	6.228	0.410216	0.11812	0.199501	0.001628	ENSG00000160299	ENST00000359568	T	0.01359	4.98	4.31	0.32	0.15878	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.17852	0.002;0.024	B;B	0.06405	0.002;0.001	T	0.43114	-0.9411	8	0.36615	T	0.2	.	5.7279	0.18022	0.5019:0.3993:0.0988:0.0	rs8131693;rs8131693	2507;2625	O95613-2;O95613	.;PCNT_HUMAN	Q	2625	ENSP00000352572:R2625Q	ENSP00000352572:R2625Q	R	+	2	0	PCNT	46674535	0.038000	0.19896	0.003000	0.11579	0.002000	0.02628	1.973000	0.40550	-0.055000	0.13244	-0.391000	0.06502	CGG	G|0.933;A|0.067	0.067	strong		0.622	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MYO7A	4647	hgsc.bcm.edu	37	11	76883797	76883797	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76883797G>A	ENST00000409709.3	+	16	2073	c.1801G>A	c.(1801-1803)Gcc>Acc	p.A601T	MYO7A_ENST00000409893.1_Missense_Mutation_p.A601T|MYO7A_ENST00000458637.2_Missense_Mutation_p.A601T|MYO7A_ENST00000409619.2_Missense_Mutation_p.A590T	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	601	Myosin motor.				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						CCCCCAGGGCGCCGAGACCAG	0.692																																					p.A601T		Atlas-SNP	.											.	MYO7A	164	.	0			c.G1801A						PASS	.						12.0	15.0	14.0					11																	76883797		1977	4041	6018	SO:0001583	missense	4647	exon16			CAGGGCGCCGAGA	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.1801G>A	11.37:g.76883797G>A	ENSP00000386331:p.Ala601Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.697112	0.48202	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	4.77	3.84	0.44239	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.80654	0.4664	L	0.37466	1.105	0.46849	D	0.999226	B;B;B	0.28291	0.206;0.085;0.123	B;B;B	0.26416	0.037;0.022;0.069	T	0.74910	-0.3503	10	0.19590	T	0.45	.	15.0945	0.72223	0.0:0.1428:0.8572:0.0	.	601;601;601	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	T	601;601;601;590;600;600;477;600	ENSP00000386331:A601T;ENSP00000386689:A601T;ENSP00000392185:A601T;ENSP00000386635:A590T	ENSP00000345075:A477T	A	+	1	0	MYO7A	76561445	0.993000	0.37304	0.994000	0.49952	0.906000	0.53458	5.244000	0.65400	1.107000	0.41642	0.549000	0.68633	GCC	.	.	none		0.692	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
MARCH2	51257	hgsc.bcm.edu	37	19	8503345	8503345	+	Missense_Mutation	SNP	G	G	C	rs34099346	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8503345G>C	ENST00000602117.1	+	5	1111	c.656G>C	c.(655-657)cGg>cCg	p.R219P	MARCH2_ENST00000215555.2_Missense_Mutation_p.R219P|MARCH2_ENST00000381035.4_Missense_Mutation_p.R149P|MARCH2_ENST00000601283.1_Intron|MARCH2_ENST00000393944.1_Missense_Mutation_p.R219P			Q9P0N8	MARH2_HUMAN	membrane-associated ring finger (C3HC4) 2, E3 ubiquitin protein ligase	219			R -> P (in dbSNP:rs34099346).		endocytosis (GO:0006897)|protein ubiquitination (GO:0016567)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(3)|ovary(3)|skin(1)|urinary_tract(1)	10						CTGAAGATCCGGGAGGCGGAC	0.617													G|||	468	0.0934505	0.0091	0.1671	5008	,	,		9415	0.002		0.167	False		,,,				2504	0.1738				p.R219P		Atlas-SNP	.											.	MARCH2	17	.	0			c.G656C						PASS	.	G	PRO/ARG,PRO/ARG,PRO/ARG	138,4268	94.4+/-133.1	3,132,2068	48.0	50.0	50.0		656,446,656	-2.2	0.8	19	dbSNP_126	50	1226,7374	238.2+/-269.8	86,1054,3160	no	missense,missense,missense	MARCH2	NM_001005415.1,NM_001005416.1,NM_016496.4	103,103,103	89,1186,5228	CC,CG,GG		14.2558,3.1321,10.4875	benign,benign,benign	219/247,149/177,219/247	8503345	1364,11642	2203	4300	6503	SO:0001583	missense	51257	exon5			AGATCCGGGAGGC	AF151074	CCDS12202.1, CCDS32894.1	19p13.2	2013-01-09	2012-02-23			ENSG00000099785		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	28038	protein-coding gene	gene with protein product		613332	"""membrane-associated ring finger (C3HC4) 2"""			11042152, 14722266	Standard	NM_016496		Approved	HSPC240, MARCH-II, RNF172	uc002mjw.3	Q9P0N8		ENST00000602117.1:c.656G>C	19.37:g.8503345G>C	ENSP00000471536:p.Arg219Pro	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_001005415	A6NP10|Q5H785|Q8N5A3|Q96B78	Missense_Mutation	SNP	ENST00000602117.1	37	CCDS12202.1	195	0.08928571428571429	6	0.012195121951219513	52	0.143646408839779	2	0.0034965034965034965	135	0.17810026385224276	G	13.58	2.279265	0.40294	0.031321	0.142558	ENSG00000099785	ENST00000393944;ENST00000215555;ENST00000381035	T;T;T	0.14022	2.54;2.54;2.54	5.33	-2.25	0.06888	.	27.369900	0.00166	N	0.000007	T	0.00012	0.0000	N	0.00966	-1.09	0.35595	P	0.19261499999999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37291	-0.9712	9	0.06494	T	0.89	-21.2424	2.2191	0.03968	0.2463:0.3846:0.2482:0.121	rs34099346	149;219	Q9P0N8-2;Q9P0N8	.;MARH2_HUMAN	P	219;219;149	ENSP00000377518:R219P;ENSP00000215555:R219P;ENSP00000370423:R149P	ENSP00000215555:R219P	R	+	2	0	MARCH2	8409345	0.999000	0.42202	0.809000	0.32408	0.021000	0.10359	1.608000	0.36847	0.009000	0.14813	-0.892000	0.02923	CGG	G|0.900;C|0.100	0.100	strong		0.617	MARCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460361.2	NM_016496	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004848	153004848	+	Silent	SNP	T	T	C	rs3795381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153004848T>C	ENST00000307098.4	+	2	92	c.27T>C	c.(25-27)ccT>ccC	p.P9P	SPRR1B_ENST00000392661.3_Silent_p.P9P	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	9	2 X 12 AA approximate repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	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)			AGAAGCAGCCTTGCACCCCAC	0.552													C|||	2474	0.49401	0.4402	0.4251	5008	,	,		16307	0.5913		0.5099	False		,,,				2504	0.499				p.P9P		Atlas-SNP	.											.	SPRR1B	18	.	0			c.T27C						PASS	.	C		2068,2338	603.3+/-390.1	482,1104,617	144.0	140.0	141.0		27	2.1	1.0	1	dbSNP_107	141	4392,4208	568.8+/-389.1	1128,2136,1036	yes	coding-synonymous	SPRR1B	NM_003125.2		1610,3240,1653	CC,CT,TT		48.9302,46.936,49.6694		9/90	153004848	6460,6546	2203	4300	6503	SO:0001819	synonymous_variant	6699	exon2			GCAGCCTTGCACC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.27T>C	1.37:g.153004848T>C		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	201	99	0.492537	NM_003125	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	37	CCDS30863.1																																																																																			T|0.497;C|0.503	0.503	strong		0.552	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
C6orf15	29113	hgsc.bcm.edu	37	6	31079894	31079894	+	Missense_Mutation	SNP	A	A	G	rs2233977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31079894A>G	ENST00000259870.3	-	2	245	c.242T>C	c.(241-243)gTg>gCg	p.V81A	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	81			V -> A (in dbSNP:rs2233977).		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						TGATGCAGGCACGCTGAGCTT	0.607													G|||	1071	0.213858	0.087	0.1974	5008	,	,		16805	0.3899		0.169	False		,,,				2504	0.2618				p.V81A		Atlas-SNP	.											C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	0			c.T242C						PASS	.	G	ALA/VAL	464,3942	764.3+/-413.3	21,422,1760	61.0	67.0	65.0		242	-8.4	0.0	6	dbSNP_98	65	1456,7144	744.7+/-407.2	131,1194,2975	yes	missense	C6orf15	NM_014070.2	64	152,1616,4735	GG,GA,AA		16.9302,10.5311,14.7624	benign	81/326	31079894	1920,11086	2203	4300	6503	SO:0001583	missense	29113	exon2			GCAGGCACGCTGA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.242T>C	6.37:g.31079894A>G	ENSP00000259870:p.Val81Ala	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	458	0.2097069597069597	53	0.10772357723577236	54	0.14917127071823205	222	0.3881118881118881	129	0.17018469656992086	G	1.094	-0.663129	0.03428	0.105311	0.169302	ENSG00000204542	ENST00000259870	T	0.05025	3.51	4.61	-8.37	0.00976	.	1.975560	0.02836	N	0.127304	T	0.00412	0.0013	N	0.01267	-0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	9	0.07644	T	0.81	-15.0007	5.3978	0.16278	0.3695:0.0:0.2882:0.3423	rs2233977;rs2233977	81	Q6UXA7	CF015_HUMAN	A	81	ENSP00000259870:V81A	ENSP00000259870:V81A	V	-	2	0	C6orf15	31187873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.201000	0.01236	-2.546000	0.00482	-1.841000	0.00585	GTG	A|0.825;G|0.175	0.175	strong		0.607	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
MUC16	94025	hgsc.bcm.edu	37	19	9071834	9071834	+	Silent	SNP	G	G	C	rs17000803	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9071834G>C	ENST00000397910.4	-	3	15815	c.15612C>G	c.(15610-15612)ccC>ccG	p.P5204P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5206	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						TTGTGTCCGTGGGAAAGCTGG	0.468													G|||	1007	0.201078	0.0946	0.2824	5008	,	,		21218	0.3254		0.167	False		,,,				2504	0.1943				p.P5204P		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,-1,3	MUC16	4315	3	0			c.C15612G						PASS	.	G		399,3425		18,363,1531	188.0	177.0	180.0		15612	-1.2	0.0	19	dbSNP_123	180	1504,6742		136,1232,2755	no	coding-synonymous	MUC16	NM_024690.2		154,1595,4286	CC,CG,GG		18.2391,10.4341,15.7664		5204/14508	9071834	1903,10167	1912	4123	6035	SO:0001819	synonymous_variant	94025	exon3			GTCCGTGGGAAAG	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.15612C>G	19.37:g.9071834G>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.792;C|0.208	0.208	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
HAPLN3	145864	hgsc.bcm.edu	37	15	89421405	89421405	+	Silent	SNP	G	G	A	rs7182726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89421405G>A	ENST00000359595.3	-	5	1093	c.879C>T	c.(877-879)atC>atT	p.I293I	HAPLN3_ENST00000562889.1_Silent_p.I355I	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	293	Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)	p.I293I(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	CCACCTTGGCGATCGTGGCAT	0.642													G|||	874	0.174521	0.1778	0.1974	5008	,	,		17816	0.1101		0.2167	False		,,,				2504	0.1769				p.I293I		Atlas-SNP	.											HAPLN3,NS,carcinoma,0,1	HAPLN3	43	1	1	Substitution - coding silent(1)	prostate(1)	c.C879T						PASS	.	G		884,3516	342.5+/-307.2	82,720,1398	160.0	147.0	151.0		879	-5.5	0.1	15	dbSNP_116	151	1896,6702	337.1+/-322.1	196,1504,2599	no	coding-synonymous	HAPLN3	NM_178232.2		278,2224,3997	AA,AG,GG		22.0516,20.0909,21.3879		293/361	89421405	2780,10218	2200	4299	6499	SO:0001819	synonymous_variant	145864	exon5			CTTGGCGATCGTG	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.879C>T	15.37:g.89421405G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	147	68	0.462585	NM_178232	A8K7P0	Silent	SNP	ENST00000359595.3	37	CCDS10346.1																																																																																			G|0.804;A|0.196	0.196	strong		0.642	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12856087	12856087	+	Missense_Mutation	SNP	C	C	T	rs141070565	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12856087C>T	ENST00000332296.7	+	4	1470	c.1367C>T	c.(1366-1368)cCc>cTc	p.P456L	PRAMEF1_ENST00000400814.3_Missense_Mutation_p.P211L	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	456					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.P456L(4)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCCCACCCCCTGCCCTTCC	0.557																																					p.P456L		Atlas-SNP	.											PRAMEF1,trunk,malignant_melanoma,0,4	PRAMEF1	78	4	4	Substitution - Missense(4)	skin(4)	c.C1367T						scavenged	.	C	LEU/PRO	154,4248		0,154,2047	61.0	69.0	66.0		1367	-2.3	0.0	1	dbSNP_134	66	288,8300		0,288,4006	no	missense	PRAMEF1	NM_023013.2	98	0,442,6053	TT,TC,CC		3.3535,3.4984,3.4026	probably-damaging	456/475	12856087	442,12548	2201	4294	6495	SO:0001583	missense	65121	exon4			CCACCCCCTGCCC	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.1367C>T	1.37:g.12856087C>T	ENSP00000332134:p.Pro456Leu	Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	379	13	0.0343008	NM_023013	Q9UQP2	Missense_Mutation	SNP	ENST00000332296.7	37	CCDS148.1	.	.	.	.	.	.	.	.	.	.	.	10.30	1.313050	0.23908	0.034984	0.033535	ENSG00000116721	ENST00000332296;ENST00000400814	T;T	0.51071	0.72;0.72	1.56	-2.32	0.06745	.	1.064360	0.07319	N	0.877252	T	0.20292	0.0488	L	0.58810	1.83	0.09310	N	1	P	0.50819	0.939	P	0.51135	0.66	T	0.19943	-1.0290	10	0.17832	T	0.49	.	0.4517	0.00502	0.2326:0.3128:0.2565:0.1982	.	456	O95521	PRAM1_HUMAN	L	456;211	ENSP00000332134:P456L;ENSP00000383616:P211L	ENSP00000332134:P456L	P	+	2	0	PRAMEF1	12778674	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.486000	0.06513	-0.706000	0.05028	0.205000	0.17691	CCC	C|0.968;T|0.032	0.032	strong		0.557	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
SNX9	51429	hgsc.bcm.edu	37	6	158330765	158330765	+	Silent	SNP	G	G	A	rs3211067	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:158330765G>A	ENST00000392185.3	+	8	945	c.774G>A	c.(772-774)agG>agA	p.R258R		NM_016224.3	NP_057308.1	Q9Y5X1	SNX9_HUMAN	sorting nexin 9	258	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|lipid tube assembly (GO:0060988)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein oligomerization (GO:0032461)|receptor-mediated endocytosis (GO:0006898)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle membrane (GO:0030659)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	1-phosphatidylinositol binding (GO:0005545)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)|Prostate(117;0.167)		OV - Ovarian serous cystadenocarcinoma(65;8.06e-18)|BRCA - Breast invasive adenocarcinoma(81;4.48e-05)		CAGATCCCAGGAAAGGCTCCA	0.408													G|||	1028	0.205272	0.2239	0.1383	5008	,	,		20959	0.1369		0.2485	False		,,,				2504	0.2536				p.R258R		Atlas-SNP	.											.	SNX9	43	.	0			c.G774A						PASS	.	G		966,3440	367.1+/-318.1	107,752,1344	170.0	166.0	167.0		774	2.8	1.0	6	dbSNP_105	167	2020,6580	352.5+/-328.7	248,1524,2528	no	coding-synonymous	SNX9	NM_016224.3		355,2276,3872	AA,AG,GG		23.4884,21.9246,22.9586		258/596	158330765	2986,10020	2203	4300	6503	SO:0001819	synonymous_variant	51429	exon8			TCCCAGGAAAGGC	AF121859	CCDS5253.1	6q25.1-q26	2008-05-22			ENSG00000130340	ENSG00000130340		"""Sorting nexins"""	14973	protein-coding gene	gene with protein product		605952				10531379, 17609109	Standard	NM_016224		Approved	SH3PX1, SDP1, SH3PXD3A	uc003qqv.1	Q9Y5X1	OTTHUMG00000015903	ENST00000392185.3:c.774G>A	6.37:g.158330765G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	68	59	0.867647	NM_016224	Q9BSI7|Q9BVM1|Q9UJH6|Q9UP20	Silent	SNP	ENST00000392185.3	37	CCDS5253.1																																																																																			G|0.778;A|0.222	0.222	strong		0.408	SNX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042856.1		
RASGRF1	5923	hgsc.bcm.edu	37	15	79298523	79298523	+	Silent	SNP	G	G	A	rs894780	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79298523G>A	ENST00000419573.3	-	15	2393	c.2119C>T	c.(2119-2121)Ctg>Ttg	p.L707L	RASGRF1_ENST00000558480.2_Intron|RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000394745.3_5'Flank	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	707	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GGGCACCTCAGCCACCTGGCA	0.607													G|||	332	0.0662939	0.0061	0.0605	5008	,	,		21301	0.0972		0.1163	False		,,,				2504	0.0685				p.L707L		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C2119T						PASS	.	G	,	96,4296	75.2+/-113.4	2,92,2102	110.0	96.0	100.0		,2119	1.3	0.1	15	dbSNP_86	100	885,7701	198.6+/-242.9	71,743,3479	no	intron,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4	,	73,835,5581	AA,AG,GG		10.3075,2.1858,7.5589	,	,707/1274	79298523	981,11997	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon15			ACCTCAGCCACCT	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.2119C>T	15.37:g.79298523G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																			G|0.921;T|0.000	.	strong		0.607	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
LPPR3	79948	hgsc.bcm.edu	37	19	814452	814452	+	Silent	SNP	C	C	T	rs3746138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:814452C>T	ENST00000520876.3	-	7	891	c.813G>A	c.(811-813)gcG>gcA	p.A271A	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Silent_p.A299A	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		271						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)										CAGCGATGCCCGCCCCGATGA	0.662													C|||	65	0.0129792	0.0008	0.0403	5008	,	,		12728	0.0109		0.0169	False		,,,				2504	0.0082				p.A299A		Atlas-SNP	.											.	.	.	.	0			c.G897A						PASS	.	C		13,4369	17.9+/-39.9	0,13,2178	26.0	27.0	27.0		897	-9.3	0.0	19	dbSNP_107	27	123,8465	58.3+/-119.8	0,123,4171	no	coding-synonymous	LPPR3	NM_024888.1		0,136,6349	TT,TC,CC		1.4322,0.2967,1.0486		299/747	814452	136,12834	2191	4294	6485	SO:0001819	synonymous_variant	0	exon6			GATGCCCGCCCCG																												ENST00000520876.3:c.813G>A	19.37:g.814452C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Silent	SNP	ENST00000520876.3	37	CCDS58636.1	36	0.016483516483516484	1	0.0020325203252032522	10	0.027624309392265192	8	0.013986013986013986	17	0.022427440633245383	C	0.417	-0.910305	0.02434	0.002967	0.014322	ENSG00000129951	ENST00000517665	.	.	.	4.66	-9.33	0.00639	.	.	.	.	.	T	0.14141	0.0342	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54589	-0.8271	4	.	.	.	-19.2679	2.3959	0.04389	0.1348:0.2259:0.3395:0.2998	rs3746138	.	.	.	R	60	.	.	G	-	1	0	AC006273.1	765452	0.000000	0.05858	0.005000	0.12908	0.063000	0.16089	-7.774000	0.00030	-4.791000	0.00031	-3.357000	0.00042	GGG	C|0.987;T|0.013	0.013	strong		0.662	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
C1orf127	148345	hgsc.bcm.edu	37	1	11008341	11008341	+	Silent	SNP	G	G	A	rs10864483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:11008341G>A	ENST00000377008.4	-	11	1796	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C	C1orf127_ENST00000377004.4_Silent_p.C617C			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	450										NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCGTTCCAGAGCACGTTTCCT	0.657													G|||	890	0.177716	0.3699	0.1254	5008	,	,		16984	0.2093		0.0557	False		,,,				2504	0.0481				p.C617C		Atlas-SNP	.											.	C1orf127	134	.	0			c.C1851T						PASS	.	G		1463,2943	459.2+/-352.2	244,975,984	59.0	68.0	65.0		1851	-0.2	0.0	1	dbSNP_120	65	364,8236	120.1+/-179.3	7,350,3943	no	coding-synonymous	C1orf127	NM_001170754.1		251,1325,4927	AA,AG,GG		4.2326,33.2047,14.0474		617/824	11008341	1827,11179	2203	4300	6503	SO:0001819	synonymous_variant	148345	exon12			TCCAGAGCACGTT	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1350C>T	1.37:g.11008341G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	72	67	0.930556	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		381	0.17445054945054944	180	0.36585365853658536	41	0.1132596685082873	115	0.20104895104895104	45	0.059366754617414245	G	3.870	-0.028045	0.07589	0.332047	0.042326	ENSG00000175262	ENST00000418570;ENST00000520253	.	.	.	3.9	-0.204	0.13200	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.44375	-0.9332	3	.	.	.	-0.1999	1.0939	0.01669	0.2064:0.1773:0.4339:0.1824	rs10864483;rs10864483	.	.	.	V	452;569	.	.	A	-	2	0	C1orf127	10930928	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.046000	0.11983	-0.020000	0.14032	0.491000	0.48974	GCT	G|0.844;A|0.156	0.156	strong		0.657	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
BTN3A1	11119	hgsc.bcm.edu	37	6	26408145	26408145	+	Missense_Mutation	SNP	T	T	A	rs144114619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26408145T>A	ENST00000289361.6	+	4	1048	c.680T>A	c.(679-681)cTc>cAc	p.L227H	BTN3A1_ENST00000414912.2_Missense_Mutation_p.L175H|BTN3A1_ENST00000476549.2_Missense_Mutation_p.L227H|BTN3A1_ENST00000425234.2_Missense_Mutation_p.L227H	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	227	Ig-like V-type 2.				activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						AGTTCCCTCCTCGGCCTGGAA	0.562													T|||	9	0.00179712	0.0	0.0014	5008	,	,		19221	0.0		0.003	False		,,,				2504	0.0051				p.L227H		Atlas-SNP	.											.	BTN3A1	80	.	0			c.T680A						PASS	.	T	HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU	5,4401		0,5,2198	158.0	146.0	150.0		524,680,680,680	0.8	0.0	6	dbSNP_134	150	35,8565		0,35,4265	yes	missense,missense,missense,missense	BTN3A1	NM_001145008.1,NM_001145009.1,NM_007048.5,NM_194441.2	99,99,99,99	0,40,6463	AA,AT,TT		0.407,0.1135,0.3076	probably-damaging,probably-damaging,probably-damaging,probably-damaging	175/462,227/379,227/514,227/353	26408145	40,12966	2203	4300	6503	SO:0001583	missense	11119	exon4			CCCTCCTCGGCCT	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.680T>A	6.37:g.26408145T>A	ENSP00000289361:p.Leu227His	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	191	83	0.434555	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	37	CCDS4608.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	12.24	1.879952	0.33162	0.001135	0.00407	ENSG00000026950	ENST00000476549;ENST00000289361;ENST00000425234;ENST00000414912	T;T;T;T	0.54866	2.24;2.24;2.24;0.55	2.0	0.812	0.18744	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.58977	0.2160	M	0.89030	3	0.09310	N	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;0.999;0.999;1.0	T	0.46762	-0.9168	9	0.87932	D	0	.	3.6881	0.08336	0.0:0.2045:0.0:0.7955	.	175;227;227;227	E9PGB4;O00481-3;O00481-2;O00481	.;.;.;BT3A1_HUMAN	H	227;227;227;175	ENSP00000420010:L227H;ENSP00000289361:L227H;ENSP00000396684:L227H;ENSP00000406667:L175H	ENSP00000289361:L227H	L	+	2	0	BTN3A1	26516124	0.037000	0.19845	0.002000	0.10522	0.061000	0.15899	1.546000	0.36179	0.229000	0.21039	0.418000	0.28097	CTC	T|0.997;A|0.003	0.003	strong		0.562	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
TEK	7010	hgsc.bcm.edu	37	9	27203002	27203002	+	Silent	SNP	G	G	A	rs45563539	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:27203002G>A	ENST00000380036.4	+	13	2536	c.2094G>A	c.(2092-2094)caG>caA	p.Q698Q	TEK_ENST00000406359.4_Silent_p.Q655Q|TEK_ENST00000519097.1_Silent_p.Q551Q	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	698	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)	CTCAGTATCAGCTCAAGGGCC	0.443													G|||	170	0.0339457	0.0038	0.0303	5008	,	,		20576	0.0456		0.0487	False		,,,				2504	0.0501				p.Q698Q		Atlas-SNP	.											.	TEK	250	.	0			c.G2094A						PASS	.	G		48,4358	48.9+/-83.8	0,48,2155	141.0	120.0	127.0		2094	-2.2	1.0	9	dbSNP_127	127	418,8182	130.3+/-188.3	10,398,3892	no	coding-synonymous	TEK	NM_000459.3		10,446,6047	AA,AG,GG		4.8605,1.0894,3.583		698/1125	27203002	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon13			GTATCAGCTCAAG	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.2094G>A	9.37:g.27203002G>A		Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	210	118	0.561905	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			G|0.961;A|0.039	0.039	strong		0.443	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
MFGE8	4240	hgsc.bcm.edu	37	15	89450546	89450546	+	Silent	SNP	C	C	T	rs1878327	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89450546C>T	ENST00000566497.1	-	3	328	c.267G>A	c.(265-267)tcG>tcA	p.S89S	MFGE8_ENST00000559997.1_5'UTR|MFGE8_ENST00000268151.7_Silent_p.S89S|MFGE8_ENST00000539437.1_Silent_p.S81S|MFGE8_ENST00000268150.8_Silent_p.S89S|MFGE8_ENST00000542878.1_Silent_p.S45S			Q08431	MFGM_HUMAN	milk fat globule-EGF factor 8 protein	89	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|phagocytosis, engulfment (GO:0006911)|phagocytosis, recognition (GO:0006910)|positive regulation of apoptotic cell clearance (GO:2000427)|single fertilization (GO:0007338)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|vesicle (GO:0031982)	phosphatidylethanolamine binding (GO:0008429)|phosphatidylserine binding (GO:0001786)	p.S89S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	22	Lung NSC(78;0.0392)|all_lung(78;0.077)					CACGCACAGACGAGGCGGCGA	0.617													T|||	3150	0.628994	0.8011	0.6138	5008	,	,		18641	0.4623		0.6322	False		,,,				2504	0.5757				p.S89S		Atlas-SNP	.											MFGE8,NS,carcinoma,0,1	MFGE8	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G267A						PASS	.	T	,	3450,950	360.4+/-315.2	1349,752,99	131.0	91.0	105.0		267,267	-10.6	0.0	15	dbSNP_92	105	5584,3014	465.8+/-366.6	1796,1992,511	no	coding-synonymous,coding-synonymous	MFGE8	NM_001114614.1,NM_005928.2	,	3145,2744,610	TT,TC,CC		35.0547,21.5909,30.497	,	89/336,89/388	89450546	9034,3964	2200	4299	6499	SO:0001819	synonymous_variant	4240	exon3			CACAGACGAGGCG	U58516	CCDS10347.1, CCDS45345.1	15q25	2009-03-25			ENSG00000140545	ENSG00000140545			7036	protein-coding gene	gene with protein product	"""sperm surface protein hP47"""	602281	"""sperm associated antigen 10"""	SPAG10		9027496, 19204935	Standard	NM_005928		Approved	SED1, EDIL1, BA46, OAcGD3S, HsT19888, MFG-E8, hP47	uc002bng.4	Q08431	OTTHUMG00000148682	ENST00000566497.1:c.267G>A	15.37:g.89450546C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	160	74	0.4625	NM_001114614	B2R6M7|Q53FU9|Q7Z3D2|Q9BTL9	Silent	SNP	ENST00000566497.1	37	CCDS10347.1																																																																																			C|0.333;T|0.667	0.667	strong		0.617	MFGE8-015	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000432804.1	NM_005928	
CCDC86	79080	hgsc.bcm.edu	37	11	60610056	60610056	+	Missense_Mutation	SNP	G	G	C	rs2074421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60610056G>C	ENST00000227520.5	+	1	513	c.459G>C	c.(457-459)caG>caC	p.Q153H	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	153	Pro-rich.		Q -> H (in dbSNP:rs2074421).		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						CCCAGCATCAGCTACCGCCGG	0.647													G|||	403	0.0804712	0.0461	0.196	5008	,	,		13962	0.0496		0.1024	False		,,,				2504	0.0542				p.Q153H		Atlas-SNP	.											.	CCDC86	24	.	0			c.G459C						PASS	.	G	HIS/GLN	244,4148		7,230,1959	24.0	30.0	28.0		459	2.5	0.1	11	dbSNP_96	28	882,7686		54,774,3456	yes	missense	CCDC86	NM_024098.3	24	61,1004,5415	CC,CG,GG		10.2941,5.5556,8.6883	probably-damaging	153/361	60610056	1126,11834	2196	4284	6480	SO:0001583	missense	79080	exon1			GCATCAGCTACCG	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.459G>C	11.37:g.60610056G>C	ENSP00000227520:p.Gln153His	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_024098	B4DY99	Missense_Mutation	SNP	ENST00000227520.5	37	CCDS7993.1	198	0.09065934065934066	24	0.04878048780487805	59	0.16298342541436464	33	0.057692307692307696	82	0.10817941952506596	G	11.56	1.673993	0.29693	0.055556	0.102941	ENSG00000110104	ENST00000227520;ENST00000339492	T	0.47528	0.84	2.46	2.46	0.29980	.	0.303860	0.26635	N	0.023285	T	0.00384	0.0012	L	0.60455	1.87	0.09310	P	0.999999999980983	D	0.69078	0.997	D	0.68353	0.957	T	0.13818	-1.0495	9	0.52906	T	0.07	.	11.0471	0.47865	0.0:0.0:1.0:0.0	rs2074421	153	Q9H6F5	CCD86_HUMAN	H	153;117	ENSP00000227520:Q153H	ENSP00000227520:Q153H	Q	+	3	2	CCDC86	60366632	0.001000	0.12720	0.113000	0.21522	0.081000	0.17604	-0.240000	0.08952	1.686000	0.51046	0.561000	0.74099	CAG	G|0.909;C|0.091	0.091	strong		0.647	CCDC86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395743.1	NM_024098	
FCGBP	8857	hgsc.bcm.edu	37	19	40392347	40392347	+	Missense_Mutation	SNP	C	C	G	rs139175656	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40392347C>G	ENST00000221347.6	-	16	8164	c.8157G>C	c.(8155-8157)caG>caC	p.Q2719H		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2719				Q -> H (in Ref. 1; BAA19526). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)		p.Q2719H(2)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGGCTCCACCTGGCCTCCAG	0.592													G|||	1513	0.302117	0.2708	0.4164	5008	,	,		15565	0.2103		0.3688	False		,,,				2504	0.2894				p.Q2719H		Atlas-SNP	.											FCGBP,NS,carcinoma,0,2	FCGBP	416	2	2	Substitution - Missense(2)	prostate(2)	c.G8157C						scavenged	.						17.0	16.0	17.0					19																	40392347		2135	4094	6229	SO:0001583	missense	8857	exon16			CTCCACCTGGCCT	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8157G>C	19.37:g.40392347C>G	ENSP00000221347:p.Gln2719His	Somatic	557	0	0		WXS	Illumina HiSeq	Phase_I	167	24	0.143713	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	0.582	-0.836839	0.02692	.	.	ENSG00000090920	ENST00000221347	T	0.76709	-1.04	2.02	-2.46	0.06461	Uncharacterised domain, cysteine-rich (2);	1.468830	0.04141	N	0.319631	T	0.53818	0.1820	N	0.04063	-0.285	0.09310	N	1	B	0.14012	0.009	B	0.20577	0.03	T	0.33904	-0.9850	10	0.37606	T	0.19	.	2.9179	0.05759	0.1094:0.305:0.4189:0.1668	.	2719	Q9Y6R7	FCGBP_HUMAN	H	2719	ENSP00000221347:Q2719H	ENSP00000221347:Q2719H	Q	-	3	2	FCGBP	45084187	0.000000	0.05858	0.060000	0.19600	0.366000	0.29705	-3.718000	0.00384	-0.933000	0.03737	-0.702000	0.03669	CAG	C|0.333;G|0.667	0.667	strong		0.592	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
MICA	100507436	hgsc.bcm.edu	37	6	31379794	31379794	+	Silent	SNP	C	C	T	rs1051797|rs386699191	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31379794C>T	ENST00000449934.2	+	4	738	c.684C>T	c.(682-684)tcC>tcT	p.S228S	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GCAGGGCTTCCAGCTTCTATC	0.587													t|||	1823	0.364018	0.4773	0.4063	5008	,	,		19466	0.2996		0.3141	False		,,,				2504	0.2986				p.S228S		Atlas-SNP	.											.	MICA	21	.	0			c.C684T						PASS	.						21.0	25.0	24.0					6																	31379794		692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			GGCTTCCAGCTTC	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.684C>T	6.37:g.31379794C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.698;T|0.302	0.302	strong		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
BAZ1A	11177	hgsc.bcm.edu	37	14	35230980	35230980	+	Missense_Mutation	SNP	C	C	T	rs45620534	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:35230980C>T	ENST00000382422.2	-	23	4553	c.4226G>A	c.(4225-4227)aGa>aAa	p.R1409K	BAZ1A_ENST00000358716.4_Missense_Mutation_p.R1377K|BAZ1A_ENST00000360310.1_Missense_Mutation_p.R1409K			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1409				R -> K (in Ref. 1; AAF70601 and 7; CAB43261). {ECO:0000305}.	chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TTGTCTTTTTCTGCATCTTCT	0.343													C|||	193	0.0385383	0.0023	0.049	5008	,	,		19306	0.0		0.0805	False		,,,				2504	0.0767				p.R1409K		Atlas-SNP	.											.	BAZ1A	128	.	0			c.G4226A						PASS	.	C	LYS/ARG,LYS/ARG	89,4317		2,85,2116	98.0	100.0	99.0		4226,4130	5.1	1.0	14	dbSNP_127	99	795,7805		42,711,3547	yes	missense,missense	BAZ1A	NM_013448.2,NM_182648.1	26,26	44,796,5663	TT,TC,CC		9.2442,2.02,6.7969	benign,benign	1409/1557,1377/1525	35230980	884,12122	2203	4300	6503	SO:0001583	missense	11177	exon24			CTTTTTCTGCATC	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.4226G>A	14.37:g.35230980C>T	ENSP00000371859:p.Arg1409Lys	Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	278	125	0.44964	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	82	0.037545787545787544	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	61	0.08047493403693931	.	13.59	2.282752	0.40394	0.0202	0.092442	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	T;T;T	0.60548	0.18;0.18;0.18	5.95	5.06	0.68205	Bromodomain (2);	0.355312	0.33712	N	0.004626	T	0.01765	0.0056	N	0.16656	0.425	0.35854	D	0.826989	B;B	0.16603	0.018;0.01	B;B	0.16722	0.016;0.007	T	0.09530	-1.0670	10	0.25751	T	0.34	.	11.0778	0.48043	0.0:0.8593:0.0:0.1407	rs45620534;rs61754297	1377;1409	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	K	1377;1409;1409;1061	ENSP00000351555:R1377K;ENSP00000371859:R1409K;ENSP00000353458:R1409K	ENSP00000351555:R1377K	R	-	2	0	BAZ1A	34300731	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.149000	0.50655	1.520000	0.48965	0.563000	0.77884	AGA	C|0.938;T|0.062	0.062	strong		0.343	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
GAD2	2572	hgsc.bcm.edu	37	10	26559571	26559571	+	Silent	SNP	G	G	C	rs1556234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:26559571G>C	ENST00000376261.3	+	10	1481	c.978G>C	c.(976-978)ggG>ggC	p.G326G	GAD2_ENST00000259271.3_Silent_p.G326G	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	326			G -> A (in dbSNP:rs2839678).		glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|cell junction (GO:0030054)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(26)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TCGCACAGGGGTTTGTTCCTT	0.458													G|||	226	0.0451278	0.0083	0.0576	5008	,	,		20591	0.0446		0.1064	False		,,,				2504	0.0235				p.G326G		Atlas-SNP	.											GAD2,NS,malignant_melanoma,+2,2	GAD2	116	2	0			c.G978C						PASS	.	G	,	100,4306	81.4+/-119.9	0,100,2103	163.0	157.0	159.0		978,978	-2.7	1.0	10	dbSNP_88	159	904,7696	200.9+/-244.5	54,796,3450	no	coding-synonymous,coding-synonymous	GAD2	NM_000818.2,NM_001134366.1	,	54,896,5553	CC,CG,GG		10.5116,2.2696,7.7195	,	326/586,326/586	26559571	1004,12002	2203	4300	6503	SO:0001819	synonymous_variant	2572	exon10			ACAGGGGTTTGTT	AJ251501	CCDS7149.1	10p13-p11.2	2003-11-11	2002-08-29		ENSG00000136750	ENSG00000136750	4.1.1.15		4093	protein-coding gene	gene with protein product		138275	"""glutamate decarboxylase 2 (pancreatic islets and brain, 65kD)"""			2039509	Standard	NM_000818		Approved	GAD65	uc001isp.2	Q05329	OTTHUMG00000017836	ENST00000376261.3:c.978G>C	10.37:g.26559571G>C		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_000818	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																			G|0.930;C|0.070	0.070	strong		0.458	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818	
CHRNA7	1139	hgsc.bcm.edu	37	15	32450704	32450704	+	Silent	SNP	G	G	A	rs201822909		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:32450704G>A	ENST00000306901.3	+	7	787	c.690G>A	c.(688-690)acG>acA	p.T230T	CHRNA7_ENST00000454250.3_Silent_p.T259T|CHRNA7_ENST00000455693.2_Silent_p.T49T	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	230					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)	p.T230T(1)|p.T140T(1)		endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	GCCGCAGGACGCTCTACTATG	0.582																																					p.T259T	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											CHRNA7_ENST00000437966,caecum,carcinoma,0,11	CHRNA7	57	11	2	Substitution - coding silent(2)	ovary(2)	c.G777A						scavenged	.						119.0	100.0	107.0					15																	32450704		2200	4297	6497	SO:0001819	synonymous_variant	1139	exon7			CAGGACGCTCTAC	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1960	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 7 (neuronal)"""	118511	"""cholinergic receptor, nicotinic, alpha polypeptide 7"""			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.690G>A	15.37:g.32450704G>A		Somatic	700	1	0.00142857		WXS	Illumina HiSeq	Phase_I	839	295	0.351609	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Silent	SNP	ENST00000306901.3	37	CCDS10027.1																																																																																			G|0.705;A|0.295	0.295	strong		0.582	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2		
CD276	80381	hgsc.bcm.edu	37	15	73995247	73995247	+	Missense_Mutation	SNP	C	C	T	rs142744437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:73995247C>T	ENST00000318443.5	+	4	855	c.553C>T	c.(553-555)Ccc>Tcc	p.P185S	CD276_ENST00000564751.1_Intron|CD276_ENST00000318424.5_Intron|CD276_ENST00000561213.1_Missense_Mutation_p.P185S|CD276_ENST00000537340.2_Missense_Mutation_p.P39S	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	185	Ig-like C2-type 1.				cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GCAGGGTGTGCCCCTGACTGG	0.622													C|||	3	0.000599042	0.0	0.0	5008	,	,		19371	0.0		0.003	False		,,,				2504	0.0				p.P185S		Atlas-SNP	.											.	CD276	29	.	0			c.C553T						PASS	.	C	SER/PRO,	1,4395	2.1+/-5.4	0,1,2197	89.0	76.0	80.0		553,	-0.7	0.0	15	dbSNP_134	80	13,8577	9.1+/-34.3	0,13,4282	no	missense,intron	CD276	NM_001024736.1,NM_025240.2	74,	0,14,6479	TT,TC,CC		0.1513,0.0227,0.1078	possibly-damaging,	185/535,	73995247	14,12972	2198	4295	6493	SO:0001583	missense	80381	exon4			GGTGTGCCCCTGA	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.553C>T	15.37:g.73995247C>T	ENSP00000320084:p.Pro185Ser	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	228	120	0.526316	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	0.107	-1.143273	0.01728	2.27E-4	0.001513	ENSG00000103855	ENST00000318443;ENST00000379823;ENST00000537340	T;T	0.76448	-1.02;-1.02	3.14	-0.671	0.11381	Immunoglobulin subtype 2 (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55561	0.1928	N	0.12502	0.225	0.09310	N	0.999994	B;B;B	0.16396	0.017;0.017;0.013	B;B;B	0.20184	0.028;0.028;0.017	T	0.39482	-0.9612	9	0.21540	T	0.41	.	6.3988	0.21626	0.3327:0.2617:0.4056:0.0	.	131;185;185	B4DK26;Q5ZPR3;Q5ZPR3-4	.;CD276_HUMAN;.	S	185;185;39	ENSP00000320084:P185S;ENSP00000441087:P39S	ENSP00000320084:P185S	P	+	1	0	CD276	71782300	0.021000	0.18746	0.011000	0.14972	0.203000	0.24098	1.959000	0.40412	0.103000	0.17682	0.313000	0.20887	CCC	C|0.999;T|0.001	0.001	strong		0.622	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
PGM5	5239	hgsc.bcm.edu	37	9	70993153	70993153	+	Silent	SNP	G	G	A	rs150515274	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:70993153G>A	ENST00000396396.1	+	2	529	c.300G>A	c.(298-300)tcG>tcA	p.S100S	PGM5_ENST00000604870.2_3'UTR|PGM5_ENST00000396392.1_Silent_p.S100S	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	100					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)			endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						GCATCTTGTCGACACCTGCGG	0.468													N|||	149	0.0297524	0.1097	0.0058	5008	,	,		15888	0.0		0.0	False		,,,				2504	0.0				p.S100S		Atlas-SNP	.											PGM5,colon,carcinoma,0,3	PGM5	80	3	0			c.G300A						scavenged	.	G		425,3977		20,385,1796	33.0	35.0	34.0		300	-6.6	0.8	9	dbSNP_134	34	3,8569		0,3,4283	no	coding-synonymous	PGM5	NM_021965.3		20,388,6079	AA,AG,GG		0.035,9.6547,3.2989		100/568	70993153	428,12546	2201	4286	6487	SO:0001819	synonymous_variant	5239	exon2			CTTGTCGACACCT	L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"""phosphoglucomutase-related protein"""	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.300G>A	9.37:g.70993153G>A		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	218	5	0.0229358	NM_021965	B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Silent	SNP	ENST00000396396.1	37	CCDS6622.2																																																																																			G|0.970;A|0.030	0.030	strong		0.468	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965	
OR13C2	392376	hgsc.bcm.edu	37	9	107367431	107367431	+	Missense_Mutation	SNP	A	A	T	rs1851716	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107367431A>T	ENST00000542196.1	-	1	520	c.478T>A	c.(478-480)Tca>Aca	p.S160T		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	160			S -> T (in dbSNP:rs1851716).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						ACAAACACTGATTGTACTGCA	0.458																																					p.S160T		Atlas-SNP	.											.	OR13C2	46	.	0			c.T478A						PASS	.						108.0	150.0	136.0					9																	107367431		2201	4300	6501	SO:0001583	missense	392376	exon1			ACACTGATTGTAC		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.478T>A	9.37:g.107367431A>T	ENSP00000438815:p.Ser160Thr	Somatic	414	0	0		WXS	Illumina HiSeq	Phase_I	335	108	0.322388	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	710	0.3250915750915751	230	0.46747967479674796	73	0.20165745856353592	303	0.5297202797202797	104	0.13720316622691292	T	0.025	-1.379759	0.01204	.	.	ENSG00000257019	ENST00000542196	T	0.00017	9.09	3.72	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	N	0.001874	T	0.00012	0.0000	N	0.00230	-1.795	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.18999	-1.0319	9	0.02654	T	1	.	7.6109	0.28129	0.1903:0.0:0.0:0.8097	rs1851716;rs59641728	160	Q8NGS9	O13C2_HUMAN	T	160	ENSP00000438815:S160T	ENSP00000438815:S160T	S	-	1	0	OR13C2	106407252	0.000000	0.05858	0.008000	0.14137	0.470000	0.32858	0.065000	0.14466	0.509000	0.28195	-0.527000	0.04329	TCA	A|0.158;T|0.842	0.842	strong		0.458	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
FYCO1	79443	hgsc.bcm.edu	37	3	46009684	46009684	+	Missense_Mutation	SNP	G	G	A	rs3733101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46009684G>A	ENST00000296137.2	-	8	1347	c.1142C>T	c.(1141-1143)aCg>aTg	p.T381M	FYCO1_ENST00000535325.1_Missense_Mutation_p.T381M	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	381			T -> M (in dbSNP:rs3733101).	T -> S (in Ref. 1; CAC33883). {ECO:0000305}.	plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)	p.T381R(1)		NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		GTCTGATGCCGTATCTGCCTT	0.567													G|||	24	0.00479233	0.0	0.0	5008	,	,		19434	0.0099		0.006	False		,,,				2504	0.0082				p.T381M		Atlas-SNP	.											FYCO1,NS,NS,0,1	FYCO1	115	1	1	Substitution - Missense(1)	NS(1)	c.C1142T						PASS	.	G	MET/THR	0,4406		0,0,2203	130.0	133.0	132.0		1142	-4.9	0.0	3	dbSNP_107	132	24,8576	17.9+/-57.8	0,24,4276	yes	missense	FYCO1	NM_024513.2	81	0,24,6479	AA,AG,GG		0.2791,0.0,0.1845	benign	381/1479	46009684	24,12982	2203	4300	6503	SO:0001583	missense	79443	exon8			GATGCCGTATCTG	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.1142C>T	3.37:g.46009684G>A	ENSP00000296137:p.Thr381Met	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	48	0.607595	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	12	0.005494505494505495	0	0.0	0	0.0	9	0.015734265734265736	3	0.00395778364116095	G	9.681	1.149199	0.21288	0.0	0.002791	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21543	2.0;2.0	4.72	-4.89	0.03103	.	1.423960	0.03853	N	0.272715	T	0.03434	0.0099	N	0.02011	-0.69	0.09310	N	1	B;B	0.16166	0.006;0.016	B;B	0.06405	0.001;0.002	T	0.31668	-0.9935	10	0.46703	T	0.11	7.8015	6.7042	0.23242	0.4859:0.0:0.4017:0.1125	rs3733101;rs52831125;rs3733101	381;381	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	M	381	ENSP00000296137:T381M;ENSP00000441178:T381M	ENSP00000296137:T381M	T	-	2	0	FYCO1	45984688	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.371000	0.07513	-1.277000	0.02411	-0.136000	0.14681	ACG	G|0.996;A|0.004	0.004	strong		0.567	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
FCGBP	8857	hgsc.bcm.edu	37	19	40408532	40408532	+	Missense_Mutation	SNP	G	G	A	rs36106401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40408532G>A	ENST00000221347.6	-	8	4314	c.4307C>T	c.(4306-4308)cCg>cTg	p.P1436L		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1436	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		P -> L (in dbSNP:rs36106401).			extracellular vesicular exosome (GO:0070062)		p.P1436L(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)			CTCGCTCCCCGGCGGGCAAGG	0.642													G|||	562	0.11222	0.0363	0.2003	5008	,	,		17719	0.0387		0.1839	False		,,,				2504	0.1544				p.P1436L		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	stomach(1)	c.C4307T						PASS	.	G	LEU/PRO	356,4050	181.9+/-209.8	15,326,1862	53.0	57.0	55.0		4307	4.8	0.0	19	dbSNP_126	55	1750,6850	318.2+/-313.6	182,1386,2732	no	missense	FCGBP	NM_003890.2	98	197,1712,4594	AA,AG,GG		20.3488,8.0799,16.1925	probably-damaging	1436/5406	40408532	2106,10900	2203	4300	6503	SO:0001583	missense	8857	exon8			CTCCCCGGCGGGC	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.4307C>T	19.37:g.40408532G>A	ENSP00000221347:p.Pro1436Leu	Somatic	429	0	0		WXS	Illumina HiSeq	Phase_I	354	162	0.457627	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	237	0.10851648351648352	21	0.042682926829268296	50	0.13812154696132597	19	0.033216783216783216	147	0.19393139841688653	G	13.46	2.242442	0.39598	0.080799	0.203488	ENSG00000090920	ENST00000221347	T	0.19532	2.14	4.8	4.8	0.61643	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.00012	0.0000	L	0.39566	1.225	0.80722	P	0.0	P	0.37864	0.61	B	0.24701	0.055	T	0.30707	-0.9969	8	0.12103	T	0.63	.	11.0692	0.47993	0.0916:0.0:0.9084:0.0	rs36106401	1436	Q9Y6R7	FCGBP_HUMAN	L	1436	ENSP00000221347:P1436L	ENSP00000221347:P1436L	P	-	2	0	FCGBP	45100372	.	.	0.046000	0.18839	0.004000	0.04260	.	.	2.240000	0.73641	0.644000	0.83932	CCG	G|0.853;A|0.147	0.147	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CCL24	6369	hgsc.bcm.edu	37	7	75442730	75442730	+	Missense_Mutation	SNP	T	T	G	rs2302006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:75442730T>G	ENST00000416943.1	-	3	178	c.85A>C	c.(85-87)Atc>Ctc	p.I29L	CCL24_ENST00000222902.2_Missense_Mutation_p.I29L	NM_002991.2	NP_002982.2	O00175	CCL24_HUMAN	chemokine (C-C motif) ligand 24	29			I -> L (in dbSNP:rs2302006). {ECO:0000269|PubMed:14702039}.		cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of inflammatory response (GO:0050729)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3						GGAGAGGGGATGACCACAGAG	0.562													T|||	1733	0.346046	0.2685	0.4063	5008	,	,		17705	0.5595		0.1839	False		,,,				2504	0.3548				p.I29L		Atlas-SNP	.											.	CCL24	11	.	0			c.A85C						PASS	.	T	LEU/ILE	1230,3176		173,884,1146	69.0	72.0	71.0		85	-0.4	0.0	7	dbSNP_100	71	1725,6875		170,1385,2745	yes	missense	CCL24	NM_002991.2	5	343,2269,3891	GG,GT,TT		20.0581,27.9165,22.7203	benign	29/120	75442730	2955,10051	2203	4300	6503	SO:0001583	missense	6369	exon2			AGGGGATGACCAC	U85768	CCDS34670.1	7q11.23	2013-02-25	2002-08-22	2002-08-23	ENSG00000106178	ENSG00000106178		"""Chemokine ligands"", ""Endogenous ligands"""	10623	protein-coding gene	gene with protein product	"""CK-beta-6"", ""myeloid progenitor inhibitory factor 2"", ""eotaxin-2"""	602495	"""small inducible cytokine subfamily A (Cys-Cys), member 24"""	SCYA24		9104803, 9598329	Standard	NM_002991		Approved	Ckb-6, MPIF-2, eotaxin-2, MPIF2	uc011kga.2	O00175	OTTHUMG00000156635	ENST00000416943.1:c.85A>C	7.37:g.75442730T>G	ENSP00000400533:p.Ile29Leu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_002991	B2R5K2	Missense_Mutation	SNP	ENST00000416943.1	37	CCDS34670.1	739	0.3383699633699634	141	0.2865853658536585	125	0.3453038674033149	325	0.5681818181818182	148	0.19525065963060687	.	6.304	0.424243	0.11928	0.279165	0.200581	ENSG00000106178	ENST00000222902;ENST00000416943	T;T	0.03689	3.84;3.84	3.61	-0.408	0.12381	Chemokine interleukin-8-like domain (1);	1.308000	0.05150	N	0.495911	T	0.00012	0.0000	L	0.37800	1.135	0.80722	P	0.0	B	0.11235	0.004	B	0.14023	0.01	T	0.35895	-0.9770	9	0.16420	T	0.52	.	9.5265	0.39167	0.0:0.0:0.5652:0.4348	rs2302006;rs11465292;rs60968338;rs2302006	29	O00175	CCL24_HUMAN	L	29	ENSP00000222902:I29L;ENSP00000400533:I29L	ENSP00000222902:I29L	I	-	1	0	CCL24	75280666	0.696000	0.27757	0.004000	0.12327	0.004000	0.04260	0.260000	0.18424	-0.058000	0.13177	-0.291000	0.09656	ATC	T|0.714;G|0.286	0.286	strong		0.562	CCL24-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344886.1	NM_002991	
KRT35	3886	hgsc.bcm.edu	37	17	39635194	39635194	+	Silent	SNP	G	G	A	rs12936485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39635194G>A	ENST00000393989.1	-	4	807	c.765C>T	c.(763-765)gaC>gaT	p.D255D	KRT35_ENST00000246639.2_Silent_p.D225D	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	255	Linker 12.|Rod.				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)				GTGGGGCAGCGTCCACCTCAA	0.557													G|||	340	0.0678914	0.0537	0.085	5008	,	,		19995	0.001		0.1183	False		,,,				2504	0.092				p.D255D		Atlas-SNP	.											.	KRT35	58	.	0			c.C765T						PASS	.	G		239,4157	132.1+/-168.6	5,229,1964	64.0	68.0	66.0		765	-9.4	0.2	17	dbSNP_121	66	886,7714	193.9+/-239.5	54,778,3468	no	coding-synonymous	KRT35	NM_002280.4		59,1007,5432	AA,AG,GG		10.3023,5.4368,8.6565		255/456	39635194	1125,11871	2198	4300	6498	SO:0001819	synonymous_variant	3886	exon4			GGCAGCGTCCACC	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.765C>T	17.37:g.39635194G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	NM_002280	O76012|Q92651	Silent	SNP	ENST00000393989.1	37	CCDS11394.2																																																																																			G|0.919;A|0.081	0.081	strong		0.557	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
ECE2	9718	hgsc.bcm.edu	37	3	183994447	183994447	+	Intron	SNP	C	C	T	rs13063766	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183994447C>T	ENST00000402825.3	+	3	480				ECE2_ENST00000404464.3_Intron|ECE2_ENST00000357474.5_Missense_Mutation_p.T73I|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000359140.4_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGGAGGGTCACCTGCCCCCAC	0.622													C|||	106	0.0211661	0.0023	0.0346	5008	,	,		16846	0.0		0.0408	False		,,,				2504	0.0389				p.T73I		Atlas-SNP	.											.	ECE2	303	.	0			c.C218T						PASS	.	C	,ILE/THR,,	23,4177		1,21,2078	19.0	21.0	20.0		,218,,	1.4	0.0	3	dbSNP_121	20	238,8178		6,226,3976	yes	intron,missense,intron,intron	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	,89,,	7,247,6054	TT,TC,CC		2.8279,0.5476,2.0688	,,,	,73/812,,	183994447	261,12355	2100	4208	6308	SO:0001627	intron_variant	9718	exon2			GGGTCACCTGCCC	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.481-233C>T	3.37:g.183994447C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_001100120	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	48	0.02197802197802198	1	0.0020325203252032522	15	0.04143646408839779	0	0.0	32	0.04221635883905013	C	16.14	3.039338	0.55003	0.005476	0.028279	ENSG00000145194	ENST00000357474;ENST00000430587	D;T	0.81908	-1.55;-1.26	3.22	1.36	0.22044	.	3.528980	0.02380	U	0.078724	T	0.38026	0.1025	N	0.08118	0	0.19300	N	0.999975	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.50882	-0.8775	10	0.33940	T	0.23	.	8.484	0.33061	0.0:0.7903:0.0:0.2097	rs13063766	73;73	B7Z1P1;O60344-5	.;.	I	73;19	ENSP00000350066:T73I;ENSP00000398444:T19I	ENSP00000350066:T73I	T	+	2	0	ECE2	185477141	0.912000	0.30974	0.046000	0.18839	0.943000	0.58893	0.900000	0.28431	0.344000	0.23847	0.462000	0.41574	ACC	C|0.977;T|0.023	0.023	strong		0.622	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
FKBP15	23307	hgsc.bcm.edu	37	9	115932012	115932012	+	Missense_Mutation	SNP	G	G	T	rs57348436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115932012G>T	ENST00000238256.3	-	26	3094	c.2977C>A	c.(2977-2979)Ccg>Acg	p.P993T		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	993			P -> T (in dbSNP:rs57348436).		endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GGAGGCAACGGGACAGCTTCC	0.592													G|||	307	0.0613019	0.0363	0.0317	5008	,	,		17489	0.0387		0.0467	False		,,,				2504	0.1544				p.P993T		Atlas-SNP	.											.	FKBP15	128	.	0			c.C2977A						PASS	.	G	THR/PRO	190,3968		5,180,1894	44.0	49.0	47.0		2977	2.7	0.0	9	dbSNP_129	47	532,7884		15,502,3691	yes	missense	FKBP15	NM_015258.1	38	20,682,5585	TT,TG,GG		6.3213,4.5695,5.742	possibly-damaging	993/1220	115932012	722,11852	2079	4208	6287	SO:0001583	missense	23307	exon26			GCAACGGGACAGC	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2977C>A	9.37:g.115932012G>T	ENSP00000238256:p.Pro993Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	115	64	0.556522	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	79	0.036172161172161175	22	0.044715447154471545	12	0.03314917127071823	11	0.019230769230769232	34	0.044854881266490766	G	9.749	1.167001	0.21621	0.045695	0.063213	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.29142	1.58;1.6	4.61	2.72	0.32119	.	.	.	.	.	T	0.03095	0.0091	L	0.51422	1.61	0.09310	N	1	B;B	0.29646	0.253;0.02	B;B	0.31337	0.128;0.018	T	0.11743	-1.0575	9	0.56958	D	0.05	0.0131	6.2186	0.20669	0.2382:0.0:0.7618:0.0	rs57348436	574;993	B4DVS2;Q5T1M5	.;FKB15_HUMAN	T	1018;993	ENSP00000416158:P1018T;ENSP00000238256:P993T	ENSP00000238256:P993T	P	-	1	0	FKBP15	114971833	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	-0.337000	0.07852	0.532000	0.28657	0.491000	0.48974	CCG	G|0.954;T|0.046	0.046	strong		0.592	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
NBAS	51594	hgsc.bcm.edu	37	2	15359012	15359012	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:15359012C>T	ENST00000281513.5	-	48	6342	c.6317G>A	c.(6316-6318)cGc>cAc	p.R2106H	NBAS_ENST00000441750.1_Missense_Mutation_p.R1986H	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2106					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CACGTGAATGCGGGGCCGCAC	0.567																																					p.R2106H		Atlas-SNP	.											NBAS,NS,carcinoma,-1,1	NBAS	246	1	0			c.G6317A						scavenged	.						57.0	61.0	60.0					2																	15359012		2203	4300	6503	SO:0001583	missense	51594	exon48			TGAATGCGGGGCC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6317G>A	2.37:g.15359012C>T	ENSP00000281513:p.Arg2106His	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	188	3	0.0159574	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.413540|5.413540	0.96072|0.96072	.|.	.|.	ENSG00000151779|ENSG00000151779	ENST00000442506|ENST00000441750;ENST00000281513	.|T;T	.|0.55052	.|0.54;0.54	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.72285|0.72285	0.3441|0.3441	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.81914	.|0.995;0.912	T|T	0.74266|0.74266	-0.3721|-0.3721	5|10	.|0.87932	.|D	.|0	.|.	18.6777|18.6777	0.91534|0.91534	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1986;2106	.|A2RRP1-2;A2RRP1	.|.;NBAS_HUMAN	T|H	1154|1986;2106	.|ENSP00000413201:R1986H;ENSP00000281513:R2106H	.|ENSP00000281513:R2106H	A|R	-|-	1|2	0|0	NBAS|NBAS	15276463|15276463	1.000000|1.000000	0.71417|0.71417	0.861000|0.861000	0.33841|0.33841	0.987000|0.987000	0.75469|0.75469	6.932000|6.932000	0.75869|0.75869	2.644000|2.644000	0.89710|0.89710	0.591000|0.591000	0.81541|0.81541	GCA|CGC	.	.	none		0.567	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
AOC1	26	hgsc.bcm.edu	37	7	150554553	150554553	+	Missense_Mutation	SNP	C	C	T	rs1049742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150554553C>T	ENST00000493429.1	+	4	1579	c.995C>T	c.(994-996)tCc>tTc	p.S332F	AOC1_ENST00000416793.2_Missense_Mutation_p.S332F|AOC1_ENST00000360937.4_Missense_Mutation_p.S332F|AOC1_ENST00000467291.1_Missense_Mutation_p.S332F			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	332			S -> F (in dbSNP:rs1049742). {ECO:0000269|PubMed:8595053, ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	CGCTCCTCCTCCGGGCTGCAG	0.667													C|||	266	0.053115	0.0877	0.0605	5008	,	,		14622	0.002		0.0785	False		,,,				2504	0.0276				p.S332F		Atlas-SNP	.											.	ABP1	92	.	0			c.C995T						PASS	.	C	PHE/SER	379,4021		22,335,1843	29.0	31.0	30.0		995	5.0	0.1	7	dbSNP_86	30	634,7962		17,600,3681	yes	missense	ABP1	NM_001091.2	155	39,935,5524	TT,TC,CC		7.3755,8.6136,7.7947	probably-damaging	332/752	150554553	1013,11983	2200	4298	6498	SO:0001583	missense	26	exon2			CCTCCTCCGGGCT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.995C>T	7.37:g.150554553C>T	ENSP00000418614:p.Ser332Phe	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	33	0.485294	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	CCDS43679.1	126	0.057692307692307696	43	0.08739837398373984	26	0.0718232044198895	0	0.0	57	0.07519788918205805	C	17.14	3.312468	0.60414	0.086136	0.073755	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000416793;ENST00000437714;ENST00000483043	T;T;T;T;T	0.04194	3.68;3.68;3.68;3.68;3.68	4.96	4.96	0.65561	Copper amine oxidase, C-terminal (3);	0.350050	0.28630	N	0.014677	T	0.00906	0.0030	M	0.87547	2.89	0.18873	N	0.999987	P;D	0.62365	0.914;0.991	P;D	0.71414	0.646;0.973	T	0.00022	-1.2336	10	0.72032	D	0.01	-17.8832	16.083	0.81017	0.0:1.0:0.0:0.0	rs1049742;rs3189948;rs1049742	332;332	C9J690;P19801	.;ABP1_HUMAN	F	332;332;332;332;208;332	ENSP00000418614:S332F;ENSP00000418328:S332F;ENSP00000354193:S332F;ENSP00000411613:S332F;ENSP00000417392:S332F	ENSP00000354193:S332F	S	+	2	0	ABP1	150185486	0.006000	0.16342	0.094000	0.20943	0.974000	0.67602	2.255000	0.43222	2.735000	0.93741	0.561000	0.74099	TCC	C|0.946;T|0.054	0.054	strong		0.667	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
HRCT1	646962	hgsc.bcm.edu	37	9	35906471	35906471	+	Missense_Mutation	SNP	C	C	T	rs76452347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35906471C>T	ENST00000354323.2	+	1	283	c.187C>T	c.(187-189)Cgg>Tgg	p.R63W		NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	63						integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						GCCCTTCCGGCGGCGGGGCCA	0.657													C|||	472	0.0942492	0.0983	0.1268	5008	,	,		11113	0.003		0.2078	False		,,,				2504	0.0429				p.R63W		Atlas-SNP	.											HRCT1,NS,carcinoma,0,2	HRCT1	14	2	0			c.C187T						PASS	.	C	TRP/ARG	500,3906	215.1+/-234.2	40,420,1743	55.0	57.0	57.0		187	1.7	0.1	9	dbSNP_131	57	1798,6800	307.2+/-308.3	187,1424,2688	yes	missense	HRCT1	NM_001039792.1	101	227,1844,4431	TT,TC,CC		20.9118,11.3482,17.6715	probably-damaging	63/116	35906471	2298,10706	2203	4299	6502	SO:0001583	missense	646962	exon1			TTCCGGCGGCGGG		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.187C>T	9.37:g.35906471C>T	ENSP00000346283:p.Arg63Trp	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	71	43	0.605634	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	254	0.1163003663003663	36	0.07317073170731707	54	0.14917127071823205	2	0.0034965034965034965	162	0.21372031662269128	C	13.61	2.289073	0.40494	0.113482	0.209118	ENSG00000196196	ENST00000354323	.	.	.	3.57	1.71	0.24356	.	0.763287	0.10681	N	0.646406	T	0.00039	0.0001	N	0.24115	0.695	0.80722	P	0.0	D	0.63880	0.993	B	0.43783	0.431	T	0.12293	-1.0553	8	0.72032	D	0.01	-9.8139	9.858	0.41096	0.0:0.4869:0.5131:0.0	.	63	Q6UXD1	HRCT1_HUMAN	W	63	.	ENSP00000346283:R63W	R	+	1	2	HRCT1	35896471	0.000000	0.05858	0.083000	0.20561	0.182000	0.23217	0.421000	0.21280	0.494000	0.27859	0.563000	0.77884	CGG	C|0.836;G|0.000;T|0.164	0.164	strong		0.657	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
AKAP12	9590	hgsc.bcm.edu	37	6	151674326	151674326	+	Missense_Mutation	SNP	A	A	C	rs3823310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151674326A>C	ENST00000253332.1	+	3	4989	c.4800A>C	c.(4798-4800)gaA>gaC	p.E1600D	AKAP12_ENST00000402676.2_Missense_Mutation_p.E1600D|AKAP12_ENST00000354675.6_Missense_Mutation_p.E1502D|AKAP12_ENST00000359755.5_Missense_Mutation_p.E1495D			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1600			E -> D (in dbSNP:rs3823310). {ECO:0000269|Ref.3}.		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)		AAGGAGAGGAACCTCAGGCCT	0.493													A|||	2198	0.438898	0.2201	0.5476	5008	,	,		22187	0.4355		0.668	False		,,,				2504	0.4254				p.E1600D	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.A4800C						PASS	.	A	ASP/GLU,ASP/GLU	1432,2974	462.3+/-353.2	231,970,1002	72.0	72.0	72.0		4800,4506	-4.3	0.0	6	dbSNP_107	72	5754,2846	672.9+/-403.0	1934,1886,480	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	45,45	2165,2856,1482	CC,CA,AA		33.093,32.5011,44.7486	benign,benign	1600/1783,1502/1685	151674326	7186,5820	2203	4300	6503	SO:0001583	missense	9590	exon4			AGAGGAACCTCAG	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.4800A>C	6.37:g.151674326A>C	ENSP00000253332:p.Glu1600Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	46	35	0.76087	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	1131	0.5178571428571429	142	0.2886178861788618	209	0.5773480662983426	272	0.4755244755244755	508	0.6701846965699209	A	7.096	0.573064	0.13623	0.325011	0.66907	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07567	3.18;3.18;3.19;3.19	4.44	-4.35	0.03656	.	0.212560	0.23738	N	0.045043	T	0.00724	0.0024	N	0.04880	-0.145	0.80722	P	0.0	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.11329	0.006;0.006;0.003	T	0.43343	-0.9397	9	0.21540	T	0.41	.	2.0017	0.03468	0.2881:0.2693:0.3241:0.1185	rs3823310;rs17229363;rs52808840;rs60827874;rs3823310	1495;1502;1600	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	D	1600;1600;1502;1495	ENSP00000384537:E1600D;ENSP00000253332:E1600D;ENSP00000346702:E1502D;ENSP00000352794:E1495D	ENSP00000253332:E1600D	E	+	3	2	AKAP12	151716019	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.729000	0.04920	-0.789000	0.04498	0.528000	0.53228	GAA	A|0.477;C|0.523	0.523	strong		0.493	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
TYRO3	7301	hgsc.bcm.edu	37	15	41862801	41862801	+	Splice_Site	SNP	G	G	T	rs200684350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:41862801G>T	ENST00000263798.3	+	12	1707		c.e12-1		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		TTTCCCCACAGTGGACAGCTT	0.527																																					.		Atlas-SNP	.											TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	0			c.1484-1G>T						scavenged	.						75.0	75.0	75.0					15																	41862801		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon12			CCCACAGTGGACA	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1484-1G>T	15.37:g.41862801G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	8	0.0930233	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916766	0.73098	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	4.99	4.99	0.66335	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4637	0.90748	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39650093	1.000000	0.71417	1.000000	0.80357	0.875000	0.50365	9.263000	0.95617	2.579000	0.87056	0.563000	0.77884	.	G|0.985;T|0.015	0.015	strong		0.527	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron
RHPN2	85415	hgsc.bcm.edu	37	19	33517515	33517515	+	Missense_Mutation	SNP	C	C	T	rs28626308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33517515C>T	ENST00000254260.3	-	3	244	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	RHPN2_ENST00000400226.4_5'UTR	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	70			R -> Q (in dbSNP:rs28626308). {ECO:0000269|PubMed:12221077}.		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)					CACTTGCTCCCGCACCTTTGA	0.562													C|||	582	0.116214	0.0575	0.0735	5008	,	,		19310	0.1508		0.0596	False		,,,				2504	0.2485				p.R70Q		Atlas-SNP	.											RHPN2,NS,carcinoma,-1,1	RHPN2	107	1	0			c.G209A						PASS	.	C	GLN/ARG	287,4119	154.8+/-188.1	14,259,1930	79.0	79.0	79.0		209	2.8	0.9	19	dbSNP_125	79	467,8133	134.7+/-192.1	13,441,3846	no	missense	RHPN2	NM_033103.4	43	27,700,5776	TT,TC,CC		5.4302,6.5138,5.7973	possibly-damaging	70/687	33517515	754,12252	2203	4300	6503	SO:0001583	missense	85415	exon3			TGCTCCCGCACCT	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.209G>A	19.37:g.33517515C>T	ENSP00000254260:p.Arg70Gln	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	29	11	0.37931	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	184	0.08424908424908426	27	0.054878048780487805	30	0.08287292817679558	79	0.1381118881118881	48	0.0633245382585752	C	13.87	2.366555	0.41902	0.065138	0.054302	ENSG00000131941	ENST00000254260	T	0.19669	2.13	3.88	2.82	0.32997	.	0.138754	0.47093	D	0.000251	T	0.00241	0.0007	M	0.69358	2.11	0.09310	P	0.999999999884797	D	0.59767	0.986	P	0.49853	0.624	T	0.09796	-1.0658	9	0.59425	D	0.04	2.4614	11.6871	0.51492	0.0:0.9106:0.0:0.0894	rs28626308	70	Q8IUC4	RHPN2_HUMAN	Q	70	ENSP00000254260:R70Q	ENSP00000254260:R70Q	R	-	2	0	RHPN2	38209355	0.984000	0.35163	0.928000	0.36995	0.038000	0.13279	2.820000	0.48057	0.953000	0.37825	0.557000	0.71058	CGG	C|0.935;T|0.065	0.065	strong		0.562	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
TMEM8A	58986	hgsc.bcm.edu	37	16	427820	427820	+	Silent	SNP	C	C	T	rs12922073	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:427820C>T	ENST00000431232.2	-	2	310	c.150G>A	c.(148-150)tcG>tcA	p.S50S	TMEM8A_ENST00000250930.3_Intron|TMEM8A_ENST00000476735.1_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	50					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						GCGGGGCCTGCGAGAAGTGCT	0.672													C|||	2580	0.515176	0.5582	0.4683	5008	,	,		14226	0.2996		0.5368	False		,,,				2504	0.6902				p.S50S		Atlas-SNP	.											.	TMEM8A	49	.	0			c.G150A						PASS	.	C		2520,1808		745,1030,389	33.0	39.0	37.0		150	-8.8	0.7	16	dbSNP_121	37	4850,3678		1444,1962,858	no	coding-synonymous	TMEM8A	NM_021259.2		2189,2992,1247	TT,TC,CC		43.1285,41.7745,42.6727		50/772	427820	7370,5486	2164	4264	6428	SO:0001819	synonymous_variant	58986	exon2			GGCCTGCGAGAAG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.150G>A	16.37:g.427820C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			A|0.000;C|0.470;G|0.000;T|0.530	0.530	strong		0.672	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
SEZ6L	23544	hgsc.bcm.edu	37	22	26692953	26692953	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26692953G>A	ENST00000248933.6	+	4	1164	c.1069G>A	c.(1069-1071)Ggg>Agg	p.G357R	SEZ6L_ENST00000360929.3_Missense_Mutation_p.G357R|SEZ6L_ENST00000402979.1_Missense_Mutation_p.G130R|SEZ6L_ENST00000403121.1_Missense_Mutation_p.G130R|SEZ6L_ENST00000404234.3_Missense_Mutation_p.G357R|SEZ6L_ENST00000343706.4_Missense_Mutation_p.G357R|SEZ6L_ENST00000529632.2_Missense_Mutation_p.G357R			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	357	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						CCTGGTGGAGGGGCAGGTAAT	0.622																																					p.G357R		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G1069A						PASS	.						60.0	47.0	52.0					22																	26692953		2203	4300	6503	SO:0001583	missense	23544	exon4			GTGGAGGGGCAGG	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.1069G>A	22.37:g.26692953G>A	ENSP00000248933:p.Gly357Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	4	0.04	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087781	0.94100	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24;0.24	5.26	5.26	0.73747	CUB (5);	0.000000	0.56097	D	0.000037	T	0.78162	0.4240	M	0.79926	2.475	0.80722	D	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	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	T	0.81420	-0.0941	10	0.87932	D	0	.	17.8539	0.88756	0.0:0.0:1.0:0.0	.	357;357;130;357;357;357;357	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	R	357;357;357;357;357;130;130	ENSP00000384772:G357R;ENSP00000437037:G357R;ENSP00000354185:G357R;ENSP00000248933:G357R;ENSP00000342661:G357R;ENSP00000384838:G130R;ENSP00000384733:G130R	ENSP00000248933:G357R	G	+	1	0	SEZ6L	25022953	1.000000	0.71417	0.997000	0.53966	0.870000	0.49936	9.244000	0.95423	2.446000	0.82766	0.655000	0.94253	GGG	.	.	none		0.622	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
DOPEY2	9980	hgsc.bcm.edu	37	21	37661405	37661405	+	Missense_Mutation	SNP	G	G	A	rs3827183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:37661405G>A	ENST00000399151.3	+	35	6501	c.6416G>A	c.(6415-6417)gGg>gAg	p.G2139E		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	2139			G -> E (in dbSNP:rs3827183). {ECO:0000269|PubMed:10231032}.		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.G2139E(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						CCCTCAGTGGGGGAGATACCC	0.398													G|||	724	0.144569	0.115	0.111	5008	,	,		18023	0.126		0.1223	False		,,,				2504	0.2505				p.G2139E		Atlas-SNP	.											DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	1	Substitution - Missense(1)	stomach(1)	c.G6416A						PASS	.	G	GLU/GLY	525,3881	239.9+/-250.9	30,465,1708	110.0	106.0	108.0		6416	2.9	0.2	21	dbSNP_107	108	1026,7574	219.0+/-257.2	70,886,3344	yes	missense	DOPEY2	NM_005128.2	98	100,1351,5052	AA,AG,GG		11.9302,11.9156,11.9253	benign	2139/2299	37661405	1551,11455	2203	4300	6503	SO:0001583	missense	9980	exon35			CAGTGGGGGAGAT	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.6416G>A	21.37:g.37661405G>A	ENSP00000382104:p.Gly2139Glu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	265	0.12133699633699634	57	0.11585365853658537	41	0.1132596685082873	71	0.12412587412587413	96	0.1266490765171504	G	15.39	2.819449	0.50633	0.119156	0.119302	ENSG00000142197	ENST00000399151	T	0.41758	0.99	4.81	2.87	0.33458	.	0.436973	0.24249	N	0.040199	T	0.00356	0.0011	L	0.56769	1.78	0.32167	P	0.582177	B;B	0.28552	0.191;0.215	B;B	0.29942	0.109;0.051	T	0.09143	-1.0688	9	0.11485	T	0.65	.	9.9191	0.41453	0.0825:0.1407:0.7768:0.0	rs3827183;rs58599312;rs3827183	2132;2139	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	E	2139	ENSP00000382104:G2139E	ENSP00000382104:G2139E	G	+	2	0	DOPEY2	36583275	0.515000	0.26210	0.199000	0.23439	0.733000	0.41908	2.524000	0.45589	1.387000	0.46486	0.563000	0.77884	GGG	G|0.873;A|0.127	0.127	strong		0.398	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
DDX58	23586	hgsc.bcm.edu	37	9	32526146	32526146	+	Missense_Mutation	SNP	G	G	A	rs10813831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:32526146G>A	ENST00000379883.2	-	1	176	c.19C>T	c.(19-21)Cgc>Tgc	p.R7C	DDX58_ENST00000545044.1_De_novo_Start_InFrame|DDX58_ENST00000379868.1_De_novo_Start_InFrame|DDX58_ENST00000379882.1_Missense_Mutation_p.R7C	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	7	CARD 1.		R -> C (in dbSNP:rs10813831). {ECO:0000269|PubMed:17974005}.		cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TGCAGGCTGCGTCGCTGCTCG	0.607													G|||	922	0.184105	0.2073	0.1628	5008	,	,		14229	0.1052		0.2773	False		,,,				2504	0.1534				p.R7C		Atlas-SNP	.											.	DDX58	82	.	0			c.C19T						PASS	.	G	CYS/ARG	1018,3388	377.1+/-322.3	122,774,1307	64.0	56.0	59.0		19	-2.1	0.0	9	dbSNP_120	59	2213,6387	375.4+/-337.8	288,1637,2375	yes	missense	DDX58	NM_014314.3	180	410,2411,3682	AA,AG,GG		25.7326,23.1049,24.8424	probably-damaging	7/926	32526146	3231,9775	2203	4300	6503	SO:0001583	missense	23586	exon1			GGCTGCGTCGCTG	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.19C>T	9.37:g.32526146G>A	ENSP00000369213:p.Arg7Cys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	416	0.19047619047619047	99	0.20121951219512196	70	0.19337016574585636	41	0.07167832167832168	206	0.2717678100263852	G	15.14	2.743956	0.49151	0.231049	0.257326	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542960	T;T	0.06371	3.4;3.31	4.02	-2.08	0.07254	.	1.305430	0.05512	N	0.560359	T	0.00012	0.0000	L	0.56769	1.78	0.49915	P	1.6099999999996673E-4	D;D	0.71674	0.997;0.998	P;P	0.53861	0.736;0.65	T	0.35773	-0.9775	9	0.87932	D	0	0.1979	8.0968	0.30833	0.0:0.2914:0.1955:0.513	rs10813831;rs17553642;rs52815553;rs59478737;rs10813831	7;7	O95786-2;O95786	.;DDX58_HUMAN	C	7	ENSP00000369212:R7C;ENSP00000369213:R7C	ENSP00000369212:R7C	R	-	1	0	DDX58	32516146	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.144000	0.10280	-0.381000	0.07882	-0.261000	0.10672	CGC	G|0.788;A|0.212	0.212	strong		0.607	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
CPN2	1370	hgsc.bcm.edu	37	3	194061907	194061907	+	Nonsense_Mutation	SNP	G	G	A	rs4974539|rs386669887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194061907G>A	ENST00000323830.3	-	2	1614	c.1525C>T	c.(1525-1527)Cag>Tag	p.Q509*	CPN2_ENST00000429275.1_Nonsense_Mutation_p.Q509*	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	509			Q -> R (in dbSNP:rs4974538). {ECO:0000269|PubMed:2378615}.	Q -> W (in Ref. 4; AAH31569/AAH42334/ AAI37399/AAI37404). {ECO:0000305}.	protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		GAGCCCTGCTGAGGAGAGAGC	0.657													G|||	1403	0.280152	0.23	0.2378	5008	,	,		19027	0.38		0.3509	False		,,,				2504	0.2025				p.Q509X		Atlas-SNP	.											.	CPN2	56	.	0			c.C1525T						PASS	.	G	stop/GLN	1186,3220	402.6+/-332.4	157,872,1174	36.0	36.0	36.0		1525	-4.4	0.0	3	dbSNP_111	36	3295,5305	477.4+/-369.6	637,2021,1642	no	stop-gained	CPN2	NM_001080513.2		794,2893,2816	AA,AG,GG		38.314,26.9178,34.4533		509/546	194061907	4481,8525	2203	4300	6503	SO:0001587	stop_gained	1370	exon2			CCTGCTGAGGAGA	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.1525C>T	3.37:g.194061907G>A	ENSP00000319464:p.Gln509*	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Nonsense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	568	0.2600732600732601	109	0.22154471544715448	76	0.20994475138121546	158	0.2762237762237762	225	0.29683377308707126	G	12.47	1.946724	0.34377	0.269178	0.38314	ENSG00000178772	ENST00000323830;ENST00000429275	.	.	.	5.41	-4.38	0.03622	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999422471	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	13.6727	0.62436	0.0:0.0809:0.2212:0.6979	rs4974539;rs17453997;rs4974539	.	.	.	X	509	.	ENSP00000319464:Q509X	Q	-	1	0	CPN2	195543602	0.011000	0.17503	0.000000	0.03702	0.010000	0.07245	0.263000	0.18478	-0.644000	0.05465	-1.014000	0.02459	CAG	G|0.680;A|0.320	0.320	strong		0.657	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
PXDNL	137902	hgsc.bcm.edu	37	8	52321686	52321686	+	Missense_Mutation	SNP	C	C	T	rs11985241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:52321686C>T	ENST00000356297.4	-	17	2598	c.2498G>A	c.(2497-2499)aGc>aAc	p.S833N	PXDNL_ENST00000543296.1_Missense_Mutation_p.S833N	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	833				S -> N (in Ref. 4; BAD18663). {ECO:0000305}.	hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCAGACGGAGCTGCACGGCCG	0.672													C|||	771	0.153954	0.1725	0.0778	5008	,	,		10650	0.2768		0.0905	False		,,,				2504	0.1217				p.S833N		Atlas-SNP	.											.	PXDNL	414	.	0			c.G2498A						PASS	.	C	ASN/SER	682,3532		50,582,1475	17.0	21.0	20.0		2498	2.6	0.0	8	dbSNP_120	20	725,7687		33,659,3514	yes	missense	PXDNL	NM_144651.4	46	83,1241,4989	TT,TC,CC		8.6186,16.1841,11.1437	benign	833/1464	52321686	1407,11219	2107	4206	6313	SO:0001583	missense	137902	exon17			ACGGAGCTGCACG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2498G>A	8.37:g.52321686C>T	ENSP00000348645:p.Ser833Asn	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	334	0.15293040293040294	85	0.17276422764227642	30	0.08287292817679558	152	0.26573426573426573	67	0.08839050131926121	C	4.452	0.083708	0.08533	0.161841	0.086186	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.73047	-0.71;-0.71	3.56	2.63	0.31362	.	0.000000	0.64402	D	0.000019	T	0.00012	0.0000	L	0.33753	1.03	0.39622	P	0.029958999999999958	B	0.25105	0.118	B	0.23716	0.048	T	0.06935	-1.0799	9	0.40728	T	0.16	.	9.8527	0.41066	0.2068:0.7932:0.0:0.0	rs11985241	833	A1KZ92	PXDNL_HUMAN	N	833	ENSP00000348645:S833N;ENSP00000444865:S833N	ENSP00000348645:S833N	S	-	2	0	PXDNL	52484239	1.000000	0.71417	0.017000	0.16124	0.034000	0.12701	5.229000	0.65316	0.553000	0.29044	0.650000	0.86243	AGC	C|0.853;T|0.147	0.147	strong		0.672	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
GOLGA4	2803	hgsc.bcm.edu	37	3	37368755	37368755	+	Missense_Mutation	SNP	T	T	A	rs62241896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:37368755T>A	ENST00000361924.2	+	14	5752	c.5378T>A	c.(5377-5379)aTg>aAg	p.M1793K	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.M1815K	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1793	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GATCAAAGTATGATAGGTCAT	0.378													T|||	984	0.196486	0.1407	0.3012	5008	,	,		20174	0.0764		0.3579	False		,,,				2504	0.1554				p.M1815K		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T5444A						PASS	.	T	LYS/MET,LYS/MET	839,3565	295.9+/-283.9	91,657,1454	87.0	89.0	88.0		5444,5378	-1.3	0.0	3	dbSNP_129	88	3377,5221	490.8+/-372.9	660,2057,1582	yes	missense,missense	GOLGA4	NM_001172713.1,NM_002078.4	95,95	751,2714,3036	AA,AT,TT		39.2766,19.0509,32.4258	benign,benign	1815/2244,1793/2231	37368755	4216,8786	2202	4299	6501	SO:0001583	missense	2803	exon15			AAAGTATGATAGG	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5378T>A	3.37:g.37368755T>A	ENSP00000354486:p.Met1793Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	520	0.23809523809523808	66	0.13414634146341464	128	0.35359116022099446	49	0.08566433566433566	277	0.3654353562005277	T	3.075	-0.190340	0.06299	0.190509	0.392766	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.21734	1.99;1.99;1.99	4.07	-1.3	0.09259	.	0.921625	0.08919	N	0.874722	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B;B;B	0.15473	0.009;0.009;0.009;0.013	B;B;B;B	0.11329	0.006;0.006;0.006;0.004	T	0.46317	-0.9200	9	0.05959	T	0.93	.	3.3512	0.07153	0.1339:0.0803:0.4148:0.371	rs62241896	1793;1793;1815;1793	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	K	1793;1815;1664	ENSP00000354486:M1793K;ENSP00000349305:M1815K;ENSP00000405842:M1664K	ENSP00000349305:M1815K	M	+	2	0	GOLGA4	37343759	0.001000	0.12720	0.000000	0.03702	0.165000	0.22458	-0.108000	0.10857	-0.306000	0.08818	0.448000	0.29417	ATG	T|0.705;A|0.295	0.295	strong		0.378	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
TCP10L	140290	hgsc.bcm.edu	37	21	33951068	33951068	+	Missense_Mutation	SNP	T	T	C	rs9622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33951068T>C	ENST00000300258.3	-	4	547	c.434A>G	c.(433-435)cAc>cGc	p.H145R	TCP10L_ENST00000472557.1_Missense_Mutation_p.H59R|LINC00846_ENST00000334165.4_lincRNA	NM_144659.5	NP_653260.1	Q8TDR4	TCP1L_HUMAN	t-complex 10-like	145			H -> R (in dbSNP:rs9622). {ECO:0000269|PubMed:10830953, ECO:0000269|Ref.3}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	protein self-association (GO:0043621)|repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)			breast(1)|central_nervous_system(1)|liver(1)|skin(1)	4						CTGATTCTTGTGGCCAGCGTA	0.433													C|||	1093	0.218251	0.2012	0.2133	5008	,	,		18820	0.2599		0.1928	False		,,,				2504	0.228				p.H145R		Atlas-SNP	.											.	TCP10L	24	.	0			c.A434G						PASS	.	C	ARG/HIS	886,3520	741.7+/-411.3	79,728,1396	179.0	154.0	163.0		434	0.5	0.0	21	dbSNP_52	163	1564,7036	745.3+/-407.3	142,1280,2878	yes	missense	TCP10L	NM_144659.5	29	221,2008,4274	CC,CT,TT		18.186,20.1089,18.8375		145/216	33951068	2450,10556	2203	4300	6503	SO:0001583	missense	140290	exon4			TTCTTGTGGCCAG	AF115967	CCDS13616.1	21p22.11	2012-09-20	2012-09-20		ENSG00000242220	ENSG00000242220			11657	protein-coding gene	gene with protein product		608365	"""t-complex 10 (a murine tcp homolog)-like"", ""t-complex 10 (mouse)-like"""			10830953	Standard	NM_144659		Approved	PRED77		Q8TDR4	OTTHUMG00000064901	ENST00000300258.3:c.434A>G	21.37:g.33951068T>C	ENSP00000300258:p.His145Arg	Somatic	266	1	0.0037594		WXS	Illumina HiSeq	Phase_I	326	139	0.42638	NM_144659	Q53EW0|Q96LN5	Missense_Mutation	SNP	ENST00000300258.3	37	CCDS13616.1	484	0.2216117216117216	97	0.19715447154471544	76	0.20994475138121546	159	0.27797202797202797	152	0.20052770448548812	C	1.066	-0.671530	0.03403	0.201089	0.18186	ENSG00000242220	ENST00000300258	T	0.22743	1.94	0.459	0.459	0.16678	.	.	.	.	.	T	0.00012	0.0000	N	0.01188	-0.97	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	7	0.02654	T	1	.	.	.	.	rs9622;rs2246107;rs6517105;rs17353914;rs9622	145	Q8TDR4	TCP1L_HUMAN	R	145	ENSP00000300258:H145R	ENSP00000300258:H145R	H	-	2	0	TCP10L	32872939	0.037000	0.19845	0.010000	0.14722	0.046000	0.14306	-0.931000	0.03967	-0.405000	0.07599	-1.063000	0.02288	CAC	T|0.791;C|0.209	0.209	strong		0.433	TCP10L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139350.1	NM_144659	
ACPP	55	hgsc.bcm.edu	37	3	132068831	132068831	+	Silent	SNP	C	C	T	rs2228402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132068831C>T	ENST00000336375.5	+	8	939	c.849C>T	c.(847-849)ctC>ctT	p.L283L	ACPP_ENST00000475741.1_Silent_p.L250L|ACPP_ENST00000351273.7_Silent_p.L283L	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	283					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						ACAAAAAACTCATCATGTATT	0.353													T|||	1981	0.395567	0.3585	0.4841	5008	,	,		21077	0.1171		0.5378	False		,,,				2504	0.5235				p.L283L		Atlas-SNP	.											.	ACPP	118	.	0			c.C849T						PASS	.	T	,	1706,2700	651.9+/-399.3	337,1032,834	138.0	123.0	128.0		849,849	-7.9	0.0	3	dbSNP_98	128	4801,3799	537.8+/-383.3	1332,2137,831	no	coding-synonymous,coding-synonymous	ACPP	NM_001099.4,NM_001134194.1	,	1669,3169,1665	TT,TC,CC		44.1744,38.7199,49.9692	,	283/387,283/419	132068831	6507,6499	2203	4300	6503	SO:0001819	synonymous_variant	55	exon8			AAAACTCATCATG		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.849C>T	3.37:g.132068831C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	37	CCDS3073.1																																																																																			C|0.529;T|0.471	0.471	strong		0.353	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	
ZGLP1	100125288	hgsc.bcm.edu	37	19	10419130	10419130	+	Silent	SNP	C	C	T	rs281417	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10419130C>T	ENST00000403903.3	-	1	1426	c.228G>A	c.(226-228)ccG>ccA	p.P76P	ZGLP1_ENST00000403352.1_5'UTR|FDX1L_ENST00000492239.1_5'Flank|FDX1L_ENST00000541276.1_Intron|CTD-2369P2.10_ENST00000452032.2_Intron	NM_001103167.1	NP_001096637.1	P0C6A0	ZGLP1_HUMAN	zinc finger, GATA-like protein 1	76					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oocyte development (GO:0048599)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.P76P(2)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(2)|ovary(1)	6						GCCCCAGGACCGGGGTGTCCT	0.657													C|||	1274	0.254393	0.3328	0.2061	5008	,	,		14662	0.1121		0.2922	False		,,,				2504	0.2904				p.P76P		Atlas-SNP	.											ZGLP1_ENST00000403903,NS,lymphoid_neoplasm,0,2	ZGLP1	18	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.G228A						PASS	.	C		1084,2734		132,820,957	21.0	24.0	23.0		228	-2.4	0.0	19	dbSNP_79	23	2622,5616		417,1788,1914	no	coding-synonymous	ZGLP1	NM_001103167.1		549,2608,2871	TT,TC,CC		31.8281,28.3918,30.7399		76/272	10419130	3706,8350	1909	4119	6028	SO:0001819	synonymous_variant	100125288	exon1			CAGGACCGGGGTG	AK096830	CCDS45959.1	19p13.2	2013-01-25			ENSG00000220201	ENSG00000220201		"""GATA zinc finger domain containing"""	37245	protein-coding gene	gene with protein product	"""GATA like protein 1"", ""GATA zinc finger domain containing 3"""	611639				16982049	Standard	NM_001103167		Approved	GLP1, GLP-1, GATAD3	uc002mnw.4	P0C6A0	OTTHUMG00000152114	ENST00000403903.3:c.228G>A	19.37:g.10419130C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001103167		Silent	SNP	ENST00000403903.3	37	CCDS45959.1																																																																																			C|0.758;T|0.242	0.242	strong		0.657	ZGLP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325278.1	NM_001103167	
SPINT3	10816	hgsc.bcm.edu	37	20	44141331	44141331	+	Missense_Mutation	SNP	A	A	G	rs6032259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:44141331A>G	ENST00000217428.6	-	2	245	c.230T>C	c.(229-231)tTg>tCg	p.L77S		NM_006652.1	NP_006643.1	P49223	SPIT3_HUMAN	serine peptidase inhibitor, Kunitz type, 3	77	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.		L -> S (in dbSNP:rs6032259).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)	1						TTCTTTCCTCAAAAAGTTGTT	0.443													G|||	2303	0.459864	0.5545	0.4481	5008	,	,		21673	0.3264		0.5109	False		,,,				2504	0.4254				p.L77S		Atlas-SNP	.											.	SPINT3	12	.	0			c.T230C						PASS	.						105.0	91.0	95.0					20																	44141331		692	1591	2283	SO:0001583	missense	10816	exon2			TTCCTCAAAAAGT	X77166	CCDS46608.1	20q12-q13.2	2012-08-20	2005-08-17		ENSG00000101446	ENSG00000101446			11248	protein-coding gene	gene with protein product		613941	"""serine protease inhibitor, Kunitz type, 3"""			21988899	Standard	NM_006652		Approved	HKIB9	uc010ghg.1	P49223	OTTHUMG00000032585	ENST00000217428.6:c.230T>C	20.37:g.44141331A>G	ENSP00000217428:p.Leu77Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	39	0.364486	NM_006652	A6NCQ6|Q6UDR8|Q96KK2	Missense_Mutation	SNP	ENST00000217428.6	37	CCDS46608.1	967	0.44276556776556775	249	0.5060975609756098	168	0.46408839779005523	165	0.28846153846153844	385	0.5079155672823219	G	0.018	-1.474504	0.01044	.	.	ENSG00000101446	ENST00000217428	T	0.56444	0.46	3.25	-6.5	0.01884	Proteinase inhibitor I2, Kunitz metazoa (6);Proteinase inhibitor I2, Kunitz, conserved site (1);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.15141	0.012	B	0.18263	0.021	T	0.29243	-1.0018	7	0.21014	T	0.42	.	1.4375	0.02346	0.2518:0.0918:0.2376:0.4187	rs6032259;rs7274991;rs52805157;rs59517836;rs6032259	77	P49223	SPIT3_HUMAN	S	77	ENSP00000217428:L77S	ENSP00000217428:L77S	L	-	2	0	SPINT3	43574745	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.126000	0.03254	-3.407000	0.00169	-1.690000	0.00728	TTG	A|0.558;G|0.442	0.442	strong		0.443	SPINT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079464.5	NM_006652	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276909	71276909	+	Silent	SNP	G	G	A	rs71272260|rs12289712	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71276909G>A	ENST00000398531.1	+	1	301	c.276G>A	c.(274-276)ggG>ggA	p.G92G	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	92	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GCTCCAAGGGGGGCTGTGGCT	0.677																																					p.G92G		Atlas-SNP	.											KRTAP5-10,rectum,carcinoma,0,3	KRTAP5-10	37	3	0			c.G276A						scavenged	.						35.0	54.0	47.0					11																	71276909		2068	4190	6258	SO:0001819	synonymous_variant	387273	exon1			CAAGGGGGGCTGT	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.276G>A	11.37:g.71276909G>A		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	95	14	0.147368	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			A|0.153;G|0.847	0.153	strong		0.677	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
PROSER3	148137	hgsc.bcm.edu	37	19	36255965	36255965	+	Silent	SNP	C	C	G	rs7252936	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36255965C>G	ENST00000544099.1	+	7	720	c.657C>G	c.(655-657)ctC>ctG	p.L219L	C19orf55_ENST00000396908.4_Silent_p.L219L			Q2NL68	PRSR3_HUMAN		219	Ser-rich.									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)			CCTCCTCCCTCAGCCCCAGCG	0.622													C|||	449	0.0896565	0.0666	0.1326	5008	,	,		20110	0.1429		0.0825	False		,,,				2504	0.0429				p.L219L		Atlas-SNP	.											.	C19orf55	39	.	0			c.C657G						PASS	.	C		249,4093		6,237,1928	136.0	149.0	145.0		657	3.3	1.0	19	dbSNP_116	145	739,7785		34,671,3557	no	coding-synonymous	C19orf55	NM_001039887.2		40,908,5485	GG,GC,CC		8.6696,5.7347,7.6792		219/481	36255965	988,11878	2171	4262	6433	SO:0001819	synonymous_variant	148137	exon7			CTCCCTCAGCCCC																												ENST00000544099.1:c.657C>G	19.37:g.36255965C>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Silent	SNP	ENST00000544099.1	37																																																																																				C|0.915;G|0.085	0.085	strong		0.622	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		
ZZZ3	26009	hgsc.bcm.edu	37	1	78098403	78098403	+	Missense_Mutation	SNP	T	T	C	rs34535037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:78098403T>C	ENST00000370801.3	-	5	1112	c.637A>G	c.(637-639)Ata>Gta	p.I213V	ZZZ3_ENST00000476275.1_5'UTR|ZZZ3_ENST00000370798.1_Intron	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	213					chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						TCACAGTTTATAACAGCTGAA	0.418													T|||	127	0.0253594	0.0015	0.049	5008	,	,		22914	0.0248		0.0219	False		,,,				2504	0.045				p.I213V		Atlas-SNP	.											.	ZZZ3	80	.	0			c.A637G						PASS	.	T	VAL/ILE	19,4387	25.3+/-52.1	0,19,2184	113.0	110.0	111.0		637	0.4	1.0	1	dbSNP_126	111	140,8460	68.7+/-131.2	1,138,4161	yes	missense	ZZZ3	NM_015534.4	29	1,157,6345	CC,CT,TT		1.6279,0.4312,1.2225	benign	213/904	78098403	159,12847	2203	4300	6503	SO:0001583	missense	26009	exon5			AGTTTATAACAGC	AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"""Zinc fingers, ZZ-type"""	24523	protein-coding gene	gene with protein product	"""ATAC component 1 homolog (Drosophila)"""					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.637A>G	1.37:g.78098403T>C	ENSP00000359837:p.Ile213Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	156	79	0.50641	NM_015534	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Missense_Mutation	SNP	ENST00000370801.3	37	CCDS677.1	42	0.019230769230769232	1	0.0020325203252032522	10	0.027624309392265192	13	0.022727272727272728	18	0.023746701846965697	T	3.784	-0.045131	0.07452	0.004312	0.016279	ENSG00000036549	ENST00000370801	.	.	.	5.49	0.375	0.16188	.	0.481200	0.23983	N	0.042651	T	0.12475	0.0303	N	0.22421	0.69	0.49389	D	0.999784	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.08289	-1.0729	8	.	.	.	.	1.7365	0.02943	0.1194:0.3162:0.2148:0.3496	rs34535037	213;213;213	Q8IYH5-4;Q8IYH5;Q8IYH5-2	.;ZZZ3_HUMAN;.	V	213	.	.	I	-	1	0	ZZZ3	77870991	0.942000	0.31987	0.999000	0.59377	0.989000	0.77384	0.288000	0.18939	0.455000	0.26910	0.528000	0.53228	ATA	T|0.984;C|0.016	0.016	strong		0.418	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1	NM_015534	
FRG1	2483	hgsc.bcm.edu	37	4	190878589	190878589	+	Missense_Mutation	SNP	A	A	G	rs561930100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:190878589A>G	ENST00000226798.4	+	6	691	c.469A>G	c.(469-471)Att>Gtt	p.I157V	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	157					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TAGCTGCTTTATTAGATGCAA	0.363													.|||	11	0.00219649	0.0015	0.0058	5008	,	,		28209	0.001		0.004	False		,,,				2504	0.0				p.I157V		Atlas-SNP	.											FRG1,NS,carcinoma,0,1	FRG1	76	1	0			c.A469G						scavenged	.						15.0	18.0	17.0					4																	190878589		2157	4266	6423	SO:0001583	missense	2483	exon6			TGCTTTATTAGAT	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.469A>G	4.37:g.190878589A>G	ENSP00000226798:p.Ile157Val	Somatic	275	4	0.0145455		WXS	Illumina HiSeq	Phase_I	295	13	0.0440678	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	10.14	1.269261	0.23221	.	.	ENSG00000109536	ENST00000226798;ENST00000524583;ENST00000531991	T;T	0.42900	2.02;0.96	4.19	4.19	0.49359	Actin cross-linking (1);	0.049103	0.85682	D	0.000000	T	0.25938	0.0632	L	0.28014	0.82	0.48696	D	0.999699	B	0.09022	0.002	B	0.18871	0.023	T	0.08086	-1.0739	10	0.20519	T	0.43	-23.3336	6.6273	0.22837	0.8897:0.0:0.1103:0.0	.	157	Q14331	FRG1_HUMAN	V	157;29;94	ENSP00000226798:I157V;ENSP00000435943:I94V	ENSP00000226798:I157V	I	+	1	0	FRG1	191115583	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	5.196000	0.65136	1.677000	0.50941	0.373000	0.22412	ATT	.	.	none		0.363	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
CHRNE	1145	hgsc.bcm.edu	37	17	4804902	4804902	+	Silent	SNP	G	G	A	rs33970119	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4804902G>A	ENST00000293780.4	-	6	529	c.519C>T	c.(517-519)gcC>gcT	p.A173A	C17orf107_ENST00000381365.3_3'UTR|CHRNE_ENST00000575637.1_5'UTR	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)	173					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	CCACCTCTTCGGCATTGTACG	0.612													G|||	100	0.0199681	0.0008	0.0461	5008	,	,		15449	0.001		0.0616	False		,,,				2504	0.0041				p.A173A		Atlas-SNP	.											.	CHRNE	25	.	0			c.C519T						PASS	.	G	,	46,4360	49.6+/-84.7	0,46,2157	147.0	118.0	128.0		519,	-4.1	0.0	17	dbSNP_126	128	535,8065	148.2+/-203.4	19,497,3784	no	coding-synonymous,utr-3	CHRNE,C17orf107	NM_000080.3,NM_001145536.1	,	19,543,5941	AA,AG,GG		6.2209,1.044,4.4672	,	173/494,	4804902	581,12425	2203	4300	6503	SO:0001819	synonymous_variant	1145	exon6			CTCTTCGGCATTG	X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1966	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, epsilon (muscle)"""	100725	"""cholinergic receptor, nicotinic, epsilon"""			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778	ENST00000293780.4:c.519C>T	17.37:g.4804902G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_000080	D3DTK6	Silent	SNP	ENST00000293780.4	37	CCDS11058.1																																																																																			G|0.958;A|0.042	0.042	strong		0.612	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3		
ZNF415	55786	hgsc.bcm.edu	37	19	53612720	53612720	+	De_novo_Start_OutOfFrame	SNP	T	T	C	rs1560099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53612720T>C	ENST00000601493.1	-	0	543				ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.Y193C|ZNF415_ENST00000440291.1_Missense_Mutation_p.Y180C|ZNF415_ENST00000455735.2_Missense_Mutation_p.Y241C|ZNF415_ENST00000421033.1_Missense_Mutation_p.Y205C|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000500065.4_Missense_Mutation_p.Y193C|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.Y241C			Q09FC8	ZN415_HUMAN	zinc finger protein 415						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		ATCAGTCCCATATTTATTAGA	0.363													T|||	834	0.166534	0.0219	0.2911	5008	,	,		21572	0.3363		0.1769	False		,,,				2504	0.0879				p.Y193C		Atlas-SNP	.											.	ZNF415	68	.	0			c.A578G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	208,4198	128.6+/-165.4	5,198,2000	106.0	96.0	99.0		578,578,578	-5.5	0.0	19	dbSNP_88	99	1385,7215	267.2+/-287.2	114,1157,3029	yes	missense,missense,missense	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	194,194,194	119,1355,5029	CC,CT,TT		16.1047,4.7208,12.2482	benign,benign,benign	193/556,193/556,193/556	53612720	1593,11413	2203	4300	6503			55786	exon4			GTCCCATATTTAT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000601493.1:c.-113A>G	19.37:g.53612720T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000601493.1	37		421	0.19276556776556777	7	0.014227642276422764	88	0.2430939226519337	199	0.3479020979020979	127	0.16754617414248021	T	4.759	0.141173	0.09083	0.047208	0.161047	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.03831	3.79;3.79;3.79;3.79;3.79;3.79	2.74	-5.49	0.02584	.	.	.	.	.	T	0.00012	0.0000	N	0.00599	-1.345	0.80722	P	0.0	B;B;D;B;B	0.76494	0.0;0.0;0.999;0.0;0.003	B;B;D;B;B	0.79784	0.0;0.0;0.993;0.0;0.004	T	0.20739	-1.0266	8	0.02654	T	1	.	5.1664	0.15088	0.1316:0.6504:0.0:0.218	rs1560099;rs3170111;rs52796533;rs56818125;rs1560099	193;241;193;180;205	F5H287;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;ZN415_HUMAN;.;.;.	C	193;193;241;205;241;180	ENSP00000243643:Y193C;ENSP00000439435:Y193C;ENSP00000396492:Y241C;ENSP00000395055:Y205C;ENSP00000388787:Y241C;ENSP00000414601:Y180C	ENSP00000243643:Y193C	Y	-	2	0	ZNF415	58304532	0.000000	0.05858	0.000000	0.03702	0.202000	0.24057	-1.377000	0.02558	-1.636000	0.01533	0.260000	0.18958	TAT	T|0.843;C|0.157	0.157	strong		0.363	ZNF415-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000464038.1	NM_018355	
IL4R	3566	hgsc.bcm.edu	37	16	27374180	27374180	+	Missense_Mutation	SNP	T	T	C	rs1805015	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:27374180T>C	ENST00000395762.2	+	11	1766	c.1507T>C	c.(1507-1509)Tcc>Ccc	p.S503P	IL4R_ENST00000380922.3_Missense_Mutation_p.S488P|IL4R_ENST00000543915.2_Missense_Mutation_p.S503P|IL4R_ENST00000170630.2_Missense_Mutation_p.S503P	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	503	Required for IRS1 activation and IL4- induced cell growth.		S -> P (lowered total IgE concentration; dbSNP:rs1805015). {ECO:0000269|PubMed:10233717, ECO:0000269|PubMed:11285129, ECO:0000269|Ref.5}.		defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						CTTCAGCAACTCCCTGAGCCA	0.622													T|||	1010	0.201677	0.4251	0.1614	5008	,	,		19105	0.0843		0.1521	False		,,,				2504	0.1002				p.S503P		Atlas-SNP	.											IL4R,colon,carcinoma,0,1	IL4R	70	1	0			c.T1507C	GRCh37	CM993667	IL4R	M	rs1805015	PASS	.	T	PRO/SER	1595,2799	491.1+/-362.0	292,1011,894	78.0	83.0	81.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1507	1.6	0.0	16	dbSNP_89	81	1391,7209	265.3+/-286.1	110,1171,3019	yes	missense	IL4R	NM_000418.2	74	402,2182,3913	CC,CT,TT		16.1744,36.2995,22.9798	possibly-damaging	503/826	27374180	2986,10008	2197	4300	6497	SO:0001583	missense	3566	exon11			AGCAACTCCCTGA	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1507T>C	16.37:g.27374180T>C	ENSP00000379111:p.Ser503Pro	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	65	26	0.4	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	458	0.2097069597069597	227	0.4613821138211382	62	0.1712707182320442	43	0.07517482517482517	126	0.1662269129287599	T	12.87	2.068150	0.36470	0.362995	0.161744	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.09255	3.0;3.0;3.0;3.0	4.99	1.57	0.23409	.	10.161500	0.00166	N	0.000000	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;P;P	0.36144	0.539;0.539;0.539	B;B;B	0.31016	0.123;0.123;0.123	T	0.45056	-0.9287	9	0.33141	T	0.24	.	6.2127	0.20638	0.0:0.2856:0.0:0.7143	rs1805015;rs17513769;rs60163518;rs1805015	488;503;503	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	P	503;503;488;503	ENSP00000379111:S503P;ENSP00000441667:S503P;ENSP00000370309:S488P;ENSP00000170630:S503P	ENSP00000170630:S503P	S	+	1	0	IL4R	27281681	0.000000	0.05858	0.001000	0.08648	0.081000	0.17604	0.118000	0.15605	0.762000	0.33152	0.459000	0.35465	TCC	T|0.773;C|0.227	0.227	strong		0.622	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
RNF31	55072	hgsc.bcm.edu	37	14	24620821	24620821	+	Missense_Mutation	SNP	A	A	T	rs149481717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24620821A>T	ENST00000324103.6	+	10	2185	c.1865A>T	c.(1864-1866)cAg>cTg	p.Q622L	RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.Q97L|RNF31_ENST00000559275.1_Missense_Mutation_p.Q471L|RNF31_ENST00000382687.3_Missense_Mutation_p.Q471L	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	622					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		CCCTTCCGCCAGCGCCTCTGG	0.652													A|||	9	0.00179712	0.0	0.0029	5008	,	,		18657	0.0		0.005	False		,,,				2504	0.002				p.Q622L		Atlas-SNP	.											.	RNF31	95	.	0			c.A1865T						PASS	.	A	LEU/GLN	6,3962		0,6,1978	34.0	37.0	36.0		1865	5.4	1.0	14	dbSNP_134	36	41,8285		0,41,4122	yes	missense	RNF31	NM_017999.4	113	0,47,6100	TT,TA,AA		0.4924,0.1512,0.3823	possibly-damaging	622/1073	24620821	47,12247	1984	4163	6147	SO:0001583	missense	55072	exon10			TCCGCCAGCGCCT	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"""RING-type (C3HC4) zinc fingers"""	16031	protein-coding gene	gene with protein product	"""HOIL-1-interacting protein"""	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1865A>T	14.37:g.24620821A>T	ENSP00000315112:p.Gln622Leu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	14.27	2.485749	0.44147	0.001512	0.004924	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.47869	0.83;0.83	5.42	5.42	0.78866	.	0.068650	0.64402	D	0.000016	T	0.34395	0.0896	L	0.56769	1.78	0.46028	D	0.998828	B;B;B	0.33171	0.301;0.278;0.4	B;B;B	0.30855	0.08;0.039;0.121	T	0.42292	-0.9460	10	0.66056	D	0.02	-11.1548	9.8917	0.41294	0.8475:0.0:0.0:0.1524	.	381;622;471	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	L	622;471	ENSP00000315112:Q622L;ENSP00000372134:Q471L	ENSP00000315112:Q622L	Q	+	2	0	RNF31	23690661	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.311000	0.59147	2.274000	0.75844	0.533000	0.62120	CAG	A|0.998;T|0.002	0.002	strong		0.652	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999	
FUT5	2527	hgsc.bcm.edu	37	19	5867191	5867191	+	Silent	SNP	G	G	A	rs10412834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5867191G>A	ENST00000588525.1	-	2	633	c.546C>T	c.(544-546)taC>taT	p.Y182Y	FUT5_ENST00000252675.5_Silent_p.Y182Y	NM_002034.2	NP_002025.2	Q11128	FUT5_HUMAN	fucosyltransferase 5 (alpha (1,3) fucosyltransferase)	182					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3-galactosyl-N-acetylglucosaminide 4-alpha-L-fucosyltransferase activity (GO:0017060)|alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12						CCAGCCAGCCGTAGGGCGTGA	0.662													G|||	452	0.0902556	0.0764	0.1124	5008	,	,		13354	0.0109		0.1531	False		,,,				2504	0.1104				p.Y182Y		Atlas-SNP	.											.	FUT5	29	.	0			c.C546T						PASS	.	G		370,3984		11,348,1818	26.0	23.0	24.0		546	-1.2	1.0	19	dbSNP_119	24	1225,7311		92,1041,3135	no	coding-synonymous	FUT5	NM_002034.2		103,1389,4953	AA,AG,GG		14.351,8.4979,12.3739		182/375	5867191	1595,11295	2177	4268	6445	SO:0001819	synonymous_variant	2527	exon2			CCAGCCGTAGGGC		CCDS12154.1	19p13.3	2013-02-26				ENSG00000130383	2.4.1.65	"""Fucosyltransferases"""	4016	protein-coding gene	gene with protein product		136835				1740457	Standard	NM_002034		Approved	FUC-TV	uc002mdo.4	Q11128	OTTHUMG00000180616	ENST00000588525.1:c.546C>T	19.37:g.5867191G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	NM_002034	A8K4X2	Silent	SNP	ENST00000588525.1	37	CCDS12154.1																																																																																			G|0.912;A|0.088	0.088	strong		0.662	FUT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452213.1	NM_002034	
SLFN13	146857	hgsc.bcm.edu	37	17	33767943	33767943	+	Missense_Mutation	SNP	C	C	T	rs138317636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33767943C>T	ENST00000285013.6	-	6	2640	c.2365G>A	c.(2365-2367)Gtg>Atg	p.V789M	SLFN13_ENST00000360502.2_Missense_Mutation_p.V471M|SLFN13_ENST00000526861.1_Missense_Mutation_p.V789M|SLFN13_ENST00000542635.1_Missense_Mutation_p.V789M|SLFN13_ENST00000533791.1_Missense_Mutation_p.V789M|SLFN13_ENST00000534689.1_Missense_Mutation_p.V471M	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	789						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)		ACATAGGTCACTATTTGCTCC	0.458																																					p.V789M		Atlas-SNP	.											.	SLFN13	79	.	0			c.G2365A						PASS	.	C	MET/VAL	0,4406		0,0,2203	78.0	76.0	77.0		2365	2.2	0.0	17	dbSNP_134	77	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SLFN13	NM_144682.5	21	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign	789/898	33767943	3,13003	2203	4300	6503	SO:0001583	missense	146857	exon6			AGGTCACTATTTG	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.2365G>A	17.37:g.33767943C>T	ENSP00000285013:p.Val789Met	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	c	8.383	0.838010	0.16891	0.0	3.49E-4	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72	3.26	2.22	0.28083	.	0.899723	0.09181	N	0.837387	T	0.78972	0.4368	L	0.53780	1.695	0.09310	N	1	P;B	0.36222	0.544;0.2	B;B	0.36989	0.238;0.037	T	0.65973	-0.6038	10	0.44086	T	0.13	.	8.2184	0.31526	0.0:0.7525:0.2475:0.0	.	471;789	Q68D06-2;Q68D06	.;SLN13_HUMAN	M	789;471;789;789;471	ENSP00000285013:V789M;ENSP00000353692:V471M;ENSP00000434439:V789M;ENSP00000444016:V789M;ENSP00000435442:V471M	ENSP00000285013:V789M	V	-	1	0	SLFN13	30792056	0.000000	0.05858	0.001000	0.08648	0.062000	0.15995	0.425000	0.21346	0.637000	0.30526	0.400000	0.26472	GTG	C|1.000;T|0.000	0.000	strong		0.458	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
KLK3	354	hgsc.bcm.edu	37	19	51361315	51361315	+	Silent	SNP	C	C	T	rs12946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51361315C>T	ENST00000326003.2	+	3	278	c.237C>T	c.(235-237)agC>agT	p.S79S	KLK3_ENST00000593997.1_Silent_p.S79S|KLK3_ENST00000360617.3_Silent_p.S79S|KLK3_ENST00000597483.1_Intron|KLK3_ENST00000595952.1_Intron	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		GTCGGCACAGCCTGTTTCATC	0.542													C|||	438	0.0874601	0.0764	0.1009	5008	,	,		21521	0.0685		0.1272	False		,,,				2504	0.0716				p.S79S	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.C237T						PASS	.	C	,,	371,4035	187.4+/-214.1	14,343,1846	69.0	59.0	62.0		237,,237	2.3	0.0	19	dbSNP_52	62	1085,7515	225.9+/-261.8	64,957,3279	yes	coding-synonymous,intron,coding-synonymous	KLK3	NM_001030047.1,NM_001030048.1,NM_001648.2	,,	78,1300,5125	TT,TC,CC		12.6163,8.4203,11.1948	,,	79/239,,79/262	51361315	1456,11550	2203	4300	6503	SO:0001819	synonymous_variant	354	exon3			GCACAGCCTGTTT	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.237C>T	19.37:g.51361315C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			C|0.890;T|0.110	0.110	strong		0.542	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
AGAP6	414189	hgsc.bcm.edu	37	10	51769799	51769799	+	Silent	SNP	C	C	T	rs61848275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:51769799C>T	ENST00000374056.4	+	7	2243	c.1845C>T	c.(1843-1845)gtC>gtT	p.V615V	AGAP6_ENST00000412531.3_Silent_p.V638V			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	615					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						GGAATGTGGTCCTGGCGCAGC	0.667													.|||	597	0.119209	0.0461	0.1542	5008	,	,		18357	0.0317		0.2654	False		,,,				2504	0.1329				p.V638V		Atlas-SNP	.											AGAP6,NS,carcinoma,0,1	AGAP6	53	1	0			c.C1914T						scavenged	.																																			SO:0001819	synonymous_variant	414189	exon8			TGTGGTCCTGGCG		CCDS44397.1	10q11.23	2013-01-10	2008-09-22	2008-09-22	ENSG00000204149	ENSG00000204149		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	23466	protein-coding gene	gene with protein product			"""centaurin, gamma-like family, member 3"""	CTGLF3			Standard	NM_001077665		Approved	bA324H6.1	uc001jix.4	Q5VW22	OTTHUMG00000018220	ENST00000374056.4:c.1845C>T	10.37:g.51769799C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	167	44	0.263473	NM_001077665		Silent	SNP	ENST00000374056.4	37																																																																																				C|0.500;T|0.500	0.500	weak		0.667	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665	
INSR	3643	hgsc.bcm.edu	37	19	7166388	7166388	+	Silent	SNP	G	G	A	rs2229429	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7166388G>A	ENST00000302850.5	-	8	1780	c.1638C>T	c.(1636-1638)gaC>gaT	p.D546D	INSR_ENST00000341500.5_Silent_p.D546D	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	546					activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	CATCCTGCCCGTCGAACTCCG	0.547													G|||	1285	0.256589	0.4834	0.1441	5008	,	,		19189	0.0655		0.1909	False		,,,				2504	0.2945				p.D546D		Atlas-SNP	.											.	INSR	265	.	0			c.C1638T						PASS	.	G	,	1901,2505	545.4+/-376.8	403,1095,705	84.0	61.0	69.0		1638,1638	-4.5	0.8	19	dbSNP_98	69	1710,6890	311.2+/-310.2	165,1380,2755	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	568,2475,3460	AA,AG,GG		19.8837,43.1457,27.7641	,	546/1383,546/1371	7166388	3611,9395	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon8			CTGCCCGTCGAAC	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.1638C>T	19.37:g.7166388G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			T|0.000;G|0.746;C|0.000;A|0.254	0.254	strong		0.547	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
GPC4	2239	hgsc.bcm.edu	37	X	132438872	132438872	+	Missense_Mutation	SNP	C	C	A	rs1129980	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:132438872C>A	ENST00000370828.3	-	7	1697	c.1173G>T	c.(1171-1173)gaG>gaT	p.E391D	GPC4_ENST00000535467.1_Missense_Mutation_p.E321D	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	391			E -> D (in dbSNP:rs1129980). {ECO:0000269|PubMed:10814714, ECO:0000269|PubMed:9787072, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					GTTTCAGTTTCTCCTTGACAT	0.433													C|||	1732	0.458808	0.5053	0.1787	3775	,	,		15716	0.3492		0.2177	False		,,,				2504	0.3773				p.E391D		Atlas-SNP	.											.	GPC4	58	.	0			c.G1173T						PASS	.	C	ASP/GLU	2289,1546		593,784,319,255,252	178.0	150.0	160.0		1173	3.4	1.0	X	dbSNP_86	160	1986,4742		209,1010,558,1209,1314	yes	missense	GPC4	NM_001448.2	45	802,1794,877,1464,1566	AA,AC,A,CC,C		29.5184,40.3129,40.4715	benign	391/557	132438872	4275,6288	2203	4300	6503	SO:0001583	missense	2239	exon7			CAGTTTCTCCTTG	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"""Proteoglycans / Cell Surface : Glypicans"""	4452	protein-coding gene	gene with protein product	"""glypican proteoglycan 4"""	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.1173G>T	X.37:g.132438872C>A	ENSP00000359864:p.Glu391Asp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	37	CCDS14637.1	654	0.39421338155515373	173	0.4914772727272727	50	0.15822784810126583	117	0.26	117	0.17410714285714285	C	12.01	1.808215	0.31961	0.596871	0.295184	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.52526	0.66;0.66	5.13	3.36	0.38483	.	0.046337	0.85682	D	0.000000	T	0.00012	0.0000	L	0.43152	1.355	0.24745	P	0.99301708	B	0.24483	0.104	B	0.30782	0.12	T	0.45279	-0.9272	9	0.23891	T	0.37	-19.7874	7.2029	0.25891	0.0:0.643:0.0:0.357	rs1129980;rs1805046;rs52808097;rs57817524;rs1129980	391	O75487	GPC4_HUMAN	D	391;385;321	ENSP00000359864:E391D;ENSP00000444959:E321D	ENSP00000359864:E391D	E	-	3	2	GPC4	132266538	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.974000	0.29436	0.948000	0.37687	0.594000	0.82650	GAG	C|0.574;A|0.426	0.426	strong		0.433	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448	
HERC2	8924	hgsc.bcm.edu	37	15	28459092	28459092	+	Silent	SNP	G	G	A	rs187225254		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459092G>A	ENST00000261609.7	-	42	6690	c.6582C>T	c.(6580-6582)gaC>gaT	p.D2194D		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)		GGTTCTCGGAGTCGGGGAAGT	0.587																																					p.D2194D		Atlas-SNP	.											.	HERC2	501	.	0			c.C6582T						PASS	.						35.0	32.0	33.0					15																	28459092		2203	4298	6501	SO:0001819	synonymous_variant	8924	exon42			CTCGGAGTCGGGG	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.6582C>T	15.37:g.28459092G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	194	12	0.0618557	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.993;A|0.007	0.007	strong		0.587	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
FRAS1	80144	hgsc.bcm.edu	37	4	79447763	79447763	+	Missense_Mutation	SNP	T	T	C	rs34670941	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:79447763T>C	ENST00000264895.6	+	70	11317	c.10877T>C	c.(10876-10878)gTt>gCt	p.V3626A		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3622					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CAGCCATGGGTTGACCCAGGA	0.478													T|||	728	0.145367	0.1755	0.0865	5008	,	,		22507	0.2272		0.1093	False		,,,				2504	0.0992				p.V3626A		Atlas-SNP	.											.	FRAS1	779	.	0			c.T10877C						PASS	.	T	ALA/VAL	652,3336		46,560,1388	50.0	53.0	52.0		10877	-0.8	0.0	4	dbSNP_126	52	832,7504		38,756,3374	yes	missense	FRAS1	NM_025074.6	64	84,1316,4762	CC,CT,TT		9.9808,16.349,12.0415	benign	3626/4013	79447763	1484,10840	1994	4168	6162	SO:0001583	missense	80144	exon70			CATGGGTTGACCC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10877T>C	4.37:g.79447763T>C	ENSP00000264895:p.Val3626Ala	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	227	106	0.46696	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	342	0.1565934065934066	96	0.1951219512195122	32	0.08839779005524862	128	0.22377622377622378	86	0.11345646437994723	T	5.318	0.243937	0.10077	0.16349	0.099808	ENSG00000138759	ENST00000264895	T	0.11063	2.81	5.75	-0.78	0.10969	.	1.100870	0.06846	N	0.796502	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48246	-0.9052	9	0.15952	T	0.53	.	11.2992	0.49295	0.0:0.406:0.0:0.594	rs34670941	3626	E9PHH6	.	A	3626	ENSP00000264895:V3626A	ENSP00000264895:V3626A	V	+	2	0	FRAS1	79666787	0.000000	0.05858	0.003000	0.11579	0.368000	0.29767	0.372000	0.20467	-0.331000	0.08501	0.397000	0.26171	GTT	T|0.854;C|0.146	0.146	strong		0.478	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MYBPC3	4607	hgsc.bcm.edu	37	11	47369443	47369443	+	Silent	SNP	G	G	A	rs11570058	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:47369443G>A	ENST00000545968.1	-	7	840	c.786C>T	c.(784-786)acC>acT	p.T262T	MYBPC3_ENST00000256993.4_Silent_p.T262T|MYBPC3_ENST00000399249.2_Silent_p.T262T	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	262					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)		CCAGGTCTCCGGTGCCCATGG	0.657													G|||	306	0.0611022	0.034	0.0807	5008	,	,		16010	0.0169		0.1352	False		,,,				2504	0.0532				p.T262T		Atlas-SNP	.											.	MYBPC3	102	.	0			c.C786T						PASS	.	G		149,3641		2,145,1748	15.0	19.0	18.0		786	-11.1	0.1	11	dbSNP_120	18	965,7183		57,851,3166	no	coding-synonymous	MYBPC3	NM_000256.3		59,996,4914	AA,AG,GG		11.8434,3.9314,9.3315		262/1275	47369443	1114,10824	1895	4074	5969	SO:0001819	synonymous_variant	4607	exon7			GTCTCCGGTGCCC	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.786C>T	11.37:g.47369443G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Silent	SNP	ENST00000545968.1	37	CCDS53621.1																																																																																			G|0.937;A|0.063	0.063	strong		0.657	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3		
OR7G3	390883	hgsc.bcm.edu	37	19	9237435	9237435	+	Silent	SNP	A	A	G	rs386806663|rs10407484	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9237435A>G	ENST00000305444.2	-	1	191	c.192T>C	c.(190-192)tcT>tcC	p.S64S		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	64						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S64S(1)		NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						AGGACAGGATAGAGAGGAGGA	0.552													G|||	2249	0.449081	0.8041	0.2421	5008	,	,		20656	0.3651		0.3141	False		,,,				2504	0.3415				p.S64S		Atlas-SNP	.											OR7G3,NS,carcinoma,0,1	OR7G3	41	1	1	Substitution - coding silent(1)	prostate(1)	c.T192C						PASS	.	G		3080,1326		1167,746,290	128.0	102.0	110.0		192	-2.5	0.0	19	dbSNP_119	110	2659,5941		386,1887,2027	no	coding-synonymous	OR7G3	NM_001001958.1		1553,2633,2317	GG,GA,AA		30.9186,30.0953,44.1258		64/313	9237435	5739,7267	2203	4300	6503	SO:0001819	synonymous_variant	390883	exon1			CAGGATAGAGAGG		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"""GPCR / Class A : Olfactory receptors"""	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.192T>C	19.37:g.9237435A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	133	57	0.428571	NM_001001958	Q6IFJ6|Q96R99	Silent	SNP	ENST00000305444.2	37	CCDS32899.1																																																																																			A|0.566;G|0.434	0.434	strong		0.552	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1		
ALPI	248	hgsc.bcm.edu	37	2	233321641	233321641	+	Silent	SNP	C	C	T	rs61732032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233321641C>T	ENST00000295463.3	+	4	410	c.333C>T	c.(331-333)agC>agT	p.S111S		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	111					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TGCCAGACAGCGCAGCCACAG	0.617													C|||	472	0.0942492	0.112	0.0807	5008	,	,		18792	0.0804		0.1064	False		,,,				2504	0.0818				p.S111S		Atlas-SNP	.											ALPI,NS,carcinoma,0,1	ALPI	64	1	0			c.C333T						scavenged	.	C		491,3915	226.5+/-242.0	31,429,1743	64.0	51.0	56.0		333	-7.8	0.6	2	dbSNP_129	56	707,7893	171.9+/-222.7	26,655,3619	no	coding-synonymous	ALPI	NM_001631.3		57,1084,5362	TT,TC,CC		8.2209,11.1439,9.2111		111/529	233321641	1198,11808	2203	4300	6503	SO:0001819	synonymous_variant	248	exon4			AGACAGCGCAGCC	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.333C>T	2.37:g.233321641C>T		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	242	108	0.446281	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			C|0.912;T|0.088	0.088	strong		0.617	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
CPED1	79974	hgsc.bcm.edu	37	7	120876835	120876835	+	Missense_Mutation	SNP	A	A	G	rs35793694	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:120876835A>G	ENST00000310396.5	+	17	2590	c.2123A>G	c.(2122-2124)gAa>gGa	p.E708G	CPED1_ENST00000450913.2_Missense_Mutation_p.E708G|CPED1_ENST00000423795.1_Missense_Mutation_p.E488G	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	708			E -> G (in dbSNP:rs35793694). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			endoplasmic reticulum (GO:0005783)											GACTACATTGAAGCCATTTTA	0.348													A|||	182	0.0363419	0.0325	0.0403	5008	,	,		15919	0.0		0.0805	False		,,,				2504	0.0307				p.E708G		Atlas-SNP	.											.	.	.	.	0			c.A2123G						PASS	.	A	GLY/GLU,GLY/GLU	200,4206	124.5+/-161.8	3,194,2006	98.0	97.0	97.0		2123,2123	4.8	1.0	7	dbSNP_126	97	684,7916	169.4+/-220.8	30,624,3646	yes	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	98,98	33,818,5652	GG,GA,AA		7.9535,4.5393,6.7969	benign,benign	708/784,708/1027	120876835	884,12122	2203	4300	6503	SO:0001583	missense	79974	exon16			ACATTGAAGCCAT		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2123A>G	7.37:g.120876835A>G	ENSP00000309772:p.Glu708Gly	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	105	0.04807692307692308	21	0.042682926829268296	16	0.04419889502762431	0	0.0	68	0.08970976253298153	A	20.3	3.965228	0.74131	0.045393	0.079535	ENSG00000106034	ENST00000310396;ENST00000450913;ENST00000423795	T;T;T	0.25085	2.15;1.82;1.83	5.86	4.75	0.60458	.	0.200573	0.43416	D	0.000573	T	0.00637	0.0021	L	0.40543	1.245	0.80722	D	1	P;P;B	0.38078	0.617;0.617;0.329	B;B;B	0.30855	0.121;0.121;0.077	T	0.03112	-1.1071	10	0.46703	T	0.11	.	10.2136	0.43156	0.6934:0.3066:0.0:0.0	rs35793694	488;708;708	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	G	708;708;488	ENSP00000309772:E708G;ENSP00000406122:E708G;ENSP00000415573:E488G	ENSP00000309772:E708G	E	+	2	0	C7orf58	120664071	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.980000	0.40618	2.238000	0.73509	0.477000	0.44152	GAA	A|0.939;G|0.061	0.061	strong		0.348	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
ATAD5	79915	hgsc.bcm.edu	37	17	29161202	29161202	+	Missense_Mutation	SNP	A	A	T	rs9910051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:29161202A>T	ENST00000321990.4	+	2	481	c.103A>T	c.(103-105)Acc>Tcc	p.T35S	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	35			T -> S (in dbSNP:rs9910051).		cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				TGACACATCTACCTGCAAAAC	0.308													T|||	1442	0.287939	0.5681	0.2305	5008	,	,		17249	0.1359		0.1163	False		,,,				2504	0.2832				p.T35S		Atlas-SNP	.											.	ATAD5	150	.	0			c.A103T						PASS	.	T	SER/THR	2097,2303	549.6+/-377.8	501,1095,604	75.0	82.0	80.0		103	5.5	1.0	17	dbSNP_119	80	960,7638	761.2+/-407.6	45,870,3384	yes	missense	ATAD5	NM_024857.3	58	546,1965,3988	TT,TA,AA		11.1654,47.6591,23.519	benign	35/1845	29161202	3057,9941	2200	4299	6499	SO:0001583	missense	79915	exon2			ACATCTACCTGCA		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.103A>T	17.37:g.29161202A>T	ENSP00000313171:p.Thr35Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	115	55	0.478261	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	518	0.23717948717948717	269	0.5467479674796748	81	0.22375690607734808	90	0.15734265734265734	78	0.10290237467018469	T	11.35	1.612102	0.28712	0.476591	0.111654	ENSG00000176208	ENST00000321990	T	0.05855	3.38	5.47	5.47	0.80525	.	0.556987	0.18338	N	0.144288	T	0.00012	0.0000	N	0.00112	-2.095	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40194	-0.9576	9	0.02654	T	1	.	6.5206	0.22272	0.1388:0.0722:0.0:0.789	rs9910051;rs52830976;rs9910051	35	Q96QE3	ATAD5_HUMAN	S	35	ENSP00000313171:T35S	ENSP00000313171:T35S	T	+	1	0	ATAD5	26185328	0.998000	0.40836	0.974000	0.42286	0.914000	0.54420	1.019000	0.30014	0.911000	0.36747	-0.257000	0.10917	ACC	A|0.786;N|0.000	.	strong		0.308	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
TMEM123	114908	hgsc.bcm.edu	37	11	102272884	102272884	+	Missense_Mutation	SNP	C	C	T	rs2155587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102272884C>T	ENST00000398136.2	-	3	631	c.211G>A	c.(211-213)Gtg>Atg	p.V71M	TMEM123_ENST00000532161.1_De_novo_Start_InFrame|TMEM123_ENST00000361236.3_Missense_Mutation_p.V52M|TMEM123_ENST00000525577.1_5'UTR	NM_052932.2	NP_443164.2	Q8N131	PORIM_HUMAN	transmembrane protein 123	71	Thr-rich.		V -> M (in dbSNP:rs2155587).		oncosis (GO:0070267)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(3)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9	all_cancers(8;0.00027)|all_epithelial(12;0.0021)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0314)|Lung(13;0.109)|all cancers(10;0.12)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0149)		GGTGGTTTCACAGTACTGTTG	0.428													C|||	283	0.0565096	0.003	0.1527	5008	,	,		17030	0.0635		0.0865	False		,,,				2504	0.0225				p.V71M		Atlas-SNP	.											.	TMEM123	16	.	0			c.G211A						PASS	.	C	MET/VAL	107,3919		2,103,1908	270.0	251.0	257.0		211	-0.6	0.0	11	dbSNP_96	257	786,7546		39,708,3419	yes	missense	TMEM123	NM_052932.2	21	41,811,5327	TT,TC,CC		9.4335,2.6577,7.2261	possibly-damaging	71/209	102272884	893,11465	2013	4166	6179	SO:0001583	missense	114908	exon3			GTTTCACAGTACT	AL050161	CCDS41702.1	11q22.1	2014-01-02			ENSG00000152558	ENSG00000152558			30138	protein-coding gene	gene with protein product	"""pro oncosis receptor inducing membrane injury gene"""	606356				11481458, 24318988	Standard	NM_052932		Approved	PORIMIN, KCT3	uc001pha.3	Q8N131	OTTHUMG00000167326	ENST00000398136.2:c.211G>A	11.37:g.102272884C>T	ENSP00000381204:p.Val71Met	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	246	131	0.53252	NM_052932	Q8IWS2|Q96QV2	Missense_Mutation	SNP	ENST00000398136.2	37	CCDS41702.1	156	0.07142857142857142	1	0.0020325203252032522	46	0.1270718232044199	43	0.07517482517482517	66	0.0870712401055409	C	11.51	1.659731	0.29515	0.026577	0.094335	ENSG00000152558	ENST00000361236;ENST00000398136;ENST00000526676	T;T;T	0.53640	1.84;1.78;0.61	5.36	-0.649	0.11461	.	4.242690	0.00639	N	0.000519	T	0.00356	0.0011	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.13594	0.008;0.008	B;B	0.18561	0.022;0.022	T	0.09596	-1.0667	9	0.45353	T	0.12	2.6989	3.637	0.08153	0.1716:0.3951:0.0:0.4334	rs2155587;rs17258581;rs52821242;rs60976972;rs2155587	52;71	Q8N131-2;Q8N131	.;PORIM_HUMAN	M	52;71;29	ENSP00000355285:V52M;ENSP00000381204:V71M;ENSP00000435842:V29M	ENSP00000355285:V52M	V	-	1	0	TMEM123	101778094	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.339000	0.01102	0.039000	0.15632	0.563000	0.77884	GTG	C|0.929;T|0.071	0.071	strong		0.428	TMEM123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394178.1	NM_052932	
RANBP2	5903	hgsc.bcm.edu	37	2	109374952	109374952	+	Silent	SNP	A	A	G	rs826549	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:109374952A>G	ENST00000283195.6	+	18	2676	c.2550A>G	c.(2548-2550)tcA>tcG	p.S850S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	850					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.S850S(1)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						GACCAGACTCAGTGCCTGATG	0.423																																					p.S850S		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,1	RANBP2	488	1	1	Substitution - coding silent(1)	stomach(1)	c.A2550G						scavenged	.	G		2554,1850		991,572,639	117.0	171.0	153.0		2550	-2.5	0.6	2	dbSNP_86	153	1455,7145		235,985,3080	no	coding-synonymous	RANBP2	NM_006267.4		1226,1557,3719	GG,GA,AA		16.9186,42.0073,30.829		850/3225	109374952	4009,8995	2202	4300	6502	SO:0001819	synonymous_variant	5903	exon18			AGACTCAGTGCCT	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.2550A>G	2.37:g.109374952A>G		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	218	91	0.417431	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																			A|0.745;G|0.255	0.255	strong		0.423	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
MANSC1	54682	hgsc.bcm.edu	37	12	12496086	12496086	+	Missense_Mutation	SNP	C	C	T	rs3741798	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:12496086C>T	ENST00000535902.1	-	2	726	c.163G>A	c.(163-165)Gta>Ata	p.V55I	MANSC1_ENST00000396349.3_Missense_Mutation_p.V21I			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	55	MANSC. {ECO:0000255|PROSITE- ProRule:PRU00341}.		V -> I (in dbSNP:rs3741798). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		GAAGTATATACGGGCTCATTG	0.388													C|||	401	0.0800719	0.0772	0.0879	5008	,	,		21408	0.0764		0.1163	False		,,,				2504	0.045				p.V55I		Atlas-SNP	.											.	MANSC1	38	.	0			c.G163A						PASS	.	C	ILE/VAL	415,3991	203.5+/-225.9	23,369,1811	170.0	168.0	168.0		163	-2.2	0.0	12	dbSNP_107	168	993,7607	215.0+/-254.5	51,891,3358	yes	missense	MANSC1	NM_018050.2	29	74,1260,5169	TT,TC,CC		11.5465,9.419,10.8258	benign	55/432	12496086	1408,11598	2203	4300	6503	SO:0001583	missense	54682	exon2			TATATACGGGCTC	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.163G>A	12.37:g.12496086C>T	ENSP00000438205:p.Val55Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_018050	Q8NEC1|Q9NW60	Missense_Mutation	SNP	ENST00000535902.1	37	CCDS8648.1	213	0.09752747252747253	44	0.08943089430894309	35	0.09668508287292818	56	0.0979020979020979	78	0.10290237467018469	C	0.032	-1.326428	0.01309	0.09419	0.115465	ENSG00000111261	ENST00000535902;ENST00000396349;ENST00000543314	T;T;T	0.36157	1.99;1.99;1.27	5.66	-2.16	0.07080	Seven cysteines (1);Seven cysteines, N-terminal (2);	1.386070	0.05028	N	0.474172	T	0.00144	0.0004	N	0.00677	-1.265	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.32613	-0.9900	9	0.02654	T	1	-5.2156	10.6695	0.45749	0.0:0.4575:0.0:0.5425	rs3741798;rs17846030;rs17859014;rs52831774;rs60985477;rs3741798	21;55	Q9NW60;Q9H8J5	.;MANS1_HUMAN	I	55;21;55	ENSP00000438205:V55I;ENSP00000379638:V21I;ENSP00000437624:V55I	ENSP00000379638:V21I	V	-	1	0	MANSC1	12387353	0.016000	0.18221	0.037000	0.18230	0.332000	0.28634	-0.418000	0.07080	-0.402000	0.07633	-1.063000	0.02288	GTA	C|0.898;T|0.102	0.102	strong		0.388	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
AP5Z1	9907	hgsc.bcm.edu	37	7	4827859	4827859	+	Missense_Mutation	SNP	G	G	A	rs77890266	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4827859G>A	ENST00000348624.4	+	12	1623	c.1529G>A	c.(1528-1530)cGg>cAg	p.R510Q	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Missense_Mutation_p.R510Q	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	510					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAGGCCTTCCGGGACCCGCAG	0.687													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		16573	0.0		0.0239	False		,,,				2504	0.0235				p.R510Q		Atlas-SNP	.											.	.	.	.	0			c.G1529A						PASS	.	G	GLN/ARG	12,3796		0,12,1892	10.0	13.0	12.0		1529	2.6	0.2	7	dbSNP_131	12	197,8015		5,187,3914	yes	missense	KIAA0415	NM_014855.2	43	5,199,5806	AA,AG,GG		2.3989,0.3151,1.7388	benign	510/808	4827859	209,11811	1904	4106	6010	SO:0001583	missense	9907	exon12			CCTTCCGGGACCC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1529G>A	7.37:g.4827859G>A	ENSP00000297562:p.Arg510Gln	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	154	68	0.441558	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	32	0.014652014652014652	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	18	0.023746701846965697	G	13.91	2.377627	0.42105	0.003151	0.023989	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44881	0.91;0.91	4.48	2.62	0.31277	.	0.079729	0.52532	N	0.000077	T	0.10121	0.0248	L	0.45228	1.405	0.38035	D	0.93527	P	0.37864	0.61	B	0.25405	0.06	T	0.04103	-1.0977	10	0.36615	T	0.2	.	8.8683	0.35300	0.1868:0.0:0.8132:0.0	.	510	O43299	K0415_HUMAN	Q	510	ENSP00000297562:R510Q;ENSP00000384980:R510Q	ENSP00000297562:R510Q	R	+	2	0	KIAA0415	4794385	0.959000	0.32827	0.180000	0.23079	0.851000	0.48451	1.465000	0.35299	0.310000	0.22990	0.478000	0.44815	CGG	G|0.986;A|0.014	0.014	strong		0.687	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
SLC7A6OS	84138	hgsc.bcm.edu	37	16	68344696	68344696	+	Missense_Mutation	SNP	C	C	T	rs3803650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68344696C>T	ENST00000263997.6	-	1	152	c.134G>A	c.(133-135)gGt>gAt	p.G45D	PRMT7_ENST00000348497.4_5'Flank|snoU13_ENST00000458872.1_RNA|PRMT7_ENST00000449359.3_5'Flank|PRMT7_ENST00000339507.5_5'Flank|PRMT7_ENST00000441236.1_5'Flank	NM_032178.2	NP_115554.2	Q96CW6	S7A6O_HUMAN	solute carrier family 7, member 6 opposite strand	45			G -> D (in dbSNP:rs3803650). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		hematopoietic progenitor cell differentiation (GO:0002244)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.034)|Epithelial(162;0.106)		TCTCTCCAAACCCTCCGACGT	0.627													c|||	3347	0.668331	0.7746	0.6816	5008	,	,		16642	0.7728		0.5437	False		,,,				2504	0.5358				p.G45D		Atlas-SNP	.											SLC7A6OS,NS,carcinoma,0,1	SLC7A6OS	22	1	0			c.G134A						PASS	.	T	ASP/GLY	3273,1123	715.1+/-408.4	1227,819,152	75.0	62.0	66.0		134	-5.3	0.0	16	dbSNP_107	66	5011,3589	627.2+/-397.9	1450,2111,739	yes	missense	SLC7A6OS	NM_032178.2	94	2677,2930,891	TT,TC,CC		41.7326,25.546,36.2573	benign	45/310	68344696	8284,4712	2198	4300	6498	SO:0001583	missense	84138	exon1			TCCAAACCCTCCG		CCDS10865.1	16q22.1	2010-03-11			ENSG00000103061	ENSG00000103061			25807	protein-coding gene	gene with protein product							Standard	NM_032178		Approved	FLJ13291	uc002evw.2	Q96CW6	OTTHUMG00000137558	ENST00000263997.6:c.134G>A	16.37:g.68344696C>T	ENSP00000263997:p.Gly45Asp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	214	212	0.990654	NM_032178	Q8TCZ3|Q9H8R8	Missense_Mutation	SNP	ENST00000263997.6	37	CCDS10865.1	1518	0.695054945054945	402	0.8170731707317073	241	0.6657458563535912	455	0.7954545454545454	420	0.554089709762533	c	8.395	0.840662	0.16891	0.74454	0.582674	ENSG00000103061	ENST00000263997	T	0.18016	2.24	5.14	-5.34	0.02705	.	0.784649	0.12366	N	0.475201	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.31251	-0.9950	9	0.12103	T	0.63	0.0062	7.5123	0.27581	0.0:0.2759:0.1293:0.5949	rs3803650;rs17554596;rs17554603;rs17845399;rs17858256;rs60471765;rs3803650	45	Q96CW6	S7A6O_HUMAN	D	45	ENSP00000263997:G45D	ENSP00000263997:G45D	G	-	2	0	SLC7A6OS	66902197	0.184000	0.23200	0.002000	0.10522	0.276000	0.26787	-0.287000	0.08388	-0.806000	0.04398	-0.124000	0.14976	GGT	C|0.334;T|0.666	0.666	strong		0.627	SLC7A6OS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268894.3	NM_032178	
LAMB3	3914	hgsc.bcm.edu	37	1	209823354	209823354	+	Silent	SNP	G	G	A	rs2228339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:209823354G>A	ENST00000356082.4	-	3	272	c.138C>T	c.(136-138)acC>acT	p.T46T	LAMB3_ENST00000367030.3_Silent_p.T46T|LAMB3_ENST00000391911.1_Silent_p.T46T	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	46	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.T46T(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)		TCAGTCCACAGGTAGATGAAG	0.617													G|||	1492	0.297923	0.2088	0.4078	5008	,	,		17612	0.3393		0.2674	False		,,,				2504	0.3292				p.T46T		Atlas-SNP	.											LAMB3,NS,carcinoma,0,1	LAMB3	136	1	1	Substitution - coding silent(1)	stomach(1)	c.C138T						PASS	.	G	,,	1002,3404	373.7+/-320.9	106,790,1307	90.0	77.0	82.0		138,138,138	5.4	1.0	1	dbSNP_107	82	2150,6450	370.0+/-335.7	277,1596,2427	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	383,2386,3734	AA,AG,GG		25.0,22.7417,24.235	,,	46/1173,46/1173,46/1173	209823354	3152,9854	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon3			TCCACAGGTAGAT	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.138C>T	1.37:g.209823354G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			G|0.739;A|0.261	0.261	strong		0.617	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
TMX4	56255	hgsc.bcm.edu	37	20	7980390	7980390	+	Silent	SNP	C	C	T	rs1012891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:7980390C>T	ENST00000246024.2	-	4	671	c.456G>A	c.(454-456)ccG>ccA	p.P152P	TMX4_ENST00000530935.1_5'UTR	NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	152					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						TTAGAGAAGCCGGGGATTTCC	0.418													C|||	1756	0.350639	0.2602	0.2939	5008	,	,		16262	0.3562		0.3111	False		,,,				2504	0.5481				p.P152P		Atlas-SNP	.											.	TMX4	39	.	0			c.G456A						PASS	.	C		1202,3204	414.1+/-336.7	160,882,1161	45.0	47.0	46.0		456	-11.5	0.2	20	dbSNP_86	46	2524,6076	411.6+/-350.5	359,1806,2135	no	coding-synonymous	TMX4	NM_021156.2		519,2688,3296	TT,TC,CC		29.3488,27.281,28.6483		152/350	7980390	3726,9280	2203	4300	6503	SO:0001819	synonymous_variant	56255	exon4			AGAAGCCGGGGAT		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.456G>A	20.37:g.7980390C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Silent	SNP	ENST00000246024.2	37	CCDS13101.1																																																																																			C|0.691;T|0.308	0.308	strong		0.418	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
NUDT5	11164	hgsc.bcm.edu	37	10	12209752	12209752	+	Silent	SNP	T	T	C	rs6686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:12209752T>C	ENST00000491614.1	-	10	1004	c.609A>G	c.(607-609)gcA>gcG	p.A203A	SEC61A2_ENST00000495368.1_3'UTR|NUDT5_ENST00000537776.1_Silent_p.A203A|NUDT5_ENST00000378937.3_Silent_p.A216A|SEC61A2_ENST00000304267.8_Intron|NUDT5_ENST00000378952.3_5'UTR			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	203					D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				CATGTTTCAGTGCTAGAGCGT	0.448													C|||	2315	0.46226	0.4251	0.5245	5008	,	,		20633	0.5575		0.4821	False		,,,				2504	0.3497				p.A203A		Atlas-SNP	.											.	NUDT5	10	.	0			c.A609G						PASS	.	C	,	1985,2421	615.9+/-392.7	459,1067,677	163.0	148.0	153.0		,609	-10.3	0.0	10	dbSNP_52	153	4282,4318	578.9+/-390.8	1067,2148,1085	no	intron,coding-synonymous	NUDT5,SEC61A2	NM_001142627.1,NM_014142.2	,	1526,3215,1762	CC,CT,TT		49.7907,45.0522,48.1855	,	,203/220	12209752	6267,6739	2203	4300	6503	SO:0001819	synonymous_variant	11164	exon10			TTTCAGTGCTAGA	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"""Nudix motif containing"""	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.609A>G	10.37:g.12209752T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	42	0.617647	NM_014142	A8K516|Q6IAG0|Q9UH49	Silent	SNP	ENST00000491614.1	37	CCDS7089.1																																																																																			T|0.523;C|0.477	0.477	strong		0.448	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1		
CS	1431	hgsc.bcm.edu	37	12	56669799	56669799	+	Silent	SNP	G	G	A	rs61738833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56669799G>A	ENST00000351328.3	-	7	959	c.769C>T	c.(769-771)Ctg>Ttg	p.L257L	CS_ENST00000542324.2_Silent_p.L244L|CS_ENST00000548567.1_Silent_p.L191L	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	257					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)		GTGAGGTACAGGCGCGTGAGC	0.478													G|||	28	0.00559105	0.0008	0.0101	5008	,	,		20736	0.0		0.0189	False		,,,				2504	0.001				p.L257L		Atlas-SNP	.											.	CS	44	.	0			c.C769T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	136.0	117.0	123.0		769	1.7	1.0	12	dbSNP_129	123	120,8480	62.4+/-124.4	2,116,4182	no	coding-synonymous	CS	NM_004077.2		2,127,6374	AA,AG,GG		1.3953,0.2497,1.0072		257/467	56669799	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	1431	exon7			GGTACAGGCGCGT		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.769C>T	12.37:g.56669799G>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	215	104	0.483721	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Silent	SNP	ENST00000351328.3	37	CCDS8913.1																																																																																			G|0.991;A|0.009	0.009	strong		0.478	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
SLC31A2	1318	hgsc.bcm.edu	37	9	115925104	115925104	+	Silent	SNP	C	C	T	rs3810906	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115925104C>T	ENST00000259392.3	+	4	472	c.339C>T	c.(337-339)gcC>gcT	p.A113A		NM_001860.2	NP_001851.1	O15432	COPT2_HUMAN	solute carrier family 31 (copper transporter), member 2	113					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|regulation of copper ion transmembrane transport (GO:1902311)	integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|recycling endosome (GO:0055037)	copper ion transmembrane transporter activity (GO:0005375)	p.A113A(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	7					Carboplatin(DB00958)|Cisplatin(DB00515)	TCATGCTGGCCGTAATGTCCT	0.483													C|||	1560	0.311502	0.2103	0.3919	5008	,	,		18268	0.4067		0.2465	False		,,,				2504	0.3599				p.A113A		Atlas-SNP	.											SLC31A2,NS,carcinoma,0,1	SLC31A2	11	1	1	Substitution - coding silent(1)	stomach(1)	c.C339T						PASS	.	C		903,3159		112,679,1240	287.0	280.0	283.0		339	-3.8	0.2	9	dbSNP_107	283	2113,6263		273,1567,2348	no	coding-synonymous	SLC31A2	NM_001860.2		385,2246,3588	TT,TC,CC		25.2268,22.2304,24.2483		113/144	115925104	3016,9422	2031	4188	6219	SO:0001819	synonymous_variant	1318	exon4			GCTGGCCGTAATG		CCDS6788.1	9q32	2013-07-17	2013-07-17		ENSG00000136867	ENSG00000136867		"""Solute carriers"""	11017	protein-coding gene	gene with protein product	"""copper transporter 2"""	603088		COPT2		9207117	Standard	NM_001860		Approved	hCTR2, CTR2	uc004bgq.3	O15432	OTTHUMG00000021037	ENST00000259392.3:c.339C>T	9.37:g.115925104C>T		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	237	121	0.510549	NM_001860		Silent	SNP	ENST00000259392.3	37	CCDS6788.1																																																																																			C|0.696;T|0.304	0.304	strong		0.483	SLC31A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055509.2	NM_001860	
TBC1D31	93594	hgsc.bcm.edu	37	8	124154697	124154697	+	Splice_Site	SNP	G	G	T	rs10101626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124154697G>T	ENST00000287380.1	+	19	2925		c.e19+1		TBC1D31_ENST00000309336.3_Intron|TBC1D31_ENST00000522420.1_Splice_Site|TBC1D31_ENST00000327098.5_Intron|TBC1D31_ENST00000521676.1_Splice_Site|TBC1D31_ENST00000518805.1_Splice_Site|TBC1D31_ENST00000378080.2_Intron	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31							centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										AGCCAAGAAGGTAAAAAATAG	0.323													G|||	1026	0.204872	0.2534	0.1614	5008	,	,		16505	0.1825		0.1948	False		,,,				2504	0.2035				.		Atlas-SNP	.											.	WDR67	97	.	0			c.2835+1G>T						PASS	.						36.0	37.0	37.0					8																	124154697		2202	4299	6501	SO:0001630	splice_region_variant	93594	exon19			AAGAAGGTAAAAA	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.2835+1G>T	8.37:g.124154697G>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_145647	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Splice_Site	SNP	ENST00000287380.1	37	CCDS6338.1	458	0.2097069597069597	130	0.26422764227642276	51	0.1408839779005525	128	0.22377622377622378	149	0.19656992084432717	G	11.00	1.509071	0.27036	.	.	ENSG00000156787	ENST00000287380;ENST00000522420;ENST00000521676;ENST00000518805	.	.	.	5.36	5.36	0.76844	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8646	0.88792	0.0:0.0:1.0:0.0	rs10101626;rs17375320;rs57669972;rs10101626	.	.	.	.	-1	.	.	.	+	.	.	WDR67	124223878	1.000000	0.71417	0.997000	0.53966	0.092000	0.18411	6.243000	0.72384	2.529000	0.85273	0.471000	0.43371	.	G|0.784;T|0.216	0.216	strong		0.323	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	Intron
OR7G3	390883	hgsc.bcm.edu	37	19	9236886	9236886	+	Silent	SNP	A	A	G	rs10424352|rs386806662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9236886A>G	ENST00000305444.2	-	1	740	c.741T>C	c.(739-741)gtT>gtC	p.V247V		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	247						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						ACAAGGAAACAACGATTAAAT	0.443													G|||	2120	0.423323	0.7095	0.245	5008	,	,		20673	0.3651		0.3141	False		,,,				2504	0.3354				p.V247V		Atlas-SNP	.											OR7G3,NS,adenocarcinoma,-1,1	OR7G3	41	1	0			c.T741C						scavenged	.	G		2859,1547	486.5+/-360.6	939,981,283	103.0	101.0	101.0		741	-5.8	0.0	19	dbSNP_119	101	2673,5927	685.0+/-404.0	386,1901,2013	no	coding-synonymous	OR7G3	NM_001001958.1		1325,2882,2296	GG,GA,AA		31.0814,35.1112,42.5342		247/313	9236886	5532,7474	2203	4300	6503	SO:0001819	synonymous_variant	390883	exon1			GGAAACAACGATT		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"""GPCR / Class A : Olfactory receptors"""	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.741T>C	19.37:g.9236886A>G		Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	134	49	0.365672	NM_001001958	Q6IFJ6|Q96R99	Silent	SNP	ENST00000305444.2	37	CCDS32899.1																																																																																			A|0.585;G|0.415	0.415	strong		0.443	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1		
HGFAC	3083	hgsc.bcm.edu	37	4	3449652	3449652	+	Missense_Mutation	SNP	G	G	A	rs16844401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3449652G>A	ENST00000382774.3	+	12	1641	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H	HGFAC_ENST00000511533.1_Missense_Mutation_p.R516H	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	509	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> H (in dbSNP:rs16844401).		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)		AAAGGGGACCGCTGTGCCACA	0.667													G|||	372	0.0742812	0.0219	0.085	5008	,	,		17199	0.0873		0.0696	False		,,,				2504	0.1288				p.R509H		Atlas-SNP	.											.	HGFAC	69	.	0			c.G1526A						PASS	.	G	HIS/ARG	123,4273	85.3+/-124.0	4,115,2079	28.0	27.0	27.0		1526	4.0	1.0	4	dbSNP_123	27	587,8005	150.3+/-205.2	16,555,3725	yes	missense	HGFAC	NM_001528.2	29	20,670,5804	AA,AG,GG		6.8319,2.798,5.4666	benign	509/656	3449652	710,12278	2198	4296	6494	SO:0001583	missense	3083	exon12			GGGACCGCTGTGC	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.1526G>A	4.37:g.3449652G>A	ENSP00000372224:p.Arg509His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_001528	Q14726|Q2M1W7|Q53X47	Missense_Mutation	SNP	ENST00000382774.3	37	CCDS3369.1	158	0.07234432234432235	18	0.036585365853658534	30	0.08287292817679558	60	0.1048951048951049	50	0.06596306068601583	G	13.39	2.223930	0.39300	0.02798	0.068319	ENSG00000109758	ENST00000382774;ENST00000511533	D;D	0.89415	-2.51;-2.48	4.02	4.02	0.46733	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.144148	0.47852	D	0.000204	T	0.09905	0.0243	N	0.15975	0.35	0.09310	P	0.9999999450782	P;B	0.51240	0.943;0.1	B;B	0.39299	0.296;0.011	T	0.64317	-0.6436	9	0.34782	T	0.22	.	14.8854	0.70564	0.0:0.0:1.0:0.0	rs16844401;rs61487417;rs16844401	516;509	D6RAR4;Q04756	.;HGFA_HUMAN	H	509;516	ENSP00000372224:R509H;ENSP00000421801:R516H	ENSP00000372224:R509H	R	+	2	0	HGFAC	3419450	0.593000	0.26840	1.000000	0.80357	0.683000	0.39861	2.662000	0.46766	2.070000	0.61991	0.563000	0.77884	CGC	G|0.935;A|0.065	0.065	strong		0.667	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
ANKRD6	22881	hgsc.bcm.edu	37	6	90338863	90338863	+	Silent	SNP	C	C	T	rs9353687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90338863C>T	ENST00000522441.1	+	15	2159	c.1518C>T	c.(1516-1518)tgC>tgT	p.C506C	ANKRD6_ENST00000369408.5_Silent_p.C471C|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000447838.2_Silent_p.C506C|ANKRD6_ENST00000520793.1_Silent_p.C447C|ANKRD6_ENST00000339746.4_Silent_p.C506C	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	506					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		AAACCTGGTGCATGTTAAAGA	0.378													C|||	841	0.167931	0.1876	0.1398	5008	,	,		18179	0.2222		0.1809	False		,,,				2504	0.092				p.C506C		Atlas-SNP	.											.	ANKRD6	51	.	0			c.C1518T						PASS	.	C	,,,,	705,2943		73,559,1192	82.0	81.0	81.0		1518,1518,1413,1341,1518	4.0	1.0	6	dbSNP_119	81	1461,6697		132,1197,2750	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANKRD6	NM_001242809.1,NM_001242811.1,NM_001242813.1,NM_001242814.1,NM_014942.4	,,,,	205,1756,3942	TT,TC,CC		17.9088,19.3257,18.3466	,,,,	506/728,506/728,471/693,447/664,506/723	90338863	2166,9640	1824	4079	5903	SO:0001819	synonymous_variant	22881	exon15			CTGGTGCATGTTA	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1518C>T	6.37:g.90338863C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	45	44	0.977778	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	37	CCDS56441.1	419	0.19184981684981686	99	0.20121951219512196	46	0.1270718232044199	131	0.229020979020979	143	0.18865435356200527	C	9.377	1.071923	0.20147	0.193257	0.179088	ENSG00000135299	ENST00000492158	.	.	.	6.07	3.97	0.46021	.	.	.	.	.	T	0.53222	0.1783	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.56245	-0.8011	3	.	.	.	-6.6477	14.3358	0.66589	0.0:0.8596:0.0:0.1404	rs9353687	.	.	.	Y	80	.	.	H	+	1	0	ANKRD6	90395584	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.526000	0.45607	1.550000	0.49438	0.655000	0.94253	CAT	C|0.815;T|0.185	0.185	strong		0.378	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
ZNF354A	6940	hgsc.bcm.edu	37	5	178140090	178140090	+	Silent	SNP	C	C	T	rs1132336	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:178140090C>T	ENST00000335815.2	-	5	986	c.789G>A	c.(787-789)acG>acA	p.T263T		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	263					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T263T(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		CTCCAGTATGCGTTATTTGAT	0.353													C|||	1318	0.263179	0.09	0.2464	5008	,	,		19499	0.3333		0.2813	False		,,,				2504	0.4182				p.T263T		Atlas-SNP	.											ZNF354A,NS,carcinoma,0,1	ZNF354A	74	1	1	Substitution - coding silent(1)	stomach(1)	c.G789A						scavenged	.	C		570,3836	251.5+/-258.2	38,494,1671	98.0	98.0	98.0		789	-5.9	0.9	5	dbSNP_86	98	2355,6245	392.0+/-343.8	322,1711,2267	no	coding-synonymous	ZNF354A	NM_005649.2		360,2205,3938	TT,TC,CC		27.3837,12.9369,22.4896		263/606	178140090	2925,10081	2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			AGTATGCGTTATT	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.789G>A	5.37:g.178140090C>T		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			C|0.762;T|0.238	0.238	strong		0.353	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
GPR61	83873	hgsc.bcm.edu	37	1	110086451	110086451	+	Silent	SNP	G	G	A	rs17575798	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110086451G>A	ENST00000527748.1	+	2	1490	c.807G>A	c.(805-807)tcG>tcA	p.S269S	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		TCACCAGCTCGGGGGCCCCCC	0.672													G|||	1086	0.216853	0.1142	0.1441	5008	,	,		15644	0.3621		0.171	False		,,,				2504	0.3047				p.S269S		Atlas-SNP	.											.	GPR61	60	.	0			c.G807A						PASS	.	G		519,3885		22,475,1705	36.0	43.0	41.0		807	-5.2	0.9	1	dbSNP_123	41	1694,6906		187,1320,2793	no	coding-synonymous	GPR61	NM_031936.4		209,1795,4498	AA,AG,GG		19.6977,11.7847,17.0178		269/452	110086451	2213,10791	2202	4300	6502	SO:0001819	synonymous_variant	83873	exon2			CAGCTCGGGGGCC	AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"""GPCR / Class A : Orphans"""	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.807G>A	1.37:g.110086451G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_031936	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Silent	SNP	ENST00000527748.1	37	CCDS801.1																																																																																			G|0.805;A|0.195	0.195	strong		0.672	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1		
INTS3	65123	hgsc.bcm.edu	37	1	153737498	153737498	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153737498G>T	ENST00000318967.2	+	20	2617	c.2049G>T	c.(2047-2049)caG>caT	p.Q683H	INTS3_ENST00000512605.1_Missense_Mutation_p.Q477H|INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000435409.2_Missense_Mutation_p.Q683H|INTS3_ENST00000456435.1_Missense_Mutation_p.Q477H	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	684					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ATCAGAAGCAGCCCAAGATTG	0.532																																					p.Q683H		Atlas-SNP	.											.	INTS3	83	.	0			c.G2049T						PASS	.						233.0	222.0	226.0					1																	153737498		2203	4300	6503	SO:0001583	missense	65123	exon20			GAAGCAGCCCAAG	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2049G>T	1.37:g.153737498G>T	ENSP00000318641:p.Gln683His	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	31	0.295238	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887087	0.52014	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	4.91	1.99	0.26369	.	0.000000	0.85682	D	0.000000	T	0.57770	0.2076	M	0.64404	1.975	0.42968	D	0.994425	D;D;D	0.64830	0.994;0.98;0.988	D;D;D	0.78314	0.991;0.948;0.977	T	0.59925	-0.7362	9	0.62326	D	0.03	.	7.1424	0.25564	0.2806:0.0:0.7194:0.0	.	477;684;683	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	H	683;477;683;477	.	ENSP00000318641:Q683H	Q	+	3	2	INTS3	152004122	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.298000	0.43602	0.258000	0.21686	0.563000	0.77884	CAG	.	.	none		0.532	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
PLCB1	23236	hgsc.bcm.edu	37	20	8770822	8770822	+	Splice_Site	SNP	C	C	T	rs2294597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:8770822C>T	ENST00000338037.6	+	31	3364	c.3337C>T	c.(3337-3339)Cta>Tta	p.L1113L	PLCB1_ENST00000378637.2_Splice_Site_p.L1113L|PLCB1_ENST00000378641.3_Splice_Site_p.L1113L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	1113					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						TTTCTTATAGCTAGAAGAAGC	0.368													C|||	1145	0.228634	0.1263	0.2219	5008	,	,		19106	0.1329		0.3022	False		,,,				2504	0.3947				p.G1113X		Atlas-SNP	.											.	PLCB1	394	.	0			c.G3337T						PASS	.	C	,	622,3784	259.2+/-262.9	54,514,1635	47.0	47.0	47.0		3337,3337	3.3	1.0	20	dbSNP_100	47	2673,5927	408.4+/-349.5	451,1771,2078	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PLCB1	NM_015192.2,NM_182734.1	,	505,2285,3713	TT,TC,CC		31.0814,14.1171,25.3345	,	1113/1217,1113/1174	8770822	3295,9711	2203	4300	6503	SO:0001630	splice_region_variant	23236	exon31			TTATAGCTAGAAG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.3337-1C>T	20.37:g.8770822C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_182734	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Nonsense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			C|0.774;T|0.226	0.226	strong		0.368	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Silent
DAAM1	23002	hgsc.bcm.edu	37	14	59789727	59789727	+	Silent	SNP	G	G	A	rs8022614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:59789727G>A	ENST00000395125.1	+	5	581	c.558G>A	c.(556-558)aaG>aaA	p.K186K	DAAM1_ENST00000360909.3_Silent_p.K186K|DAAM1_ENST00000351081.1_Silent_p.K186K	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	186	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		GCTGTATAAAGGCGTTAATGA	0.438													G|||	1685	0.336462	0.0787	0.2406	5008	,	,		20067	0.5883		0.3936	False		,,,				2504	0.4346				p.K186K		Atlas-SNP	.											.	DAAM1	95	.	0			c.G558A						PASS	.	G		526,3880	230.7+/-244.8	38,450,1715	109.0	101.0	104.0		558	3.9	1.0	14	dbSNP_116	104	3354,5246	490.0+/-372.8	668,2018,1614	no	coding-synonymous	DAAM1	NM_014992.1		706,2468,3329	AA,AG,GG		39.0,11.9383,29.8324		186/1079	59789727	3880,9126	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon6			TATAAAGGCGTTA	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.558G>A	14.37:g.59789727G>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.684;A|0.316	0.316	strong		0.438	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
HUNK	30811	hgsc.bcm.edu	37	21	33370900	33370900	+	Silent	SNP	T	T	C	rs9305483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33370900T>C	ENST00000270112.2	+	11	1908	c.1548T>C	c.(1546-1548)tcT>tcC	p.S516S		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	516					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						TGGCTTCTTCTTCCATGGAGT	0.547													T|||	3179	0.634784	0.5673	0.6383	5008	,	,		17804	0.6488		0.6173	False		,,,				2504	0.727				p.S516S		Atlas-SNP	.											.	HUNK	74	.	0			c.T1548C						PASS	.	T		2559,1847	635.3+/-396.4	750,1059,394	116.0	109.0	111.0		1548	-0.7	1.0	21	dbSNP_119	111	5481,3119	657.6+/-401.5	1771,1939,590	no	coding-synonymous	HUNK	NM_014586.1		2521,2998,984	CC,CT,TT		36.2674,41.9201,38.1824		516/715	33370900	8040,4966	2203	4300	6503	SO:0001819	synonymous_variant	30811	exon11			TTCTTCTTCCATG	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"""hormonally upregulated Neu-associated kinase"""			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1548T>C	21.37:g.33370900T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_014586		Silent	SNP	ENST00000270112.2	37	CCDS13610.1																																																																																			T|0.382;C|0.618	0.618	strong		0.547	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
EMR2	30817	hgsc.bcm.edu	37	19	14875388	14875388	+	Missense_Mutation	SNP	G	G	A	rs35612307	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14875388G>A	ENST00000315576.3	-	11	1392	c.941C>T	c.(940-942)gCc>gTc	p.A314V	EMR2_ENST00000595839.1_Missense_Mutation_p.A172V|EMR2_ENST00000596991.2_Missense_Mutation_p.A314V|EMR2_ENST00000353005.1_Missense_Mutation_p.A172V|EMR2_ENST00000392965.3_Missense_Mutation_p.A314V|EMR2_ENST00000392967.2_Missense_Mutation_p.A314V|EMR2_ENST00000392964.3_Missense_Mutation_p.A53V|EMR2_ENST00000594076.1_Missense_Mutation_p.A221V|EMR2_ENST00000346057.1_Missense_Mutation_p.A265V|EMR2_ENST00000353876.1_Missense_Mutation_p.A221V|EMR2_ENST00000594294.1_Missense_Mutation_p.A265V|EMR2_ENST00000601345.1_Missense_Mutation_p.A314V	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	314			A -> V (in dbSNP:rs35612307).		cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						GTCCCCAGGGGCCTCCAGCAG	0.622													G|||	951	0.189896	0.0946	0.3458	5008	,	,		15749	0.1667		0.2813	False		,,,				2504	0.138				p.A314V		Atlas-SNP	.											.	EMR2	99	.	0			c.C941T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	517,3887	233.9+/-246.9	37,443,1722	39.0	37.0	38.0		941,794,662,515,941,794,662	-3.3	0.0	19	dbSNP_126	38	2549,6049	406.2+/-348.7	385,1779,2135	yes	missense,missense,missense,missense,missense,missense,missense	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	64,64,64,64,64,64,64	422,2222,3857	AA,AG,GG		29.6464,11.7393,23.581	benign,benign,benign,benign,benign,benign,benign	314/824,265/775,221/731,172/682,314/813,265/764,221/720	14875388	3066,9936	2202	4299	6501	SO:0001583	missense	30817	exon10			CCAGGGGCCTCCA	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.941C>T	19.37:g.14875388G>A	ENSP00000319883:p.Ala314Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_001271052	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	508	0.2326007326007326	54	0.10975609756097561	125	0.3453038674033149	124	0.21678321678321677	205	0.2704485488126649	G	14.59	2.579958	0.46006	0.117393	0.296464	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965;ENST00000392964;ENST00000392962	T;T;T;T;T;T;T;T	0.78707	-0.91;-1.05;-0.44;0.35;1.1;-1.2;1.48;-1.09	3.77	-3.32	0.04973	.	.	.	.	.	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	B;B;B;B;B;B	0.30763	0.294;0.08;0.004;0.027;0.016;0.171	B;B;B;B;B;B	0.28011	0.057;0.027;0.002;0.037;0.01;0.085	T	0.11155	-1.0599	8	0.38643	T	0.18	.	2.2231	0.03977	0.1072:0.1584:0.2526:0.4818	rs35612307;rs62122625	314;221;172;265;314;314	E7ESD7;Q9UHX3-4;Q9UHX3-5;Q9UHX3-3;Q9UHX3;Q9UHX3-2	.;.;.;.;EMR2_HUMAN;.	V	314;314;265;221;172;314;53;265	ENSP00000319883:A314V;ENSP00000376694:A314V;ENSP00000263380:A265V;ENSP00000319454:A221V;ENSP00000319838:A172V;ENSP00000376692:A314V;ENSP00000376691:A53V;ENSP00000376689:A265V	ENSP00000319883:A314V	A	-	2	0	EMR2	14736388	0.000000	0.05858	0.000000	0.03702	0.472000	0.32918	-0.787000	0.04618	-0.240000	0.09696	0.508000	0.49915	GCC	G|0.765;A|0.235	0.235	strong		0.622	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
ZNF45	7596	hgsc.bcm.edu	37	19	44418077	44418077	+	Missense_Mutation	SNP	C	C	T	rs407731	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44418077C>T	ENST00000269973.5	-	10	2601	c.1511G>A	c.(1510-1512)aGg>aAg	p.R504K	ZNF45_ENST00000589703.1_Missense_Mutation_p.R504K|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	504			R -> K (in dbSNP:rs407731). {ECO:0000269|PubMed:15057824}.		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						CTTACCACACCTCTCGCATTT	0.493													T|||	2630	0.52516	0.3336	0.6484	5008	,	,		20800	0.7996		0.5169	False		,,,				2504	0.4223				p.R504K		Atlas-SNP	.											.	ZNF45	51	.	0			c.G1511A						PASS	.	T	LYS/ARG	1581,2825	666.0+/-401.6	294,993,916	62.0	58.0	60.0		1511	2.6	1.0	19	dbSNP_80	60	4351,4249	573.4+/-389.9	1117,2117,1066	yes	missense	ZNF45	NM_003425.3	26	1411,3110,1982	TT,TC,CC		49.407,35.8829,45.6097	benign	504/683	44418077	5932,7074	2203	4300	6503	SO:0001583	missense	7596	exon10			CCACACCTCTCGC	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.1511G>A	19.37:g.44418077C>T	ENSP00000269973:p.Arg504Lys	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	1254|1254	0.5741758241758241|0.5741758241758241	187|187	0.3800813008130081|0.3800813008130081	208|208	0.574585635359116|0.574585635359116	470|470	0.8216783216783217|0.8216783216783217	389|389	0.5131926121372031|0.5131926121372031	T|T	5.190|5.190	0.220623|0.220623	0.09863|0.09863	0.358829|0.358829	0.50593|0.50593	ENSG00000124459|ENSG00000124459	ENST00000328762|ENST00000269973	.|T	.|0.07327	.|3.2	3.61|3.61	2.56|2.56	0.30785|0.30785	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.200214	.|0.24801	.|N	.|0.035499	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01679|0.01679	-0.765|-0.765	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.06338|0.06338	-1.0832|-1.0832	5|9	0.59425|0.46703	D|T	0.04|0.11	-11.4279|-11.4279	5.9628|5.9628	0.19308|0.19308	0.0:0.0945:0.1643:0.7412|0.0:0.0945:0.1643:0.7412	rs407731;rs17712947;rs407731|rs407731;rs17712947;rs407731	.|504	.|Q02386	.|ZNF45_HUMAN	S|K	504|504	.|ENSP00000269973:R504K	ENSP00000367176:G504S|ENSP00000269973:R504K	G|R	-|-	1|2	0|0	ZNF45|ZNF45	49109917|49109917	0.000000|0.000000	0.05858|0.05858	0.997000|0.997000	0.53966|0.53966	0.974000|0.974000	0.67602|0.67602	0.794000|0.794000	0.26958|0.26958	0.096000|0.096000	0.17463|0.17463	-0.556000|-0.556000	0.04195|0.04195	GGT|AGG	C|0.480;T|0.520	0.520	strong		0.493	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
OR4C16	219428	hgsc.bcm.edu	37	11	55339652	55339652	+	Nonsense_Mutation	SNP	C	C	T	rs1459101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55339652C>T	ENST00000314634.3	+	1	49	c.49C>T	c.(49-51)Cag>Tag	p.Q17*		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				TGGATTGACACAGGATCCTTT	0.388													c|||	1265	0.252596	0.1014	0.3242	5008	,	,		18829	0.3909		0.2843	False		,,,				2504	0.2311				p.Q17X		Atlas-SNP	.											OR4C16,NS,carcinoma,-2,1	OR4C16	104	1	0			c.C49T						PASS	.	C	stop/GLN	561,3841	252.1+/-258.6	27,507,1667	132.0	122.0	125.0		49	0.8	0.0	11	dbSNP_88	125	2290,6302	386.3+/-341.8	329,1632,2335	yes	stop-gained	OR4C16	NM_001004701.2		356,2139,4002	TT,TC,CC		26.6527,12.7442,21.9409		17/311	55339652	2851,10143	2201	4296	6497	SO:0001587	stop_gained	219428	exon1			TTGACACAGGATC	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.49C>T	11.37:g.55339652C>T	ENSP00000324913:p.Gln17*	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	141	75	0.531915	NM_001004701	Q6IEV8	Nonsense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	605	0.27701465201465203	47	0.09552845528455285	126	0.34806629834254144	214	0.3741258741258741	218	0.287598944591029	C	15.62	2.886232	0.51908	0.127442	0.266527	ENSG00000181935	ENST00000314634	.	.	.	4.98	0.756	0.18421	.	0.325431	0.26677	N	0.023065	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	5.4911	0.16777	0.0:0.5122:0.3092:0.1786	rs1459101;rs52825307;rs60632881;rs1459101	.	.	.	X	17	.	ENSP00000324913:Q17X	Q	+	1	0	OR4C16	55096228	0.000000	0.05858	0.017000	0.16124	0.810000	0.45777	-1.242000	0.02908	0.253000	0.21552	0.549000	0.68633	CAG	C|0.759;T|0.241	0.241	strong		0.388	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
NOC3L	64318	hgsc.bcm.edu	37	10	96098373	96098373	+	Missense_Mutation	SNP	C	C	T	rs17517578	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:96098373C>T	ENST00000371361.3	-	18	2183	c.2083G>A	c.(2083-2085)Gct>Act	p.A695T	NOC3L_ENST00000543788.1_Missense_Mutation_p.A433T|NOC3L_ENST00000371350.1_Missense_Mutation_p.A695T	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	695			A -> T (in dbSNP:rs17517578).		fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				ACCCGCAGAGCATGCAGTTCC	0.438													C|||	553	0.110423	0.1059	0.111	5008	,	,		16705	0.003		0.1839	False		,,,				2504	0.1513				p.A695T		Atlas-SNP	.											.	NOC3L	67	.	0			c.G2083A						PASS	.	C	THR/ALA	493,3913	230.7+/-244.8	24,445,1734	100.0	98.0	99.0		2083	3.8	0.2	10	dbSNP_123	99	1376,7224	267.6+/-287.4	103,1170,3027	yes	missense	NOC3L	NM_022451.9	58	127,1615,4761	TT,TC,CC		16.0,11.1893,14.3703	benign	695/801	96098373	1869,11137	2203	4300	6503	SO:0001583	missense	64318	exon18			GCAGAGCATGCAG	AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.2083G>A	10.37:g.96098373C>T	ENSP00000360412:p.Ala695Thr	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	187	91	0.486631	NM_022451	Q9H5M6|Q9H9D8	Missense_Mutation	SNP	ENST00000371361.3	37	CCDS7433.1	222	0.10164835164835165	45	0.09146341463414634	41	0.1132596685082873	1	0.0017482517482517483	135	0.17810026385224276	C	0.836	-0.743469	0.03088	0.111893	0.16	ENSG00000173145	ENST00000543788;ENST00000371361;ENST00000371350	T;T;T	0.21734	1.99;1.99;1.99	5.63	3.77	0.43336	CCAAT-binding factor (1);	0.744226	0.13218	N	0.404571	T	0.00039	0.0001	N	0.20574	0.59	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.34477	-0.9827	9	0.25751	T	0.34	-1.7679	3.1464	0.06473	0.123:0.5555:0.1192:0.2023	rs17517578;rs52814170;rs17517578	695	Q8WTT2	NOC3L_HUMAN	T	433;695;695	ENSP00000437838:A433T;ENSP00000360412:A695T;ENSP00000360401:A695T	ENSP00000360401:A695T	A	-	1	0	NOC3L	96088363	0.004000	0.15560	0.176000	0.23000	0.002000	0.02628	0.359000	0.20233	0.844000	0.35094	-0.136000	0.14681	GCT	C|0.868;T|0.132	0.132	strong		0.438	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1	NM_022451	
RNF8	9025	hgsc.bcm.edu	37	6	37349033	37349033	+	Silent	SNP	G	G	A	rs2284922	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:37349033G>A	ENST00000373479.4	+	7	1537	c.1344G>A	c.(1342-1344)acG>acA	p.T448T	RNF8_ENST00000469731.1_Intron	NM_003958.3|NM_183078.2	NP_003949.1|NP_898901.1	O76064	RNF8_HUMAN	ring finger protein 8, E3 ubiquitin protein ligase	448					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|histone exchange (GO:0043486)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A ubiquitination (GO:0033522)|histone H2B ubiquitination (GO:0033523)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|mitotic nuclear division (GO:0007067)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|response to ionizing radiation (GO:0010212)|spermatid development (GO:0007286)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromosome, telomeric region (GO:0000781)|nucleolus (GO:0005730)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	13						AGTCCAAAACGTACTCTTTGG	0.413													A|||	2806	0.560304	0.5582	0.549	5008	,	,		22516	0.7361		0.3588	False		,,,				2504	0.5971				p.T448T		Atlas-SNP	.											RNF8,NS,carcinoma,+1,1	RNF8	78	1	0			c.G1344A						PASS	.	A	,	2285,2121	577.4+/-384.4	573,1139,491	145.0	126.0	132.0		1344,	-3.5	0.3	6	dbSNP_100	132	2973,5627	666.1+/-402.3	544,1885,1871	no	coding-synonymous,intron	RNF8	NM_003958.3,NM_183078.2	,	1117,3024,2362	AA,AG,GG		34.5698,48.1389,40.4275	,	448/486,	37349033	5258,7748	2203	4300	6503	SO:0001819	synonymous_variant	9025	exon7			CAAAACGTACTCT	AB012770	CCDS4833.1, CCDS4834.1	6p21.3	2013-01-09	2012-02-23		ENSG00000112130	ENSG00000112130		"""RING-type (C3HC4) zinc fingers"""	10071	protein-coding gene	gene with protein product		611685	"""ring finger protein (C3HC4 type) 8"", ""ring finger protein 8"""			9734811, 9852682	Standard	NM_003958		Approved	KIAA0646	uc003onq.4	O76064	OTTHUMG00000014620	ENST00000373479.4:c.1344G>A	6.37:g.37349033G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_003958	A6NN24|A8MYC0|B4DPG0|Q53H16|Q5NKW5	Silent	SNP	ENST00000373479.4	37	CCDS4834.1																																																																																			G|0.535;A|0.465	0.465	strong		0.413	RNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040403.2		
RNASEH1	246243	hgsc.bcm.edu	37	2	3597974	3597974	+	Silent	SNP	T	T	C	rs10186193	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:3597974T>C	ENST00000315212.3	-	4	853	c.498A>G	c.(496-498)ccA>ccG	p.P166P	RP13-512J5.1_ENST00000438485.1_5'Flank	NM_002936.3	NP_002927.2	O60930	RNH1_HUMAN	ribonuclease H1	166	RNase H. {ECO:0000255|PROSITE- ProRule:PRU00408}.				mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|lung(7)|ovary(1)|prostate(2)|skin(1)	13	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)			OV - Ovarian serous cystadenocarcinoma(76;0.0713)|Epithelial(75;0.167)|all cancers(51;0.22)		AAGGATGGCCTGGCCCCCAGT	0.498													C|||	1881	0.375599	0.6233	0.2305	5008	,	,		17040	0.2371		0.3479	False		,,,				2504	0.3149				p.P166P		Atlas-SNP	.											.	RNASEH1	27	.	0			c.A498G						PASS	.	C		2631,1775	521.1+/-370.4	820,991,392	110.0	124.0	119.0		498	-10.9	0.1	2	dbSNP_119	119	3150,5450	652.1+/-400.9	596,1958,1746	yes	coding-synonymous	RNASEH1	NM_002936.3		1416,2949,2138	CC,CT,TT		36.6279,40.286,44.4487		166/287	3597974	5781,7225	2203	4300	6503	SO:0001819	synonymous_variant	246243	exon4			ATGGCCTGGCCCC	AF039652	CCDS1647.1	2p25	2008-03-11			ENSG00000171865	ENSG00000171865	3.1.26.-		18466	protein-coding gene	gene with protein product	"""RNase H1"""	604123				12036296, 17964265	Standard	XR_244873		Approved		uc002qxt.3	O60930	OTTHUMG00000090279	ENST00000315212.3:c.498A>G	2.37:g.3597974T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_002936	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Silent	SNP	ENST00000315212.3	37	CCDS1647.1																																																																																			T|0.579;C|0.421	0.421	strong		0.498	RNASEH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206605.2		
USH2A	7399	hgsc.bcm.edu	37	1	215848641	215848641	+	Silent	SNP	T	T	C	rs2797235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:215848641T>C	ENST00000307340.3	-	63	12998	c.12612A>G	c.(12610-12612)acA>acG	p.T4204T	USH2A_ENST00000366943.2_Silent_p.T4204T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4204	Fibronectin type-III 27. {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)	p.T4204T(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CGGCCTGGATTGTCTGATTTC	0.413										HNSCC(13;0.011)			T|||	3454	0.689696	0.6127	0.7954	5008	,	,		21060	0.6429		0.8091	False		,,,				2504	0.6442				p.T4204T		Atlas-SNP	.											USH2A,NS,carcinoma,0,1	USH2A	1168	1	1	Substitution - coding silent(1)	stomach(1)	c.A12612G						PASS	.	T		2812,1594	665.9+/-401.6	894,1024,285	124.0	123.0	123.0		12612	-2.0	0.1	1	dbSNP_100	123	7000,1600	742.9+/-407.2	2845,1310,145	no	coding-synonymous	USH2A	NM_206933.2		3739,2334,430	CC,CT,TT		18.6047,36.1779,24.5579		4204/5203	215848641	9812,3194	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon63			CTGGATTGTCTGA	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.12612A>G	1.37:g.215848641T>C		Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	154	154	1	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			T|0.265;C|0.735	0.735	strong		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
WDYHV1	55093	hgsc.bcm.edu	37	8	124448804	124448804	+	Missense_Mutation	SNP	T	T	A	rs6470147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124448804T>A	ENST00000287387.2	+	4	471	c.346T>A	c.(346-348)Ttt>Att	p.F116I	WDYHV1_ENST00000518125.1_Intron|WDYHV1_ENST00000523356.1_Missense_Mutation_p.F116I|WDYHV1_ENST00000517609.1_3'UTR|WDYHV1_ENST00000523984.1_Missense_Mutation_p.F56I	NM_018024.1	NP_060494.1	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	116			F -> I (in dbSNP:rs6470147). {ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)	p.F116I(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						AGAAGATGCCTTTAAGTCTGA	0.393													T|||	2054	0.410144	0.3427	0.3919	5008	,	,		20506	0.5863		0.3111	False		,,,				2504	0.4346				p.F116I		Atlas-SNP	.											WDYHV1,NS,carcinoma,0,1	WDYHV1	30	1	1	Substitution - Missense(1)	stomach(1)	c.T346A						PASS	.	T	ILE/PHE	1600,2806	495.1+/-363.2	293,1014,896	200.0	169.0	179.0		346	4.4	1.0	8	dbSNP_116	179	3029,5571	466.5+/-366.8	541,1947,1812	yes	missense	WDYHV1	NM_018024.1	21	834,2961,2708	AA,AT,TT		35.2209,36.3141,35.5913	benign	116/206	124448804	4629,8377	2203	4300	6503	SO:0001583	missense	55093	exon4			GATGCCTTTAAGT	AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795			25490	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 32"""	C8orf32		12477932	Standard	NM_018024		Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000287387.2:c.346T>A	8.37:g.124448804T>A	ENSP00000287387:p.Phe116Ile	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	197	196	0.994924	NM_018024	B4DE68|Q9NW95	Missense_Mutation	SNP	ENST00000287387.2	37	CCDS6344.1	841	0.3850732600732601	140	0.2845528455284553	136	0.3756906077348066	327	0.5716783216783217	238	0.31398416886543534	T	13.35	2.211562	0.39102	0.363141	0.352209	ENSG00000156795	ENST00000287387;ENST00000523984;ENST00000523356	T;T;T	0.16597	2.33;2.33;2.33	5.78	4.42	0.53409	Protein N-terminal glutamine amidohydrolase, alpha beta roll (1);Protein N-terminal glutamine amidohydrolase (1);	0.166512	0.53938	D	0.000047	T	0.00012	0.0000	L	0.49455	1.56	0.09310	P	0.9999999999999997	B	0.23854	0.092	B	0.23574	0.047	T	0.38520	-0.9657	9	0.48119	T	0.1	-15.6241	7.2021	0.25887	0.0:0.2173:0.0:0.7827	rs6470147;rs17850382;rs52812591;rs6470147	116	Q96HA8	NTAQ1_HUMAN	I	116;56;116	ENSP00000287387:F116I;ENSP00000430427:F56I;ENSP00000428615:F116I	ENSP00000287387:F116I	F	+	1	0	WDYHV1	124517985	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	3.135000	0.50546	0.810000	0.34279	0.533000	0.62120	TTT	T|0.626;A|0.374	0.374	strong		0.393	WDYHV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381772.1	NM_018024	
OR51B6	390058	hgsc.bcm.edu	37	11	5373104	5373104	+	Missense_Mutation	SNP	A	A	G	rs5006889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373104A>G	ENST00000380219.1	+	1	367	c.367A>G	c.(367-369)Acc>Gcc	p.T123A	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	123			T -> A (in dbSNP:rs5006889).	TIRS -> AIHN (in Ref. 1; AAG41682). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGTTTCATTACCATCCGCAG	0.483													G|||	1170	0.233626	0.326	0.2349	5008	,	,		22992	0.0863		0.2644	False		,,,				2504	0.228				p.T123A		Atlas-SNP	.											.	OR51B6	53	.	0			c.A367G						PASS	.	G	ALA/THR	1247,3155	699.6+/-406.5	173,901,1127	136.0	125.0	129.0		367	5.0	1.0	11	dbSNP_113	129	2238,6356	707.6+/-405.6	309,1620,2368	yes	missense	OR51B6	NM_001004750.1	58	482,2521,3495	GG,GA,AA		26.0414,28.328,26.8159	benign	123/313	5373104	3485,9511	2201	4297	6498	SO:0001583	missense	390058	exon1			TTCATTACCATCC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.367A>G	11.37:g.5373104A>G	ENSP00000369568:p.Thr123Ala	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	169	60	0.35503	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	G	0.018	-1.478016	0.01035	0.28328	0.260414	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.24723	1.84	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	N	0.000063	T	0.00012	0.0000	N	0.00001	-3.785	0.39348	P	0.03429300000000002	B	0.02656	0.0	B	0.01281	0.0	T	0.43637	-0.9379	9	0.02654	T	1	.	12.5381	0.56152	0.0813:0.0:0.9187:0.0	rs5006889;rs5006889	123	Q9H340	O51B6_HUMAN	A	122;123	ENSP00000369568:T123A	ENSP00000369568:T123A	T	+	1	0	OR51B6	5329680	1.000000	0.71417	1.000000	0.80357	0.008000	0.06430	5.415000	0.66411	1.352000	0.45808	-0.374000	0.07098	ACC	A|0.761;G|0.239	0.239	strong		0.483	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255503	25255503	+	Missense_Mutation	SNP	G	G	C	rs116889865		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:25255503G>C	ENST00000328086.7	-	6	2387	c.1584C>G	c.(1582-1584)agC>agG	p.S528R		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	528					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)		CATACAATTTGCTCTTCCGAT	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		18493	0.0		0.001	False		,,,				2504	0.0				p.S528R		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.C1584G						PASS	.	G	ARG/SER	3,4391	6.2+/-15.9	0,3,2194	68.0	68.0	68.0		1584	4.5	1.0	16	dbSNP_133	68	7,8593	6.4+/-24.3	0,7,4293	yes	missense	ZKSCAN2	NM_001012981.4	110	0,10,6487	CC,CG,GG		0.0814,0.0683,0.077	probably-damaging	528/968	25255503	10,12984	2197	4300	6497	SO:0001583	missense	342357	exon6			CAATTTGCTCTTC	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.1584C>G	16.37:g.25255503G>C	ENSP00000331626:p.Ser528Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.80	3.700874	0.68501	6.83E-4	8.14E-4	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.41400	1.0	5.48	4.53	0.55603	SANT domain, DNA binding (1);	0.000000	0.85682	D	0.000000	T	0.55689	0.1936	L	0.52011	1.625	0.37889	D	0.930635	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.60596	-0.7232	10	0.51188	T	0.08	-19.0721	10.586	0.45284	0.0889:0.0:0.9111:0.0	.	324;528	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	R	528	ENSP00000331626:S528R	ENSP00000331626:S528R	S	-	3	2	ZKSCAN2	25163004	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.061000	0.30542	1.457000	0.47850	0.655000	0.94253	AGC	G|0.999;C|0.001	0.001	strong		0.507	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
BANF2	140836	hgsc.bcm.edu	37	20	17716416	17716416	+	Missense_Mutation	SNP	C	C	G	rs1053993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:17716416C>G	ENST00000246090.5	+	4	495	c.233C>G	c.(232-234)aCt>aGt	p.T78S	BANF2_ENST00000467330.1_3'UTR|BANF2_ENST00000545418.2_Missense_Mutation_p.T85S|BANF2_ENST00000377805.3_Missense_Mutation_p.T78S	NM_178477.4	NP_848572.3	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2	78			T -> S (in dbSNP:rs1053993).			cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(1)|prostate(3)|skin(1)	6						GCCCAGCAGACTTCTCACTGC	0.537													G|||	1965	0.392372	0.5212	0.2536	5008	,	,		17148	0.4861		0.2604	False		,,,				2504	0.3558				p.T85S		Atlas-SNP	.											.	BANF2	12	.	0			c.C254G						PASS	.	G	SER/THR,SER/THR,SER/THR	2165,2241	593.8+/-388.1	540,1085,578	178.0	148.0	158.0		233,254,233	3.4	0.1	20	dbSNP_86	158	2368,6232	703.0+/-405.3	324,1720,2256	yes	missense,missense,missense	BANF2	NM_178477.4,NM_001159495.1,NM_001014977.3	58,58,58	864,2805,2834	GG,GC,CC		27.5349,49.1375,34.8531	benign,benign,benign	78/91,85/98,78/91	17716416	4533,8473	2203	4300	6503	SO:0001583	missense	140836	exon3			AGCAGACTTCTCA	BC054871	CCDS13129.1, CCDS54449.1	20p12.1	2007-12-17	2007-12-17	2007-12-17	ENSG00000125888	ENSG00000125888			16172	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 179"""	C20orf179			Standard	NM_178477		Approved	dJ803K15.1, BAF-L, BAFL, BAF2	uc010zrs.1	Q9H503	OTTHUMG00000031949	ENST00000246090.5:c.233C>G	20.37:g.17716416C>G	ENSP00000246090:p.Thr78Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	120	64	0.533333	NM_001159495	D3DW25|F5H3F6|Q7Z4M6	Missense_Mutation	SNP	ENST00000246090.5	37	CCDS13129.1	817	0.3740842490842491	240	0.4878048780487805	105	0.2900552486187845	282	0.493006993006993	190	0.25065963060686014	G	10.90	1.481913	0.26598	0.491375	0.275349	ENSG00000125888	ENST00000545418;ENST00000377805;ENST00000246090	T;T;T	0.53640	0.61;0.61;0.61	5.43	3.36	0.38483	.	0.234635	0.35615	N	0.003098	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	0.45920	-0.9228	8	0.33940	T	0.23	.	7.6537	0.28363	0.0:0.316:0.4986:0.1855	rs1053993;rs3194554;rs1053993	85;78	F5H3F6;Q9H503	.;BAFL_HUMAN	S	85;78;78	ENSP00000439128:T85S;ENSP00000367036:T78S;ENSP00000246090:T78S	ENSP00000246090:T78S	T	+	2	0	BANF2	17664416	0.537000	0.26386	0.107000	0.21349	0.973000	0.67179	0.676000	0.25247	1.305000	0.44909	-0.216000	0.12614	ACT	C|0.647;G|0.353	0.353	strong		0.537	BANF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102261.2	NM_178477	
CCDC70	83446	hgsc.bcm.edu	37	13	52440130	52440130	+	Missense_Mutation	SNP	A	A	G	rs1054515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:52440130A>G	ENST00000242819.4	+	2	912	c.616A>G	c.(616-618)Att>Gtt	p.I206V		NM_031290.2	NP_112580.2	Q6NSX1	CCD70_HUMAN	coiled-coil domain containing 70	206			I -> V (in dbSNP:rs1054515). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)|plasma membrane (GO:0005886)				breast(1)|large_intestine(4)|lung(7)|skin(2)|urinary_tract(1)	15		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.0107)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;2.4e-08)		CAATGGCCACATTGCCGGAGA	0.607													A|||	1782	0.355831	0.2837	0.4582	5008	,	,		17971	0.4127		0.3439	False		,,,				2504	0.3344				p.I206V		Atlas-SNP	.											.	CCDC70	31	.	0			c.A616G						PASS	.	A	VAL/ILE	1286,3120	422.1+/-339.6	172,942,1089	46.0	48.0	47.0		616	-10.1	0.0	13	dbSNP_86	47	2918,5682	436.3+/-358.3	518,1882,1900	yes	missense	CCDC70	NM_031290.2	29	690,2824,2989	GG,GA,AA		33.9302,29.1875,32.3235	benign	206/234	52440130	4204,8802	2203	4300	6503	SO:0001583	missense	83446	exon2			GGCCACATTGCCG		CCDS9431.1	13q14.3	2006-02-07			ENSG00000123171	ENSG00000123171			25303	protein-coding gene	gene with protein product						11230166	Standard	NM_031290		Approved	DKFZP434K1172, FLJ25853	uc001vfu.4	Q6NSX1	OTTHUMG00000016950	ENST00000242819.4:c.616A>G	13.37:g.52440130A>G	ENSP00000242819:p.Ile206Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_031290	Q8N7A8|Q9H097	Missense_Mutation	SNP	ENST00000242819.4	37	CCDS9431.1	824	0.3772893772893773	149	0.30284552845528456	149	0.4116022099447514	268	0.46853146853146854	258	0.3403693931398417	A	0.890	-0.725974	0.03158	0.291875	0.339302	ENSG00000123171	ENST00000242819	T	0.10573	2.86	5.05	-10.1	0.00402	.	2.119790	0.02563	N	0.096983	T	0.00012	0.0000	N	0.13043	0.29	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.43491	-0.9388	9	0.06494	T	0.89	-13.9377	5.5287	0.16972	0.1325:0.3229:0.4425:0.1022	rs1054515;rs3168775;rs52819501;rs57874413;rs1054515	206	Q6NSX1	CCD70_HUMAN	V	206	ENSP00000242819:I206V	ENSP00000242819:I206V	I	+	1	0	CCDC70	51338131	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.833000	0.04396	-2.204000	0.00743	-0.648000	0.03929	ATT	A|0.658;G|0.342	0.342	strong		0.607	CCDC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045033.2	NM_031290	
DCHS1	8642	hgsc.bcm.edu	37	11	6643976	6643976	+	Silent	SNP	C	C	T	rs7122587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6643976C>T	ENST00000299441.3	-	21	9342	c.8931G>A	c.(8929-8931)caG>caA	p.Q2977Q	RP11-732A19.5_ENST00000526456.1_RNA|RP11-732A19.9_ENST00000545572.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2977					branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGGTGCTGCCTGTGACATTG	0.622													C|||	982	0.196086	0.3487	0.1816	5008	,	,		17200	0.0714		0.2157	False		,,,				2504	0.1084				p.Q2977Q		Atlas-SNP	.											.	DCHS1	277	.	0			c.G8931A						PASS	.	C		1390,3006		225,940,1033	53.0	44.0	47.0		8931	2.7	1.0	11	dbSNP_116	47	1707,6869		171,1365,2752	yes	coding-synonymous	DCHS1	NM_003737.2		396,2305,3785	TT,TC,CC		19.9044,31.6197,23.8745		2977/3299	6643976	3097,9875	2198	4288	6486	SO:0001819	synonymous_variant	8642	exon21			TGCTGCCTGTGAC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.8931G>A	11.37:g.6643976C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			C|0.764;T|0.236	0.236	strong		0.622	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
AP2M1	1173	hgsc.bcm.edu	37	3	183899832	183899832	+	Silent	SNP	C	C	T	rs8478	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183899832C>T	ENST00000292807.5	+	9	1108	c.960C>T	c.(958-960)atC>atT	p.I320I	AP2M1_ENST00000439647.1_Silent_p.I318I|AP2M1_ENST00000411763.2_Silent_p.I345I|AP2M1_ENST00000461733.1_3'UTR|EIF2B5_ENST00000444495.1_Intron|AP2M1_ENST00000382456.3_Silent_p.I318I	NM_004068.3	NP_004059.2	Q96CW1	AP2M1_HUMAN	adaptor-related protein complex 2, mu 1 subunit	320	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of protein localization to plasma membrane (GO:1903077)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	18	all_cancers(143;1.12e-10)|Ovarian(172;0.0339)		Epithelial(37;2.92e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTCAGAAGATCGAGGTGAGGA	0.542													T|||	719	0.14357	0.2421	0.1066	5008	,	,		23976	0.004		0.164	False		,,,				2504	0.1595				p.I318I		Atlas-SNP	.											.	AP2M1	35	.	0			c.C954T						PASS	.	T	,	826,3196		85,656,1270	45.0	47.0	46.0		954,960	3.8	1.0	3	dbSNP_52	46	1442,6912		119,1204,2854	yes	coding-synonymous,coding-synonymous	AP2M1	NM_001025205.1,NM_004068.3	,	204,1860,4124	TT,TC,CC		17.2612,20.537,18.3258	,	318/434,320/436	183899832	2268,10108	2011	4177	6188	SO:0001819	synonymous_variant	1173	exon8			GAAGATCGAGGTG	U36188	CCDS43177.1, CCDS43178.1	3q28	2008-07-18			ENSG00000161203	ENSG00000161203			564	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, medium 1"", ""plasma membrane adaptor AP-2 50kDA protein"", ""clathrin coat adaptor protein AP50"", ""clathrin adaptor complex AP2, mu subunit"", ""HA2 50 kDA subunit"", ""clathrin assembly protein complex 2 medium chain"", ""AP-2 mu 2 chain"""	601024		CLAPM1		8595912	Standard	NM_004068		Approved	AP50, mu2	uc003fmw.3	Q96CW1	OTTHUMG00000156822	ENST00000292807.5:c.960C>T	3.37:g.183899832C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	95	44	0.463158	NM_001025205	A6NE12|D3DNT1|P20172|P53679	Silent	SNP	ENST00000292807.5	37	CCDS43177.1																																																																																			C|0.853;T|0.147	0.147	strong		0.542	AP2M1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346013.1	NM_004068	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134815	32134815	+	Missense_Mutation	SNP	G	G	A	rs16919122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:32134815G>A	ENST00000312561.4	+	4	1340	c.926G>A	c.(925-927)cGa>cAa	p.R309Q	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	309			R -> Q (in dbSNP:rs16919122). {ECO:0000269|PubMed:10997877}.														CCTCAGAGTCGAGAAATGCTG	0.408													G|||	561	0.112021	0.1362	0.183	5008	,	,		21052	0.0655		0.1203	False		,,,				2504	0.0685				p.R309Q		Atlas-SNP	.											.	.	.	.	0			c.G926A						PASS	.	G	GLN/ARG	637,3769	275.2+/-272.4	44,549,1610	93.0	89.0	90.0		926	0.3	0.0	12	dbSNP_123	90	975,7625	211.1+/-251.8	57,861,3382	yes	missense	C12orf35	NM_018169.3	43	101,1410,4992	AA,AG,GG		11.3372,14.4576,12.3943	benign	309/1748	32134815	1612,11394	2203	4300	6503	SO:0001583	missense	55196	exon4			AGAGTCGAGAAAT	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.926G>A	12.37:g.32134815G>A	ENSP00000310338:p.Arg309Gln	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	271	0.12408424908424909	73	0.1483739837398374	67	0.1850828729281768	40	0.06993006993006994	91	0.12005277044854881	G	1.870	-0.460463	0.04508	0.144576	0.113372	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.04502	4.24;3.61	5.34	0.344	0.16006	.	0.896444	0.09336	N	0.816138	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.48151	-0.9060	8	.	.	.	.	5.1251	0.14880	0.4273:0.382:0.1907:0.0	rs16919122;rs16919122	309	Q9HCM1	CL035_HUMAN	Q	309	ENSP00000310338:R309Q;ENSP00000370442:R309Q	.	R	+	2	0	C12orf35	32026082	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	0.222000	0.17699	0.089000	0.17243	-0.378000	0.06908	CGA	G|0.878;A|0.122	0.122	strong		0.408	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
GABBR1	2550	hgsc.bcm.edu	37	6	29600104	29600104	+	Missense_Mutation	SNP	G	G	A	rs1805056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29600104G>A	ENST00000377034.4	-	2	394	c.59C>T	c.(58-60)gCg>gTg	p.A20V	GABBR1_ENST00000377016.4_Missense_Mutation_p.A20V|GABBR1_ENST00000376977.3_Missense_Mutation_p.A20V	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	20			A -> V (in dbSNP:rs1805056). {ECO:0000269|PubMed:10402495, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:9933300}.		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	GGGGGTCTgcgccccgcccgc	0.662													g|||	155	0.0309505	0.0477	0.0403	5008	,	,		14488	0.002		0.0467	False		,,,				2504	0.0153				p.A20V		Atlas-SNP	.											.	GABBR1	95	.	0			c.C59T						PASS	.		VAL/ALA,VAL/ALA	187,4033		3,181,1926	30.0	17.0	21.0		59,59	1.8	1.0	6	dbSNP_89	21	320,7952		6,308,3822	yes	missense,missense	GABBR1	NM_001470.2,NM_021904.2	64,64	9,489,5748	AA,AG,GG		3.8685,4.4313,4.0586	probably-damaging,probably-damaging	20/962,20/900	29600104	507,11985	2110	4136	6246	SO:0001583	missense	2550	exon2			GTCTGCGCCCCGC	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4070	protein-coding gene	gene with protein product	"""GABA-B receptor"""	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.59C>T	6.37:g.29600104G>A	ENSP00000366233:p.Ala20Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_021904	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Missense_Mutation	SNP	ENST00000377034.4	37	CCDS4663.1	61	0.027930402930402932	17	0.034552845528455285	15	0.04143646408839779	3	0.005244755244755245	26	0.03430079155672823	g	15.33	2.802875	0.50315	0.044313	0.038685	ENSG00000204681	ENST00000376977;ENST00000377016;ENST00000377034;ENST00000462632;ENST00000476670	T;D;T;T;T	0.83419	-1.0;-1.72;-0.48;1.48;0.93	1.81	1.81	0.25067	.	0.332794	0.18443	U	0.141084	T	0.61652	0.2364	N	0.14661	0.345	0.25961	N	0.982626	D;D;D	0.56521	0.976;0.976;0.959	P;P;P	0.52309	0.695;0.695;0.499	T	0.55198	-0.8178	10	0.39692	T	0.17	.	7.1562	0.25639	0.0:0.0:1.0:0.0	rs1805056;rs28359989	20;20;20	Q9UBS5-5;Q9UBS5-3;Q9UBS5	.;.;GABR1_HUMAN	V	20;20;20;20;25	ENSP00000366176:A20V;ENSP00000366215:A20V;ENSP00000366233:A20V;ENSP00000419755:A20V;ENSP00000417332:A25V	ENSP00000366176:A20V	A	-	2	0	GABBR1	29708083	0.988000	0.35896	1.000000	0.80357	0.827000	0.46813	1.909000	0.39917	1.323000	0.45263	0.282000	0.19409	GCG	G|0.962;A|0.038	0.038	strong		0.662	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3		
PKHD1	5314	hgsc.bcm.edu	37	6	51613012	51613012	+	Silent	SNP	C	C	T	rs143737660		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:51613012C>T	ENST00000371117.3	-	58	9677	c.9402G>A	c.(9400-9402)aaG>aaA	p.K3134K	PKHD1_ENST00000340994.4_Silent_p.K3134K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3134					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)					GTCCACTTTCCTTATAGAGAT	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		21874	0.0		0.0	False		,,,				2504	0.001				p.K3134K		Atlas-SNP	.											.	PKHD1	927	.	0			c.G9402A						PASS	.	C	,	0,4406		0,0,2203	201.0	209.0	206.0		9402,9402	3.0	0.1	6	dbSNP_134	206	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	3134/4075,3134/3397	51613012	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon58			ACTTTCCTTATAG	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.9402G>A	6.37:g.51613012C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			C|0.999;T|0.001	0.001	strong		0.463	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
DNAH3	55567	hgsc.bcm.edu	37	16	21078693	21078693	+	Silent	SNP	T	T	G	rs861424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:21078693T>G	ENST00000261383.3	-	24	3428	c.3429A>C	c.(3427-3429)gcA>gcC	p.A1143A	DNAH3_ENST00000415178.1_Silent_p.A1143A	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1143	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GAAGCTTCTCTGCCATCCGTG	0.468													G|||	2226	0.444489	0.3812	0.3732	5008	,	,		17763	0.6766		0.4215	False		,,,				2504	0.365				p.A1143A		Atlas-SNP	.											.	DNAH3	1142	.	0			c.A3429C						PASS	.	G		1821,2581	604.3+/-390.3	355,1111,735	85.0	86.0	86.0		3429	2.1	0.9	16	dbSNP_86	86	3499,5101	633.1+/-398.7	681,2137,1482	no	coding-synonymous	DNAH3	NM_017539.1		1036,3248,2217	GG,GT,TT		40.686,41.3676,40.9168		1143/4117	21078693	5320,7682	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon24			CTTCTCTGCCATC	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.3429A>C	16.37:g.21078693T>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			G|0.438;T|0.562	0.438	strong		0.468	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
PLET1	349633	hgsc.bcm.edu	37	11	112123095	112123095	+	Missense_Mutation	SNP	A	A	G	rs2564872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:112123095A>G	ENST00000338832.2	-	3	694	c.424T>C	c.(424-426)Tct>Cct	p.S142P		NM_001145024.1	NP_001138496.1	Q6UQ28	PLET1_HUMAN		142			S -> P (in dbSNP:rs2564872). {ECO:0000269|PubMed:15203209}.		cell differentiation (GO:0030154)|negative regulation of cell-matrix adhesion (GO:0001953)|positive regulation of cell migration (GO:0030335)|wound healing, spreading of epidermal cells (GO:0035313)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)				endometrium(2)	2						TTCAGAGTAGAAAGTATAGGC	0.463													A|||	3234	0.645767	0.3336	0.7176	5008	,	,		19355	0.7778		0.7217	False		,,,				2504	0.8027				p.S142P		Atlas-SNP	.											.	C11orf34	6	.	0			c.T424C						PASS	.	A	PRO/SER	553,831		110,333,249	150.0	130.0	136.0		424	2.6	0.0	11	dbSNP_100	136	2257,925		804,649,138	yes	missense	C11orf34	NM_001145024.1	74	914,982,387	GG,GA,AA		29.0698,39.9566,38.4582	probably-damaging	142/208	112123095	2810,1756	692	1591	2283	SO:0001583	missense	349633	exon3			GAGTAGAAAGTAT																												ENST00000338832.2:c.424T>C	11.37:g.112123095A>G	ENSP00000341412:p.Ser142Pro	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001145024	Q6UQ24|Q6UQ25|Q6UQ27	Missense_Mutation	SNP	ENST00000338832.2	37		1409	0.6451465201465202	157	0.31910569105691056	247	0.6823204419889503	452	0.7902097902097902	553	0.7295514511873351	A	14.29	2.492677	0.44352	0.399566	0.709302	ENSG00000188771	ENST00000338832;ENST00000527122	T;T	0.58652	0.32;0.59	3.77	2.62	0.31277	.	0.626164	0.14150	N	0.338087	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.89917	1.0	D	0.81914	0.995	T	0.28073	-1.0055	9	0.56958	D	0.05	.	7.2666	0.26234	0.7737:0.2263:0.0:0.0	rs2564872;rs58169031;rs2564872	142	Q6UQ28	PLET1_HUMAN	P	142	ENSP00000341412:S142P;ENSP00000433513:S142P	ENSP00000341412:S142P	S	-	1	0	C11orf34	111628305	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	-0.016000	0.12613	0.799000	0.34018	0.528000	0.53228	TCT	G|0.640;N|0.001	0.640	strong		0.463	C11orf34-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
NACAD	23148	hgsc.bcm.edu	37	7	45124286	45124286	+	Missense_Mutation	SNP	A	A	G	rs3735494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45124286A>G	ENST00000490531.2	-	2	1512	c.1493T>C	c.(1492-1494)gTg>gCg	p.V498A		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	498			V -> A (in dbSNP:rs3735494).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						TCTGGTAGCCACCTCCACCTG	0.602													a|||	1665	0.332468	0.354	0.4164	5008	,	,		20244	0.2857		0.335	False		,,,				2504	0.2894				p.V498A		Atlas-SNP	.											.	NACAD	44	.	0			c.T1493C						PASS	.	G	ALA/VAL	535,849		104,327,261	41.0	44.0	43.0		1493	-5.1	0.0	7	dbSNP_107	43	1119,2063		190,739,662	yes	missense	NACAD	NM_001146334.1	64	294,1066,923	GG,GA,AA		35.1666,38.6561,36.2243	possibly-damaging	498/1563	45124286	1654,2912	692	1591	2283	SO:0001583	missense	23148	exon2			GTAGCCACCTCCA	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1493T>C	7.37:g.45124286A>G	ENSP00000420477:p.Val498Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	724	0.3315018315018315	177	0.3597560975609756	144	0.39779005524861877	150	0.26223776223776224	253	0.3337730870712401	a	0.003	-2.391135	0.00200	0.386561	0.351666	ENSG00000136274	ENST00000490531	T	0.11385	2.78	2.54	-5.08	0.02929	.	.	.	.	.	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	0.31971	-0.9924	8	0.08381	T	0.77	6.4536	5.5272	0.16964	0.2234:0.0:0.2477:0.5289	rs3735494;rs3735494	498	O15069	NACAD_HUMAN	A	498	ENSP00000420477:V498A	ENSP00000420477:V498A	V	-	2	0	NACAD	45090811	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.043000	0.01413	-4.430000	0.00049	-5.108000	0.00001	GTG	A|0.677;G|0.323	0.323	strong		0.602	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
ADRA1D	146	hgsc.bcm.edu	37	20	4228779	4228779	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4228779G>T	ENST00000379453.4	-	1	942	c.826C>A	c.(826-828)Cgc>Agc	p.R276S		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	276					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)	ACGTACACGCGGCAGTACATG	0.672																																					p.R276S		Atlas-SNP	.											.	ADRA1D	36	.	0			c.C826A						PASS	.						25.0	19.0	21.0					20																	4228779		2179	4285	6464	SO:0001583	missense	146	exon1			ACACGCGGCAGTA	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.826C>A	20.37:g.4228779G>T	ENSP00000368766:p.Arg276Ser	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	37	CCDS13079.1	.	.	.	.	.	.	.	.	.	.	g	18.67	3.673764	0.67928	.	.	ENSG00000171873	ENST00000379453	T	0.38560	1.13	4.25	4.25	0.50352	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	M	0.91140	3.18	0.47862	D	0.999538	D	0.76494	0.999	D	0.80764	0.994	T	0.73895	-0.3838	10	0.87932	D	0	.	9.4862	0.38931	0.0:0.0:0.7892:0.2108	.	276	P25100	ADA1D_HUMAN	S	276	ENSP00000368766:R276S	ENSP00000368766:R276S	R	-	1	0	ADRA1D	4176779	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.525000	0.45598	2.208000	0.71279	0.552000	0.68991	CGC	.	.	none		0.672	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678	
GNAS	2778	hgsc.bcm.edu	37	20	57429163	57429163	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:57429163C>T	ENST00000306120.3	+	1	653	c.653C>T	c.(652-654)tCg>tTg	p.S218L	GNAS_ENST00000371100.4_Silent_p.I281I|GNAS_ENST00000371102.4_Silent_p.I281I|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371098.2_Intron|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000371099.2_Silent_p.I281I|GNAS_ENST00000464624.2_3'UTR			P63092	GNAS2_HUMAN	GNAS complex locus	0					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			CAGGCGCCATCGGCAGCCCAT	0.687			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.S219L	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	.	GNAS	867	.	0			c.C656T						PASS	.						14.0	15.0	15.0					20																	57429163		1811	3992	5803	SO:0001583	missense	2778	exon1			CGCCATCGGCAGC	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000306120.3:c.653C>T	20.37:g.57429163C>T	ENSP00000302237:p.Ser218Leu	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	22	0.349206	NM_001077490	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000306120.3	37		.	.	.	.	.	.	.	.	.	.	C	2.592	-0.295042	0.05532	.	.	ENSG00000087460	ENST00000306120	.	.	.	4.03	0.906	0.19314	.	.	.	.	.	T	0.23611	0.0571	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23833	-1.0177	5	0.27082	T	0.32	.	3.761	0.08604	0.0:0.5632:0.2068:0.23	.	.	.	.	L	218	.	ENSP00000302237:S218L	S	+	2	0	GNAS	56862558	0.000000	0.05858	0.008000	0.14137	0.415000	0.31203	0.170000	0.16663	0.235000	0.21160	0.561000	0.74099	TCG	.	.	none		0.687	GNAS-050	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000267987.1	NM_000516	
ATF5	22809	hgsc.bcm.edu	37	19	50435921	50435921	+	Missense_Mutation	SNP	C	C	T	rs201354210	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50435921C>T	ENST00000423777.2	+	3	798	c.421C>T	c.(421-423)Ctc>Ttc	p.L141F	ATF5_ENST00000595125.1_Missense_Mutation_p.L141F|MIR4751_ENST00000578027.1_RNA|NUP62_ENST00000352066.3_5'Flank|NUP62_ENST00000422090.2_5'Flank|CTC-326K19.6_ENST00000451973.1_Intron	NM_001193646.1	NP_001180575.1	Q9Y2D1	ATF5_HUMAN	activating transcription factor 5	141	Interaction with PTP4A1. {ECO:0000250}.				multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of astrocyte differentiation (GO:0048712)|olfactory bulb interneuron development (GO:0021891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|transcription corepressor activity (GO:0003714)			NS(1)|endometrium(2)|large_intestine(1)|skin(3)	7		all_lung(116;0.00318)|all_neural(266;0.107)|Ovarian(192;0.17)		GBM - Glioblastoma multiforme(134;0.00221)|OV - Ovarian serous cystadenocarcinoma(262;0.017)	Pseudoephedrine(DB00852)	aGCCCCCTCCCTCCCCCTGTC	0.657													C|||	47	0.00938498	0.0008	0.0058	5008	,	,		4633	0.001		0.0358	False		,,,				2504	0.0051				p.L141F	GBM(48;768 989 9196 9511 26329)	Atlas-SNP	.											.	ATF5	27	.	0			c.C421T						PASS	.	C	PHE/LEU,PHE/LEU	12,4140		0,12,2064	5.0	5.0	5.0		421,421	1.6	0.0	19		5	202,7676		3,196,3740	yes	missense,missense	ATF5	NM_001193646.1,NM_012068.5	22,22	3,208,5804	TT,TC,CC		2.5641,0.289,1.7789	possibly-damaging,possibly-damaging	141/283,141/283	50435921	214,11816	2076	3939	6015	SO:0001583	missense	22809	exon4			CCCTCCCTCCCCC	AF101388	CCDS12789.1	19q13.33	2013-09-20			ENSG00000169136	ENSG00000169136		"""basic leucine zipper proteins"""	790	protein-coding gene	gene with protein product		606398				10373550	Standard	NM_012068		Approved		uc002prd.3	Q9Y2D1	OTTHUMG00000183065	ENST00000423777.2:c.421C>T	19.37:g.50435921C>T	ENSP00000396954:p.Leu141Phe	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	80	28	0.35	NM_012068	B3KND3|Q9BSA1|Q9UNQ3	Missense_Mutation	SNP	ENST00000423777.2	37	CCDS12789.1	33	0.01510989010989011	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	28	0.036939313984168866	C	0.021	-1.431560	0.01108	0.00289	0.025641	ENSG00000169136	ENST00000423777	T	0.24538	1.85	3.77	1.6	0.23607	.	0.583879	0.14988	U	0.286856	T	0.02727	0.0082	N	0.22421	0.69	0.09310	N	1	P	0.41041	0.736	B	0.38803	0.282	T	0.13764	-1.0497	10	0.10111	T	0.7	.	6.5994	0.22693	0.0:0.7104:0.1835:0.1061	.	141	Q9Y2D1	ATF5_HUMAN	F	141	ENSP00000396954:L141F	ENSP00000396954:L141F	L	+	1	0	ATF5	55127733	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.557000	0.23454	0.272000	0.22027	0.448000	0.29417	CTC	C|0.985;T|0.015	0.015	strong		0.657	ATF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464915.2		
HGS	9146	hgsc.bcm.edu	37	17	79662067	79662067	+	Silent	SNP	A	A	G	rs34384005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79662067A>G	ENST00000329138.4	+	13	1224	c.1089A>G	c.(1087-1089)gaA>gaG	p.E363E		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	363	Interaction with SNX1. {ECO:0000250}.|Pro-rich.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			AGCCTGGGGAAGGGCACGCAG	0.672													G|||	569	0.113618	0.1172	0.049	5008	,	,		16874	0.2232		0.0716	False		,,,				2504	0.0849				p.E363E		Atlas-SNP	.											.	HGS	54	.	0			c.A1089G						PASS	.	G		439,3967	765.8+/-413.4	26,387,1790	43.0	48.0	46.0		1089	0.1	0.1	17	dbSNP_126	46	514,8084	785.6+/-407.6	15,484,3800	no	coding-synonymous	HGS	NM_004712.4		41,871,5590	GG,GA,AA		5.9781,9.9637,7.3285		363/778	79662067	953,12051	2203	4299	6502	SO:0001819	synonymous_variant	9146	exon13			TGGGGAAGGGCAC	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.1089A>G	17.37:g.79662067A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	43	13	0.302326	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	37	CCDS11784.1																																																																																			A|0.915;G|0.085	0.085	strong		0.672	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
NKPD1	284353	hgsc.bcm.edu	37	19	45655647	45655647	+	Missense_Mutation	SNP	G	G	T	rs117934605	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45655647G>T	ENST00000438936.2	-	3	1593	c.1382C>A	c.(1381-1383)gCg>gAg	p.A461E	AC005757.7_ENST00000589594.1_lincRNA|NKPD1_ENST00000589776.1_Missense_Mutation_p.A461E|NKPD1_ENST00000317951.4_Missense_Mutation_p.A683E|NKPD1_ENST00000429338.1_Missense_Mutation_p.A461E			Q17RQ9	NKPD1_HUMAN	NTPase, KAP family P-loop domain containing 1	461				A -> E (in Ref. 1; BAC03547). {ECO:0000305}.		integral component of membrane (GO:0016021)				endometrium(1)|lung(4)|prostate(2)|urinary_tract(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00863)|GBM - Glioblastoma multiforme(486;0.231)		gccctcgggcgcgcccccggT	0.731													G|||	252	0.0503195	0.003	0.0576	5008	,	,		11170	0.001		0.1252	False		,,,				2504	0.0828				p.A683E		Atlas-SNP	.											.	NKPD1	46	.	0			c.C2048A						PASS	.	G	GLU/ALA	66,3544		0,66,1739	5.0	6.0	5.0		2048	0.2	1.0	19	dbSNP_132	5	1009,6969		61,887,3041	no	missense	NKPD1	NM_198478.3	107	61,953,4780	TT,TG,GG		12.6473,1.8283,9.2768	benign	683/833	45655647	1075,10513	1805	3989	5794	SO:0001583	missense	284353	exon4			TCGGGCGCGCCCC	AK090919		19q13.32	2012-07-02		2012-07-02	ENSG00000179846	ENSG00000179846			24739	protein-coding gene	gene with protein product						14702039	Standard	NM_198478		Approved	FLJ33600	uc010xxi.2	Q17RQ9	OTTHUMG00000160521	ENST00000438936.2:c.1382C>A	19.37:g.45655647G>T	ENSP00000401739:p.Ala461Glu	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	10	9	0.9	NM_198478	B7ZLG6|D6RH15|Q8N2A2	Missense_Mutation	SNP	ENST00000438936.2	37		128	0.05860805860805861	3	0.006097560975609756	25	0.06906077348066299	0	0.0	100	0.13192612137203166	G	7.978	0.750483	0.15778	0.018283	0.126473	ENSG00000179846	ENST00000317951;ENST00000438936;ENST00000429338	T;T;T	0.47528	0.84;0.85;0.92	5.31	0.179	0.15063	.	0.291000	0.24158	N	0.041010	T	0.00328	0.0010	L	0.50333	1.59	0.52501	P	4.199999999998649E-5	B	0.15930	0.015	B	0.08055	0.003	T	0.07731	-1.0757	9	0.09843	T	0.71	-20.6459	4.8104	0.13340	0.0859:0.2863:0.4951:0.1328	.	461	Q17RQ9	NKPD1_HUMAN	E	683;461;461	ENSP00000321976:A683E;ENSP00000401739:A461E;ENSP00000404706:A461E	ENSP00000321976:A683E	A	-	2	0	NKPD1	50347487	0.001000	0.12720	1.000000	0.80357	0.789000	0.44602	0.080000	0.14802	0.571000	0.29365	0.561000	0.74099	GCG	G|0.941;T|0.059	0.059	strong		0.731	NKPD1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000360950.2	NM_198478	
SLC22A10	387775	hgsc.bcm.edu	37	11	63057925	63057925	+	Nonsense_Mutation	SNP	G	G	A	rs1790218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:63057925G>A	ENST00000332793.6	+	1	290	c.288G>A	c.(286-288)tgG>tgA	p.W96*	SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000526800.1_Nonsense_Mutation_p.W44*|SLC22A10_ENST00000544661.1_5'UTR|SLC22A10_ENST00000525620.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	96						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			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)	ATCCCCAGTGGCAGCTTCTTC	0.498													G|||	2171	0.433506	0.2663	0.5058	5008	,	,		17692	0.4692		0.5537	False		,,,				2504	0.4479				p.W96X		Atlas-SNP	.											.	SLC22A10	79	.	0			c.G288A						PASS	.	G	stop/TRP	1330,3072	443.7+/-347.1	199,932,1070	103.0	108.0	107.0		288	2.9	1.0	11	dbSNP_89	107	4901,3695	620.1+/-397.0	1401,2099,798	yes	stop-gained	SLC22A10	NM_001039752.3		1600,3031,1868	AA,AG,GG		42.9851,30.2135,47.9381		96/542	63057925	6231,6767	2201	4298	6499	SO:0001587	stop_gained	387775	exon1			CCAGTGGCAGCTT	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.288G>A	11.37:g.63057925G>A	ENSP00000327569:p.Trp96*	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	225	115	0.511111	NM_001039752	Q68CJ0	Nonsense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	1027	0.47023809523809523	137	0.2784552845528455	215	0.5939226519337016	240	0.4195804195804196	435	0.5738786279683378	G	13.07	2.126603	0.37533	0.302135	0.570149	ENSG00000184999	ENST00000332793;ENST00000526800	.	.	.	2.89	2.89	0.33648	.	0.089292	0.49916	U	0.000124	.	.	.	.	.	.	0.09310	P	0.9999999999311662	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.4093	0.27009	0.0:0.0:0.7407:0.2593	rs1790218;rs3763800;rs17709061;rs1790218	.	.	.	X	96;44	.	ENSP00000327569:W96X	W	+	3	0	SLC22A10	62814501	1.000000	0.71417	0.995000	0.50966	0.155000	0.21991	3.409000	0.52657	1.662000	0.50781	0.579000	0.79373	TGG	G|0.538;A|0.462	0.462	strong		0.498	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752	
MYO1C	4641	hgsc.bcm.edu	37	17	1373518	1373518	+	Missense_Mutation	SNP	T	T	C	rs9905106	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1373518T>C	ENST00000575158.1	-	24	2548	c.2372A>G	c.(2371-2373)cAg>cGg	p.Q791R	MYO1C_ENST00000545534.2_Missense_Mutation_p.Q802R|MYO1C_ENST00000359786.5_Missense_Mutation_p.Q826R|MYO1C_ENST00000438665.2_Missense_Mutation_p.Q807R|MYO1C_ENST00000361007.2_Missense_Mutation_p.Q791R			Q12965	MYO1E_HUMAN	myosin IC	0	Myosin tail. {ECO:0000255}.				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)		CAGGACATTCTGGGGCAGCTG	0.637													C|||	3564	0.711661	0.9183	0.7017	5008	,	,		12609	0.4196		0.7008	False		,,,				2504	0.7515				p.Q826R		Atlas-SNP	.											MYO1C,NS,carcinoma,0,2	MYO1C	57	2	0			c.A2477G						PASS	.	C	ARG/GLN,ARG/GLN,ARG/GLN	3834,498		1699,436,31	14.0	15.0	15.0		2477,2420,2372	4.9	1.0	17	dbSNP_119	15	6265,2185		2341,1583,301	yes	missense,missense,missense	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	43,43,43	4040,2019,332	CC,CT,TT		25.858,11.4958,20.9905	benign,benign,benign	826/1064,807/1045,791/1029	1373518	10099,2683	2166	4225	6391	SO:0001583	missense	4641	exon24			ACATTCTGGGGCA	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.2372A>G	17.37:g.1373518T>C	ENSP00000459174:p.Gln791Arg	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_001080779	Q14778	Missense_Mutation	SNP	ENST00000575158.1	37	CCDS11003.1	1440	0.6593406593406593	441	0.8963414634146342	256	0.7071823204419889	226	0.3951048951048951	517	0.6820580474934037	C	5.871	0.344923	0.11126	0.885042	0.74142	ENSG00000197879	ENST00000359786;ENST00000438665;ENST00000535856;ENST00000361007;ENST00000545534	D;D;D;D	0.87029	-2.19;-2.2;-2.2;-2.2	4.95	4.95	0.65309	.	0.106416	0.64402	N	0.000009	T	0.00012	0.0000	N	0.03608	-0.345	0.53005	P	3.500000000000725E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41124	-0.9526	9	0.15952	T	0.53	.	6.3336	0.21285	0.0:0.7213:0.0:0.2787	rs9905106;rs57897716	826;807	O00159;O00159-3	MYO1C_HUMAN;.	R	826;807;807;791;802	ENSP00000352834:Q826R;ENSP00000412197:Q807R;ENSP00000354283:Q791R;ENSP00000437685:Q802R	ENSP00000352834:Q826R	Q	-	2	0	MYO1C	1320268	0.998000	0.40836	0.999000	0.59377	0.215000	0.24574	1.400000	0.34577	1.334000	0.45468	-0.215000	0.12644	CAG	T|0.270;C|0.730	0.730	strong		0.637	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
CCDC34	91057	hgsc.bcm.edu	37	11	27362359	27362359	+	Missense_Mutation	SNP	T	T	G	rs17244028	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:27362359T>G	ENST00000328697.6	-	5	1464	c.791A>C	c.(790-792)gAa>gCa	p.E264A	CCDC34_ENST00000529615.1_5'UTR	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	264			E -> A (in dbSNP:rs17244028). {ECO:0000269|Ref.6}.							endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						CTCCTGTATTTCAGCTTGCTG	0.338													T|||	808	0.161342	0.056	0.2637	5008	,	,		16669	0.0734		0.34	False		,,,				2504	0.138				p.E264A		Atlas-SNP	.											.	CCDC34	48	.	0			c.A791C						PASS	.	T	ALA/GLU	479,3925	223.3+/-239.8	26,427,1749	155.0	144.0	148.0		791	5.9	1.0	11	dbSNP_123	148	3029,5569	467.1+/-367.0	545,1939,1815	yes	missense	CCDC34	NM_030771.1	107	571,2366,3564	GG,GT,TT		35.2291,10.8765,26.9805	probably-damaging	264/374	27362359	3508,9494	2202	4299	6501	SO:0001583	missense	91057	exon5			TGTATTTCAGCTT	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.791A>C	11.37:g.27362359T>G	ENSP00000330240:p.Glu264Ala	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	263	113	0.429658	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	37	CCDS31448.1	433	0.19826007326007325	33	0.06707317073170732	100	0.27624309392265195	40	0.06993006993006994	260	0.34300791556728233	T	13.88	2.367807	0.42003	0.108765	0.352291	ENSG00000109881	ENST00000328697	T	0.25250	1.81	5.92	5.92	0.95590	.	0.067529	0.56097	D	0.000022	T	0.00012	0.0000	L	0.49455	1.56	0.09310	P	1.0	D	0.52996	0.957	P	0.59595	0.86	T	0.44697	-0.9311	9	0.48119	T	0.1	-10.9812	11.2236	0.48871	0.0:0.0:0.1532:0.8468	rs17244028;rs52822831;rs17244028	264	Q96HJ3	CCD34_HUMAN	A	264	ENSP00000330240:E264A	ENSP00000330240:E264A	E	-	2	0	CCDC34	27318935	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.873000	0.56093	2.266000	0.75297	0.533000	0.62120	GAA	T|0.772;G|0.228	0.228	strong		0.338	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771	
OR5AS1	219447	hgsc.bcm.edu	37	11	55798259	55798259	+	Missense_Mutation	SNP	G	G	T	rs12224086	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55798259G>T	ENST00000313555.1	+	1	365	c.365G>T	c.(364-366)cGc>cTc	p.R122L		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, member 1	122			R -> L (in dbSNP:rs12224086).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R122L(1)		endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					GCTTATGACCGCTATGCAGCC	0.453													G|||	519	0.103634	0.0477	0.0965	5008	,	,		20013	0.1458		0.1223	False		,,,				2504	0.1217				p.R122L		Atlas-SNP	.											OR5AS1,NS,carcinoma,+1,5	OR5AS1	121	5	1	Substitution - Missense(1)	stomach(1)	c.G365T						PASS	.	G	LEU/ARG	237,4165	139.2+/-174.8	9,219,1973	133.0	109.0	117.0		365	3.6	1.0	11	dbSNP_120	117	1019,7573	218.3+/-256.7	57,905,3334	yes	missense	OR5AS1	NM_001001921.1	102	66,1124,5307	TT,TG,GG		11.8599,5.3839,9.666	probably-damaging	122/325	55798259	1256,11738	2201	4296	6497	SO:0001583	missense	219447	exon1			ATGACCGCTATGC	AB065543	CCDS31516.1	11q11	2012-08-09			ENSG00000181785	ENSG00000181785		"""GPCR / Class A : Olfactory receptors"""	15261	protein-coding gene	gene with protein product							Standard	NM_001001921		Approved		uc010riw.2	Q8N127	OTTHUMG00000166830	ENST00000313555.1:c.365G>T	11.37:g.55798259G>T	ENSP00000324111:p.Arg122Leu	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	220	117	0.531818	NM_001001921	Q6IFB8	Missense_Mutation	SNP	ENST00000313555.1	37	CCDS31516.1	251	0.11492673992673992	29	0.05894308943089431	33	0.09116022099447514	88	0.15384615384615385	101	0.13324538258575197	G	15.37	2.812972	0.50527	0.053839	0.118599	ENSG00000181785	ENST00000313555	T	0.77358	-1.09	5.46	3.59	0.41128	GPCR, rhodopsin-like superfamily (1);	0.224065	0.22821	U	0.055229	T	0.02156	0.0067	M	0.93978	3.48	0.31274	P	0.691424	P	0.47762	0.9	P	0.45538	0.484	T	0.55477	-0.8135	9	0.72032	D	0.01	.	11.0053	0.47631	0.154:0.0:0.846:0.0	rs12224086;rs12224086	122	Q8N127	O5AS1_HUMAN	L	122	ENSP00000324111:R122L	ENSP00000324111:R122L	R	+	2	0	OR5AS1	55554835	0.991000	0.36638	0.997000	0.53966	0.134000	0.20937	6.174000	0.71943	0.680000	0.31366	-0.148000	0.13756	CGC	A|0.000;G|0.900;T|0.099	0.099	strong		0.453	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921	
GP6	51206	hgsc.bcm.edu	37	19	55539049	55539049	+	Silent	SNP	C	C	T	rs5030705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55539049C>T	ENST00000417454.1	-	4	534	c.507G>A	c.(505-507)acG>acA	p.T169T	CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.7_ENST00000586961.1_RNA|CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Silent_p.T169T|CTC-550B14.6_ENST00000585492.1_RNA|GP6_ENST00000310373.3_Silent_p.T169T	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	169	Ig-like C2-type 2.				blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		CGGCGGTCACCGTGATGATGG	0.587													C|||	430	0.0858626	0.0151	0.1354	5008	,	,		15104	0.0308		0.2376	False		,,,				2504	0.047				p.T169T		Atlas-SNP	.											.	GP6	55	.	0			c.G507A						PASS	.	C	,	168,3808		6,156,1826	60.0	66.0	64.0		507,507	-8.0	0.0	19	dbSNP_113	64	1697,6651		179,1339,2656	no	coding-synonymous,coding-synonymous	GP6	NM_001083899.1,NM_016363.4	,	185,1495,4482	TT,TC,CC		20.3282,4.2254,15.1331	,	169/621,169/340	55539049	1865,10459	1988	4174	6162	SO:0001819	synonymous_variant	51206	exon4			GGTCACCGTGATG	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.507G>A	19.37:g.55539049C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_016363	Q9HCN7|Q9UIF2	Silent	SNP	ENST00000417454.1	37	CCDS46184.1																																																																																			C|0.847;T|0.153	0.153	strong		0.587	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
FZD6	8323	hgsc.bcm.edu	37	8	104312432	104312432	+	Missense_Mutation	SNP	A	A	G	rs827528	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:104312432A>G	ENST00000358755.4	+	2	414	c.97A>G	c.(97-99)Atg>Gtg	p.M33V	RP11-318M2.2_ENST00000521383.1_RNA|RP11-318M2.2_ENST00000522856.1_RNA|FZD6_ENST00000522566.1_Missense_Mutation_p.M33V|FZD6_ENST00000523739.1_Start_Codon_SNP_p.M1V|RP11-318M2.2_ENST00000523614.2_RNA|FZD6_ENST00000540287.1_5'UTR	NM_001164616.1|NM_003506.3	NP_001158088.1|NP_003497.2	O60353	FZD6_HUMAN	frizzled class receptor 6	33	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.		M -> V (in dbSNP:rs827528). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:22045688}.		angiogenesis (GO:0001525)|axonogenesis (GO:0007409)|cell proliferation in midbrain (GO:0033278)|embryonic nail plate morphogenesis (GO:0035880)|establishment of planar polarity (GO:0001736)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|platelet activation (GO:0030168)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(57;2.86e-05)|STAD - Stomach adenocarcinoma(118;0.197)			TCCCAGATGTATGAAAATGGC	0.423													A|||	852	0.170128	0.2156	0.1657	5008	,	,		20348	0.0129		0.2704	False		,,,				2504	0.1708				p.M33V		Atlas-SNP	.											FZD6,colon,carcinoma,0,1	FZD6	61	1	0			c.A97G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	930,3476	356.4+/-313.5	95,740,1368	200.0	177.0	185.0		97,1,97	-0.7	1.0	8	dbSNP_86	185	2279,6321	385.2+/-341.4	294,1691,2315	yes	missense,missense,missense	FZD6	NM_001164615.1,NM_001164616.1,NM_003506.3	21,21,21	389,2431,3683	GG,GA,AA		26.5,21.1076,24.6732	benign,benign,benign	33/707,1/675,33/707	104312432	3209,9797	2203	4300	6503	SO:0001583	missense	8323	exon2			AGATGTATGAAAA	AB012911	CCDS6298.1, CCDS55268.1	8q22.3-q23.1	2014-01-29	2014-01-29		ENSG00000164930	ENSG00000164930		"""GPCR / Class F : Frizzled receptors"""	4044	protein-coding gene	gene with protein product		603409	"""frizzled (Drosophila) homolog 6"", ""frizzled homolog 6 (Drosophila)"", ""frizzled 6, seven transmembrane spanning receptor"", ""frizzled family receptor 6"""			9480858, 14747478	Standard	NM_003506		Approved	Hfz6	uc003ylh.3	O60353	OTTHUMG00000164840	ENST00000358755.4:c.97A>G	8.37:g.104312432A>G	ENSP00000351605:p.Met33Val	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	199	92	0.462312	NM_003506	B4DRN0|Q6N0A5|Q6P9C3|Q8WXR9	Missense_Mutation	SNP	ENST00000358755.4	37	CCDS6298.1	375	0.1717032967032967	96	0.1951219512195122	72	0.19889502762430938	5	0.008741258741258742	202	0.26649076517150394	A	11.83	1.756296	0.31137	0.211076	0.265	ENSG00000164930	ENST00000522566;ENST00000358755;ENST00000523739	T;T;T	0.75938	-0.93;-0.93;-0.98	5.93	-0.683	0.11335	Frizzled domain (5);	0.614894	0.19147	N	0.121550	T	0.00012	0.0000	L	0.28400	0.85	0.09310	P	0.9999999135129	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.04307	-1.0961	9	0.38643	T	0.18	.	2.9794	0.05948	0.4952:0.1098:0.2875:0.1075	rs827528;rs57692859;rs827528	33;33	B2R9H9;O60353	.;FZD6_HUMAN	V	33;33;1	ENSP00000429055:M33V;ENSP00000351605:M33V;ENSP00000429528:M1V	ENSP00000351605:M33V	M	+	1	0	FZD6	104381608	0.093000	0.21703	0.954000	0.39281	0.985000	0.73830	-0.195000	0.09546	-0.097000	0.12307	-0.256000	0.11100	ATG	A|0.785;G|0.215;T|0.000	0.215	strong		0.423	FZD6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380560.1	NM_003506	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792171	8792171	+	Silent	SNP	T	T	C	rs11650737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8792171T>C	ENST00000447110.1	-	10	1057	c.933A>G	c.(931-933)ctA>ctG	p.L311L	PIK3R5_ENST00000581552.1_Silent_p.L311L|PIK3R5_ENST00000584803.1_Silent_p.L311L	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	311				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)	p.L311L(2)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CTGGCTGGAGTAGCTCCTGTT	0.582													C|||	1017	0.203075	0.2995	0.2839	5008	,	,		20122	0.001		0.2843	False		,,,				2504	0.1401				p.L311L	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											PIK3R5,NS,carcinoma,0,1	PIK3R5	79	1	2	Substitution - coding silent(2)	prostate(2)	c.A933G						scavenged	.	C	,	1302,3104	692.1+/-405.5	204,894,1105	51.0	56.0	54.0		933,933	3.7	1.0	17	dbSNP_120	54	2695,5905	681.3+/-403.7	418,1859,2023	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	622,2753,3128	CC,CT,TT		31.3372,29.5506,30.732	,	311/881,311/881	8792171	3997,9009	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			CTGGAGTAGCTCC	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.933A>G	17.37:g.8792171T>C		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	7	3	0.428571	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			T|0.722;C|0.278	0.278	strong		0.582	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21796784	21796784	+	Missense_Mutation	SNP	G	G	C	rs3748361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21796784G>C	ENST00000400017.2	+	18	3097	c.3097G>C	c.(3097-3099)Gag>Cag	p.E1033Q	RPGRIP1_ENST00000556336.1_Missense_Mutation_p.E690Q|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.E1033Q|RPGRIP1_ENST00000382933.4_Missense_Mutation_p.E359Q|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.E995Q|RPGRIP1_ENST00000307974.4_Missense_Mutation_p.E392Q	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	1033			E -> Q (in dbSNP:rs3748361). {ECO:0000269|PubMed:10958647, ECO:0000269|PubMed:11528500, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18682808}.		eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)		p.E649Q(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		AAATACACCAGAGGTAAGACC	0.388													G|||	1479	0.295327	0.0219	0.2291	5008	,	,		20609	0.4246		0.3419	False		,,,				2504	0.5307				p.E1033Q		Atlas-SNP	.											RPGRIP1,NS,carcinoma,0,1	RPGRIP1	213	1	1	Substitution - Missense(1)	stomach(1)	c.G3097C						PASS	.	G	GLN/GLU	265,3473		12,241,1616	72.0	66.0	68.0		3097	1.8	0.4	14	dbSNP_107	68	2888,5328		523,1842,1743	yes	missense	RPGRIP1	NM_020366.3	29	535,2083,3359	CC,CG,GG		35.1509,7.0894,26.3761	benign	1033/1287	21796784	3153,8801	1869	4108	5977	SO:0001583	missense	57096	exon18			ACACCAGAGGTAA	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.3097G>C	14.37:g.21796784G>C	ENSP00000382895:p.Glu1033Gln	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	587|587	0.26877289377289376|0.26877289377289376	13|13	0.026422764227642278|0.026422764227642278	83|83	0.2292817679558011|0.2292817679558011	227|227	0.3968531468531469|0.3968531468531469	264|264	0.3482849604221636|0.3482849604221636	G|G	0.025|0.025	-1.379822|-1.379822	0.01204|0.01204	0.070894|0.070894	0.351509|0.351509	ENSG00000092200|ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000307974|ENST00000557606	T;T;T;T;T;T;T|.	0.77489|.	-0.01;-0.79;-0.83;-0.83;-0.34;-1.1;-1.1|.	4.74|4.74	1.79|1.79	0.24919|0.24919	.|.	0.810519|.	0.11028|.	N|.	0.607627|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00162|0.00162	-1.95|-1.95	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B;B|.	0.06786|.	0.0;0.0;0.0;0.001;0.0;0.0|.	B;B;B;B;B;B|.	0.04013|.	0.001;0.001;0.001;0.001;0.001;0.0|.	T|T	0.47598|0.47598	-0.9105|-0.9105	9|4	0.06365|.	T|.	0.9|.	-9.6351|-9.6351	7.5361|7.5361	0.27710|0.27710	0.1741:0.4739:0.352:0.0|0.1741:0.4739:0.352:0.0	rs3748361;rs17254729;rs52805987;rs3748361|rs3748361;rs17254729;rs52805987;rs3748361	416;392;508;359;649;1033|.	Q96KN7-2;Q96KN7-3;G3V3I7;Q96KN7-4;Q96KN7-5;Q96KN7|.	.;.;.;.;.;RPGR1_HUMAN|.	Q|H	690;995;1033;1033;359;508;392|9	ENSP00000450445:E690Q;ENSP00000451219:E995Q;ENSP00000382895:E1033Q;ENSP00000206660:E1033Q;ENSP00000372391:E359Q;ENSP00000451262:E508Q;ENSP00000309721:E392Q|.	ENSP00000206660:E1033Q|.	E|Q	+|+	1|3	0|2	RPGRIP1|RPGRIP1	20866624|20866624	0.892000|0.892000	0.30473|0.30473	0.418000|0.418000	0.26571|0.26571	0.022000|0.022000	0.10575|0.10575	1.269000|1.269000	0.33074|0.33074	1.233000|1.233000	0.43693|0.43693	-0.153000|-0.153000	0.13522|0.13522	GAG|CAG	G|0.722;C|0.277	0.277	strong		0.388	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
MYBPC2	4606	hgsc.bcm.edu	37	19	50965272	50965272	+	Silent	SNP	T	T	C	rs25668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50965272T>C	ENST00000357701.5	+	26	3258	c.3207T>C	c.(3205-3207)tgT>tgC	p.C1069C		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	1069	Ig-like C2-type 7.				cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CCCTCAACTGTGCTGTCAGAG	0.582													C|||	3977	0.794129	0.9667	0.7824	5008	,	,		14210	0.7054		0.6789	False		,,,				2504	0.7791				p.C1069C		Atlas-SNP	.											.	MYBPC2	103	.	0			c.T3207C						PASS	.	C		3750,350		1719,312,19	33.0	34.0	34.0		3207	-7.6	0.1	19	dbSNP_72	34	5618,2748		1899,1820,464	no	coding-synonymous	MYBPC2	NM_004533.3		3618,2132,483	CC,CT,TT		32.8472,8.5366,24.8516		1069/1142	50965272	9368,3098	2050	4183	6233	SO:0001819	synonymous_variant	4606	exon26			CAACTGTGCTGTC		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.3207T>C	19.37:g.50965272T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_004533	A1L4G9	Silent	SNP	ENST00000357701.5	37	CCDS46152.1																																																																																			T|0.231;C|0.769	0.769	strong		0.582	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
KHNYN	23351	hgsc.bcm.edu	37	14	24901433	24901433	+	Silent	SNP	C	C	T	rs17795094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24901433C>T	ENST00000251343.5	+	3	1105	c.966C>T	c.(964-966)caC>caT	p.H322H	KHNYN_ENST00000556842.1_Silent_p.H322H|KHNYN_ENST00000554268.1_5'Flank|KHNYN_ENST00000553935.1_Silent_p.H322H|CBLN3_ENST00000267406.6_5'Flank|CBLN3_ENST00000555436.1_5'Flank			O15037	KHNYN_HUMAN	KH and NYN domain containing	322							RNA binding (GO:0003723)			kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(3)	24						TCTGTGTCCACCGTGAGCCTC	0.647											OREG0022627	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	392	0.0782748	0.0416	0.0965	5008	,	,		17135	0.0565		0.1014	False		,,,				2504	0.1135				p.H322H		Atlas-SNP	.											.	KHNYN	46	.	0			c.C966T						PASS	.	C		323,4083	170.5+/-200.9	12,299,1892	71.0	74.0	73.0		966	2.3	0.3	14	dbSNP_123	73	1147,7453	234.6+/-267.5	72,1003,3225	yes	coding-synonymous	KHNYN	NM_015299.2		84,1302,5117	TT,TC,CC		13.3372,7.3309,11.3025		322/679	24901433	1470,11536	2203	4300	6503	SO:0001819	synonymous_variant	23351	exon3			TGTCCACCGTGAG	AB002321	CCDS32058.1	14q11.2	2010-11-23	2009-10-14	2009-10-14	ENSG00000100441	ENSG00000100441			20166	protein-coding gene	gene with protein product			"""KIAA0323"""	KIAA0323		17114934	Standard	NM_015299		Approved		uc001wph.4	O15037		ENST00000251343.5:c.966C>T	14.37:g.24901433C>T		Somatic	114	0	0	774	WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_015299	Q86TZ6|Q8IUQ2|Q96BA9	Silent	SNP	ENST00000251343.5	37	CCDS32058.1																																																																																			C|0.904;T|0.096	0.096	strong		0.647	KHNYN-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412928.1		
WWC2	80014	hgsc.bcm.edu	37	4	184190233	184190233	+	Missense_Mutation	SNP	G	G	T	rs11941467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:184190233G>T	ENST00000403733.3	+	15	2516	c.2317G>T	c.(2317-2319)Gcc>Tcc	p.A773S	WWC2_ENST00000513834.1_Missense_Mutation_p.A724S|WWC2_ENST00000448232.2_Missense_Mutation_p.A773S|WWC2_ENST00000378925.3_Missense_Mutation_p.A675S|WWC2_ENST00000506225.1_3'UTR|WWC2_ENST00000504005.1_Missense_Mutation_p.A455S	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	773	C2.		A -> S (in dbSNP:rs11941467). {ECO:0000269|PubMed:15489334}.		negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		GTTCAGAGTCGCCATTTCCCA	0.453													G|||	500	0.0998403	0.0166	0.072	5008	,	,		18521	0.0933		0.1143	False		,,,				2504	0.2239				p.A773S		Atlas-SNP	.											.	WWC2	78	.	0			c.G2317T						PASS	.	G	SER/ALA	164,4242	109.9+/-148.2	4,156,2043	148.0	146.0	146.0		2317	3.5	1.0	4	dbSNP_120	146	947,7653	208.3+/-249.8	60,827,3413	yes	missense	WWC2	NM_024949.5	99	64,983,5456	TT,TG,GG		11.0116,3.7222,8.5422	benign	773/1193	184190233	1111,11895	2203	4300	6503	SO:0001583	missense	80014	exon15			AGAGTCGCCATTT	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2317G>T	4.37:g.184190233G>T	ENSP00000384222:p.Ala773Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	60	0.545455	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	158	0.07234432234432235	3	0.006097560975609756	29	0.08011049723756906	46	0.08041958041958042	80	0.10554089709762533	G	6.837	0.523552	0.13066	0.037222	0.110116	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232;ENST00000504005	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.35	3.5	0.40072	C2 calcium/lipid-binding domain, CaLB (1);	0.255724	0.33496	N	0.004843	T	0.00178	0.0005	N	0.12471	0.22	0.31698	N	0.641027	B;B;B	0.24186	0.044;0.01;0.099	B;B;B	0.22601	0.03;0.024;0.04	T	0.12915	-1.0529	10	0.14252	T	0.57	-6.6582	13.7162	0.62697	0.0:0.0:0.505:0.495	rs11941467;rs52814359;rs59395067;rs11941467	773;773;724	Q6AWC2-6;Q6AWC2;Q6AWC2-4	.;WWC2_HUMAN;.	S	773;675;724;773;455	ENSP00000384222:A773S;ENSP00000368205:A675S;ENSP00000425054:A724S;ENSP00000398577:A773S;ENSP00000427569:A455S	ENSP00000368205:A675S	A	+	1	0	WWC2	184427227	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	1.546000	0.36179	1.430000	0.47334	0.555000	0.69702	GCC	G|0.917;T|0.083	0.083	strong		0.453	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
TSHZ1	10194	hgsc.bcm.edu	37	18	72998526	72998526	+	Silent	SNP	G	G	A	rs34095753	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:72998526G>A	ENST00000580243.1	+	2	1512	c.1164G>A	c.(1162-1164)ccG>ccA	p.P388P	TSHZ1_ENST00000322038.5_Silent_p.P343P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	388					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CAGCGAACCCGTACGTCACGC	0.622													G|||	143	0.0285543	0.0015	0.0274	5008	,	,		19271	0.002		0.0586	False		,,,				2504	0.0624				p.P343P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G1029A						PASS	.	G		49,4357	50.9+/-86.3	1,47,2155	101.0	106.0	105.0		1029	-5.5	1.0	18	dbSNP_126	105	593,8007	158.0+/-211.6	19,555,3726	no	coding-synonymous	TSHZ1	NM_005786.4		20,602,5881	AA,AG,GG		6.8953,1.1121,4.9362		343/1033	72998526	642,12364	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GAACCCGTACGTC	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.1164G>A	18.37:g.72998526G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				G|0.955;A|0.045	0.045	strong		0.622	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103027234	103027234	+	Missense_Mutation	SNP	A	A	G	rs17301750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:103027234A>G	ENST00000375735.2	+	26	4006	c.3862A>G	c.(3862-3864)Act>Gct	p.T1288A	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.T1288A	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	1288	Stem. {ECO:0000250}.		T -> A (in dbSNP:rs17301750).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCAAAGTCGAACTATGAAGCT	0.358													A|||	382	0.076278	0.0023	0.0922	5008	,	,		15673	0.0923		0.1233	False		,,,				2504	0.1002				p.T1288A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A3862G						PASS	.	A	ALA/THR,ALA/THR	97,3585		2,93,1746	96.0	95.0	95.0		3862,3862	4.1	1.0	11	dbSNP_123	95	944,7242		58,828,3207	yes	missense,missense	DYNC2H1	NM_001080463.1,NM_001377.2	58,58	60,921,4953	GG,GA,AA		11.5319,2.6344,8.7715	benign,benign	1288/4315,1288/4308	103027234	1041,10827	1841	4093	5934	SO:0001583	missense	79659	exon26			AGTCGAACTATGA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.3862A>G	11.37:g.103027234A>G	ENSP00000364887:p.Thr1288Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	33	0.417722	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	190	0.08699633699633699	3	0.006097560975609756	33	0.09116022099447514	50	0.08741258741258741	104	0.13720316622691292	A	6.130	0.392124	0.11581	0.026344	0.115319	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.60424	0.19;0.19	5.27	4.1	0.47936	Dynein heavy chain, domain-2 (1);	0.981166	0.08306	N	0.966220	T	0.00524	0.0017	L	0.54323	1.7	0.38246	P	0.05853600000000003	B;B	0.11235	0.004;0.004	B;B	0.16722	0.016;0.014	T	0.18681	-1.0329	9	0.08599	T	0.76	.	11.2807	0.49192	0.8632:0.0:0.0:0.1368	rs17301750;rs52791460;rs17301750	1288;1288	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	A	1288	ENSP00000364887:T1288A;ENSP00000381167:T1288A	ENSP00000364887:T1288A	T	+	1	0	DYNC2H1	102532444	1.000000	0.71417	0.994000	0.49952	0.991000	0.79684	4.416000	0.59815	0.796000	0.33947	0.460000	0.39030	ACT	A|0.912;G|0.088	0.088	strong		0.358	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
TIGD1	200765	hgsc.bcm.edu	37	2	233413771	233413771	+	Silent	SNP	C	C	T	rs6752614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233413771C>T	ENST00000408957.3	-	1	1455	c.822G>A	c.(820-822)gcG>gcA	p.A274A	EIF4E2_ENST00000409322.1_5'Flank|EIF4E2_ENST00000409098.1_5'Flank|EIF4E2_ENST00000409495.1_5'Flank|EIF4E2_ENST00000409394.1_5'Flank|EIF4E2_ENST00000409167.3_5'Flank|EIF4E2_ENST00000409514.1_5'Flank|EIF4E2_ENST00000258416.3_5'Flank|MIR5001_ENST00000580185.1_RNA	NM_145702.1	NP_663748.1	Q96MW7	TIGD1_HUMAN	tigger transposable element derived 1	274	DDE.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|skin(1)	2		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;2e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|LUSC - Lung squamous cell carcinoma(224;0.00746)|Lung(119;0.00842)|GBM - Glioblastoma multiforme(43;0.233)		cagtaaaccacgctgtaaaca	0.398													T|||	2387	0.476637	0.2436	0.6138	5008	,	,		20248	0.5863		0.4692	False		,,,				2504	0.589				p.A274A		Atlas-SNP	.											TIGD1,colon,carcinoma,0,1	TIGD1	17	1	0			c.G822A						PASS	.	T		704,1944		101,502,721	12.0	14.0	13.0		822	-0.8	0.4	2	dbSNP_116	13	2228,2386		555,1118,634	no	coding-synonymous	TIGD1	NM_145702.1		656,1620,1355	TT,TC,CC		48.2878,26.5861,40.3746		274/592	233413771	2932,4330	1324	2307	3631	SO:0001819	synonymous_variant	200765	exon1			AAACCACGCTGTA		CCDS2495.1	2q37.1	2011-01-17			ENSG00000221944	ENSG00000221944			14523	protein-coding gene	gene with protein product		612972					Standard	NM_145702		Approved	EEYORE	uc002vsy.2	Q96MW7	OTTHUMG00000133260	ENST00000408957.3:c.822G>A	2.37:g.233413771C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_145702	Q6P4D2|Q6PIF9	Silent	SNP	ENST00000408957.3	37	CCDS2495.1																																																																																			C|0.535;T|0.465	0.465	strong		0.398	TIGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257037.1	NM_145702	
ALS2CL	259173	hgsc.bcm.edu	37	3	46713457	46713457	+	Silent	SNP	C	C	G	rs7625303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46713457C>G	ENST00000318962.4	-	24	2684	c.2601G>C	c.(2599-2601)acG>acC	p.T867T	ALS2CL_ENST00000383742.3_Silent_p.T214T|ALS2CL_ENST00000415953.1_Silent_p.T867T	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	867	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CCCTCGACACCGTGCCCTCAA	0.642													C|||	1254	0.250399	0.1483	0.2968	5008	,	,		17491	0.38		0.2197	False		,,,				2504	0.2536				p.T867T		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G2601C						PASS	.	C	,,	723,3683	299.8+/-286.0	58,607,1538	124.0	103.0	110.0		2601,2601,642	-10.6	0.7	3	dbSNP_116	110	1848,6752	330.1+/-319.0	197,1454,2649	no	coding-synonymous,coding-synonymous,coding-synonymous	ALS2CL	NM_001190707.1,NM_147129.3,NM_182775.2	,,	255,2061,4187	GG,GC,CC		21.4884,16.4094,19.7678	,,	867/954,867/954,214/301	46713457	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	259173	exon24			CGACACCGTGCCC	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2601G>C	3.37:g.46713457C>G		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	94	93	0.989362	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Silent	SNP	ENST00000318962.4	37	CCDS2743.1																																																																																			C|0.780;G|0.220	0.220	strong		0.642	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
RPTOR	57521	hgsc.bcm.edu	37	17	78865630	78865630	+	Silent	SNP	A	A	G	rs2289765	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:78865630A>G	ENST00000306801.3	+	18	2456	c.2094A>G	c.(2092-2094)gcA>gcG	p.A698A	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Silent_p.A540A	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	698					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						CTTCTCCAGCAACCACAGGTA	0.557													G|||	1152	0.230032	0.3343	0.1398	5008	,	,		14671	0.2321		0.1123	False		,,,				2504	0.272				p.A698A		Atlas-SNP	.											.	RPTOR	122	.	0			c.A2094G						PASS	.	G	,	1317,3089	696.3+/-406.1	197,923,1083	105.0	89.0	94.0		1620,2094	-9.4	0.0	17	dbSNP_100	94	1057,7543	770.8+/-407.7	73,911,3316	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	270,1834,4399	GG,GA,AA		12.2907,29.8911,18.2531	,	540/1178,698/1336	78865630	2374,10632	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon18			TCCAGCAACCACA		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.2094A>G	17.37:g.78865630A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			A|0.803;G|0.197	0.197	strong		0.557	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
PIEZO1	9780	hgsc.bcm.edu	37	16	88779032	88779032	+	IGR	SNP	G	G	C	rs2290896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88779032G>C	ENST00000301015.9	-	0	8072				CTU2_ENST00000453996.2_Silent_p.V152V|CTU2_ENST00000567949.1_Silent_p.V223V|CTU2_ENST00000378384.3_Silent_p.V65V|CTU2_ENST00000312060.5_Silent_p.V152V	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						CCCGGAAGGTGTTCAGCCTGC	0.692													G|||	474	0.0946486	0.0318	0.1556	5008	,	,		12054	0.127		0.1243	False		,,,				2504	0.0726				p.V152V		Atlas-SNP	.											CTU2_ENST00000453996,NS,carcinoma,0,2	CTU2	66	2	0			c.G456C						PASS	.	G	,	212,4180		4,204,1988	27.0	33.0	31.0		456,456	3.1	1.0	16	dbSNP_100	31	1191,7405		74,1043,3181	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	78,1247,5169	CC,CG,GG		13.8553,4.827,10.8023	,	152/516,152/486	88779032	1403,11585	2196	4298	6494	SO:0001628	intergenic_variant	348180	exon7			GAAGGTGTTCAGC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		16.37:g.88779032G>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			G|0.895;C|0.105	0.105	strong		0.692	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
MUC4	4585	hgsc.bcm.edu	37	3	195509939	195509939	+	Missense_Mutation	SNP	G	G	T	rs202039836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195509939G>T	ENST00000463781.3	-	2	8971	c.8512C>A	c.(8512-8514)Cct>Act	p.P2838T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2838T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.P2838T(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGGGATGGTGACA	0.592													.|||	318	0.0634984	0.0045	0.0432	5008	,	,		7871	0.0417		0.1521	False		,,,				2504	0.089				p.P2838T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	kidney(3)	c.C8512A						scavenged	.						102.0	63.0	75.0					3																	195509939		690	1569	2259	SO:0001583	missense	4585	exon2			AGGAAGGGATGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8512C>A	3.37:g.195509939G>T	ENSP00000417498:p.Pro2838Thr	Somatic	252	2	0.00793651		WXS	Illumina HiSeq	Phase_I	166	11	0.0662651	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	3.466	-0.108992	0.06924	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.55	.	.	.	.	.	.	.	.	T	0.10551	0.0258	N	0.08118	0	0.09310	N	1	P	0.38110	0.618	B	0.28638	0.092	T	0.19386	-1.0307	7	.	.	.	.	4.5444	0.12074	0.0:0.4166:0.5833:0.0	.	2710	E7ESK3	.	T	2838	ENSP00000417498:P2838T;ENSP00000420243:P2838T	.	P	-	1	0	MUC4	196994718	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.690000	0.00392	-0.000000	0.14550	0.000000	0.15137	CCT	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CNTLN	54875	hgsc.bcm.edu	37	9	17273731	17273731	+	Splice_Site	SNP	A	A	G	rs3808795	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:17273731A>G	ENST00000380647.3	+	6	934	c.850A>G	c.(850-852)Acc>Gcc	p.T284A	CNTLN_ENST00000380641.4_Splice_Site_p.T284A|CNTLN_ENST00000262360.5_Splice_Site_p.T284A|CNTLN_ENST00000425824.1_Splice_Site_p.T284A			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	284			T -> A (in dbSNP:rs3808795).		centriole-centriole cohesion (GO:0010457)|protein localization to organelle (GO:0033365)	centriole (GO:0005814)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)|protein binding, bridging (GO:0030674)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(6)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53				GBM - Glioblastoma multiforme(50;6.14e-10)		CTAATTTTAGACCTTTGAAGA	0.264													G|||	1674	0.334265	0.3298	0.245	5008	,	,		15726	0.3502		0.2853	False		,,,				2504	0.4376				p.T284A		Atlas-SNP	.											.	CNTLN	128	.	0			c.A850G						PASS	.	G	ALA/THR,ALA/THR	1134,2470		191,752,859	72.0	72.0	72.0		850,850	2.2	1.0	9	dbSNP_107	72	2199,5923		316,1567,2178	yes	missense-near-splice,missense-near-splice	CNTLN	NM_001114395.1,NM_017738.2	58,58	507,2319,3037	GG,GA,AA		27.0746,31.465,28.424	benign,benign	284/392,284/1407	17273731	3333,8393	1802	4061	5863	SO:0001630	splice_region_variant	54875	exon6			TTTTAGACCTTTG	AK000283	CCDS43789.1, CCDS47953.1	9p22.2-p22.1	2008-11-11	2008-02-08	2008-02-08	ENSG00000044459	ENSG00000044459			23432	protein-coding gene	gene with protein product		611870	"""chromosome 9 open reading frame 101"", ""chromosome 9 open reading frame 39"""	C9orf101, C9orf39		18086554	Standard	XM_005251492		Approved	FLJ20276, bA340N12.1, OTTHUMG00000019597	uc003zmy.3	Q9NXG0	OTTHUMG00000019599	ENST00000380647.3:c.850-1A>G	9.37:g.17273731A>G		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	622	0.2847985347985348	137	0.2784552845528455	94	0.2596685082872928	187	0.3269230769230769	204	0.2691292875989446	G	1.629	-0.519449	0.04171	0.31465	0.270746	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	4.48	2.17	0.27698	.	.	.	.	.	T	0.00012	0.0000	N	0.01705	-0.755	0.53688	P	2.599999999997049E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.48139	-0.9061	7	.	.	.	.	5.2808	0.15674	0.5249:0.0:0.4751:0.0	rs3808795;rs61116885;rs3808795	284;284;284	C9J1F9;Q9NXG0-2;Q9NXG0-3	.;.;.	A	284	ENSP00000370021:T284A;ENSP00000392798:T284A;ENSP00000262360:T284A;ENSP00000370015:T284A	.	T	+	1	0	CNTLN	17263731	0.565000	0.26610	0.999000	0.59377	0.871000	0.50021	0.744000	0.26245	0.456000	0.26937	-0.684000	0.03749	ACC	A|0.706;G|0.294	0.294	strong		0.264	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738	Missense_Mutation
POLDIP3	84271	hgsc.bcm.edu	37	22	43010821	43010821	+	Missense_Mutation	SNP	C	C	T	rs61744232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:43010821C>T	ENST00000252115.5	-	1	147	c.43G>A	c.(43-45)Gcg>Acg	p.A15T	RNU12_ENST00000362512.1_lincRNA|POLDIP3_ENST00000348657.2_Missense_Mutation_p.A15T|POLDIP3_ENST00000339677.6_Missense_Mutation_p.A15T	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	15					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						TTCGCCGCCGCCCCGCGCTTC	0.672													C|||	19	0.00379393	0.0	0.0115	5008	,	,		12867	0.0		0.0089	False		,,,				2504	0.002				p.A15T	Ovarian(52;967 1128 5875 19997 42537)	Atlas-SNP	.											.	POLDIP3	58	.	0			c.G43A						PASS	.	C	THR/ALA,THR/ALA	13,4393	20.2+/-43.8	0,13,2190	45.0	50.0	48.0		43,43	-1.5	0.0	22	dbSNP_129	48	93,8507	51.9+/-112.3	1,91,4208	yes	missense,missense	POLDIP3	NM_032311.3,NM_178136.1	58,58	1,104,6398	TT,TC,CC		1.0814,0.2951,0.815	benign,benign	15/422,15/393	43010821	106,12900	2203	4300	6503	SO:0001583	missense	84271	exon1			CCGCCGCCCCGCG		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"""RNA binding motif (RRM) containing"""	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.43G>A	22.37:g.43010821C>T	ENSP00000252115:p.Ala15Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_178136	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	3.855	-0.030975	0.07543	0.002951	0.010814	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	4.4	-1.47	0.08772	.	0.803483	0.11757	N	0.532429	T	0.08891	0.0220	N	0.04508	-0.205	0.09310	N	0.999995	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.0	T	0.29882	-0.9997	9	0.13470	T	0.59	-16.8684	4.6712	0.12691	0.1382:0.4646:0.0:0.3972	.	15;15;15;15	B4E0L0;Q6R954;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	T	15	.	ENSP00000252115:A15T	A	-	1	0	POLDIP3	41340765	0.001000	0.12720	0.000000	0.03702	0.689000	0.40095	0.621000	0.24418	-0.251000	0.09542	-0.259000	0.10710	GCG	C|0.995;T|0.005	0.005	strong		0.672	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311	
SPINK5	11005	hgsc.bcm.edu	37	5	147480955	147480955	+	Missense_Mutation	SNP	A	A	G	rs2303067	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:147480955A>G	ENST00000256084.7	+	14	1300	c.1258A>G	c.(1258-1260)Aaa>Gaa	p.K420E	SPINK5_ENST00000398454.1_Missense_Mutation_p.K420E|SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Missense_Mutation_p.K420E	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	420	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.		K -> E (in dbSNP:rs2303067). {ECO:0000269|PubMed:10419450, ECO:0000269|PubMed:11544479, ECO:0000269|PubMed:16374478}.		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAGGAAGGTAAATCAAGAAA	0.383													G|||	2169	0.433107	0.1989	0.6167	5008	,	,		17991	0.4851		0.4871	False		,,,				2504	0.5102				p.K420E		Atlas-SNP	.											.	SPINK5	245	.	0			c.A1258G	GRCh37	CM013815	SPINK5	M	rs2303067	PASS	.	G	GLU/LYS,GLU/LYS,GLU/LYS	946,2756		121,704,1026	124.0	110.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1258,1258,1258	2.8	0.5	5	dbSNP_100	114	4204,3986		1071,2062,962	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	56,56,56	1192,2766,1988	GG,GA,AA		48.6691,25.5538,43.3064	benign,benign,benign	420/1095,420/917,420/1065	147480955	5150,6742	1851	4095	5946	SO:0001583	missense	11005	exon14			GAAGGTAAATCAA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1258A>G	5.37:g.147480955A>G	ENSP00000256084:p.Lys420Glu	Somatic	301	1	0.00332226		WXS	Illumina HiSeq	Phase_I	242	240	0.991736	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	936	0.42857142857142855	111	0.22560975609756098	213	0.5883977900552486	263	0.4597902097902098	349	0.4604221635883905	G	0.156	-1.086008	0.01873	0.255538	0.513309	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.03801	3.8;3.8;3.8;3.8	3.72	2.84	0.33178	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	1.088120	0.07087	N	0.838072	T	0.00012	0.0000	N	0.00368	-1.59	0.58432	P	5.000000000032756E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.002	T	0.41161	-0.9524	9	0.02654	T	1	-6.8235	4.7186	0.12906	0.1116:0.0:0.6761:0.2123	rs2303067;rs17775367;rs17860505;rs52832839;rs56830970;rs2303067	420;420;420	Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;ISK5_HUMAN;.	E	420;420;401;420	ENSP00000381472:K420E;ENSP00000352936:K420E;ENSP00000421519:K401E;ENSP00000256084:K420E	ENSP00000256084:K420E	K	+	1	0	SPINK5	147461148	0.127000	0.22367	0.464000	0.27143	0.640000	0.38277	0.153000	0.16323	0.538000	0.28769	-0.128000	0.14901	AAA	A|0.569;G|0.431	0.431	strong		0.383	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
C17orf97	400566	hgsc.bcm.edu	37	17	263652	263652	+	Missense_Mutation	SNP	G	G	A	rs111543298	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:263652G>A	ENST00000360127.6	+	2	1034	c.1018G>A	c.(1018-1020)Gag>Aag	p.E340K	AC108004.3_ENST00000466740.2_RNA|C17orf97_ENST00000571106.1_Intron	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	370	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.							p.E340K(2)		breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						CCCCGACCCCGAGGCCCTCAA	0.697																																					p.E340K		Atlas-SNP	.											C17orf97_ENST00000360127,rectum,carcinoma,0,5	C17orf97	76	5	2	Substitution - Missense(2)	large_intestine(1)|pancreas(1)	c.G1018A						scavenged	.																																			SO:0001583	missense	400566	exon2			GACCCCGAGGCCC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.1018G>A	17.37:g.263652G>A	ENSP00000353245:p.Glu340Lys	Somatic	169	1	0.00591716		WXS	Illumina HiSeq	Phase_I	151	31	0.205298	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000360127.6	37	CCDS32519.2	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.456157	0.01071	.	.	ENSG00000187624	ENST00000360127	T	0.30448	1.53	2.05	-4.1	0.03940	.	.	.	.	.	T	0.10637	0.0260	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16660	-1.0395	9	0.20046	T	0.44	.	1.1152	0.01713	0.4009:0.1974:0.266:0.1357	.	340	Q6ZQX7-4	.	K	340	ENSP00000353245:E340K	ENSP00000353245:E340K	E	+	1	0	C17orf97	263998	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.847000	0.00351	-2.613000	0.00444	-1.026000	0.02426	GAG	G|0.162;A|0.838	0.838	strong		0.697	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
ARHGEF25	115557	hgsc.bcm.edu	37	12	58010163	58010163	+	Missense_Mutation	SNP	A	A	G	rs57224884|rs1564374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:58010163A>G	ENST00000286494.4	+	14	1977	c.1517A>G	c.(1516-1518)cAg>cGg	p.Q506R	AC025165.8_ENST00000444467.1_RNA|AC025165.8_ENST00000356672.3_RNA|AC025165.8_ENST00000610219.1_RNA|ARHGEF25_ENST00000333972.7_Missense_Mutation_p.Q545R|AC025165.8_ENST00000593846.1_RNA	NM_182947.3	NP_891992	Q86VW2	ARHGP_HUMAN	Rho guanine nucleotide exchange factor (GEF) 25	506			Q -> R (in dbSNP:rs1564374). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			cytosol (GO:0005829)|myofibril (GO:0030016)|plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	28						GGAAGAATTCAGCTTGGAGAT	0.617													G|||	3156	0.630192	0.5197	0.6657	5008	,	,		16921	0.7222		0.5527	False		,,,				2504	0.7393				p.Q545R		Atlas-SNP	.											.	ARHGEF25	111	.	0			c.A1634G						PASS	.	G	ARG/GLN,ARG/GLN	2353,2053		632,1089,482	74.0	73.0	73.0		1634,1517	3.7	0.4	12	dbSNP_88	73	4851,3749		1381,2089,830	yes	missense,missense	ARHGEF25	NM_001111270.1,NM_182947.2	43,43	2013,3178,1312	GG,GA,AA		43.593,46.5956,44.6102	benign,benign	545/620,506/581	58010163	7204,5802	2203	4300	6503	SO:0001583	missense	115557	exon15			GAATTCAGCTTGG		CCDS8947.1, CCDS44931.1	12q13.3	2011-11-16			ENSG00000240771	ENSG00000240771		"""Rho guanine nucleotide exchange factors"""	30275	protein-coding gene	gene with protein product	"""RAC/CDC42 exchange factor"""	610215				12547822	Standard	NM_182947		Approved	GEFT, p63RhoGEF	uc009zpy.4	Q86VW2	OTTHUMG00000152516	ENST00000286494.4:c.1517A>G	12.37:g.58010163A>G	ENSP00000286494:p.Gln506Arg	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_001111270	A6NJH5|A9CQZ6|F8W7Z4|Q8WV84|Q96E63	Missense_Mutation	SNP	ENST00000286494.4	37	CCDS8947.1	1398	0.6401098901098901	284	0.5772357723577236	222	0.6132596685082873	453	0.791958041958042	439	0.579155672823219	N	0.006	-2.114913	0.00349	0.534044	0.56407	ENSG00000240771	ENST00000333972;ENST00000286494	T;T	0.37411	1.23;1.2	4.56	3.66	0.41972	.	0.252152	0.21027	N	0.081419	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	0.39961	-0.9588	9	0.02654	T	1	.	7.6461	0.28321	0.1977:0.0:0.8023:0.0	rs1564374;rs17856409;rs17857334;rs56537767;rs1564374	545;506	F8W7Z4;Q86VW2	.;ARHGP_HUMAN	R	545;506	ENSP00000335560:Q545R;ENSP00000286494:Q506R	ENSP00000286494:Q506R	Q	+	2	0	ARHGEF25	56296430	0.247000	0.23920	0.431000	0.26735	0.122000	0.20287	0.321000	0.19558	0.659000	0.30945	-0.128000	0.14901	CAG	A|0.402;G|0.598;T|0.000	0.598	strong		0.617	ARHGEF25-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326561.1	NM_133483	
VCX2	51480	hgsc.bcm.edu	37	X	8138170	8138170	+	Missense_Mutation	SNP	C	C	G	rs75657421		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:8138170C>G	ENST00000317103.4	-	3	629	c.323G>C	c.(322-324)aGc>aCc	p.S108T		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	108	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.			S -> A (in Ref. 1; AAG41765, 2; AAF28172 and 4; AAH98113/AAH96715/AAH98163). {ECO:0000305}.						endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				TTCCACCTCGCTCTCCTGACT	0.642													G|||	3056	0.809536	0.5908	0.6427	3775	,	,		3228	0.7192		0.5775	False		,,,				2504	0.5348				p.S108T		Atlas-SNP	.											.	VCX2	16	.	0			c.G323C						PASS	.						35.0	44.0	41.0					X																	8138170		1777	3690	5467	SO:0001583	missense	51480	exon3			ACCTCGCTCTCCT	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.323G>C	X.37:g.8138170C>G	ENSP00000321309:p.Ser108Thr	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	81	72	0.888889	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	1050	0.6329113924050633	144	0.38095238095238093	131	0.5646551724137931	216	0.6352941176470588	227	0.40827338129496404	G	0.003	-2.558529	0.00136	.	.	ENSG00000177504	ENST00000317103	T	0.14022	2.54	0.0465	0.0465	0.14256	.	.	.	.	.	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	0.41466	-0.9507	7	0.02654	T	1	.	.	.	.	.	108	Q9H322	VCX2_HUMAN	T	108	ENSP00000321309:S108T	ENSP00000321309:S108T	S	-	2	0	VCX2	8098170	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	-0.361000	0.07612	-1.450000	0.01936	-1.461000	0.01025	AGC	C|0.367;G|0.633	0.633	strong		0.642	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
FAM209B	388799	hgsc.bcm.edu	37	20	55108538	55108538	+	Silent	SNP	C	C	T	rs141117316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:55108538C>T	ENST00000371325.1	+	1	237	c.141C>T	c.(139-141)aaC>aaT	p.N47N		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	47						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TTCGGCAGAACCTACCAGAGC	0.517																																					p.N47N		Atlas-SNP	.											.	.	.	.	0			c.C141T						PASS	.	C		7,4399	8.1+/-20.4	0,7,2196	173.0	145.0	155.0		141	-1.2	0.0	20	dbSNP_134	155	61,8539	24.6+/-71.5	0,61,4239	no	coding-synonymous	C20orf107	NM_001013646.2		0,68,6435	TT,TC,CC		0.7093,0.1589,0.5228		47/172	55108538	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	388799	exon1			GCAGAACCTACCA	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.141C>T	20.37:g.55108538C>T		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	346	74	0.213873	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			C|0.994;T|0.006	0.006	strong		0.517	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
PEX6	5190	hgsc.bcm.edu	37	6	42932202	42932202	+	Silent	SNP	C	C	T	rs386700658|rs1129186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42932202C>T	ENST00000304611.8	-	17	2883	c.2814G>A	c.(2812-2814)gaG>gaA	p.E938E	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	938					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)			AGCTACCTGGCTCCAGCCCTG	0.627													C|||	2472	0.49361	0.7617	0.428	5008	,	,		18458	0.1687		0.5447	False		,,,				2504	0.4601				p.E938E		Atlas-SNP	.											PEX6,colon,carcinoma,0,1	PEX6	44	1	0			c.G2814A						PASS	.	C		3222,1184	687.7+/-404.9	1178,866,159	48.0	44.0	45.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2814	4.2	0.9	6	dbSNP_86	45	4550,4050	573.4+/-389.9	1178,2194,928	no	coding-synonymous	PEX6	NM_000287.3		2356,3060,1087	TT,TC,CC		47.093,26.8724,40.243		938/981	42932202	7772,5234	2203	4300	6503	SO:0001819	synonymous_variant	5190	exon17			ACCTGGCTCCAGC	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.2814G>A	6.37:g.42932202C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Silent	SNP	ENST00000304611.8	37	CCDS4877.1																																																																																			C|0.441;T|0.559	0.559	strong		0.627	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
COL5A3	50509	hgsc.bcm.edu	37	19	10071347	10071347	+	Missense_Mutation	SNP	C	C	T	rs2277969	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10071347C>T	ENST00000264828.3	-	66	5156	c.5071G>A	c.(5071-5073)Gtc>Atc	p.V1691I		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1691	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.		V -> I (in dbSNP:rs2277969).		axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCCTGGGGGACGCTGACAGTG	0.627													C|||	1267	0.252995	0.385	0.2853	5008	,	,		17190	0.1091		0.1889	False		,,,				2504	0.2658				p.V1691I		Atlas-SNP	.											.	COL5A3	243	.	0			c.G5071A						PASS	.	C	ILE/VAL	1505,2901	476.6+/-357.7	230,1045,928	64.0	65.0	65.0		5071	1.8	0.4	19	dbSNP_100	65	1632,6968	300.4+/-304.9	139,1354,2807	yes	missense	COL5A3	NM_015719.3	29	369,2399,3735	TT,TC,CC		18.9767,34.158,24.1196	benign	1691/1746	10071347	3137,9869	2203	4300	6503	SO:0001583	missense	50509	exon66			GGGGGACGCTGAC	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.5071G>A	19.37:g.10071347C>T	ENSP00000264828:p.Val1691Ile	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	49	20	0.408163	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	469	0.21474358974358973	176	0.35772357723577236	89	0.24585635359116023	59	0.10314685314685315	145	0.19129287598944592	C	10.12	1.262374	0.23051	0.34158	0.189767	ENSG00000080573	ENST00000264828	T	0.75704	-0.96	4.03	1.81	0.25067	Fibrillar collagen, C-terminal (4);	0.297436	0.26213	U	0.025666	T	0.00012	0.0000	L	0.46157	1.445	0.52501	P	4.300000000001525E-5	B	0.15930	0.015	B	0.10450	0.005	T	0.17684	-1.0361	9	0.41790	T	0.15	.	8.4159	0.32670	0.0:0.7959:0.0:0.2041	rs2277969;rs3207622;rs59814308;rs2277969	1691	P25940	CO5A3_HUMAN	I	1691	ENSP00000264828:V1691I	ENSP00000264828:V1691I	V	-	1	0	COL5A3	9932347	0.747000	0.28283	0.354000	0.25760	0.078000	0.17371	1.637000	0.37155	0.917000	0.36895	0.462000	0.41574	GTC	C|0.770;T|0.230	0.230	strong		0.627	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
TRPM5	29850	hgsc.bcm.edu	37	11	2436201	2436201	+	Missense_Mutation	SNP	C	C	T	rs202052284		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2436201C>T	ENST00000155858.6	-	10	1564	c.1556G>A	c.(1555-1557)cGg>cAg	p.R519Q	TRPM5_ENST00000528453.1_Missense_Mutation_p.R519Q|TRPM5_ENST00000452833.1_Missense_Mutation_p.R521Q|TRPM5_ENST00000533060.1_Missense_Mutation_p.R519Q	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)		GAACAGGTCCCGCCAGGGGTT	0.711																																					p.R519Q	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1556A						PASS	.	C	GLN/ARG	1,4355		0,1,2177	23.0	29.0	27.0		1556	3.7	1.0	11		27	2,8566		0,2,4282	yes	missense	TRPM5	NM_014555.3	43	0,3,6459	TT,TC,CC		0.0233,0.023,0.0232	probably-damaging	519/1166	2436201	3,12921	2178	4284	6462	SO:0001583	missense	29850	exon10			AGGTCCCGCCAGG	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.1556G>A	11.37:g.2436201C>T	ENSP00000155858:p.Arg519Gln	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	20	16	0.8	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822268	0.71028	2.3E-4	2.33E-4	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92	3.68	3.68	0.42216	.	0.000000	0.85682	D	0.000000	D	0.87309	0.6145	L	0.46885	1.475	0.47214	D	0.999352	D;D;D	0.89917	1.0;1.0;0.993	D;D;P	0.65443	0.935;0.935;0.837	D	0.86502	0.1804	10	0.48119	T	0.1	-29.7753	9.9877	0.41852	0.2027:0.7973:0.0:0.0	.	519;521;519	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	Q	513;519;521;519;519;519	ENSP00000434383:R513Q;ENSP00000155858:R519Q;ENSP00000387965:R521Q;ENSP00000434121:R519Q;ENSP00000436809:R519Q	ENSP00000155858:R519Q	R	-	2	0	TRPM5	2392777	0.861000	0.29849	0.957000	0.39632	0.939000	0.58152	3.421000	0.52742	2.069000	0.61940	0.491000	0.48974	CGG	C|0.998;T|0.002	0.002	weak		0.711	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
SLC24A4	123041	hgsc.bcm.edu	37	14	92922900	92922900	+	Silent	SNP	G	G	A	rs77671856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92922900G>A	ENST00000532405.1	+	12	1429	c.1203G>A	c.(1201-1203)ccG>ccA	p.P401P	SLC24A4_ENST00000351924.5_Silent_p.P365P|SLC24A4_ENST00000298877.1_Silent_p.P384P|SLC24A4_ENST00000531433.1_Silent_p.P382P|SLC24A4_ENST00000556739.1_3'UTR|SLC24A4_ENST00000393265.2_Silent_p.P337P			Q8NFF2	NCKX4_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 4	401	Poly-Pro.				amelogenesis (GO:0097186)|cellular calcium ion homeostasis (GO:0006874)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|sensory perception of smell (GO:0007608)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(20)|ovary(2)|skin(1)	36		all_cancers(154;0.0347)|all_epithelial(191;0.163)		Colorectal(1;0.00242)|COAD - Colon adenocarcinoma(157;0.047)|Epithelial(152;0.0781)|READ - Rectum adenocarcinoma(1;0.176)|all cancers(159;0.182)		AGCCACCACCGCCAGAGCCAG	0.622											OREG0022876	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	858	0.171326	0.1596	0.2392	5008	,	,		16905	0.0724		0.2445	False		,,,				2504	0.1656				p.P401P	NSCLC(10;315 435 10383 28450 38798)	Atlas-SNP	.											SLC24A4,colon,carcinoma,0,1	SLC24A4	112	1	0			c.G1203A						PASS	.	G	,,	737,3659		68,601,1529	30.0	36.0	34.0		1203,1146,1011	1.1	0.2	14	dbSNP_131	34	2181,6399		274,1633,2383	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC24A4	NM_153646.3,NM_153647.3,NM_153648.3	,,	342,2234,3912	AA,AG,GG		25.4196,16.7652,22.4877	,,	401/623,382/604,337/559	92922900	2918,10058	2198	4290	6488	SO:0001819	synonymous_variant	123041	exon12			ACCACCGCCAGAG	AF520704	CCDS9903.1, CCDS45155.1, CCDS45156.1, CCDS9903.2, CCDS45155.2	14q32.12	2013-05-22			ENSG00000140090	ENSG00000140090		"""Solute carriers"""	10978	protein-coding gene	gene with protein product		609840					Standard	NM_153646		Approved	NCKX4	uc001yak.3	Q8NFF2	OTTHUMG00000167589	ENST00000532405.1:c.1203G>A	14.37:g.92922900G>A		Somatic	43	0	0	1293	WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_153646	B4DHE7|B9ZVY2|Q8N8U6|Q8NCX1|Q8NFF0|Q8NFF1	Silent	SNP	ENST00000532405.1	37	CCDS9903.2	389	0.17811355311355312	71	0.1443089430894309	93	0.2569060773480663	42	0.07342657342657342	183	0.24142480211081793	G	0.084	-1.179173	0.01633	0.167652	0.254196	ENSG00000140090	ENST00000525557	.	.	.	4.15	1.06	0.20224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.23762	-1.0179	3	.	.	.	.	6.9551	0.24565	0.1773:0.4239:0.3988:0.0	.	.	.	.	T	267	.	.	A	+	1	0	SLC24A4	91992653	0.000000	0.05858	0.203000	0.23512	0.007000	0.05969	-0.606000	0.05654	0.388000	0.25054	-0.384000	0.06662	GCC	G|0.792;A|0.208	0.208	strong		0.622	SLC24A4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395240.1	NM_153646	
COL22A1	169044	hgsc.bcm.edu	37	8	139701209	139701209	+	Missense_Mutation	SNP	G	G	T	rs4909444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:139701209G>T	ENST00000303045.6	-	37	3259	c.2813C>A	c.(2812-2814)gCt>gAt	p.A938D	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.A938D	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	938	Collagen-like 8.|Gly-rich.|Pro-rich.		A -> D (in dbSNP:rs4909444). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GAGGCCGGGAGCACCCTGTGG	0.517										HNSCC(7;0.00092)			G|||	1461	0.291733	0.2534	0.3012	5008	,	,		19616	0.1835		0.34	False		,,,				2504	0.3988				p.A938D		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2813A						PASS	.	G	ASP/ALA	1269,3137	434.1+/-343.8	198,873,1132	130.0	118.0	122.0		2813	2.7	0.4	8	dbSNP_111	122	2821,5779	444.9+/-360.8	474,1873,1953	yes	missense	COL22A1	NM_152888.1	126	672,2746,3085	TT,TG,GG		32.8023,28.8016,31.447	benign	938/1627	139701209	4090,8916	2203	4300	6503	SO:0001583	missense	169044	exon37			CCGGGAGCACCCT	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2813C>A	8.37:g.139701209G>T	ENSP00000303153:p.Ala938Asp	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	638	0.29212454212454214	142	0.2886178861788618	116	0.32044198895027626	119	0.20804195804195805	261	0.34432717678100266	G	0.686	-0.796225	0.02862	0.288016	0.328023	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.93488	-3.23;-3.23	3.63	2.74	0.32292	.	0.979358	0.08299	U	0.967174	T	0.00012	0.0000	N	0.10760	0.04	0.80722	P	0.0	B;B	0.21905	0.062;0.037	B;B	0.17098	0.017;0.007	T	0.17837	-1.0356	9	0.13470	T	0.59	.	6.2583	0.20885	0.138:0.0:0.862:0.0	rs4909444;rs17445739;rs52804110;rs60475514;rs4909444	938;938	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	D	938;938;651	ENSP00000303153:A938D;ENSP00000387655:A938D	ENSP00000303153:A938D	A	-	2	0	COL22A1	139770391	0.034000	0.19679	0.361000	0.25849	0.153000	0.21895	1.251000	0.32862	2.017000	0.59298	0.542000	0.68232	GCT	G|0.699;T|0.301	0.301	strong		0.517	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
SLC37A2	219855	hgsc.bcm.edu	37	11	124947396	124947396	+	Missense_Mutation	SNP	A	A	G	rs55752830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124947396A>G	ENST00000403796.2	+	4	587	c.286A>G	c.(286-288)Atc>Gtc	p.I96V	SLC37A2_ENST00000407458.1_Missense_Mutation_p.I96V|SLC37A2_ENST00000298280.5_Missense_Mutation_p.I96V|SLC37A2_ENST00000308074.4_Missense_Mutation_p.I96V	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	96			I -> V (in dbSNP:rs55752830).		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)		CGCCTTCCTCATCGCCTATGC	0.527													G|||	1889	0.377196	0.5348	0.3689	5008	,	,		22449	0.1468		0.3757	False		,,,				2504	0.409				p.I96V	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.A286G						PASS	.	G	VAL/ILE,VAL/ILE	2137,2265	597.0+/-388.8	528,1081,592	99.0	90.0	93.0		286,286	3.6	0.8	11	dbSNP_129	93	3034,5564	663.3+/-402.1	532,1970,1797	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	29,29	1060,3051,2389	GG,GA,AA		35.2873,48.5461,39.7769	benign,benign	96/502,96/506	124947396	5171,7829	2201	4299	6500	SO:0001583	missense	219855	exon4			TTCCTCATCGCCT	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.286A>G	11.37:g.124947396A>G	ENSP00000384407:p.Ile96Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	51	0.573034	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	742	0.33974358974358976	244	0.4959349593495935	140	0.3867403314917127	80	0.13986013986013987	278	0.36675461741424803	G	0.151	-1.091165	0.01858	0.485461	0.352873	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000532000;ENST00000308074	T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41	4.5	3.56	0.40772	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00483	-1.445	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.42666	-0.9438	9	0.07325	T	0.83	-19.5978	10.8993	0.47043	0.1591:0.0:0.8409:0.0	rs55752830;rs61753650	96;96	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	V	96;96;96;59;96	ENSP00000384407:I96V;ENSP00000385126:I96V;ENSP00000298280:I96V;ENSP00000432254:I59V;ENSP00000311833:I96V	ENSP00000298280:I96V	I	+	1	0	SLC37A2	124452606	1.000000	0.71417	0.818000	0.32626	0.004000	0.04260	2.952000	0.49097	1.128000	0.42052	-0.227000	0.12334	ATC	A|0.619;G|0.381	0.381	strong		0.527	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
OSBPL10	114884	hgsc.bcm.edu	37	3	31789582	31789582	+	Missense_Mutation	SNP	T	T	C	rs2290532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:31789582T>C	ENST00000396556.2	-	5	882	c.760A>G	c.(760-762)Aac>Gac	p.N254D	OSBPL10_ENST00000467647.1_5'UTR|OSBPL10_ENST00000438237.2_Missense_Mutation_p.N190D	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	254			N -> D (in dbSNP:rs2290532).		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)		TGCACAAGGTTCTTCTGCTGC	0.587													T|||	2141	0.427516	0.0461	0.5576	5008	,	,		17939	0.7401		0.4404	False		,,,				2504	0.5153				p.N254D		Atlas-SNP	.											.	OSBPL10	160	.	0			c.A760G						PASS	.	T	ASP/ASN,ASP/ASN	511,3895	235.5+/-248.0	30,451,1722	66.0	52.0	57.0		568,760	4.5	1.0	3	dbSNP_100	57	3774,4826	531.3+/-382.0	825,2124,1351	yes	missense,missense	OSBPL10	NM_001174060.1,NM_017784.4	23,23	855,2575,3073	CC,CT,TT		43.8837,11.5978,32.9463	benign,benign	190/701,254/765	31789582	4285,8721	2203	4300	6503	SO:0001583	missense	114884	exon5			CAAGGTTCTTCTG	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.760A>G	3.37:g.31789582T>C	ENSP00000379804:p.Asn254Asp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	1001	0.4583333333333333	27	0.054878048780487805	190	0.5248618784530387	445	0.777972027972028	339	0.4472295514511873	T	13.65	2.299228	0.40694	0.115978	0.438837	ENSG00000144645	ENST00000396556;ENST00000438237;ENST00000428241	T;T;T	0.40756	1.02;1.02;1.02	5.63	4.48	0.54585	.	0.186293	0.56097	D	0.000023	T	0.00012	0.0000	L	0.33668	1.02	0.32366	P	0.556513	D;B;B	0.63046	0.992;0.011;0.011	P;B;B	0.53360	0.724;0.006;0.009	T	0.11842	-1.0571	9	0.07325	T	0.83	-24.1001	11.4451	0.50118	0.0:0.0702:0.0:0.9298	rs2290532;rs17451508;rs52825393;rs59854988;rs2290532	190;254;22	B4E212;Q9BXB5;Q59ED9	.;OSB10_HUMAN;.	D	254;190;62	ENSP00000379804:N254D;ENSP00000406124:N190D;ENSP00000399200:N62D	ENSP00000379804:N254D	N	-	1	0	OSBPL10	31764586	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	5.965000	0.70387	0.966000	0.38159	0.459000	0.35465	AAC	C|0.372;N|0.000	0.372	strong		0.587	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		
SCD5	79966	hgsc.bcm.edu	37	4	83582064	83582064	+	Intron	SNP	G	G	T	rs3733228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:83582064G>T	ENST00000319540.4	-	3	889				SCD5_ENST00000273908.4_Missense_Mutation_p.L246M	NM_001037582.2	NP_001032671.2	Q86SK9	SCD5_HUMAN	stearoyl-CoA desaturase 5						fatty acid biosynthetic process (GO:0006633)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|stearoyl-CoA 9-desaturase activity (GO:0004768)			endometrium(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)	13		Colorectal(4;0.0323)|Hepatocellular(203;0.115)				AGAGCACGCAGCATCAAGCAG	0.443													G|||	1516	0.302716	0.0794	0.487	5008	,	,		20298	0.4762		0.2913	False		,,,				2504	0.3067				p.L246M		Atlas-SNP	.											.	SCD5	58	.	0			c.C736A						PASS	.	G	,MET/LEU	464,3942	219.1+/-236.9	28,408,1767	162.0	156.0	158.0		,736	3.9	0.0	4	dbSNP_107	158	2681,5919	430.3+/-356.5	423,1835,2042	yes	intron,missense	SCD5	NM_001037582.2,NM_024906.2	,15	451,2243,3809	TT,TG,GG		31.1744,10.5311,24.1811	,	,246/257	83582064	3145,9861	2203	4300	6503	SO:0001627	intron_variant	79966	exon4			CACGCAGCATCAA	AF389338	CCDS3595.1, CCDS34024.1	4q21.3	2013-01-25	2005-06-09	2005-06-09	ENSG00000145284	ENSG00000145284		"""Fatty acid desaturases"""	21088	protein-coding gene	gene with protein product		608370	"""stearoyl-CoA desaturase 4"""	SCD4		12477932	Standard	NM_024906		Approved	ACOD4, FLJ21032, FADS4, HSCD5	uc003hna.2	Q86SK9	OTTHUMG00000130293	ENST00000319540.4:c.569+19795C>A	4.37:g.83582064G>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_024906	B2RPG0|Q4W5Q5|Q8NDS0|Q9H7D1	Missense_Mutation	SNP	ENST00000319540.4	37	CCDS34024.1	720	0.32967032967032966	50	0.1016260162601626	163	0.45027624309392267	278	0.486013986013986	229	0.3021108179419525	G	7.902	0.734689	0.15574	0.105311	0.311744	ENSG00000145284	ENST00000273908	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25440	P	0.9881068	P	0.34826	0.471	B	0.40228	0.323	T	0.50457	-0.8826	6	0.62326	D	0.03	.	11.7991	0.52116	0.0:0.0:1.0:0.0	rs3733228;rs52806587;rs61024749;rs3733228	246	Q86SK9-2	.	M	246	.	ENSP00000273908:L246M	L	-	1	2	SCD5	83801088	0.005000	0.15991	0.005000	0.12908	0.009000	0.06853	1.546000	0.36179	2.502000	0.84385	0.585000	0.79938	CTG	G|0.729;T|0.271	0.271	strong		0.443	SCD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252635.1	NM_024906	
TBC1D8	11138	hgsc.bcm.edu	37	2	101638828	101638828	+	Silent	SNP	C	C	T	rs34685616	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:101638828C>T	ENST00000376840.4	-	16	2630	c.2631G>A	c.(2629-2631)acG>acA	p.T877T	TBC1D8_ENST00000409318.1_Silent_p.T892T			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	877					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						CGAGGATCTCCGTGTGGGCCC	0.597													C|||	289	0.0577077	0.0537	0.0634	5008	,	,		19267	0.001		0.1262	False		,,,				2504	0.047				p.T877T		Atlas-SNP	.											.	TBC1D8	169	.	0			c.G2631A						PASS	.	C		250,3870		7,236,1817	58.0	62.0	61.0		2631	-8.1	0.9	2	dbSNP_126	61	1091,7297		87,917,3190	no	coding-synonymous	TBC1D8	NM_001102426.1		94,1153,5007	TT,TC,CC		13.0067,6.068,10.7211		877/1141	101638828	1341,11167	2060	4194	6254	SO:0001819	synonymous_variant	11138	exon16			GATCTCCGTGTGG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.2631G>A	2.37:g.101638828C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	112	64	0.571429	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	37	CCDS46375.1																																																																																			C|0.922;T|0.078	0.078	strong		0.597	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
OR13C5	138799	hgsc.bcm.edu	37	9	107360922	107360922	+	Missense_Mutation	SNP	A	A	G	rs1851724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107360922A>G	ENST00000374779.2	-	1	866	c.773T>C	c.(772-774)aTg>aCg	p.M258T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	258			M -> T (in dbSNP:rs1851724).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTTCATGTACATGAGGAAGAT	0.443													A|||	3390	0.676917	0.7466	0.5937	5008	,	,		20659	0.9573		0.4235	False		,,,				2504	0.6135				p.M258T		Atlas-SNP	.											OR13C5,NS,lymphoid_neoplasm,0,1	OR13C5	60	1	0			c.T773C						PASS	.	A	THR/MET	3165,1241	706.6+/-407.4	1144,877,182	137.0	123.0	128.0		773	4.0	0.9	9	dbSNP_92	128	3648,4952	525.3+/-380.7	806,2036,1458	yes	missense	OR13C5	NM_001004482.1	81	1950,2913,1640	GG,GA,AA		42.4186,28.1661,47.6165	possibly-damaging	258/319	107360922	6813,6193	2203	4300	6503	SO:0001583	missense	138799	exon1			ATGTACATGAGGA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.773T>C	9.37:g.107360922A>G	ENSP00000363911:p.Met258Thr	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	184	85	0.461957	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	1440	0.6593406593406593	349	0.709349593495935	207	0.5718232044198895	550	0.9615384615384616	334	0.44063324538258575	A	14.53	2.562208	0.45694	0.718339	0.424186	ENSG00000255800	ENST00000374779	T	0.00164	8.64	4.03	4.03	0.46877	GPCR, rhodopsin-like superfamily (1);	0.395212	0.18447	U	0.140947	T	0.00012	0.0000	L	0.41492	1.28	0.45806	P	0.0013180000000000414	P	0.39601	0.68	P	0.45406	0.479	T	0.48536	-0.9027	9	0.51188	T	0.08	.	6.0217	0.19632	0.8838:0.0:0.1162:0.0	rs1851724;rs52797012;rs61541229;rs1851724	258	Q8NGS8	O13C5_HUMAN	T	258	ENSP00000363911:M258T	ENSP00000363911:M258T	M	-	2	0	OR13C5	106400743	0.036000	0.19791	0.947000	0.38551	0.290000	0.27261	1.107000	0.31110	1.704000	0.51252	0.347000	0.21830	ATG	A|0.421;G|0.579	0.579	strong		0.443	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
GCFC2	6936	hgsc.bcm.edu	37	2	75917161	75917161	+	Missense_Mutation	SNP	G	G	C	rs41286005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75917161G>C	ENST00000321027.3	-	9	1406	c.1273C>G	c.(1273-1275)Cag>Gag	p.Q425E	GCFC2_ENST00000541687.1_3'UTR|GCFC2_ENST00000409857.3_Missense_Mutation_p.Q387E|MRPL19_ENST00000358788.6_Intron	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	425					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	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)										gttccttcctgatggttacaa	0.363													G|||	79	0.0157748	0.0015	0.0346	5008	,	,		17322	0.0		0.0467	False		,,,				2504	0.0061				p.Q425E		Atlas-SNP	.											.	.	.	.	0			c.C1273G						PASS	.	G	GLU/GLN,GLU/GLN	47,4355	49.6+/-84.7	1,45,2155	112.0	104.0	107.0		766,1273	-1.2	1.0	2	dbSNP_127	107	371,8229	121.8+/-180.9	8,355,3937	yes	missense,missense	C2orf3	NM_001201334.1,NM_003203.4	29,29	9,400,6092	CC,CG,GG		4.314,1.0677,3.2149	benign,benign	256/613,425/782	75917161	418,12584	2201	4300	6501	SO:0001583	missense	6936	exon9			CTTCCTGATGGTT	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"""GC binding factor"""	189901	"""transcription factor 9 (binds GC-rich sequences)"", ""chromosome 2 open reading frame 3"""	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.1273C>G	2.37:g.75917161G>C	ENSP00000318690:p.Gln425Glu	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	197	93	0.472081	NM_003203	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	49	0.022435897435897436	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	34	0.044854881266490766	G	4.611	0.113483	0.08831	0.010677	0.04314	ENSG00000005436	ENST00000321027;ENST00000409857	T;T	0.12255	2.71;2.7	4.18	-1.24	0.09435	.	0.617868	0.17656	N	0.166482	T	0.01695	0.0054	N	0.17082	0.46	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.31392	-0.9945	10	0.24483	T	0.36	-0.0047	15.6725	0.77289	0.0:0.6623:0.3377:0.0	rs41286005	425	P16383	GCF_HUMAN	E	425;387	ENSP00000318690:Q425E;ENSP00000386552:Q387E	ENSP00000318690:Q425E	Q	-	1	0	C2orf3	75770669	1.000000	0.71417	0.958000	0.39756	0.358000	0.29455	2.698000	0.47068	-0.218000	0.10018	0.305000	0.20034	CAG	G|0.970;C|0.030	0.030	strong		0.363	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203	
OR9K2	441639	hgsc.bcm.edu	37	12	55524314	55524314	+	Silent	SNP	T	T	C	rs7137261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55524314T>C	ENST00000305377.5	+	1	850	c.762T>C	c.(760-762)caT>caC	p.H254H		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	254						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						TAAAGATACATTCTACTGAGG	0.383													C|||	1523	0.304113	0.4085	0.2421	5008	,	,		18723	0.1141		0.334	False		,,,				2504	0.3722				p.H254H		Atlas-SNP	.											.	OR9K2	63	.	0			c.T762C						PASS	.	C		1703,2703	652.8+/-399.5	308,1087,808	130.0	118.0	122.0		762	-1.6	0.0	12	dbSNP_116	122	2777,5823	678.6+/-403.5	456,1865,1979	no	coding-synonymous	OR9K2	NM_001005243.1		764,2952,2787	CC,CT,TT		32.2907,38.6518,34.4456		254/336	55524314	4480,8526	2203	4300	6503	SO:0001819	synonymous_variant	441639	exon1			GATACATTCTACT	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.762T>C	12.37:g.55524314T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_001005243	B9EH19|Q6IFD6	Silent	SNP	ENST00000305377.5	37	CCDS31814.1																																																																																			T|0.674;C|0.326	0.326	strong		0.383	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
PCDHGA10	56106	hgsc.bcm.edu	37	5	140793007	140793007	+	Missense_Mutation	SNP	A	A	G	rs4912751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140793007A>G	ENST00000398610.2	+	1	265	c.265A>G	c.(265-267)Atc>Gtc	p.I89V	PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	89	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		I -> V (in dbSNP:rs4912751).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCAGCTTGATCACCGCGGG	0.617													N|||	2785	0.55611	0.8941	0.6239	5008	,	,		14913	0.3254		0.4245	False		,,,				2504	0.4243				p.I89V		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.A265G						PASS	.	G	,,VAL/ILE,,,,,,,,,,,,,,VAL/ILE	3572,716		1501,570,73	58.0	74.0	69.0		,,265,,,,,,,,,,,,,,265	2.8	1.0	5	dbSNP_111	69	3663,4883		792,2079,1402	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032090.1	,,29,,,,,,,,,,,,,,29	2293,2649,1475	GG,GA,AA		42.8622,16.6978,43.6263	,,,,,,,,,,,,,,,,	,,89/937,,,,,,,,,,,,,,89/851	140793007	7235,5599	2144	4273	6417	SO:0001583	missense	56106	exon1			AGCTTGATCACCG		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.265A>G	5.37:g.140793007A>G	ENSP00000381611:p.Ile89Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	1169	0.5352564102564102	424	0.8617886178861789	217	0.5994475138121547	189	0.3304195804195804	339	0.4472295514511873	g	0.258	-1.001608	0.02128	0.833022	0.428622	ENSG00000253846	ENST00000398610	T	0.25749	1.78	5.89	2.76	0.32466	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00960	-1.095	0.49798	P	1.7800000000001148E-4	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.37197	-0.9716	8	0.02654	T	1	.	10.6926	0.45879	0.3043:0.0:0.6957:0.0	rs4912751;rs56999226;rs4912751	89;89	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	V	89	ENSP00000381611:I89V	ENSP00000381611:I89V	I	+	1	0	PCDHGA10	140773191	0.000000	0.05858	1.000000	0.80357	0.750000	0.42670	-2.080000	0.01368	0.352000	0.24053	-0.226000	0.12346	ATC	A|0.483;G|0.517	0.517	strong		0.617	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32610436	32610436	+	Silent	SNP	T	T	C	rs1048372	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32610436T>C	ENST00000343139.5	+	4	765	c.663T>C	c.(661-663)tgT>tgC	p.C221C	HLA-DQA1_ENST00000374949.2_Silent_p.C221C|HLA-DQA1_ENST00000395363.1_Silent_p.C221C	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	220			A -> T (in allele DQA1*01:04; dbSNP:rs35087390).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CTGTGGTCTGTGCCCTGGGGT	0.547													.|||	2981	0.595248	0.5492	0.7406	5008	,	,		14803	0.6647		0.6233	False		,,,				2504	0.454				p.C221C		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.T663C						PASS	.	C		1662,1358		522,618,370	138.0	118.0	126.0		663	-7.8	0.3	6	dbSNP_86	126	3147,2269		964,1219,525	no	coding-synonymous	HLA-DQA1	NM_002122.3		1486,1837,895	CC,CT,TT		41.8944,44.9669,42.9943		221/256	32610436	4809,3627	1510	2708	4218	SO:0001819	synonymous_variant	3117	exon4			GGTCTGTGCCCTG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.663T>C	6.37:g.32610436T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	291	288	0.989691	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Silent	SNP	ENST00000343139.5	37	CCDS4752.1																																																																																			T|0.391;C|0.609	0.609	strong		0.547	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
ANKRD6	22881	hgsc.bcm.edu	37	6	90333599	90333599	+	Silent	SNP	A	A	G	rs17292811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90333599A>G	ENST00000522441.1	+	12	1682	c.1041A>G	c.(1039-1041)gcA>gcG	p.A347A	ANKRD6_ENST00000369408.5_Silent_p.A312A|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000447838.2_Silent_p.A347A|ANKRD6_ENST00000520793.1_Silent_p.A288A|ANKRD6_ENST00000339746.4_Silent_p.A347A	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	347					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		AGGTGTCAGCATTTTCTGACC	0.537													A|||	4528	0.904153	0.8752	0.9193	5008	,	,		17075	0.997		0.8419	False		,,,				2504	0.9008				p.A347A		Atlas-SNP	.											.	ANKRD6	51	.	0			c.A1041G						PASS	.	A	,,,,	3748,504		1658,432,36	77.0	86.0	83.0		1041,1041,936,864,1041	-12.0	0.1	6	dbSNP_123	83	7110,1386		2982,1146,120	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANKRD6	NM_001242809.1,NM_001242811.1,NM_001242813.1,NM_001242814.1,NM_014942.4	,,,,	4640,1578,156	GG,GA,AA		16.3136,11.8532,14.8259	,,,,	347/728,347/728,312/693,288/664,347/723	90333599	10858,1890	2126	4248	6374	SO:0001819	synonymous_variant	22881	exon12			GTCAGCATTTTCT	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1041A>G	6.37:g.90333599A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	37	CCDS56441.1																																																																																			A|0.116;G|0.884	0.884	strong		0.537	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537249	88537249	+	Silent	SNP	T	T	C	rs371359066		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537249T>C	ENST00000282478.7	+	4	3468	c.3435T>C	c.(3433-3435)agT>agC	p.S1145S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1145S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1145	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagtgacagcagtg	0.567																																					p.S1145S		Atlas-SNP	.											DSPP,NS,carcinoma,0,5	DSPP	174	5	0			c.T3435C						scavenged	.						41.0	55.0	50.0					4																	88537249		1542	2816	4358	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGACAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3435T>C	4.37:g.88537249T>C		Somatic	134	7	0.0522388		WXS	Illumina HiSeq	Phase_I	137	14	0.10219	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	
IL37	27178	hgsc.bcm.edu	37	2	113674709	113674709	+	Missense_Mutation	SNP	C	C	G	rs2708943	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113674709C>G	ENST00000263326.3	+	3	191	c.149C>G	c.(148-150)cCa>cGa	p.P50R	IL37_ENST00000353225.3_Intron|IL37_ENST00000352179.3_Missense_Mutation_p.P29R|IL37_ENST00000311328.2_Missense_Mutation_p.P24R|IL37_ENST00000349806.3_Intron	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	50			P -> R (in dbSNP:rs2708943).		immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						GATCTAGGTCCAAAGGTGAAG	0.463													c|||	381	0.0760783	0.174	0.0591	5008	,	,		22327	0.001		0.0805	False		,,,				2504	0.0286				p.P50R		Atlas-SNP	.											.	IL37	56	.	0			c.C149G						PASS	.		ARG/PRO,ARG/PRO,,,ARG/PRO	730,3676	303.5+/-288.0	53,624,1526	81.0	78.0	79.0		149,86,,,71	1.0	0.0	2	dbSNP_100	79	690,7910	171.4+/-222.4	37,616,3647	yes	missense,missense,intron,intron,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1,NM_173205.1	103,103,,,103	90,1240,5173	GG,GC,CC		8.0233,16.5683,10.918	probably-damaging,probably-damaging,,,probably-damaging	50/219,29/198,,,24/193	113674709	1420,11586	2203	4300	6503	SO:0001583	missense	27178	exon3			TAGGTCCAAAGGT	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.149C>G	2.37:g.113674709C>G	ENSP00000263326:p.Pro50Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	164	0.07509157509157509	81	0.16463414634146342	26	0.0718232044198895	1	0.0017482517482517483	56	0.07387862796833773	c	12.31	1.899428	0.33535	0.165683	0.080233	ENSG00000125571	ENST00000263326;ENST00000352179;ENST00000311328	T;T;T	0.55413	0.52;0.52;0.52	2.83	0.99	0.19807	.	.	.	.	.	T	0.00178	0.0005	L	0.59436	1.845	0.80722	P	0.0	P;P;D	0.54047	0.919;0.523;0.964	P;B;P	0.47299	0.504;0.107;0.543	T	0.03433	-1.1037	8	0.33940	T	0.23	0.6927	4.8753	0.13653	0.0:0.6989:0.0:0.3011	rs2708943;rs2708943	24;29;50	Q9NZH6-2;Q9NZH6-4;Q9NZH6	.;.;IL37_HUMAN	R	50;29;24	ENSP00000263326:P50R;ENSP00000263327:P29R;ENSP00000309883:P24R	ENSP00000263326:P50R	P	+	2	0	IL37	113391180	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.147000	0.10234	0.266000	0.21894	0.645000	0.84053	CCA	C|0.903;G|0.097	0.097	strong		0.463	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
ENOX1	55068	hgsc.bcm.edu	37	13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	rs7338624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:43987003C>G	ENST00000261488.6	-	4	625	c.48G>C	c.(46-48)gaG>gaC	p.E16D	ENOX1_ENST00000412891.1_Missense_Mutation_p.E16D	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	16			E -> D (in dbSNP:rs7338624). {ECO:0000269|PubMed:19055324}.		rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TCTGAGGAAGCTCCTGGGGAA	0.498													C|||	242	0.0483227	0.1778	0.0101	5008	,	,		16486	0.0		0.0	False		,,,				2504	0.0				p.E16D		Atlas-SNP	.											.	ENOX1	158	.	0			c.G48C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	677,3729	286.3+/-278.7	49,579,1575	125.0	111.0	116.0		48,48,48	2.9	0.9	13	dbSNP_116	116	9,8591	5.7+/-21.5	0,9,4291	yes	missense,missense,missense	ENOX1	NM_001127615.1,NM_001242863.1,NM_017993.3	45,45,45	49,588,5866	GG,GC,CC		0.1047,15.3654,5.2745	benign,benign,benign	16/644,16/644,16/644	43987003	686,12320	2203	4300	6503	SO:0001583	missense	55068	exon4			AGGAAGCTCCTGG	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"""RNA binding motif (RRM) containing"""	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.48G>C	13.37:g.43987003C>G	ENSP00000261488:p.Glu16Asp	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	69	21	0.304348	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	11.61	1.690096	0.29962	0.153654	0.001047	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.44083	0.93;0.93	5.91	2.88	0.33553	.	0.688144	0.14119	N	0.340181	T	0.00109	0.0003	N	0.08118	0	0.09310	P	0.99999166027	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	9	0.19590	T	0.45	-0.328	2.7291	0.05222	0.2036:0.4159:0.0:0.3805	rs7338624;rs52798713;rs7338624	16	Q8TC92	ENOX1_HUMAN	D	16	ENSP00000261488:E16D;ENSP00000415054:E16D	ENSP00000261488:E16D	E	-	3	2	ENOX1	42885003	0.996000	0.38824	0.871000	0.34182	0.975000	0.68041	1.058000	0.30504	0.842000	0.35045	0.655000	0.94253	GAG	C|0.955;G|0.045	0.045	strong		0.498	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993	
IFI44L	10964	hgsc.bcm.edu	37	1	79093818	79093818	+	Missense_Mutation	SNP	A	A	G	rs273259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:79093818A>G	ENST00000370751.5	+	2	397	c.218A>G	c.(217-219)cAt>cGt	p.H73R	IFI44L_ENST00000476521.1_Intron|IFI44L_ENST00000342282.3_Intron	NM_006820.2	NP_006811.2	Q53G44	IF44L_HUMAN	interferon-induced protein 44-like	73			H -> R (in dbSNP:rs273259). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		defense response to virus (GO:0051607)|immune response (GO:0006955)	cytoplasm (GO:0005737)				endometrium(4)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	22						ATTAATTTACATGAAAGTTCT	0.328													G|||	2228	0.444888	0.3608	0.3545	5008	,	,		17848	0.751		0.3449	False		,,,				2504	0.41				p.H73R		Atlas-SNP	.											.	IFI44L	93	.	0			c.A218G						PASS	.	G	ARG/HIS	1658,2748	639.2+/-397.1	332,994,877	57.0	60.0	59.0		218	-6.2	0.0	1	dbSNP_79	59	2812,5788	669.2+/-402.6	463,1886,1951	yes	missense	IFI44L	NM_006820.2	29	795,2880,2828	GG,GA,AA		32.6977,37.6305,34.3688	benign	73/453	79093818	4470,8536	2203	4300	6503	SO:0001583	missense	10964	exon2			ATTTACATGAAAG	AB000115	CCDS687.2	1p22.3	2008-07-18	2004-11-12	2004-11-12	ENSG00000137959	ENSG00000137959			17817	protein-coding gene	gene with protein product		613975	"""chromosome 1 open reading frame 29"""	C1orf29			Standard	NM_006820		Approved	GS3686	uc010oro.2	Q53G44	OTTHUMG00000009724	ENST00000370751.5:c.218A>G	1.37:g.79093818A>G	ENSP00000359787:p.His73Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	72	32	0.444444	NM_006820	Q86TE1|Q96B64|Q99984	Missense_Mutation	SNP	ENST00000370751.5	37	CCDS687.2	979	0.4482600732600733	159	0.3231707317073171	115	0.31767955801104975	442	0.7727272727272727	263	0.3469656992084433	G	0.003	-2.572666	0.00133	0.376305	0.326977	ENSG00000137959	ENST00000452835;ENST00000370751;ENST00000450498	T;T;T	0.31510	1.49;3.18;2.58	3.1	-6.2	0.02072	.	4.699020	0.01184	N	0.007166	T	0.01558	0.0050	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10590	-1.0623	9	0.13853	T	0.58	.	1.5275	0.02528	0.4325:0.2384:0.1325:0.1966	rs273259;rs481313;rs52793488;rs60945929;rs273259	73	Q53G44	IF44L_HUMAN	R	73;73;50	ENSP00000409914:H73R;ENSP00000359787:H73R;ENSP00000400784:H50R	ENSP00000359787:H73R	H	+	2	0	IFI44L	78866406	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.458000	0.00121	-6.276000	0.00005	-2.893000	0.00094	CAT	G|0.407;N|0.001	0.407	strong		0.328	IFI44L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026834.3	NM_006820	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788145	3788145	+	Missense_Mutation	SNP	C	C	T	rs242018	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:3788145C>T	ENST00000252322.1	-	6	928	c.460G>A	c.(460-462)Gaa>Aaa	p.E154K	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.E154K|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.E154K	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		154			E -> K (in dbSNP:rs242018). {ECO:0000269|PubMed:15489334}.		activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TCCTCATCTTCGCCCATGTCG	0.532													C|||	1114	0.222444	0.1747	0.33	5008	,	,		20677	0.1319		0.2565	False		,,,				2504	0.2689				p.E154K		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.G460A						PASS	.	C	LYS/GLU,LYS/GLU	825,3581	327.7+/-300.2	91,643,1469	205.0	165.0	179.0		460,460	1.5	0.0	12	dbSNP_79	179	2370,6230	395.0+/-344.9	303,1764,2233	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	56,56	394,2407,3702	TT,TC,CC		27.5581,18.7245,24.5656	benign,benign	154/732,154/396	3788145	3195,9811	2203	4300	6503	SO:0001583	missense	84766	exon6			CATCTTCGCCCAT																												ENST00000252322.1:c.460G>A	12.37:g.3788145C>T	ENSP00000252322:p.Glu154Lys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	95	54	0.568421	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	488	0.22344322344322345	90	0.18292682926829268	119	0.3287292817679558	81	0.14160839160839161	198	0.2612137203166227	C	6.084	0.383782	0.11524	0.187245	0.275581	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;T;T	0.62941	-0.01;2.41;2.39	4.9	1.51	0.23008	.	0.607794	0.17497	N	0.172133	T	0.00012	0.0000	M	0.72894	2.215	0.80722	P	0.0	B;B;B	0.19817	0.039;0.008;0.008	B;B;B	0.08055	0.003;0.003;0.001	T	0.14727	-1.0462	9	0.32370	T	0.25	-0.0552	4.976	0.14140	0.0:0.5477:0.2293:0.223	rs242018;rs3803136;rs17770609;rs52791075;rs56733254;rs242018	154;154;154	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	K	154	ENSP00000409382:E154K;ENSP00000412496:E154K;ENSP00000252322:E154K	ENSP00000252322:E154K	E	-	1	0	EFCAB4B	3658406	0.005000	0.15991	0.000000	0.03702	0.006000	0.05464	1.008000	0.29872	-0.025000	0.13918	0.561000	0.74099	GAA	C|0.763;T|0.237	0.237	strong		0.532	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
RBMX	27316	hgsc.bcm.edu	37	X	135956575	135956575	+	Missense_Mutation	SNP	G	G	A	rs78646793		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135956575G>A	ENST00000320676.7	-	9	1056	c.902C>T	c.(901-903)cCg>cTg	p.P301L	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Missense_Mutation_p.P173L|RBMX_ENST00000570135.1_Missense_Mutation_p.P166L|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	301					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					ATAAGATGGCGGGGGCCCTCG	0.463																																					p.P301L		Atlas-SNP	.											.	RBMX	149	.	0			c.C902T						PASS	.						90.0	85.0	87.0					X																	135956575		2203	4300	6503	SO:0001583	missense	27316	exon9			GATGGCGGGGGCC		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.902C>T	X.37:g.135956575G>A	ENSP00000359645:p.Pro301Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	139	29	0.208633	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	13.41	2.229139	0.39399	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.77877	-1.13	5.4	5.4	0.78164	.	0.000000	0.85682	U	0.000000	T	0.75708	0.3886	L	0.61218	1.895	0.80722	D	1	B	0.30114	0.269	B	0.19666	0.026	T	0.75631	-0.3251	10	0.56958	D	0.05	.	18.4308	0.90624	0.0:0.0:1.0:0.0	.	301	P38159	HNRPG_HUMAN	L	301;288	ENSP00000359645:P301L	ENSP00000359645:P301L	P	-	2	0	RBMX	135784241	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.751000	0.85126	2.380000	0.81148	0.600000	0.82982	CCG	G|0.500;A|0.500	0.500	weak		0.463	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
NLRP14	338323	hgsc.bcm.edu	37	11	7059981	7059981	+	Missense_Mutation	SNP	G	G	A	rs61063081	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7059981G>A	ENST00000299481.4	+	2	510	c.164G>A	c.(163-165)cGg>cAg	p.R55Q		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	55	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		R -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		AAGGCCAGGCGGGAGGACCTG	0.443													G|||	482	0.096246	0.0666	0.1297	5008	,	,		18849	0.0179		0.2147	False		,,,				2504	0.0716				p.R55Q		Atlas-SNP	.											.	NLRP14	187	.	0			c.G164A						PASS	.	G	GLN/ARG	370,4032	182.9+/-210.6	13,344,1844	58.0	63.0	61.0		164	2.2	0.0	11	dbSNP_129	61	1840,6752	325.0+/-316.7	200,1440,2656	yes	missense	NLRP14	NM_176822.3	43	213,1784,4500	AA,AG,GG		21.4153,8.4053,17.0078	probably-damaging	55/1094	7059981	2210,10784	2201	4296	6497	SO:0001583	missense	338323	exon2			CCAGGCGGGAGGA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.164G>A	11.37:g.7059981G>A	ENSP00000299481:p.Arg55Gln	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	247	0.1130952380952381	24	0.04878048780487805	48	0.13259668508287292	13	0.022727272727272728	162	0.21372031662269128	G	14.50	2.554234	0.45487	0.084053	0.214153	ENSG00000158077	ENST00000299481	T	0.53857	0.6	4.22	2.23	0.28157	Pyrin (2);DEATH-like (2);	0.529188	0.15927	N	0.237859	T	0.00109	0.0003	M	0.78456	2.415	0.80722	P	0.0	D	0.76494	0.999	P	0.62089	0.898	T	0.17289	-1.0374	9	0.19147	T	0.46	.	10.4223	0.44356	0.0:0.3865:0.6135:0.0	rs61063081;rs61879042	55	Q86W24	NAL14_HUMAN	Q	55	ENSP00000299481:R55Q	ENSP00000299481:R55Q	R	+	2	0	NLRP14	7016557	0.001000	0.12720	0.000000	0.03702	0.948000	0.59901	0.751000	0.26348	0.659000	0.30945	0.655000	0.94253	CGG	G|0.835;A|0.165	0.165	strong		0.443	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
EEF2	1938	hgsc.bcm.edu	37	19	3982967	3982967	+	Silent	SNP	G	G	A	rs2230561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:3982967G>A	ENST00000309311.6	-	4	538	c.450C>T	c.(448-450)cgC>cgT	p.R150R	SNORD37_ENST00000384048.1_RNA|EEF2_ENST00000600720.1_5'Flank	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	150	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGCTTGATGCGCTCGGCAA	0.642													G|||	330	0.0658946	0.0045	0.0533	5008	,	,		16936	0.0218		0.0974	False		,,,				2504	0.1708				p.R150R	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.C450T						PASS	.	G		69,4335	62.3+/-99.4	1,67,2134	45.0	35.0	38.0		450	1.6	1.0	19	dbSNP_98	38	825,7773	185.6+/-233.3	37,751,3511	yes	coding-synonymous	EEF2	NM_001961.3		38,818,5645	AA,AG,GG		9.5953,1.5668,6.8759		150/859	3982967	894,12108	2202	4299	6501	SO:0001819	synonymous_variant	1938	exon4			CTTGATGCGCTCG	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.450C>T	19.37:g.3982967G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_001961	B2RMP5|D6W618|Q58J86	Silent	SNP	ENST00000309311.6	37	CCDS12117.1																																																																																			G|0.937;A|0.063	0.063	strong		0.642	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
SLX4	84464	hgsc.bcm.edu	37	16	3645607	3645607	+	Splice_Site	SNP	A	A	G	rs77985244	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3645607A>G	ENST00000294008.3	-	9	2652	c.2012T>C	c.(2011-2013)tTg>tCg	p.L671S		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	671			L -> S (in dbSNP:rs77985244). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						AGTTCTTACCAAGGTGCGGCC	0.667								Direct reversal of damage					G|||	311	0.0621006	0.0779	0.0735	5008	,	,		17478	0.0506		0.0646	False		,,,				2504	0.0419				p.L671S		Atlas-SNP	.											.	SLX4	173	.	0			c.T2012C						PASS	.	G	SER/LEU	402,3992	781.3+/-414.5	20,362,1815	40.0	44.0	42.0		2012	0.9	0.1	16	dbSNP_131	42	582,8018	789.1+/-407.6	15,552,3733	yes	missense-near-splice	SLX4	NM_032444.2	145	35,914,5548	GG,GA,AA		6.7674,9.1488,7.5727	benign	671/1835	3645607	984,12010	2197	4300	6497	SO:0001630	splice_region_variant	84464	exon9			CTTACCAAGGTGC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2013+1T>C	16.37:g.3645607A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	140	0.0641025641025641	44	0.08943089430894309	24	0.06629834254143646	24	0.04195804195804196	48	0.0633245382585752	G	1.261	-0.615866	0.03663	0.091488	0.067674	ENSG00000188827	ENST00000294008	T	0.00995	5.46	5.07	0.88	0.19161	.	0.839455	0.10270	N	0.694860	T	0.00012	0.0000	N	0.00162	-1.95	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39057	-0.9632	10	0.15066	T	0.55	.	7.4261	0.27100	0.4675:0.0:0.5325:0.0	.	671	Q8IY92	SLX4_HUMAN	S	671	ENSP00000294008:L671S	ENSP00000294008:L671S	L	-	2	0	SLX4	3585608	0.263000	0.24083	0.107000	0.21349	0.065000	0.16274	0.569000	0.23638	0.028000	0.15324	-0.215000	0.12644	TTG	A|0.932;G|0.068	0.068	strong		0.667	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	Missense_Mutation
CMKLR1	1240	hgsc.bcm.edu	37	12	108686008	108686008	+	Silent	SNP	C	C	G	rs1057401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:108686008C>G	ENST00000312143.7	-	3	1095	c.732G>C	c.(730-732)gtG>gtC	p.V244V	CMKLR1_ENST00000552995.1_Silent_p.V242V|CMKLR1_ENST00000550402.1_Silent_p.V244V|CMKLR1_ENST00000397688.2_Silent_p.V242V|CMKLR1_ENST00000412676.1_Silent_p.V244V	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	244					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						GCAGTTTGCACACGATGGTGA	0.552													G|||	1855	0.370407	0.6513	0.3156	5008	,	,		21024	0.0119		0.4473	False		,,,				2504	0.32				p.V244V		Atlas-SNP	.											CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	0			c.G732C						PASS	.		,,,	2563,1707		803,957,375	69.0	76.0	74.0		732,732,732,726	4.5	1.0	12	dbSNP_86	74	3973,4507		948,2077,1215	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CMKLR1	NM_001142343.1,NM_001142344.1,NM_001142345.1,NM_004072.2	,,,	1751,3034,1590	GG,GC,CC		46.8514,39.9766,48.7373	,,,	244/374,244/374,244/374,242/372	108686008	6536,6214	2135	4240	6375	SO:0001819	synonymous_variant	1240	exon3			TTTGCACACGATG	U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.732G>C	12.37:g.108686008C>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Silent	SNP	ENST00000312143.7	37	CCDS44965.1																																																																																			C|0.627;G|0.373	0.373	strong		0.552	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
MUC6	4588	hgsc.bcm.edu	37	11	1016825	1016825	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1016825G>A	ENST00000421673.2	-	31	6026	c.5976C>T	c.(5974-5976)acC>acT	p.T1992T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1992	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)		GATAGGTAGTGGTGGTCTGGA	0.552																																					p.T1992T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	0			c.C5976T						PASS	.						1487.0	1481.0	1483.0					11																	1016825		2203	4298	6501	SO:0001819	synonymous_variant	4588	exon31			GGTAGTGGTGGTC	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.5976C>T	11.37:g.1016825G>A		Somatic	953	0	0		WXS	Illumina HiSeq	Phase_I	1138	68	0.059754	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	none		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
THEMIS2	9473	hgsc.bcm.edu	37	1	28209002	28209002	+	Silent	SNP	C	C	T	rs76072311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:28209002C>T	ENST00000373921.3	+	4	1171	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D	THEMIS2_ENST00000373927.3_Intron|THEMIS2_ENST00000328928.7_Intron|THEMIS2_ENST00000373925.1_Intron	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	389	CABIT 2.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											AGGGCAGTGACGTGGATGTCT	0.657													C|||	64	0.0127796	0.0015	0.0144	5008	,	,		18604	0.0		0.0467	False		,,,				2504	0.0051				p.D389D		Atlas-SNP	.											.	.	.	.	0			c.C1167T						PASS	.	C	,,	34,4186		1,32,2077	31.0	39.0	37.0		,1167,	-1.6	0.1	1	dbSNP_131	37	451,7993		20,411,3791	no	intron,coding-synonymous,intron	C1orf38	NM_001039477.1,NM_001105556.1,NM_004848.2	,,	21,443,5868	TT,TC,CC		5.3411,0.8057,3.8298	,,	,389/644,	28209002	485,12179	2110	4222	6332	SO:0001819	synonymous_variant	9473	exon4			CAGTGACGTGGAT	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.1167C>T	1.37:g.28209002C>T		Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	161	152	0.944099	NM_001105556	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Silent	SNP	ENST00000373921.3	37	CCDS41290.1																																																																																			C|0.976;T|0.024	0.024	strong		0.657	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848	
TTLL4	9654	hgsc.bcm.edu	37	2	219610433	219610433	+	Silent	SNP	A	A	G	rs586194	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219610433A>G	ENST00000392102.1	+	7	2146	c.1806A>G	c.(1804-1806)gaA>gaG	p.E602E	TTLL4_ENST00000442769.1_Silent_p.E602E|TTLL4_ENST00000457313.1_Silent_p.E437E|TTLL4_ENST00000258398.4_Silent_p.E602E	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	602					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)		TTCCCTGGGAACAGAGGAAGT	0.507													G|||	2450	0.489217	0.9168	0.438	5008	,	,		20186	0.1409		0.4672	False		,,,				2504	0.3292				p.E602E	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.A1806G						PASS	.	G		3726,680	287.2+/-279.2	1577,572,54	50.0	49.0	49.0		1806	-0.1	1.0	2	dbSNP_83	49	4092,4508	588.7+/-392.4	992,2108,1200	no	coding-synonymous	TTLL4	NM_014640.4		2569,2680,1254	GG,GA,AA		47.5814,15.4335,39.8893		602/1200	219610433	7818,5188	2203	4300	6503	SO:0001819	synonymous_variant	9654	exon7			CTGGGAACAGAGG		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.1806A>G	2.37:g.219610433A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_014640	A8K6V5|Q8WW29	Silent	SNP	ENST00000392102.1	37	CCDS2422.1																																																																																			A|0.446;G|0.554	0.554	strong		0.507	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
CDAN1	146059	hgsc.bcm.edu	37	15	43017426	43017426	+	Silent	SNP	T	T	G	rs16957091	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43017426T>G	ENST00000356231.3	-	27	3497	c.3474A>C	c.(3472-3474)ctA>ctC	p.L1158L		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	1158					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		CCAGCTCCCGTAGCAAGAATA	0.577													G|||	2311	0.461462	0.9554	0.1916	5008	,	,		19027	0.254		0.2346	False		,,,				2504	0.4325				p.L1158L		Atlas-SNP	.											.	CDAN1	70	.	0			c.A3474C						PASS	.	G		3640,766	312.5+/-292.6	1518,604,81	69.0	64.0	66.0		3474	3.0	1.0	15	dbSNP_123	66	1955,6643	724.7+/-406.5	240,1475,2584	no	coding-synonymous	CDAN1	NM_138477.2		1758,2079,2665	GG,GT,TT		22.7378,17.3854,43.0252		1158/1228	43017426	5595,7409	2203	4299	6502	SO:0001819	synonymous_variant	146059	exon27			CTCCCGTAGCAAG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.3474A>C	15.37:g.43017426T>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	140	59	0.421429	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			T|0.565;G|0.435	0.435	strong		0.577	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
TXNDC2	84203	hgsc.bcm.edu	37	18	9886275	9886275	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9886275C>T	ENST00000306084.6	+	1	303	c.104C>T	c.(103-105)gCt>gTt	p.A35V	TXNDC2_ENST00000357775.5_Intron|TXNDC2_ENST00000536353.2_Intron|TXNDC2_ENST00000426718.3_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	35					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						GAAGGTGATGCTAATGGTAAG	0.468																																					p.A35V		Atlas-SNP	.											.	TXNDC2	168	.	0			c.C104T						PASS	.						75.0	75.0	75.0					18																	9886275		1940	4140	6080	SO:0001583	missense	84203	exon1			GTGATGCTAATGG	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.104C>T	18.37:g.9886275C>T	ENSP00000304908:p.Ala35Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	C	9.184	1.024442	0.19433	.	.	ENSG00000168454	ENST00000306084;ENST00000426718	T	0.05199	3.48	3.92	1.03	0.20045	.	.	.	.	.	T	0.03739	0.0106	L	0.27053	0.805	0.09310	N	1	B	0.26809	0.16	B	0.23275	0.045	T	0.44982	-0.9292	8	.	.	.	1.9805	2.2617	0.04068	0.1932:0.4906:0.2043:0.1119	.	35	Q86VQ3	TXND2_HUMAN	V	35	ENSP00000304908:A35V	.	A	+	2	0	TXNDC2	9876275	0.000000	0.05858	0.004000	0.12327	0.067000	0.16453	-0.468000	0.06656	0.206000	0.20587	0.563000	0.77884	GCT	.	.	none		0.468	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
TMEM199	147007	hgsc.bcm.edu	37	17	26691916	26691916	+	IGR	SNP	T	T	C	rs2277667	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:26691916T>C	ENST00000292114.3	+	0	3148				VTN_ENST00000431468.1_Silent_p.L57L|CTB-96E2.3_ENST00000591482.1_RNA|VTN_ENST00000536498.1_Silent_p.L56L|TMEM199_ENST00000509083.1_Intron|CTB-96E2.7_ENST00000577850.1_RNA|VTN_ENST00000438614.1_Silent_p.L56L|CTB-96E2.2_ENST00000555059.2_Missense_Mutation_p.T131A|SARM1_ENST00000379061.4_Intron	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199							integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6	all_lung(13;0.000354)|Lung NSC(42;0.00115)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		CCAGCTCCAGTAGCTGCCCTT	0.632													C|||	812	0.162141	0.1853	0.0821	5008	,	,		18306	0.244		0.0785	False		,,,				2504	0.1892				p.L57L		Atlas-SNP	.											.	SEBOX	20	.	0			c.A171G						PASS	.	C		721,3659		65,591,1534	58.0	68.0	64.0		171	3.2	1.0	17	dbSNP_100	64	696,7868		33,630,3619	no	coding-synonymous	SEBOX	NM_001080837.2		98,1221,5153	CC,CT,TT		8.127,16.4612,10.9472		57/217	26691916	1417,11527	2190	4282	6472	SO:0001628	intergenic_variant	645832	exon2			CTCCAGTAGCTGC	AY074907	CCDS11228.1	17q11.2	2007-12-17	2007-12-17	2007-12-17	ENSG00000244045	ENSG00000244045			18085	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 32"""	C17orf32			Standard	NM_152464		Approved	MGC45714	uc002hba.3	Q8N511	OTTHUMG00000132498		17.37:g.26691916T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001080837		Silent	SNP	ENST00000292114.3	37	CCDS11228.1																																																																																			T|0.855;C|0.145	0.145	strong		0.632	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464	
SORBS1	10580	hgsc.bcm.edu	37	10	97143826	97143826	+	Missense_Mutation	SNP	T	T	C	rs35808802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:97143826T>C	ENST00000361941.3	-	15	1480	c.1454A>G	c.(1453-1455)tAc>tGc	p.Y485C	SORBS1_ENST00000371239.1_Missense_Mutation_p.Y284C|SORBS1_ENST00000371245.3_Missense_Mutation_p.Y370C|SORBS1_ENST00000306402.6_Missense_Mutation_p.Y316C|SORBS1_ENST00000371241.1_Missense_Mutation_p.Y275C|SORBS1_ENST00000393949.1_Missense_Mutation_p.Y455C|SORBS1_ENST00000607232.1_Missense_Mutation_p.Y274C|SORBS1_ENST00000371246.2_Missense_Mutation_p.Y507C|SORBS1_ENST00000347291.4_Missense_Mutation_p.Y353C|SORBS1_ENST00000277982.5_Missense_Mutation_p.Y507C|SORBS1_ENST00000371249.2_Missense_Mutation_p.Y407C|SORBS1_ENST00000353505.5_Missense_Mutation_p.Y370C|SORBS1_ENST00000371227.4_Missense_Mutation_p.Y439C|SORBS1_ENST00000371247.2_Missense_Mutation_p.Y485C|SORBS1_ENST00000474353.2_5'UTR|SORBS1_ENST00000354106.3_Missense_Mutation_p.Y455C	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		ACCATCAATGTAGCTCATCTC	0.488													T|||	110	0.0219649	0.0038	0.0331	5008	,	,		21674	0.0		0.0537	False		,,,				2504	0.0286				p.Y507C		Atlas-SNP	.											.	SORBS1	185	.	0			c.A1520G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	48,4358	49.6+/-84.7	0,48,2155	113.0	98.0	103.0		1454,1520,1109,824,824,1220,947	2.5	1.0	10	dbSNP_126	103	510,8090	145.6+/-201.3	13,484,3803	yes	missense,missense,missense,missense,missense,missense,missense	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	194,194,194,194,194,194,194	13,532,5958	CC,CT,TT		5.9302,1.0894,4.2903	benign,benign,benign,benign,benign,benign,benign	485/1293,507/1152,370/906,275/741,275/685,407/817,316/782	97143826	558,12448	2203	4300	6503	SO:0001583	missense	10580	exon15			TCAATGTAGCTCA	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.1454A>G	10.37:g.97143826T>C	ENSP00000355136:p.Tyr485Cys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	118	64	0.542373	NM_001034955		Missense_Mutation	SNP	ENST00000361941.3	37	CCDS31255.1	54	0.024725274725274724	3	0.006097560975609756	11	0.03038674033149171	0	0.0	40	0.052770448548812667	T	11.83	1.754733	0.31046	0.010894	0.059302	ENSG00000095637	ENST00000371245;ENST00000306402;ENST00000371249;ENST00000371247;ENST00000371227;ENST00000371246;ENST00000393949;ENST00000353505;ENST00000347291;ENST00000361941;ENST00000277982;ENST00000371241;ENST00000354106;ENST00000371239	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.28895	3.41;2.85;2.9;1.59;3.05;1.59;1.59;3.41;1.59;1.59;1.59;2.85;1.59;2.83	6.17	2.53	0.30540	.	0.405041	0.18329	N	0.144554	T	0.01940	0.0061	L	0.27053	0.805	0.27793	N	0.942755	B;B;B;B;B;B;B;B;B;B;B;B;B	0.15719	0.014;0.0;0.003;0.0;0.001;0.0;0.0;0.0;0.0;0.004;0.0;0.001;0.001	B;B;B;B;B;B;B;B;B;B;B;B;B	0.17979	0.008;0.001;0.02;0.005;0.004;0.0;0.0;0.0;0.002;0.007;0.002;0.005;0.001	T	0.11203	-1.0597	10	0.38643	T	0.18	-0.6316	6.4764	0.22039	0.0:0.1931:0.1185:0.6884	rs35808802	637;284;439;407;316;275;284;370;485;507;353;455;63	B7Z9B7;B4DTX5;Q9BX66-11;Q9BX66-10;Q9BX66-9;Q9BX66-4;Q9BX66-8;Q9BX66-3;Q9BX66;Q9BX66-2;Q9BX66-6;Q9BX66-5;Q6MZY5	.;.;.;.;.;.;.;.;SRBS1_HUMAN;.;.;.;.	C	370;316;407;485;439;507;455;370;353;485;507;275;455;284	ENSP00000360291:Y370C;ENSP00000302556:Y316C;ENSP00000360295:Y407C;ENSP00000360293:Y485C;ENSP00000360271:Y439C;ENSP00000360292:Y507C;ENSP00000377521:Y455C;ENSP00000343998:Y370C;ENSP00000277985:Y353C;ENSP00000355136:Y485C;ENSP00000277982:Y507C;ENSP00000360285:Y275C;ENSP00000277984:Y455C;ENSP00000360283:Y284C	ENSP00000277982:Y507C	Y	-	2	0	SORBS1	97133816	0.978000	0.34361	0.997000	0.53966	0.849000	0.48306	-0.033000	0.12246	0.175000	0.19841	-0.904000	0.02843	TAC	T|0.963;C|0.037	0.037	strong		0.488	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
TAF7L	54457	hgsc.bcm.edu	37	X	100547805	100547805	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547805C>T	ENST00000372907.3	-	1	240	c.229G>A	c.(229-231)Gcc>Acc	p.A77T	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_5'UTR	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	77					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						TTTTCTGGGGCCTGGGCAGCA	0.557																																					p.A77T	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.G229A						PASS	.						70.0	70.0	70.0					X																	100547805		2203	4300	6503	SO:0001583	missense	54457	exon1			CTGGGGCCTGGGC	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.229G>A	X.37:g.100547805C>T	ENSP00000361998:p.Ala77Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	9.433	1.086161	0.20390	.	.	ENSG00000102387	ENST00000372907	T	0.14391	2.51	3.17	-6.35	0.01975	.	2.099320	0.02710	N	0.112725	T	0.10380	0.0254	L	0.27053	0.805	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.24835	-1.0149	10	0.51188	T	0.08	-1.4147	9.7024	0.40196	0.0:0.5863:0.2433:0.1704	.	77	Q5H9L4	TAF7L_HUMAN	T	77	ENSP00000361998:A77T	ENSP00000361998:A77T	A	-	1	0	TAF7L	100434461	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.202000	0.03023	-2.983000	0.00282	-0.340000	0.08031	GCC	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
CCDC180	100499483	hgsc.bcm.edu	37	9	100074446	100074446	+	Silent	SNP	C	C	T	rs3747504	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100074446C>T	ENST00000357054.1	+	18	1796	c.861C>T	c.(859-861)atC>atT	p.I287I	CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000529487.1_Silent_p.I148I|CCDC180_ENST00000411667.2_Silent_p.I148I|CCDC180_ENST00000375202.2_Silent_p.I148I|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_Silent_p.I287I			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	287						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.I287I(1)									AGAACACCATCGCTGCCCGAG	0.567													C|||	1380	0.275559	0.2965	0.353	5008	,	,		21122	0.2907		0.1869	False		,,,				2504	0.2679				p.I148I		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.C444T						PASS	.	C		1188,3218	416.1+/-337.4	155,878,1170	119.0	120.0	119.0		444	-10.4	0.0	9	dbSNP_107	119	1592,7008	299.0+/-304.2	146,1300,2854	no	coding-synonymous	C9orf174	NM_020893.2		301,2178,4024	TT,TC,CC		18.5116,26.9632,21.3748		148/1702	100074446	2780,10226	2203	4300	6503	SO:0001819	synonymous_variant	0	exon4			CACCATCGCTGCC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.861C>T	9.37:g.100074446C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				C|0.766;T|0.234	0.234	strong		0.567	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
MST1L	11223	hgsc.bcm.edu	37	1	17085452	17085452	+	RNA	SNP	A	A	G	rs3981980		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17085452A>G	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GAGCGGGAGCAAAATCGTGGC	0.617																																					p.F413F		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,1	.	.	1	0			c.T1239C						scavenged	.																																					11223	exon10			GGGAGCAAAATCG	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.17085452A>G		Somatic	332	9	0.0271084		WXS	Illumina HiSeq	Phase_I	310	58	0.187097	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				A|1.000;|0.000	.	weak		0.617	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792003	8792003	+	Silent	SNP	C	C	T	rs9915880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8792003C>T	ENST00000447110.1	-	10	1225	c.1101G>A	c.(1099-1101)tcG>tcA	p.S367S	PIK3R5_ENST00000581552.1_Silent_p.S367S|PIK3R5_ENST00000584803.1_Silent_p.S367S	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	367				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						GGGCCGGCCCCGAGGCCTGGG	0.627													c|||	1017	0.203075	0.2995	0.2853	5008	,	,		18342	0.001		0.2833	False		,,,				2504	0.1401				p.S367S	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.G1101A						PASS	.	C	,	1297,3109	432.8+/-343.4	203,891,1109	72.0	75.0	74.0		1101,1101	-9.0	0.1	17	dbSNP_119	74	2686,5914	427.5+/-355.6	414,1858,2028	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	617,2749,3137	TT,TC,CC		31.2326,29.4371,30.6243	,	367/881,367/881	8792003	3983,9023	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			CGGCCCCGAGGCC	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.1101G>A	17.37:g.8792003C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	21	0.362069	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			C|0.736;T|0.264	0.264	strong		0.627	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
ODF2	4957	hgsc.bcm.edu	37	9	131245130	131245130	+	Silent	SNP	G	G	A	rs139481144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131245130G>A	ENST00000434106.3	+	10	1314	c.951G>A	c.(949-951)gaG>gaA	p.E317E	ODF2_ENST00000372807.5_Silent_p.E312E|ODF2_ENST00000535026.1_3'UTR|ODF2_ENST00000393527.3_Silent_p.E293E|ODF2_ENST00000448249.3_Silent_p.E236E|ODF2_ENST00000546203.1_Silent_p.E298E|ODF2_ENST00000393533.2_Silent_p.E317E|ODF2_ENST00000444119.2_Silent_p.E293E|ODF2_ENST00000604420.1_Silent_p.E317E|ODF2_ENST00000372791.3_Silent_p.E298E|ODF2_ENST00000351030.3_Silent_p.E312E|ODF2_ENST00000372814.3_Silent_p.E361E	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	317					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						AGGACAAGGAGGTGGAAGAGC	0.537													G|||	3	0.000599042	0.0	0.0014	5008	,	,		16148	0.0		0.002	False		,,,				2504	0.0				p.E381E		Atlas-SNP	.											.	ODF2	227	.	0			c.G1143A						PASS	.	G	,,,,,,,,,,	0,4406		0,0,2203	97.0	100.0	99.0		936,951,708,879,1083,951,1143,951,894,1026,894	1.1	1.0	9	dbSNP_134	99	21,8579	14.0+/-48.4	0,21,4279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2	NM_001242352.1,NM_001242353.1,NM_001242354.1,NM_002540.4,NM_153432.1,NM_153433.1,NM_153435.1,NM_153436.1,NM_153437.2,NM_153439.1,NM_153440.1	,,,,,,,,,,	0,21,6482	AA,AG,GG		0.2442,0.0,0.1615	,,,,,,,,,,	312/825,317/830,236/577,293/806,361/702,317/830,381/894,317/658,298/639,342/654,298/639	131245130	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	4957	exon10			CAAGGAGGTGGAA	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.951G>A	9.37:g.131245130G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
GPATCH1	55094	hgsc.bcm.edu	37	19	33617583	33617583	+	Silent	SNP	C	C	T	rs6510356	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33617583C>T	ENST00000170564.2	+	19	3023	c.2709C>T	c.(2707-2709)agC>agT	p.S903S		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	903					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					CCGACAGCAGCGACAGCCAGA	0.488											OREG0025410	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1298	0.259185	0.4387	0.134	5008	,	,		16215	0.1716		0.1163	False		,,,				2504	0.3425				p.S903S	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C2709T						PASS	.	C		1821,2585	533.0+/-373.6	379,1063,761	86.0	83.0	84.0		2709	-4.2	0.7	19	dbSNP_116	84	1008,7592	216.3+/-255.4	50,908,3342	no	coding-synonymous	GPATCH1	NM_018025.2		429,1971,4103	TT,TC,CC		11.7209,41.33,21.7515		903/932	33617583	2829,10177	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon19			CAGCAGCGACAGC	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.2709C>T	19.37:g.33617583C>T		Somatic	38	0	0	841	WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.792;N|0.001	.	strong		0.488	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
ZNF385B	151126	hgsc.bcm.edu	37	2	180308028	180308028	+	Silent	SNP	C	C	T	rs2367796	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:180308028C>T	ENST00000410066.1	-	10	1968	c.1365G>A	c.(1363-1365)ggG>ggA	p.G455G	ZNF385B_ENST00000409692.1_Silent_p.G353G|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Silent_p.G379G|ZNF385B_ENST00000336917.5_Silent_p.G353G	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	455	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			TGGGCCCATGCCCAGGCCTCA	0.622													C|||	840	0.167732	0.261	0.1023	5008	,	,		15902	0.1518		0.1412	False		,,,				2504	0.1319				p.G455G	Colon(155;204 2491 32774 51842)	Atlas-SNP	.											.	ZNF385B	68	.	0			c.G1365A						PASS	.	C	,,	959,3447	351.3+/-311.2	99,761,1343	32.0	39.0	37.0		1137,1059,1365	-3.9	0.0	2	dbSNP_100	37	1244,7356	244.4+/-273.7	102,1040,3158	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF385B	NM_001113397.1,NM_001113398.1,NM_152520.4	,,	201,1801,4501	TT,TC,CC		14.4651,21.7658,16.9383	,,	379/396,353/370,455/472	180308028	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	151126	exon10			CCCATGCCCAGGC	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"""zinc finger protein 533"""	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.1365G>A	2.37:g.180308028C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Silent	SNP	ENST00000410066.1	37	CCDS33339.1																																																																																			C|0.827;T|0.173	0.173	strong		0.622	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520	
CCL8	6355	hgsc.bcm.edu	37	17	32647831	32647831	+	Missense_Mutation	SNP	A	A	C	rs1133763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:32647831A>C	ENST00000394620.1	+	3	671	c.205A>C	c.(205-207)Aaa>Caa	p.K69Q		NM_005623.2	NP_005614.2	P80075	CCL8_HUMAN	chemokine (C-C motif) ligand 8	69			K -> Q (in dbSNP:rs1133763). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9070881, ECO:0000269|PubMed:9119400}.		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)				CTTCAAGACCAAACGGGGCAA	0.512													A|||	1138	0.227236	0.0658	0.2939	5008	,	,		15216	0.2986		0.1511	False		,,,				2504	0.4029				p.K69Q		Atlas-SNP	.											.	CCL8	12	.	0			c.A205C						PASS	.	A	GLN/LYS	318,4088	162.2+/-194.2	12,294,1897	72.0	60.0	64.0		205	3.1	0.0	17	dbSNP_86	64	1384,7216	253.4+/-279.1	118,1148,3034	yes	missense	CCL8	NM_005623.2	53	130,1442,4931	CC,CA,AA		16.093,7.2174,13.0863	probably-damaging	69/100	32647831	1702,11304	2203	4300	6503	SO:0001583	missense	6355	exon3			AAGACCAAACGGG	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.205A>C	17.37:g.32647831A>C	ENSP00000378118:p.Lys69Gln	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	164	68	0.414634	NM_005623	A0AV77|P78388	Missense_Mutation	SNP	ENST00000394620.1	37	CCDS11280.1	427	0.1955128205128205	48	0.0975609756097561	103	0.2845303867403315	163	0.28496503496503495	113	0.14907651715039577	A	16.50	3.140975	0.56936	0.072174	0.16093	ENSG00000108700	ENST00000394620;ENST00000225840	T	0.05580	3.42	5.34	3.09	0.35607	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.330523	0.21877	N	0.067797	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.46020	0.871	P	0.48738	0.588	T	0.46679	-0.9174	8	0.54805	T	0.06	.	6.482	0.22067	0.8092:0.0:0.1908:0.0	rs1133763;rs3138038;rs52819306;rs56696873;rs1133763	69	P80075	CCL8_HUMAN	Q	79;69	ENSP00000378118:K79Q	ENSP00000225840:K69Q	K	+	1	0	CCL8	29671944	0.027000	0.19231	0.042000	0.18584	0.132000	0.20833	2.066000	0.41452	0.829000	0.34733	0.460000	0.39030	AAA	A|0.839;C|0.161	0.161	strong		0.512	CCL8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256376.2	NM_005623	
COL18A1	80781	hgsc.bcm.edu	37	21	46913477	46913477	+	Missense_Mutation	SNP	G	G	C	rs2230693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46913477G>C	ENST00000359759.4	+	25	3606	c.3585G>C	c.(3583-3585)caG>caC	p.Q1195H	COL18A1_ENST00000400337.2_Missense_Mutation_p.Q780H|COL18A1_ENST00000459895.1_3'UTR|COL18A1_ENST00000355480.5_Missense_Mutation_p.Q960H			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	1195	Nonhelical region 6 (NC6).		Q -> H (in dbSNP:rs2230693).		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)		GCCCTGCCCAGAAAGGAGCCA	0.692													G|||	316	0.063099	0.0961	0.0159	5008	,	,		14748	0.1022		0.008	False		,,,				2504	0.0685				p.Q960H		Atlas-SNP	.											.	COL18A1	129	.	0			c.G2880C						PASS	.	G	HIS/GLN,HIS/GLN	284,3478		12,260,1609	10.0	12.0	11.0		2880,2340	0.4	0.2	21	dbSNP_98	11	46,7972		1,44,3964	no	missense,missense	COL18A1	NM_030582.3,NM_130445.2	24,24	13,304,5573	CC,CG,GG		0.5737,7.5492,2.8014	probably-damaging,probably-damaging	960/1520,780/1340	46913477	330,11450	1881	4009	5890	SO:0001583	missense	80781	exon25			TGCCCAGAAAGGA		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.3585G>C	21.37:g.46913477G>C	ENSP00000352798:p.Gln1195His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		145	0.06639194139194139	69	0.1402439024390244	7	0.019337016574585635	63	0.11013986013986014	6	0.0079155672823219	G	12.59	1.982841	0.34942	0.075492	0.005737	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645;ENST00000342220	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22	3.37	0.37	0.16160	.	0.812506	0.10906	N	0.621078	T	0.04137	0.0115	N	0.25890	0.77	0.51012	P	9.40000000000385E-5	B;B;B	0.14805	0.011;0.009;0.009	B;B;B	0.15052	0.012;0.007;0.007	T	0.52734	-0.8536	9	0.39692	T	0.17	.	6.075	0.19911	0.0:0.1845:0.4366:0.3789	rs2230693	1195;960;780	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	H	780;780;960;1195;1195;127	ENSP00000383191:Q780H;ENSP00000347665:Q960H;ENSP00000352798:Q1195H;ENSP00000339118:Q127H	ENSP00000339118:Q127H	Q	+	3	2	COL18A1	45737905	0.000000	0.05858	0.220000	0.23810	0.671000	0.39405	-0.328000	0.07945	0.066000	0.16515	0.313000	0.20887	CAG	G|0.935;C|0.065	0.065	strong		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
EPPK1	83481	hgsc.bcm.edu	37	8	144940290	144940290	+	Missense_Mutation	SNP	C	C	G	rs201976887		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144940290C>G	ENST00000525985.1	-	2	7203	c.7132G>C	c.(7132-7134)Gac>Cac	p.D2378H				P58107	EPIPL_HUMAN	epiplakin 1	2378						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)			TCGCTGGGGTCGGCCAGGACG	0.682																																					p.D2378H		Atlas-SNP	.											EPPK1,NS,carcinoma,0,5	EPPK1	199	5	0			c.G7132C						PASS	.	C	HIS/ASP	51,4341	20.2+/-43.8	0,51,2145	315.0	292.0	300.0		7132	3.6	0.8	8		300	22,8530	7.1+/-27.0	0,22,4254	no	missense	EPPK1	NM_031308.1	81	0,73,6399	GG,GC,CC		0.2572,1.1612,0.564	probably-damaging	2378/2420	144940290	73,12871	2196	4276	6472	SO:0001583	missense	83481	exon1			TGGGGTCGGCCAG	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.7132G>C	8.37:g.144940290C>G	ENSP00000436337:p.Asp2378His	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	240	14	0.0583333	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	22.4	4.279155	0.80692	0.011612	0.002572	ENSG00000227184	ENST00000525985	T	0.74737	-0.87	4.43	3.56	0.40772	.	.	.	.	.	D	0.83133	0.5188	M	0.89785	3.06	0.42176	D	0.991666	D	0.89917	1.0	D	0.91635	0.999	D	0.86316	0.1689	9	0.62326	D	0.03	.	10.4012	0.44231	0.0:0.9038:0.0:0.0962	.	2378	E9PPU0	.	H	2378	ENSP00000436337:D2378H	ENSP00000436337:D2378H	D	-	1	0	EPPK1	145012278	1.000000	0.71417	0.773000	0.31616	0.942000	0.58702	7.555000	0.82223	1.223000	0.43536	0.591000	0.81541	GAC	.	.	weak		0.682	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
HMCN1	83872	hgsc.bcm.edu	37	1	186026474	186026474	+	Missense_Mutation	SNP	T	T	C	rs12129650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186026474T>C	ENST00000271588.4	+	46	7482	c.7253T>C	c.(7252-7254)aTa>aCa	p.I2418T	HMCN1_ENST00000367492.2_Missense_Mutation_p.I2418T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2418	Ig-like C2-type 22.		I -> T (in dbSNP:rs12129650). {ECO:0000269|PubMed:14570714, ECO:0000269|Ref.1}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						CTGCCTTCCATAACCTGGTTC	0.413													T|||	2654	0.529952	0.5393	0.6124	5008	,	,		15388	0.5675		0.496	False		,,,				2504	0.455				p.I2418T		Atlas-SNP	.											.	HMCN1	797	.	0			c.T7253C						PASS	.	T	THR/ILE	2446,1960	619.5+/-393.4	686,1074,443	115.0	115.0	115.0		7253	4.7	0.9	1	dbSNP_120	115	4387,4213	583.2+/-391.5	1138,2111,1051	yes	missense	HMCN1	NM_031935.2	89	1824,3185,1494	CC,CT,TT		48.9884,44.4848,47.4627	benign	2418/5636	186026474	6833,6173	2203	4300	6503	SO:0001583	missense	83872	exon46			CTTCCATAACCTG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7253T>C	1.37:g.186026474T>C	ENSP00000271588:p.Ile2418Thr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	39	0.410526	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1198	0.5485347985347986	254	0.516260162601626	216	0.5966850828729282	341	0.5961538461538461	387	0.5105540897097626	T	18.19	3.569521	0.65765	0.555152	0.510116	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72282	-0.64;-0.64	5.8	4.67	0.58626	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.183947	0.56097	N	0.000027	T	0.00012	0.0000	M	0.85542	2.76	0.20307	P	0.9999161177	P	0.48998	0.918	B	0.44315	0.446	T	0.47674	-0.9099	9	0.56958	D	0.05	.	11.7655	0.51928	0.0:0.0685:0.0:0.9315	rs12129650;rs52819931;rs57046032;rs12129650	2418	Q96RW7	HMCN1_HUMAN	T	2418	ENSP00000271588:I2418T;ENSP00000356462:I2418T	ENSP00000271588:I2418T	I	+	2	0	HMCN1	184293097	1.000000	0.71417	0.907000	0.35723	0.830000	0.47004	5.743000	0.68655	1.020000	0.39573	-0.263000	0.10527	ATA	C|0.538;N|0.000	0.538	strong		0.413	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
GMPPB	29925	hgsc.bcm.edu	37	3	49760431	49760431	+	Missense_Mutation	SNP	G	G	C	rs34345884	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49760431G>C	ENST00000480687.1	-	5	492	c.376C>G	c.(376-378)Cac>Gac	p.H126D	GMPPB_ENST00000308375.6_Missense_Mutation_p.H126D|GMPPB_ENST00000308388.6_Missense_Mutation_p.H126D|AMIGO3_ENST00000535833.1_5'UTR			Q9Y5P6	GMPPB_HUMAN	GDP-mannose pyrophosphorylase B	126			H -> D (in dbSNP:rs34345884).		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|mannose-1-phosphate guanylyltransferase activity (GO:0004475)			endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TGGCCATGGTGCCGGTGGAAC	0.587													G|||	44	0.00878594	0.0	0.0144	5008	,	,		21498	0.0		0.0308	False		,,,				2504	0.0031				p.H126D		Atlas-SNP	.											.	GMPPB	14	.	0			c.C376G						PASS	.	G	ASP/HIS,ASP/HIS	18,4388	26.2+/-53.5	0,18,2185	49.0	48.0	48.0		376,376	4.9	1.0	3	dbSNP_126	48	184,8414	83.1+/-145.7	2,180,4117	yes	missense,missense	GMPPB	NM_013334.2,NM_021971.1	81,81	2,198,6302	CC,CG,GG		2.14,0.4085,1.5534	benign,benign	126/388,126/361	49760431	202,12802	2203	4299	6502	SO:0001583	missense	29925	exon4			CATGGTGCCGGTG	AF135421	CCDS2802.1, CCDS2803.1	3p21.31	2008-02-05			ENSG00000173540	ENSG00000173540	2.7.7.22		22932	protein-coding gene	gene with protein product		615320					Standard	NM_013334		Approved	KIAA1851	uc003cxl.1	Q9Y5P6	OTTHUMG00000158151	ENST00000480687.1:c.376C>G	3.37:g.49760431G>C	ENSP00000418565:p.His126Asp	Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	251	125	0.498008	NM_021971	A8K6N5|Q9H7U3	Missense_Mutation	SNP	ENST00000480687.1	37	CCDS2803.1	31	0.014194139194139194	0	0.0	6	0.016574585635359115	0	0.0	25	0.032981530343007916	G	10.98	1.505629	0.26949	0.004085	0.0214	ENSG00000173540	ENST00000480687;ENST00000308375;ENST00000308388	D;D;D	0.93307	-3.2;-3.2;-3.2	4.94	4.94	0.65067	Nucleotidyl transferase (1);	0.221869	0.46145	D	0.000315	T	0.65595	0.2706	N	0.02403	-0.565	0.48135	D	0.999591	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.74044	-0.3791	10	0.14252	T	0.57	-20.3305	17.1357	0.86739	0.0:0.0:1.0:0.0	rs34345884	126;126	Q9Y5P6-2;Q9Y5P6	.;GMPPB_HUMAN	D	126	ENSP00000418565:H126D;ENSP00000309092:H126D;ENSP00000311130:H126D	ENSP00000309092:H126D	H	-	1	0	GMPPB	49735435	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.904000	0.63279	2.290000	0.77057	0.462000	0.41574	CAC	G|0.986;C|0.014	0.014	strong		0.587	GMPPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350291.1	NM_013334	
FGFBP2	83888	hgsc.bcm.edu	37	4	15964485	15964485	+	Missense_Mutation	SNP	G	G	A	rs758329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:15964485G>A	ENST00000259989.6	-	1	374	c.268C>T	c.(268-270)Cct>Tct	p.P90S	FGFBP2_ENST00000509331.1_Intron	NM_031950.3	NP_114156.1	Q9BYJ0	FGFP2_HUMAN	fibroblast growth factor binding protein 2	90			P -> S (in dbSNP:rs758329).			extracellular region (GO:0005576)				central_nervous_system(1)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	9						TTCCAGTAAGGTTTGGGGTCA	0.632													G|||	1689	0.33726	0.2194	0.2954	5008	,	,		20479	0.501		0.4722	False		,,,				2504	0.2188				p.P90S		Atlas-SNP	.											FGFBP2,colon,carcinoma,0,2	FGFBP2	22	2	0			c.C268T						PASS	.	G	SER/PRO	1068,3338	388.2+/-326.8	136,796,1271	54.0	54.0	54.0		268	1.1	0.2	4	dbSNP_86	54	3973,4627	549.9+/-385.6	947,2079,1274	yes	missense	FGFBP2	NM_031950.3	74	1083,2875,2545	AA,AG,GG		46.1977,24.2397,38.759	benign	90/224	15964485	5041,7965	2203	4300	6503	SO:0001583	missense	83888	exon1			AGTAAGGTTTGGG	AB021123	CCDS3419.1	4p15.32	2008-07-16			ENSG00000137441	ENSG00000137441			29451	protein-coding gene	gene with protein product	"""killer-specific secretory protein of 37 kDa"""	607713				11342666, 12322897	Standard	NM_031950		Approved	KSP37	uc003gon.3	Q9BYJ0	OTTHUMG00000128513	ENST00000259989.6:c.268C>T	4.37:g.15964485G>A	ENSP00000259989:p.Pro90Ser	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_031950		Missense_Mutation	SNP	ENST00000259989.6	37	CCDS3419.1	915	0.41895604395604397	121	0.2459349593495935	112	0.30939226519337015	307	0.5367132867132867	375	0.4947229551451187	G	0.169	-1.073128	0.01918	0.242397	0.461977	ENSG00000137441	ENST00000259989	T	0.12672	2.66	2.98	1.08	0.20341	.	0.651924	0.13462	U	0.386030	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.25441	0.126	B	0.22880	0.042	T	0.37009	-0.9724	9	0.21014	T	0.42	0.3963	5.9323	0.19146	0.0:0.1584:0.3635:0.4782	rs758329;rs17709603;rs758329	90	Q9BYJ0	FGFP2_HUMAN	S	90	ENSP00000259989:P90S	ENSP00000259989:P90S	P	-	1	0	FGFBP2	15573583	0.917000	0.31117	0.160000	0.22671	0.187000	0.23431	0.703000	0.25646	-0.187000	0.10516	-1.067000	0.02272	CCT	G|0.606;A|0.394	0.394	strong		0.632	FGFBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250324.1	NM_031950	
CFAP53	220136	hgsc.bcm.edu	37	18	47777244	47777244	+	Missense_Mutation	SNP	C	C	T	rs35193847	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:47777244C>T	ENST00000398545.4	-	5	997	c.880G>A	c.(880-882)Gag>Aag	p.E294K		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		TCTATCCTCTCTTGTAGGGCT	0.418													C|||	969	0.19349	0.1036	0.1787	5008	,	,		20837	0.0625		0.3926	False		,,,				2504	0.2556				p.E294K		Atlas-SNP	.											.	CCDC11	59	.	0			c.G880A						PASS	.	C	LYS/GLU	542,3210		43,456,1377	385.0	342.0	356.0		880	4.9	0.8	18	dbSNP_126	356	3112,5114		618,1876,1619	yes	missense	CCDC11	NM_145020.3	56	661,2332,2996	TT,TC,CC		37.8313,14.4456,30.5059	possibly-damaging	294/515	47777244	3654,8324	1876	4113	5989	SO:0001583	missense	220136	exon5			TCCTCTCTTGTAG																												ENST00000398545.4:c.880G>A	18.37:g.47777244C>T	ENSP00000381553:p.Glu294Lys	Somatic	399	1	0.00250627		WXS	Illumina HiSeq	Phase_I	342	342	1	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	37	CCDS11940.2	441	0.20192307692307693	49	0.09959349593495935	74	0.20441988950276244	39	0.06818181818181818	279	0.36807387862796836	C	12.00	1.807417	0.31961	0.144456	0.378313	ENSG00000172361	ENST00000398545	T	0.11821	2.74	5.81	4.94	0.65067	.	0.524458	0.21054	N	0.080955	T	0.00012	0.0000	L	0.46157	1.445	0.53688	P	2.8000000000028002E-5	P	0.37061	0.58	B	0.37550	0.253	T	0.43669	-0.9377	9	0.11794	T	0.64	-5.5184	8.4953	0.33125	0.0:0.7651:0.1536:0.0813	rs35193847;rs56682575	294	Q96M91	CCD11_HUMAN	K	294	ENSP00000381553:E294K	ENSP00000381553:E294K	E	-	1	0	CCDC11	46031242	0.587000	0.26791	0.806000	0.32338	0.006000	0.05464	2.060000	0.41394	1.471000	0.48121	0.655000	0.94253	GAG	C|0.738;T|0.262	0.262	strong		0.418	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
IER2	9592	hgsc.bcm.edu	37	19	13264398	13264398	+	Missense_Mutation	SNP	C	C	T	rs1042164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:13264398C>T	ENST00000588173.1	+	1	1610	c.398C>T	c.(397-399)gCt>gTt	p.A133V	IER2_ENST00000292433.3_Missense_Mutation_p.A133V|CTC-250I14.6_ENST00000586483.1_RNA|IER2_ENST00000587885.1_Missense_Mutation_p.A133V|CTC-250I14.6_ENST00000592882.1_RNA			Q9BTL4	IER2_HUMAN	immediate early response 2	133			A -> V (in dbSNP:rs1042164). {ECO:0000269|PubMed:2061303}.			cytoplasm (GO:0005737)				kidney(1)|lung(1)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			GGCGGGGACGCTGGACTGGTC	0.682											OREG0025291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	352	0.0702875	0.0159	0.1124	5008	,	,		13931	0.0129		0.175	False		,,,				2504	0.0654				p.A133V		Atlas-SNP	.											.	IER2	14	.	0			c.C398T						PASS	.	C	VAL/ALA	181,4157		4,173,1992	12.0	13.0	13.0		398	0.6	0.0	19	dbSNP_86	13	1425,7093		137,1151,2971	yes	missense	IER2	NM_004907.2	64	141,1324,4963	TT,TC,CC		16.7293,4.1724,12.4922	benign	133/224	13264398	1606,11250	2169	4259	6428	SO:0001583	missense	9592	exon2			GGGACGCTGGACT	M62831	CCDS12295.1	19p13.13	2008-02-05				ENSG00000160888			28871	protein-coding gene	gene with protein product						2061303	Standard	NM_004907		Approved	ETR101	uc002mwr.3	Q9BTL4		ENST00000588173.1:c.398C>T	19.37:g.13264398C>T	ENSP00000465617:p.Ala133Val	Somatic	13	0	0	686	WXS	Illumina HiSeq	Phase_I	31	17	0.548387	NM_004907	Q03827|Q2TAZ2	Missense_Mutation	SNP	ENST00000588173.1	37	CCDS12295.1	212	0.09706959706959707	10	0.02032520325203252	50	0.13812154696132597	12	0.02097902097902098	140	0.18469656992084432	C	12.81	2.050513	0.36181	0.041724	0.167293	ENSG00000160888	ENST00000292433	T	0.10288	2.89	4.18	0.597	0.17504	.	0.350700	0.20201	N	0.097097	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.10296	0.003	B	0.10450	0.005	T	0.38243	-0.9670	9	0.48119	T	0.1	-0.4452	5.1108	0.14808	0.0:0.6165:0.1694:0.2141	rs1042164;rs57863418;rs1042164	133	Q9BTL4	IER2_HUMAN	V	133	ENSP00000292433:A133V	ENSP00000292433:A133V	A	+	2	0	IER2	13125398	0.013000	0.17824	0.001000	0.08648	0.564000	0.35744	1.510000	0.35790	-0.084000	0.12595	-0.379000	0.06801	GCT	C|0.921;T|0.079	0.079	strong		0.682	IER2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453033.1	NM_004907	
SIRT1	23411	hgsc.bcm.edu	37	10	69666598	69666598	+	Silent	SNP	T	T	C	rs2273773	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:69666598T>C	ENST00000212015.6	+	5	1047	c.994T>C	c.(994-996)Ttg>Ctg	p.L332L	SIRT1_ENST00000432464.1_Silent_p.L37L|SIRT1_ENST00000406900.1_Silent_p.L29L|SIRT1_ENST00000403579.1_Silent_p.L29L	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	332	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.|Interaction with CCAR2.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						ATTCATAGCCTTGTCAGATAA	0.383													T|||	637	0.127196	0.0204	0.1297	5008	,	,		16893	0.3115		0.0755	False		,,,				2504	0.1329				p.L332L		Atlas-SNP	.											.	SIRT1	38	.	0			c.T994C						PASS	.	T	,	134,4272	95.7+/-134.4	1,132,2070	88.0	87.0	87.0		109,994	5.3	1.0	10	dbSNP_100	87	524,8076	145.7+/-201.4	13,498,3789	no	coding-synonymous,coding-synonymous	SIRT1	NM_001142498.1,NM_012238.4	,	14,630,5859	CC,CT,TT		6.093,3.0413,5.0592	,	37/453,332/748	69666598	658,12348	2203	4300	6503	SO:0001819	synonymous_variant	23411	exon5			ATAGCCTTGTCAG	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.994T>C	10.37:g.69666598T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Silent	SNP	ENST00000212015.6	37	CCDS7273.1																																																																																			T|0.910;C|0.090	0.090	strong		0.383	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1		
ITPR2	3709	hgsc.bcm.edu	37	12	26733062	26733062	+	Silent	SNP	T	T	C	rs2230375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:26733062T>C	ENST00000381340.3	-	33	4823	c.4407A>G	c.(4405-4407)aaA>aaG	p.K1469K		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1469					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TGTCTGCATGTTTCCTGTCTG	0.358													T|||	1001	0.19988	0.0885	0.2305	5008	,	,		18889	0.0764		0.3559	False		,,,				2504	0.2955				p.K1469K		Atlas-SNP	.											.	ITPR2	270	.	0			c.A4407G						PASS	.	T		466,3188		29,408,1390	164.0	146.0	151.0		4407	-8.6	0.4	12	dbSNP_98	151	2793,5383		484,1825,1779	no	coding-synonymous	ITPR2	NM_002223.2		513,2233,3169	CC,CT,TT		34.161,12.7531,27.5486		1469/2702	26733062	3259,8571	1827	4088	5915	SO:0001819	synonymous_variant	3709	exon33			TGCATGTTTCCTG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4407A>G	12.37:g.26733062T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.774;C|0.226	0.226	strong		0.358	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
COL18A1	80781	hgsc.bcm.edu	37	21	46875586	46875586	+	Missense_Mutation	SNP	C	C	G	rs61749002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46875586C>G	ENST00000359759.4	+	1	163	c.142C>G	c.(142-144)Ccc>Gcc	p.P48A	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Missense_Mutation_p.P48A			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	48					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)		GATCCCTGAGCCCCAGGGGCC	0.637													C|||	99	0.0197684	0.0688	0.0115	5008	,	,		16000	0.0		0.0	False		,,,				2504	0.0				p.P48A		Atlas-SNP	.											.	COL18A1	129	.	0			c.C142G						PASS	.	C	,ALA/PRO	243,3931		6,231,1850	52.0	69.0	63.0		,142	0.2	0.0	21	dbSNP_129	63	1,8439		0,1,4219	yes	intron,missense	COL18A1	NM_130445.2,NM_030582.3	,27	6,232,6069	GG,GC,CC		0.0118,5.8218,1.9344	,benign	,48/1520	46875586	244,12370	2087	4220	6307	SO:0001583	missense	80781	exon1			CCTGAGCCCCAGG		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.142C>G	21.37:g.46875586C>G	ENSP00000352798:p.Pro48Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	145	66	0.455172	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		54	0.024725274725274724	48	0.0975609756097561	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	C	8.524	0.869347	0.17322	0.058218	1.18E-4	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.59906	0.23;0.23	3.33	0.153	0.14897	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	1.487630	0.05437	N	0.546948	T	0.01627	0.0052	L	0.34521	1.04	0.09310	N	1	B;B	0.14438	0.01;0.002	B;B	0.17098	0.017;0.003	T	0.15407	-1.0438	10	0.87932	D	0	.	6.156	0.20338	0.0:0.5294:0.3598:0.1108	rs61749002	48;48	P39060;P39060-1	COIA1_HUMAN;.	A	48	ENSP00000347665:P48A;ENSP00000352798:P48A	ENSP00000347665:P48A	P	+	1	0	COL18A1	45700014	0.000000	0.05858	0.049000	0.19019	0.056000	0.15407	-0.676000	0.05221	-0.110000	0.12022	0.436000	0.28706	CCC	C|0.976;G|0.024	0.024	strong		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
NACAD	23148	hgsc.bcm.edu	37	7	45120248	45120248	+	Silent	SNP	G	G	A	rs1132130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45120248G>A	ENST00000490531.2	-	7	4684	c.4665C>T	c.(4663-4665)aaC>aaT	p.N1555N		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1555					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						CCATGATGGCGTTGACGATGT	0.622													G|||	539	0.107628	0.0166	0.1657	5008	,	,		20196	0.1081		0.173	False		,,,				2504	0.1217				p.N1555N		Atlas-SNP	.											.	NACAD	44	.	0			c.C4665T						PASS	.	G		49,1335		0,49,643	191.0	195.0	194.0		4665	-4.9	1.0	7	dbSNP_86	194	595,2587		48,499,1044	no	coding-synonymous	NACAD	NM_001146334.1		48,548,1687	AA,AG,GG		18.6989,3.5405,14.1042		1555/1563	45120248	644,3922	692	1591	2283	SO:0001819	synonymous_variant	23148	exon7			GATGGCGTTGACG	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.4665C>T	7.37:g.45120248G>A		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	202	97	0.480198	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			G|0.875;C|0.000;A|0.124	0.124	strong		0.622	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
TMEM261	90871	hgsc.bcm.edu	37	9	7799653	7799653	+	Missense_Mutation	SNP	G	G	T	rs1127430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:7799653G>T	ENST00000358227.4	-	1	414	c.82C>A	c.(82-84)Ccc>Acc	p.P28T	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	28			P -> T (in dbSNP:rs1127430).			integral component of membrane (GO:0016021)											GTAGCTGGGGGCGCAGGTTTG	0.662													g|||	1874	0.374201	0.264	0.5375	5008	,	,		9632	0.371		0.3926	False		,,,				2504	0.3916				p.P28T		Atlas-SNP	.											.	C9orf123	7	.	0			c.C82A						PASS	.	G	THR/PRO	1224,3182		178,868,1157	22.0	26.0	25.0		82	3.5	0.0	9	dbSNP_86	25	3382,5218		663,2056,1581	no	missense	C9orf123	NM_033428.1	38	841,2924,2738	TT,TG,GG		39.3256,27.7803,35.4144	probably-damaging	28/113	7799653	4606,8400	2203	4300	6503	SO:0001583	missense	90871	exon1			CTGGGGGCGCAGG	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.82C>A	9.37:g.7799653G>T	ENSP00000350961:p.Pro28Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_033428	A8K9B7|Q5T6Y9|Q9NT74	Missense_Mutation	SNP	ENST00000358227.4	37	CCDS34989.1	819	0.375	137	0.2784552845528455	198	0.5469613259668509	197	0.34440559440559443	287	0.3786279683377309	g	17.75	3.467238	0.63625	0.277803	0.393256	ENSG00000137038	ENST00000358227	T	0.52526	0.66	5.34	3.45	0.39498	.	0.309163	0.24041	N	0.042086	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	P;P	0.46512	0.717;0.879	B;P	0.45639	0.243;0.488	T	0.48547	-0.9026	9	0.72032	D	0.01	-4.188	8.6511	0.34035	0.0:0.166:0.6616:0.1724	rs1127430;rs3183396	28;28	Q96GE9-2;Q96GE9	.;CI123_HUMAN	T	28	ENSP00000350961:P28T	ENSP00000350961:P28T	P	-	1	0	C9orf123	7789653	0.000000	0.05858	0.003000	0.11579	0.139000	0.21198	-0.242000	0.08928	0.773000	0.33404	0.645000	0.84053	CCC	G|0.647;T|0.353	0.353	strong		0.662	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428	
CPEB3	22849	hgsc.bcm.edu	37	10	93999850	93999850	+	Silent	SNP	A	A	G	rs3824734	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:93999850A>G	ENST00000265997.4	-	2	430	c.258T>C	c.(256-258)ccT>ccC	p.P86P	CPEB3_ENST00000412050.4_Silent_p.P86P	NM_014912.4	NP_055727.3	Q8NE35	CPEB3_HUMAN	cytoplasmic polyadenylation element binding protein 3	86	Pro-rich.				3'-UTR-mediated mRNA destabilization (GO:0061158)|cellular response to amino acid stimulus (GO:0071230)|long-term memory (GO:0007616)|negative regulation of cytoplasmic translational elongation (GO:1900248)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation (GO:0017148)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of mRNA polyadenylation (GO:1900365)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|regulation of dendritic spine development (GO:0060998)|regulation of synaptic plasticity (GO:0048167)|translation (GO:0006412)	apical dendrite (GO:0097440)|CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuron projection (GO:0043005)|nucleus (GO:0005634)|synapse (GO:0045202)	mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|translation factor activity, nucleic acid binding (GO:0008135)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0869)				GCTGCTGAGGAGGCTGATGGA	0.721													G|||	3298	0.658546	0.9501	0.745	5008	,	,		9820	0.499		0.6173	False		,,,				2504	0.41				p.P86P		Atlas-SNP	.											.	CPEB3	43	.	0			c.T258C						PASS	.	G	,	3896,456		1755,386,35	13.0	15.0	14.0		258,258	-0.1	1.0	10	dbSNP_107	14	5207,3285		1622,1963,661	no	coding-synonymous,coding-synonymous	CPEB3	NM_001178137.1,NM_014912.4	,	3377,2349,696	GG,GA,AA		38.6835,10.4779,29.1264	,	86/685,86/699	93999850	9103,3741	2176	4246	6422	SO:0001819	synonymous_variant	22849	exon2			CTGAGGAGGCTGA	AB023157	CCDS31246.1, CCDS53553.1	10q23.33	2013-02-12			ENSG00000107864	ENSG00000107864		"""RNA binding motif (RRM) containing"""	21746	protein-coding gene	gene with protein product		610606				10231032, 12672660	Standard	NM_014912		Approved	KIAA0940	uc001khw.2	Q8NE35	OTTHUMG00000018756	ENST00000265997.4:c.258T>C	10.37:g.93999850A>G		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_014912	Q5T389|Q9NQJ7|Q9Y2E9	Silent	SNP	ENST00000265997.4	37	CCDS31246.1																																																																																			A|0.307;G|0.693	0.693	strong		0.721	CPEB3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049387.2	NM_014912	
LRG1	116844	hgsc.bcm.edu	37	19	4538599	4538599	+	Missense_Mutation	SNP	G	G	A	rs966384	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4538599G>A	ENST00000306390.6	-	2	857	c.397C>T	c.(397-399)Ccg>Tcg	p.P133S	CTB-50L17.14_ENST00000586020.1_Intron|LRG1_ENST00000586883.1_5'UTR	NM_052972.2	NP_443204.1	P02750	A2GL_HUMAN	leucine-rich alpha-2-glycoprotein 1	133			P -> S (in dbSNP:rs966384). {ECO:0000269|PubMed:15489334}.		brown fat cell differentiation (GO:0050873)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				NS(1)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAGGCCCGGGGGCAGCCCG	0.632													G|||	1604	0.320288	0.0862	0.4467	5008	,	,		16078	0.5308		0.3618	False		,,,				2504	0.2873				p.P133S		Atlas-SNP	.											.	LRG1	25	.	0			c.C397T						PASS	.	G	SER/PRO	566,3826		41,484,1671	24.0	30.0	28.0		397	0.9	0.0	19	dbSNP_86	28	2767,5779		455,1857,1961	yes	missense	LRG1	NM_052972.2	74	496,2341,3632	AA,AG,GG		32.3777,12.8871,25.7613	benign	133/348	4538599	3333,9605	2196	4273	6469	SO:0001583	missense	116844	exon2			GGCCCGGGGGCAG		CCDS12130.1	19p13.3	2013-09-20			ENSG00000171236	ENSG00000171236			29480	protein-coding gene	gene with protein product	"""leucine rich alpha 2 glycoprotein"""	611289				3856868, 12223515	Standard	NM_052972		Approved	LRG	uc002mau.3	P02750	OTTHUMG00000182010	ENST00000306390.6:c.397C>T	19.37:g.4538599G>A	ENSP00000302621:p.Pro133Ser	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_052972	Q8N4F5|Q96QZ4	Missense_Mutation	SNP	ENST00000306390.6	37	CCDS12130.1	770	0.3525641025641026	39	0.07926829268292683	168	0.46408839779005523	290	0.506993006993007	273	0.36015831134564646	.	4.933	0.173269	0.09391	0.128871	0.323777	ENSG00000171236	ENST00000306390	T	0.03524	3.9	4.71	0.948	0.19561	.	0.000000	0.40469	N	0.001098	T	0.00012	0.0000	L	0.38733	1.17	0.80722	P	0.0	B	0.30068	0.267	B	0.30495	0.116	T	0.32214	-0.9915	9	0.22109	T	0.4	-22.3111	6.9139	0.24349	0.0:0.3445:0.4527:0.2027	rs966384;rs17846084;rs17859086;rs57205193;rs966384	133	P02750	A2GL_HUMAN	S	133	ENSP00000302621:P133S	ENSP00000302621:P133S	P	-	1	0	LRG1	4489599	0.091000	0.21658	0.009000	0.14445	0.001000	0.01503	0.022000	0.13511	0.527000	0.28560	0.655000	0.94253	CCG	G|0.705;A|0.295	0.295	strong		0.632	LRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458654.2	NM_052972	
OR4K15	81127	hgsc.bcm.edu	37	14	20444607	20444607	+	Missense_Mutation	SNP	C	C	G	rs10135467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20444607C>G	ENST00000305051.5	+	1	1005	c.930C>G	c.(928-930)atC>atG	p.I310M		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	310			I -> M (in dbSNP:rs10135467). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ACCCTGTAATCTACACGCTAA	0.398													C|||	1099	0.219449	0.2186	0.1715	5008	,	,		17634	0.123		0.2227	False		,,,				2504	0.3507				p.I310M		Atlas-SNP	.											.	OR4K15	82	.	0			c.C930G						PASS	.	C	MET/ILE	1057,3347		121,815,1266	96.0	95.0	96.0		930	-0.4	0.9	14	dbSNP_119	96	2284,6316		289,1706,2305	no	missense	OR4K15	NM_001005486.1	10	410,2521,3571	GG,GC,CC		26.5581,24.0009,25.6921	probably-damaging	310/349	20444607	3341,9663	2202	4300	6502	SO:0001583	missense	81127	exon1			TGTAATCTACACG		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.930C>G	14.37:g.20444607C>G	ENSP00000304077:p.Ile310Met	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	184	99	0.538043	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	402	0.18406593406593408	97	0.19715447154471544	65	0.17955801104972377	66	0.11538461538461539	174	0.22955145118733508	.	12.66	2.004692	0.35320	0.240009	0.265581	ENSG00000169488	ENST00000305051	T	0.57273	0.41	3.69	-0.451	0.12214	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000087	T	0.00012	0.0000	M	0.72353	2.195	0.38036	P	0.064697	D	0.89917	1.0	D	0.76575	0.988	T	0.06716	-1.0811	9	0.87932	D	0	.	3.7838	0.08692	0.171:0.5187:0.0:0.3104	rs10135467;rs17276912;rs10135467	310	Q8NH41	OR4KF_HUMAN	M	310	ENSP00000304077:I310M	ENSP00000304077:I310M	I	+	3	3	OR4K15	19514447	0.070000	0.21116	0.927000	0.36925	0.707000	0.40811	-0.927000	0.03984	-0.217000	0.10033	0.591000	0.81541	ATC	C|0.770;G|0.230	0.230	strong		0.398	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
LRRC74A	145497	hgsc.bcm.edu	37	14	77297656	77297656	+	Missense_Mutation	SNP	G	G	A	rs142627436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:77297656G>A	ENST00000393774.3	+	3	452	c.328G>A	c.(328-330)Gtg>Atg	p.V110M	C14orf166B_ENST00000460005.1_3'UTR|C14orf166B_ENST00000450042.2_Missense_Mutation_p.V93M	NM_194287.2	NP_919263.2														breast(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(1)	18			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0306)		GGAGTCCTACGTGAACCTCAA	0.552													G|||	20	0.00399361	0.0015	0.0144	5008	,	,		19573	0.001		0.007	False		,,,				2504	0.0				p.V110M	Ovarian(165;1056 1958 32571 36789 48728)	Atlas-SNP	.											.	C14orf166B	52	.	0			c.G328A						PASS	.	G	MET/VAL	3,4403	6.2+/-15.9	0,3,2200	127.0	110.0	116.0		328	-3.2	0.0	14	dbSNP_134	116	51,8549	32.3+/-84.9	1,49,4250	yes	missense	C14orf166B	NM_194287.2	21	1,52,6450	AA,AG,GG		0.593,0.0681,0.4152	benign	110/489	77297656	54,12952	2203	4300	6503	SO:0001583	missense	145497	exon3			TCCTACGTGAACC																												ENST00000393774.3:c.328G>A	14.37:g.77297656G>A	ENSP00000377369:p.Val110Met	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_194287		Missense_Mutation	SNP	ENST00000393774.3	37	CCDS9853.2	13	0.005952380952380952	2	0.0040650406504065045	5	0.013812154696132596	1	0.0017482517482517483	5	0.006596306068601583	G	1.756	-0.488058	0.04352	6.81E-4	0.00593	ENSG00000100565	ENST00000393774;ENST00000450042	T;T	0.53857	0.6;2.28	5.66	-3.17	0.05202	.	0.327597	0.42548	N	0.000691	T	0.22742	0.0549	N	0.17278	0.47	0.80722	D	1	B	0.20550	0.046	B	0.11329	0.006	T	0.02184	-1.1199	10	0.31617	T	0.26	.	11.9366	0.52876	0.745:0.0:0.255:0.0	.	110	Q0VAA2	CN16B_HUMAN	M	110;93	ENSP00000377369:V110M;ENSP00000396260:V93M	ENSP00000216450:V110M	V	+	1	0	C14orf166B	76367409	0.001000	0.12720	0.009000	0.14445	0.921000	0.55340	-0.146000	0.10250	-0.735000	0.04837	-0.474000	0.04947	GTG	G|0.995;A|0.005	0.005	strong		0.552	C14orf166B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316592.1		
ZNF844	284391	hgsc.bcm.edu	37	19	12186857	12186857	+	Missense_Mutation	SNP	G	G	C	rs6511763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12186857G>C	ENST00000439326.3	+	4	1097	c.922G>C	c.(922-924)Gct>Cct	p.A308P	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	308			A -> P (in dbSNP:rs6511763).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TGAGGAGAAGGCTTATGAATG	0.413													.|||	1455	0.290535	0.73	0.1455	5008	,	,		21988	0.0853		0.161	False		,,,				2504	0.1442				p.A308P		Atlas-SNP	.											.	ZNF844	69	.	0			c.G922C						PASS	.	C	PRO/ALA	887,497		287,313,92	67.0	64.0	65.0		922	1.4	0.0	19	dbSNP_116	65	416,2766		25,366,1200	yes	missense	ZNF844	NM_001136501.1	27	312,679,1292	CC,CG,GG		13.0735,35.9104,28.537	benign	308/667	12186857	1303,3263	692	1591	2283	SO:0001583	missense	284391	exon4			GAGAAGGCTTATG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.922G>C	19.37:g.12186857G>C	ENSP00000392024:p.Ala308Pro	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	572	0.2619047619047619	339	0.6890243902439024	53	0.1464088397790055	53	0.09265734265734266	127	0.16754617414248021	C	1.412	-0.575281	0.03882	0.640896	0.130735	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505	T	0.10192	2.9	2.5	1.42	0.22433	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00047	-2.43	0.26978	P	0.9654259	B	0.02656	0.0	B	0.01281	0.0	T	0.33929	-0.9849	8	0.02654	T	1	.	5.9876	0.19442	0.0:0.6833:0.1951:0.1217	rs6511763;rs52826403;rs60463492;rs6511763	308	Q08AG5	ZN844_HUMAN	P	308;308;283	ENSP00000392024:A308P	ENSP00000392024:A308P	A	+	1	0	ZNF844	12047857	0.000000	0.05858	0.001000	0.08648	0.403000	0.30841	0.066000	0.14489	-0.014000	0.14175	-0.980000	0.02579	GCT	G|0.739;C|0.261	0.261	strong		0.413	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ZNF215	7762	hgsc.bcm.edu	37	11	6977109	6977109	+	Missense_Mutation	SNP	T	T	C	rs149189074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6977109T>C	ENST00000278319.5	+	7	1489	c.901T>C	c.(901-903)Ttt>Ctt	p.F301L	ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000529903.1_Intron|ZNF215_ENST00000414517.2_Missense_Mutation_p.F301L	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	301					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)		GGAGGAAGATTTTGAATGTAG	0.353													T|||	12	0.00239617	0.0	0.0014	5008	,	,		18696	0.0		0.0099	False		,,,				2504	0.001				p.F301L		Atlas-SNP	.											.	ZNF215	72	.	0			c.T901C						PASS	.	T	LEU/PHE	4,4398	8.1+/-20.4	0,4,2197	72.0	83.0	79.0		901	3.1	0.0	11	dbSNP_134	79	56,8530	31.7+/-84.0	0,56,4237	yes	missense	ZNF215	NM_013250.2	22	0,60,6434	CC,CT,TT		0.6522,0.0909,0.462	possibly-damaging	301/518	6977109	60,12928	2201	4293	6494	SO:0001583	missense	7762	exon7			GAAGATTTTGAAT	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.901T>C	11.37:g.6977109T>C	ENSP00000278319:p.Phe301Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	108	51	0.472222	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	10.32	1.318071	0.23994	9.09E-4	0.006522	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.04809	3.55;3.55	4.27	3.11	0.35812	.	0.516746	0.16372	N	0.217295	T	0.02047	0.0064	N	0.14661	0.345	0.21675	N	0.999599	B	0.22346	0.068	B	0.15484	0.013	T	0.45056	-0.9287	10	0.30854	T	0.27	-2.7081	8.4029	0.32597	0.1755:0.0:0.0:0.8245	.	301	Q9UL58	ZN215_HUMAN	L	301	ENSP00000278319:F301L;ENSP00000393202:F301L	ENSP00000278319:F301L	F	+	1	0	ZNF215	6933685	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.972000	0.29409	0.757000	0.33036	0.533000	0.62120	TTT	T|0.996;C|0.004	0.004	strong		0.353	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
RAD54B	25788	hgsc.bcm.edu	37	8	95399378	95399378	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95399378A>G	ENST00000336148.5	-	11	1943	c.1819T>C	c.(1819-1821)Tgt>Cgt	p.C607R		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	607					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			GTTGAGCTACATTCCTTTTCC	0.348								Direct reversal of damage;Homologous recombination																													p.C607R		Atlas-SNP	.											.	RAD54B	88	.	0			c.T1819C						PASS	.						101.0	94.0	97.0					8																	95399378		2203	4300	6503	SO:0001583	missense	25788	exon11			AGCTACATTCCTT	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1819T>C	8.37:g.95399378A>G	ENSP00000336606:p.Cys607Arg	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	180	81	0.45	NM_012415	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	A	7.240	0.601139	0.13939	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	D	0.88586	-2.4	5.28	-0.253	0.12996	.	1.072940	0.06949	N	0.814172	T	0.81550	0.4846	L	0.60455	1.87	0.21416	N	0.999695	B	0.33413	0.411	B	0.25506	0.061	T	0.63462	-0.6632	10	0.14656	T	0.56	-24.2196	3.5354	0.07792	0.5686:0.0:0.1549:0.2765	.	607	Q9Y620	RA54B_HUMAN	R	607;279	ENSP00000336606:C607R	ENSP00000336606:C607R	C	-	1	0	RAD54B	95468554	0.224000	0.23674	0.348000	0.25681	0.965000	0.64279	0.519000	0.22862	0.025000	0.15241	0.477000	0.44152	TGT	.	.	none		0.348	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
CACNA1S	779	hgsc.bcm.edu	37	1	201016296	201016296	+	Missense_Mutation	SNP	G	G	A	rs3850625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201016296G>A	ENST00000362061.3	-	38	4841	c.4615C>T	c.(4615-4617)Cgc>Tgc	p.R1539C	CACNA1S_ENST00000367338.3_Missense_Mutation_p.R1520C	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	1539			R -> C (in dbSNP:rs3850625). {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)	TCCTCTTGGCGTTTCATGAAC	0.532													G|||	421	0.0840655	0.0053	0.0879	5008	,	,		20380	0.0397		0.1183	False		,,,				2504	0.1984				p.R1539C		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C4615T						PASS	.	G	CYS/ARG	96,4310		2,92,2109	169.0	156.0	161.0		4615	5.2	1.0	1	dbSNP_108	161	1065,7535		66,933,3301	yes	missense	CACNA1S	NM_000069.2	180	68,1025,5410	AA,AG,GG		12.3837,2.1788,8.9266	possibly-damaging	1539/1874	201016296	1161,11845	2203	4300	6503	SO:0001583	missense	779	exon38			CTTGGCGTTTCAT	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.4615C>T	1.37:g.201016296G>A	ENSP00000355192:p.Arg1539Cys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	155	0.07097069597069597	4	0.008130081300813009	33	0.09116022099447514	24	0.04195804195804196	94	0.12401055408970976	.	18.80	3.701873	0.68501	0.021788	0.123837	ENSG00000081248	ENST00000362061;ENST00000367338	T;T	0.70282	-0.47;-0.47	5.17	5.17	0.71159	Voltage-dependent calcium channel, alpha-1 subunit, IQ domain (1);	0.047866	0.85682	D	0.000000	T	0.01976	0.0062	L	0.41492	1.28	0.09310	P	0.9999999438172	P	0.41041	0.736	B	0.39419	0.299	T	0.46938	-0.9155	9	0.72032	D	0.01	.	19.0118	0.92875	0.0:0.0:1.0:0.0	rs3850625;rs56979208;rs3850625	1539	Q13698	CAC1S_HUMAN	C	1539;1520	ENSP00000355192:R1539C;ENSP00000356307:R1520C	ENSP00000355192:R1539C	R	-	1	0	CACNA1S	199282919	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.194000	0.72082	2.575000	0.86900	0.655000	0.94253	CGC	G|0.919;A|0.081	0.081	strong		0.532	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
TMEM132C	92293	hgsc.bcm.edu	37	12	129153986	129153986	+	Missense_Mutation	SNP	G	G	A	rs4272850	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:129153986G>A	ENST00000435159.2	+	5	1330	c.1330G>A	c.(1330-1332)Gta>Ata	p.V444I	AC107020.1_ENST00000408822.1_RNA|TMEM132C_ENST00000315208.8_Missense_Mutation_p.V60I	NM_001136103.2	NP_001129575.2	Q8N3T6	T132C_HUMAN	transmembrane protein 132C	444			V -> I (in dbSNP:rs4272850).			integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(2)|prostate(2)|skin(1)	13						GAACACCGCCGTACTCACAGG	0.498													A|||	1712	0.341853	0.4523	0.3199	5008	,	,		21362	0.248		0.2783	False		,,,				2504	0.3701				p.V444I		Atlas-SNP	.											.	TMEM132C	142	.	0			c.G1330A						PASS	.	A	ILE/VAL	589,795		126,337,229	110.0	99.0	103.0		1330	1.3	0.5	12	dbSNP_111	103	802,2380		108,586,897	yes	missense	TMEM132C	NM_001136103.2	29	234,923,1126	AA,AG,GG		25.2043,42.5578,30.4643	benign	444/1109	129153986	1391,3175	692	1591	2283	SO:0001583	missense	92293	exon5			ACCGCCGTACTCA	AK126715		12q24.32	2014-06-13				ENSG00000181234			25436	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 152"""						Standard	NM_001136103		Approved	DKFZp761O2018, PPP1R152	uc021rgn.1	Q8N3T6		ENST00000435159.2:c.1330G>A	12.37:g.129153986G>A	ENSP00000410852:p.Val444Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_001136103	Q69YX8	Missense_Mutation	SNP	ENST00000435159.2	37		671	0.30723443223443225	216	0.43902439024390244	120	0.3314917127071823	130	0.22727272727272727	205	0.2704485488126649	A	0.020	-1.446847	0.01089	0.425578	0.252043	ENSG00000181234	ENST00000435159;ENST00000315208	T;T	0.11495	2.77;2.77	5.01	1.33	0.21861	.	0.000000	0.56097	N	0.000030	T	0.00012	0.0000	N	0.00538	-1.39	0.47949	P	4.450000000000287E-4	B	0.06786	0.001	B	0.08055	0.003	T	0.47235	-0.9133	9	0.02654	T	1	.	9.0375	0.36296	0.7069:0.0:0.2931:0.0	rs4272850;rs52821868;rs60998550;rs4272850	444	Q8N3T6	T132C_HUMAN	I	444;60	ENSP00000410852:V444I;ENSP00000324458:V60I	ENSP00000324458:V60I	V	+	1	0	TMEM132C	127719939	0.576000	0.26700	0.479000	0.27329	0.106000	0.19336	1.199000	0.32235	-0.273000	0.09246	-1.062000	0.02293	GTA	G|0.692;A|0.308	0.308	strong		0.498	TMEM132C-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_044062	
DCAF6	55827	hgsc.bcm.edu	37	1	168014204	168014204	+	Missense_Mutation	SNP	T	T	A	rs41271647	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:168014204T>A	ENST00000312263.6	+	14	1970	c.1766T>A	c.(1765-1767)cTt>cAt	p.L589H	DCAF6_ENST00000367840.3_Missense_Mutation_p.L666H|DCAF6_ENST00000367843.3_Missense_Mutation_p.L609H|DCAF6_ENST00000432587.2_Missense_Mutation_p.L635H	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	589					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						GACCTCAATCTTGATCGCTCT	0.423													T|||	200	0.0399361	0.003	0.0605	5008	,	,		20427	0.0		0.0915	False		,,,				2504	0.0634				p.L666H		Atlas-SNP	.											.	DCAF6	99	.	0			c.T1997A						PASS	.	T	HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU	74,4332	66.4+/-103.9	0,74,2129	118.0	127.0	124.0		1766,1997,1904,1826	-1.9	0.6	1	dbSNP_127	124	837,7763	192.8+/-238.7	39,759,3502	yes	missense,missense,missense,missense	DCAF6	NM_001017977.2,NM_001198956.1,NM_001198957.1,NM_018442.3	99,99,99,99	39,833,5631	AA,AT,TT		9.7326,1.6795,7.0045	benign,benign,benign,benign	589/861,666/952,635/921,609/881	168014204	911,12095	2203	4300	6503	SO:0001583	missense	55827	exon16			TCAATCTTGATCG	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.1766T>A	1.37:g.168014204T>A	ENSP00000311949:p.Leu589His	Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	358	175	0.488827	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	103	0.04716117216117216	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	72	0.09498680738786279	T	3.954	-0.011668	0.07727	0.016795	0.097326	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.16	-1.9	0.07665	WD40 repeat-like-containing domain (1);	0.834564	0.10756	N	0.637779	T	0.02767	0.0083	N	0.03608	-0.345	0.19300	N	0.999975	B;B;B;B	0.11235	0.001;0.004;0.0;0.002	B;B;B;B	0.14023	0.002;0.01;0.002;0.004	T	0.43940	-0.9360	9	0.14656	T	0.56	.	3.6996	0.08378	0.3525:0.2041:0.0:0.4433	rs41271647;rs61746944	635;666;589;609	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	H	609;635;589;666	ENSP00000356817:L609H;ENSP00000396238:L635H;ENSP00000311949:L589H;ENSP00000356814:L666H	ENSP00000311949:L589H	L	+	2	0	DCAF6	166280828	0.796000	0.28864	0.553000	0.28255	0.506000	0.33950	-0.069000	0.11542	-0.024000	0.13941	0.383000	0.25322	CTT	T|0.933;A|0.067	0.067	strong		0.423	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	
ZFP2	80108	hgsc.bcm.edu	37	5	178359136	178359136	+	Silent	SNP	A	A	G	rs961030	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:178359136A>G	ENST00000361362.2	+	5	1352	c.822A>G	c.(820-822)caA>caG	p.Q274Q	ZFP2_ENST00000503510.2_Silent_p.Q274Q|ZFP2_ENST00000520301.1_Silent_p.Q274Q|ZFP2_ENST00000523286.1_Silent_p.Q274Q	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	274					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	20	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)	all cancers(165;0.00655)|GBM - Glioblastoma multiforme(465;0.0302)|OV - Ovarian serous cystadenocarcinoma(192;0.0615)|Epithelial(171;0.111)		AGTGTAGTCAATGTGGAAAAG	0.388																																					p.Q274Q		Atlas-SNP	.											ZFP2,NS,carcinoma,+2,1	ZFP2	70	1	0			c.A822G						scavenged	.	A		759,3647	307.2+/-289.9	67,625,1511	73.0	74.0	74.0		822	1.1	1.0	5	dbSNP_86	74	2826,5774	444.9+/-360.8	473,1880,1947	no	coding-synonymous	ZFP2	NM_030613.2		540,2505,3458	GG,GA,AA		32.8605,17.2265,27.5642		274/462	178359136	3585,9421	2203	4300	6503	SO:0001819	synonymous_variant	80108	exon5			TAGTCAATGTGGA	AK025281	CCDS4440.1	5q35.3	2013-01-08	2012-11-27		ENSG00000198939	ENSG00000198939		"""Zinc fingers, C2H2-type"""	26138	protein-coding gene	gene with protein product			"""zinc finger protein 2 homolog (mouse)"""				Standard	NM_030613		Approved	FLJ21628, ZNF751	uc003mjn.1	Q6ZN57	OTTHUMG00000130885	ENST00000361362.2:c.822A>G	5.37:g.178359136A>G		Somatic	65	1	0.0153846		WXS	Illumina HiSeq	Phase_I	56	28	0.5	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Silent	SNP	ENST00000361362.2	37	CCDS4440.1																																																																																			A|0.718;G|0.282	0.282	strong		0.388	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613	
ZBTB2	57621	hgsc.bcm.edu	37	6	151686905	151686905	+	Silent	SNP	C	C	T	rs11155787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151686905C>T	ENST00000325144.4	-	3	1436	c.1296G>A	c.(1294-1296)gaG>gaA	p.E432E		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	432					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)|large_intestine(2)|lung(6)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.63e-11)		GACTCCCTTCCTCAAATGTGC	0.493													C|||	2123	0.423922	0.3517	0.5447	5008	,	,		21385	0.2778		0.6382	False		,,,				2504	0.3661				p.E432E		Atlas-SNP	.											.	ZBTB2	30	.	0			c.G1296A						PASS	.	C		1735,2671	516.8+/-369.3	352,1031,820	161.0	131.0	141.0		1296	5.4	1.0	6	dbSNP_120	141	5477,3123	657.0+/-401.4	1757,1963,580	yes	coding-synonymous	ZBTB2	NM_020861.1		2109,2994,1400	TT,TC,CC		36.314,39.3781,44.5487		432/515	151686905	7212,5794	2203	4300	6503	SO:0001819	synonymous_variant	57621	exon3			CCCTTCCTCAAAT	BC020172	CCDS5231.1	6q25.1	2013-01-09			ENSG00000181472	ENSG00000181472		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20868	protein-coding gene	gene with protein product						10819331	Standard	NM_020861		Approved	KIAA1483, ZNF437, bA351K16.2	uc003qoh.3	Q8N680	OTTHUMG00000015834	ENST00000325144.4:c.1296G>A	6.37:g.151686905C>T		Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	118	106	0.898305	NM_020861	A8K7C7|Q5SZ81|Q9P245	Silent	SNP	ENST00000325144.4	37	CCDS5231.1																																																																																			C|0.495;T|0.505	0.505	strong		0.493	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861	
GPRIN2	9721	hgsc.bcm.edu	37	10	46998904	46998904	+	Silent	SNP	G	G	A	rs140651048		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:46998904G>A	ENST00000374317.1	+	3	297	c.24G>A	c.(22-24)ccG>ccA	p.P8P	GPRIN2_ENST00000374314.4_Silent_p.P8P	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	8										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GCCCCGAGCCGGGTCCCTGGG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		31822	0.001		0.0	False		,,,				2504	0.0				p.P8P		Atlas-SNP	.											.	GPRIN2	94	.	0			c.G24A						PASS	.	G		1,4371		0,1,2185	51.0	71.0	64.0		24	-10.7	0.0	10	dbSNP_134	64	0,8544		0,0,4272	no	coding-synonymous	GPRIN2	NM_014696.3		0,1,6457	AA,AG,GG		0.0,0.0229,0.0077		8/459	46998904	1,12915	2186	4272	6458	SO:0001819	synonymous_variant	9721	exon3			CGAGCCGGGTCCC	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.24G>A	10.37:g.46998904G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	140	32	0.228571	NM_014696	Q5SVF0	Silent	SNP	ENST00000374317.1	37	CCDS31192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
ZNF594	84622	hgsc.bcm.edu	37	17	5087040	5087040	+	Missense_Mutation	SNP	A	A	G	rs9908414	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5087040A>G	ENST00000399604.4	-	1	652	c.512T>C	c.(511-513)aTt>aCt	p.I171T	ZNF594_ENST00000575779.1_Missense_Mutation_p.I171T			Q96JF6	ZN594_HUMAN	zinc finger protein 594	171			I -> T (in dbSNP:rs9908414).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CTGATGTATAATAAGATTTGA	0.338													a|||	1134	0.226438	0.1233	0.4265	5008	,	,		20145	0.0972		0.4354	False		,,,				2504	0.1421				p.I171T		Atlas-SNP	.											ZNF594,caecum,carcinoma,0,1	ZNF594	89	1	0			c.T512C						PASS	.						80.0	83.0	82.0					17																	5087040		1993	4200	6193	SO:0001583	missense	84622	exon2			TGTATAATAAGAT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.512T>C	17.37:g.5087040A>G	ENSP00000382513:p.Ile171Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	30	0.352941	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	604	0.2765567765567766	69	0.1402439024390244	157	0.43370165745856354	51	0.08916083916083917	327	0.4313984168865435	a	0.001	-4.054948	0.00002	.	.	ENSG00000180626	ENST00000399604	T	0.37584	1.19	2.29	-2.72	0.05968	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46871	-0.9160	8	0.08837	T	0.75	.	6.3503	0.21373	0.5162:0.0:0.4838:0.0	rs9908414;rs17178125;rs52818653;rs58970192;rs9908414	171	Q96JF6	ZN594_HUMAN	T	171	ENSP00000382513:I171T	ENSP00000382513:I171T	I	-	2	0	ZNF594	5027764	0.000000	0.05858	0.203000	0.23512	0.000000	0.00434	-1.675000	0.01947	-0.853000	0.04136	-1.319000	0.01295	ATT	A|0.710;G|0.290	0.290	strong		0.338	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
PDCD6IP	10015	hgsc.bcm.edu	37	3	33879770	33879770	+	Missense_Mutation	SNP	G	G	A	rs3203777	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:33879770G>A	ENST00000307296.3	+	9	1509	c.1132G>A	c.(1132-1134)Gtt>Att	p.V378I	PDCD6IP_ENST00000457054.2_Missense_Mutation_p.V383I			Q8WUM4	PDC6I_HUMAN	programmed cell death 6 interacting protein	378	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.|Interaction with CHMP4A, CHMP4B and CHMP4C.|Interaction with EIAV p9.		V -> I (in dbSNP:rs3203777). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell division (GO:0051301)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|membrane (GO:0016020)|vesicle (GO:0031982)	calcium-dependent protein binding (GO:0048306)|protein homodimerization activity (GO:0042803)	p.V378I(1)		central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|skin(1)|stomach(1)	23						AGCCGATTTGGTTAACAGATC	0.403													G|||	1470	0.29353	0.0151	0.2334	5008	,	,		16153	0.3442		0.4523	False		,,,				2504	0.4969				p.V383I		Atlas-SNP	.											PDCD6IP,NS,carcinoma,0,1	PDCD6IP	62	1	1	Substitution - Missense(1)	stomach(1)	c.G1147A						PASS	.	G	ILE/VAL,ILE/VAL	379,4027	189.5+/-215.6	16,347,1840	79.0	79.0	79.0		1147,1132	4.9	1.0	3	dbSNP_105	79	3810,4790	537.9+/-383.3	848,2114,1338	yes	missense,missense	PDCD6IP	NM_001162429.1,NM_013374.4	29,29	864,2461,3178	AA,AG,GG		44.3023,8.6019,32.2082	benign,benign	383/874,378/869	33879770	4189,8817	2203	4300	6503	SO:0001583	missense	10015	exon9			GATTTGGTTAACA	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.1132G>A	3.37:g.33879770G>A	ENSP00000307387:p.Val378Ile	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	144	72	0.5	NM_001162429	C5MQH7|E9PFU1|Q6NUS1|Q9BX86|Q9NUN0|Q9P2H2|Q9UKL5	Missense_Mutation	SNP	ENST00000307296.3	37	CCDS2660.1	653	0.298992673992674	12	0.024390243902439025	89	0.24585635359116023	193	0.3374125874125874	359	0.4736147757255937	G	16.33	3.093060	0.56075	0.086019	0.443023	ENSG00000170248	ENST00000307296;ENST00000457054	T;T	0.21031	2.03;2.03	4.92	4.92	0.64577	BRO1 domain (2);	0.115029	0.64402	N	0.000016	T	0.00012	0.0000	L	0.31752	0.955	0.09310	P	0.99999999172293	B;B	0.17465	0.022;0.016	B;B	0.24848	0.049;0.056	T	0.47935	-0.9078	9	0.32370	T	0.25	-17.4758	11.6058	0.51031	0.082:0.0:0.918:0.0	rs3203777;rs17274543;rs17404210;rs3203777	383;378	E9PFU1;Q8WUM4	.;PDC6I_HUMAN	I	378;383	ENSP00000307387:V378I;ENSP00000411825:V383I	ENSP00000307387:V378I	V	+	1	0	PDCD6IP	33854774	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.057000	0.89457	2.281000	0.76405	0.585000	0.79938	GTT	G|0.682;A|0.317	0.317	strong		0.403	PDCD6IP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253251.2		
FAM198A	729085	hgsc.bcm.edu	37	3	43095101	43095101	+	Missense_Mutation	SNP	A	A	G	rs536119	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:43095101A>G	ENST00000430121.2	+	3	1474	c.1379A>G	c.(1378-1380)cAg>cGg	p.Q460R	KRBOX1_ENST00000443313.1_3'UTR	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	460			Q -> R (in dbSNP:rs536119). {ECO:0000269|PubMed:14702039}.			extracellular region (GO:0005576)				endometrium(1)	1						GAGAAATGCCAGAACCCAGCC	0.597													G|||	2710	0.541134	0.4644	0.6686	5008	,	,		16542	0.6696		0.5954	False		,,,				2504	0.3661				p.Q460R		Atlas-SNP	.											.	FAM198A	23	.	0			c.A1379G						PASS	.	G	ARG/GLN	625,759		142,341,209	32.0	43.0	40.0		1379	0.7	1.0	3	dbSNP_83	40	1929,1253		582,765,244	yes	missense	FAM198A	NM_001129908.2	43	724,1106,453	GG,GA,AA		39.3777,45.159,44.0648	benign	460/576	43095101	2554,2012	692	1591	2283	SO:0001583	missense	729085	exon3			AATGCCAGAACCC	AL117530	CCDS46808.1	3p22.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000144649	ENSG00000144649			24485	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 41"""	C3orf41			Standard	NM_001129908		Approved	DKFZP434B172	uc003cmp.4	Q9UFP1	OTTHUMG00000156449	ENST00000430121.2:c.1379A>G	3.37:g.43095101A>G	ENSP00000407301:p.Gln460Arg	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	107	37	0.345794	NM_001129908	B3KR48	Missense_Mutation	SNP	ENST00000430121.2	37	CCDS46808.1	1315	0.6021062271062271	252	0.5121951219512195	253	0.6988950276243094	373	0.6520979020979021	437	0.5765171503957783	G	3.612	-0.079297	0.07141	0.45159	0.606223	ENSG00000144649	ENST00000488863;ENST00000430121	T;T	0.27104	1.69;1.69	5.62	0.681	0.17986	.	0.564021	0.18201	N	0.148503	T	0.00012	0.0000	N	0.00054	-2.38	0.58432	P	9.99999999995449E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36237	-0.9756	9	0.02654	T	1	-20.7108	6.9169	0.24365	0.322:0.1098:0.5682:0.0	rs536119;rs17469537;rs58673217;rs536119	31;460	F5H4W4;Q9UFP1	.;F198A_HUMAN	R	31;460	ENSP00000439905:Q31R;ENSP00000407301:Q460R	ENSP00000273146:Q460R	Q	+	2	0	FAM198A	43070105	0.469000	0.25846	0.965000	0.40720	0.817000	0.46193	0.166000	0.16583	-0.417000	0.07461	-0.974000	0.02594	CAG	A|0.413;G|0.587	0.587	strong		0.597	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
TACC2	10579	hgsc.bcm.edu	37	10	123970722	123970722	+	Missense_Mutation	SNP	T	T	A	rs2295876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123970722T>A	ENST00000369005.1	+	9	7122	c.6782T>A	c.(6781-6783)cTc>cAc	p.L2261H	TACC2_ENST00000513429.1_Missense_Mutation_p.L407H|TACC2_ENST00000368999.1_Missense_Mutation_p.L339H|TACC2_ENST00000360561.3_Missense_Mutation_p.L339H|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000369004.3_Missense_Mutation_p.L339H|TACC2_ENST00000453444.2_Missense_Mutation_p.L2265H|TACC2_ENST00000358010.1_Missense_Mutation_p.L407H|TACC2_ENST00000334433.3_Missense_Mutation_p.L2261H|TACC2_ENST00000260733.3_Missense_Mutation_p.L339H|TACC2_ENST00000515273.1_Missense_Mutation_p.L2265H|TACC2_ENST00000515603.1_Missense_Mutation_p.L2216H	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2261			L -> H (in dbSNP:rs2295876).		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)				GCCAAAGGGCTCTCCGTAAGG	0.567													T|||	446	0.0890575	0.0045	0.1311	5008	,	,		15915	0.1151		0.0835	False		,,,				2504	0.1524				p.L2261H		Atlas-SNP	.											.	TACC2	271	.	0			c.T6782A						PASS	.	T	HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU	117,4289	86.8+/-125.4	2,113,2088	40.0	46.0	44.0		1016,1016,1220,6782	5.0	1.0	10	dbSNP_100	44	1067,7533	224.4+/-260.8	70,927,3303	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	99,99,99,99	72,1040,5391	AA,AT,TT		12.407,2.6555,9.1035	probably-damaging,probably-damaging,probably-damaging,probably-damaging	339/1027,339/997,407/1095,2261/2949	123970722	1184,11822	2203	4300	6503	SO:0001583	missense	10579	exon9			AAGGGCTCTCCGT	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.6782T>A	10.37:g.123970722T>A	ENSP00000358001:p.Leu2261His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	183	0.08379120879120878	5	0.01016260162601626	41	0.1132596685082873	73	0.12762237762237763	64	0.08443271767810026	T	12.73	2.024084	0.35701	0.026555	0.12407	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539	T;T;T;T;T;T;T;T;T;T;T;T	0.08193	4.05;3.65;4.09;4.09;4.05;3.65;4.09;3.53;3.54;3.53;3.54;3.12	5.0	5.0	0.66597	.	0.000000	0.30686	N	0.009091	T	0.00241	0.0007	M	0.63428	1.95	0.35028	P	0.24145000000000005	D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.999;1.0;0.999;0.995;0.991;0.991;1.0	D;D;P;D;D;P;P;P;D	0.76575	0.927;0.983;0.885;0.988;0.983;0.893;0.893;0.893;0.988	T	0.05068	-1.0908	9	0.45353	T	0.12	-13.7028	9.2912	0.37789	0.1606:0.0:0.0:0.8394	rs2295876	356;2265;339;2216;2265;339;339;407;2261	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	H	2261;407;2265;2216;2261;407;2265;2251;339;339;339;339;356	ENSP00000358001:L2261H;ENSP00000425062:L407H;ENSP00000424467:L2265H;ENSP00000427618:L2216H;ENSP00000334280:L2261H;ENSP00000350701:L407H;ENSP00000395048:L2265H;ENSP00000353763:L339H;ENSP00000357995:L339H;ENSP00000422815:L339H;ENSP00000260733:L339H;ENSP00000420967:L356H	ENSP00000260733:L339H	L	+	2	0	TACC2	123960712	0.827000	0.29292	0.999000	0.59377	0.504000	0.33889	3.088000	0.50175	2.016000	0.59253	0.533000	0.62120	CTC	A|0.085;C|0.000;T|0.915	0.085	strong		0.567	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
NRG1	3084	hgsc.bcm.edu	37	8	32611970	32611970	+	Missense_Mutation	SNP	G	G	T	rs74942016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:32611970G>T	ENST00000405005.3	+	8	781	c.781G>T	c.(781-783)Gtg>Ttg	p.V261L	NRG1_ENST00000338921.4_Missense_Mutation_p.V269L|NRG1_ENST00000521670.1_Missense_Mutation_p.V261L|NRG1_ENST00000287845.5_Missense_Mutation_p.V232L|NRG1_ENST00000287842.3_Missense_Mutation_p.V258L|NRG1_ENST00000539990.1_Missense_Mutation_p.V104L|NRG1_ENST00000519301.1_Missense_Mutation_p.V211L|NRG1_ENST00000523079.1_Missense_Mutation_p.V258L|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000356819.4_Missense_Mutation_p.V266L			Q02297	NRG1_HUMAN	neuregulin 1	261				V -> L (in Ref. 10; ABQ53540). {ECO:0000305}.	activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CATCATGTGTGTGGTGGCCTA	0.527													G|||	72	0.014377	0.0008	0.0259	5008	,	,		17487	0.0		0.0467	False		,,,				2504	0.0061				p.V266L		Atlas-SNP	.											.	NRG1	260	.	0			c.G796T	GRCh37	CM066934	NRG1	M	rs74942016	PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	47,4359	48.9+/-83.8	0,47,2156	226.0	165.0	186.0		682,319,733,631,772,772,796,772,781,781	5.6	1.0	8	dbSNP_131	186	405,8195	127.5+/-185.8	12,381,3907	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159996.1,NM_001159999.1,NM_001160001.1,NM_001160004.1,NM_001160008.1,NM_013956.3,NM_013957.3,NM_013960.3,NM_013964.3	32,32,32,32,32,32,32,32,32,32	12,428,6063	TT,TG,GG		4.7093,1.0667,3.4753	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	228/608,107/309,245/625,211/591,258/460,258/421,266/646,258/638,261/463,261/641	32611970	452,12554	2203	4300	6503	SO:0001583	missense	3084	exon9			ATGTGTGTGGTGG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.781G>T	8.37:g.32611970G>T	ENSP00000384620:p.Val261Leu	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	168	76	0.452381	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	35	5.558867	0.96514	0.010667	0.047093	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000522402;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;2.63;0.14	5.62	5.62	0.85841	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;P;D;P;D;D	0.71674	0.979;0.998;0.995;0.979;0.983;0.995;0.599;0.962;0.946;0.979;0.994	D;D;D;P;D;D;B;P;P;P;D	0.85130	0.986;0.997;0.972;0.879;0.926;0.972;0.283;0.879;0.893;0.879;0.914	T	0.67722	-0.5597	10	0.72032	D	0.01	-36.9375	19.6569	0.95845	0.0:0.0:1.0:0.0	.	104;107;258;232;266;257;269;258;261;266;261	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	L	228;211;334;258;269;266;261;232;258;261;261;107;104;104	ENSP00000430053:V228L;ENSP00000429582:V211L;ENSP00000429067:V334L;ENSP00000430120:V258L;ENSP00000343395:V269L;ENSP00000349275:V266L;ENSP00000287840:V261L;ENSP00000287845:V232L;ENSP00000287842:V258L;ENSP00000384620:V261L;ENSP00000428828:V261L;ENSP00000430862:V107L;ENSP00000428411:V104L;ENSP00000439276:V104L	ENSP00000287840:V261L	V	+	1	0	NRG1	32731512	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.639000	0.89480	0.650000	0.86243	GTG	G|0.968;T|0.032	0.032	strong		0.527	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
ENTPD1	953	hgsc.bcm.edu	37	10	97599537	97599537	+	Silent	SNP	G	G	C	rs61731067	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:97599537G>C	ENST00000371205.4	+	3	517	c.234G>C	c.(232-234)gtG>gtC	p.V78V	ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000490659.1_3'UTR|ENTPD1_ENST00000453258.2_Silent_p.V85V|RP11-429G19.3_ENST00000433113.1_RNA|ENTPD1_ENST00000371203.5_5'UTR|ENTPD1_ENST00000371207.3_Silent_p.V90V|ENTPD1_ENST00000539125.1_Intron|ENTPD1_ENST00000543964.1_5'UTR			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	78					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		CAGGCGTGGTGCATCAAGTAG	0.473													G|||	260	0.0519169	0.0234	0.0663	5008	,	,		9998	0.0407		0.0596	False		,,,				2504	0.0838				p.V90V		Atlas-SNP	.											.	ENTPD1	44	.	0			c.G270C						PASS	.	G	,,,,,,	154,4252	105.6+/-144.1	3,148,2052	166.0	154.0	158.0		255,270,234,,,,234	1.5	0.4	10	dbSNP_129	158	554,8046	151.6+/-206.3	21,512,3767	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-5,utr-5,intron,coding-synonymous	ENTPD1	NM_001098175.1,NM_001164178.1,NM_001164179.1,NM_001164181.1,NM_001164182.1,NM_001164183.1,NM_001776.5	,,,,,,	24,660,5819	CC,CG,GG		6.4419,3.4952,5.4436	,,,,,,	85/518,90/523,78/470,,,,78/511	97599537	708,12298	2203	4300	6503	SO:0001819	synonymous_variant	953	exon3			CGTGGTGCATCAA	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"""CD molecules"""	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.234G>C	10.37:g.97599537G>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	136	73	0.536765	NM_001164178	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Silent	SNP	ENST00000371205.4	37	CCDS7444.1																																																																																			G|0.945;C|0.055	0.055	strong		0.473	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776	
PCDHB12	56124	hgsc.bcm.edu	37	5	140590766	140590766	+	Missense_Mutation	SNP	A	A	G	rs2910006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140590766A>G	ENST00000239450.2	+	1	2476	c.2287A>G	c.(2287-2289)Aag>Gag	p.K763E	PCDHB13_ENST00000341948.4_5'Flank|PCDHB12_ENST00000541609.1_Missense_Mutation_p.K426E	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	763			K -> E (in dbSNP:rs2910006).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGGTCAAATAAGTTCAAATT	0.502													G|||	1949	0.389177	0.7511	0.3386	5008	,	,		16246	0.1339		0.3211	False		,,,				2504	0.2689				p.K763E		Atlas-SNP	.											PCDHB12,tonsil,carcinoma,0,1	PCDHB12	179	1	0			c.A2287G						PASS	.	G	GLU/LYS	3093,1313	441.4+/-346.4	1082,929,192	74.0	75.0	75.0		2287	3.1	0.0	5	dbSNP_101	75	3042,5558	661.9+/-401.9	540,1962,1798	yes	missense	PCDHB12	NM_018932.3	56	1622,2891,1990	GG,GA,AA		35.3721,29.8003,47.1705	benign	763/796	140590766	6135,6871	2203	4300	6503	SO:0001583	missense	56124	exon1			TCAAATAAGTTCA	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.2287A>G	5.37:g.140590766A>G	ENSP00000239450:p.Lys763Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	828	0.3791208791208791	375	0.7621951219512195	124	0.3425414364640884	78	0.13636363636363635	251	0.3311345646437995	G	3.390	-0.124597	0.06795	0.701997	0.353721	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.12039	2.72;2.72	3.13	3.13	0.36017	.	.	.	.	.	T	0.00012	0.0000	N	0.00000	-4.025	0.46678	P	8.479999999999599E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41251	-0.9519	8	0.02654	T	1	.	9.4973	0.38995	0.1133:0.0:0.8867:0.0	rs2910006;rs3776095;rs17844605;rs60542532;rs2910006	763	Q9Y5F1	PCDBC_HUMAN	E	426;763;383	ENSP00000440199:K426E;ENSP00000239450:K763E	ENSP00000239450:K763E	K	+	1	0	PCDHB12	140570950	1.000000	0.71417	0.002000	0.10522	0.009000	0.06853	6.496000	0.73670	0.422000	0.26005	-0.684000	0.03749	AAG	A|0.559;G|0.441	0.441	strong		0.502	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
KIF3C	3797	hgsc.bcm.edu	37	2	26204640	26204640	+	Silent	SNP	G	G	A	rs6721440	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26204640G>A	ENST00000264712.3	-	1	726	c.147C>T	c.(145-147)gcC>gcT	p.A49A	KIF3C_ENST00000405914.1_Silent_p.A49A	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	49	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)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle transport along microtubule (GO:0072384)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCCCGGGGCGGCGCGGGGGT	0.652													A|||	2144	0.428115	0.8033	0.3386	5008	,	,		15734	0.0546		0.4553	False		,,,				2504	0.3415				p.A49A		Atlas-SNP	.											.	KIF3C	79	.	0			c.C147T						PASS	.	A		3267,1139	384.4+/-325.3	1218,831,154	62.0	70.0	67.0		147	-11.1	0.0	2	dbSNP_116	67	4142,4458	560.5+/-387.6	993,2156,1151	no	coding-synonymous	KIF3C	NM_002254.6		2211,2987,1305	AA,AG,GG		48.1628,25.8511,43.034		49/794	26204640	7409,5597	2203	4300	6503	SO:0001819	synonymous_variant	3797	exon1			CGGGGCGGCGCGG		CCDS1719.1	2p23	2008-02-05			ENSG00000084731	ENSG00000084731		"""Kinesins"""	6321	protein-coding gene	gene with protein product		602845				9480755	Standard	NM_002254		Approved		uc002rgu.2	O14782	OTTHUMG00000094797	ENST00000264712.3:c.147C>T	2.37:g.26204640G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Silent	SNP	ENST00000264712.3	37	CCDS1719.1																																																																																			G|0.496;A|0.504	0.504	strong		0.652	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1		
TTN	7273	hgsc.bcm.edu	37	2	179640255	179640255	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179640255G>A	ENST00000591111.1	-	28	6560	c.6336C>T	c.(6334-6336)taC>taT	p.Y2112Y	RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000342175.6_Silent_p.Y2066Y|TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000360870.5_Silent_p.Y2112Y|TTN_ENST00000589042.1_Silent_p.Y2112Y|TTN_ENST00000342992.6_Silent_p.Y2112Y|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Silent_p.Y2066Y|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000359218.5_Silent_p.Y2066Y			Q8WZ42	TITIN_HUMAN	titin	12800	Ig-like 10.				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)			CACCATTTTTGTACCATTCAC	0.478																																					p.Y2112Y		Atlas-SNP	.											TTN_ENST00000360870,NS,adenocarcinoma,-2,6	TTN	18412	6	0			c.C6336T						scavenged	.						80.0	85.0	83.0					2																	179640255		2203	4300	6503	SO:0001819	synonymous_variant	7273	exon28			ATTTTTGTACCAT	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.6336C>T	2.37:g.179640255G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	167	3	0.0179641	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				.	.	none		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DGCR8	54487	hgsc.bcm.edu	37	22	20074006	20074006	+	Missense_Mutation	SNP	A	A	G	rs35987994	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20074006A>G	ENST00000351989.3	+	2	949	c.520A>G	c.(520-522)Ata>Gta	p.I174V	MIR1306_ENST00000408439.1_RNA|DGCR8_ENST00000383024.2_Missense_Mutation_p.I174V|MIR3618_ENST00000580330.1_RNA|DGCR8_ENST00000407755.1_Missense_Mutation_p.I174V	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	174	Necessary for interaction with NCL.|Necessary for nuclear localization and retention.		I -> V (in dbSNP:rs35987994).		gene expression (GO:0010467)|primary miRNA processing (GO:0031053)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			NS(2)|breast(1)|endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	Colorectal(54;0.0993)					CGGGGTAGGCATAGGGGGTGA	0.552													A|||	253	0.0505192	0.0045	0.0101	5008	,	,		17805	0.0813		0.0547	False		,,,				2504	0.1053				p.I174V		Atlas-SNP	.											.	DGCR8	53	.	0			c.A520G						PASS	.	A	VAL/ILE,VAL/ILE	52,4354	52.3+/-87.9	0,52,2151	138.0	130.0	132.0		520,520	-10.8	0.0	22	dbSNP_126	132	469,8131	139.2+/-195.9	18,433,3849	yes	missense,missense	DGCR8	NM_001190326.1,NM_022720.6	29,29	18,485,6000	GG,GA,AA		5.4535,1.1802,4.0058	benign,benign	174/741,174/774	20074006	521,12485	2203	4300	6503	SO:0001583	missense	54487	exon2			GTAGGCATAGGGG	AF165527, AB050770	CCDS13773.1, CCDS54501.1	22q11.2	2013-05-02	2013-05-02		ENSG00000128191	ENSG00000128191			2847	protein-coding gene	gene with protein product		609030	"""chromosome 22 open reading frame 12"", ""DiGeorge syndrome critical region gene 8"""	C22orf12		21454614	Standard	NM_001190326		Approved	DGCRK6, Gy1, pasha	uc002zri.3	Q8WYQ5	OTTHUMG00000150503	ENST00000351989.3:c.520A>G	22.37:g.20074006A>G	ENSP00000263209:p.Ile174Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001190326	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Missense_Mutation	SNP	ENST00000351989.3	37	CCDS13773.1	96	0.04395604395604396	2	0.0040650406504065045	4	0.011049723756906077	42	0.07342657342657342	48	0.0633245382585752	A	0.118	-1.129884	0.01756	0.011802	0.054535	ENSG00000128191	ENST00000351989;ENST00000383024;ENST00000407755	T;T;T	0.29142	1.59;1.58;1.58	5.42	-10.8	0.00216	.	1.338760	0.04236	N	0.336176	T	0.00754	0.0025	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.06625	-1.0816	10	0.17832	T	0.49	5.1326	4.3344	0.11080	0.4797:0.274:0.1177:0.1286	rs35987994	174;174	Q8WYQ5-3;Q8WYQ5	.;DGCR8_HUMAN	V	174	ENSP00000263209:I174V;ENSP00000372488:I174V;ENSP00000384726:I174V	ENSP00000263209:I174V	I	+	1	0	DGCR8	18454006	0.000000	0.05858	0.011000	0.14972	0.979000	0.70002	-1.110000	0.03306	-3.838000	0.00100	-0.608000	0.04076	ATA	A|0.958;G|0.042	0.042	strong		0.552	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1		
NEB	4703	hgsc.bcm.edu	37	2	152422087	152422087	+	Silent	SNP	A	A	G	rs2288211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:152422087A>G	ENST00000172853.10	-	88	13338	c.13191T>C	c.(13189-13191)taT>taC	p.Y4397Y	NEB_ENST00000427231.2_Silent_p.Y6098Y|NEB_ENST00000604864.1_Silent_p.Y6098Y|NEB_ENST00000409198.1_Silent_p.Y4397Y|NEB_ENST00000603639.1_Silent_p.Y6098Y|NEB_ENST00000397345.3_Silent_p.Y6098Y			P20929	NEBU_HUMAN	nebulin	4397					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.Y4397Y(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		TAAAGTTAGGATAGTTTTCAA	0.388													A|||	1121	0.223842	0.0363	0.3761	5008	,	,		19432	0.3036		0.328	False		,,,				2504	0.18				p.Y6098Y		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	1	Substitution - coding silent(1)	stomach(1)	c.T18294C						PASS	.	A	,,	314,3372		8,298,1537	70.0	63.0	65.0		18294,18294,13191	1.2	1.0	2	dbSNP_100	65	2380,5802		349,1682,2060	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	357,1980,3597	GG,GA,AA		29.0882,8.5187,22.6997	,,	6098/8526,6098/8526,4397/6670	152422087	2694,9174	1843	4091	5934	SO:0001819	synonymous_variant	4703	exon116			GTTAGGATAGTTT	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.13191T>C	2.37:g.152422087A>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				A|0.732;G|0.268	0.268	strong		0.388	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
SLC12A8	84561	hgsc.bcm.edu	37	3	124802888	124802888	+	Missense_Mutation	SNP	C	C	T	rs2981482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124802888C>T	ENST00000393469.4	-	13	2040	c.1991G>A	c.(1990-1992)cGg>cAg	p.R664Q	SLC12A8_ENST00000423114.2_Missense_Mutation_p.R693Q|SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000469902.1_Missense_Mutation_p.R664Q|SLC12A8_ENST00000430155.2_Missense_Mutation_p.R465Q|SLC12A8_ENST00000314584.7_Missense_Mutation_p.R325Q	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	664			R -> Q (in dbSNP:rs2981482). {ECO:0000269|Ref.2}.		potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						CTGAGGGGACCGCAAGCTCCT	0.527													C|||	3105	0.620008	0.7995	0.5994	5008	,	,		18755	0.5813		0.5388	False		,,,				2504	0.5153				p.R664Q		Atlas-SNP	.											.	SLC12A8	81	.	0			c.G1991A						PASS	.	C	GLN/ARG,GLN/ARG	3181,915		1257,667,124	30.0	34.0	33.0		1991,1991	1.6	0.2	3	dbSNP_101	33	4378,4030		1150,2078,976	yes	missense,missense	SLC12A8	NM_001195483.1,NM_024628.5	43,43	2407,2745,1100	TT,TC,CC		47.9305,22.3389,39.5473	benign,benign	664/715,664/715	124802888	7559,4945	2048	4204	6252	SO:0001583	missense	84561	exon14			GGGGACCGCAAGC		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1991G>A	3.37:g.124802888C>T	ENSP00000377112:p.Arg664Gln	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	CCDS43143.1	1328	0.608058608058608	388	0.7886178861788617	202	0.5580110497237569	323	0.5646853146853147	415	0.5474934036939314	C	7.846	0.722884	0.15439	0.776611	0.520695	ENSG00000221955	ENST00000430155;ENST00000393469;ENST00000423114;ENST00000469902;ENST00000314584	D;D;D;D;T	0.87887	-1.82;-2.31;-2.31;-2.31;-1.46	5.42	1.63	0.23807	.	.	.	.	.	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B;B;B	0.24823	0.012;0.022;0.112	B;B;B	0.14023	0.007;0.003;0.01	T	0.41305	-0.9516	8	0.45353	T	0.12	.	5.9399	0.19187	0.0:0.5647:0.1353:0.3	rs2981482;rs59635900;rs2981482	693;664;465	A0AV02-2;A0AV02;A0AV02-3	.;S12A8_HUMAN;.	Q	465;664;693;664;325	ENSP00000415713:R465Q;ENSP00000377112:R664Q;ENSP00000404243:R693Q;ENSP00000418783:R664Q;ENSP00000323632:R325Q	ENSP00000323632:R325Q	R	-	2	0	SLC12A8	126285578	0.000000	0.05858	0.165000	0.22776	0.482000	0.33219	-0.951000	0.03885	0.669000	0.31146	-0.251000	0.11542	CGG	C|0.403;T|0.597	0.597	strong		0.527	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
SPINK5	11005	hgsc.bcm.edu	37	5	147486677	147486677	+	Silent	SNP	C	C	A	rs880687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:147486677C>A	ENST00000256084.7	+	17	1599	c.1557C>A	c.(1555-1557)ggC>ggA	p.G519G	SPINK5_ENST00000398454.1_Silent_p.G519G|SPINK5_ENST00000359874.3_Silent_p.G519G	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	519	Kazal-like 8. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G519G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTCCGTGGCCCAGATGGCA	0.468													C|||	2150	0.429313	0.1861	0.6167	5008	,	,		17269	0.4841		0.4871	False		,,,				2504	0.5092				p.G519G		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.C1557A						PASS	.	C	,,	963,3087		118,727,1180	161.0	158.0	159.0		1557,1557,1557	2.0	0.9	5	dbSNP_86	159	4279,4093		1086,2107,993	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1204,2834,2173	AA,AC,CC		48.8892,23.7778,42.1993	,,	519/1095,519/917,519/1065	147486677	5242,7180	2025	4186	6211	SO:0001819	synonymous_variant	11005	exon17			CCGTGGCCCAGAT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1557C>A	5.37:g.147486677C>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	135	134	0.992593	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			C|0.571;A|0.429	0.429	strong		0.468	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
LTA	4049	hgsc.bcm.edu	37	6	31540784	31540784	+	Missense_Mutation	SNP	C	C	A	rs1041981	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31540784C>A	ENST00000454783.1	+	3	437	c.179C>A	c.(178-180)aCc>aAc	p.T60N	TNF_ENST00000449264.2_5'Flank|LTA_ENST00000418386.2_Missense_Mutation_p.T60N	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	60			T -> N (in allele TNFB*2; dbSNP:rs1041981). {ECO:0000269|PubMed:1451807, ECO:0000269|PubMed:1670638, ECO:0000269|Ref.10, ECO:0000269|Ref.11}.		apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)			endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	GCCCACAGCACCCTCAAACCT	0.592													C|||	1951	0.389577	0.5136	0.3386	5008	,	,		15261	0.4692		0.3062	False		,,,				2504	0.2618				p.T60N		Atlas-SNP	.											.	LTA	18	.	0			c.C179A	GRCh37	CM024124	LTA	M	rs1041981	PASS	.	C	ASN/THR,ASN/THR	1543,1479		371,801,339	136.0	90.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	179,179	3.2	0.8	6	dbSNP_86	107	1793,3625		294,1205,1210	yes	missense,missense	LTA	NM_000595.2,NM_001159740.1	65,65	665,2006,1549	AA,AC,CC		33.0934,48.9411,39.5261	possibly-damaging,possibly-damaging	60/206,60/206	31540784	3336,5104	1511	2709	4220	SO:0001583	missense	4049	exon3			ACAGCACCCTCAA	X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"""Tumor necrosis factor (ligand) superfamily"""	6709	protein-coding gene	gene with protein product	"""TNF superfamily member 1"""	153440	"""lymphotoxin alpha (TNF superfamily, member 1)"""	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.179C>A	6.37:g.31540784C>A	ENSP00000403495:p.Thr60Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_001159740	Q8N4C3|Q9UKS8	Missense_Mutation	SNP	ENST00000454783.1	37	CCDS4701.1	871	0.39880952380952384	261	0.5304878048780488	114	0.3149171270718232	255	0.4458041958041958	241	0.3179419525065963	C	9.721	1.159641	0.21454	0.510589	0.330934	ENSG00000226979	ENST00000454783;ENST00000418386;ENST00000436827	T;T	0.15487	2.42;2.42	5.01	3.15	0.36227	.	0.411685	0.25552	N	0.029886	T	0.05868	0.0153	L	0.59436	1.845	0.36409	P	0.13637600000000005	B;B	0.16802	0.019;0.005	B;B	0.18561	0.022;0.005	T	0.18871	-1.0323	9	0.33141	T	0.24	-27.9588	5.2294	0.15414	0.2031:0.6916:0.0:0.1053	rs1041981;rs1800509;rs2229093;rs3181466;rs17846104;rs17859107;rs57361933;rs1041981	60;60	E7ET53;P01374	.;TNFB_HUMAN	N	60	ENSP00000403495:T60N;ENSP00000413450:T60N	ENSP00000413450:T60N	T	+	2	0	LTA	31648763	0.552000	0.26505	0.829000	0.32907	0.958000	0.62258	0.849000	0.27723	0.641000	0.30601	0.655000	0.94253	ACC	C|0.603;A|0.397	0.397	strong		0.592	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1		
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10600442G>C	ENST00000171111.5	-	4	1960	c.1413C>G	c.(1411-1413)ctC>ctG	p.L471L	KEAP1_ENST00000393623.2_Silent_p.L471L|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000588024.1_5'Flank	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	471					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)		p.L471L(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CGGCATAAAGGAGACGATTGA	0.562													C|||	2545	0.508187	0.7534	0.2983	5008	,	,		14922	0.5337		0.3549	False		,,,				2504	0.4571				p.L471L		Atlas-SNP	.											KEAP1,NS,carcinoma,0,1	KEAP1	182	1	1	Substitution - coding silent(1)	stomach(1)	c.C1413G						PASS	.	C	,	3017,1389	455.9+/-351.1	1037,943,223	77.0	63.0	68.0		1413,1413	0.6	1.0	19	dbSNP_86	68	3200,5400	653.2+/-401.0	612,1976,1712	no	coding-synonymous,coding-synonymous	KEAP1	NM_012289.3,NM_203500.1	,	1649,2919,1935	CC,CG,GG		37.2093,31.5252,47.801	,	471/625,471/625	10600442	6217,6789	2203	4300	6503	SO:0001819	synonymous_variant	9817	exon4			ATAAAGGAGACGA	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1413C>G	19.37:g.10600442G>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Silent	SNP	ENST00000171111.5	37	CCDS12239.1																																																																																			G|0.511;C|0.489	0.489	strong		0.562	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
NIPBL	25836	hgsc.bcm.edu	37	5	36985303	36985303	+	Missense_Mutation	SNP	A	A	G	rs3822471	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:36985303A>G	ENST00000282516.8	+	10	2520	c.2021A>G	c.(2020-2022)aAt>aGt	p.N674S	NIPBL_ENST00000448238.2_Missense_Mutation_p.N674S|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	674			N -> S (in dbSNP:rs3822471). {ECO:0000269|PubMed:15318302}.		brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			CCTAAACAAAATGAAAATAGA	0.373													A|||	627	0.1252	0.1021	0.1888	5008	,	,		19832	0.1329		0.1054	False		,,,				2504	0.1237				p.N674S		Atlas-SNP	.											NIPBL_ENST00000448238,NS,carcinoma,-1,2	NIPBL	513	2	0			c.A2021G						PASS	.	A	SER/ASN,SER/ASN	406,4000	203.1+/-225.7	23,360,1820	88.0	86.0	87.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2021,2021	2.3	1.0	5	dbSNP_107	87	1074,7526	223.1+/-260.0	55,964,3281	yes	missense,missense	NIPBL	NM_015384.4,NM_133433.3	46,46	78,1324,5101	GG,GA,AA		12.4884,9.2147,11.3794	benign,benign	674/2698,674/2805	36985303	1480,11526	2203	4300	6503	SO:0001583	missense	25836	exon10			AACAAAATGAAAA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.2021A>G	5.37:g.36985303A>G	ENSP00000282516:p.Asn674Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	145	80	0.551724	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	259	0.11858974358974358	55	0.11178861788617886	73	0.20165745856353592	51	0.08916083916083917	80	0.10554089709762533	A	4.339	0.062284	0.08388	0.092147	0.124884	ENSG00000164190	ENST00000282516;ENST00000448238	D;D	0.93859	-3.27;-3.3	5.98	2.31	0.28768	.	0.180790	0.47455	N	0.000240	T	0.00356	0.0011	N	0.24115	0.695	0.33515	P	0.408377	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.27739	-1.0065	9	0.07325	T	0.83	-7.3863	4.765	0.13128	0.6002:0.1633:0.2365:0.0	rs61259989	674;674	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	S	674	ENSP00000282516:N674S;ENSP00000406266:N674S	ENSP00000282516:N674S	N	+	2	0	NIPBL	37021060	0.250000	0.23951	0.999000	0.59377	0.987000	0.75469	0.421000	0.21280	0.160000	0.19432	0.528000	0.53228	AAT	A|0.879;G|0.121	0.121	strong		0.373	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
OR7A17	26333	hgsc.bcm.edu	37	19	14991439	14991439	+	Silent	SNP	T	T	G	rs34590588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14991439T>G	ENST00000327462.2	-	1	825	c.729A>C	c.(727-729)tcA>tcC	p.S243S		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					CTGAGAGGTGTGATGCACAGG	0.478													.|||	270	0.0539137	0.1354	0.0461	5008	,	,		17091	0.0159		0.0139	False		,,,				2504	0.0297				p.S243S		Atlas-SNP	.											.	OR7A17	37	.	0			c.A729C						PASS	.	C		500,3906		31,438,1734	112.0	97.0	102.0		729	1.2	0.7	19	dbSNP_126	102	256,8344		3,250,4047	no	coding-synonymous	OR7A17	NM_030901.1		34,688,5781	GG,GT,TT		2.9767,11.3482,5.8127		243/310	14991439	756,12250	2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			GAGGTGTGATGCA	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"""GPCR / Class A : Olfactory receptors"""	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.729A>C	19.37:g.14991439T>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			T|0.950;G|0.050	0.050	strong		0.478	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
MB21D2	151963	hgsc.bcm.edu	37	3	192516931	192516931	+	Silent	SNP	A	A	C	rs35594076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:192516931A>C	ENST00000392452.2	-	2	1040	c.720T>G	c.(718-720)tcT>tcG	p.S240S		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	240							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						AACCTTTGAAAGATACCACAG	0.473													A|||	15	0.00299521	0.0008	0.0	5008	,	,		21100	0.0		0.0129	False		,,,				2504	0.001				p.S240S		Atlas-SNP	.											.	MB21D2	75	.	0			c.T720G						PASS	.	A		15,4391	21.2+/-45.6	0,15,2188	105.0	97.0	100.0		720	-1.9	1.0	3	dbSNP_126	100	124,8476	63.9+/-126.0	2,120,4178	no	coding-synonymous	MB21D2	NM_178496.3		2,135,6366	CC,CA,AA		1.4419,0.3404,1.0687		240/492	192516931	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	151963	exon2			TTTGAAAGATACC	AK056276	CCDS3302.2	3q28-q29	2011-02-23	2011-02-23	2011-02-23	ENSG00000180611	ENSG00000180611			30438	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 59"""	C3orf59		12477932	Standard	NM_178496		Approved		uc011bsp.2	Q8IYB1	OTTHUMG00000155768	ENST00000392452.2:c.720T>G	3.37:g.192516931A>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	148	85	0.574324	NM_178496	Q86VD8	Silent	SNP	ENST00000392452.2	37	CCDS3302.2																																																																																			A|0.991;C|0.009	0.009	strong		0.473	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496	
ZNF585A	199704	hgsc.bcm.edu	37	19	37642922	37642922	+	Missense_Mutation	SNP	C	C	T	rs79071992	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37642922C>T	ENST00000356958.4	-	5	2137	c.1879G>A	c.(1879-1881)Gtt>Att	p.V627I	ZNF585A_ENST00000392157.2_Missense_Mutation_p.V572I|ZNF585A_ENST00000355533.2_Intron|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000292841.5_Missense_Mutation_p.V572I			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	627					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTGTGTGAACTGGCTGATGC	0.473													T|||	2515	0.502196	0.8064	0.5764	5008	,	,		19397	0.1944		0.497	False		,,,				2504	0.3609				p.V572I		Atlas-SNP	.											.	ZNF585A	117	.	0			c.G1714A						PASS	.	T	ILE/VAL,ILE/VAL	3347,1059	382.8+/-324.6	1247,853,103	35.0	33.0	34.0		1714,1714	-0.2	0.0	19	dbSNP_131	34	4355,4245	567.4+/-388.8	1103,2149,1048	no	missense,missense	ZNF585A	NM_152655.2,NM_199126.1	29,29	2350,3002,1151	TT,TC,CC		49.3605,24.0354,40.7812	benign,benign	572/715,572/715	37642922	7702,5304	2203	4300	6503	SO:0001583	missense	199704	exon6			TGTGAACTGGCTG	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"""Zinc fingers, C2H2-type"", ""-"""	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1879G>A	19.37:g.37642922C>T	ENSP00000349440:p.Val627Ile	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	241	91	0.377593	NM_199126	Q8TE95|Q96MV3	Missense_Mutation	SNP	ENST00000356958.4	37		1102	0.5045787545787546	399	0.8109756097560976	212	0.585635359116022	107	0.18706293706293706	384	0.5065963060686016	t	0.009	-1.831847	0.00584	0.759646	0.506395	ENSG00000196967	ENST00000356958;ENST00000292841;ENST00000392157	T;T;T	0.19105	2.17;2.17;2.17	3.21	-0.23	0.13090	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.198195	0.25060	N	0.033448	T	0.00012	0.0000	.	.	.	0.32492	P	0.5400860000000001	B	0.02656	0.0	B	0.04013	0.001	T	0.36792	-0.9733	8	0.02654	T	1	.	1.988	0.03440	0.1516:0.3908:0.1556:0.302	.	627	Q6P3V2	Z585A_HUMAN	I	627;572;572	ENSP00000349440:V627I;ENSP00000292841:V572I;ENSP00000375998:V572I	ENSP00000292841:V572I	V	-	1	0	ZNF585A	42334762	0.000000	0.05858	0.017000	0.16124	0.799000	0.45148	-0.917000	0.04025	-0.670000	0.05282	-2.387000	0.00228	GTT	C|0.454;T|0.546	0.546	strong		0.473	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655	
ANXA2R	389289	hgsc.bcm.edu	37	5	43039793	43039793	+	Missense_Mutation	SNP	T	T	C	rs1054428	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:43039793T>C	ENST00000314890.3	-	2	1775	c.356A>G	c.(355-357)cAg>cGg	p.Q119R	AC025171.1_ENST00000451894.2_RNA|AC025171.1_ENST00000505541.1_RNA	NM_001014279.2	NP_001014301.1	Q3ZCQ2	AX2R_HUMAN	annexin A2 receptor	119			Q -> R (in dbSNP:rs1054428). {ECO:0000269|PubMed:15489334}.														GGGAAGCTGCTGGAGCCTGAG	0.632											OREG0016598	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	919	0.183506	0.115	0.3487	5008	,	,		16771	0.0089		0.334	False		,,,				2504	0.184				p.Q119R		Atlas-SNP	.											.	.	.	.	0			c.A356G						PASS	.	T	ARG/GLN	660,3746	281.4+/-275.9	44,572,1587	77.0	84.0	82.0		356	-6.0	0.0	5	dbSNP_86	82	2812,5788	443.7+/-360.5	463,1886,1951	yes	missense	C5orf39	NM_001014279.2	43	507,2458,3538	CC,CT,TT		32.6977,14.9796,26.6954	benign	119/194	43039793	3472,9534	2203	4300	6503	SO:0001583	missense	389289	exon1			AGCTGCTGGAGCC	BC067873	CCDS34153.1	5p12	2013-08-14	2012-03-09	2012-03-09	ENSG00000177721	ENSG00000177721			33463	protein-coding gene	gene with protein product		611296	"""chromosome 5 open reading frame 39"""	C5orf39		16895901, 18636554	Standard	NM_001014279		Approved	AXIIR	uc003jnf.3	Q3ZCQ2	OTTHUMG00000162232	ENST00000314890.3:c.356A>G	5.37:g.43039793T>C	ENSP00000315915:p.Gln119Arg	Somatic	106	0	0	913	WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_001014279	Q8NHX5	Missense_Mutation	SNP	ENST00000314890.3	37	CCDS34153.1	434	0.1987179487179487	53	0.10772357723577236	132	0.36464088397790057	5	0.008741258741258742	244	0.32189973614775724	T	10.40	1.340230	0.24339	0.149796	0.326977	ENSG00000177721	ENST00000314890	T	0.32023	1.47	3.0	-6.01	0.02199	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	D	0.64830	0.994	P	0.56960	0.81	T	0.04140	-1.0974	8	0.28530	T	0.3	.	1.5697	0.02612	0.5049:0.1914:0.1277:0.1761	rs1054428;rs3172894;rs1054428	119	Q3ZCQ2	AX2R_HUMAN	R	119	ENSP00000315915:Q119R	ENSP00000315915:Q119R	Q	-	2	0	C5orf39	43075550	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.215000	0.09279	-2.514000	0.00502	-0.336000	0.08194	CAG	T|0.756;C|0.244	0.244	strong		0.632	ANXA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368030.1	NM_001014279	
AKAP12	9590	hgsc.bcm.edu	37	6	151670690	151670690	+	Silent	SNP	G	G	A	rs35341741	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151670690G>A	ENST00000253332.1	+	3	1353	c.1164G>A	c.(1162-1164)tcG>tcA	p.S388S	AKAP12_ENST00000402676.2_Silent_p.S388S|AKAP12_ENST00000354675.6_Silent_p.S290S|AKAP12_ENST00000359755.5_Silent_p.S283S|snoU13_ENST00000458767.1_RNA			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	388	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)		TCAGTGGCTCGCAGGGACCTT	0.542													G|||	397	0.0792732	0.053	0.0764	5008	,	,		18084	0.0099		0.0875	False		,,,				2504	0.18				p.S388S	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G1164A						PASS	.	G	,	234,4172	136.1+/-172.1	1,232,1970	35.0	41.0	39.0		1164,870	1.0	0.0	6	dbSNP_126	39	772,7828	181.8+/-230.4	30,712,3558	yes	coding-synonymous,coding-synonymous	AKAP12	NM_005100.3,NM_144497.2	,	31,944,5528	AA,AG,GG		8.9767,5.3109,7.7349	,	388/1783,290/1685	151670690	1006,12000	2203	4300	6503	SO:0001819	synonymous_variant	9590	exon4			TGGCTCGCAGGGA	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.1164G>A	6.37:g.151670690G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	75	7	0.0933333	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Silent	SNP	ENST00000253332.1	37	CCDS5229.1																																																																																			G|0.924;A|0.076	0.076	strong		0.542	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
TRPM7	54822	hgsc.bcm.edu	37	15	50867082	50867082	+	Silent	SNP	G	G	A	rs473357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:50867082G>A	ENST00000313478.7	-	34	5267	c.4986C>T	c.(4984-4986)taC>taT	p.Y1662Y	TRPM7_ENST00000561443.1_5'UTR|TRPM7_ENST00000560955.1_Silent_p.Y1661Y	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1662	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.				actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		TATCTTCTTTGTAAATACTTG	0.323													A|||	3063	0.611621	0.7073	0.6066	5008	,	,		17833	0.6121		0.5606	False		,,,				2504	0.5378				p.Y1662Y		Atlas-SNP	.											.	TRPM7	145	.	0			c.C4986T						PASS	.	A		2386,1224		802,782,221	81.0	79.0	79.0		4986	3.0	1.0	15	dbSNP_83	79	4591,3559		1302,1987,786	no	coding-synonymous	TRPM7	NM_017672.4		2104,2769,1007	AA,AG,GG		43.6687,33.9058,40.6718		1662/1866	50867082	6977,4783	1805	4075	5880	SO:0001819	synonymous_variant	54822	exon34			TTCTTTGTAAATA	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.4986C>T	15.37:g.50867082G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Silent	SNP	ENST00000313478.7	37	CCDS42035.1																																																																																			G|0.417;A|0.583	0.583	strong		0.323	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	
KIAA2018	205717	hgsc.bcm.edu	37	3	113379865	113379865	+	Missense_Mutation	SNP	G	G	C	rs9866806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113379865G>C	ENST00000478658.1	-	5	681	c.664C>G	c.(664-666)Cct>Gct	p.P222A	KIAA2018_ENST00000316407.4_Missense_Mutation_p.P222A|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	222			P -> A (in dbSNP:rs9866806). {ECO:0000269|PubMed:17974005}.			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						AGAGGAACAGGCTGGTTGGTA	0.483													G|||	1035	0.206669	0.1536	0.1758	5008	,	,		18612	0.2004		0.3519	False		,,,				2504	0.1575				p.P222A		Atlas-SNP	.											KIAA2018,NS,carcinoma,+1,1	KIAA2018	180	1	0			c.C664G						scavenged	.	G	ALA/PRO	577,3327		48,481,1423	65.0	70.0	68.0		664	3.0	1.0	3	dbSNP_119	68	2765,5539		483,1799,1870	yes	missense	KIAA2018	NM_001009899.2	27	531,2280,3293	CC,CG,GG		33.2972,14.7797,27.3755	benign	222/2246	113379865	3342,8866	1952	4152	6104	SO:0001583	missense	205717	exon7			GAACAGGCTGGTT	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.664C>G	3.37:g.113379865G>C	ENSP00000420721:p.Pro222Ala	Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	564	0.25824175824175827	78	0.15853658536585366	76	0.20994475138121546	120	0.2097902097902098	290	0.38258575197889183	G	7.481	0.648761	0.14516	0.147797	0.332972	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.13307	2.6;2.6	5.43	3.04	0.35103	.	0.486738	0.19311	N	0.117389	T	0.00012	0.0000	N	0.08118	0	0.37600	P	0.07947800000000005	B	0.24483	0.104	B	0.18871	0.023	T	0.48768	-0.9006	9	0.40728	T	0.16	-7.8482	1.794	0.03057	0.2708:0.1415:0.4432:0.1445	rs9866806;rs17326610;rs52791201;rs56479814;rs9866806	222	Q68DE3	K2018_HUMAN	A	222	ENSP00000320794:P222A;ENSP00000420721:P222A	ENSP00000320794:P222A	P	-	1	0	KIAA2018	114862555	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.716000	0.25836	1.179000	0.42884	0.655000	0.94253	CCT	G|0.747;C|0.253	0.253	strong		0.483	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
SPRY3	10251	hgsc.bcm.edu	37	X	155004280	155004280	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:155004280A>G	ENST00000302805.2	+	2	1178	c.747A>G	c.(745-747)caA>caG	p.Q249Q		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	249	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|regulation of signal transduction (GO:0009966)	cytoplasm (GO:0005737)|membrane (GO:0016020)						all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					ATCTGTGCCAACAGGGCTATG	0.592													A|||	970	0.19369	0.2489	0.1744	5008	,	,		20237	0.0179		0.2992	False		,,,				2504	0.2055				p.Q249Q		Atlas-SNP	.											.	SPRY3	52	.	0			c.A747G						PASS	.	A		1040,3366		132,776,1295	207.0	192.0	197.0		747	2.0	1.0	X	dbSNP_134	197	2390,6202		328,1734,2234	no	coding-synonymous	SPRY3	NM_005840.1		460,2510,3529	GG,GA,AA		27.8166,23.6042,26.3887		249/289	155004280	3430,9568	2203	4296	6499	SO:0001819	synonymous_variant	10251	exon2			GTGCCAACAGGGC	AF041038	CCDS14769.4	Xq28 and Yq12	2008-02-05	2001-11-28		ENSG00000168939	ENSG00000168939		"""Pseudoautosomal regions / PAR2"""	11271	protein-coding gene	gene with protein product	"""antagonist of FGF signaling"""	300531	"""sprouty (Drosophila) homolog 2"""			9458049	Standard	NM_005840		Approved	HSPRY3	uc004fnq.1	O43610	OTTHUMG00000022675	ENST00000302805.2:c.747A>G	X.37:g.155004280A>G		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	159	58	0.36478	NM_005840	A8K0H8	Silent	SNP	ENST00000302805.2	37	CCDS14769.4																																																																																			A|0.771;G|0.229	0.229	strong		0.592	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840	
LRRCC1	85444	hgsc.bcm.edu	37	8	86021994	86021994	+	Missense_Mutation	SNP	G	G	A	rs62525422	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:86021994G>A	ENST00000360375.3	+	2	418	c.269G>A	c.(268-270)tGc>tAc	p.C90Y	LRRCC1_ENST00000414626.2_Missense_Mutation_p.C70Y	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	90				C -> Y (in Ref. 1; BAB21855 and 2; BAG63888). {ECO:0000305}.	mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						ACAAAACTGTGCACATTAAAT	0.308													G|||	283	0.0565096	0.0083	0.0389	5008	,	,		14924	0.0149		0.0905	False		,,,				2504	0.1421				p.C90Y		Atlas-SNP	.											.	LRRCC1	212	.	0			c.G269A						PASS	.	G	TYR/CYS	73,3603		0,73,1765	60.0	55.0	57.0		269	5.5	1.0	8	dbSNP_129	57	898,7258		42,814,3222	yes	missense	LRRCC1	NM_033402.4	194	42,887,4987	AA,AG,GG		11.0103,1.9859,8.2066	probably-damaging	90/1033	86021994	971,10861	1838	4078	5916	SO:0001583	missense	85444	exon2			AACTGTGCACATT	BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.269G>A	8.37:g.86021994G>A	ENSP00000353538:p.Cys90Tyr	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Missense_Mutation	SNP	ENST00000360375.3	37	CCDS43750.1	99	0.04532967032967033	4	0.008130081300813009	16	0.04419889502762431	7	0.012237762237762238	72	0.09498680738786279	G	14.18	2.457495	0.43634	0.019859	0.110103	ENSG00000133739	ENST00000360375;ENST00000414626	T;T	0.09163	3.01;3.01	5.52	5.52	0.82312	.	0.185354	0.26871	N	0.022066	T	0.00210	0.0006	N	0.08118	0	0.33173	P	0.45148299999999997	D;P	0.54964	0.969;0.91	P;P	0.51135	0.66;0.544	T	0.31280	-0.9949	9	0.54805	T	0.06	-0.1137	12.7415	0.57255	0.075:0.0:0.925:0.0	rs62525422	70;90	Q9C099-2;Q9C099	.;LRCC1_HUMAN	Y	90;70	ENSP00000353538:C90Y;ENSP00000394695:C70Y	ENSP00000353538:C90Y	C	+	2	0	LRRCC1	86209246	1.000000	0.71417	0.997000	0.53966	0.186000	0.23388	5.294000	0.65687	2.582000	0.87167	0.591000	0.81541	TGC	G|0.925;A|0.075	0.075	strong		0.308	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
CUL9	23113	hgsc.bcm.edu	37	6	43172529	43172529	+	Silent	SNP	G	G	A	rs45496798	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43172529G>A	ENST00000252050.4	+	22	4467	c.4383G>A	c.(4381-4383)tcG>tcA	p.S1461S	CUL9_ENST00000372647.2_Silent_p.S1461S|CUL9_ENST00000354495.3_Silent_p.S1351S	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1461					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						CGGCGCCTTCGCCAGTGCTTC	0.602													g|||	38	0.00758786	0.0008	0.0072	5008	,	,		18507	0.0		0.0189	False		,,,				2504	0.0133				p.S1461S		Atlas-SNP	.											CUL9,NS,adenoma,0,1	CUL9	248	1	0			c.G4383A						PASS	.	A		12,4394	19.1+/-41.9	0,12,2191	80.0	86.0	84.0		4383	-9.9	0.0	6	dbSNP_127	84	139,8461	69.4+/-131.9	2,135,4163	no	coding-synonymous	CUL9	NM_015089.2		2,147,6354	AA,AG,GG		1.6163,0.2724,1.161		1461/2518	43172529	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon22			GCCTTCGCCAGTG	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.4383G>A	6.37:g.43172529G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	52	0.429752	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			G|0.990;A|0.010	0.010	strong		0.602	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
METTL22	79091	hgsc.bcm.edu	37	16	8722629	8722629	+	Missense_Mutation	SNP	G	G	C	rs2270286	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:8722629G>C	ENST00000381920.3	+	3	434	c.176G>C	c.(175-177)tGg>tCg	p.W59S	METTL22_ENST00000561758.1_Missense_Mutation_p.W59S	NM_024109.2	NP_077014.2	Q9BUU2	MET22_HUMAN	methyltransferase like 22	59			W -> S (in dbSNP:rs2270286).			nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			large_intestine(5)|lung(4)	9						CAAGACTCTTGGACAGATTCA	0.488													G|||	880	0.175719	0.0076	0.2061	5008	,	,		20032	0.3105		0.1889	False		,,,				2504	0.229				p.W59S		Atlas-SNP	.											.	METTL22	23	.	0			c.G176C						PASS	.	G	SER/TRP	160,3688		2,156,1766	57.0	59.0	58.0		176	-2.2	0.0	16	dbSNP_100	58	1560,6748		154,1252,2748	yes	missense	METTL22	NM_024109.2	177	156,1408,4514	CC,CG,GG		18.7771,4.158,14.1494	benign	59/405	8722629	1720,10436	1924	4154	6078	SO:0001583	missense	79091	exon3			ACTCTTGGACAGA	AK022495	CCDS10533.2	16p13.2	2014-07-15	2011-03-03	2011-03-03	ENSG00000067365	ENSG00000067365			28368	protein-coding gene	gene with protein product		615261	"""chromosome 16 open reading frame 68"""	C16orf68		24140279	Standard	XM_005255570		Approved	FLJ12433,MGC2654	uc002cyz.3	Q9BUU2	OTTHUMG00000129694	ENST00000381920.3:c.176G>C	16.37:g.8722629G>C	ENSP00000371345:p.Trp59Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	142	76	0.535211	NM_024109	B2RD29|D3DUF2|Q6XYB4|Q9HA03	Missense_Mutation	SNP	ENST00000381920.3	37	CCDS10533.2	405	0.18543956043956045	8	0.016260162601626018	69	0.19060773480662985	176	0.3076923076923077	152	0.20052770448548812	G	6.561	0.471814	0.12461	0.04158	0.187771	ENSG00000067365	ENST00000381920;ENST00000163678	T;T	0.41758	2.37;0.99	5.0	-2.18	0.07037	.	1.766790	0.03076	N	0.157894	T	0.00012	0.0000	L	0.40543	1.245	0.33131	P	0.45687999999999995	B	0.14438	0.01	B	0.09377	0.004	T	0.23297	-1.0192	9	0.11485	T	0.65	-12.35	5.5293	0.16974	0.5345:0.0:0.3172:0.1483	rs2270286;rs17746596;rs52824520;rs2270286	59	Q9BUU2	MET22_HUMAN	S	59	ENSP00000371345:W59S;ENSP00000163678:W59S	ENSP00000163678:W59S	W	+	2	0	METTL22	8630130	0.000000	0.05858	0.009000	0.14445	0.639000	0.38242	-0.392000	0.07314	-0.770000	0.04614	0.561000	0.74099	TGG	G|0.810;C|0.190	0.190	strong		0.488	METTL22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251901.1	NM_024109	
C10orf71	118461	hgsc.bcm.edu	37	10	50532812	50532812	+	Missense_Mutation	SNP	A	A	G	rs11101093	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50532812A>G	ENST00000374144.3	+	3	2510	c.2222A>G	c.(2221-2223)gAt>gGt	p.D741G	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	741			D -> G (in dbSNP:rs11101093).							endometrium(1)	1						GCCTCATTTGATGATCAGCAG	0.463													A|||	478	0.0954473	0.053	0.0663	5008	,	,		22000	0.122		0.1193	False		,,,				2504	0.1217				p.D741G		Atlas-SNP	.											.	C10orf71	179	.	0			c.A2222G						PASS	.	A	GLY/ASP,	76,1308		0,76,616	73.0	60.0	64.0		2222,	5.6	0.5	10	dbSNP_120	64	414,2768		24,366,1201	yes	missense,intron	C10orf71	NM_001135196.1,NM_199459.3	94,	24,442,1817	GG,GA,AA		13.0107,5.4913,10.7315	,	741/1436,	50532812	490,4076	692	1591	2283	SO:0001583	missense	118461	exon3			CATTTGATGATCA	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.2222A>G	10.37:g.50532812A>G	ENSP00000363259:p.Asp741Gly	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	198	97	0.489899	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	211	0.09661172161172162	32	0.06504065040650407	30	0.08287292817679558	60	0.1048951048951049	89	0.11741424802110818	A	14.84	2.655166	0.47467	0.054913	0.130107	ENSG00000177354	ENST00000374144	T	0.05081	3.5	5.64	5.64	0.86602	.	0.732696	0.11145	U	0.594792	T	0.00073	0.0002	N	0.08118	0	0.36653	P	0.12250799999999995	.	.	.	.	.	.	T	0.39781	-0.9597	7	0.54805	T	0.06	.	6.769	0.23583	0.6973:0.1449:0.0:0.1579	rs11101093;rs57806961;rs11101093	.	.	.	G	741	ENSP00000363259:D741G	ENSP00000363259:D741G	D	+	2	0	C10orf71	50202818	0.988000	0.35896	0.520000	0.27837	0.940000	0.58332	3.080000	0.50112	2.160000	0.67779	0.482000	0.46254	GAT	A|0.908;G|0.092	0.092	strong		0.463	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
SNX32	254122	hgsc.bcm.edu	37	11	65601560	65601560	+	Silent	SNP	G	G	C	rs17854357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:65601560G>C	ENST00000308342.6	+	1	449	c.24G>C	c.(22-24)ggG>ggC	p.G8G	SNX32_ENST00000531795.1_Intron	NM_152760.2	NP_689973.2	Q86XE0	SNX32_HUMAN	sorting nexin 32	8					intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)	p.G8G(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				READ - Rectum adenocarcinoma(159;0.171)		CGGAGGTTGGGAAGGAGGGCA	0.632													G|||	369	0.0736821	0.0272	0.1196	5008	,	,		5103	0.0585		0.161	False		,,,				2504	0.0297				p.G8G		Atlas-SNP	.											SNX32,NS,carcinoma,0,1	SNX32	46	1	1	Substitution - coding silent(1)	stomach(1)	c.G24C						PASS	.	G		186,3686		7,172,1757	140.0	135.0	137.0		24	0.3	0.8	11	dbSNP_123	137	1043,6373		67,909,2732	no	coding-synonymous	SNX32	NM_152760.2		74,1081,4489	CC,CG,GG		14.0642,4.8037,10.8877		8/404	65601560	1229,10059	1936	3708	5644	SO:0001819	synonymous_variant	254122	exon1			GGTTGGGAAGGAG	AK055496	CCDS8113.2	11q13.1	2008-03-11	2008-03-11	2008-03-11	ENSG00000172803	ENSG00000172803		"""Sorting nexins"""	26423	protein-coding gene	gene with protein product			"""sorting nexin 6B"""	SNX6B		16782399	Standard	XM_005273871		Approved	FLJ30934	uc001ofr.3	Q86XE0	OTTHUMG00000128491	ENST00000308342.6:c.24G>C	11.37:g.65601560G>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_152760	Q8IW53|Q96NG4	Silent	SNP	ENST00000308342.6	37	CCDS8113.2																																																																																			G|0.893;C|0.107	0.107	strong		0.632	SNX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250295.3	NM_152760	
LRBA	987	hgsc.bcm.edu	37	4	151719263	151719263	+	Silent	SNP	A	A	G	rs1129998	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:151719263A>G	ENST00000357115.3	-	34	5793	c.5550T>C	c.(5548-5550)gtT>gtC	p.V1850V	LRBA_ENST00000510413.1_Silent_p.V1850V|LRBA_ENST00000535741.1_Silent_p.V1850V|LRBA_ENST00000507224.1_Silent_p.V1850V	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	1850						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)					CCAATTCCACAACTGAACTAC	0.313													A|||	605	0.120807	0.0091	0.1081	5008	,	,		16351	0.1518		0.2624	False		,,,				2504	0.1033				p.V1850V		Atlas-SNP	.											.	LRBA	253	.	0			c.T5550C						PASS	.	A	,	230,4176	135.3+/-171.4	5,220,1978	87.0	84.0	85.0		5550,5550	3.5	1.0	4	dbSNP_86	85	2046,6548	352.1+/-328.5	248,1550,2499	yes	coding-synonymous,coding-synonymous	LRBA	NM_001199282.2,NM_006726.4	,	253,1770,4477	GG,GA,AA		23.8073,5.2202,17.5077	,	1850/2864,1850/2864	151719263	2276,10724	2203	4297	6500	SO:0001819	synonymous_variant	987	exon34			TTCCACAACTGAA	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.5550T>C	4.37:g.151719263A>G		Somatic	365	1	0.00273973		WXS	Illumina HiSeq	Phase_I	404	194	0.480198	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	37	CCDS3773.1	350	0.16025641025641027	4	0.008130081300813009	49	0.13535911602209943	102	0.17832167832167833	195	0.25725593667546176	A	9.830	1.188139	0.21954	0.052202	0.238073	ENSG00000198589	ENST00000509835	.	.	.	5.83	3.46	0.39613	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23368	-1.0190	3	.	.	.	.	4.9513	0.14015	0.7203:0.0:0.1436:0.1361	rs1129998;rs3188419;rs7674188;rs17589531;rs1129998	.	.	.	S	503	.	.	L	-	2	0	LRBA	151938713	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.750000	0.38329	1.038000	0.40049	0.528000	0.53228	TTG	A|0.839;G|0.161	0.161	strong		0.313	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155219361	155219361	+	Silent	SNP	A	A	G	rs17031387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155219361A>G	ENST00000357232.4	-	18	4739	c.4740T>C	c.(4738-4740)gaT>gaC	p.D1580D		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1580	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCAAAACTGGATCATTGTCAT	0.448													A|||	863	0.172324	0.1687	0.1138	5008	,	,		19749	0.1528		0.174	False		,,,				2504	0.2372				p.D1580D		Atlas-SNP	.											DCHS2,NS,carcinoma,-2,1	DCHS2	594	1	0			c.T4740C						PASS	.	A		804,3602	321.3+/-297.0	71,662,1470	106.0	104.0	105.0		4740	-0.0	1.0	4	dbSNP_123	105	1519,7081	287.0+/-298.0	146,1227,2927	no	coding-synonymous	DCHS2	NM_017639.3		217,1889,4397	GG,GA,AA		17.6628,18.2478,17.861		1580/2917	155219361	2323,10683	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon18			AACTGGATCATTG	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.4740T>C	4.37:g.155219361A>G		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	194	88	0.453608	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			A|0.826;G|0.174	0.174	strong		0.448	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
SVEP1	79987	hgsc.bcm.edu	37	9	113189954	113189954	+	Silent	SNP	T	T	G	rs41279045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113189954T>G	ENST00000401783.2	-	36	6228	c.5892A>C	c.(5890-5892)ggA>ggC	p.G1964G	SVEP1_ENST00000374469.1_Silent_p.G1941G|SVEP1_ENST00000297826.5_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1964	Sushi 10. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CAGGTGGTTCTCCACAGAAGA	0.517											OREG0019389	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	166	0.033147	0.0234	0.0259	5008	,	,		17532	0.0476		0.0457	False		,,,				2504	0.0235				p.G1964G		Atlas-SNP	.											.	SVEP1	326	.	0			c.A5892C						PASS	.	T		83,4071		0,83,1994	107.0	112.0	110.0		5892	0.9	1.0	9	dbSNP_127	110	357,8087		8,341,3873	no	coding-synonymous	SVEP1	NM_153366.3		8,424,5867	GG,GT,TT		4.2279,1.9981,3.4926		1964/3572	113189954	440,12158	2077	4222	6299	SO:0001819	synonymous_variant	79987	exon36			TGGTTCTCCACAG	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.5892A>C	9.37:g.113189954T>G		Somatic	128	0	0	1448	WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.963;G|0.037	0.037	strong		0.517	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
TAS2R13	50838	hgsc.bcm.edu	37	12	11061122	11061122	+	Missense_Mutation	SNP	T	T	C	rs1015443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:11061122T>C	ENST00000390677.2	-	1	1039	c.776A>G	c.(775-777)aAc>aGc	p.N259S	PRR4_ENST00000536668.1_Intron	NM_023920.2	NP_076409.1	Q9NYV9	T2R13_HUMAN	taste receptor, type 2, member 13	259			N -> S (in dbSNP:rs1015443). {ECO:0000269|PubMed:15489334}.		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|positive regulation of cytokinesis (GO:0032467)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9						GATCACTGTGTTCTGATACAG	0.388													T|||	2606	0.520367	0.1528	0.5908	5008	,	,		18568	0.7242		0.6243	False		,,,				2504	0.6503				p.N259S		Atlas-SNP	.											.	TAS2R13	29	.	0			c.A776G						PASS	.	T	SER/ASN	967,3439	363.9+/-316.7	114,739,1350	91.0	83.0	86.0		776	0.2	0.0	12	dbSNP_86	86	5005,3595	625.9+/-397.8	1470,2065,765	yes	missense	TAS2R13	NM_023920.2	46	1584,2804,2115	CC,CT,TT		41.8023,21.9473,45.9173	benign	259/304	11061122	5972,7034	2203	4300	6503	SO:0001583	missense	50838	exon1			ACTGTGTTCTGAT	AF227137	CCDS8635.1	12p13	2012-08-22			ENSG00000212128	ENSG00000212128		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14919	protein-coding gene	gene with protein product		604792				10761934, 10766242	Standard	NM_023920		Approved	T2R13, TRB3	uc001qzg.1	Q9NYV9		ENST00000390677.2:c.776A>G	12.37:g.11061122T>C	ENSP00000375095:p.Asn259Ser	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	120	116	0.966667	NM_023920	Q4G0I5|Q502V8|Q645X2	Missense_Mutation	SNP	ENST00000390677.2	37	CCDS8635.1	1180	0.5402930402930403	81	0.16463414634146342	221	0.6104972375690608	409	0.715034965034965	469	0.6187335092348285	T	4.365	0.067332	0.08388	0.219473	0.581977	ENSG00000212128	ENST00000390677	T	0.00760	5.73	2.71	0.219	0.15274	.	0.840598	0.09541	N	0.788221	T	0.00012	0.0000	N	0.13003	0.285	0.80722	P	0.0	B	0.19935	0.04	B	0.31390	0.129	T	0.00842	-1.1544	9	0.25751	T	0.34	.	4.853	0.13545	0.0:0.2661:0.0:0.7339	rs1015443;rs17743263;rs52835765;rs59560426;rs1015443	259	Q9NYV9	T2R13_HUMAN	S	259	ENSP00000375095:N259S	ENSP00000375095:N259S	N	-	2	0	TAS2R13	10952389	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-1.097000	0.03349	-0.077000	0.12752	0.377000	0.23210	AAC	T|0.499;C|0.501	0.501	strong		0.388	TAS2R13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400229.1		
IFT122	55764	hgsc.bcm.edu	37	3	129237966	129237966	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:129237966G>A	ENST00000348417.2	+	28	3485	c.3408G>A	c.(3406-3408)cgG>cgA	p.R1136R	IFT122_ENST00000507564.1_Silent_p.R1129R|IFT122_ENST00000440957.2_Silent_p.R927R|IFT122_ENST00000504021.1_Silent_p.R1013R|IFT122_ENST00000347300.2_Silent_p.R1077R|IFT122_ENST00000296266.3_Silent_p.R1187R|IFT122_ENST00000431818.2_Silent_p.R986R|IFT122_ENST00000349441.2_Silent_p.R1026R	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1136					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						AGATTCTGCGGCTAGTGGAGA	0.577																																					p.R1187R		Atlas-SNP	.											.	IFT122	117	.	0			c.G3561A						PASS	.						120.0	121.0	121.0					3																	129237966		2203	4300	6503	SO:0001819	synonymous_variant	55764	exon29			TCTGCGGCTAGTG	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3408G>A	3.37:g.129237966G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																			.	.	none		0.577	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
MAP3K9	4293	hgsc.bcm.edu	37	14	71267772	71267772	+	Silent	SNP	G	G	A	rs147891121	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:71267772G>A	ENST00000554752.2	-	2	431	c.432C>T	c.(430-432)ctC>ctT	p.L144L	MAP3K9_ENST00000381250.4_Silent_p.L144L|MAP3K9_ENST00000555993.2_Silent_p.L144L	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		CTTCCAAGGTGAGCTCCGCAA	0.438																																					p.L144L	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.C432T						PASS	.	G		0,4406		0,0,2203	57.0	58.0	58.0		432	-2.0	1.0	14	dbSNP_134	58	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MAP3K9	NM_033141.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		144/1119	71267772	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon2			CAAGGTGAGCTCC	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.432C>T	14.37:g.71267772G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				G|1.000;A|0.000	0.000	strong		0.438	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
CPN2	1370	hgsc.bcm.edu	37	3	194063153	194063153	+	Silent	SNP	G	G	A	rs3732474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194063153G>A	ENST00000323830.3	-	2	368	c.279C>T	c.(277-279)ttC>ttT	p.F93F	CPN2_ENST00000429275.1_Silent_p.F93F	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	93					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)			breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		GCAGCCCCCCGAAGGCATCCG	0.567													g|||	1300	0.259585	0.1626	0.2219	5008	,	,		20573	0.376		0.3519	False		,,,				2504	0.2025				p.F93F		Atlas-SNP	.											.	CPN2	56	.	0			c.C279T						PASS	.	A		914,3492	350.8+/-311.0	83,748,1372	91.0	89.0	90.0		279	-7.4	0.7	3	dbSNP_107	90	3287,5313	492.8+/-373.4	624,2039,1637	no	coding-synonymous	CPN2	NM_001080513.2		707,2787,3009	AA,AG,GG		38.2209,20.7444,32.3005		93/546	194063153	4201,8805	2203	4300	6503	SO:0001819	synonymous_variant	1370	exon2			CCCCCCGAAGGCA	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.279C>T	3.37:g.194063153G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Silent	SNP	ENST00000323830.3	37	CCDS33920.1																																																																																			G|0.700;A|0.300	0.300	strong		0.567	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
RADIL	55698	hgsc.bcm.edu	37	7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	rs187128776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4843307T>C	ENST00000399583.3	-	11	2556	c.2369A>G	c.(2368-2370)aAc>aGc	p.N790S	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.N550S	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	790					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N790S(1)		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)		GTCCAGGCAGTTGGCTTCCAA	0.647													T|||	63	0.0125799	0.0015	0.0187	5008	,	,		11788	0.0		0.0239	False		,,,				2504	0.0245				p.N790S		Atlas-SNP	.											RADIL,brain,glioma,0,1	RADIL	110	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2369G						PASS	.						19.0	26.0	24.0					7																	4843307		1977	4092	6069	SO:0001583	missense	55698	exon11			AGGCAGTTGGCTT	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.2369A>G	7.37:g.4843307T>C	ENSP00000382492:p.Asn790Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	72	27	0.375	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	33	0.01510989010989011	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	18	0.023746701846965697	T	0.543	-0.852823	0.02630	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.06449	3.37;3.3	4.27	3.12	0.35913	.	0.502188	0.20854	N	0.084468	T	0.00695	0.0023	N	0.08118	0	0.19300	N	0.999978	B;B	0.09022	0.0;0.002	B;B	0.01281	0.0;0.0	T	0.46925	-0.9156	10	0.23302	T	0.38	-15.6944	6.6406	0.22906	0.0:0.187:0.0:0.813	.	790;98	Q96JH8;Q75LH2	RADIL_HUMAN;.	S	790;761;524;550	ENSP00000382492:N790S;ENSP00000442966:N550S	ENSP00000320946:N761S	N	-	2	0	RADIL	4809833	0.936000	0.31750	0.004000	0.12327	0.026000	0.11368	3.515000	0.53429	0.692000	0.31613	0.459000	0.35465	AAC	T|0.985;C|0.015	0.015	strong		0.647	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
GGT1	2678	hgsc.bcm.edu	37	22	25016911	25016911	+	Missense_Mutation	SNP	C	C	T	rs199703506	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:25016911C>T	ENST00000400382.1	+	9	1362	c.607C>T	c.(607-609)Cgg>Tgg	p.R203W	GGT1_ENST00000400383.1_Missense_Mutation_p.R203W|GGT1_ENST00000248923.4_Missense_Mutation_p.R203W|GGT1_ENST00000466310.1_Intron|GGT1_ENST00000406383.2_Missense_Mutation_p.R203W|GGT1_ENST00000400380.1_Missense_Mutation_p.R203W			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	203					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.R203W(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	AAAGGTGCTTCGGGAGGGGGA	0.652																																					p.R203W		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	breast(1)	c.C607T						scavenged	.						20.0	22.0	21.0					22																	25016911		1981	4142	6123	SO:0001583	missense	2678	exon9			GTGCTTCGGGAGG	M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.607C>T	22.37:g.25016911C>T	ENSP00000383232:p.Arg203Trp	Somatic	397	4	0.0100756		WXS	Illumina HiSeq	Phase_I	475	16	0.0336842	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	16.88	3.244872	0.59103	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12;3.12	3.94	1.51	0.23008	.	0.465560	0.21948	U	0.066770	T	0.18841	0.0452	M	0.62016	1.91	0.29917	N	0.823045	D	0.76494	0.999	P	0.58970	0.849	T	0.03121	-1.1070	10	0.87932	D	0	-23.2527	10.8877	0.46976	0.3395:0.6605:0.0:0.0	.	203	P19440	GGT1_HUMAN	W	203	ENSP00000248923:R203W;ENSP00000393537:R203W;ENSP00000383232:R203W;ENSP00000383233:R203W;ENSP00000383231:R203W;ENSP00000385975:R203W	ENSP00000248923:R203W	R	+	1	2	GGT1	23346911	0.047000	0.20315	0.042000	0.18584	0.549000	0.35272	1.263000	0.33004	0.735000	0.32537	0.555000	0.69702	CGG	C|0.996;T|0.004	0.004	strong		0.652	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
C12orf43	64897	hgsc.bcm.edu	37	12	121454148	121454148	+	Missense_Mutation	SNP	C	C	T	rs11537857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121454148C>T	ENST00000288757.3	-	1	152	c.130G>A	c.(130-132)Ggg>Agg	p.G44R	C12orf43_ENST00000539736.1_Missense_Mutation_p.G44R|C12orf43_ENST00000445832.3_Missense_Mutation_p.G14R|C12orf43_ENST00000366211.2_5'UTR|C12orf43_ENST00000537817.1_Missense_Mutation_p.G14R|C12orf43_ENST00000536407.2_Missense_Mutation_p.G44R	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	44			G -> R (in dbSNP:rs16950706).							cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CTTGGCTTCCCTGCCACGTGC	0.627													C|||	170	0.0339457	0.0045	0.049	5008	,	,		14707	0.005		0.0606	False		,,,				2504	0.0654				p.G44R		Atlas-SNP	.											.	C12orf43	30	.	0			c.G130A						PASS	.	C	ARG/GLY	52,4354	48.9+/-83.8	2,48,2153	33.0	35.0	34.0		130	2.2	0.0	12	dbSNP_123	34	474,8126	134.1+/-191.5	16,442,3842	yes	missense	C12orf43	NM_022895.1	125	18,490,5995	TT,TC,CC		5.5116,1.1802,4.0443	benign	44/263	121454148	526,12480	2203	4300	6503	SO:0001583	missense	64897	exon1			GCTTCCCTGCCAC	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.130G>A	12.37:g.121454148C>T	ENSP00000288757:p.Gly44Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_022895	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	37	CCDS9210.1	75|75	0.034340659340659344|0.034340659340659344	5|5	0.01016260162601626|0.01016260162601626	21|21	0.058011049723756904|0.058011049723756904	1|1	0.0017482517482517483|0.0017482517482517483	48|48	0.0633245382585752|0.0633245382585752	C|C	13.11|13.11	2.140389|2.140389	0.37825|0.37825	0.011802|0.011802	0.055116|0.055116	ENSG00000157895|ENSG00000157895	ENST00000445832;ENST00000288757;ENST00000537817;ENST00000539736;ENST00000538296|ENST00000536407	T;T;T;T;T|.	0.44083|.	0.96;0.99;0.93;0.99;0.94|.	5.06|5.06	2.16|2.16	0.27623|0.27623	.|.	1.154110|.	0.06168|.	N|.	0.677205|.	T|T	0.02267|0.02267	0.0070|0.0070	N|N	0.08118|0.08118	0|0	0.47123|0.47123	P|P	6.730000000000347E-4|6.730000000000347E-4	B;B;B;B|.	0.27416|.	0.069;0.178;0.02;0.034|.	B;B;B;B|.	0.23419|.	0.046;0.037;0.046;0.014|.	T|T	0.20438|0.20438	-1.0275|-1.0275	9|4	0.15499|.	T|.	0.54|.	-7.2169|-7.2169	7.8635|7.8635	0.29524|0.29524	0.0:0.6737:0.2379:0.0884|0.0:0.6737:0.2379:0.0884	rs16950706;rs16950706|rs16950706;rs16950706	44;14;44;44|.	G5EA44;F5H7W8;B4DWJ9;Q96C57|.	.;.;.;CL043_HUMAN|.	R|K	14;44;14;44;14|48	ENSP00000409788:G14R;ENSP00000288757:G44R;ENSP00000442224:G14R;ENSP00000437803:G44R;ENSP00000442041:G14R|.	ENSP00000288757:G44R|.	G|R	-|-	1|2	0|0	C12orf43|C12orf43	119938531|119938531	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	0.340000|0.340000	0.19892|0.19892	0.368000|0.368000	0.24481|0.24481	0.650000|0.650000	0.86243|0.86243	GGG|AGG	T|0.040;C|0.960	0.040	strong		0.627	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
NUTM2G	441457	hgsc.bcm.edu	37	9	99699485	99699485	+	Missense_Mutation	SNP	G	G	C	rs7866127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:99699485G>C	ENST00000372322.3	+	5	1143	c.1122G>C	c.(1120-1122)gaG>gaC	p.E374D	NUTM2G_ENST00000354649.3_Missense_Mutation_p.E374D|HIATL2_ENST00000506067.1_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	374	Pro-rich.							p.E374D(1)									TCCCTGAGGAGATCCCCCCTG	0.667													.|||	552	0.110224	0.0076	0.2147	5008	,	,		16896	0.0913		0.1352	False		,,,				2504	0.1687				p.E374D		Atlas-SNP	.											FAM22G,NS,carcinoma,0,1	FAM22G	66	1	1	Substitution - Missense(1)	stomach(1)	c.G1122C						scavenged	.	G	ASP/GLU,ASP/GLU	99,3747		2,95,1826	43.0	52.0	49.0		1122,1122	0.2	0.1	9	dbSNP_116	49	941,7303		46,849,3227	no	missense,missense	FAM22G	NM_001045477.2,NM_001170741.1	45,45	48,944,5053	CC,CG,GG		11.4144,2.5741,8.6022	probably-damaging,probably-damaging	374/493,374/742	99699485	1040,11050	1923	4122	6045	SO:0001583	missense	441457	exon5			TGAGGAGATCCCC		CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152			23449	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member G"""	FAM22G			Standard	NM_001045477		Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.1122G>C	9.37:g.99699485G>C	ENSP00000361397:p.Glu374Asp	Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_001045477	A6NNI5|Q5VZR3	Missense_Mutation	SNP	ENST00000372322.3	37	CCDS55329.1	233	0.10668498168498168	8	0.016260162601626018	80	0.22099447513812154	50	0.08741258741258741	95	0.12532981530343007	.	11.65	1.701614	0.30142	0.025741	0.114144	ENSG00000188152	ENST00000354649;ENST00000372322;ENST00000375230	T;T	0.54675	0.56;1.15	1.33	0.238	0.15480	.	0.417786	0.22883	N	0.054494	T	0.00073	0.0002	M	0.76170	2.325	0.80722	P	0.0	D	0.76494	0.999	D	0.80764	0.994	T	0.05289	-1.0894	9	0.72032	D	0.01	.	5.095	0.14729	0.0:0.381:0.619:0.0	rs7866127	374	Q5VZR2-2	.	D	374;374;255	ENSP00000346670:E374D;ENSP00000361397:E374D	ENSP00000346670:E374D	E	+	3	2	FAM22G	98739306	1.000000	0.71417	0.070000	0.20053	0.027000	0.11550	0.621000	0.24418	0.105000	0.17753	0.473000	0.43528	GAG	G|0.893;C|0.107	0.107	strong		0.667	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053291.2	NM_001170741	
PNPO	55163	hgsc.bcm.edu	37	17	46020698	46020698	+	Silent	SNP	C	C	T	rs11079804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:46020698C>T	ENST00000225573.4	+	2	270	c.165C>T	c.(163-165)tcC>tcT	p.S55S	RP11-6N17.9_ENST00000582262.1_RNA|AC003665.1_ENST00000411573.2_RNA|AC003665.1_ENST00000433001.1_RNA|PNPO_ENST00000534893.1_Intron|PNPO_ENST00000434554.2_Silent_p.S55S|AC003665.1_ENST00000585280.1_RNA|PNPO_ENST00000544840.1_Silent_p.S55S|AC003665.1_ENST00000451140.2_RNA	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	55					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						ATCTGACCTCCCTTGACCCAG	0.463													C|||	814	0.16254	0.0537	0.2176	5008	,	,		20122	0.1617		0.162	False		,,,				2504	0.272				p.S55S		Atlas-SNP	.											PNPO,NS,adenoma,0,1	PNPO	18	1	0			c.C165T						PASS	.	C		330,4076	176.6+/-205.7	19,292,1892	140.0	111.0	120.0		165	-3.7	1.0	17	dbSNP_120	120	1469,7131	279.4+/-293.9	137,1195,2968	no	coding-synonymous	PNPO	NM_018129.3		156,1487,4860	TT,TC,CC		17.0814,7.4898,13.8321		55/262	46020698	1799,11207	2203	4300	6503	SO:0001819	synonymous_variant	55163	exon2			GACCTCCCTTGAC	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.165C>T	17.37:g.46020698C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	172	75	0.436047	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Silent	SNP	ENST00000225573.4	37	CCDS11522.1																																																																																			C|0.855;T|0.145	0.145	strong		0.463	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
CHM	1121	hgsc.bcm.edu	37	X	85219021	85219021	+	Silent	SNP	T	T	C	rs10217950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:85219021T>C	ENST00000357749.2	-	5	380	c.351A>G	c.(349-351)gcA>gcG	p.A117A	CHM_ENST00000537751.1_5'UTR|CHM_ENST00000467744.2_Intron	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	117					blood vessel development (GO:0001568)|protein geranylgeranylation (GO:0018344)|protein targeting to membrane (GO:0006612)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	cytosol (GO:0005829)|Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|prostate(1)	20		all_lung(315;5.41e-06)				TTTTCTGCAGTGCACCAGCTT	0.398													T|||	453	0.12	0.0098	0.1081	3775	,	,		13139	0.1052		0.2008	False		,,,				2504	0.0583				p.A117A		Atlas-SNP	.											.	CHM	57	.	0			c.A351G						PASS	.	T		150,3685		6,116,22,1510,549	56.0	49.0	51.0		351	2.1	1.0	X	dbSNP_119	51	1639,5089		145,878,471,1405,1401	no	coding-synonymous	CHM	NM_000390.2		151,994,493,2915,1950	CC,CT,C,TT,T		24.3609,3.9113,16.9365		117/654	85219021	1789,8774	2203	4300	6503	SO:0001819	synonymous_variant	1121	exon5			CTGCAGTGCACCA	X78121	CCDS14454.1, CCDS48139.1	Xq21.1-q21.3	2014-09-17			ENSG00000188419	ENSG00000188419			1940	protein-coding gene	gene with protein product		300390		TCD, DXS540		1373238	Standard	XM_006724615		Approved	REP-1	uc004eet.3	P24386	OTTHUMG00000021937	ENST00000357749.2:c.351A>G	X.37:g.85219021T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	62	61	0.983871	NM_000390	A1L4D2|O43732	Silent	SNP	ENST00000357749.2	37	CCDS14454.1																																																																																			T|0.840;C|0.160	0.160	strong		0.398	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390	
CCDC102A	92922	hgsc.bcm.edu	37	16	57555076	57555076	+	Silent	SNP	C	C	T	rs28446687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:57555076C>T	ENST00000258214.2	-	4	1071	c.825G>A	c.(823-825)gcG>gcA	p.A275A		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	275										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						TCCTGCTCAACGCCAGTTTAT	0.582													c|||	926	0.184904	0.3162	0.134	5008	,	,		17816	0.0298		0.2366	False		,,,				2504	0.1503				p.A275A		Atlas-SNP	.											.	CCDC102A	22	.	0			c.G825A						PASS	.	T		1326,3070	446.5+/-348.0	206,914,1078	137.0	114.0	122.0		825	-6.7	0.9	16	dbSNP_125	122	1908,6692	337.3+/-322.2	210,1488,2602	no	coding-synonymous	CCDC102A	NM_033212.3		416,2402,3680	TT,TC,CC		22.186,30.1638,24.8846		275/551	57555076	3234,9762	2198	4300	6498	SO:0001819	synonymous_variant	92922	exon4			GCTCAACGCCAGT	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.825G>A	16.37:g.57555076C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_033212	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																			C|0.768;T|0.232	0.232	strong		0.582	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212	
UNC13D	201294	hgsc.bcm.edu	37	17	73839326	73839326	+	Missense_Mutation	SNP	C	C	T	rs9904366	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73839326C>T	ENST00000207549.4	-	3	554	c.175G>A	c.(175-177)Gca>Aca	p.A59T	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Missense_Mutation_p.A59T	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	59			A -> T (in dbSNP:rs9904366).		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)			GTGTAGAGTGCGTCCTCGTAG	0.652									Familial Hemophagocytic Lymphohistiocytosis				C|||	78	0.0155751	0.0182	0.0216	5008	,	,		14274	0.0		0.0129	False		,,,				2504	0.0266				p.A59T		Atlas-SNP	.											.	UNC13D	68	.	0			c.G175A	GRCh37	CM066256	UNC13D	M	rs9904366	PASS	.	C	THR/ALA	63,4343	58.7+/-95.3	2,59,2142	52.0	51.0	51.0		175	3.9	0.9	17	dbSNP_119	51	147,8453	69.7+/-132.2	3,141,4156	yes	missense	UNC13D	NM_199242.2	58	5,200,6298	TT,TC,CC		1.7093,1.4299,1.6146	benign	59/1091	73839326	210,12796	2203	4300	6503	SO:0001583	missense	201294	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	AGAGTGCGTCCTC	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.175G>A	17.37:g.73839326C>T	ENSP00000207549:p.Ala59Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_199242	B4DWG9|Q9H7K5	Missense_Mutation	SNP	ENST00000207549.4	37	CCDS11730.1	30	0.013736263736263736	14	0.028455284552845527	9	0.024861878453038673	0	0.0	7	0.009234828496042216	C	14.71	2.617979	0.46736	0.014299	0.017093	ENSG00000092929	ENST00000207549;ENST00000412096;ENST00000448606	T;T	0.71461	-0.53;-0.57	4.86	3.89	0.44902	.	0.382752	0.25186	N	0.032492	T	0.35998	0.0951	L	0.43152	1.355	0.31637	N	0.648271	B	0.12013	0.005	B	0.06405	0.002	T	0.53899	-0.8373	10	0.29301	T	0.29	-11.5747	11.3402	0.49529	0.0:0.9145:0.0:0.0855	rs9904366;rs9904366	59	Q70J99	UN13D_HUMAN	T	59	ENSP00000207549:A59T;ENSP00000388093:A59T	ENSP00000207549:A59T	A	-	1	0	UNC13D	71350921	0.964000	0.33143	0.894000	0.35097	0.496000	0.33645	1.378000	0.34328	1.033000	0.39918	0.561000	0.74099	GCA	C|0.984;T|0.016	0.016	strong		0.652	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
VCAN	1462	hgsc.bcm.edu	37	5	82833369	82833369	+	Missense_Mutation	SNP	A	A	G	rs309559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:82833369A>G	ENST00000265077.3	+	8	5112	c.4547A>G	c.(4546-4548)aAa>aGa	p.K1516R	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.K529R|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1516	GAG-beta.		K -> R (in dbSNP:rs309559).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GGAACAGCCAAAAAAGGGGCA	0.448													A|||	2359	0.471046	0.5113	0.5274	5008	,	,		21484	0.3919		0.5258	False		,,,				2504	0.4018				p.K1516R		Atlas-SNP	.											.	VCAN	498	.	0			c.A4547G						PASS	.	A	,ARG/LYS,,ARG/LYS	2227,2179	587.0+/-386.6	557,1113,533	70.0	69.0	69.0		,1586,,4547	2.8	0.0	5	dbSNP_79	69	4258,4342	568.8+/-389.1	1064,2130,1106	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,26,,26	1621,3243,1639	GG,GA,AA		49.5116,49.4553,49.8616	,benign,,benign	,529/2410,,1516/3397	82833369	6485,6521	2203	4300	6503	SO:0001583	missense	1462	exon8			CAGCCAAAAAAGG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4547A>G	5.37:g.82833369A>G	ENSP00000265077:p.Lys1516Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	1060	0.48534798534798534	236	0.4796747967479675	192	0.5303867403314917	239	0.4178321678321678	393	0.5184696569920845	A	0.215	-1.033169	0.02029	0.505447	0.495116	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.84873	-1.89;-1.91;3.24	5.96	2.79	0.32731	.	0.512905	0.19591	N	0.110638	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.16802	0.019;0.011	B;B	0.19666	0.026;0.012	T	0.44452	-0.9327	9	0.29301	T	0.29	.	9.2557	0.37581	0.114:0.6976:0.0:0.1884	rs309559;rs310476;rs560411;rs3734012;rs3909225;rs16900527;rs17284461;rs59004049;rs309559	529;1516	P13611-2;P13611	.;CSPG2_HUMAN	R	1516;529;529	ENSP00000265077:K1516R;ENSP00000340062:K529R;ENSP00000426251:K529R	ENSP00000265077:K1516R	K	+	2	0	VCAN	82869125	0.002000	0.14202	0.002000	0.10522	0.000000	0.00434	0.289000	0.18957	0.852000	0.35287	-1.027000	0.02421	AAA	T|0.003;G|0.491	0.491	strong		0.448	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
SALL4	57167	hgsc.bcm.edu	37	20	50406630	50406630	+	Missense_Mutation	SNP	T	T	G	rs6091375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:50406630T>G	ENST00000217086.4	-	2	2503	c.2392A>C	c.(2392-2394)Atc>Ctc	p.I798L	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	798			I -> L (in dbSNP:rs6091375). {ECO:0000269|PubMed:12395297}.		embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TTTGACTTGATGCTTTCGGCT	0.527													T|||	329	0.0656949	0.1619	0.049	5008	,	,		18816	0.0		0.0646	False		,,,				2504	0.0164				p.I798L		Atlas-SNP	.											.	SALL4	168	.	0			c.A2392C						PASS	.	T	LEU/ILE	696,3710	294.1+/-283.0	54,588,1561	81.0	78.0	79.0		2392	-5.1	0.2	20	dbSNP_114	79	498,8102	142.2+/-198.4	14,470,3816	yes	missense	SALL4	NM_020436.3	5	68,1058,5377	GG,GT,TT		5.7907,15.7966,9.1804	benign	798/1054	50406630	1194,11812	2203	4300	6503	SO:0001583	missense	57167	exon2			ACTTGATGCTTTC	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2392A>C	20.37:g.50406630T>G	ENSP00000217086:p.Ile798Leu	Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	279	136	0.487455	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	159	0.07280219780219781	88	0.17886178861788618	22	0.06077348066298342	0	0.0	49	0.06464379947229551	T	4.686	0.127462	0.08981	0.157966	0.057907	ENSG00000101115	ENST00000217086	T	0.07800	3.16	5.67	-5.11	0.02901	.	0.990681	0.08190	N	0.984093	T	0.00012	0.0000	L	0.38175	1.15	0.20764	P	0.99985162	B	0.06786	0.001	B	0.06405	0.002	T	0.48258	-0.9051	9	0.10902	T	0.67	-18.3976	9.814	0.40840	0.0984:0.488:0.0:0.4137	rs6091375;rs52814636;rs56500327;rs6091375	798	Q9UJQ4	SALL4_HUMAN	L	798	ENSP00000217086:I798L	ENSP00000217086:I798L	I	-	1	0	SALL4	49840037	0.000000	0.05858	0.196000	0.23383	0.847000	0.48162	-1.163000	0.03138	-1.412000	0.02030	-0.408000	0.06270	ATC	T|0.917;G|0.083	0.083	strong		0.527	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
TPRX1	284355	hgsc.bcm.edu	37	19	48305654	48305654	+	Missense_Mutation	SNP	C	C	T	rs73036913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48305654C>T	ENST00000322175.3	-	2	769	c.614G>A	c.(613-615)gGc>gAc	p.G205D	TPRX1_ENST00000543508.1_Missense_Mutation_p.G195D|TPRX1_ENST00000535759.1_Missense_Mutation_p.G302D	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	205	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		tgggatcgggcctgggatcgg	0.677													G|||	184	0.0367412	0.0045	0.0432	5008	,	,		16236	0.0		0.1103	False		,,,				2504	0.0378				p.G205D	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,colon,carcinoma,0,1	TPRX1	46	1	0			c.G614A						PASS	.	C	ASP/GLY	63,3517		0,63,1727	13.0	10.0	11.0		614	-0.8	0.0	19	dbSNP_130	11	632,6154		20,592,2781	no	missense	TPRX1	NM_198479.2	94	20,655,4508	TT,TC,CC		9.3133,1.7598,6.7046	possibly-damaging	205/412	48305654	695,9671	1790	3393	5183	SO:0001583	missense	284355	exon2			ATCGGGCCTGGGA		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.614G>A	19.37:g.48305654C>T	ENSP00000323455:p.Gly205Asp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	43	21	0.488372	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	104	0.047619047619047616	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	88	0.11609498680738786	-	9.378	1.072204	0.20147	0.017598	0.093133	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	T;T;T	0.40476	1.03;1.03;1.03	0.401	-0.802	0.10889	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	P	0.49185	0.92	B	0.39805	0.31	T	0.04870	-1.0921	8	0.13108	T	0.6	.	.	.	.	.	205	Q8N7U7	TPRX1_HUMAN	D	205;302;195	ENSP00000323455:G205D;ENSP00000438832:G302D;ENSP00000438712:G195D	ENSP00000323455:G205D	G	-	2	0	TPRX1	52997466	0.001000	0.12720	0.004000	0.12327	0.004000	0.04260	-0.104000	0.10923	-0.484000	0.06763	-0.486000	0.04755	GGC	C|0.949;T|0.051	0.051	strong		0.677	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
RIN3	79890	hgsc.bcm.edu	37	14	93118229	93118229	+	Missense_Mutation	SNP	C	C	T	rs117068593	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93118229C>T	ENST00000216487.7	+	6	994	c.835C>T	c.(835-837)Cgc>Tgc	p.R279C	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	279	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				GGCCCCACGccgcccaccacc	0.721													C|||	403	0.0804712	0.0053	0.098	5008	,	,		5561	0.003		0.1869	False		,,,				2504	0.1401				p.R279C		Atlas-SNP	.											.	RIN3	81	.	0			c.C835T						PASS	.	C	CYS/ARG	154,4250	102.5+/-141.1	3,148,2051	29.0	33.0	32.0		835	3.7	1.0	14	dbSNP_132	32	1687,6911	297.4+/-303.4	157,1373,2769	no	missense	RIN3	NM_024832.3	180	160,1521,4820	TT,TC,CC		19.6208,3.4968,14.1594	probably-damaging	279/986	93118229	1841,11161	2202	4299	6501	SO:0001583	missense	79890	exon6			CCACGCCGCCCAC	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.835C>T	14.37:g.93118229C>T	ENSP00000216487:p.Arg279Cys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	177	0.08104395604395605	3	0.006097560975609756	44	0.12154696132596685	1	0.0017482517482517483	129	0.17018469656992086	C	14.37	2.515668	0.44763	0.034968	0.196208	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.08008	3.14	4.65	3.65	0.41850	.	0.936394	0.08842	N	0.885755	T	0.00039	0.0001	L	0.60455	1.87	0.09310	P	0.9999999999954712	D;D	0.89917	1.0;1.0	D;D	0.64410	0.925;0.925	T	0.18461	-1.0336	9	0.51188	T	0.08	-13.9867	15.0459	0.71827	0.1521:0.8479:0.0:0.0	.	204;279	Q6ZRC2;Q8TB24	.;RIN3_HUMAN	C	279	ENSP00000216487:R279C	ENSP00000216487:R279C	R	+	1	0	RIN3	92187982	0.977000	0.34250	0.991000	0.47740	0.617000	0.37484	1.979000	0.40608	2.157000	0.67596	0.313000	0.20887	CGC	C|0.886;T|0.114	0.114	strong		0.721	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
DOCK6	57572	hgsc.bcm.edu	37	19	11348960	11348960	+	Missense_Mutation	SNP	G	G	A	rs12609039	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11348960G>A	ENST00000294618.7	-	15	1675	c.1664C>T	c.(1663-1665)cCg>cTg	p.P555L	C19orf80_ENST00000591200.1_Intron|C19orf80_ENST00000252453.8_5'Flank|DOCK6_ENST00000319867.7_5'Flank	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	555	DHR-1.		P -> L (in dbSNP:rs12609039).		blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GAGGCTGTGCGGGTACACGTA	0.647													G|||	196	0.0391374	0.0023	0.0403	5008	,	,		16457	0.0704		0.0517	False		,,,				2504	0.0429				p.P555L		Atlas-SNP	.											.	DOCK6	104	.	0			c.C1664T						PASS	.	G	LEU/PRO	57,4017		0,57,1980	16.0	18.0	17.0		1664	4.8	1.0	19	dbSNP_120	17	615,7701		35,545,3578	yes	missense	DOCK6	NM_020812.2	98	35,602,5558	AA,AG,GG		7.3954,1.3991,5.4237	probably-damaging	555/2048	11348960	672,11718	2037	4158	6195	SO:0001583	missense	57572	exon15			CTGTGCGGGTACA		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.1664C>T	19.37:g.11348960G>A	ENSP00000294618:p.Pro555Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	87	0.03983516483516483	3	0.006097560975609756	15	0.04143646408839779	37	0.06468531468531469	32	0.04221635883905013	G	25.6	4.655909	0.88056	0.013991	0.073954	ENSG00000130158	ENST00000294618	T	0.10763	2.84	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.05547	0.0146	H	0.95645	3.7	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.47195	-0.9136	10	0.87932	D	0	-28.6951	16.638	0.85064	0.0:0.0:1.0:0.0	rs12609039;rs59939727;rs12609039	555	Q96HP0	DOCK6_HUMAN	L	555	ENSP00000294618:P555L	ENSP00000294618:P555L	P	-	2	0	DOCK6	11209960	1.000000	0.71417	0.987000	0.45799	0.779000	0.44077	9.129000	0.94430	2.211000	0.71520	0.591000	0.81541	CCG	G|0.960;A|0.040	0.040	strong		0.647	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
CSTA	1475	hgsc.bcm.edu	37	3	122056432	122056432	+	Silent	SNP	C	C	T	rs17589	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:122056432C>T	ENST00000264474.3	+	2	154	c.105C>T	c.(103-105)taC>taT	p.Y35Y	CSTA_ENST00000479204.1_Silent_p.Y35Y	NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	35					keratinocyte differentiation (GO:0030216)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|peptide cross-linking (GO:0018149)|single organismal cell-cell adhesion (GO:0016337)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			large_intestine(2)|lung(2)	4				GBM - Glioblastoma multiforme(114;0.155)		ATGAGACTTACGGAAAATTGG	0.343													C|||	1967	0.392772	0.413	0.549	5008	,	,		18411	0.0923		0.5596	False		,,,				2504	0.3926				p.Y35Y	Pancreas(26;157 1503 12440)	Atlas-SNP	.											.	CSTA	11	.	0			c.C105T						PASS	.	C		1745,2661	521.1+/-370.4	334,1077,792	117.0	120.0	119.0		105	-5.6	0.0	3	dbSNP_63	119	4876,3724	617.2+/-396.6	1363,2150,787	no	coding-synonymous	CSTA	NM_005213.3		1697,3227,1579	TT,TC,CC		43.3023,39.6051,49.0927		35/99	122056432	6621,6385	2203	4300	6503	SO:0001819	synonymous_variant	1475	exon2			GACTTACGGAAAA		CCDS3011.1	3q21	2008-04-15			ENSG00000121552	ENSG00000121552			2481	protein-coding gene	gene with protein product		184600		STF1, STFA		1674139	Standard	NM_005213		Approved		uc003eex.3	P01040	OTTHUMG00000159488	ENST00000264474.3:c.105C>T	3.37:g.122056432C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	143	57	0.398601	NM_005213	Q6IB90	Silent	SNP	ENST00000264474.3	37	CCDS3011.1																																																																																			C|0.552;T|0.448	0.448	strong		0.343	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213	
ASB17	127247	hgsc.bcm.edu	37	1	76387795	76387795	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:76387795C>T	ENST00000284142.6	-	2	790	c.651G>A	c.(649-651)gtG>gtA	p.V217V		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	217					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						TGACAGAAAGCACTCTGGAAC	0.353																																					p.V217V		Atlas-SNP	.											.	ASB17	53	.	0			c.G651A						PASS	.						80.0	68.0	72.0					1																	76387795		2203	4300	6503	SO:0001819	synonymous_variant	127247	exon2			AGAAAGCACTCTG	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"""Ankyrin repeat domain containing"""	19769	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 17"""			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.651G>A	1.37:g.76387795C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_080868	B1APB8|Q8N0X5	Silent	SNP	ENST00000284142.6	37	CCDS671.1																																																																																			.	.	none		0.353	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868	
CYP3A5	1577	hgsc.bcm.edu	37	7	99273815	99273815	+	Missense_Mutation	SNP	G	G	A	rs28383468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99273815G>A	ENST00000222982.4	-	2	187	c.88C>T	c.(88-90)Cat>Tat	p.H30Y	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000439761.1_Missense_Mutation_p.H30Y|CYP3A5_ENST00000343703.5_Missense_Mutation_p.H20Y|CYP3A5_ENST00000480723.1_5'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	30			H -> Y (in dbSNP:rs28383468). {ECO:0000269|PubMed:15469410}.		alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	AAAAGTCCATGTGTACGGGTC	0.463													G|||	17	0.00339457	0.0	0.0014	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0041				p.H30Y		Atlas-SNP	.											.	CYP3A5	46	.	0			c.C88T						PASS	.	G	TYR/HIS,TYR/HIS	6,4400	11.4+/-27.6	0,6,2197	110.0	100.0	104.0		88,88	1.9	0.0	7	dbSNP_125	104	82,8518	48.1+/-107.5	0,82,4218	yes	missense,missense	CYP3A5	NM_000777.3,NM_001190484.1	83,83	0,88,6415	AA,AG,GG		0.9535,0.1362,0.6766	,	30/503,30/141	99273815	88,12918	2203	4300	6503	SO:0001583	missense	1577	exon2			GTCCATGTGTACG	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.88C>T	7.37:g.99273815G>A	ENSP00000222982:p.His30Tyr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	124	50	0.403226	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Missense_Mutation	SNP	ENST00000222982.4	37	CCDS5672.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	0.239	-1.015455	0.02078	0.001362	0.009535	ENSG00000106258	ENST00000222982;ENST00000343703;ENST00000439761	T;T;T	0.08896	3.04;3.04;3.04	3.78	1.87	0.25490	.	0.279306	0.35320	N	0.003281	T	0.04048	0.0113	L	0.34521	1.04	0.09310	N	0.999998	B;B;B	0.14012	0.002;0.009;0.004	B;B;B	0.21151	0.021;0.033;0.012	T	0.42068	-0.9473	10	0.19147	T	0.46	.	8.2763	0.31874	0.2274:0.0:0.7726:0.0	rs28383468;rs59353336	20;30;30	F5H4S0;B7Z5I7;P20815	.;.;CP3A5_HUMAN	Y	30;20;30	ENSP00000222982:H30Y;ENSP00000342969:H20Y;ENSP00000401269:H30Y	ENSP00000222982:H30Y	H	-	1	0	CYP3A5	99111751	0.350000	0.24878	0.003000	0.11579	0.009000	0.06853	1.409000	0.34680	0.209000	0.20645	-1.644000	0.00765	CAT	G|0.994;A|0.006	0.006	strong		0.463	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
TCN2	6948	hgsc.bcm.edu	37	22	31006860	31006860	+	Missense_Mutation	SNP	A	A	G	rs9606756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:31006860A>G	ENST00000215838.3	+	2	561	c.67A>G	c.(67-69)Ata>Gta	p.I23V	TCN2_ENST00000407817.3_Missense_Mutation_p.I23V|TCN2_ENST00000405742.3_Missense_Mutation_p.I23V			P20062	TCO2_HUMAN	transcobalamin II	23			I -> V (in dbSNP:rs9606756).		cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TTTCTAAGAAATACCAGAGAT	0.502													A|||	566	0.113019	0.1581	0.196	5008	,	,		21709	0.0129		0.1133	False		,,,				2504	0.0961				p.I23V		Atlas-SNP	.											.	TCN2	44	.	0			c.A67G						PASS	.	A	VAL/ILE,VAL/ILE	678,3728	284.0+/-277.4	57,564,1582	78.0	76.0	77.0		67,67	1.3	0.0	22	dbSNP_119	77	1001,7599	213.6+/-253.5	60,881,3359	yes	missense,missense	TCN2	NM_000355.3,NM_001184726.1	29,29	117,1445,4941	GG,GA,AA		11.6395,15.3881,12.9094	benign,benign	23/428,23/401	31006860	1679,11327	2203	4300	6503	SO:0001583	missense	6948	exon2			TAAGAAATACCAG		CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"""macrocytic anemia"""	613441	"""transcobalamin II; macrocytic anemia"""			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.67A>G	22.37:g.31006860A>G	ENSP00000215838:p.Ile23Val	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_001184726	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	223	0.1021062271062271	75	0.1524390243902439	52	0.143646408839779	4	0.006993006993006993	92	0.12137203166226913	A	13.93	2.382508	0.42207	0.153881	0.116395	ENSG00000185339	ENST00000215838;ENST00000423350;ENST00000405742;ENST00000407817	T;T;T;T	0.37235	1.54;1.54;1.54;1.21	5.94	1.27	0.21489	.	0.228775	0.44902	N	0.000409	T	0.00144	0.0004	L	0.47016	1.485	0.29483	P	0.856208	B;B;B	0.17038	0.02;0.002;0.002	B;B;B	0.22601	0.04;0.026;0.026	T	0.09574	-1.0668	9	0.37606	T	0.19	-2.8261	2.0113	0.03489	0.5892:0.1357:0.1451:0.1301	rs9606756;rs11557599;rs61003488;rs9606756	23;23;23	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	V	23	ENSP00000215838:I23V;ENSP00000411529:I23V;ENSP00000385914:I23V;ENSP00000384914:I23V	ENSP00000215838:I23V	I	+	1	0	TCN2	29336860	0.122000	0.22280	0.003000	0.11579	0.378000	0.30076	0.182000	0.16900	-0.109000	0.12044	0.528000	0.53228	ATA	A|0.885;G|0.115	0.115	strong		0.502	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355	
PRMT7	54496	hgsc.bcm.edu	37	16	68389772	68389772	+	Silent	SNP	C	C	T	rs1131933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68389772C>T	ENST00000339507.5	+	17	2627	c.1797C>T	c.(1795-1797)acC>acT	p.T599T	PRMT7_ENST00000348497.4_Silent_p.T451T|PRMT7_ENST00000449359.3_Silent_p.T549T|PRMT7_ENST00000441236.1_Silent_p.T549T			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	599	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CCGAGGGCACCGTGGAGCTCA	0.677													C|||	2816	0.5623	0.5825	0.5764	5008	,	,		17878	0.7649		0.4026	False		,,,				2504	0.4806				p.T599T		Atlas-SNP	.											.	PRMT7	51	.	0			c.C1797T						PASS	.	C	,	2443,1951		678,1087,432	24.0	23.0	23.0		1647,1797	2.9	0.0	16	dbSNP_86	23	3796,4802		860,2076,1363	no	coding-synonymous,coding-synonymous	PRMT7	NM_001184824.1,NM_019023.2	,	1538,3163,1795	TT,TC,CC		44.1498,44.4015,48.0219	,	549/643,599/693	68389772	6239,6753	2197	4299	6496	SO:0001819	synonymous_variant	54496	exon17			GGGCACCGTGGAG	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.1797C>T	16.37:g.68389772C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Silent	SNP	ENST00000339507.5	37	CCDS10866.1																																																																																			C|0.488;T|0.512	0.512	strong		0.677	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
MT-ND4	4538	hgsc.bcm.edu	37	M	11251	11251	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:11251A>G	ENST00000361381.2	+	1	492	c.492A>G	c.(490-492)ctA>ctG	p.L164L	MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TK_ENST00000387421.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	164					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						CTCATCGCACTAATTTACACT	0.473																																					p.L164L		Atlas-SNP	.											.	.	.	.	0			c.A492G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CGCACTAATTTAC			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.492A>G	M.37:g.11251A>G		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.473	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
MARCH1	55016	hgsc.bcm.edu	37	4	165118796	165118796	+	Intron	SNP	G	G	A	rs2288674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:165118796G>A	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				GTTGTCCAGGGCAAGTTCTTT	0.517													G|||	1477	0.294928	0.118	0.3141	5008	,	,		16046	0.2133		0.4732	False		,,,				2504	0.4213				p.A23V		Atlas-SNP	.											.	ANP32C	59	.	0			c.C68T						PASS	.	G	,VAL/ALA	742,3664	301.0+/-286.6	71,600,1532	140.0	140.0	140.0		,68	-0.9	0.0	4	dbSNP_100	140	4245,4355	570.1+/-389.3	1048,2149,1103	no	intron,missense	ANP32C,MARCH1	NM_001166373.1,NM_012403.1	,64	1119,2749,2635	AA,AG,GG		49.3605,16.8407,38.3438	,benign	,23/235	165118796	4987,8019	2203	4300	6503	SO:0001627	intron_variant	23520	exon1			TCCAGGGCAAGTT	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-85982C>T	4.37:g.165118796G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			G|0.673;A|0.327	0.327	strong		0.517	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
PLCB3	5331	hgsc.bcm.edu	37	11	64023971	64023971	+	Silent	SNP	G	G	A	rs7943988	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64023971G>A	ENST00000540288.1	+	9	925	c.822G>A	c.(820-822)ctG>ctA	p.L274L	PLCB3_ENST00000325234.5_Silent_p.L207L|PLCB3_ENST00000279230.6_Silent_p.L274L	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	274					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						AGGCCCGGCTGCTCATCGAAA	0.637													G|||	854	0.170527	0.0227	0.1441	5008	,	,		18463	0.129		0.2982	False		,,,				2504	0.3006				p.L274L		Atlas-SNP	.											.	PLCB3	103	.	0			c.G822A						PASS	.	G	,	267,4135	147.6+/-182.1	8,251,1942	83.0	101.0	95.0		822,621	5.3	1.0	11	dbSNP_116	95	2707,5887	426.2+/-355.2	424,1859,2014	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	432,2110,3956	AA,AG,GG		31.4987,6.0654,22.884	,	274/1235,207/1168	64023971	2974,10022	2201	4297	6498	SO:0001819	synonymous_variant	5331	exon9			CCGGCTGCTCATC	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.822G>A	11.37:g.64023971G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	133	71	0.533835	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			G|0.807;A|0.193	0.193	strong		0.637	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
DEF6	50619	hgsc.bcm.edu	37	6	35288696	35288696	+	Silent	SNP	C	C	T	rs34278260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35288696C>T	ENST00000316637.5	+	10	1622	c.1617C>T	c.(1615-1617)aaC>aaT	p.N539N	DEF6_ENST00000542066.1_Silent_p.N284N	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	539						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						CCAGCACCAACGTGAAACACT	0.552													C|||	103	0.0205671	0.053	0.013	5008	,	,		18342	0.002		0.0199	False		,,,				2504	0.002				p.N539N		Atlas-SNP	.											.	DEF6	36	.	0			c.C1617T						PASS	.	C		213,4193	126.1+/-163.2	5,203,1995	56.0	50.0	52.0		1617	-6.7	0.5	6	dbSNP_126	52	185,8415	80.1+/-142.7	2,181,4117	no	coding-synonymous	DEF6	NM_022047.3		7,384,6112	TT,TC,CC		2.1512,4.8343,3.0601		539/632	35288696	398,12608	2203	4300	6503	SO:0001819	synonymous_variant	50619	exon10			CACCAACGTGAAA	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.1617C>T	6.37:g.35288696C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_022047	Q86VF4	Silent	SNP	ENST00000316637.5	37	CCDS4802.1																																																																																			C|0.970;T|0.030	0.030	strong		0.552	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047	
H2AFX	3014	hgsc.bcm.edu	37	11	118965688	118965688	+	Silent	SNP	G	G	A	rs1064180	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118965688G>A	ENST00000530167.1	-	1	489	c.417C>T	c.(415-417)gcC>gcT	p.A139A		NM_002105.2	NP_002096.1	P16104	H2AX_HUMAN	H2A histone family, member X	139					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|nucleosome assembly (GO:0006334)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)			lung(3)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		ACTCCTGGGAGGCCTGGGTGG	0.701								Chromatin Structure			OREG0021395	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	4	0.000798722	0.0	0.0	5008	,	,		10753	0.0		0.0	False		,,,				2504	0.0041				p.A139A		Atlas-SNP	.											.	H2AFX	8	.	0			c.C417T						PASS	.						17.0	21.0	20.0					11																	118965688		2196	4287	6483	SO:0001819	synonymous_variant	3014	exon1			CTGGGAGGCCTGG	X14850	CCDS8410.1	11q23.3	2011-01-27						"""Histones / Replication-independent"""	4739	protein-coding gene	gene with protein product		601772		H2AX		8076949	Standard	NM_002105		Approved		uc001pvg.3	P16104		ENST00000530167.1:c.417C>T	11.37:g.118965688G>A		Somatic	9	0	0	1492	WXS	Illumina HiSeq	Phase_I	25	12	0.48	NM_002105	Q4ZGJ7|Q6IAS5	Silent	SNP	ENST00000530167.1	37	CCDS8410.1																																																																																			G|0.999;A|0.001	0.001	weak		0.701	H2AFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388330.2	NM_002105	
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246979	47246979	+	Silent	SNP	A	A	G	rs16946912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:47246979A>G	ENST00000300404.2	+	11	1649	c.1590A>G	c.(1588-1590)gaA>gaG	p.E530E	B4GALNT2_ENST00000504681.1_Silent_p.E444E|B4GALNT2_ENST00000393354.2_Silent_p.E470E|RP11-708H21.4_ENST00000575159.1_lincRNA	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	530					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			TGGACTCAGAACTGGCTGCCC	0.527													G|||	611	0.122005	0.1641	0.0749	5008	,	,		20337	0.0218		0.1193	False		,,,				2504	0.2045				p.E530E	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.A1590G						PASS	.	G	,,	597,3809	771.2+/-413.8	34,529,1640	97.0	89.0	92.0		1410,1332,1590	0.9	0.0	17	dbSNP_123	92	904,7696	778.2+/-407.7	49,806,3445	no	coding-synonymous,coding-synonymous,coding-synonymous	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	,,	83,1335,5085	GG,GA,AA		10.5116,13.5497,11.5408	,,	470/507,444/481,530/567	47246979	1501,11505	2203	4300	6503	SO:0001819	synonymous_variant	124872	exon11			CTCAGAACTGGCT	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1590A>G	17.37:g.47246979A>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_153446	B4DZE4|Q14CP1|Q86Y40	Silent	SNP	ENST00000300404.2	37	CCDS11544.1																																																																																			A|0.888;G|0.112	0.112	strong		0.527	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446	
C1QTNF8	390664	hgsc.bcm.edu	37	16	1143496	1143496	+	Splice_Site	SNP	C	C	A	rs150337362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1143496C>A	ENST00000328449.5	-	4	1037		c.e4+1			NM_207419.3	NP_997302.2	P60827	C1QT8_HUMAN	C1q and tumor necrosis factor related protein 8							collagen trimer (GO:0005581)|extracellular region (GO:0005576)				lung(2)|prostate(1)|skin(1)	4		Hepatocellular(780;0.00369)				GGGCCCCTCACCCGGCTACAG	0.687													C|||	51	0.0101837	0.0008	0.0187	5008	,	,		9566	0.0		0.0288	False		,,,				2504	0.0082				.		Atlas-SNP	.											.	C1QTNF8	15	.	0			c.763+1G>T						PASS	.	C		10,3934		0,10,1962	4.0	6.0	5.0			-2.6	0.0	16	dbSNP_134	5	102,7936		0,102,3917	no	splice-5	C1QTNF8	NM_207419.3		0,112,5879	AA,AC,CC		1.269,0.2535,0.9347			1143496	112,11870	1972	4019	5991	SO:0001630	splice_region_variant	390664	exon5			CCCTCACCCGGCT	AY358832	CCDS32358.1	16p13.3	2014-08-12			ENSG00000184471	ENSG00000184471			31374	protein-coding gene	gene with protein product		614147				12975309	Standard	NM_207419		Approved	UNQ5829, CTRP8	uc010uuw.1	P60827	OTTHUMG00000167756	ENST00000328449.5:c.756+1G>T	16.37:g.1143496C>A		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	17	13	0.764706	NM_207419	B7U178	Splice_Site	SNP	ENST00000328449.5	37	CCDS32358.1																																																																																			C|0.984;A|0.016	0.016	strong		0.687	C1QTNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396120.1	XM_372606	Intron
P2RX7	5027	hgsc.bcm.edu	37	12	121592689	121592689	+	Missense_Mutation	SNP	T	T	C	rs17525809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121592689T>C	ENST00000546057.1	+	2	370	c.227T>C	c.(226-228)gTg>gCg	p.V76A	P2RX7_ENST00000328963.5_5'UTR|P2RX7_ENST00000541446.1_5'UTR|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_5'UTR|P2RX7_ENST00000377162.2_Missense_Mutation_p.V76A	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	76			V -> A (in dbSNP:rs17525809).		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)					GAGGAGATCGTGGAGAATGGA	0.527													T|||	250	0.0499201	0.0023	0.0663	5008	,	,		20695	0.0546		0.0676	False		,,,				2504	0.0798				p.V76A		Atlas-SNP	.											.	P2RX7	53	.	0			c.T227C						PASS	.	T	ALA/VAL	56,4350	55.5+/-91.7	1,54,2148	276.0	191.0	220.0		227	-4.0	0.0	12	dbSNP_123	220	599,8001	158.8+/-212.2	26,547,3727	yes	missense	P2RX7	NM_002562.5	64	27,601,5875	CC,CT,TT		6.9651,1.271,5.0361	benign	76/596	121592689	655,12351	2203	4300	6503	SO:0001583	missense	5027	exon2			AGATCGTGGAGAA	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.227T>C	12.37:g.121592689T>C	ENSP00000442349:p.Val76Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	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	118	0.05402930402930403	4	0.008130081300813009	26	0.0718232044198895	34	0.05944055944055944	54	0.0712401055408971	T	9.424	1.083670	0.20309	0.01271	0.069651	ENSG00000089041	ENST00000546057;ENST00000377162	T;T	0.07327	4.49;3.2	5.13	-3.96	0.04106	.	3.530630	0.00926	N	0.002653	T	0.00356	0.0011	N	0.03608	-0.345	0.09310	N	0.999999	B	0.16802	0.019	B	0.22152	0.038	T	0.42378	-0.9455	10	0.44086	T	0.13	.	7.6761	0.28486	0.0:0.5595:0.1632:0.2772	rs17525809;rs52803498;rs60836942;rs17525809	76	Q99572	P2RX7_HUMAN	A	76	ENSP00000442349:V76A;ENSP00000366367:V76A	ENSP00000261826:V76A	V	+	2	0	P2RX7	120077072	0.000000	0.05858	0.001000	0.08648	0.303000	0.27691	-1.354000	0.02614	-0.229000	0.09854	-0.415000	0.06103	GTG	T|0.944;C|0.056	0.056	strong		0.527	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
ADAL	161823	hgsc.bcm.edu	37	15	43632549	43632549	+	Splice_Site	SNP	T	T	C	rs2278857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43632549T>C	ENST00000562188.1	+	4	358	c.342T>C	c.(340-342)acT>acC	p.T114T	ADAL_ENST00000422466.2_Splice_Site_p.T114T|ADAL_ENST00000389651.4_Splice_Site_p.T114T|ADAL_ENST00000428046.3_Splice_Site_p.T114T			Q6DHV7	ADAL_HUMAN	adenosine deaminase-like	114					adenosine catabolic process (GO:0006154)|drug metabolic process (GO:0017144)|inosine biosynthetic process (GO:0046103)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	adenosine deaminase activity (GO:0004000)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|lung(2)|prostate(1)|skin(1)	7		all_cancers(109;7.96e-11)|all_epithelial(112;2.96e-09)|Lung NSC(122;8.91e-07)|all_lung(180;8.8e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;9.31e-07)		AAAATGCTACTGGTAGAATTT	0.378													C|||	2700	0.539137	0.9334	0.3343	5008	,	,		20547	0.4692		0.3221	False		,,,				2504	0.4468				p.T114T		Atlas-SNP	.											.	ADAL	48	.	0			c.T342C						PASS	.	C	,	3560,842	332.8+/-302.6	1435,690,76	72.0	79.0	77.0		342,342	-1.6	1.0	15	dbSNP_100	77	2724,5874	681.2+/-403.7	428,1868,2003	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ADAL	NM_001012969.2,NM_001159280.1	,	1863,2558,2079	CC,CT,TT		31.6818,19.1277,48.3385	,	114/268,114/329	43632549	6284,6716	2201	4299	6500	SO:0001630	splice_region_variant	161823	exon6			TGCTACTGGTAGA		CCDS32214.1, CCDS53936.1	15q15.3	2014-08-08			ENSG00000168803	ENSG00000168803			31853	protein-coding gene	gene with protein product							Standard	NM_001012969		Approved		uc010udo.2	Q6DHV7	OTTHUMG00000176646	ENST00000562188.1:c.343+1T>C	15.37:g.43632549T>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	52	0.541667	NM_001012969	A6NHZ3|B4DQM8	Silent	SNP	ENST00000562188.1	37																																																																																				T|0.487;C|0.513	0.513	strong		0.378	ADAL-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432960.1	XM_091156	Silent
DDX60	55601	hgsc.bcm.edu	37	4	169188780	169188780	+	Missense_Mutation	SNP	T	T	C	rs576619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169188780T>C	ENST00000393743.3	-	22	3283	c.2992A>G	c.(2992-2994)Att>Gtt	p.I998V		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	998			I -> V (in dbSNP:rs576619).		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)		TCAAAATGAATGTCACCATGT	0.303													T|||	406	0.0810703	0.1467	0.085	5008	,	,		14209	0.0		0.0994	False		,,,				2504	0.0542				p.I998V		Atlas-SNP	.											.	DDX60	304	.	0			c.A2992G						PASS	.	T	VAL/ILE	520,3886	239.6+/-250.7	31,458,1714	115.0	106.0	109.0		2992	-5.7	0.0	4	dbSNP_83	109	661,7939	166.8+/-218.7	21,619,3660	yes	missense	DDX60	NM_017631.5	29	52,1077,5374	CC,CT,TT		7.686,11.8021,9.0804	benign	998/1713	169188780	1181,11825	2203	4300	6503	SO:0001583	missense	55601	exon22			AATGAATGTCACC	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.2992A>G	4.37:g.169188780T>C	ENSP00000377344:p.Ile998Val	Somatic	348	1	0.00287356		WXS	Illumina HiSeq	Phase_I	335	139	0.414925	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	180	0.08241758241758242	77	0.1565040650406504	31	0.0856353591160221	0	0.0	72	0.09498680738786279	T	5.731	0.319347	0.10845	0.118021	0.07686	ENSG00000137628	ENST00000393743;ENST00000537338	T	0.16743	2.32	5.22	-5.7	0.02421	.	0.770143	0.11971	N	0.511818	T	0.00039	0.0001	N	0.16743	0.435	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.43376	-0.9395	9	0.16420	T	0.52	.	7.5868	0.27998	0.3052:0.489:0.0:0.2058	rs576619;rs52835038;rs57456959;rs576619	998	Q8IY21	DDX60_HUMAN	V	998;90	ENSP00000377344:I998V	ENSP00000377344:I998V	I	-	1	0	DDX60	169425355	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.237000	0.08990	-0.772000	0.04602	0.460000	0.39030	ATT	T|0.915;C|0.085	0.085	strong		0.303	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
TRIB3	57761	hgsc.bcm.edu	37	20	368905	368905	+	Missense_Mutation	SNP	A	A	G	rs2295490	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:368905A>G	ENST00000217233.3	+	2	804	c.251A>G	c.(250-252)cAg>cGg	p.Q84R	TRIB3_ENST00000422053.2_Missense_Mutation_p.Q111R	NM_021158.3	NP_066981.2	Q96RU7	TRIB3_HUMAN	tribbles pseudokinase 3	84	Interaction with DDIT3/CHOP.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Q -> R (in dbSNP:rs2295490). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of protein binding (GO:0032092)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|regulation of glucose transport (GO:0010827)|regulation of MAP kinase activity (GO:0043405)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|transcription corepressor activity (GO:0003714)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase regulator activity (GO:0055106)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|skin(1)	21		all_epithelial(17;0.165)|Lung NSC(37;0.191)|Breast(17;0.231)		Colorectal(46;0.101)|COAD - Colon adenocarcinoma(99;0.112)		CGGGCCTACCAGGCCCTGCAC	0.667													G|||	997	0.199081	0.1641	0.0836	5008	,	,		17047	0.1865		0.1441	False		,,,				2504	0.3978				p.Q84R	Melanoma(101;421 2374 19538)	Atlas-SNP	.											.	TRIB3	50	.	0			c.A251G	GRCh37	CM052928	TRIB3	M	rs2295490	PASS	.	G	ARG/GLN	706,3700	730.6+/-410.2	59,588,1556	34.0	36.0	35.0		251	4.5	0.5	20	dbSNP_100	35	1334,7262	727.5+/-406.6	117,1100,3081	yes	missense	TRIB3	NM_021158.3	43	176,1688,4637	GG,GA,AA		15.5188,16.0236,15.6899	benign	84/359	368905	2040,10962	2203	4298	6501	SO:0001583	missense	57761	exon2			CCTACCAGGCCCT	AF250311	CCDS12997.1	20p13-p12.2	2013-10-03	2013-10-03	2004-05-04	ENSG00000101255	ENSG00000101255			16228	protein-coding gene	gene with protein product		607898	"""chromosome 20 open reading frame 97"", ""tribbles homolog 3 (Drosophila)"""	C20orf97		12791994, 16715410	Standard	XM_005260773		Approved	dJ1103G7.3, TRB3	uc002wdm.3	Q96RU7	OTTHUMG00000031627	ENST00000217233.3:c.251A>G	20.37:g.368905A>G	ENSP00000217233:p.Gln84Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_021158	Q53GU4|Q53ZW7|Q6I9Y9|Q8TAI6|Q9H5M8|Q9NUD2	Missense_Mutation	SNP	ENST00000217233.3	37	CCDS12997.1	338	0.15476190476190477	75	0.1524390243902439	31	0.0856353591160221	125	0.21853146853146854	107	0.14116094986807387	G	5.585	0.292770	0.10567	0.160236	0.155188	ENSG00000101255	ENST00000217233;ENST00000449710;ENST00000422053	T;T;T	0.18338	2.22;2.24;2.22	4.49	4.49	0.54785	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.253277	0.20459	N	0.091939	T	0.00012	0.0000	N	0.00175	-1.925	0.50039	P	1.5699999999996272E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34378	-0.9831	9	0.17369	T	0.5	-10.8277	10.4874	0.44731	0.0958:0.0:0.9042:0.0	rs2295490;rs17856768;rs2295490	111;84	B4DMM9;Q96RU7	.;TRIB3_HUMAN	R	84;84;111	ENSP00000217233:Q84R;ENSP00000391873:Q84R;ENSP00000415416:Q111R	ENSP00000217233:Q84R	Q	+	2	0	TRIB3	316905	1.000000	0.71417	0.489000	0.27452	0.548000	0.35241	5.142000	0.64820	1.119000	0.41883	-0.215000	0.12644	CAG	A|0.840;G|0.160	0.160	strong		0.667	TRIB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077441.2	NM_021158	
DZIP1	22873	hgsc.bcm.edu	37	13	96239805	96239805	+	Missense_Mutation	SNP	G	G	A	rs11070136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:96239805G>A	ENST00000376829.2	-	20	3057	c.2206C>T	c.(2206-2208)Ccc>Tcc	p.P736S	DZIP1_ENST00000361156.3_Missense_Mutation_p.P717S|DZIP1_ENST00000347108.3_Missense_Mutation_p.P736S|DZIP1_ENST00000361396.2_Missense_Mutation_p.P717S	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	736			P -> S (in dbSNP:rs11070136). {ECO:0000269|PubMed:17974005}.		cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.P717S(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			GCGGGCTTGGGAGAATCATCA	0.542													G|||	1346	0.26877	0.3207	0.2248	5008	,	,		19768	0.1558		0.3618	False		,,,				2504	0.2505				p.P736S		Atlas-SNP	.											DZIP1,NS,carcinoma,0,1	DZIP1	195	1	1	Substitution - Missense(1)	stomach(1)	c.C2206T						PASS	.	G	SER/PRO,SER/PRO	1323,3083	444.7+/-347.4	190,943,1070	161.0	140.0	147.0		2149,2206	2.6	1.0	13	dbSNP_120	147	2927,5673	456.3+/-364.0	498,1931,1871	yes	missense,missense	DZIP1	NM_014934.3,NM_198968.2	74,74	688,2874,2941	AA,AG,GG		34.0349,30.0272,32.6772	benign,benign	717/849,736/868	96239805	4250,8756	2203	4300	6503	SO:0001583	missense	22873	exon20			GCTTGGGAGAATC	AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2206C>T	13.37:g.96239805G>A	ENSP00000366025:p.Pro736Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_198968	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	619	0.2834249084249084	160	0.3252032520325203	103	0.2845303867403315	80	0.13986013986013987	276	0.3641160949868074	G	0.013	-1.609554	0.00842	0.300272	0.340349	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.32272	1.46;1.46;1.46;1.46	5.34	2.63	0.31362	.	0.434403	0.26116	N	0.026258	T	0.00012	0.0000	L	0.43923	1.385	0.50467	P	1.2900000000004574E-4	B;B	0.12013	0.005;0.003	B;B	0.12837	0.008;0.004	T	0.44081	-0.9351	9	0.17369	T	0.5	-9.4551	4.96	0.14061	0.2465:0.1776:0.5759:0.0	rs11070136;rs52809482;rs56641201;rs60157457;rs11070136	717;736	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	S	736;717;717;736	ENSP00000257312:P736S;ENSP00000355018:P717S;ENSP00000355175:P717S;ENSP00000366025:P736S	ENSP00000257312:P736S	P	-	1	0	DZIP1	95037806	0.995000	0.38212	0.968000	0.41197	0.094000	0.18550	0.739000	0.26173	1.244000	0.43870	0.650000	0.86243	CCC	G|0.704;A|0.296	0.296	strong		0.542	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
ATG16L1	55054	hgsc.bcm.edu	37	2	234171812	234171812	+	Silent	SNP	A	A	G	rs13011156	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:234171812A>G	ENST00000392017.4	+	3	503	c.246A>G	c.(244-246)ctA>ctG	p.L82L	ATG16L1_ENST00000373525.5_Intron|ATG16L1_ENST00000347464.5_Intron|ATG16L1_ENST00000392018.1_Silent_p.L82L|ATG16L1_ENST00000392020.4_Silent_p.L82L	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	82					autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		ACAATCAGCTACAAGAAATGG	0.458													A|||	111	0.0221645	0.0023	0.0432	5008	,	,		21864	0.001		0.0636	False		,,,				2504	0.0133				p.L82L		Atlas-SNP	.											.	ATG16L1	83	.	0			c.A246G						PASS	.	A	,,,,	53,4353	52.9+/-88.7	0,53,2150	138.0	104.0	115.0		,,246,246,	-2.9	0.9	2	dbSNP_121	115	546,8054	149.4+/-204.5	21,504,3775	no	utr-5,utr-5,coding-synonymous,coding-synonymous,intron	ATG16L1	NM_001190266.1,NM_001190267.1,NM_017974.3,NM_030803.6,NM_198890.2	,,,,	21,557,5925	GG,GA,AA		6.3488,1.2029,4.6056	,,,,	,,82/589,82/608,	234171812	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	55054	exon3			TCAGCTACAAGAA	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"""WD repeat domain containing"""	21498	protein-coding gene	gene with protein product		610767	"""APG16 autophagy 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like 1 (S. cerevisiae)"""	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.246A>G	2.37:g.234171812A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_017974	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Silent	SNP	ENST00000392017.4	37	CCDS2503.2																																																																																			A|0.957;G|0.043	0.043	strong		0.458	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974	
ZBTB12	221527	hgsc.bcm.edu	37	6	31868938	31868938	+	Missense_Mutation	SNP	C	C	T	rs9394078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31868938C>T	ENST00000375527.2	-	2	320	c.145G>A	c.(145-147)Gtc>Atc	p.V49I	C2_ENST00000469372.1_Intron|C2_ENST00000452323.2_Intron	NM_181842.2	NP_862825.1	Q9Y330	ZBT12_HUMAN	zinc finger and BTB domain containing 12	49	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(5)|prostate(1)|skin(1)	10						GCCAAGATGACCTTGTGGCCT	0.632													C|||	293	0.0585064	0.0015	0.0187	5008	,	,		15657	0.2004		0.0427	False		,,,				2504	0.0337				p.V49I		Atlas-SNP	.											ZBTB12,NS,carcinoma,+2,1	ZBTB12	25	1	0			c.G145A						PASS	.	C	,ILE/VAL	29,4377	33.5+/-64.1	0,29,2174	41.0	33.0	36.0		,145	3.6	1.0	6	dbSNP_119	36	287,8313	102.9+/-164.1	14,259,4027	yes	intron,missense	C2,ZBTB12	NM_001178063.1,NM_181842.2	,29	14,288,6201	TT,TC,CC		3.3372,0.6582,2.4296	,probably-damaging	,49/460	31868938	316,12690	2203	4300	6503	SO:0001583	missense	221527	exon2			AGATGACCTTGTG	BC043609	CCDS4727.1	6p21.31	2013-01-08	2004-04-15	2004-04-16	ENSG00000204366	ENSG00000204366		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19066	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 46"""	C6orf46		9545376	Standard	NM_181842		Approved	G10, NG35, D6S59E	uc003nyd.1	Q9Y330	OTTHUMG00000031169	ENST00000375527.2:c.145G>A	6.37:g.31868938C>T	ENSP00000364677:p.Val49Ile	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	171	113	0.660819	NM_181842	B0UY00|Q5JQ98	Missense_Mutation	SNP	ENST00000375527.2	37	CCDS4727.1	130	0.05952380952380952	1	0.0020325203252032522	5	0.013812154696132596	86	0.15034965034965034	38	0.05013192612137203	C	14.26	2.482590	0.44147	0.006582	0.033372	ENSG00000204366	ENST00000375527	T	0.69040	-0.37	4.46	3.58	0.41010	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.64402	U	0.000001	T	0.38026	0.1025	L	0.45422	1.42	0.21064	P	0.999795426	B	0.27700	0.186	B	0.27500	0.08	T	0.15206	-1.0445	9	0.23891	T	0.37	.	11.1753	0.48595	0.0:0.9068:0.0:0.0932	rs9394078	49	Q9Y330	ZBT12_HUMAN	I	49	ENSP00000364677:V49I	ENSP00000364677:V49I	V	-	1	0	ZBTB12	31976917	0.995000	0.38212	1.000000	0.80357	0.996000	0.88848	1.222000	0.32515	0.861000	0.35504	0.543000	0.68304	GTC	C|0.967;T|0.033	0.033	strong		0.632	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842	
ITGAE	3682	hgsc.bcm.edu	37	17	3654980	3654980	+	Silent	SNP	A	A	G	rs11652878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3654980A>G	ENST00000263087.4	-	15	1955	c.1857T>C	c.(1855-1857)aaT>aaC	p.N619N		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	619					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		CCCAGTGTCCATTGTAGATAT	0.592													G|||	708	0.141374	0.1694	0.0908	5008	,	,		14885	0.1687		0.1093	False		,,,				2504	0.1442				p.N619N	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.T1857C						PASS	.	G		705,3701	760.6+/-413.0	61,583,1559	71.0	77.0	75.0		1857	-7.1	0.4	17	dbSNP_120	75	847,7753	780.3+/-407.7	35,777,3488	no	coding-synonymous	ITGAE	NM_002208.4		96,1360,5047	GG,GA,AA		9.8488,16.0009,11.933		619/1180	3654980	1552,11454	2203	4300	6503	SO:0001819	synonymous_variant	3682	exon15			GTGTCCATTGTAG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.1857T>C	17.37:g.3654980A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_002208	Q17RS6|Q9NZU9	Silent	SNP	ENST00000263087.4	37	CCDS32531.1																																																																																			A|0.864;G|0.136	0.136	strong		0.592	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
SPATA33	124045	hgsc.bcm.edu	37	16	89724755	89724755	+	Missense_Mutation	SNP	C	C	T	rs13329897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:89724755C>T	ENST00000301031.4	+	2	134	c.134C>T	c.(133-135)tCg>tTg	p.S45L	CHMP1A_ENST00000535997.2_5'Flank|CHMP1A_ENST00000550102.1_5'Flank|SPATA33_ENST00000579310.1_Missense_Mutation_p.S46L|CHMP1A_ENST00000547614.1_5'Flank|CHMP1A_ENST00000253475.5_5'Flank|CHMP1A_ENST00000397901.3_5'Flank|SPATA33_ENST00000568929.1_Missense_Mutation_p.S15L	NM_001271908.1|NM_153025.1	NP_001258837.1|NP_694570.1	Q96N06	SPT33_HUMAN	spermatogenesis associated 33	45			S -> L (in dbSNP:rs13329897).			cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACAGGGAGTCGGAGAAGCCT	0.612													C|||	37	0.00738818	0.0	0.013	5008	,	,		13663	0.0		0.0249	False		,,,				2504	0.0031				p.S46L		Atlas-SNP	.											.	C16orf55	6	.	0			c.C137T						PASS	.		LEU/SER	24,4370	29.9+/-59.1	0,24,2173	34.0	38.0	37.0		134	-1.5	0.0	16	dbSNP_121	37	174,8426	79.5+/-142.1	2,170,4128	yes	missense	C16orf55	NM_153025.1	145	2,194,6301	TT,TC,CC		2.0233,0.5462,1.5238	possibly-damaging	45/140	89724755	198,12796	2197	4300	6497	SO:0001583	missense	124045	exon2			GGGAGTCGGAGAA	AK056168	CCDS10983.1, CCDS62012.1, CCDS73929.1	16q24.3	2013-07-16	2013-07-05	2013-07-05	ENSG00000167523	ENSG00000167523			26463	protein-coding gene	gene with protein product		615409	"""chromosome 16 open reading frame 55"""	C16orf55		23844118	Standard	NM_153025		Approved	FLJ31606	uc010vpk.2	Q96N06	OTTHUMG00000138048	ENST00000301031.4:c.134C>T	16.37:g.89724755C>T	ENSP00000301031:p.Ser45Leu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_001271910	A8WFL2|B4DZN8	Missense_Mutation	SNP	ENST00000301031.4	37	CCDS10983.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	6.839	0.524082	0.13066	0.005462	0.020233	ENSG00000167523	ENST00000301031;ENST00000457689	T	0.40225	1.04	1.95	-1.52	0.08637	.	.	.	.	.	T	0.11665	0.0284	L	0.27053	0.805	0.09310	N	1	B;B;B	0.22851	0.004;0.076;0.008	B;B;B	0.08055	0.001;0.003;0.001	T	0.12426	-1.0548	9	0.36615	T	0.2	.	2.8748	0.05628	0.0:0.4326:0.2424:0.325	rs13329897;rs52799200;rs13329897	46;59;45	B4DZN8;Q86XC3;Q96N06	.;.;CP055_HUMAN	L	45;46	ENSP00000301031:S45L	ENSP00000301031:S45L	S	+	2	0	C16orf55	88252256	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.868000	0.04236	-0.356000	0.08187	-2.290000	0.00267	TCG	C|0.987;T|0.013	0.013	strong		0.612	SPATA33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269924.2	NM_153025	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921277	12921277	+	Silent	SNP	A	A	G	rs3204826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	264	2	0.00757576		WXS	Illumina HiSeq	Phase_I	288	9	0.03125	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	
CPNE6	9362	hgsc.bcm.edu	37	14	24545366	24545366	+	Silent	SNP	T	T	C	rs2070342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24545366T>C	ENST00000397016.2	+	12	1244	c.933T>C	c.(931-933)atT>atC	p.I311I	CPNE6_ENST00000537691.1_Silent_p.I366I|CPNE6_ENST00000216775.2_Silent_p.I311I	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	311	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		AGGTGGCCATTGACTTCACCG	0.622													C|||	2492	0.497604	0.5968	0.4337	5008	,	,		16063	0.4861		0.3579	False		,,,				2504	0.5644				p.I311I		Atlas-SNP	.											.	CPNE6	40	.	0			c.T933C						PASS	.	C		2454,1952	549.0+/-377.7	693,1068,442	47.0	45.0	46.0		933	-4.6	0.8	14	dbSNP_96	46	2986,5614	663.0+/-402.0	509,1968,1823	no	coding-synonymous	CPNE6	NM_006032.2		1202,3036,2265	CC,CT,TT		34.7209,44.3032,41.8268		311/558	24545366	5440,7566	2203	4300	6503	SO:0001819	synonymous_variant	9362	exon11			GGCCATTGACTTC	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.933T>C	14.37:g.24545366T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			T|0.579;C|0.421	0.421	strong		0.622	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
CAPN13	92291	hgsc.bcm.edu	37	2	30976058	30976058	+	Silent	SNP	C	C	T	rs2926304	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:30976058C>T	ENST00000295055.8	-	10	1124	c.948G>A	c.(946-948)tcG>tcA	p.S316S	CAPN13_ENST00000534090.2_Silent_p.S316S	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	316	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)	p.S316S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					AATCTTGACACGACATCCTGT	0.473													T|||	1922	0.383786	0.1475	0.4928	5008	,	,		21621	0.5109		0.4085	False		,,,				2504	0.4693				p.S316S		Atlas-SNP	.											CAPN13,NS,carcinoma,0,1	CAPN13	70	1	1	Substitution - coding silent(1)	stomach(1)	c.G948A						PASS	.	T		664,3172		56,552,1310	151.0	135.0	140.0		948	-2.4	1.0	2	dbSNP_101	140	3303,4941		657,1989,1476	no	coding-synonymous	CAPN13	NM_144575.2		713,2541,2786	TT,TC,CC		40.0655,17.3097,32.8394		316/670	30976058	3967,8113	1918	4122	6040	SO:0001819	synonymous_variant	92291	exon10			TTGACACGACATC		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.948G>A	2.37:g.30976058C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_144575	Q17RF0|Q580X1|Q8TE80	Silent	SNP	ENST00000295055.8	37	CCDS46252.1																																																																																			C|0.617;N|0.000	.	strong		0.473	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575	
TMEM132E	124842	hgsc.bcm.edu	37	17	32962050	32962050	+	Missense_Mutation	SNP	C	C	T	rs75594429	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:32962050C>T	ENST00000321639.5	+	8	1979	c.1651C>T	c.(1651-1653)Cac>Tac	p.H551Y		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	551						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CCGAGTGGCACACATGGTGGA	0.632													C|||	55	0.0109824	0.0008	0.0187	5008	,	,		17260	0.0		0.0358	False		,,,				2504	0.0051				p.H551Y		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C1651T						PASS	.	C	TYR/HIS	21,4385	28.1+/-56.4	0,21,2182	63.0	51.0	55.0		1651	5.2	1.0	17	dbSNP_131	55	273,8327	103.6+/-164.7	3,267,4030	yes	missense	TMEM132E	NM_207313.1	83	3,288,6212	TT,TC,CC		3.1744,0.4766,2.2605	benign	551/985	32962050	294,12712	2203	4300	6503	SO:0001583	missense	124842	exon8			GTGGCACACATGG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1651C>T	17.37:g.32962050C>T	ENSP00000316532:p.His551Tyr	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	33	0.01510989010989011	0	0.0	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	16.88	3.244653	0.59103	0.004766	0.031744	ENSG00000181291	ENST00000321639	T	0.42131	0.98	5.22	5.22	0.72569	.	0.437153	0.26331	N	0.024989	T	0.12433	0.0302	N	0.22421	0.69	0.42271	D	0.992056	B	0.23540	0.087	B	0.24394	0.053	T	0.04551	-1.0943	10	0.62326	D	0.03	-18.2352	13.6575	0.62346	0.0:0.8452:0.1548:0.0	.	551	Q6IEE7	T132E_HUMAN	Y	551	ENSP00000316532:H551Y	ENSP00000316532:H551Y	H	+	1	0	TMEM132E	29986163	0.068000	0.21057	0.996000	0.52242	0.997000	0.91878	1.410000	0.34691	2.725000	0.93324	0.498000	0.49722	CAC	C|0.979;T|0.021	0.021	strong		0.632	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
PLXNA4	91584	hgsc.bcm.edu	37	7	131864652	131864652	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:131864652G>A	ENST00000359827.3	-	20	4630	c.3668C>T	c.(3667-3669)cCg>cTg	p.P1223L	PLXNA4_ENST00000321063.4_Missense_Mutation_p.P1223L			Q9HCM2	PLXA4_HUMAN	plexin A4	1223	IPT/TIG 4.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CACCATCCCCGGGGAGTACTC	0.652																																					p.P1223L		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3668T						PASS	.						15.0	18.0	17.0					7																	131864652		2134	4237	6371	SO:0001583	missense	91584	exon20			ATCCCCGGGGAGT	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3668C>T	7.37:g.131864652G>A	ENSP00000352882:p.Pro1223Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	21	0.318182	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.549153	0.45383	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.57752	0.38;0.38	4.92	4.92	0.64577	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.097949	0.64402	D	0.000001	T	0.65133	0.2662	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58132	-0.7690	10	0.06625	T	0.88	.	18.3041	0.90175	0.0:0.0:1.0:0.0	.	1223	Q9HCM2	PLXA4_HUMAN	L	1223	ENSP00000323194:P1223L;ENSP00000352882:P1223L	ENSP00000323194:P1223L	P	-	2	0	PLXNA4	131515192	1.000000	0.71417	0.986000	0.45419	0.951000	0.60555	9.623000	0.98386	2.582000	0.87167	0.484000	0.47621	CCG	.	.	none		0.652	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
GIMAP7	168537	hgsc.bcm.edu	37	7	150217309	150217309	+	Missense_Mutation	SNP	C	C	T	rs3735080	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150217309C>T	ENST00000313543.4	+	2	404	c.247C>T	c.(247-249)Cgc>Tgc	p.R83C		NM_153236.3	NP_694968.1	Q8NHV1	GIMA7_HUMAN	GTPase, IMAP family member 7	83	AIG1-type G.		R -> C (in dbSNP:rs3735080).		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)	p.R83C(1)		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)		GGAAATCAGCCGCTGCATCAT	0.562													C|||	849	0.169529	0.0144	0.33	5008	,	,		19408	0.1587		0.2217	False		,,,				2504	0.2229				p.R83C		Atlas-SNP	.											GIMAP7,NS,carcinoma,0,1	GIMAP7	47	1	1	Substitution - Missense(1)	stomach(1)	c.C247T						PASS	.	C	CYS/ARG	218,4188	131.4+/-167.9	7,204,1992	48.0	49.0	49.0		247	-10.2	0.0	7	dbSNP_107	49	1961,6639	343.9+/-325.1	238,1485,2577	yes	missense	GIMAP7	NM_153236.3	180	245,1689,4569	TT,TC,CC		22.8023,4.9478,16.7538	probably-damaging	83/301	150217309	2179,10827	2203	4300	6503	SO:0001583	missense	168537	exon2			ATCAGCCGCTGCA	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.247C>T	7.37:g.150217309C>T	ENSP00000315474:p.Arg83Cys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_153236		Missense_Mutation	SNP	ENST00000313543.4	37	CCDS5903.1	370	0.16941391941391942	12	0.024390243902439025	94	0.2596685082872928	83	0.1451048951048951	181	0.23878627968337732	C	12.26	1.884168	0.33255	0.049478	0.228023	ENSG00000179144	ENST00000313543	T	0.07444	3.19	5.09	-10.2	0.00374	AIG1 (1);	0.922232	0.09141	N	0.842960	T	0.00012	0.0000	M	0.91249	3.19	0.80722	P	0.0	D	0.89917	1.0	D	0.67103	0.949	T	0.34254	-0.9836	9	0.87932	D	0	.	16.2376	0.82384	0.7907:0.1247:0.0846:0.0	rs3735080;rs11554998;rs17469020;rs52825973;rs57588247;rs3735080	83	Q8NHV1	GIMA7_HUMAN	C	83	ENSP00000315474:R83C	ENSP00000315474:R83C	R	+	1	0	GIMAP7	149848242	0.000000	0.05858	0.004000	0.12327	0.023000	0.10783	-1.164000	0.03135	-1.798000	0.01250	-1.107000	0.02091	CGC	C|0.840;T|0.160	0.160	strong		0.562	GIMAP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349277.1	NM_153236	
WSCD1	23302	hgsc.bcm.edu	37	17	6014188	6014188	+	Silent	SNP	C	C	T	rs74858033	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6014188C>T	ENST00000574946.1	+	7	1497	c.1107C>T	c.(1105-1107)caC>caT	p.H369H	WSCD1_ENST00000573634.1_Silent_p.H253H|WSCD1_ENST00000539421.1_Silent_p.H369H|WSCD1_ENST00000317744.5_Silent_p.H369H|WSCD1_ENST00000574232.1_Silent_p.H369H			Q658N2	WSCD1_HUMAN	WSC domain containing 1	369						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						GGGCACGGCACCTCATTGAGC	0.507													C|||	23	0.00459265	0.0	0.0029	5008	,	,		21716	0.0		0.0189	False		,,,				2504	0.002				p.H369H		Atlas-SNP	.											.	WSCD1	84	.	0			c.C1107T						PASS	.	C		13,4393	20.2+/-43.8	0,13,2190	142.0	130.0	134.0		1107	4.4	1.0	17	dbSNP_132	134	110,8490	59.8+/-121.6	1,108,4191	no	coding-synonymous	WSCD1	NM_015253.1		1,121,6381	TT,TC,CC		1.2791,0.2951,0.9457		369/576	6014188	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	23302	exon7			ACGGCACCTCATT		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.1107C>T	17.37:g.6014188C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	115	63	0.547826	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Silent	SNP	ENST00000574946.1	37	CCDS32538.1																																																																																			C|0.991;T|0.009	0.009	strong		0.507	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
PITRM1	10531	hgsc.bcm.edu	37	10	3180298	3180298	+	Silent	SNP	C	C	T	rs10175	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:3180298C>T	ENST00000224949.4	-	27	3073	c.3039G>A	c.(3037-3039)aaG>aaA	p.K1013K	PITRM1_ENST00000464395.1_5'UTR|PITRM1_ENST00000380994.1_Silent_p.K571K|PITRM1_ENST00000380989.2_Silent_p.K1014K|PITRM1_ENST00000451104.2_Silent_p.K915K			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	1013					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						CGTGTGTGCTCTTCCCAGTGC	0.607													C|||	1180	0.235623	0.2027	0.3473	5008	,	,		17500	0.1617		0.3121	False		,,,				2504	0.1984				p.K1014K		Atlas-SNP	.											.	PITRM1	109	.	0			c.G3042A						PASS	.	C	,,	989,3275		113,763,1256	46.0	51.0	49.0		3042,2745,3039	1.8	0.2	10	dbSNP_52	49	2305,6179		314,1677,2251	no	coding-synonymous,coding-synonymous,coding-synonymous	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	,,	427,2440,3507	TT,TC,CC		27.1688,23.1942,25.8393	,,	1014/1039,915/940,1013/1038	3180298	3294,9454	2132	4242	6374	SO:0001819	synonymous_variant	10531	exon27			TGTGCTCTTCCCA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.3039G>A	10.37:g.3180298C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Silent	SNP	ENST00000224949.4	37	CCDS59208.1																																																																																			C|0.756;T|0.244	0.244	strong		0.607	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
PARP15	165631	hgsc.bcm.edu	37	3	122354037	122354037	+	Silent	SNP	A	A	G	rs1106346	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:122354037A>G	ENST00000464300.2	+	11	1809	c.1743A>G	c.(1741-1743)aaA>aaG	p.K581K	PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000483793.1_Silent_p.K386K|PARP15_ENST00000493645.1_Silent_p.K278K|PARP15_ENST00000310366.4_Silent_p.K347K	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	581	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		GTGCTGGGAAAAATGGTAAGG	0.433													G|||	1794	0.358227	0.2557	0.3876	5008	,	,		18818	0.5		0.3787	False		,,,				2504	0.3088				p.K581K		Atlas-SNP	.											.	PARP15	115	.	0			c.A1743G						PASS	.	G	,	1163,3243	711.2+/-408.0	156,851,1196	66.0	59.0	61.0		1743,1041	0.9	0.0	3	dbSNP_86	61	3155,5445	652.4+/-400.9	574,2007,1719	no	coding-synonymous,coding-synonymous	PARP15	NM_001113523.1,NM_152615.1	,	730,2858,2915	GG,GA,AA		36.686,26.3958,33.2001	,	581/679,347/445	122354037	4318,8688	2203	4300	6503	SO:0001819	synonymous_variant	165631	exon11			TGGGAAAAATGGT	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1743A>G	3.37:g.122354037A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	135	72	0.533333	NM_001113523	J3KR47|Q8N1K3	Silent	SNP	ENST00000464300.2	37	CCDS46893.1																																																																																			A|0.654;G|0.346	0.346	strong		0.433	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
CROCC	9696	hgsc.bcm.edu	37	1	17264939	17264939	+	Silent	SNP	T	T	C	rs4558023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17264939T>C	ENST00000375541.5	+	11	1404	c.1335T>C	c.(1333-1335)gaT>gaC	p.D445D	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin									p.D445D(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		AGACAGAGGATGGAGAGGGGC	0.632																																					p.D445D		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	1	Substitution - coding silent(1)	prostate(1)	c.T1335C						PASS	.						19.0	16.0	17.0					1																	17264939		2178	4273	6451	SO:0001819	synonymous_variant	9696	exon11			AGAGGATGGAGAG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1335T>C	1.37:g.17264939T>C		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	508	225	0.442913	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			T|0.699;C|0.301	0.301	strong		0.632	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
ZNF566	84924	hgsc.bcm.edu	37	19	36940760	36940760	+	Silent	SNP	G	G	T	rs2967532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36940760G>T	ENST00000434377.2	-	5	457	c.376C>A	c.(376-378)Cgg>Agg	p.R126R	ZNF566_ENST00000424129.2_Silent_p.R126R|ZNF566_ENST00000454319.1_Silent_p.R127R|ZNF566_ENST00000493391.1_Silent_p.R22R|ZNF566_ENST00000392170.2_Silent_p.R127R	NM_032838.4	NP_116227.1	Q969W8	ZN566_HUMAN	zinc finger protein 566	126					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(12)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24	Esophageal squamous(110;0.162)					TTAAACTGCCGATTACATTCC	0.408													T|||	2486	0.496406	0.5968	0.3991	5008	,	,		17970	0.2669		0.5885	False		,,,				2504	0.5716				p.R127R		Atlas-SNP	.											ZNF566,mouth,carcinoma,+2,1	ZNF566	40	1	0			c.C379A						PASS	.	T	,,,	2705,1701	513.4+/-368.3	818,1069,316	163.0	165.0	164.0		379,376,376,376	-0.4	0.1	19	dbSNP_101	164	5084,3516	512.4+/-377.9	1510,2064,726	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF566	NM_001145343.1,NM_001145344.1,NM_001145345.1,NM_032838.4	,,,	2328,3133,1042	TT,TG,GG		40.8837,38.6064,40.1123	,,,	127/420,126/419,126/419,126/419	36940760	7789,5217	2203	4300	6503	SO:0001819	synonymous_variant	84924	exon5			ACTGCCGATTACA	AK074497	CCDS12494.1, CCDS46061.1, CCDS74346.1	19q13.12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	25919	protein-coding gene	gene with protein product						12477932	Standard	NM_001145343		Approved	FLJ14779, MGC12515	uc010xtf.2	Q969W8		ENST00000434377.2:c.376C>A	19.37:g.36940760G>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_001145343	B7ZL95|Q2M3J1	Silent	SNP	ENST00000434377.2	37	CCDS12494.1																																																																																			G|0.483;T|0.517	0.517	strong		0.408	ZNF566-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000341054.1	NM_032838	
RFPL3	10738	hgsc.bcm.edu	37	22	32756744	32756744	+	Silent	SNP	A	A	G	rs2076035	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:32756744A>G	ENST00000249007.4	+	2	1084	c.879A>G	c.(877-879)caA>caG	p.Q293Q	RFPL3_ENST00000397468.1_Silent_p.Q264Q|RFPL3_ENST00000382088.3_Silent_p.Q264Q|RFPL3S_ENST00000400234.1_Silent_p.P98P|RFPL3S_ENST00000382084.4_Silent_p.P69P|RFPL3S_ENST00000461833.1_5'UTR	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	293	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						ATGGTGATCAAGGTGTCTTGA	0.502																																					p.Q293Q		Atlas-SNP	.											.	RFPL3	91	.	0			c.A879G						PASS	.						116.0	101.0	106.0					22																	32756744		2203	4300	6503	SO:0001819	synonymous_variant	10738	exon2			TGATCAAGGTGTC	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.879A>G	22.37:g.32756744A>G		Somatic	261	2	0.00766284		WXS	Illumina HiSeq	Phase_I	273	215	0.787546	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			A|0.497;G|0.503	0.503	strong		0.502	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
CACNA1S	779	hgsc.bcm.edu	37	1	201047062	201047062	+	Silent	SNP	G	G	A	rs4915476	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201047062G>A	ENST00000362061.3	-	11	1790	c.1564C>T	c.(1564-1566)Ctg>Ttg	p.L522L	CACNA1S_ENST00000367338.3_Silent_p.L522L	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	522					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)	GAGATGCCCAGGGGTGTCATG	0.622													G|||	956	0.190895	0.292	0.2695	5008	,	,		18414	0.0367		0.2425	False		,,,				2504	0.1043				p.L522L		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C1564T	GRCh37	CM023570	CACNA1S	M	rs4915476	PASS	.	G		1172,3234	410.9+/-335.5	158,856,1189	77.0	61.0	66.0		1564	4.7	0.9	1	dbSNP_111	66	1915,6685	337.8+/-322.5	202,1511,2587	no	coding-synonymous	CACNA1S	NM_000069.2		360,2367,3776	AA,AG,GG		22.2674,26.6001,23.7352		522/1874	201047062	3087,9919	2203	4300	6503	SO:0001819	synonymous_variant	779	exon11			TGCCCAGGGGTGT	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.1564C>T	1.37:g.201047062G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	170	89	0.523529	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			G|0.776;A|0.224	0.224	strong		0.622	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
CWF19L1	55280	hgsc.bcm.edu	37	10	102006681	102006681	+	Silent	SNP	C	C	T	rs17112787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:102006681C>T	ENST00000354105.4	-	8	806	c.720G>A	c.(718-720)gcG>gcA	p.A240A	CWF19L1_ENST00000370379.1_5'Flank|CWF19L1_ENST00000478047.1_Intron	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	240							catalytic activity (GO:0003824)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|stomach(2)	17		Colorectal(252;0.117)		Epithelial(162;3.78e-10)|all cancers(201;3.1e-08)		CAATACTGAACGCGTAAAGAT	0.383													C|||	543	0.108427	0.1165	0.0216	5008	,	,		20065	0.3026		0.0129	False		,,,				2504	0.0573				p.A240A		Atlas-SNP	.											CWF19L1,NS,carcinoma,-1,2	CWF19L1	39	2	0			c.G720A						PASS	.	C		391,4015	194.3+/-219.2	15,361,1827	73.0	67.0	69.0		720	-4.8	1.0	10	dbSNP_123	69	150,8450	72.3+/-134.9	4,142,4154	no	coding-synonymous	CWF19L1	NM_018294.4		19,503,5981	TT,TC,CC		1.7442,8.8743,4.1596		240/539	102006681	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	55280	exon8			ACTGAACGCGTAA	AK001860	CCDS7489.1	10q24.31	2008-11-24			ENSG00000095485	ENSG00000095485			25613	protein-coding gene	gene with protein product						14702039	Standard	NM_018294		Approved	FLJ10998	uc001kqq.1	Q69YN2	OTTHUMG00000018901	ENST00000354105.4:c.720G>A	10.37:g.102006681C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Silent	SNP	ENST00000354105.4	37	CCDS7489.1																																																																																			C|0.921;T|0.079	0.079	strong		0.383	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
MUC16	94025	hgsc.bcm.edu	37	19	9077581	9077581	+	Missense_Mutation	SNP	G	G	T	rs73011014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9077581G>T	ENST00000397910.4	-	3	10068	c.9865C>A	c.(9865-9867)Cca>Aca	p.P3289T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	3290	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						GCCTCAGGTGGGGATGGGGAG	0.542													G|||	938	0.1873	0.0946	0.2536	5008	,	,		20999	0.3254		0.1322	False		,,,				2504	0.18				p.P3289T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C9865A						PASS	.	G	THR/PRO	392,3698		18,356,1671	101.0	103.0	102.0		9865	-0.8	0.0	19	dbSNP_130	102	1158,7206		72,1014,3096	yes	missense	MUC16	NM_024690.2	38	90,1370,4767	TT,TG,GG		13.8451,9.5844,12.4458	probably-damaging	3289/14508	9077581	1550,10904	2045	4182	6227	SO:0001583	missense	94025	exon3			CAGGTGGGGATGG	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.9865C>A	19.37:g.9077581G>T	ENSP00000381008:p.Pro3289Thr	Somatic	386	0	0		WXS	Illumina HiSeq	Phase_I	452	212	0.469027	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	8.427	0.847619	0.17034	0.095844	0.138451	ENSG00000181143	ENST00000397910	T	0.03181	4.02	1.67	-0.84	0.10755	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.65815	0.995	P	0.55577	0.779	T	0.53056	-0.8492	8	0.87932	D	0	.	4.138	0.10179	0.4727:0.0:0.5273:0.0	.	3289	B5ME49	.	T	3289	ENSP00000381008:P3289T	ENSP00000381008:P3289T	P	-	1	0	MUC16	8938581	0.001000	0.12720	0.000000	0.03702	0.851000	0.48451	-0.230000	0.09083	-0.166000	0.10890	0.313000	0.20887	CCA	G|0.809;T|0.191	0.191	strong		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52131119	52131119	+	Missense_Mutation	SNP	A	A	G	rs2278831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52131119A>G	ENST00000534261.2	-	6	1364	c.965T>C	c.(964-966)tTc>tCc	p.F322S	SIGLEC5_ENST00000222107.4_Missense_Mutation_p.F322S|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.F322S|SIGLEC5_ENST00000599649.1_Missense_Mutation_p.F322S|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.F322S			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	322	Ig-like C2-type 2.		F -> S (in dbSNP:rs2278831).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		AATTTGCAGGAAGCCCAGCGG	0.547													A|||	478	0.0954473	0.0983	0.0692	5008	,	,		17551	0.1419		0.0676	False		,,,				2504	0.091				p.F322S		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.T965C						PASS	.	A	SER/PHE	393,4013		13,367,1823	30.0	35.0	33.0		965	2.8	0.8	19	dbSNP_100	33	646,7954		28,590,3682	yes	missense	SIGLEC5	NM_003830.2	155	41,957,5505	GG,GA,AA		7.5116,8.9197,7.9886	benign	322/552	52131119	1039,11967	2203	4300	6503	SO:0001583	missense	8778	exon5			TGCAGGAAGCCCA	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.965T>C	19.37:g.52131119A>G	ENSP00000473238:p.Phe322Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	128	62	0.484375	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	233	0.10668498168498168	57	0.11585365853658537	41	0.1132596685082873	85	0.1486013986013986	50	0.06596306068601583	A	0.363	-0.938499	0.02340	0.089197	0.075116	ENSG00000105501	ENST00000222107;ENST00000429354	T;T	0.12879	2.64;2.64	3.88	2.84	0.33178	Immunoglobulin-like (1);	0.737030	0.11702	N	0.537799	T	0.00012	0.0000	N	0.00060	-2.34	0.45791	P	0.0013300000000000534	B	0.06786	0.001	B	0.01281	0.0	T	0.38222	-0.9671	9	0.02654	T	1	.	7.8326	0.29351	0.1179:0.0:0.8821:0.0	rs2278831;rs59229972;rs2278831	322	O15389	SIGL5_HUMAN	S	322	ENSP00000222107:F322S;ENSP00000415200:F322S	ENSP00000222107:F322S	F	-	2	0	SIGLEC5	56822931	0.891000	0.30450	0.836000	0.33094	0.029000	0.11900	0.734000	0.26101	0.968000	0.38212	-0.251000	0.11542	TTC	A|0.913;G|0.087	0.087	strong		0.547	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
SNX7	51375	hgsc.bcm.edu	37	1	99164434	99164434	+	Silent	SNP	G	G	A	rs6577322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:99164434G>A	ENST00000306121.3	+	6	1020	c.1011G>A	c.(1009-1011)gaG>gaA	p.E337E	SNX7_ENST00000370189.5_Silent_p.E273E|SNX7_ENST00000529992.1_Silent_p.E282E	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	273					apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TTGTACATGAGTACGTGCTTT	0.418													G|||	1090	0.217652	0.2088	0.2781	5008	,	,		16727	0.0595		0.2654	False		,,,				2504	0.3006				p.E337E		Atlas-SNP	.											.	SNX7	76	.	0			c.G1011A						PASS	.	G	,	964,3442	361.9+/-315.9	100,764,1339	108.0	95.0	99.0		1011,846	1.0	1.0	1	dbSNP_116	99	2519,6081	411.3+/-350.5	362,1795,2143	no	coding-synonymous,coding-synonymous	SNX7	NM_015976.4,NM_152238.3	,	462,2559,3482	AA,AG,GG		29.2907,21.8793,26.7799	,	337/452,282/397	99164434	3483,9523	2203	4300	6503	SO:0001819	synonymous_variant	51375	exon6			ACATGAGTACGTG	AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"""Sorting nexins"""	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.1011G>A	1.37:g.99164434G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	161	70	0.434783	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Silent	SNP	ENST00000306121.3	37	CCDS755.2																																																																																			G|0.762;A|0.238	0.238	strong		0.418	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2		
FAM135B	51059	hgsc.bcm.edu	37	8	139149406	139149406	+	Silent	SNP	G	G	A	rs6577876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:139149406G>A	ENST00000395297.1	-	19	4169	c.3999C>T	c.(3997-3999)ctC>ctT	p.L1333L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1333										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GTCTGTCTTTGAGGGCAGTTT	0.408										HNSCC(54;0.14)			G|||	984	0.196486	0.3101	0.2017	5008	,	,		18941	0.0139		0.2575	False		,,,				2504	0.1646				p.L1333L		Atlas-SNP	.											.	FAM135B	423	.	0			c.C3999T						PASS	.	G		1137,2587		177,783,902	153.0	151.0	152.0		3999	-0.4	0.9	8	dbSNP_116	152	2241,5981		295,1651,2165	no	coding-synonymous	FAM135B	NM_015912.3		472,2434,3067	AA,AG,GG		27.2561,30.5317,28.2772		1333/1407	139149406	3378,8568	1862	4111	5973	SO:0001819	synonymous_variant	51059	exon19			GTCTTTGAGGGCA	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.3999C>T	8.37:g.139149406G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	118	40	0.338983	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			G|0.777;A|0.223	0.223	strong		0.408	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
GLIS1	148979	hgsc.bcm.edu	37	1	54060248	54060248	+	Missense_Mutation	SNP	T	T	C	rs4307514	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:54060248T>C	ENST00000312233.2	-	3	894	c.328A>G	c.(328-330)Acg>Gcg	p.T110A		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						AGATCTCCCGTCAGAGGGGGG	0.657													C|||	1076	0.214856	0.1074	0.1599	5008	,	,		16057	0.1885		0.2962	False		,,,				2504	0.3425				p.T110A		Atlas-SNP	.											GLIS1,NS,carcinoma,0,1	GLIS1	52	1	0			c.A328G						PASS	.	C	ALA/THR	469,3885		39,391,1747	20.0	25.0	24.0		328	1.8	0.7	1	dbSNP_111	24	2634,5870		442,1750,2060	yes	missense	GLIS1	NM_147193.2	58	481,2141,3807	CC,CT,TT		30.9737,10.7717,24.1328	benign	110/621	54060248	3103,9755	2177	4252	6429	SO:0001583	missense	148979	exon3			CTCCCGTCAGAGG	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"""Zinc fingers, C2H2-type"""	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.328A>G	1.37:g.54060248T>C	ENSP00000309653:p.Thr110Ala	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	105	49	0.466667	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	469	0.21474358974358973	59	0.11991869918699187	66	0.18232044198895028	114	0.1993006993006993	230	0.3034300791556728	C	4.520	0.096571	0.08681	0.107717	0.309737	ENSG00000174332	ENST00000312233	T	0.09163	3.01	4.8	1.81	0.25067	.	0.384219	0.22553	N	0.058568	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47649	-0.9101	9	0.05436	T	0.98	.	5.5009	0.16829	0.0701:0.1254:0.5527:0.2518	rs4307514	110	Q8NBF1	GLIS1_HUMAN	A	110	ENSP00000309653:T110A	ENSP00000309653:T110A	T	-	1	0	GLIS1	53832836	0.999000	0.42202	0.685000	0.30070	0.006000	0.05464	0.857000	0.27831	0.041000	0.15688	-1.109000	0.02080	ACG	T|0.751;C|0.249	0.249	strong		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
OR4A15	81328	hgsc.bcm.edu	37	11	55135435	55135435	+	Missense_Mutation	SNP	C	C	T	rs1425193	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55135435C>T	ENST00000314706.3	+	1	76	c.76C>T	c.(76-78)Cct>Tct	p.P26S		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	26			P -> S (in dbSNP:rs1425193).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						GAGTCCAACACCTTCAGAAGA	0.398													.|||	1139	0.227436	0.0159	0.3141	5008	,	,		17645	0.3869		0.2823	False		,,,				2504	0.2311				p.P26S		Atlas-SNP	.											.	OR4A15	161	.	0			c.C76T						PASS	.	C	SER/PRO	275,4127	153.7+/-187.2	6,263,1932	62.0	58.0	59.0		76	-2.7	0.0	11	dbSNP_88	59	2281,6311	383.2+/-340.6	325,1631,2340	yes	missense	OR4A15	NM_001005275.1	74	331,1894,4272	TT,TC,CC		26.548,6.2472,19.6706	benign	26/345	55135435	2556,10438	2201	4296	6497	SO:0001583	missense	81328	exon1			CCAACACCTTCAG	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"""GPCR / Class A : Olfactory receptors"""	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.76C>T	11.37:g.55135435C>T	ENSP00000325065:p.Pro26Ser	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_001005275	Q6IFL4|Q96R65	Missense_Mutation	SNP	ENST00000314706.3	37	CCDS31500.1	564	0.25824175824175827	13	0.026422764227642278	122	0.3370165745856354	212	0.3706293706293706	217	0.2862796833773087	c	9.493	1.101203	0.20632	0.062472	0.26548	ENSG00000181958	ENST00000314706	T	0.37584	1.19	2.8	-2.65	0.06095	.	.	.	.	.	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	0.41752	-0.9491	8	0.07030	T	0.85	.	0.9311	0.01335	0.3917:0.2726:0.194:0.1417	rs1425193;rs59457328;rs1425193	26	Q8NGL6	O4A15_HUMAN	S	26	ENSP00000325065:P26S	ENSP00000325065:P26S	P	+	1	0	OR4A15	54892011	.	.	0.000000	0.03702	0.043000	0.13939	.	.	-0.268000	0.09312	0.492000	0.49549	CCT	C|0.778;T|0.222	0.222	strong		0.398	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275	
RGAG1	57529	hgsc.bcm.edu	37	X	109694685	109694685	+	Silent	SNP	T	T	A	rs2073787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:109694685T>A	ENST00000465301.2	+	3	1086	c.840T>A	c.(838-840)ggT>ggA	p.G280G	RGAG1_ENST00000540313.1_Silent_p.G280G	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	280										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CTTCTGGAGGTACATCACCCC	0.478													A|||	1412	0.37404	0.5915	0.2075	3775	,	,		16051	0.0129		0.333	False		,,,				2504	0.1411				p.G280G		Atlas-SNP	.											.	RGAG1	168	.	0			c.T840A						PASS	.	A		2908,927		948,591,421,93,150	141.0	119.0	127.0		840	2.7	0.0	X	dbSNP_96	127	2788,3940		422,1194,750,812,1122	no	coding-synonymous	RGAG1	NM_020769.2		1370,1785,1171,905,1272	AA,AT,A,TT,T		41.4388,24.1721,46.0759		280/1389	109694685	5696,4867	2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			TGGAGGTACATCA	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.840T>A	X.37:g.109694685T>A		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																			T|0.511;0|0.003	.	strong		0.478	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769	
NUP88	4927	hgsc.bcm.edu	37	17	5308377	5308377	+	Splice_Site	SNP	C	C	T	rs2301739	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5308377C>T	ENST00000573584.1	-	6	1553	c.1044G>A	c.(1042-1044)acG>acA	p.T348T		NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	348					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						CTGCACTTACCGTGTGGTCAT	0.428													C|||	1407	0.28095	0.0076	0.2579	5008	,	,		22297	0.5655		0.2316	False		,,,				2504	0.4243				p.T348T		Atlas-SNP	.											.	NUP88	47	.	0			c.G1044A						PASS	.	C		165,4241	108.6+/-147.0	0,165,2038	144.0	103.0	117.0		1044	-5.1	0.4	17	dbSNP_100	117	1622,6978	298.5+/-303.9	151,1320,2829	yes	coding-synonymous-near-splice	NUP88	NM_002532.4		151,1485,4867	TT,TC,CC		18.8605,3.7449,13.7398		348/742	5308377	1787,11219	2203	4300	6503	SO:0001630	splice_region_variant	4927	exon6			ACTTACCGTGTGG	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.1044+1G>A	17.37:g.5308377C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	191	102	0.534031	NM_002532	D3DTM2|Q9BWE5	Silent	SNP	ENST00000573584.1	37	CCDS11070.1																																																																																			C|0.806;T|0.194	0.194	strong		0.428	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	Silent
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713674	32713674	+	Silent	SNP	C	C	A	rs34357612	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32713674C>A	ENST00000374940.3	+	3	540	c.438C>A	c.(436-438)acC>acA	p.T146T		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	146	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	TCAACATCACCTGGCTGAGCA	0.502																																					p.T146T		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C438A						PASS	.						271.0	240.0	251.0					6																	32713674		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon3			CATCACCTGGCTG		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.438C>A	6.37:g.32713674C>A		Somatic	516	0	0		WXS	Illumina HiSeq	Phase_I	388	66	0.170103	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			C|0.886;A|0.114	0.114	strong		0.502	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
RP1L1	94137	hgsc.bcm.edu	37	8	10465190	10465190	+	Missense_Mutation	SNP	C	C	T	rs72494282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10465190C>T	ENST00000382483.3	-	4	6641	c.6418G>A	c.(6418-6420)Gag>Aag	p.E2140K		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2220	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				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)		GGCTGGGCCTCCCCTTCAGCC	0.617													-|||	851	0.169928	0.0991	0.134	5008	,	,		18207	0.4236		0.1113	False		,,,				2504	0.09				p.E2140K		Atlas-SNP	.											.	RP1L1	453	.	0			c.G6418A						PASS	.	T	LYS/GLU	414,3388		22,370,1509	156.0	171.0	166.0		6418	-0.5	0.0	8	dbSNP_130	166	1097,7115		77,943,3086	yes	missense	RP1L1	NM_178857.5	56	99,1313,4595	TT,TC,CC		13.3585,10.889,12.577	benign	2140/2401	10465190	1511,10503	1901	4106	6007	SO:0001583	missense	94137	exon4			GGGCCTCCCCTTC	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.6418G>A	8.37:g.10465190C>T	ENSP00000371923:p.Glu2140Lys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	141	65	0.460993	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	414	0.18956043956043955	44	0.08943089430894309	61	0.1685082872928177	229	0.40034965034965037	80	0.10554089709762533	-	5.627	0.300305	0.10678	0.10889	0.133585	ENSG00000183638	ENST00000382483	T	0.07908	3.15	1.74	-0.491	0.12045	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.33549	0.417	B	0.19666	0.026	T	0.48115	-0.9063	8	0.18276	T	0.48	.	6.3097	0.21159	0.0:0.5605:0.0:0.4395	.	2140	A6NKC6	.	K	2140	ENSP00000371923:E2140K	ENSP00000371923:E2140K	E	-	1	0	RP1L1	10502600	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.033000	0.12246	-0.382000	0.07870	-0.336000	0.08194	GAG	C|0.835;T|0.165	0.165	strong		0.617	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
MAP1A	4130	hgsc.bcm.edu	37	15	43818079	43818079	+	Missense_Mutation	SNP	G	G	A	rs62020612	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43818079G>A	ENST00000300231.5	+	4	4858	c.4408G>A	c.(4408-4410)Gcc>Acc	p.A1470T	MAP1A_ENST00000382031.1_Missense_Mutation_p.A1708T|MAP1A_ENST00000399453.1_Missense_Mutation_p.A1470T			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1470				A -> T (in Ref. 4; AAD00355). {ECO:0000305}.	microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GAAGGACAAGGCCCTGGAACC	0.428													G|||	690	0.13778	0.2005	0.1124	5008	,	,		20611	0.001		0.1918	False		,,,				2504	0.1564				p.A1470T		Atlas-SNP	.											MAP1A,colon,carcinoma,0,1	MAP1A	189	1	0			c.G4408A						PASS	.	G	THR/ALA	687,3045		70,547,1249	89.0	89.0	89.0		4408	-0.4	0.0	15	dbSNP_129	89	1570,6626		145,1280,2673	yes	missense	MAP1A	NM_002373.5	58	215,1827,3922	AA,AG,GG		19.1557,18.4084,18.9219	benign	1470/2804	43818079	2257,9671	1866	4098	5964	SO:0001583	missense	4130	exon4			GACAAGGCCCTGG	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.4408G>A	15.37:g.43818079G>A	ENSP00000300231:p.Ala1470Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	22	0.338462	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	309	0.14148351648351648	113	0.22967479674796748	46	0.1270718232044199	0	0.0	150	0.19788918205804748	G	12.15	1.852828	0.32699	0.184084	0.191557	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.21191	4.28;2.02;2.02	3.79	-0.403	0.12400	.	.	.	.	.	T	0.00012	0.0000	L	0.45228	1.405	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41342	-0.9514	8	0.18276	T	0.48	7.5049	9.2146	0.37339	0.403:0.0:0.597:0.0	rs62020612	1470	P78559	MAP1A_HUMAN	T	1708;1470;1470	ENSP00000371462:A1708T;ENSP00000382380:A1470T;ENSP00000300231:A1470T	ENSP00000300231:A1470T	A	+	1	0	MAP1A	41605371	0.000000	0.05858	0.000000	0.03702	0.573000	0.36030	-0.485000	0.06520	-0.182000	0.10602	0.563000	0.77884	GCC	G|0.831;A|0.169	0.169	strong		0.428	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792514	8792514	+	Silent	SNP	G	G	A	rs394811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8792514G>A	ENST00000447110.1	-	9	961	c.837C>T	c.(835-837)caC>caT	p.H279H	PIK3R5_ENST00000581552.1_Silent_p.H279H|PIK3R5_ENST00000584803.1_Silent_p.H279H	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	279				AKTLAELEDIFTETAEAQELASGIGDAAEARRWLRTKLQAV GEKAGFPGVLDTAKPGKLHTIPIPVARCYTYSWSQDS -> TLQNQGSSIPSPSLSPGATPTAGARTALTSCRKSCSRNRSC SSQGSWEMMKRRKRRRRRWRRTWKLMGTVPREIPCSP (in Ref. 6; AAW63122). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						TGGGGATGGTGTGGAGCTTCC	0.602													A|||	2217	0.442692	0.7254	0.4049	5008	,	,		19432	0.1786		0.3907	False		,,,				2504	0.4131				p.H279H	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.C837T						PASS	.	A	,	2908,1498	477.7+/-358.0	966,976,261	77.0	70.0	72.0		837,837	-2.2	0.9	17	dbSNP_80	72	3629,4971	624.8+/-397.6	749,2131,1420	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	1715,3107,1681	AA,AG,GG		42.1977,33.9991,49.7386	,	279/881,279/881	8792514	6537,6469	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon9			GATGGTGTGGAGC	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.837C>T	17.37:g.8792514G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			G|0.527;A|0.473	0.473	strong		0.602	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
P2RX7	5027	hgsc.bcm.edu	37	12	121600253	121600253	+	Missense_Mutation	SNP	T	T	C	rs208294	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121600253T>C	ENST00000546057.1	+	5	606	c.463T>C	c.(463-465)Tat>Cat	p.Y155H	P2RX7_ENST00000328963.5_Intron|P2RX7_ENST00000541446.1_5'UTR|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_Missense_Mutation_p.Y65H|P2RX7_ENST00000377162.2_Missense_Mutation_p.Y155H	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	155			Y -> H (in dbSNP:rs208294). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15896293, ECO:0000269|PubMed:9038151, ECO:0000269|PubMed:9826911}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGTGTAGTGTATGAAGGGAA	0.557													T|||	2654	0.529952	0.6944	0.3905	5008	,	,		17916	0.4137		0.5557	False		,,,				2504	0.5				p.Y155H		Atlas-SNP	.											.	P2RX7	53	.	0			c.T463C	GRCh37	CM056028	P2RX7	M	rs208294	PASS	.	T	HIS/TYR	3046,1360	685.0+/-404.5	1048,950,205	95.0	88.0	91.0		463	5.6	0.0	12	dbSNP_79	91	4761,3839	609.5+/-395.5	1292,2177,831	yes	missense	P2RX7	NM_002562.5	83	2340,3127,1036	CC,CT,TT		44.6395,30.867,39.9739	probably-damaging	155/596	121600253	7807,5199	2203	4300	6503	SO:0001583	missense	5027	exon5			GTAGTGTATGAAG	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.463T>C	12.37:g.121600253T>C	ENSP00000442349:p.Tyr155His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	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	1175	0.538003663003663	367	0.7459349593495935	153	0.42265193370165743	232	0.40559440559440557	423	0.558047493403694	T	17.36	3.368779	0.61624	0.69133	0.553605	ENSG00000089041	ENST00000546057;ENST00000377162;ENST00000535250	T;T;T	0.04317	3.65;3.65;3.65	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000010	T	0.00012	0.0000	M	0.81497	2.545	0.09310	P	1.0	D;D	0.69078	0.988;0.997	P;D	0.67103	0.808;0.949	T	0.02813	-1.1107	9	0.45353	T	0.12	-15.6695	13.6886	0.62531	0.0:0.0:0.0:1.0	rs208294;rs485653;rs2230909;rs17845317;rs17858156;rs61592120;rs208294	65;155	F5H7E8;Q99572	.;P2RX7_HUMAN	H	155;155;65	ENSP00000442349:Y155H;ENSP00000366367:Y155H;ENSP00000442572:Y65H	ENSP00000366367:Y155H	Y	+	1	0	P2RX7	120084636	1.000000	0.71417	0.015000	0.15790	0.583000	0.36354	6.416000	0.73332	2.121000	0.65114	0.533000	0.62120	TAT	T|0.429;C|0.571	0.571	strong		0.557	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
COL14A1	7373	hgsc.bcm.edu	37	8	121357700	121357700	+	Missense_Mutation	SNP	C	C	G	rs137867605		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:121357700C>G	ENST00000297848.3	+	45	5245	c.4975C>G	c.(4975-4977)Cct>Gct	p.P1659A	COL14A1_ENST00000247781.3_Missense_Mutation_p.P1564A|COL14A1_ENST00000309791.4_Missense_Mutation_p.P1659A	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)			TCCTGGGGAGCCTGGGAGGCC	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		16125	0.0		0.001	False		,,,				2504	0.0				p.P1659A		Atlas-SNP	.											.	COL14A1	292	.	0			c.C4975G						PASS	.	C	ALA/PRO	1,4405	2.1+/-5.4	0,1,2202	57.0	56.0	56.0		4975	5.8	1.0	8	dbSNP_134	56	10,8590	7.7+/-29.5	0,10,4290	yes	missense	COL14A1	NM_021110.1	27	0,11,6492	GG,GC,CC		0.1163,0.0227,0.0846	probably-damaging	1659/1797	121357700	11,12995	2203	4300	6503	SO:0001583	missense	7373	exon45			GGGGAGCCTGGGA		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.4975C>G	8.37:g.121357700C>G	ENSP00000297848:p.Pro1659Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	124	73	0.58871	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712324	0.89112	2.27E-4	0.001163	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.93906	-3.3;-3.3;-3.3;-3.31	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.95962	0.8685	M	0.62016	1.91	0.80722	D	1	D	0.61697	0.99	D	0.77004	0.989	D	0.94953	0.8101	10	0.39692	T	0.17	.	17.7738	0.88501	0.0:1.0:0.0:0.0	.	1659	Q05707	COEA1_HUMAN	A	1659;1659;1564;6	ENSP00000311809:P1659A;ENSP00000297848:P1659A;ENSP00000247781:P1564A;ENSP00000403640:P6A	ENSP00000247781:P1564A	P	+	1	0	COL14A1	121426881	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.773000	0.55333	2.736000	0.93811	0.555000	0.69702	CCT	C|0.999;G|0.001	0.001	strong		0.637	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
CCDC24	149473	hgsc.bcm.edu	37	1	44461822	44461822	+	Missense_Mutation	SNP	C	C	T	rs2301983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:44461822C>T	ENST00000372318.3	+	9	1085	c.914C>T	c.(913-915)gCc>gTc	p.A305V	SLC6A9_ENST00000372307.3_Intron|SLC6A9_ENST00000372306.3_Intron	NM_152499.1	NP_689712.1	Q8N4L8	CCD24_HUMAN	coiled-coil domain containing 24	305										endometrium(3)|large_intestine(2)|lung(3)|stomach(1)	9	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				GCACCCCAAGCCCCAGCCTGA	0.672													C|||	284	0.0567093	0.0113	0.0418	5008	,	,		17118	0.1141		0.0417	False		,,,				2504	0.0849				p.A305V		Atlas-SNP	.											.	CCDC24	22	.	0			c.C914T						PASS	.	C	VAL/ALA	99,4287		1,97,2095	17.0	19.0	19.0		914	3.7	0.6	1	dbSNP_100	19	335,8261		7,321,3970	yes	missense	CCDC24	NM_152499.1	64	8,418,6065	TT,TC,CC		3.8972,2.2572,3.3431	possibly-damaging	305/308	44461822	434,12548	2193	4298	6491	SO:0001583	missense	149473	exon9			CCCAAGCCCCAGC		CCDS507.1	1p34.1	2008-02-05			ENSG00000159214	ENSG00000159214			28688	protein-coding gene	gene with protein product						12477932	Standard	NM_152499		Approved	MGC45441	uc001clj.3	Q8N4L8	OTTHUMG00000008299	ENST00000372318.3:c.914C>T	1.37:g.44461822C>T	ENSP00000361392:p.Ala305Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_152499	Q6RWT2	Missense_Mutation	SNP	ENST00000372318.3	37	CCDS507.1	118	0.05402930402930403	11	0.022357723577235773	15	0.04143646408839779	64	0.11188811188811189	28	0.036939313984168866	C	19.05	3.751871	0.69533	0.022572	0.038972	ENSG00000159214	ENST00000372318	.	.	.	4.62	3.69	0.42338	.	0.170406	0.27122	N	0.020830	T	0.00666	0.0022	L	0.29908	0.895	0.24899	N	0.992112	D;D	0.60160	0.987;0.965	P;P	0.51193	0.662;0.548	T	0.00448	-1.1733	9	0.87932	D	0	-24.273	9.4507	0.38725	0.0:0.8988:0.0:0.1012	rs2301983;rs57155160	269;305	Q8N4L8-2;Q8N4L8	.;CCD24_HUMAN	V	305	.	ENSP00000361392:A305V	A	+	2	0	CCDC24	44234409	0.059000	0.20769	0.611000	0.29010	0.013000	0.08279	0.417000	0.21214	2.282000	0.76494	0.514000	0.50259	GCC	C|0.956;T|0.044	0.044	strong		0.672	CCDC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022865.1	NM_152499	
CEP131	22994	hgsc.bcm.edu	37	17	79170578	79170578	+	Missense_Mutation	SNP	C	C	T	rs4613097	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79170578C>T	ENST00000269392.4	-	15	2078	c.1831G>A	c.(1831-1833)Gcg>Acg	p.A611T	AZI1_ENST00000575907.1_Missense_Mutation_p.A611T|AZI1_ENST00000374782.3_Missense_Mutation_p.A608T|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000450824.2_Missense_Mutation_p.A608T	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		611					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			CGGCTCAGCGCCTTCTCTGTC	0.697													C|||	558	0.111422	0.1672	0.0231	5008	,	,		12656	0.1379		0.0577	False		,,,				2504	0.1268				p.A608T		Atlas-SNP	.											AZI1_ENST00000450824,NS,carcinoma,+2,2	AZI1	145	2	0			c.G1822A						scavenged	.	C	THR/ALA,THR/ALA	618,3750		42,534,1608	23.0	22.0	22.0		1822,1822	4.8	0.2	17	dbSNP_111	22	454,8114		15,424,3845	yes	missense,missense	AZI1	NM_001009811.2,NM_014984.2	58,58	57,958,5453	TT,TC,CC		5.2988,14.1484,8.287	benign,benign	608/1045,608/1081	79170578	1072,11864	2184	4284	6468	SO:0001583	missense	22994	exon15			TCAGCGCCTTCTC																												ENST00000269392.4:c.1831G>A	17.37:g.79170578C>T	ENSP00000269392:p.Ala611Thr	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37		215	0.09844322344322344	89	0.18089430894308944	10	0.027624309392265192	79	0.1381118881118881	37	0.048812664907651716	C	19.62	3.861451	0.71949	0.141484	0.052988	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.29397	1.57;1.57;1.57	4.8	4.8	0.61643	.	0.055829	0.64402	D	0.000001	T	0.00039	0.0001	N	0.17474	0.49	0.28801	P	0.898769	P;B;P;B	0.41848	0.763;0.237;0.692;0.1	B;B;B;B	0.41691	0.288;0.054;0.364;0.041	T	0.23476	-1.0187	9	0.27082	T	0.32	-20.1239	17.6263	0.88095	0.0:1.0:0.0:0.0	rs4613097	608;611;608;608	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	T	608;608;611	ENSP00000393583:A608T;ENSP00000363914:A608T;ENSP00000269392:A611T	ENSP00000269392:A611T	A	-	1	0	AZI1	76785173	1.000000	0.71417	0.214000	0.23707	0.964000	0.63967	7.084000	0.76866	2.483000	0.83821	0.313000	0.20887	GCG	C|0.909;T|0.091	0.091	strong		0.697	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
TCP10L2	401285	hgsc.bcm.edu	37	6	167592605	167592605	+	Missense_Mutation	SNP	T	T	G	rs200932131	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167592605T>G	ENST00000366832.2	+	6	895	c.764T>G	c.(763-765)gTt>gGt	p.V255G		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	255										endometrium(1)|kidney(2)|lung(3)	6						GCAGCCGGAGTTGCTGGTGAG	0.582																																					p.V255G		Atlas-SNP	.											.	TCP10L2	41	.	0			c.T764G						PASS	.																																			SO:0001583	missense	401285	exon6			CCGGAGTTGCTGG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.764T>G	6.37:g.167592605T>G	ENSP00000355797:p.Val255Gly	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	60	20	0.333333	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	.	.	.	.	.	.	.	.	.	.	N	0.018	-1.471236	0.01044	.	.	ENSG00000166984	ENST00000366832	T	0.21031	2.03	.	.	.	.	.	.	.	.	T	0.01254	0.0041	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41662	-0.9496	7	0.33141	T	0.24	.	.	.	.	.	255	B9ZVM9	TCP2L_HUMAN	G	255	ENSP00000355797:V255G	ENSP00000283507:V255G	V	+	2	0	TCP10L2	167512595	0.001000	0.12720	0.001000	0.08648	0.019000	0.09904	-0.587000	0.05780	-1.946000	0.01035	-2.069000	0.00389	GTT	T|0.926;G|0.074	0.074	strong		0.582	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
DENND1C	79958	hgsc.bcm.edu	37	19	6467910	6467910	+	Missense_Mutation	SNP	T	T	C	rs34135887|rs35173535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6467910T>C	ENST00000381480.2	-	23	2123	c.2011A>G	c.(2011-2013)Aaa>Gaa	p.K671E	DENND1C_ENST00000543576.1_Missense_Mutation_p.K627E	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	671					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						GGAGAGGGTTTGGGGTCCCCC	0.572													C|||	88	0.0175719	0.0182	0.0259	5008	,	,		15902	0.0		0.0249	False		,,,				2504	0.0215				p.K671E		Atlas-SNP	.											.	DENND1C	93	.	0			c.A2011G						PASS	.	C	GLU/LYS	83,3813		1,81,1866	43.0	44.0	44.0		2011	-4.1	0.0	19	dbSNP_126	44	203,8061		3,197,3932	yes	missense	DENND1C	NM_024898.2	56	4,278,5798	CC,CT,TT		2.4564,2.1304,2.352	benign	671/802	6467910	286,11874	1948	4132	6080	SO:0001583	missense	79958	exon23			AGGGTTTGGGGTC	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.2011A>G	19.37:g.6467910T>C	ENSP00000370889:p.Lys671Glu	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	164	78	0.47561	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	38	0.0173992673992674	10	0.02032520325203252	8	0.022099447513812154	0	0.0	20	0.026385224274406333	C	2.014	-0.426414	0.04701	0.021304	0.024564	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.12361	2.86;2.69	3.86	-4.14	0.03892	.	22.285500	0.00166	N	0.000000	T	0.01454	0.0047	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30909	-0.9962	10	0.02654	T	1	3.2145	5.2644	0.15591	0.0:0.245:0.2821:0.4729	rs35173535	671	Q8IV53	DEN1C_HUMAN	E	671;627	ENSP00000370889:K671E;ENSP00000437805:K627E	ENSP00000370889:K671E	K	-	1	0	DENND1C	6418910	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-2.672000	0.00843	-0.871000	0.04042	-1.923000	0.00514	AAA	T|0.977;C|0.023	0.023	strong		0.572	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573956	140573956	+	Missense_Mutation	SNP	G	G	A	rs554525456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140573956G>A	ENST00000239446.4	+	1	2015	c.1831G>A	c.(1831-1833)Gag>Aag	p.E611K		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	611	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			CAAGGCCACGGAGCCCGGGCT	0.706													G|||	11	0.00219649	0.0	0.0014	5008	,	,		15886	0.0		0.005	False		,,,				2504	0.0051				p.E611K		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G1831A						PASS	.						6.0	8.0	7.0					5																	140573956		1542	3066	4608	SO:0001583	missense	56126	exon1			GCCACGGAGCCCG	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.1831G>A	5.37:g.140573956G>A	ENSP00000239446:p.Glu611Lys	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	g	19.21	3.783989	0.70222	.	.	ENSG00000120324	ENST00000239446	T	0.53857	0.6	3.34	3.34	0.38264	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.72244	0.3436	M	0.79475	2.455	0.32066	N	0.595055	D	0.89917	1.0	D	0.79108	0.992	T	0.78425	-0.2209	9	0.87932	D	0	.	14.8686	0.70437	0.0:0.0:1.0:0.0	.	611	Q9UN67	PCDBA_HUMAN	K	611	ENSP00000239446:E611K	ENSP00000239446:E611K	E	+	1	0	PCDHB10	140554140	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	5.119000	0.64679	1.884000	0.54569	0.479000	0.44913	GAG	.	.	none		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
NLRP1	22861	hgsc.bcm.edu	37	17	5442790	5442790	+	Missense_Mutation	SNP	C	C	T	rs61754791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5442790C>T	ENST00000572272.1	-	7	2814	c.2815G>A	c.(2815-2817)Gtg>Atg	p.V939M	NLRP1_ENST00000354411.3_Missense_Mutation_p.V939M|NLRP1_ENST00000269280.4_Missense_Mutation_p.V939M|NLRP1_ENST00000262467.5_Missense_Mutation_p.V939M|NLRP1_ENST00000345221.3_Missense_Mutation_p.V939M|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Missense_Mutation_p.V939M			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	939					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				AGCAGTCGCACGCCAACGTCA	0.622													C|||	58	0.0115815	0.0318	0.0058	5008	,	,		18777	0.0		0.0109	False		,,,				2504	0.001				p.V939M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G2815A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	105,4301	82.9+/-121.4	3,99,2101	79.0	62.0	67.0		2815,2815,2815,2815,2815	0.5	0.0	17	dbSNP_129	67	134,8466	67.7+/-130.1	2,130,4168	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	5,229,6269	TT,TC,CC		1.5581,2.3831,1.8376	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	939/1376,939/1430,939/1474,939/1444,939/1400	5442790	239,12767	2203	4300	6503	SO:0001583	missense	22861	exon7			GTCGCACGCCAAC	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2815G>A	17.37:g.5442790C>T	ENSP00000460475:p.Val939Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	25	0.373134	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	26	0.011904761904761904	14	0.028455284552845527	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.12	2.440438	0.43326	0.023831	0.015581	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	3.7	0.477	0.16784	.	0.224064	0.22878	N	0.054551	T	0.10680	0.0261	M	0.74546	2.27	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.997;1.0	D;D;D;D;P;D	0.91635	0.912;0.999;0.997;0.982;0.896;0.982	T	0.03641	-1.1017	10	0.87932	D	0	.	2.8517	0.05560	0.2212:0.5366:0.0:0.2423	rs61754791	205;939;939;939;939;939	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	939;939;939;939;939;205	ENSP00000442029:V939M;ENSP00000262467:V939M;ENSP00000269280:V939M;ENSP00000346390:V939M;ENSP00000324366:V939M	ENSP00000262467:V939M	V	-	1	0	NLRP1	5383514	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	0.004000	0.13106	0.155000	0.19261	0.650000	0.86243	GTG	A|0.000;C|0.986;T|0.014	0.014	strong		0.622	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A	rs114397261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057635G>A	ENST00000380095.1	+	1	363	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						tgtctgctgtgtgcccgtctg	0.632													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		18765	0.002		0.001	False		,,,				2504	0.0112				p.V101M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G301A						PASS	.	A	,MET/VAL	438,3968		76,286,1841	130.0	123.0	125.0		,301	-1.7	0.0	21	dbSNP_132	125	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	76,288,6137	AA,AG,GG		0.0233,9.941,3.3841	,possibly-damaging	,101/252	46057635	440,12562	2203	4298	6501	SO:0001583	missense	353333	exon1			TGCTGTGTGCCCG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.301G>A	21.37:g.46057635G>A	ENSP00000369438:p.Val101Met	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	145	85	0.586207	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	1.285	-0.609223	0.03690	0.09941	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01430	4.9	2.86	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.09310	N	1	B	0.26195	0.144	B	0.34452	0.183	T	0.44128	-0.9348	9	0.44086	T	0.13	.	9.7593	0.40522	0.4446:0.0:0.5554:0.0	.	101	P60014	KR10A_HUMAN	M	101	ENSP00000369438:V101M	ENSP00000369438:V101M	V	+	1	0	KRTAP10-10	44882063	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.140000	0.10342	-1.728000	0.01366	-2.786000	0.00116	GTG	G|0.928;A|0.072	0.072	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
NLRP8	126205	hgsc.bcm.edu	37	19	56499279	56499279	+	Nonstop_Mutation	SNP	G	G	C	rs306457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56499279G>C	ENST00000291971.3	+	10	3218	c.3147G>C	c.(3145-3147)taG>taC	p.*1049Y	NLRP8_ENST00000590542.1_Nonstop_Mutation_p.*1030Y	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	0					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)		TTAATCCTTAGGCCGTCCAGT	0.488													g|||	3629	0.724641	0.7163	0.7767	5008	,	,		19038	0.623		0.7406	False		,,,				2504	0.7873				p.X1049Y		Atlas-SNP	.											.	NLRP8	225	.	0			c.G3147C						PASS	.	C	TYR/stop	3204,1202	709.2+/-407.7	1172,860,171	93.0	79.0	84.0		3147	0.4	0.0	19	dbSNP_79	84	6333,2267	707.6+/-405.6	2343,1647,310	yes	stop-lost	NLRP8	NM_176811.2		3515,2507,481	CC,CG,GG		26.3605,27.281,26.6723		1049/1049	56499279	9537,3469	2203	4300	6503	SO:0001578	stop_lost	126205	exon10			TCCTTAGGCCGTC	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.3147G>C	19.37:g.56499279G>C	ENSP00000291971:p.*1049Tyrext*10	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	75	25	0.333333	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	1594	0.7298534798534798	362	0.7357723577235772	284	0.7845303867403315	367	0.6416083916083916	581	0.7664907651715039	g	0.020	-1.447930	0.01080	0.72719	0.736395	ENSG00000179709	ENST00000291971	.	.	.	1.44	0.372	0.16173	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.8402	0.29393	0.0:0.7299:0.2701:0.0	rs306457;rs57526396;rs306457	.	.	.	Y	1049	.	.	X	+	3	2	NLRP8	61191091	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.284000	0.02793	-0.160000	0.11002	-2.828000	0.00107	TAG	G|0.274;C|0.726	0.726	strong		0.488	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ARSF	416	hgsc.bcm.edu	37	X	3002687	3002687	+	Silent	SNP	A	A	G	rs5983003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3002687A>G	ENST00000381127.1	+	6	1031	c.810A>G	c.(808-810)gaA>gaG	p.E270E	ARSF_ENST00000537104.1_Silent_p.E270E|ARSF_ENST00000359361.2_Silent_p.E270E	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	270					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)				TGGTGAAGGAAGCGATTTCCT	0.438													g|||	2996	0.793642	0.5998	0.5533	3775	,	,		13687	0.6935		0.4811	False		,,,				2504	0.6503				p.E270E		Atlas-SNP	.											.	ARSF	97	.	0			c.A810G						PASS	.	G	,,	2974,861		989,577,419,66,152	48.0	42.0	44.0		810,810,810	1.1	0.0	X	dbSNP_114	44	4467,2261		1050,1116,1251,262,621	no	coding-synonymous,coding-synonymous,coding-synonymous	ARSF	NM_001201538.1,NM_001201539.1,NM_004042.4	,,	2039,1693,1670,328,773	GG,GA,G,AA,A		33.6058,22.4511,29.556	,,	270/591,270/591,270/591	3002687	7441,3122	2203	4300	6503	SO:0001819	synonymous_variant	416	exon6			GAAGGAAGCGATT	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.810A>G	X.37:g.3002687A>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_004042	Q8TCC5	Silent	SNP	ENST00000381127.1	37	CCDS14123.1																																																																																			A|0.253;0|0.015	.	strong		0.438	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
MAGEA1	4100	hgsc.bcm.edu	37	X	152482796	152482796	+	Missense_Mutation	SNP	C	C	T	rs2008144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:152482796C>T	ENST00000356661.5	-	3	433	c.215G>A	c.(214-216)cGa>cAa	p.R72Q		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	72			R -> Q (in dbSNP:rs2008144).		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)					TTGCCTCTGTCGAGTGAAGTT	0.587													c|||	707	0.187285	0.1044	0.2032	3775	,	,		13088	0.3403		0.0378	False		,,,				2504	0.0481				p.R72Q		Atlas-SNP	.											.	MAGEA1	57	.	0			c.G215A						PASS	.	C	GLN/ARG	571,3264		34,414,89,1184,482	85.0	87.0	86.0		215	-2.4	0.0	X	dbSNP_92	86	327,6401		7,217,96,2204,1776	yes	missense	MAGEA1	NM_004988.4	43	41,631,185,3388,2258	TT,TC,T,CC,C		4.8603,14.8892,8.5014	possibly-damaging	72/310	152482796	898,9665	2203	4300	6503	SO:0001583	missense	4100	exon3			CTCTGTCGAGTGA		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.215G>A	X.37:g.152482796C>T	ENSP00000349085:p.Arg72Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_004988	B2RC81|O00346	Missense_Mutation	SNP	ENST00000356661.5	37	CCDS14720.1	346	0.20855937311633513	45	0.09955752212389381	50	0.16025641025641027	120	0.26905829596412556	19	0.025333333333333333	C	4.922	0.171293	0.09391	0.148892	0.048603	ENSG00000198681	ENST00000356661	T	0.04194	3.68	1.19	-2.38	0.06622	Melanoma associated antigen, MAGE, N-terminal (1);	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P	0.47910	0.902	B	0.42738	0.396	T	0.33752	-0.9856	9	0.30078	T	0.28	.	0.4318	0.00472	0.1978:0.2504:0.3123:0.2396	rs2008144;rs2008144	72	P43355	MAGA1_HUMAN	Q	72	ENSP00000349085:R72Q	ENSP00000349085:R72Q	R	-	2	0	MAGEA1	152135990	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.253000	0.01184	-1.902000	0.01094	-2.856000	0.00102	CGA	0|0.027;T|0.150	0.150	strong		0.587	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
PCDHB6	56130	hgsc.bcm.edu	37	5	140531091	140531091	+	Missense_Mutation	SNP	C	C	T	rs145637479	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140531091C>T	ENST00000231136.1	+	1	1253	c.1253C>T	c.(1252-1254)aCt>aTt	p.T418I	PCDHB6_ENST00000543635.1_Missense_Mutation_p.T282I	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	418	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)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TACAACATCACTATCACGGTC	0.522													C|||	10	0.00199681	0.0	0.0014	5008	,	,		19649	0.0		0.005	False		,,,				2504	0.0041				p.T418I		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C1253T						PASS	.	C	ILE/THR	3,4403	6.2+/-15.9	0,3,2200	122.0	122.0	122.0		1253	2.8	1.0	5	dbSNP_134	122	35,8565	24.6+/-71.5	0,35,4265	yes	missense	PCDHB6	NM_018939.2	89	0,38,6465	TT,TC,CC		0.407,0.0681,0.2922	benign	418/795	140531091	38,12968	2203	4300	6503	SO:0001583	missense	56130	exon1			ACATCACTATCAC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1253C>T	5.37:g.140531091C>T	ENSP00000231136:p.Thr418Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	8.038	0.763255	0.15914	6.81E-4	0.00407	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.03358	3.96;3.96	4.59	2.8	0.32819	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.08537	0.0212	M	0.90198	3.095	0.33677	D	0.611678	B	0.26635	0.155	B	0.39935	0.314	T	0.00852	-1.1540	9	0.72032	D	0.01	.	7.6304	0.28236	0.0:0.695:0.1449:0.1601	.	418	Q9Y5E3	PCDB6_HUMAN	I	282;418;203	ENSP00000438466:T282I;ENSP00000231136:T418I	ENSP00000231136:T418I	T	+	2	0	PCDHB6	140511275	0.001000	0.12720	0.983000	0.44433	0.020000	0.10135	0.191000	0.17076	0.474000	0.27392	-0.254000	0.11334	ACT	C|0.997;T|0.003	0.003	strong		0.522	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
CDC45	8318	hgsc.bcm.edu	37	22	19468514	19468514	+	Silent	SNP	T	T	C	rs13447189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19468514T>C	ENST00000407835.1	+	4	406	c.150T>C	c.(148-150)gtT>gtC	p.V50V	UFD1L_ENST00000399523.1_5'Flank|CDC45_ENST00000263201.1_Silent_p.V50V|CDC45_ENST00000404724.3_Silent_p.V50V|CDC45_ENST00000483431.1_3'UTR|UFD1L_ENST00000263202.10_5'Flank|UFD1L_ENST00000484101.1_5'Flank|UFD1L_ENST00000360834.4_5'Flank|CDC45_ENST00000437685.2_Silent_p.V50V			O75419	CDC45_HUMAN	cell division cycle 45	50					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						ATACGCTGGTTCCAGTTTCTG	0.398													T|||	247	0.0493211	0.0023	0.0389	5008	,	,		20562	0.0179		0.0348	False		,,,				2504	0.1677				p.V50V		Atlas-SNP	.											.	CDC45	48	.	0			c.T150C						PASS	.	T	,,	44,4362	46.0+/-80.4	0,44,2159	112.0	102.0	105.0		150,150,150	1.8	1.0	22	dbSNP_121	105	468,8132	137.9+/-194.8	16,436,3848	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC45	NM_001178010.1,NM_001178011.1,NM_003504.3	,,	16,480,6007	CC,CT,TT		5.4419,0.9986,3.9366	,,	50/599,50/521,50/567	19468514	512,12494	2203	4300	6503	SO:0001819	synonymous_variant	8318	exon3			GCTGGTTCCAGTT	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"""human CDC45"""	603465	"""CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like"", ""CDC45 cell division cycle 45-like (S. cerevisiae)"", ""cell division cycle 45 homolog (S. cerevisiae)"""	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.150T>C	22.37:g.19468514T>C		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_003504	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Silent	SNP	ENST00000407835.1	37	CCDS13762.1																																																																																			T|0.963;C|0.037	0.037	strong		0.398	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504	
NLRP12	91662	hgsc.bcm.edu	37	19	54327313	54327313	+	Missense_Mutation	SNP	C	C	A	rs34436714	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54327313C>A	ENST00000324134.6	-	1	284	c.116G>T	c.(115-117)gGa>gTa	p.G39V	NLRP12_ENST00000535162.1_Missense_Mutation_p.G39V|NLRP12_ENST00000351894.4_Missense_Mutation_p.G39V|NLRP12_ENST00000391773.1_Missense_Mutation_p.G39V|NLRP12_ENST00000354278.3_Missense_Mutation_p.G39V|NLRP12_ENST00000391775.3_Missense_Mutation_p.G39V|NLRP12_ENST00000391772.1_Missense_Mutation_p.G39V|NLRP12_ENST00000345770.5_Missense_Mutation_p.G39V	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	39	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.		G -> V (in dbSNP:rs34436714).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to cytokine stimulus (GO:0071345)|dendritic cell migration (GO:0036336)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of signal transduction (GO:0009968)|negative regulation of Toll signaling pathway (GO:0045751)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of MHC class I biosynthetic process (GO:0045345)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of interleukin-18 biosynthetic process (GO:0045381)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(36)|ovary(5)|pancreas(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	80	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.026)		CTTGCCTTCTCCCAGCTCTGT	0.607													C|||	1280	0.255591	0.3858	0.2291	5008	,	,		16894	0.1776		0.2008	False		,,,				2504	0.2352				p.K39M		Atlas-SNP	.											.	NLRP12	236	.	0			c.A116T						PASS	.	C	VAL/GLY	1619,2787	499.3+/-364.4	299,1021,883	62.0	58.0	60.0		116	4.5	0.1	19	dbSNP_126	60	1851,6749	329.8+/-318.9	195,1461,2644	yes	missense	NLRP12	NM_144687.2	109	494,2482,3527	AA,AC,CC		21.5233,36.7453,26.68	probably-damaging	39/1062	54327313	3470,9536	2203	4300	6503	SO:0001583	missense	91662	exon1			CCTTCTCCCAGCT	AY095146	CCDS12864.1, CCDS62784.1, CCDS62785.1	19q13.42	2014-09-17	2006-12-08	2006-12-08	ENSG00000142405	ENSG00000142405		"""Nucleotide-binding domain and leucine rich repeat containing"""	22938	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 12"""	609648	"""NACHT, leucine rich repeat and PYD containing 12"""	NALP12		12563287, 12019269	Standard	NM_001277129		Approved	RNO2, PYPAF7, Monarch1, PAN6, CLR19.3	uc002qcj.5	P59046	OTTHUMG00000060776	ENST00000324134.6:c.116G>T	19.37:g.54327313C>A	ENSP00000319377:p.Gly39Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1	536	0.2454212454212454	213	0.4329268292682927	87	0.24033149171270718	83	0.1451048951048951	153	0.20184696569920843	C	13.08	2.130976	0.37630	0.367453	0.215233	ENSG00000142405	ENST00000324134;ENST00000535162;ENST00000351894;ENST00000354278;ENST00000391775;ENST00000391773;ENST00000345770;ENST00000391772	T;T;T;T;T;T;T	0.61158	0.13;0.13;0.13;0.13;0.13;0.13;0.13	4.48	4.48	0.54585	Pyrin (2);DEATH-like (2);	0.183793	0.25991	N	0.027001	T	0.00012	0.0000	L	0.60845	1.875	0.09310	P	0.9999999899703	B;B;B;B	0.25772	0.134;0.028;0.111;0.051	B;B;B;B	0.25614	0.052;0.021;0.062;0.03	T	0.38672	-0.9650	9	0.36615	T	0.2	.	13.0212	0.58789	0.0:1.0:0.0:0.0	rs34436714;rs58032372;rs34436714	39;39;39;39	F2Z321;A8K407;A8MTQ2;P59046	.;.;.;NAL12_HUMAN	V	39	ENSP00000319377:G39V;ENSP00000438030:G39V;ENSP00000340473:G39V;ENSP00000346231:G39V;ENSP00000375655:G39V;ENSP00000375653:G39V;ENSP00000375652:G39V	ENSP00000319377:G39V	G	-	2	0	NLRP12	59019125	0.013000	0.17824	0.079000	0.20413	0.188000	0.23474	1.465000	0.35299	2.224000	0.72417	0.305000	0.20034	GGA	C|0.741;A|0.259	0.259	strong		0.607	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687	
PTPRH	5794	hgsc.bcm.edu	37	19	55693244	55693244	+	Missense_Mutation	SNP	T	T	C	rs2288419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55693244T>C	ENST00000376350.3	-	20	3248	c.3226A>G	c.(3226-3228)Atc>Gtc	p.I1076V	SYT5_ENST00000354308.3_5'Flank|PTPRH_ENST00000263434.5_Missense_Mutation_p.I898V|SYT5_ENST00000590851.1_5'Flank|SYT5_ENST00000537500.1_5'Flank	NM_002842.3	NP_002833.3	Q9HD43	PTPRH_HUMAN	protein tyrosine phosphatase, receptor type, H	1076	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		I -> V (in dbSNP:rs2288419).		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)		AACCGCAGGATGCACTGATGC	0.622													T|||	2010	0.401358	0.472	0.4193	5008	,	,		18931	0.4425		0.1928	False		,,,				2504	0.4652				p.I1076V		Atlas-SNP	.											.	PTPRH	139	.	0			c.A3226G						PASS	.	T	VAL/ILE,VAL/ILE	1912,2494	547.8+/-377.4	409,1094,700	123.0	116.0	118.0		2692,3226	2.2	1.0	19	dbSNP_100	118	1741,6859	315.9+/-312.5	175,1391,2734	yes	missense,missense	PTPRH	NM_001161440.1,NM_002842.3	29,29	584,2485,3434	CC,CT,TT		20.2442,43.3954,28.087	possibly-damaging,possibly-damaging	898/938,1076/1116	55693244	3653,9353	2203	4300	6503	SO:0001583	missense	5794	exon20			GCAGGATGCACTG		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.3226A>G	19.37:g.55693244T>C	ENSP00000365528:p.Ile1076Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	108	105	0.972222	NM_002842	C9JCH2|Q15426|Q2NKN9|Q2NKP0	Missense_Mutation	SNP	ENST00000376350.3	37	CCDS33110.1	748	0.3424908424908425	231	0.4695121951219512	120	0.3314917127071823	257	0.4493006993006993	140	0.18469656992084432	T	6.180	0.401308	0.11696	0.433954	0.202442	ENSG00000080031	ENST00000376350;ENST00000263434	T;T	0.10192	2.9;2.9	4.41	2.25	0.28309	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.39407	N	0.001369	T	0.00012	0.0000	L	0.31664	0.95	0.22762	P	0.99876137	P;P	0.42296	0.659;0.775	B;B	0.43658	0.228;0.426	T	0.21518	-1.0243	9	0.02654	T	1	.	6.2511	0.20845	0.0:0.0867:0.3023:0.6109	rs2288419;rs17814771;rs56666279;rs2288419	898;1076	C9JCH2;Q9HD43	.;PTPRH_HUMAN	V	1076;898	ENSP00000365528:I1076V;ENSP00000263434:I898V	ENSP00000263434:I898V	I	-	1	0	PTPRH	60385056	0.118000	0.22208	0.999000	0.59377	0.975000	0.68041	-0.083000	0.11286	0.291000	0.22468	-0.320000	0.08662	ATC	T|0.668;C|0.332	0.332	strong		0.622	PTPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452649.1		
PCDHB7	56129	hgsc.bcm.edu	37	5	140554006	140554006	+	Silent	SNP	C	C	G	rs2907329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140554006C>G	ENST00000231137.3	+	1	1764	c.1590C>G	c.(1588-1590)cgC>cgG	p.R530R		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	530	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCGAGTTCCGCGTGGGCGCCA	0.692													c|||	3163	0.631589	0.6884	0.6527	5008	,	,		16448	0.6716		0.5477	False		,,,				2504	0.5849				p.R530R		Atlas-SNP	.											PCDHB7,colon,carcinoma,+2,1	PCDHB7	231	1	0			c.C1590G						PASS	.	G		2888,1518	645.7+/-398.2	926,1036,241	53.0	59.0	57.0		1590	0.9	1.0	5	dbSNP_101	57	4849,3751	597.0+/-393.7	1370,2109,821	no	coding-synonymous	PCDHB7	NM_018940.2		2296,3145,1062	GG,GC,CC		43.6163,34.453,40.5121		530/794	140554006	7737,5269	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			GTTCCGCGTGGGC	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1590C>G	5.37:g.140554006C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			C|0.393;G|0.607	0.607	strong		0.692	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
DDX11	1663	hgsc.bcm.edu	37	12	31242861	31242861	+	Silent	SNP	A	A	C	rs200751040|rs531309221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:31242861A>C	ENST00000407793.2	+	9	1173	c.922A>C	c.(922-924)Agg>Cgg	p.R308R	DDX11_ENST00000350437.4_Silent_p.R308R|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000545668.1_Silent_p.R308R|DDX11_ENST00000542838.1_Silent_p.R308R|DDX11_ENST00000228264.6_Silent_p.R282R	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	308	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.R308R(2)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					AAAGAGGAGGAGGCAGGAGAA	0.587										Multiple Myeloma(12;0.14)				29	0.00579073	0.0038	0.0043	5008	,	,		20906	0.0099		0.007	False		,,,				2504	0.0041				p.R308R		Atlas-SNP	.											DDX11_ENST00000407793,bladder,carcinoma,0,10	DDX11	188	10	2	Substitution - coding silent(2)	kidney(2)	c.A922C						scavenged	.						5.0	7.0	6.0					12																	31242861		2036	4038	6074	SO:0001819	synonymous_variant	1663	exon9			AGGAGGAGGCAGG	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.922A>C	12.37:g.31242861A>C		Somatic	543	0	0		WXS	Illumina HiSeq	Phase_I	533	66	0.123827	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Silent	SNP	ENST00000407793.2	37	CCDS44856.1																																																																																			A|0.977;C|0.023	0.023	strong		0.587	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
HLA-C	3107	hgsc.bcm.edu	37	6	31238886	31238886	+	Missense_Mutation	SNP	A	A	G	rs77935220	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31238886A>G	ENST00000376228.5	-	3	597	c.583T>C	c.(583-585)Tac>Cac	p.Y195H	HLA-C_ENST00000383329.3_Missense_Mutation_p.Y195H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	195	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						TTCTCCAGGTATCTGCGGAGC	0.672																																					p.Y195H		Atlas-SNP	.											.	HLA-C	92	.	0			c.T583C						PASS	.						52.0	42.0	45.0					6																	31238886		2202	4298	6500	SO:0001583	missense	3107	exon3			CCAGGTATCTGCG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.583T>C	6.37:g.31238886A>G	ENSP00000365402:p.Tyr195His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	313	123	0.392971	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	94|94	0.04304029304029304|0.04304029304029304	16|16	0.032520325203252036|0.032520325203252036	35|35	0.09668508287292818|0.09668508287292818	17|17	0.02972027972027972|0.02972027972027972	26|26	0.03430079155672823|0.03430079155672823	.|.	9.585|9.585	1.124510|1.124510	0.20959|0.20959	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000415537|ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	.|T;T	.|0.01203	.|5.18;5.18	2.71|2.71	-1.2|-1.2	0.09554|0.09554	.|MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.|0.416377	.|0.17377	.|N	.|0.176439	T|T	0.00552|0.00552	0.0018|0.0018	L|L	0.55990|0.55990	1.75|1.75	0.22811|0.22811	N|N	0.998706|0.998706	.|B;B;B;B	.|0.20550	.|0.046;0.006;0.006;0.01	.|B;B;B;B	.|0.31495	.|0.131;0.036;0.059;0.105	T|T	0.41215|0.41215	-0.9521|-0.9521	5|10	.|0.48119	.|T	.|0.1	.|.	6.6487|6.6487	0.22949|0.22949	0.6285:0.0:0.3715:0.0|0.6285:0.0:0.3715:0.0	.|.	.|195;195;195;195	.|A2AEA4;A6H578;A2AEA2;P10321	.|.;.;.;1C07_HUMAN	T|H	194|195;195;195;232	.|ENSP00000365402:Y195H;ENSP00000372819:Y195H	.|ENSP00000365402:Y195H	I|Y	-|-	2|1	0|0	HLA-C|HLA-C	31346865|31346865	0.004000|0.004000	0.15560|0.15560	0.410000|0.410000	0.26471|0.26471	0.044000|0.044000	0.14063|0.14063	-0.338000|-0.338000	0.07842|0.07842	-0.240000|-0.240000	0.09696|0.09696	0.254000|0.254000	0.18369|0.18369	ATA|TAC	A|0.956;G|0.044	0.044	strong		0.672	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
C9orf62	157927	hgsc.bcm.edu	37	9	138236031	138236031	+	Silent	SNP	A	A	G	rs914398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:138236031A>G	ENST00000320778.2	+	2	387	c.237A>G	c.(235-237)ccA>ccG	p.P79P		NM_173520.2	NP_775791.1	Q8N4C0	CI062_HUMAN	chromosome 9 open reading frame 62	79																	CCGGACGCCCAGTCCTGGGCT	0.622											OREG0019607	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2629	0.52496	0.7383	0.5677	5008	,	,		18306	0.3998		0.4871	False		,,,				2504	0.3742				p.P79P		Atlas-SNP	.											.	C9orf62	1	.	0			c.A237G						PASS	.																																			SO:0001819	synonymous_variant	157927	exon2			ACGCCCAGTCCTG	BC034752	CCDS59154.1	9q34.3	2008-02-05			ENSG00000178243	ENSG00000178243			28581	protein-coding gene	gene with protein product						12477932	Standard	NM_173520		Approved	MGC35463	uc004cfo.3	Q8N4C0	OTTHUMG00000020900	ENST00000320778.2:c.237A>G	9.37:g.138236031A>G		Somatic	41	0	0	1639	WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_173520	Q5T7E2	Silent	SNP	ENST00000320778.2	37	CCDS59154.1																																																																																			A|0.488;G|0.512	0.512	strong		0.622	C9orf62-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000054980.2	NM_173520	
MYO5A	4644	hgsc.bcm.edu	37	15	52611451	52611451	+	Silent	SNP	A	A	G	rs2290332	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:52611451A>G	ENST00000399231.3	-	38	5208	c.4965T>C	c.(4963-4965)gaT>gaC	p.D1655D	MYO5A_ENST00000399233.2_Silent_p.D1652D|MYO5A_ENST00000358212.6_Silent_p.D1680D|MYO5A_ENST00000356338.6_Silent_p.D1628D|MYO5A_ENST00000553916.1_Silent_p.D1653D	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1655	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				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)		AGGTGCCCTCATCGGCGATAC	0.562													A|||	1646	0.328674	0.2867	0.2939	5008	,	,		20516	0.5774		0.1163	False		,,,				2504	0.3722				p.D1655D		Atlas-SNP	.											.	MYO5A	145	.	0			c.T4965C						PASS	.	A	,	1091,3259		143,805,1227	130.0	137.0	134.0		4965,4884	-11.4	0.1	15	dbSNP_100	134	1267,7291		107,1053,3119	no	coding-synonymous,coding-synonymous	MYO5A	NM_000259.3,NM_001142495.1	,	250,1858,4346	GG,GA,AA		14.8049,25.0805,18.2677	,	1655/1856,1628/1829	52611451	2358,10550	2175	4279	6454	SO:0001819	synonymous_variant	4644	exon38			GCCCTCATCGGCG		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.4965T>C	15.37:g.52611451A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	201	93	0.462687	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	37	CCDS42037.1																																																																																			A|0.716;G|0.284	0.284	strong		0.562	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	
ITGB4	3691	hgsc.bcm.edu	37	17	73729660	73729660	+	Missense_Mutation	SNP	G	G	A	rs61735297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73729660G>A	ENST00000200181.3	+	13	1731	c.1544G>A	c.(1543-1545)cGt>cAt	p.R515H	ITGB4_ENST00000339591.3_Missense_Mutation_p.R515H|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000450894.3_Missense_Mutation_p.R515H|ITGB4_ENST00000579662.1_Missense_Mutation_p.R515H|ITGB4_ENST00000449880.2_Missense_Mutation_p.R515H	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	515	Cysteine-rich tandem repeats.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGCTCCGGCCGTGGGGAGTGC	0.647													G|||	27	0.00539137	0.0008	0.0115	5008	,	,		13114	0.001		0.0129	False		,,,				2504	0.0041				p.R515H		Atlas-SNP	.											ITGB4,caecum,carcinoma,0,1	ITGB4	165	1	0			c.G1544A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	15,4391	22.3+/-47.3	0,15,2188	69.0	59.0	62.0		1544,1544,1544	-0.9	0.0	17	dbSNP_129	62	163,8437	76.6+/-139.3	0,163,4137	yes	missense,missense,missense	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	29,29,29	0,178,6325	AA,AG,GG		1.8953,0.3404,1.3686	benign,benign,benign	515/1823,515/1806,515/1753	73729660	178,12828	2203	4300	6503	SO:0001583	missense	3691	exon13			CCGGCCGTGGGGA		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.1544G>A	17.37:g.73729660G>A	ENSP00000200181:p.Arg515His	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	16	0.007326007326007326	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	7	0.009234828496042216	G	9.385	1.074039	0.20147	0.003404	0.018953	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.97688	-4.49;-4.49;-4.49	4.78	-0.858	0.10689	.	0.072851	0.53938	N	0.000050	D	0.88764	0.6525	L	0.38531	1.155	0.42452	D	0.992753	B;B;B;B;B	0.31485	0.303;0.325;0.015;0.031;0.031	B;B;B;B;B	0.26770	0.058;0.073;0.021;0.016;0.009	T	0.82532	-0.0410	10	0.45353	T	0.12	.	9.7846	0.40668	0.4551:0.0:0.5449:0.0	rs61735297	475;515;515;515;515	B4E3N0;P16144-5;P16144-3;A0AVL6;P16144	.;.;.;.;ITB4_HUMAN	H	431;515;515;515	ENSP00000200181:R515H;ENSP00000344079:R515H;ENSP00000400217:R515H	ENSP00000200181:R515H	R	+	2	0	ITGB4	71241255	0.974000	0.33945	0.025000	0.17156	0.421000	0.31385	2.990000	0.49401	-0.424000	0.07382	-0.263000	0.10527	CGT	G|0.988;A|0.012	0.012	strong		0.647	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
CRIM1	51232	hgsc.bcm.edu	37	2	36706780	36706780	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:36706780G>A	ENST00000280527.2	+	7	1682	c.1315G>A	c.(1315-1317)Gga>Aga	p.G439R		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	439	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				GACCGTCTGCGGACAGACCTG	0.572																																					p.G439R		Atlas-SNP	.											CRIM1,NS,carcinoma,0,1	CRIM1	88	1	0			c.G1315A						scavenged	.						135.0	130.0	132.0					2																	36706780		2203	4300	6503	SO:0001583	missense	51232	exon7			GTCTGCGGACAGA	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.1315G>A	2.37:g.36706780G>A	ENSP00000280527:p.Gly439Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	145	3	0.0206897	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Missense_Mutation	SNP	ENST00000280527.2	37	CCDS1783.1	.	.	.	.	.	.	.	.	.	.	G	18.49	3.636333	0.67130	.	.	ENSG00000150938	ENST00000280527	T	0.65549	-0.16	5.35	5.35	0.76521	von Willebrand factor, type C (4);	0.114306	0.64402	D	0.000015	T	0.70404	0.3220	L	0.31578	0.945	0.53005	D	0.999962	D	0.89917	1.0	D	0.78314	0.991	T	0.69602	-0.5101	10	0.41790	T	0.15	-12.9171	18.423	0.90598	0.0:0.0:1.0:0.0	.	439	Q9NZV1	CRIM1_HUMAN	R	439	ENSP00000280527:G439R	ENSP00000280527:G439R	G	+	1	0	CRIM1	36560284	1.000000	0.71417	0.906000	0.35671	0.875000	0.50365	7.732000	0.84908	2.668000	0.90789	0.655000	0.94253	GGA	.	.	none		0.572	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
DGKQ	1609	hgsc.bcm.edu	37	4	961373	961373	+	Silent	SNP	G	G	A	rs1377586	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:961373G>A	ENST00000273814.3	-	8	1024	c.951C>T	c.(949-951)gtC>gtT	p.V317V	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	317					blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGGACACCGTGACGAGGCGGA	0.692													g|||	2023	0.403954	0.385	0.5519	5008	,	,		10570	0.3363		0.4483	False		,,,				2504	0.3487				p.V317V	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.C951T						PASS	.			1714,2684	508.1+/-366.9	359,996,844	54.0	52.0	52.0		951	2.2	0.0	4	dbSNP_88	52	3948,4652	544.2+/-384.5	901,2146,1253	no	coding-synonymous	DGKQ	NM_001347.2		1260,3142,2097	AA,AG,GG		45.907,38.9723,43.5605		317/943	961373	5662,7336	2199	4300	6499	SO:0001819	synonymous_variant	1609	exon8			CACCGTGACGAGG	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"""diacylglycerol kinase, theta (110kD)"""	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.951C>T	4.37:g.961373G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001347	Q6P3W4	Silent	SNP	ENST00000273814.3	37	CCDS3342.1	961	0.440018315018315	210	0.4268292682926829	201	0.5552486187845304	207	0.3618881118881119	343	0.4525065963060686	g	1.498	-0.552850	0.03996	0.389723	0.45907	ENSG00000145214	ENST00000509465	.	.	.	4.97	2.2	0.27929	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20975	P	0.999812195	.	.	.	.	.	.	T	0.47018	-0.9149	3	.	.	.	.	5.0796	0.14649	0.1786:0.1789:0.6425:0.0	rs1377586;rs59339670	.	.	.	L	264	.	.	S	-	2	0	DGKQ	951373	0.999000	0.42202	0.005000	0.12908	0.021000	0.10359	0.653000	0.24902	0.131000	0.18576	0.544000	0.68410	TCA	G|0.561;A|0.439	0.439	strong		0.692	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		
MCMBP	79892	hgsc.bcm.edu	37	10	121587116	121587116	+	IGR	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:121587116C>T	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Nonsense_Mutation_p.R1075*|INPP5F_ENST00000369080.3_Nonsense_Mutation_p.R465*	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.R1075*(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						TGCCAAGATTCGAAGTTCCAT	0.483																																					p.R1075X		Atlas-SNP	.											INPP5F,NS,carcinoma,0,1	INPP5F	112	1	1	Substitution - Nonsense(1)	endometrium(1)	c.C3223T						PASS	.						97.0	97.0	97.0					10																	121587116		2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			AAGATTCGAAGTT	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		10.37:g.121587116C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Nonsense_Mutation	SNP	ENST00000360003.3	37	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	C	41	8.746755	0.98937	.	.	ENSG00000198825	ENST00000361976;ENST00000369080	.	.	.	6.02	3.07	0.35406	.	0.182665	0.46758	D	0.000275	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.7045	10.5033	0.44819	0.2383:0.6993:0.0:0.0624	.	.	.	.	X	1075;465	.	ENSP00000354519:R1075X	R	+	1	2	INPP5F	121577106	0.999000	0.42202	0.956000	0.39512	0.996000	0.88848	2.619000	0.46401	0.873000	0.35799	0.655000	0.94253	CGA	.	.	none		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
COL4A4	1286	hgsc.bcm.edu	37	2	227872995	227872995	+	Silent	SNP	T	T	C	rs2228555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227872995T>C	ENST00000396625.3	-	47	4755	c.4548A>G	c.(4546-4548)gtA>gtG	p.V1516V	COL4A4_ENST00000329662.7_Silent_p.V1513V	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1516	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GCGTGCTAAATACGGGAAGGC	0.587													C|||	3208	0.640575	0.7761	0.5432	5008	,	,		20423	0.5982		0.5199	False		,,,				2504	0.6943				p.V1516V		Atlas-SNP	.											.	COL4A4	215	.	0			c.A4548G						PASS	.	C		3066,1150		1125,816,167	50.0	58.0	55.0		4548	2.2	0.1	2	dbSNP_98	55	4342,4090		1139,2064,1013	no	coding-synonymous	COL4A4	NM_000092.4		2264,2880,1180	CC,CT,TT		48.5057,27.277,41.4295		1516/1691	227872995	7408,5240	2108	4216	6324	SO:0001819	synonymous_variant	1286	exon47			GCTAAATACGGGA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4548A>G	2.37:g.227872995T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	167	67	0.401198	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			T|0.294;G|0.193	.	strong		0.587	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
CCDC157	550631	hgsc.bcm.edu	37	22	30762140	30762140	+	Missense_Mutation	SNP	G	G	A	rs740223	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30762140G>A	ENST00000405659.1	+	3	860	c.151G>A	c.(151-153)Gac>Aac	p.D51N	CCDC157_ENST00000399824.2_Missense_Mutation_p.D51N|CCDC157_ENST00000338306.3_Missense_Mutation_p.D51N			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	51			D -> N (in dbSNP:rs740223).							central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CTGTGACCTCGACATGGTGGC	0.647													G|||	797	0.159145	0.1415	0.1571	5008	,	,		20656	0.1468		0.2694	False		,,,				2504	0.0838				p.D51N		Atlas-SNP	.											.	CCDC157	86	.	0			c.G151A						PASS	.	G	ASN/ASP	667,3739	282.5+/-276.6	55,557,1591	154.0	135.0	142.0		151	5.2	1.0	22	dbSNP_86	142	2204,6396	375.9+/-337.9	287,1630,2383	no	missense	CCDC157	NM_001017437.2	23	342,2187,3974	AA,AG,GG		25.6279,15.1384,22.0744	probably-damaging	51/753	30762140	2871,10135	2203	4300	6503	SO:0001583	missense	550631	exon3			GACCTCGACATGG	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.151G>A	22.37:g.30762140G>A	ENSP00000385357:p.Asp51Asn	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001017437	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	381	0.17445054945054944	70	0.14227642276422764	57	0.1574585635359116	71	0.12412587412587413	183	0.24142480211081793	G	35	5.588928	0.96590	0.151384	0.256279	ENSG00000187860	ENST00000399824;ENST00000405659;ENST00000338306;ENST00000445005;ENST00000430839	T;T;T;T;T	0.54479	0.57;1.46;1.46;1.09;1.09	5.25	5.25	0.73442	.	.	.	.	.	T	0.00039	0.0001	M	0.61703	1.905	0.09310	P	1.0	D	0.89917	1.0	D	0.97110	1.0	T	0.00076	-1.2119	8	0.41790	T	0.15	-20.5084	17.3819	0.87407	0.0:0.0:1.0:0.0	rs740223;rs13055115;rs17736500;rs52830809;rs740223	51	Q569K6	CC157_HUMAN	N	51	ENSP00000382720:D51N;ENSP00000385357:D51N;ENSP00000343087:D51N;ENSP00000387491:D51N;ENSP00000401837:D51N	ENSP00000343087:D51N	D	+	1	0	CCDC157	29092140	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.060000	0.93907	2.613000	0.88420	0.455000	0.32223	GAC	G|0.814;A|0.186	0.186	strong		0.647	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
KIF24	347240	hgsc.bcm.edu	37	9	34256347	34256347	+	Silent	SNP	C	C	T	rs10814083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34256347C>T	ENST00000402558.2	-	10	3282	c.3258G>A	c.(3256-3258)ggG>ggA	p.G1086G	KIF24_ENST00000379174.3_Silent_p.G952G|KIF24_ENST00000345050.2_Silent_p.G952G|KIF24_ENST00000379166.2_Silent_p.G1086G			Q5T7B8	KIF24_HUMAN	kinesin family member 24	1086					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)			CAACTGGGCCCCCTGTGCTCT	0.607													C|||	2204	0.440096	0.2685	0.4006	5008	,	,		20026	0.7351		0.3082	False		,,,				2504	0.5317				p.G1086G		Atlas-SNP	.											.	KIF24	64	.	0			c.G3258A						PASS	.	C		1226,3180	423.0+/-339.9	158,910,1135	44.0	37.0	39.0		3258	0.4	0.0	9	dbSNP_120	39	2936,5664	452.7+/-363.0	499,1938,1863	no	coding-synonymous	KIF24	NM_194313.2		657,2848,2998	TT,TC,CC		34.1395,27.8257,32.0006		1086/1369	34256347	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	347240	exon11			TGGGCCCCCTGTG	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.3258G>A	9.37:g.34256347C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Silent	SNP	ENST00000402558.2	37	CCDS6551.2	924	0.4230769230769231	142	0.2886178861788618	139	0.3839779005524862	397	0.6940559440559441	246	0.3245382585751979	C	2.713	-0.268302	0.05716	0.278257	0.341395	ENSG00000186638	ENST00000443226	.	.	.	4.81	0.37	0.16160	.	0.988720	0.08220	N	0.979213	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.40942	-0.9536	5	0.36615	T	0.2	.	6.452	0.21908	0.1277:0.6217:0.0:0.2506	rs10814083;rs58917175;rs10814083	.	.	.	R	132	.	ENSP00000414628:G132R	G	-	1	0	KIF24	34246347	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.091000	0.11146	-0.012000	0.14223	-1.119000	0.02030	GGG	C|0.626;T|0.374	0.374	strong		0.607	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		
PKD1	5310	hgsc.bcm.edu	37	16	2159996	2159996	+	Silent	SNP	G	G	A	rs9935526	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2159996G>A	ENST00000262304.4	-	15	5380	c.5172C>T	c.(5170-5172)gcC>gcT	p.A1724A	PKD1_ENST00000423118.1_Silent_p.A1724A|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1724	PKD 13. {ECO:0000255|PROSITE- ProRule:PRU00151}.			A -> T (in Ref. 2; AAC37576/AAC41765). {ECO:0000305}.	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						TCGGGGAGGCGGCCACCATCA	0.657													g|||	1084	0.216454	0.5378	0.1787	5008	,	,		16383	0.0		0.166	False		,,,				2504	0.0838				p.A1724A		Atlas-SNP	.											.	PKD1	184	.	0			c.C5172T						PASS	.	G	,	2007,2333		462,1083,625	16.0	16.0	16.0		5172,5172	-4.6	0.0	16	dbSNP_119	16	1489,7009		132,1225,2892	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	594,2308,3517	AA,AG,GG		17.5218,46.2442,27.2317	,	1724/4303,1724/4304	2159996	3496,9342	2170	4249	6419	SO:0001819	synonymous_variant	5310	exon15			GGAGGCGGCCACC	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.5172C>T	16.37:g.2159996G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	165	77	0.466667	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			G|0.724;A|0.276	0.276	strong		0.657	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
MRPL50	54534	hgsc.bcm.edu	37	9	104152846	104152846	+	Missense_Mutation	SNP	G	G	A	rs8131	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104152846G>A	ENST00000374865.4	-	2	400	c.379C>T	c.(379-381)Ctt>Ttt	p.L127F	MRPL50_ENST00000539624.1_Intron	NM_019051.2	NP_061924.1	Q8N5N7	RM50_HUMAN	mitochondrial ribosomal protein L50	127			L -> F (in dbSNP:rs8131). {ECO:0000269|PubMed:15489334}.			mitochondrion (GO:0005739)|ribosome (GO:0005840)				large_intestine(1)|lung(2)|prostate(2)	5		Acute lymphoblastic leukemia(62;0.0559)				TAGAAATCAAGAACATCTCTA	0.408													G|||	328	0.0654952	0.0038	0.0375	5008	,	,		18274	0.1111		0.0736	False		,,,				2504	0.1135				p.L127F		Atlas-SNP	.											MRPL50,colon,carcinoma,0,1	MRPL50	18	1	0			c.C379T						scavenged	.	G	PHE/LEU	52,4354	50.2+/-85.5	0,52,2151	87.0	84.0	85.0		379	5.0	1.0	9	dbSNP_52	85	557,8039	150.7+/-205.6	19,519,3760	no	missense	MRPL50	NM_019051.2	22	19,571,5911	AA,AG,GG		6.4798,1.1802,4.6839	probably-damaging	127/159	104152846	609,12393	2203	4298	6501	SO:0001583	missense	54534	exon2			AATCAAGAACATC	AK000500	CCDS6753.1	9q31.1	2012-11-14			ENSG00000136897	ENSG00000136897		"""Mitochondrial ribosomal proteins / large subunits"""	16654	protein-coding gene	gene with protein product	"""mitochondrial 39S ribosomal protein L50"""	611854					Standard	NM_019051		Approved	FLJ20493, MRP-L50	uc004bbe.2	Q8N5N7	OTTHUMG00000020384	ENST00000374865.4:c.379C>T	9.37:g.104152846G>A	ENSP00000363999:p.Leu127Phe	Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_019051	B7Z358|Q5T7E0|Q9NX15	Missense_Mutation	SNP	ENST00000374865.4	37	CCDS6753.1	134	0.06135531135531135	3	0.006097560975609756	15	0.04143646408839779	64	0.11188811188811189	52	0.06860158311345646	G	18.74	3.687591	0.68157	0.011802	0.064798	ENSG00000136897	ENST00000374865	T	0.48836	0.8	5.9	4.96	0.65561	.	0.220856	0.31709	N	0.007198	T	0.03053	0.0090	M	0.72894	2.215	0.09310	P	0.999999999958323	D	0.76494	0.999	D	0.71184	0.972	T	0.27226	-1.0080	9	0.56958	D	0.05	-6.3907	15.775	0.78207	0.0:0.1482:0.8518:0.0	rs8131;rs3174987;rs17853009;rs52827537;rs8131	127	Q8N5N7	RM50_HUMAN	F	127	ENSP00000363999:L127F	ENSP00000363999:L127F	L	-	1	0	MRPL50	103192667	0.997000	0.39634	1.000000	0.80357	0.969000	0.65631	1.279000	0.33191	2.793000	0.96121	0.563000	0.77884	CTT	G|0.950;A|0.050	0.050	strong		0.408	MRPL50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053450.1	NM_019051	
FYCO1	79443	hgsc.bcm.edu	37	3	46010077	46010077	+	Missense_Mutation	SNP	C	C	T	rs4683158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46010077C>T	ENST00000296137.2	-	8	954	c.749G>A	c.(748-750)cGg>cAg	p.R250Q	FYCO1_ENST00000535325.1_Missense_Mutation_p.R250Q	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	250			R -> Q (in dbSNP:rs4683158). {ECO:0000269|PubMed:11896456, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CATGCGCTCCCGTAGCTGCTT	0.592													T|||	4648	0.928115	0.9818	0.9135	5008	,	,		19677	1.0		0.8012	False		,,,				2504	0.9223				p.R250Q		Atlas-SNP	.											FYCO1,colon,carcinoma,-1,1	FYCO1	115	1	0			c.G749A						PASS	.	T	GLN/ARG	4160,246	143.1+/-178.2	1966,228,9	77.0	71.0	73.0		749	5.4	1.0	3	dbSNP_111	73	6662,1938	343.0+/-324.7	2562,1538,200	yes	missense	FYCO1	NM_024513.2	43	4528,1766,209	TT,TC,CC		22.5349,5.5833,16.7922	benign	250/1479	46010077	10822,2184	2203	4300	6503	SO:0001583	missense	79443	exon8			CGCTCCCGTAGCT	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.749G>A	3.37:g.46010077C>T	ENSP00000296137:p.Arg250Gln	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	2004	0.9175824175824175	484	0.983739837398374	329	0.9088397790055248	572	1.0	619	0.816622691292876	T	13.73	2.325366	0.41197	0.944167	0.774651	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.18016	2.29;2.24	5.45	5.45	0.79879	.	0.150361	0.47852	N	0.000201	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	0.38457	-0.9660	9	0.02654	T	1	-12.0565	10.1272	0.42656	0.0:0.076:0.0:0.924	rs4683158;rs17280833;rs57364286;rs4683158	250;250	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	Q	250	ENSP00000296137:R250Q;ENSP00000441178:R250Q	ENSP00000296137:R250Q	R	-	2	0	FYCO1	45985081	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.190000	0.42630	0.902000	0.36520	-0.360000	0.07572	CGG	A|0.000;C|0.136;T|0.864	0.864	strong		0.592	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
RPL4	6124	hgsc.bcm.edu	37	15	66791920	66791920	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:66791920G>A	ENST00000307961.6	-	10	1201	c.1109C>T	c.(1108-1110)gCg>gTg	p.A370V	SNORD18B_ENST00000365659.1_RNA|SNAPC5_ENST00000395589.2_5'Flank|SNAPC5_ENST00000566658.1_5'Flank|MIR4512_ENST00000583257.1_RNA|RPL4_ENST00000568588.1_Missense_Mutation_p.A276V|SNAPC5_ENST00000316634.5_5'Flank|SNAPC5_ENST00000307979.7_5'Flank|SNAPC5_ENST00000563480.2_5'Flank|SNORD18C_ENST00000362704.1_RNA	NM_000968.3	NP_000959.2	P36578	RL4_HUMAN	ribosomal protein L4	370	Lys-rich.				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)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)|urinary_tract(1)	17						GCCTGCAACCGCCGCCTTCTC	0.512																																					p.A370V		Atlas-SNP	.											.	RPL4	29	.	0			c.C1109T						PASS	.						37.0	40.0	39.0					15																	66791920		2198	4295	6493	SO:0001583	missense	6124	exon10			GCAACCGCCGCCT	AB007167	CCDS10218.1	15q22	2011-04-06			ENSG00000174444	ENSG00000174444		"""L ribosomal proteins"""	10353	protein-coding gene	gene with protein product	"""60S ribosomal protein L4"""	180479				9582194, 8268230	Standard	NM_000968		Approved	L4	uc002apv.3	P36578	OTTHUMG00000133193	ENST00000307961.6:c.1109C>T	15.37:g.66791920G>A	ENSP00000311430:p.Ala370Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	89	33	0.370787	NM_000968	A8K502|P39029|Q4VBR0|Q969Z9	Missense_Mutation	SNP	ENST00000307961.6	37	CCDS10218.1	.	.	.	.	.	.	.	.	.	.	G	8.795	0.931551	0.18131	.	.	ENSG00000174444	ENST00000307961;ENST00000432669	.	.	.	5.76	-3.16	0.05217	.	.	.	.	.	T	0.13072	0.0317	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.04013	0.001	T	0.22138	-1.0225	8	0.27082	T	0.32	.	0.968	0.01410	0.2269:0.1496:0.3465:0.2771	.	370	P36578	RL4_HUMAN	V	370	.	ENSP00000311430:A370V	A	-	2	0	RPL4	64578974	0.000000	0.05858	0.003000	0.11579	0.207000	0.24258	-0.538000	0.06120	-0.170000	0.10816	-0.785000	0.03343	GCG	.	.	none		0.512	RPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256903.2	NM_000968	
GSTA1	2938	hgsc.bcm.edu	37	6	52658962	52658962	+	Silent	SNP	T	T	C	rs1051775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:52658962T>C	ENST00000334575.5	-	5	530	c.375A>G	c.(373-375)aaA>aaG	p.K125K	GSTA1_ENST00000493331.1_5'UTR	NM_145740.3	NP_665683.1	P08263	GSTA1_HUMAN	glutathione S-transferase alpha 1	125	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|metabolic process (GO:0008152)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	12	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Glutathione(DB00143)	TTATTTTCTCTTTGATCAAGG	0.398													.|||	1142	0.228035	0.0424	0.2695	5008	,	,		18853	0.1369		0.4235	False		,,,				2504	0.3425				p.K125K		Atlas-SNP	.											.	GSTA1	40	.	0			c.A375G						PASS	.	T		476,3930	223.3+/-239.8	28,420,1755	232.0	227.0	228.0		375	1.0	0.0	6	dbSNP_86	228	3658,4942	526.0+/-380.9	787,2084,1429	no	coding-synonymous	GSTA1	NM_145740.3		815,2504,3184	CC,CT,TT		42.5349,10.8034,31.7853		125/223	52658962	4134,8872	2203	4300	6503	SO:0001819	synonymous_variant	2938	exon5			TTTCTCTTTGATC		CCDS4945.1	6p12.2	2012-06-21	2008-11-26		ENSG00000243955	ENSG00000243955	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4626	protein-coding gene	gene with protein product		138359	"""glutathione S-transferase A1"""			9503014	Standard	NM_145740		Approved		uc003paz.3	P08263	OTTHUMG00000014861	ENST00000334575.5:c.375A>G	6.37:g.52658962T>C		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	NM_145740	Q14750|Q5GHF8|Q5SZC1	Silent	SNP	ENST00000334575.5	37	CCDS4945.1																																																																																			T|0.707;C|0.293	0.293	strong		0.398	GSTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040922.1		
HEATR6	63897	hgsc.bcm.edu	37	17	58123571	58123571	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:58123571C>T	ENST00000184956.6	-	19	2805	c.2789G>A	c.(2788-2790)cGg>cAg	p.R930Q	HEATR6_ENST00000585976.1_Missense_Mutation_p.R818Q	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	930							poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	44	all_cancers(5;2.25e-13)|Breast(5;4.84e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		BRCA - Breast invasive adenocarcinoma(1;5.93e-19)|Epithelial(12;7.59e-12)|all cancers(12;1.26e-10)			TCCAAGGGCCCGGACTGCATT	0.368																																					p.R930Q		Atlas-SNP	.											HEATR6,NS,neuroblastoma,-1,1	HEATR6	98	1	0			c.G2789A						scavenged	.						67.0	69.0	68.0					17																	58123571		2203	4300	6503	SO:0001583	missense	63897	exon19			AGGGCCCGGACTG	BX640819	CCDS11623.1	17q23.2	2007-05-01				ENSG00000068097			24076	protein-coding gene	gene with protein product	"""amplified in breast cancer 1"""					12755490	Standard	NM_022070		Approved	ABC1, FLJ22087	uc002iyk.1	Q6AI08		ENST00000184956.6:c.2789G>A	17.37:g.58123571C>T	ENSP00000184956:p.Arg930Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	95	2	0.0210526	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Missense_Mutation	SNP	ENST00000184956.6	37	CCDS11623.1	.	.	.	.	.	.	.	.	.	.	C	36	5.626152	0.96671	.	.	ENSG00000068097	ENST00000184956;ENST00000393017	T	0.65364	-0.15	5.44	5.44	0.79542	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.82375	0.5023	M	0.87827	2.91	0.42790	D	0.993892	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.83745	0.0206	10	0.49607	T	0.09	-19.5213	18.7064	0.91640	0.0:1.0:0.0:0.0	.	665;930	E7ESB9;Q6AI08	.;HEAT6_HUMAN	Q	930;665	ENSP00000184956:R930Q	ENSP00000184956:R930Q	R	-	2	0	HEATR6	55478353	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.552000	0.82192	2.740000	0.93945	0.650000	0.86243	CGG	.	.	none		0.368	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070	
NIN	51199	hgsc.bcm.edu	37	14	51224417	51224417	+	Missense_Mutation	SNP	G	G	C	rs2236316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:51224417G>C	ENST00000382041.3	-	18	3521	c.3331C>G	c.(3331-3333)Cca>Gca	p.P1111A	NIN_ENST00000389868.3_Intron|NIN_ENST00000324330.9_Missense_Mutation_p.P1111A|NIN_ENST00000245441.5_Missense_Mutation_p.P1111A|NIN_ENST00000530997.2_Missense_Mutation_p.P1111A|NIN_ENST00000382043.4_Intron|NIN_ENST00000453196.1_Missense_Mutation_p.P1111A	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1111			P -> A (in dbSNP:rs2236316).		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)					TCAGTAGCTGGCTCATCCAAA	0.423			T	PDGFRB	MPD								G|||	933	0.186302	0.0628	0.2565	5008	,	,		20641	0.1617		0.2734	False		,,,				2504	0.2393				p.P1111A		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C3331G						PASS	.	G	,ALA/PRO,ALA/PRO,ALA/PRO	456,3950	217.8+/-236.0	21,414,1768	133.0	136.0	135.0		,3331,3331,3331	-4.1	0.0	14	dbSNP_98	135	2157,6443	369.9+/-335.7	277,1603,2420	yes	intron,missense,missense,missense	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,27,27,27	298,2017,4188	CC,CG,GG		25.0814,10.3495,20.0907	,benign,benign,benign	,1111/2134,1111/2047,1111/2091	51224417	2613,10393	2203	4300	6503	SO:0001583	missense	51199	exon18			TAGCTGGCTCATC	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.3331C>G	14.37:g.51224417G>C	ENSP00000371472:p.Pro1111Ala	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	157	76	0.484076	NM_020921	A6NDB8|B7WPA3|C9JSB6|C9JSG2|C9JXL2|Q5BKU3|Q6P0P6|Q9BWU6|Q9C012|Q9C013|Q9C014|Q9H5I6|Q9HAT7|Q9HBY5|Q9HCK7|Q9UH61	Missense_Mutation	SNP	ENST00000382041.3	37	CCDS32079.1	403|403	0.18452380952380953|0.18452380952380953	45|45	0.09146341463414634|0.09146341463414634	84|84	0.23204419889502761|0.23204419889502761	86|86	0.15034965034965034|0.15034965034965034	188|188	0.24802110817941952|0.24802110817941952	G|G	0.007|0.007	-2.003729|-2.003729	0.00431|0.00431	0.103495|0.103495	0.250814|0.250814	ENSG00000100503|ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853|ENST00000245441;ENST00000311149;ENST00000324292;ENST00000382041;ENST00000324330;ENST00000453196	.|T;T;T;T	.|0.06449	.|3.57;3.31;3.3;3.31	5.93|5.93	-4.1|-4.1	0.03940|0.03940	.|.	.|1.425020	.|0.04346	.|N	.|0.354818	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.09022	.|0.001;0.001;0.001;0.002	.|B;B;B;B	.|0.09377	.|0.002;0.001;0.001;0.004	T|T	0.47045|0.47045	-0.9147|-0.9147	4|9	.|0.07030	.|T	.|0.85	1.3606|1.3606	8.4876|8.4876	0.33080|0.33080	0.2578:0.3897:0.3525:0.0|0.2578:0.3897:0.3525:0.0	rs2236316;rs17719470;rs52791150;rs56485217;rs2236316|rs2236316;rs17719470;rs52791150;rs56485217;rs2236316	.|1117;1111;1111;1111	.|Q8N4C6-5;C9J066;Q8N4C6;Q8N4C6-7	.|.;.;NIN_HUMAN;.	G|A	601|1111;1094;1117;1111;1111;1111	.|ENSP00000245441:P1111A;ENSP00000371472:P1111A;ENSP00000324210:P1111A;ENSP00000412391:P1111A	.|ENSP00000245441:P1111A	A|P	-|-	2|1	0|0	NIN|NIN	50294167|50294167	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.044000|0.044000	0.14063|0.14063	-0.337000|-0.337000	0.07852|0.07852	-0.361000|-0.361000	0.08125|0.08125	0.563000|0.563000	0.77884|0.77884	GCC|CCA	G|0.805;C|0.195	0.195	strong		0.423	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
TRAP1	10131	hgsc.bcm.edu	37	16	3726074	3726074	+	Silent	SNP	G	G	C	rs61753377	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3726074G>C	ENST00000246957.5	-	7	865	c.777C>G	c.(775-777)tcC>tcG	p.S259S	TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000538171.1_Silent_p.S206S|TRAP1_ENST00000575671.1_Silent_p.S50S	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	259					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)				CCTTGCAGTCGGATTTCAGGT	0.572													G|||	203	0.0405351	0.003	0.0605	5008	,	,		16805	0.0397		0.0596	False		,,,				2504	0.0583				p.S259S		Atlas-SNP	.											TRAP1,NS,carcinoma,-2,1	TRAP1	53	1	0			c.C777G						PASS	.	G		56,4338	53.6+/-89.4	0,56,2141	109.0	105.0	106.0		777	-10.6	0.0	16	dbSNP_129	106	569,8031	154.0+/-208.3	17,535,3748	no	coding-synonymous	TRAP1	NM_016292.2		17,591,5889	CC,CG,GG		6.6163,1.2745,4.8099		259/705	3726074	625,12369	2197	4300	6497	SO:0001819	synonymous_variant	10131	exon7			GCAGTCGGATTTC	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.777C>G	16.37:g.3726074G>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Silent	SNP	ENST00000246957.5	37	CCDS10508.1																																																																																			G|0.958;C|0.042	0.042	strong		0.572	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
PTDSS2	81490	hgsc.bcm.edu	37	11	490035	490035	+	Missense_Mutation	SNP	C	C	T	rs61742833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:490035C>T	ENST00000308020.5	+	11	1444	c.1268C>T	c.(1267-1269)gCg>gTg	p.A423V		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	423					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	TCCGTCCTGGCGCTCACCTGG	0.657													T|||	238	0.047524	0.0053	0.1974	5008	,	,		15849	0.001		0.0726	False		,,,				2504	0.0204				p.A423V		Atlas-SNP	.											PTDSS2,caecum,carcinoma,-1,3	PTDSS2	27	3	0			c.C1268T						PASS	.	T	VAL/ALA	91,4315	809.3+/-416.0	1,89,2113	90.0	60.0	70.0		1268	2.6	1.0	11	dbSNP_129	70	876,7724	776.3+/-407.7	45,786,3469	yes	missense	PTDSS2	NM_030783.1	64	46,875,5582	TT,TC,CC		10.186,2.0654,7.435	benign	423/488	490035	967,12039	2203	4300	6503	SO:0001583	missense	81490	exon11			TCCTGGCGCTCAC	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.1268C>T	11.37:g.490035C>T	ENSP00000308258:p.Ala423Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_030783		Missense_Mutation	SNP	ENST00000308020.5	37	CCDS7696.1	132	0.06043956043956044	7	0.014227642276422764	70	0.19337016574585636	1	0.0017482517482517483	54	0.0712401055408971	T	6.945	0.544199	0.13312	0.020654	0.10186	ENSG00000174915	ENST00000308020	.	.	.	3.74	2.6	0.31112	.	0.151894	0.44688	N	0.000433	T	0.00039	0.0001	N	0.02539	-0.55	0.54753	P	1.3000000000040757E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.27739	-1.0065	8	0.12430	T	0.62	-7.4345	8.089	0.30790	0.0:0.1704:0.0:0.8296	rs61742833	423	Q9BVG9	PTSS2_HUMAN	V	423	.	ENSP00000308258:A423V	A	+	2	0	PTDSS2	480035	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.134000	0.50538	0.177000	0.19895	-0.361000	0.07541	GCG	C|0.925;T|0.075	0.075	strong		0.657	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
SYT14	255928	hgsc.bcm.edu	37	1	210334081	210334081	+	Silent	SNP	T	T	C	rs17188183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:210334081T>C	ENST00000472886.1	+	8	1376	c.1362T>C	c.(1360-1362)taT>taC	p.Y454Y	SYT14_ENST00000367019.1_Silent_p.Y473Y|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000537238.1_Silent_p.Y416Y|SYT14_ENST00000367015.1_Silent_p.Y416Y|SYT14_ENST00000534859.1_Silent_p.Y480Y|SYT14_ENST00000422431.1_Silent_p.Y518Y|SYT14_ENST00000399639.2_3'UTR			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	454	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		TAGATACATATGTTAAGTTAA	0.318													T|||	377	0.0752796	0.0121	0.0677	5008	,	,		17664	0.0486		0.1402	False		,,,				2504	0.1268				p.Y518Y		Atlas-SNP	.											.	SYT14	89	.	0			c.T1554C						PASS	.	T	,,,	117,4289	86.3+/-125.0	3,111,2089	76.0	76.0	76.0		1554,1419,1497,1362	4.7	1.0	1	dbSNP_123	76	1169,7431	237.2+/-269.1	83,1003,3214	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYT14	NM_001146261.1,NM_001146262.1,NM_001146264.1,NM_153262.2	,,,	86,1114,5303	CC,CT,TT		13.593,2.6555,9.8877	,,,	518/620,473/575,499/601,454/556	210334081	1286,11720	2203	4300	6503	SO:0001819	synonymous_variant	255928	exon10			TACATATGTTAAG	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"""Synaptotagmins"""	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.1362T>C	1.37:g.210334081T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_001146261	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Silent	SNP	ENST00000472886.1	37	CCDS31014.1																																																																																			T|0.914;C|0.086	0.086	strong		0.318	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262	
KAT2A	2648	hgsc.bcm.edu	37	17	40266533	40266533	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:40266533G>A	ENST00000225916.5	-	14	2162	c.2109C>T	c.(2107-2109)atC>atT	p.I703I	DHX58_ENST00000251642.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	703					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCTCCACAGGGATCTGCCTCA	0.577																																					p.I703I		Atlas-SNP	.											.	KAT2A	54	.	0			c.C2109T						PASS	.						168.0	159.0	162.0					17																	40266533		2203	4300	6503	SO:0001819	synonymous_variant	2648	exon14			CACAGGGATCTGC	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"""Chromatin-modifying enzymes / K-acetyltransferases"""	4201	protein-coding gene	gene with protein product		602301	"""GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"""	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.2109C>T	17.37:g.40266533G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_021078	Q8N1A2|Q9UCW1	Silent	SNP	ENST00000225916.5	37	CCDS11417.1																																																																																			.	.	none		0.577	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078	
CCDC137	339230	hgsc.bcm.edu	37	17	79638805	79638805	+	Missense_Mutation	SNP	C	C	T	rs11150805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79638805C>T	ENST00000329214.8	+	4	932	c.529C>T	c.(529-531)Cgg>Tgg	p.R177W		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	177			R -> W (in dbSNP:rs11150805).				poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			TAAAGTCCGACGGAAAAAGGA	0.572													C|||	535	0.106829	0.1467	0.0951	5008	,	,		18674	0.002		0.1918	False		,,,				2504	0.0818				p.R177W		Atlas-SNP	.											.	CCDC137	27	.	0			c.C529T						PASS	.	C	TRP/ARG	735,3227		70,595,1316	54.0	60.0	58.0		529	4.1	0.0	17	dbSNP_120	58	1368,6950		126,1116,2917	yes	missense	CCDC137	NM_199287.2	101	196,1711,4233	TT,TC,CC		16.4463,18.5512,17.1254	probably-damaging	177/290	79638805	2103,10177	1981	4159	6140	SO:0001583	missense	339230	exon4			GTCCGACGGAAAA	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.529C>T	17.37:g.79638805C>T	ENSP00000329360:p.Arg177Trp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	129	68	0.527132	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	243	0.11126373626373626	72	0.14634146341463414	41	0.1132596685082873	0	0.0	130	0.17150395778364116	C	12.18	1.859126	0.32884	0.185512	0.164463	ENSG00000185298	ENST00000329214	D	0.90385	-2.66	5.12	4.12	0.48240	.	0.496261	0.21184	N	0.078761	T	0.01061	0.0035	L	0.47716	1.5	0.80722	P	0.0	D	0.71674	0.998	P	0.53861	0.736	T	0.20140	-1.0284	9	0.72032	D	0.01	-9.5786	11.4747	0.50291	0.4593:0.5407:0.0:0.0	rs11150805;rs57790847;rs11150805	177	Q6PK04	CC137_HUMAN	W	177	ENSP00000329360:R177W	ENSP00000329360:R177W	R	+	1	2	CCDC137	77249210	0.000000	0.05858	0.010000	0.14722	0.041000	0.13682	0.509000	0.22707	1.082000	0.41137	0.655000	0.94253	CGG	C|0.863;T|0.137	0.137	strong		0.572	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679120	37679120	+	Missense_Mutation	SNP	G	G	C	rs139953443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:37679120G>C	ENST00000379800.3	-	1	683	c.274C>G	c.(274-276)Ctt>Gtt	p.L92V		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	92	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GGTCCCAGAAGGTCCATGACT	0.458													G|||	8	0.00159744	0.0053	0.0	5008	,	,		20187	0.0		0.001	False		,,,				2504	0.0				p.L92V		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.C274G						PASS	.	G	VAL/LEU	19,4387	26.2+/-53.5	0,19,2184	116.0	108.0	111.0		274	1.0	0.9	13	dbSNP_134	111	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CSNK1A1L	NM_145203.5	32	0,21,6482	CC,CG,GG		0.0233,0.4312,0.1615	possibly-damaging	92/338	37679120	21,12985	2203	4300	6503	SO:0001583	missense	122011	exon1			CCAGAAGGTCCAT	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.274C>G	13.37:g.37679120G>C	ENSP00000369126:p.Leu92Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	127	65	0.511811	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	16.63	3.176449	0.57692	0.004312	2.33E-4	ENSG00000180138	ENST00000379800	T	0.23348	1.91	1.01	1.01	0.19927	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.54727	0.1876	H	0.96996	3.92	0.44447	D	0.99737	D	0.63880	0.993	P	0.60173	0.87	T	0.63422	-0.6641	10	0.87932	D	0	.	7.8591	0.29499	0.0:0.0:1.0:0.0	.	92	Q8N752	KC1AL_HUMAN	V	92	ENSP00000369126:L92V	ENSP00000369126:L92V	L	-	1	0	CSNK1A1L	36577120	1.000000	0.71417	0.926000	0.36857	0.971000	0.66376	2.973000	0.49264	0.825000	0.34637	0.561000	0.74099	CTT	G|0.998;C|0.002	0.002	strong		0.458	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203	
ARHGEF15	22899	hgsc.bcm.edu	37	17	8215534	8215534	+	Silent	SNP	C	C	T	rs3744651	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8215534C>T	ENST00000361926.3	+	2	287	c.177C>T	c.(175-177)acC>acT	p.T59T	ARHGEF15_ENST00000421050.1_Silent_p.T59T	NM_173728.3	NP_776089.2	O94989	ARHGF_HUMAN	Rho guanine nucleotide exchange factor (GEF) 15	59	Pro-rich.				negative regulation of synapse maturation (GO:2000297)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|regulation of catalytic activity (GO:0050790)|retina vasculature morphogenesis in camera-type eye (GO:0061299)	cytoplasm (GO:0005737)|dendrite (GO:0030425)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(9)|large_intestine(5)|lung(11)|ovary(5)|prostate(3)|skin(2)|urinary_tract(1)	37						CAATGTGCACCCCCATCTTCT	0.617													C|||	2088	0.416933	0.4062	0.4424	5008	,	,		11137	0.6468		0.3211	False		,,,				2504	0.2751				p.T59T		Atlas-SNP	.											.	ARHGEF15	97	.	0			c.C177T						PASS	.	C	,	1667,2739	508.6+/-367.0	313,1041,849	93.0	95.0	94.0		177,177	2.1	1.0	17	dbSNP_107	94	2855,5745	447.6+/-361.6	465,1925,1910	no	coding-synonymous,coding-synonymous	ARHGEF15	NM_025014.1,NM_173728.3	,	778,2966,2759	TT,TC,CC		33.1977,37.8348,34.7686	,	59/842,59/842	8215534	4522,8484	2203	4300	6503	SO:0001819	synonymous_variant	22899	exon2			GTGCACCCCCATC	AB020722	CCDS11139.1	17p13.1	2011-11-16			ENSG00000198844	ENSG00000198844		"""Rho guanine nucleotide exchange factors"""	15590	protein-coding gene	gene with protein product	"""Rho guanine exchange factor (GEF) 15"""	608504				10048485	Standard	NM_173728		Approved	KIAA0915, Vsm-RhoGEF, ARGEF15, FLJ13791, MGC44868	uc002glc.3	O94989	OTTHUMG00000108187	ENST00000361926.3:c.177C>T	17.37:g.8215534C>T		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	318	313	0.984277	NM_025014	A8K6G1|Q8N449|Q9H8B4	Silent	SNP	ENST00000361926.3	37	CCDS11139.1	977	0.44734432234432236	210	0.4268292682926829	153	0.42265193370165743	369	0.6451048951048951	245	0.3232189973614776	c	7.455	0.643538	0.14451	0.378348	0.331977	ENSG00000198844	ENST00000455564	.	.	.	5.14	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999378766	.	.	.	.	.	.	T	0.41431	-0.9509	4	0.66056	D	0.02	-14.1856	5.1653	0.15082	0.0:0.6475:0.1706:0.182	rs3744651;rs61574661;rs3744651	.	.	.	L	21	.	ENSP00000413324:P21L	P	+	2	0	ARHGEF15	8156259	0.001000	0.12720	0.998000	0.56505	0.894000	0.52154	-0.282000	0.08445	0.358000	0.24211	-0.126000	0.14955	CCC	C|0.620;T|0.380	0.380	strong		0.617	ARHGEF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226993.2	NM_173728	
OR14A16	284532	hgsc.bcm.edu	37	1	247978135	247978135	+	Silent	SNP	C	C	A	rs12734733	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:247978135C>A	ENST00000357627.1	-	1	896	c.897G>T	c.(895-897)ggG>ggT	p.G299G		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						TTATCAACATCCCCAGAGCCA	0.353													C|||	467	0.0932508	0.0068	0.1888	5008	,	,		15546	0.003		0.1968	False		,,,				2504	0.1288				p.G299G	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.G897T						PASS	.	C		170,4234	105.6+/-144.1	5,160,2037	58.0	56.0	57.0		897	-4.3	0.0	1	dbSNP_121	57	1675,6925	298.9+/-304.1	158,1359,2783	no	coding-synonymous	OR14A16	NM_001001966.1		163,1519,4820	AA,AC,CC		19.4767,3.8601,14.1879		299/310	247978135	1845,11159	2202	4300	6502	SO:0001819	synonymous_variant	284532	exon1			CAACATCCCCAGA	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"""GPCR / Class A : Olfactory receptors"""	15022	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AT, member 1"""	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.897G>T	1.37:g.247978135C>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	107	40	0.373832	NM_001001966	Q6IF96	Silent	SNP	ENST00000357627.1	37	CCDS31097.1																																																																																			C|0.875;A|0.125	0.125	strong		0.353	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966	
RAB11FIP3	9727	hgsc.bcm.edu	37	16	570557	570557	+	Silent	SNP	T	T	C	rs11537754	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:570557T>C	ENST00000262305.4	+	13	2503	c.2115T>C	c.(2113-2115)tcT>tcC	p.S705S	RAB11FIP3_ENST00000450428.1_Silent_p.S409S|RAB11FIP3_ENST00000457159.1_Silent_p.S750S	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	705	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.				cytokinesis (GO:0000910)|endocytic recycling (GO:0032456)|vesicle-mediated transport (GO:0016192)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|endosome (GO:0005768)|intercellular bridge (GO:0045171)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(3)|lung(5)|upper_aerodigestive_tract(1)	12		Hepatocellular(16;0.0218)				CAGCCTTCTCTGAGTCCCTGG	0.592													C|||	3961	0.790935	0.8381	0.6902	5008	,	,		22357	0.9911		0.5398	False		,,,				2504	0.8507				p.S705S	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.T2115C						PASS	.	C	,	3351,1051	386.8+/-326.2	1280,791,130	156.0	144.0	148.0		1227,2115	-8.9	0.0	16	dbSNP_120	148	4640,3960	550.6+/-385.8	1267,2106,927	no	coding-synonymous,coding-synonymous	RAB11FIP3	NM_001142272.1,NM_014700.3	,	2547,2897,1057	CC,CT,TT		46.0465,23.8755,38.5402	,	409/461,705/757	570557	7991,5011	2201	4300	6501	SO:0001819	synonymous_variant	9727	exon13			CTTCTCTGAGTCC	AB014565	CCDS32351.1, CCDS45364.1	16p13.3	2013-01-10			ENSG00000090565	ENSG00000090565		"""EF-hand domain containing"""	17224	protein-coding gene	gene with protein product		608738				9734811, 11481332	Standard	NM_014700		Approved	KIAA0665, Rab11-FIP3, eferin	uc002chf.3	O75154	OTTHUMG00000047843	ENST00000262305.4:c.2115T>C	16.37:g.570557T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	37	CCDS32351.1																																																																																			T|0.353;C|0.647	0.647	strong		0.592	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700	
GALNT6	11226	hgsc.bcm.edu	37	12	51773201	51773201	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51773201T>C	ENST00000543196.2	-	2	570	c.365A>G	c.(364-366)aAg>aGg	p.K122R	GALNT6_ENST00000356317.3_Missense_Mutation_p.K122R|GALNT6_ENST00000603203.1_5'Flank			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	122					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CCACTTGCTCTTCTGAAATGC	0.567																																					p.K122R		Atlas-SNP	.											GALNT6,mouth,carcinoma,+1,1	GALNT6	63	1	0			c.A365G						scavenged	.						80.0	86.0	84.0					12																	51773201		2203	4300	6503	SO:0001583	missense	11226	exon3			TTGCTCTTCTGAA	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"""Glycosyltransferase family 2 domain containing"""	4128	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 6"""	605148	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"""			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.365A>G	12.37:g.51773201T>C	ENSP00000444171:p.Lys122Arg	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Missense_Mutation	SNP	ENST00000543196.2	37	CCDS8813.1	.	.	.	.	.	.	.	.	.	.	T	6.279	0.419608	0.11928	.	.	ENSG00000139629	ENST00000543196;ENST00000356317;ENST00000546163	T;T	0.55930	0.49;0.49	4.52	4.52	0.55395	.	0.560290	0.19274	N	0.118337	T	0.47192	0.1432	L	0.58101	1.795	0.38316	D	0.94338	B	0.18166	0.026	B	0.11329	0.006	T	0.45293	-0.9271	10	0.15066	T	0.55	.	13.7966	0.63175	0.0:0.0:0.0:1.0	.	122	Q8NCL4	GALT6_HUMAN	R	122;122;103	ENSP00000444171:K122R;ENSP00000348668:K122R	ENSP00000348668:K122R	K	-	2	0	GALNT6	50059468	0.071000	0.21146	0.989000	0.46669	0.821000	0.46438	0.335000	0.19806	2.254000	0.74563	0.533000	0.62120	AAG	.	.	none		0.567	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921333	12921333	+	Missense_Mutation	SNP	G	G	A	rs56145411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12921333G>A	ENST00000240189.2	+	4	1211	c.1124G>A	c.(1123-1125)tGc>tAc	p.C375Y		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	375			C -> R (in dbSNP:rs17039307).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCTGAGCTGCTGCTCCCAG	0.562													.|||	1359	0.271366	0.3858	0.1844	5008	,	,		27344	0.2857		0.2157	False		,,,				2504	0.2209				p.C375Y		Atlas-SNP	.											PRAMEF2,NS,carcinoma,+1,1	PRAMEF2	85	1	0			c.G1124A						scavenged	.						111.0	118.0	116.0					1																	12921333		2201	4294	6495	SO:0001583	missense	65122	exon4			TGAGCTGCTGCTC		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.1124G>A	1.37:g.12921333G>A	ENSP00000240189:p.Cys375Tyr	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	322	11	0.0341615	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	357	0.16346153846153846	115	0.23373983739837398	63	0.17403314917127072	80	0.13986013986013987	99	0.13060686015831136	g	3.142	-0.176022	0.06380	.	.	ENSG00000120952	ENST00000240189	T	0.09163	3.01	0.824	-0.682	0.11339	.	1.330770	0.04798	N	0.433017	T	0.00012	0.0000	L	0.34521	1.04	0.58432	P	1.999999999946489E-6	B	0.09022	0.002	B	0.29440	0.102	T	0.47114	-0.9142	9	0.72032	D	0.01	.	5.1225	0.14867	0.5904:0.0:0.4096:0.0	rs56145411	375	O60811	PRAM2_HUMAN	Y	375	ENSP00000240189:C375Y	ENSP00000240189:C375Y	C	+	2	0	PRAMEF2	12843920	0.000000	0.05858	0.596000	0.28811	0.002000	0.02628	-0.801000	0.04550	-2.179000	0.00767	-2.900000	0.00093	TGC	G|0.837;A|0.163	0.163	strong		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
ABI3BP	25890	hgsc.bcm.edu	37	3	100712249	100712249	+	Start_Codon_SNP	SNP	T	T	C	rs3732895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:100712249T>C	ENST00000284322.5	-	1	110	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	ABI3BP_ENST00000471714.1_Start_Codon_SNP_p.M1V|ABI3BP_ENST00000495063.1_Start_Codon_SNP_p.M1V	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	1					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						CCACCTCGCATGGGGAATGAT	0.547													C|||	1199	0.239417	0.2375	0.1484	5008	,	,		14711	0.4127		0.1292	False		,,,				2504	0.2413				p.M1V		Atlas-SNP	.											.	ABI3BP	305	.	0			c.A1G						PASS	.	C	VAL/MET	712,3240		51,610,1315	33.0	34.0	33.0		1	3.7	0.6	3	dbSNP_107	33	1026,7002		64,898,3052	yes	missense	ABI3BP	NM_015429.3	21	115,1508,4367	CC,CT,TT		12.7803,18.0162,14.5075	benign	1/1076	100712249	1738,10242	1976	4014	5990	SO:0001582	initiator_codon_variant	25890	exon1			CTCGCATGGGGAA	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.1A>G	3.37:g.100712249T>C	ENSP00000284322:p.Met1Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	509	0.23305860805860806	99	0.20121951219512196	57	0.1574585635359116	252	0.4405594405594406	101	0.13324538258575197	C	0.959	-0.703929	0.03255	0.180162	0.127803	ENSG00000154175	ENST00000471714;ENST00000284322;ENST00000495063;ENST00000530539	T;T	0.21031	2.21;2.03	5.83	3.73	0.42828	.	0.844176	0.09657	N	0.772937	T	0.00012	0.0000	.	.	.	0.22266	P	0.999242365	B	0.02656	0.0	B	0.01281	0.0	T	0.47983	-0.9074	8	0.19147	T	0.46	3.7832	7.9155	0.29816	0.0:0.7103:0.1257:0.164	rs3732895;rs52821022;rs58678259;rs3732895	1	Q7Z7G0	TARSH_HUMAN	V	1	ENSP00000420524:M1V;ENSP00000284322:M1V	ENSP00000284322:M1V	M	-	1	0	ABI3BP	102194939	0.000000	0.05858	0.611000	0.29010	0.765000	0.43378	0.399000	0.20916	0.642000	0.30620	-0.119000	0.15052	ATG	T|0.753;C|0.246	0.246	strong		0.547	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		Missense_Mutation
IFT140	9742	hgsc.bcm.edu	37	16	1608082	1608082	+	Silent	SNP	A	A	G	rs2076436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1608082A>G	ENST00000426508.2	-	19	2616	c.2253T>C	c.(2251-2253)ccT>ccC	p.P751P	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	751					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.P751P(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				ACACCATCTGAGGGATGTGGT	0.547													A|||	1740	0.347444	0.5507	0.1844	5008	,	,		18218	0.3433		0.2087	False		,,,				2504	0.3354				p.P751P		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	1	Substitution - coding silent(1)	stomach(1)	c.T2253C						PASS	.	A		2135,2263	579.6+/-385.0	518,1099,582	146.0	144.0	145.0		2253	0.7	0.3	16	dbSNP_96	145	1861,6739	333.7+/-320.7	197,1467,2636	no	coding-synonymous	IFT140	NM_014714.3		715,2566,3218	GG,GA,AA		21.6395,48.5448,30.7432		751/1463	1608082	3996,9002	2199	4300	6499	SO:0001819	synonymous_variant	9742	exon19			CATCTGAGGGATG	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.2253T>C	16.37:g.1608082A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	145	88	0.606897	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																			A|0.687;G|0.313	0.313	strong		0.547	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
FGFBP2	83888	hgsc.bcm.edu	37	4	15964670	15964670	+	Missense_Mutation	SNP	C	C	T	rs35496730	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:15964670C>T	ENST00000259989.6	-	1	189	c.83G>A	c.(82-84)aGc>aAc	p.S28N	FGFBP2_ENST00000509331.1_Intron	NM_031950.3	NP_114156.1	Q9BYJ0	FGFP2_HUMAN	fibroblast growth factor binding protein 2	28			S -> N (in dbSNP:rs35496730).			extracellular region (GO:0005576)				central_nervous_system(1)|lung(5)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	9						CTCCCCAGTGCTTCCTTGCTT	0.577													C|||	606	0.121006	0.0794	0.1297	5008	,	,		20896	0.0853		0.1541	False		,,,				2504	0.1738				p.S28N		Atlas-SNP	.											.	FGFBP2	22	.	0			c.G83A						PASS	.	C	ASN/SER	425,3981	206.5+/-228.1	21,383,1799	71.0	62.0	65.0		83	-2.1	0.0	4	dbSNP_126	65	1325,7275	259.8+/-282.9	112,1101,3087	yes	missense	FGFBP2	NM_031950.3	46	133,1484,4886	TT,TC,CC		15.407,9.6459,13.4553	benign	28/224	15964670	1750,11256	2203	4300	6503	SO:0001583	missense	83888	exon1			CCAGTGCTTCCTT	AB021123	CCDS3419.1	4p15.32	2008-07-16			ENSG00000137441	ENSG00000137441			29451	protein-coding gene	gene with protein product	"""killer-specific secretory protein of 37 kDa"""	607713				11342666, 12322897	Standard	NM_031950		Approved	KSP37	uc003gon.3	Q9BYJ0	OTTHUMG00000128513	ENST00000259989.6:c.83G>A	4.37:g.15964670C>T	ENSP00000259989:p.Ser28Asn	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_031950		Missense_Mutation	SNP	ENST00000259989.6	37	CCDS3419.1	255	0.11675824175824176	39	0.07926829268292683	52	0.143646408839779	47	0.08216783216783216	117	0.15435356200527706	C	3.733	-0.055220	0.07362	0.096459	0.15407	ENSG00000137441	ENST00000259989	T	0.16073	2.37	2.98	-2.08	0.07254	.	1.294600	0.05643	U	0.583857	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.39542	-0.9609	9	0.18276	T	0.48	0.8044	3.5788	0.07945	0.1651:0.4992:0.0:0.3357	rs35496730	28	Q9BYJ0	FGFP2_HUMAN	N	28	ENSP00000259989:S28N	ENSP00000259989:S28N	S	-	2	0	FGFBP2	15573768	0.044000	0.20184	0.000000	0.03702	0.002000	0.02628	-0.015000	0.12634	-0.762000	0.04664	-0.896000	0.02909	AGC	C|0.872;T|0.128	0.128	strong		0.577	FGFBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250324.1	NM_031950	
SNAPC4	6621	hgsc.bcm.edu	37	9	139276430	139276430	+	Silent	SNP	G	G	A	rs34850728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139276430G>A	ENST00000298532.2	-	17	2531	c.2163C>T	c.(2161-2163)caC>caT	p.H721H		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)		GGGTGGCTCTGTGCCGTAGCC	0.667													G|||	527	0.105232	0.0068	0.1081	5008	,	,		16781	0.002		0.1799	False		,,,				2504	0.2658				p.H721H		Atlas-SNP	.											.	SNAPC4	82	.	0			c.C2163T						PASS	.	G		175,4219		3,169,2025	20.0	21.0	20.0		2163	-1.1	0.0	9	dbSNP_126	20	1685,6903		166,1353,2775	no	coding-synonymous	SNAPC4	NM_003086.2		169,1522,4800	AA,AG,GG		19.6204,3.9827,14.3275		721/1470	139276430	1860,11122	2197	4294	6491	SO:0001819	synonymous_variant	6621	exon17			GGCTCTGTGCCGT	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.2163C>T	9.37:g.139276430G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			G|0.876;A|0.124	0.124	strong		0.667	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
BCDIN3D	144233	hgsc.bcm.edu	37	12	50232496	50232496	+	Silent	SNP	T	T	C	rs17260403	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:50232496T>C	ENST00000333924.4	-	2	578	c.537A>G	c.(535-537)ctA>ctG	p.L179L	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	179	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						GGAACTCCCATAGGCCATGGT	0.512											OREG0021805	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	179	0.0357428	0.0045	0.0461	5008	,	,		20862	0.001		0.1302	False		,,,				2504	0.0092				p.L179L		Atlas-SNP	.											.	BCDIN3D	20	.	0			c.A537G						PASS	.	T		92,4314	77.8+/-116.1	1,90,2112	97.0	82.0	87.0		537	-1.2	0.4	12	dbSNP_123	87	898,7702	201.8+/-245.2	44,810,3446	no	coding-synonymous	BCDIN3D	NM_181708.2		45,900,5558	CC,CT,TT		10.4419,2.0881,7.6119		179/293	50232496	990,12016	2203	4300	6503	SO:0001819	synonymous_variant	144233	exon2			CTCCCATAGGCCA		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.537A>G	12.37:g.50232496T>C		Somatic	62	0	0	968	WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_181708	A8K829	Silent	SNP	ENST00000333924.4	37	CCDS8790.1																																																																																			T|0.938;C|0.062	0.062	strong		0.512	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	
SULF1	23213	hgsc.bcm.edu	37	8	70513996	70513996	+	Silent	SNP	C	C	T	rs556585631		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:70513996C>T	ENST00000260128.4	+	10	1710	c.993C>T	c.(991-993)tcC>tcT	p.S331S	SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000419716.3_Silent_p.S331S|SULF1_ENST00000458141.2_Silent_p.S331S|SULF1_ENST00000402687.4_Silent_p.S331S	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	331					apoptotic process (GO:0006915)|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 angiogenesis (GO:0016525)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of prostatic bud formation (GO:0060686)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	Breast(64;0.0654)		Epithelial(68;0.0124)|OV - Ovarian serous cystadenocarcinoma(28;0.0265)|all cancers(69;0.0534)			AGGGGAAATCCATGCCATATG	0.448																																					p.S331S		Atlas-SNP	.											SULF1,NS,malignant_melanoma,+1,1	SULF1	153	1	0			c.C993T						scavenged	.						402.0	345.0	364.0					8																	70513996		2203	4300	6503	SO:0001819	synonymous_variant	23213	exon10			GAAATCCATGCCA	AB029000	CCDS6204.1	8q13.2	2014-09-11			ENSG00000137573	ENSG00000137573			20391	protein-coding gene	gene with protein product		610012				12368295	Standard	NM_015170		Approved	KIAA1077, SULF-1	uc003xyd.2	Q8IWU6	OTTHUMG00000164466	ENST00000260128.4:c.993C>T	8.37:g.70513996C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	291	4	0.0137457	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Silent	SNP	ENST00000260128.4	37	CCDS6204.1																																																																																			.	.	none		0.448	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170	
FER1L6	654463	hgsc.bcm.edu	37	8	125107207	125107207	+	Silent	SNP	C	C	T	rs6470220	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:125107207C>T	ENST00000522917.1	+	35	4829	c.4623C>T	c.(4621-4623)gtC>gtT	p.V1541V	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Silent_p.V1541V	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1541						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)			TCCCGGAAGTCGGGTGTAGGC	0.493													C|||	3804	0.759585	0.733	0.7003	5008	,	,		18807	0.6627		0.8728	False		,,,				2504	0.8211				p.V1541V		Atlas-SNP	.											.	FER1L6	268	.	0			c.C4623T						PASS	.	C		2907,915		1102,703,106	90.0	84.0	86.0		4623	-4.4	1.0	8	dbSNP_116	86	7120,1146		3065,990,78	no	coding-synonymous	FER1L6	NM_001039112.2		4167,1693,184	TT,TC,CC		13.864,23.9403,17.05		1541/1858	125107207	10027,2061	1911	4133	6044	SO:0001819	synonymous_variant	654463	exon35			GGAAGTCGGGTGT	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.4623C>T	8.37:g.125107207C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			C|0.200;T|0.800	0.800	strong		0.493	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
KCNQ4	9132	hgsc.bcm.edu	37	1	41285585	41285585	+	Silent	SNP	G	G	A	rs12117176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41285585G>A	ENST00000347132.5	+	6	955	c.873G>A	c.(871-873)ccG>ccA	p.P291P	KCNQ4_ENST00000509682.2_Silent_p.P291P|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	291					inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	ACAAGACACCGCACACATGGC	0.587													G|||	579	0.115615	0.0159	0.0994	5008	,	,		19143	0.247		0.1014	False		,,,				2504	0.1411				p.P291P		Atlas-SNP	.											.	KCNQ4	58	.	0			c.G873A						PASS	.	G	,	126,4280	89.7+/-128.4	3,120,2080	149.0	149.0	149.0		873,873	-11.4	0.1	1	dbSNP_120	149	731,7869	168.6+/-220.1	40,651,3609	no	coding-synonymous,coding-synonymous	KCNQ4	NM_004700.3,NM_172163.2	,	43,771,5689	AA,AG,GG		8.5,2.8597,6.5893	,	291/696,291/642	41285585	857,12149	2203	4300	6503	SO:0001819	synonymous_variant	9132	exon6			GACACCGCACACA	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.873G>A	1.37:g.41285585G>A		Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	165	155	0.939394	NM_004700	O96025	Silent	SNP	ENST00000347132.5	37	CCDS456.1	254	0.1163003663003663	6	0.012195121951219513	38	0.10497237569060773	132	0.23076923076923078	78	0.10290237467018469	G	9.673	1.147361	0.21288	0.028597	0.085	ENSG00000117013	ENST00000443478	.	.	.	5.71	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998329	.	.	.	.	.	.	T	0.06215	-1.0839	3	.	.	.	-16.3202	3.6278	0.08120	0.2009:0.2415:0.4067:0.1509	rs12117176	.	.	.	T	187	.	.	A	+	1	0	KCNQ4	41058172	0.000000	0.05858	0.133000	0.22050	0.932000	0.56968	-2.861000	0.00726	-2.601000	0.00451	-1.648000	0.00760	GCA	G|0.918;A|0.082	0.082	strong		0.587	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
MYLK3	91807	hgsc.bcm.edu	37	16	46773999	46773999	+	Missense_Mutation	SNP	C	C	A	rs28407821	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:46773999C>A	ENST00000394809.4	-	2	653	c.538G>T	c.(538-540)Gtg>Ttg	p.V180L	MYLK3_ENST00000536476.1_5'UTR	NM_182493.2	NP_872299.2	Q32MK0	MYLK3_HUMAN	myosin light chain kinase 3	180			V -> L (in dbSNP:rs28407821). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		cardiac myofibril assembly (GO:0055003)|cellular response to interleukin-1 (GO:0071347)|positive regulation of sarcomere organization (GO:0060298)|protein phosphorylation (GO:0006468)|regulation of vascular permeability involved in acute inflammatory response (GO:0002528)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|myosin light chain kinase activity (GO:0004687)	p.V180L(1)|p.V231L(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(5)|stomach(3)	37		all_cancers(37;0.00023)|all_epithelial(9;0.000543)|all_lung(18;0.00585)|Lung NSC(13;0.0496)|Breast(268;0.116)				TCAGACTGCACCCCACTGGTG	0.453													C|||	2334	0.466054	0.1203	0.464	5008	,	,		18437	0.5536		0.5984	False		,,,				2504	0.7086				p.V180L		Atlas-SNP	.											MYLK3,NS,carcinoma,0,2	MYLK3	82	2	2	Substitution - Missense(2)	stomach(2)	c.G538T						scavenged	.	C	LEU/VAL	875,3531	341.5+/-306.7	99,677,1427	202.0	176.0	185.0		538	2.6	0.1	16	dbSNP_125	185	5060,3540	631.9+/-398.5	1498,2064,738	yes	missense	MYLK3	NM_182493.2	32	1597,2741,2165	AA,AC,CC		41.1628,19.8593,45.6328	possibly-damaging	180/820	46773999	5935,7071	2203	4300	6503	SO:0001583	missense	91807	exon2			ACTGCACCCCACT	AJ247087	CCDS10723.2	16q11.2	2008-10-23			ENSG00000140795	ENSG00000140795			29826	protein-coding gene	gene with protein product	"""MLC kinase"""	612147				17885681	Standard	NM_182493		Approved	caMLCK, MLCK	uc002eei.4	Q32MK0	OTTHUMG00000132543	ENST00000394809.4:c.538G>T	16.37:g.46773999C>A	ENSP00000378288:p.Val180Leu	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_182493	B5BUL9|B7Z5U8|Q32MK1|Q96DV1	Missense_Mutation	SNP	ENST00000394809.4	37	CCDS10723.2	1020	0.46703296703296704	56	0.11382113821138211	179	0.494475138121547	316	0.5524475524475524	469	0.6187335092348285	C	12.44	1.938748	0.34189	0.198593	0.588372	ENSG00000140795	ENST00000394809	T	0.72505	-0.66	5.58	2.57	0.30868	.	0.601209	0.12878	N	0.431687	T	0.00012	0.0000	L	0.40543	1.245	0.36580	P	0.12650499999999998	B	0.09022	0.002	B	0.04013	0.001	T	0.44922	-0.9296	9	0.31617	T	0.26	.	5.3239	0.15895	0.1413:0.5918:0.0:0.2669	rs28407821;rs59283497;rs28407821	180	Q32MK0	MYLK3_HUMAN	L	180	ENSP00000378288:V180L	ENSP00000378288:V180L	V	-	1	0	MYLK3	45331500	0.026000	0.19158	0.050000	0.19076	0.007000	0.05969	1.065000	0.30592	0.400000	0.25396	-0.158000	0.13435	GTG	C|0.544;A|0.456	0.456	strong		0.453	MYLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255743.2	NM_182493	
TRIM66	9866	hgsc.bcm.edu	37	11	8671369	8671369	+	Silent	SNP	C	C	T	rs10840101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:8671369C>T	ENST00000299550.6	-	3	269	c.75G>A	c.(73-75)ctG>ctA	p.L25L	TRIM66_ENST00000531498.1_5'UTR|TRIM66_ENST00000402157.2_Silent_p.L25L	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	25						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						AAGAGCTGCACAGCCAGCGAT	0.562													C|||	742	0.148163	0.0076	0.2003	5008	,	,		19751	0.1329		0.2744	False		,,,				2504	0.1871				p.L25L		Atlas-SNP	.											.	TRIM66	45	.	0			c.G75A						PASS	.	C		70,1314		1,68,623	74.0	74.0	74.0		75	-0.9	1.0	11	dbSNP_120	74	954,2228		131,692,768	no	coding-synonymous	TRIM66	NM_014818.1		132,760,1391	TT,TC,CC		29.9811,5.0578,22.4266		25/1217	8671369	1024,3542	692	1591	2283	SO:0001819	synonymous_variant	9866	exon3			GCTGCACAGCCAG	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.75G>A	11.37:g.8671369C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_014818	Q9BQQ4	Silent	SNP	ENST00000299550.6	37																																																																																				C|0.817;T|0.183	0.183	strong		0.562	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
ARHGEF7	8874	hgsc.bcm.edu	37	13	111938511	111938511	+	Silent	SNP	T	T	C	rs72653559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:111938511T>C	ENST00000375741.2	+	18	2281	c.2031T>C	c.(2029-2031)ccT>ccC	p.P677P	ARHGEF7_ENST00000218789.5_Silent_p.P499P|ARHGEF7_ENST00000375739.2_Silent_p.P627P|ARHGEF7_ENST00000375736.4_Silent_p.P499P|ARHGEF7_ENST00000370623.3_Silent_p.P584P|ARHGEF7_ENST00000426073.2_Silent_p.P499P|ARHGEF7_ENST00000375723.1_Silent_p.P499P|ARHGEF7_ENST00000478679.1_Silent_p.P421P|ARHGEF7_ENST00000375737.5_Silent_p.P574P|ARHGEF7_ENST00000317133.5_Silent_p.P656P	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	677					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			GTAAGAGCCCTAAGACCATGA	0.468													C|||	46	0.0091853	0.0061	0.0202	5008	,	,		18205	0.0		0.0139	False		,,,				2504	0.0102				p.P677P		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.T2031C						PASS	.	C	,,,,	21,4385	824.4+/-416.5	0,21,2182	82.0	79.0	80.0		2031,1881,1497,1497,1968	1.4	1.0	13	dbSNP_130	80	138,8462	813.1+/-407.0	0,138,4162	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF7	NM_001113511.1,NM_001113512.1,NM_001113513.1,NM_003899.3,NM_145735.2	,,,,	0,159,6344	CC,CT,TT		1.6047,0.4766,1.2225	,,,,	677/804,627/754,499/647,499/647,656/783	111938511	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	8874	exon18			GAGCCCTAAGACC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.2031T>C	13.37:g.111938511T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	71	30	0.422535	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	37	CCDS45068.1																																																																																			T|0.989;C|0.011	0.011	strong		0.468	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
CENPF	1063	hgsc.bcm.edu	37	1	214820099	214820099	+	Missense_Mutation	SNP	A	A	G	rs3748697	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:214820099A>G	ENST00000366955.3	+	13	7354	c.7186A>G	c.(7186-7188)Aat>Gat	p.N2396D		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2492	2 X 177 AA tandem repeats.|Interaction with NDE1 and NDEL1.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AGAAAAAGAAAATCTGACAAA	0.323													A|||	1177	0.235024	0.0522	0.3127	5008	,	,		19895	0.122		0.4831	False		,,,				2504	0.2883				p.N2396D	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,1	CENPF	321	1	0			c.A7186G						PASS	.	A	ASP/ASN	521,3881		44,433,1724	32.0	37.0	35.0		7186	4.0	0.2	1	dbSNP_107	35	4376,4224		1112,2152,1036	yes	missense	CENPF	NM_016343.3	23	1156,2585,2760	GG,GA,AA		49.1163,11.8355,37.6634	benign	2396/3115	214820099	4897,8105	2201	4300	6501	SO:0001583	missense	1063	exon13			AAAGAAAATCTGA	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.7186A>G	1.37:g.214820099A>G	ENSP00000355922:p.Asn2396Asp	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	134	132	0.985075	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	583	0.26694139194139194	34	0.06910569105691057	128	0.35359116022099446	63	0.11013986013986014	358	0.47229551451187335	A	3.995	-0.003637	0.07773	0.118355	0.508837	ENSG00000117724	ENST00000366955	T	0.42900	0.96	5.09	3.97	0.46021	Centromere protein Cenp-F, leucine-rich repeat-containing domain (1);	0.178649	0.27008	N	0.021399	T	0.00012	0.0000	L	0.48642	1.525	0.37429	P	0.08606100000000005	B	0.15473	0.013	B	0.17433	0.018	T	0.46816	-0.9164	9	0.10902	T	0.67	.	5.1495	0.15002	0.7373:0.0:0.0925:0.1701	rs3748697;rs17737483;rs52804761;rs61185773;rs3748697	2492	P49454	CENPF_HUMAN	D	2396	ENSP00000355922:N2396D	ENSP00000355922:N2396D	N	+	1	0	CENPF	212886722	0.000000	0.05858	0.203000	0.23512	0.176000	0.22953	0.342000	0.19926	0.969000	0.38237	0.496000	0.49642	AAT	A|0.689;G|0.311	0.311	strong		0.323	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
CLPSL1	340204	hgsc.bcm.edu	37	6	35748931	35748931	+	Missense_Mutation	SNP	T	T	C	rs34109614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35748931T>C	ENST00000373861.5	+	1	138	c.44T>C	c.(43-45)tTc>tCc	p.F15S	CLPSL1_ENST00000542261.1_Missense_Mutation_p.F14S			A2RUU4	COLL1_HUMAN	colipase-like 1	15			F -> S (in dbSNP:rs34109614).		digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										CTTCTCTTCTTCTTTCTCTTC	0.532													c|||	1485	0.296526	0.3351	0.2522	5008	,	,		19574	0.2917		0.2992	False		,,,				2504	0.2781				p.F15S		Atlas-SNP	.											.	.	.	.	0			c.T44C						PASS	.	T	SER/PHE	1350,2706		224,902,902	161.0	176.0	171.0		44	-0.4	0.0	6	dbSNP_126	171	2676,5686		429,1818,1934	yes	missense	C6orf127	NM_001010886.3	155	653,2720,2836	CC,CT,TT		32.0019,33.284,32.4207	benign	15/122	35748931	4026,8392	2028	4181	6209	SO:0001583	missense	340204	exon1			TCTTCTTCTTTCT		CCDS43456.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000204140	ENSG00000204140			21251	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 127"""	C6orf127			Standard	NM_001010886		Approved	dJ510O8.6	uc003old.4	A2RUU4	OTTHUMG00000014582	ENST00000373861.5:c.44T>C	6.37:g.35748931T>C	ENSP00000362968:p.Phe15Ser	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	160	69	0.43125	NM_001010886	A7E2T6|B2RPE2|B5G4V2|B6ZDM9|Q5T9G1	Missense_Mutation	SNP	ENST00000373861.5	37	CCDS43456.1	635	0.2907509157509158	173	0.3516260162601626	89	0.24585635359116023	147	0.256993006993007	226	0.29815303430079154	c	0.006	-2.049623	0.00394	0.33284	0.320019	ENSG00000204140	ENST00000373861;ENST00000373860;ENST00000542261	T;T	0.31769	1.48;1.49	1.62	-0.45	0.12223	.	1.624490	0.04724	N	0.419874	T	0.02767	0.0083	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30966	-0.9960	9	0.48119	T	0.1	.	2.9097	0.05733	0.0:0.5052:0.2934:0.2014	rs34109614;rs58544058	15	A2RUU4	CF127_HUMAN	S	15;15;14	ENSP00000362968:F15S;ENSP00000438478:F14S	ENSP00000362967:F15S	F	+	2	0	C6orf127	35856909	0.010000	0.17322	0.000000	0.03702	0.038000	0.13279	-0.240000	0.08952	-0.170000	0.10816	-0.741000	0.03529	TTC	C|0.301;G|0.000;T|0.698	0.301	strong		0.532	CLPSL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040317.2	NM_001010886	
OBSCN	84033	hgsc.bcm.edu	37	1	228402508	228402508	+	Silent	SNP	C	C	T	rs2776853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228402508C>T	ENST00000422127.1	+	5	1581	c.1537C>T	c.(1537-1539)Ctg>Ttg	p.L513L	OBSCN_ENST00000570156.2_Silent_p.L513L|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.L513L|C1orf145_ENST00000295012.5_5'Flank	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	513					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GAAGCCTCCCCTGCAACCCCC	0.612													C|||	1381	0.275759	0.3086	0.353	5008	,	,		17070	0.1706		0.3618	False		,,,				2504	0.1963				p.L513L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C1537T						PASS	.	C	,	1272,2538		201,870,834	35.0	39.0	38.0		1537,1537	3.6	0.0	1	dbSNP_100	38	3213,5025		632,1949,1538	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	833,2819,2372	TT,TC,CC		39.0022,33.3858,37.2261	,	513/7969,513/6621	228402508	4485,7563	1905	4119	6024	SO:0001819	synonymous_variant	84033	exon5			CCTCCCCTGCAAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.1537C>T	1.37:g.228402508C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.687;T|0.313	0.313	strong		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CD300E	342510	hgsc.bcm.edu	37	17	72613589	72613589	+	Missense_Mutation	SNP	T	T	G	rs581157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72613589T>G	ENST00000328630.3	-	2	96	c.56A>C	c.(55-57)aAg>aCg	p.K19T	CD300E_ENST00000426295.2_Missense_Mutation_p.K60T|CD300E_ENST00000392619.1_Missense_Mutation_p.K46T			Q496F6	CLM2_HUMAN	CD300e molecule	19	Ig-like V-type.		K -> T (in dbSNP:rs581157). {ECO:0000269|PubMed:15557162}.		innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	19						GCCGGGGCCCTTCAGAGACAA	0.552													G|||	2172	0.433706	0.618	0.3501	5008	,	,		18373	0.3532		0.4294	False		,,,				2504	0.3313				p.K19T		Atlas-SNP	.											.	CD300E	70	.	0			c.A56C						PASS	.	G	THR/LYS	2563,1843	529.0+/-372.6	744,1075,384	41.0	37.0	38.0		56	-3.7	0.0	17	dbSNP_83	38	3781,4819	612.2+/-395.9	842,2097,1361	yes	missense	CD300E	NM_181449.2	78	1586,3172,1745	GG,GT,TT		43.9651,41.8293,48.7775	benign	19/206	72613589	6344,6662	2203	4300	6503	SO:0001583	missense	342510	exon2			GGGCCCTTCAGAG	BX648376	CCDS11702.1	17q25.1	2013-01-11	2006-03-28	2006-02-22	ENSG00000186407	ENSG00000186407		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	28874	protein-coding gene	gene with protein product		609801	"""CD300 antigen like family member E"", ""CD300e antigen"""	CD300LE		15549731, 15557162	Standard	NM_181449		Approved	IREM2, CLM2	uc002jlb.2	Q496F6	OTTHUMG00000067605	ENST00000328630.3:c.56A>C	17.37:g.72613589T>G	ENSP00000329942:p.Lys19Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_181449	B4DNS1|Q7Z7I3	Missense_Mutation	SNP	ENST00000328630.3	37	CCDS11702.1	969	0.44368131868131866	315	0.6402439024390244	126	0.34806629834254144	198	0.34615384615384615	330	0.43535620052770446	G	3.490	-0.104128	0.06967	0.581707	0.439651	ENSG00000186407	ENST00000392619;ENST00000426295;ENST00000328630;ENST00000412268	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	4.62	-3.69	0.04450	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.315838	0.22719	N	0.056466	T	0.00012	0.0000	N	0.00633	-1.31	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42932	-0.9422	9	0.22109	T	0.4	-6.1244	4.5509	0.12112	0.1653:0.5134:0.2025:0.1188	rs581157;rs17470415;rs52818557;rs59897598;rs581157	19	Q496F6	CLM2_HUMAN	T	46;60;19;21	ENSP00000376395:K46T;ENSP00000416642:K60T;ENSP00000329942:K19T;ENSP00000415488:K21T	ENSP00000329942:K19T	K	-	2	0	CD300E	70125184	0.000000	0.05858	0.002000	0.10522	0.157000	0.22087	-3.607000	0.00416	-0.592000	0.05851	-1.623000	0.00790	AAG	T|0.531;G|0.469	0.469	strong		0.552	CD300E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181449	
MR1	3140	hgsc.bcm.edu	37	1	181018236	181018236	+	Missense_Mutation	SNP	A	A	G	rs2236410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:181018236A>G	ENST00000367580.5	+	2	121	c.116A>G	c.(115-117)cAt>cGt	p.H39R	MR1_ENST00000282990.6_Missense_Mutation_p.H39R|MR1_ENST00000367579.3_Missense_Mutation_p.H39R|MR1_ENST00000434571.2_Missense_Mutation_p.H39R|MR1_ENST00000438435.2_3'UTR	NM_001531.2	NP_001522.1	Q95460	HMR1_HUMAN	major histocompatibility complex, class I-related	39	Alpha-1.|Ligand-binding.		H -> R (in dbSNP:rs2236410). {ECO:0000269|Ref.10}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	MHC class I receptor activity (GO:0032393)|peptide antigen binding (GO:0042605)	p.H39R(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	18					Antithymocyte globulin(DB00098)	GATCCCATCCATGGGGTCCCT	0.542													A|||	966	0.192891	0.1263	0.2161	5008	,	,		17473	0.3502		0.1372	False		,,,				2504	0.1616				p.H39R	Colon(174;1412 1962 45296 46549 47110)	Atlas-SNP	.											MR1,NS,carcinoma,0,1	MR1	46	1	1	Substitution - Missense(1)	stomach(1)	c.A116G						PASS	.	A	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	593,3813	258.3+/-262.4	44,505,1654	50.0	51.0	50.0		116,116,116,116	-6.8	0.0	1	dbSNP_98	50	1339,7261	262.1+/-284.2	97,1145,3058	no	missense,missense,missense,missense	MR1	NM_001194999.1,NM_001195000.1,NM_001195035.1,NM_001531.2	29,29,29,29	141,1650,4712	GG,GA,AA		15.5698,13.4589,14.8547	benign,benign,benign,benign	39/297,39/250,39/215,39/342	181018236	1932,11074	2203	4300	6503	SO:0001583	missense	3140	exon3			CCATCCATGGGGT	AF010446	CCDS1342.1, CCDS53440.1, CCDS53441.1, CCDS53442.1	1q25.3	2013-01-11	2003-03-05	2003-03-07	ENSG00000153029	ENSG00000153029		"""Immunoglobulin superfamily / C1-set domain containing"""	4975	protein-coding gene	gene with protein product		600764	"""major histocompatibility complex, class I-like sequence"""	HLALS		7624800, 9784382	Standard	NM_001194999		Approved		uc001goq.2	Q95460	OTTHUMG00000035175	ENST00000367580.5:c.116A>G	1.37:g.181018236A>G	ENSP00000356552:p.His39Arg	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	286	167	0.583916	NM_001195035	A8K2V9|B4E3B1|O97985|O97986|Q53GM1|Q95HB8|Q9MY23|Q9NPL2|Q9TQB3|Q9TQB9|Q9TQK3	Missense_Mutation	SNP	ENST00000367580.5	37	CCDS1342.1	450	0.20604395604395603	68	0.13821138211382114	73	0.20165745856353592	207	0.3618881118881119	102	0.1345646437994723	A	7.426	0.637720	0.14386	0.134589	0.155698	ENSG00000153029	ENST00000434571;ENST00000367580;ENST00000282990;ENST00000367579	T;T;T;D	0.88741	9.51;9.51;9.51;-2.42	4.78	-6.85	0.01681	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	1.135970	0.06552	N	0.745148	T	0.00012	0.0000	N	0.02120	-0.675	0.22601	P	0.998948	B;P;P;P;B	0.37276	0.158;0.589;0.589;0.473;0.0	B;B;B;B;B	0.38106	0.067;0.083;0.173;0.265;0.001	T	0.04153	-1.0973	9	0.02654	T	1	.	3.7899	0.08716	0.2244:0.5:0.1585:0.117	rs2236410;rs2236410	39;39;39;39;39	B4E3B1;Q95460-3;Q95460-2;Q95460;Q95460-4	.;.;.;HMR1_HUMAN;.	R	39	ENSP00000388504:H39R;ENSP00000356552:H39R;ENSP00000282990:H39R;ENSP00000356551:H39R	ENSP00000282990:H39R	H	+	2	0	MR1	179284859	0.000000	0.05858	0.000000	0.03702	0.213000	0.24496	0.431000	0.21444	-1.392000	0.02082	-0.425000	0.05940	CAT	A|0.833;G|0.167	0.167	strong		0.542	MR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085134.2	NM_001531	
ABCA13	154664	hgsc.bcm.edu	37	7	48287840	48287840	+	Missense_Mutation	SNP	G	G	A	rs2361519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48287840G>A	ENST00000435803.1	+	14	1688	c.1664G>A	c.(1663-1665)cGt>cAt	p.R555H		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	555			R -> H (in dbSNP:rs2361519).		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						GTTAAGGATCGTATTTTGCAA	0.378													G|||	992	0.198083	0.3003	0.1873	5008	,	,		19918	0.1508		0.1123	False		,,,				2504	0.2045				p.R555H		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G1664A						PASS	.	G	HIS/ARG	990,2674		139,712,981	57.0	55.0	56.0		1664	-8.6	0.0	7	dbSNP_100	56	924,7248		55,814,3217	yes	missense	ABCA13	NM_152701.3	29	194,1526,4198	AA,AG,GG		11.3069,27.0197,16.171	benign	555/5059	48287840	1914,9922	1832	4086	5918	SO:0001583	missense	154664	exon14			AGGATCGTATTTT	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.1664G>A	7.37:g.48287840G>A	ENSP00000411096:p.Arg555His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	409	0.18727106227106227	155	0.3150406504065041	65	0.17955801104972377	102	0.17832167832167833	87	0.11477572559366754	G	0.438	-0.899834	0.02472	0.270197	0.113069	ENSG00000179869	ENST00000435803	D	0.88201	-2.35	4.29	-8.57	0.00900	.	1.686530	0.03124	N	0.164131	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.46898	-0.9158	9	0.02654	T	1	.	15.1309	0.72523	0.3917:0.0:0.6083:0.0	rs2361519;rs4283998;rs2361519	555	Q86UQ4	ABCAD_HUMAN	H	555	ENSP00000411096:R555H	ENSP00000411096:R555H	R	+	2	0	ABCA13	48258386	0.000000	0.05858	0.002000	0.10522	0.607000	0.37147	-1.368000	0.02580	-1.979000	0.00992	-1.099000	0.02127	CGT	G|0.802;A|0.197	0.197	strong		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
FAM47C	442444	hgsc.bcm.edu	37	X	37028127	37028127	+	Silent	SNP	A	A	G	rs73631164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:37028127A>G	ENST00000358047.3	+	1	1696	c.1644A>G	c.(1642-1644)ccA>ccG	p.P548P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	548										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						ATCTCCGCCCAGAGCCTCCTG	0.612													-|||	1420	0.376159	0.6589	0.245	3775	,	,		12948	0.0982		0.0785	False		,,,				2504	0.2055				p.P548P		Atlas-SNP	.											.	FAM47C	267	.	0			c.A1644G						PASS	.	A		2974,859		997,539,441,95,130	61.0	67.0	65.0		1644	-3.3	0.0	X	dbSNP_130	65	782,5946		26,498,232,1904,1640	no	coding-synonymous	FAM47C	NM_001013736.2		1023,1037,673,1999,1770	GG,GA,G,AA,A		11.6231,22.4106,35.5648		548/1036	37028127	3756,6805	2202	4300	6502	SO:0001819	synonymous_variant	442444	exon1			CCGCCCAGAGCCT	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1644A>G	X.37:g.37028127A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001013736	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																			A|0.644;G|0.356	0.356	strong		0.612	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
KRT7	3855	hgsc.bcm.edu	37	12	52639302	52639302	+	Missense_Mutation	SNP	G	G	C	rs2608009	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52639302G>C	ENST00000331817.5	+	7	1274	c.1091G>C	c.(1090-1092)gGc>gCc	p.G364A	RP3-416H24.1_ENST00000546686.1_RNA|KRT7_ENST00000552322.1_3'UTR	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	364	Coil 2.|Rod.		G -> A (in dbSNP:rs2608009). {ECO:0000269|PubMed:10492017, ECO:0000269|PubMed:12359226, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2415537, ECO:0000269|PubMed:2459129}.		viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	CTGCAGCGGGGCAAGCAGGAT	0.642													C|||	4468	0.892173	0.9773	0.8458	5008	,	,		19790	0.9067		0.8171	False		,,,				2504	0.8722				p.G364A		Atlas-SNP	.											.	KRT7	48	.	0			c.G1091C						PASS	.	C	ALA/GLY	4129,277	141.9+/-177.2	1937,255,11	49.0	50.0	49.0		1091	3.4	0.9	12	dbSNP_100	49	6900,1700	292.3+/-300.8	2769,1362,169	no	missense	KRT7	NM_005556.3	60	4706,1617,180	CC,CG,GG		19.7674,6.2869,15.2007	benign	364/470	52639302	11029,1977	2203	4300	6503	SO:0001583	missense	3855	exon7			AGCGGGGCAAGCA		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.1091G>C	12.37:g.52639302G>C	ENSP00000329243:p.Gly364Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Missense_Mutation	SNP	ENST00000331817.5	37	CCDS8822.1	1907	0.8731684981684982	481	0.9776422764227642	285	0.787292817679558	511	0.8933566433566433	630	0.8311345646437994	C	5.066	0.197835	0.09652	0.937131	0.802326	ENSG00000135480	ENST00000331817;ENST00000422319	T	0.76316	-1.01	4.4	3.43	0.39272	Filament (1);	0.420395	0.17687	N	0.165421	T	0.00012	0.0000	N	0.00004	-3.39	0.50171	P	1.4899999999995472E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47045	-0.9147	9	0.02654	T	1	.	15.0864	0.72158	0.0:0.7332:0.2668:0.0	rs2608009;rs3741723;rs17433043;rs17856069;rs59686101;rs2608009	364	P08729	K2C7_HUMAN	A	364;340	ENSP00000329243:G364A	ENSP00000329243:G364A	G	+	2	0	KRT7	50925569	1.000000	0.71417	0.861000	0.33841	0.012000	0.07955	4.688000	0.61715	1.232000	0.43678	-0.216000	0.12614	GGC	G|0.148;C|0.852	0.852	strong		0.642	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
YAE1D1	57002	hgsc.bcm.edu	37	7	39610177	39610177	+	Missense_Mutation	SNP	A	A	G	rs6947660	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:39610177A>G	ENST00000223273.2	+	2	245	c.202A>G	c.(202-204)Aaa>Gaa	p.K68E	YAE1D1_ENST00000432096.2_Missense_Mutation_p.K68E|YAE1D1_ENST00000469737.1_3'UTR|YAE1D1_ENST00000448268.1_Missense_Mutation_p.K68E	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	68			K -> E (in dbSNP:rs6947660).														AGGTTATAAGAAAGGTGCAGA	0.368													G|||	776	0.154952	0.298	0.072	5008	,	,		18998	0.1131		0.0984	False		,,,				2504	0.1217				p.K68E		Atlas-SNP	.											.	YAE1D1	2	.	0			c.A202G						PASS	.	G	GLU/LYS	1035,3371	726.8+/-409.8	126,783,1294	133.0	136.0	135.0		202	4.1	1.0	7	dbSNP_116	135	806,7794	782.6+/-407.6	30,746,3524	yes	missense	C7orf36	NM_020192.3	56	156,1529,4818	GG,GA,AA		9.3721,23.4907,14.155	benign	68/227	39610177	1841,11165	2203	4300	6503	SO:0001583	missense	57002	exon2			TATAAGAAAGGTG	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 36"""	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.202A>G	7.37:g.39610177A>G	ENSP00000223273:p.Lys68Glu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Missense_Mutation	SNP	ENST00000223273.2	37	CCDS5459.1	339	0.15521978021978022	163	0.3313008130081301	27	0.07458563535911603	79	0.1381118881118881	70	0.09234828496042216	G	5.662	0.306799	0.10733	0.234907	0.093721	ENSG00000241127	ENST00000223273;ENST00000448268;ENST00000432096	T;T;T	0.38401	1.14;1.14;1.14	6.02	4.12	0.48240	Essential protein Yae1, N-terminal (1);	0.212623	0.48286	N	0.000186	T	0.00012	0.0000	N	0.00146	-1.995	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40813	-0.9543	9	0.02654	T	1	-8.7331	8.356	0.32331	0.1451:0.1927:0.6622:0.0	rs6947660;rs10486684;rs59204652;rs6947660	68	Q9NRH1	CG036_HUMAN	E	68	ENSP00000223273:K68E;ENSP00000400511:K68E;ENSP00000395777:K68E	ENSP00000223273:K68E	K	+	1	0	C7orf36	39576702	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	1.236000	0.32683	0.897000	0.36392	-0.790000	0.03334	AAA	A|0.858;G|0.142	0.142	strong		0.368	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192	
DSPP	1834	hgsc.bcm.edu	37	4	88535868	88535868	+	Missense_Mutation	SNP	A	A	G	rs199719429		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88535868A>G	ENST00000282478.7	+	4	2087	c.2054A>G	c.(2053-2055)aAc>aGc	p.N685S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.N685S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	685	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagcaacagcagtgat	0.483																																					p.N685S		Atlas-SNP	.											DSPP,NS,carcinoma,-1,2	DSPP	174	2	0			c.A2054G						PASS	.						116.0	132.0	127.0					4																	88535868		1684	3089	4773	SO:0001583	missense	1834	exon5			GCAGCAACAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2054A>G	4.37:g.88535868A>G	ENSP00000282478:p.Asn685Ser	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	193	21	0.108808	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	-	4.290	0.052936	0.08291	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87809	-2.3;-2.3	1.5	0.247	0.15521	.	.	.	.	.	T	0.69287	0.3094	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.54833	-0.8234	9	0.02654	T	1	0.1107	4.5905	0.12304	0.7937:0.0:0.2063:0.0	.	685	Q9NZW4	DSPP_HUMAN	S	685	ENSP00000382213:N685S;ENSP00000282478:N685S	ENSP00000282478:N685S	N	+	2	0	DSPP	88754892	0.003000	0.15002	0.026000	0.17262	0.014000	0.08584	1.419000	0.34793	0.077000	0.16863	0.139000	0.15985	AAC	.	.	weak		0.483	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
PCSK9	255738	hgsc.bcm.edu	37	1	55518416	55518416	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:55518416C>T	ENST00000302118.5	+	5	1041	c.751C>T	c.(751-753)Cgc>Tgc	p.R251C	PCSK9_ENST00000543384.1_Missense_Mutation_p.R51C|PCSK9_ENST00000452118.2_3'UTR|PCSK9_ENST00000490692.1_3'UTR	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	251	Peptidase S8.				apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.R251C(1)		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						GCGCAGCCTGCGCGTGCTCAA	0.662																																					p.R251C	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											PCSK9,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,2	PCSK9	76	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.C751T						scavenged	.						44.0	40.0	41.0					1																	55518416		2203	4300	6503	SO:0001583	missense	255738	exon5			AGCCTGCGCGTGC	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.751C>T	1.37:g.55518416C>T	ENSP00000303208:p.Arg251Cys	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	175	5	0.0285714	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.925575	0.73213	.	.	ENSG00000169174	ENST00000302118;ENST00000543384	D;D	0.89875	-2.58;-2.58	3.9	3.9	0.45041	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.000000	0.64402	D	0.000001	D	0.94971	0.8373	M	0.92507	3.315	0.58432	D	0.999993	D	0.89917	1.0	D	0.73380	0.98	D	0.95451	0.8534	10	0.87932	D	0	-22.3967	11.1944	0.48704	0.1839:0.8161:0.0:0.0	.	251	Q8NBP7	PCSK9_HUMAN	C	251;51	ENSP00000303208:R251C;ENSP00000441859:R51C	ENSP00000303208:R251C	R	+	1	0	PCSK9	55291004	0.999000	0.42202	0.999000	0.59377	0.732000	0.41865	3.578000	0.53892	1.691000	0.51100	0.563000	0.77884	CGC	.	.	none		0.662	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
ENPP5	59084	hgsc.bcm.edu	37	6	46129345	46129345	+	Silent	SNP	G	G	A	rs2235881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46129345G>A	ENST00000371383.2	-	5	1412	c.1152C>T	c.(1150-1152)acC>acT	p.T384T	ENPP5_ENST00000230565.3_Silent_p.T384T					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GTGGCATGGCGGTGATATTGA	0.458													G|||	2236	0.446486	0.1899	0.4467	5008	,	,		19626	0.4494		0.5348	False		,,,				2504	0.6994				p.T384T		Atlas-SNP	.											.	ENPP5	44	.	0			c.C1152T						PASS	.	G		1049,3357	383.7+/-325.0	126,797,1280	238.0	235.0	236.0		1152	-8.1	0.0	6	dbSNP_98	236	4592,4008	598.8+/-394.0	1220,2152,928	no	coding-synonymous	ENPP5	NM_021572.4		1346,2949,2208	AA,AG,GG		46.6047,23.8084,43.3723		384/478	46129345	5641,7365	2203	4300	6503	SO:0001819	synonymous_variant	59084	exon4			CATGGCGGTGATA	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.1152C>T	6.37:g.46129345G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	129	65	0.503876	NM_021572		Silent	SNP	ENST00000371383.2	37	CCDS4915.1																																																																																			G|0.569;T|0.002	.	strong		0.458	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
PDE4DIP	9659	hgsc.bcm.edu	37	1	144909956	144909956	+	Silent	SNP	G	G	A	rs638260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144909956G>A	ENST00000369354.3	-	17	2421	c.2232C>T	c.(2230-2232)gaC>gaT	p.D744D	PDE4DIP_ENST00000369359.4_Silent_p.D881D|PDE4DIP_ENST00000530740.1_Silent_p.D881D|PDE4DIP_ENST00000313431.9_Silent_p.D907D|PDE4DIP_ENST00000369351.3_Silent_p.D744D|PDE4DIP_ENST00000529945.1_Silent_p.D907D|PDE4DIP_ENST00000369349.3_Silent_p.D744D|PDE4DIP_ENST00000524974.1_5'Flank|PDE4DIP_ENST00000479408.2_Silent_p.D531D|PDE4DIP_ENST00000369356.4_Silent_p.D744D|PDE4DIP_ENST00000313382.9_Silent_p.D810D			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	744					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTGTGTCCAAGTCTCCTAAAA	0.363			T	PDGFRB	MPD																																p.D907D		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C2721T						PASS	.	C	,,,,	985,3421		0,985,1218	88.0	89.0	88.0		2721,2232,2430,2232,2232	0.0	0.1	1	dbSNP_83	88	1948,6652		0,1948,2352	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	,,,,	0,2933,3570	AA,AG,GG		22.6512,22.3559,22.5511	,,,,	907/1133,744/970,810/2241,744/2363,744/2347	144909956	2933,10073	2203	4300	6503	SO:0001819	synonymous_variant	9659	exon13			GTCCAAGTCTCCT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.2232C>T	1.37:g.144909956G>A		Somatic	311	0	0		WXS	Illumina HiSeq	Phase_I	371	107	0.28841	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			A|0.001;C|0.701	0.001	strong		0.363	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SIGLEC14	100049587	hgsc.bcm.edu	37	19	52149165	52149165	+	Silent	SNP	G	G	A	rs71358847	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52149165G>A	ENST00000360844.6	-	3	611	c.570C>T	c.(568-570)ccC>ccT	p.P190P	SIGLEC5_ENST00000222107.4_Intron|SIGLEC5_ENST00000534261.2_5'Flank|SIGLEC5_ENST00000429354.3_Intron|SIGLEC5_ENST00000599649.1_Intron	NM_001098612.1	NP_001092082.1	Q08ET2	SIG14_HUMAN	sialic acid binding Ig-like lectin 14	190	Ig-like C2-type 1.				cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000965)|OV - Ovarian serous cystadenocarcinoma(262;0.0195)		GGGTGGTCTCGGGGTCCAGGG	0.657													G|||	2173	0.433906	0.475	0.3963	5008	,	,		11433	0.4325		0.3429	False		,,,				2504	0.5				p.P190P		Atlas-SNP	.											.	SIGLEC14	46	.	0			c.C570T						PASS	.	G		1657,2399		519,619,890	10.0	11.0	10.0		570	-2.2	0.0	19	dbSNP_130	10	2942,5324		803,1336,1994	no	coding-synonymous	SIGLEC14	NM_001098612.1		1322,1955,2884	AA,AG,GG		35.5916,40.8531,37.3235		190/397	52149165	4599,7723	2028	4133	6161	SO:0001819	synonymous_variant	100049587	exon3			GGTCTCGGGGTCC	AY854038	CCDS42604.1	19q13.41	2013-01-29			ENSG00000254415	ENSG00000254415		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	32926	protein-coding gene	gene with protein product						17012248	Standard	NM_001098612		Approved		uc002pxf.4	Q08ET2	OTTHUMG00000165511	ENST00000360844.6:c.570C>T	19.37:g.52149165G>A		Somatic	294	1	0.00340136		WXS	Illumina HiSeq	Phase_I	512	209	0.408203	NM_001098612	Q6UXG0	Silent	SNP	ENST00000360844.6	37	CCDS42604.1																																																																																			G|0.621;A|0.379	0.379	strong		0.657	SIGLEC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466899.2	NM_001098612	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94342564	94342564	+	Missense_Mutation	SNP	C	C	A	rs3747965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:94342564C>A	ENST00000436063.2	-	2	984	c.927G>T	c.(925-927)gaG>gaT	p.E309D	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	309			E -> D (in dbSNP:rs3747965). {ECO:0000269|PubMed:12786946, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TTTCTTTCCCCTCATCTGTTA	0.378													C|||	1727	0.344848	0.0817	0.33	5008	,	,		19818	0.5565		0.325	False		,,,				2504	0.5133				p.E309D		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.G927T						PASS	.	C	ASP/GLU	505,3149		34,437,1356	65.0	54.0	58.0		927	0.4	0.0	1	dbSNP_107	58	2741,5429		446,1849,1790	yes	missense	DNTTIP2	NM_014597.4	45	480,2286,3146	AA,AC,CC		33.5496,13.8205,27.4526	possibly-damaging	309/757	94342564	3246,8578	1827	4085	5912	SO:0001583	missense	30836	exon2			TTTCCCCTCATCT	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.927G>T	1.37:g.94342564C>A	ENSP00000411010:p.Glu309Asp	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	741	0.3392857142857143	44	0.08943089430894309	124	0.3425414364640884	325	0.5681818181818182	248	0.32717678100263853	C	7.180	0.589308	0.13812	0.138205	0.335496	ENSG00000067334	ENST00000436063	T	0.22134	1.97	4.83	0.373	0.16178	.	1.095520	0.06942	N	0.813102	T	0.07324	0.0185	L	0.56769	1.78	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.35943	-0.9768	9	0.38643	T	0.18	.	4.5422	0.12064	0.2991:0.529:0.0:0.1719	rs3747965;rs17846411;rs17859454;rs52797280;rs59636660;rs3747965	309	Q5QJE6	TDIF2_HUMAN	D	309	ENSP00000411010:E309D	ENSP00000352137:E309D	E	-	3	2	DNTTIP2	94115152	0.000000	0.05858	0.001000	0.08648	0.292000	0.27327	-1.753000	0.01818	-0.083000	0.12618	-0.345000	0.07892	GAG	C|0.661;A|0.339	0.339	strong		0.378	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
WDR62	284403	hgsc.bcm.edu	37	19	36594063	36594063	+	Silent	SNP	C	C	T	rs17851502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36594063C>T	ENST00000270301.7	+	29	3453	c.3453C>T	c.(3451-3453)ctC>ctT	p.L1151L	WDR62_ENST00000401500.2_Silent_p.L1156L			O43379	WDR62_HUMAN	WD repeat domain 62	1151					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			TGCAGGTCCTCGCTGCAGGGA	0.667													C|||	607	0.121206	0.2557	0.072	5008	,	,		20422	0.0		0.1342	False		,,,				2504	0.0859				p.L1156L		Atlas-SNP	.											.	WDR62	102	.	0			c.C3468T						PASS	.	C	,	978,3428	359.6+/-314.9	106,766,1331	46.0	45.0	45.0		3468,3453	-3.1	0.0	19	dbSNP_123	45	885,7715	194.8+/-240.1	52,781,3467	yes	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	158,1547,4798	TT,TC,CC		10.2907,22.197,14.3242	,	1156/1524,1151/1519	36594063	1863,11143	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon29			GGTCCTCGCTGCA	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.3453C>T	19.37:g.36594063C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	107	64	0.598131	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			C|0.869;T|0.131	0.131	strong		0.667	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
NPLOC4	55666	hgsc.bcm.edu	37	17	79580457	79580457	+	Silent	SNP	C	C	A	rs17852306	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79580457C>A	ENST00000331134.6	-	4	488	c.273G>T	c.(271-273)acG>acT	p.T91T	NPLOC4_ENST00000539314.1_5'UTR|NPLOC4_ENST00000574344.1_5'UTR|NPLOC4_ENST00000374747.5_Silent_p.T91T	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	91					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GTGGAACTGACGTCTCCATTT	0.512													C|||	428	0.0854633	0.053	0.0303	5008	,	,		17895	0.2212		0.0437	False		,,,				2504	0.0716				p.T91T		Atlas-SNP	.											.	NPLOC4	27	.	0			c.G273T						PASS	.	C		142,3802		1,140,1831	86.0	82.0	83.0		273	-8.4	0.2	17	dbSNP_123	83	337,7965		7,323,3821	no	coding-synonymous	NPLOC4	NM_017921.2		8,463,5652	AA,AC,CC		4.0593,3.6004,3.9115		91/609	79580457	479,11767	1972	4151	6123	SO:0001819	synonymous_variant	55666	exon4			AACTGACGTCTCC	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.273G>T	17.37:g.79580457C>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Silent	SNP	ENST00000331134.6	37	CCDS45812.1																																																																																			C|0.916;A|0.084	0.084	strong		0.512	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228504591	228504591	+	Missense_Mutation	SNP	C	C	A	rs61825301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228504591C>A	ENST00000422127.1	+	51	13511	c.13467C>A	c.(13465-13467)caC>caA	p.H4489Q	OBSCN_ENST00000366707.4_Missense_Mutation_p.H2123Q|OBSCN_ENST00000366709.4_Missense_Mutation_p.H1608Q|OBSCN_ENST00000284548.11_Missense_Mutation_p.H4489Q|OBSCN_ENST00000570156.2_Missense_Mutation_p.H5446Q	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4489	Ig-like 46.			H -> Q (in Ref. 1; CAC44768). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCAGTCACCACGCCCTACTGC	0.716													c|||	728	0.145367	0.121	0.2349	5008	,	,		14096	0.1518		0.159	False		,,,				2504	0.0941				p.H5446Q		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C16338A						PASS	.		GLN/HIS,GLN/HIS	675,3615		55,565,1525	9.0	14.0	12.0		13467,13467	0.2	0.1	1	dbSNP_129	12	1406,7004		118,1170,2917	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	24,24	173,1735,4442	AA,AC,CC		16.7182,15.7343,16.3858	probably-damaging,probably-damaging	4489/7969,4489/6621	228504591	2081,10619	2145	4205	6350	SO:0001583	missense	84033	exon62			TCACCACGCCCTA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13467C>A	1.37:g.228504591C>A	ENSP00000409493:p.His4489Gln	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	36	23	0.638889	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	346	0.15842490842490842	50	0.1016260162601626	86	0.23756906077348067	87	0.1520979020979021	123	0.16226912928759896	c	12.44	1.937450	0.34189	0.157343	0.167182	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.76968	-1.06;-1.06;0.09;0.6	5.41	0.187	0.15109	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.149471	0.46758	D	0.000266	T	0.00073	0.0002	L	0.59967	1.855	0.49130	P	2.4400000000002198E-4	D;D	0.76494	0.998;0.999	P;D	0.64042	0.835;0.921	T	0.16158	-1.0412	9	0.29301	T	0.29	.	9.7878	0.40686	0.0:0.5739:0.0:0.4261	rs61825301	4489;4489	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	Q	4489;4489;2123;1608	ENSP00000284548:H4489Q;ENSP00000409493:H4489Q;ENSP00000355668:H2123Q;ENSP00000355670:H1608Q	ENSP00000284548:H4489Q	H	+	3	2	OBSCN	226571214	0.000000	0.05858	0.074000	0.20217	0.153000	0.21895	-0.722000	0.04958	-0.223000	0.09943	0.550000	0.68814	CAC	C|0.841;A|0.159	0.159	strong		0.716	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MUC16	94025	hgsc.bcm.edu	37	19	9056989	9056989	+	Missense_Mutation	SNP	C	C	G	rs4804381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9056989C>G	ENST00000397910.4	-	3	30660	c.30457G>C	c.(30457-30459)Gag>Cag	p.E10153Q		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10155	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						CCTGTGGTCTCAAAATTAGCA	0.463													C|||	932	0.186102	0.0666	0.281	5008	,	,		22984	0.3313		0.167	False		,,,				2504	0.1503				p.E10153Q		Atlas-SNP	.											.	MUC16	4315	.	0			c.G30457C						PASS	.	C	GLN/GLU	314,3536		14,286,1625	76.0	73.0	74.0		30457	-0.7	0.0	19	dbSNP_111	74	1506,6768		136,1234,2767	yes	missense	MUC16	NM_024690.2	29	150,1520,4392	GG,GC,CC		18.2016,8.1558,15.0115	possibly-damaging	10153/14508	9056989	1820,10304	1925	4137	6062	SO:0001583	missense	94025	exon3			TGGTCTCAAAATT	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.30457G>C	19.37:g.9056989C>G	ENSP00000381008:p.Glu10153Gln	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	462	0.21153846153846154	35	0.07113821138211382	93	0.2569060773480663	208	0.36363636363636365	126	0.1662269129287599	c	4.952	0.176786	0.09443	0.081558	0.182016	ENSG00000181143	ENST00000397910	T	0.40756	1.02	2.85	-0.7	0.11273	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	.	.	.	P	0.41041	0.736	B	0.40636	0.335	T	0.37596	-0.9699	8	0.87932	D	0	.	4.9506	0.14011	0.0:0.4393:0.4299:0.1308	rs4804381;rs4804381	10153	B5ME49	.	Q	10153	ENSP00000381008:E10153Q	ENSP00000381008:E10153Q	E	-	1	0	MUC16	8917989	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.107000	0.10873	-0.044000	0.13491	-0.300000	0.09419	GAG	C|0.780;G|0.220	0.220	strong		0.463	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MTCL1	23255	hgsc.bcm.edu	37	18	8825096	8825096	+	Silent	SNP	G	G	A	rs113084211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:8825096G>A	ENST00000306329.11	+	13	4545	c.4545G>A	c.(4543-4545)ccG>ccA	p.P1515P	SOGA2_ENST00000517570.1_Silent_p.P1155P|SOGA2_ENST00000400050.3_Silent_p.P1155P|SOGA2_ENST00000306285.7_Silent_p.P521P|SOGA2_ENST00000359865.3_Silent_p.P1196P|SOGA2_ENST00000518815.1_Silent_p.P521P																							TACACAGCCCGCCTGCCGTGC	0.672													G|||	20	0.00399361	0.0008	0.0029	5008	,	,		18045	0.0		0.0139	False		,,,				2504	0.0031				p.P1196P		Atlas-SNP	.											.	.	.	.	0			c.G3588A						PASS	.	G		20,4358		0,20,2169	44.0	37.0	39.0		3588	-7.8	0.1	18	dbSNP_132	39	180,8386		1,178,4104	no	coding-synonymous	CCDC165	NM_015210.3		1,198,6273	AA,AG,GG		2.1013,0.4568,1.5451		1196/1587	8825096	200,12744	2189	4283	6472	SO:0001819	synonymous_variant	23255	exon15			CAGCCCGCCTGCC																												ENST00000306329.11:c.4545G>A	18.37:g.8825096G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	NM_015210		Silent	SNP	ENST00000306329.11	37																																																																																				G|0.987;A|0.013	0.013	strong		0.672	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
COBLL1	22837	hgsc.bcm.edu	37	2	165551000	165551000	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:165551000G>A	ENST00000392717.2	-	13	3134	c.3130C>T	c.(3130-3132)Ctg>Ttg	p.L1044L	COBLL1_ENST00000194871.6_Silent_p.L1073L|COBLL1_ENST00000409184.3_Silent_p.L1006L|COBLL1_ENST00000375458.2_Silent_p.L968L|COBLL1_ENST00000342193.4_Silent_p.L1006L			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	1044						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						AAAGTCTTCAGATTTTGTGTG	0.473																																					p.L1006L		Atlas-SNP	.											.	COBLL1	122	.	0			c.C3016T						PASS	.						107.0	106.0	106.0					2																	165551000		2203	4300	6503	SO:0001819	synonymous_variant	22837	exon12			TCTTCAGATTTTG	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.3130C>T	2.37:g.165551000G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	147	65	0.442177	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	37																																																																																				.	.	none		0.473	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
TRIM3	10612	hgsc.bcm.edu	37	11	6477831	6477831	+	Silent	SNP	C	C	T	rs10606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6477831C>T	ENST00000525074.1	-	6	1519	c.1125G>A	c.(1123-1125)ccG>ccA	p.P375P	TRIM3_ENST00000529058.1_5'UTR|TRIM3_ENST00000359518.3_Silent_p.P375P|TRIM3_ENST00000536344.1_Silent_p.P256P|TRIM3_ENST00000345851.3_Silent_p.P375P|TRIM3_ENST00000537602.1_Silent_p.P297P	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	375					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P375P(1)		breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCACTGGCACCGGAAGGCGCG	0.637													C|||	940	0.1877	0.2973	0.1772	5008	,	,		18660	0.0188		0.1849	False		,,,				2504	0.2239				p.P375P	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											TRIM3,NS,lymphoid_neoplasm,0,1	TRIM3	67	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1125A						PASS	.	C	,	1261,3125		180,901,1112	31.0	31.0	31.0		1125,1125	-10.3	0.0	11	dbSNP_52	31	1738,6816		198,1342,2737	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	378,2243,3849	TT,TC,CC		20.318,28.7506,23.1762	,	375/745,375/745	6477831	2999,9941	2193	4277	6470	SO:0001819	synonymous_variant	10612	exon6			TGGCACCGGAAGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.1125G>A	11.37:g.6477831C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			C|0.791;T|0.209	0.209	strong		0.637	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
TIMELESS	8914	hgsc.bcm.edu	37	12	56827694	56827694	+	Silent	SNP	C	C	G	rs2279665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56827694C>G	ENST00000553532.1	-	3	264	c.114G>C	c.(112-114)ctG>ctC	p.L38L	TIMELESS_ENST00000229201.4_Silent_p.L38L|TIMELESS_ENST00000554616.1_Silent_p.L38L					timeless circadian clock									p.L38L(1)		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						AATAGCGGATCAGATCCTTCA	0.537													C|||	2351	0.469449	0.6505	0.3141	5008	,	,		21692	0.2619		0.5497	False		,,,				2504	0.4663				p.L38L		Atlas-SNP	.											TIMELESS,NS,carcinoma,0,1	TIMELESS	107	1	1	Substitution - coding silent(1)	stomach(1)	c.G114C						PASS	.	C		2823,1583	667.6+/-401.9	894,1035,274	112.0	111.0	111.0		114	4.6	1.0	12	dbSNP_100	111	4690,3910	605.1+/-394.9	1262,2166,872	no	coding-synonymous	TIMELESS	NM_003920.3		2156,3201,1146	GG,GC,CC		45.4651,35.9283,42.2344		38/1209	56827694	7513,5493	2203	4300	6503	SO:0001819	synonymous_variant	8914	exon3			GCGGATCAGATCC	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.114G>C	12.37:g.56827694C>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_003920		Silent	SNP	ENST00000553532.1	37	CCDS8918.1																																																																																			C|0.472;G|0.528	0.528	strong		0.537	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
TTC28	23331	hgsc.bcm.edu	37	22	28504258	28504258	+	Silent	SNP	A	A	G	rs9625409	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:28504258A>G	ENST00000397906.2	-	7	1716	c.1575T>C	c.(1573-1575)aaT>aaC	p.N525N		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	525					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						TGCCCAGGGCATTGTAGGCAT	0.572													A|||	297	0.0593051	0.0598	0.0677	5008	,	,		18711	0.002		0.0755	False		,,,				2504	0.0951				p.N525N		Atlas-SNP	.											.	TTC28	84	.	0			c.T1575C						PASS	.	A		96,1288		1,94,597	82.0	75.0	77.0		1575	-10.4	0.3	22	dbSNP_119	77	264,2918		15,234,1342	no	coding-synonymous	TTC28	NM_001145418.1		16,328,1939	GG,GA,AA		8.2967,6.9364,7.8844		525/2482	28504258	360,4206	692	1591	2283	SO:0001819	synonymous_variant	23331	exon7			CAGGGCATTGTAG	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.1575T>C	22.37:g.28504258A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			A|0.942;G|0.058	0.058	strong		0.572	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
MX1	4599	hgsc.bcm.edu	37	21	42812891	42812891	+	Silent	SNP	C	C	T	rs467960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:42812891C>T	ENST00000398600.2	+	11	1694	c.669C>T	c.(667-669)atC>atT	p.I223I	MX1_ENST00000455164.2_Silent_p.I223I|MX1_ENST00000288383.6_Silent_p.I200I|AP001610.5_ENST00000411427.1_RNA|MX1_ENST00000398598.3_Silent_p.I223I	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1	223	Dynamin-type G.|GTPase domain (Globular).				apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|response to type I interferon (GO:0034340)|response to virus (GO:0009615)|signal transduction (GO:0007165)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	27		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				ATGTGGACATCGCCACCACAG	0.572													C|||	1777	0.354832	0.3313	0.4424	5008	,	,		16676	0.1062		0.5706	False		,,,				2504	0.3589				p.I223I		Atlas-SNP	.											.	MX1	58	.	0			c.C669T						PASS	.	C	,,	1536,2870	485.8+/-360.4	277,982,944	110.0	102.0	104.0		669,669,669	-2.1	1.0	21	dbSNP_80	104	4955,3645	623.6+/-397.5	1390,2175,735	no	coding-synonymous,coding-synonymous,coding-synonymous	MX1	NM_001144925.1,NM_001178046.1,NM_002462.3	,,	1667,3157,1679	TT,TC,CC		42.3837,34.8616,49.9077	,,	223/663,223/663,223/663	42812891	6491,6515	2203	4300	6503	SO:0001819	synonymous_variant	4599	exon11			GGACATCGCCACC		CCDS13673.1, CCDS74796.1	21q22.3	2014-07-15	2014-07-15		ENSG00000157601	ENSG00000157601			7532	protein-coding gene	gene with protein product	"""interferon-inducible protein p78"""	147150	"""myxovirus (influenza) resistance 1, homolog of murine (interferon-inducible protein p78)"", ""myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)"""			17570575	Standard	XM_005260979		Approved	IFI-78K, MxA	uc010goq.3	P20591	OTTHUMG00000086755	ENST00000398600.2:c.669C>T	21.37:g.42812891C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Silent	SNP	ENST00000398600.2	37	CCDS13673.1																																																																																			C|0.547;T|0.453	0.453	strong		0.572	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		
GBA2	57704	hgsc.bcm.edu	37	9	35749845	35749845	+	5'Flank	SNP	G	G	C	rs2236288	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35749845G>C	ENST00000378103.3	-	0	0				GBA2_ENST00000378094.4_5'Flank|RGP1_ENST00000456972.2_Silent_p.P71P|RGP1_ENST00000378078.4_Silent_p.P31P|GBA2_ENST00000545786.1_5'UTR	NM_020944.2	NP_065995.1	Q9HCG7	GBA2_HUMAN	glucosidase, beta (bile acid) 2						bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|central nervous system neuron development (GO:0021954)|glucosylceramide catabolic process (GO:0006680)|glycoside catabolic process (GO:0016139)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)	beta-glucosidase activity (GO:0008422)|glucosylceramidase activity (GO:0004348)			NS(1)|kidney(3)|large_intestine(5)|lung(5)|ovary(4)|skin(3)	21	all_epithelial(49;0.167)		Lung(28;0.00416)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			ACCCCCTTCCGCCCACGGCCA	0.602													C|||	1579	0.315296	0.4811	0.232	5008	,	,		17770	0.4018		0.2127	False		,,,				2504	0.1667				p.P31P		Atlas-SNP	.											.	RGP1	60	.	0			c.G93C						PASS	.	C		1713,2251		386,941,655	51.0	55.0	54.0		93	0.4	0.7	9	dbSNP_98	54	1743,6575		184,1375,2600	no	coding-synonymous	RGP1	NM_001080496.2		570,2316,3255	CC,CG,GG		20.9546,43.2139,28.1387		31/392	35749845	3456,8826	1982	4159	6141	SO:0001631	upstream_gene_variant	9827	exon2			CCTTCCGCCCACG	AJ309567	CCDS6589.1	9p13.2	2013-09-11			ENSG00000070610	ENSG00000070610			18986	protein-coding gene	gene with protein product	"""bile acid beta-glucosidase"", ""non-lysosomal glucosylceramidase"""	609471	"""spastic paraplegia 46 (autosomal recessive)"""	SPG46		11489889, 23332916, 23332917	Standard	NM_020944		Approved	KIAA1605, AD035, DKFZp762K054	uc003zxw.3	Q9HCG7	OTTHUMG00000021024		9.37:g.35749845G>C	Exception_encountered	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_001080496	D3DRP2|Q5TCV6|Q96A51|Q96LY1|Q96SJ2|Q9H2L8	Silent	SNP	ENST00000378103.3	37	CCDS6589.1																																																																																			G|0.688;C|0.312	0.312	strong		0.602	GBA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055456.1	NM_020944	
FBXO10	26267	hgsc.bcm.edu	37	9	37537557	37537557	+	Silent	SNP	G	G	A	rs7044153	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37537557G>A	ENST00000432825.2	-	3	1017	c.969C>T	c.(967-969)gcC>gcT	p.A323A	FBXO10_ENST00000543968.1_5'Flank|FBXO10_ENST00000541829.1_Intron|RP11-613M10.8_ENST00000544475.1_5'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	323					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		GGGAGCTAGAGGCTGGGCTGG	0.607													G|||	2757	0.550519	0.3116	0.5447	5008	,	,		20557	0.6984		0.6571	False		,,,				2504	0.6155				p.A323A		Atlas-SNP	.											.	FBXO10	75	.	0			c.C969T						PASS	.	G		1554,2422		316,922,750	20.0	24.0	23.0		969	0.9	1.0	9	dbSNP_116	23	5312,3004		1693,1926,539	no	coding-synonymous	FBXO10	NM_012166.2		2009,2848,1289	AA,AG,GG		36.1231,39.0845,44.1425		323/957	37537557	6866,5426	1988	4158	6146	SO:0001819	synonymous_variant	26267	exon3			GCTAGAGGCTGGG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.969C>T	9.37:g.37537557G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Silent	SNP	ENST00000432825.2	37	CCDS47966.1																																																																																			G|0.429;A|0.571	0.571	strong		0.607	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
FYB	2533	hgsc.bcm.edu	37	5	39124367	39124367	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:39124367G>A	ENST00000351578.6	-	12	2111	c.1921C>T	c.(1921-1923)Cct>Tct	p.P641S	FYB_ENST00000505428.1_Missense_Mutation_p.P687S|FYB_ENST00000540520.1_Missense_Mutation_p.P697S|FYB_ENST00000515010.1_Missense_Mutation_p.P641S|FYB_ENST00000512982.1_Missense_Mutation_p.P687S	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	641					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			AATTGTTTAGGAGGAGCAGGG	0.353																																					p.P697S		Atlas-SNP	.											.	FYB	354	.	0			c.C2089T						PASS	.						93.0	84.0	86.0					5																	39124367		1850	4103	5953	SO:0001583	missense	2533	exon13			GTTTAGGAGGAGC	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1921C>T	5.37:g.39124367G>A	ENSP00000316460:p.Pro641Ser	Somatic	332	1	0.00301205		WXS	Illumina HiSeq	Phase_I	302	149	0.493377	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.766616	0.31228	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T;T;T	0.23950	1.88;1.88;2.01;2.01;2.01	5.52	4.64	0.57946	.	0.316489	0.33419	N	0.004937	T	0.19208	0.0461	L	0.43701	1.375	0.26889	N	0.967371	B;P	0.43094	0.376;0.799	B;B	0.35931	0.186;0.214	T	0.10706	-1.0618	10	0.22706	T	0.39	-1.5143	12.0613	0.53564	0.0:0.1728:0.8272:0.0	.	697;641	B4DLN2;O15117	.;FYB_HUMAN	S	641;641;687;687;697;687	ENSP00000316460:P641S;ENSP00000426346:P641S;ENSP00000425845:P687S;ENSP00000427114:P687S;ENSP00000442840:P697S	ENSP00000316460:P641S	P	-	1	0	FYB	39160124	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	1.917000	0.39996	1.532000	0.49169	0.650000	0.86243	CCT	.	.	none		0.353	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
FBXO39	162517	hgsc.bcm.edu	37	17	6683215	6683215	+	Missense_Mutation	SNP	C	C	T	rs4796555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6683215C>T	ENST00000321535.4	+	2	158	c.28C>T	c.(28-30)Ccc>Tcc	p.P10S		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	10			P -> S (in dbSNP:rs4796555).							NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						ACTGATCCAGCCCCAAGACCA	0.537													C|||	1626	0.324681	0.2148	0.2896	5008	,	,		20496	0.6151		0.2107	False		,,,				2504	0.316				p.P10S		Atlas-SNP	.											.	FBXO39	50	.	0			c.C28T						PASS	.	C	SER/PRO	958,3448	361.6+/-315.8	107,744,1352	89.0	85.0	86.0		28	2.3	0.9	17	dbSNP_111	86	1879,6721	334.2+/-320.9	213,1453,2634	yes	missense	FBXO39	NM_153230.2	74	320,2197,3986	TT,TC,CC		21.8488,21.7431,21.813	possibly-damaging	10/443	6683215	2837,10169	2203	4300	6503	SO:0001583	missense	162517	exon2			ATCCAGCCCCAAG	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.28C>T	17.37:g.6683215C>T	ENSP00000321386:p.Pro10Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_153230		Missense_Mutation	SNP	ENST00000321535.4	37	CCDS11082.1	740	0.33882783882783885	109	0.22154471544715448	92	0.2541436464088398	380	0.6643356643356644	159	0.20976253298153033	C	12.69	2.013227	0.35511	0.217431	0.218488	ENSG00000177294	ENST00000321535	T	0.54279	0.58	5.56	2.26	0.28386	.	0.525149	0.18834	N	0.129870	T	0.00012	0.0000	L	0.27053	0.805	0.43338	P	0.004612999999999978	B	0.17465	0.022	B	0.14023	0.01	T	0.44221	-0.9342	9	0.10902	T	0.67	-13.5396	4.7906	0.13247	0.1528:0.6137:0.1485:0.085	rs4796555;rs17794696;rs52829409;rs56480343;rs60341795;rs4796555	10	Q8N4B4	FBX39_HUMAN	S	10	ENSP00000321386:P10S	ENSP00000321386:P10S	P	+	1	0	FBXO39	6623939	0.046000	0.20272	0.902000	0.35471	0.970000	0.65996	0.928000	0.28831	0.813000	0.34350	0.561000	0.74099	CCC	C|0.730;N|0.000	.	strong		0.537	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
GPR1	2825	hgsc.bcm.edu	37	2	207041933	207041933	+	Silent	SNP	T	T	C	rs3755227|rs560796868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:207041933T>C	ENST00000407325.2	-	3	401	c.39A>G	c.(37-39)gaA>gaG	p.E13E	GPR1_ENST00000437420.1_Silent_p.E13E	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	13					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		AGGAATAGTTTTCAAATTCTT	0.358													T|||	435	0.086861	0.0045	0.0951	5008	,	,		17424	0.0724		0.1342	False		,,,				2504	0.1585				p.E13E		Atlas-SNP	.											.	GPR1	38	.	0			c.A39G						PASS	.	T	,	108,4298		4,100,2099	64.0	72.0	69.0		39,39	-3.5	0.7	2	dbSNP_107	69	1176,7422		85,1006,3208	yes	coding-synonymous,coding-synonymous	GPR1	NM_001098199.1,NM_005279.3	,	89,1106,5307	CC,CT,TT		13.6776,2.4512,9.8739	,	13/356,13/356	207041933	1284,11720	2203	4299	6502	SO:0001819	synonymous_variant	2825	exon3			ATAGTTTTCAAAT		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.39A>G	2.37:g.207041933T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	27	0.421875	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	37	CCDS2368.1																																																																																			T|0.899;C|0.101	0.101	strong		0.358	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389005	1389005	+	Missense_Mutation	SNP	T	T	C	rs71614970	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1389005T>C	ENST00000324803.4	+	1	3666	c.706T>C	c.(706-708)Tgc>Cgc	p.C236R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	236					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACGTGCCGATGCGGAGTGCC	0.672													t|||	859	0.171526	0.1059	0.245	5008	,	,		14444	0.0437		0.2913	False		,,,				2504	0.2168				p.C236R		Atlas-SNP	.											CRIPAK,rectum,NS,0,1	CRIPAK	185	1	0			c.T706C						scavenged	.						163.0	133.0	143.0					4																	1389005		2188	4292	6480	SO:0001583	missense	285464	exon1			TGCCGATGCGGAG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.706T>C	4.37:g.1389005T>C	ENSP00000323978:p.Cys236Arg	Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	63	7	0.111111	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	t	1.791	-0.479438	0.04383	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.18338	2.22	1.11	-2.23	0.06930	Post-SET domain (1);	.	.	.	.	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.32214	-0.9915	9	0.46703	T	0.11	.	2.6743	0.05077	0.0:0.3283:0.2597:0.412	.	236	Q8N1N5	CRPAK_HUMAN	R	236;178	ENSP00000323978:C236R	ENSP00000323978:C236R	C	+	1	0	CRIPAK	1379005	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.211000	0.09332	-0.571000	0.06014	-0.530000	0.04314	TGC	C|1.000;|0.000	1.000	weak		0.672	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
FCGBP	8857	hgsc.bcm.edu	37	19	40389657	40389657	+	Missense_Mutation	SNP	T	T	G	rs3746010|rs148187888		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40389657T>G	ENST00000221347.6	-	18	8532	c.8525A>C	c.(8524-8526)aAc>aCc	p.N2842T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2842	Cys-rich.			N -> T (in Ref. 1; BAA19526). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)		p.N2842T(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)			agcACCTTTGTTGACGCAGCT	0.637																																					p.N2842T		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.A8525C						scavenged	.						47.0	40.0	42.0					19																	40389657		2103	3809	5912	SO:0001583	missense	8857	exon18			CCTTTGTTGACGC	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.8525A>C	19.37:g.40389657T>G	ENSP00000221347:p.Asn2842Thr	Somatic	834	0	0		WXS	Illumina HiSeq	Phase_I	330	44	0.133333	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	t	0.013	-1.641107	0.00799	.	.	ENSG00000090920	ENST00000221347	T	0.19938	2.11	2.94	-3.79	0.04320	von Willebrand factor, type C (1);	0.689783	0.12210	N	0.489415	T	0.04952	0.0133	N	0.01219	-0.95	0.09310	N	1	B	0.19935	0.04	B	0.18871	0.023	T	0.41179	-0.9523	10	0.13108	T	0.6	.	6.0306	0.19679	0.0:0.1722:0.2977:0.5301	.	2842	Q9Y6R7	FCGBP_HUMAN	T	2842	ENSP00000221347:N2842T	ENSP00000221347:N2842T	N	-	2	0	FCGBP	45081497	0.511000	0.26179	0.068000	0.19968	0.025000	0.11179	-0.344000	0.07780	-0.736000	0.04831	-0.708000	0.03648	AAC	T|0.250;G|0.750	0.750	weak		0.637	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF236	7776	hgsc.bcm.edu	37	18	74672703	74672703	+	Missense_Mutation	SNP	A	A	G	rs183845634		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:74672703A>G	ENST00000253159.8	+	30	5503	c.5305A>G	c.(5305-5307)Atg>Gtg	p.M1769V	ZNF236_ENST00000320610.9_Missense_Mutation_p.M1771V	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1769					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)		GCAGGTGCACATGAAGAAGCA	0.552													A|||	1	0.000199681	0.0	0.0	5008	,	,		19924	0.0		0.001	False		,,,				2504	0.0				p.M1769V		Atlas-SNP	.											.	ZNF236	325	.	0			c.A5305G						PASS	.	A	VAL/MET	0,4100		0,0,2050	88.0	95.0	92.0		5305	1.8	1.0	18		92	5,8409		0,5,4202	yes	missense	ZNF236	NM_007345.3	21	0,5,6252	GG,GA,AA		0.0594,0.0,0.04	benign	1769/1846	74672703	5,12509	2050	4207	6257	SO:0001583	missense	7776	exon30			GTGCACATGAAGA	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.5305A>G	18.37:g.74672703A>G	ENSP00000253159:p.Met1769Val	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	11.72	1.724148	0.30593	0.0	5.94E-4	ENSG00000130856	ENST00000253159	T	0.10573	2.86	5.61	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.07773	0.0195	L	0.37750	1.13	0.28794	N	0.899167	B	0.24186	0.099	B	0.28465	0.09	T	0.27971	-1.0058	10	0.27785	T	0.31	.	4.7999	0.13292	0.6934:0.1236:0.065:0.118	.	1769	Q9UL36	ZN236_HUMAN	V	1769	ENSP00000253159:M1769V	ENSP00000253159:M1769V	M	+	1	0	ZNF236	72801691	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.024000	0.57218	0.058000	0.16222	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	strong		0.552	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
OR13C2	392376	hgsc.bcm.edu	37	9	107367704	107367704	+	Missense_Mutation	SNP	A	A	T	rs201900693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107367704A>T	ENST00000542196.1	-	1	247	c.205T>A	c.(205-207)Ttg>Atg	p.L69M		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	69						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CAGATGTCCAAGAAGGAGAGG	0.483													A|||	215	0.0429313	0.0893	0.0115	5008	,	,		20012	0.0476		0.004	False		,,,				2504	0.0378				p.L69M		Atlas-SNP	.											OR13C2,NS,carcinoma,0,1	OR13C2	46	1	0			c.T205A						scavenged	.						16.0	18.0	18.0					9																	107367704		2196	4277	6473	SO:0001583	missense	392376	exon1			TGTCCAAGAAGGA		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.205T>A	9.37:g.107367704A>T	ENSP00000438815:p.Leu69Met	Somatic	641	0	0		WXS	Illumina HiSeq	Phase_I	665	48	0.0721804	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	.	.	.	.	.	.	.	.	.	.	A	13.36	2.214684	0.39102	.	.	ENSG00000257019	ENST00000542196	T	0.14391	2.51	3.39	-2.32	0.06745	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29948	U	0.010786	T	0.19208	0.0461	L	0.58302	1.8	0.09310	N	1	D	0.65815	0.995	P	0.53401	0.725	T	0.09058	-1.0692	10	0.56958	D	0.05	.	9.8961	0.41320	0.3456:0.0:0.6544:0.0	.	69	Q8NGS9	O13C2_HUMAN	M	69	ENSP00000438815:L69M	ENSP00000438815:L69M	L	-	1	2	OR13C2	106407525	0.000000	0.05858	0.993000	0.49108	0.979000	0.70002	-3.903000	0.00338	-0.393000	0.07739	0.379000	0.24179	TTG	A|0.222;T|0.778	0.778	strong		0.483	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
FAF1	11124	hgsc.bcm.edu	37	1	51121198	51121198	+	Silent	SNP	T	T	C	rs11205753	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:51121198T>C	ENST00000396153.2	-	8	1111	c.660A>G	c.(658-660)gtA>gtG	p.V220V	FAF1_ENST00000371778.4_Silent_p.V220V	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	220					apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(1)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		CATTTCTCTTTACCTATGAAA	0.373													T|||	462	0.0922524	0.0182	0.0706	5008	,	,		17097	0.001		0.1113	False		,,,				2504	0.2822				p.V220V		Atlas-SNP	.											.	FAF1	64	.	1	Whole gene deletion(1)	thyroid(1)	c.A660G						PASS	.	T		169,4237	113.3+/-151.4	3,163,2037	97.0	92.0	93.0		660	3.9	1.0	1	dbSNP_120	93	1109,7491	227.6+/-262.9	78,953,3269	no	coding-synonymous	FAF1	NM_007051.2		81,1116,5306	CC,CT,TT		12.8953,3.8357,9.8262		220/651	51121198	1278,11728	2203	4300	6503	SO:0001819	synonymous_variant	11124	exon8			TCTCTTTACCTAT	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.660A>G	1.37:g.51121198T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Silent	SNP	ENST00000396153.2	37	CCDS554.1																																																																																			T|0.918;C|0.082	0.082	strong		0.373	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187698751	187698751	+	Silent	SNP	G	G	A	rs7559533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:187698751G>A	ENST00000295131.2	-	6	789	c.750C>T	c.(748-750)acC>acT	p.T250T		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	250					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CTATGCATTCGGTACACCTAA	0.368													G|||	983	0.196286	0.0976	0.2464	5008	,	,		19325	0.1131		0.2704	False		,,,				2504	0.3037				p.T250T		Atlas-SNP	.											ZSWIM2,NS,carcinoma,-1,1	ZSWIM2	119	1	0			c.C750T						PASS	.	G		550,3856	247.2+/-255.5	38,474,1691	103.0	90.0	94.0		750	-3.1	0.0	2	dbSNP_116	94	2531,6069	412.7+/-350.9	361,1809,2130	no	coding-synonymous	ZSWIM2	NM_182521.2		399,2283,3821	AA,AG,GG		29.4302,12.483,23.6891		250/634	187698751	3081,9925	2203	4300	6503	SO:0001819	synonymous_variant	151112	exon6			GCATTCGGTACAC	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.750C>T	2.37:g.187698751G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Silent	SNP	ENST00000295131.2	37	CCDS33348.1																																																																																			G|0.784;A|0.216	0.216	strong		0.368	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209864	84209864	+	Missense_Mutation	SNP	G	G	C	rs2288023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84209864G>C	ENST00000378553.5	+	11	2148	c.2024G>C	c.(2023-2025)aGt>aCt	p.S675T	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	675			S -> T (in dbSNP:rs2288023). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						CTCACTTCCAGTGGAGACAGG	0.627													G|||	1340	0.267572	0.0613	0.4063	5008	,	,		17997	0.376		0.3439	False		,,,				2504	0.2577				p.S675T		Atlas-SNP	.											DNAAF1,rectum,carcinoma,0,1	DNAAF1	81	1	0			c.G2024C						PASS	.	G	THR/SER	491,3909	225.2+/-241.2	32,427,1741	46.0	42.0	43.0		2024	-1.7	0.0	16	dbSNP_100	43	3062,5538	457.8+/-364.4	561,1940,1799	yes	missense	DNAAF1	NM_178452.4	58	593,2367,3540	CC,CG,GG		35.6047,11.1591,27.3308	benign	675/726	84209864	3553,9447	2200	4300	6500	SO:0001583	missense	123872	exon11			CTTCCAGTGGAGA	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.2024G>C	16.37:g.84209864G>C	ENSP00000367815:p.Ser675Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	659	0.3017399267399267	36	0.07317073170731707	125	0.3453038674033149	237	0.4143356643356643	261	0.34432717678100266	G	9.612	1.131548	0.21041	0.111591	0.356047	ENSG00000154099	ENST00000378553	T	0.32023	1.47	4.34	-1.74	0.08056	.	1.806150	0.03273	N	0.185064	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	2.9999999999752447E-6	B;B	0.20988	0.05;0.021	B;B	0.20184	0.028;0.008	T	0.42666	-0.9438	9	0.15066	T	0.55	0.1543	5.967	0.19330	0.2144:0.5194:0.2662:0.0	rs2288023;rs17845738;rs17858688;rs2288023	439;675	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	T	675	ENSP00000367815:S675T	ENSP00000367815:S675T	S	+	2	0	DNAAF1	82767365	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.037000	0.12164	-0.128000	0.11641	0.563000	0.77884	AGT	G|0.706;C|0.294	0.294	strong		0.627	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
ABCA5	23461	hgsc.bcm.edu	37	17	67267317	67267317	+	Missense_Mutation	SNP	T	T	C	rs557491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:67267317T>C	ENST00000392676.3	-	21	2942	c.2878A>G	c.(2878-2880)Atg>Gtg	p.M960V	ABCA5_ENST00000392677.2_Missense_Mutation_p.M961V|ABCA5_ENST00000588877.1_Missense_Mutation_p.M960V			Q8WWZ7	ABCA5_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 5	960			M -> V (in dbSNP:rs557491). {ECO:0000269|PubMed:11572484}.		cholesterol efflux (GO:0033344)|high-density lipoprotein particle remodeling (GO:0034375)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|reverse cholesterol transport (GO:0043691)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(18)|lung(19)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	54	Breast(10;3.72e-11)				Tacrolimus(DB00864)	TCTGAATGCATCACATTTAAA	0.348													T|||	2491	0.497404	0.4327	0.5893	5008	,	,		16231	0.6002		0.4404	False		,,,				2504	0.4724				p.M960V		Atlas-SNP	.											.	ABCA5	162	.	0			c.A2878G						PASS	.	T	VAL/MET,VAL/MET	1989,2417	557.9+/-379.9	441,1107,655	106.0	92.0	97.0		2878,2878	2.0	0.9	17	dbSNP_83	97	3967,4633	551.1+/-385.9	897,2173,1230	yes	missense,missense	ABCA5	NM_018672.3,NM_172232.2	21,21	1338,3280,1885	CC,CT,TT		46.1279,45.143,45.7942	benign,benign	960/1643,960/1643	67267317	5956,7050	2203	4300	6503	SO:0001583	missense	23461	exon20			AATGCATCACATT	U66672	CCDS11685.1	17q24.3	2012-03-14			ENSG00000154265	ENSG00000154265		"""ATP binding cassette transporters / subfamily A"""	35	protein-coding gene	gene with protein product		612503				8894702	Standard	NM_172232		Approved	EST90625	uc002jig.2	Q8WWZ7		ENST00000392676.3:c.2878A>G	17.37:g.67267317T>C	ENSP00000376443:p.Met960Val	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_018672	Q8IVJ2|Q96LJ1|Q96MS4|Q96PZ9|Q9NY14	Missense_Mutation	SNP	ENST00000392676.3	37	CCDS11685.1	1106	0.5064102564102564	228	0.4634146341463415	183	0.505524861878453	362	0.6328671328671329	333	0.4393139841688654	T	0.009	-1.827882	0.00584	0.45143	0.461279	ENSG00000154265	ENST00000392677;ENST00000392676	D;D	0.86497	-2.13;-2.13	5.5	1.95	0.26073	.	0.388405	0.24861	N	0.035020	T	0.00012	0.0000	N	0.13043	0.29	0.51482	P	7.199999999996098E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46442	-0.9191	8	.	.	.	.	3.3547	0.07164	0.2829:0.3545:0.0:0.3626	rs557491;rs52818855;rs60930051;rs557491	960	Q8WWZ7	ABCA5_HUMAN	V	961;960	ENSP00000376444:M961V;ENSP00000376443:M960V	.	M	-	1	0	ABCA5	64778912	0.058000	0.20735	0.853000	0.33588	0.149000	0.21700	0.306000	0.19279	0.057000	0.16193	0.482000	0.46254	ATG	T|0.519;C|0.481	0.481	strong		0.348	ABCA5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450654.1	NM_018672	
ALDH9A1	223	hgsc.bcm.edu	37	1	165648709	165648709	+	Silent	SNP	C	C	T	rs1143661	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:165648709C>T	ENST00000354775.4	-	6	1204	c.900G>A	c.(898-900)gcG>gcA	p.A300A	ALDH9A1_ENST00000538148.1_Silent_p.A206A|ALDH9A1_ENST00000461664.1_5'Flank	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	276					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TGGCCATCAGCGCCCCCTTTA	0.468													C|||	397	0.0792732	0.1702	0.0447	5008	,	,		18744	0.0179		0.0616	False		,,,				2504	0.0624				p.A300A	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.G900A						PASS	.	C		637,3769	274.9+/-272.2	55,527,1621	124.0	103.0	110.0		900	-10.7	0.3	1	dbSNP_120	110	615,7985	160.8+/-213.9	24,567,3709	no	coding-synonymous	ALDH9A1	NM_000696.3		79,1094,5330	TT,TC,CC		7.1512,14.4576,9.6263		300/519	165648709	1252,11754	2203	4300	6503	SO:0001819	synonymous_variant	223	exon6			CATCAGCGCCCCC	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.900G>A	1.37:g.165648709C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	163	93	0.570552	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	ENST00000354775.4	37	CCDS1250.2																																																																																			C|0.910;T|0.090	0.090	strong		0.468	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
CHRNA3	1136	hgsc.bcm.edu	37	15	78911181	78911181	+	Silent	SNP	T	T	C	rs8040868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78911181T>C	ENST00000326828.5	-	2	543	c.159A>G	c.(157-159)gtA>gtG	p.V53V	CHRNA3_ENST00000559941.1_5'Flank|CHRNA3_ENST00000348639.3_Silent_p.V53V	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	53					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|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)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	ACACGTTGGCTACAGGCCGGA	0.572											OREG0023334	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1645	0.328474	0.3533	0.2795	5008	,	,		18663	0.3542		0.4165	False		,,,				2504	0.2127				p.V53V		Atlas-SNP	.											.	CHRNA3	56	.	0			c.A159G						PASS	.	C	,	1475,2917	677.4+/-403.4	235,1005,956	87.0	76.0	80.0		159,159	3.9	1.0	15	dbSNP_116	80	3524,5062	631.5+/-398.5	754,2016,1523	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	989,3021,2479	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	41.0436,33.5838,38.519	,	53/506,53/490	78911181	4999,7979	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon2			GTTGGCTACAGGC		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.159A>G	15.37:g.78911181T>C		Somatic	73	0	0	1187	WXS	Illumina HiSeq	Phase_I	85	85	1	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			T|0.616;C|0.384	0.384	strong		0.572	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
C10orf120	399814	hgsc.bcm.edu	37	10	124459139	124459139	+	Silent	SNP	T	T	C	rs11813597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124459139T>C	ENST00000329446.4	-	1	199	c.168A>G	c.(166-168)tcA>tcG	p.S56S		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	56								p.S56S(1)		endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				ACCGCAACGGTGAAGCAGAAC	0.478													T|||	2233	0.445887	0.4145	0.33	5008	,	,		19618	0.5327		0.4076	False		,,,				2504	0.5204				p.S56S		Atlas-SNP	.											C10orf120,NS,carcinoma,0,1	C10orf120	55	1	1	Substitution - coding silent(1)	stomach(1)	c.A168G						PASS	.	T		1827,2579	533.7+/-373.8	391,1045,767	99.0	86.0	90.0		168	-1.2	0.0	10	dbSNP_120	90	3560,5040	518.0+/-379.2	740,2080,1480	no	coding-synonymous	C10orf120	NM_001010912.1		1131,3125,2247	CC,CT,TT		41.3953,41.4662,41.4193		56/336	124459139	5387,7619	2203	4300	6503	SO:0001819	synonymous_variant	399814	exon1			CAACGGTGAAGCA		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.168A>G	10.37:g.124459139T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1	966	0.4423076923076923	229	0.4654471544715447	143	0.39502762430939226	290	0.506993006993007	304	0.40105540897097625	T	4.042	0.005438	0.07866	0.414662	0.413953	ENSG00000183559	ENST00000432000	.	.	.	4.28	-1.2	0.09554	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.47959	-0.9076	3	.	.	.	-0.4259	6.7398	0.23428	0.0:0.0978:0.5383:0.3639	rs11813597;rs17649853;rs11813597	.	.	.	R	49	.	.	H	-	2	0	C10orf120	124449129	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.094000	0.11094	-0.300000	0.08895	-0.323000	0.08544	CAC	C|0.427;N|0.000	0.427	strong		0.478	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
OR2H2	7932	hgsc.bcm.edu	37	6	29555864	29555864	+	Missense_Mutation	SNP	C	C	T	rs1233387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29555864C>T	ENST00000383640.2	+	1	182	c.143C>T	c.(142-144)gCg>gTg	p.A48V	GABBR1_ENST00000355973.3_Intron	NM_007160.3	NP_009091.3	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H, member 2	48			A -> V (in dbSNP:rs1233387). {ECO:0000269|PubMed:10880742, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14983052}.		defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	14						CTGCTGTCTGCGCTGGACCCC	0.527													T|||	1718	0.343051	0.2685	0.3559	5008	,	,		21347	0.4831		0.2555	False		,,,				2504	0.3804				p.A48V		Atlas-SNP	.											OR2H2,NS,carcinoma,0,1	OR2H2	29	1	0			c.C143T						PASS	.	T	VAL/ALA	786,2236		100,586,825	231.0	198.0	210.0		143	2.0	0.0	6	dbSNP_87	210	1371,4047		178,1015,1516	yes	missense	OR2H2	NM_007160.3	64	278,1601,2341	TT,TC,CC		25.3045,26.0093,25.5569	benign	48/313	29555864	2157,6283	1511	2709	4220	SO:0001583	missense	7932	exon1			TGTCTGCGCTGGA		CCDS34365.1	6p22.2-p21.31	2012-08-09				ENSG00000204657		"""GPCR / Class A : Olfactory receptors"""	8253	protein-coding gene	gene with protein product		600578					Standard	XM_005249407		Approved	hs6M1-12	uc003nmr.1	O95918		ENST00000383640.2:c.143C>T	6.37:g.29555864C>T	ENSP00000373136:p.Ala48Val	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	219	120	0.547945	NM_007160	Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14	Missense_Mutation	SNP	ENST00000383640.2	37	CCDS34365.1	688	0.315018315018315	125	0.2540650406504065	109	0.3011049723756906	272	0.4755244755244755	182	0.24010554089709762	T	5.424	0.263305	0.10294	0.260093	0.253045	ENSG00000204657	ENST00000383640	T	0.01076	5.37	4.44	1.96	0.26148	GPCR, rhodopsin-like superfamily (1);	0.908400	0.09070	N	0.853071	T	0.00210	0.0006	N	0.04787	-0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35895	-0.9770	9	0.17832	T	0.49	.	0.8099	0.01091	0.1659:0.293:0.1712:0.3699	rs1233387;rs1233387	48	O95918	OR2H2_HUMAN	V	48	ENSP00000373136:A48V	ENSP00000373136:A48V	A	+	2	0	OR2H2	29663843	0.000000	0.05858	0.001000	0.08648	0.987000	0.75469	-1.347000	0.02632	-0.043000	0.13513	-0.352000	0.07741	GCG	C|0.722;T|0.278	0.278	strong		0.527	OR2H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076057.2		
COL6A5	256076	hgsc.bcm.edu	37	3	130107442	130107442	+	Silent	SNP	C	C	T	rs138213174	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130107442C>T	ENST00000432398.2	+	6	2375	c.1881C>T	c.(1879-1881)gcC>gcT	p.A627A	COL6A5_ENST00000265379.6_Silent_p.A627A	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	627	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						ACATGAAGGCCGACATCATGT	0.338													T|||	39	0.00778754	0.0	0.0101	5008	,	,		18294	0.0		0.0268	False		,,,				2504	0.0051				p.A627A		Atlas-SNP	.											.	COL6A5	205	.	0			c.C1881T						PASS	.	T		4,1380		0,4,688	46.0	37.0	40.0		1881	-11.1	0.2	3	dbSNP_134	40	78,3102		0,78,1512	no	coding-synonymous	COL6A5	NM_153264.5		0,82,2200	TT,TC,CC		2.4528,0.289,1.7967		627/2527	130107442	82,4482	692	1590	2282	SO:0001819	synonymous_variant	256076	exon6			GAAGGCCGACATC	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.1881C>T	3.37:g.130107442C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	52	17	0.326923	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				C|0.990;T|0.010	0.010	strong		0.338	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
CFAP58	159686	hgsc.bcm.edu	37	10	106159180	106159180	+	Silent	SNP	A	A	G	rs61732098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:106159180A>G	ENST00000369704.3	+	12	1871	c.1737A>G	c.(1735-1737)gaA>gaG	p.E579E	snoU13_ENST00000458914.1_RNA	NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		579						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		AAAAGCAAGAAGCTGAAGAGA	0.458													A|||	147	0.029353	0.0514	0.0072	5008	,	,		18901	0.0129		0.0109	False		,,,				2504	0.0511				p.E579E		Atlas-SNP	.											.	CCDC147	137	.	0			c.A1737G						PASS	.	A		148,4258	103.4+/-141.9	4,140,2059	73.0	72.0	72.0		1737	3.3	1.0	10	dbSNP_129	72	83,8517	48.1+/-107.5	0,83,4217	no	coding-synonymous	CCDC147	NM_001008723.1		4,223,6276	GG,GA,AA		0.9651,3.3591,1.7761		579/873	106159180	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	159686	exon12			GCAAGAAGCTGAA																												ENST00000369704.3:c.1737A>G	10.37:g.106159180A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	58	0.568627	NM_001008723	D3DRA6|Q8NA27	Silent	SNP	ENST00000369704.3	37	CCDS31282.1																																																																																			A|0.982;G|0.018	0.018	strong		0.458	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1		
PCDHGB3	56102	hgsc.bcm.edu	37	5	140803241	140803241	+	Intron	SNP	C	C	A	rs57195665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140803241C>A	ENST00000576222.1	+	1	2546				PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB8P_ENST00000502926.1_RNA|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGATTTATTTCTCTGCCTCCT	0.453													c|||	567	0.113219	0.1195	0.1499	5008	,	,		14734	0.1171		0.0596	False		,,,				2504	0.1299				p.S816Y		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.C2447A						PASS	.	C	,,,,,,,,,,,,,,,,,,TYR/SER,	476,3742		26,424,1659	33.0	37.0	36.0		,,,,,,,,,,,,,,,,,,2447,	-2.0	0.0	5	dbSNP_129	36	632,7882		25,582,3650	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,,,,,,,,,,,,,,,,144,	51,1006,5309	AA,AC,CC		7.4231,11.285,8.7025	,,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,816/838,	140803241	1108,11624	2109	4257	6366	SO:0001627	intron_variant	56105	exon1			TTATTTCTCTGCC	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+50865C>A	5.37:g.140803241C>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_032091	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			C|0.900;A|0.100	0.100	strong		0.453	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
NIPA2	81614	hgsc.bcm.edu	37	15	23021238	23021238	+	Silent	SNP	C	C	T	rs145147241|rs7170838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:23021238C>T	ENST00000337451.3	-	4	711	c.99G>A	c.(97-99)aaG>aaA	p.K33K	NIPA2_ENST00000398014.2_Silent_p.K33K|NIPA2_ENST00000398013.3_Silent_p.K33K|NIPA2_ENST00000559571.1_5'Flank|NIPA2_ENST00000539711.2_Silent_p.K33K|NIPA2_ENST00000359727.4_Silent_p.K33K	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2	33						early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	magnesium ion transmembrane transporter activity (GO:0015095)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(4)|skin(1)	15		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;1.48e-06)|Epithelial(43;1.44e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000353)		GAAGGAGGCCCTTTTTTTTCA	0.448													T|||	1130	0.225639	0.2262	0.3112	5008	,	,		16677	0.2421		0.1799	False		,,,				2504	0.1943				p.K33K		Atlas-SNP	.											NIPA2,NS,adenoma,0,1	NIPA2	49	1	0			c.G99A						PASS	.	T	,,,,,	973,3433		120,733,1350	132.0	134.0	134.0		99,99,99,99,99,99	1.4	1.0	15	dbSNP_116	134	1372,7228		126,1120,3054	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NIPA2	NM_001008860.2,NM_001008892.2,NM_001008894.2,NM_001184888.1,NM_001184889.1,NM_030922.6	,,,,,	246,1853,4404	TT,TC,CC		15.9535,22.0835,18.0301	,,,,,	33/361,33/361,33/342,33/342,33/361,33/361	23021238	2345,10661	2203	4300	6503	SO:0001819	synonymous_variant	81614	exon6			GAGGCCCTTTTTT	AY732242	CCDS73693.1, CCDS73694.1	15q11.2	2008-02-05			ENSG00000140157	ENSG00000140157			17044	protein-coding gene	gene with protein product		608146				14508708	Standard	NM_001008860		Approved		uc001yuz.3	Q8N8Q9	OTTHUMG00000129101	ENST00000337451.3:c.99G>A	15.37:g.23021238C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	43	0.413462	NM_001184889	F8W7Y8|Q96F03|Q9BVS2	Silent	SNP	ENST00000337451.3	37	CCDS10010.1																																																																																			C|0.792;T|0.208	0.208	strong		0.448	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922	
ATAD5	79915	hgsc.bcm.edu	37	17	29161503	29161503	+	Missense_Mutation	SNP	A	A	G	rs11080134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:29161503A>G	ENST00000321990.4	+	2	782	c.404A>G	c.(403-405)gAa>gGa	p.E135G	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	135			E -> G (in dbSNP:rs11080134). {ECO:0000269|PubMed:15489334}.		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)				GCTCCAATTGAAATTAGTAGC	0.289													A|||	759	0.151558	0.0673	0.2594	5008	,	,		19686	0.001		0.327	False		,,,				2504	0.1636				p.E135G		Atlas-SNP	.											.	ATAD5	150	.	0			c.A404G						PASS	.	A	GLY/GLU	482,3924		28,426,1749	118.0	135.0	130.0		404	4.2	1.0	17	dbSNP_120	130	2931,5661		496,1939,1861	yes	missense	ATAD5	NM_024857.3	98	524,2365,3610	GG,GA,AA		34.1131,10.9396,26.2579	possibly-damaging	135/1845	29161503	3413,9585	2203	4296	6499	SO:0001583	missense	79915	exon2			CAATTGAAATTAG		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.404A>G	17.37:g.29161503A>G	ENSP00000313171:p.Glu135Gly	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	380	0.17399267399267399	29	0.05894308943089431	100	0.27624309392265195	1	0.0017482517482517483	250	0.32981530343007914	A	6.597	0.478550	0.12521	0.109396	0.341131	ENSG00000176208	ENST00000321990	T	0.18502	2.21	5.35	4.24	0.50183	.	2.337970	0.01197	N	0.007499	T	0.00012	0.0000	L	0.55481	1.735	0.30194	P	0.799222	D;D	0.56746	0.977;0.961	P;B	0.50659	0.647;0.444	T	0.18713	-1.0328	9	0.38643	T	0.18	.	6.6781	0.23106	0.7905:0.0:0.0723:0.1372	rs11080134;rs17767684;rs58774345;rs11080134	135;135	Q96QE3-2;Q96QE3	.;ATAD5_HUMAN	G	135	ENSP00000313171:E135G	ENSP00000313171:E135G	E	+	2	0	ATAD5	26185629	1.000000	0.71417	0.997000	0.53966	0.400000	0.30750	1.536000	0.36072	1.067000	0.40740	0.533000	0.62120	GAA	A|0.786;G|0.214	0.214	strong		0.289	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
MAP4	4134	hgsc.bcm.edu	37	3	47958037	47958037	+	Missense_Mutation	SNP	G	G	T	rs1060407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:47958037G>T	ENST00000360240.6	-	7	1798	c.1280C>A	c.(1279-1281)tCc>tAc	p.S427Y	MAP4_ENST00000395734.3_Missense_Mutation_p.S427Y|MAP4_ENST00000426837.2_Missense_Mutation_p.S444Y|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	427	17 X 14 AA tandem repeats.		S -> Y (in dbSNP:rs1060407). {ECO:0000269|PubMed:1718985}.		cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	TATTTCTGTGGATGATATAAT	0.483													G|||	1261	0.251797	0.1165	0.3458	5008	,	,		21315	0.2629		0.2992	False		,,,				2504	0.3078				p.S427Y		Atlas-SNP	.											.	MAP4	176	.	0			c.C1280A						PASS	.	G	TYR/SER,TYR/SER	591,3815	257.0+/-261.6	36,519,1648	124.0	111.0	116.0		1280,1280	4.1	0.1	3	dbSNP_86	116	2660,5940	426.6+/-355.3	420,1820,2060	yes	missense,missense	MAP4	NM_001134364.1,NM_002375.4	144,144	456,2339,3708	TT,TG,GG		30.9302,13.4135,24.9962	benign,benign	427/1136,427/1153	47958037	3251,9755	2203	4300	6503	SO:0001583	missense	4134	exon7			TCTGTGGATGATA		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1280C>A	3.37:g.47958037G>T	ENSP00000353375:p.Ser427Tyr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	209	87	0.416268	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	506	0.2316849816849817	46	0.09349593495934959	108	0.2983425414364641	131	0.229020979020979	221	0.29155672823219	G	13.11	2.140525	0.37825	0.134135	0.309302	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.08807	3.12;3.05;3.13	4.09	4.09	0.47781	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	0.23277	P	0.99799361	P;B;B	0.45827	0.867;0.27;0.319	B;B;B	0.42062	0.374;0.151;0.073	T	0.48502	-0.9030	8	0.87932	D	0	-1.8424	14.6207	0.68582	0.0:0.0:1.0:0.0	rs1060407;rs3201295;rs3821448;rs17382401;rs61068109;rs1060407	404;427;427	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	Y	427;444;427	ENSP00000379083:S427Y;ENSP00000407602:S444Y;ENSP00000353375:S427Y	ENSP00000353375:S427Y	S	-	2	0	MAP4	47933041	0.200000	0.23398	0.112000	0.21494	0.006000	0.05464	1.868000	0.39509	2.560000	0.86352	0.561000	0.74099	TCC	G|0.754;T|0.246	0.246	strong		0.483	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
DPCR1	135656	hgsc.bcm.edu	37	6	30918400	30918400	+	Missense_Mutation	SNP	A	A	G	rs2844699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30918400A>G	ENST00000462446.1	+	2	2187	c.2159A>G	c.(2158-2160)gAg>gGg	p.E720G	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	284						integral component of membrane (GO:0016021)		p.E720G(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TCCCCAGCAGAGCCTACAGAA	0.488													-|||	1111	0.221845	0.0983	0.2118	5008	,	,		24807	0.2421		0.3579	False		,,,				2504	0.2352				p.E720G		Atlas-SNP	.											DPCR1_ENST00000462446,NS,carcinoma,0,1	DPCR1	99	1	1	Substitution - Missense(1)	endometrium(1)	c.A2159G						PASS	.	A	GLY/GLU	173,1211		8,157,527	55.0	63.0	61.0		2159	-4.1	0.0	6	dbSNP_100	61	1159,2023		217,725,649	no	missense	DPCR1	NM_080870.3	98	225,882,1176	GG,GA,AA		36.4236,12.5,29.1721	possibly-damaging	720/1394	30918400	1332,3234	692	1591	2283	SO:0001583	missense	135656	exon2			CAGCAGAGCCTAC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2159A>G	6.37:g.30918400A>G	ENSP00000417182:p.Glu720Gly	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	119	61	0.512605	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	505	0.23122710622710624	31	0.06300813008130081	75	0.20718232044198895	148	0.25874125874125875	251	0.3311345646437995	-	7.598	0.672128	0.14776	0.125	0.364236	ENSG00000168631	ENST00000462446	T	0.47177	0.85	2.04	-4.07	0.03975	.	.	.	.	.	T	0.13415	0.0325	L	0.54908	1.71	0.58432	P	1.999999999946489E-6	B	0.06786	0.001	B	0.08055	0.003	T	0.12426	-1.0548	8	0.33141	T	0.24	.	1.8675	0.03201	0.1759:0.4062:0.2689:0.149	rs2844699	720	E9PEI6	.	G	720	ENSP00000417182:E720G	ENSP00000417182:E720G	E	+	2	0	DPCR1	31026379	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.561000	0.00215	-1.885000	0.01118	0.359000	0.22050	GAG	A|0.768;G|0.232	0.232	strong		0.488	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
VIT	5212	hgsc.bcm.edu	37	2	37041480	37041480	+	Silent	SNP	G	G	A	rs17441812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37041480G>A	ENST00000389975.3	+	15	2315	c.2013G>A	c.(2011-2013)gaG>gaA	p.E671E	VIT_ENST00000379241.3_Silent_p.E649E|VIT_ENST00000401530.1_Silent_p.E650E|VIT_ENST00000404084.1_Silent_p.E623E|VIT_ENST00000497382.1_Silent_p.E340E|VIT_ENST00000379242.3_Silent_p.E686E	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	671					extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				TTTGTACAGAGTTCAACTCAC	0.522													G|||	103	0.0205671	0.0015	0.0288	5008	,	,		20102	0.0		0.0696	False		,,,				2504	0.0112				p.E686E		Atlas-SNP	.											.	VIT	138	.	0			c.G2058A						PASS	.	G	,,,	60,4346	56.8+/-93.2	0,60,2143	102.0	91.0	94.0		2013,1950,1947,2058	4.5	1.0	2	dbSNP_123	94	551,8049	150.4+/-205.3	19,513,3768	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VIT	NM_001177969.1,NM_001177970.1,NM_001177971.1,NM_053276.3	,,,	19,573,5911	AA,AG,GG		6.407,1.3618,4.6978	,,,	671/679,650/658,649/657,686/694	37041480	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	5212	exon16			TACAGAGTTCAAC	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.2013G>A	2.37:g.37041480G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			G|0.956;A|0.044	0.044	strong		0.522	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
MT-ND5	4540	hgsc.bcm.edu	37	M	12633	12633	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:12633C>A	ENST00000361567.2	+	1	297	c.297C>A	c.(295-297)tcC>tcA	p.S99S	MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	99			S -> P. {ECO:0000269|PubMed:1757091}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						GTTACATGGTCCATCATAGAA	0.368																																					p.S99S		Atlas-SNP	.											.	.	.	.	0			c.C297A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ATGGTCCATCATA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.297C>A	M.37:g.12633C>A		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	11	11	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.368	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
GRIN2B	2904	hgsc.bcm.edu	37	12	13724742	13724742	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:13724742T>C	ENST00000609686.1	-	10	2376	c.2167A>G	c.(2167-2169)Aca>Gca	p.T723A		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	723					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)	TCTTACCCTGTTTTCAGGGAG	0.418																																					p.T723A		Atlas-SNP	.											.	GRIN2B	303	.	0			c.A2167G						PASS	.						235.0	206.0	216.0					12																	13724742		2203	4300	6503	SO:0001583	missense	2904	exon10			ACCCTGTTTTCAG		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.2167A>G	12.37:g.13724742T>C	ENSP00000477455:p.Thr723Ala	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	163	7	0.0429448	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.466424	0.43839	.	.	ENSG00000150086	ENST00000279593	T	0.49720	0.77	5.66	5.66	0.87406	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.107478	0.64402	D	0.000004	T	0.40619	0.1124	L	0.33189	0.99	0.58432	D	0.999996	B	0.06786	0.001	B	0.18561	0.022	T	0.16012	-1.0417	10	0.40728	T	0.16	.	16.1922	0.82000	0.0:0.0:0.0:1.0	.	723	Q13224	NMDE2_HUMAN	A	723	ENSP00000279593:T723A	ENSP00000279593:T723A	T	-	1	0	GRIN2B	13616009	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.074000	0.57577	2.280000	0.76307	0.533000	0.62120	ACA	.	.	none		0.418	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
TNXB	7148	hgsc.bcm.edu	37	6	32029431	32029431	+	Missense_Mutation	SNP	G	G	A	rs12524664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32029431G>A	ENST00000375244.3	-	21	7436	c.7235C>T	c.(7234-7236)cCg>cTg	p.P2412L	TNXB_ENST00000375247.2_Missense_Mutation_p.P2412L			P22105	TENX_HUMAN	tenascin XB	2472	Fibronectin type-III 16. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCCCAGGAGCGGCTCCTCAGG	0.647													G|||	527	0.105232	0.2012	0.0749	5008	,	,		14003	0.0823		0.0934	False		,,,				2504	0.0327				p.P2412L		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,+1,2	TNXB	553	2	0			c.C7235T						PASS	.	G	LEU/PRO	367,1871		29,309,781	46.0	53.0	51.0		7235	4.0	1.0	6	dbSNP_120	51	312,4646		6,300,2173	no	missense	TNXB	NM_019105.6	98	35,609,2954	AA,AG,GG		6.2929,16.3986,9.4358	benign	2412/4243	32029431	679,6517	1119	2479	3598	SO:0001583	missense	7148	exon21			AGGAGCGGCTCCT	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.7235C>T	6.37:g.32029431G>A	ENSP00000364393:p.Pro2412Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	112	48	0.428571	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		269	0.12316849816849818	98	0.1991869918699187	38	0.10497237569060773	60	0.1048951048951049	73	0.09630606860158311	G	18.44	3.624587	0.66901	0.163986	0.062929	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.61980	0.22;0.06	4.0	4.0	0.46444	.	0.104175	0.43416	D	0.000567	T	0.78947	0.4364	M	0.93150	3.385	0.26478	P	0.9751589	D	0.76494	0.999	D	0.67103	0.949	D	0.85220	0.1026	9	0.87932	D	0	.	13.1106	0.59270	0.0:0.0:1.0:0.0	rs12524664;rs17201532	2412	P22105-3	.	L	2412	ENSP00000364393:P2412L;ENSP00000364396:P2412L	ENSP00000364393:P2412L	P	-	2	0	TNXB	32137409	0.990000	0.36364	0.999000	0.59377	0.792000	0.44763	2.762000	0.47597	2.038000	0.60285	0.591000	0.81541	CCG	G|0.894;A|0.106	0.106	strong		0.647	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
SMG6	23293	hgsc.bcm.edu	37	17	2203167	2203167	+	Missense_Mutation	SNP	T	T	G	rs216195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:2203167T>G	ENST00000263073.6	-	2	930	c.880A>C	c.(880-882)Aag>Cag	p.K294Q	SMG6_ENST00000544865.1_Missense_Mutation_p.K263Q	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	294	Interaction with telomeric DNA.		K -> Q (in dbSNP:rs216195).		gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						GACACTTGCTTCTTCAGTCGT	0.537													T|||	2010	0.401358	0.3222	0.2205	5008	,	,		17706	0.6736		0.2813	False		,,,				2504	0.4796				p.K294Q	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A880C						PASS	.	T	GLN/LYS,GLN/LYS	1550,2856	490.1+/-361.7	267,1016,920	89.0	79.0	83.0		787,880	5.3	1.0	17	dbSNP_79	83	2510,6090	410.5+/-350.2	357,1796,2147	yes	missense,missense	SMG6	NM_001170957.1,NM_017575.4	53,53	624,2812,3067	GG,GT,TT		29.186,35.1793,31.2164	probably-damaging,probably-damaging	263/1389,294/1420	2203167	4060,8946	2203	4300	6503	SO:0001583	missense	23293	exon2			CTTGCTTCTTCAG	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.880A>C	17.37:g.2203167T>G	ENSP00000263073:p.Lys294Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	826	0.3782051282051282	160	0.3252032520325203	79	0.21823204419889503	371	0.6486013986013986	216	0.2849604221635884	T	14.92	2.679107	0.47886	0.351793	0.29186	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.08807	3.05;3.05	5.35	5.35	0.76521	.	0.329730	0.32416	N	0.006125	T	0.00012	0.0000	L	0.29908	0.895	0.34437	P	0.300809	B	0.31077	0.307	B	0.22152	0.038	T	0.08249	-1.0731	9	0.39692	T	0.17	-10.2096	11.93	0.52841	0.0:0.0:0.1452:0.8548	rs216195;rs3826336;rs58625577;rs216195	294	Q86US8	EST1A_HUMAN	Q	294;263	ENSP00000263073:K294Q;ENSP00000443920:K263Q	ENSP00000263073:K294Q	K	-	1	0	SMG6	2149917	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.662000	0.46766	2.015000	0.59207	0.533000	0.62120	AAG	T|0.655;G|0.345	0.345	strong		0.537	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
GPR112	139378	hgsc.bcm.edu	37	X	135430044	135430044	+	Silent	SNP	T	T	C	rs877761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135430044T>C	ENST00000394143.1	+	6	4470	c.4179T>C	c.(4177-4179)acT>acC	p.T1393T	GPR112_ENST00000370652.1_Silent_p.T1393T|GPR112_ENST00000412101.1_Silent_p.T1188T|GPR112_ENST00000287534.4_Silent_p.T1330T|GPR112_ENST00000394141.1_Silent_p.T1188T	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1393					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CTCCCAGGACTGTGGAAATGA	0.448													c|||	2014	0.53351	0.5983	0.3847	3775	,	,		16408	0.255		0.3817	False		,,,				2504	0.3221				p.T1393T		Atlas-SNP	.											.	GPR112	459	.	0			c.T4179C						PASS	.			2878,957		910,628,430,94,141	170.0	160.0	163.0		4179	-1.4	0.0	X	dbSNP_86	163	3231,3497		571,1175,914,682,958	no	coding-synonymous	GPR112	NM_153834.3		1481,1803,1344,776,1099	CC,CT,C,TT,T		48.0232,24.9544,42.1661		1393/3081	135430044	6109,4454	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			CAGGACTGTGGAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4179T>C	X.37:g.135430044T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			T|0.432;0|0.003	.	strong		0.448	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
ZNF48	197407	hgsc.bcm.edu	37	16	30409241	30409241	+	Missense_Mutation	SNP	A	A	G	rs34843513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30409241A>G	ENST00000320159.2	+	2	1046	c.670A>G	c.(670-672)Ata>Gta	p.I224V	SEPT1_ENST00000570039.1_5'Flank	NM_001214906.1|NM_001214907.1|NM_001214909.1|NM_152652.2	NP_001201835.1|NP_001201836.1|NP_001201838.1|NP_689865.2	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	224			I -> V (in dbSNP:rs34843513).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)|pancreas(1)|skin(1)	21						CAAGTGTGGCATATGTGGCAA	0.627													A|||	69	0.013778	0.0151	0.0231	5008	,	,		17562	0.0		0.0278	False		,,,				2504	0.0051				p.I224V		Atlas-SNP	.											.	ZNF48	34	.	0			c.A670G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	57,4337	56.8+/-93.2	0,57,2140	45.0	51.0	49.0		670,301,670,670	-1.1	1.0	16	dbSNP_126	49	301,8299	109.4+/-169.9	4,293,4003	yes	missense,missense,missense,missense	ZNF48	NM_001214906.1,NM_001214907.1,NM_001214909.1,NM_152652.2	29,29,29,29	4,350,6143	GG,GA,AA		3.5,1.2972,2.7551	benign,benign,benign,benign	224/619,101/496,224/619,224/619	30409241	358,12636	2197	4300	6497	SO:0001583	missense	197407	exon3			TGTGGCATATGTG	M88358, AK056313	CCDS10679.1, CCDS73868.1	16p11.2	2013-01-08			ENSG00000180035	ENSG00000180035		"""Zinc fingers, C2H2-type"""	13114	protein-coding gene	gene with protein product			"""zinc finger protein 553"""	ZNF553		1505991	Standard	NM_152652		Approved	DKFZp762K013, FLJ31751, MGC43952	uc021tgi.1	Q96MX3	OTTHUMG00000048195	ENST00000320159.2:c.670A>G	16.37:g.30409241A>G	ENSP00000324056:p.Ile224Val	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	39	19	0.487179	NM_001214906	Q15920|Q4G0R3|Q69YP3|Q96IL9	Missense_Mutation	SNP	ENST00000320159.2	37	CCDS10679.1	44	0.020146520146520148	10	0.02032520325203252	11	0.03038674033149171	0	0.0	23	0.030343007915567283	A	7.802	0.713871	0.15306	0.012972	0.035	ENSG00000180035	ENST00000495929;ENST00000320159	T	0.17370	2.28	4.85	-1.06	0.10002	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.370615	0.19752	N	0.106879	T	0.01092	0.0036	N	0.01405	-0.89	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.36335	-0.9752	10	0.49607	T	0.09	-7.3888	9.7449	0.40440	0.4414:0.0:0.5586:0.0	rs34843513	224	Q96MX3	ZNF48_HUMAN	V	349;224	ENSP00000324056:I224V	ENSP00000324056:I224V	I	+	1	0	ZNF48	30316742	0.000000	0.05858	0.991000	0.47740	0.988000	0.76386	-0.486000	0.06513	-0.099000	0.12263	0.460000	0.39030	ATA	A|0.973;G|0.027	0.027	strong		0.627	ZNF48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255549.2	NM_152652	
CAV3	859	hgsc.bcm.edu	37	3	8787220	8787220	+	Silent	SNP	T	T	C	rs13087941	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:8787220T>C	ENST00000343849.2	+	2	200	c.123T>C	c.(121-123)ttT>ttC	p.F41F	CAV3_ENST00000472766.1_Intron|SSUH2_ENST00000478513.1_5'Flank|CAV3_ENST00000397368.2_Silent_p.F41F	NM_001234.4|NM_033337.2	NP_001225.1|NP_203123.1	P56539	CAV3_HUMAN	caveolin 3	41					actin filament organization (GO:0007015)|cardiac muscle cell development (GO:0055013)|caveola assembly (GO:0070836)|cell differentiation (GO:0030154)|cell growth (GO:0016049)|cholesterol homeostasis (GO:0042632)|cytoplasmic microtubule organization (GO:0031122)|endocytosis (GO:0006897)|establishment of protein localization to plasma membrane (GO:0090002)|glucose homeostasis (GO:0042593)|heart trabecula formation (GO:0060347)|membrane raft organization (GO:0031579)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)|negative regulation of cell size (GO:0045792)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of potassium ion transmembrane transport (GO:1901380)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein localization to cell surface (GO:2000009)|negative regulation of sarcomere organization (GO:0060299)|nucleus localization (GO:0051647)|plasma membrane organization (GO:0007009)|plasma membrane repair (GO:0001778)|positive regulation of caveolin-mediated endocytosis (GO:2001288)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein localization (GO:0008104)|protein localization to plasma membrane (GO:0072659)|regulation of branching involved in mammary gland duct morphogenesis (GO:0060762)|regulation of calcium ion import (GO:0090279)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart contraction (GO:0008016)|regulation of heart rate (GO:0002027)|regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900825)|regulation of membrane potential (GO:0042391)|regulation of nerve growth factor receptor activity (GO:0051394)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase B signaling (GO:0051896)|regulation of signal transduction by receptor internalization (GO:0038009)|regulation of skeletal muscle contraction (GO:0014819)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|T-tubule organization (GO:0033292)|triglyceride metabolic process (GO:0006641)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|dystrophin-associated glycoprotein complex (GO:0016010)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|connexin binding (GO:0071253)|ion channel binding (GO:0044325)|potassium channel inhibitor activity (GO:0019870)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein complex scaffold (GO:0032947)|sodium channel regulator activity (GO:0017080)	p.F41F(1)		breast(1)|kidney(2)|large_intestine(4)|lung(3)|prostate(1)	11						AGGTGGATTTTGAAGACGTGA	0.562													C|||	766	0.152955	0.2837	0.1311	5008	,	,		18630	0.0139		0.2326	False		,,,				2504	0.0532				p.F41F		Atlas-SNP	.											CAV3,NS,carcinoma,0,1	CAV3	20	1	1	Substitution - coding silent(1)	prostate(1)	c.T123C						PASS	.	C	,	1251,3155	704.6+/-407.1	175,901,1127	60.0	53.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	123,123	-7.3	0.6	3	dbSNP_121	56	2073,6527	716.8+/-406.1	242,1589,2469	no	coding-synonymous,coding-synonymous	CAV3	NM_001234.3,NM_033337.2	,	417,2490,3596	CC,CT,TT		24.1047,28.3931,25.5574	,	41/152,41/152	8787220	3324,9682	2203	4300	6503	SO:0001819	synonymous_variant	859	exon2			GGATTTTGAAGAC	AF043101	CCDS2569.1	3p25	2014-09-17			ENSG00000182533	ENSG00000182533			1529	protein-coding gene	gene with protein product	"""M-caveolin"""	601253				9536092, 9537420	Standard	NM_033337		Approved	VIP-21, LGMD1C, VIP21, LQT9	uc003brb.3	P56539	OTTHUMG00000090519	ENST00000343849.2:c.123T>C	3.37:g.8787220T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_033337	A8K777|Q3T1A4	Silent	SNP	ENST00000343849.2	37	CCDS2569.1																																																																																			T|0.791;C|0.209	0.209	strong		0.562	CAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207008.2	NM_033337	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388429	1388429	+	Missense_Mutation	SNP	G	G	A	rs79298048	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388429G>A	ENST00000324803.4	+	1	3090	c.130G>A	c.(130-132)Gcc>Acc	p.A44T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	44					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGGAGTGCCCGCCTGCTCACA	0.662													N|||	944	0.188498	0.062	0.2853	5008	,	,		16920	0.0536		0.3797	False		,,,				2504	0.2331				p.A44T		Atlas-SNP	.											CRIPAK,colon,carcinoma,0,2	CRIPAK	185	2	0			c.G130A						scavenged	.	G	THR/ALA	508,3898		29,450,1724	219.0	210.0	213.0		130	-1.5	0.0	4	dbSNP_131	213	3442,5158		673,2096,1531	no	missense	CRIPAK	NM_175918.3	58	702,2546,3255	AA,AG,GG		40.0233,11.5297,30.3706	benign	44/447	1388429	3950,9056	2203	4300	6503	SO:0001583	missense	285464	exon1			GTGCCCGCCTGCT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.130G>A	4.37:g.1388429G>A	ENSP00000323978:p.Ala44Thr	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	169	72	0.426035	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	438	0.20054945054945056	28	0.056910569105691054	99	0.27348066298342544	38	0.06643356643356643	273	0.36015831134564646	-	6.138	0.393672	0.11638	0.115297	0.400233	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.24350	1.86	1.11	-1.54	0.08584	Post-SET domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.39748	0.686	B	0.17722	0.019	T	0.47484	-0.9114	8	0.36615	T	0.2	.	3.7735	0.08650	0.1991:0.2527:0.5481:0.0	.	44	Q8N1N5	CRPAK_HUMAN	T	44;37	ENSP00000323978:A44T	ENSP00000323978:A44T	A	+	1	0	CRIPAK	1378429	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.619000	0.05572	-0.466000	0.06943	0.413000	0.27773	GCC	G|0.725;A|0.275	0.275	strong		0.662	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
PRSS58	136541	hgsc.bcm.edu	37	7	141957504	141957504	+	Silent	SNP	A	A	G	rs7786497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141957504A>G	ENST00000552471.1	-	1	343	c.24T>C	c.(22-24)gcT>gcC	p.A8A	PRSS58_ENST00000547058.2_Silent_p.A8A			Q8IYP2	PRS58_HUMAN	protease, serine, 58	8						extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			kidney(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(2)|skin(2)	19						GATTCAAGAGAGCCCAGAGGA	0.433													A|||	1399	0.279353	0.059	0.3329	5008	,	,		19561	0.5109		0.2485	False		,,,				2504	0.3323				p.A8A		Atlas-SNP	.											.	PRSS58	41	.	0			c.T24C						PASS	.	A		380,4026	193.6+/-218.7	13,354,1836	135.0	129.0	131.0		24	-0.1	0.0	7	dbSNP_116	131	2152,6448	369.5+/-335.5	269,1614,2417	no	coding-synonymous	PRSS58	NM_001001317.3		282,1968,4253	GG,GA,AA		25.0233,8.6246,19.4679		8/242	141957504	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon2			CAAGAGAGCCCAG		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.24T>C	7.37:g.141957504A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			A|0.764;G|0.236	0.236	strong		0.433	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317	
TBCD	6904	hgsc.bcm.edu	37	17	80710097	80710097	+	Missense_Mutation	SNP	G	G	T	rs11550062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80710097G>T	ENST00000355528.4	+	1	158	c.28G>T	c.(28-30)Ggc>Tgc	p.G10C	TBCD_ENST00000539345.2_Missense_Mutation_p.G10C|TBCD_ENST00000397466.2_5'UTR	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	1	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	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	
TMEM175	84286	hgsc.bcm.edu	37	4	944210	944210	+	Splice_Site	SNP	A	A	C	rs34884217	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:944210A>C	ENST00000264771.4	+	4	379	c.194A>C	c.(193-195)cAg>cCg	p.Q65P	TMEM175_ENST00000504180.1_Splice_Site|TMEM175_ENST00000508204.1_5'UTR|TMEM175_ENST00000515740.1_5'UTR	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	65			Q -> P (in dbSNP:rs34884217).			integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GTATTCCAGCAGTTCGACAGA	0.587													A|||	161	0.0321486	0.0023	0.049	5008	,	,		15929	0.001		0.0964	False		,,,				2504	0.0266				p.Q65P		Atlas-SNP	.											.	TMEM175	44	.	0			c.A194C						PASS	.	A	PRO/GLN	101,4305	79.9+/-118.3	4,93,2106	119.0	102.0	107.0		194	0.6	0.1	4	dbSNP_126	107	921,7679	203.5+/-246.5	63,795,3442	yes	missense-near-splice	TMEM175	NM_032326.2	76	67,888,5548	CC,CA,AA		10.7093,2.2923,7.8579	benign	65/505	944210	1022,11984	2203	4300	6503	SO:0001630	splice_region_variant	84286	exon4			TCCAGCAGTTCGA	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.193-1A>C	4.37:g.944210A>C		Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	237	113	0.476793	NM_032326	D3DVN4|Q8ND13	Missense_Mutation	SNP	ENST00000264771.4	37	CCDS3341.1	87|87	0.03983516483516483|0.03983516483516483	4|4	0.008130081300813009|0.008130081300813009	20|20	0.055248618784530384|0.055248618784530384	0|0	0.0|0.0	63|63	0.08311345646437995|0.08311345646437995	A|A	1.373|1.373	-0.585596|-0.585596	0.03827|0.03827	0.022923|0.022923	0.107093|0.107093	ENSG00000127419|ENSG00000127419	ENST00000507319|ENST00000264771;ENST00000514453;ENST00000514546	.|T;T;T	.|0.46451	.|0.87;1.0;0.87	4.9|4.9	0.563|0.563	0.17296|0.17296	.|.	.|0.685752	.|0.13840	.|N	.|0.359112	.|T	.|0.00300	.|0.0009	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	D|D	1|1	.|B	.|0.10296	.|0.003	.|B	.|0.10450	.|0.005	.|T	.|0.22277	.|-1.0221	.|10	.|0.30854	.|T	.|0.27	.|-4.2182	4.3737|4.3737	0.11260|0.11260	0.6118:0.1753:0.2129:0.0|0.6118:0.1753:0.2129:0.0	rs34884217|rs34884217	.|65	.|Q9BSA9	.|TM175_HUMAN	.|P	-1|65;52;65	.|ENSP00000264771:Q65P;ENSP00000425181:Q52P;ENSP00000425763:Q65P	.|ENSP00000264771:Q65P	.|Q	+|+	.|2	.|0	TMEM175|TMEM175	934210|934210	1.000000|1.000000	0.71417|0.71417	0.101000|0.101000	0.21167|0.21167	0.007000|0.007000	0.05969|0.05969	4.186000|4.186000	0.58337|0.58337	0.233000|0.233000	0.21120|0.21120	-0.396000|-0.396000	0.06452|0.06452	.|CAG	A|0.930;C|0.070	0.070	strong		0.587	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326	Missense_Mutation
EVPL	2125	hgsc.bcm.edu	37	17	74003805	74003805	+	Silent	SNP	G	G	A	rs7342882	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74003805G>A	ENST00000301607.3	-	22	5734	c.5481C>T	c.(5479-5481)atC>atT	p.I1827I	EVPL_ENST00000586740.1_Silent_p.I1849I|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1827	Globular 2.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						AGATCCCGGCGATAGGGAAGC	0.592													G|||	878	0.175319	0.5484	0.085	5008	,	,		17459	0.0089		0.0577	False		,,,				2504	0.0276				p.I1827I		Atlas-SNP	.											.	EVPL	155	.	0			c.C5481T						PASS	.	G		2087,2319	572.4+/-383.3	513,1061,629	134.0	142.0	139.0		5481	1.4	1.0	17	dbSNP_116	139	468,8132	138.6+/-195.4	17,434,3849	no	coding-synonymous	EVPL	NM_001988.2		530,1495,4478	AA,AG,GG		5.4419,47.3672,19.6448		1827/2034	74003805	2555,10451	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon22			CCCGGCGATAGGG	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.5481C>T	17.37:g.74003805G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.804;A|0.196	0.196	strong		0.592	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
ISYNA1	51477	hgsc.bcm.edu	37	19	18546678	18546678	+	Silent	SNP	T	T	C	rs2303697	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18546678T>C	ENST00000338128.8	-	8	1246	c.1029A>G	c.(1027-1029)ctA>ctG	p.L343L	ISYNA1_ENST00000578963.1_Silent_p.L215L|ISYNA1_ENST00000317018.6_Silent_p.L141L|ISYNA1_ENST00000545187.1_Silent_p.L193L|ISYNA1_ENST00000457269.4_Silent_p.L289L	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	343					inositol biosynthetic process (GO:0006021)|inositol phosphate metabolic process (GO:0043647)|phospholipid biosynthetic process (GO:0008654)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-3-phosphate synthase activity (GO:0004512)			breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	12						ATGGCGCCGATAGGTTCTCCC	0.602													C|||	2366	0.472444	0.8298	0.3732	5008	,	,		15663	0.2163		0.3479	False		,,,				2504	0.4519				p.L343L		Atlas-SNP	.											.	ISYNA1	31	.	0			c.A1029G	GRCh37	CM044082	ISYNA1	M	rs2303697	PASS	.	C	,,	3313,1093	394.0+/-329.1	1253,807,143	163.0	176.0	172.0		867,579,1029	0.8	1.0	19	dbSNP_100	172	2947,5653	668.2+/-402.5	537,1873,1890	no	coding-synonymous,coding-synonymous,coding-synonymous	ISYNA1	NM_001170938.1,NM_001170939.1,NM_016368.4	,,	1790,2680,2033	CC,CT,TT		34.2674,24.8071,48.1316	,,	289/505,193/409,343/559	18546678	6260,6746	2203	4300	6503	SO:0001819	synonymous_variant	51477	exon8			CGCCGATAGGTTC		CCDS12379.1, CCDS54234.1, CCDS62603.1	19p13.11	2014-09-04			ENSG00000105655	ENSG00000105655	5.5.1.4		29821	protein-coding gene	gene with protein product	"""myo-inositol 1-phosphate synthase"""	611670				15024000, 12941308	Standard	NM_016368		Approved	Ino1, INOS, IPS	uc002njd.2	Q9NPH2	OTTHUMG00000179027	ENST00000338128.8:c.1029A>G	19.37:g.18546678T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	124	70	0.564516	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			T|0.535;C|0.465	0.465	strong		0.602	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368	
USP10	9100	hgsc.bcm.edu	37	16	84778694	84778694	+	Missense_Mutation	SNP	T	T	C	rs2326391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84778694T>C	ENST00000219473.7	+	4	720	c.607T>C	c.(607-609)Tca>Cca	p.S203P	USP10_ENST00000570191.1_Missense_Mutation_p.S207P|USP10_ENST00000562743.1_3'UTR	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	203			S -> P (in dbSNP:rs2326391). {ECO:0000269|PubMed:15489334}.		autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						CATGCCCCCGTCAGTTACGCC	0.547													T|||	1406	0.280751	0.2337	0.121	5008	,	,		17497	0.4107		0.1531	False		,,,				2504	0.455				p.S207P		Atlas-SNP	.											.	USP10	51	.	0			c.T619C						PASS	.	T	PRO/SER	824,3138		80,664,1237	30.0	29.0	29.0		607	-2.2	0.0	16	dbSNP_100	29	1157,7163		83,991,3086	no	missense	USP10	NM_005153.2	74	163,1655,4323	CC,CT,TT		13.9062,20.7976,16.1293	benign	203/799	84778694	1981,10301	1981	4160	6141	SO:0001583	missense	9100	exon5			CCCCCGTCAGTTA	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.607T>C	16.37:g.84778694T>C	ENSP00000219473:p.Ser203Pro	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	140	52	0.371429	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	528	0.24175824175824176	114	0.23170731707317074	48	0.13259668508287292	256	0.44755244755244755	110	0.14511873350923482	T	4.094	0.015431	0.07959	0.207976	0.139063	ENSG00000103194	ENST00000219473	T	0.08282	3.11	5.17	-2.15	0.07102	.	1.297810	0.05133	N	0.492893	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.47649	-0.9101	9	0.42905	T	0.14	3.5779	7.0558	0.25099	0.0:0.4462:0.1418:0.4121	rs2326391;rs17855998	207;203	Q14694-3;Q14694	.;UBP10_HUMAN	P	203	ENSP00000219473:S203P	ENSP00000219473:S203P	S	+	1	0	USP10	83336195	0.000000	0.05858	0.000000	0.03702	0.181000	0.23173	-0.193000	0.09573	-0.758000	0.04690	0.402000	0.26972	TCA	T|0.774;C|0.226	0.226	strong		0.547	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
MRPL12	6182	hgsc.bcm.edu	37	17	79671714	79671714	+	Missense_Mutation	SNP	T	T	C	rs11546280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79671714T>C	ENST00000333676.3	+	3	458	c.313T>C	c.(313-315)Tct>Cct	p.S105P	SLC25A10_ENST00000571730.1_Missense_Mutation_p.S105P|SLC25A10_ENST00000541223.1_Missense_Mutation_p.S105P|RP13-1032I1.7_ENST00000575312.1_RNA	NM_002949.3	NP_002940.2	P52815	RM12_HUMAN	mitochondrial ribosomal protein L12	105			S -> P (in dbSNP:rs11546280).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|lung(2)|urinary_tract(1)	4	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			TGGTGTGATGTCTGGGGCTGT	0.602													C|||	508	0.101438	0.0726	0.0461	5008	,	,		18705	0.2242		0.0716	False		,,,				2504	0.0838				p.S105P		Atlas-SNP	.											.	MRPL12	12	.	0			c.T313C						PASS	.	C	PRO/SER	308,4098	796.5+/-415.4	8,292,1903	169.0	138.0	149.0		313	4.6	0.1	17	dbSNP_120	149	528,8072	795.4+/-407.5	15,498,3787	yes	missense	MRPL12	NM_002949.3	74	23,790,5690	CC,CT,TT		6.1395,6.9905,6.4278		105/199	79671714	836,12170	2203	4300	6503	SO:0001583	missense	6182	exon3			GTGATGTCTGGGG	X79865	CCDS11785.1	17q25	2012-11-14			ENSG00000262814	ENSG00000262814		"""Mitochondrial ribosomal proteins / large subunits"""	10378	protein-coding gene	gene with protein product		602375		RPML12		8626705, 9169145	Standard	NM_002949		Approved	MRPL7/L12, MRPL7		P52815	OTTHUMG00000178171	ENST00000333676.3:c.313T>C	17.37:g.79671714T>C	ENSP00000333837:p.Ser105Pro	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	56	0.388889	NM_002949	Q969U0|Q9HCA2|Q9UQJ3	Missense_Mutation	SNP	ENST00000333676.3	37	CCDS11785.1	238	0.10897435897435898	40	0.08130081300813008	15	0.04143646408839779	127	0.22202797202797203	56	0.07387862796833773	C	0.042	-1.279643	0.01410	0.069905	0.061395	ENSG00000183048	ENST00000541223;ENST00000333676;ENST00000332396	T;T	0.40756	1.02;1.02	4.62	4.62	0.57501	Ribosomal protein L7/L12, oligomerisation (1);	0.255193	0.38959	N	0.001503	T	0.00012	0.0000	N	0.00368	-1.59	0.09310	P	0.9999999999814047	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20706	-1.0267	9	0.06494	T	0.89	-19.539	8.4871	0.33078	0.0:0.8197:0.0:0.1803	rs11546280;rs11546280	105;105	B4DLN1;P52815	.;RM12_HUMAN	P	105	ENSP00000439565:S105P;ENSP00000333837:S105P	ENSP00000330017:S105P	S	+	1	0	SLC25A10	77282119	1.000000	0.71417	0.060000	0.19600	0.019000	0.09904	1.935000	0.40173	1.182000	0.42928	-0.119000	0.15052	TCT	T|0.923;C|0.077	0.077	strong		0.602	MRPL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440812.1	NM_002949	
OR4N4	283694	hgsc.bcm.edu	37	15	22382821	22382821	+	Missense_Mutation	SNP	G	G	C	rs12438969	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:22382821G>C	ENST00000328795.4	+	1	440	c.349G>C	c.(349-351)Gtg>Ctg	p.V117L	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	117						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)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		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)		ACTCCTTGTTGTGATGGCCTT	0.512																																					p.V117L		Atlas-SNP	.											.	OR4N4	108	.	0			c.G349C						PASS	.						99.0	89.0	92.0					15																	22382821		2192	4261	6453	SO:0001583	missense	283694	exon1			CTTGTTGTGATGG	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.349G>C	15.37:g.22382821G>C	ENSP00000332500:p.Val117Leu	Somatic	363	0	0		WXS	Illumina HiSeq	Phase_I	356	104	0.292135	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	560	0.2564102564102564	152	0.3089430894308943	85	0.23480662983425415	125	0.21853146853146854	198	0.2612137203166227	.	12.85	2.060507	0.36373	.	.	ENSG00000183706	ENST00000328795	T	0.05139	3.49	3.2	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000469	T	0.00012	0.0000	L	0.48362	1.52	0.80722	P	0.0	D	0.61080	0.989	P	0.51701	0.677	T	0.49661	-0.8916	9	0.42905	T	0.14	-9.0007	5.3674	0.16121	0.2721:0.0:0.7279:0.0	rs12438969	117	Q8N0Y3	OR4N4_HUMAN	L	117	ENSP00000332500:V117L	ENSP00000332500:V117L	V	+	1	0	OR4N4	19884185	0.000000	0.05858	0.753000	0.31225	0.732000	0.41865	0.654000	0.24918	0.671000	0.31185	0.184000	0.17185	GTG	.	.	weak		0.512	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
C10orf71	118461	hgsc.bcm.edu	37	10	50533776	50533776	+	Silent	SNP	C	C	G	rs10857471|rs71471341	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50533776C>G	ENST00000374144.3	+	3	3474	c.3186C>G	c.(3184-3186)ccC>ccG	p.P1062P	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1062										endometrium(1)	1						CCGGCTCCCCCGGGGAGAGCA	0.627													c|||	1737	0.346845	0.2806	0.3919	5008	,	,		15975	0.1954		0.4334	False		,,,				2504	0.4714				p.P1062P		Atlas-SNP	.											.	C10orf71	179	.	0			c.C3186G						PASS	.						10.0	14.0	13.0					10																	50533776		691	1589	2280	SO:0001819	synonymous_variant	118461	exon3			CTCCCCCGGGGAG	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.3186C>G	10.37:g.50533776C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.643;G|0.357	0.357	strong		0.627	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
FAM124B	79843	hgsc.bcm.edu	37	2	225244352	225244352	+	Missense_Mutation	SNP	G	G	A	rs61732371	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:225244352G>A	ENST00000409685.3	-	2	1571	c.1306C>T	c.(1306-1308)Ctc>Ttc	p.L436F	FAM124B_ENST00000389874.3_3'UTR	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	436										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)		AGATGAAGGAGACATTCTGAA	0.393													G|||	169	0.033746	0.0431	0.0202	5008	,	,		19858	0.0109		0.0676	False		,,,				2504	0.0194				p.L436F		Atlas-SNP	.											.	FAM124B	71	.	0			c.C1306T						PASS	.	G	PHE/LEU,	53,1331		0,53,639	54.0	49.0	51.0		1306,	-4.3	0.0	2	dbSNP_129	51	191,2991		7,177,1407	yes	missense,utr-3	FAM124B	NM_001122779.1,NM_024785.2	22,	7,230,2046	AA,AG,GG		6.0025,3.8295,5.3438	benign,	436/456,	225244352	244,4322	692	1591	2283	SO:0001583	missense	79843	exon2			GAAGGAGACATTC	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.1306C>T	2.37:g.225244352G>A	ENSP00000386895:p.Leu436Phe	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001122779	A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	CCDS46527.1	76	0.0347985347985348	8	0.016260162601626018	14	0.03867403314917127	3	0.005244755244755245	51	0.06728232189973615	G	0.082	-1.182241	0.01633	0.038295	0.060025	ENSG00000124019	ENST00000409685	T	0.31247	1.5	5.89	-4.32	0.03688	.	.	.	.	.	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	P	0.38420	0.63	B	0.37198	0.243	T	0.14727	-1.0462	9	0.37606	T	0.19	-1.0026	8.6055	0.33771	0.5495:0.0:0.3505:0.0999	.	436	Q9H5Z6	F124B_HUMAN	F	436	ENSP00000386895:L436F	ENSP00000386895:L436F	L	-	1	0	FAM124B	224952596	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.622000	0.05553	-0.956000	0.03631	-0.156000	0.13503	CTC	G|0.965;A|0.035	0.035	strong		0.393	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785	
SEPT4	5414	hgsc.bcm.edu	37	17	56598991	56598991	+	Missense_Mutation	SNP	T	T	A	rs17741424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56598991T>A	ENST00000317268.3	-	8	1108	c.932A>T	c.(931-933)gAg>gTg	p.E311V	SEPT4_ENST00000583114.1_Missense_Mutation_p.E164V|SEPT4_ENST00000317256.6_Missense_Mutation_p.E292V|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_Missense_Mutation_p.E326V|SEPT4_ENST00000426861.1_3'UTR|SEPT4_ENST00000579371.1_Missense_Mutation_p.E212V|SEPT4_ENST00000412945.3_Missense_Mutation_p.E303V|SEPT4_ENST00000580844.1_Missense_Mutation_p.E212V|SEPT4_ENST00000393086.1_Missense_Mutation_p.E292V|SEPT4_ENST00000580809.1_3'UTR	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	311	Septin-type G.		E -> V (in dbSNP:rs17741424).		apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCAAAATGCTCAATCTCCTC	0.522													T|||	218	0.0435304	0.0045	0.0533	5008	,	,		19419	0.0		0.1243	False		,,,				2504	0.0511				p.E326V		Atlas-SNP	.											SEPT4,lymph_node,lymphoid_neoplasm,0,1	SEPT4	48	1	0			c.A977T						PASS	.	T	VAL/GLU,VAL/GLU,,VAL/GLU	101,4305	80.4+/-118.8	1,99,2103	123.0	118.0	120.0		908,932,,875	5.6	1.0	17	dbSNP_123	120	1037,7563	220.1+/-257.9	69,899,3332	yes	missense,missense,utr-3,missense	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	121,121,,121	70,998,5435	AA,AT,TT		12.0581,2.2923,8.7498	possibly-damaging,possibly-damaging,,possibly-damaging	303/471,311/479,,292/460	56598991	1138,11868	2203	4300	6503	SO:0001583	missense	5414	exon9			AAATGCTCAATCT	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"""Septins"""	9165	protein-coding gene	gene with protein product	"""bradeoin"", ""septin-M"""	603696	"""peanut-like 2 (Drosophila)"""	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.932A>T	17.37:g.56598991T>A	ENSP00000321674:p.Glu311Val	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	136	47	0.345588	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Missense_Mutation	SNP	ENST00000317268.3	37	CCDS11610.1	112	0.05128205128205128	2	0.0040650406504065045	24	0.06629834254143646	0	0.0	86	0.11345646437994723	T	8.736	0.917894	0.17982	0.022923	0.120581	ENSG00000108387	ENST00000412945;ENST00000457347;ENST00000317256;ENST00000317268;ENST00000393086	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.59	5.59	0.84812	.	0.112753	0.64402	D	0.000011	T	0.00724	0.0024	L	0.41079	1.255	0.09310	P	0.999999833909	P;P;B;P;P	0.48089	0.726;0.905;0.422;0.833;0.768	P;P;P;P;P	0.54140	0.499;0.605;0.499;0.68;0.743	T	0.05616	-1.0874	9	0.62326	D	0.03	.	13.7051	0.62633	0.0:0.0:0.0:1.0	rs17741424;rs52801197;rs17741424	303;326;292;164;311	O43236-3;O43236-4;O43236-2;O43236-5;O43236	.;.;.;.;SEPT4_HUMAN	V	303;325;292;311;292	ENSP00000414779:E303V;ENSP00000321071:E292V;ENSP00000321674:E311V;ENSP00000376801:E292V	ENSP00000321071:E292V	E	-	2	0	SEPT4	53953990	1.000000	0.71417	1.000000	0.80357	0.835000	0.47333	5.151000	0.64875	2.116000	0.64780	0.455000	0.32223	GAG	T|0.923;A|0.077	0.077	strong		0.522	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68678962	68678962	+	Missense_Mutation	SNP	T	T	C	rs560096	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68678962T>C	ENST00000255078.3	+	5	713	c.602T>C	c.(601-603)tTa>tCa	p.L201S	IGHMBP2_ENST00000539224.1_Silent_p.F168F	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	201			L -> S (in dbSNP:rs560096). {ECO:0000269|PubMed:8349627}.		ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GAAGCGGTTTTATTTGCGCTG	0.522													C|||	3408	0.680511	0.6029	0.817	5008	,	,		19637	0.4633		0.8509	False		,,,				2504	0.7372				p.L201S		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.T602C						PASS	.	C	SER/LEU	2862,1538	486.4+/-360.6	939,984,277	96.0	83.0	88.0		602	-1.6	0.0	11	dbSNP_83	88	7250,1338	262.3+/-284.3	3061,1128,105	yes	missense	IGHMBP2	NM_002180.2	145	4000,2112,382	CC,CT,TT		15.5799,34.9545,22.1435	benign	201/994	68678962	10112,2876	2200	4294	6494	SO:0001583	missense	3508	exon5			CGGTTTTATTTGC	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.602T>C	11.37:g.68678962T>C	ENSP00000255078:p.Leu201Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	1535	0.7028388278388278	297	0.6036585365853658	299	0.8259668508287292	294	0.513986013986014	645	0.8509234828496042	C	1.240	-0.621672	0.03636	0.650455	0.844201	ENSG00000132740	ENST00000255078	D	0.82081	-1.57	4.93	-1.58	0.08479	DEAD-like helicase (1);	0.987546	0.08229	N	0.977827	T	0.00012	0.0000	N	0.02685	-0.53	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.33240	-0.9876	9	0.06494	T	0.89	-9.3544	5.028	0.14395	0.0944:0.3103:0.4391:0.1562	rs560096;rs731473;rs56607437;rs58736819;rs560096	201	P38935	SMBP2_HUMAN	S	201	ENSP00000255078:L201S	ENSP00000255078:L201S	L	+	2	0	IGHMBP2	68435538	0.000000	0.05858	0.000000	0.03702	0.309000	0.27889	-0.070000	0.11523	-0.414000	0.07495	-0.343000	0.07986	TTA	A|0.001;C|0.675	0.675	strong		0.522	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
C17orf96	100170841	hgsc.bcm.edu	37	17	36830727	36830727	+	Missense_Mutation	SNP	G	G	A	rs76756126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36830727G>A	ENST00000325814.5	-	1	460	c.22C>T	c.(22-24)Ccc>Tcc	p.P8S		NM_001130677.1	NP_001124149.1	A6NHQ4	CQ096_HUMAN	chromosome 17 open reading frame 96	8	Pro-rich.				neuron fate commitment (GO:0048663)												GCCAGGCGGGGCGCAGGGCAC	0.746													G|||	346	0.0690895	0.0121	0.049	5008	,	,		11987	0.0724		0.0348	False		,,,				2504	0.1922				p.P8S		Atlas-SNP	.											.	.	.	.	0			c.C22T						PASS	.						1.0	2.0	2.0					17																	36830727		436	1184	1620	SO:0001583	missense	100170841	exon1			GGCGGGGCGCAGG		CCDS45661.1	17q12	2014-04-17			ENSG00000179294	ENSG00000273604			34493	protein-coding gene	gene with protein product	"""proline rich 28"""					24550272	Standard	NM_001130677		Approved	LOC100170841, PRR28	uc010wdq.2	A6NHQ4	OTTHUMG00000188495	ENST00000325814.5:c.22C>T	17.37:g.36830727G>A	ENSP00000317905:p.Pro8Ser	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_001130677		Missense_Mutation	SNP	ENST00000325814.5	37	CCDS45661.1	99	0.04532967032967033	7	0.014227642276422764	19	0.052486187845303865	45	0.07867132867132867	28	0.036939313984168866	G	2.519	-0.311228	0.05458	.	.	ENSG00000179294	ENST00000325814	.	.	.	4.24	-1.13	0.09775	.	.	.	.	.	T	0.00784	0.0026	N	0.12182	0.205	0.19775	N	0.999956	B	0.02656	0.0	B	0.06405	0.002	T	0.19321	-1.0309	8	0.25751	T	0.34	.	3.8915	0.09120	0.3532:0.0:0.4745:0.1723	.	8	A6NHQ4	CQ096_HUMAN	S	8	.	ENSP00000317905:P8S	P	-	1	0	C17orf96	34084253	0.004000	0.15560	0.753000	0.31225	0.145000	0.21501	-0.344000	0.07780	-0.065000	0.13021	-0.448000	0.05591	CCC	G|0.953;A|0.047	0.047	strong		0.746	C17orf96-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255465.2	NM_001130677	
SLX4	84464	hgsc.bcm.edu	37	16	3656680	3656680	+	Silent	SNP	G	G	A	rs74640850	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3656680G>A	ENST00000294008.3	-	3	1195	c.555C>T	c.(553-555)gaC>gaT	p.D185D		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	185	Interaction with SLX4IP, ERCC4 and MSH2.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GAGGCTGGGAGTCGCTGTTGG	0.493								Direct reversal of damage					G|||	210	0.0419329	0.0038	0.0692	5008	,	,		19483	0.0506		0.0646	False		,,,				2504	0.0419				p.D185D		Atlas-SNP	.											SLX4,colon,carcinoma,-2,1	SLX4	173	1	0			c.C555T						PASS	.	G		65,4329	60.5+/-97.4	0,65,2132	131.0	127.0	129.0		555	1.3	0.0	16	dbSNP_131	129	582,8018	156.4+/-210.3	15,552,3733	no	coding-synonymous	SLX4	NM_032444.2		15,617,5865	AA,AG,GG		6.7674,1.4793,4.9792		185/1835	3656680	647,12347	2197	4300	6497	SO:0001819	synonymous_variant	84464	exon3			CTGGGAGTCGCTG	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.555C>T	16.37:g.3656680G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_032444	Q69YT8|Q8TF15|Q96JP1	Silent	SNP	ENST00000294008.3	37	CCDS10506.2																																																																																			G|0.954;A|0.046	0.046	strong		0.493	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
MUC6	4588	hgsc.bcm.edu	37	11	1016630	1016630	+	Silent	SNP	G	G	A	rs369775657		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1016630G>A	ENST00000421673.2	-	31	6221	c.6171C>T	c.(6169-6171)tcC>tcT	p.S2057S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2057	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)		CTGTGTGGGTGGACCCTGTGG	0.562																																					p.S2057S		Atlas-SNP	.											.	MUC6	408	.	0			c.C6171T						PASS	.	G		32,4354	2.1+/-5.4	0,32,2161	389.0	386.0	387.0		6171	-2.5	0.0	11		387	18,8558	1.2+/-3.3	0,18,4270	no	coding-synonymous	MUC6	NM_005961.2		0,50,6431	AA,AG,GG		0.2099,0.7296,0.3857		2057/2440	1016630	50,12912	2193	4288	6481	SO:0001819	synonymous_variant	4588	exon31			GTGGGTGGACCCT	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.6171C>T	11.37:g.1016630G>A		Somatic	429	0	0		WXS	Illumina HiSeq	Phase_I	446	27	0.0605381	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	weak		0.562	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ALPK2	115701	hgsc.bcm.edu	37	18	56203837	56203837	+	Silent	SNP	G	G	A	rs17065139	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:56203837G>A	ENST00000361673.3	-	5	3795	c.3582C>T	c.(3580-3582)tcC>tcT	p.S1194S	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1194						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						CAGCCACCACGGAGACCCTCG	0.552													G|||	277	0.0553115	0.1293	0.0303	5008	,	,		18795	0.0268		0.0268	False		,,,				2504	0.0317				p.S1194S		Atlas-SNP	.											.	ALPK2	487	.	0			c.C3582T						PASS	.	G		446,3960	214.1+/-233.5	22,402,1779	95.0	90.0	92.0		3582	-9.5	0.0	18	dbSNP_123	92	188,8412	84.2+/-146.7	3,182,4115	no	coding-synonymous	ALPK2	NM_052947.3		25,584,5894	AA,AG,GG		2.186,10.1226,4.8747		1194/2171	56203837	634,12372	2203	4300	6503	SO:0001819	synonymous_variant	115701	exon5			CACCACGGAGACC	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.3582C>T	18.37:g.56203837G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			G|0.949;A|0.051	0.051	strong		0.552	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947	
LRPAP1	4043	hgsc.bcm.edu	37	4	3519762	3519762	+	Splice_Site	SNP	A	A	G	rs13325	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3519762A>G	ENST00000500728.2	-	5	896	c.750T>C	c.(748-750)gcT>gcC	p.A250A	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	250	LDL receptor binding. {ECO:0000255}.				extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		GGCACTCACCAGCCTCAGTGC	0.652													.|||	492	0.0982428	0.1263	0.1369	5008	,	,		16586	0.0		0.161	False		,,,				2504	0.0695				p.A250A		Atlas-SNP	.											.	LRPAP1	29	.	0			c.T750C						PASS	.	G		691,3715	749.8+/-412.1	53,585,1565	38.0	36.0	36.0		750	-8.2	0.0	4	dbSNP_52	36	1466,7134	742.2+/-407.2	122,1222,2956	no	coding-synonymous-near-splice	LRPAP1	NM_002337.3		175,1807,4521	GG,GA,AA		17.0465,15.6832,16.5847		250/358	3519762	2157,10849	2203	4300	6503	SO:0001630	splice_region_variant	4043	exon5			CTCACCAGCCTCA		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.751+1T>C	4.37:g.3519762A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			A|0.853;G|0.147	0.147	strong		0.652	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		Silent
TEK	7010	hgsc.bcm.edu	37	9	27212856	27212856	+	Silent	SNP	C	C	T	rs45505400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:27212856C>T	ENST00000380036.4	+	17	3280	c.2838C>T	c.(2836-2838)gcC>gcT	p.A946A	TEK_ENST00000406359.4_Silent_p.A903A|TEK_ENST00000519097.1_Silent_p.A798A	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	946	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	ACTTCGCTGCCGACGTGGCCC	0.557													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		16575	0.0		0.007	False		,,,				2504	0.001				p.A946A		Atlas-SNP	.											.	TEK	250	.	0			c.C2838T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	72.0	61.0	65.0		2838	-1.5	0.9	9	dbSNP_127	65	85,8515	48.5+/-108.0	1,83,4216	no	coding-synonymous	TEK	NM_000459.3		1,92,6410	TT,TC,CC		0.9884,0.2043,0.7227		946/1125	27212856	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon17			CGCTGCCGACGTG	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.2838C>T	9.37:g.27212856C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			C|0.993;T|0.007	0.007	strong		0.557	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
GNRH2	2797	hgsc.bcm.edu	37	20	3025107	3025107	+	Missense_Mutation	SNP	C	C	T	rs6051545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3025107C>T	ENST00000245983.2	+	2	98	c.47C>T	c.(46-48)gCc>gTc	p.A16V	MRPS26_ENST00000380325.3_5'Flank|GNRH2_ENST00000359100.2_Missense_Mutation_p.A16V|GNRH2_ENST00000380346.2_Missense_Mutation_p.A16V|GNRH2_ENST00000359987.1_Missense_Mutation_p.A16V|GNRH2_ENST00000380347.2_Missense_Mutation_p.A16V	NM_001501.1	NP_001492.1	O43555	GON2_HUMAN	gonadotropin-releasing hormone 2	16			A -> V (in dbSNP:rs6051545).		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			ovary(1)|upper_aerodigestive_tract(1)	2						CTGCTGACTGCCCACCTTGGA	0.617													C|||	1203	0.240216	0.1104	0.281	5008	,	,		18857	0.372		0.173	False		,,,				2504	0.32				p.A16V		Atlas-SNP	.											.	GNRH2	15	.	0			c.C47T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	584,3822	258.6+/-262.5	36,512,1655	70.0	69.0	70.0		47,47,47	1.3	0.0	20	dbSNP_114	70	1374,7226	267.1+/-287.1	103,1168,3029	yes	missense,missense,missense	GNRH2	NM_001501.1,NM_178331.1,NM_178332.1	64,64,64	139,1680,4684	TT,TC,CC		15.9767,13.2547,15.0546	probably-damaging,probably-damaging,probably-damaging	16/121,16/114,16/113	3025107	1958,11048	2203	4300	6503	SO:0001583	missense	2797	exon2			TGACTGCCCACCT	AF036329	CCDS13040.1, CCDS13041.1, CCDS13042.1	20p13	2013-02-26			ENSG00000125787	ENSG00000125787		"""Endogenous ligands"""	4420	protein-coding gene	gene with protein product		602352				9419371, 12447356	Standard	NM_178331		Approved		uc002whr.1	O43555	OTTHUMG00000031723	ENST00000245983.2:c.47C>T	20.37:g.3025107C>T	ENSP00000245983:p.Ala16Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	69	0.594828	NM_001501	Q14C68|Q14C69|Q9BYN9|Q9BYP0	Missense_Mutation	SNP	ENST00000245983.2	37	CCDS13040.1	509	0.23305860805860806	62	0.12601626016260162	103	0.2845303867403315	207	0.3618881118881119	137	0.18073878627968337	C	14.43	2.533369	0.45073	0.132547	0.159767	ENSG00000125787	ENST00000245983;ENST00000359100;ENST00000359987;ENST00000380347;ENST00000380346	T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0	3.32	1.34	0.21922	.	.	.	.	.	T	0.00012	0.0000	N	0.10664	0.02	0.80722	P	0.0	B;B;B	0.20550	0.027;0.046;0.046	B;B;B	0.17433	0.008;0.018;0.018	T	0.46610	-0.9179	8	0.13853	T	0.58	.	6.8688	0.24108	0.0:0.7646:0.0:0.2353	rs6051545;rs6051545	16;16;16	O43555;O43555-2;O43555-3	GON2_HUMAN;.;.	V	16	ENSP00000245983:A16V;ENSP00000352003:A16V;ENSP00000353077:A16V;ENSP00000369705:A16V;ENSP00000369704:A16V	ENSP00000245983:A16V	A	+	2	0	GNRH2	2973107	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.193000	0.17116	0.407000	0.25591	0.563000	0.77884	GCC	C|0.815;T|0.185	0.185	strong		0.617	GNRH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077694.2	NM_001501	
HLA-B	3106	hgsc.bcm.edu	37	6	31324647	31324647	+	Missense_Mutation	SNP	T	T	C	rs9266183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31324647T>C	ENST00000412585.2	-	2	189	c.161A>G	c.(160-162)gAc>gGc	p.D54G		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	54	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GAACTGGGTGTCGTCCACGTA	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	137	0.0273562	0.0325	0.0418	5008	,	,		9560	0.004		0.0388	False		,,,				2504	0.0225				p.D54G		Atlas-SNP	.											.	HLA-B	54	.	0			c.A161G						PASS	.	T	GLY/ASP	143,4165		21,101,2032	36.0	29.0	32.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	161	2.0	1.0	6	dbSNP_118	32	410,7910		58,294,3808	no	missense	HLA-B	NM_005514.6	94	79,395,5840	CC,CT,TT		4.9279,3.3194,4.3792		54/363	31324647	553,12075	2154	4160	6314	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	TGGGTGTCGTCCA	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.161A>G	6.37:g.31324647T>C	ENSP00000399168:p.Asp54Gly	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	73	0.033424908424908424	21	0.042682926829268296	23	0.06353591160220995	0	0.0	29	0.03825857519788918	N	2.937	-0.219661	0.06061	0.033194	0.049279	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00012	9.33;9.33	3.2	2.03	0.26663	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.472360	0.15161	U	0.277142	T	0.00144	0.0004	M	0.87547	2.89	0.25498	N	0.987581	D;B;D	0.89917	1.0;0.001;0.999	D;B;D	0.87578	0.998;0.006;0.998	T	0.08391	-1.0724	10	0.72032	D	0.01	.	6.5793	0.22585	0.0:0.1228:0.0:0.8772	rs9266183;rs17878667;rs45487393	54;54;29	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	G	54;65	ENSP00000399168:D54G;ENSP00000405931:D65G	ENSP00000399168:D54G	D	-	2	0	HLA-B	31432626	0.854000	0.29725	1.000000	0.80357	0.008000	0.06430	0.927000	0.28818	0.450000	0.26774	-0.487000	0.04747	GAC	T|0.965;C|0.035	0.035	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ACADSB	36	hgsc.bcm.edu	37	10	124800853	124800853	+	Silent	SNP	C	C	T	rs1140591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124800853C>T	ENST00000358776.4	+	5	653	c.639C>T	c.(637-639)caC>caT	p.H213H	ACADSB_ENST00000368869.4_Silent_p.H111H|ACADSB_ENST00000496730.2_3'UTR	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	213					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	GTGCTGAGCACGCAGGGCTCT	0.413													C|||	1141	0.227835	0.2163	0.2176	5008	,	,		17755	0.1419		0.2296	False		,,,				2504	0.3374				p.H213H		Atlas-SNP	.											.	ACADSB	45	.	0			c.C639T						PASS	.	C		950,3456	362.1+/-316.0	103,744,1356	143.0	138.0	139.0		639	-9.7	0.0	10	dbSNP_86	139	2017,6583	353.4+/-329.1	222,1573,2505	no	coding-synonymous	ACADSB	NM_001609.3		325,2317,3861	TT,TC,CC		23.4535,21.5615,22.8125		213/433	124800853	2967,10039	2203	4300	6503	SO:0001819	synonymous_variant	36	exon5			TGAGCACGCAGGG	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"""acyl-Coenzyme A dehydrogenase, short/branched chain"""			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.639C>T	10.37:g.124800853C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Silent	SNP	ENST00000358776.4	37	CCDS7634.1																																																																																			A|0.000;C|0.783;G|0.000;T|0.217	0.217	strong		0.413	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52133292	52133292	+	Missense_Mutation	SNP	A	A	G	rs1973019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52133292A>G	ENST00000534261.2	-	3	614	c.215T>C	c.(214-216)gTt>gCt	p.V72A	SIGLEC5_ENST00000222107.4_Intron|SIGLEC5_ENST00000429354.3_Missense_Mutation_p.V72A|SIGLEC5_ENST00000599649.1_Intron|SIGLEC5_ENST00000570106.2_Missense_Mutation_p.V72A			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	72	Ig-like V-type.		V -> A (in dbSNP:rs1973019).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGTGGCCACAACCTCAGCGTA	0.577													G|||	482	0.096246	0.0121	0.1974	5008	,	,		15121	0.002		0.1988	False		,,,				2504	0.1299				p.V72A		Atlas-SNP	.											SIGLEC5,NS,carcinoid-endocrine_tumour,0,1	SIGLEC5	67	1	0			c.T215C						scavenged	.						6.0	6.0	6.0					19																	52133292		1790	3344	5134	SO:0001583	missense	8778	exon2			GCCACAACCTCAG	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.215T>C	19.37:g.52133292A>G	ENSP00000473238:p.Val72Ala	Somatic	785	3	0.00382166		WXS	Illumina HiSeq	Phase_I	1021	502	0.491675	NM_003830		Missense_Mutation	SNP	ENST00000534261.2	37	CCDS33088.1	.	.	.	.	.	.	.	.	.	.	a	5.405	0.259892	0.10239	.	.	ENSG00000105501	ENST00000429354	T	0.68025	-0.3	4.24	-4.0	0.04057	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.544624	0.15369	N	0.265939	T	0.46870	0.1415	N	0.25485	0.75	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.27640	-1.0068	9	0.30854	T	0.27	.	10.8806	0.46935	0.6567:0.0:0.3433:0.0	.	72	O15389	SIGL5_HUMAN	A	72	ENSP00000415200:V72A	ENSP00000415200:V72A	V	-	2	0	SIGLEC5	56825104	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.459000	0.06728	-0.793000	0.04475	-0.880000	0.02959	GTT	A|0.500;G|0.500	0.500	strong		0.577	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
ZNF286A	57335	hgsc.bcm.edu	37	17	15620481	15620481	+	Silent	SNP	C	C	T	rs2530064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15620481C>T	ENST00000464847.2	+	5	1996	c.1443C>T	c.(1441-1443)ctC>ctT	p.L481L	ZNF286A_ENST00000421016.1_Silent_p.L481L|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000413242.2_Silent_p.L481L|ZNF286A_ENST00000583566.1_Silent_p.L481L|ZNF286A_ENST00000593105.1_Silent_p.L471L			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	481					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.L481L(1)		central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		CATCAGCTCTCATTCAACATC	0.403													T|||	1613	0.322085	0.3215	0.3473	5008	,	,		18041	0.25		0.327	False		,,,				2504	0.3742				p.L481L		Atlas-SNP	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	1	Substitution - coding silent(1)	stomach(1)	c.C1443T						PASS	.						57.0	60.0	59.0					17																	15620481		2200	4294	6494	SO:0001819	synonymous_variant	57335	exon6			AGCTCTCATTCAA	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.1443C>T	17.37:g.15620481C>T		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	162	41	0.253086	NM_020652	B4DKF9|Q96JF3	Silent	SNP	ENST00000464847.2	37	CCDS11172.1																																																																																			C|0.250;T|0.750	0.750	weak		0.403	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
ENPP7	339221	hgsc.bcm.edu	37	17	77709339	77709339	+	Silent	SNP	C	C	G	rs11657217	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:77709339C>G	ENST00000328313.5	+	3	1118	c.897C>G	c.(895-897)gcC>gcG	p.A299A		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)			TGTACGATGCCCTCAAGGACG	0.592													G|||	1599	0.319289	0.4864	0.2435	5008	,	,		5034	0.1101		0.2942	False		,,,				2504	0.3885				p.A299A		Atlas-SNP	.											.	ENPP7	63	.	0			c.C897G						PASS	.	G		2062,2344	607.3+/-390.9	479,1104,620	94.0	76.0	82.0		897	-0.9	0.0	17	dbSNP_120	82	2625,5975	686.6+/-404.1	414,1797,2089	no	coding-synonymous	ENPP7	NM_178543.3		893,2901,2709	GG,GC,CC		30.5233,46.7998,36.0372		299/459	77709339	4687,8319	2203	4300	6503	SO:0001819	synonymous_variant	339221	exon3			CGATGCCCTCAAG	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.897C>G	17.37:g.77709339C>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_178543		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			C|0.672;G|0.328	0.328	strong		0.592	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
ZNF749	388567	hgsc.bcm.edu	37	19	57955244	57955244	+	Missense_Mutation	SNP	A	A	G	rs12986235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57955244A>G	ENST00000334181.4	+	3	978	c.728A>G	c.(727-729)cAg>cGg	p.Q243R	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	243			Q -> R (in dbSNP:rs12986235).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		ATTAAATATCAGCAAAATCAT	0.413													A|||	998	0.199281	0.2428	0.1931	5008	,	,		21163	0.0913		0.2883	False		,,,				2504	0.1646				p.Q243R		Atlas-SNP	.											.	ZNF749	75	.	0			c.A728G						PASS	.	A	ARG/GLN	1078,3328	384.2+/-325.2	123,832,1248	57.0	57.0	57.0		728	-0.1	0.0	19	dbSNP_121	57	2297,6303	379.7+/-339.4	306,1685,2309	yes	missense	ZNF749	NM_001023561.2	43	429,2517,3557	GG,GA,AA		26.7093,24.4666,25.9496	probably-damaging	243/779	57955244	3375,9631	2203	4300	6503	SO:0001583	missense	388567	exon3			AATATCAGCAAAA	AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"""Zinc fingers, C2H2-type"", ""-"""	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.728A>G	19.37:g.57955244A>G	ENSP00000333980:p.Gln243Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	72	71	0.986111	NM_001023561		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	449	0.20558608058608058	109	0.22154471544715448	90	0.24861878453038674	38	0.06643356643356643	212	0.2796833773087071	A	13.76	2.333168	0.41297	0.244666	0.267093	ENSG00000186230	ENST00000334181	T	0.16196	2.36	2.27	-0.122	0.13531	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.54863	1.705	0.80722	P	0.0	B	0.21225	0.053	B	0.15052	0.012	T	0.39683	-0.9602	8	0.38643	T	0.18	.	2.7912	0.05388	0.6341:0.0:0.1448:0.2211	rs12986235;rs52824955;rs60657301;rs12986235	243	O43361	ZN749_HUMAN	R	243	ENSP00000333980:Q243R	ENSP00000333980:Q243R	Q	+	2	0	ZNF749	62647056	0.000000	0.05858	0.012000	0.15200	0.338000	0.28826	-0.861000	0.04268	-0.268000	0.09312	0.254000	0.18369	CAG	A|0.771;G|0.229	0.229	strong		0.413	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1	NM_001023561	
SPICE1	152185	hgsc.bcm.edu	37	3	113222036	113222036	+	Silent	SNP	G	G	A	rs11537650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113222036G>A	ENST00000295872.4	-	3	397	c.138C>T	c.(136-138)ccC>ccT	p.P46P		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	46					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						CCAGATCTTCGGGAGTTGCCC	0.313													A|||	1223	0.244209	0.3684	0.1427	5008	,	,		14743	0.2212		0.2286	False		,,,				2504	0.1881				p.P46P		Atlas-SNP	.											.	SPICE1	130	.	0			c.C138T						PASS	.	A		1548,2858	666.6+/-401.7	277,994,932	52.0	55.0	54.0		138	5.6	1.0	3	dbSNP_120	54	1972,6626	721.7+/-406.4	228,1516,2555	no	coding-synonymous	SPICE1	NM_144718.3		505,2510,3487	AA,AG,GG		22.9356,35.1339,27.0686		46/856	113222036	3520,9484	2203	4299	6502	SO:0001819	synonymous_variant	152185	exon3			ATCTTCGGGAGTT	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.138C>T	3.37:g.113222036G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	105	53	0.504762	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			T|0.051;G|0.602;C|0.139;A|0.208	0.208	strong		0.313	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276681	71276681	+	Silent	SNP	T	T	C	rs113879786		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71276681T>C	ENST00000398531.1	+	1	73	c.48T>C	c.(46-48)ggT>ggC	p.G16G	KRTAP5-10_ENST00000376536.4_Silent_p.G16G	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	16						keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GCTGTGGGGGTTGTGGCTCCG	0.662																																					p.G16G		Atlas-SNP	.											.	KRTAP5-10	37	.	0			c.T48C						PASS	.						33.0	43.0	40.0					11																	71276681		2175	4274	6449	SO:0001819	synonymous_variant	387273	exon1			TGGGGGTTGTGGC	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.48T>C	11.37:g.71276681T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	138	39	0.282609	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			T|0.717;C|0.283	0.283	strong		0.662	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
IFIH1	64135	hgsc.bcm.edu	37	2	163124051	163124051	+	Missense_Mutation	SNP	C	C	T	rs1990760	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:163124051C>T	ENST00000263642.2	-	15	3231	c.2836G>A	c.(2836-2838)Gca>Aca	p.A946T		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	946			A -> T (associated with susceptibility to IDDM19; dbSNP:rs1990760). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16699517}.		cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						TTTTGCAGTGCTTTGTTTTCT	0.383													C|||	1786	0.356629	0.1256	0.3905	5008	,	,		19813	0.1865		0.6054	False		,,,				2504	0.5644				p.A946T		Atlas-SNP	.											.	IFIH1	102	.	0			c.G2836A	GRCh37	CM066881	IFIH1	M	rs1990760	PASS	.	C	THR/ALA	816,3590	325.3+/-299.0	85,646,1472	185.0	154.0	165.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2836	3.9	1.0	2	dbSNP_92	165	5185,3415	639.0+/-399.4	1583,2019,698	yes	missense	IFIH1	NM_022168.2	58	1668,2665,2170	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	39.7093,18.5202,46.1402	benign	946/1026	163124051	6001,7005	2203	4300	6503	SO:0001583	missense	64135	exon15			GCAGTGCTTTGTT	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2836G>A	2.37:g.163124051C>T	ENSP00000263642:p.Ala946Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	801	0.36675824175824173	56	0.11382113821138211	162	0.44751381215469616	123	0.21503496503496503	460	0.6068601583113457	C	4.264	0.048000	0.08243	0.185202	0.602907	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.43294	0.95	4.74	3.87	0.44632	C-terminal domain of RIG-I (1);	0.453841	0.25469	N	0.030455	T	0.00012	0.0000	L	0.40543	1.245	0.30279	P	0.791512	B	0.24533	0.105	B	0.19946	0.027	T	0.42447	-0.9451	9	0.12766	T	0.61	-12.3172	7.7307	0.28786	0.0:0.6931:0.0:0.3069	rs1990760;rs3761653;rs34707823;rs52819809;rs58100036;rs1990760	946	Q9BYX4	IFIH1_HUMAN	T	946	ENSP00000263642:A946T	ENSP00000263642:A946T	A	-	1	0	IFIH1	162832297	0.975000	0.34042	0.991000	0.47740	0.226000	0.24999	0.669000	0.25142	1.243000	0.43853	0.585000	0.79938	GCA	C|0.588;T|0.412	0.412	strong		0.383	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
MSH5	4439	hgsc.bcm.edu	37	6	31729359	31729359	+	Silent	SNP	A	A	G	rs707938	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31729359A>G	ENST00000375755.3	+	22	2434	c.2148A>G	c.(2146-2148)caA>caG	p.Q716Q	SAPCD1_ENST00000415669.2_5'Flank|MSH5_ENST00000431848.2_Silent_p.Q415Q|MSH5_ENST00000375740.3_Silent_p.Q734Q|MSH5_ENST00000534153.4_Silent_p.Q733Q|MSH5-SAPCD1_ENST00000493662.2_Silent_p.Q733Q|SAPCD1_ENST00000425424.1_5'Flank|MSH5_ENST00000375703.3_Silent_p.Q717Q|MSH5_ENST00000375750.3_Silent_p.Q716Q|MSH5-SAPCD1_ENST00000491552.1_3'UTR|SAPCD1-AS1_ENST00000419679.1_RNA|MSH5_ENST00000375742.3_Silent_p.Q733Q|MSH5_ENST00000395853.1_Silent_p.Q390Q	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	716					ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						TTCAGCTACAACTGCTGCCAC	0.607								Direct reversal of damage;Mismatch excision repair (MMR)					G|||	2340	0.467252	0.6929	0.4236	5008	,	,		17393	0.3512		0.3191	False		,,,				2504	0.4652				p.Q734Q		Atlas-SNP	.											.	MSH5	108	.	0			c.A2202G						PASS	.	G	,,,	2847,1559		925,997,281	47.0	53.0	51.0		2148,2202,2151,2148	2.6	1.0	6	dbSNP_86	51	2724,5876		455,1814,2031	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	,,,	1380,2811,2312	GG,GA,AA		31.6744,35.3836,42.8341	,,,	716/835,734/823,717/836,716/835	31729359	5571,7435	2203	4300	6503	SO:0001819	synonymous_variant	4439	exon22			GCTACAACTGCTG	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.2148A>G	6.37:g.31729359A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_025259	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Silent	SNP	ENST00000375755.3	37	CCDS4720.1																																																																																			A|0.573;G|0.427	0.427	strong		0.607	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
FER1L6	654463	hgsc.bcm.edu	37	8	125076589	125076589	+	Splice_Site	SNP	T	T	G	rs7012186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:125076589T>G	ENST00000522917.1	+	26	3536	c.3330T>G	c.(3328-3330)gaT>gaG	p.D1110E	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Splice_Site_p.D1110E	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1110			D -> E (in dbSNP:rs7012186).			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)			TCATTTCAGATATTTCAGATT	0.502													G|||	3873	0.773363	0.7746	0.7089	5008	,	,		18081	0.6716		0.8708	False		,,,				2504	0.8221				p.D1110E		Atlas-SNP	.											.	FER1L6	268	.	0			c.T3330G						PASS	.	G	GLU/ASP	3227,779		1300,627,76	91.0	97.0	95.0		3330	-6.3	0.0	8	dbSNP_116	95	7213,1147		3111,991,78	yes	missense-near-splice	FER1L6	NM_001039112.2	45	4411,1618,154	GG,GT,TT		13.7201,19.4458,15.575	benign	1110/1858	125076589	10440,1926	2003	4180	6183	SO:0001630	splice_region_variant	654463	exon26			TTCAGATATTTCA	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.3329-1T>G	8.37:g.125076589T>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	1698	0.7774725274725275	379	0.7703252032520326	270	0.7458563535911602	398	0.6958041958041958	651	0.8588390501319261	G	0.579	-0.837956	0.02692	0.805542	0.862799	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.80566	-1.39;-1.39	4.62	-6.3	0.02007	C2 calcium/lipid-binding domain, CaLB (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	0.41088	-0.9528	8	0.02654	T	1	.	0.5246	0.00618	0.1932:0.2396:0.2107:0.3565	rs7012186;rs57095251;rs7012186	1110	Q2WGJ9	FR1L6_HUMAN	E	1110	ENSP00000428280:D1110E;ENSP00000381982:D1110E	ENSP00000381982:D1110E	D	+	3	2	FER1L6	125145770	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.307000	0.08167	-2.111000	0.00836	-1.482000	0.00985	GAT	T|0.207;G|0.793	0.793	strong		0.502	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	Missense_Mutation
ZNF189	7743	hgsc.bcm.edu	37	9	104170227	104170227	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104170227T>G	ENST00000339664.2	+	3	306	c.177T>G	c.(175-177)gaT>gaG	p.D59E	ZNF189_ENST00000259395.4_Missense_Mutation_p.D17E|ZNF189_ENST00000374861.3_Missense_Mutation_p.D45E	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	59	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)				TGAACAGAGATAAGGATGAGG	0.358																																					p.D59E		Atlas-SNP	.											.	ZNF189	79	.	0			c.T177G						PASS	.						51.0	54.0	53.0					9																	104170227		2202	4300	6502	SO:0001583	missense	7743	exon3			CAGAGATAAGGAT	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.177T>G	9.37:g.104170227T>G	ENSP00000342019:p.Asp59Glu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	T	0.024	-1.384786	0.01194	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.05081	5.68;5.68;3.5	4.79	4.79	0.61399	Krueppel-associated box (3);	0.402704	0.21477	N	0.073890	T	0.03695	0.0105	N	0.11870	0.19	0.24556	N	0.993991	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.0;0.0;0.005	T	0.38415	-0.9662	10	0.06365	T	0.9	.	12.9471	0.58379	0.0:0.0:0.0:1.0	.	44;45;59	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	E	45;59;17	ENSP00000363995:D45E;ENSP00000342019:D59E;ENSP00000259395:D17E	ENSP00000259395:D17E	D	+	3	2	ZNF189	103210048	.	.	1.000000	0.80357	0.966000	0.64601	.	.	2.371000	0.80710	0.533000	0.62120	GAT	.	.	none		0.358	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
LGI3	203190	hgsc.bcm.edu	37	8	22006123	22006123	+	Silent	SNP	G	G	A	rs201271501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22006123G>A	ENST00000306317.2	-	8	1486	c.1197C>T	c.(1195-1197)ccC>ccT	p.P399P	LGI3_ENST00000424267.2_Silent_p.P375P	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	399					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		GATAGATGACGGGTGCCTGGG	0.632													g|||	3	0.000599042	0.0	0.0	5008	,	,		16962	0.003		0.0	False		,,,				2504	0.0				p.P399P		Atlas-SNP	.											.	LGI3	44	.	0			c.C1197T						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	76.0	62.0	67.0		1197	-10.3	0.0	8		67	0,8600		0,0,4300	no	coding-synonymous	LGI3	NM_139278.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		399/549	22006123	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	203190	exon8			GATGACGGGTGCC	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1197C>T	8.37:g.22006123G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_139278	A5PLP2|Q86TL4|Q8N296	Silent	SNP	ENST00000306317.2	37	CCDS6025.1																																																																																			G|1.000;A|0.000	0.000	strong		0.632	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
LRRC15	131578	hgsc.bcm.edu	37	3	194081635	194081635	+	Silent	SNP	T	T	C	rs923935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194081635T>C	ENST00000347624.3	-	2	223	c.138A>G	c.(136-138)gcA>gcG	p.A46A	LRRC15_ENST00000428839.1_Silent_p.A52A|LRRC15_ENST00000439944.2_Silent_p.A52A	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	46	LRRNT.				negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GGGTGGGCACTGCCACAATGC	0.622													T|||	737	0.147165	0.1566	0.1398	5008	,	,		20219	0.0685		0.2416	False		,,,				2504	0.1237				p.A52A		Atlas-SNP	.											.	LRRC15	137	.	0			c.A156G						PASS	.	T	,	739,3667	302.4+/-287.4	50,639,1514	64.0	49.0	54.0		156,138	-10.1	0.0	3	dbSNP_86	54	2214,6386	375.2+/-337.7	282,1650,2368	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	332,2289,3882	CC,CT,TT		25.7442,16.7726,22.7049	,	52/588,46/582	194081635	2953,10053	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			GGGCACTGCCACA	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.138A>G	3.37:g.194081635T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			T|0.795;C|0.205	0.205	strong		0.622	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971023	45971023	+	Missense_Mutation	SNP	G	G	T	rs478967	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45971023G>T	ENST00000391621.1	-	1	365	c.319C>A	c.(319-321)Cct>Act	p.P107T	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	107	22 X 5 AA repeats of C-C-X(3).		P -> T (in dbSNP:rs478967). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGCACACAGGCTTGCAGCAG	0.662													g|||	1139	0.227436	0.2171	0.1585	5008	,	,		20659	0.369		0.2048	False		,,,				2504	0.1677				p.P107T		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C319A						PASS	.	T	,THR/PRO	996,3408	350.8+/-311.0	91,814,1297	104.0	107.0	106.0		,319	0.7	0.0	21	dbSNP_83	106	1678,6922	302.0+/-305.7	148,1382,2770	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,38	239,2196,4067	TT,TG,GG		19.5116,22.6158,20.5629	,benign	,107/256	45971023	2674,10330	2202	4300	6502	SO:0001583	missense	386679	exon1			ACACAGGCTTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.319C>A	21.37:g.45971023G>T	ENSP00000375479:p.Pro107Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	150	74	0.493333	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	522	0.23901098901098902	101	0.20528455284552846	61	0.1685082872928177	200	0.34965034965034963	160	0.21108179419525067	g	2.743	-0.261873	0.05791	0.226158	0.195116	ENSG00000205445	ENST00000391621	T	0.04360	3.64	3.77	0.683	0.17998	.	.	.	.	.	T	0.00012	0.0000	M	0.78285	2.405	0.80722	P	0.0	B	0.25351	0.124	B	0.27887	0.084	T	0.41413	-0.9510	8	0.39692	T	0.17	.	1.2578	0.01995	0.2057:0.1724:0.4448:0.177	rs56265636	107	P60368	KR102_HUMAN	T	107	ENSP00000375479:P107T	ENSP00000375479:P107T	P	-	1	0	KRTAP10-2	44795451	0.669000	0.27502	0.004000	0.12327	0.026000	0.11368	1.776000	0.38594	0.131000	0.18576	-0.369000	0.07265	CCT	G|0.811;T|0.189	0.189	strong		0.662	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
LILRB1	10859	hgsc.bcm.edu	37	19	55143452	55143452	+	Missense_Mutation	SNP	T	T	C	rs1061680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55143452T>C	ENST00000396331.1	+	6	782	c.425T>C	c.(424-426)aTc>aCc	p.I142T	LILRB1_ENST00000434867.2_Missense_Mutation_p.I142T|LILRB1_ENST00000396321.2_Missense_Mutation_p.I142T|LILRB1_ENST00000396315.1_Missense_Mutation_p.I142T|LILRB1_ENST00000418536.2_Missense_Mutation_p.I142T|LILRB1_ENST00000427581.2_Missense_Mutation_p.I178T|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Missense_Mutation_p.I142T|LILRB1_ENST00000396317.1_Missense_Mutation_p.I142T|LILRB1_ENST00000448689.1_Missense_Mutation_p.I142T|LILRB1_ENST00000396327.3_Missense_Mutation_p.I142T|LILRB1_ENST00000324602.7_Missense_Mutation_p.I142T	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	142	Ig-like C2-type 2.		I -> T (in dbSNP:rs1061680). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20600445, ECO:0000269|PubMed:9285411}.		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)		GGGAATGTAATCCTCCAGTGT	0.552										HNSCC(37;0.09)			N|||	2190	0.4373	0.6059	0.4553	5008	,	,		18519	0.5942		0.2465	False		,,,				2504	0.2311				p.I142T		Atlas-SNP	.											LILRB1,NS,carcinoma,-1,1	LILRB1	140	1	0			c.T425C						PASS	.	C	THR/ILE,THR/ILE,THR/ILE,THR/ILE	2467,1939	549.6+/-377.8	694,1079,430	104.0	101.0	102.0		425,425,425,425	-0.6	0.0	19	dbSNP_86	102	2380,6220	700.8+/-405.2	323,1734,2243	yes	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	89,89,89,89	1017,2813,2673	CC,CT,TT		27.6744,44.0082,37.2674	benign,benign,benign,benign	142/653,142/652,142/652,142/651	55143452	4847,8159	2203	4300	6503	SO:0001583	missense	10859	exon5			ATGTAATCCTCCA	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.425T>C	19.37:g.55143452T>C	ENSP00000379622:p.Ile142Thr	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	998	0.45695970695970695	313	0.6361788617886179	153	0.42265193370165743	339	0.5926573426573427	193	0.2546174142480211	C	0.004	-2.258264	0.00265	0.559918	0.276744	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.02050	4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48;4.48	1.9	-0.625	0.11548	Immunoglobulin-like fold (1);	0.000000	0.56097	N	0.000039	T	0.00012	0.0000	N	0.00082	-2.215	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.001	T	0.13124	-1.0521	9	0.02654	T	1	.	5.3779	0.16176	0.0:0.4992:0.0:0.5008	rs1061680;rs3202770;rs17845472;rs17858351;rs58070294;rs1061680	142;142;142;142;142	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	T	142;142;142;142;142;142;142;142;178;142;142	ENSP00000379614:I142T;ENSP00000391514:I142T;ENSP00000409968:I142T;ENSP00000379622:I142T;ENSP00000379618:I142T;ENSP00000315997:I142T;ENSP00000405243:I142T;ENSP00000379623:I142T;ENSP00000395004:I178T;ENSP00000379610:I142T;ENSP00000379608:I142T	ENSP00000315997:I142T	I	+	2	0	LILRB1	59835264	0.330000	0.24705	0.001000	0.08648	0.002000	0.02628	0.437000	0.21543	-0.405000	0.07599	-1.160000	0.01791	ATC	T|0.567;C|0.433	0.433	strong		0.552	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
RASSF7	8045	hgsc.bcm.edu	37	11	562437	562437	+	Silent	SNP	G	G	A	rs11246189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:562437G>A	ENST00000397583.3	+	3	916	c.483G>A	c.(481-483)agG>agA	p.R161R	RASSF7_ENST00000524468.1_3'UTR|RP11-496I9.1_ENST00000527620.1_RNA|RP11-496I9.1_ENST00000527113.1_RNA|RASSF7_ENST00000431809.1_Silent_p.R161R|C11orf35_ENST00000329451.3_5'Flank|RASSF7_ENST00000344375.4_Silent_p.R161R|RASSF7_ENST00000397582.3_Silent_p.R161R|RASSF7_ENST00000454668.2_Silent_p.R161R	NM_003475.3	NP_003466.1	Q02833	RASF7_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 7	161					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(3)	8		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.18e-28)|Epithelial(43;6.93e-27)|OV - Ovarian serous cystadenocarcinoma(40;6.97e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGAGCTCAGGGTGCAGAGGA	0.711													G|||	784	0.15655	0.239	0.2478	5008	,	,		16375	0.0188		0.1948	False		,,,				2504	0.0828				p.R161R	Pancreas(184;1170 3913 7268)	Atlas-SNP	.											.	RASSF7	22	.	0			c.G483A						PASS	.	G	,,	938,3214		123,692,1261	14.0	13.0	13.0		483,483,483	0.5	0.5	11	dbSNP_120	13	1641,6559		163,1315,2622	no	coding-synonymous,coding-synonymous,coding-synonymous	RASSF7	NM_001143993.1,NM_001143994.1,NM_003475.3	,,	286,2007,3883	AA,AG,GG		20.0122,22.5915,20.8792	,,	161/338,161/321,161/374	562437	2579,9773	2076	4100	6176	SO:0001819	synonymous_variant	8045	exon3			GCTCAGGGTGCAG	M91083	CCDS7702.1, CCDS44505.1, CCDS44506.1	11p15.5	2008-02-22	2008-02-22	2005-09-14	ENSG00000099849	ENSG00000099849			1166	protein-coding gene	gene with protein product		143023	"""chromosome 11 open reading frame 13"""	C11orf13		1339391	Standard	NM_001143993		Approved	HRC1, HRAS1	uc001lqc.3	Q02833	OTTHUMG00000132004	ENST00000397583.3:c.483G>A	11.37:g.562437G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	107	53	0.495327	NM_001143994	G5E9N9|Q3KP41|Q3KP42	Silent	SNP	ENST00000397583.3	37	CCDS7702.1																																																																																			G|0.827;A|0.173	0.173	strong		0.711	RASSF7-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254972.2	NM_003475	
FER1L6	654463	hgsc.bcm.edu	37	8	125072426	125072426	+	Silent	SNP	T	T	C	rs4483140	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:125072426T>C	ENST00000522917.1	+	23	3086	c.2880T>C	c.(2878-2880)ccT>ccC	p.P960P	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Silent_p.P960P	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	960						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)			GGTAGGTTCCTCCTTCTGGGC	0.547													T|||	4046	0.807907	0.8691	0.7435	5008	,	,		16735	0.6915		0.8718	False		,,,				2504	0.8252				p.P960P		Atlas-SNP	.											.	FER1L6	268	.	0			c.T2880C						PASS	.	T		3807,559		1652,503,28	91.0	101.0	98.0		2880	-1.3	0.0	8	dbSNP_111	98	7376,1188		3179,1018,85	no	coding-synonymous	FER1L6	NM_001039112.2		4831,1521,113	CC,CT,TT		13.872,12.8035,13.5112		960/1858	125072426	11183,1747	2183	4282	6465	SO:0001819	synonymous_variant	654463	exon23			GGTTCCTCCTTCT	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.2880T>C	8.37:g.125072426T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	68	0.971429	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			T|0.177;C|0.823	0.823	strong		0.547	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
DNAH9	1770	hgsc.bcm.edu	37	17	11650958	11650958	+	Missense_Mutation	SNP	G	G	A	rs61743635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:11650958G>A	ENST00000262442.4	+	32	6553	c.6485G>A	c.(6484-6486)aGg>aAg	p.R2162K	DNAH9_ENST00000454412.2_Missense_Mutation_p.R2162K	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2162	AAA 2. {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)		CAGGTGCTGAGGTCCTTGCAC	0.557													G|||	430	0.0858626	0.0363	0.0562	5008	,	,		17386	0.1696		0.0895	False		,,,				2504	0.0838				p.R2162K		Atlas-SNP	.											.	DNAH9	695	.	0			c.G6485A						PASS	.	G	LYS/ARG	246,4160	143.5+/-178.5	6,234,1963	90.0	82.0	85.0		6485	2.4	1.0	17	dbSNP_129	85	798,7802	188.1+/-235.2	35,728,3537	yes	missense	DNAH9	NM_001372.3	26	41,962,5500	AA,AG,GG		9.2791,5.5833,8.0271	benign	2162/4487	11650958	1044,11962	2203	4300	6503	SO:0001583	missense	1770	exon32			TGCTGAGGTCCTT	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.6485G>A	17.37:g.11650958G>A	ENSP00000262442:p.Arg2162Lys	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	178	0.0815018315018315	16	0.032520325203252036	23	0.06353591160220995	76	0.13286713286713286	63	0.08311345646437995	G	2.495	-0.316623	0.05422	0.055833	0.092791	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.39406	1.08;1.08	4.5	2.41	0.29592	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.177992	0.48286	N	0.000193	T	0.00144	0.0004	N	0.04203	-0.255	0.09310	P	0.9999999999766689	B	0.02656	0.0	B	0.12837	0.008	T	0.23404	-1.0189	9	0.02654	T	1	.	7.5211	0.27629	0.3555:0.0:0.6445:0.0	rs61743635	2162	Q9NYC9	DYH9_HUMAN	K	2162;2162;744	ENSP00000262442:R2162K;ENSP00000414874:R2162K	ENSP00000262442:R2162K	R	+	2	0	DNAH9	11591683	0.992000	0.36948	0.999000	0.59377	0.774000	0.43823	1.256000	0.32921	0.463000	0.27118	0.557000	0.71058	AGG	G|0.922;A|0.078	0.078	strong		0.557	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
DCPS	28960	hgsc.bcm.edu	37	11	126174164	126174164	+	Silent	SNP	C	C	T	rs695029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:126174164C>T	ENST00000263579.4	+	1	518	c.189C>T	c.(187-189)ttC>ttT	p.F63F	RP11-712L6.5_ENST00000524964.1_5'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	63					cellular response to menadione (GO:0036245)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		AAATCATTTTCCTACACGGGA	0.547													C|||	1531	0.305711	0.0749	0.3905	5008	,	,		17744	0.624		0.2008	False		,,,				2504	0.3374				p.F63F		Atlas-SNP	.											DCPS,NS,carcinoma,+2,1	DCPS	33	1	0			c.C189T						PASS	.	C		466,3936	218.1+/-236.3	26,414,1761	72.0	71.0	71.0		189	3.8	0.9	11	dbSNP_83	71	1723,6873	311.4+/-310.3	160,1403,2735	no	coding-synonymous	DCPS	NM_014026.3		186,1817,4496	TT,TC,CC		20.0442,10.5861,16.8411		63/338	126174164	2189,10809	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon1			CATTTTCCTACAC	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.189C>T	11.37:g.126174164C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	85	43	0.505882	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			C|0.772;T|0.228	0.228	strong		0.547	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
SLK	9748	hgsc.bcm.edu	37	10	105762933	105762933	+	Missense_Mutation	SNP	G	G	A	rs7071400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105762933G>A	ENST00000369755.3	+	9	2542	c.1997G>A	c.(1996-1998)gGa>gAa	p.G666E	SLK_ENST00000335753.4_Missense_Mutation_p.G666E	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	666			G -> E (in dbSNP:rs7071400).		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)		AAGGCTTTAGGAAGTGAAGTT	0.393													G|||	84	0.0167732	0.059	0.0086	5008	,	,		19341	0.0		0.0	False		,,,				2504	0.0				p.G666E	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.G1997A						PASS	.	G	GLU/GLY	206,4200	127.4+/-164.3	5,196,2002	126.0	114.0	118.0		1997	-0.6	0.0	10	dbSNP_116	118	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SLK	NM_014720.2	98	5,199,6299	AA,AG,GG		0.0349,4.6754,1.607	benign	666/1236	105762933	209,12797	2203	4300	6503	SO:0001583	missense	9748	exon9			CTTTAGGAAGTGA		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.1997G>A	10.37:g.105762933G>A	ENSP00000358770:p.Gly666Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	29	0.013278388278388278	24	0.04878048780487805	5	0.013812154696132596	0	0.0	0	0.0	G	0.021	-1.419805	0.01136	0.046754	3.49E-4	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.66995	-0.24;-0.24	5.6	-0.619	0.11572	Protein kinase-like domain (1);	0.516601	0.20063	N	0.100027	T	0.09247	0.0228	N	0.17082	0.46	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.12156	0.005;0.007	T	0.05386	-1.0888	10	0.15499	T	0.54	.	6.5662	0.22513	0.3317:0.0:0.4868:0.1815	rs7071400;rs52824513;rs56426845;rs7071400	666;666	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	E	666	ENSP00000336824:G666E;ENSP00000358770:G666E	ENSP00000336824:G666E	G	+	2	0	SLK	105752923	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.468000	0.06656	-0.380000	0.07894	-1.471000	0.01009	GGA	G|0.982;A|0.018	0.018	strong		0.393	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
SMOC1	64093	hgsc.bcm.edu	37	14	70418881	70418881	+	Silent	SNP	G	G	A	rs3742909	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:70418881G>A	ENST00000381280.4	+	2	379	c.126G>A	c.(124-126)caG>caA	p.Q42Q	SMOC1_ENST00000555917.1_3'UTR|SMOC1_ENST00000361956.3_Silent_p.Q42Q	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	42	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GTGACCCACAGTGCAACCTCC	0.507													G|||	1087	0.217053	0.0076	0.3718	5008	,	,		20143	0.375		0.2634	False		,,,				2504	0.18				p.Q42Q		Atlas-SNP	.											.	SMOC1	61	.	0			c.G126A						PASS	.	G	,	272,4134	153.7+/-187.2	12,248,1943	126.0	116.0	120.0		126,126	4.5	1.0	14	dbSNP_107	120	2163,6437	372.1+/-336.5	259,1645,2396	no	coding-synonymous,coding-synonymous	SMOC1	NM_001034852.2,NM_022137.5	,	271,1893,4339	AA,AG,GG		25.1512,6.1734,18.7221	,	42/436,42/435	70418881	2435,10571	2203	4300	6503	SO:0001819	synonymous_variant	64093	exon2			CCCACAGTGCAAC	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.126G>A	14.37:g.70418881G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_001034852	A8K1S3|B2R7P5|Q96F78	Silent	SNP	ENST00000381280.4	37	CCDS9798.1																																																																																			G|0.784;A|0.216	0.216	strong		0.507	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1		
TSSK2	23617	hgsc.bcm.edu	37	22	19119545	19119545	+	Silent	SNP	C	C	T	rs45604134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19119545C>T	ENST00000399635.2	+	1	1225	c.633C>T	c.(631-633)tgC>tgT	p.C211C	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	211	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					TCATGGTCTGCGGCTCCATGC	0.597													C|||	815	0.16274	0.1195	0.134	5008	,	,		20404	0.125		0.173	False		,,,				2504	0.2699				p.C211C		Atlas-SNP	.											.	TSSK2	29	.	0			c.C633T						PASS	.	C	,	489,3917	228.1+/-243.1	30,429,1744	94.0	89.0	91.0		,633	-8.6	0.9	22	dbSNP_127	91	1589,7011	292.7+/-301.0	165,1259,2876	yes	utr-3,coding-synonymous	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,	195,1688,4620	TT,TC,CC		18.4767,11.0985,15.9772	,	,211/359	19119545	2078,10928	2203	4300	6503	SO:0001819	synonymous_variant	23617	exon1			GGTCTGCGGCTCC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.633C>T	22.37:g.19119545C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_053006	Q8IY55	Silent	SNP	ENST00000399635.2	37	CCDS13755.1																																																																																			C|0.846;T|0.154	0.154	strong		0.597	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
SCN4A	6329	hgsc.bcm.edu	37	17	62019103	62019103	+	Silent	SNP	G	G	T	rs56342400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:62019103G>T	ENST00000435607.1	-	24	4615	c.4539C>A	c.(4537-4539)atC>atA	p.I1513I	SCN4A_ENST00000578147.1_Silent_p.I1513I	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1513					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)	p.I1513I(1)		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)	ACATATCATCGATGCCCGACT	0.552													g|||	702	0.140176	0.1452	0.1254	5008	,	,		18534	0.1062		0.1968	False		,,,				2504	0.1207				p.I1513I		Atlas-SNP	.											SCN4A,NS,carcinoma,0,1	SCN4A	205	1	1	Substitution - coding silent(1)	stomach(1)	c.C4539A						PASS	.	A		587,3819	246.8+/-255.3	38,511,1654	127.0	122.0	123.0		4539	-0.3	1.0	17	dbSNP_129	123	1683,6917	304.6+/-307.0	154,1375,2771	no	coding-synonymous	SCN4A	NM_000334.4		192,1886,4425	TT,TG,GG		19.5698,13.3227,17.4535		1513/1837	62019103	2270,10736	2203	4300	6503	SO:0001819	synonymous_variant	6329	exon24			ATCATCGATGCCC	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.4539C>A	17.37:g.62019103G>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			A|0.000;C|0.000;G|0.831;T|0.168	0.168	strong		0.552	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
MTCL1	23255	hgsc.bcm.edu	37	18	8819246	8819246	+	Missense_Mutation	SNP	C	C	T	rs55676538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:8819246C>T	ENST00000306329.11	+	11	4102	c.4102C>T	c.(4102-4104)Cgc>Tgc	p.R1368C	SOGA2_ENST00000517570.1_Missense_Mutation_p.R1008C|SOGA2_ENST00000400050.3_Missense_Mutation_p.R1008C|SOGA2_ENST00000306285.7_Missense_Mutation_p.R374C|SOGA2_ENST00000359865.3_Missense_Mutation_p.R1049C|SOGA2_ENST00000518815.1_Missense_Mutation_p.R374C																							GTTCAGGAACCGCCTCCCTGA	0.572													C|||	29	0.00579073	0.0008	0.0072	5008	,	,		17313	0.0		0.0209	False		,,,				2504	0.002				p.R1049C		Atlas-SNP	.											.	.	.	.	0			c.C3145T						PASS	.	C	CYS/ARG	25,4381	31.7+/-61.6	0,25,2178	54.0	60.0	58.0		3145	-4.9	0.0	18	dbSNP_129	58	214,8386	89.7+/-151.9	3,208,4089	yes	missense	CCDC165	NM_015210.3	180	3,233,6267	TT,TC,CC		2.4884,0.5674,1.8376	benign	1049/1587	8819246	239,12767	2203	4300	6503	SO:0001583	missense	23255	exon13			AGGAACCGCCTCC																												ENST00000306329.11:c.4102C>T	18.37:g.8819246C>T	ENSP00000305027:p.Arg1368Cys	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	C	5.158	0.214684	0.09810	0.005674	0.024884	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	T;T;T;T	0.29397	2.57;2.57;2.57;1.57	5.62	-4.88	0.03113	.	0.990599	0.08201	N	0.982238	T	0.02380	0.0073	N	0.00170	-1.935	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31223	-0.9951	10	0.45353	T	0.12	-6.5151	2.7484	0.05273	0.0896:0.2449:0.1981:0.4674	rs55676538;rs62086627	1359;1049	Q9Y4B5;Q9Y4B5-3	CC165_HUMAN;.	C	1070;1008;1049;1008;374	ENSP00000429556:R1008C;ENSP00000352927:R1049C;ENSP00000382924:R1008C;ENSP00000303670:R374C	ENSP00000303670:R374C	R	+	1	0	CCDC165	8809246	0.979000	0.34478	0.019000	0.16419	0.015000	0.08874	0.414000	0.21164	-1.054000	0.03214	-2.585000	0.00167	CGC	C|0.985;T|0.015	0.015	strong		0.572	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
OR13C5	138799	hgsc.bcm.edu	37	9	107361451	107361451	+	Silent	SNP	G	G	A	rs376107801|rs201540433|rs377523807	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107361451G>A	ENST00000374779.2	-	1	337	c.244C>T	c.(244-246)Cta>Tta	p.L82L		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AAGCTCACTAGCGTGGAGGGA	0.512													A|||	3407	0.680312	0.761	0.5937	5008	,	,		19219	0.9573		0.4225	False		,,,				2504	0.6125				p.L82L		Atlas-SNP	.											.	OR13C5	60	.	0			c.C244T						PASS	.																																			SO:0001819	synonymous_variant	138799	exon1			TCACTAGCGTGGA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.244C>T	9.37:g.107361451G>A		Somatic	607	0	0		WXS	Illumina HiSeq	Phase_I	461	76	0.164859	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			.	.	weak		0.512	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
OR10G3	26533	hgsc.bcm.edu	37	14	22038659	22038659	+	Missense_Mutation	SNP	T	T	C	rs17792778	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:22038659T>C	ENST00000303532.1	-	1	216	c.217A>G	c.(217-219)Agc>Ggc	p.S73G		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	73			S -> G (in dbSNP:rs17792778).			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)		GAGGAGATGCTCATATCAATG	0.473													C|||	3562	0.711262	0.7042	0.7997	5008	,	,		22034	0.7331		0.669	False		,,,				2504	0.6789				p.S73G		Atlas-SNP	.											OR10G3,colon,carcinoma,0,2	OR10G3	40	2	0			c.A217G						PASS	.	C	GLY/SER	3071,1335	446.3+/-348.0	1079,913,211	67.0	64.0	65.0		217	2.6	1.0	14	dbSNP_123	65	5747,2853	449.3+/-362.1	1907,1933,460	yes	missense	OR10G3	NM_001005465.1	56	2986,2846,671	CC,CT,TT		33.1744,30.2996,32.2005	benign	73/314	22038659	8818,4188	2203	4300	6503	SO:0001583	missense	26533	exon1			AGATGCTCATATC		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.217A>G	14.37:g.22038659T>C	ENSP00000302437:p.Ser73Gly	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_001005465	Q6IET7|Q96R77	Missense_Mutation	SNP	ENST00000303532.1	37	CCDS32046.1	1534	0.7023809523809523	328	0.6666666666666666	281	0.7762430939226519	418	0.7307692307692307	507	0.6688654353562006	C	1.658	-0.512111	0.04200	0.697004	0.668256	ENSG00000169208	ENST00000303532	T	0.00402	7.56	4.57	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	0.123963	0.36338	N	0.002655	T	0.00012	0.0000	N	0.03253	-0.375	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.20974	-1.0259	9	0.41790	T	0.15	-3.225	6.8857	0.24199	0.0:0.5762:0.0:0.4238	rs17792778;rs57792063;rs17792778	73	Q8NGC4	O10G3_HUMAN	G	73	ENSP00000302437:S73G	ENSP00000302437:S73G	S	-	1	0	OR10G3	21108499	0.000000	0.05858	0.998000	0.56505	0.907000	0.53573	-0.085000	0.11250	0.084000	0.17077	-0.197000	0.12766	AGC	T|0.310;C|0.690	0.690	strong		0.473	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
MYO9B	4650	hgsc.bcm.edu	37	19	17316782	17316782	+	Missense_Mutation	SNP	T	T	C	rs7248508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17316782T>C	ENST00000594824.1	+	32	5225	c.5078T>C	c.(5077-5079)gTt>gCt	p.V1693A	MYO9B_ENST00000397274.2_Missense_Mutation_p.V1693A|MYO9B_ENST00000595618.1_Missense_Mutation_p.V1693A|CTD-3032J10.3_ENST00000601929.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	1693	Tail.			V -> A (in Ref. 1; AAC50402). {ECO:0000305}.	actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						GAGCCAGGCGTTGAGCCTGGC	0.667													C|||	3163	0.631589	0.708	0.6772	5008	,	,		12871	0.746		0.3917	False		,,,				2504	0.6247				p.V1693A		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.T5078C						PASS	.	C	ALA/VAL,ALA/VAL	2660,1460		885,890,285	21.0	27.0	25.0		5078,5078	4.7	0.0	19	dbSNP_116	25	3346,5022		710,1926,1548	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	64,64	1595,2816,1833	CC,CT,TT		39.9857,35.4369,48.0942	benign,benign	1693/2023,1693/2158	17316782	6006,6482	2060	4184	6244	SO:0001583	missense	4650	exon32			CAGGCGTTGAGCC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.5078T>C	19.37:g.17316782T>C	ENSP00000471367:p.Val1693Ala	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		1311	0.6002747252747253	331	0.6727642276422764	232	0.6408839779005525	445	0.777972027972028	303	0.3997361477572559	C	2.673	-0.277158	0.05679	0.645631	0.399857	ENSG00000099331	ENST00000397274;ENST00000319396	D	0.84442	-1.85	4.74	4.74	0.60224	.	0.234317	0.29676	N	0.011484	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41142	-0.9525	9	0.05959	T	0.93	.	10.8777	0.46921	0.0:0.9112:0.0:0.0888	rs7248508;rs11545735;rs7248508	1693;1693;1699	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	A	1693;38	ENSP00000380444:V1693A	ENSP00000314032:V38A	V	+	2	0	MYO9B	17177782	0.001000	0.12720	0.039000	0.18376	0.005000	0.04900	1.204000	0.32296	1.136000	0.42199	-0.215000	0.12644	GTT	T|0.406;C|0.594	0.594	strong		0.667	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
SLIT2	9353	hgsc.bcm.edu	37	4	20535275	20535275	+	Missense_Mutation	SNP	C	C	T	rs201411609		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:20535275C>T	ENST00000504154.1	+	18	2021	c.1769C>T	c.(1768-1770)aCg>aTg	p.T590M	SLIT2_ENST00000503823.1_Missense_Mutation_p.T582M|SLIT2_ENST00000503837.1_Missense_Mutation_p.T586M|SLIT2_ENST00000273739.5_Missense_Mutation_p.T594M	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	590					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						ATACTTCTTACGAGTAATCGT	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		19865	0.0		0.001	False		,,,				2504	0.0				p.T590M		Atlas-SNP	.											SLIT2,right_lower_lobe,carcinoma,-1,1	SLIT2	290	1	0			c.C1769T						scavenged	.						142.0	144.0	144.0					4																	20535275		2203	4300	6503	SO:0001583	missense	9353	exon18			TTCTTACGAGTAA	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.1769C>T	4.37:g.20535275C>T	ENSP00000422591:p.Thr590Met	Somatic	412	0	0		WXS	Illumina HiSeq	Phase_I	433	6	0.0138568	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.2	4.387353	0.82902	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.73923	0.3649	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.992	T	0.76932	-0.2776	10	0.72032	D	0.01	.	18.8776	0.92345	0.0:1.0:0.0:0.0	.	582;590	O94813-3;O94813	.;SLIT2_HUMAN	M	582;590;594;586;586	ENSP00000427548:T582M;ENSP00000422591:T590M;ENSP00000273739:T594M;ENSP00000422261:T586M	ENSP00000273739:T594M	T	+	2	0	SLIT2	20144373	1.000000	0.71417	0.934000	0.37439	0.749000	0.42624	7.723000	0.84788	2.469000	0.83416	0.561000	0.74099	ACG	C|1.000;T|0.000	0.000	strong		0.348	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
CD48	962	hgsc.bcm.edu	37	1	160650938	160650938	+	Intron	SNP	C	C	T	rs6667145	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:160650938C>T	ENST00000368046.3	-	3	740				RP11-404F10.2_ENST00000588034.1_RNA|RP11-404F10.2_ENST00000443928.2_RNA|RP11-404F10.2_ENST00000598917.2_RNA	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule						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)			TTTCTTTGTTCAAAACAACTC	0.572													C|||	398	0.0794728	0.0787	0.0879	5008	,	,		19883	0.002		0.1213	False		,,,				2504	0.1115				p.E236K		Atlas-SNP	.											.	CD48	31	.	0			c.G706A						PASS	.																																			SO:0001627	intron_variant	962	exon3			TTTGTTCAAAACA	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.652+53G>A	1.37:g.160650938C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	NM_001256030	Q5U055|Q8MGR0	Missense_Mutation	SNP	ENST00000368046.3	37	CCDS1208.1																																																																																			C|0.927;T|0.073	0.073	strong		0.572	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778	
RGPD3	653489	hgsc.bcm.edu	37	2	107084739	107084739	+	Silent	SNP	A	A	G	rs6718521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:107084739A>G	ENST00000409886.3	-	1	93	c.6T>C	c.(4-6)agT>agC	p.S2S	RGPD3_ENST00000304514.7_Silent_p.S2S	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	2					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						CCTTGCTGCAACTCATCGCGC	0.657													.|||	2209	0.441094	0.2088	0.4409	5008	,	,		12001	0.8313		0.2952	False		,,,				2504	0.5031				p.S2S		Atlas-SNP	.											.	RGPD3	316	.	0			c.T6C						PASS	.						65.0	93.0	84.0					2																	107084739		692	1591	2283	SO:0001819	synonymous_variant	653489	exon1			GCTGCAACTCATC		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.6T>C	2.37:g.107084739A>G		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	229	214	0.934498	NM_001144013	B8ZZM4	Silent	SNP	ENST00000409886.3	37	CCDS46379.1																																																																																			A|0.626;G|0.374	0.374	strong		0.657	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
CASK	8573	hgsc.bcm.edu	37	X	41604809	41604809	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:41604809G>A	ENST00000378163.1	-	4	798	c.324C>T	c.(322-324)gaC>gaT	p.D108D	CASK_ENST00000378158.1_Silent_p.D108D|CASK_ENST00000421587.2_Silent_p.D108D|CASK_ENST00000378154.1_Silent_p.D108D|CASK_ENST00000361962.4_Silent_p.D108D|CASK_ENST00000442742.2_Silent_p.D108D|CASK_ENST00000318588.9_Silent_p.D108D|CASK_ENST00000378166.4_Silent_p.D108D			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						CAAAACCAGCGTCAGCTCGCT	0.358																																					p.D108D	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.C324T						PASS	.						89.0	74.0	79.0					X																	41604809		2203	4300	6503	SO:0001819	synonymous_variant	8573	exon4			ACCAGCGTCAGCT	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"""trinucleotide repeat containing 8"""	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.324C>T	X.37:g.41604809G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Silent	SNP	ENST00000378163.1	37																																																																																				.	.	none		0.358	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688	
NMU	10874	hgsc.bcm.edu	37	4	56475338	56475338	+	Silent	SNP	G	G	A	rs3805383	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:56475338G>A	ENST00000264218.3	-	4	333	c.228C>T	c.(226-228)aaC>aaT	p.N76N	NMU_ENST00000515325.1_5'UTR|NMU_ENST00000505262.1_Silent_p.N76N|NMU_ENST00000507338.1_Silent_p.N76N|NMU_ENST00000511469.1_Silent_p.N60N	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	76					digestion (GO:0007586)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of hormone secretion (GO:0046887)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic transmission (GO:0050806)|regulation of smooth muscle contraction (GO:0006940)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|terminal bouton (GO:0043195)	receptor binding (GO:0005102)			lung(3)|ovary(1)|urinary_tract(1)	5	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		CCTCCAGTGCGTTGGATGCCT	0.363													A|||	987	0.197085	0.1362	0.1844	5008	,	,		19385	0.1042		0.2783	False		,,,				2504	0.3006				p.N76N		Atlas-SNP	.											.	NMU	17	.	0			c.C228T						PASS	.	A		658,3748	765.0+/-413.3	46,566,1591	110.0	109.0	109.0		228	-6.0	0.0	4	dbSNP_107	109	2140,6460	714.8+/-406.0	261,1618,2421	no	coding-synonymous	NMU	NM_006681.2		307,2184,4012	AA,AG,GG		24.8837,14.9342,21.5131		76/175	56475338	2798,10208	2203	4300	6503	SO:0001819	synonymous_variant	10874	exon4			CAGTGCGTTGGAT	X76029	CCDS3501.1, CCDS75125.1	4q12	2013-02-26			ENSG00000109255	ENSG00000109255		"""Endogenous ligands"""	7859	protein-coding gene	gene with protein product	"""prepro-NMU"""	605103				7619205	Standard	XM_005265713		Approved		uc003hbc.3	P48645	OTTHUMG00000102161	ENST00000264218.3:c.228C>T	4.37:g.56475338G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_006681		Silent	SNP	ENST00000264218.3	37	CCDS3501.1																																																																																			G|0.795;A|0.205	0.205	strong		0.363	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2		
ISM1	140862	hgsc.bcm.edu	37	20	13251325	13251325	+	Missense_Mutation	SNP	C	C	T	rs76665689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:13251325C>T	ENST00000262487.4	+	2	319	c.313C>T	c.(313-315)Ctt>Ttt	p.L105F	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	105						extracellular region (GO:0005576)				NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						ATCCTTTCTCCTTGATCTACC	0.488													C|||	21	0.00419329	0.0045	0.0101	5008	,	,		20403	0.0		0.008	False		,,,				2504	0.0				p.L105F		Atlas-SNP	.											.	ISM1	41	.	0			c.C313T						PASS	.	C	PHE/LEU	21,3715		0,21,1847	94.0	87.0	89.0		313	3.5	1.0	20	dbSNP_131	89	7,8223		0,7,4108	yes	missense	ISM1	NM_080826.1	22	0,28,5955	TT,TC,CC		0.0851,0.5621,0.234	possibly-damaging	105/465	13251325	28,11938	1868	4115	5983	SO:0001583	missense	140862	exon2			TTTCTCCTTGATC	AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"""chromosome 20 open reading frame 82"", ""isthmin 1 homolog (zebrafish)"""	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.313C>T	20.37:g.13251325C>T	ENSP00000262487:p.Leu105Phe	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_080826	Q8WVH9	Missense_Mutation	SNP	ENST00000262487.4	37	CCDS46579.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	16.02	3.005070	0.54254	0.005621	8.51E-4	ENSG00000101230	ENST00000262487;ENST00000447521	T;T	0.66638	-0.22;-0.07	5.71	3.45	0.39498	.	0.000000	0.85682	D	0.000000	T	0.54175	0.1842	L	0.57536	1.79	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.61559	-0.7038	10	0.52906	T	0.07	3.7228	13.6816	0.62489	0.0:0.8541:0.0:0.1459	.	105	B1AKI9	ISM1_HUMAN	F	105;59	ENSP00000262487:L105F;ENSP00000409938:L59F	ENSP00000262487:L105F	L	+	1	0	ISM1	13199325	0.996000	0.38824	1.000000	0.80357	0.988000	0.76386	2.360000	0.44151	1.417000	0.47077	0.591000	0.81541	CTT	C|0.997;T|0.003	0.003	strong		0.488	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2		
SLX4	84464	hgsc.bcm.edu	37	16	3656625	3656625	+	Missense_Mutation	SNP	G	G	A	rs79842542	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3656625G>A	ENST00000294008.3	-	3	1250	c.610C>T	c.(610-612)Cgc>Tgc	p.R204C		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	204	Interaction with SLX4IP, ERCC4 and MSH2.		R -> C (in dbSNP:rs79842542). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TGTGCTGTGCGGGGTTTGGAG	0.557								Direct reversal of damage					G|||	299	0.0597045	0.0688	0.0735	5008	,	,		19452	0.0506		0.0646	False		,,,				2504	0.0419				p.R204C		Atlas-SNP	.											SLX4,NS,carcinoma,+1,2	SLX4	173	2	0			c.C610T						PASS	.	G	CYS/ARG	343,4051	177.6+/-206.5	9,325,1863	178.0	179.0	179.0		610	3.1	0.9	16	dbSNP_131	179	583,8017	156.6+/-210.4	15,553,3732	yes	missense	SLX4	NM_032444.2	180	24,878,5595	AA,AG,GG		6.7791,7.8061,7.1264	probably-damaging	204/1835	3656625	926,12068	2197	4300	6497	SO:0001583	missense	84464	exon3			CTGTGCGGGGTTT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.610C>T	16.37:g.3656625G>A	ENSP00000294008:p.Arg204Cys	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	207	103	0.497585	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	133	0.060897435897435896	35	0.07113821138211382	26	0.0718232044198895	24	0.04195804195804196	48	0.0633245382585752	G	19.50	3.839913	0.71488	0.078061	0.067791	ENSG00000188827	ENST00000294008	T	0.05139	3.49	5.16	3.11	0.35812	.	0.085562	0.45606	D	0.000360	T	0.00936	0.0031	L	0.55990	1.75	0.46336	D	0.99899	D	0.89917	1.0	D	0.91635	0.999	T	0.00042	-1.2227	10	0.87932	D	0	.	12.8945	0.58091	0.0:0.0:0.6944:0.3056	.	204	Q8IY92	SLX4_HUMAN	C	204	ENSP00000294008:R204C	ENSP00000294008:R204C	R	-	1	0	SLX4	3596626	0.990000	0.36364	0.943000	0.38184	0.776000	0.43924	2.460000	0.45031	0.620000	0.30215	0.655000	0.94253	CGC	G|0.937;A|0.063	0.063	strong		0.557	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
MUC4	4585	hgsc.bcm.edu	37	3	195506446	195506446	+	Missense_Mutation	SNP	G	G	T	rs545270545|rs62282468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506446G>T	ENST00000463781.3	-	2	12464	c.12005C>A	c.(12004-12006)cCt>cAt	p.P4002H	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4002H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGGTGACAGGAAGAGGGGT	0.602													.|||	1028	0.205272	0.2935	0.1729	5008	,	,		9512	0.0724		0.2654	False		,,,				2504	0.184				p.P4002H		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12005A						PASS	.						16.0	13.0	14.0					3																	195506446		664	1492	2156	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.12005C>A	3.37:g.195506446G>T	ENSP00000417498:p.Pro4002His	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	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	219	0.10027472527472528	55	0.11178861788617886	35	0.09668508287292818	34	0.05944055944055944	95	0.12532981530343007	g	3.476	-0.106992	0.06924	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35605	1.46;1.3	0.764	0.764	0.18465	.	0.000000	0.25881	U	0.027698	T	0.00384	0.0012	N	0.19112	0.55	0.80722	P	0.0	D	0.61080	0.989	D	0.73380	0.98	T	0.04664	-1.0935	8	.	.	.	.	7.4763	0.27378	1.0E-4:0.0:0.9999:0.0	rs62282468	3874	E7ESK3	.	H	4002	ENSP00000417498:P4002H;ENSP00000420243:P4002H	.	P	-	2	0	MUC4	196991225	0.000000	0.05858	0.001000	0.08648	0.134000	0.20937	-0.577000	0.05847	0.724000	0.32296	0.064000	0.15345	CCT	G|0.899;T|0.101	0.101	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RNF169	254225	hgsc.bcm.edu	37	11	74546905	74546905	+	Silent	SNP	G	G	A	rs1125609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:74546905G>A	ENST00000299563.4	+	6	1270	c.1257G>A	c.(1255-1257)caG>caA	p.Q419Q		NM_001098638.1	NP_001092108.1	Q8NCN4	RN169_HUMAN	ring finger protein 169	419					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of double-strand break repair (GO:2000780)|protein ubiquitination (GO:0016567)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|site of double-strand break (GO:0035861)	K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	15						GAAGCCTGCAGAAGCAGACTT	0.488													G|||	1251	0.2498	0.171	0.1931	5008	,	,		19862	0.2609		0.2087	False		,,,				2504	0.4274				p.Q419Q		Atlas-SNP	.											RNF169,colon,carcinoma,0,1	RNF169	36	1	0			c.G1257A						PASS	.	G		652,3124		59,534,1295	96.0	97.0	97.0		1257	6.0	1.0	11	dbSNP_86	97	1577,6683		120,1337,2673	no	coding-synonymous	RNF169	NM_001098638.1		179,1871,3968	AA,AG,GG		19.092,17.2669,18.5194		419/709	74546905	2229,9807	1888	4130	6018	SO:0001819	synonymous_variant	254225	exon6			CCTGCAGAAGCAG	AB082522	CCDS41691.1	11q13.4	2008-02-05			ENSG00000166439	ENSG00000166439		"""RING-type (C3HC4) zinc fingers"""	26961	protein-coding gene	gene with protein product						12056414	Standard	NM_001098638		Approved	KIAA1991	uc001ovl.4	Q8NCN4	OTTHUMG00000165516	ENST00000299563.4:c.1257G>A	11.37:g.74546905G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_001098638	Q6N015	Silent	SNP	ENST00000299563.4	37	CCDS41691.1																																																																																			G|0.788;A|0.212	0.212	strong		0.488	RNF169-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384741.1	XM_495886	
WNT10B	7480	hgsc.bcm.edu	37	12	49359989	49359989	+	Silent	SNP	G	G	A	rs1051886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49359989G>A	ENST00000301061.4	-	5	1407	c.1059C>T	c.(1057-1059)caC>caT	p.H353H	WNT10B_ENST00000407467.1_3'UTR|WNT10B_ENST00000403957.1_3'UTR	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B	353					bone trabecula formation (GO:0060346)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cell fate commitment (GO:0045165)|cellular response to cAMP (GO:0071320)|cellular response to hydrostatic pressure (GO:0071464)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to retinoic acid (GO:0071300)|chondrocyte differentiation (GO:0002062)|fungiform papilla development (GO:0061196)|G2/M transition of mitotic cell cycle (GO:0000086)|hematopoietic stem cell proliferation (GO:0071425)|lipid metabolic process (GO:0006629)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|positive regulation of anagen (GO:0051885)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein stabilization (GO:0050821)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of skeletal muscle tissue development (GO:0048641)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			central_nervous_system(1)|large_intestine(5)|lung(12)|prostate(1)|skin(4)	23						GGAGCACGTTGTGCCCACGGC	0.622													G|||	1558	0.311102	0.1021	0.4957	5008	,	,		16965	0.4494		0.4155	False		,,,				2504	0.2127				p.H353H		Atlas-SNP	.											.	WNT10B	41	.	0			c.C1059T						PASS	.	G		692,3714	284.9+/-277.9	68,556,1579	60.0	48.0	52.0		1059	2.8	1.0	12	dbSNP_86	52	3289,5311	489.3+/-372.6	620,2049,1631	no	coding-synonymous	WNT10B	NM_003394.3		688,2605,3210	AA,AG,GG		38.2442,15.7059,30.6089		353/390	49359989	3981,9025	2203	4300	6503	SO:0001819	synonymous_variant	7480	exon5			CACGTTGTGCCCA	X97057	CCDS8775.1	12q13	2009-01-02			ENSG00000169884	ENSG00000169884		"""Wingless-type MMTV integration sites"""	12775	protein-coding gene	gene with protein product		601906				9121776, 9284937, 18515319	Standard	NM_003394		Approved	WNT-12, SHFM6	uc001rss.3	O00744	OTTHUMG00000150734	ENST00000301061.4:c.1059C>T	12.37:g.49359989G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_003394	B2R7A5|O00747|Q4VAJ4|Q4VAJ5|Q8WZ97	Silent	SNP	ENST00000301061.4	37	CCDS8775.1																																																																																			G|0.679;A|0.321	0.321	strong		0.622	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	NM_003394	
OR7A5	26659	hgsc.bcm.edu	37	19	14938248	14938248	+	Missense_Mutation	SNP	T	T	A	rs112284734	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14938248T>A	ENST00000322301.3	-	2	893	c.806A>T	c.(805-807)cAc>cTc	p.H269L	OR7A5_ENST00000601611.1_Intron|OR7A5_ENST00000594432.1_Missense_Mutation_p.H269L			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	269					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						TGCACTTGAGTGTGAGTTGCG	0.483																																					p.H269L		Atlas-SNP	.											OR7A5,rectum,carcinoma,0,1	OR7A5	43	1	0			c.A806T						PASS	.						94.0	81.0	86.0					19																	14938248		2203	4300	6503	SO:0001583	missense	26659	exon1			CTTGAGTGTGAGT	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.806A>T	19.37:g.14938248T>A	ENSP00000316955:p.His269Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	109	9	0.0825688	NM_017506	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	37	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	t	11.34	1.609869	0.28712	.	.	ENSG00000188269	ENST00000322301	T	0.00069	8.77	3.12	-0.173	0.13322	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	N	0.20445	0.575	0.09310	N	1	B	0.23990	0.095	B	0.33254	0.16	T	0.04976	-1.0914	9	0.48119	T	0.1	.	6.5609	0.22485	0.0:0.5426:0.0:0.4574	.	269	Q15622	OR7A5_HUMAN	L	269	ENSP00000316955:H269L	ENSP00000316955:H269L	H	-	2	0	OR7A5	14799248	0.000000	0.05858	0.000000	0.03702	0.320000	0.28249	-0.053000	0.11846	0.050000	0.15949	0.102000	0.15555	CAC	T|0.993;A|0.007	0.007	strong		0.483	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
MT-CYB	4519	hgsc.bcm.edu	37	M	14767	14767	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:14767T>C	ENST00000361789.2	+	1	21	c.21T>C	c.(19-21)acT>acC	p.T7T	MT-TH_ENST00000387441.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND6_ENST00000361681.2_5'Flank			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	7			T -> I (in dbSNP:rs3135031). {ECO:0000269|PubMed:10453733, ECO:0000269|PubMed:11130070, ECO:0000269|PubMed:11553319, ECO:0000269|PubMed:12022039, ECO:0000269|PubMed:1757091, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:7530363, ECO:0000269|PubMed:7623448}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						ATACGCAAAATTAACCCCCTA	0.438																																					p.T7T		Atlas-SNP	.											.	.	.	.	0			c.T21C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CAAAACTAACCCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.21T>C	M.37:g.14767T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	50	49	0.98	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				T|0.826;C|0.174	0.174	strong		0.438	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
NOS3	4846	hgsc.bcm.edu	37	7	150704250	150704250	+	Silent	SNP	C	C	G	rs2566514	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150704250C>G	ENST00000297494.3	+	17	2355	c.1998C>G	c.(1996-1998)gcC>gcG	p.A666A	NOS3_ENST00000461406.1_Silent_p.A460A	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TTGCTCGTGCCGTGGACACAC	0.701													G|||	2160	0.43131	0.5635	0.5043	5008	,	,		17098	0.3909		0.2694	False		,,,				2504	0.409				p.A666A		Atlas-SNP	.											NOS3,NS,carcinoma,+2,1	NOS3	131	1	0			c.C1998G						PASS	.	G		2195,2211	589.8+/-387.2	541,1113,549	76.0	81.0	79.0		1998	1.9	1.0	7	dbSNP_100	79	2138,6462	713.6+/-406.0	250,1638,2412	no	coding-synonymous	NOS3	NM_000603.4		791,2751,2961	GG,GC,CC		24.8605,49.8184,33.3154		666/1204	150704250	4333,8673	2203	4300	6503	SO:0001819	synonymous_variant	4846	exon17			TCGTGCCGTGGAC		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.1998C>G	7.37:g.150704250C>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_000603	Q495E5	Silent	SNP	ENST00000297494.3	37	CCDS5912.1																																																																																			C|0.648;G|0.352	0.352	strong		0.701	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603	
ASTL	431705	hgsc.bcm.edu	37	2	96798440	96798440	+	Missense_Mutation	SNP	C	C	T	rs61735195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:96798440C>T	ENST00000342380.2	-	6	475	c.476G>A	c.(475-477)cGc>cAc	p.R159H		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						CCCTCCACTGCGCCCCACACT	0.632													C|||	33	0.00658946	0.0015	0.0173	5008	,	,		19007	0.0		0.0129	False		,,,				2504	0.0061				p.R159H		Atlas-SNP	.											.	ASTL	59	.	0			c.G476A						PASS	.	C	HIS/ARG	10,4396	19.1+/-41.9	0,10,2193	61.0	61.0	61.0		476	3.7	1.0	2	dbSNP_129	61	163,8437	76.0+/-138.7	2,159,4139	yes	missense	ASTL	NM_001002036.3	29	2,169,6332	TT,TC,CC		1.8953,0.227,1.3302	probably-damaging	159/432	96798440	173,12833	2203	4300	6503	SO:0001583	missense	431705	exon6			CCACTGCGCCCCA	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"""sperm acrosomal SLLP1 binding"""	608860	"""astacin-like metalloendopeptidase (M12 family)"""			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.476G>A	2.37:g.96798440C>T	ENSP00000343674:p.Arg159His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_001002036		Missense_Mutation	SNP	ENST00000342380.2	37	CCDS33249.1	17	0.007783882783882784	0	0.0	7	0.019337016574585635	0	0.0	10	0.013192612137203167	C	18.29	3.591213	0.66219	0.00227	0.018953	ENSG00000188886	ENST00000342380	T	0.66995	-0.24	4.79	3.69	0.42338	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (1);Metallopeptidase, catalytic domain (1);	0.000000	0.47093	D	0.000244	T	0.52996	0.1769	M	0.73962	2.25	0.25993	N	0.982226	P	0.52316	0.952	P	0.46208	0.507	T	0.61262	-0.7098	10	0.59425	D	0.04	-14.8332	11.2464	0.49000	0.0:0.8911:0.0:0.1089	.	159	Q6HA08	ASTL_HUMAN	H	159	ENSP00000343674:R159H	ENSP00000343674:R159H	R	-	2	0	ASTL	96162167	0.471000	0.25862	0.977000	0.42913	0.766000	0.43426	2.049000	0.41288	2.211000	0.71520	0.551000	0.68910	CGC	C|0.991;T|0.009	0.009	strong		0.632	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1		
CACNA1H	8912	hgsc.bcm.edu	37	16	1268485	1268485	+	Silent	SNP	C	C	T	rs2738891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1268485C>T	ENST00000348261.5	+	33	5969	c.5721C>T	c.(5719-5721)ggC>ggT	p.G1907G	CACNA1H_ENST00000358590.4_Silent_p.G1901G|CACNA1H_ENST00000565831.1_Silent_p.G1901G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1907					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)	AGAGTCCGGGCGCCAGGGACG	0.692													C|||	449	0.0896565	0.0113	0.0605	5008	,	,		14302	0.0317		0.1133	False		,,,				2504	0.2515				p.G1907G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5721T						PASS	.	C	,	94,3926		0,94,1916	22.0	29.0	27.0		5703,5721	-3.0	0.0	16	dbSNP_100	27	969,7165		49,871,3147	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	49,965,5063	TT,TC,CC		11.913,2.3383,8.7461	,	1901/2348,1907/2354	1268485	1063,11091	2010	4067	6077	SO:0001819	synonymous_variant	8912	exon33			TCCGGGCGCCAGG	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.5721C>T	16.37:g.1268485C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.936;T|0.064	0.064	strong		0.692	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
ANKS1B	56899	hgsc.bcm.edu	37	12	99640428	99640428	+	Silent	SNP	T	T	C	rs3751323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:99640428T>C	ENST00000547776.2	-	13	1970	c.1971A>G	c.(1969-1971)tcA>tcG	p.S657S	ANKS1B_ENST00000550833.1_5'UTR|ANKS1B_ENST00000547010.1_Silent_p.S237S|ANKS1B_ENST00000329257.7_Silent_p.S657S	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	657						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)		CCAAAGGTTCTGAGTTATTTT	0.363													T|||	2746	0.548323	0.3926	0.5418	5008	,	,		20952	0.7937		0.3956	False		,,,				2504	0.6677				p.S657S		Atlas-SNP	.											.	ANKS1B	180	.	0			c.A1971G						PASS	.	T		1382,2260		269,844,708	79.0	72.0	74.0		1971	-0.1	0.2	12	dbSNP_107	74	3300,4856		685,1930,1463	no	coding-synonymous	ANKS1B	NM_152788.4		954,2774,2171	CC,CT,TT		40.461,37.9462,39.6847		657/1249	99640428	4682,7116	1821	4078	5899	SO:0001819	synonymous_variant	56899	exon13			AGGTTCTGAGTTA	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.1971A>G	12.37:g.99640428T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	187	96	0.513369	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1																																																																																			T|0.481;C|0.519	0.519	strong		0.363	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
MT1E	4493	hgsc.bcm.edu	37	16	56660816	56660816	+	Missense_Mutation	SNP	G	G	A	rs72818417	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:56660816G>A	ENST00000306061.6	+	3	496	c.119G>A	c.(118-120)gGc>gAc	p.G40D	MT1E_ENST00000568293.1_Missense_Mutation_p.G18D|MT1E_ENST00000330439.6_3'UTR	NM_175617.3	NP_783316.2	P04732	MT1E_HUMAN	metallothionein 1E	40	Alpha.				cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)										TGCCCCGTGGGCTGTGCCAAG	0.602													.|||	188	0.0375399	0.0008	0.0648	5008	,	,		16658	0.0		0.0775	False		,,,				2504	0.0654				p.G40D		Atlas-SNP	.											.	MT1E	7	.	0			c.G119A						PASS	.	G	ASP/GLY	68,4328	62.9+/-100.1	3,62,2133	142.0	137.0	139.0		119	2.4	0.9	16	dbSNP_131	139	656,7944	167.0+/-218.8	23,610,3667	no	missense	MT1E	NM_175617.3	94	26,672,5800	AA,AG,GG		7.6279,1.5469,5.5709	benign	40/62	56660816	724,12272	2198	4300	6498	SO:0001583	missense	4493	exon3			CCGTGGGCTGTGC	BC009699	CCDS10764.2	16q13	2008-08-11	2007-03-02		ENSG00000169715	ENSG00000169715		"""Metallothioneins"""	7397	protein-coding gene	gene with protein product		156351		MT1		6089206, 2581970	Standard	XM_005255956		Approved	MTD	uc002ejl.3	P04732	OTTHUMG00000133014	ENST00000306061.6:c.119G>A	16.37:g.56660816G>A	ENSP00000307706:p.Gly40Asp	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_175617	A2RRF7|Q86YX4|Q8TD51	Missense_Mutation	SNP	ENST00000306061.6	37	CCDS10764.2	82	0.037545787545787544	1	0.0020325203252032522	21	0.058011049723756904	0	0.0	60	0.079155672823219	G	12.49	1.955021	0.34471	0.015469	0.076279	ENSG00000169715	ENST00000306061	T	0.10288	2.89	2.39	2.39	0.29439	Metallothionein domain, vertebrate (1);Metallothionein domain (1);	.	.	.	.	T	0.00967	0.0032	.	.	.	0.80722	D	1	P	0.45240	0.854	P	0.54238	0.746	T	0.00662	-1.1621	8	0.66056	D	0.02	.	6.5445	0.22398	0.1513:0.0:0.8487:0.0	.	40	P04732	MT1E_HUMAN	D	40	ENSP00000307706:G40D	ENSP00000307706:G40D	G	+	2	0	MT1E	55218317	1.000000	0.71417	0.935000	0.37517	0.856000	0.48823	4.596000	0.61055	1.334000	0.45468	0.306000	0.20318	GGC	G|0.948;A|0.052	0.052	strong		0.602	MT1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256600.1	NM_175617	
JPH3	57338	hgsc.bcm.edu	37	16	87678165	87678165	+	Silent	SNP	G	G	A	rs3751725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:87678165G>A	ENST00000284262.2	+	2	926	c.684G>A	c.(682-684)tcG>tcA	p.S228S		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	228					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		TGCGCAAGTCGGAGTCCAAGA	0.632													G|||	931	0.185903	0.0454	0.2291	5008	,	,		13766	0.3204		0.2028	False		,,,				2504	0.1892				p.S228S		Atlas-SNP	.											.	JPH3	95	.	0			c.G684A						PASS	.	G		319,4077	161.4+/-193.6	12,295,1891	51.0	53.0	52.0		684	-10.3	0.7	16	dbSNP_107	52	1973,6627	333.2+/-320.4	223,1527,2550	no	coding-synonymous	JPH3	NM_020655.2		235,1822,4441	AA,AG,GG		22.9419,7.2566,17.6362		228/749	87678165	2292,10704	2198	4300	6498	SO:0001819	synonymous_variant	57338	exon2			CAAGTCGGAGTCC	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.684G>A	16.37:g.87678165G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	52	50	0.961538	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Silent	SNP	ENST00000284262.2	37	CCDS10962.1																																																																																			G|0.816;A|0.184	0.184	strong		0.632	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
SLC2A1	6513	hgsc.bcm.edu	37	1	43408966	43408966	+	Silent	SNP	G	G	A	rs1385129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43408966G>A	ENST00000426263.3	-	2	223	c.45C>T	c.(43-45)gcC>gcT	p.A15A	SLC2A1_ENST00000372500.3_Silent_p.A15A|SLC2A1_ENST00000415851.2_Silent_p.A15A	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	15					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	CTCCTCCCACGGCCAGCATGA	0.577													G|||	1204	0.240415	0.1543	0.3199	5008	,	,		19565	0.3185		0.2187	False		,,,				2504	0.2423				p.A15A		Atlas-SNP	.											.	SLC2A1	36	.	0			c.C45T						PASS	.	G		772,3634	311.6+/-292.2	54,664,1485	62.0	49.0	54.0		45	-5.9	1.0	1	dbSNP_88	54	1853,6747	326.0+/-317.2	216,1421,2663	no	coding-synonymous	SLC2A1	NM_006516.2		270,2085,4148	AA,AG,GG		21.5465,17.5216,20.183		15/493	43408966	2625,10381	2203	4300	6503	SO:0001819	synonymous_variant	6513	exon2			TCCCACGGCCAGC	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"""Solute carriers"""	11005	protein-coding gene	gene with protein product		138140	"""human T-cell leukemia virus (I and II) receptor"""	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.45C>T	1.37:g.43408966G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_006516	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Silent	SNP	ENST00000426263.3	37	CCDS477.1																																																																																			G|0.781;A|0.219	0.219	strong		0.577	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516	
USH2A	7399	hgsc.bcm.edu	37	1	216363590	216363590	+	Silent	SNP	C	C	T	rs56013136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:216363590C>T	ENST00000307340.3	-	20	4757	c.4371G>A	c.(4369-4371)tcG>tcA	p.S1457S	USH2A_ENST00000366943.2_Silent_p.S1457S|USH2A_ENST00000366942.3_Silent_p.S1457S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1457	Fibronectin type-III 4. {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)		GTCCTGCTCCCGAAGCACTGG	0.368										HNSCC(13;0.011)			C|||	28	0.00559105	0.0015	0.0072	5008	,	,		17343	0.0		0.0199	False		,,,				2504	0.001				p.S1457S		Atlas-SNP	.											.	USH2A	1168	.	0			c.G4371A						PASS	.	C	,	25,4381	31.7+/-61.6	0,25,2178	101.0	98.0	99.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4371,4371	-10.4	0.0	1	dbSNP_129	99	180,8420	81.2+/-143.8	2,176,4122	no	coding-synonymous,coding-synonymous	USH2A	NM_007123.5,NM_206933.2	,	2,201,6300	TT,TC,CC		2.093,0.5674,1.5762	,	1457/1547,1457/5203	216363590	205,12801	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon20			TGCTCCCGAAGCA	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.4371G>A	1.37:g.216363590C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			C|0.987;T|0.013	0.013	strong		0.368	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
PCDHGA8	9708	hgsc.bcm.edu	37	5	140773388	140773388	+	Silent	SNP	G	G	T	rs370400807|rs2240700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140773388G>T	ENST00000398604.2	+	1	1008	c.1008G>T	c.(1006-1008)tcG>tcT	p.S336S	PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	336	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTCATTTCGGTGGAAGATG	0.398													.|||	1012	0.202077	0.3169	0.1902	5008	,	,		18441	0.1548		0.1014	False		,,,				2504	0.2076				p.S336S		Atlas-SNP	.											PCDHGA8,caecum,carcinoma,+1,3	PCDHGA8	146	3	0			c.G1008T						PASS	.	G	,,,,,,,,,,,,	1171,2545		190,791,877	146.0	149.0	148.0		,1008,,,,,,,,,,,1008	-10.6	0.1	5	dbSNP_98	148	1005,7203		63,879,3162	yes	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,,,,,,,,,,,,	253,1670,4039	TT,TG,GG		12.2442,31.5124,18.2489	,,,,,,,,,,,,	,336/821,,,,,,,,,,,336/933	140773388	2176,9748	1858	4104	5962	SO:0001819	synonymous_variant	9708	exon1			CATTTCGGTGGAA	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1008G>T	5.37:g.140773388G>T		Somatic	310	0	0		WXS	Illumina HiSeq	Phase_I	237	236	0.995781	NM_014004	A7MCZ4|O15039	Silent	SNP	ENST00000398604.2	37	CCDS47291.1																																																																																			G|0.805;T|0.195	0.195	strong		0.398	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
ERCC5	2073	hgsc.bcm.edu	37	13	103504517	103504517	+	Silent	SNP	T	T	C	rs1047768	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:103504517T>C	ENST00000355739.4	+	2	1561	c.138T>C	c.(136-138)caT>caC	p.H46H	ERCC5_ENST00000535557.1_Silent_p.H46H|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.W472R	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	46	N-domain.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					GGGATCGCCATGGGAACTCAA	0.393			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	2469	0.493011	0.6778	0.3991	5008	,	,		14964	0.25		0.5845	False		,,,				2504	0.4663				p.H500H		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.T1500C						PASS	.	C	,	2912,1494	478.3+/-358.2	970,972,261	148.0	149.0	149.0		138,1500	-0.4	0.9	13	dbSNP_86	149	5045,3555	516.8+/-378.9	1464,2117,719	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2434,3089,980	CC,CT,TT		41.3372,33.9083,38.8205	,	46/1187,500/1641	103504517	7957,5049	2203	4300	6503	SO:0001819	synonymous_variant	0	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCGCCATGGGAAC	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.138T>C	13.37:g.103504517T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	120	62	0.516667	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			T|0.449;C|0.551	0.551	strong		0.393	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
HHIPL2	79802	hgsc.bcm.edu	37	1	222721288	222721288	+	Silent	SNP	C	C	T	rs4846382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:222721288C>T	ENST00000343410.6	-	1	157	c.99G>A	c.(97-99)ttG>ttA	p.L33L		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	33					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		CCACCTGGCCCAACAAGAATA	0.577													C|||	2914	0.581869	0.3124	0.7205	5008	,	,		16120	0.6379		0.6044	False		,,,				2504	0.7669				p.L33L		Atlas-SNP	.											.	HHIPL2	122	.	0			c.G99A						PASS	.	C		1464,2374		291,882,746	38.0	44.0	42.0		99	1.5	0.4	1	dbSNP_111	42	5085,3161		1574,1937,612	no	coding-synonymous	HHIPL2	NM_024746.3		1865,2819,1358	TT,TC,CC		38.3337,38.1449,45.8044		33/725	222721288	6549,5535	1919	4123	6042	SO:0001819	synonymous_variant	79802	exon1			CTGGCCCAACAAG	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.99G>A	1.37:g.222721288C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	159	80	0.503145	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			C|0.444;T|0.556	0.556	strong		0.577	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
TBX4	9496	hgsc.bcm.edu	37	17	59560685	59560685	+	Silent	SNP	C	C	T	rs2270150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:59560685C>T	ENST00000240335.1	+	8	1491	c.1446C>T	c.(1444-1446)gtC>gtT	p.V482V	TBX4_ENST00000589449.1_3'UTR|TBX4_ENST00000393853.4_Silent_p.V483V	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	482					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						AGTCTCAGGTCCGAGAGCGGG	0.622													C|||	521	0.104034	0.1188	0.1052	5008	,	,		17375	0.0268		0.1402	False		,,,				2504	0.1258				p.V482V		Atlas-SNP	.											.	TBX4	69	.	0			c.C1446T						PASS	.	C		571,3835	255.2+/-260.5	45,481,1677	59.0	61.0	61.0		1446	4.3	1.0	17	dbSNP_100	61	1184,7416	240.7+/-271.3	92,1000,3208	no	coding-synonymous	TBX4	NM_018488.2		137,1481,4885	TT,TC,CC		13.7674,12.9596,13.4938		482/546	59560685	1755,11251	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			TCAGGTCCGAGAG	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1446C>T	17.37:g.59560685C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			C|0.880;T|0.120	0.120	strong		0.622	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
NACA2	342538	hgsc.bcm.edu	37	17	59668352	59668352	+	Missense_Mutation	SNP	C	C	T	rs17531723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:59668352C>T	ENST00000521764.1	-	1	211	c.190G>A	c.(190-192)Gtc>Atc	p.V64I		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	64			V -> I (in dbSNP:rs17531723).		myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.V64I(1)		large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					GCTTTACCGACTGGTTCTTCA	0.483													C|||	727	0.145168	0.0567	0.1023	5008	,	,		21025	0.1667		0.1421	False		,,,				2504	0.2761				p.V64I		Atlas-SNP	.											NACA2,NS,carcinoma,0,1	NACA2	33	1	1	Substitution - Missense(1)	stomach(1)	c.G190A						PASS	.	C	ILE/VAL	320,4086	168.7+/-199.5	13,294,1896	180.0	164.0	170.0		190	0.8	1.0	17	dbSNP_123	170	1175,7425	238.8+/-270.1	85,1005,3210	yes	missense	NACA2	NM_199290.3	29	98,1299,5106	TT,TC,CC		13.6628,7.2628,11.4947	benign	64/216	59668352	1495,11511	2203	4300	6503	SO:0001583	missense	342538	exon1			TACCGACTGGTTC	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.190G>A	17.37:g.59668352C>T	ENSP00000427802:p.Val64Ile	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	205	96	0.468293	NM_199290	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	248	0.11355311355311355	25	0.0508130081300813	39	0.10773480662983426	73	0.12762237762237763	111	0.14643799472295516	C	15.15	2.747568	0.49257	0.072628	0.136628	ENSG00000253506	ENST00000521764	T	0.44482	0.92	0.753	0.753	0.18404	.	0.000000	0.64402	U	0.000019	T	0.00210	0.0006	M	0.61703	1.905	0.22066	P	0.999383782	B	0.15141	0.012	B	0.11329	0.006	T	0.06752	-1.0809	8	.	.	.	.	7.3227	0.26536	0.0:1.0:0.0:0.0	rs17531723;rs52831210;rs17531723	64	Q9H009	NACA2_HUMAN	I	64	ENSP00000427802:V64I	.	V	-	1	0	NACA2	57023134	1.000000	0.71417	0.985000	0.45067	0.716000	0.41182	3.351000	0.52232	0.702000	0.31825	0.411000	0.27672	GTC	C|0.884;T|0.116	0.116	strong		0.483	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
CIZ1	25792	hgsc.bcm.edu	37	9	130938661	130938661	+	Missense_Mutation	SNP	C	C	T	rs11549266	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130938661C>T	ENST00000393608.1	-	11	2114	c.1912G>A	c.(1912-1914)Gtg>Atg	p.V638M	CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000357558.5_Missense_Mutation_p.V610M|CIZ1_ENST00000277465.4_Missense_Mutation_p.V610M|CIZ1_ENST00000538431.1_Missense_Mutation_p.V638M|CIZ1_ENST00000372938.5_Missense_Mutation_p.V638M|CIZ1_ENST00000325721.8_Missense_Mutation_p.V609M|CIZ1_ENST00000372948.3_Missense_Mutation_p.V582M|CIZ1_ENST00000372954.1_Missense_Mutation_p.V558M|CIZ1_ENST00000541172.1_Missense_Mutation_p.V537M	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	638			V -> M (in dbSNP:rs11549266). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.		maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.L636_R640delLPVPR(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TCCCGGGGCACGGGCAGCAGG	0.637													C|||	273	0.0545128	0.0061	0.0692	5008	,	,		19284	0.001		0.1451	False		,,,				2504	0.0716				p.V668M		Atlas-SNP	.											CIZ1,colon,carcinoma,+1,2	CIZ1	75	2	1	Deletion - In frame(1)	breast(1)	c.G2002A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	112,4294	86.3+/-125.0	0,112,2091	101.0	102.0	102.0		1744,1912,1729,1672,1912	-0.9	0.7	9	dbSNP_120	102	1175,7425	239.3+/-270.5	79,1017,3204	yes	missense,missense,missense,missense,missense	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	21,21,21,21,21	79,1129,5295	TT,TC,CC		13.6628,2.542,9.8954	benign,benign,benign,benign,benign	582/843,638/899,577/838,558/819,638/899	130938661	1287,11719	2203	4300	6503	SO:0001583	missense	25792	exon11			GGGGCACGGGCAG	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1912G>A	9.37:g.130938661C>T	ENSP00000377232:p.Val638Met	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	40	0.519481	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Missense_Mutation	SNP	ENST00000393608.1	37	CCDS6894.1	163	0.07463369963369963	6	0.012195121951219513	35	0.09668508287292818	1	0.0017482517482517483	121	0.15963060686015831	C	2.506	-0.313975	0.05422	0.02542	0.136628	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372948;ENST00000372938;ENST00000415526	T;T;T;T;T;T;T;T;T;T	0.34072	1.38;1.54;1.53;1.7;1.54;1.97;1.7;1.39;1.54;2.14	5.42	-0.856	0.10697	.	0.495363	0.16770	N	0.200242	T	0.00039	0.0001	N	0.01874	-0.695	0.80722	P	0.0	B;B;B;P;B;P;B	0.39601	0.051;0.106;0.021;0.474;0.029;0.68;0.029	B;B;B;B;B;B;B	0.32211	0.006;0.008;0.012;0.043;0.005;0.142;0.005	T	0.30327	-0.9982	9	0.34782	T	0.22	-5.4729	5.3691	0.16131	0.1366:0.3037:0.0:0.5597	rs11549266	638;577;582;558;638;609;610	B7Z3U7;B4E0A3;Q9ULV3-4;Q9ULV3-3;Q9ULV3;Q9ULV3-2;Q5SYW2	.;.;.;.;CIZ1_HUMAN;.;.	M	558;638;638;610;609;577;537;610;582;638;560	ENSP00000362045:V558M;ENSP00000377232:V638M;ENSP00000439244:V638M;ENSP00000350169:V610M;ENSP00000320374:V609M;ENSP00000445057:V537M;ENSP00000277465:V610M;ENSP00000362039:V582M;ENSP00000362029:V638M;ENSP00000398011:V560M	ENSP00000277465:V610M	V	-	1	0	CIZ1	129978482	0.469000	0.25846	0.744000	0.31058	0.002000	0.02628	0.669000	0.25142	0.180000	0.19960	-1.281000	0.01382	GTG	C|0.908;T|0.092	0.092	strong		0.637	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
SDC3	9672	hgsc.bcm.edu	37	1	31349642	31349642	+	Silent	SNP	C	C	T	rs41269521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:31349642C>T	ENST00000339394.6	-	3	801	c.627G>A	c.(625-627)cgG>cgA	p.R209R	SDC3_ENST00000336798.7_Silent_p.R151R|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	209	Ser/Thr-rich (mucin-like).				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGAAGCCTCCGTACGCCAG	0.682													C|||	75	0.014976	0.0015	0.0331	5008	,	,		13855	0.0		0.0427	False		,,,				2504	0.0072				p.R209R		Atlas-SNP	.											.	SDC3	45	.	0			c.G627A						PASS	.	C		35,4371	37.6+/-69.7	0,35,2168	26.0	29.0	28.0		627	1.8	0.8	1	dbSNP_127	28	343,8255	115.5+/-175.4	10,323,3966	no	coding-synonymous	SDC3	NM_014654.3		10,358,6134	TT,TC,CC		3.9893,0.7944,2.9068		209/443	31349642	378,12626	2203	4299	6502	SO:0001819	synonymous_variant	9672	exon3			AAGCCTCCGTACG	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.627G>A	1.37:g.31349642C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	82	9	0.109756	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			C|0.972;G|0.000;T|0.028	0.028	strong		0.682	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
CMTM2	146225	hgsc.bcm.edu	37	16	66614008	66614008	+	Missense_Mutation	SNP	T	T	C	rs2290182	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:66614008T>C	ENST00000268595.2	+	2	516	c.365T>C	c.(364-366)aTa>aCa	p.I122T	CMTM2_ENST00000379486.2_Intron|RP11-403P17.2_ENST00000568430.1_RNA	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	122	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.		I -> T (in dbSNP:rs2290182).		chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		ACCATGGAGATATCCTTCTTC	0.473													T|||	1185	0.236621	0.2663	0.2421	5008	,	,		18787	0.3036		0.1302	False		,,,				2504	0.2331				p.I122T		Atlas-SNP	.											.	CMTM2	33	.	0			c.T365C						PASS	.	T	,THR/ILE	1173,3229	414.1+/-336.7	148,877,1176	310.0	236.0	261.0		,365	3.4	0.0	16	dbSNP_100	261	973,7627	211.3+/-251.9	63,847,3390	yes	intron,missense	CMTM2	NM_001199317.1,NM_144673.2	,89	211,1724,4566	CC,CT,TT		11.314,26.647,16.5052	,possibly-damaging	,122/249	66614008	2146,10856	2201	4300	6501	SO:0001583	missense	146225	exon2			TGGAGATATCCTT	BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"""chemokine-like factor super family 2"", ""chemokine-like factor superfamily 2"""	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.365T>C	16.37:g.66614008T>C	ENSP00000268595:p.Ile122Thr	Somatic	399	0	0		WXS	Illumina HiSeq	Phase_I	447	221	0.494407	NM_144673	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	37	CCDS10814.1	486	0.22252747252747251	135	0.27439024390243905	86	0.23756906077348067	166	0.2902097902097902	99	0.13060686015831136	T	14.64	2.595383	0.46318	0.26647	0.11314	ENSG00000140932	ENST00000268595	T	0.32988	1.43	4.51	3.42	0.39159	Marvel (1);	1.936980	0.02139	N	0.056964	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.21606	0.058	B	0.25759	0.063	T	0.21827	-1.0234	9	0.25106	T	0.35	1.0129	6.6943	0.23191	0.0:0.1041:0.0:0.8959	rs2290182;rs52805047;rs58100845;rs2290182	122	Q8TAZ6	CKLF2_HUMAN	T	122	ENSP00000268595:I122T	ENSP00000268595:I122T	I	+	2	0	CMTM2	65171509	0.017000	0.18338	0.001000	0.08648	0.037000	0.13140	3.042000	0.49815	1.059000	0.40554	0.459000	0.35465	ATA	T|0.810;C|0.190	0.190	strong		0.473	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1		
CREB3L3	84699	hgsc.bcm.edu	37	19	4154910	4154910	+	Silent	SNP	C	C	T	rs35474881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4154910C>T	ENST00000078445.2	+	2	189	c.42C>T	c.(40-42)gcC>gcT	p.A14A	CREB3L3_ENST00000252587.3_Silent_p.A5A|CREB3L3_ENST00000602257.1_Silent_p.A14A|CREB3L3_ENST00000602147.1_Silent_p.A14A|CREB3L3_ENST00000595923.1_Silent_p.A14A	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	14					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CTTCTGCTGCCTGCTCCATGG	0.622													C|||	429	0.0856629	0.0855	0.0821	5008	,	,		18561	0.0308		0.1431	False		,,,				2504	0.0859				p.A14A		Atlas-SNP	.											CREB3L3,NS,carcinoma,+1,2	CREB3L3	53	2	0			c.C42T						PASS	.	C		403,4003	199.4+/-223.0	24,355,1824	96.0	79.0	85.0		42	0.7	0.0	19	dbSNP_126	85	1175,7425	239.0+/-270.3	90,995,3215	no	coding-synonymous	CREB3L3	NM_032607.1		114,1350,5039	TT,TC,CC		13.6628,9.1466,12.1329		14/462	4154910	1578,11428	2203	4300	6503	SO:0001819	synonymous_variant	84699	exon2			TGCTGCCTGCTCC		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"""basic leucine zipper proteins"""	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.42C>T	19.37:g.4154910C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_001271997	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			C|0.881;T|0.119	0.119	strong		0.622	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
RDH12	145226	hgsc.bcm.edu	37	14	68193731	68193731	+	Missense_Mutation	SNP	G	G	A	rs17852293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68193731G>A	ENST00000551171.1	+	7	806	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	RDH12_ENST00000267502.3_Missense_Mutation_p.R161Q|RDH12_ENST00000539142.1_Missense_Mutation_p.R161Q	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	161			R -> Q (in dbSNP:rs17852293). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:16269441, ECO:0000269|PubMed:21602930}.		photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)			large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	CTCCTGGAGCGGCTAAAGGTG	0.587													G|||	527	0.105232	0.0885	0.1513	5008	,	,		20733	0.1101		0.1143	False		,,,				2504	0.0808				p.R161Q		Atlas-SNP	.											RDH12,brain,glioma,0,1	RDH12	43	1	0			c.G482A						PASS	.	G	GLN/ARG	421,3985	206.8+/-228.3	17,387,1799	70.0	63.0	65.0		482	0.7	1.0	14	dbSNP_123	65	1135,7465	233.6+/-266.8	76,983,3241	yes	missense	RDH12	NM_152443.2	43	93,1370,5040	AA,AG,GG		13.1977,9.5552,11.9637	benign	161/317	68193731	1556,11450	2203	4300	6503	SO:0001583	missense	145226	exon7			TGGAGCGGCTAAA	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19977	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 2"""	608830	"""retinol dehydrogenase 12 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.482G>A	14.37:g.68193731G>A	ENSP00000449079:p.Arg161Gln	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	87	50	0.574713	NM_152443	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	37	CCDS9787.1	241	0.11034798534798534	41	0.08333333333333333	47	0.1298342541436464	64	0.11188811188811189	89	0.11741424802110818	G	10.09	1.253769	0.22965	0.095552	0.131977	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.89415	-2.51;-2.51;-2.51	5.66	0.738	0.18319	NAD(P)-binding domain (1);	0.197807	0.44483	N	0.000444	T	0.02342	0.0072	N	0.17901	0.54	0.34473	P	0.297021	B	0.26602	0.154	B	0.21917	0.037	T	0.29119	-1.0022	9	0.25751	T	0.34	.	5.8805	0.18852	0.2948:0.0:0.5847:0.1205	rs17852293	161	Q96NR8	RDH12_HUMAN	Q	161	ENSP00000449079:R161Q;ENSP00000267502:R161Q;ENSP00000438715:R161Q	ENSP00000267502:R161Q	R	+	2	0	RDH12	67263484	1.000000	0.71417	0.984000	0.44739	0.305000	0.27757	2.495000	0.45337	-0.123000	0.11745	-0.895000	0.02911	CGG	G|0.882;A|0.118	0.118	strong		0.587	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1		
SLC12A2	6558	hgsc.bcm.edu	37	5	127469859	127469859	+	Silent	SNP	A	A	G	rs2228112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:127469859A>G	ENST00000262461.2	+	6	1380	c.1191A>G	c.(1189-1191)gaA>gaG	p.E397E	SLC12A2_ENST00000343225.4_Silent_p.E397E	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	397					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	TTTTCTAGGAACATTCCATAC	0.328													A|||	1975	0.394369	0.7337	0.3977	5008	,	,		17350	0.3294		0.1918	False		,,,				2504	0.2086				p.E397E		Atlas-SNP	.											.	SLC12A2	119	.	0			c.A1191G						PASS	.	A		2732,1674	653.5+/-399.6	854,1024,325	101.0	112.0	108.0		1191	2.5	1.0	5	dbSNP_98	108	1896,6700	334.1+/-320.8	196,1504,2598	no	coding-synonymous	SLC12A2	NM_001046.2		1050,2528,2923	GG,GA,AA		22.0568,37.9936,35.5945		397/1213	127469859	4628,8374	2203	4298	6501	SO:0001819	synonymous_variant	6558	exon6			CTAGGAACATTCC		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"""Solute carriers"""	10911	protein-coding gene	gene with protein product	"""bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1"", ""basolateral Na-K-Cl symporter"", ""protein phosphatase 1, regulatory subunit 141"""	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.1191A>G	5.37:g.127469859A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	145	64	0.441379	NM_001046	Q8N713|Q8WWH7	Silent	SNP	ENST00000262461.2	37	CCDS4144.1																																																																																			A|0.627;C|0.000;G|0.373;T|0.000	0.373	strong		0.328	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046	
RREB1	6239	hgsc.bcm.edu	37	6	7231843	7231843	+	Missense_Mutation	SNP	G	G	A	rs9379084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:7231843G>A	ENST00000349384.6	+	10	3825	c.3511G>A	c.(3511-3513)Gac>Aac	p.D1171N	RREB1_ENST00000379938.2_Missense_Mutation_p.D1171N|RREB1_ENST00000334984.6_Missense_Mutation_p.D1171N|RREB1_ENST00000379933.3_Missense_Mutation_p.D1171N	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1171			D -> N (in dbSNP:rs9379084).		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)				CGGCGGGGTGGACCTGGACTC	0.652													G|||	482	0.096246	0.0061	0.111	5008	,	,		12875	0.1587		0.1322	False		,,,				2504	0.1063				p.D1171N		Atlas-SNP	.											.	RREB1	242	.	0			c.G3511A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	96,4240		1,94,2073	11.0	15.0	14.0		3511,3511,3511,3511	5.7	1.0	6	dbSNP_119	14	939,7593		51,837,3378	yes	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	23,23,23,23	52,931,5451	AA,AG,GG		11.0056,2.214,8.0432	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1171/1688,1171/1743,1171/1477,1171/1688	7231843	1035,11833	2168	4266	6434	SO:0001583	missense	6239	exon10			GGGGTGGACCTGG	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.3511G>A	6.37:g.7231843G>A	ENSP00000305560:p.Asp1171Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	62	34	0.548387	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	236	0.10805860805860806	4	0.008130081300813009	46	0.1270718232044199	87	0.1520979020979021	99	0.13060686015831136	G	35	5.550748	0.96501	0.02214	0.110056	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.19938	2.11;2.27;2.11;2.24	5.74	5.74	0.90152	.	0.000000	0.64402	D	0.000005	T	0.32194	0.0821	M	0.63843	1.955	0.09310	P	0.9999999107708	D;D;D	0.71674	0.998;0.997;0.998	P;P;D	0.65233	0.904;0.859;0.933	T	0.01312	-1.1388	9	0.17832	T	0.49	-64.7872	19.9197	0.97082	0.0:0.0:1.0:0.0	rs9379084;rs9379084	1171;1171;1171	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	N	1171	ENSP00000369265:D1171N;ENSP00000369270:D1171N;ENSP00000305560:D1171N;ENSP00000335574:D1171N	ENSP00000335574:D1171N	D	+	1	0	RREB1	7176842	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.199000	0.95003	2.702000	0.92279	0.655000	0.94253	GAC	G|0.896;A|0.104	0.104	strong		0.652	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
FUCA2	2519	hgsc.bcm.edu	37	6	143816859	143816859	+	Silent	SNP	C	C	T	rs8161	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:143816859C>T	ENST00000002165.6	-	7	1444	c.1389G>A	c.(1387-1389)ctG>ctA	p.L463L	RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	463					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)	p.L463L(1)		endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		TCACATTAGTCAGGGCTAGAG	0.448													T|||	2116	0.422524	0.4796	0.438	5008	,	,		18597	0.4821		0.339	False		,,,				2504	0.3589				p.L463L		Atlas-SNP	.											FUCA2,NS,carcinoma,0,1	FUCA2	28	1	1	Substitution - coding silent(1)	stomach(1)	c.G1389A						PASS	.	T		2070,2336	605.8+/-390.6	486,1098,619	88.0	74.0	79.0		1389	-1.4	0.0	6	dbSNP_52	79	2938,5662	668.3+/-402.5	523,1892,1885	yes	coding-synonymous	FUCA2	NM_032020.4		1009,2990,2504	TT,TC,CC		34.1628,46.9814,38.5053		463/468	143816859	5008,7998	2203	4300	6503	SO:0001819	synonymous_variant	2519	exon7			ATTAGTCAGGGCT	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1389G>A	6.37:g.143816859C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Silent	SNP	ENST00000002165.6	37	CCDS5200.1																																																																																			C|0.585;T|0.415	0.415	strong		0.448	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
ATXN3	4287	hgsc.bcm.edu	37	14	92537354	92537354	+	Missense_Mutation	SNP	C	C	G	rs12895357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92537354C>G	ENST00000532032.1	-	10	925	c.916G>C	c.(916-918)Ggg>Cgg	p.G306R	ATXN3_ENST00000340660.6_Missense_Mutation_p.G251R|ATXN3_ENST00000503767.1_Missense_Mutation_p.G291R|ATXN3_ENST00000502250.1_Missense_Mutation_p.G127R|ATXN3_ENST00000429774.2_Missense_Mutation_p.G299R|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000545170.1_Missense_Mutation_p.G315R|ATXN3_ENST00000393287.5_Missense_Mutation_p.G306R			P54252	ATX3_HUMAN	ataxin 3	306			G -> QQQQQQQQQQQQR. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7874163, ECO:0000269|PubMed:9274833}.		actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.G306R(1)		endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		GATAGGTCCCCctgctgctgc	0.443													C|||	1382	0.275958	0.1687	0.1844	5008	,	,		15680	0.4236		0.2724	False		,,,				2504	0.3374				p.G306R	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											ATXN3,NS,carcinoma,0,2	ATXN3	46	2	1	Substitution - Missense(1)	lung(1)	c.G916C						scavenged	.	C	ARG/GLY,ARG/GLY,ALA/GLY,ALA/GLY,ALA/GLY,ALA/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ALA/GLY,ARG/GLY,ARG/GLY	496,3910		54,388,1761	97.0	75.0	82.0		871,763,233,278,113,431,553,379,706,68,916,751	0.2	0.0	14	dbSNP_121	82	1619,6981		285,1049,2966	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	ATXN3	NM_001127696.1,NM_001127697.2,NM_001164774.1,NM_001164776.1,NM_001164777.1,NM_001164778.1,NM_001164779.1,NM_001164780.1,NM_001164781.1,NM_001164782.1,NM_004993.5,NM_030660.4	125,125,60,60,60,60,125,125,125,60,125,125	339,1437,4727	GG,GC,CC		18.8256,11.2574,16.2617	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	291/347,255/311,78/89,93/104,38/49,144/155,185/241,127/183,236/292,23/34,306/362,251/307	92537354	2115,10891	2203	4300	6503	SO:0001583	missense	4287	exon10			GGTCCCCCTGCTG	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"""Ataxins"""	7106	protein-coding gene	gene with protein product		607047	"""Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"""	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.916G>C	14.37:g.92537354C>G	ENSP00000437157:p.Gly306Arg	Somatic	59	2	0.0338983		WXS	Illumina HiSeq	Phase_I	45	28	0.622222	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37		560	0.2564102564102564	88	0.17886178861788618	59	0.16298342541436464	238	0.4160839160839161	175	0.23087071240105542	C	9.580	1.123237	0.20959	0.112574	0.188256	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220	T;T;T;T;T;T;T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.93	4.78	0.191	0.15130	.	5.350120	0.00508	N	0.000162	T	0.00012	0.0000	.	.	.	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	0.08055	0.001;0.001;0.003;0.003;0.001	T	0.42430	-0.9452	8	0.35671	T	0.21	.	3.2489	0.06807	0.1547:0.5342:0.1949:0.1162	rs12895357	306;291;317;251;306	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	R	322;319;317;315;315;314;311;299;320;306;127;291;251;306;236;127;305;208;255;200	ENSP00000445618:G315R;ENSP00000389376:G299R;ENSP00000376965:G306R;ENSP00000425322:G127R;ENSP00000426697:G291R;ENSP00000339110:G251R;ENSP00000437157:G306R;ENSP00000451001:G236R;ENSP00000450642:G127R;ENSP00000451385:G305R;ENSP00000451417:G208R;ENSP00000451996:G255R;ENSP00000450641:G200R	ENSP00000339110:G251R	G	-	1	0	ATXN3	91607107	0.000000	0.05858	0.031000	0.17742	0.053000	0.15095	-1.306000	0.02735	0.441000	0.26529	0.454000	0.30748	GGG	C|0.783;G|0.217	0.217	strong		0.443	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
HMOX2	3163	hgsc.bcm.edu	37	16	4558064	4558064	+	Silent	SNP	G	G	A	rs2404579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:4558064G>A	ENST00000570646.1	+	4	1160	c.555G>A	c.(553-555)caG>caA	p.Q185Q	HMOX2_ENST00000219700.6_Silent_p.Q185Q|HMOX2_ENST00000406590.2_Silent_p.Q185Q|HMOX2_ENST00000398595.3_Silent_p.Q185Q|HMOX2_ENST00000575120.1_Silent_p.Q156Q|HMOX2_ENST00000458134.3_Silent_p.Q185Q|HMOX2_ENST00000414777.1_Silent_p.Q185Q	NM_002134.3	NP_002125.3	P30519	HMOX2_HUMAN	heme oxygenase (decycling) 2	185					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						AAGGGACCCAGTTCTACCTGT	0.577													G|||	6	0.00119808	0.0	0.0043	5008	,	,		19668	0.0		0.003	False		,,,				2504	0.0				p.Q185Q		Atlas-SNP	.											.	HMOX2	22	.	0			c.G555A						PASS	.	G	,,,	6,4388	11.4+/-27.6	0,6,2191	48.0	47.0	47.0		555,555,555,555	1.6	1.0	16	dbSNP_100	47	33,8567	22.8+/-68.1	0,33,4267	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HMOX2	NM_001127204.1,NM_001127205.1,NM_001127206.1,NM_002134.3	,,,	0,39,6458	AA,AG,GG		0.3837,0.1365,0.3001	,,,	185/317,185/317,185/317,185/317	4558064	39,12955	2197	4300	6497	SO:0001819	synonymous_variant	3163	exon4			GACCCAGTTCTAC		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.555G>A	16.37:g.4558064G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_001127205	A8MT35|D3DUD5|I3L430|O60605	Silent	SNP	ENST00000570646.1	37	CCDS10517.1																																																																																			G|0.996;A|0.004	0.004	strong		0.577	HMOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251636.2		
RASAL1	8437	hgsc.bcm.edu	37	12	113565933	113565933	+	Missense_Mutation	SNP	G	G	A	rs34598602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113565933G>A	ENST00000261729.5	-	4	488	c.173C>T	c.(172-174)aCg>aTg	p.T58M	RASAL1_ENST00000548055.1_Missense_Mutation_p.T58M|RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000546530.1_Missense_Mutation_p.T58M|RASAL1_ENST00000446861.3_Missense_Mutation_p.T58M			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	58	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		T -> M (in dbSNP:rs34598602). {ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						CAGGTGCACCGTGTACTCCTC	0.617													G|||	117	0.0233626	0.0038	0.0403	5008	,	,		15576	0.0		0.0706	False		,,,				2504	0.0133				p.T58M		Atlas-SNP	.											.	RASAL1	89	.	0			c.C173T						PASS	.	G	MET/THR,MET/THR,MET/THR	70,4336	64.1+/-101.4	0,70,2133	199.0	197.0	197.0		173,173,173	5.1	0.9	12	dbSNP_126	197	535,8065	148.8+/-204.0	17,501,3782	yes	missense,missense,missense	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	81,81,81	17,571,5915	AA,AG,GG		6.2209,1.5887,4.6517	probably-damaging,probably-damaging,probably-damaging	58/807,58/777,58/805	113565933	605,12401	2203	4300	6503	SO:0001583	missense	8437	exon4			TGCACCGTGTACT	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.173C>T	12.37:g.113565933G>A	ENSP00000261729:p.Thr58Met	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	37	CCDS9165.1	67	0.030677655677655676	5	0.01016260162601626	12	0.03314917127071823	0	0.0	50	0.06596306068601583	G	23.2	4.393216	0.83011	0.015887	0.062209	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48	5.12	5.12	0.69794	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.31765	0.0807	L	0.60455	1.87	0.48511	D	0.999668	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.975;0.993;1.0	T	0.65965	-0.6040	10	0.52906	T	0.07	.	17.315	0.87221	0.0:0.0:1.0:0.0	rs34598602	58;58;70;58;58;58	B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;RASL1_HUMAN;.	M	58	ENSP00000450244:T58M;ENSP00000261729:T58M;ENSP00000395920:T58M;ENSP00000448510:T58M	ENSP00000261729:T58M	T	-	2	0	RASAL1	112050316	1.000000	0.71417	0.939000	0.37840	0.913000	0.54294	8.924000	0.92827	2.394000	0.81467	0.491000	0.48974	ACG	G|0.957;A|0.043	0.043	strong		0.617	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
C5orf45	51149	hgsc.bcm.edu	37	5	179285752	179285752	+	Silent	SNP	G	G	A	rs10060182	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179285752G>A	ENST00000292586.6	-	1	135	c.45C>T	c.(43-45)tgC>tgT	p.C15C	C5orf45_ENST00000518235.1_Silent_p.C15C|C5orf45_ENST00000523084.1_5'UTR|CTC-241N9.1_ENST00000499601.2_5'Flank|C5orf45_ENST00000518219.1_Silent_p.C15C|C5orf45_ENST00000403396.2_Missense_Mutation_p.P31S|C5orf45_ENST00000520698.1_Silent_p.C15C|C5orf45_ENST00000521333.1_Silent_p.C15C|C5orf45_ENST00000376931.2_Silent_p.C15C	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	15										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						GGAAGAGGCGGCAGCTGCAGC	0.706													G|||	2240	0.447284	0.1687	0.5706	5008	,	,		14354	0.7589		0.2982	False		,,,				2504	0.5685				p.C15C		Atlas-SNP	.											C5orf45,colon,carcinoma,0,1	C5orf45	23	1	0			c.C45T						PASS	.	G	,	760,3204		108,544,1330	10.0	11.0	11.0		45,45	1.6	1.0	5	dbSNP_119	11	2081,5543		332,1417,2063	no	coding-synonymous,coding-synonymous	C5orf45	NM_001017987.2,NM_016175.3	,	440,1961,3393	AA,AG,GG		27.2954,19.1726,24.5167	,	15/289,15/344	179285752	2841,8747	1982	3812	5794	SO:0001819	synonymous_variant	51149	exon1			GAGGCGGCAGCTG		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.45C>T	5.37:g.179285752G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	46	28	0.608696	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Silent	SNP	ENST00000292586.6	37	CCDS34319.1	936	0.42857142857142855	86	0.17479674796747968	182	0.5027624309392266	453	0.791958041958042	215	0.2836411609498681	G	11.87	1.766751	0.31320	0.191726	0.272954	ENSG00000161010	ENST00000403396	T	0.30182	1.54	3.43	1.62	0.23740	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.43172	P	0.005027000000000004	.	.	.	.	.	.	T	0.11717	-1.0576	5	0.87932	D	0	-12.471	8.1787	0.31298	0.1954:0.0:0.8046:0.0	rs10060182;rs56833977;rs10060182	.	.	.	S	31	ENSP00000384599:P31S	ENSP00000384599:P31S	P	-	1	0	C5orf45	179218358	1.000000	0.71417	0.998000	0.56505	0.719000	0.41307	1.018000	0.30002	0.445000	0.26639	0.561000	0.74099	CCG	G|0.579;A|0.421	0.421	strong		0.706	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
PLCG2	5336	hgsc.bcm.edu	37	16	81971403	81971403	+	Silent	SNP	T	T	C	rs1071644	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81971403T>C	ENST00000359376.3	+	28	3307	c.3093T>C	c.(3091-3093)aaT>aaC	p.N1031N		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1031	PI-PLC Y-box. {ECO:0000255|PROSITE- ProRule:PRU00271}.				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						TTTCTCTCAATGGGCGCACGG	0.547													T|||	1572	0.313898	0.0764	0.3199	5008	,	,		20866	0.3442		0.504	False		,,,				2504	0.4039				p.N1031N		Atlas-SNP	.											.	PLCG2	276	.	0			c.T3093C						PASS	.	T		636,3558		55,526,1516	102.0	99.0	100.0		3093	-5.8	0.9	16	dbSNP_86	100	4490,3954		1225,2040,957	no	coding-synonymous	PLCG2	NM_002661.3		1280,2566,2473	CC,CT,TT		46.8261,15.1645,40.5602		1031/1266	81971403	5126,7512	2097	4222	6319	SO:0001819	synonymous_variant	5336	exon28			TCTCAATGGGCGC		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.3093T>C	16.37:g.81971403T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			C|0.387;N|0.000	0.387	strong		0.547	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
CDHR2	54825	hgsc.bcm.edu	37	5	176017455	176017455	+	Missense_Mutation	SNP	C	C	T	rs2291442	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176017455C>T	ENST00000510636.1	+	27	3657	c.3383C>T	c.(3382-3384)aCg>aTg	p.T1128M	CDHR2_ENST00000506348.1_Missense_Mutation_p.T1128M|CDHR2_ENST00000261944.5_Missense_Mutation_p.T1128M	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	1128			T -> M (in dbSNP:rs2291442). {ECO:0000269|PubMed:12117771, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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						GACTCGCTGACGCAGCTGCTG	0.637													c|||	1413	0.282149	0.3033	0.2334	5008	,	,		16317	0.3194		0.2445	False		,,,				2504	0.2883				p.T1128M		Atlas-SNP	.											CDHR2,colon,carcinoma,0,1	CDHR2	152	1	0			c.C3383T						PASS	.		MET/THR,MET/THR	1332,3074	446.3+/-348.0	180,972,1051	65.0	67.0	66.0		3383,3383	0.3	0.0	5	dbSNP_100	66	2337,6263	389.7+/-343.0	298,1741,2261	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	81,81	478,2713,3312	TT,TC,CC		27.1744,30.2315,28.2101	benign,benign	1128/1311,1128/1311	176017455	3669,9337	2203	4300	6503	SO:0001583	missense	54825	exon27			CGCTGACGCAGCT	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.3383C>T	5.37:g.176017455C>T	ENSP00000424565:p.Thr1128Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	114	50	0.438596	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	616	0.28205128205128205	138	0.2804878048780488	104	0.287292817679558	181	0.31643356643356646	193	0.2546174142480211	c	3.170	-0.170179	0.06461	0.302315	0.271744	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.55760	0.5;0.5;0.5	4.61	0.292	0.15737	.	.	.	.	.	T	0.00012	0.0000	N	0.17674	0.51	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.30149	-0.9988	8	0.45353	T	0.12	-2.7345	3.7294	0.08487	0.1833:0.5449:0.112:0.1598	rs2291442;rs59204096;rs2291442	1128	Q9BYE9	CDHR2_HUMAN	M	1128	ENSP00000424565:T1128M;ENSP00000261944:T1128M;ENSP00000421078:T1128M	ENSP00000261944:T1128M	T	+	2	0	CDHR2	175950061	0.000000	0.05858	0.030000	0.17652	0.184000	0.23303	-1.990000	0.01479	-0.169000	0.10834	-1.263000	0.01449	ACG	C|0.719;T|0.281	0.281	strong		0.637	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
GPC4	2239	hgsc.bcm.edu	37	X	132437337	132437337	+	Missense_Mutation	SNP	G	G	A	rs1048369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:132437337G>A	ENST00000370828.3	-	8	1849	c.1325C>T	c.(1324-1326)gCc>gTc	p.A442V	GPC4_ENST00000535467.1_Missense_Mutation_p.A372V	NM_001448.2	NP_001439.2	O75487	GPC4_HUMAN	glypican 4	442			A -> V (in dbSNP:rs1048369). {ECO:0000269|PubMed:10814714, ECO:0000269|PubMed:9787072, ECO:0000269|Ref.3}.		anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;0.000127)					GCCCTGGTTGGCTAATCCATT	0.463													G|||	1730	0.458278	0.5045	0.1787	3775	,	,		13755	0.3492		0.2167	False		,,,				2504	0.3773				p.A442V		Atlas-SNP	.											.	GPC4	58	.	0			c.C1325T						PASS	.	G	VAL/ALA	2290,1545		594,783,319,255,252	151.0	118.0	129.0		1325	4.7	1.0	X	dbSNP_86	129	1986,4742		209,1010,558,1209,1314	yes	missense	GPC4	NM_001448.2	64	803,1793,877,1464,1566	AA,AG,A,GG,G		29.5184,40.2868,40.4809	possibly-damaging	442/557	132437337	4276,6287	2203	4300	6503	SO:0001583	missense	2239	exon8			TGGTTGGCTAATC	AF030186	CCDS14637.1	Xq26.1	2008-02-05			ENSG00000076716	ENSG00000076716		"""Proteoglycans / Cell Surface : Glypicans"""	4452	protein-coding gene	gene with protein product	"""glypican proteoglycan 4"""	300168				9787072	Standard	NM_001448		Approved	K-glypican	uc004exc.1	O75487	OTTHUMG00000022434	ENST00000370828.3:c.1325C>T	X.37:g.132437337G>A	ENSP00000359864:p.Ala442Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001448	B2R6J7|B4E2C0|Q6ZMA6|Q96L43|Q9NU08|Q9UJN1|Q9UPD9	Missense_Mutation	SNP	ENST00000370828.3	37	CCDS14637.1	651	0.3924050632911392	173	0.4914772727272727	50	0.15822784810126583	117	0.26	114	0.16964285714285715	G	19.48	3.835502	0.71373	0.597132	0.295184	ENSG00000076716	ENST00000370828;ENST00000536418;ENST00000535467	T;T	0.52295	0.67;0.67	5.63	4.72	0.59763	.	0.150453	0.64402	N	0.000014	T	0.00012	0.0000	M	0.72624	2.21	0.09310	P	0.99999893531	P	0.47910	0.902	B	0.43194	0.411	T	0.47275	-0.9130	9	0.62326	D	0.03	-4.432	11.9038	0.52699	0.0899:0.0:0.9101:0.0	rs1048369;rs1805047;rs3188383;rs59667595;rs1048369	442	O75487	GPC4_HUMAN	V	442;436;372	ENSP00000359864:A442V;ENSP00000444959:A372V	ENSP00000359864:A442V	A	-	2	0	GPC4	132265003	1.000000	0.71417	1.000000	0.80357	0.517000	0.34286	6.803000	0.75180	1.052000	0.40392	-0.380000	0.06706	GCC	G|0.566;0|0.012	.	strong		0.463	GPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058338.1	NM_001448	
CCDC180	100499483	hgsc.bcm.edu	37	9	100105735	100105735	+	Silent	SNP	T	T	C	rs1947717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100105735T>C	ENST00000357054.1	+	33	3872	c.2937T>C	c.(2935-2937)tgT>tgC	p.C979C	CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000529487.1_Silent_p.C840C|CCDC180_ENST00000411667.2_Silent_p.C837C|CCDC180_ENST00000375202.2_Silent_p.C840C|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	979						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											AAGAGCATTGTAGGAAGTCCC	0.423													C|||	2973	0.59365	0.7458	0.6628	5008	,	,		17941	0.5843		0.3936	False		,,,				2504	0.5542				p.C840C		Atlas-SNP	.											.	.	.	.	0			c.T2520C						PASS	.	C		3195,1211	420.2+/-338.9	1154,887,162	123.0	113.0	116.0		2520	2.3	0.0	9	dbSNP_92	116	3980,4620	600.2+/-394.2	912,2156,1232	no	coding-synonymous	C9orf174	NM_020893.2		2066,3043,1394	CC,CT,TT		46.2791,27.4852,44.8332		840/1702	100105735	7175,5831	2203	4300	6503	SO:0001819	synonymous_variant	0	exon19			GCATTGTAGGAAG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.2937T>C	9.37:g.100105735T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	85	49	0.576471	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				T|0.445;C|0.555	0.555	strong		0.423	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
PSPC1	55269	hgsc.bcm.edu	37	13	20279879	20279879	+	Missense_Mutation	SNP	T	T	C	rs200516102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:20279879T>C	ENST00000338910.4	-	8	1468	c.1309A>G	c.(1309-1311)Atg>Gtg	p.M437V		NM_001042414.2	NP_001035879.1	Q8WXF1	PSPC1_HUMAN	paraspeckle component 1	437	Gly-rich.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23		all_cancers(29;1.25e-22)|all_lung(29;1.97e-20)|all_epithelial(30;2.29e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;4.63e-06)|Epithelial(112;2.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00256)|Lung(94;0.00975)|LUSC - Lung squamous cell carcinoma(192;0.0483)		CCAGGACCCATTGGTGGGCCA	0.473																																					p.M437V		Atlas-SNP	.											PSPC1,NS,haematopoietic_neoplasm,0,1	PSPC1	61	1	0			c.A1309G						scavenged	.						49.0	55.0	53.0					13																	20279879		1832	4086	5918	SO:0001583	missense	55269	exon9			GACCCATTGGTGG	AK001817	CCDS41870.1	13q11	2013-02-12			ENSG00000121390	ENSG00000121390		"""RNA binding motif (RRM) containing"""	20320	protein-coding gene	gene with protein product		612408				11790299	Standard	NM_001042414		Approved	PSP1, FLJ10955	uc021rgx.1	Q8WXF1	OTTHUMG00000016502	ENST00000338910.4:c.1309A>G	13.37:g.20279879T>C	ENSP00000343966:p.Met437Val	Somatic	603	9	0.0149254		WXS	Illumina HiSeq	Phase_I	697	84	0.120517	NM_001042414	Q5JTQ3|Q8NCZ9|Q8WXE8|Q9NV36	Missense_Mutation	SNP	ENST00000338910.4	37	CCDS41870.1	.	.	.	.	.	.	.	.	.	.	T	7.585	0.669496	0.14776	.	.	ENSG00000121390	ENST00000338910;ENST00000422828	T	0.13420	2.59	5.29	2.98	0.34508	.	0.178534	0.56097	D	0.000021	T	0.08044	0.0201	N	0.22421	0.69	0.30474	N	0.772982	B	0.15141	0.012	B	0.12156	0.007	T	0.25847	-1.0120	10	0.14252	T	0.57	-7.4851	9.0578	0.36416	0.0:0.0762:0.1546:0.7692	.	437	Q8WXF1	PSPC1_HUMAN	V	437;377	ENSP00000343966:M437V	ENSP00000343966:M437V	M	-	1	0	PSPC1	19177879	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	0.910000	0.28571	0.844000	0.35094	0.402000	0.26972	ATG	T|0.998;C|0.002	0.002	strong		0.473	PSPC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044037.2		
ANGPT2	285	hgsc.bcm.edu	37	8	6371303	6371303	+	Silent	SNP	A	A	G	rs17063434	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:6371303A>G	ENST00000325203.5	-	7	1569	c.1095T>C	c.(1093-1095)aaT>aaC	p.N365N	ANGPT2_ENST00000338312.6_Silent_p.N313N|ANGPT2_ENST00000415216.1_Silent_p.N364N|ANGPT2_ENST00000523120.1_Silent_p.N364N|MCPH1_ENST00000344683.5_Intron			O15123	ANGP2_HUMAN	angiopoietin 2	365	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		AGCGTTGCTGATTAGTCAGTT	0.363													A|||	222	0.0443291	0.0847	0.0389	5008	,	,		18004	0.0		0.0517	False		,,,				2504	0.0317				p.N365N		Atlas-SNP	.											.	ANGPT2	126	.	0			c.T1095C						PASS	.	A	,,,	334,4072	176.6+/-205.7	14,306,1883	106.0	107.0	107.0		1092,939,1095,	1.1	0.0	8	dbSNP_123	107	500,8100	144.0+/-200.0	13,474,3813	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ANGPT2,MCPH1	NM_001118887.1,NM_001118888.1,NM_001147.2,NM_024596.3	,,,	27,780,5696	GG,GA,AA		5.814,7.5806,6.4124	,,,	364/496,313/445,365/497,	6371303	834,12172	2203	4300	6503	SO:0001819	synonymous_variant	285	exon7			TTGCTGATTAGTC	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.1095T>C	8.37:g.6371303A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	134	71	0.529851	NM_001147	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	37	CCDS5958.1																																																																																			A|0.942;G|0.058	0.058	strong		0.363	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
IGSF10	285313	hgsc.bcm.edu	37	3	151171542	151171542	+	Silent	SNP	A	A	G	rs7621591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:151171542A>G	ENST00000282466.3	-	3	344	c.345T>C	c.(343-345)aaT>aaC	p.N115N		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	115					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTCGGACTTTATTATAGCTCA	0.323													G|||	4065	0.811701	0.8926	0.781	5008	,	,		15197	0.7649		0.7714	False		,,,				2504	0.8139				p.N115N		Atlas-SNP	.											.	IGSF10	279	.	0			c.T345C						PASS	.	G		3682,600		1589,504,48	72.0	80.0	77.0		345	1.7	1.0	3	dbSNP_116	77	6604,1968		2570,1464,252	no	coding-synonymous	IGSF10	NM_178822.4		4159,1968,300	GG,GA,AA		22.9585,14.0121,19.9782		115/2624	151171542	10286,2568	2141	4286	6427	SO:0001819	synonymous_variant	285313	exon3			GACTTTATTATAG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.345T>C	3.37:g.151171542A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			A|0.195;G|0.805	0.805	strong		0.323	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
PIEZO1	9780	hgsc.bcm.edu	37	16	88782079	88782079	+	Silent	SNP	G	G	A	rs1061228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88782079G>A	ENST00000301015.9	-	51	7746	c.7500C>T	c.(7498-7500)taC>taT	p.Y2500Y	RP5-1142A6.9_ENST00000564984.1_RNA|MIR4722_ENST00000578292.1_RNA|PIEZO1_ENST00000327397.7_Missense_Mutation_p.R356C	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	2500					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						TGAGCTTGGCGTACAACTCCT	0.617													G|||	432	0.086262	0.0159	0.1369	5008	,	,		15983	0.126		0.1193	False		,,,				2504	0.0706				p.Y2500Y		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C7500T						PASS	.						73.0	66.0	68.0					16																	88782079		692	1589	2281	SO:0001819	synonymous_variant	9780	exon51			CTTGGCGTACAAC	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.7500C>T	16.37:g.88782079G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	246	0.11263736263736264	10	0.02032520325203252	51	0.1408839779005525	94	0.16433566433566432	91	0.12005277044854881	G	10.73	1.432739	0.25813	.	.	ENSG00000103335	ENST00000451779;ENST00000327397	T	0.69926	-0.44	4.74	-2.49	0.06403	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.37292	P	0.091696	B	0.06786	0.001	B	0.04013	0.001	T	0.08700	-1.0709	7	0.87932	D	0	-15.9375	10.3786	0.44096	0.5308:0.0:0.4692:0.0	rs1061228;rs17845148;rs17857952	356	E7EUT2	.	C	2446;356	ENSP00000333704:R356C	ENSP00000333704:R356C	R	-	1	0	FAM38A	87309580	0.994000	0.37717	0.102000	0.21198	0.973000	0.67179	0.261000	0.18442	-0.670000	0.05282	-0.258000	0.10820	CGC	T|0.000;G|0.884;C|0.000;A|0.115	0.115	strong		0.617	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
DOCK11	139818	hgsc.bcm.edu	37	X	117700141	117700141	+	Silent	SNP	A	A	G	rs2286977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:117700141A>G	ENST00000276202.7	+	8	930	c.867A>G	c.(865-867)gcA>gcG	p.A289A	DOCK11_ENST00000276204.6_Silent_p.A289A	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	289					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						TAGAAACAGCACAAGGTCAGA	0.373													A|||	1459	0.38649	0.1225	0.2911	3775	,	,		12894	0.4177		0.2753	False		,,,				2504	0.4059				p.A289A		Atlas-SNP	.											.	DOCK11	185	.	0			c.A867G						PASS	.	A		707,3128		51,503,102,1078,469	70.0	70.0	70.0		867	1.6	0.6	X	dbSNP_100	70	2489,4239		317,1174,681,937,1191	no	coding-synonymous	DOCK11	NM_144658.3		368,1677,783,2015,1660	GG,GA,G,AA,A		36.9946,18.4355,30.2566		289/2074	117700141	3196,7367	2203	4300	6503	SO:0001819	synonymous_variant	139818	exon8			AACAGCACAAGGT	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.867A>G	X.37:g.117700141A>G		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	106	104	0.981132	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			0|0.012;G|0.317	0.317	strong		0.373	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
DDX18	8886	hgsc.bcm.edu	37	2	118575215	118575215	+	Missense_Mutation	SNP	C	C	G	rs1052637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:118575215C>G	ENST00000263239.2	+	2	409	c.281C>G	c.(280-282)aCc>aGc	p.T94S	DDX18_ENST00000474694.1_3'UTR	NM_006773.3	NP_006764.3	Q9NVP1	DDX18_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 18	94			T -> S (in dbSNP:rs1052637). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		ATP catabolic process (GO:0006200)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ACTGTATTAACCAATGGAGAA	0.373													C|||	2138	0.426917	0.6263	0.3602	5008	,	,		17432	0.2282		0.3688	False		,,,				2504	0.4693				p.T94S		Atlas-SNP	.											.	DDX18	79	.	0			c.C281G						PASS	.	C	SER/THR	2550,1854	590.2+/-387.3	739,1072,391	87.0	100.0	95.0		281	2.2	0.8	2	dbSNP_86	95	3143,5457	463.4+/-366.0	574,1995,1731	yes	missense	DDX18	NM_006773.3	58	1313,3067,2122	GG,GC,CC		36.5465,42.0981,43.7788	benign	94/671	118575215	5693,7311	2202	4300	6502	SO:0001583	missense	8886	exon2			TATTAACCAATGG	X98743	CCDS2120.1	2q21.2	2008-02-05	2003-06-13		ENSG00000088205	ENSG00000088205		"""DEAD-boxes"""	2741	protein-coding gene	gene with protein product		606355	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 18 (Myc-regulated)"""			8861962	Standard	NM_006773		Approved	MrDb	uc002tlh.1	Q9NVP1	OTTHUMG00000058521	ENST00000263239.2:c.281C>G	2.37:g.118575215C>G	ENSP00000263239:p.Thr94Ser	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	162	66	0.407407	NM_006773	Q6GTZ9|Q6IAU4|Q92732|Q9BQB7	Missense_Mutation	SNP	ENST00000263239.2	37	CCDS2120.1	829	0.37957875457875456	299	0.6077235772357723	126	0.34806629834254144	123	0.21503496503496503	281	0.370712401055409	C	5.931	0.355794	0.11239	0.579019	0.365465	ENSG00000088205	ENST00000263239	T	0.21031	2.03	4.01	2.2	0.27929	.	2.399920	0.01794	N	0.032491	T	0.00012	0.0000	L	0.56769	1.78	0.44539	P	0.002507000000000037	B	0.17038	0.02	B	0.11329	0.006	T	0.47873	-0.9083	9	0.05959	T	0.93	-3.7378	6.2096	0.20621	0.0:0.7687:0.0:0.2313	rs1052637;rs1583331;rs2070147;rs3171830;rs16897521;rs17852239;rs17857615;rs17857732;rs52829447;rs60628909;rs1052637	94	Q9NVP1	DDX18_HUMAN	S	94	ENSP00000263239:T94S	ENSP00000263239:T94S	T	+	2	0	DDX18	118291685	0.055000	0.20627	0.842000	0.33263	0.713000	0.41058	0.094000	0.15107	0.480000	0.27534	0.655000	0.94253	ACC	C|0.601;G|0.399	0.399	strong		0.373	DDX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129632.3	NM_006773	
CCDC34	91057	hgsc.bcm.edu	37	11	27379026	27379026	+	Missense_Mutation	SNP	C	C	T	rs138159804		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:27379026C>T	ENST00000328697.6	-	2	1095	c.422G>A	c.(421-423)cGc>cAc	p.R141H	CCDC34_ENST00000317945.6_Missense_Mutation_p.R141H	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	141										endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						TGGTGTCAGGCGGCTTTCTGG	0.428																																					p.R141H		Atlas-SNP	.											.	CCDC34	48	.	0			c.G422A						PASS	.	C	HIS/ARG,HIS/ARG	0,4404		0,0,2202	150.0	139.0	143.0		422,422	1.2	0.1	11	dbSNP_134	143	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense	CCDC34	NM_030771.1,NM_080654.2	29,29	0,3,6498	TT,TC,CC		0.0349,0.0,0.0231	benign,benign	141/374,141/230	27379026	3,12999	2202	4299	6501	SO:0001583	missense	91057	exon2			GTCAGGCGGCTTT	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.422G>A	11.37:g.27379026C>T	ENSP00000330240:p.Arg141His	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	37	CCDS31448.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825829	0.32237	0.0	3.49E-4	ENSG00000109881	ENST00000328697;ENST00000317945	T;T	0.22743	1.94;1.94	5.39	1.21	0.21127	.	0.954155	0.08803	N	0.891475	T	0.11367	0.0277	N	0.14661	0.345	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.04013	0.001;0.001	T	0.32322	-0.9911	10	0.38643	T	0.18	7.2849	4.8599	0.13579	0.0:0.4435:0.2345:0.322	.	141;141	Q96HJ3-2;Q96HJ3	.;CCD34_HUMAN	H	141	ENSP00000330240:R141H;ENSP00000321563:R141H	ENSP00000321563:R141H	R	-	2	0	CCDC34	27335602	0.026000	0.19158	0.117000	0.21633	0.190000	0.23558	0.086000	0.14935	0.361000	0.24292	-0.812000	0.03155	CGC	C|1.000;T|0.000	0.000	weak		0.428	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771	
SDC4	6385	hgsc.bcm.edu	37	20	43964514	43964514	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43964514C>T	ENST00000372733.3	-	2	146	c.107G>A	c.(106-108)cGa>cAa	p.R36Q	SDC4_ENST00000537976.1_Intron	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	36					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				GGAGAAGTATCGGCCTTCTAG	0.552			T	ROS1	NSCLC																																p.R36Q		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.G107A						PASS	.						70.0	65.0	66.0					20																	43964514		2203	4300	6503	SO:0001583	missense	6385	exon2			AAGTATCGGCCTT	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"""Proteoglycans / Cell Surface : Syndecans"""	10661	protein-coding gene	gene with protein product	"""syndecan proteoglycan 4"""	600017	"""syndecan 4 (amphiglycan, ryudocan)"""			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.107G>A	20.37:g.43964514C>T	ENSP00000361818:p.Arg36Gln	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.075721	0.36662	.	.	ENSG00000124145	ENST00000372733	T	0.30182	1.54	4.79	1.8	0.24995	.	0.602744	0.16677	N	0.204118	T	0.16685	0.0401	N	0.25426	0.745	0.27144	N	0.961575	B	0.16802	0.019	B	0.08055	0.003	T	0.30794	-0.9966	10	0.11485	T	0.65	-0.7809	7.1145	0.25409	0.0:0.7099:0.0:0.2901	.	36	P31431	SDC4_HUMAN	Q	36	ENSP00000361818:R36Q	ENSP00000361818:R36Q	R	-	2	0	SDC4	43397928	0.000000	0.05858	0.901000	0.35422	0.714000	0.41099	-1.122000	0.03267	0.201000	0.20466	0.561000	0.74099	CGA	.	.	none		0.552	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999	
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327909	+	Missense_Mutation	SNP	A	A	C	rs59310777	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:16327909A>C	ENST00000244769.4	-	8	1569	c.633T>G	c.(631-633)caT>caG	p.H211Q	ATXN1_ENST00000436367.1_Missense_Mutation_p.H211Q	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	211	Poly-Gln.			H -> HQ (in Ref. 1; CAA55793). {ECO:0000305}.	adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.H209_H211delHQH(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgatgctgatgct	0.672													A|||	1334	0.266374	0.2897	0.2161	5008	,	,		12493	0.3879		0.0964	False		,,,				2504	0.32				p.H211Q		Atlas-SNP	.											ATXN1,colon,carcinoma,0,3	ATXN1	117	3	1	Deletion - In frame(1)	prostate(1)	c.T633G						PASS	.						4.0	7.0	6.0					6																	16327909		1575	3495	5070	SO:0001583	missense	6310	exon7			CTGCTGATGCTGA	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.633T>G	6.37:g.16327909A>C	ENSP00000244769:p.His211Gln	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	39	26	0.666667	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	369	0.16895604395604397	105	0.21341463414634146	59	0.16298342541436464	150	0.26223776223776224	55	0.07255936675461741	A	5.976	0.364085	0.11296	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.50813	0.73;0.73	.	.	.	.	.	.	.	.	T	0.08358	0.0208	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.31223	-0.9951	4	0.15952	T	0.53	.	.	.	.	rs59310777	211	P54253	ATX1_HUMAN	Q	211	ENSP00000244769:H211Q;ENSP00000416360:H211Q	ENSP00000244769:H211Q	H	-	3	2	ATXN1	16435888	0.694000	0.27738	0.023000	0.16930	0.066000	0.16364	1.537000	0.36083	0.000000	0.14550	0.000000	0.15137	CAT	A|0.830;C|0.170	0.170	strong		0.672	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
VAMP8	8673	hgsc.bcm.edu	37	2	85806266	85806266	+	Silent	SNP	C	C	T	rs3731828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:85806266C>T	ENST00000263864.5	+	2	294	c.138C>T	c.(136-138)aaC>aaT	p.N46N	VAMP8_ENST00000432071.1_Silent_p.N20N|VAMP8_ENST00000409760.1_Silent_p.N46N	NM_003761.4	NP_003752.2	Q9BV40	VAMP8_HUMAN	vesicle-associated membrane protein 8	46	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				autophagic vacuole fusion (GO:0000046)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule membrane (GO:0030667)|SNARE complex (GO:0031201)		p.N46N(1)		breast(1)|endometrium(2)|large_intestine(1)|stomach(2)	6						ATCTCCGCAACAAGACAGAGG	0.542													C|||	1419	0.283347	0.3971	0.2161	5008	,	,		17696	0.3085		0.2982	False		,,,				2504	0.136				p.N46N		Atlas-SNP	.											VAMP8,NS,carcinoma,0,1	VAMP8	10	1	1	Substitution - coding silent(1)	stomach(1)	c.C138T						PASS	.	C		1556,2850	452.8+/-350.1	282,992,929	39.0	38.0	38.0		138	2.9	1.0	2	dbSNP_107	38	2352,6248	362.0+/-332.6	325,1702,2273	no	coding-synonymous	VAMP8	NM_003761.4		607,2694,3202	TT,TC,CC		27.3488,35.3155,30.0477		46/101	85806266	3908,9098	2203	4300	6503	SO:0001819	synonymous_variant	8673	exon2			CCGCAACAAGACA	AF053233	CCDS1979.1	2p12-p11.2	2013-02-13	2012-10-17		ENSG00000118640	ENSG00000118640		"""Vesicle-associated membrane proteins"""	12647	protein-coding gene	gene with protein product	"""endobrevin"""	603177				9878266, 9614193	Standard	NM_003761		Approved	EDB	uc002spt.4	Q9BV40	OTTHUMG00000130180	ENST00000263864.5:c.138C>T	2.37:g.85806266C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	11	0.275	NM_003761	O60625|Q53SP9|Q6IB09	Silent	SNP	ENST00000263864.5	37	CCDS1979.1																																																																																			C|0.698;T|0.302	0.302	strong		0.542	VAMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252498.3	NM_003761	
ZNF442	79973	hgsc.bcm.edu	37	19	12463856	12463856	+	Missense_Mutation	SNP	T	T	C	rs73921445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12463856T>C	ENST00000242804.4	-	4	733	c.151A>G	c.(151-153)Aag>Gag	p.K51E	ZNF442_ENST00000438182.1_Intron	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TACAGACTCTTCTGTGATGGA	0.438													T|||	63	0.0125799	0.0378	0.0058	5008	,	,		19281	0.0		0.008	False		,,,				2504	0.001				p.K51E		Atlas-SNP	.											.	ZNF442	102	.	0			c.A151G						PASS	.	T	GLU/LYS	139,4267	98.9+/-137.6	3,133,2067	142.0	139.0	140.0		151	1.0	0.1	19	dbSNP_130	140	33,8567	22.2+/-67.0	0,33,4267	yes	missense	ZNF442	NM_030824.2	56	3,166,6334	CC,CT,TT		0.3837,3.1548,1.3225	probably-damaging	51/628	12463856	172,12834	2203	4300	6503	SO:0001583	missense	79973	exon4			GACTCTTCTGTGA	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"""Zinc fingers, C2H2-type"", ""-"""	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.151A>G	19.37:g.12463856T>C	ENSP00000242804:p.Lys51Glu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_030824	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	25	0.011446886446886446	15	0.03048780487804878	3	0.008287292817679558	0	0.0	7	0.009234828496042216	T	16.79	3.219430	0.58560	0.031548	0.003837	ENSG00000198342	ENST00000242804	T	0.02863	4.13	1.03	1.03	0.20045	Krueppel-associated box (4);	.	.	.	.	T	0.06462	0.0166	H	0.95850	3.73	0.36021	D	0.838739	D	0.89917	1.0	D	0.87578	0.998	T	0.03202	-1.1061	9	0.87932	D	0	.	6.2028	0.20585	0.0:0.0:0.0:1.0	.	51	Q9H7R0	ZN442_HUMAN	E	51	ENSP00000242804:K51E	ENSP00000242804:K51E	K	-	1	0	ZNF442	12324856	0.683000	0.27633	0.066000	0.19879	0.547000	0.35210	1.198000	0.32223	0.710000	0.31997	0.260000	0.18958	AAG	T|0.986;C|0.014	0.014	strong		0.438	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824	
HSPB7	27129	hgsc.bcm.edu	37	1	16342237	16342237	+	Silent	SNP	A	A	G	rs1739840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16342237A>G	ENST00000311890.9	-	3	1177	c.351T>C	c.(349-351)acT>acC	p.T117T	HSPB7_ENST00000487046.1_Silent_p.T122T|HSPB7_ENST00000375718.4_Silent_p.T192T|HSPB7_ENST00000411503.1_Silent_p.T112T|HSPB7_ENST00000406363.2_Silent_p.T121T	NM_014424.4	NP_055239.1	Q9UBY9	HSPB7_HUMAN	heat shock 27kDa protein family, member 7 (cardiovascular)	117					regulation of heart contraction (GO:0008016)|response to unfolded protein (GO:0006986)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(1)|liver(1)|lung(6)|skin(1)	10		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;8.21e-08)|COAD - Colon adenocarcinoma(227;5.5e-06)|BRCA - Breast invasive adenocarcinoma(304;9.08e-05)|Kidney(64;0.000162)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		TGTTCATGACAGTGCCGTCAG	0.662													G|||	3268	0.652556	0.7216	0.4582	5008	,	,		15224	0.7639		0.5944	False		,,,				2504	0.6421				p.T117T		Atlas-SNP	.											.	HSPB7	17	.	0			c.T351C						PASS	.	G		3071,1335	442.7+/-346.8	1073,925,205	51.0	49.0	50.0		351	-9.8	0.0	1	dbSNP_89	50	5031,3567	513.5+/-378.2	1488,2055,756	no	coding-synonymous	HSPB7	NM_014424.4		2561,2980,961	GG,GA,AA		41.4864,30.2996,37.6961		117/171	16342237	8102,4902	2203	4299	6502	SO:0001819	synonymous_variant	27129	exon3			CATGACAGTGCCG	AF155908	CCDS30611.1	1p36.23-p34.3	2011-09-02	2002-08-29		ENSG00000173641	ENSG00000173641		"""Heat shock proteins / HSPB"""	5249	protein-coding gene	gene with protein product		610692	"""heat shock 27kD protein family, member 7 (cardiovascular)"""			10593960	Standard	NM_014424		Approved	cvHSP	uc001axo.2	Q9UBY9	OTTHUMG00000009531	ENST00000311890.9:c.351T>C	1.37:g.16342237A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_014424	B3KQ37|C9K0Y0|Q9NU17	Silent	SNP	ENST00000311890.9	37	CCDS30611.1																																																																																			A|0.376;G|0.624	0.624	strong		0.662	HSPB7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026334.2	NM_014424	
SLC16A6	9120	hgsc.bcm.edu	37	17	66267691	66267691	+	Missense_Mutation	SNP	A	A	T	rs7222013	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:66267691A>T	ENST00000327268.4	-	6	774	c.610T>A	c.(610-612)Ttt>Att	p.F204I	ARSG_ENST00000448504.2_Intron|SLC16A6_ENST00000580666.1_Missense_Mutation_p.F204I	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	204			F -> I (in dbSNP:rs7222013). {ECO:0000269|PubMed:9425115}.		monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	CCTCTGATAAAGATGGGTCTG	0.473													T|||	1901	0.379593	0.6853	0.3746	5008	,	,		18980	0.247		0.1928	False		,,,				2504	0.2986				p.F204I		Atlas-SNP	.											.	SLC16A6	56	.	0			c.T610A						PASS	.	T	ILE/PHE,ILE/PHE,	2758,1648	505.9+/-366.3	868,1022,313	116.0	112.0	113.0		610,610,	-0.5	0.0	17	dbSNP_116	113	2012,6588	722.1+/-406.4	239,1534,2527	yes	missense,missense,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	21,21,	1107,2556,2840	TT,TA,AA		23.3953,37.4035,36.6754	benign,benign,	204/524,204/524,	66267691	4770,8236	2203	4300	6503	SO:0001583	missense	9120	exon6			TGATAAAGATGGG	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.610T>A	17.37:g.66267691A>T	ENSP00000319991:p.Phe204Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	156	74	0.474359	NM_001174166	Q6P1X3	Missense_Mutation	SNP	ENST00000327268.4	37	CCDS11675.1	725	0.33195970695970695	326	0.6626016260162602	133	0.3674033149171271	137	0.2395104895104895	129	0.17018469656992086	T	0.008	-1.881272	0.00532	0.625965	0.233953	ENSG00000108932	ENST00000327268	T	0.03889	3.77	4.33	-0.528	0.11905	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.619301	0.16867	N	0.196264	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.08493	-1.0719	9	0.33141	T	0.24	.	6.1866	0.20500	0.1265:0.4151:0.0:0.4584	rs7222013;rs7222013	204	O15403	MOT7_HUMAN	I	204	ENSP00000319991:F204I	ENSP00000319991:F204I	F	-	1	0	SLC16A6	63779286	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-2.006000	0.01459	-0.690000	0.05142	-0.514000	0.04452	TTT	A|0.636;T|0.364	0.364	strong		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
OBSCN	84033	hgsc.bcm.edu	37	1	228505204	228505204	+	Missense_Mutation	SNP	G	G	A	rs4653942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228505204G>A	ENST00000422127.1	+	52	13645	c.13601G>A	c.(13600-13602)cGc>cAc	p.R4534H	OBSCN_ENST00000366707.4_Missense_Mutation_p.R2168H|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1653H|OBSCN_ENST00000284548.11_Missense_Mutation_p.R4534H|OBSCN_ENST00000570156.2_Missense_Mutation_p.R5491H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4534	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> H (in dbSNP:rs4653942). {ECO:0000269|PubMed:11448995}.		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTGGTGGCTCGCAGCAGCCAC	0.657													g|||	1579	0.315296	0.3941	0.2954	5008	,	,		15262	0.499		0.1869	False		,,,				2504	0.1656				p.R5491H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16472A						PASS	.		HIS/ARG,HIS/ARG	1547,2561		304,939,811	28.0	32.0	31.0		13601,13601	2.4	0.0	1	dbSNP_111	31	1632,6764		158,1316,2724	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	462,2255,3535	AA,AG,GG		19.4378,37.6582,25.4239	probably-damaging,probably-damaging	4534/7969,4534/6621	228505204	3179,9325	2054	4198	6252	SO:0001583	missense	84033	exon63			TGGCTCGCAGCAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13601G>A	1.37:g.228505204G>A	ENSP00000409493:p.Arg4534His	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	735	0.33653846153846156	188	0.3821138211382114	111	0.30662983425414364	288	0.5034965034965035	148	0.19525065963060687	g	13.05	2.120013	0.37436	0.376582	0.194378	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	4.42	2.36	0.29203	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.565277	0.16104	N	0.229422	T	0.00012	0.0000	L	0.28649	0.875	0.80722	P	0.0	P;D	0.64830	0.702;0.994	B;P	0.52672	0.295;0.706	T	0.44513	-0.9323	9	0.45353	T	0.12	.	2.8707	0.05616	0.3981:0.2307:0.3712:0.0	rs4653942;rs4653942	4534;4534	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	4534;4534;2168;1653	ENSP00000284548:R4534H;ENSP00000409493:R4534H;ENSP00000355668:R2168H;ENSP00000355670:R1653H	ENSP00000284548:R4534H	R	+	2	0	OBSCN	226571827	0.043000	0.20138	0.007000	0.13788	0.029000	0.11900	1.330000	0.33781	1.099000	0.41499	0.479000	0.44913	CGC	G|0.671;A|0.329	0.329	strong		0.657	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45479055	45479055	+	Silent	SNP	C	C	T	rs2838475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45479055C>T	ENST00000291574.4	+	6	925	c.750C>T	c.(748-750)gaC>gaT	p.D250D	TRAPPC10_ENST00000380221.3_Silent_p.D250D	NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	250					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						ACGAACTGGACGCCCTCTTCT	0.507													C|||	275	0.0549121	0.0129	0.0576	5008	,	,		16057	0.0506		0.1093	False		,,,				2504	0.0583				p.D250D		Atlas-SNP	.											.	TRAPPC10	109	.	0			c.C750T						PASS	.	C		113,4293	86.8+/-125.4	3,107,2093	72.0	59.0	63.0		750	1.0	1.0	21	dbSNP_100	63	905,7695	201.3+/-244.8	60,785,3455	no	coding-synonymous	TRAPPC10	NM_003274.4		63,892,5548	TT,TC,CC		10.5233,2.5647,7.8272		250/1260	45479055	1018,11988	2203	4300	6503	SO:0001819	synonymous_variant	7109	exon6			ACTGGACGCCCTC	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.750C>T	21.37:g.45479055C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	24	0.358209	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																			C|0.929;T|0.071	0.071	strong		0.507	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
TMEM133	83935	hgsc.bcm.edu	37	11	100863319	100863319	+	Missense_Mutation	SNP	A	A	C	rs61995873	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:100863319A>C	ENST00000303130.2	+	1	509	c.280A>C	c.(280-282)Aat>Cat	p.N94H		NM_032021.2	NP_114410.1	Q9H2Q1	TM133_HUMAN	transmembrane protein 133	94						integral component of membrane (GO:0016021)				kidney(2)|large_intestine(1)|lung(1)|prostate(1)	5		Acute lymphoblastic leukemia(157;0.000869)|all_hematologic(158;0.014)		BRCA - Breast invasive adenocarcinoma(274;0.0675)		AACTGGTCTCAATTTCCTGAA	0.413													A|||	351	0.0700879	0.0	0.1081	5008	,	,		20706	0.1855		0.0467	False		,,,				2504	0.0429				p.N94H		Atlas-SNP	.											.	TMEM133	9	.	0			c.A280C						PASS	.	A	HIS/ASN	56,4350	56.8+/-93.2	0,56,2147	189.0	176.0	180.0		280	-0.5	0.0	11	dbSNP_129	180	398,8202	127.0+/-185.4	7,384,3909	yes	missense	TMEM133	NM_032021.2	68	7,440,6056	CC,CA,AA		4.6279,1.271,3.4907	benign	94/130	100863319	454,12552	2203	4300	6503	SO:0001583	missense	83935	exon1			GGTCTCAATTTCC	AF247167	CCDS8309.1	11q22.1	2006-03-09				ENSG00000170647			24033	protein-coding gene	gene with protein product						12477932	Standard	NM_032021		Approved	AD031	uc001pgf.3	Q9H2Q1		ENST00000303130.2:c.280A>C	11.37:g.100863319A>C	ENSP00000303999:p.Asn94His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	120	69	0.575	NM_032021		Missense_Mutation	SNP	ENST00000303130.2	37	CCDS8309.1	187	0.08562271062271062	0	0.0	38	0.10497237569060773	116	0.20279720279720279	33	0.04353562005277045	A	7.288	0.610544	0.14066	0.01271	0.046279	ENSG00000170647	ENST00000303130	.	.	.	4.59	-0.537	0.11872	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.26809	0.16	B	0.29598	0.104	T	0.28554	-1.0040	7	0.87932	D	0	.	4.1765	0.10355	0.4575:0.35:0.1925:0.0	rs61995873	94	Q9H2Q1	TM133_HUMAN	H	94	.	ENSP00000303999:N94H	N	+	1	0	TMEM133	100368529	0.001000	0.12720	0.005000	0.12908	0.024000	0.10985	0.962000	0.29280	0.017000	0.15025	0.533000	0.62120	AAT	A|0.949;C|0.051	0.051	strong		0.413	TMEM133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395137.1	NM_032021	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383137	41383137	+	Silent	SNP	C	C	T	rs148915421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41383137C>T	ENST00000301146.4	-	7	1660	c.1119G>A	c.(1117-1119)agG>agA	p.R373R	CYP2A7_ENST00000291764.3_Silent_p.R322R|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	373						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			CCTTTTTAACCCTGCGGGCCA	0.542													.|||	59	0.0117812	0.0	0.0144	5008	,	,		18858	0.002		0.0457	False		,,,				2504	0.001				p.R373R		Atlas-SNP	.											CYP2A7,NS,carcinoma,-1,1	CYP2A7	71	1	0			c.G1119A						PASS	.	C	,	23,4383	28.1+/-56.4	0,23,2180	103.0	91.0	95.0		1119,966	-1.3	0.0	19	dbSNP_134	95	283,8315	98.8+/-160.4	14,255,4030	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	14,278,6210	TT,TC,CC		3.2915,0.522,2.3531	,	373/495,322/444	41383137	306,12698	2203	4299	6502	SO:0001819	synonymous_variant	1549	exon7			TTTAACCCTGCGG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1119G>A	19.37:g.41383137C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	213	94	0.441315	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			C|0.978;T|0.022	0.022	strong		0.542	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42439376	42439376	+	Silent	SNP	G	G	A	rs4923929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:42439376G>A	ENST00000382396.4	-	13	1451	c.1365C>T	c.(1363-1365)agC>agT	p.S455S	PLA2G4F_ENST00000397272.3_Silent_p.S457S			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	455	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid secretion (GO:0050482)|cellular response to antibiotic (GO:0071236)|cellular response to organic cyclic compound (GO:0071407)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|ruffle membrane (GO:0032587)|vesicle (GO:0031982)	calcium-dependent phospholipase A2 activity (GO:0047498)|lysophospholipase activity (GO:0004622)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(109;4.82e-12)|all_epithelial(112;5.64e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(94;8.97e-07)		TGAGGGACACGCTGTGGCCAC	0.582													G|||	2052	0.409744	0.534	0.3718	5008	,	,		17590	0.246		0.496	False		,,,				2504	0.3487				p.S455S		Atlas-SNP	.											PLA2G4F,NS,carcinoma,0,1	PLA2G4F	75	1	0			c.C1365T						PASS	.	G		2322,2084	604.0+/-390.2	600,1122,481	58.0	53.0	55.0		1365	-5.2	0.0	15	dbSNP_111	55	4084,4514	559.5+/-387.4	978,2128,1193	no	coding-synonymous	PLA2G4F	NM_213600.3		1578,3250,1674	AA,AG,GG		47.4994,47.2991,49.2618		455/850	42439376	6406,6598	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon13			GGACACGCTGTGG		CCDS32204.1	15q15.1	2008-09-19				ENSG00000168907	3.1.1.4		27396	protein-coding gene	gene with protein product						14702039, 15866882	Standard	NM_213600		Approved	PLA2G4F/Z	uc001zoz.3	Q68DD2		ENST00000382396.4:c.1365C>T	15.37:g.42439376G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	17	8	0.470588	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.534;A|0.466	0.466	strong		0.582	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
NEIL1	79661	hgsc.bcm.edu	37	15	75641682	75641682	+	Splice_Site	SNP	T	T	C	rs5745908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75641682T>C	ENST00000564784.1	+	3	1063		c.e3+2		NEIL1_ENST00000355059.4_Splice_Site|NEIL1_ENST00000567959.1_Intron|NEIL1_ENST00000569035.1_Splice_Site			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)						base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						GCAGTTCAGGTAGGGCCAGCA	0.632								Base excision repair (BER), DNA glycosylases					T|||	14	0.00279553	0.0	0.0072	5008	,	,		14728	0.0		0.008	False		,,,				2504	0.001				.		Atlas-SNP	.											.	NEIL1	36	.	0			c.434+2T>C						PASS	.	T		7,4251		0,7,2122	18.0	20.0	20.0			5.4	1.0	15	dbSNP_114	20	105,8207		1,103,4052	yes	splice-5	NEIL1	NM_024608.2		1,110,6174	CC,CT,TT		1.2632,0.1644,0.891			75641682	112,12458	2129	4156	6285	SO:0001630	splice_region_variant	79661	exon2			TTCAGGTAGGGCC	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.434+2T>C	15.37:g.75641682T>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_024608	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Splice_Site	SNP	ENST00000564784.1	37	CCDS10278.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	20.9	4.072179	0.76415	0.001644	0.012632	ENSG00000140398	ENST00000355059;ENST00000336572	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5906	0.68362	0.0:0.0:0.0:1.0	rs5745908;rs5745908	.	.	.	.	-1	.	.	.	+	.	.	NEIL1	73428735	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.327000	0.79147	2.042000	0.60477	0.459000	0.35465	.	T|0.993;C|0.007	0.007	strong		0.632	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	Intron
SNAPC2	6618	hgsc.bcm.edu	37	19	7986638	7986638	+	Missense_Mutation	SNP	C	C	G	rs475002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7986638C>G	ENST00000221573.6	+	3	403	c.352C>G	c.(352-354)Ctg>Gtg	p.L118V	SNAPC2_ENST00000595035.1_3'UTR|SNAPC2_ENST00000597584.1_5'UTR|CTD-3193O13.1_ENST00000564226.1_RNA	NM_003083.3	NP_003074.1	Q13487	SNPC2_HUMAN	small nuclear RNA activating complex, polypeptide 2, 45kDa	118			L -> V (in dbSNP:rs475002). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		gene expression (GO:0010467)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						GGAAGAAGCCCTGGCAGTGGC	0.602													C|||	2067	0.41274	0.2156	0.4092	5008	,	,		18527	0.5169		0.5467	False		,,,				2504	0.4366				p.L118V		Atlas-SNP	.											.	SNAPC2	20	.	0			c.C352G						PASS	.	C	VAL/LEU	1242,3164	419.6+/-338.7	175,892,1136	49.0	48.0	48.0		352	-0.5	0.8	19	dbSNP_83	48	4808,3790	607.1+/-395.2	1372,2064,863	yes	missense	SNAPC2	NM_003083.3	32	1547,2956,1999	GG,GC,CC		44.08,28.1888,46.5241	probably-damaging	118/335	7986638	6050,6954	2203	4299	6502	SO:0001583	missense	6618	exon3			GAAGCCCTGGCAG	U44898	CCDS12190.1	19p13	2008-07-22	2002-08-29			ENSG00000104976			11135	protein-coding gene	gene with protein product		605076	"""small nuclear RNA activating complex, polypeptide 2, 45kD"""			8633057	Standard	NM_003083		Approved	SNAP45, PTFdelta	uc002miw.2	Q13487		ENST00000221573.6:c.352C>G	19.37:g.7986638C>G	ENSP00000221573:p.Leu118Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_003083	B2RBZ6|D6W663|Q13486	Missense_Mutation	SNP	ENST00000221573.6	37	CCDS12190.1	974	0.445970695970696	120	0.24390243902439024	158	0.43646408839779005	288	0.5034965034965035	408	0.5382585751978892	c	15.72	2.916868	0.52546	0.281888	0.5592	ENSG00000104976	ENST00000221573	T	0.49139	0.79	4.71	-0.458	0.12182	.	0.198865	0.29861	N	0.011020	T	0.00012	0.0000	M	0.72118	2.19	0.52501	P	4.4000000000044004E-5	D	0.63046	0.992	D	0.63192	0.912	T	0.45131	-0.9282	9	0.54805	T	0.06	-14.4343	1.3297	0.02132	0.1835:0.4591:0.1586:0.1988	rs475002;rs1131167;rs11551333;rs475002	118	Q13487	SNPC2_HUMAN	V	118	ENSP00000221573:L118V	ENSP00000221573:L118V	L	+	1	2	SNAPC2	7892638	0.001000	0.12720	0.817000	0.32601	0.832000	0.47134	-0.315000	0.08081	0.200000	0.20447	0.556000	0.70494	CTG	C|0.546;G|0.454	0.454	strong		0.602	SNAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461358.1	NM_003083	
KIAA0226	9711	hgsc.bcm.edu	37	3	197427557	197427557	+	Silent	SNP	A	A	G	rs28394098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:197427557A>G	ENST00000296343.5	-	7	1187	c.1188T>C	c.(1186-1188)acT>acC	p.T396T	KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000449205.1_Silent_p.T396T|KIAA0226_ENST00000389665.5_Silent_p.T396T|KIAA0226_ENST00000273582.5_Silent_p.T336T	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	396	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		CACTGGTGACAGTGAGTGTCT	0.577													G|||	697	0.139177	0.3169	0.0677	5008	,	,		17652	0.0308		0.1034	False		,,,				2504	0.0982				p.T396T	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.T1188C						PASS	.	G	,	1134,2944		137,860,1042	77.0	80.0	79.0		1008,1188	-2.2	0.0	3	dbSNP_125	79	789,7585		38,713,3436	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	175,1573,4478	GG,GA,AA		9.422,27.8077,15.4433	,	336/928,396/973	197427557	1923,10529	2039	4187	6226	SO:0001819	synonymous_variant	9711	exon7			GGTGACAGTGAGT	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1188T>C	3.37:g.197427557A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	153	71	0.464052	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	271|271	0.12408424908424909|0.12408424908424909	142|142	0.2886178861788618|0.2886178861788618	27|27	0.07458563535911603|0.07458563535911603	24|24	0.04195804195804196|0.04195804195804196	78|78	0.10290237467018469|0.10290237467018469	G|G	6.290|6.290	0.421625|0.421625	0.11928|0.11928	0.278077|0.278077	0.09422|0.09422	ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452	.|.	.|.	.|.	5.85|5.85	-2.21|-2.21	0.06973|0.06973	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.33033|0.33033	-0.9884|-0.9884	3|3	.|.	.|.	.|.	.|.	7.4519|7.4519	0.27244|0.27244	0.411:0.2206:0.3684:0.0|0.411:0.2206:0.3684:0.0	rs28394098|rs28394098	.|.	.|.	.|.	R|P	375|155	.|.	.|.	C|L	-|-	1|2	0|0	KIAA0226|KIAA0226	198911954|198911954	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.820000|0.820000	0.46376|0.46376	-0.445000|-0.445000	0.06845|0.06845	-0.698000|-0.698000	0.05085|0.05085	-1.073000|-1.073000	0.02249|0.02249	TGT|CTG	A|0.885;G|0.115	0.115	strong		0.577	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95084131	95084131	+	Silent	SNP	G	G	A	rs34896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:95084131G>A	ENST00000379982.3	+	4	1018	c.510G>A	c.(508-510)gcG>gcA	p.A170A		NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	170	Rho-like.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		AACTAGGAGCGACCTATCTTG	0.418													G|||	2269	0.453075	0.2784	0.3343	5008	,	,		15976	0.6905		0.4294	False		,,,				2504	0.5532				p.A170A		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.G510A						PASS	.	G		1347,3059	448.1+/-348.6	202,943,1058	116.0	109.0	111.0		510	-12.1	0.4	5	dbSNP_76	111	3574,5026	518.5+/-379.3	731,2112,1457	no	coding-synonymous	RHOBTB3	NM_014899.3		933,3055,2515	AA,AG,GG		41.5581,30.5719,37.8364		170/612	95084131	4921,8085	2203	4300	6503	SO:0001819	synonymous_variant	22836	exon4			AGGAGCGACCTAT	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.510G>A	5.37:g.95084131G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_014899	A0PJA4|A8K1W9|Q8IW06	Silent	SNP	ENST00000379982.3	37	CCDS4077.1																																																																																			A|0.416;C|0.001	0.416	strong		0.418	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
UBXN11	91544	hgsc.bcm.edu	37	1	26608877	26608877	+	Silent	SNP	G	G	A	rs1134582|rs140364749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608877G>A	ENST00000374222.1	-	16	1940	c.1476C>T	c.(1474-1476)ggC>ggT	p.G492G	UBXN11_ENST00000314675.7_Silent_p.G372G|UBXN11_ENST00000374217.2_Silent_p.G459G|UBXN11_ENST00000357089.4_Silent_p.G459G|UBXN11_ENST00000374223.1_Silent_p.G249G|UBXN11_ENST00000374221.3_Silent_p.G492G			Q5T124	UBX11_HUMAN	UBX domain protein 11	492	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						cgggactggggccgggaccgg	0.721																																					p.G492G		Atlas-SNP	.											UBXN11,NS,carcinoma,0,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.C1476T						scavenged	.						33.0	40.0	38.0					1																	26608877		1787	4040	5827	SO:0001819	synonymous_variant	91544	exon16			ACTGGGGCCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1476C>T	1.37:g.26608877G>A		Somatic	33	4	0.121212		WXS	Illumina HiSeq	Phase_I	49	39	0.795918	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			G|0.870;A|0.130	0.130	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
OR52E6	390078	hgsc.bcm.edu	37	11	5862416	5862416	+	Missense_Mutation	SNP	C	C	T	rs61735020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5862416C>T	ENST00000329322.5	-	1	711	c.712G>A	c.(712-714)Gct>Act	p.A238T	OR52E6_ENST00000379946.2_Missense_Mutation_p.A242T|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGTTGAGAGCTTTGAGTCGA	0.443													C|||	43	0.00858626	0.0008	0.013	5008	,	,		19247	0.0		0.0308	False		,,,				2504	0.002				p.A238T		Atlas-SNP	.											.	OR52E6	70	.	0			c.G712A						PASS	.	C	THR/ALA	30,4364	31.7+/-61.6	0,30,2167	64.0	65.0	65.0		712	3.2	0.5	11	dbSNP_129	65	271,8317	102.3+/-163.5	5,261,4028	yes	missense	OR52E6	NM_001005167.1	58	5,291,6195	TT,TC,CC		3.1556,0.6827,2.3186	probably-damaging	238/314	5862416	301,12681	2197	4294	6491	SO:0001583	missense	390078	exon1			TGAGAGCTTTGAG	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.712G>A	11.37:g.5862416C>T	ENSP00000328878:p.Ala238Thr	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	60	0.487805	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	31	0.014194139194139194	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	27	0.03562005277044855	C	15.10	2.732139	0.48939	0.006827	0.031556	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00357	7.89;7.89	3.23	3.23	0.37069	GPCR, rhodopsin-like superfamily (1);	0.110508	0.40144	N	0.001174	T	0.00144	0.0004	M	0.67397	2.05	0.40032	D	0.975546	D	0.53462	0.96	P	0.54924	0.764	D	0.84518	0.0626	10	0.51188	T	0.08	.	13.1659	0.59571	0.0:1.0:0.0:0.0	rs61735020	238	Q96RD3	O52E6_HUMAN	T	238;242	ENSP00000328878:A238T;ENSP00000369279:A242T	ENSP00000328878:A238T	A	-	1	0	OR52E6	5818992	0.998000	0.40836	0.504000	0.27639	0.080000	0.17528	3.007000	0.49536	1.631000	0.50456	0.551000	0.68910	GCT	C|0.984;T|0.016	0.016	strong		0.443	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
ZNF132	7691	hgsc.bcm.edu	37	19	58946056	58946056	+	Missense_Mutation	SNP	G	G	A	rs1465789	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58946056G>A	ENST00000254166.3	-	3	1155	c.755C>T	c.(754-756)cCc>cTc	p.P252L		NM_003433.3	NP_003424.3	P52740	ZN132_HUMAN	zinc finger protein 132	252			P -> L (in dbSNP:rs1465789).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(1)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_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;0.0171)|Lung(386;0.182)		CAGATGGTTGGGGAGAGTGGA	0.443													A|||	2507	0.500599	0.7882	0.3818	5008	,	,		21770	0.3264		0.494	False		,,,				2504	0.3824				p.P252L		Atlas-SNP	.											.	ZNF132	56	.	0			c.C755T						PASS	.	A	LEU/PRO	3372,1034	379.7+/-323.4	1299,774,130	99.0	100.0	99.0		755	1.0	0.0	19	dbSNP_88	99	4115,4485	589.8+/-392.6	995,2125,1180	yes	missense	ZNF132	NM_003433.3	98	2294,2899,1310	AA,AG,GG		47.8488,23.468,42.4343	benign	252/707	58946056	7487,5519	2203	4300	6503	SO:0001583	missense	7691	exon3			TGGTTGGGGAGAG	U09411	CCDS12980.1	19q13.4	2013-01-08	2006-06-13			ENSG00000131849		"""Zinc fingers, C2H2-type"", ""-"""	12916	protein-coding gene	gene with protein product		604074	"""zinc finger protein 132 (clone pHZ-12)"""			7557990	Standard	NM_003433		Approved	pHZ-12	uc002qst.4	P52740		ENST00000254166.3:c.755C>T	19.37:g.58946056G>A	ENSP00000254166:p.Pro252Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	117	39	0.333333	NM_003433	Q32MI9	Missense_Mutation	SNP	ENST00000254166.3	37	CCDS12980.1	1102	0.5045787545787546	397	0.806910569105691	151	0.4171270718232044	184	0.32167832167832167	370	0.48812664907651715	A	0.024	-1.387674	0.01194	0.76532	0.478488	ENSG00000131849	ENST00000254166;ENST00000391695	T	0.13538	2.58	3.12	0.98	0.19750	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09314	-1.0680	8	0.19147	T	0.46	.	3.7082	0.08408	0.511:0.0:0.3223:0.1667	rs1465789;rs17669697;rs60250577;rs1465789	252	P52740	ZN132_HUMAN	L	252;163	ENSP00000254166:P252L	ENSP00000254166:P252L	P	-	2	0	ZNF132	63637868	0.000000	0.05858	0.002000	0.10522	0.024000	0.10985	-1.739000	0.01840	0.010000	0.14839	-1.062000	0.02293	CCC	G|0.464;A|0.536	0.536	strong		0.443	ZNF132-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467035.1	NM_003433	
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23059324	23059324	+	Missense_Mutation	SNP	C	C	G	rs20575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:23059324C>G	ENST00000221132.3	-	4	690	c.626G>C	c.(625-627)aGa>aCa	p.R209T		NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	209			R -> T (in dbSNP:rs20575). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9082980}.		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)		GTCTCACCCTCTGCTGCACTT	0.532													G|||	2902	0.579473	0.2769	0.6138	5008	,	,		17637	0.9732		0.4553	False		,,,				2504	0.6861				p.R209T		Atlas-SNP	.											.	TNFRSF10A	40	.	0			c.G626C						PASS	.	G	THR/ARG	1393,3013	689.0+/-405.1	205,983,1015	90.0	71.0	77.0		626	0.2	0.0	8	dbSNP_67	77	3944,4656	602.3+/-394.5	924,2096,1280	yes	missense	TNFRSF10A	NM_003844.3	71	1129,3079,2295	GG,GC,CC		45.8605,31.616,41.0349	benign	209/469	23059324	5337,7669	2203	4300	6503	SO:0001583	missense	8797	exon4			CACCCTCTGCTGC	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.626G>C	8.37:g.23059324C>G	ENSP00000221132:p.Arg209Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	1249	0.5718864468864469	129	0.2621951219512195	210	0.580110497237569	561	0.9807692307692307	349	0.4604221635883905	G	0.019	-1.462074	0.01062	0.31616	0.458605	ENSG00000104689	ENST00000221132;ENST00000524158	D;T	0.90620	-2.7;1.75	4.2	0.222	0.15288	TNFR/CD27/30/40/95 cysteine-rich region (4);	0.747139	0.11590	N	0.548796	T	0.00012	0.0000	N	0.00043	-2.47	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38499	-0.9658	9	0.02654	T	1	.	4.4761	0.11745	0.2821:0.3084:0.4095:0.0	rs20575;rs4871857;rs11550539;rs17398665;rs17759966;rs52835905;rs60716604;rs4871857	209	O00220	TR10A_HUMAN	T	209;7	ENSP00000221132:R209T;ENSP00000428884:R7T	ENSP00000221132:R209T	R	-	2	0	TNFRSF10A	23115269	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.139000	0.10358	-0.547000	0.06207	-0.738000	0.03535	AGA	C|0.521;G|0.478	0.478	strong		0.532	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
TKTL1	8277	hgsc.bcm.edu	37	X	153537783	153537783	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153537783C>T	ENST00000369915.3	+	3	528	c.339C>T	c.(337-339)ttC>ttT	p.F113F	TKTL1_ENST00000369912.2_Silent_p.F57F|TKTL1_ENST00000217905.7_Intron	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	113					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.F113F(1)		NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCAAGTACTTCGACAGGGCCA	0.537																																					p.F113F		Atlas-SNP	.											.	TKTL1	61	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C339T						PASS	.						252.0	213.0	226.0					X																	153537783		2203	4300	6503	SO:0001819	synonymous_variant	8277	exon3			GTACTTCGACAGG	X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.339C>T	X.37:g.153537783C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Silent	SNP	ENST00000369915.3	37	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	C	4.122	0.020848	0.08006	.	.	ENSG00000007350	ENST00000426203	.	.	.	4.64	-1.03	0.10102	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.2143	4.8078	0.13328	0.0:0.2949:0.1505:0.5547	.	.	.	.	X	96	.	.	R	+	1	2	TKTL1	153190977	0.998000	0.40836	0.927000	0.36925	0.416000	0.31233	0.367000	0.20382	-0.364000	0.08088	-0.380000	0.06706	CGA	.	.	none		0.537	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253	
ABCA12	26154	hgsc.bcm.edu	37	2	215865575	215865575	+	Silent	SNP	T	T	C	rs10498030	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:215865575T>C	ENST00000272895.7	-	22	3252	c.3033A>G	c.(3031-3033)ccA>ccG	p.P1011P	ABCA12_ENST00000389661.4_Silent_p.P693P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1011					cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GGTTGTGTGATGGAGAATTGT	0.433													T|||	979	0.195487	0.0174	0.1945	5008	,	,		18738	0.3433		0.2773	False		,,,				2504	0.2004				p.P1011P	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A3033G						PASS	.	T	,	221,4185	133.3+/-169.7	9,203,1991	160.0	166.0	164.0		2079,3033	1.7	1.0	2	dbSNP_119	164	2191,6409	373.7+/-337.1	300,1591,2409	no	coding-synonymous,coding-synonymous	ABCA12	NM_015657.3,NM_173076.2	,	309,1794,4400	CC,CT,TT		25.4767,5.0159,18.5453	,	693/2278,1011/2596	215865575	2412,10594	2203	4300	6503	SO:0001819	synonymous_variant	26154	exon22			GTGTGATGGAGAA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3033A>G	2.37:g.215865575T>C		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	229	125	0.545852	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			T|0.804;C|0.196	0.196	strong		0.433	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
TPRX1	284355	hgsc.bcm.edu	37	19	48305602	48305602	+	Silent	SNP	C	C	T	rs147608412	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48305602C>T	ENST00000322175.3	-	2	821	c.666G>A	c.(664-666)ccG>ccA	p.P222P	TPRX1_ENST00000543508.1_Silent_p.P212P|TPRX1_ENST00000535759.1_Silent_p.P319P	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	222	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)	p.P228_I231delPGPI(1)		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)		ggcctgggatcgggcctgggt	0.667													C|||	221	0.0441294	0.0295	0.0476	5008	,	,		12917	0.001		0.1103	False		,,,				2504	0.0378				p.P222P	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,NS,carcinoma,-1,1	TPRX1	46	1	1	Deletion - In frame(1)	prostate(1)	c.G666A						PASS	.	T		79,3765		0,79,1843	12.0	10.0	10.0		666	-0.8	0.0	19	dbSNP_134	10	659,7001		14,631,3185	no	coding-synonymous	TPRX1	NM_198479.2		14,710,5028	TT,TC,CC		8.6031,2.0552,6.4152		222/412	48305602	738,10766	1922	3830	5752	SO:0001819	synonymous_variant	284355	exon2			TGGGATCGGGCCT		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.666G>A	19.37:g.48305602C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			C|0.943;T|0.057	0.057	strong		0.667	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
COL27A1	85301	hgsc.bcm.edu	37	9	116931099	116931099	+	Missense_Mutation	SNP	G	G	A	rs2241671	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:116931099G>A	ENST00000356083.3	+	3	1655	c.1264G>A	c.(1264-1266)Gca>Aca	p.A422T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	422	Pro-rich.		A -> T (in dbSNP:rs2241671). {ECO:0000269|PubMed:15489334}.		extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.A422T(1)		central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CTCCCGTCCCGCAGAGAAGCC	0.592													G|||	1885	0.376398	0.3041	0.317	5008	,	,		14098	0.5129		0.4304	False		,,,				2504	0.32				p.A422T		Atlas-SNP	.											COL27A1,NS,carcinoma,0,1	COL27A1	200	1	1	Substitution - Missense(1)	stomach(1)	c.G1264A						PASS	.	G	THR/ALA	1469,2937	473.3+/-356.6	230,1009,964	115.0	137.0	130.0		1264	-8.5	0.0	9	dbSNP_98	130	3717,4883	531.2+/-381.9	788,2141,1371	yes	missense	COL27A1	NM_032888.2	58	1018,3150,2335	AA,AG,GG		43.2209,33.3409,39.8739	benign	422/1861	116931099	5186,7820	2203	4300	6503	SO:0001583	missense	85301	exon3			CGTCCCGCAGAGA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.1264G>A	9.37:g.116931099G>A	ENSP00000348385:p.Ala422Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	900	0.41208791208791207	154	0.3130081300813008	126	0.34806629834254144	303	0.5297202797202797	317	0.4182058047493404	G	8.990	0.977384	0.18812	0.333409	0.432209	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	D;D	0.90676	-2.45;-2.71	4.26	-8.53	0.00916	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B	0.10296	0.0;0.003	B;B	0.06405	0.0;0.002	T	0.22871	-1.0204	8	0.02654	T	1	.	1.1229	0.01728	0.3173:0.2275:0.0884:0.3667	rs2241671;rs17207056;rs57097923;rs2241671	422;369	Q8IZC6;Q5T1U7	CORA1_HUMAN;.	T	422;422;369;369	ENSP00000348385:A422T;ENSP00000391328:A369T	ENSP00000348385:A422T	A	+	1	0	COL27A1	115970920	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.604000	0.05667	-1.614000	0.01575	-2.761000	0.00122	GCA	G|0.596;A|0.404	0.404	strong		0.592	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
FURIN	5045	hgsc.bcm.edu	37	15	91419548	91419548	+	Missense_Mutation	SNP	C	C	T	rs148110342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91419548C>T	ENST00000268171.3	+	3	520	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	81					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GTCGCCTCACCGCCCGCGGCA	0.647													C|||	10	0.00199681	0.0	0.0101	5008	,	,		14336	0.0		0.002	False		,,,				2504	0.001				p.R81C		Atlas-SNP	.											FURIN,NS,carcinoma,-1,1	FURIN	85	1	0			c.C241T						PASS	.	C	CYS/ARG	1,4395	2.1+/-5.4	0,1,2197	62.0	69.0	66.0		241	3.7	1.0	15	dbSNP_134	66	29,8567	19.8+/-62.0	0,29,4269	yes	missense	FURIN	NM_002569.2	180	0,30,6466	TT,TC,CC		0.3374,0.0227,0.2309	probably-damaging	81/795	91419548	30,12962	2198	4298	6496	SO:0001583	missense	5045	exon3			CCTCACCGCCCGC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.241C>T	15.37:g.91419548C>T	ENSP00000268171:p.Arg81Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	4	0.0018315018315018315	0	0.0	4	0.011049723756906077	0	0.0	0	0.0	C	16.37	3.103601	0.56291	2.27E-4	0.003374	ENSG00000140564	ENST00000268171	T	0.32515	1.45	4.58	3.67	0.42095	Proteinase inhibitor, propeptide (1);	0.447962	0.23209	N	0.050699	T	0.35653	0.0939	M	0.85945	2.785	0.52501	D	0.999957	D	0.61080	0.989	P	0.48677	0.586	T	0.43750	-0.9372	10	0.39692	T	0.17	-17.545	11.108	0.48214	0.0:0.9142:0.0:0.0858	.	81	P09958	FURIN_HUMAN	C	81	ENSP00000268171:R81C	ENSP00000268171:R81C	R	+	1	0	FURIN	89220552	0.624000	0.27102	0.998000	0.56505	0.701000	0.40568	1.792000	0.38754	1.170000	0.42753	-0.266000	0.10368	CGC	C|0.998;T|0.002	0.002	strong		0.647	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
NPC1	4864	hgsc.bcm.edu	37	18	21120444	21120444	+	Missense_Mutation	SNP	T	T	C	rs1805082	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:21120444T>C	ENST00000269228.5	-	17	3126	c.2572A>G	c.(2572-2574)Att>Gtt	p.I858V	NPC1_ENST00000412552.2_Missense_Mutation_p.I540V|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	858			I -> V (common polymorphism in Japanese; dbSNP:rs1805082). {ECO:0000269|PubMed:10480349, ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCCAATCCAATATCTACTTTG	0.338													T|||	2433	0.485823	0.3646	0.611	5008	,	,		19289	0.6111		0.4583	False		,,,				2504	0.4601				p.I858V		Atlas-SNP	.											.	NPC1	114	.	0			c.A2572G						PASS	.	T	VAL/ILE	1711,2695	515.2+/-368.8	312,1087,804	109.0	96.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2572	6.1	1.0	18	dbSNP_89	101	4047,4553	556.5+/-386.9	938,2171,1191	yes	missense	NPC1	NM_000271.4	29	1250,3258,1995	CC,CT,TT		47.0581,38.8334,44.2719	benign	858/1279	21120444	5758,7248	2203	4300	6503	SO:0001583	missense	4864	exon17			ATCCAATATCTAC	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2572A>G	18.37:g.21120444T>C	ENSP00000269228:p.Ile858Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	1100	0.5036630036630036	179	0.3638211382113821	201	0.5552486187845304	367	0.6416083916083916	353	0.4656992084432718	T	17.17	3.321358	0.60634	0.388334	0.470581	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.94000	-3.33;-3.33	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.33485	1.01	0.09310	P	0.999999999248751	B;B	0.20671	0.044;0.047	B;B	0.21360	0.034;0.021	T	0.41215	-0.9521	9	0.16420	T	0.52	-30.843	16.6288	0.85011	0.0:0.0:0.0:1.0	rs1805082;rs17797474;rs1805082	869;858	Q59GR1;O15118	.;NPC1_HUMAN	V	858;540;703	ENSP00000269228:I858V;ENSP00000408606:I540V	ENSP00000269228:I858V	I	-	1	0	NPC1	19374442	1.000000	0.71417	0.985000	0.45067	0.934000	0.57294	4.947000	0.63583	2.326000	0.78906	0.533000	0.62120	ATT	T|0.533;C|0.467	0.467	strong		0.338	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
CCDC79	283847	hgsc.bcm.edu	37	16	66792714	66792714	+	Missense_Mutation	SNP	T	T	C	rs363156	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:66792714T>C	ENST00000558713.2	-	17	2030	c.1958A>G	c.(1957-1959)cAa>cGa	p.Q653R	CCDC79_ENST00000433574.1_3'UTR|CCDC79_ENST00000415744.1_3'UTR|CCDC79_ENST00000432602.1_Missense_Mutation_p.Q606R|CCDC79_ENST00000433154.1_Missense_Mutation_p.Q653R			Q8NA31	TERB1_HUMAN	coiled-coil domain containing 79	653	Interaction with TERF1. {ECO:0000250}.				meiotic telomere clustering (GO:0045141)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|skin(2)	7						ACTGAGTCGTTGTCTTCTACG	0.348													T|||	1722	0.34385	0.0681	0.3963	5008	,	,		17640	0.6161		0.3479	False		,,,				2504	0.3947				p.Q653R		Atlas-SNP	.											.	CCDC79	32	.	0			c.A1958G						PASS	.	T	ARG/GLN	172,1212		16,140,536	213.0	172.0	185.0		1958	-7.6	0.0	16	dbSNP_79	185	1152,2030		210,732,649	yes	missense	CCDC79	NM_001136505.1	43	226,872,1185	CC,CT,TT		36.2036,12.4277,28.9969	benign	653/728	66792714	1324,3242	692	1591	2283	SO:0001583	missense	283847	exon18			AGTCGTTGTCTTC	AK093213		16q22.1	2012-10-03			ENSG00000249961	ENSG00000249961			26675	protein-coding gene	gene with protein product							Standard	NM_001136505		Approved	FLJ35894	uc010viv.2	Q8NA31	OTTHUMG00000133562	ENST00000558713.2:c.1958A>G	16.37:g.66792714T>C	ENSP00000462883:p.Gln653Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001136505	A0AUW1	Missense_Mutation	SNP	ENST00000558713.2	37		804	0.36813186813186816	38	0.07723577235772358	148	0.4088397790055249	360	0.6293706293706294	258	0.3403693931398417	T	7.896	0.733318	0.15574	0.124277	0.362036	ENSG00000177461	ENST00000433154;ENST00000432602	.	.	.	4.96	-7.59	0.01308	.	.	.	.	.	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45848	-0.9233	7	0.02654	T	1	-2.038	14.4873	0.67626	0.0:0.2195:0.0:0.7805	rs363156;rs17700107;rs61213912;rs363156	653	Q8NA31	CCD79_HUMAN	R	653;606	.	ENSP00000446376:Q606R	Q	-	2	0	CCDC79	65350215	0.013000	0.17824	0.000000	0.03702	0.728000	0.41692	-1.224000	0.02959	-1.282000	0.02396	-1.010000	0.02471	CAA	T|0.651;C|0.349	0.349	strong		0.348	CCDC79-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000418864.2		
DYNC2H1	79659	hgsc.bcm.edu	37	11	103082558	103082558	+	Silent	SNP	A	A	G	rs17394217	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:103082558A>G	ENST00000375735.2	+	54	8724	c.8580A>G	c.(8578-8580)gaA>gaG	p.E2860E	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.E2860E	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	2860	AAA 4. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		TAATCCATGAATCTTGTAAAG	0.264													A|||	389	0.0776757	0.0023	0.0922	5008	,	,		14624	0.0923		0.1243	False		,,,				2504	0.1063				p.E2860E		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.A8580G						PASS	.	A	,	85,3421		2,81,1670	29.0	26.0	27.0		8580,8580	-3.2	1.0	11	dbSNP_123	27	847,7065		40,767,3149	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	42,848,4819	GG,GA,AA		10.7053,2.4244,8.1626	,	2860/4315,2860/4308	103082558	932,10486	1753	3956	5709	SO:0001819	synonymous_variant	79659	exon54			CCATGAATCTTGT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.8580A>G	11.37:g.103082558A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			A|0.913;G|0.087	0.087	strong		0.264	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
KRT8	3856	hgsc.bcm.edu	37	12	53298775	53298775	+	5'UTR	SNP	A	A	T	rs137898974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:53298775A>T	ENST00000552551.1	-	0	423				KRT8_ENST00000293308.6_5'UTR|KRT8_ENST00000546897.1_5'UTR|KRT8_ENST00000552150.1_Silent_p.P25P			P05787	K2C8_HUMAN	keratin 8						cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	TGGTAGAGGCAGGAGTGGAGG	0.602													a|||	211	0.0421326	0.0038	0.072	5008	,	,		15642	0.0		0.1312	False		,,,				2504	0.0245				p.P25P		Atlas-SNP	.											.	KRT8	41	.	0			c.T75A						PASS	.	A		69,3037		0,69,1484	9.0	10.0	10.0			0.6	0.9	12	dbSNP_134	10	648,5684		31,586,2549	no	utr-5	KRT8	NM_002273.3		31,655,4033	TT,TA,AA		10.2337,2.2215,7.5969			53298775	717,8721	1553	3166	4719	SO:0001623	5_prime_UTR_variant	3856	exon2			AGAGGCAGGAGTG	BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.-10T>A	12.37:g.53298775A>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Silent	SNP	ENST00000552551.1	37	CCDS8841.1																																																																																			A|0.935;T|0.065	0.065	strong		0.602	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
KDM2B	84678	hgsc.bcm.edu	37	12	121880520	121880520	+	Silent	SNP	G	G	A	rs3751131	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121880520G>A	ENST00000377071.4	-	19	2796	c.2724C>T	c.(2722-2724)gaC>gaT	p.D908D	KDM2B_ENST00000377069.4_Silent_p.D839D|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Silent_p.D276D	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	908					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						AGCGGGAGTGGTCGCTCTCCC	0.706													G|||	1675	0.334465	0.1566	0.4006	5008	,	,		12186	0.4534		0.4046	False		,,,				2504	0.3333				p.D908D		Atlas-SNP	.											KDM2B_ENST00000377071,colon,carcinoma,-2,2	KDM2B	218	2	0			c.C2724T						PASS	.	G	,	708,3046		79,550,1248	12.0	13.0	13.0		2517,2724	2.2	1.0	12	dbSNP_107	13	3078,5096		591,1896,1600	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	670,2446,2848	AA,AG,GG		37.656,18.8599,31.7404	,	839/1266,908/1337	121880520	3786,8142	1877	4087	5964	SO:0001819	synonymous_variant	84678	exon19			GGAGTGGTCGCTC	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2724C>T	12.37:g.121880520G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	109	62	0.568807	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.651;A|0.349	0.349	strong		0.706	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33052981	33052981	+	Missense_Mutation	SNP	C	C	A	rs14362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33052981C>A	ENST00000418931.2	+	3	735	c.619C>A	c.(619-621)Ctg>Atg	p.L207M		NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	207	Beta-2.|Ig-like C1-type.		L -> M (in allele DPB1*04:02; dbSNP:rs14362).		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						GCACACCAGCCTGGATAGTCC	0.577													.|||	399	0.0796725	0.0076	0.2464	5008	,	,		19666	0.0367		0.1163	False		,,,				2504	0.0654				p.L207M		Atlas-SNP	.											.	HLA-DPB1	28	.	0			c.C619A						PASS	.	C	MET/LEU	87,2933		2,83,1425	78.0	82.0	80.0		619	4.0	1.0	6	dbSNP_52	80	597,4819		39,519,2150	yes	missense	HLA-DPB1	NM_002121.5	15	41,602,3575	AA,AC,CC		11.0229,2.8808,8.1081	probably-damaging	207/259	33052981	684,7752	1510	2708	4218	SO:0001583	missense	3115	exon3			ACCAGCCTGGATA		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.619C>A	6.37:g.33052981C>A	ENSP00000408146:p.Leu207Met	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	219	107	0.488584	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	232	0.10622710622710622	6	0.012195121951219513	101	0.27900552486187846	30	0.05244755244755245	95	0.12532981530343007	C	15.53	2.861071	0.51482	0.028808	0.110229	ENSG00000223865	ENST00000418931;ENST00000411942;ENST00000422592;ENST00000428835	T;T	0.04758	3.56;3.56	4.04	4.04	0.47022	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.089667	0.47093	D	0.000258	T	0.12689	0.0308	M	0.91459	3.21	0.09310	P	1.0	P;B;B	0.40398	0.716;0.208;0.208	P;P;B	0.51101	0.659;0.489;0.443	T	0.00525	-1.1689	9	0.49607	T	0.09	.	14.0872	0.64964	0.0:1.0:0.0:0.0	rs14362;rs1042355;rs3176965;rs10947383;rs17358460;rs17398327;rs58897057	173;217;207	A2ALJ6;Q59GY1;P04440	.;.;DPB1_HUMAN	M	207;177;18;184	ENSP00000408146:L207M;ENSP00000412654:L184M	ENSP00000389210:L177M	L	+	1	2	HLA-DPB1	33160959	1.000000	0.71417	0.983000	0.44433	0.982000	0.71751	2.741000	0.47426	2.257000	0.74773	0.544000	0.68410	CTG	C|0.874;A|0.126	0.126	strong		0.577	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
DHODH	1723	hgsc.bcm.edu	37	16	72055078	72055078	+	Silent	SNP	G	G	A	rs148523165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:72055078G>A	ENST00000219240.4	+	5	594	c.573G>A	c.(571-573)gcG>gcA	p.A191A	DHODH_ENST00000572887.1_Silent_p.A191A|DHODH_ENST00000573922.1_Intron	NM_001361.4	NP_001352.2	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase (quinone)	191					'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of apoptotic process (GO:0043065)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of mitochondrial fission (GO:0090140)|response to caffeine (GO:0031000)|response to drug (GO:0042493)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|neuronal cell body (GO:0043025)	dihydroorotate dehydrogenase activity (GO:0004152)|dihydroorotate oxidase activity (GO:0004158)|drug binding (GO:0008144)|FMN binding (GO:0010181)|ubiquinone binding (GO:0048039)			breast(1)|endometrium(2)|large_intestine(4)|ovary(1)|skin(1)|stomach(1)	10		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)|Teriflunomide(DB08880)	TGGACGCCGCGGAGGACTACG	0.642													G|||	17	0.00339457	0.0008	0.0	5008	,	,		16661	0.0		0.0099	False		,,,				2504	0.0061				p.A191A		Atlas-SNP	.											.	DHODH	33	.	0			c.G573A						PASS	.	G		13,4125		0,13,2056	33.0	44.0	40.0		573	-5.8	0.0	16	dbSNP_134	40	105,8249		0,105,4072	no	coding-synonymous	DHODH	NM_001361.4		0,118,6128	AA,AG,GG		1.2569,0.3142,0.9446		191/396	72055078	118,12374	2069	4177	6246	SO:0001819	synonymous_variant	1723	exon5			CGCCGCGGAGGAC		CCDS42192.1	16q22.2	2012-10-02	2011-09-05		ENSG00000102967	ENSG00000102967	1.3.5.2		2867	protein-coding gene	gene with protein product		126064	"""dihydroorotate dehydrogenase"""			8211381	Standard	NM_001361		Approved		uc002fbp.3	Q02127	OTTHUMG00000178093	ENST00000219240.4:c.573G>A	16.37:g.72055078G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_001361	A8K8C8|Q6P176	Silent	SNP	ENST00000219240.4	37	CCDS42192.1																																																																																			G|0.996;A|0.004	0.004	strong		0.642	DHODH-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001361	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026138	176026138	+	Missense_Mutation	SNP	T	T	A	rs142779818|rs550332435|rs201635586|rs371149640|rs386695335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176026138T>A	ENST00000303991.4	-	2	875	c.698A>T	c.(697-699)gAg>gTg	p.E233V		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	233				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCAGGATCCTCCTTCCTCGG	0.488																																					p.E233V		Atlas-SNP	.											.	GPRIN1	77	.	0			c.A698T						PASS	.						87.0	88.0	88.0					5																	176026138		2153	4218	6371	SO:0001583	missense	114787	exon2			GGATCCTCCTTCC	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.698A>T	5.37:g.176026138T>A	ENSP00000305839:p.Glu233Val	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	106	25	0.235849	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	37	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	T	12.30	1.897302	0.33535	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.09163	3.01	4.92	2.48	0.30137	.	0.222228	0.23132	N	0.051562	T	0.12561	0.0305	M	0.77103	2.36	0.09310	N	1	B	0.30146	0.27	B	0.31337	0.128	T	0.18429	-1.0337	10	0.40728	T	0.16	-7.1862	3.6069	0.08046	0.1625:0.1858:0.0:0.6517	.	233	Q7Z2K8	GRIN1_HUMAN	V	233	ENSP00000305839:E233V	ENSP00000305839:E233V	E	-	2	0	GPRIN1	175958744	0.024000	0.19004	0.794000	0.32065	0.466000	0.32739	1.906000	0.39887	0.731000	0.32448	0.260000	0.18958	GAG	T|0.795;A|0.205	0.205	strong		0.488	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
TACC3	10460	hgsc.bcm.edu	37	4	1729660	1729660	+	Silent	SNP	C	C	T	rs1063742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1729660C>T	ENST00000313288.4	+	4	637	c.531C>T	c.(529-531)agC>agT	p.S177S		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	177					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)			TGTCTGGCAGCCCTGAGCAAG	0.562													C|||	851	0.169928	0.1331	0.196	5008	,	,		16252	0.1478		0.2634	False		,,,				2504	0.1278				p.S177S	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											TACC3,NS,carcinoma,0,1	TACC3	69	1	0			c.C531T						PASS	.	C		696,3710	291.8+/-281.7	57,582,1564	63.0	74.0	70.0		531	0.9	0.0	4	dbSNP_86	70	2130,6470	365.8+/-334.1	264,1602,2434	no	coding-synonymous	TACC3	NM_006342.1		321,2184,3998	TT,TC,CC		24.7674,15.7966,21.7284		177/839	1729660	2826,10180	2203	4300	6503	SO:0001819	synonymous_variant	10460	exon4			TGGCAGCCCTGAG	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.531C>T	4.37:g.1729660C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	159	78	0.490566	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Silent	SNP	ENST00000313288.4	37	CCDS3352.1																																																																																			C|0.805;T|0.195	0.195	strong		0.562	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
ASTN2	23245	hgsc.bcm.edu	37	9	119448979	119448979	+	Intron	SNP	C	C	T	rs10983304	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:119448979C>T	ENST00000313400.4	-	17	2907				ASTN2_ENST00000361477.3_Intron|ASTN2_ENST00000358637.4_Intron|ASTN2_ENST00000373996.3_Intron|TRIM32_ENST00000450136.1_5'Flank|TRIM32_ENST00000373983.2_5'Flank|ASTN2_ENST00000341734.4_Intron|ASTN2_ENST00000288520.5_Missense_Mutation_p.E36K|ASTN2_ENST00000361209.2_Intron			O75129	ASTN2_HUMAN	astrotactin 2						negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						CGGGTACCTTCAGTCTGCAGG	0.542													C|||	60	0.0119808	0.0015	0.013	5008	,	,		19721	0.0		0.0288	False		,,,				2504	0.0204				p.E36K		Atlas-SNP	.											.	ASTN2	307	.	0			c.G106A						PASS	.																																			SO:0001627	intron_variant	23245	exon1			TACCTTCAGTCTG	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.2807-34907G>A	9.37:g.119448979C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_198186	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		33	0.01510989010989011	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	26	0.03430079155672823	C	13.53	2.264293	0.39995	.	.	ENSG00000148219	ENST00000288520	T	0.13307	2.6	3.9	0.998	0.19857	.	.	.	.	.	T	0.02012	0.0063	.	.	.	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.41770	-0.9490	7	.	.	.	.	4.1278	0.10134	0.0:0.5889:0.1934:0.2177	rs10983304;rs52793392;rs10983304	36	O75129-4	.	K	36	ENSP00000288520:E36K	.	E	-	1	0	ASTN2	118488800	0.041000	0.20044	0.006000	0.13384	0.020000	0.10135	0.363000	0.20301	0.224000	0.20940	0.555000	0.69702	GAA	C|0.979;T|0.021	0.021	strong		0.542	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
INPP5E	56623	hgsc.bcm.edu	37	9	139324737	139324737	+	Silent	SNP	C	C	A	rs33982662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139324737C>A	ENST00000371712.3	-	9	2196	c.1794G>T	c.(1792-1794)ggG>ggT	p.G598G		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)		ACTTGTCTCGCCCCGGCCTCA	0.627													C|||	871	0.173922	0.1339	0.3069	5008	,	,		16016	0.0427		0.2555	False		,,,				2504	0.1851				p.G598G		Atlas-SNP	.											.	INPP5E	18	.	0			c.G1794T						PASS	.			583,3553		44,495,1529	56.0	47.0	50.0		1794	-7.1	0.1	9	dbSNP_126	50	2077,6059		266,1545,2257	no	coding-synonymous	INPP5E	NM_019892.4		310,2040,3786	AA,AC,CC		25.5285,14.0957,21.6754		598/645	139324737	2660,9612	2068	4068	6136	SO:0001819	synonymous_variant	56623	exon9			GTCTCGCCCCGGC	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.1794G>T	9.37:g.139324737C>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_019892	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371712.3	37	CCDS7000.1																																																																																			C|0.796;A|0.204	0.204	strong		0.627	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
PRR34	55267	hgsc.bcm.edu	37	22	46447714	46447714	+	Missense_Mutation	SNP	T	T	C	rs59929908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:46447714T>C	ENST00000396008.2	-	2	460	c.410A>G	c.(409-411)cAg>cGg	p.Q137R	FLJ27365_ENST00000381051.2_5'Flank|RP6-109B7.3_ENST00000416202.1_RNA|RP6-109B7.5_ENST00000608644.1_RNA|C22orf26_ENST00000333761.1_Missense_Mutation_p.Q137R|RP6-109B7.3_ENST00000451166.1_RNA			Q9NV39	PRR34_HUMAN		137			Q -> R (in dbSNP:rs59929908).										Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|BRCA - Breast invasive adenocarcinoma(115;0.0784)|LUAD - Lung adenocarcinoma(64;0.247)		agctcatacctgtaattccag	0.512													T|||	443	0.0884585	0.062	0.0908	5008	,	,		19210	0.1419		0.1004	False		,,,				2504	0.0552				p.Q137R		Atlas-SNP	.											.	C22orf26	1	.	0			c.A410G						PASS	.	T	ARG/GLN	135,1881		3,129,876	112.0	134.0	127.0		410	-0.3	0.0	22	dbSNP_129	127	432,3788		19,394,1697	yes	missense	C22orf26	NM_018280.2	43	22,523,2573	CC,CT,TT		10.237,6.6964,9.0924	possibly-damaging	137/139	46447714	567,5669	1008	2110	3118	SO:0001583	missense	55267	exon2			CATACCTGTAATT																												ENST00000396008.2:c.410A>G	22.37:g.46447714T>C	ENSP00000379329:p.Gln137Arg	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_018280	B0QZ24	Missense_Mutation	SNP	ENST00000396008.2	37	CCDS14071.1	224	0.10256410256410256	30	0.06097560975609756	40	0.11049723756906077	83	0.1451048951048951	71	0.09366754617414248	T	1.623	-0.521060	0.04171	0.066964	0.10237	ENSG00000182257	ENST00000396008;ENST00000333761	T;T	0.38560	1.13;1.13	0.772	-0.328	0.12690	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	P	0.42039	0.769	P	0.49332	0.607	T	0.09100	-1.0690	8	0.87932	D	0	.	2.7796	0.05357	0.0:0.3573:0.0:0.6427	rs59929908	137	Q9NV39	CV026_HUMAN	R	137	ENSP00000379329:Q137R;ENSP00000327764:Q137R	ENSP00000327764:Q137R	Q	-	2	0	C22orf26	44826378	.	.	0.003000	0.11579	0.024000	0.10985	.	.	-0.184000	0.10567	0.460000	0.39030	CAG	T|0.897;C|0.103	0.103	strong		0.512	C22orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317994.1		
PCDH12	51294	hgsc.bcm.edu	37	5	141335498	141335498	+	Missense_Mutation	SNP	C	C	T	rs164515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:141335498C>T	ENST00000231484.3	-	1	3129	c.1919G>A	c.(1918-1920)aGt>aAt	p.S640N	AC005740.6_ENST00000607378.1_RNA|PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	640	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.		S -> N (in dbSNP:rs164515). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039}.		calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCATTTCCACTGCGGATGCT	0.567													C|||	751	0.14996	0.0227	0.196	5008	,	,		19319	0.127		0.2664	False		,,,				2504	0.1933				p.S640N		Atlas-SNP	.											PCDH12,colon,carcinoma,+1,1	PCDH12	133	1	0			c.G1919A						PASS	.	C	ASN/SER	311,4095	165.4+/-196.9	11,289,1903	75.0	68.0	70.0		1919	2.7	0.0	5	dbSNP_79	70	2567,6033	418.0+/-352.6	388,1791,2121	yes	missense	PCDH12	NM_016580.2	46	399,2080,4024	TT,TC,CC		29.8488,7.0586,22.1282	benign	640/1185	141335498	2878,10128	2203	4300	6503	SO:0001583	missense	51294	exon1			TTTCCACTGCGGA	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.1919G>A	5.37:g.141335498C>T	ENSP00000231484:p.Ser640Asn	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	370	0.16941391941391942	17	0.034552845528455285	81	0.22375690607734808	71	0.12412587412587413	201	0.26517150395778366	C	0.015	-1.564822	0.00903	0.070586	0.298488	ENSG00000113555	ENST00000231484	D	0.83250	-1.7	5.38	2.7	0.31948	Cadherin (4);Cadherin-like (1);	0.728565	0.14492	N	0.316263	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.04153	-1.0973	9	0.31617	T	0.26	.	4.9107	0.13820	0.0:0.5982:0.1535:0.2483	rs164515;rs3747721;rs17208628;rs58835966;rs164515	640	Q9NPG4	PCD12_HUMAN	N	640	ENSP00000231484:S640N	ENSP00000231484:S640N	S	-	2	0	PCDH12	141315682	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	0.609000	0.24238	0.424000	0.26061	-0.136000	0.14681	AGT	C|0.796;T|0.204	0.204	strong		0.567	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
PDSS1	23590	hgsc.bcm.edu	37	10	27035396	27035396	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:27035396T>A	ENST00000376215.5	+	12	1295	c.1242T>A	c.(1240-1242)gaT>gaA	p.D414E	PDSS1_ENST00000376203.5_3'UTR|PDSS1_ENST00000470978.1_3'UTR	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	414					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						TCACAAGAGATAAATGACAAC	0.403																																					p.D414E		Atlas-SNP	.											.	PDSS1	36	.	0			c.T1242A						PASS	.						91.0	79.0	83.0					10																	27035396		2203	4300	6503	SO:0001583	missense	23590	exon12			AAGAGATAAATGA	AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"""coenzyme Q1 homolog (yeast)"""	607429	"""trans-prenyltransferase"""	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.1242T>A	10.37:g.27035396T>A	ENSP00000365388:p.Asp414Glu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_014317	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Missense_Mutation	SNP	ENST00000376215.5	37	CCDS31168.1	.	.	.	.	.	.	.	.	.	.	T	3.921	-0.018056	0.07681	.	.	ENSG00000148459	ENST00000376215;ENST00000396343	T	0.62941	-0.01	5.54	-3.27	0.05048	Terpenoid synthase (2);	0.093864	0.64402	N	0.000001	T	0.39682	0.1087	L	0.52905	1.665	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40478	-0.9561	10	0.02654	T	1	-16.2141	2.2506	0.04042	0.1373:0.2408:0.4191:0.2028	.	152;414	B4DJY1;Q5T2R2	.;DPS1_HUMAN	E	414;375	ENSP00000365388:D414E	ENSP00000365388:D414E	D	+	3	2	PDSS1	27075402	0.994000	0.37717	0.997000	0.53966	0.680000	0.39746	0.372000	0.20467	-0.207000	0.10187	-0.257000	0.10917	GAT	.	.	none		0.403	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1		
SHARPIN	81858	hgsc.bcm.edu	37	8	145154257	145154257	+	Missense_Mutation	SNP	C	C	G	rs11541804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145154257C>G	ENST00000398712.2	-	6	1281	c.845G>C	c.(844-846)aGc>aCc	p.S282T	SHARPIN_ENST00000533948.1_5'Flank	NM_030974.3	NP_112236.3	Q9H0F6	SHRPN_HUMAN	SHANK-associated RH domain interactor	282	Interaction with SHANK1. {ECO:0000250}.|Ubiquitin-like.		S -> T (in dbSNP:rs11541804).		apoptotic nuclear changes (GO:0030262)|brain development (GO:0007420)|keratinization (GO:0031424)|mitochondrion organization (GO:0007005)|negative regulation of inflammatory response (GO:0050728)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein homooligomerization (GO:0051260)|protein linear polyubiquitination (GO:0097039)|regulation of CD40 signaling pathway (GO:2000348)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|LUBAC complex (GO:0071797)|postsynaptic density (GO:0014069)	polyubiquitin binding (GO:0031593)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(2)|ovary(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.1e-42)|Epithelial(56;1.58e-40)|all cancers(56;6.12e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AGAGGCAAGGCTGCGCTCAGG	0.642													C|||	139	0.0277556	0.0045	0.0303	5008	,	,		20220	0.0		0.0835	False		,,,				2504	0.0286				p.S282T		Atlas-SNP	.											.	SHARPIN	16	.	0			c.G845C						PASS	.	C	THR/SER	65,4227		2,61,2083	56.0	66.0	63.0		845	4.6	1.0	8	dbSNP_120	63	684,7818		33,618,3600	yes	missense	SHARPIN	NM_030974.3	58	35,679,5683	GG,GC,CC		8.0452,1.5144,5.8543	probably-damaging	282/388	145154257	749,12045	2146	4251	6397	SO:0001583	missense	81858	exon6			GCAAGGCTGCGCT	AL136816	CCDS43777.1	8q24.3	2005-08-09				ENSG00000179526			25321	protein-coding gene	gene with protein product		611885				11178875, 12753155	Standard	NM_030974		Approved	DKFZP434N1923, SIPL1	uc003zba.3	Q9H0F6		ENST00000398712.2:c.845G>C	8.37:g.145154257C>G	ENSP00000381698:p.Ser282Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_030974	A6NEG3|C0L3L2|D3DWL3|Q8IXF5|Q8IXF6|Q8N2E7|Q8TB25|Q9BUE4	Missense_Mutation	SNP	ENST00000398712.2	37	CCDS43777.1	77	0.035256410256410256	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	62	0.08179419525065963	C	13.36	2.214536	0.39102	0.015144	0.080452	ENSG00000179526	ENST00000398712;ENST00000359551	T;T	0.34859	1.34;1.34	4.63	4.63	0.57726	.	0.108957	0.64402	D	0.000006	T	0.03053	0.0090	L	0.31207	0.915	0.41223	D	0.986525	D	0.76494	0.999	D	0.78314	0.991	T	0.00770	-1.1573	10	0.15066	T	0.55	.	12.8664	0.57941	0.0:1.0:0.0:0.0	rs11541804	282	Q9H0F6	SHRPN_HUMAN	T	282	ENSP00000381698:S282T;ENSP00000352551:S282T	ENSP00000352551:S282T	S	-	2	0	SHARPIN	145226245	1.000000	0.71417	0.996000	0.52242	0.450000	0.32258	5.141000	0.64814	2.424000	0.82194	0.555000	0.69702	AGC	C|0.939;G|0.061	0.061	strong		0.642	SHARPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382901.1	NM_030974	
OR51F1	256892	hgsc.bcm.edu	37	11	4790396	4790396	+	Missense_Mutation	SNP	G	G	A	rs17324609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4790396G>A	ENST00000380383.1	-	1	772	c.773C>T	c.(772-774)gCt>gTt	p.A258V	OR51F1_ENST00000343430.3_Missense_Mutation_p.A251V|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	258			A -> V (in dbSNP:rs17324609).			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)		GTAGAAGAAAGCAACTGCTCC	0.483													G|||	230	0.0459265	0.0061	0.0951	5008	,	,		20736	0.0		0.1412	False		,,,				2504	0.0143				p.A251V		Atlas-SNP	.											.	OR51F1	60	.	0			c.C752T						PASS	.	G	VAL/ALA	140,4262	98.0+/-136.7	1,138,2062	102.0	90.0	94.0		752	5.2	0.9	11	dbSNP_123	94	1159,7437	238.2+/-269.8	94,971,3233	yes	missense	OR51F1	NM_001004752.1	64	95,1109,5295	AA,AG,GG		13.483,3.1804,9.9938	possibly-damaging	251/313	4790396	1299,11699	2201	4298	6499	SO:0001583	missense	256892	exon1			AAGAAAGCAACTG	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.773C>T	11.37:g.4790396G>A	ENSP00000369744:p.Ala258Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	142	57	0.401408	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		157	0.07188644688644688	2	0.0040650406504065045	47	0.1298342541436464	0	0.0	108	0.1424802110817942	G	20.3	3.963905	0.74131	0.031804	0.13483	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.30714	1.52;1.52	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.783599	0.11487	N	0.559083	T	0.00356	0.0011	L	0.35593	1.075	0.80722	P	0.0	D	0.58970	0.984	P	0.61275	0.886	T	0.03641	-1.1017	9	0.72032	D	0.01	.	11.8249	0.52261	0.0839:0.0:0.9161:0.0	rs17324609;rs52817348;rs17324609	258	A6NGY5	O51F1_HUMAN	V	251;258	ENSP00000345163:A251V;ENSP00000369744:A258V	ENSP00000345163:A251V	A	-	2	0	OR51F1	4746972	0.602000	0.26916	0.874000	0.34290	0.923000	0.55619	2.740000	0.47418	2.728000	0.93425	0.655000	0.94253	GCT	G|0.915;A|0.085	0.085	strong		0.483	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
JPH3	57338	hgsc.bcm.edu	37	16	87678144	87678144	+	Silent	SNP	T	T	C	rs918368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:87678144T>C	ENST00000284262.2	+	2	905	c.663T>C	c.(661-663)agT>agC	p.S221S		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	221					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		CGCTGCTGAGTGGGCTGAAGC	0.657													C|||	3264	0.651757	0.7057	0.6873	5008	,	,		13897	0.7232		0.503	False		,,,				2504	0.6329				p.S221S		Atlas-SNP	.											.	JPH3	95	.	0			c.T663C						PASS	.	C		2979,1417	443.3+/-347.0	1025,929,244	47.0	51.0	49.0		663	1.3	1.0	16	dbSNP_86	49	4458,4142	547.6+/-385.2	1137,2184,979	no	coding-synonymous	JPH3	NM_020655.2		2162,3113,1223	CC,CT,TT		48.1628,32.2338,42.7747		221/749	87678144	7437,5559	2198	4300	6498	SO:0001819	synonymous_variant	57338	exon2			GCTGAGTGGGCTG	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.663T>C	16.37:g.87678144T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	63	61	0.968254	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Silent	SNP	ENST00000284262.2	37	CCDS10962.1																																																																																			T|0.400;C|0.600	0.600	strong		0.657	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
MMP3	4314	hgsc.bcm.edu	37	11	102713620	102713620	+	Missense_Mutation	SNP	T	T	C	rs679620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102713620T>C	ENST00000299855.5	-	2	389	c.133A>G	c.(133-135)Aaa>Gaa	p.K45E		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	45			K -> E (in dbSNP:rs679620). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|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)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	ACATCTTTTTTGAGGTCGTAG	0.333													C|||	3266	0.652157	0.671	0.6787	5008	,	,		18508	0.6657		0.5278	False		,,,				2504	0.7219				p.K45E		Atlas-SNP	.											MMP3,NS,carcinoma,0,1	MMP3	60	1	0			c.A133G						PASS	.	C	GLU/LYS	2815,1591	483.9+/-359.9	907,1001,295	30.0	30.0	30.0		133	-0.2	0.0	11	dbSNP_83	30	4301,4297	567.7+/-388.9	1067,2167,1065	yes	missense	MMP3	NM_002422.3	56	1974,3168,1360	CC,CT,TT		49.9767,36.1099,45.2784	benign	45/478	102713620	7116,5888	2203	4299	6502	SO:0001583	missense	4314	exon2			CTTTTTTGAGGTC	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.133A>G	11.37:g.102713620T>C	ENSP00000299855:p.Lys45Glu	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Missense_Mutation	SNP	ENST00000299855.5	37	CCDS8323.1	1373	0.6286630036630036	348	0.7073170731707317	231	0.638121546961326	384	0.6713286713286714	410	0.5408970976253298	C	1.799	-0.477598	0.04414	0.638901	0.500233	ENSG00000149968	ENST00000299855	T	0.34859	1.34	6.16	-0.221	0.13126	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	2.486670	0.02224	N	0.064238	T	0.00012	0.0000	N	0.10733	0.035	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39502	-0.9611	9	0.02654	T	1	.	6.9869	0.24733	0.0:0.2794:0.318:0.4026	rs679620;rs1051161;rs3168234;rs56822421;rs679620	45	P08254	MMP3_HUMAN	E	45	ENSP00000299855:K45E	ENSP00000299855:K45E	K	-	1	0	MMP3	102218830	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.578000	0.02125	-0.250000	0.09555	-2.364000	0.00238	AAA	T|0.428;C|0.572	0.572	strong		0.333	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
HLA-A	3105	hgsc.bcm.edu	37	6	29910402	29910402	+	Splice_Site	SNP	G	G	A	rs1136656	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910402G>A	ENST00000396634.1	+	3	413	c.72G>A	c.(70-72)gcG>gcA	p.A24A	HLA-A_ENST00000376809.5_Splice_Site_p.A24A|HLA-A_ENST00000376806.5_Splice_Site_p.A24A|HLA-A_ENST00000376802.2_Splice_Site_p.A24A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	24					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						AGACCTGGGCGGGTGAGTGCG	0.736									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|||	782	0.15615	0.1362	0.1772	5008	,	,		13109	0.2034		0.1123	False		,,,				2504	0.1646				p.A24A		Atlas-SNP	.											.	HLA-A	89	.	0			c.G72A						PASS	.	G		591,3805		42,507,1649	20.0	22.0	21.0		72	0.2	1.0	6	dbSNP_86	21	907,7677		52,803,3437	no	coding-synonymous-near-splice	HLA-A	NM_002116.7		94,1310,5086	AA,AG,GG		10.5662,13.444,11.5408		24/366	29910402	1498,11482	2198	4292	6490	SO:0001630	splice_region_variant	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CTGGGCGGGTGAG	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.73+1G>A	6.37:g.29910402G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.870;A|0.130	0.130	strong		0.736	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	Silent
THSD7A	221981	hgsc.bcm.edu	37	7	11521428	11521428	+	Silent	SNP	A	A	G	rs61996277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:11521428A>G	ENST00000423059.4	-	7	2255	c.2004T>C	c.(2002-2004)taT>taC	p.Y668Y	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	668	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CTTCACCCGCATAGGCCAGAA	0.493										HNSCC(18;0.044)			A|||	168	0.0335463	0.0068	0.0865	5008	,	,		18995	0.002		0.0636	False		,,,				2504	0.0337				p.Y668Y		Atlas-SNP	.											.	THSD7A	219	.	0			c.T2004C						PASS	.	A		78,4216		1,76,2070	122.0	118.0	119.0		2004	0.9	1.0	7	dbSNP_129	119	741,7753		34,673,3540	no	coding-synonymous	THSD7A	NM_015204.2		35,749,5610	GG,GA,AA		8.7238,1.8165,6.4044		668/1658	11521428	819,11969	2147	4247	6394	SO:0001819	synonymous_variant	221981	exon7			ACCCGCATAGGCC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2004T>C	7.37:g.11521428A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	196	94	0.479592	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			A|0.946;G|0.054	0.054	strong		0.493	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
FAM170B	170370	hgsc.bcm.edu	37	10	50339754	50339754	+	Missense_Mutation	SNP	G	G	T	rs73302786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50339754G>T	ENST00000311787.5	-	2	845	c.756C>A	c.(754-756)gaC>gaA	p.D252E	FAM170B-AS1_ENST00000443389.1_RNA|FAM170B-AS1_ENST00000435809.1_RNA|FAM170B-AS1_ENST00000442525.1_RNA	NM_001164484.1	NP_001157956.1	A6NMN3	F170B_HUMAN	family with sequence similarity 170, member B	252										central_nervous_system(1)|endometrium(1)|skin(1)	3						CCAGCTGTTGGTCATGTGCTT	0.597													G|||	857	0.171126	0.2163	0.1282	5008	,	,		19690	0.0625		0.2018	False		,,,				2504	0.2209				p.D252E		Atlas-SNP	.											.	FAM170B	20	.	0			c.C756A						PASS	.	G	GLU/ASP	340,1044		40,260,392	95.0	85.0	88.0		756	-5.6	0.0	10	dbSNP_130	88	684,2498		77,530,984	yes	missense	FAM170B	NM_001164484.1	45	117,790,1376	TT,TG,GG		21.4959,24.5665,22.4266	benign	252/284	50339754	1024,3542	692	1591	2283	SO:0001583	missense	170370	exon2			CTGTTGGTCATGT		CCDS53536.1	10q11.23	2008-11-06	2008-06-12	2008-06-12	ENSG00000172538	ENSG00000172538			19736	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 73"""	C10orf73			Standard	NM_001164484		Approved	Em:AC084727.4	uc001jhj.3	A6NMN3	OTTHUMG00000018187	ENST00000311787.5:c.756C>A	10.37:g.50339754G>T	ENSP00000308292:p.Asp252Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_001164484	Q86WY6|Q8N6K8	Missense_Mutation	SNP	ENST00000311787.5	37	CCDS53536.1	338	0.15476190476190477	106	0.21544715447154472	42	0.11602209944751381	29	0.050699300699300696	161	0.21240105540897097	G	10.97	1.500335	0.26861	0.245665	0.214959	ENSG00000172538	ENST00000311787	T	0.29917	1.55	5.37	-5.56	0.02529	.	2.209180	0.02269	N	0.068289	T	0.00012	0.0000	N	0.17474	0.49	0.80722	P	0.0	B	0.11235	0.004	B	0.13407	0.009	T	0.24764	-1.0151	9	0.02654	T	1	-11.8138	1.0815	0.01644	0.1911:0.2613:0.14:0.4075	.	252	A6NMN3	F170B_HUMAN	E	252	ENSP00000308292:D252E	ENSP00000308292:D252E	D	-	3	2	FAM170B	50009760	0.863000	0.29885	0.003000	0.11579	0.032000	0.12392	-0.061000	0.11693	-0.560000	0.06102	-0.693000	0.03709	GAC	G|0.844;T|0.156	0.156	strong		0.597	FAM170B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047974.1	XM_096317	
FZD5	7855	hgsc.bcm.edu	37	2	208632817	208632817	+	Missense_Mutation	SNP	G	G	A	rs35994626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:208632817G>A	ENST00000295417.3	-	2	1200	c.647C>T	c.(646-648)cCc>cTc	p.P216L		NM_003468.3	NP_003459.2	Q13467	FZD5_HUMAN	frizzled class receptor 5	216			P -> L (in dbSNP:rs35994626).		angiogenesis (GO:0001525)|anterior/posterior axis specification, embryo (GO:0008595)|apoptotic process (GO:0006915)|apoptotic process involved in morphogenesis (GO:0060561)|axonogenesis (GO:0007409)|brain development (GO:0007420)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|canonical Wnt signaling pathway (GO:0060070)|cell maturation (GO:0048469)|cellular response to molecule of bacterial origin (GO:0071219)|chorionic trophoblast cell differentiation (GO:0060718)|embryonic axis specification (GO:0000578)|embryonic camera-type eye development (GO:0031076)|gonad development (GO:0008406)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|neuron differentiation (GO:0030182)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic camera-type eye development (GO:0031077)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of chorionic trophoblast cell proliferation (GO:1901382)|regulation of tight junction assembly (GO:2000810)|Spemann organizer formation (GO:0060061)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell differentiation in thymus (GO:0033077)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	cell projection (GO:0042995)|cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			NS(1)|kidney(1)|lung(1)|ovary(2)|prostate(1)|skin(1)	7				LUSC - Lung squamous cell carcinoma(261;0.0703)|Epithelial(149;0.13)|Lung(261;0.134)		CGCGCAGTTGGGCACCTGGCC	0.647													G|||	124	0.0247604	0.0015	0.0346	5008	,	,		18142	0.0		0.0616	False		,,,				2504	0.0368				p.P216L		Atlas-SNP	.											.	FZD5	22	.	0			c.C647T						PASS	.	G	LEU/PRO	55,4351	50.9+/-86.3	0,55,2148	47.0	47.0	47.0		647	2.9	1.0	2	dbSNP_126	47	679,7921	166.8+/-218.7	26,627,3647	yes	missense	FZD5	NM_003468.3	98	26,682,5795	AA,AG,GG		7.8953,1.2483,5.6435	benign	216/586	208632817	734,12272	2203	4300	6503	SO:0001583	missense	7855	exon2			CAGTTGGGCACCT	U43318	CCDS33366.1	2q33.3	2014-01-29	2014-01-29		ENSG00000163251	ENSG00000163251		"""GPCR / Class F : Frizzled receptors"""	4043	protein-coding gene	gene with protein product		601723	"""frizzled (Drosophila) homolog 5"", ""chromosome 2 open reading frame 31"", ""frizzled homolog 5 (Drosophila)"", ""frizzled 5, seven transmembrane spanning receptor"", ""frizzled family receptor 5"""	C2orf31		8626800, 11408929	Standard	NM_003468		Approved	HFZ5, DKFZP434E2135	uc002vcj.3	Q13467	OTTHUMG00000154790	ENST00000295417.3:c.647C>T	2.37:g.208632817G>A	ENSP00000354607:p.Pro216Leu	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_003468	A8K2X1|B2RCZ1|Q53R22	Missense_Mutation	SNP	ENST00000295417.3	37	CCDS33366.1	56	0.02564102564102564	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	42	0.055408970976253295	G	12.13	1.845603	0.32606	0.012483	0.078953	ENSG00000163251	ENST00000295417	T	0.79845	-1.31	5.05	2.94	0.34122	.	0.294105	0.32258	N	0.006352	T	0.08358	0.0208	L	0.28192	0.835	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.43972	-0.9358	10	0.41790	T	0.15	.	3.0492	0.06164	0.1303:0.1681:0.5291:0.1726	rs35994626;rs61752181	216	Q13467	FZD5_HUMAN	L	216	ENSP00000354607:P216L	ENSP00000354607:P216L	P	-	2	0	FZD5	208341062	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	2.812000	0.47994	2.355000	0.79922	0.561000	0.74099	CCC	G|0.953;A|0.047	0.047	strong		0.647	FZD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337060.1	NM_003468	
C19orf40	91442	hgsc.bcm.edu	37	19	33467413	33467413	+	Missense_Mutation	SNP	C	C	T	rs2304103	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33467413C>T	ENST00000588258.1	+	5	583	c.473C>T	c.(472-474)tCg>tTg	p.S158L	C19orf40_ENST00000589646.1_Missense_Mutation_p.S63L|C19orf40_ENST00000590179.1_Missense_Mutation_p.S63L|C19orf40_ENST00000590281.1_Missense_Mutation_p.S158L	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	158			S -> L (in dbSNP:rs2304103).		DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					TCTGAGCCTTCGCTCCTTCGA	0.517								Direct reversal of damage			OREG0025408	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	352	0.0702875	0.0696	0.0447	5008	,	,		17031	0.0526		0.0388	False		,,,				2504	0.1401				p.S158L		Atlas-SNP	.											.	C19orf40	21	.	0			c.C473T						PASS	.	C	LEU/SER	271,4135	151.8+/-185.6	10,251,1942	98.0	92.0	94.0		473	0.7	0.0	19	dbSNP_100	94	382,8218	123.8+/-182.6	4,374,3922	yes	missense	C19orf40	NM_152266.3	145	14,625,5864	TT,TC,CC		4.4419,6.1507,5.0208	benign	158/216	33467413	653,12353	2203	4300	6503	SO:0001583	missense	91442	exon5			AGCCTTCGCTCCT	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 24kDa"""	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.473C>T	19.37:g.33467413C>T	ENSP00000466121:p.Ser158Leu	Somatic	99	0	0	840	WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Missense_Mutation	SNP	ENST00000588258.1	37	CCDS12426.1	118	0.05402930402930403	40	0.08130081300813008	19	0.052486187845303865	36	0.06293706293706294	23	0.030343007915567283	C	1.021	-0.684918	0.03328	0.061507	0.044419	ENSG00000131944	ENST00000254262	.	.	.	5.35	0.673	0.17941	RuvA domain 2-like (1);	0.773939	0.12929	N	0.427523	T	0.01029	0.0034	L	0.45581	1.43	0.09310	N	1	B	0.32731	0.382	B	0.14023	0.01	T	0.08289	-1.0729	9	0.22706	T	0.39	-3.0E-4	3.0811	0.06262	0.1547:0.5625:0.131:0.1518	rs2304103;rs52801807;rs2304103	158	Q9BTP7	FAP24_HUMAN	L	158	.	ENSP00000254262:S158L	S	+	2	0	C19orf40	38159253	0.000000	0.05858	0.012000	0.15200	0.040000	0.13550	0.859000	0.27858	0.029000	0.15352	-0.292000	0.09595	TCG	C|0.939;T|0.061	0.061	strong		0.517	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266	
CES4A	283848	hgsc.bcm.edu	37	16	67037054	67037054	+	Missense_Mutation	SNP	A	A	C	rs61744399	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67037054A>C	ENST00000326686.5	+	6	772	c.772A>C	c.(772-774)Agt>Cgt	p.S258R	CES4A_ENST00000540579.1_Missense_Mutation_p.S160R|CES4A_ENST00000338718.4_Missense_Mutation_p.S281R|CES4A_ENST00000540947.2_Missense_Mutation_p.S258R|CES4A_ENST00000541479.1_Missense_Mutation_p.S281R|CES4A_ENST00000535696.1_Missense_Mutation_p.S164R|CES4A_ENST00000398354.1_Missense_Mutation_p.S258R			Q5XG92	EST4A_HUMAN	carboxylesterase 4A	258						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			large_intestine(2)|liver(2)|lung(4)|ovary(1)	9						TTTCATCACTAGTAACCCACT	0.542													C|||	1677	0.334864	0.8033	0.1715	5008	,	,		21997	0.2312		0.0755	False		,,,				2504	0.1912				p.S258R		Atlas-SNP	.											.	CES4A	24	.	0			c.A772C						PASS	.	C	ARG/SER,ARG/SER,ARG/SER	2521,1475		801,919,278	91.0	90.0	90.0		478,490,772	1.6	0.0	16	dbSNP_129	90	632,7720		31,570,3575	yes	missense,missense,missense	CES4A	NM_001190201.1,NM_001190202.1,NM_173815.6	110,110,110	832,1489,3853	CC,CA,AA		7.567,36.9119,25.5345	benign,benign,benign	160/464,164/375,258/469	67037054	3153,9195	1998	4176	6174	SO:0001583	missense	283848	exon6			ATCACTAGTAACC	AK094783	CCDS42174.1, CCDS42174.2, CCDS54024.1, CCDS54025.1, CCDS42174.3	16q22.1	2011-10-25	2010-10-12	2010-10-12	ENSG00000172824	ENSG00000172824		"""Carboxylesterases"""	26741	protein-coding gene	gene with protein product			"""carboxylesterase 8 (putative)"""	CES8		12975309, 17364878, 20931200	Standard	NM_001190201		Approved	FLJ37464	uc010vix.2	Q5XG92		ENST00000326686.5:c.772A>C	16.37:g.67037054A>C	ENSP00000314145:p.Ser258Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	131	76	0.580153	NM_173815	A8KAJ6|B7Z349|B7Z3L2|B7Z6R3|Q6UX55|Q8N9F4	Missense_Mutation	SNP	ENST00000326686.5	37		632	0.2893772893772894	386	0.7845528455284553	61	0.1685082872928177	129	0.22552447552447552	56	0.07387862796833773	c	10.71	1.426257	0.25726	0.630881	0.07567	ENSG00000172824	ENST00000540947;ENST00000541479;ENST00000338718;ENST00000398354;ENST00000326686;ENST00000538199;ENST00000540579;ENST00000535696	T;T;T;T;T;T;T;T	0.68624	0.28;0.28;0.28;0.28;-0.34;0.28;-0.34;0.28	5.17	1.61	0.23674	Carboxylesterase, type B (1);	3.156810	0.01089	N	0.005151	T	0.00012	0.0000	N	0.25647	0.755	0.80722	P	0.0	B;B;B;B	0.13145	0.007;0.0;0.0;0.0	B;B;B;B	0.16722	0.012;0.0;0.016;0.001	T	0.45991	-0.9223	9	0.25106	T	0.35	.	2.6837	0.05101	0.3927:0.3632:0.0:0.2441	rs61744399	164;281;258;281	Q5XG92-7;F8WEE9;Q5XG92;F5H5S4	.;.;EST4A_HUMAN;.	R	258;281;281;258;258;221;160;164	ENSP00000444052:S258R;ENSP00000443175:S281R;ENSP00000340714:S281R;ENSP00000381397:S258R;ENSP00000314145:S258R;ENSP00000441103:S221R;ENSP00000441907:S160R;ENSP00000441644:S164R	ENSP00000314145:S258R	S	+	1	0	CES4A	65594555	0.000000	0.05858	0.048000	0.18961	0.178000	0.23041	-0.283000	0.08433	0.205000	0.20568	-0.211000	0.12701	AGT	A|0.791;C|0.209	0.209	strong		0.542	CES4A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_173815	
UBXN11	91544	hgsc.bcm.edu	37	1	26608849	26608849	+	Missense_Mutation	SNP	T	T	A	rs199707978		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608849T>A	ENST00000374222.1	-	16	1968	c.1504A>T	c.(1504-1506)Agt>Tgt	p.S502C	UBXN11_ENST00000314675.7_Missense_Mutation_p.S382C|UBXN11_ENST00000374217.2_Missense_Mutation_p.S469C|UBXN11_ENST00000357089.4_Missense_Mutation_p.S469C|UBXN11_ENST00000374223.1_Missense_Mutation_p.S259C|UBXN11_ENST00000374221.3_Missense_Mutation_p.S502C			Q5T124	UBX11_HUMAN	UBX domain protein 11	502	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						ggaccgggactggggccggga	0.731																																					p.S502C		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.A1504T						PASS	.						19.0	22.0	21.0					1																	26608849		1706	3905	5611	SO:0001583	missense	91544	exon16			CGGGACTGGGGCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1504A>T	1.37:g.26608849T>A	ENSP00000363339:p.Ser502Cys	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	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	.	.	.	.	.	.	.	.	.	.	-	8.284	0.816212	0.16607	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19105	2.17;2.18;2.44;2.43;2.43;2.44	.	.	.	.	.	.	.	.	T	0.10594	0.0259	N	0.08118	0	0.09310	N	0.999993	.	.	.	.	.	.	T	0.30446	-0.9978	5	0.66056	D	0.02	.	.	.	.	.	469;382;502	Q5T124-2;Q5T124-3;Q5T124	.;.;UBX11_HUMAN	C	382;259;469;502;502;469	ENSP00000324721:S382C;ENSP00000363340:S259C;ENSP00000349601:S469C;ENSP00000363338:S502C;ENSP00000363339:S502C;ENSP00000363334:S469C	ENSP00000324721:S382C	S	-	1	0	UBXN11	26481436	0.000000	0.05858	0.168000	0.22838	0.175000	0.22909	-0.694000	0.05115	0.000000	0.14550	0.000000	0.15137	AGT	.	.	weak		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
DLG5	9231	hgsc.bcm.edu	37	10	79566632	79566632	+	Silent	SNP	G	G	A	rs1058198	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:79566632G>A	ENST00000372391.2	-	26	4856	c.4851C>T	c.(4849-4851)gaC>gaT	p.D1617D	DLG5_ENST00000372388.2_Silent_p.D1277D|DLG5_ENST00000459739.1_5'UTR	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1617	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			AGAGGATGTCGTCCTTCTTAA	0.602													G|||	1315	0.26258	0.2466	0.2392	5008	,	,		16932	0.1736		0.339	False		,,,				2504	0.3139				p.D1617D		Atlas-SNP	.											.	DLG5	154	.	0			c.C4851T						PASS	.	G		1180,3226	415.4+/-337.2	169,842,1192	157.0	134.0	142.0		4851	-11.7	0.1	10	dbSNP_86	142	2978,5622	462.9+/-365.8	536,1906,1858	no	coding-synonymous	DLG5	NM_004747.3		705,2748,3050	AA,AG,GG		34.6279,26.7817,31.9699		1617/1920	79566632	4158,8848	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon26			GATGTCGTCCTTC	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.4851C>T	10.37:g.79566632G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.688;A|0.312	0.312	strong		0.602	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
FCGBP	8857	hgsc.bcm.edu	37	19	40405999	40405999	+	Missense_Mutation	SNP	C	C	A	rs7248839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40405999C>A	ENST00000221347.6	-	10	4854	c.4847G>T	c.(4846-4848)gGc>gTc	p.G1616V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1616	Cys-rich.		G -> V (in dbSNP:rs7248839).			extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCACACCATGCCTTTACCCGC	0.642													C|||	659	0.131589	0.1324	0.1916	5008	,	,		19537	0.0357		0.172	False		,,,				2504	0.1452				p.G1616V		Atlas-SNP	.											FCGBP,mouth,carcinoma,+1,1	FCGBP	416	1	0			c.G4847T						scavenged	.						80.0	60.0	67.0					19																	40405999		2201	4292	6493	SO:0001583	missense	8857	exon10			ACCATGCCTTTAC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4847G>T	19.37:g.40405999C>A	ENSP00000221347:p.Gly1616Val	Somatic	696	0	0		WXS	Illumina HiSeq	Phase_I	475	89	0.187368	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	227	0.10393772893772894	60	0.12195121951219512	41	0.1132596685082873	18	0.03146853146853147	108	0.1424802110817942	C	9.121	1.008963	0.19199	.	.	ENSG00000090920	ENST00000221347	T	0.04454	3.62	3.4	1.07	0.20283	von Willebrand factor, type C (1);	.	.	.	.	T	0.00039	0.0001	L	0.61387	1.9	0.80722	P	0.0	B	0.24963	0.115	B	0.24269	0.052	T	0.32079	-0.9920	8	0.22706	T	0.39	.	7.7598	0.28946	0.4526:0.5474:0.0:0.0	rs7248839	1616	Q9Y6R7	FCGBP_HUMAN	V	1616	ENSP00000221347:G1616V	ENSP00000221347:G1616V	G	-	2	0	FCGBP	45097839	0.003000	0.15002	0.001000	0.08648	0.014000	0.08584	0.661000	0.25023	0.128000	0.18479	0.306000	0.20318	GGC	C|0.897;A|0.103	0.103	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PEX13	5194	hgsc.bcm.edu	37	2	61258816	61258816	+	Missense_Mutation	SNP	G	G	A	rs147707348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:61258816G>A	ENST00000295030.5	+	2	393	c.355G>A	c.(355-357)Gtt>Att	p.V119I	PEX13_ENST00000472678.1_3'UTR	NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	119					cerebral cortex cell migration (GO:0021795)|fatty acid alpha-oxidation (GO:0001561)|locomotory behavior (GO:0007626)|microtubule-based peroxisome localization (GO:0060152)|neuron migration (GO:0001764)|protein import into peroxisome matrix, docking (GO:0016560)|suckling behavior (GO:0001967)	integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			CAGTAGATTTGTTCAGCAAGC	0.433													G|||	2	0.000399361	0.0	0.0	5008	,	,		20269	0.0		0.002	False		,,,				2504	0.0				p.V119I		Atlas-SNP	.											.	PEX13	27	.	0			c.G355A						PASS	.	G	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	139.0	133.0	135.0		355	5.8	1.0	2	dbSNP_134	135	22,8578	16.0+/-53.3	0,22,4278	yes	missense	PEX13	NM_002618.3	29	0,24,6479	AA,AG,GG		0.2558,0.0454,0.1845	possibly-damaging	119/404	61258816	24,12982	2203	4300	6503	SO:0001583	missense	5194	exon2			AGATTTGTTCAGC	U71374	CCDS1866.1	2p16.1	2008-08-26	2008-08-26		ENSG00000162928	ENSG00000162928			8855	protein-coding gene	gene with protein product		601789	"""peroxisome biogenesis factor 13"""			9878256	Standard	NM_002618		Approved		uc002sau.4	Q92968	OTTHUMG00000129422	ENST00000295030.5:c.355G>A	2.37:g.61258816G>A	ENSP00000295030:p.Val119Ile	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	132	70	0.530303	NM_002618	B2RCS1	Missense_Mutation	SNP	ENST00000295030.5	37	CCDS1866.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.70	3.679588	0.68042	4.54E-4	0.002558	ENSG00000162928	ENST00000295030	T	0.77098	-1.07	5.85	5.85	0.93711	Peroxin 13, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77432	0.4129	L	0.31420	0.93	0.80722	D	1	P	0.45240	0.854	P	0.49361	0.608	T	0.75525	-0.3287	10	0.38643	T	0.18	-24.2526	20.1649	0.98147	0.0:0.0:1.0:0.0	.	119	Q92968	PEX13_HUMAN	I	119	ENSP00000295030:V119I	ENSP00000295030:V119I	V	+	1	0	PEX13	61112320	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.588000	0.98232	2.753000	0.94483	0.655000	0.94253	GTT	G|0.998;A|0.002	0.002	strong		0.433	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618	
ESPNL	339768	hgsc.bcm.edu	37	2	239039637	239039637	+	Missense_Mutation	SNP	T	T	C	rs4663845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:239039637T>C	ENST00000343063.3	+	9	2545	c.2282T>C	c.(2281-2283)gTg>gCg	p.V761A	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.V393A|ESPNL_ENST00000409169.1_Missense_Mutation_p.V717A	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	761			V -> A (in dbSNP:rs4663845). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		CTCAAGACAGTGGCCTGCAGG	0.731													C|||	4325	0.863618	0.9773	0.7968	5008	,	,		13830	0.9315		0.7256	False		,,,				2504	0.8292				p.V761A		Atlas-SNP	.											.	ESPNL	63	.	0			c.T2282C						PASS	.	C	ALA/VAL	3462,136		1667,128,4	2.0	3.0	3.0		2282	2.7	0.1	2	dbSNP_111	3	5885,1463		2323,1239,112	yes	missense	ESPNL	NM_194312.2	64	3990,1367,116	CC,CT,TT		19.9102,3.7799,14.6081	benign	761/1006	239039637	9347,1599	1799	3674	5473	SO:0001583	missense	339768	exon9			AGACAGTGGCCTG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2282T>C	2.37:g.239039637T>C	ENSP00000339115:p.Val761Ala	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	1843	0.8438644688644689	479	0.9735772357723578	296	0.8176795580110497	528	0.9230769230769231	540	0.712401055408971	C	0	-2.633982	0.00114	0.962201	0.800898	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.60299	0.2;1.32;0.89	4.5	2.68	0.31781	.	0.262309	0.31989	N	0.006749	T	0.00012	0.0000	N	0.00182	-1.905	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38908	-0.9639	9	0.02654	T	1	-11.0481	7.1385	0.25541	0.0:0.6214:0.0:0.3786	rs4663845;rs13007563;rs58744855;rs4663845	717;761	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	A	761;717;393	ENSP00000339115:V761A;ENSP00000386577:V717A;ENSP00000386579:V393A	ENSP00000339115:V761A	V	+	2	0	ESPNL	238704376	0.000000	0.05858	0.057000	0.19452	0.063000	0.16089	-0.058000	0.11750	0.048000	0.15891	-0.642000	0.03964	GTG	T|0.151;C|0.849	0.849	strong		0.731	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
NRAP	4892	hgsc.bcm.edu	37	10	115370254	115370254	+	Silent	SNP	A	A	G	rs12243176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115370254A>G	ENST00000359988.3	-	31	3811	c.3567T>C	c.(3565-3567)atT>atC	p.I1189I	NRAP_ENST00000369358.4_Silent_p.I1197I|NRAP_ENST00000369360.3_Silent_p.I1162I|NRAP_ENST00000360478.3_Silent_p.I1154I	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		TCCTCCCTTCAATCTCTAACG	0.418													A|||	2351	0.469449	0.354	0.4669	5008	,	,		17753	0.6032		0.4652	False		,,,				2504	0.4939				p.I1189I		Atlas-SNP	.											.	NRAP	208	.	0			c.T3567C						PASS	.	A	,	1587,2819	495.5+/-363.3	300,987,916	178.0	150.0	160.0		3462,3567	-5.9	0.8	10	dbSNP_120	160	4166,4434	567.6+/-388.9	1004,2158,1138	no	coding-synonymous,coding-synonymous	NRAP	NM_006175.3,NM_198060.2	,	1304,3145,2054	GG,GA,AA		48.4419,36.0191,44.2334	,	1154/1696,1189/1731	115370254	5753,7253	2203	4300	6503	SO:0001819	synonymous_variant	4892	exon31			CCCTTCAATCTCT		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3567T>C	10.37:g.115370254A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_001261463		Silent	SNP	ENST00000359988.3	37	CCDS7579.1																																																																																			A|0.547;G|0.453	0.453	strong		0.418	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
GAD1	2571	hgsc.bcm.edu	37	2	171678625	171678625	+	Silent	SNP	T	T	C	rs769404	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:171678625T>C	ENST00000358196.3	+	3	661	c.111T>C	c.(109-111)caT>caC	p.H37H	GAD1_ENST00000375272.1_Silent_p.H37H|GAD1_ENST00000344257.5_Silent_p.H37H|GAD1_ENST00000429023.1_3'UTR	NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	37					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						GCGTGGCCCATGGATGCACCA	0.642													T|||	1789	0.357228	0.1596	0.3703	5008	,	,		14360	0.506		0.4324	False		,,,				2504	0.3845				p.H37H		Atlas-SNP	.											GAD1,colon,carcinoma,0,1	GAD1	79	1	0			c.T111C						scavenged	.	T	,	828,3578	312.7+/-292.7	72,684,1447	48.0	42.0	44.0		111,111	-1.7	1.0	2	dbSNP_120	44	3568,5030	494.0+/-373.7	731,2106,1462	no	coding-synonymous,coding-synonymous	GAD1	NM_000817.2,NM_013445.3	,	803,2790,2909	CC,CT,TT		41.498,18.7926,33.805	,	37/595,37/225	171678625	4396,8608	2203	4299	6502	SO:0001819	synonymous_variant	2571	exon3			GGCCCATGGATGC		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.111T>C	2.37:g.171678625T>C		Somatic	27	1	0.037037		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	37	CCDS2239.1																																																																																			T|0.654;C|0.346	0.346	strong		0.642	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
DENND6B	414918	hgsc.bcm.edu	37	22	50754466	50754466	+	Silent	SNP	C	C	T	rs62241230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50754466C>T	ENST00000413817.3	-	8	761	c.690G>A	c.(688-690)caG>caA	p.Q230Q	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	230					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										CTTGGTCAAACTGCTTCGGAG	0.627													C|||	1723	0.34405	0.2511	0.3429	5008	,	,		20386	0.2679		0.3241	False		,,,				2504	0.5695				p.Q230Q		Atlas-SNP	.											.	.	.	.	0			c.G690A						PASS	.	C		1029,3093		127,775,1159	77.0	86.0	83.0		690	2.5	0.4	22	dbSNP_129	83	2828,5558		492,1844,1857	no	coding-synonymous	FAM116B	NM_001001794.3		619,2619,3016	TT,TC,CC		33.7229,24.9636,30.8363		230/586	50754466	3857,8651	2061	4193	6254	SO:0001819	synonymous_variant	414918	exon8			GTCAAACTGCTTC	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.690G>A	22.37:g.50754466C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	655	0.2999084249084249	132	0.2682926829268293	113	0.31215469613259667	154	0.2692307692307692	256	0.33773087071240104	C	0.114	-1.135026	0.01742	0.249636	0.337229	ENSG00000205593	ENST00000433760	.	.	.	4.6	2.45	0.29901	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999614821	.	.	.	.	.	.	T	0.39187	-0.9626	3	.	.	.	-12.6833	7.1472	0.25589	0.0:0.7883:0.0:0.2117	rs62241230	.	.	.	N	251	.	.	S	-	2	0	FAM116B	49097038	0.944000	0.32072	0.423000	0.26634	0.032000	0.12392	1.553000	0.36255	1.158000	0.42547	0.491000	0.48974	AGT	C|0.691;T|0.309	0.309	strong		0.627	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
SEMA6D	80031	hgsc.bcm.edu	37	15	48053229	48053229	+	Silent	SNP	C	C	A	rs501916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:48053229C>A	ENST00000316364.5	+	4	715	c.276C>A	c.(274-276)ccC>ccA	p.P92P	SEMA6D_ENST00000558014.1_Silent_p.P92P|SEMA6D_ENST00000389428.3_Silent_p.P92P|SEMA6D_ENST00000558816.1_Silent_p.P92P|SEMA6D_ENST00000389433.2_Silent_p.P92P|SEMA6D_ENST00000358066.4_Silent_p.P92P|SEMA6D_ENST00000355997.3_Silent_p.P92P|SEMA6D_ENST00000536845.2_Silent_p.P92P|SEMA6D_ENST00000537942.1_Silent_p.P92P|SEMA6D_ENST00000389425.3_Silent_p.P92P|SEMA6D_ENST00000354744.4_Silent_p.P92P|SEMA6D_ENST00000389432.2_Silent_p.P92P	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	92	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		AAGTAATACCCAACAAGGTGA	0.353													A|||	2403	0.479832	0.5552	0.4107	5008	,	,		18970	0.6339		0.3469	False		,,,				2504	0.4049				p.P92P		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C276A						PASS	.	A	,,,,,,	2322,2074	565.1+/-381.6	599,1124,475	82.0	79.0	80.0		276,276,276,276,276,276,276	3.4	1.0	15	dbSNP_83	80	2785,5809	675.4+/-403.2	456,1873,1968	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA6D	NM_001198999.1,NM_020858.1,NM_024966.2,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	,,,,,,	1055,2997,2443	AA,AC,CC		32.4063,47.1793,39.3149	,,,,,,	92/1012,92/1012,92/477,92/999,92/1018,92/1074,92/598	48053229	5107,7883	2198	4297	6495	SO:0001819	synonymous_variant	80031	exon4			AATACCCAACAAG	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.276C>A	15.37:g.48053229C>A		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	207	97	0.468599	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			C|0.567;A|0.433	0.433	strong		0.353	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
FAM131C	348487	hgsc.bcm.edu	37	1	16384998	16384998	+	Silent	SNP	G	G	C	rs1807285	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16384998G>C	ENST00000375662.4	-	7	960	c.777C>G	c.(775-777)ccC>ccG	p.P259P	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	259	Pro-rich.									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)		GGGAGCCCGGGGGGTGGGTCC	0.716													C|||	1887	0.376797	0.4032	0.2795	5008	,	,		19381	0.4315		0.336	False		,,,				2504	0.3957				p.P259P		Atlas-SNP	.											FAM131C,NS,carcinoma,-1,2	FAM131C	21	2	0			c.C777G						PASS	.						2.0	2.0	2.0					1																	16384998		1394	3106	4500	SO:0001819	synonymous_variant	348487	exon7			GCCCGGGGGGTGG		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.777C>G	1.37:g.16384998G>C		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	14	8	0.571429	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.706;C|0.294	0.294	strong		0.716	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
HLA-A	3105	hgsc.bcm.edu	37	6	29911207	29911207	+	Missense_Mutation	SNP	G	G	A	rs1059520	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911207G>A	ENST00000396634.1	+	5	847	c.506G>A	c.(505-507)cGc>cAc	p.R169H	HLA-A_ENST00000376809.5_Missense_Mutation_p.R169H|HLA-A_ENST00000376806.5_Missense_Mutation_p.R169H|HLA-A_ENST00000376802.2_Missense_Mutation_p.R169H			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	169	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ATCACCAAGCGCAAGTGGGAG	0.647									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.R169H		Atlas-SNP	.											.	HLA-A	89	.	0			c.G506A						PASS	.						34.0	26.0	29.0					6																	29911207		1508	2704	4212	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCAAGCGCAAGTG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.506G>A	6.37:g.29911207G>A	ENSP00000379873:p.Arg169His	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	180	85	0.472222	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	710|710	0.3250915750915751|0.3250915750915751	149|149	0.30284552845528456|0.30284552845528456	124|124	0.3425414364640884|0.3425414364640884	164|164	0.2867132867132867|0.2867132867132867	273|273	0.36015831134564646|0.36015831134564646	.|.	2.879|2.879	-0.232306|-0.232306	0.05983|0.05983	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000355767|ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	.|T;T;T;T	.|0.00856	.|5.61;5.61;5.61;5.61	3.78|3.78	0.89|0.89	0.19218|0.19218	.|MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	.|0.211148	.|0.20683	.|U	.|0.087616	T|T	0.00784|0.00784	0.0026|0.0026	.|.	.|.	.|.	0.51233|0.51233	P|P	8.900000000000574E-5|8.900000000000574E-5	.|D;B;P;B;P;B;B	.|0.61080	.|0.989;0.0;0.936;0.0;0.829;0.0;0.0	.|P;B;P;B;P;B;B	.|0.61874	.|0.895;0.001;0.638;0.001;0.486;0.001;0.001	T|T	0.55933|0.55933	-0.8062|-0.8062	4|8	0.72032|0.29301	D|T	0.01|0.29	.|.	3.0116|3.0116	0.06046|0.06046	0.322:0.0:0.4849:0.1931|0.322:0.0:0.4849:0.1931	rs1059520;rs2975061;rs3179200;rs3200220;rs16896012;rs41540321|rs1059520;rs2975061;rs3179200;rs3200220;rs16896012;rs41540321	.|48;169;169;169;169;169;169	.|B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.|.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	T|H	144|169	.|ENSP00000379873:R169H;ENSP00000366002:R169H;ENSP00000366005:R169H;ENSP00000365998:R169H	ENSP00000348012:A144T|ENSP00000365998:R169H	A|R	+|+	1|2	0|0	HLA-A|HLA-A	30019186|30019186	0.000000|0.000000	0.05858|0.05858	0.011000|0.011000	0.14972|0.14972	0.034000|0.034000	0.12701|0.12701	0.075000|0.075000	0.14686|0.14686	0.052000|0.052000	0.16007|0.16007	-0.515000|-0.515000	0.04445|0.04445	GCA|CGC	A|0.308;G|0.692	0.308	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
FIGLA	344018	hgsc.bcm.edu	37	2	71012604	71012604	+	Silent	SNP	G	G	A	rs7566541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:71012604G>A	ENST00000332372.6	-	3	556	c.552C>T	c.(550-552)caC>caT	p.H184H		NM_001004311.3	NP_001004311.2	Q6QHK4	FIGLA_HUMAN	folliculogenesis specific basic helix-loop-helix	184					multicellular organismal development (GO:0007275)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			endometrium(2)|lung(3)	5						GGCGACAAGCGTGTGCTGGCT	0.468													A|||	3995	0.797724	0.9743	0.7032	5008	,	,		17286	0.9067		0.5905	False		,,,				2504	0.727				p.H184H		Atlas-SNP	.											.	FIGLA	23	.	0			c.C552T						PASS	.	A		3780,418		1696,388,15	249.0	247.0	248.0		552	-3.1	0.0	2	dbSNP_116	248	4744,3686		1343,2058,814	no	coding-synonymous	FIGLA	NM_001004311.3		3039,2446,829	AA,AG,GG		43.7248,9.9571,32.4992		184/220	71012604	8524,4104	2099	4215	6314	SO:0001819	synonymous_variant	344018	exon3			ACAAGCGTGTGCT	BC039536	CCDS46320.1	2p13.3	2013-05-21			ENSG00000183733	ENSG00000183733		"""Basic helix-loop-helix proteins"""	24669	protein-coding gene	gene with protein product	"""factor in the germline alpha"""	608697				12468641	Standard	NM_001004311		Approved	bHLHc8	uc002she.1	Q6QHK4	OTTHUMG00000153440	ENST00000332372.6:c.552C>T	2.37:g.71012604G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	135	56	0.414815	NM_001004311		Silent	SNP	ENST00000332372.6	37	CCDS46320.1																																																																																			G|0.225;A|0.774	0.774	strong		0.468	FIGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331214.1	NM_001004311	
CXorf22	170063	hgsc.bcm.edu	37	X	36007614	36007614	+	Missense_Mutation	SNP	T	T	G	rs6629027	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:36007614T>G	ENST00000297866.5	+	16	2958	c.2892T>G	c.(2890-2892)ttT>ttG	p.F964L		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	964			F -> L (in dbSNP:rs6629027). {ECO:0000269|PubMed:14702039}.					p.F964L(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						GCTATGAATTTGTTGGGTATA	0.333													G|||	1028	0.272318	0.2716	0.232	3775	,	,		12423	0.2292		0.0596	False		,,,				2504	0.2219				p.F964L		Atlas-SNP	.											.	CXorf22	272	.	1	Substitution - Missense(1)	stomach(1)	c.T2892G						PASS	.	G	LEU/PHE	1327,2506		188,756,195,687,376	137.0	115.0	122.0		2892	-4.8	0.0	X	dbSNP_116	122	399,6329		9,267,114,2152,1758	yes	missense	CXorf22	NM_152632.3	22	197,1023,309,2839,2134	GG,GT,G,TT,T		5.9304,34.6204,16.3431	benign	964/977	36007614	1726,8835	2202	4300	6502	SO:0001583	missense	170063	exon16			TGAATTTGTTGGG	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.2892T>G	X.37:g.36007614T>G	ENSP00000297866:p.Phe964Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	389	0.23447860156720915	86	0.20673076923076922	52	0.16149068322981366	91	0.19198312236286919	36	0.049723756906077346	G	0.620	-0.821362	0.02755	0.346204	0.059304	ENSG00000165164	ENST00000297866	T	0.12984	2.63	4.77	-4.83	0.03161	.	1.157710	0.06593	N	0.752410	T	0.00012	0.0000	N	0.00413	-1.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38156	-0.9674	9	0.02654	T	1	0.1628	0.9516	0.01377	0.3927:0.1076:0.1707:0.329	rs6629027;rs61474050;rs6629027	964	Q6ZTR5	CX022_HUMAN	L	964	ENSP00000297866:F964L	ENSP00000297866:F964L	F	+	3	2	CXorf22	35917535	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.145000	0.03194	-1.534000	0.01743	-0.178000	0.13098	TTT	0|0.015;G|0.213	0.213	strong		0.333	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	
LRRC69	100130742	hgsc.bcm.edu	37	8	92213022	92213022	+	Splice_Site	SNP	T	T	A	rs72666050	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:92213022T>A	ENST00000448384.2	+	7	933		c.e7+2		LRRC69_ENST00000343709.3_Splice_Site	NM_001129890.1	NP_001123362.1	Q6ZNQ3	LRC69_HUMAN	leucine rich repeat containing 69											endometrium(1)	1						CCACCAAAGGTAAATGATGCT	0.368													T|||	46	0.0091853	0.003	0.0202	5008	,	,		19526	0.0		0.0229	False		,,,				2504	0.0051				.		Atlas-SNP	.											.	LRRC69	24	.	0			c.933+2T>A						PASS	.	T		4,1380		0,4,688	225.0	186.0	198.0			5.3	1.0	8	dbSNP_130	198	52,3130		0,52,1539	yes	splice-5	LRRC69	NM_001129890.1		0,56,2227	AA,AT,TT		1.6342,0.289,1.2265			92213022	56,4510	692	1591	2283	SO:0001630	splice_region_variant	100130742	exon7			CAAAGGTAAATGA	AK130865		8q21.3	2010-07-14			ENSG00000214954	ENSG00000214954			34303	protein-coding gene	gene with protein product							Standard	NM_001129890		Approved		uc010mal.1	Q6ZNQ3	OTTHUMG00000164023	ENST00000448384.2:c.933+2T>A	8.37:g.92213022T>A		Somatic	224	1	0.00446429		WXS	Illumina HiSeq	Phase_I	215	105	0.488372	NM_001129890		Splice_Site	SNP	ENST00000448384.2	37		20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	11.31	1.600996	0.28534	0.00289	0.016342	ENSG00000214954	ENST00000343709;ENST00000448384	.	.	.	5.29	5.29	0.74685	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6207	0.51115	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRC69	92282198	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	3.978000	0.56881	2.001000	0.58596	0.459000	0.35465	.	T|0.991;A|0.009	0.009	strong		0.368	LRRC69-007	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000415207.1	NM_001129890	Intron
FAM131C	348487	hgsc.bcm.edu	37	1	16385184	16385184	+	Silent	SNP	G	G	A	rs75273615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16385184G>A	ENST00000375662.4	-	7	774	c.591C>T	c.(589-591)agC>agT	p.S197S	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	197								p.S197S(1)		large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		CGCTGGGAAGGCTGTCCTGAA	0.642																																					p.S197S		Atlas-SNP	.											FAM131C,NS,haematopoietic_neoplasm,0,1	FAM131C	21	1	1	Substitution - coding silent(1)	lung(1)	c.C591T						PASS	.						20.0	20.0	20.0					1																	16385184		2002	4131	6133	SO:0001819	synonymous_variant	348487	exon7			GGGAAGGCTGTCC		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.591C>T	1.37:g.16385184G>A		Somatic	346	0	0		WXS	Illumina HiSeq	Phase_I	383	186	0.48564	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Silent	SNP	ENST00000375662.4	37	CCDS41270.1																																																																																			G|0.740;A|0.260	0.260	strong		0.642	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
TELO2	9894	hgsc.bcm.edu	37	16	1545448	1545448	+	Missense_Mutation	SNP	A	A	G	rs2235624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1545448A>G	ENST00000262319.6	+	3	716	c.437A>G	c.(436-438)cAg>cGg	p.Q146R		NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	146			Q -> R (in dbSNP:rs2235624). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.6}.		regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				CAGCAGACGCAGCCCGGCTTC	0.682													A|||	2322	0.463658	0.2103	0.6556	5008	,	,		14106	0.5724		0.6153	False		,,,				2504	0.4018				p.Q146R		Atlas-SNP	.											.	TELO2	44	.	0			c.A437G						PASS	.	A	ARG/GLN	1135,3141		159,817,1162	15.0	14.0	14.0		437	-2.6	0.0	16	dbSNP_98	14	4963,3375		1519,1925,725	no	missense	TELO2	NM_016111.3	43	1678,2742,1887	GG,GA,AA		40.4773,26.5435,48.3431	benign	146/838	1545448	6098,6516	2138	4169	6307	SO:0001583	missense	9894	exon3			AGACGCAGCCCGG	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.437A>G	16.37:g.1545448A>G	ENSP00000262319:p.Gln146Arg	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	1120	0.5128205128205128	99	0.20121951219512196	250	0.6906077348066298	310	0.541958041958042	461	0.6081794195250659	A	4.060	0.008978	0.07912	0.265435	0.595227	ENSG00000100726	ENST00000262319	D	0.83591	-1.74	5.33	-2.64	0.06114	.	1.263210	0.05448	N	0.549007	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.31910	0.346	B	0.24269	0.052	T	0.28744	-1.0034	9	0.18276	T	0.48	-10.9661	7.4525	0.27246	0.508:0.3423:0.1497:0.0	rs2235624;rs17845529;rs17858425;rs60202364;rs2235624	146	Q9Y4R8	TELO2_HUMAN	R	146	ENSP00000262319:Q146R	ENSP00000262319:Q146R	Q	+	2	0	TELO2	1485449	0.006000	0.16342	0.004000	0.12327	0.010000	0.07245	0.588000	0.23924	-0.281000	0.09141	-1.063000	0.02288	CAG	A|0.531;G|0.469	0.469	strong		0.682	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
PASD1	139135	hgsc.bcm.edu	37	X	150791512	150791512	+	Silent	SNP	C	C	T	rs5924978	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:150791512C>T	ENST00000370357.4	+	7	767	c.522C>T	c.(520-522)tgC>tgT	p.C174C		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	174						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)					GAAATGTTTGCATTCTCAGGA	0.517													c|||	417	0.110464	0.0605	0.0951	3775	,	,		12433	0.0139		0.1213	False		,,,				2504	0.138				p.C174C		Atlas-SNP	.											.	PASD1	286	.	0			c.C522T						PASS	.	T		381,3454		16,289,60,1327,511	231.0	174.0	194.0		522	-3.2	0.0	X	dbSNP_114	194	1027,5701		54,608,311,1766,1561	no	coding-synonymous	PASD1	NM_173493.2		70,897,371,3093,2072	TT,TC,T,CC,C		15.2646,9.9348,13.3295		174/774	150791512	1408,9155	2203	4300	6503	SO:0001819	synonymous_variant	139135	exon7			TGTTTGCATTCTC	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.522C>T	X.37:g.150791512C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	114	112	0.982456	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Silent	SNP	ENST00000370357.4	37	CCDS35431.1																																																																																			C|0.879;0|0.003	.	strong		0.517	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
CRMP1	1400	hgsc.bcm.edu	37	4	5837708	5837708	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5837708C>T	ENST00000397890.2	-	11	1429	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	CRMP1_ENST00000324989.7_Silent_p.S519S|CRMP1_ENST00000512574.1_Silent_p.S403S|CRMP1_ENST00000511535.1_5'UTR	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	405					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.S519S(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CGTCGGCATCCGAGCCCACGG	0.522																																					p.S519S		Atlas-SNP	.											CRMP1,NS,carcinoma,-1,2	CRMP1	118	2	1	Substitution - coding silent(1)	stomach(1)	c.G1557A						PASS	.						149.0	135.0	140.0					4																	5837708		2203	4300	6503	SO:0001819	synonymous_variant	1400	exon11			GGCATCCGAGCCC	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1215G>A	4.37:g.5837708C>T		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	183	77	0.420765	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																			.	.	none		0.522	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21770730	21770730	+	Missense_Mutation	SNP	A	A	G	rs6571751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21770730A>G	ENST00000400017.2	+	4	574	c.574A>G	c.(574-576)Aaa>Gaa	p.K192E	RPGRIP1_ENST00000556336.1_Missense_Mutation_p.K192E|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.K192E|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.K192E	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	192			K -> E (in dbSNP:rs6571751). {ECO:0000269|PubMed:18682808}.		eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		AGTAGCCAGTAAACCCAGTGA	0.423													G|||	2390	0.477236	0.472	0.5101	5008	,	,		16887	0.3224		0.501	False		,,,				2504	0.5961				p.K192E		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.A574G						PASS	.	G	GLU/LYS	1697,2091		377,943,574	44.0	45.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	574	3.1	0.1	14	dbSNP_116	44	4112,4140		1050,2012,1064	yes	missense	RPGRIP1	NM_020366.3	56	1427,2955,1638	GG,GA,AA		49.8303,44.7994,48.2475	benign	192/1287	21770730	5809,6231	1894	4126	6020	SO:0001583	missense	57096	exon4			GCCAGTAAACCCA	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.574A>G	14.37:g.21770730A>G	ENSP00000382895:p.Lys192Glu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	991	0.45375457875457875	243	0.49390243902439024	182	0.5027624309392266	187	0.3269230769230769	379	0.5	G	0.004	-2.347412	0.00219	0.447994	0.498303	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.0	3.11	0.35812	.	1.683130	0.02576	N	0.098365	T	0.00012	0.0000	N	0.00729	-1.24	0.58432	P	5.999999999950489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.02654	T	1	-0.7479	6.5573	0.22468	0.2168:0.0:0.7832:0.0	rs6571751;rs52798683;rs59879033;rs6571751	192	Q96KN7	RPGR1_HUMAN	E	192	ENSP00000450445:K192E;ENSP00000451219:K192E;ENSP00000382895:K192E;ENSP00000206660:K192E	ENSP00000206660:K192E	K	+	1	0	RPGRIP1	20840570	0.027000	0.19231	0.062000	0.19696	0.004000	0.04260	1.415000	0.34748	0.668000	0.31126	-0.128000	0.14901	AAA	A|0.546;G|0.454	0.454	strong		0.423	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
SETMAR	6419	hgsc.bcm.edu	37	3	4354697	4354697	+	Missense_Mutation	SNP	G	G	A	rs6801634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:4354697G>A	ENST00000358065.4	+	2	339	c.272G>A	c.(271-273)cGc>cAc	p.R91H	SETMAR_ENST00000425863.1_Missense_Mutation_p.R91H|SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000462115.1_3'UTR|SETMAR_ENST00000430981.1_Missense_Mutation_p.R91H	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	91	Histone-lysine N-methyltransferase.|Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.			R -> H (in Ref. 1; BAG63636). {ECO:0000305}.	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)		TCCTGTCTCCGCCATGGAGAG	0.483								Chromatin Structure					G|||	609	0.121605	0.1014	0.1167	5008	,	,		18899	0.0982		0.16	False		,,,				2504	0.137				p.R91H		Atlas-SNP	.											.	SETMAR	30	.	0			c.G272A						PASS	.	G	HIS/ARG	458,3948	220.4+/-237.8	24,410,1769	84.0	76.0	79.0		272	1.0	0.8	3	dbSNP_116	79	1215,7385	245.6+/-274.3	70,1075,3155	yes	missense	SETMAR	NM_006515.3	29	94,1485,4924	AA,AG,GG		14.1279,10.3949,12.8633	possibly-damaging	91/685	4354697	1673,11333	2203	4300	6503	SO:0001583	missense	6419	exon2			GTCTCCGCCATGG	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.272G>A	3.37:g.4354697G>A	ENSP00000373354:p.Arg91His	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	137	67	0.489051	NM_001243723	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	273	0.125	54	0.10975609756097561	43	0.11878453038674033	54	0.0944055944055944	122	0.16094986807387862	G	9.041	0.989745	0.18966	0.103949	0.141279	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863	D;D;T	0.89552	-2.53;-2.53;-1.09	5.13	1.01	0.19927	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	.	.	.	.	T	0.01124	0.0037	M	0.64567	1.98	0.58432	P	1.0000000000287557E-6	P;P;B	0.43750	0.816;0.699;0.031	B;B;B	0.29716	0.106;0.058;0.006	T	0.41680	-0.9495	8	0.56958	D	0.05	.	3.9103	0.09201	0.1543:0.1976:0.5295:0.1185	rs6801634;rs52791578;rs58831512;rs6801634	91;78;91	E7EN68;Q53H47;C9JHK2	.;SETMR_HUMAN;.	H	91	ENSP00000373354:R91H;ENSP00000403000:R91H;ENSP00000403145:R91H	ENSP00000373354:R91H	R	+	2	0	SETMAR	4329697	0.003000	0.15002	0.809000	0.32408	0.376000	0.30014	0.089000	0.15002	0.571000	0.29365	-0.262000	0.10625	CGC	G|0.871;A|0.129	0.129	strong		0.483	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
FRAS1	80144	hgsc.bcm.edu	37	4	79437155	79437155	+	Silent	SNP	C	C	T	rs3749487	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:79437155C>T	ENST00000264895.6	+	66	10817	c.10377C>T	c.(10375-10377)acC>acT	p.T3459T		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3455					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.T3459T(2)|p.T3460T(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GCTCTGTAACCGCTGACTTCC	0.507													C|||	884	0.176518	0.177	0.1398	5008	,	,		18849	0.2242		0.2058	False		,,,				2504	0.1227				p.T3459T		Atlas-SNP	.											FRAS1_ENST00000264895,NS,carcinoma,0,2	FRAS1	779	2	3	Substitution - coding silent(3)	prostate(3)	c.C10377T						scavenged	.	C		762,3516		66,630,1443	69.0	74.0	72.0		10377	-4.6	0.7	4	dbSNP_107	72	1551,6979		140,1271,2854	no	coding-synonymous	FRAS1	NM_025074.6		206,1901,4297	TT,TC,CC		18.1829,17.8121,18.059		3459/4013	79437155	2313,10495	2139	4265	6404	SO:0001819	synonymous_variant	80144	exon66			TGTAACCGCTGAC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10377C>T	4.37:g.79437155C>T		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	150	55	0.366667	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	432	0.1978021978021978	96	0.1951219512195122	58	0.16022099447513813	128	0.22377622377622378	150	0.19788918205804748	C	1.309	-0.602724	0.03744	0.178121	0.181829	ENSG00000138759	ENST00000512123	.	.	.	5.97	-4.61	0.03380	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33929	-0.9849	3	.	.	.	.	2.7957	0.05400	0.1827:0.3609:0.0961:0.3603	rs3749487;rs57228815	.	.	.	C	1688	.	.	R	+	1	0	FRAS1	79656179	0.002000	0.14202	0.743000	0.31040	0.168000	0.22595	-1.645000	0.02000	-0.358000	0.08162	-0.606000	0.04082	CGC	C|0.803;T|0.197	0.197	strong		0.507	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
GGT1	2678	hgsc.bcm.edu	37	22	25007202	25007202	+	Missense_Mutation	SNP	A	A	G	rs2330838		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:25007202A>G	ENST00000400382.1	+	5	909	c.154A>G	c.(154-156)Aag>Gag	p.K52E	GGT1_ENST00000400383.1_Missense_Mutation_p.K52E|GGT1_ENST00000248923.4_Missense_Mutation_p.K52E|GGT1_ENST00000406383.2_Missense_Mutation_p.K52E|GGT1_ENST00000400380.1_Missense_Mutation_p.K52E			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	52			K -> E (in dbSNP:rs2330838).		arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.K52E(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	GCAGTGCTCGAAGAttgggag	0.607																																					p.K52E		Atlas-SNP	.											GGT1,NS,other,0,1	GGT1	68	1	1	Substitution - Missense(1)	pancreas(1)	c.A154G						scavenged	.																																			SO:0001583	missense	2678	exon5			TGCTCGAAGATTG	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.154A>G	22.37:g.25007202A>G	ENSP00000383232:p.Lys52Glu	Somatic	398	0	0		WXS	Illumina HiSeq	Phase_I	304	98	0.322368	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	2.776	-0.254624	0.05829	.	.	ENSG00000100031	ENST00000248923;ENST00000411974;ENST00000412658;ENST00000445029;ENST00000419133;ENST00000400382;ENST00000452551;ENST00000400383;ENST00000412898;ENST00000400380;ENST00000455483;ENST00000430289;ENST00000447416;ENST00000432867;ENST00000451366;ENST00000406383;ENST00000428855	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.20463	3.25;3.25;3.25;2.07;3.25;3.25;3.25;3.25;2.07;3.25;3.25;3.25;3.25;3.25;3.25;3.25;3.25	3.5	3.5	0.40072	.	0.140255	0.46442	N	0.000281	T	0.05044	0.0135	N	0.00823	-1.155	0.21386	N	0.999705	B	0.02656	0.0	B	0.04013	0.001	T	0.40924	-0.9537	10	0.02654	T	1	-12.471	8.7769	0.34767	0.1139:0.0:0.8861:0.0	rs2330838	52	P19440	GGT1_HUMAN	E	52	ENSP00000248923:K52E;ENSP00000389935:K52E;ENSP00000393537:K52E;ENSP00000393135:K52E;ENSP00000395271:K52E;ENSP00000383232:K52E;ENSP00000415553:K52E;ENSP00000383233:K52E;ENSP00000408151:K52E;ENSP00000383231:K52E;ENSP00000415024:K52E;ENSP00000417044:K52E;ENSP00000400621:K52E;ENSP00000398589:K52E;ENSP00000387796:K52E;ENSP00000385975:K52E;ENSP00000415068:K52E	ENSP00000248923:K52E	K	+	1	0	GGT1	23337202	1.000000	0.71417	0.890000	0.34922	0.477000	0.33069	3.277000	0.51654	0.781000	0.33589	-0.128000	0.14901	AAG	A|1.000;|0.000	.	weak		0.607	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
RGS18	64407	hgsc.bcm.edu	37	1	192153626	192153626	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:192153626G>A	ENST00000367460.3	+	5	831	c.650G>A	c.(649-651)cGc>cAc	p.R217H		NM_130782.2	NP_570138.1	Q9NS28	RGS18_HUMAN	regulator of G-protein signaling 18	217					G-protein coupled receptor signaling pathway (GO:0007186)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			kidney(1)|large_intestine(2)|lung(15)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGACGATCACGCTCATTTACC	0.348																																					p.R217H		Atlas-SNP	.											RGS18,NS,carcinoma,-1,1	RGS18	54	1	0			c.G650A						scavenged	.						93.0	86.0	88.0					1																	192153626		2203	4299	6502	SO:0001583	missense	64407	exon5			GATCACGCTCATT	AF268036	CCDS1374.1	1q31.2	2008-02-05	2007-08-14		ENSG00000150681	ENSG00000150681		"""Regulators of G-protein signaling"""	14261	protein-coding gene	gene with protein product		607192	"""regulator of G-protein signalling 18"""			11042171	Standard	NM_130782		Approved	RGS13	uc001gsg.3	Q9NS28	OTTHUMG00000035592	ENST00000367460.3:c.650G>A	1.37:g.192153626G>A	ENSP00000356430:p.Arg217His	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	218	4	0.0183486	NM_130782	B2RD23	Missense_Mutation	SNP	ENST00000367460.3	37	CCDS1374.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.654609	0.88056	.	.	ENSG00000150681	ENST00000367460	T	0.55413	0.52	5.62	5.62	0.85841	.	0.094103	0.85682	D	0.000000	T	0.60366	0.2263	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	P	0.60609	0.877	T	0.57027	-0.7881	10	0.38643	T	0.18	.	16.3945	0.83586	0.0:0.0:1.0:0.0	.	217	Q9NS28	RGS18_HUMAN	H	217	ENSP00000356430:R217H	ENSP00000356430:R217H	R	+	2	0	RGS18	190420249	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.933000	0.70130	2.648000	0.89879	0.563000	0.77884	CGC	.	.	none		0.348	RGS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086382.1	NM_130782	
LRP1B	53353	hgsc.bcm.edu	37	2	142567910	142567910	+	Missense_Mutation	SNP	T	T	C	rs12990449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:142567910T>C	ENST00000389484.3	-	2	1114	c.143A>G	c.(142-144)cAg>cGg	p.Q48R	LRP1B_ENST00000486364.1_5'UTR	NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	48	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.		Q -> R (in dbSNP:rs12990449).		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)		CAGCCAGCTCTGGGAGACACA	0.433										TSP Lung(27;0.18)			T|||	1089	0.217452	0.0658	0.1787	5008	,	,		17310	0.3532		0.2296	False		,,,				2504	0.2975				p.Q48R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A143G						PASS	.	T	ARG/GLN	427,3979	205.5+/-227.4	19,389,1795	61.0	57.0	59.0		143	4.4	1.0	2	dbSNP_121	59	1852,6748	331.2+/-319.6	211,1430,2659	yes	missense	LRP1B	NM_018557.2	43	230,1819,4454	CC,CT,TT		21.5349,9.6913,17.5227	benign	48/4600	142567910	2279,10727	2203	4300	6503	SO:0001583	missense	53353	exon2			CAGCTCTGGGAGA	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.143A>G	2.37:g.142567910T>C	ENSP00000374135:p.Gln48Arg	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	241	115	0.477178	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	471	0.21565934065934067	29	0.05894308943089431	59	0.16298342541436464	213	0.3723776223776224	170	0.22427440633245382	T	13.77	2.335108	0.41398	0.096913	0.215349	ENSG00000168702	ENST00000389484;ENST00000434794	D;D	0.95342	-3.68;-3.68	5.62	4.45	0.53987	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.173808	0.37906	N	0.001897	T	0.00012	0.0000	N	0.13235	0.315	0.35468	P	0.20288899999999999	B;B	0.06786	0.001;0.001	B;B	0.10450	0.003;0.005	T	0.08554	-1.0716	9	0.15499	T	0.54	.	7.8759	0.29592	0.0:0.072:0.1396:0.7884	rs12990449;rs52808262;rs12990449	86;48	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	R	48	ENSP00000374135:Q48R;ENSP00000413239:Q48R	ENSP00000374135:Q48R	Q	-	2	0	LRP1B	142284380	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.525000	0.53502	0.946000	0.37632	0.528000	0.53228	CAG	C|0.208;N|0.000	0.208	strong		0.433	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
GADL1	339896	hgsc.bcm.edu	37	3	30819751	30819751	+	Missense_Mutation	SNP	C	C	T	rs143542109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:30819751C>T	ENST00000282538.5	-	14	1462	c.1312G>A	c.(1312-1314)Gcc>Acc	p.A438T	GADL1_ENST00000498387.1_5'UTR	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	438					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						CAAATATTGGCATATTCAGGC	0.328													C|||	10	0.00199681	0.0	0.0058	5008	,	,		18837	0.0		0.003	False		,,,				2504	0.0031				p.A438T		Atlas-SNP	.											.	GADL1	91	.	0			c.G1312A						PASS	.	C	THR/ALA	7,4399	9.9+/-24.2	0,7,2196	64.0	69.0	67.0		1312	3.9	1.0	3	dbSNP_134	67	57,8543	35.3+/-89.8	1,55,4244	yes	missense	GADL1	NM_207359.2	58	1,62,6440	TT,TC,CC		0.6628,0.1589,0.4921	benign	438/522	30819751	64,12942	2203	4300	6503	SO:0001583	missense	339896	exon14			TATTGGCATATTC	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1312G>A	3.37:g.30819751C>T	ENSP00000282538:p.Ala438Thr	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	259	117	0.451737	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	37	CCDS2649.2	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	6.061	0.379542	0.11466	0.001589	0.006628	ENSG00000144644	ENST00000282538	T	0.37752	1.18	6.02	3.86	0.44501	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.241129	0.41938	N	0.000786	T	0.08179	0.0204	N	0.01742	-0.745	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.17289	-1.0374	10	0.02654	T	1	-3.3176	9.603	0.39617	0.0:0.7967:0.0:0.2033	.	438	Q6ZQY3	GADL1_HUMAN	T	438	ENSP00000282538:A438T	ENSP00000282538:A438T	A	-	1	0	GADL1	30794755	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.300000	0.51834	1.213000	0.43380	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.328	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359	
IFT140	9742	hgsc.bcm.edu	37	16	1614097	1614097	+	Silent	SNP	A	A	G	rs8048410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1614097A>G	ENST00000426508.2	-	17	2331	c.1968T>C	c.(1966-1968)agT>agC	p.S656S	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	656					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				GCCGGGGCTCACTCTGGTCCC	0.592													G|||	2530	0.505192	0.7179	0.3934	5008	,	,		14960	0.5675		0.2982	False		,,,				2504	0.4458				p.S656S		Atlas-SNP	.											.	IFT140	128	.	0			c.T1968C						PASS	.	G		2832,1566	488.1+/-361.1	911,1010,278	53.0	62.0	59.0		1968	-6.0	0.4	16	dbSNP_116	59	2666,5934	684.2+/-403.9	413,1840,2047	no	coding-synonymous	IFT140	NM_014714.3		1324,2850,2325	GG,GA,AA		31.0,35.6071,42.2988		656/1463	1614097	5498,7500	2199	4300	6499	SO:0001819	synonymous_variant	9742	exon17			GGGCTCACTCTGG	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1968T>C	16.37:g.1614097A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	174	89	0.511494	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																			A|0.566;G|0.434	0.434	strong		0.592	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
DNAJC13	23317	hgsc.bcm.edu	37	3	132218623	132218623	+	Missense_Mutation	SNP	G	G	T	rs3762672	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132218623G>T	ENST00000260818.6	+	38	4635	c.4387G>T	c.(4387-4389)Gct>Tct	p.A1463S		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1463			A -> S (in dbSNP:rs3762672). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9734811}.		osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CTTGACTCGTGCTAGTAAACC	0.423													T|||	3701	0.739018	0.9796	0.513	5008	,	,		17576	0.8839		0.4891	False		,,,				2504	0.682				p.A1463S		Atlas-SNP	.											.	DNAJC13	253	.	0			c.G4387T						PASS	.	T	SER/ALA	3918,488	228.5+/-243.3	1744,430,29	221.0	230.0	227.0		4387	5.2	1.0	3	dbSNP_107	227	4130,4470	590.3+/-392.7	1012,2106,1182	yes	missense	DNAJC13	NM_015268.3	99	2756,2536,1211	TT,TG,GG		48.0233,11.0758,38.1209	benign	1463/2244	132218623	8048,4958	2203	4300	6503	SO:0001583	missense	23317	exon38			ACTCGTGCTAGTA	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.4387G>T	3.37:g.132218623G>T	ENSP00000260818:p.Ala1463Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	82	49	0.597561	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	1587	0.7266483516483516	477	0.9695121951219512	197	0.5441988950276243	535	0.9353146853146853	378	0.49868073878627966	T	9.154	1.017079	0.19355	0.889242	0.480233	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.44881	0.91	5.17	5.17	0.71159	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00094	-2.165	0.47374	P	5.979999999999874E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41734	-0.9492	9	0.02654	T	1	.	12.5822	0.56397	0.0:0.0:0.139:0.8609	rs3762672;rs17411585;rs52836147;rs60113069;rs3762672	1463	O75165	DJC13_HUMAN	S	1463;110	ENSP00000260818:A1463S	ENSP00000260818:A1463S	A	+	1	0	DNAJC13	133701313	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.799000	0.69101	0.901000	0.36495	-0.375000	0.07067	GCT	G|0.315;T|0.685	0.685	strong		0.423	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
TNIP1	10318	hgsc.bcm.edu	37	5	150410219	150410219	+	3'UTR	SNP	C	C	A	rs2233311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:150410219C>A	ENST00000389378.2	-	0	2554				TNIP1_ENST00000518977.1_Missense_Mutation_p.R631I|TNIP1_ENST00000521591.1_3'UTR|TNIP1_ENST00000521423.1_5'Flank|TNIP1_ENST00000523338.1_Missense_Mutation_p.R631I|TNIP1_ENST00000524280.1_3'UTR|TNIP1_ENST00000522226.1_3'UTR|TNIP1_ENST00000520931.1_3'UTR|TNIP1_ENST00000315050.7_3'UTR	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1						defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTTGGCAATCTGAGATCAGC	0.517													C|||	535	0.106829	0.0673	0.0634	5008	,	,		18524	0.1726		0.0944	False		,,,				2504	0.136				p.R631I		Atlas-SNP	.											.	TNIP1	51	.	0			c.G1892T						PASS	.	C		95,1289		3,89,600	68.0	63.0	65.0			4.8	1.0	5	dbSNP_98	65	372,2810		24,324,1243	no	utr-3	TNIP1	NM_006058.3		27,413,1843	AA,AC,CC		11.6908,6.8642,10.2278			150410219	467,4099	692	1591	2283	SO:0001624	3_prime_UTR_variant	10318	exon18			GGCAATCTGAGAT	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.*55G>T	5.37:g.150410219C>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	44	0.60274	NM_001252393	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	236	0.10805860805860806	51	0.10365853658536585	22	0.06077348066298342	87	0.1520979020979021	76	0.10026385224274406	C	12.73	2.025598	0.35701	0.068642	0.116908	ENSG00000145901	ENST00000523338;ENST00000518977	T;T	0.11821	2.74;2.74	5.62	4.75	0.60458	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999980101	P;P	0.35628	0.513;0.513	B;B	0.36989	0.238;0.181	T	0.20739	-1.0266	7	0.49607	T	0.09	.	12.5228	0.56069	0.0:0.8324:0.1676:0.0	rs2233311;rs60477588;rs2233311	521;631	A4F1X7;A4F1W9	.;.	I	631	ENSP00000428243:R631I;ENSP00000430971:R631I	ENSP00000430971:R631I	R	-	2	0	TNIP1	150390412	0.996000	0.38824	0.959000	0.39883	0.222000	0.24845	3.585000	0.53943	1.353000	0.45828	0.448000	0.29417	AGA	G|0.000;C|0.890;A|0.109	0.109	strong		0.517	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
IFIT2	3433	hgsc.bcm.edu	37	10	91066769	91066769	+	Missense_Mutation	SNP	C	C	A	rs1727	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:91066769C>A	ENST00000371826.3	+	2	1225	c.1056C>A	c.(1054-1056)gaC>gaA	p.D352E	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	352			D -> E (in dbSNP:rs1727).		apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				AGTATGAAGACGCAGAGTATT	0.453													a|||	4401	0.878794	0.9871	0.6916	5008	,	,		20221	0.9921		0.7624	False		,,,				2504	0.8681				p.D352E		Atlas-SNP	.											.	IFIT2	39	.	0			c.C1056A						PASS	.	A	GLU/ASP	3657,195		1738,181,7	63.0	62.0	62.0		1056	2.2	1.0	10	dbSNP_36	62	6190,2082		2310,1570,256	yes	missense	IFIT2	NM_001547.4	45	4048,1751,263	AA,AC,CC		25.1692,5.0623,18.7809	benign	352/473	91066769	9847,2277	1926	4136	6062	SO:0001583	missense	3433	exon2			TGAAGACGCAGAG	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"""Tetratricopeptide (TTC) repeat domain containing"""	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.1056C>A	10.37:g.91066769C>A	ENSP00000360891:p.Asp352Glu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001547	Q5T767	Missense_Mutation	SNP	ENST00000371826.3	37	CCDS41548.1	1891	0.8658424908424909	482	0.9796747967479674	257	0.7099447513812155	568	0.993006993006993	584	0.7704485488126649	A	1.897	-0.454146	0.04540	0.949377	0.748308	ENSG00000119922	ENST00000371826	T	0.32272	1.46	4.58	2.19	0.27852	Tetratricopeptide-like helical (1);	0.848963	0.10299	N	0.691321	T	0.00012	0.0000	N	0.00583	-1.355	0.54753	P	2.0000000000020002E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.31586	-0.9938	9	0.02654	T	1	-1.7576	7.3744	0.26821	0.6564:0.2709:0.0727:0.0	rs1727;rs3168004;rs17468851;rs17846022;rs17859006;rs56477102;rs58671084;rs1727	352	P09913	IFIT2_HUMAN	E	352	ENSP00000360891:D352E	ENSP00000360891:D352E	D	+	3	2	IFIT2	91056749	0.994000	0.37717	0.985000	0.45067	0.796000	0.44982	0.637000	0.24659	0.138000	0.18790	-1.023000	0.02433	GAC	C|0.132;A|0.868	0.868	strong		0.453	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547	
AMPD3	272	hgsc.bcm.edu	37	11	10521749	10521749	+	Silent	SNP	C	C	T	rs114718879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:10521749C>T	ENST00000396554.3	+	11	2042	c.1701C>T	c.(1699-1701)taC>taT	p.Y567Y	AMPD3_ENST00000530864.1_3'UTR|AMPD3_ENST00000444303.2_Silent_p.Y399Y	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	558					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		ACAGCTACTACCTGTACTACA	0.547													C|||	62	0.0123802	0.0015	0.0173	5008	,	,		26462	0.0		0.0398	False		,,,				2504	0.0082				p.Y567Y		Atlas-SNP	.											.	AMPD3	68	.	0			c.C1701T						PASS	.	C	,,,,	20,4382	29.0+/-57.7	0,20,2181	335.0	220.0	259.0		1701,1674,1695,1674,1197	4.5	1.0	11	dbSNP_132	259	193,8395	85.0+/-147.5	8,177,4109	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	8,197,6290	TT,TC,CC		2.2473,0.4543,1.6397	,,,,	567/777,558/768,565/775,558/768,399/609	10521749	213,12777	2201	4294	6495	SO:0001819	synonymous_variant	272	exon11			CTACTACCTGTAC	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.1701C>T	11.37:g.10521749C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	163	82	0.503067	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			C|0.983;T|0.017	0.017	strong		0.547	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
VWA8	23078	hgsc.bcm.edu	37	13	42404710	42404710	+	Missense_Mutation	SNP	C	C	T	rs41288297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:42404710C>T	ENST00000379310.3	-	14	1723	c.1655G>A	c.(1654-1656)cGt>cAt	p.R552H	VWA8_ENST00000281496.6_Missense_Mutation_p.R552H	NM_015058.1	NP_055873.1	A3KMH1	VWA8_HUMAN	von Willebrand factor A domain containing 8	552						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)										CTCCTTTAAACGCATATACCT	0.378													C|||	227	0.0453275	0.087	0.0389	5008	,	,		16008	0.0		0.0417	False		,,,				2504	0.044				p.R552H		Atlas-SNP	.											.	.	.	.	0			c.G1655A						PASS	.	C	HIS/ARG,HIS/ARG	396,4010	197.4+/-221.5	28,340,1835	115.0	111.0	112.0		1655,1655	2.3	0.0	13	dbSNP_127	112	438,8162	133.6+/-191.1	13,412,3875	yes	missense,missense	KIAA0564	NM_001009814.1,NM_015058.1	29,29	41,752,5710	TT,TC,CC		5.093,8.9877,6.4124	benign,benign	552/1040,552/1906	42404710	834,12172	2203	4300	6503	SO:0001583	missense	23078	exon14			TTTAAACGCATAT	AB011136	CCDS31963.1, CCDS41881.1	13q14.11	2013-11-18	2012-08-02	2012-08-02	ENSG00000102763	ENSG00000102763			29071	protein-coding gene	gene with protein product			"""KIAA0564"""	KIAA0564		9628581	Standard	NM_015058		Approved		uc001uyj.3	A3KMH1	OTTHUMG00000016799	ENST00000379310.3:c.1655G>A	13.37:g.42404710C>T	ENSP00000368612:p.Arg552His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_015058	O60310|Q5JTP6|Q5VW08|Q7Z6I9|Q86YC9|Q8N3E4	Missense_Mutation	SNP	ENST00000379310.3	37	CCDS41881.1	72	0.03296703296703297	32	0.06504065040650407	11	0.03038674033149171	0	0.0	29	0.03825857519788918	C	12.11	1.840629	0.32513	0.089877	0.05093	ENSG00000102763	ENST00000251030;ENST00000379310;ENST00000281496	T;T	0.12039	2.92;2.72	6.06	2.3	0.28687	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.620900	0.17234	N	0.181819	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.13407	0.009	T	0.38090	-0.9677	10	0.39692	T	0.17	.	4.2991	0.10916	0.1533:0.4749:0.0:0.3718	rs41288297;rs57164625;rs61743604	552	A3KMH1	K0564_HUMAN	H	456;552;552	ENSP00000368612:R552H;ENSP00000281496:R552H	ENSP00000251030:R456H	R	-	2	0	KIAA0564	41302710	0.001000	0.12720	0.002000	0.10522	0.947000	0.59692	0.837000	0.27558	0.904000	0.36572	-0.133000	0.14855	CGT	C|0.947;T|0.053	0.053	strong		0.378	VWA8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354828.2	NM_015058	
ABRA	137735	hgsc.bcm.edu	37	8	107782395	107782395	+	Silent	SNP	G	G	A	rs11996466	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:107782395G>A	ENST00000311955.3	-	1	78	c.24C>T	c.(22-24)agC>agT	p.S8S		NM_139166.4	NP_631905.1			actin-binding Rho activating protein											breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			GGCCCTCCCCGCTTTCCTTTT	0.602													G|||	2208	0.440895	0.5643	0.304	5008	,	,		16988	0.5188		0.3579	False		,,,				2504	0.3763				p.S8S		Atlas-SNP	.											ABRA,rectum,carcinoma,-1,1	ABRA	57	1	0			c.C24T						PASS	.	G		2307,2097		630,1047,525	37.0	42.0	40.0		24	-0.0	0.2	8	dbSNP_120	40	3019,5577		533,1953,1812	no	coding-synonymous	ABRA	NM_139166.4		1163,3000,2337	AA,AG,GG		35.121,47.6158,40.9692		8/382	107782395	5326,7674	2202	4298	6500	SO:0001819	synonymous_variant	137735	exon1			CTCCCCGCTTTCC	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"""striated muscle activator of Rho-dependent signaling"""	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.24C>T	8.37:g.107782395G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	28	0.509091	NM_139166		Silent	SNP	ENST00000311955.3	37	CCDS6305.1																																																																																			G|0.575;A|0.425	0.425	strong		0.602	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166	
ATP10B	23120	hgsc.bcm.edu	37	5	159992655	159992655	+	Silent	SNP	T	T	C	rs3812005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:159992655T>C	ENST00000327245.5	-	26	5037	c.4191A>G	c.(4189-4191)gtA>gtG	p.V1397V		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1397					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTTCGTGGAGTACTGACTCTT	0.557													C|||	1787	0.356829	0.4781	0.4323	5008	,	,		19097	0.1706		0.33	False		,,,				2504	0.3589				p.V1397V		Atlas-SNP	.											.	ATP10B	201	.	0			c.A4191G						PASS	.	C		1743,2373		375,993,690	114.0	124.0	121.0		4191	-5.9	0.0	5	dbSNP_107	121	2777,5595		450,1877,1859	no	coding-synonymous	ATP10B	NM_025153.2		825,2870,2549	CC,CT,TT		33.1701,42.3469,36.1947		1397/1462	159992655	4520,7968	2058	4186	6244	SO:0001819	synonymous_variant	23120	exon26			GTGGAGTACTGAC	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.4191A>G	5.37:g.159992655T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	37	CCDS43394.1																																																																																			T|0.662;C|0.338	0.338	strong		0.557	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
MXRA5	25878	hgsc.bcm.edu	37	X	3241256	3241256	+	Missense_Mutation	SNP	T	T	C	rs5983119	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3241256T>C	ENST00000217939.6	-	5	2624	c.2470A>G	c.(2470-2472)Att>Gtt	p.I824V		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	824			I -> V (in dbSNP:rs5983119). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GGGGGAGAAATAGCAGGAAAA	0.488													C|||	2831	0.749934	0.6853	0.5216	3775	,	,		14207	0.5595		0.5288	False		,,,				2504	0.4775				p.I824V		Atlas-SNP	.											.	MXRA5	815	.	0			c.A2470G						PASS	.	C	VAL/ILE	3360,475		1270,329,491,33,80	128.0	127.0	128.0		2470	0.1	0.0	X	dbSNP_114	128	4339,2389		1019,1109,1192,300,680	yes	missense	MXRA5	NM_015419.3	29	2289,1438,1683,333,760	CC,CT,C,TT,T		35.5083,12.3859,27.1135	benign	824/2829	3241256	7699,2864	2203	4300	6503	SO:0001583	missense	25878	exon5			GAGAAATAGCAGG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2470A>G	X.37:g.3241256T>C	ENSP00000217939:p.Ile824Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	1233	0.7432188065099458	236	0.8251748251748252	131	0.5077519379844961	206	0.5885714285714285	272	0.5291828793774319	c	0.011	-1.733413	0.00687	0.876141	0.644917	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.61274	0.12	3.63	0.0923	0.14472	.	1.970240	0.02957	N	0.142505	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	0.41893	-0.9483	9	0.02654	T	1	.	2.6272	0.04933	0.1281:0.4316:0.2503:0.1899	rs5983119;rs6420602;rs17259953;rs52798373;rs58224949;rs5983119	824	Q9NR99	MXRA5_HUMAN	V	824	ENSP00000217939:I824V	ENSP00000217939:I824V	I	-	1	0	MXRA5	3251256	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.202000	0.17295	0.025000	0.15241	-0.252000	0.11476	ATT	0|0.003;C|0.749	0.749	strong		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
MRPL45	84311	hgsc.bcm.edu	37	17	36478450	36478450	+	Missense_Mutation	SNP	G	G	T	rs34749623	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36478450G>T	ENST00000312513.5	+	8	1054	c.893G>T	c.(892-894)gGa>gTa	p.G298V	GPR179_ENST00000584976.1_5'Flank	NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	298			G -> V (in dbSNP:rs34749623).			mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GAGGCACAAGGAGAGGCCCAG	0.532											OREG0024353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	172	0.034345	0.028	0.0634	5008	,	,		13089	0.0		0.0746	False		,,,				2504	0.0164				p.G298V		Atlas-SNP	.											.	MRPL45	27	.	0			c.G893T						PASS	.	G	VAL/GLY	110,4296	85.8+/-124.5	1,108,2094	70.0	70.0	70.0		893	-2.6	0.1	17	dbSNP_126	70	455,8145	135.9+/-193.0	12,431,3857	yes	missense	MRPL45	NM_032351.4	109	13,539,5951	TT,TG,GG		5.2907,2.4966,4.3441	possibly-damaging	298/307	36478450	565,12441	2203	4300	6503	SO:0001583	missense	84311	exon8			CACAAGGAGAGGC	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.893G>T	17.37:g.36478450G>T	ENSP00000308901:p.Gly298Val	Somatic	55	0	0	863	WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_032351	A1L436|Q6ZMJ5	Missense_Mutation	SNP	ENST00000312513.5	37	CCDS11326.1	84	0.038461538461538464	13	0.026422764227642278	27	0.07458563535911603	0	0.0	44	0.05804749340369393	G	5.366	0.252743	0.10185	0.024966	0.052907	ENSG00000174100	ENST00000312513	T	0.17528	2.27	5.47	-2.59	0.06209	.	0.714559	0.14201	N	0.334685	T	0.00384	0.0012	N	0.08118	0	0.20307	N	0.999917	B	0.06786	0.001	B	0.06405	0.002	T	0.36601	-0.9741	10	0.12430	T	0.62	-1.362	0.7783	0.01036	0.177:0.263:0.2657:0.2942	rs34749623;rs57663865;rs34749623	298	Q9BRJ2	RM45_HUMAN	V	298	ENSP00000308901:G298V	ENSP00000308901:G298V	G	+	2	0	MRPL45	33731977	0.000000	0.05858	0.062000	0.19696	0.285000	0.27093	-0.080000	0.11339	-0.138000	0.11434	0.632000	0.83419	GGA	G|0.956;T|0.044	0.044	strong		0.532	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
TMEM43	79188	hgsc.bcm.edu	37	3	14174427	14174427	+	Missense_Mutation	SNP	A	A	T	rs4685076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14174427A>T	ENST00000306077.4	+	6	758	c.504A>T	c.(502-504)aaA>aaT	p.K168N	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	168			K -> N (in dbSNP:rs4685076). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						TTGGCCACAAAAACCCCAGGT	0.507													A|||	1766	0.352636	0.3026	0.366	5008	,	,		18688	0.4613		0.2545	False		,,,				2504	0.3998				p.K168N		Atlas-SNP	.											.	TMEM43	33	.	0			c.A504T						PASS	.	A	ASN/LYS	1265,3141	431.8+/-343.0	191,883,1129	80.0	86.0	84.0		504	1.6	1.0	3	dbSNP_111	84	2475,6125	407.1+/-349.0	371,1733,2196	yes	missense	TMEM43	NM_024334.2	94	562,2616,3325	TT,TA,AA		28.7791,28.7108,28.756	benign	168/401	14174427	3740,9266	2203	4300	6503	SO:0001583	missense	79188	exon6			CCACAAAAACCCC	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"""arrhythmogenic right ventricular dysplasia 5"""	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.504A>T	3.37:g.14174427A>T	ENSP00000303992:p.Lys168Asn	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	37	CCDS2618.1	721	0.3301282051282051	165	0.3353658536585366	128	0.35359116022099446	234	0.4090909090909091	194	0.2559366754617414	A	15.44	2.834829	0.50951	0.287108	0.287791	ENSG00000170876	ENST00000306077	T	0.35605	1.3	5.25	1.56	0.23342	.	0.056985	0.64402	D	0.000001	T	0.00012	0.0000	L	0.27053	0.805	0.25967	P	0.9825476	B	0.28208	0.203	B	0.31016	0.123	T	0.49283	-0.8956	9	0.24483	T	0.36	-17.9328	7.8742	0.29584	0.6614:0.0:0.3386:0.0	rs4685076;rs17856367;rs4685076	168	Q9BTV4	TMM43_HUMAN	N	168	ENSP00000303992:K168N	ENSP00000303992:K168N	K	+	3	2	TMEM43	14149428	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.905000	0.28504	0.298000	0.22638	0.482000	0.46254	AAA	A|0.701;T|0.299	0.299	strong		0.507	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334	
PLK1	5347	hgsc.bcm.edu	37	16	23701313	23701313	+	Missense_Mutation	SNP	C	C	T	rs34359215		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:23701313C>T	ENST00000300093.4	+	10	1852	c.1741C>T	c.(1741-1743)Cgc>Tgc	p.R581C	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	581	POLO box 2. {ECO:0000255|PROSITE- ProRule:PRU00154}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		CAGCCGGCTCCGCTACGCCCG	0.652																																					p.R581C	Colon(12;240 564 27038 33155)	Atlas-SNP	.											.	PLK1	67	.	0			c.C1741T						PASS	.						64.0	59.0	61.0					16																	23701313		2197	4300	6497	SO:0001583	missense	5347	exon10			CGGCTCCGCTACG		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"""polo-like kinase (Drosophila)"""	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.1741C>T	16.37:g.23701313C>T	ENSP00000300093:p.Arg581Cys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	50	18	0.36	NM_005030	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.832085	0.91036	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	T	0.12672	2.66	5.13	5.13	0.70059	POLO box duplicated domain (2);	0.000000	0.85682	D	0.000000	T	0.42810	0.1219	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.50448	-0.8827	10	0.87932	D	0	-25.8067	16.0722	0.80943	0.0:1.0:0.0:0.0	rs34359215	581	P53350	PLK1_HUMAN	C	581;484	ENSP00000300093:R581C	ENSP00000300093:R581C	R	+	1	0	PLK1	23608814	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	5.740000	0.68629	2.372000	0.80975	0.555000	0.69702	CGC	.	.	weak		0.652	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030	
SNX15	29907	hgsc.bcm.edu	37	11	64799998	64799998	+	Silent	SNP	T	T	C	rs534236	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64799998T>C	ENST00000377244.3	+	3	361	c.231T>C	c.(229-231)ccT>ccC	p.P77P	RP11-399J13.3_ENST00000301886.3_3'UTR|SNX15_ENST00000352068.5_Silent_p.P77P	NM_013306.4|NM_147777.3	NP_037438.2|NP_680086.2	Q9NRS6	SNX15_HUMAN	sorting nexin 15	77	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14						AGGAGTTCCCTGCTTTCCCCC	0.627													T|||	1876	0.374601	0.2148	0.6052	5008	,	,		17784	0.1825		0.6213	False		,,,				2504	0.3712				p.P77P	Esophageal Squamous(56;269 1304 3324 8253)	Atlas-SNP	.											.	SNX15	35	.	0			c.T231C						PASS	.	T	,	1272,3130	432.0+/-343.1	181,910,1110	65.0	55.0	59.0		231,231	-7.7	0.1	11	dbSNP_83	59	5552,3042	661.1+/-401.8	1775,2002,520	no	coding-synonymous,coding-synonymous	SNX15	NM_013306.4,NM_147777.3	,	1956,2912,1630	CC,CT,TT		35.3968,28.896,47.4915	,	77/343,77/257	64799998	6824,6172	2201	4297	6498	SO:0001819	synonymous_variant	29907	exon3			GTTCCCTGCTTTC	AF175267	CCDS8089.1, CCDS8090.1	11q12	2008-05-22			ENSG00000110025	ENSG00000110025		"""Sorting nexins"""	14978	protein-coding gene	gene with protein product		605964				11208079	Standard	NM_013306		Approved			Q9NRS6	OTTHUMG00000037387	ENST00000377244.3:c.231T>C	11.37:g.64799998T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_147777	E5KQS6|Q9NRS5	Silent	SNP	ENST00000377244.3	37	CCDS8089.1	937	0.429029304029304	135	0.27439024390243905	223	0.6160220994475138	102	0.17832167832167833	477	0.6292875989445911	T	8.195	0.796932	0.16327	0.28896	0.646032	ENSG00000110025	ENST00000525648	.	.	.	4.89	-7.72	0.01250	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22745	P	0.99878566	.	.	.	.	.	.	T	0.45116	-0.9283	3	.	.	.	-21.2781	0.5102	0.00594	0.2697:0.1373:0.207:0.386	rs534236;rs17850569;rs534236	.	.	.	P	36	.	.	L	+	2	0	SNX15	64556574	0.000000	0.05858	0.061000	0.19648	0.029000	0.11900	-4.252000	0.00266	-1.237000	0.02539	-0.242000	0.12053	CTG	T|0.524;C|0.476	0.476	strong		0.627	SNX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091004.3		
TMPRSS15	5651	hgsc.bcm.edu	37	21	19713821	19713821	+	Silent	SNP	C	C	T	rs2824751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:19713821C>T	ENST00000284885.3	-	13	1506	c.1473G>A	c.(1471-1473)gcG>gcA	p.A491A		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	491	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.					brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TGTCATCCAACGCAATATCAC	0.393													t|||	920	0.183706	0.1551	0.1499	5008	,	,		21084	0.1101		0.2505	False		,,,				2504	0.2536				p.A491A		Atlas-SNP	.											TMPRSS15,NS,carcinoma,-1,1	TMPRSS15	189	1	0			c.G1473A						PASS	.	G		721,3685	758.0+/-412.8	61,599,1543	159.0	147.0	151.0		1473	-4.6	0.1	21	dbSNP_100	151	2132,6468	715.2+/-406.0	275,1582,2443	no	coding-synonymous	TMPRSS15	NM_002772.2		336,2181,3986	TT,TC,CC		24.7907,16.364,21.936		491/1020	19713821	2853,10153	2203	4300	6503	SO:0001819	synonymous_variant	5651	exon13			ATCCAACGCAATA		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1473G>A	21.37:g.19713821C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_002772	Q2NKL7	Silent	SNP	ENST00000284885.3	37	CCDS13571.1																																																																																			C|0.811;T|0.189	0.189	strong		0.393	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
ISX	91464	hgsc.bcm.edu	37	22	35463162	35463162	+	Missense_Mutation	SNP	A	A	G	rs361863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:35463162A>G	ENST00000308700.6	+	1	1034	c.82A>G	c.(82-84)Agc>Ggc	p.S28G	RP1-272J12.1_ENST00000448318.4_RNA|ISX_ENST00000404699.2_Missense_Mutation_p.S28G	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	28			S -> G (in dbSNP:rs361863). {ECO:0000269|PubMed:15489334}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						GAAGAAGCTGAGCCTGTCCTT	0.602													G|||	4006	0.79992	0.8759	0.6441	5008	,	,		18262	0.8552		0.671	False		,,,				2504	0.8834				p.S28G		Atlas-SNP	.											.	ISX	62	.	0			c.A82G						PASS	.	G	GLY/SER	3774,632	271.0+/-269.9	1618,538,47	44.0	45.0	45.0		82	5.1	1.0	22	dbSNP_79	45	5667,2933	457.9+/-364.5	1859,1949,492	yes	missense	ISX	NM_001008494.1	56	3477,2487,539	GG,GA,AA		34.1047,14.3441,27.4104	benign	28/246	35463162	9441,3565	2203	4300	6503	SO:0001583	missense	91464	exon1			AAGCTGAGCCTGT	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.82A>G	22.37:g.35463162A>G	ENSP00000311492:p.Ser28Gly	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	1669	0.7641941391941391	411	0.8353658536585366	247	0.6823204419889503	487	0.8513986013986014	524	0.6912928759894459	G	7.104	0.574716	0.13623	0.856559	0.658953	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.90324	-2.65;-2.65	5.13	5.13	0.70059	.	0.299085	0.24076	N	0.041768	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	0.44590	-0.9318	9	0.20046	T	0.44	.	9.8544	0.41077	0.0949:0.0:0.9051:0.0	rs361863;rs361863	28	Q2M1V0	ISX_HUMAN	G	28	ENSP00000311492:S28G;ENSP00000386037:S28G	ENSP00000311492:S28G	S	+	1	0	ISX	33793162	0.724000	0.28038	1.000000	0.80357	0.989000	0.77384	0.474000	0.22148	1.177000	0.42855	-0.119000	0.15052	AGC	A|0.242;G|0.758	0.758	strong		0.602	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
RDH13	112724	hgsc.bcm.edu	37	19	55559740	55559740	+	Silent	SNP	G	G	A	rs1059211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55559740G>A	ENST00000415061.3	-	5	758	c.615C>T	c.(613-615)ctC>ctT	p.L205L	RDH13_ENST00000396247.3_Silent_p.L134L|CTC-550B14.7_ENST00000593060.1_RNA|CTC-550B14.6_ENST00000585492.1_RNA	NM_001145971.1	NP_001139443.1	Q8NBN7	RDH13_HUMAN	retinol dehydrogenase 13 (all-trans/9-cis)	205					eye photoreceptor cell development (GO:0042462)|response to high light intensity (GO:0009644)|retina layer formation (GO:0010842)	mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.199)	GBM - Glioblastoma multiforme(193;0.0504)	Vitamin A(DB00162)	GGACGATGGCGAGCTTGCTCT	0.597													.|||	429	0.0856629	0.0129	0.1297	5008	,	,		19371	0.0268		0.2416	False		,,,				2504	0.0532				p.L205L		Atlas-SNP	.											.	RDH13	43	.	0			c.C615T						PASS	.	C	,	154,3816		5,144,1836	59.0	61.0	60.0		615,402	5.3	1.0	19	dbSNP_86	60	1735,6595		190,1355,2620	no	coding-synonymous,coding-synonymous	RDH13	NM_001145971.1,NM_138412.3	,	195,1499,4456	AA,AG,GG		20.8283,3.8791,15.3577	,	205/332,134/261	55559740	1889,10411	1985	4165	6150	SO:0001819	synonymous_variant	112724	exon5			GATGGCGAGCTTG		CCDS42627.1, CCDS54320.1	19q13.42	2011-09-14	2006-05-09			ENSG00000160439	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19978	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 3"""		"""retinol dehydrogenase 13 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_138412		Approved	SDR7C3	uc002qio.3	Q8NBN7		ENST00000415061.3:c.615C>T	19.37:g.55559740G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	NM_001145971	Q6UX79|Q96G88	Silent	SNP	ENST00000415061.3	37	CCDS54320.1																																																																																			G|0.867;A|0.133	0.133	strong		0.597	RDH13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451470.1	NM_138412	
PTX4	390667	hgsc.bcm.edu	37	16	1536323	1536323	+	Silent	SNP	A	A	G	rs2667671	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1536323A>G	ENST00000447419.2	-	3	1079	c.1054T>C	c.(1054-1056)Ttg>Ctg	p.L352L	PTX4_ENST00000440447.2_3'UTR|PTX4_ENST00000293922.1_Silent_p.L347L			Q96A99	PTX4_HUMAN	pentraxin 4, long	352	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						AGCAGCTGCAAGGGCAGCTCC	0.647													A|||	1553	0.310104	0.7057	0.1916	5008	,	,		16320	0.0665		0.2306	False		,,,				2504	0.1922				p.L347L		Atlas-SNP	.											PTX4,NS,carcinoma,0,1	PTX4	46	1	0			c.T1039C						PASS	.	A		2725,1673		852,1021,326	31.0	36.0	35.0		1039	2.5	0.9	16	dbSNP_100	35	1795,6805		191,1413,2696	no	coding-synonymous	PTX4	NM_001013658.1		1043,2434,3022	GG,GA,AA		20.8721,38.04,34.7746		347/474	1536323	4520,8478	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GCTGCAAGGGCAG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1054T>C	16.37:g.1536323A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				A|0.662;G|0.338	0.338	strong		0.647	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
PER3	8863	hgsc.bcm.edu	37	1	7890024	7890024	+	Missense_Mutation	SNP	T	T	G	rs201662971|rs57875989		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:7890024T>G	ENST00000361923.2	+	18	3165	c.2990T>G	c.(2989-2991)aTg>aGg	p.M997R	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.M1006R	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	997	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)	p.M997R(1)		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)		TCGCCTCCCATGAAGAATCCA	0.582																																					p.M997R		Atlas-SNP	.											PER3,NS,carcinoma,0,3	PER3	95	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.T2990G						scavenged	.						85.0	70.0	75.0					1																	7890024		2001	3894	5895	SO:0001583	missense	8863	exon18			CTCCCATGAAGAA	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.2990T>G	1.37:g.7890024T>G	ENSP00000355031:p.Met997Arg	Somatic	138	5	0.0362319		WXS	Illumina HiSeq	Phase_I	85	12	0.141176	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	.	.	.	.	.	.	.	.	.	.	T	0.033	-1.321421	0.01320	.	.	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.14640	2.49;2.49	.	.	.	Period circadian-like, C-terminal (1);	31.945600	0.01768	N	0.031022	T	0.04861	0.0131	N	0.04508	-0.205	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.25152	-1.0140	8	0.11485	T	0.65	.	.	.	.	.	997;1006;1006;997	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	R	1006;997	ENSP00000366755:M1006R;ENSP00000355031:M997R	ENSP00000355031:M997R	M	+	2	0	PER3	7812611	0.004000	0.15560	0.012000	0.15200	0.013000	0.08279	-1.043000	0.03535	-1.402000	0.02056	-1.459000	0.01027	ATG	.	.	weak		0.582	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
PKD1L1	168507	hgsc.bcm.edu	37	7	47917087	47917087	+	Splice_Site	SNP	C	C	T	rs72601626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47917087C>T	ENST00000289672.2	-	22	3713	c.3663G>A	c.(3661-3663)ccG>ccA	p.P1221P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1221	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GTCCACGTACCGGTTTTCCAG	0.582													C|||	239	0.0477236	0.0227	0.0331	5008	,	,		16430	0.0595		0.0746	False		,,,				2504	0.0521				p.P1221P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G3663A						PASS	.	C		101,4305	81.9+/-120.4	0,101,2102	148.0	138.0	141.0		3663	4.4	0.9	7	dbSNP_130	141	602,7998	159.4+/-212.7	23,556,3721	yes	coding-synonymous-near-splice	PKD1L1	NM_138295.3		23,657,5823	TT,TC,CC		7.0,2.2923,5.4052		1221/2850	47917087	703,12303	2203	4300	6503	SO:0001630	splice_region_variant	168507	exon22			ACGTACCGGTTTT	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.3663+1G>A	7.37:g.47917087C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			C|0.942;T|0.058	0.058	strong		0.582	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	Silent
P2RX4	5025	hgsc.bcm.edu	37	12	121660787	121660787	+	Silent	SNP	T	T	C	rs25643	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121660787T>C	ENST00000337233.4	+	5	773	c.465T>C	c.(463-465)tcT>tcC	p.S155S	P2RX4_ENST00000540930.1_Intron|P2RX4_ENST00000359949.7_Silent_p.S171S|P2RX4_ENST00000543171.1_Silent_p.S54S|P2RX4_ENST00000541532.1_Intron	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	155					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCAACGGGTCTGTCAAGACGT	0.562													C|||	2205	0.440296	0.4312	0.4222	5008	,	,		19659	0.3433		0.4751	False		,,,				2504	0.5297				p.S171S		Atlas-SNP	.											P2RX4,NS,carcinoma,0,1	P2RX4	27	1	0			c.T513C						scavenged	.	C		1973,2433	618.3+/-393.1	450,1073,680	141.0	105.0	117.0		465	-10.3	0.0	12	dbSNP_72	117	3906,4694	604.9+/-394.9	910,2086,1304	no	coding-synonymous	P2RX4	NM_002560.2		1360,3159,1984	CC,CT,TT		45.4186,44.7798,45.2022		155/389	121660787	5879,7127	2203	4300	6503	SO:0001819	synonymous_variant	5025	exon6			CGGGTCTGTCAAG	Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.465T>C	12.37:g.121660787T>C		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	145	74	0.510345	NM_001256796	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Silent	SNP	ENST00000337233.4	37	CCDS9214.1																																																																																			C|0.421;N|0.000;T|0.579	0.421	strong		0.562	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567	
SPICE1	152185	hgsc.bcm.edu	37	3	113176122	113176122	+	Silent	SNP	G	G	A	rs7637618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113176122G>A	ENST00000295872.4	-	13	1777	c.1518C>T	c.(1516-1518)ccC>ccT	p.P506P		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	506					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						ACAGTTTAACGGGCAACTCTT	0.468													A|||	1642	0.327875	0.5772	0.1758	5008	,	,		17892	0.2996		0.2455	False		,,,				2504	0.2127				p.P506P		Atlas-SNP	.											.	SPICE1	130	.	0			c.C1518T						PASS	.	A		2340,2066	569.8+/-382.7	626,1088,489	104.0	102.0	103.0		1518	2.0	1.0	3	dbSNP_116	103	2164,6436	713.1+/-405.9	270,1624,2406	no	coding-synonymous	SPICE1	NM_144718.3		896,2712,2895	AA,AG,GG		25.1628,46.8906,34.6302		506/856	113176122	4504,8502	2203	4300	6503	SO:0001819	synonymous_variant	152185	exon13			TTTAACGGGCAAC	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.1518C>T	3.37:g.113176122G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			G|0.662;A|0.338	0.338	strong		0.468	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	
NBN	4683	hgsc.bcm.edu	37	8	90967711	90967711	+	Silent	SNP	A	A	G	rs709816	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:90967711A>G	ENST00000265433.3	-	10	1351	c.1197T>C	c.(1195-1197)gaT>gaC	p.D399D	NBN_ENST00000409330.1_Silent_p.D317D	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	399	Interaction with MTOR, MAPKAP1 and RICTOR.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			CAGTGGGTGCATCTTGTGAAA	0.358								Homologous recombination					G|||	3048	0.608626	0.8533	0.5548	5008	,	,		17230	0.6647		0.341	False		,,,				2504	0.5337				p.D399D		Atlas-SNP	.											.	NBN	86	.	0			c.T1197C						PASS	.	G		3315,1089	391.7+/-328.2	1243,829,130	116.0	114.0	115.0		1197	-1.6	0.0	8	dbSNP_86	115	3061,5539	659.6+/-401.7	539,1983,1778	no	coding-synonymous	NBN	NM_002485.4		1782,2812,1908	GG,GA,AA		35.593,24.7275,49.0311		399/755	90967711	6376,6628	2202	4300	6502	SO:0001819	synonymous_variant	4683	exon10			GGGTGCATCTTGT	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.1197T>C	8.37:g.90967711A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Silent	SNP	ENST00000265433.3	37	CCDS6249.1																																																																																			A|0.459;G|0.541	0.541	strong		0.358	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
GPC1	2817	hgsc.bcm.edu	37	2	241405485	241405485	+	Silent	SNP	C	C	T	rs2228330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:241405485C>T	ENST00000264039.2	+	9	1703	c.1455C>T	c.(1453-1455)ggC>ggT	p.G485G	GPC1_ENST00000466624.1_3'UTR	NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	485					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		GTGACGACGGCAGCGGCTCGG	0.682													c|||	727	0.145168	0.1755	0.134	5008	,	,		15348	0.0149		0.2107	False		,,,				2504	0.1789				p.G485G		Atlas-SNP	.											.	GPC1	32	.	0			c.C1455T						PASS	.			758,3630		79,600,1515	18.0	23.0	21.0		1455	2.8	1.0	2	dbSNP_98	21	1940,6622		215,1510,2556	no	coding-synonymous	GPC1	NM_002081.2		294,2110,4071	TT,TC,CC		22.6583,17.2744,20.834		485/559	241405485	2698,10252	2194	4281	6475	SO:0001819	synonymous_variant	2817	exon9			CGACGGCAGCGGC	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1455C>T	2.37:g.241405485C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	162	79	0.487654	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	299	0.13690476190476192	85	0.17276422764227642	52	0.143646408839779	6	0.01048951048951049	156	0.20580474934036938	c	7.291	0.611022	0.14066	0.172744	0.226583	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	3.69	2.77	0.32553	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-27.6614	10.396	0.44201	0.0:0.5342:0.4658:0.0	rs2228330;rs10183272;rs2228330	.	.	.	X	525;237	.	.	Q	+	1	0	GPC1	241054158	0.134000	0.22483	0.982000	0.44146	0.770000	0.43624	0.518000	0.22847	0.610000	0.30035	0.443000	0.29094	CAG	C|0.832;T|0.168	0.168	strong		0.682	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
YIPF2	78992	hgsc.bcm.edu	37	19	11036415	11036415	+	Missense_Mutation	SNP	C	C	T	rs148361413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11036415C>T	ENST00000586748.1	-	5	486	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	YIPF2_ENST00000590329.1_Missense_Mutation_p.R105Q|C19orf52_ENST00000270502.6_5'Flank|YIPF2_ENST00000253031.2_Missense_Mutation_p.R105Q			Q9BWQ6	YIPF2_HUMAN	Yip1 domain family, member 2	105						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				cervix(1)|endometrium(1)|lung(3)|ovary(2)	7						GTGGCCAGGCCGGGGCAGCAG	0.577																																					p.R105Q		Atlas-SNP	.											.	YIPF2	13	.	0			c.G314A						PASS	.	C	GLN/ARG	0,4404		0,0,2202	90.0	74.0	80.0		314	2.5	1.0	19	dbSNP_134	80	1,8599	1.2+/-3.3	0,1,4299	no	missense	YIPF2	NM_024029.3	43	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	105/317	11036415	1,13003	2202	4300	6502	SO:0001583	missense	78992	exon5			CCAGGCCGGGGCA	BC013014	CCDS12251.1	19p13.2	2008-02-05				ENSG00000130733		"""Yip1 domain family"""	28476	protein-coding gene	gene with protein product						12477932	Standard	NM_024029		Approved	MGC3262, FinGER2	uc002mqc.3	Q9BWQ6		ENST00000586748.1:c.314G>A	19.37:g.11036415C>T	ENSP00000466055:p.Arg105Gln	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_024029		Missense_Mutation	SNP	ENST00000586748.1	37	CCDS12251.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191861	0.38707	0.0	1.16E-4	ENSG00000130733	ENST00000253031	.	.	.	4.71	2.46	0.29980	Yip1 domain (1);	0.599360	0.15816	N	0.243259	T	0.24160	0.0585	L	0.27053	0.805	0.09310	N	1	B	0.23591	0.088	B	0.14023	0.01	T	0.11060	-1.0603	9	0.27785	T	0.31	-12.2256	4.8429	0.13500	0.4337:0.4455:0.0:0.1208	.	105	Q9BWQ6	YIPF2_HUMAN	Q	105	.	ENSP00000253031:R105Q	R	-	2	0	YIPF2	10897415	0.003000	0.15002	0.998000	0.56505	0.981000	0.71138	2.003000	0.40844	0.930000	0.37217	0.542000	0.68232	CGG	C|1.000;T|0.000	0.000	strong		0.577	YIPF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453045.1	NM_024029	
TXNDC2	84203	hgsc.bcm.edu	37	18	9888069	9888069	+	Silent	SNP	A	A	G	rs2240905	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9888069A>G	ENST00000306084.6	+	2	1792	c.1593A>G	c.(1591-1593)gaA>gaG	p.E531E	TXNDC2_ENST00000357775.5_Silent_p.E464E|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	531	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						ATAAAAAAGAAGAAAAGGTGG	0.438													A|||	2778	0.554712	0.472	0.5778	5008	,	,		20063	0.8175		0.4791	False		,,,				2504	0.4571				p.E531E		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	0			c.A1593G						PASS	.	A	,	2154,2252	577.4+/-384.4	540,1074,589	43.0	44.0	44.0		1593,1392	0.3	1.0	18	dbSNP_98	44	4220,4380	568.4+/-389.0	1048,2124,1128	no	coding-synonymous,coding-synonymous	TXNDC2	NM_001098529.1,NM_032243.5	,	1588,3198,1717	GG,GA,AA		49.0698,48.8879,49.0082	,	531/554,464/487	9888069	6374,6632	2203	4300	6503	SO:0001819	synonymous_variant	84203	exon2			AAAAGAAGAAAAG	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.1593A>G	18.37:g.9888069A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	113	61	0.539823	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Silent	SNP	ENST00000306084.6	37	CCDS42414.1																																																																																			G|0.522;N|0.000	0.522	strong		0.438	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
DOCK2	1794	hgsc.bcm.edu	37	5	169461547	169461547	+	Silent	SNP	C	C	T	rs3763048	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:169461547C>T	ENST00000256935.8	+	35	3692	c.3612C>T	c.(3610-3612)acC>acT	p.T1204T	DOCK2_ENST00000540750.1_Silent_p.T265T|DOCK2_ENST00000520908.1_Silent_p.T696T|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1204	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.T1204T(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGAGCTGCACCGTGAACCTGC	0.577													T|||	2538	0.506789	0.6445	0.3271	5008	,	,		18761	0.6042		0.3489	False		,,,				2504	0.5102				p.T1204T		Atlas-SNP	.											DOCK2,caecum,carcinoma,+1,2	DOCK2	389	2	1	Substitution - coding silent(1)	stomach(1)	c.C3612T						PASS	.	T		2672,1734	518.6+/-369.8	803,1066,334	77.0	75.0	76.0		3612	-11.3	0.2	5	dbSNP_107	76	2976,5624	666.6+/-402.4	495,1986,1819	no	coding-synonymous	DOCK2	NM_004946.2		1298,3052,2153	TT,TC,CC		34.6047,39.3554,43.4261		1204/1831	169461547	5648,7358	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon35			CTGCACCGTGAAC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3612C>T	5.37:g.169461547C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			C|0.536;T|0.464	0.464	strong		0.577	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
MRPL50	54534	hgsc.bcm.edu	37	9	104152790	104152790	+	Silent	SNP	G	G	C	rs17853010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104152790G>C	ENST00000374865.4	-	2	456	c.435C>G	c.(433-435)gcC>gcG	p.A145A	MRPL50_ENST00000539624.1_Intron	NM_019051.2	NP_061924.1	Q8N5N7	RM50_HUMAN	mitochondrial ribosomal protein L50	145						mitochondrion (GO:0005739)|ribosome (GO:0005840)				large_intestine(1)|lung(2)|prostate(2)	5		Acute lymphoblastic leukemia(62;0.0559)				GCAGATTACTGGCACTGAGTT	0.423													G|||	339	0.0676917	0.0136	0.0375	5008	,	,		18514	0.1071		0.0736	False		,,,				2504	0.1155				p.A145A		Atlas-SNP	.											.	MRPL50	18	.	0			c.C435G						PASS	.	G		76,4326	65.8+/-103.3	1,74,2126	74.0	74.0	74.0		435	-1.9	0.2	9	dbSNP_123	74	555,8033	148.8+/-204.0	19,517,3758	no	coding-synonymous	MRPL50	NM_019051.2		20,591,5884	CC,CG,GG		6.4625,1.7265,4.8576		145/159	104152790	631,12359	2201	4294	6495	SO:0001819	synonymous_variant	54534	exon2			ATTACTGGCACTG	AK000500	CCDS6753.1	9q31.1	2012-11-14			ENSG00000136897	ENSG00000136897		"""Mitochondrial ribosomal proteins / large subunits"""	16654	protein-coding gene	gene with protein product	"""mitochondrial 39S ribosomal protein L50"""	611854					Standard	NM_019051		Approved	FLJ20493, MRP-L50	uc004bbe.2	Q8N5N7	OTTHUMG00000020384	ENST00000374865.4:c.435C>G	9.37:g.104152790G>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_019051	B7Z358|Q5T7E0|Q9NX15	Silent	SNP	ENST00000374865.4	37	CCDS6753.1																																																																																			G|0.013;C|0.987	0.987	weak		0.423	MRPL50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053450.1	NM_019051	
KRT15	3866	hgsc.bcm.edu	37	17	39671724	39671724	+	Splice_Site	SNP	T	T	C	rs2305556	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39671724T>C	ENST00000254043.3	-	6	4832	c.1247A>G	c.(1246-1248)aAg>aGg	p.K416R	KRT15_ENST00000393974.3_Splice_Site_p.K251R|KRT15_ENST00000393981.3_Missense_Mutation_p.K251R|KRT15_ENST00000393976.2_Splice_Site_p.K416R	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	416	Tail.		K -> R (in dbSNP:rs2305556). {ECO:0000269|PubMed:14702039}.		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				AGGCGCCTACTTGGCATCCTG	0.587													T|||	668	0.133387	0.2012	0.1354	5008	,	,		20443	0.0565		0.2107	False		,,,				2504	0.0399				p.K416R		Atlas-SNP	.											.	KRT15	60	.	0			c.A1247G						PASS	.	T	ARG/LYS	945,3461	356.9+/-313.7	96,753,1354	83.0	73.0	76.0		1247	2.5	1.0	17	dbSNP_100	76	1940,6660	339.5+/-323.2	225,1490,2585	yes	missense-near-splice	KRT15	NM_002275.3	26	321,2243,3939	CC,CT,TT		22.5581,21.448,22.1821	benign	416/457	39671724	2885,10121	2203	4300	6503	SO:0001630	splice_region_variant	3866	exon6			GCCTACTTGGCAT		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6421	protein-coding gene	gene with protein product	"""keratin-15, basic"", ""keratin-15, beta"", ""type I cytoskeletal 15"", ""cytokeratin 15"""	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.1247+1A>G	17.37:g.39671724T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_002275	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	37	CCDS11398.1	345	0.15796703296703296	99	0.20121951219512196	58	0.16022099447513813	27	0.0472027972027972	161	0.21240105540897097	T	15.25	2.776876	0.49786	0.21448	0.225581	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976;ENST00000393981	D;T;D;T	0.81499	-1.5;-0.96;-1.5;-1.44	4.71	2.51	0.30379	.	0.124418	0.35805	N	0.002962	T	0.00039	0.0001	L	0.33093	0.98	0.41345	P	0.012674999999999992	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.15484	0.013;0.012;0.012	T	0.03555	-1.1025	8	.	.	.	.	1.9768	0.03418	0.161:0.0973:0.1665:0.5752	rs2305556;rs17581965;rs58310507;rs2305556	251;416;416	A8MT21;B3KVF5;P19012	.;.;K1C15_HUMAN	R	416;251;416;251	ENSP00000254043:K416R;ENSP00000377544:K251R;ENSP00000377546:K416R;ENSP00000377550:K251R	.	K	-	2	0	KRT15	36925250	0.090000	0.21635	0.997000	0.53966	0.973000	0.67179	0.036000	0.13819	0.356000	0.24157	0.533000	0.62120	AAG	T|0.806;C|0.194	0.194	strong		0.587	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275	Missense_Mutation
ARHGAP42	143872	hgsc.bcm.edu	37	11	100792335	100792335	+	Splice_Site	SNP	G	G	A	rs75746929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:100792335G>A	ENST00000298815.8	+	6	600	c.597G>A	c.(595-597)ccG>ccA	p.P199P	ARHGAP42_ENST00000524892.2_Splice_Site_p.P165P	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	199	BAR.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGTTGAACCGGTAAGTTTCA	0.279													G|||	422	0.0842652	0.0	0.1081	5008	,	,		11980	0.2609		0.0447	False		,,,				2504	0.0399				p.P199P		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G597A						PASS	.	G		15,1369		0,15,677	32.0	26.0	28.0		597	3.5	1.0	11	dbSNP_131	28	126,3052		3,120,1466	yes	coding-synonymous-near-splice	ARHGAP42	NM_152432.2		3,135,2143	AA,AG,GG		3.9648,1.0838,3.0907		199/875	100792335	141,4421	692	1589	2281	SO:0001630	splice_region_variant	143872	exon6			TGAACCGGTAAGT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.597+1G>A	11.37:g.100792335G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				G|0.910;A|0.090	0.090	strong		0.279	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	Silent
NOTCH2	4853	hgsc.bcm.edu	37	1	120458924	120458924	+	Silent	SNP	G	G	A	rs3795666	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:120458924G>A	ENST00000256646.2	-	34	6640	c.6421C>T	c.(6421-6423)Ctg>Ttg	p.L2141L		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2141					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)		CTCTCAGACAGTTGGACCTTC	0.493			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				G|||	242	0.0483227	0.0106	0.0605	5008	,	,		23493	0.0625		0.0199	False		,,,				2504	0.1053				p.L2141L		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C6421T						PASS	.	G		68,4338	62.9+/-100.1	0,68,2135	178.0	161.0	166.0		6421	4.8	1.0	1	dbSNP_107	166	165,8435	78.1+/-140.7	1,163,4136	no	coding-synonymous	NOTCH2	NM_024408.3		1,231,6271	AA,AG,GG		1.9186,1.5433,1.7915		2141/2472	120458924	233,12773	2203	4300	6503	SO:0001819	synonymous_variant	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CAGACAGTTGGAC	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.6421C>T	1.37:g.120458924G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	164	79	0.481707	NM_024408	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																			G|0.952;A|0.048	0.048	strong		0.493	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
GEMIN4	50628	hgsc.bcm.edu	37	17	648157	648157	+	Silent	SNP	G	G	A	rs1045481	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:648157G>A	ENST00000319004.5	-	2	3244	c.3126C>T	c.(3124-3126)atC>atT	p.I1042I	GEMIN4_ENST00000576778.1_Silent_p.I1031I	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	1042					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)		CTTCAGGGCCGATGCCCTCAG	0.572													G|||	794	0.158546	0.0545	0.1772	5008	,	,		19937	0.122		0.2455	False		,,,				2504	0.2342				p.I1042I		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C3126T						PASS	.	G		363,3619		17,329,1645	45.0	44.0	44.0		3126	-2.2	1.0	17	dbSNP_86	44	2088,6240		281,1526,2357	no	coding-synonymous	GEMIN4	NM_015721.2		298,1855,4002	AA,AG,GG		25.072,9.116,19.9106		1042/1059	648157	2451,9859	1991	4164	6155	SO:0001819	synonymous_variant	50628	exon2			AGGGCCGATGCCC	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.3126C>T	17.37:g.648157G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	85	47	0.552941	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			G|0.829;A|0.172	0.172	strong		0.572	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
BOC	91653	hgsc.bcm.edu	37	3	112997554	112997554	+	Silent	SNP	A	A	G	rs775228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112997554A>G	ENST00000495514.1	+	11	2441	c.1737A>G	c.(1735-1737)aaA>aaG	p.K579K	BOC_ENST00000273395.4_Silent_p.K580K|BOC_ENST00000497495.1_3'UTR|BOC_ENST00000355385.3_Silent_p.K579K			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	579					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGGCCAGCAAAGAGCAGCAGA	0.632													G|||	3107	0.620407	0.7663	0.5418	5008	,	,		15121	0.7183		0.4781	False		,,,				2504	0.5245				p.K579K		Atlas-SNP	.											.	BOC	139	.	0			c.A1737G						PASS	.	G		3220,1152		1217,786,183	40.0	42.0	41.0		1737	4.0	1.0	3	dbSNP_86	41	3844,4684		919,2006,1339	no	coding-synonymous	BOC	NM_033254.2		2136,2792,1522	GG,GA,AA		45.075,26.3495,45.2403		579/1115	112997554	7064,5836	2186	4264	6450	SO:0001819	synonymous_variant	91653	exon11			CAGCAAAGAGCAG	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1737A>G	3.37:g.112997554A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			A|0.404;G|0.596	0.596	strong		0.632	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
HLA-A	3105	hgsc.bcm.edu	37	6	29910700	29910700	+	Silent	SNP	G	G	T	rs1059452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910700G>T	ENST00000396634.1	+	4	581	c.240G>T	c.(238-240)ggG>ggT	p.G80G	HLA-A_ENST00000376809.5_Silent_p.G80G|HLA-A_ENST00000376806.5_Silent_p.G80G|HLA-A_ENST00000376802.2_Silent_p.G80G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	80	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGCAGGAGGGGCCGGAGTATT	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.G80G		Atlas-SNP	.											.	HLA-A	89	.	0			c.G240T						PASS	.						61.0	64.0	63.0					6																	29910700		2203	4300	6503	SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGAGGGGCCGGAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.240G>T	6.37:g.29910700G>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	103	39	0.378641	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.769;T|0.231	0.231	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
OCEL1	79629	hgsc.bcm.edu	37	19	17337557	17337557	+	Missense_Mutation	SNP	G	G	T	rs10425488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17337557G>T	ENST00000215061.4	+	2	169	c.125G>T	c.(124-126)cGc>cTc	p.R42L	OCEL1_ENST00000601576.1_3'UTR|OCEL1_ENST00000601529.1_Missense_Mutation_p.R42L|OCEL1_ENST00000597836.1_5'UTR	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	42	Pro-rich.		R -> L (in dbSNP:rs10425488).							central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						CGCAGGACCCGCCCATCAGCC	0.746													G|||	385	0.076877	0.115	0.0836	5008	,	,		10155	0.001		0.0755	False		,,,				2504	0.1002				p.R42L		Atlas-SNP	.											.	OCEL1	20	.	0			c.G125T						PASS	.	G	LEU/ARG	300,3398		14,272,1563	4.0	6.0	6.0		125	3.0	0.1	19	dbSNP_119	6	480,6968		14,452,3258	no	missense	OCEL1	NM_024578.1	102	28,724,4821	TT,TG,GG		6.4447,8.1125,6.998	possibly-damaging	42/265	17337557	780,10366	1849	3724	5573	SO:0001583	missense	79629	exon2			GGACCCGCCCATC	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.125G>T	19.37:g.17337557G>T	ENSP00000215061:p.Arg42Leu	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_024578		Missense_Mutation	SNP	ENST00000215061.4	37	CCDS12351.1	142	0.06501831501831502	54	0.10975609756097561	30	0.08287292817679558	0	0.0	58	0.07651715039577836	G	16.23	3.063736	0.55432	0.081125	0.064447	ENSG00000099330	ENST00000215061	T	0.32988	1.43	3.01	3.01	0.34805	.	0.596543	0.14714	N	0.302724	T	0.00666	0.0022	N	0.19112	0.55	0.80722	P	0.0	D	0.76494	0.999	D	0.79108	0.992	T	0.04855	-1.0922	9	0.39692	T	0.17	-18.151	6.1073	0.20081	0.1412:0.0:0.8588:0.0	rs10425488	42	Q9H607	OCEL1_HUMAN	L	42	ENSP00000215061:R42L	ENSP00000215061:R42L	R	+	2	0	OCEL1	17198557	0.003000	0.15002	0.067000	0.19924	0.403000	0.30841	0.226000	0.17776	2.001000	0.58596	0.491000	0.48974	CGC	G|0.934;T|0.066	0.066	strong		0.746	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578	
WNK1	65125	hgsc.bcm.edu	37	12	994014	994014	+	Silent	SNP	C	C	T	rs10849577	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:994014C>T	ENST00000315939.6	+	19	4687	c.4044C>T	c.(4042-4044)acC>acT	p.T1348T	WNK1_ENST00000537687.1_Silent_p.T1608T|WNK1_ENST00000535572.1_Silent_p.T1101T|WNK1_ENST00000340908.4_Silent_p.T941T|WNK1_ENST00000530271.2_Silent_p.T1846T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1348					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)			GAGTCCCAACCACAGCAGCAG	0.493													C|||	580	0.115815	0.0363	0.1052	5008	,	,		19854	0.1825		0.1531	False		,,,				2504	0.1237				p.T1608T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C4824T						PASS	.	C	,,,	232,4174	138.0+/-173.8	9,214,1980	87.0	82.0	84.0		4824,3303,4044,4800	0.4	0.0	12	dbSNP_120	84	1222,7378	246.2+/-274.8	90,1042,3168	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WNK1	NM_001184985.1,NM_014823.2,NM_018979.3,NM_213655.4	,,,	99,1256,5148	TT,TC,CC		14.2093,5.2655,11.1795	,,,	1608/2643,1101/2135,1348/2383,1600/2635	994014	1454,11552	2203	4300	6503	SO:0001819	synonymous_variant	65125	exon19			CCCAACCACAGCA	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.4044C>T	12.37:g.994014C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	245	104	0.42449	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	37	CCDS8506.1																																																																																			C|0.885;T|0.115	0.115	strong		0.493	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
SLC4A10	57282	hgsc.bcm.edu	37	2	162696414	162696414	+	Silent	SNP	C	C	T	rs2084543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:162696414C>T	ENST00000446997.1	+	4	486	c.393C>T	c.(391-393)gaC>gaT	p.D131D	SLC4A10_ENST00000421911.1_Silent_p.D131D|SLC4A10_ENST00000415876.2_Silent_p.D131D|SLC4A10_ENST00000272716.5_Silent_p.D131D|SLC4A10_ENST00000493021.1_3'UTR|SLC4A10_ENST00000375514.5_Silent_p.D142D|SLC4A10_ENST00000535165.1_Silent_p.D131D	NM_001178015.1	NP_001171486.1	Q6U841	S4A10_HUMAN	solute carrier family 4, sodium bicarbonate transporter, member 10	131					bicarbonate transport (GO:0015701)|chloride transport (GO:0006821)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|symporter activity (GO:0015293)			endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(35)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60					Sodium bicarbonate(DB01390)	AAGGTGAGGACGCTGAGTGGC	0.418													T|||	348	0.0694888	0.003	0.0605	5008	,	,		16826	0.1319		0.0825	False		,,,				2504	0.0879				p.D142D		Atlas-SNP	.											.	SLC4A10	309	.	0			c.C426T						PASS	.	T	,,	61,4193		1,59,2067	136.0	139.0	138.0		393,426,393	3.2	1.0	2	dbSNP_96	138	574,7942		18,538,3702	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A10	NM_001178015.1,NM_001178016.1,NM_022058.3	,,	19,597,5769	TT,TC,CC		6.7403,1.4339,4.9726	,,	131/1119,142/1100,131/1089	162696414	635,12135	2127	4258	6385	SO:0001819	synonymous_variant	57282	exon5			TGAGGACGCTGAG		CCDS46438.1, CCDS54411.1, CCDS54412.1	2q24.2	2013-05-22	2008-09-15		ENSG00000144290	ENSG00000144290		"""Solute carriers"""	13811	protein-coding gene	gene with protein product		605556	"""solute carrier family 4, sodium bicarbonate transporter-like, member 10"""			10964153, 18319254	Standard	NM_022058		Approved	NBCn2, NCBE	uc002ubx.4	Q6U841	OTTHUMG00000153938	ENST00000446997.1:c.393C>T	2.37:g.162696414C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_001178016	B7Z1R0|B7Z2J0|B7ZLC5|B9EG69|F8W675|Q4ZFX6|Q8TCP2|Q9HCQ6	Silent	SNP	ENST00000446997.1	37	CCDS54411.1																																																																																			C|0.922;T|0.078	0.078	strong		0.418	SLC4A10-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333090.1	NM_022058	
C16orf70	80262	hgsc.bcm.edu	37	16	67173922	67173922	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67173922C>T	ENST00000219139.3	+	9	885	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	C16orf70_ENST00000569600.1_Missense_Mutation_p.R233W	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	233										cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		TGCCAAGATGCGGGTATTTGA	0.468																																					p.R233W		Atlas-SNP	.											C16orf70,NS,carcinoma,-1,1	C16orf70	38	1	0			c.C697T						scavenged	.						170.0	160.0	163.0					16																	67173922		2199	4300	6499	SO:0001583	missense	80262	exon9			AAGATGCGGGTAT	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 6"""	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510	ENST00000219139.3:c.697C>T	16.37:g.67173922C>T	ENSP00000219139:p.Arg233Trp	Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	186	3	0.016129	NM_025187	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	37	CCDS10828.1	.	.	.	.	.	.	.	.	.	.	C	12.95	2.092271	0.36952	.	.	ENSG00000125149	ENST00000219139	.	.	.	6.03	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.59088	0.2168	L	0.56769	1.78	0.58432	D	0.999995	B	0.16166	0.016	B	0.12156	0.007	T	0.59016	-0.7533	9	0.72032	D	0.01	-11.8175	12.8892	0.58061	0.3052:0.6948:0.0:0.0	.	233	Q9BSU1	CP070_HUMAN	W	233	.	ENSP00000219139:R233W	R	+	1	2	C16orf70	65731423	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.830000	0.48136	1.501000	0.48654	0.557000	0.71058	CGG	.	.	none		0.468	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573439	140573439	+	Silent	SNP	G	G	C	rs610836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140573439G>C	ENST00000239446.4	+	1	1498	c.1314G>C	c.(1312-1314)acG>acC	p.T438T		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	438	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			ACAACATAACGGTCCTGGTCT	0.587													C|||	2442	0.48762	0.5076	0.5461	5008	,	,		14303	0.5685		0.4076	False		,,,				2504	0.4182				p.T438T		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G1314C						PASS	.						82.0	79.0	80.0					5																	140573439		2203	4298	6501	SO:0001819	synonymous_variant	56126	exon1			CATAACGGTCCTG	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.1314G>C	5.37:g.140573439G>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			G|0.551;C|0.449	0.449	strong		0.587	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
C6orf57	135154	hgsc.bcm.edu	37	6	71289188	71289188	+	Nonsense_Mutation	SNP	C	C	T	rs61735710	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:71289188C>T	ENST00000370474.3	+	2	160	c.136C>T	c.(136-138)Cag>Tag	p.Q46*		NM_145267.2	NP_660310.2	Q5VUM1	SDHF4_HUMAN	chromosome 6 open reading frame 57	46			Q -> R (in dbSNP:rs1048886).		innate immune response (GO:0045087)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)				kidney(1)|lung(1)|skin(1)	3						ACTTGTCAAACAGTCCCTTAA	0.408													C|||	46	0.0091853	0.0189	0.0115	5008	,	,		14550	0.0109		0.0	False		,,,				2504	0.002				p.Q46X		Atlas-SNP	.											.	C6orf57	13	.	0			c.C136T						PASS	.	C	stop/GLN	60,4346	50.2+/-85.5	0,60,2143	112.0	110.0	111.0		136	5.8	0.1	6	dbSNP_129	111	6,8594	4.3+/-15.6	0,6,4294	yes	stop-gained	C6orf57	NM_145267.2		0,66,6437	TT,TC,CC		0.0698,1.3618,0.5075		46/109	71289188	66,12940	2203	4300	6503	SO:0001587	stop_gained	135154	exon2			GTCAAACAGTCCC	BC018085	CCDS4972.1	6q12	2011-12-13			ENSG00000154079	ENSG00000154079			20957	protein-coding gene	gene with protein product							Standard	NM_145267		Approved		uc003pfq.1	Q5VUM1	OTTHUMG00000014992	ENST00000370474.3:c.136C>T	6.37:g.71289188C>T	ENSP00000359505:p.Gln46*	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	35	7	0.2	NM_145267	E1P532	Nonsense_Mutation	SNP	ENST00000370474.3	37	CCDS4972.1	14	0.00641025641025641	6	0.012195121951219513	3	0.008287292817679558	5	0.008741258741258742	0	0.0	C	13.39	2.223702	0.39300	0.013618	6.98E-4	ENSG00000154079	ENST00000370474	.	.	.	5.82	5.82	0.92795	.	0.101718	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-6.9699	12.5617	0.56286	0.166:0.834:0.0:0.0	rs61735710	.	.	.	X	46	.	ENSP00000359505:Q46X	Q	+	1	0	C6orf57	71345909	0.918000	0.31147	0.075000	0.20258	0.206000	0.24218	0.959000	0.29240	2.742000	0.94016	0.579000	0.79373	CAG	C|0.994;T|0.006	0.006	strong		0.408	C6orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041140.1	NM_145267	
SLC38A10	124565	hgsc.bcm.edu	37	17	79220016	79220016	+	Silent	SNP	T	T	C	rs61740863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79220016T>C	ENST00000374759.3	-	16	3083	c.2700A>G	c.(2698-2700)gcA>gcG	p.A900A		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	900					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TGCCAGTGGCTGCCACCTCCT	0.627													T|||	417	0.0832668	0.0552	0.0317	5008	,	,		16081	0.1587		0.0875	False		,,,				2504	0.0757				p.A900A		Atlas-SNP	.											.	SLC38A10	133	.	0			c.A2700G						PASS	.	T		169,3819		4,161,1829	65.0	76.0	72.0		2700	1.4	0.0	17	dbSNP_129	72	704,7578		31,642,3468	no	coding-synonymous	SLC38A10	NM_001037984.1		35,803,5297	CC,CT,TT		8.5004,4.2377,7.1149		900/1120	79220016	873,11397	1994	4141	6135	SO:0001819	synonymous_variant	124565	exon16			AGTGGCTGCCACC	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2700A>G	17.37:g.79220016T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1																																																																																			A|0.000;C|0.089;G|0.000;T|0.910	0.089	strong		0.627	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
MT-CYB	4519	hgsc.bcm.edu	37	M	15452	15452	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:15452C>A	ENST00000361789.2	+	1	706	c.706C>A	c.(706-708)Ctt>Att	p.L236I	MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-ND6_ENST00000361681.2_5'Flank			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	236			L -> I (in dbSNP:rs3088309). {ECO:0000269|PubMed:10453733, ECO:0000269|PubMed:11130070, ECO:0000269|PubMed:11553319}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						TACTTCTCTTCCTTCTCTCCT	0.478											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.L236I		Atlas-SNP	.											.	.	.	.	0			c.C706A						PASS	.																																			SO:0001583	missense	0	exon1			CTCTTCCTTCTCT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.706C>A	M.37:g.15452C>A	ENSP00000354554:p.Leu236Ile	Somatic	4	0	0	585	WXS	Illumina HiSeq	Phase_I	8	8	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.478	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
GALNT15	117248	hgsc.bcm.edu	37	3	16268986	16268986	+	Silent	SNP	C	C	A	rs14576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:16268986C>A	ENST00000339732.5	+	10	2402	c.1899C>A	c.(1897-1899)atC>atA	p.I633I	GALNT15_ENST00000437509.1_Intron	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	633					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										TTGACCAGATCAATGCTGTGG	0.428													C|||	1470	0.29353	0.3359	0.3516	5008	,	,		18243	0.2034		0.3598	False		,,,				2504	0.2198				p.I633I		Atlas-SNP	.											.	.	.	.	0			c.C1899A						PASS	.	C		1431,2975	465.1+/-354.1	232,967,1004	122.0	119.0	120.0		1899	5.4	0.0	3	dbSNP_52	120	3065,5535	470.3+/-367.8	554,1957,1789	no	coding-synonymous	GALNTL2	NM_054110.4		786,2924,2793	AA,AC,CC		35.6395,32.4784,34.5687		633/640	16268986	4496,8510	2203	4300	6503	SO:0001819	synonymous_variant	117248	exon10			CCAGATCAATGCT	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1899C>A	3.37:g.16268986C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Silent	SNP	ENST00000339732.5	37	CCDS33711.1	724	0.3315018315018315	183	0.3719512195121951	147	0.40607734806629836	129	0.22552447552447552	265	0.3496042216358839	C	5.671	0.308339	0.10733	0.324784	0.356395	ENSG00000131386	ENST00000543679	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999999203764	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	.	15.0278	0.71682	0.0:1.0:0.0:0.0	rs14576;rs1394910;rs3172436;rs59745256;rs14576	.	.	.	X	163	.	ENSP00000445852:S163X	S	+	2	0	GALNTL2	16243990	0.028000	0.19301	0.012000	0.15200	0.052000	0.14988	1.745000	0.38278	2.681000	0.91329	0.655000	0.94253	TCA	C|0.670;A|0.330	0.330	strong		0.428	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
ZNF845	91664	hgsc.bcm.edu	37	19	53854397	53854397	+	Missense_Mutation	SNP	G	G	C	rs10415799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53854397G>C	ENST00000595091.1	+	5	688	c.469G>C	c.(469-471)Gaa>Caa	p.E157Q	ZNF845_ENST00000458035.1_Missense_Mutation_p.E157Q			Q96IR2	ZN845_HUMAN	zinc finger protein 845	157					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E157Q(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTTTCAGACCGAAGGGAAAAT	0.408													.|||	1723	0.34405	0.2307	0.2882	5008	,	,		21024	0.4702		0.3738	False		,,,				2504	0.3763				p.E157Q		Atlas-SNP	.											ZNF845,NS,carcinoma,0,6	ZNF845	101	6	3	Substitution - Missense(3)	kidney(2)|stomach(1)	c.G469C						PASS	.	G	GLN/GLU	332,1052		44,244,404	69.0	48.0	54.0		469	-1.4	0.0	19	dbSNP_119	54	1198,1984		230,738,623	no	missense	ZNF845	NM_138374.1	29	274,982,1027	CC,CG,GG		37.6493,23.9884,33.5085	benign	157/971	53854397	1530,3036	692	1591	2283	SO:0001583	missense	91664	exon4			CAGACCGAAGGGA	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.469G>C	19.37:g.53854397G>C	ENSP00000470005:p.Glu157Gln	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	168	73	0.434524	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	792	0.3626373626373626	129	0.2621951219512195	114	0.3149171270718232	283	0.49475524475524474	266	0.35092348284960423	G	1.231	-0.624000	0.03636	0.239884	0.376493	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.08282	3.11	1.2	-1.38	0.09027	.	.	.	.	.	T	0.00012	0.0000	L	0.48935	1.535	0.80722	P	0.0	B	0.28933	0.228	B	0.29663	0.105	T	0.42799	-0.9430	8	0.18276	T	0.48	.	3.6513	0.08205	0.1859:0.2581:0.556:0.0	rs10415799	157	Q96IR2	ZN845_HUMAN	Q	157	ENSP00000388311:E157Q	ENSP00000412086:E157Q	E	+	1	0	ZNF845	58546209	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.057000	0.14279	-0.374000	0.07967	0.411000	0.27672	GAA	G|0.643;C|0.357	0.357	strong		0.408	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
MMAA	166785	hgsc.bcm.edu	37	4	146572227	146572227	+	Silent	SNP	G	G	A	rs11721553	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:146572227G>A	ENST00000281317.5	+	5	1957	c.747G>A	c.(745-747)tcG>tcA	p.S249S	MMAA_ENST00000541599.1_Intron|RP11-557J10.4_ENST00000504555.1_RNA	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	249					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TGGGTCAGTCGGAGTTTGCTG	0.378													G|||	246	0.0491214	0.0454	0.062	5008	,	,		19828	0.0069		0.0974	False		,,,				2504	0.0389				p.S249S		Atlas-SNP	.											.	MMAA	46	.	0			c.G747A						PASS	.	G		274,4132	153.7+/-187.2	13,248,1942	242.0	221.0	228.0		747	-2.0	1.0	4	dbSNP_120	228	890,7710	200.2+/-244.0	55,780,3465	no	coding-synonymous	MMAA	NM_172250.2		68,1028,5407	AA,AG,GG		10.3488,6.2188,8.9497		249/419	146572227	1164,11842	2203	4300	6503	SO:0001819	synonymous_variant	166785	exon5			TCAGTCGGAGTTT	AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"""methylmalonic aciduria (cobalamin deficiency) type A"""			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.747G>A	4.37:g.146572227G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_172250	B3KX40|Q495G7	Silent	SNP	ENST00000281317.5	37	CCDS3766.1																																																																																			G|0.927;A|0.073	0.073	strong		0.378	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2		
OBSCN	84033	hgsc.bcm.edu	37	1	228505739	228505739	+	Missense_Mutation	SNP	G	G	A	rs3795801	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228505739G>A	ENST00000422127.1	+	53	14040	c.13996G>A	c.(13996-13998)Ggt>Agt	p.G4666S	OBSCN_ENST00000366707.4_Missense_Mutation_p.G2300S|OBSCN_ENST00000366709.4_Missense_Mutation_p.G1785S|OBSCN_ENST00000284548.11_Missense_Mutation_p.G4666S|OBSCN_ENST00000570156.2_Missense_Mutation_p.G5623S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4666	Ig-like 47.		G -> S (in dbSNP:rs3795801).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CATCCAGCCCGGTGGGCGGTT	0.627													g|||	867	0.173123	0.2216	0.2435	5008	,	,		18063	0.1518		0.159	False		,,,				2504	0.0941				p.G5623S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16867A						PASS	.		SER/GLY,SER/GLY	1019,3243		112,795,1224	87.0	97.0	94.0		13996,13996	-5.4	0.0	1	dbSNP_107	94	1469,6999		133,1203,2898	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	56,56	245,1998,4122	AA,AG,GG		17.3477,23.909,19.5444	benign,benign	4666/7969,4666/6621	228505739	2488,10242	2131	4234	6365	SO:0001583	missense	84033	exon64			CAGCCCGGTGGGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13996G>A	1.37:g.228505739G>A	ENSP00000409493:p.Gly4666Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	194	97	0.5	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	393	0.17994505494505494	94	0.1910569105691057	89	0.24585635359116023	87	0.1520979020979021	123	0.16226912928759896	g	13.43	2.235989	0.39498	0.23909	0.173477	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	4.51	-5.37	0.02681	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.102050	0.06837	N	0.794996	T	0.00012	0.0000	N	0.17800	0.525	0.80722	P	0.0	B;B	0.09022	0.002;0.002	B;B	0.09377	0.004;0.002	T	0.41484	-0.9506	9	0.07175	T	0.84	.	20.2526	0.98410	0.1567:0.0:0.8433:0.0	rs3795801;rs52803091;rs58512327;rs3795801	4666;4666	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	4666;4666;2300;1785	ENSP00000284548:G4666S;ENSP00000409493:G4666S;ENSP00000355668:G2300S;ENSP00000355670:G1785S	ENSP00000284548:G4666S	G	+	1	0	OBSCN	226572362	0.020000	0.18652	0.000000	0.03702	0.151000	0.21798	0.239000	0.18023	-1.559000	0.01688	-0.565000	0.04167	GGT	G|0.828;A|0.172	0.172	strong		0.627	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
LAMA5	3911	hgsc.bcm.edu	37	20	60899182	60899182	+	Missense_Mutation	SNP	C	C	T	rs11698080	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60899182C>T	ENST00000252999.3	-	43	5788	c.5722G>A	c.(5722-5724)Gcc>Acc	p.A1908T		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1908	Laminin EGF-like 17. {ECO:0000255|PROSITE-ProRule:PRU00460}.		A -> T (in dbSNP:rs11698080).		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)			ACACAGGGGGCGCTGGGGTCG	0.672													.|||	1077	0.215056	0.2458	0.2363	5008	,	,		15727	0.1895		0.2406	False		,,,				2504	0.1585				p.A1908T		Atlas-SNP	.											LAMA5,caecum,carcinoma,0,1	LAMA5	268	1	0			c.G5722A						PASS	.	C	THR/ALA	1186,3188		159,868,1160	21.0	24.0	23.0		5722	0.0	0.2	20	dbSNP_120	23	1879,6663		206,1467,2598	yes	missense	LAMA5	NM_005560.3	58	365,2335,3758	TT,TC,CC		21.9972,27.1148,23.7303	benign	1908/3696	60899182	3065,9851	2187	4271	6458	SO:0001583	missense	3911	exon43			AGGGGGCGCTGGG	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.5722G>A	20.37:g.60899182C>T	ENSP00000252999:p.Ala1908Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	98	57	0.581633	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	487	0.222985347985348	131	0.266260162601626	83	0.2292817679558011	104	0.18181818181818182	169	0.22295514511873352	C	9.488	1.099832	0.20552	0.271148	0.219972	ENSG00000130702	ENST00000252999	T	0.61392	0.11	4.05	0.0403	0.14208	EGF-like, laminin (4);	0.386612	0.25625	U	0.029398	T	0.00012	0.0000	L	0.33137	0.985	0.46874	P	7.700000000000484E-4	B	0.24576	0.106	B	0.13407	0.009	T	0.23619	-1.0183	9	0.19590	T	0.45	.	8.6324	0.33928	0.287:0.6297:0.0:0.0834	rs11698080;rs11698080	1908	O15230	LAMA5_HUMAN	T	1908	ENSP00000252999:A1908T	ENSP00000252999:A1908T	A	-	1	0	LAMA5	60332577	0.019000	0.18553	0.211000	0.23655	0.031000	0.12232	1.445000	0.35079	0.150000	0.19136	-0.350000	0.07774	GCC	C|0.759;T|0.241	0.241	strong		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
PTPRN2	5799	hgsc.bcm.edu	37	7	157931119	157931119	+	Silent	SNP	A	A	G	rs1130500	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:157931119A>G	ENST00000389418.4	-	7	1008	c.999T>C	c.(997-999)gcT>gcC	p.A333A	PTPRN2_ENST00000404321.2_Silent_p.A356A|PTPRN2_ENST00000389413.3_Silent_p.A333A|PTPRN2_ENST00000409483.1_Silent_p.A295A|PTPRN2_ENST00000389416.4_Silent_p.A316A	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	333					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCATCAGCTCAGCCATGCCGT	0.657													G|||	1897	0.378794	0.4516	0.4409	5008	,	,		18883	0.4663		0.2903	False		,,,				2504	0.2372				p.A333A		Atlas-SNP	.											.	PTPRN2	243	.	0			c.T999C						PASS	.		,,	1974,2432	617.8+/-393.0	443,1088,672	71.0	73.0	72.0		999,948,999	-7.1	0.0	7	dbSNP_86	72	2540,6060	691.6+/-404.5	361,1818,2121	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	804,2906,2793	GG,GA,AA		29.5349,44.8025,34.7071	,,	333/1016,316/999,333/987	157931119	4514,8492	2203	4300	6503	SO:0001819	synonymous_variant	5799	exon7			CAGCTCAGCCATG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.999T>C	7.37:g.157931119A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	96	43	0.447917	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			A|0.625;G|0.375	0.375	strong		0.657	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
PMPCA	23203	hgsc.bcm.edu	37	9	139311471	139311471	+	Silent	SNP	C	C	T	rs3812581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139311471C>T	ENST00000371717.3	+	7	711	c.702C>T	c.(700-702)aaC>aaT	p.N234N	PMPCA_ENST00000462616.1_3'UTR|PMPCA_ENST00000399219.3_Silent_p.N103N	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	234					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)		CAAAGATCAACCGAGAGGTGC	0.587													C|||	983	0.196286	0.0598	0.3069	5008	,	,		18840	0.1637		0.2744	False		,,,				2504	0.2556				p.N234N		Atlas-SNP	.											.	PMPCA	29	.	0			c.C702T						PASS	.	C		418,3988	202.1+/-225.0	25,368,1810	77.0	54.0	62.0		702	-7.9	0.0	9	dbSNP_107	62	2431,6169	402.3+/-347.4	328,1775,2197	no	coding-synonymous	PMPCA	NM_015160.1		353,2143,4007	TT,TC,CC		28.2674,9.4871,21.9053		234/526	139311471	2849,10157	2203	4300	6503	SO:0001819	synonymous_variant	23203	exon7			GATCAACCGAGAG	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.702C>T	9.37:g.139311471C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	44	0.423077	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Silent	SNP	ENST00000371717.3	37	CCDS35180.1																																																																																			C|0.785;T|0.215	0.215	strong		0.587	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160	
HLA-B	3106	hgsc.bcm.edu	37	6	31324602	31324602	+	Missense_Mutation	SNP	T	T	G	rs41562914	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31324602T>G	ENST00000412585.2	-	2	234	c.206A>C	c.(205-207)gAg>gCg	p.E69A		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	69	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.E69fs*30(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCGCGGCTCCTCTCTCGGACT	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	1344	0.268371	0.3222	0.2666	5008	,	,		7700	0.1677		0.2008	False		,,,				2504	0.3701				p.E69A		Atlas-SNP	.											.	HLA-B	54	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.A206C						PASS	.						34.0	34.0	34.0					6																	31324602		2056	4023	6079	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GGCTCCTCTCTCG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.206A>C	6.37:g.31324602T>G	ENSP00000399168:p.Glu69Ala	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	0.012	-1.657841	0.00779	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00007	9.68;9.68	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	4.848800	0.01913	U	0.040001	T	0.00039	0.0001	N	0.16833	0.445	0.09310	N	1	B;B;B	0.21309	0.002;0.001;0.054	B;B;P	0.44772	0.007;0.005;0.46	T	0.32052	-0.9921	10	0.20519	T	0.43	.	8.9744	0.35926	0.1185:0.0:0.2387:0.6428	rs9281379	69;69;44	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	A	69;80	ENSP00000399168:E69A;ENSP00000405931:E80A	ENSP00000399168:E69A	E	-	2	0	HLA-B	31432581	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.912000	0.00171	-4.011000	0.00082	-0.641000	0.03968	GAG	T|0.638;G|0.265;C|0.001;A|0.096	0.265	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
TMTC4	84899	hgsc.bcm.edu	37	13	101287404	101287404	+	Silent	SNP	G	G	A	rs2297943	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:101287404G>A	ENST00000376234.3	-	10	1380	c.1191C>T	c.(1189-1191)ccC>ccT	p.P397P	TMTC4_ENST00000328767.5_Silent_p.P286P|TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000342624.5_Silent_p.P416P	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	397						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GGTTACTCGCGGGGAGAAATG	0.488													.|||	1331	0.265775	0.0378	0.3617	5008	,	,		19380	0.3343		0.3598	False		,,,				2504	0.3384				p.P416P		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1248T						PASS	.	G	,	392,4014	192.6+/-218.0	19,354,1830	41.0	38.0	39.0		1191,1248	1.3	1.0	13	dbSNP_100	39	2920,5680	449.5+/-362.1	497,1926,1877	no	coding-synonymous,coding-synonymous	TMTC4	NM_001079669.1,NM_032813.2	,	516,2280,3707	AA,AG,GG		33.9535,8.897,25.4652	,	397/742,416/761	101287404	3312,9694	2203	4300	6503	SO:0001819	synonymous_variant	84899	exon11			ACTCGCGGGGAGA		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1191C>T	13.37:g.101287404G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	116	42	0.362069	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			G|0.737;A|0.263	0.263	strong		0.488	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
FLRT2	23768	hgsc.bcm.edu	37	14	86089032	86089032	+	Missense_Mutation	SNP	A	A	G	rs137990800	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:86089032A>G	ENST00000330753.4	+	2	1941	c.1174A>G	c.(1174-1176)Agc>Ggc	p.S392G	FLRT2_ENST00000554746.1_Missense_Mutation_p.S392G	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	392					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)			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)		TCCAAACCCTAGCAGAAGCTA	0.572													A|||	2	0.000399361	0.0	0.0014	5008	,	,		16226	0.0		0.001	False		,,,				2504	0.0				p.S392G		Atlas-SNP	.											.	FLRT2	168	.	0			c.A1174G						PASS	.	A	GLY/SER	0,4406		0,0,2203	78.0	81.0	80.0		1174	2.6	0.1	14	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	yes	missense	FLRT2	NM_013231.4	56	0,11,6492	GG,GA,AA		0.1279,0.0,0.0846	benign	392/661	86089032	11,12995	2203	4300	6503	SO:0001583	missense	23768	exon2			AACCCTAGCAGAA	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.1174A>G	14.37:g.86089032A>G	ENSP00000332879:p.Ser392Gly	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	0.009	-1.812472	0.00600	0.0	0.001279	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.56941	0.43;0.43	6.17	2.57	0.30868	.	0.309770	0.41001	N	0.000969	T	0.28234	0.0697	N	0.08118	0	0.28921	N	0.892133	B	0.02656	0.0	B	0.01281	0.0	T	0.15723	-1.0427	10	0.20046	T	0.44	-12.0086	9.8404	0.40996	0.8088:0.0:0.1912:0.0	.	392	O43155	FLRT2_HUMAN	G	392;392;45	ENSP00000332879:S392G;ENSP00000451050:S392G	ENSP00000332879:S392G	S	+	1	0	FLRT2	85158785	0.870000	0.30015	0.060000	0.19600	0.021000	0.10359	1.891000	0.39738	0.207000	0.20607	0.533000	0.62120	AGC	A|0.999;G|0.001	0.001	strong		0.572	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
OR10AD1	121275	hgsc.bcm.edu	37	12	48596546	48596546	+	Missense_Mutation	SNP	C	C	T	rs75531856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48596546C>T	ENST00000310248.2	-	1	624	c.530G>A	c.(529-531)aGc>aAc	p.S177N		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	177						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						ACAGAAGAAGCTTTCTATGTG	0.507													T|||	213	0.0425319	0.059	0.036	5008	,	,		21070	0.006		0.0924	False		,,,				2504	0.0112				p.S177N		Atlas-SNP	.											.	OR10AD1	24	.	0			c.G530A						PASS	.	T	ASN/SER	275,4131	800.4+/-415.6	8,259,1936	51.0	42.0	45.0		530	3.7	0.6	12	dbSNP_131	45	762,7838	784.1+/-407.6	30,702,3568	yes	missense	OR10AD1	NM_001004134.1	46	38,961,5504	TT,TC,CC		8.8605,6.2415,7.9732	benign	177/318	48596546	1037,11969	2203	4300	6503	SO:0001583	missense	121275	exon1			AAGAAGCTTTCTA		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.530G>A	12.37:g.48596546C>T	ENSP00000308689:p.Ser177Asn	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	99	0.04532967032967033	21	0.042682926829268296	9	0.024861878453038673	3	0.005244755244755245	66	0.0870712401055409	T	9.976	1.226799	0.22542	0.062415	0.088605	ENSG00000172640	ENST00000310248	T	0.00137	8.68	4.83	3.69	0.42338	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	N	0.000680	T	0.00012	0.0000	N	0.02345	-0.59	0.19775	N	0.999958	B	0.02656	0.0	B	0.01281	0.0	T	0.31447	-0.9943	10	0.66056	D	0.02	-26.1844	7.8654	0.29535	0.0:0.1739:0.0:0.8261	.	177	Q8NGE0	O10AD_HUMAN	N	177	ENSP00000308689:S177N	ENSP00000308689:S177N	S	-	2	0	OR10AD1	46882813	1.000000	0.71417	0.627000	0.29227	0.469000	0.32828	2.446000	0.44908	0.439000	0.26476	-0.361000	0.07541	AGC	C|0.935;T|0.065	0.065	strong		0.507	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537243	88537243	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537243C>A	ENST00000282478.7	+	4	3462	c.3429C>A	c.(3427-3429)gaC>gaA	p.D1143E	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1143E			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1143	Asp/Ser-rich.			D -> E (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.D1143D(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagtgacagcagtgaca	0.562																																					p.D1143E		Atlas-SNP	.											DSPP,NS,carcinoma,0,6	DSPP	174	6	1	Substitution - coding silent(1)	stomach(1)	c.C3429A						scavenged	.						36.0	50.0	45.0					4																	88537243		1513	2785	4298	SO:0001583	missense	1834	exon5			CAGTGACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3429C>A	4.37:g.88537243C>A	ENSP00000282478:p.Asp1143Glu	Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	129	7	0.0542636	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.530299	0.00951	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88201	-2.35;-2.35	1.37	-2.09	0.07232	.	0.760977	0.10684	N	0.646028	T	0.74313	0.3700	N	0.03608	-0.345	0.09310	N	1	D	0.58620	0.983	P	0.45406	0.479	T	0.68398	-0.5419	10	0.52906	T	0.07	-6.576	6.5853	0.22616	0.0:0.6688:0.0:0.3312	.	1143	Q9NZW4	DSPP_HUMAN	E	1143	ENSP00000382213:D1143E;ENSP00000282478:D1143E	ENSP00000282478:D1143E	D	+	3	2	DSPP	88756267	0.982000	0.34865	0.151000	0.22473	0.006000	0.05464	0.555000	0.23422	-0.845000	0.04179	-0.856000	0.03024	GAC	.	.	none		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
COL6A3	1293	hgsc.bcm.edu	37	2	238249717	238249717	+	Silent	SNP	G	G	A	rs34558385	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238249717G>A	ENST00000295550.4	-	38	8294	c.7842C>T	c.(7840-7842)agC>agT	p.S2614S	COL6A3_ENST00000353578.4_Silent_p.S2408S|COL6A3_ENST00000346358.4_Silent_p.S2414S|COL6A3_ENST00000347401.3_Silent_p.S2413S|COL6A3_ENST00000409809.1_Silent_p.S2408S|COL6A3_ENST00000472056.1_Silent_p.S2007S	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2614	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGTCCACATCGCTCCCTGCCG	0.522													G|||	218	0.0435304	0.003	0.0432	5008	,	,		16652	0.0089		0.1133	False		,,,				2504	0.0624				p.S2614S		Atlas-SNP	.											.	COL6A3	608	.	0			c.C7842T						PASS	.	G	,,	80,4326	70.9+/-108.8	1,78,2124	150.0	149.0	150.0		7842,6021,7224	-2.4	0.1	2	dbSNP_126	150	856,7744	194.9+/-240.2	43,770,3487	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	44,848,5611	AA,AG,GG		9.9535,1.8157,7.1967	,,	2614/3178,2007/2571,2408/2972	238249717	936,12070	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			CACATCGCTCCCT	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.7842C>T	2.37:g.238249717G>A		Somatic	190	1	0.00526316		WXS	Illumina HiSeq	Phase_I	212	202	0.95283	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.929;A|0.071	0.071	strong		0.522	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
TLL1	7092	hgsc.bcm.edu	37	4	166929102	166929102	+	Silent	SNP	G	G	A	rs17590218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:166929102G>A	ENST00000061240.2	+	7	1466	c.819G>A	c.(817-819)gaG>gaA	p.E273E	TLL1_ENST00000513213.1_Silent_p.E273E|TLL1_ENST00000507499.1_Silent_p.E273E	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	273	Metalloprotease. {ECO:0000250}.				cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E273E(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(21)|lung(26)|ovary(2)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	all_hematologic(180;0.221)	Melanoma(52;0.0315)|Prostate(90;0.0405)		GBM - Glioblastoma multiforme(119;0.103)		TAGGTCAAGAGTACAATTTTC	0.413													G|||	261	0.0521166	0.0454	0.0533	5008	,	,		15828	0.0883		0.0427	False		,,,				2504	0.0327				p.E273E		Atlas-SNP	.											TLL1,NS,carcinoma,0,2	TLL1	194	2	1	Substitution - coding silent(1)	prostate(1)	c.G819A						PASS	.	G	,	186,4220	118.0+/-155.7	3,180,2020	96.0	96.0	96.0		819,819	4.4	1.0	4	dbSNP_123	96	257,8343	100.3+/-161.8	5,247,4048	no	coding-synonymous,coding-synonymous	TLL1	NM_001204760.1,NM_012464.4	,	8,427,6068	AA,AG,GG		2.9884,4.2215,3.4061	,	273/393,273/1014	166929102	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	7092	exon7			TCAAGAGTACAAT	AF282732	CCDS3811.1, CCDS56342.1	4q32-q33	2008-07-29			ENSG00000038295	ENSG00000038295			11843	protein-coding gene	gene with protein product		606742				10516436	Standard	NM_012464		Approved		uc003irh.2	O43897	OTTHUMG00000161112	ENST00000061240.2:c.819G>A	4.37:g.166929102G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_001204760	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	37	CCDS3811.1																																																																																			G|0.953;A|0.047	0.047	strong		0.413	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1		
HAUS6	54801	hgsc.bcm.edu	37	9	19058483	19058483	+	Missense_Mutation	SNP	C	C	A	rs150852615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:19058483C>A	ENST00000380502.3	-	16	2749	c.2282G>T	c.(2281-2283)aGt>aTt	p.S761I	HAUS6_ENST00000380496.1_Missense_Mutation_p.S625I	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	761			S -> I (in dbSNP:rs4977493). {ECO:0000269|PubMed:15489334}.		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						ACTAATTCCACTTGATATCTG	0.323													C|||	379	0.0756789	0.0318	0.1499	5008	,	,		19354	0.0288		0.1004	False		,,,				2504	0.1053				p.S761I		Atlas-SNP	.											.	HAUS6	66	.	0			c.G2282T						PASS	.	C	ILE/SER	147,3967		4,139,1914	13.0	17.0	15.0		2282	4.2	0.6	9	dbSNP_134	15	1015,7457		56,903,3277	no	missense	HAUS6	NM_017645.3	142	60,1042,5191	AA,AC,CC		11.9806,3.5732,9.2325	probably-damaging	761/956	19058483	1162,11424	2057	4236	6293	SO:0001583	missense	54801	exon16			ATTCCACTTGATA	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.2282G>T	9.37:g.19058483C>A	ENSP00000369871:p.Ser761Ile	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	219	80	0.365297	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	169	0.07738095238095238	15	0.03048780487804878	61	0.1685082872928177	12	0.02097902097902098	81	0.10686015831134564	C	11.61	1.689967	0.29962	0.035732	0.119806	ENSG00000147874	ENST00000380502;ENST00000380496	T;T	0.27720	1.67;1.65	5.34	4.24	0.50183	.	0.232716	0.45126	D	0.000398	T	0.00144	0.0004	M	0.64997	1.995	0.80722	P	0.0	D;D;D	0.61697	0.99;0.99;0.989	P;P;P	0.61201	0.839;0.839;0.885	T	0.05767	-1.0865	9	0.72032	D	0.01	-4.5268	8.2433	0.31673	0.0:0.7116:0.1521:0.1363	.	726;625;761	Q7Z4H7-3;Q5VY60;Q7Z4H7	.;.;HAUS6_HUMAN	I	761;625	ENSP00000369871:S761I;ENSP00000369865:S625I	ENSP00000369865:S625I	S	-	2	0	HAUS6	19048483	0.995000	0.38212	0.591000	0.28745	0.369000	0.29798	1.703000	0.37846	2.483000	0.83821	0.453000	0.30009	AGT	C|1.000;|0.000	.	weak		0.323	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
B4GALNT3	283358	hgsc.bcm.edu	37	12	644337	644337	+	Missense_Mutation	SNP	G	G	A	rs2075033	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:644337G>A	ENST00000266383.5	+	2	188	c.175G>A	c.(175-177)Ggc>Agc	p.G59S		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	59			G -> S (in dbSNP:rs2075033).		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)			CACAGGGTACGGCAGCTGGAG	0.562													G|||	573	0.114417	0.1687	0.085	5008	,	,		18291	0.1389		0.0795	False		,,,				2504	0.0726				p.G59S		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G175A						PASS	.	G	SER/GLY	659,3747	273.4+/-271.3	47,565,1591	47.0	45.0	45.0		175	1.0	1.0	12	dbSNP_96	45	682,7918	167.3+/-219.0	33,616,3651	yes	missense	B4GALNT3	NM_173593.3	56	80,1181,5242	AA,AG,GG		7.9302,14.9569,10.3106	benign	59/999	644337	1341,11665	2203	4300	6503	SO:0001583	missense	283358	exon2			GGGTACGGCAGCT	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.175G>A	12.37:g.644337G>A	ENSP00000266383:p.Gly59Ser	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	274	0.12545787545787546	101	0.20528455284552846	33	0.09116022099447514	82	0.14335664335664336	58	0.07651715039577836	G	3.585	-0.084803	0.07097	0.149569	0.079302	ENSG00000139044	ENST00000266383	T	0.04654	3.58	5.47	1.01	0.19927	.	0.775582	0.12229	N	0.487621	T	0.00012	0.0000	N	0.25647	0.755	0.38237	P	0.058791999999999955	B	0.22480	0.07	B	0.08055	0.003	T	0.46048	-0.9219	9	0.21014	T	0.42	-14.5149	9.7844	0.40666	0.4047:0.0:0.5953:0.0	rs2075033;rs52814513;rs2075033	59	Q6L9W6	B4GN3_HUMAN	S	59	ENSP00000266383:G59S	ENSP00000266383:G59S	G	+	1	0	B4GALNT3	514598	0.923000	0.31300	0.966000	0.40874	0.100000	0.18952	1.065000	0.30592	0.266000	0.21894	-0.253000	0.11424	GGC	G|0.885;A|0.115	0.115	strong		0.562	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
RYR1	6261	hgsc.bcm.edu	37	19	38993547	38993547	+	Silent	SNP	C	C	T	rs2229142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38993547C>T	ENST00000359596.3	+	49	7863	c.7863C>T	c.(7861-7863)caC>caT	p.H2621H	RYR1_ENST00000355481.4_Silent_p.H2621H|RYR1_ENST00000360985.3_Silent_p.H2621H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2621	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)	p.H2621H(1)		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)	TGCTGCAGCACCTGTTGCGCC	0.622													C|||	1191	0.237819	0.2163	0.1902	5008	,	,		13091	0.3095		0.16	False		,,,				2504	0.3067				p.H2621H		Atlas-SNP	.											RYR1,NS,carcinoma,0,1	RYR1	708	1	1	Substitution - coding silent(1)	stomach(1)	c.C7863T						PASS	.	C	,	834,3572	331.0+/-301.8	81,672,1450	118.0	81.0	94.0		7863,7863	3.0	1.0	19	dbSNP_98	94	1219,7381	244.6+/-273.7	100,1019,3181	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	181,1691,4631	TT,TC,CC		14.1744,18.9287,15.785	,	2621/5039,2621/5034	38993547	2053,10953	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon49			GCAGCACCTGTTG	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.7863C>T	19.37:g.38993547C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.834;T|0.166	0.166	strong		0.622	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
CREBBP	1387	hgsc.bcm.edu	37	16	3788618	3788618	+	Missense_Mutation	SNP	G	G	A	rs398124146		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3788618G>A	ENST00000262367.5	-	26	5145	c.4336C>T	c.(4336-4338)Cgc>Tgc	p.R1446C	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1408C	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1446	Acetyl-CoA binding. {ECO:0000250|UniProtKB:Q09472}.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 coactivator activity (GO:0001105)|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)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1446C(6)|p.R1446G(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ACGGCTGTGCGGAGGCAACGT	0.413			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.R1446C		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,rectum,carcinoma,0,21	CREBBP	546	21	7	Substitution - Missense(7)	haematopoietic_and_lymphoid_tissue(4)|urinary_tract(1)|lung(1)|central_nervous_system(1)	c.C4336T						PASS	.						75.0	68.0	71.0					16																	3788618		2197	4300	6497	SO:0001583	missense	1387	exon26			CTGTGCGGAGGCA	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4336C>T	16.37:g.3788618G>A	ENSP00000262367:p.Arg1446Cys	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	17.20	3.329498	0.60743	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.94330	-3.4;-3.4	5.28	4.29	0.51040	.	0.000000	0.64402	D	0.000004	D	0.97739	0.9258	H	0.96080	3.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98988	1.0807	10	0.87932	D	0	-29.6499	15.2916	0.73870	0.0:0.0:0.8588:0.1412	.	1476;1446	Q4LE28;Q92793	.;CBP_HUMAN	C	1446;1476;1408;35	ENSP00000262367:R1446C;ENSP00000371502:R1408C	ENSP00000262367:R1446C	R	-	1	0	CREBBP	3728619	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.937000	0.63513	1.303000	0.44873	0.561000	0.74099	CGC	.	.	none		0.413	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
MDN1	23195	hgsc.bcm.edu	37	6	90448092	90448092	+	Missense_Mutation	SNP	C	C	T	rs4140446	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90448092C>T	ENST00000369393.3	-	33	4791	c.4676G>A	c.(4675-4677)aGt>aAt	p.S1559N	MDN1_ENST00000428876.1_Missense_Mutation_p.S1559N			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1559			S -> N (in dbSNP:rs4140446).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AAGATTATGACTGATGATCTG	0.423													T|||	4401	0.878794	0.795	0.902	5008	,	,		18124	0.997		0.837	False		,,,				2504	0.8967				p.S1559N		Atlas-SNP	.											.	MDN1	478	.	0			c.G4676A						PASS	.	T	ASN/SER	3498,908	350.3+/-310.7	1397,704,102	143.0	128.0	133.0		4676	-2.3	0.0	6	dbSNP_110	133	7145,1455	277.9+/-293.1	2976,1193,131	yes	missense	MDN1	NM_014611.1	46	4373,1897,233	TT,TC,CC		16.9186,20.6083,18.1685	benign	1559/5597	90448092	10643,2363	2203	4300	6503	SO:0001583	missense	23195	exon33			TTATGACTGATGA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.4676G>A	6.37:g.90448092C>T	ENSP00000358400:p.Ser1559Asn	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	99	97	0.979798	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	1916	0.8772893772893773	390	0.7926829268292683	320	0.8839779005524862	571	0.9982517482517482	635	0.837730870712401	T	8.966	0.971868	0.18736	0.793917	0.830814	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.39229	1.09;1.09	5.69	-2.32	0.06745	.	0.766934	0.12987	N	0.422800	T	0.08358	0.0208	N	0.20574	0.59	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.36744	-0.9735	9	0.17832	T	0.49	.	9.4131	0.38505	0.0:0.486:0.1107:0.4033	rs4140446;rs17228938;rs52793877;rs57929527;rs4140446	1559	Q9NU22	MDN1_HUMAN	N	1559	ENSP00000358400:S1559N;ENSP00000413970:S1559N	ENSP00000358400:S1559N	S	-	2	0	MDN1	90504813	0.727000	0.28069	0.001000	0.08648	0.646000	0.38490	0.515000	0.22801	-1.025000	0.03334	-1.242000	0.01536	AGT	C|0.154;T|0.846	0.846	strong		0.423	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
VCAN	1462	hgsc.bcm.edu	37	5	82834630	82834630	+	Silent	SNP	T	T	C	rs309557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:82834630T>C	ENST00000265077.3	+	8	6373	c.5808T>C	c.(5806-5808)ggT>ggC	p.G1936G	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Silent_p.G949G|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1936	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ATTTCAGTGGTGACTTTAGAG	0.438													T|||	2347	0.46865	0.5023	0.5288	5008	,	,		19704	0.3919		0.5258	False		,,,				2504	0.4008				p.G1936G		Atlas-SNP	.											.	VCAN	498	.	0			c.T5808C						PASS	.	T	,,,	2213,2193	588.8+/-387.0	549,1115,539	82.0	84.0	83.0		,2847,,5808	3.3	1.0	5	dbSNP_79	83	4263,4337	573.0+/-389.8	1066,2131,1103	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	1615,3246,1642	CC,CT,TT		49.5698,49.773,49.7924	,,,	,949/2410,,1936/3397	82834630	6476,6530	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			CAGTGGTGACTTT	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.5808T>C	5.37:g.82834630T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	86	43	0.5	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			T|0.507;C|0.493	0.493	strong		0.438	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
CLHC1	130162	hgsc.bcm.edu	37	2	55436934	55436934	+	Missense_Mutation	SNP	G	G	A	rs9677948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:55436934G>A	ENST00000401408.1	-	6	878	c.533C>T	c.(532-534)gCt>gTt	p.A178V	CLHC1_ENST00000406076.1_Missense_Mutation_p.A56V|CLHC1_ENST00000494539.1_Intron|CLHC1_ENST00000407122.1_Missense_Mutation_p.A178V|CLHC1_ENST00000406437.2_Intron	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	178			A -> V (in dbSNP:rs9677948). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.														TTTAGTGAGAGCATCTAGATT	0.393													G|||	1053	0.210264	0.3699	0.1715	5008	,	,		16962	0.0853		0.2137	False		,,,				2504	0.1472				p.A178V		Atlas-SNP	.											.	.	.	.	0			c.C533T						PASS	.	G	VAL/ALA,VAL/ALA	1585,2821	484.4+/-360.0	288,1009,906	48.0	46.0	46.0		167,533	3.3	0.9	2	dbSNP_119	46	1885,6709	321.3+/-315.0	224,1437,2636	yes	missense,missense	C2orf63	NM_001135598.1,NM_152385.2	64,64	512,2446,3542	AA,AG,GG		21.9339,35.9737,26.6923	benign,benign	56/465,178/587	55436934	3470,9530	2203	4297	6500	SO:0001583	missense	130162	exon6			GTGAGAGCATCTA		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.533C>T	2.37:g.55436934G>A	ENSP00000384869:p.Ala178Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	69	41	0.594203	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	37	CCDS33201.1	463	0.211996336996337	199	0.40447154471544716	60	0.16574585635359115	43	0.07517482517482517	161	0.21240105540897097	G	19.13	3.767599	0.69878	0.359737	0.219339	ENSG00000162994	ENST00000407122;ENST00000401408;ENST00000406076	T;T;T	0.19669	2.13;2.13;2.15	5.21	3.33	0.38152	.	0.382481	0.23098	N	0.051951	T	0.00012	0.0000	M	0.62723	1.935	0.19300	P	0.9999714307	P	0.52463	0.953	P	0.47744	0.556	T	0.47446	-0.9117	9	0.33141	T	0.24	-5.2384	5.1184	0.14847	0.0801:0.1438:0.6276:0.1485	rs9677948;rs17846200;rs17859215;rs52789690;rs59173455;rs9677948	178	Q8NHS4	CB063_HUMAN	V	178;178;56	ENSP00000385778:A178V;ENSP00000384869:A178V;ENSP00000385512:A56V	ENSP00000384869:A178V	A	-	2	0	C2orf63	55290438	0.991000	0.36638	0.892000	0.35008	0.942000	0.58702	2.381000	0.44336	1.195000	0.43115	0.655000	0.94253	GCT	G|0.762;A|0.238	0.238	strong		0.393	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	
FAT2	2196	hgsc.bcm.edu	37	5	150886882	150886882	+	Missense_Mutation	SNP	G	G	A	rs1105168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:150886882G>A	ENST00000261800.5	-	22	12362	c.12350C>T	c.(12349-12351)cCg>cTg	p.P4117L	CTC-251D13.1_ENST00000606930.1_RNA	NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4117			P -> L (in dbSNP:rs1105168). {ECO:0000269|PubMed:9693030}.		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)			GCTGGGTTCCGGTTGGTTGAG	0.577													G|||	3891	0.776957	0.91	0.7291	5008	,	,		20171	0.8244		0.5487	False		,,,				2504	0.817				p.P4117L		Atlas-SNP	.											.	FAT2	465	.	0			c.C12350T						PASS	.	G	LEU/PRO	3780,626	768.8+/-413.6	1633,514,56	148.0	150.0	149.0		12350	0.3	0.0	5	dbSNP_86	149	4721,3879	606.7+/-395.1	1273,2175,852	yes	missense	FAT2	NM_001447.2	98	2906,2689,908	AA,AG,GG		45.1047,14.2079,34.6379	benign	4117/4350	150886882	8501,4505	2203	4300	6503	SO:0001583	missense	2196	exon22			GGTTCCGGTTGGT	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.12350C>T	5.37:g.150886882G>A	ENSP00000261800:p.Pro4117Leu	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	198	98	0.494949	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	1560	0.7142857142857143	426	0.8658536585365854	251	0.6933701657458563	468	0.8181818181818182	415	0.5474934036939314	G	0.034	-1.314492	0.01331	0.857921	0.548953	ENSG00000086570	ENST00000261800	T	0.70749	-0.51	4.63	0.264	0.15607	.	1.165440	0.06294	N	0.699675	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	0.34551	-0.9824	9	0.09843	T	0.71	.	9.5946	0.39567	0.3745:0.0:0.6255:0.0	rs1105168;rs2304027;rs17661196;rs52796103;rs58131896;rs1105168	4117;1222	Q9NYQ8;E9PDJ8	FAT2_HUMAN;.	L	4117	ENSP00000261800:P4117L	ENSP00000261800:P4117L	P	-	2	0	FAT2	150867075	0.000000	0.05858	0.001000	0.08648	0.230000	0.25150	-0.041000	0.12084	-0.078000	0.12730	-0.150000	0.13652	CCG	G|0.304;A|0.696	0.696	strong		0.577	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
SNRNP70	6625	hgsc.bcm.edu	37	19	49611319	49611319	+	Silent	SNP	C	C	T	rs1058882	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49611319C>T	ENST00000598441.1	+	10	1157	c.933C>T	c.(931-933)ggC>ggT	p.G311G	SNRNP70_ENST00000221448.5_Silent_p.G302G			P08621	RU17_HUMAN	small nuclear ribonucleoprotein 70kDa (U1)	311	Poly-Gly.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|skin(2)	12						AGCTGCGTGGCGGCGGTGGCG	0.751													C|||	836	0.166933	0.0537	0.1499	5008	,	,		10446	0.0575		0.2962	False		,,,				2504	0.3119				p.G311G		Atlas-SNP	.											SNRNP70,NS,carcinoma,0,1	SNRNP70	30	1	0			c.C933T						PASS	.	C		302,3788		22,258,1765	6.0	10.0	9.0		933	-7.3	0.0	19	dbSNP_86	9	2319,5669		375,1569,2050	no	coding-synonymous	SNRNP70	NM_003089.4		397,1827,3815	TT,TC,CC		29.031,7.3839,21.7006		311/438	49611319	2621,9457	2045	3994	6039	SO:0001819	synonymous_variant	6625	exon10			GCGTGGCGGCGGT		CCDS12756.1, CCDS74417.1	19q13.3	2013-02-12	2008-10-29	2008-10-29		ENSG00000104852		"""RNA binding motif (RRM) containing"""	11150	protein-coding gene	gene with protein product		180740	"""small nuclear ribonucleoprotein 70kDa (RNP antigen)"""	RNPU1Z, RPU1, SNRP70			Standard	XM_005259177		Approved	U1-70K, Snp1	uc021uxh.1	P08621		ENST00000598441.1:c.933C>T	19.37:g.49611319C>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	6	5	0.833333	NM_003089	B3KUA3|P78493|P78494|Q15364|Q15686|Q15687|Q15689|Q99377|Q9UE45|Q9UE46|Q9UE47|Q9UE48|Q9UFQ6	Silent	SNP	ENST00000598441.1	37	CCDS12756.1																																																																																			C|0.830;T|0.170	0.170	strong		0.751	SNRNP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466266.1	NM_003089	
SLC39A14	23516	hgsc.bcm.edu	37	8	22262379	22262379	+	Silent	SNP	C	C	T	rs33999442	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22262379C>T	ENST00000381237.1	+	2	275	c.156C>T	c.(154-156)ggC>ggT	p.G52G	SLC39A14_ENST00000289952.5_Silent_p.G52G|SLC39A14_ENST00000240095.6_Silent_p.G52G|SLC39A14_ENST00000359741.5_Silent_p.G52G	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	52					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		ATCGGTATGGCGAGGGTGACA	0.587													C|||	827	0.165136	0.1422	0.1196	5008	,	,		19658	0.1736		0.2058	False		,,,				2504	0.1779				p.G52G		Atlas-SNP	.											.	SLC39A14	59	.	0			c.C156T						PASS	.	C	,,,	770,3636	312.7+/-292.7	67,636,1500	85.0	79.0	81.0		156,156,156,156	-8.0	0.0	8	dbSNP_126	81	1599,7001	297.8+/-303.6	152,1295,2853	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A14	NM_001128431.2,NM_001135153.1,NM_001135154.1,NM_015359.4	,,,	219,1931,4353	TT,TC,CC		18.593,17.4762,18.2147	,,,	52/493,52/493,52/482,52/493	22262379	2369,10637	2203	4300	6503	SO:0001819	synonymous_variant	23516	exon2			GTATGGCGAGGGT	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.156C>T	8.37:g.22262379C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Silent	SNP	ENST00000381237.1	37	CCDS47823.1																																																																																			C|0.817;G|0.000;T|0.183	0.183	strong		0.587	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
PDZD7	79955	hgsc.bcm.edu	37	10	102782113	102782113	+	Missense_Mutation	SNP	A	A	T	rs118098246	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:102782113A>T	ENST00000370215.3	-	5	797	c.572T>A	c.(571-573)gTg>gAg	p.V191E		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	191						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)		GCACTTCTCCACTACCAGGCG	0.617													A|||	6	0.00119808	0.0	0.0014	5008	,	,		17580	0.0		0.005	False		,,,				2504	0.0				p.V191E		Atlas-SNP	.											.	PDZD7	101	.	0			c.T572A						PASS	.	A	GLU/VAL,GLU/VAL	8,4398	14.3+/-33.2	0,8,2195	111.0	99.0	103.0		572,572	5.3	1.0	10	dbSNP_132	103	78,8522	46.3+/-105.2	0,78,4222	yes	missense,missense	PDZD7	NM_001195263.1,NM_024895.4	121,121	0,86,6417	TT,TA,AA		0.907,0.1816,0.6612	possibly-damaging,possibly-damaging	191/1034,191/518	102782113	86,12920	2203	4300	6503	SO:0001583	missense	79955	exon5			TTCTCCACTACCA	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.572T>A	10.37:g.102782113A>T	ENSP00000359234:p.Val191Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_001195263	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	A	22.3	4.275685	0.80580	0.001816	0.00907	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.12672	2.66	5.29	5.29	0.74685	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.20618	0.0496	L	0.55481	1.735	0.80722	D	1	P;D	0.89917	0.95;1.0	P;D	0.91635	0.742;0.999	T	0.06463	-1.0825	10	0.02654	T	1	.	15.2184	0.73288	1.0:0.0:0.0:0.0	.	191;191	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	E	191	ENSP00000359234:V191E	ENSP00000359234:V191E	V	-	2	0	PDZD7	102772103	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	6.096000	0.71446	2.006000	0.58801	0.379000	0.24179	GTG	A|0.996;T|0.004	0.004	strong		0.617	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895	
DOCK7	85440	hgsc.bcm.edu	37	1	62960101	62960101	+	Silent	SNP	A	A	G	rs10889335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:62960101A>G	ENST00000340370.5	-	39	4986	c.4969T>C	c.(4969-4971)Ttg>Ctg	p.L1657L	DOCK7_ENST00000251157.5_Silent_p.L1679L	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1688					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						AACCAGGTCAATCGCAGATCT	0.468													A|||	1751	0.349641	0.4228	0.3573	5008	,	,		18621	0.1815		0.3171	False		,,,				2504	0.4519				p.L1679L		Atlas-SNP	.											.	DOCK7	184	.	0			c.T5035C						PASS	.	A		1726,2680	518.5+/-369.7	350,1026,827	102.0	79.0	87.0		4969	-8.7	0.0	1	dbSNP_120	87	2870,5730	451.3+/-362.6	508,1854,1938	no	coding-synonymous	DOCK7	NM_033407.2		858,2880,2765	GG,GA,AA		33.3721,39.1739,35.3375		1657/2110	62960101	4596,8410	2203	4300	6503	SO:0001819	synonymous_variant	85440	exon40			AGGTCAATCGCAG		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.4969T>C	1.37:g.62960101A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1	667	0.30540293040293043	204	0.4146341463414634	116	0.32044198895027626	100	0.17482517482517482	247	0.3258575197889182	A	8.164	0.790280	0.16258	0.391739	0.333721	ENSG00000116641	ENST00000454575	.	.	.	5.9	-8.68	0.00859	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999740427	.	.	.	.	.	.	T	0.27365	-1.0076	3	.	.	.	.	22.854	0.99977	0.2653:0.0:0.7347:0.0	rs10889335;rs59629051;rs10889335	.	.	.	T	850	.	.	I	-	2	0	DOCK7	62732689	0.003000	0.15002	0.003000	0.11579	0.990000	0.78478	-0.049000	0.11924	-1.661000	0.01484	-0.353000	0.07706	ATT	A|0.670;G|0.330	0.330	strong		0.468	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626759	43626759	+	Missense_Mutation	SNP	G	G	A	rs574727392	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:43626759G>A	ENST00000332857.6	-	4	1956	c.1928C>T	c.(1927-1929)aCg>aTg	p.T643M	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	643					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.T643M(1)									ACCTGTGGACGTGGAGGACTG	0.572													A|||	1567	0.312899	0.2292	0.2795	5008	,	,		8461	0.5516		0.3052	False		,,,				2504	0.2117				p.T643M		Atlas-SNP	.											FAM75A6,NS,carcinoma,+1,2	.	.	2	1	Substitution - Missense(1)	breast(1)	c.C1928T						scavenged	.						8.0	7.0	7.0					9																	43626759		454	1111	1565	SO:0001583	missense	389730	exon4			GTGGACGTGGAGG		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.1928C>T	9.37:g.43626759G>A	ENSP00000329825:p.Thr643Met	Somatic	45	2	0.0444444		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001145196		Missense_Mutation	SNP	ENST00000332857.6	37	CCDS47973.1	.	.	.	.	.	.	.	.	.	.	A	2.502	-0.314968	0.05422	.	.	ENSG00000185775	ENST00000332857	T	0.06142	3.34	2.36	-4.38	0.03622	.	2.118030	0.02377	N	0.078485	T	0.03390	0.0098	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39035	-0.9633	9	0.28530	T	0.3	0.4794	4.5079	0.11898	0.5468:0.1745:0.2787:0.0	.	643	Q5VVP1	F75A6_HUMAN	M	643	ENSP00000329825:T643M	ENSP00000329825:T643M	T	-	2	0	FAM75A6	43566755	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.736000	0.04882	-1.194000	0.02684	-3.677000	0.00025	ACG	A|1.000;|0.000	1.000	weak		0.572	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
NLRP1	22861	hgsc.bcm.edu	37	17	5485367	5485367	+	Missense_Mutation	SNP	A	A	T	rs12150220	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5485367A>T	ENST00000572272.1	-	3	463	c.464T>A	c.(463-465)cTc>cAc	p.L155H	NLRP1_ENST00000354411.3_Missense_Mutation_p.L155H|NLRP1_ENST00000269280.4_Missense_Mutation_p.L155H|NLRP1_ENST00000262467.5_Missense_Mutation_p.L155H|NLRP1_ENST00000345221.3_Missense_Mutation_p.L155H|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Missense_Mutation_p.L155H			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	155			L -> H (associated with susceptibility to vitiligo and vitiligo-associated autoimmune diseases; dbSNP:rs12150220). {ECO:0000269|PubMed:11270363, ECO:0000269|PubMed:17377159}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)	p.L155H(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				TTGGTAGAGGAGTGAGGCAGA	0.478													A|||	962	0.192093	0.034	0.3674	5008	,	,		18435	0.0308		0.4443	False		,,,				2504	0.1881				p.L155H		Atlas-SNP	.											NLRP1,NS,carcinoma,0,1	NLRP1	358	1	1	Substitution - Missense(1)	prostate(1)	c.T464A	GRCh37	CM074383	NLRP1	M	rs12150220	scavenged	.	A	HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU,HIS/LEU	437,3969	204.8+/-226.9	24,389,1790	34.0	37.0	36.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	464,464,464,464,464	-1.1	0.0	17	dbSNP_120	36	3884,4716	530.3+/-381.8	877,2130,1293	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	99,99,99,99,99	901,2519,3083	TT,TA,AA		45.1628,9.9183,33.2231	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	155/1376,155/1430,155/1474,155/1444,155/1400	5485367	4321,8685	2203	4300	6503	SO:0001583	missense	22861	exon3			TAGAGGAGTGAGG	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.464T>A	17.37:g.5485367A>T	ENSP00000460475:p.Leu155His	Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	504	0.23076923076923078	20	0.04065040650406504	131	0.36187845303867405	19	0.033216783216783216	334	0.44063324538258575	A	11.80	1.745635	0.30955	0.099183	0.451628	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221	T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99	2.85	-1.07	0.09968	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;D;D;D;D	0.69078	0.997;0.997;0.994;0.997;0.994	P;P;P;P;P	0.57548	0.823;0.823;0.669;0.823;0.669	T	0.37197	-0.9716	8	0.41790	T	0.15	.	0.4436	0.00490	0.4246:0.2228:0.1358:0.2168	rs12150220;rs52798470;rs12150220	155;155;155;155;155	Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;NALP1_HUMAN;.;.	H	155	ENSP00000442029:L155H;ENSP00000262467:L155H;ENSP00000269280:L155H;ENSP00000346390:L155H;ENSP00000324366:L155H	ENSP00000262467:L155H	L	-	2	0	NLRP1	5426091	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-1.072000	0.03434	-0.277000	0.09193	0.459000	0.35465	CTC	A|0.737;T|0.263	0.263	strong		0.478	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
DNAH9	1770	hgsc.bcm.edu	37	17	11833365	11833365	+	Silent	SNP	G	G	A	rs1859887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:11833365G>A	ENST00000262442.4	+	63	12128	c.12060G>A	c.(12058-12060)acG>acA	p.T4020T	DNAH9_ENST00000608377.1_Silent_p.T332T|DNAH9_ENST00000454412.2_Intron|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4020	AAA 6. {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)		AGCCCCCCACGGGCATGCATG	0.602													G|||	1109	0.221446	0.0779	0.2637	5008	,	,		18928	0.1796		0.34	False		,,,				2504	0.3067				p.T4020T		Atlas-SNP	.											.	DNAH9	695	.	0			c.G12060A						PASS	.	G	,	491,3915	227.5+/-242.7	33,425,1745	67.0	55.0	59.0		12060,996	-10.4	0.1	17	dbSNP_92	59	2855,5745	447.1+/-361.4	482,1891,1927	no	coding-synonymous,coding-synonymous	DNAH9	NM_001372.3,NM_004662.2	,	515,2316,3672	AA,AG,GG		33.1977,11.1439,25.7266	,	4020/4487,332/799	11833365	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon63			CCCCACGGGCATG	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.12060G>A	17.37:g.11833365G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	160	88	0.55	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.743;A|0.257	0.257	strong		0.602	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ID1	3397	hgsc.bcm.edu	37	20	30193538	30193538	+	Silent	SNP	A	A	G	rs15817	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:30193538A>G	ENST00000376112.3	+	1	453	c.348A>G	c.(346-348)ggA>ggG	p.G116G	ID1_ENST00000376105.3_Silent_p.G116G|MIR3193_ENST00000578262.1_RNA	NM_002165.3	NP_002156.2	P41134	ID1_HUMAN	inhibitor of DNA binding 1, dominant negative helix-loop-helix protein	116					angiogenesis (GO:0001525)|blood vessel endothelial cell migration (GO:0043534)|blood vessel morphogenesis (GO:0048514)|BMP signaling pathway (GO:0030509)|collagen metabolic process (GO:0032963)|endothelial cell morphogenesis (GO:0001886)|heart development (GO:0007507)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein destabilization (GO:0031648)|regulation of angiogenesis (GO:0045765)|regulation of MAPK cascade (GO:0043408)|response to antibiotic (GO:0046677)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|ovary(1)|pancreas(1)	4	all_cancers(5;7.12e-06)|Lung NSC(7;3.95e-06)|all_epithelial(3;4.36e-06)|all_lung(7;6.68e-06)|all_hematologic(12;0.158)|Ovarian(7;0.198)		Epithelial(4;1.99e-05)|all cancers(5;0.000169)|Colorectal(19;0.00202)|COAD - Colon adenocarcinoma(19;0.0264)			CCGAAGTTGGAACCCCCGGGG	0.632													G|||	1436	0.286741	0.8389	0.1859	5008	,	,		16049	0.0		0.16	False		,,,				2504	0.0378				p.G116G	NSCLC(123;1618 1779 21803 28680 33854)	Atlas-SNP	.											.	ID1	12	.	0			c.A348G						PASS	.	G	,	3039,1367		1071,897,235	19.0	23.0	22.0		348,348	-3.9	0.1	20	dbSNP_52	22	1354,7244		109,1136,3054	no	coding-synonymous,coding-synonymous	ID1	NM_002165.3,NM_181353.2	,	1180,2033,3289	GG,GA,AA		15.7478,31.0259,33.7819	,	116/156,116/150	30193538	4393,8611	2203	4299	6502	SO:0001819	synonymous_variant	3397	exon1			AGTTGGAACCCCC		CCDS13185.1, CCDS13186.1	20q11	2013-05-21			ENSG00000125968	ENSG00000125968		"""Basic helix-loop-helix proteins"""	5360	protein-coding gene	gene with protein product	"""DNA-binding protein inhibitor ID-1"""	600349				8294468	Standard	NM_002165		Approved	dJ857M17.1.2, bHLHb24	uc002wwg.2	P41134	OTTHUMG00000032181	ENST00000376112.3:c.348A>G	20.37:g.30193538A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	127	58	0.456693	NM_002165	A8K537|E1P5L4|O00651|O00652|Q16371|Q16377|Q5TE66|Q5TE67|Q969Z7|Q9H0Z5|Q9H109	Silent	SNP	ENST00000376112.3	37	CCDS13185.1																																																																																			A|0.677;G|0.323	0.323	strong		0.632	ID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078550.1	NM_002165	
ITPR3	3710	hgsc.bcm.edu	37	6	33653486	33653486	+	Missense_Mutation	SNP	G	G	A	rs12528378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33653486G>A	ENST00000374316.5	+	42	6609	c.5549G>A	c.(5548-5550)cGg>cAg	p.R1850Q	ITPR3_ENST00000605930.1_Missense_Mutation_p.R1850Q			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	1850			R -> Q (in dbSNP:rs12528378).		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)	AGCCTGCGCCGGGGGCACGAG	0.657													g|||	167	0.0333466	0.0023	0.062	5008	,	,		20882	0.005		0.0984	False		,,,				2504	0.0174				p.R1850Q		Atlas-SNP	.											.	ITPR3	409	.	0			c.G5549A						PASS	.		GLN/ARG	87,4319	70.9+/-108.8	0,87,2116	66.0	62.0	63.0		5549	3.8	1.0	6	dbSNP_120	63	854,7746	189.6+/-236.3	50,754,3496	yes	missense	ITPR3	NM_002224.3	43	50,841,5612	AA,AG,GG		9.9302,1.9746,7.2351	benign	1850/2672	33653486	941,12065	2203	4300	6503	SO:0001583	missense	3710	exon41			TGCGCCGGGGGCA	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.5549G>A	6.37:g.33653486G>A	ENSP00000363435:p.Arg1850Gln	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	177	87	0.491525	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	37	CCDS4783.1	111	0.050824175824175824	3	0.006097560975609756	25	0.06906077348066299	4	0.006993006993006993	79	0.10422163588390501	G	10.28	1.306279	0.23736	0.019746	0.099302	ENSG00000096433	ENST00000374316	D	0.91843	-2.92	4.69	3.81	0.43845	.	0.392432	0.23809	N	0.044353	T	0.69637	0.3133	L	0.28400	0.85	0.19775	N	0.999952	B	0.31009	0.303	B	0.27380	0.079	T	0.58962	-0.7543	10	0.13853	T	0.58	-21.4683	5.0338	0.14423	0.1979:0.1733:0.6288:0.0	rs12528378	1850	Q14573	ITPR3_HUMAN	Q	1850	ENSP00000363435:R1850Q	ENSP00000363435:R1850Q	R	+	2	0	ITPR3	33761464	0.800000	0.28916	1.000000	0.80357	0.906000	0.53458	1.127000	0.31357	0.960000	0.38005	0.313000	0.20887	CGG	G|0.935;A|0.065	0.065	strong		0.657	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
C11orf24	53838	hgsc.bcm.edu	37	11	68030173	68030173	+	Missense_Mutation	SNP	C	C	A	rs3802746	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68030173C>A	ENST00000304271.6	-	4	692	c.290G>T	c.(289-291)gGt>gTt	p.G97V	C11orf24_ENST00000530166.1_5'UTR|C11orf24_ENST00000533310.1_Intron	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	97			G -> V (in dbSNP:rs3802746). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874}.			Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						ATCAGCTGCACCTCCTGAAGT	0.567													C|||	1920	0.383387	0.1309	0.513	5008	,	,		18929	0.4752		0.3062	False		,,,				2504	0.6176				p.G97V	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.G290T						PASS	.	C	VAL/GLY	690,3710	289.2+/-280.3	56,578,1566	133.0	98.0	110.0		290	1.5	0.0	11	dbSNP_107	110	2633,5955	425.0+/-354.8	428,1777,2089	yes	missense	C11orf24	NM_022338.3	109	484,2355,3655	AA,AC,CC		30.6591,15.6818,25.5852	probably-damaging	97/450	68030173	3323,9665	2200	4294	6494	SO:0001583	missense	53838	exon4			GCTGCACCTCCTG	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.290G>T	11.37:g.68030173C>A	ENSP00000307264:p.Gly97Val	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	199	105	0.527638	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	737	0.3374542124542125	56	0.11382113821138211	179	0.494475138121547	264	0.46153846153846156	238	0.31398416886543534	C	12.00	1.806515	0.31961	0.156818	0.306591	ENSG00000171067	ENST00000304271	T	0.55052	0.54	3.37	1.45	0.22620	.	.	.	.	.	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	D	0.65815	0.995	D	0.63877	0.919	T	0.45833	-0.9234	8	0.26408	T	0.33	3.0E-4	6.6072	0.22731	0.0:0.7456:0.0:0.2544	rs3802746;rs17855426;rs60804736;rs3802746	97	Q96F05	CK024_HUMAN	V	97	ENSP00000307264:G97V	ENSP00000307264:G97V	G	-	2	0	C11orf24	67786749	0.001000	0.12720	0.005000	0.12908	0.443000	0.32047	0.759000	0.26461	0.746000	0.32786	0.305000	0.20034	GGT	T|0.000;C|0.709;A|0.291	0.291	strong		0.567	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
LRWD1	222229	hgsc.bcm.edu	37	7	102112980	102112980	+	Silent	SNP	G	G	A	rs3800987	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:102112980G>A	ENST00000292616.5	+	13	1766	c.1614G>A	c.(1612-1614)acG>acA	p.T538T	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	538					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						GCCAGTCCACGGTGGCAGTGG	0.716													G|||	2312	0.461661	0.3139	0.5519	5008	,	,		15340	0.372		0.662	False		,,,				2504	0.4836				p.T538T		Atlas-SNP	.											LRWD1,NS,carcinoma,0,1	LRWD1	41	1	0			c.G1614A						PASS	.	G		1560,2790		317,926,932	11.0	9.0	10.0		1614	-10.2	0.0	7	dbSNP_107	10	5482,3026		1822,1838,594	no	coding-synonymous	LRWD1	NM_152892.1		2139,2764,1526	AA,AG,GG		35.5665,35.8621,45.2325		538/648	102112980	7042,5816	2175	4254	6429	SO:0001819	synonymous_variant	222229	exon13			GTCCACGGTGGCA	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.1614G>A	7.37:g.102112980G>A		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1	1113	0.5096153846153846	173	0.3516260162601626	215	0.5939226519337016	227	0.3968531468531469	498	0.6569920844327177	G	0.094	-1.162080	0.01673	0.358621	0.644335	ENSG00000161036	ENST00000488689;ENST00000468175	.	.	.	5.1	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.51767	P	6.799999999995698E-5	.	.	.	.	.	.	T	0.16719	-1.0393	3	.	.	.	-0.1259	4.6709	0.12689	0.5376:0.2198:0.0955:0.1471	rs3800987;rs10316934;rs13244777;rs17845221;rs17858035;rs17858491	.	.	.	Q	149;124	.	.	R	+	2	0	LRWD1	101899985	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-7.784000	0.00030	-3.315000	0.00189	-1.058000	0.02302	CGG	G|0.476;A|0.524	0.524	strong		0.716	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
DNAH5	1767	hgsc.bcm.edu	37	5	13865980	13865980	+	Silent	SNP	T	T	C	rs7703349	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13865980T>C	ENST00000265104.4	-	27	4256	c.4152A>G	c.(4150-4152)acA>acG	p.T1384T	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1384	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)	p.T1384T(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CTCCAGTATATGTGATGTATT	0.318									Kartagener syndrome				C|||	2347	0.46865	0.5968	0.3401	5008	,	,		18627	0.3323		0.4652	False		,,,				2504	0.5307				p.T1384T		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - coding silent(1)	stomach(1)	c.A4152G						PASS	.	C		2506,1892		718,1070,411	49.0	55.0	53.0		4152	1.8	1.0	5	dbSNP_116	53	4011,4581		985,2041,1270	no	coding-synonymous	DNAH5	NM_001369.2		1703,3111,1681	CC,CT,TT		46.683,43.0196,49.8306		1384/4625	13865980	6517,6473	2199	4296	6495	SO:0001819	synonymous_variant	1767	exon27	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTATATGTGATG	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.4152A>G	5.37:g.13865980T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	75	30	0.4	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.533;C|0.467	0.467	strong		0.318	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
CDRT1	374286	hgsc.bcm.edu	37	17	15498181	15498181	+	Silent	SNP	A	A	G	rs12601532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15498181A>G	ENST00000395906.3	-	10	1727	c.1728T>C	c.(1726-1728)gcT>gcC	p.A576A	CDRT1_ENST00000583965.1_Intron|RP11-385D13.1_ENST00000455584.2_Silent_p.A886A|CDRT1_ENST00000354433.3_Silent_p.A76A	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	576										endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		GGCATTTCACAGCTCCCTCGT	0.532													G|||	1837	0.366813	0.4697	0.3545	5008	,	,		17968	0.3899		0.2356	False		,,,				2504	0.3476				p.A576A		Atlas-SNP	.											.	CDRT1	83	.	0			c.T1728C						PASS	.	G		1590,2816		461,668,1074	88.0	105.0	99.0		1728	-11.0	0.0	17	dbSNP_120	99	1673,6927		269,1135,2896	no	coding-synonymous	CDRT1	NM_006382.3		730,1803,3970	GG,GA,AA		19.4535,36.0872,25.0884		576/753	15498181	3263,9743	2203	4300	6503	SO:0001819	synonymous_variant	374286	exon10			TTTCACAGCTCCC	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1728T>C	17.37:g.15498181A>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	140	52	0.371429	NM_006382	O43848|O95611	Silent	SNP	ENST00000395906.3	37	CCDS45619.1	654	0.29945054945054944	174	0.35365853658536583	109	0.3011049723756906	204	0.35664335664335667	167	0.22031662269129287	G	1.934	-0.445217	0.04604	0.360872	0.194535	ENSG00000251537	ENST00000455584	.	.	.	5.51	-11.0	0.00169	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20563	P	0.99988422	.	.	.	.	.	.	T	0.07347	-1.0777	3	.	.	.	.	6.3925	0.21595	0.3997:0.0791:0.4302:0.091	rs12601532	.	.	.	P	901	.	.	L	-	2	0	RP11-385D13.1	15438906	0.000000	0.05858	0.011000	0.14972	0.235000	0.25334	-3.535000	0.00439	-3.489000	0.00153	-1.922000	0.00515	CTG	A|0.715;G|0.285	0.285	strong		0.532	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
FAM71F2	346653	hgsc.bcm.edu	37	7	128312463	128312463	+	Missense_Mutation	SNP	C	C	G	rs74343948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128312463C>G	ENST00000480462.1	+	1	118	c.12C>G	c.(10-12)atC>atG	p.I4M	FAM71F2_ENST00000378704.3_Missense_Mutation_p.I4M|FAM71F2_ENST00000477515.1_Missense_Mutation_p.I4M|FAM71F2_ENST00000460349.1_3'UTR			Q6NXP2	F71F2_HUMAN	family with sequence similarity 71, member F2	4										NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(2)	7						TGAGTAAAATCAGGGGCCTCC	0.522													.|||	562	0.11222	0.034	0.1066	5008	,	,		16667	0.1657		0.1322	False		,,,				2504	0.1462				p.I4M		Atlas-SNP	.											.	FAM71F2	19	.	0			c.C12G						PASS	.	C	MET/ILE,MET/ILE	214,3556		11,192,1682	33.0	34.0	33.0		12,12	1.1	1.0	7	dbSNP_132	33	1243,6983		116,1011,2986	yes	missense,missense	FAM71F2	NM_001012454.3,NM_001128926.1	10,10	127,1203,4668	GG,GC,CC		15.1106,5.6764,12.1457	benign,benign	4/310,4/301	128312463	1457,10539	1885	4113	5998	SO:0001583	missense	346653	exon1			TAAAATCAGGGGC	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.12C>G	7.37:g.128312463C>G	ENSP00000420140:p.Ile4Met	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_001012454	Q0VGF6|Q0VGF7|Q86X39	Missense_Mutation	SNP	ENST00000480462.1	37	CCDS47701.1	241	0.11034798534798534	26	0.052845528455284556	37	0.10220994475138122	90	0.15734265734265734	88	0.11609498680738786	C	16.28	3.080033	0.55753	0.056764	0.151106	ENSG00000205085	ENST00000474069;ENST00000480462;ENST00000378704;ENST00000434001;ENST00000477515	T;T;T;T;T	0.37411	3.01;3.01;3.01;3.01;1.2	4.86	1.13	0.20643	.	0.270429	0.26248	N	0.025467	T	0.00210	0.0006	L	0.57536	1.79	0.40727	P	0.017286000000000024	D;P	0.55385	0.971;0.952	P;P	0.57620	0.824;0.671	T	0.04440	-1.0951	9	0.33940	T	0.23	0.4287	7.1167	0.25421	0.0:0.2398:0.0:0.7602	.	4;4	Q6NXP2-2;Q6NXP2	.;F71F2_HUMAN	M	4	ENSP00000418907:I4M;ENSP00000420140:I4M;ENSP00000367976:I4M;ENSP00000401654:I4M;ENSP00000419649:I4M	ENSP00000367976:I4M	I	+	3	3	FAM71F2	128099699	0.998000	0.40836	0.974000	0.42286	0.897000	0.52465	0.156000	0.16382	0.092000	0.17331	-0.140000	0.14226	ATC	C|0.884;G|0.116	0.116	strong		0.522	FAM71F2-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350537.1		
FAM131C	348487	hgsc.bcm.edu	37	1	16384999	16384999	+	Missense_Mutation	SNP	G	G	A	rs1807284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16384999G>A	ENST00000375662.4	-	7	959	c.776C>T	c.(775-777)cCc>cTc	p.P259L	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	259	Pro-rich.									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)		GGAGCCCGGGGGGTGGGTCCC	0.721													A|||	1887	0.376797	0.4032	0.2795	5008	,	,		19329	0.4315		0.336	False		,,,				2504	0.3957				p.P259L		Atlas-SNP	.											FAM131C,NS,carcinoma,0,2	FAM131C	21	2	0			c.C776T						PASS	.						2.0	3.0	3.0					1																	16384999		1408	3137	4545	SO:0001583	missense	348487	exon7			CCCGGGGGGTGGG		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.776C>T	1.37:g.16384999G>A	ENSP00000364814:p.Pro259Leu	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	618	0.28296703296703296	170	0.34552845528455284	94	0.2596685082872928	168	0.2937062937062937	186	0.24538258575197888	A	0.006	-2.029401	0.00410	.	.	ENSG00000185519	ENST00000375662	T	0.11821	2.74	4.65	-2.16	0.07080	.	1.628260	0.03484	N	0.215578	T	0.00012	0.0000	N	0.00972	-1.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43605	-0.9381	10	0.02654	T	1	.	10.8536	0.46784	0.4433:0.0:0.5567:0.0	rs1807284;rs3884147	259	Q96AQ9	F131C_HUMAN	L	259	ENSP00000364814:P259L	ENSP00000364814:P259L	P	-	2	0	FAM131C	16257586	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.041000	0.12084	-1.034000	0.03295	-1.271000	0.01417	CCC	G|0.717;A|0.283	0.283	strong		0.721	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
RASL12	51285	hgsc.bcm.edu	37	15	65347405	65347405	+	Silent	SNP	G	G	A	rs2232762	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:65347405G>A	ENST00000220062.4	-	5	909	c.633C>T	c.(631-633)acC>acT	p.T211T	RASL12_ENST00000434605.2_Silent_p.T200T|RASL12_ENST00000421977.3_Silent_p.T192T	NM_016563.2	NP_057647.1	Q9NYN1	RASLC_HUMAN	RAS-like, family 12	211					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			lung(1)|ovary(1)|skin(1)|urinary_tract(1)	4						CATGCCGCGCGGTGAGCGGGG	0.677													G|||	2122	0.423722	0.1876	0.5202	5008	,	,		17548	0.7837		0.4095	False		,,,				2504	0.318				p.T211T		Atlas-SNP	.											.	RASL12	32	.	0			c.C633T						PASS	.	G		1076,3324	371.0+/-319.8	136,804,1260	26.0	24.0	25.0		633	-10.5	0.0	15	dbSNP_98	25	3422,5176	475.0+/-369.0	689,2044,1566	no	coding-synonymous	RASL12	NM_016563.2		825,2848,2826	AA,AG,GG		39.8,24.4545,34.6053		211/267	65347405	4498,8500	2200	4299	6499	SO:0001819	synonymous_variant	51285	exon5			CCGCGCGGTGAGC	AF233588	CCDS10200.1	15q11.2-q22.33	2014-05-09			ENSG00000103710	ENSG00000103710			30289	protein-coding gene	gene with protein product	"""Ras family member Ris"""					12107412	Standard	NM_016563		Approved	RIS	uc002aoi.1	Q9NYN1	OTTHUMG00000133115	ENST00000220062.4:c.633C>T	15.37:g.65347405G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_016563	B2RC29|B4DJW2|B4DU82	Silent	SNP	ENST00000220062.4	37	CCDS10200.1																																																																																			G|0.606;A|0.394	0.394	strong		0.677	RASL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256782.2	NM_016563	
FAM174A	345757	hgsc.bcm.edu	37	5	99897866	99897866	+	Silent	SNP	G	G	A	rs6874840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:99897866G>A	ENST00000312637.4	+	2	769	c.543G>A	c.(541-543)acG>acA	p.T181T	FAM174A_ENST00000505792.1_3'UTR	NM_198507.1	NP_940909.1	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	181						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ATGACAACACGTTGTTTGATG	0.383													A|||	933	0.186302	0.2292	0.3732	5008	,	,		14098	0.0179		0.2694	False		,,,				2504	0.0838				p.T181T		Atlas-SNP	.											.	FAM174A	13	.	0			c.G543A						PASS	.	A		1013,3393	728.5+/-409.9	122,769,1312	153.0	140.0	145.0		543	-1.2	0.9	5	dbSNP_116	145	2091,6509	717.0+/-406.1	231,1629,2440	no	coding-synonymous	FAM174A	NM_198507.1		353,2398,3752	AA,AG,GG		24.314,22.9914,23.8659		181/191	99897866	3104,9902	2203	4300	6503	SO:0001819	synonymous_variant	345757	exon2			CAACACGTTGTTT	AY359108	CCDS4090.1	5q21.1	2008-06-19	2008-06-19	2008-06-19	ENSG00000174132	ENSG00000174132			24943	protein-coding gene	gene with protein product			"""transmembrane protein 157"""	TMEM157		12975309	Standard	NM_198507		Approved	UNQ1912	uc003knj.1	Q8TBP5	OTTHUMG00000128726	ENST00000312637.4:c.543G>A	5.37:g.99897866G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	217	99	0.456221	NM_198507	A8K0H4	Silent	SNP	ENST00000312637.4	37	CCDS4090.1																																																																																			G|0.774;A|0.226	0.226	strong		0.383	FAM174A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250631.2	NM_198507	
ZACN	353174	hgsc.bcm.edu	37	17	74076415	74076415	+	Missense_Mutation	SNP	G	G	A	rs2257020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74076415G>A	ENST00000334586.5	+	5	537	c.454G>A	c.(454-456)Gcc>Acc	p.A152T	ZACN_ENST00000392503.2_Intron|EXOC7_ENST00000591724.1_5'Flank	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	152			A -> T (in dbSNP:rs2257020). {ECO:0000269|PubMed:12381728, ECO:0000269|PubMed:14702039}.		ion transmembrane transport (GO:0034220)|response to zinc ion (GO:0010043)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)|ligand-gated ion channel activity (GO:0015276)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	11						CCTGGCCCTCGCCACGGAGAC	0.632													A|||	3030	0.605032	0.6384	0.4856	5008	,	,		16479	0.5188		0.6173	False		,,,				2504	0.7209				p.A152T		Atlas-SNP	.											.	ZACN	29	.	0			c.G454A						PASS	.	A	THR/ALA	2764,1642	502.5+/-365.3	895,974,334	99.0	90.0	93.0		454	4.6	1.0	17	dbSNP_100	93	5233,3367	499.6+/-375.0	1591,2051,658	yes	missense	ZACN	NM_180990.3	58	2486,3025,992	AA,AG,GG		39.1512,37.2674,38.513	benign	152/413	74076415	7997,5009	2203	4300	6503	SO:0001583	missense	353174	exon5			GCCCTCGCCACGG	AK122638	CCDS11740.2	17q25.3	2012-01-18	2008-04-17	2008-04-17	ENSG00000186919	ENSG00000186919		"""Ligand-gated ion channels / Zinc activated channels"""	29504	protein-coding gene	gene with protein product		610935	"""ligand-gated ion channel, zinc activated 1"""	LGICZ1		12381728, 16083862	Standard	NM_180990		Approved	LGICZ, L2, ZAC, ZAC1	uc002jqn.2	Q401N2	OTTHUMG00000157186	ENST00000334586.5:c.454G>A	17.37:g.74076415G>A	ENSP00000334854:p.Ala152Thr	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_180990	Q2TB29|Q6ZWK3|Q86YW4	Missense_Mutation	SNP	ENST00000334586.5	37	CCDS11740.2	1246	0.5705128205128205	325	0.6605691056910569	179	0.494475138121547	270	0.47202797202797203	472	0.6226912928759895	A	11.04	1.521398	0.27211	0.627326	0.608488	ENSG00000186919	ENST00000334586	T	0.77750	-1.12	4.6	4.6	0.57074	Neurotransmitter-gated ion-channel ligand-binding (3);	0.151015	0.43260	N	0.000582	T	0.00012	0.0000	N	0.00099	-2.14	0.09310	P	0.9999999999992408	B	0.02656	0.0	B	0.01281	0.0	T	0.47018	-0.9149	9	0.27082	T	0.32	-20.9782	8.0886	0.30786	0.9052:0.0:0.0948:0.0	rs2257020;rs16968514;rs57988082;rs2257020	152	Q401N2	ZACN_HUMAN	T	152	ENSP00000334854:A152T	ENSP00000334854:A152T	A	+	1	0	ZACN	71588010	0.954000	0.32549	0.993000	0.49108	0.775000	0.43874	0.920000	0.28705	0.804000	0.34136	-0.254000	0.11334	GCC	G|0.403;A|0.597	0.597	strong		0.632	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990	
USP20	10868	hgsc.bcm.edu	37	9	132637712	132637712	+	Silent	SNP	G	G	A	rs735115	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:132637712G>A	ENST00000315480.4	+	20	2330	c.2172G>A	c.(2170-2172)gcG>gcA	p.A724A	USP20_ENST00000358355.1_Silent_p.A724A|USP20_ENST00000372429.3_Silent_p.A724A			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	724	DUSP 1. {ECO:0000255|PROSITE- ProRule:PRU00613}.				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)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	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)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				ACACCTTCGCGGAGCCAGGCC	0.682													G|||	1041	0.207867	0.0507	0.2522	5008	,	,		17874	0.1885		0.4066	False		,,,				2504	0.2045				p.A724A		Atlas-SNP	.											.	USP20	186	.	0			c.G2172A						PASS	.	G	,,	391,3755		20,351,1702	55.0	63.0	60.0		2172,2172,2172	-10.7	0.0	9	dbSNP_86	60	3070,5360		541,1988,1686	no	coding-synonymous,coding-synonymous,coding-synonymous	USP20	NM_001008563.3,NM_001110303.2,NM_006676.6	,,	561,2339,3388	AA,AG,GG		36.4176,9.4308,27.5207	,,	724/915,724/915,724/915	132637712	3461,9115	2073	4215	6288	SO:0001819	synonymous_variant	10868	exon20			CTTCGCGGAGCCA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.2172G>A	9.37:g.132637712G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Silent	SNP	ENST00000315480.4	37	CCDS43892.1																																																																																			G|0.730;A|0.270	0.270	strong		0.682	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		
CD1D	912	hgsc.bcm.edu	37	1	158151892	158151892	+	Silent	SNP	T	T	C	rs140563679	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158151892T>C	ENST00000368171.3	+	4	898	c.399T>C	c.(397-399)caT>caC	p.H133H		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	133					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					ACTTCTTCCATGTAGCATTTC	0.498													T|||	3	0.000599042	0.0	0.0	5008	,	,		19718	0.0		0.003	False		,,,				2504	0.0				p.H133H		Atlas-SNP	.											.	CD1D	60	.	0			c.T399C						PASS	.	T		0,4406		0,0,2203	130.0	143.0	138.0		399	-9.5	0.0	1	dbSNP_134	138	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	CD1D	NM_001766.3		0,17,6486	CC,CT,TT		0.1977,0.0,0.1307		133/336	158151892	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	912	exon4			CTTCCATGTAGCA	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1637	protein-coding gene	gene with protein product		188410	"""CD1D antigen, d polypeptide"", ""CD1d antigen"""			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.399T>C	1.37:g.158151892T>C		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	218	107	0.490826	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Silent	SNP	ENST00000368171.3	37	CCDS1173.1																																																																																			T|0.999;C|0.001	0.001	strong		0.498	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766	
GALP	85569	hgsc.bcm.edu	37	19	56693620	56693620	+	Splice_Site	SNP	C	C	G	rs3745833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56693620C>G	ENST00000357330.2	+	4	298	c.216C>G	c.(214-216)atC>atG	p.I72M	GALP_ENST00000440823.1_3'UTR	NM_033106.3	NP_149097.1	Q9UBC7	GALP_HUMAN	galanin-like peptide	72			I -> M (in dbSNP:rs3745833).		behavioral response to starvation (GO:0042595)|defense response to bacterium (GO:0042742)|neuropeptide signaling pathway (GO:0007218)|regulation of appetite (GO:0032098)|response to insulin (GO:0032868)	extracellular region (GO:0005576)				lung(4)	4		Colorectal(82;0.000147)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0507)		GGAAGGCCATCGGTGAGTGAG	0.592													C|||	1630	0.325479	0.3366	0.3429	5008	,	,		17856	0.2302		0.3668	False		,,,				2504	0.3538				p.I72M		Atlas-SNP	.											.	GALP	13	.	0			c.C216G	GRCh37	CM071786	GALP	M	rs3745833	PASS	.	C	,MET/ILE	1496,2910	477.9+/-358.1	243,1010,950	166.0	140.0	149.0		,216	-2.4	0.7	19	dbSNP_107	149	3109,5491	475.6+/-369.2	555,1999,1746	yes	utr-3,missense-near-splice	GALP	NM_001145546.1,NM_033106.3	,10	798,3009,2696	GG,GC,CC		36.1512,33.9537,35.4067	,benign	,72/117	56693620	4605,8401	2203	4300	6503	SO:0001630	splice_region_variant	85569	exon4			GGCCATCGGTGAG	AF188493	CCDS12940.1, CCDS46202.1	19q13.42	2013-02-26	2007-08-24			ENSG00000197487		"""Endogenous ligands"""	24840	protein-coding gene	gene with protein product		611178				10601261	Standard	NM_033106		Approved		uc002qmo.1	Q9UBC7		ENST00000357330.2:c.217+1C>G	19.37:g.56693620C>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	46	17	0.369565	NM_033106	A1KXL3	Missense_Mutation	SNP	ENST00000357330.2	37	CCDS12940.1	685	0.31364468864468864	164	0.3333333333333333	122	0.3370165745856354	124	0.21678321678321677	275	0.3627968337730871	C	11.47	1.649411	0.29336	0.339537	0.361512	ENSG00000197487	ENST00000357330	T	0.56444	0.46	1.87	-2.37	0.06643	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.999999275268	P	0.48089	0.905	P	0.49047	0.599	T	0.13656	-1.0501	8	0.87932	D	0	0.045	0.1275	0.00070	0.2336:0.18:0.2368:0.3496	rs3745833;rs17668585;rs52824557;rs3745833	72	Q9UBC7	GALP_HUMAN	M	72	ENSP00000349884:I72M	ENSP00000349884:I72M	I	+	3	3	GALP	61385432	0.091000	0.21658	0.653000	0.29593	0.141000	0.21300	0.003000	0.13083	-0.762000	0.04664	-0.499000	0.04595	ATC	C|0.667;G|0.332	0.332	strong		0.592	GALP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457832.1	NM_033106	Missense_Mutation
EXOC3L1	283849	hgsc.bcm.edu	37	16	67222676	67222676	+	Silent	SNP	G	G	A	rs13334403	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67222676G>A	ENST00000314586.6	-	4	615	c.375C>T	c.(373-375)gcC>gcT	p.A125A	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	125	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						GCTTGTGCTGGGCAACCCGCT	0.662													G|||	405	0.0808706	0.2519	0.0187	5008	,	,		17923	0.0109		0.0268	False		,,,				2504	0.0215				p.A125A		Atlas-SNP	.											LOC283849,NS,carcinoma,-1,2	EXOC3L1	52	2	0			c.C375T						PASS	.	G		890,3506	332.5+/-302.5	96,698,1404	44.0	46.0	45.0		375	-1.6	0.1	16	dbSNP_121	45	273,8327	102.3+/-163.5	8,257,4035	no	coding-synonymous	EXOC3L1	NM_178516.3		104,955,5439	AA,AG,GG		3.1744,20.2457,8.9489		125/747	67222676	1163,11833	2198	4300	6498	SO:0001819	synonymous_variant	283849	exon4			GTGCTGGGCAACC	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.375C>T	16.37:g.67222676G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Silent	SNP	ENST00000314586.6	37	CCDS10832.1																																																																																			G|0.920;A|0.080	0.080	strong		0.662	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
PHC1	1911	hgsc.bcm.edu	37	12	9074259	9074259	+	Silent	SNP	C	C	T	rs1805741	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9074259C>T	ENST00000543824.1	+	6	701	c.369C>T	c.(367-369)ccC>ccT	p.P123P	PHC1_ENST00000536844.1_5'UTR|PHC1_ENST00000544916.1_Silent_p.P123P|PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000433083.2_Silent_p.P86P			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	123					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						TGAGCTCTCCCAGTGCTACCA	0.562													C|||	3172	0.633387	0.3782	0.5764	5008	,	,		-128	0.7202		0.7078	False		,,,				2504	0.8528				p.P123P		Atlas-SNP	.											.	PHC1	67	.	0			c.C369T						PASS	.						93.0	81.0	85.0					12																	9074259		2203	4297	6500	SO:0001819	synonymous_variant	1911	exon5			CTCTCCCAGTGCT	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.369C>T	12.37:g.9074259C>T		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	224	213	0.950893	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Silent	SNP	ENST00000543824.1	37	CCDS8597.1																																																																																			.	.	weak		0.562	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
SBF2	81846	hgsc.bcm.edu	37	11	10019879	10019879	+	Silent	SNP	G	G	A	rs16907355	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:10019879G>A	ENST00000256190.8	-	9	1046	c.909C>T	c.(907-909)ccC>ccT	p.P303P	SBF2_ENST00000527019.1_Intron	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	303			P -> L (in dbSNP:rs16907355).		cell death (GO:0008219)|myelination (GO:0042552)|positive regulation of Rab GTPase activity (GO:0032851)|protein tetramerization (GO:0051262)	membrane (GO:0016020)|vacuolar membrane (GO:0005774)	phosphatase activity (GO:0016791)|phosphatase regulator activity (GO:0019208)|phosphatidylinositol binding (GO:0035091)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(4)|endometrium(8)|kidney(2)|large_intestine(8)|lung(16)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48				all cancers(16;2.88e-11)|Epithelial(150;3.61e-10)|BRCA - Breast invasive adenocarcinoma(625;0.00887)		GAATACATTCGGGAATTTTAA	0.323													A|||	319	0.0636981	0.0257	0.0389	5008	,	,		17647	0.0238		0.0825	False		,,,				2504	0.1544				p.P303P		Atlas-SNP	.											.	SBF2	146	.	0			c.C909T						PASS	.	A		143,4259	812.1+/-416.1	1,141,2059	107.0	112.0	111.0		909	4.3	1.0	11	dbSNP_123	111	619,7969	790.7+/-407.6	26,567,3701	yes	coding-synonymous	SBF2	NM_030962.3		27,708,5760	AA,AG,GG		7.2077,3.2485,5.8661		303/1850	10019879	762,12228	2201	4294	6495	SO:0001819	synonymous_variant	81846	exon9			ACATTCGGGAATT	AB051553	CCDS31427.1	11p15.3	2014-09-17	2004-11-12	2004-11-12	ENSG00000133812	ENSG00000133812		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	2135	protein-coding gene	gene with protein product	"""myotubularin related 13"""	607697	"""Charcot-Marie-Tooth neuropathy 4B2 (autosomal recessive, with myelin outfolding)"", ""DENN/MADD domain containing 7B"""	CMT4B2		10644431	Standard	NM_030962		Approved	KIAA1766, MTMR13, DENND7B	uc001mib.2	Q86WG5	OTTHUMG00000165890	ENST00000256190.8:c.909C>T	11.37:g.10019879G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Silent	SNP	ENST00000256190.8	37	CCDS31427.1																																																																																			G|0.942;A|0.058	0.058	strong		0.323	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962	
PLIN4	729359	hgsc.bcm.edu	37	19	4512629	4512629	+	Missense_Mutation	SNP	C	C	T	rs146679364	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4512629C>T	ENST00000301286.3	-	3	1300	c.1301G>A	c.(1300-1302)aGa>aAa	p.R434K		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	434	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.R362T(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						GATGGTTCCTCTGGCCAAATT	0.547																																					p.R434K		Atlas-SNP	.											PLIN4,NS,carcinoma,0,1	PLIN4	191	1	1	Substitution - Missense(1)	breast(1)	c.G1301A						PASS	.	C	LYS/ARG	454,3580		74,306,1637	130.0	149.0	143.0		1301	3.7	0.6	19	dbSNP_134	143	397,7961		38,321,3820	yes	missense	PLIN4	NM_001080400.1	26	112,627,5457	TT,TC,CC		4.7499,11.2543,6.8673	benign	434/1358	4512629	851,11541	2017	4179	6196	SO:0001583	missense	729359	exon3			GTTCCTCTGGCCA	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.1301G>A	19.37:g.4512629C>T	ENSP00000301286:p.Arg434Lys	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	80	0.03663003663003663	43	0.08739837398373984	9	0.024861878453038673	1	0.0017482517482517483	27	0.03562005277044855	c	0.010	-1.773753	0.00640	0.112543	0.047499	ENSG00000167676	ENST00000301286	T	0.03004	4.08	4.73	3.7	0.42460	.	0.111229	0.39544	N	0.001334	T	0.00012	0.0000	N	0.00015	-2.89	0.48135	P	4.089999999999927E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.31971	-0.9924	9	0.02654	T	1	-14.0488	8.4942	0.33119	0.0:0.0956:0.0:0.9044	.	434	Q96Q06	PLIN4_HUMAN	K	434	ENSP00000301286:R434K	ENSP00000301286:R434K	R	-	2	0	PLIN4	4463629	0.017000	0.18338	0.647000	0.29507	0.011000	0.07611	0.761000	0.26489	0.687000	0.31509	-0.856000	0.03024	AGA	C|0.949;T|0.051	0.051	strong		0.547	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
TMEM187	8269	hgsc.bcm.edu	37	X	153247722	153247722	+	Missense_Mutation	SNP	C	C	T	rs2266890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153247722C>T	ENST00000369982.4	+	2	956	c.209C>T	c.(208-210)tCg>tTg	p.S70L	MIR3202-1_ENST00000580198.1_RNA	NM_003492.2	NP_003483.1	Q14656	TM187_HUMAN	transmembrane protein 187	70			S -> L (in dbSNP:rs2266890).			integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|large_intestine(1)|lung(1)|prostate(2)	5	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTGGGGCTGTCGTGGCTGCAC	0.682													c|||	1474	0.390464	0.0688	0.3588	3775	,	,		13208	0.5516		0.1421	False		,,,				2504	0.4448				p.S70L		Atlas-SNP	.											.	TMEM187	21	.	0			c.C209T						PASS	.	C	LEU/SER	412,3421		16,319,61,1297,508	36.0	36.0	36.0		209	0.2	0.0	X	dbSNP_100	36	1205,5517		72,713,348,1641,1522	yes	missense	TMEM187	NM_003492.2	145	88,1032,409,2938,2030	TT,TC,T,CC,C		17.9262,10.7488,15.3198	benign	70/262	153247722	1617,8938	2201	4296	6497	SO:0001583	missense	8269	exon2			GGCTGTCGTGGCT	X92475	CCDS14739.1	Xq28	2007-03-14	2007-03-14	2007-03-14	ENSG00000177854	ENSG00000177854			13705	protein-coding gene	gene with protein product		300059	"""chromosome X open reading frame 12"""	CXorf12		8661027	Standard	NM_003492		Approved	ITBA1, DXS9878E	uc004fjq.2	Q14656	OTTHUMG00000024220	ENST00000369982.4:c.209C>T	X.37:g.153247722C>T	ENSP00000358999:p.Ser70Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_003492	B2RC47|Q6IAV7	Missense_Mutation	SNP	ENST00000369982.4	37	CCDS14739.1	575	0.3465943339361061	29	0.06223175965665236	81	0.2682119205298013	208	0.5683060109289617	80	0.11527377521613832	c	12.03	1.815302	0.32053	0.107488	0.179262	ENSG00000177854	ENST00000369982	T	0.19394	2.15	4.13	0.241	0.15494	.	0.413516	0.15928	U	0.237814	T	0.00012	0.0000	N	0.03608	-0.345	0.53005	P	3.2999999999949736E-5	B	0.06786	0.001	B	0.01281	0.0	T	0.38265	-0.9669	9	0.39692	T	0.17	.	2.0999	0.03677	0.5872:0.1559:0.0929:0.164	rs2266890;rs12838500;rs52811742;rs61673727;rs2266890	70	Q14656	TM187_HUMAN	L	70	ENSP00000358999:S70L	ENSP00000358999:S70L	S	+	2	0	TMEM187	152900916	0.979000	0.34478	0.015000	0.15790	0.000000	0.00434	1.795000	0.38784	-0.343000	0.08351	-2.240000	0.00288	TCG	C|0.761;T|0.239	0.239	strong		0.682	TMEM187-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061093.1	NM_003492	
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1803704T>C	ENST00000260795.2	+	6	984	c.882T>C	c.(880-882)aaT>aaC	p.N294N	FGFR3_ENST00000352904.1_Silent_p.N294N|FGFR3_ENST00000440486.2_Silent_p.N294N|FGFR3_ENST00000481110.2_Silent_p.N294N|FGFR3_ENST00000412135.2_Silent_p.N294N|FGFR3_ENST00000340107.4_Silent_p.N294N|FGFR3_ENST00000474521.1_3'UTR			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	294	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.N294N(5)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGGAGGTGAATGGCAGCAAGG	0.672		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	1039	0.207468	0.3707	0.1441	5008	,	,		12849	0.0744		0.17	False		,,,				2504	0.2076				p.N294N		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	5	Substitution - coding silent(5)	upper_aerodigestive_tract(3)|skin(2)	c.T882C						scavenged	.	C	,,	1504,2902	654.3+/-399.7	251,1002,950	47.0	42.0	44.0		882,882,882	-6.8	0.9	4	dbSNP_98	44	1278,7320	749.7+/-407.4	98,1082,3119	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	349,2084,4069	CC,CT,TT		14.8639,34.1353,21.3934	,,	294/807,294/809,294/695	1803704	2782,10222	2203	4299	6502	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGTGAATGGCAGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.882T>C	4.37:g.1803704T>C		Somatic	88	1	0.0113636		WXS	Illumina HiSeq	Phase_I	108	45	0.416667	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.799;C|0.201	0.201	strong		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
CMYA5	202333	hgsc.bcm.edu	37	5	79025157	79025157	+	Missense_Mutation	SNP	A	A	G	rs10942901	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:79025157A>G	ENST00000446378.2	+	2	600	c.569A>G	c.(568-570)gAt>gGt	p.D190G		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	190			D -> G (in dbSNP:rs10942901). {ECO:0000269|PubMed:17974005}.		negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GGCATTTATGATAAAGCAAGA	0.393													A|||	835	0.166733	0.1036	0.1902	5008	,	,		17856	0.2202		0.1471	False		,,,				2504	0.2004				p.D190G		Atlas-SNP	.											.	CMYA5	643	.	0			c.A569G						PASS	.	A	GLY/ASP	388,3280		23,342,1469	45.0	44.0	44.0		569	4.9	0.0	5	dbSNP_120	44	1184,7008		98,988,3010	yes	missense	CMYA5	NM_153610.3	94	121,1330,4479	GG,GA,AA		14.4531,10.578,13.2546	probably-damaging	190/4070	79025157	1572,10288	1834	4096	5930	SO:0001583	missense	202333	exon2			TTTATGATAAAGC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.569A>G	5.37:g.79025157A>G	ENSP00000394770:p.Asp190Gly	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	155	74	0.477419	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	341	0.15613553113553114	48	0.0975609756097561	67	0.1850828729281768	114	0.1993006993006993	112	0.14775725593667546	A	11.26	1.587130	0.28268	0.10578	0.144531	ENSG00000164309	ENST00000446378	T	0.65549	-0.16	6.06	4.88	0.63580	.	0.255650	0.28082	N	0.016672	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	P	0.48407	0.91	P	0.45099	0.469	T	0.25222	-1.0138	9	0.87932	D	0	.	3.4618	0.07536	0.6482:0.1413:0.0751:0.1354	rs10942901;rs10942901	190	Q8N3K9	CMYA5_HUMAN	G	190	ENSP00000394770:D190G	ENSP00000394770:D190G	D	+	2	0	CMYA5	79060913	0.975000	0.34042	0.020000	0.16555	0.282000	0.26991	1.489000	0.35562	1.073000	0.40885	0.533000	0.62120	GAT	A|0.832;G|0.162	0.162	strong		0.393	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
TMEM261	90871	hgsc.bcm.edu	37	9	7799606	7799606	+	Silent	SNP	C	C	A	rs14059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:7799606C>A	ENST00000358227.4	-	1	461	c.129G>T	c.(127-129)ctG>ctT	p.L43L	TMEM261_ENST00000484082.1_Intron	NM_033428.1	NP_219500.1	Q96GE9	TM261_HUMAN	transmembrane protein 261	43						integral component of membrane (GO:0016021)											AGGTCTTCAACAGGCGGTGTT	0.667													c|||	1889	0.377196	0.267	0.5389	5008	,	,		10006	0.38		0.3897	False		,,,				2504	0.3957				p.L43L		Atlas-SNP	.											.	C9orf123	7	.	0			c.G129T						PASS	.	C		1229,3177	409.7+/-335.1	176,877,1150	36.0	39.0	38.0		129	-7.3	0.0	9	dbSNP_52	38	3407,5193	485.0+/-371.5	668,2071,1561	no	coding-synonymous	C9orf123	NM_033428.1		844,2948,2711	AA,AC,CC		39.6163,27.8938,35.6451		43/113	7799606	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	90871	exon1			CTTCAACAGGCGG	BC009510	CCDS34989.1	9p24.1	2014-02-21	2013-09-11	2013-09-11	ENSG00000137038	ENSG00000137038			30536	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 123"""	C9orf123		21666724	Standard	NM_033428		Approved	MGC4730	uc003zkj.3	Q96GE9	OTTHUMG00000019539	ENST00000358227.4:c.129G>T	9.37:g.7799606C>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_033428	A8K9B7|Q5T6Y9|Q9NT74	Silent	SNP	ENST00000358227.4	37	CCDS34989.1																																																																																			C|0.639;A|0.361	0.361	strong		0.667	TMEM261-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051705.1	NM_033428	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626718	140626718	+	Silent	SNP	G	G	T	rs141887199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140626718G>T	ENST00000231173.3	+	1	1572	c.1572G>T	c.(1570-1572)ctG>ctT	p.L524L		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	524	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACGAGGCCCTGCAGGCTTTCG	0.682													G|||	10	0.00199681	0.0	0.0014	5008	,	,		16283	0.0		0.005	False		,,,				2504	0.0041				p.L524L		Atlas-SNP	.											.	PCDHB15	138	.	0			c.G1572T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	69.0	80.0	76.0		1572	2.4	0.3	5	dbSNP_134	76	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	PCDHB15	NM_018935.2		0,38,6465	TT,TG,GG		0.407,0.0681,0.2922		524/788	140626718	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	56121	exon1			GGCCCTGCAGGCT	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1572G>T	5.37:g.140626718G>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	312	138	0.442308	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			G|0.997;T|0.003	0.003	strong		0.682	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
HFM1	164045	hgsc.bcm.edu	37	1	91809036	91809036	+	Silent	SNP	T	T	C	rs148872247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91809036T>C	ENST00000370425.3	-	20	2384	c.2286A>G	c.(2284-2286)tcA>tcG	p.S762S	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Silent_p.S441S	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	762					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)		AGTCCAGGGATGATAAATCAT	0.249													T|||	34	0.00678914	0.0	0.0	5008	,	,		13475	0.0		0.0	False		,,,				2504	0.0348				p.S762S		Atlas-SNP	.											.	HFM1	188	.	0			c.A2286G						PASS	.	T		1,4379		0,1,2189	27.0	27.0	27.0		2286	4.2	1.0	1	dbSNP_134	27	1,8511		0,1,4255	no	coding-synonymous	HFM1	NM_001017975.3		0,2,6444	CC,CT,TT		0.0117,0.0228,0.0155		762/1436	91809036	2,12890	2190	4256	6446	SO:0001819	synonymous_variant	164045	exon20			CAGGGATGATAAA	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.2286A>G	1.37:g.91809036T>C		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	246	113	0.45935	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	9.635	1.137319	0.21123	2.28E-4	1.17E-4	ENSG00000162669	ENST00000430465	.	.	.	5.35	4.18	0.49190	.	.	.	.	.	T	0.43787	0.1263	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	.	6.5979	0.22685	0.217:0.082:0.0:0.7009	.	.	.	.	R	18	.	.	H	-	2	0	HFM1	91581624	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.354000	0.34056	2.015000	0.59207	0.377000	0.23210	CAT	T|0.999;C|0.001	0.001	strong		0.249	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
COBL	23242	hgsc.bcm.edu	37	7	51097216	51097216	+	Missense_Mutation	SNP	G	G	A	rs17656599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:51097216G>A	ENST00000265136.7	-	10	1742	c.1577C>T	c.(1576-1578)cCa>cTa	p.P526L	COBL_ENST00000395542.2_Missense_Mutation_p.P608L	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	526			P -> L (in dbSNP:rs17656599). {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)					GGCATCCTGTGGGCAGTGGTT	0.493													G|||	228	0.0455272	0.0053	0.0865	5008	,	,		19243	0.0		0.1302	False		,,,				2504	0.0307				p.P526L	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C1577T						PASS	.	G	LEU/PRO	110,4296	84.4+/-122.9	5,100,2098	117.0	113.0	114.0		1577	0.5	0.0	7	dbSNP_123	114	1057,7543	223.3+/-260.1	77,903,3320	yes	missense	COBL	NM_015198.3	98	82,1003,5418	AA,AG,GG		12.2907,2.4966,8.9728	benign	526/1262	51097216	1167,11839	2203	4300	6503	SO:0001583	missense	23242	exon10			TCCTGTGGGCAGT	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.1577C>T	7.37:g.51097216G>A	ENSP00000265136:p.Pro526Leu	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	138	0.06318681318681318	5	0.01016260162601626	39	0.10773480662983426	0	0.0	94	0.12401055408970976	G	7.611	0.674869	0.14841	0.024966	0.122907	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000457306	T;T;T;T	0.20463	2.07;2.07;2.07;2.07	5.6	0.527	0.17084	.	2.250440	0.02046	N	0.049656	T	0.00144	0.0004	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.001;0.001;0.0;0.001;0.002	T	0.22521	-1.0214	9	0.27785	T	0.31	.	5.7387	0.18081	0.4638:0.1479:0.3883:0.0	rs17656599;rs52804892;rs17656599	526;583;526;608;68	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	L	526;418;411;608;24	ENSP00000265136:P526L;ENSP00000401204:P418L;ENSP00000413498:P411L;ENSP00000378912:P608L	ENSP00000265136:P526L	P	-	2	0	COBL	51064710	0.000000	0.05858	0.004000	0.12327	0.010000	0.07245	-1.240000	0.02914	0.447000	0.26695	0.655000	0.94253	CCA	G|0.919;A|0.081	0.081	strong		0.493	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
MAP3K19	80122	hgsc.bcm.edu	37	2	135745392	135745392	+	Silent	SNP	G	G	A	rs11888766	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:135745392G>A	ENST00000375845.3	-	7	1080	c.1050C>T	c.(1048-1050)gaC>gaT	p.D350D	MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Silent_p.D237D|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Silent_p.D367D	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	350							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										TACCATGGCAGTCAATATCCT	0.373													G|||	1199	0.239417	0.202	0.1916	5008	,	,		20554	0.1647		0.2664	False		,,,				2504	0.3732				p.D350D		Atlas-SNP	.											.	.	.	.	0			c.C1050T						PASS	.	G	,	786,3620	316.1+/-294.4	74,638,1491	62.0	60.0	60.0		,1050	-2.9	0.0	2	dbSNP_120	60	1927,6673	339.8+/-323.3	246,1435,2619	no	intron,coding-synonymous	YSK4	NM_001018046.1,NM_025052.3	,	320,2073,4110	AA,AG,GG		22.407,17.8393,20.8596	,	,350/1329	135745392	2713,10293	2203	4300	6503	SO:0001819	synonymous_variant	80122	exon7			ATGGCAGTCAATA	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.1050C>T	2.37:g.135745392G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Silent	SNP	ENST00000375845.3	37	CCDS2176.2																																																																																			G|0.781;A|0.219	0.219	strong		0.373	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
OR10G2	26534	hgsc.bcm.edu	37	14	22102745	22102745	+	Missense_Mutation	SNP	C	C	A	rs41314525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:22102745C>A	ENST00000542433.1	-	1	351	c.254G>T	c.(253-255)cGg>cTg	p.R85L		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	85			R -> L (in dbSNP:rs41314525).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CAAAATAAGCCGAGGAACGGT	0.527													.|||	1173	0.234225	0.2746	0.1859	5008	,	,		21829	0.2808		0.1948	False		,,,				2504	0.2065				p.R85L		Atlas-SNP	.											.	OR10G2	35	.	0			c.G254T						PASS	.	C	LEU/ARG	1087,3319	394.0+/-329.1	139,809,1255	61.0	56.0	58.0		254	1.6	0.5	14	dbSNP_127	58	1549,7051	291.1+/-300.1	144,1261,2895	yes	missense	OR10G2	NM_001005466.1	102	283,2070,4150	AA,AC,CC		18.0116,24.6709,20.2676	benign	85/311	22102745	2636,10370	2203	4300	6503	SO:0001583	missense	26534	exon1			ATAAGCCGAGGAA		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.254G>T	14.37:g.22102745C>A	ENSP00000445383:p.Arg85Leu	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	224	223	0.995536	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	37	CCDS32047.1	525	0.2403846153846154	131	0.266260162601626	67	0.1850828729281768	169	0.29545454545454547	158	0.20844327176781002	C	3.673	-0.067195	0.07273	0.246709	0.180116	ENSG00000255582	ENST00000542433	T	0.03212	4.01	3.79	1.65	0.23941	GPCR, rhodopsin-like superfamily (1);	0.197894	0.24848	N	0.035104	T	0.00012	0.0000	L	0.45051	1.395	0.80722	P	0.0	B	0.12630	0.006	B	0.13407	0.009	T	0.48536	-0.9027	9	0.87932	D	0	-3.183	3.1156	0.06373	0.2243:0.5309:0.0:0.2448	rs41314525;rs61755908;rs41314525	85	Q8NGC3	O10G2_HUMAN	L	85	ENSP00000445383:R85L	ENSP00000445383:R85L	R	-	2	0	OR10G2	21172585	0.000000	0.05858	0.457000	0.27056	0.045000	0.14185	0.179000	0.16840	0.760000	0.33108	0.563000	0.77884	CGG	C|0.782;A|0.218	0.218	strong		0.527	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092827	1092827	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1092827C>A	ENST00000441003.2	+	30	4673	c.4646C>A	c.(4645-4647)aCc>aAc	p.T1549N	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1550N|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.T1549N(1)|p.T1550N(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)	GTGACCCCAACCCCAACACCC	0.632																																					p.T1549N		Atlas-SNP	.											MUC2_ENST00000441003,NS,malignant_melanoma,0,2	MUC2	614	2	2	Substitution - Missense(2)	NS(2)	c.C4646A						scavenged	.						61.0	92.0	81.0					11																	1092827		1824	3332	5156	SO:0001583	missense	4583	exon30			CCCCAACCCCAAC	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.4646C>A	11.37:g.1092827C>A	ENSP00000415183:p.Thr1549Asn	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	3	0.0365854	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.215	-0.160741	0.06502	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15487	2.47;2.42	1.49	-2.04	0.07343	.	.	.	.	.	T	0.06188	0.0160	.	.	.	0.09310	N	1	P	0.41978	0.767	B	0.26310	0.068	T	0.34950	-0.9808	8	0.23891	T	0.37	.	4.9756	0.14138	0.0:0.6372:0.2131:0.1496	.	1549	E7EUV1	.	N	1549;1550	ENSP00000415183:T1549N;ENSP00000351956:T1550N	ENSP00000351956:T1550N	T	+	2	0	MUC2	1082827	0.000000	0.05858	0.000000	0.03702	0.255000	0.26057	0.798000	0.27014	-0.678000	0.05224	0.109000	0.15622	ACC	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
DIS3L2	129563	hgsc.bcm.edu	37	2	233201328	233201328	+	Silent	SNP	A	A	G	rs3811578	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233201328A>G	ENST00000409307.1	+	20	2646	c.2646A>G	c.(2644-2646)tcA>tcG	p.S882S	DIS3L2_ENST00000273009.6_Intron|DIS3L2_ENST00000325385.7_Silent_p.S882S					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CCGAGGACTCAAGCACCAGCT	0.662													A|||	1012	0.202077	0.1732	0.2579	5008	,	,		9237	0.4484		0.0865	False		,,,				2504	0.0665				p.S882S		Atlas-SNP	.											.	DIS3L2	77	.	0			c.A2646G						PASS	.	A		549,3537		37,475,1531	15.0	21.0	19.0		2646	2.9	0.7	2	dbSNP_107	19	690,7680		28,634,3523	no	coding-synonymous	DIS3L2	NM_152383.4		65,1109,5054	GG,GA,AA		8.2437,13.4361,9.947		882/886	233201328	1239,11217	2043	4185	6228	SO:0001819	synonymous_variant	129563	exon21			GGACTCAAGCACC	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.2646A>G	2.37:g.233201328A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_152383		Silent	SNP	ENST00000409307.1	37	CCDS42834.1	473	0.21657509157509158	65	0.13211382113821138	69	0.19060773480662985	279	0.48776223776223776	60	0.079155672823219	A	8.285	0.816528	0.16607	0.134361	0.082437	ENSG00000144535	ENST00000418143	.	.	.	4.06	2.89	0.33648	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22656	P	0.99888447	.	.	.	.	.	.	T	0.50013	-0.8877	3	.	.	.	.	5.6377	0.17546	0.875:0.0:0.125:0.0	rs3811578;rs3811578	.	.	.	E	163	.	.	K	+	1	0	DIS3L2	232909572	0.000000	0.05858	0.693000	0.30195	0.069000	0.16628	-0.295000	0.08298	1.622000	0.50330	0.529000	0.55759	AAG	A|0.797;G|0.203	0.203	strong		0.662	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	
PDLIM4	8572	hgsc.bcm.edu	37	5	131607020	131607020	+	Silent	SNP	G	G	A	rs147858379	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:131607020G>A	ENST00000253754.3	+	5	595	c.531G>A	c.(529-531)ccG>ccA	p.P177P	PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Silent_p.P177P|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	177				RGLPRSRDC -> EASRGAGS (in Ref. 1; CAA63767). {ECO:0000305}.			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)			GAGGCCTCCCGCGGAGCCGGG	0.657													G|||	30	0.00599042	0.0	0.0	5008	,	,		14307	0.0298		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	PDLIM4	22	.	0			c.G531A						PASS	.						20.0	25.0	23.0					5																	131607020		2202	4298	6500	SO:0001819	synonymous_variant	8572	exon5			CCTCCCGCGGAGC	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.531G>A	5.37:g.131607020G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	28	9	0.321429	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Silent	SNP	ENST00000253754.3	37	CCDS4152.1																																																																																			G|0.989;A|0.011	0.011	strong		0.657	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
MUC4	4585	hgsc.bcm.edu	37	3	195474159	195474159	+	Missense_Mutation	SNP	G	G	A	rs62284986	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195474159G>A	ENST00000346145.4	-	24	3458	c.3419C>T	c.(3418-3420)gCc>gTc	p.A1140V	MUC4_ENST00000463781.3_Missense_Mutation_p.A5376V|MUC4_ENST00000349607.4_Missense_Mutation_p.A1089V|MUC4_ENST00000475231.1_Missense_Mutation_p.A5324V	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2133					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCCGCCCAGGGCCCCAAAGAA	0.617													.|||	616	0.123003	0.1165	0.0994	5008	,	,		27753	0.0466		0.1938	False		,,,				2504	0.1544				p.A5376V		Atlas-SNP	.											.	MUC4	1505	.	0			c.C16127T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	465,3941	214.5+/-233.7	11,443,1749	73.0	72.0	72.0		3419,16127,3266	4.3	0.1	3	dbSNP_129	72	1654,6946	300.6+/-305.0	144,1366,2790	yes	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	64,64,64	155,1809,4539	AA,AG,GG		19.2326,10.5538,16.2925	probably-damaging,probably-damaging,probably-damaging	1140/1177,5376/5413,1089/1126	195474159	2119,10887	2203	4300	6503	SO:0001583	missense	4585	exon25			CCCAGGGCCCCAA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.3419C>T	3.37:g.195474159G>A	ENSP00000304207:p.Ala1140Val	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	208	62	0.298077	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000346145.4	37	CCDS3310.1	279	0.12774725274725274	53	0.10772357723577236	38	0.10497237569060773	36	0.06293706293706294	152	0.20052770448548812	g	14.14	2.445671	0.43429	0.105538	0.192326	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.51071	0.72;1.07;1.15;1.13	5.14	4.26	0.50523	.	0.574939	0.15528	N	0.257648	T	0.00073	0.0002	M	0.69823	2.125	0.80722	P	0.0	D;B;B;B;B;B	0.58268	0.982;0.068;0.068;0.041;0.041;0.068	P;B;B;B;B;B	0.48627	0.584;0.058;0.058;0.026;0.026;0.058	T	0.07868	-1.0750	9	0.72032	D	0.01	-16.8905	9.2366	0.37470	0.0999:0.0:0.9001:0.0	rs62284986	5248;1089;1140;5376;5324;2081	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	V	1089;1140;5376;5324;1876	ENSP00000338109:A1089V;ENSP00000304207:A1140V;ENSP00000417498:A5376V;ENSP00000420243:A5324V	ENSP00000304207:A1140V	A	-	2	0	MUC4	196959830	0.942000	0.31987	0.141000	0.22245	0.580000	0.36256	4.549000	0.60726	1.171000	0.42768	0.543000	0.68304	GCC	G|0.849;A|0.151	0.151	strong		0.617	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
NR4A2	4929	hgsc.bcm.edu	37	2	157184995	157184995	+	Silent	SNP	G	G	A	rs201103933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:157184995G>A	ENST00000339562.4	-	4	1277	c.915C>T	c.(913-915)tgC>tgT	p.C305C	NR4A2_ENST00000409108.2_Silent_p.C305C|NR4A2_ENST00000539077.1_Silent_p.C316C|NR4A2_ENST00000426264.1_Silent_p.C242C|NR4A2_ENST00000409572.1_Silent_p.C305C|NR4A2_ENST00000429376.1_Silent_p.C242C	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	305					adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						TGTCCACTGGGCAGTTTTTAT	0.453													G|||	2	0.000399361	0.0	0.0	5008	,	,		18722	0.0		0.0	False		,,,				2504	0.002				p.C305C		Atlas-SNP	.											.	NR4A2	82	.	0			c.C915T						PASS	.						91.0	87.0	88.0					2																	157184995		2203	4300	6503	SO:0001819	synonymous_variant	4929	exon4			CACTGGGCAGTTT	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"""Nuclear hormone receptors"""	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.915C>T	2.37:g.157184995G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	215	102	0.474419	NM_006186	Q16311|Q53RZ2|Q6NXU0	Silent	SNP	ENST00000339562.4	37	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	G	3.579	-0.085989	0.07097	.	.	ENSG00000153234	ENST00000406048	.	.	.	6.07	5.2	0.72013	.	.	.	.	.	T	0.63248	0.2495	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62153	-0.6914	4	.	.	.	.	11.2859	0.49222	0.138:0.0:0.862:0.0	.	.	.	.	S	87	.	.	P	-	1	0	NR4A2	156893241	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.696000	0.37773	1.584000	0.49913	0.655000	0.94253	CCC	G|0.999;A|0.001	0.001	weak		0.453	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2		
SCN3A	6328	hgsc.bcm.edu	37	2	165996107	165996107	+	Silent	SNP	T	T	A	rs1946892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:165996107T>A	ENST00000360093.3	-	14	2522	c.2031A>T	c.(2029-2031)acA>acT	p.T677T	SCN3A_ENST00000283254.7_Silent_p.T677T|SCN3A_ENST00000409101.3_Silent_p.T628T	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	677					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CTTCCGTTTCTGTGGTGGTGC	0.453													A|||	3178	0.634585	0.7277	0.5778	5008	,	,		16901	0.8165		0.4245	False		,,,				2504	0.5777				p.T677T		Atlas-SNP	.											.	SCN3A	544	.	0			c.A2031T						PASS	.	A	,,	2919,1487	476.4+/-357.6	956,1007,240	126.0	110.0	115.0		1884,1884,2031	1.6	1.0	2	dbSNP_92	115	3622,4978	625.1+/-397.7	767,2088,1445	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN3A	NM_001081676.1,NM_001081677.1,NM_006922.3	,,	1723,3095,1685	AA,AT,TT		42.1163,33.7494,49.7078	,,	628/1952,628/1952,677/2001	165996107	6541,6465	2203	4300	6503	SO:0001819	synonymous_variant	6328	exon14			CGTTTCTGTGGTG	AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2031A>T	2.37:g.165996107T>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																				A|0.544;N|0.000	0.544	strong		0.453	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
TESPA1	9840	hgsc.bcm.edu	37	12	55356258	55356258	+	Missense_Mutation	SNP	C	C	T	rs61733025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55356258C>T	ENST00000449076.1	-	9	1556	c.1424G>A	c.(1423-1425)cGg>cAg	p.R475Q	TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000316577.8_Missense_Mutation_p.R475Q|TESPA1_ENST00000524622.1_Missense_Mutation_p.R337Q|TESPA1_ENST00000531122.1_Missense_Mutation_p.R337Q|TESPA1_ENST00000532804.1_Missense_Mutation_p.R337Q	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	475				R -> Q (in Ref. 7; AAH44578). {ECO:0000305}.	COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											GCTTAAAGACCGACGCAGTTC	0.517													C|||	65	0.0129792	0.0015	0.0144	5008	,	,		19033	0.001		0.0447	False		,,,				2504	0.0072				p.R475Q		Atlas-SNP	.											KIAA0748_ENST00000449076,colon,carcinoma,0,3	.	.	3	0			c.G1424A						PASS	.	C	GLN/ARG,GLN/ARG	30,3882		0,30,1926	164.0	168.0	166.0		1424,1424	-3.3	0.0	12	dbSNP_129	166	344,7972		6,332,3820	yes	missense,missense	KIAA0748	NM_001098815.1,NM_001136030.1	43,43	6,362,5746	TT,TC,CC		4.1366,0.7669,3.0586	benign,benign	475/522,475/522	55356258	374,11854	1956	4158	6114	SO:0001583	missense	9840	exon9			AAAGACCGACGCA	AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"""KIAA0748"""	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.1424G>A	12.37:g.55356258C>T	ENSP00000400892:p.Arg475Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	51	0.579545	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Missense_Mutation	SNP	ENST00000449076.1	37	CCDS44913.1	39	0.017857142857142856	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	32	0.04221635883905013	C	0.612	-0.824677	0.02755	0.007669	0.041366	ENSG00000135426	ENST00000524622;ENST00000528240;ENST00000532804;ENST00000449076;ENST00000316577;ENST00000531122	T;T;T;T;T	0.46063	0.88;0.88;0.89;0.89;0.88	4.7	-3.31	0.04988	.	1.157010	0.06533	N	0.741787	T	0.05547	0.0146	N	0.17082	0.46	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.15009	-1.0452	10	0.23891	T	0.37	0.3771	6.6576	0.22996	0.0:0.2615:0.143:0.5955	rs61733025	475	A2RU30	K0748_HUMAN	Q	337;75;337;475;475;337	ENSP00000435622:R337Q;ENSP00000432030:R337Q;ENSP00000400892:R475Q;ENSP00000312679:R475Q;ENSP00000433098:R337Q	ENSP00000312679:R475Q	R	-	2	0	KIAA0748	53642525	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-3.735000	0.00380	-0.678000	0.05224	-0.345000	0.07892	CGG	C|0.976;T|0.024	0.024	strong		0.517	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815	
CSHL1	1444	hgsc.bcm.edu	37	17	61987576	61987576	+	Silent	SNP	G	G	A	rs2246207	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61987576G>A	ENST00000309894.5	-	4	416	c.417C>T	c.(415-417)agC>agT	p.S139S	CSHL1_ENST00000450719.3_Silent_p.S45S|CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000346606.6_Silent_p.S45S|CSHL1_ENST00000259003.10_Silent_p.S77S|CSHL1_ENST00000438387.2_Silent_p.S56S|CSHL1_ENST00000561003.1_Silent_p.S56S|CSHL1_ENST00000558099.1_5'UTR	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	139						extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						GATAGTCATCGCTGTCCGAGG	0.587													G|||	1952	0.389776	0.4637	0.3501	5008	,	,		19398	0.4196		0.4225	False		,,,				2504	0.2536				p.S139S		Atlas-SNP	.											CSHL1_ENST00000561003,NS,adenoma,0,2	CSHL1	42	2	0			c.C417T						PASS	.	G	,,,	2165,2241	583.4+/-385.8	538,1089,576	88.0	76.0	80.0		135,417,168,348	-4.3	0.0	17	dbSNP_100	80	3571,5029	517.8+/-379.1	751,2069,1480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSHL1	NM_001318.2,NM_022579.1,NM_022580.1,NM_022581.1	,,,	1289,3158,2056	AA,AG,GG		41.5233,49.1375,44.1027	,,,	45/129,139/223,56/140,116/200	61987576	5736,7270	2203	4300	6503	SO:0001819	synonymous_variant	1444	exon4			GTCATCGCTGTCC	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"""chorionic somatomammotropin CS-5"""	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.417C>T	17.37:g.61987576G>A		Somatic	449	1	0.00222717		WXS	Illumina HiSeq	Phase_I	313	311	0.99361	NM_022579	D3DU26|D3DU27|Q0VDB2	Silent	SNP	ENST00000309894.5	37	CCDS11652.1																																																																																			G|0.566;A|0.434	0.434	strong		0.587	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579	
BCO1	53630	hgsc.bcm.edu	37	16	81314496	81314496	+	Missense_Mutation	SNP	C	C	T	rs7501331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81314496C>T	ENST00000258168.2	+	8	1597	c.1136C>T	c.(1135-1137)gCa>gTa	p.A379V	BCMO1_ENST00000425577.2_Missense_Mutation_p.A310V	NM_017429.2	NP_059125.2														breast(2)|endometrium(1)|large_intestine(4)|lung(9)|prostate(3)|skin(3)|stomach(1)	23						ATCAAAGTGGCATCTACAACA	0.388													C|||	762	0.152157	0.0091	0.1744	5008	,	,		18135	0.1875		0.2316	False		,,,				2504	0.2117				p.A379V		Atlas-SNP	.											.	BCMO1	53	.	0			c.C1136T						PASS	.	C	VAL/ALA	224,4180	133.7+/-170.0	1,222,1979	65.0	63.0	64.0		1136	4.6	0.3	16	dbSNP_116	64	2007,6593	350.7+/-328.0	243,1521,2536	yes	missense	BCMO1	NM_017429.2	64	244,1743,4515	TT,TC,CC		23.3372,5.0863,17.1563	benign	379/548	81314496	2231,10773	2202	4300	6502	SO:0001583	missense	53630	exon8			AAGTGGCATCTAC																												ENST00000258168.2:c.1136C>T	16.37:g.81314496C>T	ENSP00000258168:p.Ala379Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_017429		Missense_Mutation	SNP	ENST00000258168.2	37	CCDS10934.1	353	0.16163003663003664	8	0.016260162601626018	65	0.17955801104972377	96	0.16783216783216784	184	0.24274406332453827	C	15.85	2.954275	0.53293	0.050863	0.233372	ENSG00000135697	ENST00000258168;ENST00000425577	D;D	0.95103	-3.61;-3.23	5.61	4.6	0.57074	.	0.904678	0.09742	N	0.761746	T	0.00271	0.0008	L	0.40543	1.245	0.80722	P	0.0	P;B	0.45044	0.849;0.12	B;B	0.40982	0.345;0.114	T	0.06391	-1.0829	9	0.30078	T	0.28	-1.633	15.431	0.75099	0.1389:0.861:0.0:0.0	rs7501331;rs52800470;rs7501331	310;379	E7EM88;Q9HAY6	.;BCDO1_HUMAN	V	379;310	ENSP00000258168:A379V;ENSP00000400586:A310V	ENSP00000258168:A379V	A	+	2	0	BCMO1	79871997	0.052000	0.20516	0.265000	0.24526	0.986000	0.74619	1.730000	0.38125	2.793000	0.96121	0.655000	0.94253	GCA	C|0.837;T|0.163	0.163	strong		0.388	BCMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269056.1		
ENTPD6	955	hgsc.bcm.edu	37	20	25187213	25187213	+	Missense_Mutation	SNP	G	G	A	rs2076559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25187213G>A	ENST00000376652.4	+	2	204	c.41G>A	c.(40-42)aGc>aAc	p.S14N	ENTPD6_ENST00000354989.5_Intron|ENTPD6_ENST00000360031.2_Missense_Mutation_p.S14N|ENTPD6_ENST00000433259.2_Missense_Mutation_p.S14N			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	14			S -> N (in dbSNP:rs2076559). {ECO:0000269|PubMed:14529283}.		response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGAAAAACGAGCTACATTTTT	0.403													G|||	1562	0.311901	0.0983	0.2349	5008	,	,		20423	0.5903		0.3469	False		,,,				2504	0.3323				p.S14N		Atlas-SNP	.											.	ENTPD6	57	.	0			c.G41A						PASS	.	G	,ASN/SER	621,3785	269.5+/-269.1	42,537,1624	104.0	97.0	100.0		,41	-0.2	0.0	20	dbSNP_96	100	2767,5833	439.7+/-359.3	431,1905,1964	yes	intron,missense	ENTPD6	NM_001114089.1,NM_001247.2	,46	473,2442,3588	AA,AG,GG		32.1744,14.0944,26.0495	,benign	,14/485	25187213	3388,9618	2203	4300	6503	SO:0001583	missense	955	exon2			AAACGAGCTACAT	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.41G>A	20.37:g.25187213G>A	ENSP00000365840:p.Ser14Asn	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	107	44	0.411215	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	755	0.3456959706959707	59	0.11991869918699187	94	0.2596685082872928	344	0.6013986013986014	258	0.3403693931398417	G	8.922	0.961415	0.18583	0.140944	0.321744	ENSG00000197586	ENST00000360031;ENST00000376652;ENST00000433259;ENST00000435520;ENST00000425813	T;T;T;T;T	0.34275	2.18;2.18;2.05;1.37;2.35	2.98	-0.162	0.13367	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B;B;B	0.30482	0.281;0.18;0.18;0.18;0.18	B;B;B;B;B	0.22152	0.038;0.038;0.038;0.017;0.017	T	0.44283	-0.9338	8	0.19590	T	0.45	.	3.4656	0.07549	0.2556:0.2143:0.5302:0.0	rs2076559;rs11539327;rs17829504;rs52811761;rs60671666;rs2076559	14;14;14;14;14	E7EP89;Q5QPI9;D3DW49;Q5QPJ2;O75354	.;.;.;.;ENTP6_HUMAN	N	14	ENSP00000353131:S14N;ENSP00000365840:S14N;ENSP00000401895:S14N;ENSP00000398844:S14N;ENSP00000390646:S14N	ENSP00000353131:S14N	S	+	2	0	ENTPD6	25135213	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.214000	0.17541	0.004000	0.14682	-0.172000	0.13284	AGC	G|0.702;A|0.298	0.298	strong		0.403	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
ANKRD50	57182	hgsc.bcm.edu	37	4	125591687	125591687	+	Silent	SNP	A	A	G	rs3733471	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:125591687A>G	ENST00000504087.1	-	4	3782	c.2745T>C	c.(2743-2745)aaT>aaC	p.N915N	ANKRD50_ENST00000515641.1_Silent_p.N736N	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	915										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CCCGCAGTGCATTTCTTCCAT	0.408													G|||	1439	0.28734	0.3933	0.2233	5008	,	,		23630	0.2629		0.2107	False		,,,				2504	0.2935				p.N915N		Atlas-SNP	.											.	ANKRD50	136	.	0			c.T2745C						PASS	.	G	,	1571,2835	667.9+/-401.9	259,1053,891	100.0	97.0	98.0		2208,2745	-6.2	0.1	4	dbSNP_107	98	1803,6797	732.6+/-406.8	203,1397,2700	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	462,2450,3591	GG,GA,AA		20.9651,35.6559,25.9419	,	736/1251,915/1430	125591687	3374,9632	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			CAGTGCATTTCTT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2745T>C	4.37:g.125591687A>G		Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	213	118	0.553991	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			A|0.742;G|0.258	0.258	strong		0.408	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
VWA5A	4013	hgsc.bcm.edu	37	11	124006993	124006993	+	Missense_Mutation	SNP	G	G	A	rs2276053	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124006993G>A	ENST00000456829.2	+	13	1768	c.1517G>A	c.(1516-1518)aGg>aAg	p.R506K	VWA5A_ENST00000392748.1_Missense_Mutation_p.R506K|VWA5A_ENST00000360334.4_Intron	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	506			R -> K (in dbSNP:rs2276053). {ECO:0000269|PubMed:9417908}.							autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						CTGACCGGGAGGATGCCAGTG	0.478													G|||	598	0.119409	0.1861	0.0764	5008	,	,		20037	0.0575		0.1014	False		,,,				2504	0.1421				p.R506K		Atlas-SNP	.											.	VWA5A	102	.	0			c.G1517A						PASS	.	G	LYS/ARG,LYS/ARG	747,3655	306.6+/-289.6	58,631,1512	79.0	76.0	77.0		1517,1517	-10.7	0.0	11	dbSNP_100	77	921,7677	204.1+/-246.9	47,827,3425	yes	missense,missense	VWA5A	NM_001130142.1,NM_014622.4	26,26	105,1458,4937	AA,AG,GG		10.7118,16.9696,12.8308	benign,benign	506/787,506/787	124006993	1668,11332	2201	4299	6500	SO:0001583	missense	4013	exon12			CCGGGAGGATGCC	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1517G>A	11.37:g.124006993G>A	ENSP00000407726:p.Arg506Lys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	233	0.10668498168498168	91	0.18495934959349594	35	0.09668508287292818	27	0.0472027972027972	80	0.10554089709762533	G	0.186	-1.057595	0.01965	0.169696	0.107118	ENSG00000110002	ENST00000456829;ENST00000392748	T;T	0.03607	3.87;3.87	5.35	-10.7	0.00240	.	3.151380	0.01991	N	0.045531	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	0.38436	-0.9661	9	0.05833	T	0.94	6.056	2.6497	0.04995	0.4098:0.1332:0.0708:0.3862	rs2276053;rs61387352;rs2276053	506	O00534	VMA5A_HUMAN	K	506	ENSP00000407726:R506K;ENSP00000376504:R506K	ENSP00000376504:R506K	R	+	2	0	VWA5A	123512203	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-2.735000	0.00802	-3.343000	0.00183	-1.099000	0.02127	AGG	G|0.883;A|0.117	0.117	strong		0.478	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
C4orf36	132989	hgsc.bcm.edu	37	4	87809020	87809020	+	Missense_Mutation	SNP	C	C	G	rs72613147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:87809020C>G	ENST00000473559.1	-	7	910	c.247G>C	c.(247-249)Gtg>Ctg	p.V83L	C4orf36_ENST00000295898.3_Missense_Mutation_p.V83L|C4orf36_ENST00000503001.1_5'Flank			Q96KX1	CD036_HUMAN	chromosome 4 open reading frame 36	83								p.V83L(1)		breast(1)|kidney(1)|lung(1)|prostate(1)	4		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00141)		AGACGCTTCACTTCATACTCC	0.378													C|||	736	0.146965	0.0121	0.1945	5008	,	,		22337	0.1825		0.1759	False		,,,				2504	0.229				p.V83L		Atlas-SNP	.											C4orf36,NS,carcinoma,0,1	C4orf36	10	1	1	Substitution - Missense(1)	prostate(1)	c.G247C						PASS	.	C	LEU/VAL	169,4237	112.1+/-150.2	7,155,2041	84.0	78.0	80.0		247	0.2	1.0	4	dbSNP_130	80	1555,7045	291.7+/-300.5	137,1281,2882	yes	missense	C4orf36	NM_144645.3	32	144,1436,4923	GG,GC,CC		18.0814,3.8357,13.2554	benign	83/118	87809020	1724,11282	2203	4300	6503	SO:0001583	missense	132989	exon4			GCTTCACTTCATA	BC016746	CCDS3615.1	4q21.3	2008-02-05			ENSG00000163633	ENSG00000163633			28386	protein-coding gene	gene with protein product						12477932	Standard	NM_144645		Approved	MGC26744	uc003hqe.4	Q96KX1	OTTHUMG00000130597	ENST00000473559.1:c.247G>C	4.37:g.87809020C>G	ENSP00000420949:p.Val83Leu	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_144645		Missense_Mutation	SNP	ENST00000473559.1	37	CCDS3615.1	323	0.1478937728937729	11	0.022357723577235773	60	0.16574585635359115	118	0.2062937062937063	134	0.17678100263852242	C	7.612	0.675093	0.14841	0.038357	0.180814	ENSG00000163633	ENST00000295898;ENST00000473559;ENST00000506308	T;T;T	0.31247	1.5;1.5;1.5	5.23	0.167	0.15006	.	0.618498	0.16276	N	0.221587	T	0.00012	0.0000	N	0.03608	-0.345	0.51767	P	6.700000000003925E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.35599	-0.9782	9	0.06099	T	0.92	-8.0956	4.5836	0.12271	0.0:0.2137:0.4169:0.3693	.	83	Q96KX1	CD036_HUMAN	L	83	ENSP00000295898:V83L;ENSP00000420949:V83L;ENSP00000421141:V83L	ENSP00000295898:V83L	V	-	1	0	C4orf36	88028044	0.888000	0.30383	0.994000	0.49952	0.447000	0.32167	0.418000	0.21230	0.137000	0.18759	-0.311000	0.09066	GTG	C|0.864;G|0.136	0.136	strong		0.378	C4orf36-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253045.2	NM_144645	
KLHL36	79786	hgsc.bcm.edu	37	16	84691044	84691044	+	Silent	SNP	C	C	T	rs3751762	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84691044C>T	ENST00000564996.1	+	3	772	c.631C>T	c.(631-633)Ctg>Ttg	p.L211L	KLHL36_ENST00000258157.5_Silent_p.L211L	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	211	BACK.				protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						GCACGACCTCCTGCAGGCCGC	0.647													C|||	1069	0.213458	0.1029	0.2795	5008	,	,		18406	0.1756		0.3439	False		,,,				2504	0.2209				p.L211L		Atlas-SNP	.											KLHL36,NS,carcinoma,0,1	KLHL36	51	1	0			c.C631T						PASS	.	C		667,3723		49,569,1577	32.0	29.0	30.0		631	5.4	1.0	16	dbSNP_107	30	2707,5885		435,1837,2024	no	coding-synonymous	KLHL36	NM_024731.2		484,2406,3601	TT,TC,CC		31.5061,15.1936,25.9898		211/617	84691044	3374,9608	2195	4296	6491	SO:0001819	synonymous_variant	79786	exon3			GACCTCCTGCAGG	AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"""Kelch-like"", ""BTB/POZ domain containing"""	17844	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 44"", ""kelch-like 36 (Drosophila)"""	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.631C>T	16.37:g.84691044C>T		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	23	22	0.956522	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	37	CCDS10948.1																																																																																			C|0.757;T|0.243	0.243	strong		0.647	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2		
PTCD1	26024	hgsc.bcm.edu	37	7	99032559	99032559	+	Missense_Mutation	SNP	G	G	A	rs150504114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99032559G>A	ENST00000292478.4	-	2	557	c.307C>T	c.(307-309)Cgc>Tgc	p.R103C	ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000555673.1_Missense_Mutation_p.R152C|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.R152C|PTCD1_ENST00000485746.1_5'UTR	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	103					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)			GCGGATTTGCGGAATAGTCTC	0.577													G|||	36	0.0071885	0.0	0.0259	5008	,	,		19143	0.0		0.0089	False		,,,				2504	0.0092				p.R152C		Atlas-SNP	.											.	.	.	.	0			c.C454T						PASS	.	G	CYS/ARG,CYS/ARG	15,4391	22.3+/-47.3	0,15,2188	127.0	136.0	133.0		454,307	6.0	0.9	7	dbSNP_134	133	121,8479	63.5+/-125.6	1,119,4180	yes	missense,missense	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	180,180	1,134,6368	AA,AG,GG		1.407,0.3404,1.0457	probably-damaging,probably-damaging	152/750,103/701	99032559	136,12870	2203	4300	6503	SO:0001583	missense	100526740	exon3			ATTTGCGGAATAG	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.307C>T	7.37:g.99032559G>A	ENSP00000292478:p.Arg103Cys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	76	0.554745	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	15	0.006868131868131868	0	0.0	13	0.03591160220994475	0	0.0	2	0.002638522427440633	G	16.59	3.166435	0.57476	0.003404	0.01407	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000555673;ENST00000430982;ENST00000430029;ENST00000419981;ENST00000413834	T;T;D;D;D;T	0.85556	-0.23;-0.21;-2.0;-1.99;-1.87;-0.21	5.97	5.97	0.96955	.	0.496389	0.23896	N	0.043488	T	0.70824	0.3268	M	0.63843	1.955	0.31971	N	0.607147	D;D	0.71674	0.998;0.996	P;P	0.55667	0.781;0.564	D	0.83520	0.0085	10	0.62326	D	0.03	-2.9079	15.1788	0.72938	0.0:0.0:0.859:0.1409	.	152;103	G3V325;O75127	.;PTCD1_HUMAN	C	103;152;103;103;103;152	ENSP00000292478:R103C;ENSP00000450995:R152C;ENSP00000390530:R103C;ENSP00000408059:R103C;ENSP00000401600:R103C;ENSP00000400168:R152C	ENSP00000400168:R152C	R	-	1	0	ATP5J2-PTCD1;PTCD1	98870495	1.000000	0.71417	0.924000	0.36721	0.089000	0.18198	5.560000	0.67332	2.837000	0.97791	0.655000	0.94253	CGC	G|0.991;A|0.009	0.009	strong		0.577	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
LZIC	84328	hgsc.bcm.edu	37	1	9992024	9992024	+	Missense_Mutation	SNP	C	C	G	rs146375448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:9992024C>G	ENST00000377223.1	-	7	686	c.439G>C	c.(439-441)Gca>Cca	p.A147P	LZIC_ENST00000377213.1_Missense_Mutation_p.A147P|LZIC_ENST00000400903.2_Missense_Mutation_p.A147P|LZIC_ENST00000541052.1_Missense_Mutation_p.A168P	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	147					response to ionizing radiation (GO:0010212)					breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)		TCATCATCTGCAGTCAGCTAA	0.453													C|||	5	0.000998403	0.0008	0.0014	5008	,	,		16195	0.0		0.003	False		,,,				2504	0.0				p.A147P		Atlas-SNP	.											LZIC,NS,carcinoma,+1,1	LZIC	11	1	0			c.G439C						PASS	.	C	PRO/ALA	1,4405	2.1+/-5.4	0,1,2202	83.0	75.0	78.0		439	3.4	1.0	1	dbSNP_134	78	12,8588	9.1+/-34.3	0,12,4288	yes	missense	LZIC	NM_032368.3	27	0,13,6490	GG,GC,CC		0.1395,0.0227,0.1	benign	147/191	9992024	13,12993	2203	4300	6503	SO:0001583	missense	84328	exon6			CATCTGCAGTCAG	AB060688	CCDS107.1	1p36.22	2008-02-05			ENSG00000162441	ENSG00000162441			17497	protein-coding gene	gene with protein product		610458				11712074	Standard	NM_032368		Approved	MGC15436	uc001aqm.3	Q8WZA0	OTTHUMG00000001804	ENST00000377223.1:c.439G>C	1.37:g.9992024C>G	ENSP00000366430:p.Ala147Pro	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	104	7	0.0673077	NM_032368	B2R6F0|B4E2N0|Q96IU1	Missense_Mutation	SNP	ENST00000377223.1	37	CCDS107.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	4.176	0.031261	0.08101	2.27E-4	0.001395	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	T;T;T;T	0.42513	0.98;0.98;0.97;0.98	5.42	3.44	0.39384	.	0.625117	0.18198	N	0.148607	T	0.12817	0.0311	N	0.00642	-1.3	0.23336	N	0.997886	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17623	-1.0363	9	.	.	.	-3.6864	10.6507	0.45647	0.1167:0.6093:0.274:0.0	.	168;147	B4E2N0;Q8WZA0	.;LZIC_HUMAN	P	147;147;168;147	ENSP00000366430:A147P;ENSP00000383695:A147P;ENSP00000437432:A168P;ENSP00000366418:A147P	.	A	-	1	0	LZIC	9914611	0.366000	0.25014	1.000000	0.80357	0.994000	0.84299	0.170000	0.16663	2.700000	0.92200	0.650000	0.86243	GCA	C|0.999;G|0.001	0.001	strong		0.453	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368	
ZNF568	374900	hgsc.bcm.edu	37	19	37441111	37441111	+	Silent	SNP	C	C	T	rs571294	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37441111C>T	ENST00000333987.7	+	7	1562	c.1056C>T	c.(1054-1056)caC>caT	p.H352H	ZNF568_ENST00000415168.1_Silent_p.H288H|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTATTGAGCACGAGAAAATTC	0.398													T|||	2936	0.586262	0.7625	0.6167	5008	,	,		20112	0.3571		0.5656	False		,,,				2504	0.5838				p.H352H		Atlas-SNP	.											.	ZNF568	106	.	0			c.C1056T						PASS	.	T	,,,,,	3270,1128		1204,862,133	70.0	78.0	75.0		1053,864,864,,,1056	3.2	0.8	19	dbSNP_83	75	4929,3661		1441,2047,807	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	ZNF568	NM_001204835.1,NM_001204836.1,NM_001204837.1,NM_001204838.1,NM_001204839.1,NM_198539.3	,,,,,	2645,2909,940	TT,TC,CC		42.6193,25.648,36.8725	,,,,,	351/644,288/581,288/581,,,352/645	37441111	8199,4789	2199	4295	6494	SO:0001819	synonymous_variant	374900	exon7			TGAGCACGAGAAA	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1056C>T	19.37:g.37441111C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Silent	SNP	ENST00000333987.7	37	CCDS42558.1																																																																																			C|0.422;T|0.578	0.578	strong		0.398	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
FAM83D	81610	hgsc.bcm.edu	37	20	37570725	37570725	+	Silent	SNP	C	C	T	rs3752293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37570725C>T	ENST00000217429.4	+	2	738	c.697C>T	c.(697-699)Ctg>Ttg	p.L233L		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	203					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				CTCTCAATTTCTGGATATGTG	0.433													T|||	2048	0.408946	0.5492	0.3847	5008	,	,		21976	0.4365		0.3419	False		,,,				2504	0.2771				p.L233L		Atlas-SNP	.											.	FAM83D	60	.	0			c.C697T						PASS	.	T		1944,1892		516,912,490	185.0	179.0	181.0		697	-3.5	0.6	20	dbSNP_107	181	2665,5621		395,1875,1873	no	coding-synonymous	FAM83D	NM_030919.2		911,2787,2363	TT,TC,CC		32.1627,49.3222,38.0218		233/616	37570725	4609,7513	1918	4143	6061	SO:0001819	synonymous_variant	81610	exon2			CAATTTCTGGATA	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 129"""	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.697C>T	20.37:g.37570725C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Silent	SNP	ENST00000217429.4	37	CCDS42872.1																																																																																			C|0.607;T|0.393	0.393	strong		0.433	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1		
GBE1	2632	hgsc.bcm.edu	37	3	81720076	81720076	+	Silent	SNP	G	G	A	rs13320194	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:81720076G>A	ENST00000429644.2	-	3	985	c.342C>T	c.(340-342)taC>taT	p.Y114Y	GBE1_ENST00000477426.1_5'UTR|GBE1_ENST00000489715.1_Silent_p.Y73Y	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	114					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)	p.Y114Y(1)		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)		CCAGTTTTTTGTATGGGTACG	0.353									Glycogen Storage Disease, type IV				A|||	527	0.105232	0.2625	0.0879	5008	,	,		16113	0.0694		0.0169	False		,,,				2504	0.0327				p.Y114Y		Atlas-SNP	.											GBE1_ENST00000429644,NS,carcinoma,0,1	GBE1	111	1	1	Substitution - coding silent(1)	stomach(1)	c.C342T						PASS	.	A		742,2890		79,584,1153	73.0	69.0	70.0		342	4.3	1.0	3	dbSNP_121	70	179,7997		2,175,3911	no	coding-synonymous	GBE1	NM_000158.3		81,759,5064	AA,AG,GG		2.1893,20.4295,7.7998		114/703	81720076	921,10887	1816	4088	5904	SO:0001819	synonymous_variant	2632	exon3	Familial Cancer Database	Andersen Disease, Brancher deficiency	TTTTTTGTATGGG		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.342C>T	3.37:g.81720076G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_000158	B3KWV3|Q96EN0	Silent	SNP	ENST00000429644.2	37	CCDS54612.1																																																																																			G|0.910;A|0.090	0.090	strong		0.353	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
HIPK4	147746	hgsc.bcm.edu	37	19	40886993	40886993	+	Missense_Mutation	SNP	C	C	T	rs11670988	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40886993C>T	ENST00000291823.2	-	3	1189	c.905G>A	c.(904-906)cGg>cAg	p.R302Q		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	302	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> Q (in dbSNP:rs11670988).		histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GAAGGTTAGCCGACTGGCCAC	0.612													C|||	371	0.0740815	0.0023	0.0403	5008	,	,		20060	0.1736		0.0905	False		,,,				2504	0.0757				p.R302Q		Atlas-SNP	.											HIPK4_ENST00000291823,larynx,carcinoma,-1,1	HIPK4	100	1	0			c.G905A						PASS	.	C	GLN/ARG	112,4286		1,110,2088	44.0	39.0	41.0		905	4.6	1.0	19	dbSNP_120	41	819,7773		34,751,3511	yes	missense	HIPK4	NM_144685.3	43	35,861,5599	TT,TC,CC		9.5321,2.5466,7.1671	possibly-damaging	302/617	40886993	931,12059	2199	4296	6495	SO:0001583	missense	147746	exon3			GTTAGCCGACTGG	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.905G>A	19.37:g.40886993C>T	ENSP00000291823:p.Arg302Gln	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	188	0.08608058608058608	3	0.006097560975609756	14	0.03867403314917127	94	0.16433566433566432	77	0.10158311345646438	C	11.64	1.700119	0.30142	0.025466	0.095321	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.21031	2.03	5.67	4.59	0.56863	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.154362	0.31092	N	0.008264	T	0.00073	0.0002	L	0.48260	1.515	0.30050	P	0.811871	P	0.52061	0.95	B	0.40864	0.342	T	0.14504	-1.0470	9	0.46703	T	0.11	.	5.3853	0.16215	0.0:0.7997:0.0:0.2003	rs11670988;rs59468898;rs11670988	302	Q8NE63	HIPK4_HUMAN	Q	302;267	ENSP00000291823:R302Q	ENSP00000291823:R302Q	R	-	2	0	HIPK4	45578833	0.490000	0.26012	0.998000	0.56505	0.035000	0.12851	1.035000	0.30216	2.677000	0.91161	0.561000	0.74099	CGG	C|0.921;T|0.079	0.079	strong		0.612	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
STAB1	23166	hgsc.bcm.edu	37	3	52558008	52558008	+	Missense_Mutation	SNP	T	T	C	rs13303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52558008T>C	ENST00000321725.6	+	67	7593	c.7517T>C	c.(7516-7518)aTg>aCg	p.M2506T		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2506			M -> T (in dbSNP:rs13303).		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)		GGCAAGCCCATGGGCTTTGGC	0.682													C|||	2747	0.548522	0.7141	0.6513	5008	,	,		15967	0.4524		0.5656	False		,,,				2504	0.3333				p.M2506T		Atlas-SNP	.											.	STAB1	178	.	0			c.T7517C						PASS	.	C	THR/MET	2867,1535		948,971,282	25.0	29.0	28.0		7517	3.6	0.0	3	dbSNP_52	28	4901,3691		1415,2071,810	yes	missense	STAB1	NM_015136.2	81	2363,3042,1092	CC,CT,TT		42.9586,34.8705,40.2186	benign	2506/2571	52558008	7768,5226	2201	4296	6497	SO:0001583	missense	23166	exon67			AGCCCATGGGCTT	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.7517T>C	3.37:g.52558008T>C	ENSP00000312946:p.Met2506Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	1301	0.5956959706959707	338	0.6869918699186992	240	0.6629834254143646	291	0.5087412587412588	432	0.5699208443271768	C	0.014	-1.584710	0.00872	0.651295	0.570414	ENSG00000010327	ENST00000321725	D	0.83837	-1.77	5.48	3.6	0.41247	.	1.170570	0.06285	N	0.698125	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	0.42447	-0.9451	9	0.08599	T	0.76	.	6.3188	0.21206	0.1217:0.6768:0.1191:0.0823	rs13303;rs1131678;rs3191793;rs4687622;rs58080543;rs13303	2506	Q9NY15	STAB1_HUMAN	T	2506	ENSP00000312946:M2506T	ENSP00000312946:M2506T	M	+	2	0	STAB1	52533048	0.000000	0.05858	0.001000	0.08648	0.040000	0.13550	-0.595000	0.05727	0.819000	0.34492	-0.930000	0.02707	ATG	T|0.423;C|0.577	0.577	strong		0.682	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
PLG	5340	hgsc.bcm.edu	37	6	161137779	161137779	+	Silent	SNP	T	T	C	rs14224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:161137779T>C	ENST00000308192.9	+	7	834	c.771T>C	c.(769-771)tgT>tgC	p.C257C		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	257	Kringle 2. {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)	GGGAACTTTGTGACATCCCCC	0.502													C|||	2253	0.44988	0.5537	0.3329	5008	,	,		18453	0.4563		0.3976	False		,,,				2504	0.4397				p.C257C		Atlas-SNP	.											.	PLG	150	.	0			c.T771C						PASS	.	C		2301,2105	575.2+/-383.9	590,1121,492	66.0	62.0	64.0		771	-6.8	0.4	6	dbSNP_52	64	3595,5005	626.7+/-397.9	759,2077,1464	no	coding-synonymous	PLG	NM_000301.3		1349,3198,1956	CC,CT,TT		41.8023,47.7758,45.3329		257/811	161137779	5896,7110	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon7			ACTTTGTGACATC	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.771T>C	6.37:g.161137779T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.540;C|0.460	0.460	strong		0.502	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
OR5I1	10798	hgsc.bcm.edu	37	11	55703011	55703011	+	Missense_Mutation	SNP	G	G	A	rs61995929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55703011G>A	ENST00000301532.3	-	1	865	c.866C>T	c.(865-867)cCg>cTg	p.P289L		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	289					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						ATAAATCAACGGATTCAGCAC	0.363													G|||	101	0.0201677	0.0045	0.036	5008	,	,		18988	0.0		0.0577	False		,,,				2504	0.0123				p.P289L		Atlas-SNP	.											OR5I1,NS,carcinoma,+1,1	OR5I1	110	1	0			c.C866T						scavenged	.	G	LEU/PRO	43,4357	46.0+/-80.4	0,43,2157	67.0	66.0	66.0		866	4.8	0.2	11	dbSNP_129	66	456,8132	135.9+/-193.0	13,430,3851	yes	missense	OR5I1	NM_006637.1	98	13,473,6008	AA,AG,GG		5.3097,0.9773,3.842	probably-damaging	289/315	55703011	499,12489	2200	4294	6494	SO:0001583	missense	10798	exon1			ATCAACGGATTCA	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.866C>T	11.37:g.55703011G>A	ENSP00000301532:p.Pro289Leu	Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_006637	Q6IEU4	Missense_Mutation	SNP	ENST00000301532.3	37	CCDS7949.1	62	0.028388278388278388	5	0.01016260162601626	17	0.04696132596685083	0	0.0	40	0.052770448548812667	G	13.48	2.250236	0.39797	0.009773	0.053097	ENSG00000167825	ENST00000301532	T	0.63417	-0.04	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	D	0.000401	T	0.42223	0.1193	H	0.98048	4.135	0.51767	D	0.999933	D	0.56746	0.977	P	0.44772	0.46	T	0.79203	-0.1900	10	0.72032	D	0.01	.	15.6672	0.77238	0.0:0.0:1.0:0.0	.	289	Q13606	OR5I1_HUMAN	L	289	ENSP00000301532:P289L	ENSP00000301532:P289L	P	-	2	0	OR5I1	55459587	1.000000	0.71417	0.247000	0.24249	0.386000	0.30323	4.095000	0.57728	2.339000	0.79563	0.643000	0.83706	CCG	G|0.964;A|0.036	0.036	strong		0.363	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
USP6	9098	hgsc.bcm.edu	37	17	5037241	5037241	+	Silent	SNP	G	G	A	rs117611547		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5037241G>A	ENST00000574788.1	+	15	2674	c.444G>A	c.(442-444)gtG>gtA	p.V148V	USP6_ENST00000332776.4_Silent_p.V148V|USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Silent_p.V148V			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	148	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.V148V(3)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						ACCTGGACGTGAGGACGACTC	0.557			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts																																p.V148V		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6_ENST00000250066,NS,carcinoma,0,3	USP6	213	3	3	Substitution - coding silent(3)	ovary(2)|skin(1)	c.G444A						scavenged	.						220.0	174.0	189.0					17																	5037241		2203	4300	6503	SO:0001819	synonymous_variant	9098	exon7			GGACGTGAGGACG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.444G>A	17.37:g.5037241G>A		Somatic	55	3	0.0545455		WXS	Illumina HiSeq	Phase_I	54	5	0.0925926	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			.	.	weak		0.557	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
NEK5	341676	hgsc.bcm.edu	37	13	52676275	52676275	+	Missense_Mutation	SNP	T	T	G	rs34756139	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:52676275T>G	ENST00000355568.4	-	10	902	c.763A>C	c.(763-765)Aaa>Caa	p.K255Q		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> Q (in dbSNP:rs34756139).		positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of striated muscle cell differentiation (GO:0051155)		ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.K312Q(1)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(11)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Breast(56;0.00173)|Lung NSC(96;0.0168)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;3.7e-08)		AAGGGCCTTTTCAAAATGGAA	0.428													T|||	361	0.0720847	0.0197	0.1167	5008	,	,		18374	0.0546		0.1173	False		,,,				2504	0.0828				p.K255Q		Atlas-SNP	.											NEK5,NS,carcinoma,0,1	NEK5	189	1	1	Substitution - Missense(1)	stomach(1)	c.A763C						PASS	.	T	GLN/LYS	174,4232	113.3+/-151.4	2,170,2031	122.0	136.0	131.0		763	4.8	1.0	13	dbSNP_126	131	980,7620	212.2+/-252.6	59,862,3379	yes	missense	NEK5	NM_199289.1	53	61,1032,5410	GG,GT,TT		11.3953,3.9492,8.8728	probably-damaging	255/709	52676275	1154,11852	2203	4300	6503	SO:0001583	missense	341676	exon10			GCCTTTTCAAAAT	BC063885	CCDS31979.1	13q14.2	2012-11-15	2012-11-15		ENSG00000197168	ENSG00000197168			7748	protein-coding gene	gene with protein product			"""NIMA (never in mitosis gene a)-related kinase 5"""			9552363	Standard	XM_006719807		Approved		uc001vge.3	Q6P3R8	OTTHUMG00000016957	ENST00000355568.4:c.763A>C	13.37:g.52676275T>G	ENSP00000347767:p.Lys255Gln	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_199289	Q5TAP5	Missense_Mutation	SNP	ENST00000355568.4	37	CCDS31979.1	200	0.09157509157509157	16	0.032520325203252036	48	0.13259668508287292	37	0.06468531468531469	99	0.13060686015831136	T	13.95	2.391323	0.42410	0.039492	0.113953	ENSG00000197168	ENST00000355568	T	0.66099	-0.19	5.98	4.81	0.61882	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.073654	0.56097	D	0.000036	T	0.01061	0.0035	N	0.17564	0.495	0.30553	P	0.765266	D	0.65815	0.995	D	0.63957	0.92	T	0.26677	-1.0096	9	0.27785	T	0.31	.	11.9924	0.53182	0.0:0.0672:0.0:0.9328	rs34756139;rs61745508	255	Q6P3R8	NEK5_HUMAN	Q	255	ENSP00000347767:K255Q	ENSP00000347767:K255Q	K	-	1	0	NEK5	51574276	1.000000	0.71417	1.000000	0.80357	0.015000	0.08874	3.451000	0.52964	1.093000	0.41377	-0.371000	0.07208	AAA	T|0.912;G|0.088	0.088	strong		0.428	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289	
FANCE	2178	hgsc.bcm.edu	37	6	35430686	35430686	+	Missense_Mutation	SNP	G	G	A	rs9462088	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35430686G>A	ENST00000229769.2	+	9	1689	c.1504G>A	c.(1504-1506)Gct>Act	p.A502T		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	502			A -> T (in dbSNP:rs9462088). {ECO:0000269|Ref.2}.		DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						CAAGTATCAGGCTAACGTGAG	0.532			"""N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	949	0.189497	0.4357	0.0533	5008	,	,		19373	0.119		0.0368	False		,,,				2504	0.183				p.A502T		Atlas-SNP	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"""Fanconi anemia, complementation group E"""		L	.	FANCE	45	.	0			c.G1504A						PASS	.	G	THR/ALA	1514,2892	481.7+/-359.2	260,994,949	129.0	128.0	129.0		1504	3.2	1.0	6	dbSNP_119	129	450,8150	135.4+/-192.6	16,418,3866	yes	missense	FANCE	NM_021922.2	58	276,1412,4815	AA,AG,GG		5.2326,34.3622,15.1007	benign	502/537	35430686	1964,11042	2203	4300	6503	SO:0001583	missense	2178	exon9	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TATCAGGCTAACG	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"""Fanconi anemia, complementation groups"""	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.1504G>A	6.37:g.35430686G>A	ENSP00000229769:p.Ala502Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_021922	A8K907|Q4ZGH2	Missense_Mutation	SNP	ENST00000229769.2	37	CCDS4805.1	306	0.1401098901098901	219	0.4451219512195122	15	0.04143646408839779	47	0.08216783216783216	25	0.032981530343007916	G	6.940	0.543122	0.13250	0.343622	0.052326	ENSG00000112039	ENST00000229769	T	0.50813	0.73	5.92	3.16	0.36331	Fanconi Anaemia group E protein, C-terminal (1);	0.528805	0.20017	N	0.100994	T	0.15522	0.0374	L	0.46157	1.445	0.38147	P	0.061378000000000044	B	0.13145	0.007	B	0.13407	0.009	T	0.10800	-1.0614	9	0.08179	T	0.78	-19.0539	7.9271	0.29880	0.2513:0.0:0.7487:0.0	rs9462088;rs11551303;rs52833726;rs9462088	502	Q9HB96	FANCE_HUMAN	T	502	ENSP00000229769:A502T	ENSP00000229769:A502T	A	+	1	0	FANCE	35538664	0.363000	0.24989	0.976000	0.42696	0.383000	0.30230	0.921000	0.28718	0.825000	0.34637	0.561000	0.74099	GCT	G|0.843;A|0.157	0.157	strong		0.532	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1		
C5orf42	65250	hgsc.bcm.edu	37	5	37196028	37196028	+	Missense_Mutation	SNP	C	C	T	rs72736758	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:37196028C>T	ENST00000508244.1	-	20	3836	c.3743G>A	c.(3742-3744)gGt>gAt	p.G1248D	C5orf42_ENST00000274258.7_Missense_Mutation_p.G129D|C5orf42_ENST00000425232.2_Missense_Mutation_p.G1248D			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1248						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AAATGCGATACCTCCTTTACA	0.383													C|||	97	0.019369	0.0045	0.0303	5008	,	,		16480	0.0		0.0398	False		,,,				2504	0.0307				p.G1248D		Atlas-SNP	.											.	C5orf42	422	.	0			c.G3743A						PASS	.	C	ASP/GLY	39,4367	43.1+/-76.7	1,37,2165	105.0	102.0	103.0		3743	5.2	0.9	5	dbSNP_130	103	369,8231	122.7+/-181.7	10,349,3941	yes	missense	C5orf42	NM_023073.3	94	11,386,6106	TT,TC,CC		4.2907,0.8852,3.137	benign	1248/3198	37196028	408,12598	2203	4300	6503	SO:0001583	missense	65250	exon21			GCGATACCTCCTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.3743G>A	5.37:g.37196028C>T	ENSP00000421690:p.Gly1248Asp	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	215	86	0.4	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	30	0.0395778364116095	C	18.05	3.537916	0.65085	0.008852	0.042907	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.27557	1.8;1.8;1.66;1.68	5.21	5.21	0.72293	.	0.153741	0.30791	N	0.008879	T	0.10766	0.0263	N	0.14661	0.345	0.32954	D	0.520092	D;D	0.76494	0.999;0.999	D;D	0.72075	0.976;0.967	T	0.24905	-1.0147	10	0.46703	T	0.11	.	12.947	0.58376	0.0:0.915:0.0:0.085	.	1248;129	E9PH94;Q9H799	.;CE042_HUMAN	D	1248;1248;129;296;129	ENSP00000421690:G1248D;ENSP00000389014:G1248D;ENSP00000274258:G129D;ENSP00000424223:G296D	ENSP00000274258:G129D	G	-	2	0	C5orf42	37231785	0.005000	0.15991	0.924000	0.36721	0.532000	0.34746	1.971000	0.40530	2.601000	0.87937	0.655000	0.94253	GGT	C|0.972;T|0.028	0.028	strong		0.383	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209634	84209634	+	Silent	SNP	C	C	G	rs2288019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84209634C>G	ENST00000378553.5	+	11	1918	c.1794C>G	c.(1792-1794)ctC>ctG	p.L598L	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	598					axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)	p.L598L(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						TGGAAAACCTCCCCACAGACA	0.468											OREG0023983	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2663	0.531749	0.5159	0.5245	5008	,	,		18997	0.5268		0.504	False		,,,				2504	0.592				p.L598L		Atlas-SNP	.											DNAAF1,NS,carcinoma,0,1	DNAAF1	81	1	1	Substitution - coding silent(1)	stomach(1)	c.C1794G						PASS	.	G		2265,2135	577.8+/-384.5	609,1047,544	81.0	72.0	75.0		1794	-3.8	0.0	16	dbSNP_100	75	4374,4226	571.9+/-389.6	1130,2114,1056	no	coding-synonymous	DNAAF1	NM_178452.4		1739,3161,1600	GG,GC,CC		49.1395,48.5227,48.9308		598/726	84209634	6639,6361	2200	4300	6500	SO:0001819	synonymous_variant	123872	exon11			AAACCTCCCCACA	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1794C>G	16.37:g.84209634C>G		Somatic	91	0	0	1227	WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Silent	SNP	ENST00000378553.5	37	CCDS10943.2																																																																																			C|0.475;G|0.525	0.525	strong		0.468	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
ALCAM	214	hgsc.bcm.edu	37	3	105264176	105264176	+	Missense_Mutation	SNP	G	G	T	rs34926152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:105264176G>T	ENST00000306107.5	+	9	1601	c.1101G>T	c.(1099-1101)atG>atT	p.M367I	ALCAM_ENST00000486979.2_Missense_Mutation_p.M316I|ALCAM_ENST00000472644.2_Missense_Mutation_p.M367I|ALCAM_ENST00000389927.4_Missense_Mutation_p.M89I	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	367	Ig-like C2-type 2.		M -> I (in dbSNP:rs34926152).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						TGGTATGGATGAAAGTAAGTA	0.383													G|||	105	0.0209665	0.0	0.0432	5008	,	,		18486	0.001		0.0537	False		,,,				2504	0.0204				p.M367I		Atlas-SNP	.											ALCAM,colon,carcinoma,+1,1	ALCAM	71	1	0			c.G1101T						PASS	.	G	ILE/MET	42,4364	45.3+/-79.5	0,42,2161	163.0	147.0	153.0		1101	5.3	1.0	3	dbSNP_126	153	432,8168	134.1+/-191.5	10,412,3878	yes	missense	ALCAM	NM_001627.3	10	10,454,6039	TT,TG,GG		5.0233,0.9532,3.6445	benign	367/584	105264176	474,12532	2203	4300	6503	SO:0001583	missense	214	exon9			ATGGATGAAAGTA	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1101G>T	3.37:g.105264176G>T	ENSP00000305988:p.Met367Ile	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	146	77	0.527397	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Missense_Mutation	SNP	ENST00000306107.5	37	CCDS33810.1	57|57	0.0260989010989011|0.0260989010989011	0|0	0.0|0.0	16|16	0.04419889502762431|0.04419889502762431	0|0	0.0|0.0	41|41	0.05408970976253298|0.05408970976253298	G|G	12.69|12.69	2.015025|2.015025	0.35511|0.35511	0.009532|0.009532	0.050233|0.050233	ENSG00000170017|ENSG00000170017	ENST00000465413|ENST00000306107;ENST00000472644;ENST00000486979;ENST00000389927	.|T;T;T;T	.|0.11712	.|2.75;2.75;2.75;2.75	5.28|5.28	5.28|5.28	0.74379|0.74379	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.170783	.|0.64402	.|D	.|0.000006	.|T	.|0.01189	.|0.0039	L|L	0.27053|0.27053	0.805|0.805	0.43793|0.43793	D|D	0.996335|0.996335	.|B;B;B	.|0.14438	.|0.01;0.001;0.001	.|B;B;B	.|0.17433	.|0.018;0.012;0.012	.|T	.|0.37934	.|-0.9684	.|10	.|0.23891	.|T	.|0.37	-23.1958|-23.1958	13.0764|13.0764	0.59089|0.59089	0.0839:0.0:0.9161:0.0|0.0839:0.0:0.9161:0.0	rs34926152|rs34926152	.|89;367;367	.|Q6ZS95;B4DTU0;Q13740	.|.;.;CD166_HUMAN	X|I	128|367;367;316;89	.|ENSP00000305988:M367I;ENSP00000419236:M367I;ENSP00000418213:M316I;ENSP00000374577:M89I	.|ENSP00000305988:M367I	E|M	+|+	1|3	0|0	ALCAM|ALCAM	106746866|106746866	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	1.421000|1.421000	0.34815|0.34815	2.618000|2.618000	0.88619|0.88619	0.563000|0.563000	0.77884|0.77884	GAA|ATG	G|0.968;T|0.032	0.032	strong		0.383	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
SLC12A4	6560	hgsc.bcm.edu	37	16	67979423	67979423	+	Silent	SNP	G	G	T	rs17851876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67979423G>T	ENST00000316341.3	-	22	3021	c.2881C>A	c.(2881-2883)Cgg>Agg	p.R961R	SLC12A4_ENST00000338335.3_3'UTR|LCAT_ENST00000264005.5_5'Flank|SLC12A4_ENST00000572037.1_Silent_p.R913R|SLC12A4_ENST00000541864.2_Silent_p.R930R|SLC12A4_ENST00000576616.1_Silent_p.R961R|CTC-479C5.17_ENST00000590594.1_lincRNA|SLC12A4_ENST00000422611.2_Silent_p.R963R|SLC12A4_ENST00000537830.2_Silent_p.R955R	NM_001145961.1|NM_005072.4	NP_001139433.1|NP_005063.1	Q9UP95	S12A4_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 4	961					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(2)|ovary(2)|prostate(4)|skin(2)|urinary_tract(3)	29		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)	Bumetanide(DB00887)|Potassium Chloride(DB00761)	CTCTCCAGCCGCAGGGCCGAG	0.592													G|||	151	0.0301518	0.0008	0.0245	5008	,	,		19721	0.0		0.0646	False		,,,				2504	0.0695				p.R963R		Atlas-SNP	.											.	SLC12A4	81	.	0			c.C2887A						PASS	.	G	,,,,	52,4342	52.9+/-88.7	0,52,2145	60.0	61.0	61.0		2863,2887,2863,2788,2881	3.4	0.9	16	dbSNP_123	61	603,7997	158.6+/-212.1	11,581,3708	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A4	NM_001145961.1,NM_001145962.1,NM_001145963.1,NM_001145964.1,NM_005072.4	,,,,	11,633,5853	TT,TG,GG		7.0116,1.1834,5.0408	,,,,	955/1080,963/1088,955/1080,930/1055,961/1086	67979423	655,12339	2197	4300	6497	SO:0001819	synonymous_variant	6560	exon21			CCAGCCGCAGGGC		CCDS10855.1, CCDS54030.1, CCDS54031.1, CCDS54032.1	16q22.1	2013-07-18	2013-07-18		ENSG00000124067	ENSG00000124067		"""Solute carriers"""	10913	protein-coding gene	gene with protein product		604119				8663127	Standard	NM_005072		Approved	KCC1	uc010ceu.2	Q9UP95	OTTHUMG00000137535	ENST00000316341.3:c.2881C>A	16.37:g.67979423G>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	113	45	0.39823	NM_001145962	B4DF69|B4DR04|B4DZ82|B7ZAV0|F5H066|F5H0S9|F5H3C0|O60632|O75893|Q13953|Q96LD5	Silent	SNP	ENST00000316341.3	37	CCDS10855.1																																																																																			G|0.959;T|0.041	0.041	strong		0.592	SLC12A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268864.4	NM_005072	
ADORA3	140	hgsc.bcm.edu	37	1	112043139	112043139	+	Silent	SNP	G	G	A	rs2789537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:112043139G>A	ENST00000241356.4	-	2	795	c.390C>T	c.(388-390)gcC>gcT	p.A130A	ADORA3_ENST00000486342.1_5'UTR|ADORA3_ENST00000369716.4_Intron|ADORA3_ENST00000369717.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	130					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	AAAGGCCCAGGGCCAGCCATA	0.507													G|||	108	0.0215655	0.0272	0.0144	5008	,	,		20977	0.0109		0.0209	False		,,,				2504	0.0307				p.A130A		Atlas-SNP	.											.	ADORA3	104	.	0			c.C390T						PASS	.	G	,,	100,4306	77.3+/-115.6	1,98,2104	84.0	94.0	90.0		390,,	0.1	1.0	1	dbSNP_100	90	160,8440	76.0+/-138.7	2,156,4142	no	coding-synonymous,intron,intron	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	,,	3,254,6246	AA,AG,GG		1.8605,2.2696,1.9991	,,	130/319,,	112043139	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	140	exon2			GCCCAGGGCCAGC	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.390C>T	1.37:g.112043139G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	60	0.550459	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Silent	SNP	ENST00000241356.4	37	CCDS839.1																																																																																			G|0.981;A|0.019	0.019	strong		0.507	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
TMEM176B	28959	hgsc.bcm.edu	37	7	150490238	150490238	+	Missense_Mutation	SNP	G	G	A	rs17256042	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150490238G>A	ENST00000447204.2	-	5	910	c.538C>T	c.(538-540)Cgg>Tgg	p.R180W	TMEM176B_ENST00000434545.1_Missense_Mutation_p.R180W|TMEM176B_ENST00000326442.5_Missense_Mutation_p.R180W|TMEM176B_ENST00000450753.2_Missense_Mutation_p.R143W|TMEM176B_ENST00000492607.1_Missense_Mutation_p.R180W|TMEM176B_ENST00000429904.2_Missense_Mutation_p.R180W	NM_014020.3	NP_054739.3	Q3YBM2	T176B_HUMAN	transmembrane protein 176B	180			R -> W (in dbSNP:rs17256042).		cell differentiation (GO:0030154)|negative regulation of dendritic cell differentiation (GO:2001199)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				cervix(1)|large_intestine(4)|lung(10)|ovary(1)|skin(3)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGACTTCGCCGCATCCATCTG	0.512													G|||	99	0.0197684	0.0076	0.0317	5008	,	,		21434	0.001		0.0577	False		,,,				2504	0.0082				p.R180W		Atlas-SNP	.											TMEM176B,NS,carcinoma,+1,2	TMEM176B	36	2	0			c.C538T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	44,4362	48.2+/-83.0	1,42,2160	150.0	125.0	133.0		538,538,427,538	-2.4	0.0	7	dbSNP_123	133	458,8142	137.1+/-194.1	13,432,3855	yes	missense,missense,missense,missense	TMEM176B	NM_001101311.1,NM_001101312.1,NM_001101314.1,NM_014020.3	101,101,101,101	14,474,6015	AA,AG,GG		5.3256,0.9986,3.8598	probably-damaging,probably-damaging,probably-damaging,probably-damaging	180/271,180/271,143/234,180/271	150490238	502,12504	2203	4300	6503	SO:0001583	missense	28959	exon5			TTCGCCGCATCCA	AF115384	CCDS5908.1, CCDS47746.1	7q36.1	2006-09-04			ENSG00000106565	ENSG00000106565			29596	protein-coding gene	gene with protein product		610385				9922225	Standard	NM_014020		Approved	LR8	uc003whu.4	Q3YBM2	OTTHUMG00000157577	ENST00000447204.2:c.538C>T	7.37:g.150490238G>A	ENSP00000410269:p.Arg180Trp	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	187	87	0.465241	NM_014020	B2RDK2|D3DWZ7|E9PAV4|Q5BJI2|Q9BT42|Q9Y609	Missense_Mutation	SNP	ENST00000447204.2	37	CCDS5908.1	60	0.027472527472527472	5	0.01016260162601626	14	0.03867403314917127	0	0.0	41	0.05408970976253298	G	11.90	1.776134	0.31411	0.009986	0.053256	ENSG00000106565	ENST00000492607;ENST00000326442;ENST00000447204;ENST00000434545;ENST00000429904;ENST00000450753;ENST00000528038	T;T;T;T;T;T	0.02498	4.27;4.27;4.27;4.27;4.27;4.27	3.1	-2.36	0.06663	.	1.402630	0.04900	N	0.451178	T	0.00845	0.0028	L	0.57536	1.79	0.09310	N	1	D;D	0.60575	0.988;0.988	P;P	0.51266	0.664;0.541	T	0.22906	-1.0203	10	0.54805	T	0.06	1.2904	2.7714	0.05335	0.2776:0.0:0.331:0.3914	rs17256042;rs52810663;rs58586485;rs17256042	143;180	E9PAV4;Q3YBM2	.;T176B_HUMAN	W	180;180;180;180;180;143;180	ENSP00000419258:R180W;ENSP00000318409:R180W;ENSP00000410269:R180W;ENSP00000413531:R180W;ENSP00000397810:R180W;ENSP00000404831:R143W	ENSP00000318409:R180W	R	-	1	2	TMEM176B	150121171	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.341000	0.19909	-0.672000	0.05266	0.280000	0.19369	CGG	G|0.964;A|0.036	0.036	strong		0.512	TMEM176B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349204.1	NM_014020	
PKD1	5310	hgsc.bcm.edu	37	16	2161087	2161087	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2161087G>C	ENST00000262304.4	-	15	4289	c.4081C>G	c.(4081-4083)Ctg>Gtg	p.L1361V	PKD1_ENST00000423118.1_Missense_Mutation_p.L1361V|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1361	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						CGGCTGGACAGCACCAGCGCC	0.652																																					p.L1361V		Atlas-SNP	.											.	PKD1	184	.	0			c.C4081G						PASS	.						35.0	37.0	37.0					16																	2161087		2193	4295	6488	SO:0001583	missense	5310	exon15			TGGACAGCACCAG	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.4081C>G	16.37:g.2161087G>C	ENSP00000262304:p.Leu1361Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	122	64	0.52459	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	4.600	0.111428	0.08831	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.45276	0.9;0.9	5.58	2.51	0.30379	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (4);	0.236328	0.35349	N	0.003270	T	0.37128	0.0992	L	0.59436	1.845	0.21915	N	0.999479	P;P	0.40638	0.702;0.725	B;P	0.47786	0.421;0.557	T	0.16719	-1.0393	10	0.09084	T	0.74	.	2.4934	0.04615	0.2134:0.125:0.5333:0.1283	.	1361;1361	P98161-3;P98161	.;PKD1_HUMAN	V	1361;1361;1042	ENSP00000262304:L1361V;ENSP00000399501:L1361V	ENSP00000262304:L1361V	L	-	1	2	PKD1	2101088	0.548000	0.26473	0.582000	0.28627	0.017000	0.09413	0.802000	0.27069	0.705000	0.31890	0.450000	0.29827	CTG	.	.	none		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155410650	155410650	+	Missense_Mutation	SNP	T	T	C	rs72731014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155410650T>C	ENST00000339452.1	-	1	2218	c.1858A>G	c.(1858-1860)Act>Gct	p.T620A	DCHS2_ENST00000456341.2_Missense_Mutation_p.T613A|DCHS2_ENST00000443500.1_Missense_Mutation_p.T620A	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1747	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(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)		CGGTCTAGAGTCCGGATAGTG	0.592													T|||	866	0.172923	0.0386	0.3084	5008	,	,		18744	0.1558		0.2137	False		,,,				2504	0.2342				p.T620A		Atlas-SNP	.											.	DCHS2	594	.	0			c.A1858G						PASS	.	T	ALA/THR,ALA/THR	77,1307		6,65,621	46.0	48.0	48.0		1858,1858	0.7	0.1	4	dbSNP_130	48	550,2632		56,438,1097	yes	missense,missense	DCHS2	NM_001142552.1,NM_001142553.1	58,58	62,503,1718	CC,CT,TT		17.2847,5.5636,13.7319	,	620/1370,620/710	155410650	627,3939	692	1591	2283	SO:0001583	missense	54798	exon1			CTAGAGTCCGGAT	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		ENST00000339452.1:c.1858A>G	4.37:g.155410650T>C	ENSP00000345062:p.Thr620Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	359	0.16437728937728938	17	0.034552845528455285	96	0.26519337016574585	81	0.14160839160839161	165	0.21767810026385223	T	1.685	-0.505419	0.04261	0.055636	0.172847	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.49432	0.78;0.78;0.78	5.17	0.658	0.17855	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.09377	0.004;0.004	T	0.30238	-0.9985	7	0.07644	T	0.81	.	0.3221	0.00305	0.2522:0.2199:0.1358:0.3921	.	620;620	E9PG03;E9PC11	.;.	A	620;620;613;620	ENSP00000345062:T620A;ENSP00000408543:T613A;ENSP00000395539:T620A	ENSP00000345062:T620A	T	-	1	0	DCHS2	155630100	0.000000	0.05858	0.103000	0.21229	0.887000	0.51463	-0.488000	0.06497	0.308000	0.22923	0.455000	0.32223	ACT	T|0.834;C|0.166	0.166	strong		0.592	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
COL17A1	1308	hgsc.bcm.edu	37	10	105836066	105836066	+	Silent	SNP	C	C	T	rs61731085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105836066C>T	ENST00000353479.5	-	5	614	c.324G>A	c.(322-324)gcG>gcA	p.A108A	COL17A1_ENST00000369733.3_Silent_p.A108A|COL17A1_ENST00000393211.3_Silent_p.A108A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	108	Nonhelical region (NC16).				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)		TACCTTCATACGCATGGCGGG	0.502													C|||	69	0.013778	0.0492	0.0043	5008	,	,		20980	0.0		0.001	False		,,,				2504	0.0				p.A108A		Atlas-SNP	.											.	COL17A1	149	.	0			c.G324A						PASS	.	C		198,4208	124.1+/-161.4	4,190,2009	203.0	202.0	202.0		324	-11.2	0.0	10	dbSNP_129	202	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	COL17A1	NM_000494.3		4,196,6303	TT,TC,CC		0.0698,4.4939,1.5685		108/1498	105836066	204,12802	2203	4300	6503	SO:0001819	synonymous_variant	1308	exon5			TTCATACGCATGG	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.324G>A	10.37:g.105836066C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			C|0.988;T|0.012	0.012	strong		0.502	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
RASGRF1	5923	hgsc.bcm.edu	37	15	79296172	79296172	+	Silent	SNP	G	G	A	rs1562008	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79296172G>A	ENST00000419573.3	-	16	2743	c.2469C>T	c.(2467-2469)ccC>ccT	p.P823P	RASGRF1_ENST00000558480.2_Silent_p.P807P|RASGRF1_ENST00000560334.1_5'UTR|RASGRF1_ENST00000394745.3_Silent_p.P39P	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	823					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						AAGGGTCTTCGGGCTTCTCAG	0.627													G|||	626	0.125	0.0272	0.1556	5008	,	,		18455	0.0942		0.2316	False		,,,				2504	0.1575				p.P823P		Atlas-SNP	.											.	RASGRF1	168	.	0			c.C2469T						PASS	.	G	,,	271,4121	149.2+/-183.4	12,247,1937	52.0	45.0	47.0		2421,2469,117	-3.4	0.3	15	dbSNP_88	47	2028,6558	338.3+/-322.7	245,1538,2510	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRF1	NM_001145648.1,NM_002891.4,NM_153815.2	,,	257,1785,4447	AA,AG,GG		23.6198,6.1703,17.7146	,,	807/1258,823/1274,39/490	79296172	2299,10679	2196	4293	6489	SO:0001819	synonymous_variant	5923	exon16			GTCTTCGGGCTTC	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.2469C>T	15.37:g.79296172G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_002891	F8VPA5|H0YKF2|J3KQP9|Q16027	Silent	SNP	ENST00000419573.3	37	CCDS10309.1																																																																																			G|0.849;A|0.151	0.151	strong		0.627	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
MRGPRF	116535	hgsc.bcm.edu	37	11	68773403	68773403	+	Silent	SNP	G	G	A	rs11544722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68773403G>A	ENST00000309099.6	-	3	757	c.375C>T	c.(373-375)tgC>tgT	p.C125C	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Silent_p.C125C	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	125						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(3)|lung(4)	7			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TAAGGAACATGCAGAGCCCCA	0.687													G|||	1164	0.232428	0.2065	0.1354	5008	,	,		14674	0.2272		0.2694	False		,,,				2504	0.3037				p.C125C		Atlas-SNP	.											.	MRGPRF	22	.	0			c.C375T						PASS	.	G	,	885,3459		100,685,1387	21.0	21.0	21.0		375,375	2.7	0.8	11	dbSNP_120	21	2185,6331		295,1595,2368	no	coding-synonymous,coding-synonymous	MRGPRF	NM_001098515.1,NM_145015.4	,	395,2280,3755	AA,AG,GG		25.6576,20.3729,23.8725	,	125/344,125/344	68773403	3070,9790	2172	4258	6430	SO:0001819	synonymous_variant	116535	exon3			GAACATGCAGAGC	AK075492	CCDS8188.1	11q13.1	2014-03-13	2004-03-25		ENSG00000172935	ENSG00000172935		"""GPCR / Class A : Orphans"""	24828	protein-coding gene	gene with protein product		607233	"""G protein-coupled receptor 168"", ""G protein-coupled receptor 140"""	GPR168, GPR140		12477932	Standard	NM_001098515		Approved	MGC21621, mrgF	uc001oop.4	Q96AM1	OTTHUMG00000167897	ENST00000309099.6:c.375C>T	11.37:g.68773403G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_001098515	B3KV43|Q8NBK8	Silent	SNP	ENST00000309099.6	37	CCDS8188.1																																																																																			G|0.763;A|0.237	0.237	strong		0.687	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015	
PLEKHB1	58473	hgsc.bcm.edu	37	11	73371842	73371842	+	Silent	SNP	C	C	G	rs147173613	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:73371842C>G	ENST00000354190.5	+	7	971	c.540C>G	c.(538-540)ccC>ccG	p.P180P	PLEKHB1_ENST00000227214.6_Silent_p.P126P|PLEKHB1_ENST00000398494.4_Silent_p.P161P|PLEKHB1_ENST00000535129.1_Silent_p.P126P|PLEKHB1_ENST00000398492.4_Silent_p.P145P|PLEKHB1_ENST00000543085.1_Silent_p.P75P	NM_021200.2	NP_067023.1	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B (evectins) member 1	180					multicellular organismal development (GO:0007275)|phototransduction (GO:0007602)|regulation of cell differentiation (GO:0045595)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	7						AGGTGGTGCCCCCCAATGCAC	0.637											OREG0021217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	24	0.00479233	0.0008	0.013	5008	,	,		17175	0.001		0.0129	False		,,,				2504	0.0				p.P180P		Atlas-SNP	.											.	PLEKHB1	16	.	0			c.C540G						PASS	.	C	,,,,	12,4134		0,12,2061	55.0	63.0	60.0		435,483,378,378,540	-6.7	0.3	11	dbSNP_134	60	121,8227		2,117,4055	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEKHB1	NM_001130033.1,NM_001130034.1,NM_001130035.1,NM_001130036.1,NM_021200.2	,,,,	2,129,6116	GG,GC,CC		1.4494,0.2894,1.0645	,,,,	145/209,161/225,126/190,126/190,180/244	73371842	133,12361	2073	4174	6247	SO:0001819	synonymous_variant	58473	exon7			GGTGCCCCCCAAT	AF081583	CCDS44672.1, CCDS44673.1, CCDS44674.1, CCDS44675.1	11q13.5-q14.1	2013-01-10	2002-11-04	2002-11-08	ENSG00000021300	ENSG00000021300		"""Pleckstrin homology (PH) domain containing"""	19079	protein-coding gene	gene with protein product		607651	"""PH domain containing, retinal 1"""	PHRET1		10585447	Standard	NM_021200		Approved	PHR1, KPL1	uc001ouc.3	Q9UF11	OTTHUMG00000168030	ENST00000354190.5:c.540C>G	11.37:g.73371842C>G		Somatic	69	0	0	1144	WXS	Illumina HiSeq	Phase_I	103	48	0.466019	NM_021200	A8K0Q5|B2RBP1|B7Z716|Q9UBF5|Q9UI37|Q9UI44	Silent	SNP	ENST00000354190.5	37	CCDS44672.1																																																																																			C|0.993;G|0.007	0.007	strong		0.637	PLEKHB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397593.1		
FAM83A	84985	hgsc.bcm.edu	37	8	124206324	124206324	+	Missense_Mutation	SNP	G	G	A	rs7813708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124206324G>A	ENST00000518448.1	+	4	2723	c.709G>A	c.(709-711)Gct>Act	p.A237T	FAM83A_ENST00000276699.6_Missense_Mutation_p.A237T|FAM83A_ENST00000546351.1_Missense_Mutation_p.A181T|FAM83A_ENST00000536633.1_Missense_Mutation_p.A237T|FAM83A_ENST00000318462.6_Missense_Mutation_p.A237T|FAM83A_ENST00000522648.1_Missense_Mutation_p.A181T			Q86UY5	FA83A_HUMAN	family with sequence similarity 83, member A	237			A -> T (in dbSNP:rs7813708). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.							breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(2)|skin(1)	17	Lung NSC(37;1.55e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			CAGGAAATTCGCTGGCCAAAT	0.478													G|||	784	0.15655	0.0219	0.1988	5008	,	,		21893	0.2133		0.2008	False		,,,				2504	0.2045				p.A237T		Atlas-SNP	.											.	FAM83A	64	.	0			c.G709A						PASS	.	G	THR/ALA,THR/ALA	254,4152	148.0+/-182.4	7,240,1956	139.0	117.0	125.0		709,709	1.2	0.3	8	dbSNP_116	125	1791,6809	324.7+/-316.6	191,1409,2700	yes	missense,missense	FAM83A	NM_032899.4,NM_207006.1	58,58	198,1649,4656	AA,AG,GG		20.8256,5.7649,15.7235	benign,benign	237/435,237/368	124206324	2045,10961	2203	4300	6503	SO:0001583	missense	84985	exon3			AAATTCGCTGGCC	BC052300	CCDS6339.1, CCDS6340.1, CCDS75784.1	8q24.13	2014-03-13			ENSG00000147689	ENSG00000147689			28210	protein-coding gene	gene with protein product						22886303	Standard	XM_005251087		Approved	MGC14128, BJ-TSA-9	uc003ypx.3	Q86UY5	OTTHUMG00000165083	ENST00000518448.1:c.709G>A	8.37:g.124206324G>A	ENSP00000428876:p.Ala237Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	113	64	0.566372	NM_032899	Q71HL2|Q8N7I1|Q96I47	Missense_Mutation	SNP	ENST00000518448.1	37	CCDS6340.1	389	0.17811355311355312	14	0.028455284552845527	70	0.19337016574585636	150	0.26223776223776224	155	0.20448548812664907	G	7.351	0.622953	0.14193	0.057649	0.208256	ENSG00000147689	ENST00000518448;ENST00000546351;ENST00000536633;ENST00000318462;ENST00000522648;ENST00000276699	T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83	5.62	1.17	0.20885	.	0.346115	0.30455	N	0.009597	T	0.00012	0.0000	N	0.17082	0.46	0.48632	P	3.1800000000004047E-4	B;B;B	0.31209	0.313;0.066;0.048	B;B;B	0.22601	0.03;0.009;0.04	T	0.41215	-0.9521	9	0.02654	T	1	-15.2663	14.8562	0.70338	0.0:0.0:0.4168:0.5832	rs7813708;rs13279798;rs17377444;rs17845132;rs17857935;rs52838187;rs59588076;rs7813708	181;237;237	Q86UY5-2;Q86UY5-3;Q86UY5	.;.;FA83A_HUMAN	T	237;181;237;237;181;237	ENSP00000428876:A237T;ENSP00000440565:A181T;ENSP00000445218:A237T;ENSP00000323034:A237T;ENSP00000427979:A181T;ENSP00000276699:A237T	ENSP00000276699:A237T	A	+	1	0	FAM83A	124275505	0.211000	0.23529	0.302000	0.25058	0.914000	0.54420	1.323000	0.33701	0.273000	0.22049	0.555000	0.69702	GCT	G|0.835;A|0.165	0.165	strong		0.478	FAM83A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381737.1	NM_032899	
OR8H2	390151	hgsc.bcm.edu	37	11	55873334	55873334	+	Silent	SNP	A	A	G	rs11227212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55873334A>G	ENST00000313503.1	+	1	816	c.816A>G	c.(814-816)caA>caG	p.Q272Q		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	272						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Q272Q(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					GAAGAGATCAAGTGGCTTCTG	0.373										HNSCC(53;0.14)			a|||	514	0.102636	0.0477	0.098	5008	,	,		17441	0.1429		0.1213	False		,,,				2504	0.1196				p.Q272Q		Atlas-SNP	.											OR8H2,NS,carcinoma,0,1	OR8H2	117	1	1	Substitution - coding silent(1)	stomach(1)	c.A816G						PASS	.	A		234,4168	127.4+/-164.3	7,220,1974	81.0	86.0	85.0		816	-0.3	0.3	11	dbSNP_120	85	1002,7588	212.1+/-252.5	54,894,3347	no	coding-synonymous	OR8H2	NM_001005200.1		61,1114,5321	GG,GA,AA		11.6647,5.3158,9.5135		272/313	55873334	1236,11756	2201	4295	6496	SO:0001819	synonymous_variant	390151	exon1			AGATCAAGTGGCT	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.816A>G	11.37:g.55873334A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	120	65	0.541667	NM_001005200	Q6IFC1	Silent	SNP	ENST00000313503.1	37	CCDS31518.1																																																																																			A|0.902;G|0.098	0.098	strong		0.373	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
APOA4	337	hgsc.bcm.edu	37	11	116691634	116691634	+	Missense_Mutation	SNP	C	C	A	rs5110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:116691634C>A	ENST00000357780.3	-	3	1254	c.1140G>T	c.(1138-1140)caG>caT	p.Q380H		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	380	Gln/Glu-rich.		Q -> H (in allele APOA-IV*2 and allele APOA-IV*0A; associated with E-187 in allele APOA-IV*0A; dbSNP:rs5110). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:15108119, ECO:0000269|PubMed:1677358, ECO:0000269|PubMed:2065039, ECO:0000269|PubMed:2351649, ECO:0000269|PubMed:3036793, ECO:0000269|PubMed:3080432}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		gctgctcctgctgctgttcct	0.612													C|||	119	0.023762	0.0038	0.0418	5008	,	,		19562	0.0		0.0656	False		,,,				2504	0.0194				p.Q380H		Atlas-SNP	.											APOA4,rectum,carcinoma,0,1	APOA4	51	1	0			c.G1140T	GRCh37	CM984162	APOA4	M	rs5110	PASS	.	C	HIS/GLN	78,4324	68.7+/-106.4	1,76,2124	54.0	47.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1140	0.1	0.1	11	dbSNP_52	50	712,7876	174.9+/-225.1	24,664,3606	yes	missense	APOA4	NM_000482.3	24	25,740,5730	AA,AC,CC		8.2906,1.7719,6.0816	benign	380/397	116691634	790,12200	2201	4294	6495	SO:0001583	missense	337	exon3			CTCCTGCTGCTGT		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.1140G>T	11.37:g.116691634C>A	ENSP00000350425:p.Gln380His	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	140	73	0.521429	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	72	0.03296703296703297	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	49	0.06464379947229551	C	4.510	0.094555	0.08632	0.017719	0.082906	ENSG00000110244	ENST00000357780	T	0.74106	-0.81	1.25	0.139	0.14798	.	.	.	.	.	T	0.05090	0.0136	N	0.22421	0.69	0.09310	N	1	B	0.24533	0.105	B	0.20955	0.032	T	0.02471	-1.1154	9	0.20046	T	0.44	.	4.2239	0.10572	0.4256:0.5744:0.0:0.0	rs5110;rs3181830;rs9282881;rs17250981;rs5110	380	P06727	APOA4_HUMAN	H	380	ENSP00000350425:Q380H	ENSP00000350425:Q380H	Q	-	3	2	APOA4	116196844	0.000000	0.05858	0.111000	0.21465	0.022000	0.10575	-0.722000	0.04958	0.041000	0.15688	0.460000	0.39030	CAG	C|0.956;A|0.044	0.044	strong		0.612	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
CCDC15	80071	hgsc.bcm.edu	37	11	124861377	124861377	+	Silent	SNP	A	A	G	rs61752520	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124861377A>G	ENST00000344762.5	+	9	2188	c.1929A>G	c.(1927-1929)ccA>ccG	p.P643P	CCDC15_ENST00000529051.1_Silent_p.P643P	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	643						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		TTAAGGAGCCATACTCTGATA	0.353													a|||	58	0.0115815	0.0015	0.0231	5008	,	,		16559	0.001		0.0348	False		,,,				2504	0.0041				p.P643P		Atlas-SNP	.											.	CCDC15	134	.	0			c.A1929G						PASS	.	G		31,3567		1,29,1769	53.0	49.0	50.0		1929	0.7	0.1	11	dbSNP_129	50	323,7809		5,313,3748	no	coding-synonymous	CCDC15	NM_025004.2		6,342,5517	GG,GA,AA		3.972,0.8616,3.0179		643/952	124861377	354,11376	1799	4066	5865	SO:0001819	synonymous_variant	80071	exon9			GGAGCCATACTCT	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.1929A>G	11.37:g.124861377A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	37	0.440476	NM_025004	Q9H8U7	Silent	SNP	ENST00000344762.5	37	CCDS44756.1																																																																																			A|0.976;G|0.024	0.024	strong		0.353	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
DPYD	1806	hgsc.bcm.edu	37	1	97770920	97770920	+	Missense_Mutation	SNP	C	C	T	rs1801160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:97770920C>T	ENST00000370192.3	-	18	2294	c.2194G>A	c.(2194-2196)Gtt>Att	p.V732I	DPYD-AS1_ENST00000422980.1_RNA	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	732			V -> I (in dbSNP:rs1801160). {ECO:0000269|PubMed:15489334}.		beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	GTGGCTGTAACGCCATTGGCA	0.453													C|||	220	0.0439297	0.0242	0.0548	5008	,	,		18214	0.0149		0.0497	False		,,,				2504	0.0869				p.V732I		Atlas-SNP	.											.	DPYD	219	.	0			c.G2194A						PASS	.	C	ILE/VAL	136,4270	99.4+/-138.0	1,134,2068	193.0	163.0	173.0		2194	5.6	0.9	1	dbSNP_89	173	402,8198	128.0+/-186.3	6,390,3904	yes	missense	DPYD	NM_000110.3	29	7,524,5972	TT,TC,CC		4.6744,3.0867,4.1366	probably-damaging	732/1026	97770920	538,12468	2203	4300	6503	SO:0001583	missense	1806	exon18			CTGTAACGCCATT	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.2194G>A	1.37:g.97770920C>T	ENSP00000359211:p.Val732Ile	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	87	0.03983516483516483	13	0.026422764227642278	26	0.0718232044198895	7	0.012237762237762238	41	0.05408970976253298	C	23.5	4.419797	0.83559	0.030867	0.046744	ENSG00000188641	ENST00000370192	T	0.73469	-0.75	5.55	5.55	0.83447	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	T	0.80969	0.4726	L	0.54908	1.71	0.80722	D	1	D	0.71674	0.998	D	0.64144	0.922	T	0.81822	-0.0756	10	0.87932	D	0	-28.4127	19.8696	0.96845	0.0:1.0:0.0:0.0	rs1801160;rs12720467;rs12720468	732	Q12882	DPYD_HUMAN	I	732	ENSP00000359211:V732I	ENSP00000359211:V732I	V	-	1	0	DPYD	97543508	1.000000	0.71417	0.918000	0.36340	0.538000	0.34931	7.442000	0.80503	2.773000	0.95371	0.585000	0.79938	GTT	C|0.955;T|0.045	0.045	strong		0.453	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
FOXI1	2299	hgsc.bcm.edu	37	5	169535450	169535450	+	Silent	SNP	G	G	C	rs56128152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:169535450G>C	ENST00000306268.6	+	2	1033	c.972G>C	c.(970-972)ccG>ccC	p.P324P	FOXI1_ENST00000449804.2_Silent_p.P229P			Q12951	FOXI1_HUMAN	forkhead box I1	324					embryo development (GO:0009790)|inner ear morphogenesis (GO:0042472)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.P324P(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Renal(175;0.000159)|Lung NSC(126;0.0267)|all_lung(126;0.04)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CCTTCTCCCCGCTCACCAACC	0.622									Pendred syndrome				G|||	25	0.00499201	0.0	0.0086	5008	,	,		17968	0.0		0.0159	False		,,,				2504	0.0031				p.P324P		Atlas-SNP	.											FOXI1,NS,carcinoma,0,1	FOXI1	70	1	1	Substitution - coding silent(1)	lung(1)	c.G972C						scavenged	.	G	,	11,4395	17.9+/-39.9	0,11,2192	103.0	78.0	86.0		972,687	-10.6	0.0	5	dbSNP_129	86	169,8431	76.6+/-139.3	2,165,4133	no	coding-synonymous,coding-synonymous	FOXI1	NM_012188.4,NM_144769.2	,	2,176,6325	CC,CG,GG		1.9651,0.2497,1.384	,	324/379,229/284	169535450	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	2299	exon2	Familial Cancer Database	Goiter-Deafness syndrome	CTCCCCGCTCACC	BC029778	CCDS4372.1, CCDS47337.1	5q34	2008-02-05			ENSG00000168269	ENSG00000168269		"""Forkhead boxes"""	3815	protein-coding gene	gene with protein product		601093		FKHL10		7957066, 8825632	Standard	NM_144769		Approved	FREAC6	uc003mai.4	Q12951	OTTHUMG00000130436	ENST00000306268.6:c.972G>C	5.37:g.169535450G>C		Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	163	83	0.509202	NM_012188	Q14518|Q66SR7|Q8N6L8	Silent	SNP	ENST00000306268.6	37	CCDS4372.1																																																																																			G|0.989;C|0.011	0.011	strong		0.622	FOXI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252827.2	NM_144769, NM_012188	
TACC3	10460	hgsc.bcm.edu	37	4	1732978	1732978	+	Missense_Mutation	SNP	G	G	A	rs17680881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1732978G>A	ENST00000313288.4	+	6	1647	c.1541G>A	c.(1540-1542)gGg>gAg	p.G514E		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	514			G -> E (in dbSNP:rs17680881). {ECO:0000269|PubMed:11298601}.		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)			CATCAGCAGGGGCAGCCTGCC	0.622													G|||	851	0.169928	0.1331	0.196	5008	,	,		19828	0.1478		0.2634	False		,,,				2504	0.1278				p.G514E	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.G1541A						PASS	.	G	GLU/GLY	695,3711	291.0+/-281.2	57,581,1565	74.0	75.0	74.0		1541	-1.7	0.0	4	dbSNP_123	74	2130,6468	364.1+/-333.4	264,1602,2433	yes	missense	TACC3	NM_006342.1	98	321,2183,3998	AA,AG,GG		24.7732,15.7739,21.7241	benign	514/839	1732978	2825,10179	2203	4299	6502	SO:0001583	missense	10460	exon6			AGCAGGGGCAGCC	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.1541G>A	4.37:g.1732978G>A	ENSP00000326550:p.Gly514Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	420	0.19230769230769232	54	0.10975609756097561	68	0.1878453038674033	95	0.1660839160839161	203	0.2678100263852243	G	16.26	3.072642	0.55646	0.157739	0.247732	ENSG00000013810	ENST00000485989;ENST00000313288	T;T	0.40225	1.04;3.03	4.02	-1.72	0.08107	.	2.240520	0.02495	N	0.089903	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;B;P	0.50528	0.936;0.009;0.915	P;B;B	0.50192	0.634;0.005;0.374	T	0.04723	-1.0931	9	0.34782	T	0.22	-1.5279	0.5462	0.00654	0.3723:0.176:0.2734:0.1782	rs17680881;rs52795866;rs17680881	514;154;514	B4DYJ1;C9JWI7;Q9Y6A5	.;.;TACC3_HUMAN	E	154;514	ENSP00000419210:G154E;ENSP00000326550:G514E	ENSP00000326550:G514E	G	+	2	0	TACC3	1702776	0.000000	0.05858	0.000000	0.03702	0.645000	0.38454	-0.981000	0.03766	-0.243000	0.09653	0.462000	0.41574	GGG	G|0.805;A|0.195	0.195	strong		0.622	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
RADIL	55698	hgsc.bcm.edu	37	7	4876100	4876100	+	Silent	SNP	G	G	A	rs138811640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4876100G>A	ENST00000399583.3	-	3	859	c.672C>T	c.(670-672)aaC>aaT	p.N224N	RADIL_ENST00000536091.1_Silent_p.N224N|RADIL_ENST00000538469.1_De_novo_Start_OutOfFrame	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	224					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N224N(1)		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)		CGGGCAGGGCGTTCACTGGGC	0.721													G|||	60	0.0119808	0.0015	0.0173	5008	,	,		12942	0.0		0.0249	False		,,,				2504	0.0215				p.N224N		Atlas-SNP	.											RADIL,brain,glioma,0,2	RADIL	110	2	1	Substitution - coding silent(1)	lung(1)	c.C672T						PASS	.	G		16,4162		0,16,2073	11.0	18.0	16.0		672	0.3	0.1	7	dbSNP_134	16	205,8153		6,193,3980	no	coding-synonymous	RADIL	NM_018059.4		6,209,6053	AA,AG,GG		2.4527,0.383,1.7629		224/1076	4876100	221,12315	2089	4179	6268	SO:0001819	synonymous_variant	55698	exon3			CAGGGCGTTCACT	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.672C>T	7.37:g.4876100G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	19	17	0.894737	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.987;A|0.013	0.013	strong		0.721	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
GGH	8836	hgsc.bcm.edu	37	8	63951312	63951312	+	Missense_Mutation	SNP	A	A	G	rs1800909	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:63951312A>G	ENST00000260118.6	-	1	418	c.16T>C	c.(16-18)Tgc>Cgc	p.C6R		NM_003878.2	NP_003869.1	Q92820	GGH_HUMAN	gamma-glutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)	6			C -> R (in dbSNP:rs1800909).		glutamine metabolic process (GO:0006541)|proteolysis (GO:0006508)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	exopeptidase activity (GO:0008238)|gamma-glutamyl-peptidase activity (GO:0034722)|omega peptidase activity (GO:0008242)			breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(6)|stomach(1)	11	Breast(64;0.0716)	all_cancers(86;0.189)|Lung NSC(129;0.0324)|all_lung(136;0.0593)|all_epithelial(80;0.131)			Folic Acid(DB00158)|Methotrexate(DB00563)	CACAGCAGGCAGCCCGGACTG	0.716													G|||	1161	0.231829	0.1672	0.2277	5008	,	,		10294	0.2192		0.2793	False		,,,				2504	0.2863				p.C6R		Atlas-SNP	.											.	GGH	32	.	0			c.T16C						PASS	.	G	ARG/CYS	752,3574		76,600,1487	10.0	10.0	10.0		16	1.1	0.0	8	dbSNP_89	10	2198,6302		290,1618,2342	no	missense	GGH	NM_003878.2	180	366,2218,3829	GG,GA,AA		25.8588,17.3833,23.0002	benign	6/319	63951312	2950,9876	2163	4250	6413	SO:0001583	missense	8836	exon1			GCAGGCAGCCCGG	U55206	CCDS6177.1	8q12.3	2008-02-05			ENSG00000137563	ENSG00000137563	3.4.19.9		4248	protein-coding gene	gene with protein product		601509				8816764, 10570974	Standard	NM_003878		Approved		uc003xuw.3	Q92820	OTTHUMG00000164365	ENST00000260118.6:c.16T>C	8.37:g.63951312A>G	ENSP00000260118:p.Cys6Arg	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_003878		Missense_Mutation	SNP	ENST00000260118.6	37	CCDS6177.1	512	0.23443223443223443	88	0.17886178861788618	83	0.2292817679558011	127	0.22202797202797203	214	0.28232189973614774	G	6.061	0.379536	0.11466	0.173833	0.258588	ENSG00000137563	ENST00000260118	T	0.21191	2.02	4.12	1.06	0.20224	.	1.412970	0.04201	N	0.329979	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	0.42258	-0.9462	9	0.24483	T	0.36	-3.9473	1.5309	0.02535	0.1969:0.1633:0.4721:0.1677	rs1800909	6	Q92820	GGH_HUMAN	R	6	ENSP00000260118:C6R	ENSP00000260118:C6R	C	-	1	0	GGH	64113866	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.797000	0.26999	-0.133000	0.11537	-0.684000	0.03749	TGC	A|0.769;G|0.231	0.231	strong		0.716	GGH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378453.1		
DYTN	391475	hgsc.bcm.edu	37	2	207527840	207527840	+	Missense_Mutation	SNP	G	G	T	rs2115591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:207527840G>T	ENST00000452335.2	-	11	1536	c.1420C>A	c.(1420-1422)Cag>Aag	p.Q474K		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	474			Q -> K (in dbSNP:rs2115591).			plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		ATGACTTTCTGTGGCATCTTT	0.507													T|||	1978	0.394968	0.643	0.4942	5008	,	,		21098	0.1716		0.3738	False		,,,				2504	0.2413				p.Q474K		Atlas-SNP	.											.	DYTN	168	.	0			c.C1420A						PASS	.	T	LYS/GLN	2301,1677		671,959,359	175.0	164.0	168.0		1420	0.3	0.0	2	dbSNP_96	168	2992,5368		531,1930,1719	yes	missense	DYTN	NM_001093730.1	53	1202,2889,2078	TT,TG,GG		35.7895,42.1569,42.9	benign	474/579	207527840	5293,7045	1989	4180	6169	SO:0001583	missense	391475	exon11			CTTTCTGTGGCAT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.1420C>A	2.37:g.207527840G>T	ENSP00000396593:p.Gln474Lys	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	267	122	0.456929	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	861	0.3942307692307692	307	0.6239837398373984	163	0.45027624309392267	109	0.19055944055944055	282	0.3720316622691293	T	0.022	-1.412533	0.01145	0.578431	0.357895	ENSG00000232125	ENST00000452335	T	0.12465	2.68	5.12	0.26	0.15588	.	.	.	.	.	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	0.40590	-0.9555	8	0.02654	T	1	-0.7123	4.8672	0.13615	0.0:0.3448:0.1647:0.4904	rs2115591;rs52796299;rs57633224;rs2115591	474	A2CJ06	DYTN_HUMAN	K	474	ENSP00000396593:Q474K	ENSP00000396593:Q474K	Q	-	1	0	DYTN	207236085	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.883000	0.28200	-0.055000	0.13244	-1.816000	0.00601	CAG	G|0.615;N|0.000	.	strong		0.507	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
NUB1	51667	hgsc.bcm.edu	37	7	151064064	151064064	+	Silent	SNP	C	C	T	rs386956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151064064C>T	ENST00000355851.4	+	9	917	c.840C>T	c.(838-840)taC>taT	p.Y280Y	NUB1_ENST00000568733.1_Silent_p.Y304Y|NUB1_ENST00000566856.1_Silent_p.Y280Y|NUB1_ENST00000413040.2_Silent_p.Y304Y	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	280					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TGGATAACTACGCCGTCCTCC	0.458													C|||	1925	0.384385	0.1634	0.4553	5008	,	,		19414	0.4603		0.6302	False		,,,				2504	0.3016				p.Y304Y		Atlas-SNP	.											NUB1,caecum,carcinoma,0,1	NUB1	31	1	0			c.C912T						PASS	.	C		867,3207		101,665,1271	75.0	74.0	74.0		840	-9.4	0.1	7	dbSNP_80	74	5179,3203		1574,2031,586	no	coding-synonymous	NUB1	NM_016118.4		1675,2696,1857	TT,TC,CC		38.2128,21.2813,48.5389		280/602	151064064	6046,6410	2037	4191	6228	SO:0001819	synonymous_variant	51667	exon9			TAACTACGCCGTC	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.840C>T	7.37:g.151064064C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37																																																																																				C|0.538;T|0.462	0.462	strong		0.458	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
TRAP1	10131	hgsc.bcm.edu	37	16	3726075	3726075	+	Missense_Mutation	SNP	G	G	A	rs61753378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3726075G>A	ENST00000246957.5	-	7	864	c.776C>T	c.(775-777)tCc>tTc	p.S259F	TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000538171.1_Missense_Mutation_p.S206F|TRAP1_ENST00000575671.1_Missense_Mutation_p.S50F	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	259					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)				CTTGCAGTCGGATTTCAGGTG	0.577													G|||	202	0.0403355	0.003	0.0605	5008	,	,		16599	0.0397		0.0596	False		,,,				2504	0.0573				p.S259F		Atlas-SNP	.											TRAP1,NS,carcinoma,-1,1	TRAP1	53	1	0			c.C776T						PASS	.	G	PHE/SER	56,4338	53.6+/-89.4	0,56,2141	112.0	108.0	109.0		776	5.3	0.1	16	dbSNP_129	109	569,8031	154.2+/-208.4	17,535,3748	yes	missense	TRAP1	NM_016292.2	155	17,591,5889	AA,AG,GG		6.6163,1.2745,4.8099	benign	259/705	3726075	625,12369	2197	4300	6497	SO:0001583	missense	10131	exon7			CAGTCGGATTTCA	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.776C>T	16.37:g.3726075G>A	ENSP00000246957:p.Ser259Phe	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	61	28	0.459016	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	37	CCDS10508.1	73	0.033424908424908424	4	0.008130081300813009	19	0.052486187845303865	18	0.03146853146853147	32	0.04221635883905013	G	16.31	3.087742	0.55968	0.012745	0.066163	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.76709	-1.04;-1.04	5.32	5.32	0.75619	Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (3);	0.712422	0.13777	N	0.363480	T	0.29355	0.0731	L	0.46157	1.445	0.29619	N	0.846341	B;B	0.34264	0.241;0.446	B;P	0.47891	0.309;0.56	T	0.63761	-0.6564	10	0.87932	D	0	-0.7703	12.1003	0.53780	0.0:0.0:0.7302:0.2698	rs61753378	206;259	F5H897;Q12931	.;TRAP1_HUMAN	F	259;206	ENSP00000246957:S259F;ENSP00000442070:S206F	ENSP00000246957:S259F	S	-	2	0	TRAP1	3666076	0.988000	0.35896	0.066000	0.19879	0.806000	0.45545	5.333000	0.65917	2.644000	0.89710	0.563000	0.77884	TCC	A|0.042;C|0.000;G|0.957	0.042	strong		0.577	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
C1orf168	199920	hgsc.bcm.edu	37	1	57257817	57257817	+	Silent	SNP	T	T	C	rs2298130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:57257817T>C	ENST00000343433.6	-	2	749	c.669A>G	c.(667-669)aaA>aaG	p.K223K	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	223										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TTTCCCAGCTTTTTCTGATAT	0.522													C|||	1259	0.251398	0.3601	0.1599	5008	,	,		16319	0.3542		0.1431	False		,,,				2504	0.1748				p.K223K		Atlas-SNP	.											.	C1orf168	102	.	0			c.A669G						PASS	.	C		1414,2990	651.2+/-399.2	224,966,1012	69.0	77.0	74.0		669	2.8	0.0	1	dbSNP_100	74	1191,7409	754.7+/-407.5	105,981,3214	no	coding-synonymous	C1orf168	NM_001004303.4		329,1947,4226	CC,CT,TT		13.8488,32.1072,20.0323		223/729	57257817	2605,10399	2202	4300	6502	SO:0001819	synonymous_variant	199920	exon2			CCAGCTTTTTCTG	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.669A>G	1.37:g.57257817T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	134	80	0.597015	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																			T|0.778;C|0.222	0.222	strong		0.522	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
CLCA2	9635	hgsc.bcm.edu	37	1	86891073	86891073	+	Missense_Mutation	SNP	G	G	A	rs11580625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:86891073G>A	ENST00000370565.4	+	2	400	c.238G>A	c.(238-240)Gta>Ata	p.V80I		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	80	Metalloprotease domain. {ECO:0000250|UniProtKB:A8K7I4}.		V -> I (in dbSNP:rs11580625).		cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CAAGAGAAGAGTATTTTTCAG	0.303													G|||	82	0.0163738	0.0045	0.0216	5008	,	,		15704	0.0		0.0517	False		,,,				2504	0.0092				p.V80I	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.G238A						PASS	.	G	ILE/VAL	37,4367	37.6+/-69.7	1,35,2166	45.0	49.0	48.0		238	3.1	1.0	1	dbSNP_120	48	361,8207	116.3+/-176.0	12,337,3935	yes	missense	CLCA2	NM_006536.5	29	13,372,6101	AA,AG,GG		4.2134,0.8401,3.0681	possibly-damaging	80/944	86891073	398,12574	2202	4284	6486	SO:0001583	missense	9635	exon2			AGAAGAGTATTTT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.238G>A	1.37:g.86891073G>A	ENSP00000359596:p.Val80Ile	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	48	0.02197802197802198	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	39	0.051451187335092345	G	16.97	3.268510	0.59540	0.008401	0.042134	ENSG00000137975	ENST00000370565;ENST00000439777	T	0.12255	2.7	5.93	3.08	0.35506	Chloride channel calcium-activated (1);	0.438333	0.23265	N	0.050093	T	0.04318	0.0119	M	0.66939	2.045	0.31514	N	0.663187	B	0.13594	0.008	B	0.16289	0.015	T	0.37033	-0.9723	10	0.19147	T	0.46	-4.1577	4.4784	0.11755	0.2942:0.0:0.5286:0.1772	rs11580625;rs11580625	80	Q9UQC9	CLCA2_HUMAN	I	80	ENSP00000359596:V80I	ENSP00000359596:V80I	V	+	1	0	CLCA2	86663661	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	0.651000	0.24873	0.429000	0.26202	-0.136000	0.14681	GTA	G|0.969;A|0.031	0.031	strong		0.303	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
GPR125	166647	hgsc.bcm.edu	37	4	22390719	22390719	+	Silent	SNP	G	G	A	rs143611399	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:22390719G>A	ENST00000334304.5	-	18	2984	c.2715C>T	c.(2713-2715)aaC>aaT	p.N905N	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	905					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(33)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	56		Breast(46;0.198)				ACTAGGGTGCGTTTGGCCGAC	0.408													A|||	7	0.00139776	0.0008	0.0	5008	,	,		17038	0.005		0.0	False		,,,				2504	0.001				p.N905N		Atlas-SNP	.											.	GPR125	118	.	0			c.C2715T						PASS	.	A		2,4404	826.0+/-416.6	0,2,2201	206.0	216.0	213.0		2715	-1.0	0.1	4	dbSNP_134	213	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	GPR125	NM_145290.2		0,7,6496	AA,AG,GG		0.0581,0.0454,0.0538		905/1322	22390719	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	166647	exon18			GGGTGCGTTTGGC	AK095866	CCDS33964.1	4p15.31	2014-08-08			ENSG00000152990	ENSG00000152990		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"""	13839	protein-coding gene	gene with protein product		612303				12565841	Standard	NM_145290		Approved	FLJ38547, PGR21	uc003gqm.2	Q8IWK6	OTTHUMG00000160926	ENST00000334304.5:c.2715C>T	4.37:g.22390719G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	101	59	0.584158	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Silent	SNP	ENST00000334304.5	37	CCDS33964.1																																																																																			G|0.999;A|0.001	0.001	strong		0.408	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3		
PCDHB11	56125	hgsc.bcm.edu	37	5	140581510	140581510	+	Silent	SNP	G	G	T	rs638054	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140581510G>T	ENST00000354757.3	+	1	2163	c.2163G>T	c.(2161-2163)tcG>tcT	p.S721S	PCDHB11_ENST00000536699.1_Silent_p.S356S	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	721					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGGCGGCCTCGGTGGGAAGCT	0.647																																					p.S721S		Atlas-SNP	.											.	PCDHB11	162	.	0			c.G2163T						PASS	.	G		184,4222		3,178,2022	99.0	109.0	106.0		2163	-5.5	0.0	5	dbSNP_83	106	1905,6695		216,1473,2611	no	coding-synonymous	PCDHB11	NM_018931.2		219,1651,4633	TT,TG,GG		22.1512,4.1761,16.0618		721/798	140581510	2089,10917	2203	4300	6503	SO:0001819	synonymous_variant	56125	exon1			GGCCTCGGTGGGA	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.2163G>T	5.37:g.140581510G>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	37	CCDS4253.1																																																																																			G|0.802;T|0.198	0.198	strong		0.647	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
BRDT	676	hgsc.bcm.edu	37	1	92442695	92442695	+	Missense_Mutation	SNP	A	A	C	rs1156281	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:92442695A>C	ENST00000362005.3	+	7	1132	c.714A>C	c.(712-714)aaA>aaC	p.K238N	BRDT_ENST00000484781.1_3'UTR|BRDT_ENST00000394530.3_Missense_Mutation_p.K192N|BRDT_ENST00000370389.2_Missense_Mutation_p.K165N|BRDT_ENST00000399546.2_Missense_Mutation_p.K238N|BRDT_ENST00000402388.1_Missense_Mutation_p.K238N	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	238			K -> N (in dbSNP:rs1156281). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TCACAGAAAAATCAGTGGCAC	0.368													A|||	947	0.189097	0.1513	0.134	5008	,	,		19037	0.3859		0.0755	False		,,,				2504	0.1933				p.K242N		Atlas-SNP	.											.	BRDT	133	.	0			c.A726C						PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	562,3844	244.3+/-253.7	39,484,1680	58.0	56.0	57.0		714,726,576,576,495,714,714	3.2	0.2	1	dbSNP_87	57	497,8103	142.2+/-198.4	18,461,3821	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	94,94,94,94,94,94,94	57,945,5501	CC,CA,AA		5.7791,12.7553,8.1424	benign,benign,benign,benign,benign,benign,benign	238/948,242/952,192/902,192/902,165/875,238/948,238/948	92442695	1059,11947	2203	4300	6503	SO:0001583	missense	676	exon6			AGAAAAATCAGTG	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.714A>C	1.37:g.92442695A>C	ENSP00000354568:p.Lys238Asn	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	405	0.18543956043956045	63	0.12804878048780488	41	0.1132596685082873	241	0.42132867132867136	60	0.079155672823219	A	13.80	2.344740	0.41498	0.127553	0.057791	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.11063	3.1;3.1;3.1;3.14;2.81;3.1	5.58	3.21	0.36854	.	1.092130	0.06940	N	0.812580	T	0.06962	0.0177	L	0.34521	1.04	0.42066	P	0.008811000000000013	D;D;P;D	0.53312	0.959;0.959;0.944;0.959	P;P;P;P	0.52343	0.503;0.503;0.696;0.503	T	0.25882	-1.0119	9	0.72032	D	0.01	-3.2232	7.8455	0.29422	0.7881:0.1391:0.0727:0.0	rs1156281;rs52816607;rs58411058;rs1156281	192;192;242;238	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	N	238;165;238;238;192;238;238	ENSP00000354568:K238N;ENSP00000359416:K165N;ENSP00000387822:K238N;ENSP00000378038:K192N;ENSP00000404969:K238N;ENSP00000384051:K238N	ENSP00000354568:K238N	K	+	3	2	BRDT	92215283	0.991000	0.36638	0.150000	0.22450	0.181000	0.23173	2.784000	0.47774	0.467000	0.27218	0.533000	0.62120	AAA	A|0.865;C|0.135	0.135	strong		0.368	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
SEC31A	22872	hgsc.bcm.edu	37	4	83795806	83795806	+	Silent	SNP	T	T	C	rs10025654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:83795806T>C	ENST00000395310.2	-	6	779	c.597A>G	c.(595-597)agA>agG	p.R199R	SEC31A_ENST00000448323.1_Silent_p.R199R|SEC31A_ENST00000264405.5_5'Flank|SEC31A_ENST00000508502.1_Silent_p.R199R|SEC31A_ENST00000513858.1_Silent_p.R199R|SEC31A_ENST00000326950.5_Silent_p.R199R|SEC31A_ENST00000508479.1_Silent_p.R199R|SEC31A_ENST00000509142.1_Silent_p.R199R|SEC31A_ENST00000505472.1_Silent_p.R199R|SEC31A_ENST00000311785.7_Silent_p.R199R|SEC31A_ENST00000348405.4_Silent_p.R199R|SEC31A_ENST00000500777.2_Silent_p.R199R|SEC31A_ENST00000443462.2_Silent_p.R194R|SEC31A_ENST00000436790.2_5'UTR|SEC31A_ENST00000432794.1_Silent_p.R199R|SEC31A_ENST00000355196.2_Silent_p.R199R|SEC31A_ENST00000505984.1_Silent_p.R199R	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	199	Interaction with SEC13.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				GCTCATTTTTTCTAAGATCCC	0.428													T|||	1766	0.352636	0.1029	0.6758	5008	,	,		18100	0.2629		0.5616	False		,,,				2504	0.3384				p.R199R		Atlas-SNP	.											.	SEC31A	227	.	0			c.A597G						PASS	.	T	,,,,,	837,3569	332.0+/-302.3	94,649,1460	130.0	128.0	129.0		597,597,597,582,597,597	-3.6	1.0	4	dbSNP_119	129	4943,3657	623.2+/-397.4	1423,2097,780	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEC31A	NM_001077206.2,NM_001077207.2,NM_001077208.2,NM_001191049.1,NM_014933.3,NM_016211.3	,,,,,	1517,2746,2240	CC,CT,TT		42.5233,18.9968,44.441	,,,,,	199/1107,199/1221,199/1206,194/1201,199/1221,199/1182	83795806	5780,7226	2203	4300	6503	SO:0001819	synonymous_variant	22872	exon6			ATTTTTTCTAAGA	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.597A>G	4.37:g.83795806T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	97	53	0.546392	NM_001077206	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1																																																																																			T|0.602;C|0.398	0.398	strong		0.428	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211	
VAV3	10451	hgsc.bcm.edu	37	1	108307727	108307727	+	Missense_Mutation	SNP	T	T	A	rs7528153	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:108307727T>A	ENST00000370056.4	-	9	1166	c.892A>T	c.(892-894)Aca>Tca	p.T298S	VAV3_ENST00000527011.1_Missense_Mutation_p.T298S|VAV3_ENST00000343258.4_5'UTR|VAV3_ENST00000371846.4_Missense_Mutation_p.T233S	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	298	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		T -> S (in dbSNP:rs7528153). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9705494}.		angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TCTTCTTTTGTCTTAGAAATG	0.343													T|||	2543	0.507788	0.5862	0.4251	5008	,	,		15591	0.3879		0.7038	False		,,,				2504	0.3824				p.T298S		Atlas-SNP	.											.	VAV3	176	.	0			c.A892T						PASS	.	T	SER/THR	2699,1707	646.4+/-398.4	816,1067,320	81.0	79.0	80.0		892	4.5	1.0	1	dbSNP_116	80	5984,2616	686.2+/-404.1	2078,1828,394	yes	missense	VAV3	NM_006113.4	58	2894,2895,714	AA,AT,TT		30.4186,38.7426,33.2385	benign	298/848	108307727	8683,4323	2203	4300	6503	SO:0001583	missense	10451	exon9			CTTTTGTCTTAGA	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.892A>T	1.37:g.108307727T>A	ENSP00000359073:p.Thr298Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	125	122	0.976	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	1199|1199	0.548992673992674|0.548992673992674	281|281	0.5711382113821138|0.5711382113821138	177|177	0.4889502762430939|0.4889502762430939	209|209	0.36538461538461536|0.36538461538461536	532|532	0.7018469656992085|0.7018469656992085	T|T	8.268|8.268	0.812619|0.812619	0.16537|0.16537	0.612574|0.612574	0.695814|0.695814	ENSG00000134215|ENSG00000134215	ENST00000490388|ENST00000370056;ENST00000527011;ENST00000371846	.|T;T;T	.|0.67345	.|-0.26;-0.26;-0.26	5.64|5.64	4.5|4.5	0.54988|0.54988	.|Dbl homology (DH) domain (5);	.|0.162982	.|0.56097	.|D	.|0.000034	T|T	0.31702|0.31702	0.0805|0.0805	L|L	0.31371|0.31371	0.925|0.925	0.22457|0.22457	P|P	0.999083523|0.999083523	.|P;B	.|0.36712	.|0.566;0.022	.|B;B	.|0.40702	.|0.338;0.038	T|T	0.14699|0.14699	-1.0463|-1.0463	4|9	.|0.10377	.|T	.|0.69	.|.	6.5647|6.5647	0.22505|0.22505	0.1382:0.0717:0.0:0.7901|0.1382:0.0717:0.0:0.7901	rs7528153;rs17229619;rs52810668;rs56826441;rs7528153|rs7528153;rs17229619;rs52810668;rs56826441;rs7528153	.|298;298	.|E9PQ97;Q9UKW4	.|.;VAV3_HUMAN	S|S	292|298;298;233	.|ENSP00000359073:T298S;ENSP00000432540:T298S;ENSP00000360912:T233S	.|ENSP00000359073:T298S	R|T	-|-	3|1	2|0	VAV3|VAV3	108109250|108109250	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.315000|1.315000	0.33608|0.33608	0.946000|0.946000	0.37632|0.37632	0.528000|0.528000	0.53228|0.53228	AGA|ACA	T|0.379;A|0.621	0.621	strong		0.343	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
PLAUR	5329	hgsc.bcm.edu	37	19	44153100	44153100	+	Missense_Mutation	SNP	A	A	G	rs4760	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44153100A>G	ENST00000340093.3	-	7	1179	c.950T>C	c.(949-951)cTc>cCc	p.L317P	PLAUR_ENST00000221264.4_Missense_Mutation_p.L272P|PLAUR_ENST00000339082.3_Intron|PLAUR_ENST00000601723.1_Missense_Mutation_p.L268P	NM_002659.3	NP_002650.1	Q03405	UPAR_HUMAN	plasminogen activator, urokinase receptor	317			L -> P (in dbSNP:rs4760). {ECO:0000269|Ref.8}.		attachment of GPI anchor to protein (GO:0016255)|blood coagulation (GO:0007596)|C-terminal protein lipidation (GO:0006501)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|chemotaxis (GO:0006935)|fibrinolysis (GO:0042730)|post-translational protein modification (GO:0043687)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|urokinase plasminogen activator signaling pathway (GO:0038195)	anchored component of membrane (GO:0031225)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)|urokinase plasminogen activator receptor activity (GO:0030377)			endometrium(1)|kidney(4)|large_intestine(5)|lung(5)|ovary(1)|stomach(1)|urinary_tract(3)	20		Prostate(69;0.0153)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Tenecteplase(DB00031)|Urokinase(DB00013)	GGTGATGGTGAGGCTGAGATG	0.602													A|||	343	0.0684904	0.0038	0.0821	5008	,	,		19100	0.0		0.1491	False		,,,				2504	0.1339				p.L317P		Atlas-SNP	.											.	PLAUR	71	.	0			c.T950C						PASS	.	A	,PRO/LEU,PRO/LEU	132,4274	95.7+/-134.4	3,126,2074	96.0	84.0	88.0		,815,950	2.9	0.1	19	dbSNP_52	88	1327,7273	259.1+/-282.5	91,1145,3064	yes	intron,missense,missense	PLAUR	NM_001005376.2,NM_001005377.2,NM_002659.3	,98,98	94,1271,5138	GG,GA,AA		15.4302,2.9959,11.2179	,probably-damaging,probably-damaging	,272/291,317/336	44153100	1459,11547	2203	4300	6503	SO:0001583	missense	5329	exon7			ATGGTGAGGCTGA		CCDS12628.1, CCDS33041.1, CCDS33042.1, CCDS74386.1	19q13	2012-03-15			ENSG00000011422	ENSG00000011422		"""CD molecules"""	9053	protein-coding gene	gene with protein product	"""urokinase-type plasminogen activator (uPA) receptor"", ""urokinase plasminogen activator surface receptor"""	173391					Standard	NM_002659		Approved	URKR, UPAR, CD87	uc002oxf.2	Q03405		ENST00000340093.3:c.950T>C	19.37:g.44153100A>G	ENSP00000339328:p.Leu317Pro	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	108	50	0.462963	NM_002659	A8K409|Q12876|Q15845|Q16887|Q6IB52|Q9BWT0|Q9NYC8|Q9UD69|Q9UEA6|Q9UM92|Q9UMV0	Missense_Mutation	SNP	ENST00000340093.3	37	CCDS12628.1	146	0.06684981684981685	1	0.0020325203252032522	26	0.0718232044198895	0	0.0	119	0.15699208443271767	A	14.78	2.637424	0.47049	0.029959	0.154302	ENSG00000011422	ENST00000340093;ENST00000221264	T;T	0.13538	2.62;2.58	3.94	2.93	0.34026	.	0.809357	0.10433	N	0.675276	T	0.00109	0.0003	L	0.55481	1.735	0.37595	P	0.07964499999999997	D;D	0.64830	0.99;0.994	D;P	0.63192	0.912;0.84	T	0.10800	-1.0614	9	0.54805	T	0.06	-5.0102	5.7743	0.18271	0.8805:0.0:0.1195:0.0	rs4760;rs3199954;rs4760	272;317	Q03405-3;Q03405	.;UPAR_HUMAN	P	317;272	ENSP00000339328:L317P;ENSP00000221264:L272P	ENSP00000221264:L272P	L	-	2	0	PLAUR	48844940	0.632000	0.27172	0.117000	0.21633	0.262000	0.26303	2.117000	0.41939	0.881000	0.35993	0.260000	0.18958	CTC	A|0.908;G|0.092	0.092	strong		0.602	PLAUR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463571.1	NM_002659	
TBC1D9	23158	hgsc.bcm.edu	37	4	141598126	141598126	+	Silent	SNP	C	C	T	rs2303911	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:141598126C>T	ENST00000442267.2	-	6	1055	c.981G>A	c.(979-981)caG>caA	p.Q327Q		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	327	GRAM 2.						calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				ACACAAACATCTGCCCCAAAA	0.428													C|||	503	0.100439	0.0991	0.072	5008	,	,		17329	0.0853		0.1581	False		,,,				2504	0.0787				p.Q327Q		Atlas-SNP	.											.	TBC1D9	198	.	0			c.G981A						PASS	.	C		443,3385		28,387,1499	120.0	117.0	118.0		981	2.7	1.0	4	dbSNP_100	118	1247,7015		83,1081,2967	no	coding-synonymous	TBC1D9	NM_015130.2		111,1468,4466	TT,TC,CC		15.0932,11.5726,13.9785		327/1267	141598126	1690,10400	1914	4131	6045	SO:0001819	synonymous_variant	23158	exon6			AAACATCTGCCCC	AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"""EF-hand domain containing"""	21710	protein-coding gene	gene with protein product			"""TBC1 domain family, member 9"""			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.981G>A	4.37:g.141598126C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_015130	A6H8U8|D3DNZ1|O94958	Silent	SNP	ENST00000442267.2	37	CCDS47136.1																																																																																			C|0.866;G|0.000;T|0.133	0.133	strong		0.428	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130	
SLFN14	342618	hgsc.bcm.edu	37	17	33880003	33880003	+	Silent	SNP	C	C	G	rs28498569	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33880003C>G	ENST00000415846.3	-	3	1685	c.1650G>C	c.(1648-1650)gtG>gtC	p.V550V	RP11-1094M14.12_ENST00000588445.1_RNA	NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	550							ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						ACAGGGAGACCACCACCAGAG	0.527													C|||	1164	0.232428	0.3782	0.2046	5008	,	,		15105	0.2976		0.0964	False		,,,				2504	0.1278				p.V550V		Atlas-SNP	.											.	SLFN14	43	.	0			c.G1650C						PASS	.	C		420,964		61,298,333	142.0	136.0	138.0		1650	-5.5	0.0	17	dbSNP_125	138	281,2901		11,259,1321	no	coding-synonymous	SLFN14	NM_001129820.1		72,557,1654	GG,GC,CC		8.8309,30.3468,15.3526		550/913	33880003	701,3865	692	1591	2283	SO:0001819	synonymous_variant	342618	exon3			GGAGACCACCACC		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.1650G>C	17.37:g.33880003C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	86	50	0.581395	NM_001129820	B2RTW9	Silent	SNP	ENST00000415846.3	37	CCDS45650.1																																																																																			C|0.765;G|0.235	0.235	strong		0.527	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
FAM207A	85395	hgsc.bcm.edu	37	21	46387078	46387078	+	Missense_Mutation	SNP	G	G	T	rs2294168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46387078G>T	ENST00000291634.6	+	4	530	c.482G>T	c.(481-483)aGc>aTc	p.S161I	FAM207A_ENST00000479127.1_3'UTR|FAM207A_ENST00000397826.3_Missense_Mutation_p.S146I	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	161																	GAGGCTGGCAGCCGGCGCCAA	0.711													G|||	547	0.109225	0.0991	0.2003	5008	,	,		13190	0.1121		0.1282	False		,,,				2504	0.0358				p.S161I		Atlas-SNP	.											C21orf70,NS,carcinoma,-1,1	.	.	1	0			c.G482T						PASS	.	G	ILE/SER	491,3883		35,421,1731	14.0	19.0	17.0		482	1.5	0.0	21	dbSNP_100	17	1032,7520		80,872,3324	no	missense	FAM207A	NM_058190.2	142	115,1293,5055	TT,TG,GG		12.0674,11.2254,11.7825	benign	161/231	46387078	1523,11403	2187	4276	6463	SO:0001583	missense	85395	exon4			CTGGCAGCCGGCG		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.482G>T	21.37:g.46387078G>T	ENSP00000291634:p.Ser161Ile	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	38	24	0.631579	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	37	CCDS13718.1	275	0.1259157509157509	56	0.11382113821138211	56	0.15469613259668508	67	0.11713286713286714	96	0.1266490765171504	G	12.01	1.809550	0.31961	0.112254	0.120674	ENSG00000160256	ENST00000291634;ENST00000397826;ENST00000458015	T;T;T	0.47177	1.01;1.01;0.85	3.44	1.53	0.23141	.	0.895789	0.09616	N	0.778288	T	0.00271	0.0008	L	0.38531	1.155	0.80722	P	0.0	P;P	0.44380	0.73;0.834	B;P	0.45506	0.316;0.483	T	0.06716	-1.0811	9	0.39692	T	0.17	-0.0034	9.4412	0.38670	0.0:0.4286:0.5714:0.0	rs2294168	146;161	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	I	161;146;146	ENSP00000291634:S161I;ENSP00000380926:S146I;ENSP00000404964:S146I	ENSP00000291634:S161I	S	+	2	0	C21orf70	45211506	0.000000	0.05858	0.006000	0.13384	0.015000	0.08874	0.202000	0.17295	0.405000	0.25532	0.563000	0.77884	AGC	G|0.887;T|0.113	0.113	strong		0.711	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190	
KDM6A	7403	hgsc.bcm.edu	37	X	44938563	44938563	+	Silent	SNP	G	G	A	rs20539	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:44938563G>A	ENST00000377967.4	+	20	3152	c.3111G>A	c.(3109-3111)caG>caA	p.Q1037Q	KDM6A_ENST00000543216.1_Silent_p.Q958Q|KDM6A_ENST00000382899.4_Silent_p.Q1044Q|KDM6A_ENST00000536777.1_Silent_p.Q992Q	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1037	Interaction with SUPT6H. {ECO:0000250}.				canonical Wnt signaling pathway (GO:0060070)|heart morphogenesis (GO:0003007)|histone H3-K4 methylation (GO:0051568)|in utero embryonic development (GO:0001701)|mesodermal cell differentiation (GO:0048333)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|regulation of gene expression (GO:0010468)|respiratory system process (GO:0003016)|somite rostral/caudal axis specification (GO:0032525)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)	p.0?(6)		NS(1)|breast(7)|central_nervous_system(27)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(24)|kidney(24)|large_intestine(9)|liver(1)|lung(21)|oesophagus(11)|pancreas(2)|prostate(5)|skin(1)|soft_tissue(1)|urinary_tract(29)	170						AATATGCACAGTACCAGGCCT	0.358			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""								G|||	837	0.221722	0.0091	0.3386	3775	,	,		12635	0.2381		0.16	False		,,,				2504	0.1933				p.Q1037Q	Colon(129;1273 1667 15230 27352 52914)	Atlas-SNP	.		Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	.	KDM6A	274	.	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)	c.G3111A						PASS	.	G		126,3709		5,103,13,1524,558	136.0	109.0	118.0		3111	0.2	1.0	X	dbSNP_67	118	1268,5460		79,761,349,1588,1523	no	coding-synonymous	KDM6A	NM_021140.2		84,864,362,3112,2081	AA,AG,A,GG,G		18.8466,3.2855,13.197		1037/1402	44938563	1394,9169	2203	4300	6503	SO:0001819	synonymous_variant	7403	exon20			TGCACAGTACCAG	AF000992	CCDS14265.1	Xp11.2	2014-09-17	2009-04-17	2009-04-17	ENSG00000147050	ENSG00000147050		"""Chromatin-modifying enzymes / K-demethylases"", ""Tetratricopeptide (TTC) repeat domain containing"""	12637	protein-coding gene	gene with protein product		300128	"""ubiquitously transcribed tetratricopeptide repeat, X chromosome"""	UTX		9499428, 9381176	Standard	XM_005272655		Approved		uc004dge.4	O15550	OTTHUMG00000021402	ENST00000377967.4:c.3111G>A	X.37:g.44938563G>A		Somatic	208	1	0.00480769		WXS	Illumina HiSeq	Phase_I	249	246	0.987952	NM_021140	Q52LL9|Q5JVQ7	Silent	SNP	ENST00000377967.4	37	CCDS14265.1	374	0.22543701024713683	7	0.014285714285714285	69	0.24820143884892087	90	0.18518518518518517	86	0.12536443148688048	G	7.673	0.687468	0.14973	0.032855	0.188466	ENSG00000147050	ENST00000414389;ENST00000433797	.	.	.	5.6	0.226	0.15353	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.16660	-1.0395	3	.	.	.	-8.1414	11.1997	0.48734	0.3721:0.0:0.6279:0.0	rs20539;rs4824526;rs17245004;rs52822280;rs4824526	.	.	.	I	635;680	.	.	V	+	1	0	KDM6A	44823507	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.819000	0.39022	-0.032000	0.13758	-0.198000	0.12761	GTA	0|0.018;A|0.156	0.156	strong		0.358	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140	
MUC4	4585	hgsc.bcm.edu	37	3	195509354	195509354	+	Missense_Mutation	SNP	C	C	T	rs556992821	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195509354C>T	ENST00000463781.3	-	2	9556	c.9097G>A	c.(9097-9099)Gca>Aca	p.A3033T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3033T	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)		CCGGTGGATGCTGAGGAAGGG	0.587													.|||	649	0.129593	0.1657	0.0893	5008	,	,		11674	0.0407		0.1899	False		,,,				2504	0.1391				p.A3033T		Atlas-SNP	.											MUC4_ENST00000463781,uveal_tract,malignant_melanoma,0,4	MUC4	1505	4	0			c.G9097A						scavenged	.						16.0	12.0	13.0					3																	195509354		652	1525	2177	SO:0001583	missense	4585	exon2			TGGATGCTGAGGA	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.9097G>A	3.37:g.195509354C>T	ENSP00000417498:p.Ala3033Thr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	103	8	0.0776699	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	10.16	1.273058	0.23221	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.55;1.54	1.18	1.18	0.20946	.	.	.	.	.	T	0.15696	0.0378	N	0.19112	0.55	0.09310	N	1	B	0.22909	0.077	B	0.06405	0.002	T	0.23619	-1.0183	8	.	.	.	.	5.4573	0.16598	0.0:0.6407:0.3593:0.0	.	2905	E7ESK3	.	T	3033	ENSP00000417498:A3033T;ENSP00000420243:A3033T	.	A	-	1	0	MUC4	196994133	0.000000	0.05858	0.021000	0.16686	0.000000	0.00434	-0.303000	0.08210	0.694000	0.31654	0.000000	0.15137	GCA	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PBDC1	51260	hgsc.bcm.edu	37	X	75394784	75394784	+	Splice_Site	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:75394784G>T	ENST00000373358.3	+	3	359	c.156G>T	c.(154-156)aaG>aaT	p.K52N	PBDC1_ENST00000373357.3_Splice_Site_p.K52N	NM_016500.3	NP_057584.2	Q9BVG4	PBDC1_HUMAN	polysaccharide biosynthesis domain containing 1	52																	TCTATTACAAGGTGAGTTGTC	0.398																																					p.K52N		Atlas-SNP	.											.	.	.	.	0			c.G156T						PASS	.						131.0	106.0	114.0					X																	75394784		2203	4300	6503	SO:0001630	splice_region_variant	51260	exon3			TTACAAGGTGAGT	BC001220	CCDS14432.1, CCDS75995.1	Xq13.2	2012-11-28	2012-11-28	2012-11-28	ENSG00000102390	ENSG00000102390			28790	protein-coding gene	gene with protein product			"""chromosome X open reading frame 26"""	CXorf26		11042152	Standard	NM_016500		Approved	MGC874	uc004ecl.1	Q9BVG4	OTTHUMG00000021876	ENST00000373358.3:c.156+1G>T	X.37:g.75394784G>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	99	99	1	NM_016500		Missense_Mutation	SNP	ENST00000373358.3	37	CCDS14432.1	.	.	.	.	.	.	.	.	.	.	G	8.506	0.865350	0.17250	.	.	ENSG00000102390	ENST00000373358;ENST00000373357	.	.	.	4.8	1.69	0.24217	Yst0336-like domain (1);	0.044941	0.85682	D	0.000000	T	0.14570	0.0352	N	0.02111	-0.68	0.37122	D	0.900873	B	0.21520	0.057	B	0.23275	0.045	T	0.04242	-1.0966	9	0.15066	T	0.55	-21.0255	0.5888	0.00724	0.2492:0.1861:0.3716:0.1931	.	52	Q9BVG4	CX026_HUMAN	N	52	.	ENSP00000362455:K52N	K	+	3	2	CXorf26	75311186	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	0.813000	0.27225	0.469000	0.27268	0.600000	0.82982	AAG	.	.	none		0.398	PBDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057294.1	NM_016500	Missense_Mutation
KRT83	3889	hgsc.bcm.edu	37	12	52708565	52708565	+	Silent	SNP	A	A	G	rs2857670	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52708565A>G	ENST00000293670.3	-	9	1394	c.1332T>C	c.(1330-1332)gaT>gaC	p.D444D	AC121757.1_ENST00000594763.1_5'Flank	NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	444	Tail.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		ACACGCAGAGATCCCCGCACA	0.667													N|||	3563	0.711462	0.8714	0.585	5008	,	,		15305	0.6776		0.6441	False		,,,				2504	0.6892				p.D444D	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.T1332C						PASS	.	G		3769,613		1629,511,51	19.0	22.0	21.0		1332	3.9	1.0	12	dbSNP_100	21	5655,2931		1870,1915,508	no	coding-synonymous	KRT83	NM_002282.3		3499,2426,559	GG,GA,AA		34.137,13.989,27.3288		444/494	52708565	9424,3544	2191	4293	6484	SO:0001819	synonymous_variant	3889	exon9			GCAGAGATCCCCG	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.1332T>C	12.37:g.52708565A>G		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	161	159	0.987578	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			A|0.272;G|0.728	0.728	strong		0.667	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
RHPN2	85415	hgsc.bcm.edu	37	19	33482821	33482821	+	Missense_Mutation	SNP	G	G	A	rs79314177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33482821G>A	ENST00000254260.3	-	13	1587	c.1552C>T	c.(1552-1554)Cgc>Tgc	p.R518C	RHPN2_ENST00000400226.4_Missense_Mutation_p.R367C|RHPN2_ENST00000588683.1_5'Flank	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	518	PDZ.				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)					GCAGTGAAGCGGATGCTTCGA	0.547													G|||	208	0.0415335	0.0	0.0288	5008	,	,		16695	0.0169		0.0368	False		,,,				2504	0.137				p.R518C		Atlas-SNP	.											.	RHPN2	107	.	0			c.C1552T						PASS	.	G	CYS/ARG	19,4387	26.2+/-53.5	0,19,2184	69.0	62.0	64.0		1552	3.1	0.6	19	dbSNP_131	64	294,8306	107.6+/-168.3	1,292,4007	no	missense	RHPN2	NM_033103.4	180	1,311,6191	AA,AG,GG		3.4186,0.4312,2.4066	benign	518/687	33482821	313,12693	2203	4300	6503	SO:0001583	missense	85415	exon13			TGAAGCGGATGCT	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.1552C>T	19.37:g.33482821G>A	ENSP00000254260:p.Arg518Cys	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	204	113	0.553922	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	47	0.02152014652014652	0	0.0	16	0.04419889502762431	10	0.017482517482517484	21	0.027704485488126648	G	12.86	2.063219	0.36373	0.004312	0.034186	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.30981	1.51;1.51	5.22	3.08	0.35506	PDZ/DHR/GLGF (1);	0.573078	0.19174	N	0.120873	T	0.05823	0.0152	L	0.41492	1.28	0.43761	D	0.996271	B	0.12013	0.005	B	0.08055	0.003	T	0.02805	-1.1108	10	0.33141	T	0.24	-5.1732	10.146	0.42764	0.1578:0.0:0.8422:0.0	.	518	Q8IUC4	RHPN2_HUMAN	C	518;248;367	ENSP00000254260:R518C;ENSP00000402244:R367C	ENSP00000254260:R518C	R	-	1	0	RHPN2	38174661	0.988000	0.35896	0.591000	0.28745	0.766000	0.43426	2.061000	0.41403	0.726000	0.32339	-0.119000	0.15052	CGC	G|0.974;A|0.026	0.026	strong		0.547	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
TGIF1	7050	hgsc.bcm.edu	37	18	3457606	3457606	+	Missense_Mutation	SNP	C	C	T	rs4468717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:3457606C>T	ENST00000330513.5	+	3	1177	c.874C>T	c.(874-876)Ccg>Tcg	p.P292S	TGIF1_ENST00000401449.1_Missense_Mutation_p.P143S|TGIF1_ENST00000343820.5_Missense_Mutation_p.P163S|TGIF1_ENST00000405385.3_Missense_Mutation_p.P143S|TGIF1_ENST00000407501.2_Missense_Mutation_p.P163S|TGIF1_ENST00000400167.2_Missense_Mutation_p.P143S|TGIF1_ENST00000472042.1_Missense_Mutation_p.P143S|TGIF1_ENST00000345133.5_Missense_Mutation_p.P143S|TGIF1_ENST00000551541.1_Missense_Mutation_p.P143S|TGIF1_ENST00000548489.2_Missense_Mutation_p.P177S	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	292			P -> L (in dbSNP:rs2229333).|P -> S (in dbSNP:rs4468717). {ECO:0000269|PubMed:10764806, ECO:0000269|Ref.3}.		determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GCCGTCATCCCCGGGATCAGT	0.537													C|||	157	0.0313498	0.0045	0.0403	5008	,	,		18684	0.001		0.0944	False		,,,				2504	0.0276				p.P292S		Atlas-SNP	.											.	TGIF1	41	.	0			c.C874T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	73,4333	67.6+/-105.2	0,73,2130	55.0	51.0	52.0		487,874,529,487,427,427,427,427	5.3	0.5	18	dbSNP_111	52	668,7932	168.4+/-220.0	26,616,3658	yes	missense,missense,missense,missense,missense,missense,missense,missense	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_173211.1,NM_174886.1	74,74,74,74,74,74,74,74	26,689,5788	TT,TC,CC		7.7674,1.6568,5.6974	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	163/273,292/402,177/287,163/273,143/253,143/253,143/253,143/253	3457606	741,12265	2203	4300	6503	SO:0001583	missense	7050	exon3			TCATCCCCGGGAT	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.874C>T	18.37:g.3457606C>T	ENSP00000327959:p.Pro292Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	168	73	0.434524	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Missense_Mutation	SNP	ENST00000330513.5	37	CCDS11834.1	95	0.043498168498168496	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	75	0.09894459102902374	C	7.176	0.588604	0.13812	0.016568	0.077674	ENSG00000177426	ENST00000552383;ENST00000401449;ENST00000548489;ENST00000549780;ENST00000405385;ENST00000343820;ENST00000407501;ENST00000551541;ENST00000345133;ENST00000330513;ENST00000549546;ENST00000400167;ENST00000472042	T;T;T;T;T;T;T;T;T;T;T;T;T	0.64438	-0.1;0.4;0.31;-0.1;0.4;0.39;0.39;0.4;0.4;0.18;0.41;0.4;0.4	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.04272	0.0118	M	0.62016	1.91	0.58432	D	0.999997	P;P;P	0.41546	0.726;0.639;0.754	B;B;B	0.42692	0.205;0.11;0.395	T	0.14783	-1.0460	10	0.39692	T	0.17	-21.8135	18.8793	0.92350	0.0:1.0:0.0:0.0	rs4468717	292;163;177	Q15583;Q15583-2;F8VZB6	TGIF1_HUMAN;.;.	S	143;143;177;143;143;163;163;143;143;292;143;143;143	ENSP00000449287:P143S;ENSP00000385206:P143S;ENSP00000447747:P177S;ENSP00000448121:P143S;ENSP00000384970:P143S;ENSP00000339631:P163S;ENSP00000384133:P163S;ENSP00000450025:P143S;ENSP00000343969:P143S;ENSP00000327959:P292S;ENSP00000449580:P143S;ENSP00000383031:P143S;ENSP00000449501:P143S	ENSP00000327959:P292S	P	+	1	0	TGIF1	3447606	1.000000	0.71417	0.514000	0.27761	0.509000	0.34042	3.633000	0.54295	2.468000	0.83385	0.467000	0.42956	CCG	C|0.945;T|0.055	0.055	strong		0.537	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
COMT	1312	hgsc.bcm.edu	37	22	19951207	19951207	+	Silent	SNP	C	C	G	rs4818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19951207C>G	ENST00000361682.6	+	4	790	c.408C>G	c.(406-408)ctC>ctG	p.L136L	COMT_ENST00000449653.1_Silent_p.L86L|COMT_ENST00000493893.1_3'UTR|MIR4761_ENST00000585066.1_RNA|COMT_ENST00000407537.1_Silent_p.L86L|COMT_ENST00000406520.3_Silent_p.L136L|COMT_ENST00000403710.1_Silent_p.L136L|COMT_ENST00000403184.1_Silent_p.L136L	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	136					cellular response to phosphate starvation (GO:0016036)|dopamine catabolic process (GO:0042420)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|learning (GO:0007612)|methylation (GO:0032259)|multicellular organismal reproductive process (GO:0048609)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of smooth muscle cell proliferation (GO:0048662)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|positive regulation of homocysteine metabolic process (GO:0050668)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	catechol O-methyltransferase activity (GO:0016206)|magnesium ion binding (GO:0000287)|O-methyltransferase activity (GO:0008171)			kidney(1)|lung(1)|ovary(1)|prostate(1)|stomach(1)	5	Colorectal(54;0.0993)				Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Methyldopa(DB00968)|Micafungin(DB01141)|S-Adenosylmethionine(DB00118)|Testosterone Propionate(DB01420)|Tolcapone(DB00323)	GGGCGAGGCTCATCACCATCG	0.632													G|||	1487	0.296925	0.1702	0.2954	5008	,	,		16301	0.3413		0.4026	False		,,,				2504	0.3149				p.L136L		Atlas-SNP	.											.	COMT	10	.	0			c.C408G	GRCh37	CM970391	COMT	M	rs4818	PASS	.	G	,,,	864,3542	740.3+/-411.2	87,690,1426	61.0	50.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	408,408,408,258	-0.3	0.2	22	dbSNP_52	54	3396,5204	637.1+/-399.2	656,2084,1560	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COMT	NM_000754.3,NM_001135161.1,NM_001135162.1,NM_007310.2	,,,	743,2774,2986	GG,GC,CC		39.4884,19.6096,32.7541	,,,	136/272,136/272,136/272,86/222	19951207	4260,8746	2203	4300	6503	SO:0001819	synonymous_variant	1312	exon4			GAGGCTCATCACC		CCDS13770.1, CCDS46663.1	22q11.21	2012-10-02			ENSG00000093010	ENSG00000093010	2.1.1.6		2228	protein-coding gene	gene with protein product		116790				1572656	Standard	NM_000754		Approved		uc002zqu.3	P21964	OTTHUMG00000150529	ENST00000361682.6:c.408C>G	22.37:g.19951207C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_000754	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	Silent	SNP	ENST00000361682.6	37	CCDS13770.1																																																																																			C|0.677;G|0.323	0.323	strong		0.632	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318936.2	NM_000754	
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	382	4	0.0104712		WXS	Illumina HiSeq	Phase_I	334	9	0.0269461	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	
ESYT2	57488	hgsc.bcm.edu	37	7	158536267	158536267	+	Missense_Mutation	SNP	T	T	C	rs2305473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158536267T>C	ENST00000251527.5	-	16	1893	c.1828A>G	c.(1828-1830)Agt>Ggt	p.S610G	ESYT2_ENST00000435514.2_Missense_Mutation_p.S45G	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	638	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CCCGAGTTACTGAGCTGGAAG	0.597													T|||	1680	0.335463	0.3994	0.1801	5008	,	,		17999	0.5843		0.17	False		,,,				2504	0.273				p.S610G		Atlas-SNP	.											.	ESYT2	70	.	0			c.A1828G						PASS	.		GLY/SER	1507,2899	479.5+/-358.5	265,977,961	123.0	97.0	106.0		1828	3.0	0.3	7	dbSNP_100	106	1469,7131	279.0+/-293.7	125,1219,2956	yes	missense	ESYT2	NM_020728.2	56	390,2196,3917	CC,CT,TT		17.0814,34.2034,22.8817	benign	610/894	158536267	2976,10030	2203	4300	6503	SO:0001583	missense	57488	exon16			AGTTACTGAGCTG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1828A>G	7.37:g.158536267T>C	ENSP00000251527:p.Ser610Gly	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	701	0.320970695970696	187	0.3800813008130081	63	0.17403314917127072	323	0.5646853146853147	128	0.16886543535620052	T	13.55	2.270957	0.40194	0.342034	0.170814	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514;ENST00000377650;ENST00000429474	T;T;T	0.24538	1.85;1.85;1.85	5.43	3.0	0.34707	C2 calcium/lipid-binding domain, CaLB (1);	0.146748	0.64402	D	0.000004	T	0.00012	0.0000	M	0.65498	2.005	0.34595	P	0.284046	P;B	0.35033	0.481;0.133	B;B	0.33454	0.164;0.065	T	0.43972	-0.9358	9	0.33940	T	0.23	-25.813	6.7082	0.23262	0.136:0.0742:0.0:0.7898	rs2305473;rs59383218;rs2305473	610;638	A0FGR8-2;A0FGR8	.;ESYT2_HUMAN	G	610;659;601;45;45;434	ENSP00000251527:S610G;ENSP00000275418:S601G;ENSP00000411488:S45G	ENSP00000251527:S610G	S	-	1	0	ESYT2	158229028	1.000000	0.71417	0.309000	0.25155	0.752000	0.42762	3.254000	0.51477	0.343000	0.23821	0.455000	0.32223	AGT	T|0.712;C|0.288	0.288	strong		0.597	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
FRAS1	80144	hgsc.bcm.edu	37	4	79455733	79455733	+	Silent	SNP	C	C	T	rs4975139	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:79455733C>T	ENST00000264895.6	+	71	11496	c.11056C>T	c.(11056-11058)Cta>Tta	p.L3686L		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3682					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TGATATGTCACTAGCAGAAAT	0.438													C|||	2579	0.514976	0.3086	0.4395	5008	,	,		21167	0.7758		0.4632	False		,,,				2504	0.6319				p.L3686L		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11056T						PASS	.	C		1271,2491		214,843,824	104.0	93.0	97.0		11056	2.4	1.0	4	dbSNP_111	97	3591,4647		790,2011,1318	no	coding-synonymous	FRAS1	NM_025074.6		1004,2854,2142	TT,TC,CC		43.5907,33.7852,40.5167		3686/4013	79455733	4862,7138	1881	4119	6000	SO:0001819	synonymous_variant	80144	exon71			ATGTCACTAGCAG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11056C>T	4.37:g.79455733C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	1143	0.5233516483516484	172	0.34959349593495936	163	0.45027624309392267	453	0.791958041958042	355	0.4683377308707124	C	5.004	0.186442	0.09495	0.337852	0.435907	ENSG00000138759	ENST00000512123	.	.	.	5.05	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999856936	.	.	.	.	.	.	T	0.20940	-1.0260	3	.	.	.	.	6.0073	0.19553	0.1323:0.6491:0.0:0.2186	rs4975139;rs58497218;rs4975139	.	.	.	I	1914	.	.	T	+	2	0	FRAS1	79674757	0.602000	0.26916	0.987000	0.45799	0.774000	0.43823	1.126000	0.31344	0.174000	0.19809	-0.216000	0.12614	ACT	C|0.484;T|0.516	0.516	strong		0.438	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
KIAA2018	205717	hgsc.bcm.edu	37	3	113377361	113377361	+	Silent	SNP	A	A	G	rs9813630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113377361A>G	ENST00000478658.1	-	5	3185	c.3168T>C	c.(3166-3168)aaT>aaC	p.N1056N	KIAA2018_ENST00000316407.4_Silent_p.N1056N|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1056						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						CTCTATCATCATTGTTCATCA	0.403													G|||	1524	0.304313	0.4387	0.2709	5008	,	,		22325	0.2183		0.3569	False		,,,				2504	0.181				p.N1056N		Atlas-SNP	.											.	KIAA2018	180	.	0			c.T3168C						PASS	.	G		1536,2330		312,912,709	149.0	138.0	142.0		3168	-2.3	0.2	3	dbSNP_119	142	2792,5470		492,1808,1831	no	coding-synonymous	KIAA2018	NM_001009899.2		804,2720,2540	GG,GA,AA		33.7933,39.731,35.686		1056/2246	113377361	4328,7800	1933	4131	6064	SO:0001819	synonymous_variant	205717	exon7			ATCATCATTGTTC	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.3168T>C	3.37:g.113377361A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	127	123	0.968504	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			A|0.657;G|0.343	0.343	strong		0.403	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180563	57180563	+	Missense_Mutation	SNP	G	G	C	rs59615456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:57180563G>C	ENST00000504228.1	+	6	1000	c.895G>C	c.(895-897)Ggt>Cgt	p.G299R	KIAA1211_ENST00000541073.1_Missense_Mutation_p.G292R|KIAA1211_ENST00000264229.6_Missense_Mutation_p.G299R			Q6ZU35	K1211_HUMAN	KIAA1211	299	Glu-rich.			G -> R (in Ref. 2; BAC86392). {ECO:0000305}.						endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GGAAGCGCCAGGTTGGGAGGA	0.716													G|||	1138	0.227236	0.1505	0.2262	5008	,	,		13699	0.2589		0.3429	False		,,,				2504	0.18				p.G299R		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G895C						PASS	.	G	ARG/GLY	622,3124		63,496,1314	5.0	7.0	7.0		895	0.0	0.0	4	dbSNP_129	7	2434,5116		429,1576,1770	no	missense	KIAA1211	NM_020722.1	125	492,2072,3084	CC,CG,GG		32.2384,16.6044,27.0538	benign	299/1234	57180563	3056,8240	1873	3775	5648	SO:0001583	missense	57482	exon8			GCGCCAGGTTGGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.895G>C	4.37:g.57180563G>C	ENSP00000423366:p.Gly299Arg	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	571	0.26144688644688646	75	0.1524390243902439	91	0.2513812154696133	148	0.25874125874125875	257	0.3390501319261214	G	7.864	0.726788	0.15439	0.166044	0.322384	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.11063	2.82;2.82;2.81	4.58	0.0276	0.14155	.	.	.	.	.	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.14578	0.011;0.011	T	0.42732	-0.9434	8	0.36615	T	0.2	-0.8935	3.6126	0.08066	0.4628:0.2149:0.3223:0.0	rs59615456;rs62310634	292;299	F5H1N7;Q6ZU35	.;K1211_HUMAN	R	299;299;292;209	ENSP00000264229:G299R;ENSP00000423366:G299R;ENSP00000444006:G292R	ENSP00000264229:G299R	G	+	1	0	KIAA1211	56875320	0.003000	0.15002	0.000000	0.03702	0.029000	0.11900	1.610000	0.36869	0.107000	0.17824	0.462000	0.41574	GGT	G|0.738;C|0.262	0.262	strong		0.716	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
C6orf211	79624	hgsc.bcm.edu	37	6	151789868	151789868	+	Missense_Mutation	SNP	G	G	A	rs35972078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151789868G>A	ENST00000367294.3	+	5	1208	c.949G>A	c.(949-951)Gct>Act	p.A317T	C6orf211_ENST00000545879.1_Missense_Mutation_p.A198T	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	317			A -> T (in dbSNP:rs35972078).							breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		CAAGTGTGGGGCTGACTGGGA	0.378													G|||	396	0.0790735	0.0658	0.0778	5008	,	,		18970	0.0159		0.1183	False		,,,				2504	0.1227				p.A317T		Atlas-SNP	.											C6orf211,NS,carcinoma,0,1	C6orf211	30	1	0			c.G949A						PASS	.	G	THR/ALA	320,4086	172.7+/-202.6	5,310,1888	85.0	87.0	86.0		949	3.0	0.7	6	dbSNP_126	86	1076,7524	225.5+/-261.6	63,950,3287	yes	missense	C6orf211	NM_024573.1	58	68,1260,5175	AA,AG,GG		12.5116,7.2628,10.7335	benign	317/442	151789868	1396,11610	2203	4300	6503	SO:0001583	missense	79624	exon5			TGTGGGGCTGACT	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.949G>A	6.37:g.151789868G>A	ENSP00000356263:p.Ala317Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_024573	Q96FC6|Q9UFY5	Missense_Mutation	SNP	ENST00000367294.3	37	CCDS5233.1	168	0.07692307692307693	30	0.06097560975609756	33	0.09116022099447514	10	0.017482517482517484	95	0.12532981530343007	G	5.785	0.329209	0.10956	0.072628	0.125116	ENSG00000146476	ENST00000367294;ENST00000545879	T;T	0.07216	3.21;3.21	6.16	3.03	0.35002	Domain of unknown function DUF89 (2);	1.279400	0.05047	N	0.477484	T	0.01558	0.0050	N	0.13168	0.305	0.58432	P	6.999999999979245E-6	B	0.06786	0.001	B	0.09377	0.004	T	0.42832	-0.9428	9	0.18276	T	0.48	.	7.1424	0.25564	0.2135:0.1503:0.6361:0.0	rs35972078	317	Q9H993	CF211_HUMAN	T	317;198	ENSP00000356263:A317T;ENSP00000444121:A198T	ENSP00000356263:A317T	A	+	1	0	C6orf211	151831561	0.942000	0.31987	0.736000	0.30914	0.262000	0.26303	1.691000	0.37721	0.908000	0.36671	0.650000	0.86243	GCT	G|0.904;A|0.096	0.096	strong		0.378	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573	
ZNF404	342908	hgsc.bcm.edu	37	19	44377669	44377669	+	Missense_Mutation	SNP	G	G	A	rs12977303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44377669G>A	ENST00000587539.1	-	3	696	c.697C>T	c.(697-699)Cat>Tat	p.H233Y	ZNF404_ENST00000324394.6_Missense_Mutation_p.H231Y	NM_001033719.2	NP_001028891.2	Q494X3	ZN404_HUMAN	zinc finger protein 404	233			H -> Y (in dbSNP:rs12977303). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|stomach(2)|urinary_tract(1)	17		Prostate(69;0.0352)				ATTTTCTGATGTTCTGTAAGG	0.373													G|||	1953	0.389976	0.0855	0.5692	5008	,	,		20854	0.5536		0.507	False		,,,				2504	0.3855				p.H230Y		Atlas-SNP	.											.	ZNF404	46	.	0			c.C688T						PASS	.	G	TYR/HIS	589,3619		55,479,1570	107.0	108.0	108.0		697	2.6	1.0	19	dbSNP_121	108	4199,4311		1058,2083,1114	yes	missense	ZNF404	NM_001033719.2	83	1113,2562,2684	AA,AG,GG		49.342,13.9971,37.6474	possibly-damaging	233/553	44377669	4788,7930	2104	4255	6359	SO:0001583	missense	342908	exon2			TCTGATGTTCTGT	XM_092027	CCDS59394.1	19q13.31	2013-01-08				ENSG00000176222		"""Zinc fingers, C2H2-type"", ""-"""	19417	protein-coding gene	gene with protein product							Standard	NM_001033719		Approved		uc002oxs.5	Q494X3		ENST00000587539.1:c.697C>T	19.37:g.44377669G>A	ENSP00000466051:p.His233Tyr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001033719	A4FU30|K7ELF2	Missense_Mutation	SNP	ENST00000587539.1	37	CCDS59394.1	943	0.4317765567765568	53	0.10772357723577236	181	0.5	326	0.5699300699300699	383	0.5052770448548812	G	12.88	2.070859	0.36566	0.139971	0.49342	ENSG00000176222	ENST00000324394	D	0.86769	-2.17	2.56	2.56	0.30785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	H	0.97365	3.99	0.36459	P	0.13344199999999995	D	0.89917	1.0	D	0.91635	0.999	T	0.03000	-1.1084	8	0.87932	D	0	.	12.2572	0.54631	0.0:0.0:1.0:0.0	rs12977303;rs52824820;rs59071427;rs12977303	233	Q494X3	ZN404_HUMAN	Y	231	ENSP00000319479:H231Y	ENSP00000319479:H231Y	H	-	1	0	ZNF404	49069509	1.000000	0.71417	0.981000	0.43875	0.212000	0.24457	5.111000	0.64628	1.444000	0.47605	0.404000	0.27445	CAT	G|0.588;A|0.412	0.412	strong		0.373	ZNF404-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460019.1	NM_001033719	
POC5	134359	hgsc.bcm.edu	37	5	75003678	75003678	+	Missense_Mutation	SNP	T	T	C	rs2307111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:75003678T>C	ENST00000428202.2	-	3	296	c.107A>G	c.(106-108)cAt>cGt	p.H36R	POC5_ENST00000510798.1_5'UTR|POC5_ENST00000446329.2_Missense_Mutation_p.H11R|POC5_ENST00000504862.1_5'UTR|RNU6-680P_ENST00000384603.1_RNA|POC5_ENST00000514838.2_Missense_Mutation_p.H36R|POC5_ENST00000380475.2_5'UTR	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	36			H -> R (in dbSNP:rs2307111). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TATAGCATAATGAAGCAGTTC	0.333													C|||	3083	0.615615	0.9244	0.4798	5008	,	,		16489	0.5347		0.3956	False		,,,				2504	0.6043				p.H36R		Atlas-SNP	.											.	POC5	82	.	0			c.A107G						PASS	.	C	ARG/HIS,ARG/HIS	3158,526		1353,452,37	41.0	40.0	40.0		107,32	5.8	0.9	5	dbSNP_100	40	3295,4875		661,1973,1451	yes	missense,missense	POC5	NM_001099271.1,NM_152408.2	29,29	2014,2425,1488	CC,CT,TT		40.3305,14.278,45.5627	benign,benign	36/576,11/551	75003678	6453,5401	1842	4085	5927	SO:0001583	missense	134359	exon3			GCATAATGAAGCA	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.107A>G	5.37:g.75003678T>C	ENSP00000410216:p.His36Arg	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	212	208	0.981132	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	1228	0.5622710622710623	442	0.8983739837398373	169	0.46685082872928174	305	0.5332167832167832	312	0.41160949868073876	C	0.187	-1.056591	0.01965	0.85722	0.403305	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000446329	T;T;T	0.19938	2.53;2.11;2.51	5.85	5.85	0.93711	.	0.053444	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00063	-2.32	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37103	-0.9720	9	0.02654	T	1	-4.8718	12.2646	0.54670	0.0:0.9214:0.0:0.0786	rs2307111;rs3186857;rs17411855;rs17563925;rs58982046;rs2307111	36;11	Q8NA72;Q8NA72-3	POC5_HUMAN;.	R	36;36;11	ENSP00000410216:H36R;ENSP00000420971:H36R;ENSP00000399481:H11R	ENSP00000410216:H36R	H	-	2	0	POC5	75039434	1.000000	0.71417	0.937000	0.37676	0.006000	0.05464	2.176000	0.42500	1.483000	0.48342	-0.119000	0.15052	CAT	T|0.429;C|0.571	0.571	strong		0.333	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
LAMC3	10319	hgsc.bcm.edu	37	9	133963008	133963008	+	Splice_Site	SNP	G	G	A	rs4740412	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:133963008G>A	ENST00000361069.4	+	26	4509	c.4376G>A	c.(4375-4377)cGg>cAg	p.R1459Q	LAMC3_ENST00000480883.1_Intron	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	1459	Domain II and I.				astrocyte development (GO:0014002)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|extracellular matrix organization (GO:0030198)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	structural molecule activity (GO:0005198)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(31)|ovary(3)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	69	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.06e-05)|Epithelial(140;0.000551)		GAAGCTGAGCGGGTACGTTTG	0.657													G|||	818	0.163339	0.0635	0.2435	5008	,	,		18447	0.0833		0.2714	False		,,,				2504	0.2127				p.R1459Q		Atlas-SNP	.											LAMC3,NS,carcinoma,-1,1	LAMC3	167	1	0			c.G4376A						PASS	.	G	GLN/ARG	359,4047	184.0+/-211.4	15,329,1859	66.0	72.0	70.0		4376	-4.3	0.1	9	dbSNP_111	70	2287,6313	383.0+/-340.6	301,1685,2314	yes	missense-near-splice	LAMC3	NM_006059.3	43	316,2014,4173	AA,AG,GG		26.593,8.148,20.3445	benign	1459/1576	133963008	2646,10360	2203	4300	6503	SO:0001630	splice_region_variant	10319	exon26			CTGAGCGGGTACG	AF041835	CCDS6938.1	9q31-q34	2013-03-01			ENSG00000050555	ENSG00000050555		"""Laminins"""	6494	protein-coding gene	gene with protein product		604349				10225960	Standard	NM_006059		Approved	DKFZp434E202	uc004caa.1	Q9Y6N6	OTTHUMG00000020819	ENST00000361069.4:c.4377+1G>A	9.37:g.133963008G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	74	35	0.472973	NM_006059	B1APX9|B1APY0|Q59H72	Missense_Mutation	SNP	ENST00000361069.4	37	CCDS6938.1	374|374	0.17124542124542125|0.17124542124542125	39|39	0.07926829268292683|0.07926829268292683	94|94	0.2596685082872928|0.2596685082872928	41|41	0.07167832167832168|0.07167832167832168	200|200	0.2638522427440633|0.2638522427440633	G|G	0.779|0.779	-0.763118|-0.763118	0.02996|0.02996	0.08148|0.08148	0.26593|0.26593	ENSG00000050555|ENSG00000050555	ENST00000355452|ENST00000361069;ENST00000355048	.|T	.|0.26518	.|1.73	4.62|4.62	-4.34|-4.34	0.03666|0.03666	.|.	.|1.674320	.|0.03126	.|N	.|0.164480	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00823|0.00823	-1.155|-1.155	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.06786	.|0.0;0.001	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.34403|0.34403	-0.9830|-0.9830	4|9	.|0.14656	.|T	.|0.56	.|.	8.3932|8.3932	0.32542|0.32542	0.2491:0.0:0.6052:0.1457|0.2491:0.0:0.6052:0.1457	rs4740412;rs17453122;rs52815542;rs4740412|rs4740412;rs17453122;rs52815542;rs4740412	.|140;1459	.|Q9UF61;Q9Y6N6	.|.;LAMC3_HUMAN	R|Q	141|1459;1471	.|ENSP00000354360:R1459Q	.|ENSP00000347156:R1471Q	G|R	+|+	1|2	0|0	LAMC3|LAMC3	132952829|132952829	0.001000|0.001000	0.12720|0.12720	0.080000|0.080000	0.20451|0.20451	0.126000|0.126000	0.20510|0.20510	-0.404000|-0.404000	0.07205|0.07205	-0.993000|-0.993000	0.03467|0.03467	-1.595000|-1.595000	0.00837|0.00837	GGG|CGG	G|0.817;A|0.183	0.183	strong		0.657	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	Missense_Mutation
LPCAT2	54947	hgsc.bcm.edu	37	16	55562466	55562466	+	Missense_Mutation	SNP	G	G	A	rs837550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:55562466G>A	ENST00000262134.5	+	3	673	c.489G>A	c.(487-489)atG>atA	p.M163I		NM_017839.4	NP_060309.2	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	163			M -> I (in dbSNP:rs837550).		glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	12						TACCTTCTATGGTATCTCGAA	0.383													G|||	2593	0.517772	0.3389	0.621	5008	,	,		15646	0.4296		0.6461	False		,,,				2504	0.6452				p.M163I		Atlas-SNP	.											.	LPCAT2	35	.	0			c.G489A						PASS	.	G	ILE/MET	1683,2713	510.8+/-367.6	297,1089,812	183.0	166.0	172.0		489	-3.8	0.0	16	dbSNP_86	172	5613,2987	665.5+/-402.3	1838,1937,525	yes	missense	LPCAT2	NM_017839.4	10	2135,3026,1337	AA,AG,GG		34.7326,38.2848,43.8596	benign	163/545	55562466	7296,5700	2198	4300	6498	SO:0001583	missense	54947	exon3			TTCTATGGTATCT	AK000488	CCDS10753.1	16q12.2	2013-01-10	2007-12-17	2007-12-17	ENSG00000087253	ENSG00000087253		"""EF-hand domain containing"""	26032	protein-coding gene	gene with protein product		612040	"""acyltransferase like 1"""	AYTL1		16704971	Standard	NM_017839		Approved	FLJ20481	uc002eie.4	Q7L5N7	OTTHUMG00000133238	ENST00000262134.5:c.489G>A	16.37:g.55562466G>A	ENSP00000262134:p.Met163Ile	Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	282	124	0.439716	NM_017839	A3KBM1|Q6MZJ6|Q9NX23	Missense_Mutation	SNP	ENST00000262134.5	37	CCDS10753.1	1137	0.5206043956043956	167	0.3394308943089431	217	0.5994475138121547	249	0.4353146853146853	504	0.6649076517150396	G	0.010	-1.747828	0.00669	0.382848	0.652674	ENSG00000087253	ENST00000262134	D	0.92911	-3.13	5.8	-3.8	0.04307	Phospholipid/glycerol acyltransferase (2);	0.588370	0.21304	N	0.076759	T	0.00012	0.0000	N	0.00894	-1.105	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.29458	-1.0011	9	0.02654	T	1	-8.4188	7.5195	0.27620	0.4753:0.0:0.3727:0.152	rs837550;rs1052664;rs3193118;rs52823221;rs57713681;rs837550	163	Q7L5N7	PCAT2_HUMAN	I	163	ENSP00000262134:M163I	ENSP00000262134:M163I	M	+	3	0	LPCAT2	54119967	0.003000	0.15002	0.006000	0.13384	0.272000	0.26649	-1.098000	0.03346	-0.392000	0.07751	-0.203000	0.12734	ATG	G|0.457;A|0.543	0.543	strong		0.383	LPCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256977.2	NM_017839	
ST14	6768	hgsc.bcm.edu	37	11	130068491	130068491	+	Silent	SNP	G	G	C	rs11827924	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:130068491G>C	ENST00000278742.5	+	14	2077	c.1659G>C	c.(1657-1659)ggG>ggC	p.G553G		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	553	LDL-receptor class A 3. {ECO:0000255|PROSITE-ProRule:PRU00124}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	GTGGGGACGGGTCCGACGAGG	0.657													g|||	589	0.117612	0.1029	0.0749	5008	,	,		13855	0.1974		0.1133	False		,,,				2504	0.09				p.G553G		Atlas-SNP	.											ST14,NS,malignant_melanoma,+1,1	ST14	82	1	0			c.G1659C						PASS	.			480,3922	222.0+/-238.9	26,428,1747	46.0	47.0	47.0		1659	-3.3	0.6	11	dbSNP_120	47	1206,7388	241.7+/-271.9	85,1036,3176	no	coding-synonymous	ST14	NM_021978.3		111,1464,4923	CC,CG,GG		14.033,10.9041,12.9732		553/856	130068491	1686,11310	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon14			GGACGGGTCCGAC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.1659G>C	11.37:g.130068491G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	191	96	0.502618	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			G|0.868;C|0.132	0.132	strong		0.657	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
MMRN1	22915	hgsc.bcm.edu	37	4	90857518	90857518	+	Missense_Mutation	SNP	T	T	A	rs200343754	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:90857518T>A	ENST00000394980.1	+	7	3006	c.2687T>A	c.(2686-2688)cTg>cAg	p.L896Q	MMRN1_ENST00000264790.2_Missense_Mutation_p.L896Q|MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000508372.1_Missense_Mutation_p.L638Q			Q13201	MMRN1_HUMAN	multimerin 1	896					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GCTCTTCAACTGCAAGTATTA	0.348													T|||	3	0.000599042	0.0	0.0	5008	,	,		19216	0.0		0.001	False		,,,				2504	0.002				p.L896Q		Atlas-SNP	.											.	MMRN1	174	.	0			c.T2687A						PASS	.	T	GLN/LEU	0,4402		0,0,2201	60.0	63.0	62.0		2687	4.1	1.0	4		62	2,8594	2.2+/-6.3	0,2,4296	no	missense	MMRN1	NM_007351.2	113	0,2,6497	AA,AT,TT		0.0233,0.0,0.0154	benign	896/1229	90857518	2,12996	2201	4298	6499	SO:0001583	missense	22915	exon6			TTCAACTGCAAGT	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2687T>A	4.37:g.90857518T>A	ENSP00000378431:p.Leu896Gln	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640952	0.47153	0.0	2.33E-4	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.68624	-0.03;-0.03;-0.34	5.3	4.1	0.47936	.	0.211787	0.33290	N	0.005070	T	0.54631	0.1870	L	0.44542	1.39	0.80722	D	1	B	0.33857	0.429	B	0.27170	0.077	T	0.57423	-0.7814	10	0.72032	D	0.01	.	10.1863	0.43000	0.2658:0.0:0.0:0.7342	.	896	Q13201	MMRN1_HUMAN	Q	896;896;638	ENSP00000378431:L896Q;ENSP00000264790:L896Q;ENSP00000426461:L638Q	ENSP00000264790:L896Q	L	+	2	0	MMRN1	91076541	0.093000	0.21703	1.000000	0.80357	0.828000	0.46876	1.331000	0.33793	1.082000	0.41137	0.533000	0.62120	CTG	T|0.999;A|0.001	0.001	weak		0.348	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
USP13	8975	hgsc.bcm.edu	37	3	179371154	179371154	+	Silent	SNP	C	C	T	rs2276803	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:179371154C>T	ENST00000263966.3	+	1	612	c.141C>T	c.(139-141)aaC>aaT	p.N47N	USP13_ENST00000496897.1_5'Flank|USP13_ENST00000482333.1_3'UTR	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	47					autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			TCTACAAGAACGAGTGCGCCT	0.687													C|||	1052	0.210064	0.3767	0.1499	5008	,	,		10066	0.1002		0.1541	False		,,,				2504	0.1984				p.N47N		Atlas-SNP	.											.	USP13	117	.	0			c.C141T						PASS	.	C		1382,2976		225,932,1022	38.0	29.0	32.0		141	1.6	1.0	3	dbSNP_100	32	1320,7238		111,1098,3070	no	coding-synonymous	USP13	NM_003940.2		336,2030,4092	TT,TC,CC		15.4242,31.7118,20.9198		47/864	179371154	2702,10214	2179	4279	6458	SO:0001819	synonymous_variant	8975	exon1			CAAGAACGAGTGC	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.141C>T	3.37:g.179371154C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Silent	SNP	ENST00000263966.3	37	CCDS3235.1																																																																																			C|0.795;T|0.205	0.205	strong		0.687	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1		
SIRT4	23409	hgsc.bcm.edu	37	12	120741382	120741382	+	Silent	SNP	G	G	A	rs61748115	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:120741382G>A	ENST00000202967.4	+	2	77	c.18G>A	c.(16-18)gcG>gcA	p.A6A		NM_012240.2	NP_036372.1			sirtuin 4											haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TGAGCTTTGCGTTGACTTTCA	0.443													G|||	419	0.0836661	0.0272	0.1902	5008	,	,		16781	0.1151		0.0537	False		,,,				2504	0.0828				p.A6A		Atlas-SNP	.											SIRT4,NS,adenoma,0,1	SIRT4	29	1	0			c.G18A						PASS	.	G		155,4251	103.4+/-141.9	4,147,2052	78.0	83.0	81.0		18	0.1	0.0	12	dbSNP_129	81	391,8209	125.8+/-184.4	7,377,3916	no	coding-synonymous	SIRT4	NM_012240.2		11,524,5968	AA,AG,GG		4.5465,3.5179,4.1981		6/315	120741382	546,12460	2203	4300	6503	SO:0001819	synonymous_variant	23409	exon2			CTTTGCGTTGACT	AF083109	CCDS9194.1	12q24.31	2010-06-25	2010-06-25		ENSG00000089163	ENSG00000089163			14932	protein-coding gene	gene with protein product		604482	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 4"", ""sirtuin (silent mating type information regulation 2 homolog) 4 (S. cerevisiae)"""			10381378	Standard	NM_012240		Approved	SIR2L4	uc001tyc.3	Q9Y6E7	OTTHUMG00000169028	ENST00000202967.4:c.18G>A	12.37:g.120741382G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	33	0.702128	NM_012240		Silent	SNP	ENST00000202967.4	37	CCDS9194.1																																																																																			G|0.947;A|0.053	0.053	strong		0.443	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240	
MUC16	94025	hgsc.bcm.edu	37	19	9084183	9084183	+	Silent	SNP	G	G	A	rs1609460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9084183G>A	ENST00000397910.4	-	1	7835	c.7632C>T	c.(7630-7632)ccC>ccT	p.P2544P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2544	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						CTGAGAGATGGGGAGTGAAGG	0.507													G|||	2085	0.416334	0.3411	0.5677	5008	,	,		20799	0.3264		0.4831	False		,,,				2504	0.4346				p.P2544P		Atlas-SNP	.											.	MUC16	4315	.	0			c.C7632T						PASS	.	G		1404,2822		255,894,964	101.0	104.0	103.0		7632	-0.4	0.2	19	dbSNP_88	103	4302,4176		1117,2068,1054	no	coding-synonymous	MUC16	NM_024690.2		1372,2962,2018	AA,AG,GG		49.2569,33.2229,44.915		2544/14508	9084183	5706,6998	2113	4239	6352	SO:0001819	synonymous_variant	94025	exon1			GAGATGGGGAGTG	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.7632C>T	19.37:g.9084183G>A		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	219	128	0.584475	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.573;A|0.427	0.427	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PCDH17	27253	hgsc.bcm.edu	37	13	58207711	58207711	+	Missense_Mutation	SNP	G	G	T	rs41292834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:58207711G>T	ENST00000377918.3	+	1	1057	c.1031G>T	c.(1030-1032)cGc>cTc	p.R344L		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	344	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CTCATCGACCGCAACGACAAT	0.647													G|||	24	0.00479233	0.0015	0.0043	5008	,	,		13628	0.0		0.0169	False		,,,				2504	0.002				p.R344L	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G1031T						PASS	.	G	LEU/ARG	9,4397	15.5+/-35.6	0,9,2194	75.0	72.0	73.0		1031	5.6	1.0	13	dbSNP_127	73	97,8503	54.4+/-115.2	0,97,4203	yes	missense	PCDH17	NM_001040429.2	102	0,106,6397	TT,TG,GG		1.1279,0.2043,0.815	benign	344/1160	58207711	106,12900	2203	4300	6503	SO:0001583	missense	27253	exon1			TCGACCGCAACGA	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1031G>T	13.37:g.58207711G>T	ENSP00000367151:p.Arg344Leu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	31	21	0.677419	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	14	0.00641025641025641	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	11.47	1.647374	0.29246	0.002043	0.011279	ENSG00000118946	ENST00000377918	T	0.59638	0.25	5.57	5.57	0.84162	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.043754	0.85682	D	0.000000	T	0.15825	0.0381	N	0.02011	-0.69	0.46149	D	0.998891	B;B	0.19935	0.016;0.04	B;B	0.17098	0.017;0.012	T	0.18777	-1.0326	9	.	.	.	.	12.8315	0.57748	0.0746:0.0:0.9254:0.0	rs41292834	344;344	O14917-2;O14917	.;PCD17_HUMAN	L	344	ENSP00000367151:R344L	.	R	+	2	0	PCDH17	57105712	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.511000	0.53400	2.640000	0.89533	0.650000	0.86243	CGC	G|0.993;T|0.007	0.007	strong		0.647	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
NLRP2	55655	hgsc.bcm.edu	37	19	55485899	55485899	+	Silent	SNP	G	G	A	rs2217659	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55485899G>A	ENST00000543010.1	+	3	455	c.312G>A	c.(310-312)aaG>aaA	p.K104K	NLRP2_ENST00000537859.1_Silent_p.K104K|NLRP2_ENST00000427260.2_Silent_p.K81K|NLRP2_ENST00000339757.7_Silent_p.K104K|NLRP2_ENST00000391721.4_Silent_p.K104K|NLRP2_ENST00000538819.1_Silent_p.K104K|NLRP2_ENST00000263437.6_Silent_p.K104K|NLRP2_ENST00000448584.2_Silent_p.K104K	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	104					positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		ATAAAAGGAAGCCTCTATCAT	0.358													.|||	887	0.177117	0.093	0.1542	5008	,	,		17526	0.3512		0.1779	False		,,,				2504	0.1268				p.K104K		Atlas-SNP	.											.	NLRP2	161	.	0			c.G312A						PASS	.	G	,,,	502,3902	229.8+/-244.2	31,440,1731	99.0	102.0	101.0		312,312,243,312	-2.6	0.0	19	dbSNP_96	101	1525,7075	285.7+/-297.3	145,1235,2920	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	176,1675,4651	AA,AG,GG		17.7326,11.3987,15.5875	,,,	104/1063,104/1041,81/1040,104/1063	55485899	2027,10977	2202	4300	6502	SO:0001819	synonymous_variant	55655	exon3			AAGGAAGCCTCTA	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.312G>A	19.37:g.55485899G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_001174082	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			G|0.829;A|0.171	0.171	strong		0.358	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
PON3	5446	hgsc.bcm.edu	37	7	95025600	95025600	+	Silent	SNP	G	G	A	rs13226149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:95025600G>A	ENST00000265627.5	-	1	73	c.63C>T	c.(61-63)ttC>ttT	p.F21F	PON3_ENST00000451904.1_Silent_p.F21F|PON1_ENST00000542556.1_Silent_p.F21F|PON3_ENST00000427422.1_Silent_p.F21F|PON3_ENST00000475439.1_5'Flank	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	21					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	TAAACGCCAGGAACATCTCCC	0.657													G|||	1526	0.304712	0.4024	0.245	5008	,	,		13487	0.1667		0.2555	False		,,,				2504	0.408				p.F21F		Atlas-SNP	.											.	PON3	59	.	0			c.C63T						PASS	.	G		1480,2926	474.1+/-356.9	236,1008,959	133.0	118.0	123.0		63	-8.7	0.0	7	dbSNP_121	123	2187,6413	373.5+/-337.0	283,1621,2396	no	coding-synonymous	PON3	NM_000940.2		519,2629,3355	AA,AG,GG		25.4302,33.5906,28.1947		21/355	95025600	3667,9339	2203	4300	6503	SO:0001819	synonymous_variant	5446	exon1			CGCCAGGAACATC	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.63C>T	7.37:g.95025600G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																			G|0.723;A|0.277	0.277	strong		0.657	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
SH3BGR	6450	hgsc.bcm.edu	37	21	40823902	40823902	+	Missense_Mutation	SNP	C	C	G	rs11575939	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:40823902C>G	ENST00000333634.4	+	1	147	c.69C>G	c.(67-69)gaC>gaG	p.D23E	SH3BGR_ENST00000458295.1_Intron|SH3BGR_ENST00000380631.1_Intron|SH3BGR_ENST00000380634.1_Intron|SH3BGR_ENST00000380637.3_Intron	NM_007341.2	NP_031367	P55822	SH3BG_HUMAN	SH3 domain binding glutamate-rich protein	23			D -> E (in dbSNP:rs11575939). {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)		GCCCAGTGGACCCCTGGGCTG	0.622													G|||	833	0.166334	0.2519	0.1369	5008	,	,		15488	0.0268		0.2058	False		,,,				2504	0.1748				p.D23E		Atlas-SNP	.											.	SH3BGR	29	.	0			c.C69G						PASS	.	G	,GLU/ASP	1010,3396	725.4+/-409.6	115,780,1308	60.0	60.0	60.0		,69	-0.2	0.0	21	dbSNP_120	60	1668,6932	736.2+/-407.0	171,1326,2803	yes	intron,missense	SH3BGR	NM_001001713.1,NM_007341.2	,45	286,2106,4111	GG,GC,CC		19.3953,22.9233,20.5905	,benign	,23/240	40823902	2678,10328	2203	4300	6503	SO:0001583	missense	6450	exon1			AGTGGACCCCTGG		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.69C>G	21.37:g.40823902C>G	ENSP00000332513:p.Asp23Glu	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	104	62	0.596154	NM_007341	A6ND59|D3DSI2|Q9BRB8	Missense_Mutation	SNP	ENST00000333634.4	37	CCDS13666.1	349	0.15979853479853479	118	0.23983739837398374	61	0.1685082872928177	15	0.026223776223776224	155	0.20448548812664907	G	0.007	-1.965622	0.00461	0.229233	0.193953	ENSG00000185437	ENST00000333634	T	0.28069	1.63	5.14	-0.25	0.13007	.	1.574460	0.04150	N	0.321084	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	0.17349	-1.0372	9	0.02654	T	1	.	2.843	0.05535	0.165:0.4108:0.284:0.1402	rs11575939;rs17856186	23	P55822	SH3BG_HUMAN	E	23	ENSP00000332513:D23E	ENSP00000332513:D23E	D	+	3	2	SH3BGR	39745772	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.805000	0.27112	-0.244000	0.09639	-0.824000	0.03097	GAC	C|0.802;G|0.198	0.198	strong		0.622	SH3BGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157377.6	NM_007341	
SLC15A3	51296	hgsc.bcm.edu	37	11	60718792	60718792	+	Missense_Mutation	SNP	C	C	T	rs150370599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60718792C>T	ENST00000227880.3	-	1	465	c.232G>A	c.(232-234)Gta>Ata	p.V78I		NM_016582.2	NP_057666.1	Q8IY34	S15A3_HUMAN	solute carrier family 15 (oligopeptide transporter), member 3	78					ion transport (GO:0006811)|peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	symporter activity (GO:0015293)			central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)	17						CCCAGGAATACCAGCGCGGCG	0.706													-|||	126	0.0251597	0.0038	0.0461	5008	,	,		8892	0.0		0.0746	False		,,,				2504	0.0143				p.V78I		Atlas-SNP	.											.	SLC15A3	34	.	0			c.G232A						PASS	.		ILE/VAL	41,3613		0,41,1786	6.0	5.0	5.0		232	-0.9	0.5	11	dbSNP_134	5	461,6997		11,439,3279	yes	missense	SLC15A3	NM_016582.2	29	11,480,5065	TT,TC,CC		6.1813,1.1221,4.5176	benign	78/582	60718792	502,10610	1827	3729	5556	SO:0001583	missense	51296	exon1			GGAATACCAGCGC	AB020598	CCDS7998.1	11q12.2	2013-07-18	2013-07-18		ENSG00000110446	ENSG00000110446		"""Solute carriers"""	18068	protein-coding gene	gene with protein product		610408	"""solute carrier family 15, member 3"""			11336635, 11741232	Standard	NM_016582		Approved	PHT2, hPTR3	uc001nqn.2	Q8IY34	OTTHUMG00000167804	ENST00000227880.3:c.232G>A	11.37:g.60718792C>T	ENSP00000227880:p.Val78Ile	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_016582	Q9P2X9	Missense_Mutation	SNP	ENST00000227880.3	37	CCDS7998.1	69	0.03159340659340659	3	0.006097560975609756	17	0.04696132596685083	0	0.0	49	0.06464379947229551	c	7.293	0.611444	0.14066	0.011221	0.061813	ENSG00000110446	ENST00000227880;ENST00000442626	T	0.58060	0.36	3.22	-0.932	0.10435	Major facilitator superfamily domain, general substrate transporter (1);	0.507607	0.14586	N	0.310574	T	0.03959	0.0111	N	0.20766	0.605	0.18873	N	0.999982	B;B	0.18461	0.028;0.001	B;B	0.18871	0.023;0.001	T	0.08146	-1.0736	10	0.15499	T	0.54	-15.8031	10.5046	0.44826	0.0:0.24:0.661:0.099	.	78;78	F5H1C8;Q8IY34	.;S15A3_HUMAN	I	78	ENSP00000227880:V78I	ENSP00000227880:V78I	V	-	1	0	SLC15A3	60475368	0.127000	0.22367	0.504000	0.27639	0.828000	0.46876	0.184000	0.16939	-0.301000	0.08882	-0.323000	0.08544	GTA	C|0.968;T|0.032	0.032	strong		0.706	SLC15A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396366.1	NM_016582	
HFM1	164045	hgsc.bcm.edu	37	1	91816313	91816313	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91816313T>C	ENST00000370425.3	-	18	2286	c.2188A>G	c.(2188-2190)Aaa>Gaa	p.K730E	HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000462405.1_Intron|HFM1_ENST00000370424.3_Missense_Mutation_p.K409E	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	730					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)		GATGGATTTTTCAAGGCTCTG	0.343																																					p.K730E		Atlas-SNP	.											.	HFM1	188	.	0			c.A2188G						PASS	.						119.0	107.0	111.0					1																	91816313		1834	4085	5919	SO:0001583	missense	164045	exon18			GATTTTTCAAGGC	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.2188A>G	1.37:g.91816313T>C	ENSP00000359454:p.Lys730Glu	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	23.5	4.421719	0.83559	.	.	ENSG00000162669	ENST00000370425;ENST00000370424;ENST00000370421	T;T	0.68181	0.03;-0.31	5.36	5.36	0.76844	.	0.000000	0.47852	U	0.000204	T	0.80433	0.4622	M	0.88031	2.925	0.80722	D	1	D;D	0.64830	0.994;0.986	D;P	0.65874	0.939;0.904	D	0.83812	0.0242	10	0.54805	T	0.06	.	15.6548	0.77124	0.0:0.0:0.0:1.0	.	409;730	A6NGI5;A2PYH4	.;HFM1_HUMAN	E	730;409;414	ENSP00000359454:K730E;ENSP00000359453:K409E	ENSP00000359450:K414E	K	-	1	0	HFM1	91588901	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.939000	0.87685	2.162000	0.67917	0.377000	0.23210	AAA	.	.	none		0.343	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
KIAA0040	9674	hgsc.bcm.edu	37	1	175129933	175129933	+	Missense_Mutation	SNP	T	T	C	rs150137790		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:175129933T>C	ENST00000423313.1	-	4	753	c.217A>G	c.(217-219)Aag>Gag	p.K73E	KIAA0040_ENST00000444639.1_Missense_Mutation_p.K73E|KIAA0040_ENST00000545251.2_Missense_Mutation_p.K73E|KIAA0040_ENST00000567124.1_5'Flank	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040	0																	tccttcttcttcttcttcttc	0.502																																					p.K73E		Atlas-SNP	.											KIAA0040,colon,carcinoma,0,1	KIAA0040	2	1	0			c.A217G						PASS	.						107.0	90.0	95.0					1																	175129933		692	1591	2283	SO:0001583	missense	9674	exon3			TCTTCTTCTTCTT	D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.217A>G	1.37:g.175129933T>C	ENSP00000462172:p.Lys73Glu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	96	6	0.0625	NM_001162895	A8K9H6|Q2NKQ0	Missense_Mutation	SNP	ENST00000423313.1	37																																																																																				.	.	none		0.502	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
ATM	472	hgsc.bcm.edu	37	11	108163487	108163487	+	Silent	SNP	C	C	T	rs1800889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:108163487C>T	ENST00000452508.2	+	31	4767	c.4578C>T	c.(4576-4578)ccC>ccT	p.P1526P	ATM_ENST00000278616.4_Silent_p.P1526P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1526					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CACTTATACCCCTTGTGTATG	0.358			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			C|||	77	0.0153754	0.003	0.0288	5008	,	,		18654	0.0		0.0398	False		,,,				2504	0.0133				p.P1526P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	ATM	1657	.	0			c.C4578T						PASS	.	C		43,4359	44.6+/-78.6	0,43,2158	197.0	173.0	181.0		4578	-0.5	0.9	11	dbSNP_89	181	438,8158	133.0+/-190.5	21,396,3881	no	coding-synonymous	ATM	NM_000051.3		21,439,6039	TT,TC,CC		5.0954,0.9768,3.7006		1526/3057	108163487	481,12517	2201	4298	6499	SO:0001819	synonymous_variant	472	exon30	Familial Cancer Database	AT, Louis-Bar syndrome	TATACCCCTTGTG	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.4578C>T	11.37:g.108163487C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	147	67	0.455782	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																			C|0.972;T|0.028	0.028	strong		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
NAT6	24142	hgsc.bcm.edu	37	3	50334592	50334592	+	Silent	SNP	G	G	A	rs374560438		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50334592G>A	ENST00000443842.1	-	2	1110	c.303C>T	c.(301-303)ttC>ttT	p.F101F	NAT6_ENST00000354862.4_Silent_p.F123F|HYAL3_ENST00000415204.1_Intron|NAT6_ENST00000443094.2_Silent_p.F101F|NAT6_ENST00000417393.1_Silent_p.F101F|HYAL3_ENST00000336307.1_Intron|HYAL3_ENST00000359051.3_Intron|HYAL3_ENST00000450982.1_Intron|HYAL3_ENST00000513170.1_Intron			Q93015	NAT6_HUMAN	N-acetyltransferase 6 (GCN5-related)	101	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					cytoplasm (GO:0005737)	N-acetyltransferase activity (GO:0008080)			endometrium(3)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GGCAGAGGGGGAAGGCATCTG	0.652																																					p.F123F		Atlas-SNP	.											.	NAT6	14	.	0			c.C369T						PASS	.	G	,,,,,,,	2,4212		0,2,2105	27.0	34.0	32.0		303,303,,,,,,369	4.6	1.0	3		32	17,8403		0,17,4193	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	HYAL3,NAT6	NM_001200016.1,NM_001200018.1,NM_001200029.1,NM_001200030.1,NM_001200031.1,NM_001200032.1,NM_003549.3,NM_012191.3	,,,,,,,	0,19,6298	AA,AG,GG		0.2019,0.0475,0.1504	,,,,,,,	101/287,101/287,,,,,,123/309	50334592	19,12615	2107	4210	6317	SO:0001819	synonymous_variant	24142	exon2			GAGGGGGAAGGCA	AF040705	CCDS43095.1, CCDS56258.1	3p21.3	2011-11-16	2008-09-24		ENSG00000243477	ENSG00000243477	2.3.1.-		30252	protein-coding gene	gene with protein product		607073	"""N-acetyltransferase 6"""			11929860, 11085536	Standard	NM_012191		Approved	FUS2		Q93015	OTTHUMG00000156939	ENST00000443842.1:c.303C>T	3.37:g.50334592G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	131	74	0.564885	NM_012191	Q93014	Silent	SNP	ENST00000443842.1	37	CCDS56258.1																																																																																			.	.	weak		0.652	NAT6-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346681.1	NM_012191	
SLFNL1	200172	hgsc.bcm.edu	37	1	41482917	41482917	+	Missense_Mutation	SNP	A	A	G	rs147062455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41482917A>G	ENST00000359345.1	-	3	3666	c.1090T>C	c.(1090-1092)Tgg>Cgg	p.W364R	SLFNL1_ENST00000372611.1_Missense_Mutation_p.W305R|SLFNL1_ENST00000372613.2_Intron|SLFNL1_ENST00000302946.8_Missense_Mutation_p.W364R|SLFNL1_ENST00000439569.2_Missense_Mutation_p.W364R|SLFNL1_ENST00000397197.2_Intron	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	364							ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				TGCCTGCACCACTCCTGGATG	0.682													A|||	10	0.00199681	0.0	0.0072	5008	,	,		17107	0.0		0.005	False		,,,				2504	0.0				p.W364R		Atlas-SNP	.											.	SLFNL1	37	.	0			c.T1090C						PASS	.	A	ARG/TRP,ARG/TRP	2,4388		0,2,2193	23.0	23.0	23.0		1090,1090	5.6	1.0	1	dbSNP_134	23	14,8572		0,14,4279	no	missense,missense	SLFNL1	NM_001168247.1,NM_144990.3	101,101	0,16,6472	GG,GA,AA		0.1631,0.0456,0.1233	probably-damaging,probably-damaging	364/408,364/408	41482917	16,12960	2195	4293	6488	SO:0001583	missense	200172	exon5			TGCACCACTCCTG	BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.1090T>C	1.37:g.41482917A>G	ENSP00000352299:p.Trp364Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	51	48	0.941176	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	A	20.3	3.971902	0.74246	4.56E-4	0.001631	ENSG00000171790	ENST00000302946;ENST00000372611;ENST00000359345;ENST00000439569	T;T;T;T	0.37915	1.17;1.42;1.17;1.17	5.57	5.57	0.84162	.	0.000000	0.47852	D	0.000220	T	0.39118	0.1066	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71656	0.974;0.915	T	0.43147	-0.9409	10	0.72032	D	0.01	-16.654	12.1224	0.53900	1.0:0.0:0.0:0.0	.	305;364	Q499Z3-2;Q499Z3	.;SLNL1_HUMAN	R	364;305;364;364	ENSP00000304401:W364R;ENSP00000361694:W305R;ENSP00000352299:W364R;ENSP00000398938:W364R	ENSP00000304401:W364R	W	-	1	0	SLFNL1	41255504	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.980000	0.70516	2.117000	0.64856	0.459000	0.35465	TGG	A|0.998;G|0.002	0.002	strong		0.682	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990	
IL16	3603	hgsc.bcm.edu	37	15	81592802	81592802	+	Silent	SNP	A	A	G	rs11073001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:81592802A>G	ENST00000302987.4	+	13	3135	c.3135A>G	c.(3133-3135)acA>acG	p.T1045T	IL16_ENST00000394652.2_Silent_p.T344T|IL16_ENST00000394660.2_Silent_p.T1045T|RP11-761I4.4_ENST00000607019.1_RNA			Q14005	IL16_HUMAN	interleukin 16	1045	Interaction with HTLV-1 tax.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CCTTGGACACAGGGTTCTCGC	0.423													G|||	1406	0.280751	0.5439	0.2507	5008	,	,		16620	0.1984		0.1799	False		,,,				2504	0.135				p.T1045T		Atlas-SNP	.											.	IL16	254	.	0			c.A3135G						PASS	.	G	,,	2092,2314	591.1+/-387.5	507,1078,618	54.0	56.0	56.0		3135,1032,3135	-10.3	0.0	15	dbSNP_120	56	1718,6882	727.5+/-406.6	190,1338,2772	no	coding-synonymous,coding-synonymous,coding-synonymous	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	,,	697,2416,3390	GG,GA,AA		19.9767,47.4807,29.2942	,,	1045/1332,344/632,1045/1333	81592802	3810,9196	2203	4300	6503	SO:0001819	synonymous_variant	3603	exon14			GGACACAGGGTTC	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3135A>G	15.37:g.81592802A>G		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			A|0.697;G|0.303	0.303	strong		0.423	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
STK31	56164	hgsc.bcm.edu	37	7	23809303	23809303	+	Silent	SNP	A	A	G	rs55860134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:23809303A>G	ENST00000355870.3	+	13	1760	c.1641A>G	c.(1639-1641)gcA>gcG	p.A547A	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Silent_p.A524A|STK31_ENST00000428484.1_Silent_p.A524A|STK31_ENST00000433467.2_Silent_p.A547A	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	547						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						CAGAAGACGCAATGGATAATA	0.358													A|||	32	0.00638978	0.0	0.0115	5008	,	,		18826	0.0		0.0179	False		,,,				2504	0.0061				p.A547A		Atlas-SNP	.											.	STK31	175	.	0			c.A1641G						PASS	.	A	,,	6,4400	11.4+/-27.6	0,6,2197	186.0	181.0	183.0		1572,1641,1572	2.9	0.1	7	dbSNP_129	183	174,8426	79.8+/-142.4	1,172,4127	no	coding-synonymous,coding-synonymous,coding-synonymous	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	,,	1,178,6324	GG,GA,AA		2.0233,0.1362,1.384	,,	524/997,547/1020,524/997	23809303	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	56164	exon13			AGACGCAATGGAT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1641A>G	7.37:g.23809303A>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	107	59	0.551402	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																			A|0.989;G|0.011	0.011	strong		0.358	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
CPED1	79974	hgsc.bcm.edu	37	7	120901695	120901695	+	Intron	SNP	G	G	A	rs10953934	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:120901695G>A	ENST00000310396.5	+	19	2777				CPED1_ENST00000450913.2_Missense_Mutation_p.D774N|CPED1_ENST00000423795.1_Missense_Mutation_p.D554N	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1							endoplasmic reticulum (GO:0005783)											gttgggtgtcgatgtccagag	0.493													A|||	1780	0.355431	0.5469	0.2709	5008	,	,		15804	0.1409		0.3857	False		,,,				2504	0.3466				p.D774N		Atlas-SNP	.											.	.	.	.	0			c.G2320A						PASS	.	A	ASN/ASP,	1858,1908		446,966,471	87.0	90.0	89.0		2320,	1.9	0.0	7	dbSNP_120	89	3188,5014		645,1898,1558	yes	missense,intron	C7orf58	NM_001105533.1,NM_024913.4	23,	1091,2864,2029	AA,AG,GG		38.8686,49.3362,42.1624	,	774/784,	120901695	5046,6922	1883	4101	5984	SO:0001627	intron_variant	79974	exon18			GGTGTCGATGTCC		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2311-4586G>A	7.37:g.120901695G>A		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	218	114	0.522936	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	744	0.34065934065934067	266	0.540650406504065	120	0.3314917127071823	77	0.1346153846153846	281	0.370712401055409	A	0.557	-0.846798	0.02671	0.493362	0.388686	ENSG00000106034	ENST00000450913;ENST00000423795	T;T	0.22945	1.94;1.93	3.06	1.91	0.25777	.	.	.	.	.	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	0.41998	-0.9477	8	0.87932	D	0	.	4.9187	0.13858	0.7298:0.0:0.2702:0.0	rs10953934;rs52822357;rs57867012;rs10953934	554;774	G5E9U2;A4D0V7-2	.;.	N	774;554	ENSP00000406122:D774N;ENSP00000415573:D554N	ENSP00000415573:D554N	D	+	1	0	C7orf58	120688931	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.439000	0.06897	0.135000	0.18707	-0.254000	0.11334	GAT	G|0.648;A|0.352	0.352	strong		0.493	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
WDYHV1	55093	hgsc.bcm.edu	37	8	124448736	124448736	+	Missense_Mutation	SNP	A	A	G	rs7014678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124448736A>G	ENST00000287387.2	+	4	403	c.278A>G	c.(277-279)aAc>aGc	p.N93S	WDYHV1_ENST00000518125.1_Intron|WDYHV1_ENST00000523356.1_Missense_Mutation_p.N93S|WDYHV1_ENST00000517609.1_3'UTR|WDYHV1_ENST00000523984.1_Missense_Mutation_p.N33S	NM_018024.1	NP_060494.1	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	93			N -> S (in dbSNP:rs7014678). {ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)	p.N93S(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						GGAGGACAGAACTTCATTTAT	0.373													G|||	2054	0.410144	0.3427	0.3919	5008	,	,		18870	0.5863		0.3111	False		,,,				2504	0.4346				p.N93S		Atlas-SNP	.											WDYHV1,NS,carcinoma,0,1	WDYHV1	30	1	1	Substitution - Missense(1)	stomach(1)	c.A278G						PASS	.	G	SER/ASN	1600,2806	665.5+/-401.5	293,1014,896	228.0	189.0	202.0		278	3.9	1.0	8	dbSNP_116	202	3029,5571	663.7+/-402.1	541,1947,1812	yes	missense	WDYHV1	NM_018024.1	46	834,2961,2708	GG,GA,AA		35.2209,36.3141,35.5913	benign	93/206	124448736	4629,8377	2203	4300	6503	SO:0001583	missense	55093	exon4			GACAGAACTTCAT	AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795			25490	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 32"""	C8orf32		12477932	Standard	NM_018024		Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000287387.2:c.278A>G	8.37:g.124448736A>G	ENSP00000287387:p.Asn93Ser	Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	249	248	0.995984	NM_018024	B4DE68|Q9NW95	Missense_Mutation	SNP	ENST00000287387.2	37	CCDS6344.1	841	0.3850732600732601	140	0.2845528455284553	136	0.3756906077348066	327	0.5716783216783217	238	0.31398416886543534	G	2.520	-0.310888	0.05458	0.363141	0.352209	ENSG00000156795	ENST00000287387;ENST00000523984;ENST00000523356	T;T;T	0.15718	2.4;2.4;2.4	5.78	3.94	0.45596	Protein N-terminal glutamine amidohydrolase, alpha beta roll (1);Protein N-terminal glutamine amidohydrolase (1);	0.228594	0.49916	N	0.000137	T	0.00012	0.0000	N	0.02345	-0.59	0.09310	P	0.9999999999999971	B	0.02656	0.0	B	0.04013	0.001	T	0.46386	-0.9195	9	0.02654	T	1	-11.8569	4.7626	0.13115	0.3066:0.1497:0.5437:0.0	rs7014678;rs17856267;rs52835877;rs60247196;rs7014678	93	Q96HA8	NTAQ1_HUMAN	S	93;33;93	ENSP00000287387:N93S;ENSP00000430427:N33S;ENSP00000428615:N93S	ENSP00000287387:N93S	N	+	2	0	WDYHV1	124517917	1.000000	0.71417	1.000000	0.80357	0.612000	0.37316	1.596000	0.36718	0.346000	0.23899	-0.119000	0.15052	AAC	A|0.626;G|0.374	0.374	strong		0.373	WDYHV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381772.1	NM_018024	
MYBPC2	4606	hgsc.bcm.edu	37	19	50957397	50957397	+	Missense_Mutation	SNP	G	G	A	rs25665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50957397G>A	ENST00000357701.5	+	17	1921	c.1870G>A	c.(1870-1872)Gtc>Atc	p.V624I		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	624	Ig-like C2-type 5.		V -> I (in dbSNP:rs25665).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		CACCAACCCCGTCGGCGAGGA	0.632													g|||	1184	0.236422	0.034	0.2824	5008	,	,		18456	0.3829		0.2515	False		,,,				2504	0.3108				p.V624I		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G1870A						PASS	.	G	ILE/VAL	263,3941		7,249,1846	34.0	38.0	37.0		1870	-0.5	0.0	19	dbSNP_72	37	1778,6626		196,1386,2620	yes	missense	MYBPC2	NM_004533.3	29	203,1635,4466	AA,AG,GG		21.1566,6.2559,16.1881	benign	624/1142	50957397	2041,10567	2102	4202	6304	SO:0001583	missense	4606	exon17			AACCCCGTCGGCG		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.1870G>A	19.37:g.50957397G>A	ENSP00000350332:p.Val624Ile	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	171	95	0.555556	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	526	0.24084249084249085	19	0.03861788617886179	91	0.2513812154696133	228	0.3986013986013986	188	0.24802110817941952	g	9.583	1.124179	0.20959	0.062559	0.211566	ENSG00000086967	ENST00000357701	T	0.68181	-0.31	3.26	-0.485	0.12067	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	15.483300	0.02223	U	0.064183	T	0.00012	0.0000	L	0.58810	1.83	0.80722	P	0.0	B	0.20052	0.041	B	0.17098	0.017	T	0.15723	-1.0427	9	0.20519	T	0.43	.	3.9465	0.09350	0.0969:0.1597:0.579:0.1645	rs25665;rs2230838;rs2272322;rs12978290;rs17804237;rs52823468;rs25665	624	Q14324	MYPC2_HUMAN	I	624	ENSP00000350332:V624I	ENSP00000350332:V624I	V	+	1	0	MYBPC2	55649209	0.007000	0.16637	0.010000	0.14722	0.324000	0.28378	1.574000	0.36482	-0.057000	0.13199	-0.555000	0.04198	GTC	G|0.772;A|0.227	0.227	strong		0.632	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
PCDH9	5101	hgsc.bcm.edu	37	13	67800935	67800935	+	Silent	SNP	G	G	A	rs9571740	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:67800935G>A	ENST00000377865.2	-	1	1772	c.1638C>T	c.(1636-1638)gaC>gaT	p.D546D	PCDH9_ENST00000544246.1_Silent_p.D546D|PCDH9_ENST00000328454.5_Silent_p.D546D|PCDH9_ENST00000377861.3_Silent_p.D546D|PCDH9_ENST00000456367.1_Silent_p.D546D			Q9HC56	PCDH9_HUMAN	protocadherin 9	546	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				forebrain development (GO:0030900)|homophilic cell adhesion (GO:0007156)	cell-cell contact zone (GO:0044291)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(33)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(3)	103		Hepatocellular(98;0.0906)|Breast(118;0.107)		GBM - Glioblastoma multiforme(99;0.00819)		GGGTCCCATTGTCCCTGGCAG	0.428													G|||	2137	0.426717	0.2163	0.4697	5008	,	,		18272	0.5536		0.5298	False		,,,				2504	0.4438				p.D546D		Atlas-SNP	.											.	PCDH9	252	.	0			c.C1638T						PASS	.	G	,	1150,3256	406.4+/-333.9	138,874,1191	84.0	87.0	86.0		1638,1638	5.8	1.0	13	dbSNP_119	86	4705,3895	603.7+/-394.7	1291,2123,886	no	coding-synonymous,coding-synonymous	PCDH9	NM_020403.4,NM_203487.2	,	1429,2997,2077	AA,AG,GG		45.2907,26.1008,45.0177	,	546/1204,546/1238	67800935	5855,7151	2203	4300	6503	SO:0001819	synonymous_variant	5101	exon2			CCCATTGTCCCTG	AF169692	CCDS9443.1, CCDS9444.1	13q21.32	2010-02-22			ENSG00000184226	ENSG00000184226		"""Cadherins / Protocadherins : Non-clustered"""	8661	protein-coding gene	gene with protein product		603581				9787079	Standard	NM_020403		Approved		uc001vik.3	Q9HC56	OTTHUMG00000017040	ENST00000377865.2:c.1638C>T	13.37:g.67800935G>A		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Silent	SNP	ENST00000377865.2	37	CCDS9444.1																																																																																			G|0.559;A|0.441	0.441	strong		0.428	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487	
MSH6	2956	hgsc.bcm.edu	37	2	48027375	48027375	+	Silent	SNP	T	T	C	rs2020913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:48027375T>C	ENST00000234420.5	+	4	2405	c.2253T>C	c.(2251-2253)aaT>aaC	p.N751N	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_Silent_p.N449N|MSH6_ENST00000540021.1_Silent_p.N621N	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	751					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATGGAACAAATGGTTCTACTG	0.443			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				T|||	120	0.0239617	0.0885	0.0043	5008	,	,		20418	0.0		0.0	False		,,,				2504	0.0				p.N751N		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T2253C						PASS	.	T		266,4140	150.3+/-184.3	8,250,1945	135.0	132.0	133.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2253	-0.9	1.0	2	dbSNP_98	133	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MSH6	NM_000179.2		8,251,6244	CC,CT,TT		0.0116,6.0372,2.0529		751/1361	48027375	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AACAAATGGTTCT	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2253T>C	2.37:g.48027375T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			T|0.980;C|0.020	0.020	strong		0.443	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
FUT8	2530	hgsc.bcm.edu	37	14	66082793	66082793	+	Missense_Mutation	SNP	A	A	C	rs2229678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:66082793A>C	ENST00000360689.5	+	4	2028	c.301A>C	c.(301-303)Aag>Cag	p.K101Q	FUT8_ENST00000394586.2_Missense_Mutation_p.K101Q|FUT8_ENST00000557164.1_5'UTR|FUT8_ENST00000394585.1_Missense_Mutation_p.K101Q|FUT8_ENST00000358307.2_5'UTR	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	101			K -> Q (in dbSNP:rs2229678).		cell migration (GO:0016477)|cellular protein metabolic process (GO:0044267)|GDP-L-fucose metabolic process (GO:0046368)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|L-fucose catabolic process (GO:0042355)|N-glycan fucosylation (GO:0036071)|N-glycan processing (GO:0006491)|oligosaccharide biosynthetic process (GO:0009312)|post-translational protein modification (GO:0043687)|protein glycosylation in Golgi (GO:0033578)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|receptor metabolic process (GO:0043112)|respiratory gaseous exchange (GO:0007585)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycoprotein 6-alpha-L-fucosyltransferase activity (GO:0008424)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00109)|OV - Ovarian serous cystadenocarcinoma(108;0.00242)|BRCA - Breast invasive adenocarcinoma(234;0.0114)		TGAAAATTACAAGAAACAGAC	0.403													A|||	30	0.00599042	0.0	0.0029	5008	,	,		19356	0.0		0.0268	False		,,,				2504	0.001				p.K101Q		Atlas-SNP	.											.	FUT8	101	.	0			c.A301C						PASS	.	A	,GLN/LYS,GLN/LYS	10,4396	15.5+/-35.6	0,10,2193	88.0	88.0	88.0		,301,301	6.0	1.0	14	dbSNP_98	88	116,8484	60.6+/-122.4	0,116,4184	yes	utr-5,missense,missense	FUT8	NM_004480.4,NM_178155.2,NM_178156.2	,53,53	0,126,6377	CC,CA,AA		1.3488,0.227,0.9688	,benign,benign	,101/576,101/576	66082793	126,12880	2203	4300	6503	SO:0001583	missense	2530	exon4			AATTACAAGAAAC	AB049740	CCDS9775.1, CCDS9776.1, CCDS9776.2	14q24.3	2013-02-26			ENSG00000033170	ENSG00000033170		"""Fucosyltransferases"""	4019	protein-coding gene	gene with protein product		602589				9368041	Standard	NM_178155		Approved		uc001xio.3	Q9BYC5	OTTHUMG00000142818	ENST00000360689.5:c.301A>C	14.37:g.66082793A>C	ENSP00000353910:p.Lys101Gln	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Missense_Mutation	SNP	ENST00000360689.5	37	CCDS9775.1	28	0.01282051282051282	0	0.0	1	0.0027624309392265192	0	0.0	27	0.03562005277044855	A	12.89	2.072310	0.36566	0.00227	0.013488	ENSG00000033170	ENST00000360689;ENST00000394586;ENST00000394585	T;T;T	0.23950	1.88;1.88;1.88	6.03	6.03	0.97812	.	0.165190	0.56097	D	0.000036	T	0.03477	0.0100	N	0.13043	0.29	0.80722	D	1	B	0.16802	0.019	B	0.14023	0.01	T	0.14531	-1.0469	10	0.15066	T	0.55	-13.7514	14.5244	0.67878	1.0:0.0:0.0:0.0	rs2229678	101	Q9BYC5	FUT8_HUMAN	Q	101	ENSP00000353910:K101Q;ENSP00000378087:K101Q;ENSP00000378086:K101Q	ENSP00000345865:K101Q	K	+	1	0	FUT8	65152546	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.778000	0.75043	2.313000	0.78055	0.455000	0.32223	AAG	A|0.990;C|0.010	0.010	strong		0.403	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388631	1388631	+	Missense_Mutation	SNP	C	C	G	rs200849975	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388631C>G	ENST00000324803.4	+	1	3292	c.332C>G	c.(331-333)cCa>cGa	p.P111R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	111					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P111R(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTCACGTGCCCATGTGGAGTG	0.667													N|||	218	0.0435304	0.0287	0.0548	5008	,	,		18151	0.006		0.0487	False		,,,				2504	0.089				p.P111R		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,2	CRIPAK	185	2	1	Substitution - Missense(1)	skin(1)	c.C332G						PASS	.						193.0	146.0	162.0					4																	1388631		2203	4299	6502	SO:0001583	missense	285464	exon1			CGTGCCCATGTGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.332C>G	4.37:g.1388631C>G	ENSP00000323978:p.Pro111Arg	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	130	31	0.238462	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.610	0.297336	0.10622	.	.	ENSG00000179979	ENST00000324803	T	0.22336	1.96	0.948	-0.0113	0.13993	Post-SET domain (1);	.	.	.	.	T	0.07548	0.0190	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	9	0.12103	T	0.63	.	2.6024	0.04869	0.0:0.4564:0.3174:0.2262	.	111	Q8N1N5	CRPAK_HUMAN	R	111	ENSP00000323978:P111R	ENSP00000323978:P111R	P	+	2	0	CRIPAK	1378631	0.005000	0.15991	0.001000	0.08648	0.013000	0.08279	-1.037000	0.03557	-0.011000	0.14247	-1.737000	0.00689	CCA	C|0.935;G|0.065	0.065	strong		0.667	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
PCLO	27445	hgsc.bcm.edu	37	7	82785304	82785304	+	Missense_Mutation	SNP	G	G	A	rs61738783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:82785304G>A	ENST00000333891.9	-	2	990	c.653C>T	c.(652-654)cCg>cTg	p.P218L	PCLO_ENST00000423517.2_Missense_Mutation_p.P218L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTTAGGAATCGGCTTGGGTGG	0.443													G|||	27	0.00539137	0.0	0.0043	5008	,	,		18249	0.0		0.0169	False		,,,				2504	0.0072				p.P218L		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,+1,5	PCLO	1506	5	0			c.C653T						PASS	.	G	LEU/PRO,LEU/PRO	11,3805		0,11,1897	83.0	88.0	86.0		653,653	4.6	0.0	7	dbSNP_129	86	141,8103		0,141,3981	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	98,98	0,152,5878	AA,AG,GG		1.7103,0.2883,1.2604	benign,benign	218/5143,218/4936	82785304	152,11908	1908	4122	6030	SO:0001583	missense	27445	exon2			GGAATCGGCTTGG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.653C>T	7.37:g.82785304G>A	ENSP00000334319:p.Pro218Leu	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	238	134	0.563025	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	4.810	0.150680	0.09185	0.002883	0.017103	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16196	2.36;2.37	5.48	4.59	0.56863	.	.	.	.	.	T	0.06645	0.0170	N	0.22421	0.69	0.24930	N	0.991927	B;B	0.16396	0.017;0.017	B;B	0.08055	0.003;0.003	T	0.15464	-1.0436	9	0.87932	D	0	.	12.7097	0.57082	0.1393:0.0:0.8607:0.0	.	218;218	Q9Y6V0-5;Q9Y6V0-6	.;.	L	218	ENSP00000334319:P218L;ENSP00000388393:P218L	ENSP00000334319:P218L	P	-	2	0	PCLO	82623240	0.613000	0.27009	0.002000	0.10522	0.071000	0.16799	4.026000	0.57232	1.301000	0.44836	0.655000	0.94253	CCG	G|0.989;A|0.011	0.011	strong		0.443	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595106	140595106	+	Missense_Mutation	SNP	C	C	G	rs2910329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140595106C>G	ENST00000341948.4	+	1	1598	c.1411C>G	c.(1411-1413)Cgc>Ggc	p.R471G		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	471	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> G (in dbSNP:rs2910329).		calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGCACATCCGCAGCGTCAG	0.642																																					p.R471G		Atlas-SNP	.											.	PCDHB13	142	.	0			c.C1411G						PASS	.	G	GLY/ARG	2957,1447		987,983,232	103.0	114.0	110.0		1411	2.8	0.3	5	dbSNP_101	110	3007,5587		534,1939,1824	no	missense	PCDHB13	NM_018933.2	125	1521,2922,2056	GG,GC,CC		34.9895,32.8565,45.884	benign	471/799	140595106	5964,7034	2202	4297	6499	SO:0001583	missense	56123	exon1			CACATCCGCAGCG	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1411C>G	5.37:g.140595106C>G	ENSP00000345491:p.Arg471Gly	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	132	67	0.507576	NM_018933	A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	CCDS4255.1	730	0.3342490842490842	324	0.6585365853658537	116	0.32044198895027626	68	0.11888111888111888	222	0.2928759894459103	N	0.012	-1.682679	0.00745	0.671435	0.349895	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.00753	5.74	3.67	2.78	0.32641	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00006	-3.25	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18335	-1.0340	8	0.02654	T	1	.	8.0096	0.30344	0.0:0.1564:0.5207:0.3228	rs2910329;rs3733685;rs17844611;rs2910329	471	Q9Y5F0	PCDBD_HUMAN	G	471	ENSP00000345491:R471G	ENSP00000345491:R471G	R	+	1	0	PCDHB13	140575290	0.345000	0.24835	0.324000	0.25361	0.611000	0.37282	1.343000	0.33930	0.185000	0.20105	-0.702000	0.03669	CGC	C|0.532;G|0.468	0.468	strong		0.642	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
FCGBP	8857	hgsc.bcm.edu	37	19	40408821	40408821	+	Missense_Mutation	SNP	C	C	G	rs11083543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40408821C>G	ENST00000221347.6	-	8	4025	c.4018G>C	c.(4018-4020)Gtg>Ctg	p.V1340L		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1340	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.		V -> L (in dbSNP:rs11083543).			extracellular vesicular exosome (GO:0070062)		p.V1340L(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCAGCACCACGGGCAGCTTC	0.577													C|||	1291	0.257788	0.121	0.4092	5008	,	,		19419	0.2173		0.3608	False		,,,				2504	0.271				p.V1340L		Atlas-SNP	.											FCGBP,caecum,carcinoma,0,2	FCGBP	416	2	1	Substitution - Missense(1)	ovary(1)	c.G4018C						PASS	.	C	LEU/VAL	611,3795		45,521,1637	23.0	20.0	21.0		4018	-0.1	0.0	19	dbSNP_120	21	2976,5622		523,1930,1846	yes	missense	FCGBP	NM_003890.2	32	568,2451,3483	GG,GC,CC		34.6127,13.8675,27.5838	probably-damaging	1340/5406	40408821	3587,9417	2203	4299	6502	SO:0001583	missense	8857	exon8			GCACCACGGGCAG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4018G>C	19.37:g.40408821C>G	ENSP00000221347:p.Val1340Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	624	0.2857142857142857	76	0.15447154471544716	148	0.4088397790055249	125	0.21853146853146854	275	0.3627968337730871	C	12.27	1.888760	0.33348	0.138675	0.346127	ENSG00000090920	ENST00000221347	T	0.58797	0.31	4.95	-0.14	0.13456	von Willebrand factor, type D domain (3);	0.451564	0.18780	N	0.131345	T	0.00012	0.0000	N	0.25031	0.7	0.80722	P	0.0	B	0.25235	0.121	B	0.21151	0.033	T	0.40232	-0.9574	9	0.11485	T	0.65	.	2.6779	0.05085	0.1375:0.4356:0.268:0.1589	rs11083543;rs11083543	1340	Q9Y6R7	FCGBP_HUMAN	L	1340	ENSP00000221347:V1340L	ENSP00000221347:V1340L	V	-	1	0	FCGBP	45100661	0.000000	0.05858	0.015000	0.15790	0.023000	0.10783	-0.881000	0.04179	0.120000	0.18254	-0.182000	0.12963	GTG	.	.	weak		0.577	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
LRRC56	115399	hgsc.bcm.edu	37	11	554047	554047	+	Missense_Mutation	SNP	G	G	A	rs12793222	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:554047G>A	ENST00000270115.7	+	14	1900	c.1400G>A	c.(1399-1401)cGg>cAg	p.R467Q		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	467			R -> Q (in dbSNP:rs12793222).							kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCTCCCCGCGGTGGTCGACA	0.672													G|||	804	0.160543	0.2345	0.2522	5008	,	,		15719	0.0476		0.1918	False		,,,				2504	0.0798				p.R467Q		Atlas-SNP	.											.	LRRC56	23	.	0			c.G1400A						PASS	.	G	GLN/ARG	1047,3359	366.6+/-317.9	127,793,1283	68.0	72.0	71.0		1400	2.2	0.0	11	dbSNP_121	71	1871,6727	326.2+/-317.3	188,1495,2616	yes	missense	LRRC56	NM_198075.3	43	315,2288,3899	AA,AG,GG		21.7609,23.7631,22.4392	possibly-damaging	467/543	554047	2918,10086	2203	4299	6502	SO:0001583	missense	115399	exon14			CCCCGCGGTGGTC		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.1400G>A	11.37:g.554047G>A	ENSP00000270115:p.Arg467Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	111	65	0.585586	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	37	CCDS7700.1	395	0.18086080586080586	124	0.25203252032520324	96	0.26519337016574585	35	0.06118881118881119	140	0.18469656992084432	G	10.68	1.419586	0.25552	0.237631	0.217609	ENSG00000161328	ENST00000270115	T	0.09163	3.01	3.14	2.23	0.28157	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.42871	0.792	B	0.31946	0.138	T	0.48433	-0.9036	8	0.20046	T	0.44	-29.9114	6.2194	0.20673	0.1395:0.0:0.8605:0.0	rs12793222;rs60751468	467	Q8IYG6	LRC56_HUMAN	Q	467	ENSP00000270115:R467Q	ENSP00000270115:R467Q	R	+	2	0	LRRC56	544047	0.101000	0.21875	0.008000	0.14137	0.004000	0.04260	0.300000	0.19156	0.897000	0.36392	0.561000	0.74099	CGG	G|0.781;A|0.219	0.219	strong		0.672	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
DDI1	414301	hgsc.bcm.edu	37	11	103908735	103908735	+	Silent	SNP	G	G	A	rs1052313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:103908735G>A	ENST00000302259.3	+	1	1428	c.1185G>A	c.(1183-1185)gaG>gaA	p.E395E	PDGFD_ENST00000393158.2_Intron|PDGFD_ENST00000302251.5_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	395							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		GACGAAAAGAGCATTAAAGCA	0.423													G|||	1847	0.36881	0.1082	0.5807	5008	,	,		20665	0.3988		0.4751	False		,,,				2504	0.4305				p.E395E		Atlas-SNP	.											.	DDI1	222	.	0			c.G1185A						PASS	.	G	,,	774,3608		80,614,1497	43.0	43.0	43.0		1185,,	4.3	0.2	11	dbSNP_86	43	4005,4579		933,2139,1220	no	coding-synonymous,intron,intron	PDGFD,DDI1	NM_001001711.2,NM_025208.4,NM_033135.3	,,	1013,2753,2717	AA,AG,GG		46.6566,17.6632,36.8579	,,	395/397,,	103908735	4779,8187	2191	4292	6483	SO:0001819	synonymous_variant	414301	exon1			AAAAGAGCATTAA		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.1185G>A	11.37:g.103908735G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	174	98	0.563218	NM_001001711	Q7Z4U6|Q8WTS3	Silent	SNP	ENST00000302259.3	37	CCDS31660.1																																																																																			G|0.625;A|0.374	0.374	strong		0.423	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711	
MUC16	94025	hgsc.bcm.edu	37	19	9069792	9069792	+	Missense_Mutation	SNP	G	G	A	rs1862458	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9069792G>A	ENST00000397910.4	-	3	17857	c.17654C>T	c.(17653-17655)tCc>tTc	p.S5885F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5887	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						CCCTTCCCAGGAAGCTGTGCT	0.502													G|||	1006	0.200879	0.0938	0.2824	5008	,	,		21349	0.3254		0.167	False		,,,				2504	0.1943				p.S5885F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C17654T						PASS	.	G	PHE/SER	403,3541		18,367,1587	175.0	160.0	165.0		17654	1.9	0.0	19	dbSNP_92	165	1510,6798		137,1236,2781	yes	missense	MUC16	NM_024690.2	155	155,1603,4368	AA,AG,GG		18.1753,10.2181,15.6138	probably-damaging	5885/14508	9069792	1913,10339	1972	4154	6126	SO:0001583	missense	94025	exon3			TCCCAGGAAGCTG	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.17654C>T	19.37:g.9069792G>A	ENSP00000381008:p.Ser5885Phe	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	479	0.21932234432234432	56	0.11382113821138211	92	0.2541436464088398	205	0.3583916083916084	126	0.1662269129287599	g	4.115	0.019520	0.08006	0.102181	0.181753	ENSG00000181143	ENST00000397910	T	0.24908	1.83	1.87	1.87	0.25490	.	.	.	.	.	T	0.00012	0.0000	L	0.46157	1.445	.	.	.	D	0.65815	0.995	D	0.69824	0.966	T	0.38090	-0.9677	8	0.87932	D	0	.	7.2365	0.26072	0.0:0.0:1.0:0.0	rs1862458;rs52791883;rs56970751;rs1862458	5885	B5ME49	.	F	5885	ENSP00000381008:S5885F	ENSP00000381008:S5885F	S	-	2	0	MUC16	8930792	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-0.065000	0.11617	1.369000	0.46134	0.305000	0.20034	TCC	G|0.798;A|0.202	0.202	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ANK3	288	hgsc.bcm.edu	37	10	61832131	61832131	+	Silent	SNP	A	A	G	rs11815168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:61832131A>G	ENST00000280772.2	-	37	8699	c.8508T>C	c.(8506-8508)caT>caC	p.H2836H	ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000373827.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2836					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CTGAGGTTATATGACATGCCA	0.408													A|||	12	0.00239617	0.0	0.0014	5008	,	,		18183	0.0		0.007	False		,,,				2504	0.0041				p.H2836H		Atlas-SNP	.											.	ANK3	703	.	0			c.T8508C						PASS	.	A	,,,	12,4394	17.9+/-39.9	0,12,2191	102.0	102.0	102.0		,,,8508	0.7	1.0	10	dbSNP_120	102	55,8545	33.8+/-87.4	0,55,4245	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	0,67,6436	GG,GA,AA		0.6395,0.2724,0.5151	,,,	,,,2836/4378	61832131	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			GGTTATATGACAT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8508T>C	10.37:g.61832131A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	116	67	0.577586	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			A|0.995;G|0.005	0.005	strong		0.408	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
GIT1	28964	hgsc.bcm.edu	37	17	27901903	27901903	+	Silent	SNP	T	T	C	rs11548560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:27901903T>C	ENST00000225394.3	-	20	2351	c.2103A>G	c.(2101-2103)tcA>tcG	p.S701S	GIT1_ENST00000579937.1_3'UTR|GIT1_ENST00000581348.1_Silent_p.S687S|GIT1_ENST00000394869.3_Silent_p.S710S|RP11-68I3.2_ENST00000581474.1_RNA	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1	701	Interaction with PXN and TGFB1I1. {ECO:0000250}.				regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				READ - Rectum adenocarcinoma(3;0.0419)|Colorectal(3;0.069)		GCAGCCGCAGTGAGCTCCGCA	0.657													T|||	53	0.0105831	0.0008	0.0245	5008	,	,		16271	0.001		0.0249	False		,,,				2504	0.0092				p.S710S	Colon(81;41 1719 20078 35068)	Atlas-SNP	.											.	GIT1	84	.	0			c.A2130G						PASS	.	T	,	17,4355		0,17,2169	10.0	11.0	10.0		2130,2103	-9.3	0.7	17	dbSNP_120	10	174,8370		1,172,4099	no	coding-synonymous,coding-synonymous	GIT1	NM_001085454.1,NM_014030.3	,	1,189,6268	CC,CT,TT		2.0365,0.3888,1.4788	,	710/771,701/762	27901903	191,12725	2186	4272	6458	SO:0001819	synonymous_variant	28964	exon21			CCGCAGTGAGCTC	AF124490	CCDS11250.1, CCDS42290.1	17p11.2	2013-01-10	2008-09-05		ENSG00000108262	ENSG00000108262		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4272	protein-coding gene	gene with protein product		608434	"""G protein-coupled receptor kinase interactor 1"""			9826657, 10896954	Standard	NM_014030		Approved		uc002heg.2	Q9Y2X7	OTTHUMG00000132730	ENST00000225394.3:c.2103A>G	17.37:g.27901903T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_001085454	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Silent	SNP	ENST00000225394.3	37	CCDS11250.1																																																																																			T|0.987;C|0.013	0.013	strong		0.657	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629809	32629809	+	Missense_Mutation	SNP	C	C	T	rs701564|rs9282122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629809C>T	ENST00000399082.3	-	2	370	c.326G>A	c.(325-327)cGt>cAt	p.R109H	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.R199H|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.R199H|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.R199H|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.R199H|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	199	Beta-1.		T -> R (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:06; dbSNP:rs1130392).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)	p.R199H(1)		breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GACATCTCCACGCTGGGGAGT	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1206	0.240815	0.1997	0.2017	5008	,	,		17689	0.3135		0.1809	False		,,,				2504	0.3108				p.R199H	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	1	Substitution - Missense(1)	pancreas(1)	c.G596A						PASS	.	T	HIS/ARG	801,3603		86,629,1487	52.0	56.0	54.0		596	-1.7	0.0	6	dbSNP_86	54	1677,6923		165,1347,2788	no	missense	HLA-DQB1	NM_002123.4	29	251,1976,4275	TT,TC,CC		19.5,18.188,19.0557	benign	199/262	32629809	2478,10526	2202	4300	6502	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCTCCACGCTGGG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.326G>A	6.37:g.32629809C>T	ENSP00000382032:p.Arg109His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		484	0.2216117216117216	96	0.1951219512195122	76	0.20994475138121546	185	0.32342657342657344	127	0.16754617414248021	.	0.734	-0.778745	0.02929	0.18188	0.195	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.03004	4.08;4.08;4.08;4.08;4.08	4.52	-1.67	0.08238	.	0.285278	0.34932	N	0.003574	T	0.01124	0.0037	.	.	.	0.80722	P	0.0	B;B;B;B	0.12630	0.003;0.006;0.001;0.001	B;B;B;B	0.09377	0.004;0.004;0.003;0.004	T	0.45760	-0.9239	8	0.56958	D	0.05	.	10.0965	0.42478	0.0:0.4447:0.0:0.5553	rs701564;rs9273944;rs9273945;rs17840138;rs34600508	199;164;199;199	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	H	109;199;199;199;199;135	ENSP00000382032:R109H;ENSP00000382029:R199H;ENSP00000364080:R199H;ENSP00000407332:R199H;ENSP00000382034:R199H	ENSP00000364080:R199H	R	-	2	0	HLA-DQB1	32737787	0.000000	0.05858	0.005000	0.12908	0.045000	0.14185	-0.443000	0.06862	-0.872000	0.04037	-1.740000	0.00687	CGT	T|0.225;C|0.775	0.225	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
OR4N4	283694	hgsc.bcm.edu	37	15	22382655	22382655	+	Missense_Mutation	SNP	A	A	C	rs535034	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:22382655A>C	ENST00000328795.4	+	1	274	c.183A>C	c.(181-183)ttA>ttC	p.L61F	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	61			L -> F (in dbSNP:rs535034). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		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)		CCCTCTATTTATTTCTGGGCA	0.453																																					p.L61F		Atlas-SNP	.											.	OR4N4	108	.	0			c.A183C						PASS	.						137.0	141.0	139.0					15																	22382655		2201	4292	6493	SO:0001583	missense	283694	exon1			CTATTTATTTCTG	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.183A>C	15.37:g.22382655A>C	ENSP00000332500:p.Leu61Phe	Somatic	498	0	0		WXS	Illumina HiSeq	Phase_I	456	107	0.234649	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	563	0.25778388278388276	168	0.34146341463414637	88	0.2430939226519337	120	0.2097902097902098	187	0.24670184696569922	.	0.004	-2.313001	0.00237	.	.	ENSG00000183706	ENST00000328795	T	0.00529	6.78	3.24	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	N	0.000108	T	0.00012	0.0000	N	0.00109	-2.105	0.50632	P	1.2000000000000899E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.15521	-1.0434	9	0.02654	T	1	-7.3442	9.6854	0.40096	0.3717:0.6283:0.0:0.0	rs535034	61	Q8N0Y3	OR4N4_HUMAN	F	61	ENSP00000332500:L61F	ENSP00000332500:L61F	L	+	3	2	OR4N4	19884019	0.000000	0.05858	1.000000	0.80357	0.244000	0.25665	-1.741000	0.01837	0.182000	0.20032	-1.043000	0.02367	TTA	A|0.776;C|0.224	0.224	strong		0.453	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
TRIM51	84767	hgsc.bcm.edu	37	11	55653164	55653164	+	Missense_Mutation	SNP	G	G	A	rs10897403	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55653164G>A	ENST00000449290.2	+	2	352	c.260G>A	c.(259-261)aGc>aAc	p.S87N	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	87						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										CAATTCCTTAGCTCTGAGGAG	0.483													N|||	2125	0.424321	0.1672	0.4928	5008	,	,		21418	0.621		0.3628	False		,,,				2504	0.5838				p.S87N		Atlas-SNP	.											.	.	.	.	0			c.G260A						PASS	.	G	ASN/SER	278,1106		31,216,445	14.0	13.0	13.0		260	0.8	0.0	11	dbSNP_120	13	1132,2048		219,694,677	no	missense	SPRYD5	NM_032681.3	46	250,910,1122	AA,AG,GG		35.5975,20.0867,30.894	possibly-damaging	87/453	55653164	1410,3154	692	1590	2282	SO:0001583	missense	84767	exon2			TCCTTAGCTCTGA	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.260G>A	11.37:g.55653164G>A	ENSP00000395086:p.Ser87Asn	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	130	59	0.453846	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		850	0.3891941391941392	70	0.14227642276422764	174	0.48066298342541436	341	0.5961538461538461	265	0.3496042216358839	.	6.212	0.407193	0.11754	0.200867	0.355975	ENSG00000124900	ENST00000449290	T	0.57436	0.4	0.803	0.803	0.18691	Zinc finger, RING/FYVE/PHD-type (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.50632	P	1.1099999999997223E-4	B	0.31989	0.35	B	0.30105	0.111	T	0.45948	-0.9226	8	0.21014	T	0.42	.	7.5005	0.27516	1.0E-4:0.0:0.9999:0.0	rs10897403;rs57159508	87	Q9BSJ1	SPRY5_HUMAN	N	87	ENSP00000395086:S87N	ENSP00000395086:S87N	S	+	2	0	SPRYD5	55409740	0.000000	0.05858	0.038000	0.18304	0.141000	0.21300	-0.576000	0.05854	0.752000	0.32923	0.152000	0.16155	AGC	G|0.613;A|0.387	0.387	strong		0.483	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
POLE	5426	hgsc.bcm.edu	37	12	133208979	133208979	+	Silent	SNP	T	T	C	rs5745022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133208979T>C	ENST00000320574.5	-	45	6295	c.6252A>G	c.(6250-6252)tcA>tcG	p.S2084S	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Silent_p.S2057S	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	2084					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GAAACATCTCTGAGAGCTCAG	0.512								DNA polymerases (catalytic subunits)					C|||	3501	0.699081	0.7844	0.7464	5008	,	,		21503	0.7788		0.5656	False		,,,				2504	0.6053				p.S2084S		Atlas-SNP	.											.	POLE	416	.	0			c.A6252G						PASS	.	C		3334,1072	390.0+/-327.5	1272,790,141	139.0	137.0	138.0		6252	-10.5	0.3	12	dbSNP_114	138	5025,3575	517.8+/-379.1	1443,2139,718	yes	coding-synonymous	POLE	NM_006231.2		2715,2929,859	CC,CT,TT		41.5698,24.3305,35.7297		2084/2287	133208979	8359,4647	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon45			CATCTCTGAGAGC		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.6252A>G	12.37:g.133208979T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	172	77	0.447674	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			T|0.339;C|0.661	0.661	strong		0.512	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634303	32634303	+	Silent	SNP	G	G	A	rs1049061|rs67851506	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32634303G>A	ENST00000399082.3	-	1	126	c.82C>T	c.(82-84)Cta>Tta	p.L28L	HLA-DQB1_ENST00000399079.3_Silent_p.L28L|HLA-DQB1_ENST00000434651.2_Silent_p.L28L|HLA-DQB1_ENST00000399084.1_Silent_p.L28L|HLA-DQB1_ENST00000374943.4_Silent_p.L28L			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	28			P -> L (in allele DQB1*06:02 and allele DQB1*06:12; dbSNP:rs1049062).|P -> S (in allele DQB1*05:01 and allele DQB1*05:02). {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)"""	TCAGCCAGTAGGGAGCTCAGC	0.592									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				G|||	1068	0.213259	0.2269	0.1513	5008	,	,		8486	0.246		0.1968	False		,,,				2504	0.2219				p.L28L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C82T						PASS	.						47.0	45.0	45.0					6																	32634303		1943	4108	6051	SO:0001819	synonymous_variant	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CCAGTAGGGAGCT		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.82C>T	6.37:g.32634303G>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	27	19	0.703704	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|0.848;A|0.152	0.152	strong		0.592	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
ZNF704	619279	hgsc.bcm.edu	37	8	81733727	81733727	+	Missense_Mutation	SNP	C	C	A	rs3907424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:81733727C>A	ENST00000327835.3	-	2	334	c.103G>T	c.(103-105)Gca>Tca	p.A35S		NM_001033723.2	NP_001028895.1	Q6ZNC4	ZN704_HUMAN	zinc finger protein 704	35			A -> S (in dbSNP:rs3907424).				metal ion binding (GO:0046872)			lung(9)|skin(1)|upper_aerodigestive_tract(1)	11	all_cancers(3;8.53e-08)|all_epithelial(4;4.59e-10)|Breast(3;2.56e-06)|Lung NSC(7;2.58e-06)|all_lung(9;9.4e-06)		BRCA - Breast invasive adenocarcinoma(6;0.00401)|Epithelial(68;0.00448)|all cancers(69;0.0277)			TTGGTGTCTGCTGTTTTCACA	0.423													C|||	912	0.182109	0.4523	0.17	5008	,	,		18807	0.001		0.1471	False		,,,				2504	0.0481				p.A35S		Atlas-SNP	.											.	ZNF704	32	.	0			c.G103T						PASS	.	C	SER/ALA	1822,2584	533.6+/-373.7	379,1064,760	323.0	302.0	309.0		103	4.1	1.0	8	dbSNP_108	309	1317,7283	257.7+/-281.7	100,1117,3083	yes	missense	ZNF704	NM_001033723.2	99	479,2181,3843	AA,AC,CC		15.314,41.3527,24.135	benign	35/413	81733727	3139,9867	2203	4300	6503	SO:0001583	missense	619279	exon2			TGTCTGCTGTTTT	AK131274	CCDS34913.1	8q21.13	2008-05-02			ENSG00000164684	ENSG00000164684			32291	protein-coding gene	gene with protein product							Standard	NM_001033723		Approved	FLJ16218, Gig1	uc003yby.2	Q6ZNC4	OTTHUMG00000164733	ENST00000327835.3:c.103G>T	8.37:g.81733727C>A	ENSP00000331462:p.Ala35Ser	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	198	80	0.40404	NM_001033723	B2RNE6|B9EGW6	Missense_Mutation	SNP	ENST00000327835.3	37	CCDS34913.1	385	0.1762820512820513	217	0.4410569105691057	59	0.16298342541436464	1	0.0017482517482517483	108	0.1424802110817942	C	14.70	2.612780	0.46631	0.413527	0.15314	ENSG00000164684	ENST00000327835;ENST00000519936	D;D	0.82526	-1.62;-1.62	5.9	4.13	0.48395	.	0.532999	0.20545	N	0.090226	T	0.00012	0.0000	L	0.36672	1.1	0.34382	P	0.30673300000000003	B	0.22683	0.073	B	0.27796	0.083	T	0.28396	-1.0045	9	0.24483	T	0.36	-5.0219	10.9668	0.47416	0.0:0.8566:0.0:0.1434	rs3907424;rs52812277;rs3907424	35	Q6ZNC4	ZN704_HUMAN	S	35	ENSP00000331462:A35S;ENSP00000427715:A35S	ENSP00000331462:A35S	A	-	1	0	ZNF704	81896282	0.999000	0.42202	0.996000	0.52242	0.998000	0.95712	1.722000	0.38042	0.852000	0.35287	0.563000	0.77884	GCA	C|0.783;A|0.217	0.217	strong		0.423	ZNF704-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379964.2	NM_001033723	
TOP1MT	116447	hgsc.bcm.edu	37	8	144406705	144406705	+	Missense_Mutation	SNP	C	C	T	rs11544484	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144406705C>T	ENST00000329245.4	-	6	800	c.766G>A	c.(766-768)Gtt>Att	p.V256I	TOP1MT_ENST00000523676.1_Missense_Mutation_p.V158I|TOP1MT_ENST00000519148.1_Missense_Mutation_p.V158I|TOP1MT_ENST00000521193.1_Missense_Mutation_p.V158I	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	256			V -> I (in dbSNP:rs11544484). {ECO:0000269|PubMed:15489334}.		DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	GAGTTCTGAACGCTCTCGGTC	0.627													C|||	1381	0.275759	0.5015	0.1873	5008	,	,		18410	0.0754		0.3121	False		,,,				2504	0.2025				p.V256I		Atlas-SNP	.											.	TOP1MT	63	.	0			c.G766A						PASS	.	C	ILE/VAL	2179,2227	584.9+/-386.1	549,1081,573	133.0	112.0	119.0		766	-7.1	0.0	8	dbSNP_120	119	2426,6174	402.5+/-347.5	368,1690,2242	yes	missense	TOP1MT	NM_052963.1	29	917,2771,2815	TT,TC,CC		28.2093,49.4553,35.4067	benign	256/602	144406705	4605,8401	2203	4300	6503	SO:0001583	missense	116447	exon6			TCTGAACGCTCTC	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.766G>A	8.37:g.144406705C>T	ENSP00000328835:p.Val256Ile	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	37	CCDS6400.1	593	0.2715201465201465	252	0.5121951219512195	73	0.20165745856353592	39	0.06818181818181818	229	0.3021108179419525	C	0.012	-1.660811	0.00772	0.494553	0.282093	ENSG00000184428	ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676;ENST00000522041;ENST00000519591	T;T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24;1.24	3.55	-7.1	0.01547	DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, DNA binding, mixed alpha/beta motif, eukaryotic-type (1);DNA topoisomerase I, DNA binding, eukaryotic-type (2);	0.581986	0.13931	N	0.352874	T	0.00012	0.0000	N	0.01656	-0.775	0.46678	P	8.439999999999559E-4	B;B	0.20164	0.042;0.01	B;B	0.19666	0.026;0.02	T	0.16041	-1.0416	9	0.02654	T	1	.	9.912	0.41411	0.0:0.4416:0.0:0.5584	rs11544484;rs61685599;rs11544484	51;256	E7ESI1;Q969P6	.;TOP1M_HUMAN	I	256;158;158;158;158;158	ENSP00000328835:V256I;ENSP00000428369:V158I;ENSP00000429169:V158I;ENSP00000429181:V158I;ENSP00000427998:V158I;ENSP00000429177:V158I	ENSP00000328835:V256I	V	-	1	0	TOP1MT	144478080	1.000000	0.71417	0.013000	0.15412	0.002000	0.02628	1.413000	0.34725	-1.752000	0.01325	-1.077000	0.02231	GTT	C|0.689;T|0.311	0.311	strong		0.627	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
FOXQ1	94234	hgsc.bcm.edu	37	6	1313470	1313470	+	Silent	SNP	C	C	T	rs4435985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:1313470C>T	ENST00000296839.2	+	1	796	c.531C>T	c.(529-531)ttC>ttT	p.F177F		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	177					hair follicle morphogenesis (GO:0031069)|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)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		ACGACTGCTTCGTCAAGGTGC	0.622													C|||	956	0.190895	0.1241	0.1167	5008	,	,		7348	0.2986		0.2048	False		,,,				2504	0.2086				p.F177F		Atlas-SNP	.											FOXQ1,NS,carcinoma,0,1	FOXQ1	8	1	0			c.C531T						PASS	.	C		619,3785		37,545,1620	43.0	45.0	44.0		531	3.8	1.0	6	dbSNP_111	44	1699,6897		159,1381,2758	no	coding-synonymous	FOXQ1	NM_033260.3		196,1926,4378	TT,TC,CC		19.765,14.0554,17.8308		177/404	1313470	2318,10682	2202	4298	6500	SO:0001819	synonymous_variant	94234	exon1			CTGCTTCGTCAAG	AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379		"""Forkhead boxes"""	20951	protein-coding gene	gene with protein product		612788				11747606, 12011061	Standard	NM_033260		Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.531C>T	6.37:g.1313470C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_033260	Q9NS06	Silent	SNP	ENST00000296839.2	37	CCDS4471.1																																																																																			C|0.811;T|0.189	0.189	strong		0.622	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043410.1	NM_033260	
SEC16B	89866	hgsc.bcm.edu	37	1	177929940	177929940	+	Silent	SNP	G	G	A	rs7413442	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:177929940G>A	ENST00000308284.6	-	7	1011	c.922C>T	c.(922-924)Ctg>Ttg	p.L308L	SEC16B_ENST00000464631.2_Silent_p.L309L|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	308					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						ATGCTGTGCAGTTCAACAAGG	0.542													G|||	1392	0.277955	0.5719	0.2003	5008	,	,		19999	0.1944		0.1819	False		,,,				2504	0.1207				p.L308L		Atlas-SNP	.											.	SEC16B	92	.	0			c.C922T						PASS	.	G		2005,2213		490,1025,594	42.0	46.0	45.0		922	-0.2	0.9	1	dbSNP_116	45	1459,7027		128,1203,2912	no	coding-synonymous	SEC16B	NM_033127.2		618,2228,3506	AA,AG,GG		17.193,47.5344,27.267		308/1061	177929940	3464,9240	2109	4243	6352	SO:0001819	synonymous_variant	89866	exon7			TGTGCAGTTCAAC	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.922C>T	1.37:g.177929940G>A		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	198	107	0.540404	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			G|0.727;A|0.273	0.273	strong		0.542	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
MUC16	94025	hgsc.bcm.edu	37	19	9086819	9086819	+	Silent	SNP	G	G	A	rs1823056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9086819G>A	ENST00000397910.4	-	1	5199	c.4996C>T	c.(4996-4998)Ctg>Ttg	p.L1666L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1666	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						CTTCTTTCCAGTGCCATGTTT	0.512													G|||	952	0.190096	0.0711	0.2709	5008	,	,		22140	0.3036		0.172	False		,,,				2504	0.1953				p.L1666L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C4996T						PASS	.	G		282,3728		5,272,1728	109.0	105.0	106.0		4996	-1.9	0.0	19	dbSNP_92	106	1490,6868		127,1236,2816	no	coding-synonymous	MUC16	NM_024690.2		132,1508,4544	AA,AG,GG		17.8272,7.0324,14.3273		1666/14508	9086819	1772,10596	2005	4179	6184	SO:0001819	synonymous_variant	94025	exon1			TTTCCAGTGCCAT	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.4996C>T	19.37:g.9086819G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	151	82	0.543046	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.811;A|0.189	0.189	strong		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ALDH7A1	501	hgsc.bcm.edu	37	5	125887715	125887715	+	Missense_Mutation	SNP	T	T	G	rs12514417	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:125887715T>G	ENST00000409134.3	-	14	1534	c.1315A>C	c.(1315-1317)Aag>Cag	p.K439Q	ALDH7A1_ENST00000553117.1_Missense_Mutation_p.K375Q|RNU6-963P_ENST00000363477.1_RNA|ALDH7A1_ENST00000447989.2_Missense_Mutation_p.K402Q	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	439			K -> Q (in dbSNP:rs12514417). {ECO:0000269|PubMed:15489334}.		cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)			endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		ATTTTTACCTTGAATTTAAAG	0.388													T|||	485	0.096845	0.0219	0.1571	5008	,	,		18638	0.1667		0.1014	False		,,,				2504	0.0787				p.K439Q		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.A1315C						PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS	196,4210	122.1+/-159.5	3,190,2010	61.0	56.0	58.0		1315,1231,1204	3.5	1.0	5	dbSNP_120	58	763,7837	180.8+/-229.6	46,671,3583	yes	missense,missense,missense	ALDH7A1	NM_001182.4,NM_001201377.1,NM_001202404.1	53,53,53	49,861,5593	GG,GT,TT		8.8721,4.4485,7.3735	benign,benign,benign	439/540,411/512,402/503	125887715	959,12047	2203	4300	6503	SO:0001583	missense	501	exon14			TTACCTTGAATTT	S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"""Aldehyde dehydrogenases"""	877	protein-coding gene	gene with protein product	"""antiquitin 1"", ""26g turgor protein homolog"", ""alpha-aminoadipic semialdehyde dehydrogenase"", ""alpha-AASA dehydrogenase"", ""delta1-piperideine-6-carboxylate dehydrogenease"", ""P6c dehydrogenase"""	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.1315A>C	5.37:g.125887715T>G	ENSP00000387123:p.Lys439Gln	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001182	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Missense_Mutation	SNP	ENST00000409134.3	37	CCDS4137.2	209	0.09569597069597069	10	0.02032520325203252	48	0.13259668508287292	83	0.1451048951048951	68	0.08970976253298153	T	12.56	1.974123	0.34848	0.044485	0.088721	ENSG00000164904	ENST00000409134;ENST00000553117;ENST00000447989;ENST00000437170	D;D;D	0.91464	-2.85;-2.85;-2.85	4.71	3.52	0.40303	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.089807	0.85682	N	0.000000	T	0.02767	0.0083	L	0.46885	1.475	0.40681	P	0.01770000000000005	B;B	0.16802	0.019;0.001	B;B	0.19666	0.026;0.002	T	0.55464	-0.8137	9	0.33141	T	0.24	.	11.7136	0.51639	0.0:0.0:0.1476:0.8524	rs12514417;rs60750352;rs12514417	402;439	E7EPT3;P49419	.;AL7A1_HUMAN	Q	439;375;402;247	ENSP00000387123:K439Q;ENSP00000448593:K375Q;ENSP00000414132:K402Q	ENSP00000387123:K439Q	K	-	1	0	ALDH7A1	125915614	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	4.745000	0.62125	0.900000	0.36469	0.533000	0.62120	AAG	T|0.916;G|0.084	0.084	strong		0.388	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182	
SASH1	23328	hgsc.bcm.edu	37	6	148854984	148854984	+	Silent	SNP	G	G	A	rs2294787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:148854984G>A	ENST00000367467.3	+	15	2287	c.1812G>A	c.(1810-1812)acG>acA	p.T604T		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	604	SH3.				positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of p38MAPK cascade (GO:1900745)|protein polyubiquitination (GO:0000209)|regulation of protein autoubiquitination (GO:1902498)|regulation of protein K63-linked ubiquitination (GO:1900044)	membrane (GO:0016020)|protein complex (GO:0043234)	mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein C-terminus binding (GO:0008022)|protein complex scaffold (GO:0032947)|protein kinase binding (GO:0019901)			breast(4)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Ovarian(120;0.0169)		OV - Ovarian serous cystadenocarcinoma(155;5.63e-11)|GBM - Glioblastoma multiforme(68;0.0701)		AAGTCGGCACGTTCAAGTTCA	0.557													G|||	258	0.0515176	0.0061	0.0749	5008	,	,		18360	0.0466		0.1034	False		,,,				2504	0.0481				p.T604T		Atlas-SNP	.											.	SASH1	123	.	0			c.G1812A						PASS	.	G		88,4318	73.6+/-111.7	1,86,2116	122.0	110.0	114.0		1812	-10.4	0.0	6	dbSNP_100	114	856,7744	196.6+/-241.5	39,778,3483	no	coding-synonymous	SASH1	NM_015278.3		40,864,5599	AA,AG,GG		9.9535,1.9973,7.2582		604/1248	148854984	944,12062	2203	4300	6503	SO:0001819	synonymous_variant	23328	exon15			CGGCACGTTCAAG	AB018333	CCDS5212.1	6q24.3	2013-01-10			ENSG00000111961	ENSG00000111961		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	19182	protein-coding gene	gene with protein product		607955				9872452, 12771949	Standard	NM_015278		Approved	KIAA0790, dJ323M4.1, SH3D6A	uc003qme.1	O94885	OTTHUMG00000015773	ENST00000367467.3:c.1812G>A	6.37:g.148854984G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Silent	SNP	ENST00000367467.3	37	CCDS5212.1																																																																																			G|0.931;A|0.069	0.069	strong		0.557	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278	
PAIP2B	400961	hgsc.bcm.edu	37	2	71429687	71429687	+	Silent	SNP	C	C	G	rs13001756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:71429687C>G	ENST00000244221.8	-	2	199	c.33G>C	c.(31-33)ccG>ccC	p.P11P		NM_020459.1	NP_065192.1	Q9ULR5	PAI2B_HUMAN	poly(A) binding protein interacting protein 2B	11					negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)	translation repressor activity, nucleic acid binding (GO:0000900)			large_intestine(1)|lung(1)	2						ATTTTACACTCGGTGATGTAT	0.373													G|||	286	0.0571086	0.0787	0.0461	5008	,	,		18724	0.0099		0.0596	False		,,,				2504	0.0818				p.P11P		Atlas-SNP	.											.	PAIP2B	7	.	0			c.G33C						PASS	.	G		353,3445		14,325,1560	157.0	151.0	153.0		33	3.3	1.0	2	dbSNP_121	153	505,7775		19,467,3654	no	coding-synonymous	PAIP2B	NM_020459.1		33,792,5214	GG,GC,CC		6.099,9.2944,7.1038		11/124	71429687	858,11220	1899	4140	6039	SO:0001819	synonymous_variant	400961	exon2			TACACTCGGTGAT		CCDS46322.1	2p13.3	2007-07-16			ENSG00000124374	ENSG00000124374			29200	protein-coding gene	gene with protein product		611018				16804161	Standard	NM_020459		Approved	KIAA1155	uc002shu.2	Q9ULR5	OTTHUMG00000153284	ENST00000244221.8:c.33G>C	2.37:g.71429687C>G		Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	289	138	0.477509	NM_020459		Silent	SNP	ENST00000244221.8	37	CCDS46322.1																																																																																			C|0.934;G|0.066	0.066	strong		0.373	PAIP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330547.2	XM_376062	
ATG16L1	55054	hgsc.bcm.edu	37	2	234183368	234183368	+	Missense_Mutation	SNP	A	A	G	rs2241880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:234183368A>G	ENST00000392017.4	+	9	1155	c.898A>G	c.(898-900)Act>Gct	p.T300A	ATG16L1_ENST00000373525.5_Missense_Mutation_p.T156A|ATG16L1_ENST00000347464.5_Missense_Mutation_p.T137A|ATG16L1_ENST00000392018.1_Missense_Mutation_p.T317A|ATG16L1_ENST00000498620.1_3'UTR|SCARNA5_ENST00000516201.1_RNA|ATG16L1_ENST00000392020.4_Missense_Mutation_p.T281A	NM_001190266.1|NM_001190267.1|NM_030803.6	NP_001177195.1|NP_001177196.1|NP_110430.5	Q676U5	A16L1_HUMAN	autophagy related 16-like 1 (S. cerevisiae)	300			T -> A (associated with susceptibility to IBD10; has no effect on the stability of the protein; enhances the cleavage and the degradation mediated by activated CASP3; results in reduced autophagy and defective clearance of intestinal pathogens; dbSNP:rs2241880). {ECO:0000269|PubMed:15620219}.		autophagic vacuole assembly (GO:0000045)|negative stranded viral RNA replication (GO:0039689)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)	autophagic vacuole (GO:0005776)|autophagic vacuole membrane (GO:0000421)|axoneme (GO:0005930)	identical protein binding (GO:0042802)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(7)|prostate(3)|skin(1)	25		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0539)		Epithelial(121;1.53e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000379)|LUSC - Lung squamous cell carcinoma(224;0.00619)|Lung(119;0.00732)|GBM - Glioblastoma multiforme(43;0.11)		CAATGTGGATACTCATCCTGG	0.473													A|||	1983	0.395966	0.3101	0.3213	5008	,	,		21225	0.3224		0.5368	False		,,,				2504	0.4959				p.T300A		Atlas-SNP	.											.	ATG16L1	83	.	0			c.A898G	GRCh37	CM070026	ATG16L1	M	rs2241880	PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	1428,2978	465.9+/-354.3	234,960,1009	181.0	149.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	646,550,841,898,409	-11.4	0.0	2	dbSNP_98	160	4506,4094	592.4+/-393.0	1198,2110,992	yes	missense,missense,missense,missense,missense	ATG16L1	NM_001190266.1,NM_001190267.1,NM_017974.3,NM_030803.6,NM_198890.2	58,58,58,58,58	1432,3070,2001	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	47.6047,32.4103,45.6251	benign,benign,benign,benign,benign	216/524,184/492,281/589,300/608,137/445	234183368	5934,7072	2203	4300	6503	SO:0001583	missense	55054	exon9			GTGGATACTCATC	AK000897	CCDS2502.2, CCDS2503.2, CCDS54438.1	2q37.1	2014-02-12	2012-06-06	2005-09-13	ENSG00000085978	ENSG00000085978		"""WD repeat domain containing"""	21498	protein-coding gene	gene with protein product		610767	"""APG16 autophagy 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like (S. cerevisiae)"", ""ATG16 autophagy related 16-like 1 (S. cerevisiae)"""	APG16L, ATG16L			Standard	NM_017974		Approved	WDR30, FLJ10035, ATG16A	uc002vty.3	Q676U5	OTTHUMG00000133619	ENST00000392017.4:c.898A>G	2.37:g.234183368A>G	ENSP00000375872:p.Thr300Ala	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	162	87	0.537037	NM_030803	A3EXK9|A3EXL0|B6ZDH0|Q6IPN1|Q6UXW4|Q6ZVZ5|Q8NCY2|Q96JV5|Q9H619	Missense_Mutation	SNP	ENST00000392017.4	37	CCDS2503.2	851	0.38965201465201466	123	0.25	136	0.3756906077348066	190	0.3321678321678322	402	0.5303430079155673	A	10.98	1.504884	0.26949	0.324103	0.523953	ENSG00000085978	ENST00000392017;ENST00000347464;ENST00000444735;ENST00000373525;ENST00000419681;ENST00000392020;ENST00000392018	T;T;T;T;T;T;T	0.48522	0.88;0.92;1.09;0.99;1.71;0.81;0.91	5.71	-11.4	0.00090	WD40 repeat-like-containing domain (1);	1.946940	0.02287	N	0.069914	T	0.00012	0.0000	N	0.04203	-0.255	0.47341	P	6.049999999999667E-4	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.0;0.001;0.005;0.0;0.001	T	0.27536	-1.0071	9	0.14252	T	0.57	.	12.6604	0.56811	0.1798:0.4806:0.3396:0.0	rs2241880;rs17607702;rs52836811;rs57853061;rs2241880	254;281;156;300;137	B7ZLM5;Q676U5-2;Q676U5-4;Q676U5;A3EXL0	.;.;.;A16L1_HUMAN;.	A	300;137;173;156;137;281;317	ENSP00000375872:T300A;ENSP00000318259:T137A;ENSP00000409215:T173A;ENSP00000362625:T156A;ENSP00000398773:T137A;ENSP00000375875:T281A;ENSP00000375873:T317A	ENSP00000318259:T137A	T	+	1	0	ATG16L1	233848107	0.000000	0.05858	0.001000	0.08648	0.985000	0.73830	-0.395000	0.07287	-1.999000	0.00967	0.528000	0.53228	ACT	G|0.422;N|0.000	0.422	strong		0.473	ATG16L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257069.2	NM_017974	
ZDHHC19	131540	hgsc.bcm.edu	37	3	195938177	195938177	+	Silent	SNP	A	A	G	rs1522394	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195938177A>G	ENST00000296326.3	-	1	89	c.10T>C	c.(10-12)Tta>Cta	p.L4L	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	4						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		GCATCCGTTAAGAGTGTCATG	0.647													A|||	1350	0.269569	0.0537	0.3098	5008	,	,		16359	0.5248		0.2704	False		,,,				2504	0.2689				p.L4L		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.T10C						PASS	.	A		357,3821		19,319,1751	96.0	121.0	113.0		10	-6.1	0.0	3	dbSNP_88	113	2005,6435		224,1557,2439	no	coding-synonymous	ZDHHC19	NM_001039617.1		243,1876,4190	GG,GA,AA		23.7559,8.5448,18.7193		4/310	195938177	2362,10256	2089	4220	6309	SO:0001819	synonymous_variant	131540	exon1			CCGTTAAGAGTGT	BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958		"""Zinc fingers, DHHC-type"""	20713	protein-coding gene	gene with protein product							Standard	XR_246038		Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.10T>C	3.37:g.195938177A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_001039617	A8MSY6|B3KVI1	Silent	SNP	ENST00000296326.3	37	CCDS43190.1																																																																																			A|0.742;G|0.258	0.258	strong		0.647	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637	
RPA1	6117	hgsc.bcm.edu	37	17	1782957	1782957	+	Silent	SNP	C	C	T	rs2230930	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1782957C>T	ENST00000254719.5	+	11	1166	c.1056C>T	c.(1054-1056)tcC>tcT	p.S352S		NM_002945.3	NP_002936.1	P27694	RFA1_HUMAN	replication protein A1, 70kDa	352					base-excision repair (GO:0006284)|DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of cell proliferation (GO:0008284)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|DNA replication factor A complex (GO:0005662)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|single-stranded DNA binding (GO:0003697)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)	10						TGGACACATCCGGGAAGGTGG	0.522								Nucleotide excision repair (NER)					c|||	1357	0.270966	0.2088	0.2392	5008	,	,		22185	0.4048		0.1779	False		,,,				2504	0.3354				p.S352S		Atlas-SNP	.											.	RPA1	48	.	0			c.C1056T						PASS	.	C		776,3630	313.8+/-293.3	73,630,1500	196.0	190.0	192.0		1056	-11.1	0.1	17	dbSNP_98	192	1342,7258	261.9+/-284.1	104,1134,3062	no	coding-synonymous	RPA1	NM_002945.3		177,1764,4562	TT,TC,CC		15.6047,17.6123,16.2848		352/617	1782957	2118,10888	2203	4300	6503	SO:0001819	synonymous_variant	6117	exon11			CACATCCGGGAAG	M63488	CCDS11014.1	17p13.3	2008-02-05	2002-08-29		ENSG00000132383	ENSG00000132383			10289	protein-coding gene	gene with protein product		179835	"""replication protein A1 (70kD)"""			8454588	Standard	NM_002945		Approved	REPA1, RPA70, HSSB, RF-A, RP-A	uc002fto.2	P27694	OTTHUMG00000090579	ENST00000254719.5:c.1056C>T	17.37:g.1782957C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	91	30	0.32967	NM_002945	A8K0Y9|Q59ES9	Silent	SNP	ENST00000254719.5	37	CCDS11014.1																																																																																			C|0.802;N|0.000	.	strong		0.522	RPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207118.2	NM_002945	
MRAP2	112609	hgsc.bcm.edu	37	6	84799185	84799185	+	Silent	SNP	C	C	T	rs2875382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:84799185C>T	ENST00000257776.4	+	4	738	c.603C>T	c.(601-603)caC>caT	p.H201H		NM_138409.2	NP_612418.2	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	201					energy homeostasis (GO:0097009)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|identical protein binding (GO:0042802)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)	p.H201H(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(4)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	19						AGACCTCACACAAAGACCTGG	0.413													T|||	1749	0.349241	0.711	0.2666	5008	,	,		20311	0.1736		0.2306	False		,,,				2504	0.2219				p.H201H		Atlas-SNP	.											MRAP2,NS,carcinoma,0,1	MRAP2	40	1	1	Substitution - coding silent(1)	stomach(1)	c.C603T						PASS	.	T		2840,1566	489.9+/-361.6	915,1010,278	94.0	100.0	98.0		603	-0.5	0.0	6	dbSNP_101	98	1802,6798	732.8+/-406.9	196,1410,2694	no	coding-synonymous	MRAP2	NM_138409.2		1111,2420,2972	TT,TC,CC		20.9535,35.5424,35.6912		201/206	84799185	4642,8364	2203	4300	6503	SO:0001819	synonymous_variant	112609	exon4			CTCACACAAAGAC	AK090775	CCDS5001.1	6q14.3	2009-10-06	2008-07-16	2008-07-16	ENSG00000135324	ENSG00000135324			21232	protein-coding gene	gene with protein product		615410	"""chromosome 6 open reading frame 117"""	C6orf117			Standard	NM_138409		Approved	bA51G5.2	uc003pkg.4	Q96G30	OTTHUMG00000015121	ENST00000257776.4:c.603C>T	6.37:g.84799185C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	52	8	0.153846	NM_138409	A8K9M1|Q8IXM9|Q8N2D1	Silent	SNP	ENST00000257776.4	37	CCDS5001.1																																																																																			C|0.654;T|0.346	0.346	strong		0.413	MRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041367.1	NM_138409	
SHPRH	257218	hgsc.bcm.edu	37	6	146234644	146234644	+	Silent	SNP	G	G	A	rs9497426	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:146234644G>A	ENST00000367505.2	-	24	4560	c.4296C>T	c.(4294-4296)tgC>tgT	p.C1432C	SHPRH_ENST00000367503.3_Silent_p.C1436C|SHPRH_ENST00000275233.7_Silent_p.C1432C|SHPRH_ENST00000438092.2_Silent_p.C1436C			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1432					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		CACAGATTGGGCAAGGTTCTG	0.299													A|||	4188	0.836262	0.9622	0.8646	5008	,	,		17843	0.8095		0.7485	False		,,,				2504	0.7638				p.C1436C		Atlas-SNP	.											.	SHPRH	169	.	0			c.C4308T						PASS	.	A	,	3349,259		1555,239,10	129.0	127.0	127.0		4296,4308	4.4	1.0	6	dbSNP_119	127	6194,1950		2344,1506,222	no	coding-synonymous,coding-synonymous	SHPRH	NM_001042683.2,NM_173082.3	,	3899,1745,232	AA,AG,GG		23.944,7.1785,18.7968	,	1432/1684,1436/1660	146234644	9543,2209	1804	4072	5876	SO:0001819	synonymous_variant	257218	exon24			GATTGGGCAAGGT	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.4296C>T	6.37:g.146234644G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Silent	SNP	ENST00000367505.2	37	CCDS43513.2																																																																																			G|0.174;A|0.826	0.826	strong		0.299	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
MAN2B1	4125	hgsc.bcm.edu	37	19	12768948	12768948	+	Missense_Mutation	SNP	T	T	C	rs35836657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12768948T>C	ENST00000456935.2	-	10	1278	c.1238A>G	c.(1237-1239)aAc>aGc	p.N413S	MAN2B1_ENST00000495617.1_Intron|MAN2B1_ENST00000221363.4_Missense_Mutation_p.N412S	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	413			N -> S (in dbSNP:rs35836657). {ECO:0000269|PubMed:22161967, ECO:0000269|PubMed:9915946}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						CTCCAGCTGGTTGCACACCTG	0.682													T|||	193	0.0385383	0.0045	0.0591	5008	,	,		10943	0.0		0.1342	False		,,,				2504	0.0112				p.N413S		Atlas-SNP	.											MAN2B1,NS,carcinoma,0,1	MAN2B1	91	1	0			c.A1238G						PASS	.	T	SER/ASN,SER/ASN	88,4318		2,84,2117	23.0	28.0	26.0		1238,1235	2.9	1.0	19	dbSNP_126	26	1034,7562		65,904,3329	yes	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	46,46	67,988,5446	CC,CT,TT		12.0289,1.9973,8.6294	benign,benign	413/1012,412/1011	12768948	1122,11880	2203	4298	6501	SO:0001583	missense	4125	exon10			AGCTGGTTGCACA		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.1238A>G	19.37:g.12768948T>C	ENSP00000395473:p.Asn413Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	129	0.059065934065934064	1	0.0020325203252032522	26	0.0718232044198895	1	0.0017482517482517483	101	0.13324538258575197	T	14.77	2.635090	0.47049	0.019973	0.120289	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	T;T	0.74632	-0.86;-0.86	4.95	2.86	0.33363	Glycoside hydrolase, family 38, central domain (2);	0.585680	0.14730	N	0.301860	T	0.01661	0.0053	M	0.62723	1.935	0.23411	P	0.99773184	B;B	0.12013	0.004;0.005	B;B	0.22601	0.035;0.04	T	0.42155	-0.9468	9	0.72032	D	0.01	-15.5093	7.6038	0.28091	0.0:0.1771:0.0:0.8229	rs35836657	412;413	G5E928;O00754	.;MA2B1_HUMAN	S	413;352;412	ENSP00000395473:N413S;ENSP00000221363:N412S	ENSP00000221363:N412S	N	-	2	0	MAN2B1	12629948	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.060000	0.41394	0.259000	0.21709	0.254000	0.18369	AAC	T|0.924;C|0.076	0.076	strong		0.682	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
LTN1	26046	hgsc.bcm.edu	37	21	30339234	30339234	+	Missense_Mutation	SNP	T	T	C	rs61735768	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:30339234T>C	ENST00000361371.5	-	10	1658	c.1579A>G	c.(1579-1581)Agc>Ggc	p.S527G	LTN1_ENST00000389195.2_Missense_Mutation_p.S573G|LTN1_ENST00000389194.2_Missense_Mutation_p.S573G			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	527					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.S527G(1)		NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						TTCAATGAGCTCTTCGGCTTC	0.383													T|||	769	0.153554	0.0424	0.2233	5008	,	,		17681	0.3839		0.1233	False		,,,				2504	0.0481				p.S573G		Atlas-SNP	.											LTN1,NS,carcinoma,0,1	LTN1	141	1	1	Substitution - Missense(1)	stomach(1)	c.A1717G						PASS	.	T	GLY/SER	278,4128	154.4+/-187.8	14,250,1939	76.0	72.0	73.0		1717	4.8	0.5	21	dbSNP_129	73	978,7622	211.3+/-251.9	55,868,3377	yes	missense	LTN1	NM_015565.2	56	69,1118,5316	CC,CT,TT		11.3721,6.3096,9.6571	benign	573/1813	30339234	1256,11750	2203	4300	6503	SO:0001583	missense	26046	exon10			ATGAGCTCTTCGG	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1579A>G	21.37:g.30339234T>C	ENSP00000354977:p.Ser527Gly	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	76	33	0.434211	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		427	0.1955128205128205	21	0.042682926829268296	74	0.20441988950276244	233	0.40734265734265734	99	0.13060686015831136	T	12.03	1.814859	0.32053	0.063096	0.113721	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000389195	T;T;T	0.24723	2.18;2.19;1.84	4.83	4.83	0.62350	Armadillo-type fold (1);	0.304482	0.38164	N	0.001788	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40887	-0.9539	9	0.62326	D	0.03	.	10.1603	0.42847	0.1487:0.0:0.0:0.8513	.	527	O94822	LTN1_HUMAN	G	573;527;573	ENSP00000373846:S573G;ENSP00000354977:S527G;ENSP00000373847:S573G	ENSP00000354977:S527G	S	-	1	0	LTN1	29261105	0.005000	0.15991	0.478000	0.27316	0.651000	0.38670	1.358000	0.34102	2.145000	0.66743	0.528000	0.53228	AGC	T|0.880;C|0.120	0.120	strong		0.383	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
ATAD3B	83858	hgsc.bcm.edu	37	1	1421531	1421531	+	Silent	SNP	C	C	A	rs819976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1421531C>A	ENST00000308647.7	+	10	1121	c.1005C>A	c.(1003-1005)acC>acA	p.T335T		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	335						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCATAGCAACCAGGAACACCA	0.642													N|||	2417	0.482628	0.8502	0.3228	5008	,	,		17732	0.622		0.0924	False		,,,				2504	0.3569				p.T335T		Atlas-SNP	.											.	ATAD3B	68	.	0			c.C1005A						PASS	.	A		3215,1191		1192,831,180	79.0	91.0	87.0		1005	1.1	0.7	1	dbSNP_86	87	617,7981		35,547,3717	no	coding-synonymous	ATAD3B	NM_031921.4		1227,1378,3897	AA,AC,CC		7.1761,27.0313,29.4679		335/649	1421531	3832,9172	2203	4299	6502	SO:0001819	synonymous_variant	83858	exon10			AGCAACCAGGAAC	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1005C>A	1.37:g.1421531C>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	211	201	0.952607	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Silent	SNP	ENST00000308647.7	37	CCDS30.1																																																																																			C|0.587;A|0.413	0.413	strong		0.642	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
CTBP2	1488	hgsc.bcm.edu	37	10	126715436	126715436	+	Intron	SNP	C	C	T	rs3781411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:126715436C>T	ENST00000337195.5	-	3	458				CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.R298Q|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000494626.2_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)		CCCCTCCGCCCGCAGAAAGGC	0.632													C|||	611	0.122005	0.1089	0.2896	5008	,	,		17635	0.0456		0.1352	False		,,,				2504	0.0859				p.R298Q		Atlas-SNP	.											.	CTBP2	100	.	0			c.G893A						PASS	.	C	,,GLN/ARG	449,3957	210.5+/-231.0	18,413,1772	43.0	45.0	44.0		,,893	4.0	1.0	10	dbSNP_107	44	1127,7473	229.1+/-263.9	66,995,3239	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,43	84,1408,5011	TT,TC,CC		13.1047,10.1906,12.1175	,,probably-damaging	,,298/986	126715436	1576,11430	2203	4300	6503	SO:0001627	intron_variant	1488	exon1			TCCGCCCGCAGAA	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12129G>A	10.37:g.126715436C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	163	66	0.404908	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	260	0.11904761904761904	48	0.0975609756097561	86	0.23756906077348067	30	0.05244755244755245	96	0.1266490765171504	C	22.1	4.249659	0.80024	0.101906	0.131047	ENSG00000175029	ENST00000309035	D	0.87571	-2.27	4.88	3.96	0.45880	.	0.086330	0.44483	D	0.000446	T	0.00241	0.0007	.	.	.	0.09310	P	1.0	D	0.76494	0.999	P	0.60345	0.873	T	0.00005	-1.2543	8	0.87932	D	0	.	14.1729	0.65522	0.0:0.923:0.0:0.077	rs3781411;rs3781411	298	P56545-2	.	Q	298	ENSP00000311825:R298Q	ENSP00000311825:R298Q	R	-	2	0	CTBP2	126705426	1.000000	0.71417	0.988000	0.46212	0.723000	0.41478	3.859000	0.55987	2.423000	0.82170	0.655000	0.94253	CGG	C|0.882;T|0.118	0.118	strong		0.632	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
DNHD1	144132	hgsc.bcm.edu	37	11	6579354	6579354	+	Silent	SNP	G	G	C	rs16915382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6579354G>C	ENST00000527990.2	+	23	8829	c.8829G>C	c.(8827-8829)ctG>ctC	p.L2943L	DNHD1_ENST00000254579.6_Silent_p.L2943L			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2943					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CAGTGGCTCTGTTGGTACCCA	0.547													G|||	1144	0.228435	0.5545	0.1599	5008	,	,		18259	0.0159		0.0994	False		,,,				2504	0.1881				p.L2943L		Atlas-SNP	.											.	DNHD1	198	.	0			c.G8829C						PASS	.	G		719,665		187,345,160	76.0	66.0	69.0		8829	-0.0	0.1	11	dbSNP_123	69	420,2762		30,360,1201	no	coding-synonymous	DNHD1	NM_144666.2		217,705,1361	CC,CG,GG		13.1992,48.0491,24.9452		2943/4754	6579354	1139,3427	692	1591	2283	SO:0001819	synonymous_variant	144132	exon25			GGCTCTGTTGGTA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8829G>C	11.37:g.6579354G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.805;C|0.195	0.195	strong		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
MYBPC2	4606	hgsc.bcm.edu	37	19	50940778	50940778	+	Splice_Site	SNP	C	C	T	rs61731791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50940778C>T	ENST00000357701.5	+	6	563	c.512C>T	c.(511-513)aCg>aTg	p.T171M		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	171					cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		TTCAAGCGTACGTAAGTGACC	0.582													N|||	127	0.0253594	0.0015	0.0807	5008	,	,		18973	0.001		0.0328	False		,,,				2504	0.0358				p.T171M		Atlas-SNP	.											MYBPC2_ENST00000357701,colon,carcinoma,0,1	MYBPC2	103	1	0			c.C512T						PASS	.		MET/THR	27,3813		0,27,1893	63.0	59.0	60.0		512	1.3	0.2	19	dbSNP_129	60	342,7896		4,334,3781	yes	missense-near-splice	MYBPC2	NM_004533.3	81	4,361,5674	TT,TC,CC		4.1515,0.7031,3.0551	benign	171/1142	50940778	369,11709	1920	4119	6039	SO:0001630	splice_region_variant	4606	exon6			AGCGTACGTAAGT		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.512+1C>T	19.37:g.50940778C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	58	0.026556776556776556	0	0.0	31	0.0856353591160221	1	0.0017482517482517483	26	0.03430079155672823	.	3.029	-0.200052	0.06219	0.007031	0.041515	ENSG00000086967	ENST00000357701	T	0.58506	0.33	3.53	1.28	0.21552	.	1.022040	0.07915	U	0.974822	T	0.02807	0.0084	L	0.52011	1.625	0.20638	N	0.999877	B	0.26041	0.14	B	0.13407	0.009	T	0.04005	-1.0985	10	0.48119	T	0.1	.	8.917	0.35587	0.0:0.7773:0.0:0.2227	rs61731791	171	Q14324	MYPC2_HUMAN	M	171	ENSP00000350332:T171M	ENSP00000350332:T171M	T	+	2	0	MYBPC2	55632590	0.140000	0.22579	0.183000	0.23137	0.081000	0.17604	0.184000	0.16939	-0.000000	0.14550	-1.512000	0.00943	ACG	C|0.969;T|0.031	0.031	strong		0.582	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	Missense_Mutation
RING1	6015	hgsc.bcm.edu	37	6	33177782	33177782	+	Silent	SNP	C	C	T	rs61736933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33177782C>T	ENST00000374656.4	+	4	538	c.330C>T	c.(328-330)atC>atT	p.I110I	RING1_ENST00000478431.1_3'UTR|MIR219-1_ENST00000362166.1_RNA	NM_002931.3	NP_002922.2	Q06587	RING1_HUMAN	ring finger protein 1	110	Necessary for transcriptional repression. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|camera-type eye morphogenesis (GO:0048593)|histone H2A monoubiquitination (GO:0035518)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(5)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|skin(4)	17						TCTCTAAGATCTATCCTAGCC	0.572													C|||	30	0.00599042	0.0015	0.0101	5008	,	,		21397	0.0		0.0169	False		,,,				2504	0.0041				p.I110I		Atlas-SNP	.											RING1,NS,carcinoma,+1,1	RING1	40	1	0			c.C330T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	71.0	63.0	66.0		330	1.2	1.0	6	dbSNP_129	66	113,8487	60.6+/-122.4	0,113,4187	no	coding-synonymous	RING1	NM_002931.3		0,127,6376	TT,TC,CC		1.314,0.3177,0.9765		110/407	33177782	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	6015	exon4			TAAGATCTATCCT		CCDS34424.1	6p21.3	2013-01-09			ENSG00000204227	ENSG00000204227		"""RING-type (C3HC4) zinc fingers"""	10018	protein-coding gene	gene with protein product		602045				1906426	Standard	NM_002931		Approved	RNF1	uc003odk.3	Q06587	OTTHUMG00000031278	ENST00000374656.4:c.330C>T	6.37:g.33177782C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	109	56	0.513761	NM_002931	A8JZZ0|Q5JP96|Q5SQW2|Q86V19	Silent	SNP	ENST00000374656.4	37	CCDS34424.1																																																																																			C|0.991;T|0.009	0.009	strong		0.572	RING1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076609.2		
ZNF443	10224	hgsc.bcm.edu	37	19	12541542	12541542	+	Missense_Mutation	SNP	C	C	T	rs74181783|rs34507016|rs386806904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12541542C>T	ENST00000301547.5	-	4	1641	c.1444G>A	c.(1444-1446)Ggg>Agg	p.G482R	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	482					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CAGGCTTTCCCAAGTTTGCAT	0.403													.|||	1958	0.390974	0.4781	0.3084	5008	,	,		20938	0.3462		0.2793	False		,,,				2504	0.4928				p.G482R		Atlas-SNP	.											.	ZNF443	63	.	0			c.G1444A						PASS	.	T	ARG/GLY	1668,2736		403,862,937	63.0	68.0	66.0		1444	0.2	0.0	19	dbSNP_126	66	1880,6720		353,1174,2773	no	missense	ZNF443	NM_005815.4	125	756,2036,3710	TT,TC,CC		21.8605,37.8747,27.2839	benign	482/672	12541542	3548,9456	2202	4300	6502	SO:0001583	missense	10224	exon4			CTTTCCCAAGTTT	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1444G>A	19.37:g.12541542C>T	ENSP00000301547:p.Gly482Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	655	0.2999084249084249	199	0.40447154471544716	97	0.26795580110497236	182	0.3181818181818182	177	0.23350923482849603	T	13.08	2.131227	0.37630	0.378747	0.218605	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.09073	3.02	1.26	0.171	0.15026	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.84846	2.72	0.48696	P	3.1000000000003247E-4	D	0.89917	1.0	D	0.97110	1.0	T	0.39522	-0.9610	8	0.72032	D	0.01	.	7.0991	0.25327	0.0:0.8344:0.0:0.1656	rs34507016	482	Q9Y2A4	ZN443_HUMAN	R	482	ENSP00000301547:G482R	ENSP00000301547:G482R	G	-	1	0	ZNF443	12402542	0.931000	0.31567	0.021000	0.16686	0.010000	0.07245	0.709000	0.25734	0.122000	0.18314	-0.359000	0.07587	GGG	TACGTT|0.500;CAAGTG|0.500	.	alt		0.403	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
MYO3A	53904	hgsc.bcm.edu	37	10	26310506	26310506	+	Silent	SNP	C	C	T	rs34067308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:26310506C>T	ENST00000265944.5	+	8	826	c.660C>T	c.(658-660)gcC>gcT	p.A220A	MYO3A_ENST00000543632.1_Silent_p.A220A|MYO3A_ENST00000376302.1_Silent_p.A220A	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						GTATCACGGCCATTGAGCTGG	0.473													C|||	176	0.0351438	0.0151	0.0504	5008	,	,		19005	0.001		0.0954	False		,,,				2504	0.0245				p.A220A		Atlas-SNP	.											.	MYO3A	371	.	0			c.C660T						PASS	.	C		132,4274	95.3+/-134.0	3,126,2074	193.0	160.0	171.0		660	1.6	1.0	10	dbSNP_126	171	857,7743	194.1+/-239.6	47,763,3490	no	coding-synonymous	MYO3A	NM_017433.4		50,889,5564	TT,TC,CC		9.9651,2.9959,7.6042		220/1617	26310506	989,12017	2203	4300	6503	SO:0001819	synonymous_variant	53904	exon8			CACGGCCATTGAG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.660C>T	10.37:g.26310506C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			C|0.933;T|0.067	0.067	strong		0.473	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
DCDC2	51473	hgsc.bcm.edu	37	6	24357796	24357796	+	Silent	SNP	G	G	A	rs33943110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:24357796G>A	ENST00000378454.3	-	1	484	c.183C>T	c.(181-183)gcC>gcT	p.A61A	KAAG1_ENST00000274766.1_5'UTR	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	61	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TGTTCCTGACGGCCCCAAAGG	0.622													G|||	161	0.0321486	0.0068	0.0605	5008	,	,		16785	0.002		0.0606	False		,,,				2504	0.0481				p.A61A		Atlas-SNP	.											.	DCDC2	53	.	0			c.C183T						PASS	.	G	,,	58,4348		1,56,2146	38.0	38.0	38.0		183,183,	-11.1	0.0	6	dbSNP_126	38	573,8027		23,527,3750	no	coding-synonymous,coding-synonymous,utr-5	DCDC2,KAAG1	NM_001195610.1,NM_016356.3,NM_181337.3	,,	24,583,5896	AA,AG,GG		6.6628,1.3164,4.8516	,,	61/477,61/477,	24357796	631,12375	2203	4300	6503	SO:0001819	synonymous_variant	51473	exon2			CCTGACGGCCCCA	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.183C>T	6.37:g.24357796G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Silent	SNP	ENST00000378454.3	37	CCDS4550.1	67	0.030677655677655676	3	0.006097560975609756	19	0.052486187845303865	2	0.0034965034965034965	43	0.05672823218997362	G	6.402	0.442341	0.12164	0.013164	0.066628	ENSG00000146038	ENST00000436313	.	.	.	5.56	-11.1	0.00147	.	.	.	.	.	T	0.23370	0.0565	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51593	-0.8686	4	.	.	.	-12.4188	6.3844	0.21552	0.2367:0.4667:0.1801:0.1165	rs33943110;rs33943110	.	.	.	L	29	.	.	P	-	2	0	DCDC2	24465775	0.000000	0.05858	0.027000	0.17364	0.687000	0.40016	-3.787000	0.00366	-3.168000	0.00226	-1.692000	0.00727	CCG	G|0.955;A|0.045	0.045	strong		0.622	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
PI16	221476	hgsc.bcm.edu	37	6	36926952	36926952	+	Missense_Mutation	SNP	A	A	G	rs113848006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36926952A>G	ENST00000373674.3	+	2	531	c.203A>G	c.(202-204)aAg>aGg	p.K68R		NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	68	SCP.				negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCTTCGCCAAGGCCTACGCA	0.652													A|||	80	0.0159744	0.0477	0.0072	5008	,	,		17606	0.0		0.0119	False		,,,				2504	0.0				p.K68R		Atlas-SNP	.											.	PI16	50	.	0			c.A203G						PASS	.	A	ARG/LYS,ARG/LYS	163,4237		2,159,2039	23.0	19.0	21.0		203,203	4.1	1.0	6	dbSNP_132	21	55,8541		0,55,4243	yes	missense,missense	PI16	NM_001199159.1,NM_153370.2	26,26	2,214,6282	GG,GA,AA		0.6398,3.7045,1.6774	probably-damaging,probably-damaging	68/464,68/464	36926952	218,12778	2200	4298	6498	SO:0001583	missense	221476	exon3			TCGCCAAGGCCTA		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.203A>G	6.37:g.36926952A>G	ENSP00000362778:p.Lys68Arg	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	38	0.0173992673992674	28	0.056910569105691054	3	0.008287292817679558	0	0.0	7	0.009234828496042216	A	23.5	4.418054	0.83449	0.037045	0.006398	ENSG00000164530	ENST00000536757;ENST00000373674	T	0.07800	3.16	5.29	4.09	0.47781	CAP domain (3);	0.128596	0.52532	D	0.000078	T	0.05914	0.0154	N	0.20685	0.6	0.31202	N	0.699673	D;P	0.57257	0.979;0.892	P;P	0.60609	0.877;0.57	T	0.18871	-1.0323	10	0.45353	T	0.12	.	11.8387	0.52342	0.8531:0.1469:0.0:0.0	.	68;68	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	R	68	ENSP00000362778:K68R	ENSP00000362778:K68R	K	+	2	0	PI16	37034930	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	3.619000	0.54196	0.809000	0.34255	0.418000	0.28097	AAG	A|0.982;G|0.018	0.018	strong		0.652	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
VPS13B	157680	hgsc.bcm.edu	37	8	100443885	100443885	+	Missense_Mutation	SNP	C	C	T	rs61753722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:100443885C>T	ENST00000358544.2	+	22	3314	c.3203C>T	c.(3202-3204)aCa>aTa	p.T1068I	VPS13B_ENST00000357162.2_Missense_Mutation_p.T1068I|VPS13B_ENST00000395996.1_Missense_Mutation_p.T1068I	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1068					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)			AAGCATCTCACACTACAGGTA	0.308													C|||	55	0.0109824	0.0	0.013	5008	,	,		15552	0.0		0.006	False		,,,				2504	0.0409				p.T1068I	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.C3203T						PASS	.	C	ILE/THR,ILE/THR	5,4401	8.1+/-20.4	0,5,2198	59.0	64.0	62.0		3203,3203	4.4	1.0	8	dbSNP_129	62	89,8511	49.4+/-109.1	1,87,4212	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	89,89	1,92,6410	TT,TC,CC		1.0349,0.1135,0.7227	probably-damaging,probably-damaging	1068/4023,1068/3998	100443885	94,12912	2203	4300	6503	SO:0001583	missense	157680	exon22			ATCTCACACTACA	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.3203C>T	8.37:g.100443885C>T	ENSP00000351346:p.Thr1068Ile	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	19	7	0.368421	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	11.46	1.645534	0.29246	0.001135	0.010349	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.46819	0.86;0.86;0.86	4.41	4.41	0.53225	.	0.119576	0.52532	D	0.000061	T	0.45054	0.1323	N	0.24115	0.695	0.53688	D	0.999974	D;D;D;B	0.71674	0.986;0.986;0.998;0.291	P;P;D;B	0.80764	0.558;0.675;0.994;0.143	T	0.42137	-0.9469	10	0.16420	T	0.52	.	17.3622	0.87354	0.0:1.0:0.0:0.0	rs61753722	1067;1068;1068;1068	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	I	1068	ENSP00000349685:T1068I;ENSP00000351346:T1068I;ENSP00000379318:T1068I	ENSP00000349685:T1068I	T	+	2	0	VPS13B	100513061	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.920000	0.75799	2.154000	0.67381	0.555000	0.69702	ACA	C|0.994;T|0.006	0.006	strong		0.308	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
ASPSCR1	79058	hgsc.bcm.edu	37	17	79941511	79941511	+	Silent	SNP	C	C	T	rs11539917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79941511C>T	ENST00000306739.4	+	3	337	c.240C>T	c.(238-240)ccC>ccT	p.P80P	ASPSCR1_ENST00000581647.1_Silent_p.P80P|ASPSCR1_ENST00000580534.1_Silent_p.P3P|ASPSCR1_ENST00000306729.7_Silent_p.P80P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	80					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			AGATGGTGCCCGCTTCCCGGA	0.622			T	TFE3	alveolar soft part sarcoma								C|||	63	0.0125799	0.0015	0.0231	5008	,	,		12243	0.0		0.0209	False		,,,				2504	0.0245				p.P80P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"""alveolar soft part sarcoma chromosome region, candidate 1"""		M	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	0			c.C240T						PASS	.	C		22,4384	29.0+/-57.7	0,22,2181	80.0	63.0	69.0		240	-8.0	0.0	17	dbSNP_120	69	162,8438	76.3+/-139.0	2,158,4140	no	coding-synonymous	ASPSCR1	NM_024083.2		2,180,6321	TT,TC,CC		1.8837,0.4993,1.4147		80/554	79941511	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon3			GGTGCCCGCTTCC	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.240C>T	17.37:g.79941511C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			C|0.988;T|0.012	0.012	strong		0.622	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	
CCDC171	203238	hgsc.bcm.edu	37	9	15784560	15784560	+	Silent	SNP	A	A	G	rs55780067	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:15784560A>G	ENST00000380701.3	+	21	3463	c.3135A>G	c.(3133-3135)gcA>gcG	p.A1045A	CCDC171_ENST00000297641.3_Silent_p.A1045A	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1045																	TAAATAATGCATTACTTCGGG	0.388													A|||	126	0.0251597	0.0008	0.0202	5008	,	,		18163	0.0		0.0557	False		,,,				2504	0.0562				p.A1045A		Atlas-SNP	.											.	.	.	.	0			c.A3135G						PASS	.	A		37,4369	41.6+/-74.8	0,37,2166	93.0	82.0	86.0		3135	-2.1	1.0	9	dbSNP_129	86	427,8173	132.3+/-190.0	11,405,3884	no	coding-synonymous	C9orf93	NM_173550.2		11,442,6050	GG,GA,AA		4.9651,0.8398,3.5676		1045/1327	15784560	464,12542	2203	4300	6503	SO:0001819	synonymous_variant	203238	exon21			TAATGCATTACTT	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.3135A>G	9.37:g.15784560A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Silent	SNP	ENST00000380701.3	37	CCDS6481.1	49	0.022435897435897436	0	0.0	9	0.024861878453038673	0	0.0	40	0.052770448548812667	A	9.759	1.169548	0.21621	0.008398	0.049651	ENSG00000164989	ENST00000449575;ENST00000432954	.	.	.	5.04	-2.06	0.07298	.	.	.	.	.	T	0.08758	0.0217	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.13255	-1.0516	4	.	.	.	-5.6568	2.304	0.04169	0.5751:0.1174:0.1948:0.1127	rs55780067;rs61745611	.	.	.	R	285;99	.	.	H	+	2	0	C9orf93	15774560	0.853000	0.29707	0.984000	0.44739	0.972000	0.66771	-0.078000	0.11375	-0.559000	0.06110	-0.266000	0.10368	CAT	A|0.966;G|0.034	0.034	strong		0.388	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100846936	100846936	+	Silent	SNP	A	A	G	rs654593	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:100846936A>G	ENST00000298815.8	+	20	2007	c.2004A>G	c.(2002-2004)ccA>ccG	p.P668P	ARHGAP42_ENST00000524892.2_Silent_p.P634P	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	668	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TTGCAACCCCATCATCTTCCA	0.473													G|||	2874	0.573882	0.2511	0.6081	5008	,	,		20996	0.997		0.4344	False		,,,				2504	0.6933				p.P668P		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2004G						PASS	.	G		471,913		83,305,304	54.0	43.0	46.0		2004	-7.1	0.1	11	dbSNP_83	46	1401,1781		313,775,503	no	coding-synonymous	ARHGAP42	NM_152432.2		396,1080,807	GG,GA,AA		44.0289,34.0318,40.9987		668/875	100846936	1872,2694	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			AACCCCATCATCT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2004A>G	11.37:g.100846936A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.462;G|0.538	0.538	strong		0.473	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
EXD1	161829	hgsc.bcm.edu	37	15	41476209	41476209	+	Missense_Mutation	SNP	T	T	C	rs522063	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:41476209T>C	ENST00000314992.5	-	10	1655	c.1465A>G	c.(1465-1467)Act>Gct	p.T489A	EXD1_ENST00000458580.2_Missense_Mutation_p.T547A	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	489			T -> A (in dbSNP:rs522063). {ECO:0000269|PubMed:14702039}.				3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						GAAACCACAGTCTTTCTGATA	0.433													C|||	4095	0.817692	0.7776	0.8314	5008	,	,		21014	0.9861		0.7286	False		,,,				2504	0.7802				p.T489A		Atlas-SNP	.											.	EXD1	52	.	0			c.A1465G						PASS	.	C	ALA/THR	3355,1051	385.6+/-325.8	1264,827,112	110.0	104.0	106.0		1465	-8.2	0.0	15	dbSNP_83	106	6284,2316	387.9+/-342.4	2279,1726,295	yes	missense	EXD1	NM_152596.2	58	3543,2553,407	CC,CT,TT		26.9302,23.8538,25.8881	benign	489/515	41476209	9639,3367	2203	4300	6503	SO:0001583	missense	161829	exon10			CCACAGTCTTTCT	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.1465A>G	15.37:g.41476209T>C	ENSP00000321029:p.Thr489Ala	Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	161	161	1	NM_152596	A8K909|B7Z839|Q6ZW94	Missense_Mutation	SNP	ENST00000314992.5	37	CCDS10072.1	1788	0.8186813186813187	370	0.7520325203252033	290	0.8011049723756906	569	0.9947552447552448	559	0.737467018469657	C	0.004	-2.313693	0.00235	0.761462	0.730698	ENSG00000178997	ENST00000314992;ENST00000458580	T;T	0.34667	1.35;1.35	5.19	-8.2	0.01045	.	0.875220	0.09993	N	0.729474	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.34950	-0.9808	9	0.02654	T	1	-8.1884	5.3328	0.15942	0.1737:0.1451:0.086:0.5952	rs522063;rs16971593;rs52831687;rs56571544;rs57762649;rs522063	547;489;287	B7Z839;Q8NHP7;Q8NHP7-2	.;EXD1_HUMAN;.	A	489;547	ENSP00000321029:T489A;ENSP00000415056:T547A	ENSP00000321029:T489A	T	-	1	0	EXD1	39263501	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.271000	0.01166	-1.897000	0.01101	-1.551000	0.00897	ACT	T|0.221;C|0.779	0.779	strong		0.433	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
DCLRE1B	64858	hgsc.bcm.edu	37	1	114448389	114448389	+	Missense_Mutation	SNP	C	C	T	rs11552449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:114448389C>T	ENST00000369563.3	+	1	627	c.181C>T	c.(181-183)Cac>Tac	p.H61Y	AP4B1_ENST00000369569.1_5'Flank|AP4B1_ENST00000369566.3_5'Flank|DCLRE1B_ENST00000466480.1_3'UTR|AP4B1_ENST00000369567.1_5'Flank|AP4B1_ENST00000256658.4_5'Flank	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	61			H -> Y (in dbSNP:rs11552449). {ECO:0000269|Ref.2}.		cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTTGCATCGTCACCTACAGGT	0.592								Other identified genes with known or suspected DNA repair function			OREG0004772	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	C|||	1213	0.242212	0.0151	0.3833	5008	,	,		16208	0.5873		0.1909	False		,,,				2504	0.1462				p.H61Y		Atlas-SNP	.											.	DCLRE1B	36	.	0			c.C181T						PASS	.	C	TYR/HIS	185,4221	116.7+/-154.6	9,167,2027	45.0	42.0	43.0		181	3.6	0.3	1	dbSNP_120	43	1495,7105	282.5+/-295.6	130,1235,2935	yes	missense	DCLRE1B	NM_022836.3	83	139,1402,4962	TT,TC,CC		17.3837,4.1988,12.9171	benign	61/533	114448389	1680,11326	2203	4300	6503	SO:0001583	missense	64858	exon1			CATCGTCACCTAC	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"""APOLLO"", ""PSO2 homolog (S. cerevisiae)"""	609683	"""DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"""				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.181C>T	1.37:g.114448389C>T	ENSP00000358576:p.His61Tyr	Somatic	79	0	0	1458	WXS	Illumina HiSeq	Phase_I	84	47	0.559524	NM_022836	Q9H9E5	Missense_Mutation	SNP	ENST00000369563.3	37	CCDS866.1	604	0.2765567765567766	14	0.028455284552845527	111	0.30662983425414364	334	0.583916083916084	145	0.19129287598944592	C	11.60	1.687518	0.29962	0.041988	0.173837	ENSG00000118655	ENST00000369563	T	0.76186	-1.0	5.56	3.57	0.40892	Beta-lactamase-like (1);	0.798476	0.12346	N	0.477046	T	0.34279	0.0892	N	0.14661	0.345	0.80722	P	0.0	B	0.25850	0.136	B	0.35182	0.197	T	0.09487	-1.0672	9	0.02654	T	1	-4.4801	8.133	0.31037	0.3264:0.5989:0.0:0.0747	rs11552449;rs12022378;rs52822912;rs12022378	61	Q9H816	DCR1B_HUMAN	Y	61	ENSP00000358576:H61Y	ENSP00000358576:H61Y	H	+	1	0	DCLRE1B	114249912	0.995000	0.38212	0.269000	0.24586	0.677000	0.39632	3.647000	0.54403	1.337000	0.45525	0.561000	0.74099	CAC	C|0.806;G|0.000;T|0.194	0.194	strong		0.592	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836	
DCP2	167227	hgsc.bcm.edu	37	5	112349109	112349109	+	Silent	SNP	C	C	T	rs149633478	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:112349109C>T	ENST00000389063.2	+	11	1389	c.1191C>T	c.(1189-1191)ttC>ttT	p.F397F	DCP2_ENST00000515408.1_Silent_p.F362F|DCP2_ENST00000543319.1_Silent_p.F186F	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	397					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		ATTGCAAGTTCCCCTTTTCAT	0.418													C|||	9	0.00179712	0.0008	0.0	5008	,	,		19749	0.0		0.001	False		,,,				2504	0.0072				p.F397F		Atlas-SNP	.											.	DCP2	34	.	0			c.C1191T						PASS	.	C	,	0,4404		0,0,2202	233.0	204.0	214.0		1086,1191	2.8	1.0	5	dbSNP_134	214	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	DCP2	NM_001242377.1,NM_152624.5	,	0,3,6499	TT,TC,CC		0.0349,0.0,0.0231	,	362/386,397/421	112349109	3,13001	2202	4300	6502	SO:0001819	synonymous_variant	167227	exon11			CAAGTTCCCCTTT	AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"""Nudix motif containing"""	24452	protein-coding gene	gene with protein product	"""nudix (nucleoside diphosphate linked moiety X)-type motif 20"", ""M(7)GpppN-mRNA hydrolase"""	609844	"""DCP2 decapping enzyme homolog (S. cerevisiae)"""			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.1191C>T	5.37:g.112349109C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	81	36	0.444444	NM_152624	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Silent	SNP	ENST00000389063.2	37	CCDS34210.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	c	9.005	0.981066	0.18812	0.0	3.49E-4	ENSG00000172795	ENST00000513585	.	.	.	5.83	2.76	0.32466	.	.	.	.	.	T	0.54598	0.1868	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43523	-0.9386	4	.	.	.	.	6.4401	0.21845	0.0:0.6123:0.1279:0.2598	.	.	.	.	S	379	.	.	P	+	1	0	DCP2	112377008	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	0.796000	0.26986	0.242000	0.21303	0.552000	0.68991	CCC	C|0.999;T|0.001	0.001	strong		0.418	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624	
GPR149	344758	hgsc.bcm.edu	37	3	154146922	154146922	+	Silent	SNP	A	A	G	rs34792862	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:154146922A>G	ENST00000389740.2	-	1	582	c.483T>C	c.(481-483)agT>agC	p.S161S		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	161					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			AGAGCAGCAGACTGGCTGCCC	0.642													A|||	814	0.16254	0.112	0.1974	5008	,	,		14601	0.246		0.1392	False		,,,				2504	0.1442				p.S161S		Atlas-SNP	.											.	GPR149	134	.	0			c.T483C						PASS	.	A		464,3572		20,424,1574	22.0	27.0	25.0		483	-2.7	0.9	3	dbSNP_126	25	1177,7171		88,1001,3085	no	coding-synonymous	GPR149	NM_001038705.1		108,1425,4659	GG,GA,AA		14.0992,11.4965,13.251		161/732	154146922	1641,10743	2018	4174	6192	SO:0001819	synonymous_variant	344758	exon1			CAGCAGACTGGCT	AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.483T>C	3.37:g.154146922A>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	63	21	0.333333	NM_001038705		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			A|0.841;G|0.159	0.159	strong		0.642	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580	
C10orf71	118461	hgsc.bcm.edu	37	10	50531524	50531524	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50531524C>T	ENST00000374144.3	+	3	1222	c.934C>T	c.(934-936)Cta>Tta	p.L312L	C10orf71_ENST00000323868.4_Silent_p.L312L			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	312								p.L312I(2)		endometrium(1)	1						CACGACCTTGCTAAGAGAACC	0.577																																					p.L312L		Atlas-SNP	.											C10orf71_ENST00000374144,NS,carcinoma,0,2	C10orf71	179	2	2	Substitution - Missense(2)	prostate(2)	c.C934T						scavenged	.						68.0	76.0	74.0					10																	50531524		2055	4201	6256	SO:0001819	synonymous_variant	118461	exon3			ACCTTGCTAAGAG	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.934C>T	10.37:g.50531524C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	55	2	0.0363636	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			.	.	none		0.577	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
TEKT3	64518	hgsc.bcm.edu	37	17	15234895	15234895	+	Missense_Mutation	SNP	C	C	T	rs7226363	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15234895C>T	ENST00000395930.1	-	3	194	c.8G>A	c.(7-9)cGt>cAt	p.R3H	TEKT3_ENST00000338696.2_Missense_Mutation_p.R3H	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	3			R -> H (in dbSNP:rs7226363).		cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		ACAACCTACACGTTCCATGAT	0.403													C|||	977	0.195088	0.1513	0.1686	5008	,	,		15690	0.2212		0.2356	False		,,,				2504	0.2045				p.R3H		Atlas-SNP	.											.	TEKT3	64	.	0			c.G8A						PASS	.	C	HIS/ARG	696,3710	290.1+/-280.8	44,608,1551	71.0	67.0	68.0		8	-11.0	0.0	17	dbSNP_116	68	2077,6523	359.3+/-331.5	269,1539,2492	yes	missense	TEKT3	NM_031898.2	29	313,2147,4043	TT,TC,CC		24.1512,15.7966,21.3209	benign	3/491	15234895	2773,10233	2203	4300	6503	SO:0001583	missense	64518	exon3			CCTACACGTTCCA	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.8G>A	17.37:g.15234895C>T	ENSP00000379263:p.Arg3His	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Missense_Mutation	SNP	ENST00000395930.1	37	CCDS11169.1	436	0.19963369963369965	70	0.14227642276422764	66	0.18232044198895028	141	0.2465034965034965	159	0.20976253298153033	C	8.891	0.954112	0.18431	0.157966	0.241512	ENSG00000125409	ENST00000395930;ENST00000338696;ENST00000536146;ENST00000539316;ENST00000543896	T;T;T;T;T	0.42513	4.15;4.15;1.56;1.56;0.97	5.51	-11.0	0.00169	.	0.900938	0.09728	N	0.763471	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.28350	0.208	B	0.13407	0.009	T	0.13255	-1.0516	9	0.38643	T	0.18	0.0046	1.0096	0.01495	0.3388:0.2037:0.2856:0.1719	rs7226363;rs52810686;rs61496150;rs7226363	3	Q9BXF9	TEKT3_HUMAN	H	3	ENSP00000379263:R3H;ENSP00000343995:R3H;ENSP00000446111:R3H;ENSP00000439713:R3H;ENSP00000444180:R3H	ENSP00000343995:R3H	R	-	2	0	TEKT3	15175620	0.006000	0.16342	0.000000	0.03702	0.001000	0.01503	0.810000	0.27183	-2.238000	0.00712	-0.878000	0.02970	CGT	C|0.794;T|0.206	0.206	strong		0.403	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
CSF3R	1441	hgsc.bcm.edu	37	1	36937878	36937878	+	Missense_Mutation	SNP	C	C	T	rs3918018	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:36937878C>T	ENST00000373106.1	-	8	1505	c.958G>A	c.(958-960)Gac>Aac	p.D320N	CSF3R_ENST00000373104.1_Missense_Mutation_p.D320N|CSF3R_ENST00000331941.5_Missense_Mutation_p.D320N|CSF3R_ENST00000373103.1_Missense_Mutation_p.D320N|CSF3R_ENST00000418048.2_Missense_Mutation_p.D320N|CSF3R_ENST00000440588.2_Missense_Mutation_p.D320N|CSF3R_ENST00000338937.5_Missense_Mutation_p.D320N|CSF3R_ENST00000361632.4_Missense_Mutation_p.D320N|CSF3R_ENST00000487540.2_5'UTR	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	320	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		D -> N (in dbSNP:rs3918018). {ECO:0000269|Ref.4}.		cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	GGGCTCCAGTCGCTCCAGTGG	0.652													C|||	50	0.00998403	0.003	0.013	5008	,	,		17681	0.0		0.0348	False		,,,				2504	0.002				p.D320N		Atlas-SNP	.											.	CSF3R	157	.	0			c.G958A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	28,4378	32.6+/-62.9	0,28,2175	52.0	64.0	60.0		958,958,958	-5.5	0.0	1	dbSNP_108	60	263,8337	96.1+/-157.9	6,251,4043	yes	missense,missense,missense	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	23,23,23	6,279,6218	TT,TC,CC		3.0581,0.6355,2.2374	benign,benign,benign	320/837,320/864,320/784	36937878	291,12715	2203	4300	6503	SO:0001583	missense	1441	exon8			TCCAGTCGCTCCA	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.958G>A	1.37:g.36937878C>T	ENSP00000362198:p.Asp320Asn	Somatic	226	0	0		WXS	Illumina HiSeq	Phase_I	197	9	0.0456853	NM_156039		Missense_Mutation	SNP	ENST00000373106.1	37	CCDS413.1	32	0.014652014652014652	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	26	0.03430079155672823	C	9.303	1.053698	0.19907	0.006355	0.030581	ENSG00000119535	ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588	T;T;T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.5;0.5;0.5;0.5	4.74	-5.51	0.02568	Fibronectin, type III (2);Immunoglobulin-like fold (1);	14.406800	0.00166	N	0.000000	T	0.13713	0.0332	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.10296	0.003;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.12553	-1.0543	10	0.22706	T	0.39	0.2998	10.7202	0.46036	0.0:0.7775:0.1041:0.1184	rs3918018;rs3918018	320;320;320;320	E1B6W6;Q99062-3;Q99062;Q99062-4	.;.;CSF3R_HUMAN;.	N	320	ENSP00000362198:D320N;ENSP00000362196:D320N;ENSP00000362195:D320N;ENSP00000355406:D320N;ENSP00000332180:D320N;ENSP00000401588:D320N;ENSP00000345013:D320N;ENSP00000397568:D320N	ENSP00000332180:D320N	D	-	1	0	CSF3R	36710465	0.004000	0.15560	0.043000	0.18650	0.514000	0.34195	-0.149000	0.10204	-1.334000	0.02244	-0.340000	0.08031	GAC	C|0.981;T|0.019	0.019	strong		0.652	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
KITLG	4254	hgsc.bcm.edu	37	12	88900891	88900891	+	Missense_Mutation	SNP	C	C	A	rs41283112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:88900891C>A	ENST00000228280.5	-	7	810	c.628G>T	c.(628-630)Gac>Tac	p.D210Y	KITLG_ENST00000378535.4_5'UTR|KITLG_ENST00000357116.4_5'UTR|KITLG_ENST00000347404.5_Missense_Mutation_p.D182Y	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	210			D -> Y (in dbSNP:rs41283112).		cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						AGGCTGGAGTCTCCAGGGGGA	0.418									Testicular Cancer, Familial Clustering of				C|||	20	0.00399361	0.0	0.0101	5008	,	,		14689	0.0		0.0099	False		,,,				2504	0.0031				p.D210Y		Atlas-SNP	.											.	KITLG	26	.	0			c.G628T						PASS	.	C	TYR/ASP,TYR/ASP	15,4391	24.3+/-50.5	0,15,2188	63.0	67.0	65.0		628,544	2.8	0.0	12	dbSNP_127	65	138,8462	68.7+/-131.2	0,138,4162	yes	missense,missense	KITLG	NM_000899.4,NM_003994.5	160,160	0,153,6350	AA,AC,CC		1.6047,0.3404,1.1764	probably-damaging,probably-damaging	210/274,182/246	88900891	153,12853	2203	4300	6503	SO:0001583	missense	4254	exon7	Familial Cancer Database		TGGAGTCTCCAGG	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"""mast cell growth factor"", ""stem cell factor"", ""steel factor"", ""familial progressive hyperpigmentation 2"""	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.628G>T	12.37:g.88900891C>A	ENSP00000228280:p.Asp210Tyr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_000899	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Missense_Mutation	SNP	ENST00000228280.5	37	CCDS31868.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	C|C	17.16|17.16	3.317419|3.317419	0.60524|0.60524	0.003404|0.003404	0.016047|0.016047	ENSG00000049130|ENSG00000049130	ENST00000378535;ENST00000228280;ENST00000347404|ENST00000537835	T;T|.	0.67523|.	-0.27;-0.27|.	5.68|5.68	2.84|2.84	0.33178|0.33178	.|.	0.350727|.	0.32819|.	N|.	0.005616|.	T|T	0.25419|0.25419	0.0618|0.0618	L|L	0.54323|0.54323	1.7|1.7	0.26217|0.26217	N|N	0.979217|0.979217	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.72982|.	0.964;0.979|.	T|T	0.34875|0.34875	-0.9811|-0.9811	10|6	0.59425|0.87932	D|D	0.04|0	-2.0558|-2.0558	3.7484|3.7484	0.08556|0.08556	0.0:0.5316:0.1938:0.2746|0.0:0.5316:0.1938:0.2746	rs41283112;rs61754238|rs41283112;rs61754238	182;210|.	P21583-2;P21583|.	.;SCF_HUMAN|.	Y|D	175;210;182|13	ENSP00000228280:D210Y;ENSP00000054216:D182Y|.	ENSP00000228280:D210Y|ENSP00000438889:E13D	D|E	-|-	1|3	0|2	KITLG|KITLG	87425022|87425022	0.712000|0.712000	0.27916|0.27916	0.041000|0.041000	0.18516|0.18516	0.359000|0.359000	0.29487|0.29487	1.040000|1.040000	0.30278|0.30278	0.735000|0.735000	0.32537|0.32537	0.655000|0.655000	0.94253|0.94253	GAC|GAG	C|0.991;A|0.009	0.009	strong		0.418	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994	
AQP3	360	hgsc.bcm.edu	37	9	33443867	33443867	+	Silent	SNP	G	G	A	rs2228333	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:33443867G>A	ENST00000297991.4	-	2	212	c.132C>T	c.(130-132)gcC>gcT	p.A44A	AQP3_ENST00000493581.1_5'UTR	NM_004925.4	NP_004916.1	Q92482	AQP3_HUMAN	aquaporin 3 (Gill blood group)	44					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)		GCACAACCTGGGCCACGGAGC	0.597													G|||	8	0.00159744	0.0	0.0	5008	,	,		17978	0.0		0.008	False		,,,				2504	0.0				p.A44A		Atlas-SNP	.											.	AQP3	18	.	0			c.C132T						PASS	.	G		5,4401	11.4+/-27.6	0,5,2198	48.0	44.0	45.0		132	0.3	1.0	9	dbSNP_98	45	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous	AQP3	NM_004925.4		0,60,6443	AA,AG,GG		0.6395,0.1135,0.4613		44/293	33443867	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	360	exon2			AACCTGGGCCACG		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.132C>T	9.37:g.33443867G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	66	22	0.333333	NM_004925	A8K843|B2RE16|D3DRL3|O00108|Q6FGT2|Q6FGW6	Silent	SNP	ENST00000297991.4	37	CCDS6542.1																																																																																			G|0.996;A|0.004	0.004	strong		0.597	AQP3-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052055.1	NM_004925	
OR13C9	286362	hgsc.bcm.edu	37	9	107380177	107380177	+	Silent	SNP	A	A	G	rs1813819	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107380177A>G	ENST00000259362.1	-	1	308	c.309T>C	c.(307-309)ctT>ctC	p.L103L		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						TGGCCAAGCCAAGGAACATCT	0.498													a|||	2155	0.430312	0.6271	0.2262	5008	,	,		20857	0.5754		0.1779	False		,,,				2504	0.4192				p.L103L		Atlas-SNP	.											.	OR13C9	42	.	0			c.T309C						PASS	.	G		2358,2048	598.6+/-389.1	674,1010,519	116.0	135.0	129.0		309	-3.7	0.9	9	dbSNP_92	129	1591,7009	286.3+/-297.7	184,1223,2893	no	coding-synonymous	OR13C9	NM_001001956.1		858,2233,3412	GG,GA,AA		18.5,46.4821,30.3629		103/319	107380177	3949,9057	2203	4300	6503	SO:0001819	synonymous_variant	286362	exon1			CAAGCCAAGGAAC		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.309T>C	9.37:g.107380177A>G		Somatic	413	0	0		WXS	Illumina HiSeq	Phase_I	384	175	0.455729	NM_001001956	Q6IFL2	Silent	SNP	ENST00000259362.1	37	CCDS35093.1																																																																																			A|0.694;G|0.306	0.306	strong		0.498	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
SLC25A22	79751	hgsc.bcm.edu	37	11	794790	794790	+	Silent	SNP	G	G	A	rs146402942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:794790G>A	ENST00000320230.5	-	3	613	c.132C>T	c.(130-132)cgC>cgT	p.R44R	SLC25A22_ENST00000531214.1_Silent_p.R44R	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22	44					L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCGTGTACACGCGCTGGCCGT	0.667																																					p.R44R	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	SLC25A22	19	.	0			c.C132T						PASS	.	G	,,	0,4396		0,0,2198	39.0	37.0	37.0		132,132,132	2.3	1.0	11	dbSNP_134	37	13,8579		0,13,4283	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC25A22	NM_001191060.1,NM_001191061.1,NM_024698.5	,,	0,13,6481	AA,AG,GG		0.1513,0.0,0.1001	,,	44/324,44/324,44/324	794790	13,12975	2198	4296	6494	SO:0001819	synonymous_variant	79751	exon3			GTACACGCGCTGG	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310	ENST00000320230.5:c.132C>T	11.37:g.794790G>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_001191061	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Silent	SNP	ENST00000320230.5	37	CCDS7715.1																																																																																			G|0.999;A|0.001	0.001	strong		0.667	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2		
DCAF4L1	285429	hgsc.bcm.edu	37	4	41984782	41984782	+	Missense_Mutation	SNP	G	G	A	rs369307123		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:41984782G>A	ENST00000333141.5	+	1	1070	c.973G>A	c.(973-975)Gaa>Aaa	p.E325K		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	325										breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						TGTGCACGAGGAAGAGGGAAT	0.562																																					p.E325K		Atlas-SNP	.											.	DCAF4L1	70	.	0			c.G973A						PASS	.	G	LYS/GLU	0,4406		0,0,2203	125.0	92.0	103.0		973	-0.3	0.7	4		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	DCAF4L1	NM_001029955.3	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	325/397	41984782	1,13005	2203	4300	6503	SO:0001583	missense	285429	exon1			CACGAGGAAGAGG	BC035027	CCDS33978.1	4p13	2013-01-09	2009-07-17	2009-07-17		ENSG00000182308		"""WD repeat domain containing"""	27723	protein-coding gene	gene with protein product			"""WD repeat domain 21B"""	WDR21B			Standard	NM_001029955		Approved		uc003gwk.2	Q3SXM0		ENST00000333141.5:c.973G>A	4.37:g.41984782G>A	ENSP00000327796:p.Glu325Lys	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	205	86	0.419512	NM_001029955	B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Missense_Mutation	SNP	ENST00000333141.5	37	CCDS33978.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245448	0.59103	0.0	1.16E-4	ENSG00000182308	ENST00000333141	T	0.70045	-0.45	0.97	-0.348	0.12613	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.285662	0.40064	N	0.001186	T	0.63165	0.2488	L	0.60455	1.87	0.31255	N	0.693609	P	0.46578	0.88	P	0.50270	0.636	T	0.62388	-0.6865	10	0.34782	T	0.22	.	5.6253	0.17478	0.0:0.0:0.6821:0.3179	.	325	Q3SXM0	DC4L1_HUMAN	K	325	ENSP00000327796:E325K	ENSP00000327796:E325K	E	+	1	0	DCAF4L1	41679539	1.000000	0.71417	0.729000	0.30791	0.811000	0.45836	1.846000	0.39289	-0.124000	0.11724	0.313000	0.20887	GAA	.	.	weak		0.562	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955	
BRAT1	221927	hgsc.bcm.edu	37	7	2578246	2578246	+	Silent	SNP	C	C	T	rs2917726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:2578246C>T	ENST00000340611.4	-	14	2179	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	BRAT1_ENST00000473879.1_5'UTR	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	641					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						CTCGGCTCGCCGCCTGCAGCA	0.716													C|||	445	0.0888578	0.0015	0.0893	5008	,	,		13448	0.2679		0.0437	False		,,,				2504	0.0685				p.A641A		Atlas-SNP	.											.	BRAT1	57	.	0			c.G1923A						PASS	.	C		48,4176		2,44,2066	10.0	12.0	11.0		1923	-1.8	0.0	7	dbSNP_101	11	433,7867		10,413,3727	no	coding-synonymous	BRAT1	NM_152743.3		12,457,5793	TT,TC,CC		5.2169,1.1364,3.8406		641/822	2578246	481,12043	2112	4150	6262	SO:0001819	synonymous_variant	221927	exon14			GCTCGCCGCCTGC	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.1923G>A	7.37:g.2578246C>T		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	37	CCDS5334.1																																																																																			C|0.772;T|0.228	0.228	strong		0.716	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
PLS1	5357	hgsc.bcm.edu	37	3	142408606	142408606	+	Silent	SNP	G	G	A	rs6793735	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142408606G>A	ENST00000337777.3	+	10	1341	c.1128G>A	c.(1126-1128)ccG>ccA	p.P376P	PLS1_ENST00000457734.2_Silent_p.P376P|PLS1_ENST00000497002.1_Silent_p.P376P	NM_002670.2	NP_002661.2	Q14651	PLSI_HUMAN	plastin 1	376	Actin-binding 1.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.P376P(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	27						ACACATACCCGTGCCTGCACA	0.368													A|||	3084	0.615815	0.9433	0.4669	5008	,	,		16287	0.3988		0.6551	False		,,,				2504	0.4622				p.P376P		Atlas-SNP	.											PLS1,NS,carcinoma,0,1	PLS1	71	1	1	Substitution - coding silent(1)	stomach(1)	c.G1128A						PASS	.	A	,,	3943,463	217.8+/-236.0	1767,409,27	124.0	120.0	122.0		1128,1128,1128	-1.1	0.9	3	dbSNP_116	122	5593,3007	465.3+/-366.5	1803,1987,510	yes	coding-synonymous,coding-synonymous,coding-synonymous	PLS1	NM_001145319.1,NM_001172312.1,NM_002670.2	,,	3570,2396,537	AA,AG,GG		34.9651,10.5084,26.68	,,	376/630,376/630,376/630	142408606	9536,3470	2203	4300	6503	SO:0001819	synonymous_variant	5357	exon10			ATACCCGTGCCTG	L20826	CCDS3125.1	3q23	2013-01-10	2010-02-10		ENSG00000120756	ENSG00000120756		"""EF-hand domain containing"""	9090	protein-coding gene	gene with protein product		602734	"""plastin 1 (I isoform)"""			8139549	Standard	NM_002670		Approved	I-plastin, Plastin-1	uc003euz.3	Q14651	OTTHUMG00000159292	ENST00000337777.3:c.1128G>A	3.37:g.142408606G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_001172312	A8K2Q1|D3DNG3|Q8NEG6	Silent	SNP	ENST00000337777.3	37	CCDS3125.1																																																																																			G|0.314;A|0.686	0.686	strong		0.368	PLS1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354435.1	NM_002670	
CERCAM	51148	hgsc.bcm.edu	37	9	131196704	131196704	+	Silent	SNP	G	G	A	rs7259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131196704G>A	ENST00000372838.4	+	11	1745	c.1347G>A	c.(1345-1347)aaG>aaA	p.K449K	CERCAM_ENST00000372842.1_Silent_p.K371K|RP11-339B21.10_ENST00000610052.1_RNA	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	449					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						TCGGACGGAAGCAGGTGAACC	0.662													G|||	1884	0.376198	0.6604	0.2089	5008	,	,		16087	0.4048		0.2117	False		,,,				2504	0.2505				p.K449K		Atlas-SNP	.											.	CERCAM	104	.	0			c.G1347A						PASS	.	G		2657,1749	623.6+/-394.2	814,1029,360	43.0	49.0	47.0		1347	3.4	1.0	9	dbSNP_52	47	1567,7033	281.2+/-294.9	134,1299,2867	no	coding-synonymous	CERCAM	NM_016174.4		948,2328,3227	AA,AG,GG		18.2209,39.6959,32.4773		449/596	131196704	4224,8782	2203	4300	6503	SO:0001819	synonymous_variant	51148	exon11			ACGGAAGCAGGTG	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"""glycosyltransferase 25 domain containing 3"""		"""cerebral cell adhesion molecule"""	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.1347G>A	9.37:g.131196704G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_016174	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Silent	SNP	ENST00000372838.4	37	CCDS6901.2																																																																																			G|0.673;A|0.327	0.327	strong		0.662	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174	
PRRC2B	84726	hgsc.bcm.edu	37	9	134334588	134334588	+	Missense_Mutation	SNP	A	A	G	rs34553878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:134334588A>G	ENST00000357304.4	+	10	1304	c.1249A>G	c.(1249-1251)Atg>Gtg	p.M417V	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.M417V|PRRC2B_ENST00000405995.1_Missense_Mutation_p.M417V	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	417			M -> V (in dbSNP:rs34553878).				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						GCAGTTGTCAATGAGCTCTGC	0.552													A|||	292	0.0583067	0.0257	0.0793	5008	,	,		18766	0.006		0.1153	False		,,,				2504	0.0828				p.M417V		Atlas-SNP	.											.	PRRC2B	266	.	0			c.A1249G						PASS	.	A	VAL/MET	216,4182	120.8+/-158.4	7,202,1990	102.0	111.0	108.0		1249	-11.2	0.0	9	dbSNP_126	108	978,7616	207.9+/-249.5	55,868,3374	yes	missense	PRRC2B	NM_013318.3	21	62,1070,5364	GG,GA,AA		11.38,4.9113,9.1903	benign	417/2230	134334588	1194,11798	2199	4297	6496	SO:0001583	missense	84726	exon10			TTGTCAATGAGCT	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.1249A>G	9.37:g.134334588A>G	ENSP00000349856:p.Met417Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	126	0.057692307692307696	14	0.028455284552845527	28	0.07734806629834254	4	0.006993006993006993	80	0.10554089709762533	A	10.93	1.489273	0.26686	0.049113	0.1138	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.02323	4.34;4.67;4.34	5.62	-11.2	0.00127	.	0.525110	0.15142	U	0.278216	T	0.00039	0.0001	N	0.22421	0.69	0.58432	D	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.48581	-0.9023	10	0.29301	T	0.29	-0.0829	0.5425	0.00647	0.2329:0.2976:0.1825:0.287	rs34553878;rs57516479	417	Q5JSZ5	PRC2B_HUMAN	V	417	ENSP00000384606:M417V;ENSP00000349856:M417V;ENSP00000398853:M417V	ENSP00000349856:M417V	M	+	1	0	PRRC2B	133324409	0.000000	0.05858	0.001000	0.08648	0.974000	0.67602	-1.201000	0.03026	-1.794000	0.01256	0.482000	0.46254	ATG	A|0.928;G|0.072	0.072	strong		0.552	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PEBP4	157310	hgsc.bcm.edu	37	8	22570904	22570904	+	Silent	SNP	C	C	T	rs386723487|rs61732772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22570904C>T	ENST00000256404.6	-	7	754	c.663G>A	c.(661-663)caG>caA	p.Q221Q	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	221						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		CTATCTCCGCCTGGTTTTTGT	0.587													C|||	55	0.0109824	0.0098	0.0072	5008	,	,		16308	0.004		0.0199	False		,,,				2504	0.0133				p.Q221Q		Atlas-SNP	.											.	PEBP4	23	.	0			c.G663A						PASS	.						71.0	78.0	76.0					8																	22570904		1953	4153	6106	SO:0001819	synonymous_variant	157310	exon7			CTCCGCCTGGTTT	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"""cousin-of-RKIP 1 protein"""	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.663G>A	8.37:g.22570904C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_144962	Q5EVA1|Q8WW74	Silent	SNP	ENST00000256404.6	37	CCDS43724.1																																																																																			C|0.986;T|0.014	0.014	strong		0.587	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
TAOK2	9344	hgsc.bcm.edu	37	16	29999225	29999225	+	Missense_Mutation	SNP	G	G	A	rs11864149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:29999225G>A	ENST00000308893.4	+	16	4675	c.3632G>A	c.(3631-3633)cGc>cAc	p.R1211H	TAOK2_ENST00000416441.2_Missense_Mutation_p.R1038H|TAOK2_ENST00000543033.1_Missense_Mutation_p.R1098H|TAOK2_ENST00000279394.3_Intron	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	1211				R -> H (in Ref. 1; AAD45616). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|focal adhesion assembly (GO:0048041)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein targeting to membrane (GO:0006612)|regulation of cell growth (GO:0001558)|regulation of cell shape (GO:0008360)|response to stress (GO:0006950)|stress-activated MAPK cascade (GO:0051403)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|mitogen-activated protein kinase kinase binding (GO:0031434)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(3)|skin(1)	22						CCTGCCTCCCGCCAGCCACTG	0.721													G|||	368	0.0734824	0.1604	0.0706	5008	,	,		11363	0.003		0.0835	False		,,,				2504	0.0204				p.R1211H		Atlas-SNP	.											.	TAOK2	142	.	0			c.G3632A						PASS	.	G	,HIS/ARG	479,3449		22,435,1507	6.0	7.0	6.0		,3632	0.6	0.1	16	dbSNP_120	6	507,7365		18,471,3447	no	intron,missense	TAOK2	NM_004783.2,NM_016151.2	,29	40,906,4954	AA,AG,GG		6.4405,12.1945,8.3559	,possibly-damaging	,1211/1236	29999225	986,10814	1964	3936	5900	SO:0001583	missense	9344	exon16			CCTCCCGCCAGCC	AB020688	CCDS10662.1, CCDS10663.1, CCDS58448.1	16p11.2	2008-02-05			ENSG00000149930	ENSG00000149930			16835	protein-coding gene	gene with protein product		613199				10048485, 9786855	Standard	NM_016151		Approved	TAO1, KIAA0881, PSK, PSK1, TAO2, MAP3K17	uc002dva.2	Q9UL54	OTTHUMG00000132111	ENST00000308893.4:c.3632G>A	16.37:g.29999225G>A	ENSP00000310094:p.Arg1211His	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	19	10	0.526316	NM_016151	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Missense_Mutation	SNP	ENST00000308893.4	37	CCDS10663.1	174	0.07967032967032966	79	0.16056910569105692	33	0.09116022099447514	1	0.0017482517482517483	61	0.08047493403693931	G	0.054	-1.241336	0.01493	0.121945	0.064405	ENSG00000149930	ENST00000308893;ENST00000543033	T;T	0.71222	-0.52;-0.55	4.04	0.591	0.17465	.	1.515130	0.04227	N	0.334654	T	0.00271	0.0008	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	0.02625	-1.1132	8	.	.	.	.	7.7362	0.28815	0.2033:0.1469:0.6498:0.0	rs11864149	1402;1038;1211	Q86V37;Q9UL54-3;Q9UL54	.;.;TAOK2_HUMAN	H	1211;1098	ENSP00000310094:R1211H;ENSP00000440336:R1098H	.	R	+	2	0	TAOK2	29906726	0.000000	0.05858	0.100000	0.21137	0.027000	0.11550	0.386000	0.20702	0.037000	0.15575	-1.119000	0.02030	CGC	G|0.914;A|0.086	0.086	strong		0.721	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151	
SLC16A9	220963	hgsc.bcm.edu	37	10	61414011	61414011	+	Missense_Mutation	SNP	G	G	T	rs2242206	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:61414011G>T	ENST00000395348.3	-	5	1409	c.773C>A	c.(772-774)aCa>aAa	p.T258K	SLC16A9_ENST00000395347.1_Missense_Mutation_p.T258K	NM_194298.2	NP_919274.1	Q7RTY1	MOT9_HUMAN	solute carrier family 16, member 9	258			T -> K (in dbSNP:rs2242206).		urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			kidney(3)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	23						GTGTGTCACTGTGGGGTTTTT	0.398													G|||	1728	0.345048	0.0696	0.3847	5008	,	,		19641	0.5804		0.2664	False		,,,				2504	0.5276				p.T258K		Atlas-SNP	.											.	SLC16A9	58	.	0			c.C773A						PASS	.	G	LYS/THR	468,3938	219.1+/-236.9	23,422,1758	226.0	214.0	218.0		773	2.0	0.0	10	dbSNP_98	218	2235,6365	379.4+/-339.3	307,1621,2372	yes	missense	SLC16A9	NM_194298.2	78	330,2043,4130	TT,TG,GG		25.9884,10.6219,20.7827	benign	258/510	61414011	2703,10303	2203	4300	6503	SO:0001583	missense	220963	exon5			GTCACTGTGGGGT	AK125791	CCDS7256.1	10q21.3	2013-07-18	2013-07-18	2004-01-21	ENSG00000165449	ENSG00000165449		"""Solute carriers"""	23520	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 9"""	614242	"""chromosome 10 open reading frame 36"", ""solute carrier family 16 (monocarboxylic acid transporters), member 9"", ""solute carrier family 16, member 9 (monocarboxylic acid transporter 9)"""	C10orf36			Standard	NM_194298		Approved	FLJ43803, MCT9	uc010qig.1	Q7RTY1	OTTHUMG00000018283	ENST00000395348.3:c.773C>A	10.37:g.61414011G>T	ENSP00000378757:p.Thr258Lys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	219	83	0.378995	NM_194298	Q6ZMI2|Q9UFH8	Missense_Mutation	SNP	ENST00000395348.3	37	CCDS7256.1	714	0.3269230769230769	48	0.0975609756097561	113	0.31215469613259667	342	0.5979020979020979	211	0.2783641160949868	G	0.004	-2.322151	0.00232	0.106219	0.259884	ENSG00000165449	ENST00000395348;ENST00000395347	T;T	0.04119	3.7;3.7	5.02	2.0	0.26442	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.506790	0.03439	N	0.209031	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.25007	0.116	B	0.22152	0.038	T	0.37384	-0.9708	9	0.05959	T	0.93	.	3.3426	0.07124	0.2824:0.0:0.4133:0.3043	rs2242206;rs52832507;rs61451304;rs2242206	258	Q7RTY1	MOT9_HUMAN	K	258	ENSP00000378757:T258K;ENSP00000378756:T258K	ENSP00000378756:T258K	T	-	2	0	SLC16A9	61084017	0.001000	0.12720	0.002000	0.10522	0.105000	0.19272	1.236000	0.32683	0.470000	0.27294	0.591000	0.81541	ACA	G|0.740;T|0.260	0.260	strong		0.398	SLC16A9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048174.2	NM_194298	
PLCE1	51196	hgsc.bcm.edu	37	10	96006281	96006281	+	Missense_Mutation	SNP	G	G	A	rs61751498	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:96006281G>A	ENST00000371380.3	+	7	3234	c.2999G>A	c.(2998-3000)aGc>aAc	p.S1000N	PLCE1_ENST00000371385.3_Missense_Mutation_p.S692N|PLCE1_ENST00000260766.3_Missense_Mutation_p.S1000N|PLCE1_ENST00000371375.1_Missense_Mutation_p.S692N			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1000					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)				ATGCTCTTCAGCGGATTATTG	0.473													G|||	4	0.000798722	0.0008	0.0014	5008	,	,		21465	0.0		0.002	False		,,,				2504	0.0				p.S1000N		Atlas-SNP	.											.	PLCE1	543	.	0			c.G2999A						PASS	.	G	ASN/SER,ASN/SER	0,3870		0,0,1935	97.0	94.0	95.0		2075,2999	4.9	1.0	10	dbSNP_129	95	25,8289		0,25,4132	yes	missense,missense	PLCE1	NM_001165979.1,NM_016341.3	46,46	0,25,6067	AA,AG,GG		0.3007,0.0,0.2052	benign,benign	692/1995,1000/2303	96006281	25,12159	1935	4157	6092	SO:0001583	missense	51196	exon8			TCTTCAGCGGATT		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.2999G>A	10.37:g.96006281G>A	ENSP00000360431:p.Ser1000Asn	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	105	46	0.438095	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	12.18	1.859484	0.32884	0.0	0.003007	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.42513	0.97;0.97;0.97;0.97	5.89	4.89	0.63831	.	0.417124	0.28828	N	0.014004	T	0.15652	0.0377	N	0.03608	-0.345	0.28282	N	0.923926	B;B;B	0.09022	0.001;0.0;0.002	B;B;B	0.08055	0.003;0.003;0.001	T	0.16512	-1.0400	10	0.15066	T	0.55	.	3.9319	0.09290	0.3175:0.0:0.6825:0.0	rs61751498	1000;692;1000	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	N	1000;1000;692;692	ENSP00000260766:S1000N;ENSP00000360431:S1000N;ENSP00000360438:S692N;ENSP00000360426:S692N	ENSP00000260766:S1000N	S	+	2	0	PLCE1	95996271	1.000000	0.71417	0.991000	0.47740	0.895000	0.52256	6.110000	0.71535	2.814000	0.96858	0.585000	0.79938	AGC	G|0.997;A|0.003	0.003	strong		0.473	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
ESPL1	9700	hgsc.bcm.edu	37	12	53682326	53682326	+	Silent	SNP	G	G	A	rs1110720	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:53682326G>A	ENST00000257934.4	+	20	4642	c.4551G>A	c.(4549-4551)ggG>ggA	p.G1517G	ESPL1_ENST00000552462.1_Silent_p.G1517G	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1517					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						CCCCAGGTGGGAAGACTCCAG	0.567											OREG0021863	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3232	0.645367	0.4327	0.6326	5008	,	,		17084	0.8204		0.6382	False		,,,				2504	0.7689				p.G1517G	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.G4551A						PASS	.	G		1951,2455		420,1111,672	27.0	26.0	26.0		4551	3.0	0.8	12	dbSNP_86	26	5464,3134		1747,1970,582	no	coding-synonymous	ESPL1	NM_012291.4		2167,3081,1254	AA,AG,GG		36.4503,44.2805,42.9791		1517/2121	53682326	7415,5589	2203	4299	6502	SO:0001819	synonymous_variant	9700	exon20			AGGTGGGAAGACT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.4551G>A	12.37:g.53682326G>A		Somatic	67	0	0	994	WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			G|0.402;A|0.598	0.598	strong		0.567	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
HABP2	3026	hgsc.bcm.edu	37	10	115334124	115334124	+	Silent	SNP	C	C	T	rs3740530	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115334124C>T	ENST00000351270.3	+	3	279	c.183C>T	c.(181-183)caC>caT	p.H61H	HABP2_ENST00000541666.1_Silent_p.H61H|HABP2_ENST00000542051.1_Silent_p.H35H|HABP2_ENST00000537906.1_Missense_Mutation_p.T50M	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	61					cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	CACTTACCCACGCTGAGAATC	0.502													C|||	2677	0.534545	0.2965	0.6354	5008	,	,		19524	0.6042		0.6183	False		,,,				2504	0.6268				p.H61H		Atlas-SNP	.											.	HABP2	52	.	0			c.C183T						PASS	.	C	,	1585,2821	493.4+/-362.7	292,1001,910	151.0	124.0	133.0		105,183	2.4	0.0	10	dbSNP_107	133	5491,3109	658.1+/-401.5	1777,1937,586	no	coding-synonymous,coding-synonymous	HABP2	NM_001177660.1,NM_004132.3	,	2069,2938,1496	TT,TC,CC		36.1512,35.9737,45.5943	,	35/535,61/561	115334124	7076,5930	2203	4300	6503	SO:0001819	synonymous_variant	3026	exon3			TACCCACGCTGAG		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.183C>T	10.37:g.115334124C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Silent	SNP	ENST00000351270.3	37	CCDS7577.1	1187	0.5434981684981685	132	0.2682926829268293	233	0.643646408839779	353	0.6171328671328671	469	0.6187335092348285	C	4.611	0.113538	0.08831	0.359737	0.638488	ENSG00000148702	ENST00000537906	.	.	.	4.31	2.41	0.29592	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	D	0.61697	0.99	P	0.48627	0.584	T	0.43180	-0.9407	6	0.87932	D	0	.	6.0471	0.19766	0.1873:0.7092:0.0:0.1035	rs3740530;rs17698474;rs59251586;rs3740530	50	F5H475	.	M	50	.	ENSP00000446135:T50M	T	+	2	0	HABP2	115324114	0.001000	0.12720	0.002000	0.10522	0.013000	0.08279	0.639000	0.24690	0.729000	0.32403	-0.261000	0.10672	ACG	C|0.467;T|0.533	0.533	strong		0.502	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
SPINK5	11005	hgsc.bcm.edu	37	5	147477551	147477551	+	Missense_Mutation	SNP	C	C	T	rs34482796	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:147477551C>T	ENST00000256084.7	+	11	1046	c.1004C>T	c.(1003-1005)gCc>gTc	p.A335V	SPINK5_ENST00000398454.1_Missense_Mutation_p.A335V|SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Missense_Mutation_p.A335V	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	335	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.		A -> V (in dbSNP:rs34482796). {ECO:0000269|PubMed:10419450, ECO:0000269|PubMed:16374478}.		anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGTGTCAAGCCTACTTGTGA	0.403													C|||	2236	0.446486	0.2534	0.6282	5008	,	,		17872	0.4802		0.4831	False		,,,				2504	0.5061				p.A335V		Atlas-SNP	.											SPINK5_ENST00000359874,colon,carcinoma,+1,2	SPINK5	245	2	0			c.C1004T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1107,2613		166,775,919	106.0	94.0	98.0		1004,1004,1004	2.7	1.0	5	dbSNP_126	98	4153,4055		1037,2079,988	yes	missense,missense,missense	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	64,64,64	1203,2854,1907	TT,TC,CC		49.403,29.7581,44.0979	benign,benign,benign	335/1095,335/917,335/1065	147477551	5260,6668	1860	4104	5964	SO:0001583	missense	11005	exon11			GTCAAGCCTACTT	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1004C>T	5.37:g.147477551C>T	ENSP00000256084:p.Ala335Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	965	0.44184981684981683	139	0.28252032520325204	218	0.6022099447513812	262	0.458041958041958	346	0.45646437994722955	C	10.64	1.408263	0.25378	0.297581	0.50597	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.05025	3.51;3.51;3.51;3.51	5.4	2.65	0.31530	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.283230	0.25386	N	0.031058	T	0.00012	0.0000	L	0.52126	1.63	0.45777	P	0.0013400000000000079	B;B;B	0.16396	0.009;0.003;0.017	B;B;B	0.23419	0.019;0.032;0.046	T	0.23261	-1.0193	9	0.33141	T	0.24	-0.5071	7.8004	0.29170	0.1326:0.7134:0.0:0.154	rs34482796;rs56847883	335;335;335	Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;ISK5_HUMAN;.	V	335;335;316;335	ENSP00000381472:A335V;ENSP00000352936:A335V;ENSP00000421519:A316V;ENSP00000256084:A335V	ENSP00000256084:A335V	A	+	2	0	SPINK5	147457744	0.931000	0.31567	0.998000	0.56505	0.757000	0.42996	0.065000	0.14466	0.095000	0.17434	-1.094000	0.02160	GCC	C|0.530;T|0.470	0.470	strong		0.403	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
MIA3	375056	hgsc.bcm.edu	37	1	222803204	222803204	+	Missense_Mutation	SNP	A	A	G	rs2936051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:222803204A>G	ENST00000344922.5	+	4	2667	c.2642A>G	c.(2641-2643)gAg>gGg	p.E881G	MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344441.6_Missense_Mutation_p.E881G|MIA3_ENST00000344507.1_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	881			E -> G (in dbSNP:rs2936051). {ECO:0000269|PubMed:9039502}.		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)				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)		GAGGACCATGAGAACACAGAG	0.502													a|||	1609	0.321286	0.3374	0.4236	5008	,	,		19303	0.3998		0.168	False		,,,				2504	0.3037				p.E881G		Atlas-SNP	.											.	MIA3	167	.	0			c.A2642G						PASS	.		GLY/GLU	1144,2716		158,828,944	35.0	36.0	35.0		2642	3.8	0.0	1	dbSNP_101	35	1457,6799		136,1185,2807	yes	missense	MIA3	NM_198551.2	98	294,2013,3751	GG,GA,AA		17.6478,29.6373,21.4675	probably-damaging	881/1908	222803204	2601,9515	1930	4128	6058	SO:0001583	missense	375056	exon4			ACCATGAGAACAC		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.2642A>G	1.37:g.222803204A>G	ENSP00000340900:p.Glu881Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	645|645	0.29532967032967034|0.29532967032967034	168|168	0.34146341463414637|0.34146341463414637	128|128	0.35359116022099446|0.35359116022099446	221|221	0.38636363636363635|0.38636363636363635	128|128	0.16886543535620052|0.16886543535620052	a|a	18.04|18.04	3.534540|3.534540	0.64972|0.64972	0.296373|0.296373	0.176478|0.176478	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831|ENST00000354906	T;T|.	0.06218|.	3.33;3.33|.	4.91|4.91	3.79|3.79	0.43588|0.43588	.|.	.|.	.|.	.|.	.|.	T|.	0.00012|.	0.0000|.	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	P|P	0.0|0.0	B;D|.	0.89917|.	0.385;1.0|.	B;D|.	0.74674|.	0.313;0.984|.	T|.	0.38499|.	-0.9658|.	8|.	0.66056|.	D|.	0.02|.	.|.	10.284|10.284	0.43556|0.43556	0.9215:0.0:0.0785:0.0|0.9215:0.0:0.0785:0.0	rs2936051;rs3748628;rs9441929;rs17163335|rs2936051;rs3748628;rs9441929;rs17163335	881;881|.	Q5JRA6-2;Q5JRA6|.	.;MIA3_HUMAN|.	G|W	881|463	ENSP00000340900:E881G;ENSP00000340587:E881G|.	ENSP00000325973:E881G|.	E|X	+|+	2|3	0|0	MIA3|MIA3	220869827|220869827	0.997000|0.997000	0.39634|0.39634	0.006000|0.006000	0.13384|0.13384	0.006000|0.006000	0.05464|0.05464	4.080000|4.080000	0.57620|0.57620	0.842000|0.842000	0.35045|0.35045	0.375000|0.375000	0.23000|0.23000	GAG|TGA	A|0.748;G|0.252	0.252	strong		0.502	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
WNK2	65268	hgsc.bcm.edu	37	9	96021254	96021254	+	Silent	SNP	G	G	A	rs55768771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:96021254G>A	ENST00000297954.4	+	11	2424	c.2424G>A	c.(2422-2424)gcG>gcA	p.A808A	WNK2_ENST00000395477.2_Silent_p.A808A|WNK2_ENST00000395475.2_Silent_p.A742A|WNK2_ENST00000427277.2_Silent_p.A420A|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Silent_p.A420A	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	808					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						CGCCCCTGGCGGGAATCGACG	0.652													G|||	29	0.00579073	0.0	0.0173	5008	,	,		13362	0.0		0.0159	False		,,,				2504	0.001				p.A808A		Atlas-SNP	.											.	WNK2	277	.	0			c.G2424A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	34.0	38.0	37.0		2424	-9.8	0.0	9	dbSNP_129	37	65,8533	37.8+/-93.5	0,65,4234	yes	coding-synonymous	WNK2	NM_006648.3		0,70,6432	AA,AG,GG		0.756,0.1135,0.5383		808/2218	96021254	70,12934	2203	4299	6502	SO:0001819	synonymous_variant	65268	exon11			CCTGGCGGGAATC	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.2424G>A	9.37:g.96021254G>A		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	200	100	0.5	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	G|G	0.469|0.469	-0.885479|-0.885479	0.02511|0.02511	0.001135|0.001135	0.00756|0.00756	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730	.|.	.|.	.|.	5.01|5.01	-9.75|-9.75	0.00506|0.00506	.|.	.|.	.|.	.|.	.|.	T|T	0.20455|0.20455	0.0492|0.0492	.|.	.|.	.|.	0.50813|0.50813	D|D	0.999895|0.999895	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.40720|0.40720	-0.9548|-0.9548	4|4	.|.	.|.	.|.	.|.	4.2626|4.2626	0.10747|0.10747	0.5387:0.099:0.2794:0.0829|0.5387:0.099:0.2794:0.0829	rs55768771;rs62622028|rs55768771;rs62622028	.|.	.|.	.|.	R|Q	412|804	.|.	.|.	G|R	+|+	1|2	0|0	WNK2|WNK2	95061075|95061075	0.025000|0.025000	0.19082|0.19082	0.000000|0.000000	0.03702|0.03702	0.058000|0.058000	0.15608|0.15608	-0.554000|-0.554000	0.06006|0.06006	-2.101000|-2.101000	0.00846|0.00846	-1.697000|-1.697000	0.00723|0.00723	GGG|CGG	G|0.993;A|0.007	0.007	strong		0.652	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
LRRC15	131578	hgsc.bcm.edu	37	3	194080983	194080983	+	Missense_Mutation	SNP	C	C	T	rs13060627	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194080983C>T	ENST00000347624.3	-	2	875	c.790G>A	c.(790-792)Gtc>Atc	p.V264I	LRRC15_ENST00000428839.1_Missense_Mutation_p.V270I|LRRC15_ENST00000439944.2_Missense_Mutation_p.V270I	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	264			V -> I (in dbSNP:rs13060627). {ECO:0000269|PubMed:11785964, ECO:0000269|PubMed:12923058}.		negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TGCATGAAGACGCTGGGTGGC	0.577													T|||	789	0.157548	0.1929	0.1412	5008	,	,		18257	0.0685		0.2406	False		,,,				2504	0.1278				p.V270I		Atlas-SNP	.											LRRC15_ENST00000439944,NS,carcinoma,0,2	LRRC15	137	2	0			c.G808A						PASS	.	T	ILE/VAL,ILE/VAL	875,3531	715.1+/-408.4	79,717,1407	142.0	153.0	150.0		808,790	3.9	1.0	3	dbSNP_121	150	2212,6388	705.2+/-405.5	283,1646,2371	no	missense,missense	LRRC15	NM_001135057.2,NM_130830.4	29,29	362,2363,3778	TT,TC,CC		25.7209,19.8593,23.7352	benign,benign	270/588,264/582	194080983	3087,9919	2203	4300	6503	SO:0001583	missense	131578	exon3			TGAAGACGCTGGG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.790G>A	3.37:g.194080983C>T	ENSP00000306276:p.Val264Ile	Somatic	235	0	0		WXS	Illumina HiSeq	Phase_I	277	140	0.505415	NM_001135057	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	397	0.18177655677655677	103	0.20934959349593496	54	0.14917127071823205	48	0.08391608391608392	192	0.2532981530343008	T	0.059	-1.229135	0.01518	0.198593	0.257209	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.24350	1.86;1.86;1.86	5.15	3.91	0.45181	.	.	.	.	.	T	0.00012	0.0000	N	0.20483	0.58	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.40515	-0.9559	8	0.11794	T	0.64	.	6.8945	0.24249	0.0:0.1407:0.209:0.6503	rs13060627;rs13060627	264;270	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	I	264;270;270	ENSP00000306276:V264I;ENSP00000389128:V270I;ENSP00000413707:V270I	ENSP00000306276:V264I	V	-	1	0	LRRC15	195562278	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	0.776000	0.26704	0.913000	0.36797	-0.254000	0.11334	GTC	C|0.796;T|0.204	0.204	strong		0.577	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
BRD3	8019	hgsc.bcm.edu	37	9	136907005	136907005	+	Silent	SNP	G	G	A	rs467387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136907005G>A	ENST00000303407.7	-	8	1469	c.1284C>T	c.(1282-1284)ccC>ccT	p.P428P	BRD3_ENST00000357885.2_Silent_p.P428P|BRD3_ENST00000371834.2_Silent_p.P428P|BRD3_ENST00000473349.1_5'Flank	NM_007371.3	NP_031397.1	Q15059	BRD3_HUMAN	bromodomain containing 3	428					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)		TGGGGGCCGCGGGGGCAGGCA	0.652			T	C15orf55	lethal midline carcinoma of young people								G|||	1680	0.335463	0.0499	0.2594	5008	,	,		15964	0.6667		0.2903	False		,,,				2504	0.4806				p.P428P		Atlas-SNP	.		Dom	yes		9	9q34	8019	bromodomain containing 3		E	.	BRD3	82	.	0			c.C1284T						PASS	.	G		377,4029	176.9+/-206.0	21,335,1847	25.0	27.0	26.0		1284	-3.5	0.0	9	dbSNP_80	26	2379,6219	371.6+/-336.3	341,1697,2261	no	coding-synonymous	BRD3	NM_007371.3		362,2032,4108	AA,AG,GG		27.6692,8.5565,21.1935		428/727	136907005	2756,10248	2203	4299	6502	SO:0001819	synonymous_variant	8019	exon8			GGCCGCGGGGGCA		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.1284C>T	9.37:g.136907005G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	192	99	0.515625	NM_007371	B1APD9|Q4G5Y3|Q5T1R7|Q8N5M3|Q92645	Silent	SNP	ENST00000303407.7	37	CCDS6980.1																																																																																			G|0.751;A|0.249	0.249	strong		0.652	BRD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055390.4	NM_007371	
UAP1L1	91373	hgsc.bcm.edu	37	9	139973582	139973582	+	Silent	SNP	C	C	G	rs75127829	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139973582C>G	ENST00000409858.3	+	4	857	c.825C>G	c.(823-825)ggC>ggG	p.G275G	UAP1L1_ENST00000360271.3_Silent_p.G152G|UAP1L1_ENST00000476184.1_3'UTR	NM_207309.2	NP_997192.2	Q3KQV9	UAP1L_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1 like 1	275							uridylyltransferase activity (GO:0070569)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		TGTTGCAGGGCGCAGACTGTG	0.706													C|||	291	0.058107	0.0015	0.0274	5008	,	,		9938	0.0427		0.0577	False		,,,				2504	0.1728				p.G275G		Atlas-SNP	.											.	UAP1L1	46	.	0			c.C825G						PASS	.	C		32,4370	32.6+/-62.9	2,28,2171	58.0	57.0	57.0		825	-10.5	0.0	9	dbSNP_132	57	382,8218	103.8+/-164.8	10,362,3928	no	coding-synonymous	UAP1L1	NM_207309.2		12,390,6099	GG,GC,CC		4.4419,0.7269,3.1841		275/508	139973582	414,12588	2201	4300	6501	SO:0001819	synonymous_variant	91373	exon4			GCAGGGCGCAGAC	AK022632	CCDS7028.2	9q34.3	2014-07-31	2014-07-31		ENSG00000197355	ENSG00000197355			28082	protein-coding gene	gene with protein product							Standard	NM_207309		Approved		uc010ncb.3	Q3KQV9	OTTHUMG00000020962	ENST00000409858.3:c.825C>G	9.37:g.139973582C>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_207309	A2AMJ8|Q5SPZ2|Q69YQ3|Q6ZR38	Silent	SNP	ENST00000409858.3	37	CCDS7028.2																																																																																			C|0.965;G|0.035	0.035	strong		0.706	UAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055216.2	XM_038063	
KIAA1211	57482	hgsc.bcm.edu	37	4	57181995	57181995	+	Missense_Mutation	SNP	C	C	T	rs3796547	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:57181995C>T	ENST00000504228.1	+	6	2432	c.2327C>T	c.(2326-2328)tCg>tTg	p.S776L	KIAA1211_ENST00000541073.1_Missense_Mutation_p.S769L|KIAA1211_ENST00000264229.6_Missense_Mutation_p.S776L			Q6ZU35	K1211_HUMAN	KIAA1211	776			S -> L (in dbSNP:rs3796547). {ECO:0000269|PubMed:14702039}.					p.S776L(1)		endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CCGGAGAAGTCGGAGATGCAC	0.597													C|||	1212	0.242013	0.1997	0.2334	5008	,	,		14559	0.254		0.34	False		,,,				2504	0.1922				p.S776L		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	1	Substitution - Missense(1)	stomach(1)	c.C2327T						PASS	.	C	LEU/SER	878,3072		96,686,1193	62.0	76.0	72.0		2327	-5.8	0.0	4	dbSNP_107	72	2849,5455		497,1855,1800	yes	missense	KIAA1211	NM_020722.1	145	593,2541,2993	TT,TC,CC		34.3088,22.2278,30.4146	benign	776/1234	57181995	3727,8527	1975	4152	6127	SO:0001583	missense	57482	exon8			AGAAGTCGGAGAT	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2327C>T	4.37:g.57181995C>T	ENSP00000423366:p.Ser776Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	575	0.2632783882783883	84	0.17073170731707318	92	0.2541436464088398	144	0.2517482517482518	255	0.33641160949868076	C	10.70	1.425095	0.25639	0.222278	0.343088	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.10668	2.85;2.85;2.85	4.79	-5.82	0.02333	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.20887	0.049;0.049	B;B	0.12156	0.007;0.007	T	0.48670	-0.9015	8	0.10111	T	0.7	0.6006	10.3039	0.43670	0.0975:0.5901:0.0:0.3124	rs3796547;rs17490484;rs58264499;rs3796547	769;776	F5H1N7;Q6ZU35	.;K1211_HUMAN	L	776;776;769;686	ENSP00000264229:S776L;ENSP00000423366:S776L;ENSP00000444006:S769L	ENSP00000264229:S776L	S	+	2	0	KIAA1211	56876752	0.000000	0.05858	0.000000	0.03702	0.197000	0.23852	-0.293000	0.08320	-1.173000	0.02758	-0.367000	0.07326	TCG	C|0.728;T|0.272	0.272	strong		0.597	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
DUSP13	51207	hgsc.bcm.edu	37	10	76855421	76855421	+	Silent	SNP	G	G	A	rs3740316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:76855421G>A	ENST00000472493.2	-	3	384	c.306C>T	c.(304-306)atC>atT	p.I102I	DUSP13_ENST00000372700.3_Silent_p.I152I|DUSP13_ENST00000607009.1_5'Flank|DUSP13_ENST00000607131.1_Silent_p.I195I|DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000464872.1_Intron|DUSP13_ENST00000478873.2_Silent_p.I238I|DUSP13_ENST00000491677.2_Silent_p.I231I|DUSP13_ENST00000605915.1_Silent_p.I124I	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	102					meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					CGTCCGCCTCGATGCCATAGT	0.557													G|||	1068	0.213259	0.233	0.2406	5008	,	,		21358	0.2649		0.166	False		,,,				2504	0.1626				p.I195I	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.C585T						PASS	.	G	,,,	952,3454	360.6+/-315.3	96,760,1347	265.0	217.0	233.0		,456,585,306	-4.5	0.9	10	dbSNP_107	233	1353,7247	263.4+/-285.0	93,1167,3040	no	utr-3,coding-synonymous,coding-synonymous,coding-synonymous	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1,NM_016364.3	,,,	189,1927,4387	AA,AG,GG		15.7326,21.6069,17.7226	,,,	,152/249,195/292,102/199	76855421	2305,10701	2203	4300	6503	SO:0001819	synonymous_variant	51207	exon5			CGCCTCGATGCCA	AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000472493.2:c.306C>T	10.37:g.76855421G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_001007273	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Silent	SNP	ENST00000472493.2	37	CCDS7346.1																																																																																			G|0.795;A|0.205	0.205	strong		0.557	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3		
ATAD3A	55210	hgsc.bcm.edu	37	1	1458150	1458150	+	Silent	SNP	T	T	C	rs1135025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1458150T>C	ENST00000378755.5	+	8	1015	c.921T>C	c.(919-921)gtT>gtC	p.V307V	ATAD3A_ENST00000378756.3_Silent_p.V259V|ATAD3A_ENST00000536055.1_Silent_p.V180V	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	307					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		TGCTGGCTGTTGGGGTCTACT	0.677													N|||	134	0.0267572	0.0507	0.0504	5008	,	,		14272	0.0109		0.0109	False		,,,				2504	0.0102				p.V307V		Atlas-SNP	.											.	ATAD3A	35	.	0			c.T921C						PASS	.	C	,,	39,4357	795.2+/-415.3	2,35,2161	40.0	52.0	48.0		777,540,921	-9.5	0.0	1	dbSNP_86	48	67,8533	811.9+/-407.1	0,67,4233	no	coding-synonymous,coding-synonymous,coding-synonymous	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	,,	2,102,6394	CC,CT,TT		0.7791,0.8872,0.8156	,,	259/587,180/508,307/635	1458150	106,12890	2198	4300	6498	SO:0001819	synonymous_variant	55210	exon8			GGCTGTTGGGGTC	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.921T>C	1.37:g.1458150T>C		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	384	346	0.901042	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Silent	SNP	ENST00000378755.5	37	CCDS31.1	44	0.020146520146520148	13	0.026422764227642278	15	0.04143646408839779	7	0.012237762237762238	9	0.011873350923482849	c	2.002	-0.429111	0.04701	0.008872	0.007791	ENSG00000197785	ENST00000339113	.	.	.	4.92	-9.49	0.00587	.	.	.	.	.	T	0.18718	0.0449	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58255	-0.7668	4	.	.	.	.	10.7083	0.45969	0.0:0.127:0.3056:0.5674	rs1135025	.	.	.	R	245	.	.	W	+	1	0	ATAD3A	1448013	0.908000	0.30866	0.008000	0.14137	0.071000	0.16799	-0.105000	0.10907	-2.425000	0.00561	-0.768000	0.03414	TGG	T|0.991;C|0.009	0.009	strong		0.677	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
TVP23C	201158	hgsc.bcm.edu	37	17	15406197	15406197	+	Missense_Mutation	SNP	A	A	T	rs12150518	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15406197A>T	ENST00000225576.3	-	6	907	c.812T>A	c.(811-813)cTg>cAg	p.L271Q	TVP23C-CDRT4_ENST00000522212.2_Intron|TVP23C_ENST00000519970.1_Intron	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	271			L -> Q (in dbSNP:rs12150518).			integral component of membrane (GO:0016021)											TCCGGATGCCAGATGAAATTT	0.562													A|||	154	0.0307508	0.0038	0.0389	5008	,	,		14672	0.0218		0.0666	False		,,,				2504	0.0337				p.L271Q		Atlas-SNP	.											.	.	.	.	0			c.T812A						PASS	.	A	,GLN/LEU	66,4338	58.1+/-94.6	1,64,2137	31.0	36.0	34.0		,812	-1.9	0.1	17	dbSNP_120	34	614,7986	159.5+/-212.8	24,566,3710	yes	intron,missense	FAM18B2,FAM18B2-CDRT4	NM_001204478.1,NM_145301.2	,113	25,630,5847	TT,TA,AA		7.1395,1.4986,5.2292	,benign	,271/277	15406197	680,12324	2202	4300	6502	SO:0001583	missense	201158	exon6			GATGCCAGATGAA	BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.812T>A	17.37:g.15406197A>T	ENSP00000225576:p.Leu271Gln	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	162	82	0.506173	NM_145301	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	37	CCDS11170.1	85	0.03891941391941392	2	0.0040650406504065045	18	0.049723756906077346	6	0.01048951048951049	59	0.07783641160949868	A	7.851	0.723912	0.15439	0.014986	0.071395	ENSG00000175106	ENST00000225576	T	0.30981	1.51	3.25	-1.86	0.07760	.	.	.	.	.	T	0.00580	0.0019	N	0.08118	0	0.34736	D	0.730257	B	0.19200	0.034	B	0.12156	0.007	T	0.23440	-1.0188	9	0.87932	D	0	-9.5616	0.3328	0.00321	0.384:0.194:0.2335:0.1885	rs12150518;rs12150518	271	Q96ET8	F18B2_HUMAN	Q	271	ENSP00000225576:L271Q	ENSP00000225576:L271Q	L	-	2	0	FAM18B2	15346922	0.983000	0.35010	0.124000	0.21820	0.386000	0.30323	0.065000	0.14466	-0.437000	0.07243	-0.621000	0.04028	CTG	A|0.951;T|0.049	0.049	strong		0.562	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2	NM_145301	
VARS2	57176	hgsc.bcm.edu	37	6	30887988	30887988	+	Silent	SNP	C	C	T	rs2249459	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30887988C>T	ENST00000321897.5	+	12	1920	c.1288C>T	c.(1288-1290)Ctg>Ttg	p.L430L	VARS2_ENST00000541562.1_Silent_p.L460L|VARS2_ENST00000542001.1_Silent_p.L290L|VARS2_ENST00000416670.2_Silent_p.L430L|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	430					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CGGGGACTGGCTGCAGGTGGT	0.562													C|||	1112	0.222045	0.0983	0.2075	5008	,	,		16319	0.247		0.3559	False		,,,				2504	0.2362				p.L460L		Atlas-SNP	.											.	VARS2	60	.	0			c.C1378T						PASS	.	C	,,	443,2579		34,375,1102	49.0	46.0	47.0		868,1378,1288	3.7	1.0	6	dbSNP_100	47	2042,3376		364,1314,1031	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	398,1689,2133	TT,TC,CC		37.6892,14.6592,29.4431	,,	290/924,460/1094,430/1064	30887988	2485,5955	1511	2709	4220	SO:0001819	synonymous_variant	57176	exon13			GACTGGCTGCAGG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1288C>T	6.37:g.30887988C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			C|0.730;T|0.270	0.270	strong		0.562	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
MICA	100507436	hgsc.bcm.edu	37	6	31379807	31379807	+	Missense_Mutation	SNP	C	C	T	rs1051798	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31379807C>T	ENST00000449934.2	+	4	751	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CTTCTATCCCCGGAATATCAT	0.582													t|||	1823	0.364018	0.4773	0.4063	5008	,	,		19217	0.2996		0.3141	False		,,,				2504	0.2986				p.R233W		Atlas-SNP	.											.	MICA	21	.	0			c.C697T						PASS	.						16.0	20.0	18.0					6																	31379807		692	1589	2281	SO:0001583	missense	100507436	exon4			TATCCCCGGAATA	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.697C>T	6.37:g.31379807C>T	ENSP00000413079:p.Arg233Trp	Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	688	0.315018315018315	200	0.4065040650406504	150	0.4143646408839779	136	0.23776223776223776	202	0.26649076517150394	N	3.279	-0.147379	0.06627	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.15017	2.46;2.46	2.52	-5.05	0.02955	.	1.658740	0.04364	N	0.357915	T	0.02304	0.0071	.	.	.	0.80722	P	0.0	B;B	0.18310	0.027;0.008	B;B	0.09377	0.004;0.002	T	0.28681	-1.0036	8	0.39692	T	0.17	.	1.8464	0.03160	0.1203:0.2683:0.332:0.2794	rs1051798;rs3192174;rs17200323;rs17845521;rs17858411;rs17883108;rs52816780;rs1051798	95;233	Q5SS58;Q96QC4	.;.	W	95;233;190;233;124	ENSP00000413079:R233W;ENSP00000402410:R124W	ENSP00000365394:R233W	R	+	1	2	MICA	31487786	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-9.749000	0.00009	-2.258000	0.00694	-3.922000	0.00016	CGG	C|0.730;T|0.270	0.270	strong		0.582	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
MYT1	4661	hgsc.bcm.edu	37	20	62863580	62863580	+	Silent	SNP	C	C	T	rs41279352	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62863580C>T	ENST00000328439.1	+	19	3103	c.2739C>T	c.(2737-2739)agC>agT	p.S913S	MYT1_ENST00000536311.1_Silent_p.S940S	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)					CTCACAGGAGCGCATCCGGCT	0.632													C|||	241	0.048123	0.0348	0.0159	5008	,	,		17828	0.0417		0.0537	False		,,,				2504	0.09				p.S913S	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											.	MYT1	152	.	0			c.C2739T						PASS	.	C		106,4300	81.9+/-120.4	1,104,2098	53.0	55.0	55.0		2739	-7.0	0.1	20	dbSNP_127	55	451,8147	135.1+/-192.4	7,437,3855	no	coding-synonymous	MYT1	NM_004535.2		8,541,5953	TT,TC,CC		5.2454,2.4058,4.2833		913/1122	62863580	557,12447	2203	4299	6502	SO:0001819	synonymous_variant	4661	exon19			CAGGAGCGCATCC	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.2739C>T	20.37:g.62863580C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000328439.1	37	CCDS13558.1																																																																																			C|0.954;T|0.046	0.046	strong		0.632	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535	
LCA5L	150082	hgsc.bcm.edu	37	21	40800371	40800371	+	Missense_Mutation	SNP	C	C	T	rs2837029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:40800371C>T	ENST00000358268.2	-	4	577	c.49G>A	c.(49-51)Ggc>Agc	p.G17S	LCA5L_ENST00000288350.3_Missense_Mutation_p.G17S|LCA5L_ENST00000485895.2_Missense_Mutation_p.G17S|LCA5L_ENST00000380671.2_Missense_Mutation_p.G17S			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	17			G -> S (in dbSNP:rs2837029).							breast(1)|cervix(1)|endometrium(3)|large_intestine(8)|lung(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	24		Prostate(19;1.2e-06)				AATGCCACGCCGAAGAAATGC	0.368													T|||	1096	0.21885	0.4259	0.1628	5008	,	,		10829	0.0268		0.2157	False		,,,				2504	0.18				p.G17S		Atlas-SNP	.											.	LCA5L	57	.	0			c.G49A						PASS	.	T	SER/GLY	1741,2665	647.6+/-398.6	357,1027,819	108.0	105.0	106.0		49	-3.1	0.0	21	dbSNP_100	106	1703,6897	738.0+/-407.0	180,1343,2777	yes	missense	LCA5L	NM_152505.3	56	537,2370,3596	TT,TC,CC		19.8023,39.5143,26.4801	benign	17/671	40800371	3444,9562	2203	4300	6503	SO:0001583	missense	150082	exon4			CCACGCCGAAGAA	AF121781	CCDS13665.1	21q22.2	2007-12-18	2007-12-18	2007-12-18	ENSG00000157578	ENSG00000157578			1255	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 13"""	C21orf13			Standard	XM_005260926		Approved	MGC33295	uc002yxu.3	O95447	OTTHUMG00000066280	ENST00000358268.2:c.49G>A	21.37:g.40800371C>T	ENSP00000351008:p.Gly17Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	456	0.2087912087912088	206	0.4186991869918699	71	0.19613259668508287	15	0.026223776223776224	164	0.21635883905013192	T	7.581	0.668727	0.14776	0.395143	0.198023	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268;ENST00000418018;ENST00000448288;ENST00000434281;ENST00000438404;ENST00000411566;ENST00000415863;ENST00000426783;ENST00000456017	T;T;T;T;T;T;T;T;T;T;T	0.77877	0.68;0.68;0.68;1.11;1.12;1.12;1.12;1.12;1.14;1.15;-1.13	5.65	-3.13	0.05266	.	1.174020	0.06017	N	0.650621	T	0.00012	0.0000	N	0.04203	-0.255	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.08086	-1.0739	9	0.02654	T	1	0.2877	3.4211	0.07393	0.1051:0.4068:0.1812:0.3069	rs2837029;rs52802136;rs58867617;rs2837029	17;17	C9JFB6;O95447	.;LCA5L_HUMAN	S	17	ENSP00000288350:G17S;ENSP00000370046:G17S;ENSP00000351008:G17S;ENSP00000404521:G17S;ENSP00000405598:G17S;ENSP00000400086:G17S;ENSP00000405130:G17S;ENSP00000412691:G17S;ENSP00000395593:G17S;ENSP00000414784:G17S;ENSP00000407065:G17S	ENSP00000288350:G17S	G	-	1	0	LCA5L	39722241	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.232000	0.02936	-0.792000	0.04480	-0.254000	0.11334	GGC	C|0.751;T|0.249	0.249	strong		0.368	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505	
SMARCAD1	56916	hgsc.bcm.edu	37	4	95173928	95173928	+	Missense_Mutation	SNP	C	C	T	rs139839410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:95173928C>T	ENST00000354268.4	+	9	1124	c.1051C>T	c.(1051-1053)Cca>Tca	p.P351S	SMARCAD1_ENST00000509418.1_5'Flank|SMARCAD1_ENST00000457823.2_Missense_Mutation_p.P351S			Q9H4L7	SMRCD_HUMAN	SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1	351			P -> Q (in dbSNP:rs17854344). {ECO:0000269|PubMed:15489334}.		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)			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)		TGTTTTTAATCCAAAGAGAGT	0.328													C|||	10	0.00199681	0.0008	0.0	5008	,	,		17385	0.0		0.0089	False		,,,				2504	0.0				p.P351S		Atlas-SNP	.											.	SMARCAD1	97	.	0			c.C1051T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	13,4393	20.2+/-43.8	0,13,2190	63.0	62.0	63.0		1051,1051,1051	4.7	1.0	4	dbSNP_134	63	118,8482	61.7+/-123.6	0,118,4182	yes	missense,missense,missense	SMARCAD1	NM_001128429.1,NM_001128430.1,NM_020159.3	74,74,74	0,131,6372	TT,TC,CC		1.3721,0.2951,1.0072	benign,benign,benign	351/1029,351/1029,351/1027	95173928	131,12875	2203	4300	6503	SO:0001583	missense	56916	exon9			TTTAATCCAAAGA	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.1051C>T	4.37:g.95173928C>T	ENSP00000346217:p.Pro351Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_001128429	B7Z799|Q05D56|Q96SX1|Q9H017|Q9H860|Q9NPU9|Q9ULU7	Missense_Mutation	SNP	ENST00000354268.4	37	CCDS3639.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	3.047	-0.196323	0.06259	0.002951	0.013721	ENSG00000163104	ENST00000359052;ENST00000457823;ENST00000354268	D;D;D	0.86497	-2.13;-2.13;-2.13	5.58	4.73	0.59995	.	0.138145	0.33438	N	0.004913	T	0.64360	0.2591	N	0.19112	0.55	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.60767	-0.7198	10	0.06891	T	0.86	-16.2353	4.6152	0.12422	0.1898:0.5119:0.2238:0.0744	.	351;351	Q9H4L7;Q9H4L7-2	SMRCD_HUMAN;.	S	351	ENSP00000351947:P351S;ENSP00000415576:P351S;ENSP00000346217:P351S	ENSP00000346217:P351S	P	+	1	0	SMARCAD1	95392951	0.773000	0.28580	0.998000	0.56505	0.957000	0.61999	0.745000	0.26259	2.630000	0.89119	0.655000	0.94253	CCA	C|0.992;T|0.008	0.008	strong		0.328	SMARCAD1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253583.1	NM_020159	
C1orf68	100129271	hgsc.bcm.edu	37	1	152692074	152692074	+	Missense_Mutation	SNP	G	G	C	rs1332500	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152692074G>C	ENST00000368775.2	+	1	77	c.77G>C	c.(76-78)aGc>aCc	p.S26T		NM_001024679.2	NP_001019850.1	Q5T750	XP32_HUMAN	chromosome 1 open reading frame 68	26			S -> T (in dbSNP:rs1332500).		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)		p.S26T(1)		NS(1)|breast(1)|lung(2)|prostate(1)|stomach(3)	8						GGGCAGGGTAGCAATGGTGCC	0.522													C|||	1749	0.349241	0.5461	0.3804	5008	,	,		17303	0.1716		0.3608	False		,,,				2504	0.2321				p.S26T		Atlas-SNP	.											C1orf68,NS,carcinoma,0,1	C1orf68	19	1	1	Substitution - Missense(1)	stomach(1)	c.G77C						PASS	.						102.0	100.0	101.0					1																	152692074		692	1591	2283	SO:0001583	missense	100129271	exon1			AGGGTAGCAATGG	AF005081	CCDS44226.1	1q21.3	2014-05-30			ENSG00000198854	ENSG00000198854			29468	protein-coding gene	gene with protein product						11698679	Standard	NM_001024679		Approved	LEP7	uc010pdu.2	Q5T750	OTTHUMG00000012401	ENST00000368775.2:c.77G>C	1.37:g.152692074G>C	ENSP00000357764:p.Ser26Thr	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	178	175	0.983146	NM_001024679	O14634	Missense_Mutation	SNP	ENST00000368775.2	37	CCDS44226.1	767	0.35119047619047616	259	0.5264227642276422	137	0.3784530386740331	103	0.18006993006993008	268	0.35356200527704484	C	0.012	-1.673937	0.00758	.	.	ENSG00000198854	ENST00000362017;ENST00000368775	T;T	0.23950	1.88;1.88	3.86	0.885	0.19188	.	0.835692	0.10039	N	0.723727	T	0.01835	0.0058	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44065	-0.9352	9	0.02654	T	1	3.1982	2.9191	0.05762	0.1703:0.3719:0.3561:0.1017	rs1332500;rs1332500	26	Q5T750	XP32_HUMAN	T	26	ENSP00000354769:S26T;ENSP00000357764:S26T	ENSP00000354769:S26T	S	+	2	0	C1orf68	150958698	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.412000	0.21131	-0.012000	0.14223	-0.908000	0.02827	AGC	G|0.655;C|0.345	0.345	strong		0.522	C1orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034521.2	NM_001024679	
MUC16	94025	hgsc.bcm.edu	37	19	9083427	9083427	+	Silent	SNP	A	A	G	rs1609453	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9083427A>G	ENST00000397910.4	-	1	8591	c.8388T>C	c.(8386-8388)gcT>gcC	p.A2796A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2796	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						CTCCAGAGCTAGCCATACCCT	0.502													G|||	1065	0.21266	0.1536	0.2752	5008	,	,		21615	0.3036		0.173	False		,,,				2504	0.1953				p.A2796A		Atlas-SNP	.											.	MUC16	4315	.	0			c.T8388C						PASS	.	G		565,3315		41,483,1416	64.0	64.0	64.0		8388	0.2	0.0	19	dbSNP_88	64	1489,6807		127,1235,2786	no	coding-synonymous	MUC16	NM_024690.2		168,1718,4202	GG,GA,AA		17.9484,14.5619,16.8693		2796/14508	9083427	2054,10122	1940	4148	6088	SO:0001819	synonymous_variant	94025	exon1			AGAGCTAGCCATA	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.8388T>C	19.37:g.9083427A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			A|0.789;G|0.211	0.211	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
C10orf71	118461	hgsc.bcm.edu	37	10	50532588	50532588	+	Missense_Mutation	SNP	C	C	G	rs10857469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50532588C>G	ENST00000374144.3	+	3	2286	c.1998C>G	c.(1996-1998)caC>caG	p.H666Q	C10orf71_ENST00000323868.4_Missense_Mutation_p.H666Q			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	666			H -> Q (in dbSNP:rs10857469).							endometrium(1)	1						TGAAGACCCACCAGCTAGAGA	0.532													C|||	478	0.0954473	0.053	0.0663	5008	,	,		19595	0.122		0.1193	False		,,,				2504	0.1217				p.H666Q		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1998G						PASS	.	C	GLN/HIS,GLN/HIS	190,3550		3,184,1683	36.0	39.0	38.0		1998,1998	-1.2	0.0	10	dbSNP_120	38	1085,7137		68,949,3094	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	24,24	71,1133,4777	GG,GC,CC		13.1963,5.0802,10.6588	benign,benign	666/1436,666/720	50532588	1275,10687	1870	4111	5981	SO:0001583	missense	118461	exon3			GACCCACCAGCTA	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.1998C>G	10.37:g.50532588C>G	ENSP00000363259:p.His666Gln	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	211	0.09661172161172162	32	0.06504065040650407	30	0.08287292817679558	60	0.1048951048951049	89	0.11741424802110818	C	11.54	1.669304	0.29604	0.050802	0.131963	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.14893	2.47;3.59	5.53	-1.24	0.09435	.	0.981567	0.08269	N	0.971860	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B	0.10296	0.003	B	0.13407	0.009	T	0.44574	-0.9319	9	0.10636	T	0.68	.	6.3808	0.21533	0.0:0.3596:0.4084:0.232	rs10857469;rs59643639;rs10857469	666	Q711Q0-3	.	Q	666	ENSP00000318713:H666Q;ENSP00000363259:H666Q	ENSP00000318713:H666Q	H	+	3	2	C10orf71	50202594	0.000000	0.05858	0.000000	0.03702	0.648000	0.38561	-0.954000	0.03873	-0.536000	0.06298	0.591000	0.81541	CAC	C|0.906;G|0.094	0.094	strong		0.532	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
ADAMTS4	9507	hgsc.bcm.edu	37	1	161168189	161168189	+	Missense_Mutation	SNP	C	C	T	rs34448954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161168189C>T	ENST00000367996.5	-	1	657	c.229G>A	c.(229-231)Gcc>Acc	p.A77T	ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Missense_Mutation_p.A77T|NDUFS2_ENST00000367993.3_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	77			A -> T (in dbSNP:rs34448954). {ECO:0000269|PubMed:9734811}.		defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	CTGGCAGGGGCGCCCGAGCCA	0.677													C|||	257	0.0513179	0.0068	0.0418	5008	,	,		15569	0.0099		0.1113	False		,,,				2504	0.0992				p.A77T		Atlas-SNP	.											ADAMTS4_ENST00000367996,rectum,carcinoma,0,2	ADAMTS4	171	2	0			c.G229A						PASS	.	C	THR/ALA	82,4276		4,74,2101	12.0	12.0	12.0		229	-6.9	0.0	1	dbSNP_126	12	831,7711		48,735,3488	yes	missense	ADAMTS4	NM_005099.4	58	52,809,5589	TT,TC,CC		9.7284,1.8816,7.0775	benign	77/838	161168189	913,11987	2179	4271	6450	SO:0001583	missense	9507	exon1			CAGGGGCGCCCGA	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.229G>A	1.37:g.161168189C>T	ENSP00000356975:p.Ala77Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	93	36	0.387097	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Missense_Mutation	SNP	ENST00000367996.5	37	CCDS1223.1	117	0.05357142857142857	7	0.014227642276422764	17	0.04696132596685083	6	0.01048951048951049	87	0.11477572559366754	C	11.17	1.560306	0.27827	0.018816	0.097284	ENSG00000158859	ENST00000367996;ENST00000367995	T;T	0.07021	3.23;3.23	5.48	-6.94	0.01633	Peptidase M12B, propeptide (1);	1.266050	0.05430	N	0.545706	T	0.00936	0.0031	N	0.08118	0	0.09310	N	0.999995	B;B	0.22346	0.004;0.068	B;B	0.27887	0.003;0.084	T	0.47018	-0.9149	10	0.28530	T	0.3	.	2.4191	0.04444	0.4451:0.2678:0.082:0.2051	rs34448954	77;77	Q5VTW1;O75173	.;ATS4_HUMAN	T	77	ENSP00000356975:A77T;ENSP00000356974:A77T	ENSP00000356974:A77T	A	-	1	0	ADAMTS4	159434813	0.000000	0.05858	0.000000	0.03702	0.828000	0.46876	-1.501000	0.02281	-0.961000	0.03609	0.491000	0.48974	GCC	C|0.946;T|0.054	0.054	strong		0.677	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
PDLIM2	64236	hgsc.bcm.edu	37	8	22442661	22442661	+	Silent	SNP	A	A	G	rs2294047	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22442661A>G	ENST00000397760.4	+	5	847	c.447A>G	c.(445-447)gcA>gcG	p.A149A	PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000409141.1_Silent_p.A149A|PDLIM2_ENST00000397761.2_Silent_p.A149A|PDLIM2_ENST00000339162.7_Silent_p.A149A|PDLIM2_ENST00000409417.1_Silent_p.A149A|PDLIM2_ENST00000265810.4_Silent_p.A149A|PDLIM2_ENST00000308354.7_Silent_p.A399A			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	149	Ser-rich.			A -> R (in Ref. 4; AAL55747). {ECO:0000305}.		actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		CTGGAGAGGCAGCCATCAGCC	0.657													G|||	2925	0.584065	0.5915	0.6527	5008	,	,		17391	0.4673		0.6123	False		,,,				2504	0.6166				p.A399A		Atlas-SNP	.											.	PDLIM2	42	.	0			c.A1197G						PASS	.	G	,,	2634,1772	517.7+/-369.5	785,1064,354	48.0	47.0	48.0		1197,447,447	-11.1	0.0	8	dbSNP_100	48	5134,3466	504.6+/-376.2	1543,2048,709	no	coding-synonymous,coding-synonymous,coding-synonymous	PDLIM2	NM_021630.5,NM_176871.3,NM_198042.3	,,	2328,3112,1063	GG,GA,AA		40.3023,40.2179,40.2737	,,	399/603,149/367,149/279	22442661	7768,5238	2203	4300	6503	SO:0001819	synonymous_variant	64236	exon5			AGAGGCAGCCATC	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.447A>G	8.37:g.22442661A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	58	0.402778	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Silent	SNP	ENST00000397760.4	37																																																																																				A|0.422;G|0.578	0.578	strong		0.657	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1		
CHAD	1101	hgsc.bcm.edu	37	17	48543154	48543154	+	Silent	SNP	G	G	A	rs2231507	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48543154G>A	ENST00000508540.1	-	2	1004	c.852C>T	c.(850-852)ccC>ccT	p.P284P	ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000541920.1_Intron|CHAD_ENST00000258969.4_Silent_p.P284P|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000502667.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	284					bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGAAGTTGGAGGGTAGCTGGT	0.577													G|||	121	0.0241613	0.0015	0.0202	5008	,	,		16822	0.0		0.0527	False		,,,				2504	0.0532				p.P284P		Atlas-SNP	.											CHAD,upper_leg,malignant_melanoma,-2,1	CHAD	36	1	0			c.C852T						PASS	.	G	,	35,4371	40.0+/-72.8	0,35,2168	206.0	176.0	186.0		852,	-3.4	0.7	17	dbSNP_98	186	406,8194	128.2+/-186.4	13,380,3907	no	coding-synonymous,intron	CHAD,ACSF2	NM_001267.2,NM_025149.4	,	13,415,6075	AA,AG,GG		4.7209,0.7944,3.3907	,	284/360,	48543154	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	1101	exon2			GTTGGAGGGTAGC	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1909	protein-coding gene	gene with protein product	"""chondroadherin proteoglycan"""	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.852C>T	17.37:g.48543154G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_001267	A8K812|Q6GTU0|Q96RJ5	Silent	SNP	ENST00000508540.1	37	CCDS11568.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
OR13D1	286365	hgsc.bcm.edu	37	9	107456933	107456933	+	Silent	SNP	C	C	T	rs12347076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107456933C>T	ENST00000318763.5	+	1	274	c.231C>T	c.(229-231)ctC>ctT	p.L77L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	77						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						ATAGCCTCCTCATTATCATCA	0.448													C|||	1354	0.270367	0.1657	0.183	5008	,	,		20502	0.4821		0.1909	False		,,,				2504	0.3374				p.L77L		Atlas-SNP	.											.	OR13D1	42	.	0			c.C231T						PASS	.	C		789,3617	319.1+/-295.9	75,639,1489	208.0	208.0	208.0		231	0.3	0.2	9	dbSNP_120	208	1824,6776	328.2+/-318.2	224,1376,2700	no	coding-synonymous	OR13D1	NM_001004484.1		299,2015,4189	TT,TC,CC		21.2093,17.9074,20.0907		77/347	107456933	2613,10393	2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			CCTCCTCATTATC		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.231C>T	9.37:g.107456933C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	179	90	0.502793	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	37	CCDS35094.1																																																																																			C|0.771;T|0.229	0.229	strong		0.448	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
UBOX5	22888	hgsc.bcm.edu	37	20	3090848	3090848	+	Silent	SNP	T	T	G	rs708973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3090848T>G	ENST00000217173.2	-	5	2001	c.1530A>C	c.(1528-1530)cgA>cgC	p.R510R	UBOX5-AS1_ENST00000446537.1_RNA|UBOX5_ENST00000348031.2_Silent_p.R456R|UBOX5-AS1_ENST00000454019.1_RNA	NM_001267584.1|NM_014948.3	NP_001254513.1|NP_055763.1			U-box domain containing 5											endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(2)|prostate(1)|skin(1)	20						CCAGGCAGGGTCGGCACAGGA	0.617													T|||	1080	0.215655	0.1543	0.2666	5008	,	,		16634	0.119		0.3111	False		,,,				2504	0.2638				p.T509P		Atlas-SNP	.											.	UBOX5	47	.	0			c.A1525C						PASS	.	T	,	731,3675	298.1+/-285.1	57,617,1529	67.0	72.0	70.0		1530,1368	-7.3	0.9	20	dbSNP_86	70	3054,5546	458.6+/-364.7	554,1946,1800	no	coding-synonymous,coding-synonymous	UBOX5	NM_014948.2,NM_199415.1	,	611,2563,3329	GG,GT,TT		35.5116,16.591,29.102	,	510/542,456/488	3090848	3785,9221	2203	4300	6503	SO:0001819	synonymous_variant	22888	exon5			GCAGGGTCGGCAC	AB020667	CCDS13046.1, CCDS13047.1	20p13	2013-01-28			ENSG00000185019	ENSG00000185019		"""RING-type (C3HC4) zinc fingers"", ""U-box domain containing"""	17777	protein-coding gene	gene with protein product						11274149	Standard	NM_014948		Approved	UIP5, KIAA0860, Ubce7ip5, RNF37	uc002whw.4	O94941	OTTHUMG00000031731	ENST00000217173.2:c.1530A>C	20.37:g.3090848T>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001267584		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1																																																																																			T|0.734;G|0.266	0.266	strong		0.617	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948	
HNRNPH1	3187	hgsc.bcm.edu	37	5	179044053	179044053	+	Splice_Site	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179044053G>A	ENST00000356731.5	-	9	2651	c.1116C>T	c.(1114-1116)taC>taT	p.Y372Y	HNRNPH1_ENST00000393432.4_Splice_Site_p.Y372Y|HNRNPH1_ENST00000442819.2_Splice_Site_p.Y372Y|HNRNPH1_ENST00000511300.2_Silent_p.Y102Y|HNRNPH1_ENST00000524180.1_5'Flank|HNRNPH1_ENST00000510411.1_Silent_p.Y372Y|HNRNPH1_ENST00000329433.6_Splice_Site_p.Y372Y			P31943	HNRH1_HUMAN	heterogeneous nuclear ribonucleoprotein H1 (H)	372	2 X 16 AA Gly-rich approximate repeats.|2 X 19 AA perfect repeats.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA splicing (GO:0043484)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|skin(1)	14						TTTGGCTACCGTAAGCACCAC	0.373																																					p.Y372Y		Atlas-SNP	.											HNRPH1,NS,carcinoma,-2,3	HNRNPH1	62	3	0			c.C1116T						scavenged	.						105.0	102.0	103.0					5																	179044053		2203	4300	6503	SO:0001630	splice_region_variant	3187	exon10			GCTACCGTAAGCA	BC001348	CCDS4446.1	5q35.3	2013-02-12		2008-04-18	ENSG00000169045	ENSG00000169045		"""RNA binding motif (RRM) containing"""	5041	protein-coding gene	gene with protein product		601035		HNRPH1		7499401	Standard	NM_005520		Approved	hnRNPH	uc003mkf.5	P31943	OTTHUMG00000130908	ENST00000356731.5:c.1117+1C>T	5.37:g.179044053G>A		Somatic	348	2	0.00574713		WXS	Illumina HiSeq	Phase_I	367	5	0.013624	NM_001257293	B3KW86|D3DWQ2|Q6IBM4	Silent	SNP	ENST00000356731.5	37	CCDS4446.1	.	.	.	.	.	.	.	.	.	.	g	12.51	1.960606	0.34565	.	.	ENSG00000169045	ENST00000521173	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	T	0.58750	0.2144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57271	-0.7840	4	.	.	.	-9.1144	8.0021	0.30304	0.192:0.0:0.808:0.0	.	.	.	.	M	247	.	.	T	-	2	0	HNRNPH1	178976659	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.877000	0.28106	2.730000	0.93505	0.644000	0.83932	ACG	.	.	none		0.373	HNRNPH1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253497.3	NM_005520	Silent
C7orf33	202865	hgsc.bcm.edu	37	7	148288135	148288135	+	Silent	SNP	C	C	T	rs111320068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:148288135C>T	ENST00000307003.2	+	1	479	c.118C>T	c.(118-120)Ctg>Ttg	p.L40L		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	40										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TGACCTTCGCCTGAGTGGGAG	0.552													C|||	131	0.0261581	0.0015	0.0908	5008	,	,		17766	0.001		0.0249	False		,,,				2504	0.0409				p.L40L		Atlas-SNP	.											.	C7orf33	28	.	0			c.C118T						PASS	.	C		39,4367	43.1+/-76.7	1,37,2165	91.0	76.0	81.0		118	1.9	0.0	7	dbSNP_132	81	296,8304	108.4+/-169.1	4,288,4008	no	coding-synonymous	C7orf33	NM_145304.2		5,325,6173	TT,TC,CC		3.4419,0.8852,2.5757		40/178	148288135	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	202865	exon1			CTTCGCCTGAGTG	BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.118C>T	7.37:g.148288135C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_145304		Silent	SNP	ENST00000307003.2	37	CCDS5890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.552	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304	
RSPH1	89765	hgsc.bcm.edu	37	21	43905887	43905887	+	Silent	SNP	C	C	T	rs2839536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43905887C>T	ENST00000291536.3	-	5	560	c.393G>A	c.(391-393)gcG>gcA	p.A131A	RSPH1_ENST00000398352.3_Silent_p.A93A	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	131					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)				large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						TGCCCGTCTCCGCGTATAAAT	0.517													C|||	1399	0.279353	0.0817	0.6182	5008	,	,		22217	0.1994		0.3728	False		,,,				2504	0.2924				p.A131A	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											.	RSPH1	36	.	0			c.G393A						PASS	.	C		626,3780	269.5+/-269.1	49,528,1626	162.0	139.0	147.0		393	-9.7	0.6	21	dbSNP_100	147	3379,5221	501.5+/-375.5	680,2019,1601	no	coding-synonymous	RSPH1	NM_080860.2		729,2547,3227	TT,TC,CC		39.2907,14.2079,30.7935		131/310	43905887	4005,9001	2203	4300	6503	SO:0001819	synonymous_variant	89765	exon5			CGTCTCCGCGTAT	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"""meichroacidin"""	609314	"""testis specific A2 homolog (mouse)"""	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.393G>A	21.37:g.43905887C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	37	CCDS13688.1																																																																																			C|0.704;T|0.296	0.296	strong		0.517	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		
MS4A6A	64231	hgsc.bcm.edu	37	11	59945789	59945789	+	Splice_Site	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:59945789A>G	ENST00000530839.1	-	5	775	c.283T>C	c.(283-285)Ttt>Ctt	p.F95L	MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000323961.3_Splice_Site_p.F95L|MS4A6A_ENST00000529054.1_Splice_Site_p.F123L|MS4A6A_ENST00000426738.2_Splice_Site_p.F50L|MS4A6A_ENST00000412309.2_Splice_Site_p.F123L|MS4A6A_ENST00000528851.1_Splice_Site_p.F95L|MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000420732.2_Splice_Site_p.F95L	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	95						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						GAGATGATAAACTAAGATAAA	0.393																																					p.F123L		Atlas-SNP	.											.	MS4A6A	85	.	0			c.T367C						PASS	.						113.0	110.0	111.0					11																	59945789		2201	4295	6496	SO:0001630	splice_region_variant	64231	exon5			TGATAAACTAAGA	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.283-1T>C	11.37:g.59945789A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	130	60	0.461538	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Missense_Mutation	SNP	ENST00000530839.1	37	CCDS7981.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.775052	0.70107	.	.	ENSG00000110077	ENST00000323961;ENST00000528851;ENST00000420732;ENST00000530839;ENST00000529054;ENST00000426738;ENST00000412309	T;T;T;T;T;T;T	0.03242	4.0;4.0;4.0;4.0;4.0;4.0;4.0	4.73	3.6	0.41247	.	0.201048	0.42821	D	0.000645	T	0.12305	0.0299	M	0.81682	2.555	0.34555	D	0.711745	D;D;D;D;P	0.55385	0.971;0.964;0.971;0.971;0.703	P;P;P;P;B	0.57548	0.716;0.728;0.823;0.823;0.342	T	0.08351	-1.0726	10	0.66056	D	0.02	.	6.9541	0.24562	0.8964:0.0:0.1036:0.0	.	50;123;123;95;95	E7EMT7;F8W9K1;E9PSA9;Q9H2W1;Q9H2W1-3	.;.;.;M4A6A_HUMAN;.	L	95;95;95;95;123;50;123	ENSP00000315878:F95L;ENSP00000431901:F95L;ENSP00000392921:F95L;ENSP00000436979:F95L;ENSP00000435844:F123L;ENSP00000392770:F50L;ENSP00000403212:F123L	ENSP00000315878:F95L	F	-	1	0	MS4A6A	59702365	1.000000	0.71417	0.772000	0.31596	0.009000	0.06853	2.298000	0.43602	0.942000	0.37525	0.533000	0.62120	TTT	.	.	none		0.393	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		Missense_Mutation
RETNLB	84666	hgsc.bcm.edu	37	3	108475974	108475974	+	Missense_Mutation	SNP	G	G	A	rs11708527	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:108475974G>A	ENST00000295755.6	-	1	257	c.59C>T	c.(58-60)cCg>cTg	p.P20L	RETNLB_ENST00000482939.1_5'Flank	NM_032579.2	NP_115968.1	Q9BQ08	RETNB_HUMAN	resistin like beta	20			P -> L (in dbSNP:rs11708527).		cell proliferation (GO:0008283)	extracellular region (GO:0005576)				endometrium(1)|kidney(3)|lung(10)|prostate(1)|skin(1)	16						AGTACTCCCCGGGTTGATCAG	0.532													G|||	1005	0.200679	0.1165	0.232	5008	,	,		19248	0.0377		0.2783	False		,,,				2504	0.3804				p.P20L		Atlas-SNP	.											RETNLB,NS,carcinoma,+1,1	RETNLB	38	1	0			c.C59T						PASS	.	G	LEU/PRO	644,3762	276.6+/-273.2	45,554,1604	68.0	62.0	64.0		59	2.5	0.0	3	dbSNP_120	64	2467,6133	405.7+/-348.6	360,1747,2193	yes	missense	RETNLB	NM_032579.2	98	405,2301,3797	AA,AG,GG		28.686,14.6164,23.9197	possibly-damaging	20/112	108475974	3111,9895	2203	4300	6503	SO:0001583	missense	84666	exon1			CTCCCCGGGTTGA	AF290873	CCDS2953.1	3q13.1	2008-02-05			ENSG00000163515	ENSG00000163515			20388	protein-coding gene	gene with protein product		605645				10921885, 12574343	Standard	NM_032579		Approved	HXCP2, FIZZ2, RELMb	uc003dxh.2	Q9BQ08	OTTHUMG00000159393	ENST00000295755.6:c.59C>T	3.37:g.108475974G>A	ENSP00000295755:p.Pro20Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_032579	Q14D27	Missense_Mutation	SNP	ENST00000295755.6	37	CCDS2953.1	352	0.16117216117216118	43	0.08739837398373984	76	0.20994475138121546	23	0.04020979020979021	210	0.2770448548812665	G	12.09	1.833577	0.32421	0.146164	0.28686	ENSG00000163515	ENST00000295755	T	0.41758	0.99	4.38	2.52	0.30459	.	0.512899	0.16570	N	0.208678	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	P	0.41848	0.763	B	0.28638	0.092	T	0.30822	-0.9965	9	0.48119	T	0.1	-0.3382	5.1548	0.15029	0.1077:0.0:0.6897:0.2027	rs11708527;rs52797386;rs57988437;rs11708527	20	Q9BQ08	RETNB_HUMAN	L	20	ENSP00000295755:P20L	ENSP00000295755:P20L	P	-	2	0	RETNLB	109958664	0.000000	0.05858	0.001000	0.08648	0.097000	0.18754	0.091000	0.15046	0.450000	0.26774	0.655000	0.94253	CCG	G|0.795;A|0.205	0.205	strong		0.532	RETNLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355093.1		
HLX	3142	hgsc.bcm.edu	37	1	221057739	221057739	+	Missense_Mutation	SNP	C	C	G	rs11578466	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:221057739C>G	ENST00000366903.6	+	4	2661	c.1160C>G	c.(1159-1161)gCc>gGc	p.A387G	HLX_ENST00000549319.1_Missense_Mutation_p.A173G	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	387	Ser-rich.		A -> G (in dbSNP:rs11578466).		cell differentiation (GO:0030154)|embryonic digestive tract morphogenesis (GO:0048557)|enteric nervous system development (GO:0048484)|liver development (GO:0001889)|multicellular organismal development (GO:0007275)|negative regulation of T-helper 2 cell differentiation (GO:0045629)|positive regulation of cell proliferation (GO:0008284)|positive regulation of organ growth (GO:0046622)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(9)|lung(11)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	32				GBM - Glioblastoma multiforme(131;0.00914)		CTGGACATGGCCCCCAGCGAC	0.652													C|||	374	0.0746805	0.0719	0.1066	5008	,	,		15491	0.001		0.162	False		,,,				2504	0.0419				p.A387G		Atlas-SNP	.											.	HLX	67	.	0			c.C1160G						PASS	.	C	GLY/ALA	351,4055	169.4+/-200.1	11,329,1863	58.0	52.0	54.0		1160	3.2	1.0	1	dbSNP_120	54	1287,7313	245.7+/-274.4	100,1087,3113	yes	missense	HLX	NM_021958.3	60	111,1416,4976	GG,GC,CC		14.9651,7.9664,12.5942	possibly-damaging	387/489	221057739	1638,11368	2203	4300	6503	SO:0001583	missense	3142	exon4			ACATGGCCCCCAG	BC033808	CCDS1527.1	1q41	2011-06-20	2007-07-26	2007-07-26	ENSG00000136630	ENSG00000136630		"""Homeoboxes / ANTP class : NKL subclass"""	4978	protein-coding gene	gene with protein product		142995	"""H2.0 (Drosophila)-like homeo box 1"", ""H2.0-like homeobox 1 (Drosophila)"", ""H2.0-like homeobox 1"""	HLX1		1676597, 7806220	Standard	NM_021958		Approved	HB24	uc001hmv.4	Q14774	OTTHUMG00000037352	ENST00000366903.6:c.1160C>G	1.37:g.221057739C>G	ENSP00000355870:p.Ala387Gly	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	171	81	0.473684	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	214	0.09798534798534798	46	0.09349593495934959	43	0.11878453038674033	0	0.0	125	0.16490765171503957	C	17.06	3.292686	0.59976	0.079664	0.149651	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;T;T	0.90676	-2.71;0.61;0.61	5.03	3.16	0.36331	.	0.487636	0.18752	N	0.132160	T	0.01061	0.0035	N	0.12746	0.255	0.30258	P	0.79347	B	0.15141	0.012	B	0.18263	0.021	T	0.39941	-0.9589	9	0.35671	T	0.21	-14.8358	8.3626	0.32367	0.0:0.7502:0.0:0.2498	rs11578466;rs11578466	387	Q14774	HLX_HUMAN	G	387;120;173	ENSP00000355870:A387G;ENSP00000408248:A120G;ENSP00000449882:A173G	ENSP00000355870:A387G	A	+	2	0	HLX	219124362	0.747000	0.28283	1.000000	0.80357	0.933000	0.57130	1.083000	0.30815	0.642000	0.30620	0.561000	0.74099	GCC	C|0.877;G|0.123	0.123	strong		0.652	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958	
OR5D16	390144	hgsc.bcm.edu	37	11	55606302	55606302	+	Silent	SNP	G	G	T	rs6591699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55606302G>T	ENST00000378396.1	+	1	75	c.75G>T	c.(73-75)ctG>ctT	p.L25L		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				ACCTGGAACTGCAAATTCCCC	0.418													N|||	3371	0.673123	0.6112	0.683	5008	,	,		17728	0.7718		0.6163	False		,,,				2504	0.7065				p.L25L		Atlas-SNP	.											OR5D16,NS,carcinoma,+1,1	OR5D16	94	1	0			c.G75T						scavenged	.	G		2788,1614		906,976,319	111.0	102.0	105.0		75	-3.2	0.0	11	dbSNP_116	105	5389,3203		1699,1991,606	no	coding-synonymous	OR5D16	NM_001005496.1		2605,2967,925	TT,TG,GG		37.2789,36.6652,37.071		25/329	55606302	8177,4817	2201	4296	6497	SO:0001819	synonymous_variant	390144	exon1			GGAACTGCAAATT	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.75G>T	11.37:g.55606302G>T		Somatic	300	2	0.00666667		WXS	Illumina HiSeq	Phase_I	276	276	1	NM_001005496	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																			G|0.350;T|0.650	0.650	strong		0.418	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
OR13A1	79290	hgsc.bcm.edu	37	10	45799451	45799451	+	Silent	SNP	C	C	T	rs17157674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45799451C>T	ENST00000553795.1	-	4	728	c.420G>A	c.(418-420)cgG>cgA	p.R140R	OR13A1_ENST00000536058.1_Silent_p.R140R|OR13A1_ENST00000374401.2_Silent_p.R140R	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						TGGCTGCGTACCGGTCATAGG	0.617													C|||	38	0.00758786	0.0265	0.0043	5008	,	,		19585	0.0		0.0	False		,,,				2504	0.0				p.R140R		Atlas-SNP	.											.	OR13A1	49	.	0			c.G420A						PASS	.	C		83,4323	69.2+/-107.0	1,81,2121	35.0	28.0	30.0		420	-6.5	0.1	10	dbSNP_123	30	0,8600		0,0,4300	no	coding-synonymous	OR13A1	NM_001004297.2		1,81,6421	TT,TC,CC		0.0,1.8838,0.6382		140/329	45799451	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	79290	exon4			TGCGTACCGGTCA	AB065728	CCDS31188.1	10q11.21	2012-10-03			ENSG00000256574	ENSG00000256574		"""GPCR / Class A : Olfactory receptors"""	14772	protein-coding gene	gene with protein product							Standard	NM_001004297		Approved		uc001jcc.1	Q8NGR1	OTTHUMG00000018080	ENST00000553795.1:c.420G>A	10.37:g.45799451C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Silent	SNP	ENST00000553795.1	37	CCDS31188.1																																																																																			C|0.992;T|0.008	0.008	strong		0.617	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297	
SALL3	27164	hgsc.bcm.edu	37	18	76753588	76753588	+	Missense_Mutation	SNP	A	A	G	rs7240860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:76753588A>G	ENST00000537592.2	+	2	1597	c.1597A>G	c.(1597-1599)Act>Gct	p.T533A	SALL3_ENST00000575389.2_Missense_Mutation_p.T533A|SALL3_ENST00000536229.3_Missense_Mutation_p.T400A	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	533			T -> A (in dbSNP:rs7240860).		forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		ACTGCCGCCCACTGTCCCTGG	0.741													A|||	3600	0.71885	0.3374	0.8242	5008	,	,		11859	0.9127		0.8459	False		,,,				2504	0.8292				p.T533A		Atlas-SNP	.											SALL3,NS,carcinoma,0,1	SALL3	162	1	0			c.A1597G						scavenged	.	A	ALA/THR	1821,2527		397,1027,750	12.0	11.0	11.0		1597	2.7	0.2	18	dbSNP_116	11	7027,1441		2953,1121,160	no	missense	SALL3	NM_171999.2	58	3350,2148,910	GG,GA,AA		17.017,41.8813,30.9613	possibly-damaging	533/1301	76753588	8848,3968	2174	4234	6408	SO:0001583	missense	27164	exon2			CCGCCCACTGTCC	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.1597A>G	18.37:g.76753588A>G	ENSP00000441823:p.Thr533Ala	Somatic	3	1	0.333333		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	1629	0.7458791208791209	158	0.32113821138211385	307	0.8480662983425414	532	0.9300699300699301	632	0.8337730870712401	A	3.488	-0.104379	0.06967	0.418813	0.82983	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.10288	2.89	5.2	2.73	0.32206	.	0.000000	0.64402	D	0.000017	T	0.00012	0.0000	M	0.70842	2.15	0.09310	P	0.999999037973	P;P	0.52577	0.712;0.954	B;B	0.43950	0.396;0.437	T	0.11155	-1.0599	9	0.42905	T	0.14	-37.6074	8.1421	0.31089	0.7253:0.1343:0.0:0.1405	rs7240860	265;533	F5GXY4;Q9BXA9	.;SALL3_HUMAN	A	533;533;265	ENSP00000441823:T533A	ENSP00000299466:T533A	T	+	1	0	SALL3	74854576	1.000000	0.71417	0.204000	0.23530	0.006000	0.05464	4.407000	0.59754	0.267000	0.21916	-0.460000	0.05396	ACT	A|0.251;G|0.749	0.749	strong		0.741	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
MMADHC	27249	hgsc.bcm.edu	37	2	150432976	150432976	+	Silent	SNP	C	C	T	rs11545261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:150432976C>T	ENST00000428879.1	-	4	957	c.453G>A	c.(451-453)caG>caA	p.Q151Q	MMADHC_ENST00000422782.2_Silent_p.Q151Q|MMADHC_ENST00000303319.5_Silent_p.Q151Q			Q9H3L0	MMAD_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblD type, with homocystinuria	151					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)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(2)	11						CTGGACATGTCTGTATTGCAC	0.338													T|||	3804	0.759585	0.447	0.7954	5008	,	,		17574	0.876		0.8907	False		,,,				2504	0.9018				p.Q151Q		Atlas-SNP	.											.	MMADHC	20	.	0			c.G453A						PASS	.	T		2274,2132	579.6+/-385.0	613,1048,542	159.0	138.0	145.0		453	0.2	1.0	2	dbSNP_120	145	7792,808	187.3+/-234.6	3521,750,29	no	coding-synonymous	MMADHC	NM_015702.2		4134,1798,571	TT,TC,CC		9.3953,48.3886,22.605		151/297	150432976	10066,2940	2203	4300	6503	SO:0001819	synonymous_variant	27249	exon5			ACATGTCTGTATT	BC023995	CCDS2189.1	2q23	2011-05-12	2009-01-08	2009-01-08	ENSG00000168288	ENSG00000168288			25221	protein-coding gene	gene with protein product		611935	"""chromosome 2 open reading frame 25"""	C2orf25		18385497	Standard	NM_015702		Approved	CL25022, cblD	uc002txc.3	Q9H3L0	OTTHUMG00000155558	ENST00000428879.1:c.453G>A	2.37:g.150432976C>T		Somatic	271	0	0		WXS	Illumina HiSeq	Phase_I	245	105	0.428571	NM_015702	B2R895|D3DP91|O95891	Silent	SNP	ENST00000428879.1	37	CCDS2189.1																																																																																			C|0.220;T|0.780	0.780	strong		0.338	MMADHC-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332312.1	NM_015702	
TRIML2	205860	hgsc.bcm.edu	37	4	189012680	189012680	+	Silent	SNP	G	G	A	rs17881718	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:189012680G>A	ENST00000512729.1	-	7	1385	c.1011C>T	c.(1009-1011)acC>acT	p.T337T	TRIML2_ENST00000326754.3_Silent_p.T362T	NM_173553.1	NP_775824.1	Q8N7C3	TRIMM_HUMAN	tripartite motif family-like 2	337	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)|response to retinoic acid (GO:0032526)		ligase activity (GO:0016874)	p.T337T(2)		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)		GGGACATCTCGGTCACATTGT	0.488													G|||	332	0.0662939	0.0484	0.0778	5008	,	,		19837	0.0139		0.1412	False		,,,				2504	0.0593				p.T337T		Atlas-SNP	.											TRIML2,NS,carcinoma,0,2	TRIML2	80	2	2	Substitution - coding silent(2)	prostate(2)	c.C1011T						PASS	.	G		285,4121	157.0+/-190.0	9,267,1927	156.0	165.0	162.0		1011	-9.9	0.0	4	dbSNP_124	162	1288,7312	255.8+/-280.5	102,1084,3114	no	coding-synonymous	TRIML2	NM_173553.1		111,1351,5041	AA,AG,GG		14.9767,6.4685,12.0944		337/388	189012680	1573,11433	2203	4300	6503	SO:0001819	synonymous_variant	205860	exon7			CATCTCGGTCACA	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.1011C>T	4.37:g.189012680G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	103	42	0.407767	NM_173553	B7Z6J6	Silent	SNP	ENST00000512729.1	37	CCDS3850.1																																																																																			G|0.888;A|0.112	0.112	strong		0.488	TRIML2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359733.1	NM_173553	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68022572	68022572	+	Missense_Mutation	SNP	G	G	A	rs200379117		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68022572G>A	ENST00000329153.5	+	3	289	c.157G>A	c.(157-159)Gca>Aca	p.A53T		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	53						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)		GCTGCTGGAGGCAGAGCAGAG	0.607																																					p.A53T		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G157A						PASS	.						35.0	41.0	39.0					14																	68022572		2129	4263	6392	SO:0001583	missense	57475	exon3			CTGGAGGCAGAGC	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.157G>A	14.37:g.68022572G>A	ENSP00000330278:p.Ala53Thr	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	263	120	0.456274	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099177	0.94197	.	.	ENSG00000054690	ENST00000329153	T	0.39229	1.09	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.67237	-0.5721	10	0.52906	T	0.07	.	14.4383	0.67298	0.0:0.0:1.0:0.0	.	53	Q9ULM0	PKHH1_HUMAN	T	53	ENSP00000330278:A53T	ENSP00000330278:A53T	A	+	1	0	PLEKHH1	67092325	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.665000	0.68052	2.476000	0.83614	0.655000	0.94253	GCA	.	.	weak		0.607	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
KPNA2	3838	hgsc.bcm.edu	37	17	66042639	66042639	+	Missense_Mutation	SNP	T	T	A	rs138669765	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:66042639T>A	ENST00000537025.2	+	11	2137	c.1517T>A	c.(1516-1518)gTt>gAt	p.V506D	KPNA2_ENST00000330459.3_Missense_Mutation_p.V506D|KPNA2_ENST00000582898.1_3'UTR			P52292	IMA1_HUMAN	karyopherin alpha 2 (RAG cohort 1, importin alpha 1)	506					cytokine-mediated signaling pathway (GO:0019221)|DNA metabolic process (GO:0006259)|NLS-bearing protein import into nucleus (GO:0006607)|regulation of DNA recombination (GO:0000018)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone deacetylase binding (GO:0042826)|nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|kidney(2)|lung(9)|prostate(1)|urinary_tract(2)	22	all_cancers(12;1.18e-09)		BRCA - Breast invasive adenocarcinoma(8;1.03e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			GATCAAAACGTTGTACCAGAA	0.363													t|||	49	0.00978435	0.0053	0.0202	5008	,	,		17124	0.0		0.0249	False		,,,				2504	0.0031				p.V506D		Atlas-SNP	.											.	KPNA2	55	.	0			c.T1517A						PASS	.	T	ASP/VAL	29,4377	35.2+/-66.4	0,29,2174	73.0	75.0	74.0		1517	5.3	1.0	17	dbSNP_134	74	270,8322	103.8+/-164.8	5,260,4031	no	missense	KPNA2	NM_002266.2	152	5,289,6205	AA,AT,TT		3.1425,0.6582,2.3004	probably-damaging	506/530	66042639	299,12699	2203	4296	6499	SO:0001583	missense	3838	exon11			AAAACGTTGTACC	U09559	CCDS32713.1	17q24.2	2013-02-14						"""Importins"", ""Armadillo repeat containing"""	6395	protein-coding gene	gene with protein product		600685		RCH1		8016130, 7754385	Standard	NM_002266		Approved	SRP1alpha, IPOA1, QIP2	uc002jgk.3	P52292		ENST00000537025.2:c.1517T>A	17.37:g.66042639T>A	ENSP00000438483:p.Val506Asp	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_002266	B9EJD6|Q53YE3|Q9BRU5	Missense_Mutation	SNP	ENST00000537025.2	37	CCDS32713.1	33	0.01510989010989011	6	0.012195121951219513	8	0.022099447513812154	0	0.0	19	0.025065963060686015	T	22.2	4.262299	0.80358	0.006582	0.031425	ENSG00000182481	ENST00000330459;ENST00000537025	T;T	0.34072	1.38;1.38	5.33	5.33	0.75918	.	0.151414	0.43579	U	0.000548	T	0.15046	0.0363	L	0.49350	1.555	0.80722	D	1	B	0.16396	0.017	B	0.10450	0.005	T	0.04650	-1.0936	10	0.62326	D	0.03	.	15.3409	0.74296	0.0:0.0:0.0:1.0	rs13105;rs1136676;rs3200135;rs16926080	506	P52292	IMA2_HUMAN	D	506	ENSP00000332455:V506D;ENSP00000438483:V506D	ENSP00000332455:V506D	V	+	2	0	KPNA2	63473101	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	6.534000	0.73833	2.019000	0.59389	0.378000	0.23410	GTT	T|0.979;A|0.021	0.021	strong		0.363	KPNA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448111.1	NM_002266	
GCFC2	6936	hgsc.bcm.edu	37	2	75923413	75923413	+	Missense_Mutation	SNP	T	T	C	rs7560262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75923413T>C	ENST00000321027.3	-	5	879	c.746A>G	c.(745-747)aAt>aGt	p.N249S	RP11-342K6.3_ENST00000604464.1_RNA|GCFC2_ENST00000541687.1_Intron|GCFC2_ENST00000409857.3_Missense_Mutation_p.N211S	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	249			N -> S (in dbSNP:rs7560262).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	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)	p.N249S(1)									TGAAGATCCATTGCCACAGGA	0.279													C|||	2771	0.553315	0.7988	0.5173	5008	,	,		14327	0.4147		0.4742	False		,,,				2504	0.4714				p.N249S		Atlas-SNP	.											C2orf3,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A746G						scavenged	.	C	SER/ASN,SER/ASN	3234,1138		1209,816,161	45.0	54.0	51.0		239,746	2.8	0.0	2	dbSNP_116	51	4041,4509		960,2121,1194	yes	missense,missense	C2orf3	NM_001201334.1,NM_003203.4	46,46	2169,2937,1355	CC,CT,TT		47.2632,26.0293,43.7007	benign,benign	80/613,249/782	75923413	7275,5647	2186	4275	6461	SO:0001583	missense	6936	exon5			GATCCATTGCCAC	AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"""GC binding factor"""	189901	"""transcription factor 9 (binds GC-rich sequences)"", ""chromosome 2 open reading frame 3"""	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.746A>G	2.37:g.75923413T>C	ENSP00000318690:p.Asn249Ser	Somatic	161	2	0.0124224		WXS	Illumina HiSeq	Phase_I	136	66	0.485294	NM_003203	A4UHQ8|O95032|Q53TY0|Q6P2F2	Missense_Mutation	SNP	ENST00000321027.3	37	CCDS1961.1	1188	0.5439560439560439	400	0.8130081300813008	194	0.5359116022099447	239	0.4178321678321678	355	0.4683377308707124	C	0.025	-1.377147	0.01214	0.739707	0.472632	ENSG00000005436	ENST00000321027;ENST00000409857;ENST00000442309	T;T;T	0.26373	2.58;2.59;1.74	4.53	2.75	0.32379	.	0.765052	0.12717	N	0.445006	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29792	-1.0000	9	0.07030	T	0.85	0.5614	8.7555	0.34643	0.0:0.744:0.0:0.256	rs7560262;rs52803963;rs58807166;rs7560262	249	P16383	GCF_HUMAN	S	249;211;174	ENSP00000318690:N249S;ENSP00000386552:N211S;ENSP00000415831:N174S	ENSP00000318690:N249S	N	-	2	0	C2orf3	75776921	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.275000	0.18698	0.433000	0.26313	-0.790000	0.03334	AAT	T|0.465;C|0.535	0.535	strong		0.279	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203	
PRDM10	56980	hgsc.bcm.edu	37	11	129772309	129772309	+	Silent	SNP	G	G	A	rs12275633	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:129772309G>A	ENST00000360871.3	-	21	3601	c.3370C>T	c.(3370-3372)Ctg>Ttg	p.L1124L	PRDM10_ENST00000526082.1_Silent_p.L1042L|PRDM10_ENST00000528746.1_Silent_p.L1085L|PRDM10_ENST00000358825.5_Silent_p.L1128L|PRDM10_ENST00000423662.2_Silent_p.L1029L|PRDM10_ENST00000304538.6_Silent_p.L991L	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	1115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TGGGGGTCCAGGGAGTCACTG	0.512													A|||	401	0.0800719	0.2912	0.0216	5008	,	,		20324	0.0		0.001	False		,,,				2504	0.0				p.L1128L		Atlas-SNP	.											.	PRDM10	120	.	0			c.C3382T						PASS	.	A	,,,	1030,3372	726.5+/-409.7	128,774,1299	280.0	239.0	252.0		3382,3370,3085,2971	-2.2	0.7	11	dbSNP_120	252	6,8588	818.8+/-406.8	0,6,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRDM10	NM_020228.2,NM_199437.1,NM_199438.1,NM_199439.1	,,,	128,780,5590	AA,AG,GG		0.0698,23.3985,7.9717	,,,	1128/1161,1124/1157,1029/1062,991/1024	129772309	1036,11960	2201	4297	6498	SO:0001819	synonymous_variant	56980	exon22			GGTCCAGGGAGTC	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.3370C>T	11.37:g.129772309G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	214	115	0.537383	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			G|0.921;A|0.079	0.079	strong		0.512	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
KIF20B	9585	hgsc.bcm.edu	37	10	91468925	91468925	+	Splice_Site	SNP	C	C	G	rs1129777	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:91468925C>G	ENST00000371728.3	+	3	214	c.149C>G	c.(148-150)gCa>gGa	p.A50G	KIF20B_ENST00000416354.1_Splice_Site_p.A50G|KIF20B_ENST00000394289.2_Splice_Site_p.A50G|KIF20B_ENST00000260753.4_Splice_Site_p.A50G	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	50			A -> G (in dbSNP:rs1129777).		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						TTTTTTAAGGCAAACAGTTTC	0.323													C|||	1047	0.209065	0.0492	0.2133	5008	,	,		15780	0.3621		0.2416	False		,,,				2504	0.2311				p.A50G		Atlas-SNP	.											.	KIF20B	191	.	0			c.C149G						PASS	.	C	GLY/ALA	324,4082	148.8+/-183.1	11,302,1890	42.0	46.0	45.0		149	-3.7	1.0	10	dbSNP_86	45	1720,6870	284.0+/-296.4	191,1338,2766	yes	missense-near-splice	KIF20B	NM_016195.2	60	202,1640,4656	GG,GC,CC		20.0233,7.3536,15.7279	benign	50/1781	91468925	2044,10952	2203	4295	6498	SO:0001630	splice_region_variant	9585	exon3			TTAAGGCAAACAG	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.148-1C>G	10.37:g.91468925C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	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		502	0.22985347985347984	27	0.054878048780487805	76	0.20994475138121546	215	0.3758741258741259	184	0.24274406332453827	C	14.83	2.652799	0.47362	0.073536	0.200233	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728;ENST00000439656;ENST00000447580	T;T;T;T;T	0.68624	-0.29;-0.28;-0.34;-0.28;2.29	5.35	-3.67	0.04476	.	1.205930	0.06061	N	0.658370	T	0.00012	0.0000	L	0.29908	0.895	0.35266	P	0.21994499999999995	P;B	0.48998	0.918;0.244	P;B	0.46110	0.504;0.159	T	0.09574	-1.0668	9	0.21540	T	0.41	0.0243	0.4388	0.00483	0.2746:0.1731:0.3032:0.249	rs1129777;rs3188038;rs3758383;rs11549427;rs52833306;rs3758383	50;50	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	G	50	ENSP00000260753:A50G;ENSP00000411545:A50G;ENSP00000377830:A50G;ENSP00000360793:A50G;ENSP00000390946:A50G	ENSP00000260753:A50G	A	+	2	0	KIF20B	91458905	0.991000	0.36638	0.985000	0.45067	0.852000	0.48524	0.276000	0.18716	-0.240000	0.09696	-0.176000	0.13171	GCA	C|0.817;G|0.183	0.183	strong		0.323	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	Missense_Mutation
ARHGEF10L	55160	hgsc.bcm.edu	37	1	17949562	17949562	+	Silent	SNP	C	C	T	rs55693639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17949562C>T	ENST00000361221.3	+	12	1251	c.1092C>T	c.(1090-1092)ttC>ttT	p.F364F	ARHGEF10L_ENST00000434513.1_Silent_p.F364F|ARHGEF10L_ENST00000375408.3_Silent_p.F142F|ARHGEF10L_ENST00000167825.4_Silent_p.F142F|ARHGEF10L_ENST00000375415.1_Silent_p.F325F|ARHGEF10L_ENST00000375420.3_Silent_p.F122F|ARHGEF10L_ENST00000452522.1_Silent_p.F325F|ARHGEF10L_ENST00000469726.1_3'UTR	NM_018125.3	NP_060595	Q9HCE6	ARGAL_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10-like	364	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(16)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	43		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00598)|COAD - Colon adenocarcinoma(227;1.62e-05)|BRCA - Breast invasive adenocarcinoma(304;1.68e-05)|Kidney(64;0.000269)|KIRC - Kidney renal clear cell carcinoma(64;0.00361)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0718)|Lung(427;0.204)		TGGTGTTCTTCCGCGTGAAGG	0.657													C|||	66	0.0131789	0.0015	0.0274	5008	,	,		18067	0.0		0.0348	False		,,,				2504	0.0102				p.F364F		Atlas-SNP	.											.	ARHGEF10L	219	.	0			c.C1092T						PASS	.	C	,	45,4361	47.5+/-82.1	0,45,2158	98.0	86.0	90.0		975,1092	1.1	1.0	1	dbSNP_129	90	472,8128	138.4+/-195.2	12,448,3840	no	coding-synonymous,coding-synonymous	ARHGEF10L	NM_001011722.2,NM_018125.3	,	12,493,5998	TT,TC,CC		5.4884,1.0213,3.9751	,	325/1241,364/1280	17949562	517,12489	2203	4300	6503	SO:0001819	synonymous_variant	55160	exon12			GTTCTTCCGCGTG	AB046846	CCDS182.1, CCDS30617.1	1p36.13	2011-11-16			ENSG00000074964	ENSG00000074964		"""Rho guanine nucleotide exchange factors"""	25540	protein-coding gene	gene with protein product	"""GrinchGEF"""	612494				10997877, 16112081	Standard	XM_005245923		Approved	FLJ10521, KIAA1626	uc001ban.3	Q9HCE6	OTTHUMG00000002514	ENST00000361221.3:c.1092C>T	1.37:g.17949562C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	114	103	0.903509	NM_018125	B7ZKS1|Q17RW1|Q3YFJ4|Q5VXI5|Q5VXI6|Q66K51|Q6P0L7|Q8NAV5|Q9NVT3	Silent	SNP	ENST00000361221.3	37	CCDS182.1																																																																																			C|0.964;T|0.036	0.036	strong		0.657	ARHGEF10L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007147.1	NM_018125	
SV2B	9899	hgsc.bcm.edu	37	15	91827264	91827264	+	Silent	SNP	C	C	T	rs2301664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91827264C>T	ENST00000394232.1	+	11	1991	c.1521C>T	c.(1519-1521)caC>caT	p.H507H	SV2B_ENST00000330276.4_Silent_p.H507H|SV2B_ENST00000545111.2_Silent_p.H356H	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	507					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			TCTACGAGCACAAGTTCATCA	0.522													T|||	642	0.128195	0.261	0.062	5008	,	,		19686	0.0506		0.0765	False		,,,				2504	0.1288				p.H507H		Atlas-SNP	.											.	SV2B	98	.	0			c.C1521T						PASS	.	T	,	1020,3376	726.5+/-409.7	111,798,1289	192.0	186.0	188.0		1068,1521	-2.2	0.4	15	dbSNP_100	188	682,7914	788.1+/-407.6	34,614,3650	no	coding-synonymous,coding-synonymous	SV2B	NM_001167580.1,NM_014848.4	,	145,1412,4939	TT,TC,CC		7.9339,23.2029,13.1004	,	356/533,507/684	91827264	1702,11290	2198	4298	6496	SO:0001819	synonymous_variant	9899	exon12			CGAGCACAAGTTC	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1521C>T	15.37:g.91827264C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			C|0.870;T|0.130	0.130	strong		0.522	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
TMEM8A	58986	hgsc.bcm.edu	37	16	426432	426432	+	Missense_Mutation	SNP	T	T	C	rs2071915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:426432T>C	ENST00000431232.2	-	6	1088	c.928A>G	c.(928-930)Atc>Gtc	p.I310V	TMEM8A_ENST00000250930.3_Missense_Mutation_p.I117V|TMEM8A_ENST00000476735.1_5'Flank	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	310			I -> V (in dbSNP:rs2071915). {ECO:0000269|PubMed:11006113, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AGGGGCTGGATGGTCACGCTC	0.647													C|||	2667	0.532548	0.6188	0.4712	5008	,	,		16721	0.3036		0.5378	False		,,,				2504	0.6902				p.I310V		Atlas-SNP	.											.	TMEM8A	49	.	0			c.A928G						PASS	.	C	VAL/ILE	2746,1652		848,1050,301	25.0	27.0	27.0		928	-9.1	0.0	16	dbSNP_96	27	4870,3724		1411,2048,838	yes	missense	TMEM8A	NM_021259.2	29	2259,3098,1139	CC,CT,TT		43.3326,37.5625,41.3793	benign	310/772	426432	7616,5376	2199	4297	6496	SO:0001583	missense	58986	exon6			GCTGGATGGTCAC	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.928A>G	16.37:g.426432T>C	ENSP00000401338:p.Ile310Val	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	48	0.615385	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	1086	0.49725274725274726	335	0.6808943089430894	179	0.494475138121547	163	0.28496503496503495	409	0.5395778364116095	C	0.012	-1.684225	0.00745	0.624375	0.566674	ENSG00000129925	ENST00000431232;ENST00000250930	T;T	0.28666	2.01;1.6	4.57	-9.13	0.00704	.	3.050000	0.00628	N	0.000477	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	0.26985	-1.0087	9	0.22109	T	0.4	-13.6961	4.298	0.10911	0.0755:0.2978:0.203:0.4237	rs2071915;rs17797276;rs17845651;rs17858585;rs56985763;rs2071915	310	Q9HCN3	TMM8A_HUMAN	V	310;117	ENSP00000401338:I310V;ENSP00000250930:I117V	ENSP00000250930:I117V	I	-	1	0	TMEM8A	366433	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.095000	0.01350	-5.232000	0.00018	-4.127000	0.00010	ATC	C|0.542;N|0.001	0.542	strong		0.647	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
CDH16	1014	hgsc.bcm.edu	37	16	66948130	66948130	+	Missense_Mutation	SNP	G	G	A	rs2271023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:66948130G>A	ENST00000299752.4	-	7	962	c.769C>T	c.(769-771)Cac>Tac	p.H257Y	CDH16_ENST00000568632.1_Missense_Mutation_p.H160Y|CDH16_ENST00000394055.3_Missense_Mutation_p.H257Y|CDH16_ENST00000570262.1_Missense_Mutation_p.H177Y|CDH16_ENST00000565796.1_Missense_Mutation_p.H257Y	NM_001204744.1|NM_001204745.1|NM_004062.3	NP_001191673.1|NP_001191674.1|NP_004053.1	O75309	CAD16_HUMAN	cadherin 16, KSP-cadherin	257	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		H -> Y (in dbSNP:rs2271023).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(3)|large_intestine(10)|lung(15)|ovary(2)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0877)|Epithelial(162;0.203)		TGGGCCATGTGGTGCGGGTAT	0.587													G|||	370	0.0738818	0.0234	0.072	5008	,	,		21563	0.2014		0.0398	False		,,,				2504	0.047				p.H257Y		Atlas-SNP	.											.	CDH16	91	.	0			c.C769T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS	130,4270	94.4+/-133.1	2,126,2072	99.0	90.0	93.0		769,769,478,769	1.0	0.3	16	dbSNP_100	93	257,8343	100.6+/-161.9	5,247,4048	yes	missense,missense,missense,missense	CDH16	NM_001204744.1,NM_001204745.1,NM_001204746.1,NM_004062.3	83,83,83,83	7,373,6120	AA,AG,GG		2.9884,2.9545,2.9769	benign,benign,benign,benign	257/808,257/791,160/733,257/830	66948130	387,12613	2200	4300	6500	SO:0001583	missense	1014	exon7			CCATGTGGTGCGG	AF016272	CCDS10823.1, CCDS56002.1, CCDS58471.1, CCDS58472.1	16q22.1	2010-01-26			ENSG00000166589	ENSG00000166589		"""Cadherins / Major cadherins"""	1755	protein-coding gene	gene with protein product		603118				9721215, 7615566	Standard	NM_004062		Approved		uc002eql.3	O75309	OTTHUMG00000137518	ENST00000299752.4:c.769C>T	16.37:g.66948130G>A	ENSP00000299752:p.His257Tyr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_004062	B4DPA8|H3BPD3|Q6UW93	Missense_Mutation	SNP	ENST00000299752.4	37	CCDS10823.1	172	0.07875457875457875	15	0.03048780487804878	22	0.06077348066298342	104	0.18181818181818182	31	0.040897097625329816	G	5.817	0.335088	0.11013	0.029545	0.029884	ENSG00000166589	ENST00000394055;ENST00000299752;ENST00000544875	T;T	0.56444	0.5;0.46	4.16	1.03	0.20045	Cadherin (2);	0.756939	0.12401	N	0.472145	T	0.00039	0.0001	N	0.25647	0.755	0.80722	P	0.0	P;P;B	0.34977	0.478;0.475;0.403	B;B;B	0.31686	0.134;0.133;0.086	T	0.09292	-1.0681	9	0.02654	T	1	-0.7045	3.0076	0.06033	0.2328:0.0:0.5406:0.2266	rs2271023;rs58280403;rs2271023	257;257;257	O75309-2;B2R7S8;O75309	.;.;CAD16_HUMAN	Y	257;257;221	ENSP00000377619:H257Y;ENSP00000299752:H257Y	ENSP00000299752:H257Y	H	-	1	0	CDH16	65505631	0.764000	0.28473	0.278000	0.24718	0.129000	0.20672	0.653000	0.24902	0.478000	0.27488	0.655000	0.94253	CAC	A|0.053;G|0.947;T|0.000	0.053	strong		0.587	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062	
MEGF6	1953	hgsc.bcm.edu	37	1	3418391	3418391	+	Silent	SNP	C	C	T	rs4648508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:3418391C>T	ENST00000356575.4	-	18	2509	c.2283G>A	c.(2281-2283)ccG>ccA	p.P761P	MEGF6_ENST00000294599.4_Silent_p.P656P	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	761	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		TCCTCCCCGGCGGACACCGGC	0.706													C|||	1433	0.286142	0.1914	0.2882	5008	,	,		13912	0.3056		0.336	False		,,,				2504	0.3415				p.P761P	Ovarian(73;978 3658)	Atlas-SNP	.											MEGF6,colon,carcinoma,0,2	MEGF6	91	2	0			c.G2283A						PASS	.	C		753,3243		71,611,1316	22.0	30.0	27.0		2283	-7.2	0.2	1	dbSNP_111	27	2575,5717		410,1755,1981	no	coding-synonymous	MEGF6	NM_001409.3		481,2366,3297	TT,TC,CC		31.054,18.8438,27.0833		761/1542	3418391	3328,8960	1998	4146	6144	SO:0001819	synonymous_variant	1953	exon18			CCCCGGCGGACAC	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.2283G>A	1.37:g.3418391C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	249	240	0.963855	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1																																																																																			C|0.703;T|0.297	0.297	strong		0.706	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
RANBP17	64901	hgsc.bcm.edu	37	5	170597190	170597190	+	Silent	SNP	G	G	A	rs36104512	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:170597190G>A	ENST00000523189.1	+	15	1931	c.1767G>A	c.(1765-1767)gaG>gaA	p.E589E	RANBP17_ENST00000521759.1_3'UTR	NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	589					mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nuclear pore (GO:0005643)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	50	Renal(175;0.000159)|Lung NSC(126;0.00751)|all_lung(126;0.0123)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			ACGTTCTAGAGACGTTCATGA	0.274			T	TRD@	ALL								A|||	489	0.0976438	0.1679	0.0461	5008	,	,		13233	0.1091		0.0427	False		,,,				2504	0.0838				p.E589E		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.G1767A						PASS	.	A		801,3605	746.8+/-411.8	67,667,1469	134.0	144.0	141.0		1767	4.9	1.0	5	dbSNP_126	141	377,8221	800.2+/-407.4	7,363,3929	no	coding-synonymous	RANBP17	NM_022897.3		74,1030,5398	AA,AG,GG		4.3847,18.1798,9.0588		589/1089	170597190	1178,11826	2203	4299	6502	SO:0001819	synonymous_variant	64901	exon15			TCTAGAGACGTTC	AF222747	CCDS34287.1	5q34	2009-01-12			ENSG00000204764	ENSG00000204764			14428	protein-coding gene	gene with protein product		606141				11024021	Standard	NM_022897		Approved		uc003mba.3	Q9H2T7	OTTHUMG00000163203	ENST00000523189.1:c.1767G>A	5.37:g.170597190G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	122	38	0.311475	NM_022897	Q8IU74	Silent	SNP	ENST00000523189.1	37	CCDS34287.1																																																																																			G|0.917;A|0.083	0.083	strong		0.274	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897	
GRM7	2917	hgsc.bcm.edu	37	3	7620828	7620828	+	Silent	SNP	G	G	A	rs1485174	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:7620828G>A	ENST00000357716.4	+	8	2509	c.2235G>A	c.(2233-2235)ggG>ggA	p.G745G	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000486284.1_Silent_p.G745G|GRM7_ENST00000403881.1_Silent_p.G745G|GRM7_ENST00000402647.2_Silent_p.G745G|GRM7_ENST00000389336.4_Silent_p.G745G	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	745			G -> E (in dbSNP:rs1485174).		adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						AAGCCAGAGGGGTTCTCAAGT	0.443													G|||	855	0.170727	0.0552	0.2565	5008	,	,		19555	0.1399		0.2932	False		,,,				2504	0.1718				p.G745G		Atlas-SNP	.											.	GRM7	223	.	0			c.G2235A						PASS	.	G	,	372,4034	187.4+/-214.1	16,340,1847	131.0	116.0	121.0		2235,2235	-11.7	0.4	3	dbSNP_88	121	2388,6212	398.3+/-346.1	338,1712,2250	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	354,2052,4097	AA,AG,GG		27.7674,8.443,21.221	,	745/916,745/923	7620828	2760,10246	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			CAGAGGGGTTCTC	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2235G>A	3.37:g.7620828G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	205	109	0.531707	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			G|0.803;A|0.197	0.197	strong		0.443	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
RASSF4	83937	hgsc.bcm.edu	37	10	45478092	45478092	+	Missense_Mutation	SNP	A	A	G	rs870957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45478092A>G	ENST00000340258.5	+	4	375	c.262A>G	c.(262-264)Aga>Gga	p.R88G	RASSF4_ENST00000374417.2_Missense_Mutation_p.R88G|RASSF4_ENST00000334940.6_Missense_Mutation_p.R70G|RASSF4_ENST00000472561.1_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	624					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)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						ATGGATGCCCAGACGGCCTAG	0.667													.|||	1406	0.280751	0.3782	0.1412	5008	,	,		19294	0.3194		0.171	False		,,,				2504	0.3211				p.R88G		Atlas-SNP	.											.	RASSF4	33	.	0			c.A262G						PASS	.	G	GLY/ARG	1484,2922	676.9+/-403.3	254,976,973	72.0	70.0	71.0		262	1.4	0.0	10	dbSNP_86	71	1499,7101	747.6+/-407.3	120,1259,2921	yes	missense	RASSF4	NM_032023.3	125	374,2235,3894	GG,GA,AA		17.4302,33.6813,22.9356	benign	88/322	45478092	2983,10023	2203	4300	6503	SO:0001583	missense	83937	exon4			ATGCCCAGACGGC	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.262A>G	10.37:g.45478092A>G	ENSP00000339692:p.Arg88Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	125	63	0.504	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000340258.5	37	CCDS7208.1	575	0.2632783882783883	189	0.38414634146341464	62	0.1712707182320442	196	0.34265734265734266	128	0.16886543535620052	G	0.027	-1.361971	0.01235	0.336813	0.174302	ENSG00000107551	ENST00000334940;ENST00000374417;ENST00000374414;ENST00000340258;ENST00000427758;ENST00000428466;ENST00000374411	T;T;T;T;T	0.30448	2.54;1.54;2.56;1.53;1.53	4.39	1.39	0.22231	.	0.619583	0.14038	N	0.345633	T	0.00012	0.0000	N	0.00621	-1.32	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47156	-0.9139	9	0.22109	T	0.4	-1.7041	5.0423	0.14465	0.1868:0.3279:0.4853:0.0	rs870957;rs11540202;rs56589186;rs57926736;rs870957	88	Q9H2L5	RASF4_HUMAN	G	70;88;88;88;88;81;179	ENSP00000334543:R70G;ENSP00000363538:R88G;ENSP00000339692:R88G;ENSP00000409767:R88G;ENSP00000413468:R81G	ENSP00000334543:R70G	R	+	1	2	RASSF4	44798098	0.087000	0.21565	0.000000	0.03702	0.002000	0.02628	0.681000	0.25320	0.069000	0.16605	-0.119000	0.15052	AGA	A|0.750;G|0.250	0.250	strong		0.667	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023	
ECD	11319	hgsc.bcm.edu	37	10	74896664	74896664	+	Missense_Mutation	SNP	T	T	C	rs36152134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:74896664T>C	ENST00000372979.4	-	13	1708	c.1502A>G	c.(1501-1503)aAt>aGt	p.N501S	ECD_ENST00000430082.2_Missense_Mutation_p.N534S|ECD_ENST00000454759.2_Missense_Mutation_p.N458S	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	501			N -> S (in dbSNP:rs36152134).		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)					ATCTGACTCATTAGGCCTTGG	0.353													T|||	884	0.176518	0.1657	0.0994	5008	,	,		13695	0.3145		0.0537	False		,,,				2504	0.2301				p.N534S		Atlas-SNP	.											.	ECD	50	.	0			c.A1601G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	664,3742	279.3+/-274.7	57,550,1596	125.0	120.0	122.0		1601,1373,1502	0.1	0.0	10	dbSNP_126	122	571,8029	151.2+/-206.0	26,519,3755	yes	missense,missense,missense	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	46,46,46	83,1069,5351	CC,CT,TT		6.6395,15.0704,9.4956	benign,benign,benign	534/678,458/602,501/645	74896664	1235,11771	2203	4300	6503	SO:0001583	missense	11319	exon14			GACTCATTAGGCC	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		ENST00000372979.4:c.1502A>G	10.37:g.74896664T>C	ENSP00000362070:p.Asn501Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	354	0.1620879120879121	99	0.20121951219512196	31	0.0856353591160221	183	0.31993006993006995	41	0.05408970976253298	T	5.212	0.224639	0.09916	0.150704	0.066395	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.16897	2.31;2.31;2.31	5.55	0.0463	0.14233	.	0.987665	0.08275	N	0.970828	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.16289	0.0;0.003;0.015	T	0.47315	-0.9127	9	0.10111	T	0.7	-5.701	3.169	0.06545	0.1272:0.0749:0.2634:0.5345	rs36152134	458;534;501	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	S	501;534;458	ENSP00000362070:N501S;ENSP00000401566:N534S;ENSP00000395786:N458S	ENSP00000362070:N501S	N	-	2	0	ECD	74566670	0.952000	0.32445	0.002000	0.10522	0.192000	0.23643	1.606000	0.36826	0.015000	0.14971	0.533000	0.62120	AAT	T|0.887;C|0.113	0.113	strong		0.353	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58549395	58549395	+	Missense_Mutation	SNP	G	G	A	rs369859464		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58549395G>A	ENST00000282326.1	+	3	438	c.191G>A	c.(190-192)cGc>cAc	p.R64H	ZSCAN1_ENST00000601162.1_Missense_Mutation_p.R64H|ZSCAN1_ENST00000391700.1_Missense_Mutation_p.R64H	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	64	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		ACGCTGTGCCGCCAGTGGCTG	0.706																																					p.R64H		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.G191A						PASS	.	G	HIS/ARG	0,4342		0,0,2171	15.0	15.0	15.0		191	-0.6	0.4	19		15	1,8511		0,1,4255	no	missense	ZSCAN1	NM_182572.3	29	0,1,6426	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging	64/409	58549395	1,12853	2171	4256	6427	SO:0001583	missense	284312	exon3			TGTGCCGCCAGTG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.191G>A	19.37:g.58549395G>A	ENSP00000282326:p.Arg64His	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737403	0.30774	0.0	1.17E-4	ENSG00000152467	ENST00000391700;ENST00000282326	T;T	0.05786	3.39;3.39	2.09	-0.628	0.11537	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.03348	0.0097	N	0.25245	0.725	0.23126	N	0.998253	P;P	0.41102	0.738;0.584	B;B	0.36134	0.218;0.054	T	0.39187	-0.9626	9	0.35671	T	0.21	.	2.1585	0.03819	0.2018:0.0:0.4923:0.3059	.	64;64	Q8NBB4;Q8NBB4-2	ZSCA1_HUMAN;.	H	64	ENSP00000375581:R64H;ENSP00000282326:R64H	ENSP00000282326:R64H	R	+	2	0	ZSCAN1	63241207	0.000000	0.05858	0.395000	0.26283	0.143000	0.21401	0.248000	0.18198	0.216000	0.20781	0.407000	0.27541	CGC	.	.	weak		0.706	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
FANCD2	2177	hgsc.bcm.edu	37	3	10089723	10089723	+	Silent	SNP	G	G	A	rs12330369		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:10089723G>A	ENST00000419585.1	+	16	1562	c.1401G>A	c.(1399-1401)acG>acA	p.T467T	FANCD2_ENST00000383807.1_Silent_p.T467T|FANCD2_ENST00000383806.1_Silent_p.T467T|FANCD2_ENST00000287647.3_Silent_p.T467T			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	467					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TTTTTGACACGTACTGCCAGC	0.388			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T467T		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253	.	0			c.G1401A						PASS	.						96.0	97.0	97.0					3																	10089723		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGACACGTACTGC	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1401G>A	3.37:g.10089723G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	117	24	0.205128	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			G|0.750;A|0.250	0.250	weak		0.388	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
MICALCL	84953	hgsc.bcm.edu	37	11	12313845	12313845	+	Splice_Site	SNP	G	G	A	rs200949393		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12313845G>A	ENST00000256186.2	+	2	420		c.e2+1			NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like						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)		CCCGCCTCAGGTGAGTGTCCC	0.527																																					.		Atlas-SNP	.											.	MICALCL	59	.	0			c.129+1G>A						PASS	.	G		2,3888		0,2,1943	107.0	106.0	106.0			5.4	1.0	11		106	1,8273		0,1,4136	yes	splice-5	MICALCL	NM_032867.2		0,3,6079	AA,AG,GG		0.0121,0.0514,0.0247			12313845	3,12161	1945	4137	6082	SO:0001630	splice_region_variant	84953	exon2			CCTCAGGTGAGTG	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.129+1G>A	11.37:g.12313845G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_032867	Q7RTP7|Q96JU6	Splice_Site	SNP	ENST00000256186.2	37	CCDS41620.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212670	0.39102	5.14E-4	1.21E-4	ENSG00000133808	ENST00000256186	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0104	0.71545	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MICALCL	12270421	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	4.368000	0.59505	2.671000	0.90904	0.591000	0.81541	.	.	.	weak		0.527	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	Intron
FHL2	2274	hgsc.bcm.edu	37	2	105977761	105977761	+	Silent	SNP	G	G	A	rs11124029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:105977761G>A	ENST00000409807.1	-	6	1153	c.819C>T	c.(817-819)ccC>ccT	p.P273P	FHL2_ENST00000358129.4_Silent_p.P273P|AC012360.6_ENST00000457290.2_RNA|FHL2_ENST00000344213.4_Silent_p.P383P|FHL2_ENST00000322142.8_Silent_p.P273P|FHL2_ENST00000336660.5_3'UTR|FHL2_ENST00000408995.1_Silent_p.P273P|FHL2_ENST00000393352.3_Silent_p.P273P|FHL2_ENST00000409177.1_Silent_p.P389P|FHL2_ENST00000393353.3_Silent_p.P273P			Q14192	FHL2_HUMAN	four and a half LIM domains 2	273	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						TCCCACAGTCGGGGCACAGGA	0.498													g|||	558	0.111422	0.0809	0.1614	5008	,	,		20874	0.0258		0.1988	False		,,,				2504	0.1155				p.P273P		Atlas-SNP	.											.	FHL2	18	.	0			c.C819T						PASS	.	A	,,,	453,3953	217.1+/-235.6	24,405,1774	117.0	110.0	113.0		819,819,819,819	-11.0	0.5	2	dbSNP_120	113	1685,6915	308.6+/-309.0	154,1377,2769	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FHL2	NM_001039492.2,NM_001450.3,NM_201555.1,NM_201557.3	,,,	178,1782,4543	AA,AG,GG		19.593,10.2814,16.4386	,,,	273/280,273/280,273/280,273/280	105977761	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	2274	exon7			ACAGTCGGGGCAC		CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641			3703	protein-coding gene	gene with protein product		602633				8753811	Standard	NM_201557		Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409807.1:c.819C>T	2.37:g.105977761G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	78	41	0.525641	NM_001039492	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Silent	SNP	ENST00000409807.1	37	CCDS2070.1																																																																																			G|0.852;A|0.148	0.148	strong		0.498	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1		
GRIN2D	2906	hgsc.bcm.edu	37	19	48908452	48908452	+	Silent	SNP	G	G	A	rs369747884		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48908452G>A	ENST00000263269.3	+	3	1015	c.927G>A	c.(925-927)tcG>tcA	p.S309S		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	309					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CAGTGCGCTCGGCTGGCTGGC	0.716													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14132	0.0		0.0	False		,,,				2504	0.0				p.S309S		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G927A						PASS	.	G		0,4306		0,0,2153	10.0	13.0	12.0		927	-8.9	0.8	19		12	2,8414		0,2,4206	no	coding-synonymous	GRIN2D	NM_000836.2		0,2,6359	AA,AG,GG		0.0238,0.0,0.0157		309/1337	48908452	2,12720	2153	4208	6361	SO:0001819	synonymous_variant	2906	exon3			GCGCTCGGCTGGC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.927G>A	19.37:g.48908452G>A		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	21	13	0.619048	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			.	.	weak		0.716	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
MST1L	11223	hgsc.bcm.edu	37	1	17086183	17086183	+	RNA	SNP	T	T	G	rs61769735	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17086183T>G	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.?(2)									CCTCGGACCCTTAGATGGACC	0.652																																					.		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,6	.	.	6	2	Unknown(2)	kidney(2)	c.716-2A>C						scavenged	.																																					11223	exon8			GGACCCTTAGATG	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.17086183T>G		Somatic	207	4	0.0193237		WXS	Illumina HiSeq	Phase_I	211	27	0.127962	NM_001271733	B7WPB1|Q13209	Splice_Site	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	6.643	0.487109	0.12641	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	rs61769735	.	.	.	.	-1	.	.	.	-	.	.	MST1P9	16958770	0.699000	0.27786	0.000000	0.03702	0.000000	0.00434	0.557000	0.23454	0.000000	0.14550	0.000000	0.15137	.	T|0.988;G|0.011	0.011	strong		0.652	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
RPRD2	23248	hgsc.bcm.edu	37	1	150445058	150445058	+	Missense_Mutation	SNP	C	C	T	rs201108869		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:150445058C>T	ENST00000369068.4	+	11	3638	c.3634C>T	c.(3634-3636)Cca>Tca	p.P1212S	RPRD2_ENST00000401000.4_Missense_Mutation_p.P1186S|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	1212	Pro-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						GCCAGTGGGGCCATCATCTGC	0.537																																					p.P1212S		Atlas-SNP	.											.	RPRD2	189	.	0			c.C3634T						PASS	.	C	SER/PRO	0,3984		0,0,1992	84.0	87.0	86.0		3634	4.6	1.0	1		86	2,8300		0,2,4149	yes	missense	RPRD2	NM_015203.3	74	0,2,6141	TT,TC,CC		0.0241,0.0,0.0163	probably-damaging	1212/1462	150445058	2,12284	1992	4151	6143	SO:0001583	missense	23248	exon11			GTGGGGCCATCAT	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"""KIAA0460"""	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.3634C>T	1.37:g.150445058C>T	ENSP00000358064:p.Pro1212Ser	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	76	0.575758	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.965007	0.53507	0.0	2.41E-4	ENSG00000163125	ENST00000401000;ENST00000369068	T;T	0.61510	0.1;0.12	4.59	4.59	0.56863	.	0.161530	0.43416	D	0.000574	T	0.57548	0.2061	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.65537	-0.6144	10	0.72032	D	0.01	-7.9501	17.1925	0.86883	0.0:1.0:0.0:0.0	.	1212;1186	Q5VT52;Q5VT52-3	RPRD2_HUMAN;.	S	1186;1212	ENSP00000383785:P1186S;ENSP00000358064:P1212S	ENSP00000358064:P1212S	P	+	1	0	RPRD2	148711682	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.389000	0.52516	2.363000	0.80096	0.563000	0.77884	CCA	.	.	weak		0.537	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
C10orf55	414236	hgsc.bcm.edu	37	10	75673879	75673879	+	Intron	SNP	C	C	T	rs2227568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75673879C>T	ENST00000409178.1	-	3	268				PLAU_ENST00000372764.3_Silent_p.N274N|PLAU_ENST00000372762.4_Silent_p.N238N|PLAU_ENST00000446342.1_Silent_p.N257N|C10orf55_ENST00000412307.2_Intron	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55											endometrium(1)	1	Prostate(51;0.0112)					CTCACCACAACGACATTGGTG	0.567													C|||	826	0.164936	0.0469	0.1081	5008	,	,		19302	0.2937		0.1581	False		,,,				2504	0.2393				p.N274N		Atlas-SNP	.											.	PLAU	47	.	0			c.C822T						PASS	.	C	,,	335,4071	175.9+/-205.1	15,305,1883	76.0	60.0	65.0		,771,822	-5.0	1.0	10	dbSNP_98	65	1403,7197	269.6+/-288.5	117,1169,3014	no	intron,coding-synonymous,coding-synonymous	PLAU,C10orf55	NM_001001791.2,NM_001145031.1,NM_002658.3	,,	132,1474,4897	TT,TC,CC		16.314,7.6033,13.3631	,,	,257/415,274/432	75673879	1738,11268	2203	4300	6503	SO:0001627	intron_variant	5328	exon8			CCACAACGACATT		CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.73-1046G>A	10.37:g.75673879C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_002658	Q3KRG4|Q8NAK4	Silent	SNP	ENST00000409178.1	37	CCDS53541.1																																																																																			C|0.859;T|0.141	0.141	strong		0.567	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791	
TPST2	8459	hgsc.bcm.edu	37	22	26936766	26936766	+	Silent	SNP	G	G	A	rs58274935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26936766G>A	ENST00000338754.4	-	3	1101	c.831C>T	c.(829-831)gtC>gtT	p.V277V	TPST2_ENST00000398110.2_Silent_p.V277V|TPST2_ENST00000403880.1_Silent_p.V277V	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	277					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						TGGACAGGGAGACACCACCGG	0.597													G|||	341	0.0680911	0.0469	0.0476	5008	,	,		18035	0.0833		0.0736	False		,,,				2504	0.09				p.V277V		Atlas-SNP	.											.	TPST2	23	.	0			c.C831T						PASS	.	G	,	191,4215	118.8+/-156.5	7,177,2019	40.0	41.0	40.0		831,831	3.0	1.0	22	dbSNP_129	40	442,8158	132.3+/-190.0	15,412,3873	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	22,589,5892	AA,AG,GG		5.1395,4.335,4.867	,	277/378,277/378	26936766	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	8459	exon3			CAGGGAGACACCA	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.831C>T	22.37:g.26936766G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	32	22	0.6875	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			G|0.952;A|0.048	0.048	strong		0.597	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
TNK2	10188	hgsc.bcm.edu	37	3	195595054	195595054	+	Silent	SNP	C	C	T	rs7516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195595054C>T	ENST00000333602.6	-	12	2687	c.2070G>A	c.(2068-2070)ccG>ccA	p.P690P	TNK2_ENST00000392400.1_Silent_p.P690P|TNK2_ENST00000428187.1_Silent_p.P722P|TNK2_ENST00000381916.2_Silent_p.P768P	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	690	Pro-rich.			Missing (in Ref. 4; AAH08884). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CACCCTGGGGCGGGAGGAACA	0.711													c|||	416	0.0830671	0.0998	0.0519	5008	,	,		11446	0.0278		0.1163	False		,,,				2504	0.1053				p.P768P		Atlas-SNP	.											TNK2_ENST00000381916,NS,carcinoma,0,3	TNK2	246	3	0			c.G2304A						PASS	.		,	401,3965		21,359,1803	10.0	12.0	11.0		2304,2070	-10.6	0.0	3	dbSNP_52	11	981,7557		42,897,3330	no	coding-synonymous,coding-synonymous	TNK2	NM_001010938.1,NM_005781.4	,	63,1256,5133	TT,TC,CC		11.4898,9.1846,10.7099	,	768/1087,690/1039	195595054	1382,11522	2183	4269	6452	SO:0001819	synonymous_variant	10188	exon13			CTGGGGCGGGAGG	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.2070G>A	3.37:g.195595054C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	15	0.3125	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Silent	SNP	ENST00000333602.6	37	CCDS33928.1																																																																																			C|0.921;T|0.079	0.079	strong		0.711	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
OR5J2	282775	hgsc.bcm.edu	37	11	55944474	55944474	+	Silent	SNP	G	G	A	rs4489763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55944474G>A	ENST00000312298.1	+	1	381	c.381G>A	c.(379-381)gtG>gtA	p.V127V		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	127						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V127V(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					TGGCCATTGTGAGTCCCTTGC	0.453													.|||	494	0.0986422	0.0499	0.0994	5008	,	,		23210	0.125		0.1163	False		,,,				2504	0.1186				p.V127V		Atlas-SNP	.											OR5J2,NS,carcinoma,0,1	OR5J2	98	1	1	Substitution - coding silent(1)	stomach(1)	c.G381A						scavenged	.	G		239,4163	140.4+/-175.9	7,225,1969	159.0	144.0	149.0		381	-9.2	0.0	11	dbSNP_111	149	999,7593	215.5+/-254.8	53,893,3350	no	coding-synonymous	OR5J2	NM_001005492.1		60,1118,5319	AA,AG,GG		11.6271,5.4294,9.5275		127/313	55944474	1238,11756	2201	4296	6497	SO:0001819	synonymous_variant	282775	exon1			CATTGTGAGTCCC	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"""GPCR / Class A : Olfactory receptors"""	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.381G>A	11.37:g.55944474G>A		Somatic	353	2	0.00566572		WXS	Illumina HiSeq	Phase_I	311	140	0.450161	NM_001005492	Q6IEU5	Silent	SNP	ENST00000312298.1	37	CCDS31522.1																																																																																			G|0.903;A|0.097	0.097	strong		0.453	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492	
CCDC88C	440193	hgsc.bcm.edu	37	14	91773568	91773568	+	Silent	SNP	T	T	C	rs1970912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:91773568T>C	ENST00000389857.6	-	18	3095	c.3009A>G	c.(3007-3009)ctA>ctG	p.L1003L		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1003					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)				ACTCCTTCTTTAGCTACAGGT	0.602													C|||	2406	0.480431	0.5522	0.4914	5008	,	,		18579	0.3552		0.5994	False		,,,				2504	0.3824				p.L1003L		Atlas-SNP	.											.	CCDC88C	192	.	0			c.A3009G						PASS	.	C		2299,1741		642,1015,363	47.0	49.0	48.0		3009	2.1	0.1	14	dbSNP_92	48	4874,3466		1434,2006,730	no	coding-synonymous	CCDC88C	NM_001080414.3		2076,3021,1093	CC,CT,TT		41.5588,43.0941,42.0598		1003/2029	91773568	7173,5207	2020	4170	6190	SO:0001819	synonymous_variant	440193	exon18			CTTCTTTAGCTAC		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.3009A>G	14.37:g.91773568T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	49	28	0.571429	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.517;N|0.000	0.517	strong		0.602	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
CWC27	10283	hgsc.bcm.edu	37	5	64273018	64273018	+	Silent	SNP	G	G	A	rs1309581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:64273018G>A	ENST00000381070.3	+	13	1426	c.1209G>A	c.(1207-1209)acG>acA	p.T403T	CWC27_ENST00000545000.1_3'UTR	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	403					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						TTGCTGAAACGCCTGAAAATG	0.358													G|||	1761	0.351637	0.2519	0.3876	5008	,	,		18195	0.3026		0.4125	False		,,,				2504	0.4489				p.T403T		Atlas-SNP	.											.	CWC27	47	.	0			c.G1209A						PASS	.	G		1287,3119	432.8+/-343.4	203,881,1119	80.0	74.0	76.0		1209	0.7	1.0	5	dbSNP_87	76	3875,4725	543.3+/-384.4	906,2063,1331	no	coding-synonymous	CWC27	NM_005869.2		1109,2944,2450	AA,AG,GG		45.0581,29.2102,39.6894		403/473	64273018	5162,7844	2203	4300	6503	SO:0001819	synonymous_variant	10283	exon13			TGAAACGCCTGAA	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.1209G>A	5.37:g.64273018G>A		Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	231	126	0.545455	NM_005869	O60529|O60530|Q96EM3	Silent	SNP	ENST00000381070.3	37	CCDS3982.2																																																																																			G|0.631;A|0.369	0.369	strong		0.358	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
HLA-A	3105	hgsc.bcm.edu	37	6	29910358	29910358	+	Missense_Mutation	SNP	C	C	G	rs1143146	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910358C>G	ENST00000396634.1	+	3	369	c.28C>G	c.(28-30)Ctc>Gtc	p.L10V	HLA-A_ENST00000376809.5_Missense_Mutation_p.L10V|HLA-A_ENST00000376806.5_Missense_Mutation_p.L10V|HLA-A_ENST00000376802.2_Missense_Mutation_p.L10V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	10					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						CCGAACCCTCCTCCTGCTACT	0.697									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|||	2531	0.505391	0.4743	0.5965	5008	,	,		15681	0.5397		0.5119	False		,,,				2504	0.4407				p.L10V		Atlas-SNP	.											.	HLA-A	89	.	0			c.C28G						PASS	.	G	VAL/LEU	2094,2312		466,1162,575	33.0	36.0	35.0		28	-0.4	0.0	6	dbSNP_86	35	4132,4458		989,2154,1152	no	missense	HLA-A	NM_002116.7	32	1455,3316,1727	GG,GC,CC		48.1024,47.5261,47.907	benign	10/366	29910358	6226,6770	2203	4295	6498	SO:0001583	missense	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ACCCTCCTCCTGC	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.28C>G	6.37:g.29910358C>G	ENSP00000379873:p.Leu10Val	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	147	144	0.979592	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	1140	0.521978021978022	230	0.46747967479674796	198	0.5469613259668509	329	0.5751748251748252	383	0.5052770448548812	.	8.451	0.853152	0.17106	0.475261	0.481024	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00801	5.7;5.68;5.7;5.71	3.71	-0.398	0.12418	.	1.184600	0.07033	N	0.828726	T	0.00144	0.0004	.	.	.	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.003	T	0.34204	-0.9838	8	0.02654	T	1	.	4.1979	0.10452	0.0:0.5233:0.1702:0.3065	rs1143146;rs2230953;rs3115640;rs3173432;rs9260121;rs41540716	10;10;10;10	Q5SRN7;P16188;Q5SRN5;P04439	.;1A30_HUMAN;.;1A03_HUMAN	V	10	ENSP00000379873:L10V;ENSP00000366002:L10V;ENSP00000366005:L10V;ENSP00000365998:L10V	ENSP00000348012:L10V	L	+	1	0	HLA-A	30018337	0.000000	0.05858	0.002000	0.10522	0.137000	0.21094	-0.182000	0.09726	-0.192000	0.10432	-0.363000	0.07495	CTC	C|0.511;G|0.489	0.489	strong		0.697	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
GDF3	9573	hgsc.bcm.edu	37	12	7848202	7848202	+	Silent	SNP	G	G	C	rs17727707	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7848202G>C	ENST00000329913.3	-	1	170	c.123C>G	c.(121-123)ccC>ccG	p.P41P		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	41					endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						GGAACTTCTGGGGTGAAGGCG	0.483													G|||	134	0.0267572	0.0023	0.0389	5008	,	,		-128	0.0		0.0686	False		,,,				2504	0.0358				p.P41P		Atlas-SNP	.											.	GDF3	68	.	0			c.C123G						PASS	.	G		68,4338	62.9+/-100.1	0,68,2135	48.0	49.0	48.0		123	-0.3	0.0	12	dbSNP_123	48	677,7923	169.1+/-220.5	39,599,3662	no	coding-synonymous	GDF3	NM_020634.1		39,667,5797	CC,CG,GG		7.8721,1.5433,5.7281		41/365	7848202	745,12261	2203	4300	6503	SO:0001819	synonymous_variant	9573	exon1			CTTCTGGGGTGAA	AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"""Endogenous ligands"""	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.123C>G	12.37:g.7848202G>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	89	50	0.561798	NM_020634	Q8NEJ4	Silent	SNP	ENST00000329913.3	37	CCDS8581.1																																																																																			G|0.951;C|0.049	0.049	strong		0.483	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1		
C1orf53	388722	hgsc.bcm.edu	37	1	197874949	197874949	+	Silent	SNP	T	T	C	rs2270763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:197874949T>C	ENST00000367393.3	+	2	291	c.288T>C	c.(286-288)gaT>gaC	p.D96D	C1orf53_ENST00000542800.1_3'UTR	NM_001024594.2	NP_001019765.1	Q5VUE5	CA053_HUMAN	chromosome 1 open reading frame 53	96										endometrium(1)|lung(1)	2						ACTATGTGGATCCAGCTACTG	0.408													T|||	1801	0.359625	0.4123	0.3948	5008	,	,		18098	0.2619		0.3668	False		,,,				2504	0.3569				p.D96D		Atlas-SNP	.											.	C1orf53	18	.	0			c.T288C						PASS	.	T		1591,2363		339,913,725	160.0	151.0	154.0		288	-0.9	1.0	1	dbSNP_100	154	2921,5421		512,1897,1762	no	coding-synonymous	C1orf53	NM_001024594.2		851,2810,2487	CC,CT,TT		35.0156,40.2377,36.6949		96/146	197874949	4512,7784	1977	4171	6148	SO:0001819	synonymous_variant	388722	exon2			TGTGGATCCAGCT	BC038214	CCDS44290.1	1q31.3	2011-01-26			ENSG00000203724	ENSG00000203724			30003	protein-coding gene	gene with protein product						15897902	Standard	NM_001024594		Approved		uc001guh.3	Q5VUE5	OTTHUMG00000035659	ENST00000367393.3:c.288T>C	1.37:g.197874949T>C		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	228	104	0.45614	NM_001024594	A1L4N2|Q5VUE4	Silent	SNP	ENST00000367393.3	37	CCDS44290.1	735	0.33653846153846156	187	0.3800813008130081	151	0.4171270718232044	139	0.243006993006993	258	0.3403693931398417	T	8.716	0.913213	0.17907	0.402377	0.350156	ENSG00000203724	ENST00000436652	.	.	.	5.73	-0.891	0.10573	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999697	.	.	.	.	.	.	T	0.43376	-0.9395	3	.	.	.	-2.0025	11.3485	0.49575	0.0:0.4741:0.0:0.5259	rs2270763;rs61130784;rs2270763	.	.	.	P	33	.	.	S	+	1	0	C1orf53	196141572	0.993000	0.37304	0.968000	0.41197	0.989000	0.77384	0.140000	0.16056	-0.399000	0.07668	-0.290000	0.09829	TCC	T|0.659;C|0.341	0.341	strong		0.408	C1orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086555.1	NM_001024594	
PGBD5	79605	hgsc.bcm.edu	37	1	230461079	230461079	+	Silent	SNP	G	G	A	rs2306813	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:230461079G>A	ENST00000525115.1	-	6	1172	c.1149C>T	c.(1147-1149)tgC>tgT	p.C383C	PGBD5_ENST00000321327.2_Silent_p.C482C|PGBD5_ENST00000530424.1_5'UTR|PGBD5_ENST00000391860.1_Silent_p.C337C			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	383						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		CATCGTATCTGCAGATGTAGC	0.527													G|||	1179	0.235423	0.1536	0.255	5008	,	,		22434	0.4901		0.1551	False		,,,				2504	0.1524				p.C452C		Atlas-SNP	.											.	PGBD5	73	.	0			c.C1356T						PASS	.	G		705,3701	295.0+/-283.4	60,585,1558	255.0	219.0	232.0		1149	4.2	1.0	1	dbSNP_100	232	1492,7108	284.2+/-296.5	122,1248,2930	no	coding-synonymous	PGBD5	NM_024554.3		182,1833,4488	AA,AG,GG		17.3488,16.0009,16.8922		383/456	230461079	2197,10809	2203	4300	6503	SO:0001819	synonymous_variant	79605	exon6			GTATCTGCAGATG	AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.1149C>T	1.37:g.230461079G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_001258311	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Silent	SNP	ENST00000525115.1	37																																																																																				G|0.791;N|0.000	.	strong		0.527	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554	
PTPRR	5801	hgsc.bcm.edu	37	12	71139664	71139664	+	Missense_Mutation	SNP	T	T	C	rs3803036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:71139664T>C	ENST00000283228.2	-	6	1393	c.941A>G	c.(940-942)aAa>aGa	p.K314R	PTPRR_ENST00000342084.4_Missense_Mutation_p.K202R|PTPRR_ENST00000378778.1_Missense_Mutation_p.K108R|PTPRR_ENST00000549308.1_Missense_Mutation_p.K69R|PTPRR_ENST00000440835.2_Missense_Mutation_p.K69R	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	314			K -> R (in dbSNP:rs3803036). {ECO:0000269|PubMed:10705342, ECO:0000269|PubMed:11147789, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7557444, ECO:0000269|Ref.4, ECO:0000269|Ref.7}.		ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		GGTGGTAGCTTTGATCTCAGG	0.522													T|||	3397	0.678315	0.2784	0.7983	5008	,	,		16192	0.9385		0.7763	False		,,,				2504	0.7648				p.K314R		Atlas-SNP	.											.	PTPRR	109	.	0			c.A941G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1674,2732	510.1+/-367.4	313,1048,842	153.0	113.0	127.0		605,323,941,206	0.6	0.8	12	dbSNP_107	127	6753,1847	730.8+/-406.8	2652,1449,199	yes	missense,missense,missense,missense	PTPRR	NM_001207015.1,NM_001207016.1,NM_002849.3,NM_130846.2	26,26,26,26	2965,2497,1041	CC,CT,TT		21.4767,37.9936,35.2068	benign,benign,benign,benign	202/546,108/452,314/658,69/413	71139664	8427,4579	2203	4300	6503	SO:0001583	missense	5801	exon6			GTAGCTTTGATCT	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.941A>G	12.37:g.71139664T>C	ENSP00000283228:p.Lys314Arg	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	175	173	0.988571	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	1576	0.7216117216117216	160	0.3252032520325203	282	0.7790055248618785	540	0.9440559440559441	594	0.783641160949868	T	9.111	1.006603	0.19199	0.379936	0.785233	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308;ENST00000550661	T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46	5.53	0.593	0.17478	.	0.382752	0.21803	N	0.068889	T	0.00012	0.0000	N	0.17474	0.49	0.51233	P	9.00000000000345E-5	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.001;0.001	T	0.22556	-1.0213	9	0.16896	T	0.51	-5.0751	9.0855	0.36579	0.0:0.3682:0.0:0.6318	rs3803036;rs52824799;rs58461104;rs3803036	163;202;108;314	B7Z998;F5GXR7;Q15256-4;Q15256	.;.;.;PTPRR_HUMAN	R	69;314;108;202;69;69	ENSP00000391750:K69R;ENSP00000283228:K314R;ENSP00000368054:K108R;ENSP00000339605:K202R;ENSP00000446943:K69R;ENSP00000449616:K69R	ENSP00000283228:K314R	K	-	2	0	PTPRR	69425931	1.000000	0.71417	0.835000	0.33067	0.903000	0.53119	0.832000	0.27490	-0.122000	0.11766	-0.261000	0.10672	AAA	T|0.322;C|0.678	0.678	strong		0.522	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
BTG1	694	hgsc.bcm.edu	37	12	92539246	92539246	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:92539246G>A	ENST00000256015.3	-	1	427	c.66C>T	c.(64-66)atC>atT	p.I22I	RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000546975.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	22					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GAAACTTGGAGATGAAGGACA	0.701			T	MYC	BCLL																																p.I22I		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	.	BTG1	30	.	0			c.C66T						PASS	.						44.0	48.0	47.0					12																	92539246		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			CTTGGAGATGAAG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.66C>T	12.37:g.92539246G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	164	8	0.0487805	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	none		0.701	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
GRIN2C	2905	hgsc.bcm.edu	37	17	72838649	72838649	+	Missense_Mutation	SNP	C	C	A	rs3744215	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72838649C>A	ENST00000293190.5	-	13	3773	c.3627G>T	c.(3625-3627)agG>agT	p.R1209S		NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	1209			R -> S (in dbSNP:rs3744215).		directional locomotion (GO:0033058)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of protein catabolic process (GO:0042177)|neuromuscular process controlling balance (GO:0050885)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to wounding (GO:0009611)|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)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(15)|ovary(2)|skin(2)|urinary_tract(1)	33	all_lung(278;0.172)|Lung NSC(278;0.207)				Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CACGGGCTACCCTGCTGATCT	0.662													C|||	1450	0.289537	0.2852	0.1931	5008	,	,		15832	0.381		0.2942	False		,,,				2504	0.2648				p.R1209S		Atlas-SNP	.											GRIN2C_ENST00000293190,NS,carcinoma,0,4	GRIN2C	144	4	0			c.G3627T						PASS	.	C	SER/ARG	1356,3050		214,928,1061	22.0	20.0	21.0		3627	-1.4	0.2	17	dbSNP_107	21	2433,6161		337,1759,2201	yes	missense	GRIN2C	NM_000835.3	110	551,2687,3262	AA,AC,CC		28.3104,30.7762,29.1462	possibly-damaging	1209/1234	72838649	3789,9211	2203	4297	6500	SO:0001583	missense	2905	exon13			GGCTACCCTGCTG		CCDS32724.1, CCDS62330.1	17q25.1	2012-08-29			ENSG00000161509	ENSG00000161509		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4587	protein-coding gene	gene with protein product		138254		NMDAR2C		9480759	Standard	NM_001278553		Approved	GluN2C	uc002jlt.1	Q14957	OTTHUMG00000044524	ENST00000293190.5:c.3627G>T	17.37:g.72838649C>A	ENSP00000293190:p.Arg1209Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	159	72	0.45283	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	37	CCDS32724.1	681	0.3118131868131868	149	0.30284552845528456	74	0.20441988950276244	229	0.40034965034965037	229	0.3021108179419525	C	14.76	2.631722	0.46944	0.307762	0.283104	ENSG00000161509	ENST00000293190	T	0.10763	2.84	4.74	-1.36	0.09085	.	0.853171	0.10019	N	0.726218	T	0.00012	0.0000	L	0.27053	0.805	0.21290	P	0.999737402	B	0.06786	0.001	B	0.04013	0.001	T	0.47971	-0.9075	9	0.59425	D	0.04	.	3.6082	0.08050	0.4273:0.3215:0.0:0.2511	rs3744215;rs56834934;rs3744215	1209	Q14957	NMDE3_HUMAN	S	1209	ENSP00000293190:R1209S	ENSP00000293190:R1209S	R	-	3	2	GRIN2C	70350244	0.000000	0.05858	0.188000	0.23233	0.666000	0.39218	0.514000	0.22786	-0.045000	0.13468	-0.258000	0.10820	AGG	C|0.689;A|0.311	0.311	strong		0.662	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1		
DCSTAMP	81501	hgsc.bcm.edu	37	8	105367121	105367121	+	Missense_Mutation	SNP	A	A	G	rs3802204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:105367121A>G	ENST00000297581.2	+	3	1095	c.1046A>G	c.(1045-1047)gAt>gGt	p.D349G	DPYS_ENST00000521601.1_Intron|DCSTAMP_ENST00000517991.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	349			D -> G (in dbSNP:rs3802204).		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)											GGAACTCAAGATATTATCCAT	0.358													A|||	593	0.118411	0.0605	0.1931	5008	,	,		20178	0.1319		0.1342	False		,,,				2504	0.1135				p.D349G		Atlas-SNP	.											.	.	.	.	0			c.A1046G						PASS	.	A	GLY/ASP	353,4053	180.1+/-208.5	18,317,1868	66.0	64.0	65.0		1046	0.3	0.0	8	dbSNP_107	65	1169,7431	237.8+/-269.5	88,993,3219	yes	missense	TM7SF4	NM_030788.2	94	106,1310,5087	GG,GA,AA		13.593,8.0118,11.7023	benign	349/471	105367121	1522,11484	2203	4300	6503	SO:0001583	missense	81501	exon3			CTCAAGATATTAT	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.1046A>G	8.37:g.105367121A>G	ENSP00000297581:p.Asp349Gly	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_030788	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	265	0.12133699633699634	33	0.06707317073170732	74	0.20441988950276244	57	0.09965034965034965	101	0.13324538258575197	A	0.797	-0.756924	0.03019	0.080118	0.13593	ENSG00000164935	ENST00000297581	T	0.30182	1.54	5.44	0.324	0.15898	Dendritic cell-specific transmembrane protein-like (1);	0.767529	0.12451	N	0.467785	T	0.00012	0.0000	L	0.28400	0.85	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.32719	-0.9896	9	0.25751	T	0.34	-0.1646	4.1981	0.10453	0.5009:0.1767:0.3224:0.0	rs3802204;rs52810559;rs56635979;rs57014874;rs3802204	349	Q9H295	TM7S4_HUMAN	G	349	ENSP00000297581:D349G	ENSP00000297581:D349G	D	+	2	0	TM7SF4	105436297	0.000000	0.05858	0.001000	0.08648	0.318000	0.28184	-0.029000	0.12329	-0.103000	0.12175	0.533000	0.62120	GAT	A|0.886;G|0.114	0.114	strong		0.358	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
LCT	3938	hgsc.bcm.edu	37	2	136575199	136575199	+	Silent	SNP	G	G	T	rs6719488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:136575199G>T	ENST00000264162.2	-	6	1429	c.1419C>A	c.(1417-1419)ggC>ggA	p.G473G	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	473	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	AGTAGGCAACGCCTGGGAGGC	0.637													G|||	1783	0.35603	0.1195	0.4323	5008	,	,		18831	0.3998		0.5954	False		,,,				2504	0.3303				p.G473G		Atlas-SNP	.											.	LCT	309	.	0			c.C1419A						PASS	.	G		1040,3366		120,800,1283	55.0	49.0	51.0		1419	-11.5	0.0	2	dbSNP_116	51	5998,2602		2180,1638,482	no	coding-synonymous	LCT	NM_002299.2		2300,2438,1765	TT,TG,GG		30.2558,23.6042,45.8865		473/1928	136575199	7038,5968	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon6			GGCAACGCCTGGG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1419C>A	2.37:g.136575199G>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.592;T|0.408	0.408	strong		0.637	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
HIST1H4B	8366	hgsc.bcm.edu	37	6	26027286	26027286	+	Silent	SNP	G	G	A	rs115249469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26027286G>A	ENST00000377364.3	-	1	194	c.195C>T	c.(193-195)aaC>aaT	p.N65N		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	65					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						CCCGGATCACGTTCTCCAGAA	0.567											OREG0017238	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	13	0.00259585	0.0008	0.0	5008	,	,		14349	0.0		0.005	False		,,,				2504	0.0072				p.N65N		Atlas-SNP	.											.	HIST1H4B	27	.	0			c.C195T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	103.0	87.0	92.0		195	0.9	1.0	6	dbSNP_132	92	31,8569	21.6+/-65.8	0,31,4269	no	coding-synonymous	HIST1H4B	NM_003544.2		0,36,6467	AA,AG,GG		0.3605,0.1135,0.2768		65/104	26027286	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	8366	exon1			GATCACGTTCTCC	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.195C>T	6.37:g.26027286G>A		Somatic	87	0	0	783	WXS	Illumina HiSeq	Phase_I	116	66	0.568965	NM_003544	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377364.3	37	CCDS4572.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544	
CASP7	840	hgsc.bcm.edu	37	10	115457264	115457264	+	Missense_Mutation	SNP	T	T	G	rs11555408	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115457264T>G	ENST00000345633.4	+	3	396	c.12T>G	c.(10-12)gaT>gaG	p.D4E	CASP7_ENST00000369321.2_Missense_Mutation_p.D37E|CASP7_ENST00000369331.4_Missense_Mutation_p.D4E|CASP7_ENST00000369315.1_Missense_Mutation_p.D4E|CASP7_ENST00000369318.3_Missense_Mutation_p.D4E	NM_033339.4	NP_203125.1	P55210	CASP7_HUMAN	caspase 7, apoptosis-related cysteine peptidase	4			D -> E (in dbSNP:rs11593766). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway (GO:0097193)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			kidney(1)|large_intestine(1)|lung(5)|ovary(1)	8		Colorectal(252;0.0946)|Breast(234;0.188)		Epithelial(162;0.012)|all cancers(201;0.014)		TGGCAGATGATCAGGGCTGTA	0.453													T|||	529	0.105631	0.146	0.0807	5008	,	,		21630	0.0883		0.1044	False		,,,				2504	0.0879				p.I79S		Atlas-SNP	.											.	CASP7	21	.	0			c.T236G						PASS	.	T	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	542,3864	246.2+/-254.9	35,472,1696	182.0	178.0	180.0		12,111,12,12	2.0	0.1	10	dbSNP_120	180	892,7708	201.3+/-244.8	59,774,3467	yes	missense,missense,missense,missense	CASP7	NM_001227.3,NM_033338.4,NM_033339.3,NM_033340.2	45,45,45,45	94,1246,5163	GG,GT,TT		10.3721,12.3014,11.0257	benign,benign,benign,benign	4/304,37/337,4/304,4/254	115457264	1434,11572	2203	4300	6503	SO:0001583	missense	840	exon2			AGATGATCAGGGC	U37448	CCDS7580.1, CCDS7581.1, CCDS7582.1, CCDS58096.1, CCDS73200.1	10q25	2006-02-17	2005-08-17		ENSG00000165806	ENSG00000165806		"""Caspases"""	1508	protein-coding gene	gene with protein product		601761	"""caspase 7, apoptosis-related cysteine protease"""			8521391, 8576161	Standard	NM_033338		Approved	MCH3, CMH-1, ICE-LAP3	uc010qsa.3	P55210	OTTHUMG00000019076	ENST00000345633.4:c.12T>G	10.37:g.115457264T>G	ENSP00000298701:p.Asp4Glu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001267057	B4DQU7|B5BU45|D3DRB8|Q13364|Q53YD5|Q5SVL0|Q5SVL3|Q96BA0	Missense_Mutation	SNP	ENST00000345633.4	37	CCDS7581.1	231	0.10576923076923077	74	0.15040650406504066	32	0.08839779005524862	45	0.07867132867132867	80	0.10554089709762533	T	13.38	2.220932	0.39201	0.123014	0.103721	ENSG00000165806	ENST00000429617;ENST00000369331;ENST00000369321;ENST00000345633;ENST00000369318;ENST00000442393;ENST00000369319;ENST00000369316;ENST00000369315	T;T;T;T;T;T	0.11495	3.74;2.77;4.28;4.37;4.37;4.37	4.39	2.04	0.26737	.	0.454251	0.19939	N	0.102697	T	0.00073	0.0002	M	0.62723	1.935	0.36861	P	0.11158199999999996	B;B;P	0.45715	0.041;0.147;0.865	B;B;P	0.45310	0.026;0.042;0.476	T	0.20974	-1.0259	9	0.30078	T	0.28	.	5.7337	0.18055	0.0:0.2196:0.0:0.7804	rs11593766;rs17845478;rs17858357;rs11593766	37;4;4	P55210-3;P55210;P55210-2	.;CASP7_HUMAN;.	E	4;4;37;4;4;4;4;4;4	ENSP00000400094:D4E;ENSP00000358337:D4E;ENSP00000358327:D37E;ENSP00000298701:D4E;ENSP00000358324:D4E;ENSP00000358321:D4E	ENSP00000298701:D4E	D	+	3	2	CASP7	115447254	0.144000	0.22641	0.110000	0.21437	0.309000	0.27889	0.009000	0.13219	0.317000	0.23160	0.533000	0.62120	GAT	T|0.889;G|0.111	0.111	strong		0.453	CASP7-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050439.1	NM_033338	
COL5A3	50509	hgsc.bcm.edu	37	19	10116508	10116508	+	Missense_Mutation	SNP	C	C	T	rs2303098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10116508C>T	ENST00000264828.3	-	3	486	c.401G>A	c.(400-402)cGc>cAc	p.R134H		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	134	Laminin G-like.		R -> H (in dbSNP:rs2303098).		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)			GGGGAGGGGGCGGAAGGGGTC	0.647													C|||	820	0.163738	0.171	0.0908	5008	,	,		15770	0.1062		0.1551	False		,,,				2504	0.274				p.R134H		Atlas-SNP	.											.	COL5A3	243	.	0			c.G401A						PASS	.	C	HIS/ARG	696,3674		61,574,1550	18.0	21.0	20.0		401	0.6	0.0	19	dbSNP_100	20	1484,7094		131,1222,2936	yes	missense	COL5A3	NM_015719.3	29	192,1796,4486	TT,TC,CC		17.3001,15.9268,16.8366	benign	134/1746	10116508	2180,10768	2185	4289	6474	SO:0001583	missense	50509	exon3			AGGGGGCGGAAGG	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.401G>A	19.37:g.10116508C>T	ENSP00000264828:p.Arg134His	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	22	9	0.409091	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	311	0.1423992673992674	101	0.20528455284552846	43	0.11878453038674033	52	0.09090909090909091	115	0.1517150395778364	C	1.837	-0.468341	0.04445	0.159268	0.173001	ENSG00000080573	ENST00000264828	T	0.02140	4.43	4.02	0.641	0.17759	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Laminin G, thrombospondin-type, N-terminal (1);	0.709518	0.13678	U	0.370381	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47005	-0.9150	9	0.39692	T	0.17	.	4.0101	0.09619	0.0:0.5817:0.1967:0.2216	rs2303098;rs59921984;rs2303098	134	P25940	CO5A3_HUMAN	H	134	ENSP00000264828:R134H	ENSP00000264828:R134H	R	-	2	0	COL5A3	9977508	0.005000	0.15991	0.000000	0.03702	0.043000	0.13939	1.375000	0.34295	0.053000	0.16036	-0.502000	0.04539	CGC	C|0.847;T|0.153	0.153	strong		0.647	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
ZNF568	374900	hgsc.bcm.edu	37	19	37441980	37441980	+	Missense_Mutation	SNP	A	A	G	rs1644634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37441980A>G	ENST00000333987.7	+	7	2431	c.1925A>G	c.(1924-1926)cAa>cGa	p.Q642R	ZNF568_ENST00000415168.1_Missense_Mutation_p.Q578R|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	642			Q -> R (in dbSNP:rs1644634).		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			GAGAGACACCAAGTATATTAA	0.353													G|||	2744	0.547923	0.6982	0.5634	5008	,	,		16777	0.3085		0.5636	False		,,,				2504	0.5644				p.Q642R		Atlas-SNP	.											.	ZNF568	106	.	0			c.A1925G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN,,,ARG/GLN	2868,1198		1013,842,178	44.0	49.0	48.0		1922,1733,1733,,,1925	-6.2	0.0	19	dbSNP_89	48	4847,3589		1427,1993,798	yes	missense,missense,missense,intron,intron,missense	ZNF568	NM_001204835.1,NM_001204836.1,NM_001204837.1,NM_001204838.1,NM_001204839.1,NM_198539.3	43,43,43,,,43	2440,2835,976	GG,GA,AA		42.5439,29.4638,38.2899	benign,benign,benign,,,benign	641/644,578/581,578/581,,,642/645	37441980	7715,4787	2033	4218	6251	SO:0001583	missense	374900	exon7			GACACCAAGTATA	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1925A>G	19.37:g.37441980A>G	ENSP00000334685:p.Gln642Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	36	22	0.611111	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	1178	0.5393772893772893	355	0.7215447154471545	206	0.569060773480663	183	0.31993006993006995	434	0.5725593667546174	G	0.267	-0.995235	0.02145	0.705362	0.574561	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.05199	3.57;3.48	4.13	-6.21	0.02065	.	.	.	.	.	T	0.00012	0.0000	N	0.11313	0.125	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31336	-0.9947	8	0.59425	D	0.04	.	5.9799	0.19401	0.4871:0.2255:0.2875:0.0	rs1644634;rs17242347;rs52798567;rs59064941;rs1644634	642	Q3ZCX4	ZN568_HUMAN	R	642;578	ENSP00000334685:Q642R;ENSP00000394514:Q578R	ENSP00000334685:Q642R	Q	+	2	0	ZNF568	42133820	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.872000	0.04219	-1.765000	0.01303	-1.861000	0.00560	CAA	A|0.447;G|0.553	0.553	strong		0.353	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
FRRS1	391059	hgsc.bcm.edu	37	1	100203648	100203648	+	Silent	SNP	C	C	T	rs7537296	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:100203648C>T	ENST00000414213.1	-	7	1354	c.753G>A	c.(751-753)caG>caA	p.Q251Q	FRRS1_ENST00000287474.5_Silent_p.Q251Q			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	251	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		CAACCATCCACTGATCATGAG	0.483													c|||	2796	0.558307	0.9402	0.4928	5008	,	,		19702	0.3909		0.3082	False		,,,				2504	0.5184				p.Q251Q		Atlas-SNP	.											.	FRRS1	50	.	0			c.G753A						PASS	.	T		3680,726	757.7+/-412.7	1536,608,59	109.0	113.0	112.0		753	-1.3	0.5	1	dbSNP_116	112	2915,5685	454.1+/-363.4	505,1905,1890	yes	coding-synonymous	FRRS1	NM_001013660.2		2041,2513,1949	TT,TC,CC		33.8953,16.4775,49.2926		251/627	100203648	6595,6411	2203	4300	6503	SO:0001819	synonymous_variant	391059	exon7			CATCCACTGATCA	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.753G>A	1.37:g.100203648C>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	179	95	0.530726	NM_001013660	A6NLN7	Silent	SNP	ENST00000414213.1	37																																																																																				C|0.486;T|0.514	0.514	strong		0.483	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
PARP15	165631	hgsc.bcm.edu	37	3	122354792	122354792	+	Missense_Mutation	SNP	G	G	A	rs12489170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:122354792G>A	ENST00000464300.2	+	12	1948	c.1882G>A	c.(1882-1884)Gga>Aga	p.G628R	PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000483793.1_Missense_Mutation_p.G433R|PARP15_ENST00000493645.1_Missense_Mutation_p.G325R|PARP15_ENST00000310366.4_Missense_Mutation_p.G394R	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	628	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.		G -> R (in dbSNP:rs12489170).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		CTTCACAAAGGGACGTGCAGG	0.478													G|||	1110	0.221645	0.0983	0.2478	5008	,	,		19992	0.4881		0.1322	False		,,,				2504	0.1871				p.G628R		Atlas-SNP	.											.	PARP15	115	.	0			c.G1882A						PASS	.	G	ARG/GLY,ARG/GLY	511,3895	236.1+/-248.4	28,455,1720	164.0	134.0	144.0		1882,1180	4.0	0.0	3	dbSNP_120	144	1138,7462	233.7+/-266.9	91,956,3253	yes	missense,missense	PARP15	NM_001113523.1,NM_152615.1	125,125	119,1411,4973	AA,AG,GG		13.2326,11.5978,12.6788	probably-damaging,probably-damaging	628/679,394/445	122354792	1649,11357	2203	4300	6503	SO:0001583	missense	165631	exon12			ACAAAGGGACGTG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1882G>A	3.37:g.122354792G>A	ENSP00000417214:p.Gly628Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	512	0.23443223443223443	48	0.0975609756097561	82	0.2265193370165746	281	0.49125874125874125	101	0.13324538258575197	G	20.7	4.030508	0.75504	0.115978	0.132326	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.16457	2.34;2.34;2.34;2.34	3.99	3.99	0.46301	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.00012	0.0000	M	0.93594	3.435	0.09310	P	0.99999999239116	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	T	0.48502	-0.9030	8	0.62326	D	0.03	.	14.7995	0.69903	0.0:0.0:1.0:0.0	rs12489170;rs60932120;rs12489170	325;394;375;433;606	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	R	628;433;375;394;325	ENSP00000417214:G628R;ENSP00000417785:G433R;ENSP00000308436:G394R;ENSP00000419488:G325R	ENSP00000308436:G394R	G	+	1	0	PARP15	123837482	1.000000	0.71417	0.030000	0.17652	0.002000	0.02628	9.647000	0.98478	2.058000	0.61347	0.650000	0.86243	GGA	G|0.823;A|0.177	0.177	strong		0.478	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
SUGP2	10147	hgsc.bcm.edu	37	19	19105259	19105259	+	Silent	SNP	G	G	A	rs4808897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19105259G>A	ENST00000601879.1	-	10	3462	c.3165C>T	c.(3163-3165)gaC>gaT	p.D1055D	AC004447.2_ENST00000594142.1_RNA|SUGP2_ENST00000600377.1_Silent_p.D1069D|SUGP2_ENST00000452918.2_Silent_p.D1055D|SUGP2_ENST00000337018.6_Silent_p.D1055D			Q8IX01	SUGP2_HUMAN	SURP and G patch domain containing 2	1055	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GCTCCTGCCCGTCAGCACCCA	0.557													G|||	204	0.0407348	0.0265	0.0692	5008	,	,		19573	0.0		0.0765	False		,,,				2504	0.045				p.D1055D		Atlas-SNP	.											SUGP2,NS,adenoma,0,1	SUGP2	107	1	0			c.C3165T						scavenged	.	G	,	127,4279	91.6+/-130.3	2,123,2078	243.0	195.0	211.0		3165,3165	-5.0	0.8	19	dbSNP_111	211	695,7905	172.7+/-223.4	29,637,3634	no	coding-synonymous,coding-synonymous	SUGP2	NM_001017392.3,NM_014884.3	,	31,760,5712	AA,AG,GG		8.0814,2.8824,6.3202	,	1055/1083,1055/1083	19105259	822,12184	2203	4300	6503	SO:0001819	synonymous_variant	10147	exon10			CTGCCCGTCAGCA	AB002363	CCDS12392.1	19p13	2013-01-28	2010-08-10	2010-08-10	ENSG00000064607	ENSG00000064607		"""G patch domain containing"""	18641	protein-coding gene	gene with protein product		607993	"""splicing factor, arginine/serine-rich 14"""	SFRS14		12594045	Standard	NM_014884		Approved	KIAA0365	uc002nkx.2	Q8IX01		ENST00000601879.1:c.3165C>T	19.37:g.19105259G>A		Somatic	128	2	0.015625		WXS	Illumina HiSeq	Phase_I	136	75	0.551471	NM_014884	C9JI71|O15071|O60369|Q5JPH7|Q8WUF7	Silent	SNP	ENST00000601879.1	37	CCDS12392.1																																																																																			G|0.940;A|0.060	0.060	strong		0.557	SUGP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464627.1	NM_001017392	
INSL4	3641	hgsc.bcm.edu	37	9	5231712	5231712	+	Silent	SNP	T	T	A	rs12720	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5231712T>A	ENST00000239316.4	+	1	294	c.189T>A	c.(187-189)cgT>cgA	p.R63R		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	63					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	insulin-like growth factor receptor binding (GO:0005159)|receptor binding (GO:0005102)			endometrium(2)|lung(2)|skin(1)|urinary_tract(1)	6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.14)		AATCTGGACGTCCCAAAGGTG	0.512													A|||	1999	0.399161	0.7337	0.3775	5008	,	,		19844	0.2222		0.2883	False		,,,				2504	0.2587				p.R63R		Atlas-SNP	.											INSL4,bladder,carcinoma,+2,1	INSL4	20	1	0			c.T189A						PASS	.	A		2877,1529	483.3+/-359.7	937,1003,263	46.0	46.0	46.0		189	0.4	0.0	9	dbSNP_52	46	2350,6250	701.5+/-405.2	305,1740,2255	no	coding-synonymous	INSL4	NM_002195.1		1242,2743,2518	AA,AT,TT		27.3256,34.7027,40.1891		63/140	5231712	5227,7779	2203	4300	6503	SO:0001819	synonymous_variant	3641	exon1			TGGACGTCCCAAA		CCDS6459.1	9p24	2008-02-05			ENSG00000120211	ENSG00000120211			6087	protein-coding gene	gene with protein product		600910				8666396, 9730618	Standard	NM_002195		Approved	EPIL	uc003ziy.3	Q14641	OTTHUMG00000019494	ENST00000239316.4:c.189T>A	9.37:g.5231712T>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_002195	A8K678|Q5W127	Silent	SNP	ENST00000239316.4	37	CCDS6459.1																																																																																			T|0.613;A|0.387	0.387	strong		0.512	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195	
PLIN4	729359	hgsc.bcm.edu	37	19	4512889	4512889	+	Silent	SNP	A	A	G	rs200699570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4512889A>G	ENST00000301286.3	-	3	1040	c.1041T>C	c.(1039-1041)acT>acC	p.T347T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	347	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CAGTTAGGACAGTCTTGGTGG	0.577													A|||	601	0.120008	0.3396	0.0706	5008	,	,		19261	0.001		0.0656	False		,,,				2504	0.0368				p.T347T		Atlas-SNP	.											.	PLIN4	191	.	0			c.T1041C						PASS	.						45.0	88.0	75.0					19																	4512889		1693	4155	5848	SO:0001819	synonymous_variant	729359	exon3			TAGGACAGTCTTG	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.1041T>C	19.37:g.4512889A>G		Somatic	288	1	0.00347222		WXS	Illumina HiSeq	Phase_I	66	64	0.969697	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.986;G|0.014	0.014	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
N4BP2	55728	hgsc.bcm.edu	37	4	40103767	40103767	+	Missense_Mutation	SNP	G	G	T	rs17511668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:40103767G>T	ENST00000261435.6	+	4	718	c.302G>T	c.(301-303)aGt>aTt	p.S101I		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	101			S -> I (in dbSNP:rs17511668).		nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TCTTCACAAAGTTTCGTTGCT	0.338													G|||	570	0.113818	0.0106	0.255	5008	,	,		16258	0.0208		0.2217	False		,,,				2504	0.138				p.S101I		Atlas-SNP	.											.	N4BP2	166	.	0			c.G302T						PASS	.	G	ILE/SER	214,4192	128.2+/-165.1	10,194,1999	79.0	78.0	78.0		302	1.3	0.0	4	dbSNP_123	78	1978,6622	343.7+/-325.0	234,1510,2556	yes	missense	N4BP2	NM_018177.4	142	244,1704,4555	TT,TG,GG		23.0,4.857,16.8538	benign	101/1771	40103767	2192,10814	2203	4300	6503	SO:0001583	missense	55728	exon4			CACAAAGTTTCGT	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.302G>T	4.37:g.40103767G>T	ENSP00000261435:p.Ser101Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	286	0.13095238095238096	6	0.012195121951219513	97	0.26795580110497236	10	0.017482517482517484	173	0.22823218997361477	G	7.215	0.596153	0.13875	0.04857	0.23	ENSG00000078177	ENST00000261435;ENST00000381804;ENST00000515550	T;T	0.33438	2.16;1.41	6.08	1.32	0.21799	.	1.086440	0.06897	N	0.805379	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P;B	0.34724	0.465;0.335	B;B	0.33521	0.165;0.08	T	0.33085	-0.9882	9	0.72032	D	0.01	-0.0785	1.7256	0.02921	0.2058:0.3217:0.3069:0.1656	rs17511668;rs17511668	101;101	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	I	101;21;21	ENSP00000261435:S101I;ENSP00000422057:S21I	ENSP00000261435:S101I	S	+	2	0	N4BP2	39780162	0.000000	0.05858	0.001000	0.08648	0.313000	0.28021	-0.144000	0.10280	-0.065000	0.13021	0.591000	0.81541	AGT	G|0.859;T|0.141	0.141	strong		0.338	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
NFE2L3	9603	hgsc.bcm.edu	37	7	26224668	26224668	+	Silent	SNP	C	C	T	rs2074566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:26224668C>T	ENST00000056233.3	+	4	1609	c.1350C>T	c.(1348-1350)tgC>tgT	p.C450C		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	450					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						TAGGTTATTGCACTGACCATG	0.423													T|||	1783	0.35603	0.5325	0.2565	5008	,	,		22551	0.5466		0.1203	False		,,,				2504	0.2342				p.C450C		Atlas-SNP	.											.	NFE2L3	77	.	0			c.C1350T						PASS	.	T		2044,2362	609.9+/-391.4	468,1108,627	156.0	167.0	163.0		1350	-5.4	0.0	7	dbSNP_96	163	865,7735	779.5+/-407.7	52,761,3487	no	coding-synonymous	NFE2L3	NM_004289.6		520,1869,4114	TT,TC,CC		10.0581,46.3913,22.3666		450/695	26224668	2909,10097	2203	4300	6503	SO:0001819	synonymous_variant	9603	exon4			TTATTGCACTGAC	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1350C>T	7.37:g.26224668C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Silent	SNP	ENST00000056233.3	37	CCDS5396.1																																																																																			C|0.790;T|0.210	0.210	strong		0.423	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340836	55340836	+	Missense_Mutation	SNP	A	A	G	rs45551936	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55340836A>G	ENST00000391728.4	+	7	1054	c.1021A>G	c.(1021-1023)Att>Gtt	p.I341V	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.I324V|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.I324V|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.I246V|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.I341V	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	341					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ACACCTGCACATTCTGATTGG	0.448													a|||	880	0.175719	0.1626	0.1729	5008	,	,		16245	0.1141		0.2992	False		,,,				2504	0.1319				p.I341V		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A1021G						PASS	.	G	VAL/ILE	529,3819		169,191,1814	273.0	207.0	230.0		1021	-1.5	0.0	19	dbSNP_127	230	1118,7184		477,164,3510	no	missense	KIR3DL1	NM_013289.2	29	646,355,5324	GG,GA,AA		13.4666,12.1665,13.0198		341/445	55340836	1647,11003	2174	4151	6325	SO:0001583	missense	3811	exon7			CTGCACATTCTGA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1021A>G	19.37:g.55340836A>G	ENSP00000375608:p.Ile341Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	31	10	0.322581	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	334	0.15293040293040294	56	0.11382113821138211	54	0.14917127071823205	57	0.09965034965034965	167	0.22031662269129287	-	0.001	-2.987940	0.00046	0.121665	0.134666	ENSG00000167633	ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T	0.00463	7.25;7.36;7.25;7.36;7.33	0.743	-1.49	0.08718	.	.	.	.	.	T	0.00012	0.0000	N	0.00879	-1.12	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	0.15435	-1.0437	8	0.02654	T	1	.	5.4332	0.16464	0.6495:0.0:0.3505:0.0	rs45551936	324;246;341	Q15702;Q14946;P43629	.;.;KI3L1_HUMAN	V	341;324;319;341;324;246	ENSP00000443350:I341V;ENSP00000442355:I324V;ENSP00000375608:I341V;ENSP00000326868:I324V;ENSP00000350901:I246V	ENSP00000326868:I324V	I	+	1	0	KIR3DL1	60032648	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.466000	0.02355	-1.524000	0.01764	-1.160000	0.01791	ATT	A|0.847;G|0.153	0.153	strong		0.448	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
TTLL11	158135	hgsc.bcm.edu	37	9	124855211	124855211	+	Missense_Mutation	SNP	C	C	T	rs61742319	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:124855211C>T	ENST00000373776.3	-	1	674	c.487G>A	c.(487-489)Gct>Act	p.A163T	TTLL11_ENST00000474723.1_5'UTR|TTLL11_ENST00000321582.5_Missense_Mutation_p.A163T	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	163					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						CCCTCCTCAGCCGCACTGGGC	0.766													C|||	1236	0.246805	0.3691	0.3271	5008	,	,		11025	0.0645		0.3012	False		,,,				2504	0.1564				p.A163T		Atlas-SNP	.											.	TTLL11	67	.	0			c.G487A						PASS	.	C	THR/ALA,THR/ALA	1219,2527		207,805,861	5.0	6.0	6.0		487,487	-3.5	0.8	9	dbSNP_129	6	1866,5634		260,1346,2144	no	missense,missense	TTLL11	NM_001139442.1,NM_194252.2	58,58	467,2151,3005	TT,TC,CC		24.88,32.5414,27.432	benign,benign	163/801,163/539	124855211	3085,8161	1873	3750	5623	SO:0001583	missense	158135	exon1			CCTCAGCCGCACT	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000373776.3:c.487G>A	9.37:g.124855211C>T	ENSP00000362881:p.Ala163Thr	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	37	CCDS6834.2	551	0.2522893772893773	184	0.37398373983739835	110	0.30386740331491713	29	0.050699300699300696	228	0.3007915567282322	C	7.277	0.608368	0.14002	0.325414	0.2488	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.06294	3.47;3.32	4.73	-3.49	0.04724	.	2587.460000	0.00357	U	0.000031	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B;B	0.11235	0.004;0.001	B;B	0.10450	0.005;0.002	T	0.48747	-0.9008	8	.	.	.	.	5.0877	0.14691	0.0941:0.3934:0.3609:0.1515	.	163;163	F8W6M1;Q8NHH1	.;TTL11_HUMAN	T	163	ENSP00000321346:A163T;ENSP00000362881:A163T	.	A	-	1	0	TTLL11	123895032	0.133000	0.22466	0.781000	0.31783	0.146000	0.21551	0.583000	0.23849	-0.487000	0.06735	-0.502000	0.04539	GCT	C|0.742;T|0.258	0.258	strong		0.766	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486	
DNAAF1	123872	hgsc.bcm.edu	37	16	84209738	84209738	+	Missense_Mutation	SNP	T	T	C	rs2288020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84209738T>C	ENST00000378553.5	+	11	2022	c.1898T>C	c.(1897-1899)tTg>tCg	p.L633S	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	633			L -> S (in dbSNP:rs2288020). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		axonemal dynein complex assembly (GO:0070286)|cilium morphogenesis (GO:0060271)|cilium movement (GO:0003341)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|inner dynein arm assembly (GO:0036159)|left/right pattern formation (GO:0060972)|lung development (GO:0030324)|motile cilium assembly (GO:0044458)|outer dynein arm assembly (GO:0036158)|regulation of cilium beat frequency (GO:0003356)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dynein binding (GO:0045502)	p.L633S(1)		NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						AAGAGGGACTTGGAAATCCGA	0.517													T|||	1339	0.267372	0.0613	0.4049	5008	,	,		17263	0.376		0.3439	False		,,,				2504	0.2577				p.L633S		Atlas-SNP	.											DNAAF1,NS,carcinoma,0,2	DNAAF1	81	2	1	Substitution - Missense(1)	stomach(1)	c.T1898C						scavenged	.	T	SER/LEU	489,3911	223.9+/-240.3	32,425,1743	37.0	39.0	38.0		1898	-3.4	0.0	16	dbSNP_100	38	3054,5546	464.9+/-366.4	558,1938,1804	yes	missense	DNAAF1	NM_178452.4	145	590,2363,3547	CC,CT,TT		35.5116,11.1136,27.2538	benign	633/726	84209738	3543,9457	2200	4300	6500	SO:0001583	missense	123872	exon11			GGGACTTGGAAAT	BC024009	CCDS10943.2	16q24.1	2012-05-03	2011-06-09	2011-06-09	ENSG00000154099	ENSG00000154099			30539	protein-coding gene	gene with protein product	"""outer row dynein assembly 7 homolog (Chlamydomonas)"""	613190	"""leucine rich repeat containing 50"""	LRRC50		19944405	Standard	NM_178452		Approved	FLJ25330, ODA7, CILD13	uc002fhl.4	Q8NEP3	OTTHUMG00000128517	ENST00000378553.5:c.1898T>C	16.37:g.84209738T>C	ENSP00000367815:p.Leu633Ser	Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	660	0.3021978021978022	36	0.07317073170731707	124	0.3425414364640884	238	0.4160839160839161	262	0.34564643799472294	T	2.115	-0.402769	0.04865	0.111136	0.355116	ENSG00000154099	ENST00000378553	T	0.32023	1.47	4.79	-3.4	0.04853	.	1.974810	0.02961	N	0.143145	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.32101	0.356;0.102	B;B	0.29598	0.104;0.034	T	0.35599	-0.9782	9	0.20519	T	0.43	-0.7212	6.0115	0.19578	0.1502:0.4791:0.0:0.3708	rs2288020;rs17728304;rs17845736;rs17858686;rs58400300;rs2288020	397;633	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	S	633	ENSP00000367815:L633S	ENSP00000367815:L633S	L	+	2	0	DNAAF1	82767239	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.092000	0.00608	-0.980000	0.03524	-0.400000	0.06385	TTG	C|0.283;N|0.000	0.283	strong		0.517	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
ASB15	142685	hgsc.bcm.edu	37	7	123277002	123277002	+	Nonsense_Mutation	SNP	T	T	A	rs140369638		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:123277002T>A	ENST00000451558.1	+	14	2255	c.1734T>A	c.(1732-1734)taT>taA	p.Y578*	ASB15_ENST00000540573.1_Nonsense_Mutation_p.Y578*|ASB15_ENST00000451215.1_Nonsense_Mutation_p.Y578*|ASB15_ENST00000434204.1_Nonsense_Mutation_p.Y578*|ASB15_ENST00000275699.3_Nonsense_Mutation_p.Y578*			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	578	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						TTAAAGAGTATGATCTCTATG	0.343													T|||	1	0.000199681	0.0	0.0	5008	,	,		15210	0.0		0.001	False		,,,				2504	0.0				p.Y578X		Atlas-SNP	.											.	ASB15	94	.	0			c.T1734A						PASS	.	T	stop/TYR	3,4401	6.2+/-15.9	0,3,2199	45.0	52.0	49.0		1734	2.6	1.0	7	dbSNP_134	49	9,8589	6.4+/-24.3	0,9,4290	yes	stop-gained	ASB15	NM_080928.3		0,12,6489	AA,AT,TT		0.1047,0.0681,0.0923		578/589	123277002	12,12990	2202	4299	6501	SO:0001587	stop_gained	142685	exon10			AGAGTATGATCTC	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"""Ankyrin repeat domain containing"""	19767	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 15"""			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.1734T>A	7.37:g.123277002T>A	ENSP00000397655:p.Tyr578*	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	116	64	0.551724	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Nonsense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	35	5.428744	0.96131	6.81E-4	0.001047	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000275699	.	.	.	5.17	2.59	0.31030	.	0.088888	0.48767	D	0.000167	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.0306	8.5691	0.33558	0.0:0.252:0.0:0.748	.	.	.	.	X	578	.	ENSP00000275699:Y578X	Y	+	3	2	ASB15	123064238	0.997000	0.39634	1.000000	0.80357	0.994000	0.84299	0.300000	0.19156	0.309000	0.22966	0.477000	0.44152	TAT	T|0.999;A|0.001	0.001	strong		0.343	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1		
POLR2D	5433	hgsc.bcm.edu	37	2	128610648	128610648	+	Silent	SNP	T	T	C	rs10210695	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:128610648T>C	ENST00000272645.4	-	2	161	c.105A>G	c.(103-105)tcA>tcG	p.S35S	POLR2D_ENST00000409955.1_Silent_p.S35S|POLR2D_ENST00000409698.1_5'UTR|POLR2D_ENST00000487079.1_Intron	NM_004805.3	NP_004796.1	O15514	RPB4_HUMAN	polymerase (RNA) II (DNA directed) polypeptide D	35					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)		TATGAACTTCTGAATTTAGAA	0.383													T|||	619	0.123602	0.2859	0.0735	5008	,	,		20607	0.0466		0.1024	False		,,,				2504	0.0409				p.S35S		Atlas-SNP	.											.	POLR2D	13	.	0			c.A105G						PASS	.	T		1219,3187	425.7+/-340.9	172,875,1156	136.0	131.0	133.0		105	-9.8	0.9	2	dbSNP_119	133	994,7606	213.9+/-253.7	49,896,3355	no	coding-synonymous	POLR2D	NM_004805.3		221,1771,4511	CC,CT,TT		11.5581,27.6668,17.0152		35/143	128610648	2213,10793	2203	4300	6503	SO:0001819	synonymous_variant	5433	exon2			AACTTCTGAATTT	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.105A>G	2.37:g.128610648T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_004805	Q52LT4	Silent	SNP	ENST00000272645.4	37	CCDS2151.1																																																																																			T|0.848;C|0.152	0.152	strong		0.383	POLR2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254388.3	NM_004805	
ZSCAN29	146050	hgsc.bcm.edu	37	15	43653649	43653649	+	Silent	SNP	G	G	A	rs62019445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43653649G>A	ENST00000396976.2	-	5	2315	c.2181C>T	c.(2179-2181)atC>atT	p.I727I	ZSCAN29_ENST00000396972.1_Silent_p.I338I|ZSCAN29_ENST00000562072.1_3'UTR|ZSCAN29_ENST00000568898.1_Silent_p.I337I	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	727					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		CTCCTGTGTGGATTCTCCTAT	0.433													G|||	142	0.0283546	0.0038	0.0519	5008	,	,		20080	0.0		0.0835	False		,,,				2504	0.0174				p.I727I		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.C2181T						PASS	.	G		79,4323	68.7+/-106.4	2,75,2124	76.0	73.0	74.0		2181	3.2	1.0	15	dbSNP_129	74	634,7964	164.3+/-216.7	20,594,3685	no	coding-synonymous	ZSCAN29	NM_152455.3		22,669,5809	AA,AG,GG		7.3738,1.7946,5.4846		727/853	43653649	713,12287	2201	4299	6500	SO:0001819	synonymous_variant	146050	exon5			TGTGTGGATTCTC	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.2181C>T	15.37:g.43653649G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	141	62	0.439716	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Silent	SNP	ENST00000396976.2	37	CCDS10095.2																																																																																			G|0.943;A|0.057	0.057	strong		0.433	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
BLM	641	hgsc.bcm.edu	37	15	91326099	91326099	+	Missense_Mutation	SNP	C	C	T	rs2227935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91326099C>T	ENST00000355112.3	+	13	2721	c.2603C>T	c.(2602-2604)cCg>cTg	p.P868L	BLM_ENST00000560136.1_3'UTR|BLM_ENST00000560509.1_Missense_Mutation_p.P868L	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	868			P -> L (in dbSNP:rs11852361). {ECO:0000269|Ref.3}.		alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TATGTATTACCGAAAAAGCCT	0.338			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome				C|||	257	0.0513179	0.0749	0.049	5008	,	,		18265	0.0		0.0736	False		,,,				2504	0.0511				p.P868L		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.C2603T						PASS	.	C	LEU/PRO	323,4073	169.8+/-200.3	10,303,1885	71.0	62.0	65.0		2603	5.5	0.9	15	dbSNP_120	65	561,8035	151.6+/-206.3	23,515,3760	yes	missense	BLM	NM_000057.2	98	33,818,5645	TT,TC,CC		6.5263,7.3476,6.8042	benign	868/1418	91326099	884,12108	2198	4298	6496	SO:0001583	missense	641	exon13	Familial Cancer Database		TATTACCGAAAAA	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.2603C>T	15.37:g.91326099C>T	ENSP00000347232:p.Pro868Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	142	70	0.492958	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	37	CCDS10363.1	116	0.05311355311355311	42	0.08536585365853659	22	0.06077348066298342	0	0.0	52	0.06860158311345646	C	19.45	3.829246	0.71258	0.073476	0.065263	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.52526	0.66	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.03520	0.0101	M	0.78049	2.395	0.09310	P	0.9999999999996407	P;P;P	0.43542	0.729;0.81;0.729	B;B;B	0.40864	0.149;0.342;0.149	T	0.46527	-0.9185	9	0.66056	D	0.02	-6.8019	16.9752	0.86311	0.0:1.0:0.0:0.0	rs2227935	868;493;868	B2RAN0;B7ZKN7;P54132	.;.;BLM_HUMAN	L	868;521;55	ENSP00000347232:P868L	ENSP00000347232:P868L	P	+	2	0	BLM	89127103	1.000000	0.71417	0.942000	0.38095	0.969000	0.65631	5.647000	0.67923	2.603000	0.88011	0.655000	0.94253	CCG	C|0.940;T|0.060	0.060	strong		0.338	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
KIAA1586	57691	hgsc.bcm.edu	37	6	56917520	56917520	+	Missense_Mutation	SNP	T	T	C	rs36113897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56917520T>C	ENST00000370733.4	+	4	430	c.223T>C	c.(223-225)Ttt>Ctt	p.F75L	KIAA1586_ENST00000545356.1_Missense_Mutation_p.F48L|KIAA1586_ENST00000488682.1_3'UTR	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	75			F -> L (in dbSNP:rs36113897).				nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			ACAGGGTGATTTTTTGCATTT	0.303													t|||	134	0.0267572	0.0061	0.0461	5008	,	,		17818	0.0		0.0865	False		,,,				2504	0.0072				p.F75L		Atlas-SNP	.											.	KIAA1586	59	.	0			c.T223C						PASS	.	T	LEU/PHE	63,4343	54.2+/-90.2	0,63,2140	45.0	50.0	48.0		223	-0.4	0.0	6	dbSNP_126	48	559,8039	147.9+/-203.2	14,531,3754	yes	missense	KIAA1586	NM_020931.2	22	14,594,5894	CC,CT,TT		6.5015,1.4299,4.7831	possibly-damaging	75/788	56917520	622,12382	2203	4299	6502	SO:0001583	missense	57691	exon4			GGTGATTTTTTGC	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.223T>C	6.37:g.56917520T>C	ENSP00000359768:p.Phe75Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	85	0.03891941391941392	3	0.006097560975609756	20	0.055248618784530384	0	0.0	62	0.08179419525065963	t	10.31	1.314933	0.23908	0.014299	0.065015	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.25749	1.78;1.79	4.11	-0.391	0.12446	.	.	.	.	.	T	0.03959	0.0111	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43015	-0.9417	9	0.25106	T	0.35	.	3.8013	0.08760	0.351:0.0:0.2649:0.3841	rs36113897;rs61738003	48;75	F5H2N6;Q9HCI6	.;K1586_HUMAN	L	75;48	ENSP00000359768:F75L;ENSP00000445507:F48L	ENSP00000359768:F75L	F	+	1	0	KIAA1586	57025479	0.003000	0.15002	0.000000	0.03702	0.942000	0.58702	-0.360000	0.07622	0.157000	0.19338	0.383000	0.25322	TTT	T|0.952;C|0.048	0.048	strong		0.303	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
KRT8	3856	hgsc.bcm.edu	37	12	53298769	53298769	+	5'UTR	SNP	A	A	G	rs1065306	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:53298769A>G	ENST00000552551.1	-	0	429				KRT8_ENST00000293308.6_5'UTR|KRT8_ENST00000546897.1_5'UTR|KRT8_ENST00000552150.1_Silent_p.S27S			P05787	K2C8_HUMAN	keratin 8						cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	TGGACATGGTAGAGGCAGGAG	0.622													g|||	1561	0.311701	0.3661	0.2608	5008	,	,		15470	0.1409		0.4264	False		,,,				2504	0.3323				p.S27S		Atlas-SNP	.											.	KRT8	41	.	0			c.T81C						PASS	.						10.0	11.0	10.0					12																	53298769		1596	3236	4832	SO:0001623	5_prime_UTR_variant	3856	exon2			CATGGTAGAGGCA	BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.-4T>C	12.37:g.53298769A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	31	15	0.483871	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Silent	SNP	ENST00000552551.1	37	CCDS8841.1																																																																																			A|0.655;G|0.345	0.345	strong		0.622	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
NAPEPLD	222236	hgsc.bcm.edu	37	7	102760511	102760511	+	Missense_Mutation	SNP	A	A	C	rs12540583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:102760511A>C	ENST00000417955.1	-	3	608	c.454T>G	c.(454-456)Tct>Gct	p.S152A	NAPEPLD_ENST00000455523.2_Missense_Mutation_p.S225A|NAPEPLD_ENST00000427257.1_Missense_Mutation_p.S152A|NAPEPLD_ENST00000341533.4_Missense_Mutation_p.S152A|NAPEPLD_ENST00000465647.1_Missense_Mutation_p.S152A			Q6IQ20	NAPEP_HUMAN	N-acyl phosphatidylethanolamine phospholipase D	152			S -> A (in dbSNP:rs12540583).		phospholipid catabolic process (GO:0009395)	extracellular vesicular exosome (GO:0070062)|photoreceptor outer segment membrane (GO:0042622)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GAAGCACGAGAGCTAAAGATG	0.502													A|||	841	0.167931	0.0946	0.1844	5008	,	,		13891	0.2768		0.0974	False		,,,				2504	0.2157				p.S152A		Atlas-SNP	.											.	NAPEPLD	49	.	0			c.T454G						PASS	.	A	ALA/SER,ALA/SER	364,4042	185.7+/-212.7	12,340,1851	169.0	132.0	144.0		454,454	-4.7	0.1	7	dbSNP_120	144	890,7710	199.9+/-243.8	51,788,3461	yes	missense,missense	NAPEPLD	NM_001122838.1,NM_198990.4	99,99	63,1128,5312	CC,CA,AA		10.3488,8.2615,9.6417	benign,benign	152/394,152/394	102760511	1254,11752	2203	4300	6503	SO:0001583	missense	222236	exon3			CACGAGAGCTAAA	BC037350, AY357337	CCDS5729.1	7q22.1	2014-03-14			ENSG00000161048	ENSG00000161048	3.1.4.54		21683	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 18, N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D"""	612334				14634025, 15820312, 18067139	Standard	NM_198990		Approved	FMP30, C7orf18, NAPE-PLD	uc003vbd.2	Q6IQ20	OTTHUMG00000157204	ENST00000417955.1:c.454T>G	7.37:g.102760511A>C	ENSP00000407112:p.Ser152Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_001122838	Q5CZ87|Q769K1	Missense_Mutation	SNP	ENST00000417955.1	37	CCDS5729.1	347	0.15888278388278387	60	0.12195121951219512	58	0.16022099447513813	159	0.27797202797202797	70	0.09234828496042216	A	13.41	2.228637	0.39399	0.082615	0.103488	ENSG00000161048	ENST00000341533;ENST00000417955;ENST00000465647;ENST00000427257;ENST00000455523	D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91	5.93	-4.69	0.03299	.	0.645957	0.17297	N	0.179417	T	0.00039	0.0001	N	0.25332	0.735	0.48762	P	2.9800000000002047E-4	B;B	0.06786	0.001;0.0	B;B	0.15052	0.012;0.002	T	0.16660	-1.0395	9	0.44086	T	0.13	-5.2249	2.2767	0.04104	0.1181:0.2271:0.3677:0.2871	rs12540583;rs12540583	225;152	B4E3B0;Q6IQ20	.;NAPEP_HUMAN	A	152;152;152;152;225	ENSP00000340093:S152A;ENSP00000407112:S152A;ENSP00000419188:S152A;ENSP00000392775:S152A;ENSP00000414364:S225A	ENSP00000340093:S152A	S	-	1	0	NAPEPLD	102547747	1.000000	0.71417	0.065000	0.19835	0.998000	0.95712	1.650000	0.37292	-0.455000	0.07054	0.482000	0.46254	TCT	A|0.876;C|0.124	0.124	strong		0.502	NAPEPLD-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347904.1	NM_198990	
TRIM10	10107	hgsc.bcm.edu	37	6	30121525	30121525	+	3'UTR	SNP	G	G	A	rs12210298	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30121525G>A	ENST00000449742.2	-	0	1742				TRIM10_ENST00000376704.3_Silent_p.D376D	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10						erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						AGCAGCCTGAGTCCCCAGGTA	0.547													G|||	76	0.0151757	0.003	0.013	5008	,	,		17602	0.002		0.0527	False		,,,				2504	0.0082				p.D376D		Atlas-SNP	.											.	TRIM10	65	.	0			c.C1128T						PASS	.	G	,	22,3000		0,22,1489	69.0	57.0	61.0		,1128	0.8	0.0	6	dbSNP_120	61	237,5181		6,225,2478	no	utr-3,coding-synonymous	TRIM10	NM_006778.3,NM_052828.2	,	6,247,3967	AA,AG,GG		4.3743,0.728,3.0687	,	,376/396	30121525	259,8181	1511	2709	4220	SO:0001624	3_prime_UTR_variant	10107	exon8			GCCTGAGTCCCCA	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10072	protein-coding gene	gene with protein product		605701	"""tripartite motif-containing 10"""	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.*221C>T	6.37:g.30121525G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	145	65	0.448276	NM_052828	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Silent	SNP	ENST00000449742.2	37	CCDS34375.1																																																																																			G|0.970;A|0.030	0.030	strong		0.547	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1		
PER1	5187	hgsc.bcm.edu	37	17	8053085	8053085	+	Silent	SNP	T	T	G	rs3027178	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8053085T>G	ENST00000317276.4	-	5	876	c.639A>C	c.(637-639)acA>acC	p.T213T	PER1_ENST00000354903.5_Silent_p.T197T|PER1_ENST00000581082.1_Silent_p.T213T	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	213	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.T213T(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GGTTCTGAAGTGTGTACTCAG	0.597			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes					T|||	1436	0.286741	0.267	0.4553	5008	,	,		20009	0.2738		0.2922	False		,,,				2504	0.2014				p.T213T		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	PER1,NS,carcinoma,0,1	PER1	104	1	1	Substitution - coding silent(1)	stomach(1)	c.A639C						PASS	.	T		1133,3273	404.0+/-332.9	147,839,1217	194.0	188.0	190.0		639	-11.1	0.0	17	dbSNP_102	190	2636,5964	424.1+/-354.6	396,1844,2060	no	coding-synonymous	PER1	NM_002616.2		543,2683,3277	GG,GT,TT		30.6512,25.7149,28.9789		213/1291	8053085	3769,9237	2203	4300	6503	SO:0001819	synonymous_variant	5187	exon5			CTGAAGTGTGTAC	AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.639A>C	17.37:g.8053085T>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_002616	B2RPA8|B4DI49|D3DTR3	Silent	SNP	ENST00000317276.4	37	CCDS11131.1																																																																																			T|0.699;G|0.301	0.301	strong		0.597	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2		
RBMX	27316	hgsc.bcm.edu	37	X	135961560	135961560	+	Missense_Mutation	SNP	C	C	G	rs80321628		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135961560C>G	ENST00000320676.7	-	2	181	c.27G>C	c.(25-27)aaG>aaC	p.K9N	RBMX_ENST00000562646.1_Missense_Mutation_p.K9N|RBMX_ENST00000431446.3_Missense_Mutation_p.K9N|RBMX_ENST00000565438.1_Intron|RBMX_ENST00000570135.1_5'UTR|SNORD61_ENST00000384252.1_RNA	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	9	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K9N(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAATGAAGAGCTTTCCTGGGC	0.413																																					p.K9N		Atlas-SNP	.											.	RBMX	149	.	1	Substitution - Missense(1)	pancreas(1)	c.G27C						PASS	.						109.0	103.0	105.0					X																	135961560		2203	4300	6503	SO:0001583	missense	27316	exon2			GAAGAGCTTTCCT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.27G>C	X.37:g.135961560C>G	ENSP00000359645:p.Lys9Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	158	35	0.221519	NM_001164803	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	19.30	3.801463	0.70682	.	.	ENSG00000147274	ENST00000431446;ENST00000320676;ENST00000449161	D;D	0.89050	-2.46;-2.46	4.66	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	U	0.000000	D	0.88507	0.6455	L	0.56340	1.77	0.09310	P	0.9999999999999992	P;B;P	0.46656	0.882;0.278;0.868	P;B;B	0.50270	0.636;0.142;0.311	D	0.91729	0.5395	9	0.72032	D	0.01	.	8.8627	0.35267	0.0:0.7507:0.0:0.2493	.	9;9;9	B4E3U4;P38159;Q8N8Y7	.;HNRPG_HUMAN;.	N	9	ENSP00000411989:K9N;ENSP00000359645:K9N	ENSP00000359645:K9N	K	-	3	2	RBMX	135789226	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.970000	0.29383	1.905000	0.55150	0.508000	0.49915	AAG	.	.	weak		0.413	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
NACC2	138151	hgsc.bcm.edu	37	9	138903635	138903635	+	Silent	SNP	G	G	A	rs9753	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:138903635G>A	ENST00000371753.1	-	5	1549	c.1491C>T	c.(1489-1491)gcC>gcT	p.A497A	NACC2_ENST00000277554.2_Silent_p.A497A			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	497					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						CCCGCCGCTCGGCGTAGATGC	0.706													G|||	743	0.148363	0.0787	0.1902	5008	,	,		10710	0.2202		0.1223	False		,,,				2504	0.1656				p.A497A		Atlas-SNP	.											NACC2,NS,carcinoma,-2,1	NACC2	16	1	0			c.C1491T						PASS	.	G		357,3943		14,329,1807	7.0	8.0	7.0		1491	-10.3	0.0	9	dbSNP_52	7	814,7610		47,720,3445	no	coding-synonymous	NACC2	NM_144653.4		61,1049,5252	AA,AG,GG		9.6629,8.3023,9.2031		497/588	138903635	1171,11553	2150	4212	6362	SO:0001819	synonymous_variant	138151	exon6			CCGCTCGGCGTAG	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.1491C>T	9.37:g.138903635G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	14	9	0.642857	NM_144653		Silent	SNP	ENST00000371753.1	37	CCDS6993.1																																																																																			G|0.844;A|0.156	0.156	strong		0.706	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653	
OR6M1	390261	hgsc.bcm.edu	37	11	123676231	123676231	+	Missense_Mutation	SNP	G	G	T	rs4936845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:123676231G>T	ENST00000309154.2	-	1	864	c.827C>A	c.(826-828)aCa>aAa	p.T276K		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, member 1	276			T -> K (in dbSNP:rs4936845).			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)		GGTCACCACTGTGATGAGGAC	0.478													G|||	1219	0.243411	0.1029	0.317	5008	,	,		17328	0.2946		0.2853	False		,,,				2504	0.2853				p.T276K		Atlas-SNP	.											OR6M1,colon,carcinoma,0,1	OR6M1	60	1	0			c.C827A						PASS	.	G	LYS/THR	540,3864	243.4+/-253.1	44,452,1706	127.0	120.0	122.0		827	3.5	0.3	11	dbSNP_111	122	2568,6030	420.5+/-353.4	389,1790,2120	yes	missense	OR6M1	NM_001005325.1	78	433,2242,3826	TT,TG,GG		29.8674,12.2616,23.904	possibly-damaging	276/314	123676231	3108,9894	2202	4299	6501	SO:0001583	missense	390261	exon1			ACCACTGTGATGA	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.827C>A	11.37:g.123676231G>T	ENSP00000311038:p.Thr276Lys	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	136	63	0.463235	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	526	0.24084249084249085	54	0.10975609756097561	94	0.2596685082872928	161	0.28146853146853146	217	0.2862796833773087	G	13.48	2.251267	0.39797	0.122616	0.298674	ENSG00000196099	ENST00000309154	T	0.00265	8.39	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34200	U	0.004164	T	0.00012	0.0000	M	0.92970	3.365	0.80722	P	0.0	P	0.41188	0.741	P	0.53809	0.735	T	0.04153	-1.0973	9	0.87932	D	0	.	6.5789	0.22583	0.1324:0.0:0.8676:0.0	rs4936845;rs52810786;rs56873896;rs4936845	276	Q8NGM8	OR6M1_HUMAN	K	276	ENSP00000311038:T276K	ENSP00000311038:T276K	T	-	2	0	OR6M1	123181441	0.010000	0.17322	0.295000	0.24960	0.731000	0.41821	1.794000	0.38774	1.754000	0.51921	0.655000	0.94253	ACA	G|0.763;T|0.237	0.237	strong		0.478	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325	
EPPK1	83481	hgsc.bcm.edu	37	8	144940331	144940331	+	Missense_Mutation	SNP	C	C	T	rs200585601		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144940331C>T	ENST00000525985.1	-	2	7162	c.7091G>A	c.(7090-7092)cGg>cAg	p.R2364Q				P58107	EPIPL_HUMAN	epiplakin 1	2364						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)	p.R2364Q(1)		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)			GTAGCCGCGCCGGTAGGCCAC	0.692																																					p.R2364Q		Atlas-SNP	.											EPPK1,NS,carcinoma,0,6	EPPK1	199	6	1	Substitution - Missense(1)	large_intestine(1)	c.G7091A						PASS	.	C	GLN/ARG	194,4166		0,194,1986	217.0	211.0	213.0		7091	0.7	1.0	8	dbSNP_134	213	66,8462		0,66,4198	no	missense	EPPK1	NM_031308.1	43	0,260,6184	TT,TC,CC		0.7739,4.4495,2.0174	benign	2364/2420	144940331	260,12628	2180	4264	6444	SO:0001583	missense	83481	exon1			CCGCGCCGGTAGG	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.7091G>A	8.37:g.144940331C>T	ENSP00000436337:p.Arg2364Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	189	21	0.111111	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	7.296	0.612142	0.14066	0.044495	0.007739	ENSG00000227184	ENST00000525985	T	0.74526	-0.85	4.42	0.661	0.17874	.	.	.	.	.	T	0.14184	0.0343	N	0.03903	-0.33	0.21579	N	0.999636	B	0.20550	0.046	B	0.12837	0.008	T	0.14254	-1.0479	9	0.02654	T	1	.	7.4216	0.27075	0.0:0.2871:0.0:0.7129	.	2364	E9PPU0	.	Q	2364	ENSP00000436337:R2364Q	ENSP00000436337:R2364Q	R	-	2	0	EPPK1	145012319	0.742000	0.28228	0.982000	0.44146	0.955000	0.61496	1.358000	0.34102	0.024000	0.15214	-0.482000	0.04802	CGG	C|0.997;T|0.003	0.003	weak		0.692	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956194	18956194	+	Silent	SNP	T	T	C	rs2014931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18956194T>C	ENST00000302797.3	-	1	362	c.138A>G	c.(136-138)gcA>gcG	p.A46A	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	46					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			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						AGAGCACAACTGCGTTTCCTG	0.587													C|||	1819	0.363219	0.3442	0.3588	5008	,	,		26113	0.3075		0.4026	False		,,,				2504	0.409				p.A46A		Atlas-SNP	.											MRGPRX1,caecum,carcinoma,-2,3	MRGPRX1	84	3	0			c.A138G						scavenged	.	C		1481,2907		203,1075,916	169.0	160.0	163.0		138	-2.1	0.0	11	dbSNP_92	163	3341,5233		595,2151,1541	no	coding-synonymous	MRGPRX1	NM_147199.3		798,3226,2457	CC,CT,TT		38.9666,33.7511,37.201		46/323	18956194	4822,8140	2194	4287	6481	SO:0001819	synonymous_variant	259249	exon1			CACAACTGCGTTT		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.138A>G	11.37:g.18956194T>C		Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	37	CCDS7846.1																																																																																			T|0.636;C|0.364	0.364	strong		0.587	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
TRIM66	9866	hgsc.bcm.edu	37	11	8662516	8662516	+	Missense_Mutation	SNP	T	T	C	rs11042023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:8662516T>C	ENST00000299550.6	-	9	1165	c.971A>G	c.(970-972)cAc>cGc	p.H324R	TRIM66_ENST00000402157.2_Missense_Mutation_p.H322R	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	324						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						TGGGGAGCAGTGGGAGCAGCA	0.622													T|||	2630	0.52516	0.5166	0.5836	5008	,	,		16172	0.4028		0.6302	False		,,,				2504	0.5133				p.H324R		Atlas-SNP	.											TRIM66,rectum,carcinoma,0,1	TRIM66	45	1	0			c.A971G						PASS	.	T	ARG/HIS	739,645		199,341,152	44.0	45.0	45.0		971	5.1	1.0	11	dbSNP_120	45	2089,1093		686,717,188	yes	missense	TRIM66	NM_014818.1	29	885,1058,340	CC,CT,TT		34.3495,46.604,38.064	probably-damaging	324/1217	8662516	2828,1738	692	1591	2283	SO:0001583	missense	9866	exon9			GAGCAGTGGGAGC	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.971A>G	11.37:g.8662516T>C	ENSP00000299550:p.His324Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	129	0.984733	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		1176	0.5384615384615384	258	0.524390243902439	200	0.5524861878453039	239	0.4178321678321678	479	0.6319261213720316	T	19.19	3.779607	0.70107	0.53396	0.656505	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.18174	2.23;2.23	5.1	5.1	0.69264	.	0.000000	0.50627	D	0.000104	T	0.00012	0.0000	M	0.69823	2.125	0.32774	P	0.503443	D	0.76494	0.999	D	0.80764	0.994	T	0.35425	-0.9789	9	0.30078	T	0.28	-15.8813	14.8856	0.70567	0.0:0.0:0.0:1.0	rs11042023;rs52817908;rs58678299;rs11042023	324	O15016	TRI66_HUMAN	R	324;322	ENSP00000299550:H324R;ENSP00000384876:H322R	ENSP00000299550:H324R	H	-	2	0	TRIM66	8619092	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	5.486000	0.66856	1.922000	0.55676	0.397000	0.26171	CAC	T|0.470;C|0.530	0.530	strong		0.622	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68701948	68701948	+	Silent	SNP	C	C	T	rs11228413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68701948C>T	ENST00000255078.3	+	11	1665	c.1554C>T	c.(1552-1554)gtC>gtT	p.V518V	IGHMBP2_ENST00000541229.1_3'UTR	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	518					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TCCGCCTCGTCAGTTTGCACA	0.582													C|||	665	0.132788	0.1483	0.1902	5008	,	,		18535	0.0208		0.2644	False		,,,				2504	0.0511				p.V518V		Atlas-SNP	.											IGHMBP2,colon,carcinoma,+2,3	IGHMBP2	83	3	0			c.C1554T						PASS	.	C		765,3635	305.5+/-289.0	68,629,1503	118.0	97.0	104.0		1554	3.0	0.5	11	dbSNP_120	104	2127,6461	352.2+/-328.6	258,1611,2425	no	coding-synonymous	IGHMBP2	NM_002180.2		326,2240,3928	TT,TC,CC		24.7671,17.3864,22.2667		518/994	68701948	2892,10096	2200	4294	6494	SO:0001819	synonymous_variant	3508	exon11			CCTCGTCAGTTTG	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.1554C>T	11.37:g.68701948C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_002180	A0PJD2|Q00443|Q14177	Silent	SNP	ENST00000255078.3	37	CCDS8187.1																																																																																			C|0.805;T|0.195	0.195	strong		0.582	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
ITPA	3704	hgsc.bcm.edu	37	20	3193978	3193978	+	Silent	SNP	G	G	A	rs8362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3193978G>A	ENST00000380113.3	+	3	330	c.138G>A	c.(136-138)caG>caA	p.Q46Q	ITPA_ENST00000483354.1_Intron|ITPA_ENST00000455664.2_Silent_p.Q29Q|ITPA_ENST00000399838.3_Intron	NM_033453.3|NM_181493.2	NP_258412.1|NP_852470.1			inosine triphosphatase (nucleoside triphosphate pyrophosphatase)											autonomic_ganglia(1)|large_intestine(3)|ovary(1)|stomach(1)	6						CGGAGTACCAGGGGGAGCCGG	0.483													G|||	2356	0.470447	0.4705	0.3055	5008	,	,		18388	0.6131		0.3022	False		,,,				2504	0.6135				p.Q46Q		Atlas-SNP	.											.	ITPA	16	.	0			c.G138A						PASS	.	G	,	2017,2389	561.6+/-380.8	466,1085,652	116.0	112.0	113.0		138,87	2.0	1.0	20	dbSNP_52	113	2404,6196	399.2+/-346.4	364,1676,2260	no	coding-synonymous,coding-synonymous	ITPA	NM_033453.2,NM_181493.1	,	830,2761,2912	AA,AG,GG		27.9535,45.7785,33.992	,	46/195,29/178	3193978	4421,8585	2203	4300	6503	SO:0001819	synonymous_variant	3704	exon3			GTACCAGGGGGAG	AF026816	CCDS13051.1, CCDS46576.1, CCDS58762.1	20p	2002-02-01			ENSG00000125877	ENSG00000125877	3.6.1.19		6176	protein-coding gene	gene with protein product		147520		C20orf37		11278832	Standard	NM_033453		Approved	HLC14-06-P, dJ794I6.3	uc002wid.4	Q9BY32	OTTHUMG00000031738	ENST00000380113.3:c.138G>A	20.37:g.3193978G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_033453		Silent	SNP	ENST00000380113.3	37	CCDS13051.1																																																																																			G|0.607;A|0.393	0.393	strong		0.483	ITPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077719.2		
CRTAP	10491	hgsc.bcm.edu	37	3	33174168	33174168	+	Silent	SNP	G	G	A	rs1135128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:33174168G>A	ENST00000320954.6	+	5	1143	c.1044G>A	c.(1042-1044)tcG>tcA	p.S348S	CRTAP_ENST00000449224.1_Silent_p.S305S	NM_006371.4	NP_006362.1	O75718	CRTAP_HUMAN	cartilage associated protein	348					chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation to 3-hydroxy-L-proline (GO:0018400)|protein stabilization (GO:0050821)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|macromolecular complex (GO:0032991)|proteinaceous extracellular matrix (GO:0005578)	protein complex binding (GO:0032403)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9						GGGGCCTCTCGGATGAGCACT	0.517													G|||	1470	0.29353	0.2451	0.268	5008	,	,		18961	0.1548		0.4354	False		,,,				2504	0.3742				p.S348S		Atlas-SNP	.											.	CRTAP	16	.	0			c.G1044A						PASS	.	G		1168,3238	411.5+/-335.8	160,848,1195	132.0	116.0	121.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1044	-6.7	0.6	3	dbSNP_86	121	3830,4770	539.0+/-383.5	872,2086,1342	no	coding-synonymous	CRTAP	NM_006371.4		1032,2934,2537	AA,AG,GG		44.5349,26.5093,38.4284		348/402	33174168	4998,8008	2203	4300	6503	SO:0001819	synonymous_variant	10491	exon5			CCTCTCGGATGAG	AJ006470	CCDS2657.1	3p22	2014-09-17			ENSG00000170275	ENSG00000170275			2379	protein-coding gene	gene with protein product	"""leprecan-like 3"""	605497				9217321, 10429950	Standard	NM_006371		Approved	CASP, LEPREL3	uc003cfl.4	O75718	OTTHUMG00000130746	ENST00000320954.6:c.1044G>A	3.37:g.33174168G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	57	0.422222	NM_006371	B2RBL6	Silent	SNP	ENST00000320954.6	37	CCDS2657.1																																																																																			G|0.639;A|0.361	0.361	strong		0.517	CRTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253246.3		
RBPJ	3516	hgsc.bcm.edu	37	4	26417136	26417136	+	Silent	SNP	T	T	C	rs2270226	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:26417136T>C	ENST00000361572.6	+	4	428	c.234T>C	c.(232-234)agT>agC	p.S78S	RBPJ_ENST00000355476.3_Silent_p.S64S|RBPJ_ENST00000348160.4_Silent_p.S65S|RBPJ_ENST00000342295.1_Silent_p.S78S|RBPJ_ENST00000511401.1_3'UTR|RBPJ_ENST00000504907.1_Silent_p.S64S|RBPJ_ENST00000507561.1_Silent_p.S43S|RBPJ_ENST00000345843.3_Silent_p.S63S|RBPJ_ENST00000342320.4_Silent_p.S64S			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	78					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				TTATGGGCAGTGGATGGAAGA	0.358													T|||	2563	0.511781	0.3328	0.683	5008	,	,		16222	0.5308		0.5606	False		,,,				2504	0.5624				p.S78S		Atlas-SNP	.											.	RBPJ	78	.	0			c.T234C						PASS	.	T	,,,	1638,2768	484.4+/-360.0	295,1048,860	82.0	89.0	87.0		234,195,189,192	2.8	1.0	4	dbSNP_100	87	4832,3768	610.4+/-395.7	1347,2138,815	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBPJ	NM_005349.2,NM_015874.3,NM_203283.1,NM_203284.1	,,,	1642,3186,1675	CC,CT,TT		43.814,37.1766,49.7463	,,,	78/501,65/488,63/486,64/487	26417136	6470,6536	2203	4300	6503	SO:0001819	synonymous_variant	3516	exon5			GGGCAGTGGATGG	L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"""suppressor of hairless homolog (Drosophila)"""	147183	"""recombining binding protein suppressor of hairless (Drosophila)"""	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.234T>C	4.37:g.26417136T>C		Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	226	107	0.473451	NM_005349	B4DY22|Q5XKH9|Q6P1N3	Silent	SNP	ENST00000361572.6	37	CCDS3437.1																																																																																			T|0.487;C|0.513	0.513	strong		0.358	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874	
WSB1	26118	hgsc.bcm.edu	37	17	25639329	25639329	+	Silent	SNP	C	C	T	rs61761626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:25639329C>T	ENST00000262394.2	+	9	1516	c.1200C>T	c.(1198-1200)ccC>ccT	p.P400P	RP11-173M1.8_ENST00000578929.1_lincRNA|WSB1_ENST00000348811.2_Silent_p.P254P	NM_015626.8	NP_056441.6	Q9Y6I7	WSB1_HUMAN	WD repeat and SOCS box containing 1	400	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	intracellular (GO:0005622)				lung(3)	3	all_cancers(1;2e-13)|all_epithelial(1;4.8e-15)|Lung NSC(42;0.00152)		BRCA - Breast invasive adenocarcinoma(3;0.0152)	UCEC - Uterine corpus endometrioid carcinoma (53;0.154)		GAGTGATGCCCACCCAAGAAG	0.483													C|||	52	0.0103834	0.0008	0.0	5008	,	,		16318	0.003		0.005	False		,,,				2504	0.044				p.P400P		Atlas-SNP	.											WSB1,NS,carcinoma,+1,1	WSB1	29	1	0			c.C1200T						scavenged	.	C	,	9,4397	12.9+/-30.5	0,9,2194	279.0	265.0	270.0		1200,762	0.5	1.0	17	dbSNP_129	270	79,8521	46.7+/-105.8	0,79,4221	no	coding-synonymous,coding-synonymous	WSB1	NM_015626.8,NM_134265.2	,	0,88,6415	TT,TC,CC		0.9186,0.2043,0.6766	,	400/422,254/276	25639329	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	26118	exon9			GATGCCCACCCAA	AF069313	CCDS11220.1, CCDS11221.1	17q11.2	2013-01-09	2011-01-25		ENSG00000109046	ENSG00000109046		"""WD repeat domain containing"""	19221	protein-coding gene	gene with protein product		610091	"""WD repeat and SOCS box-containing 1"""			10354473, 12076535	Standard	XR_243778		Approved	DKFZp564A122, DKFZp564B0482, SWIP1	uc002gzd.1	Q9Y6I7	OTTHUMG00000132293	ENST00000262394.2:c.1200C>T	17.37:g.25639329C>T		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	164	85	0.518293	NM_015626	Q9NRB1|Q9UBH9|Q9UG25|Q9UNN6|Q9Y656	Silent	SNP	ENST00000262394.2	37	CCDS11220.1																																																																																			C|0.994;T|0.006	0.006	strong		0.483	WSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255391.4	NM_015626	
OR6C68	403284	hgsc.bcm.edu	37	12	55887087	55887087	+	Missense_Mutation	SNP	G	G	T	rs12579181	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55887087G>T	ENST00000548615.1	+	1	926	c.926G>T	c.(925-927)cGt>cTt	p.R309L	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|OR6C68_ENST00000379662.1_Missense_Mutation_p.R314L	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	309						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						ATTGCATTTCGTTTAAAAAAG	0.279													T|||	1841	0.367612	0.5242	0.2334	5008	,	,		16540	0.5694		0.1938	False		,,,				2504	0.2219				p.R309L		Atlas-SNP	.											OR6C68,NS,carcinoma,+1,1	OR6C68	36	1	0			c.G926T						PASS	.	T	LEU/ARG	1956,2380		443,1070,655	19.0	23.0	22.0		926	1.8	0.0	12	dbSNP_120	22	1679,6841		190,1299,2771	yes	missense	OR6C68	NM_001005519.2	102	633,2369,3426	TT,TG,GG		19.7066,45.1107,28.2747	benign	309/313	55887087	3635,9221	2168	4260	6428	SO:0001583	missense	403284	exon1			CATTTCGTTTAAA		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"""GPCR / Class A : Olfactory receptors"""	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.926G>T	12.37:g.55887087G>T	ENSP00000448811:p.Arg309Leu	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	24	12	0.5	NM_001005519		Missense_Mutation	SNP	ENST00000548615.1	37	CCDS31826.2	806	0.36904761904761907	239	0.48577235772357724	84	0.23204419889502761	331	0.5786713286713286	152	0.20052770448548812	T	0.723	-0.782679	0.02907	0.451107	0.197066	ENSG00000205327	ENST00000379662;ENST00000548615	T;T	0.38722	1.12;1.12	4.3	1.78	0.24846	.	0.536654	0.15535	N	0.257285	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	0.45160	-0.9280	9	0.10377	T	0.69	.	1.3142	0.02104	0.2786:0.0852:0.2865:0.3497	rs12579181;rs61200712	309	A6NDL8	O6C68_HUMAN	L	314;309	ENSP00000368983:R314L;ENSP00000448811:R309L	ENSP00000368983:R314L	R	+	2	0	OR6C68	54173354	0.000000	0.05858	0.000000	0.03702	0.574000	0.36063	-0.342000	0.07801	-0.015000	0.14150	-0.333000	0.08304	CGT	G|0.703;T|0.297	0.297	strong		0.279	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1		
NXPE3	91775	hgsc.bcm.edu	37	3	101540552	101540552	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:101540552G>T	ENST00000491511.2	+	8	2390	c.1434G>T	c.(1432-1434)gtG>gtT	p.V478V	RP11-49I4.3_ENST00000490324.2_RNA|NXPE3_ENST00000422132.1_Silent_p.V478V|NXPE3_ENST00000273347.5_Silent_p.V478V|NXPE3_ENST00000477909.1_Silent_p.V478V	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	478						extracellular region (GO:0005576)											CAAAGACCGTGGTGGTCATCC	0.582																																					p.V478V		Atlas-SNP	.											.	.	.	.	0			c.G1434T						PASS	.						96.0	98.0	97.0					3																	101540552		2203	4300	6503	SO:0001819	synonymous_variant	91775	exon8			GACCGTGGTGGTC	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member C"""	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.1434G>T	3.37:g.101540552G>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Silent	SNP	ENST00000491511.2	37	CCDS2945.1																																																																																			.	.	none		0.582	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037	
TBC1D22B	55633	hgsc.bcm.edu	37	6	37252210	37252210	+	Silent	SNP	C	C	T	rs3818136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:37252210C>T	ENST00000373491.3	+	6	917	c.771C>T	c.(769-771)aaC>aaT	p.N257N		NM_017772.2	NP_060242.2	Q9NU19	TB22B_HUMAN	TBC1 domain family, member 22B	257	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|prostate(1)	15			OV - Ovarian serous cystadenocarcinoma(102;0.241)			ACTCTCGAAACGAGGAACATC	0.478													C|||	3492	0.697284	0.5734	0.6787	5008	,	,		19538	0.8462		0.6551	False		,,,				2504	0.7679				p.N257N		Atlas-SNP	.											.	TBC1D22B	37	.	0			c.C771T						PASS	.	C		2550,1856	636.0+/-396.5	738,1074,391	116.0	104.0	108.0		771	0.9	1.0	6	dbSNP_107	108	5679,2921	670.0+/-402.7	1875,1929,496	no	coding-synonymous	TBC1D22B	NM_017772.2		2613,3003,887	TT,TC,CC		33.9651,42.1244,36.7292		257/506	37252210	8229,4777	2203	4300	6503	SO:0001819	synonymous_variant	55633	exon6			TCGAAACGAGGAA	AK096340	CCDS4832.1	6p21.2	2005-01-05	2005-01-05	2005-01-05	ENSG00000065491	ENSG00000065491			21602	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 197"""	C6orf197			Standard	NM_017772		Approved	FLJ20337, dJ744I24.2	uc003onn.3	Q9NU19	OTTHUMG00000014619	ENST00000373491.3:c.771C>T	6.37:g.37252210C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_017772	A8KA28|Q32MQ8|Q5VUK9|Q6P4C3|Q7Z6P7|Q9BPV6|Q9BUT5|Q9NXB6	Silent	SNP	ENST00000373491.3	37	CCDS4832.1																																																																																			C|0.335;T|0.665	0.665	strong		0.478	TBC1D22B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040402.1	NM_017772	
MSX1	4487	hgsc.bcm.edu	37	4	4864582	4864582	+	Silent	SNP	G	G	T	rs369820958		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:4864582G>T	ENST00000382723.4	+	2	858	c.624G>T	c.(622-624)tcG>tcT	p.S208S	MSX1_ENST00000468421.1_3'UTR	NM_002448.3	NP_002439.2	P28360	MSX1_HUMAN	msh homeobox 1	208					activation of meiosis (GO:0090427)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone morphogenesis (GO:0060349)|cartilage morphogenesis (GO:0060536)|cell morphogenesis (GO:0000902)|cellular response to nicotine (GO:0071316)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|mammary gland epithelium development (GO:0061180)|mesenchymal cell proliferation (GO:0010463)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902255)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of odontogenesis (GO:0042481)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|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)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(3)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	11				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCTCCAGCTCGCTCAGCCTCA	0.632																																					p.S208S		Atlas-SNP	.											MSX1,NS,carcinoma,+1,1	MSX1	19	1	0			c.G624T						PASS	.	G		0,4406		0,0,2203	40.0	42.0	41.0		624	0.7	1.0	4		41	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MSX1	NM_002448.3		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		208/304	4864582	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4487	exon2			CAGCTCGCTCAGC	M97676	CCDS3378.2	4p16.2	2011-06-20	2006-11-21		ENSG00000163132	ENSG00000163132		"""Homeoboxes / ANTP class : NKL subclass"""	7391	protein-coding gene	gene with protein product		142983	"""msh (Drosophila) homeo box homolog 1 (formerly homeo box 7)"", ""msh homeobox homolog 1 (Drosophila)"""	HOX7		1685479, 1973146	Standard	NM_002448		Approved	HYD1, OFC5	uc003gif.3	P28360	OTTHUMG00000090335	ENST00000382723.4:c.624G>T	4.37:g.4864582G>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	119	70	0.588235	NM_002448	A0SZU5|A8K3M1|Q96NY4	Silent	SNP	ENST00000382723.4	37	CCDS3378.2																																																																																			.	.	weak		0.632	MSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206700.3		
CFAP46	54777	hgsc.bcm.edu	37	10	134691496	134691496	+	Missense_Mutation	SNP	A	A	C	rs187274296		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691496A>C	ENST00000368586.5	-	30	4201	c.4101T>G	c.(4099-4101)aaT>aaG	p.N1367K	TTC40_ENST00000368582.2_Missense_Mutation_p.N1367K	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						tactcctctcattctccttct	0.448																																					p.N1367K		Atlas-SNP	.											.	TTC40	100	.	0			c.T4101G						PASS	.																																			SO:0001583	missense	54777	exon30			CCTCTCATTCTCC																												ENST00000368586.5:c.4101T>G	10.37:g.134691496A>C	ENSP00000357575:p.Asn1367Lys	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	231	28	0.121212	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	2	0.0034965034965034965	9	0.011873350923482849	A	0.010	-1.767717	0.00645	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.04758	3.56;3.56	1.72	-2.27	0.06846	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44513	-0.9323	6	0.02654	T	1	.	2.8375	0.05519	0.237:0.4507:0.0:0.3123	.	.	.	.	K	1367	ENSP00000357575:N1367K;ENSP00000357571:N1367K	ENSP00000357571:N1367K	N	-	3	2	C10orf93	134541486	0.031000	0.19500	0.096000	0.21009	0.260000	0.26232	0.118000	0.15605	-0.489000	0.06716	0.102000	0.15555	AAT	A|0.993;C|0.007	0.007	strong		0.448	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
OR8B4	283162	hgsc.bcm.edu	37	11	124294377	124294377	+	Missense_Mutation	SNP	A	A	G	rs4057750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124294377A>G	ENST00000356130.3	-	1	412	c.391T>C	c.(391-393)Tac>Cac	p.Y131H		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	131			Y -> H (in dbSNP:rs4057750). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		GTGACCATGTAGAGCAGGGGG	0.502													A|||	1302	0.259984	0.3843	0.1931	5008	,	,		22069	0.2163		0.1978	False		,,,				2504	0.2485				p.Y131H		Atlas-SNP	.											OR8B4,NS,carcinoma,+1,1	OR8B4	60	1	0			c.T391C						PASS	.	A	HIS/TYR	1502,2900	478.5+/-358.2	263,976,962	90.0	84.0	86.0		391	4.6	0.9	11	dbSNP_108	86	1963,6635	344.7+/-325.5	219,1525,2555	no	missense	OR8B4	NM_001005196.1	83	482,2501,3517	GG,GA,AA		22.8309,34.1209,26.6538	probably-damaging	131/310	124294377	3465,9535	2201	4299	6500	SO:0001583	missense	283162	exon1			CCATGTAGAGCAG	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.391T>C	11.37:g.124294377A>G	ENSP00000348449:p.Tyr131His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	543	0.24862637362637363	214	0.4349593495934959	70	0.19337016574585636	107	0.18706293706293706	152	0.20052770448548812	a	18.02	3.530106	0.64860	0.341209	0.228309	ENSG00000198657	ENST00000356130	T	0.00392	7.58	4.62	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000198	T	0.00012	0.0000	M	0.93106	3.38	0.22156	P	0.999323742	D	0.89917	1.0	D	0.91635	0.999	T	0.44682	-0.9312	9	0.72032	D	0.01	.	14.1353	0.65284	1.0:0.0:0.0:0.0	rs4057750;rs52820788;rs4057750	131	Q96RC9	OR8B4_HUMAN	H	131	ENSP00000348449:Y131H	ENSP00000348449:Y131H	Y	-	1	0	OR8B4	123799587	1.000000	0.71417	0.928000	0.36995	0.531000	0.34715	8.756000	0.91651	2.073000	0.62155	0.533000	0.62120	TAC	A|0.742;G|0.258	0.258	strong		0.502	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
GSTA3	2940	hgsc.bcm.edu	37	6	52767193	52767193	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:52767193T>C	ENST00000211122.3	-	4	288	c.223A>G	c.(223-225)Att>Gtt	p.I75V	GSTA3_ENST00000370968.1_Missense_Mutation_p.I25V	NM_000847.4	NP_000838.3	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3	75	GST N-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)	10	Lung NSC(77;0.0912)				Glutathione(DB00143)	TTGCTGGCAATGTAGTTGAGA	0.423																																					p.I75V		Atlas-SNP	.											.	GSTA3	21	.	0			c.A223G						PASS	.						199.0	193.0	195.0					6																	52767193		2203	4300	6503	SO:0001583	missense	2940	exon4			TGGCAATGTAGTT	AF020919	CCDS4947.1	6p12.2	2012-06-21	2008-11-26		ENSG00000174156	ENSG00000174156	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4628	protein-coding gene	gene with protein product		605449	"""glutathione S-transferase A3"""			8307579, 9480897	Standard	NM_000847		Approved		uc003pbb.3	Q16772	OTTHUMG00000014865	ENST00000211122.3:c.223A>G	6.37:g.52767193T>C	ENSP00000211122:p.Ile75Val	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	202	84	0.415842	NM_000847	O43468|Q068V6|Q8WWA8|Q9H415	Missense_Mutation	SNP	ENST00000211122.3	37	CCDS4947.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.925899	0.34002	.	.	ENSG00000174156	ENST00000370968;ENST00000211122;ENST00000431899	T;T;T	0.15487	2.42;2.42;2.42	4.16	1.75	0.24633	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.055329	0.64402	D	0.000001	T	0.05868	0.0153	L	0.43646	1.37	0.36011	D	0.838043	B	0.18461	0.028	B	0.24006	0.05	T	0.11891	-1.0569	10	0.46703	T	0.11	.	8.092	0.30805	0.0:0.1721:0.0:0.8279	.	75	Q16772	GSTA3_HUMAN	V	25;75;25	ENSP00000360007:I25V;ENSP00000211122:I75V;ENSP00000399142:I25V	ENSP00000211122:I75V	I	-	1	0	GSTA3	52875152	1.000000	0.71417	0.949000	0.38748	0.738000	0.42128	2.245000	0.43133	0.263000	0.21812	0.533000	0.62120	ATT	.	.	none		0.423	GSTA3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040933.1		
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086457	46086457	+	Missense_Mutation	SNP	G	G	A	rs12483730	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46086457G>A	ENST00000360770.3	-	1	387	c.347C>T	c.(346-348)gCg>gTg	p.A116V	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	116	23 X 5 AA approximate repeats.		A -> V (in dbSNP:rs12483730).			keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						GGACGGAGCCGCATACACGAC	0.627													G|||	723	0.144369	0.0877	0.1657	5008	,	,		18686	0.0923		0.2078	False		,,,				2504	0.1943				p.A116V		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.C347T						PASS	.	G	,VAL/ALA	387,3947		21,345,1801	55.0	64.0	61.0		,347	0.4	0.0	21	dbSNP_120	61	1745,6771		173,1399,2686	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,64	194,1744,4487	AA,AG,GG		20.4908,8.9294,16.5914	,possibly-damaging	,116/147	46086457	2132,10718	2167	4258	6425	SO:0001583	missense	353323	exon1			GGAGCCGCATACA	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.347C>T	21.37:g.46086457G>A	ENSP00000354001:p.Ala116Val	Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	265	152	0.573585	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	320	0.14652014652014653	44	0.08943089430894309	61	0.1685082872928177	56	0.0979020979020979	159	0.20976253298153033	g	0.632	-0.816857	0.02776	0.089294	0.204908	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02944	4.1	2.9	0.394	0.16299	.	.	.	.	.	T	0.00012	0.0000	N	0.00507	-1.42	0.58432	P	1.0000000000287557E-6	B	0.12630	0.006	B	0.04013	0.001	T	0.44267	-0.9339	8	0.27082	T	0.32	.	4.4209	0.11479	0.6485:0.0:0.3515:0.0	rs12483730	116	P59991	KR122_HUMAN	V	116;66	ENSP00000354001:A116V	ENSP00000354001:A116V	A	-	2	0	KRTAP12-2	44910885	0.002000	0.14202	0.006000	0.13384	0.001000	0.01503	0.492000	0.22435	0.175000	0.19841	-0.481000	0.04817	GCG	G|0.846;A|0.154	0.154	strong		0.627	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
ADCYAP1	116	hgsc.bcm.edu	37	18	909561	909561	+	Silent	SNP	A	A	G	rs2231187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:909561A>G	ENST00000579794.1	+	4	734	c.456A>G	c.(454-456)aaA>aaG	p.K152K	RP11-672L10.3_ENST00000582554.1_RNA|RP11-672L10.2_ENST00000581719.2_RNA|ADCYAP1_ENST00000450565.3_Silent_p.K152K	NM_001117.3	NP_001108.2	P18509	PACA_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary)	152	Important for receptor binding.				activation of adenylate cyclase activity (GO:0007190)|ATP metabolic process (GO:0046034)|behavioral fear response (GO:0001662)|cAMP-mediated signaling (GO:0019933)|cell-cell signaling (GO:0007267)|cellular response to glucocorticoid stimulus (GO:0071385)|female pregnancy (GO:0007565)|histamine secretion (GO:0001821)|negative regulation of acute inflammatory response to antigenic stimulus (GO:0002865)|negative regulation of acute inflammatory response to non-antigenic stimulus (GO:0002878)|negative regulation of cell cycle (GO:0045786)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of Rho GTPase activity (GO:0034259)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|pituitary gland development (GO:0021983)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of somatostatin secretion (GO:0090274)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)|regulation of postsynaptic membrane potential (GO:0060078)|regulation of protein localization (GO:0032880)|response to ethanol (GO:0045471)|response to starvation (GO:0042594)|sensory perception of pain (GO:0019233)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|terminal bouton (GO:0043195)	neuropeptide hormone activity (GO:0005184)|peptide hormone receptor binding (GO:0051428)|pituitary adenylate cyclase activating polypeptide activity (GO:0016521)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						CTGTCAAGAAATACTTGGCGG	0.557													A|||	1014	0.202476	0.0802	0.2709	5008	,	,		11583	0.2411		0.3191	False		,,,				2504	0.1595				p.C152W		Atlas-SNP	.											ADCYAP1,NS,carcinoma,0,1	ADCYAP1	24	1	0			c.T456G						PASS	.	A	,	548,3858	241.8+/-252.1	36,476,1691	99.0	118.0	111.0		456,456	5.2	1.0	18	dbSNP_98	111	2798,5802	435.4+/-358.0	454,1890,1956	no	coding-synonymous,coding-synonymous	ADCYAP1	NM_001099733.1,NM_001117.3	,	490,2366,3647	GG,GA,AA		32.5349,12.4376,25.7266	,	152/177,152/177	909561	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	116	exon4			CAAGAAATACTTG	S83513	CCDS11825.1	18p11	2013-02-28			ENSG00000141433	ENSG00000141433		"""Endogenous ligands"""	241	protein-coding gene	gene with protein product	"""prepro-PACAP"""	102980				1730060	Standard	NM_001099733		Approved	PACAP	uc010dkh.4	P18509	OTTHUMG00000131479	ENST00000579794.1:c.456A>G	18.37:g.909561A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	62	0.534483	NM_001117	B2R7N4|Q52LQ0	Missense_Mutation	SNP	ENST00000579794.1	37	CCDS11825.1																																																																																			A|0.757;C|0.001	.	strong		0.557	ADCYAP1-003	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440765.3	NM_001117	
OR51B6	390058	hgsc.bcm.edu	37	11	5373334	5373334	+	Silent	SNP	A	A	G	rs5006882	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373334A>G	ENST00000380219.1	+	1	597	c.597A>G	c.(595-597)gtA>gtG	p.V199V	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	199					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCCAGTTGTAGTTTTATTTG	0.438													A|||	1170	0.233626	0.326	0.2349	5008	,	,		23806	0.0863		0.2644	False		,,,				2504	0.228				p.V199V		Atlas-SNP	.											OR51B6,NS,carcinoma,+2,1	OR51B6	53	1	0			c.A597G						scavenged	.	A		1286,3116	439.2+/-345.6	173,940,1088	242.0	217.0	226.0		597	-0.1	0.9	11	dbSNP_113	226	2270,6324	382.6+/-340.4	310,1650,2337	no	coding-synonymous	OR51B6	NM_001004750.1		483,2590,3425	GG,GA,AA		26.4138,29.214,27.3623		199/313	5373334	3556,9440	2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			AGTTGTAGTTTTA		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.597A>G	11.37:g.5373334A>G		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	166	72	0.433735	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			A|0.757;G|0.243	0.243	strong		0.438	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
DDX58	23586	hgsc.bcm.edu	37	9	32459450	32459450	+	Silent	SNP	T	T	G	rs3205166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:32459450T>G	ENST00000379883.2	-	17	2557	c.2400A>C	c.(2398-2400)gtA>gtC	p.V800V	DDX58_ENST00000379868.1_Silent_p.V597V|DDX58_ENST00000379882.1_Silent_p.V755V|DDX58_ENST00000542096.1_Silent_p.V729V	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	800	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CCTTATCAGGTACAGGTTTTG	0.363													T|||	1574	0.314297	0.202	0.3602	5008	,	,		17599	0.4524		0.3529	False		,,,				2504	0.2515				p.V800V		Atlas-SNP	.											.	DDX58	82	.	0			c.A2400C						PASS	.	T		1056,3350	386.3+/-326.1	120,816,1267	186.0	165.0	172.0		2400	-6.8	0.0	9	dbSNP_105	172	3120,5480	474.8+/-368.9	555,2010,1735	no	coding-synonymous	DDX58	NM_014314.3		675,2826,3002	GG,GT,TT		36.2791,23.9673,32.1083		800/926	32459450	4176,8830	2203	4300	6503	SO:0001819	synonymous_variant	23586	exon17			ATCAGGTACAGGT	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2400A>C	9.37:g.32459450T>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Silent	SNP	ENST00000379883.2	37	CCDS6526.1																																																																																			T|0.672;G|0.328	0.328	strong		0.363	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
TAS2R20	259295	hgsc.bcm.edu	37	12	11150054	11150054	+	Missense_Mutation	SNP	C	C	T	rs79420812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:11150054C>T	ENST00000538986.1	-	1	420	c.421G>A	c.(421-423)Gtt>Att	p.V141I	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176889.2	NP_795370.2	P59543	T2R20_HUMAN	taste receptor, type 2, member 20	141				VCH -> ICQ (in Ref. 3; AAU21140). {ECO:0000305}.	sensory perception of taste (GO:0050909)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V141I(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13						AGGTGACAAACCAAAAAGAAC	0.388													C|||	916	0.182907	0.0371	0.1225	5008	,	,		20886	0.3185		0.2227	False		,,,				2504	0.2423				p.V141I		Atlas-SNP	.											TAS2R20,NS,carcinoma,0,1	TAS2R20	17	1	1	Substitution - Missense(1)	ovary(1)	c.G421A						PASS	.	C	ILE/VAL	239,4167	139.6+/-175.2	7,225,1971	128.0	114.0	118.0		421	-5.9	0.0	12	dbSNP_131	118	1704,6896	311.7+/-310.5	167,1370,2763	yes	missense	TAS2R20	NM_176889.2	29	174,1595,4734	TT,TC,CC		19.814,5.4244,14.9393	benign	141/310	11150054	1943,11063	2203	4300	6503	SO:0001583	missense	259295	exon1			GACAAACCAAAAA	AX097732, AF494236	CCDS8639.1	12p13.2	2012-08-22			ENSG00000255837	ENSG00000255837		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19109	protein-coding gene	gene with protein product		613962	"""taste receptor, type 2, member 49"""	TAS2R49			Standard	NM_176889		Approved	T2R20, T2R56	uc001qzm.2	P59543	OTTHUMG00000162695	ENST00000538986.1:c.421G>A	12.37:g.11150054C>T	ENSP00000441624:p.Val141Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_176889	P59549|Q2HIZ4|Q496D8|Q645X9	Missense_Mutation	SNP	ENST00000538986.1	37	CCDS8639.1	402	0.18406593406593408	19	0.03861788617886179	50	0.13812154696132597	171	0.29895104895104896	162	0.21372031662269128	C	2.515	-0.312165	0.05422	0.054244	0.19814	ENSG00000255837	ENST00000538986	T	0.36340	1.26	2.93	-5.87	0.02297	.	0.867467	0.09448	U	0.800842	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.12156	0.007	T	0.39078	-0.9631	9	0.25751	T	0.34	.	1.3021	0.02081	0.4189:0.2764:0.1245:0.1802	.	141	P59543	T2R20_HUMAN	I	141	ENSP00000441624:V141I	ENSP00000441624:V141I	V	-	1	0	TAS2R20	11041321	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.252000	0.00539	-1.958000	0.01019	-0.964000	0.02622	GTT	C|0.838;T|0.162	0.162	strong		0.388	TAS2R20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370130.2	NM_176889	
CTSH	1512	hgsc.bcm.edu	37	15	79237293	79237293	+	Missense_Mutation	SNP	C	C	T	rs2289702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79237293C>T	ENST00000220166.5	-	1	140	c.31G>A	c.(31-33)Ggg>Agg	p.G11R		NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	11			G -> R (in dbSNP:rs2289702).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						AGCCAGGCCCCGGCGCAGAGC	0.721													C|||	385	0.076877	0.0151	0.0533	5008	,	,		11873	0.0714		0.1054	False		,,,				2504	0.1534				p.G11R		Atlas-SNP	.											.	CTSH	23	.	0			c.G31A						PASS	.	C	ARG/GLY	103,3647		2,99,1774	7.0	8.0	8.0		31	3.1	0.5	15	dbSNP_100	8	663,6797		26,611,3093	no	missense	CTSH	NM_004390.3	125	28,710,4867	TT,TC,CC		8.8874,2.7467,6.8332		11/336	79237293	766,10444	1875	3730	5605	SO:0001583	missense	1512	exon1			AGGCCCCGGCGCA	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.31G>A	15.37:g.79237293C>T	ENSP00000220166:p.Gly11Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	178|178	0.0815018315018315|0.0815018315018315	28|28	0.056910569105691054|0.056910569105691054	21|21	0.058011049723756904|0.058011049723756904	44|44	0.07692307692307693|0.07692307692307693	85|85	0.11213720316622691|0.11213720316622691	C|C	7.291|7.291	0.610990|0.610990	0.14066|0.14066	0.027467|0.027467	0.088874|0.088874	ENSG00000103811|ENSG00000103811	ENST00000394758|ENST00000220166;ENST00000444399	.|T	.|0.72051	.|-0.62	3.12|3.12	3.12|3.12	0.35913|0.35913	.|.	.|131.017000	.|0.00531	.|U	.|0.000202	T|T	0.04679|0.04679	0.0127|0.0127	N|N	0.19112|0.19112	0.55|0.55	0.45330|0.45330	P|P	0.0016800000000000148|0.0016800000000000148	.|D	.|0.76494	.|0.999	.|D	.|0.65323	.|0.934	T|T	0.56263|0.56263	-0.8008|-0.8008	5|9	0.49607|0.27785	T|T	0.09|0.31	.|.	9.9555|9.9555	0.41663|0.41663	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2289702|rs2289702	.|11	.|E9PF73	.|.	T|R	11|11	.|ENSP00000220166:G11R	ENSP00000378240:A11T|ENSP00000220166:G11R	A|G	-|-	1|1	0|0	CTSH|CTSH	77024348|77024348	0.001000|0.001000	0.12720|0.12720	0.483000|0.483000	0.27378|0.27378	0.004000|0.004000	0.04260|0.04260	0.281000|0.281000	0.18810|0.18810	2.040000|2.040000	0.60383|0.60383	0.491000|0.491000	0.48974|0.48974	GCC|GGG	C|0.917;T|0.083	0.083	strong		0.721	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
IVL	3713	hgsc.bcm.edu	37	1	152882981	152882981	+	Silent	SNP	A	A	T	rs62637699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152882981A>T	ENST00000368764.3	+	2	772	c.708A>T	c.(706-708)ccA>ccT	p.P236P	IVL_ENST00000392667.2_Silent_p.P90P			P07476	INVO_HUMAN	involucrin	236	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		P -> S (in dbSNP:rs17855670). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			tggagctcccacagcagcagg	0.677																																					p.P236P		Atlas-SNP	.											IVL,colon,carcinoma,+2,2	IVL	100	2	0			c.A708T						PASS	.						3.0	4.0	3.0					1																	152882981		1601	3431	5032	SO:0001819	synonymous_variant	3713	exon2			GCTCCCACAGCAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.708A>T	1.37:g.152882981A>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	22	0.275	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			A|0.696;T|0.304	0.304	strong		0.677	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
COMMD2	51122	hgsc.bcm.edu	37	3	149459413	149459413	+	Silent	SNP	C	C	T	rs11549572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:149459413C>T	ENST00000473414.1	-	5	549	c.495G>A	c.(493-495)ctG>ctA	p.L165L		NM_016094.3	NP_057178.2	Q86X83	COMD2_HUMAN	COMM domain containing 2	165	COMM. {ECO:0000255|PROSITE- ProRule:PRU00602}.									NS(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	9			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GGTCTGTCTGCAGAACTTTGG	0.428													T|||	1404	0.280351	0.6097	0.1354	5008	,	,		13701	0.2609		0.0785	False		,,,				2504	0.1656				p.L165L		Atlas-SNP	.											.	COMMD2	21	.	0			c.G495A						PASS	.	T		2304,2102	573.3+/-383.5	611,1082,510	228.0	236.0	234.0		495	3.0	0.9	3	dbSNP_120	234	693,7907	788.1+/-407.6	32,629,3639	yes	coding-synonymous	COMMD2	NM_016094.3		643,1711,4149	TT,TC,CC		8.0581,47.7077,23.0432		165/200	149459413	2997,10009	2203	4300	6503	SO:0001819	synonymous_variant	51122	exon5			TGTCTGCAGAACT	AY542158	CCDS3145.1	3q25.1	2004-02-20			ENSG00000114744	ENSG00000114744			24993	protein-coding gene	gene with protein product						15799966	Standard	NM_016094		Approved	HSPC042	uc003exj.2	Q86X83	OTTHUMG00000159616	ENST00000473414.1:c.495G>A	3.37:g.149459413C>T		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	251	136	0.541833	NM_016094	Q561V4|Q9H3L5|Q9Y5V1	Silent	SNP	ENST00000473414.1	37	CCDS3145.1																																																																																			C|0.755;T|0.245	0.245	strong		0.428	COMMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356515.1	NM_016094	
SNAPC3	6619	hgsc.bcm.edu	37	9	15459821	15459821	+	Missense_Mutation	SNP	A	A	C	rs3087653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:15459821A>C	ENST00000380821.3	+	9	1369	c.1193A>C	c.(1192-1194)gAa>gCa	p.E398A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	398			E -> A (in dbSNP:rs3087653).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		AAACTGGGGGAATTCCTTGCT	0.413													A|||	193	0.0385383	0.0416	0.0231	5008	,	,		16799	0.0		0.0596	False		,,,				2504	0.0634				p.E398A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.A1193C						PASS	.	A	ALA/GLU	145,4261	101.2+/-139.8	0,145,2058	134.0	122.0	126.0		1193	5.9	1.0	9	dbSNP_102	126	425,8175	131.8+/-189.6	13,399,3888	yes	missense	SNAPC3	NM_001039697.1	107	13,544,5946	CC,CA,AA		4.9419,3.291,4.3826	probably-damaging	398/412	15459821	570,12436	2203	4300	6503	SO:0001583	missense	6619	exon9			TGGGGGAATTCCT	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.1193A>C	9.37:g.15459821A>C	ENSP00000370200:p.Glu398Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	78	0.03571428571428571	26	0.052845528455284556	11	0.03038674033149171	0	0.0	41	0.05408970976253298	A	31	5.081553	0.94050	0.03291	0.049419	ENSG00000164975	ENST00000380821	T	0.44083	0.93	5.86	5.86	0.93980	.	0.138414	0.64402	D	0.000005	T	0.17450	0.0419	M	0.65498	2.005	0.80722	D	1	D	0.57571	0.98	P	0.53224	0.721	T	0.31447	-0.9943	10	0.56958	D	0.05	-42.6534	16.5602	0.84551	1.0:0.0:0.0:0.0	rs3087653;rs3198208;rs52828246;rs3087653	398	Q92966	SNPC3_HUMAN	A	398	ENSP00000370200:E398A	ENSP00000370200:E398A	E	+	2	0	SNAPC3	15449821	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.283000	0.78640	2.367000	0.80283	0.528000	0.53228	GAA	A|0.956;C|0.044	0.044	strong		0.413	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
OR5T2	219464	hgsc.bcm.edu	37	11	56000451	56000451	+	Silent	SNP	G	G	A	rs11227598	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56000451G>A	ENST00000313264.4	-	1	286	c.211C>T	c.(211-213)Cta>Tta	p.L71L		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	71						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L71L(1)		endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TAGATTGCTAGAAACAGGAAG	0.388													g|||	511	0.102037	0.062	0.1009	5008	,	,		21549	0.125		0.1173	False		,,,				2504	0.1176				p.L71L		Atlas-SNP	.											OR5T2,colon,carcinoma,0,2	OR5T2	107	2	1	Substitution - coding silent(1)	stomach(1)	c.C211T						PASS	.	G		277,4125	152.5+/-186.2	9,259,1933	72.0	65.0	67.0		211	-0.9	0.0	11	dbSNP_120	67	998,7594	214.3+/-254.0	54,890,3352	no	coding-synonymous	OR5T2	NM_001004746.1		63,1149,5285	AA,AG,GG		11.6155,6.2926,9.8122		71/360	56000451	1275,11719	2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			TTGCTAGAAACAG	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.211C>T	11.37:g.56000451G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	37	CCDS31523.1																																																																																			G|0.901;A|0.099	0.099	strong		0.388	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
WNT7A	7476	hgsc.bcm.edu	37	3	13896140	13896140	+	Silent	SNP	A	A	G	rs3762719	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:13896140A>G	ENST00000285018.4	-	3	763	c.459T>C	c.(457-459)tcT>tcC	p.S153S		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	153					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						GGATGTCGGCAGAGCAGCCAC	0.607													A|||	1256	0.250799	0.1293	0.2061	5008	,	,		18627	0.5813		0.17	False		,,,				2504	0.1892				p.S153S		Atlas-SNP	.											.	WNT7A	70	.	0			c.T459C						PASS	.	A		775,3631	311.1+/-291.9	70,635,1498	113.0	110.0	111.0		459	-9.5	0.9	3	dbSNP_107	111	1567,7033	293.0+/-301.1	135,1297,2868	no	coding-synonymous	WNT7A	NM_004625.3		205,1932,4366	GG,GA,AA		18.2209,17.5897,18.0071		153/350	13896140	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	7476	exon3			GTCGGCAGAGCAG	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"""Wingless-type MMTV integration sites"""	12786	protein-coding gene	gene with protein product	"""proto-oncogene Wnt7a protein"""	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.459T>C	3.37:g.13896140A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	40	23	0.575	NM_004625	Q96H90|Q9Y560	Silent	SNP	ENST00000285018.4	37	CCDS2616.1																																																																																			A|0.795;G|0.205	0.205	strong		0.607	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625	
RPN1	6184	hgsc.bcm.edu	37	3	128344786	128344786	+	Silent	SNP	G	G	A	rs1126828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:128344786G>A	ENST00000296255.3	-	7	1254	c.1206C>T	c.(1204-1206)gaC>gaT	p.D402D	RPN1_ENST00000490166.1_5'Flank|RPN1_ENST00000497289.1_Silent_p.D230D	NM_002950.3	NP_002941.1	P04843	RPN1_HUMAN	ribophorin I	402					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)|poly(A) RNA binding (GO:0044822)	p.D402D(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(2)|stomach(2)	13				GBM - Glioblastoma multiforme(114;0.189)		GGCCAAATGTGTCCAGATAGG	0.468			T	EVI1	AML								G|||	1192	0.238019	0.143	0.2003	5008	,	,		19302	0.4147		0.2137	False		,,,				2504	0.2362				p.D402D		Atlas-SNP	.		Dom	yes		3	3q21.3-q25.2	6184	ribophorin I		L	RPN1,NS,carcinoma,0,1	RPN1	39	1	1	Substitution - coding silent(1)	stomach(1)	c.C1206T						PASS	.	G		627,3779	270.1+/-269.4	48,531,1624	135.0	124.0	128.0		1206	3.1	1.0	3	dbSNP_86	128	1950,6650	343.9+/-325.1	237,1476,2587	no	coding-synonymous	RPN1	NM_002950.3		285,2007,4211	AA,AG,GG		22.6744,14.2306,19.8139		402/608	128344786	2577,10429	2203	4300	6503	SO:0001819	synonymous_variant	6184	exon7			AAATGTGTCCAGA		CCDS3051.1	3q21.3	2013-03-06			ENSG00000163902	ENSG00000163902			10381	protein-coding gene	gene with protein product	"""oligosaccharyltransferase 1 homolog (S. cerevisiae)"", ""oligosaccharyltransferase complex subunit (non-catalytic)"""	180470					Standard	NM_002950		Approved	OST1	uc003ekr.1	P04843	OTTHUMG00000159691	ENST00000296255.3:c.1206C>T	3.37:g.128344786G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_002950	B2R5Z0|D3DNB6|Q68DT1	Silent	SNP	ENST00000296255.3	37	CCDS3051.1																																																																																			G|0.779;A|0.221	0.221	strong		0.468	RPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356934.2	NM_002950	
GTF2H3	2967	hgsc.bcm.edu	37	12	124144395	124144395	+	Silent	SNP	A	A	G	rs1051793	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124144395A>G	ENST00000543341.2	+	11	769	c.738A>G	c.(736-738)ccA>ccG	p.P246P	GTF2H3_ENST00000228955.7_Silent_p.P205P	NM_001271867.1|NM_001516.3	NP_001258796.1|NP_001507.2	Q13889	TF2H3_HUMAN	general transcription factor IIH, polypeptide 3, 34kDa	246					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)|translation (GO:0006412)|viral process (GO:0016032)	core TFIIH complex (GO:0000439)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|large_intestine(4)|lung(2)|urinary_tract(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.1e-05)|Epithelial(86;0.000388)|all cancers(50;0.00362)		TCCCACCCCCAGTTCATGTTG	0.383								Nucleotide excision repair (NER)					A|||	1758	0.351038	0.6135	0.304	5008	,	,		18537	0.0615		0.3817	False		,,,				2504	0.2965				p.P246P	Melanoma(176;111 2022 3038 14733 36962)	Atlas-SNP	.											.	GTF2H3	20	.	0			c.A738G						PASS	.	A		2599,1807	640.4+/-397.3	781,1037,385	124.0	115.0	118.0		738	-7.4	0.0	12	dbSNP_86	118	3479,5121	509.8+/-377.4	699,2081,1520	no	coding-synonymous	GTF2H3	NM_001516.3		1480,3118,1905	GG,GA,AA		40.4535,41.0123,46.7323		246/309	124144395	6078,6928	2203	4300	6503	SO:0001819	synonymous_variant	2967	exon11			ACCCCCAGTTCAT	Z30093	CCDS9252.1, CCDS61275.1, CCDS73544.1	12q24.31	2012-11-05	2002-08-29		ENSG00000111358	ENSG00000111358		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	4657	protein-coding gene	gene with protein product		601750	"""general transcription factor IIH, polypeptide 3 (34kD subunit)"""			8194529	Standard	NM_001516		Approved	BTF2, TFIIH, P34	uc001ufo.2	Q13889	OTTHUMG00000168697	ENST00000543341.2:c.738A>G	12.37:g.124144395A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	193	76	0.393782	NM_001516	B2R819|B4DNZ6|Q7L0G0|Q96AT7	Silent	SNP	ENST00000543341.2	37	CCDS9252.1																																																																																			A|0.577;G|0.423	0.423	strong		0.383	GTF2H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400641.2	NM_001516	
PPARGC1A	10891	hgsc.bcm.edu	37	4	23815681	23815681	+	Silent	SNP	G	G	A	rs17574213	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:23815681G>A	ENST00000264867.2	-	8	1544	c.1425C>T	c.(1423-1425)gaC>gaT	p.D475D	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	475	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				CTGCTTCGTCGTCAAAAACAG	0.468													G|||	117	0.0233626	0.0174	0.0403	5008	,	,		19749	0.0		0.0497	False		,,,				2504	0.0164				p.D475D	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.C1425T						PASS	.	G		138,4268	98.9+/-137.6	3,132,2068	116.0	104.0	108.0		1425	0.9	1.0	4	dbSNP_123	108	580,8020	155.4+/-209.4	21,538,3741	no	coding-synonymous	PPARGC1A	NM_013261.3		24,670,5809	AA,AG,GG		6.7442,3.1321,5.5205		475/799	23815681	718,12288	2203	4300	6503	SO:0001819	synonymous_variant	10891	exon8			TTCGTCGTCAAAA	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1425C>T	4.37:g.23815681G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	140	78	0.557143	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Silent	SNP	ENST00000264867.2	37	CCDS3429.1																																																																																			G|0.955;A|0.045	0.045	strong		0.468	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
WWC2	80014	hgsc.bcm.edu	37	4	184203990	184203990	+	Silent	SNP	C	C	T	rs17291770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:184203990C>T	ENST00000403733.3	+	18	3013	c.2814C>T	c.(2812-2814)gaC>gaT	p.D938D	WWC2_ENST00000513834.1_Silent_p.D889D|WWC2_ENST00000508747.1_Silent_p.D66D|WWC2_ENST00000448232.2_Silent_p.D962D|WWC2_ENST00000504005.1_Silent_p.D620D	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	938					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TGAATGAAGACGGGAACAGGA	0.438													C|||	146	0.0291534	0.0023	0.0375	5008	,	,		20274	0.001		0.0547	False		,,,				2504	0.0624				p.D938D		Atlas-SNP	.											.	WWC2	78	.	0			c.C2814T						PASS	.	C		60,4346	52.9+/-88.7	0,60,2143	85.0	75.0	78.0		2814	-0.6	0.0	4	dbSNP_123	78	535,8063	139.4+/-196.0	21,493,3785	no	coding-synonymous	WWC2	NM_024949.5		21,553,5928	TT,TC,CC		6.2224,1.3618,4.5755		938/1193	184203990	595,12409	2203	4299	6502	SO:0001819	synonymous_variant	80014	exon18			TGAAGACGGGAAC	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.2814C>T	4.37:g.184203990C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Silent	SNP	ENST00000403733.3	37	CCDS34109.2																																																																																			C|0.961;T|0.039	0.039	strong		0.438	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
PIH1D1	55011	hgsc.bcm.edu	37	19	49949652	49949652	+	Missense_Mutation	SNP	G	G	A	rs7462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49949652G>A	ENST00000262265.5	-	9	1095	c.860C>T	c.(859-861)cCg>cTg	p.P287L	PIH1D1_ENST00000596049.1_Missense_Mutation_p.P287L|PIH1D1_ENST00000602226.1_5'UTR	NM_017916.2	NP_060386.1	Q9NWS0	PIHD1_HUMAN	PIH1 domain containing 1	287			P -> L (in dbSNP:rs7462). {ECO:0000269|PubMed:15489334}.		box C/D snoRNP assembly (GO:0000492)|epithelial cell differentiation (GO:0030855)	pre-snoRNP complex (GO:0070761)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|urinary_tract(1)	11		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00152)|GBM - Glioblastoma multiforme(486;0.0244)		AGAAGGCACCGGCAGAAGCGG	0.522													G|||	930	0.185703	0.2746	0.2032	5008	,	,		15967	0.005		0.3231	False		,,,				2504	0.0982				p.P287L		Atlas-SNP	.											.	PIH1D1	23	.	0			c.C860T						PASS	.	G	LEU/PRO	1114,3292	399.9+/-331.4	140,834,1229	60.0	59.0	59.0		860	2.2	0.0	19	dbSNP_52	59	2895,5705	453.9+/-363.3	479,1937,1884	yes	missense	PIH1D1	NM_017916.2	98	619,2771,3113	AA,AG,GG		33.6628,25.2837,30.8242	benign	287/291	49949652	4009,8997	2203	4300	6503	SO:0001583	missense	55011	exon9			GGCACCGGCAGAA	AK000650	CCDS12765.1	19q13.33	2012-07-18	2007-01-31	2007-01-31	ENSG00000104872	ENSG00000104872			26075	protein-coding gene	gene with protein product		611480		NOP17		12477932	Standard	NM_017916		Approved	FLJ20643	uc002pns.2	Q9NWS0		ENST00000262265.5:c.860C>T	19.37:g.49949652G>A	ENSP00000262265:p.Pro287Leu	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	209	94	0.449761	NM_017916	B4DGN7|B4E2X7|Q9BVL0	Missense_Mutation	SNP	ENST00000262265.5	37	CCDS12765.1	472	0.21611721611721613	148	0.3008130081300813	78	0.2154696132596685	3	0.005244755244755245	243	0.32058047493403696	G	4.396	0.073136	0.08485	0.252837	0.336628	ENSG00000104872	ENST00000262265	T	0.16457	2.34	3.32	2.25	0.28309	.	0.348457	0.26680	N	0.023057	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	0.45190	-0.9278	9	0.51188	T	0.08	-1.7009	6.9777	0.24686	0.1285:0.0:0.8715:0.0	rs7462;rs1043253;rs3182784;rs17856032;rs52817842;rs60098984;rs7462	287	Q9NWS0	PIHD1_HUMAN	L	287	ENSP00000262265:P287L	ENSP00000262265:P287L	P	-	2	0	PIH1D1	54641464	0.052000	0.20516	0.022000	0.16811	0.207000	0.24258	1.153000	0.31676	0.954000	0.37851	0.655000	0.94253	CCG	G|0.723;A|0.277	0.277	strong		0.522	PIH1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465389.2	NM_017916	
HK2	3099	hgsc.bcm.edu	37	2	75115108	75115108	+	Silent	SNP	A	A	G	rs10194657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75115108A>G	ENST00000290573.2	+	16	2898	c.2298A>G	c.(2296-2298)ctA>ctG	p.L766L	HK2_ENST00000409174.1_Silent_p.L738L	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	766	Catalytic.|Hexokinase type-2 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.L766L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						AGCGTGGACTACTCTTCCGAG	0.478													G|||	2625	0.524161	0.4236	0.4654	5008	,	,		23273	0.4821		0.6282	False		,,,				2504	0.638				p.L766L		Atlas-SNP	.											HK2,NS,carcinoma,0,1	HK2	85	1	1	Substitution - coding silent(1)	stomach(1)	c.A2298G						scavenged	.	G		2030,2376	612.6+/-392.0	471,1088,644	154.0	136.0	142.0		2298	2.6	1.0	2	dbSNP_119	142	5404,3196	484.4+/-371.4	1686,2032,582	no	coding-synonymous	HK2	NM_000189.4		2157,3120,1226	GG,GA,AA		37.1628,46.0735,42.8418		766/918	75115108	7434,5572	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon16			TGGACTACTCTTC		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.2298A>G	2.37:g.75115108A>G		Somatic	133	2	0.0150376		WXS	Illumina HiSeq	Phase_I	182	87	0.478022	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																			A|0.442;C|0.004	.	strong		0.478	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
STK36	27148	hgsc.bcm.edu	37	2	219555262	219555262	+	Missense_Mutation	SNP	G	G	A	rs1344642	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219555262G>A	ENST00000295709.3	+	14	2027	c.1748G>A	c.(1747-1749)cGg>cAg	p.R583Q	STK36_ENST00000392105.3_Missense_Mutation_p.R583Q|STK36_ENST00000392106.2_Missense_Mutation_p.R583Q|STK36_ENST00000440309.1_Missense_Mutation_p.R583Q	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CAGACTTTGCGGAGGGACAGC	0.522													G|||	2112	0.421725	0.7095	0.4107	5008	,	,		18563	0.1429		0.4235	False		,,,				2504	0.3262				p.R583Q		Atlas-SNP	.											.	STK36	111	.	0			c.G1748A						PASS	.	G	GLN/ARG	2804,1602	665.1+/-401.5	886,1032,285	69.0	67.0	68.0		1748	2.4	0.0	2	dbSNP_88	68	3775,4825	536.2+/-383.0	840,2095,1365	yes	missense	STK36	NM_015690.4	43	1726,3127,1650	AA,AG,GG		43.8953,36.3595,49.4157	possibly-damaging	583/1316	219555262	6579,6427	2203	4300	6503	SO:0001583	missense	27148	exon14			CTTTGCGGAGGGA	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.1748G>A	2.37:g.219555262G>A	ENSP00000295709:p.Arg583Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	921	0.4217032967032967	371	0.7540650406504065	146	0.40331491712707185	90	0.15734265734265734	314	0.41424802110817943	G	10.15	1.270143	0.23221	0.636405	0.438953	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.73681	-0.77;-0.77;0.56;-0.77	5.14	2.42	0.29668	Armadillo-like helical (1);	0.366067	0.19209	N	0.119992	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.26258	0.145;0.041	B;B	0.12837	0.008;0.002	T	0.41179	-0.9523	9	0.32370	T	0.25	-4.1498	8.0229	0.30419	0.2473:0.0:0.7527:0.0	rs1344642;rs17463680;rs52819602;rs59588577;rs1344642	583;583	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	Q	583	ENSP00000295709:R583Q;ENSP00000375955:R583Q;ENSP00000375954:R583Q;ENSP00000394095:R583Q	ENSP00000295709:R583Q	R	+	2	0	STK36	219263506	0.309000	0.24518	0.046000	0.18839	0.720000	0.41350	1.646000	0.37249	0.356000	0.24157	-0.136000	0.14681	CGG	G|0.530;A|0.470	0.470	strong		0.522	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
TG	7038	hgsc.bcm.edu	37	8	133975283	133975283	+	Missense_Mutation	SNP	G	G	A	rs2069561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:133975283G>A	ENST00000220616.4	+	29	5552	c.5512G>A	c.(5512-5514)Gac>Aac	p.D1838N	TG_ENST00000542445.1_Missense_Mutation_p.D208N|TG_ENST00000377869.1_Missense_Mutation_p.D1781N|TG_ENST00000519543.1_5'Flank	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1838			D -> N (in dbSNP:rs2069561). {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)		p.D1838N(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)		ATGTAGAAAAGACACAGTGCC	0.488													G|||	1737	0.346845	0.0333	0.5259	5008	,	,		19744	0.3452		0.5089	False		,,,				2504	0.4785				p.D1838N		Atlas-SNP	.											TG,NS,carcinoma,0,1	TG	416	1	1	Substitution - Missense(1)	stomach(1)	c.G5512A						PASS	.	G	ASN/ASP	530,3876	241.2+/-251.7	37,456,1710	275.0	247.0	257.0		5512	1.7	0.0	8	dbSNP_96	257	4398,4202	585.9+/-391.9	1156,2086,1058	yes	missense	TG	NM_003235.4	23	1193,2542,2768	AA,AG,GG		48.8605,12.0291,37.8902	benign	1838/2769	133975283	4928,8078	2203	4300	6503	SO:0001583	missense	7038	exon29			AGAAAAGACACAG	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.5512G>A	8.37:g.133975283G>A	ENSP00000220616:p.Asp1838Asn	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	220	219	0.995455	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	803|803	0.3676739926739927|0.3676739926739927	25|25	0.0508130081300813|0.0508130081300813	184|184	0.5082872928176796|0.5082872928176796	201|201	0.3513986013986014|0.3513986013986014	393|393	0.5184696569920845|0.5184696569920845	G|G	9.376|9.376	1.071724|1.071724	0.20147|0.20147	0.120291|0.120291	0.511395|0.511395	ENSG00000042832|ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445|ENST00000519178	T;T;T|.	0.66995|.	-0.03;-0.03;-0.24|.	4.41|4.41	1.66|1.66	0.24008|0.24008	.|.	1.854800|.	0.02283|.	N|.	0.069558|.	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;B|.	0.15930|.	0.015;0.001|.	B;B|.	0.12837|.	0.008;0.003|.	T|T	0.47898|0.47898	-0.9081|-0.9081	9|4	0.54805|.	T|.	0.06|.	.|.	6.41|6.41	0.21686|0.21686	0.3047:0.0:0.6953:0.0|0.3047:0.0:0.6953:0.0	rs2069561;rs2741220;rs3739271;rs17619883;rs52813039;rs59959331;rs2069561|rs2069561;rs2741220;rs3739271;rs17619883;rs52813039;rs59959331;rs2069561	208;1838|.	F5GWW5;P01266|.	.;THYG_HUMAN|.	N|K	1781;644;1838;208|293	ENSP00000367100:D1781N;ENSP00000220616:D1838N;ENSP00000441693:D208N|.	ENSP00000220616:D1838N|.	D|R	+|+	1|2	0|0	TG|TG	134044465|134044465	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.528000|0.528000	0.23002|0.23002	0.374000|0.374000	0.24650|0.24650	-0.251000|-0.251000	0.11542|0.11542	GAC|AGA	G|0.642;A|0.358	0.358	strong		0.488	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
MED17	9440	hgsc.bcm.edu	37	11	93529674	93529674	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:93529674C>T	ENST00000251871.3	+	7	1398	c.1111C>T	c.(1111-1113)Cta>Tta	p.L371L	snoU13_ENST00000459243.1_RNA|MED17_ENST00000533367.1_3'UTR	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	371			L -> P (in MCPHSBA). {ECO:0000269|PubMed:20950787}.		androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CCTTTATGTCCTAGAGCATAA	0.403																																					p.L371L		Atlas-SNP	.											.	MED17	37	.	0			c.C1111T						PASS	.						157.0	151.0	153.0					11																	93529674		2201	4298	6499	SO:0001819	synonymous_variant	9440	exon7			TATGTCCTAGAGC	AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"""cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)"", ""cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"""	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.1111C>T	11.37:g.93529674C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	83	4	0.0481928	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Silent	SNP	ENST00000251871.3	37	CCDS8295.1																																																																																			.	.	none		0.403	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268	
PRSS55	203074	hgsc.bcm.edu	37	8	10383138	10383138	+	Missense_Mutation	SNP	G	G	A	rs35102108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10383138G>A	ENST00000328655.3	+	1	83	c.43G>A	c.(43-45)Gga>Aga	p.G15R	PRSS51_ENST00000523024.1_RNA|PRSS55_ENST00000522210.1_Missense_Mutation_p.G15R	NM_198464.3	NP_940866.2	Q6UWB4	PRS55_HUMAN	protease, serine, 55	15				G -> R (in Ref. 3; BC033497). {ECO:0000305}.		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						CCTGGTCACGGGAACTCAGCT	0.677													G|||	928	0.185304	0.0499	0.245	5008	,	,		17372	0.3204		0.1789	False		,,,				2504	0.1933				p.G15R		Atlas-SNP	.											.	PRSS55	67	.	0			c.G43A						PASS	.	G	ARG/GLY,ARG/GLY	333,4073	176.2+/-205.4	12,309,1882	93.0	75.0	81.0		43,43	-1.0	0.0	8	dbSNP_126	81	1710,6890	312.5+/-310.9	176,1358,2766	yes	missense,missense	PRSS55	NM_198464.3,NM_001197020.1	125,125	188,1667,4648	AA,AG,GG		19.8837,7.5579,15.7081	benign,benign	15/353,15/277	10383138	2043,10963	2203	4300	6503	SO:0001583	missense	203074	exon1			GTCACGGGAACTC	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.43G>A	8.37:g.10383138G>A	ENSP00000333003:p.Gly15Arg	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_001197020	E5RJX5	Missense_Mutation	SNP	ENST00000328655.3	37	CCDS5976.1	437	0.2000915750915751	21	0.042682926829268296	92	0.2541436464088398	186	0.32517482517482516	138	0.1820580474934037	G	10.04	1.241746	0.22711	0.075579	0.198837	ENSG00000184647	ENST00000328655;ENST00000522210	D;D	0.88431	-2.38;-2.36	3.39	-0.977	0.10282	.	.	.	.	.	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	0.05099	-1.0906	8	0.66056	D	0.02	.	6.5712	0.22539	0.5624:0.0:0.4376:0.0	rs35102108;rs61067117	15	Q6UWB4	PRS55_HUMAN	R	15	ENSP00000333003:G15R;ENSP00000430459:G15R	ENSP00000333003:G15R	G	+	1	0	PRSS55	10420548	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.494000	0.22467	-0.219000	0.10003	-0.218000	0.12543	GGA	G|0.834;A|0.166	0.166	strong		0.677	PRSS55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251493.3	NM_198464	
FAM66D	100132923	hgsc.bcm.edu	37	8	11990882	11990882	+	RNA	SNP	C	C	T	rs9720235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:11990882C>T	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		GTGTCTGAAACGCCGTGGCAG	0.498													t|||	2043	0.407947	0.2897	0.5187	5008	,	,		24947	0.4077		0.4513	False		,,,				2504	0.4448				p.V213I		Atlas-SNP	.											.	.	.	.	0			c.G637A						PASS	.																																					392197	exon1			CTGAAACGCCGTG			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11990882C>T		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				C|0.499;T|0.501	0.501	strong		0.498	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
SPATA20	64847	hgsc.bcm.edu	37	17	48628160	48628160	+	Missense_Mutation	SNP	A	A	G	rs62621401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48628160A>G	ENST00000356488.4	+	10	1300	c.1217A>G	c.(1216-1218)aAa>aGa	p.K406R	SPATA20_ENST00000393244.3_Missense_Mutation_p.K362R|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Missense_Mutation_p.K422R	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	406					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			TGGACGGTCAAAGAGGTTCAG	0.637											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	300	0.0599042	0.0802	0.1282	5008	,	,		16458	0.0437		0.0258	False		,,,				2504	0.0358				p.K422R		Atlas-SNP	.											.	SPATA20	59	.	0			c.A1265G						PASS	.	A	ARG/LYS	336,4070	170.1+/-200.6	16,304,1883	77.0	88.0	84.0		1265	4.5	1.0	17	dbSNP_129	84	158,8442	72.3+/-134.9	1,156,4143	yes	missense	SPATA20	NM_022827.2	26	17,460,6026	GG,GA,AA		1.8372,7.626,3.7982	benign	422/803	48628160	494,12512	2203	4300	6503	SO:0001583	missense	64847	exon11			CGGTCAAAGAGGT		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1217A>G	17.37:g.48628160A>G	ENSP00000348878:p.Lys406Arg	Somatic	116	0	0	119	WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	106	0.048534798534798536	25	0.0508130081300813	38	0.10497237569060773	24	0.04195804195804196	19	0.025065963060686015	A	11.37	1.618228	0.28801	0.07626	0.018372	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.22743	1.94;1.94;1.94	5.64	4.5	0.54988	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	0.402857	0.29080	N	0.013202	T	0.00440	0.0014	L	0.33093	0.98	0.53005	P	3.399999999997849E-5	B;B	0.06786	0.0;0.001	B;B	0.12837	0.008;0.003	T	0.06844	-1.0804	9	0.37606	T	0.19	-10.9229	12.432	0.55578	0.8601:0.1399:0.0:0.0	rs62621401	406;422	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	R	422;406;362	ENSP00000006658:K422R;ENSP00000348878:K406R;ENSP00000376935:K362R	ENSP00000006658:K422R	K	+	2	0	SPATA20	45983159	0.774000	0.28592	0.964000	0.40570	0.170000	0.22686	3.093000	0.50217	2.152000	0.67230	0.533000	0.62120	AAA	A|0.956;G|0.044	0.044	strong		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
MMP20	9313	hgsc.bcm.edu	37	11	102477395	102477395	+	Missense_Mutation	SNP	A	A	G	rs1784423	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102477395A>G	ENST00000260228.2	-	6	836	c.824T>C	c.(823-825)gTa>gCa	p.V275A	MMP20_ENST00000544938.1_5'UTR|RP11-817J15.2_ENST00000542119.1_RNA|RP11-817J15.2_ENST00000544115.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	294					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	CCCCAGGAATACTTTCCGAGG	0.527													G|||	2103	0.419928	0.2625	0.4424	5008	,	,		19891	0.4325		0.4364	False		,,,				2504	0.5869				p.V275A		Atlas-SNP	.											.	MMP20	52	.	0			c.T824C						PASS	.	G	ALA/VAL	1359,3047	692.2+/-405.5	203,953,1047	97.0	97.0	97.0		824	4.5	0.0	11	dbSNP_89	97	3927,4671	604.8+/-394.9	867,2193,1239	yes	missense	MMP20	NM_004771.3	64	1070,3146,2286	GG,GA,AA		45.6734,30.8443,40.649	benign	275/484	102477395	5286,7718	2203	4299	6502	SO:0001583	missense	9313	exon6			AGGAATACTTTCC	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.824T>C	11.37:g.102477395A>G	ENSP00000260228:p.Val275Ala	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	138	136	0.985507	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	876	0.4010989010989011	129	0.2621951219512195	170	0.4696132596685083	248	0.43356643356643354	329	0.4340369393139842	G	0.012	-1.683853	0.00745	0.308443	0.456734	ENSG00000137674	ENST00000260228	T	0.12361	2.69	5.45	4.53	0.55603	.	1.200790	0.05857	N	0.622272	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44892	-0.9298	9	0.07175	T	0.84	.	7.9149	0.29812	0.2475:0.0:0.7525:0.0	rs1784423;rs1784423	275	O60882	MMP20_HUMAN	A	275	ENSP00000260228:V275A	ENSP00000260228:V275A	V	-	2	0	MMP20	101982605	0.005000	0.15991	0.017000	0.16124	0.020000	0.10135	0.727000	0.25999	0.855000	0.35359	-0.128000	0.14901	GTA	G|0.400;N|0.000	0.400	strong		0.527	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
ESRP1	54845	hgsc.bcm.edu	37	8	95680229	95680229	+	Silent	SNP	C	C	T	rs1549466	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95680229C>T	ENST00000433389.2	+	10	1174	c.984C>T	c.(982-984)gtC>gtT	p.V328V	ESRP1_ENST00000423620.2_Silent_p.V328V|ESRP1_ENST00000358397.5_Silent_p.V328V|ESRP1_ENST00000454170.2_Silent_p.V328V	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	328	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)		ESRP1/RAF1(4)	NS(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|urinary_tract(2)	20						AAGTCATTGTCCGCATGCGGG	0.483													C|||	1765	0.352436	0.0514	0.3804	5008	,	,		19140	0.5387		0.3897	False		,,,				2504	0.5092				p.V328V		Atlas-SNP	.											ESRP1_ENST00000433389,NS,carcinoma,+2,2	ESRP1	148	2	0			c.C984T						PASS	.	C	,,,,	393,3341		21,351,1495	61.0	60.0	60.0		984,984,984,984,984	-0.6	1.0	8	dbSNP_88	60	3101,5085		579,1943,1571	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRP1	NM_001034915.2,NM_001122825.1,NM_001122826.1,NM_001122827.1,NM_017697.3	,,,,	600,2294,3066	TT,TC,CC		37.8817,10.5249,29.3121	,,,,	328/678,328/609,328/660,328/605,328/682	95680229	3494,8426	1867	4093	5960	SO:0001819	synonymous_variant	54845	exon10			CATTGTCCGCATG	AK000178	CCDS47895.1, CCDS47896.1, CCDS47897.1, CCDS47898.1	8q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000104413	ENSG00000104413		"""RNA binding motif (RRM) containing"""	25966	protein-coding gene	gene with protein product		612959	"""RNA binding motif protein 35A"""	RBM35A		12477932	Standard	NM_017697		Approved	FLJ20171	uc003ygq.4	Q6NXG1	OTTHUMG00000164587	ENST00000433389.2:c.984C>T	8.37:g.95680229C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	138	61	0.442029	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Silent	SNP	ENST00000433389.2	37	CCDS47897.1	780	0.35714285714285715	28	0.056910569105691054	135	0.3729281767955801	307	0.5367132867132867	310	0.40897097625329815	C	9.611	1.131193	0.21041	0.105249	0.378817	ENSG00000104413	ENST00000519505	.	.	.	5.78	-0.637	0.11504	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47761	-0.9092	3	.	.	.	-9.6706	9.8714	0.41177	0.0:0.28:0.5332:0.1868	rs1549466;rs17717111;rs1549466	.	.	.	S	194	.	.	P	+	1	0	ESRP1	95749405	0.112000	0.22096	0.981000	0.43875	0.994000	0.84299	-0.523000	0.06230	-0.440000	0.07211	-0.302000	0.09304	CCG	C|0.648;T|0.352	0.352	strong		0.483	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697	
CIITA	4261	hgsc.bcm.edu	37	16	11000848	11000848	+	Missense_Mutation	SNP	G	G	C	rs4774	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:11000848G>C	ENST00000324288.8	+	11	1632	c.1499G>C	c.(1498-1500)gGc>gCc	p.G500A	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	500	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		G -> A (in dbSNP:rs4774). {ECO:0000269|PubMed:12859996, ECO:0000269|PubMed:7749984, ECO:0000269|PubMed:8402893}.		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						ATCCTAGACGGCTTCGAGGAG	0.647			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								C|||	1297	0.258986	0.2663	0.428	5008	,	,		17451	0.1329		0.2724	False		,,,				2504	0.2454				p.G500A		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	CIITA_ENST00000324288,NS,carcinoma,0,1	CIITA	92	1	0			c.G1499C						PASS	.	C	ALA/GLY	1130,3264		148,834,1215	66.0	70.0	69.0		1499	-0.8	0.0	16	dbSNP_52	69	2514,6086		389,1736,2175	yes	missense	CIITA	NM_000246.3	60	537,2570,3390	CC,CG,GG		29.2326,25.7169,28.0437	benign	500/1131	11000848	3644,9350	2197	4300	6497	SO:0001583	missense	4261	exon11			TAGACGGCTTCGA	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.1499G>C	16.37:g.11000848G>C	ENSP00000316328:p.Gly500Ala	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	573	0.2623626373626374	139	0.28252032520325204	136	0.3756906077348066	81	0.14160839160839161	217	0.2862796833773087	C	0.011	-1.704285	0.00719	0.257169	0.292326	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.81415	-1.49	5.27	-0.799	0.10901	NACHT nucleoside triphosphatase (1);	0.377447	0.22470	N	0.059640	T	0.00012	0.0000	N	0.25957	0.775	0.58432	P	6.999999999979245E-6	B;B;B	0.13145	0.001;0.007;0.0	B;B;B	0.19148	0.012;0.024;0.005	T	0.37663	-0.9696	9	0.22109	T	0.4	.	24.3173	0.99989	0.0:0.1936:0.8064:0.0	rs4774;rs1135817;rs2228237;rs3198759;rs59312217;rs4774	500;500;452	A0N0N9;P33076;F2Z2G8	.;C2TA_HUMAN;.	A	500;452	ENSP00000316328:G500A	ENSP00000316328:G500A	G	+	2	0	CIITA	10908349	0.872000	0.30054	0.011000	0.14972	0.405000	0.30901	0.706000	0.25690	-0.719000	0.04942	-0.216000	0.12614	GGC	G|0.737;C|0.263	0.263	strong		0.647	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
FBXL19	54620	hgsc.bcm.edu	37	16	30936081	30936081	+	Missense_Mutation	SNP	G	G	A	rs35675346	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30936081G>A	ENST00000380310.2	+	1	186	c.28G>A	c.(28-30)Gaa>Aaa	p.E10K	FBXL19_ENST00000565690.1_5'Flank|FBXL19-AS1_ENST00000563777.1_RNA|FBXL19_ENST00000338343.4_Intron|FBXL19_ENST00000471231.2_Intron|FBXL19_ENST00000562319.1_5'UTR	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	10					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						CGGAAAGGGGGAATCTGGGGT	0.632													g|||	1670	0.333466	0.2943	0.3501	5008	,	,		13277	0.0863		0.2505	False		,,,				2504	0.7147				p.E10K		Atlas-SNP	.											.	FBXL19	74	.	0			c.G28A						PASS	.		LYS/GLU	1003,2613		141,721,946	27.0	29.0	28.0		28	3.9	1.0	16	dbSNP_126	28	1843,6301		225,1393,2454	yes	missense	FBXL19	NM_001099784.2	56	366,2114,3400	AA,AG,GG		22.6302,27.7378,24.2007	benign	10/695	30936081	2846,8914	1808	4072	5880	SO:0001583	missense	54620	exon1			AAGGGGGAATCTG	AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"""F-boxes / Leucine-rich repeats"""	25300	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1C"""	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.28G>A	16.37:g.30936081G>A	ENSP00000369666:p.Glu10Lys	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	40	16	0.4	NM_001099784	A8MT10|Q8N789|Q9NT14	Missense_Mutation	SNP	ENST00000380310.2	37	CCDS45465.1	481	0.22023809523809523	138	0.2804878048780488	113	0.31215469613259667	37	0.06468531468531469	193	0.2546174142480211	g	11.95	1.791506	0.31685	0.277378	0.226302	ENSG00000099364	ENST00000380310	T	0.16457	2.34	3.88	3.88	0.44766	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.45648	P	0.001422999999999952	B	0.23377	0.084	B	0.14023	0.01	T	0.35475	-0.9787	8	0.02654	T	1	.	11.6992	0.51560	0.0:0.0:1.0:0.0	rs35675346;rs35675346	10	Q6PCT2	FXL19_HUMAN	K	10	ENSP00000369666:E10K	ENSP00000369666:E10K	E	+	1	0	FBXL19	30843582	0.435000	0.25577	0.961000	0.40146	0.626000	0.37791	0.240000	0.18042	1.850000	0.53721	0.306000	0.20318	GAA	G|0.772;A|0.228	0.228	strong		0.632	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085	
ACSBG1	23205	hgsc.bcm.edu	37	15	78466127	78466127	+	Missense_Mutation	SNP	T	T	C	rs2304824	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78466127T>C	ENST00000258873.4	-	13	2102	c.1897A>G	c.(1897-1899)Atg>Gtg	p.M633V	ACSBG1_ENST00000541759.1_Missense_Mutation_p.M391V|ACSBG1_ENST00000560817.1_Missense_Mutation_p.M391V	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	633			M -> V (in dbSNP:rs2304824). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811, ECO:0000269|Ref.6}.		long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						CAGAACTCCATAGCTTGTTCA	0.537													C|||	2638	0.526757	0.73	0.4409	5008	,	,		21424	0.2867		0.498	False		,,,				2504	0.59				p.M633V		Atlas-SNP	.											.	ACSBG1	79	.	0			c.A1897G						PASS	.	C	VAL/MET,VAL/MET	3021,1371	453.4+/-350.3	1031,959,206	77.0	67.0	70.0		1885,1897	-0.0	0.4	15	dbSNP_100	70	4289,4297	576.6+/-390.4	1074,2141,1078	yes	missense,missense	ACSBG1	NM_001199377.1,NM_015162.4	21,21	2105,3100,1284	CC,CT,TT		49.9534,31.2158,43.6739	benign,benign	629/721,633/725	78466127	7310,5668	2196	4293	6489	SO:0001583	missense	23205	exon13			ACTCCATAGCTTG	AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.1897A>G	15.37:g.78466127T>C	ENSP00000258873:p.Met633Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	116	49	0.422414	NM_015162	B2RB61|O75126|Q76N27|Q9HC26	Missense_Mutation	SNP	ENST00000258873.4	37	CCDS10298.1	1073	0.4913003663003663	358	0.7276422764227642	175	0.48342541436464087	165	0.28846153846153844	375	0.4947229551451187	C	1.769	-0.484813	0.04352	0.687842	0.499534	ENSG00000103740	ENST00000258873;ENST00000541759	T;T	0.34275	1.71;1.37	5.35	-0.0403	0.13872	.	0.487637	0.19405	N	0.115080	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	0.33727	-0.9857	9	0.12103	T	0.63	-14.1277	0.1445	0.00087	0.2497:0.228:0.2448:0.2775	rs2304824;rs17605786;rs17855404;rs61080752;rs2304824	633	Q96GR2	ACBG1_HUMAN	V	633;391	ENSP00000258873:M633V;ENSP00000439955:M391V	ENSP00000258873:M633V	M	-	1	0	ACSBG1	76253182	0.000000	0.05858	0.394000	0.26270	0.853000	0.48598	-0.598000	0.05706	0.105000	0.17753	-0.186000	0.12905	ATG	T|0.468;C|0.532	0.532	strong		0.537	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	
SPOCD1	90853	hgsc.bcm.edu	37	1	32279629	32279629	+	Missense_Mutation	SNP	G	G	A	rs6669563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:32279629G>A	ENST00000360482.2	-	2	1435	c.1306C>T	c.(1306-1308)Cgg>Tgg	p.R436W	SPOCD1_ENST00000533231.1_Missense_Mutation_p.R436W|SPOCD1_ENST00000257100.3_Intron|SPOCD1_ENST00000373648.2_Missense_Mutation_p.R436W	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	436			R -> W (in dbSNP:rs6669563).		negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)			p.R436W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		TCTGTGCCCCGGTCTTGGGCA	0.592													G|||	1734	0.346246	0.1876	0.4957	5008	,	,		18940	0.4226		0.4374	False		,,,				2504	0.2822				p.R436W		Atlas-SNP	.											SPOCD1,NS,carcinoma,0,2	SPOCD1	109	2	1	Substitution - Missense(1)	stomach(1)	c.C1306T						PASS	.	G	TRP/ARG	990,3416	365.9+/-317.6	118,754,1331	59.0	62.0	61.0		1306	0.2	0.0	1	dbSNP_116	61	3765,4835	527.7+/-381.2	804,2157,1339	yes	missense	SPOCD1	NM_144569.4	101	922,2911,2670	AA,AG,GG		43.7791,22.4694,36.56	probably-damaging	436/1217	32279629	4755,8251	2203	4300	6503	SO:0001583	missense	90853	exon2			TGCCCCGGTCTTG	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.1306C>T	1.37:g.32279629G>A	ENSP00000353670:p.Arg436Trp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	111	6	0.0540541	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	865	0.39606227106227104	106	0.21544715447154472	161	0.4447513812154696	260	0.45454545454545453	338	0.44591029023746703	G	10.09	1.254901	0.22965	0.224694	0.437791	ENSG00000134668	ENST00000360482;ENST00000373648;ENST00000533231	T;T;T	0.34275	1.84;1.37;1.84	3.25	0.152	0.14893	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;P	0.44044	0.825;0.733	B;B	0.36959	0.237;0.12	T	0.45011	-0.9290	8	0.87932	D	0	9.782	3.8093	0.08791	0.2419:0.202:0.556:0.0	rs6669563;rs6669563	436;436	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	W	436	ENSP00000353670:R436W;ENSP00000362752:R436W;ENSP00000435851:R436W	ENSP00000353670:R436W	R	-	1	2	SPOCD1	32052216	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	0.049000	0.14099	0.044000	0.15775	0.455000	0.32223	CGG	G|0.624;A|0.376	0.376	strong		0.592	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569	
RPTOR	57521	hgsc.bcm.edu	37	17	78854223	78854223	+	Silent	SNP	A	A	G	rs2289759	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:78854223A>G	ENST00000306801.3	+	14	1880	c.1518A>G	c.(1516-1518)caA>caG	p.Q506Q	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Intron	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	506					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						AGTCGTGCCAAGCGGACCTCG	0.597													G|||	1242	0.248003	0.1188	0.245	5008	,	,		17803	0.3879		0.2515	False		,,,				2504	0.2771				p.Q506Q		Atlas-SNP	.											.	RPTOR	122	.	0			c.A1518G						PASS	.	G	,	660,3746	763.9+/-413.2	56,548,1599	106.0	78.0	87.0		,1518	-1.3	1.0	17	dbSNP_100	87	2241,6359	708.6+/-405.7	287,1667,2346	no	intron,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	343,2215,3945	GG,GA,AA		26.0581,14.9796,22.3051	,	,506/1336	78854223	2901,10105	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon14			GTGCCAAGCGGAC		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.1518A>G	17.37:g.78854223A>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	110	48	0.436364	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			A|0.768;G|0.232	0.232	strong		0.597	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
ENPP5	59084	hgsc.bcm.edu	37	6	46135984	46135984	+	Missense_Mutation	SNP	G	G	T	rs3806995	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46135984G>T	ENST00000371383.2	-	3	276	c.16C>A	c.(16-18)Ctc>Atc	p.L6I	ENPP5_ENST00000492313.1_5'Flank|ENPP5_ENST00000230565.3_Missense_Mutation_p.L6I					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GACACCAAGAGAAATTTCGAA	0.348													G|||	2225	0.444289	0.1899	0.4467	5008	,	,		17819	0.4494		0.5298	False		,,,				2504	0.6933				p.L6I		Atlas-SNP	.											.	ENPP5	44	.	0			c.C16A						PASS	.	G	ILE/LEU	943,3191		113,717,1237	65.0	67.0	66.0		16	3.4	0.0	6	dbSNP_107	66	4445,4071		1170,2105,983	yes	missense	ENPP5	NM_021572.4	5	1283,2822,2220	TT,TG,GG		47.8041,22.8108,42.5929	benign	6/478	46135984	5388,7262	2067	4258	6325	SO:0001583	missense	59084	exon2			CCAAGAGAAATTT	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.16C>A	6.37:g.46135984G>T	ENSP00000360436:p.Leu6Ile	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_021572		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	908	0.4157509157509158	95	0.19308943089430894	178	0.49171270718232046	231	0.40384615384615385	404	0.5329815303430079	G	5.728	0.318747	0.10845	0.228108	0.521959	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.74632	-0.86;-0.86	5.26	3.41	0.39046	.	1.187990	0.05858	N	0.622403	T	0.39009	0.1062	N	0.19112	0.55	0.80722	P	0.0	B	0.13594	0.008	B	0.12837	0.008	T	0.17868	-1.0355	9	0.34782	T	0.22	-4.3671	5.3566	0.16065	0.0787:0.3349:0.4595:0.1268	rs3806995;rs52837713;rs60345511;rs3806995	6	Q9UJA9	ENPP5_HUMAN	I	6	ENSP00000360436:L6I;ENSP00000230565:L6I	ENSP00000230565:L6I	L	-	1	0	ENPP5	46243943	0.209000	0.23505	0.015000	0.15790	0.108000	0.19459	1.068000	0.30629	1.305000	0.44909	0.591000	0.81541	CTC	G|0.573;T|0.427	0.427	strong		0.348	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
ABCG8	64241	hgsc.bcm.edu	37	2	44079606	44079606	+	Silent	SNP	G	G	A	rs9282575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:44079606G>A	ENST00000272286.2	+	5	765	c.675G>A	c.(673-675)gtG>gtA	p.V225V		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	225	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	GCATTGGGGTGCAGCTCCTGT	0.687													G|||	233	0.0465256	0.0711	0.0331	5008	,	,		15945	0.001		0.0358	False		,,,				2504	0.0808				p.V225V		Atlas-SNP	.											.	ABCG8	98	.	0			c.G675A						PASS	.	G		281,4125	152.5+/-186.2	12,257,1934	34.0	40.0	38.0		675	1.4	1.0	2	dbSNP_118	38	417,8183	128.7+/-186.9	10,397,3893	no	coding-synonymous	ABCG8	NM_022437.2		22,654,5827	AA,AG,GG		4.8488,6.3777,5.3668		225/674	44079606	698,12308	2203	4300	6503	SO:0001819	synonymous_variant	64241	exon5			TGGGGTGCAGCTC	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.675G>A	2.37:g.44079606G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	37	CCDS1815.1																																																																																			G|0.949;A|0.051	0.051	strong		0.687	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
OR2T3	343173	hgsc.bcm.edu	37	1	248637046	248637046	+	Missense_Mutation	SNP	G	G	A	rs148025314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248637046G>A	ENST00000359594.2	+	1	420	c.395G>A	c.(394-396)tGc>tAc	p.C132Y		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	132						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCTGCTGTTTGCAGACCTCTC	0.557																																					p.C132Y		Atlas-SNP	.											.	OR2T3	79	.	0			c.G395A						PASS	.						38.0	36.0	37.0					1																	248637046		2193	4282	6475	SO:0001583	missense	343173	exon1			CTGTTTGCAGACC		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.395G>A	1.37:g.248637046G>A	ENSP00000352604:p.Cys132Tyr	Somatic	480	0	0		WXS	Illumina HiSeq	Phase_I	490	164	0.334694	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	643	0.2944139194139194	127	0.258130081300813	102	0.281767955801105	241	0.42132867132867136	173	0.22823218997361477	g	15.47	2.843842	0.51164	.	.	ENSG00000196539	ENST00000359594	T	0.02158	4.42	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	M	0.90425	3.115	0.33216	P	0.445929	D	0.89917	1.0	D	0.91635	0.999	T	0.43294	-0.9400	8	0.87932	D	0	.	11.721	0.51683	0.0:0.0:1.0:0.0	.	132	Q8NH03	OR2T3_HUMAN	Y	132	ENSP00000352604:C132Y	ENSP00000352604:C132Y	C	+	2	0	OR2T3	246703669	1.000000	0.71417	0.002000	0.10522	0.045000	0.14185	6.128000	0.71650	1.014000	0.39417	0.186000	0.17326	TGC	G|0.744;A|0.256	0.256	strong		0.557	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
LOXHD1	125336	hgsc.bcm.edu	37	18	44143153	44143153	+	Missense_Mutation	SNP	C	C	T	rs36086089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:44143153C>T	ENST00000398722.4	-	11	1638	c.1639G>A	c.(1639-1641)Gtg>Atg	p.V547M	LOXHD1_ENST00000441551.2_Missense_Mutation_p.V825M|LOXHD1_ENST00000536736.1_Missense_Mutation_p.V825M			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	547	PLAT 5. {ECO:0000255|PROSITE- ProRule:PRU00152}.		V -> M (in dbSNP:rs36086089).		calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						GCGCCACCCACATCTCCTGTC	0.468													C|||	417	0.0832668	0.1377	0.0519	5008	,	,		19876	0.001		0.0855	False		,,,				2504	0.1145				p.V825M		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G2473A						PASS	.	C	MET/VAL	194,1190		14,166,512	47.0	42.0	44.0		2473	4.1	0.8	18	dbSNP_126	44	276,2906		10,256,1325	yes	missense	LOXHD1	NM_144612.6	21	24,422,1837	TT,TC,CC		8.6738,14.0173,10.2935	benign	825/2212	44143153	470,4096	692	1591	2283	SO:0001583	missense	125336	exon18			CACCCACATCTCC	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1639G>A	18.37:g.44143153C>T	ENSP00000381707:p.Val547Met	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		159|159	0.07280219780219781|0.07280219780219781	71|71	0.1443089430894309|0.1443089430894309	19|19	0.052486187845303865|0.052486187845303865	0|0	0.0|0.0	69|69	0.09102902374670185|0.09102902374670185	C|C	11.71|11.71	1.721028|1.721028	0.30503|0.30503	0.140173|0.140173	0.086738|0.086738	ENSG00000167210|ENSG00000167210	ENST00000441551|ENST00000398722;ENST00000536736;ENST00000335730	.|T;T	.|0.64085	.|-0.08;-0.08	5.05|5.05	4.05|4.05	0.47172|0.47172	.|.	.|0.252404	.|0.41001	.|D	.|0.000970	T|T	0.00412|0.00412	0.0013|0.0013	L|L	0.28556|0.28556	0.865|0.865	0.09310|0.09310	P|P	1.0|1.0	.|B;B	.|0.32753	.|0.194;0.383	.|B;B	.|0.27608	.|0.056;0.081	T|T	0.14282|0.14282	-1.0478|-1.0478	4|9	.|0.45353	.|T	.|0.12	.|.	10.07|10.07	0.42328|0.42328	0.0:0.8682:0.0:0.1318|0.0:0.8682:0.0:0.1318	rs36086089;rs58426200|rs36086089;rs58426200	.|825;547	.|F5GZB4;Q8IVV2-2	.|.;.	Y|M	805|547;825;547	.|ENSP00000381707:V547M;ENSP00000444586:V825M	.|ENSP00000338222:V547M	C|V	-|-	2|1	0|0	LOXHD1|LOXHD1	42397151|42397151	0.198000|0.198000	0.23374|0.23374	0.755000|0.755000	0.31263|0.31263	0.949000|0.949000	0.60115|0.60115	0.749000|0.749000	0.26320|0.26320	2.351000|2.351000	0.79841|0.79841	0.484000|0.484000	0.47621|0.47621	TGT|GTG	C|0.919;T|0.081	0.081	strong		0.468	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
CYP2C18	1562	hgsc.bcm.edu	37	10	96447920	96447920	+	Missense_Mutation	SNP	C	C	T	rs117111102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:96447920C>T	ENST00000285979.6	+	3	569	c.370C>T	c.(370-372)Cgg>Tgg	p.R124W	CYP2C18_ENST00000339022.5_Missense_Mutation_p.R124W|CYP2C19_ENST00000464755.1_3'UTR	NM_000772.2	NP_000763.1	P33260	CP2CI_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 18	124					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	26		Colorectal(252;0.09)		all cancers(201;2.8e-06)|KIRC - Kidney renal clear cell carcinoma(50;0.0646)|Kidney(138;0.0805)	Aminophenazone(DB01424)|Antipyrine(DB01435)|Buprenorphine(DB00921)|Clobazam(DB00349)|Clotiazepam(DB01559)|Cyclophosphamide(DB00531)|Dapsone(DB00250)|Desipramine(DB01151)|Diazepam(DB00829)|Diclofenac(DB00586)|Diphenhydramine(DB01075)|Ifosfamide(DB01181)|Imipramine(DB00458)|Lansoprazole(DB00448)|Lidocaine(DB00281)|Methadone(DB00333)|Omeprazole(DB00338)|Pegvisomant(DB00082)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Propofol(DB00818)|Tolbutamide(DB01124)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vilazodone(DB06684)|Warfarin(DB00682)	GAAGGAGATCCGGCGTTTCTG	0.512													C|||	33	0.00658946	0.0015	0.0043	5008	,	,		15683	0.0129		0.0119	False		,,,				2504	0.0031				p.R124W		Atlas-SNP	.											.	CYP2C18	79	.	0			c.C370T						PASS	.	C	TRP/ARG,TRP/ARG	13,4393	20.2+/-43.8	0,13,2190	114.0	104.0	107.0		370,370	0.3	0.0	10	dbSNP_132	107	123,8477	64.9+/-127.2	1,121,4178	yes	missense,missense	CYP2C18	NM_000772.2,NM_001128925.1	101,101	1,134,6368	TT,TC,CC		1.4302,0.2951,1.0457	,	124/491,124/432	96447920	136,12870	2203	4300	6503	SO:0001583	missense	1562	exon3			GAGATCCGGCGTT	M61853	CCDS7435.1, CCDS44460.1	10q24	2003-11-12	2003-01-14		ENSG00000108242	ENSG00000108242		"""Cytochrome P450s"""	2620	protein-coding gene	gene with protein product		601131	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 18"""	CYP2C17		1896026, 2009263	Standard	NM_000772		Approved	P450IIC17, CPCI, CYP2C		P33260	OTTHUMG00000018796	ENST00000285979.6:c.370C>T	10.37:g.96447920C>T	ENSP00000285979:p.Arg124Trp	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	229	105	0.458515	NM_000772	B2R8K2|Q16703|Q16751|Q4VAT5|Q6GRG1	Missense_Mutation	SNP	ENST00000285979.6	37	CCDS7435.1	17	0.007783882783882784	1	0.0020325203252032522	2	0.0055248618784530384	8	0.013986013986013986	6	0.0079155672823219	c	15.57	2.872772	0.51695	0.002951	0.014302	ENSG00000108242	ENST00000339022;ENST00000285979	T;T	0.42513	0.97;0.97	4.63	0.268	0.15626	.	0.000000	0.64402	U	0.000002	T	0.65780	0.2724	H	0.98833	4.345	0.09310	N	0.999996	P;D	0.89917	0.494;1.0	B;D	0.71414	0.196;0.973	T	0.62469	-0.6848	10	0.87932	D	0	.	7.1123	0.25396	0.5723:0.3418:0.0:0.0859	.	124;124	Q4VAT5;P33260	.;CP2CI_HUMAN	W	124	ENSP00000341293:R124W;ENSP00000285979:R124W	ENSP00000285979:R124W	R	+	1	2	CYP2C18	96437910	0.001000	0.12720	0.000000	0.03702	0.803000	0.45373	-0.089000	0.11180	-0.264000	0.09365	0.306000	0.20318	CGG	C|0.990;T|0.010	0.010	strong		0.512	CYP2C18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049486.1	NM_000772	
TCP10L2	401285	hgsc.bcm.edu	37	6	167585654	167585654	+	Missense_Mutation	SNP	G	G	A	rs142318145	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167585654G>A	ENST00000366832.2	+	2	153	c.22G>A	c.(22-24)Gcc>Acc	p.A8T		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	8										endometrium(1)|kidney(2)|lung(3)	6						TCAGCTCGAGGCCAGGGAGCC	0.672													G|||	75	0.014976	0.0083	0.0216	5008	,	,		17957	0.0		0.0298	False		,,,				2504	0.0194				p.A8T		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G22A						PASS	.	G	THR/ALA	23,1361		0,23,669	22.0	33.0	29.0		22	1.7	0.0	6	dbSNP_134	29	78,3104		3,72,1516	no	missense	TCP10L2	NM_001145121.1	58	3,95,2185	AA,AG,GG		2.4513,1.6618,2.212	benign	8/354	167585654	101,4465	692	1591	2283	SO:0001583	missense	401285	exon2			CTCGAGGCCAGGG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.22G>A	6.37:g.167585654G>A	ENSP00000355797:p.Ala8Thr	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	92	14	0.152174	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	38	0.0173992673992674	4	0.008130081300813009	8	0.022099447513812154	0	0.0	26	0.03430079155672823	g	11.39	1.625678	0.28889	0.016618	0.024513	ENSG00000166984	ENST00000486697;ENST00000366832	T	0.19938	2.11	2.61	1.69	0.24217	.	.	.	.	.	T	0.05135	0.0137	L	0.51422	1.61	0.09310	N	1	P	0.40731	0.728	B	0.32342	0.144	T	0.32079	-0.9920	9	0.21540	T	0.41	.	7.2095	0.25925	0.0:0.2794:0.7206:0.0	.	8	B9ZVM9	TCP2L_HUMAN	T	8	ENSP00000355797:A8T	ENSP00000283507:A8T	A	+	1	0	TCP10L2	167505644	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	0.226000	0.17776	0.388000	0.25054	0.416000	0.27883	GCC	G|0.982;A|0.018	0.018	strong		0.672	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
PHF2	5253	hgsc.bcm.edu	37	9	96407983	96407983	+	Silent	SNP	C	C	T	rs9695734	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:96407983C>T	ENST00000359246.4	+	4	739	c.372C>T	c.(370-372)acC>acT	p.T124T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	124					liver development (GO:0001889)|negative regulation of chromatin silencing at rDNA (GO:0061188)|protein demethylation (GO:0006482)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K9 specific) (GO:0032454)|iron ion binding (GO:0005506)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;9.11e-28)		ACGGCTTCACCGAGCCCATCC	0.622													C|||	530	0.105831	0.1241	0.0764	5008	,	,		20102	0.0506		0.161	False		,,,				2504	0.1022				p.T124T		Atlas-SNP	.											PHF2,NS,carcinoma,0,1	PHF2	113	1	0			c.C372T						PASS	.	C		536,3870	244.3+/-253.7	28,480,1695	81.0	75.0	77.0		372	-9.2	0.2	9	dbSNP_119	77	1498,7102	284.7+/-296.8	119,1260,2921	yes	coding-synonymous	PHF2	NM_005392.3		147,1740,4616	TT,TC,CC		17.4186,12.1652,15.6389		124/1097	96407983	2034,10972	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon4			CTTCACCGAGCCC	AF043725	CCDS35069.1	9q22	2013-01-28			ENSG00000197724	ENSG00000197724		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	8920	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1E"", ""centromere protein 35"""	604351				10051327, 20129925	Standard	NM_005392		Approved	KIAA0662, JHDM1E, CENP-35	uc004aub.3	O75151	OTTHUMG00000020253	ENST00000359246.4:c.372C>T	9.37:g.96407983C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			C|0.853;T|0.147	0.147	strong		0.622	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392	
PCDHAC1	56135	hgsc.bcm.edu	37	5	140307284	140307284	+	Silent	SNP	G	G	A	rs155361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140307284G>A	ENST00000253807.2	+	1	807	c.807G>A	c.(805-807)caG>caA	p.Q269Q	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.Q269Q|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	269	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGAAGTCCAGTACTCCCTAA	0.552													a|||	2868	0.572684	0.7231	0.5865	5008	,	,		20798	0.6071		0.5169	False		,,,				2504	0.3814				p.Q269Q		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.G807A						PASS	.	A	,,,,,,,,,,,,,,,,,	3126,1280	435.7+/-344.4	1109,908,186	82.0	76.0	78.0		807,,,,,,,,,,,,,,,,,807	2.5	1.0	5	dbSNP_79	78	4374,4226	572.3+/-389.7	1091,2192,1017	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	2200,3100,1203	AA,AG,GG		49.1395,29.0513,42.3343	,,,,,,,,,,,,,,,,,	269/964,,,,,,,,,,,,,,,,,269/819	140307284	7500,5506	2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			AGTCCAGTACTCC	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.807G>A	5.37:g.140307284G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			G|0.421;A|0.579	0.579	strong		0.552	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
IGSF10	285313	hgsc.bcm.edu	37	3	151165678	151165678	+	Silent	SNP	T	T	C	rs9871952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:151165678T>C	ENST00000282466.3	-	4	2090	c.2091A>G	c.(2089-2091)caA>caG	p.Q697Q		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	697					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ATGTACGGAGTTGTGCACCTG	0.498													C|||	3938	0.786342	0.8185	0.7695	5008	,	,		20283	0.7649		0.7724	False		,,,				2504	0.7914				p.Q697Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.A2091G						PASS	.	C		3583,823	330.4+/-301.5	1464,655,84	75.0	70.0	72.0		2091	-10.5	0.0	3	dbSNP_119	72	6533,2067	357.9+/-330.9	2494,1545,261	no	coding-synonymous	IGSF10	NM_178822.4		3958,2200,345	CC,CT,TT		24.0349,18.6791,22.2205		697/2624	151165678	10116,2890	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon4			ACGGAGTTGTGCA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.2091A>G	3.37:g.151165678T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	174	173	0.994253	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			T|0.213;C|0.787	0.787	strong		0.498	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
TNNT1	7138	hgsc.bcm.edu	37	19	55658387	55658387	+	Missense_Mutation	SNP	T	T	C	rs112562759	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55658387T>C	ENST00000588981.1	-	3	239	c.35A>G	c.(34-36)gAg>gGg	p.E12G	TNNT1_ENST00000291901.8_Missense_Mutation_p.E12G|TNNT1_ENST00000585321.2_5'Flank|TNNT1_ENST00000356783.5_Missense_Mutation_p.E12G|TNNT1_ENST00000587758.1_Missense_Mutation_p.E12G|TNNT1_ENST00000592920.1_5'UTR|TNNT1_ENST00000587465.2_5'Flank|TNNT1_ENST00000588426.1_Missense_Mutation_p.S4G|TNNT1_ENST00000536926.1_Missense_Mutation_p.E12G	NM_003283.4	NP_003274.3	P13805	TNNT1_HUMAN	troponin T type 1 (skeletal, slow)	12					muscle filament sliding (GO:0030049)|negative regulation of muscle contraction (GO:0045932)|skeletal muscle contraction (GO:0003009)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	cytosol (GO:0005829)|troponin complex (GO:0005861)	tropomyosin binding (GO:0005523)			endometrium(2)|kidney(3)|lung(4)|ovary(1)	10			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		TTCCGGCTGCTCCCTGCGGAC	0.687													t|||	180	0.0359425	0.0053	0.0533	5008	,	,		11636	0.0		0.0984	False		,,,				2504	0.0378				p.E12G		Atlas-SNP	.											.	TNNT1	28	.	0			c.A35G						PASS	.		GLY/GLU,GLY/GLU,GLY/GLU	77,4329	62.9+/-100.1	1,75,2127	38.0	35.0	36.0		35,35,35	2.1	1.0	19	dbSNP_132	36	840,7760	174.3+/-224.6	45,750,3505	yes	missense,missense,missense	TNNT1	NM_003283.4,NM_001126133.1,NM_001126132.1	98,98,98	46,825,5632	CC,CT,TT		9.7674,1.7476,7.0506	benign,benign,benign	12/279,12/252,12/263	55658387	917,12089	2203	4300	6503	SO:0001583	missense	7138	exon3			GGCTGCTCCCTGC		CCDS12917.1, CCDS46185.1, CCDS59421.1	19q13.4	2014-09-17	2005-09-12			ENSG00000105048			11948	protein-coding gene	gene with protein product	"""slow skeletal muscle troponin T"", ""troponin T1, skeletal, slow"", ""nemaline myopathy type 5"""	191041	"""troponin T1, skeletal, slow"""			1505979	Standard	XM_006723343		Approved	ANM, STNT, TNT, TNTS, FLJ98147, MGC104241, NEM5	uc002qjb.4	P13805		ENST00000588981.1:c.35A>G	19.37:g.55658387T>C	ENSP00000467176:p.Glu12Gly	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	166	87	0.524096	NM_001126132	O95472|Q16061|Q5U0E1	Missense_Mutation	SNP	ENST00000588981.1	37	CCDS12917.1	96	0.04395604395604396	3	0.006097560975609756	18	0.049723756906077346	0	0.0	75	0.09894459102902374	t	16.12	3.032760	0.54790	0.017476	0.097674	ENSG00000105048	ENST00000291901;ENST00000356783;ENST00000536926;ENST00000429737	D;D;D	0.99663	-6.33;-5.15;-5.15	2.1	2.1	0.27182	.	0.000000	0.51477	U	0.000088	T	0.70692	0.3253	L	0.54323	1.7	0.44579	D	0.997542	B;B;B;B	0.18741	0.03;0.02;0.02;0.03	B;B;B;B	0.08055	0.002;0.003;0.003;0.002	T	0.83074	-0.0141	10	0.54805	T	0.06	-6.0213	6.2044	0.20593	0.0:0.0:0.0:1.0	.	12;12;12;12	Q56R94;P13805-2;P13805-3;P13805	.;.;.;TNNT1_HUMAN	G	12;12;12;31	ENSP00000291901:E12G;ENSP00000349233:E12G;ENSP00000439640:E12G	ENSP00000291901:E12G	E	-	2	0	TNNT1	60350199	1.000000	0.71417	0.995000	0.50966	0.468000	0.32798	2.013000	0.40942	1.227000	0.43598	0.324000	0.21423	GAG	T|0.942;C|0.058	0.058	strong		0.687	TNNT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451825.2	NM_003283	
MUC6	4588	hgsc.bcm.edu	37	11	1013987	1013987	+	Missense_Mutation	SNP	G	G	A	rs10902268	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1013987G>A	ENST00000421673.2	-	32	7104	c.7054C>T	c.(7054-7056)Cgg>Tgg	p.R2352W		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2352	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				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)		TGCTGCTCCCGCACACTGCAG	0.662													G|||	608	0.121406	0.0681	0.2579	5008	,	,		16970	0.1607		0.0984	False		,,,				2504	0.0798				p.R2352W		Atlas-SNP	.											.	MUC6	408	.	0			c.C7054T						PASS	.	G	TRP/ARG	283,3923		3,277,1823	23.0	27.0	25.0		7054	-1.4	0.0	11	dbSNP_120	25	739,7667		29,681,3493	yes	missense	MUC6	NM_005961.2	101	32,958,5316	AA,AG,GG		8.7913,6.7285,8.1034	probably-damaging	2352/2440	1013987	1022,11590	2103	4203	6306	SO:0001583	missense	4588	exon32			GCTCCCGCACACT	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.7054C>T	11.37:g.1013987G>A	ENSP00000406861:p.Arg2352Trp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	285	0.1304945054945055	35	0.07113821138211382	76	0.20994475138121546	96	0.16783216783216784	78	0.10290237467018469	G	8.606	0.888082	0.17540	0.067285	0.087913	ENSG00000184956	ENST00000421673	T	0.20332	2.08	3.81	-1.4	0.08968	Cystine knot, C-terminal (2);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.56968	0.978	B	0.37422	0.249	T	0.40327	-0.9569	8	0.59425	D	0.04	.	5.5228	0.16941	0.129:0.0:0.4081:0.4629	rs10902268	2352	Q6W4X9	MUC6_HUMAN	W	2352	ENSP00000406861:R2352W	ENSP00000406861:R2352W	R	-	1	2	MUC6	1003987	0.000000	0.05858	0.000000	0.03702	0.216000	0.24613	0.132000	0.15891	-0.353000	0.08224	0.453000	0.30009	CGG	G|0.877;A|0.123	0.123	strong		0.662	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
DAGLA	747	hgsc.bcm.edu	37	11	61511133	61511133	+	Silent	SNP	G	G	A	rs3741251	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:61511133G>A	ENST00000257215.5	+	20	2417	c.2301G>A	c.(2299-2301)gcG>gcA	p.A767A	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	767					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		AGCGGCTGGCGGCGGAGCTGC	0.716													G|||	902	0.180112	0.0772	0.2176	5008	,	,		9840	0.1478		0.163	False		,,,				2504	0.3436				p.A767A		Atlas-SNP	.											.	DAGLA	109	.	0			c.G2301A						PASS	.	G		307,3765		11,285,1740	17.0	22.0	20.0		2301	-6.2	0.0	11	dbSNP_107	20	1129,6939		80,969,2985	no	coding-synonymous	DAGLA	NM_006133.2		91,1254,4725	AA,AG,GG		13.9936,7.5393,11.8287		767/1043	61511133	1436,10704	2036	4034	6070	SO:0001819	synonymous_variant	747	exon20			GCTGGCGGCGGAG	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.2301G>A	11.37:g.61511133G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																			G|0.868;A|0.132	0.132	strong		0.716	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
C3orf18	51161	hgsc.bcm.edu	37	3	50598396	50598396	+	Silent	SNP	G	G	A	rs41291736	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50598396G>A	ENST00000357203.3	-	5	899	c.360C>T	c.(358-360)gaC>gaT	p.D120D	C3orf18_ENST00000426034.1_Silent_p.D120D|C3orf18_ENST00000486175.1_5'UTR|C3orf18_ENST00000422619.1_Silent_p.D68D|C3orf18_ENST00000449241.1_Silent_p.D120D|C3orf18_ENST00000441239.1_Silent_p.D100D	NM_016210.4	NP_057294.2	Q9UK00	CC018_HUMAN	chromosome 3 open reading frame 18	120						integral component of membrane (GO:0016021)				lung(1)|pancreas(1)|skin(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000278)|KIRC - Kidney renal clear cell carcinoma(197;0.0175)|Kidney(197;0.0207)		CAGAGGCGGCGTCCCGCCCAT	0.632													G|||	280	0.0559105	0.0242	0.0937	5008	,	,		18530	0.0		0.1243	False		,,,				2504	0.0593				p.D120D		Atlas-SNP	.											.	C3orf18	12	.	0			c.C360T						PASS	.	G	,,,	179,4227	115.9+/-153.8	2,175,2026	95.0	83.0	87.0		360,360,300,360	-4.8	0.1	3	dbSNP_127	87	1140,7460	234.9+/-267.6	68,1004,3228	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C3orf18	NM_001171740.2,NM_001171741.2,NM_001171743.2,NM_016210.4	,,,	70,1179,5254	AA,AG,GG		13.2558,4.0626,10.1415	,,,	120/163,120/163,100/143,120/163	50598396	1319,11687	2203	4300	6503	SO:0001819	synonymous_variant	51161	exon5			GGCGGCGTCCCGC	AF188706	CCDS2829.1, CCDS54589.1	3p21.3	2006-01-11			ENSG00000088543	ENSG00000088543			24837	protein-coding gene	gene with protein product						12477932	Standard	NM_016210		Approved	G20	uc010hlp.3	Q9UK00	OTTHUMG00000156854	ENST00000357203.3:c.360C>T	3.37:g.50598396G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_016210	C9JNP0	Silent	SNP	ENST00000357203.3	37	CCDS2829.1																																																																																			G|0.908;A|0.092	0.092	strong		0.632	C3orf18-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346260.2	NM_016210	
MUC4	4585	hgsc.bcm.edu	37	3	195513126	195513126	+	Silent	SNP	G	G	A	rs62282488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195513126G>A	ENST00000463781.3	-	2	5784	c.5325C>T	c.(5323-5325)acC>acT	p.T1775T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T1775T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CAGGAAGTGGGGTGGCGTGAG	0.592													.|||	468	0.0934505	0.0144	0.1023	5008	,	,		35328	0.0466		0.1958	False		,,,				2504	0.137				p.T1775T		Atlas-SNP	.											.	MUC4	1505	.	0			c.C5325T						PASS	.	G	,,	38,1346		0,38,654	62.0	60.0	60.0		,5325,		0.0	3	dbSNP_129	60	548,2634		55,438,1098	no	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	55,476,1752	AA,AG,GG		17.2219,2.7457,12.834	,,	,1775/5413,	195513126	586,3980	692	1591	2283	SO:0001819	synonymous_variant	4585	exon2			AAGTGGGGTGGCG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.5325C>T	3.37:g.195513126G>A		Somatic	673	1	0.00148588		WXS	Illumina HiSeq	Phase_I	478	120	0.251046	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.897;A|0.103	0.103	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CEP131	22994	hgsc.bcm.edu	37	17	79169641	79169641	+	Silent	SNP	G	G	A	rs61741559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79169641G>A	ENST00000269392.4	-	16	2266	c.2019C>T	c.(2017-2019)caC>caT	p.H673H	AZI1_ENST00000374782.3_Silent_p.H670H|AZI1_ENST00000575907.1_Silent_p.H673H|AZI1_ENST00000450824.2_Silent_p.H670H|RP11-455O6.2_ENST00000571085.1_RNA	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		673					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)			TCACCAGCTCGTGCTGCGCCT	0.642													G|||	619	0.123602	0.1815	0.0288	5008	,	,		18248	0.1379		0.0577	False		,,,				2504	0.1656				p.H670H		Atlas-SNP	.											.	AZI1	145	.	0			c.C2010T						PASS	.	G	,	676,3730	284.0+/-277.4	51,574,1578	121.0	99.0	107.0		2010,2010	-8.2	0.0	17	dbSNP_129	107	467,8133	138.3+/-195.1	16,435,3849	no	coding-synonymous,coding-synonymous	AZI1	NM_001009811.2,NM_014984.2	,	67,1009,5427	AA,AG,GG		5.4302,15.3427,8.7883	,	670/1045,670/1081	79169641	1143,11863	2203	4300	6503	SO:0001819	synonymous_variant	22994	exon16			CAGCTCGTGCTGC																												ENST00000269392.4:c.2019C>T	17.37:g.79169641G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	51	23	0.45098	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																				G|0.907;A|0.093	0.093	strong		0.642	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
FBXW8	26259	hgsc.bcm.edu	37	12	117402583	117402583	+	Missense_Mutation	SNP	G	G	C	rs141777878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117402583G>C	ENST00000309909.5	+	5	841	c.759G>C	c.(757-759)gaG>gaC	p.E253D	FBXW8_ENST00000455858.2_Missense_Mutation_p.E187D			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	253					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		AGGACGAGGAGGATGAGCCTG	0.532													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.001				p.E253D		Atlas-SNP	.											.	FBXW8	53	.	0			c.G759C						PASS	.	G	ASP/GLU,ASP/GLU	4,4402	8.1+/-20.4	0,4,2199	183.0	159.0	167.0		561,759	4.3	1.0	12	dbSNP_134	167	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	FBXW8	NM_012174.1,NM_153348.2	45,45	0,9,6494	CC,CG,GG		0.0581,0.0908,0.0692	possibly-damaging,possibly-damaging	187/533,253/599	117402583	9,12997	2203	4300	6503	SO:0001583	missense	26259	exon5			CGAGGAGGATGAG	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13597	protein-coding gene	gene with protein product		609073	"""F-box only protein 29"", ""F-box and WD-40 domain protein 8"""	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.759G>C	12.37:g.117402583G>C	ENSP00000310686:p.Glu253Asp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	83	47	0.566265	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	G	15.67	2.901463	0.52227	9.08E-4	5.81E-4	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.09163	3.02;3.01	5.28	4.33	0.51752	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.195075	0.45126	D	0.000397	T	0.09818	0.0241	L	0.48642	1.525	0.28382	N	0.919506	P;P	0.49559	0.925;0.774	B;B	0.40285	0.325;0.236	T	0.18808	-1.0325	10	0.13108	T	0.6	-32.349	13.4249	0.61020	0.0:0.0:0.7974:0.2026	.	253;187	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	D	253;187;187	ENSP00000310686:E253D;ENSP00000389144:E187D	ENSP00000310686:E253D	E	+	3	2	FBXW8	115886966	0.999000	0.42202	1.000000	0.80357	0.924000	0.55760	0.860000	0.27871	2.906000	0.99361	0.655000	0.94253	GAG	G|0.999;C|0.001	0.001	strong		0.532	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257296	114257296	+	Missense_Mutation	SNP	A	A	G	rs199845792	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:114257296A>G	ENST00000306507.5	+	1	636	c.463A>G	c.(463-465)Atc>Gtc	p.I155V		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	155					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I155V(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GCAGAACAGCATCCGCCACAA	0.662																																					p.I155V		Atlas-SNP	.											FOXD4L1,colon,carcinoma,-2,3	FOXD4L1	48	3	1	Substitution - Missense(1)	skin(1)	c.A463G						scavenged	.						33.0	42.0	39.0					2																	114257296		1859	3671	5530	SO:0001583	missense	200350	exon1			AACAGCATCCGCC	AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.463A>G	2.37:g.114257296A>G	ENSP00000302756:p.Ile155Val	Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	317	58	0.182965	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	18.09	3.545708	0.65198	.	.	ENSG00000184492	ENST00000306507	D	0.96427	-4.01	2.57	2.57	0.30868	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);Transcription factor, fork head, conserved site (1);	0.000000	0.31859	U	0.006943	D	0.97009	0.9023	M	0.67517	2.055	0.54753	D	0.999981	D	0.67145	0.996	D	0.83275	0.996	D	0.96223	0.9162	10	0.66056	D	0.02	.	8.6531	0.34046	1.0:0.0:0.0:0.0	.	155	Q9NU39	FX4L1_HUMAN	V	155	ENSP00000302756:I155V	ENSP00000302756:I155V	I	+	1	0	FOXD4L1	113973766	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.565000	0.60836	1.190000	0.43042	0.155000	0.16302	ATC	A|0.985;G|0.015	0.015	strong		0.662	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
ZNF385D	79750	hgsc.bcm.edu	37	3	21552486	21552486	+	Silent	SNP	C	C	T	rs150360612		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:21552486C>T	ENST00000281523.2	-	4	824	c.306G>A	c.(304-306)acG>acA	p.T102T	ZNF385D_ENST00000494118.1_5'UTR	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	102						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.T102T(1)		NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						TGGCATGTTTCGTGCCTTTGT	0.453																																					p.T102T		Atlas-SNP	.											ZNF385D,caecum,carcinoma,0,2	ZNF385D	93	2	1	Substitution - coding silent(1)	skin(1)	c.G306A						scavenged	.						226.0	185.0	199.0					3																	21552486		2203	4300	6503	SO:0001819	synonymous_variant	79750	exon4			ATGTTTCGTGCCT	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.306G>A	3.37:g.21552486C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	175	5	0.0285714	NM_024697		Silent	SNP	ENST00000281523.2	37	CCDS2636.1																																																																																			.	.	weak		0.453	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
WSCD1	23302	hgsc.bcm.edu	37	17	6023792	6023792	+	Silent	SNP	C	C	T	rs16955477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6023792C>T	ENST00000574946.1	+	9	1929	c.1539C>T	c.(1537-1539)agC>agT	p.S513S	WSCD1_ENST00000573634.1_Silent_p.S397S|WSCD1_ENST00000539421.1_Silent_p.S513S|WSCD1_ENST00000317744.5_Silent_p.S513S|WSCD1_ENST00000574232.1_Silent_p.S513S			Q658N2	WSCD1_HUMAN	WSC domain containing 1	513						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						TGTCTGTGAGCGAGGAGCGGC	0.667													C|||	80	0.0159744	0.0	0.0259	5008	,	,		17440	0.002		0.0378	False		,,,				2504	0.0225				p.S513S		Atlas-SNP	.											.	WSCD1	84	.	0			c.C1539T						PASS	.	C		30,4376	36.0+/-67.5	0,30,2173	80.0	76.0	77.0		1539	-2.3	1.0	17	dbSNP_123	77	353,8247	119.2+/-178.6	6,341,3953	no	coding-synonymous	WSCD1	NM_015253.1		6,371,6126	TT,TC,CC		4.1047,0.6809,2.9448		513/576	6023792	383,12623	2203	4300	6503	SO:0001819	synonymous_variant	23302	exon9			TGTGAGCGAGGAG		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.1539C>T	17.37:g.6023792C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	45	0.542169	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Silent	SNP	ENST00000574946.1	37	CCDS32538.1																																																																																			C|0.974;T|0.026	0.026	strong		0.667	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
SPRR4	163778	hgsc.bcm.edu	37	1	152944594	152944594	+	Silent	SNP	C	C	T	rs3170863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152944594C>T	ENST00000328051.2	+	2	277	c.228C>T	c.(226-228)agC>agT	p.S76S		NM_173080.1	NP_775103.1	Q96PI1	SPRR4_HUMAN	small proline-rich protein 4	76	Gln-rich.				keratinization (GO:0031424)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)				lung(1)|prostate(1)	2	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTCCAAGAGCAAACAGAAGT	0.527													T|||	3131	0.6252	0.8306	0.4986	5008	,	,		21757	0.6319		0.5656	False		,,,				2504	0.4918				p.S76S		Atlas-SNP	.											.	SPRR4	8	.	0			c.C228T						PASS	.	T		3425,981	368.1+/-318.5	1336,753,114	125.0	100.0	108.0		228	2.5	0.9	1	dbSNP_105	108	4912,3688	528.4+/-381.4	1434,2044,822	no	coding-synonymous	SPRR4	NM_173080.1		2770,2797,936	TT,TC,CC		42.8837,22.2651,35.8988		76/80	152944594	8337,4669	2203	4300	6503	SO:0001819	synonymous_variant	163778	exon2			CAAGAGCAAACAG	AF335109	CCDS1031.1	1q21.3	2008-02-05	2006-11-29		ENSG00000184148	ENSG00000184148			23173	protein-coding gene	gene with protein product						11719550, 11279051	Standard	NM_173080		Approved		uc001fav.1	Q96PI1	OTTHUMG00000012450	ENST00000328051.2:c.228C>T	1.37:g.152944594C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	164	162	0.987805	NM_173080	Q2M1Y7|Q5T522	Silent	SNP	ENST00000328051.2	37	CCDS1031.1																																																																																			C|0.355;T|0.645	0.645	strong		0.527	SPRR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034663.1	NM_173080	
UBR1	197131	hgsc.bcm.edu	37	15	43299467	43299467	+	Missense_Mutation	SNP	A	A	C	rs141543407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43299467A>C	ENST00000290650.4	-	30	3303	c.3225T>G	c.(3223-3225)agT>agG	p.S1075R	UBR1_ENST00000568782.1_5'UTR|UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1075					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TAGAGTAGTCACTGACTGCTG	0.423																																					p.S1075R		Atlas-SNP	.											.	UBR1	124	.	0			c.T3225G						PASS	.	A	ARG/SER	0,4406		0,0,2203	62.0	56.0	58.0		3225	5.0	1.0	15	dbSNP_134	58	1,8597	1.2+/-3.3	0,1,4298	no	missense	UBR1	NM_174916.2	110	0,1,6501	CC,CA,AA		0.0116,0.0,0.0077	benign	1075/1750	43299467	1,13003	2203	4299	6502	SO:0001583	missense	197131	exon30			GTAGTCACTGACT		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3225T>G	15.37:g.43299467A>C	ENSP00000290650:p.Ser1075Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.879865	0.33162	0.0	1.16E-4	ENSG00000159459	ENST00000290650	T	0.50277	0.75	4.99	4.99	0.66335	.	0.403021	0.31507	N	0.007537	T	0.28532	0.0706	L	0.32530	0.975	0.80722	D	1	B	0.31125	0.309	B	0.19391	0.025	T	0.10086	-1.0645	10	0.13853	T	0.58	0.1735	6.762	0.23546	0.7868:0.0:0.0763:0.1369	.	1075	Q8IWV7	UBR1_HUMAN	R	1075	ENSP00000290650:S1075R	ENSP00000290650:S1075R	S	-	3	2	UBR1	41086759	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.608000	0.46308	2.096000	0.63516	0.533000	0.62120	AGT	A|0.999;C|0.001	0.001	strong		0.423	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592120	1592120	+	Intron	SNP	G	G	T	rs1135201		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1592120G>T	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Missense_Mutation_p.R106S|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Missense_Mutation_p.R106S|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TTACTGATGCGGATGGAAAAG	0.512																																					p.R106S		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,carcinoma,0,1	SIRPB1	83	1	0			c.C316A						scavenged	.						105.0	121.0	117.0					20																	1592120		448	1337	1785	SO:0001627	intron_variant	10326	exon2			TGATGCGGATGGA	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8394C>A	20.37:g.1592120G>T		Somatic	601	0	0		WXS	Illumina HiSeq	Phase_I	22	18	0.818182	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	560	0.2564102564102564	150	0.3048780487804878	74	0.20441988950276244	183	0.31993006993006995	153	0.20184696569920843	.	2.402	-0.337253	0.05278	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.65364	-0.15	2.65	-2.79	0.05841	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.52266	1.64	0.34870	D	0.743495	B	0.31435	0.323	B	0.31869	0.137	T	0.37753	-0.9692	9	0.37606	T	0.19	.	4.2858	0.10855	0.1304:0.0:0.2968:0.5727	rs1135201;rs3197735	106	Q5TFQ8	SIRBL_HUMAN	S	106	ENSP00000279477:R106S	ENSP00000279477:R106S	R	-	1	0	SIRPB1	1540120	0.081000	0.21417	0.142000	0.22268	0.020000	0.10135	0.000000	0.12993	-0.294000	0.08973	-2.062000	0.00397	CGC	G|0.744;T|0.256	0.256	strong		0.512	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
IVL	3713	hgsc.bcm.edu	37	1	152882610	152882610	+	Missense_Mutation	SNP	A	A	G	rs2229496	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152882610A>G	ENST00000368764.3	+	2	401	c.337A>G	c.(337-339)Aca>Gca	p.T113A	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	113			T -> A (in dbSNP:rs2229496).		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCAGGAGAAAACACAAAGGGA	0.493													G|||	2072	0.413738	0.6808	0.2997	5008	,	,		21641	0.5615		0.1083	False		,,,				2504	0.2955				p.T113A		Atlas-SNP	.											.	IVL	100	.	0			c.A337G						PASS	.	G	ALA/THR	2534,1872	542.0+/-375.9	740,1054,409	57.0	60.0	59.0		337	-0.6	0.0	1	dbSNP_98	59	789,7811	783.7+/-407.6	38,713,3549	yes	missense	IVL	NM_005547.2	58	778,1767,3958	GG,GA,AA		9.1744,42.4875,25.5497	benign	113/586	152882610	3323,9683	2203	4300	6503	SO:0001583	missense	3713	exon2			GAGAAAACACAAA	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.337A>G	1.37:g.152882610A>G	ENSP00000357753:p.Thr113Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	856	0.39194139194139194	342	0.6951219512195121	101	0.27900552486187846	333	0.5821678321678322	80	0.10554089709762533	G	0.819	-0.749185	0.03065	0.575125	0.091744	ENSG00000163207	ENST00000368764	T	0.06849	3.25	3.65	-0.585	0.11698	.	.	.	.	.	T	0.00637	0.0021	N	0.02539	-0.55	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44982	-0.9292	8	0.08381	T	0.77	.	4.9328	0.13926	0.51:0.164:0.326:0.0	rs2229496;rs2339485;rs59054145;rs2229496	113	P07476	INVO_HUMAN	A	113	ENSP00000357753:T113A	ENSP00000357753:T113A	T	+	1	0	IVL	151149234	0.000000	0.05858	0.000000	0.03702	0.189000	0.23516	-0.796000	0.04575	-0.530000	0.06349	-0.441000	0.05720	ACA	A|0.668;G|0.332	0.332	strong		0.493	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
XKR9	389668	hgsc.bcm.edu	37	8	71593425	71593425	+	Silent	SNP	G	G	A	rs6991329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:71593425G>A	ENST00000408926.3	+	3	666	c.132G>A	c.(130-132)gcG>gcA	p.A44A	XKR9_ENST00000520273.1_Intron|XKR9_ENST00000520030.1_Silent_p.A44A	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	44						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	Breast(64;0.0716)		Epithelial(68;0.00301)|all cancers(69;0.0165)|OV - Ovarian serous cystadenocarcinoma(28;0.0524)|BRCA - Breast invasive adenocarcinoma(89;0.166)			GTGCTTTAGCGTTAAGCTTTA	0.363													A|||	1263	0.252196	0.2269	0.2939	5008	,	,		18749	0.0734		0.5159	False		,,,				2504	0.1697				p.A44A		Atlas-SNP	.											.	XKR9	43	.	0			c.G132A						PASS	.	A		1156,3250	713.8+/-408.3	158,840,1205	270.0	265.0	267.0		132	0.5	1.0	8	dbSNP_116	267	4412,4188	569.1+/-389.1	1145,2122,1033	no	coding-synonymous	XKR9	NM_001011720.1		1303,2962,2238	AA,AG,GG		48.6977,26.2369,42.811		44/374	71593425	5568,7438	2203	4300	6503	SO:0001819	synonymous_variant	389668	exon3			TTTAGCGTTAAGC	AY534247	CCDS34905.1	8q13.3	2006-01-12	2006-01-12			ENSG00000221947			20937	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 9"""				Standard	NM_001287258		Approved		uc003xyq.3	Q5GH70		ENST00000408926.3:c.132G>A	8.37:g.71593425G>A		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	255	252	0.988235	NM_001011720	B2RNS9|B9EH74	Silent	SNP	ENST00000408926.3	37	CCDS34905.1																																																																																			G|0.625;A|0.375	0.375	strong		0.363	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720	
GRID2IP	392862	hgsc.bcm.edu	37	7	6591008	6591008	+	Silent	SNP	C	C	T	rs73059373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6591008C>T	ENST00000457091.2	-	1	59	c.60G>A	c.(58-60)cgG>cgA	p.R20R		NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	20	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.		R -> Q (in dbSNP:rs11761490).		long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						AGCCACCTAGCCGGAAGCCAA	0.652													C|||	778	0.155351	0.3812	0.1081	5008	,	,		11775	0.0526		0.0736	False		,,,				2504	0.0736				p.R20R		Atlas-SNP	.											GRID2IP_ENST00000457091,NS,carcinoma,0,2	GRID2IP	82	2	0			c.G60A						scavenged	.						7.0	9.0	9.0					7																	6591008		687	1585	2272	SO:0001819	synonymous_variant	392862	exon1			ACCTAGCCGGAAG		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.60G>A	7.37:g.6591008C>T		Somatic	46	2	0.0434783		WXS	Illumina HiSeq	Phase_I	60	58	0.966667	NM_001145118		Silent	SNP	ENST00000457091.2	37	CCDS47537.1																																																																																			C|0.859;T|0.141	0.141	strong		0.652	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
FCRL4	83417	hgsc.bcm.edu	37	1	157559122	157559122	+	Missense_Mutation	SNP	C	C	T	rs11582663	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:157559122C>T	ENST00000271532.1	-	3	314	c.179G>A	c.(178-180)cGg>cAg	p.R60Q	FCRL4_ENST00000448509.2_5'Flank	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	60	Ig-like C2-type 1.		R -> Q (in dbSNP:rs11582663).		immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				CCAGTAGTGCCGATGATACCA	0.517													C|||	234	0.0467252	0.0045	0.0692	5008	,	,		19974	0.001		0.1581	False		,,,				2504	0.0204				p.R60Q		Atlas-SNP	.											.	FCRL4	95	.	0			c.G179A						PASS	.	C	GLN/ARG	136,4270	98.0+/-136.7	5,126,2072	109.0	93.0	99.0		179	-3.9	0.0	1	dbSNP_120	99	1305,7295	257.9+/-281.7	88,1129,3083	yes	missense	FCRL4	NM_031282.2	43	93,1255,5155	TT,TC,CC		15.1744,3.0867,11.0795	benign	60/516	157559122	1441,11565	2203	4300	6503	SO:0001583	missense	83417	exon3			TAGTGCCGATGAT	AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.179G>A	1.37:g.157559122C>T	ENSP00000271532:p.Arg60Gln	Somatic	384	0	0		WXS	Illumina HiSeq	Phase_I	394	202	0.51269	NM_031282	Q96PJ3|Q96RE0	Missense_Mutation	SNP	ENST00000271532.1	37	CCDS1166.1	157	0.07188644688644688	4	0.008130081300813009	29	0.08011049723756906	0	0.0	124	0.16358839050131926	C	0.693	-0.793811	0.02862	0.030867	0.151744	ENSG00000163518	ENST00000271532	T	0.54279	0.58	1.95	-3.9	0.04181	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.13286	0.0322	L	0.36672	1.1	0.80722	P	0.0	B	0.24043	0.096	B	0.23419	0.046	T	0.18241	-1.0343	8	0.38643	T	0.18	.	0.1358	0.00078	0.342:0.2316:0.1692:0.2572	rs11582663;rs52802570;rs59243416;rs11582663	60	Q96PJ5	FCRL4_HUMAN	Q	60	ENSP00000271532:R60Q	ENSP00000271532:R60Q	R	-	2	0	FCRL4	155825746	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.398000	0.02066	-1.082000	0.02213	CGG	C|0.911;T|0.089	0.089	strong		0.517	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282	
FMN2	56776	hgsc.bcm.edu	37	1	240371469	240371469	+	Silent	SNP	C	C	T	rs199920451		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	74	8	0.108108		WXS	Illumina HiSeq	Phase_I	66	6	0.0909091	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	
XRCC3	7517	hgsc.bcm.edu	37	14	104165753	104165753	+	Missense_Mutation	SNP	G	G	A	rs861539	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:104165753G>A	ENST00000553264.1	-	6	1518	c.722C>T	c.(721-723)aCg>aTg	p.T241M	XRCC3_ENST00000554974.1_Missense_Mutation_p.T36M|KLC1_ENST00000452929.2_Intron|XRCC3_ENST00000555055.1_Missense_Mutation_p.T241M|XRCC3_ENST00000445556.1_Missense_Mutation_p.T241M|RP11-73M18.8_ENST00000602422.1_RNA|KLC1_ENST00000555836.1_Intron|KLC1_ENST00000348520.6_Intron|KLC1_ENST00000554280.1_Intron|KLC1_ENST00000334553.6_Intron|XRCC3_ENST00000554913.1_Missense_Mutation_p.T241M|XRCC3_ENST00000555832.1_5'Flank|XRCC3_ENST00000352127.7_Missense_Mutation_p.T241M|KLC1_ENST00000557450.1_Intron			O43542	XRCC3_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 3	241			T -> M (in CMM6 susceptibility; associated with cutaneous malignant melanoma; dbSNP:rs861539). {ECO:0000269|PubMed:11059748, ECO:0000269|PubMed:9660962, ECO:0000269|Ref.2}.		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|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)|response to organic substance (GO:0010033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)	p.T241M(1)		endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Melanoma(154;0.155)|all_epithelial(191;0.19)		Epithelial(152;0.239)		CTCACGCAGCGTGGCCCCCAG	0.637								Direct reversal of damage;Homologous recombination					G|||	1086	0.216853	0.1906	0.2291	5008	,	,		17489	0.0734		0.3936	False		,,,				2504	0.2096				p.T241M		Atlas-SNP	.											XRCC3,NS,carcinoma,0,1	XRCC3	16	1	1	Substitution - Missense(1)	prostate(1)	c.C722T	GRCh37	CM003625	XRCC3	M	rs861539	PASS	.	G	MET/THR,MET/THR,,MET/THR,	950,3452		98,754,1349	19.0	22.0	21.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	722,722,,722,	1.4	0.0	14	dbSNP_86	21	3252,5346		640,1972,1687	yes	missense,missense,intron,missense,intron	KLC1,XRCC3	NM_001100118.1,NM_001100119.1,NM_001130107.1,NM_005432.3,NM_182923.3	81,81,,81,	738,2726,3036	AA,AG,GG		37.8227,21.5811,32.3231	benign,benign,,benign,	241/347,241/347,,241/347,	104165753	4202,8798	2201	4299	6500	SO:0001583	missense	7517	exon8			CGCAGCGTGGCCC	AF035586	CCDS9984.1	14q32.3	2006-05-04				ENSG00000126215			12830	protein-coding gene	gene with protein product	"""RAD51-like"""	600675				7603995	Standard	NM_001100118		Approved		uc001ynz.4	O43542		ENST00000553264.1:c.722C>T	14.37:g.104165753G>A	ENSP00000451974:p.Thr241Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_005432	O43568|Q9BU18	Missense_Mutation	SNP	ENST00000553264.1	37	CCDS9984.1	546	0.25	94	0.1910569105691057	96	0.26519337016574585	52	0.09090909090909091	304	0.40105540897097625	G	11.27	1.589788	0.28357	0.215811	0.378227	ENSG00000126215	ENST00000554913;ENST00000352127;ENST00000553264;ENST00000555055;ENST00000445556;ENST00000554974	T;T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05;1.05	4.78	1.35	0.21983	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.561051	0.19129	N	0.121979	T	0.00012	0.0000	L	0.38531	1.155	0.58432	P	5.000000000032756E-6	P	0.36171	0.541	B	0.34824	0.19	T	0.47355	-0.9124	9	0.26408	T	0.33	-18.8536	12.3156	0.54955	0.0:0.0:0.2693:0.7307	rs861539;rs1734804;rs3212111;rs17435402;rs17850783;rs56934996;rs861539	241	O43542	XRCC3_HUMAN	M	241;241;241;241;241;36	ENSP00000451362:T241M;ENSP00000343392:T241M;ENSP00000451974:T241M;ENSP00000452598:T241M;ENSP00000412990:T241M;ENSP00000451361:T36M	ENSP00000343392:T241M	T	-	2	0	XRCC3	103235506	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	0.642000	0.24735	0.376000	0.24707	0.462000	0.41574	ACG	G|0.729;A|0.271	0.271	strong		0.637	XRCC3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414631.1	NM_005432	
SLC6A5	9152	hgsc.bcm.edu	37	11	20622975	20622975	+	Missense_Mutation	SNP	G	G	A	rs1443547	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:20622975G>A	ENST00000525748.1	+	2	577	c.304G>A	c.(304-306)Ggc>Agc	p.G102S		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	102			G -> S (in dbSNP:rs1443547). {ECO:0000269|PubMed:10381548}.		glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	AGAGGCGCAAGGCGCGCAGGC	0.701													G|||	2032	0.405751	0.447	0.3804	5008	,	,		14053	0.3651		0.3847	False		,,,				2504	0.4315				p.G102S		Atlas-SNP	.											.	SLC6A5	151	.	0			c.G304A						PASS	.	G	SER/GLY	1916,2474		441,1034,720	16.0	19.0	18.0		304	-4.0	0.0	11	dbSNP_88	18	2871,5697		529,1813,1942	no	missense	SLC6A5	NM_004211.3	56	970,2847,2662	AA,AG,GG		33.5084,43.6446,36.9424	benign	102/798	20622975	4787,8171	2195	4284	6479	SO:0001583	missense	9152	exon2			GCGCAAGGCGCGC	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.304G>A	11.37:g.20622975G>A	ENSP00000434364:p.Gly102Ser	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	10	6	0.6	NM_004211	O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	806	0.36904761904761907	202	0.4105691056910569	126	0.34806629834254144	201	0.3513986013986014	277	0.3654353562005277	G	1.537	-0.542827	0.04053	0.436446	0.335084	ENSG00000165970	ENST00000525748	T	0.70631	-0.5	5.37	-3.96	0.04106	.	1.669100	0.02954	N	0.142135	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13176	-1.0519	9	0.07175	T	0.84	.	6.8887	0.24216	0.5281:0.227:0.2449:0.0	rs1443547;rs1443547	102	Q9Y345	SC6A5_HUMAN	S	102	ENSP00000434364:G102S	ENSP00000298923:G102S	G	+	1	0	SLC6A5	20579551	0.000000	0.05858	0.000000	0.03702	0.164000	0.22412	-0.675000	0.05227	-0.904000	0.03876	0.462000	0.41574	GGC	G|0.607;A|0.393	0.393	strong		0.701	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
HEPN1	641654	hgsc.bcm.edu	37	11	124789828	124789828	+	Missense_Mutation	SNP	A	A	T	rs78859654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124789828A>T	ENST00000408930.5	+	1	683	c.182A>T	c.(181-183)cAc>cTc	p.H61L	HEPACAM_ENST00000298251.4_3'UTR	NM_001037558.2	NP_001032647.2	Q6WQI6	HEPN1_HUMAN	hepatocellular carcinoma, down-regulated 1	61						cytoplasm (GO:0005737)				large_intestine(1)|lung(1)|stomach(1)	3	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;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0287)		GATTACTGCCACTCCTATGAA	0.502													A|||	292	0.0583067	0.0545	0.0432	5008	,	,		20285	0.0288		0.0934	False		,,,				2504	0.0685				p.H61L		Atlas-SNP	.											HEPN1,NS,haematopoietic_neoplasm,0,1	HEPN1	11	1	0			c.A182T						scavenged	.	A	LEU/HIS,	225,3603		2,221,1691	81.0	82.0	82.0		182,	-3.4	0.0	11	dbSNP_131	82	728,7558		38,652,3453	yes	missense,utr-3	HEPACAM,HEPN1	NM_001037558.2,NM_152722.4	99,	40,873,5144	TT,TA,AA		8.7859,5.8777,7.8669	benign,	61/89,	124789828	953,11161	1914	4143	6057	SO:0001583	missense	641654	exon1			ACTGCCACTCCTA	BC148521	CCDS41729.1	11q24	2013-07-02	2011-02-11		ENSG00000221932	ENSG00000221932			34400	protein-coding gene	gene with protein product	"""cancer susceptibility gene HEPN1"""	611641	"""HEPACAM opposite strand 1"""			12971969, 23548416	Standard	NM_001037558		Approved		uc001qbj.1	Q6WQI6	OTTHUMG00000165939	ENST00000408930.5:c.182A>T	11.37:g.124789828A>T	ENSP00000386143:p.His61Leu	Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	201	96	0.477612	NM_001037558		Missense_Mutation	SNP	ENST00000408930.5	37	CCDS41729.1	119	0.05448717948717949	24	0.04878048780487805	10	0.027624309392265192	15	0.026223776223776224	70	0.09234828496042216	A	5.592	0.294002	0.10567	0.058777	0.087859	ENSG00000221932	ENST00000408930	T	0.53640	0.61	3.92	-3.39	0.04868	.	.	.	.	.	T	0.01092	0.0036	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14172	-1.0482	7	0.87932	D	0	.	2.9735	0.05930	0.3248:0.2998:0.0:0.3754	.	61	Q6WQI6	HEPN1_HUMAN	L	61	ENSP00000386143:H61L	ENSP00000386143:H61L	H	+	2	0	HEPN1	124295038	0.000000	0.05858	0.000000	0.03702	0.045000	0.14185	0.242000	0.18087	-0.804000	0.04410	-1.571000	0.00872	CAC	A|0.939;T|0.061	0.061	strong		0.502	HEPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387129.1	NM_001037558	
LRP1B	53353	hgsc.bcm.edu	37	2	141267573	141267573	+	Silent	SNP	G	G	A	rs35821928	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:141267573G>A	ENST00000389484.3	-	52	9293	c.8322C>T	c.(8320-8322)tgC>tgT	p.C2774C		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2774	LDL-receptor class A 17. {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)	p.C2774W(1)		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)		GTCGGGGCACGCAGGCACGAG	0.532										TSP Lung(27;0.18)			G|||	174	0.0347444	0.0257	0.0432	5008	,	,		19643	0.0		0.0716	False		,,,				2504	0.0389				p.C2774C	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	1	Substitution - Missense(1)	lung(1)	c.C8322T						PASS	.	G		140,4266	98.0+/-136.7	4,132,2067	128.0	116.0	120.0		8322	-1.7	1.0	2	dbSNP_126	120	692,7908	170.9+/-221.9	29,634,3637	no	coding-synonymous	LRP1B	NM_018557.2		33,766,5704	AA,AG,GG		8.0465,3.1775,6.397		2774/4600	141267573	832,12174	2203	4300	6503	SO:0001819	synonymous_variant	53353	exon52			GGGCACGCAGGCA	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.8322C>T	2.37:g.141267573G>A		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	152	85	0.559211	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			G|0.946;A|0.054	0.054	strong		0.532	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786230	75786230	+	Silent	SNP	C	C	T	rs149559986		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:75786230C>T	ENST00000478296.1	-	4	2670	c.2394G>A	c.(2392-2394)agG>agA	p.R798R	ZNF717_ENST00000400845.3_Silent_p.R841R|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Silent_p.R848R|MIR4273_ENST00000582824.1_RNA			Q9BY31	ZN717_HUMAN	zinc finger protein 717	838					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						AGAAAGTTTTCCTACATTCAT	0.393																																					p.R848R		Atlas-SNP	.											ZNF717,NS,carcinoma,0,1	ZNF717	160	1	0			c.G2544A						scavenged	.						3.0	3.0	3.0					3																	75786230		442	1082	1524	SO:0001819	synonymous_variant	100131827	exon5			AGTTTTCCTACAT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.2394G>A	3.37:g.75786230C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	42	0.677419	NM_001128223		Silent	SNP	ENST00000478296.1	37																																																																																				C|0.620;T|0.380	0.380	strong		0.393	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
RYR1	6261	hgsc.bcm.edu	37	19	38956839	38956839	+	Silent	SNP	C	C	T	rs2228070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38956839C>T	ENST00000359596.3	+	24	2979	c.2979C>T	c.(2977-2979)aaC>aaT	p.N993N	RYR1_ENST00000355481.4_Silent_p.N993N|RYR1_ENST00000360985.3_Silent_p.N993N			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	993	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ATGGGCACAACGTGTGGGCCC	0.682													C|||	1222	0.24401	0.084	0.2176	5008	,	,		15689	0.4266		0.2237	False		,,,				2504	0.3119				p.N993N		Atlas-SNP	.											.	RYR1	708	.	0			c.C2979T						PASS	.	C	,	452,3952	211.2+/-231.4	23,406,1773	42.0	43.0	42.0		2979,2979	-6.4	0.8	19	dbSNP_98	42	1934,6662	329.3+/-318.7	241,1452,2605	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	264,1858,4378	TT,TC,CC		22.4988,10.2634,18.3538	,	993/5039,993/5034	38956839	2386,10614	2202	4298	6500	SO:0001819	synonymous_variant	6261	exon24			GCACAACGTGTGG	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.2979C>T	19.37:g.38956839C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	77	46	0.597403	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			C|0.798;T|0.202	0.202	strong		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
CXorf58	254158	hgsc.bcm.edu	37	X	23928489	23928489	+	Missense_Mutation	SNP	C	C	T	rs2707164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:23928489C>T	ENST00000379211.3	+	2	619	c.70C>T	c.(70-72)Cgc>Tgc	p.R24C	APOO_ENST00000379226.4_5'Flank|APOO_ENST00000379220.3_5'Flank	NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58	24			R -> C (in dbSNP:rs2707164). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						ACAAAAAGTTCGCAGAGTACA	0.373													C|||	1397	0.370066	0.1505	0.4294	3775	,	,		15069	0.2381		0.5139	False		,,,				2504	0.1462				p.R24C		Atlas-SNP	.											.	CXorf58	53	.	0			c.C70T						PASS	.	C	CYS/ARG,CYS/ARG	942,2893		112,572,146,948,425	131.0	96.0	108.0		70,70	-0.7	0.0	X	dbSNP_100	108	4745,1983		1222,987,1314,219,558	yes	missense,missense	CXorf58	NM_001169574.1,NM_152761.2	180,180	1334,1559,1460,1167,983	TT,TC,T,CC,C		29.4738,24.5632,46.1611	probably-damaging,probably-damaging	24/331,24/333	23928489	5687,4876	2203	4300	6503	SO:0001583	missense	254158	exon2			AAAGTTCGCAGAG	AK058173	CCDS14209.1	Xp22.11	2012-11-28			ENSG00000165182	ENSG00000165182			26356	protein-coding gene	gene with protein product							Standard	NM_152761		Approved	FLJ25444	uc004daz.1	Q96LI9	OTTHUMG00000021258	ENST00000379211.3:c.70C>T	X.37:g.23928489C>T	ENSP00000368511:p.Arg24Cys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_152761		Missense_Mutation	SNP	ENST00000379211.3	37	CCDS14209.1	772	0.4653405666063894	69	0.15065502183406113	104	0.4126984126984127	99	0.21153846153846154	260	0.49429657794676807	C	6.635	0.485625	0.12641	0.245632	0.705262	ENSG00000165182	ENST00000379211	T	0.32753	1.44	3.44	-0.668	0.11392	.	1.597720	0.03958	N	0.289533	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.67145	0.996	P	0.47573	0.55	T	0.42932	-0.9422	9	0.37606	T	0.19	10.0265	6.5671	0.22519	0.0:0.3254:0.5532:0.1214	rs2707164;rs17322469;rs52793631;rs58445345;rs2707164	24	Q96LI9	CX058_HUMAN	C	24	ENSP00000368511:R24C	ENSP00000368511:R24C	R	+	1	0	CXorf58	23838410	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.158000	0.16422	-0.274000	0.09232	0.600000	0.82982	CGC	0|0.003;T|0.491	0.491	strong		0.373	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761	
SYMPK	8189	hgsc.bcm.edu	37	19	46352122	46352122	+	Silent	SNP	A	A	G	rs2303014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46352122A>G	ENST00000245934.7	-	6	556	c.312T>C	c.(310-312)atT>atC	p.I104I		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	104	Interaction with HSF1.				cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		GCAGCAACTCAATGTCTCGCT	0.512													A|||	619	0.123602	0.031	0.2233	5008	,	,		24932	0.0952		0.1581	False		,,,				2504	0.1718				p.I104I		Atlas-SNP	.											SYMPK,colon,carcinoma,-2,1	SYMPK	104	1	0			c.T312C						PASS	.	A		237,4169	138.8+/-174.5	5,227,1971	144.0	124.0	131.0		312	-5.2	0.9	19	dbSNP_100	131	1270,7330	253.2+/-279.0	98,1074,3128	no	coding-synonymous	SYMPK	NM_004819.2		103,1301,5099	GG,GA,AA		14.7674,5.379,11.587		104/1275	46352122	1507,11499	2203	4300	6503	SO:0001819	synonymous_variant	8189	exon6			CAACTCAATGTCT	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.312T>C	19.37:g.46352122A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	146	72	0.493151	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			A|0.892;G|0.108	0.108	strong		0.512	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
NIN	51199	hgsc.bcm.edu	37	14	51225132	51225132	+	Silent	SNP	G	G	T	rs2073349	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:51225132G>T	ENST00000382041.3	-	18	2806	c.2616C>A	c.(2614-2616)gcC>gcA	p.A872A	NIN_ENST00000389868.3_Intron|NIN_ENST00000324330.9_Silent_p.A872A|NIN_ENST00000245441.5_Silent_p.A872A|NIN_ENST00000530997.2_Silent_p.A872A|NIN_ENST00000382043.4_Intron|NIN_ENST00000453196.1_Silent_p.A872A	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	872					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)					GCAGCTCCTGGGCTTCCGCAC	0.512			T	PDGFRB	MPD								G|||	1941	0.38758	0.3033	0.4712	5008	,	,		18934	0.5099		0.3628	False		,,,				2504	0.3415				p.A872A		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.C2616A						PASS	.	G	,,,	1273,3133	433.9+/-343.8	175,923,1105	69.0	65.0	67.0		,2616,2616,2616	4.8	1.0	14	dbSNP_96	67	3163,5437	479.5+/-370.1	594,1975,1731	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,,,	769,2898,2836	TT,TG,GG		36.7791,28.8924,34.1073	,,,	,872/2134,872/2047,872/2091	51225132	4436,8570	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon18			CTCCTGGGCTTCC	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.2616C>A	14.37:g.51225132G>T		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	222	94	0.423423	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	879	0.4024725274725275	129	0.2621951219512195	175	0.48342541436464087	295	0.5157342657342657	280	0.36939313984168864	G	7.370	0.626620	0.14257	0.288924	0.367791	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.82	4.85	0.62838	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998826	.	.	.	.	.	.	T	0.50197	-0.8856	3	.	.	.	-0.0545	16.7684	0.85529	0.0:0.0:0.8626:0.1374	rs2073349;rs60896995;rs2073349	.	.	.	T	363	.	.	P	-	1	0	NIN	50294882	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	2.971000	0.49248	2.756000	0.94617	0.561000	0.74099	CCA	G|0.635;T|0.365	0.365	strong		0.512	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
MS4A4A	51338	hgsc.bcm.edu	37	11	60070176	60070176	+	Missense_Mutation	SNP	A	A	G	rs6591561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60070176A>G	ENST00000337908.4	+	5	622	c.532A>G	c.(532-534)Atg>Gtg	p.M178V	MS4A4A_ENST00000355131.3_Missense_Mutation_p.M159V|MS4A4A_ENST00000395016.3_Missense_Mutation_p.M159V|MS4A4A_ENST00000532114.1_Intron	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	178			M -> V (in dbSNP:rs6591561).			integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						TCATGGGACTATGTCCATCTT	0.388													A|||	1648	0.329073	0.3525	0.1844	5008	,	,		19686	0.3849		0.331	False		,,,				2504	0.3405				p.M178V		Atlas-SNP	.											.	MS4A4A	76	.	0			c.A532G						PASS	.	A	VAL/MET,VAL/MET	1386,3020	456.9+/-351.5	209,968,1026	150.0	130.0	137.0		475,532	-5.8	0.0	11	dbSNP_116	137	2497,6103	410.8+/-350.3	369,1759,2172	yes	missense,missense	MS4A4A	NM_024021.3,NM_148975.2	21,21	578,2727,3198	GG,GA,AA		29.0349,31.4571,29.8555	benign,benign	159/221,178/240	60070176	3883,9123	2203	4300	6503	SO:0001583	missense	51338	exon5			GGGACTATGTCCA	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"""membrane-spanning 4-domains, subfamily A, member 4"""	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.532A>G	11.37:g.60070176A>G	ENSP00000338648:p.Met178Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	203	97	0.477833	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Missense_Mutation	SNP	ENST00000337908.4	37	CCDS7982.1	705	0.3228021978021978	178	0.3617886178861789	83	0.2292817679558011	210	0.36713286713286714	234	0.3087071240105541	A	0	-2.795470	0.00076	0.314571	0.290349	ENSG00000110079	ENST00000337908;ENST00000355131;ENST00000395016	T;T;T	0.02158	4.42;4.42;4.42	2.89	-5.79	0.02354	.	2.898180	0.01956	N	0.043012	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	0.41052	-0.9530	9	0.12430	T	0.62	9.3152	2.14	0.03772	0.1566:0.1123:0.4253:0.3058	rs6591561;rs11552430;rs52837371;rs58618649;rs6591561	178	Q96JQ5	M4A4A_HUMAN	V	178;159;159	ENSP00000338648:M178V;ENSP00000347252:M159V;ENSP00000378462:M159V	ENSP00000338648:M178V	M	+	1	0	MS4A4A	59826752	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.866000	0.00093	-4.728000	0.00034	-2.713000	0.00133	ATG	A|0.685;G|0.315	0.315	strong		0.388	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2		
AZU1	566	hgsc.bcm.edu	37	19	831865	831865	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:831865G>A	ENST00000233997.2	+	5	765	c.744G>A	c.(742-744)ccG>ccA	p.P248P		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	248			Missing (in 50% of the molecules).		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)		ACCCGGGACCGGGGCCAGCCT	0.711																																					p.P248P		Atlas-SNP	.											.	AZU1	31	.	0			c.G744A						PASS	.						27.0	33.0	31.0					19																	831865		2189	4270	6459	SO:0001819	synonymous_variant	566	exon5			GGGACCGGGGCCA	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.744G>A	19.37:g.831865G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			.	.	none		0.711	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
IDO2	169355	hgsc.bcm.edu	37	8	39871135	39871135	+	Silent	SNP	C	C	T	rs2001923	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39871135C>T	ENST00000389060.4	+	9	771	c.771C>T	c.(769-771)tcC>tcT	p.S257S	IDO2_ENST00000502986.2_Silent_p.S270S|IDO2_ENST00000343295.4_3'UTR			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	257					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						AAGGAGTTTCCCAAGAGCCCC	0.498													C|||	381	0.0760783	0.1785	0.0692	5008	,	,		17581	0.002		0.0577	False		,,,				2504	0.0378				p.S270S		Atlas-SNP	.											IDO2_ENST00000502986,trunk,malignant_melanoma,+1,1	IDO2	78	1	0			c.C810T						scavenged	.	C		646,3172		54,538,1317	103.0	99.0	100.0		810	-4.0	0.0	8	dbSNP_92	100	462,7788		13,436,3676	no	coding-synonymous	IDO2	NM_194294.2		67,974,4993	TT,TC,CC		5.6,16.9199,9.1813		270/421	39871135	1108,10960	1909	4125	6034	SO:0001819	synonymous_variant	169355	exon10			AGTTTCCCAAGAG	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.771C>T	8.37:g.39871135C>T		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	128	74	0.578125	NM_194294	A4UD41	Silent	SNP	ENST00000389060.4	37																																																																																				C|0.932;T|0.068	0.068	strong		0.498	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
LPPR1	54886	hgsc.bcm.edu	37	9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	rs41296085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:103947810T>G	ENST00000374874.3	+	2	473	c.34T>G	c.(34-36)Tcc>Gcc	p.S12A	LPPR1_ENST00000395056.2_Missense_Mutation_p.S12A|LPPR1_ENST00000494890.1_3'UTR	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		12					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										ACGAAGTTATTCCATCATCCC	0.338													T|||	42	0.00838658	0.0	0.0144	5008	,	,		16008	0.0		0.0169	False		,,,				2504	0.0153				p.S12A		Atlas-SNP	.											.	.	.	.	0			c.T34G						PASS	.	T	ALA/SER,ALA/SER	17,4389	24.3+/-50.5	0,17,2186	221.0	202.0	208.0		34,34	5.9	1.0	9	dbSNP_127	208	133,8467	67.3+/-129.8	1,131,4168	yes	missense,missense	LPPR1	NM_017753.2,NM_207299.1	99,99	1,148,6354	GG,GT,TT		1.5465,0.3858,1.1533	benign,benign	12/326,12/326	103947810	150,12856	2203	4300	6503	SO:0001583	missense	0	exon2			AGTTATTCCATCA																												ENST00000374874.3:c.34T>G	9.37:g.103947810T>G	ENSP00000364008:p.Ser12Ala	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	207	99	0.478261	NM_207299	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000374874.3	37	CCDS6751.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	15.22	2.768539	0.49680	0.003858	0.015465	ENSG00000148123	ENST00000374874;ENST00000456287;ENST00000374871;ENST00000395056	T;T;T	0.38077	1.16;1.16;1.16	5.93	5.93	0.95920	.	0.431258	0.25774	N	0.028386	T	0.23094	0.0558	M	0.65498	2.005	0.34363	D	0.691192	B	0.02656	0.0	B	0.08055	0.003	T	0.40384	-0.9566	10	0.34782	T	0.22	-32.2815	14.3318	0.66561	0.0:0.0:0.0:1.0	rs41296085;rs61755095	12	Q8TBJ4	LPPR1_HUMAN	A	12	ENSP00000364008:S12A;ENSP00000410223:S12A;ENSP00000378496:S12A	ENSP00000364005:S12A	S	+	1	0	RP11-35N6.1	102987631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	2.271000	0.75665	0.533000	0.62120	TCC	T|0.990;G|0.010	0.010	strong		0.338	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
PSMD5	5711	hgsc.bcm.edu	37	9	123583192	123583192	+	Silent	SNP	A	A	G	rs1060817	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:123583192A>G	ENST00000210313.3	-	9	1256	c.1182T>C	c.(1180-1182)gaT>gaC	p.D394D	PSMD5_ENST00000604848.1_Silent_p.D51D|PSMD5_ENST00000373904.5_Silent_p.D351D	NM_001270427.1|NM_005047.3	NP_001257356.1|NP_005038.1	Q16401	PSMD5_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5	394					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						GCTCCAGTGGATCCCGAGATA	0.453													A|||	2446	0.488419	0.1626	0.6571	5008	,	,		21160	0.4673		0.5895	False		,,,				2504	0.727				p.D394D		Atlas-SNP	.											.	PSMD5	34	.	0			c.T1182C						PASS	.	A		1017,3389	375.9+/-321.8	109,799,1295	86.0	87.0	87.0		1182	1.0	0.9	9	dbSNP_86	87	5113,3487	633.9+/-398.8	1514,2085,701	no	coding-synonymous	PSMD5	NM_005047.2		1623,2884,1996	GG,GA,AA		40.5465,23.0822,47.1321		394/505	123583192	6130,6876	2203	4300	6503	SO:0001819	synonymous_variant	5711	exon9			CAGTGGATCCCGA	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.1182T>C	9.37:g.123583192A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_005047	B4DZM8|Q15045|Q4VXG8	Silent	SNP	ENST00000210313.3	37	CCDS6824.1																																																																																			A|0.532;G|0.468	0.468	strong		0.453	PSMD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053825.2	NM_005047	
GATB	5188	hgsc.bcm.edu	37	4	152609826	152609826	+	Silent	SNP	A	A	C	rs62327344	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:152609826A>C	ENST00000515812.1	-	9	1180	c.1164T>G	c.(1162-1164)acT>acG	p.T388T	PET112_ENST00000507592.1_5'Flank|PET112_ENST00000263985.6_Silent_p.T429T														p.T429T(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	23						AGCCCAGAAAAGTGTTGAGGA	0.443													A|||	42	0.00838658	0.0	0.0101	5008	,	,		18209	0.0		0.0328	False		,,,				2504	0.002				p.T429T		Atlas-SNP	.											PET112,NS,carcinoma,0,1	PET112	43	1	1	Substitution - coding silent(1)	prostate(1)	c.T1287G						PASS	.	A		26,4380	32.6+/-62.9	0,26,2177	138.0	139.0	139.0		1287	0.1	0.0	4	dbSNP_129	139	364,8236	120.8+/-180.0	9,346,3945	no	coding-synonymous	PET112	NM_004564.2		9,372,6122	CC,CA,AA		4.2326,0.5901,2.9986		429/558	152609826	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	5188	exon10			CAGAAAAGTGTTG																												ENST00000515812.1:c.1164T>G	4.37:g.152609826A>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_004564		Silent	SNP	ENST00000515812.1	37																																																																																				A|0.977;C|0.023	0.023	strong		0.443	PET112-002	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365672.1		
IGF2BP2	10644	hgsc.bcm.edu	37	3	185542653	185542653	+	Silent	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:185542653T>A	ENST00000382199.2	-	1	191	c.96A>T	c.(94-96)ggA>ggT	p.G32G	IGF2BP2_ENST00000457616.2_Silent_p.G32G|IGF2BP2_ENST00000346192.3_Silent_p.G32G	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	32	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GCAGGACCTGTCCCGCCAGGG	0.657																																					p.G32G		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.A96T						PASS	.						24.0	25.0	25.0					3																	185542653		2197	4294	6491	SO:0001819	synonymous_variant	10644	exon1			GACCTGTCCCGCC	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"""RNA binding motif (RRM) containing"""	28867	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 2"""	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.96A>T	3.37:g.185542653T>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	187	81	0.433155	NM_001007225	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Silent	SNP	ENST00000382199.2	37	CCDS3273.2																																																																																			.	.	none		0.657	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548	
HSD17B12	51144	hgsc.bcm.edu	37	11	43702530	43702530	+	Silent	SNP	A	A	G	rs56168061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:43702530A>G	ENST00000278353.4	+	1	272	c.153A>G	c.(151-153)gaA>gaG	p.E51E	HSD17B12_ENST00000395700.4_Silent_p.E51E|HSD17B12_ENST00000529261.1_Intron	NM_016142.2	NP_057226.1	Q53GQ0	DHB12_HUMAN	hydroxysteroid (17-beta) dehydrogenase 12	51					cellular lipid metabolic process (GO:0044255)|estrogen biosynthetic process (GO:0006703)|extracellular matrix organization (GO:0030198)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cell-substrate adhesion (GO:0010811)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|integral component of membrane (GO:0016021)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|heparin binding (GO:0008201)			endometrium(2)|large_intestine(4)|lung(4)	10						GGCTCGGAGAATGGGCAGGTG	0.697													A|||	511	0.102037	0.0817	0.1066	5008	,	,		11188	0.001		0.1938	False		,,,				2504	0.136				p.E51E	Ovarian(58;548 1143 13948 16572 34258)	Atlas-SNP	.											HSD17B12,NS,carcinoma,0,1	HSD17B12	25	1	0			c.A153G						PASS	.	A		399,3997		19,361,1818	17.0	19.0	18.0		153	1.8	1.0	11	dbSNP_129	18	1843,6753		215,1413,2670	no	coding-synonymous	HSD17B12	NM_016142.2		234,1774,4488	GG,GA,AA		21.4402,9.0764,17.2568		51/313	43702530	2242,10750	2198	4298	6496	SO:0001819	synonymous_variant	51144	exon1			CGGAGAATGGGCA	AF078850	CCDS7905.1	11q11	2011-09-20				ENSG00000149084	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18646	protein-coding gene	gene with protein product	"""3-ketoacyl-CoA reductase"", ""short chain dehydrogenase/reductase family 12C, member 1"""	609574				12482854, 19027726	Standard	NM_016142		Approved	KAR, SDR12C1	uc001mxq.4	Q53GQ0		ENST00000278353.4:c.153A>G	11.37:g.43702530A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_016142	A8K9B0|D3DR23|Q96EA9|Q96JU2|Q9Y6G8	Silent	SNP	ENST00000278353.4	37	CCDS7905.1																																																																																			A|0.873;G|0.127	0.127	strong		0.697	HSD17B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389594.1		
TBC1D14	57533	hgsc.bcm.edu	37	4	7006636	7006636	+	Missense_Mutation	SNP	G	G	C	rs11731231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:7006636G>C	ENST00000409757.4	+	8	1460	c.1336G>C	c.(1336-1338)Gaa>Caa	p.E446Q	TBC1D14_ENST00000446947.2_Missense_Mutation_p.E59Q|TBC1D14_ENST00000410031.1_Missense_Mutation_p.E218Q|TBC1D14_ENST00000448507.1_Missense_Mutation_p.E446Q|TBC1D14_ENST00000451522.2_Missense_Mutation_p.E166Q	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	446	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		E -> Q (in dbSNP:rs11731231).		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						AGGAGGCTCTGAAGTGGAGAA	0.458													G|||	8	0.00159744	0.0	0.0	5008	,	,		16696	0.0		0.006	False		,,,				2504	0.002				p.E446Q		Atlas-SNP	.											.	TBC1D14	110	.	0			c.G1336C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	4,4402	8.1+/-20.4	0,4,2199	108.0	110.0	109.0		1336,496,1336	5.3	0.0	4	dbSNP_120	109	45,8555	29.6+/-80.5	0,45,4255	yes	missense,missense,missense	TBC1D14	NM_001113361.1,NM_001113363.1,NM_020773.2	29,29,29	0,49,6454	CC,CG,GG		0.5233,0.0908,0.3767	benign,benign,benign	446/694,166/414,446/694	7006636	49,12957	2203	4300	6503	SO:0001583	missense	57533	exon8			GGCTCTGAAGTGG	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.1336G>C	4.37:g.7006636G>C	ENSP00000386921:p.Glu446Gln	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	37	CCDS3394.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	17.41	3.381565	0.61845	9.08E-4	0.005233	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000439515;ENST00000446947	T;T;T;T;T;T	0.33216	3.46;3.46;3.43;3.44;1.42;3.0	5.27	5.27	0.74061	Rab-GAP/TBC domain (4);	0.405543	0.28718	N	0.014366	T	0.33323	0.0859	M	0.63843	1.955	0.80722	D	1	B;B;B	0.22211	0.059;0.003;0.066	B;B;B	0.36092	0.097;0.009;0.217	T	0.23583	-1.0184	10	0.49607	T	0.09	-2.7179	18.059	0.89371	0.0:0.0:1.0:0.0	rs11731231;rs52800326;rs11731231	59;166;446	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	Q	446;446;218;166;65;59	ENSP00000404041:E446Q;ENSP00000386921:E446Q;ENSP00000386343:E218Q;ENSP00000388886:E166Q;ENSP00000389082:E65Q;ENSP00000405875:E59Q	ENSP00000386921:E446Q	E	+	1	0	TBC1D14	7057537	0.408000	0.25360	0.029000	0.17559	0.574000	0.36063	3.009000	0.49552	2.722000	0.93159	0.655000	0.94253	GAA	G|0.997;C|0.003	0.003	strong		0.458	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773	
KIF15	56992	hgsc.bcm.edu	37	3	44884647	44884647	+	Missense_Mutation	SNP	C	C	A	rs3804583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:44884647C>A	ENST00000326047.4	+	30	3765	c.3616C>A	c.(3616-3618)Ctg>Atg	p.L1206M	KIF15_ENST00000425755.1_Missense_Mutation_p.L841M	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	1206			L -> M (in dbSNP:rs3804583).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AAACCTACGCCTGGAAAGTCA	0.413													C|||	2643	0.527756	0.1573	0.5303	5008	,	,		19620	0.8492		0.5159	False		,,,				2504	0.7076				p.L1206M		Atlas-SNP	.											.	KIF15	103	.	0			c.C3616A						PASS	.	C	MET/LEU	938,3468	356.1+/-313.4	114,710,1379	84.0	90.0	88.0		3616	3.5	0.9	3	dbSNP_107	88	4161,4439	565.0+/-388.4	986,2189,1125	yes	missense	KIF15	NM_020242.2	15	1100,2899,2504	AA,AC,CC		48.3837,21.2892,39.205	benign	1206/1389	44884647	5099,7907	2203	4300	6503	SO:0001583	missense	56992	exon30			CTACGCCTGGAAA	AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.3616C>A	3.37:g.44884647C>A	ENSP00000324020:p.Leu1206Met	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	37	CCDS33744.1	1180	0.5402930402930403	88	0.17886178861788618	201	0.5552486187845304	505	0.8828671328671329	386	0.5092348284960422	C	16.43	3.120522	0.56613	0.212892	0.483837	ENSG00000163808	ENST00000326047;ENST00000425755	T;T	0.70164	-0.46;1.75	5.36	3.52	0.40303	.	0.626542	0.13005	N	0.421302	T	0.00012	0.0000	L	0.48642	1.525	0.32754	P	0.505993	B	0.21225	0.053	B	0.18263	0.021	T	0.34004	-0.9846	9	0.36615	T	0.2	.	9.7004	0.40182	0.1219:0.7566:0.0:0.1215	rs3804583;rs17631354;rs52789435;rs58380355;rs3804583	1206	Q9NS87	KIF15_HUMAN	M	1206;841	ENSP00000324020:L1206M;ENSP00000389982:L841M	ENSP00000324020:L1206M	L	+	1	2	KIF15	44859651	0.802000	0.28943	0.913000	0.36048	0.970000	0.65996	0.526000	0.22971	1.367000	0.46095	0.591000	0.81541	CTG	C|0.543;A|0.457	0.457	strong		0.413	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
MRPL19	9801	hgsc.bcm.edu	37	2	75882399	75882399	+	Silent	SNP	G	G	A	rs17689863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75882399G>A	ENST00000393909.2	+	6	892	c.867G>A	c.(865-867)tcG>tcA	p.S289S	MRPL19_ENST00000409374.1_Silent_p.S289S|MRPL19_ENST00000358788.6_Intron	NM_014763.3	NP_055578.2	P49406	RM19_HUMAN	mitochondrial ribosomal protein L19	289					translation (GO:0006412)	mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(6)	8						TTGAAGCGTCGAAAAGGTCTT	0.343													G|||	883	0.176318	0.0182	0.2305	5008	,	,		16035	0.1637		0.2435	False		,,,				2504	0.2955				p.S289S		Atlas-SNP	.											.	MRPL19	21	.	0			c.G867A						PASS	.	G		175,3491		3,169,1661	64.0	60.0	62.0		867	-8.2	0.0	2	dbSNP_123	62	2084,6072		263,1558,2257	no	coding-synonymous	MRPL19	NM_014763.3		266,1727,3918	AA,AG,GG		25.5517,4.7736,19.1084		289/293	75882399	2259,9563	1833	4078	5911	SO:0001819	synonymous_variant	9801	exon6			AGCGTCGAAAAGG	AB051621	CCDS1960.2	2p11.1-q11.2	2012-09-13			ENSG00000115364	ENSG00000115364		"""Mitochondrial ribosomal proteins / large subunits"""	14052	protein-coding gene	gene with protein product	"""39S ribosomal protein L19"""	611832				11543634, 17309879	Standard	XM_006712155		Approved	MRP-L15, RPML15, KIAA0104, RLX1	uc002snl.3	P49406	OTTHUMG00000129990	ENST00000393909.2:c.867G>A	2.37:g.75882399G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	154	55	0.357143	NM_014763	Q53TX9|Q96Q52	Silent	SNP	ENST00000393909.2	37	CCDS1960.2																																																																																			G|0.829;A|0.171	0.171	strong		0.343	MRPL19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252256.1	NM_014763	
XIRP2	129446	hgsc.bcm.edu	37	2	168099738	168099738	+	Silent	SNP	T	T	C	rs10497323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168099738T>C	ENST00000409195.1	+	9	1925	c.1836T>C	c.(1834-1836)ggT>ggC	p.G612G	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.G390G|XIRP2_ENST00000295237.9_Silent_p.G612G|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	437					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGCTGGTGGTGATGTGAAAT	0.428													C|||	1763	0.352037	0.5719	0.255	5008	,	,		19983	0.3284		0.169	False		,,,				2504	0.3364				p.G612G		Atlas-SNP	.											.	XIRP2	914	.	0			c.T1836C						PASS	.	C	,,,,	1921,2051		459,1003,524	88.0	92.0	91.0		,,1170,,1836	-5.3	0.7	2	dbSNP_119	91	1298,6980		100,1098,2941	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	559,2101,3465	CC,CT,TT		15.6801,48.3635,26.2776	,,,,	,,390/3328,,612/3550	168099738	3219,9031	1986	4139	6125	SO:0001819	synonymous_variant	129446	exon9			TGGTGGTGATGTG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.1836T>C	2.37:g.168099738T>C		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	258	115	0.445736	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			T|0.689;C|0.311	0.311	strong		0.428	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
CDK7	1022	hgsc.bcm.edu	37	5	68531253	68531253	+	Silent	SNP	C	C	T	rs2972388	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:68531253C>T	ENST00000256443.3	+	2	202	c.99C>T	c.(97-99)aaC>aaT	p.N33N	CDK7_ENST00000514676.1_Silent_p.N33N|CDK7_ENST00000513629.1_3'UTR|CDK7_ENST00000502604.1_5'UTR	NM_001799.3	NP_001790.1	P50613	CDK7_HUMAN	cyclin-dependent kinase 7	33	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				7-methylguanosine mRNA capping (GO:0006370)|androgen receptor signaling pathway (GO:0030521)|ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA-dependent ATPase activity (GO:0008094)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription coactivator activity (GO:0003713)			endometrium(1)|lung(2)	3		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)		GAGATAAGAACACCAACCAAA	0.323								Nucleotide excision repair (NER)					T|||	3154	0.629792	0.7693	0.6427	5008	,	,		20512	0.499		0.5427	False		,,,				2504	0.6564				p.N33N		Atlas-SNP	.											.	CDK7	48	.	0			c.C99T						PASS	.	T		3116,1290	438.2+/-345.2	1097,922,184	135.0	148.0	143.0		99	4.0	1.0	5	dbSNP_101	143	4639,3961	551.9+/-386.0	1273,2093,934	no	coding-synonymous	CDK7	NM_001799.3		2370,3015,1118	TT,TC,CC		46.0581,29.2783,40.3737		33/347	68531253	7755,5251	2203	4300	6503	SO:0001819	synonymous_variant	1022	exon2			TAAGAACACCAAC		CCDS3999.1	5q12.1	2012-11-05	2007-11-21		ENSG00000134058	ENSG00000134058		"""Cyclin-dependent kinases"", ""General transcription factor IIH complex subunits"""	1778	protein-coding gene	gene with protein product		601955	"""cyclin-dependent kinase 7 (homolog of Xenopus MO15 cdk-activating kinase)"", ""cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating kinase)"""			8069918	Standard	NM_001799		Approved	CAK1, CDKN7, MO15, STK1, CAK	uc003jvs.4	P50613	OTTHUMG00000099358	ENST00000256443.3:c.99C>T	5.37:g.68531253C>T		Somatic	295	2	0.00677966		WXS	Illumina HiSeq	Phase_I	248	248	1	NM_001799	Q9BS60|Q9UE19	Silent	SNP	ENST00000256443.3	37	CCDS3999.1																																																																																			C|0.407;T|0.593	0.593	strong		0.323	CDK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216802.3	NM_001799	
ERAP1	51752	hgsc.bcm.edu	37	5	96124330	96124330	+	Missense_Mutation	SNP	T	T	C	rs30187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96124330T>C	ENST00000443439.2	-	11	1649	c.1583A>G	c.(1582-1584)aAg>aGg	p.K528R	CTD-2260A17.1_ENST00000602972.1_RNA|ERAP1_ENST00000296754.3_Missense_Mutation_p.K528R|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000514604.1_5'Flank	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	528			K -> R (in dbSNP:rs30187). {ECO:0000269|PubMed:11481040, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:9628581, ECO:0000269|Ref.3}.		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)		GGGAAAACCCTTCTGCAGTGT	0.502													T|||	2986	0.596246	0.5976	0.5951	5008	,	,		21336	0.5466		0.6501	False		,,,				2504	0.591				p.K528R		Atlas-SNP	.											.	ERAP1	59	.	0			c.A1583G	GRCh37	CM020528	ERAP1	M	rs30187	PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	2629,1777	644.3+/-398.0	783,1063,357	169.0	129.0	142.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1583,1583,1583	6.2	1.0	5	dbSNP_76	142	5533,3067	659.8+/-401.7	1768,1997,535	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	26,26,26	2551,3060,892	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	35.6628,40.3314,37.2443	benign,benign,benign	528/942,528/942,528/949	96124330	8162,4844	2203	4300	6503	SO:0001583	missense	51752	exon11			AAACCCTTCTGCA	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.1583A>G	5.37:g.96124330T>C	ENSP00000406304:p.Lys528Arg	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	184	182	0.98913	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	1288	0.5897435897435898	283	0.5752032520325203	211	0.5828729281767956	292	0.5104895104895105	502	0.662269129287599	T	20.6	4.012271	0.75046	0.596686	0.643372	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.04654	3.58;3.58	6.17	6.17	0.99709	.	0.044645	0.85682	D	0.000000	T	0.00012	0.0000	M	0.86178	2.8	0.22796	P	0.99872577	D;D	0.71674	0.991;0.998	P;D	0.70016	0.889;0.967	T	0.29336	-1.0015	9	0.22706	T	0.39	.	16.4837	0.84171	0.0:0.0:0.0:1.0	rs30187;rs60932799;rs30187	528;528	Q9NZ08;Q9NZ08-2	ERAP1_HUMAN;.	R	528	ENSP00000296754:K528R;ENSP00000406304:K528R	ENSP00000296754:K528R	K	-	2	0	ERAP1	96150086	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.362000	0.79507	2.371000	0.80710	0.533000	0.62120	AAG	C|0.606;N|0.001	0.606	strong		0.502	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
ABCC6	368	hgsc.bcm.edu	37	16	16281007	16281007	+	Missense_Mutation	SNP	A	A	G	rs12931472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:16281007A>G	ENST00000205557.7	-	14	1870	c.1841T>C	c.(1840-1842)gTc>gCc	p.V614A	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	614			V -> A (in dbSNP:rs12931472). {ECO:0000269|PubMed:10835642, ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:11776382, ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	TGAGTCTACGACACCAGGGTC	0.602											OREG0023640	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1700	0.339457	0.3328	0.4957	5008	,	,		16349	0.1518		0.5	False		,,,				2504	0.2658				p.V614A		Atlas-SNP	.											.	ABCC6	110	.	0			c.T1841C						PASS	.	G	ALA/VAL	1687,2707	649.8+/-398.9	316,1055,826	50.0	41.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1841	3.8	0.0	16	dbSNP_121	44	4342,4258	571.3+/-389.5	1096,2150,1054	yes	missense	ABCC6	NM_001171.5	64	1412,3205,1880	GG,GA,AA		49.5116,38.3933,46.3983	benign	614/1504	16281007	6029,6965	2197	4300	6497	SO:0001583	missense	368	exon14			TCTACGACACCAG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1841T>C	16.37:g.16281007A>G	ENSP00000205557:p.Val614Ala	Somatic	44	0	0	709	WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	817	0.3740842490842491	178	0.3617886178861789	174	0.48066298342541436	91	0.1590909090909091	374	0.49340369393139843	G	4.895	0.166267	0.09339	0.383933	0.504884	ENSG00000091262	ENST00000205557;ENST00000456970;ENST00000546056	D;D	0.90069	-2.56;-2.61	4.84	3.85	0.44370	.	0.663319	0.12998	N	0.421879	T	0.00012	0.0000	N	0.03983	-0.305	0.58432	P	5.000000000032756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38672	-0.9650	9	0.19147	T	0.46	.	3.5818	0.07957	0.0941:0.1734:0.5664:0.1661	rs12931472;rs52812178;rs56825606;rs12931472	626;614	F5GWQ0;O95255	.;MRP6_HUMAN	A	614;614;626	ENSP00000205557:V614A;ENSP00000405002:V614A	ENSP00000205557:V614A	V	-	2	0	ABCC6	16188508	0.006000	0.16342	0.002000	0.10522	0.011000	0.07611	1.037000	0.30241	0.432000	0.26286	-0.215000	0.12644	GTC	A|0.599;G|0.400	0.400	strong		0.602	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
ASMTL	8623	hgsc.bcm.edu	37	X	1537881	1537881	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:1537881C>T	ENST00000381317.3	-	10	1404	c.1372G>A	c.(1372-1374)Gtg>Atg	p.V458M	ASMTL_ENST00000416733.2_Missense_Mutation_p.V382M|ASMTL_ENST00000381333.4_Missense_Mutation_p.V442M|ASMTL_ENST00000534940.1_Missense_Mutation_p.V400M	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	458	ASMT-like.		V -> M (in dbSNP:rs4503285). {ECO:0000269|PubMed:15489334}.			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)				CCACCTCCCACGTCGCAGGCG	0.612													c|||	1330	0.265575	0.3056	0.3127	5008	,	,		15599	0.2163		0.2247	False		,,,				2504	0.271				p.V458M		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1372A						PASS	.		MET/VAL,MET/VAL,MET/VAL	1063,2945		147,769,1088	30.0	42.0	38.0		1198,1324,1372	0.6	0.3	X	dbSNP_134	38	2099,6171		278,1543,2314	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	21,21,21	425,2312,3402	TT,TC,CC		25.3809,26.522,25.7534	possibly-damaging,possibly-damaging,possibly-damaging	400/564,442/606,458/622	1537881	3162,9116	2004	4135	6139	SO:0001583	missense	8623	exon10			CTCCCACGTCGCA	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.1372G>A	X.37:g.1537881C>T	ENSP00000370718:p.Val458Met	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	563	0.25778388278388276	137	0.2784552845528455	119	0.3287292817679558	129	0.22552447552447552	178	0.23482849604221637	c	5.889	0.348066	0.11126	0.26522	0.253809	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	1.58	0.547	0.17202	O-methyltransferase, family 2 (1);	0.209188	0.30293	U	0.009956	T	0.00012	0.0000	M	0.64170	1.965	0.09310	N	1	D;D;D	0.59357	0.973;0.985;0.973	P;B;B	0.46253	0.509;0.405;0.322	T	0.29336	-1.0015	10	0.66056	D	0.02	.	2.9037	0.05714	0.4205:0.2351:0.3444:0.0	rs4503285;rs17855417;rs4503285	382;442;458	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	M	382;400;442;458	ENSP00000410578:V382M;ENSP00000446410:V400M;ENSP00000370734:V442M;ENSP00000370718:V458M	ENSP00000370718:V458M	V	-	1	0	ASMTL	1497881	1.000000	0.71417	0.298000	0.25002	0.157000	0.22087	0.547000	0.23299	-0.451000	0.07097	0.100000	0.15512	GTG	C|0.757;T|0.243	0.243	strong		0.612	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
RAD50	10111	hgsc.bcm.edu	37	5	131924538	131924538	+	Missense_Mutation	SNP	A	A	G	rs200017020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:131924538A>G	ENST00000265335.6	+	8	1598	c.1211A>G	c.(1210-1212)cAa>cGa	p.Q404R	RAD50_ENST00000378823.3_Missense_Mutation_p.Q265R			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	404					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGAGAGACAAGAAGGGGAA	0.358								Homologous recombination					A|||	2	0.000399361	0.0	0.0	5008	,	,		16369	0.002		0.0	False		,,,				2504	0.0				p.Q404R		Atlas-SNP	.											.	RAD50	246	.	0			c.A1211G						PASS	.						77.0	77.0	77.0					5																	131924538		2203	4300	6503	SO:0001583	missense	10111	exon8			AGAGACAAGAAGG	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"""RAD50 (S. cerevisiae) homolog"""			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.1211A>G	5.37:g.131924538A>G	ENSP00000265335:p.Gln404Arg	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	174	95	0.545977	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	9.857	1.195145	0.22037	.	.	ENSG00000113522	ENST00000378823;ENST00000265335;ENST00000453394	T;T;T	0.09073	3.51;3.02;3.02	5.97	4.8	0.61643	.	0.173879	0.52532	D	0.000075	T	0.09992	0.0245	L	0.57536	1.79	0.33889	D	0.637111	B	0.30511	0.282	B	0.26517	0.07	T	0.10132	-1.0643	10	0.32370	T	0.25	-11.145	11.8328	0.52305	0.8688:0.0:0.0:0.1312	.	404	Q92878	RAD50_HUMAN	R	265;404;404	ENSP00000368100:Q265R;ENSP00000265335:Q404R;ENSP00000400049:Q404R	ENSP00000265335:Q404R	Q	+	2	0	RAD50	131952437	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.243000	0.51392	1.062000	0.40625	-0.333000	0.08304	CAA	A|1.000;G|0.000	0.000	strong		0.358	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732	
METTL16	79066	hgsc.bcm.edu	37	17	2323517	2323517	+	Missense_Mutation	SNP	C	C	T	rs17834783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:2323517C>T	ENST00000263092.6	-	10	1563	c.1436G>A	c.(1435-1437)aGt>aAt	p.S479N	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Missense_Mutation_p.S261N	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	479			S -> N (in dbSNP:rs17834783). {ECO:0000269|PubMed:15489334}.				methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(9)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	19						GCCTTGACAACTTTCCAAAAC	0.612													C|||	133	0.0265575	0.0076	0.036	5008	,	,		17914	0.0		0.0577	False		,,,				2504	0.0409				p.S479N		Atlas-SNP	.											.	METTL16	75	.	0			c.G1436A						PASS	.	C	ASN/SER	51,3845		2,47,1899	121.0	129.0	126.0		1436	3.6	0.3	17	dbSNP_123	126	646,7630		20,606,3512	yes	missense	METTL16	NM_024086.3	46	22,653,5411	TT,TC,CC		7.8057,1.309,5.7263	benign	479/563	2323517	697,11475	1948	4138	6086	SO:0001583	missense	79066	exon10			TGACAACTTTCCA	AK027410	CCDS42232.1	17p13.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000127804	ENSG00000127804			28484	protein-coding gene	gene with protein product			"""methyltransferase 10 domain containing"""	METT10D		18021804	Standard	NM_024086		Approved	MGC3329	uc002fut.3	Q86W50		ENST00000263092.6:c.1436G>A	17.37:g.2323517C>T	ENSP00000263092:p.Ser479Asn	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	66	20	0.30303	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	63	0.028846153846153848	6	0.012195121951219513	12	0.03314917127071823	0	0.0	45	0.059366754617414245	C	6.548	0.469345	0.12461	0.01309	0.078057	ENSG00000127804	ENST00000263092;ENST00000537138;ENST00000538844	T;T	0.47177	0.89;0.85	5.65	3.62	0.41486	.	0.875556	0.10532	N	0.663709	T	0.02193	0.0068	L	0.36672	1.1	0.09310	N	0.999999	B	0.18610	0.029	B	0.17722	0.019	T	0.07046	-1.0793	10	0.25106	T	0.35	.	7.918	0.29829	0.0:0.753:0.1608:0.0862	rs17834783;rs17854652;rs52796630;rs61363252;rs17834783	479	Q86W50	MET16_HUMAN	N	479;159;261	ENSP00000263092:S479N;ENSP00000443633:S261N	ENSP00000263092:S479N	S	-	2	0	METTL16	2270267	0.144000	0.22641	0.290000	0.24890	0.144000	0.21451	0.444000	0.21661	0.715000	0.32103	0.644000	0.83932	AGT	C|0.956;T|0.044	0.044	strong		0.612	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086	
OR51B6	390058	hgsc.bcm.edu	37	11	5373006	5373006	+	Missense_Mutation	SNP	T	T	C	rs7483122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373006T>C	ENST00000380219.1	+	1	269	c.269T>C	c.(268-270)aTt>aCt	p.I90T	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	90			I -> T (in dbSNP:rs7483122). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CACAGGGAGATTGGCCATGGA	0.468													T|||	1172	0.234026	0.3275	0.2349	5008	,	,		22609	0.0863		0.2644	False		,,,				2504	0.228				p.I90T		Atlas-SNP	.											.	OR51B6	53	.	0			c.T269C						PASS	.	T	THR/ILE	1298,3104	441.6+/-346.4	177,944,1080	131.0	123.0	126.0		269	5.0	1.0	11	dbSNP_116	126	2268,6326	382.1+/-340.3	310,1648,2339	yes	missense	OR51B6	NM_001004750.1	89	487,2592,3419	CC,CT,TT		26.3905,29.4866,27.4392	benign	90/313	5373006	3566,9430	2201	4297	6498	SO:0001583	missense	390058	exon1			GGGAGATTGGCCA		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.269T>C	11.37:g.5373006T>C	ENSP00000369568:p.Ile90Thr	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	58	0.371795	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	473	0.21657509157509158	160	0.3252032520325203	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	T	13.29	2.191954	0.38707	0.294866	0.263905	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00605	6.27	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000053	T	0.00012	0.0000	H	0.96889	3.9	0.22947	P	0.99852053	B	0.34290	0.447	B	0.34242	0.178	T	0.14839	-1.0458	9	0.66056	D	0.02	.	13.6838	0.62504	0.0:0.0:0.0:1.0	rs7483122;rs52804602;rs59784769;rs7483122	90	Q9H340	O51B6_HUMAN	T	89;90	ENSP00000369568:I90T	ENSP00000369568:I90T	I	+	2	0	OR51B6	5329582	1.000000	0.71417	0.955000	0.39395	0.480000	0.33159	4.774000	0.62339	2.103000	0.63969	0.374000	0.22700	ATT	T|0.768;C|0.232	0.232	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
FHOD1	29109	hgsc.bcm.edu	37	16	67268008	67268008	+	Missense_Mutation	SNP	G	G	A	rs77958237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67268008G>A	ENST00000258201.4	-	13	1845	c.1598C>T	c.(1597-1599)cCt>cTt	p.P533L		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	533	FH1.			P -> L (in Ref. 6; BAD92821). {ECO:0000305}.	positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		TGCACGGGTAGGGAGCTCCCA	0.612													G|||	164	0.0327476	0.0393	0.0331	5008	,	,		12559	0.0208		0.0368	False		,,,				2504	0.0317				p.P533L		Atlas-SNP	.											.	FHOD1	86	.	0			c.C1598T						PASS	.	G	LEU/PRO	237,4159	138.8+/-174.5	6,225,1967	86.0	93.0	91.0		1598	0.5	0.0	16	dbSNP_131	91	324,8276	112.7+/-172.9	10,304,3986	yes	missense	FHOD1	NM_013241.2	98	16,529,5953	AA,AG,GG		3.7674,5.3913,4.3167	probably-damaging	533/1165	67268008	561,12435	2198	4300	6498	SO:0001583	missense	29109	exon13			CGGGTAGGGAGCT	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.1598C>T	16.37:g.67268008G>A	ENSP00000258201:p.Pro533Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	127	57	0.448819	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	37	CCDS10834.1	68	0.031135531135531136	23	0.046747967479674794	12	0.03314917127071823	10	0.017482517482517484	23	0.030343007915567283	G	0.050	-1.252792	0.01469	0.053913	0.037674	ENSG00000135723	ENST00000258201	T	0.33216	1.42	4.95	0.493	0.16878	.	0.554699	0.20217	N	0.096794	T	0.02083	0.0065	N	0.19112	0.55	0.23180	N	0.998161	B;B	0.12630	0.006;0.0	B;B	0.08055	0.003;0.0	T	0.21793	-1.0235	10	0.16896	T	0.51	.	6.0291	0.19671	0.1684:0.2879:0.5438:0.0	.	112;533	B4DVN5;Q9Y613	.;FHOD1_HUMAN	L	533	ENSP00000258201:P533L	ENSP00000258201:P533L	P	-	2	0	FHOD1	65825509	0.185000	0.23213	0.002000	0.10522	0.057000	0.15508	0.677000	0.25262	0.118000	0.18165	0.561000	0.74099	CCT	G|0.958;A|0.042	0.042	strong		0.612	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939674	12939674	+	Silent	SNP	C	C	G	rs28546260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12939674C>G	ENST00000235349.5	-	4	1198	c.1128G>C	c.(1126-1128)ctG>ctC	p.L376L		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	376					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.L376L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGCAGCGGCTCAGGGCAGGCA	0.498													c|||	579	0.115615	0.1362	0.1023	5008	,	,		20404	0.1399		0.1123	False		,,,				2504	0.0757				p.L376L		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,2	PRAMEF4	62	2	1	Substitution - coding silent(1)	prostate(1)	c.G1128C						scavenged	.	C		435,2561		63,309,1126	95.0	99.0	97.0		1128	1.5	0.5	1	dbSNP_130	97	620,4750		69,482,2134	no	coding-synonymous	PRAMEF4	NM_001009611.2		132,791,3260	GG,GC,CC		11.5456,14.5194,12.6106		376/479	12939674	1055,7311	1498	2685	4183	SO:0001819	synonymous_variant	400735	exon4			GCGGCTCAGGGCA		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"""-"""	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.1128G>C	1.37:g.12939674C>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_001009611	Q5LJB5	Silent	SNP	ENST00000235349.5	37	CCDS30592.1																																																																																			C|0.879;G|0.121	0.121	strong		0.498	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
OR13C5	138799	hgsc.bcm.edu	37	9	107361129	107361129	+	Missense_Mutation	SNP	C	C	T	rs4117966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107361129C>T	ENST00000374779.2	-	1	659	c.566G>A	c.(565-567)tGt>tAt	p.C189Y		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	189			C -> Y (in dbSNP:rs4117966).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						GATGTCAGCACAGGCCAGTTT	0.388													C|||	1820	0.363419	0.3994	0.2133	5008	,	,		24769	0.5645		0.1789	False		,,,				2504	0.4039				p.C189Y		Atlas-SNP	.											.	OR13C5	60	.	0			c.G566A						PASS	.	C	TYR/CYS	1567,2839	492.0+/-362.3	283,1001,919	183.0	169.0	173.0		566	4.2	0.3	9	dbSNP_108	173	1660,6940	306.8+/-308.1	182,1296,2822	no	missense	OR13C5	NM_001004482.1	194	465,2297,3741	TT,TC,CC		19.3023,35.5651,24.8116	probably-damaging	189/319	107361129	3227,9779	2203	4300	6503	SO:0001583	missense	138799	exon1			TCAGCACAGGCCA		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.566G>A	9.37:g.107361129C>T	ENSP00000363911:p.Cys189Tyr	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	376	184	0.489362	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	700	0.32051282051282054	174	0.35365853658536583	72	0.19889502762430938	322	0.5629370629370629	132	0.1741424802110818	C	19.12	3.766581	0.69878	0.355651	0.193023	ENSG00000255800	ENST00000374779	T	0.00462	7.26	4.17	4.17	0.49024	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40469	U	0.001090	T	0.00012	0.0000	H	0.97077	3.935	0.28200	P	0.9273963000000001	D	0.89917	1.0	D	0.97110	1.0	T	0.13124	-1.0521	9	0.87932	D	0	.	14.0519	0.64742	0.0:1.0:0.0:0.0	rs4117966;rs52805780;rs57944987;rs4117966	189	Q8NGS8	O13C5_HUMAN	Y	189	ENSP00000363911:C189Y	ENSP00000363911:C189Y	C	-	2	0	OR13C5	106400950	0.971000	0.33674	0.337000	0.25536	0.483000	0.33249	2.706000	0.47135	2.169000	0.68431	0.531000	0.56144	TGT	C|0.726;T|0.274	0.274	strong		0.388	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
CFAP61	26074	hgsc.bcm.edu	37	20	20144772	20144772	+	Missense_Mutation	SNP	G	G	A	rs6081901	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:20144772G>A	ENST00000245957.5	+	11	1181	c.1105G>A	c.(1105-1107)Gta>Ata	p.V369I	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Missense_Mutation_p.V369I|C20orf26_ENST00000377306.1_Missense_Mutation_p.V369I|C20orf26_ENST00000377309.2_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		369			V -> I (in dbSNP:rs6081901). {ECO:0000269|PubMed:15489334}.							NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		GGCATCGCTCGTACTGCCTGA	0.488													A|||	2298	0.458866	0.559	0.4265	5008	,	,		17163	0.2778		0.5497	False		,,,				2504	0.4397				p.V369I		Atlas-SNP	.											.	C20orf26	188	.	0			c.G1105A						PASS	.	A	ILE/VAL,ILE/VAL	2423,1983	557.4+/-379.7	674,1075,454	132.0	122.0	125.0		1105,1105	-2.9	0.0	20	dbSNP_114	125	4808,3792	537.6+/-383.2	1359,2090,851	yes	missense,missense	C20orf26	NM_001167816.1,NM_015585.3	29,29	2033,3165,1305	AA,AG,GG		44.093,45.0068,44.4026	benign,benign	369/471,369/1238	20144772	7231,5775	2203	4300	6503	SO:0001583	missense	26074	exon11			TCGCTCGTACTGC																												ENST00000245957.5:c.1105G>A	20.37:g.20144772G>A	ENSP00000245957:p.Val369Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	1001	0.4583333333333333	284	0.5772357723577236	158	0.43646408839779005	147	0.256993006993007	412	0.5435356200527705	A	7.318	0.616292	0.14129	0.549932	0.55907	ENSG00000089101	ENST00000340348;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000451767	T;T;T	0.07114	3.22;3.22;3.22	5.05	-2.89	0.05665	.	3.546850	0.00970	N	0.003235	T	0.00012	0.0000	N	0.14661	0.345	0.58432	P	2.9999999999752447E-6	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.0;0.0;0.0;0.001	T	0.45160	-0.9280	9	0.17832	T	0.49	.	0.4809	0.00547	0.2484:0.2739:0.2489:0.2287	rs6081901;rs17398861;rs17856819;rs56641477;rs58930563;rs6081901	369;369;324;369	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	I	324;369;369;369;369	ENSP00000245957:V369I;ENSP00000366521:V369I;ENSP00000414537:V369I	ENSP00000245957:V369I	V	+	1	0	C20orf26	20092772	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.461000	0.06712	-0.700000	0.05070	-1.046000	0.02355	GTA	G|0.482;A|0.518	0.518	strong		0.488	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
MUC20	200958	hgsc.bcm.edu	37	3	195453257	195453257	+	Missense_Mutation	SNP	G	G	A	rs3828406	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195453257G>A	ENST00000447234.2	+	2	1909	c.1783G>A	c.(1783-1785)Gca>Aca	p.A595T	MUC20_ENST00000445522.2_Missense_Mutation_p.A560T|MUC20_ENST00000320736.6_Missense_Mutation_p.A424T|MUC20_ENST00000436408.1_Missense_Mutation_p.A595T	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	595	Involved in oligomerization.|Thr-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)				NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CATGGACATCGCAACCAAGGG	0.582																																					p.A424T		Atlas-SNP	.											.	MUC20	84	.	0			c.G1270A						PASS	.		THR/ALA,THR/ALA	1253,2893		58,1137,878	62.0	60.0	61.0		1165,1270	4.5	0.0	3	dbSNP_107	61	2926,5464		178,2570,1447	no	missense,missense	MUC20	NM_001098516.1,NM_152673.2	58,58	236,3707,2325	AA,AG,GG		34.8749,30.2219,33.336	benign,benign	389/504,424/539	195453257	4179,8357	2073	4195	6268	SO:0001583	missense	200958	exon3			GACATCGCAACCA	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.1783G>A	3.37:g.195453257G>A	ENSP00000414350:p.Ala595Thr	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	155	48	0.309677	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		802|802	0.36721611721611724|0.36721611721611724	178|178	0.3617886178861789|0.3617886178861789	124|124	0.3425414364640884|0.3425414364640884	251|251	0.4388111888111888|0.4388111888111888	249|249	0.32849604221635886|0.32849604221635886	A|A	1.905|1.905	-0.452224|-0.452224	0.04540|0.04540	0.302219|0.302219	0.348749|0.348749	ENSG00000176945|ENSG00000176945	ENST00000381954;ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522|ENST00000423938	T;T;T;T|.	0.12361|.	3.1;3.04;3.26;2.69|.	4.48|4.48	4.48|4.48	0.54585|0.54585	.|.	0.826684|.	0.10455|.	N|.	0.672700|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01048|0.01048	-1.04|-1.04	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.44726|0.44726	-0.9309|-0.9309	9|4	0.02654|.	T|.	1|.	-0.0298|-0.0298	7.0355|7.0355	0.24991|0.24991	0.8978:0.0:0.1022:0.0|0.8978:0.0:0.1022:0.0	rs3828406;rs9870845|rs3828406;rs9870845	424|.	E9PH32|.	.|.	T|H	406;595;424;595;560|6	ENSP00000414350:A595T;ENSP00000325431:A424T;ENSP00000396774:A595T;ENSP00000405629:A560T|.	ENSP00000325431:A424T|.	A|R	+|+	1|2	0|0	MUC20|MUC20	196938928|196938928	0.001000|0.001000	0.12720|0.12720	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	1.433000|1.433000	0.34947|0.34947	0.859000|0.859000	0.35456|0.35456	-0.375000|-0.375000	0.07067|0.07067	GCA|CGC	G|0.643;A|0.357	0.357	strong		0.582	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
CCDC137	339230	hgsc.bcm.edu	37	17	79634774	79634774	+	Missense_Mutation	SNP	A	A	T	rs61742303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79634774A>T	ENST00000329214.8	+	2	553	c.150A>T	c.(148-150)aaA>aaT	p.K50N	OXLD1_ENST00000571503.1_5'Flank|OXLD1_ENST00000374741.3_5'Flank|OXLD1_ENST00000573786.1_5'Flank	NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	50							poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			AGAAGAAGAAAGTGAACTGCA	0.493													A|||	537	0.107228	0.1467	0.0951	5008	,	,		17005	0.002		0.1928	False		,,,				2504	0.0828				p.K50N		Atlas-SNP	.											.	CCDC137	27	.	0			c.A150T						PASS	.	A	ASN/LYS	722,3022		70,582,1220	58.0	62.0	61.0		150	0.8	1.0	17	dbSNP_129	61	1370,6838		127,1116,2861	yes	missense	CCDC137	NM_199287.2	94	197,1698,4081	TT,TA,AA		16.691,19.2842,17.5033	probably-damaging	50/290	79634774	2092,9860	1872	4104	5976	SO:0001583	missense	339230	exon2			GAAGAAAGTGAAC	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.150A>T	17.37:g.79634774A>T	ENSP00000329360:p.Lys50Asn	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	244	0.11172161172161173	72	0.14634146341463414	41	0.1132596685082873	0	0.0	131	0.17282321899736147	A	17.85	3.491233	0.64074	0.192842	0.16691	ENSG00000185298	ENST00000329214	D	0.90788	-2.73	4.26	0.759	0.18438	.	0.625364	0.15478	N	0.260244	T	0.01353	0.0044	M	0.78637	2.42	0.31061	P	0.714183	D	0.58268	0.982	P	0.54924	0.764	T	0.41179	-0.9523	9	0.72032	D	0.01	0.0104	7.9003	0.29731	0.6186:0.0:0.3814:0.0	rs61742303	50	Q6PK04	CC137_HUMAN	N	50	ENSP00000329360:K50N	ENSP00000329360:K50N	K	+	3	2	CCDC137	77245179	0.956000	0.32656	0.997000	0.53966	0.879000	0.50718	0.792000	0.26929	0.221000	0.20879	0.460000	0.39030	AAA	A|0.867;T|0.133	0.133	strong		0.493	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
OR4C46	119749	hgsc.bcm.edu	37	11	51515912	51515912	+	Missense_Mutation	SNP	C	C	T	rs77689730	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:51515912C>T	ENST00000328188.1	+	1	631	c.631C>T	c.(631-633)Ctc>Ttc	p.L211F		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						AAACTTTGCCCTCCTGCTGGT	0.517													.|||	978	0.195288	0.1626	0.1671	5008	,	,		20373	0.2262		0.0954	False		,,,				2504	0.3303				p.L211F		Atlas-SNP	.											OR4C46,NS,carcinoma,-2,1	OR4C46	96	1	0			c.C631T						scavenged	.	C	PHE/LEU	708,3694		58,592,1551	123.0	106.0	111.0		631	0.3	0.0	11	dbSNP_131	111	902,7690		54,794,3448	yes	missense	OR4C46	NM_001004703.1	22	112,1386,4999	TT,TC,CC		10.4981,16.0836,12.3903	benign	211/310	51515912	1610,11384	2201	4296	6497	SO:0001583	missense	119749	exon1			TTTGCCCTCCTGC		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.631C>T	11.37:g.51515912C>T	ENSP00000329056:p.Leu211Phe	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	147	2	0.0136054	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	354	0.1620879120879121	89	0.18089430894308944	53	0.1464088397790055	145	0.2534965034965035	67	0.08839050131926121	.	0.623	-0.820491	0.02755	0.160836	0.104981	ENSG00000185926	ENST00000328188	T	0.42131	0.98	2.47	0.291	0.15732	GPCR, rhodopsin-like superfamily (1);	0.425624	0.17845	N	0.160070	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B	0.20988	0.05	B	0.29077	0.098	T	0.28618	-1.0038	9	0.51188	T	0.08	.	4.736	0.12988	0.2095:0.6582:0.0:0.1323	.	211	A6NHA9	O4C46_HUMAN	F	211	ENSP00000329056:L211F	ENSP00000329056:L211F	L	+	1	0	OR4C46	51372488	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.168000	0.01270	-0.027000	0.13873	-1.492000	0.00969	CTC	C|0.864;T|0.136	0.136	strong		0.517	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
KRT32	3882	hgsc.bcm.edu	37	17	39620399	39620399	+	Silent	SNP	C	C	T	rs12948056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39620399C>T	ENST00000225899.3	-	5	1030	c.927G>A	c.(925-927)caG>caA	p.Q309Q		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	309	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				TGATGTCTGACTGGTAGTTCT	0.582													C|||	1523	0.304113	0.2095	0.3818	5008	,	,		21394	0.3145		0.4215	False		,,,				2504	0.2454				p.Q309Q		Atlas-SNP	.											KRT32,rectum,carcinoma,0,1	KRT32	57	1	0			c.G927A						PASS	.	C		935,3471	357.1+/-313.8	98,739,1366	175.0	132.0	147.0		927	4.1	1.0	17	dbSNP_121	147	3179,5421	481.6+/-370.7	611,1957,1732	no	coding-synonymous	KRT32	NM_002278.3		709,2696,3098	TT,TC,CC		36.9651,21.2211,31.6316		309/449	39620399	4114,8892	2203	4300	6503	SO:0001819	synonymous_variant	3882	exon5			GTCTGACTGGTAG	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.927G>A	17.37:g.39620399C>T		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_002278		Silent	SNP	ENST00000225899.3	37	CCDS11393.1																																																																																			C|0.683;N|0.000	.	strong		0.582	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
MUC16	94025	hgsc.bcm.edu	37	19	9060085	9060085	+	Missense_Mutation	SNP	C	C	T	rs4804382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9060085C>T	ENST00000397910.4	-	3	27564	c.27361G>A	c.(27361-27363)Gct>Act	p.A9121T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	9123	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						CTCATAAGAGCGGTCATCTGT	0.493													c|||	1008	0.201278	0.0938	0.2824	5008	,	,		23200	0.3254		0.167	False		,,,				2504	0.1963				p.A9121T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G27361A						PASS	.	T	THR/ALA	406,3520		19,368,1576	90.0	84.0	86.0		27361	-0.8	0.0	19	dbSNP_111	86	1512,6774		137,1238,2768	no	missense	MUC16	NM_024690.2	58	156,1606,4344	TT,TC,CC		18.2476,10.3413,15.7059	benign	9121/14508	9060085	1918,10294	1963	4143	6106	SO:0001583	missense	94025	exon3			TAAGAGCGGTCAT	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.27361G>A	19.37:g.9060085C>T	ENSP00000381008:p.Ala9121Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	160	95	0.59375	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	479	0.21932234432234432	56	0.11382113821138211	92	0.2541436464088398	205	0.3583916083916084	126	0.1662269129287599	c	6.642	0.486880	0.12641	0.103413	0.182476	ENSG00000181143	ENST00000397910	T	0.16597	2.33	1.7	-0.777	0.10981	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.46582	-0.9181	8	0.87932	D	0	.	2.2742	0.04098	0.2376:0.3365:0.0:0.426	rs4804382;rs52817559;rs4804382	9121	B5ME49	.	T	9121	ENSP00000381008:A9121T	ENSP00000381008:A9121T	A	-	1	0	MUC16	8921085	0.000000	0.05858	0.000000	0.03702	0.113000	0.19764	-0.563000	0.05943	-0.829000	0.04268	-0.965000	0.02619	GCT	C|0.786;T|0.214	0.214	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
NCKAP5	344148	hgsc.bcm.edu	37	2	133540176	133540176	+	Missense_Mutation	SNP	A	A	G	rs2278752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:133540176A>G	ENST00000409261.1	-	14	4581	c.4208T>C	c.(4207-4209)gTa>gCa	p.V1403A	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000317721.6_Missense_Mutation_p.V1403A|NCKAP5_ENST00000405974.3_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1403			V -> A (in dbSNP:rs2278752).							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						TTCCCCAAGTACAGCCACATT	0.612													A|||	359	0.0716853	0.1339	0.0173	5008	,	,		15117	0.1111		0.0089	False		,,,				2504	0.0501				p.V1403A		Atlas-SNP	.											.	NCKAP5	322	.	0			c.T4208C						PASS	.	A	ALA/VAL,	466,3524		27,412,1556	46.0	49.0	48.0		4208,	-1.3	0.0	2	dbSNP_100	48	69,8235		0,69,4083	yes	missense,intron	NCKAP5	NM_207363.2,NM_207481.3	64,	27,481,5639	GG,GA,AA		0.8309,11.6792,4.3517	benign,	1403/1910,	133540176	535,11759	1995	4152	6147	SO:0001583	missense	344148	exon14			CCAAGTACAGCCA	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.4208T>C	2.37:g.133540176A>G	ENSP00000387128:p.Val1403Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	87	29	0.333333	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	156	0.07142857142857142	68	0.13821138211382114	8	0.022099447513812154	73	0.12762237762237763	7	0.009234828496042216	A	0.973	-0.699419	0.03279	0.116792	0.008309	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10005	2.92;2.92	5.5	-1.27	0.09347	.	0.957602	0.08400	N	0.951506	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47623	-0.9103	9	0.12430	T	0.62	.	6.5714	0.22541	0.6839:0.2177:0.0984:0.0	rs2278752;rs2278752	1403	O14513	NCKP5_HUMAN	A	1403	ENSP00000387128:V1403A;ENSP00000380603:V1403A	ENSP00000380603:V1403A	V	-	2	0	NCKAP5	133256646	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.098000	0.11024	-0.333000	0.08476	0.533000	0.62120	GTA	A|0.931;G|0.069	0.069	strong		0.612	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
BCAS4	55653	hgsc.bcm.edu	37	20	49411698	49411698	+	Missense_Mutation	SNP	G	G	T	rs2272962	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:49411698G>T	ENST00000358791.5	+	1	268	c.168G>T	c.(166-168)gaG>gaT	p.E56D	BCAS4_ENST00000262591.5_Missense_Mutation_p.E56D|BCAS4_ENST00000485049.1_3'UTR|BCAS4_ENST00000609336.1_Missense_Mutation_p.E26D|BCAS4_ENST00000371608.2_Missense_Mutation_p.E56D	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	56			E -> D (in dbSNP:rs2272962).			cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						TGACCCCCGAGCCTGGGGCCG	0.721													G|||	779	0.155551	0.093	0.1585	5008	,	,		8914	0.1329		0.1968	False		,,,				2504	0.2188				p.E56D		Atlas-SNP	.											.	BCAS4	41	.	0			c.G168T						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	179,2153		4,171,991	1.0	2.0	2.0		168,168,168	2.8	1.0	20	dbSNP_100	2	626,4430		16,594,1918	yes	missense,missense,missense	BCAS4	NM_001010974.1,NM_017843.3,NM_198799.2	45,45,45	20,765,2909	TT,TG,GG		12.3813,7.6758,10.896	benign,benign,benign	56/159,56/212,56/204	49411698	805,6583	1166	2528	3694	SO:0001583	missense	55653	exon1			CCCCGAGCCTGGG	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.168G>T	20.37:g.49411698G>T	ENSP00000351642:p.Glu56Asp	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	19	8	0.421053	NM_198799	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	Missense_Mutation	SNP	ENST00000358791.5	37	CCDS33487.1	306|306	0.1401098901098901|0.1401098901098901	58|58	0.11788617886178862|0.11788617886178862	45|45	0.12430939226519337|0.12430939226519337	61|61	0.10664335664335664|0.10664335664335664	142|142	0.18733509234828497|0.18733509234828497	G|G	9.245|9.245	1.039207|1.039207	0.19669|0.19669	0.076758|0.076758	0.123813|0.123813	ENSG00000124243|ENSG00000124243	ENST00000358791;ENST00000262591;ENST00000355583;ENST00000371608|ENST00000445038	T;T;T|.	0.46451|.	1.88;0.9;0.87|.	4.77|4.77	2.77|2.77	0.32553|0.32553	.|.	0.376195|.	0.29246|.	N|.	0.012709|.	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.28274|0.28274	0.84|0.84	0.44055|0.44055	P|P	0.003210000000000046|0.003210000000000046	D;B;D;D|.	0.76494|.	0.999;0.039;0.999;0.999|.	D;B;D;D|.	0.79108|.	0.992;0.042;0.992;0.992|.	T|T	0.14172|0.14172	-1.0482|-1.0482	9|4	0.12430|.	T|.	0.62|.	-23.8746|-23.8746	7.8073|7.8073	0.29211|0.29211	0.205:0.0:0.795:0.0|0.205:0.0:0.795:0.0	rs2272962|rs2272962	56;56;56;56|.	Q8TDM0-2;Q8TDM0-3;Q8TDM0;F8WE92|.	.;.;BCAS4_HUMAN;.|.	D|I	56|31	ENSP00000351642:E56D;ENSP00000262591:E56D;ENSP00000360669:E56D|.	ENSP00000262591:E56D|.	E|S	+|+	3|2	2|0	BCAS4|BCAS4	48845105|48845105	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.329000|0.329000	0.28539|0.28539	0.885000|0.885000	0.28227|0.28227	0.995000|0.995000	0.38917|0.38917	0.484000|0.484000	0.47621|0.47621	GAG|AGC	G|0.867;T|0.133	0.133	strong		0.721	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079700.1	NM_017843	
ATP13A2	23400	hgsc.bcm.edu	37	1	17314702	17314702	+	Silent	SNP	C	C	T	rs3738815	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17314702C>T	ENST00000326735.8	-	25	2823	c.2790G>A	c.(2788-2790)tcG>tcA	p.S930S	RP1-37C10.3_ENST00000446261.1_RNA|ATP13A2_ENST00000341676.5_Silent_p.S886S|ATP13A2_ENST00000452699.1_Silent_p.S925S			Q9NQ11	AT132_HUMAN	ATPase type 13A2	930					cell death (GO:0008219)|cellular response to manganese ion (GO:0071287)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Colorectal(325;0.000147)|Breast(348;0.00104)|Renal(390;0.00145)|Lung NSC(340;0.00566)|all_lung(284;0.00797)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|COAD - Colon adenocarcinoma(227;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;1.99e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.182)		AGACGCTGAACGAAGTGTCAA	0.607													C|||	1457	0.290935	0.1369	0.3429	5008	,	,		21211	0.5774		0.2058	False		,,,				2504	0.2546				p.S930S		Atlas-SNP	.											ATP13A2,NS,carcinoma,-1,1	ATP13A2	85	1	0			c.G2790A						PASS	.	C	,,	659,3747	280.5+/-275.4	56,547,1600	142.0	127.0	132.0		2775,2658,2790	-11.0	0.0	1	dbSNP_107	132	1657,6943	305.7+/-307.6	145,1367,2788	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP13A2	NM_001141973.1,NM_001141974.1,NM_022089.2	,,	201,1914,4388	TT,TC,CC		19.2674,14.9569,17.8072	,,	925/1176,886/1159,930/1181	17314702	2316,10690	2203	4300	6503	SO:0001819	synonymous_variant	23400	exon25			GCTGAACGAAGTG	AL354615	CCDS175.1, CCDS44072.1, CCDS44073.1	1p36	2014-09-17			ENSG00000159363	ENSG00000159363		"""ATPases / P-type"", ""Parkinson disease"""	30213	protein-coding gene	gene with protein product		610513	"""Parkinson disease (autosomal recessive) 9 (Kufor-Rakeb syndrome)"""	PARK9		15381061, 16964263	Standard	XM_005245809		Approved	HSA9947, CLN12	uc001baa.2	Q9NQ11	OTTHUMG00000002293	ENST00000326735.8:c.2790G>A	1.37:g.17314702C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	140	135	0.964286	NM_022089	O75700|Q5JXY1|Q5JXY2|Q6S9Z9	Silent	SNP	ENST00000326735.8	37	CCDS175.1																																																																																			C|0.770;T|0.230	0.230	strong		0.607	ATP13A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006617.1	NM_022089	
CCDC146	57639	hgsc.bcm.edu	37	7	76871113	76871113	+	Silent	SNP	A	A	G	rs17230060	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:76871113A>G	ENST00000285871.4	+	4	472	c.345A>G	c.(343-345)gcA>gcG	p.A115A	CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	115								p.A115A(1)		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)				TTCCAGAAGCATTCTCCACGG	0.403													A|||	353	0.0704872	0.0068	0.072	5008	,	,		19981	0.0516		0.163	False		,,,				2504	0.0798				p.A115A		Atlas-SNP	.											CCDC146,NS,carcinoma,0,1	CCDC146	87	1	1	Substitution - coding silent(1)	stomach(1)	c.A345G						PASS	.	A		140,4266	100.7+/-139.4	2,136,2065	112.0	111.0	112.0		345	-11.4	0.0	7	dbSNP_123	112	1373,7227	267.4+/-287.2	114,1145,3041	no	coding-synonymous	CCDC146	NM_020879.2		116,1281,5106	GG,GA,AA		15.9651,3.1775,11.6331		115/956	76871113	1513,11493	2203	4300	6503	SO:0001819	synonymous_variant	57639	exon4			AGAAGCATTCTCC	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.345A>G	7.37:g.76871113A>G		Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	277	126	0.454874	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																			A|0.896;G|0.104	0.104	strong		0.403	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
HOXD1	3231	hgsc.bcm.edu	37	2	177054769	177054769	+	Missense_Mutation	SNP	G	G	A	rs6710142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:177054769G>A	ENST00000331462.4	+	2	1109	c.886G>A	c.(886-888)Gcc>Acc	p.A296T	HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000452365.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000436126.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	296			A -> T (in dbSNP:rs6710142).		embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		TCTGGCCACGGCCATTCCTGT	0.542													G|||	937	0.187101	0.3313	0.147	5008	,	,		15751	0.0149		0.2515	False		,,,				2504	0.1319				p.A296T		Atlas-SNP	.											.	HOXD1	33	.	0			c.G886A						PASS	.	G	THR/ALA	1314,3092	441.8+/-346.5	190,934,1079	109.0	117.0	114.0		886	1.3	0.0	2	dbSNP_116	114	2020,6580	351.5+/-328.3	242,1536,2522	yes	missense	HOXD1	NM_024501.1	58	432,2470,3601	AA,AG,GG		23.4884,29.823,25.6343	benign	296/329	177054769	3334,9672	2203	4300	6503	SO:0001583	missense	3231	exon2			GCCACGGCCATTC		CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"""Homeoboxes / ANTP class : HOXL subclass"""	5132	protein-coding gene	gene with protein product		142987	"""homeo box D1"""	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.886G>A	2.37:g.177054769G>A	ENSP00000328598:p.Ala296Thr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_024501	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	CCDS2271.1	394	0.1804029304029304	147	0.29878048780487804	58	0.16022099447513813	6	0.01048951048951049	183	0.24142480211081793	G	6.383	0.438828	0.12104	0.29823	0.234884	ENSG00000128645	ENST00000331462	D	0.90676	-2.71	5.66	1.3	0.21679	Homeodomain-like (1);	0.139876	0.33272	N	0.005099	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.17852	0.024;0.009	B;B	0.12156	0.005;0.007	T	0.03684	-1.1013	9	0.12766	T	0.61	.	3.1673	0.06540	0.2697:0.1163:0.4955:0.1186	rs6710142	296;296	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	T	296	ENSP00000328598:A296T	ENSP00000328598:A296T	A	+	1	0	HOXD1	176763015	0.001000	0.12720	0.002000	0.10522	0.428000	0.31595	0.921000	0.28718	0.325000	0.23359	0.655000	0.94253	GCC	G|0.768;A|0.232	0.232	strong		0.542	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2		
PSCA	8000	hgsc.bcm.edu	37	8	143763490	143763490	+	Silent	SNP	T	T	C	rs2978982	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143763490T>C	ENST00000301258.4	+	3	368	c.285T>C	c.(283-285)gcT>gcC	p.A95A		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	104	UPAR/Ly6.					anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					AGCCGGCTGCTGCCATCCTTG	0.662													C|||	2030	0.405351	0.3676	0.5072	5008	,	,		15544	0.3413		0.4473	False		,,,				2504	0.407				p.A95A		Atlas-SNP	.											.	PSCA	9	.	0			c.T285C						PASS	.	C		1728,2590		364,1000,795	31.0	36.0	34.0		285	-4.0	0.0	8	dbSNP_101	34	3823,4711		882,2059,1326	no	coding-synonymous	PSCA	NM_005672.4		1246,3059,2121	CC,CT,TT		44.7973,40.0185,43.1917		95/115	143763490	5551,7301	2159	4267	6426	SO:0001819	synonymous_variant	8000	exon3			GGCTGCTGCCATC	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.285T>C	8.37:g.143763490T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	73	25	0.342466	NM_005672	Q6UW92	Silent	SNP	ENST00000301258.4	37	CCDS47925.2																																																																																			T|0.576;C|0.424	0.424	strong		0.662	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
GLYATL3	389396	hgsc.bcm.edu	37	6	49494241	49494241	+	Missense_Mutation	SNP	A	A	G	rs9367359	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:49494241A>G	ENST00000371197.4	+	6	594	c.481A>G	c.(481-483)Aat>Gat	p.N161D		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	161						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						GAGTGTTGCCAATGCGGATCT	0.507													G|||	2439	0.487021	0.407	0.3674	5008	,	,		19001	0.4573		0.6322	False		,,,				2504	0.5613				p.N161D		Atlas-SNP	.											.	GLYATL3	19	.	0			c.A481G						PASS	.	G	ASP/ASN	625,759		132,361,199	86.0	75.0	78.0		481	6.1	0.6	6	dbSNP_119	78	2050,1132		660,730,201	yes	missense	GLYATL3	NM_001010904.1	23	792,1091,400	GG,GA,AA		35.5751,45.159,41.4148	benign	161/289	49494241	2675,1891	692	1591	2283	SO:0001583	missense	389396	exon6			GTTGCCAATGCGG		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.481A>G	6.37:g.49494241A>G	ENSP00000360240:p.Asn161Asp	Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	161	160	0.993789	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	1054	0.4826007326007326	198	0.4024390243902439	147	0.40607734806629836	222	0.3881118881118881	487	0.6424802110817942	G	0.274	-0.991050	0.02162	0.45159	0.644249	ENSG00000203972	ENST00000371197	T	0.11712	2.75	6.06	6.06	0.98353	Acyl-CoA N-acyltransferase (2);Glycine N-acyltransferase, N-terminal (1);	0.157276	0.56097	N	0.000033	T	0.00936	0.0031	N	0.00483	-1.445	0.53005	P	3.399999999997849E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45775	-0.9238	9	0.11794	T	0.64	-1.7093	11.5712	0.50834	0.0814:0.0:0.9186:0.0	rs9367359;rs52799300;rs9367359	161	Q5SZD4	GLYL3_HUMAN	D	161	ENSP00000360240:N161D	ENSP00000360240:N161D	N	+	1	0	GLYATL3	49602200	0.992000	0.36948	0.589000	0.28718	0.003000	0.03518	3.040000	0.49799	1.593000	0.50029	-0.119000	0.15052	AAT	A|0.510;G|0.490	0.490	strong		0.507	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
COL15A1	1306	hgsc.bcm.edu	37	9	101778265	101778265	+	Missense_Mutation	SNP	G	G	T	rs2297603	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:101778265G>T	ENST00000375001.3	+	11	1934	c.1511G>T	c.(1510-1512)gGt>gTt	p.G504V		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	504	4 X tandem repeats.|Nonhelical region 1 (NC1).		G -> V (in dbSNP:rs2297603).		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)				CAGGGTCCTGGTGATGAAGAA	0.592													G|||	427	0.0852636	0.0053	0.1196	5008	,	,		16779	0.2133		0.0885	False		,,,				2504	0.0337				p.G504V		Atlas-SNP	.											COL15A1,brain,glioma,0,1	COL15A1	211	1	0			c.G1511T						PASS	.	G	VAL/GLY	93,4313	73.6+/-111.7	2,89,2112	66.0	62.0	63.0		1511	-1.9	0.0	9	dbSNP_100	63	929,7671	201.3+/-244.8	48,833,3419	yes	missense	COL15A1	NM_001855.3	109	50,922,5531	TT,TG,GG		10.8023,2.1108,7.8579	probably-damaging	504/1389	101778265	1022,11984	2203	4300	6503	SO:0001583	missense	1306	exon11			GTCCTGGTGATGA	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.1511G>T	9.37:g.101778265G>T	ENSP00000364140:p.Gly504Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	238	0.10897435897435898	8	0.016260162601626018	47	0.1298342541436464	115	0.20104895104895104	68	0.08970976253298153	G	8.560	0.877531	0.17395	0.021108	0.108023	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89875	-2.58	3.93	-1.87	0.07737	.	15.702500	0.00604	N	0.000385	T	0.00384	0.0012	L	0.50333	1.59	0.80722	P	0.0	B	0.14438	0.01	B	0.10450	0.005	T	0.41645	-0.9497	9	0.66056	D	0.02	.	1.185	0.01853	0.2164:0.343:0.278:0.1626	rs2297603;rs17617726;rs52813576;rs2297603	504	P39059	COFA1_HUMAN	V	504;474	ENSP00000364140:G504V	ENSP00000364140:G504V	G	+	2	0	COL15A1	100818086	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	0.248000	0.18198	-0.153000	0.11137	0.650000	0.86243	GGT	G|0.909;T|0.091	0.091	strong		0.592	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
GPR112	139378	hgsc.bcm.edu	37	X	135430483	135430483	+	Missense_Mutation	SNP	T	T	C	rs912002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135430483T>C	ENST00000394143.1	+	6	4909	c.4618T>C	c.(4618-4620)Tct>Cct	p.S1540P	GPR112_ENST00000370652.1_Missense_Mutation_p.S1540P|GPR112_ENST00000412101.1_Missense_Mutation_p.S1335P|GPR112_ENST00000287534.4_Missense_Mutation_p.S1477P|GPR112_ENST00000394141.1_Missense_Mutation_p.S1335P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1540			S -> P (in dbSNP:rs912002).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					AACTAAATCTTCTAAAACAAT	0.418													t|||	1764	0.467285	0.4251	0.3573	3775	,	,		14599	0.255		0.3797	False		,,,				2504	0.3221				p.S1540P		Atlas-SNP	.											.	GPR112	459	.	0			c.T4618C						PASS	.		PRO/SER	2110,1725		493,813,311,326,260	96.0	94.0	95.0		4618	1.7	0.1	X	dbSNP_86	95	3223,3505		567,1177,912,684,960	yes	missense	GPR112	NM_153834.3	74	1060,1990,1223,1010,1220	CC,CT,C,TT,T		47.9043,44.9804,49.5124	probably-damaging	1540/3081	135430483	5333,5230	2203	4300	6503	SO:0001583	missense	139378	exon6			AAATCTTCTAAAA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.4618T>C	X.37:g.135430483T>C	ENSP00000377699:p.Ser1540Pro	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	754	0.45449065702230257	137	0.37027027027027026	83	0.2902097902097902	103	0.22391304347826088	190	0.3242320819112628	t	14.52	2.560180	0.45590	0.550196	0.479043	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.40756	1.06;1.06;1.02;1.13;1.02	3.02	1.66	0.24008	.	.	.	.	.	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	D;D;D	0.76494	0.997;0.999;0.998	D;D;D	0.80764	0.986;0.994;0.987	T	0.44483	-0.9325	8	0.87932	D	0	.	4.2365	0.10628	0.3093:0.0:0.0:0.6907	rs912002;rs52799687;rs61339577;rs912002	1477;1335;1540	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	P	1540;1540;1335;1477;1335	ENSP00000377699:S1540P;ENSP00000359686:S1540P;ENSP00000416526:S1335P;ENSP00000287534:S1477P;ENSP00000377697:S1335P	ENSP00000287534:S1477P	S	+	1	0	GPR112	135258149	0.316000	0.24580	0.086000	0.20670	0.250000	0.25880	0.927000	0.28818	1.195000	0.43115	0.378000	0.23410	TCT	0|0.015;C|0.478	0.478	strong		0.418	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
MEIOB	254528	hgsc.bcm.edu	37	16	1894912	1894912	+	Silent	SNP	C	C	T	rs9806826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1894912C>T	ENST00000397344.3	-	10	1025	c.831G>A	c.(829-831)acG>acA	p.T277T	MEIOB_ENST00000452149.2_Silent_p.T277T|MEIOB_ENST00000470044.1_Silent_p.T70T|LA16c-429E7.1_ENST00000570247.1_RNA|MEIOB_ENST00000412554.2_Silent_p.T277T|MEIOB_ENST00000325962.3_Silent_p.T277T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	277					double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										CCAGAACATTCGTTTCTTTAT	0.279													T|||	1854	0.370208	0.3548	0.3242	5008	,	,		17509	0.4246		0.3141	False		,,,				2504	0.4254				p.T277T		Atlas-SNP	.											C16orf73_ENST00000412554,NS,carcinoma,-1,2	.	.	2	0			c.G831A						PASS	.	T	,	1467,2921	665.6+/-401.6	242,983,969	50.0	51.0	50.0		831,831	0.8	0.0	16	dbSNP_119	50	2459,6107	685.3+/-404.0	374,1711,2198	no	coding-synonymous,coding-synonymous	C16orf73	NM_001163560.2,NM_152764.2	,	616,2694,3167	TT,TC,CC		28.7065,33.4321,30.3072	,	277/472,277/443	1894912	3926,9028	2194	4283	6477	SO:0001819	synonymous_variant	254528	exon10			AACATTCGTTTCT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.831G>A	16.37:g.1894912C>T		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	169	65	0.384615	NM_001163560	B1AK39|C9J0S1|Q96RY0	Silent	SNP	ENST00000397344.3	37	CCDS10449.2																																																																																			C|0.681;T|0.319	0.319	strong		0.279	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
SPINK8	646424	hgsc.bcm.edu	37	3	48360992	48360992	+	Missense_Mutation	SNP	T	T	G	rs11718350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:48360992T>G	ENST00000434006.1	-	3	233	c.234A>C	c.(232-234)aaA>aaC	p.K78N		NM_001080525.1	NP_001073994.1	P0C7L1	ISK8_HUMAN	serine peptidase inhibitor, Kazal type 8 (putative)	78	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		K -> N (in dbSNP:rs11718350).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|kidney(1)	2				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		CTTACAGAATTTTGGAGCACA	0.428													T|||	844	0.16853	0.0318	0.1772	5008	,	,		21625	0.123		0.2843	False		,,,				2504	0.2751				p.K78N		Atlas-SNP	.											.	SPINK8	5	.	0			c.A234C						PASS	.	T	ASN/LYS	229,3597		9,211,1693	127.0	126.0	126.0		234	2.4	0.4	3	dbSNP_120	126	2501,5759		396,1709,2025	yes	missense	SPINK8	NM_001080525.1	94	405,1920,3718	GG,GT,TT		30.2785,5.9854,22.5881	possibly-damaging	78/98	48360992	2730,9356	1913	4130	6043	SO:0001583	missense	646424	exon3			CAGAATTTTGGAG		CCDS46822.1	3p21.31	2011-08-31			ENSG00000229453	ENSG00000229453		"""Serine peptidase inhibitors, Kazal type"""	33160	protein-coding gene	gene with protein product						16930550	Standard	NM_001080525		Approved		uc003csq.1	P0C7L1	OTTHUMG00000156832	ENST00000434006.1:c.234A>C	3.37:g.48360992T>G	ENSP00000407497:p.Lys78Asn	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_001080525		Missense_Mutation	SNP	ENST00000434006.1	37	CCDS46822.1	363	0.1662087912087912	18	0.036585365853658534	70	0.19337016574585636	63	0.11013986013986014	212	0.2796833773087071	T	12.28	1.889555	0.33348	0.059854	0.302785	ENSG00000229453	ENST00000434006	T	0.75154	-0.91	3.58	2.39	0.29439	Proteinase inhibitor I1, Kazal (2);	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	P	0.43826	0.818	B	0.39617	0.305	T	0.06356	-1.0831	7	0.20519	T	0.43	.	6.9836	0.24715	0.0:0.0:0.2345:0.7655	rs11718350;rs11718350	78	P0C7L1	ISK8_HUMAN	N	78	ENSP00000407497:K78N	ENSP00000407497:K78N	K	-	3	2	SPINK8	48335996	0.002000	0.14202	0.359000	0.25824	0.346000	0.29079	0.234000	0.17930	0.729000	0.32403	0.528000	0.53228	AAA	T|0.820;G|0.180	0.180	strong		0.428	SPINK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346123.1	NM_001080525	
OBSCN	84033	hgsc.bcm.edu	37	1	228465346	228465346	+	Intron	SNP	A	A	G	rs493945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228465346A>G	ENST00000422127.1	+	25	6798				OBSCN_ENST00000359599.6_Intron|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000284548.11_Intron|RP5-1139B12.3_ENST00000602947.1_RNA|RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000570156.2_Missense_Mutation_p.N2674D	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)				GCCCACTGACAACGTGCGCAT	0.647													A|||	1653	0.330072	0.3585	0.3617	5008	,	,		15447	0.378		0.3638	False		,,,				2504	0.1851				p.N2674D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.A8020G						PASS	.																																			SO:0001627	intron_variant	84033	exon29			ACTGACAACGTGC	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.6755-109A>G	1.37:g.228465346A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	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																																																																																			A|0.659;G|0.341	0.341	strong		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	3'UTR	SNP	G	G	A	rs1047057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000356226.4_3'UTR|FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000357555.5_Silent_p.L703L|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000369060.4_3'UTR	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.L703L(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86.0	84.0	85.0		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.*259C>T	10.37:g.123239112G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	102	100	0.980392	NM_001144915	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
PINX1	54984	hgsc.bcm.edu	37	8	10623240	10623240	+	Missense_Mutation	SNP	T	T	C	rs17711777	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10623240T>C	ENST00000314787.3	-	7	777	c.658A>G	c.(658-660)Aca>Gca	p.T220A	SOX7_ENST00000554914.1_Intron|CTD-2135J3.3_ENST00000506149.2_RNA|CTD-2135J3.3_ENST00000519568.1_RNA|SOX7_ENST00000553390.1_Intron|PINX1_ENST00000519088.1_3'UTR|PINX1_ENST00000426190.2_3'UTR	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1	220			T -> A (in dbSNP:rs17711777).		mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)			kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		TCTTTACCTGTGGCCTCTTTA	0.547													T|||	160	0.0319489	0.003	0.1282	5008	,	,		15723	0.001		0.0487	False		,,,				2504	0.0174				p.T220A		Atlas-SNP	.											.	PINX1	38	.	0			c.A658G						PASS	.	T	ALA/THR	69,3787		0,69,1859	111.0	119.0	116.0		658	0.9	0.1	8	dbSNP_123	116	561,7701		24,513,3594	yes	missense	PINX1	NM_017884.4	58	24,582,5453	CC,CT,TT		6.7901,1.7894,5.1989		220/329	10623240	630,11488	1928	4131	6059	SO:0001583	missense	54984	exon7			TACCTGTGGCCTC	AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"""G patch domain containing"""	30046	protein-coding gene	gene with protein product	"""PIN2 interacting protein 1"", ""liver-related putative tumor suppressor"""	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.658A>G	8.37:g.10623240T>C	ENSP00000318966:p.Thr220Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	83	24	0.289157	NM_017884	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Missense_Mutation	SNP	ENST00000314787.3	37	CCDS47801.1	77	0.035256410256410256	2	0.0040650406504065045	36	0.09944751381215469	0	0.0	39	0.051451187335092345	T	0.780	-0.762596	0.02996	0.017894	0.067901	ENSG00000254093	ENST00000314787	T	0.10288	2.89	5.56	0.905	0.19307	.	0.922202	0.09372	N	0.811105	T	0.00144	0.0004	N	0.08118	0	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.44467	-0.9326	9	0.06625	T	0.88	.	7.0549	0.25093	0.0:0.4498:0.0:0.5502	rs17711777;rs52837746;rs17711777	220	Q96BK5	PINX1_HUMAN	A	220	ENSP00000318966:T220A	ENSP00000318966:T220A	T	-	1	0	PINX1	10660650	0.119000	0.22226	0.053000	0.19242	0.005000	0.04900	0.278000	0.18753	0.132000	0.18615	-0.274000	0.10170	ACA	T|0.963;C|0.037	0.037	strong		0.547	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884	
DOCK1	1793	hgsc.bcm.edu	37	10	129242515	129242515	+	Silent	SNP	G	G	A	rs11371	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:129242515G>A	ENST00000280333.6	+	50	5431	c.5322G>A	c.(5320-5322)agG>agA	p.R1774R		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1774					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TTACACCAAGGGCCAAGCTCA	0.572													G|||	1690	0.33746	0.2133	0.2824	5008	,	,		19267	0.4653		0.3658	False		,,,				2504	0.3834				p.R1774R		Atlas-SNP	.											.	DOCK1	188	.	0			c.G5322A						PASS	.	G		911,3281		108,695,1293	85.0	96.0	92.0		5277	1.9	0.8	10	dbSNP_52	92	3176,5248		615,1946,1651	no	coding-synonymous	DOCK1	NM_001380.3		723,2641,2944	AA,AG,GG		37.7018,21.7319,32.3954		1759/1851	129242515	4087,8529	2096	4212	6308	SO:0001819	synonymous_variant	1793	exon50			ACCAAGGGCCAAG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5322G>A	10.37:g.129242515G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.667;A|0.333	0.333	strong		0.572	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
FCN1	2219	hgsc.bcm.edu	37	9	137804360	137804360	+	Silent	SNP	A	A	G	rs2274845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:137804360A>G	ENST00000371806.3	-	7	661	c.570T>C	c.(568-570)aaT>aaC	p.N190N		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	190	B domain; contributes to trimerization.|Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		GGATGTTGTCATTCCCCAGCC	0.642													.|||	3342	0.667332	0.91	0.4654	5008	,	,		16568	0.4673		0.6213	False		,,,				2504	0.7362				p.N190N		Atlas-SNP	.											.	FCN1	62	.	0			c.T570C						PASS	.	G		3813,593	258.9+/-262.7	1664,485,54	64.0	58.0	60.0		570	-7.1	0.0	9	dbSNP_100	60	5366,3234	486.6+/-371.9	1641,2084,575	no	coding-synonymous	FCN1	NM_002003.3		3305,2569,629	GG,GA,AA		37.6047,13.4589,29.4249		190/327	137804360	9179,3827	2203	4300	6503	SO:0001819	synonymous_variant	2219	exon7			GTTGTCATTCCCC	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"""Fibrinogen C domain containing"""	3623	protein-coding gene	gene with protein product		601252	"""ficolin (collagen/fibrinogen domain-containing) 1"""			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.570T>C	9.37:g.137804360A>G		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_002003	Q5VYV5|Q92596	Silent	SNP	ENST00000371806.3	37	CCDS6985.1																																																																																			A|0.323;G|0.677	0.677	strong		0.642	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003	
NPC1	4864	hgsc.bcm.edu	37	18	21119777	21119777	+	Silent	SNP	G	G	A	rs1140458	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:21119777G>A	ENST00000269228.5	-	18	3347	c.2793C>T	c.(2791-2793)aaC>aaT	p.N931N	NPC1_ENST00000412552.2_Silent_p.N613N|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	931					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GTACTGACTAGTTGTCCAGCT	0.527													G|||	2424	0.484026	0.3646	0.611	5008	,	,		18099	0.6111		0.4573	False		,,,				2504	0.4519				p.N931N		Atlas-SNP	.											NPC1,NS,carcinoma,0,1	NPC1	114	1	0			c.C2793T						PASS	.	G		1709,2697	513.7+/-368.4	311,1087,805	56.0	52.0	53.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2793	4.4	1.0	18	dbSNP_86	53	4040,4560	553.0+/-386.2	936,2168,1196	no	coding-synonymous	NPC1	NM_000271.4		1247,3255,2001	AA,AG,GG		46.9767,38.788,44.2027		931/1279	21119777	5749,7257	2203	4300	6503	SO:0001819	synonymous_variant	4864	exon18			TGACTAGTTGTCC	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2793C>T	18.37:g.21119777G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	49	0.471154	NM_000271	B4DET3|Q9P130	Silent	SNP	ENST00000269228.5	37	CCDS11878.1																																																																																			T|0.094;G|0.438;C|0.101;A|0.366	0.366	strong		0.527	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
VPS8	23355	hgsc.bcm.edu	37	3	184700426	184700426	+	Missense_Mutation	SNP	C	C	T	rs11555405	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:184700426C>T	ENST00000437079.3	+	41	3664	c.3493C>T	c.(3493-3495)Cac>Tac	p.H1165Y	VPS8_ENST00000446204.2_Missense_Mutation_p.H1073Y|VPS8_ENST00000287546.4_Missense_Mutation_p.H1165Y|VPS8_ENST00000436792.2_Missense_Mutation_p.H1163Y	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	1165			H -> Y (in dbSNP:rs11555405). {ECO:0000269|PubMed:17974005}.				zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_cancers(143;2.51e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.02e-33)|OV - Ovarian serous cystadenocarcinoma(80;4.81e-22)			TCCTCATCTACACTCTGAAGG	0.398													C|||	1432	0.285942	0.0174	0.3285	5008	,	,		16904	0.506		0.2883	False		,,,				2504	0.3896				p.H1165Y		Atlas-SNP	.											.	VPS8	109	.	0			c.C3493T						PASS	.	C	TYR/HIS,TYR/HIS	184,3598		2,180,1709	77.0	68.0	71.0		3493,3487	5.1	0.0	3	dbSNP_120	71	2082,6166		255,1572,2297	yes	missense,missense	VPS8	NM_001009921.2,NM_015303.3	83,83	257,1752,4006	TT,TC,CC		25.2425,4.8652,18.8362	benign,benign	1165/1429,1163/1427	184700426	2266,9764	1891	4124	6015	SO:0001583	missense	23355	exon40			CATCTACACTCTG	AK056661	CCDS46972.1	3q27.2	2006-07-07	2006-07-07	2006-07-07	ENSG00000156931	ENSG00000156931			29122	protein-coding gene	gene with protein product			"""KIAA0804"""	KIAA0804		9872452	Standard	NM_001009921		Approved	FLJ32099	uc003fpb.1	Q8N3P4	OTTHUMG00000156707	ENST00000437079.3:c.3493C>T	3.37:g.184700426C>T	ENSP00000397879:p.His1165Tyr	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	235	114	0.485106	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	659	0.3017399267399267	11	0.022357723577235773	127	0.35082872928176795	290	0.506993006993007	231	0.30474934036939316	C	4.147	0.025712	0.08054	0.048652	0.252425	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	6.05	5.09	0.68999	.	0.413977	0.28983	N	0.013505	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.13145	0.0;0.007;0.0	B;B;B	0.15870	0.0;0.014;0.0	T	0.41413	-0.9510	9	0.02654	T	1	-17.2505	9.2184	0.37362	0.0:0.824:0.0:0.176	rs11555405;rs13095607;rs52814306;rs61568357;rs11555405	1165;1073;1163	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	Y	1165;1165;1163;1073	ENSP00000287546:H1165Y;ENSP00000397879:H1165Y;ENSP00000404704:H1163Y;ENSP00000405483:H1073Y	ENSP00000287546:H1165Y	H	+	1	0	VPS8	186183120	0.000000	0.05858	0.008000	0.14137	0.700000	0.40528	0.339000	0.19875	1.408000	0.46895	0.650000	0.86243	CAC	C|0.726;T|0.274	0.274	strong		0.398	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303	
ATAD3C	219293	hgsc.bcm.edu	37	1	1387764	1387764	+	Missense_Mutation	SNP	G	G	A	rs9793256	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1387764G>A	ENST00000378785.2	+	3	1167	c.172G>A	c.(172-174)Ggg>Agg	p.G58R		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	58							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CACCTTGTTTGGGGAAGGATT	0.567													N|||	1402	0.279952	0.1967	0.3314	5008	,	,		20431	0.3849		0.1571	False		,,,				2504	0.3742				p.G58R		Atlas-SNP	.											.	ATAD3C	23	.	0			c.G172A						PASS	.	G	ARG/GLY	238,1146		17,204,471	128.0	110.0	116.0		172	2.2	1.0	1	dbSNP_119	116	515,2667		57,401,1133	no	missense	ATAD3C	NM_001039211.2	125	74,605,1604	AA,AG,GG		16.1848,17.1965,16.4915	probably-damaging	58/412	1387764	753,3813	692	1591	2283	SO:0001583	missense	219293	exon3			TTGTTTGGGGAAG	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.172G>A	1.37:g.1387764G>A	ENSP00000368062:p.Gly58Arg	Somatic	260	2	0.00769231		WXS	Illumina HiSeq	Phase_I	306	287	0.937908	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	556	0.25457875457875456	122	0.24796747967479674	99	0.27348066298342544	217	0.3793706293706294	118	0.15567282321899736	.	6.701	0.497956	0.12762	0.171965	0.161848	ENSG00000215915	ENST00000378785	D	0.94687	-3.49	2.18	2.18	0.27775	ATPase family AAA domain-containing protein 3, domain of unknown function DUF3523 (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.80616	2.505	0.09310	P	0.9999999850473	D	0.76494	0.999	D	0.77557	0.99	T	0.00000	-1.5390	9	0.59425	D	0.04	.	11.6938	0.51532	0.0:0.0:1.0:0.0	rs9793256	58	Q5T2N8	ATD3C_HUMAN	R	58	ENSP00000368062:G58R	ENSP00000368062:G58R	G	+	1	0	ATAD3C	1377627	1.000000	0.71417	1.000000	0.80357	0.211000	0.24417	7.824000	0.86668	1.224000	0.43551	0.194000	0.17425	GGG	G|0.744;A|0.256	0.256	strong		0.567	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
FAM129A	116496	hgsc.bcm.edu	37	1	184764681	184764681	+	Silent	SNP	G	G	A	rs35545276	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:184764681G>A	ENST00000367511.3	-	14	2410	c.2217C>T	c.(2215-2217)caC>caT	p.H739H	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	739	Glu-rich.				negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CTTGGGGAACGTGGCTCTCCC	0.532													G|||	188	0.0375399	0.0371	0.0418	5008	,	,		18593	0.001		0.0676	False		,,,				2504	0.0419				p.H739H		Atlas-SNP	.											.	FAM129A	98	.	0			c.C2217T						PASS	.	G		210,4196	129.8+/-166.5	2,206,1995	127.0	135.0	132.0		2217	-5.6	0.0	1	dbSNP_126	132	547,8053	149.7+/-204.7	16,515,3769	no	coding-synonymous	FAM129A	NM_052966.2		18,721,5764	AA,AG,GG		6.3605,4.7662,5.8204		739/929	184764681	757,12249	2203	4300	6503	SO:0001819	synonymous_variant	116496	exon14			GGGAACGTGGCTC	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.2217C>T	1.37:g.184764681G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Silent	SNP	ENST00000367511.3	37	CCDS1364.1																																																																																			G|0.954;A|0.046	0.046	strong		0.532	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
SEC16A	9919	hgsc.bcm.edu	37	9	139371342	139371342	+	Silent	SNP	G	G	A	rs11999525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139371342G>A	ENST00000371706.3	-	1	225	c.192C>T	c.(190-192)ccC>ccT	p.P64P	SEC16A_ENST00000431893.2_Silent_p.P64P|SEC16A_ENST00000313050.7_Silent_p.P242P|SEC16A_ENST00000290037.6_Silent_p.P64P			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	64					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)		TGGTGGCACAGGGCACCCCGC	0.657													G|||	663	0.132388	0.0454	0.2493	5008	,	,		17667	0.0546		0.2396	False		,,,				2504	0.137				p.P242P		Atlas-SNP	.											SEC16A_NM_014866.1,NS,carcinoma,0,2	SEC16A	249	2	0			c.C726T						PASS	.	G		308,3908		9,290,1809	25.0	29.0	28.0		726	-5.4	0.0	9	dbSNP_120	28	2070,6362		237,1596,2383	no	coding-synonymous	SEC16A	NM_014866.1		246,1886,4192	AA,AG,GG		24.5493,7.3055,18.8014		242/2358	139371342	2378,10270	2108	4216	6324	SO:0001819	synonymous_variant	9919	exon3			GGCACAGGGCACC	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.192C>T	9.37:g.139371342G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.849;A|0.151	0.151	strong		0.657	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
GLS2	27165	hgsc.bcm.edu	37	12	56865338	56865338	+	Missense_Mutation	SNP	A	A	G	rs2657879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56865338A>G	ENST00000311966.4	-	18	2020	c.1742T>C	c.(1741-1743)cTc>cCc	p.L581P	GLS2_ENST00000476991.1_5'Flank|MIP_ENST00000555551.1_5'Flank	NM_013267.2	NP_037399.2	Q9UI32	GLSL_HUMAN	glutaminase 2 (liver, mitochondrial)	581			L -> P (in dbSNP:rs2657879). {ECO:0000269|Ref.3}.		cellular amino acid biosynthetic process (GO:0008652)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate secretion (GO:0014047)|glutamine metabolic process (GO:0006541)|neurotransmitter secretion (GO:0007269)|reactive oxygen species metabolic process (GO:0072593)|regulation of apoptotic process (GO:0042981)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	glutaminase activity (GO:0004359)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13					L-Glutamine(DB00130)	AGTTTCAGAGAGTGTGTAGGA	0.512													A|||	643	0.128395	0.0371	0.2392	5008	,	,		21065	0.0823		0.2127	False		,,,				2504	0.1339				p.L581P		Atlas-SNP	.											.	GLS2	42	.	0			c.T1742C						PASS	.	A	PRO/LEU	289,4117	159.2+/-191.8	8,273,1922	74.0	66.0	69.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1742	3.1	0.9	12	dbSNP_100	69	1601,6999	297.9+/-303.7	147,1307,2846	yes	missense	GLS2	NM_013267.2	98	155,1580,4768	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	18.6163,6.5592,14.5318	benign	581/603	56865338	1890,11116	2203	4300	6503	SO:0001583	missense	27165	exon18			TCAGAGAGTGTGT		CCDS8921.1, CCDS73482.1	12q13	2013-01-10			ENSG00000135423	ENSG00000135423		"""Ankyrin repeat domain containing"""	29570	protein-coding gene	gene with protein product		606365				11130979, 10620514	Standard	NM_013267		Approved	GA, GLS, LGA, hLGA	uc001slj.3	Q9UI32	OTTHUMG00000140379	ENST00000311966.4:c.1742T>C	12.37:g.56865338A>G	ENSP00000310447:p.Leu581Pro	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_013267	B7Z8Q9|Q8IX91|Q9NYY2|Q9UI31	Missense_Mutation	SNP	ENST00000311966.4	37	CCDS8921.1	299	0.13690476190476192	21	0.042682926829268296	77	0.212707182320442	48	0.08391608391608392	153	0.20184696569920843	A	2.497	-0.316008	0.05422	0.065592	0.186163	ENSG00000135423	ENST00000311966	T	0.30182	1.54	5.6	3.08	0.35506	.	0.387987	0.25590	N	0.029624	T	0.00012	0.0000	L	0.37630	1.12	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.23190	-1.0195	9	0.28530	T	0.3	-19.7846	6.3142	0.21180	0.7659:0.0:0.2341:0.0	rs2657879;rs17442734;rs2657879	581	Q9UI32	GLSL_HUMAN	P	581	ENSP00000310447:L581P	ENSP00000310447:L581P	L	-	2	0	GLS2	55151605	0.286000	0.24305	0.897000	0.35233	0.041000	0.13682	1.374000	0.34283	0.678000	0.31325	0.533000	0.62120	CTC	A|0.864;G|0.136	0.136	strong		0.512	GLS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277113.1	NM_013267	
BHLHE40	8553	hgsc.bcm.edu	37	3	5024771	5024771	+	Silent	SNP	T	T	C	rs908078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:5024771T>C	ENST00000256495.3	+	5	1236	c.633T>C	c.(631-633)ggT>ggC	p.G211G		NM_003670.2	NP_003661.1	O14503	BHE40_HUMAN	basic helix-loop-helix family, member e40	211					circadian regulation of gene expression (GO:0032922)|entrainment of circadian clock by photoperiod (GO:0043153)|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)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|MRF binding (GO:0043426)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)	12						CGGCCAAAGGTTCGGAAGGTC	0.592													C|||	791	0.157947	0.0855	0.2435	5008	,	,		17832	0.1915		0.1471	False		,,,				2504	0.1718				p.G211G		Atlas-SNP	.											.	BHLHE40	35	.	0			c.T633C						PASS	.	C		388,4018	786.8+/-414.8	15,358,1830	42.0	46.0	45.0		633	3.8	1.0	3	dbSNP_86	45	1334,7266	752.8+/-407.4	91,1152,3057	no	coding-synonymous	BHLHE40	NM_003670.2		106,1510,4887	CC,CT,TT		15.5116,8.8062,13.24		211/413	5024771	1722,11284	2203	4300	6503	SO:0001819	synonymous_variant	8553	exon5			CAAAGGTTCGGAA	AB004066	CCDS2565.1	3p26	2009-01-12	2009-01-12	2009-01-12	ENSG00000134107	ENSG00000134107		"""Basic helix-loop-helix proteins"""	1046	protein-coding gene	gene with protein product	"""differentially expressed in chondrocytes 1"", "" differentiated embryo chondrocyte expressed gene 1"""	604256	"""basic helix-loop-helix domain containing, class B, 2"""	STRA13, BHLHB2		9240428, 10449910, 18557763	Standard	NM_003670		Approved	DEC1, bHLHe40	uc003bqf.3	O14503	OTTHUMG00000119035	ENST00000256495.3:c.633T>C	3.37:g.5024771T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	20	0.333333	NM_003670	Q96TD3	Silent	SNP	ENST00000256495.3	37	CCDS2565.1																																																																																			T|0.855;C|0.145	0.145	strong		0.592	BHLHE40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239244.2	NM_003670	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33568789	33568789	+	Silent	SNP	T	T	G	rs10971566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:33568789T>G	ENST00000290943.6	+	15	2985	c.2889T>G	c.(2887-2889)ctT>ctG	p.L963L	ANKRD18B_ENST00000426460.2_3'UTR	NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	963										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						TTGAAAATCTTAATAGTATAG	0.393													.|||	1000	0.199681	0.0454	0.2695	5008	,	,		16912	0.2143		0.3161	False		,,,				2504	0.2239				p.L962L		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.T2886G						PASS	.																																			SO:0001819	synonymous_variant	441459	exon15			AAATCTTAATAGT			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2889T>G	9.37:g.33568789T>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				T|0.756;G|0.244	0.244	strong		0.393	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
BST1	683	hgsc.bcm.edu	37	4	15733454	15733454	+	Silent	SNP	A	A	C	rs1058212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:15733454A>C	ENST00000265016.4	+	9	1138	c.943A>C	c.(943-945)Agg>Cgg	p.R315R	BST1_ENST00000382346.3_Silent_p.R330R	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	315					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)	p.R315R(2)		central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						GCTGGCTTCCAGGACTCAACT	0.493													G|||	931	0.185903	0.115	0.0951	5008	,	,		16685	0.502		0.0308	False		,,,				2504	0.18				p.R315R		Atlas-SNP	.											BST1,colon,carcinoma,0,3	BST1	30	3	2	Substitution - coding silent(2)	stomach(1)|central_nervous_system(1)	c.A943C						PASS	.	G		506,3900		26,454,1723	55.0	52.0	53.0		943	4.0	0.0	4	dbSNP_86	53	260,8340		3,254,4043	no	coding-synonymous	BST1	NM_004334.2		29,708,5766	CC,CA,AA		3.0233,11.4843,5.8896		315/319	15733454	766,12240	2203	4300	6503	SO:0001819	synonymous_variant	683	exon9			GCTTCCAGGACTC	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.943A>C	4.37:g.15733454A>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Silent	SNP	ENST00000265016.4	37	CCDS3416.1																																																																																			A|0.883;C|0.117	0.117	strong		0.493	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
FBXO15	201456	hgsc.bcm.edu	37	18	71740743	71740743	+	Missense_Mutation	SNP	A	A	G	rs35815390	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:71740743A>G	ENST00000419743.2	-	10	1565	c.1486T>C	c.(1486-1488)Tat>Cat	p.Y496H	FBXO15_ENST00000269500.5_Missense_Mutation_p.Y420H|FBXO15_ENST00000580806.1_5'UTR	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	496			Y -> H (in dbSNP:rs35815390).			SCF ubiquitin ligase complex (GO:0019005)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		ATACTAAGATAAAGGACCAGG	0.408													a|||	144	0.028754	0.0038	0.0331	5008	,	,		19793	0.001		0.0746	False		,,,				2504	0.0409				p.Y496H		Atlas-SNP	.											FBXO15_ENST00000419743,lymph_node,lymphoid_neoplasm,0,2	FBXO15	97	2	0			c.T1486C						PASS	.		HIS/TYR,HIS/TYR	64,4342	60.5+/-97.4	1,62,2140	191.0	189.0	190.0		1486,1258	3.5	0.5	18	dbSNP_126	190	702,7898	174.0+/-224.4	33,636,3631	yes	missense,missense	FBXO15	NM_001142958.1,NM_152676.2	83,83	34,698,5771	GG,GA,AA		8.1628,1.4526,5.8896	probably-damaging,probably-damaging	496/511,420/435	71740743	766,12240	2203	4300	6503	SO:0001583	missense	201456	exon10			TAAGATAAAGGAC	AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"""F-boxes /  ""other"""""	13617	protein-coding gene	gene with protein product		609093	"""F-box only protein 15"""			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1486T>C	18.37:g.71740743A>G	ENSP00000393154:p.Tyr496His	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	173	95	0.549133	NM_001142958	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	37	CCDS45884.1	75	0.034340659340659344	2	0.0040650406504065045	15	0.04143646408839779	1	0.0017482517482517483	57	0.07519788918205805	a	16.14	3.037868	0.54896	0.014526	0.081628	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.41758	0.99;0.99	5.9	3.51	0.40186	.	0.591425	0.19477	N	0.113320	T	0.05364	0.0142	M	0.66939	2.045	0.36126	D	0.845824	D;D	0.57899	0.981;0.981	P;P	0.57371	0.819;0.819	T	0.32161	-0.9917	10	0.87932	D	0	-35.7152	9.2734	0.37686	0.8473:0.0:0.1527:0.0	rs35815390;rs61752026	496;420	B3KST3;Q8NCQ5	.;FBX15_HUMAN	H	420;496	ENSP00000269500:Y420H;ENSP00000393154:Y496H	ENSP00000269500:Y420H	Y	-	1	0	FBXO15	69891723	0.999000	0.42202	0.472000	0.27241	0.375000	0.29983	3.125000	0.50469	0.486000	0.27676	0.529000	0.55759	TAT	A|0.951;G|0.049	0.049	strong		0.408	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676	
GSTM5	2949	hgsc.bcm.edu	37	1	110257835	110257835	+	Silent	SNP	C	C	T	rs386634508|rs67757008|rs78183574	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110257835C>T	ENST00000256593.3	+	7	598	c.540C>T	c.(538-540)aaC>aaT	p.N180N	GSTM5_ENST00000369813.1_Silent_p.N139N|GSTM5_ENST00000369812.5_Silent_p.N199N|GSTM5_ENST00000492718.1_3'UTR	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	180	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)			NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	CCTTCCTAAACTTGAAGGACT	0.478													C|||	703	0.140375	0.3941	0.0663	5008	,	,		19824	0.001		0.0845	False		,,,				2504	0.0511				p.N180N		Atlas-SNP	.											GSTM5,brain,glioma,0,2	GSTM5	89	2	0			c.C540T						scavenged	.																																			SO:0001819	synonymous_variant	2949	exon7			CCTAAACTTGAAG	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.540C>T	1.37:g.110257835C>T		Somatic	446	4	0.00896861		WXS	Illumina HiSeq	Phase_I	473	236	0.498943	NM_000851	A8K0V8|Q6PD78	Silent	SNP	ENST00000256593.3	37	CCDS811.1																																																																																			C|0.907;T|0.093	0.093	strong		0.478	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851	
OBSCN	84033	hgsc.bcm.edu	37	1	228407260	228407260	+	Intron	SNP	G	G	A	rs1771484	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228407260G>A	ENST00000422127.1	+	8	2697				OBSCN_ENST00000570156.2_Silent_p.E963E|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000284548.11_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACAGCTGTGAGGCCAGGGGAC	0.642													G|||	1388	0.277157	0.3147	0.3487	5008	,	,		19787	0.1746		0.3588	False		,,,				2504	0.1973				p.E963E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2889A						PASS	.																																			SO:0001627	intron_variant	84033	exon9			CTGTGAGGCCAGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2653+2271G>A	1.37:g.228407260G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.718;A|0.282	0.282	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
DDX60L	91351	hgsc.bcm.edu	37	4	169279364	169279364	+	Silent	SNP	C	C	T	rs11736382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169279364C>T	ENST00000511577.1	-	38	5302	c.5055G>A	c.(5053-5055)ttG>ttA	p.L1685L	DDX60L_ENST00000260184.7_Silent_p.L1685L			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1685							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AGGTTTGACTCAATTGTTTAA	0.299													C|||	109	0.0217652	0.0038	0.0346	5008	,	,		15501	0.0		0.0706	False		,,,				2504	0.0092				p.L1685L		Atlas-SNP	.											.	DDX60L	116	.	0			c.G5055A						PASS	.	C		43,3569		0,43,1763	121.0	113.0	115.0		5055	0.4	0.0	4	dbSNP_120	115	541,7617		17,507,3555	no	coding-synonymous	DDX60L	NM_001012967.1		17,550,5318	TT,TC,CC		6.6315,1.1905,4.9618		1685/1707	169279364	584,11186	1806	4079	5885	SO:0001819	synonymous_variant	91351	exon38			TTGACTCAATTGT	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.5055G>A	4.37:g.169279364C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.960;T|0.040	0.040	strong		0.299	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
MXRA5	25878	hgsc.bcm.edu	37	X	3235724	3235724	+	Missense_Mutation	SNP	C	C	T	rs1635242	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3235724C>T	ENST00000217939.6	-	6	6152	c.5998G>A	c.(5998-6000)Ggc>Agc	p.G2000S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2000	Ig-like C2-type 4.		G -> S (in dbSNP:rs1635242). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				GTGATGCGGCCCTCCACGGGG	0.602													C|||	2623	0.694834	0.5386	0.5043	3775	,	,		14459	0.5595		0.5258	False		,,,				2504	0.4785				p.G2000S		Atlas-SNP	.											.	MXRA5	815	.	0			c.G5998A						PASS	.	C	SER/GLY	2674,1161		783,702,406,147,165	46.0	43.0	44.0		5998	3.5	0.7	X	dbSNP_89	44	4341,2387		1020,1108,1193,300,679	yes	missense	MXRA5	NM_015419.3	56	1803,1810,1599,447,844	TT,TC,T,CC,C		35.4786,30.2738,33.5889	benign	2000/2829	3235724	7015,3548	2203	4300	6503	SO:0001583	missense	25878	exon6			TGCGGCCCTCCAC	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5998G>A	X.37:g.3235724C>T	ENSP00000217939:p.Gly2000Ser	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	67	0.985294	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	1154	0.6955997588908981	184	0.5679012345679012	127	0.4810606060606061	206	0.5885714285714285	272	0.5271317829457365	c	6.436	0.448618	0.12223	0.697262	0.645214	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.78126	-1.15	3.55	3.55	0.40652	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.239206	0.20393	U	0.093219	T	0.00012	0.0000	L	0.38649	1.16	0.36763	P	0.11658199999999996	B	0.25048	0.117	B	0.33454	0.164	T	0.46498	-0.9187	9	0.14656	T	0.56	.	6.6556	0.22986	0.0:0.7548:0.0:0.2452	rs1635242;rs52807899;rs58318664;rs1635242	2000	Q9NR99	MXRA5_HUMAN	S	2000	ENSP00000217939:G2000S	ENSP00000217939:G2000S	G	-	1	0	MXRA5	3245724	0.005000	0.15991	0.677000	0.29947	0.217000	0.24651	0.838000	0.27572	1.399000	0.46721	0.544000	0.68410	GGC	C|0.319;T|0.681	0.681	strong		0.602	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
FBN3	84467	hgsc.bcm.edu	37	19	8176640	8176640	+	Missense_Mutation	SNP	C	C	T	rs12975322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8176640C>T	ENST00000600128.1	-	32	4390	c.3976G>A	c.(3976-3978)Gtc>Atc	p.V1326I	FBN3_ENST00000601739.1_Missense_Mutation_p.V1326I|FBN3_ENST00000270509.2_Missense_Mutation_p.V1326I			Q75N90	FBN3_HUMAN	fibrillin 3	1326	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		V -> I (in dbSNP:rs12975322). {ECO:0000269|PubMed:11347906}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TCCTGGGAGACGCATTCATCC	0.622													C|||	1416	0.282748	0.2322	0.3905	5008	,	,		10528	0.4206		0.2326	False		,,,				2504	0.184				p.V1326I		Atlas-SNP	.											FBN3,colon,carcinoma,0,1	FBN3	300	1	0			c.G3976A						PASS	.	C	ILE/VAL	1126,3280	396.3+/-330.0	135,856,1212	50.0	49.0	49.0		3976	1.7	0.0	19	dbSNP_121	49	2080,6520	357.9+/-330.9	242,1596,2462	yes	missense	FBN3	NM_032447.3	29	377,2452,3674	TT,TC,CC		24.186,25.5561,24.6502	benign	1326/2810	8176640	3206,9800	2203	4300	6503	SO:0001583	missense	84467	exon31			GGGAGACGCATTC		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.3976G>A	19.37:g.8176640C>T	ENSP00000470498:p.Val1326Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	683	0.31272893772893773	129	0.2621951219512195	126	0.34806629834254144	248	0.43356643356643354	180	0.23746701846965698	C	8.020	0.759456	0.15846	0.255561	0.24186	ENSG00000142449	ENST00000270509	D	0.87179	-2.22	3.95	1.72	0.24424	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.503112	0.19831	U	0.105085	T	0.00012	0.0000	N	0.03917	-0.325	0.80722	P	0.0	P	0.36535	0.557	B	0.29440	0.102	T	0.35847	-0.9772	9	0.37606	T	0.19	.	6.808	0.23788	0.0:0.6905:0.0:0.3095	rs12975322;rs56654013;rs12975322	1326	Q75N90	FBN3_HUMAN	I	1326	ENSP00000270509:V1326I	ENSP00000270509:V1326I	V	-	1	0	FBN3	8082640	0.000000	0.05858	0.000000	0.03702	0.324000	0.28378	-0.922000	0.04004	0.131000	0.18576	0.313000	0.20887	GTC	C|0.722;T|0.278	0.278	strong		0.622	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
LINC00283	100874057	hgsc.bcm.edu	37	13	103397937	103397937	+	RNA	SNP	T	T	G	rs9300759	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:103397937T>G	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		CATTTGGGATTCACTAAAGTT	0.388													T|||	1370	0.273562	0.3419	0.2406	5008	,	,		21063	0.4087		0.174	False		,,,				2504	0.1677				p.N1704H		Atlas-SNP	.											.	.	.	.	0			c.A5110C						PASS	.	T	HIS/ASN	456,928		76,304,312	135.0	115.0	121.0		5110	0.9	0.0	13	dbSNP_119	121	632,2548		70,492,1028	yes	missense	CCDC168	NM_001146197.1	68	146,796,1340	GG,GT,TT		19.8742,32.948,23.8387		1704/7082	103397937	1088,3476	692	1590	2282			643677	exon4			TGGGATTCACTAA			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.103397937T>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				T|0.697;G|0.303	0.303	strong		0.388	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
LY75	4065	hgsc.bcm.edu	37	2	160676350	160676350	+	Missense_Mutation	SNP	T	T	C	rs17827158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:160676350T>C	ENST00000263636.4	-	29	4067	c.4040A>G	c.(4039-4041)aAg>aGg	p.K1347R	LY75-CD302_ENST00000505052.1_Missense_Mutation_p.K1347R|LY75_ENST00000554112.1_Missense_Mutation_p.K1347R|LY75_ENST00000553424.1_Missense_Mutation_p.K1347R|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.K1347R	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1347	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.		K -> R (in dbSNP:rs17827158).		endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AGCCAAAAACTTCTCATTTTT	0.363													T|||	365	0.0728834	0.0567	0.0807	5008	,	,		17662	0.0079		0.1044	False		,,,				2504	0.1237				p.K1347R		Atlas-SNP	.											.	LY75	151	.	0			c.A4040G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	309,4097	162.9+/-194.8	17,275,1911	81.0	86.0	84.0		4040,4040,4040	2.0	0.1	2	dbSNP_123	84	901,7699	202.1+/-245.5	52,797,3451	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	26,26,26	69,1072,5362	CC,CT,TT		10.4767,7.0132,9.3034	benign,benign,benign	1347/1874,1347/1818,1347/1723	160676350	1210,11796	2203	4300	6503	SO:0001583	missense	4065	exon29			AAAAACTTCTCAT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.4040A>G	2.37:g.160676350T>C	ENSP00000263636:p.Lys1347Arg	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	161	0.07371794871794872	38	0.07723577235772358	45	0.12430939226519337	3	0.005244755244755245	75	0.09894459102902374	T	8.685	0.905974	0.17760	0.070132	0.104767	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07908	3.15;3.15;3.15;3.15;3.15	5.65	1.98	0.26296	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	.	.	.	.	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	B;B;B	0.11235	0.003;0.004;0.004	B;B;B	0.14023	0.009;0.01;0.006	T	0.42916	-0.9423	8	0.15952	T	0.53	-4.5352	1.4096	0.02288	0.1352:0.206:0.1403:0.5185	rs17827158;rs52833817;rs17827158	1347;1347;1347	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	R	1347	ENSP00000451511:K1347R;ENSP00000451446:K1347R;ENSP00000263636:K1347R;ENSP00000423463:K1347R;ENSP00000421035:K1347R	ENSP00000423463:K1347R	K	-	2	0	LY75;LY75-CD302	160384596	0.000000	0.05858	0.114000	0.21550	0.746000	0.42486	0.646000	0.24797	0.403000	0.25479	0.482000	0.46254	AAG	T|0.915;C|0.085	0.085	strong		0.363	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
BTNL2	56244	hgsc.bcm.edu	37	6	32362639	32362639	+	Silent	SNP	G	G	A	rs41535850	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32362639G>A	ENST00000374993.1	-	6	1241	c.1242C>T	c.(1240-1242)caC>caT	p.H414H	BTNL2_ENST00000414363.1_Silent_p.H204H|BTNL2_ENST00000544175.1_Silent_p.H137H|BTNL2_ENST00000540315.1_Silent_p.H204H|BTNL2_ENST00000429232.2_3'UTR|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Silent_p.H320H|BTNL2_ENST00000454136.3_Silent_p.H414H	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	414						integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						GGAACAGCCCGTGGCTGCCTT	0.557													g|||	821	0.163938	0.1422	0.1599	5008	,	,		21164	0.1587		0.163	False		,,,				2504	0.2025				p.H414H		Atlas-SNP	.											.	BTNL2	50	.	0			c.C1242T						PASS	.			551,3855	248.1+/-256.1	28,495,1680	210.0	203.0	205.0		1242	-9.9	0.0	6	dbSNP_127	205	1241,7359	248.3+/-276.0	92,1057,3151	no	coding-synonymous	BTNL2	NM_019602.1		120,1552,4831	AA,AG,GG		14.4302,12.5057,13.7783		414/456	32362639	1792,11214	2203	4300	6503	SO:0001819	synonymous_variant	56244	exon6			CAGCCCGTGGCTG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1242C>T	6.37:g.32362639G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	113	48	0.424779	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				G|0.859;A|0.141	0.141	strong		0.557	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
ACSF3	197322	hgsc.bcm.edu	37	16	89199651	89199651	+	Silent	SNP	G	G	A	rs12447947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:89199651G>A	ENST00000317447.4	+	8	1724	c.1347G>A	c.(1345-1347)ctG>ctA	p.L449L	ACSF3_ENST00000378345.4_Silent_p.L184L|ACSF3_ENST00000406948.3_Silent_p.L449L	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	449					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)		CATTCACCCTGGATGGCTGGT	0.557													G|||	728	0.145367	0.0295	0.2608	5008	,	,		18812	0.0109		0.3608	False		,,,				2504	0.137				p.L449L		Atlas-SNP	.											.	ACSF3	40	.	0			c.G1347A						PASS	.	G	,	320,4076	170.9+/-201.2	16,288,1894	61.0	61.0	61.0		1347,1347	-9.6	0.0	16	dbSNP_120	61	3095,5505	472.3+/-368.3	573,1949,1778	no	coding-synonymous,coding-synonymous	ACSF3	NM_001127214.2,NM_174917.3	,	589,2237,3672	AA,AG,GG		35.9884,7.2793,26.2773	,	449/577,449/577	89199651	3415,9581	2198	4300	6498	SO:0001819	synonymous_variant	197322	exon8			CACCCTGGATGGC	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.1347G>A	16.37:g.89199651G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	33	0.6	NM_174917	A8K4J8|C9JQL6|Q6INA0|Q8N2F7	Silent	SNP	ENST00000317447.4	37	CCDS10974.1																																																																																			G|0.746;A|0.254	0.254	strong		0.557	ACSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269919.1	NM_174917	
KRT40	125115	hgsc.bcm.edu	37	17	39139348	39139348	+	Silent	SNP	A	A	G	rs16968859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39139348A>G	ENST00000398486.2	-	4	640	c.480T>C	c.(478-480)ctT>ctC	p.L160L	KRT40_ENST00000377755.4_Silent_p.L160L	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	160	Coil 1B.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				GCTGTACAGCAAGTCTAGAAT	0.328													A|||	789	0.157548	0.1415	0.1715	5008	,	,		16670	0.1548		0.1302	False		,,,				2504	0.2004				p.L160L		Atlas-SNP	.											.	KRT40	27	.	0			c.T480C						PASS	.	A		480,3200		29,422,1389	174.0	169.0	171.0		480	-8.8	0.9	17	dbSNP_123	171	889,7303		48,793,3255	no	coding-synonymous	KRT40	NM_182497.3		77,1215,4644	GG,GA,AA		10.8521,13.0435,11.5313		160/432	39139348	1369,10503	1840	4096	5936	SO:0001819	synonymous_variant	125115	exon4			TACAGCAAGTCTA	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.480T>C	17.37:g.39139348A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	37	CCDS42320.1																																																																																			A|0.859;G|0.141	0.141	strong		0.328	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
DPCR1	135656	hgsc.bcm.edu	37	6	30920890	30920890	+	Missense_Mutation	SNP	G	G	A	rs2240804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30920890G>A	ENST00000462446.1	+	3	4206	c.4178G>A	c.(4177-4179)cGg>cAg	p.R1393Q	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.R235Q			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	517						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CCTTCCCCACGGTGATCTTGG	0.562													g|||	909	0.18151	0.0446	0.196	5008	,	,		18705	0.1776		0.3419	False		,,,				2504	0.1953				p.R1393Q		Atlas-SNP	.											.	DPCR1	99	.	0			c.G4178A						PASS	.		GLN/ARG	430,3976	209.5+/-230.2	23,384,1796	102.0	77.0	86.0		4178	-1.6	0.1	6	dbSNP_98	86	3114,5486	477.2+/-369.6	544,2026,1730	yes	missense	DPCR1	NM_080870.3	43	567,2410,3526	AA,AG,GG		36.2093,9.7594,27.249	probably-damaging	1393/1394	30920890	3544,9462	2203	4300	6503	SO:0001583	missense	135656	exon3			CCCCACGGTGATC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.4178G>A	6.37:g.30920890G>A	ENSP00000417182:p.Arg1393Gln	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	472	0.21611721611721613	20	0.04065040650406504	68	0.1878453038674033	126	0.2202797202797203	258	0.3403693931398417	g	19.26	3.793411	0.70452	0.097594	0.362093	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.29917	1.55;1.68	3.72	-1.63	0.08345	.	.	.	.	.	T	0.09642	0.0237	L	0.46157	1.445	0.80722	P	0.0	B	0.31989	0.35	B	0.32149	0.141	T	0.23868	-1.0176	8	0.87932	D	0	.	4.2277	0.10589	0.4629:0.1878:0.3492:0.0	rs2240804;rs17427055;rs52811115;rs60056207;rs2240804	1393	E9PEI6	.	Q	1393;517;235	ENSP00000417182:R1393Q;ENSP00000305948:R235Q	ENSP00000305948:R235Q	R	+	2	0	DPCR1	31028869	0.000000	0.05858	0.076000	0.20297	0.585000	0.36419	-0.186000	0.09670	-0.238000	0.09724	0.574000	0.79327	CGG	G|0.759;A|0.241	0.241	strong		0.562	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
MPDZ	8777	hgsc.bcm.edu	37	9	13183486	13183486	+	Silent	SNP	T	T	C	rs34704118	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:13183486T>C	ENST00000319217.7	-	19	2827	c.2580A>G	c.(2578-2580)ttA>ttG	p.L860L	MPDZ_ENST00000381015.4_Silent_p.L860L|MPDZ_ENST00000541718.1_Silent_p.L860L|MPDZ_ENST00000536827.1_Silent_p.L860L|MPDZ_ENST00000381022.2_Silent_p.L860L|MPDZ_ENST00000546205.1_Silent_p.L860L|MPDZ_ENST00000447879.1_Silent_p.L860L	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	860					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CATGAAGAGATAAAATAGAGG	0.408													T|||	7	0.00139776	0.0	0.0072	5008	,	,		18769	0.0		0.001	False		,,,				2504	0.001				p.L860L		Atlas-SNP	.											MPDZ_ENST00000541718,colon,carcinoma,-2,2	MPDZ	324	2	0			c.A2580G						PASS	.	T		4,3782		0,4,1889	93.0	91.0	92.0		2580	0.8	0.8	9	dbSNP_126	92	55,8201		0,55,4073	no	coding-synonymous	MPDZ	NM_003829.3		0,59,5962	CC,CT,TT		0.6662,0.1057,0.49		860/2042	13183486	59,11983	1893	4128	6021	SO:0001819	synonymous_variant	8777	exon19			AAGAGATAAAATA	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2580A>G	9.37:g.13183486T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				T|0.997;C|0.003	0.003	strong		0.408	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
MAP2K2	5605	hgsc.bcm.edu	37	19	4117528	4117528	+	Silent	SNP	G	G	A	rs8157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4117528G>A	ENST00000262948.5	-	2	445	c.192C>T	c.(190-192)gtC>gtT	p.V64V	MAP2K2_ENST00000599345.1_5'UTR|MAP2K2_ENST00000394867.4_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	64					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	TGAGTTCGCCGACCTTGGCTT	0.592													G|||	292	0.0583067	0.0825	0.0317	5008	,	,		16277	0.0228		0.0596	False		,,,				2504	0.0798				p.V64V		Atlas-SNP	.											.	MAP2K2	72	.	0			c.C192T						PASS	.	G		306,4100	165.4+/-196.9	14,278,1911	91.0	86.0	88.0		192	-4.7	1.0	19	dbSNP_52	88	515,8085	145.7+/-201.4	21,473,3806	no	coding-synonymous	MAP2K2	NM_030662.3		35,751,5717	AA,AG,GG		5.9884,6.9451,6.3125		64/401	4117528	821,12185	2203	4300	6503	SO:0001819	synonymous_variant	5605	exon2			TTCGCCGACCTTG	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.192C>T	19.37:g.4117528G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			G|0.943;A|0.057	0.057	strong		0.592	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
DNMT3L	29947	hgsc.bcm.edu	37	21	45675997	45675997	+	Missense_Mutation	SNP	C	C	T	rs142917827		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45675997C>T	ENST00000418993.1	-	7	1040	c.557G>A	c.(556-558)aGg>aAg	p.R186K	DNMT3L_ENST00000270172.3_Missense_Mutation_p.R186K	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	186					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		TGGCTGTCTCCTCCACACAGG	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		13853	0.0		0.001	False		,,,				2504	0.0				p.R186K		Atlas-SNP	.											.	DNMT3L	33	.	0			c.G557A						PASS	.	C	LYS/ARG,LYS/ARG	1,4405	2.1+/-5.4	0,1,2202	108.0	108.0	108.0		557,557	1.1	0.3	21	dbSNP_134	108	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense	DNMT3L	NM_013369.2,NM_175867.1	26,26	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign,benign	186/388,186/387	45675997	18,12988	2203	4300	6503	SO:0001583	missense	29947	exon7			TGTCTCCTCCACA	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"""cytosine-5-methyltransferase 3-like protein"", ""human cytosine-5-methyltransferase 3-like protein"""	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.557G>A	21.37:g.45675997C>T	ENSP00000412862:p.Arg186Lys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	183	98	0.535519	NM_013369	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.006	-2.100319	0.00360	2.27E-4	0.001977	ENSG00000142182	ENST00000270172;ENST00000418993;ENST00000431166	T;T;T	0.73258	-0.73;-0.73;-0.73	3.44	1.07	0.20283	.	0.493499	0.20721	N	0.086902	T	0.29620	0.0739	N	0.01091	-1.02	0.24720	N	0.993155	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36648	-0.9739	10	0.02654	T	1	-19.7411	4.7202	0.12915	0.0:0.3025:0.0:0.6975	.	186;186	Q9UJW3-2;Q9UJW3	.;DNM3L_HUMAN	K	186;186;171	ENSP00000270172:R186K;ENSP00000412862:R186K;ENSP00000400242:R171K	ENSP00000270172:R186K	R	-	2	0	DNMT3L	44500425	0.992000	0.36948	0.271000	0.24616	0.065000	0.16274	2.203000	0.42752	0.118000	0.18165	-0.379000	0.06801	AGG	C|0.999;T|0.001	0.001	strong		0.478	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369	
PKP2	5318	hgsc.bcm.edu	37	12	33003762	33003762	+	Missense_Mutation	SNP	A	A	G	rs397516992		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:33003762A>G	ENST00000070846.6	-	5	1340	c.1316T>C	c.(1315-1317)gTa>gCa	p.V439A	PKP2_ENST00000340811.4_Missense_Mutation_p.V439A	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	439					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					CAGCCGAGGTACCCCATTTAG	0.438																																					p.V439A		Atlas-SNP	.											PKP2,right_upper_lobe,carcinoma,-1,1	PKP2	110	1	0			c.T1316C						scavenged	.						128.0	126.0	127.0					12																	33003762		2203	4300	6503	SO:0001583	missense	5318	exon5			CGAGGTACCCCAT	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.1316T>C	12.37:g.33003762A>G	ENSP00000070846:p.Val439Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	141	3	0.0212766	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	A	13.77	2.337206	0.41398	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.75704	-0.96;0.53	4.7	4.7	0.59300	Armadillo-like helical (1);Armadillo-type fold (1);	0.239191	0.35677	N	0.003053	T	0.75354	0.3838	M	0.71206	2.165	0.27146	N	0.96152	P;P;P	0.40000	0.649;0.698;0.518	B;B;B	0.43990	0.311;0.438;0.164	T	0.73059	-0.4102	10	0.87932	D	0	-10.5033	9.8173	0.40860	0.8467:0.0:0.0:0.1533	.	439;439;439	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	A	439	ENSP00000342800:V439A;ENSP00000070846:V439A	ENSP00000070846:V439A	V	-	2	0	PKP2	32895029	1.000000	0.71417	0.041000	0.18516	0.671000	0.39405	5.344000	0.65981	1.880000	0.54463	0.379000	0.24179	GTA	.	.	none		0.438	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
PBRM1	55193	hgsc.bcm.edu	37	3	52584787	52584787	+	Silent	SNP	T	T	C	rs2251219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52584787T>C	ENST00000296302.7	-	28	4657	c.4656A>G	c.(4654-4656)ccA>ccG	p.P1552P	PBRM1_ENST00000394830.3_Silent_p.P1445P|PBRM1_ENST00000410007.1_Silent_p.P1472P|PBRM1_ENST00000409114.3_Silent_p.P1515P|PBRM1_ENST00000409057.1_Silent_p.P1497P|PBRM1_ENST00000356770.4_Silent_p.P1465P|PBRM1_ENST00000337303.4_Silent_p.P1445P|SMIM4_ENST00000476842.1_Intron|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000409767.1_Silent_p.P1460P			Q86U86	PB1_HUMAN	polybromo 1	1552	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GACTTCCACCTGGTGCTGGAG	0.468			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	1618	0.323083	0.1452	0.4654	5008	,	,		20114	0.4296		0.4195	False		,,,				2504	0.2536				p.P1445P		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.A4335G						PASS	.	T	,,	766,3640	313.0+/-292.9	65,636,1502	80.0	74.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4395,4335,4335	3.5	1.0	3	dbSNP_100	76	3517,5083	512.3+/-377.9	740,2037,1523	yes	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	805,2673,3025	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	40.8953,17.3854,32.931	,,	1465/1603,1445/1583,1445/1583	52584787	4283,8723	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon28			TCCACCTGGTGCT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4656A>G	3.37:g.52584787T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	118	55	0.466102	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.654;C|0.346	0.346	strong		0.468	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
STK16	8576	hgsc.bcm.edu	37	2	220113145	220113145	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220113145A>G	ENST00000409638.3	+	8	954	c.782A>G	c.(781-783)cAt>cGt	p.H261R	GLB1L_ENST00000295759.7_5'Flank|STK16_ENST00000409516.3_Missense_Mutation_p.H143R|STK16_ENST00000409260.1_Missense_Mutation_p.H306R|GLB1L_ENST00000392089.2_5'Flank|STK16_ENST00000396738.2_Missense_Mutation_p.H261R|STK16_ENST00000409743.1_Missense_Mutation_p.H229R|TUBA4A_ENST00000498660.1_5'Flank	NM_001008910.2	NP_001008910.1	O75716	STK16_HUMAN	serine/threonine kinase 16	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|protein autophosphorylation (GO:0046777)	Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			skin(1)	1		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTCCACAGGCATTCTTCAGCA	0.567																																					p.H261R	Pancreas(34;887 922 17165 36961 39622)	Atlas-SNP	.											.	STK16	22	.	0			c.A782G						PASS	.						128.0	135.0	133.0					2																	220113145		2088	4216	6304	SO:0001583	missense	8576	exon8			ACAGGCATTCTTC	AF060798	CCDS42822.1	2q35	2010-04-16			ENSG00000115661	ENSG00000115661			11394	protein-coding gene	gene with protein product		604719				9712705	Standard	NM_001008910		Approved	PKL12, MPSK	uc002vko.2	O75716	OTTHUMG00000154520	ENST00000409638.3:c.782A>G	2.37:g.220113145A>G	ENSP00000386928:p.His261Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001008910	A8K9H9|Q5U0F8|Q96KI2|Q9BUH4|Q9UEN3|Q9UP78	Missense_Mutation	SNP	ENST00000409638.3	37	CCDS42822.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.534997	0.45073	.	.	ENSG00000115661	ENST00000409638;ENST00000396738;ENST00000409516;ENST00000409260;ENST00000409743	T;T;T;T;T	0.73363	2.13;2.13;-0.74;-0.74;2.13	4.98	4.98	0.66077	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.301734	0.37530	N	0.002044	T	0.64405	0.2595	L	0.27944	0.81	0.48288	D	0.999628	B;B;B	0.33022	0.394;0.084;0.084	B;B;B	0.33042	0.072;0.157;0.026	T	0.68629	-0.5358	10	0.72032	D	0.01	-3.1791	14.8415	0.70230	1.0:0.0:0.0:0.0	.	143;306;261	B4DPS1;B8ZZN3;O75716	.;.;STK16_HUMAN	R	261;261;143;306;229	ENSP00000386928:H261R;ENSP00000379964:H261R;ENSP00000386309:H143R;ENSP00000387156:H306R;ENSP00000386553:H229R	ENSP00000379964:H261R	H	+	2	0	STK16	219821389	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.637000	0.74304	2.098000	0.63641	0.459000	0.35465	CAT	.	.	none		0.567	STK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335679.1		
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970718	45970718	+	Silent	SNP	C	C	T	rs233238	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45970718C>T	ENST00000391621.1	-	1	670	c.624G>A	c.(622-624)ccG>ccA	p.P208P	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	208	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						GCTGGCAGCACGGAGAGGAAG	0.642													C|||	1331	0.265775	0.357	0.1715	5008	,	,		20976	0.3641		0.2068	False		,,,				2504	0.1687				p.P208P		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G624A						PASS	.	C	,	1465,2941	472.6+/-356.4	247,971,985	119.0	126.0	124.0		,624	-5.0	0.0	21	dbSNP_79	124	1696,6904	311.7+/-310.5	158,1380,2762	no	intron,coding-synonymous	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,	405,2351,3747	TT,TC,CC		19.7209,33.2501,24.3042	,	,208/256	45970718	3161,9845	2203	4300	6503	SO:0001819	synonymous_variant	386679	exon1			GCAGCACGGAGAG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.624G>A	21.37:g.45970718C>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	85	28	0.329412	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			C|0.742;T|0.258	0.258	strong		0.642	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
NUP153	9972	hgsc.bcm.edu	37	6	17629004	17629004	+	Silent	SNP	T	T	C	rs78541395	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:17629004T>C	ENST00000262077.2	-	18	3425	c.3426A>G	c.(3424-3426)aaA>aaG	p.K1142K	NUP153_ENST00000537253.1_Silent_p.K1173K	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	1142					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)			AATTCTCATCTTTGGTTTGCT	0.413													T|||	10	0.00199681	0.0015	0.0029	5008	,	,		15099	0.0		0.006	False		,,,				2504	0.0				p.K1142K		Atlas-SNP	.											.	NUP153	116	.	0			c.A3426G						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	98.0	101.0	100.0		3426	5.6	1.0	6	dbSNP_132	100	70,8530	42.2+/-99.7	0,70,4230	no	coding-synonymous	NUP153	NM_005124.2		0,76,6427	CC,CT,TT		0.814,0.1362,0.5843		1142/1476	17629004	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	9972	exon18			CTCATCTTTGGTT	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.3426A>G	6.37:g.17629004T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Silent	SNP	ENST00000262077.2	37	CCDS4541.1																																																																																			T|0.996;C|0.004	0.004	strong		0.413	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		
QSER1	79832	hgsc.bcm.edu	37	11	32996805	32996805	+	Silent	SNP	C	C	T	rs11032076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:32996805C>T	ENST00000399302.2	+	12	5318	c.4983C>T	c.(4981-4983)gtC>gtT	p.V1661V	QSER1_ENST00000527788.1_Silent_p.V1422V	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1661										breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AGTTTGCTGTCGATCCAGAGA	0.308													c|||	295	0.0589058	0.0015	0.0994	5008	,	,		15385	0.005		0.1481	False		,,,				2504	0.0716				p.V1661V		Atlas-SNP	.											QSER1,caecum,carcinoma,0,1	QSER1	153	1	0			c.C4983T						PASS	.	T		98,3494		2,94,1700	97.0	92.0	93.0		4983	-2.5	1.0	11	dbSNP_120	93	1124,7000		72,980,3010	no	coding-synonymous	QSER1	NM_001076786.1		74,1074,4710	TT,TC,CC		13.8355,2.7283,10.4302		1661/1736	32996805	1222,10494	1796	4062	5858	SO:0001819	synonymous_variant	79832	exon12			TGCTGTCGATCCA	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.4983C>T	11.37:g.32996805C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_001076786	Q6ZU30|Q6ZUR5	Silent	SNP	ENST00000399302.2	37	CCDS41631.1	158	0.07234432234432235	1	0.0020325203252032522	44	0.12154696132596685	3	0.005244755244755245	110	0.14511873350923482	c	7.557	0.663876	0.14710	0.027283	0.138355	ENSG00000060749	ENST00000524678	.	.	.	5.67	-2.55	0.06288	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.21999	-1.0229	3	.	.	.	.	6.1626	0.20372	0.2699:0.3365:0.0:0.3936	rs11032076;rs17756863;rs61521589;rs11032076	.	.	.	L	682	.	.	S	+	2	0	QSER1	32953381	0.998000	0.40836	0.972000	0.41901	0.923000	0.55619	0.465000	0.22004	-0.725000	0.04901	-1.873000	0.00551	TCG	C|0.907;T|0.093	0.093	strong		0.308	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774	
DNPEP	23549	hgsc.bcm.edu	37	2	220250232	220250232	+	Missense_Mutation	SNP	G	G	C	rs115897075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220250232G>C	ENST00000273075.4	-	8	908	c.688C>G	c.(688-690)Ctc>Gtc	p.L230V	DNPEP_ENST00000373972.1_Missense_Mutation_p.L155V|DNPEP_ENST00000523282.1_Missense_Mutation_p.L238V|AC053503.4_ENST00000420563.1_RNA	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	220					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGGACATGAGGACCGAATGG	0.607													G|||	21	0.00419329	0.0008	0.0014	5008	,	,		20324	0.0		0.0189	False		,,,				2504	0.0				p.L230V		Atlas-SNP	.											.	DNPEP	40	.	0			c.C688G						PASS	.	G	VAL/LEU	11,4079		0,11,2034	52.0	56.0	54.0		688	4.8	1.0	2	dbSNP_132	54	126,8226		1,124,4051	yes	missense	DNPEP	NM_012100.2	32	1,135,6085	CC,CG,GG		1.5086,0.2689,1.1011	probably-damaging	230/486	220250232	137,12305	2045	4176	6221	SO:0001583	missense	23549	exon8			ACATGAGGACCGA		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.688C>G	2.37:g.220250232G>C	ENSP00000273075:p.Leu230Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	141	55	0.390071	NM_012100	Q9BW44|Q9NUV5	Missense_Mutation	SNP	ENST00000273075.4	37	CCDS42823.1	16	0.007326007326007326	1	0.0020325203252032522	0	0.0	0	0.0	15	0.01978891820580475	G	26.6	4.756807	0.89843	0.002689	0.015086	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000535056;ENST00000429013;ENST00000322176	.	.	.	4.82	4.82	0.62117	Peptidase M18, domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.66436	0.2789	M	0.79123	2.44	0.80722	D	1	D;D;D;D;D	0.63046	0.992;0.992;0.992;0.992;0.992	P;P;P;D;P	0.66497	0.882;0.882;0.882;0.944;0.882	T	0.76772	-0.2836	9	0.56958	D	0.05	-0.3566	17.7194	0.88347	0.0:0.0:1.0:0.0	.	238;230;238;220;230	E7ETB3;B7Z822;B7Z7F0;Q9ULA0;Q53SB6	.;.;.;DNPEP_HUMAN;.	V	230;230;155;238;123;216;245	.	ENSP00000273075:L230V	L	-	1	0	DNPEP	219958476	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.835000	0.92100	2.503000	0.84419	0.655000	0.94253	CTC	G|0.990;C|0.010	0.010	strong		0.607	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	
CPEB1	64506	hgsc.bcm.edu	37	15	83296073	83296073	+	Missense_Mutation	SNP	C	C	T	rs61733713	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:83296073C>T	ENST00000562019.1	-	2	377	c.61G>A	c.(61-63)Gca>Aca	p.A21T	CPEB1_ENST00000568757.1_5'UTR|CPEB1_ENST00000568128.1_Missense_Mutation_p.A21T|CPEB1_ENST00000563800.1_Missense_Mutation_p.A48T|CPEB1_ENST00000450751.2_5'UTR			Q9BZB8	CPEB1_HUMAN	cytoplasmic polyadenylation element binding protein 1	21					cellular response to amino acid stimulus (GO:0071230)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|mRNA processing (GO:0006397)|negative regulation of cytoplasmic translation (GO:2000766)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|ribonucleoprotein complex (GO:0030529)	metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|nucleotide binding (GO:0000166)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(1)|skin(1)	28			BRCA - Breast invasive adenocarcinoma(143;0.229)			AGAGCAGGTGCTTCCTGGTTG	0.403													C|||	39	0.00778754	0.0	0.0058	5008	,	,		19995	0.0		0.0209	False		,,,				2504	0.0143				p.A21T		Atlas-SNP	.											.	CPEB1	114	.	0			c.G61A						PASS	.	C	THR/ALA	5,3771		0,5,1883	95.0	92.0	93.0		61	4.8	1.0	15	dbSNP_129	93	129,8107		0,129,3989	yes	missense	CPEB1	NM_030594.3	58	0,134,5872	TT,TC,CC		1.5663,0.1324,1.1156	benign	21/562	83296073	134,11878	1888	4118	6006	SO:0001583	missense	64506	exon2			CAGGTGCTTCCTG	AF329402	CCDS42072.1, CCDS45329.1, CCDS45330.1, CCDS42072.2, CCDS45329.2, CCDS45330.2	15q25.1	2008-02-05				ENSG00000214575			21744	protein-coding gene	gene with protein product		607342				11223249	Standard	NM_001079533		Approved	FLJ13203, CPEB	uc002biv.3	Q9BZB8		ENST00000562019.1:c.61G>A	15.37:g.83296073C>T	ENSP00000457836:p.Ala21Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	37	0.480519	NM_030594	B7Z6C6|Q86W46|Q8IV41|Q9BZB7|Q9H8V5	Missense_Mutation	SNP	ENST00000562019.1	37		21	0.009615384615384616	0	0.0	3	0.008287292817679558	0	0.0	18	0.023746701846965697	C	10.88	1.475021	0.26511	0.001324	0.015663	ENSG00000214575	ENST00000450751;ENST00000398593	.	.	.	5.77	4.85	0.62838	.	0.349128	0.26334	U	0.024979	T	0.15912	0.0383	N	0.08118	0	0.80722	D	1	B;B;B	0.15473	0.0;0.005;0.013	B;B;B	0.09377	0.001;0.003;0.004	T	0.05750	-1.0866	9	0.17832	T	0.49	-0.2195	10.2922	0.43603	0.0:0.7936:0.1364:0.07	rs61733713	21;21;21	Q9BZB8-3;Q9BZB8;E7ET70	.;CPEB1_HUMAN;.	T	21	.	ENSP00000381593:A21T	A	-	1	0	CPEB1	81093128	0.999000	0.42202	0.962000	0.40283	0.767000	0.43475	1.910000	0.39927	1.420000	0.47138	0.650000	0.86243	GCA	C|0.989;T|0.011	0.011	strong		0.403	CPEB1-006	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000421102.1	NM_030594	
SSC5D	284297	hgsc.bcm.edu	37	19	56030009	56030009	+	Missense_Mutation	SNP	C	C	T	rs925878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56030009C>T	ENST00000389623.6	+	14	4389	c.4366C>T	c.(4366-4368)Ccc>Tcc	p.P1456S		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1456	Pro-rich.			P -> S (in Ref. 1; ACJ02751). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						TCCCCTTGACCCCCTCACCCT	0.632													-|||	822	0.164137	0.0825	0.1902	5008	,	,		13016	0.2212		0.173	False		,,,				2504	0.1881				p.P1456S		Atlas-SNP	.											.	SSC5D	65	.	0			c.C4366T						PASS	.						48.0	43.0	44.0					19																	56030009		692	1591	2283	SO:0001583	missense	284297	exon14			CTTGACCCCCTCA		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.4366C>T	19.37:g.56030009C>T	ENSP00000374274:p.Pro1456Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Missense_Mutation	SNP	ENST00000389623.6	37	CCDS46196.1	408	0.18681318681318682	49	0.09959349593495935	82	0.2265193370165746	144	0.2517482517482518	133	0.17546174142480211	-	9.441	1.088029	0.20390	.	.	ENSG00000179954	ENST00000389623	T	0.01145	5.27	3.41	-0.807	0.10872	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.38243	-0.9670	8	0.39692	T	0.17	.	5.8496	0.18685	0.4305:0.395:0.1745:0.0	rs925878;rs52789735;rs60801143;rs925878	1456	A1L4H1	SRCRL_HUMAN	S	1456	ENSP00000374274:P1456S	ENSP00000374274:P1456S	P	+	1	0	SSC5D	60721821	0.002000	0.14202	0.000000	0.03702	0.139000	0.21198	0.636000	0.24644	-0.296000	0.08947	0.282000	0.19409	CCC	C|0.809;T|0.191	0.191	strong		0.632	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
HINFP	25988	hgsc.bcm.edu	37	11	119005132	119005132	+	Missense_Mutation	SNP	C	C	T	rs100803	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:119005132C>T	ENST00000350777.2	+	10	1541	c.1478C>T	c.(1477-1479)gCc>gTc	p.A493V		NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	493	Interaction with NPAT.		A -> V (in dbSNP:rs100803). {ECO:0000269|PubMed:15489334}.		DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						CCTCCCCCAGCCCCTGAGCCA	0.562											OREG0021397	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2012	0.401757	0.1687	0.2839	5008	,	,		19450	0.7183		0.4433	False		,,,				2504	0.4315				p.A493V		Atlas-SNP	.											.	HINFP	50	.	0			c.C1478T						PASS	.	C	VAL/ALA,VAL/ALA	843,3557	330.4+/-301.5	75,693,1432	43.0	48.0	46.0		1478,1478	-0.7	0.0	11	dbSNP_83	46	3610,4980	518.7+/-379.3	790,2030,1475	yes	missense,missense	HINFP	NM_015517.4,NM_198971.2	64,64	865,2723,2907	TT,TC,CC		42.0256,19.1591,34.2802	benign,benign	493/518,493/518	119005132	4453,8537	2200	4295	6495	SO:0001583	missense	25988	exon11			CCCCAGCCCCTGA	AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"""Zinc fingers, C2H2-type"""	17850	protein-coding gene	gene with protein product	"""histone nuclear factor P"""	607099	"""MBD2-interacting zinc finger 1"", ""MBD2-interacting zinc finger"""	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.1478C>T	11.37:g.119005132C>T	ENSP00000318085:p.Ala493Val	Somatic	43	0	0	1492	WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_015517	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	37	CCDS8414.1	966	0.4423076923076923	90	0.18292682926829268	120	0.3314917127071823	422	0.7377622377622378	334	0.44063324538258575	C	5.618	0.298738	0.10622	0.191591	0.420256	ENSG00000172273	ENST00000350777	T	0.10099	2.91	4.9	-0.697	0.11284	.	1.282940	0.05442	N	0.547761	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.23833	-1.0177	9	0.36615	T	0.2	-0.0432	2.4679	0.04557	0.1403:0.4289:0.2726:0.1583	rs100803;rs753835;rs3741335;rs3889924;rs17844880;rs17856531;rs17857597;rs17857666;rs17858206;rs61095432	493	Q9BQA5	HINFP_HUMAN	V	493	ENSP00000318085:A493V	ENSP00000318085:A493V	A	+	2	0	HINFP	118510342	0.002000	0.14202	0.000000	0.03702	0.091000	0.18340	-0.098000	0.11024	-0.001000	0.14495	-0.136000	0.14681	GCC	C|0.611;T|0.389	0.389	strong		0.562	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517	
BLM	641	hgsc.bcm.edu	37	15	91354521	91354521	+	Missense_Mutation	SNP	G	G	A	rs7167216	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91354521G>A	ENST00000355112.3	+	21	4079	c.3961G>A	c.(3961-3963)Gta>Ata	p.V1321I	BLM_ENST00000560509.1_Missense_Mutation_p.V1190I|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1321			V -> I (in dbSNP:rs7167216). {ECO:0000269|Ref.3}.		alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			GGAAATACCCGTATCTTCCCA	0.498			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome				G|||	336	0.0670927	0.0953	0.0461	5008	,	,		17172	0.0238		0.0795	False		,,,				2504	0.0757				p.V1321I		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.G3961A						PASS	.	G	ILE/VAL	408,3988	200.4+/-223.7	15,378,1805	78.0	78.0	78.0		3961	-4.8	0.0	15	dbSNP_116	78	571,8025	154.8+/-208.9	23,525,3750	yes	missense	BLM	NM_000057.2	29	38,903,5555	AA,AG,GG		6.6426,9.2812,7.5354	benign	1321/1418	91354521	979,12013	2198	4298	6496	SO:0001583	missense	641	exon21	Familial Cancer Database		ATACCCGTATCTT	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3961G>A	15.37:g.91354521G>A	ENSP00000347232:p.Val1321Ile	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	20	0.289855	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	37	CCDS10363.1	146	0.06684981684981685	53	0.10772357723577236	20	0.055248618784530384	16	0.027972027972027972	57	0.07519788918205805	G	15.20	2.763600	0.49574	0.092812	0.066426	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.45668	0.89	5.87	-4.78	0.03209	.	0.860286	0.10474	N	0.670404	T	0.00496	0.0016	N	0.16903	0.455	0.80722	P	0.0	B;B	0.14438	0.01;0.01	B;B	0.08055	0.003;0.003	T	0.04178	-1.0971	9	0.33141	T	0.24	-15.1605	17.0924	0.86625	0.1226:0.0:0.8774:0.0	rs7167216;rs52814749;rs7167216	1321;1321	B2RAN0;P54132	.;BLM_HUMAN	I	1321;951;508	ENSP00000347232:V1321I	ENSP00000347232:V1321I	V	+	1	0	BLM	89155525	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.668000	0.05268	-1.050000	0.03230	-0.150000	0.13652	GTA	G|0.928;A|0.072	0.072	strong		0.498	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
TSHZ1	10194	hgsc.bcm.edu	37	18	73000005	73000005	+	Silent	SNP	G	G	A	rs34878160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:73000005G>A	ENST00000580243.1	+	2	2991	c.2643G>A	c.(2641-2643)ccG>ccA	p.P881P	TSHZ1_ENST00000322038.5_Silent_p.P836P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	881					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		AGCTGTCACCGGTCCACAAGA	0.632													G|||	69	0.013778	0.0023	0.0231	5008	,	,		19125	0.0		0.0457	False		,,,				2504	0.0041				p.P836P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G2508A						PASS	.	G		47,4359	49.6+/-84.7	0,47,2156	52.0	49.0	50.0		2508	-3.1	0.8	18	dbSNP_126	50	323,8277	114.6+/-174.5	7,309,3984	no	coding-synonymous	TSHZ1	NM_005786.4		7,356,6140	AA,AG,GG		3.7558,1.0667,2.8448		836/1033	73000005	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GTCACCGGTCCAC	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2643G>A	18.37:g.73000005G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				G|0.972;A|0.028	0.028	strong		0.632	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
TNXB	7148	hgsc.bcm.edu	37	6	32010272	32010272	+	Missense_Mutation	SNP	T	T	A	rs17421133	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32010272T>A	ENST00000375244.3	-	40	12371	c.12170A>T	c.(12169-12171)aAc>aTc	p.N4057I	TNXB_ENST00000451343.1_Missense_Mutation_p.N486I|TNXB_ENST00000375247.2_Missense_Mutation_p.N4055I			P22105	TENX_HUMAN	tenascin XB	4102	Fibronectin type-III 32. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCAAAACACGTTCAGGGGCCG	0.667													T|||	1087	0.217053	0.0212	0.3761	5008	,	,		19961	0.2202		0.34	False		,,,				2504	0.2393				p.N4055I		Atlas-SNP	.											TNXB_ENST00000375247,colon,carcinoma,0,3	TNXB	553	3	0			c.A12164T						PASS	.	T	ILE/ASN,ILE/ASN	228,2794		17,194,1300	52.0	46.0	48.0		12164,1457	3.3	0.8	6	dbSNP_131	48	1707,3711		266,1175,1268	no	missense,missense	TNXB	NM_019105.6,NM_032470.3	149,149	283,1369,2568	AA,AT,TT		31.5061,7.5447,22.9265	possibly-damaging,possibly-damaging	4055/4243,486/674	32010272	1935,6505	1511	2709	4220	SO:0001583	missense	7148	exon40			AACACGTTCAGGG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.12170A>T	6.37:g.32010272T>A	ENSP00000364393:p.Asn4057Ile	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	282	127	0.450355	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		566	0.2591575091575092	17	0.034552845528455285	146	0.40331491712707185	132	0.23076923076923078	271	0.3575197889182058	t	14.60	2.582663	0.46006	0.075447	0.315061	ENSG00000168477	ENST00000375244;ENST00000451343;ENST00000375247	T;T;T	0.77229	-1.08;-1.08;-1.08	4.45	3.29	0.37713	.	0.834350	0.10489	N	0.668630	T	0.65933	0.2739	L	0.37561	1.115	0.80722	P	0.0	D	0.61080	0.989	P	0.57371	0.819	T	0.59804	-0.7385	9	0.54805	T	0.06	.	4.5535	0.12126	0.1704:0.0936:0.0:0.736	rs17421133;rs28361046;rs17421133	4055	P22105-3	.	I	4057;486;4055	ENSP00000364393:N4057I;ENSP00000407685:N486I;ENSP00000364396:N4055I	ENSP00000364393:N4057I	N	-	2	0	TNXB	32118251	0.000000	0.05858	0.797000	0.32132	0.994000	0.84299	0.054000	0.14205	0.764000	0.33197	0.456000	0.33151	AAC	T|0.754;A|0.246	0.246	strong		0.667	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60986019	60986019	+	Missense_Mutation	SNP	A	A	C	rs2236200	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60986019A>C	ENST00000252998.1	-	14	2066	c.1910T>G	c.(1909-1911)cTg>cGg	p.L637R		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	637			L -> R (in dbSNP:rs2236200). {ECO:0000269|PubMed:15489334}.			extracellular space (GO:0005615)		p.L637R(1)									AGTGGCTGTCAGTTTCCTTCT	0.642													A|||	758	0.151358	0.0106	0.1859	5008	,	,		16833	0.2262		0.2505	False		,,,				2504	0.138				p.L637R		Atlas-SNP	.											C20orf151,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T1910G						scavenged	.	A	ARG/LEU	231,4175	134.9+/-171.1	6,219,1978	104.0	103.0	103.0		1910	1.3	0.0	20	dbSNP_98	103	2167,6433	369.9+/-335.7	296,1575,2429	yes	missense	C20orf151	NM_080833.2	102	302,1794,4407	CC,CA,AA		25.1977,5.2429,18.4376	probably-damaging	637/665	60986019	2398,10608	2203	4300	6503	SO:0001583	missense	140893	exon14			GCTGTCAGTTTCC	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.1910T>G	20.37:g.60986019A>C	ENSP00000252998:p.Leu637Arg	Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	375	0.1717032967032967	7	0.014227642276422764	71	0.19613259668508287	113	0.19755244755244755	184	0.24274406332453827	A	8.227	0.803891	0.16467	0.052429	0.251977	ENSG00000130701	ENST00000252998	T	0.24908	1.83	2.42	1.32	0.21799	.	0.219840	0.20847	N	0.084581	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D	0.57899	0.981	P	0.56960	0.81	T	0.22591	-1.0212	9	0.54805	T	0.06	-3.8159	4.1038	0.10026	0.8238:0.0:0.1762:0.0	rs2236200;rs57636275;rs2236200	637	Q8NC74	CT151_HUMAN	R	637	ENSP00000252998:L637R	ENSP00000252998:L637R	L	-	2	0	C20orf151	60419414	0.000000	0.05858	0.006000	0.13384	0.041000	0.13682	0.033000	0.13754	0.374000	0.24650	0.402000	0.26972	CTG	A|0.827;C|0.173	0.173	strong		0.642	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
SCN10A	6336	hgsc.bcm.edu	37	3	38764998	38764998	+	Missense_Mutation	SNP	A	A	G	rs12632942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38764998A>G	ENST00000449082.2	-	18	3274	c.3275T>C	c.(3274-3276)cTa>cCa	p.L1092P		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1092			L -> P (in dbSNP:rs12632942).		AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	ctcaggatctAGGCAGTCCAC	0.612													G|||	1100	0.219649	0.121	0.121	5008	,	,		19013	0.376		0.2465	False		,,,				2504	0.2342				p.L1092P		Atlas-SNP	.											.	SCN10A	359	.	0			c.T3275C						PASS	.	G	PRO/LEU	625,3781	767.2+/-413.5	47,531,1625	77.0	65.0	69.0		3275	-0.5	0.0	3	dbSNP_120	69	2236,6364	705.7+/-405.5	288,1660,2352	yes	missense	SCN10A	NM_006514.2	98	335,2191,3977	GG,GA,AA		26.0,14.1852,21.9975	benign	1092/1957	38764998	2861,10145	2203	4300	6503	SO:0001583	missense	6336	exon18			GGATCTAGGCAGT	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.3275T>C	3.37:g.38764998A>G	ENSP00000390600:p.Leu1092Pro	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	518	0.23717948717948717	53	0.10772357723577236	48	0.13259668508287292	237	0.4143356643356643	180	0.23746701846965698	G	7.645	0.681641	0.14907	0.141852	0.26	ENSG00000185313	ENST00000449082	D	0.83419	-1.72	4.65	-0.53	0.11898	Sodium ion transport-associated (1);	0.254741	0.39544	N	0.001332	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.799999999996249E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30736	-0.9968	9	0.19147	T	0.46	.	11.785	0.52037	0.2804:0.0:0.7196:0.0	rs12632942;rs52795271;rs61060144;rs12632942	1092	Q9Y5Y9	SCNAA_HUMAN	P	1092	ENSP00000390600:L1092P	ENSP00000390600:L1092P	L	-	2	0	SCN10A	38740002	0.004000	0.15560	0.010000	0.14722	0.896000	0.52359	0.034000	0.13776	-0.637000	0.05516	-0.227000	0.12334	CTA	A|0.777;G|0.223	0.223	strong		0.612	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
PPM1N	147699	hgsc.bcm.edu	37	19	46002007	46002007	+	Missense_Mutation	SNP	C	C	T	rs140525169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46002007C>T	ENST00000451287.2	+	1	277	c.277C>T	c.(277-279)Ccc>Tcc	p.P93S	PPM1N_ENST00000456399.2_Intron|PPM1N_ENST00000401593.1_5'Flank|PPM1N_ENST00000396735.2_5'Flank|PPM1N_ENST00000401705.1_Intron|RTN2_ENST00000344680.4_5'Flank|RTN2_ENST00000590526.1_5'Flank|PPM1N_ENST00000324688.4_Missense_Mutation_p.P15S|PPM1N_ENST00000396737.2_Intron|RTN2_ENST00000589384.1_5'Flank|PPM1N_ENST00000396736.2_5'Flank|RTN2_ENST00000245923.4_5'Flank	NM_001080401.1	NP_001073870.1	Q8N819	PPM1N_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	93	PP2C-like.						magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)	9						ACCTGGTCTGCCCCCGGGCTG	0.697													C|||	22	0.00439297	0.0	0.0202	5008	,	,		13709	0.0		0.008	False		,,,				2504	0.0				p.P93S		Atlas-SNP	.											.	PPM1N	25	.	0			c.C277T						PASS	.		SER/PRO	4,3664		0,4,1830	4.0	4.0	4.0		277	2.7	0.7	19	dbSNP_134	4	43,7527		0,43,3742	yes	missense	PPM1N	NM_001080401.1	74	0,47,5572	TT,TC,CC		0.568,0.1091,0.4182	benign	93/431	46002007	47,11191	1834	3785	5619	SO:0001583	missense	147699	exon1			GGTCTGCCCCCGG	AK097444	CCDS46115.1	19q13.32	2012-04-17			ENSG00000213889	ENSG00000213889		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	26845	protein-coding gene	gene with protein product							Standard	NM_001080401		Approved	FLJ40125	uc002pce.3	Q8N819	OTTHUMG00000140397	ENST00000451287.2:c.277C>T	19.37:g.46002007C>T	ENSP00000397050:p.Pro93Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_001080401	Q6P662	Missense_Mutation	SNP	ENST00000451287.2	37	CCDS46115.1	10	0.004578754578754579	0	0.0	4	0.011049723756906077	0	0.0	6	0.0079155672823219	C	11.30	1.596641	0.28445	0.001091	0.00568	ENSG00000213889	ENST00000451287;ENST00000396734;ENST00000324688	T;T	0.16073	2.37;2.37	3.7	2.65	0.31530	Protein phosphatase 2C-like (5);	0.472599	0.19719	U	0.107624	T	0.07683	0.0193	N	0.17922	0.545	0.26556	N	0.973825	B	0.22346	0.068	B	0.28385	0.089	T	0.24693	-1.0153	10	0.29301	T	0.29	6.4503	9.423	0.38563	0.0:0.7837:0.2163:0.0	.	93	Q8N819	PPM1N_HUMAN	S	93;93;15	ENSP00000397050:P93S;ENSP00000321761:P15S	ENSP00000321761:P15S	P	+	1	0	PPM1N	50693847	0.008000	0.16893	0.704000	0.30370	0.507000	0.33981	0.602000	0.24134	1.129000	0.42072	0.313000	0.20887	CCC	C|0.995;T|0.005	0.005	strong		0.697	PPM1N-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326517.2	NM_001080401	
ABCB8	11194	hgsc.bcm.edu	37	7	150733025	150733025	+	Silent	SNP	T	T	A	rs2303926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150733025T>A	ENST00000297504.6	+	8	1101	c.1035T>A	c.(1033-1035)cgT>cgA	p.R345R	ABCB8_ENST00000477719.1_Silent_p.R328R|ABCB8_ENST00000477092.1_Silent_p.R328R|ABCB8_ENST00000542328.1_Silent_p.R240R|ABCB8_ENST00000356058.4_Silent_p.R365R|ABCB8_ENST00000498578.1_Silent_p.R328R|ABCB8_ENST00000358849.4_Silent_p.R328R			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	345	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	GGACTGTGCGTGCCTTCGCCA	0.622													T|||	1505	0.300519	0.3306	0.219	5008	,	,		19863	0.2778		0.2863	False		,,,				2504	0.3558				p.R328R		Atlas-SNP	.											ABCB8,rectum,carcinoma,+1,2	ABCB8	65	2	0			c.T984A						PASS	.	T		1335,3071	445.7+/-347.8	195,945,1063	80.0	65.0	70.0		984	-10.0	0.3	7	dbSNP_100	70	2803,5797	442.7+/-360.2	480,1843,1977	no	coding-synonymous	ABCB8	NM_007188.3		675,2788,3040	AA,AT,TT		32.593,30.2996,31.8161		328/719	150733025	4138,8868	2203	4300	6503	SO:0001819	synonymous_variant	11194	exon7			TGTGCGTGCCTTC	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1035T>A	7.37:g.150733025T>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	54	25	0.462963	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Silent	SNP	ENST00000297504.6	37		632	0.2893772893772894	175	0.3556910569105691	80	0.22099447513812154	157	0.2744755244755245	220	0.29023746701846964	T	3.131	-0.178409	0.06380	0.302996	0.32593	ENSG00000197150	ENST00000491920	.	.	.	5.34	-9.97	0.00440	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999998351	.	.	.	.	.	.	T	0.27502	-1.0072	3	.	.	.	1.4811	5.0431	0.14469	0.176:0.0819:0.5759:0.1662	rs2303926;rs11553419;rs17448656;rs60135809	.	.	.	S	61	.	.	C	+	1	0	ABCB8	150363958	0.097000	0.21791	0.277000	0.24703	0.177000	0.22998	-0.630000	0.05502	-2.005000	0.00959	-2.213000	0.00299	TGC	T|0.697;A|0.303	0.303	strong		0.622	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
VMAC	400673	hgsc.bcm.edu	37	19	5908969	5908969	+	Missense_Mutation	SNP	G	G	A	rs10404195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5908969G>A	ENST00000339485.3	+	2	359	c.326G>A	c.(325-327)cGc>cAc	p.R109H	CAPS_ENST00000588776.1_5'Flank|AC104532.4_ENST00000591109.1_RNA|AC104532.2_ENST00000588891.1_Intron	NM_001017921.3	NP_001017921.1	Q2NL98	VMAC_HUMAN	vimentin-type intermediate filament associated coiled-coil protein	109						cytoplasm (GO:0005737)				lung(1)	1						GACATCTGCCGCCGCCGGCCA	0.721													G|||	525	0.104832	0.149	0.1311	5008	,	,		11910	0.0119		0.1302	False		,,,				2504	0.0961				p.R109H		Atlas-SNP	.											VMAC,NS,carcinoma,0,1	VMAC	5	1	0			c.G326A						PASS	.	G	HIS/ARG	599,3805		47,505,1650	21.0	22.0	22.0		326	-0.9	0.1	19	dbSNP_119	22	1242,7356		95,1052,3152	yes	missense	VMAC	NM_001017921.3	29	142,1557,4802	AA,AG,GG		14.4452,13.6013,14.1594	benign	109/170	5908969	1841,11161	2202	4299	6501	SO:0001583	missense	400673	exon2			TCTGCCGCCGCCG	BC110802	CCDS32881.1	19p13.3	2012-04-23			ENSG00000187650	ENSG00000187650			33803	protein-coding gene	gene with protein product						14985129	Standard	NM_001017921		Approved		uc002mds.4	Q2NL98		ENST00000339485.3:c.326G>A	19.37:g.5908969G>A	ENSP00000343348:p.Arg109His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	77	38	0.493506	NM_001017921	B3KW55	Missense_Mutation	SNP	ENST00000339485.3	37	CCDS32881.1	236	0.10805860805860806	72	0.14634146341463414	60	0.16574585635359115	8	0.013986013986013986	96	0.1266490765171504	G	3.845	-0.033031	0.07543	0.136013	0.144452	ENSG00000187650	ENST00000339485	.	.	.	4.4	-0.847	0.10730	.	0.602001	0.15669	N	0.250469	T	0.00073	0.0002	L	0.29908	0.895	0.58432	P	5.000000000032756E-6	B	0.12630	0.006	B	0.08055	0.003	T	0.10451	-1.0629	8	0.33141	T	0.24	-4.2626	7.651	0.28348	0.4534:0.0:0.5466:0.0	rs10404195	109	Q2NL98	VMAC_HUMAN	H	109	.	ENSP00000343348:R109H	R	+	2	0	VMAC	5859969	0.010000	0.17322	0.050000	0.19076	0.091000	0.18340	0.105000	0.15333	0.032000	0.15435	-0.448000	0.05591	CGC	G|0.872;A|0.128	0.128	strong		0.721	VMAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452220.2	NM_001017921	
CXorf22	170063	hgsc.bcm.edu	37	X	35988996	35988996	+	Silent	SNP	T	T	C	rs6632446	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:35988996T>C	ENST00000297866.5	+	11	1992	c.1926T>C	c.(1924-1926)ctT>ctC	p.L642L		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	642										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						CAATGTATCTTAAATATTTAA	0.318													T|||	759	0.20106	0.0908	0.2046	3775	,	,		12660	0.2292		0.0547	False		,,,				2504	0.2157				p.L642L		Atlas-SNP	.											.	CXorf22	272	.	0			c.T1926C						PASS	.	T		485,3348		25,365,70,1241,501	32.0	30.0	30.0		1926	-0.7	0.0	X	dbSNP_116	30	377,6341		8,256,105,2162,1761	no	coding-synonymous	CXorf22	NM_152632.3		33,621,175,3403,2262	CC,CT,C,TT,T		5.6118,12.6533,8.1698		642/977	35988996	862,9689	2202	4292	6494	SO:0001819	synonymous_variant	170063	exon11			GTATCTTAAATAT	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.1926T>C	X.37:g.35988996T>C		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_152632	Q5JRM8|Q8N6X8	Silent	SNP	ENST00000297866.5	37	CCDS14237.2																																																																																			T|0.861;C|0.139	0.139	strong		0.318	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	
PLIN4	729359	hgsc.bcm.edu	37	19	4512636	4512636	+	Missense_Mutation	SNP	A	A	C	rs140230284|rs386806138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4512636A>C	ENST00000301286.3	-	3	1293	c.1294T>G	c.(1294-1296)Ttg>Gtg	p.L432V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	432	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CCTCTGGCCAAATTCATGGCA	0.552																																					p.L432V		Atlas-SNP	.											PLIN4_ENST00000301286,caecum,carcinoma,0,4	PLIN4	191	4	0			c.T1294G						PASS	.	A	VAL/LEU	240,3794		55,130,1832	122.0	147.0	139.0		1294	-9.5	0.0	19	dbSNP_134	139	165,8197		33,99,4049	no	missense	PLIN4	NM_001080400.1	32	88,229,5881	CC,CA,AA		1.9732,5.9494,3.2672	benign	432/1358	4512636	405,11991	2017	4181	6198	SO:0001583	missense	729359	exon3			TGGCCAAATTCAT	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.1294T>G	19.37:g.4512636A>C	ENSP00000301286:p.Leu432Val	Somatic	179	1	0.00558659		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	56	0.02564102564102564	36	0.07317073170731707	6	0.016574585635359115	0	0.0	14	0.018469656992084433	C	0.046	-1.266936	0.01433	0.059494	0.019732	ENSG00000167676	ENST00000301286	T	0.03065	4.06	4.73	-9.46	0.00597	.	0.585786	0.15154	N	0.277551	T	0.00073	0.0002	N	0.00135	-2.02	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20706	-1.0267	10	0.02654	T	1	-14.0824	6.7295	0.23375	0.1975:0.1757:0.0:0.6268	.	432	Q96Q06	PLIN4_HUMAN	V	432	ENSP00000301286:L432V	ENSP00000301286:L432V	L	-	1	2	PLIN4	4463636	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-4.177000	0.00279	-1.887000	0.01115	-2.171000	0.00323	TTG	A|0.966;C|0.034	0.034	strong		0.552	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
NLRP5	126206	hgsc.bcm.edu	37	19	56549510	56549510	+	Missense_Mutation	SNP	T	T	C	rs16986899	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56549510T>C	ENST00000390649.3	+	10	2735	c.2735T>C	c.(2734-2736)aTg>aCg	p.M912T		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	912			M -> T (in dbSNP:rs16986899). {ECO:0000269|PubMed:11925379}.		cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.M912T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CAGGGAGTAATGCCTCTCAGT	0.532													C|||	1327	0.264976	0.4486	0.1398	5008	,	,		21362	0.3006		0.1889	False		,,,				2504	0.1472				p.M912T		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - Missense(1)	stomach(1)	c.T2735C						scavenged	.	C	THR/MET	1623,2587		320,983,802	132.0	134.0	133.0		2735	-3.1	0.0	19	dbSNP_123	133	1407,7041		129,1149,2946	yes	missense	NLRP5	NM_153447.4	81	449,2132,3748	CC,CT,TT		16.6548,38.5511,23.9374	benign	912/1201	56549510	3030,9628	2105	4224	6329	SO:0001583	missense	126206	exon10			GAGTAATGCCTCT	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2735T>C	19.37:g.56549510T>C	ENSP00000375063:p.Met912Thr	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	166	71	0.427711	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	580	0.26556776556776557	208	0.42276422764227645	57	0.1574585635359116	178	0.3111888111888112	137	0.18073878627968337	C	0.711	-0.787261	0.02907	0.385511	0.166548	ENSG00000171487	ENST00000390649	T	0.51817	0.69	3.59	-3.09	0.05331	.	1.126530	0.06995	N	0.822221	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40739	-0.9547	9	0.34782	T	0.22	.	2.2949	0.04147	0.2037:0.4503:0.2034:0.1426	rs16986899;rs52814735;rs60032233;rs16986899	912	P59047	NALP5_HUMAN	T	912	ENSP00000375063:M912T	ENSP00000375063:M912T	M	+	2	0	NLRP5	61241322	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.013000	0.12678	-1.137000	0.02888	-1.292000	0.01352	ATG	T|0.731;C|0.269	0.269	strong		0.532	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
HLA-A	3105	hgsc.bcm.edu	37	6	29912042	29912042	+	Missense_Mutation	SNP	G	G	A	rs150028516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29912042G>A	ENST00000396634.1	+	6	1104	c.763G>A	c.(763-765)Gtg>Atg	p.V255M	HLA-A_ENST00000376809.5_Missense_Mutation_p.V255M|HLA-A_ENST00000376806.5_Missense_Mutation_p.V255M|HLA-A_ENST00000376802.2_Missense_Mutation_p.V255M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	255	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.V255M(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CACGGAGCTCGTGGAGACCAG	0.637									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	860	0.171725	0.1051	0.2262	5008	,	,		17643	0.2242		0.2127	False		,,,				2504	0.1268				p.V255M		Atlas-SNP	.											HLA-A,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	HLA-A	89	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.G763A						scavenged	.						32.0	38.0	36.0					6																	29912042		1509	2697	4206	SO:0001583	missense	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGCTCGTGGAGA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.763G>A	6.37:g.29912042G>A	ENSP00000379873:p.Val255Met	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	150	24	0.16	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.542	1.113576	0.20795	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000536480;ENST00000376809;ENST00000376802	T;T;T;T	0.02890	4.12;4.12;4.12;4.12	3.69	0.88	0.19161	Immunoglobulin-like (4);Immunoglobulin C1-set (8);Immunoglobulin-like fold (4);	1.039740	0.07764	U	0.950678	T	0.07143	0.0181	M	0.87682	2.9	0.21527	N	0.999656	D;D;D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	0.983;1.0;0.999;1.0;0.999;1.0;1.0	T	0.15578	-1.0432	10	0.72032	D	0.01	.	5.5915	0.17303	0.3615:0.0:0.6385:0.0	.	134;255;255;255;255;255;255	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	M	255;255;43;255;255	ENSP00000379873:V255M;ENSP00000366002:V255M;ENSP00000366005:V255M;ENSP00000365998:V255M	ENSP00000365998:V255M	V	+	1	0	HLA-A	30020021	0.125000	0.22332	0.677000	0.29947	0.503000	0.33858	0.399000	0.20916	0.365000	0.24400	-0.674000	0.03794	GTG	A|1.000;|0.000	1.000	weak		0.637	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CPT2	1376	hgsc.bcm.edu	37	1	53679229	53679229	+	Missense_Mutation	SNP	A	A	G	rs1799822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:53679229A>G	ENST00000371486.3	+	5	2454	c.1939A>G	c.(1939-1941)Atg>Gtg	p.M647V	RP5-1024G6.2_ENST00000452466.1_RNA|C1orf123_ENST00000470385.1_5'Flank	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	647			M -> V (common polymorphism; confirmed at protein level; dbSNP:rs1799822). {ECO:0000269|PubMed:14605500, ECO:0000269|PubMed:1528846, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17488105, ECO:0000269|PubMed:18306170, ECO:0000269|PubMed:9600456, ECO:0000269|PubMed:9758712}.		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	CTTAGAAGACATGTTTGATGC	0.483													A|||	503	0.100439	0.0227	0.1542	5008	,	,		20518	0.0853		0.2068	False		,,,				2504	0.0736				p.M647V		Atlas-SNP	.											.	CPT2	34	.	0			c.A1939G						PASS	.	A	VAL/MET	240,4166	140.8+/-176.2	7,226,1970	88.0	80.0	83.0		1939	5.9	1.0	1	dbSNP_89	83	1937,6663	341.9+/-324.3	208,1521,2571	yes	missense	CPT2	NM_000098.2	21	215,1747,4541	GG,GA,AA		22.5233,5.4471,16.7384	benign	647/659	53679229	2177,10829	2203	4300	6503	SO:0001583	missense	1376	exon5			GAAGACATGTTTG	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1939A>G	1.37:g.53679229A>G	ENSP00000360541:p.Met647Val	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	280	0.1282051282051282	14	0.028455284552845527	68	0.1878453038674033	54	0.0944055944055944	144	0.18997361477572558	A	17.02	3.280726	0.59758	0.054471	0.225233	ENSG00000157184	ENST00000371486	D	0.90133	-2.62	5.9	5.9	0.94986	.	0.189419	0.56097	D	0.000031	T	0.00178	0.0005	L	0.31752	0.955	0.23371	P	0.99781582	B	0.09022	0.002	B	0.13407	0.009	T	0.11665	-1.0578	9	0.44086	T	0.13	-32.7754	16.3322	0.83039	1.0:0.0:0.0:0.0	rs1799822;rs17377870;rs17848486;rs17849929;rs17857680;rs52797123;rs1799822	647	P23786	CPT2_HUMAN	V	647	ENSP00000360541:M647V	ENSP00000360541:M647V	M	+	1	0	CPT2	53451817	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.445000	0.80570	2.251000	0.74343	0.528000	0.53228	ATG	A|0.854;G|0.146	0.146	strong		0.483	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
HRH4	59340	hgsc.bcm.edu	37	18	22056766	22056766	+	Missense_Mutation	SNP	C	C	T	rs11665084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:22056766C>T	ENST00000256906.4	+	3	513	c.413C>T	c.(412-414)gCc>gTc	p.A138V	HRH4_ENST00000426880.2_Intron	NM_001160166.1|NM_021624.3	NP_001153638.1|NP_067637.2	Q9H3N8	HRH4_HUMAN	histamine receptor H4	138			A -> V (in dbSNP:rs11665084). {ECO:0000269|PubMed:10973974}.		inflammatory response (GO:0006954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of MAPK cascade (GO:0043408)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	all_cancers(21;0.000545)|all_epithelial(16;6.56e-06)|Lung NSC(20;0.0027)|all_lung(20;0.0085)|Colorectal(14;0.0361)|Ovarian(20;0.0991)				Amitriptyline(DB00321)|Amoxapine(DB00543)|Chlorpromazine(DB00477)|Clozapine(DB00363)|Doxepin(DB01142)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Mianserin(DB06148)|Olanzapine(DB00334)	CTGATGGTGGCCGTTTGGGTG	0.393													C|||	286	0.0571086	0.0106	0.134	5008	,	,		21696	0.0347		0.0964	False		,,,				2504	0.0481				p.A138V		Atlas-SNP	.											.	HRH4	46	.	0			c.C413T						PASS	.	C	,,VAL/ALA	112,4294	86.8+/-125.4	1,110,2092	199.0	186.0	191.0		,,413	4.9	0.9	18	dbSNP_120	191	839,7761	192.7+/-238.6	42,755,3503	yes	intron,utr-3,missense	HRH4	NM_001143828.1,NM_001160166.1,NM_021624.3	,,64	43,865,5595	TT,TC,CC		9.7558,2.542,7.312	,,probably-damaging	,,138/391	22056766	951,12055	2203	4300	6503	SO:0001583	missense	59340	exon3			TGGTGGCCGTTTG	AF312230	CCDS11887.1, CCDS45841.1	18q11.2	2012-08-08			ENSG00000134489	ENSG00000134489		"""GPCR / Class A : Histamine receptors"""	17383	protein-coding gene	gene with protein product		606792				11118334, 10973974	Standard	NM_021624		Approved	H4R, HH4R, AXOR35, GPCR105, GPRv53	uc002kvi.3	Q9H3N8	OTTHUMG00000131945	ENST00000256906.4:c.413C>T	18.37:g.22056766C>T	ENSP00000256906:p.Ala138Val	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	230	112	0.486957	NM_021624	B0YJ19|B2KJ48|Q4G0I6|Q9GZQ0	Missense_Mutation	SNP	ENST00000256906.4	37	CCDS11887.1	146	0.06684981684981685	3	0.006097560975609756	41	0.1132596685082873	28	0.04895104895104895	74	0.09762532981530343	C	14.63	2.593668	0.46214	0.02542	0.097558	ENSG00000134489	ENST00000256906	T	0.36878	1.23	5.79	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.213135	0.40640	N	0.001050	T	0.00496	0.0016	L	0.45352	1.415	0.09310	P	0.9999999999999928	B	0.27068	0.167	B	0.30716	0.119	T	0.08452	-1.0721	9	0.02654	T	1	-9.9961	9.3701	0.38248	0.0:0.7796:0.1457:0.0747	rs11665084;rs17203335;rs52834131;rs60698202;rs11665084	138	Q9H3N8	HRH4_HUMAN	V	138	ENSP00000256906:A138V	ENSP00000256906:A138V	A	+	2	0	HRH4	20310764	0.727000	0.28069	0.917000	0.36280	0.864000	0.49448	1.414000	0.34736	1.405000	0.46838	0.655000	0.94253	GCC	C|0.930;T|0.070	0.070	strong		0.393	HRH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254904.1		
SLFN14	342618	hgsc.bcm.edu	37	17	33884804	33884804	+	Missense_Mutation	SNP	T	T	C	rs10512472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33884804T>C	ENST00000415846.3	-	1	313	c.278A>G	c.(277-279)cAg>cGg	p.Q93R		NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	93			Q -> R (in dbSNP:rs10512472).				ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						AAGGTATTTCTGTGAACCTGA	0.433													T|||	1178	0.235224	0.2284	0.2522	5008	,	,		20357	0.3056		0.172	False		,,,				2504	0.2249				p.Q93R		Atlas-SNP	.											.	SLFN14	43	.	0			c.A278G						PASS	.	T	ARG/GLN	288,1096		36,216,440	88.0	71.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	278	4.3	1.0	17	dbSNP_119	76	549,2633		44,461,1086	yes	missense	SLFN14	NM_001129820.1	43	80,677,1526	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	17.2533,20.8092,18.3311	possibly-damaging	93/913	33884804	837,3729	692	1591	2283	SO:0001583	missense	342618	exon1			TATTTCTGTGAAC		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.278A>G	17.37:g.33884804T>C	ENSP00000391101:p.Gln93Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_001129820	B2RTW9	Missense_Mutation	SNP	ENST00000415846.3	37	CCDS45650.1	505	0.23122710622710624	111	0.22560975609756098	95	0.26243093922651933	179	0.3129370629370629	120	0.158311345646438	T	14.25	2.478941	0.44044	0.208092	0.172533	ENSG00000236320	ENST00000415846	T	0.01998	4.51	4.28	4.28	0.50868	.	.	.	.	.	T	0.00012	0.0000	L	0.45422	1.42	0.47621	P	5.209999999999937E-4	P	0.43094	0.799	B	0.34722	0.188	T	0.52646	-0.8548	8	0.62326	D	0.03	-3.1007	9.9792	0.41802	0.0:0.0:0.0:1.0	rs10512472;rs61277257;rs10512472	93	P0C7P3	SLN14_HUMAN	R	93	ENSP00000391101:Q93R	ENSP00000391101:Q93R	Q	-	2	0	SLFN14	30908917	0.985000	0.35326	1.000000	0.80357	0.998000	0.95712	1.662000	0.37418	1.908000	0.55244	0.533000	0.62120	CAG	T|0.743;C|0.257	0.257	strong		0.433	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
SETD6	79918	hgsc.bcm.edu	37	16	58552921	58552921	+	Silent	SNP	G	G	A	rs3607	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58552921G>A	ENST00000219315.4	+	8	1460	c.1410G>A	c.(1408-1410)gaG>gaA	p.E470E	SETD6_ENST00000310682.2_Silent_p.E446E|SETD6_ENST00000394266.4_Silent_p.E401E			Q8TBK2	SETD6_HUMAN	SET domain containing 6	470					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						AGTTGTTGGAGCTGACAAGTT	0.398													A|||	3854	0.769569	0.8026	0.7104	5008	,	,		23078	0.9544		0.5616	False		,,,				2504	0.7904				p.E470E		Atlas-SNP	.											.	SETD6	27	.	0			c.G1410A						PASS	.	A	,	3326,1070	388.6+/-327.0	1268,790,140	69.0	69.0	69.0		1410,1338	3.2	0.3	16	dbSNP_36	69	4723,3877	543.7+/-384.5	1309,2105,886	no	coding-synonymous,coding-synonymous	SETD6	NM_001160305.1,NM_024860.2	,	2577,2895,1026	AA,AG,GG		45.0814,24.3403,38.0656	,	470/474,446/450	58552921	8049,4947	2198	4300	6498	SO:0001819	synonymous_variant	79918	exon8			GTTGGAGCTGACA	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.1410G>A	16.37:g.58552921G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_001160305	A8K380|B5ME38|Q9H787	Silent	SNP	ENST00000219315.4	37	CCDS54013.1																																																																																			G|0.344;A|0.656	0.656	strong		0.398	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
CELSR1	9620	hgsc.bcm.edu	37	22	46930107	46930107	+	Silent	SNP	C	C	T	rs8141744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:46930107C>T	ENST00000262738.3	-	1	2960	c.2961G>A	c.(2959-2961)gtG>gtA	p.V987V	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Silent_p.V987V	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	987	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CCAAGATGGTCACCTGGATTT	0.567													C|||	882	0.176118	0.2708	0.1225	5008	,	,		19808	0.0585		0.2276	False		,,,				2504	0.1544				p.V987V		Atlas-SNP	.											.	CELSR1	242	.	0			c.G2961A						PASS	.	C		1044,3360	382.3+/-324.4	109,826,1267	97.0	95.0	96.0		2961	4.4	0.9	22	dbSNP_116	96	2111,6489	363.2+/-333.1	263,1585,2452	no	coding-synonymous	CELSR1	NM_014246.1		372,2411,3719	TT,TC,CC		24.5465,23.7057,24.2618		987/3015	46930107	3155,9849	2202	4300	6502	SO:0001819	synonymous_variant	9620	exon1			GATGGTCACCTGG	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.2961G>A	22.37:g.46930107C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	209	102	0.488038	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			C|0.794;T|0.206	0.206	strong		0.567	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
HCFC1	3054	hgsc.bcm.edu	37	X	153218365	153218365	+	Silent	SNP	C	C	A	rs3027878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153218365C>A	ENST00000310441.7	-	19	5508	c.4542G>T	c.(4540-4542)ctG>ctT	p.L1514L	HCFC1_ENST00000369984.4_Silent_p.L1558L|HCFC1_ENST00000354233.3_Silent_p.L1445L	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1514					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCCGTGGCGGCAGCTGCTGGC	0.652											OREG0003630	type=REGULATORY REGION|Gene=BC010606|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	1449	0.383841	0.0461	0.3545	3775	,	,		12036	0.5784		0.1223	False		,,,				2504	0.4458				p.L1514L		Atlas-SNP	.											.	HCFC1	284	.	0			c.G4542T						PASS	.	C		227,2954		14,161,38,1163,467	5.0	7.0	6.0		4542	2.7	1.0	X	dbSNP_102	6	899,5363		55,536,253,1709,1409	no	coding-synonymous	HCFC1	NM_005334.2		69,697,291,2872,1876	AA,AC,A,CC,C		14.3564,7.1361,11.9242		1514/2036	153218365	1126,8317	1843	3962	5805	SO:0001819	synonymous_variant	3054	exon19			TGGCGGCAGCTGC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.4542G>T	X.37:g.153218365C>A		Somatic	32	0	0	1753	WXS	Illumina HiSeq	Phase_I	44	44	1	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1	561	0.33815551537070526	17	0.035864978902953586	79	0.2598684210526316	219	0.6257142857142857	70	0.09943181818181818	C	3.074	-0.190417	0.06299	0.071361	0.143564	ENSG00000172534	ENST00000444191	.	.	.	5.49	2.7	0.31948	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999945694	.	.	.	.	.	.	T	0.44050	-0.9353	3	.	.	.	.	7.5733	0.27920	0.2955:0.3935:0.311:0.0	rs3027878;rs3752391;rs58600880	.	.	.	S	89	.	.	A	-	1	0	HCFC1	152871559	1.000000	0.71417	0.980000	0.43619	0.323000	0.28346	0.475000	0.22164	0.194000	0.20326	0.513000	0.50165	GCC	C|0.637;A|0.363	0.363	strong		0.652	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
AGFG2	3268	hgsc.bcm.edu	37	7	100160264	100160264	+	Missense_Mutation	SNP	T	T	C	rs17855473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100160264T>C	ENST00000300176.4	+	8	1168	c.1046T>C	c.(1045-1047)aTg>aCg	p.M349T	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	349				M -> T (in Ref. 2; AAH17329). {ECO:0000305}.	regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCTGTCACGATGGGCGGCGGC	0.647													C|||	910	0.181709	0.3449	0.1455	5008	,	,		15023	0.0188		0.1869	False		,,,				2504	0.1493				p.M349T		Atlas-SNP	.											AGFG2,NS,carcinoma,0,1	AGFG2	44	1	0			c.T1046C						PASS	.	C	THR/MET	1380,3026	671.4+/-402.5	209,962,1032	31.0	32.0	32.0		1046	3.6	0.0	7	dbSNP_123	32	1612,6988	723.3+/-406.5	148,1316,2836	yes	missense	AGFG2	NM_006076.4	81	357,2278,3868	CC,CT,TT		18.7442,31.3209,23.0048	benign	349/482	100160264	2992,10014	2203	4300	6503	SO:0001583	missense	3268	exon8			TCACGATGGGCGG	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1046T>C	7.37:g.100160264T>C	ENSP00000300176:p.Met349Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	365|365	0.1671245421245421|0.1671245421245421	170|170	0.34552845528455284|0.34552845528455284	52|52	0.143646408839779|0.143646408839779	2|2	0.0034965034965034965|0.0034965034965034965	141|141	0.18601583113456466|0.18601583113456466	C|C	0.029|0.029	-1.347421|-1.347421	0.01266|0.01266	0.313209|0.313209	0.187442|0.187442	ENSG00000106351|ENSG00000106351	ENST00000300176|ENST00000429987	T|.	0.20738|.	2.05|.	4.51|4.51	3.64|3.64	0.41730|0.41730	.|.	0.880910|.	0.10039|.	N|.	0.723737|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00308|0.00308	-1.67|-1.67	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.42396|0.42396	-0.9454|-0.9454	9|4	0.16896|.	T|.	0.51|.	-19.9228|-19.9228	8.6556|8.6556	0.34062|0.34062	0.0:0.854:0.0:0.146|0.0:0.854:0.0:0.146	rs17855473;rs17855473|rs17855473;rs17855473	349|.	O95081|.	AGFG2_HUMAN|.	T|R	349|91	ENSP00000300176:M349T|.	ENSP00000300176:M349T|.	M|W	+|+	2|1	0|0	AGFG2|AGFG2	99998200|99998200	0.002000|0.002000	0.14202|0.14202	0.001000|0.001000	0.08648|0.08648	0.006000|0.006000	0.05464|0.05464	0.912000|0.912000	0.28597|0.28597	0.524000|0.524000	0.28502|0.28502	-1.653000|-1.653000	0.00756|0.00756	ATG|TGG	T|0.797;C|0.203	0.203	strong		0.647	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
MYH7B	57644	hgsc.bcm.edu	37	20	33584289	33584289	+	Silent	SNP	C	C	T	rs3746438	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:33584289C>T	ENST00000262873.7	+	27	3302	c.3210C>T	c.(3208-3210)acC>acT	p.T1070T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1028						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)			GCGCGCTGACCAAGGCCAAGC	0.701													C|||	2201	0.439497	0.2738	0.6326	5008	,	,		17071	0.5893		0.495	False		,,,				2504	0.3149				p.T1070T		Atlas-SNP	.											.	MYH7B	145	.	0			c.C3210T						PASS	.	C		1395,3007	418.0+/-338.2	225,945,1031	27.0	33.0	31.0		3210	0.6	1.0	20	dbSNP_107	31	3800,4790	512.2+/-377.9	823,2154,1318	no	coding-synonymous	MYH7B	NM_020884.3		1048,3099,2349	TT,TC,CC		44.2375,31.6901,39.9861		1070/1984	33584289	5195,7797	2201	4295	6496	SO:0001819	synonymous_variant	57644	exon29			GCTGACCAAGGCC	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.3210C>T	20.37:g.33584289C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	98	59	0.602041	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			C|0.542;T|0.458	0.458	strong		0.701	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
CLU	1191	hgsc.bcm.edu	37	8	27462481	27462481	+	Silent	SNP	A	A	G	rs7982	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27462481A>G	ENST00000316403.10	-	5	1194	c.789T>C	c.(787-789)caT>caC	p.H263H	CLU_ENST00000405140.3_Silent_p.H263H|CLU_ENST00000546343.1_Silent_p.H274H|CLU_ENST00000560366.1_Silent_p.H315H|CLU_ENST00000523500.1_Silent_p.H263H			P10909	CLUS_HUMAN	clusterin	263					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		AGGCCGGGCTATGGAAGTGGA	0.557													G|||	3328	0.664537	0.5749	0.6556	5008	,	,		15953	0.7887		0.6143	False		,,,				2504	0.7157				p.H263H		Atlas-SNP	.											.	CLU	54	.	0			c.T789C						PASS	.	G		2590,1816	532.6+/-373.5	738,1114,351	108.0	108.0	108.0		789	-0.9	0.0	8	dbSNP_52	108	5186,3414	503.4+/-375.9	1573,2040,687	no	coding-synonymous	CLU	NM_203339.2		2311,3154,1038	GG,GA,AA		39.6977,41.2165,40.2122		263/450	27462481	7776,5230	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon5			CGGGCTATGGAAG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.789T>C	8.37:g.27462481A>G		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	121	118	0.975207	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1	1422	0.6510989010989011	270	0.5487804878048781	232	0.6408839779005525	461	0.8059440559440559	459	0.6055408970976254	G	4.591	0.109767	0.08780	0.587835	0.603023	ENSG00000120885	ENST00000522098	.	.	.	3.68	-0.917	0.10485	.	.	.	.	.	.	.	.	.	.	.	0.54753	P	1.3000000000040757E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.6694	4.8125	0.13351	0.4259:0.1521:0.422:0.0	rs7982;rs1049263;rs1532280;rs3189370;rs17349487;rs17850671;rs17851750;rs60199999	.	.	.	Q	126	.	.	X	-	1	0	CLU	27518398	0.001000	0.12720	0.003000	0.11579	0.190000	0.23558	-0.719000	0.04974	-0.708000	0.05015	-0.213000	0.12676	TAG	G|0.610;C|0.000;A|0.390	0.610	strong		0.557	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
ELOVL4	6785	hgsc.bcm.edu	37	6	80626375	80626375	+	Missense_Mutation	SNP	T	T	C	rs3812153	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:80626375T>C	ENST00000369816.4	-	6	1195	c.895A>G	c.(895-897)Atg>Gtg	p.M299V		NM_022726.3	NP_073563.1	Q9GZR5	ELOV4_HUMAN	ELOVL fatty acid elongase 4	299			M -> V (in dbSNP:rs3812153). {ECO:0000269|PubMed:11138005, ECO:0000269|PubMed:12592226}.		cellular lipid metabolic process (GO:0044255)|detection of visible light (GO:0009584)|fatty acid biosynthetic process (GO:0006633)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)	G-protein coupled photoreceptor activity (GO:0008020)|transferase activity (GO:0016740)			central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;1.83e-05)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.011)		BRCA - Breast invasive adenocarcinoma(397;0.0168)	Alpha-Linolenic Acid(DB00132)	TTTTCTATCATGAGTTGTTTT	0.368													C|||	1210	0.241613	0.2458	0.1974	5008	,	,		17007	0.2282		0.1153	False		,,,				2504	0.411				p.M299V		Atlas-SNP	.											.	ELOVL4	46	.	0			c.A895G	GRCh37	CM052232	ELOVL4	M	rs3812153	PASS	.	C	VAL/MET	1008,3398	728.9+/-410.0	120,768,1315	102.0	91.0	95.0		895	5.6	0.4	6	dbSNP_107	95	939,7661	775.1+/-407.7	56,827,3417	yes	missense	ELOVL4	NM_022726.3	21	176,1595,4732	CC,CT,TT		10.9186,22.8779,14.97	benign	299/315	80626375	1947,11059	2203	4300	6503	SO:0001583	missense	6785	exon6			CTATCATGAGTTG	AF277094	CCDS4992.1	6q14	2013-01-08	2011-05-25		ENSG00000118402	ENSG00000118402			14415	protein-coding gene	gene with protein product	"""cancer/testis antigen 118"""	605512	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 4"""	STGD2, STGD3		11138005	Standard	NM_022726		Approved	CT118	uc003pja.4	Q9GZR5	OTTHUMG00000015087	ENST00000369816.4:c.895A>G	6.37:g.80626375T>C	ENSP00000358831:p.Met299Val	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_022726	B2R6B5|Q5TCS2|Q86YJ1|Q9H139	Missense_Mutation	SNP	ENST00000369816.4	37	CCDS4992.1	406	0.1858974358974359	134	0.27235772357723576	75	0.20718232044198895	116	0.20279720279720279	81	0.10686015831134564	C	0.008	-1.901284	0.00517	0.228779	0.109186	ENSG00000118402	ENST00000369816	T	0.15834	2.39	5.61	5.61	0.85477	.	0.432752	0.24920	N	0.034550	T	0.03520	0.0101	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34453	-0.9828	9	0.25106	T	0.35	-4.8075	13.9098	0.63860	0.0:0.9272:0.0:0.0728	rs3812153;rs52819344;rs57220964;rs3812153	299	Q9GZR5	ELOV4_HUMAN	V	299	ENSP00000358831:M299V	ENSP00000358831:M299V	M	-	1	0	ELOVL4	80683094	0.878000	0.30173	0.426000	0.26672	0.034000	0.12701	1.850000	0.39328	1.388000	0.46506	-0.226000	0.12346	ATG	T|0.831;C|0.169	0.169	strong		0.368	ELOVL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041315.1		
CLCA1	1179	hgsc.bcm.edu	37	1	86947975	86947975	+	Silent	SNP	A	A	T	rs1321694	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:86947975A>T	ENST00000234701.3	+	6	996	c.645A>T	c.(643-645)gtA>gtT	p.V215V	CLCA1_ENST00000394711.1_Silent_p.V215V			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	215					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)		TCAATAAAGTAACAGGACTCT	0.398													A|||	1841	0.367612	0.2443	0.2939	5008	,	,		20995	0.505		0.3728	False		,,,				2504	0.4397				p.V215V		Atlas-SNP	.											.	CLCA1	109	.	0			c.A645T						PASS	.	A		1116,3290	398.8+/-331.0	140,836,1227	136.0	123.0	128.0		645	-2.2	0.1	1	dbSNP_88	128	3044,5556	467.7+/-367.1	534,1976,1790	no	coding-synonymous	CLCA1	NM_001285.3		674,2812,3017	TT,TA,AA		35.3953,25.3291,31.9852		215/915	86947975	4160,8846	2203	4300	6503	SO:0001819	synonymous_variant	1179	exon5			TAAAGTAACAGGA		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.645A>T	1.37:g.86947975A>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_001285	B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	37	CCDS709.1																																																																																			T|0.353;N|0.000	0.353	strong		0.398	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1	NM_001285	
SELPLG	6404	hgsc.bcm.edu	37	12	109017672	109017672	+	Missense_Mutation	SNP	G	G	C	rs63748999|rs372173288|rs540144714	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109017672G>C	ENST00000550948.1	-	2	636	c.412C>G	c.(412-414)Ccc>Gcc	p.P138A	SELPLG_ENST00000388962.3_Intron|SELPLG_ENST00000228463.6_Missense_Mutation_p.P154A			Q14242	SELPL_HUMAN	selectin P ligand	138	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GCCTCCGTGGGCACTGGTTGA	0.617													C|||	441	0.0880591	0.0272	0.0504	5008	,	,		19574	0.2034		0.0795	False		,,,				2504	0.0869				p.P154A		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,0,14	SELPLG	138	14	0			c.C460G						scavenged	.						160.0	124.0	137.0					12																	109017672		2199	4278	6477	SO:0001583	missense	6404	exon2			CCGTGGGCACTGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.412C>G	12.37:g.109017672G>C	ENSP00000447752:p.Pro138Ala	Somatic	179	3	0.0167598		WXS	Illumina HiSeq	Phase_I	158	44	0.278481	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	C	0.375	-0.932076	0.02359	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.27402	1.67;1.67	3.23	-6.47	0.01902	.	.	.	.	.	T	0.07188	0.0182	N	0.02539	-0.55	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24154	-1.0168	9	0.02654	T	1	-1.189	3.3056	0.06998	0.2007:0.2624:0.3957:0.1411	.	154;138	B7Z5C7;Q14242	.;SELPL_HUMAN	A	138;154	ENSP00000447752:P138A;ENSP00000228463:P154A	ENSP00000228463:P154A	P	-	1	0	SELPLG	107541801	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.940000	0.00329	-1.755000	0.01320	-0.339000	0.08088	CCC	.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
RBM11	54033	hgsc.bcm.edu	37	21	15599466	15599466	+	Missense_Mutation	SNP	A	A	G	rs7280643	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:15599466A>G	ENST00000400577.3	+	5	707	c.698A>G	c.(697-699)cAc>cGc	p.H233R	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	233					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)	p.H233R(1)		endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		AAATGGACTCACCAACAACCA	0.428													A|||	530	0.105831	0.1831	0.0807	5008	,	,		22211	0.0198		0.1103	False		,,,				2504	0.1033				p.H233R		Atlas-SNP	.											RBM11,NS,carcinoma,0,1	RBM11	41	1	1	Substitution - Missense(1)	stomach(1)	c.A698G						PASS	.	A	ARG/HIS	641,3235		58,525,1355	208.0	200.0	203.0		698	3.5	0.3	21	dbSNP_116	203	958,7314		37,884,3215	yes	missense	RBM11	NM_144770.3	29	95,1409,4570	GG,GA,AA		11.5812,16.5377,13.1627	benign	233/282	15599466	1599,10549	1938	4136	6074	SO:0001583	missense	54033	exon5			GGACTCACCAACA	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"""RNA binding motif (RRM) containing"""	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.698A>G	21.37:g.15599466A>G	ENSP00000383421:p.His233Arg	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	202	0.0924908424908425	84	0.17073170731707318	25	0.06906077348066299	5	0.008741258741258742	88	0.11609498680738786	A	7.001	0.554944	0.13436	0.165377	0.115812	ENSG00000185272	ENST00000400577	T	0.08546	3.08	4.72	3.54	0.40534	.	.	.	.	.	T	0.00039	0.0001	L	0.47716	1.5	0.58432	P	9.000000000036756E-6	B	0.30763	0.294	B	0.24974	0.057	T	0.39251	-0.9623	8	0.23302	T	0.38	-2.9027	9.3897	0.38365	0.8398:0.0:0.0:0.1602	rs7280643	233	P57052	RBM11_HUMAN	R	233	ENSP00000383421:H233R	ENSP00000383421:H233R	H	+	2	0	RBM11	14521337	0.000000	0.05858	0.267000	0.24556	0.677000	0.39632	0.143000	0.16115	0.873000	0.35799	0.528000	0.53228	CAC	A|0.907;G|0.093	0.093	strong		0.428	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770	
IFI30	10437	hgsc.bcm.edu	37	19	18285944	18285944	+	Missense_Mutation	SNP	G	G	A	rs11554159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18285944G>A	ENST00000407280.3	+	2	402	c.227G>A	c.(226-228)cGa>cAa	p.R76Q	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	76				R -> Q (in Ref. 7; AAH31020). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)			endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						GGTGGCTGCCGAGCCTTCCTG	0.582													G|||	910	0.181709	0.2398	0.1816	5008	,	,		19461	0.0655		0.2704	False		,,,				2504	0.1319				p.R76Q		Atlas-SNP	.											.	IFI30	12	.	0			c.G227A						PASS	.	G	GLN/ARG	905,3225		94,717,1254	41.0	46.0	44.0		227	4.2	0.5	19	dbSNP_120	44	2157,6253		274,1609,2322	yes	missense	IFI30	NM_006332.3	43	368,2326,3576	AA,AG,GG		25.648,21.9128,24.4179	probably-damaging	76/251	18285944	3062,9478	2065	4205	6270	SO:0001583	missense	10437	exon2			GCTGCCGAGCCTT	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"""gamma-interferon-inducible lysosomal thiol reductase"", ""interferon gamma-inducible protein 30 preproprotein"""	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.227G>A	19.37:g.18285944G>A	ENSP00000384886:p.Arg76Gln	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	130	74	0.569231	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Missense_Mutation	SNP	ENST00000407280.3	37	CCDS46015.1	424	0.19413919413919414	110	0.22357723577235772	74	0.20441988950276244	39	0.06818181818181818	201	0.26517150395778366	G	17.49	3.402221	0.62288	0.219128	0.25648	ENSG00000216490	ENST00000407280	.	.	.	5.25	4.22	0.49857	.	.	.	.	.	T	0.00012	0.0000	L	0.48642	1.525	0.20403	P	0.9999051197	D	0.69078	0.997	P	0.54629	0.757	T	0.05289	-1.0894	7	0.41790	T	0.15	-50.735	12.4977	0.55937	0.082:0.0:0.918:0.0	rs11554159;rs17852874;rs11554159	76	P13284	GILT_HUMAN	Q	76	.	ENSP00000384886:R76Q	R	+	2	0	IFI30	18146944	1.000000	0.71417	0.476000	0.27291	0.000000	0.00434	5.701000	0.68325	1.230000	0.43646	-0.339000	0.08088	CGA	G|0.789;A|0.211	0.211	strong		0.582	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332	
C6orf15	29113	hgsc.bcm.edu	37	6	31079264	31079264	+	Missense_Mutation	SNP	C	C	T	rs2233984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31079264C>T	ENST00000259870.3	-	2	875	c.872G>A	c.(871-873)gGt>gAt	p.G291D		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	291	Pro-rich.		G -> D (in dbSNP:rs2233984).		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GTTATTGATACCTGGGTATAG	0.532													C|||	521	0.104034	0.0068	0.0994	5008	,	,		15975	0.2361		0.0785	False		,,,				2504	0.1288				p.G291D		Atlas-SNP	.											C6orf15,NS,carcinoma,-1,1	C6orf15	29	1	0			c.G872A						PASS	.	C	ASP/GLY	54,3498		0,54,1722	55.0	57.0	56.0		872	0.1	0.0	6	dbSNP_98	56	463,6601		21,421,3090	yes	missense	C6orf15	NM_014070.2	94	21,475,4812	TT,TC,CC		6.5544,1.5203,4.87	probably-damaging	291/326	31079264	517,10099	1776	3532	5308	SO:0001583	missense	29113	exon2			TTGATACCTGGGT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.872G>A	6.37:g.31079264C>T	ENSP00000259870:p.Gly291Asp	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	213	0.09752747252747253	8	0.016260162601626018	29	0.08011049723756906	122	0.21328671328671328	54	0.0712401055408971	C	12.76	2.035246	0.35893	0.015203	0.065544	ENSG00000204542	ENST00000259870	T	0.09163	3.01	4.21	0.0657	0.14358	.	0.132959	0.34411	N	0.003986	T	0.13756	0.0333	M	0.69823	2.125	0.48395	P	3.570000000000517E-4	D	0.89917	1.0	D	0.70935	0.971	T	0.02294	-1.1181	9	0.52906	T	0.07	-11.2596	8.2102	0.31479	0.4442:0.4117:0.1441:0.0	rs2233984;rs3823389;rs59556962;rs2233984	291	Q6UXA7	CF015_HUMAN	D	291	ENSP00000259870:G291D	ENSP00000259870:G291D	G	-	2	0	C6orf15	31187243	0.276000	0.24211	0.014000	0.15608	0.045000	0.14185	0.536000	0.23129	-0.212000	0.10109	-0.195000	0.12781	GGT	C|0.921;T|0.079	0.079	strong		0.532	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
RP1L1	94137	hgsc.bcm.edu	37	8	10465344	10465344	+	Missense_Mutation	SNP	C	C	A	rs11778341	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10465344C>A	ENST00000382483.3	-	4	6487	c.6264G>T	c.(6262-6264)caG>caT	p.Q2088H		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2168	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				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)		CTTCTGCCTCCTGGGCATCTA	0.627													-|||	822	0.164137	0.0991	0.1268	5008	,	,		19051	0.4117		0.1024	False		,,,				2504	0.0869				p.Q2088H		Atlas-SNP	.											.	RP1L1	453	.	0			c.G6264T						PASS	.	C	HIS/GLN	419,3549		21,377,1586	138.0	153.0	148.0		6264	-0.4	0.0	8	dbSNP_120	148	1025,7249		67,891,3179	yes	missense	RP1L1	NM_178857.5	24	88,1268,4765	AA,AC,CC		12.3882,10.5595,11.7955	possibly-damaging	2088/2401	10465344	1444,10798	1984	4137	6121	SO:0001583	missense	94137	exon4			TGCCTCCTGGGCA	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.6264G>T	8.37:g.10465344C>A	ENSP00000371923:p.Gln2088His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	389	0.17811355311355312	44	0.08943089430894309	58	0.16022099447513813	213	0.3723776223776224	74	0.09762532981530343	-	3.844	-0.033276	0.07543	0.105595	0.123882	ENSG00000183638	ENST00000382483	T	0.07908	3.15	1.74	-0.363	0.12556	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.36616	0.561	B	0.26416	0.069	T	0.48990	-0.8985	8	0.42905	T	0.14	.	4.2496	0.10688	0.0:0.3496:0.0:0.6504	rs11778341	2088	A6NKC6	.	H	2088	ENSP00000371923:Q2088H	ENSP00000371923:Q2088H	Q	-	3	2	RP1L1	10502754	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-2.680000	0.00837	0.033000	0.15463	-0.350000	0.07774	CAG	C|0.846;A|0.154	0.154	strong		0.627	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
DHX38	9785	hgsc.bcm.edu	37	16	72130203	72130203	+	Silent	SNP	C	C	G	rs1050361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:72130203C>G	ENST00000268482.3	+	2	656	c.147C>G	c.(145-147)ctC>ctG	p.L49L	TXNL4B_ENST00000423037.1_5'Flank|TXNL4B_ENST00000268483.3_5'Flank|DHX38_ENST00000536867.1_Silent_p.L49L|TXNL4B_ENST00000426362.2_5'Flank	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	49					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.L49L(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)				CTTCATTACTCGGACTGGACT	0.552													G|||	2570	0.513179	0.8094	0.3588	5008	,	,		19448	0.3542		0.3986	False		,,,				2504	0.5041				p.L49L	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.C147G						PASS	.	G		3193,1203	418.7+/-338.4	1177,839,182	60.0	55.0	57.0		147	2.6	1.0	16	dbSNP_86	57	3668,4932	622.1+/-397.3	776,2116,1408	no	coding-synonymous	DHX38	NM_014003.3		1953,2955,1590	GG,GC,CC		42.6512,27.3658,47.2068		49/1228	72130203	6861,6135	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon2			ATTACTCGGACTG	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.147C>G	16.37:g.72130203C>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	137	54	0.394161	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			C|0.490;G|0.510	0.510	strong		0.552	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
NLRP1	22861	hgsc.bcm.edu	37	17	5436263	5436263	+	Missense_Mutation	SNP	C	C	T	rs2301582	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5436263C>T	ENST00000572272.1	-	11	3174	c.3175G>A	c.(3175-3177)Gtg>Atg	p.V1059M	NLRP1_ENST00000354411.3_Missense_Mutation_p.V1029M|NLRP1_ENST00000269280.4_Missense_Mutation_p.V1059M|NLRP1_ENST00000262467.5_Missense_Mutation_p.V1063M|NLRP1_ENST00000345221.3_Missense_Mutation_p.V1059M|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Missense_Mutation_p.V1029M			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	1059			V -> M (in dbSNP:rs2301582).		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				GGAGAAGGCACGCACAAGAGT	0.607													C|||	923	0.184305	0.0787	0.3573	5008	,	,		17458	0.0228		0.3738	False		,,,				2504	0.1759				p.V1063M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G3187A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	567,3839	254.6+/-260.1	35,497,1671	89.0	78.0	82.0		3187,3175,3175,3085,3085	0.8	0.0	17	dbSNP_100	82	3421,5179	504.5+/-376.2	664,2093,1543	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	699,2590,3214	TT,TC,CC		39.7791,12.8688,30.6628	benign,benign,benign,benign,benign	1063/1376,1059/1430,1059/1474,1029/1444,1029/1400	5436263	3988,9018	2203	4300	6503	SO:0001583	missense	22861	exon11			AAGGCACGCACAA	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.3175G>A	17.37:g.5436263C>T	ENSP00000460475:p.Val1059Met	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_001033053	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	464	0.21245421245421245	46	0.09349593495934959	123	0.3397790055248619	16	0.027972027972027972	279	0.36807387862796836	C	8.966	0.971710	0.18736	0.128688	0.397791	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.71817	-0.6;-0.6;-0.58;-0.48;-0.58	3.94	0.836	0.18891	.	1.178250	0.06625	N	0.758189	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P;P;P;P;B	0.42039	0.434;0.769;0.769;0.658;0.769;0.095	B;B;B;B;B;B	0.24701	0.055;0.037;0.037;0.017;0.037;0.01	T	0.17653	-1.0362	9	0.49607	T	0.09	.	6.2112	0.20630	0.1028:0.3672:0.53:0.0	rs2301582;rs17765850;rs52830015;rs56943859;rs2301582	325;1029;1029;1059;1059;1063	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	1063;1063;1059;1029;1059;325	ENSP00000442029:V1063M;ENSP00000262467:V1063M;ENSP00000269280:V1059M;ENSP00000346390:V1029M;ENSP00000324366:V1059M	ENSP00000262467:V1063M	V	-	1	0	NLRP1	5376987	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.977000	0.03782	0.255000	0.21593	-0.236000	0.12185	GTG	C|0.738;T|0.262	0.262	strong		0.607	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
SIM1	6492	hgsc.bcm.edu	37	6	100868721	100868721	+	Missense_Mutation	SNP	G	G	A	rs3734355	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:100868721G>A	ENST00000369208.3	-	10	1894	c.1112C>T	c.(1111-1113)gCc>gTc	p.A371V	SIM1_ENST00000262901.4_Missense_Mutation_p.A371V			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	371	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.		A -> V (in dbSNP:rs3734355).		cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.A371V(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		CCGGGATTTGGCCCCCTTTCT	0.517													G|||	894	0.178514	0.0053	0.2089	5008	,	,		15370	0.4067		0.1471	False		,,,				2504	0.1881				p.A371V		Atlas-SNP	.											SIM1,NS,carcinoma,0,1	SIM1	173	1	1	Substitution - Missense(1)	stomach(1)	c.C1112T						scavenged	.	G	VAL/ALA	139,4267	97.6+/-136.3	2,135,2066	111.0	104.0	106.0		1112	2.9	1.0	6	dbSNP_107	106	1172,7428	239.3+/-270.5	62,1048,3190	yes	missense	SIM1	NM_005068.2	64	64,1183,5256	AA,AG,GG		13.6279,3.1548,10.08	benign	371/767	100868721	1311,11695	2203	4300	6503	SO:0001583	missense	6492	exon9			GATTTGGCCCCCT	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1112C>T	6.37:g.100868721G>A	ENSP00000358210:p.Ala371Val	Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	81	13	0.160494	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	432	0.1978021978021978	7	0.014227642276422764	76	0.20994475138121546	236	0.4125874125874126	113	0.14907651715039577	G	15.06	2.722664	0.48728	0.031548	0.136279	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.33438	1.41;1.41	5.8	2.86	0.33363	Single-minded, C-terminal (2);	0.916570	0.09543	N	0.788056	T	0.06645	0.0170	N	0.19112	0.55	0.35594	P	0.19266700000000003	B	0.10296	0.003	B	0.12156	0.007	T	0.30592	-0.9973	9	0.27785	T	0.31	.	4.3759	0.11270	0.0874:0.3246:0.4629:0.1251	rs3734355;rs3734355	371	P81133	SIM1_HUMAN	V	371	ENSP00000358210:A371V;ENSP00000262901:A371V	ENSP00000262901:A371V	A	-	2	0	SIM1	100975442	0.941000	0.31946	1.000000	0.80357	0.987000	0.75469	1.394000	0.34509	1.466000	0.48025	-0.157000	0.13467	GCC	G|0.857;A|0.143	0.143	strong		0.517	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
DOCK1	1793	hgsc.bcm.edu	37	10	129249676	129249676	+	Silent	SNP	C	C	T	rs2229604	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:129249676C>T	ENST00000280333.6	+	52	5692	c.5583C>T	c.(5581-5583)tcC>tcT	p.S1861S		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1861					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		CGGTGGACTCCGGGATCGTGC	0.582													C|||	2116	0.422524	0.2337	0.4986	5008	,	,		17386	0.4593		0.497	False		,,,				2504	0.5092				p.S1861S		Atlas-SNP	.											.	DOCK1	188	.	0			c.C5583T						PASS	.	C		1097,3077		154,789,1144	43.0	51.0	48.0		5538	-10.4	0.1	10	dbSNP_98	48	4170,4256		1036,2098,1079	no	coding-synonymous	DOCK1	NM_001380.3		1190,2887,2223	TT,TC,CC		49.4897,26.2817,41.8016		1846/1851	129249676	5267,7333	2087	4213	6300	SO:0001819	synonymous_variant	1793	exon52			GGACTCCGGGATC	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.5583C>T	10.37:g.129249676C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				C|0.571;T|0.429	0.429	strong		0.582	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
PDZD3	79849	hgsc.bcm.edu	37	11	119059404	119059404	+	Missense_Mutation	SNP	G	G	A	rs1815811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:119059404G>A	ENST00000531114.1	+	7	1862	c.1313G>A	c.(1312-1314)cGg>cAg	p.R438Q	PDZD3_ENST00000322712.4_Missense_Mutation_p.R358Q|PDZD3_ENST00000355547.5_Missense_Mutation_p.R372Q|PDZD3_ENST00000525131.1_Missense_Mutation_p.R359Q|PDZD3_ENST00000392817.2_Missense_Mutation_p.R438Q			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	438				R -> Q (in Ref. 2; BAC76050 and 5; AAH29042). {ECO:0000305}.	cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		GCCTCGCCCCGGGGCAGCAGC	0.607													A|||	3330	0.664936	0.6014	0.4251	5008	,	,		17325	0.879		0.5716	False		,,,				2504	0.7965				p.R372Q		Atlas-SNP	.											.	PDZD3	42	.	0			c.G1115A						PASS	.	A	GLN/ARG,GLN/ARG	2590,1810	529.0+/-372.6	778,1034,388	58.0	54.0	56.0		1115,1073	-1.8	0.0	11	dbSNP_92	56	4672,3918	545.1+/-384.7	1256,2160,879	yes	missense,missense	PDZD3	NM_001168468.1,NM_024791.3	43,43	2034,3194,1267	AA,AG,GG		45.6112,41.1364,44.0955	benign,benign	372/506,358/492	119059404	7262,5728	2200	4295	6495	SO:0001583	missense	79849	exon9			CGCCCCGGGGCAG	AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"""PDZ domain containing 2"""	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1313G>A	11.37:g.119059404G>A	ENSP00000431164:p.Arg438Gln	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_001168468	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Missense_Mutation	SNP	ENST00000531114.1	37		1384	0.6336996336996337	297	0.6036585365853658	170	0.4696132596685083	493	0.8618881118881119	424	0.5593667546174143	A	3.171	-0.170042	0.06461	0.588636	0.543888	ENSG00000172367	ENST00000525131;ENST00000531114;ENST00000355547;ENST00000322712;ENST00000454065;ENST00000392817	T;T;T;T;T	0.73047	1.61;1.58;1.62;-0.71;1.58	5.21	-1.83	0.07833	PDZ/DHR/GLGF (1);	1.300320	0.05375	N	0.536080	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B;B;B;B	0.09022	0.0;0.002;0.001;0.001	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.27773	-1.0064	9	0.09338	T	0.73	0.0036	6.3572	0.21408	0.3089:0.3595:0.3317:0.0	rs1815811;rs4127379;rs17545150;rs17845869;rs17858844;rs60088554;rs1815811	359;438;372;358	E9PPZ1;Q86UT5;Q86UT5-2;B0YJ61	.;NHRF4_HUMAN;.;.	Q	359;438;372;358;372;438	ENSP00000434559:R359Q;ENSP00000431164:R438Q;ENSP00000347742:R372Q;ENSP00000327107:R358Q;ENSP00000376564:R438Q	ENSP00000327107:R358Q	R	+	2	0	PDZD3	118564614	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.042000	0.13949	-0.564000	0.06070	-0.254000	0.11334	CGG	G|0.395;A|0.605	0.605	strong		0.607	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1	NM_024791	
ZNF570	148268	hgsc.bcm.edu	37	19	37975379	37975379	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37975379G>A	ENST00000330173.1	+	5	1384	c.855G>A	c.(853-855)caG>caA	p.Q285Q	ZNF570_ENST00000586475.1_Silent_p.Q341Q|ZNF570_ENST00000388801.3_Silent_p.Q82Q	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	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)			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)			CCTTCAGTCAGAATGCACACC	0.423																																					p.Q285Q		Atlas-SNP	.											.	ZNF570	58	.	0			c.G855A						PASS	.						72.0	69.0	70.0					19																	37975379		2203	4300	6503	SO:0001819	synonymous_variant	148268	exon5			CAGTCAGAATGCA	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.855G>A	19.37:g.37975379G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	39	16	0.410256	NM_144694	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																			.	.	none		0.423	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694	
DMBT1	1755	hgsc.bcm.edu	37	10	124351954	124351954	+	Silent	SNP	G	G	A	rs4752722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124351954G>A	ENST00000338354.3	+	20	2449	c.2343G>A	c.(2341-2343)tcG>tcA	p.S781S	DMBT1_ENST00000368909.3_Silent_p.S781S|DMBT1_ENST00000368955.3_Silent_p.S771S|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000344338.3_Silent_p.S771S|DMBT1_ENST00000330163.4_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	781	SRCR 6. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				GGGCCACGTCGGCCCCAGGAA	0.617													g|||	1864	0.372204	0.5469	0.2435	5008	,	,		17432	0.4395		0.1511	False		,,,				2504	0.3855				p.S781S	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G2343A						PASS	.	A	,,	1880,2108		461,958,575	179.0	145.0	156.0		,2343,2313	-7.7	0.0	10	dbSNP_111	156	1157,7105		170,817,3144	no	intron,coding-synonymous,coding-synonymous	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	,,	631,1775,3719	AA,AG,GG		14.0039,47.1414,24.7918	,,	,781/2414,771/2404	124351954	3037,9213	1994	4131	6125	SO:0001819	synonymous_variant	1755	exon20			CACGTCGGCCCCA		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.2343G>A	10.37:g.124351954G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	128	89	0.695312	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				G|0.732;A|0.268	0.268	strong		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
CHRDL1	91851	hgsc.bcm.edu	37	X	109931856	109931856	+	Silent	SNP	T	T	C	rs5943053	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:109931856T>C	ENST00000372045.1	-	9	1064	c.933A>G	c.(931-933)aaA>aaG	p.K311K	CHRDL1_ENST00000444321.2_Silent_p.K317K|CHRDL1_ENST00000372042.1_Silent_p.K318K|CHRDL1_ENST00000394797.4_Silent_p.K317K|CHRDL1_ENST00000434224.1_Silent_p.K238K|CHRDL1_ENST00000482160.1_Silent_p.K238K|CHRDL1_ENST00000218054.4_Silent_p.K317K			Q9BU40	CRDL1_HUMAN	chordin-like 1	311	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				BMP signaling pathway (GO:0030509)|cell differentiation (GO:0030154)|compound eye development (GO:0048749)|eye development (GO:0001654)|negative regulation of BMP signaling pathway (GO:0030514)|nervous system development (GO:0007399)|ossification (GO:0001503)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(12)|liver(1)|lung(15)|prostate(1)|skin(1)	31						CCTTGCAGCATTTTCCGTCTA	0.433													c|||	1464	0.387815	0.6339	0.2003	3775	,	,		12311	0.0079		0.3211	False		,,,				2504	0.1595				p.K318K		Atlas-SNP	.											.	CHRDL1	78	.	0			c.A954G						PASS	.		,,,	3008,827		998,560,452,74,119	187.0	173.0	178.0		954,951,714,951	2.1	1.0	X	dbSNP_114	178	2670,4058		395,1166,714,867,1158	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHRDL1	NM_001143981.1,NM_001143982.1,NM_001143983.2,NM_145234.3	,,,	1393,1726,1166,941,1277	CC,CT,C,TT,T		39.6849,21.5645,46.2463	,,,	318/459,317/458,238/379,317/457	109931856	5678,4885	2203	4300	6503	SO:0001819	synonymous_variant	91851	exon9			GCAGCATTTTCCG	AL049176	CCDS14553.1, CCDS48148.1, CCDS48149.1, CCDS48150.1, CCDS48148.2	Xq23	2014-01-31			ENSG00000101938	ENSG00000101938			29861	protein-coding gene	gene with protein product		300350	"""megalocornea 1 (X-linked)"""	MGC1		11441185, 11118896, 22284829	Standard	NM_001143981		Approved	NRLN1, CHL	uc004eow.3	Q9BU40	OTTHUMG00000022199	ENST00000372045.1:c.933A>G	X.37:g.109931856T>C		Somatic	101	1	0.00990099		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_001143981	B1AKD0|B4DMP3|D3DUY6|E9PGS5|Q539E4|Q9Y3H7	Silent	SNP	ENST00000372045.1	37																																																																																				C|0.491;G|0.000;T|0.508	0.491	strong		0.433	CHRDL1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057912.1	NM_145234	
DHX38	9785	hgsc.bcm.edu	37	16	72137561	72137561	+	Silent	SNP	G	G	A	rs2240243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:72137561G>A	ENST00000268482.3	+	13	2207	c.1698G>A	c.(1696-1698)acG>acA	p.T566T	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	566	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CTCAGCTGACGCAGTACCTGC	0.552													A|||	2368	0.472843	0.7814	0.3112	5008	,	,		19860	0.3105		0.3519	False		,,,				2504	0.4622				p.T566T	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.G1698A						PASS	.	A		3037,1359	451.2+/-349.6	1063,911,224	123.0	98.0	107.0		1698	-2.3	1.0	16	dbSNP_98	107	3170,5430	655.0+/-401.2	571,2028,1701	no	coding-synonymous	DHX38	NM_014003.3		1634,2939,1925	AA,AG,GG		36.8605,30.9145,47.7608		566/1228	72137561	6207,6789	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon13			GCTGACGCAGTAC	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.1698G>A	16.37:g.72137561G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	119	55	0.462185	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			G|0.533;A|0.467	0.467	strong		0.552	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
NXPE1	120400	hgsc.bcm.edu	37	11	114393652	114393652	+	Missense_Mutation	SNP	C	C	T	rs10891692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:114393652C>T	ENST00000424269.1	-	4	1056	c.1057G>A	c.(1057-1059)Gga>Aga	p.G353R	NXPE1_ENST00000251921.2_Missense_Mutation_p.G211R|NXPE1_ENST00000536271.1_Missense_Mutation_p.G69R			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	353			G -> R (in dbSNP:rs10891692).			extracellular region (GO:0005576)											GTAGAGTCTCCCAGGAGGTAA	0.358													C|||	1864	0.372204	0.2534	0.3069	5008	,	,		18462	0.6687		0.337	False		,,,				2504	0.3098				p.G211R		Atlas-SNP	.											FAM55A,NS,adenoma,0,1	NXPE1	8	1	0			c.G631A						PASS	.	C	ARG/GLY	1194,3208	416.5+/-337.6	159,876,1166	97.0	85.0	89.0		631	4.5	1.0	11	dbSNP_120	89	2963,5629	459.2+/-364.8	496,1971,1829	yes	missense	FAM55A	NM_152315.2	125	655,2847,2995	TT,TC,CC		34.4856,27.124,31.9917	probably-damaging	211/406	114393652	4157,8837	2201	4296	6497	SO:0001583	missense	120400	exon5			AGTCTCCCAGGAG	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.1057G>A	11.37:g.114393652C>T	ENSP00000411690:p.Gly353Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		864	0.3956043956043956	121	0.2459349593495935	110	0.30386740331491713	380	0.6643356643356644	253	0.3337730870712401	C	22.8	4.332185	0.81801	0.27124	0.344856	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.73258	-0.73;-0.73;-0.73	4.46	4.46	0.54185	.	0.000000	0.64402	D	0.000005	T	0.00012	0.0000	M	0.93594	3.435	0.23784	P	0.99685252	D	0.89917	1.0	D	0.97110	1.0	T	0.52503	-0.8567	9	0.87932	D	0	.	15.4186	0.74991	0.0:1.0:0.0:0.0	rs10891692;rs57749610;rs10891692	353	Q8N323	FA55A_HUMAN	R	69;211;353	ENSP00000445200:G69R;ENSP00000251921:G211R;ENSP00000411690:G353R	ENSP00000251921:G211R	G	-	1	0	FAM55A	113898862	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.585000	0.67497	2.408000	0.81797	0.650000	0.86243	GGA	C|0.645;T|0.355	0.355	strong		0.358	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
NID2	22795	hgsc.bcm.edu	37	14	52478315	52478315	+	Silent	SNP	A	A	G	rs1051069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:52478315A>G	ENST00000216286.5	-	17	3506	c.3507T>C	c.(3505-3507)gcT>gcC	p.A1169A	NID2_ENST00000541773.1_Silent_p.A1068A	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1169					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GTTCCAGACCAGCACGGCTGA	0.498													N|||	3458	0.690495	0.7859	0.745	5008	,	,		19929	0.7738		0.5378	False		,,,				2504	0.5941				p.A1169A		Atlas-SNP	.											NID2,NS,carcinoma,-1,1	NID2	201	1	0			c.T3507C						scavenged	.	G		3311,1095	394.4+/-329.3	1248,815,140	150.0	123.0	132.0		3507	-0.7	0.0	14	dbSNP_86	132	4660,3940	550.8+/-385.8	1281,2098,921	no	coding-synonymous	NID2	NM_007361.3		2529,2913,1061	GG,GA,AA		45.814,24.8525,38.7129		1169/1376	52478315	7971,5035	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon17			CAGACCAGCACGG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3507T>C	14.37:g.52478315A>G		Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1	1479	0.6771978021978022	386	0.7845528455284553	260	0.7182320441988951	438	0.7657342657342657	395	0.521108179419525	G	0.851	-0.738684	0.03111	0.751475	0.54186	ENSG00000087303	ENST00000556572	.	.	.	5.92	-0.731	0.11151	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.25847	-1.0120	3	.	.	.	.	5.6379	0.17546	0.176:0.4591:0.2713:0.0937	rs1051069;rs3191452;rs17831519;rs17846144;rs17859152;rs59260357;rs1051069	.	.	.	R	438	.	.	W	-	1	0	NID2	51548065	0.015000	0.18098	0.000000	0.03702	0.058000	0.15608	-0.734000	0.04893	-0.721000	0.04929	-0.812000	0.03155	TGG	A|0.354;G|0.646	0.646	strong		0.498	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
TRIM37	4591	hgsc.bcm.edu	37	17	57158552	57158552	+	Missense_Mutation	SNP	G	G	A	rs61758100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:57158552G>A	ENST00000262294.7	-	6	657	c.398C>T	c.(397-399)gCa>gTa	p.A133V	TRIM37_ENST00000393065.2_Missense_Mutation_p.A99V|TRIM37_ENST00000393066.3_Missense_Mutation_p.A133V|TRIM37_ENST00000376149.3_Missense_Mutation_p.A11V	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	133					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|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(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					ATAAATTTCTGCCAAAGGTTT	0.388									Mulibrey Nanism				G|||	10	0.00199681	0.0008	0.0014	5008	,	,		11696	0.0		0.008	False		,,,				2504	0.0				p.A133V		Atlas-SNP	.											.	TRIM37	105	.	0			c.C398T						PASS	.	G	VAL/ALA,VAL/ALA	11,4395	17.9+/-39.9	0,11,2192	112.0	111.0	111.0		398,398	5.6	1.0	17	dbSNP_129	111	79,8521	45.8+/-104.6	0,79,4221	yes	missense,missense	TRIM37	NM_001005207.2,NM_015294.3	64,64	0,90,6413	AA,AG,GG		0.9186,0.2497,0.692	benign,benign	133/965,133/965	57158552	90,12916	2203	4300	6503	SO:0001583	missense	4591	exon6	Familial Cancer Database	Perheentupa syndrome	ATTTCTGCCAAAG	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	7523	protein-coding gene	gene with protein product	"""RING-B-box-coiled-coil protein"""	605073	"""tripartite motif-containing 37"""	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.398C>T	17.37:g.57158552G>A	ENSP00000262294:p.Ala133Val	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	59	18	0.305085	NM_015294	Q7Z3E6|Q8IYF7|Q8WYF7	Missense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	28.2	4.902602	0.92035	0.002497	0.009186	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	T;T;T;T	0.64991	0.39;0.39;-0.13;0.39	5.62	5.62	0.85841	B-box, C-terminal (1);	0.072084	0.56097	D	0.000028	T	0.37237	0.0996	N	0.08118	0	0.80722	D	1	B;B;B	0.31931	0.148;0.347;0.057	B;B;B	0.32465	0.054;0.146;0.032	T	0.39461	-0.9613	10	0.33141	T	0.24	-11.1031	18.2379	0.89956	0.0:0.0:1.0:0.0	rs61758100	99;11;133	F8WEE6;O94972-2;O94972	.;.;TRI37_HUMAN	V	133;133;11;99	ENSP00000376785:A133V;ENSP00000262294:A133V;ENSP00000365319:A11V;ENSP00000376784:A99V	ENSP00000262294:A133V	A	-	2	0	TRIM37	54513334	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	2.661000	0.90470	0.650000	0.86243	GCA	G|0.994;A|0.006	0.006	strong		0.388	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294	
BTN1A1	696	hgsc.bcm.edu	37	6	26509330	26509330	+	Missense_Mutation	SNP	C	C	G	rs9393728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26509330C>G	ENST00000244513.6	+	7	1575	c.1509C>G	c.(1507-1509)gaC>gaG	p.D503E		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	503			D -> E (in dbSNP:rs9393728). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8611614, ECO:0000269|Ref.3}.			extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						TGGGGGAGGACTCTGCCCCTA	0.527													C|||	2849	0.56889	0.5159	0.5879	5008	,	,		3909	0.746		0.4423	False		,,,				2504	0.5746				p.D503E		Atlas-SNP	.											.	BTN1A1	68	.	0			c.C1509G						PASS	.	C	GLU/ASP	2297,2109	597.9+/-389.0	593,1111,499	96.0	100.0	98.0		1509	-1.9	0.0	6	dbSNP_119	98	4047,4553	555.1+/-386.6	986,2075,1239	yes	missense	BTN1A1	NM_001732.2	45	1579,3186,1738	GG,GC,CC		47.0581,47.8665,48.7775	benign	503/527	26509330	6344,6662	2203	4300	6503	SO:0001583	missense	696	exon7			GGAGGACTCTGCC	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.1509C>G	6.37:g.26509330C>G	ENSP00000244513:p.Asp503Glu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	1125	0.5151098901098901	203	0.41260162601626016	199	0.5497237569060773	394	0.6888111888111889	329	0.4340369393139842	C	0.514	-0.865325	0.02590	0.521335	0.470581	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.34472	1.36	5.05	-1.89	0.07689	.	0.635484	0.14826	N	0.296156	T	0.03827	0.0108	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.36187	-0.9758	9	0.02654	T	1	.	4.4229	0.11490	0.2574:0.418:0.0:0.3246	rs9393728	503	Q13410	BT1A1_HUMAN	E	503;471	ENSP00000244513:D503E	ENSP00000244513:D503E	D	+	3	2	BTN1A1	26617309	0.000000	0.05858	0.000000	0.03702	0.243000	0.25628	-1.754000	0.01816	-0.191000	0.10448	0.563000	0.77884	GAC	C|0.505;G|0.495	0.495	strong		0.527	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
COL6A6	131873	hgsc.bcm.edu	37	3	130311398	130311398	+	Missense_Mutation	SNP	C	C	T	rs73868925	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130311398C>T	ENST00000358511.6	+	13	4317	c.4286C>T	c.(4285-4287)gCc>gTc	p.A1429V	COL6A6_ENST00000453409.2_Missense_Mutation_p.A1429V	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1429	Triple-helical region.			A -> V (in Ref. 3; CAH10639). {ECO:0000305}.	cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.A1429V(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						GAAAGAGGAGCCCCTGGACCA	0.408													C|||	847	0.169129	0.1467	0.1326	5008	,	,		18058	0.2222		0.0954	False		,,,				2504	0.2464				p.A1429V		Atlas-SNP	.											COL6A6,NS,carcinoma,0,1	COL6A6	497	1	1	Substitution - Missense(1)	stomach(1)	c.C4286T						PASS	.	C	VAL/ALA	458,3246		30,398,1424	78.0	74.0	76.0		4286	0.9	0.1	3	dbSNP_130	76	675,7515		34,607,3454	yes	missense	COL6A6	NM_001102608.1	64	64,1005,4878	TT,TC,CC		8.2418,12.365,9.5258	probably-damaging	1429/2264	130311398	1133,10761	1852	4095	5947	SO:0001583	missense	131873	exon13			GAGGAGCCCCTGG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.4286C>T	3.37:g.130311398C>T	ENSP00000351310:p.Ala1429Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	326|326	0.14926739926739926|0.14926739926739926	101|101	0.20528455284552846|0.20528455284552846	41|41	0.1132596685082873|0.1132596685082873	119|119	0.20804195804195805|0.20804195804195805	65|65	0.08575197889182058|0.08575197889182058	C|C	7.361|7.361	0.624892|0.624892	0.14193|0.14193	0.12365|0.12365	0.082418|0.082418	ENSG00000206384|ENSG00000206384	ENST00000358511;ENST00000453409|ENST00000511332	D;D|.	0.93712|.	-3.27;-3.27|.	5.83|5.83	0.884|0.884	0.19182|0.19182	.|.	0.343233|.	0.21348|.	N|.	0.076003|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.17474|0.17474	0.49|0.49	0.80722|0.80722	P|P	0.0|0.0	B|.	0.09022|.	0.002|.	B|.	0.12156|.	0.007|.	T|T	0.31503|0.31503	-0.9941|-0.9941	9|4	0.11485|.	T|.	0.65|.	.|.	1.6101|1.6101	0.02692|0.02692	0.1497:0.4563:0.1464:0.2476|0.1497:0.4563:0.1464:0.2476	.|.	1429|.	A6NMZ7|.	CO6A6_HUMAN|.	V|S	1429|208	ENSP00000351310:A1429V;ENSP00000399236:A1429V|.	ENSP00000351310:A1429V|.	A|P	+|+	2|1	0|0	COL6A6|COL6A6	131794088|131794088	0.004000|0.004000	0.15560|0.15560	0.141000|0.141000	0.22245|0.22245	0.498000|0.498000	0.33706|0.33706	-0.053000|-0.053000	0.11846|0.11846	0.363000|0.363000	0.24346|0.24346	-0.302000|-0.302000	0.09304|0.09304	GCC|CCC	C|0.864;T|0.136	0.136	strong		0.408	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
TRIM59	286827	hgsc.bcm.edu	37	3	160156951	160156951	+	Silent	SNP	C	C	T	rs1141023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:160156951C>T	ENST00000309784.4	-	3	206	c.21G>A	c.(19-21)gaG>gaA	p.E7E	TRIM59_ENST00000543469.1_Silent_p.E7E|RP11-432B6.3_ENST00000483754.1_Silent_p.E7E	NM_173084.2	NP_775107.1	Q8IWR1	TRI59_HUMAN	tripartite motif containing 59	7					innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral entry into host cell (GO:0046597)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|urinary_tract(3)	15			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GACAAGTTAACTCTTCCTCAA	0.328													C|||	412	0.0822684	0.0045	0.1009	5008	,	,		18066	0.0397		0.1839	False		,,,				2504	0.1135				p.E7E		Atlas-SNP	.											.	TRIM59	42	.	0			c.G21A						PASS	.	C		168,4236	101.2+/-139.8	4,160,2038	40.0	39.0	40.0		21	2.0	1.0	3	dbSNP_86	40	1742,6852	284.4+/-296.6	178,1386,2733	no	coding-synonymous	TRIM59	NM_173084.2		182,1546,4771	TT,TC,CC		20.27,3.8147,14.6946		7/404	160156951	1910,11088	2202	4297	6499	SO:0001819	synonymous_variant	286827	exon3			AGTTAACTCTTCC	AY159379	CCDS3190.1	3q26	2013-01-09	2011-01-25		ENSG00000213186	ENSG00000213186		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	30834	protein-coding gene	gene with protein product			"""tripartite motif-containing 57"", ""tripartite motif-containing 59"""	TRIM57		12095697	Standard	NM_173084		Approved	TSBF1, Mrf1, RNF104	uc003fdm.3	Q8IWR1	OTTHUMG00000159034	ENST00000309784.4:c.21G>A	3.37:g.160156951C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	153	82	0.535948	NM_173084	A8K5G9|D3DNL9	Silent	SNP	ENST00000309784.4	37	CCDS3190.1																																																																																			C|0.882;T|0.118	0.118	strong		0.328	TRIM59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352963.1	NM_173084	
TULP4	56995	hgsc.bcm.edu	37	6	158910698	158910698	+	Missense_Mutation	SNP	G	G	A	rs12206717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:158910698G>A	ENST00000367097.3	+	9	2922	c.1565G>A	c.(1564-1566)aGt>aAt	p.S522N	TULP4_ENST00000367094.2_Missense_Mutation_p.S522N	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	522			S -> N (in dbSNP:rs12206717).		intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		ATTGAGCTGAGTGATGACTGG	0.468													G|||	159	0.0317492	0.0038	0.0476	5008	,	,		18706	0.001		0.0527	False		,,,				2504	0.0685				p.S522N		Atlas-SNP	.											.	TULP4	137	.	0			c.G1565A						PASS	.	G	ASN/SER,ASN/SER	72,4334	65.8+/-103.3	0,72,2131	153.0	138.0	143.0		1565,1565	5.6	1.0	6	dbSNP_120	143	509,8091	145.3+/-201.0	7,495,3798	yes	missense,missense	TULP4	NM_001007466.1,NM_020245.3	46,46	7,567,5929	AA,AG,GG		5.9186,1.6341,4.4672	benign,benign	522/679,522/1544	158910698	581,12425	2203	4300	6503	SO:0001583	missense	56995	exon9			AGCTGAGTGATGA		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1565G>A	6.37:g.158910698G>A	ENSP00000356064:p.Ser522Asn	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	87	13	0.149425	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	59	0.027014652014652016	3	0.006097560975609756	20	0.055248618784530384	0	0.0	36	0.047493403693931395	G	15.69	2.908482	0.52333	0.016341	0.059186	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.62105	0.05;0.85	5.57	5.57	0.84162	.	0.085022	0.85682	D	0.000000	T	0.26085	0.0636	N	0.03115	-0.41	0.48087	D	0.999588	B;B	0.13145	0.002;0.007	B;B	0.13407	0.009;0.008	T	0.14671	-1.0464	10	0.20046	T	0.44	-14.0086	19.5416	0.95277	0.0:0.0:1.0:0.0	rs12206717;rs52817462;rs12206717	522;522	Q9NRJ4-2;Q9NRJ4	.;TULP4_HUMAN	N	522	ENSP00000356064:S522N;ENSP00000356061:S522N	ENSP00000356061:S522N	S	+	2	0	TULP4	158830686	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.954000	0.63631	2.614000	0.88457	0.655000	0.94253	AGT	G|0.962;A|0.038	0.038	strong		0.468	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
SLC38A10	124565	hgsc.bcm.edu	37	17	79226362	79226362	+	Silent	SNP	G	G	A	rs3803767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79226362G>A	ENST00000374759.3	-	13	1961	c.1578C>T	c.(1576-1578)caC>caT	p.H526H	SLC38A10_ENST00000288439.5_Silent_p.H526H	NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	526					amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TTCCGCCCGCGTGTCTGGATG	0.617													g|||	342	0.0682907	0.0136	0.0303	5008	,	,		17561	0.1488		0.0865	False		,,,				2504	0.0675				p.H526H		Atlas-SNP	.											.	SLC38A10	133	.	0			c.C1578T						PASS	.		,	130,4276	91.6+/-130.3	3,124,2076	68.0	60.0	63.0		1578,1578	2.7	0.0	17	dbSNP_107	63	733,7867	174.9+/-225.1	35,663,3602	no	coding-synonymous,coding-synonymous	SLC38A10	NM_001037984.1,NM_138570.2	,	38,787,5678	AA,AG,GG		8.5233,2.9505,6.6354	,	526/1120,526/781	79226362	863,12143	2203	4300	6503	SO:0001819	synonymous_variant	124565	exon13			GCCCGCGTGTCTG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.1578C>T	17.37:g.79226362G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Silent	SNP	ENST00000374759.3	37	CCDS42397.1																																																																																			G|0.930;A|0.070	0.070	strong		0.617	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
KRT7	3855	hgsc.bcm.edu	37	12	52631313	52631313	+	Missense_Mutation	SNP	A	A	G	rs6580870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52631313A>G	ENST00000331817.5	+	3	740	c.557A>G	c.(556-558)cAc>cGc	p.H186R		NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	186	Coil 1B.|Rod.		H -> R (in dbSNP:rs6580870). {ECO:0000269|PubMed:10492017, ECO:0000269|PubMed:12359226, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:2415537, ECO:0000269|PubMed:2459129}.		viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	GAAATTAACCACCGCACAGCT	0.532													G|||	4367	0.872005	0.9198	0.8386	5008	,	,		18808	0.9028		0.8191	False		,,,				2504	0.8538				p.H186R		Atlas-SNP	.											.	KRT7	48	.	0			c.A557G						PASS	.	G	ARG/HIS	3958,448	212.2+/-232.1	1781,396,26	151.0	138.0	142.0		557	-2.7	0.0	12	dbSNP_116	142	6920,1680	308.1+/-308.7	2785,1350,165	yes	missense	KRT7	NM_005556.3	29	4566,1746,191	GG,GA,AA		19.5349,10.168,16.3617	benign	186/470	52631313	10878,2128	2203	4300	6503	SO:0001583	missense	3855	exon3			TTAACCACCGCAC		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.557A>G	12.37:g.52631313A>G	ENSP00000329243:p.His186Arg	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Missense_Mutation	SNP	ENST00000331817.5	37	CCDS8822.1	1880	0.8608058608058609	448	0.9105691056910569	284	0.7845303867403315	516	0.9020979020979021	632	0.8337730870712401	G	1.820	-0.472602	0.04445	0.89832	0.804651	ENSG00000135480	ENST00000331817;ENST00000543899;ENST00000422319;ENST00000551537	T	0.79653	-1.29	4.87	-2.67	0.06059	Filament (1);	1.841890	0.03217	N	0.176927	T	0.00012	0.0000	N	0.00088	-2.19	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.47686	-0.9098	9	0.10902	T	0.67	.	14.85	0.70289	0.8325:0.0:0.1675:0.0	rs6580870;rs11558309;rs17415162;rs17856070;rs60098934;rs6580870	186;186	F8VZY5;P08729	.;K2C7_HUMAN	R	186;186;162;186	ENSP00000329243:H186R	ENSP00000329243:H186R	H	+	2	0	KRT7	50917580	0.001000	0.12720	0.002000	0.10522	0.057000	0.15508	-0.038000	0.12144	-0.702000	0.05056	-1.050000	0.02344	CAC	A|0.149;G|0.851	0.851	strong		0.532	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
RSAD1	55316	hgsc.bcm.edu	37	17	48557348	48557348	+	Missense_Mutation	SNP	T	T	C	rs2290861	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48557348T>C	ENST00000258955.2	+	3	462	c.377T>C	c.(376-378)tTg>tCg	p.L126S		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	126			L -> S (in dbSNP:rs2290861). {ECO:0000269|PubMed:15489334}.		porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			CCTGCAGACTTGGAAGTCACA	0.602											OREG0024566	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2928	0.584665	0.9107	0.5807	5008	,	,		16031	0.2222		0.6272	False		,,,				2504	0.4765				p.L126S		Atlas-SNP	.											.	RSAD1	36	.	0			c.T377C						PASS	.	C	SER/LEU	3823,583	256.7+/-261.4	1665,493,45	54.0	61.0	58.0		377	4.6	0.4	17	dbSNP_100	58	5392,3208	483.4+/-371.1	1701,1990,609	yes	missense	RSAD1	NM_018346.1	145	3366,2483,654	CC,CT,TT		37.3023,13.232,29.1481	benign	126/443	48557348	9215,3791	2203	4300	6503	SO:0001583	missense	55316	exon3			CAGACTTGGAAGT	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.377T>C	17.37:g.48557348T>C	ENSP00000258955:p.Leu126Ser	Somatic	117	0	0	955	WXS	Illumina HiSeq	Phase_I	120	118	0.983333	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Missense_Mutation	SNP	ENST00000258955.2	37	CCDS11569.1	1273	0.5828754578754579	446	0.9065040650406504	233	0.643646408839779	124	0.21678321678321677	470	0.6200527704485488	C	14.85	2.657426	0.47467	0.86768	0.626977	ENSG00000136444	ENST00000258955	T	0.81078	-1.45	4.64	4.64	0.57946	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	0.213136	0.37219	N	0.002184	T	0.00012	0.0000	L	0.28556	0.865	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.35201	-0.9798	9	0.22706	T	0.39	-4.2282	12.7363	0.57225	0.0:0.919:0.0:0.081	rs2290861;rs17857388;rs52827597;rs58626410;rs2290861	126	Q9HA92	RSAD1_HUMAN	S	126	ENSP00000258955:L126S	ENSP00000258955:L126S	L	+	2	0	RSAD1	45912347	0.500000	0.26091	0.416000	0.26546	0.958000	0.62258	4.393000	0.59665	1.182000	0.42928	-0.320000	0.08662	TTG	T|0.339;C|0.661	0.661	strong		0.602	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346	
DSPP	1834	hgsc.bcm.edu	37	4	88536917	88536917	+	Missense_Mutation	SNP	G	G	A	rs199901845		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88536917G>A	ENST00000282478.7	+	4	3136	c.3103G>A	c.(3103-3105)Gat>Aat	p.D1035N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1035N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	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.D1035N(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)		tgacagcagcgatagcagtga	0.522																																					p.D1035N		Atlas-SNP	.											DSPP,NS,carcinoma,-2,3	DSPP	174	3	1	Substitution - Missense(1)	kidney(1)	c.G3103A						PASS	.						62.0	68.0	66.0					4																	88536917		1560	2750	4310	SO:0001583	missense	1834	exon5			AGCAGCGATAGCA	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.3103G>A	4.37:g.88536917G>A	ENSP00000282478:p.Asp1035Asn	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	134	21	0.156716	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	5.819	0.335399	0.11013	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88664	-2.41;-2.41	1.43	0.544	0.17185	.	.	.	.	.	T	0.73999	0.3659	L	0.29908	0.895	0.18873	N	0.999989	B	0.30542	0.284	B	0.13407	0.009	T	0.59783	-0.7389	9	0.06494	T	0.89	-6.585	4.0989	0.10004	0.2347:0.0:0.7653:0.0	.	1035	Q9NZW4	DSPP_HUMAN	N	1035	ENSP00000382213:D1035N;ENSP00000282478:D1035N	ENSP00000282478:D1035N	D	+	1	0	DSPP	88755941	0.238000	0.23825	0.544000	0.28141	0.014000	0.08584	1.337000	0.33862	0.180000	0.19960	-0.791000	0.03333	GAT	.	.	weak		0.522	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37482458	37482458	+	Splice_Site	SNP	C	C	A	rs201148397	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37482458C>A	ENST00000346753.3	-	8	981	c.865G>T	c.(865-867)Gtg>Ttg	p.V289L	TMPRSS6_ENST00000381792.2_Splice_Site_p.V280L|TMPRSS6_ENST00000406725.1_Splice_Site_p.V280L|TMPRSS6_ENST00000442782.2_Splice_Site_p.V289L|TMPRSS6_ENST00000406856.1_Splice_Site_p.V280L	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	289	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.V289M(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						CAGCCGTACACCCTGGCAGAA	0.692													C|||	4	0.000798722	0.0	0.0	5008	,	,		10759	0.0		0.004	False		,,,				2504	0.0				p.V289L		Atlas-SNP	.											TMPRSS6_ENST00000442782,NS,carcinoma,0,2	TMPRSS6	99	2	1	Substitution - Missense(1)	lung(1)	c.G865T						PASS	.	C	LEU/VAL	3,4351		0,3,2174	11.0	11.0	11.0		865	3.5	1.0	22		11	10,8520		0,10,4255	yes	missense-near-splice	TMPRSS6	NM_153609.2	32	0,13,6429	AA,AC,CC		0.1172,0.0689,0.1009	benign	289/812	37482458	13,12871	2177	4265	6442	SO:0001630	splice_region_variant	164656	exon8			CGTACACCCTGGC	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.864-1G>T	22.37:g.37482458C>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	155	83	0.535484	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	CCDS13941.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	0.511	-0.866458	0.02590	6.89E-4	0.001172	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000442782	T;T;T;T;T	0.57595	0.39;0.39;0.39;0.39;0.39	4.55	3.49	0.39957	CUB (1);	0.275088	0.29987	N	0.010693	T	0.24774	0.0601	N	0.12746	0.255	0.33001	D	0.526307	B;B;B	0.18013	0.025;0.004;0.002	B;B;B	0.15484	0.013;0.003;0.001	T	0.30387	-0.9980	10	0.02654	T	1	.	5.9111	0.19029	0.0:0.4755:0.3987:0.1258	.	289;280;289	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	L	280;289;280;280;289	ENSP00000371211:V280L;ENSP00000334962:V289L;ENSP00000385453:V280L;ENSP00000384964:V280L;ENSP00000397691:V289L	ENSP00000334962:V289L	V	-	1	0	TMPRSS6	35812404	1.000000	0.71417	0.999000	0.59377	0.358000	0.29455	1.579000	0.36536	2.071000	0.62044	0.655000	0.94253	GTG	C|0.999;A|0.001	0.001	strong		0.692	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	Missense_Mutation
KDM4C	23081	hgsc.bcm.edu	37	9	7046901	7046901	+	Missense_Mutation	SNP	C	C	G	rs1407856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:7046901C>G	ENST00000381309.3	+	16	2864	c.2299C>G	c.(2299-2301)Caa>Gaa	p.Q767E	KDM4C_ENST00000535193.1_Missense_Mutation_p.Q789E|KDM4C_ENST00000543771.1_Missense_Mutation_p.Q767E|KDM4C_ENST00000381306.3_Missense_Mutation_p.Q767E|KDM4C_ENST00000428870.2_Missense_Mutation_p.Q454E|KDM4C_ENST00000536108.1_Missense_Mutation_p.Q586E|KDM4C_ENST00000442236.2_Missense_Mutation_p.Q512E	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	767			Q -> E (in dbSNP:rs1407856).		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						TGCTCTTAAGCAAACGAAGAA	0.368													C|||	1127	0.22504	0.025	0.2723	5008	,	,		20955	0.2937		0.171	False		,,,				2504	0.4468				p.Q789E		Atlas-SNP	.											KDM4C_ENST00000381306,NS,chondrosarcoma,-2,2	KDM4C	186	2	0			c.C2365G						PASS	.	C	GLU/GLN,GLU/GLN,GLU/GLN,GLU/GLN	233,4173	136.5+/-172.5	10,213,1980	171.0	155.0	160.0		2299,2299,2365,2299	2.5	1.0	9	dbSNP_88	160	1519,7081	286.5+/-297.7	135,1249,2916	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	29,29,29,29	145,1462,4896	GG,GC,CC		17.6628,5.2882,13.4707	benign,benign,benign,benign	767/1048,767/814,789/836,767/1057	7046901	1752,11254	2203	4300	6503	SO:0001583	missense	23081	exon16			CTTAAGCAAACGA	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.2299C>G	9.37:g.7046901C>G	ENSP00000370710:p.Gln767Glu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	73	0.561538	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	406	0.1858974358974359	24	0.04878048780487805	90	0.24861878453038674	155	0.270979020979021	137	0.18073878627968337	C	8.625	0.892374	0.17613	0.052882	0.176628	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870;ENST00000420847	T;T;T;T;T;T;T;T	0.17691	2.55;2.55;2.55;2.55;2.55;2.26;2.55;2.55	5.44	2.53	0.30540	.	0.275088	0.41823	N	0.000819	T	0.00012	0.0000	L	0.52011	1.625	0.27847	P	0.9408761	B;B;B;B;B	0.21381	0.055;0.001;0.002;0.0;0.001	B;B;B;B;B	0.24974	0.057;0.005;0.004;0.004;0.003	T	0.37979	-0.9682	9	0.21540	T	0.41	-35.9624	16.679	0.85287	0.0:0.6856:0.3144:0.0	rs1407856;rs52835630;rs1407856	512;767;789;767;767	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	E	789;767;767;767;512;586;454;111	ENSP00000442382:Q789E;ENSP00000445427:Q767E;ENSP00000370710:Q767E;ENSP00000370707:Q767E;ENSP00000409353:Q512E;ENSP00000440656:Q586E;ENSP00000405739:Q454E;ENSP00000400127:Q111E	ENSP00000370707:Q767E	Q	+	1	0	KDM4C	7036901	1.000000	0.71417	1.000000	0.80357	0.468000	0.32798	2.162000	0.42367	0.377000	0.24735	-0.175000	0.13238	CAA	C|0.833;G|0.167	0.167	strong		0.368	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
TGFA	7039	hgsc.bcm.edu	37	2	70677994	70677994	+	Silent	SNP	G	G	A	rs2166975	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:70677994G>A	ENST00000295400.6	-	6	727	c.480C>T	c.(478-480)gtC>gtT	p.V160V	TGFA_ENST00000445399.1_Intron|TGFA_ENST00000444975.1_Silent_p.V166V|TGFA_ENST00000418333.2_Silent_p.V159V|TGFA_ENST00000450929.1_Silent_p.V165V	NM_001099691.2|NM_003236.3	NP_001093161.1|NP_003227.1	P01135	TGFA_HUMAN	transforming growth factor, alpha	160					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|mammary gland alveolus development (GO:0060749)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell division (GO:0051781)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mitosis (GO:0045840)|response to drug (GO:0042493)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)	p.V160V(1)		haematopoietic_and_lymphoid_tissue(1)|lung(2)|prostate(1)	4						GGGCTCTTCAGACCACTGGCA	0.537													G|||	1039	0.207468	0.1309	0.1326	5008	,	,		19477	0.2877		0.2565	False		,,,				2504	0.2311				p.V160V		Atlas-SNP	.											TGFA,NS,lymphoid_neoplasm,0,1	TGFA	14	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C480T						PASS	.	G	,	729,3677	292.7+/-282.2	51,627,1525	62.0	50.0	54.0		477,480	2.1	1.0	2	dbSNP_96	54	2330,6270	374.2+/-337.3	324,1682,2294	no	coding-synonymous,coding-synonymous	TGFA	NM_001099691.2,NM_003236.3	,	375,2309,3819	AA,AG,GG		27.093,16.5456,23.5199	,	159/160,160/161	70677994	3059,9947	2203	4300	6503	SO:0001819	synonymous_variant	7039	exon6			TCTTCAGACCACT		CCDS1905.1, CCDS46316.1	2p13	2012-10-02			ENSG00000163235	ENSG00000163235			11765	protein-coding gene	gene with protein product		190170				3459638, 10552925	Standard	NM_003236		Approved		uc002sgs.4	P01135	OTTHUMG00000129669	ENST00000295400.6:c.480C>T	2.37:g.70677994G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	205	117	0.570732	NM_003236	A8K286|Q15577|Q53SK7|Q9BS56|Q9UEI3|Q9UKM1|Q9UKM2|Q9UKM3	Silent	SNP	ENST00000295400.6	37	CCDS1905.1																																																																																			G|0.782;A|0.218	0.218	strong		0.537	TGFA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251870.2		
SLCO2B1	11309	hgsc.bcm.edu	37	11	74883577	74883577	+	Missense_Mutation	SNP	G	G	A	rs12422149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:74883577G>A	ENST00000289575.5	+	7	1330	c.935G>A	c.(934-936)cGa>cAa	p.R312Q	SLCO2B1_ENST00000532236.1_Missense_Mutation_p.R196Q|SLCO2B1_ENST00000531756.1_Missense_Mutation_p.R57Q|SLCO2B1_ENST00000526660.1_3'UTR|SLCO2B1_ENST00000525650.1_Missense_Mutation_p.R168Q|SLCO2B1_ENST00000454962.2_Missense_Mutation_p.R85Q|SLCO2B1_ENST00000428359.2_Missense_Mutation_p.R290Q|SLCO2B1_ENST00000341411.4_Missense_Mutation_p.R85Q	NM_007256.4	NP_009187	O94956	SO2B1_HUMAN	solute carrier organic anion transporter family, member 2B1	312			R -> Q (in dbSNP:rs12422149).		liver development (GO:0001889)|sodium-independent icosanoid transport (GO:0071718)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid transmembrane transporter activity (GO:0015125)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(2)|endometrium(1)|large_intestine(7)|lung(20)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	39					Acetic acid(DB03166)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Digoxin(DB00390)|Dinoprostone(DB00917)|Ergoloid mesylate(DB01049)|Estradiol(DB00783)|Estrone(DB00655)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Glyburide(DB01016)|Ibuprofen(DB01050)|Iloprost(DB01088)|Latanoprost(DB00654)|Montelukast(DB00471)|Niacin(DB00627)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Tolbutamide(DB01124)	CAGTTTCGGCGAAAGGTCTTA	0.562													G|||	1051	0.209864	0.0923	0.3646	5008	,	,		19572	0.3204		0.0954	False		,,,				2504	0.2628				p.R312Q		Atlas-SNP	.											.	SLCO2B1	84	.	0			c.G935A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	409,3991	202.8+/-225.5	20,369,1811	103.0	88.0	93.0		869,503,935	-2.2	0.0	11	dbSNP_120	93	869,7717	195.8+/-240.9	40,789,3464	yes	missense,missense,missense	SLCO2B1	NM_001145211.2,NM_001145212.2,NM_007256.4	43,43,43	60,1158,5275	AA,AG,GG		10.1211,9.2955,9.8414	benign,benign,benign	290/688,168/566,312/710	74883577	1278,11708	2200	4293	6493	SO:0001583	missense	11309	exon7			TTCGGCGAAAGGT	AB026256	CCDS8235.1, CCDS44683.1, CCDS53679.1	11q13	2013-05-22	2003-11-25	2003-11-26				"""Solute carriers"""	10962	protein-coding gene	gene with protein product		604988	"""solute carrier family 21 (organic anion transporter), member 9"""	SLC21A9			Standard	NM_007256		Approved	OATP-B, OATP2B1	uc001owb.3	O94956		ENST00000289575.5:c.935G>A	11.37:g.74883577G>A	ENSP00000289575:p.Arg312Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_007256	A8K2G9|B4DGA9|B4DTB0|E7ERN5|E9PPU8|Q9H2Z0|Q9UFU1	Missense_Mutation	SNP	ENST00000289575.5	37	CCDS8235.1	442	0.20238095238095238	58	0.11788617886178862	106	0.292817679558011	205	0.3583916083916084	73	0.09630606860158311	G	14.19	2.460877	0.43736	0.092955	0.101211	ENSG00000137491	ENST00000289575;ENST00000341411;ENST00000532236;ENST00000531756;ENST00000525650;ENST00000454962;ENST00000428359	T;T;T;T;T;T;T	0.80738	1.16;-1.41;-1.41;-1.41;-1.41;-1.41;1.16	5.65	-2.21	0.06973	Major facilitator superfamily domain, general substrate transporter (1);	0.773311	0.11037	N	0.606507	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B;B;B;B	0.29037	0.147;0.147;0.231;0.147	B;B;B;B	0.20384	0.029;0.029;0.029;0.029	T	0.09185	-1.0686	9	0.13853	T	0.58	.	6.2971	0.21091	0.5347:0.1582:0.3071:0.0	rs12422149;rs56415681;rs59614522;rs12422149	168;57;85;312	E9PPU8;E9PPJ4;O94956-2;O94956	.;.;.;SO2B1_HUMAN	Q	312;85;196;57;168;85;290	ENSP00000289575:R312Q;ENSP00000341286:R85Q;ENSP00000434112:R196Q;ENSP00000432650:R57Q;ENSP00000436324:R168Q;ENSP00000389653:R85Q;ENSP00000388912:R290Q	ENSP00000289575:R312Q	R	+	2	0	SLCO2B1	74561225	0.001000	0.12720	0.000000	0.03702	0.272000	0.26649	-0.094000	0.11094	-0.241000	0.09681	-0.136000	0.14681	CGA	G|0.836;A|0.164	0.164	strong		0.562	SLCO2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383933.1	NM_007256	
RAET1G	353091	hgsc.bcm.edu	37	6	150239330	150239330	+	Silent	SNP	C	C	T	rs17079029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:150239330C>T	ENST00000367360.2	-	4	889	c.822G>A	c.(820-822)agG>agA	p.R274R	RAET1E-AS1_ENST00000605899.1_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		AAAGGACTCTCCTCAGCAGCC	0.597													N|||	1137	0.227037	0.1021	0.111	5008	,	,		21265	0.5367		0.1511	False		,,,				2504	0.2372				p.R274R		Atlas-SNP	.											.	RAET1G	31	.	0			c.G822A						PASS	.	C		489,3917	227.8+/-242.9	24,441,1738	102.0	109.0	106.0		822	-4.1	0.0	6	dbSNP_123	106	1131,7469	233.9+/-267.0	83,965,3252	no	coding-synonymous	RAET1G	NM_001001788.2		107,1406,4990	TT,TC,CC		13.1512,11.0985,12.4558		274/335	150239330	1620,11386	2203	4300	6503	SO:0001819	synonymous_variant	353091	exon4			GACTCTCCTCAGC	AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"""retinoic acid early transcript 1G pseudogene"""			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.822G>A	6.37:g.150239330C>T		Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	148	122	0.824324	NM_001001788		Silent	SNP	ENST00000367360.2	37	CCDS43514.1																																																																																			C|0.785;T|0.215	0.215	strong		0.597	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2		
DGCR14	8220	hgsc.bcm.edu	37	22	19122665	19122665	+	Silent	SNP	C	C	T	rs2240111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19122665C>T	ENST00000252137.6	-	9	1102	c.1059G>A	c.(1057-1059)gaG>gaA	p.E353E		NM_022719.2	NP_073210.1	Q96DF8	DGC14_HUMAN	DiGeorge syndrome critical region gene 14	353					mRNA splicing, via spliceosome (GO:0000398)|nervous system development (GO:0007399)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)	16	Colorectal(54;0.0993)					GACCCAGCCGCTCCCTGCGGC	0.647													C|||	832	0.166134	0.1203	0.1326	5008	,	,		15434	0.121		0.1869	False		,,,				2504	0.2771				p.E353E		Atlas-SNP	.											.	DGCR14	43	.	0			c.G1059A						PASS	.	C		513,3893	236.1+/-248.4	31,451,1721	68.0	61.0	64.0		1059	1.4	1.0	22	dbSNP_98	64	1729,6871	312.5+/-310.9	187,1355,2758	no	coding-synonymous	DGCR14	NM_022719.2		218,1806,4479	TT,TC,CC		20.1047,11.6432,17.2382		353/477	19122665	2242,10764	2203	4300	6503	SO:0001819	synonymous_variant	8220	exon9			CAGCCGCTCCCTG	L77566	CCDS13756.1	22q11.21	2007-02-20			ENSG00000100056	ENSG00000100056			16817	protein-coding gene	gene with protein product		601755	"""DiGeorge syndrome critical region gene 13"""	DGCR13		8776594, 9063747	Standard	NM_022719		Approved	DGSI, Es2el, ES2, DGS-H	uc002zou.3	Q96DF8	OTTHUMG00000150119	ENST00000252137.6:c.1059G>A	22.37:g.19122665C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	140	75	0.535714	NM_022719	Q49AH7|Q9BTZ4	Silent	SNP	ENST00000252137.6	37	CCDS13756.1																																																																																			C|0.835;A|0.001	.	strong		0.647	DGCR14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316432.2		
ARID4A	5926	hgsc.bcm.edu	37	14	58830978	58830978	+	Missense_Mutation	SNP	A	A	G	rs2230098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:58830978A>G	ENST00000355431.3	+	20	2544	c.2171A>G	c.(2170-2172)aAt>aGt	p.N724S	ARID4A_ENST00000395168.3_Missense_Mutation_p.N724S|ARID4A_ENST00000431317.2_Missense_Mutation_p.N724S|ARID4A_ENST00000348476.3_Missense_Mutation_p.N724S	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	724			N -> S (in dbSNP:rs2230098).		erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						CTAGAAAAAAATGAAAATTTG	0.294													A|||	102	0.0203674	0.0053	0.0288	5008	,	,		14410	0.0		0.0636	False		,,,				2504	0.0112				p.N724S		Atlas-SNP	.											ARID4A_ENST00000355431,NS,carcinoma,0,2	ARID4A	222	2	0			c.A2171G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	63,3987		1,61,1963	33.0	38.0	37.0		2171,2171,2171	-3.3	0.6	14	dbSNP_98	37	380,8028		11,358,3835	yes	missense,missense,missense	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	46,46,46	12,419,5798	GG,GA,AA		4.5195,1.5556,3.5559	benign,benign,benign	724/1258,724/1204,724/1189	58830978	443,12015	2025	4204	6229	SO:0001583	missense	5926	exon20			AAAAAAATGAAAA	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2171A>G	14.37:g.58830978A>G	ENSP00000347602:p.Asn724Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	77	0.035256410256410256	4	0.008130081300813009	16	0.04419889502762431	0	0.0	57	0.07519788918205805	A	1.661	-0.511356	0.04231	0.015556	0.045195	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.13657	2.59;2.57;2.58;2.57;2.58	5.8	-3.3	0.05003	.	0.814284	0.12258	N	0.485033	T	0.00210	0.0006	N	0.02916	-0.46	0.23304	N	0.997945	B;B;B	0.14438	0.003;0.001;0.01	B;B;B	0.12156	0.002;0.001;0.007	T	0.35599	-0.9782	10	0.06757	T	0.87	-2.9787	0.4068	0.00434	0.2723:0.2304:0.2701:0.2272	rs2230098;rs17214261;rs57895685;rs2230098	724;724;724	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	S	724;724;724;724;402	ENSP00000347602:N724S;ENSP00000344556:N724S;ENSP00000378597:N724S;ENSP00000397368:N724S;ENSP00000416053:N402S	ENSP00000344556:N724S	N	+	2	0	ARID4A	57900731	0.500000	0.26091	0.624000	0.29186	0.971000	0.66376	-0.200000	0.09478	-0.464000	0.06963	0.528000	0.53228	AAT	A|0.960;G|0.040	0.040	strong		0.294	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634369	32634369	+	Missense_Mutation	SNP	C	C	A	rs1049056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32634369C>A	ENST00000399082.3	-	1	60	c.16G>T	c.(16-18)Gct>Tct	p.A6S	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.A6S|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.A6S|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.A6S|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.A6S			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	6			A -> S (in allele DQB1*05:01 and allele DQB1*05:02; dbSNP:rs1049056).		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)"""	ATCCGCAAAGCCTTCTTCCAA	0.527									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1072	0.214058	0.2322	0.1527	5008	,	,		13934	0.2411		0.2008	False		,,,				2504	0.2188				p.A6S	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G16T						PASS	.	C	SER/ALA	803,3049		125,553,1248	41.0	40.0	41.0		16	-0.0	0.0	6	dbSNP_86	41	1475,6725		255,965,2880	yes	missense	HLA-DQB1	NM_002123.4	99	380,1518,4128	AA,AC,CC		17.9878,20.8463,18.9014	benign	6/262	32634369	2278,9774	1926	4100	6026	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GCAAAGCCTTCTT		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.16G>T	6.37:g.32634369C>A	ENSP00000382032:p.Ala6Ser	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	25	18	0.72	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		456	0.2087912087912088	125	0.2540650406504065	70	0.19337016574585636	90	0.15734265734265734	171	0.22559366754617413	.	11.39	1.624062	0.28889	0.208463	0.179878	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.05786	3.39;6.02;6.02;5.99;5.99	4.09	-0.0275	0.13926	.	2.706550	0.03300	U	0.188815	T	0.01835	0.0058	L	0.41415	1.275	0.80722	P	0.0	B;B;B;B	0.28512	0.214;0.004;0.002;0.002	B;B;B;B	0.24848	0.056;0.012;0.01;0.008	T	0.44314	-0.9336	9	0.56958	D	0.05	.	3.2401	0.06778	0.3581:0.4329:0.0:0.209	rs1049056;rs3189132	16;6;6;6	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	S	6	ENSP00000382032:A6S;ENSP00000382029:A6S;ENSP00000364080:A6S;ENSP00000407332:A6S;ENSP00000382034:A6S	ENSP00000364080:A6S	A	-	1	0	HLA-DQB1	32742347	0.001000	0.12720	0.024000	0.17045	0.005000	0.04900	0.222000	0.17699	0.070000	0.16634	0.460000	0.39030	GCT	C|0.811;A|0.189	0.189	strong		0.527	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
C6orf223	221416	hgsc.bcm.edu	37	6	43970658	43970658	+	Missense_Mutation	SNP	T	T	A	rs115402675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43970658T>A	ENST00000336600.5	+	4	544	c.524T>A	c.(523-525)cTt>cAt	p.L175H	C6orf223_ENST00000439969.2_3'UTR|RP5-1120P11.1_ENST00000422059.1_RNA|C6orf223_ENST00000448947.2_3'UTR|C6orf223_ENST00000442114.2_Missense_Mutation_p.L155H|RP5-1120P11.1_ENST00000607590.1_RNA	NM_001171992.1|NM_153246.4	NP_001165463.1|NP_694978.2	Q8N319	CF223_HUMAN	chromosome 6 open reading frame 223	175								p.L175H(1)		central_nervous_system(1)|lung(2)|pancreas(1)|prostate(1)|urinary_tract(1)	6	all_cancers(18;2.28e-07)|all_epithelial(2;1.62e-08)|Lung NSC(15;0.000172)|all_lung(25;0.000533)|Hepatocellular(11;0.00309)|Ovarian(13;0.0437)		all cancers(41;0.00141)|Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.217)			GAGTCCCTTCTTCGCGGCCTC	0.731													T|||	243	0.0485224	0.0711	0.0403	5008	,	,		9653	0.0476		0.0457	False		,,,				2504	0.0276				p.L175H		Atlas-SNP	.											C6orf223,NS,carcinoma,0,1	C6orf223	14	1	1	Substitution - Missense(1)	pancreas(1)	c.T524A						PASS	.	T	HIS/LEU,	261,4095		7,247,1924	11.0	15.0	14.0		524,	-4.4	0.0	6	dbSNP_132	14	263,8263		4,255,4004	yes	missense,utr-3	C6orf223	NM_153246.4,NM_001171992.1	99,	11,502,5928	AA,AT,TT		3.0847,5.9917,4.0677	probably-damaging,	175/243,	43970658	524,12358	2178	4263	6441	SO:0001583	missense	221416	exon4			CCCTTCTTCGCGG	BC032706	CCDS34459.1, CCDS55016.1	6p21.1	2012-09-05			ENSG00000181577	ENSG00000181577			28692	protein-coding gene	gene with protein product						12477932	Standard	NM_153246		Approved	MGC45491	uc003own.3	Q8N319	OTTHUMG00000014753	ENST00000336600.5:c.524T>A	6.37:g.43970658T>A	ENSP00000426159:p.Leu175His	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	22	0.594595	NM_153246	E9PB59|Q8N575	Missense_Mutation	SNP	ENST00000336600.5	37	CCDS34459.1	112	0.05128205128205128	34	0.06910569105691057	18	0.049723756906077346	23	0.04020979020979021	37	0.048812664907651716	T	10.08	1.252805	0.22965	0.059917	0.030847	ENSG00000181577	ENST00000336600	T	0.44482	0.92	3.15	-4.4	0.03600	.	1.404370	0.05315	N	0.525593	T	0.12646	0.0307	N	0.08118	0	0.09310	N	0.999996	D	0.55385	0.971	P	0.50490	0.642	T	0.07693	-1.0759	10	0.87932	D	0	.	5.4409	0.16509	0.0:0.218:0.5041:0.2779	.	175	Q8N319	CF223_HUMAN	H	175	ENSP00000426159:L175H	ENSP00000426159:L175H	L	+	2	0	C6orf223	44078636	0.000000	0.05858	0.000000	0.03702	0.235000	0.25334	0.573000	0.23699	-0.896000	0.03915	-0.496000	0.04628	CTT	T|0.955;A|0.045	0.045	strong		0.731	C6orf223-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040702.3	NM_153246	
DSG1	1828	hgsc.bcm.edu	37	18	28913599	28913599	+	Silent	SNP	C	C	T	rs12967407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:28913599C>T	ENST00000257192.4	+	7	944	c.732C>T	c.(730-732)ggC>ggT	p.G244G		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	244	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			ACCGAGATGGCGGGGCAGATG	0.423													C|||	1641	0.327676	0.292	0.2882	5008	,	,		18910	0.0665		0.501	False		,,,				2504	0.4949				p.G244G		Atlas-SNP	.											DSG1,colon,carcinoma,+2,1	DSG1	176	1	0			c.C732T	GRCh37	CM014354	DSG1	M	rs12967407	scavenged	.	C		1396,3010	460.0+/-352.4	216,964,1023	141.0	127.0	132.0		732	-11.6	0.2	18	dbSNP_121	132	4281,4319	575.4+/-390.2	1043,2195,1062	no	coding-synonymous	DSG1	NM_001942.2		1259,3159,2085	TT,TC,CC		49.7791,31.6841,43.6491		244/1050	28913599	5677,7329	2203	4300	6503	SO:0001819	synonymous_variant	1828	exon7			AGATGGCGGGGCA	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.732C>T	18.37:g.28913599C>T		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	137	61	0.445255	NM_001942	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																			C|0.616;T|0.384	0.384	strong		0.423	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605344	84605344	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:84605344G>A	ENST00000344803.2	+	3	292	c.245G>A	c.(244-246)tGg>tAg	p.W82*		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	82					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTCCCAGACTGGAAAAGTTTC	0.433																																					p.W82X		Atlas-SNP	.											.	.	.	.	0			c.G245A						PASS	.						83.0	77.0	79.0					9																	84605344		1855	4089	5944	SO:0001587	stop_gained	389763	exon3			CAGACTGGAAAAG		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.245G>A	9.37:g.84605344G>A	ENSP00000341988:p.Trp82*	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	138	59	0.427536	NM_001001670		Nonsense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.828944	0.32329	.	.	ENSG00000214929	ENST00000344803	.	.	.	2.82	-3.37	0.04898	.	1.436640	0.04947	N	0.459585	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	10.638	4.091	0.09970	0.3449:0.3377:0.3174:0.0	.	.	.	.	X	82	.	ENSP00000341988:W82X	W	+	2	0	FAM75D1	83795164	0.039000	0.19947	0.000000	0.03702	0.000000	0.00434	0.316000	0.19469	-0.774000	0.04590	-0.902000	0.02854	TGG	.	.	none		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
GLTPD2	388323	hgsc.bcm.edu	37	17	4693054	4693054	+	Splice_Site	SNP	G	G	A	rs12951761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4693054G>A	ENST00000331264.7	+	4	392	c.339G>A	c.(337-339)gaG>gaA	p.E113E		NM_001014985.2	NP_001014985	A6NH11	GLTD2_HUMAN	glycolipid transfer protein domain containing 2	113						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						TCGCCCGCAGGTTCCTGACTC	0.682													G|||	2567	0.51258	0.7557	0.5216	5008	,	,		14032	0.4494		0.4722	False		,,,				2504	0.2843				p.E113E		Atlas-SNP	.											.	GLTPD2	15	.	0			c.G339A						PASS	.	G		3050,1318		1085,880,219	22.0	22.0	22.0		339	0.3	1.0	17	dbSNP_121	22	4087,4467		995,2097,1185	no	coding-synonymous-near-splice	GLTPD2	NM_001014985.2		2080,2977,1404	AA,AG,GG		47.7788,30.174,44.7686		113/292	4693054	7137,5785	2184	4277	6461	SO:0001630	splice_region_variant	388323	exon4			CCGCAGGTTCCTG	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.339-1G>A	17.37:g.4693054G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_001014985	A7E2T2	Silent	SNP	ENST00000331264.7	37	CCDS32534.1																																																																																			G|0.443;A|0.557	0.557	strong		0.682	GLTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439781.1	NM_001014985	Silent
SLC30A8	169026	hgsc.bcm.edu	37	8	118184783	118184783	+	Missense_Mutation	SNP	C	C	T	rs13266634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:118184783C>T	ENST00000456015.2	+	8	973	c.973C>T	c.(973-975)Cgg>Tgg	p.R325W	SLC30A8_ENST00000521243.1_Missense_Mutation_p.R276W|SLC30A8_ENST00000427715.2_Missense_Mutation_p.R276W|SLC30A8_ENST00000519688.1_Missense_Mutation_p.R276W	NM_173851.2	NP_776250.2	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8	325			R -> Q (in dbSNP:rs16889462).|R -> W (in dbSNP:rs13266634). {ECO:0000269|PubMed:17293876}.		cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			AGCAGCCAGCCGGGACAGCCA	0.488													C|||	1278	0.255192	0.0741	0.2666	5008	,	,		19655	0.4573		0.2833	False		,,,				2504	0.2546				p.R325W	Ovarian(162;1202 1922 6011 16223 52092)	Atlas-SNP	.											.	SLC30A8	102	.	0			c.C973T	GRCh37	CM072050	SLC30A8	M	rs13266634	PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	426,3980	206.2+/-227.9	18,390,1795	85.0	83.0	84.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	826,826,826,826,973	-1.8	0.9	8	dbSNP_121	84	2564,6036	418.7+/-352.8	398,1768,2134	yes	missense,missense,missense,missense,missense	SLC30A8	NM_001172811.1,NM_001172813.1,NM_001172814.1,NM_001172815.1,NM_173851.2	101,101,101,101,101	416,2158,3929	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	29.814,9.6686,22.9894	benign,benign,benign,benign,benign	276/321,276/321,276/321,276/321,325/370	118184783	2990,10016	2203	4300	6503	SO:0001583	missense	169026	exon8			GCCAGCCGGGACA		CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"""Solute carriers"""	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000456015.2:c.973C>T	8.37:g.118184783C>T	ENSP00000415011:p.Arg325Trp	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	90	60	0.666667	NM_173851	A0AVP9|A5YM39|B4DPE0|Q8TCL3	Missense_Mutation	SNP	ENST00000456015.2	37	CCDS6322.1	616	0.28205128205128205	41	0.08333333333333333	95	0.26243093922651933	263	0.4597902097902098	217	0.2862796833773087	C	11.92	1.783088	0.31593	0.096686	0.29814	ENSG00000164756	ENST00000521243;ENST00000427715;ENST00000519688;ENST00000456015	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.15	-1.75	0.08031	.	1.130630	0.06487	N	0.733902	T	0.00012	0.0000	L	0.49778	1.585	0.54753	P	1.2000000000012001E-5	B	0.09022	0.002	B	0.04013	0.001	T	0.42982	-0.9419	9	0.62326	D	0.03	0.3986	0.8731	0.01218	0.2334:0.3419:0.1149:0.3098	rs13266634;rs17813302;rs57876063;rs13266634	325	Q8IWU4	ZNT8_HUMAN	W	276;276;276;325	ENSP00000428545:R276W;ENSP00000407505:R276W;ENSP00000431069:R276W;ENSP00000415011:R325W	ENSP00000407505:R276W	R	+	1	2	SLC30A8	118253964	0.000000	0.05858	0.922000	0.36590	0.584000	0.36387	-0.403000	0.07214	-0.224000	0.09928	0.650000	0.86243	CGG	C|0.758;T|0.242	0.242	strong		0.488	SLC30A8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381205.1	NM_173851	
STX16	8675	hgsc.bcm.edu	37	20	57244493	57244493	+	Silent	SNP	G	G	A	rs2296524	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:57244493G>A	ENST00000371141.4	+	5	1264	c.540G>A	c.(538-540)caG>caA	p.Q180Q	STX16-NPEPL1_ENST00000530122.1_Silent_p.Q180Q|STX16_ENST00000496003.1_Intron|STX16_ENST00000361830.3_Silent_p.Q180Q|STX16_ENST00000355957.5_Silent_p.Q163Q|STX16_ENST00000361770.5_Silent_p.Q163Q|STX16_ENST00000359617.4_Silent_p.Q127Q|STX16_ENST00000358029.4_Silent_p.Q176Q|STX16_ENST00000371132.4_Silent_p.Q159Q	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	180					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			GGCACGCACAGTCAGGCTACC	0.562													G|||	2376	0.474441	0.5008	0.4553	5008	,	,		17396	0.4147		0.5	False		,,,				2504	0.4877				p.Q180Q		Atlas-SNP	.											.	STX16	36	.	0			c.G540A						PASS	.	G	,,,,	2120,2260		535,1050,605	16.0	18.0	18.0		540,528,489,381,477	3.9	1.0	20	dbSNP_100	18	4561,3997		1239,2083,957	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STX16	NM_001001433.2,NM_001134772.2,NM_001134773.2,NM_001204868.1,NM_003763.5	,,,,	1774,3133,1562	AA,AG,GG		46.7048,48.4018,48.3614	,,,,	180/326,176/322,163/309,127/273,159/305	57244493	6681,6257	2190	4279	6469	SO:0001819	synonymous_variant	8675	exon5			CGCACAGTCAGGC	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.540G>A	20.37:g.57244493G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	37	CCDS13468.1																																																																																			G|0.492;A|0.508	0.508	strong		0.562	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766045	27766045	+	Missense_Mutation	SNP	A	A	G	rs5926895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:27766045A>G	ENST00000451261.2	+	5	1432	c.1033A>G	c.(1033-1035)Acc>Gcc	p.T345A		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	345			T -> A (in dbSNP:rs5926895).							central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TGTTGTCTTCACCATTGACCT	0.478													A|||	627	0.166093	0.0613	0.1427	3775	,	,		14904	0.0575		0.2714	False		,,,				2504	0.1186				p.T345A		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A1033G						PASS	.	A	ALA/THR	164,1045		7,129,21,381,154	89.0	62.0	70.0		1033	0.1	0.0	X	dbSNP_114	70	886,1505		111,355,309,334,482	yes	missense	DCAF8L2	NM_001136533.1	58	118,484,330,715,636	GG,GA,G,AA,A		37.0556,13.5649,29.1667	benign	345/632	27766045	1050,2550	692	1591	2283	SO:0001583	missense	347442	exon1			GTCTTCACCATTG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1033A>G	X.37:g.27766045A>G	ENSP00000462745:p.Thr345Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			A|0.784;0|0.046	.	strong		0.478	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
SLC41A1	254428	hgsc.bcm.edu	37	1	205767885	205767885	+	Silent	SNP	G	G	A	rs708727	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:205767885G>A	ENST00000367137.3	-	6	1770	c.756C>T	c.(754-756)aaC>aaT	p.N252N	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	252					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	17	Breast(84;0.0799)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			GTGTGGCCACGTTGTCTGGGT	0.577													G|||	708	0.141374	0.0227	0.2291	5008	,	,		18060	0.003		0.3966	False		,,,				2504	0.1196				p.N252N		Atlas-SNP	.											SLC41A1,colon,carcinoma,0,1	SLC41A1	46	1	0			c.C756T						PASS	.	G		368,4038	187.4+/-214.1	24,320,1859	103.0	96.0	99.0		756	-2.1	1.0	1	dbSNP_86	99	3492,5108	511.3+/-377.7	710,2072,1518	no	coding-synonymous	SLC41A1	NM_173854.4		734,2392,3377	AA,AG,GG		40.6047,8.3522,29.6786		252/514	205767885	3860,9146	2203	4300	6503	SO:0001819	synonymous_variant	254428	exon6			GGCCACGTTGTCT	AJ514402	CCDS30988.1	1q32.1	2013-07-17	2013-07-17		ENSG00000133065	ENSG00000133065		"""Solute carriers"""	19429	protein-coding gene	gene with protein product		610801				12810078, 18367447	Standard	NM_173854		Approved	MgtE	uc001hdh.1	Q8IVJ1	OTTHUMG00000036000	ENST00000367137.3:c.756C>T	1.37:g.205767885G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	253	253	1	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Silent	SNP	ENST00000367137.3	37	CCDS30988.1																																																																																			G|0.751;A|0.249	0.249	strong		0.577	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1		
ITIH3	3699	hgsc.bcm.edu	37	3	52833805	52833805	+	Missense_Mutation	SNP	C	C	A	rs3617	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52833805C>A	ENST00000449956.2	+	9	949	c.943C>A	c.(943-945)Caa>Aaa	p.Q315K	ITIH3_ENST00000465243.2_3'UTR|ITIH3_ENST00000416872.2_Missense_Mutation_p.Q315K	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	315	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		Q -> K (in dbSNP:rs3617). {ECO:0000269|PubMed:7681778}.		hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GGAAGATATGCAAGAGGAAGA	0.537													A|||	2723	0.54373	0.7663	0.6095	5008	,	,		19671	0.4137		0.4841	False		,,,				2504	0.3916				p.Q315K		Atlas-SNP	.											ITIH3_ENST00000449956,NS,carcinoma,0,2	ITIH3	132	2	0			c.C943A						PASS	.	A	LYS/GLN	2690,1098		934,822,138	60.0	64.0	63.0		943	4.2	0.0	3	dbSNP_36	63	3852,4422		917,2018,1202	yes	missense	ITIH3	NM_002217.3	53	1851,2840,1340	AA,AC,CC		46.5555,28.9863,45.7636	benign	315/891	52833805	6542,5520	1894	4137	6031	SO:0001583	missense	3699	exon9			GATATGCAAGAGG		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"""pre-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha-trypsin inhibitor heavy chain H3"""	146650	"""inter-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha (globulin) inhibitor H3"""			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.943C>A	3.37:g.52833805C>A	ENSP00000415769:p.Gln315Lys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Missense_Mutation	SNP	ENST00000449956.2	37	CCDS46845.1	1234	0.565018315018315	366	0.7439024390243902	226	0.6243093922651933	269	0.47027972027972026	373	0.4920844327176781	A	1.453	-0.564539	0.03939	0.710137	0.465555	ENSG00000162267	ENST00000398670;ENST00000536431;ENST00000273291;ENST00000416872;ENST00000449956	D;D	0.82803	-1.65;-1.65	5.33	4.15	0.48705	von Willebrand factor, type A (3);	0.296777	0.41500	N	0.000863	T	0.00012	0.0000	N	0.01091	-1.02	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46638	-0.9177	9	0.15066	T	0.55	-9.9923	11.8647	0.52486	0.5731:0.4269:0.0:0.0	rs3617;rs52792886;rs59027071;rs3617	315;315	E7ET33;Q06033	.;ITIH3_HUMAN	K	315;303;310;315;315	ENSP00000413922:Q315K;ENSP00000415769:Q315K	ENSP00000273291:Q310K	Q	+	1	0	ITIH3	52808845	0.000000	0.05858	0.004000	0.12327	0.164000	0.22412	0.355000	0.20163	0.453000	0.26858	-0.256000	0.11100	CAA	T|0.010;G|0.001	.	strong		0.537	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217	
HELZ	9931	hgsc.bcm.edu	37	17	65103373	65103373	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:65103373T>C	ENST00000358691.5	-	31	5319	c.5153A>G	c.(5152-5154)cAg>cGg	p.Q1718R	HELZ_ENST00000580168.1_Missense_Mutation_p.Q1719R	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1718						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)					TTGATGATTCTGTATTTGTAC	0.453																																					p.Q1718R		Atlas-SNP	.											.	HELZ	160	.	0			c.A5153G						PASS	.						185.0	192.0	190.0					17																	65103373		1974	4156	6130	SO:0001583	missense	9931	exon31			TGATTCTGTATTT	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.5153A>G	17.37:g.65103373T>C	ENSP00000351524:p.Gln1718Arg	Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	315	147	0.466667	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.815470	0.32145	.	.	ENSG00000198265	ENST00000358691	D	0.88201	-2.35	5.31	4.2	0.49525	.	0.067201	0.64402	D	0.000013	T	0.80909	0.4714	L	0.29908	0.895	0.44048	D	0.996786	P;P	0.37466	0.596;0.596	B;B	0.29785	0.107;0.107	T	0.79995	-0.1568	10	0.87932	D	0	-4.8142	12.192	0.54277	0.0:0.0:0.1429:0.8571	.	1719;1718	B7ZLW2;P42694	.;HELZ_HUMAN	R	1718	ENSP00000351524:Q1718R	ENSP00000351524:Q1718R	Q	-	2	0	HELZ	62533835	1.000000	0.71417	0.982000	0.44146	0.993000	0.82548	2.537000	0.45702	0.827000	0.34685	0.472000	0.43445	CAG	.	.	none		0.453	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
LKAAEAR1	198437	hgsc.bcm.edu	37	20	62714783	62714783	+	3'UTR	SNP	C	C	G	rs6010717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62714783C>G	ENST00000302096.4	-	0	729				OPRL1_ENST00000336866.2_Intron|C20orf201_ENST00000308906.2_Silent_p.A226A|OPRL1_ENST00000349451.3_5'Flank|OPRL1_ENST00000355631.4_Intron			Q8TD35	LKAM1_HUMAN																			CACTCTCAGTCGCCGTCACCG	0.647													C|||	3128	0.624601	0.6422	0.6628	5008	,	,		12748	0.7093		0.6531	False		,,,				2504	0.4571				p.A226A		Atlas-SNP	.											C20orf201,NS,carcinoma,0,1	C20orf201	4	1	0			c.G678C						PASS	.	C	,,	2796,1604		875,1046,279	21.0	23.0	22.0		,678,	1.4	0.0	20	dbSNP_114	22	5362,3220		1675,2012,604	no	intron,coding-synonymous,intron	OPRL1,C20orf201	NM_000913.4,NM_001007125.1,NM_182647.2	,,	2550,3058,883	GG,GC,CC		37.5204,36.4545,37.1591	,,	,226/241,	62714783	8158,4824	2200	4291	6491	SO:0001624	3_prime_UTR_variant	198437	exon2			CTCAGTCGCCGTC																												ENST00000302096.4:c.*5G>C	20.37:g.62714783C>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001007125	Q8N419|Q8TD36	Silent	SNP	ENST00000302096.4	37																																																																																				C|0.368;G|0.632	0.632	strong		0.647	C20orf201-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000080270.2		
DHTKD1	55526	hgsc.bcm.edu	37	10	12131218	12131218	+	Silent	SNP	C	C	T	rs3740016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:12131218C>T	ENST00000263035.4	+	5	1013	c.951C>T	c.(949-951)aaC>aaT	p.N317N	DHTKD1_ENST00000465617.1_Intron	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	317					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.N317N(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			CTCCAGACAACTCAGCCCAGC	0.597													C|||	255	0.0509185	0.0061	0.0504	5008	,	,		18289	0.0179		0.1133	False		,,,				2504	0.0818				p.N317N		Atlas-SNP	.											DHTKD1,NS,carcinoma,0,1	DHTKD1	104	1	1	Substitution - coding silent(1)	stomach(1)	c.C951T						PASS	.	C		112,4294	84.4+/-122.9	3,106,2094	53.0	55.0	54.0		951	-1.3	0.0	10	dbSNP_107	54	1066,7534	222.7+/-259.7	60,946,3294	no	coding-synonymous	DHTKD1	NM_018706.5		63,1052,5388	TT,TC,CC		12.3953,2.542,9.0574		317/920	12131218	1178,11828	2203	4300	6503	SO:0001819	synonymous_variant	55526	exon5			AGACAACTCAGCC	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.951C>T	10.37:g.12131218C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Silent	SNP	ENST00000263035.4	37	CCDS7087.1																																																																																			C|0.923;T|0.077	0.077	strong		0.597	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706	
VARS2	57176	hgsc.bcm.edu	37	6	30882634	30882634	+	Silent	SNP	C	C	T	rs1264302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30882634C>T	ENST00000321897.5	+	1	653	c.21C>T	c.(19-21)gcC>gcT	p.A7A	VARS2_ENST00000541562.1_Silent_p.A37A|VARS2_ENST00000542001.1_Intron|VARS2_ENST00000416670.2_Silent_p.A7A			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	7					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						TGCCTCTCGCCTCTTTTCGAC	0.562													C|||	1112	0.222045	0.0983	0.2075	5008	,	,		19658	0.247		0.3559	False		,,,				2504	0.2362				p.A37A		Atlas-SNP	.											.	VARS2	60	.	0			c.C111T						PASS	.	C	,,	439,2579		33,373,1103	52.0	57.0	55.0		,111,21	-0.9	0.0	6	dbSNP_87	55	2036,3380		362,1312,1034	no	intron,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	395,1685,2137	TT,TC,CC		37.5923,14.5461,29.3455	,,	,37/1094,7/1064	30882634	2475,5959	1509	2708	4217	SO:0001819	synonymous_variant	57176	exon2			TCTCGCCTCTTTT	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.21C>T	6.37:g.30882634C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			C|0.733;T|0.267	0.267	strong		0.562	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
XIRP2	129446	hgsc.bcm.edu	37	2	168104199	168104199	+	Silent	SNP	C	C	T	rs7581190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168104199C>T	ENST00000409195.1	+	9	6386	c.6297C>T	c.(6295-6297)gaC>gaT	p.D2099D	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.D1877D|XIRP2_ENST00000295237.9_Silent_p.D2099D|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1924					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGAATCAGACAGGGCAGTGA	0.383													C|||	865	0.172724	0.2882	0.1196	5008	,	,		18181	0.12		0.1123	False		,,,				2504	0.1708				p.D2099D		Atlas-SNP	.											.	XIRP2	914	.	0			c.C6297T						PASS	.	C	,,,,	971,2885		131,709,1088	56.0	52.0	53.0		,,5631,,6297	4.1	0.9	2	dbSNP_116	53	800,7504		42,716,3394	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	173,1425,4482	TT,TC,CC		9.6339,25.1815,14.5641	,,,,	,,1877/3328,,2099/3550	168104199	1771,10389	1928	4152	6080	SO:0001819	synonymous_variant	129446	exon9			ATCAGACAGGGCA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6297C>T	2.37:g.168104199C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	130	68	0.523077	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			C|0.840;T|0.160	0.160	strong		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
NRXN3	9369	hgsc.bcm.edu	37	14	79181226	79181226	+	Silent	SNP	C	C	T	rs1004212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:79181226C>T	ENST00000554719.1	+	5	1160	c.669C>T	c.(667-669)acC>acT	p.T223T	NRXN3_ENST00000335750.5_Silent_p.T223T	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	0	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|angiogenesis (GO:0001525)|learning (GO:0007612)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(23)|lung(40)|ovary(3)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(9)|urinary_tract(1)	104		Renal(4;0.00876)		BRCA - Breast invasive adenocarcinoma(234;0.00544)|Kidney(3;0.029)|KIRC - Kidney renal clear cell carcinoma(182;0.223)		TTCTCCCCACCGAGCTGTGGA	0.597													C|||	984	0.196486	0.3366	0.1066	5008	,	,		19461	0.0625		0.1471	False		,,,				2504	0.2597				p.T223T		Atlas-SNP	.											.	NRXN3	342	.	0			c.C669T						PASS	.	C		1298,3108	438.6+/-345.4	204,890,1109	86.0	73.0	77.0		669	-11.7	0.1	14	dbSNP_86	77	1263,7337	251.8+/-278.1	89,1085,3126	no	coding-synonymous	NRXN3	NM_004796.4		293,1975,4235	TT,TC,CC		14.686,29.4598,19.6909		223/1062	79181226	2561,10445	2203	4300	6503	SO:0001819	synonymous_variant	9369	exon5			CCCCACCGAGCTG	AB018286	CCDS9870.1, CCDS9871.1, CCDS45145.1, CCDS61515.1	14q31	2010-01-19				ENSG00000021645			8010	protein-coding gene	gene with protein product		600567	"""chromosome 14 open reading frame 60"""	C14orf60		11944992, 12379233	Standard	NM_004796		Approved	KIAA0743	uc001xun.4	Q9HDB5		ENST00000554719.1:c.669C>T	14.37:g.79181226C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	209	110	0.526316	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Silent	SNP	ENST00000554719.1	37	CCDS9870.1																																																																																			C|0.808;T|0.192	0.192	strong		0.597	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250	
ZC3H3	23144	hgsc.bcm.edu	37	8	144623574	144623574	+	Missense_Mutation	SNP	T	T	C	rs2242093	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144623574T>C	ENST00000262577.5	-	1	49	c.18A>G	c.(16-18)atA>atG	p.I6M	RP11-661A12.5_ENST00000530600.1_RNA|7SK_ENST00000517300.1_RNA	NM_015117.2	NP_055932.2	Q8IXZ2	ZC3H3_HUMAN	zinc finger CCCH-type containing 3	6			I -> M (in dbSNP:rs2242093). {ECO:0000269|PubMed:15489334}.		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)			GCCGCCGTAATATCTCCTTTT	0.716													T|||	873	0.174321	0.0129	0.1009	5008	,	,		13418	0.4573		0.1561	False		,,,				2504	0.1718				p.I6M		Atlas-SNP	.											.	ZC3H3	75	.	0			c.A18G						PASS	.	T	MET/ILE	141,4265	97.6+/-136.3	3,135,2065	37.0	44.0	41.0		18	0.1	0.8	8	dbSNP_98	41	1378,7214	259.0+/-282.4	125,1128,3043	yes	missense	ZC3H3	NM_015117.2	10	128,1263,5108	CC,CT,TT		16.0382,3.2002,11.6864	possibly-damaging	6/949	144623574	1519,11479	2203	4296	6499	SO:0001583	missense	23144	exon1			CCGTAATATCTCC	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.18A>G	8.37:g.144623574T>C	ENSP00000262577:p.Ile6Met	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_015117	Q14163|Q8N4E2|Q9BUS4	Missense_Mutation	SNP	ENST00000262577.5	37	CCDS6402.1	437	0.2000915750915751	10	0.02032520325203252	54	0.14917127071823205	252	0.4405594405594406	121	0.15963060686015831	T	14.60	2.585265	0.46110	0.032002	0.160382	ENSG00000014164	ENST00000262577	T	0.02656	4.21	3.71	0.0969	0.14492	.	1.554190	0.04131	N	0.317912	T	0.00012	0.0000	N	0.22421	0.69	0.53688	P	2.8000000000028002E-5	B	0.23185	0.081	B	0.18871	0.023	T	0.44997	-0.9291	9	0.36615	T	0.2	-0.7387	6.9799	0.24698	0.0:0.6088:0.0:0.3912	rs2242093;rs61035733;rs2242093	6	Q8IXZ2	ZC3H3_HUMAN	M	6	ENSP00000262577:I6M	ENSP00000262577:I6M	I	-	3	3	ZC3H3	144694717	0.958000	0.32768	0.762000	0.31397	0.895000	0.52256	0.140000	0.16056	0.154000	0.19237	0.454000	0.30748	ATA	T|0.850;C|0.150	0.150	strong		0.716	ZC3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382011.2	NM_015117	
GPR144	347088	hgsc.bcm.edu	37	9	127215778	127215778	+	Missense_Mutation	SNP	C	C	T	rs67997410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:127215778C>T	ENST00000334810.1	+	4	802	c.802C>T	c.(802-804)Ctc>Ttc	p.L268F				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	268	Pentaxin.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						GCGTCACGCCCTCAGCGGCAA	0.756													T|||	3825	0.763778	0.9486	0.7363	5008	,	,		6605	0.8631		0.5736	False		,,,				2504	0.6268				p.L268F		Atlas-SNP	.											GPR144,rectum,carcinoma,0,1	GPR144	33	1	0			c.C802T						PASS	.						4.0	5.0	4.0					9																	127215778		654	1509	2163	SO:0001583	missense	347088	exon4			CACGCCCTCAGCG	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.802C>T	9.37:g.127215778C>T	ENSP00000335156:p.Leu268Phe	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1591	0.7284798534798534	428	0.8699186991869918	247	0.6823204419889503	488	0.8531468531468531	428	0.5646437994722955	T	0.219	-1.029965	0.02045	.	.	ENSG00000180264	ENST00000334810	T	0.51817	0.69	3.81	2.61	0.31194	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.00205	-1.85	0.52501	P	4.199999999998649E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.27606	-1.0069	8	0.12103	T	0.63	.	4.8806	0.13677	0.1631:0.0944:0.0:0.7425	.	268	Q7Z7M1	GP144_HUMAN	F	268	ENSP00000335156:L268F	ENSP00000335156:L268F	L	+	1	0	GPR144	126255599	1.000000	0.71417	0.629000	0.29254	0.351000	0.29236	3.633000	0.54295	-0.045000	0.13468	-0.817000	0.03123	CTC	C|0.271;T|0.729	0.729	strong		0.756	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
LCORL	254251	hgsc.bcm.edu	37	4	17886146	17886146	+	Missense_Mutation	SNP	A	A	G	rs17526944	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:17886146A>G	ENST00000382226.5	-	7	1114	c.1006T>C	c.(1006-1008)Tat>Cat	p.Y336H	LCORL_ENST00000382224.1_Missense_Mutation_p.Y252H|LCORL_ENST00000539056.1_Intron|LCORL_ENST00000326877.4_Intron	NM_001166139.1	NP_001159611.1	Q8N3X6	LCORL_HUMAN	ligand dependent nuclear receptor corepressor-like	336					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)			kidney(1)|large_intestine(1)|lung(1)|prostate(1)	4						CTGTCCTTATATGAATAACTA	0.388													A|||	139	0.0277556	0.0008	0.0245	5008	,	,		19488	0.0		0.0577	False		,,,				2504	0.0644				p.Y336H		Atlas-SNP	.											.	LCORL	60	.	0			c.T1006C						PASS	.	A	HIS/TYR,	14,1370		0,14,678	96.0	80.0	85.0		1006,	4.2	1.0	4	dbSNP_123	85	207,2973		8,191,1391	yes	missense,intron	LCORL	NM_001166139.1,NM_153686.7	83,	8,205,2069	GG,GA,AA		6.5094,1.0116,4.8422	,	336/603,	17886146	221,4343	692	1590	2282	SO:0001583	missense	254251	exon7			CCTTATATGAATA		CCDS3425.1, CCDS54749.1	4p15.32	2006-06-14			ENSG00000178177	ENSG00000178177			30776	protein-coding gene	gene with protein product		611799				12560079	Standard	NM_153686		Approved	MLR1, FLJ30696	uc021xmr.1	Q8N3X6	OTTHUMG00000128538	ENST00000382226.5:c.1006T>C	4.37:g.17886146A>G	ENSP00000371661:p.Tyr336His	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	166	75	0.451807	NM_001166139	Q96NK1	Missense_Mutation	SNP	ENST00000382226.5	37	CCDS54749.1	59	0.027014652014652016	3	0.006097560975609756	14	0.03867403314917127	0	0.0	42	0.055408970976253295	A	3.788	-0.044233	0.07452	0.010116	0.065094	ENSG00000178177	ENST00000382224;ENST00000382226	.	.	.	5.34	4.16	0.48862	.	0.808427	0.11700	N	0.538015	T	0.02571	0.0078	N	0.08118	0	0.34042	D	0.655142	.	.	.	.	.	.	T	0.19647	-1.0299	7	0.25106	T	0.35	.	11.1628	0.48526	0.9277:0.0:0.0723:0.0	rs17526944;rs17526944	.	.	.	H	252;336	.	ENSP00000371659:Y252H	Y	-	1	0	LCORL	17495244	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.093000	0.50217	0.986000	0.38683	0.533000	0.62120	TAT	A|0.972;G|0.028	0.028	strong		0.388	LCORL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_153686	
C2orf16	84226	hgsc.bcm.edu	37	2	27801403	27801403	+	Missense_Mutation	SNP	C	C	G	rs1919125	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27801403C>G	ENST00000408964.2	+	1	2015	c.1964C>G	c.(1963-1965)aCt>aGt	p.T655S		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	655			T -> S (in dbSNP:rs1919125).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AGTCCATGTACTCAAGTGAAG	0.393													T|||	3303	0.659545	0.7368	0.6888	5008	,	,		21823	0.8462		0.498	False		,,,				2504	0.5082				p.T655S		Atlas-SNP	.											.	C2orf16	357	.	0			c.C1964G						PASS	.	T	SER/THR	2616,1152		902,812,170	97.0	95.0	95.0		1964	-0.7	0.0	2	dbSNP_92	95	4085,4151		1029,2027,1062	yes	missense	C2orf16	NM_032266.3	58	1931,2839,1232	GG,GC,CC		49.5993,30.5732,44.1769	benign	655/1985	27801403	6701,5303	1884	4118	6002	SO:0001583	missense	84226	exon1			CATGTACTCAAGT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1964C>G	2.37:g.27801403C>G	ENSP00000386190:p.Thr655Ser	Somatic	298	1	0.0033557		WXS	Illumina HiSeq	Phase_I	250	106	0.424	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	1448	0.663003663003663	359	0.7296747967479674	229	0.6325966850828729	490	0.8566433566433567	370	0.48812664907651715	T	0.082	-1.181599	0.01633	0.694268	0.495993	ENSG00000221843	ENST00000408964	T	0.05649	3.41	4.27	-0.677	0.11357	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.12218	-1.0556	8	0.10377	T	0.69	.	5.683	0.17786	0.0:0.2722:0.5177:0.2101	rs1919125;rs17756208;rs60093522;rs1919125	655	Q68DN1	CB016_HUMAN	S	655	ENSP00000386190:T655S	ENSP00000386190:T655S	T	+	2	0	C2orf16	27654907	0.001000	0.12720	0.040000	0.18447	0.033000	0.12548	-0.497000	0.06428	-0.356000	0.08187	-1.482000	0.00985	ACT	C|0.375;G|0.625	0.625	strong		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
POLR3A	11128	hgsc.bcm.edu	37	10	79744042	79744042	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:79744042G>T	ENST00000372371.3	-	25	3394	c.3257C>A	c.(3256-3258)aCa>aAa	p.T1086K		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1086					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			TAGCTGTGCTGTGATAATTGG	0.458																																					p.T1086K		Atlas-SNP	.											.	POLR3A	104	.	0			c.C3257A						PASS	.						111.0	97.0	102.0					10																	79744042		2203	4300	6503	SO:0001583	missense	11128	exon25			TGTGCTGTGATAA	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.3257C>A	10.37:g.79744042G>T	ENSP00000361446:p.Thr1086Lys	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.717429	0.68844	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.77489	-1.1	5.62	5.62	0.85841	RNA polymerase Rpb1, domain 5 (1);	0.051059	0.85682	D	0.000000	D	0.87951	0.6307	M	0.80508	2.5	0.80722	D	1	P	0.48998	0.918	P	0.60345	0.873	D	0.87312	0.2312	9	.	.	.	-17.2577	19.6607	0.95868	0.0:0.0:1.0:0.0	.	1086	O14802	RPC1_HUMAN	K	1086;1065	ENSP00000361446:T1086K	.	T	-	2	0	POLR3A	79414048	1.000000	0.71417	0.970000	0.41538	0.983000	0.72400	7.320000	0.79064	2.660000	0.90430	0.650000	0.86243	ACA	.	.	none		0.458	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	
PRDM15	63977	hgsc.bcm.edu	37	21	43236176	43236176	+	Silent	SNP	G	G	A	rs4075967	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43236176G>A	ENST00000269844.3	-	26	3485	c.3375C>T	c.(3373-3375)caC>caT	p.H1125H	PRDM15_ENST00000538201.1_Silent_p.H779H|PRDM15_ENST00000422911.1_Silent_p.H816H|PRDM15_ENST00000447207.2_Silent_p.H759H|PRDM15_ENST00000398548.1_Silent_p.H796H	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1125					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GGCGCAGCGCGTGCTTGGTCT	0.637													g|||	886	0.176917	0.1324	0.2248	5008	,	,		18307	0.2054		0.1879	False		,,,				2504	0.1626				p.H1125H		Atlas-SNP	.											.	PRDM15	110	.	0			c.C3375T						PASS	.		,	679,3727	286.0+/-278.5	51,577,1575	146.0	104.0	118.0		2388,3375	0.6	1.0	21	dbSNP_108	118	1998,6602	350.1+/-327.7	230,1538,2532	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	281,2115,4107	AA,AG,GG		23.2326,15.4108,20.5828	,	796/1179,1125/1508	43236176	2677,10329	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon26			CAGCGCGTGCTTG	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3375C>T	21.37:g.43236176G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	164	87	0.530488	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			G|0.802;A|0.198	0.198	strong		0.637	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
PDXDC1	23042	hgsc.bcm.edu	37	16	15129970	15129970	+	Silent	SNP	A	A	G	rs7200543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15129970A>G	ENST00000396410.4	+	23	2302	c.2205A>G	c.(2203-2205)ctA>ctG	p.L735L	PDXDC1_ENST00000447912.2_Silent_p.L644L|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Silent_p.L707L|PDXDC1_ENST00000569715.1_Silent_p.L708L|PDXDC1_ENST00000325823.7_Silent_p.L720L|PDXDC1_ENST00000563679.1_Silent_p.L753L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	735					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGGAGCGCCTATCCAGTGGGC	0.582													G|||	1728	0.345048	0.1846	0.5331	5008	,	,		18589	0.371		0.3062	False		,,,				2504	0.4417				p.L735L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A2205G						PASS	.	G		989,3405	730.4+/-410.2	119,751,1327	120.0	120.0	120.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2205	4.7	0.1	16	dbSNP_116	120	2587,6013	689.7+/-404.4	359,1869,2072	yes	coding-synonymous	PDXDC1	NM_015027.2		478,2620,3399	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0814,22.508,27.5204		735/789	15129970	3576,9418	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon23			GCGCCTATCCAGT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.2205A>G	16.37:g.15129970A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			A|0.706;G|0.294	0.294	strong		0.582	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
DNHD1	144132	hgsc.bcm.edu	37	11	6524072	6524072	+	Missense_Mutation	SNP	A	A	C	rs11605196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6524072A>C	ENST00000527990.2	+	2	836	c.836A>C	c.(835-837)cAg>cCg	p.Q279P	DNHD1_ENST00000354685.3_Missense_Mutation_p.Q279P|DNHD1_ENST00000254579.6_Missense_Mutation_p.Q279P			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	279			Q -> P (in dbSNP:rs11605196).		microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CTGGATAGCCAGGTGATGACT	0.502													A|||	499	0.0996406	0.0408	0.147	5008	,	,		20522	0.0169		0.1789	False		,,,				2504	0.1493				p.Q279P		Atlas-SNP	.											.	DNHD1	198	.	0			c.A836C						PASS	.	A	PRO/GLN,PRO/GLN	277,4125	155.2+/-188.4	10,257,1934	122.0	102.0	109.0		836,836	4.5	0.0	11	dbSNP_120	109	1636,6956	302.2+/-305.8	165,1306,2825	yes	missense,missense	DNHD1	NM_144666.2,NM_173589.3	76,76	175,1563,4759	CC,CA,AA		19.041,6.2926,14.7222	benign,benign	279/4754,279/598	6524072	1913,11081	2201	4296	6497	SO:0001583	missense	144132	exon3			ATAGCCAGGTGAT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.836A>C	11.37:g.6524072A>C	ENSP00000436180:p.Gln279Pro	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_173589	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	224	0.10256410256410256	26	0.052845528455284556	46	0.1270718232044199	11	0.019230769230769232	141	0.18601583113456466	A	11.40	1.627054	0.28978	0.062926	0.19041	ENSG00000179532	ENST00000254579;ENST00000354685;ENST00000527990	T;T;T	0.27890	1.64;2.65;1.64	5.64	4.52	0.55395	.	0.540708	0.18166	N	0.149607	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	P;B	0.44578	0.838;0.004	B;B	0.41813	0.367;0.004	T	0.18178	-1.0345	9	0.28530	T	0.3	.	8.2343	0.31616	0.9095:0.0:0.0905:0.0	rs11605196;rs52824639;rs11605196	279;279	Q96M86;Q96M86-4	DNHD1_HUMAN;.	P	279	ENSP00000254579:Q279P;ENSP00000346716:Q279P;ENSP00000436180:Q279P	ENSP00000254579:Q279P	Q	+	2	0	DNHD1	6480648	0.000000	0.05858	0.019000	0.16419	0.032000	0.12392	0.115000	0.15540	0.971000	0.38288	0.460000	0.39030	CAG	A|0.862;C|0.138	0.138	strong		0.502	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
ZAK	51776	hgsc.bcm.edu	37	2	174055646	174055646	+	Silent	SNP	T	T	C	rs35853276	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:174055646T>C	ENST00000375213.3	+	6	517	c.439T>C	c.(439-441)Ttg>Ctg	p.L147L	MLTK_ENST00000480606.1_3'UTR|MLTK_ENST00000539448.1_Silent_p.L147L|MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000409176.2_Silent_p.L147L|MLTK_ENST00000431503.2_Silent_p.L46L|MLK7-AS1_ENST00000419609.1_RNA|MLTK_ENST00000338983.3_Silent_p.L147L	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		147	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										TGATGGAGTATTGAAGGTAGG	0.269													T|||	715	0.142772	0.3071	0.0821	5008	,	,		19235	0.0		0.1103	False		,,,				2504	0.1442				p.L147L		Atlas-SNP	.											.	ZAK	62	.	0			c.T439C						PASS	.	T	,	1068,3338	368.3+/-318.6	120,828,1255	67.0	76.0	73.0		439,439	-0.3	0.8	2	dbSNP_126	73	874,7720	195.1+/-240.3	49,776,3472	no	coding-synonymous,coding-synonymous	ZAK	NM_016653.2,NM_133646.2	,	169,1604,4727	CC,CT,TT		10.1699,24.2397,14.9385	,	147/801,147/456	174055646	1942,11058	2203	4297	6500	SO:0001819	synonymous_variant	0	exon6			GGAGTATTGAAGG																												ENST00000375213.3:c.439T>C	2.37:g.174055646T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_133646	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Silent	SNP	ENST00000375213.3	37	CCDS42777.1																																																																																			T|0.858;C|0.142	0.142	strong		0.269	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255401.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1248960	1248960	+	Silent	SNP	G	G	A	rs2075855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1248960G>A	ENST00000529681.1	+	7	781	c.723G>A	c.(721-723)acG>acA	p.T241T	MUC5B_ENST00000447027.1_Silent_p.T241T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	241	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ATGGGCCCACGGAGCAGTGCC	0.701													g|||	304	0.0607029	0.0219	0.1037	5008	,	,		14179	0.0456		0.0765	False		,,,				2504	0.0818				p.T241T		Atlas-SNP	.											MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	0			c.G723A						PASS	.	G		76,3702		0,76,1813	17.0	19.0	18.0		723	-7.0	0.8	11	dbSNP_96	18	483,7555		10,463,3546	no	coding-synonymous	MUC5B	NM_002458.2		10,539,5359	AA,AG,GG		6.009,2.0116,4.7309		241/5763	1248960	559,11257	1889	4019	5908	SO:0001819	synonymous_variant	727897	exon7			GCCCACGGAGCAG	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.723G>A	11.37:g.1248960G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.929;A|0.071	0.071	strong		0.701	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SP140	11262	hgsc.bcm.edu	37	2	231149097	231149097	+	Missense_Mutation	SNP	T	T	C	rs4972945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231149097T>C	ENST00000392045.3	+	16	1649	c.1535T>C	c.(1534-1536)aTg>aCg	p.M512T	SP140_ENST00000343805.6_Missense_Mutation_p.M452T|SP140_ENST00000417495.3_Missense_Mutation_p.M398T|SP140_ENST00000350136.5_Missense_Mutation_p.M381T|SP140_ENST00000486687.2_Missense_Mutation_p.M436T|SP140_ENST00000420434.3_Missense_Mutation_p.M485T	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	512			M -> T (in dbSNP:rs4972945).		defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AGAATGAGAATGAGAAGGCAG	0.383													T|||	384	0.0766773	0.0076	0.1095	5008	,	,		19523	0.1052		0.1272	False		,,,				2504	0.0654				p.M512T		Atlas-SNP	.											.	SP140	121	.	0			c.T1535C						PASS	.	T	THR/MET	83,3701		0,83,1809	105.0	115.0	112.0		1535	-5.8	0.0	2	dbSNP_111	112	993,7223		69,855,3184	yes	missense	SP140	NM_007237.4	81	69,938,4993	CC,CT,TT		12.0862,2.1934,8.9667	benign	512/868	231149097	1076,10924	1892	4108	6000	SO:0001583	missense	11262	exon16			TGAGAATGAGAAG	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.1535T>C	2.37:g.231149097T>C	ENSP00000375899:p.Met512Thr	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	206	101	0.490291	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	193	0.08836996336996338	7	0.014227642276422764	39	0.10773480662983426	58	0.10139860139860139	89	0.11741424802110818	T	2.324	-0.354881	0.05138	0.021934	0.120862	ENSG00000079263	ENST00000486687;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T;T	0.55760	0.71;0.98;0.77;0.5;0.79	2.91	-5.82	0.02333	.	.	.	.	.	T	0.00271	0.0008	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B	0.12013	0.0;0.0;0.0;0.005	B;B;B;B	0.09377	0.001;0.0;0.001;0.004	T	0.07121	-1.0789	8	0.29301	T	0.29	0.4595	1.4524	0.02378	0.1897:0.3793:0.1736:0.2575	rs4972945;rs12466261;rs16826973;rs52790583;rs4972945	485;398;452;512	E7EUR5;E7ESH9;E9PFJ6;Q13342	.;.;.;LY10_HUMAN	T	436;381;512;398;452;485	ENSP00000440107:M436T;ENSP00000345846:M381T;ENSP00000375899:M512T;ENSP00000342096:M452T;ENSP00000398210:M485T	ENSP00000342096:M452T	M	+	2	0	SP140	230857341	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.118000	0.01325	-1.695000	0.01423	-1.658000	0.00752	ATG	T|0.878;C|0.122	0.122	strong		0.383	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237	
SLC25A32	81034	hgsc.bcm.edu	37	8	104427359	104427359	+	5'Flank	SNP	A	A	C	rs3134295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:104427359A>C	ENST00000297578.4	-	0	0				DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'Flank|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000297579.5_Missense_Mutation_p.R47S	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	CGGGGCACAGACACTACGTCA	0.667													c|||	2145	0.428315	0.4985	0.4294	5008	,	,		16891	0.3462		0.4722	False		,,,				2504	0.3722				p.R47S		Atlas-SNP	.											DCAF13,NS,carcinoma,0,1	DCAF13	66	1	0			c.A141C						PASS	.	-	SER/ARG,	2186,2220		537,1112,554	46.0	45.0	45.0		141,	1.0	0.0	8	dbSNP_103	45	3825,4775		878,2069,1353	yes	missense,utr-5	DCAF13,SLC25A32	NM_015420.6,NM_030780.3	110,	1415,3181,1907	CC,CA,AA		44.4767,49.6142,46.2171	benign,	47/598,	104427359	6011,6995	2203	4300	6503	SO:0001631	upstream_gene_variant	25879	exon1			GCACAGACACTAC	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		8.37:g.104427359A>C	Exception_encountered	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_015420	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	983	0.4500915750915751	244	0.4959349593495935	170	0.4696132596685083	203	0.3548951048951049	366	0.48284960422163586	C	2.986	-0.209151	0.06140	0.496142	0.444767	ENSG00000164934	ENST00000297579	T	0.76968	-1.06	4.05	0.973	0.19710	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.53688	P	2.599999999997049E-5	.	.	.	.	.	.	T	0.34725	-0.9817	5	0.02654	T	1	1.0596	2.054	0.03577	0.357:0.3658:0.174:0.1032	rs3134295;rs52825097;rs57877210;rs3134295	.	.	.	S	47	ENSP00000297579:R47S	ENSP00000297579:R47S	R	+	3	2	DCAF13	104496535	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.250000	0.00540	0.137000	0.18759	-0.127000	0.14921	AGA	A|0.537;C|0.463	0.463	strong		0.667	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
STAMBPL1	57559	hgsc.bcm.edu	37	10	90673024	90673024	+	Missense_Mutation	SNP	G	G	A	rs12254856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90673024G>A	ENST00000371926.3	+	6	1545	c.587G>A	c.(586-588)aGt>aAt	p.S196N	STAMBPL1_ENST00000371924.1_Missense_Mutation_p.S196N|STAMBPL1_ENST00000371922.1_Missense_Mutation_p.S30N|STAMBPL1_ENST00000371927.3_Missense_Mutation_p.S196N	NM_020799.3	NP_065850.1	Q96FJ0	STALP_HUMAN	STAM binding protein-like 1	196			S -> N (in dbSNP:rs12254856).			membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			breast(2)|endometrium(1)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|skin(1)	11		Colorectal(252;0.0381)		Colorectal(12;6.38e-05)|COAD - Colon adenocarcinoma(12;7.75e-05)		CAAATGCGAAGTCAGCAAACC	0.483													G|||	448	0.0894569	0.1437	0.0879	5008	,	,		20632	0.003		0.1252	False		,,,				2504	0.0695				p.S196N		Atlas-SNP	.											.	STAMBPL1	63	.	0			c.G587A						PASS	.	G	ASN/SER	705,3701	294.7+/-283.3	56,593,1554	123.0	112.0	116.0		587	3.8	0.0	10	dbSNP_120	116	1228,7372	246.7+/-275.0	83,1062,3155	yes	missense	STAMBPL1	NM_020799.2	46	139,1655,4709	AA,AG,GG		14.2791,16.0009,14.8624	benign	196/437	90673024	1933,11073	2203	4300	6503	SO:0001583	missense	57559	exon6			TGCGAAGTCAGCA	AB037794	CCDS7391.1	10q23.32	2006-11-08			ENSG00000138134	ENSG00000138134			24105	protein-coding gene	gene with protein product	"""associated molecule with the SH3 domain of STAM (AMSH) like protein"", ""associated molecule with the SH3 domain of STAM (AMSH) - Family Protein"""	612352				12810066, 12943674	Standard	NM_020799		Approved	AMSH-LP, KIAA1373, AMSH-FP, FLJ31524, ALMalpha, bA399O19.2	uc001kfk.4	Q96FJ0	OTTHUMG00000018702	ENST00000371926.3:c.587G>A	10.37:g.90673024G>A	ENSP00000360994:p.Ser196Asn	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	139	58	0.417266	NM_020799	B3KPA7|Q5T9N4|Q5T9N9|Q7Z420|Q9P2H4	Missense_Mutation	SNP	ENST00000371926.3	37	CCDS7391.1	199	0.09111721611721611	76	0.15447154471544716	31	0.0856353591160221	0	0.0	92	0.12137203166226913	G	7.055	0.565156	0.13498	0.160009	0.142791	ENSG00000138134	ENST00000371926;ENST00000371927;ENST00000371924;ENST00000371922	T;T;T;T	0.23147	1.95;1.92;1.95;1.97	5.71	3.85	0.44370	.	0.739495	0.13578	N	0.377556	T	0.00039	0.0001	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.0	T	0.33904	-0.9850	9	0.17832	T	0.49	-0.1177	4.5957	0.12329	0.1762:0.0:0.647:0.1769	rs12254856;rs52814383;rs60304840;rs12254856	196;196	Q96FJ0-2;Q96FJ0	.;STALP_HUMAN	N	196;196;196;30	ENSP00000360994:S196N;ENSP00000360995:S196N;ENSP00000360992:S196N;ENSP00000360990:S30N	ENSP00000360990:S30N	S	+	2	0	STAMBPL1	90663004	0.005000	0.15991	0.048000	0.18961	0.681000	0.39784	0.402000	0.20965	1.406000	0.46857	0.650000	0.86243	AGT	G|0.874;A|0.126	0.126	strong		0.483	STAMBPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049283.1	NM_020799	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847069	100847069	+	Missense_Mutation	SNP	G	G	A	rs569336	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:100847069G>A	ENST00000298815.8	+	20	2140	c.2137G>A	c.(2137-2139)Gtt>Att	p.V713I	ARHGAP42_ENST00000524892.2_Missense_Mutation_p.V679I	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	713	Ser-rich.			V -> I (in Ref. 3; BAB71456). {ECO:0000305}.	signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						CCCAGGAGACGTTTCCCCACC	0.488													G|||	2485	0.496206	0.1505	0.5274	5008	,	,		21331	0.997		0.2883	False		,,,				2504	0.6391				p.V713I		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.G2137A						PASS	.	G	ILE/VAL	307,1077		34,239,419	64.0	49.0	54.0		2137	2.4	0.0	11	dbSNP_83	54	987,2195		160,667,764	yes	missense	ARHGAP42	NM_152432.2	29	194,906,1183	AA,AG,GG		31.0182,22.1821,28.3399	benign	713/875	100847069	1294,3272	692	1591	2283	SO:0001583	missense	143872	exon20			GGAGACGTTTCCC			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2137G>A	11.37:g.100847069G>A	ENSP00000298815:p.Val713Ile	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	117	59	0.504274	NM_152432	Q96M56	Missense_Mutation	SNP	ENST00000298815.8	37		1052	0.4816849816849817	87	0.17682926829268292	168	0.46408839779005523	572	1.0	225	0.29683377308707126	G	3.367	-0.129186	0.06753	0.221821	0.310182	ENSG00000165895	ENST00000524892;ENST00000298815	T;T	0.06849	3.25;3.34	5.7	2.36	0.29203	.	.	.	.	.	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	0.37753	-0.9692	8	0.33141	T	0.24	.	12.4883	0.55885	0.2148:0.0:0.7852:0.0	rs569336;rs52827090;rs58116702;rs569336	713	A6NI28	RHG42_HUMAN	I	679;713	ENSP00000431776:V679I;ENSP00000298815:V713I	ENSP00000298815:V713I	V	+	1	0	ARHGAP42	100352279	0.011000	0.17503	0.008000	0.14137	0.397000	0.30659	1.390000	0.34464	0.760000	0.33108	0.655000	0.94253	GTT	G|0.552;A|0.448	0.448	strong		0.488	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
SIRPB1	10326	hgsc.bcm.edu	37	20	1551485	1551485	+	Silent	SNP	C	C	T	rs2254458	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1551485C>T	ENST00000381605.4	-	4	1114	c.1050G>A	c.(1048-1050)gcG>gcA	p.A350A	SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	350					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						CCTTCTGGTGCGCTGAGATCT	0.478													.|||	3766	0.751997	0.8472	0.585	5008	,	,		19374	0.7917		0.6511	False		,,,				2504	0.8047				p.A350A		Atlas-SNP	.											SIRPB1,NS,carcinoma,-1,1	SIRPB1	83	1	0			c.G1050A						PASS	.	C	,	3546,860		1431,684,88	179.0	170.0	173.0		,1050	-5.2	0.0	20	dbSNP_100	173	5611,2989		1835,1941,524	no	intron,coding-synonymous	SIRPB1	NM_001083910.2,NM_006065.3	,	3266,2625,612	TT,TC,CC		34.7558,19.5188,29.594	,	,350/399	1551485	9157,3849	2203	4300	6503	SO:0001819	synonymous_variant	10326	exon4			CTGGTGCGCTGAG	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.1050G>A	20.37:g.1551485C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	109	107	0.981651	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			C|0.290;T|0.710	0.710	strong		0.478	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
NID1	4811	hgsc.bcm.edu	37	1	236141174	236141174	+	Missense_Mutation	SNP	T	T	C	rs3213190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:236141174T>C	ENST00000264187.6	-	20	3819	c.3737A>G	c.(3736-3738)cAg>cGg	p.Q1246R	NID1_ENST00000366595.3_Missense_Mutation_p.Q1113R	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1246			Q -> R (in dbSNP:rs3213190). {ECO:0000269|PubMed:2471408, ECO:0000269|PubMed:2574658, ECO:0000269|PubMed:7557988}.		basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	TCTTCATTTCTGTTCGATACA	0.502													C|||	1724	0.344249	0.385	0.2608	5008	,	,		21512	0.6131		0.1451	False		,,,				2504	0.2761				p.Q1246R		Atlas-SNP	.											.	NID1	196	.	0			c.A3737G						PASS	.	C	ARG/GLN	1539,2867	671.9+/-402.5	257,1025,921	109.0	106.0	107.0		3737	2.8	1.0	1	dbSNP_106	107	1504,7096	748.1+/-407.3	123,1258,2919	yes	missense	NID1	NM_002508.2	43	380,2283,3840	CC,CT,TT		17.4884,34.9296,23.3969	benign	1246/1248	236141174	3043,9963	2203	4300	6503	SO:0001583	missense	4811	exon20			CATTTCTGTTCGA	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3737A>G	1.37:g.236141174T>C	ENSP00000264187:p.Gln1246Arg	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	712	0.326007326007326	174	0.35365853658536583	86	0.23756906077348067	348	0.6083916083916084	104	0.13720316622691292	C	5.517	0.280385	0.10458	0.349296	0.174884	ENSG00000116962	ENST00000264187;ENST00000366595	T;D	0.86769	-1.48;-2.17	5.67	2.79	0.32731	.	0.054020	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00075	-2.25	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45440	-0.9261	9	0.02654	T	1	.	7.3131	0.26485	0.1194:0.6886:0.0:0.1919	rs3213190;rs3768077;rs60739893;rs3213190	1113;1246	P14543-2;P14543	.;NID1_HUMAN	R	1246;1113	ENSP00000264187:Q1246R;ENSP00000355554:Q1113R	ENSP00000264187:Q1246R	Q	-	2	0	NID1	234207797	0.971000	0.33674	0.953000	0.39169	0.928000	0.56348	0.131000	0.15870	0.072000	0.16694	-0.226000	0.12346	CAG	T|0.706;C|0.293	0.293	strong		0.502	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
OR51B6	390058	hgsc.bcm.edu	37	11	5372856	5372856	+	Missense_Mutation	SNP	A	A	G	rs4910756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5372856A>G	ENST00000380219.1	+	1	119	c.119A>G	c.(118-120)aAt>aGt	p.N40S	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	40			N -> S (in dbSNP:rs4910756). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTTCTTGGCAATGGCACTCTT	0.473													A|||	755	0.150759	0.2254	0.1556	5008	,	,		22235	0.0188		0.2147	False		,,,				2504	0.1166				p.N40S		Atlas-SNP	.											.	OR51B6	53	.	0			c.A119G						PASS	.	A	SER/ASN	869,3533	340.5+/-306.2	85,699,1417	174.0	138.0	150.0		119	4.0	1.0	11	dbSNP_111	150	1824,6770	327.2+/-317.7	205,1414,2678	yes	missense	OR51B6	NM_001004750.1	46	290,2113,4095	GG,GA,AA		21.2241,19.741,20.7218	probably-damaging	40/313	5372856	2693,10303	2201	4297	6498	SO:0001583	missense	390058	exon1			TTGGCAATGGCAC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.119A>G	11.37:g.5372856A>G	ENSP00000369568:p.Asn40Ser	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	242	125	0.516529	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	320	0.14652014652014653	100	0.2032520325203252	59	0.16298342541436464	4	0.006993006993006993	157	0.20712401055408972	A	18.26	3.584023	0.65992	0.19741	0.212241	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.75477	-0.94	5.15	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000025	T	0.00271	0.0008	H	0.96805	3.885	0.27891	P	0.9393456	P	0.35307	0.494	B	0.41202	0.35	T	0.36504	-0.9745	9	0.72032	D	0.01	.	9.8577	0.41094	0.9186:0.0:0.0814:0.0	rs4910756;rs17186878;rs52833327;rs58240740;rs4910756	40	Q9H340	O51B6_HUMAN	S	39;40	ENSP00000369568:N40S	ENSP00000369568:N40S	N	+	2	0	OR51B6	5329432	1.000000	0.71417	0.962000	0.40283	0.949000	0.60115	6.909000	0.75735	0.978000	0.38470	0.455000	0.32223	AAT	A|0.824;G|0.176	0.176	strong		0.473	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
MUSK	4593	hgsc.bcm.edu	37	9	113459655	113459655	+	Silent	SNP	C	C	T	rs41279051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113459655C>T	ENST00000374448.4	+	5	671	c.537C>T	c.(535-537)aaC>aaT	p.N179N	MUSK_ENST00000416899.2_Silent_p.N179N|MUSK_ENST00000189978.5_Silent_p.N179N|MUSK_ENST00000374440.3_Silent_p.N61N|MUSK_ENST00000374439.1_Silent_p.N61N	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	179	Ig-like 2.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N179N(3)		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						GGATTCATAACGTACAAAAGG	0.448													C|||	611	0.122005	0.0068	0.072	5008	,	,		15690	0.1974		0.171	False		,,,				2504	0.1851				p.N179N		Atlas-SNP	.											MUSK,colon,carcinoma,+1,7	MUSK	112	7	3	Substitution - coding silent(3)	stomach(1)|kidney(1)|central_nervous_system(1)	c.C537T						PASS	.	C	,,	136,3704		0,136,1784	169.0	165.0	167.0		537,537,537	4.7	1.0	9	dbSNP_127	167	1435,6849		119,1197,2826	no	coding-synonymous,coding-synonymous,coding-synonymous	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	,,	119,1333,4610	TT,TC,CC		17.3225,3.5417,12.9578	,,	179/784,179/774,179/870	113459655	1571,10553	1920	4142	6062	SO:0001819	synonymous_variant	4593	exon5			TCATAACGTACAA	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.537C>T	9.37:g.113459655C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Silent	SNP	ENST00000374448.4	37	CCDS48005.1																																																																																			C|0.866;T|0.134	0.134	strong		0.448	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
FAM83E	54854	hgsc.bcm.edu	37	19	49116438	49116438	+	Silent	SNP	A	A	G	rs376524	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49116438A>G	ENST00000263266.3	-	1	381	c.192T>C	c.(190-192)gtT>gtC	p.V64V	FAM83E_ENST00000595110.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	64										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)		CCAAGCCCTGAACCTCATCCG	0.677													G|||	1674	0.334265	0.3298	0.4251	5008	,	,		15077	0.4702		0.2147	False		,,,				2504	0.2587				p.V64V		Atlas-SNP	.											FAM83E,colon,carcinoma,0,1	FAM83E	34	1	0			c.T192C						PASS	.	G		1189,3091		181,827,1132	25.0	32.0	30.0		192	1.9	0.2	19	dbSNP_80	30	1730,6790		188,1354,2718	no	coding-synonymous	FAM83E	NM_017708.3		369,2181,3850	GG,GA,AA		20.3052,27.7804,22.8047		64/479	49116438	2919,9881	2140	4260	6400	SO:0001819	synonymous_variant	54854	exon1			GCCCTGAACCTCA	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.192T>C	19.37:g.49116438A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_017708	Q9NXK1	Silent	SNP	ENST00000263266.3	37	CCDS42587.1																																																																																			A|0.708;G|0.292	0.292	strong		0.677	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
APH1B	83464	hgsc.bcm.edu	37	15	63569902	63569902	+	Missense_Mutation	SNP	C	C	T	rs117618017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:63569902C>T	ENST00000261879.5	+	1	150	c.80C>T	c.(79-81)aCc>aTc	p.T27I	APH1B_ENST00000380343.4_Missense_Mutation_p.T27I	NM_001145646.1|NM_031301.3	NP_001139118.1|NP_112591.2	Q8WW43	APH1B_HUMAN	APH1B gamma secretase subunit	27				T -> I (in Ref. 4; AAQ89061). {ECO:0000305}.	apoptotic signaling pathway (GO:0097190)|membrane protein intracellular domain proteolysis (GO:0031293)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	peptidase activity (GO:0008233)	p.T27I(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	12						ACCATCGCCACCGAGCCGTTG	0.682													C|||	222	0.0443291	0.0045	0.0879	5008	,	,		8198	0.0		0.1352	False		,,,				2504	0.0194				p.T27I		Atlas-SNP	.											APH1B,NS,lymphoid_neoplasm,0,3	APH1B	27	3	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C80T						scavenged	.	C	ILE/THR,ILE/THR	129,4277	93.0+/-131.7	4,121,2078	49.0	49.0	49.0		80,80	1.0	0.0	15	dbSNP_132	49	1099,7501	226.9+/-262.5	68,963,3269	yes	missense,missense	APH1B	NM_001145646.1,NM_031301.3	89,89	72,1084,5347	TT,TC,CC		12.7791,2.9278,9.4418	probably-damaging,probably-damaging	27/217,27/258	63569902	1228,11778	2203	4300	6503	SO:0001583	missense	83464	exon1			TCGCCACCGAGCC	AY358698	CCDS10184.1, CCDS45276.1	15q22.2	2013-05-01	2013-05-01		ENSG00000138613	ENSG00000138613			24080	protein-coding gene	gene with protein product		607630	"""anterior pharynx defective 1 homolog B (C. elegans)"""			12110170, 11230166	Standard	NM_031301		Approved	PSFL, APH-1B, DKFZp564D0372	uc002ama.3	Q8WW43	OTTHUMG00000132863	ENST00000261879.5:c.80C>T	15.37:g.63569902C>T	ENSP00000261879:p.Thr27Ile	Somatic	44	1	0.0227273		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_001145646	A8K589|Q564N3|Q6UWQ1|Q9H0S0	Missense_Mutation	SNP	ENST00000261879.5	37	CCDS10184.1	138	0.06318681318681318	5	0.01016260162601626	35	0.09668508287292818	0	0.0	98	0.12928759894459102	C	7.955	0.745633	0.15710	0.029278	0.127791	ENSG00000138613	ENST00000380343;ENST00000261879;ENST00000380340	T;T;T	0.43688	0.94;0.94;0.94	4.11	0.961	0.19638	.	0.534132	0.18319	N	0.144870	T	0.00328	0.0010	M	0.62723	1.935	0.80722	P	0.0	P;P	0.38677	0.642;0.521	B;B	0.37650	0.193;0.255	T	0.04029	-1.0983	9	0.37606	T	0.19	-2.1163	1.1628	0.01809	0.1834:0.4361:0.1783:0.2022	.	27;27	Q564N3;Q8WW43	.;APH1B_HUMAN	I	27	ENSP00000369700:T27I;ENSP00000261879:T27I;ENSP00000369697:T27I	ENSP00000261879:T27I	T	+	2	0	APH1B	61356955	0.013000	0.17824	0.005000	0.12908	0.350000	0.29205	1.171000	0.31896	0.098000	0.17522	-0.719000	0.03609	ACC	C|0.915;T|0.085	0.085	strong		0.682	APH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256337.1	NM_031301	
CCL25	6370	hgsc.bcm.edu	37	19	8121360	8121360	+	Missense_Mutation	SNP	A	A	G	rs2032887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8121360A>G	ENST00000390669.3	+	3	352	c.302A>G	c.(301-303)cAc>cGc	p.H101R	CCL25_ENST00000315626.4_Intron|CCL25_ENST00000253451.4_Missense_Mutation_p.H101R			O15444	CCL25_HUMAN	chemokine (C-C motif) ligand 25	101			H -> R (in dbSNP:rs2032887).		cell chemotaxis (GO:0060326)|cell surface receptor signaling pathway (GO:0007166)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of cell-matrix adhesion (GO:0001954)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR10 chemokine receptor binding (GO:0031735)|chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|hormone activity (GO:0005179)			NS(1)|endometrium(1)|lung(1)|skin(1)|urinary_tract(1)	5						GCAAAGCTCCACCACAACACG	0.582													G|||	1090	0.217652	0.261	0.3458	5008	,	,		15391	0.0942		0.2475	False		,,,				2504	0.1646				p.H101R		Atlas-SNP	.											.	CCL25	12	.	0			c.A302G						PASS	.	G	ARG/HIS,ARG/HIS	1023,3111		133,757,1177	63.0	69.0	67.0		302,302	-3.0	0.0	19	dbSNP_94	67	2044,6362		254,1536,2413	yes	missense,missense	CCL25	NM_001201359.1,NM_005624.3	29,29	387,2293,3590	GG,GA,AA		24.316,24.746,24.4577	benign,benign	101/150,101/151	8121360	3067,9473	2067	4203	6270	SO:0001583	missense	6370	exon4			AGCTCCACCACAA	U86358	CCDS12194.1, CCDS56080.1	19p13.2	2013-02-25	2002-08-22	2002-08-23	ENSG00000131142	ENSG00000131142		"""Chemokine ligands"", ""Endogenous ligands"""	10624	protein-coding gene	gene with protein product	"""Ck beta-15"", ""thymus expressed chemokine"", ""TECKvar"""	602565	"""small inducible cytokine subfamily A (Cys-Cys), member 25"""	SCYA25		9285413, 9722960	Standard	NM_005624		Approved	TECK, Ckb15	uc002mjd.3	O15444	OTTHUMG00000141287	ENST00000390669.3:c.302A>G	19.37:g.8121360A>G	ENSP00000375086:p.His101Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_001201359	A1L4J4|A6NI52|A8K9E7|B5MCA5|Q96KJ7	Missense_Mutation	SNP	ENST00000390669.3	37	CCDS12194.1	485	0.22206959706959706	118	0.23983739837398374	117	0.32320441988950277	62	0.10839160839160839	188	0.24802110817941952	G	0.245	-1.011107	0.02095	0.24746	0.24316	ENSG00000131142	ENST00000253451;ENST00000390669	T;T	0.03717	3.83;3.83	2.29	-3.03	0.05429	Chemokine interleukin-8-like domain (1);	2.002980	0.02513	N	0.091738	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48525	-0.9028	9	0.25751	T	0.34	-2.4313	1.0069	0.01488	0.4783:0.1585:0.2067:0.1565	rs2032887;rs2228086;rs17304026;rs52836751;rs59402983;rs2032887	101;101	O15444;A6NI52	CCL25_HUMAN;.	R	101	ENSP00000253451:H101R;ENSP00000375086:H101R	ENSP00000253451:H101R	H	+	2	0	CCL25	8027360	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.544000	0.00933	-1.514000	0.01786	-2.251000	0.00283	CAC	A|0.785;G|0.215	0.215	strong		0.582	CCL25-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280522.1	NM_005624	
WDR81	124997	hgsc.bcm.edu	37	17	1629969	1629969	+	Silent	SNP	C	C	T	rs80035274|rs587780499	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1629969C>T	ENST00000409644.1	+	1	1716	c.1716C>T	c.(1714-1716)caC>caT	p.H572H	WDR81_ENST00000437219.2_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_Intron|WDR81_ENST00000309182.5_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	572	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.				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)		TGGACGCCCACACTCACCTGG	0.622													C|||	681	0.135982	0.0507	0.2147	5008	,	,		17737	0.1647		0.2078	False		,,,				2504	0.092				p.H572H		Atlas-SNP	.											WDR81_ENST00000409644,NS,carcinoma,0,1	WDR81	180	1	0			c.C1716T						PASS	.						12.0	15.0	14.0					17																	1629969		692	1589	2281	SO:0001819	synonymous_variant	124997	exon1			CGCCCACACTCAC	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.1716C>T	17.37:g.1629969C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.833;T|0.167	0.167	strong		0.622	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
HEATR5B	54497	hgsc.bcm.edu	37	2	37232822	37232822	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37232822T>C	ENST00000233099.5	-	30	4953	c.4858A>G	c.(4858-4860)Acc>Gcc	p.T1620A	HEATR5B_ENST00000354531.2_Missense_Mutation_p.T1620A	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	1620						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TCTAGCAAGGTATGTAAGGCC	0.413																																					p.T1620A		Atlas-SNP	.											HEATR5B,NS,carcinoma,+2,1	HEATR5B	185	1	0			c.A4858G						scavenged	.						140.0	128.0	132.0					2																	37232822		2203	4300	6503	SO:0001583	missense	54497	exon30			GCAAGGTATGTAA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.4858A>G	2.37:g.37232822T>C	ENSP00000233099:p.Thr1620Ala	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	135	2	0.0148148	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	T	2.228	-0.376801	0.05000	.	.	ENSG00000008869	ENST00000233099;ENST00000354531	T;T	0.45276	0.9;0.9	5.63	5.63	0.86233	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.22898	0.0553	N	0.08118	0	0.58432	D	0.999998	B	0.06786	0.001	B	0.09377	0.004	T	0.11518	-1.0584	10	0.07175	T	0.84	-14.8362	15.87	0.79108	0.0:0.0:0.0:1.0	.	1620	Q9P2D3	HTR5B_HUMAN	A	1620	ENSP00000233099:T1620A;ENSP00000346531:T1620A	ENSP00000233099:T1620A	T	-	1	0	HEATR5B	37086326	1.000000	0.71417	0.374000	0.26016	0.266000	0.26442	7.809000	0.86057	2.145000	0.66743	0.533000	0.62120	ACC	.	.	none		0.413	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
METTL4	64863	hgsc.bcm.edu	37	18	2554915	2554915	+	Silent	SNP	G	G	A	rs61749937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:2554915G>A	ENST00000574538.1	-	4	1357	c.582C>T	c.(580-582)gaC>gaT	p.D194D	snoU109_ENST00000459316.1_RNA|METTL4_ENST00000319888.6_Silent_p.D194D	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	194					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						AACTGCAGGCGTCAAGTGGTA	0.393													G|||	75	0.014976	0.0318	0.0086	5008	,	,		20011	0.0		0.0239	False		,,,				2504	0.0031				p.D194D		Atlas-SNP	.											.	METTL4	40	.	0			c.C582T						PASS	.	G		124,4282	91.6+/-130.3	4,116,2083	120.0	113.0	115.0		582	2.0	0.5	18	dbSNP_129	115	95,8505	54.0+/-114.7	1,93,4206	no	coding-synonymous	METTL4	NM_022840.3		5,209,6289	AA,AG,GG		1.1047,2.8143,1.6838		194/473	2554915	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	64863	exon4			GCAGGCGTCAAGT		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.582C>T	18.37:g.2554915G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	172	71	0.412791	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Silent	SNP	ENST00000574538.1	37	CCDS11826.1																																																																																			G|0.984;A|0.016	0.016	strong		0.393	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
KRT40	125115	hgsc.bcm.edu	37	17	39135207	39135207	+	Missense_Mutation	SNP	A	A	G	rs386797018|rs150812789	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39135207A>G	ENST00000398486.2	-	8	1205	c.1045T>C	c.(1045-1047)Tgt>Cgt	p.C349R	KRT40_ENST00000377755.4_Missense_Mutation_p.C349R	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	349	Coil 2.|Rod.			C -> R (in Ref. 1; CAH10353). {ECO:0000305}.		intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				TCGATCAGACACTGAATTTGG	0.582													A|||	1082	0.216054	0.0628	0.317	5008	,	,		16221	0.251		0.2425	False		,,,				2504	0.2883				p.C349R		Atlas-SNP	.											KRT40,NS,carcinoma,+2,1	KRT40	27	1	0			c.T1045C						PASS	.	A	ARG/CYS	340,4062	169.8+/-200.3	12,316,1873	90.0	99.0	96.0		1045	3.2	1.0	17	dbSNP_134	96	1951,6639	334.5+/-321.0	205,1541,2549	yes	missense	KRT40	NM_182497.3	180	217,1857,4422	GG,GA,AA		22.7125,7.7238,17.6339	benign	349/432	39135207	2291,10701	2201	4295	6496	SO:0001583	missense	125115	exon8			TCAGACACTGAAT	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1045T>C	17.37:g.39135207A>G	ENSP00000381500:p.Cys349Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	120	59	0.491667	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	465	0.2129120879120879	29	0.05894308943089431	111	0.30662983425414364	135	0.23601398601398602	190	0.25065963060686014	A	11.18	1.562779	0.27915	0.077238	0.227125	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.87729	-2.29;-2.29	5.56	3.25	0.37280	Filament (1);	0.000000	0.36519	N	0.002560	T	0.00012	0.0000	N	0.26092	0.79	0.22156	P	0.999322654	B	0.14012	0.009	B	0.17979	0.02	T	0.03112	-1.1071	9	0.24483	T	0.36	.	13.2354	0.59967	0.4595:0.5404:0.0:0.0	.	349	Q6A162	K1C40_HUMAN	R	349	ENSP00000366984:C349R;ENSP00000381500:C349R	ENSP00000366984:C349R	C	-	1	0	KRT40	36388733	0.000000	0.05858	0.998000	0.56505	0.967000	0.64934	-0.302000	0.08221	0.438000	0.26450	0.533000	0.62120	TGT	A|0.787;G|0.213	0.213	strong		0.582	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
OPA1	4976	hgsc.bcm.edu	37	3	193374964	193374964	+	Silent	SNP	T	T	C	rs9851685	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:193374964T>C	ENST00000392438.3	+	21	2343	c.2109T>C	c.(2107-2109)gcT>gcC	p.A703A	OPA1_ENST00000361908.3_Silent_p.A740A|OPA1_ENST00000361150.2_Silent_p.A704A|OPA1_ENST00000361828.2_Silent_p.A721A|OPA1_ENST00000361510.2_Silent_p.A758A|OPA1_ENST00000361715.2_Silent_p.A722A	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	703					apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		TTAAAGAGGCTGTTAAGGAAG	0.388													C|||	2336	0.466454	0.5862	0.4697	5008	,	,		16355	0.3571		0.4563	False		,,,				2504	0.4254				p.A758A		Atlas-SNP	.											.	OPA1	79	.	0			c.T2274C						PASS	.	C	,,,,,,,	2475,1931	547.6+/-377.3	693,1089,421	100.0	104.0	102.0		2109,2001,2055,2112,2163,2166,2220,2274	0.1	1.0	3	dbSNP_119	102	3991,4609	599.5+/-394.1	907,2177,1216	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OPA1	NM_015560.2,NM_130831.2,NM_130832.2,NM_130833.2,NM_130834.2,NM_130835.2,NM_130836.2,NM_130837.2	,,,,,,,	1600,3266,1637	CC,CT,TT		46.407,43.8266,49.7155	,,,,,,,	703/961,667/925,685/943,704/962,721/979,722/980,740/998,758/1016	193374964	6466,6540	2203	4300	6503	SO:0001819	synonymous_variant	4976	exon23			AGAGGCTGTTAAG	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"""mitochondrial dynamin-like GTPase"", ""dynamin-like guanosine triphosphatase"", ""Dynamin-like 120 kDa protein, mitochondrial"""	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.2109T>C	3.37:g.193374964T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_130837	D3DNW4	Silent	SNP	ENST00000392438.3	37	CCDS43186.1																																																																																			T|0.517;C|0.483	0.483	strong		0.388	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
NDUFS4	4724	hgsc.bcm.edu	37	5	52942197	52942197	+	Silent	SNP	A	A	G	rs31303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:52942197A>G	ENST00000296684.5	+	3	340	c.312A>G	c.(310-312)agA>agG	p.R104R		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	104					brain development (GO:0007420)|cAMP-mediated signaling (GO:0019933)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|positive regulation of fibroblast proliferation (GO:0048146)|reactive oxygen species metabolic process (GO:0072593)|regulation of protein phosphorylation (GO:0001932)|respiratory electron transport chain (GO:0022904)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(3)	10		Lung NSC(810;8.27e-05)|Breast(144;0.0848)				TTGATACCAGAGAGCGATGGG	0.363													G|||	4007	0.80012	0.857	0.8199	5008	,	,		17523	0.7946		0.7565	False		,,,				2504	0.7597				p.R104R		Atlas-SNP	.											.	NDUFS4	17	.	0			c.A312G						PASS	.	G		3751,655	281.6+/-276.1	1589,573,41	140.0	136.0	137.0		312	1.0	1.0	5	dbSNP_76	137	6556,2044	356.0+/-330.1	2494,1568,238	no	coding-synonymous	NDUFS4	NM_002495.2		4083,2141,279	GG,GA,AA		23.7674,14.8661,20.752		104/176	52942197	10307,2699	2203	4300	6503	SO:0001819	synonymous_variant	4724	exon3			TACCAGAGAGCGA	AF020351	CCDS3960.1	5q11.1	2011-07-04	2002-08-29		ENSG00000164258	ENSG00000164258		"""Mitochondrial respiratory chain complex / Complex I"""	7711	protein-coding gene	gene with protein product	"""complex I 18kDa subunit"""	602694	"""NADH dehydrogenase (ubiquinone) Fe-S protein 4 (18kD) (NADH-coenzyme Q reductase)"""			9463323, 9763677	Standard	NM_002495		Approved	AQDQ, CI-18	uc003jpe.2	O43181	OTTHUMG00000096987	ENST00000296684.5:c.312A>G	5.37:g.52942197A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_002495	Q9BS69	Silent	SNP	ENST00000296684.5	37	CCDS3960.1																																																																																			A|0.211;G|0.789	0.789	strong		0.363	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495	
PCDHB6	56130	hgsc.bcm.edu	37	5	140529938	140529938	+	Missense_Mutation	SNP	G	G	A	rs141476251	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140529938G>A	ENST00000231136.1	+	1	100	c.100G>A	c.(100-102)Gta>Ata	p.V34I	PCDHB6_ENST00000543635.1_Intron	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	34	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCAGTATTCCGTATTGGAGGA	0.493													G|||	10	0.00199681	0.0	0.0014	5008	,	,		16736	0.0		0.005	False		,,,				2504	0.0041				p.V34I		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G100A						PASS	.	G	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	154.0	155.0	155.0		100	3.1	0.0	5	dbSNP_134	155	35,8565	24.6+/-71.5	0,35,4265	yes	missense	PCDHB6	NM_018939.2	29	0,38,6465	AA,AG,GG		0.407,0.0681,0.2922	benign	34/795	140529938	38,12968	2203	4300	6503	SO:0001583	missense	56130	exon1			TATTCCGTATTGG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.100G>A	5.37:g.140529938G>A	ENSP00000231136:p.Val34Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	12.20	1.867611	0.32977	6.81E-4	0.00407	ENSG00000113211	ENST00000231136	T	0.35789	1.29	4.9	3.09	0.35607	Cadherin, N-terminal (1);Cadherin (1);	.	.	.	.	T	0.19604	0.0471	L	0.35414	1.06	0.52501	D	0.999956	B	0.02656	0.0	B	0.18561	0.022	T	0.04115	-1.0976	9	0.51188	T	0.08	.	8.4024	0.32594	0.2392:0.0:0.7608:0.0	.	34	Q9Y5E3	PCDB6_HUMAN	I	34	ENSP00000231136:V34I	ENSP00000231136:V34I	V	+	1	0	PCDHB6	140510122	0.013000	0.17824	0.023000	0.16930	0.355000	0.29361	0.182000	0.16900	0.559000	0.29153	0.561000	0.74099	GTA	G|0.997;A|0.003	0.003	strong		0.493	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
ZNF844	284391	hgsc.bcm.edu	37	19	12187210	12187210	+	Silent	SNP	A	A	G	rs6511764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187210A>G	ENST00000439326.3	+	4	1450	c.1275A>G	c.(1273-1275)gtA>gtG	p.V425V	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	425					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						TAAGCAGTGTAGTAAAGCCTT	0.428													.|||	1455	0.290535	0.73	0.1455	5008	,	,		23733	0.0853		0.161	False		,,,				2504	0.1442				p.V425V		Atlas-SNP	.											ZNF844,right_upper_lobe,carcinoma,0,2	ZNF844	69	2	0			c.A1275G						scavenged	.	G		883,501		287,309,96	54.0	57.0	56.0		1275	0.5	0.0	19	dbSNP_116	56	413,2769		25,363,1203	no	coding-synonymous	ZNF844	NM_001136501.1		312,672,1299	GG,GA,AA		12.9793,36.1994,28.3837		425/667	12187210	1296,3270	692	1591	2283	SO:0001819	synonymous_variant	284391	exon4			CAGTGTAGTAAAG	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1275A>G	19.37:g.12187210A>G		Somatic	42	1	0.0238095		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_001136501	Q5JPI8	Silent	SNP	ENST00000439326.3	37	CCDS45985.1																																																																																			A|0.772;G|0.228	0.228	strong		0.428	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
PSD3	23362	hgsc.bcm.edu	37	8	18656805	18656805	+	Splice_Site	SNP	G	G	A	rs2306825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:18656805G>A	ENST00000327040.8	-	8	2184	c.2082C>T	c.(2080-2082)caC>caT	p.H694H	PSD3_ENST00000440756.2_Silent_p.H694H|PSD3_ENST00000523619.1_Splice_Site_p.H629H|PSD3_ENST00000286485.8_Splice_Site_p.H160H	NM_015310.3	NP_056125.3	Q9NYI0	PSD3_HUMAN	pleckstrin and Sec7 domain containing 3	694	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				Colorectal(111;0.0281)|READ - Rectum adenocarcinoma(644;0.183)		CCACACTTACGTGGCCATGTA	0.383													A|||	1077	0.215056	0.2413	0.1744	5008	,	,		18395	0.3046		0.163	False		,,,				2504	0.1697				p.H694H		Atlas-SNP	.											.	PSD3	142	.	0			c.C2082T						PASS	.	A	,	899,3507	741.0+/-411.2	96,707,1400	127.0	117.0	121.0		2082,480	0.3	1.0	8	dbSNP_100	121	1345,7255	756.5+/-407.5	106,1133,3061	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PSD3	NM_015310.3,NM_206909.2	,	202,1840,4461	AA,AG,GG		15.6395,20.404,17.2536	,	694/1048,160/514	18656805	2244,10762	2203	4300	6503	SO:0001630	splice_region_variant	23362	exon8			ACTTACGTGGCCA	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.2082+1C>T	8.37:g.18656805G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_015310	A6NFQ4|E9KL50|Q6B003|Q9Y2F1	Silent	SNP	ENST00000327040.8	37	CCDS43720.1	445	0.20375457875457875	102	0.2073170731707317	55	0.15193370165745856	171	0.29895104895104896	117	0.15435356200527706	A	9.446	1.089325	0.20390	0.20404	0.156395	ENSG00000156011	ENST00000520858	.	.	.	5.64	0.35	0.16037	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.118	0.42603	0.6465:0.0:0.3535:0.0	rs2306825;rs59963167;rs2306825	.	.	.	X	127	.	.	Q	-	1	0	PSD3	18701085	0.836000	0.29430	0.992000	0.48379	0.629000	0.37895	-0.048000	0.11944	-0.383000	0.07858	-0.268000	0.10319	CAA	G|0.811;A|0.189	0.189	strong		0.383	PSD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374867.1	NM_015310	Silent
PLBD1	79887	hgsc.bcm.edu	37	12	14656768	14656768	+	Missense_Mutation	SNP	G	G	C	rs1600	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:14656768G>C	ENST00000240617.5	-	11	2252	c.1600C>G	c.(1600-1602)Cca>Gca	p.P534A		NM_024829.5	NP_079105.4	Q6P4A8	PLBL1_HUMAN	phospholipase B domain containing 1	534			P -> A (in dbSNP:rs1600). {ECO:0000269|PubMed:15489334}.		glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	16						TAGACCTCTGGCATGCCCTGA	0.413													G|||	2572	0.513578	0.6437	0.5778	5008	,	,		16482	0.38		0.4573	False		,,,				2504	0.4877				p.P534A		Atlas-SNP	.											.	PLBD1	36	.	0			c.C1600G						PASS	.	G	ALA/PRO	2761,1645	659.2+/-400.5	865,1031,307	126.0	121.0	123.0		1600	5.0	1.0	12	dbSNP_36	123	4021,4579	556.1+/-386.8	934,2153,1213	yes	missense	PLBD1	NM_024829.5	27	1799,3184,1520	CC,CG,GG		46.7558,37.3355,47.8548	probably-damaging	534/554	14656768	6782,6224	2203	4300	6503	SO:0001583	missense	79887	exon11			CCTCTGGCATGCC	BC000909	CCDS31751.1	12p13.1	2013-10-11			ENSG00000121316	ENSG00000121316			26215	protein-coding gene	gene with protein product	"""PLB homolog 1 (Dictyostelium)"""					15193148, 19019078	Standard	NM_024829		Approved	FLJ22662	uc001rcc.1	Q6P4A8	OTTHUMG00000168821	ENST00000240617.5:c.1600C>G	12.37:g.14656768G>C	ENSP00000240617:p.Pro534Ala	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	151	74	0.490066	NM_024829	A8K4E9|Q9BVV3|Q9H625	Missense_Mutation	SNP	ENST00000240617.5	37	CCDS31751.1	1077	0.49313186813186816	318	0.6463414634146342	192	0.5303867403314917	216	0.3776223776223776	351	0.4630606860158311	G	24.1	4.492333	0.84962	0.626645	0.467558	ENSG00000121316	ENST00000240617	T	0.24350	1.86	5.86	4.97	0.65823	.	0.049601	0.85682	N	0.000000	T	0.00012	0.0000	M	0.94021	3.485	0.09310	P	0.99999827061	D	0.89917	1.0	D	0.83275	0.996	T	0.46233	-0.9206	9	0.72032	D	0.01	-14.3777	15.8105	0.78561	0.0:0.1351:0.8649:0.0	rs1600;rs3168592;rs3789995;rs17844869;rs17855851;rs17857584;rs1600	534	Q6P4A8	PLBL1_HUMAN	A	534	ENSP00000240617:P534A	ENSP00000240617:P534A	P	-	1	0	PLBD1	14548035	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	9.434000	0.97515	1.613000	0.50231	-0.172000	0.13284	CCA	G|0.490;C|0.510	0.510	strong		0.413	PLBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401203.1	NM_024829	
CSMD2	114784	hgsc.bcm.edu	37	1	34238283	34238283	+	Missense_Mutation	SNP	T	T	C	rs474474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:34238283T>C	ENST00000338325.1	-	7	969	c.557A>G	c.(556-558)cAc>cGc	p.H186R	CSMD2_ENST00000373381.4_Missense_Mutation_p.H578R			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	538	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				GTCACCGTGGTGAAACCGGGA	0.537													C|||	1901	0.379593	0.5333	0.317	5008	,	,		19833	0.2659		0.2406	False		,,,				2504	0.4765				p.H538R		Atlas-SNP	.											.	CSMD2	946	.	0			c.A1613G						PASS	.	C	ARG/HIS	2143,2263	596.7+/-388.7	525,1093,585	111.0	105.0	107.0		1613	-1.3	0.9	1	dbSNP_83	107	2291,6309	706.5+/-405.5	301,1689,2310	yes	missense	CSMD2	NM_052896.3	29	826,2782,2895	CC,CT,TT		26.6395,48.6382,34.092	benign	538/3488	34238283	4434,8572	2203	4300	6503	SO:0001583	missense	114784	exon13			CCGTGGTGAAACC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000338325.1:c.557A>G	1.37:g.34238283T>C	ENSP00000340311:p.His186Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000338325.1	37		682	0.31227106227106227	238	0.483739837398374	96	0.26519337016574585	168	0.2937062937062937	180	0.23746701846965698	C	9.737	1.163742	0.21538	0.486382	0.266395	ENSG00000121904	ENST00000373381;ENST00000338325	T;T	0.62941	-0.01;-0.01	6.06	-1.29	0.09288	Complement control module (2);Sushi/SCR/CCP (3);	0.180087	0.50627	N	0.000119	T	0.00012	0.0000	N	0.01284	-0.91	0.09310	P	0.999999999946275	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.41197	-0.9522	9	0.10636	T	0.68	.	6.7188	0.23318	0.1097:0.4467:0.0:0.4436	rs474474;rs56977083;rs474474	538;578	Q7Z408;E7EUA6	CSMD2_HUMAN;.	R	578;186	ENSP00000362479:H578R;ENSP00000340311:H186R	ENSP00000241312:H538R	H	-	2	0	CSMD2	34010870	0.032000	0.19561	0.934000	0.37439	0.987000	0.75469	-0.069000	0.11542	-0.514000	0.06488	-0.733000	0.03571	CAC	T|0.662;C|0.338	0.338	strong		0.537	CSMD2-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000036404.2	NM_052896	
SDHA	6389	hgsc.bcm.edu	37	5	236617	236617	+	Silent	SNP	G	G	T	rs200223188	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:236617G>T	ENST00000264932.6	+	10	1450	c.1335G>T	c.(1333-1335)tcG>tcT	p.S445S	SDHA_ENST00000510361.1_Silent_p.S397S|SDHA_ENST00000504309.1_Silent_p.S445S	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	309	4	0.012945		WXS	Illumina HiSeq	Phase_I	315	4	0.0126984	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	
TNK2	10188	hgsc.bcm.edu	37	3	195594805	195594805	+	Silent	SNP	A	A	G	rs1056749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195594805A>G	ENST00000333602.6	-	12	2936	c.2319T>C	c.(2317-2319)gcT>gcC	p.A773A	TNK2_ENST00000392400.1_Silent_p.A773A|TNK2_ENST00000428187.1_Silent_p.A805A|TNK2_ENST00000381916.2_Silent_p.A851A	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	773	EBD domain. {ECO:0000250}.|Pro-rich.			Missing (in Ref. 4; AAH08884). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	GGGGAGGGGAAGCAGGTCCAG	0.746													a|||	593	0.118411	0.1505	0.0865	5008	,	,		11184	0.0327		0.175	False		,,,				2504	0.1278				p.A851A		Atlas-SNP	.											TNK2_ENST00000381916,NS,carcinoma,0,3	TNK2	246	3	0			c.T2553C						scavenged	.		,	451,3449		26,399,1525	5.0	7.0	6.0		2553,2319	-1.4	0.8	3	dbSNP_86	6	1067,6843		74,919,2962	no	coding-synonymous,coding-synonymous	TNK2	NM_001010938.1,NM_005781.4	,	100,1318,4487	GG,GA,AA		13.4893,11.5641,12.8535	,	851/1087,773/1039	195594805	1518,10292	1950	3955	5905	SO:0001819	synonymous_variant	10188	exon13			AGGGGAAGCAGGT	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.2319T>C	3.37:g.195594805A>G		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	11	5	0.454545	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Silent	SNP	ENST00000333602.6	37	CCDS33928.1																																																																																			A|0.886;G|0.114	0.114	strong		0.746	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609192	32609192	+	Missense_Mutation	SNP	A	A	G	rs1142323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32609192A>G	ENST00000343139.5	+	2	290	c.188A>G	c.(187-189)gAg>gGg	p.E63G	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.E63G|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.E63G	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	63	Alpha-1.		G -> E (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:06, allele DQA1*01:07, allele DQA1*02:01, allele DQA1*03:01, allele DQA1*03:02 and allele DQA1*03:03; dbSNP:rs1142323).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GTGGACCTGGAGAGGAAGGAG	0.517													.|||	1419	0.283347	0.3275	0.3487	5008	,	,		13238	0.246		0.3002	False		,,,				2504	0.1984				p.E63G		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.A188G						PASS	.	A	GLY/GLU	1153,3243		338,477,1383	112.0	96.0	101.0		188	1.4	0.0	6	dbSNP_86	101	2081,6451		569,943,2754	no	missense	HLA-DQA1	NM_002122.3	98	907,1420,4137	GG,GA,AA		24.3905,26.2284,25.0155	benign	63/256	32609192	3234,9694	2198	4266	6464	SO:0001583	missense	3117	exon2			ACCTGGAGAGGAA		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.188A>G	6.37:g.32609192A>G	ENSP00000339398:p.Glu63Gly	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	107	30	0.280374	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	645|645	0.29532967032967034|0.29532967032967034	162|162	0.32926829268292684|0.32926829268292684	134|134	0.3701657458563536|0.3701657458563536	133|133	0.23251748251748253|0.23251748251748253	216|216	0.2849604221635884|0.2849604221635884	.|.	0.083|0.083	-1.179542|-1.179542	0.01633|0.01633	0.262284|0.262284	0.243905|0.243905	ENSG00000196735|ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949|ENST00000486548	T;T;T;T|.	0.00808|.	5.67;5.67;5.67;5.67|.	3.84|3.84	1.4|1.4	0.22301|0.22301	.|.	0.860258|.	0.10150|.	U|.	0.709694|.	T|T	0.18676|0.18676	0.0448|0.0448	N|N	0.25825|0.25825	0.765|0.765	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.13145|.	0.007;0.001|.	B;B|.	0.14023|.	0.01;0.002|.	T|T	0.09975|0.09975	-1.0650|-1.0650	9|4	0.25751|.	T|.	0.34|.	.|.	9.286|9.286	0.37758|0.37758	0.8976:0.0:0.1024:0.0|0.8976:0.0:0.1024:0.0	rs1142323;rs3205985;rs9272691;rs12722053;rs17840125;rs36219700|rs1142323;rs3205985;rs9272691;rs12722053;rs17840125;rs36219700	69;63|.	Q59F33;G4XQK2|.	.;.|.	G|G	63|36	ENSP00000339398:E63G;ENSP00000378767:E63G;ENSP00000437302:E63G;ENSP00000364087:E63G|.	ENSP00000339398:E63G|.	E|R	+|+	2|1	0|2	HLA-DQA1|HLA-DQA1	32717170|32717170	0.011000|0.011000	0.17503|0.17503	0.013000|0.013000	0.15412|0.15412	0.002000|0.002000	0.02628|0.02628	0.495000|0.495000	0.22483|0.22483	0.191000|0.191000	0.20236|0.20236	-1.271000|-1.271000	0.01417|0.01417	GAG|AGA	A|0.709;G|0.291	0.291	strong		0.517	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726774	32726774	+	Missense_Mutation	SNP	C	C	T	rs200716952		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32726774C>T	ENST00000437316.2	-	3	562	c.499G>A	c.(499-501)Gcc>Acc	p.A167T	HLA-DQB2_ENST00000411527.1_Missense_Mutation_p.A167T|HLA-DQB2_ENST00000435145.2_Missense_Mutation_p.A167T			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	171	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)	p.A167T(1)		endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						ACAACACCGGCTGTCTCCTCC	0.542																																					p.A167T		Atlas-SNP	.											HLA-DQB2,NS,carcinoma,0,4	HLA-DQB2	22	4	1	Substitution - Missense(1)	kidney(1)	c.G499A						PASS	.																																			SO:0001583	missense	3120	exon3			CACCGGCTGTCTC	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.499G>A	6.37:g.32726774C>T	ENSP00000396330:p.Ala167Thr	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	197	19	0.0964467	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Missense_Mutation	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	C	10.03	1.238159	0.22711	.	.	ENSG00000232629	ENST00000437316;ENST00000435145;ENST00000411527	T;T;T	0.02812	4.15;4.15;4.15	3.43	2.56	0.30785	.	0.330401	0.23935	U	0.043113	T	0.00967	0.0032	L	0.33189	0.99	0.23425	N	0.997708	B;B	0.19073	0.001;0.033	B;B	0.26310	0.014;0.068	T	0.47394	-0.9121	10	0.33940	T	0.23	.	8.9215	0.35615	0.0:0.8839:0.0:0.1161	.	167;167	A2ADX3;Q5SR06	.;.	T	167	ENSP00000396330:A167T;ENSP00000410512:A167T;ENSP00000390431:A167T	ENSP00000390431:A167T	A	-	1	0	HLA-DQB2	32834752	0.000000	0.05858	0.869000	0.34112	0.359000	0.29487	0.045000	0.14013	0.784000	0.33661	-0.333000	0.08304	GCC	C|0.997;T|0.003	0.003	weak		0.542	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
TSR2	90121	hgsc.bcm.edu	37	X	54469894	54469894	+	Silent	SNP	T	T	C	rs36032873	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:54469894T>C	ENST00000375151.4	+	3	255	c.234T>C	c.(232-234)gaT>gaC	p.D78D		NM_058163.1	NP_477511.1	Q969E8	TSR2_HUMAN	TSR2, 20S rRNA accumulation, homolog (S. cerevisiae)	78					rRNA processing (GO:0006364)					breast(1)|endometrium(3)|lung(2)	6						ACGAGTTTGATACAGTTGTGG	0.517													t|||	19	0.00503311	0.0023	0.0072	3775	,	,		13203	0.0		0.0099	False		,,,				2504	0.001				p.D78D		Atlas-SNP	.											.	TSR2	15	.	0			c.T234C						PASS	.			2,3833		0,2,0,1630,571	141.0	123.0	129.0		234	2.1	0.9	X	dbSNP_126	129	38,6690		0,28,10,2400,1862	no	coding-synonymous	TSR2	NM_058163.1		0,30,10,4030,2433	CC,CT,C,TT,T		0.5648,0.0522,0.3787		78/192	54469894	40,10523	2203	4300	6503	SO:0001819	synonymous_variant	90121	exon3			GTTTGATACAGTT	BC007699	CCDS14358.1	Xp11.22	2008-10-01			ENSG00000158526	ENSG00000158526			25455	protein-coding gene	gene with protein product	"""WGG motif containing 1"""					9417904	Standard	NM_058163		Approved	DT1P1A10, RP1-112K5.2, WGG1	uc004dte.3	Q969E8	OTTHUMG00000021628	ENST00000375151.4:c.234T>C	X.37:g.54469894T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_058163		Silent	SNP	ENST00000375151.4	37	CCDS14358.1																																																																																			T|0.996;C|0.004	0.004	strong		0.517	TSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056802.1	NM_058163	
FAXDC2	10826	hgsc.bcm.edu	37	5	154203121	154203121	+	Missense_Mutation	SNP	C	C	T	rs17641488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:154203121C>T	ENST00000326080.5	-	6	821	c.398G>A	c.(397-399)cGc>cAc	p.R133H	FAXDC2_ENST00000517938.1_Missense_Mutation_p.R110H|FAXDC2_ENST00000523997.1_5'UTR	NM_032385.3	NP_115761.2	Q96IV6	FXDC2_HUMAN	fatty acid hydroxylase domain containing 2	133			R -> H (in dbSNP:rs17641488).		fatty acid biosynthetic process (GO:0006633)	integral component of membrane (GO:0016021)	iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)										AAGAACTGTGCGGATAGACTG	0.547													C|||	171	0.0341454	0.0038	0.0476	5008	,	,		21856	0.0089		0.0716	False		,,,				2504	0.0532				p.R133H		Atlas-SNP	.											.	.	.	.	0			c.G398A						PASS	.	C	HIS/ARG	56,3932		0,56,1938	93.0	97.0	96.0		398	-0.7	0.1	5	dbSNP_123	96	764,7524		33,698,3413	yes	missense	C5orf4	NM_032385.3	29	33,754,5351	TT,TC,CC		9.2181,1.4042,6.6797	benign	133/334	154203121	820,11456	1994	4144	6138	SO:0001583	missense	10826	exon6			ACTGTGCGGATAG	AF159165	CCDS43390.1	5q31-q32	2013-03-04	2013-03-04	2013-03-04	ENSG00000170271	ENSG00000170271		"""Fatty acid hydroxylase domain containing"""	1334	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 4"""	C5orf4		10843801	Standard	NM_032385		Approved	FLJ13758	uc003lvs.4	Q96IV6	OTTHUMG00000164141	ENST00000326080.5:c.398G>A	5.37:g.154203121C>T	ENSP00000320604:p.Arg133His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	97	0.95098	NM_032385	B4DIE1|Q9BSX6|Q9H8C7	Missense_Mutation	SNP	ENST00000326080.5	37	CCDS43390.1	86	0.039377289377289376	3	0.006097560975609756	17	0.04696132596685083	7	0.012237762237762238	59	0.07783641160949868	C	8.348	0.830349	0.16749	0.014042	0.092181	ENSG00000170271	ENST00000326080;ENST00000517938;ENST00000519501	T;T;T	0.41758	0.99;0.99;0.99	4.77	-0.743	0.11105	.	1.165880	0.06023	N	0.651658	T	0.01222	0.0040	L	0.60455	1.87	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.12268	-1.0554	10	0.15952	T	0.53	.	0.5084	0.00591	0.3582:0.2622:0.1333:0.2463	rs17641488;rs52831482;rs17641488	133	Q96IV6	CE004_HUMAN	H	133;110;110	ENSP00000320604:R133H;ENSP00000430286:R110H;ENSP00000429837:R110H	ENSP00000320604:R133H	R	-	2	0	C5orf4	154183314	0.000000	0.05858	0.102000	0.21198	0.996000	0.88848	-1.086000	0.03386	-0.171000	0.10797	0.561000	0.74099	CGC	C|0.950;T|0.050	0.050	strong		0.547	FAXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377429.1	NM_032385	
TRIM46	80128	hgsc.bcm.edu	37	1	155149718	155149718	+	Silent	SNP	G	G	A	rs3814316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155149718G>A	ENST00000334634.4	+	5	861	c.861G>A	c.(859-861)acG>acA	p.T287T	TRIM46_ENST00000545012.1_Silent_p.T161T|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000368385.4_Silent_p.T287T|TRIM46_ENST00000392451.2_Silent_p.T287T|RP11-201K10.3_ENST00000473363.2_Intron|TRIM46_ENST00000543729.1_Silent_p.T294T|TRIM46_ENST00000368382.1_Silent_p.T264T|TRIM46_ENST00000368383.3_Silent_p.T287T	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	287						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			ACCAGGACACGGTACAGACCC	0.617													G|||	2233	0.445887	0.2194	0.5706	5008	,	,		21930	0.7629		0.3579	False		,,,				2504	0.4274				p.T287T		Atlas-SNP	.											TRIM46,colon,carcinoma,0,1	TRIM46	79	1	0			c.G861A						PASS	.	G		1205,3201	421.1+/-339.2	169,867,1167	120.0	110.0	114.0		861	-10.7	0.1	1	dbSNP_107	114	3060,5540	470.6+/-367.9	533,1994,1773	no	coding-synonymous	TRIM46	NM_025058.3		702,2861,2940	AA,AG,GG		35.5814,27.3491,32.7926		287/760	155149718	4265,8741	2203	4300	6503	SO:0001819	synonymous_variant	80128	exon5			GGACACGGTACAG		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.861G>A	1.37:g.155149718G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	125	68	0.544	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Silent	SNP	ENST00000334634.4	37	CCDS1097.1																																																																																			G|0.609;A|0.391	0.391	strong		0.617	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167592571G>A	ENST00000366832.2	+	6	861	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	244										endometrium(1)|kidney(2)|lung(3)	6						TTCCCAGGCCGCCACGCTGCA	0.592																																					p.A244T		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G730A						PASS	.						23.0	28.0	27.0					6																	167592571		692	1591	2283	SO:0001583	missense	401285	exon6			CAGGCCGCCACGC		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.730G>A	6.37:g.167592571G>A	ENSP00000355797:p.Ala244Thr	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	61	15	0.245902	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	87	0.03983516483516483	17	0.034552845528455285	12	0.03314917127071823	14	0.024475524475524476	44	0.05804749340369393	c	8.486	0.860926	0.17178	.	.	ENSG00000166984	ENST00000366832	T	0.13901	2.55	1.87	-1.19	0.09585	.	.	.	.	.	T	0.00906	0.0030	N	0.11560	0.145	0.09310	N	1	B	0.32968	0.392	B	0.17433	0.018	T	0.43718	-0.9374	9	0.02654	T	1	.	2.6095	0.04887	0.3443:0.2689:0.3868:0.0	rs28690444	244	B9ZVM9	TCP2L_HUMAN	T	244	ENSP00000355797:A244T	ENSP00000283507:A244T	A	+	1	0	TCP10L2	167512561	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.863000	0.04259	-0.321000	0.08627	-1.962000	0.00476	GCC	G|0.965;A|0.035	0.035	strong		0.592	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
ALKBH5	54890	hgsc.bcm.edu	37	17	18088094	18088094	+	Silent	SNP	C	C	T	rs11078411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18088094C>T	ENST00000399138.4	+	1	542	c.537C>T	c.(535-537)caC>caT	p.H179H	RP11-258F1.1_ENST00000583062.1_RNA|RP11-258F1.1_ENST00000577847.1_RNA|ALKBH5_ENST00000541285.1_Intron	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	179					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					TGGTGGAGCACCGCGTCATCC	0.667													C|||	899	0.179513	0.3011	0.1873	5008	,	,		16289	0.0119		0.2078	False		,,,				2504	0.1534				p.H179H	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											.	ALKBH5	24	.	0			c.C537T						PASS	.	C		1136,3026		162,812,1107	34.0	39.0	38.0		537	5.0	1.0	17	dbSNP_120	38	1748,6626		174,1400,2613	no	coding-synonymous	ALKBH5	NM_017758.3		336,2212,3720	TT,TC,CC		20.8741,27.2946,23.0057		179/395	18088094	2884,9652	2081	4187	6268	SO:0001819	synonymous_variant	54890	exon1			GGAGCACCGCGTC	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"""Alkylation repair homologs"""	25996	protein-coding gene	gene with protein product		613303	"""oxoglutarate and iron-dependent oxygenase domain containing"", ""alkB, alkylation repair homolog 5 (E. coli)"""	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.537C>T	17.37:g.18088094C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	93	90	0.967742	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Silent	SNP	ENST00000399138.4	37	CCDS42272.1																																																																																			C|0.787;T|0.213	0.213	strong		0.667	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758	
LYPD6B	130576	hgsc.bcm.edu	37	2	150071221	150071221	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:150071221G>A	ENST00000409029.1	+	7	751	c.549G>A	c.(547-549)ctG>ctA	p.L183L	LYPD6B_ENST00000409642.3_Silent_p.L207L|LYPD6B_ENST00000409876.1_Silent_p.L183L|LYPD6B_ENST00000498249.1_3'UTR|LYPD6B_ENST00000280115.7_Silent_p.L207L			Q8NI32	LPD6B_HUMAN	LY6/PLAUR domain containing 6B	183						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	11						TTCCATTGCTGTGATGCCACC	0.507																																					p.L207L		Atlas-SNP	.											LYPD6B,NS,carcinoma,+2,1	LYPD6B	25	1	0			c.G621A						scavenged	.						157.0	158.0	158.0					2																	150071221		2068	4202	6270	SO:0001819	synonymous_variant	130576	exon7			ATTGCTGTGATGC		CCDS46423.1	2q23.2	2012-07-20			ENSG00000150556	ENSG00000150556			27018	protein-coding gene	gene with protein product	"""cancer/testis antigen 116"""					18360792	Standard	NM_177964		Approved	CT116, LYPD7	uc002twv.1	Q8NI32	OTTHUMG00000153743	ENST00000409029.1:c.549G>A	2.37:g.150071221G>A		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	187	4	0.0213904	NM_177964	D3DP90|Q53TK0|Q7Z747|Q8IXK7	Silent	SNP	ENST00000409029.1	37																																																																																				.	.	none		0.507	LYPD6B-003	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000332299.2	NM_177964	
CCDC183	84960	hgsc.bcm.edu	37	9	139694521	139694521	+	Missense_Mutation	SNP	T	T	G	rs4546744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139694521T>G	ENST00000338005.6	+	4	373	c.338T>G	c.(337-339)cTg>cGg	p.L113R	RP11-216L13.18_ENST00000471502.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.L143R|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		113			L -> R (in dbSNP:rs4546744).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		CTGATCCACCTGGTGCGGCGG	0.667													T|||	1327	0.264976	0.3003	0.2954	5008	,	,		10067	0.2421		0.2177	False		,,,				2504	0.2679				p.L113R		Atlas-SNP	.											KIAA1984,NS,carcinoma,0,1	KIAA1984	39	1	0			c.T338G						PASS	.	T	ARG/LEU	1040,3066		153,734,1166	14.0	17.0	16.0		338	4.8	1.0	9	dbSNP_111	16	1716,6654		209,1298,2678	yes	missense	KIAA1984	NM_001039374.4	102	362,2032,3844	GG,GT,TT		20.5018,25.3288,22.0904	probably-damaging	113/535	139694521	2756,9720	2053	4185	6238	SO:0001583	missense	84960	exon4			TCCACCTGGTGCG																												ENST00000338005.6:c.338T>G	9.37:g.139694521T>G	ENSP00000338013:p.Leu113Arg	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	513	0.2348901098901099	132	0.2682926829268293	98	0.27071823204419887	124	0.21678321678321677	159	0.20976253298153033	T	20.4	3.987669	0.74589	0.253288	0.205018	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.11495	2.77	4.85	4.85	0.62838	.	0.569511	0.13099	U	0.413906	T	0.00012	0.0000	M	0.61703	1.905	0.24583	P	0.99386576	D	0.57257	0.979	P	0.59487	0.858	T	0.37549	-0.9701	9	0.15952	T	0.53	-15.2278	10.827	0.46638	0.0:0.0:0.0:1.0	rs4546744;rs60974315;rs4546744	113	Q5T5S1	K1984_HUMAN	R	113	ENSP00000338013:L113R	ENSP00000338013:L113R	L	+	2	0	KIAA1984	138814342	0.931000	0.31567	1.000000	0.80357	0.960000	0.62799	0.669000	0.25142	1.808000	0.52836	0.379000	0.24179	CTG	T|0.772;G|0.228	0.228	strong		0.667	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
ULBP1	80329	hgsc.bcm.edu	37	6	150285209	150285209	+	Silent	SNP	G	G	C	rs61742437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:150285209G>C	ENST00000229708.3	+	1	67	c.24G>C	c.(22-24)gcG>gcC	p.A8A		NM_025218.2	NP_079494.1	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1	8					antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			large_intestine(3)|lung(5)|pancreas(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)		CCAGCCCCGCGTTCCTTCTGT	0.642													G|||	875	0.17472	0.4569	0.1124	5008	,	,		14283	0.0109		0.1064	False		,,,				2504	0.0767				p.A8A		Atlas-SNP	.											.	ULBP1	25	.	0			c.G24C						PASS	.	G		1724,2682	502.2+/-365.2	354,1016,833	43.0	48.0	46.0		24	0.7	0.0	6	dbSNP_129	46	808,7792	184.3+/-232.3	37,734,3529	no	coding-synonymous	ULBP1	NM_025218.2		391,1750,4362	CC,CG,GG		9.3953,39.1285,19.4679		8/245	150285209	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	80329	exon1			CCCCGCGTTCCTT	AF304377	CCDS5223.1	6q25	2003-04-29			ENSG00000111981	ENSG00000111981			14893	protein-coding gene	gene with protein product		605697				11239445, 11827464	Standard	XM_005267151		Approved	RAET1I	uc003qnp.3	Q9BZM6	OTTHUMG00000015810	ENST00000229708.3:c.24G>C	6.37:g.150285209G>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	12	0.116505	NM_025218	Q5VY81|Q8IZW3|Q8IZX6	Silent	SNP	ENST00000229708.3	37	CCDS5223.1																																																																																			G|0.819;C|0.181	0.181	strong		0.642	ULBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042677.2		
TBX1	6899	hgsc.bcm.edu	37	22	19751829	19751829	+	Silent	SNP	C	C	T	rs2301558	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19751829C>T	ENST00000329705.7	+	5	793	c.664C>T	c.(664-666)Cta>Tta	p.L222L	TBX1_ENST00000332710.4_Silent_p.L222L|TBX1_ENST00000359500.3_Silent_p.L222L	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	222					angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				GACCAACAACCTACTGGACGA	0.652													C|||	1709	0.341254	0.6203	0.3127	5008	,	,		15515	0.1171		0.2087	False		,,,				2504	0.3517				p.L222L		Atlas-SNP	.											.	TBX1	62	.	0			c.C664T						PASS	.	C	,,	2475,1929	622.7+/-394.0	699,1077,426	89.0	78.0	82.0		664,664,664	0.4	1.0	22	dbSNP_100	82	1998,6602	348.2+/-326.9	220,1558,2522	no	coding-synonymous,coding-synonymous,coding-synonymous	TBX1	NM_005992.1,NM_080646.1,NM_080647.1	,,	919,2635,2948	TT,TC,CC		23.2326,43.8011,34.3971	,,	222/373,222/399,222/496	19751829	4473,8531	2202	4300	6502	SO:0001819	synonymous_variant	6899	exon5			AACAACCTACTGG	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.664C>T	22.37:g.19751829C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	40	37	0.925	NM_080647	C6G493|C6G494|O43436|Q96RJ2	Silent	SNP	ENST00000329705.7	37	CCDS13766.1																																																																																			C|0.672;T|0.328	0.328	strong		0.652	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632724	32632724	+	Missense_Mutation	SNP	C	C	T	rs1049083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32632724C>T	ENST00000399084.1	-	3	408	c.230G>A	c.(229-231)gGg>gAg	p.G77E	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.G77E|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.G77E|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.G77E|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	77	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)"""	GCGGTACACCCCCACGTCGCT	0.637									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	973	0.194289	0.2277	0.2104	5008	,	,		5885	0.1855		0.2048	False		,,,				2504	0.136				p.G77E	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G230A						PASS	.	C	GLU/GLY	676,3592		107,462,1565	39.0	39.0	39.0		230	3.2	0.8	6	dbSNP_86	39	1404,7062		214,976,3043	yes	missense	HLA-DQB1	NM_002123.4	98	321,1438,4608	TT,TC,CC		16.584,15.8388,16.3342	benign	77/262	32632724	2080,10654	2134	4233	6367	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TACACCCCCACGT		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.230G>A	6.37:g.32632724C>T	ENSP00000382034:p.Gly77Glu	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	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	379	0.17353479853479853	96	0.1951219512195122	67	0.1850828729281768	90	0.15734265734265734	126	0.1662269129287599	.	12.14	1.849919	0.32699	0.158388	0.16584	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00512	6.89;6.89;6.89;6.89	4.06	3.18	0.36537	.	0.372434	0.26556	N	0.023704	T	0.00356	0.0011	.	.	.	0.29233	P	0.873134	D;B;B;P;B	0.59767	0.986;0.171;0.105;0.493;0.171	P;B;B;B;B	0.50314	0.637;0.194;0.126;0.26;0.126	T	0.63157	-0.6700	8	0.72032	D	0.01	.	9.5212	0.39135	0.0:0.894:0.0:0.106	rs1049083;rs3189164;rs12722126;rs16868387	87;77;42;77;77	Q59F80;A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.;.	E	77	ENSP00000382029:G77E;ENSP00000364080:G77E;ENSP00000407332:G77E;ENSP00000382034:G77E	ENSP00000364080:G77E	G	-	2	0	HLA-DQB1	32740702	0.896000	0.30565	0.796000	0.32109	0.013000	0.08279	1.734000	0.38166	0.934000	0.37316	0.305000	0.20034	GGG	C|0.828;T|0.172	0.172	strong		0.637	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
LAMC3	10319	hgsc.bcm.edu	37	9	133914570	133914570	+	Silent	SNP	G	G	A	rs2293518	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:133914570G>A	ENST00000361069.4	+	6	1351	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	LAMC3_ENST00000480883.1_3'UTR	NM_006059.3	NP_006050.3	Q9Y6N6	LAMC3_HUMAN	laminin, gamma 3	406	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		GCAAGCCCACGGTGACTGGCT	0.647													T|||	776	0.154952	0.1104	0.2061	5008	,	,		19185	0.1399		0.2445	False		,,,				2504	0.1022				p.T406T		Atlas-SNP	.											LAMC3,NS,adenoma,0,1	LAMC3	167	1	0			c.G1218A						PASS	.	T		505,3901		30,445,1728	65.0	59.0	61.0		1218	-10.2	0.0	9	dbSNP_100	61	2181,6419		277,1627,2396	no	coding-synonymous	LAMC3	NM_006059.3		307,2072,4124	AA,AG,GG		25.3605,11.4616,20.652		406/1576	133914570	2686,10320	2203	4300	6503	SO:0001819	synonymous_variant	10319	exon6			GCCCACGGTGACT	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.1218G>A	9.37:g.133914570G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_006059	B1APX9|B1APY0|Q59H72	Silent	SNP	ENST00000361069.4	37	CCDS6938.1																																																																																			G|0.809;A|0.191	0.191	strong		0.647	LAMC3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054717.3	NM_006059	
TPR	7175	hgsc.bcm.edu	37	1	186291512	186291512	+	Silent	SNP	T	T	C	rs10911846	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186291512T>C	ENST00000367478.4	-	45	6695	c.6399A>G	c.(6397-6399)acA>acG	p.T2133T		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	2133					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)		TACTTGGAACTGTTCTGTCTT	0.338			T	NTRK1	papillary thyroid								T|||	151	0.0301518	0.0446	0.013	5008	,	,		20682	0.001		0.0388	False		,,,				2504	0.044				p.T2133T		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A6399G						PASS	.	T		166,3574		1,164,1705	109.0	104.0	105.0		6399	-5.4	0.9	1	dbSNP_120	105	367,7849		11,345,3752	no	coding-synonymous	TPR	NM_003292.2		12,509,5457	CC,CT,TT		4.4669,4.4385,4.458		2133/2364	186291512	533,11423	1870	4108	5978	SO:0001819	synonymous_variant	7175	exon45			TGGAACTGTTCTG	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.6399A>G	1.37:g.186291512T>C		Somatic	311	1	0.00321543		WXS	Illumina HiSeq	Phase_I	324	165	0.509259	NM_003292	Q15655|Q5SWY0|Q99968	Silent	SNP	ENST00000367478.4	37	CCDS41446.1																																																																																			T|0.965;C|0.035	0.035	strong		0.338	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
SPATA20	64847	hgsc.bcm.edu	37	17	48628470	48628470	+	Missense_Mutation	SNP	T	T	A	rs9913430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48628470T>A	ENST00000356488.4	+	11	1530	c.1447T>A	c.(1447-1449)Tca>Aca	p.S483T	SPATA20_ENST00000393244.3_Missense_Mutation_p.S439T|SPATA20_ENST00000511937.1_3'UTR|SPATA20_ENST00000006658.6_Missense_Mutation_p.S499T	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	483			S -> T (in dbSNP:rs9913430). {ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	catalytic activity (GO:0003824)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;9.38e-09)			CTTGCTCAATTCAGGGCTGGA	0.637											OREG0024568	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1785	0.35643	0.7542	0.3617	5008	,	,		13551	0.0843		0.2773	False		,,,				2504	0.1769				p.S499T		Atlas-SNP	.											SPATA20,colon,carcinoma,0,1	SPATA20	59	1	0			c.T1495A						scavenged	.	A	THR/SER	2995,1409	454.5+/-350.7	1020,955,227	35.0	33.0	34.0		1495	-6.5	0.0	17	dbSNP_119	34	2359,6241	696.9+/-404.9	312,1735,2253	yes	missense	SPATA20	NM_022827.2	58	1332,2690,2480	AA,AT,TT		27.4302,31.9936,41.1719	benign	499/803	48628470	5354,7650	2202	4300	6502	SO:0001583	missense	64847	exon12			CTCAATTCAGGGC		CCDS11571.1, CCDS58563.1, CCDS58564.1	17q21.33	2011-03-17			ENSG00000006282	ENSG00000006282			26125	protein-coding gene	gene with protein product	"""hypothetical protein FLJ21347"""	613939				12477932	Standard	NM_022827		Approved	FLJ21347, SSP411, Tisp78	uc002ird.3	Q8TB22	OTTHUMG00000162162	ENST00000356488.4:c.1447T>A	17.37:g.48628470T>A	ENSP00000348878:p.Ser483Thr	Somatic	69	1	0.0144928	119	WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	736	0.336996336996337	345	0.7012195121951219	128	0.35359116022099446	54	0.0944055944055944	209	0.2757255936675462	A	0.808	-0.753198	0.03041	0.680064	0.274302	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.29142	1.58;1.58;1.58	5.95	-6.46	0.01908	Six-hairpin glycosidase (1);Six-hairpin glycosidase-like (1);	1.194140	0.05720	N	0.597621	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.31138	-0.9954	9	0.08599	T	0.76	-33.8639	6.734	0.23399	0.2286:0.0:0.3033:0.4681	rs9913430;rs17855970;rs58643872;rs9913430	483;499	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	T	499;483;439	ENSP00000006658:S499T;ENSP00000348878:S483T;ENSP00000376935:S439T	ENSP00000006658:S499T	S	+	1	0	SPATA20	45983469	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.109000	0.10840	-2.343000	0.00623	-1.068000	0.02270	TCA	T|0.605;A|0.395	0.395	strong		0.637	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827	
ARPC1B	10095	hgsc.bcm.edu	37	7	98985781	98985781	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:98985781C>T	ENST00000451682.1	+	6	598	c.289C>T	c.(289-291)Cgg>Tgg	p.R97W	ARPC1B_ENST00000252725.5_Missense_Mutation_p.R97W|ARPC1B_ENST00000474880.1_3'UTR|ARPC1A_ENST00000432884.2_3'UTR			O15143	ARC1B_HUMAN	actin related protein 2/3 complex, subunit 1B, 41kDa	97					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)			GCGGATCAACCGGGCTGCCCG	0.607																																					p.R97W		Atlas-SNP	.											ARPC1B,NS,carcinoma,-2,1	ARPC1B	41	1	0			c.C289T						scavenged	.						59.0	57.0	58.0					7																	98985781		2203	4300	6503	SO:0001583	missense	10095	exon4			ATCAACCGGGCTG	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.289C>T	7.37:g.98985781C>T	ENSP00000389631:p.Arg97Trp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	184	3	0.0163043	NM_005720	Q9BU00	Missense_Mutation	SNP	ENST00000451682.1	37	CCDS5661.1	.	.	.	.	.	.	.	.	.	.	c	29.3	4.998202	0.93227	.	.	ENSG00000130429	ENST00000443222;ENST00000414376;ENST00000252725;ENST00000455009;ENST00000417330;ENST00000431816;ENST00000427217;ENST00000458033;ENST00000451682	T;T;T;T;T;T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22;-0.22	5.39	4.5	0.54988	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.86053	0.5841	M	0.93150	3.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.90106	0.4188	10	0.87932	D	0	-38.5745	15.5621	0.76256	0.1393:0.8607:0.0:0.0	.	97;97	A4D275;O15143	.;ARC1B_HUMAN	W	97	ENSP00000413173:R97W;ENSP00000398620:R97W;ENSP00000252725:R97W;ENSP00000410238:R97W;ENSP00000403324:R97W;ENSP00000398110:R97W;ENSP00000403211:R97W;ENSP00000388802:R97W;ENSP00000389631:R97W	ENSP00000252725:R97W	R	+	1	2	ARPC1B	98823717	1.000000	0.71417	0.980000	0.43619	0.948000	0.59901	3.969000	0.56816	1.407000	0.46875	-0.277000	0.10078	CGG	.	.	none		0.607	ARPC1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335894.1	NM_005720	
CATSPERD	257062	hgsc.bcm.edu	37	19	5749171	5749171	+	Missense_Mutation	SNP	A	A	G	rs72983139	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5749171A>G	ENST00000381624.3	+	11	1025	c.964A>G	c.(964-966)Atc>Gtc	p.I322V	CATSPERD_ENST00000381614.2_5'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	322					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											CAATCTGGGCATCGTGCCAAG	0.438													a|||	398	0.0794728	0.1672	0.036	5008	,	,		19033	0.0119		0.0249	False		,,,				2504	0.1176				p.I322V		Atlas-SNP	.											.	.	.	.	0			c.A964G						PASS	.		VAL/ILE	513,3223		33,447,1388	88.0	88.0	88.0		964	-6.5	0.0	19	dbSNP_130	88	189,8025		0,189,3918	yes	missense	TMEM146	NM_152784.3	29	33,636,5306	GG,GA,AA		2.3009,13.7313,5.8745	benign	322/799	5749171	702,11248	1868	4107	5975	SO:0001583	missense	257062	exon11			CTGGGCATCGTGC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.964A>G	19.37:g.5749171A>G	ENSP00000371037:p.Ile322Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	120	0.054945054945054944	87	0.17682926829268292	14	0.03867403314917127	2	0.0034965034965034965	17	0.022427440633245383	a	0.139	-1.103923	0.01828	0.137313	0.023009	ENSG00000174898	ENST00000394548;ENST00000381624	T	0.25912	1.77	3.26	-6.52	0.01872	.	2.007800	0.03422	N	0.206446	T	0.00039	0.0001	N	0.14661	0.345	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.04013	0.001	T	0.22068	-1.0227	9	0.20046	T	0.44	-0.2315	3.3693	0.07215	0.3218:0.0:0.3244:0.3538	.	322	Q86XM0	TM146_HUMAN	V	248;322	ENSP00000371037:I322V	ENSP00000371037:I322V	I	+	1	0	TMEM146	5700171	0.000000	0.05858	0.000000	0.03702	0.138000	0.21146	-0.433000	0.06948	-1.175000	0.02751	-0.671000	0.03813	ATC	A|0.957;G|0.043	0.043	strong		0.438	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
KLHL33	123103	hgsc.bcm.edu	37	14	20897676	20897676	+	Missense_Mutation	SNP	T	T	C	rs1953225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20897676T>C	ENST00000344581.4	-	3	1256	c.1034A>G	c.(1033-1035)gAg>gGg	p.E345G		NM_001109997.2	NP_001103467.2	A6NCF5	KLH33_HUMAN	kelch-like family member 33	345			E -> G (in dbSNP:rs1953225).									all_cancers(95;0.00123)		Epithelial(56;7.57e-08)|all cancers(55;8.63e-07)	GBM - Glioblastoma multiforme(265;0.0223)|READ - Rectum adenocarcinoma(17;0.193)		GACATTGAGCTCAGGGTTGTA	0.498													T|||	1298	0.259185	0.3812	0.134	5008	,	,		20948	0.2718		0.2097	False		,,,				2504	0.2209				p.E345G		Atlas-SNP	.											.	KLHL33	37	.	0			c.A1034G						PASS	.	T	GLY/GLU	448,936		84,280,328	187.0	163.0	170.0		1034	5.3	1.0	14	dbSNP_92	170	605,2577		57,491,1043	yes	missense	KLHL33	NM_001109997.2	98	141,771,1371	CC,CT,TT		19.0132,32.3699,23.0618	probably-damaging	345/534	20897676	1053,3513	692	1591	2283	SO:0001583	missense	123103	exon3			TTGAGCTCAGGGT		CCDS53882.1	14q11.2	2013-10-15	2013-02-22		ENSG00000185271	ENSG00000185271		"""Kelch-like"""	31952	protein-coding gene	gene with protein product			"""kelch-like 33 (Drosophila)"""				Standard	NM_001109997		Approved		uc010tli.2	A6NCF5	OTTHUMG00000170982	ENST00000344581.4:c.1034A>G	14.37:g.20897676T>C	ENSP00000341549:p.Glu345Gly	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	55	22	0.4	NM_001109997		Missense_Mutation	SNP	ENST00000344581.4	37	CCDS53882.1	526	0.24084249084249085	173	0.3516260162601626	50	0.13812154696132597	153	0.2674825174825175	150	0.19788918205804748	T	8.186	0.795008	0.16327	0.323699	0.190132	ENSG00000185271	ENST00000344581	T	0.79554	-1.28	5.34	5.34	0.76211	Kelch-type beta propeller (1);	0.269175	0.36034	N	0.002825	T	0.00012	0.0000	L	0.39085	1.19	0.80722	P	0.0	B	0.16603	0.018	B	0.18871	0.023	T	0.05115	-1.0905	9	0.56958	D	0.05	.	12.9404	0.58340	0.0:0.0:0.0:1.0	rs1953225;rs17242641;rs57704167;rs1953225	345	A6NCF5	KLH33_HUMAN	G	345	ENSP00000341549:E345G	ENSP00000341549:E345G	E	-	2	0	KLHL33	19967516	0.003000	0.15002	0.986000	0.45419	0.965000	0.64279	1.324000	0.33712	2.242000	0.73789	0.533000	0.62120	GAG	T|0.747;C|0.253	0.253	strong		0.498	KLHL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411038.1	XM_063481	
KIF24	347240	hgsc.bcm.edu	37	9	34257979	34257979	+	Splice_Site	SNP	C	C	T	rs76547823	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34257979C>T	ENST00000402558.2	-	10	1650	c.1626G>A	c.(1624-1626)cgG>cgA	p.R542R	KIF24_ENST00000379174.3_Splice_Site_p.R408R|KIF24_ENST00000345050.2_Splice_Site_p.R408R|KIF24_ENST00000379166.2_Splice_Site_p.R542R			Q5T7B8	KIF24_HUMAN	kinesin family member 24	542	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)	p.R24R(1)|p.R542R(1)		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)			GTTCTTTGACCCTGTAAATAA	0.358													C|||	239	0.0477236	0.0038	0.0533	5008	,	,		20301	0.1647		0.003	False		,,,				2504	0.0286				p.R542R		Atlas-SNP	.											KIF24,NS,carcinoma,0,2	KIF24	64	2	2	Substitution - coding silent(2)	stomach(2)	c.G1626A						scavenged	.	C		18,4386	21.2+/-45.6	0,18,2184	86.0	96.0	93.0		1626	3.7	1.0	9	dbSNP_131	93	46,8554	27.9+/-77.7	0,46,4254	yes	coding-synonymous-near-splice	KIF24	NM_194313.2		0,64,6438	TT,TC,CC		0.5349,0.4087,0.4922		542/1369	34257979	64,12940	2202	4300	6502	SO:0001630	splice_region_variant	347240	exon11			TTTGACCCTGTAA	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.1626-1G>A	9.37:g.34257979C>T		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	142	75	0.528169	NM_194313	Q2TB93|Q5T7B5|Q5T7B7|Q6ZU97|Q6ZUZ2|Q86XZ0|Q9NV43	Silent	SNP	ENST00000402558.2	37	CCDS6551.2																																																																																			C|0.977;T|0.023	0.023	strong		0.358	KIF24-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052150.5		Silent
TOPBP1	11073	hgsc.bcm.edu	37	3	133329943	133329943	+	Silent	SNP	G	G	A	rs1444601	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:133329943G>A	ENST00000260810.5	-	25	4209	c.4078C>T	c.(4078-4080)Ctg>Ttg	p.L1360L		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1360					cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						ATTCCAGTCAGAACATCAAGT	0.418								Other conserved DNA damage response genes					A|||	3416	0.682109	0.7829	0.634	5008	,	,		17725	0.626		0.7465	False		,,,				2504	0.5716				p.L1360L	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.C4078T						PASS	.	A		2917,841		1131,655,93	195.0	182.0	186.0		4078	0.4	1.0	3	dbSNP_88	186	6028,2192		2227,1574,309	no	coding-synonymous	TOPBP1	NM_007027.3		3358,2229,402	AA,AG,GG		26.6667,22.3789,25.3214		1360/1523	133329943	8945,3033	1879	4110	5989	SO:0001819	synonymous_variant	11073	exon25			CAGTCAGAACATC	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4078C>T	3.37:g.133329943G>A		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	235	234	0.995745	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																			G|0.298;A|0.702	0.702	strong		0.418	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
DPPA3	359787	hgsc.bcm.edu	37	12	7867847	7867847	+	Missense_Mutation	SNP	G	G	C	rs2024320	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7867847G>C	ENST00000345088.2	+	2	268	c.151G>C	c.(151-153)Gaa>Caa	p.E51Q		NM_199286.2	NP_954980.1	Q6W0C5	DPPA3_HUMAN	developmental pluripotency associated 3	51			E -> Q (in dbSNP:rs2024320).		chromatin modification (GO:0016568)|embryonic cleavage (GO:0040016)|negative regulation of DNA demethylation (GO:1901536)|protection of DNA demethylation of female pronucleus (GO:0044726)|regulation of genetic imprinting (GO:2000653)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(2)	8				Kidney(36;0.0887)		CGCTAGTAGCGAATCTGTTTC	0.463													G|||	1091	0.217851	0.1884	0.2349	5008	,	,		-128	0.1845		0.3121	False		,,,				2504	0.183				p.E51Q		Atlas-SNP	.											DPPA3,NS,carcinoma,0,1	DPPA3	26	1	0			c.G151C						PASS	.	G	GLN/GLU	943,3463	357.6+/-314.0	99,745,1359	80.0	82.0	81.0		151	-4.9	0.0	12	dbSNP_94	81	2638,5962	421.6+/-353.8	417,1804,2079	no	missense	DPPA3	NM_199286.2	29	516,2549,3438	CC,CG,GG		30.6744,21.4026,27.5334	benign	51/160	7867847	3581,9425	2203	4300	6503	SO:0001583	missense	359787	exon2			AGTAGCGAATCTG	AY317075	CCDS8582.1	12p13.31	2012-10-02			ENSG00000187569	ENSG00000187569			19199	protein-coding gene	gene with protein product		608408					Standard	NM_199286		Approved	Stella	uc001qtf.3	Q6W0C5	OTTHUMG00000168434	ENST00000345088.2:c.151G>C	12.37:g.7867847G>C	ENSP00000339250:p.Glu51Gln	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	143	67	0.468531	NM_199286	Q0P5U3|Q6JZS6	Missense_Mutation	SNP	ENST00000345088.2	37	CCDS8582.1	535	0.24496336996336995	100	0.2032520325203252	88	0.2430939226519337	108	0.1888111888111888	239	0.3153034300791557	G	2.265	-0.368323	0.05069	0.214026	0.306744	ENSG00000187569	ENST00000345088	T	0.46063	0.88	2.48	-4.95	0.03048	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.28299	-1.0048	8	0.48119	T	0.1	0.0024	8.0509	0.30577	0.165:0.5213:0.3137:0.0	rs2024320;rs2024320	51	Q6W0C5	DPPA3_HUMAN	Q	51	ENSP00000339250:E51Q	ENSP00000339250:E51Q	E	+	1	0	DPPA3	7759114	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.670000	0.00844	-2.785000	0.00359	-1.250000	0.01514	GAA	G|0.700;C|0.300	0.300	strong		0.463	DPPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399718.1	NM_199286	
LCT	3938	hgsc.bcm.edu	37	2	136555659	136555659	+	Missense_Mutation	SNP	T	T	C	rs2322659	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:136555659T>C	ENST00000264162.2	-	13	4926	c.4916A>G	c.(4915-4917)aAt>aGt	p.N1639S		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1639	4 X approximate repeats.		N -> S (in dbSNP:rs2322659). {ECO:0000269|PubMed:1902057}.		carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CATCACCTCATTGTAATCTCC	0.582											OREG0014998	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2217	0.442692	0.3011	0.4669	5008	,	,		19883	0.4623		0.6382	False		,,,				2504	0.3957				p.N1639S		Atlas-SNP	.											LCT,NS,carcinoma,-1,2	LCT	309	2	0			c.A4916G						PASS	.	T	SER/ASN	1794,2612		346,1102,755	121.0	108.0	113.0		4916	-8.9	0.0	2	dbSNP_100	113	6240,2360		2335,1570,395	yes	missense	LCT	NM_002299.2	46	2681,2672,1150	CC,CT,TT		27.4419,40.7172,38.2285	benign	1639/1928	136555659	8034,4972	2203	4300	6503	SO:0001583	missense	3938	exon13			ACCTCATTGTAAT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4916A>G	2.37:g.136555659T>C	ENSP00000264162:p.Asn1639Ser	Somatic	48	0	0	1626	WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	1066	0.4880952380952381	132	0.2682926829268293	180	0.4972375690607735	262	0.458041958041958	492	0.6490765171503958	T	9.982	1.228511	0.22542	0.407172	0.725581	ENSG00000115850	ENST00000264162	T	0.30182	1.54	5.76	-8.89	0.00785	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.634460	0.18103	N	0.151626	T	0.00012	0.0000	N	0.12961	0.28	0.80722	P	0.0	B	0.15473	0.013	B	0.20767	0.031	T	0.37709	-0.9694	9	0.33940	T	0.23	0.1499	10.073	0.42345	0.0:0.2833:0.4665:0.2502	rs2322659;rs3739023;rs61091462;rs2322659	1639	P09848	LPH_HUMAN	S	1639	ENSP00000264162:N1639S	ENSP00000264162:N1639S	N	-	2	0	LCT	136272129	0.000000	0.05858	0.000000	0.03702	0.963000	0.63663	-0.869000	0.04232	-1.651000	0.01504	0.533000	0.62120	AAT	T|0.466;C|0.534	0.534	strong		0.582	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
C2CD2	25966	hgsc.bcm.edu	37	21	43327793	43327793	+	Silent	SNP	C	C	T	rs3746904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43327793C>T	ENST00000380486.3	-	9	1360	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S	C2CD2_ENST00000329623.7_Silent_p.S218S	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	373						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						AGCCCAGCACCGAGCTGCCGC	0.642													C|||	1832	0.365815	0.3169	0.4683	5008	,	,		15888	0.3859		0.3509	False		,,,				2504	0.3538				p.S373S		Atlas-SNP	.											C2CD2,NS,carcinoma,0,1	C2CD2	47	1	0			c.G1119A						PASS	.	C	,	1580,2826		320,940,943	22.0	25.0	24.0		1119,654	-7.6	0.0	21	dbSNP_107	24	3014,5586		524,1966,1810	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	844,2906,2753	TT,TC,CC		35.0465,35.8602,35.3222	,	373/697,218/542	43327793	4594,8412	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon9			CAGCACCGAGCTG	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.1119G>A	21.37:g.43327793C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1																																																																																			C|0.655;T|0.345	0.345	strong		0.642	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
GCC1	79571	hgsc.bcm.edu	37	7	127224286	127224286	+	Silent	SNP	A	A	G	rs3735642	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:127224286A>G	ENST00000321407.2	-	1	1375	c.951T>C	c.(949-951)gaT>gaC	p.D317D	GCC1_ENST00000497650.1_Intron	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	317					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						GCAGCCGGGGATCTGGCTGAT	0.498											OREG0003809	type=REGULATORY REGION|Gene=GCC1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	1536	0.306709	0.1452	0.2248	5008	,	,		20208	0.7034		0.2147	False		,,,				2504	0.2689				p.D317D		Atlas-SNP	.											.	GCC1	83	.	0			c.T951C						PASS	.	G		697,3709	761.1+/-413.0	64,569,1570	94.0	91.0	92.0		951	2.1	1.0	7	dbSNP_107	92	1695,6905	738.3+/-407.1	155,1385,2760	no	coding-synonymous	GCC1	NM_024523.5		219,1954,4330	GG,GA,AA		19.7093,15.8193,18.3915		317/776	127224286	2392,10614	2203	4300	6503	SO:0001819	synonymous_variant	79571	exon1			CCGGGGATCTGGC	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"""golgi coiled-coil 1"""			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.951T>C	7.37:g.127224286A>G		Somatic	191	0	0	1555	WXS	Illumina HiSeq	Phase_I	162	69	0.425926	NM_024523	Q9H6N7	Silent	SNP	ENST00000321407.2	37	CCDS5796.1																																																																																			A|0.765;G|0.235	0.235	strong		0.498	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523	
TRIOBP	11078	hgsc.bcm.edu	37	22	38151170	38151170	+	Silent	SNP	G	G	A	rs11704996	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38151170G>A	ENST00000406386.3	+	14	5805	c.5550G>A	c.(5548-5550)gtG>gtA	p.V1850V	TRIOBP_ENST00000403663.2_Silent_p.V137V|TRIOBP_ENST00000407319.2_Silent_p.V137V	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1850	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)					AGTACGCGGTGCAGCGCAACT	0.617													G|||	198	0.0395367	0.0348	0.062	5008	,	,		20784	0.0248		0.0517	False		,,,				2504	0.0327				p.V1850V		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,+2,2	TRIOBP	262	2	0			c.G5550A						PASS	.	G	,,	244,4162	140.0+/-175.5	7,230,1966	63.0	48.0	53.0		5550,411,411	0.9	1.0	22	dbSNP_120	53	467,8133	136.2+/-193.3	7,453,3840	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIOBP	NM_001039141.2,NM_007032.5,NM_138632.2	,,	14,683,5806	AA,AG,GG		5.4302,5.5379,5.4667	,,	1850/2366,137/653,137/432	38151170	711,12295	2203	4300	6503	SO:0001819	synonymous_variant	11078	exon14			CGCGGTGCAGCGC	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.5550G>A	22.37:g.38151170G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1	98	0.04487179487179487	13	0.026422764227642278	27	0.07458563535911603	20	0.03496503496503497	38	0.05013192612137203	G	13.99	2.403323	0.42613	0.055379	0.054302	ENSG00000100106	ENST00000428075	.	.	.	4.77	0.926	0.19430	.	.	.	.	.	T	0.08313	0.0207	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03852	-1.0998	4	.	.	.	.	7.9551	0.30038	0.1565:0.2781:0.5653:0.0	rs11704996	.	.	.	T	91	.	.	A	+	1	0	TRIOBP	36481116	1.000000	0.71417	0.990000	0.47175	0.983000	0.72400	0.803000	0.27083	0.395000	0.25257	0.655000	0.94253	GCA	G|0.950;A|0.050	0.050	strong		0.617	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
UBR4	23352	hgsc.bcm.edu	37	1	19447819	19447819	+	Silent	SNP	T	T	C	rs35802543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:19447819T>C	ENST00000375254.3	-	68	10032	c.10005A>G	c.(10003-10005)gcA>gcG	p.A3335A	UBR4_ENST00000375267.2_Silent_p.A3335A|UBR4_ENST00000375218.3_5'Flank|UBR4_ENST00000375217.2_Silent_p.A3328A|UBR4_ENST00000375226.2_Silent_p.A3311A	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3335					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		AGGCTGCCAGTGCAGCGAGCA	0.577													T|||	230	0.0459265	0.0477	0.0461	5008	,	,		2685	0.001		0.1064	False		,,,				2504	0.0276				p.A3335A		Atlas-SNP	.											.	UBR4	415	.	0			c.A10005G						PASS	.	T		260,4146	148.4+/-182.8	8,244,1951	56.0	59.0	58.0		10005	-9.1	0.5	1	dbSNP_126	58	969,7631	211.5+/-252.1	59,851,3390	no	coding-synonymous	UBR4	NM_020765.2		67,1095,5341	CC,CT,TT		11.2674,5.901,9.4495		3335/5184	19447819	1229,11777	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon68			TGCCAGTGCAGCG	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.10005A>G	1.37:g.19447819T>C		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	260	230	0.884615	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			T|0.921;C|0.079	0.079	strong		0.577	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
DRP2	1821	hgsc.bcm.edu	37	X	100490933	100490933	+	Missense_Mutation	SNP	G	G	C	rs7066252	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100490933G>C	ENST00000395209.3	+	4	729	c.202G>C	c.(202-204)Gtt>Ctt	p.V68L	DRP2_ENST00000402866.1_Missense_Mutation_p.V68L|DRP2_ENST00000541709.1_5'UTR|DRP2_ENST00000538510.1_Missense_Mutation_p.V68L	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	68			V -> L (in dbSNP:rs7066252).		central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(10)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	31						GAACGGGTCTGTTGGTGCCTC	0.517													G|||	414	0.109669	0.1014	0.098	3775	,	,		15204	0.0714		0.1153	False		,,,				2504	0.0245				p.V68L		Atlas-SNP	.											.	DRP2	98	.	0			c.G202C						PASS	.	G	,LEU/VAL	533,3302		37,393,66,1202,505	182.0	146.0	158.0		,202	-1.7	0.7	X	dbSNP_116	158	882,5846		29,562,262,1837,1610	yes	utr-5,missense	DRP2	NM_001171184.1,NM_001939.2	,32	66,955,328,3039,2115	CC,CG,C,GG,G		13.1094,13.8983,13.3958	,benign	,68/958	100490933	1415,9148	2203	4300	6503	SO:0001583	missense	1821	exon4			GGGTCTGTTGGTG	U43519	CCDS14480.2, CCDS55465.1	Xq22	2008-02-05			ENSG00000102385	ENSG00000102385			3032	protein-coding gene	gene with protein product		300052				8640231	Standard	NM_001939		Approved		uc004egz.2	Q13474	OTTHUMG00000022020	ENST00000395209.3:c.202G>C	X.37:g.100490933G>C	ENSP00000378635:p.Val68Leu	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Missense_Mutation	SNP	ENST00000395209.3	37	CCDS14480.2	200	0.12055455093429777	35	0.07743362831858407	24	0.07100591715976332	17	0.03125	55	0.07724719101123595	G	12.53	1.966418	0.34659	0.138983	0.131094	ENSG00000102385	ENST00000402866;ENST00000395209;ENST00000538510	T;T;T	0.05513	3.43;3.43;3.43	5.11	-1.66	0.08265	.	0.936492	0.08956	N	0.869385	T	0.00039	0.0001	L	0.36672	1.1	0.09310	P	0.9999999790665	B	0.02656	0.0	B	0.01281	0.0	T	0.45934	-0.9227	9	0.59425	D	0.04	-1.0308	1.1364	0.01755	0.2713:0.2665:0.3243:0.1379	rs7066252;rs17257627;rs52795917;rs7066252	68	Q13474	DRP2_HUMAN	L	68	ENSP00000385038:V68L;ENSP00000378635:V68L;ENSP00000441051:V68L	ENSP00000362007:V68L	V	+	1	0	DRP2	100377589	0.848000	0.29623	0.658000	0.29665	0.809000	0.45718	-0.569000	0.05902	-0.651000	0.05415	0.600000	0.82982	GTT	0|0.014;C|0.134	0.134	strong		0.517	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939	
ABR	29	hgsc.bcm.edu	37	17	1028676	1028676	+	Missense_Mutation	SNP	C	C	T	rs117732533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1028676C>T	ENST00000302538.5	-	2	234	c.88G>A	c.(88-90)Gac>Aac	p.D30N	ABR_ENST00000544583.2_5'UTR|ABR_ENST00000574437.1_5'UTR	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	30					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CCCTCTCCGTCGTACTCGTCC	0.627													C|||	21	0.00419329	0.0	0.0058	5008	,	,		12183	0.0		0.0169	False		,,,				2504	0.0				p.D30N	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.G88A						PASS	.	C	,ASN/ASP	8,4398	14.3+/-33.2	0,8,2195	112.0	103.0	106.0		,88	5.5	1.0	17	dbSNP_132	106	90,8510	51.5+/-111.7	1,88,4211	yes	utr-5,missense	ABR	NM_001159746.1,NM_021962.2	,23	1,96,6406	TT,TC,CC		1.0465,0.1816,0.7535	,benign	,30/860	1028676	98,12908	2203	4300	6503	SO:0001583	missense	29	exon2			CTCCGTCGTACTC	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	81	protein-coding gene	gene with protein product		600365	"""active BCR-related gene"""			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.88G>A	17.37:g.1028676C>T	ENSP00000303909:p.Asp30Asn	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	37	CCDS10999.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	C	16.51	3.142274	0.57044	0.001816	0.010465	ENSG00000159842	ENST00000302538	T	0.21361	2.01	5.46	5.46	0.80206	.	0.182095	0.48286	D	0.000187	T	0.08133	0.0203	L	0.40543	1.245	0.80722	D	1	P	0.36438	0.553	B	0.25291	0.059	T	0.05241	-1.0897	10	0.23302	T	0.38	.	16.8188	0.85740	0.0:1.0:0.0:0.0	.	30	Q12979	ABR_HUMAN	N	30	ENSP00000303909:D30N	ENSP00000303909:D30N	D	-	1	0	ABR	975426	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	5.071000	0.64382	2.567000	0.86603	0.561000	0.74099	GAC	C|0.992;T|0.008	0.008	strong		0.627	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		
LRRN1	57633	hgsc.bcm.edu	37	3	3886919	3886919	+	Silent	SNP	C	C	T	rs3749348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:3886919C>T	ENST00000319331.3	+	2	1355	c.594C>T	c.(592-594)atC>atT	p.I198I	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	198						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		TTCTCATGATCGGAGAAAACC	0.393													C|||	1060	0.211661	0.2943	0.1455	5008	,	,		18416	0.2619		0.1024	False		,,,				2504	0.2076				p.I198I		Atlas-SNP	.											.	LRRN1	82	.	0			c.C594T						PASS	.	C		1036,3370	371.2+/-319.9	112,812,1279	117.0	126.0	123.0		594	1.8	1.0	3	dbSNP_107	123	1051,7549	220.8+/-258.4	61,929,3310	no	coding-synonymous	LRRN1	NM_020873.5		173,1741,4589	TT,TC,CC		12.2209,23.5134,16.0464		198/717	3886919	2087,10919	2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			CATGATCGGAGAA	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.594C>T	3.37:g.3886919C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			C|0.817;T|0.183	0.183	strong		0.393	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
MT-CYB	4519	hgsc.bcm.edu	37	M	15607	15607	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:15607A>G	ENST00000361789.2	+	1	861	c.861A>G	c.(859-861)aaA>aaG	p.K287K	MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-ND6_ENST00000361681.2_5'Flank			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	287					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						GTCCCTAACAAACTAGGAGGC	0.453											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.K287K		Atlas-SNP	.											.	.	.	.	0			c.A861G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TAACAAACTAGGA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.861A>G	M.37:g.15607A>G		Somatic	8	0	0	585	WXS	Illumina HiSeq	Phase_I	6	6	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.453	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
CBWD6	644019	hgsc.bcm.edu	37	9	69247582	69247582	+	Splice_Site	SNP	G	G	C	rs201502273		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:69247582G>C	ENST00000377457.5	-	5	536		c.e5-1		CBWD6_ENST00000377449.1_Splice_Site|CBWD6_ENST00000382399.4_Intron	NM_001085457.1	NP_001078926.1	Q4V339	CBWD6_HUMAN	COBW domain containing 6								ATP binding (GO:0005524)			lung(4)	4						GCCACTGCACGTGAAAATATA	0.289																																					.		Atlas-SNP	.											CBWD6,NS,neuroblastoma,0,1	CBWD6	19	1	0			c.431-1C>G						scavenged	.						19.0	13.0	15.0					9																	69247582		1960	3639	5599	SO:0001630	splice_region_variant	644019	exon6			CTGCACGTGAAAA		CCDS43827.1	9q13	2006-06-30			ENSG00000204790	ENSG00000204790			31978	protein-coding gene	gene with protein product							Standard	NM_001085457		Approved	OTTHUMG00000066820	uc004afj.4	Q4V339	OTTHUMG00000066820	ENST00000377457.5:c.431-1C>G	9.37:g.69247582G>C		Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	46	8	0.173913	NM_001085457		Splice_Site	SNP	ENST00000377457.5	37	CCDS43827.1	.	.	.	.	.	.	.	.	.	.	g	8.385	0.838326	0.16891	.	.	ENSG00000204790	ENST00000377457;ENST00000377450;ENST00000377449;ENST00000377445;ENST00000536466	.	.	.	2.63	2.63	0.31362	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.326	0.37993	0.0:0.7769:0.2231:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CBWD6	68537402	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	5.187000	0.65087	0.454000	0.26884	-1.123000	0.02005	.	G|0.500;C|0.500	0.500	weak		0.289	CBWD6-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143172.2	XM_928822	Intron
CEP70	80321	hgsc.bcm.edu	37	3	138289221	138289221	+	Missense_Mutation	SNP	C	C	T	rs1673607	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:138289221C>T	ENST00000264982.3	-	6	670	c.404G>A	c.(403-405)aGt>aAt	p.S135N	CEP70_ENST00000478673.1_5'UTR|CEP70_ENST00000484888.1_Missense_Mutation_p.S135N|CEP70_ENST00000464035.1_Missense_Mutation_p.S135N|CEP70_ENST00000481834.1_Missense_Mutation_p.S135N|CEP70_ENST00000542237.1_Missense_Mutation_p.S115N|CEP70_ENST00000489254.1_Intron	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	135			S -> N (in dbSNP:rs1673607). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						GCAAGCCCTACTTAGTGATTC	0.368													T|||	3459	0.690695	0.5923	0.7061	5008	,	,		18718	0.9425		0.5338	False		,,,				2504	0.7147				p.S135N		Atlas-SNP	.											.	CEP70	51	.	0			c.G404A						PASS	.	T	ASN/SER	2629,1775	524.9+/-371.5	780,1069,353	148.0	139.0	142.0		404	-0.5	1.0	3	dbSNP_89	142	4739,3857	541.6+/-384.0	1322,2095,881	yes	missense	CEP70	NM_024491.2	46	2102,3164,1234	TT,TC,CC		44.8697,40.3043,43.3231	benign	135/598	138289221	7368,5632	2202	4298	6500	SO:0001583	missense	80321	exon6			GCCCTACTTAGTG	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.404G>A	3.37:g.138289221C>T	ENSP00000264982:p.Ser135Asn	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	285	122	0.42807	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	37	CCDS3102.1	1487	0.6808608058608059	293	0.5955284552845529	238	0.6574585635359116	543	0.9493006993006993	413	0.5448548812664907	T	0.197	-1.047852	0.01981	0.596957	0.551303	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000484888;ENST00000474781;ENST00000481834;ENST00000468900;ENST00000462419;ENST00000464035	T;T;T;T;T;T;T;T	0.46451	1.44;1.44;1.44;1.44;1.44;0.87;0.87;0.88	4.98	-0.474	0.12108	.	0.608657	0.17900	N	0.158213	T	0.00012	0.0000	N	0.01277	-0.915	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.24297	-1.0164	9	0.07325	T	0.83	-10.1296	4.2353	0.10623	0.1737:0.3805:0.0:0.4458	rs1673607;rs17845490;rs17856867;rs17858371;rs52817699;rs56945954;rs1673607	115;135;135	F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;CEP70_HUMAN	N	135;115;135;117;135;114;115;135	ENSP00000264982:S135N;ENSP00000444128:S115N;ENSP00000419231:S135N;ENSP00000419833:S117N;ENSP00000417465:S135N;ENSP00000418131:S114N;ENSP00000417819:S115N;ENSP00000419743:S135N	ENSP00000264982:S135N	S	-	2	0	CEP70	139771911	0.994000	0.37717	0.989000	0.46669	0.193000	0.23685	0.029000	0.13666	-0.140000	0.11394	-1.017000	0.02453	AGT	C|0.378;T|0.622	0.622	strong		0.368	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
PPIL2	23759	hgsc.bcm.edu	37	22	22039199	22039199	+	Silent	SNP	C	C	T	rs861833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:22039199C>T	ENST00000335025.8	+	10	802	c.711C>T	c.(709-711)aaC>aaT	p.N237N	PPIL2_ENST00000398831.3_Silent_p.N237N|PPIL2_ENST00000412327.1_Silent_p.N237N|PPIL2_ENST00000492445.2_Silent_p.N237N|PPIL2_ENST00000406385.1_Silent_p.N237N|PPIL2_ENST00000456792.2_Silent_p.N216N					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					ACAAGCTGAACGCTGTGAGTG	0.617													C|||	347	0.0692891	0.0053	0.0994	5008	,	,		17632	0.001		0.1799	False		,,,				2504	0.091				p.N237N		Atlas-SNP	.											PPIL2,colon,carcinoma,0,1	PPIL2	38	1	0			c.C711T						PASS	.	C	,,	136,4268	97.6+/-136.3	3,130,2069	46.0	48.0	47.0		711,711,711	-5.7	0.5	22	dbSNP_86	47	1394,7206	266.8+/-286.9	115,1164,3021	no	coding-synonymous,coding-synonymous,coding-synonymous	PPIL2	NM_014337.3,NM_148175.2,NM_148176.2	,,	118,1294,5090	TT,TC,CC		16.2093,3.0881,11.7656	,,	237/521,237/521,237/528	22039199	1530,11474	2202	4300	6502	SO:0001819	synonymous_variant	23759	exon10			GCTGAACGCTGTG		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"""U-box domain containing"""	9261	protein-coding gene	gene with protein product	"""U-box domain containing 7"""	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.711C>T	22.37:g.22039199C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_014337		Silent	SNP	ENST00000335025.8	37	CCDS13793.1																																																																																			C|0.901;T|0.099	0.099	strong		0.617	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		
SLIT3	6586	hgsc.bcm.edu	37	5	168244447	168244447	+	Silent	SNP	C	C	G	rs4867964	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:168244447C>G	ENST00000519560.1	-	8	1070	c.651G>C	c.(649-651)ctG>ctC	p.L217L	SLIT3_ENST00000404867.3_Silent_p.L217L|SLIT3_ENST00000332966.8_Silent_p.L217L	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	217	LRRCT 1.				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)			AGTCGCAGTACAGGTGGTTGG	0.612													C|||	730	0.145767	0.2753	0.085	5008	,	,		16531	0.0605		0.1054	False		,,,				2504	0.1431				p.L217L	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.G651C						PASS	.	C		1094,3312	394.9+/-329.4	157,780,1266	55.0	51.0	53.0		651	4.6	1.0	5	dbSNP_111	53	1020,7580	216.7+/-255.6	56,908,3336	no	coding-synonymous	SLIT3	NM_003062.2		213,1688,4602	GG,GC,CC		11.8605,24.8298,16.254		217/1524	168244447	2114,10892	2203	4300	6503	SO:0001819	synonymous_variant	6586	exon8			GCAGTACAGGTGG	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.651G>C	5.37:g.168244447C>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	120	57	0.475	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Silent	SNP	ENST00000519560.1	37	CCDS4369.1																																																																																			C|0.847;G|0.153	0.153	strong		0.612	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
LRRC15	131578	hgsc.bcm.edu	37	3	194081089	194081089	+	Silent	SNP	C	C	T	rs11713861	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194081089C>T	ENST00000347624.3	-	2	769	c.684G>A	c.(682-684)ctG>ctA	p.L228L	LRRC15_ENST00000428839.1_Silent_p.L234L|LRRC15_ENST00000439944.2_Silent_p.L234L	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	228					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GGTTCTGCTGCAGAGCCAGTT	0.557													C|||	738	0.147364	0.1573	0.1398	5008	,	,		18899	0.0685		0.2416	False		,,,				2504	0.1237				p.L234L		Atlas-SNP	.											.	LRRC15	137	.	0			c.G702A						PASS	.	C	,	736,3670	302.4+/-287.4	50,636,1517	158.0	164.0	162.0		702,684	-4.0	1.0	3	dbSNP_120	162	2214,6386	377.6+/-338.6	283,1648,2369	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	333,2284,3886	TT,TC,CC		25.7442,16.7045,22.6818	,	234/588,228/582	194081089	2950,10056	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			CTGCTGCAGAGCC	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.684G>A	3.37:g.194081089C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	199	118	0.592965	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			C|0.792;T|0.208	0.208	strong		0.557	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
CLYBL	171425	hgsc.bcm.edu	37	13	100511247	100511247	+	Missense_Mutation	SNP	G	G	A	rs35680839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:100511247G>A	ENST00000376360.1	+	3	409	c.382G>A	c.(382-384)Gtc>Atc	p.V128I	CLYBL_ENST00000444838.2_Missense_Mutation_p.V128I|CLYBL_ENST00000339105.4_Missense_Mutation_p.V128I|CLYBL_ENST00000376354.1_Missense_Mutation_p.V128I|CLYBL_ENST00000376355.3_Missense_Mutation_p.V128I			Q8N0X4	CLYBL_HUMAN	citrate lyase beta like	128			V -> I (in dbSNP:rs35680839).			mitochondrion (GO:0005739)	lyase activity (GO:0016829)|metal ion binding (GO:0046872)			NS(1)|kidney(6)|large_intestine(6)|lung(10)|skin(2)	25	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					GCAATCCCGGGTCCTTCCTTC	0.493													G|||	273	0.0545128	0.0	0.0764	5008	,	,		17544	0.1558		0.0487	False		,,,				2504	0.0143				p.V128I		Atlas-SNP	.											.	CLYBL	48	.	0			c.G382A						PASS	.	G	ILE/VAL	51,4355	50.9+/-86.3	0,51,2152	74.0	69.0	71.0		382	4.2	1.0	13	dbSNP_126	71	391,8209	124.4+/-183.2	15,361,3924	yes	missense	CLYBL	NM_206808.2	29	15,412,6076	AA,AG,GG		4.5465,1.1575,3.3984	benign	128/341	100511247	442,12564	2203	4300	6503	SO:0001583	missense	171425	exon3			TCCCGGGTCCTTC	AF428253	CCDS32002.1	13q32.3	2011-04-08			ENSG00000125246	ENSG00000125246			18355	protein-coding gene	gene with protein product		609686					Standard	XM_005254030		Approved	CLB	uc001vok.3	Q8N0X4	OTTHUMG00000017278	ENST00000376360.1:c.382G>A	13.37:g.100511247G>A	ENSP00000365538:p.Val128Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_206808	Q5W0F7|Q8TDH8	Missense_Mutation	SNP	ENST00000376360.1	37	CCDS32002.1	160	0.07326007326007326	0	0.0	26	0.0718232044198895	102	0.17832167832167833	32	0.04221635883905013	G	13.06	2.124978	0.37533	0.011575	0.045465	ENSG00000125246	ENST00000376355;ENST00000376360;ENST00000444838;ENST00000376354;ENST00000339105;ENST00000416504;ENST00000443887	T;T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59;1.59	5.91	4.17	0.49024	Aldehyde-lyase domain (1);Pyruvate/Phosphoenolpyruvate kinase (2);	0.352028	0.32655	N	0.005815	T	0.00039	0.0001	L	0.40543	1.245	0.26918	P	0.9667446	B;B;B	0.20550	0.034;0.046;0.034	B;B;B	0.22152	0.029;0.017;0.038	T	0.15009	-1.0452	9	0.26408	T	0.33	-16.5761	10.1485	0.42778	0.2151:0.0:0.7849:0.0	rs35680839	128;128;128	B4DU60;Q8N0X4-2;Q8N0X4	.;.;CLYBL_HUMAN	I	128;128;128;128;128;45;45	ENSP00000365533:V128I;ENSP00000365538:V128I;ENSP00000404768:V128I;ENSP00000365532:V128I;ENSP00000342991:V128I;ENSP00000403408:V45I;ENSP00000401586:V45I	ENSP00000342991:V128I	V	+	1	0	CLYBL	99309248	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.470000	0.53100	1.503000	0.48686	0.655000	0.94253	GTC	G|0.956;A|0.044	0.044	strong		0.493	CLYBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045611.1		
SOS2	6655	hgsc.bcm.edu	37	14	50585248	50585248	+	Silent	SNP	C	C	T	rs2227276	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:50585248C>T	ENST00000216373.5	-	23	4087	c.3813G>A	c.(3811-3813)ccG>ccA	p.P1271P	SOS2_ENST00000543680.1_Silent_p.P1238P|VCPKMT_ENST00000395860.2_5'Flank|VCPKMT_ENST00000395859.2_5'Flank	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1271					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					AGCATCGACGCGGTACCCTTG	0.517													C|||	1218	0.243211	0.2201	0.2435	5008	,	,		17245	0.4315		0.1461	False		,,,				2504	0.18				p.P1271P		Atlas-SNP	.											.	SOS2	195	.	0			c.G3813A						PASS	.	C		883,3523	342.8+/-307.3	89,705,1409	145.0	120.0	128.0		3813	-3.7	1.0	14	dbSNP_98	128	1355,7245	264.9+/-285.8	113,1129,3058	no	coding-synonymous	SOS2	NM_006939.2		202,1834,4467	TT,TC,CC		15.7558,20.0409,17.2074		1271/1333	50585248	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon23			TCGACGCGGTACC	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.3813G>A	14.37:g.50585248C>T		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	153	81	0.529412	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			T|0.202;C|0.798	0.202	strong		0.517	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
CCDC61	729440	hgsc.bcm.edu	37	19	46518651	46518651	+	Missense_Mutation	SNP	A	A	G	rs7895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46518651A>G	ENST00000595358.1	+	7	860	c.811A>G	c.(811-813)Acg>Gcg	p.T271A	CCDC61_ENST00000536603.1_Intron|CCDC61_ENST00000594087.1_Intron|CCDC61_ENST00000263284.2_Missense_Mutation_p.T328A	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	271						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		CCGGCTGAAGACGCTGACCAG	0.721													A|||	575	0.114816	0.053	0.0663	5008	,	,		6141	0.1081		0.1392	False		,,,				2504	0.2147				p.T271A		Atlas-SNP	.											.	CCDC61	32	.	0			c.A811G						PASS	.		ALA/THR	188,3606		4,180,1713	14.0	16.0	16.0		982	0.1	0.8	19	dbSNP_52	16	995,7003		50,895,3054	yes	missense	CCDC61	NM_001080402.1	58	54,1075,4767	GG,GA,AA		12.4406,4.9552,10.0322	benign	328/532	46518651	1183,10609	1897	3999	5896	SO:0001583	missense	729440	exon7			CTGAAGACGCTGA		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.811A>G	19.37:g.46518651A>G	ENSP00000471454:p.Thr271Ala	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	32	11	0.34375	NM_001267723	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	224	0.10256410256410256	27	0.054878048780487805	28	0.07734806629834254	71	0.12412587412587413	98	0.12928759894459102	A	12.21	1.868702	0.32977	0.049552	0.124406	ENSG00000104983	ENST00000263284	.	.	.	3.86	0.117	0.14652	.	0.282143	0.36303	N	0.002663	T	0.00300	0.0009	L	0.36672	1.1	0.09310	P	0.99999999003817	B	0.02656	0.0	B	0.06405	0.002	T	0.03184	-1.1063	8	0.38643	T	0.18	-7.0451	3.1397	0.06451	0.5895:0.0:0.2303:0.1802	rs7895;rs17349438	271	Q9Y6R9	CCD61_HUMAN	A	328	.	ENSP00000263284:T328A	T	+	1	0	CCDC61	51210491	0.995000	0.38212	0.816000	0.32577	0.823000	0.46562	1.816000	0.38992	0.058000	0.16222	0.249000	0.18162	ACG	A|0.897;G|0.103	0.103	strong		0.721	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	
OR51I2	390064	hgsc.bcm.edu	37	11	5475118	5475118	+	Missense_Mutation	SNP	A	A	G	rs12577167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5475118A>G	ENST00000341449.2	+	1	481	c.400A>G	c.(400-402)Act>Gct	p.T134A	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	134			T -> A (in dbSNP:rs12577167).		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)		GCGCTATGCAACTGTGCTCAC	0.478													A|||	965	0.192692	0.0666	0.1628	5008	,	,		24623	0.3581		0.1282	False		,,,				2504	0.2802				p.T134A		Atlas-SNP	.											.	OR51I2	76	.	0			c.A400G						PASS	.	A	ALA/THR	307,4095	165.8+/-197.2	16,275,1910	159.0	148.0	152.0		400	1.8	0.8	11	dbSNP_120	152	1091,7503	227.6+/-262.9	70,951,3276	yes	missense	OR51I2	NM_001004754.2	58	86,1226,5186	GG,GA,AA		12.6949,6.9741,10.7572	benign	134/313	5475118	1398,11598	2201	4297	6498	SO:0001583	missense	390064	exon1			TATGCAACTGTGC	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.400A>G	11.37:g.5475118A>G	ENSP00000341987:p.Thr134Ala	Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	259	128	0.494208	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	383	0.17536630036630035	36	0.07317073170731707	57	0.1574585635359116	186	0.32517482517482516	104	0.13720316622691292	A	9.901	1.206760	0.22205	0.069741	0.126949	ENSG00000187918	ENST00000341449	T	0.00545	6.67	5.58	1.77	0.24775	GPCR, rhodopsin-like superfamily (1);	0.185807	0.37857	N	0.001913	T	0.00012	0.0000	L	0.31207	0.915	0.58432	P	1.999999999946489E-6	B	0.09022	0.002	B	0.06405	0.002	T	0.47433	-0.9118	9	0.45353	T	0.12	.	2.1499	0.03797	0.444:0.1251:0.0742:0.3567	rs12577167;rs52795804;rs61607180;rs12577167	134	Q9H344	O51I2_HUMAN	A	134	ENSP00000341987:T134A	ENSP00000341987:T134A	T	+	1	0	OR51I2	5431694	0.000000	0.05858	0.845000	0.33349	0.907000	0.53573	-1.476000	0.02333	0.520000	0.28426	0.533000	0.62120	ACT	A|0.857;G|0.143	0.143	strong		0.478	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
SETD4	54093	hgsc.bcm.edu	37	21	37417997	37417997	+	Silent	SNP	G	G	A	rs79501672	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:37417997G>A	ENST00000399215.1	-	5	1981	c.609C>T	c.(607-609)acC>acT	p.T203T	SETD4_ENST00000399205.1_Silent_p.T179T|SETD4_ENST00000481477.1_5'UTR|SETD4_ENST00000399207.1_Silent_p.T203T|SETD4_ENST00000332131.4_Silent_p.T203T|SETD4_ENST00000399208.2_Silent_p.T203T|SETD4_ENST00000399201.1_Silent_p.T179T|SETD4_ENST00000399212.1_Silent_p.T179T			Q9NVD3	SETD4_HUMAN	SET domain containing 4	203	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						TGGTGTTGACGGTGCACCAAG	0.582													G|||	35	0.00698882	0.0015	0.0086	5008	,	,		18209	0.001		0.0258	False		,,,				2504	0.0				p.T203T		Atlas-SNP	.											.	SETD4	37	.	0			c.C609T						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	70.0	61.0	64.0		609,609	-10.2	0.2	21	dbSNP_132	64	139,8461	69.4+/-131.9	0,139,4161	no	coding-synonymous,coding-synonymous	SETD4	NM_001007259.1,NM_017438.3	,	0,153,6350	AA,AG,GG		1.6163,0.3177,1.1764	,	203/308,203/441	37417997	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	54093	exon6			GTTGACGGTGCAC	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.609C>T	21.37:g.37417997G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	138	69	0.5	NM_001007259	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Silent	SNP	ENST00000399215.1	37	CCDS13640.1																																																																																			G|0.989;A|0.011	0.011	strong		0.582	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144060802	144060802	+	Missense_Mutation	SNP	C	C	T	rs3823677		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:144060802C>T	ENST00000056217.5	+	2	1214	c.1040C>T	c.(1039-1041)aCc>aTc	p.T347I	ARHGEF5_ENST00000471847.2_5'Flank	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	347					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					AAGAGTCAAACCTTTTTGGGA	0.527																																					p.T347I		Atlas-SNP	.											ARHGEF5,colon,carcinoma,+1,1	ARHGEF5	73	1	0			c.C1040T						scavenged	.						62.0	56.0	58.0					7																	144060802		2079	3981	6060	SO:0001583	missense	7984	exon2			GTCAAACCTTTTT	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.1040C>T	7.37:g.144060802C>T	ENSP00000056217:p.Thr347Ile	Somatic	462	2	0.004329		WXS	Illumina HiSeq	Phase_I	1202	541	0.450083	NM_005435	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	764	0.3498168498168498	142	0.2886178861788618	126	0.34806629834254144	284	0.4965034965034965	212	0.2796833773087071	c	8.471	0.857559	0.17106	.	.	ENSG00000050327	ENST00000056217	T	0.73047	-0.71	3.54	-2.18	0.07037	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.44802	-0.9304	7	.	.	.	-0.3178	0.5401	0.00644	0.2016:0.2872:0.2203:0.2909	.	347	Q12774	ARHG5_HUMAN	I	347	ENSP00000056217:T347I	.	T	+	2	0	ARHGEF5	143691735	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.478000	0.06575	-0.083000	0.12618	-0.235000	0.12190	ACC	.	.	weak		0.527	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
MYO7A	4647	hgsc.bcm.edu	37	11	76922868	76922868	+	Silent	SNP	C	C	T	rs41298757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76922868C>T	ENST00000409709.3	+	46	6512	c.6240C>T	c.(6238-6240)tcC>tcT	p.S2080S	MYO7A_ENST00000458637.2_Silent_p.S2042S|MYO7A_ENST00000409619.2_Silent_p.S2031S|MYO7A_ENST00000605744.1_3'UTR	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2080	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CCCCATAGTCCATCGTCGCCT	0.627													C|||	80	0.0159744	0.0038	0.0173	5008	,	,		19295	0.0		0.0507	False		,,,				2504	0.0123				p.S2080S		Atlas-SNP	.											.	MYO7A	164	.	0			c.C6240T						PASS	.	C	,	39,4353	38.4+/-70.7	1,37,2158	46.0	47.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6240,6126	0.5	0.9	11	dbSNP_127	47	371,8199	119.7+/-179.0	11,349,3925	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	12,386,6083	TT,TC,CC		4.3291,0.888,3.1631	,	2080/2216,2042/2176	76922868	410,12552	2196	4285	6481	SO:0001819	synonymous_variant	4647	exon46			ATAGTCCATCGTC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6240C>T	11.37:g.76922868C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	43	25	0.581395	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			C|0.975;T|0.025	0.025	strong		0.627	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
C1orf68	100129271	hgsc.bcm.edu	37	1	152692472	152692472	+	Missense_Mutation	SNP	A	A	C	rs873775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152692472A>C	ENST00000368775.2	+	1	475	c.475A>C	c.(475-477)Act>Cct	p.T159P		NM_001024679.2	NP_001019850.1	Q5T750	XP32_HUMAN	chromosome 1 open reading frame 68	159	Cys-rich.		T -> P (in dbSNP:rs873775).		epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)		p.T159P(1)		NS(1)|breast(1)|lung(2)|prostate(1)|stomach(3)	8						GTACTGTGTCACTGACCCATG	0.592													C|||	1749	0.349241	0.5461	0.3804	5008	,	,		19221	0.1716		0.3608	False		,,,				2504	0.2321				p.T159P		Atlas-SNP	.											C1orf68,NS,malignant_melanoma,-1,2	C1orf68	19	2	1	Substitution - Missense(1)	stomach(1)	c.A475C						PASS	.	C	PRO/THR	693,691		176,341,175	110.0	103.0	105.0		475	5.4	0.8	1	dbSNP_86	105	1114,2068		190,734,667	yes	missense	C1orf68	NM_001024679.2	38	366,1075,842	CC,CA,AA		35.0094,49.9277,39.5751	benign	159/251	152692472	1807,2759	692	1591	2283	SO:0001583	missense	100129271	exon1			TGTGTCACTGACC	AF005081	CCDS44226.1	1q21.3	2014-05-30			ENSG00000198854	ENSG00000198854			29468	protein-coding gene	gene with protein product						11698679	Standard	NM_001024679		Approved	LEP7	uc010pdu.2	Q5T750	OTTHUMG00000012401	ENST00000368775.2:c.475A>C	1.37:g.152692472A>C	ENSP00000357764:p.Thr159Pro	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	206	204	0.990291	NM_001024679	O14634	Missense_Mutation	SNP	ENST00000368775.2	37	CCDS44226.1	767	0.35119047619047616	259	0.5264227642276422	137	0.3784530386740331	103	0.18006993006993008	268	0.35356200527704484	C	0.348	-0.946669	0.02304	0.500723	0.350094	ENSG00000198854	ENST00000362017;ENST00000368775	T;T	0.18174	2.23;2.23	5.4	5.4	0.78164	.	0.000000	0.40302	N	0.001132	T	0.01523	0.0049	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42447	-0.9451	9	0.11485	T	0.65	-6.6677	12.041	0.53452	0.1727:0.8273:0.0:0.0	rs873775;rs3829884;rs56870105;rs873775	159	Q5T750	XP32_HUMAN	P	159	ENSP00000354769:T159P;ENSP00000357764:T159P	ENSP00000354769:T159P	T	+	1	0	C1orf68	150959096	0.607000	0.26958	0.769000	0.31535	0.287000	0.27160	2.046000	0.41260	1.452000	0.47756	-0.225000	0.12378	ACT	A|0.656;C|0.344	0.344	strong		0.592	C1orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034521.2	NM_001024679	
C6orf15	29113	hgsc.bcm.edu	37	6	31079643	31079643	+	Missense_Mutation	SNP	T	T	C	rs1265054	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31079643T>C	ENST00000259870.3	-	2	496	c.493A>G	c.(493-495)Aag>Gag	p.K165E	PSORS1C1_ENST00000259881.9_5'Flank	NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	165			K -> E (in dbSNP:rs1265054). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15217361}.		extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						AGTGAAGCCTTGGGTGAGAGG	0.622													C|||	2664	0.531949	0.5461	0.5663	5008	,	,		16512	0.4871		0.5149	False		,,,				2504	0.5521				p.K165E		Atlas-SNP	.											.	C6orf15	29	.	0			c.A493G						PASS	.	C	GLU/LYS	2085,1527		598,889,319	32.0	36.0	35.0		493	2.5	0.0	6	dbSNP_87	35	3923,3145		1130,1663,741	yes	missense	C6orf15	NM_014070.2	56	1728,2552,1060	CC,CT,TT		44.4963,42.2757,43.7453	benign	165/326	31079643	6008,4672	1806	3534	5340	SO:0001583	missense	29113	exon2			AAGCCTTGGGTGA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.493A>G	6.37:g.31079643T>C	ENSP00000259870:p.Lys165Glu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	1130	0.5173992673992674	276	0.5609756097560976	206	0.569060773480663	269	0.47027972027972026	379	0.5	C	0.241	-1.013881	0.02095	0.577243	0.555037	ENSG00000204542	ENST00000259870	T	0.04758	3.56	4.26	2.48	0.30137	.	0.718931	0.12470	N	0.466075	T	0.00384	0.0012	N	0.00801	-1.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45175	-0.9279	9	0.02654	T	1	-0.2097	6.2277	0.20718	0.0:0.6796:0.0:0.3204	rs1265054;rs3800281;rs57021105;rs1265054	165	Q6UXA7	CF015_HUMAN	E	165	ENSP00000259870:K165E	ENSP00000259870:K165E	K	-	1	0	C6orf15	31187622	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.109000	0.10840	0.110000	0.17919	-0.764000	0.03450	AAG	T|0.473;C|0.527	0.527	strong		0.622	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
MUC6	4588	hgsc.bcm.edu	37	11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	rs199592093		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1017522T>G	ENST00000421673.2	-	31	5329	c.5279A>C	c.(5278-5280)gAa>gCa	p.E1760A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1760	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGAGGTGACTTCAGGATGGTG	0.567																																					p.E1760A		Atlas-SNP	.											.	MUC6	408	.	0			c.A5279C						PASS	.						751.0	715.0	727.0					11																	1017522		2200	4294	6494	SO:0001583	missense	4588	exon31			GTGACTTCAGGAT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5279A>C	11.37:g.1017522T>G	ENSP00000406861:p.Glu1760Ala	Somatic	479	0	0		WXS	Illumina HiSeq	Phase_I	596	32	0.0536913	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	0.655	-0.808100	0.02819	.	.	ENSG00000184956	ENST00000421673	T	0.20332	2.08	0.235	0.235	0.15431	.	.	.	.	.	T	0.25195	0.0612	L	0.38175	1.15	0.09310	N	1	D	0.67145	0.996	D	0.70227	0.968	T	0.11966	-1.0566	8	0.05833	T	0.94	.	.	.	.	.	1760	Q6W4X9	MUC6_HUMAN	A	1760	ENSP00000406861:E1760A	ENSP00000406861:E1760A	E	-	2	0	MUC6	1007522	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-3.356000	0.00499	0.263000	0.21812	0.260000	0.18958	GAA	.	.	weak		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
GIMAP6	474344	hgsc.bcm.edu	37	7	150325175	150325175	+	Missense_Mutation	SNP	C	C	T	rs13234724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150325175C>T	ENST00000328902.5	-	3	727	c.511G>A	c.(511-513)Ggc>Agc	p.G171S	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	171	AIG1-type G.		G -> S (in dbSNP:rs13234724). {ECO:0000269|PubMed:14702039}.			cytosol (GO:0005829)	GTP binding (GO:0005525)	p.G171S(1)		endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCCAGGGAGCCGCCAGCCAGG	0.612													C|||	900	0.179712	0.0651	0.3141	5008	,	,		16739	0.1944		0.1948	False		,,,				2504	0.2086				p.G241S		Atlas-SNP	.											GIMAP6,NS,carcinoma,+2,2	GIMAP6	60	2	1	Substitution - Missense(1)	lung(1)	c.G721A						PASS	.	C	SER/GLY	382,4024	192.6+/-218.0	17,348,1838	109.0	111.0	110.0		511	3.4	0.0	7	dbSNP_121	110	1755,6845	316.2+/-312.6	188,1379,2733	yes	missense	GIMAP6	NM_024711.5	56	205,1727,4571	TT,TC,CC		20.407,8.67,16.4309	possibly-damaging	171/293	150325175	2137,10869	2203	4300	6503	SO:0001583	missense	474344	exon3			GGGAGCCGCCAGC	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.511G>A	7.37:g.150325175C>T	ENSP00000330374:p.Gly171Ser	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	371	0.16987179487179488	36	0.07317073170731707	84	0.23204419889502761	94	0.16433566433566432	157	0.20712401055408972	C	16.63	3.175495	0.57692	0.0867	0.20407	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.05319	3.46	4.29	3.39	0.38822	AIG1 (1);	1.131570	0.06429	N	0.723757	T	0.00012	0.0000	L	0.43554	1.36	0.47905	P	4.5600000000001195E-4	P;D	0.54964	0.704;0.969	B;B	0.41088	0.218;0.347	T	0.41520	-0.9504	9	0.13108	T	0.6	.	10.0873	0.42425	0.0:0.7967:0.2033:0.0	rs13234724;rs52799454;rs60245186;rs13234724	171;91	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	S	171;232	ENSP00000330374:G171S	ENSP00000330374:G171S	G	-	1	0	GIMAP6	149956108	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.478000	0.22212	1.008000	0.39264	0.561000	0.74099	GGC	C|0.832;G|0.000;T|0.168	0.168	strong		0.612	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711	
ZNF610	162963	hgsc.bcm.edu	37	19	52856955	52856955	+	Silent	SNP	C	C	T	rs1961205	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52856955C>T	ENST00000403906.3	+	4	540	c.84C>T	c.(82-84)gaC>gaT	p.D28D	ZNF610_ENST00000327920.8_Silent_p.D28D|ZNF610_ENST00000321287.8_Silent_p.D28D|ZNF610_ENST00000601151.1_Silent_p.D28D	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	28	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D28D(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		CATTCATGGACGTGGCCATCG	0.418													c|||	2073	0.413938	0.3903	0.3357	5008	,	,		17553	0.4504		0.3926	False		,,,				2504	0.4857				p.D28D		Atlas-SNP	.											ZNF610,NS,carcinoma,+1,2	ZNF610	84	2	1	Substitution - coding silent(1)	stomach(1)	c.C84T						PASS	.	T	,,,	1815,2591	533.0+/-373.6	373,1069,761	96.0	96.0	96.0		84,84,84,84	-2.9	0.6	19	dbSNP_92	96	3259,5341	489.0+/-372.5	619,2021,1660	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	,,,	992,3090,2421	TT,TC,CC		37.8953,41.1938,39.0128	,,,	28/463,28/463,28/420,28/463	52856955	5074,7932	2203	4300	6503	SO:0001819	synonymous_variant	162963	exon4			CATGGACGTGGCC	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.84C>T	19.37:g.52856955C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_001161427	A8K4C3|Q86YH8|Q8NDS9	Silent	SNP	ENST00000403906.3	37	CCDS12851.1																																																																																			C|0.610;T|0.390	0.390	strong		0.418	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
MYOM2	9172	hgsc.bcm.edu	37	8	2037833	2037833	+	Silent	SNP	G	G	C	rs2294061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:2037833G>C	ENST00000262113.4	+	15	1788	c.1647G>C	c.(1645-1647)tcG>tcC	p.S549S	MYOM2_ENST00000523438.1_5'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	549	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		CTTTGTAGTCGGTGGTGGGGA	0.557													C|||	1122	0.224042	0.4244	0.1628	5008	,	,		18049	0.2083		0.162	False		,,,				2504	0.0767				p.S549S		Atlas-SNP	.											.	MYOM2	251	.	0			c.G1647C						PASS	.	C		1674,2732	650.5+/-399.1	321,1032,850	64.0	65.0	65.0		1647	-5.2	0.0	8	dbSNP_100	65	1257,7343	756.6+/-407.5	92,1073,3135	no	coding-synonymous	MYOM2	NM_003970.2		413,2105,3985	CC,CG,GG		14.6163,37.9936,22.5358		549/1466	2037833	2931,10075	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon15			GTAGTCGGTGGTG		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.1647G>C	8.37:g.2037833G>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			G|0.783;C|0.217	0.217	strong		0.557	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
ITPR2	3709	hgsc.bcm.edu	37	12	26810777	26810777	+	Silent	SNP	T	T	C	rs2291264	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:26810777T>C	ENST00000381340.3	-	18	2471	c.2055A>G	c.(2053-2055)tcA>tcG	p.S685S		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	685					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)	CAATGTCATCTGAAAGGATGG	0.408													C|||	1990	0.397364	0.1921	0.4524	5008	,	,		19311	0.6518		0.3628	False		,,,				2504	0.409				p.S685S		Atlas-SNP	.											.	ITPR2	270	.	0			c.A2055G						PASS	.	C		830,2970		97,636,1167	114.0	106.0	108.0		2055	-4.6	0.1	12	dbSNP_100	108	2898,5330		505,1888,1721	no	coding-synonymous	ITPR2	NM_002223.2		602,2524,2888	CC,CT,TT		35.2212,21.8421,30.9943		685/2702	26810777	3728,8300	1900	4114	6014	SO:0001819	synonymous_variant	3709	exon18			GTCATCTGAAAGG	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.2055A>G	12.37:g.26810777T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	138	83	0.601449	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.606;C|0.394	0.394	strong		0.408	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
REC8	9985	hgsc.bcm.edu	37	14	24642348	24642348	+	Silent	SNP	C	C	T	rs11547058	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24642348C>T	ENST00000311457.3	+	5	881	c.282C>T	c.(280-282)caC>caT	p.H94H	REC8_ENST00000559919.1_Silent_p.H94H			O95072	REC8_HUMAN	REC8 meiotic recombination protein	94					double-strand break repair via homologous recombination (GO:0000724)|fertilization (GO:0009566)|linear element assembly (GO:0030999)|male meiosis I (GO:0007141)|meiotic nuclear division (GO:0007126)|oocyte maturation (GO:0001556)|reciprocal meiotic recombination (GO:0007131)|seminiferous tubule development (GO:0072520)|sister chromatid cohesion (GO:0007062)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)	condensed nuclear chromosome kinetochore (GO:0000778)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear meiotic cohesin complex (GO:0034991)|nucleus (GO:0005634)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	15				GBM - Glioblastoma multiforme(265;0.00839)		ACATCCAGCACATCTTGGAGC	0.592													C|||	625	0.1248	0.0499	0.0749	5008	,	,		18589	0.3175		0.1402	False		,,,				2504	0.047				p.H94H	NSCLC(139;1764 2537 12868 49041)	Atlas-SNP	.											.	REC8	47	.	0			c.C282T						PASS	.	C	,	236,3932		6,224,1854	79.0	85.0	83.0		282,282	0.9	1.0	14	dbSNP_120	83	886,7552		54,778,3387	no	coding-synonymous,coding-synonymous	REC8	NM_001048205.1,NM_005132.2	,	60,1002,5241	TT,TC,CC		10.5001,5.6622,8.9005	,	94/547,94/547	24642348	1122,11484	2084	4219	6303	SO:0001819	synonymous_variant	9985	exon4			CCAGCACATCTTG	AF006264	CCDS41932.1	14q11.2-q12	2013-08-06	2013-08-06	2007-04-03		ENSG00000100918			16879	protein-coding gene	gene with protein product		608193	"""REC8-like 1 (yeast)"", ""REC8 homolog (yeast)"""	REC8L1		10207075, 15935783, 12759374	Standard	NM_005132		Approved	Rec8p, kleisin-alpha	uc001wms.3	O95072		ENST00000311457.3:c.282C>T	14.37:g.24642348C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_001048205	A8K576|D3DS62|Q658V5|Q6IA92|Q8WUV8|Q9BTF2|Q9NVQ9	Silent	SNP	ENST00000311457.3	37	CCDS41932.1																																																																																			C|0.862;T|0.138	0.138	strong		0.592	REC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415889.3	NM_005132	
UBXN11	91544	hgsc.bcm.edu	37	1	26608873	26608873	+	Missense_Mutation	SNP	T	T	A	rs1134583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608873T>A	ENST00000374222.1	-	16	1944	c.1480A>T	c.(1480-1482)Agt>Tgt	p.S494C	UBXN11_ENST00000314675.7_Missense_Mutation_p.S374C|UBXN11_ENST00000374217.2_Missense_Mutation_p.S461C|UBXN11_ENST00000357089.4_Missense_Mutation_p.S461C|UBXN11_ENST00000374223.1_Missense_Mutation_p.S251C|UBXN11_ENST00000374221.3_Missense_Mutation_p.S494C			Q5T124	UBX11_HUMAN	UBX domain protein 11	494	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggactggggccggga	0.711																																					p.S494C		Atlas-SNP	.											UBXN11,NS,carcinoma,0,1	UBXN11	54	1	1	Deletion - In frame(1)	ovary(1)	c.A1480T						scavenged	.						28.0	33.0	32.0					1																	26608873		1776	4034	5810	SO:0001583	missense	91544	exon16			CGGGACTGGGGCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1480A>T	1.37:g.26608873T>A	ENSP00000363339:p.Ser494Cys	Somatic	30	1	0.0333333		WXS	Illumina HiSeq	Phase_I	45	35	0.777778	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	T	10.17	1.275650	0.23307	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19250	2.16;2.17;2.43;2.41;2.41;2.43	1.27	-0.135	0.13477	.	.	.	.	.	T	0.08268	0.0206	N	0.08118	0	0.09310	N	0.999997	P;P;P;P	0.50819	0.939;0.893;0.939;0.9	B;B;B;B	0.37601	0.187;0.187;0.254;0.129	T	0.21895	-1.0232	9	0.66056	D	0.02	.	5.0204	0.14358	0.0:0.3611:0.0:0.6389	rs1134583;rs17838089	461;456;374;494	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	C	374;251;461;494;494;461	ENSP00000324721:S374C;ENSP00000363340:S251C;ENSP00000349601:S461C;ENSP00000363338:S494C;ENSP00000363339:S494C;ENSP00000363334:S461C	ENSP00000324721:S374C	S	-	1	0	UBXN11	26481460	0.000000	0.05858	0.011000	0.14972	0.011000	0.07611	-1.315000	0.02713	-0.170000	0.10816	-0.582000	0.04134	AGT	T|0.870;A|0.130	0.130	strong		0.711	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
HLA-A	3105	hgsc.bcm.edu	37	6	29911306	29911306	+	Missense_Mutation	SNP	C	C	T	rs9391665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911306C>T	ENST00000396634.1	+	5	946	c.605C>T	c.(604-606)aCg>aTg	p.T202M	HLA-A_ENST00000376809.5_Missense_Mutation_p.T202M|HLA-A_ENST00000376806.5_Missense_Mutation_p.T202M|HLA-A_ENST00000376802.2_Missense_Mutation_p.T202M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	202	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGGAAGGAGACGCTGCAGCGC	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.T202M		Atlas-SNP	.											HLA-A,NS,adenoma,0,2	HLA-A	89	2	0			c.C605T						PASS	.						48.0	42.0	44.0					6																	29911306		1509	2706	4215	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGGAGACGCTGCA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.605C>T	6.37:g.29911306C>T	ENSP00000379873:p.Thr202Met	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	130	24	0.184615	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	308	0.14102564102564102	84	0.17073170731707318	56	0.15469613259668508	56	0.0979020979020979	112	0.14775725593667546	.	3.947	-0.013107	0.07727	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00848	5.62;5.62;5.62;5.62	3.54	1.66	0.24008	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	1.297700	0.06193	U	0.681759	T	0.01976	0.0062	M	0.83953	2.67	0.80722	P	0.0	D;B;D;B;D;B;B	0.89917	0.998;0.013;1.0;0.025;1.0;0.008;0.025	D;B;D;B;D;B;B	0.91635	0.99;0.025;0.999;0.053;0.999;0.014;0.053	T	0.43147	-0.9409	9	0.87932	D	0	.	3.0431	0.06145	0.2126:0.5463:0.0:0.2411	rs9391665	81;202;202;202;202;202;202	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	M	202	ENSP00000379873:T202M;ENSP00000366002:T202M;ENSP00000366005:T202M;ENSP00000365998:T202M	ENSP00000365998:T202M	T	+	2	0	HLA-A	30019285	0.000000	0.05858	0.241000	0.24154	0.380000	0.30137	-2.455000	0.01003	0.798000	0.33994	0.485000	0.47835	ACG	C|0.855;T|0.145	0.145	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ERCC6	2074	hgsc.bcm.edu	37	10	50667105	50667105	+	Missense_Mutation	SNP	T	T	C	rs2228529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50667105T>C	ENST00000355832.5	-	21	4316	c.4238A>G	c.(4237-4239)cAg>cGg	p.Q1413R	ERCC6_ENST00000542458.1_Missense_Mutation_p.Q783R|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1413	Ubiquitin-binding domain (UBD).		Q -> R (in dbSNP:rs2228529). {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						AGAAGCTTCCTGCAGGTGCCC	0.557								Direct reversal of damage;Nucleotide excision repair (NER)					T|||	896	0.178914	0.1248	0.2089	5008	,	,		16314	0.0437		0.2078	False		,,,				2504	0.3405				p.P1413R		Atlas-SNP	.											ERCC6,NS,carcinoma,0,1	ERCC6	162	1	0			c.C4238G						PASS	.	T	ARG/GLN	596,3810	259.5+/-263.1	58,480,1665	101.0	97.0	98.0		4238	-4.9	0.0	10	dbSNP_98	98	1864,6736	332.7+/-320.2	196,1472,2632	yes	missense	ERCC6	NM_000124.2	43	254,1952,4297	CC,CT,TT		21.6744,13.527,18.9143	benign	1413/1494	50667105	2460,10546	2203	4300	6503	SO:0001583	missense	2074	exon21			GCTTCCTGCAGGT	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.4238A>G	10.37:g.50667105T>C	ENSP00000348089:p.Gln1413Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	143	0.986207	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	340	0.15567765567765568	61	0.12398373983739837	82	0.2265193370165746	30	0.05244755244755245	167	0.22031662269129287	T	10.54	1.379579	0.24944	0.13527	0.216744	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.82619	-1.63;-1.38	5.5	-4.93	0.03066	.	.	.	.	.	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B	0.25521	0.128	B	0.16722	0.016	T	0.02015	-1.1229	8	0.15952	T	0.53	1.3308	9.0549	0.36399	0.1418:0.0:0.3427:0.5155	rs2228529;rs17775071;rs52790262;rs61459256;rs2228529	1413	Q03468	ERCC6_HUMAN	R	1413;790;783	ENSP00000348089:Q1413R;ENSP00000445134:Q783R	ENSP00000348089:Q1413R	Q	-	2	0	ERCC6	50337111	0.000000	0.05858	0.000000	0.03702	0.342000	0.28953	0.101000	0.15251	-0.673000	0.05259	-0.316000	0.08728	CAG	T|0.826;C|0.173	0.173	strong		0.557	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
COL18A1	80781	hgsc.bcm.edu	37	21	46875683	46875683	+	Missense_Mutation	SNP	C	C	G	rs61739237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46875683C>G	ENST00000359759.4	+	1	260	c.239C>G	c.(238-240)cCt>cGt	p.P80R	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Missense_Mutation_p.P80R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	80					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)		CCTGGCAGCCCTGAGCCACCC	0.677													C|||	99	0.0197684	0.0688	0.0115	5008	,	,		16653	0.0		0.0	False		,,,				2504	0.0				p.P80R		Atlas-SNP	.											.	COL18A1	129	.	0			c.C239G						PASS	.	C	,ARG/PRO	249,3887		6,237,1825	45.0	58.0	54.0		,239	1.3	0.0	21	dbSNP_129	54	1,8375		0,1,4187	yes	intron,missense	COL18A1	NM_130445.2,NM_030582.3	,103	6,238,6012	GG,GC,CC		0.0119,6.0203,1.9981	,benign	,80/1520	46875683	250,12262	2068	4188	6256	SO:0001583	missense	80781	exon1			GCAGCCCTGAGCC		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.239C>G	21.37:g.46875683C>G	ENSP00000352798:p.Pro80Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	114	47	0.412281	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		54	0.024725274725274724	50	0.1016260162601626	4	0.011049723756906077	0	0.0	0	0.0	C	7.818	0.717135	0.15372	0.060203	1.19E-4	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.32515	1.45;1.45	3.31	1.34	0.21922	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	2.030890	0.02888	N	0.133800	T	0.00845	0.0028	L	0.42245	1.32	0.09310	N	1	B;B	0.14805	0.011;0.009	B;B	0.17433	0.018;0.011	T	0.27123	-1.0083	10	0.72032	D	0.01	.	10.5387	0.45020	0.0:0.6186:0.3814:0.0	rs61739237	80;80	P39060;P39060-1	COIA1_HUMAN;.	R	80	ENSP00000347665:P80R;ENSP00000352798:P80R	ENSP00000347665:P80R	P	+	2	0	COL18A1	45700111	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.377000	0.20552	0.174000	0.19809	0.491000	0.48974	CCT	C|0.976;G|0.024	0.024	strong		0.677	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
CWC22	57703	hgsc.bcm.edu	37	2	180810358	180810358	+	Missense_Mutation	SNP	C	C	T	rs71425650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:180810358C>T	ENST00000410053.3	-	20	2524	c.2225G>A	c.(2224-2226)aGg>aAg	p.R742K	CWC22_ENST00000295749.6_Missense_Mutation_p.R742K	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	742				R -> K (in Ref. 4; AAH31216). {ECO:0000305}.	mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						TTTTTGTTTCCTATCATTTGT	0.383													C|||	923	0.184305	0.1377	0.366	5008	,	,		18007	0.2302		0.1153	False		,,,				2504	0.1421				p.R742K		Atlas-SNP	.											.	CWC22	62	.	0			c.G2225A						PASS	.	C	LYS/ARG	507,3201		39,429,1386	114.0	104.0	107.0		2225	2.2	0.1	2	dbSNP_130	107	895,7289		62,771,3259	yes	missense	CWC22	NM_020943.2	26	101,1200,4645	TT,TC,CC		10.936,13.6731,11.7894	benign	742/909	180810358	1402,10490	1854	4092	5946	SO:0001583	missense	57703	exon20			TGTTTCCTATCAT		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein b"""	615186	"""CWC22 spliceosome-associated protein homolog (S. cerevisiae)"""			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.2225G>A	2.37:g.180810358C>T	ENSP00000387006:p.Arg742Lys	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	148	78	0.527027	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	37	CCDS46465.1	403	0.18452380952380953	72	0.14634146341463414	111	0.30662983425414364	129	0.22552447552447552	91	0.12005277044854881	C	11.89	1.772201	0.31411	0.136731	0.10936	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.23348	2.08;2.08;1.91	5.02	2.2	0.27929	.	0.387378	0.29073	N	0.013232	T	0.00012	0.0000	L	0.46157	1.445	0.36605	P	0.12509400000000004	B	0.21905	0.062	B	0.21708	0.036	T	0.40979	-0.9534	9	0.28530	T	0.3	-1.6659	7.522	0.27633	0.0:0.7334:0.0:0.2666	.	742	Q9HCG8	CWC22_HUMAN	K	742	ENSP00000387006:R742K;ENSP00000295749:R742K;ENSP00000384159:R742K	ENSP00000295749:R742K	R	-	2	0	CWC22	180518603	0.998000	0.40836	0.093000	0.20910	0.545000	0.35147	1.491000	0.35583	0.628000	0.30357	0.655000	0.94253	AGG	C|0.832;T|0.168	0.168	strong		0.383	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943	
DHCR7	1717	hgsc.bcm.edu	37	11	71152459	71152459	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71152459C>T	ENST00000355527.3	-	6	716	c.440G>A	c.(439-441)gGc>gAc	p.G147D	DHCR7_ENST00000407721.2_Missense_Mutation_p.G147D	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	147			G -> D (in SLOS). {ECO:0000269|PubMed:10677299}.		blood vessel development (GO:0001568)|cell differentiation (GO:0030154)|cholesterol biosynthetic process (GO:0006695)|lung development (GO:0030324)|multicellular organism growth (GO:0035264)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|regulation of cholesterol biosynthetic process (GO:0045540)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear outer membrane (GO:0005640)	7-dehydrocholesterol reductase activity (GO:0047598)			endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(1)|skin(1)	19						GGCTTGCAGGCCATTGATCTG	0.547									Smith-Lemli-Opitz syndrome																												p.G147D		Atlas-SNP	.											DHCR7_ENST00000355527,NS,haematopoietic_neoplasm,-1,2	DHCR7	98	2	0			c.G440A	GRCh37	CM000680	DHCR7	M		PASS	.						135.0	105.0	115.0					11																	71152459		2200	4294	6494	SO:0001583	missense	1717	exon6	Familial Cancer Database	SLOS type I & II	TGCAGGCCATTGA	AF034544	CCDS8200.1	11q13.4	2014-09-17	2004-02-13				1.3.1.21		2860	protein-coding gene	gene with protein product		602858	"""Smith-Lemli-Opitz syndrome"""	SLOS		9465114, 9634533	Standard	NM_001360		Approved		uc001oql.3	Q9UBM7		ENST00000355527.3:c.440G>A	11.37:g.71152459C>T	ENSP00000347717:p.Gly147Asp	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	142	68	0.478873	NM_001163817	B2R6Z2|O60492|O60717	Missense_Mutation	SNP	ENST00000355527.3	37	CCDS8200.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.128197	0.56721	.	.	ENSG00000172893	ENST00000407721;ENST00000355527;ENST00000524694;ENST00000527316;ENST00000526780	D;D;D;D	0.99523	-4.85;-4.85;-4.85;-6.08	4.14	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.99625	0.9863	H	0.94306	3.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97590	1.0116	10	0.87932	D	0	-30.5655	14.271	0.66152	0.0:1.0:0.0:0.0	.	147	Q9UBM7	DHCR7_HUMAN	D	147;147;159;115;147	ENSP00000384739:G147D;ENSP00000347717:G147D;ENSP00000435047:G115D;ENSP00000435668:G147D	ENSP00000347717:G147D	G	-	2	0	DHCR7	70830107	1.000000	0.71417	0.838000	0.33150	0.133000	0.20885	6.765000	0.74965	2.035000	0.60131	0.313000	0.20887	GGC	.	.	none		0.547	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360	
ARL16	339231	hgsc.bcm.edu	37	17	79650828	79650828	+	Missense_Mutation	SNP	T	T	G	rs8066889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79650828T>G	ENST00000397498.4	-	1	126	c.28A>C	c.(28-30)Agc>Cgc	p.S10R	ARL16_ENST00000573392.1_5'Flank|ARL16_ENST00000574938.1_5'Flank|ARL16_ENST00000576135.1_5'Flank|ARL16_ENST00000570561.1_5'Flank|HGS_ENST00000329138.4_5'Flank	NM_001040025.1	NP_001035114.1	Q0P5N6	ARL16_HUMAN	ADP-ribosylation factor-like 16	10			S -> R (in dbSNP:rs8066889).		small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|lung(4)|skin(1)	7	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			GCGCCGCGGCTCAAGGCCCGC	0.632													G|||	1243	0.248203	0.3578	0.1556	5008	,	,		12437	0.2292		0.2604	False		,,,				2504	0.1728				p.S10R		Atlas-SNP	.											.	ARL16	14	.	0			c.A28C						PASS	.	G	ARG/SER	1280,2528		237,806,861	14.0	17.0	16.0		28	0.8	0.0	17	dbSNP_116	16	1807,6371		212,1383,2494	yes	missense	ARL16	NM_001040025.1	110	449,2189,3355	GG,GT,TT		22.0959,33.6134,25.755	benign	10/198	79650828	3087,8899	1904	4089	5993	SO:0001583	missense	339231	exon1			CGCGGCTCAAGGC		CCDS45813.1	17q25.3	2014-05-09				ENSG00000214087		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	27902	protein-coding gene	gene with protein product						12477932	Standard	NM_001040025		Approved		uc002kbf.3	Q0P5N6		ENST00000397498.4:c.28A>C	17.37:g.79650828T>G	ENSP00000380635:p.Ser10Arg	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	21	20	0.952381	NM_001040025		Missense_Mutation	SNP	ENST00000397498.4	37	CCDS45813.1	573	0.2623626373626374	193	0.39227642276422764	62	0.1712707182320442	135	0.23601398601398602	183	0.24142480211081793	G	10.73	1.431804	0.25813	0.336134	0.220959	ENSG00000214087	ENST00000397498	T	0.70749	-0.51	4.35	0.805	0.18703	.	0.727362	0.09205	U	0.834153	T	0.00012	0.0000	L	0.34521	1.04	0.51012	P	9.199999999998099E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.26224	-1.0109	9	0.72032	D	0.01	.	8.4458	0.32841	0.0:0.133:0.4606:0.4064	rs8066889;rs59418595;rs8066889	10	Q0P5N6	ARL16_HUMAN	R	10	ENSP00000380635:S10R	ENSP00000380635:S10R	S	-	1	0	ARL16	77261233	0.004000	0.15560	0.003000	0.11579	0.002000	0.02628	0.878000	0.28126	0.263000	0.21812	-0.121000	0.15023	AGC	T|0.736;G|0.264	0.264	strong		0.632	ARL16-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440514.1	XM_290777	
C7orf62	219557	hgsc.bcm.edu	37	7	88423881	88423881	+	Missense_Mutation	SNP	T	T	C	rs2293583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:88423881T>C	ENST00000297203.2	-	2	561	c.376A>G	c.(376-378)Att>Gtt	p.I126V	ZNF804B_ENST00000333190.4_Intron	NM_152706.3	NP_689919.1	Q8TBZ9	CG062_HUMAN	chromosome 7 open reading frame 62	126			I -> V (in dbSNP:rs2293583).							NS(1)|breast(1)|endometrium(3)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	30						ATTTGTTGAATAAAAAATACT	0.348													T|||	609	0.121605	0.1051	0.062	5008	,	,		21075	0.124		0.0875	False		,,,				2504	0.2188				p.I126V		Atlas-SNP	.											.	C7orf62	63	.	0			c.A376G						PASS	.	T	VAL/ILE,	488,3918	225.9+/-241.6	22,444,1737	49.0	51.0	50.0		376,	1.1	0.0	7	dbSNP_100	50	691,7909	171.4+/-222.4	35,621,3644	yes	missense,intron	C7orf62,ZNF804B	NM_152706.2,NM_181646.2	29,	57,1065,5381	CC,CT,TT		8.0349,11.0758,9.065	benign,	126/254,	88423881	1179,11827	2203	4300	6503	SO:0001583	missense	219557	exon2			GTTGAATAAAAAA	BC028365	CCDS34678.1	7q21.13	2013-10-11			ENSG00000164645	ENSG00000164645			22402	protein-coding gene	gene with protein product						12690205	Standard	NM_152706		Approved	MGC26647	uc003ujv.3	Q8TBZ9	OTTHUMG00000153859	ENST00000297203.2:c.376A>G	7.37:g.88423881T>C	ENSP00000297203:p.Ile126Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_152706		Missense_Mutation	SNP	ENST00000297203.2	37	CCDS34678.1	210	0.09615384615384616	51	0.10365853658536585	31	0.0856353591160221	65	0.11363636363636363	63	0.08311345646437995	T	0.804	-0.754563	0.03041	0.110758	0.080349	ENSG00000164645	ENST00000297203	T	0.15256	2.44	6.06	1.07	0.20283	.	0.617976	0.17229	N	0.182026	T	0.00241	0.0007	L	0.48362	1.52	0.80722	P	0.0	B	0.17268	0.021	B	0.15484	0.013	T	0.20706	-1.0267	9	0.25751	T	0.34	-18.19	5.3759	0.16164	0.0:0.1703:0.3664:0.4632	rs2293583;rs2293583	126	Q8TBZ9	CG062_HUMAN	V	126	ENSP00000297203:I126V	ENSP00000297203:I126V	I	-	1	0	C7orf62	88261817	0.003000	0.15002	0.009000	0.14445	0.042000	0.13812	-0.033000	0.12246	0.164000	0.19529	-0.263000	0.10527	ATT	T|0.902;C|0.098	0.098	strong		0.348	C7orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332714.1	NM_152706	
FCGBP	8857	hgsc.bcm.edu	37	19	40392631	40392631	+	Missense_Mutation	SNP	G	G	A	rs80068592	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40392631G>A	ENST00000221347.6	-	16	7880	c.7873C>T	c.(7873-7875)Ccc>Tcc	p.P2625S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2625	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGAGAGTCGGGCACCACCTCC	0.642													G|||	1353	0.270168	0.1808	0.4121	5008	,	,		18489	0.2093		0.3569	False		,,,				2504	0.2638				p.P2625S		Atlas-SNP	.											.	FCGBP	416	.	0			c.C7873T						PASS	.						14.0	17.0	16.0					19																	40392631		2165	4278	6443	SO:0001583	missense	8857	exon16			AGTCGGGCACCAC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.7873C>T	19.37:g.40392631G>A	ENSP00000221347:p.Pro2625Ser	Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	390	126	0.323077	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	7.277	0.608327	0.14002	.	.	ENSG00000090920	ENST00000221347	T	0.18657	2.2	2.66	2.66	0.31614	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.27731	0.0682	M	0.71920	2.185	0.37706	P	0.07559199999999999	P	0.41131	0.739	P	0.48304	0.573	T	0.29761	-1.0001	8	0.02654	T	1	.	12.5273	0.56093	0.0:0.0:1.0:0.0	.	2625	Q9Y6R7	FCGBP_HUMAN	S	2625	ENSP00000221347:P2625S	ENSP00000221347:P2625S	P	-	1	0	FCGBP	45084471	0.034000	0.19679	0.110000	0.21437	0.008000	0.06430	0.899000	0.28417	1.495000	0.48549	0.298000	0.19748	CCC	G|0.772;A|0.228	0.228	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329851	55329851	+	Missense_Mutation	SNP	A	A	G	rs145262243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55329851A>G	ENST00000391728.4	+	3	185	c.152A>G	c.(151-153)tAt>tGt	p.Y51C	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.Y51C	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	51	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CGGTGTCACTATCGTCATAGG	0.517													a|||	25	0.00499201	0.0	0.0144	5008	,	,		13050	0.0		0.008	False		,,,				2504	0.0072				p.Y51C		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A152G						PASS	.	A	CYS/TYR	6,4344		0,6,2169	101.0	102.0	101.0		152	-2.5	0.0	19	dbSNP_134	101	100,8154		20,60,4047	no	missense	KIR3DL1	NM_013289.2	194	20,66,6216	GG,GA,AA		1.2115,0.1379,0.841		51/445	55329851	106,12498	2175	4127	6302	SO:0001583	missense	3811	exon3			GTCACTATCGTCA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.152A>G	19.37:g.55329851A>G	ENSP00000375608:p.Tyr51Cys	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	35	20	0.571429	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	9	0.004120879120879121	0	0.0	6	0.016574585635359115	0	0.0	3	0.00395778364116095	A	9.452	1.090889	0.20471	0.001379	0.012115	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.12361	2.69;2.69;2.69;2.69;2.69	1.25	-2.51	0.06365	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14743	0.0356	M	0.75447	2.3	0.09310	N	1	D;B	0.89917	1.0;0.022	D;B	0.91635	0.999;0.034	T	0.11591	-1.0581	9	0.66056	D	0.02	.	2.0319	0.03531	0.3118:0.4675:0.0:0.2207	.	51;51	F6QF33;P43629	.;KI3L1_HUMAN	C	51;51;51;29;51;51	ENSP00000384528:Y51C;ENSP00000443350:Y51C;ENSP00000442355:Y51C;ENSP00000375608:Y51C;ENSP00000326868:Y51C	ENSP00000326868:Y51C	Y	+	2	0	KIR3DL1	60021663	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.542000	0.06091	-0.292000	0.08999	-1.429000	0.01096	TAT	A|0.992;G|0.008	0.008	strong		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
TRIM17	51127	hgsc.bcm.edu	37	1	228602459	228602459	+	Silent	SNP	G	G	A	rs142505325	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228602459G>A	ENST00000366697.2	-	1	1271	c.315C>T	c.(313-315)ccC>ccT	p.P105P	TRIM17_ENST00000295033.3_Silent_p.P105P|TRIM17_ENST00000366698.2_Silent_p.P105P|TRIM17_ENST00000456946.2_Silent_p.P105P			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	105					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)				AAAGCTTGAGGGGCTCGTGGT	0.657													G|||	12	0.00239617	0.0	0.0014	5008	,	,		17247	0.0		0.004	False		,,,				2504	0.0072				p.P105P		Atlas-SNP	.											.	TRIM17	66	.	0			c.C315T						PASS	.	G	,,	0,4406		0,0,2203	77.0	84.0	82.0		315,315,315	0.3	1.0	1	dbSNP_134	82	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	,,	0,10,6493	AA,AG,GG		0.1163,0.0,0.0769	,,	105/478,105/344,105/478	228602459	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	51127	exon2			CTTGAGGGGCTCG	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.315C>T	1.37:g.228602459G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_001024940	B4DVJ2|Q5VST8	Silent	SNP	ENST00000366697.2	37	CCDS1571.1																																																																																			G|0.999;A|0.001	0.001	strong		0.657	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102	
PHIP	55023	hgsc.bcm.edu	37	6	79657391	79657391	+	Silent	SNP	G	G	A	rs1984195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:79657391G>A	ENST00000275034.4	-	36	4322	c.4155C>T	c.(4153-4155)gtC>gtT	p.V1385V	PHIP_ENST00000479165.1_5'UTR	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1385	Bromo 2. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		AAATAAGTCTGACATCTTTAC	0.338													G|||	2545	0.508187	0.3018	0.4611	5008	,	,		17684	0.6835		0.4791	False		,,,				2504	0.6697				p.V1385V		Atlas-SNP	.											.	PHIP	177	.	0			c.C4155T						PASS	.	G		1368,3038	454.0+/-350.5	210,948,1045	145.0	137.0	140.0		4155	4.4	1.0	6	dbSNP_92	140	4234,4366	571.4+/-389.5	1037,2160,1103	no	coding-synonymous	PHIP	NM_017934.5		1247,3108,2148	AA,AG,GG		49.2326,31.0486,43.0724		1385/1822	79657391	5602,7404	2203	4300	6503	SO:0001819	synonymous_variant	55023	exon36			AAGTCTGACATCT	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.4155C>T	6.37:g.79657391G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	58	9	0.155172	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			G|0.542;A|0.458	0.458	strong		0.338	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
RSPH10B	222967	hgsc.bcm.edu	37	7	6005323	6005323	+	Missense_Mutation	SNP	C	C	T	rs200962894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6005323C>T	ENST00000405415.1	-	3	661	c.275G>A	c.(274-276)cGt>cAt	p.R92H	RSPH10B_ENST00000337579.3_Missense_Mutation_p.R92H|RSPH10B_ENST00000404406.1_Missense_Mutation_p.R92H|RSPH10B_ENST00000535104.1_5'Flank|RSPH10B_ENST00000441023.2_Missense_Mutation_p.R92H			P0C881	R10B1_HUMAN	radial spoke head 10 homolog B (Chlamydomonas)	92										breast(1)|kidney(1)|lung(4)|ovary(1)|skin(4)	11		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0974)		ATACAGCCCACGAACCTTTTC	0.438													C|||	294	0.0587061	0.0166	0.121	5008	,	,		13170	0.0149		0.1362	False		,,,				2504	0.0368				p.R92H		Atlas-SNP	.											RSPH10B,NS,carcinoma,0,2	RSPH10B	28	2	0			c.G275A						scavenged	.						4.0	4.0	4.0					7																	6005323		1653	3655	5308	SO:0001583	missense	222967	exon4			AGCCCACGAACCT		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.275G>A	7.37:g.6005323C>T	ENSP00000385443:p.Arg92His	Somatic	962	0	0		WXS	Illumina HiSeq	Phase_I	1317	358	0.27183	NM_173565	A6NMW7|Q86ST9|Q8NE68	Missense_Mutation	SNP	ENST00000405415.1	37	CCDS34598.1	104	0.047619047619047616	9	0.018292682926829267	29	0.08011049723756906	2	0.0034965034965034965	64	0.08443271767810026	C	4.777	0.144454	0.09134	.	.	ENSG00000155026	ENST00000405415;ENST00000404406;ENST00000337579;ENST00000441023	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.73	0.597	0.17504	.	0.588391	0.17861	N	0.159518	T	0.01156	0.0038	N	0.21508	0.67	0.09310	N	1	B	0.26876	0.162	B	0.24394	0.053	T	0.05903	-1.0857	10	0.42905	T	0.14	.	5.1232	0.14871	0.0:0.4291:0.1466:0.4243	.	92	P0C881	R10B1_HUMAN	H	92	ENSP00000385443:R92H;ENSP00000384097:R92H;ENSP00000338556:R92H;ENSP00000400988:R92H	ENSP00000338556:R92H	R	-	2	0	RSPH10B	5971849	0.011000	0.17503	0.159000	0.22649	0.202000	0.24057	0.078000	0.14761	0.040000	0.15660	0.561000	0.74099	CGT	C|0.950;T|0.050	0.050	strong		0.438	RSPH10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325465.2	NM_173565	
BST1	683	hgsc.bcm.edu	37	4	15713446	15713446	+	Silent	SNP	C	C	T	rs2302463	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:15713446C>T	ENST00000265016.4	+	4	663	c.468C>T	c.(466-468)tcC>tcT	p.S156S	BST1_ENST00000382346.3_Silent_p.S171S	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	156					humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)	p.S156S(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						ATTACCAATCCTGCCCTACAT	0.393													C|||	420	0.0838658	0.0703	0.0288	5008	,	,		21378	0.1895		0.0199	False		,,,				2504	0.0982				p.S156S		Atlas-SNP	.											BST1,NS,carcinoma,0,1	BST1	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C468T						PASS	.	C		358,4048	183.3+/-210.9	12,334,1857	144.0	139.0	141.0		468	1.9	1.0	4	dbSNP_100	141	233,8367	95.4+/-157.2	1,231,4068	no	coding-synonymous	BST1	NM_004334.2		13,565,5925	TT,TC,CC		2.7093,8.1253,4.5441		156/319	15713446	591,12415	2203	4300	6503	SO:0001819	synonymous_variant	683	exon4			CCAATCCTGCCCT	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.468C>T	4.37:g.15713446C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	117	45	0.384615	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Silent	SNP	ENST00000265016.4	37	CCDS3416.1	165	0.07554945054945054	27	0.054878048780487805	12	0.03314917127071823	111	0.19405594405594406	15	0.01978891820580475	C	5.214	0.224934	0.09916	0.081253	0.027093	ENSG00000109743	ENST00000505785	.	.	.	5.64	1.87	0.25490	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999761068	.	.	.	.	.	.	T	0.17198	-1.0377	3	.	.	.	-19.4162	2.0425	0.03553	0.1628:0.5085:0.1575:0.1713	rs2302463;rs11548108;rs2302463	.	.	.	L	52	.	.	P	+	2	0	BST1	15322544	0.998000	0.40836	0.963000	0.40424	0.492000	0.33523	0.227000	0.17795	0.278000	0.22164	-0.126000	0.14955	CCT	C|0.946;T|0.054	0.054	strong		0.393	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
LTBP2	4053	hgsc.bcm.edu	37	14	74992800	74992800	+	Silent	SNP	A	A	G	rs699374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:74992800A>G	ENST00000261978.4	-	14	2792	c.2406T>C	c.(2404-2406)acT>acC	p.T802T	LTBP2_ENST00000556690.1_Silent_p.T802T	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	802					protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		CAGGTGCATGAGTGACACTGG	0.557													G|||	1897	0.378794	0.5416	0.4107	5008	,	,		19672	0.3294		0.2843	False		,,,				2504	0.2843				p.T802T		Atlas-SNP	.											LTBP2,NS,adenoma,0,1	LTBP2	158	1	0			c.T2406C						PASS	.	G		2176,2228	573.6+/-383.6	528,1120,554	110.0	85.0	93.0		2406	1.6	0.0	14	dbSNP_86	93	2419,6181	677.9+/-403.4	327,1765,2208	no	coding-synonymous	LTBP2	NM_000428.2		855,2885,2762	GG,GA,AA		28.1279,49.4096,35.3353		802/1822	74992800	4595,8409	2202	4300	6502	SO:0001819	synonymous_variant	4053	exon14			TGCATGAGTGACA		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.2406T>C	14.37:g.74992800A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_000428	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	37	CCDS9831.1																																																																																			A|0.644;G|0.356	0.356	strong		0.557	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	
LAMA2	3908	hgsc.bcm.edu	37	6	129612808	129612808	+	Silent	SNP	A	A	G	rs1027199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:129612808A>G	ENST00000421865.2	+	20	2848	c.2799A>G	c.(2797-2799)caA>caG	p.Q933Q		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	933	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		GCCACAGTCAAACTGGACAGT	0.463													A|||	1572	0.313898	0.3313	0.2233	5008	,	,		17620	0.4742		0.2256	False		,,,				2504	0.2802				p.Q933Q		Atlas-SNP	.											.	LAMA2	481	.	0			c.A2799G						PASS	.	A	,	1407,2999	460.7+/-352.7	226,955,1022	101.0	88.0	92.0		2799,2799	-1.9	0.0	6	dbSNP_86	92	1954,6646	344.1+/-325.2	235,1484,2581	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	461,2439,3603	GG,GA,AA		22.7209,31.9337,25.8419	,	933/3123,933/3119	129612808	3361,9645	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon20			CAGTCAAACTGGA	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.2799A>G	6.37:g.129612808A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			A|0.726;G|0.274	0.274	strong		0.463	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
SLC22A10	387775	hgsc.bcm.edu	37	11	63064823	63064823	+	Silent	SNP	T	T	C	rs576641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:63064823T>C	ENST00000332793.6	+	3	557	c.555T>C	c.(553-555)atT>atC	p.I185I	SLC22A10_ENST00000535888.1_5'UTR|SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000544661.1_Silent_p.I30I|SLC22A10_ENST00000525620.1_3'UTR	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	185						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			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)	AGCTTGCCATTACTGACACCT	0.413													C|||	2801	0.559305	0.6551	0.5677	5008	,	,		17382	0.4692		0.6064	False		,,,				2504	0.4683				p.I185I		Atlas-SNP	.											.	SLC22A10	79	.	0			c.T555C						PASS	.	C		2707,1445		888,931,257	170.0	170.0	170.0		555	1.3	0.0	11	dbSNP_83	170	5353,3123		1709,1935,594	no	coding-synonymous	SLC22A10	NM_001039752.3		2597,2866,851	CC,CT,TT		36.8452,34.8025,36.1736		185/542	63064823	8060,4568	2076	4238	6314	SO:0001819	synonymous_variant	387775	exon3			TGCCATTACTGAC	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.555T>C	11.37:g.63064823T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	170	90	0.529412	NM_001039752	Q68CJ0	Silent	SNP	ENST00000332793.6	37	CCDS41661.1																																																																																			T|0.413;C|0.587	0.587	strong		0.413	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752	
NID2	22795	hgsc.bcm.edu	37	14	52509501	52509501	+	Splice_Site	SNP	T	T	C	rs3818186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:52509501T>C	ENST00000216286.5	-	6	1577	c.1578A>G	c.(1576-1578)gaA>gaG	p.E526E	NID2_ENST00000541773.1_Splice_Site_p.E473E	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	526					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GTCAATTACCTTCAGGCAGAC	0.517													t|||	1936	0.386581	0.3933	0.4222	5008	,	,		19771	0.5466		0.2505	False		,,,				2504	0.3272				p.E526E		Atlas-SNP	.											.	NID2	201	.	0			c.A1578G						PASS	.	T		1573,2833	489.6+/-361.5	277,1019,907	117.0	104.0	109.0		1578	5.8	1.0	14	dbSNP_107	109	2127,6473	363.9+/-333.3	250,1627,2423	yes	coding-synonymous-near-splice	NID2	NM_007361.3		527,2646,3330	CC,CT,TT		24.7326,35.7013,28.4484		526/1376	52509501	3700,9306	2203	4300	6503	SO:0001630	splice_region_variant	22795	exon6			ATTACCTTCAGGC	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1579+1A>G	14.37:g.52509501T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1																																																																																			T|0.667;C|0.333	0.333	strong		0.517	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		Silent
PEBP4	157310	hgsc.bcm.edu	37	8	22584718	22584718	+	Missense_Mutation	SNP	T	T	C	rs1129474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22584718T>C	ENST00000256404.6	-	5	464	c.373A>G	c.(373-375)Aaa>Gaa	p.K125E	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	125			K -> E (in dbSNP:rs1129474). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)		p.K125E(1)		breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		ATCTTCCCTTTCTTCAGGTCG	0.552													T|||	2497	0.498602	0.7458	0.5749	5008	,	,		18949	0.2798		0.4672	False		,,,				2504	0.3681				p.K125E		Atlas-SNP	.											PEBP4,NS,carcinoma,0,1	PEBP4	23	1	1	Substitution - Missense(1)	stomach(1)	c.A373G						PASS	.	T	GLU/LYS	2792,1180		984,824,178	64.0	71.0	69.0		373	3.3	0.2	8	dbSNP_86	69	3985,4303		951,2083,1110	yes	missense	PEBP4	NM_144962.2	56	1935,2907,1288	CC,CT,TT		48.0816,29.708,44.7227	benign	125/228	22584718	6777,5483	1986	4144	6130	SO:0001583	missense	157310	exon5			TCCCTTTCTTCAG	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"""cousin-of-RKIP 1 protein"""	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.373A>G	8.37:g.22584718T>C	ENSP00000256404:p.Lys125Glu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	81	42	0.518519	NM_144962	Q5EVA1|Q8WW74	Missense_Mutation	SNP	ENST00000256404.6	37	CCDS43724.1	1052	0.4816849816849817	362	0.7357723577235772	202	0.5580110497237569	141	0.2465034965034965	347	0.4577836411609499	T	11.80	1.747447	0.30955	0.70292	0.480816	ENSG00000134020	ENST00000256404	T	0.40756	1.02	4.47	3.31	0.37934	.	1.360170	0.04715	N	0.418228	T	0.00012	0.0000	N	0.21373	0.66	0.80722	P	0.0	B	0.22146	0.065	B	0.18561	0.022	T	0.45116	-0.9283	9	0.39692	T	0.17	-2.3351	6.1388	0.20249	0.0:0.1147:0.0:0.8853	rs1129474;rs2271529;rs57266891;rs1129474	125	Q96S96	PEBP4_HUMAN	E	125	ENSP00000256404:K125E	ENSP00000256404:K125E	K	-	1	0	PEBP4	22640663	0.018000	0.18449	0.210000	0.23637	0.019000	0.09904	0.388000	0.20735	1.783000	0.52377	0.482000	0.46254	AAA	T|0.516;C|0.484	0.484	strong		0.552	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
PELI1	57162	hgsc.bcm.edu	37	2	64327592	64327592	+	Silent	SNP	T	T	C	rs329497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:64327592T>C	ENST00000358912.4	-	4	685	c.243A>G	c.(241-243)ttA>ttG	p.L81L	PELI1_ENST00000466177.2_5'UTR	NM_020651.3	NP_065702.2	Q96FA3	PELI1_HUMAN	pellino E3 ubiquitin protein ligase 1	81					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell proliferation (GO:0042130)|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 protein ubiquitination (GO:0031398)|positive regulation of toll-like receptor 3 signaling pathway (GO:0034141)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|protein K48-linked ubiquitination (GO:0070936)|response to dsRNA (GO:0043331)|response to lipopolysaccharide (GO:0032496)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	19						GGGCCCGAGATAAAGTATATG	0.343													T|||	1754	0.35024	0.0688	0.3112	5008	,	,		15865	0.752		0.2992	False		,,,				2504	0.3967				p.L81L		Atlas-SNP	.											.	PELI1	34	.	0			c.A243G						PASS	.	T		535,3871	241.5+/-251.9	33,469,1701	168.0	148.0	155.0		243	0.1	1.0	2	dbSNP_79	155	2617,5983	424.1+/-354.6	403,1811,2086	no	coding-synonymous	PELI1	NM_020651.3		436,2280,3787	CC,CT,TT		30.4302,12.1425,24.235		81/419	64327592	3152,9854	2203	4300	6503	SO:0001819	synonymous_variant	57162	exon4			CCGAGATAAAGTA		CCDS1876.1	2p13.3	2012-02-23	2012-02-23		ENSG00000197329	ENSG00000197329		"""Pellino homologs"""	8827	protein-coding gene	gene with protein product		614797	"""pellino (Drosophila) homolog 1"", ""pellino homolog 1 (Drosophila)"""			11306823, 16951688	Standard	NM_020651		Approved		uc002sct.4	Q96FA3	OTTHUMG00000129511	ENST00000358912.4:c.243A>G	2.37:g.64327592T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	107	48	0.448598	NM_020651	Q96SM0|Q9GZY5|Q9HCX0	Silent	SNP	ENST00000358912.4	37	CCDS1876.1																																																																																			T|0.705;C|0.295	0.295	strong		0.343	PELI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251686.1	NM_020651	
KCNK13	56659	hgsc.bcm.edu	37	14	90651079	90651079	+	Missense_Mutation	SNP	G	G	A	rs150186575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:90651079G>A	ENST00000282146.4	+	2	1400	c.959G>A	c.(958-960)cGg>cAg	p.R320Q		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	320					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				GGCAGCGTCCGGAACCGCTGC	0.597																																					p.R320Q		Atlas-SNP	.											.	KCNK13	76	.	0			c.G959A						PASS	.						65.0	69.0	68.0					14																	90651079		2203	4300	6503	SO:0001583	missense	56659	exon2			GCGTCCGGAACCG	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.959G>A	14.37:g.90651079G>A	ENSP00000282146:p.Arg320Gln	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	141	74	0.524823	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	G	8.030	0.761526	0.15914	.	.	ENSG00000152315	ENST00000282146	T	0.12255	2.7	5.28	-0.111	0.13576	.	2.504590	0.01759	N	0.030439	T	0.11879	0.0289	L	0.36672	1.1	0.46981	D	0.999276	B	0.06786	0.001	B	0.09377	0.004	T	0.46219	-0.9207	10	0.07813	T	0.8	.	10.1408	0.42734	0.3118:0.0:0.6882:0.0	.	320	Q9HB14	KCNKD_HUMAN	Q	320	ENSP00000282146:R320Q	ENSP00000282146:R320Q	R	+	2	0	KCNK13	89720832	0.952000	0.32445	0.001000	0.08648	0.007000	0.05969	4.029000	0.57253	-0.355000	0.08199	0.655000	0.94253	CGG	G|0.999;T|0.001	.	alt		0.597	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054	
DST	667	hgsc.bcm.edu	37	6	56505175	56505175	+	Silent	SNP	T	T	A	rs113432929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56505175T>A	ENST00000361203.3	-	14	1630	c.1623A>T	c.(1621-1623)tcA>tcT	p.S541S	DST_ENST00000446842.2_Silent_p.S215S|DST_ENST00000421834.2_Silent_p.S541S|DST_ENST00000370769.4_Silent_p.S541S|DST_ENST00000370754.5_Silent_p.S719S|DST_ENST00000312431.6_Silent_p.S541S|DST_ENST00000518935.1_Silent_p.S215S|DST_ENST00000244364.6_Silent_p.S215S|DST_ENST00000370765.6_Silent_p.S215S|DST_ENST00000370788.2_Silent_p.S541S			Q03001	DYST_HUMAN	dystonin	541					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)			AAGTCATCCCTGATGACAGGC	0.483													T|||	11	0.00219649	0.0	0.0	5008	,	,		18999	0.0		0.005	False		,,,				2504	0.0061				p.S215S		Atlas-SNP	.											.	DST	1427	.	0			c.A645T						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	139.0	141.0	141.0		645,645	-4.8	0.6	6	dbSNP_132	141	36,8564	25.1+/-72.6	0,36,4264	yes	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	0,40,6463	AA,AT,TT		0.4186,0.0908,0.3076	,	215/2650,215/5172	56505175	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			CATCCCTGATGAC	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.1623A>T	6.37:g.56505175T>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	69	0.442308	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				T|0.997;A|0.003	0.003	strong		0.483	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
NPBWR2	2832	hgsc.bcm.edu	37	20	62737318	62737318	+	Silent	SNP	G	G	A	rs13036542	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62737318G>A	ENST00000369768.1	-	1	1206	c.867C>T	c.(865-867)ccC>ccT	p.P289P		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	289					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					GTGGGGTCTGGGGCAGGTCCG	0.617													G|||	2247	0.448682	0.348	0.5245	5008	,	,		14518	0.6091		0.4821	False		,,,				2504	0.3313				p.P289P		Atlas-SNP	.											.	NPBWR2	36	.	0			c.C867T						PASS	.	G		1589,2815	492.0+/-362.3	282,1025,895	147.0	102.0	117.0		867	-0.2	0.0	20	dbSNP_121	117	4045,4551	554.9+/-386.6	969,2107,1222	no	coding-synonymous	NPBWR2	NM_005286.2		1251,3132,2117	AA,AG,GG		47.0568,36.0808,43.3385		289/334	62737318	5634,7366	2202	4298	6500	SO:0001819	synonymous_variant	2832	exon1			GGTCTGGGGCAGG	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.867C>T	20.37:g.62737318G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_005286	Q6NWQ6|Q9H4K3	Silent	SNP	ENST00000369768.1	37	CCDS13557.1																																																																																			G|0.545;A|0.455	0.455	strong		0.617	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
ELFN2	114794	hgsc.bcm.edu	37	22	37770066	37770066	+	Silent	SNP	G	G	T	rs8142615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37770066G>T	ENST00000402918.2	-	3	2294	c.1509C>A	c.(1507-1509)atC>atA	p.I503I	RP1-63G5.5_ENST00000430883.1_RNA|RP1-63G5.8_ENST00000609322.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	503					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					TGCGCACCTCGATATAGTTGC	0.672													G|||	1998	0.398962	0.4924	0.5403	5008	,	,		17217	0.3502		0.3608	False		,,,				2504	0.2618				p.I503I		Atlas-SNP	.											ELFN2,colon,carcinoma,0,1	ELFN2	89	1	0			c.C1509A						PASS	.	G		2242,2164	558.0+/-379.9	561,1120,522	47.0	49.0	48.0		1509	-4.5	0.9	22	dbSNP_116	48	3169,5429	454.9+/-363.6	595,1979,1725	no	coding-synonymous	ELFN2	NM_052906.3		1156,3099,2247	TT,TG,GG		36.8574,49.1148,41.6103		503/821	37770066	5411,7593	2203	4299	6502	SO:0001819	synonymous_variant	114794	exon3			CACCTCGATATAG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.1509C>A	22.37:g.37770066G>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	37	CCDS33642.1																																																																																			G|0.597;T|0.403	0.403	strong		0.672	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906	
INSR	3643	hgsc.bcm.edu	37	19	7163154	7163154	+	Silent	SNP	G	G	A	rs2963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7163154G>A	ENST00000302850.5	-	9	2060	c.1918C>T	c.(1918-1920)Ctg>Ttg	p.L640L	AC010311.1_ENST00000581768.1_RNA|INSR_ENST00000341500.5_Silent_p.L640L	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	640	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of MAPK activity (GO:0000187)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|carbohydrate metabolic process (GO:0005975)|cellular response to growth factor stimulus (GO:0071363)|cellular response to insulin stimulus (GO:0032869)|epidermis development (GO:0008544)|exocrine pancreas development (GO:0031017)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|insulin receptor signaling pathway (GO:0008286)|male sex determination (GO:0030238)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of developmental growth (GO:0048639)|positive regulation of DNA replication (GO:0045740)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of glycolytic process (GO:0045821)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of respiratory burst (GO:0060267)|protein autophosphorylation (GO:0046777)|protein heterotetramerization (GO:0051290)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction by phosphorylation (GO:0023014)|transformation of host cell by virus (GO:0019087)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|insulin receptor complex (GO:0005899)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|insulin binding (GO:0043559)|insulin receptor substrate binding (GO:0043560)|insulin-activated receptor activity (GO:0005009)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor II binding (GO:0031995)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|PTB domain binding (GO:0051425)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(1)|central_nervous_system(4)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(4)|prostate(4)|skin(3)|stomach(2)|urinary_tract(2)	66					"""""""Insulin(DB00071)|""""Insulin(DB08914)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	TTCCACTTCAGAATAATCTGG	0.517													A|||	800	0.159744	0.2723	0.0692	5008	,	,		15100	0.0367		0.0646	False		,,,				2504	0.2965				p.L640L		Atlas-SNP	.											.	INSR	265	.	0			c.C1918T						PASS	.	A	,	1034,3372	723.9+/-409.4	118,798,1287	163.0	167.0	166.0		1918,1918	-6.3	0.0	19	dbSNP_36	166	681,7919	788.0+/-407.6	33,615,3652	no	coding-synonymous,coding-synonymous	INSR	NM_000208.2,NM_001079817.1	,	151,1413,4939	AA,AG,GG		7.9186,23.468,13.1862	,	640/1383,640/1371	7163154	1715,11291	2203	4300	6503	SO:0001819	synonymous_variant	3643	exon9			ACTTCAGAATAAT	M10051	CCDS12176.1, CCDS42487.1	19p13.3-p13.2	2013-02-11				ENSG00000171105		"""CD molecules"", ""Fibronectin type III domain containing"""	6091	protein-coding gene	gene with protein product		147670				2983222	Standard	NM_000208		Approved	CD220	uc002mgd.1	P06213		ENST00000302850.5:c.1918C>T	19.37:g.7163154G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	159	50	0.314465	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			G|0.876;A|0.124	0.124	strong		0.517	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1		
RAD52	5893	hgsc.bcm.edu	37	12	1022569	1022569	+	Nonsense_Mutation	SNP	A	A	C	rs4987208	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:1022569A>C	ENST00000358495.3	-	12	1383	c.1245T>G	c.(1243-1245)taT>taG	p.Y415*	RAD52_ENST00000430095.2_Nonsense_Mutation_p.Y415*|RAD52_ENST00000539046.1_Nonsense_Mutation_p.Y338*|RAD52_ENST00000535376.1_5'UTR	NM_134424.2	NP_602296.2	P43351	RAD52_HUMAN	RAD52 homolog (S. cerevisiae)	415					DNA recombinase assembly (GO:0000730)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	all_cancers(10;0.0119)|all_epithelial(11;0.0171)|all_lung(10;0.0521)|Ovarian(42;0.0816)|Lung NSC(10;0.0987)		OV - Ovarian serous cystadenocarcinoma(31;0.00123)|BRCA - Breast invasive adenocarcinoma(9;0.0323)			AAGATGGATCATATTTCCTTT	0.388								Homologous recombination					A|||	111	0.0221645	0.0015	0.1182	5008	,	,		21288	0.0		0.008	False		,,,				2504	0.0194				p.Y415X		Atlas-SNP	.											.	RAD52	27	.	0			c.T1245G	GRCh37	CM051217	RAD52	M	rs4987208	PASS	.	A	stop/TYR	20,3686		0,20,1833	225.0	214.0	217.0		1245	1.8	0.4	12	dbSNP_113	217	156,8054		3,150,3952	yes	stop-gained	RAD52	NM_134424.2		3,170,5785	CC,CA,AA		1.9001,0.5397,1.477		415/419	1022569	176,11740	1853	4105	5958	SO:0001587	stop_gained	5893	exon12			TGGATCATATTTC		CCDS8507.2	12p13-p12.2	2008-08-05	2001-11-28		ENSG00000002016	ENSG00000002016			9824	protein-coding gene	gene with protein product		600392	"""RAD52 (S. cerevisiae) homolog"""			7774919, 18313388	Standard	XM_005253721		Approved		uc001qis.1	P43351	OTTHUMG00000090361	ENST00000358495.3:c.1245T>G	12.37:g.1022569A>C	ENSP00000351284:p.Tyr415*	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	163	89	0.546012	NM_134424	Q13205|Q9Y5T7|Q9Y5T8|Q9Y5T9	Nonsense_Mutation	SNP	ENST00000358495.3	37	CCDS8507.2	39	0.017857142857142856	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	8	0.010554089709762533	A	17.04	3.286626	0.59867	0.005397	0.019001	ENSG00000002016	ENST00000358495;ENST00000430095;ENST00000539046	.	.	.	4.71	1.8	0.24995	.	0.233424	0.35936	N	0.002896	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-27.9708	3.866	0.09016	0.2958:0.4811:0.1427:0.0805	rs4987208;rs17403546;rs4987208	.	.	.	X	415;415;338	.	ENSP00000351284:Y415X	Y	-	3	2	RAD52	892830	0.981000	0.34729	0.386000	0.26170	0.590000	0.36582	0.639000	0.24690	0.044000	0.15775	-2.411000	0.00221	TAT	A|0.979;C|0.021	0.021	strong		0.388	RAD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206733.2	NM_134424	
STX2	2054	hgsc.bcm.edu	37	12	131306314	131306314	+	Missense_Mutation	SNP	C	C	G	rs17564	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:131306314C>G	ENST00000392373.2	-	3	219	c.125G>C	c.(124-126)aGt>aCt	p.S42T	STX2_ENST00000261653.6_Missense_Mutation_p.S42T	NM_194356.2	NP_919337.1	P32856	STX2_HUMAN	syntaxin 2	42			S -> T (in dbSNP:rs6486602).		acrosome reaction (GO:0007340)|cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|intracellular protein transport (GO:0006886)|organ morphogenesis (GO:0009887)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|signal transduction (GO:0007165)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)	calcium-dependent protein binding (GO:0048306)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)	16	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.79e-06)|all cancers(50;5.27e-05)|Epithelial(86;5.29e-05)		TTTATCAATACTGTTTCTAAT	0.383													C|||	3025	0.604034	0.2141	0.6499	5008	,	,		17814	0.872		0.6571	False		,,,				2504	0.7679				p.S42T		Atlas-SNP	.											.	STX2	66	.	0			c.G125C						PASS	.	C	THR/SER,THR/SER	1217,3189	421.9+/-339.5	176,865,1162	148.0	133.0	138.0		125,125	-0.5	0.0	12	dbSNP_116	138	5651,2949	667.2+/-402.4	1856,1939,505	yes	missense,missense	STX2	NM_001980.2,NM_194356.1	58,58	2032,2804,1667	GG,GC,CC		34.2907,27.6214,47.1936	benign,benign	42/288,42/289	131306314	6868,6138	2203	4300	6503	SO:0001583	missense	2054	exon3			TCAATACTGTTTC	D14582	CCDS9269.1, CCDS9270.1	12q24	2008-02-05	2006-04-25	2006-04-25	ENSG00000111450	ENSG00000111450			3403	protein-coding gene	gene with protein product		132350	"""epimorphin"""	STX2B, STX2C, STX2A, EPIM		8938452, 15943887	Standard	NM_001980		Approved	EPM	uc001uio.4	P32856	OTTHUMG00000168365	ENST00000392373.2:c.125G>C	12.37:g.131306314C>G	ENSP00000376178:p.Ser42Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	113	55	0.486726	NM_194356	Q86VW8	Missense_Mutation	SNP	ENST00000392373.2	37	CCDS9270.1	1345	0.6158424908424909	110	0.22357723577235772	223	0.6160220994475138	501	0.8758741258741258	511	0.6741424802110818	C	2.614	-0.290165	0.05568	0.276214	0.657093	ENSG00000111450	ENST00000261653;ENST00000392373	T;T	0.17370	2.28;2.28	4.48	-0.508	0.11980	t-SNARE (1);Syntaxin, N-terminal (2);	0.633406	0.17716	N	0.164408	T	0.00012	0.0000	N	0.25485	0.75	0.80722	P	0.0	B;B;B	0.32893	0.332;0.185;0.389	B;B;B	0.36766	0.076;0.034;0.232	T	0.18023	-1.0350	9	0.15499	T	0.54	-21.5042	5.4155	0.16372	0.0:0.5118:0.1425:0.3457	rs6486602;rs11551010;rs52823741;rs6486602	42;42;42	P32856-3;P32856-2;P32856	.;.;STX2_HUMAN	T	42	ENSP00000261653:S42T;ENSP00000376178:S42T	ENSP00000261653:S42T	S	-	2	0	STX2	129872267	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.070000	0.11523	0.006000	0.14734	-1.786000	0.00637	AGT	C|0.443;G|0.557	0.557	strong		0.383	STX2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399455.2	NM_194356	
WDR64	128025	hgsc.bcm.edu	37	1	241901757	241901757	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:241901757G>A	ENST00000366552.2	+	10	1464	c.1257G>A	c.(1255-1257)atG>atA	p.M419I	WDR64_ENST00000437684.2_Missense_Mutation_p.M419I	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	419										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TTTACTCTATGATATATGATG	0.393																																					p.M419I		Atlas-SNP	.											WDR64_ENST00000366552,NS,carcinoma,+2,1	WDR64	234	1	0			c.G1257A						scavenged	.						114.0	106.0	109.0					1																	241901757		2203	4300	6503	SO:0001583	missense	128025	exon10			CTCTATGATATAT	AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1257G>A	1.37:g.241901757G>A	ENSP00000355510:p.Met419Ile	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	133	3	0.0225564	NM_144625	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		.	.	.	.	.	.	.	.	.	.	G	14.16	2.452906	0.43531	.	.	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.37411	1.79;1.26;1.2	6.07	6.07	0.98685	.	0.059387	0.64402	N	0.000001	T	0.46444	0.1393	N	0.24115	0.695	0.39928	D	0.974255	D	0.63880	0.993	D	0.70227	0.968	T	0.28964	-1.0027	10	0.31617	T	0.26	-28.5347	17.5761	0.87949	0.0:0.0:1.0:0.0	.	139	D1MPS4	.	I	419;419;190	ENSP00000355510:M419I;ENSP00000402446:M419I;ENSP00000406656:M190I	ENSP00000355510:M419I	M	+	3	0	WDR64	239968380	1.000000	0.71417	0.912000	0.35992	0.815000	0.46073	5.849000	0.69465	2.885000	0.99019	0.655000	0.94253	ATG	.	.	none		0.393	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
MAP4K1	11184	hgsc.bcm.edu	37	19	39101772	39101772	+	Splice_Site	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39101772C>T	ENST00000591517.1	-	11	757	c.729G>A	c.(727-729)tgG>tgA	p.W243*	MAP4K1_ENST00000423454.2_Intron|MAP4K1_ENST00000586296.1_Splice_Site_p.W243*|MAP4K1_ENST00000589002.1_Intron|MAP4K1_ENST00000589130.1_Splice_Site_p.W239*|MAP4K1_ENST00000396857.2_Splice_Site_p.W243*	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	243	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGGCAGCCGACCTTGGGAAGA	0.577																																					p.W243X		Atlas-SNP	.											.	MAP4K1	165	.	0			c.G729A						PASS	.						99.0	110.0	106.0					19																	39101772		1982	4153	6135	SO:0001630	splice_region_variant	11184	exon11			AGCCGACCTTGGG	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6863	protein-coding gene	gene with protein product	"""hematopoietic progenitor kinase 1"""	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.729-1G>A	19.37:g.39101772C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	164	65	0.396341	NM_007181		Nonsense_Mutation	SNP	ENST00000591517.1	37	CCDS59385.1	.	.	.	.	.	.	.	.	.	.	C	37	6.181791	0.97352	.	.	ENSG00000104814	ENST00000396857;ENST00000221409	.	.	.	4.21	4.21	0.49690	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4865	0.75571	0.0:1.0:0.0:0.0	.	.	.	.	X	243	.	ENSP00000221409:W243X	W	-	3	0	MAP4K1	43793612	1.000000	0.71417	0.999000	0.59377	0.823000	0.46562	7.190000	0.77755	2.175000	0.68902	0.555000	0.69702	TGG	.	.	none		0.577	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600	Nonsense_Mutation
IVL	3713	hgsc.bcm.edu	37	1	152883680	152883680	+	Silent	SNP	A	A	G	rs7535306	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152883680A>G	ENST00000368764.3	+	2	1471	c.1407A>G	c.(1405-1407)caA>caG	p.Q469Q	IVL_ENST00000392667.2_Silent_p.Q323Q			P07476	INVO_HUMAN	involucrin	469	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGAGAAGCAACTGGAGCTCC	0.617													G|||	2071	0.413538	0.6808	0.2997	5008	,	,		18638	0.5615		0.1083	False		,,,				2504	0.2945				p.Q469Q		Atlas-SNP	.											IVL,NS,lymphoid_neoplasm,+1,1	IVL	100	1	0			c.A1407G						PASS	.	G		2401,1947		681,1039,454	42.0	50.0	48.0		1407	-4.9	0.0	1	dbSNP_116	48	752,7780		41,670,3555	yes	coding-synonymous	IVL	NM_005547.2		722,1709,4009	GG,GA,AA		8.8139,44.7792,24.4798		469/586	152883680	3153,9727	2174	4266	6440	SO:0001819	synonymous_variant	3713	exon2			GAAGCAACTGGAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1407A>G	1.37:g.152883680A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	115	54	0.469565	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			A|0.667;G|0.333	0.333	strong		0.617	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549607	32549607	+	Missense_Mutation	SNP	T	T	G	rs17405219		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32549607T>G	ENST00000360004.5	-	3	484	c.379A>C	c.(379-381)Aag>Cag	p.K127Q		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	127	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|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						ACAGTCACCTTAGGTTGGACT	0.507										Multiple Myeloma(14;0.17)																											p.K127Q		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A379C						PASS	.						35.0	45.0	42.0					6																	32549607		1506	2702	4208	SO:0001583	missense	3123	exon3			TCACCTTAGGTTG	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.379A>C	6.37:g.32549607T>G	ENSP00000353099:p.Lys127Gln	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	93	24	0.258065	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	10.23	1.293786	0.23564	.	.	ENSG00000196126	ENST00000360004	T	0.08984	3.03	3.87	1.02	0.19986	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.096500	0.06813	N	0.790766	T	0.03053	0.0090	L	0.45470	1.425	0.09310	N	1	B	0.16603	0.018	B	0.12156	0.007	T	0.44787	-0.9305	10	0.45353	T	0.12	.	9.15	0.36957	0.0:0.0:0.3428:0.6572	rs17881211;rs17882382;rs28732333	127	P01911	2B1F_HUMAN	Q	127	ENSP00000353099:K127Q	ENSP00000353099:K127Q	K	-	1	0	HLA-DRB1	32657585	0.000000	0.05858	0.038000	0.18304	0.075000	0.17131	-0.089000	0.11180	0.451000	0.26802	0.372000	0.22366	AAG	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PAX7	5081	hgsc.bcm.edu	37	1	19018405	19018405	+	Silent	SNP	G	G	A	rs2076020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:19018405G>A	ENST00000375375.3	+	5	1342	c.744G>A	c.(742-744)gaG>gaA	p.E248E	PAX7_ENST00000400661.3_Silent_p.E246E|PAX7_ENST00000420770.2_Silent_p.E248E	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	248					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)		ACACCCGCGAGGAGCTGGCGC	0.602			T	FOXO1A	alveolar rhabdomyosarcoma								G|||	506	0.101038	0.0061	0.0865	5008	,	,		19361	0.251		0.0557	False		,,,				2504	0.1319				p.E248E		Atlas-SNP	.		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	PAX7_ENST00000420770,NS,carcinoma,+2,2	PAX7	127	2	0			c.G744A						PASS	.	G	,,	74,4330	64.1+/-101.4	0,74,2128	42.0	38.0	39.0		744,744,738	2.9	1.0	1	dbSNP_96	39	452,8146	132.2+/-189.8	13,426,3860	no	coding-synonymous,coding-synonymous,coding-synonymous	PAX7	NM_001135254.1,NM_002584.2,NM_013945.2	,,	13,500,5988	AA,AG,GG		5.257,1.6803,4.0455	,,	248/506,248/521,246/519	19018405	526,12476	2202	4299	6501	SO:0001819	synonymous_variant	5081	exon5			CCGCGAGGAGCTG	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.744G>A	1.37:g.19018405G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	83	75	0.903614	NM_002584	E9PFV9|Q0VA99|Q2PJS5	Silent	SNP	ENST00000375375.3	37	CCDS186.1																																																																																			G|0.933;A|0.067	0.067	strong		0.602	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584	
CEP89	84902	hgsc.bcm.edu	37	19	33372814	33372814	+	Missense_Mutation	SNP	G	G	A	rs34626245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33372814G>A	ENST00000305768.5	-	18	2159	c.2071C>T	c.(2071-2073)Cgg>Tgg	p.R691W		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	691					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						TGCAGGTGCCGCATCTCCTGC	0.647													g|||	412	0.0822684	0.0908	0.0634	5008	,	,		15791	0.0536		0.0567	False		,,,				2504	0.1401				p.R691W		Atlas-SNP	.											.	CEP89	82	.	0			c.C2071T						PASS	.	G	TRP/ARG	334,4072	163.3+/-195.1	14,306,1883	40.0	29.0	33.0		2071	-2.0	0.4	19	dbSNP_126	33	496,8104	135.4+/-192.6	12,472,3816	yes	missense	CEP89	NM_032816.3	101	26,778,5699	AA,AG,GG		5.7674,7.5806,6.3817	probably-damaging	691/784	33372814	830,12176	2203	4300	6503	SO:0001583	missense	84902	exon18			GGTGCCGCATCTC	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.2071C>T	19.37:g.33372814G>A	ENSP00000306105:p.Arg691Trp	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	37	23	0.621622	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	152	0.0695970695970696	46	0.09349593495934959	31	0.0856353591160221	35	0.06118881118881119	40	0.052770448548812667	g	13.87	2.367291	0.41902	0.075806	0.057674	ENSG00000121289	ENST00000305768	T	0.33865	1.39	5.76	-2.01	0.07410	.	0.352765	0.26503	N	0.024006	T	0.02455	0.0075	L	0.48642	1.525	0.09310	P	0.999999999619637	D	0.89917	1.0	D	0.77004	0.989	T	0.26189	-1.0110	9	0.87932	D	0	-6.3898	11.6902	0.51510	0.0:0.0639:0.5813:0.3548	rs34626245	691	Q96ST8	CEP89_HUMAN	W	691	ENSP00000306105:R691W	ENSP00000306105:R691W	R	-	1	2	CEP89	38064654	0.831000	0.29352	0.430000	0.26722	0.089000	0.18198	-0.413000	0.07123	-0.837000	0.04223	-0.408000	0.06270	CGG	G|0.930;A|0.070	0.070	strong		0.647	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
MXRA5	25878	hgsc.bcm.edu	37	X	3228891	3228891	+	Silent	SNP	A	A	G	rs1635235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3228891A>G	ENST00000217939.6	-	7	7507	c.7353T>C	c.(7351-7353)acT>acC	p.T2451T		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	2451	Ig-like C2-type 9.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TCTCCCGCACAGTGGTGATGG	0.592													a|||	2307	0.611126	0.357	0.4769	3775	,	,		13540	0.5575		0.4781	False		,,,				2504	0.4714				p.T2451T		Atlas-SNP	.											.	MXRA5	815	.	0			c.T7353C						PASS	.	A		1882,1952		393,815,281,424,289	68.0	41.0	50.0		7353	-7.1	0.1	X	dbSNP_89	50	3871,2849		806,1194,1065,428,799	no	coding-synonymous	MXRA5	NM_015419.3		1199,2009,1346,852,1088	GG,GA,G,AA,A		42.3958,49.0871,45.4899		2451/2829	3228891	5753,4801	2202	4292	6494	SO:0001819	synonymous_variant	25878	exon7			CCGCACAGTGGTG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.7353T>C	X.37:g.3228891A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			A|0.431;0|0.003	.	strong		0.592	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
OR4C46	119749	hgsc.bcm.edu	37	11	51516191	51516191	+	Missense_Mutation	SNP	G	G	A	rs140000110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:51516191G>A	ENST00000328188.1	+	1	910	c.910G>A	c.(910-912)Gac>Aac	p.D304N		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	304						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TAGTAGAAAGGACATTTCAGG	0.348													.|||	22	0.00439297	0.0008	0.0101	5008	,	,		17524	0.0		0.0099	False		,,,				2504	0.0041				p.D304N		Atlas-SNP	.											.	OR4C46	96	.	0			c.G910A						PASS	.	G	ASN/ASP	6,4388		0,6,2191	43.0	39.0	40.0		910	-0.3	0.0	11	dbSNP_134	40	52,8520		0,52,4234	no	missense	OR4C46	NM_001004703.1	23	0,58,6425	AA,AG,GG		0.6066,0.1365,0.4473	benign	304/310	51516191	58,12908	2197	4286	6483	SO:0001583	missense	119749	exon1			AGAAAGGACATTT		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.910G>A	11.37:g.51516191G>A	ENSP00000329056:p.Asp304Asn	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	52	16	0.307692	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	14	0.00641025641025641	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	8	0.010554089709762533	.	4.023	0.001768	0.07819	0.001365	0.006066	ENSG00000185926	ENST00000328188	T	0.00002	9.87	2.17	-0.354	0.12591	.	1.447940	0.05319	U	0.526276	T	0.00039	0.0001	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.01024	-1.1477	10	0.48119	T	0.1	.	7.0293	0.24958	0.0:0.0:0.3551:0.6449	.	304	A6NHA9	O4C46_HUMAN	N	304	ENSP00000329056:D304N	ENSP00000329056:D304N	D	+	1	0	OR4C46	51372767	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.151000	0.10175	0.225000	0.20959	0.186000	0.17326	GAC	G|0.995;A|0.005	0.005	strong		0.348	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
ADAD2	161931	hgsc.bcm.edu	37	16	84229559	84229559	+	Silent	SNP	T	T	C	rs2303238	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84229559T>C	ENST00000315906.5	+	7	1243	c.1191T>C	c.(1189-1191)agT>agC	p.S397S	ADAD2_ENST00000268624.3_Silent_p.S479S|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	397	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						TGTCAGCCAGTGACAAGCTGG	0.682													C|||	4033	0.805312	0.9902	0.6844	5008	,	,		15650	0.7123		0.7883	False		,,,				2504	0.7546				p.S479S		Atlas-SNP	.											ADAD2,NS,carcinoma,0,1	ADAD2	46	1	0			c.T1437C						PASS	.	C	,	4179,213		1996,187,13	18.0	22.0	20.0		1191,1437	-11.0	0.0	16	dbSNP_100	20	6642,1950		2591,1460,245	no	coding-synonymous,coding-synonymous	ADAD2	NM_001145400.1,NM_139174.3	,	4587,1647,258	CC,CT,TT		22.6955,4.8497,16.659	,	397/584,479/666	84229559	10821,2163	2196	4296	6492	SO:0001819	synonymous_variant	161931	exon8			AGCCAGTGACAAG	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1191T>C	16.37:g.84229559T>C		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	31	30	0.967742	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																			T|0.179;C|0.821	0.821	strong		0.682	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
TPX2	22974	hgsc.bcm.edu	37	20	30382315	30382315	+	Silent	SNP	A	A	G	rs3203770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:30382315A>G	ENST00000300403.6	+	15	2325	c.1797A>G	c.(1795-1797)agA>agG	p.R599R	TPX2_ENST00000340513.4_Silent_p.R635R	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	599					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			AGACTGACAGAAGAGGTGCTC	0.488													A|||	1122	0.224042	0.5454	0.1599	5008	,	,		18629	0.0		0.2346	False		,,,				2504	0.0552				p.R599R		Atlas-SNP	.											.	TPX2	61	.	0			c.A1797G						PASS	.	A		2046,2360	566.7+/-382.0	471,1104,628	111.0	104.0	107.0		1797	0.3	0.6	20	dbSNP_105	107	1814,6786	326.8+/-317.6	191,1432,2677	no	coding-synonymous	TPX2	NM_012112.4		662,2536,3305	GG,GA,AA		21.093,46.4367,29.6786		599/748	30382315	3860,9146	2203	4300	6503	SO:0001819	synonymous_variant	22974	exon15			TGACAGAAGAGGT	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1797A>G	20.37:g.30382315A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	67	41	0.61194	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Silent	SNP	ENST00000300403.6	37	CCDS13190.1																																																																																			A|0.722;G|0.278	0.278	strong		0.488	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
FCGR2B	2213	hgsc.bcm.edu	37	1	161642985	161642985	+	Silent	SNP	G	G	A	rs182968886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161642985G>A	ENST00000358671.5	+	4	693	c.612G>A	c.(610-612)ctG>ctA	p.L204L	FCGR2B_ENST00000367961.4_Silent_p.L197L|FCGR2B_ENST00000428605.2_Silent_p.L204L|FCGR2B_ENST00000367960.5_Silent_p.L197L|FCGR2B_ENST00000403078.3_Silent_p.L204L|FCGR2B_ENST00000367962.4_Silent_p.L204L|RP11-25K21.1_ENST00000453111.1_RNA|FCGR2B_ENST00000236937.9_Silent_p.L204L	NM_001002275.2|NM_004001.4	NP_001002275.1|NP_003992.3	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)	204	Ig-like C2-type 2.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)						all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Antithymocyte globulin(DB00098)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	GCTACACGCTGTACTCATCCA	0.517			T	?	ALL								G|||	552	0.110224	0.1694	0.0821	5008	,	,		21322	0.006		0.0944	False		,,,				2504	0.1738				p.L204L		Atlas-SNP	.		Dom	yes		1	1q23	2213	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""		L	.	FCGR2B	33	.	0			c.G612A						PASS	.	G	,,,,	717,3669		101,515,1577	42.0	43.0	43.0		609,612,609,591,612	-6.2	0.0	1		43	1003,7593		66,871,3361	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCGR2B	NM_001002273.2,NM_001002274.2,NM_001002275.2,NM_001190828.1,NM_004001.4	,,,,	167,1386,4938	AA,AG,GG		11.6682,16.3475,13.2491	,,,,	203/291,204/292,203/310,197/304,204/311	161642985	1720,11262	2193	4298	6491	SO:0001819	synonymous_variant	2213	exon4			CACGCTGTACTCA	BC031992	CCDS30924.1, CCDS30925.1, CCDS53414.1	1q23	2013-01-11	2005-02-02		ENSG00000072694	ENSG00000072694		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3618	protein-coding gene	gene with protein product		604590	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""	FCG2, FCGR2		2139735	Standard	NM_004001		Approved	CD32, CD32B	uc001gaz.2	P31994	OTTHUMG00000034470	ENST00000358671.5:c.612G>A	1.37:g.161642985G>A		Somatic	526	2	0.00380228		WXS	Illumina HiSeq	Phase_I	673	579	0.860327	NM_001002274	A6H8N3|O95649|Q53X85|Q5VXA9|Q8NIA1	Silent	SNP	ENST00000358671.5	37	CCDS30924.1																																																																																			G|0.895;A|0.105	0.105	strong		0.517	FCGR2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083337.4	NM_004001	
AXIN2	8313	hgsc.bcm.edu	37	17	63554591	63554591	+	Missense_Mutation	SNP	G	G	A	rs2240308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:63554591G>A	ENST00000375702.5	-	1	256	c.148C>T	c.(148-150)Cct>Tct	p.P50S	AXIN2_ENST00000307078.5_Missense_Mutation_p.P50S|CTD-2535L24.2_ENST00000577662.1_3'UTR			Q9Y2T1	AXIN2_HUMAN	axin 2	50			S -> P (in polymorphism associated with increased risk of lung cancer; dbSNP:rs2240308). {ECO:0000269|PubMed:16820935}.	QPGVGKGQVTKPMSVSSNTRRNEDGL -> HHGGQGPGHQT HVCLFQHQAERRWV (in Ref. 2; AAF22799). {ECO:0000305}.	bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GAAGAGACAGGCATGGGTTTG	0.662									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				G|||	1691	0.33766	0.0666	0.5159	5008	,	,		15989	0.3234		0.4702	False		,,,				2504	0.456				p.P50S		Atlas-SNP	.											.	AXIN2	92	.	0			c.C148T	GRCh37	CM066739	AXIN2	M	rs2240308	PASS	.	G	SER/PRO	596,3810	261.6+/-264.4	46,504,1653	54.0	56.0	55.0		148	2.8	0.8	17	dbSNP_98	55	4539,4061	590.3+/-392.6	1195,2149,956	yes	missense	AXIN2	NM_004655.3	74	1241,2653,2609	AA,AG,GG		47.2209,13.527,39.4818	benign	50/844	63554591	5135,7871	2203	4300	6503	SO:0001583	missense	8313	exon2	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	AGACAGGCATGGG	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.148C>T	17.37:g.63554591G>A	ENSP00000364854:p.Pro50Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		759	0.3475274725274725	42	0.08536585365853659	171	0.4723756906077348	176	0.3076923076923077	370	0.48812664907651715	G	1.053	-0.675392	0.03378	0.13527	0.527791	ENSG00000168646	ENST00000307078;ENST00000544103;ENST00000375702	T;T;T	0.76578	-0.05;-1.03;-0.04	4.74	2.75	0.32379	.	0.600804	0.16571	N	0.208652	T	0.00012	0.0000	.	.	.	0.22330	P	0.999193277	B	0.02656	0.0	B	0.01281	0.0	T	0.36480	-0.9746	8	0.05620	T	0.96	-7.6866	7.627	0.28218	0.2676:0.0:0.7324:0.0	rs2240308;rs52824132;rs60904566;rs2240308	50	E7ES00	.	S	50	ENSP00000302625:P50S;ENSP00000441151:P50S;ENSP00000364854:P50S	ENSP00000302625:P50S	P	-	1	0	AXIN2	60985053	0.999000	0.42202	0.834000	0.33040	0.020000	0.10135	0.923000	0.28757	0.980000	0.38523	0.561000	0.74099	CCT	G|0.641;A|0.359	0.359	strong		0.662	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	
RASEF	158158	hgsc.bcm.edu	37	9	85627408	85627408	+	Missense_Mutation	SNP	G	G	A	rs4146960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:85627408G>A	ENST00000376447.3	-	5	1044	c.784C>T	c.(784-786)Cgc>Tgc	p.R262C		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	262			R -> C (in dbSNP:rs4146960). {ECO:0000269|PubMed:16015647}.		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						TGACTTACGCGTTTTGATTGT	0.333													G|||	2764	0.551917	0.5136	0.4611	5008	,	,		18315	0.7292		0.5089	False		,,,				2504	0.5297				p.R262C		Atlas-SNP	.											RASEF,NS,carcinoma,+2,1	RASEF	69	1	0			c.C784T						PASS	.	G	CYS/ARG	2190,2210	576.3+/-384.2	537,1116,547	118.0	98.0	105.0		784	3.0	1.0	9	dbSNP_110	105	4423,4173	571.9+/-389.6	1118,2187,993	yes	missense	RASEF	NM_152573.2	180	1655,3303,1540	AA,AG,GG		48.5458,49.7727,49.1151	benign	262/741	85627408	6613,6383	2200	4298	6498	SO:0001583	missense	158158	exon5			TTACGCGTTTTGA	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.784C>T	9.37:g.85627408G>A	ENSP00000365630:p.Arg262Cys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_152573	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	1212	0.554945054945055	248	0.5040650406504065	178	0.49171270718232046	411	0.7185314685314685	375	0.4947229551451187	G	12.29	1.892430	0.33442	0.497727	0.514542	ENSG00000165105	ENST00000376447	T	0.61859	0.07	5.16	2.98	0.34508	.	0.356470	0.30781	N	0.008885	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999999363687	B	0.31599	0.33	B	0.11329	0.006	T	0.31861	-0.9928	9	0.38643	T	0.18	.	11.2467	0.49002	0.0:0.0:0.4574:0.5426	rs4146960;rs11567608;rs17085954;rs52833047;rs57486058;rs4146960	262	Q8IZ41	RASEF_HUMAN	C	262	ENSP00000365630:R262C	ENSP00000365630:R262C	R	-	1	0	RASEF	84817228	0.994000	0.37717	0.963000	0.40424	0.893000	0.52053	1.731000	0.38135	1.268000	0.44264	0.603000	0.83216	CGC	G|0.470;A|0.530	0.530	strong		0.333	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573	
CC2D2A	57545	hgsc.bcm.edu	37	4	15516389	15516389	+	Silent	SNP	C	C	T	rs2286976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:15516389C>T	ENST00000503292.1	+	10	957	c.777C>T	c.(775-777)caC>caT	p.H259H	CC2D2A_ENST00000389652.5_Silent_p.H210H|CC2D2A_ENST00000424120.1_Silent_p.H259H|CC2D2A_ENST00000513811.1_3'UTR|CC2D2A_ENST00000413206.1_Silent_p.H259H	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	259					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						GCTTAGATCACGTGGCTGACG	0.428													C|||	481	0.0960463	0.0431	0.0303	5008	,	,		18626	0.3492		0.0268	False		,,,				2504	0.0245				p.H259H		Atlas-SNP	.											.	CC2D2A	158	.	0			c.C777T						PASS	.	C		200,3754		3,194,1780	142.0	142.0	142.0		777	-8.1	0.0	4	dbSNP_100	142	228,8098		1,226,3936	no	coding-synonymous	CC2D2A	NM_001080522.2		4,420,5716	TT,TC,CC		2.7384,5.0582,3.4853		259/1621	15516389	428,11852	1977	4163	6140	SO:0001819	synonymous_variant	57545	exon10			AGATCACGTGGCT	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"""Meckel syndrome, type 6"""	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.777C>T	4.37:g.15516389C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Silent	SNP	ENST00000503292.1	37	CCDS47026.1																																																																																			C|0.900;T|0.100	0.100	strong		0.428	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
DNAH14	127602	hgsc.bcm.edu	37	1	225155191	225155191	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:225155191C>G	ENST00000445597.2	+	7	938	c.938C>G	c.(937-939)tCc>tGc	p.S313C	DNAH14_ENST00000366850.3_Missense_Mutation_p.S186C|DNAH14_ENST00000439375.2_Missense_Mutation_p.S186C|DNAH14_ENST00000366848.1_Missense_Mutation_p.S186C|DNAH14_ENST00000430092.1_Missense_Mutation_p.S186C|DNAH14_ENST00000400952.3_Missense_Mutation_p.S186C|DNAH14_ENST00000366849.1_Missense_Mutation_p.S186C			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	313					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						AGTCCTAAATCCCTTTACAAT	0.308																																					p.S186C		Atlas-SNP	.											.	DNAH14	300	.	0			c.C557G						PASS	.						152.0	144.0	147.0					1																	225155191		1824	4085	5909	SO:0001583	missense	127602	exon6			CTAAATCCCTTTA	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.938C>G	1.37:g.225155191C>G	ENSP00000409472:p.Ser313Cys	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_144989	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.155|9.155	1.017345|1.017345	0.19355|0.19355	.|.	.|.	ENSG00000185842|ENSG00000185842	ENST00000433124|ENST00000445597;ENST00000430092;ENST00000366850;ENST00000400952;ENST00000366849;ENST00000366848;ENST00000439375	.|T;T;T;T;T;T;T	.|0.34275	.|2.46;1.44;1.37;1.4;1.44;1.37;1.44	5.63|5.63	-2.47|-2.47	0.06442|0.06442	.|.	.|2.216230	.|0.02014	.|N	.|0.047252	T|T	0.29321|0.29321	0.0730|0.0730	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.28584	.|0.071;0.216;0.071;0.042	.|B;B;B;B	.|0.30572	.|0.117;0.117;0.117;0.054	T|T	0.35895|0.35895	-0.9770|-0.9770	4|9	.|0.48119	.|T	.|0.1	.|.	9.1048|9.1048	0.36692|0.36692	0.0:0.4285:0.4519:0.1195|0.0:0.4285:0.4519:0.1195	.|.	.|186;186;186;313	.|Q0VDD8-4;Q0VDD8-3;Q0VDD8-2;Q0VDD8	.|.;.;.;DYH14_HUMAN	A|C	84|313;186;186;186;186;186;186	.|ENSP00000409472:S313C;ENSP00000414402:S186C;ENSP00000355815:S186C;ENSP00000383737:S186C;ENSP00000355814:S186C;ENSP00000355813:S186C;ENSP00000392061:S186C	.|ENSP00000355813:S186C	P|S	+|+	1|2	0|0	DNAH14|DNAH14	223221814|223221814	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.573000|0.573000	0.36030|0.36030	0.045000|0.045000	0.14013|0.14013	-0.324000|-0.324000	0.08589|0.08589	0.543000|0.543000	0.68304|0.68304	CCC|TCC	.	.	none		0.308	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
DMRT3	58524	hgsc.bcm.edu	37	9	990840	990840	+	Silent	SNP	C	C	T	rs7021244	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:990840C>T	ENST00000190165.2	+	2	1292	c.1254C>T	c.(1252-1254)gtC>gtT	p.V418V		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	418					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		CTACCAGCGTCTTCAGAAGCT	0.547													C|||	929	0.185503	0.0113	0.1758	5008	,	,		19419	0.2312		0.2167	False		,,,				2504	0.3487				p.V418V		Atlas-SNP	.											DMRT3,NS,carcinoma,+2,2	DMRT3	83	2	0			c.C1254T						PASS	.	C		218,4188	130.6+/-167.2	5,208,1990	85.0	66.0	73.0		1254	5.2	1.0	9	dbSNP_116	73	1914,6686	339.0+/-323.0	227,1460,2613	no	coding-synonymous	DMRT3	NM_021240.2		232,1668,4603	TT,TC,CC		22.2558,4.9478,16.3924		418/473	990840	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	58524	exon2			CAGCGTCTTCAGA	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1254C>T	9.37:g.990840C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Silent	SNP	ENST00000190165.2	37	CCDS6443.1																																																																																			C|0.827;N|0.000	.	strong		0.547	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
SLC25A10	1468	hgsc.bcm.edu	37	17	79682051	79682051	+	Silent	SNP	C	C	T	rs3204270	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79682051C>T	ENST00000350690.5	+	2	248	c.162C>T	c.(160-162)acC>acT	p.T54T	SLC25A10_ENST00000571730.1_Silent_p.T209T|SLC25A10_ENST00000541223.1_Silent_p.T209T|SLC25A10_ENST00000545862.1_Silent_p.T11T|SLC25A10_ENST00000331531.5_Silent_p.T54T	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	54					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)			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)	TGGTGCGTACCGACGGCATCC	0.667													C|||	204	0.0407348	0.0068	0.0548	5008	,	,		19512	0.001		0.1272	False		,,,				2504	0.0286				p.T54T		Atlas-SNP	.											SLC25A10,NS,carcinoma,0,2	SLC25A10	24	2	0			c.C162T						PASS	.	C		100,4296	79.9+/-118.3	2,96,2100	57.0	42.0	47.0		162	-7.7	0.1	17	dbSNP_105	47	887,7711	195.6+/-240.8	44,799,3456	no	coding-synonymous	SLC25A10	NM_012140.3		46,895,5556	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	10.3164,2.2748,7.5958		54/288	79682051	987,12007	2198	4299	6497	SO:0001819	synonymous_variant	1468	exon2			GCGTACCGACGGC		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.162C>T	17.37:g.79682051C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Silent	SNP	ENST00000350690.5	37	CCDS11786.1																																																																																			C|0.937;G|0.000;T|0.062	0.062	strong		0.667	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1		
FAM3D	131177	hgsc.bcm.edu	37	3	58625875	58625875	+	Missense_Mutation	SNP	C	C	A	rs33966924	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:58625875C>A	ENST00000358781.2	-	7	662	c.352G>T	c.(352-354)Gca>Tca	p.A118S		NM_138805.2	NP_620160.1	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	118			A -> S (in dbSNP:rs33966924).		negative regulation of insulin secretion (GO:0046676)	extracellular region (GO:0005576)	cytokine activity (GO:0005125)			large_intestine(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)		ATGTCAAATGCCTTCTGTCCC	0.552													C|||	398	0.0794728	0.0552	0.1297	5008	,	,		21088	0.001		0.1769	False		,,,				2504	0.0573				p.A118S		Atlas-SNP	.											.	FAM3D	29	.	0			c.G352T						PASS	.	C	SER/ALA	361,4045	185.7+/-212.7	13,335,1855	257.0	213.0	228.0		352	-4.4	0.0	3	dbSNP_126	228	1567,7033	293.0+/-301.1	156,1255,2889	yes	missense	FAM3D	NM_138805.2	99	169,1590,4744	AA,AC,CC		18.2209,8.1934,14.8239	benign	118/225	58625875	1928,11078	2203	4300	6503	SO:0001583	missense	131177	exon7			CAAATGCCTTCTG	AF494381	CCDS2893.1	3p21.1	2008-07-18			ENSG00000198643	ENSG00000198643			18665	protein-coding gene	gene with protein product		608619				12160727	Standard	NM_138805		Approved	EF7, OIT1	uc003dkq.3	Q96BQ1	OTTHUMG00000159148	ENST00000358781.2:c.352G>T	3.37:g.58625875C>A	ENSP00000351632:p.Ala118Ser	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_138805	Q547G2	Missense_Mutation	SNP	ENST00000358781.2	37	CCDS2893.1	215	0.09844322344322344	29	0.05894308943089431	55	0.15193370165745856	1	0.0017482517482517483	130	0.17150395778364116	C	8.959	0.969981	0.18659	0.081934	0.182209	ENSG00000198643	ENST00000358781;ENST00000483787;ENST00000489857	T;T;T	0.51325	0.71;1.99;1.55	5.49	-4.43	0.03568	.	1.461070	0.03576	N	0.229351	T	0.00039	0.0001	N	0.01576	-0.805	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.07751	-1.0756	9	0.20046	T	0.44	-0.4704	6.4739	0.22024	0.2845:0.2233:0.0:0.4922	rs33966924	118	Q96BQ1	FAM3D_HUMAN	S	118;117;81	ENSP00000351632:A118S;ENSP00000417099:A117S;ENSP00000417453:A81S	ENSP00000351632:A118S	A	-	1	0	FAM3D	58600915	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.939000	0.03933	-0.496000	0.06650	-0.302000	0.09304	GCA	C|0.868;A|0.132	0.132	strong		0.552	FAM3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353494.1	NM_138805	
LRIG1	26018	hgsc.bcm.edu	37	3	66432717	66432717	+	Missense_Mutation	SNP	T	T	C	rs148946048	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:66432717T>C	ENST00000273261.3	-	16	3121	c.2597A>G	c.(2596-2598)aAt>aGt	p.N866S	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.N843S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	866					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)		AATGTGCCCATTGGCCTGAGG	0.567													T|||	36	0.0071885	0.0265	0.0014	5008	,	,		20726	0.0		0.0	False		,,,				2504	0.0				p.N866S		Atlas-SNP	.											.	LRIG1	138	.	0			c.A2597G						PASS	.	T	SER/ASN	72,4334	67.0+/-104.6	1,70,2132	143.0	144.0	143.0		2597	1.6	0.9	3	dbSNP_134	143	3,8597	3.0+/-9.4	0,3,4297	yes	missense	LRIG1	NM_015541.2	46	1,73,6429	CC,CT,TT		0.0349,1.6341,0.5767	benign	866/1094	66432717	75,12931	2203	4300	6503	SO:0001583	missense	26018	exon16			TGCCCATTGGCCT	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.2597A>G	3.37:g.66432717T>C	ENSP00000273261:p.Asn866Ser	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	55	0.55	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	T	12.51	1.960779	0.34565	0.016341	3.49E-4	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.67171	-0.14;-0.25	5.5	1.56	0.23342	.	0.106092	0.64402	N	0.000008	T	0.36331	0.0963	L	0.45581	1.43	0.33964	D	0.645981	B;B;B	0.15141	0.009;0.001;0.012	B;B;B	0.17979	0.02;0.005;0.005	T	0.46190	-0.9209	10	0.34782	T	0.22	.	5.3801	0.16186	0.0:0.2128:0.1362:0.651	.	843;866;866	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	866;843;769	ENSP00000273261:N866S;ENSP00000373208:N843S	ENSP00000273261:N866S	N	-	2	0	LRIG1	66515407	0.940000	0.31905	0.906000	0.35671	0.814000	0.46013	0.909000	0.28558	0.373000	0.24621	-0.264000	0.10439	AAT	T|0.995;C|0.005	0.005	strong		0.567	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
AVL9	23080	hgsc.bcm.edu	37	7	32598656	32598656	+	Silent	SNP	C	C	T	rs2290214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:32598656C>T	ENST00000318709.4	+	10	1016	c.795C>T	c.(793-795)tcC>tcT	p.S265S	AVL9_ENST00000409301.1_Silent_p.S265S|AVL9_ENST00000404479.1_Silent_p.S265S	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	265					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TTTCTGCATCCACTGCTGATG	0.463													C|||	1206	0.240815	0.3306	0.1744	5008	,	,		18209	0.1319		0.165	False		,,,				2504	0.3569				p.S265S		Atlas-SNP	.											.	AVL9	66	.	0			c.C795T						PASS	.	C		1448,2958	467.9+/-355.0	235,978,990	89.0	85.0	86.0		795	0.1	0.0	7	dbSNP_100	86	1407,7193	270.4+/-288.9	114,1179,3007	no	coding-synonymous	AVL9	NM_015060.1		349,2157,3997	TT,TC,CC		16.3605,32.8643,21.9514		265/649	32598656	2855,10151	2203	4300	6503	SO:0001819	synonymous_variant	23080	exon10			TGCATCCACTGCT	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.795C>T	7.37:g.32598656C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	37	CCDS34613.1																																																																																			C|0.781;T|0.219	0.219	strong		0.463	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
MXRA5	25878	hgsc.bcm.edu	37	X	3238167	3238167	+	Silent	SNP	T	T	G	rs1635245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3238167T>G	ENST00000217939.6	-	5	5713	c.5559A>C	c.(5557-5559)ccA>ccC	p.P1853P		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1853	Ig-like C2-type 3.					extracellular vesicular exosome (GO:0070062)		p.P1853P(1)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TGAGGATTTGTGGCTTTTCCC	0.517													G|||	1777	0.470728	0.3169	0.4006	3775	,	,		11504	0.2728		0.4583	False		,,,				2504	0.3517				p.P1853P		Atlas-SNP	.											.	MXRA5	815	.	1	Substitution - coding silent(1)	stomach(1)	c.A5559C						PASS	.	G		1614,2221		275,813,251,544,320	98.0	85.0	89.0		5559	0.4	0.1	X	dbSNP_89	89	3839,2889		793,1187,1066,448,806	no	coding-synonymous	MXRA5	NM_015419.3		1068,2000,1317,992,1126	GG,GT,G,TT,T		42.94,42.086,48.3764		1853/2829	3238167	5453,5110	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			GATTTGTGGCTTT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5559A>C	X.37:g.3238167T>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	101	100	0.990099	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			T|0.500;G|0.500	0.500	strong		0.517	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
DNAH5	1767	hgsc.bcm.edu	37	5	13754394	13754394	+	Silent	SNP	C	C	T	rs2401809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13754394C>T	ENST00000265104.4	-	62	10577	c.10473G>A	c.(10471-10473)acG>acA	p.T3491T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3491					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CACTGATGAGCGTGGAAGCTG	0.398									Kartagener syndrome				C|||	1644	0.328275	0.3298	0.2911	5008	,	,		18118	0.122		0.3847	False		,,,				2504	0.5072				p.T3491T		Atlas-SNP	.											.	DNAH5	868	.	0			c.G10473A						PASS	.	C		1493,2913	475.5+/-357.3	240,1013,950	127.0	121.0	123.0		10473	-7.5	0.1	5	dbSNP_100	123	3128,5472	475.8+/-369.2	559,2010,1731	no	coding-synonymous	DNAH5	NM_001369.2		799,3023,2681	TT,TC,CC		36.3721,33.8856,35.5298		3491/4625	13754394	4621,8385	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon62	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GATGAGCGTGGAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.10473G>A	5.37:g.13754394C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	235	127	0.540426	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			C|0.669;T|0.331	0.331	strong		0.398	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
NFX1	4799	hgsc.bcm.edu	37	9	33369943	33369943	+	Silent	SNP	G	G	A	rs2230122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:33369943G>A	ENST00000379540.3	+	24	3392	c.3330G>A	c.(3328-3330)gaG>gaA	p.E1110E		NM_002504.4	NP_002495.2	Q12986	NFX1_HUMAN	nuclear transcription factor, X-box binding 1	1110					inflammatory response (GO:0006954)|negative regulation of MHC class II biosynthetic process (GO:0045347)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25			LUSC - Lung squamous cell carcinoma(29;0.00506)	GBM - Glioblastoma multiforme(74;0.224)		TAACCAAGGAGCCAATAATTG	0.363													G|||	174	0.0347444	0.0038	0.0634	5008	,	,		18926	0.0		0.0964	False		,,,				2504	0.0286				p.E1110E		Atlas-SNP	.											.	NFX1	85	.	0			c.G3330A						PASS	.	G		70,4336	64.1+/-101.4	0,70,2133	80.0	76.0	77.0		3330	2.2	1.0	9	dbSNP_98	77	819,7781	189.6+/-236.3	43,733,3524	no	coding-synonymous	NFX1	NM_002504.4		43,803,5657	AA,AG,GG		9.5233,1.5887,6.8353		1110/1121	33369943	889,12117	2203	4300	6503	SO:0001819	synonymous_variant	4799	exon24			CAAGGAGCCAATA	U19759	CCDS6538.1, CCDS6539.1, CCDS6540.1	9p12	2013-12-13			ENSG00000086102	ENSG00000086102			7803	protein-coding gene	gene with protein product		603255				7964459, 2511169	Standard	NM_002504		Approved	NFX2, MGC20369, Tex42, TEG-42	uc003zsq.3	Q12986	OTTHUMG00000019772	ENST00000379540.3:c.3330G>A	9.37:g.33369943G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	100	60	0.6	NM_002504	A8K6H8|Q5VXW6|Q96EL5|Q9BXI1	Silent	SNP	ENST00000379540.3	37	CCDS6538.1																																																																																			G|0.943;A|0.057	0.057	strong		0.363	NFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052069.1		
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049939	69049939	+	Missense_Mutation	SNP	G	G	T	rs4241344	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:69049939G>T	ENST00000295381.3	+	10	2084	c.1665G>T	c.(1663-1665)agG>agT	p.R555S	ARHGAP25_ENST00000409202.3_Missense_Mutation_p.R556S|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.R549S|ARHGAP25_ENST00000409030.3_Missense_Mutation_p.R548S|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.R249S|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.R516S	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	555			R -> S (in dbSNP:rs4241344). {ECO:0000269|PubMed:14702039}.		regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CTTTGCAGAGGATGGTCCAAG	0.448													G|||	1332	0.265974	0.1725	0.3156	5008	,	,		20655	0.4435		0.1869	False		,,,				2504	0.2556				p.R556S		Atlas-SNP	.											.	ARHGAP25	175	.	0			c.G1668T						PASS	.	G	SER/ARG,SER/ARG,SER/ARG,SER/ARG	758,3646	286.0+/-278.5	53,652,1497	70.0	78.0	75.0		1668,1647,1548,1644	3.5	0.7	2	dbSNP_111	75	1644,6956	282.4+/-295.5	170,1304,2826	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	110,110,110,110	223,1956,4323	TT,TG,GG		19.1163,17.2116,18.4712	benign,benign,benign,benign	556/647,549/640,516/607,548/639	69049939	2402,10602	2202	4300	6502	SO:0001583	missense	9938	exon10			GCAGAGGATGGTC	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1665G>T	2.37:g.69049939G>T	ENSP00000295381:p.Arg555Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		554|554	0.25366300366300365|0.25366300366300365	78|78	0.15853658536585366|0.15853658536585366	109|109	0.3011049723756906|0.3011049723756906	224|224	0.3916083916083916|0.3916083916083916	143|143	0.18865435356200527|0.18865435356200527	G|G	2.826|2.826	-0.243736|-0.243736	0.05906|0.05906	0.172116|0.172116	0.191163|0.191163	ENSG00000163219|ENSG00000163219	ENST00000497259|ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844	.|T;T;T;T;T;T	.|0.38560	.|3.05;3.05;2.8;1.13;1.13;1.13	5.42|5.42	3.55|3.55	0.40652|0.40652	.|.	.|0.731496	.|0.14039	.|N	.|0.345562	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.26403|0.26403	P|P	0.976394|0.976394	.|B;B;B;B;B	.|0.06786	.|0.001;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.04013	.|0.001;0.0;0.0;0.0;0.0	T|T	0.43925|0.43925	-0.9361|-0.9361	4|9	.|0.07030	.|T	.|0.85	.|.	1.9238|1.9238	0.03313|0.03313	0.1885:0.154:0.4993:0.1582|0.1885:0.154:0.4993:0.1582	rs4241344;rs52800040;rs60408659;rs4241344|rs4241344;rs52800040;rs60408659;rs4241344	.|516;556;549;548;555	.|E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.|.;.;.;.;RHG25_HUMAN	V|S	415|555;556;516;548;549;549;540;249	.|ENSP00000295381:R555S;ENSP00000386911:R556S;ENSP00000420583:R516S;ENSP00000386863:R548S;ENSP00000386241:R549S;ENSP00000417467:R249S	.|ENSP00000295381:R555S	G|R	+|+	2|3	0|2	ARHGAP25|ARHGAP25	68903443|68903443	0.001000|0.001000	0.12720|0.12720	0.746000|0.746000	0.31095|0.31095	0.615000|0.615000	0.37417|0.37417	0.193000|0.193000	0.17116|0.17116	0.698000|0.698000	0.31739|0.31739	0.557000|0.557000	0.71058|0.71058	GGA|AGG	G|0.789;T|0.211	0.211	strong		0.448	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
KRT83	3889	hgsc.bcm.edu	37	12	52710715	52710715	+	Silent	SNP	G	G	A	rs2857669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52710715G>A	ENST00000293670.3	-	5	905	c.843C>T	c.(841-843)gcC>gcT	p.A281A		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	281	Coil 2.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.A281A(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCTTGATCTCGGCAACGATGC	0.582													g|||	1882	0.375799	0.5008	0.317	5008	,	,		21064	0.1885		0.4095	False		,,,				2504	0.407				p.A281A	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,0,1	KRT83	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C843T						PASS	.	G		2158,2248	582.7+/-385.6	552,1054,597	172.0	142.0	152.0		843	-3.3	0.5	12	dbSNP_100	152	3532,5068	515.1+/-378.5	722,2088,1490	no	coding-synonymous	KRT83	NM_002282.3		1274,3142,2087	AA,AG,GG		41.0698,48.9787,43.749		281/494	52710715	5690,7316	2203	4300	6503	SO:0001819	synonymous_variant	3889	exon5			GATCTCGGCAACG	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.843C>T	12.37:g.52710715G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	174	76	0.436782	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			G|0.593;A|0.407	0.407	strong		0.582	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
PRAMEF4	400735	hgsc.bcm.edu	37	1	12939664	12939664	+	Missense_Mutation	SNP	A	A	T	rs28452936	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12939664A>T	ENST00000235349.5	-	4	1208	c.1138T>A	c.(1138-1140)Ttt>Att	p.F380I		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	380					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.F380I(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(3)|skin(1)	24	Ovarian(185;0.249)	Lung NSC(185;3.67e-05)|all_lung(284;4.03e-05)|Renal(390;0.000147)|Breast(348;0.000278)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTGAGCTCAAAGCAGCGGCTC	0.507													a|||	579	0.115615	0.1362	0.1023	5008	,	,		20417	0.1399		0.1123	False		,,,				2504	0.0757				p.F380I		Atlas-SNP	.											PRAMEF4,NS,carcinoma,0,1	PRAMEF4	62	1	1	Substitution - Missense(1)	prostate(1)	c.T1138A						scavenged	.	T	ILE/PHE	433,2563		63,307,1128	87.0	90.0	89.0		1138	-1.9	0.0	1	dbSNP_131	89	614,4742		68,478,2132	no	missense	PRAMEF4	NM_001009611.2	21	131,785,3260	TT,TA,AA		11.4638,14.4526,12.5359	probably-damaging	380/479	12939664	1047,7305	1498	2678	4176	SO:0001583	missense	400735	exon4			GCTCAAAGCAGCG		CCDS30592.1	1p36.21	2013-01-17			ENSG00000243073	ENSG00000243073		"""-"""	31971	protein-coding gene	gene with protein product							Standard	NM_001009611		Approved	RP5-845O24.6	uc001aun.2	O60810	OTTHUMG00000001987	ENST00000235349.5:c.1138T>A	1.37:g.12939664A>T	ENSP00000235349:p.Phe380Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	108	5	0.0462963	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	269	0.12316849816849818	54	0.10975609756097561	44	0.12154696132596685	70	0.12237762237762238	101	0.13324538258575197	A	8.167	0.790796	0.16258	0.144526	0.114638	ENSG00000243073	ENST00000235349	T	0.09817	2.94	1.48	-1.9	0.07665	.	1.401010	0.04101	N	0.312866	T	0.00073	0.0002	L	0.35723	1.085	0.80722	P	0.0	B	0.11235	0.004	B	0.09377	0.004	T	0.40534	-0.9558	9	0.52906	T	0.07	.	2.3209	0.04211	0.4402:0.2822:0.0:0.2776	.	380	O60810	PRAM4_HUMAN	I	380	ENSP00000235349:F380I	ENSP00000235349:F380I	F	-	1	0	PRAMEF4	12862251	0.000000	0.05858	0.002000	0.10522	0.024000	0.10985	-1.237000	0.02922	-0.479000	0.06813	0.329000	0.21502	TTT	A|0.881;T|0.119	0.119	strong		0.507	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611	
PKD1	5310	hgsc.bcm.edu	37	16	2152129	2152129	+	Silent	SNP	A	A	G	rs144582212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2152129A>G	ENST00000262304.4	-	26	9538	c.9330T>C	c.(9328-9330)ccT>ccC	p.P3110P	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Silent_p.P3110P	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3110					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						GCCCACAGAAAGGGATGGCGC	0.667													g|||	695	0.138778	0.3911	0.0994	5008	,	,		16303	0.0		0.0815	False		,,,				2504	0.0276				p.P3110P		Atlas-SNP	.											PKD1,NS,carcinoma,0,1	PKD1	184	1	0			c.T9330C						scavenged	.																																			SO:0001819	synonymous_variant	5310	exon26			ACAGAAAGGGATG	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.9330T>C	16.37:g.2152129A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	125	18	0.144	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.500;G|0.500	0.500	weak		0.667	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
C2orf57	165100	hgsc.bcm.edu	37	2	232457857	232457857	+	Silent	SNP	T	T	C	rs17199614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:232457857T>C	ENST00000313965.2	+	1	283	c.195T>C	c.(193-195)tcT>tcC	p.S65S		NM_152614.2	NP_689827.2	Q53QW1	CB057_HUMAN	chromosome 2 open reading frame 57	65										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)		TATCAACATCTGGAGACAAAG	0.532													T|||	73	0.0145767	0.0023	0.0346	5008	,	,		21049	0.0		0.0368	False		,,,				2504	0.0092				p.S65S		Atlas-SNP	.											.	C2orf57	35	.	0			c.T195C						PASS	.	T		34,4372	39.2+/-71.8	1,32,2170	117.0	121.0	120.0		195	-2.3	0.0	2	dbSNP_123	120	333,8267	115.3+/-175.2	6,321,3973	no	coding-synonymous	C2orf57	NM_152614.2		7,353,6143	CC,CT,TT		3.8721,0.7717,2.8218		65/396	232457857	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	165100	exon1			AACATCTGGAGAC	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.195T>C	2.37:g.232457857T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	37	0.402174	NM_152614	Q8N4F2	Silent	SNP	ENST00000313965.2	37	CCDS2487.1																																																																																			T|0.976;C|0.024	0.024	strong		0.532	C2orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256962.1	NM_152614	
NUP210	23225	hgsc.bcm.edu	37	3	13395475	13395475	+	Missense_Mutation	SNP	G	G	C	rs2280085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:13395475G>C	ENST00000254508.5	-	17	2543	c.2461C>G	c.(2461-2463)Cct>Gct	p.P821A		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	821			P -> A (in dbSNP:rs2280085).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(10)|liver(1)|lung(16)|ovary(7)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	66	all_neural(104;0.187)					GGCAGCTCAGGCTCGATGCTG	0.622													G|||	1044	0.208466	0.2126	0.1729	5008	,	,		19709	0.2897		0.165	False		,,,				2504	0.1892				p.P821A		Atlas-SNP	.											.	NUP210	182	.	0			c.C2461G						PASS	.	G	ALA/PRO	929,3477	333.6+/-303.0	108,713,1382	31.0	26.0	27.0		2461	2.3	0.0	3	dbSNP_100	27	1423,7175	252.6+/-278.6	121,1181,2997	yes	missense	NUP210	NM_024923.2	27	229,1894,4379	CC,CG,GG		16.5504,21.0849,18.0867	benign	821/1888	13395475	2352,10652	2203	4299	6502	SO:0001583	missense	23225	exon17			GCTCAGGCTCGAT	AB020713	CCDS33704.1	3p25	2008-02-05			ENSG00000132182	ENSG00000132182			30052	protein-coding gene	gene with protein product		607703				2184032, 7504063	Standard	NM_024923		Approved	GP210, POM210, FLJ22389, KIAA0906	uc003bxv.1	Q8TEM1	OTTHUMG00000157268	ENST00000254508.5:c.2461C>G	3.37:g.13395475G>C	ENSP00000254508:p.Pro821Ala	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	193	99	0.512953	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	454	0.2078754578754579	84	0.17073170731707318	59	0.16298342541436464	185	0.32342657342657344	126	0.1662269129287599	G	0.017	-1.499222	0.01001	0.210849	0.165504	ENSG00000132182	ENST00000254508	T	0.49432	0.78	5.23	2.31	0.28768	.	0.560572	0.18343	N	0.144138	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	B;B	0.23249	0.082;0.049	B;B	0.25140	0.058;0.039	T	0.33650	-0.9860	9	0.09338	T	0.73	0.0042	4.1682	0.10317	0.1349:0.3424:0.4056:0.1171	rs2280085;rs2280085	821;821	Q8TEM1-2;Q8TEM1	.;PO210_HUMAN	A	821	ENSP00000254508:P821A	ENSP00000254508:P821A	P	-	1	0	NUP210	13370475	0.400000	0.25295	0.002000	0.10522	0.072000	0.16883	2.121000	0.41977	0.247000	0.21414	0.563000	0.77884	CCT	G|0.807;C|0.193	0.193	strong		0.622	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923	
OR7D2	162998	hgsc.bcm.edu	37	19	9296664	9296664	+	Silent	SNP	T	T	C	rs56246934	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9296664T>C	ENST00000344248.2	+	1	386	c.207T>C	c.(205-207)gtT>gtC	p.V69V		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	69					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						TGTCCTGGGTTGACATCTGTT	0.537													T|||	1136	0.226837	0.0787	0.2003	5008	,	,		19645	0.2768		0.3012	False		,,,				2504	0.318				p.V69V		Atlas-SNP	.											.	OR7D2	55	.	0			c.T207C						PASS	.	T		491,3915	228.5+/-243.3	18,455,1730	126.0	117.0	120.0		207	-4.4	0.0	19	dbSNP_129	120	2569,6031	417.1+/-352.3	359,1851,2090	no	coding-synonymous	OR7D2	NM_175883.2		377,2306,3820	CC,CT,TT		29.8721,11.1439,23.5276		69/313	9296664	3060,9946	2203	4300	6503	SO:0001819	synonymous_variant	162998	exon1			CTGGGTTGACATC	AK095468	CCDS32900.1	19p13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.207T>C	19.37:g.9296664T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_175883	Q6IFJ7|Q8N133	Silent	SNP	ENST00000344248.2	37	CCDS32900.1																																																																																			T|0.761;C|0.239	0.239	strong		0.537	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1		
CYP39A1	51302	hgsc.bcm.edu	37	6	46620240	46620240	+	Missense_Mutation	SNP	C	C	T	rs61661828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46620240C>T	ENST00000275016.2	-	1	283	c.80G>A	c.(79-81)cGt>cAt	p.R27H	SLC25A27_ENST00000371347.5_5'Flank|SLC25A27_ENST00000452689.2_5'Flank|SLC25A27_ENST00000411689.2_5'Flank	NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	27					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						CGGGGGTCTACGCAAATTCTT	0.448													C|||	11	0.00219649	0.0	0.0014	5008	,	,		18732	0.0		0.0099	False		,,,				2504	0.0				p.R27H		Atlas-SNP	.											.	CYP39A1	41	.	0			c.G80A						PASS	.	C	HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	225.0	239.0	234.0		80	-0.9	0.0	6	dbSNP_129	234	66,8534	39.8+/-96.3	0,66,4234	yes	missense	CYP39A1	NM_016593.3	29	0,72,6431	TT,TC,CC		0.7674,0.1362,0.5536	possibly-damaging	27/470	46620240	72,12934	2203	4300	6503	SO:0001583	missense	51302	exon1			GGTCTACGCAAAT	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.80G>A	6.37:g.46620240C>T	ENSP00000275016:p.Arg27His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	15.30	2.791895	0.50102	0.001362	0.007674	ENSG00000146233	ENST00000275016	D	0.86562	-2.14	5.29	-0.864	0.10666	.	0.829219	0.10808	N	0.631887	T	0.53190	0.1781	N	0.19112	0.55	0.09310	N	1	B;B	0.22604	0.072;0.072	B;B	0.11329	0.006;0.006	T	0.42361	-0.9456	10	0.44086	T	0.13	-0.4009	1.1221	0.01727	0.2188:0.3202:0.1073:0.3537	.	27;27	B7Z786;Q9NYL5	.;CP39A_HUMAN	H	27	ENSP00000275016:R27H	ENSP00000275016:R27H	R	-	2	0	CYP39A1	46728199	0.000000	0.05858	0.000000	0.03702	0.610000	0.37248	-0.000000	0.12993	-0.148000	0.11234	-0.768000	0.03414	CGT	C|0.995;T|0.005	0.005	strong		0.448	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
ZMIZ1	57178	hgsc.bcm.edu	37	10	81064950	81064950	+	Silent	SNP	G	G	C	rs34305410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:81064950G>C	ENST00000334512.5	+	20	2888	c.2316G>C	c.(2314-2316)ctG>ctC	p.L772L	ZMIZ1_ENST00000446377.2_5'Flank	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	772					artery morphogenesis (GO:0048844)|cell aging (GO:0007569)|developmental growth (GO:0048589)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)|vitellogenesis (GO:0007296)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(1)	30	all_cancers(46;0.0292)|Breast(12;8.52e-05)|all_epithelial(25;0.000854)|Prostate(51;0.00985)		Epithelial(14;0.00256)|all cancers(16;0.00726)|Colorectal(32;0.229)			ACCTGCAGCTGAATTGCGAGA	0.597													G|||	248	0.0495208	0.1309	0.0173	5008	,	,		18593	0.0089		0.0308	False		,,,				2504	0.0235				p.L772L		Atlas-SNP	.											.	ZMIZ1	101	.	0			c.G2316C						PASS	.	G		357,4049	184.0+/-211.4	18,321,1864	125.0	104.0	111.0		2316	5.3	1.0	10	dbSNP_126	111	213,8387	90.6+/-152.8	3,207,4090	no	coding-synonymous	ZMIZ1	NM_020338.3		21,528,5954	CC,CG,GG		2.4767,8.1026,4.3826		772/1068	81064950	570,12436	2203	4300	6503	SO:0001819	synonymous_variant	57178	exon20			GCAGCTGAATTGC	AB033050	CCDS7357.1	10q22.3	2012-11-30	2006-10-24	2006-10-24	ENSG00000108175	ENSG00000108175		"""Zinc fingers, MIZ-type"""	16493	protein-coding gene	gene with protein product		607159	"""retinoic acid induced 17"""	RAI17		15626329	Standard	NM_020338		Approved	RP11-519K18.1, KIAA1224, FLJ13541, hZIMP10, Zimp10, MIZ	uc001kaf.2	Q9ULJ6	OTTHUMG00000018560	ENST00000334512.5:c.2316G>C	10.37:g.81064950G>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_020338	Q5JSH9|Q7Z7E6	Silent	SNP	ENST00000334512.5	37	CCDS7357.1																																																																																			G|0.957;C|0.043	0.043	strong		0.597	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338	
MAGEH1	28986	hgsc.bcm.edu	37	X	55479299	55479299	+	Silent	SNP	G	G	A	rs11545211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:55479299G>A	ENST00000342972.1	+	1	762	c.492G>A	c.(490-492)ggG>ggA	p.G164G	hsa-mir-4536-2_ENST00000583537.1_RNA	NM_014061.3	NP_054780.2	Q9H213	MAGH1_HUMAN	melanoma antigen family H, 1	164	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				apoptotic process (GO:0006915)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|skin(2)	15						TCTTCTGGGGGCCCCGAGCAC	0.507													g|||	1003	0.265695	0.0303	0.3256	3775	,	,		13589	0.2837		0.2237	False		,,,				2504	0.2311				p.G164G		Atlas-SNP	.											.	MAGEH1	37	.	0			c.G492A						PASS	.			291,3544		14,220,43,1398,528	94.0	91.0	92.0		492	-3.2	0.1	X	dbSNP_120	92	1902,4826		182,1001,537,1245,1335	no	coding-synonymous	MAGEH1	NM_014061.3		196,1221,580,2643,1863	AA,AG,A,GG,G		28.2699,7.588,20.7611		164/220	55479299	2193,8370	2203	4300	6503	SO:0001819	synonymous_variant	28986	exon1			CTGGGGGCCCCGA	AF320912	CCDS14369.1	Xp11.22	2008-02-05			ENSG00000187601	ENSG00000187601			24092	protein-coding gene	gene with protein product		300548				12414813, 9485030	Standard	NM_014061		Approved	APR1	uc004dum.3	Q9H213	OTTHUMG00000021655	ENST00000342972.1:c.492G>A	X.37:g.55479299G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_014061	B2R8V9|Q5JRJ3|Q9Y5M2	Silent	SNP	ENST00000342972.1	37	CCDS14369.1																																																																																			0|0.003;A|0.216	0.216	strong		0.507	MAGEH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056868.1	NM_014061	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970812	45970812	+	Missense_Mutation	SNP	G	G	A	rs2329834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45970812G>A	ENST00000391621.1	-	1	576	c.530C>T	c.(529-531)cCg>cTg	p.P177L	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	177	22 X 5 AA repeats of C-C-X(3).		P -> L (in dbSNP:rs2329834).			keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CTGCTGACACGGGGAGGAGGT	0.607													G|||	2742	0.547524	0.5015	0.5735	5008	,	,		20805	0.371		0.6163	False		,,,				2504	0.7025				p.P177L		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C530T						PASS	.	G	,LEU/PRO	2134,2272	574.5+/-383.8	503,1128,572	114.0	117.0	116.0		,530	-1.6	0.0	21	dbSNP_100	116	5441,3159	650.5+/-400.7	1729,1983,588	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,98	2232,3111,1160	AA,AG,GG		36.7326,48.434,41.7577	,benign	,177/256	45970812	7575,5431	2203	4300	6503	SO:0001583	missense	386679	exon1			TGACACGGGGAGG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.530C>T	21.37:g.45970812G>A	ENSP00000375479:p.Pro177Leu	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	121	69	0.570248	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	1087	0.4977106227106227	225	0.4573170731707317	226	0.6243093922651933	185	0.32342657342657344	451	0.5949868073878628	g	1.411	-0.575612	0.03882	0.48434	0.632674	ENSG00000205445	ENST00000391621	T	0.01295	5.04	2.98	-1.58	0.08479	.	.	.	.	.	T	0.00012	0.0000	M	0.91818	3.245	0.80722	P	0.0	B	0.16802	0.019	B	0.13407	0.009	T	0.18085	-1.0348	8	0.40728	T	0.16	.	3.9041	0.09174	0.0988:0.2783:0.4817:0.1412	rs2329834;rs2329834	177	P60368	KR102_HUMAN	L	177	ENSP00000375479:P177L	ENSP00000375479:P177L	P	-	2	0	KRTAP10-2	44795240	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.958000	0.03857	-0.221000	0.09973	-4.721000	0.00003	CCG	G|0.491;A|0.509	0.509	strong		0.607	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
COL6A5	256076	hgsc.bcm.edu	37	3	130134492	130134492	+	Missense_Mutation	SNP	T	T	C	rs16827497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130134492T>C	ENST00000432398.2	+	23	5259	c.4765T>C	c.(4765-4767)Tca>Cca	p.S1589P	COL6A5_ENST00000265379.6_Missense_Mutation_p.S1589P	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1589	Triple-helical region.		S -> P (in dbSNP:rs16827497).		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						ACTAAAGGGGTCACAGGGAAA	0.443													T|||	2260	0.451278	0.3321	0.4914	5008	,	,		16996	0.1875		0.7674	False		,,,				2504	0.5307				p.S1589P		Atlas-SNP	.											.	COL6A5	205	.	0			c.T4765C						PASS	.	T	PRO/SER	584,800		125,334,233	67.0	63.0	64.0		4765	-5.3	0.0	3	dbSNP_123	64	2417,765		931,555,105	yes	missense	COL6A5	NM_153264.5	74	1056,889,338	CC,CT,TT		24.0415,42.1965,34.2751	benign	1589/2527	130134492	3001,1565	692	1591	2283	SO:0001583	missense	256076	exon23			AAGGGGTCACAGG	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.4765T>C	3.37:g.130134492T>C	ENSP00000390895:p.Ser1589Pro	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	271	271	1	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		1078	0.4935897435897436	183	0.3719512195121951	197	0.5441988950276243	97	0.16958041958041958	601	0.7928759894459103	T	7.235	0.600083	0.13939	0.421965	0.759585	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.94280	-3.39;-3.39	3.81	-5.28	0.02755	.	.	.	.	.	T	0.00012	0.0000	N	0.00504	-1.425	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.37549	-0.9701	8	0.25106	T	0.35	.	5.9244	0.19101	0.0:0.3035:0.4473:0.2492	rs16827497;rs16827497	1589	A8TX70-2	.	P	1589	ENSP00000390895:S1589P;ENSP00000265379:S1589P	ENSP00000265379:S1589P	S	+	1	0	COL6A5	131617182	0.000000	0.05858	0.000000	0.03702	0.141000	0.21300	-2.755000	0.00789	-1.043000	0.03258	0.454000	0.30748	TCA	T|0.539;C|0.461	0.461	strong		0.443	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
PRODH2	58510	hgsc.bcm.edu	37	19	36303664	36303664	+	Missense_Mutation	SNP	G	G	C	rs3848666	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36303664G>C	ENST00000301175.3	-	2	289	c.272C>G	c.(271-273)cCc>cGc	p.P91R		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	91			P -> R (in dbSNP:rs3848666).		proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCCCCTGGAGGGGGGACCAGC	0.637													g|||	272	0.0543131	0.0061	0.0965	5008	,	,		18695	0.0		0.1561	False		,,,				2504	0.0409				p.P91R		Atlas-SNP	.											.	PRODH2	68	.	0			c.C272G						PASS	.	A	ARG/PRO	147,4259	99.4+/-138.0	3,141,2059	42.0	42.0	42.0		272	0.6	0.0	19	dbSNP_108	42	1425,7175	267.9+/-287.5	126,1173,3001	yes	missense	PRODH2	NM_021232.1	103	129,1314,5060	CC,CG,GG		16.5698,3.3364,12.0867	benign	91/537	36303664	1572,11434	2203	4300	6503	SO:0001583	missense	58510	exon2			CTGGAGGGGGGAC	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.272C>G	19.37:g.36303664G>C	ENSP00000301175:p.Pro91Arg	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	127	67	0.527559	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	166	0.076007326007326	5	0.01016260162601626	45	0.12430939226519337	0	0.0	116	0.15303430079155672	g	6.252	0.414685	0.11870	0.033364	0.165698	ENSG00000250799	ENST00000301175	T	0.23754	1.89	5.19	0.647	0.17796	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.58432	P	1.999999999946489E-6	B	0.11235	0.004	B	0.06405	0.002	T	0.31110	-0.9955	8	0.35671	T	0.21	.	6.956	0.24572	0.2961:0.1194:0.5845:0.0	rs3848666;rs52793092;rs3848666	91	Q9UF12	PROD2_HUMAN	R	91	ENSP00000301175:P91R	ENSP00000301175:P91R	P	-	2	0	PRODH2	40995504	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.765000	0.26546	0.103000	0.17682	-2.308000	0.00257	CCC	G|0.901;C|0.099	0.099	strong		0.637	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
CCDC74B	91409	hgsc.bcm.edu	37	2	130897234	130897234	+	Missense_Mutation	SNP	C	C	T	rs3177472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130897234C>T	ENST00000310463.6	-	8	1174	c.1037G>A	c.(1036-1038)cGt>cAt	p.R346H	MED15P9_ENST00000427638.1_RNA|CCDC74B_ENST00000409943.3_Missense_Mutation_p.R280H|CCDC74B_ENST00000392984.3_Missense_Mutation_p.R448H	NM_207310.2	NP_997193.1	Q96LY2	CC74B_HUMAN	coiled-coil domain containing 74B	346			R -> H (in dbSNP:rs3177472).							endometrium(2)|large_intestine(1)|lung(3)	6	Colorectal(110;0.1)					CAGGATGGCACGCTCCGCCAC	0.647													.|||	1873	0.374002	0.2655	0.4294	5008	,	,		16507	0.4435		0.3489	False		,,,				2504	0.4356				p.R346H		Atlas-SNP	.											.	CCDC74B	27	.	0			c.G1037A						PASS	.	C	HIS/ARG	1297,3105		182,933,1086	38.0	35.0	36.0		1037	3.8	0.0	2	dbSNP_105	36	3129,5469		573,1983,1743	no	missense	CCDC74B	NM_207310.1	29	755,2916,2829	TT,TC,CC		36.3922,29.4639,34.0462	benign	346/381	130897234	4426,8574	2201	4299	6500	SO:0001583	missense	91409	exon8			ATGGCACGCTCCG		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.1037G>A	2.37:g.130897234C>T	ENSP00000308873:p.Arg346His	Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	283	148	0.522968	NM_207310	Q6NW18	Missense_Mutation	SNP	ENST00000310463.6	37	CCDS2155.1	831|831	0.3804945054945055|0.3804945054945055	150|150	0.3048780487804878|0.3048780487804878	143|143	0.39502762430939226|0.39502762430939226	271|271	0.4737762237762238|0.4737762237762238	267|267	0.35224274406332456|0.35224274406332456	.|.	6.361|6.361	0.434632|0.434632	0.12045|0.12045	0.294639|0.294639	0.363922|0.363922	ENSG00000152076|ENSG00000152076	ENST00000409943;ENST00000310463;ENST00000392984|ENST00000409488	T;T;T|.	0.33654|.	1.4;1.4;1.4|.	4.68|4.68	3.81|3.81	0.43845|0.43845	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.53005|0.53005	P|P	3.399999999997849E-5|3.399999999997849E-5	P;B;B|.	0.48911|.	0.917;0.098;0.238|.	B;B;B|.	0.35931|.	0.214;0.015;0.027|.	T|T	0.48479|0.48479	-0.9032|-0.9032	8|5	0.20046|0.87932	T|D	0.44|0	.|.	10.9461|10.9461	0.47301|0.47301	0.0:0.9061:0.0:0.0938|0.0:0.9061:0.0:0.0938	rs3177472;rs3748871;rs10928957;rs58536532|rs3177472;rs3748871;rs10928957;rs58536532	448;280;346|.	E7ESC5;Q96LY2-2;Q96LY2|.	.;.;CC74B_HUMAN|.	H|M	280;346;448|240	ENSP00000386294:R280H;ENSP00000308873:R346H;ENSP00000376710:R448H|.	ENSP00000308873:R346H|ENSP00000386250:V240M	R|V	-|-	2|1	0|0	CCDC74B|CCDC74B	130613704|130613704	0.009000|0.009000	0.17119|0.17119	0.013000|0.013000	0.15412|0.15412	0.017000|0.017000	0.09413|0.09413	1.024000|1.024000	0.30077|0.30077	1.105000|1.105000	0.41606|0.41606	0.455000|0.455000	0.32223|0.32223	CGT|GTG	C|0.654;T|0.346	0.346	strong		0.647	CCDC74B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254522.3	NM_207310	
JPH3	57338	hgsc.bcm.edu	37	16	87678302	87678302	+	Missense_Mutation	SNP	C	C	T	rs144403955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:87678302C>T	ENST00000284262.2	+	2	1063	c.821C>T	c.(820-822)gCg>gTg	p.A274V		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	274					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GCCGAGCTGGCGGTCATCGAG	0.667													C|||	4	0.000798722	0.0	0.0014	5008	,	,		12745	0.001		0.001	False		,,,				2504	0.001				p.A274V		Atlas-SNP	.											.	JPH3	95	.	0			c.C821T						PASS	.	C	VAL/ALA	0,4396		0,0,2198	75.0	68.0	70.0		821	4.9	0.9	16	dbSNP_134	70	15,8585	11.9+/-42.8	0,15,4285	yes	missense	JPH3	NM_020655.2	64	0,15,6483	TT,TC,CC		0.1744,0.0,0.1154	benign	274/749	87678302	15,12981	2198	4300	6498	SO:0001583	missense	57338	exon2			AGCTGGCGGTCAT	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.821C>T	16.37:g.87678302C>T	ENSP00000284262:p.Ala274Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	3	0.0013736263736263737	0	0.0	0	0.0	1	0.0017482517482517483	2	0.002638522427440633	C	13.94	2.387189	0.42308	0.0	0.001744	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.46819	0.86	4.91	4.91	0.64330	.	0.252030	0.40144	N	0.001172	T	0.28466	0.0704	N	0.08118	0	0.38661	D	0.952087	B	0.06786	0.001	B	0.09377	0.004	T	0.13926	-1.0491	10	0.13470	T	0.59	.	17.1059	0.86663	0.0:1.0:0.0:0.0	.	274	Q8WXH2	JPH3_HUMAN	V	137;274	ENSP00000284262:A274V	ENSP00000284262:A274V	A	+	2	0	JPH3	86235803	0.998000	0.40836	0.884000	0.34674	0.875000	0.50365	3.934000	0.56553	2.286000	0.76751	0.561000	0.74099	GCG	C|0.998;T|0.002	0.002	strong		0.667	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
FOXK2	3607	hgsc.bcm.edu	37	17	80543901	80543901	+	Silent	SNP	C	C	T	rs61737960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80543901C>T	ENST00000335255.5	+	7	1575	c.1401C>T	c.(1399-1401)gtC>gtT	p.V467V	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	467					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			AGCCACCCGTCGTGCAGACGG	0.627													C|||	58	0.0115815	0.0121	0.0202	5008	,	,		16342	0.0		0.0179	False		,,,				2504	0.0102				p.V467V		Atlas-SNP	.											.	FOXK2	46	.	0			c.C1401T						PASS	.	C		30,4370	37.6+/-69.7	0,30,2170	66.0	53.0	58.0		1401	-10.6	0.0	17	dbSNP_129	58	173,8413	79.2+/-141.9	2,169,4122	no	coding-synonymous	FOXK2	NM_004514.3		2,199,6292	TT,TC,CC		2.0149,0.6818,1.5632		467/661	80543901	203,12783	2200	4293	6493	SO:0001819	synonymous_variant	3607	exon7			ACCCGTCGTGCAG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1401C>T	17.37:g.80543901C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			C|0.986;T|0.014	0.014	strong		0.627	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
ADAD2	161931	hgsc.bcm.edu	37	16	84229436	84229436	+	Silent	SNP	G	G	A	rs62049905	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84229436G>A	ENST00000315906.5	+	7	1120	c.1068G>A	c.(1066-1068)tcG>tcA	p.S356S	ADAD2_ENST00000268624.3_Silent_p.S438S|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	356	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CCCCCACCTCGGAAGGTGGCC	0.706													G|||	1575	0.314497	0.2784	0.4438	5008	,	,		14714	0.2292		0.3211	False		,,,				2504	0.3528				p.S438S		Atlas-SNP	.											ADAD2,NS,carcinoma,0,1	ADAD2	46	1	0			c.G1314A						PASS	.	G	,	1219,3093		170,879,1107	14.0	16.0	15.0		1068,1314	-9.4	0.0	16	dbSNP_129	15	2560,5934		420,1720,2107	no	coding-synonymous,coding-synonymous	ADAD2	NM_001145400.1,NM_139174.3	,	590,2599,3214	AA,AG,GG		30.1389,28.2699,29.5096	,	356/584,438/666	84229436	3779,9027	2156	4247	6403	SO:0001819	synonymous_variant	161931	exon8			CACCTCGGAAGGT	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.1068G>A	16.37:g.84229436G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	40	26	0.65	NM_139174	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																			G|0.696;A|0.304	0.304	strong		0.706	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
DEFB108B	245911	hgsc.bcm.edu	37	11	71548544	71548544	+	Missense_Mutation	SNP	A	A	G	rs7120658	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71548544A>G	ENST00000328698.1	+	2	158	c.158A>G	c.(157-159)cAa>cGa	p.Q53R	DEFB108B_ENST00000529157.1_3'UTR	NM_001002035.1	NP_001002035.1	Q8NET1	D108B_HUMAN	defensin, beta 108B	53			Q -> R (in dbSNP:rs7120658). {ECO:0000269|PubMed:12734011}.		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)		p.Q53R(1)		endometrium(1)|kidney(1)|lung(2)|skin(1)	5						TTAAATAGCCAACCCTGCTGC	0.468													.|||	2688	0.536741	0.6589	0.3934	5008	,	,		14957	0.3631		0.5984	False		,,,				2504	0.589				p.Q53R		Atlas-SNP	.											DEFB108B,arm,malignant_melanoma,0,1	DEFB108B	6	1	1	Substitution - Missense(1)	skin(1)	c.A158G						scavenged	.	G	ARG/GLN	2797,1603		907,983,310	85.0	94.0	90.0		158	-0.8	0.0	11	dbSNP_116	90	5174,3408		1581,2012,698	no	missense	DEFB108B	NM_001002035.1	43	2488,2995,1008	GG,GA,AA		39.711,36.4318,38.5996	benign	53/74	71548544	7971,5011	2200	4291	6491	SO:0001583	missense	245911	exon2			ATAGCCAACCCTG	AF529416	CCDS31631.1	11q13.4	2011-03-29			ENSG00000184276	ENSG00000184276		"""Defensins, beta"""	29966	protein-coding gene	gene with protein product							Standard	NM_001002035		Approved		uc010rqr.2	Q8NET1	OTTHUMG00000167533	ENST00000328698.1:c.158A>G	11.37:g.71548544A>G	ENSP00000333234:p.Gln53Arg	Somatic	206	1	0.00485437		WXS	Illumina HiSeq	Phase_I	192	90	0.46875	NM_001002035		Missense_Mutation	SNP	ENST00000328698.1	37	CCDS31631.1	1033	0.47298534798534797	277	0.5630081300813008	148	0.4088397790055249	187	0.3269230769230769	421	0.5554089709762533	.	1.034	-0.680836	0.03353	0.635682	0.60289	ENSG00000184276	ENST00000328698	T	0.10382	2.88	1.33	-0.755	0.11061	.	0.972177	0.08316	N	0.964541	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41305	-0.9516	8	0.02654	T	1	.	5.2055	0.15289	0.5933:0.0:0.4067:0.0	rs7120658;rs58471012	53	Q8NET1	D108B_HUMAN	R	53	ENSP00000333234:Q53R	ENSP00000333234:Q53R	Q	+	2	0	DEFB108B	71226192	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.990000	0.03732	-0.735000	0.04837	-1.511000	0.00944	CAA	.	.	weak		0.468	DEFB108B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394945.1	NM_001002035	
HLA-DOB	3112	hgsc.bcm.edu	37	6	32783086	32783086	+	Silent	SNP	A	A	G	rs7383287	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32783086A>G	ENST00000438763.2	-	2	192	c.96T>C	c.(94-96)gaT>gaC	p.D32D	TAP2_ENST00000452392.2_Intron	NM_002120.3	NP_002111.1	P13765	DOB_HUMAN	major histocompatibility complex, class II, DO beta	32	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	9						GAATCACAAAATCTTCTGGAA	0.458													A|||	663	0.132388	0.1831	0.1268	5008	,	,		20437	0.0308		0.1839	False		,,,				2504	0.1196				p.D32D		Atlas-SNP	.											.	HLA-DOB	17	.	0			c.T96C						PASS	.	A		806,3600	322.3+/-297.6	83,640,1480	102.0	100.0	101.0		96	4.3	1.0	6	dbSNP_116	101	1822,6778	325.4+/-316.9	209,1404,2687	yes	coding-synonymous	HLA-DOB	NM_002120.3		292,2044,4167	GG,GA,AA		21.186,18.2932,20.2061		32/274	32783086	2628,10378	2203	4300	6503	SO:0001819	synonymous_variant	3112	exon2			CACAAAATCTTCT		CCDS4754.1	6p21.3	2013-01-11			ENSG00000241106	ENSG00000241106		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4937	protein-coding gene	gene with protein product		600629					Standard	NM_002120		Approved			P13765	OTTHUMG00000031213	ENST00000438763.2:c.96T>C	6.37:g.32783086A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	158	79	0.5	NM_002120	B0V0Y0|Q29746|Q29825|Q6FHC2	Silent	SNP	ENST00000438763.2	37	CCDS4754.1	270	0.12362637362637363	61	0.12398373983739837	45	0.12430939226519337	20	0.03496503496503497	144	0.18997361477572558	A	10.40	1.339479	0.24339	0.182932	0.21186	ENSG00000241106	ENST00000447394	.	.	.	4.28	4.28	0.50868	.	.	.	.	.	T	0.42743	0.1216	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.41787	-0.9489	3	.	.	.	.	11.651	0.51288	1.0:0.0:0.0:0.0	rs7383287;rs17429396;rs29029540;rs45459295;rs60007806;rs7383287	.	.	.	L	19	.	.	F	-	1	0	HLA-DOB	32891064	0.981000	0.34729	1.000000	0.80357	0.992000	0.81027	0.298000	0.19120	1.907000	0.55213	0.486000	0.48141	TTT	A|0.838;G|0.162	0.162	strong		0.458	HLA-DOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076439.1	NM_002120	
FGL1	2267	hgsc.bcm.edu	37	8	17743051	17743051	+	Missense_Mutation	SNP	A	A	T	rs61745164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17743051A>T	ENST00000398056.2	-	4	828	c.13T>A	c.(13-15)Ttc>Atc	p.F5I	FGL1_ENST00000381840.2_Missense_Mutation_p.F5I|RP11-156K13.2_ENST00000519368.1_RNA|FGL1_ENST00000522444.1_Missense_Mutation_p.F5I|FGL1_ENST00000381841.2_Missense_Mutation_p.F5I|FGL1_ENST00000518650.1_Missense_Mutation_p.F5I|FGL1_ENST00000427924.1_Missense_Mutation_p.F5I|FGL1_ENST00000398054.1_Missense_Mutation_p.F5I			Q08830	FGL1_HUMAN	fibrinogen-like 1	5					adipose tissue development (GO:0060612)|cholesterol metabolic process (GO:0008203)|regulation of glucose metabolic process (GO:0010906)|response to stilbenoid (GO:0035634)	extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)	13				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		ATGAAACTGAACACCTTTGCC	0.373													A|||	96	0.0191693	0.0008	0.0173	5008	,	,		16995	0.0		0.0368	False		,,,				2504	0.047				p.F5I		Atlas-SNP	.											.	FGL1	31	.	0			c.T13A						PASS	.	A	ILE/PHE,ILE/PHE,ILE/PHE,ILE/PHE	18,4388	27.2+/-55.0	0,18,2185	81.0	80.0	80.0		13,13,13,13	-5.5	0.0	8	dbSNP_129	80	194,8406	86.1+/-148.5	3,188,4109	yes	missense,missense,missense,missense	FGL1	NM_004467.3,NM_147203.2,NM_201552.1,NM_201553.1	21,21,21,21	3,206,6294	TT,TA,AA		2.2558,0.4085,1.63	benign,benign,benign,benign	5/313,5/313,5/313,5/313	17743051	212,12794	2203	4300	6503	SO:0001583	missense	2267	exon3			AACTGAACACCTT	D14446	CCDS6004.1	8p22	2013-02-06			ENSG00000104760	ENSG00000104760		"""Fibrinogen C domain containing"""	3695	protein-coding gene	gene with protein product		605776				8390249	Standard	NM_004467		Approved	HFREP-1	uc003wyb.3	Q08830	OTTHUMG00000096989	ENST00000398056.2:c.13T>A	8.37:g.17743051A>T	ENSP00000381133:p.Phe5Ile	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	34	15	0.441176	NM_201553	A6NKU4|Q4PJH9|Q53YF1|Q8NG32|Q96KW6|Q96QM6	Missense_Mutation	SNP	ENST00000398056.2	37	CCDS6004.1	41	0.018772893772893772	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	30	0.0395778364116095	A	10.43	1.347170	0.24426	0.004085	0.022558	ENSG00000104760	ENST00000221204;ENST00000398056;ENST00000522444;ENST00000381841;ENST00000427924;ENST00000398054;ENST00000381840;ENST00000518650	T;T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67;0.67	3.54	-5.54	0.02544	.	1.261060	0.05952	N	0.639060	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.007	B;B	0.11329	0.006;0.004	T	0.07908	-1.0748	10	0.21540	T	0.41	.	0.5177	0.00606	0.2502:0.1422:0.1898:0.4178	rs61745164	5;5	Q8NG32;Q08830	.;FGL1_HUMAN	I	5	ENSP00000381133:F5I;ENSP00000429757:F5I;ENSP00000371263:F5I;ENSP00000401952:F5I;ENSP00000381131:F5I;ENSP00000371262:F5I;ENSP00000428430:F5I	ENSP00000221204:F5I	F	-	1	0	FGL1	17787331	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.081000	0.03403	-1.202000	0.02655	-0.531000	0.04308	TTC	A|0.973;T|0.027	0.027	strong		0.373	FGL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375254.1	NM_004467	
DDX49	54555	hgsc.bcm.edu	37	19	19030571	19030571	+	Silent	SNP	C	C	T	rs2231992	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19030571C>T	ENST00000247003.4	+	1	88	c.21C>T	c.(19-21)ctC>ctT	p.L7L	COPE_ENST00000349893.4_5'Flank|DDX49_ENST00000438170.2_5'UTR|COPE_ENST00000600932.1_5'Flank|AC002985.3_ENST00000596918.1_Intron|COPE_ENST00000351079.4_5'Flank|COPE_ENST00000262812.4_5'Flank	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	7							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			TCGCGGAGCTCGGGCTGTCAT	0.672													C|||	129	0.0257588	0.0598	0.0216	5008	,	,		15532	0.0		0.0318	False		,,,				2504	0.0031				p.L7L		Atlas-SNP	.											.	DDX49	37	.	0			c.C21T						PASS	.	C		237,4165		5,227,1969	30.0	32.0	31.0		21	-2.7	0.9	19	dbSNP_98	31	358,8234		9,340,3947	no	coding-synonymous	DDX49	NM_019070.4		14,567,5916	TT,TC,CC		4.1667,5.3839,4.579		7/484	19030571	595,12399	2201	4296	6497	SO:0001819	synonymous_variant	54555	exon1			GGAGCTCGGGCTG		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"""DEAD-boxes"""	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.21C>T	19.37:g.19030571C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	131	71	0.541985	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Silent	SNP	ENST00000247003.4	37	CCDS12390.1																																																																																			C|0.958;T|0.042	0.042	strong		0.672	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070	
FSTL4	23105	hgsc.bcm.edu	37	5	132652281	132652281	+	Missense_Mutation	SNP	C	C	T	rs17683306	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:132652281C>T	ENST00000265342.7	-	5	722	c.473G>A	c.(472-474)cGt>cAt	p.R158H		NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	158			R -> H (in dbSNP:rs17683306).			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)			TGGCTGCAGACGGGTCTGGAG	0.532											OREG0016777	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	173	0.0345447	0.0083	0.0562	5008	,	,		17956	0.001		0.0954	False		,,,				2504	0.0266				p.R158H		Atlas-SNP	.											.	FSTL4	74	.	0			c.G473A						PASS	.	C	HIS/ARG	89,4317	74.1+/-112.3	2,85,2116	71.0	74.0	73.0		473	1.4	0.0	5	dbSNP_123	73	943,7657	207.9+/-249.5	51,841,3408	yes	missense	FSTL4	NM_015082.1	29	53,926,5524	TT,TC,CC		10.9651,2.02,7.9348	benign	158/843	132652281	1032,11974	2203	4300	6503	SO:0001583	missense	23105	exon5			TGCAGACGGGTCT	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.473G>A	5.37:g.132652281C>T	ENSP00000265342:p.Arg158His	Somatic	133	0	0	1597	WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_015082	Q8TBU0|Q9UPU1	Missense_Mutation	SNP	ENST00000265342.7	37	CCDS34238.1	101	0.04624542124542125	7	0.014227642276422764	21	0.058011049723756904	0	0.0	73	0.09630606860158311	C	8.534	0.871664	0.17322	0.0202	0.109651	ENSG00000053108	ENST00000265342	T	0.59638	0.25	5.41	1.44	0.22558	.	0.629297	0.17508	N	0.171731	T	0.01222	0.0040	L	0.56769	1.78	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.02491	-1.1151	10	0.31617	T	0.26	-13.9029	8.1927	0.31379	0.0:0.546:0.0:0.454	rs17683306;rs52798602;rs17683306	158	Q6MZW2	FSTL4_HUMAN	H	158	ENSP00000265342:R158H	ENSP00000265342:R158H	R	-	2	0	FSTL4	132680180	0.000000	0.05858	0.031000	0.17742	0.141000	0.21300	-0.624000	0.05540	0.304000	0.22809	0.561000	0.74099	CGT	C|0.936;T|0.064	0.064	strong		0.532	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
PWWP2A	114825	hgsc.bcm.edu	37	5	159520661	159520661	+	Silent	SNP	T	T	C	rs56251777	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:159520661T>C	ENST00000307063.7	-	2	1030	c.996A>G	c.(994-996)gaA>gaG	p.E332E	PWWP2A_ENST00000523662.1_Silent_p.E332E|PWWP2A_ENST00000456329.3_Silent_p.E332E	NM_001130864.1	NP_001124336.1	Q96N64	PWP2A_HUMAN	PWWP domain containing 2A	332										kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	5	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)			TTTCCTTTTTTTCAGCAACAA	0.333													T|||	152	0.0303514	0.0083	0.0519	5008	,	,		21301	0.001		0.0845	False		,,,				2504	0.0194				p.E332E		Atlas-SNP	.											.	PWWP2A	64	.	0			c.A996G						PASS	.	T	,	64,3586		0,64,1761	122.0	104.0	109.0		996,996	0.2	1.0	5	dbSNP_129	109	764,7414		36,692,3361	no	coding-synonymous,coding-synonymous	PWWP2A	NM_001130864.1,NM_052927.2	,	36,756,5122	CC,CT,TT		9.3421,1.7534,7.0003	,	332/756,332/561	159520661	828,11000	1825	4089	5914	SO:0001819	synonymous_variant	114825	exon2			CTTTTTTTCAGCA		CCDS47331.1, CCDS47332.1, CCDS58990.1	5q33.3	2011-03-23			ENSG00000170234	ENSG00000170234			29406	protein-coding gene	gene with protein product							Standard	NM_052927		Approved	KIAA1935	uc011ded.2	Q96N64	OTTHUMG00000163546	ENST00000307063.7:c.996A>G	5.37:g.159520661T>C		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_052927	G5EA07|Q2HJJ2|Q8IYR3|Q96PV3	Silent	SNP	ENST00000307063.7	37	CCDS47332.1																																																																																			T|0.946;C|0.054	0.054	strong		0.333	PWWP2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374092.1		
PTPRB	5787	hgsc.bcm.edu	37	12	70990054	70990054	+	Missense_Mutation	SNP	T	T	C	rs2465811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:70990054T>C	ENST00000261266.5	-	3	408	c.379A>G	c.(379-381)Agc>Ggc	p.S127G	PTPRB_ENST00000551525.1_Missense_Mutation_p.S344G|PTPRB_ENST00000334414.6_Missense_Mutation_p.S345G|PTPRB_ENST00000451516.2_Missense_Mutation_p.S127G|PTPRB_ENST00000550358.1_Missense_Mutation_p.S345G|PTPRB_ENST00000538708.1_Missense_Mutation_p.S127G|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550857.1_Missense_Mutation_p.S127G	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	127	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.		S -> G (in dbSNP:rs2465811). {ECO:0000269|PubMed:2170109}.		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)			ACATGCAAGCTGGTTGAAGTC	0.393													T|||	1603	0.320088	0.4402	0.2363	5008	,	,		15448	0.3026		0.2604	False		,,,				2504	0.2965				p.S345G		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1033G	GRCh37	CM086290	PTPRB	M	rs2465811	PASS	.	T	GLY/SER,GLY/SER,GLY/SER,GLY/SER	1481,2253		289,903,675	61.0	59.0	60.0		1033,379,379,379	5.8	0.8	12	dbSNP_100	60	2290,5936		310,1670,2133	yes	missense,missense,missense,missense	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	56,56,56,56	599,2573,2808	CC,CT,TT		27.8386,39.6626,31.5301	benign,benign,benign,benign	345/2216,127/1908,127/1908,127/1998	70990054	3771,8189	1867	4113	5980	SO:0001583	missense	5787	exon5			GCAAGCTGGTTGA	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.379A>G	12.37:g.70990054T>C	ENSP00000261266:p.Ser127Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	669	0.30631868131868134	209	0.4247967479674797	90	0.24861878453038674	175	0.30594405594405594	195	0.25725593667546176	T	10.86	1.471193	0.26423	0.396626	0.278386	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.089006	0.85682	D	0.000000	T	0.00012	0.0000	M	0.70275	2.135	0.25955	P	0.9827042	B;B;B;B;B;B;B;B	0.30482	0.001;0.001;0.008;0.281;0.008;0.007;0.003;0.007	B;B;B;B;B;B;B;B	0.35688	0.008;0.008;0.052;0.208;0.013;0.026;0.03;0.026	T	0.30119	-0.9989	9	0.59425	D	0.04	.	16.1596	0.81693	0.0:0.0:0.0:1.0	rs2465811;rs52801085;rs59164378;rs2465811	127;127;224;345;344;345;127;345	P23467-2;F5H3G6;Q6ZR19;Q6ZTX7;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;.;PTPRB_HUMAN;.	G	345;127;345;345;127;127;127;344;224	ENSP00000334928:S345G;ENSP00000393028:S127G;ENSP00000448058:S345G;ENSP00000438927:S127G;ENSP00000447302:S127G;ENSP00000261266:S127G;ENSP00000448349:S344G;ENSP00000446982:S224G	ENSP00000261266:S127G	S	-	1	0	PTPRB	69276321	1.000000	0.71417	0.821000	0.32701	0.029000	0.11900	4.003000	0.57061	2.216000	0.71823	0.533000	0.62120	AGC	C|0.325;N|0.000	0.325	strong		0.393	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
ZNF320	162967	hgsc.bcm.edu	37	19	53384197	53384197	+	Silent	SNP	A	A	G	rs61745485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53384197A>G	ENST00000595635.1	-	8	1683	c.1182T>C	c.(1180-1182)ttT>ttC	p.F394F	ZNF320_ENST00000600930.1_Intron|ZNF320_ENST00000391781.2_Silent_p.F394F|ZNF320_ENST00000597909.1_Intron	NM_207333.2	NP_997216.2	A2RRD8	ZN320_HUMAN	zinc finger protein 320	394					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(4)|large_intestine(5)|liver(1)|lung(10)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(134;0.0534)		CTTTTGTACTAAAAACCTTGC	0.403													.|||	334	0.0666933	0.143	0.0288	5008	,	,		23267	0.0437		0.0487	False		,,,				2504	0.0327				p.F394F		Atlas-SNP	.											.	ZNF320	67	.	0			c.T1182C						PASS	.	A		569,3837		26,517,1660	91.0	87.0	88.0		1182	-0.3	0.0	19	dbSNP_129	88	353,8247		5,343,3952	no	coding-synonymous	ZNF320	NM_207333.2		31,860,5612	GG,GA,AA		4.1047,12.9142,7.089		394/510	53384197	922,12084	2203	4300	6503	SO:0001819	synonymous_variant	162967	exon4			TGTACTAAAAACC	AF086262	CCDS33095.1	19q13.41	2014-09-04			ENSG00000182986	ENSG00000182986		"""Zinc fingers, C2H2-type"", ""-"""	13842	protein-coding gene	gene with protein product		606427				11536051	Standard	XM_006723059		Approved	ZFPL, DKFZp686G16228	uc002qag.3	A2RRD8	OTTHUMG00000182797	ENST00000595635.1:c.1182T>C	19.37:g.53384197A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_207333	Q8NDR6	Silent	SNP	ENST00000595635.1	37	CCDS33095.1																																																																																			A|0.933;G|0.067	0.067	strong		0.403	ZNF320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463771.1	NM_207333	
CASP9	842	hgsc.bcm.edu	37	1	15832543	15832543	+	Missense_Mutation	SNP	T	T	C	rs1052576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15832543T>C	ENST00000333868.5	-	5	756	c.662A>G	c.(661-663)cAg>cGg	p.Q221R	CASP9_ENST00000375890.4_Missense_Mutation_p.Q138R|CASP9_ENST00000348549.5_Intron|CASP9_ENST00000546424.1_Missense_Mutation_p.Q221R	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	221			Q -> R (in dbSNP:rs1052576). {ECO:0000269|PubMed:8663294, ECO:0000269|Ref.9}.		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		GTGGTCCTGCTGCGCCAGCTC	0.582													C|||	2929	0.584864	0.7398	0.4986	5008	,	,		17997	0.6538		0.5149	False		,,,				2504	0.4376				p.Q221R		Atlas-SNP	.											.	CASP9	40	.	0			c.A662G						PASS	.	C	ARG/GLN,ARG/GLN	3101,1305	440.4+/-346.0	1101,899,203	75.0	72.0	73.0		662,413	-9.5	0.0	1	dbSNP_86	73	4542,4058	558.4+/-387.2	1215,2112,973	yes	missense,missense	CASP9	NM_001229.3,NM_032996.2	43,43	2316,3011,1176	CC,CT,TT		47.186,29.6187,41.2348	benign,benign	221/417,138/334	15832543	7643,5363	2203	4300	6503	SO:0001583	missense	842	exon5			TCCTGCTGCGCCA	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.662A>G	1.37:g.15832543T>C	ENSP00000330237:p.Gln221Arg	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	249	235	0.943775	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	1310	0.5998168498168498	363	0.7378048780487805	181	0.5	359	0.6276223776223776	407	0.5369393139841688	C	6.397	0.441447	0.12164	0.703813	0.52814	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000375874;ENST00000375890;ENST00000447522	T;T;T;T	0.20069	2.1;2.1;2.1;2.1	5.89	-9.49	0.00587	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);Peptidase C14, ICE, catalytic subunit p20 (1);	1.548680	0.02844	N	0.128269	T	0.00012	0.0000	N	0.02708	-0.52	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.46693	-0.9173	9	0.02654	T	1	.	15.8974	0.79344	0.0:0.1079:0.0739:0.8181	rs1052576;rs2266730;rs3192987;rs58780274;rs1052576	221;221	P55211;F8VVS7	CASP9_HUMAN;.	R	221;221;65;138;138	ENSP00000449584:Q221R;ENSP00000330237:Q221R;ENSP00000365051:Q138R;ENSP00000396540:Q138R	ENSP00000330237:Q221R	Q	-	2	0	CASP9	15705130	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-1.738000	0.01842	-2.385000	0.00590	-2.575000	0.00170	CAG	T|0.410;C|0.590	0.590	strong		0.582	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
FRAS1	80144	hgsc.bcm.edu	37	4	79455714	79455714	+	Silent	SNP	C	C	G	rs4975070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:79455714C>G	ENST00000264895.6	+	71	11477	c.11037C>G	c.(11035-11037)ccC>ccG	p.P3679P		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3675					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TAATGGATCCCAATACATCTG	0.448													C|||	2579	0.514976	0.3086	0.4395	5008	,	,		20789	0.7758		0.4632	False		,,,				2504	0.6319				p.P3679P		Atlas-SNP	.											.	FRAS1	779	.	0			c.C11037G						PASS	.	C		1279,2509		215,849,830	128.0	115.0	119.0		11037	3.2	1.0	4	dbSNP_111	119	3593,4649		791,2011,1319	no	coding-synonymous	FRAS1	NM_025074.6		1006,2860,2149	GG,GC,CC		43.5938,33.7645,40.4988		3679/4013	79455714	4872,7158	1894	4121	6015	SO:0001819	synonymous_variant	80144	exon71			GGATCCCAATACA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.11037C>G	4.37:g.79455714C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	1143	0.5233516483516484	172	0.34959349593495936	163	0.45027624309392267	453	0.791958041958042	355	0.4683377308707124	C	6.186	0.402486	0.11696	0.337645	0.435938	ENSG00000138759	ENST00000512123	.	.	.	5.05	3.2	0.36748	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33523	-0.9865	3	.	.	.	.	9.0976	0.36649	0.2536:0.6722:0.0:0.0741	rs4975070;rs61687904;rs4975070	.	.	.	E	1908	.	.	Q	+	1	0	FRAS1	79674738	0.997000	0.39634	1.000000	0.80357	0.777000	0.43975	0.493000	0.22451	2.336000	0.79503	0.591000	0.81541	CAA	C|0.485;G|0.515	0.515	strong		0.448	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PIM3	415116	hgsc.bcm.edu	37	22	50354819	50354819	+	Silent	SNP	C	C	A	rs11541025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50354819C>A	ENST00000360612.4	+	2	567	c.132C>A	c.(130-132)gcC>gcA	p.A44A		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	44	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		AGGTGGGCGCCGTGCTGGGTA	0.766													c|||	1862	0.371805	0.3676	0.2867	5008	,	,		6787	0.3383		0.2922	False		,,,				2504	0.5542				p.A44A		Atlas-SNP	.											.	PIM3	15	.	0			c.C132A						PASS	.	G		1402,2728		306,790,969	6.0	6.0	6.0		132	-4.2	0.3	22	dbSNP_120	6	2589,5681		503,1583,2049	no	coding-synonymous	PIM3	NM_001001852.3		809,2373,3018	AA,AC,CC		31.3059,33.9467,32.1855		44/327	50354819	3991,8409	2065	4135	6200	SO:0001819	synonymous_variant	415116	exon2			GGGCGCCGTGCTG	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"""pim-3 oncogene"""			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.132C>A	22.37:g.50354819C>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	24	24	1	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Silent	SNP	ENST00000360612.4	37	CCDS33678.1																																																																																			C|0.669;A|0.331	0.331	strong		0.766	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852	
BEST1	7439	hgsc.bcm.edu	37	11	61719387	61719387	+	Silent	SNP	T	T	C	rs1800007	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:61719387T>C	ENST00000378043.4	+	2	752	c.109T>C	c.(109-111)Tta>Cta	p.L37L	BEST1_ENST00000534553.1_Intron|BEST1_ENST00000449131.2_Intron|BEST1_ENST00000378042.3_5'UTR|BEST1_ENST00000301774.9_Intron|BEST1_ENST00000435278.2_Silent_p.L37L	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1	37					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TGGCGAGTTCTTAATCTTCCT	0.572													T|||	3408	0.680511	0.7988	0.5893	5008	,	,		15117	0.8978		0.3052	False		,,,				2504	0.7474				p.L37L		Atlas-SNP	.											.	BEST1	85	.	0			c.T109C						PASS	.	T	,	3153,1251	703.6+/-407.0	1136,881,185	112.0	114.0	113.0		,109	-1.9	0.9	11	dbSNP_89	113	2663,5935	428.0+/-355.8	435,1793,2071	no	intron,coding-synonymous	BEST1	NM_001139443.1,NM_004183.3	,	1571,2674,2256	CC,CT,TT		30.9723,28.406,44.7316	,	,37/586	61719387	5816,7186	2202	4299	6501	SO:0001819	synonymous_variant	7439	exon2			GAGTTCTTAATCT	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.109T>C	11.37:g.61719387T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_004183	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			T|0.448;C|0.552	0.552	strong		0.572	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
OBSL1	23363	hgsc.bcm.edu	37	2	220417266	220417266	+	Missense_Mutation	SNP	C	C	T	rs59332477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220417266C>T	ENST00000404537.1	-	18	5356	c.5300G>A	c.(5299-5301)cGa>cAa	p.R1767Q	OBSL1_ENST00000373876.1_Missense_Mutation_p.R1675Q|OBSL1_ENST00000265318.4_3'UTR	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1767					cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACCTTCCTGTCGGATGCGGAC	0.731													C|||	1886	0.376597	0.3495	0.5202	5008	,	,		10361	0.3819		0.4583	False		,,,				2504	0.2219				p.R1767Q		Atlas-SNP	.											.	OBSL1	120	.	0			c.G5300A						PASS	.	C	GLN/ARG	1409,2443		283,843,800	9.0	13.0	12.0		5300	4.6	1.0	2	dbSNP_129	12	3644,4534		865,1914,1310	yes	missense	OBSL1	NM_015311.2	43	1148,2757,2110	TT,TC,CC		44.5586,36.5784,42.0033	probably-damaging	1767/1897	220417266	5053,6977	1926	4089	6015	SO:0001583	missense	23363	exon18			TCCTGTCGGATGC	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.5300G>A	2.37:g.220417266C>T	ENSP00000385636:p.Arg1767Gln	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	15	12	0.8	NM_015311	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	913	0.41804029304029305	163	0.3313008130081301	168	0.46408839779005523	228	0.3986013986013986	354	0.46701846965699206	C	22.2	4.252406	0.80135	0.365784	0.445586	ENSG00000124006	ENST00000404537;ENST00000373876	T;T	0.66995	-0.24;-0.24	4.61	4.61	0.57282	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.41356	1.27	0.09310	P	1.0	D	0.89917	1.0	D	0.85130	0.997	T	0.44997	-0.9291	8	0.20519	T	0.43	.	14.2902	0.66273	0.0:1.0:0.0:0.0	rs59332477;rs62191611	1767	O75147	OBSL1_HUMAN	Q	1767;1675	ENSP00000385636:R1767Q;ENSP00000362983:R1675Q	ENSP00000362983:R1675Q	R	-	2	0	OBSL1	220125510	0.997000	0.39634	1.000000	0.80357	0.840000	0.47671	3.585000	0.53943	2.390000	0.81377	0.655000	0.94253	CGA	C|0.582;T|0.418	0.418	strong		0.731	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
CERS4	79603	hgsc.bcm.edu	37	19	8321946	8321946	+	Silent	SNP	T	T	C	rs36247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8321946T>C	ENST00000251363.5	+	9	1026	c.726T>C	c.(724-726)tcT>tcC	p.S242S	CERS4_ENST00000559336.1_Silent_p.S242S|CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000558331.1_Silent_p.S191S|CERS4_ENST00000559450.1_Silent_p.S242S	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	242	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										ACGATTCCTCTGACTACCTGC	0.602													C|||	2191	0.4375	0.4259	0.3862	5008	,	,		17309	0.4504		0.328	False		,,,				2504	0.589				p.S242S		Atlas-SNP	.											.	.	.	.	0			c.T726C						PASS	.	C		1879,2527	630.2+/-395.4	415,1049,739	223.0	210.0	214.0		726	-9.5	0.0	19	dbSNP_76	214	2769,5831	678.9+/-403.5	449,1871,1980	no	coding-synonymous	CERS4	NM_024552.2		864,2920,2719	CC,CT,TT		32.1977,42.6464,35.7374		242/395	8321946	4648,8358	2203	4300	6503	SO:0001819	synonymous_variant	79603	exon9			TTCCTCTGACTAC		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.726T>C	19.37:g.8321946T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	151	70	0.463576	NM_024552	D6W665	Silent	SNP	ENST00000251363.5	37	CCDS12197.1																																																																																			T|0.623;C|0.376	0.376	strong		0.602	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
DNHD1	144132	hgsc.bcm.edu	37	11	6550309	6550309	+	Missense_Mutation	SNP	G	G	A	rs2344829	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6550309G>A	ENST00000527990.2	+	10	2305	c.2305G>A	c.(2305-2307)Ggg>Agg	p.G769R	DNHD1_ENST00000254579.6_Missense_Mutation_p.G769R			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	769					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CACAAAAGGCGGGTTGCTGCT	0.527													A|||	3582	0.715256	0.6422	0.6527	5008	,	,		20739	0.874		0.6292	False		,,,				2504	0.7832				p.G769R		Atlas-SNP	.											.	DNHD1	198	.	0			c.G2305A						PASS	.	A	ARG/GLY	894,490		284,326,82	142.0	136.0	138.0		2305	3.0	1.0	11	dbSNP_100	138	2137,1045		722,693,176	yes	missense	DNHD1	NM_144666.2	125	1006,1019,258	AA,AG,GG		32.841,35.4046,33.618	benign	769/4754	6550309	3031,1535	692	1591	2283	SO:0001583	missense	144132	exon12			AAAGGCGGGTTGC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.2305G>A	11.37:g.6550309G>A	ENSP00000436180:p.Gly769Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1538	0.7042124542124543	330	0.6707317073170732	235	0.649171270718232	487	0.8513986013986014	486	0.6411609498680739	A	5.682	0.310322	0.10733	0.645954	0.67159	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.25579	1.79;1.79	5.54	3.02	0.34903	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16364	-1.0405	8	0.27082	T	0.32	.	6.0678	0.19873	0.6721:0.2398:0.0882:0.0	rs2344829;rs52815182;rs58903745;rs2344829	769	Q96M86	DNHD1_HUMAN	R	769;769;35	ENSP00000254579:G769R;ENSP00000436180:G769R	ENSP00000254579:G769R	G	+	1	0	DNHD1	6506885	0.799000	0.28903	0.992000	0.48379	0.938000	0.57974	1.170000	0.31883	0.928000	0.37168	-0.269000	0.10298	GGG	G|0.292;A|0.708	0.708	strong		0.527	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
SPACA7	122258	hgsc.bcm.edu	37	13	113052388	113052388	+	Silent	SNP	A	A	G	rs2296895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113052388A>G	ENST00000283550.3	+	3	244	c.177A>G	c.(175-177)ttA>ttG	p.L59L	SPACA7_ENST00000375699.3_Silent_p.L28L	NM_145248.4	NP_660291.2	Q96KW9	SPAC7_HUMAN	sperm acrosome associated 7	59						acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)				large_intestine(5)|lung(4)|skin(3)|urinary_tract(1)	13						AGGAGATTTTAGATCTGAATA	0.488													G|||	3379	0.67472	0.8154	0.6196	5008	,	,		20762	0.624		0.5696	False		,,,				2504	0.684				p.L59L		Atlas-SNP	.											SPACA7,NS,adenoma,0,1	SPACA7	36	1	0			c.A177G						PASS	.	G		3464,942	356.9+/-313.7	1368,728,107	142.0	137.0	138.0		177	2.8	0.0	13	dbSNP_100	138	5061,3535	514.4+/-378.4	1515,2031,752	no	coding-synonymous	SPACA7	NM_145248.4		2883,2759,859	GG,GA,AA		41.1238,21.3799,34.4332		59/196	113052388	8525,4477	2203	4298	6501	SO:0001819	synonymous_variant	122258	exon3			GATTTTAGATCTG	BC016750	CCDS9524.1	13q34	2013-10-11	2011-03-15	2011-03-15	ENSG00000153498	ENSG00000153498			29575	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 28"""	C13orf28		22495889	Standard	NM_145248		Approved		uc001vsd.2	Q96KW9	OTTHUMG00000017365	ENST00000283550.3:c.177A>G	13.37:g.113052388A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	81	52	0.641975	NM_145248	Q5T8L1	Silent	SNP	ENST00000283550.3	37	CCDS9524.1																																																																																			A|0.363;G|0.637	0.637	strong		0.488	SPACA7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045820.2	NM_145248	
RGL4	266747	hgsc.bcm.edu	37	22	24036563	24036563	+	Silent	SNP	G	G	A	rs2070447	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:24036563G>A	ENST00000290691.5	+	5	2112	c.942G>A	c.(940-942)tcG>tcA	p.S314S	RGL4_ENST00000401461.1_Silent_p.S178S|AP000347.2_ENST00000417194.1_RNA|KB-1572G7.2_ENST00000421064.1_RNA|GUSBP11_ENST00000455485.1_RNA	NM_153615.1	NP_705843.1	Q8IZJ4	RGDSR_HUMAN	ral guanine nucleotide dissociation stimulator-like 4	314	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(3)	15						ACTTCTCCTCGGTGCACGTCA	0.587													g|||	595	0.11881	0.0113	0.1009	5008	,	,		20074	0.2798		0.0915	False		,,,				2504	0.1391				p.S314S		Atlas-SNP	.											.	RGL4	29	.	0			c.G942A						PASS	.	G		128,4278	93.9+/-132.6	6,116,2081	164.0	108.0	127.0		942	-3.8	0.0	22	dbSNP_96	127	741,7859	178.6+/-228.0	38,665,3597	no	coding-synonymous	RGL4	NM_153615.1		44,781,5678	AA,AG,GG		8.6163,2.9051,6.6815		314/474	24036563	869,12137	2203	4300	6503	SO:0001819	synonymous_variant	266747	exon5			CTCCTCGGTGCAC		CCDS13811.1	22q11.23	2008-02-22			ENSG00000159496	ENSG00000159496			31911	protein-coding gene	gene with protein product	"""RalGDS related oncogene"""	612214				9178890, 10851075	Standard	NM_153615		Approved	Rgr	uc002zxn.3	Q8IZJ4	OTTHUMG00000150711	ENST00000290691.5:c.942G>A	22.37:g.24036563G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_153615	Q495L8	Silent	SNP	ENST00000290691.5	37	CCDS13811.1																																																																																			G|0.908;A|0.092	0.092	strong		0.587	RGL4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319711.1	NM_153615	
FAM120B	84498	hgsc.bcm.edu	37	6	170626943	170626943	+	Silent	SNP	T	T	C	rs3800266	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:170626943T>C	ENST00000476287.1	+	2	573	c.465T>C	c.(463-465)tcT>tcC	p.S155S	FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000540480.1_Silent_p.S167S|FAM120B_ENST00000537664.1_Silent_p.S178S	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	155					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		CTTTGTGTTCTTTGCAGGAAG	0.468													C|||	799	0.159545	0.0749	0.2046	5008	,	,		20185	0.2817		0.1252	False		,,,				2504	0.1513				p.S155S		Atlas-SNP	.											.	FAM120B	108	.	0			c.T465C						PASS	.	C		421,3985	787.1+/-414.8	23,375,1805	81.0	79.0	80.0		465	-12.1	0.0	6	dbSNP_107	80	1214,7386	761.9+/-407.6	95,1024,3181	no	coding-synonymous	FAM120B	NM_032448.1		118,1399,4986	CC,CT,TT		14.1163,9.5552,12.5711		155/911	170626943	1635,11371	2203	4300	6503	SO:0001819	synonymous_variant	84498	exon2			GTGTTCTTTGCAG	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.465T>C	6.37:g.170626943T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	91	10	0.10989	NM_032448	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																			T|0.857;C|0.143	0.143	strong		0.468	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448	
TSC2	7249	hgsc.bcm.edu	37	16	2138269	2138269	+	Silent	SNP	T	T	C	rs137854091|rs1748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2138269T>C	ENST00000219476.3	+	41	5832	c.5202T>C	c.(5200-5202)gaT>gaC	p.D1734D	TSC2_ENST00000401874.2_Silent_p.D1667D|TSC2_ENST00000353929.4_Silent_p.D1691D|MIR1225_ENST00000408729.1_RNA|TSC2_ENST00000350773.4_Silent_p.D1711D|TSC2_ENST00000382538.6_Silent_p.D1619D|TSC2_ENST00000439673.2_Silent_p.D1631D|TSC2_ENST00000568454.1_Silent_p.D1678D	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1734	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				ACCCCACCGATATCTACCCCT	0.652			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				C|||	1384	0.276358	0.7481	0.1988	5008	,	,		14957	0.0		0.1839	False		,,,				2504	0.0736				p.D1734D		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.T5202C						PASS	.	C	,,	2789,1607	496.0+/-363.4	885,1019,294	96.0	103.0	101.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5202,5001,5133	3.2	1.0	16	dbSNP_36	101	1531,7067	745.9+/-407.3	140,1251,2908	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	1025,2270,3202	CC,CT,TT		17.8065,36.556,33.2461	,,	1734/1808,1667/1741,1711/1785	2138269	4320,8674	2198	4299	6497	SO:0001819	synonymous_variant	7249	exon41	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CACCGATATCTAC	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.5202T>C	16.37:g.2138269T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	86	31	0.360465	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			T|0.695;G|0.000;C|0.305;A|0.000	0.305	strong		0.652	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
HOXB1	3211	hgsc.bcm.edu	37	17	46608030	46608030	+	Silent	SNP	G	G	A	rs12946855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:46608030G>A	ENST00000239174.6	-	1	329	c.237C>T	c.(235-237)tcC>tcT	p.S79S	HOXB1_ENST00000577092.1_Silent_p.S79S	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	79					anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCGAGGGCGCGGAGCTGGGGA	0.662													G|||	672	0.134185	0.1172	0.1225	5008	,	,		13599	0.0972		0.2048	False		,,,				2504	0.1309				p.S79S		Atlas-SNP	.											.	HOXB1	67	.	0			c.C237T						PASS	.	G		555,3849		34,487,1681	37.0	43.0	41.0		237	-8.7	0.4	17	dbSNP_121	41	1764,6832		179,1406,2713	no	coding-synonymous	HOXB1	NM_002144.3		213,1893,4394	AA,AG,GG		20.5212,12.6022,17.8385		79/302	46608030	2319,10681	2202	4298	6500	SO:0001819	synonymous_variant	3211	exon1			GGGCGCGGAGCTG		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.237C>T	17.37:g.46608030G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_002144	Q4VB03	Silent	SNP	ENST00000239174.6	37	CCDS32675.1																																																																																			G|0.833;A|0.167	0.167	strong		0.662	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138418910	138418910	+	Silent	SNP	G	G	A	rs1026435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:138418910G>A	ENST00000310018.2	-	16	1944	c.1662C>T	c.(1660-1662)ttC>ttT	p.F554F	ATP6V0A4_ENST00000393054.1_Silent_p.F554F|ATP6V0A4_ENST00000353492.4_Silent_p.F554F	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	554			F -> L (in dbSNP:rs1026435).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GGATGACACCGAAAACCATCT	0.438													G|||	3589	0.716653	0.6074	0.7709	5008	,	,		19455	0.8403		0.7147	False		,,,				2504	0.7004				p.F554F		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C1662T						PASS	.	G	,,	2681,1725	649.7+/-398.9	815,1051,337	167.0	138.0	148.0		1662,1662,1662	-11.0	0.0	7	dbSNP_86	148	6205,2395	700.8+/-405.2	2232,1741,327	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	,,	3047,2792,664	AA,AG,GG		27.8488,39.1512,31.6777	,,	554/841,554/841,554/841	138418910	8886,4120	2203	4300	6503	SO:0001819	synonymous_variant	50617	exon15			GACACCGAAAACC	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1662C>T	7.37:g.138418910G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_130841	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																			G|0.304;A|0.696	0.696	strong		0.438	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
HNF1A	6927	hgsc.bcm.edu	37	12	121435342	121435342	+	Silent	SNP	C	C	T	rs544842497|rs2259820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121435342C>T	ENST00000257555.6	+	7	1601	c.1375C>T	c.(1375-1377)Ctg>Ttg	p.L459L	HNF1A_ENST00000538626.1_Silent_p.L41L|HNF1A_ENST00000544413.1_Silent_p.L459L|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000400024.2_Silent_p.L459L|HNF1A_ENST00000541395.1_Silent_p.L459L			P20823	HNF1A_HUMAN	HNF1 homeobox A	459					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTGACCACCCTGCAGCCCGT	0.667									Hepatic Adenoma, Familial Clustering of				c|||	1586	0.316693	0.1089	0.3501	5008	,	,		17758	0.4732		0.3161	False		,,,				2504	0.4131				p.L459L		Atlas-SNP	.											.	HNF1A	302	.	0			c.C1375T						PASS	.	C		529,3877	232.0+/-245.7	41,447,1715	33.0	35.0	34.0		1375	4.6	1.0	12	dbSNP_100	34	2675,5923	412.6+/-350.9	434,1807,2058	no	coding-synonymous	HNF1A	NM_000545.5		475,2254,3773	TT,TC,CC		31.1119,12.0064,24.6386		459/632	121435342	3204,9800	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	ACCACCCTGCAGC	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.1375C>T	12.37:g.121435342C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			C|0.718;T|0.282	0.282	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
CALCRL	10203	hgsc.bcm.edu	37	2	188245439	188245439	+	Missense_Mutation	SNP	A	A	G	rs61739909		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:188245439A>G	ENST00000409998.1	-	7	1041	c.260T>C	c.(259-261)cTc>cCc	p.L87P	AC007319.1_ENST00000453517.1_RNA|AC007319.1_ENST00000412276.1_RNA|CALCRL_ENST00000410068.1_Missense_Mutation_p.L87P|CALCRL_ENST00000392370.3_Missense_Mutation_p.L87P			Q16602	CALRL_HUMAN	calcitonin receptor-like	87					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			ATCAGGGCAGAGCTGCATTGA	0.408													A|||	1	0.000199681	0.0	0.0	5008	,	,		13904	0.0		0.001	False		,,,				2504	0.0				p.L87P		Atlas-SNP	.											.	CALCRL	73	.	0			c.T260C						PASS	.	A	PRO/LEU	0,4406		0,0,2203	68.0	66.0	67.0		260	-0.0	1.0	2	dbSNP_129	67	21,8579	14.6+/-50.1	1,19,4280	yes	missense	CALCRL	NM_005795.4	98	1,19,6483	GG,GA,AA		0.2442,0.0,0.1615	benign	87/462	188245439	21,12985	2203	4300	6503	SO:0001583	missense	10203	exon5			GGGCAGAGCTGCA	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"""GPCR / Class B : Calcitonin receptors"""	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.260T>C	2.37:g.188245439A>G	ENSP00000386972:p.Leu87Pro	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	174	96	0.551724	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.249542	0.39797	0.0	0.002442	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.46063	0.88;0.88;0.88	5.42	-0.0292	0.13919	GPCR, family 2, secretin-like, conserved site (1);GPCR, family 2, extracellular hormone receptor domain (3);	0.519591	0.18887	N	0.128407	T	0.15522	0.0374	N	0.04335	-0.225	0.47949	D	0.999551	B	0.31519	0.327	B	0.37267	0.245	T	0.25537	-1.0129	10	0.02654	T	1	.	4.3429	0.11119	0.518:0.1646:0.0:0.3174	.	87	Q16602	CALRL_HUMAN	P	87	ENSP00000376177:L87P;ENSP00000386972:L87P;ENSP00000387190:L87P	ENSP00000376177:L87P	L	-	2	0	CALCRL	187953684	0.998000	0.40836	0.996000	0.52242	0.996000	0.88848	0.409000	0.21082	-0.162000	0.10964	0.528000	0.53228	CTC	A|0.999;G|0.001	0.001	strong		0.408	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795	
SLC39A14	23516	hgsc.bcm.edu	37	8	22262321	22262321	+	Missense_Mutation	SNP	T	T	C	rs896378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22262321T>C	ENST00000381237.1	+	2	217	c.98T>C	c.(97-99)cTg>cCg	p.L33P	SLC39A14_ENST00000289952.5_Missense_Mutation_p.L33P|SLC39A14_ENST00000240095.6_Missense_Mutation_p.L33P|SLC39A14_ENST00000359741.5_Missense_Mutation_p.L33P	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	33			L -> P (in dbSNP:rs896378). {ECO:0000269|PubMed:15489334}.		cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		GCTTCATCCCTGGGTGCACCA	0.602													C|||	3150	0.628994	0.7617	0.5288	5008	,	,		18688	0.6974		0.504	False		,,,				2504	0.5787				p.L33P		Atlas-SNP	.											.	SLC39A14	59	.	0			c.T98C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	3134,1272	430.8+/-342.7	1107,920,176	93.0	94.0	94.0		98,98,98,98	-2.4	0.0	8	dbSNP_86	94	4056,4544	593.0+/-393.1	952,2152,1196	yes	missense,missense,missense,missense	SLC39A14	NM_001128431.2,NM_001135153.1,NM_001135154.1,NM_015359.4	98,98,98,98	2059,3072,1372	CC,CT,TT		47.1628,28.8697,44.7178	benign,benign,benign,benign	33/493,33/493,33/482,33/493	22262321	7190,5816	2203	4300	6503	SO:0001583	missense	23516	exon2			CATCCCTGGGTGC	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.98T>C	8.37:g.22262321T>C	ENSP00000370635:p.Leu33Pro	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Missense_Mutation	SNP	ENST00000381237.1	37	CCDS47823.1	1361	0.6231684981684982	364	0.7398373983739838	199	0.5497237569060773	414	0.7237762237762237	384	0.5065963060686016	C	9.809	1.182733	0.21870	0.711303	0.471628	ENSG00000104635	ENST00000359741;ENST00000520644;ENST00000240095;ENST00000381237;ENST00000289952;ENST00000524285;ENST00000520832;ENST00000519960;ENST00000522881;ENST00000517552	T;T;T;T;T;T;T;T;T;T	0.68025	-0.28;0.87;-0.3;-0.28;-0.28;0.87;0.73;0.78;0.78;0.79	5.48	-2.43	0.06522	.	1.717850	0.02385	N	0.079140	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42999	-0.9418	9	0.23891	T	0.37	0.4749	2.1354	0.03760	0.1041:0.3154:0.2047:0.3758	rs896378;rs17263733;rs17856493;rs896378	33;33;33	Q15043-2;Q15043;B6EU88	.;S39AE_HUMAN;.	P	33	ENSP00000352779:L33P;ENSP00000428789:L33P;ENSP00000240095:L33P;ENSP00000370635:L33P;ENSP00000289952:L33P;ENSP00000430315:L33P;ENSP00000428905:L33P;ENSP00000430629:L33P;ENSP00000429328:L33P;ENSP00000430564:L33P	ENSP00000240095:L33P	L	+	2	0	SLC39A14	22318266	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.407000	0.02488	-0.359000	0.08150	-0.355000	0.07637	CTG	C|0.584;N|0.000	0.584	strong		0.602	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993884	96993884	+	Silent	SNP	A	A	G	rs1048675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:96993884A>G	ENST00000439118.2	+	3	1766	c.1515A>G	c.(1513-1515)ccA>ccG	p.P505P	ITPRIPL1_ENST00000361124.4_Silent_p.P513P|ITPRIPL1_ENST00000536814.1_Silent_p.P497P|ITPRIPL1_ENST00000542887.1_Silent_p.P497P	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	505						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.P513P(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						TGACCATCCCAATCCCTAAGA	0.522													G|||	1903	0.379992	0.2784	0.317	5008	,	,		19077	0.2778		0.3191	False		,,,				2504	0.7301				p.P513P		Atlas-SNP	.											ITPRIPL1,NS,carcinoma,0,1	ITPRIPL1	58	1	1	Substitution - coding silent(1)	stomach(1)	c.A1539G						PASS	.	G	,,,	1245,3161	705.2+/-407.2	178,889,1136	69.0	67.0	68.0		1515,1491,1491,1539	-11.3	0.1	2	dbSNP_86	68	2885,5715	672.5+/-402.9	508,1869,1923	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ITPRIPL1	NM_001008949.2,NM_001163523.1,NM_001163524.1,NM_178495.5	,,,	686,2758,3059	GG,GA,AA		33.5465,28.2569,31.7546	,,,	505/556,497/548,497/548,513/564	96993884	4130,8876	2203	4300	6503	SO:0001819	synonymous_variant	150771	exon1			CATCCCAATCCCT		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"""KIAA1754-like"", ""inositol 1,4,5-triphosphate receptor interacting protein-like 1"""	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.1515A>G	2.37:g.96993884A>G		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	119	56	0.470588	NM_178495	F5H1L8|Q8NE61	Silent	SNP	ENST00000439118.2	37	CCDS46360.1	629	0.288003663003663	128	0.2601626016260163	113	0.31215469613259667	146	0.25524475524475526	242	0.31926121372031663	G	3.885	-0.025099	0.07589	0.282569	0.335465	ENSG00000198885	ENST00000420728	.	.	.	5.65	-11.3	0.00108	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.31482	P	0.667034	.	.	.	.	.	.	T	0.07809	-1.0753	3	.	.	.	-15.6452	7.7271	0.28765	0.3095:0.4735:0.1489:0.0681	rs1048675;rs3171926;rs58857385;rs1048675	.	.	.	R	537	.	.	Q	+	2	0	ITPRIPL1	96357611	0.012000	0.17670	0.061000	0.19648	0.970000	0.65996	-1.787000	0.01764	-2.991000	0.00279	-0.808000	0.03180	CAA	A|0.691;C|0.000;G|0.309	0.309	strong		0.522	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495	
FANCM	57697	hgsc.bcm.edu	37	14	45644589	45644589	+	Missense_Mutation	SNP	G	G	T	rs1367580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:45644589G>T	ENST00000267430.5	+	14	2717	c.2632G>T	c.(2632-2634)Gta>Tta	p.V878L	FANCM_ENST00000542564.2_Missense_Mutation_p.V852L	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	878			V -> L (in dbSNP:rs1367580). {ECO:0000269|PubMed:10997877}.		DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TATAGATTCTGTAGATAATGA	0.279								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				T|||	1163	0.232228	0.4478	0.1729	5008	,	,		17096	0.128		0.1282	False		,,,				2504	0.1973				p.V878L		Atlas-SNP	.											.	FANCM	225	.	0			c.G2632T						PASS	.	T	LEU/VAL	1460,2928		243,974,977	45.0	52.0	50.0		2632	4.1	0.0	14	dbSNP_88	50	1020,7556		62,896,3330	yes	missense	FANCM	NM_020937.2	32	305,1870,4307	TT,TG,GG		11.8937,33.2726,19.1299	benign	878/2049	45644589	2480,10484	2194	4288	6482	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GATTCTGTAGATA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.2632G>T	14.37:g.45644589G>T	ENSP00000267430:p.Val878Leu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	469	0.21474358974358973	228	0.4634146341463415	57	0.1574585635359116	75	0.13111888111888112	109	0.1437994722955145	T	0	-2.589270	0.00128	0.332726	0.118937	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.16324	2.94;2.93;2.35	5.24	4.08	0.47627	.	1.095180	0.06954	N	0.815069	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48536	-0.9027	9	0.02654	T	1	.	6.7797	0.23638	0.0:0.0815:0.1533:0.7651	rs1367580;rs3759676;rs52832869;rs61645397;rs1367580	852;878	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	L	878;852;394	ENSP00000267430:V878L;ENSP00000442493:V852L;ENSP00000452033:V394L	ENSP00000267430:V878L	V	+	1	0	FANCM	44714339	0.653000	0.27358	0.003000	0.11579	0.027000	0.11550	0.856000	0.27818	0.383000	0.24910	-0.335000	0.08231	GTA	G|0.796;T|0.204	0.204	strong		0.279	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447194	10447194	+	Missense_Mutation	SNP	T	T	G	rs73224493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:10447194T>G	ENST00000326756.3	-	3	1197	c.759A>C	c.(757-759)caA>caC	p.Q253H		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	253					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						ACCACTTATTTTGAAATGTAG	0.413													T|||	34	0.00678914	0.0	0.0086	5008	,	,		20499	0.0		0.0129	False		,,,				2504	0.0153				p.Q253H		Atlas-SNP	.											.	ZNF518B	116	.	0			c.A759C						PASS	.	T	HIS/GLN	12,4394	19.1+/-41.9	0,12,2191	201.0	201.0	201.0		759	-8.6	0.0	4	dbSNP_130	201	178,8422	80.6+/-143.3	3,172,4125	yes	missense	ZNF518B	NM_053042.2	24	3,184,6316	GG,GT,TT		2.0698,0.2724,1.4609	probably-damaging	253/1075	10447194	190,12816	2203	4300	6503	SO:0001583	missense	85460	exon3			CTTATTTTGAAAT	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.759A>C	4.37:g.10447194T>G	ENSP00000317614:p.Gln253His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	15	0.006868131868131868	0	0.0	5	0.013812154696132596	0	0.0	10	0.013192612137203167	T	25.7	4.661540	0.88154	0.002724	0.020698	ENSG00000178163	ENST00000326756	T	0.01705	4.68	6.17	-8.62	0.00881	.	0.669526	0.13673	N	0.370739	T	0.00552	0.0018	L	0.29908	0.895	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.45338	-0.9268	10	0.62326	D	0.03	-7.1486	1.381	0.02230	0.1578:0.268:0.2401:0.3342	.	253	Q9C0D4	Z518B_HUMAN	H	253	ENSP00000317614:Q253H	ENSP00000317614:Q253H	Q	-	3	2	ZNF518B	10056292	0.004000	0.15560	0.000000	0.03702	0.595000	0.36748	-0.737000	0.04877	-1.440000	0.01960	0.533000	0.62120	CAA	T|0.987;G|0.013	0.013	strong		0.413	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
IVL	3713	hgsc.bcm.edu	37	1	152883608	152883608	+	Silent	SNP	G	G	A	rs7545413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152883608G>A	ENST00000368764.3	+	2	1399	c.1335G>A	c.(1333-1335)caG>caA	p.Q445Q	IVL_ENST00000392667.2_Silent_p.Q299Q			P07476	INVO_HUMAN	involucrin	445	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ATCTGGAGCAGCAGCAGGGGC	0.632													g|||	2065	0.41234	0.6808	0.2997	5008	,	,		19909	0.5615		0.1083	False		,,,				2504	0.2883				p.Q445Q		Atlas-SNP	.											.	IVL	100	.	0			c.G1335A						PASS	.	G		2399,1957		689,1021,468	22.0	26.0	25.0		1335	2.2	0.0	1	dbSNP_116	25	760,7786		39,682,3552	no	coding-synonymous	IVL	NM_005547.2		728,1703,4020	AA,AG,GG		8.893,44.9265,24.4846		445/586	152883608	3159,9743	2178	4273	6451	SO:0001819	synonymous_variant	3713	exon2			GGAGCAGCAGCAG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1335G>A	1.37:g.152883608G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_005547	Q5T7P4	Silent	SNP	ENST00000368764.3	37	CCDS1030.1																																																																																			G|0.664;A|0.336	0.336	strong		0.632	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
FAM46D	169966	hgsc.bcm.edu	37	X	79698593	79698593	+	Missense_Mutation	SNP	C	C	G	rs1113265	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:79698593C>G	ENST00000308293.5	+	3	794	c.555C>G	c.(553-555)gaC>gaG	p.D185E	FAM46D_ENST00000538312.1_Missense_Mutation_p.D185E	NM_152630.4	NP_689843.1	Q8NEK8	FA46D_HUMAN	family with sequence similarity 46, member D	185			D -> E (in dbSNP:rs1113265). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.							kidney(1)|large_intestine(6)|liver(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23						CCATGTTAGACTTCTACAGTG	0.388													C|||	1406	0.37245	0.2685	0.4207	3775	,	,		15522	0.0615		0.5199	False		,,,				2504	0.1779				p.D185E		Atlas-SNP	.											.	FAM46D	69	.	0			c.C555G						PASS	.	C	GLU/ASP,GLU/ASP	1500,2332		247,778,228,606,342	67.0	64.0	65.0		555,555	-8.8	0.1	X	dbSNP_86	65	4774,1951		1219,991,1345,217,526	yes	missense,missense	FAM46D	NM_001170574.1,NM_152630.4	45,45	1466,1769,1573,823,868	GG,GC,G,CC,C		29.0112,39.1441,40.5702	benign,benign	185/390,185/390	79698593	6274,4283	2201	4298	6499	SO:0001583	missense	169966	exon5			GTTAGACTTCTAC	BX537938	CCDS14446.1	Xq21.1	2009-08-18			ENSG00000174016	ENSG00000174016			28399	protein-coding gene	gene with protein product	"""cancer/testis antigen 112"""					12477932	Standard	NM_152630		Approved	MGC26999, CT1.26, CT112	uc004edl.1	Q8NEK8	OTTHUMG00000021902	ENST00000308293.5:c.555C>G	X.37:g.79698593C>G	ENSP00000308575:p.Asp185Glu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	62	62	1	NM_001170574	B2R9Q6|Q7Z3F6|Q8NHU1	Missense_Mutation	SNP	ENST00000308293.5	37	CCDS14446.1	709	0.4273658830620856	85	0.20238095238095238	107	0.41796875	23	0.04151624548736462	278	0.5325670498084292	C	0.008	-1.924635	0.00493	0.391441	0.709888	ENSG00000174016	ENST00000538312;ENST00000308293	T;T	0.21031	2.03;2.03	4.8	-8.75	0.00834	Domain of unknown function DUF1693 (1);	2.784390	0.01166	N	0.006750	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.45131	-0.9282	9	0.02654	T	1	-0.0151	3.1878	0.06607	0.2954:0.0963:0.0925:0.5158	rs1113265;rs1113265	185	Q8NEK8	FA46D_HUMAN	E	185	ENSP00000443410:D185E;ENSP00000308575:D185E	ENSP00000308575:D185E	D	+	3	2	FAM46D	79585249	0.482000	0.25948	0.050000	0.19076	0.702000	0.40608	-0.369000	0.07533	-2.291000	0.00666	-0.996000	0.02517	GAC	C|0.503;0|0.028	.	strong		0.388	FAM46D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057338.1	NM_152630	
FAM207A	85395	hgsc.bcm.edu	37	21	46396659	46396659	+	Missense_Mutation	SNP	G	G	C	rs3737075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46396659G>C	ENST00000291634.6	+	6	682	c.634G>C	c.(634-636)Gtg>Ctg	p.V212L	FAM207A_ENST00000479127.1_3'UTR|FAM207A_ENST00000397826.3_Missense_Mutation_p.V197L	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	212			V -> L (in dbSNP:rs3737075).														CAGCCCCCTGGTGGCCATCGG	0.632													G|||	762	0.152157	0.2042	0.2522	5008	,	,		15848	0.1091		0.165	False		,,,				2504	0.0419				p.V212L		Atlas-SNP	.											.	.	.	.	0			c.G634C						PASS	.	G	LEU/VAL	905,3417		109,687,1365	11.0	12.0	12.0		634	0.0	1.0	21	dbSNP_107	12	1335,7185		112,1111,3037	no	missense	FAM207A	NM_058190.2	32	221,1798,4402	CC,CG,GG		15.669,20.9394,17.4428	benign	212/231	46396659	2240,10602	2161	4260	6421	SO:0001583	missense	85395	exon6			CCCCTGGTGGCCA		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.634G>C	21.37:g.46396659G>C	ENSP00000291634:p.Val212Leu	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	32	8	0.25	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	37	CCDS13718.1	364	0.16666666666666666	104	0.21138211382113822	67	0.1850828729281768	66	0.11538461538461539	127	0.16754617414248021	G	0.367	-0.935981	0.02340	0.209394	0.15669	ENSG00000160256	ENST00000291634;ENST00000397826	T;T	0.41065	1.01;1.01	4.35	0.0344	0.14183	.	0.627114	0.15229	N	0.273539	T	0.00012	0.0000	N	0.01352	-0.895	0.46478	P	9.320000000000439E-4	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.27331	-1.0077	9	0.02654	T	1	-6.2649	2.8182	0.05464	0.1701:0.3614:0.364:0.1045	rs3737075;rs4819002;rs60509357	197;212	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	L	212;197	ENSP00000291634:V212L;ENSP00000380926:V197L	ENSP00000291634:V212L	V	+	1	0	C21orf70	45221087	0.000000	0.05858	0.967000	0.41034	0.040000	0.13550	-0.231000	0.09069	0.181000	0.19994	-0.321000	0.08615	GTG	G|0.835;C|0.165	0.165	strong		0.632	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190	
COL18A1	80781	hgsc.bcm.edu	37	21	46896312	46896312	+	Silent	SNP	G	G	T	rs2230688	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46896312G>T	ENST00000359759.4	+	5	2112	c.2091G>T	c.(2089-2091)acG>acT	p.T697T	COL18A1_ENST00000400337.2_Silent_p.T282T|COL18A1_ENST00000355480.5_Silent_p.T462T			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	697	Nonhelical region 1 (NC1).				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)		CCGTCACCACGCCACCCTTGG	0.637													T|||	1141	0.227835	0.3744	0.1225	5008	,	,		16215	0.2927		0.0984	False		,,,				2504	0.1708				p.T462T		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1386T						PASS	.	T	,	1253,2817		203,847,985	50.0	54.0	52.0		1386,846	0.7	0.1	21	dbSNP_98	52	801,7539		42,717,3411	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	245,1564,4396	TT,TG,GG		9.6043,30.7862,16.5512	,	462/1520,282/1340	46896312	2054,10356	2035	4170	6205	SO:0001819	synonymous_variant	80781	exon5			CACCACGCCACCC		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.2091G>T	21.37:g.46896312G>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				A|0.000;C|0.000;G|0.800;T|0.199	0.199	strong		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
KCNE1L	23630	hgsc.bcm.edu	37	X	108868153	108868153	+	Missense_Mutation	SNP	G	G	A	rs17003955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:108868153G>A	ENST00000372101.2	-	1	240	c.97C>T	c.(97-99)Cct>Tct	p.P33S		NM_012282.2	NP_036414.1	Q9UJ90	KCE1L_HUMAN	KCNE1-like	33			P -> S (in dbSNP:rs17003955).		atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|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 transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cation channel activity (GO:2001257)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)			endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	6						CTGGGACGAGGGCCAGCGCCC	0.662													G|||	196	0.0519205	0.0023	0.0447	3775	,	,		5645	0.001		0.1292	False		,,,				2504	0.0317				p.P33S		Atlas-SNP	.											.	KCNE1L	8	.	0			c.C97T						PASS	.	G	SER/PRO	63,3719		1,53,8,1561,544	13.0	12.0	13.0		97	1.0	0.0	X	dbSNP_123	13	946,5695		35,595,281,1768,1564	yes	missense	KCNE1L	NM_012282.2	74	36,648,289,3329,2108	AA,AG,A,GG,G		14.2448,1.6658,9.6805	probably-damaging	33/143	108868153	1009,9414	2167	4243	6410	SO:0001583	missense	23630	exon1			GACGAGGGCCAGC	AJ012743	CCDS14547.1	Xq22.3	2008-02-05	2004-06-09		ENSG00000176076	ENSG00000176076		"""Potassium channels"""	6241	protein-coding gene	gene with protein product		300328	"""potassium voltage-gated channel, Isk-related family, member 1-like"""			10493825	Standard	NM_012282		Approved		uc004eoh.3	Q9UJ90	OTTHUMG00000022189	ENST00000372101.2:c.97C>T	X.37:g.108868153G>A	ENSP00000361173:p.Pro33Ser	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	20	19	0.95	NM_012282		Missense_Mutation	SNP	ENST00000372101.2	37	CCDS14547.1	117	0.0705244122965642	2	0.0040650406504065045	15	0.04261363636363636	1	0.0017482517482517483	80	0.11267605633802817	G	0.016	-1.531352	0.00951	0.016658	0.142448	ENSG00000176076	ENST00000372101	T	0.69040	-0.37	3.83	1.04	0.20106	.	0.800139	0.11004	N	0.610174	T	0.00328	0.0010	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.05037	-1.0910	9	0.38643	T	0.18	-10.6832	0.5599	0.00677	0.3188:0.1707:0.3329:0.1777	rs17003955	33	Q9UJ90	KCE1L_HUMAN	S	33	ENSP00000361173:P33S	ENSP00000361173:P33S	P	-	1	0	KCNE1L	108754809	0.385000	0.25172	0.005000	0.12908	0.016000	0.09150	1.045000	0.30341	0.085000	0.17107	0.292000	0.19580	CCT	0|0.009;A|0.075	0.075	strong		0.662	KCNE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057892.1	NM_012282	
ENPP7	339221	hgsc.bcm.edu	37	17	77704912	77704912	+	Missense_Mutation	SNP	T	T	C	rs8074547	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:77704912T>C	ENST00000328313.5	+	1	232	c.11T>C	c.(10-12)cTg>cCg	p.L4P		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)			ATGAGAGGCCTGGCCGTCCTC	0.662													C|||	2518	0.502796	0.6543	0.3314	5008	,	,		16389	0.5159		0.3777	False		,,,				2504	0.5348				p.L4P		Atlas-SNP	.											.	ENPP7	63	.	0			c.T11C						PASS	.	C	PRO/LEU	2436,1854		728,980,437	12.0	14.0	13.0		11	-8.9	0.0	17	dbSNP_116	13	3025,5387		579,1867,1760	no	missense	ENPP7	NM_178543.3	98	1307,2847,2197	CC,CT,TT		35.9605,43.2168,42.9932	benign	4/459	77704912	5461,7241	2145	4206	6351	SO:0001583	missense	339221	exon1			GAGGCCTGGCCGT	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.11T>C	17.37:g.77704912T>C	ENSP00000332656:p.Leu4Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	1035	0.4739010989010989	322	0.6544715447154471	125	0.3453038674033149	311	0.5437062937062938	277	0.3654353562005277	C	7.464	0.645289	0.14451	0.567832	0.359605	ENSG00000182156	ENST00000328313	T	0.75704	-0.96	4.59	-8.85	0.00799	.	2.885830	0.01093	N	0.005223	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	0.23154	-1.0196	9	0.49607	T	0.09	3.7928	2.7864	0.05375	0.169:0.1576:0.4144:0.2591	rs8074547;rs17857254;rs60998994	4	Q6UWV6	ENPP7_HUMAN	P	4	ENSP00000332656:L4P	ENSP00000332656:L4P	L	+	2	0	ENPP7	75319507	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.578000	0.02125	-1.753000	0.01323	-0.974000	0.02594	CTG	T|0.556;C|0.444	0.444	strong		0.662	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
KCNG4	93107	hgsc.bcm.edu	37	16	84270476	84270476	+	Missense_Mutation	SNP	G	G	A	rs11646443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84270476G>A	ENST00000308251.4	-	2	684	c.616C>T	c.(616-618)Cgg>Tgg	p.R206W	KCNG4_ENST00000568181.1_Missense_Mutation_p.R206W	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	206			R -> W (in dbSNP:rs11646443).		protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						TCGCGCAGCCGGTTCATGCAC	0.682													G|||	1371	0.273762	0.2262	0.2507	5008	,	,		15093	0.1161		0.3628	False		,,,				2504	0.4254				p.R206W		Atlas-SNP	.											.	KCNG4	71	.	0			c.C616T						PASS	.	G	TRP/ARG	1081,3315		131,819,1248	26.0	28.0	27.0		616	3.0	0.4	16	dbSNP_120	27	2877,5719		495,1887,1916	yes	missense	KCNG4	NM_172347.2	101	626,2706,3164	AA,AG,GG		33.4691,24.5905,30.4649	benign	206/520	84270476	3958,9034	2198	4298	6496	SO:0001583	missense	93107	exon2			GCAGCCGGTTCAT	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.616C>T	16.37:g.84270476G>A	ENSP00000312129:p.Arg206Trp	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	519	0.23763736263736263	94	0.1910569105691057	91	0.2513812154696133	62	0.10839160839160839	272	0.35883905013192613	G	11.56	1.675051	0.29783	0.245905	0.334691	ENSG00000168418	ENST00000308251	D	0.97016	-4.21	5.11	3.0	0.34707	.	0.882556	0.09392	U	0.808448	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.21381	0.028;0.055	B;B	0.14578	0.009;0.011	T	0.04386	-1.0955	9	0.39692	T	0.17	.	5.8407	0.18633	0.0983:0.0:0.4371:0.4646	rs11646443;rs17736772;rs11646443	206;206	Q8TDN1;Q8TDN1-2	KCNG4_HUMAN;.	W	206	ENSP00000312129:R206W	ENSP00000312129:R206W	R	-	1	2	KCNG4	82827977	0.249000	0.23941	0.367000	0.25926	0.856000	0.48823	1.442000	0.35046	0.386000	0.24997	0.549000	0.68633	CGG	G|0.721;A|0.279	0.279	strong		0.682	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
MUC5B	727897	hgsc.bcm.edu	37	11	1266479	1266479	+	Missense_Mutation	SNP	G	G	T	rs202133597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1266479G>T	ENST00000529681.1	+	31	8427	c.8369G>T	c.(8368-8370)gGg>gTg	p.G2790V	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.G2793V	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2790	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)		CCTTCCACGGGGACTTCCCAC	0.667																																					p.G2790V		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.G8369T						scavenged	.						19.0	24.0	22.0					11																	1266479		1776	3932	5708	SO:0001583	missense	727897	exon31			CCACGGGGACTTC	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.8369G>T	11.37:g.1266479G>T	ENSP00000436812:p.Gly2790Val	Somatic	333	6	0.018018		WXS	Illumina HiSeq	Phase_I	350	16	0.0457143	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	2.799	-0.249517	0.05867	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.24723	1.84;2.02	1.58	-1.18	0.09617	.	.	.	.	.	T	0.06050	0.0157	N	0.00436	-1.5	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31447	-0.9943	9	0.87932	D	0	.	3.1646	0.06531	0.0:0.421:0.2369:0.3421	.	3373;2793	A7Y9J9;E9PBJ0	.;.	V	2790;2793;2762;2750	ENSP00000436812:G2790V;ENSP00000415793:G2793V	ENSP00000343037:G2762V	G	+	2	0	MUC5B	1223055	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-4.009000	0.00314	-0.877000	0.04012	-1.241000	0.01538	GGG	G|0.728;T|0.273	0.273	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SHROOM2	357	hgsc.bcm.edu	37	X	9863112	9863112	+	Silent	SNP	A	A	G	rs6530341	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:9863112A>G	ENST00000380913.3	+	4	1254	c.1164A>G	c.(1162-1164)ccA>ccG	p.P388P		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	388					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				CGGGCTGCCCACAGGAGGCCC	0.677													A|||	786	0.208212	0.1672	0.1974	3775	,	,		10580	0.2669		0.0905	False		,,,				2504	0.0695				p.P388P		Atlas-SNP	.											.	SHROOM2	139	.	0			c.A1164G						PASS	.	A		865,2957		89,557,130,984,432	19.0	16.0	17.0		1164	-8.6	0.0	X	dbSNP_116	17	928,5788		49,587,243,1791,1619	no	coding-synonymous	SHROOM2	NM_001649.2		138,1144,373,2775,2051	GG,GA,G,AA,A		13.8177,22.6321,17.0146		388/1617	9863112	1793,8745	2192	4289	6481	SO:0001819	synonymous_variant	357	exon4			CTGCCCACAGGAG	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.1164A>G	X.37:g.9863112A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	37	CCDS14135.1																																																																																			A|0.805;0|0.004	.	strong		0.677	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388350	1388350	+	Silent	SNP	G	G	A	rs77782813		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388350G>A	ENST00000324803.4	+	1	3011	c.51G>A	c.(49-51)acG>acA	p.T17T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	17					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTGCTCACACGTGCCCATGTG	0.577																																					p.T17T		Atlas-SNP	.											.	CRIPAK	185	.	0			c.G51A						PASS	.	G		1231,3175		0,1231,972	148.0	151.0	150.0		51	-0.8	0.0	4	dbSNP_131	150	2931,5669		0,2931,1369	no	coding-synonymous	CRIPAK	NM_175918.3		0,4162,2341	AA,AG,GG		34.0814,27.9392,32.0006		17/447	1388350	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	285464	exon1			TCACACGTGCCCA	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.51G>A	4.37:g.1388350G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	176	29	0.164773	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																			G|0.858;A|0.142	0.142	strong		0.577	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
TUBAL3	79861	hgsc.bcm.edu	37	10	5435918	5435918	+	Silent	SNP	G	G	A	rs7097775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5435918G>A	ENST00000380419.3	-	4	940	c.903C>T	c.(901-903)gcC>gcT	p.A301A	TUBAL3_ENST00000479328.1_Silent_p.A261A	NM_024803.2	NP_079079.1	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	301					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.A301A(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(7)|prostate(2)|skin(3)	25						ACTCAAAGCAGGCAGTGGTGA	0.537													G|||	3346	0.668131	0.7436	0.7695	5008	,	,		22968	0.6478		0.6561	False		,,,				2504	0.5276				p.A301A		Atlas-SNP	.											TUBAL3,NS,carcinoma,0,1	TUBAL3	54	1	2	Substitution - coding silent(2)	prostate(2)	c.C903T						PASS	.	G	,	3206,1200	709.5+/-407.8	1177,852,174	132.0	123.0	126.0		783,903	-3.2	0.9	10	dbSNP_116	126	5524,3076	659.9+/-401.7	1773,1978,549	no	coding-synonymous,coding-synonymous	TUBAL3	NM_001171864.1,NM_024803.2	,	2950,2830,723	AA,AG,GG		35.7674,27.2356,32.8771	,	261/407,301/447	5435918	8730,4276	2203	4300	6503	SO:0001819	synonymous_variant	79861	exon4			AAAGCAGGCAGTG	AK025318	CCDS7066.2, CCDS53491.1	10p15.1	2007-03-15			ENSG00000178462	ENSG00000178462		"""Tubulins"""	23534	protein-coding gene	gene with protein product							Standard	NM_024803		Approved	FLJ21665	uc001ihy.3	A6NHL2	OTTHUMG00000017595	ENST00000380419.3:c.903C>T	10.37:g.5435918G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	139	59	0.42446	NM_024803	B4DKL2|Q4QQJ5|Q9H6Z0	Silent	SNP	ENST00000380419.3	37	CCDS7066.2																																																																																			G|0.324;A|0.676	0.676	strong		0.537	TUBAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046548.2	NM_024803	
PLEKHD1	400224	hgsc.bcm.edu	37	14	69966850	69966850	+	Silent	SNP	G	G	A	rs4902723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:69966850G>A	ENST00000322564.7	+	2	380	c.168G>A	c.(166-168)gaG>gaA	p.E56E		NM_001161498.1	NP_001154970.1	A6NEE1	PLHD1_HUMAN	pleckstrin homology domain containing, family D (with coiled-coil domains) member 1	56	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(1)|endometrium(1)|kidney(2)	4						TCATCAAAGAGAGCTTTCTGC	0.488													G|||	662	0.132188	0.1747	0.1556	5008	,	,		20606	0.0446		0.1282	False		,,,				2504	0.1524				p.E56E		Atlas-SNP	.											.	PLEKHD1	24	.	0			c.G168A						PASS	.	G		211,1173		16,179,497	126.0	110.0	115.0		168	2.5	1.0	14	dbSNP_111	115	461,2721		28,405,1158	no	coding-synonymous	PLEKHD1	NM_001161498.1		44,584,1655	AA,AG,GG		14.4877,15.2457,14.7175		56/507	69966850	672,3894	692	1591	2283	SO:0001819	synonymous_variant	400224	exon2			CAAAGAGAGCTTT	AK126770	CCDS53903.1	14q24.1	2013-01-10	2011-05-04		ENSG00000175985	ENSG00000175985		"""Pleckstrin homology (PH) domain containing"""	20148	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family D (with M protein repeats) member 1"""				Standard	NM_001161498		Approved	UPF0639	uc010ttf.1	A6NEE1		ENST00000322564.7:c.168G>A	14.37:g.69966850G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	127	48	0.377953	NM_001161498	B9EJC2	Silent	SNP	ENST00000322564.7	37	CCDS53903.1																																																																																			G|0.881;A|0.119	0.119	strong		0.488	PLEKHD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412451.2	NM_001161498	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596641	48596641	+	Silent	SNP	A	A	G	rs75539159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48596641A>G	ENST00000310248.2	-	1	529	c.435T>C	c.(433-435)ctT>ctC	p.L145L		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	145						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						CAGTTCCCACAAGCCTGACAC	0.478													a|||	123	0.0245607	0.0076	0.0317	5008	,	,		24313	0.0		0.0815	False		,,,				2504	0.0092				p.L145L		Atlas-SNP	.											.	OR10AD1	24	.	0			c.T435C						PASS	.	-		90,4316	76.2+/-114.5	0,90,2113	75.0	67.0	70.0		435	-0.4	0.0	12	dbSNP_131	70	713,7887	174.6+/-224.8	27,659,3614	no	coding-synonymous	OR10AD1	NM_001004134.1		27,749,5727	GG,GA,AA		8.2907,2.0427,6.1741		145/318	48596641	803,12203	2203	4300	6503	SO:0001819	synonymous_variant	121275	exon1			TCCCACAAGCCTG		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.435T>C	12.37:g.48596641A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	169	71	0.420118	NM_001004134	B9EGT9|Q6IFA8	Silent	SNP	ENST00000310248.2	37	CCDS31787.1																																																																																			A|0.949;G|0.051	0.051	strong		0.478	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
LRIG1	26018	hgsc.bcm.edu	37	3	66434643	66434643	+	Missense_Mutation	SNP	T	T	C	rs2306272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:66434643T>C	ENST00000273261.3	-	14	2367	c.1843A>G	c.(1843-1845)Atg>Gtg	p.M615V	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.M639V	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	615	Ig-like C2-type 2.		M -> V (in dbSNP:rs2306272). {ECO:0000269|PubMed:11414704, ECO:0000269|PubMed:17974005}.		innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AGGCGGGCCATGGTGGTGGTC	0.577													T|||	1814	0.36222	0.1513	0.2435	5008	,	,		17527	0.7341		0.2922	False		,,,				2504	0.4202				p.M615V		Atlas-SNP	.											.	LRIG1	138	.	0			c.A1843G						PASS	.	T	VAL/MET	637,3769	274.6+/-272.0	45,547,1611	192.0	184.0	186.0		1843	5.0	1.0	3	dbSNP_100	186	2358,6242	394.7+/-344.8	337,1684,2279	yes	missense	LRIG1	NM_015541.2	21	382,2231,3890	CC,CT,TT		27.4186,14.4576,23.0278	benign	615/1094	66434643	2995,10011	2203	4300	6503	SO:0001583	missense	26018	exon14			GGGCCATGGTGGT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1843A>G	3.37:g.66434643T>C	ENSP00000273261:p.Met615Val	Somatic	272	2	0.00735294		WXS	Illumina HiSeq	Phase_I	276	273	0.98913	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	830	0.38003663003663	82	0.16666666666666666	106	0.292817679558011	418	0.7307692307692307	224	0.2955145118733509	T	8.389	0.839336	0.16891	0.144576	0.274186	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.65916	1.06;-0.18	6.17	5.0	0.66597	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.379169	0.31936	N	0.006822	T	0.00012	0.0000	N	0.05467	-0.045	0.34993	P	0.24476699999999996	B;B	0.13145	0.006;0.007	B;B	0.19666	0.015;0.026	T	0.37596	-0.9699	9	0.27082	T	0.32	.	12.8497	0.57850	0.1223:0.0:0.0:0.8776	rs2306272;rs52808080;rs59543444;rs2306272	639;615	Q96JA1-2;Q96JA1	.;LRIG1_HUMAN	V	615;639;518	ENSP00000273261:M615V;ENSP00000373208:M639V	ENSP00000273261:M615V	M	-	1	0	LRIG1	66517333	0.990000	0.36364	0.989000	0.46669	0.306000	0.27790	6.232000	0.72313	1.126000	0.42016	0.533000	0.62120	ATG	T|0.707;C|0.293	0.293	strong		0.577	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
ERAP2	64167	hgsc.bcm.edu	37	5	96231056	96231056	+	Missense_Mutation	SNP	T	T	G	rs34261036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96231056T>G	ENST00000437043.3	+	7	1943	c.1232T>G	c.(1231-1233)cTg>cGg	p.L411R	ERAP2_ENST00000379904.4_Missense_Mutation_p.L366R|CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	411			L -> R (in dbSNP:rs34261036).		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)		TATCCAGAGCTGCAATTTGTA	0.343													T|||	13	0.00259585	0.0015	0.0	5008	,	,		17876	0.0		0.002	False		,,,				2504	0.0092				p.L411R		Atlas-SNP	.											.	ERAP2	77	.	0			c.T1232G						PASS	.	T	ARG/LEU,ARG/LEU	4,4402	8.1+/-20.4	0,4,2199	136.0	133.0	134.0		1232,1232	4.7	0.7	5	dbSNP_126	134	41,8559	27.4+/-76.7	0,41,4259	yes	missense,missense	ERAP2	NM_001130140.1,NM_022350.3	102,102	0,45,6458	GG,GT,TT		0.4767,0.0908,0.346	probably-damaging,probably-damaging	411/961,411/961	96231056	45,12961	2203	4300	6503	SO:0001583	missense	64167	exon7			CAGAGCTGCAATT	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.1232T>G	5.37:g.96231056T>G	ENSP00000400376:p.Leu411Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	0	0.0	3	0.00395778364116095	T	18.69	3.677983	0.68042	9.08E-4	0.004767	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904	T;T;T;T	0.02763	4.17;4.17;4.17;4.17	4.74	4.74	0.60224	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.50627	D	0.000108	T	0.16557	0.0398	M	0.84683	2.71	0.80722	D	1	D;P	0.57571	0.98;0.915	D;D	0.72982	0.964;0.979	T	0.00380	-1.1776	10	0.87932	D	0	.	13.5065	0.61486	0.0:0.0:0.0:1.0	rs34261036	366;411	Q6P179-3;Q6P179	.;ERAP2_HUMAN	R	411;411;411;366	ENSP00000400376:L411R;ENSP00000421175:L411R;ENSP00000421849:L411R;ENSP00000369235:L366R	ENSP00000369235:L366R	L	+	2	0	ERAP2	96256812	0.989000	0.36119	0.697000	0.30258	0.966000	0.64601	5.502000	0.66956	1.904000	0.55121	0.460000	0.39030	CTG	T|0.997;G|0.003	0.003	strong		0.343	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
CPS1	1373	hgsc.bcm.edu	37	2	211481257	211481257	+	Silent	SNP	C	C	G	rs2287599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211481257C>G	ENST00000233072.5	+	21	2875	c.2679C>G	c.(2677-2679)ggC>ggG	p.G893G	CPS1_ENST00000430249.2_Silent_p.G899G|CPS1_ENST00000451903.2_Silent_p.G442G	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	893					anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CACTGAAAGGCCTCAACAGGT	0.393													G|||	3251	0.649161	0.9107	0.4885	5008	,	,		17249	0.5248		0.5537	False		,,,				2504	0.636				p.G899G		Atlas-SNP	.											.	CPS1	485	.	0			c.C2697G						PASS	.	G	,,	3783,623	269.2+/-268.9	1624,535,44	144.0	146.0	146.0		2697,1326,2679	-0.1	1.0	2	dbSNP_100	146	4830,3770	531.5+/-382.0	1333,2164,803	no	coding-synonymous,coding-synonymous,coding-synonymous	CPS1	NM_001122633.2,NM_001122634.2,NM_001875.4	,,	2957,2699,847	GG,GC,CC		43.8372,14.1398,33.7767	,,	899/1507,442/1050,893/1501	211481257	8613,4393	2203	4300	6503	SO:0001819	synonymous_variant	1373	exon22			GAAAGGCCTCAAC	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.2679C>G	2.37:g.211481257C>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	37	CCDS2393.1																																																																																			C|0.357;G|0.643	0.643	strong		0.393	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
DLG1	1739	hgsc.bcm.edu	37	3	196865242	196865242	+	Missense_Mutation	SNP	C	C	T	rs1134986	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196865242C>T	ENST00000419354.1	-	10	1119	c.833G>A	c.(832-834)cGa>cAa	p.R278Q	DLG1_ENST00000450955.1_Missense_Mutation_p.R245Q|DLG1_ENST00000392382.2_Missense_Mutation_p.R245Q|DLG1_ENST00000448528.2_Missense_Mutation_p.R278Q|DLG1_ENST00000422288.1_Missense_Mutation_p.R227Q|DLG1_ENST00000357674.4_Missense_Mutation_p.R245Q|DLG1_ENST00000443183.1_Missense_Mutation_p.R162Q|DLG1_ENST00000346964.2_Missense_Mutation_p.R278Q|DLG1_ENST00000452595.1_Missense_Mutation_p.R162Q|DLG1_ENST00000314062.3_Missense_Mutation_p.R227Q			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	278	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.		R -> Q (in dbSNP:rs1134986). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7937897}.		actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TTCATTTACTCGTAATATACA	0.274													C|||	641	0.127995	0.0106	0.1225	5008	,	,		11825	0.0714		0.1441	False		,,,				2504	0.3323				p.R278Q		Atlas-SNP	.											.	DLG1	120	.	0			c.G833A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	111,4293	85.3+/-124.0	1,109,2092	98.0	87.0	91.0		833,734,485,485,833	5.3	1.0	3	dbSNP_86	91	1267,7333	248.6+/-276.2	77,1113,3110	yes	missense,missense,missense,missense,missense	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	43,43,43,43,43	78,1222,5202	TT,TC,CC		14.7326,2.5204,10.5967	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	278/905,245/893,162/801,162/789,278/927	196865242	1378,11626	2202	4300	6502	SO:0001583	missense	1739	exon10			TTTACTCGTAATA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.833G>A	3.37:g.196865242C>T	ENSP00000407531:p.Arg278Gln	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001098424	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	37	CCDS43194.1	201	0.09203296703296704	12	0.024390243902439025	41	0.1132596685082873	45	0.07867132867132867	103	0.1358839050131926	C	18.79	3.698977	0.68501	0.025204	0.147326	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000452595;ENST00000422288;ENST00000448528;ENST00000443183;ENST00000392382;ENST00000450955;ENST00000447466	T;T;T;T;T;T;T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74;1.74	5.31	5.31	0.75309	PDZ/DHR/GLGF (4);	0.071278	0.56097	D	0.000038	T	0.00210	0.0006	N	0.17922	0.545	0.09310	P	0.999999887938	P;P;D;D;D;P;D	0.76494	0.579;0.799;0.999;0.999;0.999;0.919;0.999	B;B;D;D;D;P;D	0.68039	0.219;0.124;0.909;0.909;0.955;0.475;0.955	T	0.01748	-1.1282	9	0.41790	T	0.15	.	18.3166	0.90223	0.0:1.0:0.0:0.0	rs1134986;rs1949471;rs3197402;rs17419616;rs52815342;rs61476238;rs1134986	245;162;162;162;245;278;278	Q12959-4;E9PG21;E7EWL7;B4DGU1;Q12959-3;Q12959;Q12959-2	.;.;.;.;.;DLG1_HUMAN;.	Q	278;278;245;278;227;278;162;227;278;162;245;245;87	ENSP00000345731:R278Q;ENSP00000350303:R245Q;ENSP00000321087:R227Q;ENSP00000407531:R278Q;ENSP00000398939:R162Q;ENSP00000413238:R227Q;ENSP00000391732:R278Q;ENSP00000396658:R162Q;ENSP00000376187:R245Q;ENSP00000411278:R245Q;ENSP00000398702:R87Q	ENSP00000321087:R227Q	R	-	2	0	DLG1	198349639	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.445000	0.80570	2.633000	0.89246	0.563000	0.77884	CGA	C|0.882;T|0.118	0.118	strong		0.274	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
FHAD1	114827	hgsc.bcm.edu	37	1	15599025	15599025	+	Splice_Site	SNP	G	G	A	rs75432354	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15599025G>A	ENST00000375998.4	+	2	300	c.300G>A	c.(298-300)ccG>ccA	p.P100P	FHAD1_ENST00000358897.4_Splice_Site_p.P100P|FHAD1_ENST00000417793.1_Splice_Site_p.P100P|FHAD1_ENST00000375999.3_Splice_Site_p.P100P			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	100	Pro-rich.									skin(1)|stomach(1)	2						ATCCACCTCCGGTGAGTCCGG	0.592											OREG0013125	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	639	0.127596	0.0234	0.1571	5008	,	,		17268	0.1409		0.164	False		,,,				2504	0.1963				p.P100P		Atlas-SNP	.											.	FHAD1	78	.	0			c.G300A						PASS	.	G		51,1333		1,49,642	28.0	26.0	27.0		300	3.3	0.9	1	dbSNP_131	27	513,2669		48,417,1126	yes	coding-synonymous-near-splice	FHAD1	NM_052929.1		49,466,1768	AA,AG,GG		16.1219,3.685,12.3522		100/1413	15599025	564,4002	692	1591	2283	SO:0001630	splice_region_variant	114827	exon3			ACCTCCGGTGAGT	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.300+1G>A	1.37:g.15599025G>A		Somatic	48	0	0	704	WXS	Illumina HiSeq	Phase_I	66	7	0.106061	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Silent	SNP	ENST00000375998.4	37																																																																																				G|0.874;A|0.126	0.126	strong		0.592	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	Silent
NMD3	51068	hgsc.bcm.edu	37	3	160956548	160956548	+	Silent	SNP	A	A	G	rs11539155	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:160956548A>G	ENST00000460469.1	+	8	1142	c.687A>G	c.(685-687)caA>caG	p.Q229Q	NMD3_ENST00000472947.1_Silent_p.Q229Q|NMD3_ENST00000351193.2_Silent_p.Q229Q			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	229					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			TGATCTCTCAAGATATCCATA	0.294													A|||	275	0.0549121	0.0061	0.0591	5008	,	,		17776	0.0516		0.0308	False		,,,				2504	0.1462				p.Q229Q		Atlas-SNP	.											.	NMD3	49	.	0			c.A687G						PASS	.	A		48,4354	48.2+/-83.0	1,46,2154	100.0	100.0	100.0		687	-3.4	1.0	3	dbSNP_120	100	298,8296	107.6+/-168.3	5,288,4004	no	coding-synonymous	NMD3	NM_015938.3		6,334,6158	GG,GA,AA		3.4675,1.0904,2.6624		229/504	160956548	346,12650	2201	4297	6498	SO:0001819	synonymous_variant	51068	exon9			CTCTCAAGATATC	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"""NMD3 homolog (S. cerevisiae)"""			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.687A>G	3.37:g.160956548A>G		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	258	113	0.437984	NM_015938	D3DNM7|Q9Y2Z6	Silent	SNP	ENST00000460469.1	37	CCDS3194.1																																																																																			A|0.972;G|0.028	0.028	strong		0.294	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938	
SCRIB	23513	hgsc.bcm.edu	37	8	144895018	144895018	+	Silent	SNP	C	C	T	rs75171224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144895018C>T	ENST00000320476.3	-	8	762	c.756G>A	c.(754-756)caG>caA	p.Q252Q	SCRIB_ENST00000356994.2_Silent_p.Q252Q|MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000377533.3_Silent_p.Q171Q	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	252	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)			GCAGCAGGTTCTGGGACAGCA	0.706													C|||	24	0.00479233	0.0008	0.0072	5008	,	,		14449	0.0		0.0169	False		,,,				2504	0.001				p.Q252Q	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G756A						PASS	.	C	,	8,4398	14.3+/-33.2	0,8,2195	35.0	35.0	35.0		756,756	4.2	1.0	8	dbSNP_131	35	140,8456	64.6+/-126.8	1,138,4159	no	coding-synonymous,coding-synonymous	SCRIB	NM_015356.3,NM_182706.3	,	1,146,6354	TT,TC,CC		1.6287,0.1816,1.1383	,	252/1631,252/1656	144895018	148,12854	2203	4298	6501	SO:0001819	synonymous_variant	23513	exon8			CAGGTTCTGGGAC	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.756G>A	8.37:g.144895018C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	57	40	0.701754	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1																																																																																			C|0.991;T|0.009	0.009	strong		0.706	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088319	17088319	+	Missense_Mutation	SNP	G	G	T	rs3745335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17088319G>T	ENST00000443236.1	-	15	1789	c.1758C>A	c.(1756-1758)gaC>gaA	p.D586E	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	539						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						TCACACACACGTCGACCTCAG	0.597													g|||	1748	0.349042	0.503	0.3012	5008	,	,		17953	0.2837		0.2863	False		,,,				2504	0.3067				p.D586E		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C1758A						PASS	.	G	GLU/ASP	1694,2282		352,990,646	31.0	38.0	36.0		1758	-4.9	0.0	19	dbSNP_107	36	2249,6059		294,1661,2199	yes	missense	CPAMD8	NM_015692.2	45	646,2651,2845	TT,TG,GG		27.0703,42.6056,32.0987	benign	586/1933	17088319	3943,8341	1988	4154	6142	SO:0001583	missense	27151	exon15			ACACACGTCGACC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1758C>A	19.37:g.17088319G>T	ENSP00000402505:p.Asp586Glu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	749|749	0.34294871794871795|0.34294871794871795	244|244	0.4959349593495935|0.4959349593495935	114|114	0.3149171270718232|0.3149171270718232	167|167	0.291958041958042|0.291958041958042	224|224	0.2955145118733509|0.2955145118733509	g|g	1.841|1.841	-0.467320|-0.467320	0.04476|0.04476	0.426056|0.426056	0.270703|0.270703	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|T	.|0.63744	.|-0.06	2.45|2.45	-4.91|-4.91	0.03085|0.03085	Alpha-2-macroglobulin, N-terminal 2 (1);|.	1.225170|.	0.06333|.	U|.	0.706515|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.16307|0.16307	0.4|0.4	0.27253|0.27253	P|P	0.9588331|0.9588331	B|.	0.09022|.	0.002|.	B|.	0.18871|.	0.023|.	T|T	0.38650|0.38650	-0.9651|-0.9651	8|5	0.05620|.	T|.	0.96|.	.|.	1.0551|1.0551	0.01588|0.01588	0.1807:0.1571:0.437:0.2253|0.1807:0.1571:0.437:0.2253	rs3745335;rs57288934;rs3745335|rs3745335;rs57288934;rs3745335	539|.	Q8IZJ3|.	CPMD8_HUMAN|.	E|K	586|597	.|ENSP00000402505:T597K	ENSP00000291440:D586E|.	D|T	-|-	3|2	2|0	CPAMD8|CPAMD8	16949319|16949319	0.133000|0.133000	0.22466|0.22466	0.028000|0.028000	0.17463|0.17463	0.151000|0.151000	0.21798|0.21798	-0.780000|-0.780000	0.04654|0.04654	-2.316000|-2.316000	0.00645|0.00645	-1.631000|-1.631000	0.00782|0.00782	GAC|ACG	.	.	weak		0.597	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
PDLIM4	8572	hgsc.bcm.edu	37	5	131607080	131607080	+	Silent	SNP	A	A	G	rs270619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:131607080A>G	ENST00000253754.3	+	5	655	c.591A>G	c.(589-591)ccA>ccG	p.P197P	PDLIM4_ENST00000484620.1_3'UTR|PDLIM4_ENST00000379018.3_Silent_p.P197P|P4HA2_ENST00000471826.1_Intron	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	197							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)			TGCGGGAGCCAGCCGAGCCCG	0.692													G|||	1453	0.290136	0.5242	0.1023	5008	,	,		13386	0.4673		0.1123	False		,,,				2504	0.1074				p.P197P		Atlas-SNP	.											.	PDLIM4	22	.	0			c.A591G						PASS	.	G	,	1918,2482		441,1036,723	20.0	28.0	26.0		591,591	-10.3	0.0	5	dbSNP_79	26	906,7688		57,792,3448	no	coding-synonymous,coding-synonymous	PDLIM4	NM_001131027.1,NM_003687.3	,	498,1828,4171	GG,GA,AA		10.5422,43.5909,21.7331	,	197/247,197/331	131607080	2824,10170	2200	4297	6497	SO:0001819	synonymous_variant	8572	exon5			GGAGCCAGCCGAG	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.591A>G	5.37:g.131607080A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	37	10	0.27027	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Silent	SNP	ENST00000253754.3	37	CCDS4152.1																																																																																			A|0.766;G|0.233	0.233	strong		0.692	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687	
HSPA4	3308	hgsc.bcm.edu	37	5	132387979	132387979	+	Missense_Mutation	SNP	T	T	A	rs61745470	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:132387979T>A	ENST00000304858.2	+	1	326	c.37T>A	c.(37-39)Tgc>Agc	p.C13S		NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	13					chaperone-mediated protein complex assembly (GO:0051131)|protein import into mitochondrial outer membrane (GO:0045040)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|stomach(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CTTCCAGAGCTGCTACGTCGC	0.701													T|||	49	0.00978435	0.0053	0.0159	5008	,	,		15553	0.0		0.0308	False		,,,				2504	0.0				p.C13S	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.T37A						PASS	.	T	SER/CYS	22,4374		0,22,2176	18.0	20.0	19.0		37	4.6	1.0	5	dbSNP_129	19	157,8427		4,149,4139	yes	missense	HSPA4	NM_002154.3	112	4,171,6315	AA,AT,TT		1.829,0.5005,1.379	probably-damaging	13/841	132387979	179,12801	2198	4292	6490	SO:0001583	missense	3308	exon1			CAGAGCTGCTACG	AB023420	CCDS4166.1	5q31.1	2011-09-07	2002-08-29		ENSG00000170606	ENSG00000170606		"""Heat shock proteins / HSP70"""	5237	protein-coding gene	gene with protein product	"""hsp70 RY"""	601113	"""heat shock 70kD protein 4"""			8335910	Standard	NM_002154		Approved	HS24/P52, HSPH2	uc003kyj.3	P34932	OTTHUMG00000129012	ENST00000304858.2:c.37T>A	5.37:g.132387979T>A	ENSP00000302961:p.Cys13Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	54	27	0.5	NM_002154	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	31	0.014194139194139194	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	22	0.029023746701846966	T	33	5.245183	0.95272	0.005005	0.01829	ENSG00000170606	ENST00000304858;ENST00000321956;ENST00000537974	T	0.00614	6.21	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.00384	0.0012	N	0.03930	-0.32	0.80722	D	1	D	0.62365	0.991	D	0.78314	0.991	D	0.88767	0.3261	10	0.20046	T	0.44	-6.2875	14.4551	0.67411	0.0:0.0:0.0:1.0	rs61745470	13	P34932	HSP74_HUMAN	S	13	ENSP00000302961:C13S	ENSP00000302961:C13S	C	+	1	0	HSPA4	132415878	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.267000	0.78462	2.048000	0.60808	0.533000	0.62120	TGC	T|0.985;A|0.015	0.015	strong		0.701	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431	
PTCD1	26024	hgsc.bcm.edu	37	7	99022873	99022873	+	Missense_Mutation	SNP	C	C	T	rs147045279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99022873C>T	ENST00000292478.4	-	6	1532	c.1282G>A	c.(1282-1284)Gca>Aca	p.A428T	PTCD1_ENST00000555673.1_Missense_Mutation_p.A477T|ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.A477T	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	428					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)			AGGGCCACTGCGGTGAGGGCT	0.662													G|||	11	0.00219649	0.0	0.0	5008	,	,		17554	0.0		0.001	False		,,,				2504	0.0102				p.A477T		Atlas-SNP	.											.	.	.	.	0			c.G1429A						PASS	.	G	THR/ALA,THR/ALA	2,4404		0,2,2201	96.0	96.0	96.0		1429,1282	2.8	0.0	7	dbSNP_134	96	13,8587		0,13,4287	yes	missense,missense	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	58,58	0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153	benign,benign	477/750,428/701	99022873	15,12991	2203	4300	6503	SO:0001583	missense	100526740	exon7			CCACTGCGGTGAG	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.1282G>A	7.37:g.99022873C>T	ENSP00000292478:p.Ala428Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	92	51	0.554348	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	9.484	1.098951	0.20552	4.54E-4	0.001512	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000438524;ENST00000555673;ENST00000413834	T;T;T	0.64803	-0.12;-0.09;-0.09	5.66	2.75	0.32379	.	0.719311	0.14379	N	0.323285	T	0.38719	0.1051	N	0.14661	0.345	0.09310	N	1	B;B	0.21753	0.06;0.036	B;B	0.18263	0.021;0.005	T	0.20806	-1.0264	10	0.15952	T	0.53	-2.2895	6.6526	0.22971	0.3204:0.1307:0.5489:0.0	.	477;428	G3V325;O75127	.;PTCD1_HUMAN	T	428;210;477;477	ENSP00000292478:A428T;ENSP00000450995:A477T;ENSP00000400168:A477T	ENSP00000400168:A477T	A	-	1	0	ATP5J2-PTCD1;PTCD1	98860809	0.005000	0.15991	0.015000	0.15790	0.007000	0.05969	0.090000	0.15025	0.275000	0.22094	-0.216000	0.12614	GCA	C|1.000;T|0.000	0.000	strong		0.662	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
TMEM244	253582	hgsc.bcm.edu	37	6	130154686	130154686	+	Missense_Mutation	SNP	A	A	G	rs4629709	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:130154686A>G	ENST00000368143.1	-	4	320	c.238T>C	c.(238-240)Ttt>Ctt	p.F80L	TMEM244_ENST00000438392.1_Missense_Mutation_p.F80L	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	80			F -> L (in dbSNP:rs4629709).			integral component of membrane (GO:0016021)											GGAACAAAAAACAATCCACAA	0.348													G|||	3076	0.614217	0.6687	0.5101	5008	,	,		17740	0.3611		0.7744	False		,,,				2504	0.7106				p.F80L		Atlas-SNP	.											.	.	.	.	0			c.T238C						PASS	.	G	LEU/PHE	3062,1344	449.2+/-349.0	1062,938,203	126.0	122.0	123.0		238	4.8	0.9	6	dbSNP_111	123	7045,1555	290.1+/-299.6	2900,1245,155	yes	missense	C6orf191	NM_001010876.1	22	3962,2183,358	GG,GA,AA		18.0814,30.5039,22.2897	benign	80/129	130154686	10107,2899	2203	4300	6503	SO:0001583	missense	253582	exon4			CAAAAAACAATCC		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.238T>C	6.37:g.130154686A>G	ENSP00000357125:p.Phe80Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_001010876		Missense_Mutation	SNP	ENST00000368143.1	37	CCDS34536.1	1322	0.6053113553113553	334	0.6788617886178862	208	0.574585635359116	199	0.3479020979020979	581	0.7664907651715039	G	5.332	0.246588	0.10130	0.694961	0.819186	ENSG00000203756	ENST00000368143;ENST00000438392	T;T	0.33865	1.39;1.39	4.8	4.8	0.61643	.	0.085531	0.47852	N	0.000203	T	0.02494	0.0076	N	0.00621	-1.32	0.49213	P	2.3200000000000998E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.41251	-0.9519	9	0.02654	T	1	-19.0081	7.7395	0.28833	0.0851:0.0:0.7547:0.1603	rs4629709;rs52812966;rs60692248;rs4629709	80	Q5VVB8	CF191_HUMAN	L	80	ENSP00000357125:F80L;ENSP00000403755:F80L	ENSP00000357125:F80L	F	-	1	0	C6orf191	130196379	0.885000	0.30320	0.927000	0.36925	0.974000	0.67602	0.230000	0.17852	1.147000	0.42369	-0.128000	0.14901	TTT	A|0.296;G|0.704	0.704	strong		0.348	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
LASP1	3927	hgsc.bcm.edu	37	17	37070658	37070658	+	Silent	SNP	A	A	G	rs525989	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:37070658A>G	ENST00000318008.6	+	5	769	c.438A>G	c.(436-438)tcA>tcG	p.S146S	LASP1_ENST00000433206.2_Silent_p.S90S|LASP1_ENST00000435347.3_Silent_p.S146S	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	146					ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						GTCGGGATTCACAGGACGGCA	0.627			T	MLL	AML								G|||	3389	0.676717	0.9175	0.5519	5008	,	,		14614	0.5933		0.6471	False		,,,				2504	0.5562				p.S146S		Atlas-SNP	.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	LASP1,colon,carcinoma,0,3	LASP1	24	3	0			c.A438G						PASS	.	G		3809,595	250.9+/-257.8	1657,495,50	27.0	33.0	31.0		438	0.4	0.6	17	dbSNP_83	31	5638,2962	443.3+/-360.3	1872,1894,534	no	coding-synonymous	LASP1	NM_006148.2		3529,2389,584	GG,GA,AA		34.4419,13.5104,27.3531		146/262	37070658	9447,3557	2202	4300	6502	SO:0001819	synonymous_variant	3927	exon5			GGATTCACAGGAC		CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.438A>G	17.37:g.37070658A>G		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	173	93	0.537572	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Silent	SNP	ENST00000318008.6	37	CCDS11331.1																																																																																			A|0.285;G|0.715	0.715	strong		0.627	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148	
DISP2	85455	hgsc.bcm.edu	37	15	40660566	40660566	+	Silent	SNP	G	G	A	rs72733420	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:40660566G>A	ENST00000267889.3	+	8	2340	c.2253G>A	c.(2251-2253)gcG>gcA	p.A751A	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	751					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		GCTTCGACGCGGAGTATCGCC	0.721													G|||	543	0.108427	0.087	0.1354	5008	,	,		11032	0.0188		0.1968	False		,,,				2504	0.1196				p.A751A		Atlas-SNP	.											DISP2,NS,carcinoma,0,1	DISP2	86	1	0			c.G2253A						scavenged	.	G		423,3975		25,373,1801	24.0	28.0	26.0		2253	-9.6	0.0	15	dbSNP_132	26	1823,6771		193,1437,2667	no	coding-synonymous	DISP2	NM_033510.1		218,1810,4468	AA,AG,GG		21.2125,9.618,17.2876		751/1402	40660566	2246,10746	2199	4297	6496	SO:0001819	synonymous_variant	85455	exon8			CGACGCGGAGTAT	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2253G>A	15.37:g.40660566G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	31	13	0.419355	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			G|0.847;A|0.153	0.153	strong		0.721	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
LAMB2	3913	hgsc.bcm.edu	37	3	49161004	49161004	+	Silent	SNP	C	C	A	rs34967349	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49161004C>A	ENST00000418109.1	-	26	4022	c.3858G>T	c.(3856-3858)gtG>gtT	p.V1286V	USP19_ENST00000417901.1_5'Flank|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000453664.1_5'Flank|LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Silent_p.V1286V|USP19_ENST00000398892.3_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1286	Domain II.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCTCATCTTGCACATCTGTCA	0.537													C|||	12	0.00239617	0.0	0.0058	5008	,	,		24506	0.0		0.008	False		,,,				2504	0.0				p.V1286V		Atlas-SNP	.											.	LAMB2	156	.	0			c.G3858T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	133.0	122.0	126.0		3858	0.8	1.0	3	dbSNP_126	126	50,8550	32.8+/-85.7	0,50,4250	no	coding-synonymous	LAMB2	NM_002292.3		0,57,6446	AA,AC,CC		0.5814,0.1589,0.4383		1286/1799	49161004	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	3913	exon25			ATCTTGCACATCT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.3858G>T	3.37:g.49161004C>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																			C|0.996;A|0.004	0.004	strong		0.537	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
MT-ATP6	4508	hgsc.bcm.edu	37	M	8697	8697	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:8697G>A	ENST00000361899.2	+	1	171	c.171G>A	c.(169-171)atG>atA	p.M57I	MT-ND4L_ENST00000361335.1_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TC_ENST00000387405.1_RNA|MT-TK_ENST00000387421.1_RNA			P00846	ATP6_HUMAN	mitochondrially encoded ATP synthase 6	57					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)			breast(2)|endometrium(7)|kidney(8)|prostate(1)	18						TCAAAACAAATGATAGCCATA	0.403																																					p.M57M		Atlas-SNP	.											.	.	.	.	0			c.G171A						PASS	.																																			SO:0001583	missense	0	exon1			ACAAATGATAACC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198899	ENSG00000198899		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7414	protein-coding gene	gene with protein product		516060	"""ATP synthase 6"", ""spicular retinitis pigmentosa with dementia, seizures, ataxia, proximal muscle weakness and sensory deficit"""	MTATP6, RP		7219534	Standard			Approved	ATP6, ATPase-6, Su6m		P00846		ENST00000361899.2:c.171G>A	M.37:g.8697G>A	ENSP00000354632:p.Met57Ile	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	ENST00000361899	Q34772|Q5S8W5|Q5S9E7|Q5S9I6|Q5SA31|Q6RPB7|Q6VHC0|Q6VHE0|Q6WQF4|Q7YCC1|Q7YCF8|Q7YCG1|Q85KU8|Q85KX1|Q85L05|Q8HNQ4|Q8HNQ8|Q8WCX6|Q9B2U5|Q9B2Z2	Silent	SNP	ENST00000361899.2	37																																																																																				.	.	none		0.403	MT-ATP6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024031	
OR51B6	390058	hgsc.bcm.edu	37	11	5373562	5373562	+	Missense_Mutation	SNP	C	C	A	rs5024042	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373562C>A	ENST00000380219.1	+	1	825	c.825C>A	c.(823-825)agC>agA	p.S275R	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	275			S -> R (in dbSNP:rs5024042). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACAATGAGCTACATCCACT	0.393													C|||	1164	0.232428	0.326	0.2349	5008	,	,		23831	0.0863		0.2644	False		,,,				2504	0.2219				p.S275R		Atlas-SNP	.											.	OR51B6	53	.	0			c.C825A						PASS	.	C	ARG/SER	1287,3115	438.8+/-345.5	173,941,1087	199.0	181.0	187.0		825	2.3	1.0	11	dbSNP_113	187	2270,6324	382.2+/-340.3	310,1650,2337	yes	missense	OR51B6	NM_001004750.1	110	483,2591,3424	AA,AC,CC		26.4138,29.2367,27.37	probably-damaging	275/313	5373562	3557,9439	2201	4297	6498	SO:0001583	missense	390058	exon1			AATGAGCTACATC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.825C>A	11.37:g.5373562C>A	ENSP00000369568:p.Ser275Arg	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	209	107	0.511962	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	C	15.09	2.730424	0.48939	0.292367	0.264138	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00262	8.4	5.13	2.3	0.28687	GPCR, rhodopsin-like superfamily (1);	0.091548	0.48286	D	0.000198	T	0.00012	0.0000	M	0.90759	3.145	0.39650	P	0.02954599999999996	D	0.89917	1.0	D	0.97110	1.0	T	0.46498	-0.9187	9	0.72032	D	0.01	.	9.0581	0.36419	0.0:0.7606:0.0:0.2394	rs5024042;rs52807625;rs58117426;rs5024042	275	Q9H340	O51B6_HUMAN	R	274;275	ENSP00000369568:S275R	ENSP00000369568:S275R	S	+	3	2	OR51B6	5330138	0.000000	0.05858	0.967000	0.41034	0.805000	0.45488	-0.398000	0.07259	0.347000	0.23924	-0.142000	0.14014	AGC	C|0.767;A|0.233	0.233	strong		0.393	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
THBS2	7058	hgsc.bcm.edu	37	6	169632219	169632219	+	Silent	SNP	G	G	A	rs35935937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:169632219G>A	ENST00000366787.3	-	14	2256	c.2007C>T	c.(2005-2007)ggC>ggT	p.G669G	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	669	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.G669G(1)		NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CGCTGAAGTGGCCCAGGTAGA	0.632													G|||	960	0.191693	0.1218	0.2161	5008	,	,		16580	0.2679		0.17	False		,,,				2504	0.2127				p.G669G	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											THBS2,NS,carcinoma,0,1	THBS2	230	1	1	Substitution - coding silent(1)	stomach(1)	c.C2007T						PASS	.	G		538,3868	241.2+/-251.7	41,456,1706	205.0	177.0	187.0		2007	-0.2	1.0	6	dbSNP_126	187	1347,7253	263.1+/-284.8	124,1099,3077	no	coding-synonymous	THBS2	NM_003247.2		165,1555,4783	AA,AG,GG		15.6628,12.2106,14.4933		669/1173	169632219	1885,11121	2203	4300	6503	SO:0001819	synonymous_variant	7058	exon14			GAAGTGGCCCAGG		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.2007C>T	6.37:g.169632219G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	78	6	0.0769231	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|0.839;C|0.000;A|0.161	0.161	strong		0.632	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
TAS2R5	54429	hgsc.bcm.edu	37	7	141490238	141490238	+	Missense_Mutation	SNP	G	G	T	rs2227264	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141490238G>T	ENST00000247883.4	+	1	222	c.77G>T	c.(76-78)aGc>aTc	p.S26I		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	26			S -> I (in dbSNP:rs2227264).		chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					GGAAATGGAAGCCTGGTGGTC	0.512													t|||	2266	0.452476	0.2065	0.5648	5008	,	,		20485	0.7014		0.4672	False		,,,				2504	0.4335				p.S26I		Atlas-SNP	.											.	TAS2R5	33	.	0			c.G77T						PASS	.	T	ILE/SER	1124,3282	717.0+/-408.7	149,826,1228	96.0	96.0	96.0		77	3.4	0.0	7	dbSNP_98	96	4239,4361	582.2+/-391.4	1039,2161,1100	yes	missense	TAS2R5	NM_018980.2	142	1188,2987,2328	TT,TG,GG		49.2907,25.5107,41.2348	benign	26/300	141490238	5363,7643	2203	4300	6503	SO:0001583	missense	54429	exon1			ATGGAAGCCTGGT	AF227132	CCDS5869.1	7q31.3-q32	2012-08-22			ENSG00000127366	ENSG00000127366		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14912	protein-coding gene	gene with protein product		605062					Standard	NM_018980		Approved	T2R5	uc003vwr.1	Q9NYW4	OTTHUMG00000157632	ENST00000247883.4:c.77G>T	7.37:g.141490238G>T	ENSP00000247883:p.Ser26Ile	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	182	86	0.472527	NM_018980	Q645W0|Q75MV7	Missense_Mutation	SNP	ENST00000247883.4	37	CCDS5869.1	1069	0.48946886446886445	120	0.24390243902439024	196	0.5414364640883977	404	0.7062937062937062	349	0.4604221635883905	T	3.131	-0.178496	0.06380	0.255107	0.492907	ENSG00000127366	ENST00000247883	T	0.35236	1.32	4.59	3.43	0.39272	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27905	-1.0060	8	0.45353	T	0.12	.	4.8795	0.13672	0.0:0.0979:0.1869:0.7152	rs2227264;rs17523954;rs52799831;rs2227264	26	Q9NYW4	TA2R5_HUMAN	I	26	ENSP00000247883:S26I	ENSP00000247883:S26I	S	+	2	0	TAS2R5	141136707	0.000000	0.05858	0.012000	0.15200	0.004000	0.04260	-0.001000	0.12947	0.279000	0.22186	-0.256000	0.11100	AGC	G|0.549;N|0.000	.	strong		0.512	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1		
PCDHB16	57717	hgsc.bcm.edu	37	5	140564263	140564263	+	Missense_Mutation	SNP	C	C	T	rs17844666	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140564263C>T	ENST00000361016.2	+	1	3284	c.2129C>T	c.(2128-2130)gCg>gTg	p.A710V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	710				A -> V (in Ref. 3; BAB13447). {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)			CTGTTCGTGGCGGTGCGGCTG	0.692													C|||	1351	0.269768	0.0477	0.3055	5008	,	,		16208	0.5288		0.2306	False		,,,				2504	0.318				p.A710V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C2129T						PASS	.	C	VAL/ALA	241,4151		11,219,1966	71.0	81.0	78.0		2129	0.9	0.3	5	dbSNP_123	78	1847,6725		206,1435,2645	no	missense	PCDHB16	NM_020957.1	64	217,1654,4611	TT,TC,CC		21.5469,5.4872,16.1061	benign	710/777	140564263	2088,10876	2196	4286	6482	SO:0001583	missense	57717	exon1			TCGTGGCGGTGCG	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.2129C>T	5.37:g.140564263C>T	ENSP00000354293:p.Ala710Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	79	45	0.56962	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	571	0.26144688644688646	15	0.03048780487804878	88	0.2430939226519337	300	0.5244755244755245	168	0.22163588390501318	c	14.19	2.461805	0.43736	0.054872	0.215469	ENSG00000196963	ENST00000361016	T	0.15603	2.41	3.91	0.912	0.19349	.	0.524287	0.14313	N	0.327546	T	0.00012	0.0000	M	0.84773	2.715	0.80722	P	0.0	B	0.16396	0.017	B	0.18263	0.021	T	0.32613	-0.9900	9	0.42905	T	0.14	.	7.2915	0.26368	0.0:0.2524:0.5685:0.179	rs61742755	710	Q9NRJ7	PCDBG_HUMAN	V	710	ENSP00000354293:A710V	ENSP00000354293:A710V	A	+	2	0	PCDHB16	140544447	0.000000	0.05858	0.256000	0.24389	0.269000	0.26545	-1.952000	0.01528	0.115000	0.18071	0.479000	0.44913	GCG	C|0.931;T|0.069	0.069	strong		0.692	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
GCC1	79571	hgsc.bcm.edu	37	7	127222157	127222157	+	Silent	SNP	G	G	A	rs3735644	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:127222157G>A	ENST00000321407.2	-	2	2663	c.2239C>T	c.(2239-2241)Ctg>Ttg	p.L747L	GCC1_ENST00000497650.1_5'Flank	NM_024523.5	NP_078799.2	Q96CN9	GCC1_HUMAN	GRIP and coiled-coil domain containing 1	747	GRIP. {ECO:0000255|PROSITE- ProRule:PRU00250}.				protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						AAGATAGTCAGTATGGCTGTG	0.527													G|||	1357	0.270966	0.0166	0.2147	5008	,	,		22088	0.7034		0.2127	False		,,,				2504	0.2689				p.L747L		Atlas-SNP	.											.	GCC1	83	.	0			c.C2239T						PASS	.	G		239,4167	139.2+/-174.8	5,229,1969	204.0	198.0	200.0		2239	3.0	0.9	7	dbSNP_107	200	1688,6912	310.0+/-309.6	154,1380,2766	no	coding-synonymous	GCC1	NM_024523.5		159,1609,4735	AA,AG,GG		19.6279,5.4244,14.8162		747/776	127222157	1927,11079	2203	4300	6503	SO:0001819	synonymous_variant	79571	exon2			TAGTCAGTATGGC	AF525417	CCDS5796.1	7q22.3	2004-03-05	2003-10-17		ENSG00000179562	ENSG00000179562			19095	protein-coding gene	gene with protein product		607418	"""golgi coiled-coil 1"""			10209125	Standard	NM_024523		Approved	FLJ22035, GCC88, GCC1P, MGC20706	uc003vma.3	Q96CN9	OTTHUMG00000023590	ENST00000321407.2:c.2239C>T	7.37:g.127222157G>A		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	226	111	0.49115	NM_024523	Q9H6N7	Silent	SNP	ENST00000321407.2	37	CCDS5796.1																																																																																			G|0.799;A|0.201	0.201	strong		0.527	GCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059911.3	NM_024523	
ERMP1	79956	hgsc.bcm.edu	37	9	5787439	5787439	+	Missense_Mutation	SNP	T	T	C	rs148237651		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5787439T>C	ENST00000339450.5	-	14	2630	c.2541A>G	c.(2539-2541)atA>atG	p.I847M	ERMP1_ENST00000543230.1_3'UTR|ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_3'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	847						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)		CCTGCACTTCTATCCAGAACT	0.473																																					p.I847M		Atlas-SNP	.											.	ERMP1	63	.	0			c.A2541G						PASS	.	T	MET/ILE	0,4406		0,0,2203	110.0	108.0	108.0		2541	-3.8	1.0	9	dbSNP_134	108	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ERMP1	NM_024896.2	10	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	847/905	5787439	3,13003	2203	4300	6503	SO:0001583	missense	79956	exon14			CACTTCTATCCAG	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.2541A>G	9.37:g.5787439T>C	ENSP00000340427:p.Ile847Met	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.538188	0.27475	0.0	3.49E-4	ENSG00000099219	ENST00000339450	T	0.53206	0.63	5.77	-3.81	0.04294	.	0.089070	0.85682	D	0.000000	T	0.50939	0.1645	L	0.55990	1.75	0.80722	D	1	D	0.71674	0.998	D	0.66602	0.945	T	0.51092	-0.8749	10	0.33940	T	0.23	-20.1147	7.7681	0.28991	0.3034:0.0:0.3774:0.3192	.	847	Q7Z2K6	ERMP1_HUMAN	M	847	ENSP00000340427:I847M	ENSP00000340427:I847M	I	-	3	3	ERMP1	5777439	0.996000	0.38824	0.989000	0.46669	0.032000	0.12392	0.236000	0.17967	-0.521000	0.06426	-0.472000	0.04984	ATA	T|1.000;C|0.000	0.000	weak		0.473	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
DDX60L	91351	hgsc.bcm.edu	37	4	169327191	169327191	+	Silent	SNP	C	C	T	rs3762856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169327191C>T	ENST00000511577.1	-	24	3370	c.3123G>A	c.(3121-3123)aaG>aaA	p.K1041K	DDX60L_ENST00000505890.1_Silent_p.K1041K|DDX60L_ENST00000260184.7_Silent_p.K1041K			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1041							ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		TAATGACTATCTTATTCTTAA	0.303													T|||	1636	0.326677	0.1944	0.2867	5008	,	,		17223	0.4048		0.3489	False		,,,				2504	0.4305				p.K1041K		Atlas-SNP	.											.	DDX60L	116	.	0			c.G3123A						PASS	.	T		721,2901		75,571,1165	86.0	73.0	77.0		3123	2.5	0.5	4	dbSNP_107	77	2547,5665		402,1743,1961	no	coding-synonymous	DDX60L	NM_001012967.1		477,2314,3126	TT,TC,CC		31.0156,19.9061,27.6153		1041/1707	169327191	3268,8566	1811	4106	5917	SO:0001819	synonymous_variant	91351	exon24			GACTATCTTATTC	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.3123G>A	4.37:g.169327191C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.674;T|0.326	0.326	strong		0.303	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
NT5C2	22978	hgsc.bcm.edu	37	10	104934709	104934709	+	Missense_Mutation	SNP	T	T	C	rs10883841	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:104934709T>C	ENST00000404739.3	-	1	30	c.7A>G	c.(7-9)Acc>Gcc	p.T3A	NT5C2_ENST00000343289.5_Missense_Mutation_p.T3A|NT5C2_ENST00000470299.1_Missense_Mutation_p.T3A|NT5C2_ENST00000369857.4_Intron			P49902	5NTC_HUMAN	5'-nucleotidase, cytosolic II	3			T -> A (in dbSNP:rs10883841). {ECO:0000269|Ref.4}.		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)	CTCCAGGAGGTTGACATTTTA	0.338													T|||	384	0.0766773	0.0098	0.0735	5008	,	,		18019	0.1528		0.1382	False		,,,				2504	0.0276				p.T3A		Atlas-SNP	.											.	NT5C2	41	.	0			c.A7G						PASS	.	T	ALA/THR,ALA/THR	150,4256	104.3+/-142.8	5,140,2058	167.0	156.0	160.0		7,7	5.3	1.0	10	dbSNP_120	160	1282,7318	253.7+/-279.3	80,1122,3098	yes	missense,missense	NT5C2	NM_001134373.1,NM_012229.3	58,58	85,1262,5156	CC,CT,TT		14.907,3.4044,11.0103	benign,benign	3/562,3/562	104934709	1432,11574	2203	4300	6503	SO:0001583	missense	22978	exon3			AGGAGGTTGACAT	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.7A>G	10.37:g.104934709T>C	ENSP00000383960:p.Thr3Ala	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_012229	B7Z382|D3DR91|Q5JUV5	Missense_Mutation	SNP	ENST00000404739.3	37	CCDS7544.1	211	0.09661172161172162	4	0.008130081300813009	33	0.09116022099447514	64	0.11188811188811189	110	0.14511873350923482	T	15.42	2.827812	0.50845	0.034044	0.14907	ENSG00000076685	ENST00000343289;ENST00000404739;ENST00000452156	T;T;T	0.17528	2.27;2.27;2.27	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.00073	0.0002	N	0.19112	0.55	0.09310	P	1.0	B	0.11235	0.004	B	0.04013	0.001	T	0.17501	-1.0367	9	0.45353	T	0.12	-9.8069	14.2241	0.65848	0.0:0.0:0.0:1.0	rs10883841;rs17734400;rs52813987;rs57885563;rs10883841	3	P49902	5NTC_HUMAN	A	3	ENSP00000339479:T3A;ENSP00000383960:T3A;ENSP00000396468:T3A	ENSP00000339479:T3A	T	-	1	0	NT5C2	104924699	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	6.255000	0.72466	1.986000	0.57962	0.477000	0.44152	ACC	T|0.899;C|0.101	0.101	strong		0.338	NT5C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050121.1	NM_012229	
CCHCR1	54535	hgsc.bcm.edu	37	6	31110786	31110786	+	Silent	SNP	T	T	A	rs12364	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31110786T>A	ENST00000376266.5	-	17	2300	c.2178A>T	c.(2176-2178)gcA>gcT	p.A726A	CCHCR1_ENST00000451521.2_Silent_p.A779A|CCHCR1_ENST00000396263.2_Silent_p.A673A|CCHCR1_ENST00000396268.3_Silent_p.A815A	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	726					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CAGGTGCAGATGCTGAACACT	0.537													T|||	714	0.142572	0.1596	0.1369	5008	,	,		20599	0.0952		0.173	False		,,,				2504	0.1411				p.A815A		Atlas-SNP	.											.	CCHCR1	68	.	0			c.A2445T						PASS	.	T	,,	518,2500		36,446,1027	292.0	339.0	322.0		2337,2445,2178	-6.8	0.0	6	dbSNP_52	322	897,4521		78,741,1890	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	114,1187,2917	AA,AT,TT		16.5559,17.1637,16.7734	,,	779/836,815/872,726/783	31110786	1415,7021	1509	2709	4218	SO:0001819	synonymous_variant	54535	exon17			TGCAGATGCTGAA	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.2178A>T	6.37:g.31110786T>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			T|0.846;A|0.154	0.154	strong		0.537	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
MET	4233	hgsc.bcm.edu	37	7	116339315	116339315	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:116339315G>A	ENST00000318493.6	+	2	364	c.177G>A	c.(175-177)gaG>gaA	p.E59E	MET_ENST00000436117.2_Silent_p.E59E|MET_ENST00000397752.3_Silent_p.E59E			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TTCTACATGAGCATCACATTT	0.443			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.E59E		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.G177A						PASS	.						104.0	101.0	102.0					7																	116339315		1947	4135	6082	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ACATGAGCATCAC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.177G>A	7.37:g.116339315G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	129	58	0.449612	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			.	.	none		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
ZWINT	11130	hgsc.bcm.edu	37	10	58118569	58118569	+	Missense_Mutation	SNP	T	T	C	rs370677108		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:58118569T>C	ENST00000373944.3	-	6	658	c.620A>G	c.(619-621)cAg>cGg	p.Q207R	ZWINT_ENST00000460654.1_5'UTR|ZWINT_ENST00000361148.6_Intron|ZWINT_ENST00000395405.1_Missense_Mutation_p.Q207R|ZWINT_ENST00000318387.2_Missense_Mutation_p.Q87R			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	207					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						AACTTACCTCTGCAGCTTGTC	0.522																																					p.Q207R		Atlas-SNP	.											.	ZWINT	39	.	0			c.A620G						PASS	.	T	ARG/GLN,ARG/GLN,	0,4406		0,0,2203	136.0	130.0	132.0		620,620,	4.5	1.0	10		132	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron	ZWINT	NM_007057.3,NM_032997.2,NM_001005413.1	43,43,	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging,probably-damaging,	207/278,207/278,	58118569	1,13005	2203	4300	6503	SO:0001583	missense	11130	exon6			TACCTCTGCAGCT	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.620A>G	10.37:g.58118569T>C	ENSP00000363055:p.Gln207Arg	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	243	117	0.481481	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Missense_Mutation	SNP	ENST00000373944.3	37	CCDS7249.1	.	.	.	.	.	.	.	.	.	.	T	11.24	1.581660	0.28180	0.0	1.16E-4	ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000318387	T;T;T	0.50548	0.74;0.74;0.74	4.48	4.48	0.54585	.	0.154517	0.30911	N	0.008632	T	0.59622	0.2207	M	0.62723	1.935	0.29902	N	0.824315	D	0.63046	0.992	P	0.60541	0.876	T	0.61446	-0.7061	10	0.87932	D	0	.	10.4401	0.44460	0.0:0.0:0.0:1.0	.	207	O95229	ZWINT_HUMAN	R	207;207;87	ENSP00000363055:Q207R;ENSP00000378801:Q207R;ENSP00000322850:Q87R	ENSP00000322850:Q87R	Q	-	2	0	ZWINT	57788575	0.992000	0.36948	1.000000	0.80357	0.070000	0.16714	1.076000	0.30729	2.237000	0.73441	0.533000	0.62120	CAG	.	.	none		0.522	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1		
ALPP	250	hgsc.bcm.edu	37	2	233243981	233243981	+	Missense_Mutation	SNP	A	A	T	rs13026692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233243981A>T	ENST00000392027.2	+	3	534	c.265A>T	c.(265-267)Ata>Tta	p.I89L	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	89			I -> L (in dbSNP:rs13026692). {ECO:0000269|PubMed:15489334}.		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)		GGGGCCTGAGATACCCCTGGC	0.552													a|||	1947	0.388778	0.2496	0.4611	5008	,	,		19167	0.5377		0.337	False		,,,				2504	0.4254				p.I89L		Atlas-SNP	.											ALPP,NS,carcinoma,0,1	ALPP	53	1	0			c.A265T						PASS	.	A	LEU/ILE	1184,3222		157,870,1176	100.0	100.0	100.0		265	-0.2	0.1	2	dbSNP_121	100	2714,5886		437,1840,2023	yes	missense	ALPP	NM_001632.3	5	594,2710,3199	TT,TA,AA		31.5581,26.8724,29.9708	benign	89/536	233243981	3898,9108	2203	4300	6503	SO:0001583	missense	250	exon3			CCTGAGATACCCC	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.265A>T	2.37:g.233243981A>T	ENSP00000375881:p.Ile89Leu	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	162	71	0.438272	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	817	0.3740842490842491	110	0.22357723577235772	151	0.4171270718232044	301	0.5262237762237763	255	0.33641160949868076	.	11.92	1.781661	0.31502	0.268724	0.315581	ENSG00000163283	ENST00000392027	D	0.95724	-3.79	2.47	-0.159	0.13379	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.285447	0.37809	N	0.001939	T	0.00012	0.0000	N	0.01874	-0.695	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.47433	-0.9118	9	0.66056	D	0.02	.	4.3616	0.11205	0.6235:0.1681:0.2084:0.0	rs13026692;rs57554920;rs13026692	89	P05187	PPB1_HUMAN	L	89	ENSP00000375881:I89L	ENSP00000375881:I89L	I	+	1	0	ALPP	232952225	0.950000	0.32346	0.117000	0.21633	0.049000	0.14656	2.236000	0.43052	-0.152000	0.11156	0.248000	0.18094	ATA	A|0.675;T|0.325	0.325	strong		0.552	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
CFAP70	118491	hgsc.bcm.edu	37	10	75056863	75056863	+	Silent	SNP	A	A	C	rs6480692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75056863A>C	ENST00000310715.3	-	16	1911	c.1791T>G	c.(1789-1791)ctT>ctG	p.L597L	TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000401621.2_Silent_p.L597L|TTC18_ENST00000355577.3_Silent_p.L66L|TTC18_ENST00000394865.1_Silent_p.L597L	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		597						extracellular vesicular exosome (GO:0070062)		p.L597L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					TAAATGTCTGAAGTTCCTCCT	0.403													C|||	890	0.177716	0.177	0.0994	5008	,	,		19536	0.3105		0.0547	False		,,,				2504	0.2239				p.L597L		Atlas-SNP	.											TTC18,NS,carcinoma,-2,2	TTC18	106	2	1	Substitution - coding silent(1)	stomach(1)	c.T1791G						PASS	.	C		659,3747	764.7+/-413.3	56,547,1600	222.0	199.0	207.0		1791	0.0	1.0	10	dbSNP_116	207	573,8027	793.6+/-407.5	27,519,3754	no	coding-synonymous	TTC18	NM_145170.3		83,1066,5354	CC,CA,AA		6.6628,14.9569,9.4726		597/1122	75056863	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	118491	exon16			TGTCTGAAGTTCC																												ENST00000310715.3:c.1791T>G	10.37:g.75056863A>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Silent	SNP	ENST00000310715.3	37	CCDS7324.3																																																																																			A|0.870;C|0.130	0.130	strong		0.403	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
RASAL1	8437	hgsc.bcm.edu	37	12	113554946	113554946	+	Silent	SNP	G	G	A	rs34456143	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113554946G>A	ENST00000261729.5	-	9	978	c.663C>T	c.(661-663)acC>acT	p.T221T	RASAL1_ENST00000548055.1_Silent_p.T221T|RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000546530.1_Silent_p.T221T|RASAL1_ENST00000446861.3_Silent_p.T221T			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	221					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						TCTGCTGGAGGGTCTTTGGAG	0.632													G|||	277	0.0553115	0.0083	0.085	5008	,	,		18411	0.0		0.1511	False		,,,				2504	0.0562				p.T221T		Atlas-SNP	.											.	RASAL1	89	.	0			c.C663T						PASS	.	G	,,	150,4256	104.7+/-143.2	2,146,2055	52.0	49.0	50.0		663,663,663	2.5	0.9	12	dbSNP_126	50	1279,7321	253.6+/-279.2	93,1093,3114	no	coding-synonymous,coding-synonymous,coding-synonymous	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	,,	95,1239,5169	AA,AG,GG		14.8721,3.4044,10.9872	,,	221/807,221/777,221/805	113554946	1429,11577	2203	4300	6503	SO:0001819	synonymous_variant	8437	exon9			CTGGAGGGTCTTT	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.663C>T	12.37:g.113554946G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Silent	SNP	ENST00000261729.5	37	CCDS9165.1																																																																																			G|0.898;A|0.102	0.102	strong		0.632	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
MUC5B	727897	hgsc.bcm.edu	37	11	1268064	1268064	+	Silent	SNP	C	C	T	rs200948102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1268064C>T	ENST00000529681.1	+	31	10012	c.9954C>T	c.(9952-9954)gcC>gcT	p.A3318A	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.A3321A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3318	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCTTCACAGCCACCCCCTCCT	0.652													c|||	1636	0.326677	0.2156	0.3256	5008	,	,		19867	0.5387		0.2853	False		,,,				2504	0.3016				p.A3318A		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C9954T						PASS	.						15.0	28.0	24.0					11																	1268064		1776	4009	5785	SO:0001819	synonymous_variant	727897	exon31			CACAGCCACCCCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.9954C>T	11.37:g.1268064C>T		Somatic	279	0	0		WXS	Illumina HiSeq	Phase_I	270	106	0.392593	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	3.753	-0.051234	0.07407	.	.	ENSG00000117983	ENST00000538459	.	.	.	3.18	0.963	0.19649	.	.	.	.	.	T	0.15392	0.0371	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.38908	-0.9639	4	0.02654	T	1	.	6.2137	0.20644	0.3708:0.4477:0.1814:0.0	.	.	.	.	Y	201	.	ENSP00000442622:H201Y	H	+	1	0	MUC5B	1224640	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.998000	0.03701	-0.041000	0.13558	0.305000	0.20034	CAC	C|0.846;T|0.154	0.154	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
B3GNTL1	146712	hgsc.bcm.edu	37	17	80904844	80904844	+	Missense_Mutation	SNP	C	C	T	rs7225887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80904844C>T	ENST00000320865.3	-	12	1034	c.1021G>A	c.(1021-1023)Gcc>Acc	p.A341T	B3GNTL1_ENST00000576599.1_Missense_Mutation_p.A230T	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	341			A -> T (in dbSNP:rs7225887).				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)			TCCTCAAAGGCGCCCCCTGTG	0.622													C|||	781	0.15595	0.0582	0.2046	5008	,	,		14879	0.1577		0.2535	False		,,,				2504	0.1513				p.A341T		Atlas-SNP	.											B3GNTL1,NS,carcinoma,+2,1	B3GNTL1	40	1	0			c.G1021A						PASS	.	C	THR/ALA	319,4081		5,309,1886	56.0	47.0	50.0		1021	4.0	1.0	17	dbSNP_116	50	1806,6778		189,1428,2675	yes	missense	B3GNTL1	NM_001009905.1	58	194,1737,4561	TT,TC,CC		21.0391,7.25,16.3663	benign	341/362	80904844	2125,10859	2200	4292	6492	SO:0001583	missense	146712	exon12			CAAAGGCGCCCCC	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.1021G>A	17.37:g.80904844C>T	ENSP00000319979:p.Ala341Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_001009905	Q6GV30|Q8WUT3	Missense_Mutation	SNP	ENST00000320865.3	37	CCDS32778.1	380	0.17399267399267399	30	0.06097560975609756	76	0.20994475138121546	90	0.15734265734265734	184	0.24274406332453827	C	12.22	1.871294	0.33069	0.0725	0.210391	ENSG00000175711	ENST00000320865	T	0.41400	1.0	4.0	4.0	0.46444	.	0.419285	0.23201	N	0.050795	T	0.00012	0.0000	N	0.19112	0.55	0.36786	P	0.115429	B	0.15473	0.013	B	0.08055	0.003	T	0.17289	-1.0374	8	.	.	.	-14.9116	14.4067	0.67088	0.0:1.0:0.0:0.0	rs7225887;rs17344847;rs52802513;rs57810247;rs7225887	341	Q67FW5	B3GNL_HUMAN	T	341	ENSP00000319979:A341T	.	A	-	1	0	B3GNTL1	78498133	0.136000	0.22515	0.965000	0.40720	0.950000	0.60333	3.322000	0.52007	2.171000	0.68590	0.563000	0.77884	GCC	C|0.840;T|0.160	0.160	strong		0.622	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
ZNF532	55205	hgsc.bcm.edu	37	18	56648756	56648756	+	Silent	SNP	C	C	T	rs61733373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:56648756C>T	ENST00000336078.4	+	10	4094	c.3318C>T	c.(3316-3318)caC>caT	p.H1106H	ZNF532_ENST00000591230.1_Silent_p.H1106H|ZNF532_ENST00000591083.1_Silent_p.H1106H|ZNF532_ENST00000589288.1_Silent_p.H1106H|ZNF532_ENST00000588956.1_3'UTR|ZNF532_ENST00000591808.1_Silent_p.H1106H	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1106					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)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TGGAGAAGCACGTCCAGCTGA	0.473													C|||	324	0.0646965	0.0061	0.0519	5008	,	,		20176	0.0188		0.1252	False		,,,				2504	0.138				p.H1106H		Atlas-SNP	.											.	ZNF532	108	.	0			c.C3318T						PASS	.	C		105,4301	81.9+/-120.4	0,105,2098	128.0	120.0	123.0		3318	2.3	1.0	18	dbSNP_129	123	1153,7447	236.8+/-268.9	80,993,3227	no	coding-synonymous	ZNF532	NM_018181.4		80,1098,5325	TT,TC,CC		13.407,2.3831,9.6725		1106/1302	56648756	1258,11748	2203	4300	6503	SO:0001819	synonymous_variant	55205	exon10			GAAGCACGTCCAG	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3318C>T	18.37:g.56648756C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	195	106	0.54359	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Silent	SNP	ENST00000336078.4	37	CCDS11969.1																																																																																			C|0.910;T|0.090	0.090	strong		0.473	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
ZNF835	90485	hgsc.bcm.edu	37	19	57176482	57176482	+	Missense_Mutation	SNP	C	C	T	rs12462469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57176482C>T	ENST00000537055.2	-	2	316	c.85G>A	c.(85-87)Gaa>Aaa	p.E29K		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	29			E -> K (in dbSNP:rs12462469). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						TCCTGGTTTTCCTGCAGGTCC	0.607													.|||	2065	0.41234	0.4531	0.379	5008	,	,		15832	0.4702		0.3131	False		,,,				2504	0.4233				p.E29K		Atlas-SNP	.											.	ZNF835	106	.	0			c.G85A						PASS	.	C	LYS/GLU	1677,2285		367,943,671	75.0	79.0	78.0		85	1.1	0.0	19	dbSNP_120	78	2491,5819		372,1747,2036	yes	missense	ZNF835	NM_001005850.2	56	739,2690,2707	TT,TC,CC		29.9759,42.3271,33.9635	benign	29/538	57176482	4168,8104	1981	4155	6136	SO:0001583	missense	90485	exon2			GGTTTTCCTGCAG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.85G>A	19.37:g.57176482C>T	ENSP00000444747:p.Glu29Lys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	865	0.39606227106227104	232	0.4715447154471545	128	0.35359116022099446	264	0.46153846153846156	241	0.3179419525065963	C	8.447	0.852126	0.17034	0.423271	0.299759	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06142	3.34	2.19	1.09	0.20402	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.26318	0.146	B	0.24974	0.057	T	0.38735	-0.9647	8	0.06236	T	0.91	.	6.5636	0.22499	0.0:0.6963:0.3037:0.0	rs12462469	51	Q9Y2P0	ZN835_HUMAN	K	51;29	ENSP00000444747:E29K	ENSP00000341756:E51K	E	-	1	0	ZNF835	61868294	0.000000	0.05858	0.007000	0.13788	0.062000	0.15995	0.145000	0.16157	0.467000	0.27218	0.491000	0.48974	GAA	C|0.621;T|0.379	0.379	strong		0.607	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
DLG5	9231	hgsc.bcm.edu	37	10	79584178	79584178	+	Silent	SNP	G	G	C	rs1248629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:79584178G>C	ENST00000372391.2	-	14	2351	c.2346C>G	c.(2344-2346)cgC>cgG	p.R782R	DLG5_ENST00000372388.2_Silent_p.R782R|DLG5_ENST00000459739.1_5'Flank	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	782	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			CCTGGCAGCTGCGCAGCAGAG	0.582													C|||	3727	0.744209	0.8737	0.7795	5008	,	,		21623	0.7282		0.6491	False		,,,				2504	0.6585				p.R782R		Atlas-SNP	.											.	DLG5	154	.	0			c.C2346G						PASS	.	C		3698,708	295.6+/-283.7	1559,580,64	86.0	65.0	72.0		2346	-3.3	0.9	10	dbSNP_87	72	5618,2982	461.0+/-365.3	1842,1934,524	no	coding-synonymous	DLG5	NM_004747.3		3401,2514,588	CC,CG,GG		34.6744,16.069,28.3715		782/1920	79584178	9316,3690	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon14			GCAGCTGCGCAGC	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.2346C>G	10.37:g.79584178G>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.288;C|0.712	0.712	strong		0.582	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
SEC24D	9871	hgsc.bcm.edu	37	4	119736796	119736796	+	Silent	SNP	A	A	C	rs2389688	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:119736796A>C	ENST00000280551.6	-	5	721	c.483T>G	c.(481-483)ccT>ccG	p.P161P	SEC24D_ENST00000419654.2_5'UTR|SEC24D_ENST00000379735.5_Silent_p.P161P			O94855	SC24D_HUMAN	SEC24 family member D	161	Pro-rich.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.P161P(1)		breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						GCAAAATGGAAGGCTGTGGAG	0.562													c|||	2188	0.436901	0.2436	0.5807	5008	,	,		18170	0.5506		0.4354	False		,,,				2504	0.4806				p.P161P		Atlas-SNP	.											SEC24D,NS,carcinoma,0,1	SEC24D	96	1	1	Substitution - coding silent(1)	prostate(1)	c.T483G						PASS	.	T		1283,3123	700.8+/-406.7	192,899,1112	238.0	212.0	221.0		483	-11.4	0.0	4	dbSNP_100	221	3875,4725	608.7+/-395.4	892,2091,1317	no	coding-synonymous	SEC24D	NM_014822.2		1084,2990,2429	CC,CA,AA		45.0581,29.1194,39.6586		161/1033	119736796	5158,7848	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon5			AATGGAAGGCTGT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.483T>G	4.37:g.119736796A>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	129	128	0.992248	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			T|0.108;G|0.070	.	strong		0.562	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
PEX14	5195	hgsc.bcm.edu	37	1	10596341	10596341	+	Silent	SNP	C	C	T	rs12375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:10596341C>T	ENST00000356607.4	+	3	236	c.156C>T	c.(154-156)ttC>ttT	p.F52F	PEX14_ENST00000538836.1_Intron|PEX14_ENST00000492696.1_3'UTR	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	52					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		GGAGAGCATTCCTAAAGAAGA	0.562													C|||	1142	0.228035	0.0658	0.4265	5008	,	,		16571	0.2004		0.3141	False		,,,				2504	0.2464				p.F52F		Atlas-SNP	.											.	PEX14	40	.	0			c.C156T						PASS	.	C		472,3934	220.7+/-238.1	30,412,1761	52.0	50.0	51.0		156	3.4	1.0	1	dbSNP_52	51	2770,5830	432.8+/-357.2	469,1832,1999	no	coding-synonymous	PEX14	NM_004565.2		499,2244,3760	TT,TC,CC		32.2093,10.7127,24.927		52/378	10596341	3242,9764	2203	4300	6503	SO:0001819	synonymous_variant	5195	exon3			AGCATTCCTAAAG	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.156C>T	1.37:g.10596341C>T		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	193	20	0.103627	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			C|0.770;T|0.230	0.230	strong		0.562	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
NPBWR1	2831	hgsc.bcm.edu	37	8	53853160	53853160	+	Silent	SNP	T	T	C	rs75387626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:53853160T>C	ENST00000331251.3	+	1	2170	c.693T>C	c.(691-693)caT>caC	p.H231H		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	231					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCCGGCTGCATGCCATGCGGC	0.667													T|||	170	0.0339457	0.0023	0.0245	5008	,	,		16708	0.0079		0.0527	False		,,,				2504	0.091				p.H231H		Atlas-SNP	.											.	NPBWR1	38	.	0			c.T693C						PASS	.	T		28,4360		0,28,2166	30.0	17.0	21.0		693	-2.3	1.0	8	dbSNP_132	21	291,8255		5,281,3987	no	coding-synonymous	NPBWR1	NM_005285.3		5,309,6153	CC,CT,TT		3.4051,0.6381,2.4664		231/329	53853160	319,12615	2194	4273	6467	SO:0001819	synonymous_variant	2831	exon1			GCTGCATGCCATG	BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.693T>C	8.37:g.53853160T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_005285	Q6NTC7	Silent	SNP	ENST00000331251.3	37	CCDS6151.1																																																																																			T|0.975;C|0.025	0.025	strong		0.667	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
MYH14	79784	hgsc.bcm.edu	37	19	50760716	50760716	+	Silent	SNP	C	C	G	rs378811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50760716C>G	ENST00000596571.1	+	15	2082	c.2082C>G	c.(2080-2082)cgC>cgG	p.R694R	MYH14_ENST00000598205.1_Silent_p.R702R|MYH14_ENST00000440075.2_Silent_p.R735R|MYH14_ENST00000262269.8_Silent_p.R735R|MYH14_ENST00000425460.1_Silent_p.R702R|MYH14_ENST00000376970.2_Silent_p.R727R|MYH14_ENST00000601313.1_Silent_p.R735R			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	694	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GTTTTGTCCGCTGCATTGTCC	0.612													C|||	1792	0.357827	0.3374	0.3026	5008	,	,		19529	0.374		0.4026	False		,,,				2504	0.362				p.R735R		Atlas-SNP	.											MYH14_ENST00000262269,NS,carcinoma,0,4	MYH14	261	4	0			c.C2205G						PASS	.	C	,,	1336,2946		217,902,1022	31.0	34.0	33.0		2106,2205,2082	4.5	1.0	19	dbSNP_80	33	3603,4903		771,2061,1421	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	988,2963,2443	GG,GC,CC		42.3583,31.2004,38.6221	,,	702/2004,735/2037,694/1996	50760716	4939,7849	2141	4253	6394	SO:0001819	synonymous_variant	79784	exon18			TGTCCGCTGCATT	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2082C>G	19.37:g.50760716C>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.617;G|0.383	0.383	strong		0.612	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
LILRA6	79168	hgsc.bcm.edu	37	19	54745665	54745665	+	Missense_Mutation	SNP	C	C	T	rs1052966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54745665C>T	ENST00000396365.2	-	4	484	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRA6_ENST00000391735.3_Missense_Mutation_p.G149R|LILRA6_ENST00000245621.5_Missense_Mutation_p.G149R|LILRA6_ENST00000440558.2_Missense_Mutation_p.G149R|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000419410.2_Missense_Mutation_p.G149R|LILRA6_ENST00000270464.5_Missense_Mutation_p.G149R	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	149			G -> R (in dbSNP:rs1052966).		immune system process (GO:0002376)	integral component of membrane (GO:0016021)		p.G149R(2)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTGATATCCCTTCTGTGAG	0.582																																					p.G149R		Atlas-SNP	.											LILRA6,NS,carcinoma,+1,4	LILRA6	75	4	2	Substitution - Missense(2)	large_intestine(2)	c.G445A						scavenged	.						25.0	40.0	35.0					19																	54745665		2106	4268	6374	SO:0001583	missense	79168	exon4			GATATCCCTTCTG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.445G>A	19.37:g.54745665C>T	ENSP00000379651:p.Gly149Arg	Somatic	606	2	0.00330033		WXS	Illumina HiSeq	Phase_I	700	107	0.152857	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825878	0.32237	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;3.85;2.76;2.76	3.1	-6.21	0.02065	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.12050	0.0293	L	0.39326	1.205	0.09310	N	1	P;B;P;P;B;P	0.41978	0.64;0.037;0.767;0.555;0.383;0.716	P;B;B;B;B;B	0.47044	0.535;0.085;0.444;0.211;0.344;0.276	T	0.27773	-1.0064	10	0.44086	T	0.13	.	4.765	0.13128	0.0:0.4155:0.3207:0.2638	rs1052966;rs3193450;rs13346484	149;149;149;149;149;149	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	R	149	ENSP00000390120:G149R;ENSP00000270464:G149R;ENSP00000411227:G149R;ENSP00000375615:G149R;ENSP00000379651:G149R;ENSP00000245621:G149R	ENSP00000245621:G149R	G	-	1	0	LILRA6	59437477	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	-2.553000	0.00927	-1.315000	0.02297	0.162000	0.16502	GGA	C|0.972;T|0.028	0.028	strong		0.582	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
KIF19	124602	hgsc.bcm.edu	37	17	72346868	72346868	+	Missense_Mutation	SNP	C	C	T	rs2382644	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72346868C>T	ENST00000389916.4	+	12	1549	c.1411C>T	c.(1411-1413)Cgg>Tgg	p.R471W		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	471			R -> W (in dbSNP:rs2382644). {ECO:0000269|PubMed:14702039}.		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						GAAGTCCCGCCGGGCCCTCAA	0.617													c|||	487	0.0972444	0.0408	0.1009	5008	,	,		17704	0.2163		0.0954	False		,,,				2504	0.0501				p.R471W		Atlas-SNP	.											.	KIF19	102	.	0			c.C1411T						PASS	.		TRP/ARG	173,4233	111.2+/-149.4	2,169,2032	55.0	54.0	54.0		1411	-11.5	0.0	17	dbSNP_100	54	834,7764	186.4+/-233.9	50,734,3515	yes	missense	KIF19	NM_153209.3	101	52,903,5547	TT,TC,CC		9.6999,3.9265,7.7438	probably-damaging	471/999	72346868	1007,11997	2203	4299	6502	SO:0001583	missense	124602	exon12			TCCCGCCGGGCCC	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.1411C>T	17.37:g.72346868C>T	ENSP00000374566:p.Arg471Trp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	247	0.1130952380952381	25	0.0508130081300813	36	0.09944751381215469	110	0.19230769230769232	76	0.10026385224274406	c	15.18	2.757543	0.49468	0.039265	0.096999	ENSG00000196169	ENST00000551294;ENST00000389916	T;T	0.74632	-0.86;-0.63	5.75	-11.5	0.00074	.	.	.	.	.	T	0.00412	0.0013	L	0.59436	1.845	0.80722	P	0.0	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	P;D;P;P	0.64687	0.895;0.928;0.854;0.854	T	0.79633	-0.1722	8	0.51188	T	0.08	.	22.6567	0.99974	0.8052:0.1948:0.0:0.0	rs2382644	471;429;429;471	Q2TAC6;F8VW50;Q2TAC6-3;Q2TAC6-2	KIF19_HUMAN;.;.;.	W	429;471	ENSP00000449134:R429W;ENSP00000374566:R471W	ENSP00000374566:R471W	R	+	1	2	KIF19	69858463	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.597000	0.05713	-2.595000	0.00454	-0.152000	0.13540	CGG	C|0.910;T|0.090	0.090	strong		0.617	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388693	1388693	+	Missense_Mutation	SNP	C	C	G	rs78906219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388693C>G	ENST00000324803.4	+	1	3354	c.394C>G	c.(394-396)Cat>Gat	p.H132D		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	132					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.H132D(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACGTGCCCATGCGGAGTG	0.697													N|||	864	0.172524	0.112	0.2421	5008	,	,		13504	0.0546		0.2783	False		,,,				2504	0.2178				p.H132D		Atlas-SNP	.											CRIPAK,caecum,carcinoma,0,2	CRIPAK	185	2	1	Substitution - Missense(1)	skin(1)	c.C394G						scavenged	.						68.0	69.0	68.0					4																	1388693		2197	4291	6488	SO:0001583	missense	285464	exon1			CGTGCCCATGCGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.394C>G	4.37:g.1388693C>G	ENSP00000323978:p.His132Asp	Somatic	54	1	0.0185185		WXS	Illumina HiSeq	Phase_I	66	24	0.363636	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	0.898|0.898	-0.723180|-0.723180	0.03158|0.03158	.|.	.|.	ENSG00000179979|ENSG00000179979	ENST00000324803|ENST00000382944	T|.	0.18657|.	2.2|.	0.666|0.666	-0.474|-0.474	0.12108|0.12108	.|.	.|.	.|.	.|.	.|.	T|T	0.12178|0.12178	0.0296|0.0296	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	0.33929|0.33929	-0.9849|-0.9849	8|5	0.28530|0.05833	T|T	0.3|0.94	.|.	2.4426|2.4426	0.04498|0.04498	0.0:0.4251:0.3263:0.2486|0.0:0.4251:0.3263:0.2486	.|.	132|.	Q8N1N5|.	CRPAK_HUMAN|.	D|R	132|115	ENSP00000323978:H132D|.	ENSP00000323978:H132D|ENSP00000372402:P115R	H|P	+|+	1|2	0|0	CRIPAK|CRIPAK	1378693|1378693	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-1.786000|-1.786000	0.01766|0.01766	-0.170000|-0.170000	0.10816|0.10816	-1.737000|-1.737000	0.00689|0.00689	CAT|CCA	G|1.000;|0.000	1.000	weak		0.697	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919231	51919231	+	Silent	SNP	A	A	G	rs112584540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919231A>G	ENST00000339313.5	-	5	1061	c.945T>C	c.(943-945)gcT>gcC	p.A315A	CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Silent_p.A257A|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Silent_p.A232A|SIGLEC10_ENST00000439889.2_Silent_p.A257A|SIGLEC10_ENST00000353836.5_Silent_p.A315A|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Silent_p.A267A|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.A315A			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	315	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CTGAATCCCCAGCCTTCACCC	0.677													a|||	19	0.00379393	0.0015	0.0058	5008	,	,		18136	0.0		0.0089	False		,,,				2504	0.0041				p.A315A		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T945C						PASS	.						41.0	46.0	45.0					19																	51919231		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			ATCCCCAGCCTTC	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.945T>C	19.37:g.51919231A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	120	41	0.341667	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.994;G|0.006	0.006	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
MCM3AP	8888	hgsc.bcm.edu	37	21	47685939	47685939	+	Silent	SNP	A	A	G	rs2839181	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47685939A>G	ENST00000397708.1	-	12	3185	c.2931T>C	c.(2929-2931)caT>caC	p.H977H	MCM3AP_ENST00000291688.1_Silent_p.H977H			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	977	SAC3 homology.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					ACACAGGGGTATGACGAGGGA	0.592													G|||	2112	0.421725	0.4879	0.5274	5008	,	,		17981	0.2788		0.4344	False		,,,				2504	0.3916				p.H977H		Atlas-SNP	.											MCM3AP,NS,carcinoma,0,1	MCM3AP	146	1	0			c.T2931C						PASS	.	G		2198,2208	589.5+/-387.1	554,1090,559	109.0	114.0	113.0		2931	-1.0	0.0	21	dbSNP_100	113	3967,4633	602.2+/-394.5	935,2097,1268	no	coding-synonymous	MCM3AP	NM_003906.3		1489,3187,1827	GG,GA,AA		46.1279,49.8865,47.4012		977/1981	47685939	6165,6841	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon11			AGGGGTATGACGA	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.2931T>C	21.37:g.47685939A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			A|0.554;G|0.446	0.446	strong		0.592	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
FER1L6	654463	hgsc.bcm.edu	37	8	125061895	125061895	+	Silent	SNP	G	G	A	rs4870887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:125061895G>A	ENST00000522917.1	+	22	2978	c.2772G>A	c.(2770-2772)aaG>aaA	p.K924K	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6-AS2_ENST00000601180.1_RNA|FER1L6_ENST00000399018.1_Silent_p.K924K	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	924						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)			CTGTTGTGAAGCTGGCTGACC	0.473													G|||	2409	0.48103	0.5038	0.4452	5008	,	,		18205	0.506		0.492	False		,,,				2504	0.4387				p.K924K		Atlas-SNP	.											FER1L6,colon,carcinoma,+2,2	FER1L6	268	2	0			c.G2772A						PASS	.	G		1806,2076		419,968,554	74.0	80.0	78.0		2772	-0.2	0.4	8	dbSNP_111	78	4147,4161		1063,2021,1070	yes	coding-synonymous	FER1L6	NM_001039112.2		1482,2989,1624	AA,AG,GG		49.9157,46.5224,48.8351		924/1858	125061895	5953,6237	1941	4154	6095	SO:0001819	synonymous_variant	654463	exon22			TGTGAAGCTGGCT	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.2772G>A	8.37:g.125061895G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	210	88	0.419048	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			G|0.501;A|0.498	0.498	strong		0.473	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
GPR108	56927	hgsc.bcm.edu	37	19	6737516	6737516	+	Silent	SNP	C	C	T	rs11539591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6737516C>T	ENST00000264080.7	-	1	98	c.72G>A	c.(70-72)gtG>gtA	p.V24V	GPR108_ENST00000430424.4_5'Flank|TRIP10_ENST00000313285.8_5'Flank|TRIP10_ENST00000600428.1_5'Flank|TRIP10_ENST00000313244.9_5'Flank|TRIP10_ENST00000596758.1_5'Flank	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	24						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						CCAGCAGCAGCACCAGAAGTA	0.726													C|||	466	0.0930511	0.0408	0.2291	5008	,	,		11089	0.002		0.172	False		,,,				2504	0.0798				p.V24V		Atlas-SNP	.											.	GPR108	35	.	0			c.G72A						PASS	.	C		159,3439		5,149,1645	4.0	8.0	7.0		72	3.0	0.8	19	dbSNP_120	7	1213,6641		77,1059,2791	no	coding-synonymous	GPR108	NM_001080452.1		82,1208,4436	TT,TC,CC		15.4444,4.4191,11.9804		24/544	6737516	1372,10080	1799	3927	5726	SO:0001819	synonymous_variant	56927	exon1			CAGCAGCACCAGA		CCDS42479.1	19p13.3	2014-01-30				ENSG00000125734		"""GPCR / Unclassified : 7TM orphan receptors"""	17829	protein-coding gene	gene with protein product							Standard	NM_001080452		Approved	LUSTR2	uc002mfp.3	Q9NPR9	OTTHUMG00000170129	ENST00000264080.7:c.72G>A	19.37:g.6737516C>T		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_001080452	B9EJD7	Silent	SNP	ENST00000264080.7	37	CCDS42479.1	217	0.09935897435897435	27	0.054878048780487805	71	0.19613259668508287	1	0.0017482517482517483	118	0.15567282321899736	C	8.583	0.882728	0.17467	0.044191	0.154444	ENSG00000125734	ENST00000549846	.	.	.	4.1	3.04	0.35103	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999994513	.	.	.	.	.	.	T	0.07309	-1.0779	3	.	.	.	-19.2802	9.5993	0.39593	0.0:0.786:0.214:0.0	rs11539591	.	.	.	T	24	.	.	A	-	1	0	GPR108	6688516	0.212000	0.23540	0.829000	0.32907	0.497000	0.33675	0.038000	0.13862	0.919000	0.36945	0.555000	0.69702	GCT	C|0.900;T|0.100	0.100	strong		0.726	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2		
MUC2	4583	hgsc.bcm.edu	37	11	1094690	1094690	+	Silent	SNP	C	C	T	rs10794291	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1094690C>T	ENST00000441003.2	+	31	5805	c.5778C>T	c.(5776-5778)acC>acT	p.T1926T	MUC2_ENST00000333592.6_Silent_p.T214T|MUC2_ENST00000361558.6_Silent_p.T64T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4288					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)	GTACCACGACCGGGTCATCTT	0.632													C|||	3780	0.754792	0.848	0.7363	5008	,	,		16819	0.9325		0.5099	False		,,,				2504	0.7106				p.T1922T		Atlas-SNP	.											.	MUC2	614	.	0			c.C5766T						PASS	.			3333,889		1331,671,109	76.0	94.0	88.0		5763	-3.9	0.0	11	dbSNP_120	88	4221,4213		1081,2059,1077	no	coding-synonymous	MUC2	NM_002457.2		2412,2730,1186	TT,TC,CC		49.9526,21.0564,40.3129		1921/2813	1094690	7554,5102	2111	4217	6328	SO:0001819	synonymous_variant	4583	exon32			CACGACCGGGTCA	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.5778C>T	11.37:g.1094690C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				C|0.311;T|0.689	0.689	strong		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FBXW10	10517	hgsc.bcm.edu	37	17	18653145	18653145	+	Missense_Mutation	SNP	C	C	G	rs200535885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18653145C>G	ENST00000395665.4	+	3	1002	c.781C>G	c.(781-783)Ctg>Gtg	p.L261V	FBXW10_ENST00000301938.4_Missense_Mutation_p.L261V|FBXW10_ENST00000395667.1_Missense_Mutation_p.L261V|FBXW10_ENST00000308799.4_Missense_Mutation_p.L261V			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	261										NS(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						ATTGGTTGACCTGGATGACAT	0.473																																					p.L261V		Atlas-SNP	.											.	FBXW10	82	.	0			c.C781G						PASS	.						129.0	103.0	112.0					17																	18653145		2203	4297	6500	SO:0001583	missense	10517	exon3			GTTGACCTGGATG	BC028364	CCDS11199.2, CCDS11199.3, CCDS58524.1	17p11	2013-01-09	2007-02-08	2004-07-21	ENSG00000171931	ENSG00000171931		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1211	protein-coding gene	gene with protein product		611679	"""chromosome 17 open reading frame 1A"", ""F-box and WD-40 domain protein 10"""	C17orf1, C17orf1A		9787083, 7586531	Standard	NM_001267585		Approved	SM2SH2, HREP, Fbw10	uc002guk.3	Q5XX13	OTTHUMG00000059048	ENST00000395665.4:c.781C>G	17.37:g.18653145C>G	ENSP00000379025:p.Leu261Val	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	491	135	0.274949	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Missense_Mutation	SNP	ENST00000395665.4	37	CCDS11199.3	.	.	.	.	.	.	.	.	.	.	C	9.289	1.050026	0.19827	.	.	ENSG00000171931	ENST00000395667;ENST00000308799;ENST00000301938;ENST00000395665	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	2.48	-1.27	0.09347	.	0.000000	0.28908	U	0.013760	T	0.23649	0.0572	M	0.65975	2.015	0.09310	N	1	B;B;B;B	0.19583	0.037;0.037;0.022;0.016	B;B;B;B	0.19148	0.024;0.024;0.011;0.024	T	0.15780	-1.0425	10	0.31617	T	0.26	.	3.914	0.09214	0.0:0.3418:0.3911:0.2671	.	261;261;261;261	Q5XX13-3;Q5XX13-2;Q5XX13;Q5XX13-4	.;.;FBW10_HUMAN;.	V	261	ENSP00000379026:L261V;ENSP00000310382:L261V;ENSP00000306937:L261V;ENSP00000379025:L261V	ENSP00000306937:L261V	L	+	1	2	FBXW10	18593870	0.154000	0.22792	0.008000	0.14137	0.738000	0.42128	0.251000	0.18257	-0.391000	0.07763	-0.507000	0.04495	CTG	.	.	weak		0.473	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456	
NPHP4	261734	hgsc.bcm.edu	37	1	5937168	5937168	+	Silent	SNP	G	G	A	rs3747992	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:5937168G>A	ENST00000378156.4	-	20	3067	c.2802C>T	c.(2800-2802)cgC>cgT	p.R934R	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	934					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)		CGCTCGTCCCGCGCCGGCCCA	0.637													G|||	2271	0.453474	0.2859	0.4597	5008	,	,		16650	0.7341		0.4225	False		,,,				2504	0.4182				p.R934R		Atlas-SNP	.											NPHP4,NS,carcinoma,0,2	NPHP4	119	2	0			c.C2802T						PASS	.	G		1224,2996		180,864,1066	14.0	18.0	17.0		2802	-0.8	0.0	1	dbSNP_107	17	3227,5183		649,1929,1627	no	coding-synonymous	NPHP4	NM_015102.3		829,2793,2693	AA,AG,GG		38.371,29.0047,35.2415		934/1427	5937168	4451,8179	2110	4205	6315	SO:0001819	synonymous_variant	261734	exon20			CGTCCCGCGCCGG	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.2802C>T	1.37:g.5937168G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	182	167	0.917582	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	37	CCDS44052.1																																																																																			G|0.536;A|0.464	0.464	strong		0.637	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
MFSD4	148808	hgsc.bcm.edu	37	1	205561372	205561372	+	Silent	SNP	C	C	T	rs7529077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:205561372C>T	ENST00000367147.4	+	7	1347	c.1254C>T	c.(1252-1254)ttC>ttT	p.F418F	MFSD4_ENST00000536357.1_Silent_p.F331F|RNU6-418P_ENST00000384035.1_RNA|MFSD4_ENST00000539267.1_Silent_p.F418F	NM_181644.4	NP_857595.3	Q8N468	MFSD4_HUMAN	major facilitator superfamily domain containing 4	418					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0908)			GCAGCACCTTCCCCAGCATGC	0.637											OREG0014160	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	671	0.133986	0.2171	0.1311	5008	,	,		12809	0.0149		0.2187	False		,,,				2504	0.0593				p.F418F		Atlas-SNP	.											.	MFSD4	46	.	0			c.C1254T						PASS	.	C		958,3448	352.8+/-311.9	105,748,1350	89.0	67.0	75.0		1254	2.7	1.0	1	dbSNP_116	75	1940,6660	333.2+/-320.4	218,1504,2578	no	coding-synonymous	MFSD4	NM_181644.4		323,2252,3928	TT,TC,CC		22.5581,21.7431,22.282		418/515	205561372	2898,10108	2203	4300	6503	SO:0001819	synonymous_variant	148808	exon7			CACCTTCCCCAGC	BC036549	CCDS1455.1	1q32.1	2008-02-05			ENSG00000174514	ENSG00000174514			25433	protein-coding gene	gene with protein product							Standard	NM_181644		Approved	DKFZp761N1114, FLJ34577, UNQ3064, FLJ25004	uc001hcv.4	Q8N468	OTTHUMG00000037197	ENST00000367147.4:c.1254C>T	1.37:g.205561372C>T		Somatic	113	0	0	2153	WXS	Illumina HiSeq	Phase_I	159	73	0.459119	NM_181644	B7Z8X3|Q6UY25|Q8NAY0|Q8TCP4	Silent	SNP	ENST00000367147.4	37	CCDS1455.1																																																																																			C|0.812;T|0.188	0.188	strong		0.637	MFSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090391.1	NM_181644	
LPP	4026	hgsc.bcm.edu	37	3	188478055	188478055	+	Silent	SNP	C	C	T	rs6771786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:188478055C>T	ENST00000312675.4	+	8	1641	c.1395C>T	c.(1393-1395)tgC>tgT	p.C465C	LPP_ENST00000543006.1_Silent_p.C465C	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	465	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		AAGCATACTGCGAGCCCTGCT	0.458			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								C|||	15	0.00299521	0.0	0.0029	5008	,	,		19555	0.001		0.0099	False		,,,				2504	0.002				p.C465C		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.C1395T						PASS	.	C	,,	6,4400	11.4+/-27.6	0,6,2197	140.0	131.0	134.0		1395,954,1395	-5.8	0.8	3	dbSNP_116	134	80,8520	47.2+/-106.3	1,78,4221	no	coding-synonymous,coding-synonymous,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	1,84,6418	TT,TC,CC		0.9302,0.1362,0.6612	,,	465/613,318/466,465/613	188478055	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon8			ATACTGCGAGCCC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1395C>T	3.37:g.188478055C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			C|0.994;T|0.006	0.006	strong		0.458	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
UQCR10	29796	hgsc.bcm.edu	37	22	30163526	30163526	+	Missense_Mutation	SNP	A	A	G	rs76013375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30163526A>G	ENST00000330029.6	+	1	169	c.139A>G	c.(139-141)Atc>Gtc	p.I47V	ZMAT5_ENST00000397781.3_5'Flank|ZMAT5_ENST00000344318.3_5'Flank|UQCR10_ENST00000401406.3_Missense_Mutation_p.I47V	NM_001003684.1|NM_013387.3	NP_001003684.1|NP_037519.2	Q9UDW1	QCR9_HUMAN	ubiquinol-cytochrome c reductase, complex III subunit X	47			I -> V (in dbSNP:rs14115).		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)	5						CTACGACCACATCAACGAGGG	0.602													A|||	739	0.147564	0.3389	0.0951	5008	,	,		17136	0.0853		0.0467	False		,,,				2504	0.0941				p.I47V		Atlas-SNP	.											.	UQCR10	10	.	0			c.A139G						PASS	.	A	VAL/ILE,VAL/ILE	1043,2937		125,793,1072	36.0	41.0	39.0		139,139	4.6	1.0	22	dbSNP_131	39	425,7883		14,397,3743	yes	missense,missense	UQCR10	NM_001003684.1,NM_013387.3	29,29	139,1190,4815	GG,GA,AA		5.1156,26.206,11.9466	benign,benign	47/63,47/64	30163526	1468,10820	1990	4154	6144	SO:0001583	missense	29796	exon1			GACCACATCAACG	AB028598	CCDS46680.1, CCDS46681.1	22q12.2	2011-07-04			ENSG00000184076	ENSG00000184076		"""Mitochondrial respiratory chain complex / Complex III"""	30863	protein-coding gene	gene with protein product	"""ubiquinol-cytochrome c reductase, complex III subunit X, 7.2kDa"", ""complex III subunit 9"""	610843				11042152	Standard	NM_013387		Approved	HSPC051, UCRC, QCR9, UCCR7.2	uc003agq.1	Q9UDW1	OTTHUMG00000151283	ENST00000330029.6:c.139A>G	22.37:g.30163526A>G	ENSP00000332887:p.Ile47Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	15	0.3	NM_001003684	B5MCM5|Q9T2V6	Missense_Mutation	SNP	ENST00000330029.6	37	CCDS46680.1	288	0.13186813186813187	164	0.3333333333333333	28	0.07734806629834254	56	0.0979020979020979	40	0.052770448548812667	A	13.79	2.341566	0.41498	0.26206	0.051156	ENSG00000184076	ENST00000330029;ENST00000401406;ENST00000406782	T;T	0.42900	0.96;0.96	5.73	4.63	0.57726	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.37359	P	0.088862	B;B	0.27932	0.004;0.194	B;B	0.29785	0.006;0.107	T	0.38564	-0.9655	7	0.16420	T	0.52	-0.3172	9.2483	0.37541	0.818:0.182:0.0:0.0	rs14115;rs2286123;rs17003399;rs60363153;rs14115	47;47	Q9UDW1;Q9UDW1-2	QCR9_HUMAN;.	V	47	ENSP00000332887:I47V;ENSP00000384962:I47V	ENSP00000332887:I47V	I	+	1	0	UQCR10	28493526	0.876000	0.30132	1.000000	0.80357	0.960000	0.62799	0.609000	0.24238	2.196000	0.70406	0.456000	0.33151	ATC	A|0.883;G|0.117	0.117	strong		0.602	UQCR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322081.1	NM_013387	
VENTX	27287	hgsc.bcm.edu	37	10	135053784	135053784	+	Missense_Mutation	SNP	A	A	G	rs148086757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:135053784A>G	ENST00000325980.9	+	3	1262	c.751A>G	c.(751-753)Atg>Gtg	p.M251V		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	251					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)		CCTGTGTGCTATGCCACAGAC	0.667													a|||	28	0.00559105	0.0	0.013	5008	,	,		9132	0.001		0.008	False		,,,				2504	0.0102				p.M251V		Atlas-SNP	.											.	VENTX	24	.	0			c.A751G						PASS	.	A	VAL/MET	1,4105		0,1,2052	15.0	17.0	17.0		751	0.9	0.0	10	dbSNP_134	17	32,8112		0,32,4040	yes	missense	VENTX	NM_014468.2	21	0,33,6092	GG,GA,AA		0.3929,0.0244,0.2694	benign	251/259	135053784	33,12217	2053	4072	6125	SO:0001583	missense	27287	exon3			TGTGCTATGCCAC	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.751A>G	10.37:g.135053784A>G	ENSP00000357556:p.Met251Val	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	41	15	0.365854	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	a	7.807	0.714805	0.15306	2.44E-4	0.003929	ENSG00000151650	ENST00000325980	D	0.89939	-2.59	2.96	0.867	0.19085	.	0.369811	0.17386	U	0.176135	T	0.68540	0.3012	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.63152	-0.6701	10	0.62326	D	0.03	.	7.6583	0.28388	0.4764:0.5236:0.0:0.0	.	251	O95231	VENTX_HUMAN	V	251	ENSP00000357556:M251V	ENSP00000357556:M251V	M	+	1	0	VENTX	134903774	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.801000	0.04550	0.052000	0.16007	-0.447000	0.05616	ATG	A|0.995;G|0.005	0.005	strong		0.667	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
PKD1	5310	hgsc.bcm.edu	37	16	2161796	2161796	+	Silent	SNP	G	G	A	rs75510884	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2161796G>A	ENST00000262304.4	-	15	3580	c.3372C>T	c.(3370-3372)gcC>gcT	p.A1124A	PKD1_ENST00000423118.1_Silent_p.A1124A|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1124	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGGGCAGGGAGGCGCGCACGC	0.692													a|||	574	0.114617	0.2935	0.111	5008	,	,		15825	0.0		0.0944	False		,,,				2504	0.0143				p.A1124A		Atlas-SNP	.											PKD1,colon,carcinoma,-2,1	PKD1	184	1	0			c.C3372T						PASS	.	G	,	1061,3315		141,779,1268	20.0	21.0	21.0		3372,3372	-10.3	0.0	16	dbSNP_131	21	832,7746		55,722,3512	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	196,1501,4780	AA,AG,GG		9.6992,24.2459,14.6132	,	1124/4303,1124/4304	2161796	1893,11061	2188	4289	6477	SO:0001819	synonymous_variant	5310	exon15			CAGGGAGGCGCGC	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.3372C>T	16.37:g.2161796G>A		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			G|0.854;A|0.146	0.146	strong		0.692	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
GSPT1	2935	hgsc.bcm.edu	37	16	11969985	11969985	+	Silent	SNP	C	C	T	rs369462446		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:11969985C>T	ENST00000563468.1	-	11	1262	c.1236G>A	c.(1234-1236)gcG>gcA	p.A412A	GSPT1_ENST00000420576.2_Silent_p.A412A|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000439887.2_Silent_p.A549A|GSPT1_ENST00000434724.2_Silent_p.A550A			P15170	ERF3A_HUMAN	G1 to S phase transition 1	412					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						TATGCAGCACCGCATTATAGC	0.333																																					p.A550A		Atlas-SNP	.											.	GSPT1	71	.	0			c.G1650A						PASS	.	C	,,	2,4392		0,2,2195	180.0	182.0	182.0		1647,1236,1650	3.0	1.0	16		182	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GSPT1	NM_001130006.1,NM_001130007.1,NM_002094.3	,,	0,2,6495	TT,TC,CC		0.0,0.0455,0.0154	,,	549/637,412/500,550/638	11969985	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	2935	exon13			CAGCACCGCATTA	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		ENST00000563468.1:c.1236G>A	16.37:g.11969985C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	122	56	0.459016	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	37	CCDS45414.1																																																																																			.	.	weak		0.333	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094	
CBLC	23624	hgsc.bcm.edu	37	19	45296806	45296806	+	Missense_Mutation	SNP	C	C	T	rs3208856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45296806C>T	ENST00000270279.3	+	8	1276	c.1213C>T	c.(1213-1215)Cac>Tac	p.H405Y	CBLC_ENST00000341505.4_Missense_Mutation_p.H359Y	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	405	Interaction with RET.		H -> Y (in dbSNP:rs3208856). {ECO:0000269|PubMed:10362357, ECO:0000269|PubMed:10571044}.		cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				CTACCAGTTCCACGGTCAGGC	0.647			M		AML								C|||	97	0.019369	0.0446	0.0173	5008	,	,		18105	0.0		0.0229	False		,,,				2504	0.0031				p.H405Y		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C1213T						PASS	.	C	TYR/HIS,TYR/HIS	186,4220		7,172,2024	48.0	41.0	43.0		1075,1213	4.2	0.0	19	dbSNP_105	43	312,8288		8,296,3996	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	83,83	15,468,6020	TT,TC,CC		3.6279,4.2215,3.829	benign,benign	359/429,405/475	45296806	498,12508	2203	4300	6503	SO:0001583	missense	23624	exon8			CAGTTCCACGGTC	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.1213C>T	19.37:g.45296806C>T	ENSP00000270279:p.His405Tyr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_012116	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	40	0.018315018315018316	13	0.026422764227642278	9	0.024861878453038673	0	0.0	18	0.023746701846965697	.	12.81	2.049017	0.36181	0.042215	0.036279	ENSG00000142273	ENST00000270279;ENST00000341505	D;D	0.86627	-2.14;-2.15	4.25	4.25	0.50352	.	0.965075	0.08514	N	0.934465	T	0.55561	0.1928	N	0.24115	0.695	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.09377	0.004;0.002	T	0.63871	-0.6539	10	0.66056	D	0.02	-0.0544	14.5453	0.68027	0.0:1.0:0.0:0.0	rs3208856;rs3208856	359;405	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	Y	405;359	ENSP00000270279:H405Y;ENSP00000340250:H359Y	ENSP00000270279:H405Y	H	+	1	0	CBLC	49988646	0.001000	0.12720	0.005000	0.12908	0.022000	0.10575	1.208000	0.32345	2.369000	0.80426	0.555000	0.69702	CAC	C|0.972;G|0.000;T|0.028	0.028	strong		0.647	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
MYOM2	9172	hgsc.bcm.edu	37	8	2057298	2057298	+	Silent	SNP	C	C	T	rs2280897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:2057298C>T	ENST00000262113.4	+	25	3297	c.3156C>T	c.(3154-3156)aaC>aaT	p.N1052N	MYOM2_ENST00000523438.1_Silent_p.N477N	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1052					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)		TTATTATTAACGACAGAGAAG	0.463													C|||	715	0.142772	0.028	0.1643	5008	,	,		17457	0.2827		0.1441	False		,,,				2504	0.137				p.N1052N		Atlas-SNP	.											.	MYOM2	251	.	0			c.C3156T						PASS	.	C		181,4225	115.4+/-153.4	4,173,2026	90.0	86.0	87.0		3156	-6.1	0.5	8	dbSNP_100	87	1186,7414	241.0+/-271.5	93,1000,3207	no	coding-synonymous	MYOM2	NM_003970.2		97,1173,5233	TT,TC,CC		13.7907,4.108,10.5105		1052/1466	2057298	1367,11639	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon25			TATTAACGACAGA		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.3156C>T	8.37:g.2057298C>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			C|0.875;T|0.125	0.125	strong		0.463	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
DEFB127	140850	hgsc.bcm.edu	37	20	139576	139576	+	Missense_Mutation	SNP	C	C	A	rs16995685	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:139576C>A	ENST00000382388.3	+	2	286	c.211C>A	c.(211-213)Cgt>Agt	p.R71S		NM_139074.3	NP_620713.1	Q9H1M4	DB127_HUMAN	defensin, beta 127	71			R -> S (in dbSNP:rs16995685). {ECO:0000269|PubMed:11854508}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			AAAGCCACCTCGTCCAAAGCC	0.388													C|||	1623	0.324081	0.0431	0.3487	5008	,	,		20057	0.5407		0.3419	False		,,,				2504	0.4448				p.R71S		Atlas-SNP	.											.	DEFB127	15	.	0			c.C211A						PASS	.	C	SER/ARG	399,4007	199.4+/-223.0	18,363,1822	109.0	93.0	98.0		211	1.2	0.0	20	dbSNP_123	98	3030,5570	466.8+/-366.9	519,1992,1789	yes	missense	DEFB127	NM_139074.2	110	537,2355,3611	AA,AC,CC		35.2326,9.0558,26.3648	benign	71/100	139576	3429,9577	2203	4300	6503	SO:0001583	missense	140850	exon2			CCACCTCGTCCAA	AY358796	CCDS12991.1	20p13	2008-02-01	2002-05-09	2002-05-10	ENSG00000088782	ENSG00000088782		"""Defensins, beta"""	16206	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 73"""	C20orf73		11854508	Standard	NM_139074		Approved	bA530N10.2, DEF-27	uc002wcy.2	Q9H1M4	OTTHUMG00000031617	ENST00000382388.3:c.211C>A	20.37:g.139576C>A	ENSP00000371825:p.Arg71Ser	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	185	92	0.497297	NM_139074	Q14DW7	Missense_Mutation	SNP	ENST00000382388.3	37	CCDS12991.1	702	0.32142857142857145	19	0.03861788617886179	135	0.3729281767955801	287	0.5017482517482518	261	0.34432717678100266	C	0.491	-0.875449	0.02550	0.090558	0.352326	ENSG00000088782	ENST00000382388	T	0.15256	2.44	3.26	1.24	0.21308	.	0.768263	0.10589	N	0.656961	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.21520	0.057	B	0.20184	0.028	T	0.45512	-0.9256	8	0.26408	T	0.33	-0.2158	4.0324	0.09714	0.2294:0.6438:0.0:0.1268	rs16995685;rs16995685	71	Q9H1M4	DB127_HUMAN	S	71	ENSP00000371825:R71S	ENSP00000371825:R71S	R	+	1	0	DEFB127	87576	0.004000	0.15560	0.003000	0.11579	0.001000	0.01503	0.595000	0.24029	0.367000	0.24454	-0.657000	0.03884	CGT	C|0.718;A|0.282	0.282	strong		0.388	DEFB127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077429.1	NM_139074	
AKAP13	11214	hgsc.bcm.edu	37	15	86123216	86123216	+	Silent	SNP	A	A	G	rs112396662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:86123216A>G	ENST00000394518.2	+	7	2012	c.1917A>G	c.(1915-1917)tcA>tcG	p.S639S	AKAP13_ENST00000361243.2_Silent_p.S639S|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	639					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						AAACAAATTCATCTCATGCTC	0.453													A|||	6	0.00119808	0.0	0.0014	5008	,	,		22520	0.0		0.005	False		,,,				2504	0.0				p.S639S	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.A1917G						PASS	.	A	,	10,4394	15.5+/-35.6	0,10,2192	142.0	127.0	132.0		1917,1917	-1.3	0.0	15	dbSNP_132	132	85,8513	48.1+/-107.5	0,85,4214	no	coding-synonymous,coding-synonymous	AKAP13	NM_006738.4,NM_007200.3	,	0,95,6406	GG,GA,AA		0.9886,0.2271,0.7307	,	639/2818,639/2814	86123216	95,12907	2202	4299	6501	SO:0001819	synonymous_variant	11214	exon7			AAATTCATCTCAT	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.1917A>G	15.37:g.86123216A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Silent	SNP	ENST00000394518.2	37	CCDS32319.1																																																																																			A|0.994;G|0.006	0.006	strong		0.453	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
ALPK1	80216	hgsc.bcm.edu	37	4	113353052	113353052	+	Silent	SNP	C	C	T	rs17044681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:113353052C>T	ENST00000458497.1	+	11	2628	c.2349C>T	c.(2347-2349)tcC>tcT	p.S783S	ALPK1_ENST00000504176.2_Silent_p.S705S|ALPK1_ENST00000177648.9_Silent_p.S783S	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	783							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CTAGTCCCTCCTGGGTTGACC	0.493													C|||	247	0.0493211	0.0197	0.0749	5008	,	,		19375	0.001		0.1501	False		,,,				2504	0.0174				p.S783S		Atlas-SNP	.											.	ALPK1	125	.	0			c.C2349T						PASS	.	C	,	173,4233	114.2+/-152.2	5,163,2035	56.0	55.0	55.0		2349,2349	-1.1	0.1	4	dbSNP_123	55	1189,7411	239.9+/-270.8	75,1039,3186	no	coding-synonymous,coding-synonymous	ALPK1	NM_001102406.1,NM_025144.3	,	80,1202,5221	TT,TC,CC		13.8256,3.9265,10.4721	,	783/1245,783/1245	113353052	1362,11644	2203	4300	6503	SO:0001819	synonymous_variant	80216	exon11			TCCCTCCTGGGTT	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2349C>T	4.37:g.113353052C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	37	CCDS3697.1																																																																																			C|0.912;T|0.088	0.088	strong		0.493	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
IZUMO1	284359	hgsc.bcm.edu	37	19	49244220	49244220	+	Missense_Mutation	SNP	G	G	A	rs66877153|rs2307019|rs386810061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49244220G>A	ENST00000332955.2	-	10	1545	c.998C>T	c.(997-999)gCg>gTg	p.A333V	RASIP1_ENST00000594232.1_5'Flank|RASIP1_ENST00000222145.4_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	333			A -> V (in dbSNP:rs2307019). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15759005, ECO:0000269|PubMed:18082733}.		cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TTGCTCGGCCGCTCCACTGCC	0.512													G|||	2573	0.513778	0.3162	0.5461	5008	,	,		18313	0.8323		0.4473	False		,,,				2504	0.498				p.A333V		Atlas-SNP	.											.	IZUMO1	30	.	0			c.C998T						PASS	.	G	VAL/ALA	1423,2983	463.2+/-353.5	246,931,1026	113.0	98.0	103.0		998	-0.8	0.0	19	dbSNP_100	103	3753,4847	529.8+/-381.7	794,2165,1341	yes	missense	IZUMO1	NM_182575.2	64	1040,3096,2367	AA,AG,GG		43.6395,32.2969,39.797	benign	333/351	49244220	5176,7830	2203	4300	6503	SO:0001583	missense	284359	exon10			TCGGCCGCTCCAC	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.998C>T	19.37:g.49244220G>A	ENSP00000327786:p.Ala333Val	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	67	0.609091	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	1004	0.4597069597069597	121	0.2459349593495935	178	0.49171270718232046	422	0.7377622377622378	283	0.3733509234828496	G	9.027	0.986244	0.18889	0.322969	0.436395	ENSG00000182264	ENST00000332955	T	0.25912	1.77	4.09	-0.804	0.10882	.	2.476250	0.02608	N	0.101765	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.40776	-0.9545	9	0.19147	T	0.46	0.0138	5.0059	0.14288	0.1805:0.0:0.5356:0.2839	rs2307019;rs58096827;rs2307019	333	Q8IYV9	IZUM1_HUMAN	V	333	ENSP00000327786:A333V	ENSP00000327786:A333V	A	-	2	0	IZUMO1	53936032	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.272000	0.08560	-0.225000	0.09913	-2.067000	0.00394	GCG	AA|0.500;CG|0.500	.	alt		0.512	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	
TSPYL4	23270	hgsc.bcm.edu	37	6	116575116	116575116	+	Missense_Mutation	SNP	G	G	T	rs17524614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:116575116G>T	ENST00000420283.1	-	1	145	c.56C>A	c.(55-57)gCt>gAt	p.A19D	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	19					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		GTCGGGAGCAGCCAGGCCGCC	0.622													G|||	509	0.101637	0.0106	0.2089	5008	,	,		16134	0.1101		0.1501	False		,,,				2504	0.09				p.A19D		Atlas-SNP	.											.	TSPYL4	18	.	0			c.C56A						PASS	.	G	ASP/ALA	108,3832		3,102,1865	19.0	23.0	21.0		56	1.3	0.0	6	dbSNP_123	21	1016,7262		57,902,3180	yes	missense	TSPYL4	NM_021648.4	126	60,1004,5045	TT,TG,GG		12.2735,2.7411,9.1995	benign	19/415	116575116	1124,11094	1970	4139	6109	SO:0001583	missense	23270	exon1			GGAGCAGCCAGGC		CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.56C>A	6.37:g.116575116G>T	ENSP00000410943:p.Ala19Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	75	8	0.106667	NM_021648	B4DYQ2|O94828|Q96GW8	Missense_Mutation	SNP	ENST00000420283.1	37	CCDS5106.1	276	0.12637362637362637	8	0.016260162601626018	73	0.20165745856353592	71	0.12412587412587413	124	0.16358839050131926	G	12.35	1.911171	0.33721	0.027411	0.122735	ENSG00000187189	ENST00000420283	T	0.26660	1.72	4.12	1.34	0.21922	.	.	.	.	.	T	0.08358	0.0208	L	0.55481	1.735	0.80722	P	0.0	P	0.42409	0.779	B	0.36885	0.235	T	0.14144	-1.0483	8	0.52906	T	0.07	-0.0586	4.1276	0.10134	0.2135:0.1949:0.5916:0.0	rs17524614	19	Q9UJ04	TSYL4_HUMAN	D	19	ENSP00000410943:A19D	ENSP00000410943:A19D	A	-	2	0	TSPYL4	116681809	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.137000	0.15995	0.285000	0.22329	0.462000	0.41574	GCT	G|0.876;T|0.124	0.124	strong		0.622	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
HERC2	8924	hgsc.bcm.edu	37	15	28459227	28459227	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459227C>T	ENST00000261609.7	-	41	6658	c.6550G>A	c.(6550-6552)Gaa>Aaa	p.E2184K		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.E2184K(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)		CCCACCCCTTCGGAAGGCCTT	0.542																																					p.E2184K		Atlas-SNP	.											HERC2,NS,carcinoma,0,1	HERC2	501	1	2	Substitution - Missense(2)	prostate(2)	c.G6550A						scavenged	.																																			SO:0001583	missense	8924	exon41			CCCCTTCGGAAGG	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.6550G>A	15.37:g.28459227C>T	ENSP00000261609:p.Glu2184Lys	Somatic	192	1	0.00520833		WXS	Illumina HiSeq	Phase_I	245	22	0.0897959	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	6.061	0.379606	0.11466	.	.	ENSG00000128731	ENST00000261609	T	0.38077	1.16	5.43	3.53	0.40419	.	0.245102	0.40385	N	0.001107	T	0.22003	0.0530	N	0.19112	0.55	0.50171	D	0.999857	B	0.10296	0.003	B	0.06405	0.002	T	0.04242	-1.0966	10	0.24483	T	0.36	.	10.3512	0.43937	0.1352:0.7947:0.0:0.0701	.	2184	O95714	HERC2_HUMAN	K	2184	ENSP00000261609:E2184K	ENSP00000261609:E2184K	E	-	1	0	HERC2	26132822	1.000000	0.71417	0.009000	0.14445	0.018000	0.09664	5.747000	0.68689	0.640000	0.30582	0.484000	0.47621	GAA	.	.	none		0.542	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629955	32629955	+	Silent	SNP	C	C	T	rs1063321	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629955C>T	ENST00000399082.3	-	2	224	c.180G>A	c.(178-180)tcG>tcA	p.S60S	HLA-DQB1_ENST00000399079.3_Silent_p.S150S|HLA-DQB1_ENST00000434651.2_Silent_p.S150S|HLA-DQB1_ENST00000399084.1_Silent_p.S150S|HLA-DQB1_ENST00000374943.4_Silent_p.S150S|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	150	Beta-1.		T -> S (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04 and allele DQB1*02:05; dbSNP:rs9274405).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	AATCTGTCACCGAGCAGACCA	0.552									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				c|||	1961	0.391573	0.3147	0.5447	5008	,	,		12272	0.4712		0.3867	False		,,,				2504	0.3098				p.S150S	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G450A						PASS	.						27.0	25.0	26.0					6																	32629955		1960	4141	6101	SO:0001819	synonymous_variant	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TGTCACCGAGCAG		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.180G>A	6.37:g.32629955C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	98	23	0.234694	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399082.3	37																																																																																				C|0.370;T|0.630	0.630	strong		0.552	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
SNED1	25992	hgsc.bcm.edu	37	2	241991875	241991875	+	Silent	SNP	G	G	A	rs57214830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:241991875G>A	ENST00000310397.8	+	15	2073	c.2073G>A	c.(2071-2073)cgG>cgA	p.R691R	SNED1_ENST00000469006.1_3'UTR|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.R691R|SNED1_ENST00000401884.1_Silent_p.R691R|SNED1_ENST00000405547.3_Silent_p.R691R	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	691	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		TGGGACGCCGGTGCCAGGCAG	0.637													G|||	1286	0.256789	0.2126	0.245	5008	,	,		17592	0.4067		0.1928	False		,,,				2504	0.2362				p.R691R		Atlas-SNP	.											.	SNED1	76	.	0			c.G2073A						PASS	.	G		800,3316		93,614,1351	43.0	49.0	47.0		2073	2.2	1.0	2	dbSNP_129	47	1433,6939		134,1165,2887	yes	coding-synonymous	SNED1	NM_001080437.1		227,1779,4238	AA,AG,GG		17.1166,19.4363,17.8812		691/1414	241991875	2233,10255	2058	4186	6244	SO:0001819	synonymous_variant	25992	exon15			ACGCCGGTGCCAG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.2073G>A	2.37:g.241991875G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1																																																																																			G|0.756;A|0.244	0.244	strong		0.637	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
WDR45B	56270	hgsc.bcm.edu	37	17	80573888	80573888	+	Silent	SNP	G	G	A	rs147083174	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80573888G>A	ENST00000392325.4	-	10	1136	c.942C>T	c.(940-942)gaC>gaT	p.D314D	WDR45B_ENST00000571835.1_5'Flank	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	314																	AGTAGCTGCCGTCTGCACAAA	0.498													G|||	19	0.00379393	0.003	0.0072	5008	,	,		18962	0.0		0.0089	False		,,,				2504	0.001				p.D314D		Atlas-SNP	.											.	.	.	.	0			c.C942T						PASS	.	G		8,4398	12.9+/-30.5	0,8,2195	119.0	100.0	107.0		942	-2.3	0.9	17	dbSNP_134	107	74,8526	44.0+/-102.2	0,74,4226	yes	coding-synonymous	WDR45L	NM_019613.3		0,82,6421	AA,AG,GG		0.8605,0.1816,0.6305		314/345	80573888	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	56270	exon10			GCTGCCGTCTGCA	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.942C>T	17.37:g.80573888G>A		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_019613	O95328|Q2MCP6|Q6IBN2	Silent	SNP	ENST00000392325.4	37	CCDS11815.2																																																																																			G|0.995;A|0.005	0.005	strong		0.498	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110489620	110489620	+	Silent	SNP	A	A	T	rs1783148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110489620A>T	ENST00000378402.5	+	53	9188	c.9084A>T	c.(9082-9084)acA>acT	p.T3028T		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3028					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GACCAGCCACATATAAGTACA	0.378										HNSCC(38;0.096)			A|||	2135	0.426318	0.3828	0.5187	5008	,	,		19204	0.3284		0.337	False		,,,				2504	0.6125				p.T3028T		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A9084T						PASS	.	A		1421,2329		289,843,743	63.0	58.0	60.0		9084	-5.7	0.5	8	dbSNP_89	60	3000,5224		571,1858,1683	no	coding-synonymous	PKHD1L1	NM_177531.4		860,2701,2426	TT,TA,AA		36.4786,37.8933,36.9217		3028/4244	110489620	4421,7553	1875	4112	5987	SO:0001819	synonymous_variant	93035	exon53			AGCCACATATAAG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9084A>T	8.37:g.110489620A>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			A|0.634;T|0.366	0.366	strong		0.378	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
OR11H12	440153	hgsc.bcm.edu	37	14	19378322	19378322	+	Missense_Mutation	SNP	G	G	A	rs201485834		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:19378322G>A	ENST00000550708.1	+	1	801	c.729G>A	c.(727-729)atG>atA	p.M243I		NM_001013354.1|NM_001197287.1	NP_001013372.1|NP_001184216.1	B2RN74	O11HC_HUMAN	olfactory receptor, family 11, subfamily H, member 12	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGTTGGGTATGCCTTCAAGCA	0.428																																					p.M243I		Atlas-SNP	.											OR11H12,NS,malignant_melanoma,+1,1	OR11H12	58	1	0			c.G729A						scavenged	.						3.0	1.0	1.0					14																	19378322		201	443	644	SO:0001583	missense	440153	exon1			GGGTATGCCTTCA		CCDS32017.1	14q11.2	2013-01-25			ENSG00000257115	ENSG00000257115		"""GPCR / Class A : Olfactory receptors"""	30738	protein-coding gene	gene with protein product							Standard	NM_001013354		Approved		uc010tkp.2	B2RN74	OTTHUMG00000170298	ENST00000550708.1:c.729G>A	14.37:g.19378322G>A	ENSP00000449002:p.Met243Ile	Somatic	566	0	0		WXS	Illumina HiSeq	Phase_I	632	12	0.0189873	NM_001013354		Missense_Mutation	SNP	ENST00000550708.1	37	CCDS32017.1	.	.	.	.	.	.	.	.	.	.	g	0.944	-0.708542	0.03230	.	.	ENSG00000257115	ENST00000550708	T	0.00021	9.03	0.585	0.585	0.17428	GPCR, rhodopsin-like superfamily (1);	0.483801	0.17283	N	0.179914	T	0.00039	0.0001	N	0.02876	-0.465	0.22675	N	0.998867	B	0.13594	0.008	B	0.12837	0.008	T	0.18366	-1.0339	9	0.02654	T	1	.	3.0137	0.06052	0.3477:0.0:0.6523:0.0	.	243	B2RN74	O11HC_HUMAN	I	243	ENSP00000449002:M243I	ENSP00000449002:M243I	M	+	3	0	CR383656.1	18448322	0.000000	0.05858	0.847000	0.33407	0.095000	0.18619	-0.623000	0.05546	0.619000	0.30197	0.064000	0.15345	ATG	.	.	weak		0.428	OR11H12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408402.1	NM_001013354	
HTR1A	3350	hgsc.bcm.edu	37	5	63257310	63257310	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:63257310C>T	ENST00000323865.3	-	1	470	c.237G>A	c.(235-237)gcG>gcA	p.A79A	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	79					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.A79A(1)		cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GGTCGGTGACCGCCAAAGAGC	0.597																																					p.A79A		Atlas-SNP	.											HTR1A,colon,carcinoma,-1,2	HTR1A	128	2	1	Substitution - coding silent(1)	lung(1)	c.G237A						PASS	.						43.0	49.0	47.0					5																	63257310		2203	4300	6503	SO:0001819	synonymous_variant	3350	exon1			GGTGACCGCCAAA	AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5286	protein-coding gene	gene with protein product		109760	"""5-hydroxytryptamine (serotonin) receptor 1A"""	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.237G>A	5.37:g.63257310C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	155	62	0.4	NM_000524	Q6LAE7	Silent	SNP	ENST00000323865.3	37	CCDS34168.1																																																																																			.	.	none		0.597	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524	
ALKBH5	54890	hgsc.bcm.edu	37	17	18111598	18111598	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18111598G>A	ENST00000399138.4	+	4	1078	c.1073G>A	c.(1072-1074)cGg>cAg	p.R358Q	ALKBH5_ENST00000541285.1_Missense_Mutation_p.R17Q	NM_017758.3	NP_060228.3	Q6P6C2	ALKB5_HUMAN	AlkB family member 5, RNA demethylase	358					cell differentiation (GO:0030154)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|oxidative single-stranded RNA demethylation (GO:0035553)|response to hypoxia (GO:0001666)|spermatogenesis (GO:0007283)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidative RNA demethylase activity (GO:0035515)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|skin(1)	10	all_neural(463;0.228)					ACACACCGGCGGAGGGGTAGC	0.597																																					p.R358Q	Ovarian(166;154 1953 40235 46283 46309)	Atlas-SNP	.											ALKBH5,NS,carcinoma,+1,1	ALKBH5	24	1	0			c.G1073A						PASS	.						57.0	66.0	63.0					17																	18111598		1967	4139	6106	SO:0001583	missense	54890	exon4			ACCGGCGGAGGGG	AK000315	CCDS42272.1	17p11.2	2014-07-23	2014-07-23	2006-02-09	ENSG00000091542	ENSG00000091542	1.14.11.-	"""Alkylation repair homologs"""	25996	protein-coding gene	gene with protein product		613303	"""oxoglutarate and iron-dependent oxygenase domain containing"", ""alkB, alkylation repair homolog 5 (E. coli)"""	OFOXD1		11997338, 24778178	Standard	NM_017758		Approved	FLJ20308	uc010cpw.3	Q6P6C2	OTTHUMG00000059397	ENST00000399138.4:c.1073G>A	17.37:g.18111598G>A	ENSP00000382091:p.Arg358Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_017758	B4DVJ4|D3DXC6|Q9NXD6	Missense_Mutation	SNP	ENST00000399138.4	37	CCDS42272.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.978141	0.92982	.	.	ENSG00000091542	ENST00000261650;ENST00000500385;ENST00000399138	.	.	.	5.91	5.91	0.95273	.	0.098908	0.64402	D	0.000003	T	0.67468	0.2896	L	0.27053	0.805	0.58432	D	0.999998	D	0.71674	0.998	D	0.72982	0.979	T	0.68209	-0.5469	9	0.56958	D	0.05	-18.2953	20.2963	0.98556	0.0:0.0:1.0:0.0	.	358	Q6P6C2-2	.	Q	358;347;358	.	ENSP00000261650:R358Q	R	+	2	0	ALKBH5	18052323	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.135000	0.71696	2.813000	0.96785	0.655000	0.94253	CGG	.	.	none		0.597	ALKBH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132069.3	NM_017758	
MICA	100507436	hgsc.bcm.edu	37	6	31379823	31379823	+	Missense_Mutation	SNP	C	C	G	rs1051799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31379823C>G	ENST00000449934.2	+	4	767	c.713C>G	c.(712-714)aCc>aGc	p.T238S	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				ATCATACTGACCTGGCGTCAG	0.602													c|||	1823	0.364018	0.4773	0.4063	5008	,	,		18600	0.2996		0.3141	False		,,,				2504	0.2986				p.T238S		Atlas-SNP	.											.	MICA	21	.	0			c.C713G						PASS	.						17.0	19.0	18.0					6																	31379823		692	1588	2280	SO:0001583	missense	100507436	exon4			TACTGACCTGGCG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.713C>G	6.37:g.31379823C>G	ENSP00000413079:p.Thr238Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	727	0.33287545787545786	205	0.4166666666666667	155	0.4281767955801105	147	0.256993006993007	220	0.29023746701846964	c	8.349	0.830533	0.16749	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.02812	4.15;4.15	2.52	-0.436	0.12275	.	1.351150	0.05555	U	0.568191	T	0.00724	0.0024	.	.	.	0.80722	P	0.0	B;B	0.23735	0.09;0.007	B;B	0.27076	0.076;0.033	T	0.48725	-0.9010	8	0.42905	T	0.14	.	2.5921	0.04845	0.2201:0.3535:0.0:0.4264	rs1051799;rs3192175;rs17200337;rs17845522;rs17858412;rs17881640;rs1051799	100;238	Q5SS58;Q96QC4	.;.	S	100;238;195;238;129	ENSP00000413079:T238S;ENSP00000402410:T129S	ENSP00000365394:T238S	T	+	2	0	MICA	31487802	0.026000	0.19158	0.013000	0.15412	0.012000	0.07955	-0.351000	0.07711	0.021000	0.15133	0.444000	0.29173	ACC	C|0.703;G|0.297	0.297	strong		0.602	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
NCOR2	9612	hgsc.bcm.edu	37	12	124886979	124886979	+	Silent	SNP	C	C	T	rs202047482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124886979C>T	ENST00000405201.1	-	14	1611	c.1611G>A	c.(1609-1611)gaG>gaA	p.E537E	NCOR2_ENST00000404121.2_Silent_p.E107E|NCOR2_ENST00000397355.1_Silent_p.E537E|NCOR2_ENST00000429285.2_Silent_p.E536E|NCOR2_ENST00000404621.1_Silent_p.E536E|NCOR2_ENST00000356219.3_Silent_p.E537E			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	537					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)		CGTTCTCCACCTCCGGcttct	0.637													C|||	2	0.000399361	0.0	0.0014	5008	,	,		15261	0.0		0.001	False		,,,				2504	0.0				p.E537E		Atlas-SNP	.											.	NCOR2	475	.	0			c.G1611A						PASS	.	C	,,	0,4292		0,0,2146	97.0	119.0	112.0		1608,1608,1611	-7.6	0.1	12		112	6,8488		0,6,4241	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,6,6387	TT,TC,CC		0.0706,0.0,0.0469	,,	536/2459,536/2505,537/2515	124886979	6,12780	2146	4247	6393	SO:0001819	synonymous_variant	9612	exon16			CTCCACCTCCGGC	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.1611G>A	12.37:g.124886979C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	122	70	0.57377	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			C|0.999;T|0.001	0.001	weak		0.637	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
CH25H	9023	hgsc.bcm.edu	37	10	90966546	90966546	+	Silent	SNP	C	C	T	rs4078488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90966546C>T	ENST00000371852.2	-	1	525	c.504G>A	c.(502-504)gcG>gcA	p.A168A		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	168					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		GCGTTGCCAGCGCGAACGAGG	0.577													C|||	1388	0.277157	0.0083	0.2579	5008	,	,		23251	0.7351		0.1332	False		,,,				2504	0.3303				p.A168A		Atlas-SNP	.											CH25H,NS,carcinoma,-1,1	CH25H	19	1	0			c.G504A						PASS	.	C		113,4293	86.8+/-125.4	5,103,2095	144.0	136.0	139.0		504	-0.9	1.0	10	dbSNP_108	139	975,7625	211.8+/-252.3	54,867,3379	no	coding-synonymous	CH25H	NM_003956.3		59,970,5474	TT,TC,CC		11.3372,2.5647,8.3654		168/273	90966546	1088,11918	2203	4300	6503	SO:0001819	synonymous_variant	9023	exon1			TGCCAGCGCGAAC	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.504G>A	10.37:g.90966546C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	37	CCDS7400.1																																																																																			C|0.850;T|0.150	0.150	strong		0.577	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557488	32557488	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32557488C>T	ENST00000360004.5	-	1	137	c.32G>A	c.(31-33)tGc>tAc	p.C11Y		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	11					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CGCTGTCATGCAGGAGCCTCC	0.577										Multiple Myeloma(14;0.17)																											p.C11Y		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,-1,1	HLA-DRB1	41	1	0			c.G32A						scavenged	.						86.0	104.0	97.0					6																	32557488		1511	2709	4220	SO:0001583	missense	3123	exon1			GTCATGCAGGAGC	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.32G>A	6.37:g.32557488C>T	ENSP00000353099:p.Cys11Tyr	Somatic	274	2	0.00729927		WXS	Illumina HiSeq	Phase_I	246	9	0.0365854	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	10.06	1.246241	0.22796	.	.	ENSG00000196126	ENST00000360004	T	0.00249	8.44	4.68	3.81	0.43845	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	N	0.25201	0.72	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29792	-1.0000	9	0.51188	T	0.08	.	8.4755	0.33009	0.0:0.8948:0.0:0.1052	rs1059551;rs3200258	11	P01911	2B1F_HUMAN	Y	11	ENSP00000353099:C11Y	ENSP00000353099:C11Y	C	-	2	0	HLA-DRB1	32665466	0.003000	0.15002	0.042000	0.18584	0.005000	0.04900	0.146000	0.16180	1.198000	0.43158	0.462000	0.41574	TGC	.	.	none		0.577	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ACSL5	51703	hgsc.bcm.edu	37	10	114169276	114169276	+	Missense_Mutation	SNP	A	A	G	rs3736946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:114169276A>G	ENST00000393081.1	+	7	851	c.544A>G	c.(544-546)Atg>Gtg	p.M182V	RP11-324O2.3_ENST00000594870.2_RNA|RP11-324O2.3_ENST00000449782.2_RNA|RP11-324O2.3_ENST00000598447.1_RNA|RP11-324O2.6_ENST00000424422.1_RNA|ACSL5_ENST00000356116.1_Missense_Mutation_p.M238V|ACSL5_ENST00000369410.3_5'Flank|ACSL5_ENST00000354273.4_Missense_Mutation_p.M182V|ACSL5_ENST00000354655.4_Missense_Mutation_p.M182V|ACSL5_ENST00000433418.1_Missense_Mutation_p.M182V	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	182			M -> V (in dbSNP:rs3736946).		cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		TGATATCGCCATGGTGATCTG	0.473													A|||	348	0.0694888	0.0166	0.0922	5008	,	,		21098	0.0942		0.0944	False		,,,				2504	0.0736				p.M238V		Atlas-SNP	.											.	ACSL5	51	.	0			c.A712G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	164,4242	109.1+/-147.4	2,160,2041	140.0	128.0	132.0		712,544,544	3.6	0.0	10	dbSNP_107	132	981,7619	213.1+/-253.2	60,861,3379	yes	missense,missense,missense	ACSL5	NM_016234.3,NM_203379.1,NM_203380.1	21,21,21	62,1021,5420	GG,GA,AA		11.407,3.7222,8.8036	benign,benign,benign	238/740,182/684,182/684	114169276	1145,11861	2203	4300	6503	SO:0001583	missense	51703	exon7			ATCGCCATGGTGA	AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"""Acyl-CoA synthetase family"""	16526	protein-coding gene	gene with protein product	"""FACL5 for fatty acid coenzyme A ligase 5"", ""long-chain acyl-CoA synthetase 5"", ""long-chain fatty acid coenzyme A ligase 5"", ""fatty-acid-Coenzyme A ligase, long-chain 5"""	605677	"""fatty-acid-Coenzyme A ligase, long-chain 5"""	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.544A>G	10.37:g.114169276A>G	ENSP00000376796:p.Met182Val	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	123	66	0.536585	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	187	0.08562271062271062	12	0.024390243902439025	39	0.10773480662983426	67	0.11713286713286714	69	0.09102902374670185	A	0.018	-1.479455	0.01035	0.037222	0.11407	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273	T;T;T;T;T	0.35421	1.31;1.31;1.31;1.31;1.31	5.9	3.59	0.41128	AMP-dependent synthetase/ligase (1);	0.505950	0.23206	N	0.050724	T	0.00144	0.0004	N	0.00560	-1.38	0.09310	P	0.9999999999999734	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.18272	-1.0342	9	0.10377	T	0.69	-0.0774	4.471	0.11712	0.6974:0.0:0.1588:0.1439	rs3736946;rs17674729;rs52794801;rs3736946	182;238;182	A6GV77;Q9ULC5-3;Q9ULC5	.;.;ACSL5_HUMAN	V	182;182;238;182;182	ENSP00000346680:M182V;ENSP00000376796:M182V;ENSP00000348429:M238V;ENSP00000403647:M182V;ENSP00000346223:M182V	ENSP00000346223:M182V	M	+	1	0	ACSL5	114159266	0.024000	0.19004	0.009000	0.14445	0.384000	0.30261	2.784000	0.47774	0.506000	0.28125	0.533000	0.62120	ATG	A|0.915;G|0.085	0.085	strong		0.473	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234	
ENPP4	22875	hgsc.bcm.edu	37	6	46107752	46107752	+	Missense_Mutation	SNP	C	C	G	rs7451713	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46107752C>G	ENST00000321037.4	+	2	662	c.432C>G	c.(430-432)caC>caG	p.H144Q		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	144			H -> Q (in dbSNP:rs7451713). {ECO:0000269|PubMed:14702039}.		blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						TACCCATTCACGATACCATCT	0.413													C|||	2262	0.451677	0.2186	0.4467	5008	,	,		20687	0.4444		0.5348	False		,,,				2504	0.6922				p.H144Q		Atlas-SNP	.											.	ENPP4	44	.	0			c.C432G						PASS	.	C	GLN/HIS	1130,3276	402.4+/-332.3	149,832,1222	184.0	171.0	176.0		432	2.1	0.9	6	dbSNP_116	176	4587,4013	597.7+/-393.8	1220,2147,933	yes	missense	ENPP4	NM_014936.4	24	1369,2979,2155	GG,GC,CC		46.6628,25.6468,43.9566	benign	144/454	46107752	5717,7289	2203	4300	6503	SO:0001583	missense	22875	exon2			CATTCACGATACC	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.432C>G	6.37:g.46107752C>G	ENSP00000318066:p.His144Gln	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	129	48	0.372093	NM_014936	A8K5G1|Q7L2N1	Missense_Mutation	SNP	ENST00000321037.4	37	CCDS34468.1	927	0.42445054945054944	106	0.21544715447154472	178	0.49171270718232046	235	0.41083916083916083	408	0.5382585751978892	C	9.135	1.012363	0.19277	0.256468	0.533372	ENSG00000001561	ENST00000321037;ENST00000371401	T	0.71698	-0.59	5.97	2.08	0.27032	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.351086	0.36665	N	0.002465	T	0.28101	0.0693	N	0.16201	0.385	0.28757	P	0.9011321999999999	B	0.22909	0.077	B	0.28709	0.093	T	0.06716	-1.0811	9	0.09084	T	0.74	-13.6269	10.5855	0.45280	0.0:0.7418:0.0:0.2582	rs7451713;rs7451713	144	Q9Y6X5	ENPP4_HUMAN	Q	144	ENSP00000318066:H144Q	ENSP00000318066:H144Q	H	+	3	2	ENPP4	46215711	0.994000	0.37717	0.929000	0.37066	0.507000	0.33981	0.713000	0.25794	0.088000	0.17205	-0.345000	0.07892	CAC	C|0.562;G|0.438	0.438	strong		0.413	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2		
PKHD1	5314	hgsc.bcm.edu	37	6	51483961	51483961	+	Missense_Mutation	SNP	T	T	C	rs9381994	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:51483961T>C	ENST00000371117.3	-	67	12418	c.12143A>G	c.(12142-12144)cAa>cGa	p.Q4048R	RP3-335N17.2_ENST00000454361.1_RNA|RP3-335N17.2_ENST00000589278.2_RNA|RP3-335N17.2_ENST00000587000.1_RNA	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	4048			Q -> R (in dbSNP:rs9381994). {ECO:0000269|PubMed:11919560, ECO:0000269|PubMed:12846734}.		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)					TTTCTTCTCTTGGGAAAGCCC	0.547													T|||	2833	0.565695	0.4546	0.6023	5008	,	,		17670	0.6131		0.5487	False		,,,				2504	0.6585				p.Q4048R		Atlas-SNP	.											PKHD1,colon,carcinoma,0,2	PKHD1	927	2	0			c.A12143G						PASS	.	T	ARG/GLN	2120,2286	573.9+/-383.6	521,1078,604	42.0	45.0	44.0		12143	4.0	1.0	6	dbSNP_119	44	4719,3881	605.1+/-394.9	1297,2125,878	yes	missense	PKHD1	NM_138694.3	43	1818,3203,1482	CC,CT,TT		45.1279,48.1162,47.4166	benign	4048/4075	51483961	6839,6167	2203	4300	6503	SO:0001583	missense	5314	exon67			TTCTCTTGGGAAA	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.12143A>G	6.37:g.51483961T>C	ENSP00000360158:p.Gln4048Arg	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1216	0.5567765567765568	222	0.45121951219512196	215	0.5939226519337016	357	0.6241258741258742	422	0.5567282321899736	T	10.82	1.457689	0.26161	0.481162	0.548721	ENSG00000170927	ENST00000371117	D	0.86164	-2.08	5.27	3.95	0.45737	.	0.000000	0.45606	D	0.000358	T	0.63141	0.2486	L	0.31664	0.95	0.09310	P	0.999999999928248	B	0.18863	0.031	B	0.19148	0.024	T	0.54227	-0.8325	9	0.25106	T	0.35	.	5.3886	0.16231	0.0:0.155:0.0:0.845	rs9381994;rs56843543;rs9381994	4048	P08F94	PKHD1_HUMAN	R	4048	ENSP00000360158:Q4048R	ENSP00000360158:Q4048R	Q	-	2	0	PKHD1	51591920	0.634000	0.27190	1.000000	0.80357	0.266000	0.26442	0.430000	0.21428	2.128000	0.65567	0.533000	0.62120	CAA	T|0.458;C|0.542	0.542	strong		0.547	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PTX4	390667	hgsc.bcm.edu	37	16	1537874	1537874	+	Missense_Mutation	SNP	G	G	A	rs7202502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1537874G>A	ENST00000447419.2	-	2	264	c.239C>T	c.(238-240)gCg>gTg	p.A80V	PTX4_ENST00000440447.2_Missense_Mutation_p.A80V|PTX4_ENST00000293922.1_Missense_Mutation_p.A75V			Q96A99	PTX4_HUMAN	pentraxin 4, long	80						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GCTCTCTTCCGCCAGGCTCCG	0.632													G|||	532	0.10623	0.3147	0.0476	5008	,	,		16770	0.0119		0.0358	False		,,,				2504	0.0358				p.A75V		Atlas-SNP	.											PTX4,colon,carcinoma,0,1	PTX4	46	1	0			c.C224T						PASS	.	G	VAL/ALA	1235,3153		169,897,1128	93.0	95.0	94.0		224	-1.6	0.0	16	dbSNP_116	94	301,8279		6,289,3995	yes	missense	PTX4	NM_001013658.1	64	175,1186,5123	AA,AG,GG		3.5082,28.1449,11.8445	benign	75/474	1537874	1536,11432	2194	4290	6484	SO:0001583	missense	390667	exon2			TCTTCCGCCAGGC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.239C>T	16.37:g.1537874G>A	ENSP00000445277:p.Ala80Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		200	0.09157509157509157	148	0.3008130081300813	20	0.055248618784530384	6	0.01048951048951049	26	0.03430079155672823	G	7.797	0.712742	0.15306	0.281449	0.035082	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.05139	3.6;3.49	5.58	-1.58	0.08479	.	1.177010	0.06210	N	0.684847	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	P	0.42248	0.774	B	0.30572	0.117	T	0.42716	-0.9435	9	0.12103	T	0.63	.	0.4208	0.00456	0.2557:0.1407:0.3152:0.2884	rs7202502;rs56872109	75	Q96A99-2	.	V	80;75	ENSP00000445277:A80V;ENSP00000293922:A75V	ENSP00000293922:A75V	A	-	2	0	PTX4	1477875	0.005000	0.15991	0.001000	0.08648	0.003000	0.03518	0.197000	0.17197	-0.527000	0.06374	-0.251000	0.11542	GCG	G|0.894;A|0.106	0.106	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
EPM2A	7957	hgsc.bcm.edu	37	6	146007332	146007332	+	Silent	SNP	C	C	T	rs35230590	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:146007332C>T	ENST00000367519.3	-	2	927	c.402G>A	c.(400-402)ggG>ggA	p.G134G	EPM2A_ENST00000496228.1_5'UTR	NM_005670.3	NP_005661.1	O95278	EPM2A_HUMAN	epilepsy, progressive myoclonus type 2A, Lafora disease (laforin)	134					autophagy (GO:0006914)|carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|habituation (GO:0046959)|inositol phosphate dephosphorylation (GO:0046855)|nervous system development (GO:0007399)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polysome (GO:0005844)	carbohydrate phosphatase activity (GO:0019203)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|starch binding (GO:2001070)			kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	7		Ovarian(120;0.162)		OV - Ovarian serous cystadenocarcinoma(155;3.38e-07)|GBM - Glioblastoma multiforme(68;0.0203)		CATTGGTGTGCCCAGTGGCCT	0.418													C|||	611	0.122005	0.0008	0.3314	5008	,	,		17112	0.0089		0.2266	False		,,,				2504	0.1462				p.G134G		Atlas-SNP	.											.	EPM2A	21	.	0			c.G402A						PASS	.	C	,	204,4202	126.1+/-163.2	7,190,2006	175.0	150.0	159.0		402,402	3.8	1.0	6	dbSNP_126	159	2127,6473	367.5+/-334.7	256,1615,2429	no	coding-synonymous,coding-synonymous	EPM2A	NM_001018041.1,NM_005670.3	,	263,1805,4435	TT,TC,CC		24.7326,4.63,17.9225	,	134/318,134/332	146007332	2331,10675	2203	4300	6503	SO:0001819	synonymous_variant	7957	exon2			GGTGTGCCCAGTG	AF284580	CCDS5206.1	6q24	2011-06-09			ENSG00000112425	ENSG00000112425		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3413	protein-coding gene	gene with protein product		607566	"""epilepsy, progressive myoclonus type 2, Lafora disease (laforin)"""			9222970, 7485240	Standard	XM_006715564		Approved	LDE, LD	uc003qkw.3	B3EWF7	OTTHUMG00000015747	ENST00000367519.3:c.402G>A	6.37:g.146007332C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	90	77	0.855556	NM_005670	B3KMU5|B4DRZ2|O95483|Q5T3F5|Q6IS15|Q8IU96|Q8IX24|Q8IX25|Q9BS66|Q9UEN2	Silent	SNP	ENST00000367519.3	37	CCDS5206.1	309	0.14148351648351648	1	0.0020325203252032522	129	0.356353591160221	2	0.0034965034965034965	177	0.23350923482849603	C	9.721	1.159735	0.21454	0.0463	0.247326	ENSG00000112425	ENST00000450221;ENST00000435470	D;D	0.96554	-3.06;-4.05	5.6	3.81	0.43845	.	0.000000	0.85682	D	0.000000	D	0.95589	0.8566	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	D	0.95635	0.8693	6	0.66056	D	0.02	-32.4686	10.7796	0.46369	0.0:0.7916:0.0:0.2084	rs35230590;rs61748671	.	.	.	D	34;54	ENSP00000414900:G34D;ENSP00000405913:G54D	ENSP00000405913:G54D	G	-	2	0	EPM2A	146049025	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.678000	0.25277	1.357000	0.45904	0.491000	0.48974	GGC	C|0.823;T|0.177	0.177	strong		0.418	EPM2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042564.1		
UTP20	27340	hgsc.bcm.edu	37	12	101776996	101776996	+	Missense_Mutation	SNP	G	G	C	rs1061436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101776996G>C	ENST00000261637.4	+	59	8008	c.7834G>C	c.(7834-7836)Gag>Cag	p.E2612Q		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2612			E -> Q (in dbSNP:rs1061436).		endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						GGTGAAGGAAGAGCTCGGCAG	0.532													G|||	435	0.086861	0.0182	0.1153	5008	,	,		14588	0.0278		0.165	False		,,,				2504	0.1401				p.E2612Q		Atlas-SNP	.											.	UTP20	222	.	0			c.G7834C						PASS	.	G	GLN/GLU	169,4237	111.2+/-149.4	4,161,2038	62.0	70.0	67.0		7834	2.4	0.0	12	dbSNP_86	67	1432,7168	275.4+/-291.8	119,1194,2987	yes	missense	UTP20	NM_014503.2	29	123,1355,5025	CC,CG,GG		16.6512,3.8357,12.3097	benign	2612/2786	101776996	1601,11405	2203	4300	6503	SO:0001583	missense	27340	exon59			AAGGAAGAGCTCG	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.7834G>C	12.37:g.101776996G>C	ENSP00000261637:p.Glu2612Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	203	0.09294871794871795	11	0.022357723577235773	46	0.1270718232044199	16	0.027972027972027972	130	0.17150395778364116	G	12.10	1.836371	0.32421	0.038357	0.166512	ENSG00000120800	ENST00000261637	T	0.04970	3.52	5.46	2.43	0.29744	.	0.501020	0.18522	N	0.138727	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.35656	0.514	B	0.25291	0.059	T	0.43734	-0.9373	9	0.15499	T	0.54	-4.2624	10.1662	0.42882	0.0699:0.2572:0.6729:0.0	rs1061436;rs3202548;rs3816569;rs17415284;rs1061436	2612	O75691	UTP20_HUMAN	Q	2612	ENSP00000261637:E2612Q	ENSP00000261637:E2612Q	E	+	1	0	UTP20	100301127	0.416000	0.25424	0.002000	0.10522	0.001000	0.01503	2.618000	0.46393	0.657000	0.30906	0.643000	0.83706	GAG	G|0.878;C|0.122	0.122	strong		0.532	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
ZNF212	7988	hgsc.bcm.edu	37	7	148936878	148936878	+	Missense_Mutation	SNP	G	G	T	rs11548535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:148936878G>T	ENST00000335870.2	+	1	137	c.9G>T	c.(7-9)gaG>gaT	p.E3D		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	3					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|ovary(1)|prostate(1)	9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			CCATGGCGGAGTCGGCGCCTG	0.736													G|||	343	0.0684904	0.0234	0.062	5008	,	,		11880	0.003		0.1352	False		,,,				2504	0.1329				p.E3D		Atlas-SNP	.											.	ZNF212	28	.	0			c.G9T						PASS	.	G	ASP/GLU	133,4113		4,125,1994	9.0	12.0	11.0		9	3.8	1.0	7	dbSNP_130	11	1070,7270		62,946,3162	no	missense	ZNF212	NM_012256.3	45	66,1071,5156	TT,TG,GG		12.8297,3.1324,9.5582	benign	3/496	148936878	1203,11383	2123	4170	6293	SO:0001583	missense	7988	exon1			GGCGGAGTCGGCG	U38864	CCDS5896.1	7q36.1	2013-01-08			ENSG00000170260	ENSG00000170260		"""Zinc fingers, C2H2-type"", ""-"""	13004	protein-coding gene	gene with protein product		602386				9169157	Standard	NM_012256		Approved	C2H2-150	uc003wfp.3	Q9UDV6	OTTHUMG00000158968	ENST00000335870.2:c.9G>T	7.37:g.148936878G>T	ENSP00000338572:p.Glu3Asp	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	41	22	0.536585	NM_012256	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	37	CCDS5896.1	141	0.06456043956043957	14	0.028455284552845527	22	0.06077348066298342	3	0.005244755244755245	102	0.1345646437994723	G	15.69	2.908566	0.52439	0.031324	0.128297	ENSG00000170260	ENST00000335870	T	0.09445	2.98	4.66	3.76	0.43208	.	0.000000	0.45867	D	0.000326	T	0.00073	0.0002	N	0.19112	0.55	0.32824	P	0.49688299999999996	B	0.22080	0.064	B	0.17979	0.02	T	0.33803	-0.9854	9	0.30854	T	0.27	-10.8146	10.8729	0.46894	0.0:0.1903:0.8097:0.0	.	3	Q9UDV6	ZN212_HUMAN	D	3	ENSP00000338572:E3D	ENSP00000338572:E3D	E	+	3	2	ZNF212	148567811	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.277000	0.51654	1.291000	0.44653	0.655000	0.94253	GAG	G|0.935;T|0.065	0.065	strong		0.736	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256	
PTPRN2	5799	hgsc.bcm.edu	37	7	157396697	157396697	+	Silent	SNP	G	G	A	rs17853260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:157396697G>A	ENST00000389418.4	-	16	2424	c.2415C>T	c.(2413-2415)ccC>ccT	p.P805P	PTPRN2_ENST00000404321.2_Silent_p.P828P|PTPRN2_ENST00000389413.3_Silent_p.P776P|PTPRN2_ENST00000409483.1_Silent_p.P767P|PTPRN2_ENST00000389416.4_Silent_p.P788P	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	805	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CACTTACGATGGGGCTAGCGT	0.622													G|||	599	0.119609	0.0129	0.1628	5008	,	,		18666	0.006		0.334	False		,,,				2504	0.1299				p.P805P		Atlas-SNP	.											PTPRN2,NS,carcinoma,0,1	PTPRN2	243	1	0			c.C2415T						PASS	.		,,	300,4106	163.6+/-195.4	10,280,1913	112.0	85.0	94.0		2415,2364,2328	4.4	1.0	7	dbSNP_123	94	2910,5690	454.6+/-363.5	514,1882,1904	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	524,2162,3817	AA,AG,GG		33.8372,6.8089,24.6809	,,	805/1016,788/999,776/987	157396697	3210,9796	2203	4300	6503	SO:0001819	synonymous_variant	5799	exon16			TACGATGGGGCTA	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2415C>T	7.37:g.157396697G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_002847	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.779;A|0.221	0.221	strong		0.622	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29911056	29911056	+	Missense_Mutation	SNP	A	A	C	rs281864748|rs1071743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911056A>C	ENST00000396634.1	+	5	696	c.355A>C	c.(355-357)Atc>Ctc	p.I119L	HLA-A_ENST00000376809.5_Missense_Mutation_p.I119L|HLA-A_ENST00000376806.5_Missense_Mutation_p.I119L|HLA-A_ENST00000376802.2_Missense_Mutation_p.I119L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	119	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	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						TTCTCACACCATCCAGATAAT	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)			a|||	878	0.175319	0.1808	0.2046	5008	,	,		10611	0.2054		0.1203	False		,,,				2504	0.1728				p.I119L		Atlas-SNP	.											.	HLA-A	89	.	0			c.A355C	GRCh37	CP044519	HLA-A	X	rs1071743	PASS	.	A	LEU/ILE	482,2480		95,292,1094	20.0	16.0	18.0		355	-7.6	0.0	6	dbSNP_86	18	714,4540		156,402,2069	yes	missense	HLA-A	NM_002116.7	5	251,694,3163	CC,CA,AA		13.5896,16.2728,14.557	benign	119/366	29911056	1196,7020	1481	2627	4108	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CACACCATCCAGA	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.355A>C	6.37:g.29911056A>C	ENSP00000379873:p.Ile119Leu	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	78	49	0.628205	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	427	0.1955128205128205	74	0.15040650406504066	92	0.2541436464088398	163	0.28496503496503495	98	0.12928759894459102	.	0.297	-0.976066	0.02215	0.162728	0.135896	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00634	6.07;6.07;6.07;6.07	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);	0.616012	0.12023	U	0.506774	T	0.00039	0.0001	N	0.00510	-1.415	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	0.12156	0.002;0.004;0.003;0.007;0.003	T	0.51772	-0.8663	9	0.09590	T	0.72	.	2.0308	0.03529	0.1108:0.2405:0.1996:0.4491	rs1071743;rs2231015;rs3179186;rs3200168;rs3200169;rs12721700;rs17433765;rs28749149;rs41544415	119;119;119;119;119	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	L	119	ENSP00000379873:I119L;ENSP00000366002:I119L;ENSP00000366005:I119L;ENSP00000365998:I119L	ENSP00000348012:I119L	I	+	1	0	HLA-A	30019035	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-10.433000	0.00006	-7.084000	0.00001	-2.496000	0.00192	ATC	A|0.782;C|0.180;G|0.037	0.180	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
BFSP1	631	hgsc.bcm.edu	37	20	17479617	17479617	+	Silent	SNP	G	G	A	rs11537702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:17479617G>A	ENST00000377873.3	-	6	843	c.804C>T	c.(802-804)aaC>aaT	p.N268N	BFSP1_ENST00000377868.2_Silent_p.N143N|BFSP1_ENST00000544874.1_Silent_p.N129N|BFSP1_ENST00000536626.1_Silent_p.N129N	NM_001195.3	NP_001186.1	Q12934	BFSP1_HUMAN	beaded filament structural protein 1, filensin	268	Coil 2.|Rod.				cell maturation (GO:0048469)|lens fiber cell development (GO:0070307)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)|structural constituent of eye lens (GO:0005212)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(7)|prostate(2)|skin(1)|stomach(1)	18						CAATCTGCTCGTTATAAAGCT	0.507													G|||	113	0.0225639	0.003	0.0346	5008	,	,		20099	0.0		0.0696	False		,,,				2504	0.0153				p.N268N		Atlas-SNP	.											.	BFSP1	55	.	0			c.C804T						PASS	.	G	,	62,4344	59.3+/-96.0	2,58,2143	149.0	135.0	140.0		429,804	-12.1	0.0	20	dbSNP_120	140	677,7923	169.3+/-220.7	32,613,3655	no	coding-synonymous,coding-synonymous	BFSP1	NM_001161705.1,NM_001195.3	,	34,671,5798	AA,AG,GG		7.8721,1.4072,5.682	,	143/541,268/666	17479617	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	631	exon6			CTGCTCGTTATAA	Y16717	CCDS13126.1, CCDS54448.1, CCDS63229.1	20p12.1	2014-06-05			ENSG00000125864	ENSG00000125864		"""Intermediate filaments type VI, eye lens intermediate filaments"""	1040	protein-coding gene	gene with protein product		603307				9787085	Standard	NM_001161705		Approved	CP94, CP115, LIFL-H, filensin	uc002wpo.3	Q12934	OTTHUMG00000031940	ENST00000377873.3:c.804C>T	20.37:g.17479617G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_001195	F5H0G1|O43595|O76034|O95676|Q8IVZ6|Q9HBX4	Silent	SNP	ENST00000377873.3	37	CCDS13126.1																																																																																			G|0.955;A|0.045	0.045	strong		0.507	BFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078119.6	NM_001195	
FAM210B	116151	hgsc.bcm.edu	37	20	54940148	54940148	+	Silent	SNP	C	C	T	rs148836702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:54940148C>T	ENST00000371384.3	+	2	283	c.192C>T	c.(190-192)ccC>ccT	p.P64P		NM_080821.2	NP_543011.2	Q96KR6	F210B_HUMAN	family with sequence similarity 210, member B	64						integral component of membrane (GO:0016021)											CACAGGACCCCAGCCAGGCCA	0.498													C|||	7	0.00139776	0.0	0.0	5008	,	,		19155	0.001		0.005	False		,,,				2504	0.001				p.P64P		Atlas-SNP	.											.	.	.	.	0			c.C192T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	47.0	43.0	45.0		192	3.2	0.4	20	dbSNP_134	45	22,8578	15.3+/-51.7	0,22,4278	no	coding-synonymous	C20orf108	NM_080821.2		0,23,6480	TT,TC,CC		0.2558,0.0227,0.1768		64/193	54940148	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	116151	exon2			GGACCCCAGCCAG	AL121914	CCDS13450.1	20q13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000124098	ENSG00000124098			16102	protein-coding gene	gene with protein product	"""hypothetical protein LOC116151"""		"""chromosome 20 open reading frame 108"""	C20orf108		11780052	Standard	NM_080821		Approved	dJ1167H4.1, DKFZP434A1114	uc002xxc.3	Q96KR6	OTTHUMG00000032793	ENST00000371384.3:c.192C>T	20.37:g.54940148C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_080821	B2RBQ9|E1P5Y7|Q8WVN2|Q9BYL6|Q9H418	Silent	SNP	ENST00000371384.3	37	CCDS13450.1																																																																																			C|0.998;T|0.002	0.002	strong		0.498	FAM210B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079800.2	NM_080821	
ISM2	145501	hgsc.bcm.edu	37	14	77950699	77950699	+	Silent	SNP	G	G	A	rs141373850		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:77950699G>A	ENST00000342219.4	-	3	650	c.594C>T	c.(592-594)caC>caT	p.H198H	ISM2_ENST00000393684.3_Silent_p.H110H|ISM2_ENST00000493585.1_Silent_p.H198H|ISM2_ENST00000429906.1_Silent_p.H117H|ISM2_ENST00000412904.1_Intron	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	198						extracellular region (GO:0005576)		p.H198H(1)		endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						TCAAGGTTGCGTGGACCAATT	0.627													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21110	0.0		0.0	False		,,,				2504	0.0				p.H198H		Atlas-SNP	.											ISM2,colon,carcinoma,0,1	ISM2	68	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C594T						scavenged	.	G	,	0,4406		0,0,2203	99.0	93.0	95.0		594,594	1.0	0.9	14	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ISM2	NM_182509.3,NM_199296.2	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	198/293,198/572	77950699	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	145501	exon3			GGTTGCGTGGACC	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"""thrombospondin and AMOP containing isthmin-like 1"""	612684	"""thrombospondin, type I domain-containing 3"", ""thrombospondin, type I, domain containing 3"", ""isthmin 2 homolog (zebrafish)"""	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.594C>T	14.37:g.77950699G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Silent	SNP	ENST00000342219.4	37	CCDS9864.1																																																																																			G|1.000;A|0.000	0.000	weak		0.627	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509	
USP19	10869	hgsc.bcm.edu	37	3	49146612	49146612	+	Missense_Mutation	SNP	G	G	A	rs79965514		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49146612G>A	ENST00000398888.2	-	26	4054	c.3736C>T	c.(3736-3738)Cgg>Tgg	p.R1246W	USP19_ENST00000434032.2_Missense_Mutation_p.R1347W|USP19_ENST00000398898.2_Intron|USP19_ENST00000453664.1_Intron|USP19_ENST00000398896.1_Intron|USP19_ENST00000398892.3_Missense_Mutation_p.R1286W|USP19_ENST00000417901.1_Intron	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1246					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)		TGCCAAATCCGGGAAGCCTAG	0.682													G|||	1	0.000199681	0.0	0.0	5008	,	,		17126	0.001		0.0	False		,,,				2504	0.0				p.R1347W		Atlas-SNP	.											.	USP19	158	.	0			c.C4039T						PASS	.						7.0	9.0	8.0					3																	49146612		1839	3927	5766	SO:0001583	missense	10869	exon27			AAATCCGGGAAGC	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.3736C>T	3.37:g.49146612G>A	ENSP00000381863:p.Arg1246Trp	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	103	30	0.291262	NM_001199160	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	19.42	3.823416	0.71143	.	.	ENSG00000172046	ENST00000398892;ENST00000398888;ENST00000434032	T;T;T	0.20463	2.07;2.17;2.17	5.3	4.43	0.53597	.	0.730358	0.12840	N	0.434921	T	0.16557	0.0398	N	0.19112	0.55	0.41423	D	0.987818	B;B;B	0.11235	0.004;0.004;0.001	B;B;B	0.08055	0.002;0.003;0.0	T	0.04078	-1.0979	10	0.59425	D	0.04	-2.2965	13.9763	0.64275	0.0724:0.0:0.9276:0.0	.	1347;1246;1286	E9PEG8;O94966;B5MEG5	.;UBP19_HUMAN;.	W	1286;1246;1347	ENSP00000381867:R1286W;ENSP00000381863:R1246W;ENSP00000401197:R1347W	ENSP00000381863:R1246W	R	-	1	2	USP19	49121616	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.009000	0.88606	1.473000	0.48159	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.682	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105889349	105889349	+	Silent	SNP	G	G	A	rs11676273	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:105889349G>A	ENST00000393359.2	-	10	2361	c.1935C>T	c.(1933-1935)ctC>ctT	p.L645L	TGFBRAP1_ENST00000258449.1_Silent_p.L645L			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	645					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						CAGATTTCTGGAGCAGCCGCC	0.557													G|||	582	0.116214	0.0091	0.2219	5008	,	,		17007	0.0804		0.2207	False		,,,				2504	0.1155				p.L645L	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											TGFBRAP1,NS,carcinoma,-2,1	TGFBRAP1	70	1	0			c.C1935T						scavenged	.	G	,	181,4225	113.3+/-151.4	2,177,2024	38.0	42.0	40.0		1935,1935	-3.9	1.0	2	dbSNP_120	40	1778,6822	317.4+/-313.2	173,1432,2695	yes	coding-synonymous,coding-synonymous	TGFBRAP1	NM_001142621.1,NM_004257.4	,	175,1609,4719	AA,AG,GG		20.6744,4.108,15.0623	,	645/861,645/861	105889349	1959,11047	2203	4300	6503	SO:0001819	synonymous_variant	9392	exon10			TTTCTGGAGCAGC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.1935C>T	2.37:g.105889349G>A		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																			G|0.864;A|0.135	0.135	strong		0.557	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
TRIM39	56658	hgsc.bcm.edu	37	6	30297505	30297505	+	Silent	SNP	C	C	T	rs1264581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30297505C>T	ENST00000396547.1	+	2	571	c.411C>T	c.(409-411)gcC>gcT	p.A137A	TRIM39_ENST00000396548.1_Silent_p.A137A|TRIM39_ENST00000540416.1_Silent_p.A137A|TRIM39_ENST00000396551.3_Silent_p.A137A|TRIM39_ENST00000376656.4_Silent_p.A137A|TRIM39_ENST00000376659.5_Silent_p.A137A|HCG18_ENST00000412685.2_RNA|TRIM39-RPP21_ENST00000513556.1_Silent_p.A49A|HCG18_ENST00000413358.2_RNA|HCG18_ENST00000426882.1_RNA			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	137				A -> P (in Ref. 1; BAB16374). {ECO:0000305}.	apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CCCACCGGGCCCACACCGTTG	0.557													C|||	248	0.0495208	0.0053	0.0331	5008	,	,		20139	0.0258		0.0835	False		,,,				2504	0.1104				p.A137A		Atlas-SNP	.											.	TRIM39	56	.	0			c.C411T						PASS	.	C	,,	49,2967		0,49,1459	68.0	72.0	70.0		411,411,411	1.2	1.0	6	dbSNP_87	70	400,5014		11,378,2318	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM39,TRIM39-RPP21	NM_001199119.1,NM_021253.3,NM_172016.2	,,	11,427,3777	TT,TC,CC		7.3883,1.6247,5.3262	,,	137/504,137/519,137/489	30297505	449,7981	1508	2707	4215	SO:0001819	synonymous_variant	56658	exon3			CCGGGCCCACACC	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.411C>T	6.37:g.30297505C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	139	68	0.489209	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Silent	SNP	ENST00000396547.1	37	CCDS34377.1	81	0.03708791208791209	3	0.006097560975609756	13	0.03591160220994475	7	0.012237762237762238	58	0.07651715039577836	C	10.30	1.312291	0.23908	0.016247	0.073883	ENSG00000204599	ENST00000420746	.	.	.	5.35	1.24	0.21308	.	.	.	.	.	T	0.36717	0.0977	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20207	-1.0282	4	.	.	.	.	5.82	0.18522	0.0:0.592:0.1461:0.2619	rs1264581;rs6939888;rs17188498;rs17850231;rs17853355;rs58793944;rs1264581	.	.	.	L	67	.	.	P	+	2	0	TRIM39	30405484	0.841000	0.29509	0.998000	0.56505	0.990000	0.78478	0.240000	0.18042	0.380000	0.24823	0.555000	0.69702	CCC	C|0.951;T|0.049	0.049	strong		0.557	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
FAM221B	392307	hgsc.bcm.edu	37	9	35826038	35826038	+	Missense_Mutation	SNP	T	T	C	rs13294245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35826038T>C	ENST00000423537.2	-	2	390	c.121A>G	c.(121-123)Aag>Gag	p.K41E	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	41			K -> E (in dbSNP:rs13294245). {ECO:0000269|PubMed:15489334}.							endometrium(2)|kidney(1)|lung(4)	7						GTGGAAGGCTTCAAGAAGCTT	0.537											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	1203	0.240216	0.2474	0.2017	5008	,	,		20084	0.375		0.2008	False		,,,				2504	0.1595				p.K41E		Atlas-SNP	.											.	FAM221B	38	.	0			c.A121G						PASS	.		GLU/LYS	894,2904		111,672,1116	81.0	83.0	82.0		121	1.9	0.0	9	dbSNP_121	82	1590,6608		150,1290,2659	yes	missense	C9orf128	NM_001012446.2	56	261,1962,3775	CC,CT,TT		19.395,23.5387,20.7069	benign	41/403	35826038	2484,9512	1899	4099	5998	SO:0001583	missense	392307	exon2			AAGGCTTCAAGAA	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 128"""	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.121A>G	9.37:g.35826038T>C	ENSP00000415299:p.Lys41Glu	Somatic	84	0	0	858	WXS	Illumina HiSeq	Phase_I	84	38	0.452381	NM_001012446	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	CCDS43799.2	572	0.2619047619047619	126	0.25609756097560976	82	0.2265193370165746	220	0.38461538461538464	144	0.18997361477572558	c	9.080	0.999048	0.19121	0.235387	0.19395	ENSG00000204930	ENST00000423537;ENST00000377984;ENST00000472182	T;T;T	0.26373	2.84;2.56;1.74	3.8	1.91	0.25777	.	0.511663	0.16358	N	0.217901	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45659	-0.9246	9	0.02654	T	1	.	4.0585	0.09827	0.0:0.5692:0.2061:0.2248	rs13294245	41	A6H8Z2	CI128_HUMAN	E	41	ENSP00000415299:K41E;ENSP00000367222:K41E;ENSP00000420279:K41E	ENSP00000367222:K41E	K	-	1	0	C9orf128	35816038	0.001000	0.12720	0.019000	0.16419	0.374000	0.29953	-0.007000	0.12810	0.201000	0.20466	-0.779000	0.03376	AAG	T|0.758;C|0.242	0.242	strong		0.537	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446	
PAPLN	89932	hgsc.bcm.edu	37	14	73716774	73716774	+	Silent	SNP	G	G	A	rs177393	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:73716774G>A	ENST00000554301.1	+	5	580	c.417G>A	c.(415-417)acG>acA	p.T139T	PAPLN_ENST00000555445.1_Silent_p.T139T|PAPLN_ENST00000427855.1_Silent_p.T139T|PAPLN_ENST00000340738.5_Silent_p.T139T|PAPLN_ENST00000381166.3_Silent_p.T139T			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	139						basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		TTGATGGGACGCCCTGCGAGC	0.637													G|||	1679	0.335264	0.4576	0.2925	5008	,	,		17768	0.1458		0.3042	False		,,,				2504	0.4274				p.T139T		Atlas-SNP	.											.	PAPLN	180	.	0			c.G417A						PASS	.	G		1913,2493	541.0+/-375.7	395,1123,685	104.0	78.0	87.0		417	-9.7	0.6	14	dbSNP_79	87	2771,5829	434.6+/-357.8	460,1851,1989	no	coding-synonymous	PAPLN	NM_173462.3		855,2974,2674	AA,AG,GG		32.2209,43.4181,36.0141		139/1252	73716774	4684,8322	2203	4300	6503	SO:0001819	synonymous_variant	89932	exon6			TGGGACGCCCTGC	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.417G>A	14.37:g.73716774G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	45	0.428571	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Silent	SNP	ENST00000554301.1	37																																																																																				G|0.667;A|0.333	0.333	strong		0.637	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
CLCA2	9635	hgsc.bcm.edu	37	1	86909582	86909582	+	Missense_Mutation	SNP	G	G	A	rs1413426	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:86909582G>A	ENST00000370565.4	+	10	1763	c.1601G>A	c.(1600-1602)gGt>gAt	p.G534D		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	534			G -> D (in dbSNP:rs1413426).		cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		CAGGCCAGTGGTCCTCCTGAG	0.393													G|||	513	0.102436	0.1362	0.1052	5008	,	,		16996	0.0585		0.0934	False		,,,				2504	0.1094				p.G534D	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.G1601A						PASS	.	G	ASP/GLY	588,3818	258.0+/-262.2	36,516,1651	146.0	134.0	138.0		1601	3.2	0.0	1	dbSNP_88	138	706,7894	174.2+/-224.5	30,646,3624	yes	missense	CLCA2	NM_006536.5	94	66,1162,5275	AA,AG,GG		8.2093,13.3454,9.9493	benign	534/944	86909582	1294,11712	2203	4300	6503	SO:0001583	missense	9635	exon10			CCAGTGGTCCTCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1601G>A	1.37:g.86909582G>A	ENSP00000359596:p.Gly534Asp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	97	49	0.505155	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	192	0.08791208791208792	57	0.11585365853658537	41	0.1132596685082873	27	0.0472027972027972	67	0.08839050131926121	G	0.037	-1.303422	0.01353	0.133454	0.082093	ENSG00000137975	ENST00000370565	T	0.34667	1.35	5.13	3.25	0.37280	Domain of unknown function DUF1973 (1);	0.835260	0.10867	N	0.625379	T	0.09642	0.0237	L	0.45137	1.4	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.27773	-1.0064	9	0.13853	T	0.58	-4.0188	3.444	0.07474	0.206:0.0:0.4484:0.3456	rs1413426;rs2390058;rs17099757;rs52811376;rs1413426	534	Q9UQC9	CLCA2_HUMAN	D	534	ENSP00000359596:G534D	ENSP00000359596:G534D	G	+	2	0	CLCA2	86682170	0.000000	0.05858	0.016000	0.15963	0.077000	0.17291	0.705000	0.25675	0.746000	0.32786	0.650000	0.86243	GGT	G|0.904;A|0.096	0.096	strong		0.393	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
BOC	91653	hgsc.bcm.edu	37	3	112991312	112991312	+	Silent	SNP	C	C	T	rs3814398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112991312C>T	ENST00000495514.1	+	7	1427	c.723C>T	c.(721-723)atC>atT	p.I241I	BOC_ENST00000273395.4_Silent_p.I241I|BOC_ENST00000355385.3_Silent_p.I241I			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	241	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			AAACCATCATCGTCACCAAAG	0.627													C|||	1386	0.276757	0.2073	0.3732	5008	,	,		18873	0.3978		0.1879	False		,,,				2504	0.2689				p.I241I		Atlas-SNP	.											.	BOC	139	.	0			c.C723T						PASS	.	C		902,3504	348.0+/-309.7	94,714,1395	162.0	154.0	157.0		723	-5.9	0.9	3	dbSNP_107	157	1332,7268	261.2+/-283.7	111,1110,3079	no	coding-synonymous	BOC	NM_033254.2		205,1824,4474	TT,TC,CC		15.4884,20.4721,17.1767		241/1115	112991312	2234,10772	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon7			CATCATCGTCACC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.723C>T	3.37:g.112991312C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	156	66	0.423077	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.788;T|0.212	0.212	strong		0.627	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
HHLA3	11147	hgsc.bcm.edu	37	1	70820880	70820880	+	Silent	SNP	G	G	A	rs55863806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:70820880G>A	ENST00000359875.5	+	1	386	c.246G>A	c.(244-246)gcG>gcA	p.A82A	HHLA3_ENST00000432224.1_Silent_p.A82A|ANKRD13C_ENST00000370944.4_5'Flank|HHLA3_ENST00000486110.1_3'UTR|ANKRD13C_ENST00000262346.6_5'Flank|HHLA3_ENST00000370940.5_Intron|HHLA3_ENST00000361764.4_Intron|HHLA3_ENST00000531950.1_Silent_p.A82A	NM_001036645.1	NP_001031722.1	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3	82										large_intestine(3)|lung(1)	4						aattaaaAGCGGAGGCGGGGA	0.453													G|||	467	0.0932508	0.0325	0.0908	5008	,	,		19262	0.0605		0.1044	False		,,,				2504	0.1994				p.A82A		Atlas-SNP	.											.	HHLA3	11	.	0			c.G246A						PASS	.	G	,,	175,4231	111.6+/-149.8	5,165,2033	36.0	38.0	37.0		,246,	-3.4	0.0	1	dbSNP_129	37	788,7812	183.6+/-231.8	27,734,3539	no	intron,coding-synonymous,intron	HHLA3	NM_001031693.2,NM_001036645.1,NM_001036646.1	,,	32,899,5572	AA,AG,GG		9.1628,3.9719,7.4043	,,	,82/115,	70820880	963,12043	2203	4300	6503	SO:0001819	synonymous_variant	11147	exon1			AAAAGCGGAGGCG	AF126164	CCDS649.1, CCDS30752.1, CCDS30753.1	1p31.1	2008-02-05			ENSG00000197568	ENSG00000197568			4906	protein-coding gene	gene with protein product		604372				10444326	Standard	NR_027404		Approved		uc001dfa.3	Q9XRX5	OTTHUMG00000009346	ENST00000359875.5:c.246G>A	1.37:g.70820880G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001036645	D3DQ74|Q5VZP2|Q96FH5|Q9XRX4	Silent	SNP	ENST00000359875.5	37	CCDS30753.1																																																																																			G|0.926;A|0.074	0.074	strong		0.453	HHLA3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025911.2	NM_007071	
APCDD1L	164284	hgsc.bcm.edu	37	20	57045765	57045765	+	Missense_Mutation	SNP	A	A	G	rs3946003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:57045765A>G	ENST00000371149.3	-	2	318	c.88T>C	c.(88-90)Tgc>Cgc	p.C30R	APCDD1L_ENST00000439429.1_Missense_Mutation_p.C41R	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	30			C -> R (in dbSNP:rs3946003).			integral component of membrane (GO:0016021)				large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			CAGCGCAGGCAGCTGCCCCCG	0.662													G|||	2308	0.460863	0.618	0.4265	5008	,	,		13648	0.3998		0.3688	False		,,,				2504	0.4305				p.C30R		Atlas-SNP	.											.	APCDD1L	48	.	0			c.T88C						PASS	.	G	ARG/CYS	2249,1989		639,971,509	24.0	21.0	22.0		88	1.8	0.0	20	dbSNP_108	22	2836,5450		534,1768,1841	yes	missense	APCDD1L	NM_153360.1	180	1173,2739,2350	GG,GA,AA		34.2264,46.9325,40.602	benign	30/502	57045765	5085,7439	2119	4143	6262	SO:0001583	missense	164284	exon2			GCAGGCAGCTGCC	AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.88T>C	20.37:g.57045765A>G	ENSP00000360191:p.Cys30Arg	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	NM_153360		Missense_Mutation	SNP	ENST00000371149.3	37	CCDS13467.1	968	0.4432234432234432	297	0.6036585365853658	161	0.4447513812154696	231	0.40384615384615385	279	0.36807387862796836	G	0.016	-1.528342	0.00959	0.530675	0.342264	ENSG00000198768	ENST00000371149;ENST00000439429;ENST00000425773	T;T;T	0.28895	2.66;2.65;1.59	4.88	1.78	0.24846	.	1.184280	0.06181	N	0.679412	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45498	-0.9257	9	0.02654	T	1	-1.6941	3.6523	0.08208	0.3072:0.0:0.3177:0.3751	rs3946003;rs59320716	41;30	F5H6V6;Q8NCL9	.;APCDL_HUMAN	R	30;41;41	ENSP00000360191:C30R;ENSP00000413261:C41R;ENSP00000396856:C41R	ENSP00000360191:C30R	C	-	1	0	APCDD1L	56479171	0.187000	0.23238	0.001000	0.08648	0.047000	0.14425	0.784000	0.26816	-0.034000	0.13713	-0.119000	0.15052	TGC	A|0.555;G|0.445	0.445	strong		0.662	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360	
SVEP1	79987	hgsc.bcm.edu	37	9	113168501	113168501	+	Missense_Mutation	SNP	A	A	G	rs41278435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113168501A>G	ENST00000401783.2	-	38	9715	c.9379T>C	c.(9379-9381)Tct>Cct	p.S3127P	SVEP1_ENST00000374469.1_Missense_Mutation_p.S3104P|SVEP1_ENST00000297826.5_Missense_Mutation_p.S1053P	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3127	Sushi 29. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TTGGCGACAGACGGTGGGGAC	0.522													A|||	166	0.033147	0.0227	0.0259	5008	,	,		19193	0.0476		0.0467	False		,,,				2504	0.0235				p.S3127P		Atlas-SNP	.											.	SVEP1	326	.	0			c.T9379C						PASS	.	A	PRO/SER	80,3906		0,80,1913	114.0	120.0	118.0		9379	-6.0	0.0	9	dbSNP_127	118	352,7980		8,336,3822	yes	missense	SVEP1	NM_153366.3	74	8,416,5735	GG,GA,AA		4.2247,2.007,3.5071	possibly-damaging	3127/3572	113168501	432,11886	1993	4166	6159	SO:0001583	missense	79987	exon38			CGACAGACGGTGG	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.9379T>C	9.37:g.113168501A>G	ENSP00000384917:p.Ser3127Pro	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	146	66	0.452055	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	82	0.037545787545787544	9	0.018292682926829267	15	0.04143646408839779	20	0.03496503496503497	38	0.05013192612137203	A	4.145	0.025223	0.08054	0.02007	0.042247	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.64085	-0.08;-0.08;-0.08	5.69	-6.0	0.02206	Complement control module (2);Sushi/SCR/CCP (3);	0.882616	0.10320	N	0.688843	T	0.08403	0.0209	L	0.41356	1.27	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.16928	-1.0386	10	0.22706	T	0.39	.	0.9383	0.01350	0.2956:0.2781:0.12:0.3064	rs41278435	3127	Q4LDE5	SVEP1_HUMAN	P	3127;3104;1053	ENSP00000384917:S3127P;ENSP00000363593:S3104P;ENSP00000297826:S1053P	ENSP00000297826:S1053P	S	-	1	0	SVEP1	112208322	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-0.035000	0.12205	-0.535000	0.06307	-0.438000	0.05819	TCT	A|0.964;G|0.036	0.036	strong		0.522	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CRTAP	10491	hgsc.bcm.edu	37	3	33174156	33174156	+	Silent	SNP	T	T	G	rs1135127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:33174156T>G	ENST00000320954.6	+	5	1131	c.1032T>G	c.(1030-1032)acT>acG	p.T344T	CRTAP_ENST00000449224.1_Silent_p.T301T	NM_006371.4	NP_006362.1	O75718	CRTAP_HUMAN	cartilage associated protein	344					chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation to 3-hydroxy-L-proline (GO:0018400)|protein stabilization (GO:0050821)|spermatogenesis (GO:0007283)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|macromolecular complex (GO:0032991)|proteinaceous extracellular matrix (GO:0005578)	protein complex binding (GO:0032403)	p.T344T(1)		breast(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9						ACAGGGACACTTGGGGCCTCT	0.522													T|||	1470	0.29353	0.2451	0.268	5008	,	,		18251	0.1548		0.4354	False		,,,				2504	0.3742				p.T344T		Atlas-SNP	.											CRTAP,NS,carcinoma,0,1	CRTAP	16	1	1	Substitution - coding silent(1)	stomach(1)	c.T1032G						PASS	.	T		1168,3238	411.5+/-335.8	160,848,1195	143.0	126.0	132.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1032	1.5	1.0	3	dbSNP_86	132	3831,4769	539.1+/-383.5	873,2085,1342	no	coding-synonymous	CRTAP	NM_006371.4		1033,2933,2537	GG,GT,TT		44.5465,26.5093,38.4361		344/402	33174156	4999,8007	2203	4300	6503	SO:0001819	synonymous_variant	10491	exon5			GGACACTTGGGGC	AJ006470	CCDS2657.1	3p22	2014-09-17			ENSG00000170275	ENSG00000170275			2379	protein-coding gene	gene with protein product	"""leprecan-like 3"""	605497				9217321, 10429950	Standard	NM_006371		Approved	CASP, LEPREL3	uc003cfl.4	O75718	OTTHUMG00000130746	ENST00000320954.6:c.1032T>G	3.37:g.33174156T>G		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	147	62	0.421769	NM_006371	B2RBL6	Silent	SNP	ENST00000320954.6	37	CCDS2657.1																																																																																			T|0.645;G|0.355	0.355	strong		0.522	CRTAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253246.3		
TSC1	7248	hgsc.bcm.edu	37	9	135782221	135782221	+	Splice_Site	SNP	T	T	C	rs7862221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135782221T>C	ENST00000298552.3	-	14	1556	c.1335A>G	c.(1333-1335)gaA>gaG	p.E445E	TSC1_ENST00000545250.1_Splice_Site_p.E394E|TSC1_ENST00000440111.2_Splice_Site_p.E445E	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	445					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)		CAGGTGGCTCTTCTGAAGAGA	0.378			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				T|||	694	0.138578	0.233	0.0965	5008	,	,		17568	0.0744		0.1441	False		,,,				2504	0.1012				p.E445E		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.A1335G						PASS	.	T	,,	965,3441	356.1+/-313.4	119,727,1357	77.0	70.0	73.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1335,1332,1182	3.3	1.0	9	dbSNP_116	73	1258,7342	244.6+/-273.7	102,1054,3144	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	TSC1	NM_000368.4,NM_001162426.1,NM_001162427.1	,,	221,1781,4501	CC,CT,TT		14.6279,21.902,17.0921	,,	445/1165,444/1164,394/1114	135782221	2223,10783	2203	4300	6503	SO:0001630	splice_region_variant	7248	exon14	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TGGCTCTTCTGAA	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.1334-1A>G	9.37:g.135782221T>C		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																			T|0.841;C|0.159	0.159	strong		0.378	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		Silent
CR1L	1379	hgsc.bcm.edu	37	1	207870916	207870916	+	Missense_Mutation	SNP	G	G	A	rs201832831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:207870916G>A	ENST00000508064.2	+	6	991	c.931G>A	c.(931-933)Ggg>Agg	p.G311R	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	311	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)		p.G319W(1)|p.G311W(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CTTTTCACCCGGGCAGGAAGT	0.557													g|||	5	0.000998403	0.0	0.0	5008	,	,		18305	0.004		0.0	False		,,,				2504	0.001				p.G311R		Atlas-SNP	.											.	CR1L	97	.	2	Substitution - Missense(2)	lung(2)	c.G931A						PASS	.	G	ARG/GLY	1,3789		0,1,1894	151.0	149.0	149.0		931	1.5	0.0	1		149	1,8223		0,1,4111	no	missense	CR1L	NM_175710.1	125	0,2,6005	AA,AG,GG		0.0122,0.0264,0.0166	probably-damaging	311/570	207870916	2,12012	1895	4112	6007	SO:0001583	missense	1379	exon6			TCACCCGGGCAGG	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.931G>A	1.37:g.207870916G>A	ENSP00000421736:p.Gly311Arg	Somatic	394	0	0		WXS	Illumina HiSeq	Phase_I	480	231	0.48125	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	.	12.71	2.018389	0.35606	2.64E-4	1.22E-4	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.71698	-0.59	2.53	1.55	0.23275	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.75295	0.3830	M	0.81614	2.55	0.09310	N	0.999996	D	0.89917	1.0	D	0.68353	0.957	T	0.64702	-0.6345	9	0.87932	D	0	.	5.7056	0.17907	0.1679:0.0:0.8321:0.0	.	311	Q2VPA4	CR1L_HUMAN	R	311	ENSP00000421736:G311R	ENSP00000434864:G255R	G	+	1	0	CR1L	205937539	0.009000	0.17119	0.001000	0.08648	0.005000	0.04900	0.673000	0.25203	0.354000	0.24105	0.298000	0.19748	GGG	G|0.999;A|0.001	0.001	strong		0.557	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
BAG3	9531	hgsc.bcm.edu	37	10	121432139	121432139	+	Missense_Mutation	SNP	C	C	T	rs144585878		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:121432139C>T	ENST00000369085.3	+	3	1186	c.880C>T	c.(880-882)Cgt>Tgt	p.R294C		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	294					brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of apoptotic process (GO:0043066)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|Z disc (GO:0030018)		p.R294C(1)		endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(5)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	20		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)		CTCGCCCATCCGTGTGCACAC	0.647																																					p.R294C		Atlas-SNP	.											BAG3,NS,carcinoma,-1,2	BAG3	42	2	1	Substitution - Missense(1)	large_intestine(1)	c.C880T						scavenged	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	46.0	53.0	51.0		880	5.6	0.9	10	dbSNP_134	51	0,8600		0,0,4300	no	missense	BAG3	NM_004281.3	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	294/576	121432139	1,13005	2203	4300	6503	SO:0001583	missense	9531	exon3			CCCATCCGTGTGC	AF095193	CCDS7615.1	10q25.2-q26.2	2014-09-17			ENSG00000151929	ENSG00000151929			939	protein-coding gene	gene with protein product		603883				9873016, 18094623	Standard	XM_005270287		Approved		uc001lem.3	O95817	OTTHUMG00000019155	ENST00000369085.3:c.880C>T	10.37:g.121432139C>T	ENSP00000358081:p.Arg294Cys	Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_004281	A8K5L8|Q3B763|Q9NT20|Q9P120	Missense_Mutation	SNP	ENST00000369085.3	37	CCDS7615.1	.	.	.	.	.	.	.	.	.	.	C	16.23	3.065057	0.55432	2.27E-4	0.0	ENSG00000151929	ENST00000369085;ENST00000450186	T;T	0.77620	-0.97;-1.11	5.57	5.57	0.84162	.	0.163364	0.44483	D	0.000444	T	0.79997	0.4543	L	0.34521	1.04	0.43863	D	0.996469	D;D	0.89917	1.0;1.0	P;P	0.60117	0.869;0.869	T	0.81097	-0.1087	10	0.59425	D	0.04	-10.8689	14.0117	0.64500	0.2746:0.7254:0.0:0.0	.	294;294	O95817;Q53GY1	BAG3_HUMAN;.	C	294;236	ENSP00000358081:R294C;ENSP00000410036:R236C	ENSP00000358081:R294C	R	+	1	0	BAG3	121422129	1.000000	0.71417	0.886000	0.34754	0.341000	0.28922	2.553000	0.45837	2.636000	0.89361	0.467000	0.42956	CGT	C|1.000;T|0.000	0.000	weak		0.647	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281	
HDGFRP2	84717	hgsc.bcm.edu	37	19	4493708	4493708	+	Silent	SNP	A	A	G	rs892161	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4493708A>G	ENST00000301284.4	+	7	751	c.687A>G	c.(685-687)ccA>ccG	p.P229P	HDGFRP2_ENST00000586684.1_Silent_p.P229P	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		229	Ser-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGAAGGCGCCATCAGCCTCCG	0.697													g|||	2915	0.582069	0.6702	0.6484	5008	,	,		12206	0.4236		0.6243	False		,,,				2504	0.5358				p.P229P		Atlas-SNP	.											HDGF2,NS,carcinoma,0,1	.	.	1	0			c.A687G						PASS	.		,	2808,1320		1014,780,270	12.0	15.0	14.0		687,687	-9.9	0.0	19	dbSNP_86	14	5167,3075		1714,1739,668	no	coding-synonymous,coding-synonymous	HDGFRP2	NM_001001520.1,NM_032631.2	,	2728,2519,938	GG,GA,AA		37.3089,31.9767,35.5295	,	229/677,229/676	4493708	7975,4395	2064	4121	6185	SO:0001819	synonymous_variant	0	exon7			GGCGCCATCAGCC																												ENST00000301284.4:c.687A>G	19.37:g.4493708A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	Silent	SNP	ENST00000301284.4	37	CCDS42472.1																																																																																			A|0.431;G|0.569	0.569	strong		0.697	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
LAMB1	3912	hgsc.bcm.edu	37	7	107569517	107569517	+	Silent	SNP	A	A	G	rs1131398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:107569517A>G	ENST00000222399.6	-	31	5109	c.4879T>C	c.(4879-4881)Tta>Cta	p.L1627L	LAMB1_ENST00000393561.1_Silent_p.L1651L|LAMB1_ENST00000474380.1_5'Flank	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1627	Domain I.				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						ACCGAAGTTAACAGGTTCTGG	0.398													G|||	2171	0.433506	0.5492	0.3963	5008	,	,		19007	0.4583		0.3857	False		,,,				2504	0.3272				p.L1627L		Atlas-SNP	.											.	LAMB1	185	.	0			c.T4879C						PASS	.	G		2366,2040	566.5+/-381.9	618,1130,455	305.0	281.0	289.0		4879	4.2	0.9	7	dbSNP_86	289	3532,5068	632.0+/-398.6	719,2094,1487	no	coding-synonymous	LAMB1	NM_002291.2		1337,3224,1942	GG,GA,AA		41.0698,46.3005,45.3483		1627/1787	107569517	5898,7108	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon31			AAGTTAACAGGTT	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.4879T>C	7.37:g.107569517A>G		Somatic	267	0	0		WXS	Illumina HiSeq	Phase_I	243	117	0.481481	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			A|0.547;G|0.453	0.453	strong		0.398	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
SPACA7	122258	hgsc.bcm.edu	37	13	113053470	113053470	+	Missense_Mutation	SNP	T	T	A	rs10816	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113053470T>A	ENST00000283550.3	+	4	399	c.332T>A	c.(331-333)gTc>gAc	p.V111D	SPACA7_ENST00000375699.3_Missense_Mutation_p.V80D	NM_145248.4	NP_660291.2	Q96KW9	SPAC7_HUMAN	sperm acrosome associated 7	111			V -> D (in dbSNP:rs10816). {ECO:0000269|PubMed:15489334}.			acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)				large_intestine(5)|lung(4)|skin(3)|urinary_tract(1)	13						GGCATTGAGGTCAAAATTTCC	0.423													A|||	3340	0.666933	0.7905	0.6081	5008	,	,		18900	0.624		0.5716	False		,,,				2504	0.684				p.V111D		Atlas-SNP	.											SPACA7,NS,adenoma,0,1	SPACA7	36	1	0			c.T332A						PASS	.	A	ASP/VAL	3445,961	360.9+/-315.4	1357,731,115	70.0	71.0	71.0		332	0.4	0.0	13	dbSNP_52	71	5185,3415	503.2+/-375.9	1577,2031,692	yes	missense	SPACA7	NM_145248.4	152	2934,2762,807	AA,AT,TT		39.7093,21.8112,33.646	benign	111/196	113053470	8630,4376	2203	4300	6503	SO:0001583	missense	122258	exon4			TTGAGGTCAAAAT	BC016750	CCDS9524.1	13q34	2013-10-11	2011-03-15	2011-03-15	ENSG00000153498	ENSG00000153498			29575	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 28"""	C13orf28		22495889	Standard	NM_145248		Approved		uc001vsd.2	Q96KW9	OTTHUMG00000017365	ENST00000283550.3:c.332T>A	13.37:g.113053470T>A	ENSP00000283550:p.Val111Asp	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	93	52	0.55914	NM_145248	Q5T8L1	Missense_Mutation	SNP	ENST00000283550.3	37	CCDS9524.1	1381	0.6323260073260073	382	0.7764227642276422	229	0.6325966850828729	344	0.6013986013986014	426	0.5620052770448549	A	0.743	-0.775762	0.02951	0.781888	0.602907	ENSG00000153498	ENST00000283550;ENST00000414180;ENST00000443541;ENST00000375699	T;T;T;T	0.39787	1.06;1.06;1.06;1.06	3.03	0.446	0.16602	.	.	.	.	.	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	0.36383	-0.9750	8	0.09843	T	0.71	-4.0574	0.5289	0.00625	0.4371:0.2203:0.129:0.2136	rs10816;rs1132162;rs3192694;rs11554437;rs17294556;rs17845503;rs17858390;rs60368660;rs10816	111	Q96KW9	SPAC7_HUMAN	D	111;99;97;80	ENSP00000283550:V111D;ENSP00000416096:V99D;ENSP00000406733:V97D;ENSP00000364851:V80D	ENSP00000283550:V111D	V	+	2	0	SPACA7	112101471	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.204000	0.09425	-0.169000	0.10834	-0.265000	0.10407	GTC	T|0.343;A|0.657	0.657	strong		0.423	SPACA7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045820.2	NM_145248	
GPR113	165082	hgsc.bcm.edu	37	2	26536299	26536299	+	Silent	SNP	C	C	G	rs11886746	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26536299C>G	ENST00000311519.1	-	9	1418	c.1419G>C	c.(1417-1419)ccG>ccC	p.P473P	GPR113_ENST00000333478.6_Silent_p.P274P|GPR113_ENST00000421160.2_Silent_p.P404P|GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000541401.1_Silent_p.P76P	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	473					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTGTGGACCGGCCCCCAGA	0.647													g|||	2002	0.39976	0.4856	0.3228	5008	,	,		18410	0.3353		0.328	False		,,,				2504	0.4785				p.P473P		Atlas-SNP	.											.	GPR113	134	.	0			c.G1419C						PASS	.	A	,,	2072,2334		494,1084,625	31.0	30.0	30.0		1419,1212,822	-0.3	0.0	2	dbSNP_120	30	2780,5820		446,1888,1966	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	,,	940,2972,2591	GG,GC,CC		32.3256,47.0268,37.3059	,,	473/1080,404/998,274/874	26536299	4852,8154	2203	4300	6503	SO:0001819	synonymous_variant	165082	exon9			GTGGACCGGCCCC	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.1419G>C	2.37:g.26536299C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Silent	SNP	ENST00000311519.1	37	CCDS46239.1																																																																																			C|0.631;G|0.369	0.369	strong		0.647	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
CAPZA2	830	hgsc.bcm.edu	37	7	116528240	116528240	+	Silent	SNP	C	C	T	rs4808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:116528240C>T	ENST00000361183.3	+	2	238	c.99C>T	c.(97-99)ttC>ttT	p.F33F	CAPZA2_ENST00000458284.2_Silent_p.F33F|CAPZA2_ENST00000490693.1_Silent_p.F33F	NM_006136.2	NP_006127.1	P47755	CAZA2_HUMAN	capping protein (actin filament) muscle Z-line, alpha 2	33					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|WASH complex (GO:0071203)				endometrium(2)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	13	all_cancers(3;8.53e-08)|all_epithelial(6;7.79e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)		GBM - Glioblastoma multiforme(2;5.01e-06)|STAD - Stomach adenocarcinoma(10;0.000512)|all cancers(2;0.00326)			ATGAGGTTTTCAATGGTGAGT	0.348													T|||	1620	0.323482	0.3888	0.3098	5008	,	,		14813	0.3948		0.2346	False		,,,				2504	0.2628				p.F33F		Atlas-SNP	.											.	CAPZA2	29	.	0			c.C99T						PASS	.	T		1642,2764	658.2+/-400.4	311,1020,872	85.0	89.0	87.0		99	3.5	1.0	7	dbSNP_52	87	1973,6623	722.1+/-406.4	222,1529,2547	no	coding-synonymous	CAPZA2	NM_006136.2		533,2549,3419	TT,TC,CC		22.9525,37.2674,27.8034		33/287	116528240	3615,9387	2203	4298	6501	SO:0001819	synonymous_variant	830	exon2			GGTTTTCAATGGT		CCDS5768.1	7q31.2-q31.3	2008-07-18			ENSG00000198898	ENSG00000198898			1490	protein-coding gene	gene with protein product	"""F-actin capping protein alpha-2 subunit"""	601571					Standard	NM_006136		Approved	CAPZ, CAPPA2	uc003vil.3	P47755	OTTHUMG00000023185	ENST00000361183.3:c.99C>T	7.37:g.116528240C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_006136	B4DG50	Silent	SNP	ENST00000361183.3	37	CCDS5768.1	684	0.3131868131868132	188	0.3821138211382114	104	0.287292817679558	213	0.3723776223776224	179	0.23614775725593667	t	11.85	1.762539	0.31228	0.372674	0.229525	ENSG00000198898	ENST00000464223;ENST00000484325	.	.	.	5.86	3.5	0.40072	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999997	.	.	.	.	.	.	T	0.28586	-1.0039	4	0.87932	D	0	-16.2536	9.1722	0.37089	0.0:0.2116:0.0:0.7884	rs4808;rs2188696;rs9641572;rs11540709;rs56433270;rs4808	.	.	.	L	11	.	ENSP00000420640:S11L	S	+	2	0	CAPZA2	116315476	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	1.798000	0.38814	0.143000	0.18926	-0.346000	0.07831	TCA	C|0.707;T|0.293	0.293	strong		0.348	CAPZA2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059506.4	NM_006136	
KRTAP3-3	85293	hgsc.bcm.edu	37	17	39150284	39150284	+	Silent	SNP	A	A	G	rs2010201	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39150284A>G	ENST00000391586.1	-	1	101	c.66T>C	c.(64-66)tcT>tcC	p.S22S		NM_033185.2	NP_149441.1	Q9BYR6	KRA33_HUMAN	keratin associated protein 3-3	22	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			lung(2)|prostate(2)	4		Breast(137;0.00043)				AGGATTTGTCAGAGGAGCAGA	0.582													A|||	2379	0.47504	0.6377	0.4784	5008	,	,		17574	0.5		0.2913	False		,,,				2504	0.4162				p.S22S		Atlas-SNP	.											.	KRTAP3-3	11	.	0			c.T66C						PASS	.	A		2510,1896	625.1+/-394.5	720,1070,413	90.0	90.0	90.0		66	-11.2	0.0	17	dbSNP_92	90	2274,6318	374.7+/-337.5	295,1684,2317	no	coding-synonymous	KRTAP3-3	NM_033185.2		1015,2754,2730	GG,GA,AA		26.4665,43.0322,36.8057		22/99	39150284	4784,8214	2203	4296	6499	SO:0001819	synonymous_variant	85293	exon1			TTTGTCAGAGGAG	AJ406933	CCDS32643.1	17q21.2	2013-06-25			ENSG00000212899	ENSG00000212899		"""Keratin associated proteins"""	18890	protein-coding gene	gene with protein product						11279113	Standard	NM_033185		Approved	KAP3.3	uc002hvr.1	Q9BYR6	OTTHUMG00000133591	ENST00000391586.1:c.66T>C	17.37:g.39150284A>G		Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	211	115	0.545024	NM_033185	Q52LP0|Q6NTD4	Silent	SNP	ENST00000391586.1	37	CCDS32643.1																																																																																			A|0.598;G|0.402	0.402	strong		0.582	KRTAP3-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257695.1		
PREX2	80243	hgsc.bcm.edu	37	8	68864728	68864728	+	Silent	SNP	G	G	A	rs61753697	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:68864728G>A	ENST00000288368.4	+	1	376	c.99G>A	c.(97-99)aaG>aaA	p.K33K	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	33	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						AGCTCCAGAAGACCGAGCGGG	0.716													G|||	1569	0.313299	0.0499	0.366	5008	,	,		12054	0.5228		0.3062	False		,,,				2504	0.4233				p.K33K		Atlas-SNP	.											PREX2_ENST00000354677,NS,carcinoma,0,2	PREX2	614	2	0			c.G99A						PASS	.	G	,	410,3994		23,364,1815	29.0	29.0	29.0		99,99	5.4	1.0	8	dbSNP_129	29	2586,6014		414,1758,2128	no	coding-synonymous,coding-synonymous	PREX2	NM_024870.2,NM_025170.4	,	437,2122,3943	AA,AG,GG		30.0698,9.3097,23.0391	,	33/1607,33/980	68864728	2996,10008	2202	4300	6502	SO:0001819	synonymous_variant	80243	exon1			CCAGAAGACCGAG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.99G>A	8.37:g.68864728G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.766;A|0.234	0.234	strong		0.716	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505159	37505159	+	Missense_Mutation	SNP	G	G	A	rs34552277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:37505159G>A	ENST00000602533.1	+	32	2851	c.2752G>A	c.(2752-2754)Gca>Aca	p.A918T	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.A1037T|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.A918T			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	974					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						TTGTGAAAGAGCAAGGGAACT	0.328													G|||	1140	0.227636	0.4145	0.1556	5008	,	,		16013	0.1558		0.2227	False		,,,				2504	0.1053				p.A918T		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.G2752A						PASS	.	G	THR/ALA	1411,2197		283,845,676	66.0	62.0	63.0		2752	0.0	0.0	10	dbSNP_126	63	1900,6242		225,1450,2396	yes	missense	ANKRD30A	NM_052997.2	58	508,2295,3072	AA,AG,GG		23.3358,39.1075,28.1787	possibly-damaging	918/1342	37505159	3311,8439	1804	4071	5875	SO:0001583	missense	91074	exon32			GAAAGAGCAAGGG	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.2752G>A	10.37:g.37505159G>A	ENSP00000473551:p.Ala918Thr	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	135	52	0.385185	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		513	0.2348901098901099	192	0.3902439024390244	72	0.19889502762430938	82	0.14335664335664336	167	0.22031662269129287	g	0.666	-0.803974	0.02819	0.391075	0.233358	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.06371	3.31;3.31	2.63	-0.00398	0.14023	.	.	.	.	.	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B	0.25486	0.127	B	0.22601	0.04	T	0.43798	-0.9369	8	0.14252	T	0.57	.	3.8812	0.09079	0.1959:0.0:0.4221:0.382	rs34552277;rs60808216	974	Q9BXX3	AN30A_HUMAN	T	918;1037	ENSP00000354432:A918T;ENSP00000363792:A1037T	ENSP00000354432:A918T	A	+	1	0	ANKRD30A	37545165	0.021000	0.18746	0.006000	0.13384	0.032000	0.12392	-0.375000	0.07475	-0.250000	0.09555	0.313000	0.20887	GCA	G|0.768;A|0.232	0.232	strong		0.328	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
ALK	238	hgsc.bcm.edu	37	2	29449819	29449819	+	Silent	SNP	C	C	T	rs2293563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29449819C>T	ENST00000389048.3	-	18	3942	c.3036G>A	c.(3034-3036)acG>acA	p.T1012T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1012			T -> M (in dbSNP:rs35073634). {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)	p.T1012T(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CAGCCAGCACCGTCCCGTGGT	0.542			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	851	0.169928	0.2277	0.147	5008	,	,		21422	0.119		0.1928	False		,,,				2504	0.137				p.T1012T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,0,1	ALK	533	1	1	Substitution - coding silent(1)	stomach(1)	c.G3036A						PASS	.	C		974,3432	366.4+/-317.8	105,764,1334	202.0	180.0	187.0		3036	-10.8	0.1	2	dbSNP_100	187	1492,7108	283.2+/-296.0	137,1218,2945	no	coding-synonymous	ALK	NM_004304.4		242,1982,4279	TT,TC,CC		17.3488,22.1062,18.9605		1012/1621	29449819	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	238	exon18	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGCACCGTCCCG	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.3036G>A	2.37:g.29449819C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			C|0.816;T|0.184	0.184	strong		0.542	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
GRM7	2917	hgsc.bcm.edu	37	3	7620789	7620789	+	Silent	SNP	T	T	C	rs1485175	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:7620789T>C	ENST00000357716.4	+	8	2470	c.2196T>C	c.(2194-2196)taT>taC	p.Y732Y	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000486284.1_Silent_p.Y732Y|GRM7_ENST00000403881.1_Silent_p.Y732Y|GRM7_ENST00000402647.2_Silent_p.Y732Y|GRM7_ENST00000389336.4_Silent_p.Y732Y	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	732					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TCATAGACTATGATGAACACA	0.423													T|||	2632	0.525559	0.5703	0.5144	5008	,	,		18820	0.4355		0.5835	False		,,,				2504	0.5061				p.Y732Y		Atlas-SNP	.											.	GRM7	223	.	0			c.T2196C						PASS	.	T	,	2528,1878	631.3+/-395.6	723,1082,398	132.0	114.0	120.0		2196,2196	-0.1	1.0	3	dbSNP_88	120	4815,3785	614.9+/-396.3	1334,2147,819	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	2057,3229,1217	CC,CT,TT		44.0116,42.6237,43.5414	,	732/916,732/923	7620789	7343,5663	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			AGACTATGATGAA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2196T>C	3.37:g.7620789T>C		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	266	140	0.526316	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			T|0.451;C|0.549	0.549	strong		0.423	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
GZMB	3002	hgsc.bcm.edu	37	14	25100282	25100282	+	Missense_Mutation	SNP	A	A	G	rs2236338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:25100282A>G	ENST00000216341.4	-	5	845	c.739T>C	c.(739-741)Tac>Cac	p.Y247H	RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Missense_Mutation_p.Y202H|GZMB_ENST00000415355.3_Missense_Mutation_p.Y235H|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Missense_Mutation_p.Y281H			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	247			Y -> H (in dbSNP:rs2236338). {ECO:0000269|PubMed:12721789, ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.Y247H(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		TGTAGTTAGTAGCGTTTCATG	0.478													G|||	1462	0.291933	0.3298	0.2075	5008	,	,		18111	0.2986		0.2495	False		,,,				2504	0.3374				p.Y247H		Atlas-SNP	.											GZMB,NS,carcinoma,0,1	GZMB	73	1	1	Substitution - Missense(1)	stomach(1)	c.T739C	GRCh37	CM033777	GZMB	M	rs2236338	PASS	.	G	HIS/TYR	1401,3005	688.4+/-405.0	213,975,1015	234.0	227.0	229.0		739	-1.6	0.0	14	dbSNP_98	229	2050,6550	719.9+/-406.3	255,1540,2505	yes	missense	GZMB	NM_004131.4	83	468,2515,3520	GG,GA,AA		23.8372,31.7975,26.5339	benign	247/248	25100282	3451,9555	2203	4300	6503	SO:0001583	missense	3002	exon5			GTTAGTAGCGTTT	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.739T>C	14.37:g.25100282A>G	ENSP00000216341:p.Tyr247His	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	270	136	0.503704	NM_004131	Q8N1D2|Q9UCC1	Missense_Mutation	SNP	ENST00000216341.4	37	CCDS9633.1	585	0.26785714285714285	163	0.3313008130081301	82	0.2265193370165746	148	0.25874125874125875	192	0.2532981530343008	G	0.858	-0.736322	0.03111	0.317975	0.238372	ENSG00000100453	ENST00000415355;ENST00000216341;ENST00000382542;ENST00000382540;ENST00000382539	D;D;D;D	0.90261	-2.55;-2.53;-2.6;-2.64	4.88	-1.58	0.08479	.	1.357460	0.05613	N	0.578444	T	0.00012	0.0000	N	0.20986	0.625	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.003	T	0.02758	-1.1114	9	0.39692	T	0.17	.	3.5013	0.07674	0.3485:0.0:0.2432:0.4082	rs2236338;rs17856857;rs52792984;rs56781976;rs2236338	235;247	Q6XGZ4;P10144	.;GRAB_HUMAN	H	235;247;281;202;152	ENSP00000387385:Y235H;ENSP00000216341:Y247H;ENSP00000371982:Y281H;ENSP00000371980:Y202H	ENSP00000216341:Y247H	Y	-	1	0	GZMB	24170122	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.197000	0.09518	-0.409000	0.07553	-0.119000	0.15052	TAC	A|0.729;G|0.271	0.271	strong		0.478	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
TMEM18	129787	hgsc.bcm.edu	37	2	677295	677295	+	Silent	SNP	C	C	T	rs3210390	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:677295C>T	ENST00000281017.3	-	1	144	c.51G>A	c.(49-51)gtG>gtA	p.V17V	AC092159.2_ENST00000445418.1_RNA|TMEM18_ENST00000355654.2_5'Flank|AC092159.2_ENST00000435573.1_RNA|TMEM18_ENST00000405941.3_5'Flank	NM_152834.2	NP_690047.2	Q96B42	TMM18_HUMAN	transmembrane protein 18	17					cell migration (GO:0016477)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(1)|lung(7)|ovary(1)	10	all_hematologic(175;0.0429)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;5.27e-05)|all_epithelial(98;2.11e-06)|Ovarian(717;0.0253)		all cancers(51;1.95e-21)|Epithelial(75;9.47e-21)|OV - Ovarian serous cystadenocarcinoma(76;8.15e-18)|GBM - Glioblastoma multiforme(21;0.0285)		TTACCGTGAGCACGGCTGGGA	0.677													C|||	603	0.120407	0.2458	0.0865	5008	,	,		11272	0.0129		0.1004	False		,,,				2504	0.1063				p.V17V		Atlas-SNP	.											.	TMEM18	22	.	0			c.G51A						PASS	.	C		958,3448		105,748,1350	40.0	32.0	35.0		51	-2.6	0.1	2	dbSNP_105	35	949,7649		53,843,3403	no	coding-synonymous	TMEM18	NM_152834.2		158,1591,4753	TT,TC,CC		11.0375,21.7431,14.6647		17/141	677295	1907,11097	2203	4299	6502	SO:0001819	synonymous_variant	129787	exon1			CGTGAGCACGGCT	AL137269	CCDS33141.1	2p25.3	2008-02-05			ENSG00000151353	ENSG00000151353			25257	protein-coding gene	gene with protein product		613220				12477932	Standard	NM_152834		Approved	DKFZp434C1714	uc002qwl.3	Q96B42	OTTHUMG00000151381	ENST00000281017.3:c.51G>A	2.37:g.677295C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_152834	D6W4X9|Q8N5H2|Q9NTH3	Silent	SNP	ENST00000281017.3	37	CCDS33141.1																																																																																			C|0.864;T|0.136	0.136	strong		0.677	TMEM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322427.1	NM_152834	
COL5A3	50509	hgsc.bcm.edu	37	19	10081322	10081322	+	Silent	SNP	G	G	A	rs61729461	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10081322G>A	ENST00000264828.3	-	54	3997	c.3912C>T	c.(3910-3912)ggC>ggT	p.G1304G		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1304	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)			gcccgggggcgccgggcTCCC	0.602													g|||	360	0.071885	0.1626	0.0418	5008	,	,		8644	0.0159		0.0885	False		,,,				2504	0.0112				p.G1304G		Atlas-SNP	.											COL5A3,NS,carcinoma,0,2	COL5A3	243	2	0			c.C3912T						PASS	.			581,3727		25,531,1598	7.0	9.0	8.0		3912	-4.8	0.3	19	dbSNP_129	8	696,7692		35,626,3533	no	coding-synonymous	COL5A3	NM_015719.3		60,1157,5131	AA,AG,GG		8.2976,13.4865,10.0583		1304/1746	10081322	1277,11419	2154	4194	6348	SO:0001819	synonymous_variant	50509	exon54			GGGGGCGCCGGGC	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.3912C>T	19.37:g.10081322G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			G|0.915;A|0.085	0.085	strong		0.602	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
LRP1B	53353	hgsc.bcm.edu	37	2	141116447	141116447	+	Missense_Mutation	SNP	G	G	T	rs35546150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:141116447G>T	ENST00000389484.3	-	73	12171	c.11200C>A	c.(11200-11202)Caa>Aaa	p.Q3734K		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3734	LDL-receptor class A 31. {ECO:0000255|PROSITE-ProRule:PRU00124}.		Q -> K (in dbSNP:rs35546150).		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)		TTGCACATTTGCTCCGACTGT	0.388										TSP Lung(27;0.18)			G|||	225	0.0449281	0.0492	0.0144	5008	,	,		16732	0.0327		0.0437	False		,,,				2504	0.0746				p.Q3734K	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C11200A						PASS	.	G	LYS/GLN	201,4205	123.7+/-161.0	6,189,2008	193.0	173.0	180.0		11200	1.0	1.0	2	dbSNP_126	180	332,8266	115.0+/-174.9	5,322,3972	yes	missense	LRP1B	NM_018557.2	53	11,511,5980	TT,TG,GG		3.8614,4.562,4.0987	benign	3734/4600	141116447	533,12471	2203	4299	6502	SO:0001583	missense	53353	exon73			ACATTTGCTCCGA	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.11200C>A	2.37:g.141116447G>T	ENSP00000374135:p.Gln3734Lys	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	167	84	0.502994	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	98	0.04487179487179487	35	0.07113821138211382	7	0.019337016574585635	20	0.03496503496503497	36	0.047493403693931395	G	4.602	0.111819	0.08831	0.04562	0.038614	ENSG00000168702	ENST00000389484;ENST00000544579	T	0.58652	0.32	5.46	0.967	0.19674	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.152498	0.44483	N	0.000455	T	0.03434	0.0099	N	0.16098	0.37	0.33987	D	0.648668	B	0.02656	0.0	B	0.01281	0.0	T	0.10382	-1.0632	10	0.15499	T	0.54	.	15.1551	0.72733	0.0:0.0:0.3747:0.6253	rs35546150	3734	Q9NZR2	LRP1B_HUMAN	K	3734;3672	ENSP00000374135:Q3734K	ENSP00000374135:Q3734K	Q	-	1	0	LRP1B	140832917	1.000000	0.71417	0.977000	0.42913	0.906000	0.53458	3.121000	0.50438	-0.149000	0.11215	-0.282000	0.10007	CAA	G|0.960;T|0.040	0.040	strong		0.388	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596254	48596254	+	Silent	SNP	A	A	C	rs11830378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48596254A>C	ENST00000310248.2	-	1	916	c.822T>G	c.(820-822)ccT>ccG	p.P274P		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	274						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GGAGGGAGAAAGGTTTGTCTT	0.483													A|||	212	0.0423323	0.059	0.036	5008	,	,		22069	0.006		0.0924	False		,,,				2504	0.0102				p.P274P		Atlas-SNP	.											OR10AD1,colon,carcinoma,-1,1	OR10AD1	24	1	0			c.T822G						PASS	.	A		275,4131	155.5+/-188.7	8,259,1936	122.0	122.0	122.0		822	0.8	1.0	12	dbSNP_120	122	764,7836	181.9+/-230.5	30,704,3566	no	coding-synonymous	OR10AD1	NM_001004134.1		38,963,5502	CC,CA,AA		8.8837,6.2415,7.9886		274/318	48596254	1039,11967	2203	4300	6503	SO:0001819	synonymous_variant	121275	exon1			GGAGAAAGGTTTG		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.822T>G	12.37:g.48596254A>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	100	45	0.45	NM_001004134	B9EGT9|Q6IFA8	Silent	SNP	ENST00000310248.2	37	CCDS31787.1																																																																																			A|0.938;C|0.062	0.062	strong		0.483	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
ATP13A5	344905	hgsc.bcm.edu	37	3	193081122	193081122	+	Missense_Mutation	SNP	G	G	T	rs12637558	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:193081122G>T	ENST00000342358.4	-	3	404	c.287C>A	c.(286-288)tCc>tAc	p.S96Y		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	96			S -> Y (in dbSNP:rs12637558). {ECO:0000269|PubMed:14702039}.			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.S96F(1)|p.S96Y(1)		NS(1)|autonomic_ganglia(2)|breast(1)|endometrium(6)|kidney(4)|large_intestine(15)|liver(2)|lung(26)|ovary(5)|prostate(1)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76	all_cancers(143;1.08e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;5.56e-18)|LUSC - Lung squamous cell carcinoma(58;6.08e-06)|Lung(62;6.49e-06)	GBM - Glioblastoma multiforme(46;0.000307)		CTTCAGTGTGGATAAGTAGAG	0.398													G|||	2083	0.415935	0.2133	0.4337	5008	,	,		18153	0.5764		0.4125	False		,,,				2504	0.5153				p.S96Y		Atlas-SNP	.											ATP13A5,NS,carcinoma,0,2	ATP13A5	171	2	2	Substitution - Missense(2)	ovary(1)|NS(1)	c.C287A						PASS	.	G	TYR/SER	1146,3260	409.1+/-334.9	155,836,1212	98.0	96.0	97.0		287	4.2	1.0	3	dbSNP_120	97	3666,4934	527.1+/-381.1	807,2052,1441	yes	missense	ATP13A5	NM_198505.2	144	962,2888,2653	TT,TG,GG		42.6279,26.01,36.9983	probably-damaging	96/1219	193081122	4812,8194	2203	4300	6503	SO:0001583	missense	344905	exon3			AGTGTGGATAAGT	AK122613	CCDS33914.1	3q29	2010-04-20			ENSG00000187527	ENSG00000187527		"""ATPases / P-type"""	31789	protein-coding gene	gene with protein product							Standard	NM_198505		Approved	FLJ16025	uc011bsq.2	Q4VNC0	OTTHUMG00000156101	ENST00000342358.4:c.287C>A	3.37:g.193081122G>T	ENSP00000341942:p.Ser96Tyr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	893	0.4088827838827839	119	0.241869918699187	143	0.39502762430939226	323	0.5646853146853147	308	0.40633245382585753	G	16.92	3.255259	0.59321	0.2601	0.426279	ENSG00000187527	ENST00000342358;ENST00000446087	T;T	0.44881	0.91;0.91	5.06	4.17	0.49024	.	0.195010	0.36893	N	0.002353	T	0.00012	0.0000	M	0.73962	2.25	0.29320	P	0.867429	P	0.36733	0.567	B	0.41764	0.366	T	0.48980	-0.8986	9	0.59425	D	0.04	-6.0887	13.2983	0.60311	0.0:0.0:0.84:0.16	rs12637558;rs59613984	96	Q4VNC0	AT135_HUMAN	Y	96;118	ENSP00000341942:S96Y;ENSP00000389416:S118Y	ENSP00000341942:S96Y	S	-	2	0	ATP13A5	194563816	1.000000	0.71417	0.987000	0.45799	0.953000	0.61014	3.546000	0.53656	1.428000	0.47296	0.655000	0.94253	TCC	G|0.618;T|0.382	0.382	strong		0.398	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
OR13C8	138802	hgsc.bcm.edu	37	9	107331504	107331504	+	Missense_Mutation	SNP	C	C	A	rs7026705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107331504C>A	ENST00000335040.1	+	1	56	c.56C>A	c.(55-57)gCc>gAc	p.A19D		NM_001004483.1	NP_001004483.1	Q8NGS7	O13C8_HUMAN	olfactory receptor, family 13, subfamily C, member 8	19			A -> D (in dbSNP:rs7026705).			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						GGGCTTTCTGCCCACCCAAAG	0.413													C|||	3233	0.645567	0.6475	0.5937	5008	,	,		19478	0.9464		0.4254	False		,,,				2504	0.5961				p.A19D		Atlas-SNP	.											.	OR13C8	77	.	0			c.C56A						PASS	.	C	ASP/ALA	2734,1672	658.2+/-400.4	856,1022,325	150.0	151.0	151.0		56	-1.6	0.9	9	dbSNP_116	151	3638,4962	524.4+/-380.5	800,2038,1462	yes	missense	OR13C8	NM_001004483.1	126	1656,3060,1787	AA,AC,CC		42.3023,37.9483,48.9928	benign	19/321	107331504	6372,6634	2203	4300	6503	SO:0001583	missense	138802	exon1			TTTCTGCCCACCC		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.56C>A	9.37:g.107331504C>A	ENSP00000334068:p.Ala19Asp	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_001004483	Q5VVG0|Q96R44	Missense_Mutation	SNP	ENST00000335040.1	37	CCDS35090.1	1400	0.6410256410256411	317	0.6443089430894309	206	0.569060773480663	542	0.9475524475524476	335	0.4419525065963061	C	2.567	-0.300408	0.05532	0.620517	0.423023	ENSG00000186943	ENST00000335040	T	0.00433	7.43	4.97	-1.64	0.08318	.	0.513993	0.17887	N	0.158677	T	0.00012	0.0000	N	0.01202	-0.96	0.58432	P	9.99999999995449E-6	B	0.09022	0.002	B	0.08055	0.003	T	0.39099	-0.9630	9	0.02654	T	1	.	8.9508	0.35788	0.5703:0.3539:0.0:0.0758	rs7026705;rs52790597;rs57774899;rs7026705	19	Q8NGS7	O13C8_HUMAN	D	19	ENSP00000334068:A19D	ENSP00000334068:A19D	A	+	2	0	OR13C8	106371325	0.000000	0.05858	0.866000	0.34008	0.588000	0.36517	-1.544000	0.02192	-0.066000	0.12998	-0.169000	0.13324	GCC	C|0.434;A|0.566	0.566	strong		0.413	OR13C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053480.1		
FMNL2	114793	hgsc.bcm.edu	37	2	153468107	153468107	+	Silent	SNP	C	C	T	rs35776654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:153468107C>T	ENST00000288670.9	+	11	1417	c.1050C>T	c.(1048-1050)gaC>gaT	p.D350D		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	350	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)		p.D350D(1)		central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						TAGGCCTGGACGAATACTTGG	0.393													C|||	260	0.0519169	0.0053	0.0576	5008	,	,		18613	0.0069		0.1392	False		,,,				2504	0.0675				p.D350D		Atlas-SNP	.											FMNL2,NS,carcinoma,0,1	FMNL2	75	1	1	Substitution - coding silent(1)	prostate(1)	c.C1050T						PASS	.	C		86,3704		0,86,1809	86.0	76.0	79.0		1050	-0.6	1.0	2	dbSNP_126	79	1167,7075		91,985,3045	no	coding-synonymous	FMNL2	NM_052905.3		91,1071,4854	TT,TC,CC		14.1592,2.2691,10.4139		350/1093	153468107	1253,10779	1895	4121	6016	SO:0001819	synonymous_variant	114793	exon11			CCTGGACGAATAC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1050C>T	2.37:g.153468107C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																			C|0.918;T|0.082	0.082	strong		0.393	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
EXOSC1	51013	hgsc.bcm.edu	37	10	99205731	99205731	+	Silent	SNP	A	A	G	rs4919098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99205731A>G	ENST00000370902.3	-	1	43	c.12T>C	c.(10-12)ccT>ccC	p.P4P	EXOSC1_ENST00000370885.4_Silent_p.P4P|ZDHHC16_ENST00000393760.1_5'Flank|ZDHHC16_ENST00000353979.3_5'Flank|EXOSC1_ENST00000471049.1_5'Flank|ZDHHC16_ENST00000370846.4_5'Flank|ZDHHC16_ENST00000352634.4_5'Flank|ZDHHC16_ENST00000345745.5_5'Flank|ZDHHC16_ENST00000370854.3_5'Flank|EXOSC1_ENST00000485122.2_Silent_p.P4P|ZDHHC16_ENST00000370842.2_5'Flank|EXOSC1_ENST00000370886.5_Silent_p.P4P	NM_016046.3	NP_057130.1	Q9Y3B2	EXOS1_HUMAN	exosome component 1	4					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|endometrium(1)|lung(5)	7		Renal(717;0.000147)|Colorectal(252;0.00205)|Ovarian(717;0.00965)		all cancers(201;8.29e-42)|Epithelial(162;5.7e-33)|BRCA - Breast invasive adenocarcinoma(275;0.000315)|Kidney(138;0.000832)|KIRC - Kidney renal clear cell carcinoma(50;0.00269)|STAD - Stomach adenocarcinoma(243;0.202)		AGTATCTCACAGGTGGCGCCA	0.557											OREG0020413	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	479	0.095647	0.0938	0.111	5008	,	,		17552	0.0764		0.1223	False		,,,				2504	0.0798				p.P4P		Atlas-SNP	.											.	EXOSC1	8	.	0			c.T12C						PASS	.	G		482,3924	782.5+/-414.6	33,416,1754	108.0	99.0	102.0		12	-3.7	0.8	10	dbSNP_111	102	1157,7443	765.0+/-407.6	81,995,3224	no	coding-synonymous	EXOSC1	NM_016046.3		114,1411,4978	GG,GA,AA		13.4535,10.9396,12.6019		4/196	99205731	1639,11367	2203	4300	6503	SO:0001819	synonymous_variant	51013	exon1			TCTCACAGGTGGC	AF151866	CCDS7459.1	10q24	2004-03-26			ENSG00000171311	ENSG00000171311			17286	protein-coding gene	gene with protein product	"""CSL4 exosomal core protein homolog (yeast)"""	606493				11812149, 11719186	Standard	XR_246092		Approved	hCsl4p, Csl4p, CSL4, Ski4p, SKI4, CGI-108, p13	uc001kni.3	Q9Y3B2	OTTHUMG00000018854	ENST00000370902.3:c.12T>C	10.37:g.99205731A>G		Somatic	76	0	0	1341	WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_016046	B2R9B3|Q5JTH3	Silent	SNP	ENST00000370902.3	37	CCDS7459.1																																																																																			A|0.888;G|0.112	0.112	strong		0.557	EXOSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049680.1		
Unknown	0	hgsc.bcm.edu	37	17	17326604	17326604	+	IGR	SNP	C	C	T	rs370938128|rs7225976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:17326604C>T								NT5M (75629 upstream) : Y_RNA (37153 downstream)																							CATGATGGGGCAAATGCCAGA	0.473													T|||	2100	0.419329	0.7912	0.2651	5008	,	,		23244	0.1875		0.3201	False		,,,				2504	0.3671				p.A140V		Atlas-SNP	.											.	.	.	.	0			c.C419T						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			ATGGGGCAAATGC																													17.37:g.17326604C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	21	20	0.952381	NM_001243312		Missense_Mutation	SNP		37																																																																																				C|0.662;T|0.338	0.338	strong	0	0.473								
ANP32E	81611	hgsc.bcm.edu	37	1	150199123	150199123	+	Silent	SNP	G	G	T	rs7522034	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:150199123G>T	ENST00000314136.8	-	5	867	c.498C>A	c.(496-498)ggC>ggA	p.G166G	ANP32E_ENST00000436748.2_Silent_p.G125G|ANP32E_ENST00000369119.3_Silent_p.G118G|ANP32E_ENST00000369116.4_Silent_p.G34G|ANP32E_ENST00000533654.1_Missense_Mutation_p.A111E|ANP32E_ENST00000369114.5_Intron|ANP32E_ENST00000369115.2_Silent_p.G34G	NM_001136478.2|NM_001280559.1|NM_030920.3	NP_001129950.1|NP_001267488.1|NP_112182.1	Q9BTT0	AN32E_HUMAN	acidic (leucine-rich) nuclear phosphoprotein 32 family, member E	166	Asp/Glu-rich (highly acidic).				histone exchange (GO:0043486)|negative regulation of catalytic activity (GO:0043086)	cytoplasmic membrane-bounded vesicle (GO:0016023)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	histone binding (GO:0042393)|phosphatase inhibitor activity (GO:0019212)			breast(3)|endometrium(3)|lung(7)|skin(1)|urinary_tract(1)	15	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CATCTTCATCGCCATCTTTAA	0.418													T|||	3015	0.602037	0.9228	0.4683	5008	,	,		19153	0.5456		0.4304	False		,,,				2504	0.498				p.G166G		Atlas-SNP	.											ANP32E,NS,adenoma,0,1	ANP32E	28	1	0			c.C498A						PASS	.	T	,,	3621,785	315.8+/-294.3	1488,645,70	109.0	98.0	102.0		375,354,498	-3.2	1.0	1	dbSNP_116	102	3578,5022	627.1+/-397.9	744,2090,1466	no	coding-synonymous,coding-synonymous,coding-synonymous	ANP32E	NM_001136478.2,NM_001136479.1,NM_030920.3	,,	2232,2735,1536	TT,TG,GG		41.6047,17.8166,44.6486	,,	125/228,118/221,166/269	150199123	7199,5807	2203	4300	6503	SO:0001819	synonymous_variant	81611	exon5			TTCATCGCCATCT	AK092672	CCDS946.1, CCDS44214.1, CCDS44215.1, CCDS60245.1	1q22	2008-02-05			ENSG00000143401	ENSG00000143401		"""ANP32 acidic nuclear phosphoproteins"""	16673	protein-coding gene	gene with protein product		609611				12438741	Standard	NM_030920		Approved	LANPL, MGC5350, LANP-L	uc001etw.3	Q9BTT0	OTTHUMG00000012547	ENST00000314136.8:c.498C>A	1.37:g.150199123G>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_030920	B4E0I6|E9PEA6|Q5TB18|Q5TB20|Q8N1S4|Q8WWW9	Silent	SNP	ENST00000314136.8	37	CCDS946.1	1220	0.5586080586080586	445	0.9044715447154471	157	0.43370165745856354	288	0.5034965034965035	330	0.43535620052770446	T	0.022	-1.416738	0.01136	0.821834	0.416047	ENSG00000143401	ENST00000533654	T	0.00333	8.07	4.71	-3.24	0.05094	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999945053	B	0.02656	0.0	B	0.01281	0.0	T	0.06285	-1.0835	7	0.15066	T	0.55	.	1.3997	0.02268	0.3882:0.0817:0.2172:0.3129	rs7522034;rs60000686;rs7522034	111	E9PLC4	.	E	111	ENSP00000435215:A111E	ENSP00000435215:A111E	A	-	2	0	ANP32E	148465747	0.993000	0.37304	0.988000	0.46212	0.046000	0.14306	0.015000	0.13355	-0.475000	0.06852	-0.363000	0.07495	GCG	G|0.433;T|0.567	0.567	strong		0.418	ANP32E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035056.1	NM_030920	
CHRNA2	1135	hgsc.bcm.edu	37	8	27328511	27328511	+	Missense_Mutation	SNP	G	G	A	rs2472553	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27328511G>A	ENST00000520933.2	-	1	218	c.65C>T	c.(64-66)aCc>aTc	p.T22I	CHRNA2_ENST00000240132.2_Missense_Mutation_p.T22I|CHRNA2_ENST00000407991.1_Missense_Mutation_p.T22I			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	22			T -> I (in dbSNP:rs2472553).		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	ACCTGCTGGGGTCAGAAGGAG	0.542													G|||	1107	0.221046	0.1921	0.1945	5008	,	,		20986	0.4325		0.1372	False		,,,				2504	0.1472				p.T22I		Atlas-SNP	.											.	CHRNA2	48	.	0			c.C65T						PASS	.	G	ILE/THR	810,3596	322.9+/-297.8	75,660,1468	78.0	69.0	72.0		65	-2.5	0.0	8	dbSNP_100	72	1125,7475	232.1+/-265.8	78,969,3253	yes	missense	CHRNA2	NM_000742.3	89	153,1629,4721	AA,AG,GG		13.0814,18.384,14.8777	benign	22/530	27328511	1935,11071	2203	4300	6503	SO:0001583	missense	1135	exon2			GCTGGGGTCAGAA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.65C>T	8.37:g.27328511G>A	ENSP00000429616:p.Thr22Ile	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	550	0.2518315018315018	93	0.18902439024390244	69	0.19060773480662985	291	0.5087412587412588	97	0.1279683377308707	G	0	-2.672280	0.00104	0.18384	0.130814	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132;ENST00000524096;ENST00000518712;ENST00000521921	T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51	4.42	-2.5	0.06384	.	3.327300	0.00649	N	0.000552	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	0.36744	-0.9735	9	0.02654	T	1	.	5.1178	0.14845	0.4675:0.1607:0.3719:0.0	rs2472553;rs57302661;rs2472553	22;22	B4DK19;Q15822	.;ACHA2_HUMAN	I	22	ENSP00000385026:T22I;ENSP00000429616:T22I;ENSP00000240132:T22I;ENSP00000430422:T22I;ENSP00000430856:T22I;ENSP00000429953:T22I	ENSP00000240132:T22I	T	-	2	0	CHRNA2	27384428	0.793000	0.28825	0.004000	0.12327	0.072000	0.16883	0.305000	0.19254	-0.388000	0.07797	-0.794000	0.03295	ACC	G|0.819;A|0.181	0.181	strong		0.542	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388635	1388635	+	Silent	SNP	T	T	C	rs74518227	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388635T>C	ENST00000324803.4	+	1	3296	c.336T>C	c.(334-336)tgT>tgC	p.C112C		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	112					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.C112C(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGTGCCCATGTGGAGTGCCCG	0.672													N|||	258	0.0515176	0.0348	0.0548	5008	,	,		16946	0.0069		0.0507	False		,,,				2504	0.1186				p.C112C		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,4	CRIPAK	185	4	1	Substitution - coding silent(1)	prostate(1)	c.T336C						scavenged	.						189.0	145.0	160.0					4																	1388635		2203	4299	6502	SO:0001819	synonymous_variant	285464	exon1			CCCATGTGGAGTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.336T>C	4.37:g.1388635T>C		Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	132	30	0.227273	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	5.811	0.333996	0.11013	.	.	ENSG00000179979	ENST00000382944	.	.	.	0.948	-1.08	0.09936	.	.	.	.	.	T	0.21427	0.0516	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.27123	-1.0083	5	0.25106	T	0.35	.	4.049	0.09786	0.3111:0.0:0.0:0.6889	.	.	.	.	R	96	.	ENSP00000372402:W96R	W	+	1	0	CRIPAK	1378635	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-1.127000	0.03251	-0.202000	0.10268	0.102000	0.15555	TGG	T|0.937;C|0.063	0.063	strong		0.672	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
BMP1	649	hgsc.bcm.edu	37	8	22021037	22021037	+	5'Flank	SNP	C	C	A	rs4715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22021037C>A	ENST00000306385.5	+	0	0				SFTPC_ENST00000522109.1_Missense_Mutation_p.T138N|BMP1_ENST00000306349.8_5'Flank|SFTPC_ENST00000521315.1_Missense_Mutation_p.T138N|SFTPC_ENST00000318561.3_Missense_Mutation_p.T138N|BMP1_ENST00000397814.3_5'Flank|SFTPC_ENST00000520605.1_Missense_Mutation_p.T85N|SFTPC_ENST00000524255.1_Missense_Mutation_p.T85N|SFTPC_ENST00000437090.2_Missense_Mutation_p.T138N|BMP1_ENST00000397816.3_5'Flank|BMP1_ENST00000354870.5_5'Flank	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1						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)		GAGGCTCTCACTAGAAAAGTC	0.552													C|||	989	0.197484	0.0318	0.2507	5008	,	,		19997	0.2688		0.2644	False		,,,				2504	0.2413				p.T138N		Atlas-SNP	.											.	SFTPC	19	.	0			c.C413A	GRCh37	CM040798	SFTPC	M	rs4715	PASS	.	C	ASN/THR,ASN/THR,ASN/THR	241,3641		12,217,1712	76.0	77.0	77.0		413,413,413	2.5	0.4	8	dbSNP_52	77	2277,6019		308,1661,2179	yes	missense,missense,missense	SFTPC	NM_001172357.1,NM_001172410.1,NM_003018.3	65,65,65	320,1878,3891	AA,AC,CC		27.447,6.2081,20.6766	benign,benign,benign	138/192,138/198,138/198	22021037	2518,9660	1941	4148	6089	SO:0001631	upstream_gene_variant	6440	exon4			CTCTCACTAGAAA		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		8.37:g.22021037C>A	Exception_encountered	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	119	60	0.504202	NM_003018	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	464	0.21245421245421245	19	0.03861788617886179	95	0.26243093922651933	146	0.25524475524475526	204	0.2691292875989446	C	18.99	3.740275	0.69304	0.062081	0.27447	ENSG00000168484	ENST00000318561;ENST00000521315;ENST00000437090;ENST00000520605;ENST00000522109;ENST00000524255;ENST00000523296	T;T;T;T;T;T;T	0.79749	-1.3;-1.3;-1.3;-1.3;-1.3;-1.3;-1.3	5.49	2.47	0.30058	.	0.507841	0.18215	N	0.148061	T	0.00039	0.0001	.	.	.	0.54753	P	1.799999999996249E-5	P;B;P	0.51933	0.949;0.002;0.896	P;B;P	0.54815	0.761;0.004;0.602	T	0.01156	-1.1434	8	0.49607	T	0.09	-1.1419	7.5391	0.27727	0.0:0.7072:0.0:0.2928	rs4715;rs1126717;rs2269331;rs3181906;rs8192341;rs11552818;rs17353998;rs17856155;rs52790253;rs57605652;rs4715	138;138;138	E9PGX3;C9JYF6;E5RI92	.;.;.	N	138;138;138;85;138;85;85	ENSP00000316152:T138N;ENSP00000430410:T138N;ENSP00000407931:T138N;ENSP00000430266:T85N;ENSP00000429496:T138N;ENSP00000429552:T85N;ENSP00000429619:T85N	ENSP00000316152:T138N	T	+	2	0	SFTPC	22076982	0.001000	0.12720	0.423000	0.26634	0.922000	0.55478	0.920000	0.28705	0.200000	0.20447	0.655000	0.94253	ACT	C|0.796;A|0.204	0.204	strong		0.552	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
STEAP2	261729	hgsc.bcm.edu	37	7	89856644	89856644	+	Silent	SNP	C	C	T	rs2016903	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:89856644C>T	ENST00000287908.3	+	3	1245	c.852C>T	c.(850-852)taC>taT	p.Y284Y	STEAP2_ENST00000394621.2_Silent_p.Y284Y|STEAP2_ENST00000394626.1_Silent_p.Y284Y|STEAP2_ENST00000394622.2_Silent_p.Y284Y|STEAP2_ENST00000394632.1_Silent_p.Y284Y|STEAP2_ENST00000394629.2_Silent_p.Y284Y|STEAP2_ENST00000402625.2_Silent_p.Y284Y	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	284	Ferric oxidoreductase.				copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					AACTTTATTACGGCACCAAGT	0.408													C|||	392	0.0782748	0.0136	0.0821	5008	,	,		18256	0.0149		0.2097	False		,,,				2504	0.093				p.Y284Y		Atlas-SNP	.											STEAP2_ENST00000394626,NS,adenoma,0,2	STEAP2	78	2	0			c.C852T						PASS	.	C	,,	251,4155	144.6+/-179.5	12,227,1964	87.0	85.0	86.0		852,852,852	-5.2	1.0	7	dbSNP_92	86	1939,6661	340.8+/-323.8	220,1499,2581	no	coding-synonymous,coding-synonymous,coding-synonymous	STEAP2	NM_001040665.1,NM_001040666.1,NM_152999.3	,,	232,1726,4545	TT,TC,CC		22.5465,5.6968,16.8384	,,	284/491,284/455,284/491	89856644	2190,10816	2203	4300	6503	SO:0001819	synonymous_variant	261729	exon4			TTATTACGGCACC	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"""prostate cancer associated protein 1"", ""six transmembrane epithelial antigen of the prostate 2"""	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.852C>T	7.37:g.89856644C>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	180	85	0.472222	NM_001244946	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Silent	SNP	ENST00000287908.3	37	CCDS5615.1																																																																																			C|0.869;T|0.131	0.131	strong		0.408	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999	
ITPA	3704	hgsc.bcm.edu	37	20	3204084	3204084	+	Silent	SNP	G	G	A	rs9101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3204084G>A	ENST00000380113.3	+	8	753	c.561G>A	c.(559-561)gaG>gaA	p.E187E	ITPA_ENST00000483354.1_3'UTR|ITPA_ENST00000455664.2_Silent_p.E170E|ITPA_ENST00000399838.3_Silent_p.E146E	NM_033453.3|NM_181493.2	NP_258412.1|NP_852470.1			inosine triphosphatase (nucleoside triphosphate pyrophosphatase)											autonomic_ganglia(1)|large_intestine(3)|ovary(1)|stomach(1)	6						AGCTGCAGGAGTACTTTGGCA	0.632													G|||	1705	0.340455	0.0832	0.2781	5008	,	,		18199	0.5089		0.3091	False		,,,				2504	0.591				p.E187E		Atlas-SNP	.											ITPA,NS,carcinoma,0,1	ITPA	16	1	0			c.G561A						PASS	.	G	,	495,3911	227.8+/-242.9	31,433,1739	50.0	40.0	43.0		561,510	-5.4	0.2	20	dbSNP_52	43	2458,6142	401.9+/-347.3	377,1704,2219	no	coding-synonymous,coding-synonymous	ITPA	NM_033453.2,NM_181493.1	,	408,2137,3958	AA,AG,GG		28.5814,11.2347,22.7049	,	187/195,170/178	3204084	2953,10053	2203	4300	6503	SO:0001819	synonymous_variant	3704	exon8			GCAGGAGTACTTT	AF026816	CCDS13051.1, CCDS46576.1, CCDS58762.1	20p	2002-02-01			ENSG00000125877	ENSG00000125877	3.6.1.19		6176	protein-coding gene	gene with protein product		147520		C20orf37		11278832	Standard	NM_033453		Approved	HLC14-06-P, dJ794I6.3	uc002wid.4	Q9BY32	OTTHUMG00000031738	ENST00000380113.3:c.561G>A	20.37:g.3204084G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_033453		Silent	SNP	ENST00000380113.3	37	CCDS13051.1																																																																																			G|0.729;A|0.271	0.271	strong		0.632	ITPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077719.2		
POU2F1	5451	hgsc.bcm.edu	37	1	167358837	167358837	+	Missense_Mutation	SNP	A	A	G	rs142378150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:167358837A>G	ENST00000541643.3	+	10	919	c.757A>G	c.(757-759)Aca>Gca	p.T253A	POU2F1_ENST00000367866.2_Missense_Mutation_p.T276A|POU2F1_ENST00000452019.1_3'UTR|POU2F1_ENST00000420254.3_Missense_Mutation_p.T253A|POU2F1_ENST00000429375.2_Missense_Mutation_p.T213A|POU2F1_ENST00000367862.5_Missense_Mutation_p.T265A|POU2F1_ENST00000367865.1_3'UTR			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	253					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						AGCAACCCCAACACGCACAAT	0.458													A|||	2	0.000399361	0.0	0.0	5008	,	,		20298	0.0		0.002	False		,,,				2504	0.0				p.T276A		Atlas-SNP	.											.	POU2F1	120	.	0			c.A826G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	6,4400	11.4+/-27.6	0,6,2197	131.0	136.0	134.0		793,637,826	5.8	1.0	1	dbSNP_134	134	35,8565	25.1+/-72.6	0,35,4265	yes	missense,missense,missense	POU2F1	NM_001198783.1,NM_001198786.1,NM_002697.3	58,58,58	0,41,6462	GG,GA,AA		0.407,0.1362,0.3152	probably-damaging,probably-damaging,probably-damaging	265/756,213/704,276/767	167358837	41,12965	2203	4300	6503	SO:0001583	missense	5451	exon9			ACCCCAACACGCA	BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"""Homeoboxes / POU class"""	9212	protein-coding gene	gene with protein product		164175	"""POU domain class 2, transcription factor 1"""	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.757A>G	1.37:g.167358837A>G	ENSP00000441285:p.Thr253Ala	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Missense_Mutation	SNP	ENST00000541643.3	37		.	.	.	.	.	.	.	.	.	.	A	19.63	3.863521	0.71949	0.001362	0.00407	ENSG00000143190	ENST00000367866;ENST00000429375;ENST00000367865;ENST00000420254;ENST00000541643;ENST00000367862;ENST00000443275	T;D;T;T;T;T;T	0.86097	-1.09;-2.07;-1.09;-1.09;-1.09;-1.09;-1.09	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.88250	0.6386	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.61697	0.984;0.971;0.99;0.99;0.984	D;P;D;D;D	0.73380	0.935;0.79;0.971;0.98;0.935	D	0.87855	0.2660	10	0.41790	T	0.15	.	16.1747	0.81844	1.0:0.0:0.0:0.0	.	213;253;265;251;253	B4E029;P14859-4;P14859-2;P14859-3;P14859	.;.;.;.;PO2F1_HUMAN	A	276;213;251;253;253;265;161	ENSP00000356840:T276A;ENSP00000401217:T213A;ENSP00000356839:T251A;ENSP00000414660:T253A;ENSP00000441285:T253A;ENSP00000356836:T265A;ENSP00000415993:T161A	ENSP00000356836:T265A	T	+	1	0	POU2F1	165625461	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.923000	0.92808	2.225000	0.72522	0.455000	0.32223	ACA	A|0.997;G|0.003	0.003	strong		0.458	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697	
GNAO1	2775	hgsc.bcm.edu	37	16	56377748	56377748	+	Intron	SNP	A	A	G	rs1799917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:56377748A>G	ENST00000262493.6	+	6	1569				GNAO1_ENST00000262494.7_Silent_p.K317K	NM_020988.2	NP_066268.1	P09471	GNAO_HUMAN	guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O						adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|dopamine receptor signaling pathway (GO:0007212)|forebrain development (GO:0030900)|locomotory behavior (GO:0007626)|muscle contraction (GO:0006936)|negative regulation of calcium ion transport (GO:0051926)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|regulation of heart contraction (GO:0008016)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to morphine (GO:0043278)	heterotrimeric G-protein complex (GO:0005834)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	corticotropin-releasing hormone receptor 1 binding (GO:0051430)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|mu-type opioid receptor binding (GO:0031852)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)	17		all_neural(199;0.159)				CAGCCCACAAAGAGATCTACA	0.562													G|||	2053	0.409944	0.6286	0.2435	5008	,	,		13508	0.2242		0.326	False		,,,				2504	0.5102				p.K317K		Atlas-SNP	.											.	GNAO1	95	.	0			c.A951G						PASS	.	G	,	2506,1890	541.3+/-375.7	701,1104,393	203.0	128.0	153.0		,951	4.4	1.0	16	dbSNP_89	153	2997,5603	664.4+/-402.2	532,1933,1835	no	intron,coding-synonymous	GNAO1	NM_020988.2,NM_138736.2	,	1233,3037,2228	GG,GA,AA		34.8488,42.9936,42.3438	,	,317/355	56377748	5503,7493	2198	4300	6498	SO:0001627	intron_variant	2775	exon8			CCACAAAGAGATC		CCDS10756.1, CCDS10757.1	16q13	2008-08-01			ENSG00000087258	ENSG00000087258			4389	protein-coding gene	gene with protein product		139311				1899283, 11395521	Standard	NM_020988		Approved	G-ALPHA-o	uc002eit.4	P09471	OTTHUMG00000133241	ENST00000262493.6:c.723+6976A>G	16.37:g.56377748A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_138736	P29777|Q8TD72|Q9UMV4	Silent	SNP	ENST00000262493.6	37	CCDS10756.1																																																																																			A|0.609;G|0.391	0.391	strong		0.562	GNAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256981.2	NM_020988	
ATP10D	57205	hgsc.bcm.edu	37	4	47584046	47584046	+	Missense_Mutation	SNP	G	G	A	rs1058793	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:47584046G>A	ENST00000273859.3	+	21	3987	c.3718G>A	c.(3718-3720)Gtt>Att	p.V1240I	ATP10D_ENST00000512393.1_3'UTR	NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1240			V -> I (in dbSNP:rs1058793). {ECO:0000269|PubMed:15489334}.		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						TCTGTTCATCGTTCTCCTCCA	0.443													A|||	1500	0.299521	0.3268	0.2493	5008	,	,		21392	0.5724		0.16	False		,,,				2504	0.1605				p.V1240I		Atlas-SNP	.											.	ATP10D	168	.	0			c.G3718A						PASS	.	A	ILE/VAL	1292,3114	699.3+/-406.5	184,924,1095	223.0	203.0	210.0		3718	5.0	1.0	4	dbSNP_86	210	1408,7192	753.2+/-407.4	132,1144,3024	yes	missense	ATP10D	NM_020453.3	29	316,2068,4119	AA,AG,GG		16.3721,29.3236,20.7596	benign	1240/1427	47584046	2700,10306	2203	4300	6503	SO:0001583	missense	57205	exon21			TTCATCGTTCTCC	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.3718G>A	4.37:g.47584046G>A	ENSP00000273859:p.Val1240Ile	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	288	144	0.5	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	661	0.30265567765567764	150	0.3048780487804878	84	0.23204419889502761	317	0.5541958041958042	110	0.14511873350923482	A	6.782	0.513172	0.12944	0.293236	0.163721	ENSG00000145246	ENST00000273859	T	0.51574	0.7	5.01	5.01	0.66863	.	0.175907	0.48767	N	0.000173	T	0.00012	0.0000	N	0.04787	-0.16	0.09310	P	1.0	B	0.06786	0.001	B	0.01281	0.0	T	0.44697	-0.9311	9	0.02654	T	1	-9.8089	7.6262	0.28214	0.8372:0.0:0.1628:0.0	rs1058793;rs3199442;rs3749586;rs17423647;rs17653691;rs52814581;rs56674990;rs1058793	1240	Q9P241	AT10D_HUMAN	I	1240	ENSP00000273859:V1240I	ENSP00000273859:V1240I	V	+	1	0	ATP10D	47278803	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.764000	0.68826	0.947000	0.37659	-0.332000	0.08345	GTT	G|0.747;A|0.253	0.253	strong		0.443	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
KIAA0922	23240	hgsc.bcm.edu	37	4	154387597	154387597	+	Silent	SNP	G	G	C	rs71620317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:154387597G>C	ENST00000409663.3	+	1	100	c.48G>C	c.(46-48)gcG>gcC	p.A16A	KIAA0922_ENST00000409959.3_Silent_p.A16A|KIAA0922_ENST00000440693.1_Silent_p.A16A	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	16						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				GCCGCACCGCGGCGGCCGTGA	0.741													-|||	2539	0.506989	0.848	0.2839	5008	,	,		5547	0.3254		0.3887	False		,,,				2504	0.5133				p.A16A		Atlas-SNP	.											.	KIAA0922	214	.	0			c.G48C						PASS	.						2.0	4.0	4.0					4																	154387597		533	1352	1885	SO:0001819	synonymous_variant	23240	exon1			CACCGCGGCGGCC	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.48G>C	4.37:g.154387597G>C		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			G|0.548;C|0.452	0.452	strong		0.741	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
OR2T29	343563	hgsc.bcm.edu	37	1	248722723	248722723	+	Nonsense_Mutation	SNP	G	G	A	rs200037558	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248722723G>A	ENST00000328570.3	-	1	74	c.70C>T	c.(70-72)Caa>Taa	p.Q24*	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTTTGGATTGTCTGAAGAGT	0.488													.|||	375	0.0748802	0.0507	0.0519	5008	,	,		17026	0.1538		0.0288	False		,,,				2504	0.09				p.Q24X		Atlas-SNP	.											.	OR2T29	8	.	0			c.C70T						PASS	.						54.0	33.0	40.0					1																	248722723		2203	4296	6499	SO:0001587	stop_gained	343563	exon1			TGGATTGTCTGAA		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"""GPCR / Class A : Olfactory receptors"""	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.70C>T	1.37:g.248722723G>A	ENSP00000331774:p.Gln24*	Somatic	599	0	0		WXS	Illumina HiSeq	Phase_I	468	147	0.314103	NM_001004694		Nonsense_Mutation	SNP	ENST00000328570.3	37	CCDS55695.1	.	.	.	.	.	.	.	.	.	.	g	9.785	1.176272	0.21704	.	.	ENSG00000182783	ENST00000328570	.	.	.	2.73	2.73	0.32206	.	0.522929	0.16025	N	0.233106	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	10.8901	0.46990	0.0:0.0:1.0:0.0	.	.	.	.	X	24	.	ENSP00000331774:Q24X	Q	-	1	0	OR2T29	246789346	0.000000	0.05858	0.901000	0.35422	0.099000	0.18886	-1.361000	0.02597	1.371000	0.46172	0.196000	0.17591	CAA	G|0.996;A|0.004	0.004	strong		0.488	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694	
MYO18B	84700	hgsc.bcm.edu	37	22	26157068	26157068	+	Missense_Mutation	SNP	C	C	G	rs61734946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26157068C>G	ENST00000407587.2	+	2	178	c.9C>G	c.(7-9)atC>atG	p.I3M	MYO18B_ENST00000335473.7_Missense_Mutation_p.I3M|MYO18B_ENST00000536101.1_Missense_Mutation_p.I3M			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	3				I -> M (in Ref. 2; CAC70712). {ECO:0000305}.		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						GCATGGCCATCTCATCACGCC	0.597													C|||	386	0.0770767	0.0129	0.1225	5008	,	,		22190	0.002		0.1839	False		,,,				2504	0.0992				p.I3M		Atlas-SNP	.											.	MYO18B	322	.	0			c.C9G						PASS	.	C	MET/ILE	177,4215	101.2+/-139.8	6,165,2025	106.0	106.0	106.0		9	-0.9	1.0	22	dbSNP_129	106	1622,6946	293.2+/-301.3	163,1296,2825	yes	missense	MYO18B	NM_032608.5	10	169,1461,4850	GG,GC,CC		18.9309,4.0301,13.8812	benign	3/2568	26157068	1799,11161	2196	4284	6480	SO:0001583	missense	84700	exon2			GGCCATCTCATCA	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.9C>G	22.37:g.26157068C>G	ENSP00000386096:p.Ile3Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		202	0.0924908424908425	8	0.016260162601626018	50	0.13812154696132597	2	0.0034965034965034965	142	0.18733509234828497	C	18.05	3.537953	0.65085	0.040301	0.189309	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.90069	-2.59;-2.59;-2.61	5.3	-0.902	0.10537	.	0.000000	0.36972	N	0.002309	T	0.00936	0.0031	L	0.56769	1.78	0.40843	P	0.016317000000000026	D	0.76494	0.999	D	0.87578	0.998	T	0.53479	-0.8433	9	0.87932	D	0	.	2.6094	0.04887	0.3227:0.327:0.0:0.3503	rs61734946	3	F5GYU7	.	M	3	ENSP00000441229:I3M;ENSP00000334563:I3M;ENSP00000386096:I3M	ENSP00000334563:I3M	I	+	3	3	MYO18B	24487068	0.993000	0.37304	0.998000	0.56505	0.988000	0.76386	0.036000	0.13819	0.029000	0.15352	-0.194000	0.12790	ATC	C|0.888;G|0.112	0.112	strong		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
IL4R	3566	hgsc.bcm.edu	37	16	27356203	27356203	+	Missense_Mutation	SNP	A	A	G	rs1805010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:27356203A>G	ENST00000395762.2	+	5	482	c.223A>G	c.(223-225)Atc>Gtc	p.I75V	IL4R_ENST00000380922.3_Missense_Mutation_p.I60V|IL4R_ENST00000543915.2_Missense_Mutation_p.I75V|IL4R_ENST00000170630.2_Missense_Mutation_p.I75V|IL4R_ENST00000449195.1_Missense_Mutation_p.I75V	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	75			I -> F (in dbSNP:rs1805010).|I -> L (in dbSNP:rs1805010).|I -> V (associated with atopic asthma and cedar pollen sensitization; dbSNP:rs1805010). {ECO:0000269|PubMed:10390422, ECO:0000269|PubMed:14657871, ECO:0000269|PubMed:9070874, ECO:0000269|PubMed:9620765, ECO:0000269|Ref.5}.		defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						CCACACGTGTATCCCTGAGAA	0.632													G|||	2286	0.45647	0.4811	0.4251	5008	,	,		15543	0.5159		0.4254	False		,,,				2504	0.4162				p.I75V		Atlas-SNP	.											.	IL4R	70	.	0			c.A223G	GRCh37	CM983400	IL4R	M	rs1805010	PASS	.	G	VAL/ILE,VAL/ILE	2189,2205	589.1+/-387.1	542,1105,550	81.0	66.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	223,223	0.2	0.3	16	dbSNP_89	71	3853,4747	609.8+/-395.6	858,2137,1305	yes	missense,missense	IL4R	NM_000418.2,NM_001008699.1	29,29	1400,3242,1855	GG,GA,AA		44.8023,49.8179,46.4984	benign,benign	75/826,75/228	27356203	6042,6952	2197	4300	6497	SO:0001583	missense	3566	exon5			ACGTGTATCCCTG	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.223A>G	16.37:g.27356203A>G	ENSP00000379111:p.Ile75Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	1019	0.4665750915750916	240	0.4878048780487805	168	0.46408839779005523	296	0.5174825174825175	315	0.4155672823218997	G	0.017	-1.489913	0.01018	0.498179	0.448023	ENSG00000077238	ENST00000380925;ENST00000449195;ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19	3.4	0.172	0.15031	Interleukin-4 receptor alpha chain, N-terminal (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	1.415690	0.04499	N	0.380973	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.43196	-0.9406	9	0.02654	T	1	-25.804	6.3201	0.21213	0.5679:0.0:0.4321:0.0	rs1805010;rs3024558;rs3116576;rs17513665;rs1805010	60;75;75	B4E076;P24394;P24394-2	.;IL4RA_HUMAN;.	V	75;75;75;75;60;75	ENSP00000410322:I75V;ENSP00000379111:I75V;ENSP00000441667:I75V;ENSP00000370309:I60V;ENSP00000170630:I75V	ENSP00000170630:I75V	I	+	1	0	IL4R	27263704	0.708000	0.27876	0.313000	0.25210	0.013000	0.08279	-0.173000	0.09854	-0.161000	0.10983	-0.642000	0.03964	ATC	A|0.524;G|0.476	0.476	strong		0.632	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
CHRNA2	1135	hgsc.bcm.edu	37	8	27327369	27327369	+	Missense_Mutation	SNP	C	C	T	rs548268816		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27327369C>T	ENST00000520933.2	-	2	356	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	CHRNA2_ENST00000240132.2_Missense_Mutation_p.R68Q|CHRNA2_ENST00000407991.1_Missense_Mutation_p.R68Q			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	68					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)	p.R68Q(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GTTGTAGCCCCGGAAGAGGTG	0.632																																					p.R68Q		Atlas-SNP	.											CHRNA2,caecum,carcinoma,-1,2	CHRNA2	48	2	1	Substitution - Missense(1)	endometrium(1)	c.G203A						PASS	.						87.0	86.0	86.0					8																	27327369		2203	4300	6503	SO:0001583	missense	1135	exon3			TAGCCCCGGAAGA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.203G>A	8.37:g.27327369C>T	ENSP00000429616:p.Arg68Gln	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.237311	0.39498	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132;ENST00000524096;ENST00000518712	T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05	4.77	3.89	0.44902	Neurotransmitter-gated ion-channel ligand-binding (3);	0.410909	0.25143	N	0.032809	T	0.47488	0.1448	L	0.33753	1.03	0.09310	N	1	B;B	0.33073	0.396;0.396	B;B	0.33568	0.166;0.166	T	0.41251	-0.9519	10	0.45353	T	0.12	.	6.9775	0.24683	0.0:0.7318:0.1747:0.0935	.	68;68	B4DK19;Q15822	.;ACHA2_HUMAN	Q	68	ENSP00000385026:R68Q;ENSP00000429616:R68Q;ENSP00000240132:R68Q;ENSP00000430422:R68Q;ENSP00000430856:R68Q	ENSP00000240132:R68Q	R	-	2	0	CHRNA2	27383286	0.000000	0.05858	0.789000	0.31954	0.875000	0.50365	0.006000	0.13152	1.380000	0.46344	0.561000	0.74099	CGG	.	.	none		0.632	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
DUS1L	64118	hgsc.bcm.edu	37	17	80020812	80020812	+	Silent	SNP	C	C	T	rs11542332	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80020812C>T	ENST00000354321.7	-	4	920	c.435G>A	c.(433-435)acG>acA	p.T145T	DUS1L_ENST00000306796.5_Silent_p.T145T			Q6P1R4	DUS1L_HUMAN	dihydrouridine synthase 1-like (S. cerevisiae)	145							flavin adenine dinucleotide binding (GO:0050660)|tRNA dihydrouridine synthase activity (GO:0017150)			breast(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	6	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;0.0211)			GGATTTTGCACGTGACAGGAA	0.612													c|||	638	0.127396	0.2617	0.1225	5008	,	,		18591	0.0377		0.0537	False		,,,				2504	0.1176				p.T145T		Atlas-SNP	.											DUS1L,colon,carcinoma,-1,1	DUS1L	25	1	0			c.G435A						PASS	.	C		959,3445	360.1+/-315.1	102,755,1345	63.0	61.0	62.0		435	-7.2	0.7	17	dbSNP_120	62	409,8191	128.0+/-186.3	9,391,3900	no	coding-synonymous	DUS1L	NM_022156.3		111,1146,5245	TT,TC,CC		4.7558,21.7757,10.5198		145/474	80020812	1368,11636	2202	4300	6502	SO:0001819	synonymous_variant	64118	exon5			TTTGCACGTGACA		CCDS32775.1	17q25.3	2005-08-09				ENSG00000169718			30086	protein-coding gene	gene with protein product						12477932	Standard	NM_022156		Approved	PP3111, DUS1	uc002kdr.4	Q6P1R4		ENST00000354321.7:c.435G>A	17.37:g.80020812C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_022156	A6NHV4|Q96AI3	Silent	SNP	ENST00000354321.7	37	CCDS32775.1																																																																																			C|0.901;T|0.099	0.099	strong		0.612	DUS1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442347.1	NM_022156	
FN3KRP	79672	hgsc.bcm.edu	37	17	80676896	80676896	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80676896C>T	ENST00000269373.6	+	2	329	c.256C>T	c.(256-258)Ctg>Ttg	p.L86L	RP11-388C12.1_ENST00000574471.1_lincRNA|FN3KRP_ENST00000535965.1_Silent_p.L36L	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	86							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			CGGGAGCGTGCTGGTGATGGA	0.547																																					p.L86L		Atlas-SNP	.											.	FN3KRP	31	.	0			c.C256T						PASS	.						105.0	103.0	104.0					17																	80676896		2203	4300	6503	SO:0001819	synonymous_variant	79672	exon2			AGCGTGCTGGTGA	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.256C>T	17.37:g.80676896C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	109	59	0.541284	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	37	CCDS11817.1																																																																																			.	.	none		0.547	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
MAML3	55534	hgsc.bcm.edu	37	4	140640527	140640527	+	Missense_Mutation	SNP	G	G	A	rs61743025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:140640527G>A	ENST00000509479.2	-	5	4223	c.3367C>T	c.(3367-3369)Cca>Tca	p.P1123S	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)					TCGTCCCCTGGCCCGCCTTTG	0.537													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18196	0.0		0.003	False		,,,				2504	0.0				p.P1119S		Atlas-SNP	.											.	MAML3	192	.	0			c.C3355T						PASS	.	G	,,SER/PRO	1,4041		0,1,2020	47.0	52.0	50.0		,,3367	5.0	0.8	4	dbSNP_129	50	25,8321		0,25,4148	yes	intron,intron,missense	MGST2,MAML3	NM_001204366.1,NM_001204367.1,NM_018717.4	,,74	0,26,6168	AA,AG,GG		0.2995,0.0247,0.2099	,,probably-damaging	,,1123/1139	140640527	26,12362	2021	4173	6194	SO:0001583	missense	55534	exon6			CCCCTGGCCCGCC	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.3367C>T	4.37:g.140640527G>A	ENSP00000421180:p.Pro1123Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	14.26	2.483745	0.44147	2.47E-4	0.002995	ENSG00000196782	ENST00000509479;ENST00000538400	T	0.24151	1.87	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000003	T	0.50565	0.1623	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.47849	-0.9085	10	0.10377	T	0.69	.	18.623	0.91327	0.0:0.0:1.0:0.0	.	1123;1119	E7EVW8;Q96JK9	.;MAML3_HUMAN	S	1123;430	ENSP00000421180:P1123S	ENSP00000421180:P1123S	P	-	1	0	MAML3	140859977	1.000000	0.71417	0.778000	0.31720	0.978000	0.69477	4.784000	0.62411	2.461000	0.83175	0.591000	0.81541	CCA	G|0.999;A|0.001	0.001	strong		0.537	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
RALGAPB	57148	hgsc.bcm.edu	37	20	37198582	37198582	+	Missense_Mutation	SNP	C	C	T	rs142678293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37198582C>T	ENST00000262879.6	+	27	4290	c.4006C>T	c.(4006-4008)Ccc>Tcc	p.P1336S	RALGAPB_ENST00000397042.3_Missense_Mutation_p.P1333S|RALGAPB_ENST00000397038.1_Missense_Mutation_p.P1115S|RALGAPB_ENST00000397040.1_Missense_Mutation_p.P1336S			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1336	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CCCTGTTCCTCCCCTTGGACC	0.453													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18979	0.0		0.004	False		,,,				2504	0.0				p.P1336S		Atlas-SNP	.											.	RALGAPB	134	.	0			c.C4006T						PASS	.	C	SER/PRO	5,4401	9.9+/-24.2	0,5,2198	102.0	87.0	92.0		4006	5.6	1.0	20	dbSNP_134	92	68,8532	41.2+/-98.3	1,66,4233	yes	missense	RALGAPB	NM_020336.2	74	1,71,6431	TT,TC,CC		0.7907,0.1135,0.5613	possibly-damaging	1336/1495	37198582	73,12933	2203	4300	6503	SO:0001583	missense	57148	exon27			GTTCCTCCCCTTG	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.4006C>T	20.37:g.37198582C>T	ENSP00000262879:p.Pro1336Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	138	66	0.478261	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	16.06	3.015096	0.54468	0.001135	0.007907	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000397038;ENST00000397040;ENST00000438490	D;D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25;-3.25	5.64	5.64	0.86602	Rap/ran-GAP (1);	0.052081	0.85682	D	0.000000	D	0.87904	0.6295	L	0.28400	0.85	0.80722	D	1	P;P	0.44139	0.827;0.827	B;B	0.44044	0.439;0.439	D	0.87073	0.2161	10	0.22109	T	0.4	.	19.7154	0.96115	0.0:1.0:0.0:0.0	.	1333;1336	A2A2E9;Q86X10	.;RLGPB_HUMAN	S	1336;1333;1115;1336;1165	ENSP00000262879:P1336S;ENSP00000380235:P1333S;ENSP00000380231:P1115S;ENSP00000380233:P1336S;ENSP00000416646:P1165S	ENSP00000262879:P1336S	P	+	1	0	RALGAPB	36631996	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.601000	0.82783	2.664000	0.90586	0.655000	0.94253	CCC	C|0.995;T|0.005	0.005	strong		0.453	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
COL6A5	256076	hgsc.bcm.edu	37	3	130125116	130125116	+	Missense_Mutation	SNP	G	G	C	rs1497312	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130125116G>C	ENST00000432398.2	+	17	4924	c.4430G>C	c.(4429-4431)tGt>tCt	p.C1477S	COL6A5_ENST00000265379.6_Missense_Mutation_p.C1477S	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1477	Triple-helical region.		C -> S (in dbSNP:rs1497312).		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						TTTTAGGGCTGTCATGGATTT	0.343													C|||	2264	0.452077	0.3389	0.4885	5008	,	,		19056	0.1855		0.7664	False		,,,				2504	0.5307				p.C1477S		Atlas-SNP	.											.	COL6A5	205	.	0			c.G4430C						PASS	.						143.0	105.0	117.0					3																	130125116		692	1591	2283	SO:0001583	missense	256076	exon17			AGGGCTGTCATGG	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.4430G>C	3.37:g.130125116G>C	ENSP00000390895:p.Cys1477Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		1083	0.4958791208791209	189	0.38414634146341464	198	0.5469613259668509	96	0.16783216783216784	600	0.7915567282321899	C	7.821	0.717721	0.15372	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.94046	-3.34;-3.34	5.56	0.227	0.15359	.	.	.	.	.	T	0.00012	0.0000	N	0.03917	-0.325	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40403	-0.9565	8	0.10111	T	0.7	.	0.9297	0.01332	0.2359:0.311:0.1289:0.3242	rs1497312;rs59992209;rs1497312	1477	A8TX70-2	.	S	1477	ENSP00000390895:C1477S;ENSP00000265379:C1477S	ENSP00000265379:C1477S	C	+	2	0	COL6A5	131607806	0.000000	0.05858	0.000000	0.03702	0.364000	0.29643	-0.617000	0.05584	-0.070000	0.12908	-1.104000	0.02111	TGT	G|0.545;C|0.455	0.455	strong		0.343	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
PFKM	5213	hgsc.bcm.edu	37	12	48526659	48526659	+	Silent	SNP	G	G	A	rs2228501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48526659G>A	ENST00000312352.7	+	5	285	c.246G>A	c.(244-246)acG>acA	p.T82T	PFKM_ENST00000395233.2_Silent_p.T82T|PFKM_ENST00000340802.6_Silent_p.T153T|PFKM_ENST00000359794.5_Silent_p.T82T|PFKM_ENST00000551804.1_Silent_p.T82T|PFKM_ENST00000547587.1_Silent_p.T82T	NM_001166687.1	NP_001160159.1	P08237	PFKAM_HUMAN	phosphofructokinase, muscle	82	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|muscle cell cellular homeostasis (GO:0046716)|positive regulation of insulin secretion (GO:0032024)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	6-phosphofructokinase complex (GO:0005945)|apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|fructose binding (GO:0070061)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			NS(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	35						AGGGAGGCACGGTGATTGGAA	0.537													G|||	136	0.0271565	0.0136	0.0346	5008	,	,		22079	0.0		0.0835	False		,,,				2504	0.0102				p.T153T		Atlas-SNP	.											.	PFKM	117	.	0			c.G459A						PASS	.	G	,,,	116,4290	87.3+/-125.9	0,116,2087	54.0	45.0	48.0		246,459,246,246	-9.1	0.3	12	dbSNP_98	48	725,7875	173.9+/-224.3	31,663,3606	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PFKM	NM_000289.5,NM_001166686.1,NM_001166687.1,NM_001166688.1	,,,	31,779,5693	AA,AG,GG		8.4302,2.6328,6.4662	,,,	82/781,153/852,82/781,82/781	48526659	841,12165	2203	4300	6503	SO:0001819	synonymous_variant	5213	exon7			AGGCACGGTGATT	M26066	CCDS8760.1, CCDS53786.1	12q13.11	2014-06-13					2.7.1.11		8877	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 122"""	610681	"""phosphofructokinase, polypeptide X"""	PFKX			Standard	NM_001166686		Approved	PFK-1, PPP1R122	uc001rrb.2	P08237		ENST00000312352.7:c.246G>A	12.37:g.48526659G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001166686	J3KNX3|Q16814|Q16815|Q6ZTT1	Silent	SNP	ENST00000312352.7	37	CCDS8760.1																																																																																			G|0.947;A|0.053	0.053	strong		0.537	PFKM-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406490.1	NM_000289	
CD5	921	hgsc.bcm.edu	37	11	60893235	60893235	+	Missense_Mutation	SNP	C	C	T	rs2229177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60893235C>T	ENST00000347785.3	+	10	1578	c.1412C>T	c.(1411-1413)gCt>gTt	p.A471V		NM_014207.3	NP_055022.2	P06127	CD5_HUMAN	CD5 molecule	471			A -> V (in dbSNP:rs2229177). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3093892, ECO:0000269|PubMed:8740779, ECO:0000269|Ref.3}.		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)		CTGGAAGGGGCTCTGCATCGC	0.582													C|||	3461	0.691094	0.5083	0.6628	5008	,	,		17773	0.9881		0.5517	False		,,,				2504	0.7955				p.A471V		Atlas-SNP	.											CD5,colon,carcinoma,0,1	CD5	52	1	0			c.C1412T						PASS	.	C	VAL/ALA	2337,2069	606.6+/-390.8	618,1101,484	90.0	97.0	94.0		1412	5.0	1.0	11	dbSNP_98	94	4328,4270	578.3+/-390.7	1087,2154,1058	yes	missense	CD5	NM_014207.3	64	1705,3255,1542	TT,TC,CC		49.6627,46.9587,48.7465	probably-damaging	471/496	60893235	6665,6339	2203	4299	6502	SO:0001583	missense	921	exon10			AAGGGGCTCTGCA	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.1412C>T	11.37:g.60893235C>T	ENSP00000342681:p.Ala471Val	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_014207	A0N0P4|A8K9I3	Missense_Mutation	SNP	ENST00000347785.3	37	CCDS8000.1	1457	0.6671245421245421	250	0.508130081300813	234	0.6464088397790055	565	0.9877622377622378	408	0.5382585751978892	C	21.3	4.129368	0.77549	0.530413	0.503373	ENSG00000110448	ENST00000347785	T	0.31510	1.49	5.01	5.01	0.66863	.	0.000000	0.52532	D	0.000080	T	0.00012	0.0000	L	0.34521	1.04	0.25198	P	0.9900787	D	0.89917	1.0	D	0.67548	0.952	T	0.13710	-1.0499	9	0.72032	D	0.01	-29.4228	16.4824	0.84161	0.0:1.0:0.0:0.0	rs2229177;rs13328900;rs17630076;rs17852465;rs52809925;rs58650951;rs2229177	471	P06127	CD5_HUMAN	V	471	ENSP00000342681:A471V	ENSP00000342681:A471V	A	+	2	0	CD5	60649811	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	4.534000	0.60622	2.313000	0.78055	0.462000	0.41574	GCT	C|0.419;T|0.581	0.581	strong		0.582	CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396465.2	NM_014207	
CSRP2BP	57325	hgsc.bcm.edu	37	20	18142564	18142564	+	Silent	SNP	A	A	G	rs3828013	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:18142564A>G	ENST00000435364.3	+	5	1124	c.783A>G	c.(781-783)aaA>aaG	p.K261K	CSRP2BP_ENST00000377681.3_Silent_p.K260K|CSRP2BP_ENST00000489634.2_Silent_p.K133K	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	261					chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)	p.K261K(2)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						TAAAAGAGAAAAGGTCTCGAA	0.443													A|||	590	0.117812	0.0446	0.1455	5008	,	,		18468	0.1349		0.1302	False		,,,				2504	0.1667				p.K261K		Atlas-SNP	.											CSRP2BP,NS,carcinoma,0,2	CSRP2BP	80	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.A783G						PASS	.	A		317,4089	160.3+/-192.7	17,283,1903	119.0	138.0	132.0		783	-1.0	0.9	20	dbSNP_107	132	1067,7533	219.9+/-257.8	71,925,3304	no	coding-synonymous	CSRP2BP	NM_020536.4		88,1208,5207	GG,GA,AA		12.407,7.1947,10.6412		261/783	18142564	1384,11622	2203	4300	6503	SO:0001819	synonymous_variant	57325	exon5			AGAGAAAAGGTCT	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"""cysteine rich protein 2 binding protein"", ""ATAC component 2 homolog (Drosophila)"""					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.783A>G	20.37:g.18142564A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	69	0.971831	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Silent	SNP	ENST00000435364.3	37	CCDS13133.1																																																																																			A|0.896;G|0.104	0.104	strong		0.443	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28305212	28305212	+	Missense_Mutation	SNP	C	C	T	rs2830585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:28305212C>T	ENST00000284987.5	-	5	1962	c.1841G>A	c.(1840-1842)cGc>cAc	p.R614H	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	614	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.		R -> H (in dbSNP:rs2830585). {ECO:0000269|PubMed:10464288}.		defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						ACTGCAGGAGCGGTAGATGGC	0.512													C|||	495	0.0988419	0.0484	0.1138	5008	,	,		18116	0.0992		0.1799	False		,,,				2504	0.0726				p.R614H	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											ADAMTS5,colon,carcinoma,-1,6	ADAMTS5	184	6	0			c.G1841A						PASS	.	C	HIS/ARG	319,4087	171.6+/-201.8	10,299,1894	153.0	105.0	121.0		1841	6.0	1.0	21	dbSNP_100	121	1372,7228	266.9+/-287.0	123,1126,3051	yes	missense	ADAMTS5	NM_007038.3	29	133,1425,4945	TT,TC,CC		15.9535,7.2401,13.0017	probably-damaging	614/931	28305212	1691,11315	2203	4300	6503	SO:0001583	missense	11096	exon5			CAGGAGCGGTAGA	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1841G>A	21.37:g.28305212C>T	ENSP00000284987:p.Arg614His	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	267	0.12225274725274725	25	0.0508130081300813	41	0.1132596685082873	65	0.11363636363636363	136	0.17941952506596306	C	35	5.473629	0.96291	0.072401	0.159535	ENSG00000154736	ENST00000284987	T	0.55930	0.49	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.00496	0.0016	M	0.87269	2.87	0.09310	P	0.9999999848425	D	0.89917	1.0	D	0.91635	0.999	T	0.09443	-1.0674	9	0.87932	D	0	.	20.5666	0.99351	0.0:1.0:0.0:0.0	rs2830585;rs17595455;rs59709407;rs2830585	614	Q9UNA0	ATS5_HUMAN	H	614	ENSP00000284987:R614H	ENSP00000284987:R614H	R	-	2	0	ADAMTS5	27227083	1.000000	0.71417	0.998000	0.56505	0.835000	0.47333	7.487000	0.81328	2.854000	0.98071	0.655000	0.94253	CGC	C|0.872;T|0.128	0.128	strong		0.512	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
VCPKMT	79609	hgsc.bcm.edu	37	14	50583083	50583083	+	Missense_Mutation	SNP	G	G	T	rs11157729	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:50583083G>T	ENST00000395860.2	-	1	192	c.188C>A	c.(187-189)gCc>gAc	p.A63D	VCPKMT_ENST00000395859.2_Missense_Mutation_p.A63D	NM_024558.2	NP_078834.2	Q9H867	MT21D_HUMAN	valosin containing protein lysine (K) methyltransferase	63			A -> D (in dbSNP:rs11157729).		peptidyl-lysine trimethylation (GO:0018023)	cytoplasm (GO:0005737)	protein-lysine N-methyltransferase activity (GO:0016279)										CAGCGCGTGGGCCCCGTCGCC	0.667													G|||	1252	0.25	0.2216	0.245	5008	,	,		12014	0.4603		0.1461	False		,,,				2504	0.182				p.A63D		Atlas-SNP	.											.	METTL21D	11	.	0			c.C188A						PASS	.	G	ASP/ALA,ASP/ALA	876,3530	312.2+/-292.5	86,704,1413	22.0	27.0	25.0		188,188	4.2	0.4	14	dbSNP_120	25	1343,7257	252.3+/-278.5	107,1129,3064	yes	missense,missense	METTL21D	NM_001040662.1,NM_024558.2	126,126	193,1833,4477	TT,TG,GG		15.6163,19.882,17.0614	benign,benign	63/195,63/230	50583083	2219,10787	2203	4300	6503	SO:0001583	missense	79609	exon1			GCGTGGGCCCCGT	AK023982	CCDS9696.2, CCDS41951.1	14q21.3	2013-09-30	2013-09-30	2013-09-30	ENSG00000100483	ENSG00000100483			20352	protein-coding gene	gene with protein product		615260	"""chromosome 14 open reading frame 138"", ""methyltransferase like 21D"""	C14orf138, METTL21D		22948820	Standard	NR_049738		Approved	VCP-KMT	uc001wxo.1	Q9H867	OTTHUMG00000029531	ENST00000395860.2:c.188C>A	14.37:g.50583083G>T	ENSP00000379201:p.Ala63Asp	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_024558	B7ZLA3|B7ZLA4|Q2M2X3|Q86T12	Missense_Mutation	SNP	ENST00000395860.2	37	CCDS9696.2	527	0.2413003663003663	93	0.18902439024390244	72	0.19889502762430938	252	0.4405594405594406	110	0.14511873350923482	G	13.02	2.111626	0.37242	0.19882	0.156163	ENSG00000100483	ENST00000395859;ENST00000395860	T;T	0.06933	3.24;3.24	6.06	4.2	0.49525	.	0.741259	0.12068	N	0.502470	T	0.00012	0.0000	L	0.35288	1.05	0.80722	P	0.0	B;B	0.21381	0.055;0.055	B;B	0.21546	0.023;0.035	T	0.42582	-0.9443	9	0.15499	T	0.54	0.0014	6.6147	0.22771	0.0678:0.1304:0.6662:0.1355	rs11157729;rs57168136	63;63	B7ZLA4;Q9H867	.;MT21D_HUMAN	D	63	ENSP00000379200:A63D;ENSP00000379201:A63D	ENSP00000379200:A63D	A	-	2	0	METTL21D	49652833	0.008000	0.16893	0.394000	0.26270	0.985000	0.73830	0.585000	0.23879	0.849000	0.35215	0.650000	0.86243	GCC	G|0.812;T|0.188	0.188	strong		0.667	VCPKMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276877.1	NM_024558	
SMCR8	140775	hgsc.bcm.edu	37	17	18219835	18219835	+	Silent	SNP	T	T	C	rs3829956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18219835T>C	ENST00000406438.3	+	1	1212	c.732T>C	c.(730-732)atT>atC	p.I244I	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	244						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						AGTCCATCATTGAACATCAAG	0.488													T|||	1076	0.214856	0.1452	0.2421	5008	,	,		22242	0.3185		0.2435	False		,,,				2504	0.1534				p.I244I		Atlas-SNP	.											.	SMCR8	62	.	0			c.T732C						PASS	.	T		684,3722	288.4+/-279.8	65,554,1584	69.0	56.0	60.0		732	-0.1	1.0	17	dbSNP_107	60	2196,6404	371.9+/-336.4	284,1628,2388	no	coding-synonymous	SMCR8	NM_144775.2		349,2182,3972	CC,CT,TT		25.5349,15.5243,22.1436		244/938	18219835	2880,10126	2203	4300	6503	SO:0001819	synonymous_variant	140775	exon1			CATCATTGAACAT	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.732T>C	17.37:g.18219835T>C		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Silent	SNP	ENST00000406438.3	37	CCDS11195.2																																																																																			T|0.772;C|0.228	0.228	strong		0.488	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
TRIOBP	11078	hgsc.bcm.edu	37	22	38122448	38122448	+	Silent	SNP	C	C	T	rs739137	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38122448C>T	ENST00000406386.3	+	7	4140	c.3885C>T	c.(3883-3885)agC>agT	p.S1295S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1295					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)					AGTGCAGCAGCGGGGGCCGCA	0.726													C|||	1686	0.336661	0.1543	0.2867	5008	,	,		13163	0.5863		0.3877	False		,,,				2504	0.3088				p.S1295S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C3885T						PASS	.	C		648,3004		99,450,1277	5.0	7.0	6.0		3885	3.6	1.0	22	dbSNP_86	6	3246,4490		767,1712,1389	no	coding-synonymous	TRIOBP	NM_001039141.2		866,2162,2666	TT,TC,CC		41.9597,17.7437,34.1939		1295/2366	38122448	3894,7494	1826	3868	5694	SO:0001819	synonymous_variant	11078	exon7			CAGCAGCGGGGGC	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.3885C>T	22.37:g.38122448C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.621;T|0.379	0.379	strong		0.726	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
TAF1C	9013	hgsc.bcm.edu	37	16	84218565	84218565	+	Silent	SNP	T	T	C	rs2230126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84218565T>C	ENST00000567759.1	-	2	212	c.30A>G	c.(28-30)gcA>gcG	p.A10A	TAF1C_ENST00000341690.6_Intron|TAF1C_ENST00000566732.1_Silent_p.A10A|TAF1C_ENST00000378541.4_Silent_p.A10A|TAF1C_ENST00000541676.1_Intron|TAF1C_ENST00000565544.1_5'Flank|TAF1C_ENST00000570117.1_Intron	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	10					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						TCAGAAACAATGCAGGGCGGA	0.617													C|||	990	0.197684	0.2421	0.0749	5008	,	,		19474	0.2639		0.1521	False		,,,				2504	0.2035				p.A10A		Atlas-SNP	.											.	TAF1C	60	.	0			c.A30G						PASS	.	C	,	973,3427	721.9+/-409.2	111,751,1338	41.0	35.0	37.0		30,	-8.0	0.0	16	dbSNP_98	37	1252,7346	754.5+/-407.5	82,1088,3129	no	coding-synonymous,intron	TAF1C	NM_005679.3,NM_139353.2	,	193,1839,4467	CC,CT,TT		14.5615,22.1136,17.118	,	10/870,	84218565	2225,10773	2200	4299	6499	SO:0001819	synonymous_variant	9013	exon2			AAACAATGCAGGG	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.30A>G	16.37:g.84218565T>C		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_001243156	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			T|0.829;C|0.171	0.171	strong		0.617	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
PRPF19	27339	hgsc.bcm.edu	37	11	60666341	60666341	+	Silent	SNP	G	G	A	rs3763840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60666341G>A	ENST00000227524.4	-	12	1252	c.1047C>T	c.(1045-1047)tcC>tcT	p.S349S		NM_014502.4	NP_055317.1			pre-mRNA processing factor 19											haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	22						TACAGCAGCCGGAGGTCTCAT	0.393											OREG0020994	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	1545	0.308506	0.1422	0.3905	5008	,	,		19784	0.3194		0.3887	False		,,,				2504	0.3814				p.S349S		Atlas-SNP	.											.	PRPF19	62	.	0			c.C1047T						PASS	.	A		808,3598		68,672,1463	21.0	19.0	20.0		1047	-9.2	0.8	11	dbSNP_107	20	3438,5160		693,2052,1554	no	coding-synonymous	PRPF19	NM_014502.4		761,2724,3017	AA,AG,GG		39.986,18.3386,32.6515		349/505	60666341	4246,8758	2203	4299	6502	SO:0001819	synonymous_variant	27339	exon12			GCAGCCGGAGGTC	BC018698	CCDS7995.1	11q12.2	2014-05-20	2013-06-10	2005-04-01	ENSG00000110107	ENSG00000110107		"""WD repeat domain containing"", ""U-box domain containing"""	17896	protein-coding gene	gene with protein product	"""nuclear matrix protein NMP200 related to splicing factor PRP19"", ""psoralen 4"""	608330	"""PRP19/PSO4 homolog (S. cerevisiae)"", ""PRP19/PSO4 pre-mRNA processing factor 19 homolog (S. cerevisiae)"""	PRP19		12960389	Standard	NM_014502		Approved	UBOX4, NMP200, PSO4, hPSO4	uc001nqf.3	Q9UMS4	OTTHUMG00000167798	ENST00000227524.4:c.1047C>T	11.37:g.60666341G>A		Somatic	176	0	0	1047	WXS	Illumina HiSeq	Phase_I	220	215	0.977273	NM_014502		Silent	SNP	ENST00000227524.4	37	CCDS7995.1																																																																																			G|0.691;A|0.309	0.309	strong		0.393	PRPF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396334.1	NM_014502	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42373810	42373810	+	Missense_Mutation	SNP	G	G	C	rs11635685	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:42373810G>C	ENST00000290472.3	-	11	918	c.824C>G	c.(823-825)cCt>cGt	p.P275R		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	275	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		P -> R (in dbSNP:rs11635685).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		CAGCTCCTCAGGGCTGTGGCA	0.632													G|||	1486	0.296725	0.1316	0.4712	5008	,	,		19169	0.4127		0.3419	False		,,,				2504	0.2301				p.P275R		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.C824G						PASS	.	G	ARG/PRO	774,3632	309.7+/-291.2	65,644,1494	54.0	57.0	56.0		824	3.7	0.6	15	dbSNP_120	56	2981,5617	454.3+/-363.5	520,1941,1838	yes	missense	PLA2G4D	NM_178034.3	103	585,2585,3332	CC,CG,GG		34.6709,17.567,28.8757	benign	275/819	42373810	3755,9249	2203	4299	6502	SO:0001583	missense	283748	exon11			TCCTCAGGGCTGT	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.824C>G	15.37:g.42373810G>C	ENSP00000290472:p.Pro275Arg	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	712	0.326007326007326	54	0.10975609756097561	159	0.43922651933701656	231	0.40384615384615385	268	0.35356200527704484	G	10.80	1.451887	0.26074	0.17567	0.346709	ENSG00000159337	ENST00000290472	T	0.01265	5.08	4.58	3.65	0.41850	Lysophospholipase, catalytic domain (2);	0.408988	0.23157	N	0.051293	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	1.0	B	0.18166	0.026	B	0.17433	0.018	T	0.39272	-0.9622	9	0.54805	T	0.06	-4.4823	9.2915	0.37789	0.0:0.1573:0.68:0.1627	rs11635685;rs11635685	275	Q86XP0	PA24D_HUMAN	R	275	ENSP00000290472:P275R	ENSP00000290472:P275R	P	-	2	0	PLA2G4D	40161102	0.961000	0.32948	0.649000	0.29536	0.003000	0.03518	2.683000	0.46943	1.035000	0.39972	0.650000	0.86243	CCT	G|0.713;C|0.287	0.287	strong		0.632	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
OTUD5	55593	hgsc.bcm.edu	37	X	48783183	48783183	+	Silent	SNP	G	G	C	rs141488277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:48783183G>C	ENST00000156084.4	-	6	1278	c.1218C>G	c.(1216-1218)tcC>tcG	p.S406S	OTUD5_ENST00000484499.1_5'Flank|OTUD5_ENST00000396743.3_Silent_p.S401S|OTUD5_ENST00000428668.2_Silent_p.S184S|OTUD5_ENST00000376488.3_Silent_p.S401S	NM_017602.3	NP_060072.1	Q96G74	OTUD5_HUMAN	OTU deubiquitinase 5	406					innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)	ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(3)|lung(6)|pancreas(2)	13						ACTGCAGGTAGGATTCCCGAG	0.572													G|||	5	0.0013245	0.0	0.0014	3775	,	,		13554	0.0		0.001	False		,,,				2504	0.0031				p.S406S		Atlas-SNP	.											.	OTUD5	66	.	0			c.C1218G						PASS	.	G	,,,	0,3835		0,0,0,1632,571	102.0	75.0	85.0		1203,1203,552,1218	2.4	1.0	X	dbSNP_134	85	31,6697		0,22,9,2406,1863	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTUD5	NM_001136157.1,NM_001136158.1,NM_001136159.1,NM_017602.3	,,,	0,22,9,4038,2434	CC,CG,C,GG,G		0.4608,0.0,0.2935	,,,	401/567,401/567,184/350,406/572	48783183	31,10532	2203	4300	6503	SO:0001819	synonymous_variant	55593	exon6			CAGGTAGGATTCC		CCDS14313.1, CCDS48104.1, CCDS48105.1	Xp11.23	2014-06-09	2014-02-24		ENSG00000068308	ENSG00000068308		"""OTU domain containing"""	25402	protein-coding gene	gene with protein product		300713	"""OTU domain containing 5"""			24143256	Standard	NM_001136157		Approved	DKFZp761A052, DUBA	uc004dlu.3	Q96G74	OTTHUMG00000024130	ENST00000156084.4:c.1218C>G	X.37:g.48783183G>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	30	30	1	NM_017602	B4DGG7|G5E9D7|Q4KMN9|Q8N6T5|Q9H650|Q9H9U0|Q9NT65	Silent	SNP	ENST00000156084.4	37	CCDS14313.1																																																																																			G|0.998;C|0.002	0.002	strong		0.572	OTUD5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000060799.1	NM_017602	
TEF	7008	hgsc.bcm.edu	37	22	41790179	41790179	+	Silent	SNP	G	G	A	rs17365991	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:41790179G>A	ENST00000266304.4	+	3	671	c.555G>A	c.(553-555)ccG>ccA	p.P185P	TEF_ENST00000406644.3_Silent_p.P155P	NM_003216.3	NP_003207.1	Q10587	TEF_HUMAN	thyrotrophic embryonic factor	185	Pro-rich (proline/acidic region (PAR)).				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						ACTTCAATCCGGACCCCGCCG	0.567													G|||	90	0.0179712	0.003	0.0288	5008	,	,		16633	0.003		0.0507	False		,,,				2504	0.0123				p.P185P		Atlas-SNP	.											.	TEF	21	.	0			c.G555A						PASS	.	G	,	44,4362	46.7+/-81.2	0,44,2159	86.0	89.0	88.0		465,555	-6.4	0.9	22	dbSNP_123	88	447,8153	135.1+/-192.4	8,431,3861	no	coding-synonymous,coding-synonymous	TEF	NM_001145398.1,NM_003216.2	,	8,475,6020	AA,AG,GG		5.1977,0.9986,3.7752	,	155/274,185/304	41790179	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	7008	exon3			CAATCCGGACCCC		CCDS14014.1, CCDS46716.1	22q13.2	2013-01-10			ENSG00000167074	ENSG00000167074		"""basic leucine zipper proteins"""	11722	protein-coding gene	gene with protein product		188595				7835883, 15665112	Standard	NM_001145398		Approved	KIAA1655	uc003azy.4	Q10587	OTTHUMG00000150968	ENST00000266304.4:c.555G>A	22.37:g.41790179G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	71	23	0.323944	NM_003216	B0QYS8|B2RC22|Q15729|Q7Z3J7|Q8IU94|Q96TG4	Silent	SNP	ENST00000266304.4	37	CCDS14014.1	57	0.0260989010989011	2	0.0040650406504065045	10	0.027624309392265192	3	0.005244755244755245	42	0.055408970976253295	G	9.184	1.024330	0.19433	0.009986	0.051977	ENSG00000167074	ENST00000413942	.	.	.	5.78	-6.36	0.01969	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31861	-0.9928	4	.	.	.	-14.0578	1.4557	0.02384	0.2829:0.3399:0.1884:0.1888	rs17365991;rs59727856;rs17365991	.	.	.	Q	151	.	.	R	+	2	0	TEF	40120125	0.000000	0.05858	0.903000	0.35520	0.978000	0.69477	-2.554000	0.00926	-1.214000	0.02614	-1.259000	0.01468	CGG	G|0.970;A|0.030	0.030	strong		0.567	TEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320692.1	NM_003216	
RREB1	6239	hgsc.bcm.edu	37	6	7247344	7247344	+	Missense_Mutation	SNP	C	C	A	rs35742417	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:7247344C>A	ENST00000349384.6	+	11	4810	c.4496C>A	c.(4495-4497)tCc>tAc	p.S1499Y	RREB1_ENST00000379938.2_Missense_Mutation_p.S1554Y|RREB1_ENST00000334984.6_Intron|RREB1_ENST00000379933.3_Missense_Mutation_p.S1499Y	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1499			S -> Y (in dbSNP:rs35742417).		multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S1499Y(1)		breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				AAGACAGACTCCCCCAAAAGC	0.617													C|||	638	0.127396	0.239	0.0908	5008	,	,		17771	0.0357		0.161	False		,,,				2504	0.0624				p.S1554Y		Atlas-SNP	.											RREB1,NS,carcinoma,0,1	RREB1	242	1	1	Substitution - Missense(1)	stomach(1)	c.C4661A						PASS	.	C	TYR/SER,TYR/SER,,TYR/SER	897,3509	329.3+/-301.0	101,695,1407	74.0	71.0	72.0		4496,4661,,4496	3.4	1.0	6	dbSNP_126	72	1381,7219	251.8+/-278.1	104,1173,3023	yes	missense,missense,intron,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	144,144,,144	205,1868,4430	AA,AC,CC		16.0581,20.3586,17.515	benign,benign,,benign	1499/1688,1554/1743,,1499/1688	7247344	2278,10728	2203	4300	6503	SO:0001583	missense	6239	exon12			CAGACTCCCCCAA	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4496C>A	6.37:g.7247344C>A	ENSP00000305560:p.Ser1499Tyr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	130	58	0.446154	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	297	0.13598901098901098	105	0.21341463414634146	35	0.09668508287292818	25	0.043706293706293704	132	0.1741424802110818	C	11.75	1.731099	0.30684	0.203586	0.160581	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384	T;T;T	0.08193	3.12;3.12;3.12	5.24	3.42	0.39159	.	0.762218	0.11459	N	0.561966	T	0.02727	0.0082	L	0.40543	1.245	0.44798	P	0.0021999999999999797	B;P	0.36315	0.07;0.547	B;B	0.37888	0.123;0.26	T	0.44528	-0.9322	9	0.41790	T	0.15	-28.114	4.3196	0.11011	0.1154:0.4061:0.3851:0.0934	rs35742417;rs61234629	1499;1554	Q92766;Q92766-2	RREB1_HUMAN;.	Y	1499;1554;1499	ENSP00000369265:S1499Y;ENSP00000369270:S1554Y;ENSP00000305560:S1499Y	ENSP00000305560:S1499Y	S	+	2	0	RREB1	7192343	0.999000	0.42202	0.963000	0.40424	0.943000	0.58893	2.107000	0.41844	1.215000	0.43411	-0.254000	0.11334	TCC	C|0.843;A|0.157	0.157	strong		0.617	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
B4GALT4	8702	hgsc.bcm.edu	37	3	118948716	118948716	+	Silent	SNP	G	G	A	rs4422294	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:118948716G>A	ENST00000483209.1	-	3	872	c.231C>T	c.(229-231)tgC>tgT	p.C77C	B4GALT4_ENST00000467604.1_Silent_p.C77C|B4GALT4_ENST00000460321.1_Intron|B4GALT4_ENST00000359213.3_Silent_p.C77C|B4GALT4_ENST00000393765.2_Silent_p.C77C|B4GALT4_ENST00000471675.1_Silent_p.C30C|B4GALT4-AS1_ENST00000470790.1_RNA			O60513	B4GT4_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 4	77					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)|membrane lipid metabolic process (GO:0006643)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.C77C(1)		breast(2)|endometrium(1)|large_intestine(1)|lung(6)|skin(2)|stomach(2)	14				GBM - Glioblastoma multiforme(114;0.222)	N-Acetyl-D-glucosamine(DB00141)	ACACAGAAGGGCAGTTGTCAA	0.373													G|||	968	0.193291	0.0378	0.3084	5008	,	,		20926	0.246		0.3022	False		,,,				2504	0.1554				p.C77C		Atlas-SNP	.											B4GALT4,NS,carcinoma,0,1	B4GALT4	30	1	1	Substitution - coding silent(1)	stomach(1)	c.C231T						PASS	.	G	,	342,4064	177.6+/-206.5	17,308,1878	138.0	128.0	132.0		231,231	-2.9	0.8	3	dbSNP_111	132	2540,6060	414.1+/-351.3	372,1796,2132	no	coding-synonymous,coding-synonymous	B4GALT4	NM_003778.3,NM_212543.1	,	389,2104,4010	AA,AG,GG		29.5349,7.7621,22.159	,	77/345,77/345	118948716	2882,10124	2203	4300	6503	SO:0001819	synonymous_variant	8702	exon4			AGAAGGGCAGTTG	AF022367	CCDS2986.1	3q13.3	2013-02-19			ENSG00000121578	ENSG00000121578		"""Beta 4-glycosyltransferases"""	927	protein-coding gene	gene with protein product		604015				9597550	Standard	NM_003778		Approved	beta4Gal-T4	uc003eci.3	O60513	OTTHUMG00000159358	ENST00000483209.1:c.231C>T	3.37:g.118948716G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	123	48	0.390244	NM_212543	Q68D68|Q9BSW3|Q9C078	Silent	SNP	ENST00000483209.1	37	CCDS2986.1																																																																																			G|0.776;A|0.224	0.224	strong		0.373	B4GALT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354925.2	NM_003778	
CAPN13	92291	hgsc.bcm.edu	37	2	30980940	30980940	+	Missense_Mutation	SNP	C	C	T	rs508405	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:30980940C>T	ENST00000295055.8	-	8	1014	c.838G>A	c.(838-840)Gcc>Acc	p.A280T	CAPN13_ENST00000465960.2_5'UTR|CAPN13_ENST00000534090.2_Missense_Mutation_p.A280T	NM_144575.2	NP_653176.2	Q6MZZ7	CAN13_HUMAN	calpain 13	280	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		A -> T (in dbSNP:rs508405). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	30	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.155)					CTCCATTCGGCCTCGCCCCAG	0.542													T|||	3957	0.790136	0.9622	0.7464	5008	,	,		17705	0.7619		0.6889	False		,,,				2504	0.7219				p.A280T		Atlas-SNP	.											.	CAPN13	70	.	0			c.G838A	GRCh37	CM065993	CAPN13	M	rs508405	PASS	.	T	THR/ALA	3480,344		1583,314,15	37.0	45.0	43.0		838	-5.9	0.0	2	dbSNP_83	43	5641,2607		1923,1795,406	yes	missense	CAPN13	NM_144575.2	58	3506,2109,421	TT,TC,CC		31.6077,8.9958,24.445	benign	280/670	30980940	9121,2951	1912	4124	6036	SO:0001583	missense	92291	exon8			ATTCGGCCTCGCC		CCDS46252.1	2p22-p21	2008-02-05			ENSG00000162949	ENSG00000162949			16663	protein-coding gene	gene with protein product		610228				11675017	Standard	NM_144575		Approved	FLJ23523	uc021vfm.1	Q6MZZ7	OTTHUMG00000152053	ENST00000295055.8:c.838G>A	2.37:g.30980940C>T	ENSP00000295055:p.Ala280Thr	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_144575	Q17RF0|Q580X1|Q8TE80	Missense_Mutation	SNP	ENST00000295055.8	37	CCDS46252.1	1677	0.7678571428571429	466	0.9471544715447154	265	0.7320441988950276	421	0.736013986013986	525	0.6926121372031663	T	0.011	-1.692667	0.00731	0.910042	0.683923	ENSG00000162949	ENST00000295055;ENST00000534090	D;D	0.87650	-2.28;-2.28	4.86	-5.94	0.02247	Peptidase C2, calpain, catalytic domain (3);	0.662303	0.15778	N	0.245066	T	0.00012	0.0000	N	0.01618	-0.8	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39396	-0.9616	9	0.22706	T	0.39	.	3.2965	0.06968	0.1219:0.4165:0.2478:0.2138	rs508405;rs17396453;rs58723439;rs508405	280	Q6MZZ7	CAN13_HUMAN	T	280	ENSP00000295055:A280T;ENSP00000431298:A280T	ENSP00000295055:A280T	A	-	1	0	CAPN13	30834444	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.356000	0.07661	-0.687000	0.05162	-1.327000	0.01280	GCC	C|0.223;T|0.777	0.777	strong		0.542	CAPN13-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325101.2	NM_144575	
IL37	27178	hgsc.bcm.edu	37	2	113674721	113674721	+	Missense_Mutation	SNP	A	A	G	rs2723183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113674721A>G	ENST00000263326.3	+	3	203	c.161A>G	c.(160-162)aAc>aGc	p.N54S	IL37_ENST00000353225.3_Intron|IL37_ENST00000352179.3_Missense_Mutation_p.N33S|IL37_ENST00000311328.2_Missense_Mutation_p.N28S|IL37_ENST00000349806.3_Intron	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	54			N -> S (in dbSNP:rs2723183).		immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						AAGGTGAAGAACTTAAACCCG	0.453													a|||	381	0.0760783	0.174	0.0591	5008	,	,		23132	0.001		0.0805	False		,,,				2504	0.0286				p.N54S		Atlas-SNP	.											.	IL37	56	.	0			c.A161G						PASS	.		SER/ASN,SER/ASN,,,SER/ASN	730,3676	303.5+/-288.0	53,624,1526	97.0	92.0	93.0		161,98,,,83	-4.9	0.0	2	dbSNP_100	93	690,7910	171.4+/-222.4	37,616,3647	yes	missense,missense,intron,intron,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1,NM_173205.1	46,46,,,46	90,1240,5173	GG,GA,AA		8.0233,16.5683,10.918	benign,benign,,,benign	54/219,33/198,,,28/193	113674721	1420,11586	2203	4300	6503	SO:0001583	missense	27178	exon3			TGAAGAACTTAAA	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.161A>G	2.37:g.113674721A>G	ENSP00000263326:p.Asn54Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	164	0.07509157509157509	81	0.16463414634146342	26	0.0718232044198895	1	0.0017482517482517483	56	0.07387862796833773	a	0.011	-1.694978	0.00731	0.165683	0.080233	ENSG00000125571	ENST00000263326;ENST00000352179;ENST00000311328	T;T;T	0.55413	0.52;0.52;0.52	2.83	-4.93	0.03066	.	3.743050	0.00861	N	0.001925	T	0.00073	0.0002	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.12630	0.006;0.002;0.003	B;B;B	0.11329	0.006;0.006;0.002	T	0.06427	-1.0827	9	0.08837	T	0.75	3.5312	0.7615	0.01008	0.1566:0.2185:0.2869:0.338	rs2723183;rs59283496;rs2723183	28;33;54	Q9NZH6-2;Q9NZH6-4;Q9NZH6	.;.;IL37_HUMAN	S	54;33;28	ENSP00000263326:N54S;ENSP00000263327:N33S;ENSP00000309883:N28S	ENSP00000263326:N54S	N	+	2	0	IL37	113391192	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.677000	0.00839	-1.324000	0.02272	-1.080000	0.02220	AAC	A|0.903;G|0.097	0.097	strong		0.453	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255242	25255242	+	Missense_Mutation	SNP	T	T	A	rs8059494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:25255242T>A	ENST00000328086.7	-	6	2648	c.1845A>T	c.(1843-1845)gaA>gaT	p.E615D		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	615			E -> D (in dbSNP:rs8059494). {ECO:0000269|PubMed:15489334}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	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)		AGCCTGTAGGTTCCTGGGGTT	0.527													T|||	387	0.0772764	0.0166	0.1095	5008	,	,		19226	0.1419		0.1014	False		,,,				2504	0.045				p.E615D		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.A1845T						PASS	.	T	ASP/GLU	162,4232	107.8+/-146.2	2,158,2037	146.0	133.0	137.0		1845	-0.7	0.2	16	dbSNP_116	137	1098,7502	229.1+/-263.9	58,982,3260	yes	missense	ZKSCAN2	NM_001012981.4	45	60,1140,5297	AA,AT,TT		12.7674,3.6868,9.6968	probably-damaging	615/968	25255242	1260,11734	2197	4300	6497	SO:0001583	missense	342357	exon6			TGTAGGTTCCTGG	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.1845A>T	16.37:g.25255242T>A	ENSP00000331626:p.Glu615Asp	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	212	99	0.466981	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	203	0.09294871794871795	4	0.008130081300813009	46	0.1270718232044199	76	0.13286713286713286	77	0.10158311345646438	T	14.87	2.665893	0.47677	0.036868	0.127674	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.08370	3.1	5.69	-0.66	0.11421	.	0.182168	0.39083	N	0.001480	T	0.00073	0.0002	L	0.54323	1.7	0.43489	P	0.004278000000000004	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.29274	-1.0017	9	0.51188	T	0.08	-7.6498	0.9316	0.01336	0.1508:0.2588:0.1563:0.4342	rs8059494;rs8059494	411;615	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	D	615	ENSP00000331626:E615D	ENSP00000331626:E615D	E	-	3	2	ZKSCAN2	25162743	0.251000	0.23961	0.224000	0.23877	0.942000	0.58702	-0.161000	0.10026	-0.093000	0.12396	0.533000	0.62120	GAA	T|0.895;A|0.105	0.105	strong		0.527	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
CFAP44	55779	hgsc.bcm.edu	37	3	113146130	113146130	+	Missense_Mutation	SNP	T	T	C	rs386664769|rs59722850	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113146130T>C	ENST00000295868.2	-	3	319	c.157A>G	c.(157-159)Aaa>Gaa	p.K53E	WDR52-AS1_ENST00000473329.1_RNA|WDR52-AS1_ENST00000498480.1_RNA|WDR52_ENST00000393845.2_Missense_Mutation_p.K53E	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						CCTTCCCCTTTGGTAAATGTT	0.323													C|||	1365	0.272564	0.0734	0.268	5008	,	,		18333	0.5129		0.2555	False		,,,				2504	0.3149				p.K53E		Atlas-SNP	.											.	WDR52	151	.	0			c.A157G						PASS	.	C	GLU/LYS,GLU/LYS	514,3892	777.6+/-414.2	38,438,1727	161.0	140.0	147.0		157,157	3.5	0.5	3	dbSNP_129	147	1974,6626	722.6+/-406.4	233,1508,2559	yes	missense,missense	WDR52	NM_001164496.1,NM_018338.3	56,56	271,1946,4286	CC,CT,TT		22.9535,11.6659,19.1296	benign,benign	53/1855,53/983	113146130	2488,10518	2203	4300	6503	SO:0001583	missense	55779	exon3			CCCCTTTGGTAAA																												ENST00000295868.2:c.157A>G	3.37:g.113146130T>C	ENSP00000295868:p.Lys53Glu	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	208	102	0.490385	NM_001164496		Missense_Mutation	SNP	ENST00000295868.2	37	CCDS2972.1	600	0.27472527472527475	38	0.07723577235772358	82	0.2265193370165746	288	0.5034965034965035	192	0.2532981530343008	C	1.365	-0.587740	0.03799	0.116659	0.229535	ENSG00000206530	ENST00000393845;ENST00000295868;ENST00000473143	T;T;T	0.44482	2.98;1.07;0.92	4.43	3.53	0.40419	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.21220	P	0.999758682	B	0.02656	0.0	B	0.01281	0.0	T	0.47182	-0.9137	8	0.02654	T	1	.	6.2418	0.20795	0.0:0.7138:0.1866:0.0996	rs59722850	53	Q96MT7	WDR52_HUMAN	E	53	ENSP00000377428:K53E;ENSP00000295868:K53E;ENSP00000419671:K53E	ENSP00000295868:K53E	K	-	1	0	WDR52	114628820	0.618000	0.27051	0.548000	0.28192	0.006000	0.05464	1.006000	0.29847	0.771000	0.33359	-0.128000	0.14901	AAA	T|0.784;C|0.216	0.216	strong		0.323	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
ADAM21	8747	hgsc.bcm.edu	37	14	70924613	70924613	+	Nonsense_Mutation	SNP	C	C	T	rs138262361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:70924613C>T	ENST00000603540.1	+	2	655	c.397C>T	c.(397-399)Cga>Tga	p.R133*	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Nonsense_Mutation_p.R133*	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	133					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TGGGGGCTTTCGAGGAGTATT	0.448																																					p.R133X		Atlas-SNP	.											ADAM21_ENST00000267499,NS,carcinoma,0,6	ADAM21	181	6	0			c.C397T						scavenged	.						74.0	86.0	82.0					14																	70924613		2202	4300	6502	SO:0001587	stop_gained	8747	exon2			GGCTTTCGAGGAG	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.397C>T	14.37:g.70924613C>T	ENSP00000474385:p.Arg133*	Somatic	117	1	0.00854701		WXS	Illumina HiSeq	Phase_I	131	10	0.0763359	NM_003813	O43507|Q2VPC6|Q32MR0	Nonsense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	C	9.227	1.034843	0.19590	.	.	ENSG00000139985	ENST00000267499	.	.	.	3.76	3.76	0.43208	.	0.682149	0.11938	U	0.515009	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	12.162	0.54109	0.1717:0.8283:0.0:0.0	.	.	.	.	X	133	.	ENSP00000267499:R133X	R	+	1	2	ADAM21	69994366	0.003000	0.15002	0.322000	0.25334	0.071000	0.16799	1.122000	0.31295	2.090000	0.63153	0.557000	0.71058	CGA	C|0.993;T|0.007	0.007	strong		0.448	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
KCNG4	93107	hgsc.bcm.edu	37	16	84256410	84256410	+	Missense_Mutation	SNP	C	C	T	rs7196482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84256410C>T	ENST00000308251.4	-	3	1041	c.973G>A	c.(973-975)Ggg>Agg	p.G325R		NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	325			G -> R (in dbSNP:rs7196482).		protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						TAGGAGCTCCCGCTCGGCCTC	0.677													C|||	885	0.176717	0.2156	0.1686	5008	,	,		17359	0.0506		0.2266	False		,,,				2504	0.2086				p.G325R		Atlas-SNP	.											.	KCNG4	71	.	0			c.G973A						PASS	.	C	ARG/GLY	942,3458	340.2+/-306.1	109,724,1367	30.0	33.0	32.0		973	-2.7	0.0	16	dbSNP_116	32	1922,6678	321.7+/-315.2	212,1498,2590	no	missense	KCNG4	NM_172347.2	125	321,2222,3957	TT,TC,CC		22.3488,21.4091,22.0308	probably-damaging	325/520	84256410	2864,10136	2200	4300	6500	SO:0001583	missense	93107	exon3			AGCTCCCGCTCGG	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.973G>A	16.37:g.84256410C>T	ENSP00000312129:p.Gly325Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	77	34	0.441558	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	369	0.16895604395604397	101	0.20528455284552846	63	0.17403314917127072	26	0.045454545454545456	179	0.23614775725593667	C	8.185	0.794792	0.16327	0.214091	0.223488	ENSG00000168418	ENST00000308251	D	0.97041	-4.22	5.61	-2.74	0.05932	Ion transport (1);	0.310951	0.34268	N	0.004108	T	0.00552	0.0018	M	0.75085	2.285	0.58432	P	6.999999999979245E-6	D	0.56521	0.976	P	0.51516	0.672	T	0.50642	-0.8804	9	0.72032	D	0.01	.	8.1708	0.31254	0.0:0.3567:0.1088:0.5345	rs7196482;rs59048729;rs7196482	325	Q8TDN1	KCNG4_HUMAN	R	325	ENSP00000312129:G325R	ENSP00000312129:G325R	G	-	1	0	KCNG4	82813911	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.117000	0.10708	-0.433000	0.07286	0.655000	0.94253	GGG	C|0.810;T|0.190	0.190	strong		0.677	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
ZNF45	7596	hgsc.bcm.edu	37	19	44418343	44418343	+	Silent	SNP	C	C	T	rs406968	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44418343C>T	ENST00000269973.5	-	10	2335	c.1245G>A	c.(1243-1245)ccG>ccA	p.P415P	ZNF45_ENST00000589703.1_Silent_p.P415P|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	415					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						CACACTGATACGGTTTCTCTC	0.463													C|||	2629	0.52496	0.3343	0.647	5008	,	,		22173	0.7996		0.5169	False		,,,				2504	0.4213				p.P415P		Atlas-SNP	.											ZNF45,caecum,carcinoma,0,1	ZNF45	51	1	0			c.G1245A						PASS	.	C		1581,2825	494.1+/-362.9	294,993,916	90.0	85.0	87.0		1245	-7.4	0.4	19	dbSNP_80	87	4352,4248	581.0+/-391.2	1118,2116,1066	no	coding-synonymous	ZNF45	NM_003425.3		1412,3109,1982	TT,TC,CC		49.3953,35.8829,45.6174		415/683	44418343	5933,7073	2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			CTGATACGGTTTC	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.1245G>A	19.37:g.44418343C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	37	CCDS12632.1																																																																																			C|0.504;T|0.496	0.496	strong		0.463	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
TBRG4	9238	hgsc.bcm.edu	37	7	45140914	45140914	+	Silent	SNP	C	C	T	rs1042984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45140914C>T	ENST00000258770.3	-	10	1858	c.1737G>A	c.(1735-1737)ctG>ctA	p.L579L	TBRG4_ENST00000494076.1_Silent_p.L579L|TBRG4_ENST00000395655.4_Silent_p.L469L|TBRG4_ENST00000361278.3_Silent_p.L469L	NM_004749.3	NP_004740.2	Q969Z0	TBRG4_HUMAN	transforming growth factor beta regulator 4	579	RAP. {ECO:0000255|PROSITE- ProRule:PRU00619}.				cell cycle arrest (GO:0007050)|cellular respiration (GO:0045333)|positive regulation of cell proliferation (GO:0008284)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|large_intestine(2)|lung(8)|skin(1)|stomach(2)	17						CAAAGCGACCCAGCAAGTCCT	0.577													C|||	237	0.0473243	0.0741	0.0331	5008	,	,		20634	0.0159		0.0497	False		,,,				2504	0.0511				p.L590L		Atlas-SNP	.											.	TBRG4	52	.	0			c.G1770A						PASS	.	C	,,	347,4059	180.5+/-208.7	19,309,1875	81.0	81.0	81.0		1737,1407,1407	4.8	1.0	7	dbSNP_86	81	412,8188	129.0+/-187.1	11,390,3899	no	coding-synonymous,coding-synonymous,coding-synonymous	TBRG4	NM_004749.2,NM_030900.2,NM_199122.1	,,	30,699,5774	TT,TC,CC		4.7907,7.8756,5.8358	,,	579/632,469/522,469/522	45140914	759,12247	2203	4300	6503	SO:0001819	synonymous_variant	9238	exon10			GCGACCCAGCAAG	AB023165	CCDS5501.1, CCDS5502.1	7p13	2006-07-07			ENSG00000136270	ENSG00000136270			17443	protein-coding gene	gene with protein product	"""FAST kinase domains 4"", ""cell cycle progression 2 protein"""	611325				9383053	Standard	NM_004749		Approved	Cpr2, KIAA0948, H_TD2522F11.8, FASTKD4	uc011kcd.3	Q969Z0	OTTHUMG00000129247	ENST00000258770.3:c.1737G>A	7.37:g.45140914C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_001261834	A4D2L2|A4D2L3|D3DVL5|D3DVL6|O14710|Q53GI8|Q8NDM4|Q9BUC6|Q9Y2F6	Silent	SNP	ENST00000258770.3	37	CCDS5501.1																																																																																			C|0.946;T|0.054	0.054	strong		0.577	TBRG4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251351.1	NM_030900	
C16orf62	57020	hgsc.bcm.edu	37	16	19693627	19693627	+	Silent	SNP	C	C	T	rs117014682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:19693627C>T	ENST00000251143.5	+	28	2454	c.2442C>T	c.(2440-2442)agC>agT	p.S814S	C16orf62_ENST00000448695.1_Silent_p.S664S|C16orf62_ENST00000543152.1_Silent_p.S563S|C16orf62_ENST00000542263.1_Silent_p.S810S|C16orf62_ENST00000438132.3_Silent_p.S903S|C16orf62_ENST00000417362.2_Silent_p.S721S			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	814						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						AGGACAACAGCGATGAGAAAA	0.517													C|||	41	0.0081869	0.0	0.0029	5008	,	,		10676	0.0		0.0239	False		,,,				2504	0.0153				p.S903S		Atlas-SNP	.											.	C16orf62	164	.	0			c.C2709T						PASS	.	C		27,4367	32.6+/-62.9	0,27,2170	164.0	140.0	148.0		2709	-7.4	0.0	16	dbSNP_132	148	209,8391	89.7+/-151.9	3,203,4094	no	coding-synonymous	C16orf62	NM_020314.5		3,230,6264	TT,TC,CC		2.4302,0.6145,1.8162		903/1053	19693627	236,12758	2197	4300	6497	SO:0001819	synonymous_variant	57020	exon28			CAACAGCGATGAG		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.2442C>T	16.37:g.19693627C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	149	73	0.489933	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																				C|0.985;T|0.015	0.015	strong		0.517	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695695	45695695	+	Silent	SNP	G	G	A	rs1153849	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:45695695G>A	ENST00000305560.6	+	1	1167	c.1068G>A	c.(1066-1068)agG>agA	p.R356R	SPATA5L1_ENST00000559860.1_Silent_p.R356R|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	356						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		CGCTGCGTAGGCCCGGGAGAT	0.677													A|||	3094	0.617812	0.8676	0.5706	5008	,	,		14893	0.8145		0.2753	False		,,,				2504	0.4632				p.R356R		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.G1068A						PASS	.	A		3242,1100		1234,774,163	33.0	39.0	37.0		1068	-0.1	1.0	15	dbSNP_87	37	2239,6277		311,1617,2330	no	coding-synonymous	SPATA5L1	NM_024063.2		1545,2391,2493	AA,AG,GG		26.2917,25.3339,42.6272		356/754	45695695	5481,7377	2171	4258	6429	SO:0001819	synonymous_variant	79029	exon1			GCGTAGGCCCGGG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1068G>A	15.37:g.45695695G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	37	CCDS10123.1																																																																																			G|0.415;A|0.585	0.585	strong		0.677	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
FRS2	10818	hgsc.bcm.edu	37	12	69967862	69967862	+	Silent	SNP	G	G	A	rs547497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:69967862G>A	ENST00000550389.1	+	7	900	c.654G>A	c.(652-654)gcG>gcA	p.A218A	FRS2_ENST00000397997.2_Silent_p.A218A|FRS2_ENST00000299293.2_Silent_p.A218A|FRS2_ENST00000549921.1_Silent_p.A218A	NM_001278353.1|NM_001278357.1	NP_001265282.1|NP_001265286.1	Q8WU20	FRS2_HUMAN	fibroblast growth factor receptor substrate 2	218					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification, embryo (GO:0008595)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation with mouth forming second (GO:0001702)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|lens fiber cell development (GO:0070307)|neuroblast proliferation (GO:0007405)|neurotrophin TRK receptor signaling pathway (GO:0048011)|optic placode formation involved in camera-type eye formation (GO:0046619)|organ induction (GO:0001759)|phosphatidylinositol-mediated signaling (GO:0048015)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|regulation of apoptotic process (GO:0042981)|regulation of epithelial cell proliferation (GO:0050678)|regulation of ERK1 and ERK2 cascade (GO:0070372)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fibroblast growth factor receptor binding (GO:0005104)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatase activator activity (GO:0019211)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.A218A(1)		autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Breast(13;2.15e-06)|Esophageal squamous(21;0.187)		Epithelial(6;2.94e-18)|Lung(24;9.68e-05)|OV - Ovarian serous cystadenocarcinoma(12;0.000984)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.0151)|Kidney(9;0.143)|LUSC - Lung squamous cell carcinoma(43;0.24)			CATTGGAGGCGAGGGTTTCTA	0.433													G|||	2319	0.463059	0.4894	0.5303	5008	,	,		18815	0.2708		0.4662	False		,,,				2504	0.5746				p.A218A		Atlas-SNP	.											FRS2_ENST00000299293,NS,carcinoma,0,1	FRS2	88	1	1	Substitution - coding silent(1)	stomach(1)	c.G654A						PASS	.	G	,	1870,1962		476,918,522	86.0	83.0	84.0		654,654	-8.1	0.7	12	dbSNP_83	84	3984,4266		985,2014,1126	no	coding-synonymous,coding-synonymous	FRS2	NM_001042555.1,NM_006654.3	,	1461,2932,1648	AA,AG,GG		48.2909,48.7996,48.4522	,	218/509,218/509	69967862	5854,6228	1916	4125	6041	SO:0001819	synonymous_variant	10818	exon10			GGAGGCGAGGGTT	AF036717	CCDS41809.1	12q15	2008-02-05				ENSG00000166225			16971	protein-coding gene	gene with protein product		607743				8761293, 9660748	Standard	NM_001278351		Approved	SNT-1, FRS2alpha, SNT1, FRS2A	uc001suz.3	Q8WU20		ENST00000550389.1:c.654G>A	12.37:g.69967862G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001042555	B0LPF2|B2R684|O43558|Q7LDQ6	Silent	SNP	ENST00000550389.1	37	CCDS41809.1																																																																																			G|0.554;A|0.446	0.446	strong		0.433	FRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403760.1	NM_006654	
C9orf156	51531	hgsc.bcm.edu	37	9	100672338	100672338	+	Missense_Mutation	SNP	C	C	T	rs2282192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100672338C>T	ENST00000375119.3	-	4	1046	c.970G>A	c.(970-972)Gtg>Atg	p.V324M	C9orf156_ENST00000478126.1_5'UTR	NM_016481.3	NP_057565.3	Q9BU70	NAP1_HUMAN	chromosome 9 open reading frame 156	324			V -> M (in dbSNP:rs2282192).		viral process (GO:0016032)		hydrolase activity (GO:0016787)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)	13		Acute lymphoblastic leukemia(62;0.158)				GCAGGAACCACGCTGCGGGGA	0.592													C|||	2951	0.589257	0.7935	0.4553	5008	,	,		19915	0.7788		0.2704	False		,,,				2504	0.5409				p.V324M		Atlas-SNP	.											C9orf156,NS,meningioma,0,1	C9orf156	35	1	0			c.G970A						PASS	.	C	MET/VAL	3121,1285	699.7+/-406.5	1113,895,195	58.0	53.0	54.0		970	-3.4	0.0	9	dbSNP_100	54	2332,6268	389.4+/-342.9	311,1710,2279	yes	missense	C9orf156	NM_016481.3	21	1424,2605,2474	TT,TC,CC		27.1163,29.1648,41.9268	benign	324/442	100672338	5453,7553	2203	4300	6503	SO:0001583	missense	51531	exon4			GAACCACGCTGCG	AK023069	CCDS6730.1	9q31.1	2011-03-02			ENSG00000136932	ENSG00000136932			30967	protein-coding gene	gene with protein product	"""Nef (lentivirus myristoylated factor) associated protein 1"""						Standard	NM_016481		Approved	HSPC219, NAP1	uc004axv.1	Q9BU70	OTTHUMG00000021007	ENST00000375119.3:c.970G>A	9.37:g.100672338C>T	ENSP00000364260:p.Val324Met	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_016481	Q5T113|Q86SK0|Q9NXJ7|Q9P0Q7	Missense_Mutation	SNP	ENST00000375119.3	37	CCDS6730.1	1203	0.5508241758241759	391	0.7947154471544715	152	0.4198895027624309	445	0.777972027972028	215	0.2836411609498681	C	10.47	1.360029	0.24598	0.708352	0.271163	ENSG00000136932	ENST00000375119;ENST00000375118	T;T	0.47528	0.84;0.84	5.03	-3.42	0.04825	Uncharacterised domain UPF0066, YaeB-like domain (1);	1.123640	0.06526	N	0.740603	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	B;B	0.18610	0.029;0.007	B;B	0.13407	0.009;0.001	T	0.39502	-0.9611	9	0.44086	T	0.13	-0.2542	1.5546	0.02582	0.1786:0.3526:0.102:0.3668	rs2282192;rs52801806;rs61011015;rs2282192	178;324	Q5T114;Q9BU70	.;NAP1_HUMAN	M	324;178	ENSP00000364260:V324M;ENSP00000364259:V178M	ENSP00000364259:V178M	V	-	1	0	C9orf156	99712159	0.000000	0.05858	0.001000	0.08648	0.222000	0.24845	-0.162000	0.10012	-0.506000	0.06558	-1.559000	0.00887	GTG	C|0.504;T|0.496	0.496	strong		0.592	C9orf156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055401.1	NM_016481	
TNRC18	84629	hgsc.bcm.edu	37	7	5353344	5353344	+	Missense_Mutation	SNP	G	G	A	rs12532973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5353344G>A	ENST00000430969.1	-	27	7526	c.7178C>T	c.(7177-7179)cCg>cTg	p.P2393L	TNRC18_ENST00000399537.4_Missense_Mutation_p.P2393L	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2393	Pro-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGGCTGCGGCGGTGCCGGGCG	0.711													g|||	449	0.0896565	0.0605	0.1758	5008	,	,		11080	0.0605		0.1044	False		,,,				2504	0.0828				p.P2393L		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7178T						PASS	.	A	LEU/PRO	195,2925		8,179,1373	11.0	13.0	13.0		7178	2.9	0.0	7	dbSNP_120	13	764,6376		35,694,2841	no	missense	TNRC18	NM_001080495.2	98	43,873,4214	AA,AG,GG		10.7003,6.25,9.347	benign	2393/2969	5353344	959,9301	1560	3570	5130	SO:0001583	missense	84629	exon27			TGCGGCGGTGCCG	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.7178C>T	7.37:g.5353344G>A	ENSP00000395538:p.Pro2393Leu	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	28	21	0.75	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	203	0.09294871794871795	34	0.06910569105691057	51	0.1408839779005525	33	0.057692307692307696	85	0.11213720316622691	g	0.006	-2.116432	0.00349	0.0625	0.107003	ENSG00000182095	ENST00000399537;ENST00000430969	T;T	0.12361	2.69;2.71	4.73	2.94	0.34122	.	0.800836	0.10212	N	0.701975	T	0.00109	0.0003	L	0.46157	1.445	0.80722	P	0.0	B	0.11235	0.004	B	0.06405	0.002	T	0.26780	-1.0093	9	0.20519	T	0.43	.	9.7442	0.40437	0.1538:0.0:0.8462:0.0	rs12532973	2393	O15417	TNC18_HUMAN	L	2393	ENSP00000382452:P2393L;ENSP00000395538:P2393L	ENSP00000382452:P2393L	P	-	2	0	TNRC18	5319870	0.730000	0.28100	0.001000	0.08648	0.000000	0.00434	4.155000	0.58131	0.442000	0.26555	-0.927000	0.02713	CCG	G|0.908;A|0.092	0.092	strong		0.711	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
LCLAT1	253558	hgsc.bcm.edu	37	2	30863092	30863092	+	Silent	SNP	C	C	T	rs12467646	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:30863092C>T	ENST00000309052.4	+	7	1061	c.852C>T	c.(850-852)caC>caT	p.H284H	LCLAT1_ENST00000540623.1_Silent_p.H246H|LCLAT1_ENST00000379509.3_Silent_p.H246H|LCLAT1_ENST00000491680.2_3'UTR	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	284					cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						TCCACTTTCACGTCCACCGGT	0.512													C|||	842	0.168131	0.0923	0.2205	5008	,	,		18550	0.2222		0.1173	False		,,,				2504	0.2301				p.H284H		Atlas-SNP	.											.	LCLAT1	51	.	0			c.C852T						PASS	.	C	,	375,4031	190.9+/-216.7	20,335,1848	100.0	96.0	97.0		738,852	0.4	1.0	2	dbSNP_120	97	1150,7450	236.8+/-268.9	94,962,3244	no	coding-synonymous,coding-synonymous	LCLAT1	NM_001002257.1,NM_182551.3	,	114,1297,5092	TT,TC,CC		13.3721,8.5111,11.7254	,	246/377,284/415	30863092	1525,11481	2203	4300	6503	SO:0001819	synonymous_variant	253558	exon7			CTTTCACGTCCAC	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"""lysocardiolipin acyltransferase"""	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.852C>T	2.37:g.30863092C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_182551	A6H8Z7|Q8N1Q7	Silent	SNP	ENST00000309052.4	37	CCDS1772.1																																																																																			C|0.872;T|0.128	0.128	strong		0.512	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551	
OR13C2	392376	hgsc.bcm.edu	37	9	107367612	107367612	+	Silent	SNP	C	C	T	rs55706329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107367612C>T	ENST00000542196.1	-	1	339	c.297G>A	c.(295-297)gtG>gtA	p.V99V		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GGAACATCTGCACTGCACAGC	0.517													C|||	1853	0.370008	0.4962	0.2089	5008	,	,		23529	0.5129		0.175	False		,,,				2504	0.3671				p.V99V		Atlas-SNP	.											.	OR13C2	46	.	0			c.G297A						PASS	.	C		2203,2203		462,1279,462	141.0	129.0	133.0		297	-7.1	0.0	9	dbSNP_129	133	1617,6983		132,1353,2815	no	coding-synonymous	OR13C2	NM_001004481.1		594,2632,3277	TT,TC,CC		18.8023,50.0,29.3711		99/319	107367612	3820,9186	2203	4300	6503	SO:0001819	synonymous_variant	392376	exon1			CATCTGCACTGCA		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.297G>A	9.37:g.107367612C>T		Somatic	455	0	0		WXS	Illumina HiSeq	Phase_I	529	206	0.389414	NM_001004481	B9EGV8|Q6IF54	Silent	SNP	ENST00000542196.1	37	CCDS35092.1																																																																																			C|0.652;T|0.348	0.348	strong		0.517	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
IMPG1	3617	hgsc.bcm.edu	37	6	76640803	76640803	+	Missense_Mutation	SNP	G	G	A	rs10943299	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:76640803G>A	ENST00000369950.3	-	15	2299	c.2110C>T	c.(2110-2112)Cgg>Tgg	p.R704W	IMPG1_ENST00000369963.3_3'UTR|Y_RNA_ENST00000363170.1_RNA	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TCCTCAGTCCGTTCGTTCTTT	0.542													g|||	450	0.0898562	0.0862	0.0821	5008	,	,		19099	0.003		0.1402	False		,,,				2504	0.138				p.R704W	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C2110T						PASS	.	A	TRP/ARG	419,3987	204.5+/-226.7	21,377,1805	88.0	71.0	77.0		2110	-7.6	0.0	6	dbSNP_120	77	1243,7357	249.0+/-276.5	81,1081,3138	yes	missense	IMPG1	NM_001563.2	101	102,1458,4943	AA,AG,GG		14.4535,9.5098,12.7787	benign	704/798	76640803	1662,11344	2203	4300	6503	SO:0001583	missense	3617	exon15			CAGTCCGTTCGTT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2110C>T	6.37:g.76640803G>A	ENSP00000358966:p.Arg704Trp	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	72	61	0.847222	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	189	0.08653846153846154	49	0.09959349593495935	28	0.07734806629834254	0	0.0	112	0.14775725593667546	g	0.009	-1.809098	0.00606	0.095098	0.144535	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.15834	2.41;2.39	5.45	-7.59	0.01308	Epidermal growth factor-like, type 3 (1);	0.900030	0.09563	N	0.785241	T	0.00666	0.0022	N	0.00510	-1.415	0.36734	P	0.11815600000000004	B	0.02656	0.0	B	0.01281	0.0	T	0.33445	-0.9868	9	0.02654	T	1	.	8.3239	0.32145	0.3945:0.2022:0.4034:0.0	rs10943299;rs52822464;rs10943299	704	Q17R60	IMPG1_HUMAN	W	704;65	ENSP00000358966:R704W;ENSP00000358968:R65W	ENSP00000358966:R704W	R	-	1	2	IMPG1	76697523	0.200000	0.23398	0.001000	0.08648	0.029000	0.11900	0.417000	0.21214	-2.374000	0.00599	-2.927000	0.00089	CGG	G|0.883;A|0.117	0.117	strong		0.542	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
SVEP1	79987	hgsc.bcm.edu	37	9	113209195	113209195	+	Missense_Mutation	SNP	T	T	G	rs1889323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113209195T>G	ENST00000401783.2	-	25	4582	c.4246A>C	c.(4246-4248)Aaa>Caa	p.K1416Q	SVEP1_ENST00000374469.1_Missense_Mutation_p.K1393Q|SVEP1_ENST00000302728.8_Missense_Mutation_p.K1416Q|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1416	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		K -> Q (in dbSNP:rs1889323).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TCACACCTTTTGCCTGAAAAT	0.343													T|||	568	0.113419	0.0401	0.1037	5008	,	,		19021	0.0327		0.1561	False		,,,				2504	0.2587				p.K1416Q		Atlas-SNP	.											.	SVEP1	326	.	0			c.A4246C						PASS	.	T	GLN/LYS	152,2988		5,142,1423	87.0	79.0	82.0		4246	4.8	1.0	9	dbSNP_92	82	1038,5840		81,876,2482	yes	missense	SVEP1	NM_153366.3	53	86,1018,3905	GG,GT,TT		15.0916,4.8408,11.8786	benign	1416/3572	113209195	1190,8828	1570	3439	5009	SO:0001583	missense	79987	exon25			ACCTTTTGCCTGA	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.4246A>C	9.37:g.113209195T>G	ENSP00000384917:p.Lys1416Gln	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	185	0.08470695970695971	17	0.034552845528455285	36	0.09944751381215469	17	0.02972027972027972	115	0.1517150395778364	T	13.99	2.401177	0.42613	0.048408	0.150916	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	D;D;D	0.86562	-2.14;-2.14;-2.14	5.95	4.8	0.61643	EGF (1);EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.351938	0.39407	N	0.001370	T	0.01661	0.0053	L	0.42744	1.35	0.40196	P	0.022534000000000054	B;B	0.15719	0.014;0.007	B;B	0.18871	0.023;0.003	T	0.50206	-0.8855	9	0.13108	T	0.6	.	13.096	0.59192	0.0:0.0:0.1385:0.8615	rs1889323;rs52835560;rs57327200;rs1889323	1416;1416	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	Q	1416;1393;1416	ENSP00000384917:K1416Q;ENSP00000363593:K1393Q;ENSP00000304118:K1416Q	ENSP00000304118:K1416Q	K	-	1	0	SVEP1	112249016	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.923000	0.56469	1.057000	0.40506	0.533000	0.62120	AAA	T|0.902;G|0.098	0.098	strong		0.343	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OR2T3	343173	hgsc.bcm.edu	37	1	248637291	248637291	+	Missense_Mutation	SNP	G	G	A	rs1770109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248637291G>A	ENST00000359594.2	+	1	665	c.640G>A	c.(640-642)Gcc>Acc	p.A214T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A214T(1)		breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATGCTTCTCGCCCCCATCAT	0.557													.|||	954	0.190495	0.1263	0.1916	5008	,	,		17132	0.2867		0.1064	False		,,,				2504	0.2638				p.A214T		Atlas-SNP	.											OR2T3,trunk,malignant_melanoma,0,1	OR2T3	79	1	1	Substitution - Missense(1)	skin(1)	c.G640A						scavenged	.						211.0	168.0	182.0					1																	248637291		2136	4233	6369	SO:0001583	missense	343173	exon1			CTTCTCGCCCCCA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.640G>A	1.37:g.248637291G>A	ENSP00000352604:p.Ala214Thr	Somatic	335	3	0.00895522		WXS	Illumina HiSeq	Phase_I	207	39	0.188406	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	537	0.24587912087912087	86	0.17479674796747968	71	0.19613259668508287	238	0.4160839160839161	142	0.18733509234828497	g	13.03	2.115628	0.37339	.	.	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	-2.22	0.06952	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10629	0.01	0.09310	N	1	P	0.39535	0.677	B	0.33568	0.166	T	0.42275	-0.9461	9	0.56958	D	0.05	.	0.5423	0.00647	0.2646:0.2059:0.3262:0.2032	rs1770109	214	Q8NH03	OR2T3_HUMAN	T	214	ENSP00000352604:A214T	ENSP00000352604:A214T	A	+	1	0	OR2T3	246703914	0.000000	0.05858	0.163000	0.22734	0.269000	0.26545	-1.638000	0.02013	0.011000	0.14865	0.186000	0.17326	GCC	G|0.754;A|0.246	0.246	strong		0.557	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
MT-CO2	4513	hgsc.bcm.edu	37	M	7853	7853	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:7853G>A	ENST00000361739.1	+	1	268	c.268G>A	c.(268-270)Gtc>Atc	p.V90I	MT-TA_ENST00000387392.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-ATP8_ENST00000361851.1_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TC_ENST00000387405.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TW_ENST00000387382.1_RNA			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	90					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						TAACAGACGAGGTCAACGATC	0.502																																					p.V90I		Atlas-SNP	.											.	.	.	.	0			c.G268A						PASS	.																																			SO:0001583	missense	5743	exon1			GACGAGGTCAACG			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.268G>A	M.37:g.7853G>A	ENSP00000354876:p.Val90Ile	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	ENST00000361739	Q37526	Missense_Mutation	SNP	ENST00000361739.1	37																																																																																				.	.	none		0.502	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029	
TPTE	7179	hgsc.bcm.edu	37	21	10959799	10959799	+	Splice_Site	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:10959799C>T	ENST00000361285.4	-	8	504	c.175G>A	c.(175-177)Gtg>Atg	p.V59M	TPTE_ENST00000298232.7_Splice_Site_p.V41M|TPTE_ENST00000342420.5_Intron|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	59					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		CGTGCTAACACACTTTAGCCA	0.328																																					p.V59M		Atlas-SNP	.											TPTE_ENST00000361285,right_lower_lobe,carcinoma,+2,4	TPTE	513	4	0			c.G175A						scavenged	.						95.0	90.0	92.0					21																	10959799		2203	4300	6503	SO:0001630	splice_region_variant	7179	exon8			CTAACACACTTTA	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.174-1G>A	21.37:g.10959799C>T		Somatic	529	5	0.0094518		WXS	Illumina HiSeq	Phase_I	521	9	0.0172745	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	c	0.513	-0.865468	0.02590	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000328758	D;D	0.94828	-3.35;-3.53	1.36	0.129	0.14739	.	0.593958	0.14931	N	0.290096	T	0.78874	0.4352	N	0.01048	-1.04	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.0	T	0.70096	-0.4966	10	0.29301	T	0.29	0.2742	4.868	0.13618	0.0:0.2316:0.0:0.7684	.	41;59	P56180-2;P56180	.;TPTE_HUMAN	M	41;59;41	ENSP00000298232:V41M;ENSP00000355208:V59M	ENSP00000298232:V41M	V	-	1	0	TPTE	9981670	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.416000	0.07097	-0.415000	0.07484	-3.038000	0.00071	GTG	.	.	none		0.328	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		Missense_Mutation
HLA-B	3106	hgsc.bcm.edu	37	6	31323353	31323353	+	Silent	SNP	G	G	A	rs2257269	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31323353G>A	ENST00000412585.2	-	4	664	c.636C>T	c.(634-636)caC>caT	p.H212H		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	212	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						GGTGGGTCACGTGTGTCTTTG	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				g|||	2004	0.40016	0.3775	0.4524	5008	,	,		18484	0.4018		0.4066	False		,,,				2504	0.3855				p.H212H		Atlas-SNP	.											.	HLA-B	54	.	0			c.C636T						PASS	.	A		1860,2546		400,1060,743	84.0	87.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	636	-6.4	0.0	6	dbSNP_100	86	3620,4980		747,2126,1427	no	coding-synonymous	HLA-B	NM_005514.6		1147,3186,2170	AA,AG,GG		42.093,42.2152,42.1344		212/363	31323353	5480,7526	2203	4300	6503	SO:0001819	synonymous_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	GGTCACGTGTGTC	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.636C>T	6.37:g.31323353G>A		Somatic	163	1	0.00613497		WXS	Illumina HiSeq	Phase_I	242	238	0.983471	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			G|0.600;A|0.400	0.400	strong		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SLC39A4	55630	hgsc.bcm.edu	37	8	145641328	145641328	+	Missense_Mutation	SNP	C	C	T	rs17855765	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145641328C>T	ENST00000301305.3	-	2	445	c.340G>A	c.(340-342)Gct>Act	p.A114T	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.A89T	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	114			A -> T (in dbSNP:rs17855765). {ECO:0000269|PubMed:12032886, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			CCAGCCCGAGCGTCCTCACAG	0.721													C|||	1874	0.374201	0.2761	0.379	5008	,	,		14156	0.37		0.5209	False		,,,				2504	0.3569				p.A114T		Atlas-SNP	.											SLC39A4_ENST00000276833,NS,carcinoma,0,2	SLC39A4	54	2	0			c.G340A						PASS	.	C	THR/ALA,THR/ALA	1238,3114		198,842,1136	13.0	15.0	15.0		265,340	-3.7	0.0	8	dbSNP_123	15	4378,4180		1181,2016,1082	yes	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	58,58	1379,2858,2218	TT,TC,CC		48.8432,28.4467,43.5012	benign,benign	89/623,114/648	145641328	5616,7294	2176	4279	6455	SO:0001583	missense	55630	exon2			CCCGAGCGTCCTC	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.340G>A	8.37:g.145641328C>T	ENSP00000301305:p.Ala114Thr	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	952	0.4358974358974359	162	0.32926829268292684	149	0.4116022099447514	230	0.4020979020979021	411	0.5422163588390502	C	6.069	0.380958	0.11466	0.284467	0.511568	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.56941	0.43;0.43	4.3	-3.67	0.04476	.	0.827299	0.10373	N	0.682547	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;P	0.43352	0.429;0.804	B;B	0.31101	0.039;0.124	T	0.43343	-0.9397	9	0.25106	T	0.35	-14.0618	10.6355	0.45563	0.0:0.492:0.0:0.508	rs17855765;rs61412194;rs17855765	114;89	Q6P5W5;A6NDY5	S39A4_HUMAN;.	T	89;114	ENSP00000276833:A89T;ENSP00000301305:A114T	ENSP00000276833:A89T	A	-	1	0	SLC39A4	145612136	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.006000	0.03671	-0.547000	0.06207	0.306000	0.20318	GCT	C|0.574;T|0.426	0.426	strong		0.721	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
ZNF443	10224	hgsc.bcm.edu	37	19	12541795	12541795	+	Missense_Mutation	SNP	C	C	A	rs35699767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12541795C>A	ENST00000301547.5	-	4	1388	c.1191G>T	c.(1189-1191)caG>caT	p.Q397H	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	397			Q -> H (in dbSNP:rs35699767).		apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						CTTTCCCACACTGCTTGCATT	0.418													.|||	1958	0.390974	0.4781	0.3084	5008	,	,		24055	0.3462		0.2793	False		,,,				2504	0.4928				p.Q397H		Atlas-SNP	.											.	ZNF443	63	.	0			c.G1191T						PASS	.	C	HIS/GLN	1960,2446	553.7+/-378.8	413,1134,656	189.0	173.0	178.0		1191	-2.7	0.0	19	dbSNP_126	178	2464,6136	406.4+/-348.8	372,1720,2208	no	missense	ZNF443	NM_005815.4	24	785,2854,2864	AA,AC,CC		28.6512,44.4848,34.0151	benign	397/672	12541795	4424,8582	2203	4300	6503	SO:0001583	missense	10224	exon4			CCCACACTGCTTG	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1191G>T	19.37:g.12541795C>A	ENSP00000301547:p.Gln397His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	753	0.3447802197802198	230	0.46747967479674796	107	0.2955801104972376	200	0.34965034965034963	216	0.2849604221635884	C	9.220	1.033143	0.19590	0.444848	0.286512	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.07567	3.18	1.37	-2.74	0.05932	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.31420	0.93	0.58432	P	5.000000000032756E-6	B	0.28470	0.213	B	0.36464	0.225	T	0.46665	-0.9175	8	0.66056	D	0.02	.	2.7523	0.05284	0.2056:0.3353:0.0:0.4591	rs35699767;rs58115314;rs62114864	397	Q9Y2A4	ZN443_HUMAN	H	397	ENSP00000301547:Q397H	ENSP00000301547:Q397H	Q	-	3	2	ZNF443	12402795	0.000000	0.05858	0.007000	0.13788	0.086000	0.17979	-3.155000	0.00580	-1.130000	0.02914	-0.384000	0.06662	CAG	C|0.657;A|0.343	0.343	strong		0.418	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
COL18A1	80781	hgsc.bcm.edu	37	21	46896303	46896303	+	Silent	SNP	C	C	G	rs2230687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46896303C>G	ENST00000359759.4	+	5	2103	c.2082C>G	c.(2080-2082)ccC>ccG	p.P694P	COL18A1_ENST00000400337.2_Silent_p.P279P|COL18A1_ENST00000355480.5_Silent_p.P459P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	694	Nonhelical region 1 (NC1).				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)		CGCCACCCCCCGTCACCACGC	0.642													G|||	1229	0.245407	0.4342	0.1311	5008	,	,		16164	0.2956		0.0984	False		,,,				2504	0.1708				p.P459P		Atlas-SNP	.											.	COL18A1	129	.	0			c.C1377G						PASS	.	G	,	1445,2563		285,875,844	45.0	48.0	47.0		1377,837	-7.7	0.0	21	dbSNP_98	47	778,7534		43,692,3421	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	328,1567,4265	GG,GC,CC		9.36,36.0529,18.0438	,	459/1520,279/1340	46896303	2223,10097	2004	4156	6160	SO:0001819	synonymous_variant	80781	exon5			ACCCCCCGTCACC		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.2082C>G	21.37:g.46896303C>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.793;G|0.207	0.207	strong		0.642	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509383	195509383	+	Missense_Mutation	SNP	G	G	T	rs559708827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195509383G>T	ENST00000463781.3	-	2	9527	c.9068C>A	c.(9067-9069)aCc>aAc	p.T3023N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3023N	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.T3023N(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)		ATGAAGAGGGGTGGCGTGACC	0.592													.|||	58	0.0115815	0.0091	0.0043	5008	,	,		10271	0.0357		0.004	False		,,,				2504	0.0031				p.T3023N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.C9068A						scavenged	.						27.0	20.0	22.0					3																	195509383		669	1569	2238	SO:0001583	missense	4585	exon2			AGAGGGGTGGCGT	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.9068C>A	3.37:g.195509383G>T	ENSP00000417498:p.Thr3023Asn	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	117	2	0.017094	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.525	0.465067	0.12402	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.52	.	.	.	.	.	.	.	.	T	0.23846	0.0577	N	0.08118	0	0.19775	N	0.999958	P	0.51653	0.947	P	0.55965	0.788	T	0.17048	-1.0382	7	.	.	.	.	7.5518	0.27802	0.0:0.0:1.0:0.0	.	2895	E7ESK3	.	N	3023	ENSP00000417498:T3023N;ENSP00000420243:T3023N	.	T	-	2	0	MUC4	196994162	0.013000	0.17824	0.041000	0.18516	0.000000	0.00434	0.698000	0.25571	0.482000	0.27582	0.000000	0.15137	ACC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HLA-A	3105	hgsc.bcm.edu	37	6	29911069	29911069	+	Missense_Mutation	SNP	A	A	T	rs1136697	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911069A>T	ENST00000396634.1	+	5	709	c.368A>T	c.(367-369)tAt>tTt	p.Y123F	HLA-A_ENST00000376809.5_Missense_Mutation_p.Y123F|HLA-A_ENST00000376806.5_Missense_Mutation_p.Y123F|HLA-A_ENST00000376802.2_Missense_Mutation_p.Y123F			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	123	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	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						CAGATAATGTATGGCTGCGAC	0.677									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	775	0.154752	0.1248	0.1787	5008	,	,		11512	0.2083		0.1133	False		,,,				2504	0.1656				p.Y123F		Atlas-SNP	.											.	HLA-A	89	.	0			c.A368T						PASS	.	T	PHE/TYR	425,2563		55,315,1124	23.0	19.0	20.0		368	-7.6	0.0	6	dbSNP_86	20	610,4736		76,458,2139	no	missense	HLA-A	NM_002116.7	22	131,773,3263	TT,TA,AA		11.4104,14.2236,12.419	benign	123/366	29911069	1035,7299	1494	2673	4167	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TAATGTATGGCTG	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.368A>T	6.37:g.29911069A>T	ENSP00000379873:p.Tyr123Phe	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	88	55	0.625	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	343	0.15705128205128205	47	0.09552845528455285	73	0.20165745856353592	147	0.256993006993007	76	0.10026385224274406	.	9.834	1.189139	0.21954	0.142236	0.114104	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00012	9.32;9.32;9.32;9.32	3.78	-7.56	0.01322	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	0.554096	0.13304	N	0.398029	T	0.00039	0.0001	L	0.55213	1.73	0.80722	P	0.0	B;B;B;B;B;B;B	0.09022	0.002;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.13407	0.002;0.008;0.003;0.004;0.009;0.008;0.004	T	0.50092	-0.8868	9	0.42905	T	0.14	.	2.5426	0.04730	0.1991:0.3075:0.0729:0.4206	rs1136697;rs3179188;rs3200172;rs11539958;rs16867784;rs17423985;rs41544021	2;123;123;123;123;123;123	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	F	123	ENSP00000379873:Y123F;ENSP00000366002:Y123F;ENSP00000366005:Y123F;ENSP00000365998:Y123F	ENSP00000348012:Y123F	Y	+	2	0	HLA-A	30019048	0.000000	0.05858	0.000000	0.03702	0.168000	0.22595	-4.451000	0.00232	-3.773000	0.00109	-0.510000	0.04470	TAT	A|0.871;T|0.129	0.129	strong		0.677	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
CEP83	51134	hgsc.bcm.edu	37	12	94769758	94769758	+	Silent	SNP	A	A	G	rs4761611	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:94769758A>G	ENST00000397809.5	-	8	1386	c.837T>C	c.(835-837)cgT>cgC	p.R279R	CCDC41_ENST00000547575.1_Silent_p.R279R|CCDC41_ENST00000339839.5_Silent_p.R279R|CCDC41_ENST00000397807.2_Silent_p.R246R|CCDC41_ENST00000549352.1_5'UTR	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		271					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						CTTTTTCCAAACGTTCTGCCC	0.284													G|||	4175	0.833666	0.9864	0.7767	5008	,	,		14477	0.9633		0.667	False		,,,				2504	0.7055				p.R279R		Atlas-SNP	.											.	CCDC41	59	.	0			c.T837C						PASS	.	G	,	3369,245		1576,217,14	79.0	74.0	75.0		837,837	0.8	1.0	12	dbSNP_111	75	5268,2876		1718,1832,522	no	coding-synonymous,coding-synonymous	CCDC41	NM_001042399.1,NM_016122.2	,	3294,2049,536	GG,GA,AA		35.3143,6.7792,26.5436	,	279/702,279/702	94769758	8637,3121	1807	4072	5879	SO:0001819	synonymous_variant	51134	exon8			TTCCAAACGTTCT																												ENST00000397809.5:c.837T>C	12.37:g.94769758A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_016122	A4FVB1|Q08AP1	Silent	SNP	ENST00000397809.5	37	CCDS41820.1																																																																																			A|0.153;G|0.847	0.847	strong		0.284	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		
APOBEC3G	60489	hgsc.bcm.edu	37	22	39477123	39477123	+	Silent	SNP	T	T	C	rs5757465	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39477123T>C	ENST00000407997.3	+	3	714	c.357T>C	c.(355-357)ttT>ttC	p.F119F	APOBEC3G_ENST00000452957.2_Silent_p.F119F|APOBEC3G_ENST00000461827.1_3'UTR	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	119					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.F119F(1)		central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					TGACCATCTTTGTTGCCCGCC	0.557													T|||	1425	0.284545	0.0287	0.3977	5008	,	,		16691	0.2242		0.4473	False		,,,				2504	0.4448				p.F119F		Atlas-SNP	.											APOBEC3G_ENST00000407997,NS,carcinoma,0,1	APOBEC3G	69	1	1	Substitution - coding silent(1)	stomach(1)	c.T357C						PASS	.	T		391,4015		18,355,1830	102.0	90.0	94.0		357	-4.9	0.0	22	dbSNP_114	94	3739,4861		831,2077,1392	no	coding-synonymous	APOBEC3G	NM_021822.3		849,2432,3222	CC,CT,TT		43.4767,8.8743,31.7546		119/385	39477123	4130,8876	2203	4300	6503	SO:0001819	synonymous_variant	60489	exon3			CATCTTTGTTGCC	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"""Apolipoprotein B mRNA editing enzymes"""	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.357T>C	22.37:g.39477123T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	100	40	0.4	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Silent	SNP	ENST00000407997.3	37	CCDS13984.1																																																																																			T|0.692;C|0.308	0.308	strong		0.557	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822	
ATE1	11101	hgsc.bcm.edu	37	10	123670575	123670575	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123670575G>T	ENST00000224652.6	-	5	514	c.429C>A	c.(427-429)ctC>ctA	p.L143L	ATE1_ENST00000543447.1_Silent_p.L28L|ATE1_ENST00000540606.1_Silent_p.L136L|ATE1_ENST00000535655.1_5'UTR|ATE1_ENST00000369043.3_Silent_p.L143L|ATE1_ENST00000369040.3_Silent_p.L47L	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	143					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)	p.L143L(1)		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)				TGTCATCACTGAGTGTTTTAA	0.378																																					p.L143L		Atlas-SNP	.											ATE1,mouth,carcinoma,0,1	ATE1	67	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C429A						PASS	.						136.0	139.0	138.0					10																	123670575		2203	4300	6503	SO:0001819	synonymous_variant	11101	exon5			ATCACTGAGTGTT	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.429C>A	10.37:g.123670575G>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	188	104	0.553191	NM_001001976	O95261|Q5SQQ3|Q8WW04	Silent	SNP	ENST00000224652.6	37	CCDS31300.1	.	.	.	.	.	.	.	.	.	.	G	0.199	-1.046145	0.01997	.	.	ENSG00000107669	ENST00000423243	.	.	.	5.78	-2.6	0.06190	.	.	.	.	.	T	0.18173	0.0436	.	.	.	0.28353	N	0.920826	.	.	.	.	.	.	T	0.27400	-1.0075	4	.	.	.	-12.2001	0.864	0.01199	0.242:0.2723:0.2842:0.2015	.	.	.	.	K	140	.	.	Q	-	1	0	ATE1	123660565	0.003000	0.15002	0.000000	0.03702	0.179000	0.23085	-0.111000	0.10807	-0.488000	0.06726	-0.253000	0.11424	CAG	.	.	none		0.378	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	
ATRIP	84126	hgsc.bcm.edu	37	3	48501936	48501936	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:48501936C>T	ENST00000320211.3	+	8	1596	c.1483C>T	c.(1483-1485)Cta>Tta	p.L495L	ATRIP_ENST00000346691.4_Silent_p.L495L|ATRIP_ENST00000412052.1_Silent_p.L402L|ATRIP_ENST00000357105.6_Silent_p.L368L	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	495					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)	microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)	22				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		AGTCGTCTCCCTATTACTGTC	0.557								Other conserved DNA damage response genes																													p.L495L		Atlas-SNP	.											ATRIP,NS,carcinoma,-2,1	ATRIP	41	1	0			c.C1483T						scavenged	.						87.0	89.0	88.0					3																	48501936		2203	4300	6503	SO:0001819	synonymous_variant	84126	exon8			GTCTCCCTATTAC	AF451323	CCDS2767.1, CCDS2768.1, CCDS59449.1, CCDS59450.1	3p24.3-p22.1	2007-06-20			ENSG00000164053	ENSG00000164053			33499	protein-coding gene	gene with protein product		606605				11721054	Standard	NM_130384		Approved	FLJ12343, MGC20625, MGC21482, MGC26740	uc003ctf.2	Q8WXE1	OTTHUMG00000133532	ENST00000320211.3:c.1483C>T	3.37:g.48501936C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	141	2	0.0141844	NM_130384	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Silent	SNP	ENST00000320211.3	37	CCDS2768.1																																																																																			.	.	none		0.557	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384	
ZNF180	7733	hgsc.bcm.edu	37	19	44981883	44981883	+	Missense_Mutation	SNP	C	C	G	rs1897820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44981883C>G	ENST00000221327.4	-	5	1096	c.815G>C	c.(814-816)tGc>tCc	p.C272S	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.C247S|ZNF180_ENST00000592529.1_Missense_Mutation_p.C245S	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	272			C -> S (in dbSNP:rs1897820). {ECO:0000269|PubMed:12743021}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				AAATCCATAGCATTTATCTTT	0.328													G|||	2176	0.434505	0.6218	0.2939	5008	,	,		18677	0.4177		0.4583	False		,,,				2504	0.274				p.C272S	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.G815C						PASS	.	G	SER/CYS	2621,1785	516.3+/-369.1	784,1053,366	76.0	83.0	81.0		815	4.2	0.0	19	dbSNP_92	81	3685,4911	615.7+/-396.4	800,2085,1413	yes	missense	ZNF180	NM_013256.3	112	1584,3138,1779	GG,GC,CC		42.8688,40.5129,48.5002	benign	272/693	44981883	6306,6696	2203	4298	6501	SO:0001583	missense	7733	exon5			CCATAGCATTTAT	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.815G>C	19.37:g.44981883C>G	ENSP00000221327:p.Cys272Ser	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	164	80	0.487805	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	993	0.45467032967032966	277	0.5630081300813008	118	0.3259668508287293	258	0.45104895104895104	340	0.44854881266490765	G	2.681	-0.275458	0.05679	0.594871	0.428688	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.05649	3.41;3.43	5.3	4.2	0.49525	.	0.366777	0.20138	N	0.098426	T	0.00012	0.0000	N	0.03608	-0.345	0.49915	P	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	0.17319	-1.0373	9	0.36615	T	0.2	-0.6346	9.886	0.41262	0.0:0.1515:0.6916:0.1568	rs1897820;rs52836449;rs1897820	247;271;272	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	S	272;247	ENSP00000221327:C272S;ENSP00000375818:C247S	ENSP00000221327:C272S	C	-	2	0	ZNF180	49673723	0.000000	0.05858	0.019000	0.16419	0.310000	0.27922	0.026000	0.13599	1.237000	0.43756	-0.120000	0.15030	TGC	C|0.530;G|0.470	0.470	strong		0.328	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
C7orf33	202865	hgsc.bcm.edu	37	7	148288020	148288020	+	Start_Codon_SNP	SNP	G	G	T	rs62624492	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:148288020G>T	ENST00000307003.2	+	1	364	c.3G>T	c.(1-3)atG>atT	p.M1I		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	1										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TTGCCAAAATGCAAGTGGAAG	0.542													G|||	137	0.0273562	0.0076	0.0893	5008	,	,		20107	0.001		0.0239	False		,,,				2504	0.0409				p.M1I		Atlas-SNP	.											.	C7orf33	28	.	0			c.G3T						PASS	.	G	ILE/MET	54,4352	52.9+/-88.7	1,52,2150	49.0	51.0	50.0		3	-3.8	0.0	7	dbSNP_129	50	291,8309	107.2+/-168.0	4,283,4013	yes	missense	C7orf33	NM_145304.2	10	5,335,6163	TT,TG,GG		3.3837,1.2256,2.6526	benign	1/178	148288020	345,12661	2203	4300	6503	SO:0001582	initiator_codon_variant	202865	exon1			CAAAATGCAAGTG	BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.3G>T	7.37:g.148288020G>T	ENSP00000304071:p.Met1Ile	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_145304		Missense_Mutation	SNP	ENST00000307003.2	37	CCDS5890.1	41	0.018772893772893772	4	0.008130081300813009	21	0.058011049723756904	0	0.0	16	0.021108179419525065	G	6.790	0.514812	0.12944	0.012256	0.033837	ENSG00000170279	ENST00000307003	.	.	.	3.77	-3.77	0.04346	.	.	.	.	.	T	0.05502	0.0145	.	.	.	0.54753	D	0.999982	B	0.12013	0.005	B	0.12156	0.007	T	0.08827	-1.0703	7	0.87932	D	0	.	0.8787	0.01230	0.3112:0.29:0.2515:0.1473	rs62624492	1	Q8WU49	CG033_HUMAN	I	1	.	ENSP00000304071:M1I	M	+	3	0	C7orf33	147918953	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.382000	0.07408	-1.036000	0.03287	0.563000	0.77884	ATG	G|0.974;T|0.026	0.026	strong		0.542	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304	Missense_Mutation
ZMAT4	79698	hgsc.bcm.edu	37	8	40438757	40438757	+	Missense_Mutation	SNP	T	T	C	rs17851751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:40438757T>C	ENST00000297737.6	-	6	747	c.601A>G	c.(601-603)Acc>Gcc	p.T201A	ZMAT4_ENST00000315769.7_Missense_Mutation_p.T125A	NM_024645.2	NP_078921.1	Q9H898	ZMAT4_HUMAN	zinc finger, matrin-type 4	201			T -> A (in dbSNP:rs17851751). {ECO:0000269|PubMed:15489334}.			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18	Ovarian(28;0.00724)|Colorectal(14;0.0468)	all_cancers(7;0.00936)|all_epithelial(6;3.53e-06)|all_lung(54;0.0318)|Lung NSC(58;0.0919)|Esophageal squamous(32;0.15)|Hepatocellular(245;0.152)	LUSC - Lung squamous cell carcinoma(45;0.00722)			CTGCAGATGGTACATCTGTAA	0.458													T|||	710	0.141773	0.0688	0.2147	5008	,	,		18996	0.002		0.3121	False		,,,				2504	0.1575				p.T201A		Atlas-SNP	.											ZMAT4,NS,adenoma,0,1	ZMAT4	47	1	0			c.A601G						scavenged	.	T	ALA/THR,ALA/THR	447,3959	214.8+/-234.0	23,401,1779	206.0	167.0	180.0		373,601	4.5	1.0	8	dbSNP_123	180	2594,6006	419.9+/-353.2	359,1876,2065	yes	missense,missense	ZMAT4	NM_001135731.1,NM_024645.2	58,58	382,2277,3844	CC,CT,TT		30.1628,10.1453,23.3815	benign,benign	125/154,201/230	40438757	3041,9965	2203	4300	6503	SO:0001583	missense	79698	exon6			AGATGGTACATCT	AK023904	CCDS34885.1, CCDS47848.1	8p11.21	2012-10-05	2010-09-15		ENSG00000165061	ENSG00000165061		"""Zinc fingers, matrin-type"""	25844	protein-coding gene	gene with protein product						12477932	Standard	NM_024645		Approved	FLJ13842	uc003xnr.3	Q9H898	OTTHUMG00000164049	ENST00000297737.6:c.601A>G	8.37:g.40438757T>C	ENSP00000297737:p.Thr201Ala	Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_024645	Q8WUT8	Missense_Mutation	SNP	ENST00000297737.6	37	CCDS34885.1	336	0.15384615384615385	37	0.07520325203252033	68	0.1878453038674033	0	0.0	231	0.30474934036939316	T	13.31	2.198852	0.38806	0.101453	0.301628	ENSG00000165061	ENST00000315769;ENST00000297737;ENST00000519406	T;T;T	0.41065	2.01;2.01;1.01	5.65	4.49	0.54785	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.473547	0.25352	N	0.031295	T	0.00012	0.0000	L	0.27053	0.805	0.38791	P	0.04502099999999998	B;B	0.20671	0.001;0.047	B;B	0.22386	0.001;0.039	T	0.35724	-0.9777	9	0.24483	T	0.36	-27.2282	9.5492	0.39299	0.0:0.0828:0.0:0.9172	rs17851751;rs17851751	125;201	Q9H898-2;Q9H898	.;ZMAT4_HUMAN	A	125;201;201	ENSP00000319785:T125A;ENSP00000297737:T201A;ENSP00000428423:T201A	ENSP00000297737:T201A	T	-	1	0	ZMAT4	40557914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.601000	0.46249	0.971000	0.38288	0.533000	0.62120	ACC	T|0.790;C|0.210	0.210	strong		0.458	ZMAT4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376950.1	NM_024645	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33802156	33802156	+	Missense_Mutation	SNP	T	T	G	rs3744372	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33802156T>G	ENST00000260908.7	-	4	1670	c.1553A>C	c.(1552-1554)tAc>tCc	p.Y518S	SLFN12L_ENST00000361112.4_Missense_Mutation_p.Y547S|SLFN12L_ENST00000449046.1_Missense_Mutation_p.Y549S|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	518			Y -> S (in dbSNP:rs3744372).			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)	p.Y549S(4)|p.Y547S(2)		breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						AGGGCTCAAGTAGAAGATCTT	0.378													T|||	1145	0.228634	0.3238	0.1239	5008	,	,		19142	0.1587		0.164	False		,,,				2504	0.3129				p.Y518S		Atlas-SNP	.											SLFN12L_ENST00000449046,NS,carcinoma,0,6	SLFN12L	140	6	6	Substitution - Missense(6)	endometrium(3)|kidney(3)	c.A1553C						PASS	.	T	SER/TYR	413,971		63,287,342	258.0	196.0	215.0		1553	-4.3	0.0	17	dbSNP_107	215	483,2699		45,393,1153	yes	missense	SLFN12L	NM_001195790.1	144	108,680,1495	GG,GT,TT		15.1791,29.841,19.6233	probably-damaging	518/589	33802156	896,3670	692	1591	2283	SO:0001583	missense	100506736	exon4			CTCAAGTAGAAGA	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.1553A>C	17.37:g.33802156T>G	ENSP00000437635:p.Tyr518Ser	Somatic	363	1	0.00275482		WXS	Illumina HiSeq	Phase_I	358	199	0.555866	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	37	CCDS56026.1	426	0.19505494505494506	161	0.32723577235772355	51	0.1408839779005525	95	0.1660839160839161	119	0.15699208443271767	T	6.676	0.493246	0.12702	0.29841	0.151791	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.03717	3.84;3.94;3.83	2.15	-4.3	0.03710	.	.	.	.	.	T	0.00012	0.0000	L	0.35854	1.095	0.80722	P	0.0	B	0.17038	0.02	B	0.10450	0.005	T	0.47045	-0.9147	8	0.22706	T	0.39	.	3.7984	0.08749	0.0:0.2959:0.3946:0.3095	rs3744372;rs12941986;rs3744372	547	Q6IEE8-2	.	S	518;547;549	ENSP00000437635:Y518S;ENSP00000354412:Y547S;ENSP00000389348:Y549S	ENSP00000437635:Y518S	Y	-	2	0	SLFN12L	30826269	0.000000	0.05858	0.001000	0.08648	0.636000	0.38137	-1.878000	0.01630	-1.542000	0.01725	0.164000	0.16699	TAC	.	.	weak		0.378	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
ATP10A	57194	hgsc.bcm.edu	37	15	25981223	25981223	+	Silent	SNP	C	C	G	rs75541743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:25981223C>G	ENST00000356865.6	-	3	831	c.720G>C	c.(718-720)ctG>ctC	p.L240L	RNA5SP390_ENST00000410191.1_RNA	NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	240					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GAAACCTACTCAGGTCGTTGT	0.458													C|||	59	0.0117812	0.003	0.0159	5008	,	,		20150	0.0		0.0328	False		,,,				2504	0.0112				p.L240L		Atlas-SNP	.											.	ATP10A	270	.	0			c.G720C						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	157.0	106.0	123.0		720	1.4	0.9	15	dbSNP_132	123	238,8362	97.0+/-158.7	4,230,4066	no	coding-synonymous	ATP10A	NM_024490.3		4,254,6245	GG,GC,CC		2.7674,0.5447,2.0145		240/1500	25981223	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon3			CCTACTCAGGTCG	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.720G>C	15.37:g.25981223C>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	83	49	0.590361	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			C|0.981;G|0.019	0.019	strong		0.458	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
BMP1	649	hgsc.bcm.edu	37	8	22059323	22059323	+	Silent	SNP	C	C	T	rs61729094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22059323C>T	ENST00000306385.5	+	16	2785	c.2115C>T	c.(2113-2115)gaC>gaT	p.D705D	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	705	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		CAGACAAGGACGAGTGCTCCA	0.602													C|||	178	0.0355431	0.0151	0.0274	5008	,	,		20185	0.0506		0.0288	False		,,,				2504	0.0603				p.D705D		Atlas-SNP	.											.	BMP1	131	.	0			c.C2115T						PASS	.	C		37,4369	41.6+/-74.8	1,35,2167	68.0	56.0	60.0		2115	1.9	1.0	8	dbSNP_129	60	193,8407	84.2+/-146.7	2,189,4109	no	coding-synonymous	BMP1	NM_006129.4		3,224,6276	TT,TC,CC		2.2442,0.8398,1.7684		705/987	22059323	230,12776	2203	4300	6503	SO:0001819	synonymous_variant	649	exon16			CAAGGACGAGTGC		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.2115C>T	8.37:g.22059323C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			C|0.979;T|0.021	0.021	strong		0.602	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
ZNF584	201514	hgsc.bcm.edu	37	19	58928299	58928299	+	Silent	SNP	A	A	T	rs11668757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58928299A>T	ENST00000306910.4	+	4	937	c.414A>T	c.(412-414)gcA>gcT	p.A138A	ZNF584_ENST00000593920.1_Silent_p.A93A|ZNF584_ENST00000599238.1_3'UTR|ZNF584_ENST00000596921.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA|ZNF584_ENST00000322834.7_3'UTR	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	138					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(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		AGCATGGGGCAGCTTTCCCAC	0.517													A|||	647	0.129193	0.0401	0.1729	5008	,	,		18513	0.0546		0.2495	False		,,,				2504	0.1718				p.A138A		Atlas-SNP	.											.	ZNF584	31	.	0			c.A414T						PASS	.	A		268,4138	151.0+/-185.0	8,252,1943	148.0	112.0	124.0		414	0.7	0.0	19	dbSNP_120	124	1790,6810	322.9+/-315.8	186,1418,2696	no	coding-synonymous	ZNF584	NM_173548.1		194,1670,4639	TT,TA,AA		20.814,6.0826,15.8235		138/422	58928299	2058,10948	2203	4300	6503	SO:0001819	synonymous_variant	201514	exon4			TGGGGCAGCTTTC	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"""Zinc fingers, C2H2-type"", ""-"""	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.414A>T	19.37:g.58928299A>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	92	47	0.51087	NM_173548	A8K203	Silent	SNP	ENST00000306910.4	37	CCDS12979.1																																																																																			A|0.846;T|0.154	0.154	strong		0.517	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548	
CDAN1	146059	hgsc.bcm.edu	37	15	43020983	43020983	+	Missense_Mutation	SNP	G	G	A	rs8023524	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43020983G>A	ENST00000356231.3	-	20	2694	c.2671C>T	c.(2671-2673)Cgc>Tgc	p.R891C		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	891			R -> C (in dbSNP:rs8023524).		chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		TCTGCCTGGCGCACCAGATCT	0.567													G|||	1317	0.262979	0.4924	0.1282	5008	,	,		16633	0.0496		0.1859	False		,,,				2504	0.3476				p.R891C		Atlas-SNP	.											.	CDAN1	70	.	0			c.C2671T						PASS	.	G	CYS/ARG	1886,2520	539.6+/-375.3	396,1094,713	59.0	47.0	51.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2671	3.8	1.0	15	dbSNP_116	51	1620,6978	299.4+/-304.4	158,1304,2837	yes	missense	CDAN1	NM_138477.2	180	554,2398,3550	AA,AG,GG		18.8416,42.8053,26.9609	probably-damaging	891/1228	43020983	3506,9498	2203	4299	6502	SO:0001583	missense	146059	exon20			CCTGGCGCACCAG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2671C>T	15.37:g.43020983G>A	ENSP00000348564:p.Arg891Cys	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	149	69	0.463087	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	461	0.21108058608058608	219	0.4451219512195122	50	0.13812154696132597	37	0.06468531468531469	155	0.20448548812664907	G	18.56	3.650453	0.67472	0.428053	0.188416	ENSG00000140326	ENST00000356231;ENST00000267892	T	0.77877	-1.13	5.77	3.79	0.43588	.	0.789671	0.12571	N	0.457342	T	0.00012	0.0000	L	0.44542	1.39	0.29758	P	0.835791	D;D	0.63880	0.987;0.993	B;P	0.45712	0.409;0.491	T	0.31251	-0.9950	9	0.56958	D	0.05	-0.5786	8.3908	0.32526	0.0729:0.0:0.6087:0.3184	rs8023524;rs52797272;rs8023524	891;889	Q8IWY9;C9K0H8	CDAN1_HUMAN;.	C	891;889	ENSP00000348564:R891C	ENSP00000267892:R889C	R	-	1	0	CDAN1	40808275	0.697000	0.27767	0.961000	0.40146	0.994000	0.84299	0.862000	0.27899	1.447000	0.47661	0.561000	0.74099	CGC	G|0.749;A|0.251	0.251	strong		0.567	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
CSNK2A2	1459	hgsc.bcm.edu	37	16	58201631	58201631	+	Silent	SNP	G	G	A	rs55748630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58201631G>A	ENST00000262506.3	-	7	765	c.582C>T	c.(580-582)gcC>gcT	p.A194A	CSNK2A2_ENST00000566813.1_5'UTR	NM_001896.2	NP_001887.1	P19784	CSK22_HUMAN	casein kinase 2, alpha prime polypeptide	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)	1						AGTACCTTGAGGCTACACGAA	0.438													G|||	4	0.000798722	0.0	0.0	5008	,	,		18027	0.001		0.003	False		,,,				2504	0.0				p.A194A	Melanoma(54;119 1219 18349 35700 39738)	Atlas-SNP	.											.	CSNK2A2	25	.	0			c.C582T						PASS	.	G		2,4394	4.2+/-10.8	0,2,2196	110.0	98.0	102.0		582	0.9	1.0	16	dbSNP_129	102	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	CSNK2A2	NM_001896.2		0,53,6445	AA,AG,GG		0.593,0.0455,0.4078		194/351	58201631	53,12943	2198	4300	6498	SO:0001819	synonymous_variant	1459	exon7			CCTTGAGGCTACA	M55268	CCDS10794.1	16q21	2013-01-17			ENSG00000070770	ENSG00000070770			2459	protein-coding gene	gene with protein product		115442				2174700, 1766873	Standard	NM_001896		Approved	CSNK2A1	uc002enc.3	P19784	OTTHUMG00000133488	ENST00000262506.3:c.582C>T	16.37:g.58201631G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_001896		Silent	SNP	ENST00000262506.3	37	CCDS10794.1																																																																																			G|0.997;A|0.003	0.003	strong		0.438	CSNK2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257386.2	NM_001896	
ZNF175	7728	hgsc.bcm.edu	37	19	52090014	52090014	+	Missense_Mutation	SNP	C	C	T	rs35625154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52090014C>T	ENST00000262259.2	+	5	788	c.430C>T	c.(430-432)Cgc>Tgc	p.R144C	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	144					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		GGATGCTGACCGCACAAAGAA	0.378													C|||	217	0.0433307	0.0204	0.072	5008	,	,		20658	0.001		0.1083	False		,,,				2504	0.0307				p.R144C		Atlas-SNP	.											.	ZNF175	65	.	0			c.C430T						PASS	.	C	CYS/ARG	143,4263	101.2+/-139.8	3,137,2063	83.0	81.0	82.0		430	0.1	0.0	19	dbSNP_126	82	991,7609	213.5+/-253.4	63,865,3372	yes	missense	ZNF175	NM_007147.2	180	66,1002,5435	TT,TC,CC		11.5233,3.2456,8.7191	possibly-damaging	144/712	52090014	1134,11872	2203	4300	6503	SO:0001583	missense	7728	exon5			GCTGACCGCACAA	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.430C>T	19.37:g.52090014C>T	ENSP00000262259:p.Arg144Cys	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	183	85	0.464481	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	124	0.056776556776556776	11	0.022357723577235773	31	0.0856353591160221	1	0.0017482517482517483	81	0.10686015831134564	C	5.249	0.231416	0.09969	0.032456	0.115233	ENSG00000105497	ENST00000262259	T	0.08008	3.14	2.2	0.0506	0.14294	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.46205	-0.9208	9	0.37606	T	0.19	.	2.9571	0.05880	0.0:0.4625:0.2397:0.2978	rs35625154;rs61739662	144	Q9Y473	ZN175_HUMAN	C	144	ENSP00000262259:R144C	ENSP00000262259:R144C	R	+	1	0	ZNF175	56781826	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.571000	0.05889	0.090000	0.17273	-0.119000	0.15052	CGC	C|0.918;T|0.082	0.082	strong		0.378	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
CD163	9332	hgsc.bcm.edu	37	12	7637769	7637769	+	Missense_Mutation	SNP	G	G	A	rs61729512	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7637769G>A	ENST00000359156.4	-	11	2904	c.2702C>T	c.(2701-2703)aCg>aTg	p.T901M	CD163_ENST00000396620.3_Missense_Mutation_p.T934M|CD163_ENST00000432237.2_Missense_Mutation_p.T901M|CD163_ENST00000541972.1_Missense_Mutation_p.T889M|CD163_ENST00000539632.1_5'UTR	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	901	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CTGCCACAGCGTGTCAGGTCC	0.527													G|||	567	0.113219	0.028	0.2839	5008	,	,		-128	0.0149		0.1272	False		,,,				2504	0.1943				p.T901M		Atlas-SNP	.											CD163,colon,carcinoma,0,1	CD163	221	1	0			c.C2702T						PASS	.	G	MET/THR,MET/THR	226,4180	135.3+/-171.4	5,216,1982	118.0	115.0	116.0		2702,2702	2.8	0.0	12	dbSNP_129	116	953,7647	209.1+/-250.4	47,859,3394	yes	missense,missense	CD163	NM_004244.5,NM_203416.3	81,81	52,1075,5376	AA,AG,GG		11.0814,5.1294,9.065	benign,benign	901/1157,901/1122	7637769	1179,11827	2203	4300	6503	SO:0001583	missense	9332	exon11			CACAGCGTGTCAG	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.2702C>T	12.37:g.7637769G>A	ENSP00000352071:p.Thr901Met	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	CCDS8578.1	197	0.0902014652014652	13	0.026422764227642278	79	0.21823204419889503	7	0.012237762237762238	98	0.12928759894459102	G	10.82	1.457842	0.26161	0.051294	0.110814	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.54	2.77	0.32553	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.582142	0.16463	N	0.213310	T	0.00039	0.0001	M	0.79693	2.465	0.80722	P	0.0	B;P;B	0.45348	0.403;0.856;0.236	B;B;B	0.37451	0.075;0.25;0.033	T	0.10636	-1.0621	9	0.29301	T	0.29	.	9.5133	0.39091	0.2324:0.0:0.7676:0.0	.	934;901;901	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	M	901;889;934;901	ENSP00000352071:T901M;ENSP00000444071:T889M;ENSP00000379863:T934M;ENSP00000403885:T901M	ENSP00000352071:T901M	T	-	2	0	CD163	7529036	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.948000	0.29096	0.413000	0.25759	-0.133000	0.14855	ACG	G|0.905;A|0.095	0.095	strong		0.527	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
PRRT4	401399	hgsc.bcm.edu	37	7	127999645	127999645	+	Missense_Mutation	SNP	C	C	T	rs56272205	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:127999645C>T	ENST00000446477.2	-	3	714	c.401G>A	c.(400-402)cGg>cAg	p.R134Q	PRRT4_ENST00000435512.1_Missense_Mutation_p.R134Q|PRRT4_ENST00000489835.2_Missense_Mutation_p.R134Q|PRRT4_ENST00000535159.1_Missense_Mutation_p.R134Q	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	134						integral component of membrane (GO:0016021)				endometrium(4)|prostate(1)	5						CCCAGAGCGCCGGGATGTGGA	0.647													C|||	612	0.122204	0.0847	0.0994	5008	,	,		14883	0.1131		0.162	False		,,,				2504	0.1575				p.R134Q		Atlas-SNP	.											PRRT4,caecum,carcinoma,0,1	PRRT4	31	1	0			c.G401A						PASS	.	C	GLN/ARG,GLN/ARG	102,1282		2,98,592	14.0	18.0	17.0		401,401	-0.4	0.0	7	dbSNP_129	17	507,2675		45,417,1129	yes	missense,missense	PRRT4	NM_001174164.1,NM_001114726.2	43,43	47,515,1721	TT,TC,CC		15.9334,7.3699,13.3377	benign,benign	134/900,134/430	127999645	609,3957	692	1591	2283	SO:0001583	missense	401399	exon3			GAGCGCCGGGATG	BC063892	CCDS47698.1, CCDS47698.2, CCDS55160.1	7q32.1	2011-10-10			ENSG00000224940	ENSG00000224940		"""Proline-rich transmembrane proteins"""	37280	protein-coding gene	gene with protein product							Standard	NM_001114726		Approved		uc022aky.1	C9JH25	OTTHUMG00000157714	ENST00000446477.2:c.401G>A	7.37:g.127999645C>T	ENSP00000415026:p.Arg134Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	92	36	0.391304	NM_001174164	A4D0Z9|C9JVW7	Missense_Mutation	SNP	ENST00000446477.2	37	CCDS55160.1	273	0.125	45	0.09146341463414634	41	0.1132596685082873	82	0.14335664335664336	105	0.13852242744063326	C	5.695	0.312812	0.10789	0.073699	0.159334	ENSG00000224940	ENST00000489835;ENST00000446477;ENST00000535159;ENST00000435512;ENST00000489517;ENST00000464607;ENST00000495931	.	.	.	5.27	-0.37	0.12530	.	.	.	.	.	T	0.00109	0.0003	N	0.22421	0.69	0.80722	P	0.0	B;B	0.32128	0.357;0.307	B;B	0.26969	0.075;0.031	T	0.18023	-1.0350	7	0.25106	T	0.35	-0.5031	9.8115	0.40826	0.0916:0.5967:0.3116:0.0	rs56272205;rs61746550	134;134	C9JH25;C9JH25-2	PRRT4_HUMAN;.	Q	134	.	ENSP00000410779:R134Q	R	-	2	0	PRRT4	127786881	0.217000	0.23597	0.008000	0.14137	0.004000	0.04260	0.510000	0.22723	-0.060000	0.13132	-0.353000	0.07706	CGG	A|0.000;C|0.874;T|0.126	0.126	strong		0.647	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
PKD1	5310	hgsc.bcm.edu	37	16	2160503	2160503	+	Silent	SNP	T	T	G	rs71385734	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2160503T>G	ENST00000262304.4	-	15	4873	c.4665A>C	c.(4663-4665)gcA>gcC	p.A1555A	PKD1_ENST00000423118.1_Silent_p.A1555A|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1555	PKD 11. {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						CCGTGCGGCTTGCATTGACGA	0.652													g|||	1110	0.221645	0.556	0.1787	5008	,	,		17751	0.0		0.167	False		,,,				2504	0.0849				p.A1555A		Atlas-SNP	.											PKD1,colon,carcinoma,0,1	PKD1	184	1	0			c.A4665C						PASS	.	G	,	2130,2262	571.7+/-383.1	517,1096,583	54.0	57.0	56.0		4665,4665	4.4	1.0	16	dbSNP_130	56	1537,7045	730.5+/-406.8	133,1271,2887	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	650,2367,3470	GG,GT,TT		17.9096,48.4973,28.2642	,	1555/4303,1555/4304	2160503	3667,9307	2196	4291	6487	SO:0001819	synonymous_variant	5310	exon15			GCGGCTTGCATTG	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.4665A>C	16.37:g.2160503T>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			T|0.738;G|0.262	0.262	strong		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
EVPL	2125	hgsc.bcm.edu	37	17	74006317	74006317	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74006317T>C	ENST00000301607.3	-	22	3222	c.2969A>G	c.(2968-2970)cAg>cGg	p.Q990R	EVPL_ENST00000586740.1_Missense_Mutation_p.Q1012R	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	990	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CAGGTCTGCCTGCAGGCCAGC	0.637																																					p.Q990R		Atlas-SNP	.											.	EVPL	155	.	0			c.A2969G						PASS	.						39.0	43.0	42.0					17																	74006317		2203	4300	6503	SO:0001583	missense	2125	exon22			TCTGCCTGCAGGC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.2969A>G	17.37:g.74006317T>C	ENSP00000301607:p.Gln990Arg	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	54	0.534653	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	12.10	1.836978	0.32421	.	.	ENSG00000167880	ENST00000301607	T	0.66815	-0.23	4.72	3.63	0.41609	.	0.198103	0.44285	D	0.000466	T	0.56877	0.2015	L	0.53780	1.695	0.33077	D	0.536119	B;B	0.16396	0.017;0.013	B;B	0.16289	0.015;0.005	T	0.64728	-0.6339	10	0.66056	D	0.02	-42.4684	5.9853	0.19430	0.1469:0.081:0.0:0.772	.	1012;990	B7ZLH8;Q92817	.;EVPL_HUMAN	R	990	ENSP00000301607:Q990R	ENSP00000301607:Q990R	Q	-	2	0	EVPL	71517912	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	5.028000	0.64115	1.887000	0.54652	0.402000	0.26972	CAG	.	.	none		0.637	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
LRRC1	55227	hgsc.bcm.edu	37	6	53762092	53762092	+	Missense_Mutation	SNP	A	A	G	rs9349688	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:53762092A>G	ENST00000370888.1	+	7	854	c.577A>G	c.(577-579)Att>Gtt	p.I193V		NM_018214.4	NP_060684.4	Q9BTT6	LRRC1_HUMAN	leucine rich repeat containing 1	193			I -> V (in dbSNP:rs9349688). {ECO:0000269|PubMed:12200217}.			cytoplasm (GO:0005737)|membrane (GO:0016020)				cervix(1)|endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20	Lung NSC(77;0.0147)			BRCA - Breast invasive adenocarcinoma(397;0.0745)		GCCAGAATCAATTGGAGCCCT	0.353													A|||	599	0.119609	0.0045	0.2262	5008	,	,		18662	0.2659		0.0845	False		,,,				2504	0.0849				p.I193V		Atlas-SNP	.											.	LRRC1	59	.	0			c.A577G						PASS	.	A	VAL/ILE	112,4294	84.4+/-122.9	1,110,2092	66.0	63.0	64.0		577	3.9	0.9	6	dbSNP_119	64	792,7806	183.9+/-232.0	42,708,3549	yes	missense	LRRC1	NM_018214.4	29	43,818,5641	GG,GA,AA		9.2114,2.542,6.9517	benign	193/525	53762092	904,12100	2203	4299	6502	SO:0001583	missense	55227	exon7			GAATCAATTGGAG	AF332199	CCDS4953.2	6p12.2	2014-07-30	2003-11-19		ENSG00000137269	ENSG00000137269			14307	protein-coding gene	gene with protein product		608195	"""leucine-rich repeat-containing 1"""				Standard	NM_018214		Approved	dJ523E19.1, LANO, FLJ10775, FLJ11834	uc003pcd.1	Q9BTT6	OTTHUMG00000014885	ENST00000370888.1:c.577A>G	6.37:g.53762092A>G	ENSP00000359925:p.Ile193Val	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	22	12	0.545455	NM_018214	Q5TGN3|Q9HAC0|Q9NVF1	Missense_Mutation	SNP	ENST00000370888.1	37	CCDS4953.2	302	0.1382783882783883	3	0.006097560975609756	73	0.20165745856353592	160	0.27972027972027974	66	0.0870712401055409	A	13.74	2.327872	0.41197	0.02542	0.092114	ENSG00000137269	ENST00000370888	T	0.23348	1.91	5.09	3.92	0.45320	.	0.000000	0.85682	D	0.000000	T	0.14700	0.0355	L	0.52206	1.635	0.09310	P	1.0	B	0.34329	0.449	B	0.43658	0.426	T	0.09250	-1.0683	9	0.21014	T	0.42	.	10.3946	0.44192	0.9224:0.0:0.0776:0.0	rs9349688;rs52825999;rs57548957;rs9349688	193	Q9BTT6	LRRC1_HUMAN	V	193	ENSP00000359925:I193V	ENSP00000359925:I193V	I	+	1	0	LRRC1	53870051	1.000000	0.71417	0.890000	0.34922	0.851000	0.48451	4.633000	0.61318	0.882000	0.36016	-0.274000	0.10170	ATT	A|0.905;G|0.095	0.095	strong		0.353	LRRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040970.2	NM_025168	
TRIM55	84675	hgsc.bcm.edu	37	8	67062583	67062583	+	Silent	SNP	G	G	A	rs61738600	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:67062583G>A	ENST00000315962.4	+	7	1240	c.867G>A	c.(865-867)tcG>tcA	p.S289S	TRIM55_ENST00000350034.4_Intron|TRIM55_ENST00000276573.7_Silent_p.S289S|TRIM55_ENST00000353317.5_Silent_p.S289S	NM_184085.1	NP_908973.1	Q9BYV6	TRI55_HUMAN	tripartite motif containing 55	289	COS. {ECO:0000255|PROSITE- ProRule:PRU00586}.				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)			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)			GCAGAATCTCGGAAGCATCAA	0.358													G|||	390	0.0778754	0.2201	0.0375	5008	,	,		19996	0.0		0.0477	False		,,,				2504	0.0256				p.S289S		Atlas-SNP	.											.	TRIM55	91	.	0			c.G867A						PASS	.	G	,,,	777,3629	312.5+/-292.6	70,637,1496	98.0	98.0	98.0		867,867,867,	-5.8	0.8	8	dbSNP_129	98	407,8193	129.0+/-187.1	11,385,3904	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	TRIM55	NM_033058.2,NM_184085.1,NM_184086.1,NM_184087.1	,,,	81,1022,5400	AA,AG,GG		4.7326,17.635,9.1035	,,,	289/541,289/549,289/453,	67062583	1184,11822	2203	4300	6503	SO:0001819	synonymous_variant	84675	exon7			AATCTCGGAAGCA	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.867G>A	8.37:g.67062583G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	132	67	0.507576	NM_184086	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Silent	SNP	ENST00000315962.4	37	CCDS6184.1																																																																																			G|0.917;A|0.083	0.083	strong		0.358	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085	
UPF1	5976	hgsc.bcm.edu	37	19	18967721	18967721	+	Silent	SNP	C	C	T	rs34677724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18967721C>T	ENST00000599848.1	+	14	2102	c.1893C>T	c.(1891-1893)gcC>gcT	p.A631A	UPF1_ENST00000262803.5_Silent_p.A620A			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	631					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GTGTGGGCGCCGGTGACCCGA	0.632													C|||	208	0.0415335	0.1188	0.0245	5008	,	,		18272	0.0		0.0318	False		,,,				2504	0.002				p.A620A		Atlas-SNP	.											.	UPF1	88	.	0			c.C1860T						PASS	.	C		461,3945	217.4+/-235.8	29,403,1771	64.0	59.0	61.0		1860	-8.8	0.1	19	dbSNP_126	61	345,8255	116.6+/-176.3	8,329,3963	no	coding-synonymous	UPF1	NM_002911.3		37,732,5734	TT,TC,CC		4.0116,10.463,6.1971		620/1119	18967721	806,12200	2203	4300	6503	SO:0001819	synonymous_variant	5976	exon14			GGGCGCCGGTGAC	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.1893C>T	19.37:g.18967721C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	193	92	0.476684	NM_002911	O00239|O43343|Q86Z25|Q92842	Silent	SNP	ENST00000599848.1	37																																																																																				C|0.942;T|0.058	0.058	strong		0.632	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911	
SPECC1L	23384	hgsc.bcm.edu	37	22	24718408	24718408	+	Missense_Mutation	SNP	G	G	A	rs55723436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:24718408G>A	ENST00000314328.9	+	5	1745	c.1460G>A	c.(1459-1461)cGc>cAc	p.R487H	SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.R487H|SPECC1L_ENST00000541492.1_Missense_Mutation_p.R487H|SPECC1L_ENST00000437398.1_Missense_Mutation_p.R487H|SPECC1L_ENST00000416735.1_Intron	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	487					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						AAAAGTGGGCGCTATATGGAA	0.423													G|||	18	0.00359425	0.0008	0.0058	5008	,	,		22148	0.0		0.0099	False		,,,				2504	0.0031				p.R487H		Atlas-SNP	.											.	SPECC1L	85	.	0			c.G1460A						PASS	.	G	HIS/ARG,HIS/ARG	9,4397	16.8+/-37.8	0,9,2194	88.0	89.0	89.0		1460,1460	5.4	1.0	22	dbSNP_129	89	80,8520	45.8+/-104.6	0,80,4220	yes	missense,missense	SPECC1L	NM_001145468.1,NM_015330.2	29,29	0,89,6414	AA,AG,GG		0.9302,0.2043,0.6843	probably-damaging,probably-damaging	487/1118,487/1118	24718408	89,12917	2203	4300	6503	SO:0001583	missense	23384	exon4			GTGGGCGCTATAT	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.1460G>A	22.37:g.24718408G>A	ENSP00000325785:p.Arg487His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	27.1	4.796160	0.90453	0.002043	0.009302	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000421374;ENST00000314328;ENST00000541492	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.17280	0.0415	L	0.45581	1.43	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.70716	0.97;0.893	T	0.00085	-1.2098	10	0.56958	D	0.05	-15.9709	18.1791	0.89771	0.0:0.0:1.0:0.0	rs55723436	487;487	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	H	515;487;487;487;487	ENSP00000393363:R487H;ENSP00000405671:R487H;ENSP00000325785:R487H;ENSP00000439633:R487H	ENSP00000325785:R487H	R	+	2	0	SPECC1L	23048408	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.647000	0.98478	2.550000	0.86006	0.591000	0.81541	CGC	G|0.993;A|0.007	0.007	strong		0.423	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
MUC4	4585	hgsc.bcm.edu	37	3	195506750	195506750	+	Missense_Mutation	SNP	G	G	C	rs62282471	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506750G>C	ENST00000463781.3	-	2	12160	c.11701C>G	c.(11701-11703)Cac>Gac	p.H3901D	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3901D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGGGTGGCGTGACGTGTGGAT	0.592													.|||	553	0.110423	0.0287	0.1095	5008	,	,		8303	0.0536		0.2256	False		,,,				2504	0.1616				p.H3901D		Atlas-SNP	.											.	MUC4	1505	.	0			c.C11701G						PASS	.						9.0	9.0	9.0					3																	195506750		524	1014	1538	SO:0001583	missense	4585	exon2			TGGCGTGACGTGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11701C>G	3.37:g.195506750G>C	ENSP00000417498:p.His3901Asp	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	75	57	0.76	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	86	0.039377289377289376	11	0.022357723577235773	16	0.04419889502762431	6	0.01048951048951049	53	0.06992084432717678	g	2.283	-0.364168	0.05103	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31247	1.55;1.5	.	.	.	.	.	.	.	.	T	0.00967	0.0032	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.01281	0.0	T	0.18053	-1.0349	7	.	.	.	.	5.4844	0.16741	1.0E-4:0.348:0.652:0.0	rs62282471	3773	E7ESK3	.	D	3901	ENSP00000417498:H3901D;ENSP00000420243:H3901D	.	H	-	1	0	MUC4	196991529	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-3.212000	0.00555	-2.418000	0.00566	-2.366000	0.00237	CAC	G|0.967;C|0.033	0.033	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ALMS1	7840	hgsc.bcm.edu	37	2	73680508	73680508	+	Missense_Mutation	SNP	G	G	C	rs6546839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73680508G>C	ENST00000264448.6	+	8	6962	c.6851G>C	c.(6850-6852)cGt>cCt	p.R2284P	ALMS1_ENST00000409009.1_Missense_Mutation_p.R2242P|ALMS1_ENST00000377715.1_Missense_Mutation_p.R2284P	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2284			R -> P (in dbSNP:rs6546839).		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						CCCCTTGCCCGTTTCAGAGAT	0.398													C|||	1825	0.364417	0.8782	0.3919	5008	,	,		20366	0.0089		0.2276	False		,,,				2504	0.1575				p.R2284P		Atlas-SNP	.											.	ALMS1	384	.	0			c.G6851C						PASS	.	C	PRO/ARG	2723,947		1024,675,136	72.0	73.0	73.0		6851	5.5	1.0	2	dbSNP_116	73	1952,6200		222,1508,2346	yes	missense	ALMS1	NM_015120.4	103	1246,2183,2482	CC,CG,GG		23.945,25.8038,39.5449	benign	2284/4168	73680508	4675,7147	1835	4076	5911	SO:0001583	missense	7840	exon8			TTGCCCGTTTCAG	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.6851G>C	2.37:g.73680508G>C	ENSP00000264448:p.Arg2284Pro	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	78	39	0.5	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	737	0.3374542124542125	425	0.8638211382113821	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	C	3.609	-0.079949	0.07141	0.741962	0.23945	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.11385	3.65;3.65;2.78	5.49	5.49	0.81192	.	0.132997	0.35291	N	0.003301	T	0.00012	0.0000	N	0.00413	-1.525	0.49299	P	2.2900000000003473E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32295	-0.9912	9	0.02654	T	1	.	12.855	0.57880	0.0:0.8363:0.1637:0.0	rs6546839;rs17434138;rs17848860;rs61596780;rs6546839	2284;2242;2284	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	P	2242;2284;2284	ENSP00000386627:R2242P;ENSP00000264448:R2284P;ENSP00000366944:R2284P	ENSP00000264448:R2284P	R	+	2	0	ALMS1	73534016	0.983000	0.35010	1.000000	0.80357	0.958000	0.62258	2.660000	0.46749	1.481000	0.48307	-0.120000	0.15030	CGT	G|0.687;C|0.313	0.313	strong		0.398	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
COL4A4	1286	hgsc.bcm.edu	37	2	227954599	227954599	+	Missense_Mutation	SNP	G	G	A	rs2229814	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227954599G>A	ENST00000396625.3	-	21	1651	c.1444C>T	c.(1444-1446)Cca>Tca	p.P482S	COL4A4_ENST00000329662.7_Missense_Mutation_p.P482S	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	482	Triple-helical region.		P -> S (in dbSNP:rs2229814). {ECO:0000269|PubMed:11961012, ECO:0000269|PubMed:12631110}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TCTCCTTTTGGGCCTCTTCCT	0.483													A|||	2747	0.548522	0.5113	0.6081	5008	,	,		13414	0.5198		0.498	False		,,,				2504	0.638				p.P482S		Atlas-SNP	.											.	COL4A4	215	.	0			c.C1444T						PASS	.	A	SER/PRO	1967,1779		523,921,429	118.0	108.0	111.0		1444	0.3	0.8	2	dbSNP_98	111	4115,4087		1044,2027,1030	yes	missense	COL4A4	NM_000092.4	74	1567,2948,1459	AA,AG,GG		49.8293,47.4907,49.0961	benign	482/1691	227954599	6082,5866	1873	4101	5974	SO:0001583	missense	1286	exon21			CTTTTGGGCCTCT		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.1444C>T	2.37:g.227954599G>A	ENSP00000379866:p.Pro482Ser	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	226	112	0.495575	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	1130	0.5173992673992674	244	0.4959349593495935	212	0.585635359116022	287	0.5017482517482518	387	0.5105540897097626	A	0.121	-1.125898	0.01770	0.525093	0.501707	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.90133	-2.62;-2.53	5.74	0.339	0.15979	.	.	.	.	.	T	0.00012	0.0000	M	0.80332	2.49	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48536	-0.9027	8	0.09590	T	0.72	.	1.2219	0.01926	0.3311:0.2894:0.0874:0.2921	rs2229814;rs3736633;rs17644431;rs52828973;rs3736633	482	P53420	CO4A4_HUMAN	S	482	ENSP00000379866:P482S;ENSP00000328553:P482S	ENSP00000328553:P482S	P	-	1	0	COL4A4	227662843	0.533000	0.26354	0.750000	0.31169	0.512000	0.34134	0.624000	0.24462	0.089000	0.17243	-0.360000	0.07572	CCA	G|0.449;T|0.045	.	strong		0.483	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340835	55340835	+	Silent	SNP	C	C	T	rs45459293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55340835C>T	ENST00000391728.4	+	7	1053	c.1020C>T	c.(1018-1020)caC>caT	p.H340H	KIR3DL1_ENST00000541392.1_Silent_p.H323H|KIR3DL1_ENST00000326542.7_Silent_p.H323H|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000358178.4_Silent_p.H245H|KIR3DL1_ENST00000538269.1_Silent_p.H340H	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	340					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		GACACCTGCACATTCTGATTG	0.448													c|||	526	0.105032	0.0938	0.1427	5008	,	,		16236	0.001		0.2475	False		,,,				2504	0.0542				p.H340H		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.C1020T						PASS	.	C		157,4191		77,3,2094	273.0	207.0	230.0		1020	-1.5	0.0	19	dbSNP_127	230	730,7570		355,20,3775	no	coding-synonymous	KIR3DL1	NM_013289.2		432,23,5869	TT,TC,CC		8.7952,3.6109,7.013		340/445	55340835	887,11761	2174	4150	6324	SO:0001819	synonymous_variant	3811	exon7			CCTGCACATTCTG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1020C>T	19.37:g.55340835C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	31	10	0.322581	NM_013289	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																			C|0.913;T|0.087	0.087	strong		0.448	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
SLC26A2	1836	hgsc.bcm.edu	37	5	149360630	149360630	+	Missense_Mutation	SNP	C	C	T	rs78676079	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149360630C>T	ENST00000286298.4	+	3	1742	c.1474C>T	c.(1474-1476)Cgg>Tgg	p.R492W		NM_000112.3	NP_000103.2	P50443	S26A2_HUMAN	solute carrier family 26 (anion exchanger), member 2	492					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)|ion transport (GO:0006811)|ossification (GO:0001503)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(1)|prostate(2)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TGTAAATCTACGGGGAGCCCT	0.418													C|||	38	0.00758786	0.0	0.0086	5008	,	,		20441	0.001		0.0229	False		,,,				2504	0.0082				p.R492W		Atlas-SNP	.											SLC26A2,NS,NS,0,1	SLC26A2	48	1	0			c.C1474T	GRCh37	CM010436	SLC26A2	M	rs78676079	PASS	.	C	TRP/ARG	12,4394	19.1+/-41.9	0,12,2191	91.0	92.0	92.0		1474	6.2	1.0	5	dbSNP_131	92	187,8413	84.5+/-147.0	4,179,4117	yes	missense	SLC26A2	NM_000112.3	101	4,191,6308	TT,TC,CC		2.1744,0.2724,1.5301	probably-damaging	492/740	149360630	199,12807	2203	4300	6503	SO:0001583	missense	1836	exon3			AATCTACGGGGAG	U14528	CCDS4300.1	5q31-q34	2014-09-17	2013-07-18		ENSG00000155850	ENSG00000155850		"""Solute carriers"""	10994	protein-coding gene	gene with protein product		606718	"""solute carrier family 26 (sulfate transporter), member 2"""	DTD		7923357	Standard	NM_000112		Approved	DTDST	uc003lrh.3	P50443	OTTHUMG00000130054	ENST00000286298.4:c.1474C>T	5.37:g.149360630C>T	ENSP00000286298:p.Arg492Trp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_000112	A8K2U3|B2R6J1|Q6N051	Missense_Mutation	SNP	ENST00000286298.4	37	CCDS4300.1	23	0.010531135531135532	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	19	0.025065963060686015	C	17.56	3.420306	0.62622	0.002724	0.021744	ENSG00000155850	ENST00000286298	D	0.92805	-3.11	6.17	6.17	0.99709	Sulphate transporter (1);	0.000000	0.85682	D	0.000000	D	0.90769	0.7102	M	0.80508	2.5	0.53688	D	0.999972	D	0.89917	1.0	D	0.97110	1.0	D	0.90641	0.4575	10	0.72032	D	0.01	.	16.1415	0.81528	0.1927:0.8073:0.0:0.0	.	492	P50443	S26A2_HUMAN	W	492	ENSP00000286298:R492W	ENSP00000286298:R492W	R	+	1	2	SLC26A2	149340823	0.991000	0.36638	1.000000	0.80357	0.953000	0.61014	1.936000	0.40183	2.941000	0.99782	0.655000	0.94253	CGG	C|0.985;T|0.015	0.015	strong		0.418	SLC26A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252333.2	NM_000112	
OR6C74	254783	hgsc.bcm.edu	37	12	55641075	55641075	+	Missense_Mutation	SNP	A	A	G	rs7301705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55641075A>G	ENST00000343870.4	+	1	94	c.4A>G	c.(4-6)Aga>Gga	p.R2G		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	2			R -> G (in dbSNP:rs7301705).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						ATCAACTATGAGAAACCATAC	0.318													A|||	1105	0.220647	0.1248	0.2291	5008	,	,		16842	0.0794		0.333	False		,,,				2504	0.3742				p.R2G		Atlas-SNP	.											.	OR6C74	52	.	0			c.A4G						PASS	.	A	GLY/ARG	688,3716	271.3+/-270.1	48,592,1562	101.0	99.0	100.0		4	-0.7	0.1	12	dbSNP_116	100	2714,5886	416.3+/-352.1	425,1864,2011	yes	missense	OR6C74	NM_001005490.1	125	473,2456,3573	GG,GA,AA		31.5581,15.6222,26.1612	benign	2/313	55641075	3402,9602	2202	4300	6502	SO:0001583	missense	254783	exon1			ACTATGAGAAACC		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"""GPCR / Class A : Olfactory receptors"""	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.4A>G	12.37:g.55641075A>G	ENSP00000342836:p.Arg2Gly	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	93	37	0.397849	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	454	0.2078754578754579	66	0.13414634146341464	95	0.26243093922651933	46	0.08041958041958042	247	0.3258575197889182	a	10.26	1.302047	0.23736	0.156222	0.315581	ENSG00000197706	ENST00000343870	T	0.01665	4.7	4.83	-0.667	0.11395	.	0.415391	0.20729	N	0.086750	T	0.00012	0.0000	N	0.16368	0.405	0.53005	P	3.900000000001125E-5	B	0.10296	0.003	B	0.19946	0.027	T	0.46610	-0.9179	9	0.40728	T	0.16	.	5.0269	0.14389	0.495:0.2724:0.2326:0.0	rs7301705;rs52817965;rs61689751;rs7301705	2	A6NCV1	O6C74_HUMAN	G	2	ENSP00000342836:R2G	ENSP00000342836:R2G	R	+	1	2	OR6C74	53927342	0.376000	0.25098	0.080000	0.20451	0.147000	0.21601	-0.260000	0.08708	-0.178000	0.10672	0.450000	0.29827	AGA	A|0.753;G|0.247	0.247	strong		0.318	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
STXBP3	6814	hgsc.bcm.edu	37	1	109338861	109338861	+	Silent	SNP	G	G	C	rs1127635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:109338861G>C	ENST00000370008.3	+	14	1166	c.1116G>C	c.(1114-1116)ctG>ctC	p.L372L		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	372					blood coagulation (GO:0007596)|membrane organization (GO:0061024)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|neutrophil degranulation (GO:0043312)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein heterooligomerization (GO:0051291)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	syntaxin binding (GO:0019905)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(3)|urinary_tract(1)	13		all_epithelial(167;0.000154)|all_lung(203;0.00026)|Lung NSC(277;0.000508)		Colorectal(144;0.0386)|Lung(183;0.104)|COAD - Colon adenocarcinoma(174;0.137)|Epithelial(280;0.231)		TTAAGGACCTGGCACTTGGAA	0.353													G|||	1650	0.329473	0.2731	0.3213	5008	,	,		18139	0.1925		0.4334	False		,,,				2504	0.4458				p.L372L		Atlas-SNP	.											.	STXBP3	44	.	0			c.G1116C						PASS	.	G		1335,3071	440.4+/-346.0	212,911,1080	57.0	57.0	57.0		1116	4.9	1.0	1	dbSNP_86	57	3818,4782	536.8+/-383.1	825,2168,1307	no	coding-synonymous	STXBP3	NM_007269.2		1037,3079,2387	CC,CG,GG		44.3953,30.2996,39.6202		372/593	109338861	5153,7853	2203	4300	6503	SO:0001819	synonymous_variant	6814	exon14			GGACCTGGCACTT	D63506	CCDS790.1	1p13.3	2008-02-05			ENSG00000116266	ENSG00000116266			11446	protein-coding gene	gene with protein product		608339				10194441	Standard	NM_007269		Approved	UNC-18C	uc001dvy.3	O00186	OTTHUMG00000011122	ENST00000370008.3:c.1116G>C	1.37:g.109338861G>C		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	259	125	0.482625	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Silent	SNP	ENST00000370008.3	37	CCDS790.1																																																																																			G|0.624;C|0.375	0.375	strong		0.353	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269	
SLC7A7	9056	hgsc.bcm.edu	37	14	23282110	23282110	+	Splice_Site	SNP	A	A	G	rs8018462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23282110A>G	ENST00000397532.3	-	2	1023	c.498T>C	c.(496-498)atT>atC	p.I166I	SLC7A7_ENST00000555702.1_Splice_Site_p.I166I|SLC7A7_ENST00000285850.7_Splice_Site_p.I166I|SLC7A7_ENST00000397528.4_Splice_Site_p.I166I|SLC7A7_ENST00000554517.1_Intron|SLC7A7_ENST00000397529.2_Splice_Site_p.I166I			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7	166					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)		CCCACTTACAAATGCAGGCAG	0.577													G|||	2915	0.582069	0.4939	0.6758	5008	,	,		11733	0.7847		0.5189	False		,,,				2504	0.4908				p.I166I		Atlas-SNP	.											.	SLC7A7	36	.	0			c.T498C						PASS	.	G	,,	2053,2347		483,1087,630	31.0	31.0	31.0		498,498,498	3.9	1.0	14	dbSNP_116	31	4535,4049		1220,2095,977	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SLC7A7	NM_001126105.2,NM_001126106.2,NM_003982.3	,,	1703,3182,1607	GG,GA,AA		47.1692,46.6591,49.2606	,,	166/512,166/512,166/512	23282110	6588,6396	2200	4292	6492	SO:0001630	splice_region_variant	9056	exon3			CTTACAAATGCAG	AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"""Solute carriers"""	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692	ENST00000397532.3:c.499+1T>C	14.37:g.23282110A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001126105	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Silent	SNP	ENST00000397532.3	37	CCDS9574.1																																																																																			A|0.461;G|0.539	0.539	strong		0.577	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3		Silent
NECAB2	54550	hgsc.bcm.edu	37	16	84012104	84012104	+	Silent	SNP	T	T	C	rs925331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84012104T>C	ENST00000305202.4	+	3	299	c.282T>C	c.(280-282)ctT>ctC	p.L94L	NECAB2_ENST00000565691.1_Missense_Mutation_p.L20S	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	94	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.|EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						ATGGCGTCCTTAATGAGAAAG	0.512													C|||	1641	0.327676	0.7988	0.2262	5008	,	,		21000	0.1181		0.1163	False		,,,				2504	0.1963				p.L94L		Atlas-SNP	.											.	NECAB2	36	.	0			c.T282C						PASS	.	C		3051,1349	448.5+/-348.7	1060,931,209	156.0	139.0	145.0		282	0.5	0.5	16	dbSNP_86	145	911,7689	778.0+/-407.7	63,785,3452	yes	coding-synonymous	NECAB2	NM_019065.2		1123,1716,3661	CC,CT,TT		10.593,30.6591,30.4769		94/387	84012104	3962,9038	2200	4300	6500	SO:0001819	synonymous_variant	54550	exon3			CGTCCTTAATGAG	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.282T>C	16.37:g.84012104T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	59	33	0.559322	NM_019065	A2RRG3|O75547|Q6ZSK0	Silent	SNP	ENST00000305202.4	37	CCDS10940.1																																																																																			T|0.692;C|0.308	0.308	strong		0.512	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
DTYMK	1841	hgsc.bcm.edu	37	2	242618050	242618050	+	Silent	SNP	A	A	G	rs1131195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:242618050A>G	ENST00000305784.2	-	4	552	c.345T>C	c.(343-345)gaT>gaC	p.D115D		NM_001165031.1|NM_012145.3	NP_001158503.1|NP_036277.2	P23919	KTHY_HUMAN	deoxythymidylate kinase (thymidylate kinase)	115					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|cellular response to growth factor stimulus (GO:0071363)|dTDP biosynthetic process (GO:0006233)|dTTP biosynthetic process (GO:0006235)|myoblast differentiation (GO:0045445)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside monophosphate phosphorylation (GO:0046940)|nucleotide phosphorylation (GO:0046939)|response to cadmium ion (GO:0046686)|response to estrogen (GO:0043627)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|nucleoside phosphate kinase activity (GO:0050145)|thymidylate kinase activity (GO:0004798)			NS(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		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;1.6e-33)|all cancers(36;3.57e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.23e-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)		GTTTACACCAATCTAGGGAAA	0.488													A|||	1703	0.340056	0.357	0.5	5008	,	,		17644	0.1994		0.4324	False		,,,				2504	0.2536				p.D115D		Atlas-SNP	.											.	DTYMK	9	.	0			c.T345C						PASS	.	A	,	1510,2896	478.8+/-358.3	252,1006,945	40.0	47.0	45.0		,345	-5.3	0.7	2	dbSNP_86	45	3658,4934	521.5+/-379.9	806,2046,1444	no	intron,coding-synonymous	DTYMK	NM_001165031.1,NM_012145.3	,	1058,3052,2389	GG,GA,AA		42.5745,34.2714,39.76	,	,115/213	242618050	5168,7830	2203	4296	6499	SO:0001819	synonymous_variant	1841	exon4			ACACCAATCTAGG	X54729	CCDS2552.1	2q37	2008-02-05			ENSG00000168393	ENSG00000168393	2.7.4.9		3061	protein-coding gene	gene with protein product	"""dTMP kinase"", ""thymidylate (dTMP) kinase"""	188345				2017365, 8024690	Standard	NM_001165031		Approved	CDC8, TYMK, TMPK	uc002wbz.2	P23919	OTTHUMG00000133409	ENST00000305784.2:c.345T>C	2.37:g.242618050A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_012145	B7ZW70|Q6FGX1|Q9BUX4	Silent	SNP	ENST00000305784.2	37	CCDS2552.1	783	0.3585164835164835	176	0.35772357723577236	175	0.48342541436464087	112	0.1958041958041958	320	0.42216358839050133	A	1.800	-0.477370	0.04414	0.342714	0.425745	ENSG00000168393	ENST00000420144	.	.	.	5.35	-5.33	0.02713	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999672201	.	.	.	.	.	.	T	0.43669	-0.9377	3	.	.	.	-24.1626	5.232	0.15426	0.5787:0.1843:0.1573:0.0798	rs1131195;rs1803264;rs3190874;rs4675906;rs17413605;rs17572987;rs17849537	.	.	.	T	111	.	.	I	-	2	0	DTYMK	242266723	0.003000	0.15002	0.743000	0.31040	0.340000	0.28889	-1.710000	0.01888	-1.261000	0.02462	-0.290000	0.09829	ATT	A|0.622;G|0.378	0.378	strong		0.488	DTYMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257266.2	NM_012145	
VARS2	57176	hgsc.bcm.edu	37	6	30890483	30890483	+	Splice_Site	SNP	G	G	T	rs2074506	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30890483G>T	ENST00000321897.5	+	21	2670	c.2038G>T	c.(2038-2040)Gtg>Ttg	p.V680L	VARS2_ENST00000541562.1_Splice_Site_p.V710L|VARS2_ENST00000542001.1_Splice_Site_p.V540L|VARS2_ENST00000416670.2_Splice_Site_p.V680L|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	680			V -> L (in dbSNP:rs2074506). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CCATCCCCAGGTGCTGCAGGA	0.612													G|||	1112	0.222045	0.0983	0.2075	5008	,	,		17917	0.247		0.3559	False		,,,				2504	0.2362				p.V710L		Atlas-SNP	.											.	VARS2	60	.	0			c.G2128T						PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL	440,2578		34,372,1103	37.0	40.0	39.0		1618,2128,2038	5.3	1.0	6	dbSNP_96	39	2039,3375		365,1309,1033	yes	missense-near-splice,missense-near-splice,missense-near-splice	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	32,32,32	399,1681,2136	TT,TG,GG		37.6616,14.5792,29.3999	possibly-damaging,possibly-damaging,possibly-damaging	540/924,710/1094,680/1064	30890483	2479,5953	1509	2707	4216	SO:0001630	splice_region_variant	57176	exon22			CCCCAGGTGCTGC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2038-1G>T	6.37:g.30890483G>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	530	0.24267399267399267	31	0.06300813008130081	74	0.20441988950276244	162	0.28321678321678323	263	0.3469656992084433	G	12.84	2.057783	0.36277	0.145792	0.376616	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.06449	3.56;3.56;3.3;3.55	5.31	5.31	0.75309	Aminoacyl-tRNA synthetase, class Ia (1);	0.292747	0.37178	N	0.002216	T	0.03348	0.0097	L	0.31664	0.95	0.09310	P	0.9999999999999999	P;B;B	0.37423	0.594;0.001;0.001	B;B;B	0.38842	0.283;0.005;0.008	T	0.48198	-0.9056	9	0.42905	T	0.14	-12.41	16.4624	0.84064	0.0:0.0:1.0:0.0	rs2074506;rs3998498;rs17776725;rs52796508;rs59650369;rs2074506	118;710;680	Q5ST30-2;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	L	680;680;540;710	ENSP00000316092:V680L;ENSP00000394802:V680L;ENSP00000438200:V540L;ENSP00000441000:V710L	ENSP00000316092:V680L	V	+	1	0	VARS2	30998462	1.000000	0.71417	1.000000	0.80357	0.842000	0.47809	3.911000	0.56378	2.505000	0.84491	0.561000	0.74099	GTG	G|0.734;T|0.266	0.266	strong		0.612	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	Missense_Mutation
CMTR2	55783	hgsc.bcm.edu	37	16	71318577	71318577	+	Missense_Mutation	SNP	T	T	C	rs3803704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:71318577T>C	ENST00000338099.5	-	3	1583	c.1247A>G	c.(1246-1248)aAt>aGt	p.N416S	CMTR2_ENST00000434935.2_Missense_Mutation_p.N416S			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	416			N -> S (in dbSNP:rs3803704). {ECO:0000269|PubMed:14702039}.		7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TAGCCAATTATTTCTGGAAAG	0.308													T|||	1392	0.277955	0.2852	0.4784	5008	,	,		19429	0.2103		0.2485	False		,,,				2504	0.226				p.N416S		Atlas-SNP	.											FTSJD1,NS,carcinoma,0,1	FTSJD1	70	1	0			c.A1247G						PASS	.	T	SER/ASN,SER/ASN	1132,3258		165,802,1228	29.0	31.0	30.0		1247,1247	2.5	1.0	16	dbSNP_107	30	2152,6412		279,1594,2409	yes	missense,missense	FTSJD1	NM_001099642.1,NM_018348.5	46,46	444,2396,3637	CC,CT,TT		25.1284,25.7859,25.3512	benign,benign	416/771,416/771	71318577	3284,9670	2195	4282	6477	SO:0001583	missense	55783	exon3			CAATTATTTCTGG	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.1247A>G	16.37:g.71318577T>C	ENSP00000337512:p.Asn416Ser	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	128	71	0.554688	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	643	0.2944139194139194	149	0.30284552845528456	164	0.4530386740331492	132	0.23076923076923078	198	0.2612137203166227	T	0.906	-0.720809	0.03182	0.257859	0.251284	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.13307	2.6;2.6	5.95	2.53	0.30540	.	0.329703	0.36200	N	0.002739	T	0.00012	0.0000	L	0.46157	1.445	0.33937	P	0.35721899999999995	B	0.06786	0.001	B	0.06405	0.002	T	0.46303	-0.9201	9	0.11794	T	0.64	0.0132	8.9128	0.35563	0.0:0.2118:0.0:0.7882	rs3803704;rs52799996;rs60429579;rs3803704	416	Q8IYT2	FTSJ1_HUMAN	S	416	ENSP00000337512:N416S;ENSP00000411148:N416S	ENSP00000337512:N416S	N	-	2	0	FTSJD1	69876078	0.994000	0.37717	1.000000	0.80357	0.989000	0.77384	0.147000	0.16202	0.503000	0.28060	0.402000	0.26972	AAT	T|0.735;C|0.265	0.265	strong		0.308	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
KMT2C	58508	hgsc.bcm.edu	37	7	151932990	151932990	+	Missense_Mutation	SNP	C	C	T	rs76844681		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151932990C>T	ENST00000262189.6	-	16	2899	c.2681G>A	c.(2680-2682)cGg>cAg	p.R894Q	KMT2C_ENST00000355193.2_Missense_Mutation_p.R894Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	894					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TCGAGGTCTCCGCTTTCCTGG	0.502																																					p.R894Q		Atlas-SNP	.											MLL3_ENST00000355193,NS,malignant_melanoma,+1,4	MLL3	1564	4	0			c.G2681A						scavenged	.						33.0	34.0	33.0					7																	151932990		2202	4295	6497	SO:0001583	missense	58508	exon16			GGTCTCCGCTTTC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2681G>A	7.37:g.151932990C>T	ENSP00000262189:p.Arg894Gln	Somatic	147	1	0.00680272		WXS	Illumina HiSeq	Phase_I	117	12	0.102564	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.710284	0.89018	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.89485	-2.5;-2.52	5.1	5.1	0.69264	.	0.000000	0.42294	D	0.000721	D	0.93314	0.7869	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.93742	0.7051	10	0.66056	D	0.02	.	17.0444	0.86498	0.0:1.0:0.0:0.0	.	894	Q8NEZ4	MLL3_HUMAN	Q	894	ENSP00000262189:R894Q;ENSP00000347325:R894Q	ENSP00000262189:R894Q	R	-	2	0	MLL3	151563923	1.000000	0.71417	0.996000	0.52242	0.951000	0.60555	7.268000	0.78473	2.530000	0.85305	0.650000	0.86243	CGG	C|0.999;T|0.001	0.001	weak		0.502	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
RALGAPA2	57186	hgsc.bcm.edu	37	20	20565512	20565512	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:20565512T>A	ENST00000202677.7	-	19	2534	c.2527A>T	c.(2527-2529)Aag>Tag	p.K843*		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	843					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						AACTTACTCTTCTGTCTTTCC	0.358																																					p.K843X		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.A2527T						PASS	.						155.0	153.0	154.0					20																	20565512		1833	4097	5930	SO:0001587	stop_gained	57186	exon19			TACTCTTCTGTCT	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.2527A>T	20.37:g.20565512T>A	ENSP00000202677:p.Lys843*	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	75	36	0.48	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Nonsense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	38|38	7.167061|7.167061	0.98107|0.98107	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000202677|ENST00000430436	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.301070|.	0.35291|.	N|.	0.003317|.	.|T	.|0.64811	.|0.2632	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71130	.|-0.4682	.|3	0.02654|.	T|.	1|.	.|.	13.4407|13.4407	0.61112|0.61112	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|S	843|659	.|.	ENSP00000202677:K843X|.	K|R	-|-	1|3	0|2	RALGAPA2|RALGAPA2	20513512|20513512	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.124000|0.124000	0.20399|0.20399	4.597000|4.597000	0.61062|0.61062	2.217000|2.217000	0.71921|0.71921	0.482000|0.482000	0.46254|0.46254	AAG|AGA	.	.	none		0.358	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
VLDLR	7436	hgsc.bcm.edu	37	9	2644799	2644799	+	Missense_Mutation	SNP	T	T	C	rs142885301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:2644799T>C	ENST00000382100.3	+	8	1488	c.1132T>C	c.(1132-1134)Tac>Cac	p.Y378H	VLDLR_ENST00000382099.2_Missense_Mutation_p.Y378H	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	378	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		AGTTATAGGCTACGAGTGTGA	0.413																																					p.Y378H		Atlas-SNP	.											.	VLDLR	68	.	0			c.T1132C						PASS	.	T	HIS/TYR,HIS/TYR	1,4405	2.1+/-5.4	0,1,2202	95.0	95.0	95.0		1132,1132	5.8	1.0	9	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	VLDLR	NM_001018056.1,NM_003383.3	83,83	0,2,6501	CC,CT,TT		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	378/846,378/874	2644799	2,13004	2203	4300	6503	SO:0001583	missense	7436	exon8			ATAGGCTACGAGT		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"""Low density lipoprotein receptors"""	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.1132T>C	9.37:g.2644799T>C	ENSP00000371532:p.Tyr378His	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.797534	0.90538	2.27E-4	1.16E-4	ENSG00000147852	ENST00000382100;ENST00000382099;ENST00000382092	D;D	0.96913	-4.17;-4.17	5.83	5.83	0.93111	Growth factor, receptor (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.48286	D	0.000194	D	0.97046	0.9035	L	0.52573	1.65	0.53688	D	0.999971	D;D;D	0.57257	0.979;0.964;0.964	D;P;P	0.65874	0.939;0.87;0.87	D	0.96766	0.9565	10	0.39692	T	0.17	.	16.1968	0.82036	0.0:0.0:0.0:1.0	.	378;378;378	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	H	378;378;257	ENSP00000371532:Y378H;ENSP00000371531:Y378H	ENSP00000371524:Y257H	Y	+	1	0	VLDLR	2634799	1.000000	0.71417	0.967000	0.41034	0.975000	0.68041	5.983000	0.70540	2.225000	0.72522	0.533000	0.62120	TAC	T|0.999;C|0.001	0.001	strong		0.413	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383	
TIMM17A	10440	hgsc.bcm.edu	37	1	201934578	201934578	+	Missense_Mutation	SNP	G	G	A	rs4648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201934578G>A	ENST00000367287.4	+	5	373	c.337G>A	c.(337-339)Gtt>Att	p.V113I	TIMM17A_ENST00000482943.1_3'UTR	NM_006335.2	NP_006326.1	Q99595	TI17A_HUMAN	translocase of inner mitochondrial membrane 17 homolog A (yeast)	113			V -> I (in dbSNP:rs4648).		cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial inner membrane presequence translocase complex (GO:0005744)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)	p.V113I(1)		kidney(1)|lung(3)|stomach(1)	5						AGTGGCCATGGTTGGGTCAGC	0.408													G|||	308	0.0615016	0.0348	0.0793	5008	,	,		17451	0.0377		0.0855	False		,,,				2504	0.0849				p.V113I		Atlas-SNP	.											TIMM17A,NS,carcinoma,0,1	TIMM17A	17	1	1	Substitution - Missense(1)	stomach(1)	c.G337A						PASS	.	G	ILE/VAL	203,4203	125.7+/-162.9	5,193,2005	120.0	119.0	120.0		337	5.4	1.0	1	dbSNP_52	120	785,7815	184.5+/-232.4	38,709,3553	yes	missense	TIMM17A	NM_006335.2	29	43,902,5558	AA,AG,GG		9.1279,4.6074,7.5965	possibly-damaging	113/172	201934578	988,12018	2203	4300	6503	SO:0001583	missense	10440	exon5			GCCATGGTTGGGT	AF106622	CCDS1417.1	1q32.1	2008-05-23			ENSG00000134375	ENSG00000134375			17315	protein-coding gene	gene with protein product		605057				8893850, 10339406	Standard	NM_006335		Approved	TIM17, TIM17A	uc001gxc.3	Q99595	OTTHUMG00000035806	ENST00000367287.4:c.337G>A	1.37:g.201934578G>A	ENSP00000356256:p.Val113Ile	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	186	79	0.424731	NM_006335	B2RDM5|Q9BWF5	Missense_Mutation	SNP	ENST00000367287.4	37	CCDS1417.1	134	0.06135531135531135	17	0.034552845528455285	30	0.08287292817679558	24	0.04195804195804196	63	0.08311345646437995	G	15.88	2.962682	0.53507	0.046074	0.091279	ENSG00000134375	ENST00000367287	T	0.30448	1.53	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.01092	0.0036	L	0.32530	0.975	0.09310	P	0.9999999863806	P	0.34546	0.456	B	0.39706	0.307	T	0.06303	-1.0834	9	0.25106	T	0.35	-9.3561	16.9249	0.86173	0.0:0.0:1.0:0.0	rs4648;rs1139869;rs11555425;rs17341773;rs17353525;rs34611715;rs56531632;rs34611715	113	Q99595	TI17A_HUMAN	I	113	ENSP00000356256:V113I	ENSP00000356256:V113I	V	+	1	0	TIMM17A	200201201	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.121000	0.71602	2.663000	0.90544	0.655000	0.94253	GTT	G|0.929;A|0.071	0.071	strong		0.408	TIMM17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087092.1	NM_006335	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77325325	77325325	+	Missense_Mutation	SNP	G	G	T	rs35478105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:77325325G>T	ENST00000282849.5	-	21	3658	c.3240C>A	c.(3238-3240)agC>agA	p.S1080R	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1080	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		S -> R (in dbSNP:rs35478105). {ECO:0000269|PubMed:14702039}.		eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S1080R(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						AGCCCTTCTCGCTGCACTTCA	0.498													G|||	1141	0.227835	0.0303	0.245	5008	,	,		21167	0.1101		0.5159	False		,,,				2504	0.3078				p.S1080R		Atlas-SNP	.											ADAMTS18,NS,carcinoma,0,1	ADAMTS18	270	1	1	Substitution - Missense(1)	stomach(1)	c.C3240A						PASS	.	G	ARG/SER	525,3871	238.7+/-250.0	33,459,1706	211.0	213.0	213.0		3240	-4.8	0.9	16	dbSNP_126	213	4260,4340	573.4+/-389.9	1045,2170,1085	yes	missense	ADAMTS18	NM_199355.2	110	1078,2629,2791	TT,TG,GG		49.5349,11.9427,36.819	possibly-damaging	1080/1222	77325325	4785,8211	2198	4300	6498	SO:0001583	missense	170692	exon21			CTTCTCGCTGCAC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3240C>A	16.37:g.77325325G>T	ENSP00000282849:p.Ser1080Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	597	0.2733516483516483	19	0.03861788617886179	103	0.2845303867403315	79	0.1381118881118881	396	0.5224274406332454	G	16.99	3.274610	0.59649	0.119427	0.495349	ENSG00000140873	ENST00000282849	T	0.53857	0.6	5.8	-4.75	0.03239	.	0.275715	0.40469	N	0.001099	T	0.00012	0.0000	N	0.13198	0.31	0.45704	P	0.0013840000000000519	B	0.27765	0.188	B	0.31191	0.125	T	0.39702	-0.9601	9	0.14656	T	0.56	.	10.3361	0.43850	0.6058:0.0983:0.2959:0.0	rs35478105;rs61749043	1080	Q8TE60	ATS18_HUMAN	R	1080	ENSP00000282849:S1080R	ENSP00000282849:S1080R	S	-	3	2	ADAMTS18	75882826	0.036000	0.19791	0.928000	0.36995	0.846000	0.48090	-0.545000	0.06069	-0.629000	0.05575	-0.253000	0.11424	AGC	G|0.665;T|0.335	0.335	strong		0.498	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
FNDC9	408263	hgsc.bcm.edu	37	5	156770133	156770133	+	Missense_Mutation	SNP	C	C	T	rs10037485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:156770133C>T	ENST00000312349.4	-	2	599	c.412G>A	c.(412-414)Gtc>Atc	p.V138I	CYFIP2_ENST00000541131.1_Intron|CYFIP2_ENST00000442283.2_Intron|CYFIP2_ENST00000318218.6_Intron|CYFIP2_ENST00000522463.1_Intron|CYFIP2_ENST00000435847.2_Intron|CYFIP2_ENST00000347377.6_Intron|CYFIP2_ENST00000521420.1_Intron|CYFIP2_ENST00000377576.3_Intron	NM_001001343.3	NP_001001343.2	Q8TBE3	FNDC9_HUMAN	fibronectin type III domain containing 9	138			V -> I (in dbSNP:rs10037485).			integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	9						TGGCAACGGACACACCAGAAC	0.607											OREG0016977	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	926	0.184904	0.379	0.1499	5008	,	,		19536	0.006		0.2048	False		,,,				2504	0.1115				p.V138I		Atlas-SNP	.											.	FNDC9	22	.	0			c.G412A						PASS	.	C	ILE/VAL,,,	1515,2891	480.6+/-358.9	263,989,951	63.0	61.0	62.0		412,,,	-3.8	1.0	5	dbSNP_119	62	1873,6727	332.9+/-320.3	198,1477,2625	yes	missense,intron,intron,intron	CYFIP2,FNDC9	NM_001001343.3,NM_001037332.2,NM_001037333.1,NM_014376.2	29,,,	461,2466,3576	TT,TC,CC		21.7791,34.3849,26.0495	benign,,,	138/225,,,	156770133	3388,9618	2203	4300	6503	SO:0001583	missense	408263	exon2			AACGGACACACCA	BC022570	CCDS4337.1	5q33.3	2013-02-11	2011-01-25	2011-01-25	ENSG00000172568	ENSG00000172568		"""Fibronectin type III domain containing"""	33547	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 40"""	C5orf40			Standard	NM_001001343		Approved	MGC27121	uc003lwu.2	Q8TBE3	OTTHUMG00000130248	ENST00000312349.4:c.412G>A	5.37:g.156770133C>T	ENSP00000310594:p.Val138Ile	Somatic	107	0	0	1781	WXS	Illumina HiSeq	Phase_I	97	97	1	NM_001001343	A8K0Y6	Missense_Mutation	SNP	ENST00000312349.4	37	CCDS4337.1	391	0.17902930402930403	177	0.3597560975609756	58	0.16022099447513813	3	0.005244755244755245	153	0.20184696569920843	C	2.095	-0.407568	0.04832	0.343849	0.217791	ENSG00000172568	ENST00000312349;ENST00000520782	T;T	0.64438	-0.1;-0.1	4.98	-3.79	0.04320	.	0.869052	0.09919	N	0.738787	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	0.33523	-0.9865	9	0.09843	T	0.71	-25.0468	1.7212	0.02912	0.1406:0.3395:0.2868:0.2332	rs10037485;rs52826537;rs10037485	138	Q8TBE3	FNDC9_HUMAN	I	138	ENSP00000310594:V138I;ENSP00000429434:V138I	ENSP00000310594:V138I	V	-	1	0	FNDC9	156702711	0.000000	0.05858	0.987000	0.45799	0.658000	0.38924	-0.750000	0.04808	-0.056000	0.13221	-0.339000	0.08088	GTC	C|0.765;T|0.235	0.235	strong		0.607	FNDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252573.2	NM_001001343	
DBH	1621	hgsc.bcm.edu	37	9	136518097	136518097	+	Silent	SNP	A	A	G	rs77905	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136518097A>G	ENST00000393056.2	+	9	1422	c.1410A>G	c.(1408-1410)acA>acG	p.T470T	DBH-AS1_ENST00000425189.1_RNA	NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	470					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)	p.T470T(1)		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)	CGTACAACACAGAAGACCGGG	0.612													G|||	3111	0.621206	0.5703	0.5937	5008	,	,		19413	0.9038		0.5199	False		,,,				2504	0.5225				p.T470T		Atlas-SNP	.											DBH,NS,carcinoma,0,2	DBH	86	2	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A1410G						PASS	.	G		2522,1884	542.8+/-376.1	710,1102,391	122.0	100.0	107.0		1410	-1.4	0.6	9	dbSNP_78	107	4312,4288	576.8+/-390.5	1082,2148,1070	no	coding-synonymous	DBH	NM_000787.3		1792,3250,1461	GG,GA,AA		49.8605,42.7599,47.455		470/618	136518097	6834,6172	2203	4300	6503	SO:0001819	synonymous_variant	1621	exon9			CAACACAGAAGAC	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.1410A>G	9.37:g.136518097A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_000787	Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	37	CCDS6977.2																																																																																			G|0.581;N|0.000	0.581	strong		0.612	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
RAB11FIP4	84440	hgsc.bcm.edu	37	17	29857460	29857460	+	Silent	SNP	G	G	A	rs61731602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:29857460G>A	ENST00000325874.8	+	14	1999	c.1770G>A	c.(1768-1770)gcG>gcA	p.A590A	RAB11FIP4_ENST00000394744.2_Silent_p.A488A	NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	590	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.|Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				CTCTGGCTGCGGAGATAGACA	0.592													G|||	457	0.091254	0.0113	0.2003	5008	,	,		17485	0.0833		0.174	False		,,,				2504	0.045				p.A590A		Atlas-SNP	.											.	RAB11FIP4	65	.	0			c.G1770A						PASS	.	G		152,4254	104.3+/-142.8	6,140,2057	88.0	89.0	88.0		1770	-10.9	0.7	17	dbSNP_129	88	1406,7194	269.7+/-288.6	120,1166,3014	no	coding-synonymous	RAB11FIP4	NM_032932.3		126,1306,5071	AA,AG,GG		16.3488,3.4498,11.9791		590/638	29857460	1558,11448	2203	4300	6503	SO:0001819	synonymous_variant	84440	exon14			GGCTGCGGAGATA	AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"""EF-hand domain containing"""	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.1770G>A	17.37:g.29857460G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_032932	Q52LI1|Q8N829|Q8NDT7|Q969D8	Silent	SNP	ENST00000325874.8	37	CCDS11267.1																																																																																			G|0.878;A|0.122	0.122	strong		0.592	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932	
SP140L	93349	hgsc.bcm.edu	37	2	231258150	231258150	+	Missense_Mutation	SNP	C	C	T	rs7590429	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231258150C>T	ENST00000415673.2	+	13	1215	c.1129C>T	c.(1129-1131)Cca>Tca	p.P377S	SP140L_ENST00000243810.6_Missense_Mutation_p.P377S|SP140L_ENST00000396563.4_Missense_Mutation_p.P342S|SP140L_ENST00000444636.1_Missense_Mutation_p.P377S	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	377			P -> S (in dbSNP:rs7590429).			nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						ACCTAATCCTCCAAGAATATA	0.353													C|||	2087	0.416733	0.4811	0.3919	5008	,	,		19709	0.2143		0.4404	False		,,,				2504	0.5317				p.P377S		Atlas-SNP	.											.	SP140L	68	.	0			c.C1129T						PASS	.	C	SER/PRO	1657,2025		374,909,558	64.0	63.0	63.0		1129	2.1	0.1	2	dbSNP_116	63	3556,4600		781,1994,1303	yes	missense	SP140L	NM_138402.4	74	1155,2903,1861	TT,TC,CC		43.5998,45.0027,44.0362	benign	377/581	231258150	5213,6625	1841	4078	5919	SO:0001583	missense	93349	exon13			AATCCTCCAAGAA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.1129C>T	2.37:g.231258150C>T	ENSP00000397911:p.Pro377Ser	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	50	17	0.34	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	812	0.3717948717948718	223	0.4532520325203252	131	0.36187845303867405	133	0.23251748251748253	325	0.4287598944591029	C	8.266	0.812214	0.16537	0.450027	0.435998	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	3.94	2.13	0.27403	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B;B	0.27625	0.183;0.089	B;B	0.32393	0.145;0.068	T	0.41645	-0.9497	8	0.38643	T	0.18	.	6.5031	0.22180	0.0:0.7764:0.0:0.2236	rs7590429;rs52792690;rs56807857;rs7590429	342;377	Q9H930-2;Q9H930-4	.;.	S	377;377;377;342	ENSP00000395195:P377S;ENSP00000397911:P377S;ENSP00000243810:P377S;ENSP00000379811:P342S	ENSP00000243810:P377S	P	+	1	0	SP140L	230966394	0.081000	0.21417	0.055000	0.19348	0.004000	0.04260	1.716000	0.37981	0.436000	0.26393	-0.966000	0.02617	CCA	C|0.605;T|0.395	0.395	strong		0.353	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
FKBP5	2289	hgsc.bcm.edu	37	6	35544942	35544942	+	Silent	SNP	G	G	A	rs34866878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35544942G>A	ENST00000539068.1	-	10	1297	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	FKBP5_ENST00000536438.1_Silent_p.N365N|FKBP5_ENST00000357266.4_Silent_p.N365N|FKBP5_ENST00000540787.1_Silent_p.N186N	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	365					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						ACTCAAACTCGTTCATGAGCA	0.483													G|||	334	0.0666933	0.2239	0.0245	5008	,	,		18453	0.001		0.0179	False		,,,				2504	0.002				p.N365N		Atlas-SNP	.											.	FKBP5	64	.	0			c.C1095T						PASS	.	G	,,	815,3591	326.1+/-299.4	68,679,1456	161.0	154.0	156.0		1095,1095,1095	-3.6	0.8	6	dbSNP_126	156	225,8375	92.8+/-154.8	5,215,4080	no	coding-synonymous,coding-synonymous,coding-synonymous	FKBP5	NM_001145775.1,NM_001145776.1,NM_004117.3	,,	73,894,5536	AA,AG,GG		2.6163,18.4975,7.9963	,,	365/458,365/458,365/458	35544942	1040,11966	2203	4300	6503	SO:0001819	synonymous_variant	2289	exon11			AAACTCGTTCATG	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"""Tetratricopeptide (TTC) repeat domain containing"""	3721	protein-coding gene	gene with protein product		602623	"""FK506-binding protein 5"""			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.1095C>T	6.37:g.35544942G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	168	90	0.535714	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	37	CCDS4808.1																																																																																			G|0.928;A|0.072	0.072	strong		0.483	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2		
TCP10L2	401285	hgsc.bcm.edu	37	6	167592601	167592601	+	Missense_Mutation	SNP	G	G	A	rs200019718	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167592601G>A	ENST00000366832.2	+	6	891	c.760G>A	c.(760-762)Gga>Aga	p.G254R		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	254										endometrium(1)|kidney(2)|lung(3)	6						GGCAGCAGCCGGAGTTGCTGG	0.577																																					p.G254R		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G760A						PASS	.																																			SO:0001583	missense	401285	exon6			GCAGCCGGAGTTG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.760G>A	6.37:g.167592601G>A	ENSP00000355797:p.Gly254Arg	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	60	18	0.3	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	.	.	.	.	.	.	.	.	.	.	g	7.547	0.661865	0.14645	.	.	ENSG00000166984	ENST00000366832	T	0.41065	1.01	.	.	.	.	.	.	.	.	T	0.20981	0.0505	N	0.24115	0.695	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.13522	-1.0506	7	0.06891	T	0.86	.	.	.	.	.	254	B9ZVM9	TCP2L_HUMAN	R	254	ENSP00000355797:G254R	ENSP00000283507:G254R	G	+	1	0	TCP10L2	167512591	0.001000	0.12720	0.002000	0.10522	0.027000	0.11550	0.333000	0.19768	0.159000	0.19401	0.162000	0.16502	GGA	G|0.941;A|0.059	0.059	strong		0.577	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
INCENP	3619	hgsc.bcm.edu	37	11	61908440	61908440	+	Missense_Mutation	SNP	T	T	C	rs2277283	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:61908440T>C	ENST00000394818.3	+	10	1719	c.1517T>C	c.(1516-1518)aTg>aCg	p.M506T	INCENP_ENST00000278849.4_Missense_Mutation_p.M506T	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	506			M -> T (in dbSNP:rs2277283).		chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CAGATGCTCATGACCCCGACC	0.642													T|||	853	0.170327	0.1498	0.1916	5008	,	,		19216	0.0744		0.3002	False		,,,				2504	0.1483				p.M506T		Atlas-SNP	.											.	INCENP	122	.	0			c.T1517C						PASS	.	T	THR/MET,THR/MET	777,3627	310.8+/-291.8	67,643,1492	77.0	76.0	77.0		1517,1517	5.5	1.0	11	dbSNP_100	77	2670,5928	428.7+/-356.0	422,1826,2051	yes	missense,missense	INCENP	NM_001040694.1,NM_020238.2	81,81	489,2469,3543	CC,CT,TT		31.0537,17.6431,26.5113	probably-damaging,probably-damaging	506/919,506/915	61908440	3447,9555	2202	4299	6501	SO:0001583	missense	3619	exon10			TGCTCATGACCCC	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1517T>C	11.37:g.61908440T>C	ENSP00000378295:p.Met506Thr	Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	178	177	0.994382	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	440	0.20146520146520147	79	0.16056910569105692	79	0.21823204419889503	39	0.06818181818181818	243	0.32058047493403696	T	15.33	2.802715	0.50315	0.176431	0.310537	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.39997	1.05;1.05	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000004	T	0.00012	0.0000	L	0.57536	1.79	0.21184	P	0.9997604	P;D;D	0.76494	0.568;0.999;0.998	P;D;D	0.77557	0.472;0.99;0.977	T	0.16364	-1.0405	9	0.35671	T	0.21	.	13.5006	0.61452	0.0:0.0:0.0:1.0	rs2277283;rs17707972	506;506;506	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	T	506	ENSP00000378295:M506T;ENSP00000278849:M506T	ENSP00000278849:M506T	M	+	2	0	INCENP	61665016	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.826000	0.75298	2.081000	0.62600	0.533000	0.62120	ATG	T|0.764;C|0.236;A|0.000	0.236	strong		0.642	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
CLCA2	9635	hgsc.bcm.edu	37	1	86904588	86904588	+	Silent	SNP	C	C	T	rs11161830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:86904588C>T	ENST00000370565.4	+	7	1164	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	334	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TACAACAAGCCGCAGAATTTT	0.398													C|||	546	0.109026	0.1679	0.111	5008	,	,		20635	0.0546		0.0944	False		,,,				2504	0.0992				p.A334A	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C1002T						PASS	.	C		752,3654	307.2+/-289.9	68,616,1519	83.0	85.0	84.0		1002	0.9	1.0	1	dbSNP_120	84	708,7892	174.2+/-224.5	30,648,3622	no	coding-synonymous	CLCA2	NM_006536.5		98,1264,5141	TT,TC,CC		8.2326,17.0676,11.2256		334/944	86904588	1460,11546	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon7			ACAAGCCGCAGAA		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1002C>T	1.37:g.86904588C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			C|0.892;T|0.108	0.108	strong		0.398	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
OAS3	4940	hgsc.bcm.edu	37	12	113398974	113398974	+	Silent	SNP	C	C	T	rs141839417	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113398974C>T	ENST00000228928.7	+	8	1935	c.1756C>T	c.(1756-1758)Ctg>Ttg	p.L586L	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	586	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						CTTCGCAGAGCTGCGGAGGAA	0.592													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18585	0.0		0.003	False		,,,				2504	0.001				p.L586L		Atlas-SNP	.											.	OAS3	63	.	0			c.C1756T						PASS	.	C		3,4031		0,3,2014	57.0	60.0	59.0		1756	3.8	0.8	12	dbSNP_134	59	32,8344		0,32,4156	no	coding-synonymous	OAS3	NM_006187.2		0,35,6170	TT,TC,CC		0.382,0.0744,0.282		586/1088	113398974	35,12375	2017	4188	6205	SO:0001819	synonymous_variant	4940	exon8			GCAGAGCTGCGGA	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.1756C>T	12.37:g.113398974C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_006187	Q2HJ14|Q9H3P5	Silent	SNP	ENST00000228928.7	37	CCDS44981.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
COL6A2	1292	hgsc.bcm.edu	37	21	47552449	47552449	+	Missense_Mutation	SNP	A	A	C	rs11910483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47552449A>C	ENST00000300527.4	+	28	3147	c.3043A>C	c.(3043-3045)Atc>Ctc	p.I1015L		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	1015	Nonhelical region.		I -> L (in dbSNP:rs11910483).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CGACCGCTTCATCCGCTGGAT	0.697													A|||	106	0.0211661	0.0756	0.0072	5008	,	,		13410	0.0		0.001	False		,,,				2504	0.0				p.I1015L		Atlas-SNP	.											.	COL6A2	351	.	0			c.A3043C						PASS	.	A	LEU/ILE	281,4115		10,261,1927	38.0	32.0	34.0		3043	4.4	1.0	21	dbSNP_120	34	4,8592		0,4,4294	yes	missense	COL6A2	NM_001849.3	5	10,265,6221	CC,CA,AA		0.0465,6.3922,2.1937	possibly-damaging	1015/1020	47552449	285,12707	2198	4298	6496	SO:0001583	missense	1292	exon28			CGCTTCATCCGCT	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.3043A>C	21.37:g.47552449A>C	ENSP00000300527:p.Ile1015Leu	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	40	0.018315018315018316	37	0.07520325203252033	3	0.008287292817679558	0	0.0	0	0.0	A	11.98	1.799818	0.31869	0.063922	4.65E-4	ENSG00000142173	ENST00000300527	T	0.77098	-1.07	4.4	4.4	0.53042	.	0.115804	0.56097	D	0.000028	T	0.16557	0.0398	L	0.53249	1.67	0.80722	D	1	P	0.44690	0.841	P	0.45449	0.481	T	0.49835	-0.8897	10	0.32370	T	0.25	-18.2856	13.6411	0.62251	1.0:0.0:0.0:0.0	rs11910483	1015	P12110	CO6A2_HUMAN	L	1015	ENSP00000300527:I1015L	ENSP00000300527:I1015L	I	+	1	0	COL6A2	46376877	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	2.891000	0.48617	1.628000	0.50416	0.247000	0.18012	ATC	A|0.975;C|0.025	0.025	strong		0.697	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
VPS41	27072	hgsc.bcm.edu	37	7	38765883	38765883	+	Missense_Mutation	SNP	C	C	T	rs1059508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:38765883C>T	ENST00000310301.4	-	29	2582	c.2528G>A	c.(2527-2529)cGt>cAt	p.R843H	VPS41_ENST00000395969.2_Missense_Mutation_p.R818H	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	843			R -> H (in dbSNP:rs1059508).		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						TCCTGGTCCACGGTTCTTAGC	0.363													C|||	26	0.00519169	0.0008	0.0086	5008	,	,		19627	0.0		0.0149	False		,,,				2504	0.0041				p.R843H		Atlas-SNP	.											.	VPS41	102	.	0			c.G2528A						PASS	.	C	HIS/ARG,HIS/ARG	24,4382	29.9+/-59.1	0,24,2179	134.0	121.0	125.0		2528,2453	4.6	1.0	7	dbSNP_86	125	238,8362	96.1+/-157.9	6,226,4068	yes	missense,missense	VPS41	NM_014396.3,NM_080631.3	29,29	6,250,6247	TT,TC,CC		2.7674,0.5447,2.0145	probably-damaging,probably-damaging	843/855,818/830	38765883	262,12744	2203	4300	6503	SO:0001583	missense	27072	exon29			GGTCCACGGTTCT	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.2528G>A	7.37:g.38765883C>T	ENSP00000309457:p.Arg843His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	C	25.2	4.611545	0.87258	0.005447	0.027674	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.22539	1.96;1.95	5.51	4.64	0.57946	.	0.161261	0.56097	D	0.000040	T	0.11495	0.0280	L	0.43152	1.355	0.49389	D	0.999789	D;D;D	0.71674	0.996;0.998;0.998	P;P;P	0.53689	0.732;0.72;0.72	T	0.00496	-1.1705	10	0.52906	T	0.07	-10.0176	13.8427	0.63449	0.0:0.9262:0.0:0.0738	rs1059508;rs3200206;rs52817418;rs56614845;rs1059508	843;818;843	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	H	843;818	ENSP00000309457:R843H;ENSP00000379297:R818H	ENSP00000309457:R843H	R	-	2	0	VPS41	38732408	1.000000	0.71417	0.980000	0.43619	0.991000	0.79684	6.463000	0.73530	1.329000	0.45376	0.650000	0.86243	CGT	C|0.986;T|0.014	0.014	strong		0.363	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
C11orf16	56673	hgsc.bcm.edu	37	11	8947586	8947586	+	Missense_Mutation	SNP	C	C	G	rs11042127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:8947586C>G	ENST00000326053.5	-	5	734	c.628G>C	c.(628-630)Gtc>Ctc	p.V210L	C11orf16_ENST00000528998.1_5'Flank|C11orf16_ENST00000525780.1_Missense_Mutation_p.V210L	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	210			V -> L (in dbSNP:rs11042127). {ECO:0000269|Ref.2}.							central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		ACCGACTGGACCCCACCTAGG	0.502													C|||	1245	0.248602	0.2307	0.2003	5008	,	,		16469	0.377		0.1918	False		,,,				2504	0.2331				p.V210L		Atlas-SNP	.											.	C11orf16	43	.	0			c.G628C						PASS	.	C	LEU/VAL	961,3441	357.9+/-314.1	95,771,1335	75.0	84.0	81.0		628	5.1	0.0	11	dbSNP_120	81	1547,7045	286.3+/-297.7	138,1271,2887	yes	missense	C11orf16	NM_020643.2	32	233,2042,4222	GG,GC,CC		18.0051,21.831,19.3012	probably-damaging	210/468	8947586	2508,10486	2201	4296	6497	SO:0001583	missense	56673	exon5			ACTGGACCCCACC	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.628G>C	11.37:g.8947586C>G	ENSP00000318999:p.Val210Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_020643	Q53FB2|Q8N6Y9	Missense_Mutation	SNP	ENST00000326053.5	37	CCDS7794.1	548	0.2509157509157509	109	0.22154471544715448	79	0.21823204419889503	213	0.3723776223776224	147	0.19393139841688653	C	11.19	1.567084	0.28003	0.21831	0.180051	ENSG00000176029	ENST00000525780;ENST00000326053	T;T	0.25912	1.77;1.77	6.07	5.14	0.70334	.	0.540684	0.17983	N	0.155467	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	B;B	0.28178	0.202;0.202	B;B	0.26202	0.039;0.067	T	0.39722	-0.9600	9	0.40728	T	0.16	-3.3055	15.681	0.77367	0.0:0.8639:0.1361:0.0	rs11042127;rs59695846;rs11042127	210;210	Q9NQ32-2;Q9NQ32	.;CK016_HUMAN	L	210	ENSP00000436818:V210L;ENSP00000318999:V210L	ENSP00000318999:V210L	V	-	1	0	C11orf16	8904162	0.607000	0.26958	0.025000	0.17156	0.196000	0.23810	3.759000	0.55227	1.536000	0.49237	0.655000	0.94253	GTC	C|0.787;G|0.213	0.213	strong		0.502	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907708	12907708	+	Silent	SNP	A	A	G	rs4026149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12907708A>G	ENST00000317869.6	-	2	660	c.435T>C	c.(433-435)cgT>cgC	p.R145R		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	145						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						ATAGACGTTGACGTTTCGAGG	0.483																																					p.R145R		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,-1,1	HNRNPCL1	68	1	0			c.T435C						scavenged	.						120.0	124.0	122.0					1																	12907708		2201	4297	6498	SO:0001819	synonymous_variant	343069	exon2			ACGTTGACGTTTC	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.435T>C	1.37:g.12907708A>G		Somatic	174	25	0.143678		WXS	Illumina HiSeq	Phase_I	204	16	0.0784314	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			A|0.667;G|0.333	0.333	strong		0.483	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
SLC1A5	6510	hgsc.bcm.edu	37	19	47282162	47282162	+	Silent	SNP	G	G	A	rs2070246	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:47282162G>A	ENST00000542575.2	-	5	1456	c.828C>T	c.(826-828)taC>taT	p.Y276Y	SLC1A5_ENST00000434726.2_Silent_p.Y74Y|SLC1A5_ENST00000412532.2_Silent_p.Y48Y|SLC1A5_ENST00000594991.1_Silent_p.Y100Y	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	276					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)	CCACAGGGGCGTACCTGATCA	0.582													G|||	1673	0.334065	0.4463	0.4294	5008	,	,		17783	0.2629		0.2177	False		,,,				2504	0.3078				p.Y276Y		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C828T						PASS	.	G	,,	1896,2510	542.8+/-376.1	408,1080,715	132.0	111.0	118.0		144,222,828	-2.2	0.8	19	dbSNP_96	118	1778,6822	320.3+/-314.5	199,1380,2721	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC1A5	NM_001145144.1,NM_001145145.1,NM_005628.2	,,	607,2460,3436	AA,AG,GG		20.6744,43.0322,28.2485	,,	48/314,74/340,276/542	47282162	3674,9332	2203	4300	6503	SO:0001819	synonymous_variant	6510	exon5			AGGGGCGTACCTG	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.828C>T	19.37:g.47282162G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	40	0.588235	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	37	CCDS12692.1																																																																																			G|0.704;A|0.296	0.296	strong		0.582	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
PFKP	5214	hgsc.bcm.edu	37	10	3150898	3150898	+	Silent	SNP	C	C	T	rs11251721	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:3150898C>T	ENST00000381125.4	+	9	952	c.876C>T	c.(874-876)gtC>gtT	p.V292V	PFKP_ENST00000381075.2_Silent_p.V284V	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	292	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TGCAGCTTGTCGTCACGCAGC	0.562													c|||	692	0.138179	0.1543	0.2075	5008	,	,		17981	0.0536		0.2018	False		,,,				2504	0.089				p.V292V		Atlas-SNP	.											.	PFKP	182	.	0			c.C876T						PASS	.	T	,	704,3702	294.4+/-283.1	65,574,1564	132.0	114.0	120.0		852,876	-5.7	0.1	10	dbSNP_120	120	1731,6869	315.7+/-312.4	172,1387,2741	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	237,1961,4305	TT,TC,CC		20.1279,15.9782,18.7221	,	284/777,292/785	3150898	2435,10571	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon9			GCTTGTCGTCACG	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.876C>T	10.37:g.3150898C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	170	93	0.547059	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																			C|0.826;T|0.174	0.174	strong		0.562	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
DMBT1	1755	hgsc.bcm.edu	37	10	124358498	124358498	+	Missense_Mutation	SNP	T	T	G	rs144489236	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124358498T>G	ENST00000338354.3	+	26	3271	c.3165T>G	c.(3163-3165)atT>atG	p.I1055M	DMBT1_ENST00000368909.3_Missense_Mutation_p.I1055M|DMBT1_ENST00000368955.3_Missense_Mutation_p.I1045M|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368956.2_Missense_Mutation_p.I556M|DMBT1_ENST00000344338.3_Missense_Mutation_p.I1045M|DMBT1_ENST00000330163.4_Missense_Mutation_p.I556M			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1055	SRCR 8. {ECO:0000255|PROSITE- ProRule:PRU00196}.				defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CAGGACCCATTGTCCTGGATG	0.597													t|||	100	0.0199681	0.0023	0.0706	5008	,	,		19043	0.001		0.0427	False		,,,				2504	0.0041				p.I1055M	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	0			c.T3165G						PASS	.	T	MET/ILE,MET/ILE,MET/ILE	22,3952		0,22,1965	148.0	145.0	146.0		1668,3165,3135	-0.3	0.0	10	dbSNP_134	146	259,8081		0,259,3911	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	10,10,10	0,281,5876	GG,GT,TT		3.1055,0.5536,2.282	probably-damaging,probably-damaging,probably-damaging	556/1786,1055/2414,1045/2404	124358498	281,12033	1987	4170	6157	SO:0001583	missense	1755	exon26			ACCCATTGTCCTG		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.3165T>G	10.37:g.124358498T>G	ENSP00000342210:p.Ile1055Met	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	92	51	0.554348	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		57	0.0260989010989011	3	0.006097560975609756	18	0.049723756906077346	1	0.0017482517482517483	35	0.04617414248021108	T	15.03	2.713206	0.48517	0.005536	0.031055	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.61510	0.1;0.1;0.1;0.1;0.1;0.1	3.57	-0.309	0.12769	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.35615	U	0.003084	T	0.40595	0.1123	M	0.93638	3.44	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.998;0.999	D;D;D;D;D	0.87578	0.998;0.972;0.998;0.947;0.969	T	0.67337	-0.5696	10	0.72032	D	0.01	.	8.7996	0.34901	0.0:0.3675:0.0:0.6325	.	562;1055;556;1045;1055	Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	M	1055;1055;1055;1055;1055;1055;556;1045;556;556;1055;1045;556	ENSP00000342210:I1055M;ENSP00000343175:I1045M;ENSP00000327747:I556M;ENSP00000357905:I1055M;ENSP00000357951:I1045M;ENSP00000357952:I556M	ENSP00000331522:I556M	I	+	3	3	DMBT1	124348488	0.000000	0.05858	0.006000	0.13384	0.155000	0.21991	-2.933000	0.00687	-0.009000	0.14296	0.456000	0.33151	ATT	T|0.976;G|0.024	0.024	strong		0.597	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
ATP2C2	9914	hgsc.bcm.edu	37	16	84494275	84494275	+	Silent	SNP	C	C	T	rs2241640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84494275C>T	ENST00000262429.4	+	24	2438	c.2349C>T	c.(2347-2349)ccC>ccT	p.P783P	RP11-517C16.2_ENST00000565700.1_RNA|ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Silent_p.P812P	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	783					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						GGGTAGAGCCCGTTGACAAAG	0.552													C|||	2365	0.472244	0.4077	0.5043	5008	,	,		19852	0.6349		0.4304	False		,,,				2504	0.4121				p.P783P		Atlas-SNP	.											ATP2C2,colon,carcinoma,+1,1	ATP2C2	75	1	0			c.C2349T						PASS	.	C		1676,2484		338,1000,742	114.0	123.0	120.0		2349	-9.7	0.5	16	dbSNP_98	120	3744,4716		842,2060,1328	no	coding-synonymous	ATP2C2	NM_014861.2		1180,3060,2070	TT,TC,CC		44.2553,40.2885,42.9477		783/947	84494275	5420,7200	2080	4230	6310	SO:0001819	synonymous_variant	9914	exon24			AGAGCCCGTTGAC	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.2349C>T	16.37:g.84494275C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	95	50	0.526316	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Silent	SNP	ENST00000262429.4	37	CCDS42207.1																																																																																			C|0.513;T|0.487	0.487	strong		0.552	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
PRAME	23532	hgsc.bcm.edu	37	22	22899234	22899234	+	Missense_Mutation	SNP	A	A	G	rs1129172	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:22899234A>G	ENST00000398741.1	-	3	325	c.19T>C	c.(19-21)Tgg>Cgg	p.W7R	LL22NC03-63E9.3_ENST00000407120.1_5'Flank|PRAME_ENST00000424204.2_5'Flank|PRAME_ENST00000398743.2_Missense_Mutation_p.W7R|PRAME_ENST00000485532.1_5'Flank|PRAME_ENST00000405655.3_Missense_Mutation_p.W7R|PRAME_ENST00000543184.1_Missense_Mutation_p.W7R|PRAME_ENST00000402697.1_Missense_Mutation_p.W7R|PRAME_ENST00000406503.1_Missense_Mutation_p.W7R|PRAME_ENST00000539862.1_5'Flank	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	7			W -> R (in dbSNP:rs2266988). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)	p.W7R(2)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		CTTCTTACCCACAAACGCCTT	0.562													G|||	3537	0.70627	0.7564	0.6931	5008	,	,		14575	0.752		0.5944	False		,,,				2504	0.7157				p.W7R	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											PRAME,NS,carcinoma,0,4	PRAME	78	4	2	Substitution - Missense(2)	prostate(1)|central_nervous_system(1)	c.T19C						PASS	.	G	ARG/TRP,ARG/TRP,ARG/TRP,ARG/TRP,ARG/TRP	3252,1154	408.6+/-334.7	1206,840,157	186.0	164.0	171.0		19,19,19,19,19	2.8	0.4	22	dbSNP_100	171	4922,3678	523.7+/-380.4	1402,2118,780	yes	missense,missense,missense,missense,missense	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	101,101,101,101,101	2608,2958,937	GG,GA,AA		42.7674,26.1916,37.1521	benign,benign,benign,benign,benign	7/510,7/510,7/510,7/510,7/510	22899234	8174,4832	2203	4300	6503	SO:0001583	missense	23532	exon3			TTACCCACAAACG	U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.19T>C	22.37:g.22899234A>G	ENSP00000381726:p.Trp7Arg	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	1490	0.6822344322344323	378	0.7682926829268293	235	0.649171270718232	422	0.7377622377622378	455	0.600263852242744	g	0.393	-0.922440	0.02396	0.738084	0.572326	ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000402697;ENST00000439106;ENST00000420709;ENST00000406503;ENST00000403441	T;T;T;T;T;T;T;T;T	0.10477	2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87;2.87	2.78	2.78	0.32641	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.33482	P	0.41245699999999996	B	0.02656	0.0	B	0.01281	0.0	T	0.34054	-0.9844	8	0.02654	T	1	.	5.8996	0.18960	0.1457:0.0:0.8543:0.0	rs2266988;rs17497986;rs57013465	7	P78395	PRAME_HUMAN	R	7	ENSP00000381728:W7R;ENSP00000445675:W7R;ENSP00000381726:W7R;ENSP00000384343:W7R;ENSP00000385198:W7R;ENSP00000407320:W7R;ENSP00000412318:W7R;ENSP00000384058:W7R;ENSP00000385091:W7R	ENSP00000381726:W7R	W	-	1	0	PRAME	21229234	0.547000	0.26465	0.392000	0.26245	0.002000	0.02628	0.671000	0.25172	0.765000	0.33221	-0.213000	0.12676	TGG	G|0.653;N|0.000	0.653	strong		0.562	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953	
CNR2	1269	hgsc.bcm.edu	37	1	24201162	24201162	+	Missense_Mutation	SNP	G	G	A	rs2229579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:24201162G>A	ENST00000374472.4	-	2	1107	c.946C>T	c.(946-948)Cac>Tac	p.H316Y	CNR2_ENST00000536471.1_Missense_Mutation_p.H316Y	NM_001841.2	NP_001832.1	P34972	CNR2_HUMAN	cannabinoid receptor 2 (macrophage)	316			H -> Y (in dbSNP:rs2229579). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18286196, ECO:0000269|Ref.5}.		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)	TTCTTCCAGTGAGCCAGGCAG	0.552													G|||	538	0.107428	0.0045	0.1081	5008	,	,		21093	0.2143		0.0885	False		,,,				2504	0.1554				p.H316Y		Atlas-SNP	.											.	CNR2	78	.	0			c.C946T						PASS	.	G	TYR/HIS	105,4301	80.9+/-119.3	2,101,2100	93.0	95.0	94.0		946	0.7	0.0	1	dbSNP_98	94	859,7741	197.3+/-242.0	34,791,3475	yes	missense	CNR2	NM_001841.2	83	36,892,5575	AA,AG,GG		9.9884,2.3831,7.412	benign	316/361	24201162	964,12042	2203	4300	6503	SO:0001583	missense	1269	exon2			TCCAGTGAGCCAG	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.946C>T	1.37:g.24201162G>A	ENSP00000363596:p.His316Tyr	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	192	19	0.0989583	NM_001841	C6ES44|Q4VBK8|Q5JRH7|Q6B0G7|Q6NSY0	Missense_Mutation	SNP	ENST00000374472.4	37	CCDS245.1	219	0.10027472527472528	1	0.0020325203252032522	30	0.08287292817679558	119	0.20804195804195805	69	0.09102902374670185	G	0.505	-0.868974	0.02570	0.023831	0.099884	ENSG00000188822	ENST00000374472;ENST00000536471	T;T	0.36878	1.23;1.23	5.21	0.728	0.18260	.	1.823760	0.02519	N	0.092394	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.30870	0.298	B	0.24974	0.057	T	0.11397	-1.0589	9	0.12430	T	0.62	.	4.3273	0.11046	0.0722:0.2569:0.4207:0.2501	rs2229579;rs3820021;rs52824290;rs2229579	316	P34972	CNR2_HUMAN	Y	316	ENSP00000363596:H316Y;ENSP00000442830:H316Y	ENSP00000363596:H316Y	H	-	1	0	CNR2	24073749	0.000000	0.05858	0.006000	0.13384	0.092000	0.18411	0.023000	0.13533	0.151000	0.19162	0.563000	0.77884	CAC	G|0.906;T|0.006	.	strong		0.552	CNR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038949.1	NM_001841	
UBXN11	91544	hgsc.bcm.edu	37	1	26612460	26612460	+	Silent	SNP	G	G	A	rs11247900	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26612460G>A	ENST00000374222.1	-	10	1092	c.628C>T	c.(628-630)Ctg>Ttg	p.L210L	UBXN11_ENST00000374217.2_Silent_p.L177L|UBXN11_ENST00000314675.7_Silent_p.L90L|UBXN11_ENST00000436301.2_Silent_p.L135L|UBXN11_ENST00000357089.4_Silent_p.L177L|UBXN11_ENST00000374223.1_5'UTR|UBXN11_ENST00000374221.3_Silent_p.L210L|UBXN11_ENST00000535108.1_Silent_p.L52L			Q5T124	UBX11_HUMAN	UBX domain protein 11	210						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						TCTACCACCAGCTCACTAAGA	0.632											OREG0013265	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	646	0.128994	0.202	0.1066	5008	,	,		17288	0.0228		0.1909	False		,,,				2504	0.092				p.L210L		Atlas-SNP	.											.	UBXN11	54	.	0			c.C628T						PASS	.	G	,,	591,3317		48,495,1411	38.0	41.0	40.0		268,529,628	2.9	1.0	1	dbSNP_120	40	1366,6934		103,1160,2887	no	coding-synonymous,coding-synonymous,coding-synonymous	UBXN11	NM_001077262.1,NM_145345.2,NM_183008.2	,,	151,1655,4298	AA,AG,GG		16.4578,15.1228,16.0305	,,	90/401,177/488,210/521	26612460	1957,10251	1954	4150	6104	SO:0001819	synonymous_variant	91544	exon10			CCACCAGCTCACT	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.628C>T	1.37:g.26612460G>A		Somatic	173	1	0.00578035	788	WXS	Illumina HiSeq	Phase_I	138	125	0.905797	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			G|0.862;A|0.138	0.138	strong		0.632	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
RBM20	282996	hgsc.bcm.edu	37	10	112544125	112544125	+	Missense_Mutation	SNP	C	C	T	rs189569984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:112544125C>T	ENST00000369519.3	+	4	1422	c.1364C>T	c.(1363-1365)tCg>tTg	p.S455L		NM_001134363.1	NP_001127835.1	Q5T481	RBM20_HUMAN	RNA binding motif protein 20	455					heart development (GO:0007507)|mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(4)|kidney(3)|large_intestine(1)|ovary(1)|skin(2)	12						ATACTTGGTTCGGCAGAGGGA	0.498													C|||	10	0.00199681	0.0	0.0058	5008	,	,		20892	0.0		0.006	False		,,,				2504	0.0				p.S455L		Atlas-SNP	.											RBM20,colon,carcinoma,-1,1	RBM20	50	1	0			c.C1364T						PASS	.	C	LEU/SER	0,1384		0,0,692	96.0	80.0	85.0		1364	5.5	0.0	10		85	33,3149		0,33,1558	yes	missense	RBM20	NM_001134363.1	145	0,33,2250	TT,TC,CC		1.0371,0.0,0.7227	benign	455/1228	112544125	33,4533	692	1591	2283	SO:0001583	missense	282996	exon4			TTGGTTCGGCAGA	BX648563	CCDS44477.1	10q25.3	2014-09-17			ENSG00000203867	ENSG00000203867		"""RNA binding motif (RRM) containing"""	27424	protein-coding gene	gene with protein product		613171					Standard	NM_001134363		Approved		uc001kzf.2	Q5T481	OTTHUMG00000019043	ENST00000369519.3:c.1364C>T	10.37:g.112544125C>T	ENSP00000358532:p.Ser455Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_001134363	A6NIP5|B5A868|Q5JVI1	Missense_Mutation	SNP	ENST00000369519.3	37	CCDS44477.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	C	15.92	2.976591	0.53720	0.0	0.010371	ENSG00000203867	ENST00000369519;ENST00000539821	D	0.90844	-2.74	5.54	5.54	0.83059	.	.	.	.	.	T	0.78629	0.4313	N	0.24115	0.695	0.09310	N	1	P	0.37997	0.614	B	0.25614	0.062	T	0.72833	-0.4173	9	0.33141	T	0.24	.	17.6723	0.88222	0.0:1.0:0.0:0.0	.	455	Q5T481	RBM20_HUMAN	L	455	ENSP00000358532:S455L	ENSP00000358532:S455L	S	+	2	0	RBM20	112534115	0.606000	0.26949	0.007000	0.13788	0.013000	0.08279	5.011000	0.64011	2.589000	0.87451	0.655000	0.94253	TCG	C|0.999;T|0.001	0.001	strong		0.498	RBM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050339.2	NM_001134363	
WDR25	79446	hgsc.bcm.edu	37	14	100847707	100847707	+	Missense_Mutation	SNP	A	A	G	rs2273800	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:100847707A>G	ENST00000335290.6	+	2	672	c.446A>G	c.(445-447)cAt>cGt	p.H149R	WDR25_ENST00000542471.2_5'Flank|WDR25_ENST00000402312.3_Missense_Mutation_p.H149R|WDR25_ENST00000554175.1_Missense_Mutation_p.H149R|WDR25_ENST00000554998.1_Missense_Mutation_p.H149R	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	149			H -> R (in dbSNP:rs2273800). {ECO:0000269|PubMed:14702039}.							central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				TCATCTTTCCATGCTCAAAGT	0.478													G|||	3240	0.646965	0.6596	0.4597	5008	,	,		20301	0.4742		0.7266	False		,,,				2504	0.8589				p.H149R		Atlas-SNP	.											.	WDR25	37	.	0			c.A446G						PASS	.	G	ARG/HIS,ARG/HIS	2936,1470	468.9+/-355.3	975,986,242	78.0	87.0	84.0		446,446	-1.2	0.0	14	dbSNP_100	84	6456,2144	367.1+/-334.6	2416,1624,260	yes	missense,missense	WDR25	NM_001161476.1,NM_024515.4	29,29	3391,2610,502	GG,GA,AA		24.9302,33.3636,27.7872	benign,benign	149/545,149/545	100847707	9392,3614	2203	4300	6503	SO:0001583	missense	79446	exon2			CTTTCCATGCTCA	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.446A>G	14.37:g.100847707A>G	ENSP00000334148:p.His149Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	37	CCDS32157.1	1294	0.5924908424908425	334	0.6788617886178862	173	0.47790055248618785	234	0.4090909090909091	553	0.7295514511873351	G	5.735	0.320138	0.10845	0.666364	0.750698	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000554175	T;T;T;T	0.58797	0.31;0.31;0.31;2.32	5.0	-1.17	0.09648	.	2.187880	0.01480	N	0.016632	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	0.38351	-0.9665	9	0.15499	T	0.54	5.3075	5.8489	0.18681	0.5579:0.1496:0.2925:0.0	rs2273800;rs17207794;rs56514452;rs60906078;rs2273800	149	Q64LD2	WDR25_HUMAN	R	149	ENSP00000450661:H149R;ENSP00000385540:H149R;ENSP00000334148:H149R;ENSP00000450727:H149R	ENSP00000334148:H149R	H	+	2	0	WDR25	99917460	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.387000	0.20718	-0.751000	0.04734	-1.082000	0.02213	CAT	A|0.330;G|0.670	0.670	strong		0.478	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515	
DNAAF3	352909	hgsc.bcm.edu	37	19	55671374	55671374	+	Silent	SNP	C	C	T	rs891187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55671374C>T	ENST00000524407.2	-	10	1089	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	DNAAF3_ENST00000527223.2_Silent_p.P419P|DNAAF3_ENST00000587789.2_5'UTR|TNNI3_ENST00000590463.1_5'Flank|TNNI3_ENST00000344887.5_5'Flank|DNAAF3_ENST00000391720.4_Silent_p.P399P|CTD-2587H24.5_ENST00000591665.1_RNA|CTD-2587H24.4_ENST00000587871.1_Missense_Mutation_p.D14N|DNAAF3_ENST00000455045.1_Silent_p.P298P			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	352					axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											ATTCCGGGGTCGGGGCTGCTG	0.602													g|||	1662	0.331869	0.6407	0.1744	5008	,	,		8607	0.2361		0.175	False		,,,				2504	0.2863				p.P419P		Atlas-SNP	.											.	.	.	.	0			c.G1257A						PASS	.	G		2095,1631		578,939,346	31.0	36.0	34.0		1197	-8.6	0.0	19	dbSNP_86	34	1382,6830		122,1138,2846	no	coding-synonymous	C19orf51	NM_178837.3		700,2077,3192	TT,TC,CC		16.829,43.7735,29.1255		399/589	55671374	3477,8461	1863	4106	5969	SO:0001819	synonymous_variant	352909	exon10			CGGGGTCGGGGCT	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.1056G>A	19.37:g.55671374C>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	92	0.968421	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Silent	SNP	ENST00000524407.2	37	CCDS59422.1	639	0.2925824175824176	314	0.6382113821138211	68	0.1878453038674033	127	0.22202797202797203	130	0.17150395778364116	G	12.82	2.053034	0.36181	0.562265	0.16829	ENSG00000167646	ENST00000530077	.	.	.	4.28	-8.56	0.00904	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.04140	-1.0974	3	.	.	.	-0.0814	10.3913	0.44171	0.6474:0.1736:0.179:0.0	rs891187;rs17855199;rs891187	.	.	.	N	10	.	.	D	-	1	0	C19orf51	60363186	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.852000	0.00731	-3.114000	0.00240	-1.583000	0.00853	GAC	C|0.700;T|0.300	0.300	strong		0.602	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
TEX33	339669	hgsc.bcm.edu	37	22	37398195	37398195	+	Missense_Mutation	SNP	C	C	T	rs743749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37398195C>T	ENST00000405091.2	-	4	423	c.172G>A	c.(172-174)Gct>Act	p.A58T	TEX33_ENST00000402860.3_5'UTR|TEX33_ENST00000381821.1_Missense_Mutation_p.A58T			O43247	TEX33_HUMAN	testis expressed 33	58																	CTGCCTTGAGCGCTGGCTCCC	0.627													C|||	1375	0.274561	0.1384	0.219	5008	,	,		15007	0.5357		0.2276	False		,,,				2504	0.2771				p.A58T		Atlas-SNP	.											.	TEX33	25	.	0			c.G172A						PASS	.	C	THR/ALA,	220,1164		21,178,493	15.0	18.0	17.0		172,	-2.6	0.0	22	dbSNP_86	17	601,2581		55,491,1045	yes	missense,utr-5	C22orf33	NM_001163857.1,NM_178552.3	58,	76,669,1538	TT,TC,CC		18.8875,15.896,17.9807	benign,	58/281,	37398195	821,3745	692	1591	2283	SO:0001583	missense	339669	exon3			CTTGAGCGCTGGC	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.172G>A	22.37:g.37398195C>T	ENSP00000386118:p.Ala58Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	73	27	0.369863	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Missense_Mutation	SNP	ENST00000405091.2	37	CCDS54524.1	634	0.2902930402930403	77	0.1565040650406504	68	0.1878453038674033	325	0.5681818181818182	164	0.21635883905013192	.	0.174	-1.068853	0.01918	0.15896	0.188875	ENSG00000185264	ENST00000405091;ENST00000381821	.	.	.	3.63	-2.63	0.06133	.	1.975310	0.02280	N	0.069327	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	0.40664	-0.9551	8	0.08179	T	0.78	-0.0709	7.0083	0.24848	0.0:0.1186:0.5945:0.2869	rs743749;rs57196762;rs743749	58	O43247	EAN57_HUMAN	T	58	.	ENSP00000371243:A58T	A	-	1	0	C22orf33	35728141	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-1.712000	0.01885	-0.382000	0.07870	-0.247000	0.11927	GCT	C|0.715;T|0.285	0.285	strong		0.627	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552	
PSMD2	5708	hgsc.bcm.edu	37	3	184020542	184020542	+	Missense_Mutation	SNP	G	G	T	rs11545169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:184020542G>T	ENST00000310118.4	+	7	1497	c.939G>T	c.(937-939)gaG>gaT	p.E313D	PSMD2_ENST00000435761.1_Missense_Mutation_p.E154D|EIF2B5_ENST00000444495.1_Intron|PSMD2_ENST00000439383.1_Missense_Mutation_p.E183D	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	313			E -> D (in dbSNP:rs11545169). {ECO:0000269|PubMed:14702039}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	ATGTCGAGGAGTATGAGGACC	0.517													G|||	385	0.076877	0.0061	0.1081	5008	,	,		22477	0.0327		0.159	False		,,,				2504	0.1115				p.E313D	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											.	PSMD2	56	.	0			c.G939T						PASS	.	G	ASP/GLU	131,4275	94.8+/-133.5	4,123,2076	156.0	142.0	147.0		939	1.3	1.0	3	dbSNP_120	147	1385,7215	268.9+/-288.1	105,1175,3020	yes	missense	PSMD2	NM_002808.3	45	109,1298,5096	TT,TG,GG		16.1047,2.9732,11.6562	benign	313/909	184020542	1516,11490	2203	4300	6503	SO:0001583	missense	5708	exon7			CGAGGAGTATGAG	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"""Proteasome (prosome, macropain) subunits"""	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.939G>T	3.37:g.184020542G>T	ENSP00000310129:p.Glu313Asp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	133	76	0.571429	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Missense_Mutation	SNP	ENST00000310118.4	37	CCDS3258.1	189	0.08653846153846154	4	0.008130081300813009	43	0.11878453038674033	14	0.024475524475524476	128	0.16886543535620052	G	6.311	0.425408	0.11987	0.029732	0.161047	ENSG00000175166	ENST00000310118;ENST00000538096;ENST00000435761;ENST00000439383	T;T;T	0.25414	1.8;1.8;1.8	5.16	1.32	0.21799	Armadillo-type fold (1);	0.050554	0.85682	D	0.000000	T	0.00039	0.0001	N	0.01464	-0.85	0.25305	P	0.9892453	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.40924	-0.9537	9	0.02654	T	1	-29.291	8.9541	0.35807	0.4502:0.0:0.5498:0.0	rs11545169;rs52807591;rs11545169	154;313	E9PCS3;Q13200	.;PSMD2_HUMAN	D	313;305;154;183	ENSP00000310129:E313D;ENSP00000402618:E154D;ENSP00000416028:E183D	ENSP00000310129:E313D	E	+	3	2	PSMD2	185503236	0.997000	0.39634	0.999000	0.59377	0.862000	0.49288	0.422000	0.21296	0.126000	0.18424	-0.199000	0.12753	GAG	G|0.896;T|0.104	0.104	strong		0.517	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38673298	38673298	+	Missense_Mutation	SNP	C	C	G	rs3745945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38673298C>G	ENST00000222345.6	+	16	4857	c.4348C>G	c.(4348-4350)Cct>Gct	p.P1450A	CTB-102L5.7_ENST00000594299.1_RNA	NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1450			P -> A (in dbSNP:rs3745945).		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)			CTCCAAGCAGCCTGTACGCAA	0.617													C|||	262	0.0523163	0.0008	0.0893	5008	,	,		13199	0.0466		0.0835	False		,,,				2504	0.0695				p.P1450A		Atlas-SNP	.											.	SIPA1L3	150	.	0			c.C4348G						PASS	.	C	ALA/PRO	68,4338	63.5+/-100.7	0,68,2135	64.0	73.0	70.0		4348	4.4	1.0	19	dbSNP_107	70	632,7968	161.7+/-214.6	24,584,3692	yes	missense	SIPA1L3	NM_015073.1	27	24,652,5827	GG,GC,CC		7.3488,1.5433,5.3821	possibly-damaging	1450/1782	38673298	700,12306	2203	4300	6503	SO:0001583	missense	23094	exon16			AAGCAGCCTGTAC	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.4348C>G	19.37:g.38673298C>G	ENSP00000222345:p.Pro1450Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	126	0.057692307692307696	1	0.0020325203252032522	35	0.09668508287292818	30	0.05244755244755245	60	0.079155672823219	C	13.53	2.265710	0.40095	0.015433	0.073488	ENSG00000105738	ENST00000222345	T	0.74209	-0.82	5.48	4.39	0.52855	.	0.177792	0.37095	N	0.002245	T	0.02380	0.0073	N	0.14661	0.345	0.32284	N	0.567252	B	0.11235	0.004	B	0.08055	0.003	T	0.14144	-1.0483	10	0.36615	T	0.2	-5.8179	8.1936	0.31383	0.2752:0.5798:0.145:0.0	rs3745945;rs17640341;rs3745945	1450	O60292	SI1L3_HUMAN	A	1450	ENSP00000222345:P1450A	ENSP00000222345:P1450A	P	+	1	0	SIPA1L3	43365138	0.875000	0.30112	1.000000	0.80357	0.987000	0.75469	1.042000	0.30303	2.562000	0.86427	0.555000	0.69702	CCT	C|0.942;G|0.058	0.058	strong		0.617	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
OR5AK2	390181	hgsc.bcm.edu	37	11	56757021	56757021	+	Silent	SNP	G	G	A	rs61886711	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56757021G>A	ENST00000326855.2	+	1	675	c.633G>A	c.(631-633)ggG>ggA	p.G211G		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						TATTCACTGGGTTGGTCGTCA	0.428													.|||	817	0.163139	0.1263	0.1081	5008	,	,		23024	0.1458		0.2177	False		,,,				2504	0.2137				p.G211G		Atlas-SNP	.											.	OR5AK2	45	.	0			c.G633A						PASS	.	G		548,3854	250.3+/-257.4	35,478,1688	241.0	214.0	223.0		633	2.9	0.3	11	dbSNP_129	223	1572,7020	294.2+/-301.7	125,1322,2849	no	coding-synonymous	OR5AK2	NM_001005323.1		160,1800,4537	AA,AG,GG		18.2961,12.4489,16.3152		211/310	56757021	2120,10874	2201	4296	6497	SO:0001819	synonymous_variant	390181	exon1			CACTGGGTTGGTC	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.633G>A	11.37:g.56757021G>A		Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	386	176	0.455959	NM_001005323	B2RNZ9	Silent	SNP	ENST00000326855.2	37	CCDS31538.1																																																																																			G|0.829;A|0.171	0.171	strong		0.428	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
KRT5	3852	hgsc.bcm.edu	37	12	52912909	52912909	+	Missense_Mutation	SNP	G	G	T	rs641615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52912909G>T	ENST00000252242.4	-	2	981	c.591C>A	c.(589-591)gaC>gaA	p.D197E		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	197	Coil 1A.|Rod.		D -> E (in dbSNP:rs641615). {ECO:0000269|PubMed:2447486, ECO:0000269|PubMed:2476664}.		cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCCACTTGGTGTCCAGAACCT	0.532													G|||	1077	0.215056	0.1089	0.2233	5008	,	,		19702	0.3393		0.2823	False		,,,				2504	0.1554				p.D197E		Atlas-SNP	.											.	KRT5	88	.	0			c.C591A						PASS	.						58.0	51.0	54.0					12																	52912909		2202	4296	6498	SO:0001583	missense	3852	exon2			CTTGGTGTCCAGA		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.591C>A	12.37:g.52912909G>T	ENSP00000252242:p.Asp197Glu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	116	37	0.318966	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Missense_Mutation	SNP	ENST00000252242.4	37	CCDS8830.1	555	0.2541208791208791	58	0.11788617886178862	91	0.2513812154696133	199	0.3479020979020979	207	0.27308707124010556	G	5.448	0.267812	0.10349	.	.	ENSG00000186081	ENST00000252242;ENST00000456000;ENST00000549420	T;T	0.72282	-0.64;-0.64	5.31	2.41	0.29592	Filament (1);	0.000000	0.64402	D	0.000015	T	0.00012	0.0000	N	0.00001	-3.76	0.38288	P	0.05736600000000003	B	0.18741	0.03	B	0.15052	0.012	T	0.46105	-0.9215	9	0.02654	T	1	.	7.4373	0.27162	0.0684:0.3532:0.4752:0.1032	rs641615;rs1042272;rs3176960;rs3181708;rs17400360;rs59010565	197	P13647	K2C5_HUMAN	E	197;162;87	ENSP00000252242:D197E;ENSP00000447209:D87E	ENSP00000252242:D197E	D	-	3	2	KRT5	51199176	0.997000	0.39634	1.000000	0.80357	0.999000	0.98932	0.484000	0.22308	0.792000	0.33850	0.655000	0.94253	GAC	G|0.790;T|0.210	0.210	strong		0.532	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
SETMAR	6419	hgsc.bcm.edu	37	3	4358210	4358210	+	Silent	SNP	A	A	G	rs7647539	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:4358210A>G	ENST00000358065.4	+	3	1402	c.1335A>G	c.(1333-1335)cgA>cgG	p.R445R	SETMAR_ENST00000425863.1_Silent_p.R306R|SUMF1_ENST00000534863.1_Intron	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	445	Mariner transposase Hsmar1.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA integration (GO:0015074)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of chromosome organization (GO:2001251)|positive regulation of double-strand break repair via nonhomologous end joining (GO:2001034)|transposition, DNA-mediated (GO:0006313)	chromosome (GO:0005694)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|histone-lysine N-methyltransferase activity (GO:0018024)|protein homodimerization activity (GO:0042803)|structure-specific DNA binding (GO:0043566)|transposase activity (GO:0004803)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)	9		Melanoma(143;0.0657)		Epithelial(13;0.0025)|OV - Ovarian serous cystadenocarcinoma(96;0.011)|all cancers(10;0.0114)		cggtcgttcgacatttgaagc	0.423								Chromatin Structure					G|||	2081	0.415535	0.8865	0.2954	5008	,	,		14865	0.1062		0.3559	False		,,,				2504	0.2444				p.R445R		Atlas-SNP	.											.	SETMAR	30	.	0			c.A1335G						PASS	.	G		3505,895		1406,693,101	13.0	15.0	14.0		1335	0.2	0.7	3	dbSNP_116	14	2843,5743		487,1869,1937	no	coding-synonymous	SETMAR	NM_006515.3		1893,2562,2038	GG,GA,AA		33.112,20.3409,48.8834		445/685	4358210	6348,6638	2200	4293	6493	SO:0001819	synonymous_variant	6419	exon3			CGTTCGACATTTG	U80776	CCDS2563.2, CCDS58814.1, CCDS63528.1	3p26.2	2013-01-31			ENSG00000170364	ENSG00000170364			10762	protein-coding gene	gene with protein product		609834				9461395	Standard	NM_006515		Approved	metnase	uc011asp.2	Q53H47	OTTHUMG00000090265	ENST00000358065.4:c.1335A>G	3.37:g.4358210A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	42	40	0.952381	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Silent	SNP	ENST00000358065.4	37	CCDS2563.2																																																																																			A|0.558;G|0.442	0.442	strong		0.423	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515	
TRIM45	80263	hgsc.bcm.edu	37	1	117659352	117659352	+	Missense_Mutation	SNP	C	C	T	rs3738413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:117659352C>T	ENST00000256649.4	-	3	1764	c.1238G>A	c.(1237-1239)cGg>cAg	p.R413Q	TRIM45_ENST00000369464.3_Missense_Mutation_p.R395Q|TRIM45_ENST00000369461.3_Missense_Mutation_p.R356Q	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	413			R -> Q (in dbSNP:rs3738413).		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)		CTGTTTCTCCCGGGCTCTGTG	0.488													C|||	457	0.091254	0.0605	0.1037	5008	,	,		18743	0.1329		0.0915	False		,,,				2504	0.0808				p.R413Q		Atlas-SNP	.											.	TRIM45	55	.	0			c.G1238A						PASS	.	C	GLN/ARG,GLN/ARG	273,4133	152.5+/-186.2	9,255,1939	74.0	74.0	74.0		1184,1238	5.1	1.0	1	dbSNP_107	74	913,7687	202.3+/-245.6	44,825,3431	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	43,43	53,1080,5370	TT,TC,CC		10.6163,6.1961,9.1189	probably-damaging,probably-damaging	395/563,413/581	117659352	1186,11820	2203	4300	6503	SO:0001583	missense	80263	exon3			TTCTCCCGGGCTC		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.1238G>A	1.37:g.117659352C>T	ENSP00000256649:p.Arg413Gln	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_025188	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	208	0.09523809523809523	30	0.06097560975609756	41	0.1132596685082873	65	0.11363636363636363	72	0.09498680738786279	C	19.62	3.861999	0.71949	0.061961	0.106163	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	D;D;D	0.84730	-1.89;-1.89;-1.89	5.09	5.09	0.68999	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.277176	0.34046	N	0.004311	D	0.84032	0.5383	L	0.46157	1.445	0.23150	P	0.9982136	D;D	0.71674	0.998;0.996	P;P	0.58391	0.838;0.833	T	0.81267	-0.1010	9	0.25106	T	0.35	-19.4447	15.8106	0.78561	0.0:1.0:0.0:0.0	rs3738413;rs52793171;rs60562050;rs3738413	395;413	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	Q	413;395;356	ENSP00000256649:R413Q;ENSP00000358476:R395Q;ENSP00000358473:R356Q	ENSP00000256649:R413Q	R	-	2	0	TRIM45	117460875	0.628000	0.27138	0.991000	0.47740	0.752000	0.42762	0.670000	0.25157	2.646000	0.89796	0.563000	0.77884	CGG	C|0.909;T|0.091	0.091	strong		0.488	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188	
TYSND1	219743	hgsc.bcm.edu	37	10	71905695	71905695	+	Silent	SNP	A	A	G	rs35587847|rs10999158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:71905695A>G	ENST00000287078.6	-	1	647	c.648T>C	c.(646-648)ggT>ggC	p.G216G	TYSND1_ENST00000494143.1_5'Flank|TYSND1_ENST00000335494.5_Silent_p.G216G	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	216					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						GCAATGGCGCACCCTTGGGCA	0.701													G|||	1634	0.326278	0.3775	0.2911	5008	,	,		12458	0.0615		0.4791	False		,,,				2504	0.3978				p.G216G		Atlas-SNP	.											.	TYSND1	20	.	0			c.T648C						PASS	.	G	,	1632,2678		358,916,881	11.0	13.0	12.0		648,648	0.9	1.0	10	dbSNP_120	12	3557,4851		845,1867,1492	no	coding-synonymous,coding-synonymous	TYSND1	NM_001040273.1,NM_173555.2	,	1203,2783,2373	GG,GA,AA		42.3049,37.8654,40.8004	,	216/399,216/567	71905695	5189,7529	2155	4204	6359	SO:0001819	synonymous_variant	219743	exon1			TGGCGCACCCTTG	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.648T>C	10.37:g.71905695A>G		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Silent	SNP	ENST00000287078.6	37	CCDS31213.1																																																																																			A|0.679;G|0.321	0.321	strong		0.701	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555	
PPM1F	9647	hgsc.bcm.edu	37	22	22287862	22287862	+	Silent	SNP	G	G	A	rs2027789	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:22287862G>A	ENST00000263212.5	-	5	753	c.648C>T	c.(646-648)aaC>aaT	p.N216N	PPM1F_ENST00000538191.1_Silent_p.N112N|PPM1F_ENST00000397495.4_Silent_p.N216N|PPM1F_ENST00000407142.1_Silent_p.N48N	NM_014634.3	NP_055449.1	P49593	PPM1F_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1F	216					cellular response to drug (GO:0035690)|histone dephosphorylation (GO:0016576)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of stress fiber assembly (GO:0051496)	cytosol (GO:0005829)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	calmodulin-dependent protein phosphatase activity (GO:0033192)|metal ion binding (GO:0046872)|phosphatase activity (GO:0016791)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	12	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.155)		GGCGGGCAGCGTTGGTGTGCA	0.632													G|||	1237	0.247005	0.2874	0.2939	5008	,	,		17553	0.0863		0.4006	False		,,,				2504	0.1667				p.N216N		Atlas-SNP	.											.	PPM1F	34	.	0			c.C648T						PASS	.	G		1232,3174	425.1+/-340.7	161,910,1132	69.0	59.0	63.0		648	-8.1	0.0	22	dbSNP_94	63	3386,5214	501.0+/-375.3	671,2044,1585	no	coding-synonymous	PPM1F	NM_014634.3		832,2954,2717	AA,AG,GG		39.3721,27.9619,35.5067		216/455	22287862	4618,8388	2203	4300	6503	SO:0001819	synonymous_variant	9647	exon5			GGCAGCGTTGGTG	D13640	CCDS13796.1	22q11.22	2012-04-17	2010-03-05		ENSG00000100034	ENSG00000100034	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19388	protein-coding gene	gene with protein product	"""partner of PIX 2"", ""Ca(2+)/calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1F (PP2C domain containing)"""			11864573, 11559703	Standard	NM_014634		Approved	FEM-2, KIAA0015, POPX2, CaMKPase, CAMKP	uc002zvp.2	P49593	OTTHUMG00000150835	ENST00000263212.5:c.648C>T	22.37:g.22287862G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_014634	A8K6G3|B7Z2C3|Q96PM2	Silent	SNP	ENST00000263212.5	37	CCDS13796.1																																																																																			G|0.665;A|0.335	0.335	strong		0.632	PPM1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320267.2	NM_014634	
SLC44A4	80736	hgsc.bcm.edu	37	6	31842598	31842598	+	Missense_Mutation	SNP	T	T	A	rs12661281	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31842598T>A	ENST00000229729.6	-	6	388	c.368A>T	c.(367-369)gAc>gTc	p.D123V	SLC44A4_ENST00000375562.4_Intron|SLC44A4_ENST00000544672.1_Missense_Mutation_p.D47V|SLC44A4_ENST00000465707.1_5'UTR	NM_025257.2	NP_079533.2	Q53GD3	CTL4_HUMAN	solute carrier family 44, member 4	123			D -> V (in dbSNP:rs12661281).		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)	AGTCCATGGGTCCTCCGGGCA	0.542													T|||	473	0.0944489	0.0068	0.183	5008	,	,		20016	0.1022		0.1491	False		,,,				2504	0.0859				p.D123V		Atlas-SNP	.											.	SLC44A4	67	.	0			c.A368T						PASS	.	T	,VAL/ASP,VAL/ASP	127,4279	93.4+/-132.2	1,125,2077	71.0	75.0	73.0		,140,368	-9.7	0.0	6	dbSNP_120	73	1322,7278	261.2+/-283.7	90,1142,3068	yes	intron,missense,missense	SLC44A4	NM_001178044.1,NM_001178045.1,NM_025257.2	,152,152	91,1267,5145	AA,AT,TT		15.3721,2.8824,11.141	,benign,benign	,47/635,123/711	31842598	1449,11557	2203	4300	6503	SO:0001583	missense	80736	exon6			CATGGGTCCTCCG	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.368A>T	6.37:g.31842598T>A	ENSP00000229729:p.Asp123Val	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	105	59	0.561905	NM_025257	A2BED3|B0UXX8|B0UZY8|B4DU94|B4DWM2|E9PEK7|Q5JP84|Q5JQ93|Q658S8|Q6UX89|Q8TEW4|Q96C58|Q96K59|Q9Y332	Missense_Mutation	SNP	ENST00000229729.6	37	CCDS4724.2	248|248	0.11355311355311355|0.11355311355311355	6|6	0.012195121951219513|0.012195121951219513	67|67	0.1850828729281768|0.1850828729281768	69|69	0.12062937062937062|0.12062937062937062	106|106	0.13984168865435356|0.13984168865435356	T|T	11.13|11.13	1.549042|1.549042	0.27652|0.27652	0.028824|0.028824	0.153721|0.153721	ENSG00000204385|ENSG00000204385	ENST00000229729;ENST00000544672|ENST00000414427	T;T|.	0.18657|.	2.2;2.2|.	4.9|4.9	-9.67|-9.67	0.00531|0.00531	.|.	3.055490|.	0.00649|.	N|.	0.000555|.	T|T	0.06872|0.06872	0.0175|0.0175	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|.	0.04013|.	0.001|.	T|T	0.13710|0.13710	-1.0499|-1.0499	9|4	0.49607|.	T|.	0.09|.	-27.1204|-27.1204	10.1697|10.1697	0.42902|0.42902	0.075:0.0:0.3333:0.5917|0.075:0.0:0.3333:0.5917	rs12661281;rs52792968;rs12661281|rs12661281;rs52792968;rs12661281	123|.	Q53GD3|.	CTL4_HUMAN|.	V|S	123;47|119	ENSP00000229729:D123V;ENSP00000444109:D47V|.	ENSP00000229729:D123V|.	D|T	-|-	2|1	0|0	SLC44A4|SLC44A4	31950577|31950577	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.103000|0.103000	0.19146|0.19146	-3.226000|-3.226000	0.00550|0.00550	-2.288000|-2.288000	0.00668|0.00668	-0.144000|-0.144000	0.13903|0.13903	GAC|ACC	T|0.871;A|0.129	0.129	strong		0.542	SLC44A4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076234.3		
SLC22A14	9389	hgsc.bcm.edu	37	3	38355225	38355225	+	Missense_Mutation	SNP	G	G	A	rs73064822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38355225G>A	ENST00000273173.4	+	7	1262	c.1171G>A	c.(1171-1173)Gtc>Atc	p.V391I	SLC22A14_ENST00000448498.1_Missense_Mutation_p.V391I	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	391					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)		CAGGTTTACCGTCAGTTACAC	0.582													G|||	836	0.166933	0.1626	0.196	5008	,	,		15883	0.2063		0.1859	False		,,,				2504	0.092				p.V391I		Atlas-SNP	.											.	SLC22A14	64	.	0			c.G1171A						PASS	.	G	ILE/VAL	729,3677	300.1+/-286.2	63,603,1537	93.0	86.0	89.0		1171	-6.2	0.0	3	dbSNP_130	89	1434,7166	273.8+/-290.9	127,1180,2993	yes	missense	SLC22A14	NM_004803.3	29	190,1783,4530	AA,AG,GG		16.6744,16.5456,16.6308	benign	391/595	38355225	2163,10843	2203	4300	6503	SO:0001583	missense	9389	exon7			TTTACCGTCAGTT	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.1171G>A	3.37:g.38355225G>A	ENSP00000273173:p.Val391Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	51	21	0.411765	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	414	0.18956043956043955	86	0.17479674796747968	74	0.20441988950276244	112	0.1958041958041958	142	0.18733509234828497	G	2.686	-0.274360	0.05679	0.165456	0.166744	ENSG00000144671	ENST00000448498;ENST00000423219;ENST00000273173	T;T	0.74106	-0.81;-0.81	3.6	-6.15	0.02105	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.740334	0.12590	N	0.455649	T	0.00109	0.0003	L	0.39898	1.24	0.80722	P	0.0	B	0.14805	0.011	B	0.15870	0.014	T	0.01874	-1.1256	9	0.42905	T	0.14	.	11.7661	0.51930	0.3639:0.0:0.6361:0.0	.	391	Q9Y267	S22AE_HUMAN	I	391	ENSP00000396283:V391I;ENSP00000273173:V391I	ENSP00000273173:V391I	V	+	1	0	SLC22A14	38330229	0.000000	0.05858	0.000000	0.03702	0.540000	0.34992	-1.703000	0.01900	-1.385000	0.02101	-0.339000	0.08088	GTC	G|0.825;A|0.175	0.175	strong		0.582	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
DOCK8	81704	hgsc.bcm.edu	37	9	271638	271638	+	Missense_Mutation	SNP	C	C	T	rs506121	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:271638C>T	ENST00000453981.1	+	2	177	c.65C>T	c.(64-66)gCg>gTg	p.A22V	DOCK8_ENST00000432829.2_5'UTR|DOCK8_ENST00000469391.1_5'Flank|RP11-59O6.3_ENST00000429661.1_RNA			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	22				A -> V (in Ref. 1; BAE45254). {ECO:0000305}.	blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TATTCTTCAGCGGAAATAAGG	0.348													C|||	1541	0.307708	0.2776	0.2767	5008	,	,		21157	0.375		0.341	False		,,,				2504	0.2669				p.A22V		Atlas-SNP	.											.	DOCK8	401	.	0			c.C65T						PASS	.	C	VAL/ALA	405,979		72,261,359	148.0	120.0	128.0		65	4.1	1.0	9	dbSNP_83	128	1051,2131		168,715,708	yes	missense	DOCK8	NM_203447.3	64	240,976,1067	TT,TC,CC		33.0295,29.263,31.8879	possibly-damaging	22/2100	271638	1456,3110	692	1591	2283	SO:0001583	missense	81704	exon2			CTTCAGCGGAAAT	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.65C>T	9.37:g.271638C>T	ENSP00000408464:p.Ala22Val	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	57	37	0.649123	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	683	0.31272893772893773	121	0.2459349593495935	102	0.281767955801105	216	0.3776223776223776	244	0.32189973614775724	C	15.91	2.971367	0.53614	0.29263	0.330295	ENSG00000107099	ENST00000453981;ENST00000287364	T	0.18174	2.23	5.88	4.05	0.47172	.	.	.	.	.	T	0.00012	0.0000	L	0.37850	1.14	0.09310	P	0.9999999999999373	B	0.06786	0.001	B	0.01281	0.0	T	0.41270	-0.9518	8	0.72032	D	0.01	.	10.1042	0.42524	0.0:0.8454:0.0:0.1546	rs506121;rs52809292;rs56483158;rs56808348;rs506121	22	Q8NF50	DOCK8_HUMAN	V	22	ENSP00000408464:A22V	ENSP00000287364:A22V	A	+	2	0	DOCK8	261638	0.975000	0.34042	0.974000	0.42286	0.974000	0.67602	1.418000	0.34782	0.839000	0.34971	0.557000	0.71058	GCG	C|0.688;T|0.312	0.312	strong		0.348	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919237	51919237	+	Silent	SNP	C	C	T	rs199590261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919237C>T	ENST00000339313.5	-	5	1055	c.939G>A	c.(937-939)gtG>gtA	p.V313V	CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Silent_p.V255V|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Silent_p.V230V|SIGLEC10_ENST00000439889.2_Silent_p.V255V|SIGLEC10_ENST00000353836.5_Silent_p.V313V|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Silent_p.V265V|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Silent_p.V313V			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	313	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CCCCAGCCTTCACCCCGGGCA	0.677													c|||	19	0.00379393	0.0015	0.0058	5008	,	,		16746	0.0		0.0089	False		,,,				2504	0.0041				p.V313V		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.G939A						PASS	.						38.0	43.0	42.0					19																	51919237		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			AGCCTTCACCCCG	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.939G>A	19.37:g.51919237C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	109	33	0.302752	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			C|0.994;T|0.006	0.006	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
SERPINA1	5265	hgsc.bcm.edu	37	14	94844843	94844843	+	Missense_Mutation	SNP	T	T	G	rs1303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:94844843T>G	ENST00000448921.1	-	7	1772	c.1200A>C	c.(1198-1200)gaA>gaC	p.E400D	SERPINA1_ENST00000437397.1_Missense_Mutation_p.E400D|SERPINA1_ENST00000393087.4_Missense_Mutation_p.E400D|SERPINA1_ENST00000449399.3_Missense_Mutation_p.E400D|SERPINA1_ENST00000404814.4_Missense_Mutation_p.E400D|SERPINA1_ENST00000440909.1_Missense_Mutation_p.E400D|SERPINA1_ENST00000355814.4_Missense_Mutation_p.E400D|SERPINA1_ENST00000393088.4_Missense_Mutation_p.E400D	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	400			E -> D (in M2 and M3; associated with H- 125 in M2; dbSNP:rs1303). {ECO:0000269|PubMed:17650587, ECO:0000269|PubMed:2394452}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.E400D(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		TGGTATTTTGTTCAATCATTA	0.512													T|||	1404	0.280351	0.0923	0.3573	5008	,	,		18671	0.3165		0.2485	False		,,,				2504	0.4755				p.E400D		Atlas-SNP	.											SERPINA1,NS,carcinoma,0,1	SERPINA1	51	1	1	Substitution - Missense(1)	stomach(1)	c.A1200C						PASS	.	T	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	472,3934	224.3+/-240.5	28,416,1759	118.0	125.0	123.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1200,1200,1200,1200,1200,1200,1200,1200,1200,1200,1200	-9.0	0.0	14	dbSNP_36	123	2222,6378	376.9+/-338.3	305,1612,2383	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	SERPINA1	NM_000295.4,NM_001002235.2,NM_001002236.2,NM_001127700.1,NM_001127701.1,NM_001127702.1,NM_001127703.1,NM_001127704.1,NM_001127705.1,NM_001127706.1,NM_001127707.1	45,45,45,45,45,45,45,45,45,45,45	333,2028,4142	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	25.8372,10.7127,20.7135	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	400/419,400/419,400/419,400/419,400/419,400/419,400/419,400/419,400/419,400/419,400/419	94844843	2694,10312	2203	4300	6503	SO:0001583	missense	5265	exon7			ATTTTGTTCAATC	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"""Serine (or cysteine) peptidase inhibitors"""	8941	protein-coding gene	gene with protein product	"""protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"""	107400	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"""	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.1200A>C	14.37:g.94844843T>G	ENSP00000416066:p.Glu400Asp	Somatic	247	1	0.00404858		WXS	Illumina HiSeq	Phase_I	283	136	0.480565	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Missense_Mutation	SNP	ENST00000448921.1	37	CCDS9925.1	495	0.22664835164835165	34	0.06910569105691057	117	0.32320441988950277	167	0.291958041958042	177	0.23350923482849603	T	0.331	-0.956393	0.02267	0.107127	0.258372	ENSG00000197249	ENST00000440909;ENST00000448921;ENST00000437397;ENST00000355814;ENST00000393087;ENST00000393088;ENST00000404814;ENST00000449399	D;D;D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	4.51	-9.02	0.00741	Serpin domain (3);	0.494653	0.17631	N	0.167400	T	0.00012	0.0000	N	0.04746	-0.17	0.80722	P	0.0	B	0.02656	0.0	B	0.14023	0.01	T	0.46527	-0.9185	9	0.02654	T	1	.	0.4433	0.00489	0.2324:0.1647:0.2353:0.3676	rs1303;rs17579;rs3191110;rs52815346;rs61680487;rs1303	400	P01009	A1AT_HUMAN	D	400	ENSP00000390299:E400D;ENSP00000416066:E400D;ENSP00000408474:E400D;ENSP00000348068:E400D;ENSP00000376802:E400D;ENSP00000376803:E400D;ENSP00000385960:E400D;ENSP00000416354:E400D	ENSP00000348068:E400D	E	-	3	2	SERPINA1	93914596	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.088000	0.00297	-1.732000	0.01359	-1.287000	0.01368	GAA	T|0.775;G|0.225	0.225	strong		0.512	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235	
GLCCI1	113263	hgsc.bcm.edu	37	7	8125964	8125964	+	Silent	SNP	C	C	T	rs929509	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:8125964C>T	ENST00000223145.5	+	8	1997	c.1440C>T	c.(1438-1440)tcC>tcT	p.S480S		NM_138426.3	NP_612435.1	Q86VQ1	GLCI1_HUMAN	glucocorticoid induced transcript 1	480						cytoplasm (GO:0005737)		p.S480S(1)		endometrium(4)|large_intestine(4)|lung(13)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	25		Ovarian(82;0.0608)		UCEC - Uterine corpus endometrioid carcinoma (126;0.206)		TCAAGAACTCCCCTAACTCTG	0.498													T|||	3744	0.747604	0.8797	0.7507	5008	,	,		19666	0.7312		0.666	False		,,,				2504	0.6677				p.S480S		Atlas-SNP	.											GLCCI1,NS,carcinoma,0,1	GLCCI1	50	1	1	Substitution - coding silent(1)	stomach(1)	c.C1440T						PASS	.	T		3769,637	277.5+/-273.7	1621,527,55	192.0	212.0	205.0		1440	-0.1	1.0	7	dbSNP_86	205	5937,2663	428.4+/-355.9	2042,1853,405	no	coding-synonymous	GLCCI1	NM_138426.2		3663,2380,460	TT,TC,CC		30.9651,14.4576,25.3729		480/548	8125964	9706,3300	2203	4300	6503	SO:0001819	synonymous_variant	113263	exon8			GAACTCCCCTAAC	BC050291	CCDS34601.1	7p22.2	2008-08-18			ENSG00000106415	ENSG00000106415			18713	protein-coding gene	gene with protein product		614283					Standard	NM_138426		Approved	GIG18, FAM117C, TSSN1	uc003srk.4	Q86VQ1	OTTHUMG00000151984	ENST00000223145.5:c.1440C>T	7.37:g.8125964C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	139	138	0.992806	NM_138426	A4D103|Q96FD0	Silent	SNP	ENST00000223145.5	37	CCDS34601.1																																																																																			C|0.255;T|0.745	0.745	strong		0.498	GLCCI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324672.1	NM_138426	
BBS10	79738	hgsc.bcm.edu	37	12	76740149	76740149	+	Missense_Mutation	SNP	G	G	A	rs35676114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:76740149G>A	ENST00000393262.3	-	2	1699	c.1616C>T	c.(1615-1617)cCa>cTa	p.P539L		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	539			P -> L (in dbSNP:rs35676114). {ECO:0000269|PubMed:20120035}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|regulation of protein complex assembly (GO:0043254)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell projection (GO:0042995)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						CTTGAGTAATGGTTCATAATA	0.358									Bardet-Biedl syndrome				G|||	168	0.0335463	0.0023	0.0375	5008	,	,		19330	0.0		0.0746	False		,,,				2504	0.0654				p.P539L		Atlas-SNP	.											BBS10,NS,carcinoma,-1,1	BBS10	46	1	0			c.C1616T						scavenged	.	G	LEU/PRO	79,4327	68.7+/-106.4	1,77,2125	131.0	127.0	128.0		1616	0.8	0.0	12	dbSNP_126	128	638,7962	163.8+/-216.2	24,590,3686	yes	missense	BBS10	NM_024685.3	98	25,667,5811	AA,AG,GG		7.4186,1.793,5.5128	benign	539/724	76740149	717,12289	2203	4300	6503	SO:0001583	missense	79738	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	AGTAATGGTTCAT	BC026355	CCDS9014.2	12q21.2	2014-06-17	2006-04-28	2006-04-28	ENSG00000179941	ENSG00000179941		"""Heat Shock Proteins / Chaperonins"""	26291	protein-coding gene	gene with protein product		610148	"""chromosome 12 open reading frame 58"""	C12orf58		16582908	Standard	NM_024685		Approved	FLJ23560	uc001syd.1	Q8TAM1	OTTHUMG00000147352	ENST00000393262.3:c.1616C>T	12.37:g.76740149G>A	ENSP00000376946:p.Pro539Leu	Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_024685	Q96CW2|Q9H5D2	Missense_Mutation	SNP	ENST00000393262.3	37	CCDS9014.2	77	0.035256410256410256	3	0.006097560975609756	19	0.052486187845303865	0	0.0	55	0.07255936675461741	G	0.021	-1.422772	0.01126	0.01793	0.074186	ENSG00000179941	ENST00000393262	D	0.84589	-1.87	4.95	0.792	0.18625	.	0.883658	0.09546	N	0.787526	T	0.25606	0.0623	L	0.43152	1.355	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.43442	-0.9391	10	0.33940	T	0.23	-0.7605	8.2402	0.31656	0.4803:0.0:0.5197:0.0	rs35676114	539	Q8TAM1	BBS10_HUMAN	L	539	ENSP00000376946:P539L	ENSP00000376946:P539L	P	-	2	0	BBS10	75264280	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	0.335000	0.19806	0.038000	0.15604	0.655000	0.94253	CCA	G|0.948;A|0.052	0.052	strong		0.358	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685	
DEFB129	140881	hgsc.bcm.edu	37	20	210306	210306	+	Missense_Mutation	SNP	C	C	G	rs1053783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:210306C>G	ENST00000246105.4	+	2	477	c.446C>G	c.(445-447)aCc>aGc	p.T149S		NM_080831.3	NP_543021.1	Q9H1M3	DB129_HUMAN	defensin, beta 129	149			T -> S (in dbSNP:rs1053783).		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(1)|ovary(1)|stomach(1)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			AAGAGTAACACCAAAGAAAGC	0.502													C|||	1248	0.249201	0.469	0.1196	5008	,	,		18729	0.2351		0.0915	False		,,,				2504	0.2209				p.T149S		Atlas-SNP	.											.	DEFB129	24	.	0			c.C446G						PASS	.	C	SER/THR	1840,2566	536.8+/-374.6	389,1062,752	136.0	123.0	127.0		446	2.3	0.0	20	dbSNP_86	127	774,7826	183.5+/-231.7	37,700,3563	yes	missense	DEFB129	NM_080831.3	58	426,1762,4315	GG,GC,CC		9.0,41.7612,20.0984	probably-damaging	149/184	210306	2614,10392	2203	4300	6503	SO:0001583	missense	140881	exon2			GTAACACCAAAGA	AY358186	CCDS12992.1	20p13	2010-03-30	2002-05-09	2002-05-10	ENSG00000125903	ENSG00000125903		"""Defensins, beta"""	16218	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 87"""	C20orf87		11854508	Standard	NM_080831		Approved	bA530N10.3, DEFB-29	uc002wda.3	Q9H1M3	OTTHUMG00000031618	ENST00000246105.4:c.446C>G	20.37:g.210306C>G	ENSP00000246105:p.Thr149Ser	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_080831	Q8NES7	Missense_Mutation	SNP	ENST00000246105.4	37	CCDS12992.1	459	0.21016483516483517	222	0.45121951219512196	43	0.11878453038674033	127	0.22202797202797203	67	0.08839050131926121	C	14.43	2.533782	0.45073	0.417612	0.09	ENSG00000125903	ENST00000246105	T	0.38401	1.14	4.25	2.27	0.28462	.	0.739381	0.12150	N	0.494997	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.41978	0.767	B	0.33196	0.159	T	0.48175	-0.9058	9	0.49607	T	0.09	-9.4267	6.8928	0.24238	0.0:0.7886:0.0:0.2114	rs1053783;rs3194381;rs52805850;rs59902862;rs1053783	149	Q9H1M3	DB129_HUMAN	S	149	ENSP00000246105:T149S	ENSP00000246105:T149S	T	+	2	0	DEFB129	158306	0.001000	0.12720	0.018000	0.16275	0.084000	0.17831	0.085000	0.14912	0.725000	0.32318	0.462000	0.41574	ACC	C|0.798;G|0.202	0.202	strong		0.502	DEFB129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077430.2	NM_080831	
NUDT10	170685	hgsc.bcm.edu	37	X	51076018	51076018	+	Silent	SNP	C	C	T	rs12846945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:51076018C>T	ENST00000376006.3	+	2	421	c.201C>T	c.(199-201)taC>taT	p.Y67Y	NUDT10_ENST00000356450.2_Silent_p.Y67Y	NM_153183.2	NP_694853.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 10	232					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(1)|prostate(3)|upper_aerodigestive_tract(1)	16	Ovarian(276;0.236)					GAGAGGTGTACGAAGAGGCGG	0.642													C|||	371	0.0982781	0.0953	0.0576	3775	,	,		9846	0.0119		0.1233	False		,,,				2504	0.0706				p.Y67Y	NSCLC(90;1817 2035 37909 38249)	Atlas-SNP	.											.	NUDT10	28	.	0			c.C201T						PASS	.	C		516,3319		29,384,74,1219,497	47.0	57.0	54.0		201	0.3	1.0	X	dbSNP_121	54	1094,5634		68,651,307,1709,1565	no	coding-synonymous	NUDT10	NM_153183.2		97,1035,381,2928,2062	TT,TC,T,CC,C		16.2604,13.455,15.2419		67/165	51076018	1610,8953	2203	4300	6503	SO:0001819	synonymous_variant	170685	exon2			GGTGTACGAAGAG	AF469196	CCDS35278.1	Xp11.22-p11.1	2014-05-20			ENSG00000122824	ENSG00000122824		"""Nudix motif containing"""	17621	protein-coding gene	gene with protein product		300527				12105228	Standard	NM_153183		Approved	DIPP3a, hDIPP3alpha	uc004dph.3	Q8NFP7	OTTHUMG00000021530	ENST00000376006.3:c.201C>T	X.37:g.51076018C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	145	138	0.951724	NM_153183	Q8NBN1|Q8NCB9|Q8NG25	Silent	SNP	ENST00000376006.3	37	CCDS35278.1																																																																																			C|0.864;T|0.136	0.136	strong		0.642	NUDT10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056578.1	NM_153183	
USP31	57478	hgsc.bcm.edu	37	16	23098422	23098422	+	Missense_Mutation	SNP	A	A	G	rs13339649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:23098422A>G	ENST00000219689.7	-	9	1612	c.1613T>C	c.(1612-1614)aTa>aCa	p.I538T		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0	DUSP 1. {ECO:0000255|PROSITE- ProRule:PRU00613}.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		CCTTTCTACTATTGGGTGGCA	0.373													G|||	1212	0.242013	0.1528	0.3876	5008	,	,		17229	0.1577		0.333	False		,,,				2504	0.2526				p.I538T		Atlas-SNP	.											.	USP31	122	.	0			c.T1613C						PASS	.	G	THR/ILE	784,3610	739.3+/-411.1	61,662,1474	43.0	41.0	41.0		1613	5.2	0.3	16	dbSNP_121	41	2719,5881	672.8+/-403.0	451,1817,2032	yes	missense	USP31	NM_020718.3	89	512,2479,3506	GG,GA,AA		31.6163,17.8425,26.9586	benign	538/1353	23098422	3503,9491	2197	4300	6497	SO:0001583	missense	57478	exon9			TCTACTATTGGGT	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.1613T>C	16.37:g.23098422A>G	ENSP00000219689:p.Ile538Thr	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	146	69	0.472603	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	553	0.2532051282051282	79	0.16056910569105692	122	0.3370165745856354	101	0.17657342657342656	251	0.3311345646437995	G	0.103	-1.149700	0.01714	0.178425	0.316163	ENSG00000103404	ENST00000219689	T	0.05855	3.38	5.16	5.16	0.70880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.216830	0.38605	N	0.001629	T	0.00012	0.0000	N	0.01824	-0.7	0.09310	P	0.9999999999999974	B	0.02656	0.0	B	0.01281	0.0	T	0.44097	-0.9350	9	0.06099	T	0.92	-1.3192	13.0274	0.58823	0.0773:0.0:0.9227:0.0	rs13339649;rs17796752;rs52819210;rs57007803;rs13339649	538	Q70CQ4	UBP31_HUMAN	T	538	ENSP00000219689:I538T	ENSP00000219689:I538T	I	-	2	0	USP31	23005923	1.000000	0.71417	0.349000	0.25694	0.180000	0.23129	6.345000	0.72995	1.194000	0.43101	-0.349000	0.07799	ATA	A|0.742;G|0.258	0.258	strong		0.373	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
ERO1LB	56605	hgsc.bcm.edu	37	1	236381825	236381825	+	Missense_Mutation	SNP	G	G	C	rs1055851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:236381825G>C	ENST00000354619.5	-	16	1596	c.1395C>G	c.(1393-1395)caC>caG	p.H465Q	GPR137B_ENST00000477559.1_Intron	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	465			H -> Q (in dbSNP:rs1055851). {ECO:0000269|PubMed:10818100}.		4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	ATTACCTACTGTGTTGTAATA	0.323													G|||	2851	0.569289	0.4803	0.5821	5008	,	,		15123	0.8839		0.4006	False		,,,				2504	0.5297				p.H465Q		Atlas-SNP	.											.	ERO1LB	48	.	0			c.C1395G						PASS	.	G	GLN/HIS	2147,2251	560.0+/-380.4	511,1125,563	57.0	63.0	61.0		1395	4.6	1.0	1	dbSNP_86	61	3443,5119	496.6+/-374.3	679,2085,1517	yes	missense	ERO1LB	NM_019891.3	24	1190,3210,2080	CC,CG,GG		40.2126,48.8176,43.1327	benign	465/468	236381825	5590,7370	2199	4281	6480	SO:0001583	missense	56605	exon16			CCTACTGTGTTGT	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.1395C>G	1.37:g.236381825G>C	ENSP00000346635:p.His465Gln	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	204	84	0.411765	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Missense_Mutation	SNP	ENST00000354619.5	37	CCDS31064.1	1234	0.565018315018315	229	0.4654471544715447	209	0.5773480662983426	509	0.8898601398601399	287	0.3786279683377309	G	9.953	1.220760	0.22457	0.488176	0.402126	ENSG00000086619	ENST00000354619	T	0.29397	1.57	5.54	4.62	0.57501	.	0.301526	0.36932	N	0.002322	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999999994	B	0.06786	0.001	B	0.04013	0.001	T	0.37731	-0.9693	9	0.21014	T	0.42	-19.4628	10.5749	0.45221	0.0766:0.169:0.7544:0.0	rs1055851;rs1749597;rs3196339;rs10317930;rs12735870;rs52808904;rs1055851	465	Q86YB8	ERO1B_HUMAN	Q	465	ENSP00000346635:H465Q	ENSP00000346635:H465Q	H	-	3	2	ERO1LB	234448448	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.371000	0.20450	2.600000	0.87896	0.650000	0.86243	CAC	G|0.530;C|0.470	0.470	strong		0.323	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
DCPS	28960	hgsc.bcm.edu	37	11	126215285	126215285	+	Missense_Mutation	SNP	G	G	A	rs140377449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:126215285G>A	ENST00000263579.4	+	6	1120	c.791G>A	c.(790-792)cGa>cAa	p.R264Q	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	264					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)		GACCATCTGCGAGTATACCTG	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		18562	0.0		0.0	False		,,,				2504	0.002				p.R264Q		Atlas-SNP	.											.	DCPS	33	.	0			c.G791A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	205.0	133.0	157.0		791	5.2	0.2	11	dbSNP_134	157	11,8585	8.4+/-32.0	0,11,4287	yes	missense	DCPS	NM_014026.3	43	0,11,6488	AA,AG,GG		0.128,0.0,0.0846	probably-damaging	264/338	126215285	11,12987	2201	4298	6499	SO:0001583	missense	28960	exon6			ATCTGCGAGTATA	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.791G>A	11.37:g.126215285G>A	ENSP00000263579:p.Arg264Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	54	23	0.425926	NM_014026	Q8NHL8|Q9Y2S5	Missense_Mutation	SNP	ENST00000263579.4	37	CCDS8473.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.344847	0.82022	0.0	0.00128	ENSG00000110063	ENST00000263579	D	0.96200	-3.94	5.16	5.16	0.70880	Histidine triad, conserved site (1);Histidine triad-like motif (1);	0.000000	0.85682	D	0.000000	D	0.98385	0.9463	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99364	1.0918	10	0.66056	D	0.02	-12.5139	18.7289	0.91726	0.0:0.0:1.0:0.0	.	264	Q96C86	DCPS_HUMAN	Q	264	ENSP00000263579:R264Q	ENSP00000263579:R264Q	R	+	2	0	DCPS	125720495	1.000000	0.71417	0.226000	0.23910	0.260000	0.26232	9.476000	0.97823	2.421000	0.82119	0.555000	0.69702	CGA	G|0.999;A|0.001	0.001	strong		0.667	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925520	47925520	+	Missense_Mutation	SNP	C	C	T	rs141646493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47925520C>T	ENST00000289672.2	-	18	3019	c.2969G>A	c.(2968-2970)cGg>cAg	p.R990Q		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	990	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TGAAGGTTCCCGTGAGAATGG	0.587													c|||	9	0.00179712	0.0023	0.0029	5008	,	,		15149	0.0		0.004	False		,,,				2504	0.0				p.R990Q		Atlas-SNP	.											PKD1L1,colon,carcinoma,-1,1	PKD1L1	328	1	0			c.G2969A						scavenged	.	T	GLN/ARG	14,4392	22.3+/-47.3	0,14,2189	94.0	86.0	89.0		2969	-8.7	0.0	7	dbSNP_134	89	62,8538	39.8+/-96.3	1,60,4239	yes	missense	PKD1L1	NM_138295.3	43	1,74,6428	TT,TC,CC		0.7209,0.3177,0.5843	possibly-damaging	990/2850	47925520	76,12930	2203	4300	6503	SO:0001583	missense	168507	exon18			GGTTCCCGTGAGA	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.2969G>A	7.37:g.47925520C>T	ENSP00000289672:p.Arg990Gln	Somatic	145	2	0.0137931		WXS	Illumina HiSeq	Phase_I	194	98	0.505155	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	c	5.043	0.193531	0.09599	0.003177	0.007209	ENSG00000158683	ENST00000289672	T	0.19938	2.11	4.97	-8.7	0.00851	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	165.707000	0.00166	N	0.000000	T	0.04588	0.0125	N	0.08118	0	0.09310	N	1	B	0.28605	0.217	B	0.14578	0.011	T	0.18366	-1.0339	10	0.19590	T	0.45	0.4961	1.9019	0.03269	0.1463:0.1646:0.3674:0.3217	.	990	Q8TDX9	PK1L1_HUMAN	Q	990	ENSP00000289672:R990Q	ENSP00000289672:R990Q	R	-	2	0	PKD1L1	47892045	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.006000	0.01459	-2.302000	0.00657	-0.835000	0.03068	CGG	C|0.995;T|0.005	0.005	strong		0.587	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
LRIT3	345193	hgsc.bcm.edu	37	4	110773067	110773067	+	Missense_Mutation	SNP	G	G	A	rs4698797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:110773067G>A	ENST00000594814.1	+	2	524	c.524G>A	c.(523-525)aGc>aAc	p.S175N	LRIT3_ENST00000327908.3_De_novo_Start_OutOfFrame|LRIT3_ENST00000379920.3_Missense_Mutation_p.S130N	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	175			S -> N (in dbSNP:rs4698797). {ECO:0000269|PubMed:15489334}.		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)		TTCCTGGAGAGCTGGACTCAT	0.478													G|||	2363	0.471845	0.4009	0.3948	5008	,	,		18697	0.4901		0.6382	False		,,,				2504	0.4325				p.S175N		Atlas-SNP	.											.	LRIT3	107	.	0			c.G524A						PASS	.	G	ASN/SER	624,760		133,358,201	34.0	27.0	29.0		389	3.8	1.0	4	dbSNP_111	29	2064,1118		682,700,209	yes	missense	LRIT3	NM_198506.2	46	815,1058,410	AA,AG,GG		35.1351,45.0867,41.1301	possibly-damaging	130/635	110773067	2688,1878	692	1591	2283	SO:0001583	missense	345193	exon2			TGGAGAGCTGGAC	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.524G>A	4.37:g.110773067G>A	ENSP00000469759:p.Ser175Asn	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	99	97	0.979798	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	1116	0.510989010989011	193	0.39227642276422764	164	0.4530386740331492	279	0.48776223776223776	480	0.633245382585752	G	16.17	3.047368	0.55110	0.450867	0.648649	ENSG00000183423	ENST00000379920	T	0.55760	0.5	5.61	3.78	0.43462	.	0.137829	0.64402	D	0.000005	T	0.00012	0.0000	N	0.12471	0.22	0.09310	P	1.0	D	0.54047	0.964	P	0.57283	0.817	T	0.28618	-1.0038	9	0.14252	T	0.57	.	8.2395	0.31652	0.0:0.117:0.5263:0.3568	rs4698797;rs56515492;rs57791998;rs4698797	130	Q3SXY7	LRIT3_HUMAN	N	130	ENSP00000369252:S130N	ENSP00000369252:S130N	S	+	2	0	LRIT3	110992516	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	5.263000	0.65507	2.793000	0.96121	0.655000	0.94253	AGC	G|0.486;A|0.514	0.514	strong		0.478	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
CCPG1	9236	hgsc.bcm.edu	37	15	55664220	55664220	+	Silent	SNP	G	G	A	rs3203152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:55664220G>A	ENST00000310958.6	-	6	775	c.477C>T	c.(475-477)gaC>gaT	p.D159D	CCPG1_ENST00000569205.1_Silent_p.D159D|MIR628_ENST00000385229.1_RNA|CCPG1_ENST00000442196.3_Silent_p.D159D|DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000425574.3_Silent_p.D159D	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	159	Interaction with MCF2L and SRC. {ECO:0000250}.				cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		TTGATTCATCGTCACTAGGCT	0.378													G|||	877	0.17512	0.4811	0.0706	5008	,	,		18918	0.0089		0.0855	False		,,,				2504	0.0992				p.D159D		Atlas-SNP	.											.	CCPG1	74	.	0			c.C477T						PASS	.	G	,,,	1495,2167		307,881,643	64.0	61.0	62.0		477,477,477,477	-11.9	0.0	15	dbSNP_105	62	735,7439		29,677,3381	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CCPG1	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_020739.3	,,,	336,1558,4024	AA,AG,GG		8.9919,40.8247,18.8408	,,,	159/808,159/425,159/758,159/758	55664220	2230,9606	1831	4087	5918	SO:0001819	synonymous_variant	9236	exon6			TTCATCGTCACTA	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.477C>T	15.37:g.55664220G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Silent	SNP	ENST00000310958.6	37	CCDS42039.1																																																																																			G|0.852;A|0.148	0.148	strong		0.378	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
CROCC	9696	hgsc.bcm.edu	37	1	17265507	17265507	+	Missense_Mutation	SNP	C	C	T	rs201951425	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17265507C>T	ENST00000375541.5	+	12	1547	c.1478C>T	c.(1477-1479)cCg>cTg	p.P493L	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGCGGACCCCGTCCCCACCG	0.736																																					p.P493L		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.C1478T						scavenged	.	C	LEU/PRO	55,4215		0,55,2080	11.0	11.0	11.0		1478	5.4	1.0	1	dbSNP_134	11	247,8075		0,247,3914	no	missense	CROCC	NM_014675.3	98	0,302,5994	TT,TC,CC		2.968,1.2881,2.3983	probably-damaging	493/2018	17265507	302,12290	2135	4161	6296	SO:0001583	missense	9696	exon12			GGACCCCGTCCCC	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.1478C>T	1.37:g.17265507C>T	ENSP00000364691:p.Pro493Leu	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	12	8	0.666667	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	36	0.016483516483516484	9	0.018292682926829267	7	0.019337016574585635	0	0.0	20	0.026385224274406333	C	15.49	2.847709	0.51164	0.012881	0.02968	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.11385	2.78	5.39	5.39	0.77823	.	.	.	.	.	T	0.08268	0.0206	L	0.55481	1.735	0.50813	D	0.99989	D;P;D	0.65815	0.981;0.803;0.995	B;B;P	0.59115	0.421;0.095;0.852	T	0.00200	-1.1927	9	0.27785	T	0.31	.	14.606	0.68478	0.0:0.8534:0.1466:0.0	.	356;356;493	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	L	493;374	ENSP00000364691:P493L	ENSP00000364691:P493L	P	+	2	0	CROCC	17138094	0.934000	0.31675	0.991000	0.47740	0.293000	0.27360	5.113000	0.64640	2.702000	0.92279	0.561000	0.74099	CCG	C|0.983;T|0.017	0.017	strong		0.736	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
WNT7A	7476	hgsc.bcm.edu	37	3	13896284	13896284	+	Silent	SNP	C	C	T	rs12639607	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:13896284C>T	ENST00000285018.4	-	3	619	c.315G>A	c.(313-315)gcG>gcA	p.A105A		NM_004625.3	NP_004616.2	O00755	WNT7A_HUMAN	wingless-type MMTV integration site family, member 7A	105					asymmetric protein localization (GO:0008105)|canonical Wnt signaling pathway (GO:0060070)|cartilage condensation (GO:0001502)|cell fate commitment (GO:0045165)|cell proliferation in forebrain (GO:0021846)|cellular response to transforming growth factor beta stimulus (GO:0071560)|central nervous system vasculogenesis (GO:0022009)|cerebellar granule cell differentiation (GO:0021707)|chondrocyte differentiation (GO:0002062)|dorsal/ventral pattern formation (GO:0009953)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment of cell polarity (GO:0030010)|lens fiber cell development (GO:0070307)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neurogenesis (GO:0050768)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|non-canonical Wnt signaling pathway (GO:0035567)|oviduct development (GO:0060066)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|positive regulation of JNK cascade (GO:0046330)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of axon diameter (GO:0031133)|response to estradiol (GO:0032355)|sex differentiation (GO:0007548)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration (GO:0014834)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|stem cell development (GO:0048864)|synapse organization (GO:0050808)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway involved in wound healing, spreading of epidermal cells (GO:0035659)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	24						CGTAGGTGAACGCAGCCTCCC	0.627													c|||	1109	0.221446	0.0257	0.1916	5008	,	,		19482	0.5813		0.17	False		,,,				2504	0.1892				p.A105A		Atlas-SNP	.											WNT7A,caecum,carcinoma,-1,3	WNT7A	70	3	0			c.G315A						PASS	.	T		270,4136	801.7+/-415.6	7,256,1940	64.0	63.0	63.0		315	0.6	1.0	3	dbSNP_120	63	1563,7037	744.7+/-407.2	133,1297,2870	no	coding-synonymous	WNT7A	NM_004625.3		140,1553,4810	TT,TC,CC		18.1744,6.128,14.0935		105/350	13896284	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	7476	exon3			GGTGAACGCAGCC	D83175	CCDS2616.1	3p25	2008-07-18			ENSG00000154764	ENSG00000154764		"""Wingless-type MMTV integration sites"""	12786	protein-coding gene	gene with protein product	"""proto-oncogene Wnt7a protein"""	601570				8893824, 9161407	Standard	NM_004625		Approved		uc003bye.1	O00755	OTTHUMG00000129803	ENST00000285018.4:c.315G>A	3.37:g.13896284C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	32	22	0.6875	NM_004625	Q96H90|Q9Y560	Silent	SNP	ENST00000285018.4	37	CCDS2616.1																																																																																			C|0.826;T|0.174	0.174	strong		0.627	WNT7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252031.2	NM_004625	
LAT	27040	hgsc.bcm.edu	37	16	28997997	28997997	+	Silent	SNP	G	G	A	rs1131543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:28997997G>A	ENST00000360872.5	+	6	525	c.447G>A	c.(445-447)gcG>gcA	p.A149A	RP11-264B17.3_ENST00000569969.1_RNA|RP11-264B17.5_ENST00000561471.1_RNA|LAT_ENST00000354453.4_Silent_p.A139A|LAT_ENST00000454369.2_Silent_p.A119A|LAT_ENST00000395456.2_Silent_p.A120A|LAT_ENST00000563964.1_3'UTR|LAT_ENST00000395461.3_Silent_p.A156A|LAT_ENST00000564277.1_Silent_p.A119A|LAT_ENST00000566177.1_Silent_p.A148A			O43561	LAT_HUMAN	linker for activation of T cells	149					blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|gene expression (GO:0010467)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|lymphocyte homeostasis (GO:0002260)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|regulation of T cell activation (GO:0050863)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|immunological synapse (GO:0001772)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|SH3/SH2 adaptor activity (GO:0005070)			large_intestine(2)|lung(3)|urinary_tract(1)	6		Hepatocellular(780;0.244)				GTGAGGATGCGGATGAGGATG	0.647													G|||	1198	0.239217	0.1142	0.1772	5008	,	,		16317	0.3125		0.3052	False		,,,				2504	0.3088				p.A156A		Atlas-SNP	.											.	LAT	22	.	0			c.G468A						PASS	.	G	,,,	621,3773	268.0+/-268.2	46,529,1622	88.0	78.0	81.0		360,357,468,447	-8.6	0.0	16	dbSNP_86	81	2797,5803	443.4+/-360.4	460,1877,1963	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAT	NM_001014987.1,NM_001014988.1,NM_001014989.1,NM_014387.3	,,,	506,2406,3585	AA,AG,GG		32.5233,14.1329,26.3044	,,,	120/234,119/233,156/270,149/263	28997997	3418,9576	2197	4300	6497	SO:0001819	synonymous_variant	27040	exon8			GGATGCGGATGAG	AF036905	CCDS10647.1, CCDS32425.1, CCDS45455.1, CCDS53999.1	16q13	2011-11-01			ENSG00000213658	ENSG00000213658			18874	protein-coding gene	gene with protein product	"""linker for activation of T cells, transmembrane adaptor"""	602354				9489702	Standard	NM_014387		Approved	LAT1	uc010vdj.2	O43561	OTTHUMG00000131761	ENST00000360872.5:c.447G>A	16.37:g.28997997G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	90	52	0.577778	NM_001014989	B7WPI0|C7C5T6|G5E9K3|O43919	Silent	SNP	ENST00000360872.5	37	CCDS10647.1																																																																																			G|0.742;A|0.258	0.258	strong		0.647	LAT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254688.2		
CMTM1	113540	hgsc.bcm.edu	37	16	66600479	66600479	+	Silent	SNP	G	G	A	rs7193473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:66600479G>A	ENST00000457188.2	+	1	184	c.63G>A	c.(61-63)ccG>ccA	p.P21P	CMTM1_ENST00000529506.1_5'UTR|CMTM1_ENST00000533666.1_Silent_p.P21P|CMTM1_ENST00000336328.6_Silent_p.P21P|CKLF-CMTM1_ENST00000527729.1_Intron|CMTM1_ENST00000535705.1_Silent_p.P21P|CMTM1_ENST00000533953.1_Silent_p.P21P|CMTM1_ENST00000528324.1_Silent_p.P21P|CMTM1_ENST00000379500.2_Silent_p.P21P|CMTM1_ENST00000531885.1_Silent_p.P21P|CMTM1_ENST00000332695.7_Silent_p.P21P|CMTM1_ENST00000328020.6_Silent_p.P21P	NM_181269.2	NP_851786.1	Q8IZ96	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain containing 1	21	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0702)|Epithelial(162;0.222)		TGAAACAACCGGAGACTGCCG	0.617													A|||	1606	0.320687	0.5643	0.2723	5008	,	,		12627	0.3006		0.1362	False		,,,				2504	0.2362				p.P21P		Atlas-SNP	.											.	CMTM1	34	.	0			c.G63A						PASS	.	A	,,,,,,,,,,	2276,2126	578.7+/-384.7	572,1132,497	76.0	67.0	70.0		,,,63,63,63,63,63,63,63,63	-5.2	0.0	16	dbSNP_116	70	1031,7569	771.9+/-407.7	71,889,3340	no	intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CMTM1,CKLF-CMTM1	NM_001202509.1,NM_001204098.1,NM_001204099.1,NM_052999.3,NM_181268.2,NM_181269.2,NM_181270.2,NM_181271.2,NM_181272.2,NM_181283.2,NM_181296.2	,,,,,,,,,,	643,2021,3837	AA,AG,GG		11.9884,48.2962,25.4345	,,,,,,,,,,	,,,21/287,21/232,21/170,21/115,21/123,21/117,21/62,21/29	66600479	3307,9695	2201	4300	6501	SO:0001819	synonymous_variant	113540	exon1			ACAACCGGAGACT	AF278577	CCDS10810.1, CCDS10811.1, CCDS10812.2, CCDS45503.1, CCDS45504.1, CCDS54019.1, CCDS54020.1, CCDS54021.1	16q22.1	2009-10-06	2005-11-08	2005-11-08	ENSG00000089505	ENSG00000089505			19172	protein-coding gene	gene with protein product		607884	"""chemokine-like factor super family 1"", ""chemokine-like factor superfamily 1"""	CKLFSF1		12782130	Standard	NM_181268		Approved	CKLFH1a, CKLFH	uc002epr.4	Q8IZ96	OTTHUMG00000137502	ENST00000457188.2:c.63G>A	16.37:g.66600479G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	136	80	0.588235	NM_181271	Q2PPY5|Q6PEV5|Q8IU76|Q8IU83|Q8IU86|Q8IU93|Q8IZ87|Q8IZ88|Q8IZ89|Q8IZ90|Q8IZ91|Q8IZ92|Q8IZ93|Q8IZ94|Q8IZ95|Q96JC2|Q96JC3	Silent	SNP	ENST00000457188.2	37	CCDS45503.1																																																																																			G|0.721;A|0.279	0.279	strong		0.617	CMTM1-015	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390261.2	NM_052999	
FGL1	2267	hgsc.bcm.edu	37	8	17731935	17731935	+	Missense_Mutation	SNP	T	T	C	rs35311020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17731935T>C	ENST00000398056.2	-	6	1155	c.340A>G	c.(340-342)Atg>Gtg	p.M114V	FGL1_ENST00000381840.2_Missense_Mutation_p.M114V|FGL1_ENST00000522444.1_Missense_Mutation_p.M114V|FGL1_ENST00000381841.2_Missense_Mutation_p.M114V|FGL1_ENST00000518650.1_Missense_Mutation_p.M114V|FGL1_ENST00000427924.1_Missense_Mutation_p.M114V|FGL1_ENST00000398054.1_Missense_Mutation_p.M114V			Q08830	FGL1_HUMAN	fibrinogen-like 1	114	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		M -> V (in dbSNP:rs35311020).		adipose tissue development (GO:0060612)|cholesterol metabolic process (GO:0008203)|regulation of glucose metabolic process (GO:0010906)|response to stilbenoid (GO:0035634)	extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)	13				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		CCATCGGACATGTCACAATAA	0.383													T|||	30	0.00599042	0.0008	0.0029	5008	,	,		16782	0.0		0.007	False		,,,				2504	0.0204				p.M114V		Atlas-SNP	.											.	FGL1	31	.	0			c.A340G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET,VAL/MET	5,4401	9.9+/-24.2	0,5,2198	139.0	136.0	137.0		340,340,340,340	5.1	1.0	8	dbSNP_126	137	63,8537	38.8+/-94.9	0,63,4237	no	missense,missense,missense,missense	FGL1	NM_004467.3,NM_147203.2,NM_201552.1,NM_201553.1	21,21,21,21	0,68,6435	CC,CT,TT		0.7326,0.1135,0.5228	probably-damaging,probably-damaging,probably-damaging,probably-damaging	114/313,114/313,114/313,114/313	17731935	68,12938	2203	4300	6503	SO:0001583	missense	2267	exon5			CGGACATGTCACA	D14446	CCDS6004.1	8p22	2013-02-06			ENSG00000104760	ENSG00000104760		"""Fibrinogen C domain containing"""	3695	protein-coding gene	gene with protein product		605776				8390249	Standard	NM_004467		Approved	HFREP-1	uc003wyb.3	Q08830	OTTHUMG00000096989	ENST00000398056.2:c.340A>G	8.37:g.17731935T>C	ENSP00000381133:p.Met114Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_201553	A6NKU4|Q4PJH9|Q53YF1|Q8NG32|Q96KW6|Q96QM6	Missense_Mutation	SNP	ENST00000398056.2	37	CCDS6004.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	21.1	4.097638	0.76870	0.001135	0.007326	ENSG00000104760	ENST00000221204;ENST00000398056;ENST00000521427;ENST00000522444;ENST00000381841;ENST00000427924;ENST00000398054;ENST00000381840;ENST00000518650	T;T;T;T;T;T;T	0.25749	1.78;1.78;1.78;1.78;1.78;1.78;1.78	5.11	5.11	0.69529	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.071198	0.85682	D	0.000000	T	0.47710	0.1460	M	0.85630	2.765	0.58432	D	0.999992	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.998;0.992;0.992	T	0.60801	-0.7191	10	0.66056	D	0.02	.	15.2528	0.73561	0.0:0.0:0.0:1.0	rs35311020	84;114;114	E7ERS0;Q8NG32;Q08830	.;.;FGL1_HUMAN	V	114;114;84;114;114;114;114;114;114	ENSP00000381133:M114V;ENSP00000429757:M114V;ENSP00000371263:M114V;ENSP00000401952:M114V;ENSP00000381131:M114V;ENSP00000371262:M114V;ENSP00000428430:M114V	ENSP00000221204:M114V	M	-	1	0	FGL1	17776215	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.333000	0.79214	2.072000	0.62099	0.454000	0.30748	ATG	T|0.994;C|0.006	0.006	strong		0.383	FGL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375254.1	NM_004467	
CFP	5199	hgsc.bcm.edu	37	X	47483800	47483800	+	Silent	SNP	G	G	A	rs1048118	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:47483800G>A	ENST00000396992.3	-	9	1404	c.1284C>T	c.(1282-1284)aaC>aaT	p.N428N	CFP_ENST00000247153.3_Silent_p.N428N	NM_001145252.1	NP_001138724.1	P27918	PROP_HUMAN	complement factor properdin	428	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	18						AGAAGGTCACGTTCTTCTCGC	0.582													G|||	781	0.206887	0.205	0.1801	3775	,	,		12485	0.0169		0.1759	False		,,,				2504	0.1953				p.N428N		Atlas-SNP	.											.	CFP	43	.	0			c.C1284T						PASS	.	G	,	892,2943		76,596,144,960,427	174.0	113.0	134.0		1284,1284	-10.6	0.3	X	dbSNP_86	134	1624,5104		149,922,404,1357,1468	no	coding-synonymous,coding-synonymous	CFP	NM_001145252.1,NM_002621.2	,	225,1518,548,2317,1895	AA,AG,A,GG,G		24.1379,23.2595,23.819	,	428/470,428/470	47483800	2516,8047	2203	4300	6503	SO:0001819	synonymous_variant	5199	exon9			GGTCACGTTCTTC	M83652	CCDS14282.1	Xp11.4	2014-09-17	2006-03-02	2006-03-02	ENSG00000126759	ENSG00000126759		"""Complement system"""	8864	protein-coding gene	gene with protein product		300383	"""properdin P factor, complement"""	PFC		1783405	Standard	NM_001145252		Approved		uc004dih.3	P27918	OTTHUMG00000021451	ENST00000396992.3:c.1284C>T	X.37:g.47483800G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_001145252	O15134|O15135|O15136|O75826	Silent	SNP	ENST00000396992.3	37	CCDS14282.1																																																																																			G|0.777;0|0.004	.	strong		0.582	CFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056435.2	NM_002621	
ARHGAP5	394	hgsc.bcm.edu	37	14	32561340	32561340	+	Missense_Mutation	SNP	G	G	A	rs78337553		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:32561340G>A	ENST00000345122.3	+	2	1780	c.1465G>A	c.(1465-1467)Gag>Aag	p.E489K	ARHGAP5_ENST00000432921.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.E489K|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.E489K|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000433497.1_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	489	FF 4.				cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|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)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.E489K(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		AGCCAAAGAAGAGTTTCAAGA	0.343																																					p.E489K	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											ARHGAP5,NS,carcinoma,0,1	ARHGAP5	166	1	1	Substitution - Missense(1)	stomach(1)	c.G1465A						scavenged	.						60.0	61.0	61.0					14																	32561340		2203	4298	6501	SO:0001583	missense	394	exon2			AAAGAAGAGTTTC	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.1465G>A	14.37:g.32561340G>A	ENSP00000371897:p.Glu489Lys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	119	7	0.0588235	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741262	0.69304	.	.	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	6.02	6.02	0.97574	FF domain (2);	0.044905	0.85682	D	0.000000	T	0.39009	0.1062	N	0.22421	0.69	0.80722	D	1	P;P	0.42296	0.734;0.775	P;P	0.52066	0.562;0.689	T	0.11060	-1.0603	10	0.62326	D	0.03	.	20.547	0.99278	0.0:0.0:1.0:0.0	.	489;489	Q13017-2;Q13017	.;RHG05_HUMAN	K	489	ENSP00000452222:E489K;ENSP00000441692:E489K;ENSP00000371897:E489K;ENSP00000393307:E489K	ENSP00000371897:E489K	E	+	1	0	ARHGAP5	31631091	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.850000	0.98022	0.650000	0.86243	GAG	G|0.999;A|0.001	0.001	weak		0.343	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
SETD6	79918	hgsc.bcm.edu	37	16	58550484	58550484	+	Silent	SNP	G	G	A	rs3743567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58550484G>A	ENST00000219315.4	+	4	629	c.579G>A	c.(577-579)ctG>ctA	p.L193L	SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000310682.2_Silent_p.L169L|SETD6_ENST00000394266.4_Intron			Q8TBK2	SETD6_HUMAN	SET domain containing 6	193	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						CCATCGTGCTGCCCTTCATGG	0.617													G|||	691	0.137979	0.0953	0.1182	5008	,	,		16684	0.1796		0.0795	False		,,,				2504	0.227				p.L193L		Atlas-SNP	.											.	SETD6	27	.	0			c.G579A						PASS	.	G	,	401,3995	199.8+/-223.2	17,367,1814	104.0	109.0	107.0		579,507	2.3	1.0	16	dbSNP_107	107	825,7775	190.7+/-237.1	39,747,3514	no	coding-synonymous,coding-synonymous	SETD6	NM_001160305.1,NM_024860.2	,	56,1114,5328	AA,AG,GG		9.593,9.1219,9.4337	,	193/474,169/450	58550484	1226,11770	2198	4300	6498	SO:0001819	synonymous_variant	79918	exon4			CGTGCTGCCCTTC	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.579G>A	16.37:g.58550484G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	109	42	0.385321	NM_001160305	A8K380|B5ME38|Q9H787	Silent	SNP	ENST00000219315.4	37	CCDS54013.1																																																																																			G|0.896;A|0.104	0.104	strong		0.617	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
ZNF585A	199704	hgsc.bcm.edu	37	19	37644051	37644051	+	Silent	SNP	T	T	C	rs57916401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37644051T>C	ENST00000356958.4	-	5	1008	c.750A>G	c.(748-750)gcA>gcG	p.A250A	ZNF585A_ENST00000392157.2_Silent_p.A195A|ZNF585A_ENST00000355533.2_Silent_p.A195A|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000292841.5_Silent_p.A195A			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	250					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTGTGTGAATGCTTTGCCAC	0.448													C|||	1702	0.339856	0.5431	0.4078	5008	,	,		19448	0.0933		0.3628	False		,,,				2504	0.2474				p.A195A		Atlas-SNP	.											.	ZNF585A	117	.	0			c.A585G						PASS	.	C	,	2336,2070	570.9+/-383.0	584,1168,451	151.0	150.0	150.0		585,585	-5.4	0.2	19	dbSNP_129	150	3066,5528	660.0+/-401.7	544,1978,1775	no	coding-synonymous,coding-synonymous	ZNF585A	NM_152655.2,NM_199126.1	,	1128,3146,2226	CC,CT,TT		35.6761,46.9814,41.5538	,	195/715,195/715	37644051	5402,7598	2203	4297	6500	SO:0001819	synonymous_variant	199704	exon6			TGTGAATGCTTTG	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"""Zinc fingers, C2H2-type"", ""-"""	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.750A>G	19.37:g.37644051T>C		Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	255	121	0.47451	NM_199126	Q8TE95|Q96MV3	Silent	SNP	ENST00000356958.4	37																																																																																				T|0.630;C|0.370	0.370	strong		0.448	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655	
FBXO45	200933	hgsc.bcm.edu	37	3	196295974	196295974	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196295974C>T	ENST00000311630.6	+	1	416	c.119C>T	c.(118-120)cCc>cTc	p.P40L	WDR53_ENST00000433160.1_5'Flank|FBXO45_ENST00000440469.1_Intron|WDR53_ENST00000429115.1_5'Flank|WDR53_ENST00000332629.5_5'Flank	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	40	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		ggccggcTGCCCAGCCGGGTG	0.771																																					p.P40L		Atlas-SNP	.											.	FBXO45	18	.	0			c.C119T						PASS	.						2.0	3.0	3.0					3																	196295974		1415	3033	4448	SO:0001583	missense	200933	exon1			GGCTGCCCAGCCG	AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"""F-boxes /  ""other"""""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.119C>T	3.37:g.196295974C>T	ENSP00000310332:p.Pro40Leu	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_001105573	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	c	23.0	4.361705	0.82353	.	.	ENSG00000174013	ENST00000311630	D	0.99709	-6.48	4.78	4.78	0.61160	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.124714	0.56097	N	0.000035	D	0.99760	0.9903	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.97050	0.9763	10	0.87932	D	0	.	16.7012	0.85349	0.0:1.0:0.0:0.0	.	40	P0C2W1	FBSP1_HUMAN	L	40	ENSP00000310332:P40L	ENSP00000310332:P40L	P	+	2	0	FBXO45	197780371	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	4.709000	0.61867	2.214000	0.71695	0.531000	0.56144	CCC	.	.	none		0.771	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2		
FBXO46	23403	hgsc.bcm.edu	37	19	46216642	46216642	+	Missense_Mutation	SNP	G	G	T	rs11537711	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46216642G>T	ENST00000317683.3	-	2	245	c.112C>A	c.(112-114)Cct>Act	p.P38T		NM_001080469.1	NP_001073938.1	Q6PJ61	FBX46_HUMAN	F-box protein 46	38										breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	15		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00568)|GBM - Glioblastoma multiforme(486;0.0844)|Epithelial(262;0.201)		CCAGGCTCAGGGCAGGCTGAT	0.692													G|||	586	0.117013	0.1082	0.1441	5008	,	,		13636	0.0833		0.1123	False		,,,				2504	0.1493				p.P38T		Atlas-SNP	.											.	FBXO46	34	.	0			c.C112A						PASS	.	G	THR/PRO	465,3531		26,413,1559	20.0	25.0	23.0		112	-2.8	0.1	19	dbSNP_120	23	1016,7286		64,888,3199	yes	missense	FBXO46	NM_001080469.1	38	90,1301,4758	TT,TG,GG		12.238,11.6366,12.0426	benign	38/604	46216642	1481,10817	1998	4151	6149	SO:0001583	missense	23403	exon2			GCTCAGGGCAGGC	BC021978	CCDS46116.1	19q13.3	2008-02-05	2004-06-15	2004-06-16		ENSG00000177051		"""F-boxes /  ""other"""""	25069	protein-coding gene	gene with protein product		609117	"""F-box only protein 34-like"""	FBXO34L		9585442	Standard	NM_001080469		Approved	20D7-FC4, Fbx46	uc002pcz.3	Q6PJ61		ENST00000317683.3:c.112C>A	19.37:g.46216642G>T	ENSP00000410007:p.Pro38Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_001080469		Missense_Mutation	SNP	ENST00000317683.3	37	CCDS46116.1	211	0.09661172161172162	46	0.09349593495934959	43	0.11878453038674033	39	0.06818181818181818	83	0.10949868073878628	G	0.001	-3.274999	0.00020	0.116366	0.12238	ENSG00000177051	ENST00000317683	.	.	.	3.8	-2.8	0.05823	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.43977	P	0.003337999999999952	B	0.02656	0.0	B	0.04013	0.001	T	0.25916	-1.0118	7	0.16896	T	0.51	-1.5752	0.581	0.00712	0.3145:0.1558:0.3437:0.186	rs11537711;rs11537711	38	Q6PJ61	FBX46_HUMAN	T	38	.	ENSP00000410007:P38T	P	-	1	0	FBXO46	50908482	0.000000	0.05858	0.063000	0.19743	0.036000	0.12997	-0.721000	0.04963	-0.539000	0.06273	-0.266000	0.10368	CCT	G|0.898;T|0.102	0.102	strong		0.692	FBXO46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459661.1	XM_371179	
EML6	400954	hgsc.bcm.edu	37	2	55119771	55119771	+	Missense_Mutation	SNP	T	T	A	rs200933456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:55119771T>A	ENST00000356458.6	+	18	3240	c.2720T>A	c.(2719-2721)tTt>tAt	p.F907Y		NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	907						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						GGGCCTGTGTTTGCTATGTAT	0.413													T|||	3	0.000599042	0.0	0.0014	5008	,	,		19318	0.0		0.0	False		,,,				2504	0.002				p.F907Y		Atlas-SNP	.											.	EML6	85	.	0			c.T2720A						PASS	.	T	TYR/PHE	0,1384		0,0,692	275.0	242.0	252.0		2720	5.6	1.0	2		252	9,3173		0,9,1582	yes	missense	EML6	NM_001039753.2	22	0,9,2274	AA,AT,TT		0.2828,0.0,0.1971	possibly-damaging	907/1959	55119771	9,4557	692	1591	2283	SO:0001583	missense	400954	exon18			CTGTGTTTGCTAT		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.2720T>A	2.37:g.55119771T>A	ENSP00000348842:p.Phe907Tyr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_001039753	A8MUB5|B6ZDG7	Missense_Mutation	SNP	ENST00000356458.6	37	CCDS46286.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.994989	0.93167	0.0	0.002828	ENSG00000214595	ENST00000356458	T	0.01258	5.09	5.55	5.55	0.83447	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.52532	U	0.000079	T	0.06554	0.0168	L	0.58354	1.805	0.50313	D	0.999862	D	0.67145	0.996	D	0.66084	0.941	T	0.10359	-1.0633	10	0.72032	D	0.01	.	15.6956	0.77494	0.0:0.0:0.0:1.0	.	907	Q6ZMW3	EMAL6_HUMAN	Y	907	ENSP00000348842:F907Y	ENSP00000348842:F907Y	F	+	2	0	EML6	54973275	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.608000	0.82898	2.110000	0.64415	0.477000	0.44152	TTT	T|0.995;A|0.005	0.005	strong		0.413	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
PDE1C	5137	hgsc.bcm.edu	37	7	31793087	31793087	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:31793087C>T	ENST00000396191.1	-	18	2496	c.2041G>A	c.(2041-2043)Gat>Aat	p.D681N	PDE1C_ENST00000321453.7_Missense_Mutation_p.D681N|PDE1C_ENST00000396193.1_Missense_Mutation_p.D741N	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	681					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GGATGCTCATCAGTTTTCTTT	0.453																																					p.D741N		Atlas-SNP	.											PDE1C_ENST00000396193,right_upper_lobe,carcinoma,0,2	PDE1C	465	2	0			c.G2221A						scavenged	.						259.0	253.0	255.0					7																	31793087		876	1991	2867	SO:0001583	missense	5137	exon19			GCTCATCAGTTTT	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.2041G>A	7.37:g.31793087C>T	ENSP00000379494:p.Asp681Asn	Somatic	157	1	0.00636943		WXS	Illumina HiSeq	Phase_I	124	62	0.5	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.590817	0.66219	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453	T;T;T	0.73789	-0.78;-0.77;-0.77	5.36	5.36	0.76844	.	0.378221	0.29892	N	0.010933	T	0.65533	0.2700	L	0.27053	0.805	0.80722	D	1	B;B	0.17667	0.023;0.023	B;B	0.20184	0.028;0.021	T	0.63328	-0.6662	10	0.87932	D	0	.	16.103	0.81201	0.0:1.0:0.0:0.0	.	741;681	E9PE92;Q14123	.;PDE1C_HUMAN	N	741;681;681	ENSP00000379496:D741N;ENSP00000379494:D681N;ENSP00000318105:D681N	ENSP00000318105:D681N	D	-	1	0	PDE1C	31759612	0.998000	0.40836	0.996000	0.52242	0.939000	0.58152	4.150000	0.58098	2.789000	0.95967	0.591000	0.81541	GAT	.	.	none		0.453	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
PCDHGA11	56105	hgsc.bcm.edu	37	5	140801104	140801104	+	Missense_Mutation	SNP	T	T	C	rs11167744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140801104T>C	ENST00000398587.2	+	1	343	c.310T>C	c.(310-312)Ttt>Ctt	p.F104L	PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_Missense_Mutation_p.F104L	NM_018914.2|NM_032092.1	NP_061737.1|NP_114481.1	Q9Y5H2	PCDGB_HUMAN	protocadherin gamma subfamily A, 11	104	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		F -> L (in dbSNP:rs11167744).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(8)|kidney(3)|large_intestine(9)|lung(22)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCTCCTGTTTTTTAAATAT	0.498													t|||	567	0.113219	0.1195	0.1499	5008	,	,		17586	0.1181		0.0596	False		,,,				2504	0.1288				p.F104L		Atlas-SNP	.											.	PCDHGA11	128	.	0			c.T310C						PASS	.	T	,,,LEU/PHE,,,,,,,,,,,,,,,LEU/PHE,LEU/PHE	469,3667		25,419,1624	32.0	37.0	36.0		,,,310,,,,,,,,,,,,,,,310,310	-3.1	1.0	5	dbSNP_120	36	624,7896		25,574,3661	yes	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032091.1,NM_032092.1	,,,22,,,,,,,,,,,,,,,22,22	50,993,5285	CC,CT,TT		7.3239,11.3395,8.6362	,,,,,,,,,,,,,,,,,,,	,,,104/936,,,,,,,,,,,,,,,104/838,104/751	140801104	1093,11563	2068	4260	6328	SO:0001583	missense	56105	exon1			TCCTGTTTTTTAA	AF152505	CCDS47294.1, CCDS54930.1, CCDS75345.1	5q31	2010-01-26			ENSG00000253873	ENSG00000253873		"""Cadherins / Protocadherins : Clustered"""	8698	other	protocadherin		606298				10380929	Standard	NM_018914		Approved	PCDH-GAMMA-A11		Q9Y5H2	OTTHUMG00000164055	ENST00000398587.2:c.310T>C	5.37:g.140801104T>C	ENSP00000381589:p.Phe104Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_032091	B7ZVY8|Q9Y5D8|Q9Y5D9	Missense_Mutation	SNP	ENST00000398587.2	37	CCDS47294.1	220	0.10073260073260074	53	0.10772357723577236	47	0.1298342541436464	69	0.12062937062937062	51	0.06728232189973615	t	2.098	-0.406756	0.04832	0.113395	0.073239	ENSG00000253873	ENST00000398587;ENST00000518882	T;T	0.24350	1.86;1.86	5.93	-3.06	0.05379	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	1.496170	0.06373	N	0.713909	T	0.00039	0.0001	N	0.00300	-1.685	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.32824	-0.9892	9	0.02654	T	1	.	0.9188	0.01310	0.4206:0.1385:0.1628:0.2782	rs11167744;rs61342402;rs11167744	104;104;104	Q9Y5H2;Q9Y5H2-3;Q9Y5H2-2	PCDGB_HUMAN;.;.	L	104	ENSP00000381589:F104L;ENSP00000428333:F104L	ENSP00000381589:F104L	F	+	1	0	PCDHGA11	140781288	0.000000	0.05858	0.979000	0.43373	0.990000	0.78478	-3.692000	0.00391	-0.129000	0.11620	0.482000	0.46254	TTT	T|0.896;C|0.104	0.104	strong		0.498	PCDHGA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376974.1	NM_018914	
EFR3A	23167	hgsc.bcm.edu	37	8	132982824	132982824	+	Missense_Mutation	SNP	A	A	G	rs1051221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:132982824A>G	ENST00000254624.5	+	10	1318	c.1093A>G	c.(1093-1095)Aac>Gac	p.N365D	EFR3A_ENST00000519656.1_Missense_Mutation_p.N329D|EFR3A_ENST00000334503.4_Missense_Mutation_p.N365D	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	365			N -> D (in dbSNP:rs1051221). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)				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)			AGGCAGTGTCAACTTAAATAC	0.393													A|||	2248	0.448882	0.5265	0.5	5008	,	,		17156	0.3125		0.5089	False		,,,				2504	0.3865				p.N365D		Atlas-SNP	.											.	EFR3A	96	.	0			c.A1093G						PASS	.	A	ASP/ASN	2335,2071	607.3+/-390.9	624,1087,492	113.0	112.0	112.0		1093	-1.1	0.0	8	dbSNP_86	112	4195,4405	568.1+/-389.0	1019,2157,1124	yes	missense	EFR3A	NM_015137.4	23	1643,3244,1616	GG,GA,AA		48.7791,47.0041,49.7924	benign	365/822	132982824	6530,6476	2203	4300	6503	SO:0001583	missense	23167	exon10			AGTGTCAACTTAA	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.1093A>G	8.37:g.132982824A>G	ENSP00000254624:p.Asn365Asp	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	91	90	0.989011	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	37	CCDS34942.2	1005	0.46016483516483514	266	0.540650406504065	188	0.5193370165745856	167	0.291958041958042	384	0.5065963060686016	A	7.915	0.737328	0.15574	0.529959	0.487791	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.32023	1.47;1.47;1.47	5.68	-1.11	0.09840	Armadillo-like helical (1);Armadillo-type fold (1);	1.359000	0.04269	N	0.341810	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.15930	0.015	B	0.22152	0.038	T	0.48536	-0.9027	9	0.46703	T	0.11	0.3366	5.6	0.17349	0.5414:0.0:0.3371:0.1215	rs1051221;rs56516663;rs1051221	365	Q14156	EFR3A_HUMAN	D	365;365;365;329	ENSP00000254624:N365D;ENSP00000334769:N365D;ENSP00000428086:N329D	ENSP00000254624:N365D	N	+	1	0	EFR3A	133052006	0.062000	0.20869	0.001000	0.08648	0.358000	0.29455	0.548000	0.23314	-0.399000	0.07668	0.477000	0.44152	AAC	A|0.517;C|0.002	.	strong		0.393	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	
GPIHBP1	338328	hgsc.bcm.edu	37	8	144295154	144295154	+	Silent	SNP	C	C	T	rs61747644	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144295154C>T	ENST00000330824.2	+	1	87	c.12C>T	c.(10-12)ctC>ctT	p.L4L		NM_178172.3	NP_835466.1	Q8IV16	HDBP1_HUMAN	glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1	4					cholesterol homeostasis (GO:0042632)|intracellular protein transport (GO:0006886)|positive regulation of chylomicron remnant clearance (GO:0090321)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein import (GO:0017038)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|protein transmembrane transport (GO:0071806)|response to heparin (GO:0071503)|transcytosis (GO:0045056)|triglyceride homeostasis (GO:0070328)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|external side of plasma membrane (GO:0009897)|high-density lipoprotein particle (GO:0034364)	chylomicron binding (GO:0035478)|lipase binding (GO:0035473)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|protein transmembrane transporter activity (GO:0008320)			lung(2)	2	all_cancers(97;6.49e-11)|all_epithelial(106;2.77e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TGAAGGCGCTCGGGGCTGTCC	0.672													C|||	707	0.141174	0.0219	0.2003	5008	,	,		17046	0.1667		0.2018	False		,,,				2504	0.1718				p.L4L		Atlas-SNP	.											.	GPIHBP1	12	.	0			c.C12T						PASS	.	C		232,4148		8,216,1966	28.0	29.0	29.0		12	-2.1	0.0	8	dbSNP_129	29	1593,6979		152,1289,2845	no	coding-synonymous	GPIHBP1	NM_178172.3		160,1505,4811	TT,TC,CC		18.5838,5.2968,14.0905		4/185	144295154	1825,11127	2190	4286	6476	SO:0001819	synonymous_variant	338328	exon1			GGCGCTCGGGGCT	AF088057	CCDS34954.1	8q24.3	2014-07-14	2008-02-07						24945	protein-coding gene	gene with protein product	"""endothelial cell LPL transporter"""	612757	"""GPI anchored high density lipoprotein binding protein 1"""			12496272, 17883852, 17620854, 17403372	Standard	NM_178172		Approved	LOC338328, GPI-HBP1	uc003yxu.2	Q8IV16		ENST00000330824.2:c.12C>T	8.37:g.144295154C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	190	190	1	NM_178172	Q6P3T2|Q86W15	Silent	SNP	ENST00000330824.2	37	CCDS34954.1																																																																																			C|0.860;T|0.140	0.140	strong		0.672	GPIHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381113.1	NM_178172	
HAGHL	84264	hgsc.bcm.edu	37	16	778820	778820	+	Silent	SNP	G	G	A	rs12448432	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:778820G>A	ENST00000341413.4	+	7	806	c.525G>A	c.(523-525)acG>acA	p.T175T	HAGHL_ENST00000561546.1_Silent_p.T175T|HAGHL_ENST00000564545.1_Missense_Mutation_p.A84T|HAGHL_ENST00000564537.1_Missense_Mutation_p.A202T|HAGHL_ENST00000389703.3_Silent_p.T175T|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000549114.1_Missense_Mutation_p.A202T|NARFL_ENST00000562862.1_5'Flank			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	175							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				ACGAGCACACGCTTAGCAACC	0.667													G|||	1975	0.394369	0.1573	0.4625	5008	,	,		9189	0.7569		0.2376	False		,,,				2504	0.454				p.T175T	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.G525A						PASS	.	G		563,3815	238.7+/-250.0	32,499,1658	26.0	27.0	26.0		525	-8.2	0.0	16	dbSNP_120	26	1796,6786	299.9+/-304.7	197,1402,2692	no	coding-synonymous	HAGHL	NM_032304.2		229,1901,4350	AA,AG,GG		20.9275,12.8598,18.2022		175/283	778820	2359,10601	2189	4291	6480	SO:0001819	synonymous_variant	84264	exon6			GCACACGCTTAGC	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.525G>A	16.37:g.778820G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	89	53	0.595506	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37		865	0.39606227106227104	82	0.16666666666666666	148	0.4088397790055249	436	0.7622377622377622	199	0.262532981530343	G	15.03	2.712967	0.48517	0.128598	0.209275	ENSG00000103253	ENST00000549114;ENST00000389701	D	0.87103	-2.21	4.27	-8.21	0.01041	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999590043	B	0.11235	0.004	B	0.12837	0.008	T	0.34551	-0.9824	6	.	.	.	-20.0695	1.828	0.03125	0.4147:0.1648:0.2828:0.1376	rs12448432;rs61367184;rs12448432	202	Q6PII5-3	.	T	202;203	ENSP00000447170:A202T	.	A	+	1	0	HAGHL	718821	0.002000	0.14202	0.002000	0.10522	0.426000	0.31534	-1.023000	0.03607	-1.455000	0.01923	-0.258000	0.10820	GCT	G|0.733;A|0.267	0.267	strong		0.667	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
FAHD1	81889	hgsc.bcm.edu	37	16	1877494	1877494	+	Silent	SNP	T	T	C	rs3743854	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1877494T>C	ENST00000427358.2	+	1	270	c.264T>C	c.(262-264)gcT>gcC	p.A88A	HAGH_ENST00000455446.2_5'Flank|FAHD1_ENST00000382668.4_Silent_p.A88A|HAGH_ENST00000566709.1_5'Flank|HAGH_ENST00000397356.3_5'Flank|HAGH_ENST00000397353.2_5'Flank|FAHD1_ENST00000382666.4_Silent_p.A88A	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	88						cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						TCCCCGAGGCTGCGGCCATGG	0.677													C|||	1007	0.201078	0.1831	0.2262	5008	,	,		18027	0.1746		0.1809	False		,,,				2504	0.2556				p.A88A		Atlas-SNP	.											.	FAHD1	18	.	0			c.T264C						PASS	.	C	,,	775,3617		82,611,1503	33.0	36.0	35.0		264,264,264	1.3	1.0	16	dbSNP_107	35	1312,7276		110,1092,3092	no	coding-synonymous,coding-synonymous,coding-synonymous	FAHD1	NM_001018104.2,NM_001142398.1,NM_031208.3	,,	192,1703,4595	CC,CT,TT		15.2771,17.6457,16.0786	,,	88/249,88/227,88/225	1877494	2087,10893	2196	4294	6490	SO:0001819	synonymous_variant	81889	exon1			CGAGGCTGCGGCC	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 36"""	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.264T>C	16.37:g.1877494T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Silent	SNP	ENST00000427358.2	37	CCDS10448.1																																																																																			T|0.840;C|0.160	0.160	strong		0.677	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605350	84605350	+	Missense_Mutation	SNP	G	G	C	rs367877053		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:84605350G>C	ENST00000344803.2	+	3	298	c.251G>C	c.(250-252)aGt>aCt	p.S84T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	84					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GACTGGAAAAGTTTCCAGAGA	0.433																																					p.S84T		Atlas-SNP	.											.	.	.	.	0			c.G251C						PASS	.	G	THR/SER	0,3710		0,0,1855	85.0	79.0	81.0		251	-5.6	0.0	9		81	1,8179		0,1,4089	no	missense	FAM75D1	NM_001001670.2	58	0,1,5944	CC,CG,GG		0.0122,0.0,0.0084	benign	84/1577	84605350	1,11889	1855	4090	5945	SO:0001583	missense	389763	exon3			GGAAAAGTTTCCA		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.251G>C	9.37:g.84605350G>C	ENSP00000341988:p.Ser84Thr	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.766413	0.00651	0.0	1.22E-4	ENSG00000214929	ENST00000344803	T	0.05081	3.5	2.82	-5.63	0.02474	.	16.493900	0.00166	N	0.000000	T	0.02304	0.0071	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35574	-0.9783	10	0.18276	T	0.48	18.5219	1.232	0.01945	0.1706:0.3724:0.205:0.252	.	84	Q6ZQQ2	F75D1_HUMAN	T	84	ENSP00000341988:S84T	ENSP00000341988:S84T	S	+	2	0	FAM75D1	83795170	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.865000	0.01649	-4.130000	0.00071	-1.316000	0.01300	AGT	.	.	weak		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
IGSF10	285313	hgsc.bcm.edu	37	3	151171439	151171439	+	Missense_Mutation	SNP	A	A	C	rs7619322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:151171439A>C	ENST00000282466.3	-	3	447	c.448T>G	c.(448-450)Tat>Gat	p.Y150D		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	150			Y -> D (in dbSNP:rs7619322).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TTGAGCCCATAAAAAACCTCT	0.423													A|||	3645	0.727835	0.6891	0.7075	5008	,	,		16508	0.745		0.7435	False		,,,				2504	0.7607				p.Y150D		Atlas-SNP	.											.	IGSF10	279	.	0			c.T448G						PASS	.	A	ASP/TYR	3031,1375	682.8+/-404.2	1038,955,210	75.0	82.0	79.0		448	-2.5	0.0	3	dbSNP_116	79	6262,2338	702.1+/-405.3	2290,1682,328	yes	missense	IGSF10	NM_178822.4	160	3328,2637,538	CC,CA,AA		27.186,31.2074,28.5484	possibly-damaging	150/2624	151171439	9293,3713	2203	4300	6503	SO:0001583	missense	285313	exon3			GCCCATAAAAAAC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.448T>G	3.37:g.151171439A>C	ENSP00000282466:p.Tyr150Asp	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	1613	0.7385531135531136	357	0.725609756097561	254	0.7016574585635359	431	0.7534965034965035	571	0.7532981530343008	A	15.79	2.936281	0.52972	0.687926	0.72814	ENSG00000152580	ENST00000282466	T	0.51574	0.7	5.53	-2.47	0.06442	.	0.700710	0.12290	N	0.482074	T	0.00012	0.0000	N	0.02916	-0.46	0.30101	P	0.807391	P	0.50710	0.938	P	0.55087	0.768	T	0.47058	-0.9146	9	0.30854	T	0.27	.	0.6669	0.00852	0.4402:0.1168:0.2:0.243	rs7619322;rs52823444;rs60638999;rs7619322	150	Q6WRI0	IGS10_HUMAN	D	150	ENSP00000282466:Y150D	ENSP00000282466:Y150D	Y	-	1	0	IGSF10	152654129	1.000000	0.71417	0.026000	0.17262	0.939000	0.58152	2.414000	0.44627	-0.442000	0.07190	0.528000	0.53228	TAT	A|0.276;C|0.724	0.724	strong		0.423	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
MICA	100507436	hgsc.bcm.edu	37	6	31378977	31378977	+	Missense_Mutation	SNP	G	G	A	rs1051792	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31378977G>A	ENST00000449934.2	+	3	508	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GGAATGGACAGTGCCCCAGTC	0.517													g|||	1827	0.364816	0.4788	0.4078	5008	,	,		20742	0.3006		0.3141	False		,,,				2504	0.2986				p.V152M		Atlas-SNP	.											.	MICA	21	.	0			c.G454A						PASS	.	G	MET/VAL	580,804		132,316,244	100.0	85.0	89.0		454	-0.6	0.0	6	dbSNP_86	89	919,2263		126,667,798	no	missense	MICA	NM_001177519.1	21	258,983,1042	AA,AG,GG		28.8812,41.9075,32.8296	probably-damaging	152/333	31378977	1499,3067	692	1591	2283	SO:0001583	missense	100507436	exon3			TGGACAGTGCCCC	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.454G>A	6.37:g.31378977G>A	ENSP00000413079:p.Val152Met	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	152	152	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	800|800	0.3663003663003663|0.3663003663003663	228|228	0.4634146341463415|0.4634146341463415	169|169	0.46685082872928174|0.46685082872928174	160|160	0.27972027972027974|0.27972027972027974	243|243	0.32058047493403696|0.32058047493403696	.|N	0.869|0.869	-0.732690|-0.732690	0.03135|0.03135	0.419075|0.419075	0.288812|0.288812	ENSG00000204520|ENSG00000204520	ENST00000399172|ENST00000364810;ENST00000449934	.|T	.|0.00730	.|5.77	1.41|1.41	-0.635|-0.635	0.11512|0.11512	.|.	.|.	.|.	.|.	.|.	.|T	.|0.00440	.|0.0014	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|D	.|0.53462	.|0.96	.|P	.|0.51550	.|0.673	.|T	.|0.51841	.|-0.8654	.|7	.|0.40728	.|T	.|0.16	.|.	2.6169|2.6169	0.04906|0.04906	0.3636:0.2644:0.372:0.0|0.3636:0.2644:0.372:0.0	rs1051792;rs3192169;rs3819270;rs16897487;rs17845518;rs17858408;rs17885687;rs1051792|rs1051792;rs3192169;rs3819270;rs16897487;rs17845518;rs17858408;rs17885687;rs1051792	.|152	.|Q96QC4	.|.	.|M	-1|152	.|ENSP00000413079:V152M	.|ENSP00000365394:V152M	.|V	+|+	.|1	.|0	MICA|MICA	31486956|31486956	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.136000|0.136000	0.15974|0.15974	-0.189000|-0.189000	0.10482|0.10482	-0.667000|-0.667000	0.03836|0.03836	.|GTG	G|0.653;A|0.347	0.347	strong		0.517	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
VSTM1	284415	hgsc.bcm.edu	37	19	54545186	54545186	+	Silent	SNP	C	C	T	rs73058793	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54545186C>T	ENST00000338372.2	-	7	712	c.537G>A	c.(535-537)ccG>ccA	p.P179P	VSTM1_ENST00000366170.2_Silent_p.P91P|VSTM1_ENST00000376626.1_Silent_p.P148P|VSTM1_ENST00000425006.2_3'UTR	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	179					immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		CCTCCTGCTCCGGAAGTTTGG	0.493													C|||	907	0.18111	0.1384	0.2896	5008	,	,		17447	0.0645		0.331	False		,,,				2504	0.1278				p.P179P		Atlas-SNP	.											.	VSTM1	30	.	0			c.G537A						PASS	.	C		745,3661	304.1+/-288.3	66,613,1524	55.0	56.0	55.0		537	-6.1	0.0	19	dbSNP_130	55	2663,5937	426.5+/-355.3	400,1863,2037	no	coding-synonymous	VSTM1	NM_198481.3		466,2476,3561	TT,TC,CC		30.9651,16.9088,26.2033		179/237	54545186	3408,9598	2203	4300	6503	SO:0001819	synonymous_variant	284415	exon7			CTGCTCCGGAAGT	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.537G>A	19.37:g.54545186C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Silent	SNP	ENST00000338372.2	37	CCDS12872.1																																																																																			C|0.755;T|0.245	0.245	strong		0.493	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	
CH25H	9023	hgsc.bcm.edu	37	10	90966996	90966996	+	Silent	SNP	C	C	G	rs10887932	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90966996C>G	ENST00000371852.2	-	1	75	c.54G>C	c.(52-54)ctG>ctC	p.L18L		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	18					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		GCTGCAGGAACAGCTGCCCGG	0.622													C|||	1404	0.280351	0.0083	0.2637	5008	,	,		19159	0.7371		0.1392	False		,,,				2504	0.3344				p.L18L		Atlas-SNP	.											.	CH25H	19	.	0			c.G54C						PASS	.	C		121,4283		6,109,2087	18.0	22.0	20.0		54	-2.1	0.2	10	dbSNP_120	20	1020,7578		63,894,3342	no	coding-synonymous	CH25H	NM_003956.3		69,1003,5429	GG,GC,CC		11.8632,2.7475,8.7756		18/273	90966996	1141,11861	2202	4299	6501	SO:0001819	synonymous_variant	9023	exon1			CAGGAACAGCTGC	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.54G>C	10.37:g.90966996C>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	99	49	0.494949	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	37	CCDS7400.1																																																																																			C|0.834;G|0.166	0.166	strong		0.622	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
JRK	8629	hgsc.bcm.edu	37	8	143747271	143747271	+	RNA	SNP	C	C	G	rs2978973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143747271C>G	ENST00000507178.2	-	0	539							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				tgttggagtccgagctggcga	0.647													C|||	1985	0.396366	0.3268	0.2781	5008	,	,		17020	0.4821		0.3459	False		,,,				2504	0.5378				p.S69S		Atlas-SNP	.											.	.	.	.	0			c.G207C						PASS	.	C	,	1309,2955		206,897,1029	34.0	42.0	39.0		207,207	-3.7	1.0	8	dbSNP_101	39	2770,5688		463,1844,1922	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	669,2741,2951	GG,GC,CC		32.7501,30.6989,32.0626	,	69/557,69/569	143747271	4079,8643	2132	4229	6361			8629	exon2			GGAGTCCGAGCTG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143747271C>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	32	0.390244	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				C|0.634;G|0.366	0.366	strong		0.647	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
BBOX1	8424	hgsc.bcm.edu	37	11	27147270	27147270	+	Silent	SNP	G	G	A	rs1044273	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:27147270G>A	ENST00000529202.1	+	7	1245	c.906G>A	c.(904-906)gtG>gtA	p.V302V	BBOX1_ENST00000525090.1_Silent_p.V302V|RP11-1L12.3_ENST00000526061.1_RNA|BBOX1_ENST00000528583.1_Silent_p.V302V|RP11-1L12.3_ENST00000525302.1_RNA|BBOX1_ENST00000263182.3_Silent_p.V302V|RP11-1L12.3_ENST00000530430.1_RNA			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	302					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	tatttgatgtgcctgttgaaa	0.368													G|||	464	0.0926518	0.1097	0.0922	5008	,	,		17585	0.001		0.1889	False		,,,				2504	0.0654				p.V302V		Atlas-SNP	.											BBOX1,right_lower_lobe,carcinoma,+2,1	BBOX1	46	1	0			c.G906A						PASS	.	G		486,3918	223.3+/-239.8	26,434,1742	94.0	80.0	84.0		906	-7.1	0.7	11	dbSNP_86	84	1606,6992	295.2+/-302.3	141,1324,2834	no	coding-synonymous	BBOX1	NM_003986.2		167,1758,4576	AA,AG,GG		18.6788,11.0354,16.0898		302/388	27147270	2092,10910	2202	4299	6501	SO:0001819	synonymous_variant	8424	exon8			TGATGTGCCTGTT	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.906G>A	11.37:g.27147270G>A		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Silent	SNP	ENST00000529202.1	37	CCDS7862.1																																																																																			G|0.866;A|0.134	0.134	strong		0.368	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986	
ST18	9705	hgsc.bcm.edu	37	8	53071461	53071461	+	Silent	SNP	G	G	A	rs2278152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:53071461G>A	ENST00000276480.7	-	15	2486	c.1803C>T	c.(1801-1803)gcC>gcT	p.A601A		NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	601					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(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				GGCCTACCTTGGCATGCAGAC	0.547													G|||	471	0.0940495	0.0061	0.1383	5008	,	,		19027	0.1399		0.1183	False		,,,				2504	0.1094				p.A601A		Atlas-SNP	.											ST18,NS,carcinoma,-2,1	ST18	212	1	0			c.C1803T						PASS	.	G		127,4279	93.4+/-132.2	1,125,2077	103.0	105.0	105.0		1803	6.1	1.0	8	dbSNP_100	105	961,7639	210.4+/-251.3	63,835,3402	no	coding-synonymous	ST18	NM_014682.2		64,960,5479	AA,AG,GG		11.1744,2.8824,8.3654		601/1048	53071461	1088,11918	2203	4300	6503	SO:0001819	synonymous_variant	9705	exon15			TACCTTGGCATGC	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"""Zinc fingers, C2HC-type containing"""	18695	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 3"""		"""zinc finger protein 387"", ""suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"""	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.1803C>T	8.37:g.53071461G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_014682	Q17RY1	Silent	SNP	ENST00000276480.7	37	CCDS6149.1																																																																																			G|0.914;A|0.086	0.086	strong		0.547	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377867.1		
ALMS1	7840	hgsc.bcm.edu	37	2	73679280	73679280	+	Missense_Mutation	SNP	A	A	G	rs6546838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73679280A>G	ENST00000264448.6	+	8	5734	c.5623A>G	c.(5623-5625)Ata>Gta	p.I1875V	ALMS1_ENST00000409009.1_Missense_Mutation_p.I1833V|ALMS1_ENST00000377715.1_Missense_Mutation_p.I1875V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1875	34 X 47 AA approximate tandem repeat.		I -> V (in dbSNP:rs6546838).		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						TTTGAAAGCAATAGGGGTTCC	0.443													G|||	1797	0.358826	0.8585	0.3919	5008	,	,		18751	0.0089		0.2276	False		,,,				2504	0.1554				p.I1875V		Atlas-SNP	.											.	ALMS1	384	.	0			c.A5623G						PASS	.	G	VAL/ILE	2708,1020		995,718,151	62.0	61.0	62.0		5623	-3.3	0.0	2	dbSNP_116	62	1951,6229		221,1509,2360	yes	missense	ALMS1	NM_015120.4	29	1216,2227,2511	GG,GA,AA		23.8509,27.3605,39.125	benign	1875/4168	73679280	4659,7249	1864	4090	5954	SO:0001583	missense	7840	exon8			AAAGCAATAGGGG	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.5623A>G	2.37:g.73679280A>G	ENSP00000264448:p.Ile1875Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	731	0.3347069597069597	419	0.8516260162601627	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	G	0.013	-1.607239	0.00842	0.726395	0.238509	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.12879	3.53;3.53;2.64	4.38	-3.33	0.04958	.	2.320940	0.02370	N	0.077734	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.001	T	0.33137	-0.9880	9	0.02654	T	1	.	5.2394	0.15464	0.2773:0.0:0.2757:0.447	rs6546838;rs17434110;rs52790418;rs60669356;rs6546838	1875;1833;1875	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	V	1833;1875;1875	ENSP00000386627:I1833V;ENSP00000264448:I1875V;ENSP00000366944:I1875V	ENSP00000264448:I1875V	I	+	1	0	ALMS1	73532788	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.185000	0.09684	-0.997000	0.03450	-1.234000	0.01563	ATA	A|0.663;G|0.337	0.337	strong		0.443	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ZNF415	55786	hgsc.bcm.edu	37	19	53612989	53612989	+	Silent	SNP	A	A	G	rs1054484	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53612989A>G	ENST00000500065.4	-	4	642	c.309T>C	c.(307-309)gaT>gaC	p.D103D	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000243643.4_Silent_p.D103D|ZNF415_ENST00000440291.1_Silent_p.D90D|ZNF415_ENST00000455735.2_Silent_p.D151D|ZNF415_ENST00000421033.1_Silent_p.D115D|ZNF415_ENST00000601215.1_3'UTR|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000448501.1_Silent_p.D151D	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	151					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D103D(1)		breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		AATTTCTTTCATCATCTCTCC	0.378													A|||	819	0.163538	0.0219	0.2896	5008	,	,		19563	0.3224		0.1769	False		,,,				2504	0.0879				p.D103D		Atlas-SNP	.											ZNF415,NS,carcinoma,0,1	ZNF415	68	1	1	Substitution - coding silent(1)	stomach(1)	c.T309C						PASS	.	A	,,	208,4198	128.6+/-165.4	5,198,2000	139.0	126.0	130.0		309,309,309	0.5	0.0	19	dbSNP_86	130	1386,7214	267.2+/-287.2	115,1156,3029	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	,,	120,1354,5029	GG,GA,AA		16.1163,4.7208,12.2559	,,	103/556,103/556,103/556	53612989	1594,11412	2203	4300	6503	SO:0001819	synonymous_variant	55786	exon4			TCTTTCATCATCT	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.309T>C	19.37:g.53612989A>G		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	285	130	0.45614	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																			A|0.848;G|0.152	0.152	strong		0.378	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
FN1	2335	hgsc.bcm.edu	37	2	216229692	216229692	+	Silent	SNP	A	A	G	rs11651	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:216229692A>G	ENST00000359671.1	-	43	7153	c.6888T>C	c.(6886-6888)taT>taC	p.Y2296Y	FN1_ENST00000421182.1_Silent_p.Y2150Y|FN1_ENST00000354785.4_Silent_p.Y2387Y|FN1_ENST00000432072.2_Silent_p.Y2177Y|FN1_ENST00000345488.5_Silent_p.Y2094Y|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000443816.1_Silent_p.Y2175Y|FN1_ENST00000357867.4_Silent_p.Y2086Y|FN1_ENST00000323926.6_Silent_p.Y2356Y|FN1_ENST00000446046.1_Silent_p.Y2240Y|FN1_ENST00000336916.4_Silent_p.Y2265Y|FN1_ENST00000346544.3_Silent_p.Y2121Y|FN1_ENST00000356005.4_Silent_p.Y2206Y			P02751	FINC_HUMAN	fibronectin 1	2296	Fibrin-binding 2.|Fibronectin type-I 12. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TCCCATCATCATAACACGTTG	0.488													A|||	1416	0.282748	0.0651	0.3127	5008	,	,		23128	0.2986		0.3141	False		,,,				2504	0.5072				p.Y2387Y		Atlas-SNP	.											FN1_ENST00000354785,NS,carcinoma,0,2	FN1	521	2	0			c.T7161C						scavenged	.	A	,,,,	445,3959		25,395,1782	152.0	92.0	112.0		6795,6258,6618,6720,7161	-8.3	0.1	2	dbSNP_52	112	2780,5816		463,1854,1981	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FN1	NM_002026.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	,,,,	488,2249,3763	GG,GA,AA		32.3406,10.1045,24.8077	,,,,	2265/2356,2086/2177,2206/2297,2240/2331,2387/2478	216229692	3225,9775	2202	4298	6500	SO:0001819	synonymous_variant	2335	exon44			ATCATCATAACAC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.6888T>C	2.37:g.216229692A>G		Somatic	78	1	0.0128205		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																				A|0.771;G|0.229	0.229	strong		0.488	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
HELB	92797	hgsc.bcm.edu	37	12	66725160	66725160	+	Missense_Mutation	SNP	C	C	T	rs1185244	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:66725160C>T	ENST00000247815.4	+	12	2956	c.2897C>T	c.(2896-2898)cCg>cTg	p.P966L		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	966			P -> L (in dbSNP:rs1185244). {ECO:0000269|PubMed:14702039}.		DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		GCAGATTTTCCGTCCCCACGG	0.502													c|||	2393	0.477835	0.382	0.6138	5008	,	,		19343	0.5585		0.4205	False		,,,				2504	0.4867				p.P966L		Atlas-SNP	.											.	HELB	90	.	0			c.C2897T						PASS	.	C	LEU/PRO	1686,2720	512.1+/-368.0	333,1020,850	67.0	61.0	63.0		2897	2.4	0.0	12	dbSNP_87	63	3712,4888	530.2+/-381.7	805,2102,1393	yes	missense	HELB	NM_033647.2	98	1138,3122,2243	TT,TC,CC		43.1628,38.266,41.5039	benign	966/1088	66725160	5398,7608	2203	4300	6503	SO:0001583	missense	92797	exon12			ATTTTCCGTCCCC	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.2897C>T	12.37:g.66725160C>T	ENSP00000247815:p.Pro966Leu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	1088	0.4981684981684982	214	0.4349593495934959	208	0.574585635359116	338	0.5909090909090909	328	0.43271767810026385	c	8.303	0.820277	0.16678	0.38266	0.431628	ENSG00000127311	ENST00000247815	T	0.12039	2.72	5.24	2.41	0.29592	.	0.765215	0.11887	N	0.519971	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.16166	0.016	B	0.06405	0.002	T	0.33752	-0.9856	8	.	.	.	-1.1376	7.2998	0.26413	0.1454:0.6934:0.0:0.1611	rs1185244;rs1691825;rs17180686;rs1185244	966	Q8NG08	HELB_HUMAN	L	966	ENSP00000247815:P966L	.	P	+	2	0	HELB	65011427	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.076000	0.14712	0.216000	0.20781	-1.836000	0.00589	CCG	C|0.561;T|0.439	0.439	strong		0.502	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
ANGPT2	285	hgsc.bcm.edu	37	8	6377433	6377433	+	Silent	SNP	C	C	T	rs1961222	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:6377433C>T	ENST00000325203.5	-	5	1356	c.882G>A	c.(880-882)acG>acA	p.T294T	ANGPT2_ENST00000338312.6_Silent_p.T242T|ANGPT2_ENST00000415216.1_Silent_p.T293T|ANGPT2_ENST00000523120.1_Silent_p.T293T|MCPH1_ENST00000344683.5_Intron			O15123	ANGP2_HUMAN	angiopoietin 2	294	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to growth factor stimulus (GO:0071363)|germ cell development (GO:0007281)|glomerulus vasculature development (GO:0072012)|leukocyte migration (GO:0050900)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of positive chemotaxis (GO:0050928)|organ regeneration (GO:0031100)|positive regulation of angiogenesis (GO:0045766)|response to activity (GO:0014823)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to radiation (GO:0009314)|signal transduction (GO:0007165)|Tie signaling pathway (GO:0048014)	cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17		Hepatocellular(245;0.0663)		Colorectal(4;0.0142)|READ - Rectum adenocarcinoma(4;0.19)|COAD - Colon adenocarcinoma(4;0.226)		AGATGCCATTCGTGGTGTGTC	0.433													C|||	750	0.14976	0.0121	0.2104	5008	,	,		19696	0.0516		0.3419	False		,,,				2504	0.1963				p.T294T		Atlas-SNP	.											.	ANGPT2	126	.	0			c.G882A						PASS	.	C	,,,	268,4138	151.0+/-185.0	7,254,1942	365.0	313.0	330.0		879,726,882,	-9.7	0.0	8	dbSNP_92	330	2903,5697	455.6+/-363.8	468,1967,1865	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ANGPT2,MCPH1	NM_001118887.1,NM_001118888.1,NM_001147.2,NM_024596.3	,,,	475,2221,3807	TT,TC,CC		33.7558,6.0826,24.3811	,,,	293/496,242/445,294/497,	6377433	3171,9835	2203	4300	6503	SO:0001819	synonymous_variant	285	exon5			GCCATTCGTGGTG	AF004327	CCDS5958.1, CCDS47761.1	8p23	2013-02-06			ENSG00000091879	ENSG00000091879		"""Fibrinogen C domain containing"""	485	protein-coding gene	gene with protein product		601922				9545648	Standard	NM_001147		Approved	Ang2	uc003wqj.4	O15123	OTTHUMG00000090365	ENST00000325203.5:c.882G>A	8.37:g.6377433C>T		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	220	93	0.422727	NM_001147	A0AV38|A8K205|B7ZLM7|Q9NRR7|Q9P2Y7	Silent	SNP	ENST00000325203.5	37	CCDS5958.1																																																																																			C|0.786;T|0.214	0.214	strong		0.433	ANGPT2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206737.1	NM_001147	
TAF6L	10629	hgsc.bcm.edu	37	11	62543326	62543326	+	Missense_Mutation	SNP	C	C	T	rs76769410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62543326C>T	ENST00000294168.3	+	2	272	c.71C>T	c.(70-72)aCg>aTg	p.T24M	TMEM223_ENST00000527073.1_Intron	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	24					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						GCGGAGAGCACGGGCCTGGAG	0.637													C|||	13	0.00259585	0.0015	0.0014	5008	,	,		18124	0.0		0.008	False		,,,				2504	0.002				p.T24M		Atlas-SNP	.											.	TAF6L	39	.	0			c.C71T						PASS	.	C	MET/THR	9,4393	16.8+/-37.8	0,9,2192	69.0	68.0	68.0		71	3.9	1.0	11	dbSNP_131	68	78,8520	45.4+/-104.0	2,74,4223	yes	missense	TAF6L	NM_006473.3	81	2,83,6415	TT,TC,CC		0.9072,0.2045,0.6692	possibly-damaging	24/623	62543326	87,12913	2201	4299	6500	SO:0001583	missense	10629	exon2			AGAGCACGGGCCT	BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227			17305	protein-coding gene	gene with protein product		602946	"""TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425	Standard	NM_006473		Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.71C>T	11.37:g.62543326C>T	ENSP00000294168:p.Thr24Met	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	33	0.578947	NM_006473	B2RAT0|Q96HA6	Missense_Mutation	SNP	ENST00000294168.3	37	CCDS8035.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	12.19	1.864603	0.32977	0.002045	0.009072	ENSG00000162227	ENST00000294168;ENST00000526261;ENST00000529509	T;T;T	0.42131	0.98;0.98;0.98	4.78	3.86	0.44501	Histone-fold (2);TATA box binding protein associated factor (TAF) (2);	0.211038	0.39615	N	0.001303	T	0.15478	0.0373	N	0.11427	0.14	0.80722	D	1	B;B	0.22146	0.013;0.065	B;B	0.17098	0.006;0.017	T	0.04522	-1.0945	10	0.37606	T	0.19	1.1681	7.4374	0.27164	0.0:0.8078:0.0:0.1922	.	24;24	B4DVM4;Q9Y6J9	.;TAF6L_HUMAN	M	24	ENSP00000294168:T24M;ENSP00000435116:T24M;ENSP00000434662:T24M	ENSP00000294168:T24M	T	+	2	0	TAF6L	62299902	0.996000	0.38824	0.963000	0.40424	0.968000	0.65278	3.349000	0.52217	1.364000	0.46038	0.561000	0.74099	ACG	C|0.995;T|0.005	0.005	strong		0.637	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395352.1	NM_006473	
JSRP1	126306	hgsc.bcm.edu	37	19	2252990	2252990	+	Missense_Mutation	SNP	C	C	G	rs80043033	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:2252990C>G	ENST00000300961.6	-	6	513	c.449G>C	c.(448-450)gGg>gCg	p.G150A	JSRP1_ENST00000586471.2_Missense_Mutation_p.G150A|MIR4321_ENST00000592276.1_RNA	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	150	Pro-rich.		G -> A (polymorphism affecting excitation/contraction coupling in muscle fibers; the sensitivity of CACNA1S voltage sensor is shifted to higher depolarizing voltages in cells carrying this variant; dbSNP:rs80043033). {ECO:0000269|PubMed:22927026}.		protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTGCCTCCCCAGGGACGGC	0.692													C|||	899	0.179513	0.0091	0.1916	5008	,	,		13576	0.3234		0.2376	False		,,,				2504	0.1933				p.G150A		Atlas-SNP	.											.	JSRP1	18	.	0			c.G449C						PASS	.	C	ALA/GLY	182,4192		3,176,2008	23.0	22.0	22.0		449	2.7	0.0	19	dbSNP_131	22	1727,6863		177,1373,2745	no	missense	JSRP1	NM_144616.3	60	180,1549,4753	GG,GC,CC		20.1048,4.161,14.7254	probably-damaging	150/332	2252990	1909,11055	2187	4295	6482	SO:0001583	missense	126306	exon6			GCCTCCCCAGGGA	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"""homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"""	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.449G>C	19.37:g.2252990C>G	ENSP00000300961:p.Gly150Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	437	0.2000915750915751	5	0.01016260162601626	68	0.1878453038674033	188	0.32867132867132864	176	0.23218997361477572	C	15.49	2.849180	0.51270	0.04161	0.201048	ENSG00000167476	ENST00000300961	T	0.59083	0.29	3.88	2.73	0.32206	.	0.642264	0.13741	N	0.365988	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P	0.36199	0.543	B	0.37387	0.248	T	0.29243	-1.0018	9	0.18276	T	0.48	-30.0495	8.7648	0.34696	0.0:0.767:0.233:0.0	.	150	Q96MG2	JSPR1_HUMAN	A	150	ENSP00000300961:G150A	ENSP00000300961:G150A	G	-	2	0	JSRP1	2203990	0.009000	0.17119	0.007000	0.13788	0.007000	0.05969	1.062000	0.30555	2.169000	0.68431	0.561000	0.74099	GGG	C|0.842;G|0.158	0.158	strong		0.692	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
ZSCAN31	64288	hgsc.bcm.edu	37	6	28297368	28297368	+	Silent	SNP	G	G	A	rs41269297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:28297368G>A	ENST00000414429.1	-	6	996	c.93C>T	c.(91-93)aaC>aaT	p.N31N	ZSCAN31_ENST00000439158.1_Silent_p.N31N|ZSCAN31_ENST00000396838.2_Silent_p.N31N|ZSCAN31_ENST00000446474.1_Intron|ZSCAN31_ENST00000481934.1_5'Flank|ZSCAN31_ENST00000344279.6_Silent_p.N31N			Q96LW9	ZSC31_HUMAN	zinc finger and SCAN domain containing 31	31					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GGCCAGAAAAGTTGTTCCCTC	0.512													G|||	99	0.0197684	0.0015	0.0288	5008	,	,		16448	0.0		0.0547	False		,,,				2504	0.0225				p.N31N		Atlas-SNP	.											.	.	.	.	0			c.C93T						PASS	.	G	,,,	50,4356	48.9+/-83.8	1,48,2154	88.0	91.0	90.0		93,93,93,93	0.7	0.0	6	dbSNP_127	90	436,8164	133.0+/-190.5	13,410,3877	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF323	NM_001135215.1,NM_001135216.1,NM_030899.4,NM_145909.2	,,,	14,458,6031	AA,AG,GG		5.0698,1.1348,3.7367	,,,	31/407,31/407,31/407,31/407	28297368	486,12520	2203	4300	6503	SO:0001819	synonymous_variant	64288	exon2			AGAAAAGTTGTTC		CCDS4649.1, CCDS59001.1	6p	2013-01-09	2013-01-08	2013-01-08	ENSG00000235109	ENSG00000235109		"""-"", ""Zinc fingers, C2H2-type"""	14097	protein-coding gene	gene with protein product		610794	"""zinc finger protein 310 pseudogene"", ""zinc finger protein 323"""	ZNF310P, ZNF323			Standard	NM_001135216		Approved		uc003nla.3	Q96LW9	OTTHUMG00000014518	ENST00000414429.1:c.93C>T	6.37:g.28297368G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_030899	Q6P178|Q8WWS5	Silent	SNP	ENST00000414429.1	37	CCDS4649.1																																																																																			G|0.972;A|0.028	0.028	strong		0.512	ZSCAN31-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346804.1	NM_030899	
ENPP4	22875	hgsc.bcm.edu	37	6	46108916	46108916	+	Silent	SNP	C	C	G	rs9472696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46108916C>G	ENST00000321037.4	+	3	1184	c.954C>G	c.(952-954)gcC>gcG	p.A318A		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	318					blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						TTTTGGTTGCCGATGAAGGCT	0.333													C|||	468	0.0934505	0.1339	0.0576	5008	,	,		17451	0.1716		0.0656	False		,,,				2504	0.0123				p.A318A		Atlas-SNP	.											.	ENPP4	44	.	0			c.C954G						PASS	.	C		607,3799	264.7+/-266.2	50,507,1646	92.0	83.0	86.0		954	-0.6	1.0	6	dbSNP_119	86	586,8008	155.4+/-209.4	15,556,3726	no	coding-synonymous	ENPP4	NM_014936.4		65,1063,5372	GG,GC,CC		6.8187,13.7767,9.1769		318/454	46108916	1193,11807	2203	4297	6500	SO:0001819	synonymous_variant	22875	exon3			GGTTGCCGATGAA	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.954C>G	6.37:g.46108916C>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_014936	A8K5G1|Q7L2N1	Silent	SNP	ENST00000321037.4	37	CCDS34468.1																																																																																			C|0.901;G|0.099	0.099	strong		0.333	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2		
EDA2R	60401	hgsc.bcm.edu	37	X	65824986	65824986	+	Missense_Mutation	SNP	C	C	T	rs1385699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:65824986C>T	ENST00000374719.3	-	3	226	c.170G>A	c.(169-171)aGa>aAa	p.R57K	EDA2R_ENST00000253392.5_Missense_Mutation_p.R57K|EDA2R_ENST00000396050.1_Missense_Mutation_p.R57K|EDA2R_ENST00000456230.2_Missense_Mutation_p.R57K|EDA2R_ENST00000451436.2_Intron|EDA2R_ENST00000450752.1_Missense_Mutation_p.R57K	NM_021783.3	NP_068555	Q9HAV5	TNR27_HUMAN	ectodysplasin A2 receptor	57			R -> K (in dbSNP:rs1385699).		cell differentiation (GO:0030154)|embryo development (GO:0009790)|epidermis development (GO:0008544)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						ACTCTGACATCTGTGGTGGCC	0.542													C|||	2512	0.66543	0.0333	0.6326	3775	,	,		13681	0.7569		0.6123	False		,,,				2504	0.6646				p.R57K		Atlas-SNP	.											.	EDA2R	30	.	0			c.G170A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	547,3288		36,393,82,1203,489	131.0	76.0	95.0		170,170,170	4.0	1.0	X	dbSNP_88	95	5367,1361		1599,731,1438,98,434	yes	missense,missense,missense	EDA2R	NM_001199687.2,NM_001242310.1,NM_021783.3	26,26,26	1635,1124,1520,1301,923	TT,TC,T,CC,C		20.2289,14.2634,44.0121	benign,benign,benign	57/298,57/319,57/298	65824986	5914,4649	2203	4300	6503	SO:0001583	missense	60401	exon2			TGACATCTGTGGT	AF298812	CCDS14386.1, CCDS56603.1	Xq11.1	2013-05-22			ENSG00000131080	ENSG00000131080		"""Tumor necrosis factor receptor superfamily"""	17756	protein-coding gene	gene with protein product		300276				11039935	Standard	NM_021783		Approved	XEDAR, EDA-A2R, EDAA2R, TNFRSF27	uc004dwt.2	Q9HAV5	OTTHUMG00000021736	ENST00000374719.3:c.170G>A	X.37:g.65824986C>T	ENSP00000363851:p.Arg57Lys	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	81	0.987805	NM_001242310	Q5VYX9|Q5VYY0|Q6UWM2|Q8IZA6	Missense_Mutation	SNP	ENST00000374719.3	37	CCDS14386.1	1144	0.6895720313441832	26	0.05416666666666667	146	0.6636363636363637	284	1.0	326	0.6877637130801688	C	7.543	0.661064	0.14645	0.142634	0.797711	ENSG00000131080	ENST00000374719;ENST00000396050;ENST00000253392;ENST00000456230;ENST00000450752	T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13	4.04	4.04	0.47022	TNFR/CD27/30/40/95 cysteine-rich region (4);	0.314080	0.26542	N	0.023785	T	0.00012	0.0000	N	0.15975	0.35	0.09310	P	0.9999999999996072	B;B	0.33826	0.001;0.427	B;B	0.31245	0.002;0.126	T	0.51647	-0.8679	9	0.02654	T	1	-10.3612	12.6999	0.57026	0.0:1.0:0.0:0.0	rs1385699;rs52832922;rs61534432;rs1385699	57;57	Q9HAV5-2;Q9HAV5	.;TNR27_HUMAN	K	57	ENSP00000363851:R57K;ENSP00000379365:R57K;ENSP00000253392:R57K;ENSP00000393935:R57K;ENSP00000402929:R57K	ENSP00000253392:R57K	R	-	2	0	EDA2R	65741711	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.661000	0.54503	1.841000	0.53522	0.600000	0.82982	AGA	C|0.436;0|0.005	.	strong		0.542	EDA2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057002.1	NM_021783	
HTR3D	200909	hgsc.bcm.edu	37	3	183753777	183753777	+	Missense_Mutation	SNP	G	G	A	rs36092077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183753777G>A	ENST00000382489.3	+	3	269	c.269G>A	c.(268-270)cGg>cAg	p.R90Q	HTR3D_ENST00000334128.2_Intron|HTR3D_ENST00000428798.2_Intron|HTR3D_ENST00000453435.1_Intron	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	90					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	caccatgcccggccTTGGCAC	0.537													g|||	1198	0.239217	0.1838	0.2579	5008	,	,		18463	0.4345		0.1819	False		,,,				2504	0.1585				p.R90Q		Atlas-SNP	.											.	HTR3D	65	.	0			c.G269A						PASS	.		,GLN/ARG,	245,1139		19,207,466	29.0	27.0	28.0		,269,	-1.2	0.0	3	dbSNP_126	28	585,2597		64,457,1070	yes	intron,missense,intron	HTR3D	NM_001145143.1,NM_001163646.1,NM_182537.2	,43,	83,664,1536	AA,AG,GG		18.3847,17.7023,18.1778	,benign,	,90/455,	183753777	830,3736	692	1591	2283	SO:0001583	missense	200909	exon3			ATGCCCGGCCTTG	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.269G>A	3.37:g.183753777G>A	ENSP00000371929:p.Arg90Gln	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Missense_Mutation	SNP	ENST00000382489.3	37	CCDS54685.1	516	0.23626373626373626	78	0.15853658536585366	66	0.18232044198895028	227	0.3968531468531469	145	0.19129287598944592	g	0.024	-1.388639	0.01185	0.177023	0.183847	ENSG00000186090	ENST00000382489	T	0.74842	-0.88	1.41	-1.24	0.09435	Neurotransmitter-gated ion-channel ligand-binding (3);	738.728000	0.00166	N	0.000002	T	0.00012	0.0000	N	0.04508	-0.205	0.51767	P	6.300000000003525E-5	B	0.13594	0.008	B	0.14023	0.01	T	0.13764	-1.0497	9	0.13108	T	0.6	.	3.949	0.09361	0.6575:0.0:0.3425:0.0	rs36092077	90	Q70Z44	5HT3D_HUMAN	Q	90	ENSP00000371929:R90Q	ENSP00000371929:R90Q	R	+	2	0	HTR3D	185236471	0.157000	0.22836	0.009000	0.14445	0.014000	0.08584	1.118000	0.31246	-0.277000	0.09193	-0.224000	0.12420	CGG	G|0.763;A|0.237	0.237	strong		0.537	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	
CFAP46	54777	hgsc.bcm.edu	37	10	134691472	134691472	+	Missense_Mutation	SNP	C	C	A	rs181912601	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691472C>A	ENST00000368586.5	-	30	4225	c.4125G>T	c.(4123-4125)aaG>aaT	p.K1375N	TTC40_ENST00000368582.2_Missense_Mutation_p.K1375N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						tactcctctccttctccttct	0.463													C|||	47	0.00938498	0.0076	0.0086	5008	,	,		17464	0.002		0.0119	False		,,,				2504	0.0174				p.K1375N		Atlas-SNP	.											.	TTC40	100	.	0			c.G4125T						PASS	.																																			SO:0001583	missense	54777	exon30			CCTCTCCTTCTCC																												ENST00000368586.5:c.4125G>T	10.37:g.134691472C>A	ENSP00000357575:p.Lys1375Asn	Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	255	66	0.258824	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	17	0.007783882783882784	5	0.01016260162601626	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	3.434	-0.115527	0.06881	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.06218	3.33;3.33	0.536	-0.606	0.11619	.	.	.	.	.	T	0.02688	0.0081	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.41413	-0.9510	5	0.32370	T	0.25	.	.	.	.	.	.	.	.	N	1375	ENSP00000357575:K1375N;ENSP00000357571:K1375N	ENSP00000357571:K1375N	K	-	3	2	C10orf93	134541462	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.744000	0.04839	-1.743000	0.01340	-1.817000	0.00601	AAG	C|0.992;A|0.008	0.008	strong		0.463	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
F7	2155	hgsc.bcm.edu	37	13	113773159	113773159	+	Missense_Mutation	SNP	G	G	A	rs6046	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113773159G>A	ENST00000375581.3	+	9	1273	c.1238G>A	c.(1237-1239)cGg>cAg	p.R413Q	F7_ENST00000541084.1_Missense_Mutation_p.R344Q|F7_ENST00000346342.3_Missense_Mutation_p.R391Q	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	413	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> G (in FA7D). {ECO:0000269|PubMed:18976247}.|R -> Q (may be associated with decreased susceptibility to myocardial infarction; dbSNP:rs6046). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10984565, ECO:0000269|PubMed:16292673, ECO:0000269|PubMed:8043443, ECO:0000269|PubMed:8844208, ECO:0000269|Ref.6}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	ACCCACTACCGGGGCACGTGG	0.627													G|||	693	0.138379	0.1172	0.1225	5008	,	,		15937	0.0466		0.1113	False		,,,				2504	0.3006				p.R413Q		Atlas-SNP	.											.	F7	49	.	0			c.G1238A	GRCh37	CM074160|CM940396	F7	M	rs6046	PASS	.	G	GLN/ARG,GLN/ARG	516,3886	218.7+/-236.7	32,452,1717	27.0	28.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1238,1172	-4.6	0.0	13	dbSNP_52	28	914,7684	192.4+/-238.4	56,802,3441	yes	missense,missense	F7	NM_000131.3,NM_019616.2	43,43	88,1254,5158	AA,AG,GG		10.6304,11.7219,11.0	benign,benign	413/467,391/445	113773159	1430,11570	2201	4299	6500	SO:0001583	missense	2155	exon9			ACTACCGGGGCAC		CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"""eptacog alfa"", ""FVII coagulation protein"", ""factor VII"""	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.1238G>A	13.37:g.113773159G>A	ENSP00000364731:p.Arg413Gln	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_000131	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Missense_Mutation	SNP	ENST00000375581.3	37	CCDS9528.1	206	0.09432234432234432	55	0.11178861788617886	42	0.11602209944751381	30	0.05244755244755245	79	0.10422163588390501	G	7.007	0.556041	0.13436	0.117219	0.106304	ENSG00000057593	ENST00000346342;ENST00000541084;ENST00000375581	D;D;D	0.81579	-1.51;-1.51;-1.51	4.11	-4.6	0.03390	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.744753	0.11868	N	0.521729	T	0.01592	0.0051	L	0.35854	1.095	0.80722	P	0.0	B;B;B	0.30889	0.092;0.254;0.299	B;B;B	0.14578	0.011;0.005;0.008	T	0.03017	-1.1082	9	0.40728	T	0.16	.	5.9568	0.19277	0.5017:0.0:0.3766:0.1217	rs6046;rs532977;rs36209568;rs6046	344;391;413	F5H8B0;P08709-2;P08709	.;.;FA7_HUMAN	Q	391;344;413	ENSP00000329546:R391Q;ENSP00000442051:R344Q;ENSP00000364731:R413Q	ENSP00000329546:R391Q	R	+	2	0	F7	112821160	0.036000	0.19791	0.003000	0.11579	0.015000	0.08874	0.104000	0.15313	-1.032000	0.03304	-0.518000	0.04402	CGG	T|0.001;G|0.877;C|0.007;A|0.115	0.115	strong		0.627	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045838.4	NM_000131	
ZRANB3	84083	hgsc.bcm.edu	37	2	135988416	135988416	+	Missense_Mutation	SNP	C	C	T	rs935615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:135988416C>T	ENST00000264159.6	-	13	1737	c.1621G>A	c.(1621-1623)Gaa>Aaa	p.E541K	ZRANB3_ENST00000401392.1_Missense_Mutation_p.E541K|ZRANB3_ENST00000536680.1_Missense_Mutation_p.E541K|ZRANB3_ENST00000412849.1_5'UTR	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	541			E -> K (in dbSNP:rs935615).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		CTCTTTGATTCGTCACAGGAG	0.373													C|||	1329	0.265375	0.3306	0.2651	5008	,	,		17479	0.2173		0.1312	False		,,,				2504	0.365				p.E541K		Atlas-SNP	.											.	ZRANB3	109	.	0			c.G1621A						PASS	.	C	LYS/GLU	1148,2536		187,774,881	94.0	90.0	91.0		1621	4.9	1.0	2	dbSNP_86	91	819,7359		49,721,3319	yes	missense	ZRANB3	NM_032143.2	56	236,1495,4200	TT,TC,CC		10.0147,31.1618,16.5824	benign	541/1080	135988416	1967,9895	1842	4089	5931	SO:0001583	missense	84083	exon13			TTGATTCGTCACA	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1621G>A	2.37:g.135988416C>T	ENSP00000264159:p.Glu541Lys	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	234	106	0.452991	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	456	0.2087912087912088	154	0.3130081300813008	89	0.24585635359116023	110	0.19230769230769232	103	0.1358839050131926	C	11.87	1.768362	0.31320	0.311618	0.100147	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	D;D;D	0.91011	-2.77;-2.77;-2.75	5.79	4.92	0.64577	.	0.610939	0.17895	N	0.158391	T	0.00012	0.0000	L	0.43152	1.355	0.43982	P	0.003326999999999969	B;B	0.13594	0.005;0.008	B;B	0.08055	0.002;0.003	T	0.03060	-1.1077	9	0.30854	T	0.27	1.0835	10.2509	0.43368	0.0:0.8461:0.0:0.1539	rs935615;rs52822236;rs58782931;rs935615	541;541	Q5FWF4;Q5FWF4-3	ZRAB3_HUMAN;.	K	6;6;541;541;541	ENSP00000383979:E541K;ENSP00000264159:E541K;ENSP00000441320:E541K	ENSP00000264159:E541K	E	-	1	0	ZRANB3	135704886	0.929000	0.31497	0.994000	0.49952	0.398000	0.30690	1.338000	0.33873	1.461000	0.47929	-0.244000	0.11960	GAA	C|0.797;T|0.203	0.203	strong		0.373	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
TTC23L	153657	hgsc.bcm.edu	37	5	34840841	34840841	+	Missense_Mutation	SNP	A	A	G	rs6451173	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:34840841A>G	ENST00000505624.1	+	2	168	c.65A>G	c.(64-66)cAt>cGt	p.H22R	CTD-2517O10.6_ENST00000606401.1_RNA|TTC23L_ENST00000514080.1_3'UTR	NM_144725.3	NP_653326.3	Q6PF05	TT23L_HUMAN	tetratricopeptide repeat domain 23-like	22			H -> R (in dbSNP:rs6451173). {ECO:0000269|PubMed:14702039}.							breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(9)|prostate(2)|stomach(1)|urinary_tract(1)	22						TTCTGCTTCCATATGTAAGTA	0.478													G|||	2693	0.53774	0.8986	0.4121	5008	,	,		17940	0.256		0.5457	False		,,,				2504	0.4213				p.H22R		Atlas-SNP	.											.	TTC23L	47	.	0			c.A65G						PASS	.	G	ARG/HIS	3405,559		1472,461,49	198.0	193.0	195.0		65	-1.2	0.0	5	dbSNP_116	195	4521,3857		1196,2129,864	yes	missense	TTC23L	NM_144725.3	29	2668,2590,913	GG,GA,AA		46.0372,14.1019,35.7803	benign	22/362	34840841	7926,4416	1982	4189	6171	SO:0001583	missense	153657	exon2			GCTTCCATATGTA		CCDS54840.1	5p13.2	2008-07-14			ENSG00000205838	ENSG00000205838			26355	protein-coding gene	gene with protein product						12477932	Standard	NM_144725		Approved	FLJ25439	uc003jiu.3	Q6PF05	OTTHUMG00000162020	ENST00000505624.1:c.65A>G	5.37:g.34840841A>G	ENSP00000422188:p.His22Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	133	59	0.443609	NM_144725	Q6RGS4|Q8N7R3|Q96LJ2	Missense_Mutation	SNP	ENST00000505624.1	37	CCDS54840.1	1163	0.5325091575091575	430	0.8739837398373984	163	0.45027624309392267	146	0.25524475524475526	424	0.5593667546174143	G	0.541	-0.853436	0.02630	0.858981	0.539628	ENSG00000205838	ENST00000505624;ENST00000535797	T	0.12361	2.69	5.34	-1.25	0.09405	.	0.904334	0.09368	N	0.811725	T	0.00012	0.0000	M	0.63428	1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.47381	-0.9122	9	0.05721	T	0.95	-9.946	5.6206	0.17455	0.557:0.0:0.3192:0.1237	rs6451173;rs17523522;rs17857470;rs52815487;rs58670304;rs6451173	22	Q6PF05	TT23L_HUMAN	R	22	ENSP00000422188:H22R	ENSP00000425242:H22R	H	+	2	0	TTC23L	34876598	0.013000	0.17824	0.046000	0.18839	0.162000	0.22319	0.234000	0.17930	-0.345000	0.08325	-1.110000	0.02074	CAT	A|0.457;G|0.543	0.543	strong		0.478	TTC23L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366819.1	NM_144725	
OSBPL1A	114876	hgsc.bcm.edu	37	18	21752366	21752366	+	Silent	SNP	A	A	G	rs2077984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:21752366A>G	ENST00000319481.3	-	22	2381	c.2175T>C	c.(2173-2175)taT>taC	p.Y725Y	OSBPL1A_ENST00000357041.4_Silent_p.Y343Y|RNA5SP452_ENST00000363004.1_RNA|OSBPL1A_ENST00000399443.3_Silent_p.Y212Y	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A	725					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					CCACATTGCCATACTGTTCGA	0.388													G|||	605	0.120807	0.3222	0.0317	5008	,	,		19396	0.0724		0.0169	False		,,,				2504	0.0685				p.Y725Y		Atlas-SNP	.											.	OSBPL1A	94	.	0			c.T2175C						PASS	.	G	,,	1165,3241	712.6+/-408.1	158,849,1196	204.0	178.0	187.0		1029,636,2175	-8.7	0.5	18	dbSNP_96	187	126,8474	813.9+/-407.0	0,126,4174	no	coding-synonymous,coding-synonymous,coding-synonymous	OSBPL1A	NM_001242508.1,NM_018030.4,NM_080597.3	,,	158,975,5370	GG,GA,AA		1.4651,26.4412,9.9262	,,	343/569,212/438,725/951	21752366	1291,11715	2203	4300	6503	SO:0001819	synonymous_variant	114876	exon22			ATTGCCATACTGT	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944	ENST00000319481.3:c.2175T>C	18.37:g.21752366A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	132	73	0.55303	NM_080597	B7Z7D3|Q9BZF5|Q9NW87	Silent	SNP	ENST00000319481.3	37	CCDS11884.1																																																																																			A|0.894;G|0.106	0.106	strong		0.388	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
MYBPC1	4604	hgsc.bcm.edu	37	12	102036305	102036305	+	Silent	SNP	C	C	T	rs2293468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:102036305C>T	ENST00000550270.1	+	9	699	c.699C>T	c.(697-699)gaC>gaT	p.D233D	MYBPC1_ENST00000547405.1_Silent_p.D207D|MYBPC1_ENST00000549145.1_Silent_p.D246D|MYBPC1_ENST00000553190.1_Silent_p.D233D|MYBPC1_ENST00000361466.2_Silent_p.D258D|MYBPC1_ENST00000551300.1_Silent_p.D134D|MYBPC1_ENST00000547509.1_Silent_p.D219D|MYBPC1_ENST00000392934.3_Silent_p.D220D|MYBPC1_ENST00000536007.1_Silent_p.D214D|MYBPC1_ENST00000452455.2_Silent_p.D233D|MYBPC1_ENST00000545503.2_Silent_p.D233D|MYBPC1_ENST00000361685.2_Silent_p.D258D|MYBPC1_ENST00000360610.2_Silent_p.D233D|MYBPC1_ENST00000441232.1_Silent_p.D233D|MYBPC1_ENST00000541119.1_Silent_p.D221D|MYBPC1_ENST00000550501.1_Intron			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	233				GITDLR -> ESPTCS (in Ref. 1; CAA46987). {ECO:0000305}.	cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myofibril (GO:0030016)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	57						GAATCACCGACCTGCGCGGCA	0.627													C|||	1474	0.294329	0.289	0.2493	5008	,	,		19254	0.3879		0.2823	False		,,,				2504	0.2495				p.D258D		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C774T						PASS	.	C	,,,	1283,3123	433.3+/-343.5	197,889,1117	88.0	71.0	76.0		774,774,699,699	3.4	1.0	12	dbSNP_100	76	2466,6134	403.5+/-347.8	343,1780,2177	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYBPC1	NM_002465.2,NM_206819.1,NM_206820.1,NM_206821.1	,,,	540,2669,3294	TT,TC,CC		28.6744,29.1194,28.8252	,,,	258/1172,258/1149,233/1142,233/1124	102036305	3749,9257	2203	4300	6503	SO:0001819	synonymous_variant	4604	exon11			CACCGACCTGCGC		CCDS9083.1, CCDS9084.1, CCDS9085.1, CCDS55877.1, CCDS58268.1, CCDS58269.1, CCDS58270.1, CCDS58271.1, CCDS58272.1, CCDS58273.1	12q23.2	2013-02-11	2001-11-28		ENSG00000196091	ENSG00000196091		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7549	protein-coding gene	gene with protein product		160794	"""myosin-binding protein C, slow-type"""			8375400, 16918501	Standard	NM_002465		Approved		uc010svs.2	Q00872	OTTHUMG00000170274	ENST00000550270.1:c.699C>T	12.37:g.102036305C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Silent	SNP	ENST00000550270.1	37	CCDS9085.1																																																																																			C|0.704;T|0.296	0.296	strong		0.627	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
MICAL3	57553	hgsc.bcm.edu	37	22	18304891	18304891	+	Missense_Mutation	SNP	C	C	T	rs45544141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18304891C>T	ENST00000441493.2	-	24	3705	c.3353G>A	c.(3352-3354)cGt>cAt	p.R1118H		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1118	Glu-rich.				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)		GCACGGCAAACGCAGCTCTCT	0.612													T|||	431	0.0860623	0.1422	0.0389	5008	,	,		18656	0.0823		0.0586	False		,,,				2504	0.0757				p.R1118H		Atlas-SNP	.											ENSG00000093100,NS,carcinoma,-1,1	MICAL3	53	1	0			c.G3353A						PASS	.	T	HIS/ARG	589,3687		39,511,1588	69.0	76.0	74.0		3353	0.4	0.0	22	dbSNP_127	74	456,8016		8,440,3788	yes	missense	MICAL3	NM_015241.2	29	47,951,5376	TT,TC,CC		5.3824,13.7746,8.1974	benign	1118/2003	18304891	1045,11703	2138	4236	6374	SO:0001583	missense	57553	exon24			GGCAAACGCAGCT	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.3353G>A	22.37:g.18304891C>T	ENSP00000416015:p.Arg1118His	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	43	14	0.325581	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	189|189	0.08653846153846154|0.08653846153846154	67|67	0.13617886178861788|0.13617886178861788	17|17	0.04696132596685083|0.04696132596685083	54|54	0.0944055944055944|0.0944055944055944	51|51	0.06728232189973615|0.06728232189973615	T|T	8.088|8.088	0.773828|0.773828	0.16051|0.16051	0.137746|0.137746	0.053824|0.053824	ENSG00000093100|ENSG00000093100	ENST00000441493|ENST00000252134	T|.	0.64991|.	-0.13|.	3.91|3.91	0.398|0.398	0.16319|0.16319	.|.	.|.	.|.	.|.	.|.	T|T	0.00271|0.00271	0.0008|0.0008	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	P|P	0.0|0.0	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|T	0.16217|0.16217	-1.0410|-1.0410	8|4	0.25751|.	T|.	0.34|.	.|.	7.1303|7.1303	0.25497|0.25497	0.0:0.6945:0.1538:0.1517|0.0:0.6945:0.1538:0.1517	rs45544141;rs59033817;rs61741772|rs45544141;rs59033817;rs61741772	1118|.	Q7RTP6|.	MICA3_HUMAN|.	H|I	1118|100	ENSP00000416015:R1118H|.	ENSP00000416015:R1118H|.	R|V	-|-	2|1	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16684891|16684891	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.041000|0.041000	0.13927|0.13927	-0.346000|-0.346000	0.08312|0.08312	-1.263000|-1.263000	0.01449|0.01449	CGT|GTT	C|0.921;G|0.000;T|0.079	0.079	strong		0.612	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
PALLD	23022	hgsc.bcm.edu	37	4	169432841	169432841	+	Silent	SNP	G	G	A	rs1806729	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169432841G>A	ENST00000505667.1	+	2	359	c.186G>A	c.(184-186)aaG>aaA	p.K62K	PALLD_ENST00000261509.6_Silent_p.K62K|PALLD_ENST00000333488.4_5'UTR|PALLD_ENST00000335742.7_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	62					cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		ACTCGGAAAAGGAGATCTCGC	0.507									Pancreatic Cancer, Familial Clustering of				G|||	1182	0.236022	0.2231	0.1844	5008	,	,		18749	0.1925		0.329	False		,,,				2504	0.2393				p.K62K	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.G186A						PASS	.	G	,	1040,3366	361.4+/-315.7	139,762,1302	39.0	40.0	40.0		186,186	3.7	1.0	4	dbSNP_92	40	2789,5811	426.7+/-355.4	460,1869,1971	no	coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_016081.3	,	599,2631,3273	AA,AG,GG		32.4302,23.6042,29.4403	,	62/1124,62/1107	169432841	3829,9177	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GGAAAAGGAGATC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.186G>A	4.37:g.169432841G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			G|0.728;A|0.272	0.272	strong		0.507	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
C15orf56	644809	hgsc.bcm.edu	37	15	40544617	40544617	+	Missense_Mutation	SNP	G	G	A	rs55863440	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:40544617G>A	ENST00000319503.3	-	2	376	c.355C>T	c.(355-357)Cca>Tca	p.P119S	C15orf56_ENST00000559727.1_3'UTR|PAK6_ENST00000453867.1_Intron|PAK6_ENST00000260404.4_Intron|PAK6_ENST00000560346.1_Intron|PAK6_ENST00000455577.2_Intron|PAK6_ENST00000542403.2_5'Flank|PAK6_ENST00000441369.1_Intron|RP11-133K1.2_ENST00000558658.1_Intron	NM_001039905.1	NP_001034994.1	Q8N910	CO056_HUMAN	chromosome 15 open reading frame 56	119			P -> S (in dbSNP:rs55863440).							lung(1)	1		all_cancers(109;1.62e-14)|all_epithelial(112;7.09e-12)|Lung NSC(122;3.4e-09)|all_lung(180;6.88e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.28e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0503)		CAAGCAGGTGGAGAGAAAGAG	0.736													G|||	791	0.157947	0.0499	0.1988	5008	,	,		11428	0.0873		0.3052	False		,,,				2504	0.1963				p.P119S		Atlas-SNP	.											.	C15orf56	3	.	0			c.C355T						PASS	.	G	,,,SER/PRO	417,3971		19,379,1796	17.0	21.0	20.0		,,,355	-3.0	0.0	15	dbSNP_129	20	2822,5768		478,1866,1951	yes	intron,intron,intron,missense	PAK6,C15orf56	NM_001128628.1,NM_001128629.1,NM_020168.4,NM_001039905.1	,,,74	497,2245,3747	AA,AG,GG		32.8522,9.5032,24.9576	,,,benign	,,,119/162	40544617	3239,9739	2194	4295	6489	SO:0001583	missense	644809	exon2			CAGGTGGAGAGAA		CCDS32197.1	15q15.1	2012-05-30			ENSG00000176753	ENSG00000176753			33868	protein-coding gene	gene with protein product							Standard	NM_001039905		Approved	FLJ38596	uc001zla.2	Q8N910	OTTHUMG00000172399	ENST00000319503.3:c.355C>T	15.37:g.40544617G>A	ENSP00000315794:p.Pro119Ser	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	21	11	0.52381	NM_001039905		Missense_Mutation	SNP	ENST00000319503.3	37	CCDS32197.1	384	0.17582417582417584	30	0.06097560975609756	85	0.23480662983425415	40	0.06993006993006994	229	0.3021108179419525	G	12.42	1.932278	0.34096	0.095032	0.328522	ENSG00000176753	ENST00000319503	T	0.32272	1.46	4.2	-3.04	0.05412	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.22414	0.069	B	0.21360	0.034	T	0.43669	-0.9377	8	0.87932	D	0	.	3.0052	0.06026	0.18:0.4429:0.2494:0.1276	rs55863440	119	Q8N910	CO056_HUMAN	S	119	ENSP00000315794:P119S	ENSP00000315794:P119S	P	-	1	0	C15orf56	38331909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.857000	0.04286	-0.735000	0.04837	-1.134000	0.01955	CCA	G|0.812;A|0.188	0.188	strong		0.736	C15orf56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418370.2	NM_001039905	
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:14542654C>A	ENST00000358970.5	-	1	491	c.492G>T	c.(490-492)acG>acT	p.T164T	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	164								p.T164T(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TGTTCATGTCCGTGTCCCTGA	0.592																																					p.T164T		Atlas-SNP	.											POTEC,NS,carcinoma,-1,5	POTEC	129	5	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G492T						scavenged	.						260.0	241.0	247.0					18																	14542654		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			CATGTCCGTGTCC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.492G>T	18.37:g.14542654C>A		Somatic	529	6	0.0113422		WXS	Illumina HiSeq	Phase_I	589	6	0.0101868	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	none		0.592	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
UBR3	130507	hgsc.bcm.edu	37	2	170917648	170917648	+	Silent	SNP	A	A	G	rs10203212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:170917648A>G	ENST00000272793.5	+	34	4895	c.4845A>G	c.(4843-4845)ctA>ctG	p.L1615L	UBR3_ENST00000418381.1_Silent_p.L1615L|UBR3_ENST00000392631.1_Silent_p.L436L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	1615					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						TAAGTGAACTATTTAAAGGAA	0.313													A|||	1663	0.332069	0.3185	0.1945	5008	,	,		16483	0.4077		0.2525	False		,,,				2504	0.4519				p.L1615L		Atlas-SNP	.											.	UBR3	182	.	0			c.A4845G						PASS	.	A		1437,2969	452.2+/-349.9	229,979,995	78.0	84.0	82.0		4845	-10.7	0.5	2	dbSNP_119	82	2198,6398	370.9+/-336.0	287,1624,2387	no	coding-synonymous	UBR3	NM_172070.3		516,2603,3382	GG,GA,AA		25.57,32.6146,27.9572		1615/1889	170917648	3635,9367	2203	4298	6501	SO:0001819	synonymous_variant	130507	exon34			TGAACTATTTAAA	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.4845A>G	2.37:g.170917648A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	142	78	0.549296	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37		662	0.3031135531135531	168	0.34146341463414637	80	0.22099447513812154	219	0.38286713286713286	195	0.25725593667546176	A	7.125	0.578734	0.13686	0.326146	0.2557	ENSG00000144357	ENST00000392632	.	.	.	6.06	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999070877	.	.	.	.	.	.	T	0.24012	-1.0172	3	.	.	.	.	6.0718	0.19893	0.2412:0.2378:0.4365:0.0844	rs10203212;rs61612763;rs10203212	.	.	.	C	677	.	.	Y	+	2	0	UBR3	170625894	0.049000	0.20398	0.451000	0.26982	0.929000	0.56500	-0.900000	0.04097	-2.018000	0.00943	-1.237000	0.01550	TAT	A|0.719;G|0.281	0.281	strong		0.313	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
ERAP1	51752	hgsc.bcm.edu	37	5	96121524	96121524	+	Silent	SNP	C	C	T	rs469783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96121524C>T	ENST00000443439.2	-	13	1977	c.1911G>A	c.(1909-1911)gcG>gcA	p.A637A	CTD-2260A17.1_ENST00000602972.1_RNA|ERAP1_ENST00000296754.3_Silent_p.A637A|CTD-2260A17.1_ENST00000512856.1_RNA|ERAP1_ENST00000514604.1_5'UTR	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	637					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)		TAATGAGACTCGCCCGATCAT	0.418													.|||	2790	0.557109	0.5855	0.5403	5008	,	,		19825	0.5427		0.5577	False		,,,				2504	0.545				p.A637A		Atlas-SNP	.											.	ERAP1	59	.	0			c.G1911A						PASS	.	C	,,	2531,1875	631.8+/-395.7	719,1093,391	148.0	117.0	128.0		1911,1911,1911	-1.1	1.0	5	dbSNP_80	128	4793,3807	612.2+/-395.9	1329,2135,836	no	coding-synonymous,coding-synonymous,coding-synonymous	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	,,	2048,3228,1227	TT,TC,CC		44.2674,42.5556,43.6875	,,	637/942,637/942,637/949	96121524	7324,5682	2203	4300	6503	SO:0001819	synonymous_variant	51752	exon13			GAGACTCGCCCGA	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.1911G>A	5.37:g.96121524C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Silent	SNP	ENST00000443439.2	37	CCDS47250.1																																																																																			C|0.451;T|0.549	0.549	strong		0.418	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
TENM2	57451	hgsc.bcm.edu	37	5	167689162	167689162	+	Missense_Mutation	SNP	G	G	A	rs370473451		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:167689162G>A	ENST00000518659.1	+	29	7711	c.7672G>A	c.(7672-7674)Ggt>Agt	p.G2558S	TENM2_ENST00000545108.1_Missense_Mutation_p.G2557S|TENM2_ENST00000520394.1_Missense_Mutation_p.G2319S|TENM2_ENST00000519204.1_Missense_Mutation_p.G2437S|TENM2_ENST00000403607.2_Missense_Mutation_p.G2382S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2558					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)										AGAGAAAGCAGGTCACTGGTT	0.547																																					p.G2549S		Atlas-SNP	.											.	.	.	.	0			c.G7645A						PASS	.	G	SER/GLY	0,4040		0,0,2020	34.0	35.0	35.0		7645	5.4	1.0	5		35	1,8379		0,1,4189	no	missense	ODZ2	NM_001122679.1	56	0,1,6209	AA,AG,GG		0.0119,0.0,0.0081	probably-damaging	2549/2766	167689162	1,12419	2020	4190	6210	SO:0001583	missense	57451	exon29			AAAGCAGGTCACT	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.7672G>A	5.37:g.167689162G>A	ENSP00000429430:p.Gly2558Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	G	18.78	3.697687	0.68386	0.0	1.19E-4	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.88896	-1.97;-1.96;-2.07;-2.43;-2.44	5.42	5.42	0.78866	.	0.102393	0.64402	D	0.000002	D	0.90397	0.6994	N	0.24115	0.695	0.58432	D	0.999992	D;D;D	0.89917	0.999;0.991;1.0	D;P;D	0.83275	0.974;0.842;0.996	D	0.87772	0.2606	10	0.21540	T	0.41	.	19.5868	0.95493	0.0:0.0:1.0:0.0	.	2557;2558;2319	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	2558;2557;2437;2319;2382	ENSP00000429430:G2558S;ENSP00000438635:G2557S;ENSP00000428964:G2437S;ENSP00000427874:G2319S;ENSP00000384905:G2382S	ENSP00000384905:G2382S	G	+	1	0	ODZ2	167621740	1.000000	0.71417	0.977000	0.42913	0.886000	0.51366	9.809000	0.99208	2.694000	0.91930	0.655000	0.94253	GGT	.	.	weak		0.547	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
OR7G1	125962	hgsc.bcm.edu	37	19	9226192	9226192	+	Missense_Mutation	SNP	A	A	G	rs6511874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9226192A>G	ENST00000541538.1	-	1	247	c.248T>C	c.(247-249)gTg>gCg	p.V83A	OR7G1_ENST00000293614.1_Missense_Mutation_p.V83A	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	83			V -> A (in dbSNP:rs6511874).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						TTGGATGTTCACTAGGATCTT	0.458													G|||	1722	0.34385	0.6188	0.1369	5008	,	,		21639	0.3244		0.1918	False		,,,				2504	0.2955				p.V83A		Atlas-SNP	.											OR7G1,right_lower_lobe,carcinoma,+1,1	OR7G1	53	1	0			c.T248C						scavenged	.	G	ALA/VAL	2369,2037	566.0+/-381.8	616,1137,450	227.0	227.0	227.0		248	-2.5	0.6	19	dbSNP_116	227	1491,7109	749.6+/-407.4	125,1241,2934	yes	missense	OR7G1	NM_001005192.2	64	741,2378,3384	GG,GA,AA		17.3372,46.2324,29.6786	benign	83/312	9226192	3860,9146	2203	4300	6503	SO:0001583	missense	125962	exon1			ATGTTCACTAGGA		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"""GPCR / Class A : Olfactory receptors"""	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.248T>C	19.37:g.9226192A>G	ENSP00000444134:p.Val83Ala	Somatic	186	2	0.0107527		WXS	Illumina HiSeq	Phase_I	181	95	0.524862	NM_001005192	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	653	0.298992673992674	291	0.5914634146341463	44	0.12154696132596685	181	0.31643356643356646	137	0.18073878627968337	g	1.871	-0.460294	0.04508	0.537676	0.173372	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.02158	4.42;4.42	2.88	-2.47	0.06442	GPCR, rhodopsin-like superfamily (1);	0.562648	0.13220	N	0.404446	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.19200	0.034	B	0.23852	0.049	T	0.26608	-1.0098	9	0.40728	T	0.16	.	0.8776	0.01227	0.4554:0.1247:0.175:0.2449	rs6511874;rs52807155;rs59528971;rs6511874	83	Q8NGA0	OR7G1_HUMAN	A	83	ENSP00000293614:V83A;ENSP00000444134:V83A	ENSP00000293614:V83A	V	-	2	0	OR7G1	9087192	0.000000	0.05858	0.569000	0.28460	0.017000	0.09413	-1.370000	0.02575	-1.123000	0.02940	-1.677000	0.00738	GTG	A|0.686;G|0.314	0.314	strong		0.458	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1		
PNKD	25953	hgsc.bcm.edu	37	2	219206738	219206738	+	Silent	SNP	C	C	A	rs34745867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219206738C>A	ENST00000273077.4	+	7	703	c.652C>A	c.(652-654)Cgg>Agg	p.R218R	AC021016.8_ENST00000411433.1_RNA|PNKD_ENST00000258362.3_Silent_p.R194R|PNKD_ENST00000436005.2_Silent_p.R158R	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia	218					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)		CAGCGTGGGACGGCTTCAGAT	0.597													C|||	28	0.00559105	0.0023	0.0101	5008	,	,		19253	0.0		0.0169	False		,,,				2504	0.001				p.R218R		Atlas-SNP	.											.	PNKD	58	.	0			c.C652A						PASS	.	C	,	18,4388	25.3+/-52.1	0,18,2185	132.0	109.0	117.0		652,580	2.7	1.0	2	dbSNP_126	117	222,8378	93.1+/-155.1	4,214,4082	no	coding-synonymous,coding-synonymous	PNKD	NM_015488.4,NM_022572.4	,	4,232,6267	AA,AC,CC		2.5814,0.4085,1.8453	,	218/386,194/362	219206738	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	25953	exon7			GTGGGACGGCTTC		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.652C>A	2.37:g.219206738C>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_015488	A8K1F2|Q96A48|Q9BU26|Q9NSX4|Q9ULN6|Q9Y4T1	Silent	SNP	ENST00000273077.4	37	CCDS2411.1																																																																																			C|0.982;A|0.018	0.018	strong		0.597	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2		
ACAP3	116983	hgsc.bcm.edu	37	1	1231656	1231656	+	Silent	SNP	G	G	A	rs1749951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1231656G>A	ENST00000354700.5	-	16	1544	c.1342C>T	c.(1342-1344)Ctg>Ttg	p.L448L	ACAP3_ENST00000353662.3_Silent_p.L406L|ACAP3_ENST00000379037.2_5'Flank	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	448	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						TGGACACCCAGGCTCCTGGAG	0.706													g|||	251	0.0501198	0.0219	0.0216	5008	,	,		12504	0.0873		0.0378	False		,,,				2504	0.0828				p.L448L		Atlas-SNP	.											.	ACAP3	87	.	0			c.C1342T						PASS	.			50,4264		1,48,2108	23.0	23.0	23.0		1342	0.6	1.0	1	dbSNP_89	23	323,8149		6,311,3919	no	coding-synonymous	ACAP3	NM_030649.2		7,359,6027	AA,AG,GG		3.8126,1.159,2.9173		448/835	1231656	373,12413	2157	4236	6393	SO:0001819	synonymous_variant	116983	exon16			CACCCAGGCTCCT	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16754	protein-coding gene	gene with protein product			"""centaurin, beta 5"""	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.1342C>T	1.37:g.1231656G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	121	9	0.0743802	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Silent	SNP	ENST00000354700.5	37	CCDS19.2																																																																																			G|0.963;A|0.037	0.037	strong		0.706	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649	
OR5P3	120066	hgsc.bcm.edu	37	11	7847472	7847472	+	Silent	SNP	C	C	T	rs1482793	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7847472C>T	ENST00000328375.1	-	1	47	c.48G>A	c.(46-48)ggG>ggA	p.G16G	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153445.1	NP_703146.1	Q8WZ94	OR5P3_HUMAN	olfactory receptor, family 5, subfamily P, member 3	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	15				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCTCAGATAACCCCAAAAGAG	0.348													C|||	2223	0.44389	0.0726	0.5937	5008	,	,		19327	0.4762		0.6292	False		,,,				2504	0.6155				p.G16G		Atlas-SNP	.											.	OR5P3	44	.	0			c.G48A						PASS	.	C		723,3615		122,479,1568	44.0	45.0	45.0		48	-4.9	0.0	11	dbSNP_88	45	5273,3283		1672,1929,677	no	coding-synonymous	OR5P3	NM_153445.1		1794,2408,2245	TT,TC,CC		38.3707,16.6667,46.5022		16/312	7847472	5996,6898	2169	4278	6447	SO:0001819	synonymous_variant	120066	exon1			AGATAACCCCAAA	AF158377	CCDS7783.1	11p15.4	2012-08-09			ENSG00000182334	ENSG00000182334		"""GPCR / Class A : Olfactory receptors"""	14784	protein-coding gene	gene with protein product							Standard	NM_153445		Approved	JCG1	uc010rbg.2	Q8WZ94	OTTHUMG00000165669	ENST00000328375.1:c.48G>A	11.37:g.7847472C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_153445	Q6IFE1|Q8NGM2	Silent	SNP	ENST00000328375.1	37	CCDS7783.1																																																																																			C|0.504;T|0.496	0.496	strong		0.348	OR5P3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385697.1	NM_153445	
FAT2	2196	hgsc.bcm.edu	37	5	150905485	150905485	+	Silent	SNP	C	C	T	rs36092108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:150905485C>T	ENST00000261800.5	-	17	10362	c.10350G>A	c.(10348-10350)ctG>ctA	p.L3450L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3450	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTGGGTCACTCAGGATCAGCT	0.567													C|||	480	0.0958466	0.0038	0.0173	5008	,	,		20940	0.1756		0.0338	False		,,,				2504	0.2577				p.L3450L		Atlas-SNP	.											.	FAT2	465	.	0			c.G10350A						PASS	.	C		72,4334	64.1+/-101.4	1,70,2132	46.0	44.0	45.0		10350	3.3	1.0	5	dbSNP_126	45	414,8186	128.8+/-187.0	12,390,3898	no	coding-synonymous	FAT2	NM_001447.2		13,460,6030	TT,TC,CC		4.814,1.6341,3.7367		3450/4350	150905485	486,12520	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon17			GTCACTCAGGATC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10350G>A	5.37:g.150905485C>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	134	0.06135531135531135	2	0.0040650406504065045	11	0.03038674033149171	96	0.16783216783216784	25	0.032981530343007916	C	9.730	1.161976	0.21538	0.016341	0.04814	ENSG00000086570	ENST00000520200	.	.	.	5.2	3.32	0.38043	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06570	-1.0819	3	.	.	.	.	10.5378	0.45016	0.1415:0.5853:0.2732:0.0	rs36092108	.	.	.	K	309	.	.	E	-	1	0	FAT2	150885678	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.390000	0.44416	0.630000	0.30394	0.544000	0.68410	GAG	C|0.954;T|0.046	0.046	strong		0.567	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
GPR171	29909	hgsc.bcm.edu	37	3	150917000	150917000	+	Silent	SNP	T	T	G	rs3773614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:150917000T>G	ENST00000309180.5	-	3	404	c.174A>C	c.(172-174)acA>acC	p.T58T	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_013308.3	NP_037440.3	O14626	GP171_HUMAN	G protein-coupled receptor 171	58					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(4)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	15			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGAAATCGGCTGTAAGCAAAT	0.413													T|||	591	0.118011	0.2194	0.085	5008	,	,		18283	0.0704		0.0666	False		,,,				2504	0.1063				p.T58T		Atlas-SNP	.											.	GPR171	36	.	0			c.A174C						PASS	.	T	,	897,3509	346.7+/-309.1	88,721,1394	85.0	83.0	84.0		174,	-6.9	0.0	3	dbSNP_107	84	608,7992	160.0+/-213.2	17,574,3709	no	coding-synonymous,intron	GPR171,MED12L	NM_013308.3,NM_053002.4	,	105,1295,5103	GG,GT,TT		7.0698,20.3586,11.5716	,	58/320,	150917000	1505,11501	2203	4300	6503	SO:0001819	synonymous_variant	29909	exon3			ATCGGCTGTAAGC	AF002986	CCDS3155.1	3q25.1	2012-08-21			ENSG00000174946	ENSG00000174946		"""GPCR / Class A : Orphans"""	30057	protein-coding gene	gene with protein product	"""platelet activating receptor homolog"""					9370294	Standard	NM_013308		Approved	H963	uc003eyq.4	O14626	OTTHUMG00000159861	ENST00000309180.5:c.174A>C	3.37:g.150917000T>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	205	86	0.419512	NM_013308	D3DNJ4|Q8IV06	Silent	SNP	ENST00000309180.5	37	CCDS3155.1																																																																																			T|0.882;G|0.118	0.118	strong		0.413	GPR171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357793.1	NM_013308	
FOXK1	221937	hgsc.bcm.edu	37	7	4802035	4802035	+	Silent	SNP	A	A	G	rs1053753	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4802035A>G	ENST00000328914.4	+	9	2142	c.2142A>G	c.(2140-2142)gtA>gtG	p.V714V	FOXK1_ENST00000446823.1_Silent_p.V551V	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		GTGGTGCTGTAACCACACCGG	0.701													G|||	1465	0.292532	0.6785	0.121	5008	,	,		12597	0.0704		0.1471	False		,,,				2504	0.271				p.V714V		Atlas-SNP	.											.	FOXK1	64	.	0			c.A2142G						PASS	.	G		2104,2054		524,1056,499	12.0	14.0	14.0		2142	-5.3	0.0	7	dbSNP_86	14	1140,7002		97,946,3028	no	coding-synonymous	FOXK1	NM_001037165.1		621,2002,3527	GG,GA,AA		14.0015,49.3987,26.374		714/734	4802035	3244,9056	2079	4071	6150	SO:0001819	synonymous_variant	221937	exon9			TGCTGTAACCACA	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.2142A>G	7.37:g.4802035A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	27	17	0.62963	NM_001037165		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																			A|0.728;G|0.272	0.272	strong		0.701	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
PSMB5	5693	hgsc.bcm.edu	37	14	23504021	23504021	+	Missense_Mutation	SNP	G	G	A	rs11543947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23504021G>A	ENST00000361611.6	-	1	333	c.70C>T	c.(70-72)Cgt>Tgt	p.R24C	PSMB5_ENST00000493471.2_Missense_Mutation_p.R24C|PSMB5_ENST00000425762.2_Intron|AL132780.1_ENST00000385031.1_RNA|PSMB5_ENST00000460922.2_Missense_Mutation_p.R24C	NM_002797.3	NP_002788.1	P28074	PSB5_HUMAN	proteasome (prosome, macropain) subunit, beta type, 5	24			R -> C (in dbSNP:rs11543947).		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)|response to oxidative stress (GO:0006979)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	7	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.0121)	Bortezomib(DB00188)|Carfilzomib(DB08889)	AGATCTGCACGACCCCCAAGT	0.582													G|||	180	0.0359425	0.0234	0.0288	5008	,	,		16780	0.001		0.0626	False		,,,				2504	0.0665				p.R24C		Atlas-SNP	.											.	PSMB5	31	.	0			c.C70T						PASS	.	G	,CYS/ARG,CYS/ARG	169,4237	110.8+/-149.0	5,159,2039	55.0	53.0	54.0		,70,70	3.4	1.0	14	dbSNP_120	54	711,7889	174.5+/-224.7	22,667,3611	yes	intron,missense,missense	PSMB5	NM_001130725.1,NM_001144932.1,NM_002797.3	,180,180	27,826,5650	AA,AG,GG		8.2674,3.8357,6.7661	,probably-damaging,probably-damaging	,24/204,24/264	23504021	880,12126	2203	4300	6503	SO:0001583	missense	5693	exon1			CTGCACGACCCCC	D29011	CCDS9584.1, CCDS45083.1, CCDS45084.1	14q11.2	2008-08-29			ENSG00000100804	ENSG00000100804		"""Proteasome (prosome, macropain) subunits"""	9542	protein-coding gene	gene with protein product		600306				8066462, 8811196	Standard	NM_001130725		Approved	X, MB1	uc001wii.3	P28074	OTTHUMG00000028713	ENST00000361611.6:c.70C>T	14.37:g.23504021G>A	ENSP00000355325:p.Arg24Cys	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_001144932	B2R4N9|B4DUM9|D3DS43|E9PAV2|Q16242|Q6PEW2|Q7Z3B5|Q86T01|Q9TNN9	Missense_Mutation	SNP	ENST00000361611.6	37	CCDS9584.1	67	0.030677655677655676	10	0.02032520325203252	11	0.03038674033149171	1	0.0017482517482517483	45	0.059366754617414245	G	15.41	2.824549	0.50739	0.038357	0.082674	ENSG00000100804	ENST00000361611;ENST00000493471;ENST00000460922	T;T;T	0.51071	0.72;0.72;0.72	5.22	3.37	0.38596	.	0.462115	0.23461	N	0.047933	T	0.01489	0.0048	N	0.19112	0.55	0.80722	D	1	B;B	0.13145	0.007;0.0	B;B	0.08055	0.003;0.0	T	0.04090	-1.0978	10	0.59425	D	0.04	-0.5438	4.4264	0.11505	0.0814:0.2848:0.4874:0.1464	rs11543947;rs52796051;rs56952751;rs11543947	24;24	P28074-2;P28074	.;PSB5_HUMAN	C	24	ENSP00000355325:R24C;ENSP00000452424:R24C;ENSP00000451286:R24C	ENSP00000334973:R24C	R	-	1	0	PSMB5	22573861	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	1.316000	0.33620	0.570000	0.29347	0.555000	0.69702	CGT	G|0.946;A|0.054	0.054	strong		0.582	PSMB5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071695.4	NM_002797	
LILRB3	11025	hgsc.bcm.edu	37	19	54721320	54721320	+	Missense_Mutation	SNP	C	C	G	rs1053002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54721320C>G	ENST00000391750.1	-	13	1753	c.1617G>C	c.(1615-1617)caG>caC	p.Q539H	LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Missense_Mutation_p.Q539H|LILRB3_ENST00000407860.2_Missense_Mutation_p.Q556H|LILRB3_ENST00000424807.1_Missense_Mutation_p.Q539H|LILRB3_ENST00000346401.6_Missense_Mutation_p.Q551H|LILRA6_ENST00000419410.2_Missense_Mutation_p.Q540H|LILRB3_ENST00000245620.9_Missense_Mutation_p.Q540H|LILRA6_ENST00000270464.5_Missense_Mutation_p.Q540H			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	539			Q -> H (in dbSNP:rs1053002). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACGTCACTGCCTGGGGGTCTT	0.577																																					p.Q540H		Atlas-SNP	.											LILRB3,NS,carcinoma,-2,1	LILRB3	67	1	0			c.G1620C						PASS	.						97.0	102.0	100.0					19																	54721320		2202	4300	6502	SO:0001583	missense	11025	exon12			CACTGCCTGGGGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1617G>C	19.37:g.54721320C>G	ENSP00000375630:p.Gln539His	Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	301	106	0.352159	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	256	0.11721611721611722	140	0.2845528455284553	37	0.10220994475138122	3	0.005244755244755245	76	0.10026385224274406	C	6.747	0.506690	0.12883	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00531	6.77;6.77;6.79;6.78;6.84;6.76;6.77;6.79	2.47	-2.73	0.05950	.	.	.	.	.	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	B;D;B;B;D;D;D	0.76494	0.095;0.988;0.226;0.004;0.967;0.999;0.994	B;P;B;B;P;P;D	0.68765	0.028;0.816;0.068;0.007;0.77;0.894;0.96	T	0.51403	-0.8710	8	0.59425	D	0.04	.	2.8244	0.05481	0.2046:0.4038:0.0:0.3916	rs1053002;rs3193491	556;539;540;551;556;539;540	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	H	539;539;551;540;556;539;540;540	ENSP00000375630:Q539H;ENSP00000412771:Q539H;ENSP00000345184:Q551H;ENSP00000245620:Q540H;ENSP00000384274:Q556H;ENSP00000390120:Q539H;ENSP00000270464:Q540H;ENSP00000411227:Q540H	ENSP00000270464:Q540H	Q	-	3	2	LILRB3;LILRA6	59413132	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.903000	0.04084	-0.478000	0.06823	0.413000	0.27773	CAG	C|0.891;G|0.109	0.109	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
ZNF589	51385	hgsc.bcm.edu	37	3	48282695	48282695	+	Missense_Mutation	SNP	A	A	G	rs9847953	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:48282695A>G	ENST00000354698.3	+	1	106	c.34A>G	c.(34-36)Act>Gct	p.T12A	ZNF589_ENST00000427617.2_Missense_Mutation_p.T12A|ZNF589_ENST00000440261.2_Missense_Mutation_p.T12A|ZNF589_ENST00000412564.1_Missense_Mutation_p.T12A	NM_016089.2	NP_057173.2	Q86UQ0	ZN589_HUMAN	zinc finger protein 589	12			T -> A (in dbSNP:rs9847953). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)|lung(1)|ovary(1)|skin(1)	4				BRCA - Breast invasive adenocarcinoma(193;0.000649)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		ACTGGGCTGGACTGCGGAAGG	0.682													G|||	1179	0.235423	0.264	0.2161	5008	,	,		13191	0.121		0.2913	False		,,,				2504	0.271				p.T12A	Colon(9;319 328 25374 27611 50948)	Atlas-SNP	.											ZNF589,NS,carcinoma,0,2	ZNF589	20	2	0			c.A34G						PASS	.	G	ALA/THR	1069,2907		162,745,1081	24.0	29.0	27.0		34	-2.0	0.0	3	dbSNP_119	27	2570,5764		419,1732,2016	yes	missense	ZNF589	NM_016089.2	58	581,2477,3097	GG,GA,AA		30.8375,26.8863,29.5613	benign	12/365	48282695	3639,8671	1988	4167	6155	SO:0001583	missense	51385	exon1			GGCTGGACTGCGG	AF114816	CCDS43085.1	3p21	2013-01-08			ENSG00000164048	ENSG00000164048		"""Zinc fingers, C2H2-type"", ""-"""	16747	protein-coding gene	gene with protein product						10029171	Standard	NM_016089		Approved	SZF1	uc003csl.4	Q86UQ0	OTTHUMG00000156833	ENST00000354698.3:c.34A>G	3.37:g.48282695A>G	ENSP00000346729:p.Thr12Ala	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_016089	Q86UC9|Q9BRI6|Q9BRY3|Q9Y611|Q9Y612	Missense_Mutation	SNP	ENST00000354698.3	37	CCDS43085.1	489	0.2239010989010989	123	0.25	86	0.23756906077348067	64	0.11188811188811189	216	0.2849604221635884	G	6.344	0.431497	0.12045	0.268863	0.308375	ENSG00000164048	ENST00000354698;ENST00000427617;ENST00000412564;ENST00000440261	T;T;T;T	0.05717	3.4;4.81;4.75;4.98	1.32	-1.99	0.07457	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.0	T	0.42632	-0.9440	8	0.07175	T	0.84	.	3.5587	0.07874	0.5199:0.2168:0.2633:0.0	rs9847953;rs9847953	12;12	B4DQF9;Q86UQ0	.;ZN589_HUMAN	A	12	ENSP00000346729:T12A;ENSP00000392719:T12A;ENSP00000404398:T12A;ENSP00000408719:T12A	ENSP00000346729:T12A	T	+	1	0	ZNF589	48257699	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.672000	0.05244	-1.395000	0.02074	-0.471000	0.05019	ACT	A|0.753;G|0.247	0.247	strong		0.682	ZNF589-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346124.1	NM_016089	
SEC14L4	284904	hgsc.bcm.edu	37	22	30888527	30888527	+	Missense_Mutation	SNP	C	C	T	rs17738540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30888527C>T	ENST00000255858.7	-	8	681	c.598G>A	c.(598-600)Gtg>Atg	p.V200M	RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000540456.1_Missense_Mutation_p.V185M|SEC14L4_ENST00000392772.2_Missense_Mutation_p.V146M|SEC14L4_ENST00000381982.3_Missense_Mutation_p.V200M|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	200	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		V -> M (in dbSNP:rs17738540).			integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	TTGAAGGCCACGGGGAACAGT	0.542													C|||	737	0.147165	0.1036	0.2824	5008	,	,		21138	0.0397		0.2296	False		,,,				2504	0.136				p.V200M		Atlas-SNP	.											.	SEC14L4	43	.	0			c.G598A						PASS	.	C	MET/VAL,MET/VAL	542,3864	243.4+/-253.1	29,484,1690	116.0	86.0	97.0		598,598	2.8	0.9	22	dbSNP_123	97	1936,6664	341.2+/-323.9	216,1504,2580	yes	missense,missense	SEC14L4	NM_001161368.1,NM_174977.3	21,21	245,1988,4270	TT,TC,CC		22.5116,12.3014,19.0527	probably-damaging,probably-damaging	200/361,200/407	30888527	2478,10528	2203	4300	6503	SO:0001583	missense	284904	exon8			AGGCCACGGGGAA	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.598G>A	22.37:g.30888527C>T	ENSP00000255858:p.Val200Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	128	57	0.445312	NM_001161368	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	37	CCDS13878.1	338	0.15476190476190477	61	0.12398373983739837	85	0.23480662983425415	22	0.038461538461538464	170	0.22427440633245382	c	15.27	2.783085	0.49891	0.123014	0.225116	ENSG00000133488	ENST00000255858;ENST00000540456;ENST00000392772;ENST00000381982	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	4.93	2.76	0.32466	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.064498	0.64402	D	0.000008	T	0.00144	0.0004	L	0.55743	1.74	0.09310	P	0.9999999999999748	D;D;D	0.89917	0.999;1.0;0.999	D;P;D	0.63033	0.91;0.904;0.91	T	0.03184	-1.1063	9	0.56958	D	0.05	-15.301	11.4606	0.50208	0.0:0.8379:0.0:0.1621	rs17738540;rs52838073;rs17738540	146;185;200	B3KSF0;G3V1L4;Q9UDX3	.;.;S14L4_HUMAN	M	200;185;146;200	ENSP00000255858:V200M;ENSP00000440848:V185M;ENSP00000376525:V146M;ENSP00000371412:V200M	ENSP00000255858:V200M	V	-	1	0	SEC14L4	29218527	0.896000	0.30565	0.855000	0.33649	0.633000	0.38033	1.804000	0.38873	1.199000	0.43173	0.591000	0.81541	GTG	C|0.837;N|0.000	.	strong		0.542	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
H2BFWT	158983	hgsc.bcm.edu	37	X	103267865	103267865	+	Missense_Mutation	SNP	C	C	T	rs553509	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:103267865C>T	ENST00000217926.5	-	1	394	c.368G>A	c.(367-369)cGc>cAc	p.R123H	H2BFM_ENST00000243297.5_5'Flank	NM_001002916.3	NP_001002916.3	Q7Z2G1	H2BWT_HUMAN	H2B histone family, member W, testis-specific	123			R -> H (in dbSNP:rs553509). {ECO:0000269|PubMed:15475252, ECO:0000269|PubMed:15489334}.			membrane (GO:0016020)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	16						GCGGGCCAGGCGACCAGCCTC	0.647													.|||	2193	0.580927	0.438	0.3098	3775	,	,		13169	0.4603		0.5089	False		,,,				2504	0.4325				p.R123H		Atlas-SNP	.											.	H2BFWT	33	.	0			c.G368A						PASS	.	C	HIS/ARG	2258,1577		574,775,335,283,236	36.0	33.0	34.0		368	-2.7	0.0	X	dbSNP_83	34	4476,2251		1080,1091,1225,257,646	yes	missense	H2BFWT	NM_001002916.3	29	1654,1866,1560,540,882	TT,TC,T,CC,C		33.4622,41.1213,36.2431	benign	123/176	103267865	6734,3828	2203	4299	6502	SO:0001583	missense	158983	exon1			GCCAGGCGACCAG	BC038109	CCDS35362.1	Xq22.2	2011-01-27			ENSG00000123569	ENSG00000123569		"""Histones / Replication-independent"""	27252	protein-coding gene	gene with protein product		300507				12477932	Standard	NM_001002916		Approved		uc004elr.3	Q7Z2G1	OTTHUMG00000022120	ENST00000217926.5:c.368G>A	X.37:g.103267865C>T	ENSP00000354723:p.Arg123His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	89	84	0.94382	NM_001002916	B1AK72|Q147W3	Missense_Mutation	SNP	ENST00000217926.5	37	CCDS35362.1	968	0.5834840265220012	141	0.375	88	0.32116788321167883	170	0.4146341463414634	271	0.5132575757575758	.	9.810	1.182830	0.21870	0.588787	0.665378	ENSG00000123569	ENST00000217926	T	0.27890	1.64	2.84	-2.67	0.06059	Histone-fold (2);Histone core (1);	1.333640	0.06752	U	0.780175	T	0.00012	0.0000	L	0.43598	1.365	0.80722	P	0.0	B	0.16166	0.016	B	0.17098	0.017	T	0.44143	-0.9347	9	0.62326	D	0.03	.	3.36	0.07182	0.3156:0.366:0.0:0.3184	rs553509;rs17340491;rs58833763	123	Q7Z2G1	H2BWT_HUMAN	H	123	ENSP00000354723:R123H	ENSP00000354723:R123H	R	-	2	0	H2BFWT	103154521	0.994000	0.37717	0.000000	0.03702	0.000000	0.00434	0.783000	0.26802	-0.944000	0.03686	-0.849000	0.03036	CGC	C|0.378;0|0.003	.	strong		0.647	H2BFWT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057756.2	NM_001002916	
NUTM2F	54754	hgsc.bcm.edu	37	9	97082699	97082699	+	Missense_Mutation	SNP	G	G	A	rs10993163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:97082699G>A	ENST00000253262.4	-	5	1179	c.1159C>T	c.(1159-1161)Cct>Tct	p.P387S	NUTM2F_ENST00000341207.4_Missense_Mutation_p.P372S|NUTM2F_ENST00000335456.7_Missense_Mutation_p.P372S	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	387	Pro-rich.																ATCTCCTCAGGGACCTTGGTC	0.672													.|||	919	0.183506	0.115	0.2637	5008	,	,		15860	0.3571		0.0586	False		,,,				2504	0.1687				p.P387S		Atlas-SNP	.											.	FAM22F	72	.	0			c.C1159T						PASS	.	G	SER/PRO	403,3523		24,355,1584	49.0	59.0	56.0		1159	1.2	0.0	9	dbSNP_120	56	394,7870		9,376,3747	no	missense	FAM22F	NM_017561.1	74	33,731,5331	AA,AG,GG		4.7677,10.2649,6.5381	probably-damaging	387/757	97082699	797,11393	1963	4132	6095	SO:0001583	missense	54754	exon5			CCTCAGGGACCTT		CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1159C>T	9.37:g.97082699G>A	ENSP00000253262:p.Pro387Ser	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	377	0.17261904761904762	53	0.10772357723577236	83	0.2292817679558011	191	0.3339160839160839	50	0.06596306068601583	.	12.41	1.930455	0.34096	0.102649	0.047677	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207	T;T;T	0.34472	1.36;2.07;2.07	1.2	1.2	0.21068	Nuclear Testis protein, C-terminal (1);	0.125438	0.36972	N	0.002302	T	0.00012	0.0000	M	0.76170	2.325	0.58432	P	8.000000000008E-6	D	0.89917	1.0	D	0.97110	1.0	T	0.15321	-1.0441	9	0.87932	D	0	.	8.3567	0.32335	0.0:0.0:1.0:0.0	rs10993163	387	A1L443	FA22F_HUMAN	S	372;387;372	ENSP00000335067:P372S;ENSP00000253262:P387S;ENSP00000343865:P372S	ENSP00000253262:P387S	P	-	1	0	FAM22F	96122520	0.060000	0.20803	0.018000	0.16275	0.013000	0.08279	1.765000	0.38481	0.992000	0.38840	0.456000	0.33151	CCT	G|0.856;A|0.144	0.144	strong		0.672	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
WASF3	10810	hgsc.bcm.edu	37	13	27250823	27250823	+	Silent	SNP	T	T	C	rs3764108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:27250823T>C	ENST00000335327.5	+	7	856	c.678T>C	c.(676-678)caT>caC	p.H226H	WASF3_ENST00000361042.4_Intron	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	226					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		GTGTGTACCATGGAGCGTCTT	0.512													C|||	1635	0.326478	0.466	0.2666	5008	,	,		17792	0.1081		0.3161	False		,,,				2504	0.4162				p.H226H		Atlas-SNP	.											.	WASF3	68	.	0			c.T678C						PASS	.	C		2000,2406	614.5+/-392.4	479,1042,682	172.0	161.0	165.0		678	-0.2	1.0	13	dbSNP_107	165	2736,5864	680.9+/-403.7	424,1888,1988	no	coding-synonymous	WASF3	NM_006646.5		903,2930,2670	CC,CT,TT		31.814,45.3926,36.414		226/503	27250823	4736,8270	2203	4300	6503	SO:0001819	synonymous_variant	10810	exon7			GTACCATGGAGCG	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.678T>C	13.37:g.27250823T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_006646	O94974|Q86VQ2	Silent	SNP	ENST00000335327.5	37	CCDS9318.1																																																																																			T|0.660;C|0.340	0.340	strong		0.512	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1		
NBN	4683	hgsc.bcm.edu	37	8	90990479	90990479	+	Missense_Mutation	SNP	C	C	G	rs1805794	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:90990479C>G	ENST00000265433.3	-	5	707	c.553G>C	c.(553-555)Gag>Cag	p.E185Q	NBN_ENST00000409330.1_Missense_Mutation_p.E103Q	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	185	Mediates interaction with SP100. {ECO:0000250}.		E -> Q (in dbSNP:rs1805794). {ECO:0000269|PubMed:14684699, ECO:0000269|PubMed:14688016, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9590180, ECO:0000269|PubMed:9590181, ECO:0000269|Ref.7}.		blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTCTTGGACTCAACTGCTTTC	0.299								Homologous recombination					G|||	1788	0.357029	0.2307	0.3761	5008	,	,		16191	0.4673		0.3062	False		,,,				2504	0.453				p.E185Q		Atlas-SNP	.											.	NBN	86	.	0			c.G553C	GRCh37	CM034886	NBN	M	rs1805794	PASS	.	G	GLN/GLU	1030,3376	725.4+/-409.6	125,780,1298	87.0	86.0	87.0		553	3.1	1.0	8	dbSNP_92	87	2697,5903	682.4+/-403.8	413,1871,2016	yes	missense	NBN	NM_002485.4	29	538,2651,3314	GG,GC,CC		31.3605,23.3772,28.656	benign	185/755	90990479	3727,9279	2203	4300	6503	SO:0001583	missense	4683	exon5			TGGACTCAACTGC	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.553G>C	8.37:g.90990479C>G	ENSP00000265433:p.Glu185Gln	Somatic	262	0	0		WXS	Illumina HiSeq	Phase_I	213	85	0.399061	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	726	0.3324175824175824	110	0.22357723577235772	122	0.3370165745856354	261	0.4562937062937063	233	0.3073878627968338	G	3.805	-0.040880	0.07452	0.233772	0.313605	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387;ENST00000517772	T;T;T	0.71222	0.43;0.51;-0.55	5.96	3.08	0.35506	.	0.222293	0.47093	N	0.000243	T	0.00012	0.0000	N	0.01454	-0.855	0.53688	P	2.8000000000028002E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.39623	-0.9605	9	0.02654	T	1	-2.2013	13.9393	0.64046	0.0:0.4497:0.4384:0.1119	rs1805794;rs3174084;rs1805794	185	O60934	NBN_HUMAN	Q	185;103;185;103	ENSP00000265433:E185Q;ENSP00000386924:E103Q;ENSP00000428717:E103Q	ENSP00000265433:E185Q	E	-	1	0	NBN	91059655	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	2.133000	0.42093	0.091000	0.17302	-0.120000	0.15030	GAG	C|0.681;G|0.319	0.319	strong		0.299	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
ALPK1	80216	hgsc.bcm.edu	37	4	113351822	113351822	+	Silent	SNP	G	G	A	rs61747381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:113351822G>A	ENST00000458497.1	+	11	1398	c.1119G>A	c.(1117-1119)ggG>ggA	p.G373G	ALPK1_ENST00000504176.2_Silent_p.G295G|ALPK1_ENST00000177648.9_Silent_p.G373G	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	373							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		GGGAGACAGGGACGGTCCATG	0.512													G|||	192	0.0383387	0.0023	0.1081	5008	,	,		20318	0.001		0.0447	False		,,,				2504	0.0695				p.G373G		Atlas-SNP	.											.	ALPK1	125	.	0			c.G1119A						PASS	.	G	,	51,4355	50.9+/-86.3	0,51,2152	78.0	68.0	71.0		1119,1119	-1.6	0.0	4	dbSNP_129	71	477,8123	140.3+/-196.8	9,459,3832	no	coding-synonymous,coding-synonymous	ALPK1	NM_001102406.1,NM_025144.3	,	9,510,5984	AA,AG,GG		5.5465,1.1575,4.0597	,	373/1245,373/1245	113351822	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	80216	exon11			GACAGGGACGGTC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.1119G>A	4.37:g.113351822G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	33	0.39759	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Silent	SNP	ENST00000458497.1	37	CCDS3697.1																																																																																			G|0.963;A|0.037	0.037	strong		0.512	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
FLNC	2318	hgsc.bcm.edu	37	7	128477547	128477547	+	Silent	SNP	T	T	C	rs2291561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128477547T>C	ENST00000325888.8	+	4	1056	c.795T>C	c.(793-795)ggT>ggC	p.G265G	FLNC_ENST00000346177.6_Silent_p.G265G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	265					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCAAACCTGGTGCCCCTGTTC	0.597													C|||	606	0.121006	0.1218	0.062	5008	,	,		14951	0.121		0.1093	False		,,,				2504	0.1738				p.G265G		Atlas-SNP	.											FLNC,NS,carcinoma,0,1	FLNC	339	1	0			c.T795C						PASS	.	C	,	529,3827	714.4+/-408.4	36,457,1685	133.0	144.0	141.0		795,795	-5.9	0.9	7	dbSNP_100	141	952,7638	757.3+/-407.5	49,854,3392	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	85,1311,5077	CC,CT,TT		11.0827,12.1442,11.4398	,	265/2693,265/2726	128477547	1481,11465	2178	4295	6473	SO:0001819	synonymous_variant	2318	exon4			ACCTGGTGCCCCT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.795T>C	7.37:g.128477547T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			T|0.881;C|0.119	0.119	strong		0.597	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
HRNR	388697	hgsc.bcm.edu	37	1	152189016	152189016	+	Missense_Mutation	SNP	G	G	A	rs200517377		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152189016G>A	ENST00000368801.2	-	3	5164	c.5089C>T	c.(5089-5091)Cgt>Tgt	p.R1697C	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1697					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)			GAAGACTGACGGGAGCCAGAC	0.632																																					p.R1697C		Atlas-SNP	.											HRNR,NS,carcinoma,0,4	HRNR	403	4	0			c.C5089T						scavenged	.						57.0	73.0	68.0					1																	152189016		1629	3176	4805	SO:0001583	missense	388697	exon3			ACTGACGGGAGCC	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.5089C>T	1.37:g.152189016G>A	ENSP00000357791:p.Arg1697Cys	Somatic	293	1	0.00341297		WXS	Illumina HiSeq	Phase_I	272	16	0.0588235	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	G	3.089	-0.187379	0.06299	.	.	ENSG00000197915	ENST00000368801	T	0.01647	4.71	3.82	-7.65	0.01281	.	.	.	.	.	T	0.00440	0.0014	L	0.38175	1.15	0.09310	N	1	B	0.13594	0.008	B	0.06405	0.002	T	0.43988	-0.9357	9	0.56958	D	0.05	.	3.7438	0.08540	0.0806:0.2135:0.2435:0.4624	.	1697	Q86YZ3	HORN_HUMAN	C	1697	ENSP00000357791:R1697C	ENSP00000357791:R1697C	R	-	1	0	HRNR	150455640	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.680000	0.00395	-2.946000	0.00295	-1.447000	0.01057	CGT	.	.	weak		0.632	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
PIK3R6	146850	hgsc.bcm.edu	37	17	8733110	8733110	+	Splice_Site	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8733110C>T	ENST00000434064.2	-	9	802		c.e9-1		PIK3R6_ENST00000311434.9_Splice_Site			Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										ACAAGGTCACCTGCAGAAAGG	0.632																																					.		Atlas-SNP	.											.	.	.	.	0			c.803-1G>A						PASS	.						51.0	61.0	58.0					17																	8733110		1949	3988	5937	SO:0001630	splice_region_variant	146850	exon11			GGTCACCTGCAGA	AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"""chromosome 17 open reading frame 38"""	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000434064.2:c.1463-1G>A	17.37:g.8733110C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	12	0.342857	NM_001010855	Q658R3	Splice_Site	SNP	ENST00000434064.2	37																																																																																				.	.	none		0.632	PIK3R6-002	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000400327.2	NM_001010855	Intron
IL4R	3566	hgsc.bcm.edu	37	16	27357927	27357927	+	Silent	SNP	C	C	T	rs2234895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:27357927C>T	ENST00000395762.2	+	6	760	c.501C>T	c.(499-501)aaC>aaT	p.N167N	IL4R_ENST00000380922.3_Silent_p.N152N|IL4R_ENST00000543915.2_Silent_p.N167N|IL4R_ENST00000170630.2_Silent_p.N167N|IL4R_ENST00000449195.1_Silent_p.N167N	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	167	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						GGAGTGAAAACGACCCGGCAG	0.547													C|||	236	0.0471246	0.0454	0.0447	5008	,	,		18856	0.0		0.0924	False		,,,				2504	0.0532				p.T9M		Atlas-SNP	.											.	IL4R	70	.	0			c.C26T						PASS	.	C	,	249,4145	145.0+/-179.8	6,237,1954	125.0	121.0	122.0		501,501	-0.6	0.0	16	dbSNP_98	122	761,7839	181.3+/-230.0	33,695,3572	no	coding-synonymous,coding-synonymous	IL4R	NM_000418.2,NM_001008699.1	,	39,932,5526	TT,TC,CC		8.8488,5.6668,7.7728	,	167/826,167/228	27357927	1010,11984	2197	4300	6497	SO:0001819	synonymous_variant	3566	exon5			TGAAAACGACCCG	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.501C>T	16.37:g.27357927C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	49	16	0.326531	NM_001257997	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			C|0.931;T|0.069	0.069	strong		0.547	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
FAM149A	25854	hgsc.bcm.edu	37	4	187088248	187088248	+	Missense_Mutation	SNP	C	C	T	rs9991339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187088248C>T	ENST00000356371.5	+	12	2164	c.2164C>T	c.(2164-2166)Cgg>Tgg	p.R722W	FAM149A_ENST00000389354.5_Missense_Mutation_p.R431W|FAM149A_ENST00000502970.1_Missense_Mutation_p.R431W|FAM149A_ENST00000514153.1_Missense_Mutation_p.R431W|FAM149A_ENST00000227065.4_Missense_Mutation_p.R431W|FAM149A_ENST00000503432.1_Missense_Mutation_p.R431W			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	722			R -> W (in dbSNP:rs9991339).							breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		CCACACGTTCCGGGTGGGTTC	0.463													C|||	355	0.0708866	0.1725	0.1066	5008	,	,		19329	0.0218		0.0239	False		,,,				2504	0.0072				p.R431W		Atlas-SNP	.											.	FAM149A	52	.	0			c.C1291T						PASS	.	C	TRP/ARG,TRP/ARG	696,3710	291.5+/-281.6	57,582,1564	56.0	55.0	55.0		1291,1291	1.7	0.2	4	dbSNP_119	55	228,8372	93.5+/-155.5	3,222,4075	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	101,101	60,804,5639	TT,TC,CC		2.6512,15.7966,7.1044	probably-damaging,probably-damaging	431/483,431/483	187088248	924,12082	2203	4300	6503	SO:0001583	missense	25854	exon11			ACGTTCCGGGTGG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.2164C>T	4.37:g.187088248C>T	ENSP00000348732:p.Arg722Trp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		128|128	0.05860805860805861|0.05860805860805861	72|72	0.14634146341463414|0.14634146341463414	26|26	0.0718232044198895|0.0718232044198895	14|14	0.024475524475524476|0.024475524475524476	16|16	0.021108179419525065|0.021108179419525065	C|C	9.228|9.228	1.035096|1.035096	0.19590|0.19590	0.157966|0.157966	0.026512|0.026512	ENSG00000109794|ENSG00000109794	ENST00000512271|ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	.|T;T;T;T;T;T	.|0.17370	.|2.31;2.28;2.31;2.31;2.31;2.31	5.72|5.72	1.68|1.68	0.24146|0.24146	.|.	.|0.221406	.|0.38605	.|N	.|0.001632	T|T	0.00073|0.00073	0.0002|0.0002	M|M	0.71581|0.71581	2.175|2.175	0.09310|0.09310	P|P	0.9999999999939376|0.9999999999939376	.|B;P	.|0.40931	.|0.432;0.733	.|B;B	.|0.31101	.|0.051;0.124	T|T	0.13150|0.13150	-1.0520|-1.0520	4|9	.|0.72032	.|D	.|0.01	-3.889|-3.889	6.8148|6.8148	0.23824|0.23824	0.1555:0.6509:0.0:0.1935|0.1555:0.6509:0.0:0.1935	rs9991339;rs52834541;rs59351672;rs9991339|rs9991339;rs52834541;rs59351672;rs9991339	.|722;722	.|A5PLN7-3;A5PLN7	.|.;F149A_HUMAN	L|W	108|431;722;431;431;431;431	.|ENSP00000426835:R431W;ENSP00000348732:R722W;ENSP00000227065:R431W;ENSP00000427155:R431W;ENSP00000424380:R431W;ENSP00000374005:R431W	.|ENSP00000227065:R431W	P|R	+|+	2|1	0|2	FAM149A|FAM149A	187325242|187325242	0.953000|0.953000	0.32496|0.32496	0.156000|0.156000	0.22583|0.22583	0.003000|0.003000	0.03518|0.03518	0.638000|0.638000	0.24674|0.24674	0.369000|0.369000	0.24510|0.24510	0.591000|0.591000	0.81541|0.81541	CCG|CGG	C|0.931;T|0.069	0.069	strong		0.463	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
PDDC1	347862	hgsc.bcm.edu	37	11	772490	772490	+	Silent	SNP	G	G	A	rs12224894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:772490G>A	ENST00000319863.8	-	5	408	c.387C>T	c.(385-387)gcC>gcT	p.A129A	PDDC1_ENST00000442059.2_Silent_p.A79A|PDDC1_ENST00000397472.2_Silent_p.A129A|PDDC1_ENST00000526325.1_Silent_p.A129A|PDDC1_ENST00000529966.1_5'UTR|PDDC1_ENST00000524550.1_Silent_p.A93A	NM_182612.2	NP_872418.1	Q8NB37	PDDC1_HUMAN	Parkinson disease 7 domain containing 1	129						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(3)|urinary_tract(1)	5		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;3.66e-26)|Epithelial(43;2.43e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-19)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGCACAGGGCGGCGACACCGT	0.667													g|||	1539	0.307308	0.1687	0.5893	5008	,	,		17437	0.2827		0.4354	False		,,,				2504	0.1881				p.A129A		Atlas-SNP	.											.	PDDC1	16	.	0			c.C387T						PASS	.			957,3449		101,755,1347	145.0	130.0	135.0		387	-8.5	0.1	11	dbSNP_120	135	4144,4456		1005,2134,1161	no	coding-synonymous	PDDC1	NM_182612.2		1106,2889,2508	AA,AG,GG		48.186,21.7204,39.2204		129/221	772490	5101,7905	2203	4300	6503	SO:0001819	synonymous_variant	347862	exon5			CAGGGCGGCGACA	AK128653	CCDS7713.1	11p15.5	2005-10-26			ENSG00000177225	ENSG00000177225			26616	protein-coding gene	gene with protein product							Standard	XM_005252898		Approved	FLJ34283	uc001lrc.3	Q8NB37	OTTHUMG00000133315	ENST00000319863.8:c.387C>T	11.37:g.772490G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	18	0.339623	NM_182612	B7ZKW5|Q2NL76|Q6ZQY0|Q8NAE0	Silent	SNP	ENST00000319863.8	37	CCDS7713.1																																																																																			G|0.633;A|0.367	0.367	strong		0.667	PDDC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258051.2	NM_182612	
SIDT1	54847	hgsc.bcm.edu	37	3	113252042	113252042	+	Silent	SNP	C	C	T	rs3732799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113252042C>T	ENST00000264852.4	+	1	900	c.174C>T	c.(172-174)ctC>ctT	p.L58L	SIDT1_ENST00000393830.3_Silent_p.L58L	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	58					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TGGTGAACCTCAGCACCGAGA	0.627													C|||	769	0.153554	0.2829	0.072	5008	,	,		14272	0.1647		0.0855	False		,,,				2504	0.0951				p.L58L		Atlas-SNP	.											.	SIDT1	99	.	0			c.C174T						PASS	.	C		1104,3302	373.0+/-320.6	135,834,1234	31.0	30.0	31.0		174	4.7	1.0	3	dbSNP_107	31	718,7882	169.3+/-220.7	19,680,3601	no	coding-synonymous	SIDT1	NM_017699.2		154,1514,4835	TT,TC,CC		8.3488,25.0567,14.0089		58/828	113252042	1822,11184	2203	4300	6503	SO:0001819	synonymous_variant	54847	exon1			GAACCTCAGCACC	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.174C>T	3.37:g.113252042C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	109	70	0.642202	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																			C|0.857;T|0.143	0.143	strong		0.627	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
USP16	10600	hgsc.bcm.edu	37	21	30407208	30407208	+	Silent	SNP	G	G	A	rs61735763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:30407208G>A	ENST00000334352.4	+	5	522	c.291G>A	c.(289-291)acG>acA	p.T97T	USP16_ENST00000399976.2_Silent_p.T97T|USP16_ENST00000535828.1_Intron|USP16_ENST00000399975.3_Silent_p.T97T	NM_001032410.1	NP_001027582.1			ubiquitin specific peptidase 16											breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(2)	34						ACTATCTGACGCCAAGATCTG	0.418													G|||	196	0.0391374	0.0484	0.0259	5008	,	,		17697	0.001		0.0487	False		,,,				2504	0.0654				p.T97T	Melanoma(92;625 1444 27493 34101 44971)	Atlas-SNP	.											.	USP16	65	.	0			c.G291A						PASS	.	G	,,	150,4256	104.7+/-143.2	1,148,2054	174.0	151.0	159.0		291,291,291	-6.9	0.0	21	dbSNP_129	159	361,8239	120.4+/-179.7	7,347,3946	no	coding-synonymous,coding-synonymous,coding-synonymous	USP16	NM_001001992.1,NM_001032410.1,NM_006447.2	,,	8,495,6000	AA,AG,GG		4.1977,3.4044,3.929	,,	97/823,97/824,97/824	30407208	511,12495	2203	4300	6503	SO:0001819	synonymous_variant	10600	exon4			TCTGACGCCAAGA	AF126736	CCDS13583.1, CCDS42912.1	21q21	2008-04-11	2005-08-08		ENSG00000156256	ENSG00000156256		"""Ubiquitin-specific peptidases"""	12614	protein-coding gene	gene with protein product		604735	"""ubiquitin specific protease 16"""			12838346	Standard	NM_006447		Approved	Ubp-M	uc002ymy.3	Q9Y5T5	OTTHUMG00000078802	ENST00000334352.4:c.291G>A	21.37:g.30407208G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	150	85	0.566667	NM_006447		Silent	SNP	ENST00000334352.4	37	CCDS13583.1																																																																																			G|0.961;A|0.039	0.039	strong		0.418	USP16-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171847.1		
COL18A1	80781	hgsc.bcm.edu	37	21	46899857	46899857	+	Silent	SNP	C	C	T	rs1131101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46899857C>T	ENST00000359759.4	+	9	2556	c.2535C>T	c.(2533-2535)gaC>gaT	p.D845D	COL18A1_ENST00000400337.2_Silent_p.D430D|COL18A1_ENST00000355480.5_Silent_p.D610D			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	845	Triple-helical region 2 (COL2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTCCAGGGGACGTAGGTCCCA	0.692													C|||	788	0.157348	0.2874	0.0735	5008	,	,		16974	0.1081		0.0696	False		,,,				2504	0.182				p.D610D		Atlas-SNP	.											.	COL18A1	129	.	0			c.C1830T						PASS	.	C	,	1059,2917		135,789,1064	61.0	73.0	69.0		1830,1290	-1.8	0.6	21	dbSNP_86	69	547,7773		18,511,3631	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	153,1300,4695	TT,TC,CC		6.5745,26.6348,13.0612	,	610/1520,430/1340	46899857	1606,10690	1988	4160	6148	SO:0001819	synonymous_variant	80781	exon9			AGGGGACGTAGGT		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2535C>T	21.37:g.46899857C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	40	26	0.65	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.888;T|0.112	0.112	strong		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
CFAP70	118491	hgsc.bcm.edu	37	10	75035257	75035257	+	Missense_Mutation	SNP	T	T	C	rs4294502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75035257T>C	ENST00000310715.3	-	23	2950	c.2830A>G	c.(2830-2832)Aac>Gac	p.N944D	TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000401621.2_Missense_Mutation_p.N944D|TTC18_ENST00000355577.3_Missense_Mutation_p.N413D|TTC18_ENST00000394865.1_Missense_Mutation_p.N944D|DNAJC9-AS1_ENST00000440197.2_RNA	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		944			N -> D (in dbSNP:rs4294502).			extracellular vesicular exosome (GO:0070062)		p.N944D(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					TTGGCAAAGTTCTTCTTAAGA	0.478													C|||	1149	0.229433	0.3525	0.1239	5008	,	,		18523	0.3105		0.0636	False		,,,				2504	0.2249				p.N944D		Atlas-SNP	.											TTC18,NS,carcinoma,0,1	TTC18	106	1	1	Substitution - Missense(1)	stomach(1)	c.A2830G						PASS	.	C	ASP/ASN	1382,3024	689.1+/-405.1	214,954,1035	226.0	213.0	217.0		2830	5.9	1.0	10	dbSNP_111	217	618,7982	791.7+/-407.5	31,556,3713	yes	missense	TTC18	NM_145170.3	23	245,1510,4748	CC,CT,TT		7.186,31.3663,15.3775	benign	944/1122	75035257	2000,11006	2203	4300	6503	SO:0001583	missense	118491	exon23			CAAAGTTCTTCTT																												ENST00000310715.3:c.2830A>G	10.37:g.75035257T>C	ENSP00000310829:p.Asn944Asp	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	457	0.20924908424908426	187	0.3800813008130081	40	0.11049723756906077	183	0.31993006993006995	47	0.06200527704485488	C	7.528	0.658154	0.14645	0.313663	0.07186	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	T;T;T;T	0.62105	0.05;0.05;0.34;0.34	5.87	5.87	0.94306	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.109437	0.64402	N	0.000010	T	0.00012	0.0000	N	0.01874	-0.695	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.17107	-1.0380	9	0.02654	T	1	-2.9252	13.0531	0.58966	0.0:0.9225:0.0:0.0775	rs4294502;rs52829733;rs61409923;rs4294502	944	Q5T0N1	TTC18_HUMAN	D	944;944;944;351;944	ENSP00000310829:N944D;ENSP00000384479:N944D;ENSP00000409527:N351D;ENSP00000378334:N944D	ENSP00000310829:N944D	N	-	1	0	TTC18	74705263	1.000000	0.71417	1.000000	0.80357	0.777000	0.43975	2.353000	0.44089	1.510000	0.48803	-0.119000	0.15052	AAC	T|0.811;C|0.189	0.189	strong		0.478	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
DCHS2	54798	hgsc.bcm.edu	37	4	155410667	155410667	+	Missense_Mutation	SNP	G	G	A	rs55810732	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155410667G>A	ENST00000339452.1	-	1	2201	c.1841C>T	c.(1840-1842)gCg>gTg	p.A614V	DCHS2_ENST00000456341.2_Missense_Mutation_p.A607V|DCHS2_ENST00000443500.1_Missense_Mutation_p.A614V	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1739	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(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)		AGTGCTGATCGCACCGCTTTC	0.597													G|||	860	0.171725	0.0356	0.3084	5008	,	,		18458	0.1558		0.2117	False		,,,				2504	0.2342				p.A614V		Atlas-SNP	.											DCHS2_ENST00000443500,NS,carcinoma,+1,2	DCHS2	594	2	0			c.C1841T						PASS	.	G	VAL/ALA,VAL/ALA	78,1306		6,66,620	48.0	48.0	48.0		1841,1841	0.1	0.0	4	dbSNP_129	48	554,2628		56,442,1093	yes	missense,missense	DCHS2	NM_001142552.1,NM_001142553.1	64,64	62,508,1713	AA,AG,GG		17.4104,5.6358,13.8414	,	614/1370,614/710	155410667	632,3934	692	1591	2283	SO:0001583	missense	54798	exon1			CTGATCGCACCGC	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		ENST00000339452.1:c.1841C>T	4.37:g.155410667G>A	ENSP00000345062:p.Ala614Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	60	0.618557	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	359	0.16437728937728938	17	0.034552845528455285	96	0.26519337016574585	81	0.14160839160839161	165	0.21767810026385223	G	0	-2.743134	0.00087	0.056358	0.174104	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.49720	0.77;0.77;0.77	5.17	0.0543	0.14310	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.30765	-0.9967	7	0.02654	T	1	.	9.3402	0.38076	0.6058:0.0:0.3942:0.0	rs55810732	614;614	E9PG03;E9PC11	.;.	V	614;614;607;614	ENSP00000345062:A614V;ENSP00000408543:A607V;ENSP00000395539:A614V	ENSP00000345062:A614V	A	-	2	0	DCHS2	155630117	0.000000	0.05858	0.002000	0.10522	0.037000	0.13140	0.599000	0.24089	-0.096000	0.12329	-1.298000	0.01336	GCG	G|0.837;A|0.163	0.163	strong		0.597	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
KIAA1429	25962	hgsc.bcm.edu	37	8	95541371	95541371	+	Silent	SNP	T	T	A	rs957446	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95541371T>A	ENST00000297591.5	-	7	882	c.807A>T	c.(805-807)cgA>cgT	p.R269R	KIAA1429_ENST00000421249.2_Silent_p.R269R|KIAA1429_ENST00000437199.1_Silent_p.R269R	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	269	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			TGTCTACTGTTCGTCGATCAT	0.443													A|||	3516	0.702077	0.6558	0.7435	5008	,	,		20289	0.8056		0.5636	False		,,,				2504	0.771				p.R269R		Atlas-SNP	.											KIAA1429_ENST00000421249,NS,carcinoma,-1,4	KIAA1429	176	4	0			c.A807T						PASS	.	A	,	2774,1632	500.5+/-364.7	887,1000,316	459.0	350.0	387.0		807,807	-2.4	0.9	8	dbSNP_86	387	4755,3845	538.9+/-383.5	1303,2149,848	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	2190,3149,1164	AA,AT,TT		44.7093,37.0404,42.1113	,	269/1813,269/1148	95541371	7529,5477	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon7			TACTGTTCGTCGA	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.807A>T	8.37:g.95541371T>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	197	193	0.979695	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			A|0.628;T|0.372	0.628	strong		0.443	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912002	45912002	+	Missense_Mutation	SNP	A	A	C	rs735482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45912002A>C	ENST00000309424.3	+	3	1264	c.776A>C	c.(775-777)aAa>aCa	p.K259T	ERCC1_ENST00000588738.1_5'Flank|PPP1R13L_ENST00000418234.2_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.K261T|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	259			K -> T (in dbSNP:rs735482).		rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		CCCAAAGGGAAAGAAACCTTC	0.547													C|||	1436	0.286741	0.3109	0.2233	5008	,	,		15739	0.4613		0.1322	False		,,,				2504	0.2781				p.K259T		Atlas-SNP	.											.	CD3EAP	27	.	0			c.A776C						PASS	.	C	,,THR/LYS	1193,3213	689.1+/-405.1	169,855,1179	67.0	70.0	69.0		,,776	-1.8	0.0	19	dbSNP_86	69	1160,7440	741.9+/-407.2	81,998,3221	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,78	250,1853,4400	CC,CA,AA		13.4884,27.0767,18.0917	,,benign	,,259/511	45912002	2353,10653	2203	4300	6503	SO:0001583	missense	10849	exon3			AAGGGAAAGAAAC	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.776A>C	19.37:g.45912002A>C	ENSP00000310966:p.Lys259Thr	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	570	0.260989010989011	131	0.266260162601626	72	0.19889502762430938	259	0.4527972027972028	108	0.1424802110817942	C	8.088	0.773935	0.16051	0.270767	0.134884	ENSG00000117877	ENST00000309424	T	0.11495	2.77	5.06	-1.76	0.08006	.	0.717583	0.12315	N	0.479769	T	0.00012	0.0000	N	0.00621	-1.32	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42749	-0.9433	9	0.14656	T	0.56	0.2029	1.8433	0.03154	0.1195:0.3621:0.259:0.2595	rs735482;rs61340218;rs735482	261;259	O15446-2;O15446	.;RPA34_HUMAN	T	259	ENSP00000310966:K259T	ENSP00000310966:K259T	K	+	2	0	CD3EAP	50603842	0.006000	0.16342	0.007000	0.13788	0.245000	0.25701	0.192000	0.17096	-0.095000	0.12351	-0.217000	0.12591	AAA	A|0.771;C|0.229	0.229	strong		0.547	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
ERCC6L2	375748	hgsc.bcm.edu	37	9	98638288	98638288	+	Start_Codon_SNP	SNP	A	A	G	rs690528	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:98638288A>G	ENST00000288985.7	+	1	306	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	LINC00476_ENST00000429781.1_RNA	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	1					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)										CGGGTGTTACATGCAGCCGGG	0.726													G|||	1264	0.252396	0.1029	0.2896	5008	,	,		15448	0.3423		0.3082	False		,,,				2504	0.2781				p.M1V		Atlas-SNP	.											C9orf102,NS,carcinoma,0,2	.	.	2	0			c.A1G						PASS	.	G	VAL/MET	561,3725		45,471,1627	7.0	9.0	8.0		1	-3.7	0.0	9	dbSNP_83	8	2502,5908		422,1658,2125	no	missense	C9orf102	NM_001010895.2	21	467,2129,3752	GG,GA,AA		29.7503,13.0891,24.1257	benign	1/713	98638288	3063,9633	2143	4205	6348	SO:0001582	initiator_codon_variant	375748	exon1			TGTTACATGCAGC	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.1A>G	9.37:g.98638288A>G	ENSP00000288985:p.Met1Val	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_001010895	A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Missense_Mutation	SNP	ENST00000288985.7	37	CCDS35072.1	608	0.2783882783882784	64	0.13008130081300814	111	0.30662983425414364	196	0.34265734265734266	237	0.31266490765171506	G	0.019	-1.460743	0.01062	0.130891	0.297503	ENSG00000182150	ENST00000288985	D	0.89050	-2.46	3.26	-3.74	0.04385	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	5.000000000032756E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06092	-1.0846	7	0.87932	D	0	.	6.0461	0.19760	0.473:0.1408:0.3862:0.0	rs690528;rs13301906;rs16910324;rs61146597	1	Q5T890	RAD26_HUMAN	V	1	ENSP00000288985:M1V	ENSP00000288985:M1V	M	+	1	0	C9orf102	97678109	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-1.326000	0.02266	-1.988000	0.00451	ATG	A|0.717;G|0.283	0.283	strong		0.726	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	Missense_Mutation
KRTAP9-8	83901	hgsc.bcm.edu	37	17	39394674	39394674	+	Missense_Mutation	SNP	A	A	G	rs62065317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39394674A>G	ENST00000254072.6	+	1	378	c.371A>G	c.(370-372)aAc>aGc	p.N124S		NM_031963.2	NP_114169.2	Q9BYQ0	KRA98_HUMAN	keratin associated protein 9-8	124	15 X 5 AA repeats of C-C-[RQVSGE]- [SPSNQ]-[TASPI].			N -> S (in Ref. 1; CAC27589 and 3; AAH74981/AAH74982). {ECO:0000305}.		keratin filament (GO:0045095)				lung(8)|ovary(1)|prostate(1)	10		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			TGTGGCTCCAACTGCTGCCAG	0.622													.|||	3922	0.783147	0.8918	0.8372	5008	,	,		17273	0.631		0.7356	False		,,,				2504	0.8037				p.N124S		Atlas-SNP	.											.	KRTAP9-8	29	.	0			c.A371G						PASS	.						46.0	62.0	56.0					17																	39394674		2095	4297	6392	SO:0001583	missense	83901	exon1			GCTCCAACTGCTG	AJ406950	CCDS42334.1	17q21.2	2013-06-25			ENSG00000187272	ENSG00000187272		"""Keratin associated proteins"""	17231	protein-coding gene	gene with protein product						11279113	Standard	NM_031963		Approved	KAP9.8	uc002hwh.4	Q9BYQ0	OTTHUMG00000133604	ENST00000254072.6:c.371A>G	17.37:g.39394674A>G	ENSP00000254072:p.Asn124Ser	Somatic	297	0	0		WXS	Illumina HiSeq	Phase_I	357	121	0.338936	NM_031963		Missense_Mutation	SNP	ENST00000254072.6	37	CCDS42334.1	1624	0.7435897435897436	404	0.8211382113821138	299	0.8259668508287292	368	0.6433566433566433	553	0.7295514511873351	.	1.224	-0.626180	0.03610	.	.	ENSG00000187272	ENST00000254072	T	0.01084	5.36	2.86	-0.595	0.11660	.	.	.	.	.	T	0.00012	0.0000	N	0.00175	-1.925	0.58432	P	1.0000000000287557E-6	B	0.12630	0.006	B	0.01281	0.0	T	0.30736	-0.9968	8	0.02654	T	1	.	0.4937	0.00568	0.2555:0.1943:0.3519:0.1982	rs62065317	124	Q9BYQ0	KRA98_HUMAN	S	124	ENSP00000254072:N124S	ENSP00000254072:N124S	N	+	2	0	KRTAP9-8	36648200	0.751000	0.28327	0.956000	0.39512	0.271000	0.26615	-0.260000	0.08708	0.033000	0.15463	-0.673000	0.03796	AAC	.	.	weak		0.622	KRTAP9-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257712.1		
GALNTL5	168391	hgsc.bcm.edu	37	7	151684256	151684256	+	Missense_Mutation	SNP	A	A	G	rs61729490	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151684256A>G	ENST00000392800.2	+	5	802	c.548A>G	c.(547-549)gAa>gGa	p.E183G	GALNTL5_ENST00000431418.2_Missense_Mutation_p.E183G	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	183	Catalytic subdomain A.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GATTTGAAAGAAAAACTAGAC	0.343													A|||	1105	0.220647	0.2587	0.2334	5008	,	,		17777	0.2063		0.16	False		,,,				2504	0.2372				p.E183G		Atlas-SNP	.											.	GALNTL5	87	.	0			c.A548G						PASS	.	A	GLY/GLU	988,3418	345.4+/-308.5	118,752,1333	39.0	42.0	41.0		548	-2.6	0.1	7	dbSNP_129	41	1372,7228	253.6+/-279.2	116,1140,3044	yes	missense	GALNTL5	NM_145292.3	98	234,1892,4377	GG,GA,AA		15.9535,22.424,18.1455	benign	183/444	151684256	2360,10646	2203	4300	6503	SO:0001583	missense	168391	exon5			TGAAAGAAAAACT	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.548A>G	7.37:g.151684256A>G	ENSP00000376548:p.Glu183Gly	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	452	0.20695970695970695	129	0.2621951219512195	89	0.24585635359116023	109	0.19055944055944055	125	0.16490765171503957	a	10.49	1.364965	0.24684	0.22424	0.159535	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.63744	-0.06;-0.06	4.3	-2.57	0.06248	Glycosyl transferase, family 2 (1);	0.713546	0.11949	N	0.513859	T	0.00012	0.0000	L	0.31157	0.91	0.58432	P	1.0000000000287557E-6	B	0.15719	0.014	B	0.17722	0.019	T	0.16660	-1.0395	9	0.21540	T	0.41	.	5.0715	0.14609	0.4889:0.2522:0.2588:0.0	rs61729490	183	Q7Z4T8	GLTL5_HUMAN	G	183	ENSP00000392582:E183G;ENSP00000376548:E183G	ENSP00000376548:E183G	E	+	2	0	GALNTL5	151315189	1.000000	0.71417	0.068000	0.19968	0.914000	0.54420	2.000000	0.40816	-0.301000	0.08882	0.454000	0.30748	GAA	A|0.814;G|0.186	0.186	strong		0.343	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
SLC4A1	6521	hgsc.bcm.edu	37	17	42328846	42328846	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42328846G>A	ENST00000262418.6	-	18	2577	c.2422C>T	c.(2422-2424)Cgc>Tgc	p.R808C	AC003102.1_ENST00000399246.2_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	808	Membrane (anion exchange).		R -> C (in SPH4; Jablonec). {ECO:0000269|PubMed:7530501}.|R -> H (in SPH4; Nara). {ECO:0000269|PubMed:10745622}.		anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		AGCAAGATGCGGTCAAAGAGC	0.587																																					p.R808C		Atlas-SNP	.											SLC4A1,NS,carcinoma,+1,2	SLC4A1	104	2	0			c.C2422T	GRCh37	CM951172	SLC4A1	M		PASS	.						130.0	116.0	121.0					17																	42328846		2203	4300	6503	SO:0001583	missense	6521	exon18			AGATGCGGTCAAA		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.2422C>T	17.37:g.42328846G>A	ENSP00000262418:p.Arg808Cys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	138	47	0.34058	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.454721	0.84209	.	.	ENSG00000004939	ENST00000262418	D	0.86694	-2.16	5.22	5.22	0.72569	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96200	0.8761	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97607	1.0127	10	0.87932	D	0	.	18.7637	0.91864	0.0:0.0:1.0:0.0	.	808	P02730	B3AT_HUMAN	C	808	ENSP00000262418:R808C	ENSP00000262418:R808C	R	-	1	0	SLC4A1	39684372	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.507000	0.81676	2.579000	0.87056	0.561000	0.74099	CGC	.	.	none		0.587	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
SERPINH1	871	hgsc.bcm.edu	37	11	75282882	75282882	+	Silent	SNP	G	G	A	rs585821	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:75282882G>A	ENST00000524558.1	+	5	2446	c.1011G>A	c.(1009-1011)ttG>ttA	p.L337L	SERPINH1_ENST00000533603.1_Silent_p.L337L|SERPINH1_ENST00000525876.1_Silent_p.L120L|SERPINH1_ENST00000358171.3_Silent_p.L337L			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	337					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					AGGCCGACTTGTCACGCATGT	0.587													G|||	1887	0.376797	0.4758	0.3775	5008	,	,		18407	0.2073		0.2972	False		,,,				2504	0.499				p.L337L		Atlas-SNP	.											.	SERPINH1	33	.	0			c.G1011A						PASS	.	G	,	1940,2460	550.6+/-378.1	437,1066,697	66.0	51.0	56.0		1011,1011	2.3	1.0	11	dbSNP_83	56	2609,5977	420.8+/-353.5	377,1855,2061	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	814,2921,2758	AA,AG,GG		30.3867,44.0909,35.03	,	337/419,337/419	75282882	4549,8437	2200	4293	6493	SO:0001819	synonymous_variant	871	exon5			CGACTTGTCACGC	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.1011G>A	11.37:g.75282882G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			G|0.662;A|0.338	0.338	strong		0.587	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
ACSL1	2180	hgsc.bcm.edu	37	4	185701549	185701549	+	Silent	SNP	G	G	T	rs1803898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:185701549G>T	ENST00000515030.1	-	5	739	c.414C>A	c.(412-414)atC>atA	p.I138I	ACSL1_ENST00000504342.1_Silent_p.I138I|ACSL1_ENST00000281455.2_Silent_p.I138I|ACSL1_ENST00000513317.1_Silent_p.I138I|ACSL1_ENST00000507295.1_Intron|ACSL1_ENST00000504900.1_Silent_p.I138I|ACSL1_ENST00000437665.3_5'UTR|ACSL1_ENST00000454703.2_5'UTR			P33121	ACSL1_HUMAN	acyl-CoA synthetase long-chain family member 1	138					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)	AGCCCTTCTGGATCAGTGCTG	0.463													G|||	805	0.160743	0.0303	0.1729	5008	,	,		18206	0.0645		0.3489	False		,,,				2504	0.2342				p.I138I		Atlas-SNP	.											.	ACSL1	77	.	0			c.C414A						PASS	.	G		323,4083	170.9+/-201.2	9,305,1889	134.0	136.0	135.0		414	4.0	1.0	4	dbSNP_89	135	2890,5710	452.5+/-363.0	474,1942,1884	no	coding-synonymous	ACSL1	NM_001995.2		483,2247,3773	TT,TG,GG		33.6047,7.3309,24.704		138/699	185701549	3213,9793	2203	4300	6503	SO:0001819	synonymous_variant	2180	exon5			CTTCTGGATCAGT	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.414C>A	4.37:g.185701549G>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_001995	B7Z452|D3DP57|P41215|Q8N8V7|Q8TA99	Silent	SNP	ENST00000515030.1	37	CCDS3839.1																																																																																			G|0.787;T|0.213	0.213	strong		0.463	ACSL1-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361112.2	NM_001995	
CABLES1	91768	hgsc.bcm.edu	37	18	20793995	20793995	+	Silent	SNP	G	G	A	rs2304301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:20793995G>A	ENST00000256925.7	+	4	1065	c.1065G>A	c.(1063-1065)ccG>ccA	p.P355P	CABLES1_ENST00000420687.2_Silent_p.P90P|CABLES1_ENST00000585061.1_Intron|CABLES1_ENST00000400473.2_Silent_p.P28P|TMEM241_ENST00000450466.2_Intron	NM_001100619.2	NP_001094089.1	Q8TDN4	CABL1_HUMAN	Cdk5 and Abl enzyme substrate 1	355	Interacts with CDK3. {ECO:0000250}.				blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|nervous system development (GO:0007399)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)	cytosol (GO:0005829)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)	p.P355P(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|stomach(1)	11	all_cancers(21;0.000102)|all_epithelial(16;2.48e-06)|Lung NSC(20;0.00696)|all_lung(20;0.0197)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CAGTGCTGCCGTATCGCGACA	0.388													G|||	191	0.038139	0.0598	0.013	5008	,	,		21114	0.0456		0.0288	False		,,,				2504	0.0286				p.P355P		Atlas-SNP	.											CABLES1,NS,carcinoma,0,1	CABLES1	32	1	1	Substitution - coding silent(1)	stomach(1)	c.G1065A						PASS	.	G	,	187,3587		6,175,1706	133.0	119.0	123.0		1065,270	2.8	1.0	18	dbSNP_100	123	168,8070		3,162,3954	no	coding-synonymous,coding-synonymous	CABLES1	NM_001100619.2,NM_138375.2	,	9,337,5660	AA,AG,GG		2.0393,4.955,2.9554	,	355/634,90/369	20793995	355,11657	1887	4119	6006	SO:0001819	synonymous_variant	91768	exon4			GCTGCCGTATCGC	BC037218	CCDS42417.1, CCDS42418.1, CCDS58615.1	18q11.2	2005-08-16				ENSG00000134508			25097	protein-coding gene	gene with protein product		609194				12477932	Standard	NM_138375		Approved	HsT2563, FLJ35924	uc002kuc.2	Q8TDN4		ENST00000256925.7:c.1065G>A	18.37:g.20793995G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	49	0.597561	NM_001100619	B4DK60|Q8N3Y8|Q8NA22|Q9BTG1	Silent	SNP	ENST00000256925.7	37	CCDS42417.1																																																																																			G|0.970;A|0.030	0.030	strong		0.388	CABLES1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445198.2	NM_138375	
TRPV1	7442	hgsc.bcm.edu	37	17	3486702	3486702	+	Missense_Mutation	SNP	G	G	A	rs224534	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3486702G>A	ENST00000571088.1	-	9	1619	c.1406C>T	c.(1405-1407)aCt>aTt	p.T469I	SHPK_ENST00000572705.1_Missense_Mutation_p.T469I|TRPV1_ENST00000576351.1_Missense_Mutation_p.T459I|TRPV1_ENST00000399756.4_Missense_Mutation_p.T469I|TRPV1_ENST00000425167.2_Missense_Mutation_p.T480I|TRPV1_ENST00000310522.5_Missense_Mutation_p.T409I|TRPV1_ENST00000399759.3_Missense_Mutation_p.T469I|TRPV1_ENST00000174621.6_Missense_Mutation_p.T467I	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	469			T -> I (in dbSNP:rs224534). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:11243859}.		calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	ATAGTCTCCAGTTTTTTCCAT	0.448													G|||	1893	0.377995	0.0378	0.353	5008	,	,		21155	0.7679		0.3718	False		,,,				2504	0.4601				p.T469I	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.C1406T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	325,3491		18,289,1601	60.0	57.0	58.0		1406,1406,1406,1406	4.1	0.1	17	dbSNP_79	58	2842,5430		493,1856,1787	yes	missense,missense,missense,missense	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	89,89,89,89	511,2145,3388	AA,AG,GG		34.3569,8.5168,26.1995	benign,benign,benign,benign	469/840,469/840,469/840,469/840	3486702	3167,8921	1908	4136	6044	SO:0001583	missense	7442	exon9			TCTCCAGTTTTTT	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1406C>T	17.37:g.3486702G>A	ENSP00000461007:p.Thr469Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	881	0.4033882783882784	26	0.052845528455284556	137	0.3784530386740331	428	0.7482517482517482	290	0.38258575197889183	G	5.282	0.237389	0.10023	0.085168	0.343569	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.91631	-2.88;-2.88;-2.88;-2.88;-2.88	5.12	4.12	0.48240	.	0.568097	0.19342	N	0.116624	T	0.00012	0.0000	M	0.67397	2.05	0.80722	P	0.0	B;B;B;B	0.34181	0.025;0.083;0.042;0.44	B;B;B;B	0.31016	0.056;0.025;0.025;0.123	T	0.50127	-0.8864	9	0.42905	T	0.14	-23.1286	3.7328	0.08499	0.0975:0.1713:0.5771:0.1541	rs224534;rs60157790;rs224534	469;467;409;480	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	I	469;469;467;480;409	ENSP00000382661:T469I;ENSP00000382659:T469I;ENSP00000174621:T467I;ENSP00000409627:T480I;ENSP00000311692:T409I	ENSP00000174621:T467I	T	-	2	0	TRPV1	3433451	0.947000	0.32204	0.080000	0.20451	0.060000	0.15804	2.864000	0.48404	1.225000	0.43566	0.655000	0.94253	ACT	G|0.613;A|0.387	0.387	strong		0.448	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
HLA-A	3105	hgsc.bcm.edu	37	6	29912098	29912098	+	Silent	SNP	G	G	A	rs142475339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29912098G>A	ENST00000396634.1	+	6	1160	c.819G>A	c.(817-819)gtG>gtA	p.V273V	HLA-A_ENST00000376809.5_Silent_p.V273V|HLA-A_ENST00000376806.5_Silent_p.V273V|HLA-A_ENST00000376802.2_Silent_p.V273V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	273	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CTGTGGTGGTGCCTTCTGGAG	0.637									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	776	0.154952	0.1354	0.1758	5008	,	,		17674	0.2034		0.1123	False		,,,				2504	0.1605				p.V273V		Atlas-SNP	.											.	HLA-A	89	.	0			c.G819A						PASS	.	A		410,2612		28,354,1129	36.0	34.0	35.0		819	2.8	1.0	6	dbSNP_127	35	582,4828		35,512,2158	no	coding-synonymous	HLA-A	NM_002116.7		63,866,3287	AA,AG,GG		10.7579,13.5672,11.7647		273/366	29912098	992,7440	1511	2705	4216	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGTGGTGCCTTCT	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.819G>A	6.37:g.29912098G>A		Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	171	92	0.538012	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.871;A|0.129	0.129	strong		0.637	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SGCD	6444	hgsc.bcm.edu	37	5	155771579	155771579	+	Silent	SNP	T	T	C	rs1801193	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:155771579T>C	ENST00000435422.3	+	2	568	c.81T>C	c.(79-81)taT>taC	p.Y27Y	SGCD_ENST00000517913.1_Silent_p.Y28Y|SGCD_ENST00000447401.1_Silent_p.Y28Y|SGCD_ENST00000337851.4_Silent_p.Y28Y	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	27					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TGGGGATTTATGGCTGGCGGA	0.493													C|||	2431	0.485423	0.2436	0.464	5008	,	,		16931	0.7937		0.4473	False		,,,				2504	0.5491				p.Y28Y		Atlas-SNP	.											.	SGCD	52	.	0			c.T84C						PASS	.	C	,,	1034,2886		143,748,1069	110.0	118.0	116.0		84,81,84	-2.0	1.0	5	dbSNP_89	116	3575,4709		751,2073,1318	no	coding-synonymous,coding-synonymous,coding-synonymous	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	,,	894,2821,2387	CC,CT,TT		43.1555,26.3776,37.7663	,,	28/291,27/290,28/257	155771579	4609,7595	1960	4142	6102	SO:0001819	synonymous_variant	6444	exon3			GATTTATGGCTGG	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"""sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"""			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.81T>C	5.37:g.155771579T>C		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	245	242	0.987755	NM_000337	A8K9S9|Q53XA5|Q99644	Silent	SNP	ENST00000435422.3	37	CCDS47327.1																																																																																			T|0.516;C|0.484	0.484	strong		0.493	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
CPNE4	131034	hgsc.bcm.edu	37	3	131268824	131268824	+	Silent	SNP	T	T	C	rs11915192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:131268824T>C	ENST00000512055.1	-	18	3395	c.1269A>G	c.(1267-1269)tcA>tcG	p.S423S	CPNE4_ENST00000429747.1_Silent_p.S423S|CPNE4_ENST00000502818.1_Silent_p.S441S|CPNE4_ENST00000512332.1_Silent_p.S441S|CPNE4_ENST00000511604.1_Silent_p.S423S			Q96A23	CPNE4_HUMAN	copine IV	423	VWFA.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CCTCTGACGCTGACTTGGCAA	0.517													T|||	878	0.175319	0.2443	0.1268	5008	,	,		20206	0.1141		0.1352	False		,,,				2504	0.2209				p.S423S		Atlas-SNP	.											.	CPNE4	112	.	0			c.A1269G						PASS	.	T		952,3454	360.9+/-315.4	98,756,1349	157.0	135.0	142.0		1269	1.2	1.0	3	dbSNP_120	142	1191,7409	242.9+/-272.7	67,1057,3176	no	coding-synonymous	CPNE4	NM_130808.1		165,1813,4525	CC,CT,TT		13.8488,21.6069,16.477		423/558	131268824	2143,10863	2203	4300	6503	SO:0001819	synonymous_variant	131034	exon14			TGACGCTGACTTG	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"""copine 8"""	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.1269A>G	3.37:g.131268824T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_130808	D3DNC5|Q8TEX1	Silent	SNP	ENST00000512055.1	37	CCDS3072.1																																																																																			T|0.840;C|0.160	0.160	strong		0.517	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	
ITPR2	3709	hgsc.bcm.edu	37	12	26811045	26811045	+	Silent	SNP	T	T	C	rs12313993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:26811045T>C	ENST00000381340.3	-	17	2321	c.1905A>G	c.(1903-1905)tcA>tcG	p.S635S		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	635					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)	CACACAGATCTGACAAATAAT	0.318													T|||	1032	0.20607	0.3918	0.1383	5008	,	,		16624	0.0139		0.1779	False		,,,				2504	0.2301				p.S635S		Atlas-SNP	.											.	ITPR2	270	.	0			c.A1905G						PASS	.	T		1328,2312		228,872,720	71.0	64.0	66.0		1905	-3.0	1.0	12	dbSNP_120	66	1400,6760		124,1152,2804	no	coding-synonymous	ITPR2	NM_002223.2		352,2024,3524	CC,CT,TT		17.1569,36.4835,23.1186		635/2702	26811045	2728,9072	1820	4080	5900	SO:0001819	synonymous_variant	3709	exon17			CAGATCTGACAAA	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.1905A>G	12.37:g.26811045T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	75	48	0.64	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.814;C|0.186	0.186	strong		0.318	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
SSTR5	6755	hgsc.bcm.edu	37	16	1129441	1129441	+	Silent	SNP	G	G	A	rs34608001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1129441G>A	ENST00000293897.4	+	1	661	c.573G>A	c.(571-573)ccG>ccA	p.P191P	SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000397547.2_Silent_p.P191P|SSTR5_ENST00000562758.1_Silent_p.P191P	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	191					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)	CCAGCTGGCCGGAGCCCGTGG	0.687													G|||	59	0.0117812	0.0008	0.0231	5008	,	,		13403	0.0		0.0298	False		,,,				2504	0.0123				p.P191P		Atlas-SNP	.											.	SSTR5	36	.	0			c.G573A						PASS	.	G	,	19,4333		1,17,2158	23.0	27.0	26.0		573,573	-9.5	0.7	16	dbSNP_126	26	215,8347		2,211,4068	no	coding-synonymous,coding-synonymous	SSTR5	NM_001053.3,NM_001172560.1	,	3,228,6226	AA,AG,GG		2.5111,0.4366,1.812	,	191/365,191/365	1129441	234,12680	2176	4281	6457	SO:0001819	synonymous_variant	6755	exon2			CTGGCCGGAGCCC	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.573G>A	16.37:g.1129441G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	37	CCDS10429.1																																																																																			G|0.983;A|0.017	0.017	strong		0.687	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
ANKRD17	26057	hgsc.bcm.edu	37	4	73956736	73956736	+	Silent	SNP	G	G	A	rs6855349	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:73956736G>A	ENST00000358602.4	-	29	6725	c.6609C>T	c.(6607-6609)ctC>ctT	p.L2203L	ANKRD17_ENST00000509867.2_Silent_p.L2090L|ANKRD17_ENST00000330838.6_Silent_p.L1952L	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2203					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GATTGACACTGAGGACTGCAA	0.458													G|||	1762	0.351837	0.2375	0.2968	5008	,	,		20331	0.3849		0.4483	False		,,,				2504	0.4121				p.L2203L		Atlas-SNP	.											.	ANKRD17	214	.	0			c.C6609T						PASS	.	G	,	1217,3189	422.5+/-339.8	185,847,1171	134.0	141.0	139.0		6609,5856	3.7	1.0	4	dbSNP_116	139	3585,5015	519.3+/-379.4	736,2113,1451	no	coding-synonymous,coding-synonymous	ANKRD17	NM_032217.3,NM_198889.1	,	921,2960,2622	AA,AG,GG		41.686,27.6214,36.9214	,	2203/2604,1952/2353	73956736	4802,8204	2203	4300	6503	SO:0001819	synonymous_variant	26057	exon29			GACACTGAGGACT	AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.6609C>T	4.37:g.73956736G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	179	79	0.441341	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																			G|0.639;A|0.361	0.361	strong		0.458	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130830	52130830	+	Silent	SNP	C	C	A	rs8107754	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52130830C>A	ENST00000534261.2	-	7	1566	c.1167G>T	c.(1165-1167)ggG>ggT	p.G389G	SIGLEC5_ENST00000222107.4_Silent_p.G389G|SIGLEC5_ENST00000429354.3_Silent_p.G389G|SIGLEC5_ENST00000599649.1_Silent_p.G389G|SIGLEC5_ENST00000570106.2_Silent_p.G389G			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	389					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		TGGCCCAGGGCCCAGCTGAGC	0.662													C|||	1646	0.328674	0.382	0.5562	5008	,	,		15906	0.0089		0.4602	False		,,,				2504	0.2894				p.G389G		Atlas-SNP	.											SIGLEC5,NS,carcinoma,-1,1	SIGLEC5	67	1	0			c.G1167T						PASS	.	C		1864,2542	534.0+/-373.9	378,1108,717	47.0	46.0	46.0		1167	3.0	0.9	19	dbSNP_116	46	4136,4464	559.5+/-387.4	996,2144,1160	no	coding-synonymous	SIGLEC5	NM_003830.2		1374,3252,1877	AA,AC,CC		48.093,42.3059,46.1326		389/552	52130830	6000,7006	2203	4300	6503	SO:0001819	synonymous_variant	8778	exon6			CCAGGGCCCAGCT	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1167G>T	19.37:g.52130830C>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_003830		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																			C|0.575;A|0.425	0.425	strong		0.662	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
SPINK5	11005	hgsc.bcm.edu	37	5	147481430	147481430	+	Silent	SNP	A	A	G	rs6896303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:147481430A>G	ENST00000256084.7	+	15	1431	c.1389A>G	c.(1387-1389)ggA>ggG	p.G463G	SPINK5_ENST00000398454.1_Silent_p.G463G|SPINK5_ENST00000359874.3_Silent_p.G463G	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	463	Kazal-like 7. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G463G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCCAGATGGAAAAATGCATG	0.502													G|||	2168	0.432907	0.1989	0.6167	5008	,	,		16733	0.4851		0.4861	False		,,,				2504	0.5102				p.G463G		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.A1389G						PASS	.	G	,,	956,2828		123,710,1059	108.0	105.0	106.0		1389,1389,1389	0.3	0.7	5	dbSNP_116	106	4220,4016		1070,2080,968	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1193,2790,2027	GG,GA,AA		48.7615,25.2643,43.0616	,,	463/1095,463/917,463/1065	147481430	5176,6844	1892	4118	6010	SO:0001819	synonymous_variant	11005	exon15			AGATGGAAAAATG	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1389A>G	5.37:g.147481430A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			A|0.545;G|0.455	0.455	strong		0.502	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144879090	144879090	+	Missense_Mutation	SNP	T	T	C	rs1778120	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144879090T>C	ENST00000369354.3	-	27	4549	c.4360A>G	c.(4360-4362)Aaa>Gaa	p.K1454E	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.K1590E|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.K1590E|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.K1454E|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.K1410E|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1454				K -> E (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)		AGTCCATTTTTTGGGAGCTGG	0.522			T	PDGFRB	MPD																																p.K1454E		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A4360G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS	485,3921		0,485,1718	128.0	141.0	137.0		4228,4360,4360	5.3	0.9	1	dbSNP_89	137	1137,7463		0,1137,3163	no	missense,missense,missense	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	56,56,56	0,1622,4881	CC,CT,TT		13.2209,11.0077,12.4712	probably-damaging,probably-damaging,probably-damaging	1410/2241,1454/2363,1454/2347	144879090	1622,11384	2203	4300	6503	SO:0001583	missense	9659	exon27			CATTTTTTGGGAG	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.4360A>G	1.37:g.144879090T>C	ENSP00000358360:p.Lys1454Glu	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	247	75	0.303644	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	580	0.26556776556776557	104	0.21138211382113822	110	0.30386740331491713	170	0.2972027972027972	196	0.25857519788918204	T	14.22	2.470544	0.43942	0.110077	0.132209	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01787	4.64;4.75;4.73;4.73;4.74	5.29	5.29	0.74685	.	.	.	.	.	T	0.02767	0.0083	L	0.48362	1.52	0.39961	D	0.974669	D;D	0.67145	0.996;0.991	P;P	0.61874	0.895;0.815	T	0.57394	-0.7819	9	0.46703	T	0.11	.	11.5395	0.50659	0.0:0.0:0.0:1.0	rs1778120	1410;1454	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	E	1410;1454;1454;1590;1590	ENSP00000327209:K1410E;ENSP00000358360:K1454E;ENSP00000358363:K1454E;ENSP00000435654:K1590E;ENSP00000358366:K1590E	ENSP00000327209:K1410E	K	-	1	0	PDE4DIP	143590447	0.002000	0.14202	0.939000	0.37840	0.994000	0.84299	1.133000	0.31430	2.232000	0.73038	0.482000	0.46254	AAA	T|0.003;G|0.264	.	strong		0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
IL10RA	3587	hgsc.bcm.edu	37	11	117859209	117859209	+	Silent	SNP	G	G	A	rs4252249|rs397724954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:117859209G>A	ENST00000227752.3	+	2	300	c.180G>A	c.(178-180)gcG>gcA	p.A60A	IL10RA_ENST00000545409.1_5'UTR|IL10RA_ENST00000541785.1_Silent_p.A40A|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	60					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		ATGAAGTGGCGCTCCTGAGGT	0.532													G|||	629	0.125599	0.1694	0.1859	5008	,	,		19073	0.0625		0.1123	False		,,,				2504	0.1022				p.A60A		Atlas-SNP	.											.	IL10RA	46	.	0			c.G180A						PASS	.	G		693,3709	288.1+/-279.7	42,609,1550	78.0	70.0	73.0		180	-4.7	0.0	11	dbSNP_111	73	912,7680	201.4+/-244.9	58,796,3442	no	coding-synonymous	IL10RA	NM_001558.3		100,1405,4992	AA,AG,GG		10.6145,15.7428,12.3519		60/579	117859209	1605,11389	2201	4296	6497	SO:0001819	synonymous_variant	3587	exon2			AGTGGCGCTCCTG	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.180G>A	11.37:g.117859209G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			G|0.876;A|0.124	0.124	strong		0.532	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
DGKH	160851	hgsc.bcm.edu	37	13	42793479	42793479	+	Silent	SNP	G	G	A	rs180870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:42793479G>A	ENST00000337343.4	+	27	3348	c.3327G>A	c.(3325-3327)gaG>gaA	p.E1109E	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000540693.1_Silent_p.E1109E|DGKH_ENST00000261491.5_Silent_p.E1109E|DGKH_ENST00000379274.2_Silent_p.E973E|DGKH_ENST00000538674.1_Silent_p.E864E|DGKH_ENST00000536612.1_Silent_p.E973E	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1109					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		ACCCAAATGAGGATGAGGTAT	0.363													G|||	3139	0.626797	0.5976	0.634	5008	,	,		17423	0.7341		0.6879	False		,,,				2504	0.4877				p.E1109E		Atlas-SNP	.											.	DGKH	106	.	0			c.G3327A						PASS	.	G	,,,,	2711,1695	653.5+/-399.6	836,1039,328	130.0	137.0	135.0		3327,2919,2919,3327,3327	1.0	1.0	13	dbSNP_79	135	5877,2723	680.7+/-403.7	2021,1835,444	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	2857,2874,772	AA,AG,GG		31.6628,38.4703,33.9689	,,,,	1109/1165,973/1101,973/1085,1109/1165,1109/1221	42793479	8588,4418	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon28			AAATGAGGATGAG	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.3327G>A	13.37:g.42793479G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	82	42	0.512195	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			G|0.337;A|0.663	0.663	strong		0.363	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
OR52K2	119774	hgsc.bcm.edu	37	11	4471473	4471473	+	Missense_Mutation	SNP	C	C	T	rs7934336	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4471473C>T	ENST00000325719.4	+	1	949	c.904C>T	c.(904-906)Cgt>Tgt	p.R302C		NM_001005172.2	NP_001005172.2	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K, member 2	302			R -> C (in dbSNP:rs7934336).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|skin(6)	25		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAAGCAAATCCGTGAGAGCAT	0.498													C|||	633	0.126398	0.3737	0.0706	5008	,	,		21207	0.0347		0.0298	False		,,,				2504	0.0256				p.R302C		Atlas-SNP	.											.	OR52K2	61	.	0			c.C904T						PASS	.	C	CYS/ARG	1407,2995	463.6+/-353.6	216,975,1010	96.0	92.0	94.0		904	2.2	1.0	11	dbSNP_116	94	235,8361	94.7+/-156.6	4,227,4067	yes	missense	OR52K2	NM_001005172.2	180	220,1202,5077	TT,TC,CC		2.7338,31.9627,12.6327	benign	302/315	4471473	1642,11356	2201	4298	6499	SO:0001583	missense	119774	exon1			CAAATCCGTGAGA	AB065791	CCDS31351.1	11p15.4	2012-08-09			ENSG00000181963	ENSG00000181963		"""GPCR / Class A : Olfactory receptors"""	15223	protein-coding gene	gene with protein product							Standard	NM_001005172		Approved		uc001lyz.2	Q8NGK3	OTTHUMG00000165703	ENST00000325719.4:c.904C>T	11.37:g.4471473C>T	ENSP00000318956:p.Arg302Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	97	48	0.494845	NM_001005172	A8MUY8|B2RP35|Q6IFK4	Missense_Mutation	SNP	ENST00000325719.4	37	CCDS31351.1	275	0.1259157509157509	206	0.4186991869918699	24	0.06629834254143646	23	0.04020979020979021	22	0.029023746701846966	C	8.510	0.866352	0.17250	0.319627	0.027338	ENSG00000181963	ENST00000325719	T	0.58358	0.34	4.16	2.24	0.28232	.	0.139494	0.32785	N	0.005660	T	0.00012	0.0000	M	0.79614	2.46	0.27898	P	0.9390894	B	0.18310	0.027	B	0.11329	0.006	T	0.25433	-1.0132	9	0.87932	D	0	.	6.7791	0.23636	0.1741:0.7276:0.0:0.0984	rs7934336;rs52810694;rs7934336	302	Q8NGK3	O52K2_HUMAN	C	302	ENSP00000318956:R302C	ENSP00000318956:R302C	R	+	1	0	OR52K2	4428049	0.817000	0.29147	0.990000	0.47175	0.395000	0.30598	2.067000	0.41461	0.387000	0.25024	0.586000	0.80456	CGT	C|0.868;T|0.132	0.132	strong		0.498	OR52K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385844.1	NM_001005172	
PCDHGB6	56100	hgsc.bcm.edu	37	5	140788264	140788264	+	Silent	SNP	C	C	T	rs58047392	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140788264C>T	ENST00000520790.1	+	1	495	c.495C>T	c.(493-495)aaC>aaT	p.N165N	PCDHGA9_ENST00000573521.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	165	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAAACATAAACTCAATTAAAG	0.343													.|||	995	0.198682	0.3064	0.1902	5008	,	,		18324	0.1528		0.1014	False		,,,				2504	0.2065				p.N165N		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.C495T						PASS	.	C	,,,,,,,,,,,,,,,	1141,2505		187,767,869	30.0	30.0	30.0		,,,,,,,,,,,,,495,,495	3.2	0.9	5	dbSNP_129	30	1000,7176		63,874,3151	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,,,	250,1641,4020	TT,TC,CC		12.2309,31.2946,18.1103	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,165/931,,165/821	140788264	2141,9681	1823	4088	5911	SO:0001819	synonymous_variant	56100	exon1			CATAAACTCAATT	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"""Cadherins / Protocadherins : Clustered"""	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.495C>T	5.37:g.140788264C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_032100	Q9Y5C5	Silent	SNP	ENST00000520790.1	37	CCDS54929.1																																																																																			C|0.824;T|0.176	0.176	strong		0.343	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
DGKG	1608	hgsc.bcm.edu	37	3	186006566	186006566	+	Silent	SNP	T	T	C	rs710443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:186006566T>C	ENST00000265022.3	-	6	1016	c.477A>G	c.(475-477)gtA>gtG	p.V159V	DGKG_ENST00000344484.4_Silent_p.V159V|DGKG_ENST00000382164.4_Silent_p.V159V|DGKG_ENST00000544847.1_Silent_p.V159V	NM_001080744.1|NM_001080745.1|NM_001346.2	NP_001074213.1|NP_001074214.1|NP_001337.2	P49619	DGKG_HUMAN	diacylglycerol kinase, gamma 90kDa	159					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|neuron development (GO:0048666)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	42	all_cancers(143;3.26e-12)|Ovarian(172;0.0315)|Breast(254;0.247)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)	GBM - Glioblastoma multiforme(93;0.0657)	Phosphatidylserine(DB00144)	CCTTCAGGTATACCACTGGGG	0.577													C|||	3485	0.695887	0.6936	0.6974	5008	,	,		16536	0.7103		0.6978	False		,,,				2504	0.681				p.V159V		Atlas-SNP	.											.	DGKG	98	.	0			c.A477G						PASS	.	C	,,	3039,1367	452.8+/-350.1	1054,931,218	129.0	139.0	136.0		477,477,477	0.8	1.0	3	dbSNP_86	136	5916,2684	430.4+/-356.5	2023,1870,407	no	coding-synonymous,coding-synonymous,coding-synonymous	DGKG	NM_001080744.1,NM_001080745.1,NM_001346.2	,,	3077,2801,625	CC,CT,TT		31.2093,31.0259,31.1472	,,	159/767,159/753,159/792	186006566	8955,4051	2203	4300	6503	SO:0001819	synonymous_variant	1608	exon6			CAGGTATACCACT	AF020945	CCDS3274.1, CCDS43181.1, CCDS43182.1	3q27-q28	2013-01-10	2002-08-29		ENSG00000058866	ENSG00000058866	2.7.1.107	"""EF-hand domain containing"""	2853	protein-coding gene	gene with protein product		601854	"""diacylglycerol kinase, gamma (90kD)"""	DAGK3		8034597	Standard	NM_001080744		Approved		uc003fqa.3	P49619	OTTHUMG00000156617	ENST00000265022.3:c.477A>G	3.37:g.186006566T>C		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	133	130	0.977444	NM_001346	B2RAH4|Q2M1H4|Q5FWG1	Silent	SNP	ENST00000265022.3	37	CCDS3274.1																																																																																			T|0.313;C|0.687	0.687	strong		0.577	DGKG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344800.3		
FAT4	79633	hgsc.bcm.edu	37	4	126336703	126336703	+	Silent	SNP	T	T	C	rs17009618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:126336703T>C	ENST00000394329.3	+	5	6598	c.6585T>C	c.(6583-6585)aaT>aaC	p.N2195N	FAT4_ENST00000335110.5_Silent_p.N493N	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2195	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GCATTGTTAATGGTAATACCA	0.413													T|||	1025	0.204673	0.1452	0.2738	5008	,	,		20411	0.2262		0.1461	False		,,,				2504	0.274				p.N2195N		Atlas-SNP	.											FAT4_ENST00000394329,colon,carcinoma,0,2	FAT4	1752	2	0			c.T6585C						PASS	.	T		576,3830	257.7+/-262.0	37,502,1664	166.0	150.0	156.0		6585	-5.6	0.0	4	dbSNP_123	156	1154,7446	236.9+/-269.0	82,990,3228	no	coding-synonymous	FAT4	NM_024582.4		119,1492,4892	CC,CT,TT		13.4186,13.0731,13.3016		2195/4982	126336703	1730,11276	2203	4300	6503	SO:0001819	synonymous_variant	79633	exon5			TGTTAATGGTAAT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.6585T>C	4.37:g.126336703T>C		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	157	84	0.535032	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			T|0.848;C|0.152	0.152	strong		0.413	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
TMEM204	79652	hgsc.bcm.edu	37	16	1591962	1591962	+	Silent	SNP	G	G	A	rs2076443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1591962G>A	ENST00000566264.1	+	2	1024	c.321G>A	c.(319-321)acG>acA	p.T107T	IFT140_ENST00000426508.2_Intron|TMEM204_ENST00000253934.5_Silent_p.T107T	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	107					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				TGGTGGCCACGGCCGCGCTCA	0.701													G|||	1534	0.30631	0.4228	0.1599	5008	,	,		18178	0.3423		0.1918	False		,,,				2504	0.3333				p.T107T		Atlas-SNP	.											TMEM204,NS,carcinoma,0,1	TMEM204	29	1	0			c.G321A						PASS	.	G	,	1554,2760		288,978,891	30.0	37.0	35.0		,321	-11.5	0.2	16	dbSNP_96	35	1649,6841		166,1317,2762	no	intron,coding-synonymous	IFT140,TMEM204	NM_014714.3,NM_024600.4	,	454,2295,3653	AA,AG,GG		19.4229,36.0223,25.0156	,	,107/227	1591962	3203,9601	2157	4245	6402	SO:0001819	synonymous_variant	79652	exon2			GGCCACGGCCGCG		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"""chromosome 16 open reading frame 30"""	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.321G>A	16.37:g.1591962G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	70	48	0.685714	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Silent	SNP	ENST00000566264.1	37	CCDS42098.1																																																																																			G|0.746;A|0.254	0.254	strong		0.701	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600	
DST	667	hgsc.bcm.edu	37	6	56482801	56482801	+	Missense_Mutation	SNP	C	C	G	rs6459166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56482801C>G	ENST00000370765.6	-	23	6138	c.6031G>C	c.(6031-6033)Gtt>Ctt	p.V2011L	DST_ENST00000446842.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			GGTGTCAAAACCTTCACCAGT	0.393													G|||	2012	0.401757	0.5817	0.4063	5008	,	,		19088	0.2669		0.3976	False		,,,				2504	0.2986				p.V2011L		Atlas-SNP	.											.	DST	1427	.	0			c.G6031C						PASS	.	G	LEU/VAL,	2424,1982	558.7+/-380.1	642,1140,421	138.0	134.0	135.0		6031,	5.5	1.0	6	dbSNP_116	135	3679,4921	621.2+/-397.2	802,2075,1423	yes	missense,intron	DST	NM_001723.5,NM_015548.4	32,	1444,3215,1844	GG,GC,CC		42.7791,44.9841,46.9245	,	2011/2650,	56482801	6103,6903	2203	4300	6503	SO:0001583	missense	667	exon23			TCAAAACCTTCAC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000370765.6:c.6031G>C	6.37:g.56482801C>G	ENSP00000359801:p.Val2011Leu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000370765.6	37	CCDS4959.1	875	0.40064102564102566	289	0.5873983739837398	156	0.430939226519337	145	0.2534965034965035	285	0.3759894459102902	G	1.427	-0.571209	0.03882	0.550159	0.427791	ENSG00000151914	ENST00000370765	T	0.12984	2.63	5.49	5.49	0.81192	.	.	.	.	.	T	0.03434	0.0099	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36383	-0.9750	7	0.17832	T	0.49	.	12.8068	0.57618	0.0:0.125:0.745:0.13	rs6459166;rs17674623;rs57901071;rs6459166	2011	Q03001-3	.	L	2011	ENSP00000359801:V2011L	ENSP00000359801:V2011L	V	-	1	0	DST	56590760	1.000000	0.71417	0.999000	0.59377	0.954000	0.61252	1.942000	0.40243	1.332000	0.45431	-0.224000	0.12420	GTT	C|0.569;G|0.431	0.431	strong		0.393	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723	
GSX1	219409	hgsc.bcm.edu	37	13	28367061	28367061	+	Silent	SNP	A	A	G	rs1231058	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:28367061A>G	ENST00000302945.2	+	1	282	c.234A>G	c.(232-234)ctA>ctG	p.L78L		NM_145657.1	NP_663632.1	Q9H4S2	GSX1_HUMAN	GS homeobox 1	78					adenohypophysis development (GO:0021984)|hypothalamus development (GO:0021854)|neuron fate commitment (GO:0048663)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spinal cord association neuron differentiation (GO:0021527)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	4		Lung SC(185;0.0161)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	GBM - Glioblastoma multiforme(144;0.0402)|all cancers(112;0.0404)|OV - Ovarian serous cystadenocarcinoma(117;0.197)		cgcTGCCTCTACTCAAGGCTT	0.751													G|||	4592	0.916933	0.9834	0.8732	5008	,	,		10675	0.997		0.7972	False		,,,				2504	0.8988				p.L78L		Atlas-SNP	.											.	GSX1	20	.	0			c.A234G						PASS	.	G		3048,136		1461,126,5	2.0	3.0	3.0		234	1.1	1.0	13	dbSNP_87	3	5457,1143		2229,999,72	no	coding-synonymous	GSX1	NM_145657.1		3690,1125,77	GG,GA,AA		17.3182,4.2714,13.0724		78/265	28367061	8505,1279	1592	3300	4892	SO:0001819	synonymous_variant	219409	exon1			GCCTCTACTCAAG	AB044157	CCDS9326.1	13q12.2	2012-03-09		2007-07-26	ENSG00000169840	ENSG00000169840		"""Homeoboxes / ANTP class : HOXL subclass"""	20374	protein-coding gene	gene with protein product				GSH1			Standard	NM_145657		Approved	Gsh-1	uc001urr.1	Q9H4S2	OTTHUMG00000016637	ENST00000302945.2:c.234A>G	13.37:g.28367061A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_145657	Q9UD62	Silent	SNP	ENST00000302945.2	37	CCDS9326.1																																																																																			A|0.104;G|0.896	0.896	strong		0.751	GSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044309.2	NM_145657	
CHFR	55743	hgsc.bcm.edu	37	12	133435716	133435716	+	Silent	SNP	T	T	G	rs35011845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133435716T>G	ENST00000432561.2	-	8	958	c.885A>C	c.(883-885)ccA>ccC	p.P295P	CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000450056.2_Silent_p.P283P|CHFR_ENST00000537522.1_5'Flank|CHFR_ENST00000443047.2_Silent_p.P203P|CHFR_ENST00000315585.7_Silent_p.P254P|CHFR_ENST00000266880.7_Silent_p.P295P			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	295					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		CCATCTTGTCTGGCTTCCCAG	0.592													T|||	712	0.142173	0.0106	0.1585	5008	,	,		18006	0.1726		0.2793	False		,,,				2504	0.136				p.P295P		Atlas-SNP	.											.	CHFR	83	.	0			c.A885C						PASS	.	T	,,,,	223,4183	137.3+/-173.1	9,205,1989	216.0	124.0	155.0		885,885,849,609,762	-11.0	0.1	12	dbSNP_126	155	2569,6031	417.4+/-352.4	384,1801,2115	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	,,,,	393,2006,4104	GG,GT,TT		29.8721,5.0613,21.467	,,,,	295/665,295/664,283/653,203/573,254/624	133435716	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	55743	exon8			CTTGTCTGGCTTC	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.885A>C	12.37:g.133435716T>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	92	35	0.380435	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Silent	SNP	ENST00000432561.2	37	CCDS53849.1																																																																																			T|0.796;G|0.204	0.204	strong		0.592	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
RTP2	344892	hgsc.bcm.edu	37	3	187419764	187419764	+	Silent	SNP	G	G	A	rs150707467		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:187419764G>A	ENST00000358241.1	-	1	581	c.153C>T	c.(151-153)caC>caT	p.H51H	RP11-211G3.3_ENST00000437407.1_5'Flank|RP11-211G3.3_ENST00000449623.1_5'Flank	NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	51					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)		TGCCTGAGGCGTGCTGCTCCA	0.627																																					p.H51H		Atlas-SNP	.											RTP2,right_upper_lobe,carcinoma,-2,1	RTP2	38	1	0			c.C153T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	98.0	102.0	100.0		153	-6.0	0.9	3	dbSNP_134	100	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	RTP2	NM_001004312.2		0,9,6494	AA,AG,GG		0.093,0.0227,0.0692		51/226	187419764	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	344892	exon1			TGAGGCGTGCTGC	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.153C>T	3.37:g.187419764G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	124	65	0.524194	NM_001004312	Q6NVH4	Silent	SNP	ENST00000358241.1	37	CCDS33911.1																																																																																			G|1.000;A|0.000	0.000	weak		0.627	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312	
ACSM5	54988	hgsc.bcm.edu	37	16	20441084	20441084	+	Silent	SNP	T	T	C	rs8063682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:20441084T>C	ENST00000331849.4	+	8	1233	c.1086T>C	c.(1084-1086)acT>acC	p.T362T		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	362					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						AACACCAGACTGGTGTGGAGC	0.597													C|||	2717	0.542532	0.7428	0.2867	5008	,	,		16542	0.755		0.3211	False		,,,				2504	0.4622				p.T362T		Atlas-SNP	.											ACSM5,right_upper_lobe,carcinoma,+2,1	ACSM5	101	1	0			c.T1086C						PASS	.	C		2925,1481		1058,809,336	81.0	86.0	84.0		1086	-8.9	0.1	16	dbSNP_116	84	2735,5861		558,1619,2121	no	coding-synonymous	ACSM5	NM_017888.2		1616,2428,2457	CC,CT,TT		31.8171,33.6133,43.5318		362/580	20441084	5660,7342	2203	4298	6501	SO:0001819	synonymous_variant	54988	exon8			CCAGACTGGTGTG		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1086T>C	16.37:g.20441084T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	18	0.4	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Silent	SNP	ENST00000331849.4	37	CCDS10585.1																																																																																			T|0.550;C|0.450	0.450	strong		0.597	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
MUC7	4589	hgsc.bcm.edu	37	4	71346701	71346701	+	Missense_Mutation	SNP	C	C	G	rs6826961	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71346701C>G	ENST00000304887.5	+	3	430	c.240C>G	c.(238-240)aaC>aaG	p.N80K	MUC7_ENST00000413702.1_Missense_Mutation_p.N80K|MUC7_ENST00000456088.1_Missense_Mutation_p.N80K|MUC7_ENST00000514512.1_3'UTR	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	80			N -> K (in dbSNP:rs6826961).		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)			CACCTAATAACCCCCCCAAAT	0.458													C|||	1554	0.310304	0.2973	0.196	5008	,	,		20095	0.4077		0.2207	False		,,,				2504	0.4008				p.N80K		Atlas-SNP	.											.	MUC7	91	.	0			c.C240G						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN	1322,3084	445.9+/-347.8	195,932,1076	122.0	120.0	121.0		240,240,240	-3.1	0.0	4	dbSNP_116	121	2029,6571	353.4+/-329.1	227,1575,2498	yes	missense,missense,missense	MUC7	NM_152291.2,NM_001145007.1,NM_001145006.1	94,94,94	422,2507,3574	GG,GC,CC		23.593,30.0045,25.765	benign,benign,benign	80/378,80/378,80/378	71346701	3351,9655	2203	4300	6503	SO:0001583	missense	4589	exon4			TAATAACCCCCCC	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.240C>G	4.37:g.71346701C>G	ENSP00000302021:p.Asn80Lys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	162	159	0.981481	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	603	0.2760989010989011	144	0.2926829268292683	67	0.1850828729281768	216	0.3776223776223776	176	0.23218997361477572	C	0.004	-2.263479	0.00262	0.300045	0.23593	ENSG00000171195	ENST00000413702;ENST00000505411;ENST00000456088;ENST00000304887	T;T;T;T	0.52526	0.67;0.66;0.67;0.67	1.55	-3.1	0.05315	.	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.12630	0.006	B	0.10450	0.005	T	0.41787	-0.9489	8	0.11794	T	0.64	.	0.0984	0.00046	0.2439:0.1942:0.2126:0.3492	rs6826961;rs52803154;rs6826961	80	Q8TAX7	MUC7_HUMAN	K	80	ENSP00000407422:N80K;ENSP00000427594:N80K;ENSP00000400585:N80K;ENSP00000302021:N80K	ENSP00000302021:N80K	N	+	3	2	MUC7	71381290	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.185000	0.00567	-1.398000	0.02066	-0.344000	0.07964	AAC	C|0.738;G|0.262	0.262	strong		0.458	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
PEA15	8682	hgsc.bcm.edu	37	1	160182943	160182943	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:160182943T>C	ENST00000360472.4	+	3	404	c.216T>C	c.(214-216)cgT>cgC	p.R72R	PEA15_ENST00000488858.1_3'UTR|PEA15_ENST00000368076.1_Silent_p.R93R|PEA15_ENST00000368077.1_Silent_p.R50R	NM_003768.3	NP_003759.1	Q15121	PEA15_HUMAN	phosphoprotein enriched in astrocytes 15	72	DED. {ECO:0000255|PROSITE- ProRule:PRU00065}.				apoptotic process (GO:0006915)|carbohydrate transport (GO:0008643)|DNA damage checkpoint (GO:0000077)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of glucose import (GO:0046325)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|response to morphine (GO:0043278)|transport (GO:0006810)	cytoplasm (GO:0005737)|microtubule associated complex (GO:0005875)				large_intestine(1)|lung(4)	5	all_cancers(52;3.11e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TCTCCCGCCGTCCTGACCTAC	0.542																																					p.R72R		Atlas-SNP	.											PEA15,NS,carcinoma,+1,1	PEA15	7	1	0			c.T216C						scavenged	.						202.0	174.0	183.0					1																	160182943		2203	4300	6503	SO:0001819	synonymous_variant	8682	exon3			CCGCCGTCCTGAC	Y13736	CCDS1199.1, CCDS72954.1	1q21.1	2008-07-18			ENSG00000162734	ENSG00000162734			8822	protein-coding gene	gene with protein product	"""Phosphoprotein enriched in astrocytes, 15kD"", ""homolog of mouse MAT-1 oncogene"""	603434				9205133	Standard	XM_005245564		Approved	HMAT1, MAT1, PED, PEA-15, MAT1H, HUMMAT1H	uc001fvk.3	Q15121	OTTHUMG00000031605	ENST00000360472.4:c.216T>C	1.37:g.160182943T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	206	6	0.0291262	NM_003768	B1AKZ3|O00511	Silent	SNP	ENST00000360472.4	37	CCDS1199.1																																																																																			.	.	none		0.542	PEA15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077407.1	NM_003768	
REPIN1	29803	hgsc.bcm.edu	37	7	150068933	150068933	+	Silent	SNP	T	T	C	rs6722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150068933T>C	ENST00000425389.2	+	1	681	c.603T>C	c.(601-603)gcT>gcC	p.A201A	RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000397281.2_Silent_p.A201A|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000444957.1_Silent_p.A201A|REPIN1_ENST00000540729.1_Silent_p.A201A|REPIN1_ENST00000489432.2_Silent_p.A258A|REPIN1_ENST00000466559.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	201					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			TGCACGTAGCTGAGGCCCTGG	0.746													C|||	2082	0.415735	0.4894	0.2176	5008	,	,		11294	0.4673		0.3181	False		,,,				2504	0.5041				p.A258A		Atlas-SNP	.											REPIN1_ENST00000489432,NS,carcinoma,0,2	REPIN1	74	2	0			c.T774C						PASS	.	C	,,,	1586,2058		384,818,620	8.0	10.0	10.0		774,603,603,603	-2.6	0.8	7	dbSNP_52	10	2511,5575		452,1607,1984	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	,,,	836,2425,2604	CC,CT,TT		31.0537,43.5236,34.9275	,,,	258/625,201/568,201/568,201/568	150068933	4097,7633	1822	4043	5865	SO:0001819	synonymous_variant	29803	exon3			CGTAGCTGAGGCC	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.603T>C	7.37:g.150068933T>C		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Silent	SNP	ENST00000425389.2	37	CCDS43677.1																																																																																			T|0.574;C|0.426	0.426	strong		0.746	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
RCN1	5954	hgsc.bcm.edu	37	11	32124978	32124978	+	Silent	SNP	T	T	C	rs4876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:32124978T>C	ENST00000054950.3	+	5	1133	c.840T>C	c.(838-840)caT>caC	p.H280H	RCN1_ENST00000532942.1_Silent_p.H229H|RP1-65P5.3_ENST00000533009.1_RNA	NM_002901.2	NP_002892.1	Q15293	RCN1_HUMAN	reticulocalbin 1, EF-hand calcium binding domain	280	EF-hand 6. {ECO:0000255|PROSITE- ProRule:PRU00448}.				camera-type eye development (GO:0043010)|in utero embryonic development (GO:0001701)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)	17	Lung SC(675;0.225)					ATTATGATCATGCACAGGCTG	0.448													.|||	2399	0.479034	0.23	0.464	5008	,	,		21509	0.6776		0.501	False		,,,				2504	0.5992				p.H280H		Atlas-SNP	.											.	RCN1	37	.	0			c.T840C						PASS	.	T		1139,3265	404.2+/-333.0	149,841,1212	82.0	84.0	84.0		840	-7.4	0.5	11	dbSNP_52	84	4491,4107	589.9+/-392.6	1154,2183,962	no	coding-synonymous	RCN1	NM_002901.2		1303,3024,2174	CC,CT,TT		47.7669,25.8629,43.301		280/332	32124978	5630,7372	2202	4299	6501	SO:0001819	synonymous_variant	5954	exon5			TGATCATGCACAG	D42073	CCDS7876.1	11p13	2013-01-10			ENSG00000049449	ENSG00000049449		"""EF-hand domain containing"""	9934	protein-coding gene	gene with protein product	"""proliferation-inducing gene 20"""	602735		RCN		9192846, 8586628	Standard	NM_002901		Approved	Rcal, PIG20, FLJ37041	uc010reb.2	Q15293		ENST00000054950.3:c.840T>C	11.37:g.32124978T>C		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	192	185	0.963542	NM_002901	B7Z1M1|D3DR00	Silent	SNP	ENST00000054950.3	37	CCDS7876.1																																																																																			.	.	weak		0.448	RCN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388510.1	NM_002901	
DMD	1756	hgsc.bcm.edu	37	X	31496350	31496350	+	Missense_Mutation	SNP	C	C	T	rs1800280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:31496350C>T	ENST00000357033.4	-	59	9016	c.8810G>A	c.(8809-8811)cGg>cAg	p.R2937Q	DMD_ENST00000359836.1_Missense_Mutation_p.R477Q|DMD_ENST00000343523.2_Missense_Mutation_p.R477Q|DMD_ENST00000474231.1_Missense_Mutation_p.R477Q|DMD_ENST00000378677.2_Missense_Mutation_p.R2933Q|DMD_ENST00000541735.1_Missense_Mutation_p.R477Q|DMD_ENST00000445312.1_5'Flank|DMD_ENST00000378707.3_Missense_Mutation_p.R477Q	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	2937			Q -> R (in dbSNP:rs1800280). {ECO:0000269|PubMed:12359139, ECO:0000269|PubMed:15772651, ECO:0000269|PubMed:7849724}.		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				TTGAAGTTCCCGGAGTCTTTC	0.537													T|||	3329	0.881854	0.7579	0.6254	3775	,	,		12784	0.7034		0.7147	False		,,,				2504	0.4755				p.R2937Q		Atlas-SNP	.											.	DMD	2127	.	0			c.G8810A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	3786,47		1589,41,567,1,4	63.0	52.0	56.0		8786,8810,8441,8798,8441,4787,4778,1430,623,1430,1430,1430,1430	4.2	1.0	X	dbSNP_89	56	6319,409		2144,277,1754,7,118	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3,NM_004013.2,NM_004014.2,NM_004020.3,NM_004021.2,NM_004022.2,NM_004023.2	43,43,43,43,43,43,43,43,43,43,43,43,43	3733,318,2321,8,122	TT,TC,T,CC,C		6.0791,1.2262,4.3178	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	2929/3678,2937/3686,2814/3563,2933/3682,2814/3563,1596/2345,1593/2342,477/1226,208/957,477/1116,477/1244,477/1231,477/1134	31496350	10105,456	2202	4300	6502	SO:0001583	missense	1756	exon59			AGTTCCCGGAGTC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.8810G>A	X.37:g.31496350C>T	ENSP00000354923:p.Arg2937Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	1554	0.9367088607594937	262	1.0	160	0.7272727272727273	264	0.9103448275862069	380	0.8715596330275229	T	6.596	0.478310	0.12521	0.987738	0.939209	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000474231	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	5.4	4.23	0.50019	.	0.000000	0.35615	N	0.003095	T	0.00012	0.0000	.	.	.	0.49213	P	2.3499999999998522E-4	B;B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.001;0.001;0.001;0.001;0.001;0.001	T	0.42481	-0.9449	8	0.07482	T	0.82	.	8.899	0.35484	0.0:0.154:0.0:0.846	rs1800280;rs52818081;rs57666470;rs1800280	2933;1596;1593;477;477;477;477;477;2814	E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3	.;.;.;.;.;.;.;.;.	Q	2929;1596;1593;633;2933;2937;477;477;2937;2814;477;477;477	ENSP00000350765:R633Q;ENSP00000367948:R2933Q;ENSP00000354923:R2937Q;ENSP00000352894:R477Q;ENSP00000340057:R477Q;ENSP00000367979:R477Q;ENSP00000444119:R477Q;ENSP00000417123:R477Q	ENSP00000340057:R477Q	R	-	2	0	DMD	31406271	0.998000	0.40836	1.000000	0.80357	0.659000	0.38960	0.871000	0.28023	0.789000	0.33779	-0.407000	0.06327	CGG	0|0.014;T|0.929	0.929	strong		0.537	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CD6	923	hgsc.bcm.edu	37	11	60785464	60785464	+	Missense_Mutation	SNP	G	G	A	rs2074233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60785464G>A	ENST00000313421.7	+	11	2002	c.1816G>A	c.(1816-1818)Ggc>Agc	p.G606S	CD6_ENST00000346437.4_Missense_Mutation_p.G533S|CD6_ENST00000344028.5_Missense_Mutation_p.G574S|CD6_ENST00000352009.5_Missense_Mutation_p.G574S|CD6_ENST00000452451.2_Missense_Mutation_p.G565S	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	606			G -> S (in dbSNP:rs2074233).		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						GGAGCTGGCCGGCACCCAGCC	0.592													G|||	515	0.102835	0.0113	0.1239	5008	,	,		16050	0.0972		0.2425	False		,,,				2504	0.0736				p.G606S	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.G1816A						PASS	.	G	SER/GLY	242,4154		7,228,1963	40.0	45.0	43.0		1816	4.3	0.5	11	dbSNP_96	43	2106,6470		275,1556,2457	yes	missense	CD6	NM_006725.3	56	282,1784,4420	AA,AG,GG		24.5569,5.505,18.1005	benign	606/669	60785464	2348,10624	2198	4288	6486	SO:0001583	missense	923	exon11			CTGGCCGGCACCC		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.1816G>A	11.37:g.60785464G>A	ENSP00000323280:p.Gly606Ser	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	295	0.13507326007326007	9	0.018292682926829267	52	0.143646408839779	52	0.09090909090909091	182	0.24010554089709762	G	18.21	3.572591	0.65765	0.05505	0.245569	ENSG00000013725	ENST00000344028;ENST00000346437;ENST00000313421;ENST00000452451;ENST00000352009	T;T;T;T;T	0.03358	4.07;3.96;4.24;4.03;4.59	5.18	4.26	0.50523	.	1.155780	0.06749	N	0.779732	T	0.00012	0.0000	M	0.66939	2.045	0.54753	P	1.0999999999983245E-5	B;B;B;B	0.34329	0.449;0.449;0.275;0.115	B;B;B;B	0.32677	0.092;0.15;0.03;0.026	T	0.41662	-0.9496	9	0.56958	D	0.05	.	9.6111	0.39663	0.0971:0.0:0.9029:0.0	rs2074233	565;574;606;606	P30203-5;P30203-4;P30203;Q8N4Q7	.;.;CD6_HUMAN;.	S	574;533;606;565;574	ENSP00000344108:G574S;ENSP00000345566:G533S;ENSP00000323280:G606S;ENSP00000390676:G565S;ENSP00000340628:G574S	ENSP00000323280:G606S	G	+	1	0	CD6	60542040	0.984000	0.35163	0.500000	0.27589	0.910000	0.53928	2.285000	0.43487	1.185000	0.42971	0.313000	0.20887	GGC	G|0.830;A|0.170	0.170	strong		0.592	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
RBM33	155435	hgsc.bcm.edu	37	7	155532600	155532600	+	Silent	SNP	C	C	T	rs200834081	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:155532600C>T	ENST00000401878.3	+	12	2127	c.1929C>T	c.(1927-1929)tcC>tcT	p.S643S		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	643	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)		ACCACCTGTCCGTCCCGCCCC	0.711													C|||	9	0.00179712	0.0	0.0029	5008	,	,		7050	0.0		0.006	False		,,,				2504	0.001				p.S643S		Atlas-SNP	.											.	RBM33	157	.	0			c.C1929T						PASS	.	C		8,4238		0,8,2115	18.0	20.0	19.0		1929	-10.3	0.0	7		19	49,8235		0,49,4093	no	coding-synonymous	RBM33	NM_053043.2		0,57,6208	TT,TC,CC		0.5915,0.1884,0.4549		643/1171	155532600	57,12473	2123	4142	6265	SO:0001819	synonymous_variant	155435	exon12			CCTGTCCGTCCCG	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.1929C>T	7.37:g.155532600C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	171	82	0.479532	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	Silent	SNP	ENST00000401878.3	37	CCDS5941.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	5.306	0.241868	0.10077	0.001884	0.005915	ENSG00000184863	ENST00000392761	.	.	.	5.13	-10.3	0.00346	.	.	.	.	.	T	0.16300	0.0392	.	.	.	0.27325	N	0.95695	.	.	.	.	.	.	T	0.10291	-1.0636	4	.	.	.	.	6.4841	0.22079	0.188:0.5415:0.0882:0.1823	.	.	.	.	L	415	.	.	P	+	2	0	RBM33	155225361	0.000000	0.05858	0.000000	0.03702	0.585000	0.36419	-3.524000	0.00442	-2.774000	0.00363	-0.518000	0.04402	CCG	C|0.998;T|0.002	0.002	strong		0.711	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408	
GPR112	139378	hgsc.bcm.edu	37	X	135429503	135429503	+	Missense_Mutation	SNP	C	C	A	rs4829830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135429503C>A	ENST00000394143.1	+	6	3929	c.3638C>A	c.(3637-3639)aCc>aAc	p.T1213N	GPR112_ENST00000370652.1_Missense_Mutation_p.T1213N|GPR112_ENST00000412101.1_Missense_Mutation_p.T1008N|GPR112_ENST00000287534.4_Missense_Mutation_p.T1150N|GPR112_ENST00000394141.1_Missense_Mutation_p.T1008N	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1213			T -> N (in dbSNP:rs4829830).		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GTTGATGAGACCACACCCTCA	0.473													c|||	1760	0.466225	0.4289	0.3573	3775	,	,		15390	0.246		0.3797	False		,,,				2504	0.3221				p.T1213N		Atlas-SNP	.											.	GPR112	459	.	0			c.C3638A						PASS	.		ASN/THR	2122,1713		502,805,313,325,258	214.0	183.0	193.0		3638	-1.5	0.0	X	dbSNP_111	193	3220,3508		566,1176,912,686,960	yes	missense	GPR112	NM_153834.3	65	1068,1981,1225,1011,1218	AA,AC,A,CC,C		47.8597,44.6675,49.4272	benign	1213/3081	135429503	5342,5221	2203	4300	6503	SO:0001583	missense	139378	exon6			ATGAGACCACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.3638C>A	X.37:g.135429503C>A	ENSP00000377699:p.Thr1213Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	106	103	0.971698	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	746	0.4496684749849307	138	0.372972972972973	83	0.2902097902097902	99	0.21063829787234042	190	0.3242320819112628	c	6.546	0.469051	0.12461	0.553325	0.478597	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.33865	1.43;1.43;1.39;1.52;1.39	2.98	-1.46	0.08800	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.15930	0.015;0.001;0.001	B;B;B	0.14578	0.011;0.003;0.001	T	0.46190	-0.9209	8	0.37606	T	0.19	.	0.3457	0.00341	0.2044:0.3206:0.1987:0.2763	rs4829830;rs58174019;rs4829830	1150;1008;1213	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	N	1213;1213;1008;1150;1008	ENSP00000377699:T1213N;ENSP00000359686:T1213N;ENSP00000416526:T1008N;ENSP00000287534:T1150N;ENSP00000377697:T1008N	ENSP00000287534:T1150N	T	+	2	0	GPR112	135257169	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.312000	0.08113	-0.347000	0.08299	-0.313000	0.08912	ACC	0|0.015;A|0.479	0.479	strong		0.473	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
MMP27	64066	hgsc.bcm.edu	37	11	102576382	102576382	+	Missense_Mutation	SNP	G	G	A	rs12099177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102576382G>A	ENST00000260229.4	-	1	155	c.64C>T	c.(64-66)Cgg>Tgg	p.R22W		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	22			R -> W (in dbSNP:rs12099177).		collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R22W(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	TCCGTCATCCGGACTAAGGGA	0.363													G|||	844	0.16853	0.1687	0.1455	5008	,	,		19020	0.2996		0.0666	False		,,,				2504	0.1544				p.R22W		Atlas-SNP	.											MMP27,NS,carcinoma,0,1	MMP27	84	1	1	Substitution - Missense(1)	stomach(1)	c.C64T						scavenged	.	G	TRP/ARG	741,3665	301.0+/-286.6	67,607,1529	99.0	106.0	104.0		64	0.5	0.0	11	dbSNP_120	104	550,8048	150.4+/-205.3	15,520,3764	yes	missense	MMP27	NM_022122.2	101	82,1127,5293	AA,AG,GG		6.3968,16.818,9.9277	possibly-damaging	22/514	102576382	1291,11713	2203	4299	6502	SO:0001583	missense	64066	exon1			TCATCCGGACTAA	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.64C>T	11.37:g.102576382G>A	ENSP00000260229:p.Arg22Trp	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	193	91	0.471503	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	340	0.15567765567765568	93	0.18902439024390244	43	0.11878453038674033	161	0.28146853146853146	43	0.05672823218997362	G	10.72	1.429129	0.25726	0.16818	0.063968	ENSG00000137675	ENST00000260229	T	0.36520	1.25	4.98	0.533	0.17121	.	1.468070	0.05201	U	0.505000	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.21606	0.058	B	0.20384	0.029	T	0.33548	-0.9864	9	0.66056	D	0.02	.	3.9186	0.09234	0.0821:0.1352:0.4882:0.2945	rs12099177;rs60819172;rs12099177	22	Q9H306	MMP27_HUMAN	W	22	ENSP00000260229:R22W	ENSP00000260229:R22W	R	-	1	2	MMP27	102081592	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.091000	0.30915	0.330000	0.23485	0.655000	0.94253	CGG	G|0.882;A|0.118	0.118	strong		0.363	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
SHC2	25759	hgsc.bcm.edu	37	19	425182	425182	+	Silent	SNP	G	G	A	rs61735134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:425182G>A	ENST00000264554.6	-	10	1223	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	408	CH1.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCTCCTCGTGGTCCGGGGGGC	0.682													G|||	165	0.0329473	0.0166	0.0548	5008	,	,		13644	0.001		0.0885	False		,,,				2504	0.0153				p.D408D		Atlas-SNP	.											.	SHC2	47	.	0			c.C1224T						PASS	.	G		82,3680		1,80,1800	26.0	31.0	29.0		1224	4.2	0.1	19	dbSNP_129	29	688,7496		30,628,3434	no	coding-synonymous	SHC2	NM_012435.2		31,708,5234	AA,AG,GG		8.4066,2.1797,6.4457		408/583	425182	770,11176	1881	4092	5973	SO:0001819	synonymous_variant	25759	exon10			CTCGTGGTCCGGG	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"""SH2 domain containing"""	29869	protein-coding gene	gene with protein product	"""neuronal Shc adaptor homolog"""	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1224C>T	19.37:g.425182G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	126	62	0.492063	NM_012435	O60230|Q9NPL5|Q9UCX4	Silent	SNP	ENST00000264554.6	37	CCDS45891.1																																																																																			G|0.950;A|0.050	0.050	strong		0.682	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3		
TTC5	91875	hgsc.bcm.edu	37	14	20764585	20764585	+	Silent	SNP	A	A	C	rs1953552	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20764585A>C	ENST00000258821.3	-	6	716	c.660T>G	c.(658-660)gcT>gcG	p.A220A		NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	220					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)	p.A220A(1)		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)		GATTGCTAGAAGCTTTTCTGT	0.438													A|||	2009	0.401158	0.2322	0.5274	5008	,	,		18439	0.4772		0.4821	False		,,,				2504	0.3783				p.A220A		Atlas-SNP	.											TTC5,NS,carcinoma,0,1	TTC5	34	1	1	Substitution - coding silent(1)	prostate(1)	c.T660G						PASS	.	A		1164,3242	410.9+/-335.5	146,872,1185	204.0	196.0	199.0		660	-1.6	1.0	14	dbSNP_92	199	4320,4280	579.1+/-390.8	1086,2148,1066	no	coding-synonymous	TTC5	NM_138376.2		1232,3020,2251	CC,CA,AA		49.7674,26.4185,42.1652		220/441	20764585	5484,7522	2203	4300	6503	SO:0001819	synonymous_variant	91875	exon6			GCTAGAAGCTTTT	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.660T>G	14.37:g.20764585A>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	115	35	0.304348	NM_138376	A8MQ18|Q96HF9	Silent	SNP	ENST00000258821.3	37	CCDS9546.1	981	0.4491758241758242	123	0.25	198	0.5469613259668509	297	0.5192307692307693	363	0.4788918205804749	A	11.22	1.573249	0.28092	0.264185	0.502326	ENSG00000136319	ENST00000423949	.	.	.	5.1	-1.63	0.08345	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45848	-0.9233	3	.	.	.	.	1.3033	0.02083	0.2526:0.118:0.1541:0.4753	rs1953552;rs11550386;rs1953552	.	.	.	V	165	.	.	F	-	1	0	TTC5	19834425	0.961000	0.32948	0.992000	0.48379	0.996000	0.88848	-0.043000	0.12043	-0.349000	0.08274	0.533000	0.62120	TTC	A|0.575;C|0.425	0.425	strong		0.438	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376	
PSCA	8000	hgsc.bcm.edu	37	8	143763547	143763547	+	Silent	SNP	C	C	A	rs1045531	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143763547C>A	ENST00000301258.4	+	3	425	c.342C>A	c.(340-342)ctC>ctA	p.L114L		NM_005672.4	NP_005663.2	O43653	PSCA_HUMAN	prostate stem cell antigen	123						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)	2	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CCGGCCAGCTCTAGGCTCTGG	0.706													A|||	2013	0.401957	0.354	0.5072	5008	,	,		13713	0.3423		0.4473	False		,,,				2504	0.407				p.L114L		Atlas-SNP	.											.	PSCA	9	.	0			c.C342A						PASS	.	A		1450,2534		293,864,835	13.0	15.0	14.0		342	1.4	0.3	8	dbSNP_86	14	3740,4612		857,2026,1293	no	coding-synonymous	PSCA	NM_005672.4		1150,2890,2128	AA,AC,CC		44.7797,36.3956,42.072		114/115	143763547	5190,7146	1992	4176	6168	SO:0001819	synonymous_variant	8000	exon3			CCAGCTCTAGGCT	AF043498	CCDS47925.1, CCDS47925.2	8q24.2	2004-02-03				ENSG00000167653			9500	protein-coding gene	gene with protein product		602470				9465086	Standard	NM_005672		Approved		uc022bcd.1	O43653		ENST00000301258.4:c.342C>A	8.37:g.143763547C>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_005672	Q6UW92	Silent	SNP	ENST00000301258.4	37	CCDS47925.2																																																																																			C|0.584;A|0.416	0.416	strong		0.706	PSCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367112.2	NM_005672	
CFAP46	54777	hgsc.bcm.edu	37	10	134694391	134694391	+	Missense_Mutation	SNP	A	A	G	rs145022957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134694391A>G	ENST00000368586.5	-	28	3873	c.3773T>C	c.(3772-3774)gTc>gCc	p.V1258A	TTC40_ENST00000368582.2_Missense_Mutation_p.V1258A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TGGCTCAGGGACATCGCCGGG	0.677													a|||	47	0.00938498	0.0	0.0086	5008	,	,		15270	0.002		0.0129	False		,,,				2504	0.0266				p.V1258A		Atlas-SNP	.											.	TTC40	100	.	0			c.T3773C						PASS	.																																			SO:0001583	missense	54777	exon28			TCAGGGACATCGC																												ENST00000368586.5:c.3773T>C	10.37:g.134694391A>G	ENSP00000357575:p.Val1258Ala	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	30	14	0.466667	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	a	0.006	-2.077388	0.00375	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.40756	2.99;1.02	2.26	-1.98	0.07480	.	.	.	.	.	T	0.09247	0.0228	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25398	-1.0133	6	0.02654	T	1	.	4.0251	0.09683	0.3732:0.3518:0.275:0.0	.	.	.	.	A	1258	ENSP00000357575:V1258A;ENSP00000357571:V1258A	ENSP00000357571:V1258A	V	-	2	0	C10orf93	134544381	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.712000	0.05013	-0.573000	0.05998	-1.948000	0.00487	GTC	A|0.993;G|0.007	0.007	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
NPVF	64111	hgsc.bcm.edu	37	7	25266400	25266400	+	Silent	SNP	G	G	A	rs2717851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:25266400G>A	ENST00000222674.2	-	2	430	c.384C>T	c.(382-384)ccC>ccT	p.P128P		NM_022150.3	NP_071433	Q9HCQ7	NPVF_HUMAN	neuropeptide VF precursor	128					negative regulation of gonadotropin secretion (GO:0032277)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						CAAACCTTTGGGGCAGGTTAG	0.473													G|||	1394	0.278355	0.3722	0.3184	5008	,	,		19591	0.1468		0.2773	False		,,,				2504	0.2597				p.P128P		Atlas-SNP	.											.	NPVF	36	.	0			c.C384T						PASS	.	G		1581,2825	493.6+/-362.7	276,1029,898	214.0	201.0	206.0		384	1.0	1.0	7	dbSNP_100	206	2424,6176	401.8+/-347.3	341,1742,2217	no	coding-synonymous	NPVF	NM_022150.3		617,2771,3115	AA,AG,GG		28.186,35.8829,30.7935		128/197	25266400	4005,9001	2203	4300	6503	SO:0001819	synonymous_variant	64111	exon2			CCTTTGGGGCAGG	AB040290	CCDS5395.1	7p21-p15	2013-02-28	2006-10-06	2006-10-06	ENSG00000105954	ENSG00000105954		"""Endogenous ligands"""	13782	protein-coding gene	gene with protein product	"""RFamide-related peptide precursor"", ""FMRFamide-related peptide precursor"""		"""chromosome 7 open reading frame 9"""	C7orf9		11951088, 11173868	Standard	NM_022150		Approved	RFRP	uc003sxo.3	Q9HCQ7	OTTHUMG00000128509	ENST00000222674.2:c.384C>T	7.37:g.25266400G>A		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	197	94	0.477157	NM_022150	A4D164|Q7LE27|Q96PI9	Silent	SNP	ENST00000222674.2	37	CCDS5395.1																																																																																			G|0.702;A|0.298	0.298	strong		0.473	NPVF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250315.1	NM_022150	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329854	55329854	+	Missense_Mutation	SNP	G	G	A	rs144994606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55329854G>A	ENST00000391728.4	+	3	188	c.155G>A	c.(154-156)cGt>cAt	p.R52H	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.R52H|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.R52H|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.R52H|KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.R52H	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	52	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TGTCACTATCGTCATAGGTTT	0.517													g|||	617	0.123203	0.0915	0.1657	5008	,	,		13130	0.001		0.2247	False		,,,				2504	0.1575				p.R52H		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.G155A						PASS	.	G	HIS/ARG	523,3827		81,361,1733	98.0	101.0	100.0		155	-2.3	0.0	19	dbSNP_134	100	2261,5995		614,1033,2481	no	missense	KIR3DL1	NM_013289.2	29	695,1394,4214	AA,AG,GG		27.3861,12.023,22.0847		52/445	55329854	2784,9822	2175	4128	6303	SO:0001583	missense	3811	exon3			ACTATCGTCATAG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.155G>A	19.37:g.55329854G>A	ENSP00000375608:p.Arg52His	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	34	19	0.558824	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	318	0.14560439560439561	40	0.08130081300813008	68	0.1878453038674033	0	0.0	210	0.2770448548812665	G	1.011	-0.687880	0.03328	0.12023	0.273861	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71	1.15	-2.29	0.06805	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.26042	0.785	0.80722	P	0.0	B;B	0.11235	0.002;0.004	B;B	0.10450	0.003;0.005	T	0.45338	-0.9268	8	0.42905	T	0.14	.	5.2208	0.15368	0.4452:0.0:0.5548:0.0	.	52;52	F6QF33;P43629	.;KI3L1_HUMAN	H	52;52;52;30;52;52	ENSP00000384528:R52H;ENSP00000443350:R52H;ENSP00000442355:R52H;ENSP00000375608:R52H;ENSP00000326868:R52H	ENSP00000326868:R52H	R	+	2	0	KIR3DL1	60021666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.812000	0.04496	-0.923000	0.03785	-1.109000	0.02080	CGT	G|0.854;A|0.146	0.146	strong		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
USP6NL	9712	hgsc.bcm.edu	37	10	11504752	11504752	+	Silent	SNP	T	T	C	rs12570211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:11504752T>C	ENST00000609104.1	-	15	2569	c.2175A>G	c.(2173-2175)ccA>ccG	p.P725P	USP6NL_ENST00000379237.2_Silent_p.P748P|USP6NL_ENST00000277575.5_Silent_p.P742P	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	725					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						AATCCACTGGTGGAATGATCA	0.478													t|||	498	0.0994409	0.0234	0.062	5008	,	,		21454	0.1319		0.0656	False		,,,				2504	0.2301				p.P742P		Atlas-SNP	.											.	USP6NL	57	.	0			c.A2226G						PASS	.	T	,	95,3711		1,93,1809	90.0	89.0	89.0		2226,2175	-2.3	1.0	10	dbSNP_120	89	516,7744		18,480,3632	no	coding-synonymous,coding-synonymous	USP6NL	NM_001080491.2,NM_014688.2	,	19,573,5441	CC,CT,TT		6.247,2.4961,5.0638	,	742/846,725/829	11504752	611,11455	1903	4130	6033	SO:0001819	synonymous_variant	9712	exon14			CACTGGTGGAATG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.2175A>G	10.37:g.11504752T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Silent	SNP	ENST00000609104.1	37	CCDS53492.1																																																																																			T|0.917;C|0.083	0.083	strong		0.478	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
SH2D4A	63898	hgsc.bcm.edu	37	8	19190491	19190491	+	Silent	SNP	A	A	G	rs1574288	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:19190491A>G	ENST00000265807.3	+	3	618	c.207A>G	c.(205-207)aaA>aaG	p.K69K	SH2D4A_ENST00000518040.1_Silent_p.K24K|SH2D4A_ENST00000519207.1_Silent_p.K69K	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	69					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TTCATTGGAAACTTGGAGCTG	0.398													G|||	1117	0.223043	0.3858	0.1527	5008	,	,		15903	0.1438		0.2266	False		,,,				2504	0.1309				p.K69K		Atlas-SNP	.											.	SH2D4A	49	.	0			c.A207G						PASS	.	G	,,	1590,2816	665.4+/-401.5	301,988,914	168.0	160.0	163.0		207,72,207	-3.0	1.0	8	dbSNP_88	163	2056,6544	719.1+/-406.2	252,1552,2496	no	coding-synonymous,coding-synonymous,coding-synonymous	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	,,	553,2540,3410	GG,GA,AA		23.907,36.0872,28.0332	,,	69/455,24/410,69/455	19190491	3646,9360	2203	4300	6503	SO:0001819	synonymous_variant	63898	exon3			TTGGAAACTTGGA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.207A>G	8.37:g.19190491A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Silent	SNP	ENST00000265807.3	37	CCDS6009.1																																																																																			A|0.739;G|0.261	0.261	strong		0.398	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
BAZ1A	11177	hgsc.bcm.edu	37	14	35331288	35331288	+	Silent	SNP	G	G	A	rs17592803	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:35331288G>A	ENST00000382422.2	-	2	681	c.354C>T	c.(352-354)gtC>gtT	p.V118V	BAZ1A_ENST00000553853.1_5'UTR|BAZ1A_ENST00000358716.4_Silent_p.V118V|BAZ1A_ENST00000360310.1_Silent_p.V118V			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	118	Required for association with the CHRAC1/POLE3 complex.|Required for interaction with NCOR1.|WAC. {ECO:0000255|PROSITE- ProRule:PRU00475}.				chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		CAGTTTCTTCGACAAAATATC	0.343													G|||	182	0.0363419	0.0023	0.0418	5008	,	,		20464	0.0		0.0775	False		,,,				2504	0.0736				p.V118V		Atlas-SNP	.											.	BAZ1A	128	.	0			c.C354T						PASS	.	G	,	94,4312	75.2+/-113.4	2,90,2111	140.0	135.0	136.0		354,354	3.0	1.0	14	dbSNP_123	136	819,7781	190.3+/-236.8	38,743,3519	no	coding-synonymous,coding-synonymous	BAZ1A	NM_013448.2,NM_182648.1	,	40,833,5630	AA,AG,GG		9.5233,2.1335,7.0198	,	118/1557,118/1525	35331288	913,12093	2203	4300	6503	SO:0001819	synonymous_variant	11177	exon3			TTCTTCGACAAAA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.354C>T	14.37:g.35331288G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	162	70	0.432099	NM_182648	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			G|0.940;A|0.060	0.060	strong		0.343	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
PARP4	143	hgsc.bcm.edu	37	13	25058867	25058867	+	Missense_Mutation	SNP	C	C	T	rs143070451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25058867C>T	ENST00000381989.3	-	12	1477	c.1372G>A	c.(1372-1374)Gta>Ata	p.V458I		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	458	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTTCCACTACTTTGGGTAAA	0.453																																					p.V458I		Atlas-SNP	.											PARP4,NS,carcinoma,0,5	PARP4	142	5	0			c.G1372A						scavenged	.						136.0	138.0	137.0					13																	25058867		2203	4297	6500	SO:0001583	missense	143	exon12			CCACTACTTTGGG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1372G>A	13.37:g.25058867C>T	ENSP00000371419:p.Val458Ile	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	129	22	0.170543	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	47	0.02152014652014652	23	0.046747967479674794	2	0.0055248618784530384	7	0.012237762237762238	15	0.01978891820580475	C	16.65	3.183039	0.57800	.	.	ENSG00000102699	ENST00000381989	T	0.13901	2.55	4.35	3.4	0.38934	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.162995	0.39985	N	0.001218	T	0.01523	0.0049	L	0.41906	1.305	0.26728	N	0.970657	P	0.37708	0.606	B	0.39904	0.313	T	0.12528	-1.0544	10	0.42905	T	0.14	-16.8693	5.0719	0.14611	0.0:0.7642:0.0:0.2358	.	458	Q9UKK3	PARP4_HUMAN	I	458	ENSP00000371419:V458I	ENSP00000371419:V458I	V	-	1	0	PARP4	23956867	0.210000	0.23517	0.999000	0.59377	0.973000	0.67179	0.932000	0.28884	2.229000	0.72834	0.650000	0.86243	GTA	.	.	weak		0.453	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
PML	5371	hgsc.bcm.edu	37	15	74328206	74328206	+	Intron	SNP	G	G	C	rs743582	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:74328206G>C	ENST00000268058.3	+	7	1806				PML_ENST00000565898.1_Intron|PML_ENST00000569965.1_Intron|PML_ENST00000564428.1_Intron|PML_ENST00000354026.6_Missense_Mutation_p.A754P|PML_ENST00000268059.6_Missense_Mutation_p.A802P|PML_ENST00000359928.4_Intron|PML_ENST00000563500.1_3'UTR|PML_ENST00000395135.3_Intron|PML_ENST00000436891.3_3'UTR|PML_ENST00000395132.2_Intron|PML_ENST00000435786.2_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						GCCTCTGGAAGCCTCTCCAAT	0.622			T	"""RARA, PAX5"""	"""APL, ALL"""								G|||	785	0.156749	0.1127	0.0591	5008	,	,		14618	0.2371		0.0964	False		,,,				2504	0.2648				p.A802P		Atlas-SNP	.		Dom	yes		15	15q22	5371	promyelocytic leukemia		L	.	PML	169	.	0			c.G2404C						PASS	.	G	,,PRO/ALA,,,,,,PRO/ALA	441,3955	196.0+/-220.5	18,405,1775	82.0	101.0	95.0		,,2404,,,,,,2260	1.2	0.0	15	dbSNP_86	95	815,7779	185.0+/-232.9	37,741,3519	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	,,27,,,,,,27	55,1146,5294	CC,CG,GG		9.4834,10.0318,9.669	,,,,,,,,	,,802/830,,,,,,754/782	74328206	1256,11734	2198	4297	6495	SO:0001627	intron_variant	5371	exon8			CTGGAAGCCTCTC	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+1335G>C	15.37:g.74328206G>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	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	258	0.11813186813186813	47	0.09552845528455285	24	0.06629834254143646	120	0.2097902097902098	67	0.08839050131926121	G	9.783	1.175788	0.21704	0.100318	0.094834	ENSG00000140464	ENST00000268059;ENST00000354026	.	.	.	3.17	1.22	0.21188	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.11235	0.004;0.004	B;B	0.10450	0.005;0.005	T	0.19192	-1.0313	7	0.54805	T	0.06	.	4.5986	0.12341	0.1275:0.2266:0.6459:0.0	rs743582;rs743582	754;802	P29590-13;P29590-8	.;.	P	802;754	.	ENSP00000268059:A802P	A	+	1	0	PML	72115259	0.000000	0.05858	0.000000	0.03702	0.146000	0.21551	0.631000	0.24568	0.355000	0.24131	0.456000	0.33151	GCC	G|0.888;C|0.112	0.112	strong		0.622	PML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269021.3	NM_002675	
MICA	100507436	hgsc.bcm.edu	37	6	31378510	31378510	+	Silent	SNP	G	G	A	rs1063632	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31378510G>A	ENST00000449934.2	+	2	315	c.261G>A	c.(259-261)agG>agA	p.R87R	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GAGAGACCAGGGACTTGACAG	0.562													g|||	323	0.0644968	0.0825	0.0533	5008	,	,		20627	0.0665		0.0736	False		,,,				2504	0.0368				p.R87R		Atlas-SNP	.											.	MICA	21	.	0			c.G261A						PASS	.	G		74,1310		4,66,622	86.0	93.0	91.0		261	0.2	0.0	6	dbSNP_86	91	232,2950		9,214,1368	yes	coding-synonymous	MICA	NM_001177519.1		13,280,1990	AA,AG,GG		7.291,5.3468,6.7017		87/333	31378510	306,4260	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon2			GACCAGGGACTTG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.261G>A	6.37:g.31378510G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1	148	0.06776556776556776	35	0.07113821138211382	24	0.06629834254143646	40	0.06993006993006994	49	0.06464379947229551	N	5.261	0.233652	0.09969	0.053468	0.07291	ENSG00000204520	ENST00000376222	.	.	.	2.36	0.17	0.15021	.	.	.	.	.	T	0.10895	0.0266	.	.	.	0.80722	P	0.0	P	0.50156	0.932	B	0.43536	0.423	T	0.08659	-1.0711	5	.	.	.	.	2.3117	0.04188	0.1866:0.0:0.5125:0.3009	rs1063632;rs3204663;rs16899594;rs17179745;rs17200193;rs17851451;rs17881564;rs1063632	7	Q5SS58	.	R	7	.	.	G	+	1	0	MICA	31486489	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.302000	0.08221	0.366000	0.24427	0.306000	0.20318	GGA	G|0.927;A|0.073	0.073	strong		0.562	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751301	19751301	+	Silent	SNP	C	C	T	rs140548354		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19751301C>T	ENST00000400113.3	-	4	926	c.822G>A	c.(820-822)ccG>ccA	p.P274P		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	274					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		CTGAGATGACCGGGGCGTAGG	0.607																																					p.P274P		Atlas-SNP	.											TUBA3C,bladder,carcinoma,-2,1	TUBA3C	166	1	0			c.G822A						scavenged	.						123.0	114.0	117.0					13																	19751301		2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			GATGACCGGGGCG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.822G>A	13.37:g.19751301C>T		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	226	10	0.0442478	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			C|0.999;T|0.001	0.001	weak		0.607	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
DNAJB13	374407	hgsc.bcm.edu	37	11	73670645	73670645	+	Silent	SNP	T	T	C	rs653263	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:73670645T>C	ENST00000339764.1	+	3	1030	c.279T>C	c.(277-279)caT>caC	p.H93H		NM_153614.2	NP_705842.2	P59910	DJB13_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 13	93					protein folding (GO:0006457)					large_intestine(3)|lung(2)	5	Breast(11;7.42e-05)					ACGTCTTCCATGGCAAACCTG	0.507													t|||	3010	0.601038	0.8971	0.5663	5008	,	,		15368	0.4534		0.4751	False		,,,				2504	0.5072				p.H93H		Atlas-SNP	.											.	DNAJB13	28	.	0			c.T279C						PASS	.			3532,868	744.3+/-411.5	1428,676,96	113.0	97.0	102.0		279	-8.4	0.2	11	dbSNP_83	102	3949,4637	549.7+/-385.6	918,2113,1262	no	coding-synonymous	DNAJB13	NM_153614.2		2346,2789,1358	CC,CT,TT		45.9935,19.7273,42.3918		93/317	73670645	7481,5505	2200	4293	6493	SO:0001819	synonymous_variant	374407	exon3			CTTCCATGGCAAA	AF516185	CCDS8227.1	11q13.3	2011-09-02	2010-04-21		ENSG00000187726	ENSG00000187726		"""Heat shock proteins / DNAJ (HSP40)"""	30718	protein-coding gene	gene with protein product	"""radial spoke 16 homolog A (Chlamydomonas)"""	610263	"""DnaJ (Hsp40) related, subfamily B, member 13"""				Standard	NM_153614		Approved	TSARG6, RSPH16A	uc001ouo.3	P59910	OTTHUMG00000168093	ENST00000339764.1:c.279T>C	11.37:g.73670645T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_153614	B3LEP4|Q8IZW5	Silent	SNP	ENST00000339764.1	37	CCDS8227.1																																																																																			T|0.418;C|0.582	0.582	strong		0.507	DNAJB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398100.1	NM_153614	
KCNQ2	3785	hgsc.bcm.edu	37	20	62046277	62046277	+	Missense_Mutation	SNP	C	C	T	rs540103798		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62046277C>T	ENST00000359125.2	-	13	1678	c.1504G>A	c.(1504-1506)Gcg>Acg	p.A502T	KCNQ2_ENST00000370224.1_Missense_Mutation_p.A474T|KCNQ2_ENST00000357249.2_Missense_Mutation_p.A484T|KCNQ2_ENST00000344462.4_Missense_Mutation_p.A472T|KCNQ2_ENST00000360480.3_Missense_Mutation_p.A474T|KCNQ2_ENST00000354587.3_Missense_Mutation_p.A474T|KCNQ2_ENST00000359689.1_Missense_Mutation_p.A502T	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	502					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TGCCGTGACGCGGCACCCTTG	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		10795	0.0		0.0	False		,,,				2504	0.001				p.A502T		Atlas-SNP	.											KCNQ2,colon,carcinoma,+2,1	KCNQ2	201	1	0			c.G1504A						scavenged	.						70.0	79.0	76.0					20																	62046277		2203	4300	6503	SO:0001583	missense	3785	exon13			GTGACGCGGCACC	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1504G>A	20.37:g.62046277C>T	ENSP00000352035:p.Ala502Thr	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	2	0.0212766	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Missense_Mutation	SNP	ENST00000359125.2	37	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	C	9.994	1.231584	0.22626	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222	D;D;D;D;D;D;D;D;D;D	0.99598	-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26;-6.26	5.15	5.15	0.70609	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.213493	0.39341	N	0.001389	D	0.97939	0.9322	N	0.25485	0.75	0.32363	N	0.556854	B;B;B;B	0.25904	0.112;0.112;0.112;0.137	B;B;B;B	0.22753	0.016;0.016;0.016;0.041	D	0.99970	1.1964	10	0.36615	T	0.2	0.9468	14.3393	0.66614	0.149:0.851:0.0:0.0	.	474;484;472;502	O43526-3;O43526-2;O43526-4;O43526	.;.;.;KCNQ2_HUMAN	T	484;502;472;474;502;472;474;462;474;474	ENSP00000349789:A484T;ENSP00000352035:A502T;ENSP00000359246:A472T;ENSP00000346601:A474T;ENSP00000352718:A502T;ENSP00000399612:A472T;ENSP00000353668:A474T;ENSP00000339611:A462T;ENSP00000359244:A474T;ENSP00000359242:A474T	ENSP00000339611:A462T	A	-	1	0	KCNQ2	61516721	0.169000	0.23002	0.455000	0.27031	0.180000	0.23129	0.736000	0.26130	2.390000	0.81377	0.478000	0.44815	GCG	.	.	none		0.672	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
ZP3	7784	hgsc.bcm.edu	37	7	76069629	76069629	+	Silent	SNP	G	G	A	rs73363163		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:76069629G>A	ENST00000394857.3	+	6	952	c.894G>A	c.(892-894)aaG>aaA	p.K298K	ZP3_ENST00000336517.4_Silent_p.K247K|ZP3_ENST00000416245.1_Silent_p.K122K|ZP3_ENST00000467555.1_3'UTR	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	298	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						AACTCAACAAGGCCTGTTCCT	0.522																																					p.K298K		Atlas-SNP	.											.	ZP3	32	.	0			c.G894A						PASS	.	A	,	291,4111		0,291,1910	89.0	82.0	84.0		894,741	-0.7	1.0	7	dbSNP_131	84	1567,7031		10,1547,2742	no	coding-synonymous,coding-synonymous	ZP3	NM_001110354.1,NM_007155.5	,	10,1838,4652	AA,AG,GG		18.2252,6.6106,14.2923	,	298/425,247/374	76069629	1858,11142	2201	4299	6500	SO:0001819	synonymous_variant	7784	exon6			CAACAAGGCCTGT	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.894G>A	7.37:g.76069629G>A		Somatic	504	0	0		WXS	Illumina HiSeq	Phase_I	1165	378	0.324464	NM_001110354	Q06633|Q29RW0	Silent	SNP	ENST00000394857.3	37	CCDS47618.1	399	0.18269230769230768	83	0.16869918699186992	65	0.17955801104972377	89	0.1555944055944056	162	0.21372031662269128	A	1.322	-0.599172	0.03744	0.066106	0.182252	ENSG00000188372	ENST00000394860	.	.	.	4.33	-0.658	0.11428	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01021	-1.1478	4	.	.	.	-23.2076	10.8429	0.46726	0.3399:0.0:0.6601:0.0	.	.	.	.	K	120	.	.	R	+	2	0	ZP3	75907565	1.000000	0.71417	0.968000	0.41197	0.203000	0.24098	0.911000	0.28584	-0.255000	0.09486	-0.361000	0.07541	AGG	.	.	weak		0.522	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
NOTCH3	4854	hgsc.bcm.edu	37	19	15299048	15299048	+	Missense_Mutation	SNP	G	G	A	rs114207045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15299048G>A	ENST00000263388.2	-	9	1565	c.1490C>T	c.(1489-1491)tCg>tTg	p.S497L		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	497	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.S497L(1)		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)			GTCCTCACCCGAGGGGCAGGT	0.562													G|||	37	0.00738818	0.0106	0.0086	5008	,	,		15109	0.001		0.006	False		,,,				2504	0.0102				p.S497L		Atlas-SNP	.											NOTCH3,rectum,carcinoma,0,1	NOTCH3	340	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1490T						PASS	.	G	LEU/SER	46,4360		0,46,2157	27.0	26.0	26.0		1490	5.0	1.0	19	dbSNP_132	26	52,8544		0,52,4246	yes	missense	NOTCH3	NM_000435.2	145	0,98,6403	AA,AG,GG		0.6049,1.044,0.7537	benign	497/2322	15299048	98,12904	2203	4298	6501	SO:0001583	missense	4854	exon9			TCACCCGAGGGGC	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.1490C>T	19.37:g.15299048G>A	ENSP00000263388:p.Ser497Leu	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	47	16	0.340426	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	15	0.006868131868131868	4	0.008130081300813009	7	0.019337016574585635	0	0.0	4	0.005277044854881266	g	13.27	2.185760	0.38609	0.01044	0.006049	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.86694	-2.16	5.04	5.04	0.67666	EGF (1);EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.27705	N	0.018199	T	0.66694	0.2815	N	0.16708	0.43	0.41468	D	0.988085	B;B	0.22146	0.031;0.065	B;B	0.21708	0.02;0.036	T	0.70353	-0.4895	10	0.26408	T	0.33	.	17.1812	0.86855	0.0:0.0:1.0:0.0	.	500;497	Q59FL3;Q9UM47	.;NOTC3_HUMAN	L	497;499	ENSP00000263388:S497L	ENSP00000263388:S497L	S	-	2	0	NOTCH3	15160048	0.788000	0.28762	0.965000	0.40720	0.908000	0.53690	4.305000	0.59110	2.347000	0.79759	0.556000	0.70494	TCG	G|0.991;A|0.009	0.009	strong		0.562	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
MOCOS	55034	hgsc.bcm.edu	37	18	33828916	33828916	+	Silent	SNP	A	A	G	rs55701019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:33828916A>G	ENST00000261326.5	+	10	2013	c.1992A>G	c.(1990-1992)gaA>gaG	p.E664E		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CTCTTGAGGAAAATAGTGAAC	0.408													A|||	34	0.00678914	0.0219	0.0058	5008	,	,		20756	0.0		0.001	False		,,,				2504	0.0				p.E664E		Atlas-SNP	.											.	MOCOS	84	.	0			c.A1992G						PASS	.	A		63,4343	59.3+/-96.0	0,63,2140	98.0	94.0	95.0		1992	-1.8	0.1	18	dbSNP_129	95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MOCOS	NM_017947.2		0,65,6438	GG,GA,AA		0.0233,1.4299,0.4998		664/889	33828916	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	55034	exon10			TGAGGAAAATAGT	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.1992A>G	18.37:g.33828916A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_017947		Silent	SNP	ENST00000261326.5	37	CCDS11919.1																																																																																			A|0.995;G|0.005	0.005	strong		0.408	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
ZMYM5	9205	hgsc.bcm.edu	37	13	20413021	20413021	+	Missense_Mutation	SNP	T	T	C	rs41292167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:20413021T>C	ENST00000337963.4	-	5	955	c.691A>G	c.(691-693)Aca>Gca	p.T231A	RP11-61K9.2_ENST00000422148.2_RNA|ZMYM5_ENST00000382907.4_Intron|ZMYM5_ENST00000382905.4_Missense_Mutation_p.T231A	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	231			T -> A (in dbSNP:rs41292167).			nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		TGTTGGGCTGTAGGCTGGAAA	0.438													T|||	487	0.0972444	0.1687	0.0735	5008	,	,		18398	0.0813		0.0924	False		,,,				2504	0.0389				p.T231A		Atlas-SNP	.											.	ZMYM5	73	.	0			c.A691G						PASS	.	T	,ALA/THR,ALA/THR	702,3704	291.3+/-281.4	61,580,1562	204.0	203.0	203.0		,691,691	-0.3	0.2	13	dbSNP_127	203	591,8009	157.6+/-211.2	16,559,3725	yes	intron,missense,missense	ZMYM5	NM_001039649.2,NM_001039650.2,NM_001142684.1	,58,58	77,1139,5287	CC,CT,TT		6.8721,15.9328,9.9416	,benign,benign	,231/383,231/670	20413021	1293,11713	2203	4300	6503	SO:0001583	missense	9205	exon5			GGGCTGTAGGCTG	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"""Zinc fingers, MYM type"""	13029	protein-coding gene	gene with protein product			"""zinc finger protein 237"""	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.691A>G	13.37:g.20413021T>C	ENSP00000337034:p.Thr231Ala	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	169	93	0.550296	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		192	0.08791208791208792	70	0.14227642276422764	26	0.0718232044198895	35	0.06118881118881119	61	0.08047493403693931	T	12.66	2.004845	0.35415	0.159328	0.068721	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382905	T;T;T	0.41065	1.01;1.01;1.01	4.67	-0.334	0.12666	.	0.324108	0.34386	N	0.004013	T	0.00073	0.0002	N	0.22421	0.69	0.45791	P	0.0013290000000000246	B;B	0.20780	0.048;0.032	B;B	0.15870	0.013;0.014	T	0.07635	-1.0762	9	0.42905	T	0.14	-1.8158	4.8425	0.13498	0.4731:0.0:0.3778:0.1491	rs41292167;rs56860401	231;231	Q9UJ78;Q9UJ78-1	ZMYM5_HUMAN;.	A	231;221;231	ENSP00000337034:T231A;ENSP00000445779:T221A;ENSP00000372361:T231A	ENSP00000337034:T231A	T	-	1	0	ZMYM5	19311021	1.000000	0.71417	0.159000	0.22649	0.918000	0.54935	0.848000	0.27710	0.073000	0.16731	-0.542000	0.04241	ACA	T|0.903;C|0.097	0.097	strong		0.438	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242	
PTX4	390667	hgsc.bcm.edu	37	16	1536499	1536499	+	Missense_Mutation	SNP	G	G	T	rs2745097	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1536499G>T	ENST00000447419.2	-	3	903	c.878C>A	c.(877-879)gCc>gAc	p.A293D	PTX4_ENST00000440447.2_Missense_Mutation_p.P145T|PTX4_ENST00000293922.1_Missense_Mutation_p.A288D			Q96A99	PTX4_HUMAN	pentraxin 4, long	293	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						GGCTCGCAGGGCAGTGACGAA	0.642													G|||	1399	0.279353	0.5983	0.1744	5008	,	,		17855	0.0665		0.2296	False		,,,				2504	0.1933				p.A288D		Atlas-SNP	.											.	PTX4	46	.	0			c.C863A						PASS	.	G	ASP/ALA	2329,2069	598.7+/-389.1	611,1107,481	62.0	66.0	64.0		863	3.6	0.2	16	dbSNP_100	64	1830,6770	327.1+/-317.7	191,1448,2661	yes	missense	PTX4	NM_001013658.1	126	802,2555,3142	TT,TG,GG		21.2791,47.0441,31.9972	benign	288/474	1536499	4159,8839	2199	4300	6499	SO:0001583	missense	390667	exon3			CGCAGGGCAGTGA		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.878C>A	16.37:g.1536499G>T	ENSP00000445277:p.Ala293Asp	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	67	0.471831	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		570	0.260989010989011	283	0.5752032520325203	67	0.1850828729281768	33	0.057692307692307696	187	0.24670184696569922	G	9.665	1.145245	0.21288	0.529559	0.212791	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06528	3.29;3.29	5.58	3.6	0.41247	.	0.615939	0.16451	N	0.213852	T	0.00012	0.0000	N	0.03029	-0.43	0.44834	P	0.0021569999999999645	B	0.15473	0.013	B	0.15484	0.013	T	0.18840	-1.0324	9	0.45353	T	0.12	.	14.376	0.66879	0.0:0.7622:0.2378:0.0	rs2745097;rs2745097	288	Q96A99-2	.	D	293;288	ENSP00000445277:A293D;ENSP00000293922:A288D	ENSP00000293922:A288D	A	-	2	0	PTX4	1476500	0.001000	0.12720	0.244000	0.24202	0.012000	0.07955	1.124000	0.31320	0.703000	0.31848	0.655000	0.94253	GCC	G|0.692;T|0.308	0.308	strong		0.642	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
FAT2	2196	hgsc.bcm.edu	37	5	150924769	150924769	+	Silent	SNP	G	G	A	rs998076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:150924769G>A	ENST00000261800.5	-	9	5931	c.5919C>T	c.(5917-5919)taC>taT	p.Y1973Y		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1973	Cadherin 17. {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)			CAGCTGCCCAGTAGACATCCT	0.468													A|||	580	0.115815	0.1717	0.0836	5008	,	,		21717	0.1329		0.0924	False		,,,				2504	0.0695				p.Y1973Y		Atlas-SNP	.											.	FAT2	465	.	0			c.C5919T						PASS	.	A		681,3725	746.9+/-411.8	57,567,1579	56.0	59.0	58.0		5919	0.8	0.0	5	dbSNP_86	58	613,7987	788.8+/-407.6	20,573,3707	no	coding-synonymous	FAT2	NM_001447.2		77,1140,5286	AA,AG,GG		7.1279,15.4562,9.9493		1973/4350	150924769	1294,11712	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon9			TGCCCAGTAGACA	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.5919C>T	5.37:g.150924769G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.887;A|0.113	0.113	strong		0.468	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
ACKR2	1238	hgsc.bcm.edu	37	3	42906116	42906116	+	Missense_Mutation	SNP	T	T	C	rs2228467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:42906116T>C	ENST00000422265.1	+	3	297	c.122T>C	c.(121-123)gTg>gCg	p.V41A	RP11-141M3.5_ENST00000471537.1_RNA|ACKR2_ENST00000442925.1_Missense_Mutation_p.V41A|KRBOX1_ENST00000426937.1_Intron|CYP8B1_ENST00000437102.1_Intron|ACKR2_ENST00000273145.2_Missense_Mutation_p.V41A	NM_001296.4	NP_001287.2	O00590	ACKR2_HUMAN	atypical chemokine receptor 2	41			V -> A (in dbSNP:rs2228467).		chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|multicellular organismal development (GO:0007275)|neutrophil activation (GO:0042119)|receptor-mediated endocytosis (GO:0006898)	actin filament (GO:0005884)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-X-C chemokine receptor activity (GO:0016494)|chemokine receptor activity (GO:0004950)|scavenger receptor activity (GO:0005044)										AAGGATGCAGTGGTGTCCTTT	0.507													T|||	95	0.0189696	0.0023	0.0231	5008	,	,		20079	0.001		0.0696	False		,,,				2504	0.0051				p.V41A		Atlas-SNP	.											.	CCBP2	49	.	0			c.T122C						PASS	.	T	ALA/VAL	53,4353	52.9+/-88.7	0,53,2150	172.0	147.0	156.0		122	5.5	0.5	3	dbSNP_98	156	582,8018	155.2+/-209.3	14,554,3732	yes	missense	CCBP2	NM_001296.4	64	14,607,5882	CC,CT,TT		6.7674,1.2029,4.8824	probably-damaging	41/385	42906116	635,12371	2203	4300	6503	SO:0001583	missense	1238	exon3			ATGCAGTGGTGTC	U94888	CCDS2706.1	3p21.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144648	ENSG00000144648		"""GPCR / Class A : Chemokine receptors : Atypical"""	1565	protein-coding gene	gene with protein product		602648	"""chemokine binding protein 2"""	CMKBR9, CCBP2		9364936, 9405404, 16148	Standard	NM_001296		Approved	CCR10, D6, CCR9	uc003cme.3	O00590	OTTHUMG00000133040	ENST00000422265.1:c.122T>C	3.37:g.42906116T>C	ENSP00000416996:p.Val41Ala	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	217	118	0.543779	NM_001296	B2R8Y8|O00537|Q53YA1|Q86UN9|Q96A02	Missense_Mutation	SNP	ENST00000422265.1	37	CCDS2706.1	65	0.02976190476190476	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	52	0.06860158311345646	T	13.25	2.179733	0.38511	0.012029	0.067674	ENSG00000144648	ENST00000442925;ENST00000422265;ENST00000273145	T;T;T	0.37235	1.21;1.21;1.21	5.52	5.52	0.82312	.	0.000000	0.42964	D	0.000640	T	0.02267	0.0070	L	0.28014	0.82	0.25789	N	0.984634	D;P	0.53151	0.958;0.919	P;P	0.44447	0.45;0.45	T	0.01729	-1.1286	9	.	.	.	.	13.0188	0.58773	0.0:0.0:0.0:1.0	rs2228467;rs61511756;rs2228467	41;41	O00590;Q7Z7I1	CCBP2_HUMAN;.	A	41	ENSP00000396150:V41A;ENSP00000416996:V41A;ENSP00000273145:V41A	.	V	+	2	0	CCBP2	42881120	0.985000	0.35326	0.490000	0.27465	0.154000	0.21943	2.284000	0.43478	2.096000	0.63516	0.460000	0.39030	GTG	T|0.958;C|0.042	0.042	strong		0.507	ACKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256645.2	NM_001296	
HS1BP3	64342	hgsc.bcm.edu	37	2	20824559	20824559	+	Silent	SNP	C	C	T	rs2305457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:20824559C>T	ENST00000304031.3	-	5	742	c.717G>A	c.(715-717)gaG>gaA	p.E239E		NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	239							phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAAGAGCCCCTCATCAGGGT	0.612													C|||	1380	0.275559	0.0333	0.366	5008	,	,		18239	0.4881		0.2614	False		,,,				2504	0.3344				p.E239E		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G717A						PASS	.	C		325,4081	170.1+/-200.6	9,307,1887	74.0	81.0	79.0		717	0.7	0.3	2	dbSNP_100	79	2227,6373	378.2+/-338.8	303,1621,2376	no	coding-synonymous	HS1BP3	NM_022460.3		312,1928,4263	TT,TC,CC		25.8953,7.3763,19.6217		239/393	20824559	2552,10454	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon5			GAGCCCCTCATCA		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.717G>A	2.37:g.20824559C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	78	46	0.589744	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1	629	0.288003663003663	21	0.042682926829268296	125	0.3453038674033149	284	0.4965034965034965	199	0.262532981530343	C	0.179	-1.064030	0.01934	0.073763	0.258953	ENSG00000118960	ENST00000445102	.	.	.	4.7	0.696	0.18075	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.47661	-0.9100	3	.	.	.	-5.486	3.0218	0.06078	0.172:0.3953:0.3349:0.0978	rs2305457;rs2305457	.	.	.	R	32	.	.	G	-	1	0	HS1BP3	20688040	0.000000	0.05858	0.278000	0.24718	0.003000	0.03518	-0.441000	0.06879	0.580000	0.29522	-0.176000	0.13171	GGG	C|0.772;T|0.228	0.228	strong		0.612	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
SLX4	84464	hgsc.bcm.edu	37	16	3639977	3639977	+	Missense_Mutation	SNP	G	G	A	rs3827530	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3639977G>A	ENST00000294008.3	-	12	4302	c.3662C>T	c.(3661-3663)gCg>gTg	p.A1221V		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1221	Interaction with PLK1 and TERF2-TERF2IP.		A -> V (in dbSNP:rs3827530). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CTCCGGCAGCGCCCCCTCATC	0.607								Direct reversal of damage					G|||	206	0.0411342	0.0038	0.0648	5008	,	,		15712	0.0496		0.0646	False		,,,				2504	0.0419				p.A1221V		Atlas-SNP	.											SLX4,bladder,carcinoma,-1,2	SLX4	173	2	0			c.C3662T						PASS	.	G	VAL/ALA	65,4329	56.2+/-92.4	0,65,2132	44.0	49.0	47.0		3662	-3.8	0.0	16	dbSNP_107	47	575,8025	151.6+/-206.3	14,547,3739	yes	missense	SLX4	NM_032444.2	64	14,612,5871	AA,AG,GG		6.686,1.4793,4.9254	benign	1221/1835	3639977	640,12354	2197	4300	6497	SO:0001583	missense	84464	exon12			GGCAGCGCCCCCT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3662C>T	16.37:g.3639977G>A	ENSP00000294008:p.Ala1221Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	128	59	0.460938	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	99	0.04532967032967033	5	0.01016260162601626	22	0.06077348066298342	24	0.04195804195804196	48	0.0633245382585752	G	12.15	1.851826	0.32699	0.014793	0.06686	ENSG00000188827	ENST00000294008	T	0.24151	1.87	5.61	-3.84	0.04256	.	1.988680	0.02298	N	0.070905	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B	0.16802	0.019	B	0.04013	0.001	T	0.16719	-1.0393	10	0.29301	T	0.29	.	5.056	0.14533	0.1975:0.2828:0.4409:0.0788	rs3827530;rs3827530	1221	Q8IY92	SLX4_HUMAN	V	1221	ENSP00000294008:A1221V	ENSP00000294008:A1221V	A	-	2	0	SLX4	3579978	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.220000	0.09215	-0.446000	0.07149	-0.226000	0.12346	GCG	G|0.954;A|0.046	0.046	strong		0.607	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
CRLF2	64109	hgsc.bcm.edu	37	X	1321349	1321349	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:1321349C>T	ENST00000381567.3	-	4	405	c.406G>A	c.(406-408)Gtg>Atg	p.V136M	CRLF2_ENST00000381566.1_Missense_Mutation_p.V136M|CRLF2_ENST00000467626.1_5'UTR	NM_022148.2	NP_071431.2	Q9HC73	CRLF2_HUMAN	cytokine receptor-like factor 2	136	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				immunoglobulin secretion involved in immune response (GO:0002380)|inflammatory response (GO:0006954)|T-helper 2 cell cytokine production (GO:0035745)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|lung(9)	20		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)				GAACACGTCACCGTCACTGCA	0.582			"""Mis, T"""	"""P2RY8, IGH@"""	"""B-ALL, Downs associated ALL"""								c|||	54	0.0107827	0.0166	0.0144	5008	,	,		17300	0.0		0.0209	False		,,,				2504	0.001				p.V136M		Atlas-SNP	.		Dom	yes		"""X,Y"""	Xp22.3; Yp11.3	64109	cytokine receptor-like factor 2		L	.	CRLF2	24	.	0			c.G406A						PASS	.	C	MET/VAL,MET/VAL	59,4125		0,59,2033	245.0	261.0	256.0		70,406	0.3	0.0	X	dbSNP_134	256	215,8199		2,211,3994	yes	missense,missense	CRLF2	NM_001012288.1,NM_022148.2	21,21	2,270,6027	TT,TC,CC		2.5553,1.4101,2.1749	probably-damaging,probably-damaging	24/152,136/372	1321349	274,12324	2092	4207	6299	SO:0001583	missense	64109	exon4			ACGTCACCGTCAC	AF142570	CCDS75944.1, CCDS75945.1	Xp22.3 and Yp11.3	2011-10-07			ENSG00000205755	ENSG00000205755		"""Pseudoautosomal regions / PAR1"""	14281	protein-coding gene	gene with protein product		300357, 400023				11237741, 11474172	Standard	NM_022148		Approved	CRL2, TSLPR	uc004cpk.2	Q9HC73	OTTHUMG00000067432	ENST00000381567.3:c.406G>A	X.37:g.1321349C>T	ENSP00000370979:p.Val136Met	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	392	185	0.471939	NM_022148	Q9H5R3	Missense_Mutation	SNP	ENST00000381567.3	37		27	0.012362637362637362	7	0.014227642276422764	5	0.013812154696132596	0	0.0	15	0.01978891820580475	c	11.07	1.530642	0.27387	0.014101	0.025553	ENSG00000205755	ENST00000381567;ENST00000400841;ENST00000381566	T;T;T	0.73152	-0.72;-0.72;-0.72	2.11	0.315	0.15852	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.651350	0.13895	U	0.355319	T	0.57562	0.2062	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.76071	0.987	T	0.58183	-0.7681	9	0.66056	D	0.02	-27.2059	3.9216	0.09245	0.0:0.3462:0.0:0.6538	.	136	Q9HC73	CRLF2_HUMAN	M	136	ENSP00000370979:V136M;ENSP00000383641:V136M;ENSP00000370978:V136M	ENSP00000370978:V136M	V	-	1	0	CRLF2	1281349	0.001000	0.12720	0.000000	0.03702	0.008000	0.06430	0.035000	0.13797	-0.021000	0.14009	0.367000	0.22151	GTG	C|0.987;T|0.013	0.013	strong		0.582	CRLF2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_022148	
TMEM99	147184	hgsc.bcm.edu	37	17	38991053	38991053	+	Silent	SNP	T	T	A	rs3169915|rs386796999	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38991053T>A	ENST00000301665.3	+	3	589	c.285T>A	c.(283-285)ctT>ctA	p.L95L		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	95			L -> R (in dbSNP:rs1044806). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				GAGAAGGACTTCTTCTTCCTT	0.468													T|||	544	0.108626	0.1248	0.1182	5008	,	,		19724	0.004		0.1928	False		,,,				2504	0.1012				p.L95L		Atlas-SNP	.											.	TMEM99	21	.	0			c.T285A						PASS	.	T	,,	427,3447		27,373,1537	201.0	197.0	199.0		285,285,285	0.2	0.1	17	dbSNP_105	199	1612,6680		151,1310,2685	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	,,	178,1683,4222	AA,AT,TT		19.4404,11.0222,16.7598	,,	95/259,95/259,95/259	38991053	2039,10127	1937	4146	6083	SO:0001819	synonymous_variant	147184	exon3			AGGACTTCTTCTT	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.285T>A	17.37:g.38991053T>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	171	81	0.473684	NM_001195386	B4DQ34|Q96BP9	Silent	SNP	ENST00000301665.3	37	CCDS42319.1																																																																																			T|0.873;A|0.127	0.127	strong		0.468	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
TUBA3D	113457	hgsc.bcm.edu	37	2	132237927	132237927	+	Missense_Mutation	SNP	C	C	A	rs200147665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:132237927C>A	ENST00000321253.6	+	4	768	c.661C>A	c.(661-663)Cgt>Agt	p.R221S		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	221					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.R221S(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		GGACATTGAACGTCCCACGTA	0.542																																					p.R221S	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											TUBA3D,trunk,malignant_melanoma,0,1	TUBA3D	60	1	1	Substitution - Missense(1)	skin(1)	c.C661A						scavenged	.						62.0	76.0	71.0					2																	132237927		2203	4296	6499	SO:0001583	missense	113457	exon4			ATTGAACGTCCCA	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"""Tubulins"""	24071	protein-coding gene	gene with protein product	"""alpha-tubulin isotype H2-alpha"""					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.661C>A	2.37:g.132237927C>A	ENSP00000326042:p.Arg221Ser	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	328	54	0.164634	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	37	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	c	3.464	-0.109452	0.06924	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	T	0.68903	-0.36	2.24	1.33	0.21861	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.44483	U	0.000448	T	0.58666	0.2138	L	0.47190	1.495	0.44036	D	0.996764	B	0.17465	0.022	B	0.32805	0.153	T	0.55049	-0.8201	10	0.87932	D	0	.	6.8167	0.23835	0.0:0.8406:0.0:0.1594	.	221	Q13748	TBA3C_HUMAN	S	221	ENSP00000326042:R221S	ENSP00000326042:R221S	R	+	1	0	TUBA3D	131954397	1.000000	0.71417	0.987000	0.45799	0.044000	0.14063	2.392000	0.44433	0.267000	0.21916	0.194000	0.17425	CGT	C|0.500;A|0.500	0.500	weak		0.542	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386	
SIM2	6493	hgsc.bcm.edu	37	21	38117040	38117040	+	Silent	SNP	G	G	A	rs2073416	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:38117040G>A	ENST00000290399.6	+	10	1792	c.1179G>A	c.(1177-1179)tcG>tcA	p.S393S	SIM2_ENST00000430056.3_Silent_p.S393S	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	393	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				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						AATACAGCTCGTTCCAAATGG	0.617													G|||	1377	0.27496	0.3835	0.1787	5008	,	,		17396	0.2292		0.2237	False		,,,				2504	0.2965				p.S393S		Atlas-SNP	.											.	SIM2	55	.	0			c.G1179A						PASS	.	G	,	1605,2799		306,993,903	28.0	27.0	27.0		1179,1179	-8.8	0.5	21	dbSNP_96	27	1829,6771		192,1445,2663	no	coding-synonymous,coding-synonymous	SIM2	NM_005069.3,NM_009586.2	,	498,2438,3566	AA,AG,GG		21.2674,36.4441,26.4073	,	393/668,393/571	38117040	3434,9570	2202	4300	6502	SO:0001819	synonymous_variant	6493	exon10			CAGCTCGTTCCAA		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.1179G>A	21.37:g.38117040G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	37	CCDS13646.1	548	0.2509157509157509	178	0.3617886178861789	71	0.19613259668508287	123	0.21503496503496503	176	0.23218997361477572	G	9.051	0.991992	0.18966	0.364441	0.212674	ENSG00000159263	ENST00000431229	.	.	.	5.05	-8.81	0.00813	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999497838	.	.	.	.	.	.	T	0.36939	-0.9727	3	.	.	.	.	2.7046	0.05158	0.2843:0.3866:0.173:0.1561	rs2073416;rs52820127;rs2073416	.	.	.	I	331	.	.	V	+	1	0	SIM2	37038910	0.865000	0.29922	0.459000	0.27081	0.990000	0.78478	-0.257000	0.08745	-1.581000	0.01642	-0.320000	0.08662	GTT	G|0.736;A|0.264	0.264	strong		0.617	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
PDE1C	5137	hgsc.bcm.edu	37	7	31855569	31855569	+	Silent	SNP	G	G	A	rs2302450	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:31855569G>A	ENST00000396191.1	-	15	2237	c.1782C>T	c.(1780-1782)gcC>gcT	p.A594A	PDE1C_ENST00000321453.7_Silent_p.A594A|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396193.1_Silent_p.A654A|PDE1C_ENST00000396182.2_Silent_p.A594A|PDE1C_ENST00000396184.3_Silent_p.A594A	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	594					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.A594A(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	ATGACTTCTCGGCTTTGGAGT	0.448													A|||	1175	0.234625	0.2451	0.2046	5008	,	,		22184	0.1667		0.2704	False		,,,				2504	0.2751				p.A654A		Atlas-SNP	.											PDE1C_ENST00000396191,NS,carcinoma,0,2	PDE1C	465	2	2	Substitution - coding silent(2)	stomach(2)	c.C1962T						PASS	.	A	,,,,	1024,3382	727.8+/-409.9	133,758,1312	230.0	222.0	225.0		1782,1782,1962,1782,1782	-8.8	0.4	7	dbSNP_100	225	2092,6508	717.1+/-406.1	254,1584,2462	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE1C	NM_001191056.1,NM_001191057.1,NM_001191058.1,NM_001191059.1,NM_005020.2	,,,,	387,2342,3774	AA,AG,GG		24.3256,23.241,23.9582	,,,,	594/635,594/710,654/770,594/710,594/635	31855569	3116,9890	2203	4300	6503	SO:0001819	synonymous_variant	5137	exon16			CTTCTCGGCTTTG	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1782C>T	7.37:g.31855569G>A		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	229	99	0.432314	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	37	CCDS55099.1																																																																																			G|0.761;A|0.239	0.239	strong		0.448	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
C17orf80	55028	hgsc.bcm.edu	37	17	71232990	71232990	+	Missense_Mutation	SNP	C	C	A	rs61729639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:71232990C>A	ENST00000535032.2	+	2	1482	c.1369C>A	c.(1369-1371)Cgc>Agc	p.R457S	C17orf80_ENST00000359042.2_Missense_Mutation_p.R457S|C17orf80_ENST00000582793.1_Intron|C17orf80_ENST00000426147.2_Missense_Mutation_p.R457S|C17orf80_ENST00000577615.1_Missense_Mutation_p.R457S|C17orf80_ENST00000268942.8_Missense_Mutation_p.R457S|FAM104A_ENST00000583178.1_5'Flank|C17orf80_ENST00000255557.4_Missense_Mutation_p.R457S			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80	457						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			GAAGACTCTTCGCAGCTGCAT	0.562													C|||	120	0.0239617	0.0015	0.0418	5008	,	,		17739	0.001		0.0358	False		,,,				2504	0.0532				p.R457S		Atlas-SNP	.											.	C17orf80	37	.	0			c.C1369A						PASS	.	C	SER/ARG,SER/ARG,SER/ARG	36,4370	40.0+/-72.8	0,36,2167	63.0	60.0	61.0		1369,1369,1369	1.1	0.0	17	dbSNP_129	61	423,8177	130.8+/-188.7	17,389,3894	yes	missense,missense,missense	C17orf80	NM_001100621.1,NM_001100622.1,NM_017941.4	110,110,110	17,425,6061	AA,AC,CC		4.9186,0.8171,3.5291	benign,benign,benign	457/574,457/584,457/610	71232990	459,12547	2203	4300	6503	SO:0001583	missense	55028	exon3			ACTCTTCGCAGCT	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.1369C>A	17.37:g.71232990C>A	ENSP00000440551:p.Arg457Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_001100621	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Missense_Mutation	SNP	ENST00000535032.2	37	CCDS11694.1	75	0.034340659340659344	15	0.03048780487804878	20	0.055248618784530384	5	0.008741258741258742	35	0.04617414248021108	C	8.821	0.937505	0.18206	0.008171	0.049186	ENSG00000141219	ENST00000255557;ENST00000359042;ENST00000268942;ENST00000426147;ENST00000535032	T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82	5.51	1.14	0.20703	.	1.035730	0.07645	N	0.930920	T	0.00328	0.0010	N	0.00677	-1.265	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.002	T	0.39603	-0.9606	10	0.02654	T	1	0.5057	7.0804	0.25227	0.0:0.5952:0.0:0.4048	rs61729639	457;457;457;457	B7Z7E5;Q9BSJ5;Q9BSJ5-2;Q9BSJ5-3	.;CQ080_HUMAN;.;.	S	457	ENSP00000255557:R457S;ENSP00000351937:R457S;ENSP00000268942:R457S;ENSP00000396970:R457S;ENSP00000440551:R457S	ENSP00000255557:R457S	R	+	1	0	C17orf80	68744585	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.131000	0.10482	-0.012000	0.14223	0.655000	0.94253	CGC	C|0.964;A|0.036	0.036	strong		0.562	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1	NM_017941	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68704264	68704264	+	Silent	SNP	C	C	T	rs546382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68704264C>T	ENST00000255078.3	+	13	2427	c.2316C>T	c.(2314-2316)tcC>tcT	p.S772S		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	772	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.|SS DNA-binding. {ECO:0000250}.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			ACGACAGTTCCGGGGAAGGGA	0.647													C|||	1233	0.246206	0.0991	0.1571	5008	,	,		18079	0.2133		0.3042	False		,,,				2504	0.4826				p.S772S		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.C2316T						PASS	.	C		561,3839	249.0+/-256.6	46,469,1685	56.0	52.0	53.0		2316	-3.7	0.1	11	dbSNP_83	53	2655,5933	425.3+/-354.9	408,1839,2047	no	coding-synonymous	IGHMBP2	NM_002180.2		454,2308,3732	TT,TC,CC		30.9152,12.75,24.7613		772/994	68704264	3216,9772	2200	4294	6494	SO:0001819	synonymous_variant	3508	exon13			CAGTTCCGGGGAA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.2316C>T	11.37:g.68704264C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_002180	A0PJD2|Q00443|Q14177	Silent	SNP	ENST00000255078.3	37	CCDS8187.1																																																																																			C|0.761;T|0.239	0.239	strong		0.647	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
MYH7B	57644	hgsc.bcm.edu	37	20	33581955	33581955	+	Silent	SNP	G	G	A	rs2425012	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:33581955G>A	ENST00000262873.7	+	25	2669	c.2577G>A	c.(2575-2577)gcG>gcA	p.A859A		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	817						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)			CTAGGGATGCGCTGTTCACCA	0.557													G|||	1987	0.396765	0.171	0.621	5008	,	,		20265	0.5546		0.4861	False		,,,				2504	0.2883				p.A859A		Atlas-SNP	.											.	MYH7B	145	.	0			c.G2577A						PASS	.	G		922,3332		107,708,1312	91.0	97.0	95.0		2577	0.1	1.0	20	dbSNP_100	95	3623,4885		760,2103,1391	no	coding-synonymous	MYH7B	NM_020884.3		867,2811,2703	AA,AG,GG		42.5835,21.6737,35.6135		859/1984	33581955	4545,8217	2127	4254	6381	SO:0001819	synonymous_variant	57644	exon27			GGATGCGCTGTTC	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.2577G>A	20.37:g.33581955G>A		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			G|0.585;A|0.415	0.415	strong		0.557	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
GLYATL3	389396	hgsc.bcm.edu	37	6	49479750	49479750	+	Missense_Mutation	SNP	T	T	C	rs13193063	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:49479750T>C	ENST00000371197.4	+	2	160	c.47T>C	c.(46-48)aTg>aCg	p.M16T		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	16						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.M16T(1)		NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						CTGGAGAAAATGTTGAAGAGT	0.318													T|||	912	0.182109	0.0537	0.1931	5008	,	,		11526	0.2044		0.333	False		,,,				2504	0.1697				p.M16T		Atlas-SNP	.											GLYATL3,NS,carcinoma,0,1	GLYATL3	19	1	1	Substitution - Missense(1)	kidney(1)	c.T47C						PASS	.						237.0	204.0	214.0					6																	49479750		692	1591	2283	SO:0001583	missense	389396	exon2			AGAAAATGTTGAA		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.47T>C	6.37:g.49479750T>C	ENSP00000360240:p.Met16Thr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	438	0.20054945054945056	29	0.05894308943089431	73	0.20165745856353592	94	0.16433566433566432	242	0.31926121372031663	T	11.00	1.509980	0.27036	.	.	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.13538	2.58;2.58	5.8	5.8	0.92144	Glycine N-acyltransferase, N-terminal (1);	0.349316	0.32970	N	0.005433	T	0.06142	0.0159	L	0.48986	1.54	0.36788	P	0.11531100000000005	B	0.31459	0.324	B	0.31390	0.129	T	0.25467	-1.0131	9	0.19590	T	0.45	-1.7855	12.5278	0.56096	0.0:0.0:0.0:1.0	rs13193063;rs17663633;rs13193063	16	Q5SZD4	GLYL3_HUMAN	T	16	ENSP00000360240:M16T;ENSP00000440029:M16T	ENSP00000360240:M16T	M	+	2	0	GLYATL3	49587709	0.923000	0.31300	0.746000	0.31095	0.992000	0.81027	1.779000	0.38624	2.215000	0.71742	0.472000	0.43445	ATG	C|0.179;N|0.000	0.179	strong		0.318	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
PDCD1LG2	80380	hgsc.bcm.edu	37	9	5557708	5557708	+	Missense_Mutation	SNP	T	T	C	rs7854413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5557708T>C	ENST00000397747.3	+	5	970	c.722T>C	c.(721-723)aTa>aCa	p.I241T	PDCD1LG2_ENST00000397745.2_Missense_Mutation_p.I151T	NM_025239.3	NP_079515.2	Q9BQ51	PD1L2_HUMAN	programmed cell death 1 ligand 2	241			I -> T (in dbSNP:rs7854413).		immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(2)|lung(4)|prostate(2)	8	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000767)|Lung(218;0.112)		GCCACAGTGATAGCCCTAAGA	0.448													T|||	1402	0.279952	0.6422	0.1326	5008	,	,		22607	0.1151		0.1034	False		,,,				2504	0.2464				p.I241T		Atlas-SNP	.											.	PDCD1LG2	16	.	0			c.T722C						PASS	.	T	THR/ILE	2425,1981	617.9+/-393.1	669,1087,447	195.0	181.0	185.0		722	2.4	0.0	9	dbSNP_116	185	825,7775	190.0+/-236.6	32,761,3507	yes	missense	PDCD1LG2	NM_025239.3	89	701,1848,3954	CC,CT,TT		9.593,44.9614,24.9885	possibly-damaging	241/274	5557708	3250,9756	2203	4300	6503	SO:0001583	missense	80380	exon5			CAGTGATAGCCCT	AF344424	CCDS6465.1	9p24.2	2014-01-30			ENSG00000197646	ENSG00000197646		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	18731	protein-coding gene	gene with protein product	"""B7 dendritic cell molecule"""	605723				11224527	Standard	NM_025239		Approved	PD-L2, Btdc, PDL2, bA574F11.2, CD273, B7-DC	uc003zjg.4	Q9BQ51	OTTHUMG00000019504	ENST00000397747.3:c.722T>C	9.37:g.5557708T>C	ENSP00000380855:p.Ile241Thr	Somatic	256	1	0.00390625		WXS	Illumina HiSeq	Phase_I	227	103	0.453745	NM_025239	Q14CN8|Q5T7Z6|Q6JXL8|Q6JXL9	Missense_Mutation	SNP	ENST00000397747.3	37	CCDS6465.1	496	0.2271062271062271	304	0.6178861788617886	49	0.13535911602209943	68	0.11888111888111888	75	0.09894459102902374	T	9.427	1.084533	0.20309	0.550386	0.09593	ENSG00000197646	ENST00000397745;ENST00000397747	T;T	0.14640	2.49;5.07	4.68	2.37	0.29283	.	0.328448	0.26112	N	0.026269	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P;B;B	0.43750	0.816;0.301;0.123	B;B;B	0.37239	0.244;0.184;0.02	T	0.25882	-1.0119	9	0.72032	D	0.01	10.8254	5.7861	0.18334	0.0:0.2107:0.0:0.7893	rs7854413;rs52819168;rs58013146;rs7854413	241;151;241	A4GW21;Q9BQ51-2;Q9BQ51	.;.;PD1L2_HUMAN	T	151;241	ENSP00000380853:I151T;ENSP00000380855:I241T	ENSP00000380853:I151T	I	+	2	0	PDCD1LG2	5547708	0.002000	0.14202	0.003000	0.11579	0.003000	0.03518	0.297000	0.19101	0.337000	0.23665	-0.250000	0.11733	ATA	T|0.745;C|0.255	0.255	strong		0.448	PDCD1LG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051634.1	NM_025239	
SIDT1	54847	hgsc.bcm.edu	37	3	113286405	113286405	+	Silent	SNP	C	C	T	rs2292511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113286405C>T	ENST00000264852.4	+	3	1089	c.363C>T	c.(361-363)aaC>aaT	p.N121N	SIDT1_ENST00000393830.3_Silent_p.N121N	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	121					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						GGAGCTACAACTATCAAGAAG	0.478													C|||	1617	0.322883	0.267	0.2565	5008	,	,		18650	0.5873		0.2326	False		,,,				2504	0.2658				p.N121N		Atlas-SNP	.											SIDT1,NS,carcinoma,0,1	SIDT1	99	1	0			c.C363T						scavenged	.	C		1182,3224	416.7+/-337.7	158,866,1179	87.0	82.0	84.0		363	4.2	1.0	3	dbSNP_100	84	1759,6841	318.2+/-313.6	166,1427,2707	no	coding-synonymous	SIDT1	NM_017699.2		324,2293,3886	TT,TC,CC		20.4535,26.8271,22.6126		121/828	113286405	2941,10065	2203	4300	6503	SO:0001819	synonymous_variant	54847	exon3			CTACAACTATCAA	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.363C>T	3.37:g.113286405C>T		Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																			C|0.717;T|0.283	0.283	strong		0.478	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
APBB1	322	hgsc.bcm.edu	37	11	6415463	6415463	+	IGR	SNP	G	G	A	rs1050239	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6415463G>A	ENST00000609360.1	-	0	2642				SMPD1_ENST00000527275.1_Missense_Mutation_p.G507R|APBB1_ENST00000526240.1_5'Flank|SMPD1_ENST00000299397.3_Missense_Mutation_p.G464R|SMPD1_ENST00000356761.2_Missense_Mutation_p.G452R|SMPD1_ENST00000342245.4_Missense_Mutation_p.G508R	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)						apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		AAACTACTCCGGGAGCTCTCA	0.572													G|||	751	0.14996	0.1127	0.2061	5008	,	,		19877	0.1548		0.2078	False		,,,				2504	0.0961				p.G508R	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											.	SMPD1	108	.	0			c.G1522A	GRCh37	CM067719	SMPD1	M	rs1050239	PASS	.	G	ARG/GLY,ARG/GLY	604,3798	263.1+/-265.3	47,510,1644	73.0	68.0	70.0		1522,1519	3.8	0.7	11	dbSNP_86	70	1970,6622	347.7+/-326.7	225,1520,2551	yes	missense,missense	SMPD1	NM_000543.4,NM_001007593.2	125,125	272,2030,4195	AA,AG,GG		22.9283,13.721,19.8091	probably-damaging,probably-damaging	508/632,507/631	6415463	2574,10420	2201	4296	6497	SO:0001628	intergenic_variant	6609	exon6			TACTCCGGGAGCT	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213			11.37:g.6415463G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_000543	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37		393	0.17994505494505494	62	0.12601626016260162	74	0.20441988950276244	104	0.18181818181818182	153	0.20184696569920843	G	16.88	3.243976	0.58995	0.13721	0.229283	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.68	3.77	0.43336	.	0.251288	0.31859	N	0.006941	T	0.00271	0.0008	M	0.78801	2.425	0.27835	P	0.9413038	D;D;D	0.65815	0.994;0.978;0.995	P;P;P	0.56648	0.742;0.541;0.803	T	0.02075	-1.1218	9	0.26408	T	0.33	-23.2629	10.4429	0.44477	0.0951:0.0:0.9049:0.0	rs1050239;rs2229724;rs3168313;rs11605169;rs17413429;rs60448991;rs1050239	507;464;506	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	R	464;452;508;507	ENSP00000299397:G464R;ENSP00000349203:G452R;ENSP00000340409:G508R;ENSP00000435350:G507R	ENSP00000299397:G464R	G	+	1	0	SMPD1	6372039	1.000000	0.71417	0.672000	0.29872	0.714000	0.41099	6.226000	0.72277	1.218000	0.43458	0.462000	0.41574	GGG	G|0.815;A|0.185	0.185	strong		0.572	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
IFT140	9742	hgsc.bcm.edu	37	16	1574863	1574863	+	Silent	SNP	G	G	A	rs2235640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1574863G>A	ENST00000426508.2	-	23	3282	c.2919C>T	c.(2917-2919)gcC>gcT	p.A973A	IFT140_ENST00000361339.5_Silent_p.A167A	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	973					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				AGTGCAGCGCGGCGTCCATCT	0.677													G|||	1157	0.23103	0.239	0.1268	5008	,	,		13427	0.3214		0.171	False		,,,				2504	0.2628				p.A973A		Atlas-SNP	.											.	IFT140	128	.	0			c.C2919T						PASS	.	G		916,3482	345.7+/-308.6	97,722,1380	49.0	59.0	56.0		2919	-11.1	0.0	16	dbSNP_98	56	1529,7071	284.7+/-296.8	127,1275,2898	no	coding-synonymous	IFT140	NM_014714.3		224,1997,4278	AA,AG,GG		17.7791,20.8276,18.8106		973/1463	1574863	2445,10553	2199	4300	6499	SO:0001819	synonymous_variant	9742	exon23			CAGCGCGGCGTCC	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.2919C>T	16.37:g.1574863G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Silent	SNP	ENST00000426508.2	37	CCDS10439.1																																																																																			G|0.803;A|0.197	0.197	strong		0.677	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
CDC20	991	hgsc.bcm.edu	37	1	43825644	43825644	+	Silent	SNP	T	T	C	rs839763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43825644T>C	ENST00000372462.1	+	4	635	c.432T>C	c.(430-432)taT>taC	p.Y144Y	CDC20_ENST00000310955.6_Silent_p.Y144Y|CDC20_ENST00000478882.1_3'UTR|RP1-92O14.3_ENST00000424948.1_RNA			Q12834	CDC20_HUMAN	cell division cycle 20	144					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|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 cell proliferation (GO:0008284)|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 ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCACAGGTTATCAGAACAGAC	0.522													C|||	1147	0.229034	0.2436	0.3674	5008	,	,		18701	0.1071		0.3708	False		,,,				2504	0.091				p.Y144Y	Esophageal Squamous(137;1154 1759 10362 10401 46925)	Atlas-SNP	.											.	CDC20	34	.	0			c.T432C						PASS	.	C		1242,3164	703.7+/-407.0	170,902,1131	151.0	165.0	160.0		432	4.8	1.0	1	dbSNP_86	160	3288,5312	645.7+/-400.2	641,2006,1653	no	coding-synonymous	CDC20	NM_001255.2		811,2908,2784	CC,CT,TT		38.2326,28.1888,34.8301		144/500	43825644	4530,8476	2203	4300	6503	SO:0001819	synonymous_variant	991	exon5			AGGTTATCAGAAC	U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"""WD repeat domain containing"""	1723	protein-coding gene	gene with protein product		603618	"""CDC20 (cell division cycle 20, S. cerevisiae, homolog)"", ""CDC20 cell division cycle 20 homolog (S. cerevisiae)"", ""cell division cycle 20 homolog (S. cerevisiae)"""			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.432T>C	1.37:g.43825644T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001255	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Silent	SNP	ENST00000372462.1	37	CCDS484.1																																																																																			T|0.728;C|0.272	0.272	strong		0.522	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255	
VPS41	27072	hgsc.bcm.edu	37	7	38805215	38805215	+	Missense_Mutation	SNP	C	C	T	rs62444122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:38805215C>T	ENST00000310301.4	-	16	1348	c.1294G>A	c.(1294-1296)Gaa>Aaa	p.E432K	VPS41_ENST00000395969.2_Missense_Mutation_p.E407K	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	432					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						TTATAAACTTCATATTCCCAG	0.318													C|||	107	0.0213658	0.0053	0.0245	5008	,	,		14043	0.0		0.0765	False		,,,				2504	0.0061				p.E432K		Atlas-SNP	.											.	VPS41	102	.	0			c.G1294A						PASS	.	C	LYS/GLU,LYS/GLU	75,4329	65.3+/-102.7	0,75,2127	65.0	67.0	66.0		1294,1219	5.5	1.0	7	dbSNP_129	66	633,7963	161.1+/-214.1	33,567,3698	yes	missense,missense	VPS41	NM_014396.3,NM_080631.3	56,56	33,642,5825	TT,TC,CC		7.3639,1.703,5.4462	probably-damaging,probably-damaging	432/855,407/830	38805215	708,12292	2202	4298	6500	SO:0001583	missense	27072	exon16			AAACTTCATATTC	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.1294G>A	7.37:g.38805215C>T	ENSP00000309457:p.Glu432Lys	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	22	10	0.454545	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	87	0.03983516483516483	4	0.008130081300813009	15	0.04143646408839779	0	0.0	68	0.08970976253298153	C	23.3	4.396391	0.83011	0.01703	0.073639	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.17370	2.28;2.28	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.01523	0.0049	M	0.75777	2.31	0.80722	D	1	D;D;D	0.63880	0.993;0.993;0.993	P;P;P	0.54629	0.757;0.757;0.757	T	0.00092	-1.2083	10	0.29301	T	0.29	-23.3687	19.3294	0.94280	0.0:1.0:0.0:0.0	rs62444122	432;407;432	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	K	432;407	ENSP00000309457:E432K;ENSP00000379297:E407K	ENSP00000309457:E432K	E	-	1	0	VPS41	38771740	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.685000	0.61693	2.584000	0.87258	0.460000	0.39030	GAA	C|0.951;T|0.049	0.049	strong		0.318	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
INPP4A	3631	hgsc.bcm.edu	37	2	99193496	99193496	+	Silent	SNP	C	C	T	rs2230388	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:99193496C>T	ENST00000523221.1	+	23	2691	c.2691C>T	c.(2689-2691)agC>agT	p.S897S	INPP4A_ENST00000074304.5_Silent_p.S897S|INPP4A_ENST00000409463.1_Silent_p.S226S|INPP4A_ENST00000409540.3_Silent_p.S858S|INPP4A_ENST00000545415.1_Silent_p.S858S|INPP4A_ENST00000409851.3_Silent_p.S892S|INPP4A_ENST00000409016.4_Silent_p.S858S			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	897					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						GCTGCAAGAGCGCTAAGGACC	0.612													C|||	1284	0.25639	0.1589	0.2968	5008	,	,		17232	0.2937		0.2714	False		,,,				2504	0.3057				p.S897S		Atlas-SNP	.											.	INPP4A	205	.	0			c.C2691T						PASS	.	C	,,,	704,3520		63,578,1471	62.0	66.0	65.0		2691,2676,2574,2574	-3.1	1.0	2	dbSNP_98	65	2195,6257		291,1613,2322	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	354,2191,3793	TT,TC,CC		25.9702,16.6667,22.87	,,,	897/978,892/973,858/955,858/939	99193496	2899,9777	2112	4226	6338	SO:0001819	synonymous_variant	3631	exon25			CAAGAGCGCTAAG	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.2691C>T	2.37:g.99193496C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	241	234	0.970954	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			C|0.753;T|0.247	0.247	strong		0.612	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519158	48519158	+	Missense_Mutation	SNP	C	C	T	rs34129198	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48519158C>T	ENST00000339841.2	+	4	395	c.217C>T	c.(217-219)Cgc>Tgc	p.R73C	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	73	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		AGATTACCCACGCTGTATCTT	0.463													c|||	810	0.161741	0.2103	0.1254	5008	,	,		20377	0.0724		0.1531	False		,,,				2504	0.2229				p.R73C		Atlas-SNP	.											.	ELSPBP1	29	.	0			c.C217T						PASS	.	C	CYS/ARG	884,3522	343.3+/-307.6	86,712,1405	106.0	83.0	91.0		217	2.2	0.9	19	dbSNP_126	91	1294,7306	256.1+/-280.7	91,1112,3097	yes	missense	ELSPBP1	NM_022142.4	180	177,1824,4502	TT,TC,CC		15.0465,20.0635,16.7461	probably-damaging	73/224	48519158	2178,10828	2203	4300	6503	SO:0001583	missense	64100	exon4			TACCCACGCTGTA	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.217C>T	19.37:g.48519158C>T	ENSP00000340660:p.Arg73Cys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	38	0.469136	NM_022142	Q96RT0|Q9H4C8	Missense_Mutation	SNP	ENST00000339841.2	37	CCDS12708.1	325	0.1488095238095238	107	0.21747967479674796	59	0.16298342541436464	47	0.08216783216783216	112	0.14775725593667546	C	9.088	1.000976	0.19121	0.200635	0.150465	ENSG00000169393	ENST00000339841	T	0.10005	2.92	3.4	2.21	0.28008	Fibronectin, type II, collagen-binding (3);Kringle-like fold (1);	0.186449	0.24554	N	0.037536	T	0.00012	0.0000	L	0.35414	1.06	0.40606	P	0.018378000000000005	P	0.35226	0.491	B	0.27608	0.081	T	0.45425	-0.9262	9	0.38643	T	0.18	.	7.0708	0.25177	0.2693:0.7306:0.0:0.0	rs34129198	73	Q96BH3	ESPB1_HUMAN	C	73	ENSP00000340660:R73C	ENSP00000340660:R73C	R	+	1	0	ELSPBP1	53210970	0.868000	0.29978	0.938000	0.37757	0.306000	0.27790	1.077000	0.30741	1.817000	0.53016	0.543000	0.68304	CGC	C|0.837;T|0.163	0.163	strong		0.463	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713625	32713625	+	Missense_Mutation	SNP	C	C	T	rs116163401		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32713625C>T	ENST00000374940.3	+	3	491	c.389C>T	c.(388-390)aCc>aTc	p.T130I		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	130	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	CAGCCCAACACCCTCATCTGT	0.507																																					p.T130I		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C389T						PASS	.						233.0	188.0	204.0					6																	32713625		1511	2709	4220	SO:0001583	missense	3118	exon3			CCAACACCCTCAT		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.389C>T	6.37:g.32713625C>T	ENSP00000364076:p.Thr130Ile	Somatic	352	0	0		WXS	Illumina HiSeq	Phase_I	344	31	0.0901163	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Missense_Mutation	SNP	ENST00000374940.3	37	CCDS4753.1	.	.	.	.	.	.	.	.	.	.	.	4.868	0.161426	0.09287	.	.	ENSG00000237541	ENST00000374940	T	0.00646	6.0	3.06	-0.952	0.10366	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.640493	0.14599	N	0.309723	T	0.00271	0.0008	L	0.38649	1.16	0.30248	N	0.79432	B	0.24618	0.107	B	0.32724	0.151	T	0.24941	-1.0146	10	0.26408	T	0.33	.	6.9609	0.24597	0.0:0.3016:0.0:0.6984	.	130	P01906	DQA2_HUMAN	I	130	ENSP00000364076:T130I	ENSP00000364076:T130I	T	+	2	0	HLA-DQA2	32821603	0.587000	0.26791	0.996000	0.52242	0.133000	0.20885	0.068000	0.14531	-0.173000	0.10761	0.174000	0.16983	ACC	C|0.998;T|0.002	0.002	weak		0.507	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
COL18A1	80781	hgsc.bcm.edu	37	21	46896294	46896294	+	Silent	SNP	G	G	A	rs2230686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46896294G>A	ENST00000359759.4	+	5	2094	c.2073G>A	c.(2071-2073)gcG>gcA	p.A691A	COL18A1_ENST00000400337.2_Silent_p.A276A|COL18A1_ENST00000355480.5_Silent_p.A456A			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	691	Nonhelical region 1 (NC1).				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)		GGCTCCCCGCGCCACCCCCCG	0.642													G|||	480	0.0958466	0.23	0.0303	5008	,	,		15771	0.0794		0.007	False		,,,				2504	0.0695				p.A456A		Atlas-SNP	.											COL18A1,right_upper_lobe,carcinoma,+1,1	COL18A1	129	1	0			c.G1368A						PASS	.	G	,	779,3193		83,613,1290	42.0	46.0	44.0		1368,828	0.9	0.0	21	dbSNP_98	44	59,8235		1,57,4089	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	84,670,5379	AA,AG,GG		0.7114,19.6123,6.8319	,	456/1520,276/1340	46896294	838,11428	1986	4147	6133	SO:0001819	synonymous_variant	80781	exon5			CCCCGCGCCACCC		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.2073G>A	21.37:g.46896294G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	56	28	0.5	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				G|0.933;A|0.067	0.067	strong		0.642	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53639438	53639438	+	Missense_Mutation	SNP	C	C	T	rs3213758	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:53639438C>T	ENST00000379925.3	-	26	3840	c.3790G>A	c.(3790-3792)Gac>Aac	p.D1264N	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.D1184N|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.D1218N|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.D1230N	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1264			D -> N (in dbSNP:rs3213758). {ECO:0000269|PubMed:19430481}.|D -> Y (in patients with Leber congenital amaurosis). {ECO:0000269|PubMed:19430481}.		camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)	p.D1264N(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				TGAAACATGTCGGCAAGGTCG	0.532													c|||	496	0.0990415	0.0068	0.0461	5008	,	,		18644	0.3125		0.0636	False		,,,				2504	0.0777				p.D1264N		Atlas-SNP	.											RPGRIP1L,NS,carcinoma,0,1	RPGRIP1L	118	1	1	Substitution - Missense(1)	stomach(1)	c.G3790A						PASS	.	T	ASN/ASP,ASN/ASP	59,4337	56.2+/-92.4	0,59,2139	187.0	140.0	156.0		3550,3790	1.6	0.0	16	dbSNP_106	156	474,8126	140.5+/-197.0	12,450,3838	yes	missense,missense	RPGRIP1L	NM_001127897.1,NM_015272.2	23,23	12,509,5977	TT,TC,CC		5.5116,1.3421,4.1013	benign,benign	1184/1236,1264/1316	53639438	533,12463	2198	4300	6498	SO:0001583	missense	23322	exon26			ACATGTCGGCAAG		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"""fantom homolog"", ""Meckel syndrome, type 5"", ""protein phosphatase 1, regulatory subunit 134"""	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3790G>A	16.37:g.53639438C>T	ENSP00000369257:p.Asp1264Asn	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_015272	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	220	0.10073260073260074	6	0.012195121951219513	13	0.03591160220994475	154	0.2692307692307692	47	0.06200527704485488	c	6.690	0.495913	0.12762	0.013421	0.055116	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.69806	-0.43;-0.43	5.81	1.6	0.23607	.	0.427079	0.24552	N	0.037548	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	1.0000000000287557E-6	B;D	0.52996	0.007;0.957	B;B	0.38985	0.005;0.287	T	0.10917	-1.0609	9	0.40728	T	0.16	-0.6026	11.031	0.47772	0.0:0.7119:0.0923:0.1959	rs3213758;rs61235315;rs3213758	1264;1184	Q68CZ1;Q68CZ1-2	FTM_HUMAN;.	N	1264;1184	ENSP00000369257:D1264N;ENSP00000262135:D1184N	ENSP00000262135:D1184N	D	-	1	0	RPGRIP1L	52196939	0.073000	0.21202	0.000000	0.03702	0.007000	0.05969	1.190000	0.32126	-0.097000	0.12307	-2.426000	0.00216	GAC	C|0.927;T|0.073	0.073	strong		0.532	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
ESYT2	57488	hgsc.bcm.edu	37	7	158534381	158534381	+	Silent	SNP	G	G	C	rs59980573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158534381G>C	ENST00000251527.5	-	17	2147	c.2082C>G	c.(2080-2082)ccC>ccG	p.P694P	ESYT2_ENST00000435514.2_Silent_p.P129P	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	722					endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CGGCCTCAGGGGGCTGGGCCT	0.637													G|||	1701	0.339657	0.4085	0.1888	5008	,	,		15915	0.5813		0.171	False		,,,				2504	0.2781				p.P694P		Atlas-SNP	.											.	ESYT2	70	.	0			c.C2082G						PASS	.			1517,2889	475.3+/-357.3	269,979,955	37.0	40.0	39.0		2082	-9.7	0.0	7	dbSNP_129	39	1395,7205	266.0+/-286.5	104,1187,3009	no	coding-synonymous	ESYT2	NM_020728.2		373,2166,3964	CC,CG,GG		16.2209,34.4303,22.3897		694/894	158534381	2912,10094	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon17			CTCAGGGGGCTGG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2082C>G	7.37:g.158534381G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			G|0.740;C|0.260	0.260	strong		0.637	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
MAP1A	4130	hgsc.bcm.edu	37	15	43817406	43817406	+	Silent	SNP	T	T	C	rs71471869|rs480108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43817406T>C	ENST00000300231.5	+	4	4185	c.3735T>C	c.(3733-3735)gaT>gaC	p.D1245D	MAP1A_ENST00000382031.1_Silent_p.D1483D|MAP1A_ENST00000399453.1_Silent_p.D1245D			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1245			D -> N (in dbSNP:rs12912505).		microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	AGGCCGAGGATACCTCTCACC	0.547													C|||	2649	0.528954	0.9728	0.3329	5008	,	,		18861	0.4177		0.2962	False		,,,				2504	0.4223				p.D1245D		Atlas-SNP	.											.	MAP1A	189	.	0			c.T3735C						PASS	.	C		3579,723		1500,579,72	94.0	110.0	105.0		3735	0.9	0.1	15	dbSNP_83	105	2490,5988		361,1768,2110	no	coding-synonymous	MAP1A	NM_002373.5		1861,2347,2182	CC,CT,TT		29.3701,16.8061,47.4883		1245/2804	43817406	6069,6711	2151	4239	6390	SO:0001819	synonymous_variant	4130	exon4			CGAGGATACCTCT	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3735T>C	15.37:g.43817406T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	37	CCDS42031.1																																																																																			T|0.539;C|0.461	0.461	strong		0.547	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
OR5D13	390142	hgsc.bcm.edu	37	11	55541284	55541284	+	Missense_Mutation	SNP	G	G	A	rs11230983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55541284G>A	ENST00000361760.1	+	1	371	c.371G>A	c.(370-372)cGt>cAt	p.R124H		NM_001001967.1	NP_001001967.1	Q8NGL4	OR5DD_HUMAN	olfactory receptor, family 5, subfamily D, member 13	124			R -> H (in dbSNP:rs11230983).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R124H(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(1)|lung(20)|ovary(1)|pancreas(2)|skin(2)|stomach(1)|urinary_tract(1)	40		all_epithelial(135;0.196)				GCTTATGACCGTTTTGTGGCA	0.438													A|||	514	0.102636	0.0514	0.0994	5008	,	,		20064	0.1448		0.1223	False		,,,				2504	0.1104				p.R124H		Atlas-SNP	.											OR5D13,caecum,carcinoma,0,2	OR5D13	96	2	1	Substitution - Missense(1)	stomach(1)	c.G371A						PASS	.	A	HIS/ARG	241,4159	804.0+/-415.7	10,221,1969	238.0	231.0	234.0		371	2.4	0.1	11	dbSNP_120	234	1021,7571	771.9+/-407.7	56,909,3331	yes	missense	OR5D13	NM_001001967.1	29	66,1130,5300	AA,AG,GG		11.8831,5.4773,9.7137	benign	124/315	55541284	1262,11730	2200	4296	6496	SO:0001583	missense	390142	exon1			ATGACCGTTTTGT	BK004394	CCDS31507.1	11q11	2012-08-09			ENSG00000198877	ENSG00000198877		"""GPCR / Class A : Olfactory receptors"""	15280	protein-coding gene	gene with protein product							Standard	NM_001001967		Approved		uc010ril.2	Q8NGL4	OTTHUMG00000166807	ENST00000361760.1:c.371G>A	11.37:g.55541284G>A	ENSP00000354800:p.Arg124His	Somatic	299	0	0		WXS	Illumina HiSeq	Phase_I	323	143	0.442724	NM_001001967	Q6IF68|Q6IFC9	Missense_Mutation	SNP	ENST00000361760.1	37	CCDS31507.1	250	0.11446886446886446	30	0.06097560975609756	33	0.09116022099447514	87	0.1520979020979021	100	0.13192612137203166	A	9.062	0.994853	0.19043	0.054773	0.118831	ENSG00000198877	ENST00000361760	T	0.77489	-1.1	3.3	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.339612	0.16661	N	0.204770	T	0.01320	0.0043	M	0.83384	2.64	0.49299	P	2.2500000000003073E-4	B	0.16166	0.016	B	0.17098	0.017	T	0.51505	-0.8697	9	0.62326	D	0.03	-0.0508	11.9762	0.53094	0.1038:0.0:0.8962:0.0	rs11230983;rs52789774;rs58654024;rs11230983	124	Q8NGL4	OR5DD_HUMAN	H	124	ENSP00000354800:R124H	ENSP00000354800:R124H	R	+	2	0	OR5D13	55297860	0.199000	0.23386	0.079000	0.20413	0.000000	0.00434	2.879000	0.48522	0.251000	0.21505	-1.682000	0.00735	CGT	G|0.898;A|0.102	0.102	strong		0.438	OR5D13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391511.1	NM_001001967	
OR10R2	343406	hgsc.bcm.edu	37	1	158450238	158450238	+	Missense_Mutation	SNP	G	G	A	rs3820678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158450238G>A	ENST00000368152.1	+	1	571	c.571G>A	c.(571-573)Gcc>Acc	p.A191T	RP11-144L1.4_ENST00000419738.1_RNA|RP11-144L1.4_ENST00000426251.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	191			A -> T (in dbSNP:rs3820678).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					TTTTTGTAGCGCCAACAAAGT	0.433													G|||	916	0.182907	0.1437	0.147	5008	,	,		22883	0.1935		0.2187	False		,,,				2504	0.2137				p.A191T		Atlas-SNP	.											OR10R2,colon,carcinoma,-1,1	OR10R2	81	1	0			c.G571A						PASS	.	G	THR/ALA	614,3792	268.0+/-268.2	47,520,1636	144.0	137.0	139.0		571	1.2	0.9	1	dbSNP_107	139	1757,6843	318.8+/-313.9	170,1417,2713	yes	missense	OR10R2	NM_001004472.1	58	217,1937,4349	AA,AG,GG		20.4302,13.9355,18.23	benign	191/336	158450238	2371,10635	2203	4300	6503	SO:0001583	missense	343406	exon1			TGTAGCGCCAACA	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"""GPCR / Class A : Olfactory receptors"""	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.571G>A	1.37:g.158450238G>A	ENSP00000357134:p.Ala191Thr	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	213	96	0.450704	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	37	CCDS30898.1	425	0.1945970695970696	64	0.13008130081300814	59	0.16298342541436464	129	0.22552447552447552	173	0.22823218997361477	g	13.56	2.272389	0.40194	0.139355	0.204302	ENSG00000198965	ENST00000368152	T	0.36699	1.24	4.48	1.21	0.21127	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.05868	0.0153	N	0.12527	0.23	0.49915	P	1.6799999999994597E-4	B	0.32829	0.386	B	0.25884	0.064	T	0.29150	-1.0021	8	0.30078	T	0.28	.	5.88	0.18850	0.1009:0.0:0.3717:0.5274	rs3820678;rs17629439;rs56509961;rs57211339;rs3820678	191	Q8NGX6	O10R2_HUMAN	T	191	ENSP00000357134:A191T	ENSP00000357134:A191T	A	+	1	0	OR10R2	156716862	0.000000	0.05858	0.897000	0.35233	0.946000	0.59487	-1.780000	0.01775	0.466000	0.27193	0.655000	0.94253	GCC	G|0.816;A|0.184	0.184	strong		0.433	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558314	140558314	+	Silent	SNP	T	T	C	rs17844487	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140558314T>C	ENST00000239444.2	+	1	944	c.699T>C	c.(697-699)gtT>gtC	p.V233V	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	233	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACATTGAAGTTGTCGATGTCA	0.512													T|||	673	0.134385	0.0136	0.1441	5008	,	,		25997	0.3333		0.0805	False		,,,				2504	0.1411				p.V233V		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T699C						PASS	.						177.0	223.0	207.0					5																	140558314		2200	4217	6417	SO:0001819	synonymous_variant	56128	exon1			TGAAGTTGTCGAT	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.699T>C	5.37:g.140558314T>C		Somatic	985	0	0		WXS	Illumina HiSeq	Phase_I	205	48	0.234146	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			T|0.929;C|0.071	0.071	strong		0.512	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
VCX2	51480	hgsc.bcm.edu	37	X	8138080	8138080	+	Missense_Mutation	SNP	G	G	C	rs1058239	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:8138080G>C	ENST00000317103.4	-	3	719	c.413C>G	c.(412-414)aCc>aGc	p.T138S		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	138			T -> S (in dbSNP:rs1058239). {ECO:0000269|PubMed:10607842, ECO:0000269|PubMed:10903929, ECO:0000269|PubMed:15489334}.							endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				AACTTAGTCGGTGCTCTCGGA	0.527													C|||	3375	0.89404	0.7292	0.6859	3775	,	,		6534	0.7321		0.6243	False		,,,				2504	0.5818				p.T138S		Atlas-SNP	.											.	VCX2	16	.	0			c.C413G						PASS	.	C	SER/THR	3610,213		1462,158,528,9,37	70.0	70.0	70.0		413	0.2	0.0	X	dbSNP_86	70	5406,1298		1572,751,1511,100,347	yes	missense	VCX2	NM_016378.2	58	3034,909,2039,109,384	CC,CG,C,GG,G		19.3616,5.5715,14.3536	benign	138/140	8138080	9016,1511	2194	4281	6475	SO:0001583	missense	51480	exon3			TAGTCGGTGCTCT	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.413C>G	X.37:g.8138080G>C	ENSP00000321309:p.Thr138Ser	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	197	197	1	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	1504	0.9065702230259193	255	0.9514925373134329	170	0.85	277	0.9295302013422819	326	0.7056277056277056	C	0.003	-2.419037	0.00188	0.944285	0.806384	ENSG00000177504	ENST00000317103	T	0.15139	2.45	0.189	0.189	0.15119	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.09022	0.002	B	0.01281	0.0	T	0.36768	-0.9734	7	0.02654	T	1	.	.	.	.	rs1058239;rs3198854;rs1058239	138	Q9H322	VCX2_HUMAN	S	138	ENSP00000321309:T138S	ENSP00000321309:T138S	T	-	2	0	VCX2	8098080	0.106000	0.21978	0.003000	0.11579	0.003000	0.03518	-0.409000	0.07160	-0.759000	0.04684	-0.752000	0.03492	ACC	G|0.122;C|0.878	0.878	strong		0.527	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
COL27A1	85301	hgsc.bcm.edu	37	9	117050998	117050998	+	Missense_Mutation	SNP	G	G	A	rs10982134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:117050998G>A	ENST00000356083.3	+	43	4452	c.4061G>A	c.(4060-4062)cGa>cAa	p.R1354Q		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1354	Collagen-like 12.|Pro-rich.|Triple-helical region.		R -> Q (in dbSNP:rs10982134).		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						GTGGGTGATCGAGGAGACCGC	0.622													G|||	2122	0.423722	0.2436	0.4467	5008	,	,		16464	0.629		0.2922	False		,,,				2504	0.5746				p.R1354Q		Atlas-SNP	.											COL27A1,NS,carcinoma,+1,1	COL27A1	200	1	0			c.G4061A						PASS	.	G	GLN/ARG	1136,3270	403.5+/-332.8	151,834,1218	64.0	68.0	67.0		4061	1.8	1.0	9	dbSNP_120	67	2772,5828	439.0+/-359.1	449,1874,1977	yes	missense	COL27A1	NM_032888.2	43	600,2708,3195	AA,AG,GG		32.2326,25.783,30.0477	benign	1354/1861	117050998	3908,9098	2203	4300	6503	SO:0001583	missense	85301	exon43			GTGATCGAGGAGA	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.4061G>A	9.37:g.117050998G>A	ENSP00000348385:p.Arg1354Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	105	43	0.409524	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	843	0.385989010989011	116	0.23577235772357724	146	0.40331491712707185	357	0.6241258741258742	224	0.2955145118733509	G	13.36	2.214824	0.39102	0.25783	0.322326	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.90788	-2.73	4.77	1.84	0.25277	.	.	.	.	.	T	0.00012	0.0000	N	0.17474	0.49	0.27045	P	0.9639178	B	0.16166	0.016	B	0.09377	0.004	T	0.42103	-0.9471	8	0.10902	T	0.67	.	7.1776	0.25753	0.1735:0.1452:0.6813:0.0	rs10982134;rs56444233;rs59519437;rs10982134	1354	Q8IZC6	CORA1_HUMAN	Q	1354	ENSP00000348385:R1354Q	ENSP00000348385:R1354Q	R	+	2	0	COL27A1	116090819	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	1.987000	0.40687	0.544000	0.28883	0.491000	0.48974	CGA	G|0.655;A|0.345	0.345	strong		0.622	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
WWC2	80014	hgsc.bcm.edu	37	4	184236868	184236868	+	Missense_Mutation	SNP	G	G	A	rs4862155	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:184236868G>A	ENST00000403733.3	+	23	3764	c.3565G>A	c.(3565-3567)Gct>Act	p.A1189T	WWC2_ENST00000513834.1_Missense_Mutation_p.A1140T|WWC2_ENST00000508747.1_Missense_Mutation_p.A317T|WWC2_ENST00000448232.2_Missense_Mutation_p.A1213T|WWC2_ENST00000504005.1_Missense_Mutation_p.A871T	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	1189			A -> T (in dbSNP:rs4862155). {ECO:0000269|PubMed:17974005}.		negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		ATCCCTGCCAGCTGATGATGT	0.363													G|||	195	0.0389377	0.0234	0.0375	5008	,	,		19449	0.0228		0.0537	False		,,,				2504	0.0624				p.A1189T		Atlas-SNP	.											.	WWC2	78	.	0			c.G3565A						PASS	.	G	THR/ALA	121,4285	89.7+/-128.4	3,115,2085	96.0	84.0	88.0		3565	4.5	0.0	4	dbSNP_111	88	544,8056	150.6+/-205.5	21,502,3777	yes	missense	WWC2	NM_024949.5	58	24,617,5862	AA,AG,GG		6.3256,2.7463,5.113	probably-damaging	1189/1193	184236868	665,12341	2203	4300	6503	SO:0001583	missense	80014	exon23			CTGCCAGCTGATG	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.3565G>A	4.37:g.184236868G>A	ENSP00000384222:p.Ala1189Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	109	64	0.587156	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	88	0.040293040293040296	12	0.024390243902439025	19	0.052486187845303865	18	0.03146853146853147	39	0.051451187335092345	G	13.93	2.384963	0.42308	0.027463	0.063256	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61	5.31	4.47	0.54385	.	0.181999	0.37623	N	0.002003	T	0.19087	0.0458	M	0.78049	2.395	0.80722	D	1	D;B;D;D	0.63046	0.992;0.248;0.992;0.985	P;B;P;P	0.61592	0.891;0.112;0.891;0.802	T	0.54437	-0.8294	10	0.72032	D	0.01	-3.1407	13.9248	0.63955	0.0724:0.0:0.9276:0.0	rs4862155;rs52802328;rs61473673;rs4862155	1213;1189;317;1140	Q6AWC2-6;Q6AWC2;Q6AWC2-7;Q6AWC2-4	.;WWC2_HUMAN;.;.	T	1189;1140;1213;871;317	ENSP00000384222:A1189T;ENSP00000425054:A1140T;ENSP00000398577:A1213T;ENSP00000427569:A871T;ENSP00000420835:A317T	ENSP00000384222:A1189T	A	+	1	0	WWC2	184473862	1.000000	0.71417	0.026000	0.17262	0.166000	0.22503	8.426000	0.90273	1.486000	0.48398	0.655000	0.94253	GCT	G|0.953;A|0.047	0.047	strong		0.363	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
PFKP	5214	hgsc.bcm.edu	37	10	3155698	3155698	+	Silent	SNP	C	C	T	rs4881086	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:3155698C>T	ENST00000381125.4	+	13	1435	c.1359C>T	c.(1357-1359)ttC>ttT	p.F453F	PFKP_ENST00000381075.2_Silent_p.F445F	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	453	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		TTGACGGCTTCGCCAAGGGCC	0.672													C|||	1340	0.267572	0.3215	0.3127	5008	,	,		17197	0.1349		0.2485	False		,,,				2504	0.319				p.F453F		Atlas-SNP	.											PFKP_ENST00000381075,NS,carcinoma,0,2	PFKP	182	2	0			c.C1359T						PASS	.	C	,	1255,3151	419.1+/-338.5	210,835,1158	39.0	36.0	37.0		1335,1359	-10.3	0.0	10	dbSNP_111	37	2232,6368	367.3+/-334.7	277,1678,2345	yes	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	487,2513,3503	TT,TC,CC		25.9535,28.4839,26.8107	,	445/777,453/785	3155698	3487,9519	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon13			CGGCTTCGCCAAG	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1359C>T	10.37:g.3155698C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	28	0.411765	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	562	0.2573260073260073	164	0.3333333333333333	123	0.3397790055248619	85	0.1486013986013986	190	0.25065963060686014	C	0.187	-1.056887	0.01965	0.284839	0.259535	ENSG00000067057	ENST00000413079	.	.	.	5.16	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999564984	.	.	.	.	.	.	T	0.07986	-1.0744	3	.	.	.	.	12.2192	0.54425	0.0:0.2036:0.2044:0.5919	rs4881086;rs11542773;rs17285564;rs60582502;rs4881086	.	.	.	C	17	.	.	R	+	1	0	PFKP	3145698	0.000000	0.05858	0.004000	0.12327	0.016000	0.09150	-3.262000	0.00535	-3.323000	0.00187	-1.844000	0.00574	CGC	C|0.734;T|0.266	0.266	strong		0.672	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
OASL	8638	hgsc.bcm.edu	37	12	121471337	121471337	+	Silent	SNP	G	G	A	rs3213545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121471337G>A	ENST00000257570.5	-	2	678	c.408C>T	c.(406-408)ctC>ctT	p.L136L	OASL_ENST00000339275.5_Silent_p.L136L	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	136					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)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGGTGAAGACGAGAGCATCGG	0.602													G|||	1568	0.313099	0.1293	0.2839	5008	,	,		19668	0.4692		0.3072	False		,,,				2504	0.4274				p.L136L	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.C408T						PASS	.	G	,	645,3761	274.6+/-272.0	46,553,1604	120.0	101.0	108.0	http://www.ncbi.nlm.nih.gov/pubmed?term	408,408	-2.8	0.0	12	dbSNP_106	108	2585,6015	421.5+/-353.7	411,1763,2126	no	coding-synonymous,coding-synonymous	OASL	NM_003733.2,NM_198213.1	,	457,2316,3730	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0581,14.6391,24.8347	,	136/515,136/256	121471337	3230,9776	2203	4300	6503	SO:0001819	synonymous_variant	8638	exon2			GAAGACGAGAGCA	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.408C>T	12.37:g.121471337G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	95	56	0.589474	NM_198213	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Silent	SNP	ENST00000257570.5	37	CCDS9211.1																																																																																			G|0.722;A|0.278	0.278	strong		0.602	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733	
RXFP2	122042	hgsc.bcm.edu	37	13	32367214	32367214	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32367214G>A	ENST00000298386.2	+	16	1846	c.1775G>A	c.(1774-1776)gGa>gAa	p.G592E	RXFP2_ENST00000380314.1_Missense_Mutation_p.G568E	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	592					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		TATTCTCTTGGAATTTTCCTA	0.294																																					p.G592E		Atlas-SNP	.											RXFP2,colon,carcinoma,0,1	RXFP2	95	1	0			c.G1775A						scavenged	.						30.0	34.0	33.0					13																	32367214		2188	4292	6480	SO:0001583	missense	122042	exon16			CTCTTGGAATTTT	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"""GPCR / Class A : Relaxin family peptide receptors"""	17318	protein-coding gene	gene with protein product		606655	"""leucine-rich repeat-containing G protein-coupled receptor 8"""	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1775G>A	13.37:g.32367214G>A	ENSP00000298386:p.Gly592Glu	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	68	3	0.0441176	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673744	0.67928	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.37235	1.21;1.21	5.73	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.102880	0.64402	D	0.000003	T	0.55401	0.1918	M	0.70275	2.135	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.65684	0.937;0.937	T	0.53920	-0.8370	10	0.28530	T	0.3	.	13.8607	0.63559	0.0:0.0:0.8462:0.1538	.	568;592	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	E	568;592	ENSP00000369670:G568E;ENSP00000298386:G592E	ENSP00000298386:G592E	G	+	2	0	RXFP2	31265214	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.997000	0.49457	1.412000	0.46977	0.655000	0.94253	GGA	.	.	none		0.294	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234952	26234952	+	Silent	SNP	A	A	G	rs2050948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26234952A>G	ENST00000244534.5	-	1	264	c.210T>C	c.(208-210)gcT>gcC	p.A70A		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	70	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				CATCGTAGCCAGCAGCCGCAA	0.552													G|||	844	0.16853	0.2262	0.1124	5008	,	,		15592	0.1022		0.1571	False		,,,				2504	0.2106				p.A70A		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.T210C						PASS	.	G		849,3557		77,695,1431	66.0	75.0	72.0		210	-10.5	0.1	6	dbSNP_94	72	1152,7448		70,1012,3218	no	coding-synonymous	HIST1H1D	NM_005320.2		147,1707,4649	GG,GA,AA		13.3953,19.2692,15.3852		70/222	26234952	2001,11005	2203	4300	6503	SO:0001819	synonymous_variant	3007	exon1			GTAGCCAGCAGCC	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.210T>C	6.37:g.26234952A>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	144	68	0.472222	NM_005320	B2R751|Q2M2I2	Silent	SNP	ENST00000244534.5	37	CCDS4597.1																																																																																			A|0.855;G|0.145	0.145	strong		0.552	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
TUBGCP5	114791	hgsc.bcm.edu	37	15	22846897	22846897	+	Missense_Mutation	SNP	G	G	A	rs145668941	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:22846897G>A	ENST00000283645.4	+	8	902	c.772G>A	c.(772-774)Gtt>Att	p.V258I	TUBGCP5_ENST00000453949.2_Missense_Mutation_p.V258I	NM_052903.4	NP_443135.3	Q96RT8	GCP5_HUMAN	tubulin, gamma complex associated protein 5	258					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gamma-tubulin ring complex (GO:0008274)|microtubule (GO:0005874)|nucleus (GO:0005634)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(5)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(23)|prostate(1)|skin(2)|urinary_tract(1)	46		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;2.86e-06)|Epithelial(43;2.63e-05)|BRCA - Breast invasive adenocarcinoma(123;0.000949)		TCCATTGTATGTTCCAGATGA	0.348													G|||	17	0.00339457	0.0	0.0101	5008	,	,		18227	0.0		0.005	False		,,,				2504	0.0051				p.V258I		Atlas-SNP	.											.	TUBGCP5	82	.	0			c.G772A						PASS	.	G	ILE/VAL,ILE/VAL	7,4399		0,7,2196	147.0	127.0	134.0		772,772	1.9	0.9	15	dbSNP_134	134	87,8513		0,87,4213	yes	missense,missense	TUBGCP5	NM_001102610.1,NM_052903.4	29,29	0,94,6409	AA,AG,GG		1.0116,0.1589,0.7227	benign,benign	258/1025,258/1025	22846897	94,12912	2203	4300	6503	SO:0001583	missense	114791	exon8			TTGTATGTTCCAG	AB067486	CCDS73697.1, CCDS73698.1	15q11.1	2014-04-17			ENSG00000153575	ENSG00000275835			18600	protein-coding gene	gene with protein product	"""gamma-tubulin complex component GCP5"""	608147				11694571	Standard	NM_052903		Approved	GCP5, KIAA1899	uc001yur.4	Q96RT8	OTTHUMG00000188371	ENST00000283645.4:c.772G>A	15.37:g.22846897G>A	ENSP00000283645:p.Val258Ile	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	22	0.392857	NM_052903	E9PB12|Q6IQ52|Q96PY8	Missense_Mutation	SNP	ENST00000283645.4	37	CCDS10008.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	.	10.20	1.285405	0.23478	0.001589	0.010116	ENSG00000153575	ENST00000283645;ENST00000453949	T;T	0.22539	1.95;1.95	4.93	1.93	0.25924	.	0.337379	0.28338	N	0.015706	T	0.07773	0.0195	N	0.24115	0.695	0.31201	N	0.699825	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10870	-1.0611	10	0.33940	T	0.23	-9.0585	4.4546	0.11637	0.3066:0.0:0.5464:0.147	.	258;258	Q96RT8;E9PB12	GCP5_HUMAN;.	I	258	ENSP00000283645:V258I;ENSP00000409217:V258I	ENSP00000283645:V258I	V	+	1	0	TUBGCP5	20398338	0.978000	0.34361	0.945000	0.38365	0.997000	0.91878	1.660000	0.37397	0.236000	0.21180	0.655000	0.94253	GTT	G|0.993;A|0.007	0.007	strong		0.348	TUBGCP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250998.2	NM_052903	
SLC5A8	160728	hgsc.bcm.edu	37	12	101552075	101552075	+	Silent	SNP	G	G	A	rs2671444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101552075G>A	ENST00000536262.2	-	14	2220	c.1662C>T	c.(1660-1662)taC>taT	p.Y554Y		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						TGGTTAGTATGTATCTGGGGT	0.353													A|||	3771	0.752995	0.9032	0.6023	5008	,	,		14022	0.8115		0.6352	False		,,,				2504	0.7178				p.Y554Y	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.C1662T						PASS	.	A		3818,586	256.4+/-261.2	1654,510,38	130.0	160.0	150.0		1662	1.5	0.2	12	dbSNP_100	150	5531,3067	470.7+/-367.9	1770,1991,538	no	coding-synonymous	SLC5A8	NM_145913.3		3424,2501,576	AA,AG,GG		35.6711,13.3061,28.0957		554/611	101552075	9349,3653	2202	4299	6501	SO:0001819	synonymous_variant	160728	exon14			TAGTATGTATCTG	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"""Solute carriers"""	19119	protein-coding gene	gene with protein product		608044	"""solute carrier family 5 (iodide transporter), member 8"""			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1662C>T	12.37:g.101552075G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_145913		Silent	SNP	ENST00000536262.2	37	CCDS9080.1																																																																																			G|0.279;A|0.721	0.721	strong		0.353	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913	
KIF17	57576	hgsc.bcm.edu	37	1	21042094	21042094	+	Silent	SNP	G	G	A	rs12046928	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:21042094G>A	ENST00000247986.2	-	2	580	c.270C>T	c.(268-270)taC>taT	p.Y90Y	KIF17_ENST00000400463.3_Silent_p.Y90Y|KIF17_ENST00000375044.1_De_novo_Start_OutOfFrame			Q9P2E2	KIF17_HUMAN	kinesin family member 17	90	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CTGTCTGGCCGTAGGCAAAGA	0.647													G|||	1404	0.280351	0.0741	0.1614	5008	,	,		19859	0.7232		0.1451	False		,,,				2504	0.3262				p.Y90Y		Atlas-SNP	.											.	KIF17	130	.	0			c.C270T						PASS	.	G	,	369,4037	187.1+/-213.8	14,341,1848	98.0	83.0	88.0		270,270	-5.7	0.9	1	dbSNP_120	88	1106,7494	230.8+/-265.0	82,942,3276	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	96,1283,5124	AA,AG,GG		12.8605,8.3749,11.3409	,	90/1029,90/1030	21042094	1475,11531	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon2			CTGGCCGTAGGCA	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.270C>T	1.37:g.21042094G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			G|0.810;A|0.190	0.190	strong		0.647	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
RNPEP	6051	hgsc.bcm.edu	37	1	201969082	201969082	+	Silent	SNP	G	G	A	rs1130790	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201969082G>A	ENST00000295640.4	+	6	1186	c.1143G>A	c.(1141-1143)caG>caA	p.Q381Q	RP11-465N4.4_ENST00000419190.1_RNA|RP11-465N4.4_ENST00000415582.1_RNA|RNPEP_ENST00000367286.3_Silent_p.Q342Q|RNPEP_ENST00000471105.1_3'UTR	NM_020216.3	NP_064601.3	Q9H4A4	AMPB_HUMAN	arginyl aminopeptidase (aminopeptidase B)	381					leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|metalloexopeptidase activity (GO:0008235)|zinc ion binding (GO:0008270)	p.Q381Q(1)		breast(1)|endometrium(4)|large_intestine(4)|lung(6)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(1967;3.23e-08)|Colorectal(1306;0.005)		TGCTGCGTCAGCACATGGACA	0.577											OREG0014093	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1545	0.308506	0.1558	0.438	5008	,	,		18265	0.3978		0.4284	False		,,,				2504	0.2076				p.Q381Q	GBM(19;39 479 7473 13131 19462)	Atlas-SNP	.											RNPEP,NS,carcinoma,0,2	RNPEP	39	2	1	Substitution - coding silent(1)	stomach(1)	c.G1143A						PASS	.	G		802,3604	320.2+/-296.5	72,658,1473	96.0	83.0	87.0		1143	4.3	1.0	1	dbSNP_86	87	3723,4877	529.8+/-381.7	795,2133,1372	no	coding-synonymous	RNPEP	NM_020216.3		867,2791,2845	AA,AG,GG		43.2907,18.2025,34.7916		381/651	201969082	4525,8481	2203	4300	6503	SO:0001819	synonymous_variant	6051	exon6			GCGTCAGCACATG	BC001064	CCDS1418.1	1q32	2008-02-05			ENSG00000176393	ENSG00000176393	3.4.11.6		10078	protein-coding gene	gene with protein product		602675				9533033, 10467730	Standard	NM_020216		Approved		uc001gxd.3	Q9H4A4	OTTHUMG00000035866	ENST00000295640.4:c.1143G>A	1.37:g.201969082G>A		Somatic	119	0	0	2125	WXS	Illumina HiSeq	Phase_I	170	93	0.547059	NM_020216	Q9BVM9|Q9H1D4|Q9NPT7	Silent	SNP	ENST00000295640.4	37	CCDS1418.1																																																																																			G|0.652;A|0.348	0.348	strong		0.577	RNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087345.1	NM_020216	
PRPF39	55015	hgsc.bcm.edu	37	14	45564675	45564675	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:45564675C>T	ENST00000355765.6	+	2	403	c.233C>T	c.(232-234)cCt>cTt	p.P78L		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	78					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						GCAAATTTCCCTCCAGAATAT	0.398																																					p.P78L		Atlas-SNP	.											.	PRPF39	46	.	0			c.C233T						PASS	.						40.0	40.0	40.0					14																	45564675		1996	4194	6190	SO:0001583	missense	55015	exon2			ATTTCCCTCCAGA	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.233C>T	14.37:g.45564675C>T	ENSP00000348010:p.Pro78Leu	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	C	18.84	3.710181	0.68730	.	.	ENSG00000185246	ENST00000355765;ENST00000553605	T	0.50548	0.74	5.72	5.72	0.89469	.	.	.	.	.	T	0.49064	0.1535	N	0.22421	0.69	0.80722	D	1	P	0.47962	0.903	P	0.53266	0.722	T	0.28427	-1.0044	9	0.23891	T	0.37	-12.9614	19.4498	0.94862	0.0:1.0:0.0:0.0	.	78	Q86UA1	PRP39_HUMAN	L	78	ENSP00000348010:P78L	ENSP00000348010:P78L	P	+	2	0	PRPF39	44634425	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.130000	0.77235	2.702000	0.92279	0.591000	0.81541	CCT	.	.	none		0.398	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
BTRC	8945	hgsc.bcm.edu	37	10	103298099	103298099	+	Missense_Mutation	SNP	G	G	T	rs4151060	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:103298099G>T	ENST00000370187.3	+	13	1745	c.1627G>T	c.(1627-1629)Gca>Tca	p.A543S	BTRC_ENST00000493877.1_3'UTR|BTRC_ENST00000408038.2_Missense_Mutation_p.A507S|BTRC_ENST00000393441.4_Missense_Mutation_p.A502S	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	543			A -> S (in dbSNP:rs4151060).		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|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 dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		CCGTGCTCCTGCAGGGACACT	0.453													G|||	69	0.013778	0.0061	0.0187	5008	,	,		16448	0.0		0.0447	False		,,,				2504	0.0031				p.A543S		Atlas-SNP	.											.	BTRC	64	.	0			c.G1627T						PASS	.	G	SER/ALA,SER/ALA	50,4356	51.6+/-87.1	0,50,2153	93.0	99.0	97.0		1519,1627	5.9	1.0	10	dbSNP_110	97	411,8189	129.8+/-187.9	10,391,3899	yes	missense,missense	BTRC	NM_003939.3,NM_033637.2	99,99	10,441,6052	TT,TG,GG		4.7791,1.1348,3.5445	benign,benign	507/570,543/606	103298099	461,12545	2203	4300	6503	SO:0001583	missense	8945	exon13			GCTCCTGCAGGGA	Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1144	protein-coding gene	gene with protein product		603482	"""beta-transducin repeat containing"""			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.1627G>T	10.37:g.103298099G>T	ENSP00000359206:p.Ala543Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_033637	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	37	CCDS7512.1	40	0.018315018315018316	3	0.006097560975609756	7	0.019337016574585635	0	0.0	30	0.0395778364116095	G	15.10	2.732020	0.48939	0.011348	0.047791	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	T;T;T	0.59224	1.33;1.33;0.28	5.86	5.86	0.93980	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.08891	0.0220	N	0.05031	-0.125	0.80722	D	1	B;B;B	0.14438	0.0;0.0;0.01	B;B;B	0.22152	0.003;0.004;0.038	T	0.10132	-1.0643	10	0.16896	T	0.51	-14.6456	20.1858	0.98214	0.0:0.0:1.0:0.0	rs4151060;rs12783576;rs52831690;rs59128439;rs4151060	517;507;543	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	S	543;502;507	ENSP00000359206:A543S;ENSP00000377088:A502S;ENSP00000385339:A507S	ENSP00000359206:A543S	A	+	1	0	BTRC	103288089	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.442000	0.97566	2.777000	0.95525	0.591000	0.81541	GCA	G|0.972;T|0.028	0.028	strong		0.453	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637	
GSTM5	2949	hgsc.bcm.edu	37	1	110257836	110257836	+	Silent	SNP	T	T	C	rs386634508|rs67757008|rs61744262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110257836T>C	ENST00000256593.3	+	7	599	c.541T>C	c.(541-543)Ttg>Ctg	p.L181L	GSTM5_ENST00000369813.1_Silent_p.L140L|GSTM5_ENST00000369812.5_Silent_p.L200L|GSTM5_ENST00000492718.1_3'UTR	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	181	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)			NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	CTTCCTAAACTTGAAGGACTT	0.483													T|||	703	0.140375	0.3941	0.0663	5008	,	,		19875	0.001		0.0845	False		,,,				2504	0.0511				p.L181L		Atlas-SNP	.											GSTM5,brain,glioma,0,4	GSTM5	89	4	0			c.T541C						PASS	.						176.0	197.0	190.0					1																	110257836		2203	4300	6503	SO:0001819	synonymous_variant	2949	exon7			CTAAACTTGAAGG	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.541T>C	1.37:g.110257836T>C		Somatic	447	2	0.00447427		WXS	Illumina HiSeq	Phase_I	473	239	0.505285	NM_000851	A8K0V8|Q6PD78	Silent	SNP	ENST00000256593.3	37	CCDS811.1																																																																																			CAAATC|0.500;TAAACT|0.500	.	alt		0.483	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851	
ZGRF1	55345	hgsc.bcm.edu	37	4	113524723	113524723	+	Missense_Mutation	SNP	G	G	A	rs17669218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:113524723G>A	ENST00000505019.1	-	10	3058	c.2933C>T	c.(2932-2934)aCa>aTa	p.T978I	C4orf21_ENST00000309071.5_Missense_Mutation_p.T978I	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		978			T -> I (in dbSNP:rs17669218).			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)		TAACTCTGGTGTCTCTGTCAT	0.388													G|||	184	0.0367412	0.0068	0.0648	5008	,	,		17252	0.0		0.1183	False		,,,				2504	0.0112				p.T978I		Atlas-SNP	.											.	C4orf21	223	.	0			c.C2933T						PASS	.	G	ILE/THR	76,4330	67.0+/-104.6	1,74,2128	216.0	176.0	190.0		2933	1.6	0.0	4	dbSNP_123	190	866,7734	195.9+/-241.0	46,774,3480	yes	missense	C4orf21	NM_018392.4	89	47,848,5608	AA,AG,GG		10.0698,1.7249,7.2428	probably-damaging	978/2105	113524723	942,12064	2203	4300	6503	SO:0001583	missense	55345	exon10			TCTGGTGTCTCTG																												ENST00000505019.1:c.2933C>T	4.37:g.113524723G>A	ENSP00000424737:p.Thr978Ile	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	120	50	0.416667	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		117	0.05357142857142857	2	0.0040650406504065045	22	0.06077348066298342	0	0.0	93	0.12269129287598944	G	11.10	1.539541	0.27563	0.017249	0.100698	ENSG00000138658	ENST00000505019;ENST00000309071	D;T	0.81821	-1.54;1.88	5.38	1.63	0.23807	.	0.602886	0.15072	N	0.282141	T	0.03095	0.0091	L	0.60455	1.87	0.80722	P	0.0	B;B	0.24186	0.099;0.069	B;B	0.24701	0.034;0.055	T	0.47861	-0.9084	9	0.87932	D	0	0.4098	4.8825	0.13686	0.1598:0.0:0.5436:0.2966	rs17669218;rs52823729;rs57738409;rs17669218	978;978	Q86YA3;G5EA02	CD021_HUMAN;.	I	978	ENSP00000424737:T978I;ENSP00000309095:T978I	ENSP00000309095:T978I	T	-	2	0	C4orf21	113744172	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.313000	0.19415	-0.012000	0.14223	-0.266000	0.10368	ACA	G|0.937;A|0.063	0.063	strong		0.388	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
BACH2	60468	hgsc.bcm.edu	37	6	90660319	90660319	+	Silent	SNP	T	T	C	rs9451298	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90660319T>C	ENST00000257749.4	-	7	2213	c.1506A>G	c.(1504-1506)gtA>gtG	p.V502V	RP3-512E2.2_ENST00000445838.1_RNA|BACH2_ENST00000343122.3_Silent_p.V502V|RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000537989.1_Silent_p.V502V	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	502						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)	p.V502V(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		CTTTGATTGGTACCGGGCAGC	0.662													C|||	1555	0.310503	0.4251	0.1931	5008	,	,		17279	0.2361		0.2773	False		,,,				2504	0.3497				p.V502V		Atlas-SNP	.											BACH2_ENST00000257749,NS,carcinoma,0,3	BACH2	224	3	1	Substitution - coding silent(1)	stomach(1)	c.A1506G						PASS	.	C	,	1636,2770	644.3+/-398.0	306,1024,873	51.0	59.0	56.0		1506,1506	5.3	1.0	6	dbSNP_119	56	2434,6166	683.4+/-403.9	355,1724,2221	no	coding-synonymous,coding-synonymous	BACH2	NM_001170794.1,NM_021813.2	,	661,2748,3094	CC,CT,TT		28.3023,37.1312,31.2932	,	502/842,502/842	90660319	4070,8936	2203	4300	6503	SO:0001819	synonymous_variant	60468	exon5			GATTGGTACCGGG	AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.1506A>G	6.37:g.90660319T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																			T|0.695;C|0.305	0.305	strong		0.662	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813	
COQ7	10229	hgsc.bcm.edu	37	16	19085298	19085298	+	Missense_Mutation	SNP	C	C	T	rs11074359	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:19085298C>T	ENST00000321998.5	+	3	374	c.308C>T	c.(307-309)aCg>aTg	p.T103M	COQ7_ENST00000544894.2_Missense_Mutation_p.T65M|COQ7_ENST00000569127.1_Missense_Mutation_p.T80M|COQ7_ENST00000568985.1_Missense_Mutation_p.T103M	NM_016138.4	NP_057222.2	Q99807	COQ7_HUMAN	coenzyme Q7 homolog, ubiquinone (yeast)	103	2 X approximate tandem repeats.		T -> M (in dbSNP:rs11074359). {ECO:0000269|PubMed:10373327, ECO:0000269|PubMed:10501970, ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9020081}.		age-dependent response to oxidative stress (GO:0001306)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|in utero embryonic development (GO:0001701)|mitochondrial ATP synthesis coupled electron transport (GO:0042775)|mitochondrion morphogenesis (GO:0070584)|neural tube formation (GO:0001841)|neurogenesis (GO:0022008)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|skin(3)|urinary_tract(1)	10						TTGATGGTTACGTTCAGGGTC	0.448													C|||	2878	0.574681	0.2655	0.6196	5008	,	,		19214	0.8145		0.6461	False		,,,				2504	0.6401				p.T103M		Atlas-SNP	.											.	COQ7	16	.	0			c.C308T						PASS	.	C	MET/THR,MET/THR	1489,2905	475.2+/-357.2	229,1031,937	125.0	104.0	111.0		194,308	5.9	0.3	16	dbSNP_120	111	5496,3104	657.7+/-401.5	1773,1950,577	yes	missense,missense	COQ7	NM_001190983.1,NM_016138.4	81,81	2002,2981,1514	TT,TC,CC		36.093,33.8871,46.2444	possibly-damaging,possibly-damaging	65/180,103/218	19085298	6985,6009	2197	4300	6497	SO:0001583	missense	10229	exon3			TGGTTACGTTCAG	U81276	CCDS10574.1, CCDS53993.1	16p12.3	2008-05-14	2001-11-28		ENSG00000167186	ENSG00000167186			2244	protein-coding gene	gene with protein product		601683	"""coenzyme Q, 7 (rat, yeast) homolog"""			9020081, 10373325	Standard	NM_016138		Approved	CLK-1, CAT5	uc002dfr.3	Q99807	OTTHUMG00000131455	ENST00000321998.5:c.308C>T	16.37:g.19085298C>T	ENSP00000322316:p.Thr103Met	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	160	75	0.46875	NM_016138	B2RDA9|Q9BTT7|Q9H0T5|Q9UEW5|Q9UNR5	Missense_Mutation	SNP	ENST00000321998.5	37	CCDS10574.1	1329	0.6085164835164835	146	0.2967479674796748	225	0.6215469613259669	473	0.8269230769230769	485	0.6398416886543535	C	18.35	3.605641	0.66445	0.338871	0.63907	ENSG00000167186	ENST00000321998;ENST00000544894	T;T	0.43688	0.94;0.94	5.91	5.91	0.95273	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);	0.424017	0.29616	N	0.011650	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	P	0.47034	0.889	P	0.50109	0.631	T	0.13791	-1.0496	9	0.66056	D	0.02	-4.7588	19.9089	0.97019	0.0:1.0:0.0:0.0	rs11074359;rs17357840;rs60588972;rs11074359	103	Q99807	COQ7_HUMAN	M	103;65	ENSP00000322316:T103M;ENSP00000442923:T65M	ENSP00000322316:T103M	T	+	2	0	COQ7	18992799	0.228000	0.23718	0.328000	0.25416	0.913000	0.54294	3.071000	0.50041	2.793000	0.96121	0.655000	0.94253	ACG	C|0.434;T|0.566	0.566	strong		0.448	COQ7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254275.3	NM_016138	
GPR112	139378	hgsc.bcm.edu	37	X	135426693	135426693	+	Missense_Mutation	SNP	A	A	G	rs4829829	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135426693A>G	ENST00000394143.1	+	6	1119	c.828A>G	c.(826-828)atA>atG	p.I276M	GPR112_ENST00000370652.1_Missense_Mutation_p.I276M|GPR112_ENST00000412101.1_Missense_Mutation_p.I71M|GPR112_ENST00000287534.4_Missense_Mutation_p.I213M|GPR112_ENST00000394141.1_Missense_Mutation_p.I71M	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	276			I -> M (in dbSNP:rs4829829). {ECO:0000269|Ref.2}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					GCATACCTATATTTGCAACTG	0.363													a|||	1702	0.450861	0.4228	0.3545	3775	,	,		15401	0.2024		0.3738	False		,,,				2504	0.3241				p.I276M		Atlas-SNP	.											.	GPR112	459	.	0			c.A828G						PASS	.		MET/ILE	2087,1748		484,812,307,336,264	199.0	154.0	169.0		828	-8.6	0.0	X	dbSNP_111	169	3203,3525		555,1185,908,688,964	yes	missense	GPR112	NM_153834.3	10	1039,1997,1215,1024,1228	GG,GA,G,AA,A		47.607,45.5802,49.9195	benign	276/3081	135426693	5290,5273	2203	4300	6503	SO:0001583	missense	139378	exon6			ACCTATATTTGCA	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.828A>G	X.37:g.135426693A>G	ENSP00000377699:p.Ile276Met	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	710	0.4279686558167571	138	0.372972972972973	80	0.27972027972027974	76	0.15702479338842976	187	0.3191126279863481	a	2.435	-0.329891	0.05314	0.544198	0.47607	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.30448	1.55;1.55;1.53;1.66;1.53	4.27	-8.55	0.00908	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.09377	0.004;0.004;0.002	T	0.43228	-0.9404	8	0.37606	T	0.19	.	0.3544	0.00354	0.2435:0.2422:0.2647:0.2496	rs4829829;rs59872615;rs4829829	213;71;276	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	M	276;276;71;213;71	ENSP00000377699:I276M;ENSP00000359686:I276M;ENSP00000416526:I71M;ENSP00000287534:I213M;ENSP00000377697:I71M	ENSP00000287534:I213M	I	+	3	3	GPR112	135254359	0.001000	0.12720	0.000000	0.03702	0.050000	0.14768	-0.872000	0.04219	-2.190000	0.00757	-0.485000	0.04761	ATA	A|0.517;0|0.025	.	strong		0.363	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
ZNF131	7690	hgsc.bcm.edu	37	5	43161351	43161351	+	Splice_Site	SNP	G	G	A	rs71627581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:43161351G>A	ENST00000399534.1	+	5	416	c.372G>A	c.(370-372)agG>agA	p.R124R	ZNF131_ENST00000509931.1_Intron|ZNF131_ENST00000306938.4_Splice_Site_p.R124R|ZNF131_ENST00000509156.1_Splice_Site_p.R124R|ZNF131_ENST00000505606.2_Splice_Site_p.R124R|ZNF131_ENST00000509634.1_Splice_Site_p.R124R			P52739	ZN131_HUMAN	zinc finger protein 131	124					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	17						TGTATTTCAGGAACAAAGAAA	0.323													G|||	180	0.0359425	0.003	0.0591	5008	,	,		18963	0.002		0.1193	False		,,,				2504	0.0133				p.R124R		Atlas-SNP	.											.	ZNF131	51	.	0			c.G372A						PASS	.	G		79,3525		0,79,1723	63.0	59.0	60.0		372	0.6	1.0	5	dbSNP_130	60	851,7277		44,763,3257	yes	coding-synonymous-near-splice	ZNF131	NM_003432.1		44,842,4980	AA,AG,GG		10.47,2.192,7.927		124/590	43161351	930,10802	1802	4064	5866	SO:0001630	splice_region_variant	7690	exon5			TTTCAGGAACAAA	U09410	CCDS43313.1	5p12	2013-01-09	2006-06-13		ENSG00000172262	ENSG00000172262		"""Zinc fingers, C2H2-type"", ""-"", ""BTB/POZ domain containing"""	12915	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 35"""	604073	"""zinc finger protein 131 (clone pHZ-10)"""				Standard	XM_005248359		Approved	ZBTB35, pHZ-10	uc003jnk.3	P52739	OTTHUMG00000162223	ENST00000399534.1:c.372-1G>A	5.37:g.43161351G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_003432	B4DRL3|Q6PIF0	Silent	SNP	ENST00000399534.1	37																																																																																				G|0.937;A|0.063	0.063	strong		0.323	ZNF131-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000367982.1	NM_003432	Silent
SERPINC1	462	hgsc.bcm.edu	37	1	173878832	173878832	+	Silent	SNP	T	T	C	rs5878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:173878832T>C	ENST00000367698.3	-	5	1129	c.1011A>G	c.(1009-1011)caA>caG	p.Q337Q	SERPINC1_ENST00000494024.1_5'Flank	NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	337					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	CCAGCCACTCTTGCAGCACCT	0.552													C|||	2683	0.535743	0.8442	0.3732	5008	,	,		20073	0.5923		0.3469	False		,,,				2504	0.3701				p.Q337Q		Atlas-SNP	.											.	SERPINC1	57	.	0			c.A1011G						PASS	.	C		3358,1048	383.0+/-324.7	1281,796,126	164.0	160.0	161.0		1011	3.5	1.0	1	dbSNP_52	161	2992,5608	666.0+/-402.3	516,1960,1824	no	coding-synonymous	SERPINC1	NM_000488.3		1797,2756,1950	CC,CT,TT		34.7907,23.7857,48.8236		337/465	173878832	6350,6656	2203	4300	6503	SO:0001819	synonymous_variant	462	exon5			CCACTCTTGCAGC	X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"""Serine (or cysteine) peptidase inhibitors"""	775	protein-coding gene	gene with protein product	"""antithrombin III"", ""signal peptide antithrombin part 1"", ""coding sequence signal peptide antithrombin part 1"", ""antithrombin (aa 375-432)"""	107300	"""serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"""	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.1011A>G	1.37:g.173878832T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_000488	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Silent	SNP	ENST00000367698.3	37	CCDS1313.1																																																																																			T|0.482;C|0.518	0.518	strong		0.552	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488	
OR6Q1	219952	hgsc.bcm.edu	37	11	57799183	57799183	+	Silent	SNP	C	C	T	rs7123727	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57799183C>T	ENST00000302622.3	+	1	782	c.759C>T	c.(757-759)agC>agT	p.S253S	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	253						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				CTGTGGTGAGCCTCTTCTATG	0.517													C|||	754	0.150559	0.0938	0.1614	5008	,	,		22234	0.1022		0.2823	False		,,,				2504	0.1339				p.S253S		Atlas-SNP	.											.	OR6Q1	58	.	0			c.C759T						PASS	.	C		497,3905	230.4+/-244.6	30,437,1734	183.0	157.0	166.0		759	3.3	0.9	11	dbSNP_116	166	2503,6089	410.7+/-350.2	351,1801,2144	no	coding-synonymous	OR6Q1	NM_001005186.2		381,2238,3878	TT,TC,CC		29.1318,11.2903,23.0876		253/318	57799183	3000,9994	2201	4296	6497	SO:0001819	synonymous_variant	219952	exon1			GGTGAGCCTCTTC	AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"""GPCR / Class A : Olfactory receptors"""	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.759C>T	11.37:g.57799183C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	169	89	0.526627	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Silent	SNP	ENST00000302622.3	37	CCDS31541.1																																																																																			C|0.778;T|0.222	0.222	strong		0.517	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
HECTD4	283450	hgsc.bcm.edu	37	12	112600883	112600883	+	Silent	SNP	C	C	T	rs183882784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:112600883C>T	ENST00000430131.2	-	74	12962	c.11817G>A	c.(11815-11817)ccG>ccA	p.P3939P	HECTD4_ENST00000550722.1_Silent_p.P4215P|HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000377560.5_Silent_p.P4189P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3939	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										TCATGGGGTACGGGGGCACAT	0.602													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		16711	0.001		0.006	False		,,,				2504	0.0051				p.P4227P		Atlas-SNP	.											.	.	.	.	0			c.G12681A						PASS	.	C		6,4042		0,6,2018	89.0	98.0	95.0		12567	-11.6	0.1	12		95	63,8265		0,63,4101	no	coding-synonymous	C12orf51	NM_001109662.2		0,69,6119	TT,TC,CC		0.7565,0.1482,0.5575		4189/4247	112600883	69,12307	2024	4164	6188	SO:0001819	synonymous_variant	283450	exon75			GGGGTACGGGGGC	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.11817G>A	12.37:g.112600883C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	178	86	0.483146	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.602	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
PCDHB7	56129	hgsc.bcm.edu	37	5	140554606	140554606	+	Silent	SNP	T	T	C	rs11741863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140554606T>C	ENST00000231137.3	+	1	2364	c.2190T>C	c.(2188-2190)ttT>ttC	p.F730F	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	730					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGGCCCCTTTCCACGACATC	0.647													T|||	1352	0.269968	0.0484	0.3055	5008	,	,		22194	0.5278		0.2296	False		,,,				2504	0.32				p.F730F		Atlas-SNP	.											PCDHB7,caecum,carcinoma,0,1	PCDHB7	231	1	0			c.T2190C						PASS	.	T		219,4187		9,201,1993	82.0	130.0	114.0		2190	-3.4	0.5	5	dbSNP_120	114	1407,7193		209,989,3102	no	coding-synonymous	PCDHB7	NM_018940.2		218,1190,5095	CC,CT,TT		16.3605,4.9705,12.5019		730/794	140554606	1626,11380	2203	4300	6503	SO:0001819	synonymous_variant	56129	exon1			CCCCTTTCCACGA	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2190T>C	5.37:g.140554606T>C		Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			T|0.805;C|0.195	0.195	strong		0.647	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
TULP4	56995	hgsc.bcm.edu	37	6	158927651	158927651	+	Silent	SNP	A	A	G	rs3828712	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:158927651A>G	ENST00000367097.3	+	14	5914	c.4557A>G	c.(4555-4557)ctA>ctG	p.L1519L	TULP4_ENST00000367094.2_3'UTR	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	1519	TUB.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		CGTACATTCTAGACTTCCAGT	0.542													A|||	2156	0.430511	0.4985	0.3948	5008	,	,		18291	0.3661		0.3549	False		,,,				2504	0.5082				p.L1519L		Atlas-SNP	.											.	TULP4	137	.	0			c.A4557G						PASS	.	A	,	2212,2194	589.8+/-387.2	543,1126,534	151.0	128.0	136.0		,4557	2.0	1.0	6	dbSNP_107	136	3019,5581	465.5+/-366.5	536,1947,1817	no	utr-3,coding-synonymous	TULP4	NM_001007466.1,NM_020245.3	,	1079,3073,2351	GG,GA,AA		35.1047,49.7957,40.2199	,	,1519/1544	158927651	5231,7775	2203	4300	6503	SO:0001819	synonymous_variant	56995	exon14			CATTCTAGACTTC		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.4557A>G	6.37:g.158927651A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	68	55	0.808824	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	37	CCDS34561.1																																																																																			A|0.590;G|0.410	0.410	strong		0.542	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
AXL	558	hgsc.bcm.edu	37	19	41745608	41745608	+	Missense_Mutation	SNP	A	A	C	rs199928489		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41745608A>C	ENST00000301178.4	+	10	1485	c.1295A>C	c.(1294-1296)cAg>cCg	p.Q432P	AXL_ENST00000593513.1_Missense_Mutation_p.Q164P|AXL_ENST00000359092.3_Intron	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	432					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						GGGCAAGCACAGCCAGTCCAC	0.572													a|||	1	0.000199681	0.0	0.0	5008	,	,		21079	0.0		0.001	False		,,,				2504	0.0				p.Q432P		Atlas-SNP	.											.	AXL	126	.	0			c.A1295C						PASS	.		,PRO/GLN	1,4405		0,1,2202	287.0	234.0	252.0		,1295	3.2	1.0	19		252	1,8599		0,1,4299	no	intron,missense	AXL	NM_001699.4,NM_021913.3	,76	0,2,6501	CC,CA,AA		0.0116,0.0227,0.0154	,possibly-damaging	,432/895	41745608	2,13004	2203	4300	6503	SO:0001583	missense	558	exon10			AAGCACAGCCAGT	M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.1295A>C	19.37:g.41745608A>C	ENSP00000301178:p.Gln432Pro	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	NM_021913	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	37	CCDS12575.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	N	8.956	0.969405	0.18659	2.27E-4	1.16E-4	ENSG00000167601	ENST00000301178	T	0.75260	-0.92	4.29	3.25	0.37280	.	0.612388	0.15184	N	0.275979	T	0.47002	0.1422	N	0.08118	0	0.80722	D	1	B	0.31931	0.347	B	0.23018	0.043	T	0.29610	-1.0006	10	0.29301	T	0.29	-5.3294	4.8946	0.13744	0.6168:0.1953:0.0:0.1879	.	432	P30530	UFO_HUMAN	P	432	ENSP00000301178:Q432P	ENSP00000301178:Q432P	Q	+	2	0	AXL	46437448	1.000000	0.71417	0.997000	0.53966	0.847000	0.48162	1.875000	0.39578	0.686000	0.31488	0.307000	0.20424	CAG	A|1.000;C|0.000	0.000	strong		0.572	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2		
LRP5L	91355	hgsc.bcm.edu	37	22	25753321	25753321	+	Silent	SNP	G	G	A	rs9624807	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:25753321G>A	ENST00000402785.2	-	2	435	c.339C>T	c.(337-339)cgC>cgT	p.R113R	LRP5L_ENST00000402859.2_Silent_p.R113R|LRP5L_ENST00000444995.3_Silent_p.R113R			A4QPB2	LRP5L_HUMAN	low density lipoprotein receptor-related protein 5-like	113					canonical Wnt signaling pathway (GO:0060070)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)		Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(2)	6						TGACCAGCACGCGCAGCTCCT	0.597													G|||	409	0.0816693	0.1301	0.0663	5008	,	,		16078	0.001		0.1133	False		,,,				2504	0.0777				p.R113R		Atlas-SNP	.											.	LRP5L	23	.	0			c.C339T						PASS	.	G	,	599,3803	261.6+/-264.4	43,513,1645	116.0	99.0	105.0		339,339	-0.2	0.1	22	dbSNP_119	105	970,7630	210.4+/-251.3	66,838,3396	no	coding-synonymous,coding-synonymous	LRP5L	NM_001135772.1,NM_182492.2	,	109,1351,5041	AA,AG,GG		11.2791,13.6075,12.0674	,	113/253,113/253	25753321	1569,11433	2201	4300	6501	SO:0001819	synonymous_variant	91355	exon4			CAGCACGCGCAGC	AL137651	CCDS33626.1	22q11.23	2013-05-30			ENSG00000100068	ENSG00000100068			25323	protein-coding gene	gene with protein product							Standard	NM_182492		Approved	DKFZp434O0213	uc011ajz.2	A4QPB2	OTTHUMG00000150900	ENST00000402785.2:c.339C>T	22.37:g.25753321G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	148	81	0.547297	NM_001135772	B0QYF3|B0QYF4|B2RPI5	Silent	SNP	ENST00000402785.2	37	CCDS33626.1																																																																																			G|0.895;A|0.105	0.105	strong		0.597	LRP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320477.2	NM_182492	
EPN3	55040	hgsc.bcm.edu	37	17	48619249	48619249	+	Missense_Mutation	SNP	C	C	A	rs4794159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48619249C>A	ENST00000268933.3	+	10	2209	c.1630C>A	c.(1630-1632)Ccg>Acg	p.P544T	EPN3_ENST00000541226.1_3'UTR|EPN3_ENST00000537145.1_Missense_Mutation_p.P572T	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	544	3 X 3 AA repeats of N-P-F.		P -> T (in dbSNP:rs4794159). {ECO:0000269|PubMed:14702039}.			clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CGCGGGCGAGCCGGGCAGGCC	0.721													C|||	1854	0.370208	0.5227	0.4481	5008	,	,		11892	0.1091		0.4642	False		,,,				2504	0.2812				p.P544T		Atlas-SNP	.											EPN3,NS,carcinoma,0,1	EPN3	32	1	0			c.C1630A						PASS	.	C	THR/PRO	2124,2270		539,1046,612	17.0	21.0	19.0		1630	5.1	0.0	17	dbSNP_111	19	3968,4620		958,2052,1284	no	missense	EPN3	NM_017957.2	38	1497,3098,1896	AA,AC,CC		46.204,48.3386,46.9265	possibly-damaging	544/633	48619249	6092,6890	2197	4294	6491	SO:0001583	missense	55040	exon10			GGCGAGCCGGGCA	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.1630C>A	17.37:g.48619249C>A	ENSP00000268933:p.Pro544Thr	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	806	0.36904761904761907	236	0.4796747967479675	166	0.4585635359116022	62	0.10839160839160839	342	0.45118733509234826	C	17.75	3.467176	0.63625	0.483386	0.46204	ENSG00000049283	ENST00000268933;ENST00000537145	T;T	0.45276	0.9;0.9	5.13	5.13	0.70059	.	0.831291	0.10264	N	0.695608	T	0.00012	0.0000	M	0.62154	1.92	0.09310	P	1.0	P;P	0.43352	0.804;0.764	B;P	0.45428	0.36;0.48	T	0.48536	-0.9027	9	0.20519	T	0.43	-4.8223	18.1664	0.89729	0.0:1.0:0.0:0.0	rs4794159	572;544	F6QWW5;Q9H201	.;EPN3_HUMAN	T	544;572	ENSP00000268933:P544T;ENSP00000439512:P572T	ENSP00000268933:P544T	P	+	1	0	EPN3	45974248	0.998000	0.40836	0.016000	0.15963	0.172000	0.22775	5.548000	0.67255	2.406000	0.81754	0.491000	0.48974	CCG	C|0.565;A|0.435	0.435	strong		0.721	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
HSPB7	27129	hgsc.bcm.edu	37	1	16344402	16344402	+	Silent	SNP	G	G	A	rs945416	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16344402G>A	ENST00000311890.9	-	1	883	c.57C>T	c.(55-57)tcC>tcT	p.S19S	HSPB7_ENST00000487046.1_Silent_p.S19S|HSPB7_ENST00000545268.1_Silent_p.S19S|HSPB7_ENST00000375718.4_Intron|HSPB7_ENST00000411503.1_Silent_p.S19S|HSPB7_ENST00000406363.2_Silent_p.S19S	NM_014424.4	NP_055239.1	Q9UBY9	HSPB7_HUMAN	heat shock 27kDa protein family, member 7 (cardiovascular)	19	Poly-Ser.|Required for localization to SC35 splicing speckles.				regulation of heart contraction (GO:0008016)|response to unfolded protein (GO:0006986)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(1)|liver(1)|lung(6)|skin(1)	10		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;8.21e-08)|COAD - Colon adenocarcinoma(227;5.5e-06)|BRCA - Breast invasive adenocarcinoma(304;9.08e-05)|Kidney(64;0.000162)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		aggaggaagaggaagaggaaT	0.647													G|||	3250	0.648962	0.7103	0.4553	5008	,	,		17584	0.7639		0.5934	False		,,,				2504	0.6421				p.S19S		Atlas-SNP	.											HSPB7,NS,carcinoma,-1,1	HSPB7	17	1	0			c.C57T						PASS	.	G		3001,1405	679.7+/-403.7	1020,961,222	45.0	44.0	44.0		57	0.2	0.7	1	dbSNP_86	44	5029,3571	623.4+/-397.5	1489,2051,760	no	coding-synonymous	HSPB7	NM_014424.4		2509,3012,982	AA,AG,GG		41.5233,31.8883,38.2593		19/171	16344402	8030,4976	2203	4300	6503	SO:0001819	synonymous_variant	27129	exon1			GGAAGAGGAAGAG	AF155908	CCDS30611.1	1p36.23-p34.3	2011-09-02	2002-08-29		ENSG00000173641	ENSG00000173641		"""Heat shock proteins / HSPB"""	5249	protein-coding gene	gene with protein product		610692	"""heat shock 27kD protein family, member 7 (cardiovascular)"""			10593960	Standard	NM_014424		Approved	cvHSP	uc001axo.2	Q9UBY9	OTTHUMG00000009531	ENST00000311890.9:c.57C>T	1.37:g.16344402G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_014424	B3KQ37|C9K0Y0|Q9NU17	Silent	SNP	ENST00000311890.9	37	CCDS30611.1																																																																																			G|0.357;A|0.643	0.643	strong		0.647	HSPB7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026334.2	NM_014424	
OR6K3	391114	hgsc.bcm.edu	37	1	158687163	158687163	+	Missense_Mutation	SNP	G	G	A	rs28568406	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158687163G>A	ENST00000368146.1	-	1	790	c.791C>T	c.(790-792)cCg>cTg	p.P264L	OR6K3_ENST00000368145.1_Missense_Mutation_p.P248L			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	264			P -> L (in dbSNP:rs28568406). {ECO:0000269|PubMed:14983052}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					AAAGAATATCGGGAAGACCAT	0.453													A|||	1948	0.388978	0.4773	0.4323	5008	,	,		22981	0.4474		0.3966	False		,,,				2504	0.1708				p.P248L		Atlas-SNP	.											.	OR6K3	101	.	0			c.C743T						PASS	.	A	LEU/PRO	2096,2310	603.5+/-390.1	496,1104,603	131.0	112.0	118.0		743	3.8	0.0	1	dbSNP_125	118	3256,5344	649.7+/-400.6	613,2030,1657	yes	missense	OR6K3	NM_001005327.2	98	1109,3134,2260	AA,AG,GG		37.8605,47.5715,41.1502	benign	248/316	158687163	5352,7654	2203	4300	6503	SO:0001583	missense	391114	exon1			AATATCGGGAAGA	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.791C>T	1.37:g.158687163G>A	ENSP00000357128:p.Pro264Leu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_001005327	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		913	0.41804029304029305	225	0.4573170731707317	152	0.4198895027624309	238	0.4160839160839161	298	0.39313984168865435	A	1.380	-0.583678	0.03827	0.475715	0.378605	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.32988	1.43;1.43	3.77	3.77	0.43336	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01092	0.0036	N	0.00022	-2.74	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.43196	-0.9406	8	0.07325	T	0.83	.	8.466	0.32956	0.9021:0.0:0.0979:0.0	rs28568406;rs52822126;rs57495154	264	Q8NGY3	OR6K3_HUMAN	L	248;264	ENSP00000357127:P248L;ENSP00000357128:P264L	ENSP00000357127:P248L	P	-	2	0	OR6K3	156953787	0.000000	0.05858	0.001000	0.08648	0.446000	0.32137	0.037000	0.13840	0.606000	0.29965	-0.516000	0.04426	CCG	G|0.585;A|0.415	0.415	strong		0.453	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			
ATXN3	4287	hgsc.bcm.edu	37	14	92548785	92548785	+	Missense_Mutation	SNP	C	C	T	rs1048755	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92548785C>T	ENST00000532032.1	-	8	643	c.634G>A	c.(634-636)Gtg>Atg	p.V212M	ATXN3_ENST00000340660.6_Missense_Mutation_p.V157M|ATXN3_ENST00000503767.1_Missense_Mutation_p.V197M|ATXN3_ENST00000502250.1_Missense_Mutation_p.V33M|ATXN3_ENST00000393287.5_Missense_Mutation_p.V212M|ATXN3_ENST00000429774.2_Missense_Mutation_p.V197M|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000545170.1_Missense_Mutation_p.V212M			P54252	ATX3_HUMAN	ataxin 3	212			V -> M (in dbSNP:rs1048755). {ECO:0000269|PubMed:7874163, ECO:0000269|PubMed:9274833, ECO:0000269|Ref.4}.		actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		GCTTCTAACACTCGTTCCAGG	0.398													C|||	1628	0.32508	0.3767	0.1455	5008	,	,		17313	0.4405		0.2237	False		,,,				2504	0.3681				p.V212M	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											.	ATXN3	46	.	0			c.G634A						PASS	.	C	MET/VAL,MET/VAL,,,,,MET/VAL,MET/VAL,MET/VAL,,MET/VAL,MET/VAL	1462,2944	472.2+/-356.3	252,958,993	132.0	118.0	123.0		589,481,,,,,271,97,424,,634,469	3.3	1.0	14	dbSNP_86	123	2087,6513	361.6+/-332.4	291,1505,2504	yes	missense,missense,intron,intron,intron,intron,missense,missense,missense,intron,missense,missense	ATXN3	NM_001127696.1,NM_001127697.2,NM_001164774.1,NM_001164776.1,NM_001164777.1,NM_001164778.1,NM_001164779.1,NM_001164780.1,NM_001164781.1,NM_001164782.1,NM_004993.5,NM_030660.4	21,21,,,,,21,21,21,,21,21	543,2463,3497	TT,TC,CC		24.2674,33.182,27.2874	benign,benign,,,,,benign,benign,benign,,benign,benign	197/347,161/311,,,,,91/241,33/183,142/292,,212/362,157/307	92548785	3549,9457	2203	4300	6503	SO:0001583	missense	4287	exon8			CTAACACTCGTTC	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"""Ataxins"""	7106	protein-coding gene	gene with protein product		607047	"""Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"""	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.634G>A	14.37:g.92548785C>T	ENSP00000437157:p.Val212Met	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	125	69	0.552	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Missense_Mutation	SNP	ENST00000532032.1	37		671	0.30723443223443225	196	0.3983739837398374	49	0.13535911602209943	252	0.4405594405594406	174	0.22955145118733508	C	13.32	2.203207	0.38905	0.33182	0.242674	ENSG00000066427	ENST00000545278;ENST00000539555;ENST00000537884;ENST00000545170;ENST00000447800;ENST00000359819;ENST00000393289;ENST00000429774;ENST00000539454;ENST00000393287;ENST00000502250;ENST00000503767;ENST00000340660;ENST00000532032;ENST00000555381;ENST00000557311;ENST00000554592;ENST00000554672;ENST00000553491;ENST00000556220;ENST00000506466	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.33865	2.16;2.16;2.17;1.82;2.18;1.84;1.82;1.44;1.39;1.86;1.42;1.43;1.41;1.45	5.29	3.26	0.37387	.	0.533463	0.20675	N	0.087770	T	0.00012	0.0000	L	0.29908	0.895	0.46678	P	8.420000000000094E-4	B;B;B;B;B	0.25390	0.028;0.011;0.112;0.125;0.019	B;B;B;B;B	0.28232	0.043;0.01;0.087;0.087;0.036	T	0.47222	-0.9134	9	0.38643	T	0.18	.	11.6072	0.51039	0.1327:0.7949:0.0:0.0724	rs1048755;rs3188793;rs17807768;rs52836282;rs57139965;rs1048755	212;197;212;157;212	P54252;E9PB63;F5H096;P54252-3;P54252-2	ATX3_HUMAN;.;.;.;.	M	212;212;212;212;212;212;212;197;211;212;33;197;157;212;142;33;211;114;161;106;146	ENSP00000445618:V212M;ENSP00000389376:V197M;ENSP00000376965:V212M;ENSP00000425322:V33M;ENSP00000426697:V197M;ENSP00000339110:V157M;ENSP00000437157:V212M;ENSP00000451001:V142M;ENSP00000450642:V33M;ENSP00000451385:V211M;ENSP00000451417:V114M;ENSP00000451996:V161M;ENSP00000450641:V106M;ENSP00000435571:V146M	ENSP00000339110:V157M	V	-	1	0	ATXN3	91618538	0.993000	0.37304	0.995000	0.50966	0.984000	0.73092	2.237000	0.43061	1.243000	0.43853	0.485000	0.47835	GTG	C|0.699;T|0.301	0.301	strong		0.398	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
AP5Z1	9907	hgsc.bcm.edu	37	7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	rs11549840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4821352G>C	ENST00000348624.4	+	3	427	c.333G>C	c.(331-333)caG>caC	p.Q111H	AP5Z1_ENST00000401897.1_Missense_Mutation_p.Q111H	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	111					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACAGCCGGCAGCTGAGCCTGG	0.662													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		17920	0.0		0.0249	False		,,,				2504	0.0235				p.Q111H		Atlas-SNP	.											.	.	.	.	0			c.G333C						PASS	.	G	HIS/GLN	13,4247		0,13,2117	21.0	26.0	24.0		333	2.1	0.8	7	dbSNP_120	24	205,8303		4,197,4053	yes	missense	KIAA0415	NM_014855.2	24	4,210,6170	CC,CG,GG		2.4095,0.3052,1.7074	possibly-damaging	111/808	4821352	218,12550	2130	4254	6384	SO:0001583	missense	9907	exon3			CCGGCAGCTGAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.333G>C	7.37:g.4821352G>C	ENSP00000297562:p.Gln111His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	114	57	0.5	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	G	10.63	1.404230	0.25378	0.003052	0.024095	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44482	0.92;0.92	5.08	2.13	0.27403	.	0.485095	0.20242	N	0.096270	T	0.13970	0.0338	M	0.63428	1.95	0.24747	N	0.993007	B	0.23316	0.083	B	0.20184	0.028	T	0.12941	-1.0528	10	0.27785	T	0.31	.	5.8299	0.18574	0.1763:0.2946:0.5291:0.0	rs11549840	111	O43299	K0415_HUMAN	H	111	ENSP00000297562:Q111H;ENSP00000384980:Q111H	ENSP00000297562:Q111H	Q	+	3	2	KIAA0415	4787878	0.601000	0.26907	0.815000	0.32552	0.847000	0.48162	-0.102000	0.10956	0.256000	0.21614	0.655000	0.94253	CAG	G|0.986;C|0.014	0.014	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
TAF7L	54457	hgsc.bcm.edu	37	X	100532621	100532621	+	Missense_Mutation	SNP	T	T	C	rs35899692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100532621T>C	ENST00000372907.3	-	9	933	c.922A>G	c.(922-924)Agc>Ggc	p.S308G	TAF7L_ENST00000356784.1_Missense_Mutation_p.S222G|TAF7L_ENST00000372905.2_Missense_Mutation_p.S222G|TAF7L_ENST00000324762.6_Missense_Mutation_p.S222G	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	308			S -> G (in dbSNP:rs35899692). {ECO:0000269|PubMed:16597641, ECO:0000269|PubMed:17714218}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						TGCTTGTGGCTGCTCATTCCC	0.458													t|||	681	0.180397	0.1906	0.1066	3775	,	,		12247	0.2014		0.1203	False		,,,				2504	0.0317				p.S308G	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.A922G						PASS	.		GLY/SER,GLY/SER	940,2895		118,583,121,931,450	187.0	181.0	183.0		664,922	3.3	0.0	X	dbSNP_126	183	912,5816		32,572,276,1824,1596	yes	missense,missense	TAF7L	NM_001168474.1,NM_024885.3	56,56	150,1155,397,2755,2046	CC,CT,C,TT,T		13.5553,24.5111,17.5329	benign,benign	222/377,308/463	100532621	1852,8711	2203	4300	6503	SO:0001583	missense	54457	exon9			TGTGGCTGCTCAT	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.922A>G	X.37:g.100532621T>C	ENSP00000361998:p.Ser308Gly	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	334	0.20132610006027726	62	0.14553990610328638	26	0.07784431137724551	78	0.16049382716049382	53	0.0748587570621469	t	0.796	-0.757255	0.03019	0.245111	0.135553	ENSG00000102387	ENST00000372907;ENST00000372905;ENST00000324762;ENST00000356784	T;T;T;T	0.22539	3.68;1.95;1.95;2.94	5.18	3.35	0.38373	.	1.401140	0.04389	N	0.362069	T	0.00012	0.0000	N	0.02721	-0.515	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.24261	-1.0165	9	0.02654	T	1	-0.2224	11.1985	0.48728	0.0:0.8329:0.0:0.1671	rs35899692	308;222	Q5H9L4;Q5H9L4-3	TAF7L_HUMAN;.	G	308;222;222;222	ENSP00000361998:S308G;ENSP00000361996:S222G;ENSP00000320283:S222G;ENSP00000349235:S222G	ENSP00000320283:S222G	S	-	1	0	TAF7L	100419277	0.025000	0.19082	0.001000	0.08648	0.000000	0.00434	2.394000	0.44450	1.041000	0.40125	-0.291000	0.09656	AGC	0|0.013;C|0.185	0.185	strong		0.458	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
PRKCD	5580	hgsc.bcm.edu	37	3	53220215	53220215	+	Silent	SNP	G	G	A	rs2230494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:53220215G>A	ENST00000394729.2	+	12	1447	c.1119G>A	c.(1117-1119)gaG>gaA	p.E373E	PRKCD_ENST00000330452.3_Silent_p.E373E	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	373	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	GCAGAGGAGAGTACTTTGCCA	0.602													G|||	1413	0.282149	0.3411	0.2925	5008	,	,		20269	0.2202		0.2863	False		,,,				2504	0.2546				p.E373E		Atlas-SNP	.											PRKCD_ENST00000394729,NS,adenoma,0,2	PRKCD	124	2	0			c.G1119A						PASS	.	G	,	1417,2989	464.7+/-354.0	231,955,1017	97.0	87.0	90.0		1119,1119	2.3	0.5	3	dbSNP_98	90	2442,6158	402.0+/-347.3	338,1766,2196	no	coding-synonymous,coding-synonymous	PRKCD	NM_006254.3,NM_212539.1	,	569,2721,3213	AA,AG,GG		28.3953,32.1607,29.6709	,	373/677,373/677	53220215	3859,9147	2203	4300	6503	SO:0001819	synonymous_variant	5580	exon12			AGGAGAGTACTTT		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.1119G>A	3.37:g.53220215G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Silent	SNP	ENST00000394729.2	37	CCDS2870.1																																																																																			A|0.289;C|0.000;G|0.710;N|0.000	0.289	strong		0.602	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1		
CACNA1A	773	hgsc.bcm.edu	37	19	13387904	13387904	+	Silent	SNP	A	A	G	rs16030	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:13387904A>G	ENST00000360228.5	-	23	3860	c.3861T>C	c.(3859-3861)ttT>ttC	p.F1287F	CACNA1A_ENST00000573710.2_Silent_p.F1288F	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1288					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCTCAAAGGTAAAGACGCCTG	0.463											OREG0025295	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	835	0.166733	0.0938	0.2147	5008	,	,		19438	0.0923		0.2475	False		,,,				2504	0.2249				p.F1288F		Atlas-SNP	.											.	CACNA1A	715	.	0			c.T3864C						PASS	.	A	,,,,	329,3505		9,311,1597	107.0	97.0	100.0		3873,3864,3861,3864,3873	1.1	1.0	19	dbSNP_54	100	1792,6458		188,1416,2521	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	197,1727,4118	GG,GA,AA		21.7212,8.5811,17.5521	,,,,	1291/2267,1288/2262,1287/2507,1288/2264,1291/2513	13387904	2121,9963	1917	4125	6042	SO:0001819	synonymous_variant	773	exon23			AAAGGTAAAGACG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3861T>C	19.37:g.13387904A>G		Somatic	71	0	0	687	WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			A|0.841;G|0.159	0.159	strong		0.463	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
FOLH1	2346	hgsc.bcm.edu	37	11	49227620	49227620	+	Splice_Site	SNP	A	A	G	rs202676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:49227620A>G	ENST00000256999.2	-	2	483	c.223T>C	c.(223-225)Tat>Cat	p.Y75H	FOLH1_ENST00000356696.3_Splice_Site_p.Y75H|FOLH1_ENST00000533034.1_Splice_Site_p.Y60H|FOLH1_ENST00000343844.4_5'UTR|FOLH1_ENST00000340334.7_Splice_Site_p.Y60H	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	75			Y -> H (in dbSNP:rs202676). {ECO:0000269|PubMed:9838072}.		folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	TGTACTTACTATAAGAACTTC	0.294													A|||	1935	0.386382	0.6021	0.2896	5008	,	,		16366	0.3155		0.2256	False		,,,				2504	0.4018				p.Y75H		Atlas-SNP	.											.	FOLH1	141	.	0			c.T223C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR,,HIS/TYR	2305,2095	599.3+/-389.2	593,1119,488	68.0	68.0	68.0		223,178,178,,223	1.9	0.9	11	dbSNP_79	68	1924,6662	337.1+/-322.1	206,1512,2575	yes	missense-near-splice,missense-near-splice,missense-near-splice,utr-5,missense-near-splice	FOLH1	NM_001014986.1,NM_001193471.1,NM_001193472.1,NM_001193473.1,NM_004476.1	83,83,83,,83	799,2631,3063	GG,GA,AA		22.4086,47.6136,32.5658	benign,benign,benign,,benign	75/720,60/736,60/705,,75/751	49227620	4229,8757	2200	4293	6493	SO:0001630	splice_region_variant	2346	exon2			CTTACTATAAGAA	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.224+1T>C	11.37:g.49227620A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	755	0.3456959706959707	288	0.5853658536585366	96	0.26519337016574585	197	0.34440559440559443	174	0.22955145118733508	A	0.951	-0.706256	0.03255	0.523864	0.224086	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724;ENST00000529117	T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1	4.29	1.93	0.25924	.	0.293789	0.24436	N	0.038558	T	0.00012	0.0000	N	0.11724	0.165	0.09310	P	0.9999999999994258	B;B;B;B;B	0.13145	0.007;0.0;0.0;0.004;0.0	B;B;B;B;B	0.17722	0.019;0.002;0.0;0.012;0.0	T	0.43163	-0.9408	9	0.41790	T	0.15	.	7.8033	0.29187	0.7216:0.0:0.2784:0.0	rs202676;rs7937199;rs52836105;rs58342698;rs202676	60;60;60;75;75	Q04609-9;Q04609-7;A4UU13;Q04609-8;Q04609	.;.;.;.;FOLH1_HUMAN	H	75;75;60;60;75;18	ENSP00000256999:Y75H;ENSP00000349129:Y75H;ENSP00000344131:Y60H;ENSP00000431463:Y60H;ENSP00000431577:Y18H	ENSP00000256999:Y75H	Y	-	1	0	FOLH1	49184196	0.800000	0.28916	0.906000	0.35671	0.393000	0.30537	0.183000	0.16919	0.011000	0.14865	-1.186000	0.01703	TAT	A|0.657;G|0.343	0.343	strong		0.294	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	Missense_Mutation
FLG	2312	hgsc.bcm.edu	37	1	152285621	152285621	+	Missense_Mutation	SNP	T	T	A	rs145627745	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152285621T>A	ENST00000368799.1	-	3	1776	c.1741A>T	c.(1741-1743)Acc>Tcc	p.T581S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	581	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAGTGCCTGGTGCCGTCTCCT	0.567									Ichthyosis				-|||	15	0.00299521	0.0	0.0014	5008	,	,		18116	0.0		0.0089	False		,,,				2504	0.0051				p.T581S		Atlas-SNP	.											FLG,NS,carcinoma,+1,1	FLG	900	1	0			c.A1741T						PASS	.	A	SER/THR	13,4393		0,13,2190	392.0	368.0	376.0		1741	-4.3	0.0	1	dbSNP_134	376	101,8499		2,97,4201	no	missense	FLG	NM_002016.1	58	2,110,6391	AA,AT,TT		1.1744,0.2951,0.8765	benign	581/4062	152285621	114,12892	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCCTGGTGCCGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1741A>T	1.37:g.152285621T>A	ENSP00000357789:p.Thr581Ser	Somatic	285	0	0		WXS	Illumina HiSeq	Phase_I	338	184	0.544379	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	-	1.132	-0.652029	0.03506	0.002951	0.011744	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01548	4.78	2.15	-4.3	0.03710	.	.	.	.	.	T	0.00109	0.0003	N	0.00265	-1.74	0.09310	N	1	B	0.23316	0.083	B	0.28139	0.086	T	0.37361	-0.9709	9	0.06365	T	0.9	.	0.4631	0.00519	0.1939:0.3015:0.2321:0.2724	.	581	P20930	FILA_HUMAN	S	581;113	ENSP00000357789:T581S	ENSP00000357789:T581S	T	-	1	0	FLG	150552245	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.125000	0.00079	-3.882000	0.00095	-1.828000	0.00595	ACC	T|0.993;A|0.007	0.007	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
MEFV	4210	hgsc.bcm.edu	37	16	3297175	3297175	+	Silent	SNP	T	T	C	rs224207	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3297175T>C	ENST00000219596.1	-	5	1467	c.1428A>G	c.(1426-1428)caA>caG	p.Q476Q	MEFV_ENST00000339854.4_Silent_p.Q296Q|MEFV_ENST00000536379.1_Silent_p.Q265Q|MEFV_ENST00000541159.1_Silent_p.Q265Q	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	476	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						AGAAATGCTCTTGCTGCTCCA	0.582													T|||	3258	0.650559	0.649	0.6239	5008	,	,		21091	0.6528		0.5577	False		,,,				2504	0.7648				p.Q476Q		Atlas-SNP	.											MEFV_ENST00000541159,NS,carcinoma,-2,2	MEFV	170	2	0			c.A1428G						PASS	.	T	,	2810,1584	663.6+/-401.2	888,1034,275	166.0	152.0	157.0		1428,795	-9.1	0.2	16	dbSNP_79	157	4578,4022	596.9+/-393.7	1248,2082,970	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2136,3116,1245	CC,CT,TT		46.7674,36.0492,43.143	,	476/782,265/446	3297175	7388,5606	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon5			ATGCTCTTGCTGC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1428A>G	16.37:g.3297175T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	168	86	0.511905	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			T|0.407;C|0.593	0.593	strong		0.582	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
SRSF6	6431	hgsc.bcm.edu	37	20	42088708	42088708	+	Silent	SNP	G	G	A	rs61733949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:42088708G>A	ENST00000244020.3	+	4	523	c.417G>A	c.(415-417)gcG>gcA	p.A139A		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	139	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						TAACCTATGCGGATGCCCACA	0.413													G|||	157	0.0313498	0.0023	0.0461	5008	,	,		20861	0.0169		0.0716	False		,,,				2504	0.0337				p.A139A		Atlas-SNP	.											.	SRSF6	37	.	0			c.G417A						PASS	.	G		50,4356	51.6+/-87.1	0,50,2153	123.0	123.0	123.0		417	-1.5	1.0	20	dbSNP_129	123	549,8051	150.4+/-205.3	13,523,3764	no	coding-synonymous	SRSF6	NM_006275.5		13,573,5917	AA,AG,GG		6.3837,1.1348,4.6056		139/345	42088708	599,12407	2203	4300	6503	SO:0001819	synonymous_variant	6431	exon4			CTATGCGGATGCC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10788	protein-coding gene	gene with protein product	"""pre-mRNA splicing factor SRP55"", ""SR splicing factor 6"""	601944	"""splicing factor, arginine/serine-rich 6"""	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.417G>A	20.37:g.42088708G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Silent	SNP	ENST00000244020.3	37	CCDS13318.1																																																																																			G|0.956;A|0.044	0.044	strong		0.413	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275	
MSH2	4436	hgsc.bcm.edu	37	2	47637439	47637439	+	Silent	SNP	C	C	T	rs1800151	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:47637439C>T	ENST00000233146.2	+	3	796	c.573C>T	c.(571-573)ctC>ctT	p.L191L	MSH2_ENST00000406134.1_Silent_p.L191L|MSH2_ENST00000543555.1_Silent_p.L125L	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	191					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGGCTCTCCTCATCCAGATTG	0.463			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	97	0.019369	0.0696	0.0072	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L191L		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.C573T						PASS	.	C		254,4152	146.9+/-181.5	4,246,1953	182.0	176.0	178.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	573	1.6	1.0	2	dbSNP_89	178	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MSH2	NM_000251.1		4,250,6249	TT,TC,CC		0.0465,5.7649,1.9837		191/935	47637439	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	4436	exon3	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTCCTCATCCAG	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.573C>T	2.37:g.47637439C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	98	49	0.5	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
KHDRBS2	202559	hgsc.bcm.edu	37	6	62390920	62390920	+	Missense_Mutation	SNP	G	G	A	rs61753606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:62390920G>A	ENST00000281156.4	-	9	1276	c.998C>T	c.(997-999)cCg>cTg	p.P333L	RP1-240B8.3_ENST00000511849.2_RNA	NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TGACCTTTGCGGTGGTGCCTT	0.478													G|||	29	0.00579073	0.003	0.0086	5008	,	,		16587	0.0		0.0139	False		,,,				2504	0.0051				p.P333L		Atlas-SNP	.											KHDRBS2,NS,carcinoma,+1,2	KHDRBS2	103	2	0			c.C998T						PASS	.	G	LEU/PRO	13,4393	21.2+/-45.6	0,13,2190	186.0	130.0	149.0		998	5.1	0.8	6	dbSNP_129	149	141,8459	70.0+/-132.6	1,139,4160	no	missense	KHDRBS2	NM_152688.2	98	1,152,6350	AA,AG,GG		1.6395,0.2951,1.1841	benign	333/350	62390920	154,12852	2203	4300	6503	SO:0001583	missense	202559	exon9			CTTTGCGGTGGTG	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"""Sam68-like mammalian protein 1"""	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.998C>T	6.37:g.62390920G>A	ENSP00000281156:p.Pro333Leu	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	88	69	0.784091	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	37	CCDS4963.1	15	0.006868131868131868	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	10.68	1.419456	0.25552	0.002951	0.016395	ENSG00000112232	ENST00000281156	T	0.44083	0.93	5.13	5.13	0.70059	.	0.316534	0.34411	N	0.003988	T	0.14960	0.0361	N	0.15975	0.35	0.43959	D	0.996637	B	0.19817	0.039	B	0.11329	0.006	T	0.05241	-1.0897	10	0.56958	D	0.05	.	12.3163	0.54958	0.0783:0.0:0.9217:0.0	rs61753606	333	Q5VWX1	KHDR2_HUMAN	L	333	ENSP00000281156:P333L	ENSP00000281156:P333L	P	-	2	0	KHDRBS2	62448879	1.000000	0.71417	0.847000	0.33407	0.169000	0.22640	4.271000	0.58902	2.541000	0.85698	0.650000	0.86243	CCG	G|0.987;A|0.013	0.013	strong		0.478	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688	
SLC2A4	6517	hgsc.bcm.edu	37	17	7187123	7187123	+	Silent	SNP	T	T	C	rs5435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:7187123T>C	ENST00000317370.8	+	4	658	c.390T>C	c.(388-390)aaT>aaC	p.N130N	SLC2A4_ENST00000571308.1_Silent_p.N130N|RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000424875.2_Silent_p.N120N	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	130					amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						GCCTGGCCAATGCTGCTGCCT	0.602													C|||	3493	0.697484	0.913	0.6081	5008	,	,		19792	0.625		0.6064	False		,,,				2504	0.638				p.N130N		Atlas-SNP	.											.	SLC2A4	44	.	0			c.T390C						PASS	.	C		3716,690	288.1+/-279.7	1576,564,63	68.0	61.0	63.0		390	-11.5	0.0	17	dbSNP_52	63	5363,3237	487.6+/-372.2	1696,1971,633	no	coding-synonymous	SLC2A4	NM_001042.2		3272,2535,696	CC,CT,TT		37.6395,15.6605,30.1938		130/510	7187123	9079,3927	2203	4300	6503	SO:0001819	synonymous_variant	6517	exon4			GGCCAATGCTGCT	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"""Solute carriers"""	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.390T>C	17.37:g.7187123T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_001042	Q05BQ3|Q14CX2	Silent	SNP	ENST00000317370.8	37	CCDS11097.1																																																																																			C|0.701;N|0.001	0.701	strong		0.602	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3		
IGSF9B	22997	hgsc.bcm.edu	37	11	133801990	133801990	+	Silent	SNP	G	G	A	rs375960322		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:133801990G>A	ENST00000321016.8	-	8	1316	c.1086C>T	c.(1084-1086)gaC>gaT	p.D362D	IGSF9B_ENST00000533871.2_Silent_p.D362D			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	362	Ig-like 4.				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)		GGGGACGGCCGTCCTTGTTCC	0.607																																					p.D362D		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C1086T						PASS	.			0,4278		0,0,2139	70.0	86.0	81.0		1086	-8.2	0.8	11		81	1,8453		0,1,4226	no	coding-synonymous	IGSF9B	NM_014987.1		0,1,6365	AA,AG,GG		0.0118,0.0,0.0079		362/1350	133801990	1,12731	2139	4227	6366	SO:0001819	synonymous_variant	22997	exon8			ACGGCCGTCCTTG	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.1086C>T	11.37:g.133801990G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	155	84	0.541936	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				.	.	weak		0.607	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751229	19751229	+	Silent	SNP	T	T	C	rs36216108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19751229T>C	ENST00000400113.3	-	4	998	c.894A>G	c.(892-894)ccA>ccG	p.P298P		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	298					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TCTGATTGGCTGGCTCGAAGC	0.607													T|||	185	0.0369409	0.0045	0.0793	5008	,	,		19564	0.0198		0.0596	False		,,,				2504	0.045				p.P298P		Atlas-SNP	.											TUBA3C,NS,carcinoma,-1,1	TUBA3C	166	1	0			c.A894G						scavenged	.	T		77,4329	68.7+/-106.4	1,75,2127	168.0	144.0	152.0		894	-1.0	1.0	13	dbSNP_126	152	509,8091	145.1+/-200.9	20,469,3811	no	coding-synonymous	TUBA3C	NM_006001.2		21,544,5938	CC,CT,TT		5.9186,1.7476,4.5056		298/451	19751229	586,12420	2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			ATTGGCTGGCTCG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.894A>G	13.37:g.19751229T>C		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	221	86	0.38914	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			T|0.955;C|0.045	0.045	strong		0.607	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
RBMX	27316	hgsc.bcm.edu	37	X	135956342	135956342	+	Missense_Mutation	SNP	C	C	G	rs72615484	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135956342C>G	ENST00000320676.7	-	9	1289	c.1135G>C	c.(1135-1137)Gga>Cga	p.G379R	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Missense_Mutation_p.G251R|RBMX_ENST00000570135.1_Missense_Mutation_p.G244R|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	379	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GATCGGCTTCCTCCACGGCCA	0.498																																					p.G379R		Atlas-SNP	.											.	RBMX	149	.	0			c.G1135C						PASS	.						47.0	48.0	48.0					X																	135956342		2195	4274	6469	SO:0001583	missense	27316	exon9			GGCTTCCTCCACG		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1135G>C	X.37:g.135956342C>G	ENSP00000359645:p.Gly379Arg	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	240	107	0.445833	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	12.97	2.097656	0.37048	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.80653	-1.4	5.54	5.54	0.83059	.	0.000000	0.85682	U	0.000000	D	0.88235	0.6382	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86056	0.1529	10	0.29301	T	0.29	.	18.509	0.90909	0.0:1.0:0.0:0.0	.	379	P38159	HNRPG_HUMAN	R	379;366	ENSP00000359645:G379R	ENSP00000359645:G379R	G	-	1	0	RBMX	135784008	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.692000	0.84203	2.313000	0.78055	0.508000	0.49915	GGA	C|0.500;G|0.500	0.500	strong		0.498	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
CHD9	80205	hgsc.bcm.edu	37	16	53283966	53283966	+	Silent	SNP	G	G	A	rs8052283	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:53283966G>A	ENST00000398510.3	+	16	3936	c.3849G>A	c.(3847-3849)caG>caA	p.Q1283Q	CHD9_ENST00000564845.1_Silent_p.Q1283Q|CHD9_ENST00000566029.1_Silent_p.Q1283Q|Y_RNA_ENST00000391280.1_RNA|CHD9_ENST00000447540.1_Silent_p.Q1283Q			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1283	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GGAATCCTCAGAATGATCTTC	0.318													A|||	1526	0.304712	0.3699	0.1902	5008	,	,		14840	0.247		0.2962	False		,,,				2504	0.3661				p.Q1283Q		Atlas-SNP	.											.	CHD9	203	.	0			c.G3849A						PASS	.	A		1220,2424		199,822,801	73.0	70.0	71.0		3849	2.0	1.0	16	dbSNP_116	71	2559,5583		401,1757,1913	no	coding-synonymous	CHD9	NM_025134.4		600,2579,2714	AA,AG,GG		31.4296,33.4797,32.0635		1283/2882	53283966	3779,8007	1822	4071	5893	SO:0001819	synonymous_variant	80205	exon17			TCCTCAGAATGAT	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.3849G>A	16.37:g.53283966G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	89	39	0.438202	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	37																																																																																				G|0.692;A|0.308	0.308	strong		0.318	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
TBC1D32	221322	hgsc.bcm.edu	37	6	121577370	121577370	+	Missense_Mutation	SNP	T	T	C	rs7745023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:121577370T>C	ENST00000398212.2	-	16	1844	c.1795A>G	c.(1795-1797)Ata>Gta	p.I599V	TBC1D32_ENST00000275159.6_Missense_Mutation_p.I599V	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	599			I -> V (in dbSNP:rs7745023).		cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)	p.I599V(1)									CCAGAAAATATAGAAATATCT	0.353													T|||	1306	0.260783	0.0424	0.2954	5008	,	,		18165	0.1111		0.5855	False		,,,				2504	0.3517				p.I599V		Atlas-SNP	.											C6orf170,NS,carcinoma,0,1	C6orf170	146	1	1	Substitution - Missense(1)	prostate(1)	c.A1795G						PASS	.	T	VAL/ILE	468,3146		39,390,1378	62.0	57.0	59.0		1795	-0.5	0.5	6	dbSNP_116	59	4710,3436		1354,2002,717	yes	missense	C6orf170	NM_152730.4	29	1393,2392,2095	CC,CT,TT		42.1802,12.9496,44.0306	benign	599/1258	121577370	5178,6582	1807	4073	5880	SO:0001583	missense	221322	exon16			AAAATATAGAAAT	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.1795A>G	6.37:g.121577370T>C	ENSP00000381270:p.Ile599Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	70	6	0.0857143	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	639	0.2925824175824176	29	0.05894308943089431	121	0.3342541436464088	51	0.08916083916083917	438	0.5778364116094987	T	2.501	-0.315202	0.05422	0.129496	0.578198	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.16073	2.37;2.37	5.21	-0.469	0.12142	.	0.775342	0.12424	N	0.470190	T	0.01695	0.0054	N	0.15975	0.35	0.44261	P	0.0028839999999999977	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.46762	-0.9168	9	0.02654	T	1	-15.6923	5.6919	0.17835	0.0:0.3939:0.3466:0.2596	rs7745023;rs13208594;rs52836518;rs58699322;rs7745023	599;599	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	V	599	ENSP00000275159:I599V;ENSP00000381270:I599V	ENSP00000275159:I599V	I	-	1	0	C6orf170	121619069	0.857000	0.29778	0.468000	0.27192	0.460000	0.32559	0.019000	0.13444	0.057000	0.16193	-1.156000	0.01807	ATA	T|0.674;C|0.326	0.326	strong		0.353	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
SLC2A1	6513	hgsc.bcm.edu	37	1	43396414	43396414	+	Silent	SNP	G	G	A	rs11537641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43396414G>A	ENST00000426263.3	-	4	577	c.399C>T	c.(397-399)tgC>tgT	p.C133C	SLC2A1_ENST00000372500.3_Silent_p.C133C|SLC2A1_ENST00000475162.1_5'UTR|SLC2A1_ENST00000415851.2_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	133					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	TGGTCAGGCCGCAGTACACAC	0.622													G|||	708	0.141374	0.0802	0.2133	5008	,	,		21408	0.1022		0.1909	False		,,,				2504	0.1626				p.C133C		Atlas-SNP	.											.	SLC2A1	36	.	0			c.C399T	GRCh37	CM044065	SLC2A1	M	rs11537641	PASS	.	G		423,3983	204.1+/-226.4	17,389,1797	66.0	59.0	61.0		399	-6.7	0.8	1	dbSNP_120	61	1709,6891	311.3+/-310.3	167,1375,2758	no	coding-synonymous	SLC2A1	NM_006516.2		184,1764,4555	AA,AG,GG		19.8721,9.6005,16.3924		133/493	43396414	2132,10874	2203	4300	6503	SO:0001819	synonymous_variant	6513	exon4			CAGGCCGCAGTAC	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"""Solute carriers"""	11005	protein-coding gene	gene with protein product		138140	"""human T-cell leukemia virus (I and II) receptor"""	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.399C>T	1.37:g.43396414G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	46	25	0.543478	NM_006516	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Silent	SNP	ENST00000426263.3	37	CCDS477.1																																																																																			G|0.840;A|0.160	0.160	strong		0.622	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516	
TMEM132B	114795	hgsc.bcm.edu	37	12	125834095	125834095	+	Silent	SNP	C	C	A	rs1491893	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:125834095C>A	ENST00000299308.3	+	2	158	c.150C>A	c.(148-150)tcC>tcA	p.S50S	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	50						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CAGAGGAGTCCTTTTTCCTTA	0.532													C|||	1374	0.274361	0.1838	0.3458	5008	,	,		17454	0.2728		0.3012	False		,,,				2504	0.32				p.S50S		Atlas-SNP	.											.	TMEM132B	207	.	0			c.C150A						PASS	.	C		793,3097		79,635,1231	132.0	133.0	132.0		150	2.0	0.4	12	dbSNP_88	132	2441,5849		364,1713,2068	no	coding-synonymous	TMEM132B	NM_052907.2		443,2348,3299	AA,AC,CC		29.4451,20.3856,26.5517		50/1079	125834095	3234,8946	1945	4145	6090	SO:0001819	synonymous_variant	114795	exon2			GGAGTCCTTTTTC	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.150C>A	12.37:g.125834095C>A		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	139	70	0.503597	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			C|0.737;A|0.262	0.262	strong		0.532	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
COL27A1	85301	hgsc.bcm.edu	37	9	117002517	117002517	+	Silent	SNP	C	C	T	rs2014134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:117002517C>T	ENST00000356083.3	+	20	3136	c.2745C>T	c.(2743-2745)atC>atT	p.I915I		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	915	Collagen-like 5.|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						CAGGAGACATCGGCCCCCCTG	0.637													C|||	1593	0.318091	0.1505	0.4827	5008	,	,		19595	0.1895		0.3847	False		,,,				2504	0.4918				p.I915I		Atlas-SNP	.											.	COL27A1	200	.	0			c.C2745T						PASS	.	C		855,3551	336.5+/-304.4	92,671,1440	80.0	78.0	78.0		2745	-4.4	1.0	9	dbSNP_92	78	3257,5343	490.3+/-372.8	645,1967,1688	no	coding-synonymous	COL27A1	NM_032888.2		737,2638,3128	TT,TC,CC		37.8721,19.4054,31.6162		915/1861	117002517	4112,8894	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon20			AGACATCGGCCCC	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.2745C>T	9.37:g.117002517C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	50	23	0.46	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			C|0.700;T|0.300	0.300	strong		0.637	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
UBASH3A	53347	hgsc.bcm.edu	37	21	43854985	43854985	+	Silent	SNP	A	A	C	rs17114925	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43854985A>C	ENST00000319294.6	+	10	1345	c.1314A>C	c.(1312-1314)ccA>ccC	p.P438P	UBASH3A_ENST00000398367.1_Silent_p.P400P|UBASH3A_ENST00000291535.6_Silent_p.P400P	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	438	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						GCAGTCTGCCAAGACGGAGTC	0.438													C|||	1253	0.2502	0.4864	0.2017	5008	,	,		23312	0.2073		0.1262	False		,,,				2504	0.137				p.P438P		Atlas-SNP	.											.	UBASH3A	72	.	0			c.A1314C						PASS	.	C	,	1918,2488	624.6+/-394.4	424,1070,709	109.0	104.0	105.0		1200,1314	2.7	0.5	21	dbSNP_123	105	1259,7341	761.0+/-407.6	105,1049,3146	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	529,2119,3855	CC,CA,AA		14.6395,43.5315,24.4272	,	400/624,438/662	43854985	3177,9829	2203	4300	6503	SO:0001819	synonymous_variant	53347	exon10			TCTGCCAAGACGG	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1314A>C	21.37:g.43854985A>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	70	32	0.457143	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			A|0.750;C|0.250	0.250	strong		0.438	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
MRPL19	9801	hgsc.bcm.edu	37	2	75879359	75879359	+	Missense_Mutation	SNP	G	G	A	rs41382847	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75879359G>A	ENST00000393909.2	+	3	338	c.313G>A	c.(313-315)Gta>Ata	p.V105I	MRPL19_ENST00000409374.1_Missense_Mutation_p.V105I|MRPL19_ENST00000358788.6_Missense_Mutation_p.V105I	NM_014763.3	NP_055578.2	P49406	RM19_HUMAN	mitochondrial ribosomal protein L19	105					translation (GO:0006412)	mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(6)	8						AAGGAGAAAAGTACTCCACAT	0.343													G|||	35	0.00698882	0.0008	0.0115	5008	,	,		15222	0.0		0.0149	False		,,,				2504	0.0112				p.V105I		Atlas-SNP	.											.	MRPL19	21	.	0			c.G313A						PASS	.	G	ILE/VAL	3,3617		0,3,1807	73.0	71.0	72.0		313	-0.5	1.0	2	dbSNP_127	72	74,8042		1,72,3985	yes	missense	MRPL19	NM_014763.3	29	1,75,5792	AA,AG,GG		0.9118,0.0829,0.6561	benign	105/293	75879359	77,11659	1810	4058	5868	SO:0001583	missense	9801	exon3			AGAAAAGTACTCC	AB051621	CCDS1960.2	2p11.1-q11.2	2012-09-13			ENSG00000115364	ENSG00000115364		"""Mitochondrial ribosomal proteins / large subunits"""	14052	protein-coding gene	gene with protein product	"""39S ribosomal protein L19"""	611832				11543634, 17309879	Standard	XM_006712155		Approved	MRP-L15, RPML15, KIAA0104, RLX1	uc002snl.3	P49406	OTTHUMG00000129990	ENST00000393909.2:c.313G>A	2.37:g.75879359G>A	ENSP00000377486:p.Val105Ile	Somatic	371	0	0		WXS	Illumina HiSeq	Phase_I	349	177	0.507163	NM_014763	Q53TX9|Q96Q52	Missense_Mutation	SNP	ENST00000393909.2	37	CCDS1960.2	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	12.24	1.877138	0.33162	8.29E-4	0.009118	ENSG00000115364	ENST00000393909;ENST00000409374	.	.	.	4.85	-0.463	0.12164	Translation protein SH3-like (1);	0.350899	0.32736	N	0.005705	T	0.50222	0.1603	M	0.69185	2.1	0.80722	D	1	B	0.20887	0.049	B	0.32022	0.139	T	0.48603	-0.9021	9	0.33940	T	0.23	-6.8784	10.7534	0.46221	0.3156:0.0:0.6844:0.0	rs41382847	105	P49406	RM19_HUMAN	I	105	.	ENSP00000377486:V105I	V	+	1	0	MRPL19	75732867	1.000000	0.71417	0.976000	0.42696	0.971000	0.66376	2.018000	0.40991	-0.205000	0.10219	-0.145000	0.13849	GTA	G|0.992;A|0.008	0.008	strong		0.343	MRPL19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252256.1	NM_014763	
MAK	4117	hgsc.bcm.edu	37	6	10775600	10775600	+	Missense_Mutation	SNP	G	G	A	rs567083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:10775600G>A	ENST00000313243.2	-	12	1940	c.1558C>T	c.(1558-1560)Ccc>Tcc	p.P520S	RP11-637O19.3_ENST00000480294.1_Intron|MAK_ENST00000354489.2_Missense_Mutation_p.P520S|MAK_ENST00000538030.1_3'UTR|MAK_ENST00000474039.1_Missense_Mutation_p.P520S|SYCP2L_ENST00000543878.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase	520			P -> S (in dbSNP:rs567083). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				GCCCCAACGGGTCCCAGTGAC	0.453													G|||	99	0.0197684	0.0015	0.0908	5008	,	,		20809	0.0		0.0209	False		,,,				2504	0.0133				p.P520S		Atlas-SNP	.											.	MAK	47	.	0			c.C1558T						PASS	.	G	SER/PRO,SER/PRO	19,4387	26.2+/-53.5	0,19,2184	200.0	199.0	199.0		1558,1558	3.4	0.9	6	dbSNP_83	199	179,8421	81.8+/-144.4	2,175,4123	yes	missense,missense	MAK	NM_001242385.1,NM_005906.4	74,74	2,194,6307	AA,AG,GG		2.0814,0.4312,1.5224	benign,benign	520/584,520/624	10775600	198,12808	2203	4300	6503	SO:0001583	missense	4117	exon12			CAACGGGTCCCAG		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1558C>T	6.37:g.10775600G>A	ENSP00000313021:p.Pro520Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	196	98	0.5	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	43	0.019688644688644688	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	15	0.01978891820580475	G	2.302	-0.359970	0.05103	0.004312	0.020814	ENSG00000111837	ENST00000313243;ENST00000354489	T;T	0.71461	-0.57;-0.57	6.17	3.36	0.38483	.	0.165506	0.53938	N	0.000048	T	0.27098	0.0664	N	0.20685	0.6	0.48571	D	0.999672	B	0.09022	0.002	B	0.09377	0.004	T	0.17137	-1.0379	10	0.08381	T	0.77	.	6.315	0.21186	0.1638:0.1538:0.6825:0.0	rs567083;rs1627871;rs17640406;rs52803991;rs567083	520	P20794	MAK_HUMAN	S	520	ENSP00000313021:P520S;ENSP00000346484:P520S	ENSP00000313021:P520S	P	-	1	0	MAK	10883586	0.831000	0.29352	0.918000	0.36340	0.161000	0.22273	0.171000	0.16685	0.884000	0.36064	0.655000	0.94253	CCC	A|0.017;C|0.006	0.017	strong		0.453	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964196	88964196	+	Missense_Mutation	SNP	T	T	A	rs801840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:88964196T>A	ENST00000333190.4	+	4	2509	c.1900T>A	c.(1900-1902)Ttt>Att	p.F634I		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	634			F -> I (in dbSNP:rs801840). {ECO:0000269|PubMed:12690205}.				metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			CATCTCTAGGTTTAAAAAGCA	0.418										HNSCC(36;0.09)			A|||	2607	0.520567	0.7738	0.3415	5008	,	,		19885	0.7153		0.2346	False		,,,				2504	0.3988				p.F634I		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T1900A						PASS	.	A	ILE/PHE	3011,1395	456.1+/-351.2	1021,969,213	80.0	84.0	83.0		1900	4.3	0.7	7	dbSNP_86	83	2036,6564	719.1+/-406.2	234,1568,2498	yes	missense	ZNF804B	NM_181646.2	21	1255,2537,2711	AA,AT,TT		23.6744,31.6614,38.8052	benign	634/1350	88964196	5047,7959	2203	4300	6503	SO:0001583	missense	219578	exon4			TCTAGGTTTAAAA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1900T>A	7.37:g.88964196T>A	ENSP00000329638:p.Phe634Ile	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	1073	0.4913003663003663	374	0.7601626016260162	130	0.35911602209944754	390	0.6818181818181818	179	0.23614775725593667	A	6.795	0.515659	0.12944	0.683386	0.236744	ENSG00000182348	ENST00000333190	T	0.04015	3.73	5.48	4.33	0.51752	.	0.169739	0.42294	D	0.000738	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06643	-1.0815	9	0.51188	T	0.08	-4.6357	7.8499	0.29448	0.8102:0.0:0.0666:0.1232	rs801840;rs1721758;rs56634318;rs801840	634	A4D1E1	Z804B_HUMAN	I	634	ENSP00000329638:F634I	ENSP00000329638:F634I	F	+	1	0	ZNF804B	88802132	1.000000	0.71417	0.702000	0.30337	0.028000	0.11728	3.085000	0.50151	0.518000	0.28383	-0.265000	0.10407	TTT	T|0.483;A|0.517	0.517	strong		0.418	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
NRAP	4892	hgsc.bcm.edu	37	10	115370274	115370274	+	Missense_Mutation	SNP	T	T	C	rs10749138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115370274T>C	ENST00000359988.3	-	31	3791	c.3547A>G	c.(3547-3549)Att>Gtt	p.I1183V	NRAP_ENST00000369358.4_Missense_Mutation_p.I1191V|NRAP_ENST00000369360.3_Missense_Mutation_p.I1156V|NRAP_ENST00000360478.3_Missense_Mutation_p.I1148V	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		GTGCCTGGAATGACACATGCA	0.433													T|||	2318	0.462859	0.3321	0.4669	5008	,	,		17368	0.5992		0.4652	False		,,,				2504	0.4939				p.I1183V		Atlas-SNP	.											NRAP,head_neck,carcinoma,0,1	NRAP	208	1	0			c.A3547G						PASS	.	T	VAL/ILE,VAL/ILE	1472,2934	475.2+/-357.2	261,950,992	178.0	151.0	160.0		3442,3547	0.6	1.0	10	dbSNP_120	160	4163,4437	567.5+/-388.9	1002,2159,1139	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	29,29	1263,3109,2131	CC,CT,TT		48.407,33.409,43.3262	benign,benign	1148/1696,1183/1731	115370274	5635,7371	2203	4300	6503	SO:0001583	missense	4892	exon31			CTGGAATGACACA		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3547A>G	10.37:g.115370274T>C	ENSP00000353078:p.Ile1183Val	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	981	0.4491758241758242	149	0.30284552845528456	173	0.47790055248618785	325	0.5681818181818182	334	0.44063324538258575	T	7.807	0.714817	0.15306	0.33409	0.48407	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.15256	2.64;2.66;2.52;2.44	5.85	0.626	0.17670	.	0.409872	0.29438	N	0.012143	T	0.00012	0.0000	N	0.16790	0.44	0.48395	P	3.6000000000002697E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45745	-0.9240	9	0.02654	T	1	.	9.7306	0.40359	0.0:0.335:0.0:0.665	rs10749138;rs52826105;rs57988639;rs10749138	1148;1183	Q86VF7-4;Q86VF7	.;NRAP_HUMAN	V	1191;1156;1183;1148	ENSP00000358365:I1191V;ENSP00000358367:I1156V;ENSP00000353078:I1183V;ENSP00000353666:I1148V	ENSP00000353078:I1183V	I	-	1	0	NRAP	115360264	0.993000	0.37304	0.996000	0.52242	0.264000	0.26372	0.173000	0.16724	-0.123000	0.11745	0.528000	0.53228	ATT	T|0.556;C|0.444	0.444	strong		0.433	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
MCM4	4173	hgsc.bcm.edu	37	8	48885436	48885436	+	Missense_Mutation	SNP	T	T	A	rs762679	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:48885436T>A	ENST00000262105.2	+	13	2157	c.1948T>A	c.(1948-1950)Ttg>Atg	p.L650M	MCM4_ENST00000523944.1_Missense_Mutation_p.L650M	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	650	MCM.		L -> M (in dbSNP:rs762679). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7601140, ECO:0000269|PubMed:8265339}.		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			biliary_tract(1)|breast(1)|endometrium(7)|kidney(4)|large_intestine(5)|lung(16)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	44		all_cancers(86;0.026)|all_epithelial(80;0.000748)|Lung NSC(129;0.00327)|all_lung(136;0.00354)				GATCTTCCTCTTGCTGGACCC	0.522													A|||	4578	0.914137	0.941	0.9222	5008	,	,		20472	1.0		0.8449	False		,,,				2504	0.8548				p.L650M		Atlas-SNP	.											.	MCM4	97	.	0			c.T1948A						PASS	.	A	MET/LEU,MET/LEU	4069,337	176.2+/-205.4	1878,313,12	85.0	78.0	80.0		1948,1948	5.3	1.0	8	dbSNP_86	80	7285,1315	258.7+/-282.2	3095,1095,110	yes	missense,missense	MCM4	NM_005914.3,NM_182746.2	15,15	4973,1408,122	AA,AT,TT		15.2907,7.6487,12.7018	benign,benign	650/864,650/864	48885436	11354,1652	2203	4300	6503	SO:0001583	missense	4173	exon14			TTCCTCTTGCTGG		CCDS6143.1	8q12-q13	2008-02-05	2007-04-04		ENSG00000104738	ENSG00000104738			6947	protein-coding gene	gene with protein product		602638	"""MCM4 minichromosome maintenance deficient 4 (S. cerevisiae)"""	CDC21		7601140	Standard	NM_005914		Approved	CDC54, hCdc21, P1-Cdc21, MGC33310	uc003xql.2	P33991	OTTHUMG00000164205	ENST00000262105.2:c.1948T>A	8.37:g.48885436T>A	ENSP00000262105:p.Leu650Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_182746	Q8NEH1|Q99658	Missense_Mutation	SNP	ENST00000262105.2	37	CCDS6143.1	1999	0.9152930402930403	474	0.9634146341463414	325	0.8977900552486188	572	1.0	628	0.8284960422163589	A	9.559	1.117856	0.20877	0.923513	0.847093	ENSG00000104738	ENST00000523944;ENST00000262105;ENST00000396826;ENST00000429229	T;T	0.13778	2.56;2.56	5.32	5.32	0.75619	ATPase, AAA+ type, core (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.11818	0.18	0.09310	P	1.0	B	0.09022	0.002	B	0.14578	0.011	T	0.42982	-0.9419	9	0.07325	T	0.83	-35.9772	10.7376	0.46135	0.8581:0.0:0.0:0.1419	rs762679;rs11556050;rs17287704;rs17694934;rs17856910;rs52801162;rs762679	650	P33991	MCM4_HUMAN	M	650;650;637;610	ENSP00000430194:L650M;ENSP00000262105:L650M	ENSP00000262105:L650M	L	+	1	2	MCM4	49047989	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.133000	0.77259	0.967000	0.38186	-0.364000	0.07487	TTG	T|0.104;A|0.896	0.896	strong		0.522	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914	
ABCA1	19	hgsc.bcm.edu	37	9	107620867	107620867	+	Missense_Mutation	SNP	C	C	T	rs2230806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107620867C>T	ENST00000374736.3	-	7	1050	c.656G>A	c.(655-657)aGg>aAg	p.R219K	ABCA1_ENST00000423487.2_Missense_Mutation_p.R219K	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	219			R -> K (common polymorphism; associated with a decreased severity of CAD; dbSNP:rs2230806). {ECO:0000269|PubMed:10938021, ECO:0000269|PubMed:11238261, ECO:0000269|PubMed:11257261, ECO:0000269|PubMed:11476965, ECO:0000269|PubMed:12624133, ECO:0000269|PubMed:12966036, ECO:0000269|PubMed:15520867}.		apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.R219K(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	CAGTTTCTCCCTTGGTAGGCC	0.468													C|||	2202	0.439696	0.7103	0.3487	5008	,	,		19674	0.4147		0.2425	False		,,,				2504	0.3671				p.R219K		Atlas-SNP	.											ABCA1,NS,carcinoma,0,1	ABCA1	244	1	1	Substitution - Missense(1)	stomach(1)	c.G656A	GRCh37	CM030397	ABCA1	M	rs2230806	PASS	.	C	LYS/ARG	2672,1734	648.2+/-398.7	820,1032,351	154.0	151.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	656	0.1	0.2	9	dbSNP_98	152	2420,6180	400.1+/-346.7	322,1776,2202	yes	missense	ABCA1	NM_005502.3	26	1142,2808,2553	TT,TC,CC		28.1395,39.3554,39.1512	benign	219/2262	107620867	5092,7914	2203	4300	6503	SO:0001583	missense	19	exon7			TTCTCCCTTGGTA	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.656G>A	9.37:g.107620867C>T	ENSP00000363868:p.Arg219Lys	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	137	77	0.562044	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	916	0.4194139194139194	356	0.7235772357723578	127	0.35082872928176795	250	0.4370629370629371	183	0.24142480211081793	C	7.792	0.711767	0.15306	0.606446	0.281395	ENSG00000165029	ENST00000374736;ENST00000423487	D;D	0.94931	-2.23;-3.56	6.17	0.0573	0.14322	.	0.632115	0.18950	N	0.126712	T	0.00012	0.0000	N	0.04880	-0.145	0.28835	P	0.896936	B	0.02656	0.0	B	0.01281	0.0	T	0.46119	-0.9214	9	0.16896	T	0.51	.	8.2419	0.31665	0.0:0.3764:0.0:0.6236	rs2230806;rs2234884;rs2853572;rs52801000;rs61696010;rs2230806	219	O95477	ABCA1_HUMAN	K	219	ENSP00000363868:R219K;ENSP00000416623:R219K	ENSP00000363868:R219K	R	-	2	0	ABCA1	106660688	0.825000	0.29262	0.227000	0.23927	0.534000	0.34807	0.318000	0.19504	0.083000	0.17047	0.655000	0.94253	AGG	C|0.587;T|0.413	0.413	strong		0.468	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
ZNF354A	6940	hgsc.bcm.edu	37	5	178139442	178139442	+	Silent	SNP	T	T	G	rs1132338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:178139442T>G	ENST00000335815.2	-	5	1634	c.1437A>C	c.(1435-1437)tcA>tcC	p.S479S		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	479					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S479S(1)		breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		GAATGAGAGCTGAACTCTGTC	0.393													t|||	1429	0.285343	0.1694	0.2522	5008	,	,		20228	0.3343		0.2813	False		,,,				2504	0.4192				p.S479S		Atlas-SNP	.											ZNF354A,NS,carcinoma,0,1	ZNF354A	74	1	1	Substitution - coding silent(1)	stomach(1)	c.A1437C						scavenged	.	G		870,3536	333.1+/-302.8	94,682,1427	122.0	115.0	118.0		1437	0.9	1.0	5	dbSNP_86	118	2291,6309	377.8+/-338.7	324,1643,2333	no	coding-synonymous	ZNF354A	NM_005649.2		418,2325,3760	GG,GT,TT		26.6395,19.7458,24.3042		479/606	178139442	3161,9845	2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			GAGAGCTGAACTC	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1437A>C	5.37:g.178139442T>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	62	13	0.209677	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			.	.	weak		0.393	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
LRP1	4035	hgsc.bcm.edu	37	12	57539082	57539082	+	Missense_Mutation	SNP	C	C	T	rs1800127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57539082C>T	ENST00000243077.3	+	6	1116	c.650C>T	c.(649-651)gCc>gTc	p.A217V	LRP1_ENST00000338962.4_Missense_Mutation_p.A217V|LRP1_ENST00000553277.1_Missense_Mutation_p.A217V|RP11-545N8.3_ENST00000555461.1_RNA|RP11-545N8.3_ENST00000554476.1_RNA|LRP1_ENST00000554174.1_Missense_Mutation_p.A217V	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	217			A -> V (in dbSNP:rs1800127).		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)	CTGAGTGGGGCCCAGGTGTCT	0.587													C|||	35	0.00698882	0.0	0.0173	5008	,	,		20985	0.0		0.0199	False		,,,				2504	0.0031				p.A217V		Atlas-SNP	.											.	LRP1	428	.	0			c.C650T						PASS	.	C	VAL/ALA	18,4388	25.3+/-52.1	0,18,2185	88.0	58.0	68.0		650	4.2	1.0	12	dbSNP_89	68	191,8409	84.0+/-146.5	3,185,4112	yes	missense	LRP1	NM_002332.2	64	3,203,6297	TT,TC,CC		2.2209,0.4085,1.607	benign	217/4545	57539082	209,12797	2203	4300	6503	SO:0001583	missense	4035	exon6			GTGGGGCCCAGGT	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.650C>T	12.37:g.57539082C>T	ENSP00000243077:p.Ala217Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	22	0.010073260073260074	0	0.0	8	0.022099447513812154	0	0.0	14	0.018469656992084433	C	16.44	3.124040	0.56613	0.004085	0.022209	ENSG00000123384	ENST00000553277;ENST00000243077;ENST00000338962;ENST00000554174	D;D;D;D	0.91351	-2.57;-2.83;-2.53;-2.83	5.08	4.19	0.49359	Six-bladed beta-propeller, TolB-like (1);	0.281286	0.28821	N	0.014040	T	0.78660	0.4318	L	0.55743	1.74	0.29803	N	0.832289	B;B;B;B	0.09022	0.002;0.002;0.002;0.001	B;B;B;B	0.08055	0.003;0.001;0.003;0.001	T	0.75883	-0.3160	10	0.35671	T	0.21	.	11.3799	0.49750	0.0:0.911:0.0:0.089	rs1800127	217;217;217;217	Q86SW0;Q07954;Q6PJ72;Q7Z7K9	.;LRP1_HUMAN;.;.	V	217	ENSP00000451449:A217V;ENSP00000243077:A217V;ENSP00000341264:A217V;ENSP00000451737:A217V	ENSP00000243077:A217V	A	+	2	0	LRP1	55825349	0.851000	0.29673	1.000000	0.80357	0.967000	0.64934	1.424000	0.34848	2.826000	0.97356	0.655000	0.94253	GCC	C|0.987;T|0.013	0.013	strong		0.587	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
ANKRD36	375248	hgsc.bcm.edu	37	2	97869979	97869979	+	Missense_Mutation	SNP	G	G	T	rs111515821		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:97869979G>T	ENST00000461153.2	+	50	3284	c.3040G>T	c.(3040-3042)Gat>Tat	p.D1014Y	ANKRD36_ENST00000420699.2_Missense_Mutation_p.D1014Y			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	1014								p.D1014Y(5)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						AGGAAAAAAGGATGGAGAAAA	0.328																																					p.D1014Y		Atlas-SNP	.											ANKRD36_ENST00000420699,bladder,carcinoma,0,8	ANKRD36	170	8	5	Substitution - Missense(5)	endometrium(2)|skin(2)|kidney(1)	c.G3040T						scavenged	.						29.0	35.0	33.0					2																	97869979		692	1589	2281	SO:0001583	missense	375248	exon50			AAAAAGGATGGAG	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.3040G>T	2.37:g.97869979G>T	ENSP00000419530:p.Asp1014Tyr	Somatic	29	3	0.103448		WXS	Illumina HiSeq	Phase_I	25	3	0.12	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	.	2.724	-0.265945	0.05754	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000461694	T;T	0.76578	-1.03;-1.03	0.63	0.63	0.17693	.	.	.	.	.	T	0.79287	0.4420	L	0.38175	1.15	0.09310	N	1	D	0.71674	0.998	D	0.69654	0.965	T	0.66440	-0.5923	8	0.52906	T	0.07	.	.	.	.	.	1014	A6QL64	AN36A_HUMAN	Y	1014;1014;376	ENSP00000419530:D1014Y;ENSP00000391950:D1014Y	ENSP00000391950:D1014Y	D	+	1	0	ANKRD36	97233706	0.010000	0.17322	0.018000	0.16275	0.005000	0.04900	0.408000	0.21065	0.612000	0.30071	0.175000	0.17021	GAT	.	.	weak		0.328	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5		
RP1L1	94137	hgsc.bcm.edu	37	8	10465399	10465399	+	Missense_Mutation	SNP	T	T	A	rs11782670	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10465399T>A	ENST00000382483.3	-	4	6432	c.6209A>T	c.(6208-6210)gAg>gTg	p.E2070V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2150	25 X 16 AA approximate tandem repeats of [ED]-[AT]-[PQ]-[ED]-[AVT]-E-[GKE]-[ED]- [AMT]-Q-[EPK]-[EAT]-[TSELP]-[EG]- [EGSQDI]-[AVIE].				cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				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)		CTCCTGGACCTCCCCTTCAGC	0.622													-|||	808	0.161342	0.0832	0.1254	5008	,	,		17815	0.4187		0.1034	False		,,,				2504	0.0869				p.E2070V		Atlas-SNP	.											RP1L1,NS,carcinoma,+1,1	RP1L1	453	1	0			c.A6209T						PASS	.	-	VAL/GLU	363,3759		13,337,1711	118.0	133.0	128.0		6209	0.7	0.0	8	dbSNP_120	128	1032,7336		66,900,3218	yes	missense	RP1L1	NM_178857.5	121	79,1237,4929	AA,AT,TT		12.3327,8.8064,11.1689	probably-damaging	2070/2401	10465399	1395,11095	2061	4184	6245	SO:0001583	missense	94137	exon4			TGGACCTCCCCTT	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.6209A>T	8.37:g.10465399T>A	ENSP00000371923:p.Glu2070Val	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	88	41	0.465909	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	382	0.1749084249084249	37	0.07520325203252033	57	0.1574585635359116	214	0.3741258741258741	74	0.09762532981530343	-	8.554	0.876171	0.17395	0.088064	0.123327	ENSG00000183638	ENST00000382483	T	0.04917	3.53	0.674	0.674	0.17946	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.63046	0.992	P	0.60682	0.878	T	0.50642	-0.8804	8	0.32370	T	0.25	.	5.241	0.15471	0.0:0.0:0.0:1.0	rs11782670	2070	A6NKC6	.	V	2070	ENSP00000371923:E2070V	ENSP00000371923:E2070V	E	-	2	0	RP1L1	10502809	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	0.163000	0.16520	0.541000	0.28827	0.392000	0.25879	GAG	T|0.847;A|0.153	0.153	strong		0.622	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
TMEM119	338773	hgsc.bcm.edu	37	12	108986031	108986031	+	Silent	SNP	C	C	T	rs74504010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:108986031C>T	ENST00000392806.3	-	2	297	c.129G>A	c.(127-129)gaG>gaA	p.E43E		NM_181724.2	NP_859075.2	Q4V9L6	TM119_HUMAN	transmembrane protein 119	43					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				large_intestine(2)|lung(3)|ovary(1)|skin(1)	7						AGCCCTCGGCCTCCCCACTAC	0.706													C|||	832	0.166134	0.0053	0.1297	5008	,	,		11135	0.3145		0.164	False		,,,				2504	0.2587				p.E43E		Atlas-SNP	.											TMEM119,NS,carcinoma,0,1	TMEM119	31	1	0			c.G129A						PASS	.	C		156,4214		6,144,2035	8.0	11.0	10.0		129	0.4	1.0	12	dbSNP_131	10	1399,7135		129,1141,2997	no	coding-synonymous	TMEM119	NM_181724.2		135,1285,5032	TT,TC,CC		16.3933,3.5698,12.0505		43/284	108986031	1555,11349	2185	4267	6452	SO:0001819	synonymous_variant	338773	exon2			CTCGGCCTCCCCA	AK075501	CCDS9119.1	12q23.3	2014-02-12				ENSG00000183160			27884	protein-coding gene	gene with protein product						12975309	Standard	NM_181724		Approved		uc001tng.3	Q4V9L6		ENST00000392806.3:c.129G>A	12.37:g.108986031C>T		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	20	14	0.7	NM_181724	Q6UXE5|Q8N2F5	Silent	SNP	ENST00000392806.3	37	CCDS9119.1																																																																																			C|0.827;T|0.173	0.173	strong		0.706	TMEM119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403900.1	NM_181724	
CFAP74	85452	hgsc.bcm.edu	37	1	1896440	1896440	+	IGR	SNP	G	G	A	rs16824585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1896440G>A								TMEM52 (45728 upstream) : C1orf222 (23122 downstream)																							GTGCGCTCCAGGATGTCCTTG	0.647													g|||	1085	0.216653	0.2489	0.2032	5008	,	,		16690	0.2718		0.2276	False		,,,				2504	0.1145				p.L488L		Atlas-SNP	.											.	KIAA1751	92	.	0			c.C1462T						PASS	.			949,3145		126,697,1224	40.0	44.0	43.0		1462	2.2	1.0	1	dbSNP_123	43	2052,6326		258,1536,2395	no	coding-synonymous	KIAA1751	NM_001080484.1		384,2233,3619	AA,AG,GG		24.4927,23.1803,24.0619		488/763	1896440	3001,9471	2047	4189	6236	SO:0001628	intergenic_variant	85452	exon13			GCTCCAGGATGTC																													1.37:g.1896440G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	104	93	0.894231	NM_001080484		Silent	SNP		37																																																																																				G|0.764;A|0.236	0.236	strong	0	0.647								
CEP135	9662	hgsc.bcm.edu	37	4	56885581	56885581	+	Silent	SNP	T	T	C	rs61753870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:56885581T>C	ENST00000257287.4	+	23	3199	c.3075T>C	c.(3073-3075)aaT>aaC	p.N1025N		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	1025					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					AACTTTCAAATGAGAGACATA	0.348													T|||	111	0.0221645	0.003	0.0793	5008	,	,		17641	0.002		0.0318	False		,,,				2504	0.0184				p.N1025N		Atlas-SNP	.											.	CEP135	115	.	0			c.T3075C						PASS	.	T		35,4371	39.2+/-71.8	0,35,2168	64.0	61.0	62.0		3075	2.5	1.0	4	dbSNP_129	62	238,8362	95.2+/-157.0	5,228,4067	no	coding-synonymous	CEP135	NM_025009.3		5,263,6235	CC,CT,TT		2.7674,0.7944,2.099		1025/1141	56885581	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	9662	exon23			TTCAAATGAGAGA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.3075T>C	4.37:g.56885581T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Silent	SNP	ENST00000257287.4	37	CCDS33986.1																																																																																			T|0.978;C|0.022	0.022	strong		0.348	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
UNC5C	8633	hgsc.bcm.edu	37	4	96166270	96166270	+	Silent	SNP	C	C	T	rs35120448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:96166270C>T	ENST00000453304.1	-	6	1149	c.801G>A	c.(799-801)acG>acA	p.T267T	UNC5C_ENST00000506749.1_Silent_p.T267T	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	267	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CAGACCACTCCGTCCAGGTGG	0.512													C|||	116	0.0231629	0.0159	0.0346	5008	,	,		17093	0.0		0.0537	False		,,,				2504	0.0174				p.T267T		Atlas-SNP	.											UNC5C,NS,carcinoma,-1,1	UNC5C	141	1	0			c.G801A						PASS	.	C		97,4309	78.3+/-116.7	3,91,2109	64.0	55.0	58.0		801	-5.9	1.0	4	dbSNP_126	58	444,8156	133.1+/-190.7	8,428,3864	no	coding-synonymous	UNC5C	NM_003728.3		11,519,5973	TT,TC,CC		5.1628,2.2015,4.1596		267/932	96166270	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon6			CCACTCCGTCCAG	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.801G>A	4.37:g.96166270C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.961;T|0.039	0.039	strong		0.512	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967981	49967981	+	Silent	SNP	T	T	G	rs11558188	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49967981T>G	ENST00000293350.4	+	12	1693	c.1530T>G	c.(1528-1530)gtT>gtG	p.V510V	ALDH16A1_ENST00000455361.2_Silent_p.V459V|ALDH16A1_ENST00000433981.2_Silent_p.V345V|CTD-3148I10.9_ENST00000599536.1_3'UTR|ALDH16A1_ENST00000540132.1_Silent_p.V347V	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	510						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GCCTCGCTGTTCCCTCAACCC	0.612													T|||	1051	0.209864	0.3396	0.2277	5008	,	,		14798	0.005		0.335	False		,,,				2504	0.1043				p.V510V		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.T1530G						PASS	.	T	,	1368,3038	451.4+/-349.7	214,940,1049	126.0	132.0	130.0		1377,1530	-9.3	0.0	19	dbSNP_120	130	3014,5586	465.2+/-366.4	527,1960,1813	yes	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	741,2900,2862	GG,GT,TT		35.0465,31.0486,33.6921	,	459/752,510/803	49967981	4382,8624	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon12			CGCTGTTCCCTCA	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1530T>G	19.37:g.49967981T>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			T|0.692;G|0.308	0.308	strong		0.612	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
LASP1	3927	hgsc.bcm.edu	37	17	37054772	37054772	+	Splice_Site	SNP	C	C	T	rs1130638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:37054772C>T	ENST00000318008.6	+	4	688	c.357C>T	c.(355-357)aaC>aaT	p.N119N	LASP1_ENST00000433206.2_Splice_Site_p.N63N|LASP1_ENST00000435347.3_Splice_Site_p.N119N	NM_006148.2	NP_006139.1	Q14847	LASP1_HUMAN	LIM and SH3 protein 1	119					ion transport (GO:0006811)|positive regulation of signal transduction (GO:0009967)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	ion transmembrane transporter activity (GO:0015075)|SH3/SH2 adaptor activity (GO:0005070)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(4)|urinary_tract(2)	9						AGATCAGTAACGTGAGCTCTT	0.577			T	MLL	AML								C|||	1164	0.232428	0.1415	0.317	5008	,	,		20211	0.1042		0.4056	False		,,,				2504	0.2495				p.N119N		Atlas-SNP	.		Dom	yes		17	17q11-q21.3	3927	LIM and SH3 protein 1		L	LASP1,colon,carcinoma,0,1	LASP1	24	1	0			c.C357T						PASS	.	C		655,3163		68,519,1322	81.0	65.0	70.0		357	-5.1	0.9	17	dbSNP_86	70	2987,4269		669,1649,1310	yes	coding-synonymous-near-splice	LASP1	NM_006148.2		737,2168,2632	TT,TC,CC		41.1659,17.1556,32.8878		119/262	37054772	3642,7432	1909	3628	5537	SO:0001630	splice_region_variant	3927	exon4			CAGTAACGTGAGC		CCDS11331.1, CCDS62164.1	17q11-q21.3	2008-07-18			ENSG00000002834	ENSG00000002834			6513	protein-coding gene	gene with protein product		602920				7490069	Standard	NM_006148		Approved	MLN50, Lasp-1	uc010cvq.3	Q14847	OTTHUMG00000133182	ENST00000318008.6:c.357+1C>T	17.37:g.37054772C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_006148	B4DGQ0|Q96ED2|Q96IG0	Silent	SNP	ENST00000318008.6	37	CCDS11331.1																																																																																			C|0.731;T|0.269	0.269	strong		0.577	LASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256890.3	NM_006148	Silent
C15orf52	388115	hgsc.bcm.edu	37	15	40627845	40627845	+	Silent	SNP	G	G	A	rs55641696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:40627845G>A	ENST00000559313.1	-	11	1134	c.1119C>T	c.(1117-1119)agC>agT	p.S373S	C15orf52_ENST00000397536.2_Silent_p.S163S	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	373							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		GCTCCATCCCGCTCTGCTTCT	0.647													G|||	733	0.146366	0.0855	0.1686	5008	,	,		17103	0.0278		0.2803	False		,,,				2504	0.1973				p.S373S		Atlas-SNP	.											.	C15orf52	47	.	0			c.C1119T						PASS	.	G		443,3913		25,393,1760	43.0	44.0	44.0		1119	0.1	0.0	15	dbSNP_129	44	2221,6283		313,1595,2344	no	coding-synonymous	C15orf52	NM_207380.2		338,1988,4104	AA,AG,GG		26.1171,10.1699,20.7154		373/535	40627845	2664,10196	2178	4252	6430	SO:0001819	synonymous_variant	388115	exon11			CATCCCGCTCTGC	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.1119C>T	15.37:g.40627845G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Silent	SNP	ENST00000559313.1	37	CCDS10055.2																																																																																			G|0.836;A|0.164	0.164	strong		0.647	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380	
SYT3	84258	hgsc.bcm.edu	37	19	51128661	51128661	+	Silent	SNP	T	T	C	rs16986142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51128661T>C	ENST00000338916.4	-	6	2196	c.1563A>G	c.(1561-1563)gtA>gtG	p.V521V	SYT3_ENST00000600079.1_Silent_p.V521V|SYT3_ENST00000593901.1_Silent_p.V521V|SYT3_ENST00000544769.1_Silent_p.V521V	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	521	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		AGTCGTAGTCTACCACGGCGA	0.677													c|||	3494	0.697684	0.8752	0.7795	5008	,	,		11656	0.3095		0.836	False		,,,				2504	0.6575				p.V521V		Atlas-SNP	.											.	SYT3	85	.	0			c.A1563G						PASS	.	C	,,	3766,580		1632,502,39	44.0	35.0	38.0		1563,1563,1563	-2.0	1.0	19	dbSNP_123	38	7193,1299		3049,1095,102	no	coding-synonymous,coding-synonymous,coding-synonymous	SYT3	NM_001160328.1,NM_001160329.1,NM_032298.2	,,	4681,1597,141	CC,CT,TT		15.2967,13.3456,14.6362	,,	521/591,521/591,521/591	51128661	10959,1879	2173	4246	6419	SO:0001819	synonymous_variant	84258	exon6			GTAGTCTACCACG	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"""Synaptotagmins"""	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.1563A>G	19.37:g.51128661T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_032298	Q8N5Z1|Q8N640	Silent	SNP	ENST00000338916.4	37	CCDS12798.1																																																																																			T|0.228;C|0.772	0.772	strong		0.677	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298	
HEATR5A	25938	hgsc.bcm.edu	37	14	31858209	31858209	+	Missense_Mutation	SNP	C	C	T	rs7157977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:31858209C>T	ENST00000389961.3	-	6	756	c.757G>A	c.(757-759)Gcc>Acc	p.A253T	HEATR5A_ENST00000439727.1_5'Flank|HEATR5A_ENST00000439348.1_Missense_Mutation_p.A253T|HEATR5A_ENST00000543095.2_Missense_Mutation_p.A259T|HEATR5A_ENST00000404677.3_Missense_Mutation_p.A259T			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	253										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		TGACGTGAGGCTGCTATGACA	0.368													C|||	1557	0.310903	0.1195	0.3429	5008	,	,		20952	0.3353		0.4205	False		,,,				2504	0.409				p.A259T		Atlas-SNP	.											.	HEATR5A	181	.	0			c.G775A						PASS	.																																			SO:0001583	missense	25938	exon7			GTGAGGCTGCTAT	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.757G>A	14.37:g.31858209C>T	ENSP00000374611:p.Ala253Thr	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	37	37	1	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		734	0.3360805860805861	57	0.11585365853658537	138	0.3812154696132597	214	0.3741258741258741	325	0.4287598944591029	C	14.32	2.501006	0.44455	.	.	ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000543095;ENST00000404677	T;T;T;T	0.08102	3.13;3.13;3.13;3.13	5.6	5.6	0.85130	.	.	.	.	.	T	0.00012	0.0000	N	0.10972	0.075	0.38151	P	0.06126900000000002	B	0.06786	0.001	B	0.06405	0.002	T	0.46843	-0.9162	8	0.13853	T	0.58	.	11.0175	0.47698	0.1998:0.6792:0.121:0.0	rs7157977;rs56643289;rs58492332;rs7157977	259	B5MC49	.	T	253;253;259;259	ENSP00000374611:A253T;ENSP00000405407:A253T;ENSP00000437968:A259T;ENSP00000384646:A259T	ENSP00000374611:A253T	A	-	1	0	HEATR5A	30927960	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	2.388000	0.44398	2.629000	0.89072	0.491000	0.48974	GCC	C|0.676;N|0.000	.	strong		0.368	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	
PCOLCE	5118	hgsc.bcm.edu	37	7	100205365	100205365	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100205365C>T	ENST00000223061.5	+	8	1398	c.1118C>T	c.(1117-1119)tCt>tTt	p.S373F		NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	373	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GACCTGCCTTCTCCACCCACT	0.552																																					p.S373F		Atlas-SNP	.											.	PCOLCE	37	.	0			c.C1118T						PASS	.						154.0	146.0	149.0					7																	100205365		2203	4300	6503	SO:0001583	missense	5118	exon8			TGCCTTCTCCACC	L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"""procollagen, type 1, COOH-terminal proteinase enhancer"", ""procollagen C-proteinase enhancer 1"""	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.1118C>T	7.37:g.100205365C>T	ENSP00000223061:p.Ser373Phe	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_002593	B2R9E1|O14550	Missense_Mutation	SNP	ENST00000223061.5	37	CCDS5700.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518752	0.44763	.	.	ENSG00000106333	ENST00000223061	T	0.23552	1.9	4.42	3.5	0.40072	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.587059	0.17803	N	0.161488	T	0.38348	0.1037	L	0.44542	1.39	0.09310	N	1	D	0.65815	0.995	D	0.68943	0.961	T	0.07597	-1.0764	10	0.54805	T	0.06	-6.1274	9.2378	0.37477	0.2159:0.7841:0.0:0.0	.	373	Q15113	PCOC1_HUMAN	F	373	ENSP00000223061:S373F	ENSP00000223061:S373F	S	+	2	0	PCOLCE	100043301	0.082000	0.21442	0.994000	0.49952	0.730000	0.41778	1.614000	0.36911	1.017000	0.39495	0.462000	0.41574	TCT	.	.	none		0.552	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345285.1	NM_002593	
SLC34A3	142680	hgsc.bcm.edu	37	9	140127051	140127051	+	Missense_Mutation	SNP	G	G	A	rs532224704|rs34372115	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140127051G>A	ENST00000538474.1	+	4	424	c.200G>A	c.(199-201)cGc>cAc	p.R67H	SLC34A3_ENST00000361134.2_Missense_Mutation_p.R67H	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	67			R -> H (in dbSNP:rs34372115). {ECO:0000269|PubMed:16358215}.		cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGCAGGCTGCGCCGCGTGGCC	0.687													g|||	506	0.101038	0.0045	0.0447	5008	,	,		13428	0.2004		0.1093	False		,,,				2504	0.1605				p.R67H		Atlas-SNP	.											.	SLC34A3	32	.	0			c.G200A						PASS	.		HIS/ARG,HIS/ARG,HIS/ARG	72,4322		0,72,2125	27.0	31.0	30.0		200,200,200	-7.5	0.0	9	dbSNP_126	30	766,7796		51,664,3566	no	missense,missense,missense	SLC34A3	NM_001177316.1,NM_001177317.1,NM_080877.2	29,29,29	51,736,5691	AA,AG,GG		8.9465,1.6386,6.468	benign,benign,benign	67/600,67/600,67/600	140127051	838,12118	2197	4281	6478	SO:0001583	missense	142680	exon4			GGCTGCGCCGCGT	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"""Solute carriers"""	20305	protein-coding gene	gene with protein product		609826	"""solute carrier family 34 (sodium phosphate), member 3"""			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.200G>A	9.37:g.140127051G>A	ENSP00000442397:p.Arg67His	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	51	36	0.705882	NM_001177317	A2BFA1	Missense_Mutation	SNP	ENST00000538474.1	37	CCDS7038.1	214	0.09798534798534798	4	0.008130081300813009	18	0.049723756906077346	109	0.19055944055944055	83	0.10949868073878628	g	5.524	0.281558	0.10458	0.016386	0.089465	ENSG00000198569	ENST00000538474;ENST00000361134	T;T	0.32753	1.44;1.44	3.74	-7.47	0.01365	.	1.350550	0.04922	N	0.455209	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.20009	-1.0288	9	0.12430	T	0.62	-0.2955	6.8531	0.24026	0.4062:0.0:0.4785:0.1153	rs34372115;rs59053592	67	Q8N130	NPT2C_HUMAN	H	67	ENSP00000442397:R67H;ENSP00000355353:R67H	ENSP00000355353:R67H	R	+	2	0	SLC34A3	139246872	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.079000	0.14782	-2.569000	0.00469	-0.347000	0.07816	CGC	G|0.924;A|0.076	0.076	strong		0.687	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877	
ASCC3	10973	hgsc.bcm.edu	37	6	101166095	101166095	+	Silent	SNP	G	G	A	rs41288423	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:101166095G>A	ENST00000369162.2	-	12	2279	c.1935C>T	c.(1933-1935)ctC>ctT	p.L645L	ASCC3_ENST00000522650.1_Silent_p.L645L	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	645	Helicase ATP-binding 1. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.L645L(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		CAGACAGTCCGAGAATCCTTA	0.323													G|||	2297	0.458666	0.4735	0.3948	5008	,	,		15981	0.3135		0.4771	False		,,,				2504	0.6145				p.L645L		Atlas-SNP	.											ASCC3,NS,carcinoma,0,2	ASCC3	205	2	1	Substitution - coding silent(1)	stomach(1)	c.C1935T						PASS	.	G		2022,2384	562.7+/-381.0	475,1072,656	112.0	108.0	109.0		1935	0.4	1.0	6	dbSNP_127	109	4273,4327	575.0+/-390.2	1079,2115,1106	no	coding-synonymous	ASCC3	NM_006828.2		1554,3187,1762	AA,AG,GG		49.686,45.892,48.4007		645/2203	101166095	6295,6711	2203	4300	6503	SO:0001819	synonymous_variant	10973	exon12			CAGTCCGAGAATC	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.1935C>T	6.37:g.101166095G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	37	0.925	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Silent	SNP	ENST00000369162.2	37	CCDS5046.1																																																																																			G|0.528;A|0.472	0.472	strong		0.323	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
USP17L22	100287513	hgsc.bcm.edu	37	4	9270328	9270328	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	714	6	0.00840336		WXS	Illumina HiSeq	Phase_I	475	11	0.0231579	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	
ACPP	55	hgsc.bcm.edu	37	3	132075554	132075554	+	Silent	SNP	T	T	C	rs3181784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132075554T>C	ENST00000336375.5	+	10	1083	c.993T>C	c.(991-993)taT>taC	p.Y331Y	ACPP_ENST00000475741.1_Silent_p.Y298Y|ACPP_ENST00000351273.7_Silent_p.Y331Y	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	331					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)	p.Y331Y(2)		NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						AGATGTACTATCGGAATGAGA	0.537													T|||	1520	0.303514	0.3245	0.3761	5008	,	,		16201	0.0804		0.3767	False		,,,				2504	0.3783				p.Y331Y		Atlas-SNP	.											ACPP_ENST00000351273,NS,carcinoma,0,4	ACPP	118	4	2	Substitution - coding silent(2)	prostate(2)	c.T993C						PASS	.	T	,	1430,2976	465.5+/-354.2	235,960,1008	138.0	127.0	131.0		993,993	-4.3	0.9	3	dbSNP_105	131	3304,5296	494.5+/-373.8	634,2036,1630	no	coding-synonymous,coding-synonymous	ACPP	NM_001099.4,NM_001134194.1	,	869,2996,2638	CC,CT,TT		38.4186,32.4557,36.3986	,	331/387,331/419	132075554	4734,8272	2203	4300	6503	SO:0001819	synonymous_variant	55	exon10			GTACTATCGGAAT		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.993T>C	3.37:g.132075554T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	107	37	0.345794	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	37	CCDS3073.1	616	0.28205128205128205	156	0.3170731707317073	141	0.38950276243093923	38	0.06643356643356643	281	0.370712401055409	T	9.892	1.204508	0.22205	0.324557	0.384186	ENSG00000014257	ENST00000507647	.	.	.	5.67	-4.32	0.03688	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999822262	.	.	.	.	.	.	T	0.25813	-1.0121	3	.	.	.	.	12.3643	0.55221	0.0:0.5521:0.0:0.4479	rs3181784;rs17182933;rs17408313	.	.	.	T	16	.	.	I	+	2	0	ACPP	133558244	0.994000	0.37717	0.936000	0.37596	0.939000	0.58152	0.006000	0.13152	-1.077000	0.03121	-0.408000	0.06270	ATC	T|0.657;C|0.343	0.343	strong		0.537	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	
VEZT	55591	hgsc.bcm.edu	37	12	95681554	95681554	+	Silent	SNP	C	C	T	rs12424550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:95681554C>T	ENST00000436874.1	+	9	1548	c.1443C>T	c.(1441-1443)caC>caT	p.H481H	RNU6-808P_ENST00000391233.1_RNA|VEZT_ENST00000356859.4_3'UTR|VEZT_ENST00000261219.6_Silent_p.H433H	NM_017599.3	NP_060069.3	Q9HBM0	VEZA_HUMAN	vezatin, adherens junctions transmembrane protein	481					chordate embryonic development (GO:0043009)|single organismal cell-cell adhesion (GO:0016337)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stereocilia ankle link complex (GO:0002142)				endometrium(2)|kidney(3)|large_intestine(1)|lung(14)|ovary(2)|upper_aerodigestive_tract(1)	23						TTCAGCCCCACGTTCAAGCAA	0.393													C|||	495	0.0988419	0.0144	0.1095	5008	,	,		16082	0.1776		0.1382	False		,,,				2504	0.0838				p.H481H		Atlas-SNP	.											.	VEZT	106	.	0			c.C1443T						PASS	.	C		131,3631		1,129,1751	56.0	51.0	52.0		1443	-2.0	1.0	12	dbSNP_120	52	1280,6920		97,1086,2917	no	coding-synonymous	VEZT	NM_017599.3		98,1215,4668	TT,TC,CC		15.6098,3.4822,11.7957		481/780	95681554	1411,10551	1881	4100	5981	SO:0001819	synonymous_variant	55591	exon9			GCCCCACGTTCAA	AF216644	CCDS44954.1	12q22	2011-02-15			ENSG00000028203	ENSG00000028203			18258	protein-coding gene	gene with protein product						11080149, 16199027, 21156161	Standard	NM_017599		Approved	DKFZP761C241	uc001tdz.2	Q9HBM0	OTTHUMG00000170182	ENST00000436874.1:c.1443C>T	12.37:g.95681554C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_017599	Q6P1Q3|Q9H2F4|Q9H2U5|Q9NT70|Q9NVW0|Q9UF91	Silent	SNP	ENST00000436874.1	37	CCDS44954.1																																																																																			C|0.882;T|0.118	0.118	strong		0.393	VEZT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407804.2	NM_017599	
CHPF	79586	hgsc.bcm.edu	37	2	220404648	220404648	+	Silent	SNP	C	C	T	rs1043833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220404648C>T	ENST00000243776.6	-	4	2033	c.1785G>A	c.(1783-1785)ctG>ctA	p.L595L	CHPF_ENST00000535926.1_Silent_p.L433L	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	595					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CCATGAGGCGCAGTGGTGAGG	0.652													C|||	1534	0.30631	0.1884	0.4841	5008	,	,		17935	0.2748		0.4523	False		,,,				2504	0.2219				p.L595L		Atlas-SNP	.											.	CHPF	56	.	0			c.G1785A						PASS	.	C	,	1096,3310		126,844,1233	53.0	59.0	57.0		1299,1785	-0.6	0.8	2	dbSNP_86	57	3967,4625		933,2101,1262	no	coding-synonymous,coding-synonymous	CHPF	NM_001195731.1,NM_024536.5	,	1059,2945,2495	TT,TC,CC		46.1709,24.8752,38.9521	,	433/614,595/776	220404648	5063,7935	2203	4296	6499	SO:0001819	synonymous_variant	79586	exon4			GAGGCGCAGTGGT	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24291	protein-coding gene	gene with protein product	"""chondroitin sulfate synthase 2"""	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1785G>A	2.37:g.220404648C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	229	120	0.524017	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																			C|0.645;T|0.355	0.355	strong		0.652	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536	
C2orf83	56918	hgsc.bcm.edu	37	2	228476140	228476140	+	Nonsense_Mutation	SNP	C	C	T	rs2176186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:228476140C>T	ENST00000264387.4	-	3	509	c.423G>A	c.(421-423)tgG>tgA	p.W141*	C2orf83_ENST00000409066.1_3'UTR	NM_020161.3	NP_064546.3	Q53S99	CB083_HUMAN	chromosome 2 open reading frame 83	141					transport (GO:0006810)	membrane (GO:0016020)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(2)	11						TAGAATGGCTCCAGAGCACCG	0.473													T|||	1572	0.313898	0.2254	0.3401	5008	,	,		18581	0.4058		0.2753	False		,,,				2504	0.3599				p.W141X		Atlas-SNP	.											.	C2orf83	15	.	0			c.G423A						PASS	.	T	,stop/TRP	1024,3382	727.6+/-409.9	113,798,1292	159.0	154.0	156.0		,423	-1.8	0.0	2	dbSNP_96	156	2628,5972	687.1+/-404.2	382,1864,2054	yes	utr-3,stop-gained	C2orf83	NM_001162483.1,NM_020161.3	,	495,2662,3346	TT,TC,CC		30.5581,23.241,28.0793	,	,141/151	228476140	3652,9354	2203	4300	6503	SO:0001587	stop_gained	56918	exon3			ATGGCTCCAGAGC		CCDS33388.1, CCDS54434.1	2q36.3	2008-09-16			ENSG00000042304	ENSG00000042304			25344	protein-coding gene	gene with protein product							Standard	NM_020161		Approved	DKFZp547H025	uc002vph.3	Q53S99	OTTHUMG00000153550	ENST00000264387.4:c.423G>A	2.37:g.228476140C>T	ENSP00000264387:p.Trp141*	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	272	143	0.525735	NM_020161	A2RRG6|B8ZZI8|Q9NPW4	Nonsense_Mutation	SNP	ENST00000264387.4	37	CCDS33388.1	671	0.30723443223443225	112	0.22764227642276422	117	0.32320441988950277	241	0.42132867132867136	201	0.26517150395778366	T	9.224	1.034135	0.19590	0.23241	0.305581	ENSG00000042304	ENST00000264387	.	.	.	2.28	-1.83	0.07833	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.0887	0.09960	0.0:0.4167:0.2121:0.3712	rs2176186;rs3762469;rs60183513;rs2176186	.	.	.	X	141	.	ENSP00000264387:W141X	W	-	3	0	C2orf83	228184384	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	0.799000	0.27028	-0.890000	0.03945	-1.480000	0.00990	TGG	C|0.703;T|0.297	0.297	strong		0.473	C2orf83-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331607.1	NM_020161	
CD3EAP	10849	hgsc.bcm.edu	37	19	45912343	45912343	+	Missense_Mutation	SNP	A	A	G	rs762562	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45912343A>G	ENST00000309424.3	+	3	1605	c.1117A>G	c.(1117-1119)Aag>Gag	p.K373E	ERCC1_ENST00000588738.1_5'Flank|PPP1R13L_ENST00000418234.2_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.K375E|ERCC1_ENST00000300853.3_3'UTR|ERCC1_ENST00000423698.2_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	373			K -> E (in dbSNP:rs762562).		rRNA transcription (GO:0009303)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	11		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0251)		AGAAGGAGCGAAGCCTCAGGC	0.617													G|||	1436	0.286741	0.3109	0.2233	5008	,	,		16994	0.4613		0.1322	False		,,,				2504	0.2781				p.K373E		Atlas-SNP	.											CD3EAP,NS,carcinoma,0,1	CD3EAP	27	1	0			c.A1117G						PASS	.	G	,,GLU/LYS	1183,3221		168,847,1187	39.0	48.0	45.0		,,1117	1.6	0.0	19	dbSNP_86	45	1150,7450		79,992,3229	yes	utr-3,utr-3,missense	ERCC1,CD3EAP	NM_001166049.1,NM_001983.3,NM_012099.1	,,56	247,1839,4416	GG,GA,AA		13.3721,26.8619,17.9406	,,benign	,,373/511	45912343	2333,10671	2202	4300	6502	SO:0001583	missense	10849	exon3			GGAGCGAAGCCTC	U86751	CCDS12661.1, CCDS74397.1	19q13.3	2008-02-05	2006-03-28			ENSG00000117877			24219	protein-coding gene	gene with protein product	"""CD3 epsilon associated protein"", ""antisense to ERCC 1"""	107325	"""CD3e antigen, epsilon polypeptide associated protein"""			10373416, 9426281, 15226435	Standard	XM_005258425		Approved	ASE-1, CAST, PAF49	uc002pbq.1	O15446		ENST00000309424.3:c.1117A>G	19.37:g.45912343A>G	ENSP00000310966:p.Lys373Glu	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	570	0.260989010989011	131	0.266260162601626	72	0.19889502762430938	259	0.4527972027972028	108	0.1424802110817942	G	1.401	-0.578050	0.03854	0.268619	0.133721	ENSG00000117877	ENST00000309424	T	0.09911	2.93	5.4	1.59	0.23543	.	0.794983	0.10950	N	0.616167	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47071	-0.9145	9	0.02654	T	1	-2.1051	5.1222	0.14865	0.3446:0.1515:0.5039:0.0	rs762562;rs56437955;rs60195558;rs762562	375;373	O15446-2;O15446	.;RPA34_HUMAN	E	373	ENSP00000310966:K373E	ENSP00000310966:K373E	K	+	1	0	CD3EAP	50604183	0.005000	0.15991	0.000000	0.03702	0.013000	0.08279	0.970000	0.29383	0.267000	0.21916	-0.215000	0.12644	AAG	A|0.774;G|0.226	0.226	strong		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099	
KIAA1211	57482	hgsc.bcm.edu	37	4	57182647	57182647	+	Silent	SNP	G	G	A	rs3822003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:57182647G>A	ENST00000504228.1	+	6	3084	c.2979G>A	c.(2977-2979)gcG>gcA	p.A993A	KIAA1211_ENST00000541073.1_Silent_p.A986A|KIAA1211_ENST00000264229.6_Silent_p.A993A			Q6ZU35	K1211_HUMAN	KIAA1211	993	Pro-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					CTCGCCGAGCGGGGAGGCCGG	0.667													G|||	949	0.189497	0.0174	0.2061	5008	,	,		13721	0.253		0.339	False		,,,				2504	0.1912				p.A993A		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G2979A						PASS	.	G		297,3731		13,271,1730	34.0	43.0	40.0		2979	-10.1	0.0	4	dbSNP_107	40	2817,5535		481,1855,1840	no	coding-synonymous	KIAA1211	NM_020722.1		494,2126,3570	AA,AG,GG		33.7284,7.3734,25.1535		993/1234	57182647	3114,9266	2014	4176	6190	SO:0001819	synonymous_variant	57482	exon8			CCGAGCGGGGAGG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.2979G>A	4.37:g.57182647G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			G|0.773;A|0.227	0.227	strong		0.667	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
SLC16A4	9122	hgsc.bcm.edu	37	1	110925550	110925550	+	Silent	SNP	T	T	G	rs35653868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110925550T>G	ENST00000369779.4	-	3	375	c.126A>C	c.(124-126)gcA>gcC	p.A42A	SLC16A4_ENST00000472422.2_Silent_p.A42A|SLC16A4_ENST00000497687.1_Intron|SLC16A4_ENST00000437429.2_Intron|SLC16A4_ENST00000541986.1_Intron|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Silent_p.A42A	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	42					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAAAGAAAATTGCAAAAGTCT	0.418													T|||	118	0.0235623	0.0015	0.0346	5008	,	,		21003	0.0		0.0845	False		,,,				2504	0.0072				p.A42A		Atlas-SNP	.											.	SLC16A4	47	.	0			c.A126C						PASS	.	T	,,,,	67,4339	62.3+/-99.4	0,67,2136	111.0	108.0	109.0		126,,,126,126	-4.2	1.0	1	dbSNP_126	109	638,7962	164.2+/-216.6	29,580,3691	no	coding-synonymous,intron,intron,coding-synonymous,coding-synonymous	SLC16A4	NM_001201546.1,NM_001201547.1,NM_001201548.1,NM_001201549.1,NM_004696.2	,,,,	29,647,5827	GG,GT,TT		7.4186,1.5207,5.4206	,,,,	42/440,,,42/320,42/488	110925550	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	9122	exon3			GAAAATTGCAAAA	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.126A>C	1.37:g.110925550T>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_001201546	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	37	CCDS823.1																																																																																			T|0.946;G|0.054	0.054	strong		0.418	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
C18orf54	162681	hgsc.bcm.edu	37	18	51887123	51887123	+	Silent	SNP	C	C	T	rs1657904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:51887123C>T	ENST00000300091.5	+	2	513	c.181C>T	c.(181-183)Cta>Tta	p.L61L	STARD6_ENST00000577499.1_5'Flank|STARD6_ENST00000581310.1_5'Flank|C18orf54_ENST00000578138.1_Intron|STARD6_ENST00000584040.1_5'Flank|C18orf54_ENST00000382911.4_Silent_p.L61L	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	61						extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		TGATTTTGATCTAGGCCAAAT	0.348													C|||	305	0.0609026	0.0946	0.0432	5008	,	,		18617	0.0079		0.0646	False		,,,				2504	0.0787				p.L61L		Atlas-SNP	.											.	C18orf54	40	.	0			c.C181T						PASS	.	C		386,4020	194.0+/-219.0	17,352,1834	104.0	105.0	105.0		181	0.9	0.0	18	dbSNP_89	105	521,8079	146.8+/-202.3	15,491,3794	no	coding-synonymous	C18orf54	NM_173529.4		32,843,5628	TT,TC,CC		6.0581,8.7608,6.9737		61/373	51887123	907,12099	2203	4300	6503	SO:0001819	synonymous_variant	162681	exon2			TTTGATCTAGGCC	AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"""lung adenoma susceptibility protein 2"""	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.181C>T	18.37:g.51887123C>T		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Silent	SNP	ENST00000300091.5	37	CCDS11956.1																																																																																			C|0.932;T|0.068	0.068	strong		0.348	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529	
MZT2B	80097	hgsc.bcm.edu	37	2	130939163	130939163	+	5'Flank	SNP	G	G	T	rs146359515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130939163G>T	ENST00000281871.6	+	0	0				SMPD4_ENST00000339679.7_5'UTR|SMPD4_ENST00000431183.2_Missense_Mutation_p.F4L|SMPD4_ENST00000443958.2_5'UTR|SMPD4_ENST00000351288.6_Missense_Mutation_p.F4L|SMPD4_ENST00000409031.1_Missense_Mutation_p.F4L|SMPD4_ENST00000473720.1_5'UTR|SMPD4_ENST00000426662.2_5'UTR|SMPD4_ENST00000453750.1_Missense_Mutation_p.F4L|AC018804.1_ENST00000578074.1_RNA|MZT2B_ENST00000409255.1_5'Flank|SMPD4_ENST00000452225.2_5'UTR	NM_025029.3	NP_079305.2	Q6NZ67	MZT2B_HUMAN	mitotic spindle organizing protein 2B							centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				lung(1)	1						CCACGGCGCCGAAAGTCGTCA	0.677													.|||	18	0.00359425	0.0	0.0086	5008	,	,		12025	0.0		0.0119	False		,,,				2504	0.0				p.F4L		Atlas-SNP	.											.	SMPD4	67	.	0			c.C12A						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	7,3753		0,7,1873	8.0	11.0	10.0		12,12,12	0.2	1.0	2	dbSNP_134	10	85,8099		0,85,4007	no	missense,missense,missense	SMPD4	NM_001171083.2,NM_017751.4,NM_017951.4	22,22,22	0,92,5880	TT,TG,GG		1.0386,0.1862,0.7703	benign,benign,benign	4/765,4/838,4/867	130939163	92,11852	1880	4092	5972	SO:0001631	upstream_gene_variant	55627	exon1			GGCGCCGAAAGTC	BC066296	CCDS2157.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000152082	ENSG00000152082			25886	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2B"""	613450	"""family with sequence similarity 128, member B"""	FAM128B		20360068	Standard	NM_025029		Approved	FLJ14346, MOZART2B	uc002tqu.3	Q6NZ67	OTTHUMG00000131625		2.37:g.130939163G>T	Exception_encountered	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_017751	Q96CG4	Missense_Mutation	SNP	ENST00000281871.6	37	CCDS2157.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	N	8.707	0.911139	0.17833	0.001862	0.010386	ENSG00000136699	ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750	.	.	.	3.38	0.175	0.15045	.	.	.	.	.	T	0.21550	0.0519	N	0.19112	0.55	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.05683	-1.0870	7	.	.	.	.	3.9534	0.09379	0.1266:0.0:0.4426:0.4308	.	4;4;4	E7ESA2;B4DM23;B1PBA3	.;.;.	L	4	.	.	F	-	3	2	SMPD4	130655633	0.722000	0.28017	0.965000	0.40720	0.152000	0.21847	-0.022000	0.12480	-0.086000	0.12550	0.455000	0.32223	TTC	G|0.996;T|0.004	0.004	strong		0.677	MZT2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254518.1	NM_025029	
MIA3	375056	hgsc.bcm.edu	37	1	222802376	222802376	+	Missense_Mutation	SNP	A	A	G	rs2936052	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:222802376A>G	ENST00000344922.5	+	4	1839	c.1814A>G	c.(1813-1815)aAa>aGa	p.K605R	MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344441.6_Missense_Mutation_p.K605R|MIA3_ENST00000344507.1_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	605			K -> R (in dbSNP:rs2936052).		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.K605R(2)		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)		AATGGGGCCAAACTGCACACG	0.473													A|||	1472	0.29393	0.3222	0.3977	5008	,	,		20855	0.3085		0.168	False		,,,				2504	0.2965				p.K605R		Atlas-SNP	.											MIA3,NS,carcinoma,0,2	MIA3	167	2	2	Substitution - Missense(2)	prostate(1)|stomach(1)	c.A1814G						PASS	.	A	ARG/LYS	1151,2895		158,835,1030	89.0	93.0	92.0		1814	-1.2	0.0	1	dbSNP_101	92	1464,6890		135,1194,2848	yes	missense	MIA3	NM_198551.2	26	293,2029,3878	GG,GA,AA		17.5245,28.4478,21.0887	benign	605/1908	222802376	2615,9785	2023	4177	6200	SO:0001583	missense	375056	exon4			GGGCCAAACTGCA		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.1814A>G	1.37:g.222802376A>G	ENSP00000340900:p.Lys605Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	593	0.2715201465201465	166	0.33739837398373984	121	0.3342541436464088	178	0.3111888111888112	128	0.16886543535620052	A	8.754	0.922005	0.17982	0.284478	0.175245	ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831	T;T	0.04603	3.59;3.59	4.32	-1.21	0.09524	.	.	.	.	.	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	B;B	0.12630	0.002;0.006	B;B	0.08055	0.003;0.003	T	0.42882	-0.9425	8	0.42905	T	0.14	.	4.7772	0.13185	0.4785:0.2848:0.2367:0.0	rs2936052;rs9441838;rs17163324	605;605	Q5JRA6-2;Q5JRA6	.;MIA3_HUMAN	R	605	ENSP00000340900:K605R;ENSP00000340587:K605R	ENSP00000325973:K605R	K	+	2	0	MIA3	220868999	0.009000	0.17119	0.000000	0.03702	0.017000	0.09413	2.198000	0.42705	-0.458000	0.07023	0.254000	0.18369	AAA	A|0.758;G|0.242	0.242	strong		0.473	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551	
PCDHB6	56130	hgsc.bcm.edu	37	5	140530529	140530529	+	Missense_Mutation	SNP	G	G	A	rs3776096	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140530529G>A	ENST00000231136.1	+	1	691	c.691G>A	c.(691-693)Gtt>Att	p.V231I	PCDHB6_ENST00000543635.1_Missense_Mutation_p.V95I	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	231	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> I (in dbSNP:rs3776096).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCAGATCCAGGTTTTGGACAT	0.587													G|||	1341	0.267772	0.0129	0.3141	5008	,	,		17417	0.5298		0.2416	False		,,,				2504	0.3364				p.V231I		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G691A						PASS	.	G	ILE/VAL	189,4217	119.2+/-156.9	3,183,2017	44.0	48.0	46.0		691	3.1	0.1	5	dbSNP_107	46	1988,6612	343.6+/-325.0	232,1524,2544	yes	missense	PCDHB6	NM_018939.2	29	235,1707,4561	AA,AG,GG		23.1163,4.2896,16.7384	benign	231/795	140530529	2177,10829	2203	4300	6503	SO:0001583	missense	56130	exon1			ATCCAGGTTTTGG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.691G>A	5.37:g.140530529G>A	ENSP00000231136:p.Val231Ile	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	575	0.2632783882783883	7	0.014227642276422764	92	0.2541436464088398	301	0.5262237762237763	175	0.23087071240105542	G	13.78	2.339532	0.41398	0.042896	0.231163	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.61510	0.1;0.1	4.85	3.06	0.35304	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.45698	1.435	0.33384	P	0.424759	B	0.27316	0.175	B	0.33339	0.162	T	0.46775	-0.9167	8	0.44086	T	0.13	.	10.3152	0.43732	0.2167:0.0:0.7833:0.0	rs3776096;rs17844430;rs52836452;rs58825835;rs3776096	231	Q9Y5E3	PCDB6_HUMAN	I	95;231;16	ENSP00000438466:V95I;ENSP00000231136:V231I	ENSP00000231136:V231I	V	+	1	0	PCDHB6	140510713	1.000000	0.71417	0.079000	0.20413	0.849000	0.48306	4.095000	0.57728	0.566000	0.29273	0.561000	0.74099	GTT	G|0.783;A|0.217	0.217	strong		0.587	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
OR10K2	391107	hgsc.bcm.edu	37	1	158390252	158390252	+	Silent	SNP	T	T	G	rs12239443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158390252T>G	ENST00000314902.2	-	1	404	c.405A>C	c.(403-405)ctA>ctC	p.L135L		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	135						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					CATGTCCCATTAGCACTGAGT	0.502													G|||	1453	0.290136	0.2526	0.2709	5008	,	,		21765	0.1687		0.4592	False		,,,				2504	0.3057				p.L135L		Atlas-SNP	.											.	OR10K2	69	.	0			c.A405C						PASS	.	G		1183,3223	710.9+/-407.9	164,855,1184	185.0	176.0	179.0		405	0.8	0.4	1	dbSNP_120	179	3770,4830	616.0+/-396.4	808,2154,1338	no	coding-synonymous	OR10K2	NM_001004476.1		972,3009,2522	GG,GT,TT		43.8372,26.8498,38.0824		135/313	158390252	4953,8053	2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			TCCCATTAGCACT	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.405A>C	1.37:g.158390252T>G		Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	219	106	0.484018	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			T|0.635;G|0.365	0.365	strong		0.502	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
COL6A5	256076	hgsc.bcm.edu	37	3	130116684	130116684	+	Missense_Mutation	SNP	G	G	A	rs79867908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130116684G>A	ENST00000432398.2	+	9	4320	c.3826G>A	c.(3826-3828)Gtc>Atc	p.V1276I	COL6A5_ENST00000265379.6_Missense_Mutation_p.V1276I	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1276	Nonhelical region.|VWFA 7. {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						GCAAGTCAACGTCAGTGGGCC	0.478													G|||	621	0.124002	0.0893	0.1484	5008	,	,		19854	0.1825		0.0577	False		,,,				2504	0.1616				p.V1276I		Atlas-SNP	.											.	COL6A5	205	.	0			c.G3826A						PASS	.	G	ILE/VAL	125,1259		1,123,568	171.0	147.0	154.0		3826	2.5	0.0	3	dbSNP_131	154	204,2978		13,178,1400	yes	missense	COL6A5	NM_153264.5	29	14,301,1968	AA,AG,GG		6.4111,9.0318,7.2054	probably-damaging	1276/2527	130116684	329,4237	692	1591	2283	SO:0001583	missense	256076	exon9			GTCAACGTCAGTG	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.3826G>A	3.37:g.130116684G>A	ENSP00000390895:p.Val1276Ile	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	134	73	0.544776	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		235	0.10760073260073261	47	0.09552845528455285	50	0.13812154696132597	103	0.18006993006993008	35	0.04617414248021108	G	2.328	-0.353967	0.05173	0.090318	0.064111	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.37058	1.22;1.22	5.26	2.48	0.30137	.	.	.	.	.	T	0.00073	0.0002	M	0.61703	1.905	0.80722	P	0.0	B	0.23937	0.094	B	0.23574	0.047	T	0.11842	-1.0571	8	0.23891	T	0.37	.	6.3888	0.21576	0.2273:0.1332:0.6395:0.0	.	1276	A8TX70-2	.	I	1276	ENSP00000390895:V1276I;ENSP00000265379:V1276I	ENSP00000265379:V1276I	V	+	1	0	COL6A5	131599374	0.388000	0.25197	0.003000	0.11579	0.096000	0.18686	0.752000	0.26362	0.222000	0.20900	-0.215000	0.12644	GTC	G|0.891;A|0.109	0.109	strong		0.478	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
GRIN3A	116443	hgsc.bcm.edu	37	9	104432873	104432873	+	Silent	SNP	T	T	G	rs942142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104432873T>G	ENST00000361820.3	-	3	2421	c.1821A>C	c.(1819-1821)gcA>gcC	p.A607A		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	607					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)	CATTTTTCCATGCTCCATACT	0.483													G|||	1339	0.267372	0.1241	0.3617	5008	,	,		21363	0.2183		0.4056	False		,,,				2504	0.3027				p.A607A		Atlas-SNP	.											.	GRIN3A	186	.	0			c.A1821C						PASS	.	G		789,3617	752.7+/-412.3	73,643,1487	94.0	79.0	84.0		1821	1.3	1.0	9	dbSNP_86	84	3550,5050	630.2+/-398.3	726,2098,1476	no	coding-synonymous	GRIN3A	NM_133445.2		799,2741,2963	GG,GT,TT		41.2791,17.9074,33.3615		607/1116	104432873	4339,8667	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			TTTCCATGCTCCA		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.1821A>C	9.37:g.104432873T>G		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			T|0.683;G|0.317	0.317	strong		0.483	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
CEP131	22994	hgsc.bcm.edu	37	17	79182778	79182778	+	Silent	SNP	T	T	C	rs62075318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79182778T>C	ENST00000269392.4	-	3	469	c.222A>G	c.(220-222)agA>agG	p.R74R	AZI1_ENST00000575907.1_Silent_p.R74R|AZI1_ENST00000374782.3_Silent_p.R74R|AZI1_ENST00000450824.2_Silent_p.R74R	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		74					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TGTTGGATCTTCTAAGGTTGT	0.592													T|||	2096	0.41853	0.0227	0.6095	5008	,	,		18179	0.626		0.4443	False		,,,				2504	0.5777				p.R74R		Atlas-SNP	.											AZI1_ENST00000450824,NS,carcinoma,0,4	AZI1	145	4	0			c.A222G						PASS	.	T	,	442,3964	208.8+/-229.8	26,390,1787	79.0	78.0	78.0		222,222	-9.5	0.0	17	dbSNP_129	78	4061,4539	553.6+/-386.3	971,2119,1210	no	coding-synonymous,coding-synonymous	AZI1	NM_001009811.2,NM_014984.2	,	997,2509,2997	CC,CT,TT		47.2209,10.0318,34.6225	,	74/1045,74/1081	79182778	4503,8503	2203	4300	6503	SO:0001819	synonymous_variant	22994	exon3			GGATCTTCTAAGG																												ENST00000269392.4:c.222A>G	17.37:g.79182778T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																				T|0.621;C|0.379	0.379	strong		0.592	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
KIAA1755	85449	hgsc.bcm.edu	37	20	36869516	36869516	+	Missense_Mutation	SNP	C	C	A	rs1205434	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36869516C>A	ENST00000279024.4	-	3	1288	c.1017G>T	c.(1015-1017)aaG>aaT	p.K339N		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	339			K -> N (in dbSNP:rs1205434). {ECO:0000269|PubMed:11214970}.							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)				AGCTTTCTGGCTTTGTGCAAG	0.498													C|||	1291	0.257788	0.1808	0.2262	5008	,	,		19642	0.2679		0.3201	False		,,,				2504	0.3098				p.K339N		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G1017T						PASS	.	C	ASN/LYS	886,3520	338.6+/-305.4	94,698,1411	141.0	157.0	151.0		1017	3.1	0.8	20	dbSNP_87	151	2844,5756	439.9+/-359.4	504,1836,1960	yes	missense	KIAA1755	NM_001029864.1	94	598,2534,3371	AA,AC,CC		33.0698,20.1089,28.6791	possibly-damaging	339/1201	36869516	3730,9276	2203	4300	6503	SO:0001583	missense	85449	exon3			TTCTGGCTTTGTG	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.1017G>T	20.37:g.36869516C>A	ENSP00000279024:p.Lys339Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	592	0.27106227106227104	104	0.21138211382113822	85	0.23480662983425415	149	0.26048951048951047	254	0.33509234828496043	C	15.96	2.985908	0.53934	0.201089	0.330698	ENSG00000149633	ENST00000279024	T	0.63580	-0.05	5.23	3.13	0.36017	.	0.412203	0.20484	N	0.091427	T	0.00012	0.0000	M	0.62723	1.935	0.41623	P	0.011029999999999984	B	0.15473	0.013	B	0.14023	0.01	T	0.15607	-1.0431	9	0.62326	D	0.03	.	7.9862	0.30213	0.0:0.7368:0.167:0.0961	rs1205434;rs52834934;rs61689240;rs1205434	339	Q5JYT7	K1755_HUMAN	N	339	ENSP00000279024:K339N	ENSP00000279024:K339N	K	-	3	2	KIAA1755	36302930	0.003000	0.15002	0.824000	0.32777	0.122000	0.20287	0.488000	0.22371	1.403000	0.46800	0.655000	0.94253	AAG	C|0.710;A|0.290	0.290	strong		0.498	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
VWA5A	4013	hgsc.bcm.edu	37	11	124006972	124006972	+	Missense_Mutation	SNP	G	G	T	rs2276054	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124006972G>T	ENST00000456829.2	+	13	1747	c.1496G>T	c.(1495-1497)aGc>aTc	p.S499I	VWA5A_ENST00000392748.1_Missense_Mutation_p.S499I|VWA5A_ENST00000360334.4_Intron	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	499			S -> I (in dbSNP:rs2276054). {ECO:0000269|PubMed:9417908}.							autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						AGATTAATCAGCTATGCCCAG	0.483													T|||	612	0.122204	0.1952	0.0764	5008	,	,		20012	0.0585		0.1014	False		,,,				2504	0.1431				p.S499I		Atlas-SNP	.											.	VWA5A	102	.	0			c.G1496T						PASS	.	T	ILE/SER,ILE/SER	752,3650	754.8+/-412.5	59,634,1508	99.0	93.0	95.0		1496,1496	5.3	0.2	11	dbSNP_100	95	921,7677	777.0+/-407.7	47,827,3425	yes	missense,missense	VWA5A	NM_001130142.1,NM_014622.4	142,142	106,1461,4933	TT,TG,GG		10.7118,17.0831,12.8692	benign,benign	499/787,499/787	124006972	1673,11327	2201	4299	6500	SO:0001583	missense	4013	exon12			TAATCAGCTATGC	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1496G>T	11.37:g.124006972G>T	ENSP00000407726:p.Ser499Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	242	0.1108058608058608	100	0.2032520325203252	35	0.09668508287292818	27	0.0472027972027972	80	0.10554089709762533	T	1.862	-0.462433	0.04508	0.170831	0.107118	ENSG00000110002	ENST00000456829;ENST00000392748	T;T	0.03272	3.99;3.99	5.35	5.35	0.76521	.	0.700441	0.14059	N	0.344167	T	0.00012	0.0000	N	0.00275	-1.725	0.09310	P	0.999999999355486	B	0.02656	0.0	B	0.01281	0.0	T	0.35919	-0.9769	9	0.06757	T	0.87	-2.4723	10.8285	0.46647	0.0:0.0:0.1591:0.8409	rs2276054;rs52794146;rs2276054	499	O00534	VMA5A_HUMAN	I	499	ENSP00000407726:S499I;ENSP00000376504:S499I	ENSP00000376504:S499I	S	+	2	0	VWA5A	123512182	0.995000	0.38212	0.185000	0.23176	0.416000	0.31233	3.428000	0.52792	0.868000	0.35678	-0.264000	0.10439	AGC	G|0.877;T|0.123	0.123	strong		0.483	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
NLRP2	55655	hgsc.bcm.edu	37	19	55494651	55494651	+	Missense_Mutation	SNP	A	A	G	rs34804158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55494651A>G	ENST00000543010.1	+	6	1728	c.1585A>G	c.(1585-1587)Acc>Gcc	p.T529A	NLRP2_ENST00000537859.1_Missense_Mutation_p.T507A|NLRP2_ENST00000427260.2_Missense_Mutation_p.T506A|NLRP2_ENST00000339757.7_Missense_Mutation_p.T507A|NLRP2_ENST00000391721.4_Missense_Mutation_p.T505A|NLRP2_ENST00000538819.1_Missense_Mutation_p.T505A|NLRP2_ENST00000263437.6_Missense_Mutation_p.T526A|NLRP2_ENST00000448584.2_Missense_Mutation_p.T529A	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	529			T -> A (in dbSNP:rs34804158). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.5}.		positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		GGACGGCCACACCTGGGACAT	0.552													A|||	601	0.120008	0.0946	0.1599	5008	,	,		18263	0.0437		0.2664	False		,,,				2504	0.0542				p.T529A		Atlas-SNP	.											.	NLRP2	161	.	0			c.A1585G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR	495,3911	229.4+/-244.0	37,421,1745	85.0	78.0	80.0		1585,1519,1516,1585	-3.6	0.0	19	dbSNP_126	80	2134,6466	362.1+/-332.6	282,1570,2448	no	missense,missense,missense,missense	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	58,58,58,58	319,1991,4193	GG,GA,AA		24.814,11.2347,20.2137	benign,benign,benign,benign	529/1063,507/1041,506/1040,529/1063	55494651	2629,10377	2203	4300	6503	SO:0001583	missense	55655	exon6			GGCCACACCTGGG	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.1585A>G	19.37:g.55494651A>G	ENSP00000445135:p.Thr529Ala	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	95	60	0.631579	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	355	0.16254578754578755	47	0.09552845528455285	80	0.22099447513812154	27	0.0472027972027972	201	0.26517150395778366	a	0.003	-2.412806	0.00191	0.112347	0.24814	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.73575	-0.71;-0.65;-0.65;-0.71;-0.65;-0.76;-0.65;-0.71	1.79	-3.59	0.04583	.	4.553140	0.00508	N	0.000163	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.003;0.001	T	0.02498	-1.1150	9	0.15066	T	0.55	.	4.0483	0.09783	0.4464:0.1874:0.3662:0.0	rs34804158;rs61729730	507;505;529	Q9NX02-2;Q9NX02-4;Q9NX02	.;.;NALP2_HUMAN	A	529;505;507;529;507;506;505;526	ENSP00000445135:T529A;ENSP00000375601:T505A;ENSP00000344074:T507A;ENSP00000409370:T529A;ENSP00000440601:T507A;ENSP00000402474:T506A;ENSP00000441133:T505A;ENSP00000263437:T526A	ENSP00000263437:T526A	T	+	1	0	NLRP2	60186463	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.048000	0.03517	-1.449000	0.01938	-1.277000	0.01392	ACC	A|0.808;G|0.192	0.192	strong		0.552	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
MACF1	23499	hgsc.bcm.edu	37	1	39549983	39549983	+	Silent	SNP	G	G	A	rs3736890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:39549983G>A	ENST00000372915.3	+	1	180	c.93G>A	c.(91-93)tcG>tcA	p.S31S	MACF1_ENST00000317713.7_Silent_p.S31S|MACF1_ENST00000539005.1_Silent_p.S31S|MACF1_ENST00000361689.2_Silent_p.S31S|MACF1_ENST00000602421.1_Silent_p.S31S|MACF1_ENST00000484793.1_Silent_p.S31S|MACF1_ENST00000545844.1_Silent_p.S31S|MACF1_ENST00000567887.1_Silent_p.S31S			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	31	Actin-binding.				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)			GCGAGCGGTCGGGGAGCCTGT	0.607													A|||	492	0.0982428	0.0522	0.111	5008	,	,		17702	0.0456		0.2058	False		,,,				2504	0.0951				p.S31S		Atlas-SNP	.											.	MACF1	909	.	0			c.G93A						PASS	.	A		331,4075	792.9+/-415.2	18,295,1890	63.0	55.0	58.0		93	-0.0	1.0	1	dbSNP_107	58	1609,6991	740.1+/-407.1	160,1289,2851	no	coding-synonymous	MACF1	NM_012090.4		178,1584,4741	AA,AG,GG		18.7093,7.5125,14.9162		31/5431	39549983	1940,11066	2203	4300	6503	SO:0001819	synonymous_variant	23499	exon3			GCGGTCGGGGAGC	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.93G>A	1.37:g.39549983G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																				G|0.867;A|0.133	0.133	strong		0.607	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
MCUR1	63933	hgsc.bcm.edu	37	6	13801615	13801615	+	Missense_Mutation	SNP	T	T	C	rs3180196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:13801615T>C	ENST00000379170.4	-	4	784	c.646A>G	c.(646-648)Act>Gct	p.T216A		NM_001031713.3	NP_001026883.1	Q96AQ8	MCUR1_HUMAN	mitochondrial calcium uniporter regulator 1	216			T -> A (in dbSNP:rs3180196).		calcium ion import (GO:0070509)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)	integral component of mitochondrial inner membrane (GO:0031305)		p.T216A(1)									TGCTGAAAAGTGATTTCCTAG	0.353													T|||	625	0.1248	0.0068	0.0879	5008	,	,		20323	0.3026		0.1779	False		,,,				2504	0.0726				p.T216A		Atlas-SNP	.											CCDC90A,NS,carcinoma,0,1	CCDC90A	15	1	1	Substitution - Missense(1)	stomach(1)	c.A646G						PASS	.	T	ALA/THR	150,4254	101.2+/-139.8	5,140,2057	90.0	93.0	92.0		646	4.0	1.0	6	dbSNP_105	92	1312,7286	259.1+/-282.5	102,1108,3089	yes	missense	CCDC90A	NM_001031713.3	58	107,1248,5146	CC,CT,TT		15.2594,3.406,11.2444	benign	216/360	13801615	1462,11540	2202	4299	6501	SO:0001583	missense	63933	exon4			GAAAAGTGATTTC	BC016850	CCDS35495.1	6p23	2013-03-13	2013-03-13	2013-03-13	ENSG00000050393	ENSG00000050393			21097	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 79"", ""coiled-coil domain containing 90A"""	C6orf79, CCDC90A		23178883	Standard	NM_001031713		Approved	FLJ20958	uc003nbc.2	Q96AQ8	OTTHUMG00000014279	ENST00000379170.4:c.646A>G	6.37:g.13801615T>C	ENSP00000368468:p.Thr216Ala	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_001031713	Q96JS7|Q9H7F8	Missense_Mutation	SNP	ENST00000379170.4	37	CCDS35495.1	344	0.1575091575091575	6	0.012195121951219513	43	0.11878453038674033	160	0.27972027972027974	135	0.17810026385224276	T	11.88	1.771192	0.31320	0.03406	0.152594	ENSG00000050393	ENST00000379170	T	0.40756	1.02	5.18	3.97	0.46021	.	0.379516	0.32134	N	0.006529	T	0.06872	0.0175	N	0.11560	0.145	0.09310	P	0.9999999999999991	B	0.30068	0.267	B	0.24701	0.055	T	0.22312	-1.0220	9	0.08837	T	0.75	-6.6486	8.5551	0.33476	0.0:0.1617:0.0:0.8383	rs3180196;rs3207308;rs57009899;rs3180196	216	Q96AQ8	CC90A_HUMAN	A	216	ENSP00000368468:T216A	ENSP00000368468:T216A	T	-	1	0	CCDC90A	13909594	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.978000	0.49305	0.874000	0.35823	0.533000	0.62120	ACT	T|0.880;C|0.120	0.120	strong		0.353	MCUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039909.3	NM_022102	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557477	32557477	+	Silent	SNP	G	G	A	rs150644773	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32557477G>A	ENST00000360004.5	-	1	148	c.43C>T	c.(43-45)Ctg>Ttg	p.L15L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	15					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GTCACTGTCAGCGCTGTCATG	0.592										Multiple Myeloma(14;0.17)																											p.L15L		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	0			c.C43T						PASS	.						87.0	106.0	99.0					6																	32557477		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon1			CTGTCAGCGCTGT	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.43C>T	6.37:g.32557477G>A		Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	261	21	0.0804598	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.868;A|0.132	0.132	strong		0.592	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ESYT2	57488	hgsc.bcm.edu	37	7	158590740	158590740	+	Missense_Mutation	SNP	A	A	T	rs13233513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158590740A>T	ENST00000251527.5	-	3	609	c.544T>A	c.(544-546)Tgc>Agc	p.C182S	ESYT2_ENST00000497111.1_5'UTR	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	210					endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						ATAAATTGGCAAATGAAAGGC	0.428													A|||	488	0.0974441	0.1316	0.0519	5008	,	,		16595	0.1101		0.1054	False		,,,				2504	0.0624				p.C182S		Atlas-SNP	.											.	ESYT2	70	.	0			c.T544A						PASS	.		SER/CYS	578,3828	254.3+/-259.9	32,514,1657	71.0	72.0	71.0		544	5.2	1.0	7	dbSNP_121	71	929,7671	204.5+/-247.2	48,833,3419	yes	missense	ESYT2	NM_020728.2	112	80,1347,5076	TT,TA,AA		10.8023,13.1185,11.587	probably-damaging	182/894	158590740	1507,11499	2203	4300	6503	SO:0001583	missense	57488	exon3			ATTGGCAAATGAA	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.544T>A	7.37:g.158590740A>T	ENSP00000251527:p.Cys182Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	221	0.10119047619047619	54	0.10975609756097561	23	0.06353591160220995	63	0.11013986013986014	81	0.10686015831134564	A	15.27	2.783083	0.49891	0.131185	0.108023	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000429474	T;T	0.76709	-1.04;-1.04	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.04048	0.0113	L	0.42245	1.32	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.51601	-0.8685	9	0.15066	T	0.55	-0.7953	14.4687	0.67501	1.0:0.0:0.0:0.0	rs13233513;rs52821058;rs13233513	210;182	A0FGR8-6;A0FGR8-2	.;.	S	182;210;152;6	ENSP00000251527:C182S;ENSP00000275418:C152S	ENSP00000251527:C182S	C	-	1	0	ESYT2	158283501	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.559000	0.90708	2.072000	0.62099	0.454000	0.30748	TGC	A|0.887;T|0.113	0.113	strong		0.428	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
FRG1	2483	hgsc.bcm.edu	37	4	190876283	190876283	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:190876283C>A	ENST00000226798.4	+	5	631	c.409C>A	c.(409-411)Caa>Aaa	p.Q137K	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	137					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ACCAAGAGAACAATGGGAACC	0.353																																					p.Q137K		Atlas-SNP	.											.	FRG1	76	.	0			c.C409A						PASS	.						88.0	87.0	87.0					4																	190876283		2203	4300	6503	SO:0001583	missense	2483	exon5			AGAGAACAATGGG	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.409C>A	4.37:g.190876283C>A	ENSP00000226798:p.Gln137Lys	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	271	20	0.0738007	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	16.72	3.202137	0.58234	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.49139	2.03;0.79	4.04	4.04	0.47022	Actin cross-linking (1);	0.103449	0.64402	D	0.000002	T	0.54902	0.1887	M	0.88377	2.95	0.80722	D	1	B	0.11235	0.004	B	0.15484	0.013	T	0.60078	-0.7333	10	0.42905	T	0.14	-3.5101	14.1451	0.65347	0.0:1.0:0.0:0.0	.	137	Q14331	FRG1_HUMAN	K	137;74	ENSP00000226798:Q137K;ENSP00000435943:Q74K	ENSP00000226798:Q137K	Q	+	1	0	FRG1	191113277	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.292000	0.78731	1.964000	0.57103	0.567000	0.79289	CAA	.	.	none		0.353	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
LUZP4	51213	hgsc.bcm.edu	37	X	114541197	114541197	+	Missense_Mutation	SNP	A	A	G	rs143490659		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:114541197A>G	ENST00000371920.3	+	4	777	c.770A>G	c.(769-771)aAa>aGa	p.K257R	LUZP4_ENST00000451986.2_Missense_Mutation_p.K175R	NM_016383.3	NP_057467.1	Q9P127	LUZP4_HUMAN	leucine zipper protein 4	257						nucleus (GO:0005634)				endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	14						GCCACTCAGAAAGATCTCATA	0.468													N|||	8	0.00211921	0.0023	0.0014	3775	,	,		13181	0.001		0.003	False		,,,				2504	0.0				p.K257R		Atlas-SNP	.											.	LUZP4	51	.	0			c.A770G						PASS	.						127.0	112.0	117.0					X																	114541197		2203	4300	6503	SO:0001583	missense	51213	exon4			CTCAGAAAGATCT	AF124430	CCDS14567.1	Xq24	2009-03-25			ENSG00000102021	ENSG00000102021			24971	protein-coding gene	gene with protein product	"""cancer/testis antigen 28"""	300616				12032826, 11051238	Standard	XM_005268343		Approved	HOM-TES-85, CT-8, CT28	uc004eqa.3	Q9P127	OTTHUMG00000022234	ENST00000371920.3:c.770A>G	X.37:g.114541197A>G	ENSP00000360988:p.Lys257Arg	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	235	40	0.170213	NM_016383	B3KSD6	Missense_Mutation	SNP	ENST00000371920.3	37	CCDS14567.1	.	.	.	.	.	.	.	.	.	.	N	1.327	-0.597898	0.03771	.	.	ENSG00000102021	ENST00000451986;ENST00000371920	T;T	0.78481	-1.18;-1.18	3.83	-0.00659	0.14012	.	.	.	.	.	T	0.49745	0.1575	N	0.03050	-0.425	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30031	-0.9992	9	0.13108	T	0.6	.	8.879	0.35363	0.527:0.0:0.473:0.0	.	175;257	B3KSD6;Q9P127	.;LUZP4_HUMAN	R	175;257	ENSP00000411212:K175R;ENSP00000360988:K257R	ENSP00000360988:K257R	K	+	2	0	LUZP4	114447453	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.608000	0.05641	-0.580000	0.05944	-3.453000	0.00036	AAA	.	.	weak		0.468	LUZP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057972.1	NM_016383	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57080352	57080352	+	Missense_Mutation	SNP	G	G	A	rs12801000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57080352G>A	ENST00000532437.1	-	4	2121	c.1810C>T	c.(1810-1812)Ccc>Tcc	p.P604S	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P604S			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	604	Acidic.|Pro-rich.			P -> S (in Ref. 1; AAM15531). {ECO:0000305}.	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)				GTAGCCAGGGGGAGAGGGGAC	0.637													G|||	101	0.0201677	0.0023	0.0389	5008	,	,		18898	0.002		0.0447	False		,,,				2504	0.0245				p.P604S		Atlas-SNP	.											TNKS1BP1,caecum,carcinoma,+1,1	TNKS1BP1	148	1	0			c.C1810T						PASS	.	G	SER/PRO	46,4356	46.0+/-80.4	0,46,2155	53.0	59.0	57.0		1810	1.9	0.0	11	dbSNP_121	57	399,8193	125.5+/-184.1	8,383,3905	yes	missense	TNKS1BP1	NM_033396.2	74	8,429,6060	AA,AG,GG		4.6439,1.045,3.4247	benign	604/1730	57080352	445,12549	2201	4296	6497	SO:0001583	missense	85456	exon5			CCAGGGGGAGAGG	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.1810C>T	11.37:g.57080352G>A	ENSP00000437271:p.Pro604Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	136	56	0.411765	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	G	12.00	1.805475	0.31961	0.01045	0.046439	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.34275	1.37;1.37	3.89	1.9	0.25705	.	0.255524	0.20503	U	0.091051	T	0.03915	0.0110	L	0.27053	0.805	0.09310	N	1	P	0.36909	0.573	B	0.37780	0.258	T	0.04678	-1.0934	10	0.62326	D	0.03	-0.7947	7.0645	0.25143	0.0:0.1818:0.6143:0.2039	rs12801000	604	Q9C0C2	TB182_HUMAN	S	604	ENSP00000350990:P604S;ENSP00000437271:P604S	ENSP00000350990:P604S	P	-	1	0	TNKS1BP1	56836928	0.002000	0.14202	0.002000	0.10522	0.834000	0.47266	0.618000	0.24373	0.271000	0.22005	0.462000	0.41574	CCC	G|0.968;A|0.032	0.032	strong		0.637	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
EXOC6	54536	hgsc.bcm.edu	37	10	94714427	94714427	+	Missense_Mutation	SNP	C	C	G	rs11187225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:94714427C>G	ENST00000260762.6	+	16	1581	c.1567C>G	c.(1567-1569)Ctg>Gtg	p.L523V	EXOC6_ENST00000371547.4_Missense_Mutation_p.L539V|EXOC6_ENST00000443748.2_Missense_Mutation_p.L420V|EXOC6_ENST00000371552.4_Missense_Mutation_p.L518V	NM_019053.4	NP_061926.3	Q8TAG9	EXOC6_HUMAN	exocyst complex component 6	523			L -> V (in dbSNP:rs11187225).		cellular protein metabolic process (GO:0044267)|erythrocyte differentiation (GO:0030218)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	exocyst (GO:0000145)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	26		Colorectal(252;0.123)				ATCAACAAATCTGCTGCTGAC	0.303													C|||	400	0.0798722	0.0719	0.1686	5008	,	,		15169	0.004		0.1024	False		,,,				2504	0.0828				p.L523V		Atlas-SNP	.											.	EXOC6	147	.	0			c.C1567G						PASS	.	C	VAL/LEU,VAL/LEU	303,4103	163.6+/-195.4	13,277,1913	83.0	87.0	86.0		1552,1567	4.9	1.0	10	dbSNP_120	86	888,7706	199.6+/-243.6	41,806,3450	yes	missense,missense	EXOC6	NM_001013848.2,NM_019053.4	32,32	54,1083,5363	GG,GC,CC		10.3328,6.877,9.1615	benign,benign	518/800,523/805	94714427	1191,11809	2203	4297	6500	SO:0001583	missense	54536	exon16			ACAAATCTGCTGC	BC028395	CCDS7424.2, CCDS31247.1	10q23.33	2013-01-22	2006-11-07	2006-11-07	ENSG00000138190	ENSG00000138190			23196	protein-coding gene	gene with protein product		609672	"""SEC15-like 1 (S. cerevisiae)"""	SEC15L1		8889548	Standard	NM_001013848		Approved	SEC15L, FLJ1125, DKFZp761I2124, MGC33397, Sec15p, EXOC6A	uc001kig.3	Q8TAG9	OTTHUMG00000018767	ENST00000260762.6:c.1567C>G	10.37:g.94714427C>G	ENSP00000260762:p.Leu523Val	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_019053	E9PHI3|Q5VXH8|Q9NZ24	Missense_Mutation	SNP	ENST00000260762.6	37	CCDS7424.2	174	0.07967032967032966	40	0.08130081300813008	57	0.1574585635359116	4	0.006993006993006993	73	0.09630606860158311	C	11.62	1.694277	0.30052	0.06877	0.103328	ENSG00000138190	ENST00000371547;ENST00000371552;ENST00000443748;ENST00000260762	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.82	4.92	0.64577	.	0.070231	0.56097	D	0.000023	T	0.00178	0.0005	M	0.68593	2.085	0.09310	P	0.999999585624	B;P;B;B;B;B	0.37548	0.212;0.599;0.201;0.368;0.201;0.201	B;P;B;B;B;B	0.48189	0.058;0.57;0.129;0.271;0.088;0.088	T	0.17992	-1.0351	9	0.34782	T	0.22	-6.9176	6.9157	0.24359	0.0:0.7117:0.0:0.2883	rs11187225;rs52826641;rs11187225	539;420;515;476;523;518	F2Z2Q3;E7EW84;B4DEZ1;B2RDH5;Q8TAG9;E9PHI3	.;.;.;.;EXOC6_HUMAN;.	V	539;518;420;523	ENSP00000360602:L539V;ENSP00000360607:L518V;ENSP00000396206:L420V;ENSP00000260762:L523V	ENSP00000260762:L523V	L	+	1	2	EXOC6	94704407	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.627000	0.54252	1.478000	0.48253	0.655000	0.94253	CTG	C|0.912;G|0.088	0.088	strong		0.303	EXOC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049410.2	NM_019053	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204199614	204199614	+	Missense_Mutation	SNP	C	C	T	rs10900562	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204199614C>T	ENST00000272203.3	-	18	2826	c.2510G>A	c.(2509-2511)aGg>aAg	p.R837K	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.R857K	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	837			R -> K (in dbSNP:rs10900562). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			CCGCTTCTCCCTCATGGAGCC	0.652													T|||	2557	0.510583	0.6914	0.5375	5008	,	,		13874	0.4802		0.4334	False		,,,				2504	0.3579				p.R837K		Atlas-SNP	.											PLEKHA6,colon,carcinoma,0,1	PLEKHA6	115	1	0			c.G2510A						PASS	.	T	LYS/ARG	2895,1507		980,935,286	22.0	21.0	22.0		2510	2.9	1.0	1	dbSNP_120	22	3909,4671		909,2091,1290	yes	missense	PLEKHA6	NM_014935.2	26	1889,3026,1576	TT,TC,CC		45.5594,34.2344,47.589	benign	837/1049	204199614	6804,6178	2201	4290	6491	SO:0001583	missense	22874	exon18			TTCTCCCTCATGG	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2510G>A	1.37:g.204199614C>T	ENSP00000272203:p.Arg837Lys	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	1131	0.5178571428571429	332	0.6747967479674797	193	0.5331491712707183	277	0.48426573426573427	329	0.4340369393139842	T	9.062	0.994763	0.19043	0.657656	0.455594	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.22743	1.94;2.4	5.24	2.91	0.33838	.	0.157126	0.56097	N	0.000034	T	0.00012	0.0000	N	0.10972	0.075	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.30707	-0.9969	9	0.15499	T	0.54	-21.9669	9.0092	0.36131	0.0:0.216:0.0:0.7839	rs10900562;rs58953574;rs10900562	837	Q9Y2H5	PKHA6_HUMAN	K	837;857	ENSP00000272203:R837K;ENSP00000402046:R857K	ENSP00000272203:R837K	R	-	2	0	PLEKHA6	202466237	1.000000	0.71417	0.999000	0.59377	0.790000	0.44656	3.200000	0.51051	0.026000	0.15269	-1.390000	0.01156	AGG	C|0.466;T|0.534	0.534	strong		0.652	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
COL18A1	80781	hgsc.bcm.edu	37	21	46899872	46899872	+	Silent	SNP	C	C	A	rs1131102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46899872C>A	ENST00000359759.4	+	9	2571	c.2550C>A	c.(2548-2550)ggC>ggA	p.G850G	COL18A1_ENST00000400337.2_Silent_p.G435G|COL18A1_ENST00000355480.5_Silent_p.G615G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	850	Triple-helical region 2 (COL2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GTCCCAAGGGCGACAAGGTGA	0.662													C|||	703	0.140375	0.2247	0.0706	5008	,	,		17006	0.1081		0.0696	False		,,,				2504	0.182				p.G615G		Atlas-SNP	.											COL18A1_ENST00000359759,NS,carcinoma,+1,2	COL18A1	129	2	0			c.C1845A						PASS	.	C	,	868,3160		100,668,1246	68.0	83.0	78.0		1845,1305	-8.0	0.7	21	dbSNP_86	78	544,7794		18,508,3643	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	118,1176,4889	AA,AC,CC		6.5243,21.5492,11.4184	,	615/1520,435/1340	46899872	1412,10954	2014	4169	6183	SO:0001819	synonymous_variant	80781	exon9			CAAGGGCGACAAG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2550C>A	21.37:g.46899872C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	38	24	0.631579	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.896;A|0.104	0.104	strong		0.662	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
CYP4F2	8529	hgsc.bcm.edu	37	19	15990431	15990431	+	Missense_Mutation	SNP	C	C	T	rs2108622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15990431C>T	ENST00000221700.6	-	11	1392	c.1297G>A	c.(1297-1299)Gtg>Atg	p.V433M		NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TCCGGCCACACAGCTGGGTTG	0.577													.|||	1186	0.236821	0.0825	0.2378	5008	,	,		18423	0.2143		0.2903	False		,,,				2504	0.4131				p.V433M		Atlas-SNP	.											.	CYP4F2	97	.	0			c.G1297A	GRCh37	CM074767	CYP4F2	M	rs2108622	PASS	.	C	MET/VAL	428,3978	208.5+/-229.5	23,382,1798	110.0	118.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1297	1.7	0.9	19	dbSNP_96	115	2504,6096	410.8+/-350.3	379,1746,2175	yes	missense	CYP4F2	NM_001082.3	21	402,2128,3973	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	29.1163,9.714,22.5434	probably-damaging	433/521	15990431	2932,10074	2203	4300	6503	SO:0001583	missense	8529	exon11			GCCACACAGCTGG	U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.1297G>A	19.37:g.15990431C>T	ENSP00000221700:p.Val433Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_001082		Missense_Mutation	SNP	ENST00000221700.6	37	CCDS12336.1	470	0.21520146520146521	42	0.08536585365853659	103	0.2845303867403315	118	0.2062937062937063	207	0.27308707124010556	c	14.01	2.407803	0.42715	0.09714	0.291163	ENSG00000186115	ENST00000221700;ENST00000392846	T	0.70749	-0.51	2.78	1.72	0.24424	.	0.000000	0.56097	U	0.000026	T	0.00039	0.0001	M	0.90019	3.08	0.09310	P	1.0	D	0.89917	1.0	D	0.73380	0.98	T	0.02156	-1.1204	9	0.72032	D	0.01	.	7.54	0.27733	0.0:0.8612:0.0:0.1388	rs2108622;rs52819608;rs57319528;rs2108622	433	P78329	CP4F2_HUMAN	M	433;284	ENSP00000221700:V433M	ENSP00000221700:V433M	V	-	1	0	CYP4F2	15851431	0.942000	0.31987	0.926000	0.36857	0.526000	0.34562	1.995000	0.40767	0.476000	0.27440	0.491000	0.48974	GTG	C|0.779;T|0.221	0.221	strong		0.577	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460372.3	NM_001082	
HEPACAM	220296	hgsc.bcm.edu	37	11	124794688	124794688	+	Silent	SNP	C	C	T	rs112686308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124794688C>T	ENST00000298251.4	-	2	768	c.363G>A	c.(361-363)gaG>gaA	p.E121E		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		AGATCTCGACCTCATAGGTGC	0.567													C|||	90	0.0179712	0.0008	0.0101	5008	,	,		21918	0.001		0.0348	False		,,,				2504	0.047				p.E121E		Atlas-SNP	.											.	HEPACAM	64	.	0			c.G363A						PASS	.	C		39,4363	44.6+/-78.6	0,39,2162	180.0	168.0	172.0		363	1.8	1.0	11	dbSNP_132	172	349,8249	118.3+/-177.8	10,329,3960	no	coding-synonymous	HEPACAM	NM_152722.4		10,368,6122	TT,TC,CC		4.0591,0.886,2.9846		121/417	124794688	388,12612	2201	4299	6500	SO:0001819	synonymous_variant	220296	exon2			CTCGACCTCATAG	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26361	protein-coding gene	gene with protein product	"""glial cell adhesion molecule"""	611642	"""hepatocyte cell adhesion molecule"""			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.363G>A	11.37:g.124794688C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	123	72	0.585366	NM_152722		Silent	SNP	ENST00000298251.4	37	CCDS8456.1																																																																																			C|0.973;T|0.027	0.027	strong		0.567	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722	
AP4B1	10717	hgsc.bcm.edu	37	1	114438951	114438951	+	Missense_Mutation	SNP	A	A	G	rs1217401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:114438951A>G	ENST00000369569.1	-	8	1719	c.1439T>C	c.(1438-1440)tTg>tCg	p.L480S	AP4B1_ENST00000369567.1_Missense_Mutation_p.L312S|AP4B1-AS1_ENST00000419536.1_RNA|AP4B1_ENST00000256658.4_Missense_Mutation_p.L480S|AP4B1_ENST00000462591.1_5'UTR	NM_001253852.1	NP_001240781.1	Q9Y6B7	AP4B1_HUMAN	adaptor-related protein complex 4, beta 1 subunit	480			L -> S (in dbSNP:rs1217401). {ECO:0000269|PubMed:10066790, ECO:0000269|Ref.3}.		intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|trans-Golgi network (GO:0005802)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(3)|prostate(3)	25	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.1e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AAGGCGCAGCAAAGCAGTGAG	0.453													A|||	1888	0.376997	0.8003	0.2536	5008	,	,		20016	0.0794		0.2694	False		,,,				2504	0.3098				p.L480S		Atlas-SNP	.											.	AP4B1	72	.	0			c.T1439C						PASS	.	A	SER/LEU	3017,1389	689.6+/-405.1	1046,925,232	158.0	154.0	155.0		1439	6.0	0.9	1	dbSNP_87	155	2679,5921	430.6+/-356.6	424,1831,2045	yes	missense	AP4B1	NM_006594.2	145	1470,2756,2277	GG,GA,AA		31.1512,31.5252,43.7952	possibly-damaging	480/740	114438951	5696,7310	2203	4300	6503	SO:0001583	missense	10717	exon9			CGCAGCAAAGCAG	AF092094	CCDS865.1	1p13.2	2012-03-30			ENSG00000134262	ENSG00000134262			572	protein-coding gene	gene with protein product	"""beta 4 subunit of AP-4"""	607245	"""spastic paraplegia 47"""	SPG47		10066790	Standard	NM_006594		Approved	BETA-4	uc001eeb.3	Q9Y6B7	OTTHUMG00000011943	ENST00000369569.1:c.1439T>C	1.37:g.114438951A>G	ENSP00000358582:p.Leu480Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_006594	B7Z4X3|Q59EJ4|Q96CL6	Missense_Mutation	SNP	ENST00000369569.1	37	CCDS865.1	756	0.34615384615384615	390	0.7926829268292683	103	0.2845303867403315	54	0.0944055944055944	209	0.2757255936675462	A	15.36	2.810246	0.50421	0.684748	0.311512	ENSG00000134262	ENST00000369567;ENST00000369569;ENST00000256658	T;T;T	0.24538	1.85;1.85;1.85	6.04	6.04	0.98038	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.389021	0.27996	N	0.017016	T	0.09598	0.0236	N	0.10809	0.05	0.09310	P	1.0	B;B;B;B	0.22541	0.071;0.008;0.033;0.001	B;B;B;B	0.30105	0.111;0.02;0.111;0.007	T	0.13442	-1.0509	9	0.52906	T	0.07	-2.4422	16.5885	0.84745	1.0:0.0:0.0:0.0	rs1217401;rs3170575;rs58628725;rs1217401	480;312;480;381	B2RBF6;B1ALD0;Q9Y6B7;B4DTG3	.;.;AP4B1_HUMAN;.	S	312;480;480	ENSP00000358580:L312S;ENSP00000358582:L480S;ENSP00000256658:L480S	ENSP00000256658:L480S	L	-	2	0	AP4B1	114240474	1.000000	0.71417	0.868000	0.34077	0.986000	0.74619	6.230000	0.72301	2.317000	0.78254	0.460000	0.39030	TTG	A|0.589;G|0.411	0.411	strong		0.453	AP4B1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033037.1	NM_006594	
NKAPL	222698	hgsc.bcm.edu	37	6	28228342	28228342	+	Missense_Mutation	SNP	A	A	G	rs1679709	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:28228342A>G	ENST00000343684.3	+	1	1245	c.1193A>G	c.(1192-1194)gAg>gGg	p.E398G	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	398			E -> G (in dbSNP:rs1679709). {ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						AAGACAAAAGAGAAAGATGAC	0.373													G|||	4257	0.85004	0.7458	0.8732	5008	,	,		18349	0.872		0.8837	False		,,,				2504	0.9172				p.E398G		Atlas-SNP	.											.	NKAPL	72	.	0			c.A1193G						PASS	.	G	GLY/GLU	3268,1138	401.9+/-332.2	1209,850,144	64.0	61.0	62.0		1193	4.6	1.0	6	dbSNP_89	62	7393,1207	243.1+/-272.8	3182,1029,89	yes	missense	NKAPL	NM_001007531.1	98	4391,1879,233	GG,GA,AA		14.0349,25.8284,18.0301	benign	398/403	28228342	10661,2345	2203	4300	6503	SO:0001583	missense	222698	exon1			CAAAAGAGAAAGA	BC038240	CCDS34353.1	6p21.33	2008-02-05	2007-08-16	2007-08-16	ENSG00000189134	ENSG00000189134			21584	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 194"""	C6orf194			Standard	NM_001007531		Approved	bA424I5.1	uc003nkt.4	Q5M9Q1	OTTHUMG00000014517	ENST00000343684.3:c.1193A>G	6.37:g.28228342A>G	ENSP00000345716:p.Glu398Gly	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	1860	0.8516483516483516	381	0.774390243902439	317	0.8756906077348067	493	0.8618881118881119	669	0.8825857519788918	G	6.557	0.471002	0.12461	0.741716	0.859651	ENSG00000189134	ENST00000343684	T	0.13420	2.59	4.63	4.63	0.57726	.	0.000000	0.85682	N	0.000000	T	0.01320	0.0043	N	0.02539	-0.55	0.51233	P	8.399999999997299E-5	B	0.09022	0.002	B	0.01281	0.0	T	0.43360	-0.9396	9	0.02654	T	1	-8.7747	11.0692	0.47993	0.091:0.0:0.909:0.0	rs1679709;rs52790887;rs61104738;rs1679709	398	Q5M9Q1	NKAPL_HUMAN	G	398	ENSP00000345716:E398G	ENSP00000345716:E398G	E	+	2	0	NKAPL	28336321	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.244000	0.78228	1.322000	0.45245	-0.119000	0.15052	GAG	A|0.162;G|0.838	0.838	strong		0.373	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1		
HABP2	3026	hgsc.bcm.edu	37	10	115350597	115350597	+	IGR	SNP	G	G	A	rs1885434	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115350597G>A	ENST00000351270.3	+	0	3009				NRAP_ENST00000369358.4_Missense_Mutation_p.R1574C|NRAP_ENST00000369360.3_Missense_Mutation_p.R1539C|NRAP_ENST00000359988.3_Missense_Mutation_p.R1566C|NRAP_ENST00000360478.3_Missense_Mutation_p.R1531C	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2						cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	TCGACACTGCGGTACCCGATC	0.567													G|||	1803	0.360024	0.4221	0.4683	5008	,	,		20268	0.2996		0.3042	False		,,,				2504	0.319				p.R1566C		Atlas-SNP	.											.	NRAP	208	.	0			c.C4696T						PASS	.	G	CYS/ARG,CYS/ARG	1797,2609	528.9+/-372.5	358,1081,764	100.0	89.0	92.0		4591,4696	3.8	1.0	10	dbSNP_92	92	2996,5604	464.3+/-366.2	502,1992,1806	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	180,180	860,3073,2570	AA,AG,GG		34.8372,40.7853,36.8522	probably-damaging,probably-damaging	1531/1696,1566/1731	115350597	4793,8213	2203	4300	6503	SO:0001628	intergenic_variant	4892	exon40			CACTGCGGTACCC		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073		10.37:g.115350597G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	142	80	0.56338	NM_001261463	A8K467|B7Z8U5|F5H5M6|O00663	Missense_Mutation	SNP	ENST00000351270.3	37	CCDS7577.1	771	0.35302197802197804	205	0.4166666666666667	150	0.4143646408839779	187	0.3269230769230769	229	0.3021108179419525	G	14.40	2.522821	0.44866	0.407853	0.348372	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478;ENST00000369350	T;T;T;T	0.18338	2.37;2.4;2.32;2.22	5.69	3.83	0.44106	.	0.248699	0.43747	N	0.000538	T	0.00012	0.0000	M	0.67625	2.065	0.22127	P	0.999347263	B;B;B;B	0.19331	0.035;0.014;0.024;0.014	B;B;B;B	0.17722	0.006;0.008;0.019;0.008	T	0.40478	-0.9561	9	0.52906	T	0.07	.	11.8775	0.52556	0.1974:0.0:0.8026:0.0	rs1885434;rs52826513;rs56506201;rs58665055;rs1885434	688;1566;1531;1566	B1ANW7;A0AVL2;Q86VF7-4;Q86VF7	.;.;.;NRAP_HUMAN	C	1574;1539;1566;1531;688	ENSP00000358365:R1574C;ENSP00000358367:R1539C;ENSP00000353078:R1566C;ENSP00000353666:R1531C	ENSP00000353078:R1566C	R	-	1	0	NRAP	115340587	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	3.514000	0.53422	0.756000	0.33013	0.561000	0.74099	CGC	G|0.640;A|0.360	0.360	strong		0.567	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
ADAM18	8749	hgsc.bcm.edu	37	8	39468070	39468070	+	Missense_Mutation	SNP	A	A	C	rs139114737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39468070A>C	ENST00000265707.5	+	6	412	c.367A>C	c.(367-369)Atc>Ctc	p.I123L	ADAM18_ENST00000520772.1_Missense_Mutation_p.I123L|ADAM18_ENST00000379866.1_Missense_Mutation_p.I123L|ADAM18_ENST00000541111.1_Intron	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	123					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			GTTTGAAAATATCAGTTATGG	0.289													a|||	22	0.00439297	0.0106	0.0072	5008	,	,		16258	0.0		0.003	False		,,,				2504	0.0				p.I123L		Atlas-SNP	.											.	ADAM18	169	.	0			c.A367C						PASS	.	G	LEU/ILE,LEU/ILE	31,4357	33.5+/-64.1	0,31,2163	37.0	38.0	38.0		367,367	-3.8	0.5	8	dbSNP_134	38	11,8575	8.4+/-32.0	0,11,4282	yes	missense,missense	ADAM18	NM_001190956.1,NM_014237.2	5,5	0,42,6445	CC,CA,AA		0.1281,0.7065,0.3237	benign,benign	123/183,123/740	39468070	42,12932	2194	4293	6487	SO:0001583	missense	8749	exon6			GAAAATATCAGTT	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.367A>C	8.37:g.39468070A>C	ENSP00000265707:p.Ile123Leu	Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	225	93	0.413333	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	10	0.004578754578754579	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	a	8.502	0.864400	0.17250	0.007065	0.001281	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.05513	3.43;3.43;3.43	5.25	-3.75	0.04372	Peptidase M12B, propeptide (1);	0.750320	0.11876	N	0.521007	T	0.04272	0.0118	L	0.40543	1.245	0.29468	N	0.857287	B;B;B	0.26845	0.133;0.161;0.056	B;B;B	0.39152	0.192;0.292;0.042	T	0.45818	-0.9235	10	0.22109	T	0.4	.	6.7801	0.23640	0.5203:0.0:0.3672:0.1125	.	123;123;123	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	L	123;123;123;79	ENSP00000265707:I123L;ENSP00000369195:I123L;ENSP00000429908:I123L	ENSP00000265707:I123L	I	+	1	0	ADAM18	39587227	0.275000	0.24201	0.488000	0.27440	0.089000	0.18198	-0.094000	0.11094	-0.734000	0.04843	-2.260000	0.00280	ATC	A|0.997;C|0.003	0.003	strong		0.289	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
THNSL1	79896	hgsc.bcm.edu	37	10	25312689	25312689	+	Silent	SNP	A	A	G	rs4748997	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:25312689A>G	ENST00000524413.1	+	3	884	c.537A>G	c.(535-537)ggA>ggG	p.G179G	THNSL1_ENST00000376356.4_Silent_p.G179G			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	179						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(5)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28					L-Threonine(DB00156)	AGAATTCTGGAACATCTATGA	0.358													A|||	1542	0.307907	0.0749	0.4308	5008	,	,		19714	0.4851		0.2714	False		,,,				2504	0.3906				p.G179G		Atlas-SNP	.											.	THNSL1	70	.	0			c.A537G						PASS	.	A		410,3996	190.2+/-216.2	26,358,1819	58.0	61.0	60.0		537	0.7	0.6	10	dbSNP_111	60	2451,6149	396.6+/-345.4	334,1783,2183	no	coding-synonymous	THNSL1	NM_024838.4		360,2141,4002	GG,GA,AA		28.5,9.3055,21.9975		179/744	25312689	2861,10145	2203	4300	6503	SO:0001819	synonymous_variant	79896	exon3			TTCTGGAACATCT	AK025655	CCDS7147.1	10p12.31	2008-02-05	2007-06-20		ENSG00000185875	ENSG00000185875			26160	protein-coding gene	gene with protein product		611260	"""threonine synthase-like 1 (bacterial)"""			12477932	Standard	NM_024838		Approved	FLJ22002	uc001isi.4	Q8IYQ7	OTTHUMG00000017828	ENST00000524413.1:c.537A>G	10.37:g.25312689A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_024838	B3KWL1|D3DRV3|Q5VV21	Silent	SNP	ENST00000524413.1	37	CCDS7147.1																																																																																			A|0.746;G|0.254	0.254	strong		0.358	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
EXOC3L1	283849	hgsc.bcm.edu	37	16	67219107	67219107	+	Missense_Mutation	SNP	G	G	C	rs9939768	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67219107G>C	ENST00000314586.6	-	11	1921	c.1681C>G	c.(1681-1683)Caa>Gaa	p.Q561E	KIAA0895L_ENST00000561621.1_5'Flank|KIAA0895L_ENST00000563902.1_5'Flank|KIAA0895L_ENST00000563831.2_5'Flank|EXOC3L1_ENST00000562887.1_5'Flank|KIAA0895L_ENST00000290881.7_5'Flank	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	561			Q -> E (in dbSNP:rs9939768).		exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CACACACTTTGCAGGAGCTCA	0.642													C|||	1001	0.19988	0.5113	0.0735	5008	,	,		17024	0.0248		0.0686	False		,,,				2504	0.184				p.Q561E		Atlas-SNP	.											.	EXOC3L1	52	.	0			c.C1681G						PASS	.	C	GLU/GLN	1842,2554	608.3+/-391.1	395,1052,751	45.0	56.0	52.0		1681	3.7	0.7	16	dbSNP_119	52	595,8005	777.5+/-407.7	28,539,3733	yes	missense	EXOC3L1	NM_178516.3	29	423,1591,4484	CC,CG,GG		6.9186,41.9017,18.7519	benign	561/747	67219107	2437,10559	2198	4300	6498	SO:0001583	missense	283849	exon11			CACTTTGCAGGAG	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.1681C>G	16.37:g.67219107G>C	ENSP00000325674:p.Gln561Glu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	326	0.14926739926739926	233	0.4735772357723577	33	0.09116022099447514	12	0.02097902097902098	48	0.0633245382585752	C	5.850	0.340979	0.11069	0.419017	0.069186	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.05649	3.41;3.41	5.6	3.66	0.41972	.	0.572106	0.19996	N	0.101441	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.42258	-0.9462	9	0.06236	T	0.91	-7.604	6.6796	0.23113	0.0:0.6955:0.1467:0.1578	rs9939768;rs52823978;rs9939768	458;458;561	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	E	561;458;463	ENSP00000325674:Q561E;ENSP00000439910:Q458E	ENSP00000325008:Q463E	Q	-	1	0	EXOC3L1	65776608	0.110000	0.22057	0.717000	0.30585	0.064000	0.16182	0.707000	0.25704	0.334000	0.23590	-0.215000	0.12644	CAA	G|0.838;C|0.162	0.162	strong		0.642	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
RUFY1	80230	hgsc.bcm.edu	37	5	179036433	179036433	+	Silent	SNP	G	G	A	rs17355294	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179036433G>A	ENST00000319449.4	+	18	2052	c.2040G>A	c.(2038-2040)ctG>ctA	p.L680L	RUFY1_ENST00000377001.2_3'UTR|RUFY1_ENST00000508797.1_3'UTR|RUFY1_ENST00000393438.2_Silent_p.L572L|RUFY1_ENST00000437570.2_Silent_p.L572L	NM_025158.4	NP_079434.3	Q96T51	RUFY1_HUMAN	RUN and FYVE domain containing 1	680					endocytosis (GO:0006897)|regulation of endocytosis (GO:0030100)	cytoplasm (GO:0005737)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	lipid binding (GO:0008289)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;0.00018)|all_epithelial(37;8.37e-05)|Renal(175;0.000159)|Lung NSC(126;0.00108)|all_lung(126;0.00195)	all_cancers(40;0.0322)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCAACGAGCTGGCCCTGCCCT	0.647										HNSCC(44;0.11)			G|||	1361	0.271765	0.2912	0.3084	5008	,	,		15099	0.1706		0.4284	False		,,,				2504	0.1626				p.L680L		Atlas-SNP	.											.	RUFY1	101	.	0			c.G2040A						PASS	.	G	,,	1450,2956		244,962,997	79.0	61.0	67.0		1716,1716,2040	1.2	1.0	5	dbSNP_123	67	3769,4831		852,2065,1383	no	coding-synonymous,coding-synonymous,coding-synonymous	RUFY1	NM_001040451.1,NM_001040452.1,NM_025158.3	,,	1096,3027,2380	AA,AG,GG		43.8256,32.9097,40.1276	,,	572/601,572/601,680/709	179036433	5219,7787	2203	4300	6503	SO:0001819	synonymous_variant	80230	exon18			CGAGCTGGCCCTG	AF361055	CCDS4445.2, CCDS34312.1	5q35.3	2008-02-05			ENSG00000176783	ENSG00000176783		"""Zinc fingers, FYVE domain containing"""	19760	protein-coding gene	gene with protein product		610327				11877430	Standard	NM_001040451		Approved	FLJ22251, ZFYVE12, RABIP4	uc003mka.2	Q96T51	OTTHUMG00000130913	ENST00000319449.4:c.2040G>A	5.37:g.179036433G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	28	0.538462	NM_025158	Q59FF3|Q71S93|Q9H6I3	Silent	SNP	ENST00000319449.4	37	CCDS4445.2																																																																																			G|0.620;A|0.380	0.380	strong		0.647	RUFY1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253505.2	NM_001040451	
PPAP2C	8612	hgsc.bcm.edu	37	19	282753	282753	+	Splice_Site	SNP	G	G	A	rs1138439	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:282753G>A	ENST00000269812.3	-	4	588	c.539C>T	c.(538-540)gCg>gTg	p.A180V	PPAP2C_ENST00000434325.2_Splice_Site_p.A124V|PPAP2C_ENST00000327790.3_Splice_Site_p.A201V	NM_003712.2|NM_177526.1	NP_003703.1|NP_803545.1	O43688	LPP2_HUMAN	phosphatidic acid phosphatase type 2C	180			A -> V (in dbSNP:rs1138439).		dephosphorylation (GO:0016311)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidate phosphatase activity (GO:0008195)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(1)|skin(1)	5		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGACTCACCGCCAAGAACAC	0.537													.|||	1826	0.364617	0.4682	0.4323	5008	,	,		16201	0.1181		0.4602	False		,,,				2504	0.3323				p.A201V		Atlas-SNP	.											PPAP2C_ENST00000269812,caecum,carcinoma,0,5	PPAP2C	38	5	0			c.C602T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	2049,2357		479,1091,633	121.0	103.0	109.0		539,371,602	-0.1	0.4	19	dbSNP_86	109	3724,4876		824,2076,1400	yes	missense-near-splice,missense-near-splice,missense-near-splice	PPAP2C	NM_003712.2,NM_177526.1,NM_177543.1	64,64,64	1303,3167,2033	AA,AG,GG		43.3023,46.5048,44.3872	benign,benign,benign	180/289,124/233,201/310	282753	5773,7233	2203	4300	6503	SO:0001630	splice_region_variant	8612	exon4			CTCACCGCCAAGA	AF035959	CCDS12023.1, CCDS12024.1, CCDS45889.1	19p13	2009-05-27				ENSG00000141934	3.1.3.4		9230	protein-coding gene	gene with protein product		607126				9570154, 9607309	Standard	NM_177543		Approved	PAP-2c, LPP2	uc002loh.3	O43688		ENST00000269812.3:c.540+1C>T	19.37:g.282753G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_177543	A6NLV0|E9PAY8	Missense_Mutation	SNP	ENST00000269812.3	37	CCDS12023.1	815	0.3731684981684982	210	0.4268292682926829	153	0.42265193370165743	88	0.15384615384615385	364	0.48021108179419525	.	6.371	0.436500	0.12104	0.465048	0.433023	ENSG00000141934	ENST00000269812;ENST00000327790;ENST00000434325	T;T;T	0.75367	-0.93;-0.93;-0.93	4.73	-0.069	0.13753	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.209140	0.39687	N	0.001299	T	0.00012	0.0000	L	0.42581	1.335	0.22479	P	0.999061563	B;B	0.21309	0.032;0.054	B;B	0.24006	0.05;0.033	T	0.43147	-0.9409	9	0.33141	T	0.24	-21.5272	8.9489	0.35776	0.3281:0.0:0.6719:0.0	rs1138439;rs1802137;rs3202329;rs10407115;rs52811693;rs57859690;rs10407115	180;201	O43688;O43688-2	LPP2_HUMAN;.	V	180;201;124	ENSP00000269812:A180V;ENSP00000329697:A201V;ENSP00000388565:A124V	ENSP00000269812:A180V	A	-	2	0	PPAP2C	233753	1.000000	0.71417	0.424000	0.26647	0.000000	0.00434	6.075000	0.71261	-0.160000	0.11002	-1.008000	0.02478	GCG	T|0.071;G|0.466;C|0.124;A|0.339	0.339	strong		0.537	PPAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451777.2		Missense_Mutation
PPP6R1	22870	hgsc.bcm.edu	37	19	55752662	55752662	+	Missense_Mutation	SNP	T	T	C	rs200841391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55752662T>C	ENST00000412770.2	-	9	1672	c.1106A>G	c.(1105-1107)aAt>aGt	p.N369S	PPP6R1_ENST00000587283.1_Missense_Mutation_p.N369S	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	369	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						GGCTGCATCATTGGCGCTCAG	0.687													T|||	6	0.00119808	0.0015	0.0029	5008	,	,		11133	0.0		0.002	False		,,,				2504	0.0				p.N369S		Atlas-SNP	.											.	PPP6R1	63	.	0			c.A1106G						PASS	.	T	SER/ASN	2,4224		0,2,2111	25.0	30.0	29.0		1106	2.8	0.8	19		29	9,8481		0,9,4236	yes	missense	PPP6R1	NM_014931.3	46	0,11,6347	CC,CT,TT		0.106,0.0473,0.0865	benign	369/882	55752662	11,12705	2113	4245	6358	SO:0001583	missense	22870	exon9			GCATCATTGGCGC	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.1106A>G	19.37:g.55752662T>C	ENSP00000414202:p.Asn369Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	128	61	0.476562	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	17.04	3.286210	0.59867	4.73E-4	0.00106	ENSG00000105063	ENST00000412770	T	0.66815	-0.23	4.98	2.81	0.32909	.	0.000000	0.64402	D	0.000017	T	0.63628	0.2527	M	0.62723	1.935	0.34351	D	0.689847	P	0.45986	0.87	P	0.48334	0.574	T	0.65529	-0.6146	10	0.19590	T	0.45	-21.6412	6.5383	0.22367	0.1379:0.0786:0.0:0.7835	.	369	Q9UPN7	PP6R1_HUMAN	S	369	ENSP00000414202:N369S	ENSP00000414202:N369S	N	-	2	0	PPP6R1	60444474	0.533000	0.26354	0.751000	0.31187	0.782000	0.44232	0.629000	0.24538	0.296000	0.22592	0.379000	0.24179	AAT	T|0.998;C|0.002	0.002	strong		0.687	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
ESYT2	57488	hgsc.bcm.edu	37	7	158528269	158528269	+	Silent	SNP	C	C	G	rs35914882	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158528269C>G	ENST00000251527.5	-	20	2576	c.2511G>C	c.(2509-2511)gtG>gtC	p.V837V	ESYT2_ENST00000435514.2_Silent_p.V272V	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	865	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Required for phosphatidylinositol 4,5- bisphosphate-dependent location at the cell membrane.				endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)	p.V837V(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						TTCTCCTCTGCACTTCTGGTA	0.443													C|||	449	0.0896565	0.1256	0.0591	5008	,	,		19516	0.0427		0.1252	False		,,,				2504	0.0746				p.V837V		Atlas-SNP	.											ESYT2,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ESYT2	70	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G2511C						PASS	.			511,3895	233.6+/-246.7	24,463,1716	139.0	143.0	141.0		2511	1.7	1.0	7	dbSNP_126	141	1086,7514	226.4+/-262.1	63,960,3277	no	coding-synonymous	ESYT2	NM_020728.2		87,1423,4993	GG,GC,CC		12.6279,11.5978,12.2789		837/894	158528269	1597,11409	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon20			CCTCTGCACTTCT	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2511G>C	7.37:g.158528269C>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			C|0.876;G|0.124	0.124	strong		0.443	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
SPRR1B	6699	hgsc.bcm.edu	37	1	153004983	153004983	+	Silent	SNP	C	C	T	rs12195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153004983C>T	ENST00000307098.4	+	2	227	c.162C>T	c.(160-162)ccC>ccT	p.P54P	SPRR1B_ENST00000392661.3_Intron	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	54	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	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)			CCAAAGTGCCCGAGCCCTGCC	0.627													T|||	2492	0.497604	0.441	0.4265	5008	,	,		14910	0.5923		0.5179	False		,,,				2504	0.5061				p.P54P		Atlas-SNP	.											.	SPRR1B	18	.	1	Deletion - In frame(1)	ovary(1)	c.C162T						PASS	.	T		2076,2330	605.2+/-390.5	490,1096,617	113.0	114.0	113.0		162	0.6	1.0	1	dbSNP_52	113	4494,4102	561.2+/-387.7	1233,2028,1037	no	coding-synonymous	SPRR1B	NM_003125.2		1723,3124,1654	TT,TC,CC		47.7199,47.1176,49.4693		54/90	153004983	6570,6432	2203	4298	6501	SO:0001819	synonymous_variant	6699	exon2			AGTGCCCGAGCCC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.162C>T	1.37:g.153004983C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	158	78	0.493671	NM_003125	B2R5H7|P22529|P22530|Q5T524	Silent	SNP	ENST00000307098.4	37	CCDS30863.1																																																																																			C|0.493;T|0.507	0.507	strong		0.627	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
C5orf45	51149	hgsc.bcm.edu	37	5	179267949	179267949	+	Missense_Mutation	SNP	T	T	C	rs248248	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179267949T>C	ENST00000292586.6	-	6	550	c.460A>G	c.(460-462)Agg>Ggg	p.R154G	C5orf45_ENST00000518235.1_Missense_Mutation_p.R154G|C5orf45_ENST00000523084.1_Missense_Mutation_p.R20G|C5orf45_ENST00000523267.1_Intron|C5orf45_ENST00000518219.1_Missense_Mutation_p.R154G|C5orf45_ENST00000403396.2_Missense_Mutation_p.R196G|C5orf45_ENST00000520698.1_Missense_Mutation_p.R99G|C5orf45_ENST00000521333.1_Intron|C5orf45_ENST00000376931.2_Missense_Mutation_p.R99G	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	154			R -> G (in dbSNP:rs248248). {ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						ACGGTGCTCCTGCTCCACTTC	0.637													C|||	4241	0.846845	0.9546	0.8458	5008	,	,		17216	0.8958		0.7097	False		,,,				2504	0.7924				p.R154G		Atlas-SNP	.											.	C5orf45	23	.	0			c.A460G						PASS	.	C	GLY/ARG,GLY/ARG	4006,400		1825,356,22	48.0	40.0	43.0		295,460	1.6	0.9	5	dbSNP_79	43	6075,2525		2179,1717,404	yes	missense,missense	C5orf45	NM_001017987.2,NM_016175.3	125,125	4004,2073,426	CC,CT,TT		29.3605,9.0785,22.4896	benign,benign	99/289,154/344	179267949	10081,2925	2203	4300	6503	SO:0001583	missense	51149	exon6			TGCTCCTGCTCCA		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.460A>G	5.37:g.179267949T>C	ENSP00000292586:p.Arg154Gly	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	37	CCDS34319.1	1803	0.8255494505494505	470	0.9552845528455285	284	0.7845303867403315	518	0.9055944055944056	531	0.7005277044854882	C	10.26	1.299845	0.23650	0.909215	0.706395	ENSG00000161010	ENST00000403396;ENST00000518235;ENST00000520698;ENST00000376931;ENST00000518219;ENST00000523084;ENST00000292586	T;T;T;T;T;T;T	0.34275	2.02;2.02;2.02;2.12;2.02;1.37;3.19	2.48	1.61	0.23674	.	0.559511	0.14611	N	0.309040	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B	0.29671	0.007;0.0;0.017;0.0;0.254	B;B;B;B;B	0.24006	0.005;0.001;0.015;0.0;0.05	T	0.14254	-1.0479	9	0.31617	T	0.26	2.5157	5.1283	0.14896	0.0:0.2362:0.5245:0.2393	rs248248;rs1643449;rs17857459;rs52812364;rs58313372;rs248248	99;154;99;154;196	E7EMV9;B7Z1T6;E9PAK6;Q6NTE8;Q6NTE8-2	.;.;.;CE045_HUMAN;.	G	196;154;99;99;154;20;154	ENSP00000384599:R196G;ENSP00000430298:R154G;ENSP00000427849:R99G;ENSP00000366130:R99G;ENSP00000428460:R154G;ENSP00000429107:R20G;ENSP00000292586:R154G	ENSP00000292586:R154G	R	-	1	2	C5orf45	179200555	0.316000	0.24580	0.907000	0.35723	0.101000	0.19017	0.596000	0.24044	0.191000	0.20236	-0.957000	0.02645	AGG	T|0.191;C|0.809	0.809	strong		0.637	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
DHX38	9785	hgsc.bcm.edu	37	16	72139184	72139184	+	Silent	SNP	C	C	A	rs2074626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:72139184C>A	ENST00000268482.3	+	17	2825	c.2316C>A	c.(2314-2316)gcC>gcA	p.A772A	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	772	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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.A772A(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)				ACGCGCCTGCCCTGGCTGTGC	0.577													C|||	2385	0.476238	0.7799	0.3156	5008	,	,		18831	0.3085		0.3559	False		,,,				2504	0.4765				p.A772A	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,NS,carcinoma,0,2	DHX38	91	2	1	Substitution - coding silent(1)	prostate(1)	c.C2316A						scavenged	.	C		3042,1354	691.3+/-405.4	1066,910,222	71.0	66.0	68.0		2316	1.2	0.9	16	dbSNP_96	68	3215,5385	484.9+/-371.5	593,2029,1678	no	coding-synonymous	DHX38	NM_014003.3		1659,2939,1900	AA,AC,CC		37.3837,30.8007,48.1456		772/1228	72139184	6257,6739	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon17			GCCTGCCCTGGCT	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.2316C>A	16.37:g.72139184C>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	78	44	0.564103	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			C|0.529;A|0.471	0.471	strong		0.577	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
PADI2	11240	hgsc.bcm.edu	37	1	17405814	17405814	+	Missense_Mutation	SNP	C	C	T	rs148233687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17405814C>T	ENST00000375486.4	-	11	1318	c.1255G>A	c.(1255-1257)Gtg>Atg	p.V419M	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000375481.1_Missense_Mutation_p.V419M|PADI2_ENST00000444885.2_Missense_Mutation_p.V303M	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	419					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	TTGCCGTTCACGGTCACTGGG	0.597													C|||	5	0.000998403	0.0	0.0043	5008	,	,		15043	0.0		0.002	False		,,,				2504	0.0				p.V419M		Atlas-SNP	.											.	PADI2	72	.	0			c.G1255A						PASS	.	C	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	65.0	65.0	65.0		1255	5.0	1.0	1	dbSNP_134	65	16,8584	11.9+/-42.8	0,16,4284	yes	missense	PADI2	NM_007365.2	21	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	probably-damaging	419/666	17405814	18,12988	2203	4300	6503	SO:0001583	missense	11240	exon11			CGTTCACGGTCAC	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1255G>A	1.37:g.17405814C>T	ENSP00000364635:p.Val419Met	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	57	48	0.842105	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	28.5	4.926678	0.92319	4.54E-4	0.00186	ENSG00000117115	ENST00000375486;ENST00000444885;ENST00000375481	T;T;T	0.30182	1.54;1.54;1.54	4.97	4.97	0.65823	Protein-arginine deiminase, C-terminal (1);	0.244684	0.41500	D	0.000874	T	0.52773	0.1755	M	0.85197	2.74	0.51233	D	0.999919	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.938	T	0.62676	-0.6804	10	0.56958	D	0.05	-20.6685	17.3265	0.87249	0.0:1.0:0.0:0.0	.	303;419	B4DIU3;Q9Y2J8	.;PADI2_HUMAN	M	419;303;419	ENSP00000364635:V419M;ENSP00000405894:V303M;ENSP00000364630:V419M	ENSP00000364630:V419M	V	-	1	0	PADI2	17278401	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	7.127000	0.77210	2.758000	0.94735	0.561000	0.74099	GTG	C|0.999;T|0.001	0.001	strong		0.597	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
R3HDML	140902	hgsc.bcm.edu	37	20	42965863	42965863	+	Silent	SNP	C	C	T	rs3746570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:42965863C>T	ENST00000217043.2	+	1	238	c.66C>T	c.(64-66)aaC>aaT	p.N22N		NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	22						extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			AGGCAGTGAACGCCTTGATAA	0.662													C|||	798	0.159345	0.1369	0.2392	5008	,	,		16802	0.0913		0.1551	False		,,,				2504	0.2076				p.N22N		Atlas-SNP	.											.	R3HDML	33	.	0			c.C66T						PASS	.	C		673,3733	274.3+/-271.8	56,561,1586	43.0	42.0	42.0		66	-8.9	0.0	20	dbSNP_107	42	1302,7296	246.7+/-275.0	96,1110,3093	no	coding-synonymous	R3HDML	NM_178491.2		152,1671,4679	TT,TC,CC		15.1431,15.2746,15.1876		22/254	42965863	1975,11029	2203	4299	6502	SO:0001819	synonymous_variant	140902	exon1			AGTGAACGCCTTG	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing-like"""				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.66C>T	20.37:g.42965863C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_178491		Silent	SNP	ENST00000217043.2	37	CCDS13329.1																																																																																			C|0.845;T|0.155	0.155	strong		0.662	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491	
ARHGEF7	8874	hgsc.bcm.edu	37	13	111870037	111870037	+	Silent	SNP	T	T	C	rs2296354	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:111870037T>C	ENST00000375741.2	+	6	793	c.543T>C	c.(541-543)gaT>gaC	p.D181D	ARHGEF7_ENST00000544132.1_5'UTR|ARHGEF7_ENST00000218789.5_Silent_p.D3D|ARHGEF7_ENST00000375739.2_Silent_p.D131D|ARHGEF7_ENST00000375736.4_Silent_p.D3D|ARHGEF7_ENST00000370623.3_Silent_p.D88D|ARHGEF7_ENST00000426073.2_Silent_p.D3D|ARHGEF7_ENST00000375723.1_Silent_p.D3D|ARHGEF7_ENST00000375737.5_Silent_p.D78D|ARHGEF7_ENST00000317133.5_Silent_p.D160D	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	181					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			ACATGACCGATAATAGCAACA	0.388													T|||	1246	0.248802	0.025	0.1225	5008	,	,		18731	0.6825		0.174	False		,,,				2504	0.271				p.D181D		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.T543C						PASS	.	T	,,,,	223,4183	134.5+/-170.7	3,217,1983	115.0	109.0	111.0		543,393,9,9,480	-3.1	0.4	13	dbSNP_100	111	1437,7163	276.7+/-292.4	115,1207,2978	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF7	NM_001113511.1,NM_001113512.1,NM_001113513.1,NM_003899.3,NM_145735.2	,,,,	118,1424,4961	CC,CT,TT		16.7093,5.0613,12.7633	,,,,	181/804,131/754,3/647,3/647,160/783	111870037	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	8874	exon6			GACCGATAATAGC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.543T>C	13.37:g.111870037T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	140	87	0.621429	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Silent	SNP	ENST00000375741.2	37	CCDS45068.1																																																																																			T|0.807;C|0.193	0.193	strong		0.388	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
NDUFS4	4724	hgsc.bcm.edu	37	5	52856504	52856504	+	Silent	SNP	G	G	C	rs2279516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:52856504G>C	ENST00000296684.5	+	1	40	c.12G>C	c.(10-12)gtG>gtC	p.V4V		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	4					brain development (GO:0007420)|cAMP-mediated signaling (GO:0019933)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|positive regulation of fibroblast proliferation (GO:0048146)|reactive oxygen species metabolic process (GO:0072593)|regulation of protein phosphorylation (GO:0001932)|respiratory electron transport chain (GO:0022904)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(3)	10		Lung NSC(810;8.27e-05)|Breast(144;0.0848)				TGGCGGCGGTGTCAATGTCAG	0.542													C|||	3410	0.680911	0.8298	0.6715	5008	,	,		15969	0.6448		0.5934	False		,,,				2504	0.6135				p.V4V		Atlas-SNP	.											.	NDUFS4	17	.	0			c.G12C						PASS	.	C		3524,882	344.4+/-308.1	1407,710,86	120.0	106.0	111.0		12	3.8	1.0	5	dbSNP_100	111	5080,3520	513.9+/-378.3	1501,2078,721	no	coding-synonymous	NDUFS4	NM_002495.2		2908,2788,807	CC,CG,GG		40.9302,20.0182,33.8459		4/176	52856504	8604,4402	2203	4300	6503	SO:0001819	synonymous_variant	4724	exon1			GGCGGTGTCAATG	AF020351	CCDS3960.1	5q11.1	2011-07-04	2002-08-29		ENSG00000164258	ENSG00000164258		"""Mitochondrial respiratory chain complex / Complex I"""	7711	protein-coding gene	gene with protein product	"""complex I 18kDa subunit"""	602694	"""NADH dehydrogenase (ubiquinone) Fe-S protein 4 (18kD) (NADH-coenzyme Q reductase)"""			9463323, 9763677	Standard	NM_002495		Approved	AQDQ, CI-18	uc003jpe.2	O43181	OTTHUMG00000096987	ENST00000296684.5:c.12G>C	5.37:g.52856504G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_002495	Q9BS69	Silent	SNP	ENST00000296684.5	37	CCDS3960.1																																																																																			G|0.338;C|0.662	0.662	strong		0.542	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495	
HEATR4	399671	hgsc.bcm.edu	37	14	73969610	73969610	+	Silent	SNP	G	G	A	rs11626122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:73969610G>A	ENST00000553558.1	-	11	2415	c.2094C>T	c.(2092-2094)caC>caT	p.H698H	HEATR4_ENST00000560393.1_Silent_p.H651H|HEATR4_ENST00000334988.2_Silent_p.H698H	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	698										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TGATTATGTCGTGCACCTCTT	0.493													G|||	926	0.184904	0.0787	0.268	5008	,	,		19315	0.2867		0.174	False		,,,				2504	0.1759				p.H698H		Atlas-SNP	.											.	HEATR4	126	.	0			c.C2094T						PASS	.	G	,	427,3979	209.5+/-230.2	20,387,1796	164.0	142.0	150.0		2094,2094	1.4	0.8	14	dbSNP_120	150	1174,7426	239.3+/-270.5	86,1002,3212	no	coding-synonymous,coding-synonymous	HEATR4	NM_001220484.1,NM_203309.2	,	106,1389,5008	AA,AG,GG		13.6512,9.6913,12.3097	,	698/1027,698/1027	73969610	1601,11405	2203	4300	6503	SO:0001819	synonymous_variant	399671	exon10			TATGTCGTGCACC	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2094C>T	14.37:g.73969610G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	48	0.461538	NM_203309	B7Z7V9|E9KL41	Silent	SNP	ENST00000553558.1	37	CCDS9815.2																																																																																			G|0.841;A|0.159	0.159	strong		0.493	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
LAMA5	3911	hgsc.bcm.edu	37	20	60895697	60895697	+	Missense_Mutation	SNP	C	C	T	rs2297587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60895697C>T	ENST00000252999.3	-	50	6743	c.6677G>A	c.(6676-6678)cGc>cAc	p.R2226H		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2226	Domain II and I.		R -> H (in dbSNP:rs2297587).		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)			CGTCTCATGGCGGGGGCCCAG	0.706													.|||	935	0.186701	0.152	0.219	5008	,	,		13119	0.1855		0.2376	False		,,,				2504	0.1595				p.R2226H		Atlas-SNP	.											.	LAMA5	268	.	0			c.G6677A						PASS	.		HIS/ARG	888,3386		124,640,1373	10.0	14.0	13.0		6677	-0.2	0.0	20	dbSNP_100	13	1876,6580		239,1398,2591	yes	missense	LAMA5	NM_005560.3	29	363,2038,3964	TT,TC,CC		22.1854,20.7768,21.7125	benign	2226/3696	60895697	2764,9966	2137	4228	6365	SO:0001583	missense	3911	exon50			TCATGGCGGGGGC	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.6677G>A	20.37:g.60895697C>T	ENSP00000252999:p.Arg2226His	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	428	0.19597069597069597	80	0.16260162601626016	78	0.2154696132596685	101	0.17657342657342656	169	0.22295514511873352	-	12.18	1.859616	0.32884	0.207768	0.221854	ENSG00000130702	ENST00000252999	T	0.10005	2.92	4.23	-0.196	0.13232	Laminin I (1);	0.716055	0.13292	N	0.398926	T	0.00012	0.0000	L	0.29908	0.895	0.53688	P	2.8999999999945736E-5	B	0.18310	0.027	B	0.10450	0.005	T	0.47235	-0.9133	9	0.15952	T	0.53	.	5.2616	0.15576	0.0:0.5371:0.1381:0.3247	rs2297587;rs57072194;rs2297587	2226	O15230	LAMA5_HUMAN	H	2226	ENSP00000252999:R2226H	ENSP00000252999:R2226H	R	-	2	0	LAMA5	60329092	0.003000	0.15002	0.009000	0.14445	0.014000	0.08584	-0.041000	0.12084	-0.080000	0.12685	-0.330000	0.08379	CGC	C|0.805;T|0.195	0.195	strong		0.706	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
NFE2L3	9603	hgsc.bcm.edu	37	7	26224382	26224382	+	Missense_Mutation	SNP	C	C	T	rs151210268		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:26224382C>T	ENST00000056233.3	+	4	1323	c.1064C>T	c.(1063-1065)aCc>aTc	p.T355I		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	355					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						CCTGAGCAAACCCTTCCTGGA	0.393																																					p.T355I		Atlas-SNP	.											.	NFE2L3	77	.	0			c.C1064T						PASS	.						92.0	87.0	89.0					7																	26224382		2203	4300	6503	SO:0001583	missense	9603	exon4			AGCAAACCCTTCC	AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.1064C>T	7.37:g.26224382C>T	ENSP00000056233:p.Thr355Ile	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	296	30	0.101351	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Missense_Mutation	SNP	ENST00000056233.3	37	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	C	8.880	0.951479	0.18431	.	.	ENSG00000050344	ENST00000056233;ENST00000398175	T	0.34667	1.35	4.72	0.691	0.18045	.	1.195610	0.05551	N	0.567511	T	0.33962	0.0881	L	0.61218	1.895	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.36841	-0.9731	10	0.72032	D	0.01	-0.0642	2.8465	0.05545	0.2149:0.3371:0.3156:0.1324	.	355	Q9Y4A8	NF2L3_HUMAN	I	355;61	ENSP00000056233:T355I	ENSP00000056233:T355I	T	+	2	0	NFE2L3	26190907	0.000000	0.05858	0.001000	0.08648	0.788000	0.44548	-0.445000	0.06845	-0.000000	0.14550	0.591000	0.81541	ACC	.	.	weak		0.393	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
PBXIP1	57326	hgsc.bcm.edu	37	1	154919080	154919080	+	Missense_Mutation	SNP	C	C	T	rs2061690	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:154919080C>T	ENST00000368463.3	-	10	1141	c.1070G>A	c.(1069-1071)gGt>gAt	p.G357D	PBXIP1_ENST00000498553.1_5'Flank|PBXIP1_ENST00000368465.1_Missense_Mutation_p.G328D|PBXIP1_ENST00000542459.1_Missense_Mutation_p.G202D|PBXIP1_ENST00000539880.1_Missense_Mutation_p.G184D	NM_020524.2	NP_065385.2	Q96AQ6	PBIP1_HUMAN	pre-B-cell leukemia homeobox interacting protein 1	357			G -> D (in dbSNP:rs2061690). {ECO:0000269|PubMed:10825160, ECO:0000269|PubMed:14702039}.		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)			TGGGCCTCTACCCCCACTGAG	0.672													C|||	2584	0.515974	0.1498	0.6297	5008	,	,		16333	0.8958		0.4334	False		,,,				2504	0.6237				p.G357D		Atlas-SNP	.											.	PBXIP1	59	.	0			c.G1070A						PASS	.	C	ASP/GLY	893,3513	341.5+/-306.7	90,713,1400	51.0	47.0	48.0		1070	3.6	0.3	1	dbSNP_94	48	3740,4860	528.4+/-381.4	826,2088,1386	yes	missense	PBXIP1	NM_020524.2	94	916,2801,2786	TT,TC,CC		43.4884,20.2678,35.622	benign	357/732	154919080	4633,8373	2203	4300	6503	SO:0001583	missense	57326	exon10			CCTCTACCCCCAC	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.1070G>A	1.37:g.154919080C>T	ENSP00000357448:p.Gly357Asp	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_020524	Q5T174|Q5T176|Q9H8X6|Q9HA02|Q9HD85	Missense_Mutation	SNP	ENST00000368463.3	37	CCDS1074.1	1134	0.5192307692307693	85	0.17276422764227642	211	0.5828729281767956	507	0.8863636363636364	331	0.4366754617414248	C	3.845	-0.032974	0.07543	0.202678	0.434884	ENSG00000163346	ENST00000368465;ENST00000368463;ENST00000351146;ENST00000539880;ENST00000543593;ENST00000542459	T;T;T;T	0.13196	2.61;2.65;2.69;2.67	4.49	3.57	0.40892	.	0.000000	0.36932	N	0.002324	T	0.03095	0.0091	L	0.36672	1.1	0.80722	P	0.0	B	0.23540	0.087	B	0.25759	0.063	T	0.38672	-0.9650	9	0.12766	T	0.61	-9.241	6.9331	0.24451	0.0:0.7945:0.0:0.2054	rs2061690;rs3753643;rs52834797;rs59260875;rs2061690	357	Q96AQ6	PBIP1_HUMAN	D	328;357;357;184;133;202	ENSP00000357450:G328D;ENSP00000357448:G357D;ENSP00000440142:G184D;ENSP00000438584:G202D	ENSP00000295523:G357D	G	-	2	0	PBXIP1	153185704	0.000000	0.05858	0.276000	0.24689	0.038000	0.13279	0.459000	0.21908	1.107000	0.41642	0.563000	0.77884	GGT	C|0.565;T|0.435	0.435	strong		0.672	PBXIP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090943.1	NM_020524	
GON4L	54856	hgsc.bcm.edu	37	1	155735012	155735012	+	Missense_Mutation	SNP	T	T	C	rs2297775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155735012T>C	ENST00000368331.1	-	21	4300	c.4252A>G	c.(4252-4254)Atg>Gtg	p.M1418V	GON4L_ENST00000361040.5_Missense_Mutation_p.M1418V|GON4L_ENST00000437809.1_Missense_Mutation_p.M1418V|GON4L_ENST00000271883.5_Missense_Mutation_p.M1418V|GON4L_ENST00000471341.1_5'UTR	NM_001282858.1|NM_001282860.1	NP_001269787.1|NP_001269789.1	Q3T8J9	GON4L_HUMAN	gon-4-like (C. elegans)	1418			M -> V (in dbSNP:rs2297775). {ECO:0000269|PubMed:11230166}.		regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(4)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|prostate(3)|skin(2)|stomach(1)|urinary_tract(1)	45	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)|all_neural(408;0.195)					TCAGGATCCATTGAGGACAAA	0.502													T|||	1774	0.354233	0.1815	0.3256	5008	,	,		21690	0.6865		0.2972	False		,,,				2504	0.3241				p.M1418V		Atlas-SNP	.											GON4L,colon,carcinoma,+2,1	GON4L	392	1	0			c.A4252G						PASS	.	T	VAL/MET,VAL/MET	913,3493	350.5+/-310.9	106,701,1396	93.0	91.0	92.0		4252,4252	-4.4	0.0	1	dbSNP_100	92	2611,5989	423.3+/-354.3	407,1797,2096	yes	missense,missense	GON4L	NM_001037533.1,NM_032292.4	21,21	513,2498,3492	CC,CT,TT		30.3605,20.7217,27.0952	benign,benign	1418/2241,1418/1530	155735012	3524,9482	2203	4300	6503	SO:0001583	missense	54856	exon21			GATCCATTGAGGA	AB046826	CCDS1121.1, CCDS44242.1, CCDS60296.1	1q22	2013-10-31	2006-11-08	2006-02-16	ENSG00000116580	ENSG00000116580			25973	protein-coding gene	gene with protein product		610393	"""gon-4 homolog (C.elegans)"""	GON4		16545939, 21454521	Standard	XM_005245283		Approved	FLJ20203, GON-4	uc001fly.1	Q3T8J9	OTTHUMG00000014106	ENST00000368331.1:c.4252A>G	1.37:g.155735012T>C	ENSP00000357315:p.Met1418Val	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	177	66	0.372881	NM_001037533	B7ZBL4|Q14C93|Q3T8J8|Q5VYZ5|Q5W0D5|Q6AWA6|Q6P1Q6|Q7Z3L3|Q8IY79|Q9BQI1|Q9HCG6	Missense_Mutation	SNP	ENST00000368331.1	37		879	0.4024725274725275	94	0.1910569105691057	133	0.3674033149171271	416	0.7272727272727273	236	0.3113456464379947	T	6.973	0.549433	0.13374	0.207217	0.303605	ENSG00000116580	ENST00000437809;ENST00000368331;ENST00000271883;ENST00000361040	T;T;T;T	0.10763	3.05;3.05;3.05;2.84	5.04	-4.4	0.03600	.	1.379720	0.04358	N	0.357025	T	0.02970	0.0088	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.36817	-0.9732	9	0.27082	T	0.32	.	16.1992	0.82057	0.0:0.6548:0.0:0.3452	rs2297775;rs52792030;rs2297775	1418;1418;1418	Q3T8J9-2;Q3T8J9;Q3T8J9-3	.;GON4L_HUMAN;.	V	1418	ENSP00000396117:M1418V;ENSP00000357315:M1418V;ENSP00000271883:M1418V;ENSP00000354322:M1418V	ENSP00000271883:M1418V	M	-	1	0	GON4L	154001636	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.619000	0.05572	-1.090000	0.03069	0.529000	0.55759	ATG	T|0.667;C|0.333	0.333	strong		0.502	GON4L-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_032292	
WDR88	126248	hgsc.bcm.edu	37	19	33655144	33655144	+	Silent	SNP	C	C	T	rs1981827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33655144C>T	ENST00000355868.3	+	9	1198	c.1122C>T	c.(1120-1122)aaC>aaT	p.N374N	WDR88_ENST00000361680.2_Silent_p.N374N	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	374										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					TTAGCAACAACAAGAAATGGA	0.383													C|||	882	0.176118	0.115	0.1239	5008	,	,		21226	0.1607		0.1282	False		,,,				2504	0.3609				p.N374N		Atlas-SNP	.											.	WDR88	50	.	0			c.C1122T						PASS	.	C		505,3901	234.2+/-247.1	31,443,1729	158.0	147.0	151.0		1122	4.1	0.9	19	dbSNP_92	151	961,7639	210.0+/-251.0	39,883,3378	no	coding-synonymous	WDR88	NM_173479.3		70,1326,5107	TT,TC,CC		11.1744,11.4616,11.2717		374/473	33655144	1466,11540	2203	4300	6503	SO:0001819	synonymous_variant	126248	exon9			CAACAACAAGAAA	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.1122C>T	19.37:g.33655144C>T		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_173479	Q8NEF8	Silent	SNP	ENST00000355868.3	37	CCDS12429.1																																																																																			C|0.874;T|0.126	0.126	strong		0.383	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
RAB3IL1	5866	hgsc.bcm.edu	37	11	61675644	61675644	+	Missense_Mutation	SNP	T	T	C	rs174477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:61675644T>C	ENST00000394836.2	-	2	303	c.146A>G	c.(145-147)cAa>cGa	p.Q49R	RAB3IL1_ENST00000301773.5_Missense_Mutation_p.Q96R	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	49			Q -> R (in dbSNP:rs174477).		positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|liver(1)|lung(4)|skin(3)|urinary_tract(1)	14						CTCCTGGCCTTGGGCCTCCTC	0.682													T|||	369	0.0736821	0.0998	0.0807	5008	,	,		15756	0.0		0.1451	False		,,,				2504	0.0358				p.Q96R		Atlas-SNP	.											RAB3IL1,NS,carcinoma,0,1	RAB3IL1	39	1	0			c.A287G						PASS	.	T	ARG/GLN	439,3883		20,399,1742	8.0	9.0	9.0		146	-1.3	0.1	11	dbSNP_79	9	1141,7311		89,963,3174	no	missense	RAB3IL1	NM_013401.2	43	109,1362,4916	CC,CT,TT		13.4998,10.1573,12.3689	benign	49/383	61675644	1580,11194	2161	4226	6387	SO:0001583	missense	5866	exon2			TGGCCTTGGGCCT	AF084557	CCDS8014.1, CCDS60809.1	11q12.2	2008-02-01			ENSG00000167994	ENSG00000167994			9780	protein-coding gene	gene with protein product							Standard	NM_013401		Approved		uc001nso.4	Q8TBN0	OTTHUMG00000167524	ENST00000394836.2:c.146A>G	11.37:g.61675644T>C	ENSP00000378313:p.Gln49Arg	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_001271686	Q86V32|Q9P1Q8	Missense_Mutation	SNP	ENST00000394836.2	37	CCDS8014.1	193	0.08836996336996338	53	0.10772357723577236	34	0.09392265193370165	0	0.0	106	0.13984168865435356	T	6.248	0.413969	0.11870	0.101573	0.134998	ENSG00000167994	ENST00000394836;ENST00000301773;ENST00000531922	T;T;T	0.44881	0.91;0.91;0.91	4.73	-1.31	0.09230	.	0.527456	0.16430	N	0.214781	T	0.00144	0.0004	L	0.44542	1.39	0.80722	P	0.0	P;B	0.41265	0.744;0.089	B;B	0.31495	0.131;0.021	T	0.07385	-1.0775	9	0.41790	T	0.15	1.193	0.4651	0.00523	0.1991:0.3048:0.203:0.2931	rs174477	96;49	Q8TBN0-2;Q8TBN0	.;R3GEF_HUMAN	R	49;96;96	ENSP00000378313:Q49R;ENSP00000301773:Q96R;ENSP00000435444:Q96R	ENSP00000301773:Q96R	Q	-	2	0	RAB3IL1	61432220	0.013000	0.17824	0.103000	0.21229	0.109000	0.19521	-0.071000	0.11505	-0.066000	0.12998	0.459000	0.35465	CAA	T|0.917;C|0.083	0.083	strong		0.682	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401	
WDR62	284403	hgsc.bcm.edu	37	19	36574063	36574063	+	Silent	SNP	C	C	T	rs45567532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36574063C>T	ENST00000270301.7	+	11	1470	c.1470C>T	c.(1468-1470)gaC>gaT	p.D490D	WDR62_ENST00000401500.2_Silent_p.D490D			O43379	WDR62_HUMAN	WD repeat domain 62	490					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)			CACCCATGGACGTGAAAGCCG	0.602													C|||	631	0.125998	0.2723	0.0764	5008	,	,		18269	0.0		0.1342	False		,,,				2504	0.0849				p.D490D		Atlas-SNP	.											.	WDR62	102	.	0			c.C1470T						PASS	.	C	,	1029,3377	373.0+/-320.6	115,799,1289	54.0	49.0	50.0		1470,1470	-9.1	0.4	19	dbSNP_127	50	887,7713	195.5+/-240.7	54,779,3467	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	169,1578,4756	TT,TC,CC		10.314,23.3545,14.7317	,	490/1524,490/1519	36574063	1916,11090	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon11			CATGGACGTGAAA	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.1470C>T	19.37:g.36574063C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			C|0.864;T|0.136	0.136	strong		0.602	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
AMTN	401138	hgsc.bcm.edu	37	4	71388551	71388551	+	Missense_Mutation	SNP	A	A	G	rs7660807	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71388551A>G	ENST00000339336.4	+	3	264	c.134A>G	c.(133-135)aAt>aGt	p.N45S	AMTN_ENST00000504451.1_Missense_Mutation_p.N44S	NM_212557.2	NP_997722.1	Q6UX39	AMTN_HUMAN	amelotin	45			N -> S (in dbSNP:rs7660807).		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|odontogenesis of dentin-containing tooth (GO:0042475)	basal lamina (GO:0005605)|cell-cell junction (GO:0005911)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)|skin(1)	19			Lung(101;0.235)			CAGCAGTCAAATCAGGTAAGA	0.423													A|||	522	0.104233	0.0061	0.0591	5008	,	,		18816	0.2014		0.1004	False		,,,				2504	0.1728				p.N45S		Atlas-SNP	.											.	AMTN	28	.	0			c.A134G						PASS	.	A	SER/ASN	87,4319	72.5+/-110.5	0,87,2116	179.0	184.0	182.0		134	1.4	1.0	4	dbSNP_116	182	706,7894	173.6+/-224.1	29,648,3623	yes	missense	AMTN	NM_212557.2	46	29,735,5739	GG,GA,AA		8.2093,1.9746,6.0972	benign	45/210	71388551	793,12213	2203	4300	6503	SO:0001583	missense	401138	exon3			AGTCAAATCAGGT	AY358528	CCDS3542.1, CCDS68716.1	4q13.3	2006-12-12			ENSG00000187689	ENSG00000187689			33188	protein-coding gene	gene with protein product		610912				16304441	Standard	NM_001286731		Approved	UNQ689, RSTI689	uc003hfk.1	Q6UX39	OTTHUMG00000129906	ENST00000339336.4:c.134A>G	4.37:g.71388551A>G	ENSP00000341013:p.Asn45Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_212557	Q0P503|Q0P506	Missense_Mutation	SNP	ENST00000339336.4	37	CCDS3542.1	218	0.09981684981684982	1	0.0020325203252032522	22	0.06077348066298342	116	0.20279720279720279	79	0.10422163588390501	A	14.98	2.697081	0.48202	0.019746	0.082093	ENSG00000187689	ENST00000339336;ENST00000504451	T;T	0.33654	1.41;1.4	5.37	1.44	0.22558	.	0.449617	0.20956	N	0.082650	T	0.00039	0.0001	L	0.34521	1.04	0.41348	P	0.012650999999999968	B;B	0.24368	0.102;0.102	B;B	0.21151	0.033;0.033	T	0.14282	-1.0478	9	0.48119	T	0.1	-0.8317	5.5572	0.17123	0.574:0.3367:0.0892:0.0	rs7660807;rs52816620;rs58045335;rs7660807	44;45	Q6UX39-2;Q6UX39	.;AMTN_HUMAN	S	45;44	ENSP00000341013:N45S;ENSP00000422452:N44S	ENSP00000341013:N45S	N	+	2	0	AMTN	71423140	0.872000	0.30054	0.994000	0.49952	0.943000	0.58893	-0.247000	0.08866	0.032000	0.15435	0.533000	0.62120	AAT	A|0.919;G|0.081	0.081	strong		0.423	AMTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252157.1	NM_212557	
PTCHD2	57540	hgsc.bcm.edu	37	1	11589911	11589911	+	Silent	SNP	G	G	A	rs2076468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:11589911G>A	ENST00000294484.6	+	15	3135	c.2997G>A	c.(2995-2997)ccG>ccA	p.P999P	PTCHD2_ENST00000389575.3_Silent_p.P999P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	999					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCGGGAAGCCGGCGGTGCGGC	0.622													G|||	913	0.182308	0.0726	0.0994	5008	,	,		16735	0.4385		0.1064	False		,,,				2504	0.2035				p.P999P		Atlas-SNP	.											.	PTCHD2	193	.	0			c.G2997A						PASS	.	G		353,3581		18,317,1632	59.0	75.0	70.0		2997	-9.9	0.0	1	dbSNP_96	70	1166,7122		73,1020,3051	no	coding-synonymous	PTCHD2	NM_020780.1		91,1337,4683	AA,AG,GG		14.0685,8.9731,12.4284		999/1393	11589911	1519,10703	1967	4144	6111	SO:0001819	synonymous_variant	57540	exon15			GAAGCCGGCGGTG	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.2997G>A	1.37:g.11589911G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	127	14	0.110236	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	37	CCDS41247.1																																																																																			G|0.816;A|0.184	0.184	strong		0.622	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
PKD1L1	168507	hgsc.bcm.edu	37	7	47930148	47930148	+	Silent	SNP	C	C	T	rs118004103	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47930148C>T	ENST00000289672.2	-	16	2717	c.2667G>A	c.(2665-2667)tcG>tcA	p.S889S		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	889	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.S889S(1)	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						ACCTGAACGCCGAGTCAGGGT	0.562													C|||	113	0.0225639	0.0151	0.0216	5008	,	,		18953	0.0179		0.0129	False		,,,				2504	0.0481				p.S889S		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	1	Substitution - coding silent(1)	stomach(1)	c.G2667A						PASS	.	C		65,4341	61.7+/-98.7	1,63,2139	76.0	71.0	73.0		2667	-10.9	0.0	7	dbSNP_132	73	195,8405	87.1+/-149.5	1,193,4106	no	coding-synonymous	PKD1L1	NM_138295.3		2,256,6245	TT,TC,CC		2.2674,1.4753,1.9991		889/2850	47930148	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon16			GAACGCCGAGTCA	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.2667G>A	7.37:g.47930148C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			C|0.980;T|0.020	0.020	strong		0.562	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
VARS	7407	hgsc.bcm.edu	37	6	31748820	31748820	+	Silent	SNP	G	G	A	rs707926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31748820G>A	ENST00000375663.3	-	22	3065	c.2625C>T	c.(2623-2625)gaC>gaT	p.D875D	VARS_ENST00000482996.1_5'UTR|Y_RNA_ENST00000364685.1_RNA	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	875					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	CATAGATGACGTCCAGGGGAT	0.627													G|||	1282	0.25599	0.3623	0.2594	5008	,	,		20231	0.1796		0.1988	False		,,,				2504	0.2474				p.D875D		Atlas-SNP	.											.	VARS	76	.	0			c.C2625T						PASS	.	G		992,2030		171,650,690	129.0	97.0	109.0		2625	-8.7	0.7	6	dbSNP_86	109	909,4509		80,749,1880	yes	coding-synonymous	VARS	NM_006295.2		251,1399,2570	AA,AG,GG		16.7774,32.8259,22.5237		875/1265	31748820	1901,6539	1511	2709	4220	SO:0001819	synonymous_variant	7407	exon22			GATGACGTCCAGG	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.2625C>T	6.37:g.31748820G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Silent	SNP	ENST00000375663.3	37	CCDS34412.1	545	0.24954212454212454	166	0.33739837398373984	94	0.2596685082872928	126	0.2202797202797203	159	0.20976253298153033	G	8.542	0.873530	0.17322	0.328259	0.167774	ENSG00000204394	ENST00000428445	.	.	.	5.01	-8.66	0.00866	.	.	.	.	.	T	0.27313	0.0670	.	.	.	0.09310	P	0.9999999999999912	.	.	.	.	.	.	T	0.21177	-1.0253	3	.	.	.	-25.3922	14.9309	0.70914	0.3898:0.0:0.6102:0.0	rs707926;rs741883;rs4993764;rs17850963;rs61056503;rs707926	.	.	.	C	193	.	.	R	-	1	0	VARS	31856799	0.152000	0.22762	0.670000	0.29842	0.837000	0.47467	-0.370000	0.07523	-1.836000	0.01190	-0.982000	0.02568	CGT	G|0.770;A|0.230	0.230	strong		0.627	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	
CHMP4C	92421	hgsc.bcm.edu	37	8	82670412	82670412	+	Silent	SNP	G	G	A	rs62514262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:82670412G>A	ENST00000297265.4	+	4	712	c.519G>A	c.(517-519)caG>caA	p.Q173Q		NM_152284.3	NP_689497.1	Q96CF2	CHM4C_HUMAN	charged multivesicular body protein 4C	173	Intramolecular interaction with N- terminus. {ECO:0000250}.				abscission (GO:0009838)|cytokinesis checkpoint (GO:0031565)|endosomal transport (GO:0016197)|membrane organization (GO:0061024)|negative regulation of cytokinesis (GO:0032466)|positive regulation of viral release from host cell (GO:1902188)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|membrane (GO:0016020)|midbody (GO:0030496)	protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	10						AATTGGAACAGGAGGAATTAA	0.428													G|||	92	0.0183706	0.0023	0.0375	5008	,	,		19447	0.001		0.0447	False		,,,				2504	0.0174				p.Q173Q		Atlas-SNP	.											CHMP4C,NS,carcinoma,0,1	CHMP4C	28	1	0			c.G519A						PASS	.	G		41,4365	43.8+/-77.6	0,41,2162	109.0	108.0	108.0		519	3.5	1.0	8	dbSNP_129	108	417,8183	129.8+/-187.9	14,389,3897	no	coding-synonymous	CHMP4C	NM_152284.3		14,430,6059	AA,AG,GG		4.8488,0.9305,3.5215		173/234	82670412	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	92421	exon4			GGAACAGGAGGAA	AK000049	CCDS6233.1	8q21.13	2011-09-21	2011-09-21		ENSG00000164695	ENSG00000164695		"""Charged multivesicular body proteins"""	30599	protein-coding gene	gene with protein product	"""Snf7 homologue associated with Alix 3"""	610899	"""chromatin modifying protein 4C"""			12860994 , 14678797	Standard	NM_152284		Approved	MGC22825, Shax3, VPS32C	uc003ycl.3	Q96CF2	OTTHUMG00000164726	ENST00000297265.4:c.519G>A	8.37:g.82670412G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	79	40	0.506329	NM_152284	B2RBZ1	Silent	SNP	ENST00000297265.4	37	CCDS6233.1																																																																																			G|0.966;A|0.034	0.034	strong		0.428	CHMP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379927.1	NM_152284	
PLOD1	5351	hgsc.bcm.edu	37	1	12009955	12009955	+	Silent	SNP	C	C	T	rs7529452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12009955C>T	ENST00000196061.4	+	3	321	c.294C>T	c.(292-294)ttC>ttT	p.F98F	PLOD1_ENST00000376369.3_Silent_p.F145F|PLOD1_ENST00000485046.1_3'UTR	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	98					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)	TCATTCTCTTCGCAGACAGGT	0.567													C|||	1341	0.267772	0.0159	0.3357	5008	,	,		17922	0.3631		0.3052	False		,,,				2504	0.4233				p.F98F		Atlas-SNP	.											.	PLOD1	75	.	0			c.C294T						PASS	.	C		300,4106	164.0+/-195.7	12,276,1915	120.0	125.0	123.0		294	3.1	1.0	1	dbSNP_116	123	2682,5918	431.2+/-356.7	419,1844,2037	no	coding-synonymous	PLOD1	NM_000302.3		431,2120,3952	TT,TC,CC		31.186,6.8089,22.9279		98/728	12009955	2982,10024	2203	4300	6503	SO:0001819	synonymous_variant	5351	exon3			TCTCTTCGCAGAC	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.294C>T	1.37:g.12009955C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	104	92	0.884615	NM_000302	B4DR87|Q96AV9|Q9H132	Silent	SNP	ENST00000196061.4	37	CCDS142.1																																																																																			C|0.767;T|0.233	0.233	strong		0.567	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302	
CDAN1	146059	hgsc.bcm.edu	37	15	43028592	43028592	+	Silent	SNP	G	G	A	rs7167392	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43028592G>A	ENST00000356231.3	-	2	500	c.477C>T	c.(475-477)ccC>ccT	p.P159P		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	159					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		TGGGGCGGCTGGGGCTGCCAG	0.736													G|||	1305	0.260583	0.4365	0.1427	5008	,	,		10276	0.0546		0.2227	False		,,,				2504	0.3579				p.P159P		Atlas-SNP	.											.	CDAN1	70	.	0			c.C477T						PASS	.	G		1658,2690		315,1028,831	16.0	19.0	18.0		477	-2.9	0.3	15	dbSNP_116	18	1804,6730		201,1402,2664	no	coding-synonymous	CDAN1	NM_138477.2		516,2430,3495	AA,AG,GG		21.139,38.1325,26.8747		159/1228	43028592	3462,9420	2174	4267	6441	SO:0001819	synonymous_variant	146059	exon2			GCGGCTGGGGCTG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.477C>T	15.37:g.43028592G>A		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			G|0.766;A|0.234	0.234	strong		0.736	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
FDXR	2232	hgsc.bcm.edu	37	17	72862593	72862593	+	Missense_Mutation	SNP	C	C	T	rs690514	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72862593C>T	ENST00000293195.5	-	4	446	c.368G>A	c.(367-369)cGg>cAg	p.R123Q	FDXR_ENST00000583917.1_Missense_Mutation_p.R124Q|FDXR_ENST00000582944.1_Missense_Mutation_p.R115Q|FDXR_ENST00000413947.2_Missense_Mutation_p.R154Q|FDXR_ENST00000442102.2_Missense_Mutation_p.R166Q|FDXR_ENST00000455107.2_Missense_Mutation_p.R79Q|FDXR_ENST00000544854.1_Missense_Mutation_p.R71Q|FDXR_ENST00000581530.1_Missense_Mutation_p.R123Q|FDXR_ENST00000581969.1_5'UTR|FDXR_ENST00000420580.2_Intron	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase	123			R -> Q (in dbSNP:rs690514). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2845396, ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	GTAGGCCTCCCGCAGCTCCGG	0.662													C|||	927	0.185104	0.0333	0.1571	5008	,	,		17901	0.378		0.2147	False		,,,				2504	0.181				p.R166Q		Atlas-SNP	.											FDXR_ENST00000581530,NS,carcinoma,0,4	FDXR	68	4	0			c.G497A						PASS	.	C	GLN/ARG,GLN/ARG	287,4119	150.7+/-184.7	7,273,1923	34.0	29.0	31.0		368,368	-2.0	1.0	17	dbSNP_83	31	1895,6703	315.5+/-312.3	198,1499,2602	yes	missense,missense	FDXR	NM_004110.3,NM_024417.2	43,43	205,1772,4525	TT,TC,CC		22.04,6.5138,16.7795	benign,benign	123/498,123/492	72862593	2182,10822	2203	4299	6502	SO:0001583	missense	2232	exon4			GCCTCCCGCAGCT	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"""adrenodoxin-NADP(+) reductase"", ""adrenodoxin reductase"""	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.368G>A	17.37:g.72862593C>T	ENSP00000293195:p.Arg123Gln	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	37	CCDS58593.1	465	0.2129120879120879	16	0.032520325203252036	59	0.16298342541436464	224	0.3916083916083916	166	0.21899736147757257	C	11.28	1.591102	0.28357	0.065138	0.2204	ENSG00000161513	ENST00000544854;ENST00000293195;ENST00000455107;ENST00000442102;ENST00000413947	T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.38;-0.38	5.05	-1.99	0.07457	.	0.565182	0.18746	N	0.132305	T	0.00012	0.0000	N	0.25825	0.765	0.22629	P	0.99891839	B;B;B;B;B;B;B;B	0.21905	0.005;0.028;0.062;0.005;0.003;0.006;0.003;0.011	B;B;B;B;B;B;B;B	0.17979	0.02;0.01;0.015;0.013;0.004;0.009;0.004;0.02	T	0.38457	-0.9660	9	0.27785	T	0.31	2.9856	11.0447	0.47852	0.0:0.2718:0.0:0.7282	rs690514;rs1130204;rs2228624;rs690514	166;154;121;71;123;115;123;123	B4DHX5;E7EQC1;B4DDI9;B7Z7G2;Q6GSK2;B4DX24;P22570;P22570-2	.;.;.;.;.;.;ADRO_HUMAN;.	Q	71;123;79;166;154	ENSP00000445432:R71Q;ENSP00000293195:R123Q;ENSP00000390875:R79Q;ENSP00000416515:R166Q;ENSP00000408595:R154Q	ENSP00000293195:R123Q	R	-	2	0	FDXR	70374188	0.000000	0.05858	0.953000	0.39169	0.431000	0.31685	-1.415000	0.02469	-0.351000	0.08249	-0.367000	0.07326	CGG	C|0.813;T|0.187	0.187	strong		0.662	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110	
OR6K6	128371	hgsc.bcm.edu	37	1	158725080	158725080	+	Missense_Mutation	SNP	C	C	T	rs16841001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158725080C>T	ENST00000368144.2	+	1	571	c.475C>T	c.(475-477)Cgt>Tgt	p.R159C		NM_001005184.1	NP_001005184.1	Q8NGW6	OR6K6_HUMAN	olfactory receptor, family 6, subfamily K, member 6	159			R -> C (in dbSNP:rs16841001).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(5)|lung(17)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_hematologic(112;0.0378)					CAATCCACTCCGTTACCCAAC	0.468													C|||	518	0.103435	0.0431	0.1095	5008	,	,		24956	0.1667		0.1541	False		,,,				2504	0.0634				p.R159C		Atlas-SNP	.											.	OR6K6	81	.	0			c.C475T						PASS	.	C	CYS/ARG	249,4157	143.8+/-178.8	8,233,1962	131.0	109.0	116.0		475	5.5	1.0	1	dbSNP_123	116	1132,7468	233.7+/-266.9	80,972,3248	yes	missense	OR6K6	NM_001005184.1	180	88,1205,5210	TT,TC,CC		13.1628,5.6514,10.6182	benign	159/344	158725080	1381,11625	2203	4300	6503	SO:0001583	missense	128371	exon1			CCACTCCGTTACC	BK004198	CCDS30904.1	1q23.1	2012-08-09			ENSG00000180433	ENSG00000180433		"""GPCR / Class A : Olfactory receptors"""	15033	protein-coding gene	gene with protein product							Standard	NM_001005184		Approved		uc001fsw.1	Q8NGW6	OTTHUMG00000022772	ENST00000368144.2:c.475C>T	1.37:g.158725080C>T	ENSP00000357126:p.Arg159Cys	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	130	71	0.546154	NM_001005184	B9EIM8|Q5VUU9|Q6IFR4	Missense_Mutation	SNP	ENST00000368144.2	37	CCDS30904.1	282	0.12912087912087913	23	0.046747967479674794	37	0.10220994475138122	100	0.17482517482517482	122	0.16094986807387862	C	14.81	2.646762	0.47258	0.056514	0.131628	ENSG00000180433	ENST00000368144	T	0.02280	4.36	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.319150	0.22869	N	0.054656	T	0.01976	0.0062	M	0.62209	1.925	0.21762	P	0.999551967	B	0.32507	0.373	B	0.26094	0.066	T	0.45673	-0.9245	9	0.56958	D	0.05	-2.2299	18.27	0.90065	0.0:1.0:0.0:0.0	rs16841001;rs52808207;rs16841001	159	Q8NGW6	OR6K6_HUMAN	C	159	ENSP00000357126:R159C	ENSP00000357126:R159C	R	+	1	0	OR6K6	156991704	0.706000	0.27856	1.000000	0.80357	0.782000	0.44232	2.968000	0.49224	2.848000	0.98002	0.655000	0.94253	CGT	C|0.885;T|0.115	0.115	strong		0.468	OR6K6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059065.2	NM_001005184	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	rs537300122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38119902A>G	ENST00000406386.3	+	7	1594	c.1339A>G	c.(1339-1341)Aca>Gca	p.T447A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	447					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T447A(3)		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)					CAGTAGAGCTACACGAGACAA	0.587													A|||	50	0.00998403	0.0	0.0029	5008	,	,		19561	0.0337		0.0119	False		,,,				2504	0.002				p.T447A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	3	Substitution - Missense(3)	prostate(2)|skin(1)	c.A1339G						scavenged	.						60.0	64.0	63.0					22																	38119902		1870	4095	5965	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1339A>G	22.37:g.38119902A>G	ENSP00000384312:p.Thr447Ala	Somatic	225	3	0.0133333		WXS	Illumina HiSeq	Phase_I	276	15	0.0543478	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	5.040	0.193024	0.09599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19806	2.12	2.54	2.54	0.30619	.	.	.	.	.	T	0.23727	0.0574	L	0.36672	1.1	0.19945	N	0.999945	P	0.52463	0.953	P	0.53988	0.739	T	0.07558	-1.0766	9	0.30854	T	0.27	.	6.7436	0.23449	1.0:0.0:0.0:0.0	.	447	Q9H2D6	TARA_HUMAN	A	447	ENSP00000384312:T447A	ENSP00000384312:T447A	T	+	1	0	TRIOBP	36449848	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-0.062000	0.11674	1.059000	0.40554	0.113000	0.15668	ACA	.	.	none		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
ZNF180	7733	hgsc.bcm.edu	37	19	44981375	44981375	+	Silent	SNP	T	T	C	rs954314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44981375T>C	ENST00000221327.4	-	5	1604	c.1323A>G	c.(1321-1323)caA>caG	p.Q441Q	AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Silent_p.Q416Q|ZNF180_ENST00000592529.1_Silent_p.Q414Q	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	441					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				ACTTTCCACATTGATTGCATT	0.393													T|||	804	0.160543	0.1513	0.1729	5008	,	,		19777	0.002		0.338	False		,,,				2504	0.1452				p.Q441Q	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											ZNF180,caecum,carcinoma,0,1	ZNF180	103	1	0			c.A1323G						PASS	.	T		872,3534	333.6+/-303.0	88,696,1419	75.0	77.0	76.0		1323	-5.9	0.9	19	dbSNP_86	76	2776,5824	439.2+/-359.1	460,1856,1984	no	coding-synonymous	ZNF180	NM_013256.3		548,2552,3403	CC,CT,TT		32.2791,19.7912,28.0486		441/693	44981375	3648,9358	2203	4300	6503	SO:0001819	synonymous_variant	7733	exon5			TCCACATTGATTG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.1323A>G	19.37:g.44981375T>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	126	60	0.47619	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																			T|0.760;C|0.240	0.240	strong		0.393	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
PKLR	5313	hgsc.bcm.edu	37	1	155260383	155260383	+	Silent	SNP	G	G	T	rs1052176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155260383G>T	ENST00000342741.4	-	11	1743	c.1705C>A	c.(1705-1707)Cgg>Agg	p.R569R	PKLR_ENST00000392414.3_Silent_p.R538R	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	569			R -> Q (in PKRD; dbSNP:rs61755431). {ECO:0000269|PubMed:21794208}.		ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	CTTAGCACCCGCATGATGTTG	0.617													G|||	2196	0.438498	0.4879	0.3271	5008	,	,		16703	0.6895		0.2803	False		,,,				2504	0.3548				p.R569R		Atlas-SNP	.											.	PKLR	70	.	0			c.C1705A						PASS	.		,	2139,2267	578.7+/-384.7	529,1081,593	75.0	58.0	64.0		1705,1612	-0.0	1.0	1	dbSNP_86	64	2299,6301	387.1+/-342.1	315,1669,2316	no	coding-synonymous,coding-synonymous	PKLR	NM_000298.5,NM_181871.3	,	844,2750,2909	TT,TG,GG		26.7326,48.5474,34.1227	,	569/575,538/544	155260383	4438,8568	2203	4300	6503	SO:0001819	synonymous_variant	5313	exon11			GCACCCGCATGAT	BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.1705C>A	1.37:g.155260383G>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_000298	O75758|P11973	Silent	SNP	ENST00000342741.4	37	CCDS1109.1																																																																																			G|0.583;T|0.417	0.417	strong		0.617	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298	
SERPINA9	327657	hgsc.bcm.edu	37	14	94935901	94935901	+	Missense_Mutation	SNP	G	G	C	rs12879019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:94935901G>C	ENST00000380365.3	-	2	355	c.277C>G	c.(277-279)Cag>Gag	p.Q93E	SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000448305.2_Missense_Mutation_p.Q13E|SERPINA9_ENST00000298845.7_Intron|SERPINA9_ENST00000337425.5_Missense_Mutation_p.Q111E|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000546329.1_Missense_Mutation_p.Q75E			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	93				Q -> E (in Ref. 4; BAG62686). {ECO:0000305}.	negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TGGAGAATCTGGGTCTTGGTG	0.577													G|||	893	0.178315	0.0106	0.1787	5008	,	,		18172	0.3472		0.2356	False		,,,				2504	0.1718				p.Q111E		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C331G						PASS	.	G	,GLU/GLN	184,4086		4,176,1955	77.0	83.0	81.0		,331	4.1	1.0	14	dbSNP_121	81	1745,6787		192,1361,2713	yes	intron,missense	SERPINA9	NM_001042518.1,NM_175739.3	,29	196,1537,4668	CC,CG,GG		20.4524,4.3091,15.068	,benign	,111/436	94935901	1929,10873	2135	4266	6401	SO:0001583	missense	327657	exon2			GAATCTGGGTCTT	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.277C>G	14.37:g.94935901G>C	ENSP00000369723:p.Gln93Glu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		446	0.2042124542124542	7	0.014227642276422764	71	0.19613259668508287	192	0.3356643356643357	176	0.23218997361477572	G	10.76	1.441231	0.25900	0.043091	0.204524	ENSG00000170054	ENST00000448305;ENST00000337425;ENST00000380365;ENST00000546329	D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37	4.12	4.12	0.48240	Serpin domain (3);	0.110623	0.39341	U	0.001386	T	0.00012	0.0000	L	0.53780	1.695	0.29507	P	0.854496	P;P;P;P	0.48230	0.907;0.837;0.907;0.805	P;P;P;P	0.53593	0.664;0.669;0.517;0.73	T	0.51795	-0.8660	9	0.02654	T	1	.	13.3858	0.60795	0.0:0.1591:0.8409:0.0	rs12879019;rs17825566;rs52793329;rs12879019	75;93;13;111	Q86WD7-4;Q86WD7;Q86WD7-6;Q86WD7-7	.;SPA9_HUMAN;.;.	E	13;111;93;75	ENSP00000414092:Q13E;ENSP00000337133:Q111E;ENSP00000369723:Q93E;ENSP00000445476:Q75E	ENSP00000337133:Q111E	Q	-	1	0	SERPINA9	94005654	1.000000	0.71417	0.991000	0.47740	0.803000	0.45373	4.681000	0.61663	2.014000	0.59158	0.462000	0.41574	CAG	G|0.779;C|0.221	0.221	strong		0.577	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
PRAM1	84106	hgsc.bcm.edu	37	19	8564469	8564469	+	Missense_Mutation	SNP	C	C	G	rs371461475|rs4990821	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8564469C>G	ENST00000423345.4	-	2	743	c.223G>C	c.(223-225)Gag>Cag	p.E75Q	PRAM1_ENST00000255612.3_Missense_Mutation_p.E75Q			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	123	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						TCAGTGACCTCAGGCGGCGGG	0.642													C|||	1814	0.36222	0.6346	0.2968	5008	,	,		12296	0.1587		0.3062	False		,,,				2504	0.3078				p.E75Q		Atlas-SNP	.											.	PRAM1	53	.	0			c.G223C						PASS	.						41.0	53.0	49.0					19																	8564469		1849	4082	5931	SO:0001583	missense	84106	exon2			TGACCTCAGGCGG	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.223G>C	19.37:g.8564469C>G	ENSP00000408342:p.Glu75Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	61	22	0.360656	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	824	0.3772893772893773	382	0.7764227642276422	110	0.30386740331491713	82	0.14335664335664336	250	0.32981530343007914	c	8.200	0.797994	0.16327	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.14144	2.53;2.53	3.74	-1.55	0.08558	.	2.531360	0.02280	N	0.069320	T	0.00012	0.0000	L	0.41824	1.3	0.80722	P	0.0	B;B	0.33940	0.433;0.433	B;B	0.27887	0.084;0.084	T	0.36065	-0.9763	9	0.24483	T	0.36	.	6.2323	0.20742	0.0:0.3333:0.4737:0.193	rs4990821	75;123	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	Q	75	ENSP00000255612:E75Q;ENSP00000408342:E75Q	ENSP00000255612:E75Q	E	-	1	0	PRAM1	8470469	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.203000	0.09438	-0.252000	0.09528	-0.187000	0.12897	GAG	C|0.656;G|0.344	0.344	strong		0.642	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
MKL1	57591	hgsc.bcm.edu	37	22	40814636	40814636	+	Silent	SNP	C	C	T	rs4821944	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:40814636C>T	ENST00000355630.3	-	12	2396	c.1806G>A	c.(1804-1806)gcG>gcA	p.A602A	MKL1_ENST00000402042.1_Silent_p.A552A|MKL1_ENST00000407029.1_Silent_p.A602A|MKL1_ENST00000396617.3_Silent_p.A602A	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	602	Pro-rich.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						TGGCTGGGGCCGCCAGGCTGG	0.701			T	RBM15	acute megakaryocytic leukemia								C|||	983	0.196286	0.1324	0.1988	5008	,	,		10064	0.0099		0.3052	False		,,,				2504	0.3609				p.A602A		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1	69	.	0			c.G1806A						PASS	.	C		645,3593		64,517,1538	7.0	10.0	9.0		1806	-9.1	0.0	22	dbSNP_111	9	2472,5952		376,1720,2116	no	coding-synonymous	MKL1	NM_020831.3		440,2237,3654	TT,TC,CC		29.3447,15.2194,24.617		602/932	40814636	3117,9545	2119	4212	6331	SO:0001819	synonymous_variant	57591	exon12			TGGGGCCGCCAGG	AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.1806G>A	22.37:g.40814636C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Silent	SNP	ENST00000355630.3	37	CCDS14003.1																																																																																			C|0.829;T|0.171	0.171	strong		0.701	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831	
TTLL4	9654	hgsc.bcm.edu	37	2	219602499	219602499	+	Missense_Mutation	SNP	G	G	C	rs3731877	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219602499G>C	ENST00000392102.1	+	3	440	c.100G>C	c.(100-102)Gag>Cag	p.E34Q	TTLL4_ENST00000442769.1_Missense_Mutation_p.E34Q|TTLL4_ENST00000457313.1_Intron|TTLL4_ENST00000258398.4_Missense_Mutation_p.E34Q	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	34			E -> Q (in dbSNP:rs3731877). {ECO:0000269|PubMed:8724849}.		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)		CACGCCACCTGAGAAACCCTC	0.557													G|||	2020	0.403355	0.6006	0.4222	5008	,	,		19525	0.1409		0.4662	False		,,,				2504	0.3292				p.E34Q	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											TTLL4,brain,glioma,0,1	TTLL4	96	1	0			c.G100C						PASS	.	G	GLN/GLU	2578,1828	637.9+/-396.8	756,1066,381	65.0	67.0	66.0		100	5.5	1.0	2	dbSNP_107	66	4082,4518	561.4+/-387.8	987,2108,1205	yes	missense	TTLL4	NM_014640.4	29	1743,3174,1586	CC,CG,GG		47.4651,41.4889,48.7929	probably-damaging	34/1200	219602499	6660,6346	2203	4300	6503	SO:0001583	missense	9654	exon3			CCACCTGAGAAAC		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.100G>C	2.37:g.219602499G>C	ENSP00000375951:p.Glu34Gln	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	136	71	0.522059	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	910	0.4166666666666667	317	0.6443089430894309	151	0.4171270718232044	90	0.15734265734265734	352	0.46437994722955145	G	15.17	2.754812	0.49362	0.585111	0.474651	ENSG00000135912	ENST00000415717;ENST00000392102;ENST00000437755;ENST00000442769;ENST00000424644;ENST00000258398	T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75	5.53	5.53	0.82687	.	0.114147	0.39475	N	0.001342	T	0.00012	0.0000	L	0.34521	1.04	0.39370	P	0.03393400000000002	P;P	0.37330	0.59;0.59	B;B	0.33196	0.159;0.159	T	0.28808	-1.0032	9	0.66056	D	0.02	.	13.9947	0.64390	0.0:0.151:0.849:0.0	rs3731877;rs52824369;rs3731877	34;34	E7EX20;Q14679	.;TTLL4_HUMAN	Q	34	ENSP00000411228:E34Q;ENSP00000375951:E34Q;ENSP00000391342:E34Q;ENSP00000396555:E34Q;ENSP00000405485:E34Q;ENSP00000258398:E34Q	ENSP00000258398:E34Q	E	+	1	0	TTLL4	219310743	0.985000	0.35326	0.992000	0.48379	0.444000	0.32077	3.127000	0.50484	2.601000	0.87937	0.563000	0.77884	GAG	G|0.525;C|0.475	0.475	strong		0.557	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
UBR7	55148	hgsc.bcm.edu	37	14	93673655	93673655	+	Missense_Mutation	SNP	G	G	A	rs2286653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93673655G>A	ENST00000013070.6	+	1	255	c.19G>A	c.(19-21)Gcc>Acc	p.A7T	UBR7_ENST00000416753.1_5'UTR|RP11-371E8.4_ENST00000557574.1_Intron|RP11-371E8.4_ENST00000557048.1_Intron|C14orf142_ENST00000306954.4_5'Flank	NM_175748.3	NP_786924.2	Q8N806	UBR7_HUMAN	ubiquitin protein ligase E3 component n-recognin 7 (putative)	7							ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(2)|lung(12)|urinary_tract(1)	19						AGCCGAGGGCGCCGCTGGGCG	0.711											OREG0022885	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	567	0.113219	0.1649	0.1239	5008	,	,		14192	0.1022		0.0755	False		,,,				2504	0.0859				p.A7T		Atlas-SNP	.											.	UBR7	36	.	0			c.G19A						PASS	.	G	THR/ALA	646,3664		45,556,1554	29.0	24.0	26.0		19	-10.4	0.0	14	dbSNP_100	26	644,7820		32,580,3620	yes	missense	UBR7	NM_175748.3	58	77,1136,5174	AA,AG,GG		7.6087,14.9884,10.0986	benign	7/426	93673655	1290,11484	2155	4232	6387	SO:0001583	missense	55148	exon1			GAGGGCGCCGCTG	AK001345	CCDS9909.1	14q32.12	2008-06-23	2008-06-23	2008-06-23		ENSG00000012963		"""Ubiquitin protein ligase E3 component n-recognins"""	20344	protein-coding gene	gene with protein product		613816	"""chromosome 14 open reading frame 130"""	C14orf130		18162545	Standard	NM_175748		Approved		uc001ybm.4	Q8N806		ENST00000013070.6:c.19G>A	14.37:g.93673655G>A	ENSP00000013070:p.Ala7Thr	Somatic	35	0	0	1299	WXS	Illumina HiSeq	Phase_I	77	50	0.649351	NM_175748	Q86U21|Q86UA9|Q96BY0|Q9NVV6	Missense_Mutation	SNP	ENST00000013070.6	37	CCDS9909.1	223|223	0.1021062271062271|0.1021062271062271	72|72	0.14634146341463414|0.14634146341463414	39|39	0.10773480662983426|0.10773480662983426	53|53	0.09265734265734266|0.09265734265734266	59|59	0.07783641160949868|0.07783641160949868	G|G	12.28|12.28	1.891509|1.891509	0.33442|0.33442	0.149884|0.149884	0.076087|0.076087	ENSG00000012963|ENSG00000012963	ENST00000013070;ENST00000554232;ENST00000556871|ENST00000555113	T;T;T|.	0.80566|.	-1.39;-1.39;-1.39|.	5.19|5.19	-10.4|-10.4	0.00318|0.00318	.|.	2.178760|.	0.01514|.	N|.	0.018052|.	T|T	0.00073|0.00073	0.0002|0.0002	N|N	0.08118|0.08118	0|0	0.51482|0.51482	P|P	7.199999999996098E-5|7.199999999996098E-5	B|.	0.24426|.	0.103|.	B|.	0.14023|.	0.01|.	T|T	0.15492|0.15492	-1.0435|-1.0435	9|4	0.11794|.	T|.	0.64|.	-0.0587|-0.0587	8.7543|8.7543	0.34637|0.34637	0.0758:0.1653:0.5791:0.1797|0.0758:0.1653:0.5791:0.1797	rs2286653|rs2286653	7|.	Q8N806|.	UBR7_HUMAN|.	T|H	7|6	ENSP00000013070:A7T;ENSP00000450645:A7T;ENSP00000451022:A7T|.	ENSP00000013070:A7T|.	A|R	+|+	1|2	0|0	UBR7|UBR7	92743408|92743408	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.115000|0.115000	0.19883|0.19883	-1.215000|-1.215000	0.02985|0.02985	-2.311000|-2.311000	0.00649|0.00649	-1.527000|-1.527000	0.00925|0.00925	GCC|CGC	G|0.886;A|0.114	0.114	strong		0.711	UBR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412693.1	NM_175748	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T	rs10107826|rs374790272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22960654C>T	ENST00000356864.3	+	1	552	c.20C>T	c.(19-21)aCc>aTc	p.T7I	TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR|TNFRSF10C_ENST00000397703.2_Missense_Mutation_p.T47I	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		ATCCCCAAGACCCTAAAGTTC	0.711													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14783	0.0		0.004	False		,,,				2504	0.0				p.T7I		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C20T						PASS	.	C	ILE/THR	443,3961	170.9+/-201.2	25,393,1784	79.0	59.0	66.0		20	0.6	0.0	8	dbSNP_119	66	12,8584	5.7+/-21.5	0,12,4286	yes	missense	TNFRSF10C	NM_003841.3	89	25,405,6070	TT,TC,CC		0.1396,10.059,3.5	probably-damaging	7/260	22960654	455,12545	2202	4298	6500	SO:0001583	missense	8794	exon1			CCAAGACCCTAAA	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.20C>T	8.37:g.22960654C>T	ENSP00000349324:p.Thr7Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	56	0.02564102564102564	50	0.1016260162601626	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	4.995	0.184796	0.09495	0.10059	0.001396	ENSG00000173535	ENST00000397703;ENST00000356864;ENST00000544885	T	0.62364	0.03	1.76	0.639	0.17747	.	2.630870	0.02547	U	0.095275	T	0.01627	0.0052	N	0.19112	0.55	0.52099	P	5.100000000002325E-5	B	0.21225	0.053	B	0.06405	0.002	T	0.08186	-1.0734	9	0.52906	T	0.07	.	4.4054	0.11407	0.0:0.717:0.0:0.283	rs10107826;rs10107826	7	O14798	TR10C_HUMAN	I	47;7;7	ENSP00000349324:T7I	ENSP00000349324:T7I	T	+	2	0	TNFRSF10C	23016599	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.737000	0.04877	-0.010000	0.14271	0.205000	0.17691	ACC	C|0.958;T|0.042	0.042	strong		0.711	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
OR10H2	26538	hgsc.bcm.edu	37	19	15839174	15839174	+	Silent	SNP	C	C	T	rs2285956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15839174C>T	ENST00000305899.3	+	1	341	c.321C>T	c.(319-321)ttC>ttT	p.F107F		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	107						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)					CCTTCAGCTTCGGCTTCACCC	0.642																																					p.F107F		Atlas-SNP	.											.	OR10H2	59	.	0			c.C321T						PASS	.						60.0	56.0	58.0					19																	15839174		2202	4277	6479	SO:0001819	synonymous_variant	26538	exon1			CAGCTTCGGCTTC	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.321C>T	19.37:g.15839174C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	250	110	0.44	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			T|1.000;|0.000	1.000	weak		0.642	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
XRN1	54464	hgsc.bcm.edu	37	3	142078759	142078759	+	Missense_Mutation	SNP	C	C	T	rs73238159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142078759C>T	ENST00000264951.4	-	30	3526	c.3409G>A	c.(3409-3411)Gat>Aat	p.D1137N	XRN1_ENST00000392981.2_Missense_Mutation_p.D1137N	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1137					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						AATAGTACATCGGCTTCTCTA	0.318													C|||	417	0.0832668	0.0303	0.0821	5008	,	,		16090	0.0952		0.1451	False		,,,				2504	0.0798				p.D1137N		Atlas-SNP	.											.	XRN1	138	.	0			c.G3409A						PASS	.	C	ASN/ASP,ASN/ASP	206,4200	126.6+/-163.6	4,198,2001	69.0	71.0	70.0		3409,3409	5.5	1.0	3	dbSNP_130	70	1151,7447	233.7+/-266.9	75,1001,3223	yes	missense,missense	XRN1	NM_001042604.1,NM_019001.3	23,23	79,1199,5224	TT,TC,CC		13.3868,4.6754,10.4353	benign,benign	1137/1694,1137/1707	142078759	1357,11647	2203	4299	6502	SO:0001583	missense	54464	exon30			GTACATCGGCTTC	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.3409G>A	3.37:g.142078759C>T	ENSP00000264951:p.Asp1137Asn	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	219	0.10027472527472528	14	0.028455284552845527	30	0.08287292817679558	64	0.11188811188811189	111	0.14643799472295516	C	28.2	4.902564	0.92035	0.046754	0.133868	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.33216	1.42;1.42	5.51	5.51	0.81932	.	0.056674	0.64402	D	0.000001	T	0.00271	0.0008	L	0.61036	1.89	0.09310	P	1.0	P;P	0.52170	0.951;0.919	P;B	0.46940	0.532;0.332	T	0.00185	-1.1943	9	0.42905	T	0.14	-17.9298	19.427	0.94746	0.0:1.0:0.0:0.0	.	1137;1137	Q8IZH2-2;Q8IZH2	.;XRN1_HUMAN	N	1137	ENSP00000264951:D1137N;ENSP00000376707:D1137N	ENSP00000264951:D1137N	D	-	1	0	XRN1	143561449	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.656000	0.74396	2.573000	0.86826	0.655000	0.94253	GAT	C|0.901;T|0.099	0.099	strong		0.318	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
TRIML1	339976	hgsc.bcm.edu	37	4	189061036	189061036	+	Silent	SNP	C	C	T	rs76826594	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:189061036C>T	ENST00000332517.3	+	1	464	c.324C>T	c.(322-324)gaC>gaT	p.D108D	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	108					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		TCTCCGATGACGAGCAGGGTG	0.627													C|||	550	0.109824	0.0772	0.1167	5008	,	,		18564	0.0437		0.2227	False		,,,				2504	0.1012				p.D108D	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											TRIML1,NS,carcinoma,+1,1	TRIML1	126	1	0			c.C324T						PASS	.	C		418,3988	202.8+/-225.5	26,366,1811	45.0	43.0	43.0		324	-10.1	0.0	4	dbSNP_131	43	1823,6777	322.8+/-315.7	194,1435,2671	no	coding-synonymous	TRIML1	NM_178556.3		220,1801,4482	TT,TC,CC		21.1977,9.4871,17.2305		108/469	189061036	2241,10765	2203	4300	6503	SO:0001819	synonymous_variant	339976	exon1			CGATGACGAGCAG	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.324C>T	4.37:g.189061036C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	160	86	0.5375	NM_178556	Q96BE5	Silent	SNP	ENST00000332517.3	37	CCDS3851.1																																																																																			C|0.830;T|0.170	0.170	strong		0.627	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
LBR	3930	hgsc.bcm.edu	37	1	225603029	225603029	+	Silent	SNP	T	T	C	rs61749339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:225603029T>C	ENST00000338179.2	-	7	968	c.843A>G	c.(841-843)gtA>gtG	p.V281V	LBR_ENST00000487054.1_5'Flank|LBR_ENST00000272163.4_Silent_p.V281V	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	281					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		GCGTTCCTTCTACAACCTTAA	0.269													T|||	28	0.00559105	0.0	0.0058	5008	,	,		18270	0.0		0.0169	False		,,,				2504	0.0072				p.V281V		Atlas-SNP	.											.	LBR	54	.	0			c.A843G						PASS	.	T	,	10,4374		0,10,2182	32.0	32.0	32.0		843,843	0.4	1.0	1	dbSNP_129	32	138,8426		1,136,4145	no	coding-synonymous,coding-synonymous	LBR	NM_002296.3,NM_194442.2	,	1,146,6327	CC,CT,TT		1.6114,0.2281,1.143	,	281/616,281/616	225603029	148,12800	2192	4282	6474	SO:0001819	synonymous_variant	3930	exon7			TCCTTCTACAACC	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"""Tudor domain containing"""	6518	protein-coding gene	gene with protein product	"""tudor domain containing 18"""	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.843A>G	1.37:g.225603029T>C		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	177	82	0.463277	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Silent	SNP	ENST00000338179.2	37	CCDS1545.1																																																																																			T|0.991;C|0.009	0.009	strong		0.269	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296	
ARNT2	9915	hgsc.bcm.edu	37	15	80884025	80884025	+	Missense_Mutation	SNP	G	G	A	rs4072568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:80884025G>A	ENST00000303329.4	+	18	2200	c.2035G>A	c.(2035-2037)Ggt>Agt	p.G679S	ARNT2_ENST00000533983.1_Missense_Mutation_p.G668S|ARNT2_ENST00000527771.1_Missense_Mutation_p.G668S	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	679			G -> S (in dbSNP:rs4072568). {ECO:0000269|PubMed:9205841}.		central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			CCAGCAGCCCGGTCAGACTGA	0.637													G|||	561	0.112021	0.1377	0.1066	5008	,	,		18357	0.003		0.166	False		,,,				2504	0.138				p.G679S		Atlas-SNP	.											ARNT2,NS,carcinoma,-1,1	ARNT2	88	1	0			c.G2035A						PASS	.	G	SER/GLY	602,3804	263.8+/-265.7	33,536,1634	111.0	107.0	108.0		2035	1.7	1.0	15	dbSNP_108	108	1684,6916	309.4+/-309.4	182,1320,2798	yes	missense	ARNT2	NM_014862.3	56	215,1856,4432	AA,AG,GG		19.5814,13.6632,17.5765	benign	679/718	80884025	2286,10720	2203	4300	6503	SO:0001583	missense	9915	exon18			CAGCCCGGTCAGA	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"""Basic helix-loop-helix proteins"""	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.2035G>A	15.37:g.80884025G>A	ENSP00000307479:p.Gly679Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	105	36	0.342857	NM_014862	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	239	0.10943223443223443	72	0.14634146341463414	45	0.12430939226519337	0	0.0	122	0.16094986807387862	G	10.84	1.462974	0.26248	0.136632	0.195814	ENSG00000172379	ENST00000360062;ENST00000303329	T	0.03920	3.76	5.07	1.74	0.24563	.	0.276124	0.39274	N	0.001420	T	0.00012	0.0000	N	0.02011	-0.69	0.35400	P	0.20852800000000005	B	0.06786	0.001	B	0.06405	0.002	T	0.46992	-0.9151	9	0.11794	T	0.64	.	6.8547	0.24034	0.4281:0.0:0.5719:0.0	rs4072568;rs17608916;rs52827902;rs56876472;rs4072568	679	Q9HBZ2	ARNT2_HUMAN	S	668;679	ENSP00000307479:G679S	ENSP00000307479:G679S	G	+	1	0	ARNT2	78671080	1.000000	0.71417	0.976000	0.42696	0.991000	0.79684	2.649000	0.46656	0.533000	0.28675	0.313000	0.20887	GGT	G|0.856;A|0.144	0.144	strong		0.637	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
PDDC1	347862	hgsc.bcm.edu	37	11	771034	771034	+	Silent	SNP	A	A	G	rs7930569	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:771034A>G	ENST00000319863.8	-	7	636	c.615T>C	c.(613-615)acT>acC	p.T205T	PDDC1_ENST00000442059.2_Silent_p.T155T|PDDC1_ENST00000397472.2_Intron|PDDC1_ENST00000526325.1_Intron|PDDC1_ENST00000529966.1_5'UTR|PDDC1_ENST00000524550.1_Silent_p.T169T	NM_182612.2	NP_872418.1	Q8NB37	PDDC1_HUMAN	Parkinson disease 7 domain containing 1	205						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(3)|urinary_tract(1)	5		all_cancers(49;1.13e-08)|all_epithelial(84;2.95e-05)|Breast(177;0.000286)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.159)|all_lung(207;0.198)		all cancers(45;3.66e-26)|Epithelial(43;2.43e-25)|OV - Ovarian serous cystadenocarcinoma(40;1.33e-19)|BRCA - Breast invasive adenocarcinoma(625;4.29e-05)|Lung(200;0.0582)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGGCCGGGACAGTGGAGCTGG	0.657													a|||	2166	0.432508	0.3064	0.6037	5008	,	,		15794	0.5605		0.4433	False		,,,				2504	0.3384				p.T205T		Atlas-SNP	.											.	PDDC1	16	.	0			c.T615C						PASS	.	A		1507,2897	469.0+/-355.3	269,969,964	54.0	53.0	53.0		615	-9.1	0.1	11	dbSNP_116	53	4227,4373	563.8+/-388.2	1042,2143,1115	no	coding-synonymous	PDDC1	NM_182612.2		1311,3112,2079	GG,GA,AA		49.1512,34.2189,44.0941		205/221	771034	5734,7270	2202	4300	6502	SO:0001819	synonymous_variant	347862	exon7			CGGGACAGTGGAG	AK128653	CCDS7713.1	11p15.5	2005-10-26			ENSG00000177225	ENSG00000177225			26616	protein-coding gene	gene with protein product							Standard	XM_005252898		Approved	FLJ34283	uc001lrc.3	Q8NB37	OTTHUMG00000133315	ENST00000319863.8:c.615T>C	11.37:g.771034A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_182612	B7ZKW5|Q2NL76|Q6ZQY0|Q8NAE0	Silent	SNP	ENST00000319863.8	37	CCDS7713.1	1074	0.49175824175824173	157	0.31910569105691056	210	0.580110497237569	363	0.6346153846153846	344	0.45382585751978893	A	7.217	0.596652	0.13875	0.342189	0.491512	ENSG00000177225	ENST00000465313	.	.	.	4.55	-9.09	0.00717	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999833531	.	.	.	.	.	.	T	0.34875	-0.9811	3	.	.	.	.	4.568	0.12196	0.2365:0.0898:0.4958:0.1779	rs7930569;rs58747471;rs7930569	.	.	.	R	56	.	.	C	-	1	0	PDDC1	761034	0.000000	0.05858	0.114000	0.21550	0.679000	0.39708	-1.347000	0.02632	-2.024000	0.00936	-0.464000	0.05259	TGT	A|0.556;G|0.444	0.444	strong		0.657	PDDC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258051.2	NM_182612	
ITIH5	80760	hgsc.bcm.edu	37	10	7679393	7679393	+	Silent	SNP	C	C	T	rs6602256	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:7679393C>T	ENST00000256861.6	-	5	528	c.450G>A	c.(448-450)aaG>aaA	p.K150K	ITIH5_ENST00000397145.2_Silent_p.K150K|ITIH5_ENST00000397146.2_Silent_p.K150K|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000446830.2_5'UTR	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	150	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						CGGCTTTGTCCTTGCTGGGAA	0.557													C|||	2248	0.448882	0.6089	0.2233	5008	,	,		18914	0.4623		0.3121	False		,,,				2504	0.5194				p.K150K		Atlas-SNP	.											.	ITIH5	343	.	0			c.G450A						PASS	.	C	,	2491,1915	625.8+/-394.6	702,1087,414	65.0	72.0	70.0		450,450	3.9	1.0	10	dbSNP_116	70	2694,5906	432.1+/-357.0	428,1838,2034	no	coding-synonymous,coding-synonymous	ITIH5	NM_001001851.2,NM_030569.6	,	1130,2925,2448	TT,TC,CC		31.3256,43.4635,39.8662	,	150/703,150/943	7679393	5185,7821	2203	4300	6503	SO:0001819	synonymous_variant	80760	exon5			TTTGTCCTTGCTG			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.450G>A	10.37:g.7679393C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				C|0.587;T|0.413	0.413	strong		0.557	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
SYMPK	8189	hgsc.bcm.edu	37	19	46341824	46341824	+	Silent	SNP	C	C	T	rs17850110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46341824C>T	ENST00000245934.7	-	10	1381	c.1137G>A	c.(1135-1137)ccG>ccA	p.P379P		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	379					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		AGGTCCCCGACGGGCCTGGCT	0.592													T|||	726	0.144968	0.1074	0.2334	5008	,	,		18331	0.0952		0.1571	False		,,,				2504	0.1718				p.P379P		Atlas-SNP	.											.	SYMPK	104	.	0			c.G1137A						PASS	.	T		476,3930	782.3+/-414.6	26,424,1753	66.0	58.0	60.0		1137	-11.7	0.0	19	dbSNP_123	60	1271,7329	759.8+/-407.6	98,1075,3127	no	coding-synonymous	SYMPK	NM_004819.2		124,1499,4880	TT,TC,CC		14.7791,10.8034,13.4323		379/1275	46341824	1747,11259	2203	4300	6503	SO:0001819	synonymous_variant	8189	exon10			CCCCGACGGGCCT	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.1137G>A	19.37:g.46341824C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			C|0.873;G|0.000;T|0.127	0.127	strong		0.592	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
FAM129A	116496	hgsc.bcm.edu	37	1	184765072	184765072	+	Missense_Mutation	SNP	A	A	G	rs28927681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:184765072A>G	ENST00000367511.3	-	14	2019	c.1826T>C	c.(1825-1827)cTg>cCg	p.L609P	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	609				L -> P (in Ref. 7; BAB84965). {ECO:0000305}.	negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CTCACTACCCAGAACTCCTGG	0.547													a|||	1011	0.201877	0.5477	0.0908	5008	,	,		18374	0.0823		0.0825	False		,,,				2504	0.0593				p.L609P		Atlas-SNP	.											FAM129A,NS,carcinoma,-1,2	FAM129A	98	2	0			c.T1826C						PASS	.	G	PRO/LEU	2016,2390	533.1+/-373.6	468,1080,655	63.0	69.0	67.0		1826	-3.5	0.0	1	dbSNP_125	67	625,7975	156.6+/-210.4	22,581,3697	yes	missense	FAM129A	NM_052966.2	98	490,1661,4352	GG,GA,AA		7.2674,45.7558,20.306	benign	609/929	184765072	2641,10365	2203	4300	6503	SO:0001583	missense	116496	exon14			CTACCCAGAACTC	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.1826T>C	1.37:g.184765072A>G	ENSP00000356481:p.Leu609Pro	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	395	0.18086080586080586	257	0.5223577235772358	37	0.10220994475138122	41	0.07167832167832168	60	0.079155672823219	a	7.583	0.669083	0.14776	0.457558	0.072674	ENSG00000135842	ENST00000367511	T	0.09911	2.93	5.67	-3.55	0.04639	.	2.968870	0.00698	N	0.000769	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.46803	-0.9165	9	0.07325	T	0.83	3.6762	14.2079	0.65746	0.6039:0.0:0.3961:0.0	rs28927681;rs56623820;rs28927681	609	Q9BZQ8	NIBAN_HUMAN	P	609	ENSP00000356481:L609P	ENSP00000356481:L609P	L	-	2	0	FAM129A	183031695	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.348000	0.07740	-1.574000	0.01657	-2.676000	0.00143	CTG	G|0.177;A|0.823	0.177	strong		0.547	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
KRTAP5-3	387266	hgsc.bcm.edu	37	11	1628948	1628948	+	Missense_Mutation	SNP	G	G	A	rs117085626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1628948G>A	ENST00000399685.1	-	1	745	c.668C>T	c.(667-669)tCc>tTc	p.S223F		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	223	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		GGACTGGGAGGAGCAGGGCTT	0.602													g|||	312	0.0623003	0.0061	0.1138	5008	,	,		19294	0.002		0.1352	False		,,,				2504	0.089				p.S223F		Atlas-SNP	.											.	KRTAP5-3	33	.	0			c.C668T						PASS	.	G	PHE/SER	122,4282	89.7+/-128.4	4,114,2084	157.0	162.0	160.0		668	2.1	0.6	11	dbSNP_132	160	1066,7532	224.5+/-260.9	64,938,3297	no	missense	KRTAP5-3	NM_001012708.2	155	68,1052,5381	AA,AG,GG		12.3982,2.7702,9.1371	possibly-damaging	223/239	1628948	1188,11814	2202	4299	6501	SO:0001583	missense	387266	exon1			TGGGAGGAGCAGG	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"""Keratin associated proteins"""	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.668C>T	11.37:g.1628948G>A	ENSP00000382592:p.Ser223Phe	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	118	56	0.474576	NM_001012708	Q6PL44|Q701N3	Missense_Mutation	SNP	ENST00000399685.1	37	CCDS41591.1	147	0.0673076923076923	3	0.006097560975609756	51	0.1408839779005525	0	0.0	93	0.12269129287598944	G	4.922	0.171317	0.09391	0.027702	0.123982	ENSG00000196224	ENST00000399685	T	0.00995	5.46	3.02	2.1	0.27182	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.41921	P	0.00948300000000002	P	0.36249	0.545	B	0.35607	0.206	T	0.54629	-0.8265	8	0.56958	D	0.05	.	10.0527	0.42225	0.0:0.7914:0.2086:0.0	.	223	Q6L8H2	KRA53_HUMAN	F	223	ENSP00000382592:S223F	ENSP00000382592:S223F	S	-	2	0	KRTAP5-3	1585524	0.997000	0.39634	0.623000	0.29173	0.119000	0.20118	0.255000	0.18333	0.608000	0.30000	-0.748000	0.03510	TCC	G|0.917;A|0.083	0.083	strong		0.602	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
OR51A2	401667	hgsc.bcm.edu	37	11	4976077	4976077	+	Missense_Mutation	SNP	T	T	G	rs2570573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4976077T>G	ENST00000380371.1	-	1	866	c.867A>C	c.(865-867)aaA>aaC	p.K289N	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	289			K -> N (in dbSNP:rs2570573).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(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)		AAACAATTGGTTTCATCAGCG	0.418																																					p.K289N		Atlas-SNP	.											OR51A2,NS,carcinoma,-2,1	OR51A2	40	1	0			c.A867C						scavenged	.		ASN/LYS	597,3473		223,151,1661	84.0	67.0	73.0		867	-4.2	0.9	11	dbSNP_100	73	1533,5907		543,447,2730	yes	missense	OR51A2	NM_001004748.1	94	766,598,4391	GG,GT,TT		20.6048,14.6683,18.5056	benign	289/314	4976077	2130,9380	2035	3720	5755	SO:0001583	missense	401667	exon1			AATTGGTTTCATC	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.867A>C	11.37:g.4976077T>G	ENSP00000369729:p.Lys289Asn	Somatic	7	7	1		WXS	Illumina HiSeq	Phase_I	40	39	0.975	NM_001004748		Missense_Mutation	SNP	ENST00000380371.1	37	CCDS31368.1	.	.	.	.	.	.	.	.	.	.	-	0.004	-2.278436	0.00254	0.146683	0.206048	ENSG00000205496	ENST00000380371	T	0.49139	0.79	3.45	-4.21	0.03812	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00000	-4.29	0.49389	P	2.1099999999996122E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.39482	-0.9612	8	0.02654	T	1	.	9.3539	0.38155	0.2085:0.0:0.6632:0.1283	rs2570573;rs2959192;rs61436556;rs2570573	289	Q8NGJ7	O51A2_HUMAN	N	289	ENSP00000369729:K289N	ENSP00000369729:K289N	K	-	3	2	OR51A2	4932653	0.112000	0.22096	0.886000	0.34754	0.012000	0.07955	-0.640000	0.05440	-1.567000	0.01671	-1.260000	0.01463	AAA	T|0.952;G|0.048	0.048	strong		0.418	OR51A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142809.1	NM_001004748	
GABBR1	2550	hgsc.bcm.edu	37	6	29581110	29581110	+	Silent	SNP	A	A	G	rs17854217	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29581110A>G	ENST00000377034.4	-	12	1811	c.1476T>C	c.(1474-1476)ggT>ggC	p.G492G	GABBR1_ENST00000355973.3_Silent_p.G375G|GABBR1_ENST00000377012.4_Silent_p.G375G|GABBR1_ENST00000377016.4_Silent_p.G430G|GABBR1_ENST00000376977.3_Silent_p.G492G	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	492					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CCAGGCGCACACCAGAACGGC	0.557													G|||	529	0.105631	0.0946	0.0807	5008	,	,		17545	0.12		0.0974	False		,,,				2504	0.1319				p.G492G		Atlas-SNP	.											.	GABBR1	95	.	0			c.T1476C						PASS	.	G	,,	272,2750		10,252,1249	106.0	116.0	112.0		1476,1125,1290	-11.7	0.1	6	dbSNP_123	112	561,4855		35,491,2182	no	coding-synonymous,coding-synonymous,coding-synonymous	GABBR1	NM_001470.2,NM_021903.2,NM_021904.2	,,	45,743,3431	GG,GA,AA		10.3582,9.0007,9.872	,,	492/962,375/845,430/900	29581110	833,7605	1511	2708	4219	SO:0001819	synonymous_variant	2550	exon12			GCGCACACCAGAA	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4070	protein-coding gene	gene with protein product	"""GABA-B receptor"""	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1476T>C	6.37:g.29581110A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1																																																																																			A|0.902;G|0.098	0.098	strong		0.557	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3		
NCAPH	23397	hgsc.bcm.edu	37	2	97020049	97020049	+	Silent	SNP	T	T	C	rs3731935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:97020049T>C	ENST00000240423.4	+	9	1174	c.1131T>C	c.(1129-1131)gaT>gaC	p.D377D	NCAPH_ENST00000427946.1_Silent_p.D241D|NCAPH_ENST00000455200.1_Silent_p.D366D	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	377					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.D377D(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				ATGCCAACGATGAACCTGACC	0.532													T|||	1398	0.279153	0.0416	0.2334	5008	,	,		14804	0.2232		0.2763	False		,,,				2504	0.6933				p.D377D		Atlas-SNP	.											NCAPH,NS,carcinoma,+2,2	NCAPH	67	2	1	Substitution - coding silent(1)	stomach(1)	c.T1131C						PASS	.	T		351,4055	181.5+/-209.5	10,331,1862	149.0	144.0	145.0		1131	1.9	0.6	2	dbSNP_107	145	2470,6130	406.5+/-348.9	363,1744,2193	no	coding-synonymous	NCAPH	NM_015341.3		373,2075,4055	CC,CT,TT		28.7209,7.9664,21.69		377/742	97020049	2821,10185	2203	4300	6503	SO:0001819	synonymous_variant	23397	exon9			CAACGATGAACCT	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"""barren (Drosophila) homolog"", ""barren homolog (Drosophila)"", ""barren homolog 1 (Drosophila)"""	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.1131T>C	2.37:g.97020049T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_015341	B4E189|Q8TB87	Silent	SNP	ENST00000240423.4	37	CCDS2021.1																																																																																			T|0.781;C|0.219	0.219	strong		0.532	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341	
ABAT	18	hgsc.bcm.edu	37	16	8844389	8844389	+	Silent	SNP	C	C	T	rs2229157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:8844389C>T	ENST00000396600.2	+	5	1247	c.309C>T	c.(307-309)gtC>gtT	p.V103V	ABAT_ENST00000268251.8_Silent_p.V103V|ABAT_ENST00000569156.1_Silent_p.V103V|ABAT_ENST00000425191.2_Silent_p.V103V|ABAT_ENST00000567812.1_Silent_p.V118V	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	103					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	TCTCCTCTGTCCCCATAGGTA	0.478													C|||	525	0.104832	0.0303	0.0994	5008	,	,		20366	0.1756		0.1034	False		,,,				2504	0.138				p.V103V		Atlas-SNP	.											.	ABAT	46	.	0			c.C309T						PASS	.	C	,,	200,4194	122.5+/-159.9	5,190,2002	173.0	158.0	163.0		309,309,309	-1.8	1.0	16	dbSNP_127	163	968,7632	206.3+/-248.5	51,866,3383	no	coding-synonymous,coding-synonymous,coding-synonymous	ABAT	NM_000663.4,NM_001127448.1,NM_020686.5	,,	56,1056,5385	TT,TC,CC		11.2558,4.5517,8.9888	,,	103/501,103/501,103/501	8844389	1168,11826	2197	4300	6497	SO:0001819	synonymous_variant	18	exon5			CTCTGTCCCCATA	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"""4-aminobutyrate transaminase"""	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.309C>T	16.37:g.8844389C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Silent	SNP	ENST00000396600.2	37	CCDS10534.1																																																																																			C|0.901;T|0.099	0.099	strong		0.478	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686	
BRWD1	54014	hgsc.bcm.edu	37	21	40652142	40652142	+	Silent	SNP	G	G	A	rs2836972	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:40652142G>A	ENST00000333229.2	-	9	1191	c.864C>T	c.(862-864)taC>taT	p.Y288Y	BRWD1_ENST00000380800.3_Silent_p.Y288Y|BRWD1_ENST00000342449.3_Silent_p.Y288Y	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	288					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TGGAAACCATGTATCTTTGAG	0.358													G|||	1077	0.215056	0.3003	0.2176	5008	,	,		17091	0.0367		0.3171	False		,,,				2504	0.1769				p.Y288Y	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											BRWD1_ENST00000333229,NS,carcinoma,0,2	BRWD1	325	2	0			c.C864T						PASS	.	G	,	1337,3069	446.1+/-347.9	176,985,1042	80.0	75.0	77.0		864,864	4.5	1.0	21	dbSNP_100	77	2995,5605	462.1+/-365.6	527,1941,1832	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	703,2926,2874	AA,AG,GG		34.8256,30.345,33.3077	,	288/2321,288/2270	40652142	4332,8674	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon9			AACCATGTATCTT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.864C>T	21.37:g.40652142G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1																																																																																			G|0.693;A|0.307	0.307	strong		0.358	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
IPPK	64768	hgsc.bcm.edu	37	9	95396712	95396712	+	Missense_Mutation	SNP	G	G	A	rs2277170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:95396712G>A	ENST00000287996.3	-	11	1402	c.1126C>T	c.(1126-1128)Ctt>Ttt	p.L376F	IPPK_ENST00000375522.1_Missense_Mutation_p.L48F	NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	376			L -> F (in dbSNP:rs2277170).		inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						TCAGTGGAAAGGTCAAGCAGC	0.453											OREG0019315	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	234	0.0467252	0.0015	0.0288	5008	,	,		18801	0.0476		0.0348	False		,,,				2504	0.1319				p.L376F		Atlas-SNP	.											.	IPPK	34	.	0			c.C1126T						PASS	.	G	PHE/LEU	32,4374	36.0+/-67.5	0,32,2171	106.0	88.0	94.0		1126	4.8	0.7	9	dbSNP_100	94	465,8135	138.1+/-194.9	18,429,3853	yes	missense	IPPK	NM_022755.5	22	18,461,6024	AA,AG,GG		5.407,0.7263,3.8213	probably-damaging	376/492	95396712	497,12509	2203	4300	6503	SO:0001583	missense	64768	exon11			TGGAAAGGTCAAG	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 12"""	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.1126C>T	9.37:g.95396712G>A	ENSP00000287996:p.Leu376Phe	Somatic	88	0	0	1312	WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_022755	Q5T9F7|Q9H7V8	Missense_Mutation	SNP	ENST00000287996.3	37	CCDS6699.1	56	0.02564102564102564	0	0.0	12	0.03314917127071823	19	0.033216783216783216	25	0.032981530343007916	G	18.19	3.568436	0.65651	0.007263	0.05407	ENSG00000127080	ENST00000287996;ENST00000375522	T;T	0.32515	1.45;1.45	5.71	4.8	0.61643	.	0.240288	0.43416	D	0.000566	T	0.13756	0.0333	M	0.64997	1.995	0.41718	D	0.989496	D;D	0.76494	0.999;0.983	D;P	0.72338	0.977;0.876	T	0.18493	-1.0335	10	0.14656	T	0.56	-5.6458	16.8525	0.85998	0.0:0.1285:0.8714:0.0	rs2277170;rs2277170	376;75	Q9H8X2;B3KVX7	IPPK_HUMAN;.	F	376;48	ENSP00000287996:L376F;ENSP00000364672:L48F	ENSP00000287996:L376F	L	-	1	0	IPPK	94436533	1.000000	0.71417	0.720000	0.30636	0.974000	0.67602	4.656000	0.61483	1.527000	0.49086	0.561000	0.74099	CTT	G|0.961;A|0.039	0.039	strong		0.453	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755	
DNAH1	25981	hgsc.bcm.edu	37	3	52407041	52407041	+	Silent	SNP	C	C	T	rs1546737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52407041C>T	ENST00000420323.2	+	44	7218	c.6957C>T	c.(6955-6957)caC>caT	p.H2319H		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2319	AAA 3. {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)		GGATGGACCACGGCGGCTGGT	0.622													C|||	1004	0.200479	0.0129	0.2651	5008	,	,		13907	0.1776		0.3459	False		,,,				2504	0.2822				p.H2319H		Atlas-SNP	.											.	DNAH1	534	.	0			c.C6957T						PASS	.	C		257,3885		14,229,1828	46.0	51.0	50.0		6957	-3.1	0.6	3	dbSNP_88	50	2780,5618		476,1828,1895	no	coding-synonymous	DNAH1	NM_015512.4		490,2057,3723	TT,TC,CC		33.1031,6.2047,24.2185		2319/4266	52407041	3037,9503	2071	4199	6270	SO:0001819	synonymous_variant	25981	exon44			GGACCACGGCGGC	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.6957C>T	3.37:g.52407041C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			C|0.781;T|0.219	0.219	strong		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
METRNL	284207	hgsc.bcm.edu	37	17	81043039	81043039	+	Silent	SNP	A	A	G	rs9908756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:81043039A>G	ENST00000320095.7	+	2	521	c.396A>G	c.(394-396)ccA>ccG	p.P132P	METRNL_ENST00000571814.1_Silent_p.P50P|METRNL_ENST00000570778.1_Silent_p.P50P	NM_001004431.1	NP_001004431.1	Q641Q3	METRL_HUMAN	meteorin, glial cell differentiation regulator-like	132					brown fat cell differentiation (GO:0050873)|fat cell differentiation (GO:0045444)|negative regulation of inflammatory response (GO:0050728)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of energy homeostasis (GO:2000507)|response to cold (GO:0009409)|response to muscle activity (GO:0014850)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hormone activity (GO:0005179)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	8	Breast(20;0.000443)|all_neural(118;0.0779)		BRCA - Breast invasive adenocarcinoma(99;0.0517)|OV - Ovarian serous cystadenocarcinoma(97;0.0868)			TGCTGGTACCAGACGGGGACG	0.637													G|||	3940	0.786741	0.8517	0.7507	5008	,	,		15514	0.9167		0.6213	False		,,,				2504	0.7607				p.P132P		Atlas-SNP	.											METRNL,NS,carcinoma,0,1	METRNL	29	1	0			c.A396G						PASS	.	G		3646,760	298.4+/-285.3	1520,606,77	38.0	48.0	45.0		396	-1.6	0.0	17	dbSNP_119	45	5266,3334	485.5+/-371.6	1630,2006,664	no	coding-synonymous	METRNL	NM_001004431.1		3150,2612,741	GG,GA,AA		38.7674,17.2492,31.4778		132/312	81043039	8912,4094	2203	4300	6503	SO:0001819	synonymous_variant	284207	exon2			GGTACCAGACGGG	AK093748	CCDS32779.1	17q25.3	2004-12-01				ENSG00000176845			27584	protein-coding gene	gene with protein product							Standard	NM_001004431		Approved		uc002kgh.3	Q641Q3		ENST00000320095.7:c.396A>G	17.37:g.81043039A>G		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	140	59	0.421429	NM_001004431	B3KSJ5|Q86VM0	Silent	SNP	ENST00000320095.7	37	CCDS32779.1																																																																																			A|0.262;G|0.738	0.738	strong		0.637	METRNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438902.1	NM_001004431	
SRPK3	26576	hgsc.bcm.edu	37	X	153049535	153049535	+	Silent	SNP	A	A	G	rs4898444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153049535A>G	ENST00000370101.3	+	10	1060	c.1014A>G	c.(1012-1014)ccA>ccG	p.P338P	SRPK3_ENST00000393786.3_Intron|SRPK3_ENST00000370100.1_Intron|SRPK3_ENST00000370108.3_Intron|SRPK3_ENST00000489426.1_Silent_p.P405P|SRPK3_ENST00000370104.1_Silent_p.P337P	NM_001170760.1|NM_014370.3	NP_001164231.1|NP_055185.2	Q9UPE1	SRPK3_HUMAN	SRSF protein kinase 3	338	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|muscle tissue development (GO:0060537)|skeletal muscle tissue development (GO:0007519)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(4)|ovary(2)|pancreas(2)|urinary_tract(1)	13	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CCCCCGCCCCAGGGGGCGGCC	0.692													G|||	2278	0.603444	0.3964	0.4539	3775	,	,		10079	0.631		0.2664	False		,,,				2504	0.547				p.P338P	Esophageal Squamous(167;766 3400 32156)	Atlas-SNP	.											.	SRPK3	63	.	0			c.A1014G						PASS	.	G	,,	1774,2049		401,698,274,530,291	20.0	24.0	23.0		1011,,1014	-9.0	0.0	X	dbSNP_111	23	2344,4361		315,1065,649,1041,1214	no	coding-synonymous,intron,coding-synonymous	SRPK3	NM_001170760.1,NM_001170761.1,NM_014370.3	,,	716,1763,923,1571,1505	GG,GA,G,AA,A		34.959,46.4033,39.1147	,,	337/567,,338/568	153049535	4118,6410	2194	4284	6478	SO:0001819	synonymous_variant	26576	exon10			CGCCCCAGGGGGC	AF027406	CCDS35441.1, CCDS55537.1, CCDS55538.1	Xq28	2010-06-23	2010-06-23	2006-08-17	ENSG00000184343	ENSG00000184343			11402	protein-coding gene	gene with protein product			"""serine/threonine kinase 23"", ""SFRS protein kinase 3"""	STK23		16140986	Standard	NM_014370		Approved	MSSK1	uc004fil.3	Q9UPE1	OTTHUMG00000024207	ENST00000370101.3:c.1014A>G	X.37:g.153049535A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	45	45	1	NM_014370	Q13583|Q4F970|Q562F5|Q9UM62	Silent	SNP	ENST00000370101.3	37	CCDS35441.1																																																																																			A|0.477;G|0.523	0.523	strong		0.692	SRPK3-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354501.1	NM_014370	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135722264	135722264	+	Missense_Mutation	SNP	A	A	G	rs17197552	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:135722264A>G	ENST00000264977.3	+	2	2541	c.1924A>G	c.(1924-1926)Agt>Ggt	p.S642G	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	642			S -> G (in dbSNP:rs17197552).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGTCTGTAGAAGTCCTGTTGG	0.423													A|||	865	0.172724	0.1505	0.1412	5008	,	,		17582	0.0288		0.2783	False		,,,				2504	0.2648				p.S642G		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A1924G						PASS	.	A	,GLY/SER	770,3634	291.0+/-281.2	64,642,1496	82.0	77.0	79.0		,1924	3.5	1.0	3	dbSNP_123	79	2708,5892	418.8+/-352.9	415,1878,2007	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,56	479,2520,3503	GG,GA,AA		31.4884,17.4841,26.7456	,benign	,642/1151	135722264	3478,9526	2202	4300	6502	SO:0001583	missense	5523	exon2			TGTAGAAGTCCTG	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.1924A>G	3.37:g.135722264A>G	ENSP00000264977:p.Ser642Gly	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	185	96	0.518919	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	340	0.15567765567765568	66	0.13414634146341464	57	0.1574585635359116	13	0.022727272727272728	204	0.2691292875989446	A	9.126	1.010279	0.19277	0.174841	0.314884	ENSG00000073711	ENST00000264977	T	0.06218	3.33	5.83	3.47	0.39725	.	0.643751	0.17330	N	0.178150	T	0.00012	0.0000	N	0.24115	0.695	0.09310	P	0.999999999742355	B	0.02656	0.0	B	0.04013	0.001	T	0.47636	-0.9102	9	0.44086	T	0.13	.	8.2194	0.31532	0.8457:0.0:0.1543:0.0	rs17197552;rs52827295;rs17197552	642	Q06190	P2R3A_HUMAN	G	642	ENSP00000264977:S642G	ENSP00000264977:S642G	S	+	1	0	PPP2R3A	137204954	0.878000	0.30173	0.996000	0.52242	0.962000	0.63368	1.520000	0.35899	0.481000	0.27557	0.460000	0.39030	AGT	A|0.779;G|0.221	0.221	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
RPTOR	57521	hgsc.bcm.edu	37	17	78919558	78919558	+	Silent	SNP	C	C	T	rs1567962	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:78919558C>T	ENST00000306801.3	+	26	3479	c.3117C>T	c.(3115-3117)gcC>gcT	p.A1039A	RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000544334.2_Silent_p.A881A	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1039					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						CGTGCATCGCCGTAGCCGACA	0.592													C|||	1876	0.374601	0.3918	0.3285	5008	,	,		15480	0.4544		0.334	False		,,,				2504	0.3436				p.A1039A		Atlas-SNP	.											.	RPTOR	122	.	0			c.C3117T						PASS	.	C	,	1678,2728	509.6+/-367.3	324,1030,849	79.0	69.0	72.0		2643,3117	-1.0	0.8	17	dbSNP_88	72	3033,5567	466.6+/-366.8	545,1943,1812	no	coding-synonymous,coding-synonymous	RPTOR	NM_001163034.1,NM_020761.2	,	869,2973,2661	TT,TC,CC		35.2674,38.0844,36.2217	,	881/1178,1039/1336	78919558	4711,8295	2203	4300	6503	SO:0001819	synonymous_variant	57521	exon26			CATCGCCGTAGCC		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.3117C>T	17.37:g.78919558C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	71	29	0.408451	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			C|0.632;T|0.368	0.368	strong		0.592	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573442	140573442	+	Silent	SNP	C	C	G	rs622424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140573442C>G	ENST00000239446.4	+	1	1501	c.1317C>G	c.(1315-1317)gtC>gtG	p.V439V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	439	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			ACATAACGGTCCTGGTCTCCG	0.592													G|||	2442	0.48762	0.5076	0.5461	5008	,	,		13937	0.5685		0.4076	False		,,,				2504	0.4182				p.V439V		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1317G						PASS	.						80.0	77.0	78.0					5																	140573442		2203	4299	6502	SO:0001819	synonymous_variant	56126	exon1			AACGGTCCTGGTC	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.1317C>G	5.37:g.140573442C>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	120	118	0.983333	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.549;G|0.451	0.451	strong		0.592	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
POLM	27434	hgsc.bcm.edu	37	7	44121936	44121936	+	Silent	SNP	C	C	A	rs3218655	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:44121936C>A	ENST00000242248.5	-	1	203	c.102G>T	c.(100-102)ctG>ctT	p.L34L	POLM_ENST00000395831.3_Silent_p.L34L|POLM_ENST00000335195.6_Silent_p.L34L	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	34	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						GAGGCTCGACCAGGTAGATGG	0.736								DNA polymerases (catalytic subunits)					C|||	853	0.170327	0.2163	0.1844	5008	,	,		9905	0.1111		0.1491	False		,,,				2504	0.181				p.L34L		Atlas-SNP	.											.	POLM	50	.	0			c.G102T						PASS	.	C		772,3464		79,614,1425	7.0	8.0	8.0		102	4.4	1.0	7	dbSNP_106	8	995,7359		69,857,3251	no	coding-synonymous	POLM	NM_013284.2		148,1471,4676	AA,AC,CC		11.9105,18.2247,14.0349		34/495	44121936	1767,10823	2118	4177	6295	SO:0001819	synonymous_variant	27434	exon1			CTCGACCAGGTAG	AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"""DNA polymerases"""	9185	protein-coding gene	gene with protein product	"""Pol iota"""	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.102G>T	7.37:g.44121936C>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	22	6	0.272727	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Silent	SNP	ENST00000242248.5	37	CCDS34625.1																																																																																			C|0.841;A|0.159	0.159	strong		0.736	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284	
NDUFV2	4729	hgsc.bcm.edu	37	18	9122638	9122638	+	Missense_Mutation	SNP	G	G	C	rs148158107	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9122638G>C	ENST00000318388.6	+	5	542	c.428G>C	c.(427-429)cGa>cCa	p.R143P	RP11-21J18.1_ENST00000579126.1_RNA|RP11-143J12.2_ENST00000582375.1_RNA|NDUFV2_ENST00000400033.1_Missense_Mutation_p.R146P|NDUFV2_ENST00000465096.1_3'UTR|RP11-143J12.2_ENST00000583081.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	143					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.R143P(1)		breast(1)|lung(4)|ovary(1)|stomach(1)	7						TGCATGCTTCGAAACTCTGAC	0.373																																					p.R143P		Atlas-SNP	.											NDUFV2,colon,carcinoma,+1,3	NDUFV2	17	3	1	Substitution - Missense(1)	stomach(1)	c.G428C						scavenged	.						101.0	90.0	94.0					18																	9122638		2203	4300	6503	SO:0001583	missense	4729	exon5			TGCTTCGAAACTC	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7717	protein-coding gene	gene with protein product	"""complex I 24kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"""	600532	"""NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"""			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.428G>C	18.37:g.9122638G>C	ENSP00000327268:p.Arg143Pro	Somatic	236	2	0.00847458		WXS	Illumina HiSeq	Phase_I	271	18	0.0664207	NM_021074	Q9BV41	Missense_Mutation	SNP	ENST00000318388.6	37	CCDS11842.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.399441	0.83120	.	.	ENSG00000178127	ENST00000318388;ENST00000400033	T;T	0.49720	0.78;0.77	5.93	5.93	0.95920	Thioredoxin-like fold (2);	0.054528	0.85682	D	0.000000	T	0.78272	0.4257	H	0.95611	3.695	0.80722	D	1	D	0.64830	0.994	D	0.69307	0.963	T	0.79412	-0.1814	10	0.29301	T	0.29	-4.6044	20.3397	0.98756	0.0:0.0:1.0:0.0	.	143	P19404	NDUV2_HUMAN	P	143;146	ENSP00000327268:R143P;ENSP00000382908:R146P	ENSP00000327268:R143P	R	+	2	0	NDUFV2	9112638	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.623000	0.98386	2.803000	0.96430	0.585000	0.79938	CGA	G|0.996;C|0.005	0.005	strong		0.373	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074	
PNPLA6	10908	hgsc.bcm.edu	37	19	7614888	7614888	+	Silent	SNP	C	C	G	rs62111288	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7614888C>G	ENST00000221249.6	+	17	2018	c.1587C>G	c.(1585-1587)ccC>ccG	p.P529P	PNPLA6_ENST00000450331.3_Silent_p.P529P|PNPLA6_ENST00000414982.3_Silent_p.P577P|PNPLA6_ENST00000545201.2_Silent_p.P503P|PNPLA6_ENST00000594864.1_3'UTR|PNPLA6_ENST00000600737.1_Silent_p.P568P	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	568					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						TAGCGCAGCCCGGGGAACTGG	0.642													c|||	25	0.00499201	0.0	0.0173	5008	,	,		16991	0.0		0.0099	False		,,,				2504	0.0031				p.P577P		Atlas-SNP	.											.	PNPLA6	163	.	0			c.C1731G						PASS	.	G	,,,,	9,4397	15.5+/-35.6	0,9,2194	108.0	94.0	99.0		1731,1509,1587,1704,1587	-10.3	0.0	19	dbSNP_129	99	125,8475	63.9+/-126.0	1,123,4176	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	,,,,	1,132,6370	GG,GC,CC		1.4535,0.2043,1.0303	,,,,	577/1376,503/1301,529/1328,568/1366,529/1328	7614888	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	10908	exon16			GCAGCCCGGGGAA	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.1587C>G	19.37:g.7614888C>G		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	67	0.563025	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	37	CCDS32891.1																																																																																			C|0.990;G|0.010	0.010	strong		0.642	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
XIRP2	129446	hgsc.bcm.edu	37	2	168107491	168107491	+	Missense_Mutation	SNP	A	A	G	rs3749004	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168107491A>G	ENST00000409195.1	+	9	9678	c.9589A>G	c.(9589-9591)Atc>Gtc	p.I3197V	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.I2975V|XIRP2_ENST00000295237.9_Missense_Mutation_p.I3197V|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3022					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CAAAGGGGCCATCCCATGTCC	0.473													A|||	992	0.198083	0.326	0.1326	5008	,	,		18868	0.12		0.1233	False		,,,				2504	0.229				p.I3197V		Atlas-SNP	.											.	XIRP2	914	.	0			c.A9589G						PASS	.	A	,,,VAL/ILE,VAL/ILE	1086,2824		160,766,1029	81.0	84.0	83.0		,,,9589,8923	-4.1	0.0	2	dbSNP_107	83	924,7380		56,812,3284	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,29,29	216,1578,4313	GG,GA,AA		11.1272,27.7749,16.4565	,,,benign,benign	,,,3197/3550,2975/3328	168107491	2010,10204	1955	4152	6107	SO:0001583	missense	129446	exon9			GGGGCCATCCCAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.9589A>G	2.37:g.168107491A>G	ENSP00000386840:p.Ile3197Val	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	386	0.17673992673992675	172	0.34959349593495936	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	A	0.111	-1.138744	0.01742	0.277749	0.111272	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02631	4.22;4.22;4.22	5.45	-4.1	0.03940	.	1.015070	0.07871	N	0.967851	T	0.00012	0.0000	N	0.25144	0.715	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.002;0.004;0.003	T	0.46345	-0.9198	9	0.19590	T	0.45	-0.4673	4.6634	0.12653	0.6565:0.0998:0.146:0.0977	rs3749004;rs52810850;rs58049014;rs3749004	3022;3022;2975	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	V	3197;3197;2975;611	ENSP00000386840:I3197V;ENSP00000295237:I3197V;ENSP00000387255:I2975V	ENSP00000295237:I3197V	I	+	1	0	XIRP2	167815737	0.000000	0.05858	0.001000	0.08648	0.776000	0.43924	0.291000	0.18994	-0.431000	0.07307	0.377000	0.23210	ATC	A|0.817;G|0.183	0.183	strong		0.473	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
SIGLEC5	8778	hgsc.bcm.edu	37	19	52130488	52130488	+	Silent	SNP	G	G	A	rs17740650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52130488G>A	ENST00000534261.2	-	8	1695	c.1296C>T	c.(1294-1296)ctC>ctT	p.L432L	SIGLEC5_ENST00000222107.4_Silent_p.L432L|SIGLEC5_ENST00000429354.3_Silent_p.L432L|SIGLEC5_ENST00000599649.1_Silent_p.L432L|SIGLEC5_ENST00000570106.2_Silent_p.L432L			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	432					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		CTCCTGTCCCGAGGTTCGATC	0.557													G|||	1226	0.244808	0.1392	0.1599	5008	,	,		19796	0.6329		0.1133	False		,,,				2504	0.183				p.L432L		Atlas-SNP	.											.	SIGLEC5	67	.	0			c.C1296T						PASS	.	G		652,3754	279.3+/-274.7	43,566,1594	97.0	84.0	88.0		1296	-0.2	0.0	19	dbSNP_123	88	939,7661	205.9+/-248.2	53,833,3414	no	coding-synonymous	SIGLEC5	NM_003830.2		96,1399,5008	AA,AG,GG		10.9186,14.798,12.2328		432/552	52130488	1591,11415	2203	4300	6503	SO:0001819	synonymous_variant	8778	exon7			TGTCCCGAGGTTC	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1296C>T	19.37:g.52130488G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	39	11	0.282051	NM_003830		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																			G|0.811;A|0.188	0.188	strong		0.557	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830	
C18orf54	162681	hgsc.bcm.edu	37	18	51888173	51888173	+	Silent	SNP	G	G	A	rs79359715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:51888173G>A	ENST00000300091.5	+	3	776	c.444G>A	c.(442-444)acG>acA	p.T148T	C18orf54_ENST00000578138.1_Intron|C18orf54_ENST00000382911.4_Silent_p.T148T	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	148						extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		GTCACCGAACGAGCAAGAAAA	0.418													G|||	111	0.0221645	0.0038	0.0331	5008	,	,		9331	0.003		0.0616	False		,,,				2504	0.0184				p.T148T		Atlas-SNP	.											.	C18orf54	40	.	0			c.G444A						PASS	.	G		54,4352	53.6+/-89.4	0,54,2149	85.0	72.0	77.0		444	0.0	0.0	18	dbSNP_132	77	507,8093	144.3+/-200.2	15,477,3808	no	coding-synonymous	C18orf54	NM_173529.4		15,531,5957	AA,AG,GG		5.8953,1.2256,4.3134		148/373	51888173	561,12445	2203	4300	6503	SO:0001819	synonymous_variant	162681	exon3			CCGAACGAGCAAG	AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"""lung adenoma susceptibility protein 2"""	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.444G>A	18.37:g.51888173G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	183	77	0.420765	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Silent	SNP	ENST00000300091.5	37	CCDS11956.1																																																																																			G|0.959;A|0.041	0.041	strong		0.418	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529	
SYNRG	11276	hgsc.bcm.edu	37	17	35902225	35902225	+	Silent	SNP	C	C	G	rs3110623	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:35902225C>G	ENST00000339208.6	-	15	3191	c.3051G>C	c.(3049-3051)ccG>ccC	p.P1017P	SYNRG_ENST00000346661.4_Silent_p.P1017P|SYNRG_ENST00000345615.4_Silent_p.P939P|SYNRG_ENST00000591288.1_Silent_p.P811P|SYNRG_ENST00000585472.1_Silent_p.P938P|SYNRG_ENST00000502449.2_Silent_p.P894P|SYNRG_ENST00000394378.2_Silent_p.P939P	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	1017					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						AACATTCGTTCGGGGTTTCTT	0.473													G|||	2704	0.539936	0.6157	0.3775	5008	,	,		18396	0.6548		0.4036	False		,,,				2504	0.5746				p.P1017P		Atlas-SNP	.											.	SYNRG	101	.	0			c.G3051C						PASS	.	G	,,,,,,	2423,1983	548.4+/-377.5	678,1067,458	78.0	83.0	81.0		2817,2814,2682,2433,3051,2817,2817	2.9	1.0	17	dbSNP_103	81	3100,5500	653.0+/-401.0	567,1966,1767	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	,,,,,,	1245,3033,2225	GG,GC,CC		36.0465,45.0068,42.465	,,,,,,	939/1237,938/1236,894/1180,811/1109,1017/1315,939/1225,939/1260	35902225	5523,7483	2203	4300	6503	SO:0001819	synonymous_variant	11276	exon15			TTCGTTCGGGGTT	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.3051G>C	17.37:g.35902225C>G		Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Silent	SNP	ENST00000339208.6	37	CCDS11321.1																																																																																			G|0.461;C|0.539	0.461	strong		0.473	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
UGT3A1	133688	hgsc.bcm.edu	37	5	35965611	35965611	+	Silent	SNP	A	A	G	rs61733467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:35965611A>G	ENST00000274278.3	-	4	1077	c.720T>C	c.(718-720)ctT>ctC	p.L240L	UGT3A1_ENST00000503189.1_Silent_p.L240L|UGT3A1_ENST00000333811.4_Silent_p.L186L|UGT3A1_ENST00000513233.1_Intron|UGT3A1_ENST00000507113.1_Silent_p.L206L	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	240						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)			CTTTCAGTAGAAGATGAGACA	0.448													A|||	56	0.0111821	0.0393	0.0058	5008	,	,		20825	0.0		0.0	False		,,,				2504	0.0				p.L240L		Atlas-SNP	.											.	UGT3A1	95	.	0			c.T720C						PASS	.	A	,	155,4251	104.3+/-142.8	2,151,2050	116.0	120.0	118.0		558,720	1.8	0.9	5	dbSNP_129	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	UGT3A1	NM_001171873.1,NM_152404.3	,	2,152,6349	GG,GA,AA		0.0116,3.5179,1.1994	,	186/253,240/524	35965611	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	133688	exon4			CAGTAGAAGATGA		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.720T>C	5.37:g.35965611A>G		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	223	114	0.511211	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Silent	SNP	ENST00000274278.3	37	CCDS3913.1																																																																																			A|0.988;G|0.012	0.012	strong		0.448	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404	
VNN2	8875	hgsc.bcm.edu	37	6	133077063	133077063	+	Silent	SNP	T	T	C	rs1883613	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:133077063T>C	ENST00000326499.6	-	3	580	c.456A>G	c.(454-456)acA>acG	p.T152T	VNN2_ENST00000525270.1_Silent_p.T99T|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000526192.1_5'UTR|VNN2_ENST00000525289.1_Silent_p.T152T	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	152	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TAGGAGGACATGTGGAGTCAC	0.453													T|||	1582	0.315895	0.261	0.4395	5008	,	,		15412	0.2351		0.34	False		,,,				2504	0.3609				p.T152T		Atlas-SNP	.											.	VNN2	83	.	0			c.A456G						PASS	.	T	,,	1281,3125	434.9+/-344.1	177,927,1099	153.0	130.0	138.0		456,456,297	-10.1	0.0	6	dbSNP_92	138	3002,5598	464.2+/-366.2	489,2024,1787	no	coding-synonymous,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	666,2951,2886	CC,CT,TT		34.907,29.074,32.931	,,	152/300,152/521,99/468	133077063	4283,8723	2203	4300	6503	SO:0001819	synonymous_variant	8875	exon3			AGGACATGTGGAG	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.456A>G	6.37:g.133077063T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	69	12	0.173913	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			T|0.682;C|0.318	0.318	strong		0.453	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
CCM2	83605	hgsc.bcm.edu	37	7	45113170	45113170	+	Splice_Site	SNP	G	G	A	rs2289367	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45113170G>A	ENST00000258781.6	+	8	1064	c.915G>A	c.(913-915)acG>acA	p.T305T	CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000541586.1_Splice_Site_p.T247T|CCM2_ENST00000475551.1_Splice_Site_p.T299T|CCM2_ENST00000474617.1_Splice_Site_p.T208T|CCM2_ENST00000544363.1_Splice_Site_p.T214T|CCM2_ENST00000381112.3_Splice_Site_p.T326T	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	305	Harmonin homology domain.				blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						ACATGCTGACGGTAGGCCTCC	0.657													G|||	1101	0.219848	0.2277	0.2752	5008	,	,		17768	0.1895		0.2078	False		,,,				2504	0.2137				p.T326T		Atlas-SNP	.											CCM2,NS,carcinoma,0,1	CCM2	42	1	0			c.G978A						PASS	.	G	,,,	1127,3279	398.5+/-330.9	133,861,1209	52.0	43.0	46.0		978,741,642,915	-0.2	1.0	7	dbSNP_100	46	1830,6770	323.2+/-315.9	202,1426,2672	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CCM2	NM_001029835.2,NM_001167934.1,NM_001167935.1,NM_031443.3	,,,	335,2287,3881	AA,AG,GG		21.2791,25.5788,22.7357	,,,	326/466,247/387,214/354,305/445	45113170	2957,10049	2203	4300	6503	SO:0001630	splice_region_variant	83605	exon8			GCTGACGGTAGGC	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.915+1G>A	7.37:g.45113170G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Silent	SNP	ENST00000258781.6	37	CCDS5500.1																																																																																			G|0.779;A|0.221	0.221	strong		0.657	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	Silent
FKBP15	23307	hgsc.bcm.edu	37	9	115931593	115931593	+	Silent	SNP	G	G	A	rs1128122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115931593G>A	ENST00000238256.3	-	26	3513	c.3396C>T	c.(3394-3396)acC>acT	p.T1132T		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1132					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						TGTGGGGACCGGTGGAGCTAG	0.597													G|||	306	0.0611022	0.0363	0.0317	5008	,	,		19298	0.0387		0.0467	False		,,,				2504	0.1534				p.T1132T		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,-1,2	FKBP15	128	2	0			c.C3396T						PASS	.	G		187,4009		5,177,1916	73.0	77.0	76.0		3396	-1.1	0.0	9	dbSNP_86	76	534,7892		15,504,3694	no	coding-synonymous	FKBP15	NM_015258.1		20,681,5610	AA,AG,GG		6.3375,4.4566,5.7122		1132/1220	115931593	721,11901	2098	4213	6311	SO:0001819	synonymous_variant	23307	exon26			GGGACCGGTGGAG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3396C>T	9.37:g.115931593G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	161	67	0.416149	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.953;A|0.047	0.047	strong		0.597	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
HK3	3101	hgsc.bcm.edu	37	5	176315822	176315822	+	Silent	SNP	G	G	T	rs61749652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176315822G>T	ENST00000292432.5	-	9	1049	c.958C>A	c.(958-960)Cgg>Agg	p.R320R		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	320	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCACCAGCCGCACCAGCTCA	0.637													G|||	79	0.0157748	0.0144	0.0072	5008	,	,		16439	0.0		0.0268	False		,,,				2504	0.0286				p.R320R		Atlas-SNP	.											HK3_ENST00000292432,NS,carcinoma,0,2	HK3	210	2	0			c.C958A						PASS	.	G		108,4298	83.4+/-121.9	1,106,2096	46.0	49.0	48.0		958	3.5	1.0	5	dbSNP_129	48	170,8430	78.6+/-141.3	6,158,4136	no	coding-synonymous	HK3	NM_002115.2		7,264,6232	TT,TG,GG		1.9767,2.4512,2.1375		320/924	176315822	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3101	exon9			CCAGCCGCACCAG		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.958C>A	5.37:g.176315822G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			G|0.979;T|0.021	0.021	strong		0.637	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
CCT8	10694	hgsc.bcm.edu	37	21	30437344	30437344	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:30437344T>C	ENST00000286788.4	-	7	913	c.707A>G	c.(706-708)gAt>gGt	p.D236G	CCT8_ENST00000540844.1_Missense_Mutation_p.D163G|CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000542732.1_Missense_Mutation_p.D217G	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	236					'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						TATTTTTGCATCTTTGACAGA	0.378																																					p.D236G		Atlas-SNP	.											.	CCT8	38	.	0			c.A707G						PASS	.						193.0	175.0	181.0					21																	30437344		2203	4300	6503	SO:0001583	missense	10694	exon7			TTTGCATCTTTGA	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"""Heat Shock Proteins / Chaperonins"""	1623	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 112"""	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.707A>G	21.37:g.30437344T>C	ENSP00000286788:p.Asp236Gly	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580704	0.65992	.	.	ENSG00000156261	ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	T;T;T	0.67865	-0.29;-0.29;-0.29	5.25	5.25	0.73442	.	0.043440	0.85682	D	0.000000	T	0.58694	0.2140	L	0.38649	1.16	0.80722	D	1	B;B;B;B;B	0.32653	0.018;0.006;0.018;0.014;0.379	B;B;B;B;B	0.33339	0.043;0.007;0.027;0.016;0.162	T	0.59794	-0.7387	10	0.42905	T	0.14	-23.8735	15.6084	0.76692	0.0:0.0:0.0:1.0	.	163;217;236;235;236	B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.;.;.;.;TCPQ_HUMAN	G	235;236;217;163	ENSP00000286788:D236G;ENSP00000444984:D217G;ENSP00000442730:D163G	ENSP00000286788:D236G	D	-	2	0	CCT8	29359215	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.728000	0.68531	2.326000	0.78906	0.533000	0.62120	GAT	.	.	none		0.378	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1		
GPR151	134391	hgsc.bcm.edu	37	5	145894896	145894896	+	Missense_Mutation	SNP	G	G	C	rs7709485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145894896G>C	ENST00000311104.2	-	1	857	c.781C>G	c.(781-783)Ctc>Gtc	p.L261V		NM_194251.2	NP_919227.2	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	261			L -> V (in dbSNP:rs7709485).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(2)	14			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCCACAAGAGAGCAGAGATG	0.502													G|||	1713	0.342053	0.2519	0.183	5008	,	,		19667	0.7669		0.1958	False		,,,				2504	0.2894				p.L261V	Pancreas(78;420 1386 18535 37114 49710)	Atlas-SNP	.											.	GPR151	35	.	0			c.C781G						PASS	.	G	VAL/LEU	1027,3379	378.5+/-322.9	120,787,1296	59.0	61.0	61.0		781	-1.6	0.0	5	dbSNP_116	61	1726,6874	314.9+/-312.0	172,1382,2746	yes	missense	GPR151	NM_194251.2	32	292,2169,4042	CC,CG,GG		20.0698,23.3091,21.1672	benign	261/420	145894896	2753,10253	2203	4300	6503	SO:0001583	missense	134391	exon1			ACAAGAGAGCAGA	AY255557	CCDS34266.1	5q32	2012-08-21						"""GPCR / Class A : Orphans"""	23624	protein-coding gene	gene with protein product	"""galanin receptor 4"""					12679517	Standard	NM_194251		Approved	PGR7, GALR4	uc003lod.1	Q8TDV0		ENST00000311104.2:c.781C>G	5.37:g.145894896G>C	ENSP00000308733:p.Leu261Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_194251	Q86SN8|Q8NGV2	Missense_Mutation	SNP	ENST00000311104.2	37	CCDS34266.1	792	0.3626373626373626	114	0.23170731707317074	79	0.21823204419889503	457	0.798951048951049	142	0.18733509234828497	G	0.255	-1.003594	0.02128	0.233091	0.200698	ENSG00000173250	ENST00000311104	T	0.37584	1.19	5.91	-1.58	0.08479	GPCR, rhodopsin-like superfamily (1);	0.302038	0.34110	N	0.004255	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	B	0.09022	0.002	B	0.14578	0.011	T	0.33033	-0.9884	9	0.13853	T	0.58	.	9.1674	0.37060	0.0:0.4239:0.2966:0.2795	rs7709485;rs17506353;rs52809074;rs58222574;rs7709485	261	Q8TDV0	GP151_HUMAN	V	261	ENSP00000308733:L261V	ENSP00000308733:L261V	L	-	1	0	GPR151	145875089	0.004000	0.15560	0.002000	0.10522	0.022000	0.10575	-0.025000	0.12413	-0.538000	0.06281	-0.175000	0.13238	CTC	G|0.723;C|0.277	0.277	strong		0.502	GPR151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373457.1	NM_194251	
SCN1A	6323	hgsc.bcm.edu	37	2	166903445	166903445	+	Silent	SNP	T	T	C	rs7580482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:166903445T>C	ENST00000303395.4	-	9	1211	c.1212A>G	c.(1210-1212)gtA>gtG	p.V404V	SCN1A_ENST00000375405.3_Silent_p.V404V|SCN1A_ENST00000409050.1_Silent_p.V404V|AC010127.3_ENST00000595268.1_RNA|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Silent_p.V404V|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	404					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAATGACCAATACAAAAAATA	0.398													C|||	3552	0.709265	0.5582	0.7363	5008	,	,		18617	0.8909		0.6909	False		,,,				2504	0.726				p.V404V		Atlas-SNP	.											.	SCN1A	641	.	0			c.A1212G						PASS	.	C	,,,	2512,1894	544.5+/-376.5	703,1106,394	103.0	100.0	101.0		1212,1212,1212,1212	2.6	1.0	2	dbSNP_116	101	5807,2793	442.2+/-360.0	1948,1911,441	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	2651,3017,835	CC,CT,TT		32.4767,42.9868,36.0372	,,,	404/2010,404/1982,404/2010,404/1999	166903445	8319,4687	2203	4300	6503	SO:0001819	synonymous_variant	6323	exon9			GACCAATACAAAA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1212A>G	2.37:g.166903445T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	130	127	0.976923	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			.	.	none		0.398	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
PCLO	27445	hgsc.bcm.edu	37	7	82435033	82435033	+	Silent	SNP	C	C	T	rs12668093	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:82435033C>T	ENST00000333891.9	-	21	15241	c.14904G>A	c.(14902-14904)ggG>ggA	p.G4968G		NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GATTAGTCTCCCCTGCAGTGC	0.498													C|||	1049	0.209465	0.3381	0.0965	5008	,	,		17481	0.2837		0.1412	False		,,,				2504	0.1094				p.G4968G		Atlas-SNP	.											.	PCLO	1506	.	0			c.G14904A						PASS	.	C		1160,2876		172,816,1030	63.0	66.0	65.0		14904	3.9	1.0	7	dbSNP_120	65	1135,7253		77,981,3136	no	coding-synonymous	PCLO	NM_033026.5		249,1797,4166	TT,TC,CC		13.5312,28.7413,18.4723		4968/5143	82435033	2295,10129	2018	4194	6212	SO:0001819	synonymous_variant	27445	exon21			AGTCTCCCCTGCA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.14904G>A	7.37:g.82435033C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	55	0.413534	NM_033026		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			C|0.773;T|0.227	0.227	strong		0.498	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
CADPS	8618	hgsc.bcm.edu	37	3	62578336	62578336	+	Silent	SNP	C	C	T	rs17066673	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:62578336C>T	ENST00000383710.4	-	7	1762	c.1413G>A	c.(1411-1413)gcG>gcA	p.A471A	CADPS_ENST00000357948.3_Silent_p.A471A|CADPS_ENST00000283269.9_Silent_p.A471A	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	471	C2.				catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TGTCCTCCAACGCCAGGACGC	0.567													G|||	327	0.0652955	0.0756	0.049	5008	,	,		21175	0.0734		0.0547	False		,,,				2504	0.0654				p.A471A		Atlas-SNP	.											CADPS,brain,glioma,-2,1	CADPS	387	1	0			c.G1413A						PASS	.	G	,,	313,4093		7,299,1897	152.0	133.0	139.0		1413,1413,1413	3.5	1.0	3	dbSNP_123	139	314,8286		6,302,3992	no	coding-synonymous,coding-synonymous,coding-synonymous	CADPS	NM_003716.3,NM_183393.2,NM_183394.2	,,	13,601,5889	TT,TC,CC		3.6512,7.1039,4.8209	,,	471/1354,471/1275,471/1315	62578336	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	8618	exon7			CTCCAACGCCAGG	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.1413G>A	3.37:g.62578336C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	37	CCDS46858.1																																																																																			C|0.946;T|0.054	0.054	strong		0.567	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
TENM4	26011	hgsc.bcm.edu	37	11	78565314	78565314	+	Missense_Mutation	SNP	C	C	G	rs17137261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:78565314C>G	ENST00000278550.7	-	12	1978	c.1516G>C	c.(1516-1518)Gag>Cag	p.E506Q		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	506			E -> Q (in dbSNP:rs17137261).		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)										CTCCGCGCCTCCTGGGTTAGG	0.587													C|||	155	0.0309505	0.0068	0.0504	5008	,	,		16854	0.0317		0.0487	False		,,,				2504	0.0307				p.E506Q		Atlas-SNP	.											.	.	.	.	0			c.G1516C						PASS	.	C	GLN/GLU	17,1367		0,17,675	12.0	14.0	14.0		1516	5.1	1.0	11	dbSNP_123	14	117,3065		5,107,1479	yes	missense	ODZ4	NM_001098816.2	29	5,124,2154	GG,GC,CC		3.6769,1.2283,2.9347	possibly-damaging	506/2770	78565314	134,4432	692	1591	2283	SO:0001583	missense	26011	exon12			GCGCCTCCTGGGT	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.1516G>C	11.37:g.78565314C>G	ENSP00000278550:p.Glu506Gln	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	15	9	0.6	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	79	0.036172161172161175	4	0.008130081300813009	21	0.058011049723756904	17	0.02972027972027972	37	0.048812664907651716	C	20.2	3.954131	0.73902	0.012283	0.036769	ENSG00000149256	ENST00000278550	T	0.21932	1.98	5.07	5.07	0.68467	.	0.174787	0.49305	D	0.000153	T	0.01592	0.0051	L	0.34521	1.04	0.53005	D	0.999968	P	0.39391	0.671	B	0.29785	0.107	T	0.08973	-1.0696	9	.	.	.	.	18.6486	0.91421	0.0:1.0:0.0:0.0	rs17137261	506	Q6N022	TEN4_HUMAN	Q	506	ENSP00000278550:E506Q	.	E	-	1	0	ODZ4	78242962	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.651000	0.83577	2.631000	0.89168	0.561000	0.74099	GAG	C|0.969;G|0.031	0.031	strong		0.587	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
LHX8	431707	hgsc.bcm.edu	37	1	75622616	75622616	+	Silent	SNP	C	C	T	rs941032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:75622616C>T	ENST00000294638.5	+	9	1513	c.849C>T	c.(847-849)caC>caT	p.H283H	LHX8_ENST00000356261.3_Silent_p.H273H	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	283					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						ACAAGAAACACGTCAGTCCTA	0.502													C|||	1973	0.39397	0.4758	0.3026	5008	,	,		17790	0.2063		0.3907	False		,,,				2504	0.545				p.H283H		Atlas-SNP	.											.	LHX8	73	.	0			c.C849T						PASS	.	C		2044,2362	566.8+/-382.0	484,1076,643	291.0	261.0	272.0		849	-3.0	0.8	1	dbSNP_86	272	3551,5049	517.5+/-379.0	748,2055,1497	yes	coding-synonymous	LHX8	NM_001001933.1		1232,3131,2140	TT,TC,CC		41.2907,46.3913,43.0186		283/357	75622616	5595,7411	2203	4300	6503	SO:0001819	synonymous_variant	431707	exon9			GAAACACGTCAGT	AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"""Homeoboxes / LIM class"""	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.849C>T	1.37:g.75622616C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	159	159	1	NM_001001933	E9PGE3	Silent	SNP	ENST00000294638.5	37	CCDS30756.1																																																																																			C|0.598;N|0.000	.	strong		0.502	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933	
HLTF	6596	hgsc.bcm.edu	37	3	148759325	148759325	+	Silent	SNP	T	T	C	rs2290725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148759325T>C	ENST00000310053.5	-	20	2521	c.2328A>G	c.(2326-2328)gcA>gcG	p.A776A	HLTF_ENST00000392912.2_Silent_p.A776A|HLTF_ENST00000494055.1_Silent_p.A776A|HLTF_ENST00000465259.1_Silent_p.A775A	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	776					chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A776A(1)		breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AAAATACATGTGCACAATGTG	0.378													T|||	1581	0.315695	0.32	0.3098	5008	,	,		17556	0.3353		0.337	False		,,,				2504	0.272				p.A776A		Atlas-SNP	.											.	HLTF	87	.	1	Substitution - coding silent(1)	lung(1)	c.A2328G						PASS	.	T	,	1331,3075	447.5+/-348.4	219,893,1091	134.0	129.0	131.0		2328,2328	3.7	1.0	3	dbSNP_100	131	2639,5961	427.5+/-355.6	404,1831,2065	no	coding-synonymous,coding-synonymous	HLTF	NM_003071.3,NM_139048.2	,	623,2724,3156	CC,CT,TT		30.686,30.2088,30.5244	,	776/1010,776/1010	148759325	3970,9036	2203	4300	6503	SO:0001819	synonymous_variant	6596	exon20			TACATGTGCACAA	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.2328A>G	3.37:g.148759325T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Silent	SNP	ENST00000310053.5	37	CCDS33875.1																																																																																			T|0.692;C|0.308	0.308	strong		0.378	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
GALNT7	51809	hgsc.bcm.edu	37	4	174090004	174090004	+	Silent	SNP	G	G	A	rs3733477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:174090004G>A	ENST00000265000.4	+	1	101	c.18G>A	c.(16-18)ggG>ggA	p.G6G	RP11-10K16.1_ENST00000499322.2_RNA|GALNT7_ENST00000512285.1_Silent_p.G6G|RP11-10K16.1_ENST00000510523.1_RNA|RP11-10K16.1_ENST00000500914.2_RNA	NM_017423.2	NP_059119.2	Q86SF2	GALT7_HUMAN	polypeptide N-acetylgalactosaminyltransferase 7	6					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|kidney(3)|large_intestine(5)|liver(1)|lung(9)	19		Prostate(90;0.0132)|Renal(120;0.0183)|Melanoma(52;0.0749)|all_hematologic(60;0.107)|all_neural(102;0.122)		all cancers(43;1.87e-18)|Epithelial(43;3.44e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-09)|STAD - Stomach adenocarcinoma(60;0.0019)|GBM - Glioblastoma multiforme(59;0.0119)|LUSC - Lung squamous cell carcinoma(193;0.0199)		TGAAGATTGGGTTCATCTTAC	0.667													G|||	3213	0.641573	0.5825	0.5231	5008	,	,		7096	0.7183		0.7018	False		,,,				2504	0.6646				p.G6G		Atlas-SNP	.											.	GALNT7	61	.	0			c.G18A						PASS	.	G		2679,1727	646.0+/-398.3	831,1017,355	150.0	132.0	138.0		18	2.2	1.0	4	dbSNP_107	138	5837,2763	677.0+/-403.3	1997,1843,460	no	coding-synonymous	GALNT7	NM_017423.2		2828,2860,815	AA,AG,GG		32.1279,39.1966,34.5225		6/658	174090004	8516,4490	2203	4300	6503	SO:0001819	synonymous_variant	51809	exon1			GATTGGGTTCATC	AJ002744	CCDS3815.1	4q31.1	2014-03-13	2014-03-13		ENSG00000109586	ENSG00000109586		"""Glycosyltransferase family 2 domain containing"""	4129	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 7"""	605005	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7)"""			10544240	Standard	NM_017423		Approved	GALNAC-T7	uc003isz.4	Q86SF2	OTTHUMG00000160817	ENST00000265000.4:c.18G>A	4.37:g.174090004G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	102	56	0.54902	NM_017423	B3KQU3|Q7Z5W7|Q9UJ28	Silent	SNP	ENST00000265000.4	37	CCDS3815.1																																																																																			T|0.000;G|0.353;A|0.647	0.647	strong		0.667	GALNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362456.2	NM_017423	
SULF2	55959	hgsc.bcm.edu	37	20	46365636	46365636	+	Missense_Mutation	SNP	C	C	T	rs56218501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:46365636C>T	ENST00000359930.4	-	3	1077	c.226G>A	c.(226-228)Gcg>Acg	p.A76T	SULF2_ENST00000467815.1_Missense_Mutation_p.A76T|SULF2_ENST00000484875.1_Missense_Mutation_p.A76T|SULF2_ENST00000478766.1_5'UTR|SULF2_ENST00000361612.4_Missense_Mutation_p.A76T	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	76			A -> T (in dbSNP:rs56218501). {ECO:0000269|PubMed:10574462}.		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						ATGAAGTGCGCCCCGCCCTGC	0.607													C|||	389	0.0776757	0.0061	0.1354	5008	,	,		18064	0.001		0.2167	False		,,,				2504	0.0695				p.A76T		Atlas-SNP	.											SULF2,colon,carcinoma,+2,3	SULF2	131	3	0			c.G226A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	168,4238	110.8+/-149.0	8,152,2043	206.0	164.0	178.0		226,226,226	5.4	1.0	20	dbSNP_129	178	1848,6752	331.5+/-319.7	219,1410,2671	yes	missense,missense,missense	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	58,58,58	227,1562,4714	TT,TC,CC		21.4884,3.813,15.5005	benign,benign,benign	76/871,76/871,76/868	46365636	2016,10990	2203	4300	6503	SO:0001583	missense	55959	exon3			AGTGCGCCCCGCC	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.226G>A	20.37:g.46365636C>T	ENSP00000353007:p.Ala76Thr	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	192	99	0.515625	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	218	0.09981684981684982	2	0.0040650406504065045	60	0.16574585635359115	0	0.0	156	0.20580474934036938	C	13.86	2.362478	0.41902	0.03813	0.214884	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.98455	-4.94;-4.94;-4.94;-4.94;-4.94	5.44	5.44	0.79542	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.103148	0.64402	D	0.000002	T	0.00754	0.0025	N	0.05534	-0.03	0.23809	P	0.99678531	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.09377	0.002;0.002;0.004	T	0.55405	-0.8146	9	0.27785	T	0.31	-14.4645	8.5077	0.33197	0.1539:0.7697:0.0:0.0764	rs56218501;rs61741658	76;76;76	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	T	76	ENSP00000353007:A76T;ENSP00000418290:A76T;ENSP00000354662:A76T;ENSP00000418442:A76T;ENSP00000410026:A76T	ENSP00000353007:A76T	A	-	1	0	SULF2	45799043	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	2.973000	0.49264	2.559000	0.86315	0.561000	0.74099	GCG	C|0.856;G|0.000;T|0.144	0.144	strong		0.607	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
NTNG2	84628	hgsc.bcm.edu	37	9	135073967	135073967	+	Silent	SNP	C	C	T	rs3739930	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135073967C>T	ENST00000393229.3	+	3	1604	c.828C>T	c.(826-828)taC>taT	p.Y276Y	NTNG2_ENST00000360670.3_Silent_p.Y276Y|NTNG2_ENST00000372179.3_Silent_p.Y276Y|NTNG2_ENST00000393228.4_Silent_p.Y276Y	NM_032536.2	NP_115925.2	Q96CW9	NTNG2_HUMAN	netrin G2	276	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				axonogenesis (GO:0007409)	anchored component of plasma membrane (GO:0046658)|axon (GO:0030424)				central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	29				OV - Ovarian serous cystadenocarcinoma(145;1.23e-05)|Epithelial(140;0.000173)		AGTACTTCTACGCCATCTCCA	0.597													C|||	476	0.0950479	0.0477	0.0793	5008	,	,		20170	0.119		0.1223	False		,,,				2504	0.1176				p.Y276Y		Atlas-SNP	.											NTNG2,NS,carcinoma,0,1	NTNG2	66	1	0			c.C828T						PASS	.	C		193,4207		8,177,2015	32.0	37.0	36.0		828	-6.4	0.8	9	dbSNP_107	36	969,7619		54,861,3379	no	coding-synonymous	NTNG2	NM_032536.2		62,1038,5394	TT,TC,CC		11.2832,4.3864,8.9467		276/531	135073967	1162,11826	2200	4294	6494	SO:0001819	synonymous_variant	84628	exon3			CTTCTACGCCATC	AB058760	CCDS6946.1	9q34	2013-03-01	2003-12-02	2003-12-03	ENSG00000196358	ENSG00000196358		"""Netrins"""	14288	protein-coding gene	gene with protein product	"""Netrin-G2"""		"""netrin G1"""	NTNG1			Standard	NM_032536		Approved	KIAA1857, Lmnt2	uc004cbh.2	Q96CW9	OTTHUMG00000020835	ENST00000393229.3:c.828C>T	9.37:g.135073967C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	133	67	0.503759	NM_032536	Q5JUJ2|Q6UXY0|Q96JH0	Silent	SNP	ENST00000393229.3	37	CCDS6946.1																																																																																			C|0.909;T|0.091	0.091	strong		0.597	NTNG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054779.1	NM_032536	
CPED1	79974	hgsc.bcm.edu	37	7	120776097	120776097	+	Missense_Mutation	SNP	C	C	G	rs41281692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:120776097C>G	ENST00000310396.5	+	14	2119	c.1652C>G	c.(1651-1653)gCa>gGa	p.A551G	CPED1_ENST00000450913.2_Missense_Mutation_p.A551G|CPED1_ENST00000423795.1_Missense_Mutation_p.A331G	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	551			A -> G (in dbSNP:rs41281692). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			endoplasmic reticulum (GO:0005783)											tttttaGCTGCAGTTCCACAA	0.244													C|||	2468	0.492812	0.202	0.6167	5008	,	,		13094	0.8552		0.4801	False		,,,				2504	0.4376				p.A551G		Atlas-SNP	.											.	.	.	.	0			c.C1652G						PASS	.	C	GLY/ALA,GLY/ALA	1135,3261		154,827,1217	39.0	41.0	41.0		1652,1652	-0.5	0.0	7	dbSNP_127	41	3790,4796		851,2088,1354	yes	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	60,60	1005,2915,2571	GG,GC,CC		44.1416,25.8189,37.9371	benign,benign	551/784,551/1027	120776097	4925,8057	2198	4293	6491	SO:0001583	missense	79974	exon13			TAGCTGCAGTTCC		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.1652C>G	7.37:g.120776097C>G	ENSP00000309772:p.Ala551Gly	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	1154	0.5283882783882784	99	0.20121951219512196	208	0.574585635359116	486	0.8496503496503497	361	0.4762532981530343	C	8.454	0.853694	0.17106	0.258189	0.441416	ENSG00000106034	ENST00000310396;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T	0.33216	2.18;1.86;1.83;1.42	5.35	-0.512	0.11966	.	1.087170	0.06929	N	0.810857	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.33238	0.001;0.403;0.0	B;B;B	0.36289	0.003;0.221;0.001	T	0.25082	-1.0142	9	0.24483	T	0.36	.	2.6608	0.05026	0.3459:0.2989:0.0:0.3551	rs41281692;rs58426784;rs61746432	331;551;551	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	G	551;551;331;331	ENSP00000309772:A551G;ENSP00000406122:A551G;ENSP00000415573:A331G;ENSP00000391952:A331G	ENSP00000309772:A551G	A	+	2	0	C7orf58	120563333	0.000000	0.05858	0.000000	0.03702	0.123000	0.20343	-0.738000	0.04871	0.040000	0.15660	0.585000	0.79938	GCA	C|0.571;G|0.429	0.429	strong		0.244	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
NLRP11	204801	hgsc.bcm.edu	37	19	56329334	56329334	+	Silent	SNP	G	G	C	rs8113630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56329334G>C	ENST00000589093.1	-	2	300	c.207C>G	c.(205-207)ctC>ctG	p.L69L	NLRP11_ENST00000589824.2_Silent_p.L69L|NLRP11_ENST00000360133.3_Silent_p.L69L|NLRP11_ENST00000443188.1_Silent_p.L69L|NLRP11_ENST00000592953.1_Intron			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	69	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.						ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		ATATGCTGAAGAGCATATTCC	0.428													G|||	410	0.081869	0.1959	0.0504	5008	,	,		19709	0.0		0.0596	False		,,,				2504	0.0573				p.L69L		Atlas-SNP	.											.	NLRP11	139	.	0			c.C207G						PASS	.	G		774,3632	314.9+/-293.9	64,646,1493	148.0	135.0	139.0		207	-5.4	0.0	19	dbSNP_116	139	626,7974	162.2+/-214.9	27,572,3701	no	coding-synonymous	NLRP11	NM_145007.3		91,1218,5194	CC,CG,GG		7.2791,17.567,10.7643		69/1034	56329334	1400,11606	2203	4300	6503	SO:0001819	synonymous_variant	204801	exon4			GCTGAAGAGCATA	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.207C>G	19.37:g.56329334G>C		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	147	69	0.469388	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Silent	SNP	ENST00000589093.1	37	CCDS12935.1																																																																																			G|0.900;C|0.100	0.100	strong		0.428	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
BAIAP3	8938	hgsc.bcm.edu	37	16	1391150	1391150	+	Missense_Mutation	SNP	A	A	C	rs115198116	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1391150A>C	ENST00000324385.5	+	7	752	c.594A>C	c.(592-594)aaA>aaC	p.K198N	BAIAP3_ENST00000426824.3_Missense_Mutation_p.K163N|BAIAP3_ENST00000562208.1_Missense_Mutation_p.K140N|BAIAP3_ENST00000397489.1_Missense_Mutation_p.K180N|BAIAP3_ENST00000397488.2_Missense_Mutation_p.K180N|BAIAP3_ENST00000421665.2_Missense_Mutation_p.K163N|BAIAP3_ENST00000568887.1_Missense_Mutation_p.K135N	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	198	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				ATGCCCTGAAAGTCTCTGTCA	0.667													A|||	5	0.000998403	0.0	0.0	5008	,	,		16618	0.0		0.004	False		,,,				2504	0.001				p.K198N		Atlas-SNP	.											.	BAIAP3	88	.	0			c.A594C						PASS	.	A	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	3,4395	6.2+/-15.9	0,3,2196	63.0	59.0	61.0		489,489,420,405,594	4.9	1.0	16	dbSNP_132	61	44,8556	28.5+/-78.6	0,44,4256	yes	missense,missense,missense,missense,missense	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	94,94,94,94,94	0,47,6452	CC,CA,AA		0.5116,0.0682,0.3616	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	163/1117,163/1153,140/1130,135/1125,198/1188	1391150	47,12951	2199	4300	6499	SO:0001583	missense	8938	exon7			CCTGAAAGTCTCT	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.594A>C	16.37:g.1391150A>C	ENSP00000324510:p.Lys198Asn	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	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	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	12.63	1.996807	0.35226	6.82E-4	0.005116	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45;-0.45	4.86	4.86	0.63082	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.055119	0.64402	D	0.000001	T	0.57373	0.2049	L	0.28014	0.82	0.45354	D	0.998349	D;P;D;D;D	0.76494	0.997;0.636;0.999;0.999;0.992	D;B;D;D;D	0.72075	0.91;0.417;0.976;0.976;0.947	T	0.59182	-0.7502	10	0.15499	T	0.54	-20.0092	7.1269	0.25477	0.9012:0.0:0.0988:0.0	.	163;215;140;198;180	E7EUB9;B4DGA2;B4DIK3;O94812;A2A2B2	.;.;.;BAIP3_HUMAN;.	N	163;180;198;180;163	ENSP00000407242:K163N;ENSP00000380625:K180N;ENSP00000324510:K198N;ENSP00000380626:K180N;ENSP00000409533:K163N	ENSP00000324510:K198N	K	+	3	2	BAIAP3	1331151	1.000000	0.71417	0.999000	0.59377	0.350000	0.29205	2.678000	0.46900	2.042000	0.60477	0.260000	0.18958	AAA	A|0.998;C|0.002	0.002	strong		0.667	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
ZNF638	27332	hgsc.bcm.edu	37	2	71654175	71654175	+	Missense_Mutation	SNP	G	G	A	rs1804020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:71654175G>A	ENST00000409544.1	+	24	5806	c.5176G>A	c.(5176-5178)Gtg>Atg	p.V1726M	ZNF638_ENST00000409407.1_Missense_Mutation_p.V666M|ZNF638_ENST00000355812.3_3'UTR|ZNF638_ENST00000264447.4_Missense_Mutation_p.V1726M	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1726			V -> M (in dbSNP:rs1804020). {ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|lung(28)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|urinary_tract(1)	63						TTCTTCTCAGGTGCCCGAAGA	0.383													A|||	1719	0.343251	0.2262	0.2435	5008	,	,		19941	0.7034		0.2376	False		,,,				2504	0.3098				p.V1726M		Atlas-SNP	.											ZNF638,tonsil,carcinoma,0,1	ZNF638	179	1	0			c.G5176A						PASS	.	A	MET/VAL,MET/VAL	1105,3301	720.2+/-409.0	146,813,1244	122.0	125.0	124.0		5176,5176	3.3	1.0	2	dbSNP_89	124	2047,6553	719.4+/-406.3	260,1527,2513	yes	missense,missense	ZNF638	NM_001014972.1,NM_014497.3	21,21	406,2340,3757	AA,AG,GG		23.8023,25.0794,24.235	benign,benign	1726/1979,1726/1979	71654175	3152,9854	2203	4300	6503	SO:0001583	missense	27332	exon24			TCTCAGGTGCCCG	D83032	CCDS1917.1	2p13.1	2013-02-12	2004-07-29	2004-07-30	ENSG00000075292	ENSG00000075292		"""RNA binding motif (RRM) containing"""	17894	protein-coding gene	gene with protein product		614349	"""zinc finger, matrin-like"""	ZFML		8647861	Standard	NM_014497		Approved	NP220, MGC26130, Zfp638	uc002shy.3	Q14966	OTTHUMG00000129735	ENST00000409544.1:c.5176G>A	2.37:g.71654175G>A	ENSP00000386433:p.Val1726Met	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	753	0.3447802197802198	101	0.20528455284552846	93	0.2569060773480663	376	0.6573426573426573	183	0.24142480211081793	A	1.046	-0.677433	0.03378	0.250794	0.238023	ENSG00000075292	ENST00000264447;ENST00000409544;ENST00000409407	T;T;T	0.30448	1.53;1.53;1.94	5.85	3.35	0.38373	.	0.089095	0.49916	N	0.000133	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.99999999834298	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37220	-0.9715	9	0.19590	T	0.45	-6.9875	5.2117	0.15320	0.6696:0.1557:0.1747:0.0	rs1804020;rs3198783;rs57778009;rs1804020	1726;1726	Q14966-3;Q14966	.;ZN638_HUMAN	M	1726;1726;666	ENSP00000264447:V1726M;ENSP00000386433:V1726M;ENSP00000386813:V666M	ENSP00000264447:V1726M	V	+	1	0	ZNF638	71507683	0.993000	0.37304	1.000000	0.80357	0.957000	0.61999	0.199000	0.17237	1.048000	0.40298	-0.254000	0.11334	GTG	G|0.710;A|0.290	0.290	strong		0.383	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497	
ADAM19	8728	hgsc.bcm.edu	37	5	156918850	156918850	+	Missense_Mutation	SNP	C	C	T	rs2287749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:156918850C>T	ENST00000517905.1	-	17	2023	c.1979G>A	c.(1978-1980)gGc>gAc	p.G660D	ADAM19_ENST00000257527.4_Missense_Mutation_p.G660D|ADAM19_ENST00000430702.2_Missense_Mutation_p.G393D|ADAM19_ENST00000394020.1_Missense_Mutation_p.G662D			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	660	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CACCCCATGGCCATTGCACTT	0.562													C|||	266	0.053115	0.0477	0.0548	5008	,	,		19065	0.004		0.1163	False		,,,				2504	0.045				p.G660D		Atlas-SNP	.											.	ADAM19	216	.	0			c.G1979A						PASS	.	C	ASP/GLY	278,4128	155.2+/-188.4	9,260,1934	130.0	99.0	109.0		1979	5.2	0.9	5	dbSNP_100	109	1093,7507	228.3+/-263.4	72,949,3279	yes	missense	ADAM19	NM_033274.3	94	81,1209,5213	TT,TC,CC		12.7093,6.3096,10.5413	probably-damaging	660/919	156918850	1371,11635	2203	4300	6503	SO:0001583	missense	8728	exon17			CCATGGCCATTGC	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.1979G>A	5.37:g.156918850C>T	ENSP00000428654:p.Gly660Asp	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	109	108	0.990826	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		146|146	0.06684981684981685|0.06684981684981685	25|25	0.0508130081300813|0.0508130081300813	23|23	0.06353591160220995|0.06353591160220995	3|3	0.005244755244755245|0.005244755244755245	95|95	0.12532981530343007|0.12532981530343007	C|C	18.83|18.83	3.706748|3.706748	0.68615|0.68615	0.063096|0.063096	0.127093|0.127093	ENSG00000135074|ENSG00000135074	ENST00000517374|ENST00000430702;ENST00000257527;ENST00000394020;ENST00000517905	.|D;D;D;D	.|0.97232	.|-4.3;-4.3;-4.3;-4.3	5.23|5.23	5.23|5.23	0.72850|0.72850	.|Epidermal growth factor-like, type 3 (1);	.|0.000000	.|0.64402	.|D	.|0.000004	T|T	0.35008|0.35008	0.0917|0.0917	M|M	0.72118|0.72118	2.19|2.19	0.58432|0.58432	D|D	0.999999|0.999999	.|P;P;P	.|0.49696	.|0.91;0.855;0.927	.|P;B;P	.|0.49561	.|0.48;0.287;0.615	T|T	0.55457|0.55457	-0.8138|-0.8138	5|10	.|0.62326	.|D	.|0.03	.|.	13.1525|13.1525	0.59498|0.59498	0.0:0.9234:0.0:0.0766|0.0:0.9234:0.0:0.0766	rs2287749;rs17600513;rs56991851;rs2287749|rs2287749;rs17600513;rs56991851;rs2287749	.|660;660;393	.|Q9H013-2;Q9H013;E9PD32	.|.;ADA19_HUMAN;.	T|D	231|393;660;662;660	.|ENSP00000414088:G393D;ENSP00000257527:G660D;ENSP00000377588:G662D;ENSP00000428654:G660D	.|ENSP00000257527:G660D	A|G	-|-	1|2	0|0	ADAM19|ADAM19	156851428|156851428	1.000000|1.000000	0.71417|0.71417	0.907000|0.907000	0.35723|0.35723	0.429000|0.429000	0.31625|0.31625	4.977000|4.977000	0.63792|0.63792	2.451000|2.451000	0.82905|0.82905	0.563000|0.563000	0.77884|0.77884	GCC|GGC	C|0.911;T|0.089	0.089	strong		0.562	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389161	1389161	+	Missense_Mutation	SNP	A	A	G	rs71614973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1389161A>G	ENST00000324803.4	+	1	3822	c.862A>G	c.(862-864)Agt>Ggt	p.S288G		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	288					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCCGATGTGGAGTGCCCGCCT	0.687													A|||	1051	0.209864	0.1362	0.2983	5008	,	,		13955	0.0536		0.3748	False		,,,				2504	0.2382				p.S288G		Atlas-SNP	.											.	CRIPAK	185	.	0			c.A862G						PASS	.						127.0	128.0	128.0					4																	1389161		2202	4298	6500	SO:0001583	missense	285464	exon1			ATGTGGAGTGCCC	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.862A>G	4.37:g.1389161A>G	ENSP00000323978:p.Ser288Gly	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	92	27	0.293478	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	A	1.586	-0.530434	0.04112	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.21734	1.99	0.815	-1.63	0.08345	.	.	.	.	.	T	0.06917	0.0176	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.39761	-0.9598	8	0.07175	T	0.84	.	2.8991	0.05700	0.2283:0.0:0.4427:0.329	.	288	Q8N1N5	CRPAK_HUMAN	G	288;230	ENSP00000323978:S288G	ENSP00000323978:S288G	S	+	1	0	CRIPAK	1379161	0.046000	0.20272	0.000000	0.03702	0.001000	0.01503	-1.350000	0.02624	-1.564000	0.01678	-0.530000	0.04314	AGT	G|1.000;|0.000	1.000	weak		0.687	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SIGLEC6	946	hgsc.bcm.edu	37	19	52033158	52033158	+	Missense_Mutation	SNP	C	C	T	rs35931837	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52033158C>T	ENST00000425629.3	-	5	986	c.832G>A	c.(832-834)Ggc>Agc	p.G278S	SIGLEC6_ENST00000474054.1_5'Flank|SIGLEC6_ENST00000343300.4_Missense_Mutation_p.G278S|SIGLEC6_ENST00000359982.4_Missense_Mutation_p.G289S|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.G226S|SIGLEC6_ENST00000391797.3_Missense_Mutation_p.G267S|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.G262S	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	278	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		GGGGGGTTGCCGTCAGCATCA	0.622													C|||	368	0.0734824	0.0038	0.2363	5008	,	,		15730	0.002		0.1183	False		,,,				2504	0.0798				p.G289S		Atlas-SNP	.											SIGLEC6_ENST00000425629,NS,carcinoma,+2,2	SIGLEC6	142	2	0			c.G865A						scavenged	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	116,4288	82.9+/-121.4	2,112,2088	76.0	86.0	83.0		676,865,799,832,784,832	1.5	0.9	19	dbSNP_126	83	938,7662	203.2+/-246.3	62,814,3424	no	missense,missense,missense,missense,missense,missense	SIGLEC6	NM_001177547.1,NM_001177548.1,NM_001177549.1,NM_001245.5,NM_198845.4,NM_198846.4	56,56,56,56,56,56	64,926,5512	TT,TC,CC		10.907,2.634,8.1052	benign,benign,benign,benign,benign,benign	226/402,289/390,267/343,278/454,262/438,278/354	52033158	1054,11950	2202	4300	6502	SO:0001583	missense	946	exon5			GGTTGCCGTCAGC	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.832G>A	19.37:g.52033158C>T	ENSP00000401502:p.Gly278Ser	Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_001177548	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	178	0.0815018315018315	4	0.008130081300813009	71	0.19613259668508287	0	0.0	103	0.1358839050131926	C	0.011	-1.691978	0.00731	0.02634	0.10907	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000359982;ENST00000436458;ENST00000343300	T;T;T;T;T	0.81163	-1.46;-1.29;-1.29;-1.29;-1.29	3.71	1.55	0.23275	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.297955	0.23995	N	0.042527	T	0.00073	0.0002	N	0.03917	-0.325	0.38054	P	0.06411100000000003	B;B;B;B;B;B	0.17852	0.002;0.0;0.016;0.007;0.024;0.009	B;B;B;B;B;B	0.09377	0.002;0.002;0.004;0.003;0.004;0.002	T	0.05451	-1.0884	9	0.02654	T	1	.	5.3372	0.15965	0.0:0.254:0.0:0.746	rs35931837	289;226;267;278;262;278	F8WA78;C9JBE5;O43699-4;O43699-2;O43699-3;O43699	.;.;.;.;.;SIGL6_HUMAN	S	251;262;278;289;226;278	ENSP00000344064:G251S;ENSP00000401502:G278S;ENSP00000353071:G289S;ENSP00000410679:G226S;ENSP00000345907:G278S	ENSP00000345907:G278S	G	-	1	0	SIGLEC6	56724970	0.083000	0.21467	0.902000	0.35471	0.038000	0.13279	-0.302000	0.08221	0.150000	0.19136	-0.492000	0.04666	GGC	C|0.914;T|0.086	0.086	strong		0.622	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
PRND	23627	hgsc.bcm.edu	37	20	4705718	4705718	+	Missense_Mutation	SNP	C	C	T	rs2245220	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4705718C>T	ENST00000305817.2	+	2	592	c.521C>T	c.(520-522)aCg>aTg	p.T174M		NM_012409.2	NP_036541.2	Q9UKY0	PRND_HUMAN	prion protein 2 (dublet)	174			T -> M (common polymorphism; dbSNP:rs2245220). {ECO:0000269|PubMed:10525406, ECO:0000269|PubMed:10825657, ECO:0000269|PubMed:11702213, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.		protein homooligomerization (GO:0051260)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	13						ATCTGGCTCACGGTGAAATAA	0.577													T|||	2480	0.495208	0.6702	0.3646	5008	,	,		19250	0.253		0.4871	False		,,,				2504	0.6094				p.T174M		Atlas-SNP	.											PRND,caecum,carcinoma,0,1	PRND	34	1	0			c.C521T	GRCh37	CM014824	PRND	M	rs2245220	PASS	.	T	MET/THR	2798,1608		897,1004,302	22.0	21.0	21.0		521	2.2	0.0	20	dbSNP_100	21	4200,4392		1030,2140,1126	yes	missense	PRND	NM_012409.2	81	1927,3144,1428	TT,TC,CC		48.8827,36.4957,46.1609	benign	174/177	4705718	6998,6000	2203	4296	6499	SO:0001583	missense	23627	exon2			GGCTCACGGTGAA	AF106918	CCDS13081.1	20p13	2013-09-19			ENSG00000171864	ENSG00000171864			15748	protein-coding gene	gene with protein product	"""prion-like protein doppel"""	604263				10525406, 10577243	Standard	NM_012409		Approved	DPL, dJ1068H6.4, DOPPEL, PrPLP	uc002wkz.3	Q9UKY0	OTTHUMG00000031789	ENST00000305817.2:c.521C>T	20.37:g.4705718C>T	ENSP00000306900:p.Thr174Met	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	76	34	0.447368	NM_012409	A7U7M5|Q9H311|Q9H312|Q9NTM4	Missense_Mutation	SNP	ENST00000305817.2	37	CCDS13081.1	1004	0.4597069597069597	345	0.7012195121951219	140	0.3867403314917127	151	0.263986013986014	368	0.48548812664907653	T	8.922	0.961269	0.18583	0.635043	0.488827	ENSG00000171864	ENST00000305817	D	0.88664	-2.41	4.7	2.23	0.28157	Prion/Doppel protein, beta-ribbon domain (1);	0.787074	0.11050	N	0.605177	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43766	-0.9371	9	0.38643	T	0.18	-13.5917	3.7704	0.08639	0.0:0.2044:0.1882:0.6074	rs2245220;rs17736407;rs17846360;rs17859396;rs52805311;rs61599564;rs2245220	174	Q9UKY0	PRND_HUMAN	M	174	ENSP00000306900:T174M	ENSP00000306900:T174M	T	+	2	0	PRND	4653718	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	0.864000	0.27926	0.253000	0.21552	-0.381000	0.06696	ACG	C|0.492;T|0.508	0.508	strong		0.577	PRND-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077827.2	NM_012409	
NPW	283869	hgsc.bcm.edu	37	16	2070200	2070200	+	Missense_Mutation	SNP	G	G	C	rs11248906	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2070200G>C	ENST00000566435.1	+	1	655	c.142G>C	c.(142-144)Gag>Cag	p.E48Q	NPW_ENST00000329610.4_Missense_Mutation_p.E100Q			Q8N729	NPW_HUMAN	neuropeptide W	100					feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				kidney(1)	1						GGAGCTGTGGGAGACGCGACG	0.756													G|||	465	0.0928514	0.0567	0.1311	5008	,	,		10039	0.0		0.2256	False		,,,				2504	0.0736				p.E100Q		Atlas-SNP	.											.	NPW	4	.	0			c.G298C						PASS	.	G	GLN/GLU	242,3078		11,220,1429	7.0	8.0	7.0		298	2.1	0.1	16	dbSNP_120	7	1359,6037		104,1151,2443	yes	missense	NPW	NM_001099456.2	29	115,1371,3872	CC,CG,GG		18.3748,7.2892,14.9403	benign	100/166	2070200	1601,9115	1660	3698	5358	SO:0001583	missense	283869	exon1			CTGTGGGAGACGC	AB084276	CCDS42102.1	16p13.3	2013-02-26			ENSG00000183971	ENSG00000183971		"""Endogenous ligands"""	30509	protein-coding gene	gene with protein product	"""prepro-neuropeptide W"""	607997				12118011, 12401809	Standard	NM_001099456		Approved	PPL8	uc002coh.4	Q8N729	OTTHUMG00000176914	ENST00000566435.1:c.142G>C	16.37:g.2070200G>C	ENSP00000456974:p.Glu48Gln	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	13	12	0.923077	NM_001099456		Missense_Mutation	SNP	ENST00000566435.1	37		243	0.11126373626373626	21	0.042682926829268296	57	0.1574585635359116	0	0.0	165	0.21767810026385223	g	10.79	1.451090	0.26074	0.072892	0.183748	ENSG00000183971	ENST00000329610	T	0.50548	0.74	3.08	2.12	0.27331	.	0.406531	0.21498	U	0.073573	T	0.00039	0.0001	N	0.17082	0.46	0.58432	P	4.000000000004E-6	D	0.63046	0.992	P	0.57620	0.824	T	0.06092	-1.0846	9	0.51188	T	0.08	.	6.1772	0.20451	0.1452:0.0:0.8548:0.0	rs11248906	100	Q8N729	NPW_HUMAN	Q	100	ENSP00000330070:E100Q	ENSP00000330070:E100Q	E	+	1	0	NPW	2010201	0.004000	0.15560	0.091000	0.20842	0.107000	0.19398	0.835000	0.27531	0.652000	0.30806	0.400000	0.26472	GAG	G|0.881;C|0.119	0.119	strong		0.756	NPW-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000434312.1	NM_001099456	
NECAB2	54550	hgsc.bcm.edu	37	16	84030848	84030848	+	Silent	SNP	C	C	T	rs7193267	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84030848C>T	ENST00000305202.4	+	9	840	c.823C>T	c.(823-825)Ctg>Ttg	p.L275L	NECAB2_ENST00000567703.1_3'UTR|NECAB2_ENST00000565691.1_Silent_p.L192L	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	275						cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						GCAGCAGCGCCTGTCAGATGA	0.607													C|||	17	0.00339457	0.0015	0.0072	5008	,	,		16661	0.0		0.0099	False		,,,				2504	0.0				p.L275L		Atlas-SNP	.											.	NECAB2	36	.	0			c.C823T						PASS	.	C		14,4386	21.2+/-45.6	0,14,2186	188.0	136.0	154.0		823	4.5	0.9	16	dbSNP_116	154	99,8501	54.4+/-115.2	1,97,4202	no	coding-synonymous	NECAB2	NM_019065.2		1,111,6388	TT,TC,CC		1.1512,0.3182,0.8692		275/387	84030848	113,12887	2200	4300	6500	SO:0001819	synonymous_variant	54550	exon9			CAGCGCCTGTCAG	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.823C>T	16.37:g.84030848C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	133	64	0.481203	NM_019065	A2RRG3|O75547|Q6ZSK0	Silent	SNP	ENST00000305202.4	37	CCDS10940.1																																																																																			C|0.992;T|0.008	0.008	strong		0.607	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
C5orf60	285679	hgsc.bcm.edu	37	5	179069912	179069912	+	Missense_Mutation	SNP	C	C	T	rs75942553	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179069912C>T	ENST00000448248.2	-	4	666	c.641G>A	c.(640-642)aGc>aAc	p.S214N	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	214	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						TGATAGGGTGCTCGCAGGTGG	0.602													-|||	305	0.0609026	0.0257	0.0663	5008	,	,		17687	0.0843		0.0755	False		,,,				2504	0.0654				p.S214N		Atlas-SNP	.											.	C5orf60	24	.	0			c.G641A						PASS	.	C	ASN/SER	39,1345		0,39,653	72.0	73.0	72.0		641	0.1	0.0	5	dbSNP_131	72	277,2905		14,249,1328	no	missense	C5orf60	NM_001142306.1	46	14,288,1981	TT,TC,CC		8.7052,2.8179,6.9207	probably-damaging	214/278	179069912	316,4250	692	1591	2283	SO:0001583	missense	285679	exon4			AGGGTGCTCGCAG	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.641G>A	5.37:g.179069912C>T	ENSP00000404583:p.Ser214Asn	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	383	200	0.522193	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	132	0.06043956043956044	14	0.028455284552845527	22	0.06077348066298342	44	0.07692307692307693	52	0.06860158311345646	c	10.63	1.403766	0.25291	0.028179	0.087052	ENSG00000204661	ENST00000448248	T	0.24723	1.84	0.118	0.118	0.14667	.	.	.	.	.	T	0.00875	0.0029	L	0.42245	1.32	0.09310	N	1	P;P	0.51449	0.945;0.945	P;P	0.51866	0.682;0.682	T	0.07309	-1.0779	8	0.10902	T	0.67	.	.	.	.	.	214;214	A6NFR6-2;A6NFR6-4	.;.	N	214	ENSP00000404583:S214N	ENSP00000404583:S214N	S	-	2	0	C5orf60	179002518	0.065000	0.20965	0.044000	0.18714	0.025000	0.11179	0.197000	0.17197	0.191000	0.20236	0.194000	0.17425	AGC	C|0.934;T|0.066	0.066	strong		0.602	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
FAM208B	54906	hgsc.bcm.edu	37	10	5784151	5784151	+	Missense_Mutation	SNP	A	A	G	rs45575338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5784151A>G	ENST00000328090.5	+	14	3044	c.2419A>G	c.(2419-2421)Atc>Gtc	p.I807V	RP11-336A10.2_ENST00000411512.2_RNA	NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	807			I -> V (in dbSNP:rs45575338).														TCAGAACAAAATCATACGATC	0.398													G|||	704	0.140575	0.0719	0.2378	5008	,	,		18896	0.1498		0.1909	False		,,,				2504	0.1033				p.I807V		Atlas-SNP	.											C10orf18,NS,carcinoma,-2,1	.	.	1	0			c.A2419G						PASS	.	G	VAL/ILE	281,3451		10,261,1595	125.0	114.0	117.0		2419	4.7	0.1	10	dbSNP_127	117	1714,6484		184,1346,2569	yes	missense	FAM208B	NM_017782.4	29	194,1607,4164	GG,GA,AA		20.9075,7.5295,16.7225	benign	807/2431	5784151	1995,9935	1866	4099	5965	SO:0001583	missense	54906	exon14			AACAAAATCATAC	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.2419A>G	10.37:g.5784151A>G	ENSP00000328426:p.Ile807Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	376	0.17216117216117216	38	0.07723577235772358	91	0.2513812154696133	101	0.17657342657342656	146	0.19261213720316622	G	0.530	-0.858420	0.02610	0.075295	0.209075	ENSG00000108021	ENST00000328090	T	0.03524	3.9	5.57	4.66	0.58398	.	0.229969	0.30538	N	0.009413	T	0.00012	0.0000	N	0.00088	-2.19	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38178	-0.9673	9	0.02654	T	1	.	4.2655	0.10761	0.1442:0.1241:0.6039:0.1278	rs45575338	807	Q5VWN6	F208B_HUMAN	V	807	ENSP00000328426:I807V	ENSP00000328426:I807V	I	+	1	0	C10orf18	5824157	0.152000	0.22762	0.139000	0.22197	0.842000	0.47809	0.156000	0.16382	0.718000	0.32166	-0.119000	0.15052	ATC	A|0.816;G|0.184	0.184	strong		0.398	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
TMEM187	8269	hgsc.bcm.edu	37	X	153248248	153248248	+	Silent	SNP	G	G	A	rs13397	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153248248G>A	ENST00000369982.4	+	2	1482	c.735G>A	c.(733-735)acG>acA	p.T245T	MIR3202-1_ENST00000580198.1_RNA	NM_003492.2	NP_003483.1	Q14656	TM187_HUMAN	transmembrane protein 187	245						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|large_intestine(1)|lung(1)|prostate(2)	5	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGTTTCTGACGCATTTCAACA	0.542													G|||	1314	0.348079	0.0219	0.3184	3775	,	,		16262	0.5298		0.1153	False		,,,				2504	0.4233				p.T245T		Atlas-SNP	.											.	TMEM187	21	.	0			c.G735A						PASS	.	G		164,3671		2,133,27,1497,544	100.0	88.0	92.0		735	-8.7	0.0	X	dbSNP_52	92	949,5779		47,584,271,1797,1601	no	coding-synonymous	TMEM187	NM_003492.2		49,717,298,3294,2145	AA,AG,A,GG,G		14.1052,4.2764,10.5368		245/262	153248248	1113,9450	2203	4300	6503	SO:0001819	synonymous_variant	8269	exon2			TCTGACGCATTTC	X92475	CCDS14739.1	Xq28	2007-03-14	2007-03-14	2007-03-14	ENSG00000177854	ENSG00000177854			13705	protein-coding gene	gene with protein product		300059	"""chromosome X open reading frame 12"""	CXorf12		8661027	Standard	NM_003492		Approved	ITBA1, DXS9878E	uc004fjq.2	Q14656	OTTHUMG00000024220	ENST00000369982.4:c.735G>A	X.37:g.153248248G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	114	114	1	NM_003492	B2RC47|Q6IAV7	Silent	SNP	ENST00000369982.4	37	CCDS14739.1																																																																																			0|0.003;A|0.194	0.194	strong		0.542	TMEM187-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061093.1	NM_003492	
EYS	346007	hgsc.bcm.edu	37	6	65300143	65300143	+	Missense_Mutation	SNP	G	G	C	rs16895517	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65300143G>C	ENST00000370621.3	-	26	6143	c.5617C>G	c.(5617-5619)Ctg>Gtg	p.L1873V	EYS_ENST00000370616.2_Missense_Mutation_p.L1873V|EYS_ENST00000503581.1_Missense_Mutation_p.L1873V			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1873			L -> V (in dbSNP:rs16895517). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TGAGGTGCCAGAATGGATTCC	0.428													G|||	457	0.091254	0.0061	0.1167	5008	,	,		19844	0.1567		0.0984	False		,,,				2504	0.1135				p.L1873V		Atlas-SNP	.											.	EYS	527	.	0			c.C5617G						PASS	.	G	VAL/LEU	39,1345		1,37,654	124.0	119.0	120.0		5617	2.0	0.0	6	dbSNP_123	120	445,2737		41,363,1187	yes	missense	EYS	NM_001142800.1	32	42,400,1841	CC,CG,GG		13.9849,2.8179,10.6001	possibly-damaging	1873/3145	65300143	484,4082	692	1591	2283	SO:0001583	missense	346007	exon26			GTGCCAGAATGGA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.5617C>G	6.37:g.65300143G>C	ENSP00000359655:p.Leu1873Val	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	89	86	0.966292	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		211	0.09661172161172162	2	0.0040650406504065045	44	0.12154696132596685	86	0.15034965034965034	79	0.10422163588390501	G	0.007	-1.981510	0.00448	0.028179	0.139849	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84660	-1.88;-1.85;-1.85	5.96	1.96	0.26148	.	.	.	.	.	T	0.46521	0.1397	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.02214	-1.1194	8	0.23891	T	0.37	.	6.1373	0.20241	0.0956:0.2973:0.4963:0.1108	rs16895517;rs52800058;rs16895517	1873;1873	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	V	1873	ENSP00000424243:L1873V;ENSP00000359655:L1873V;ENSP00000359650:L1873V	ENSP00000359650:L1873V	L	-	1	2	EYS	65356864	0.000000	0.05858	0.000000	0.03702	0.406000	0.30931	-0.025000	0.12413	-0.138000	0.11434	-0.795000	0.03280	CTG	G|0.909;C|0.091	0.091	strong		0.428	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
HHAT	55733	hgsc.bcm.edu	37	1	210577901	210577901	+	Missense_Mutation	SNP	T	T	C	rs34228541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:210577901T>C	ENST00000367010.1	+	6	789	c.562T>C	c.(562-564)Tgc>Cgc	p.C188R	HHAT_ENST00000391905.3_Missense_Mutation_p.C188R|HHAT_ENST00000541565.1_Intron|HHAT_ENST00000545154.1_Missense_Mutation_p.C189R|HHAT_ENST00000308852.6_Missense_Mutation_p.C143R|HHAT_ENST00000545781.1_Missense_Mutation_p.C125R|HHAT_ENST00000413764.2_Missense_Mutation_p.C188R|HHAT_ENST00000537898.1_Missense_Mutation_p.C123R|HHAT_ENST00000261458.3_Missense_Mutation_p.C188R	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	188			C -> R (in dbSNP:rs34228541). {ECO:0000269|PubMed:14702039}.		multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		CCTGGAGCTCTGCTGGCAGCA	0.527													T|||	405	0.0808706	0.034	0.111	5008	,	,		20164	0.002		0.1789	False		,,,				2504	0.1033				p.C189R		Atlas-SNP	.											HHAT,NS,carcinoma,-2,1	HHAT	66	1	0			c.T565C						PASS	.	T	ARG/CYS,,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	239,4167	139.6+/-175.2	6,227,1970	101.0	88.0	92.0		562,,562,565,367,562	5.5	1.0	1	dbSNP_126	92	1603,6997	297.3+/-303.3	163,1277,2860	yes	missense,intron,missense,missense,missense,missense	HHAT	NM_001122834.2,NM_001170564.1,NM_001170580.1,NM_001170587.1,NM_001170588.1,NM_018194.4	180,,180,180,180,180	169,1504,4830	CC,CT,TT		18.6395,5.4244,14.1627	probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging	188/494,,188/494,189/495,123/429,188/494	210577901	1842,11164	2203	4300	6503	SO:0001583	missense	55733	exon5			GAGCTCTGCTGGC	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.562T>C	1.37:g.210577901T>C	ENSP00000355977:p.Cys188Arg	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Missense_Mutation	SNP	ENST00000367010.1	37	CCDS1495.1	202	0.0924908424908425	23	0.046747967479674794	40	0.11049723756906077	0	0.0	139	0.18337730870712401	T	24.0	4.487403	0.84854	0.054244	0.186395	ENSG00000054392	ENST00000413764;ENST00000545154;ENST00000537898;ENST00000391905;ENST00000545781;ENST00000261458;ENST00000308852;ENST00000367010;ENST00000426968	T;T;T;T;T;T;T;T;T	0.25749	2.01;2.0;2.1;1.97;2.02;2.01;2.05;2.01;1.78	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	M	0.80183	2.485	0.09310	P	0.999999999893868	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.999;1.0;1.0	T	0.00728	-1.1591	9	0.34782	T	0.22	-39.1205	15.3723	0.74573	0.0:0.0:0.0:1.0	rs34228541	143;189;123;188	B7Z2U8;F5H444;B7Z5I1;Q5VTY9	.;.;.;HHAT_HUMAN	R	188;189;123;188;125;188;143;188;60	ENSP00000416845:C188R;ENSP00000438468:C189R;ENSP00000442625:C123R;ENSP00000375773:C188R;ENSP00000439229:C125R;ENSP00000261458:C188R;ENSP00000308628:C143R;ENSP00000355977:C188R;ENSP00000413399:C60R	ENSP00000261458:C188R	C	+	1	0	HHAT	208644524	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	7.100000	0.76989	2.107000	0.64212	0.482000	0.46254	TGC	T|0.874;C|0.126	0.126	strong		0.527	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792093	8792093	+	Silent	SNP	G	G	A	rs16957702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8792093G>A	ENST00000447110.1	-	10	1135	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	PIK3R5_ENST00000581552.1_Silent_p.D337D|PIK3R5_ENST00000584803.1_Silent_p.D337D	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	337				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						CACAGTGCCCGTCAGTTTCCA	0.612													G|||	1017	0.203075	0.2995	0.2839	5008	,	,		18474	0.001		0.2843	False		,,,				2504	0.1401				p.D337D	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.C1011T						PASS	.	G	,	1302,3104	437.8+/-345.1	204,894,1105	106.0	102.0	103.0		1011,1011	-10.5	0.0	17	dbSNP_123	103	2694,5906	430.6+/-356.6	418,1858,2024	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	622,2752,3129	AA,AG,GG		31.3256,29.5506,30.7243	,	337/881,337/881	8792093	3996,9010	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			GTGCCCGTCAGTT	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.1011C>T	17.37:g.8792093G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			G|0.734;A|0.266	0.266	strong		0.612	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
FAM209A	200232	hgsc.bcm.edu	37	20	55099977	55099977	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:55099977A>G	ENST00000371328.3	+	1	436	c.113A>G	c.(112-114)tAc>tGc	p.Y38C	GCNT7_ENST00000243913.4_Intron|FAM209A_ENST00000481560.1_3'UTR	NM_001012971.3	NP_001012989.2	Q5JX71	F209A_HUMAN	family with sequence similarity 209, member A	38						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)											AAGGTGCAATACGGAGAGCAC	0.517																																					p.Y38C		Atlas-SNP	.											.	.	.	.	0			c.A113G						PASS	.						158.0	143.0	148.0					20																	55099977		2203	4300	6503	SO:0001583	missense	200232	exon1			TGCAATACGGAGA	AL109806	CCDS33493.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000124103	ENSG00000124103			16100	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 106"""	C20orf106			Standard	NM_001012971		Approved	dJ1153D9.3		Q5JX71	OTTHUMG00000032799	ENST00000371328.3:c.113A>G	20.37:g.55099977A>G	ENSP00000360379:p.Tyr38Cys	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	181	22	0.121547	NM_001012971	Q05C43	Missense_Mutation	SNP	ENST00000371328.3	37	CCDS33493.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.160435	0.00321	.	.	ENSG00000124103	ENST00000371328	T	0.06687	3.27	5.51	4.52	0.55395	.	0.114561	0.39544	N	0.001338	T	0.02304	0.0071	N	0.00926	-1.1	0.30465	N	0.773854	B	0.02656	0.0	B	0.01281	0.0	T	0.33548	-0.9864	10	0.02654	T	1	-14.443	10.2141	0.43158	0.0936:0.0:0.9064:0.0	.	38	Q5JX71	CT106_HUMAN	C	38	ENSP00000360379:Y38C	ENSP00000360379:Y38C	Y	+	2	0	C20orf106	54533384	0.384000	0.25164	0.682000	0.30024	0.001000	0.01503	1.980000	0.40618	1.302000	0.44855	-0.621000	0.04028	TAC	.	.	none		0.517	FAM209A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079815.2		
FAT1	2195	hgsc.bcm.edu	37	4	187509931	187509931	+	Missense_Mutation	SNP	C	C	T	rs192609167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187509931C>T	ENST00000441802.2	-	27	13791	c.13582G>A	c.(13582-13584)Gag>Aag	p.E4528K		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4528					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						GCGGGCGCCTCGAAGTGTCTT	0.562										HNSCC(5;0.00058)			C|||	3	0.000599042	0.0	0.0014	5008	,	,		17560	0.0		0.002	False		,,,				2504	0.0				p.E4528K	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G13582A						PASS	.	C	LYS/GLU	5,4159		0,5,2077	60.0	70.0	67.0		13582	5.4	0.0	4		67	67,8369		0,67,4151	yes	missense	FAT1	NM_005245.3	56	0,72,6228	TT,TC,CC		0.7942,0.1201,0.5714	benign	4528/4589	187509931	72,12528	2082	4218	6300	SO:0001583	missense	2195	exon27			GCGCCTCGAAGTG	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.13582G>A	4.37:g.187509931C>T	ENSP00000406229:p.Glu4528Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	110	49	0.445455	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.46|13.46	2.243967|2.243967	0.39697|0.39697	0.001201|0.001201	0.007942|0.007942	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772	T|.	0.38077|.	1.16|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.411428|.	0.30311|.	N|.	0.009906|.	T|T	0.67420|0.67420	0.2891|0.2891	M|M	0.62723|0.62723	1.935|1.935	0.58432|0.58432	D|D	0.999994|0.999994	P|.	0.42337|.	0.776|.	B|.	0.26770|.	0.073|.	T|T	0.68232|0.68232	-0.5463|-0.5463	10|5	0.21014|.	T|.	0.42|.	.|.	19.3098|19.3098	0.94182|0.94182	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4528|.	Q14517|.	FAT1_HUMAN|.	K|Q	4528;4530|307	ENSP00000406229:E4528K|.	ENSP00000260147:E4530K|.	E|R	-|-	1|2	0|0	FAT1|FAT1	187746925|187746925	1.000000|1.000000	0.71417|0.71417	0.043000|0.043000	0.18650|0.18650	0.008000|0.008000	0.06430|0.06430	7.309000|7.309000	0.78937|0.78937	2.800000|2.800000	0.96347|0.96347	0.455000|0.455000	0.32223|0.32223	GAG|CGA	C|0.999;T|0.001	0.001	strong		0.562	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
LCT	3938	hgsc.bcm.edu	37	2	136561557	136561557	+	Silent	SNP	G	G	A	rs2304371	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:136561557G>A	ENST00000264162.2	-	11	4616	c.4606C>T	c.(4606-4608)Ctg>Ttg	p.L1536L		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1536	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	GGCTCATTCAGCGTGATCCAA	0.522													G|||	3306	0.660144	0.4047	0.7507	5008	,	,		20923	0.7758		0.7485	False		,,,				2504	0.7311				p.L1536L		Atlas-SNP	.											.	LCT	309	.	0			c.C4606T						PASS	.	G		2172,2234	585.3+/-386.2	536,1100,567	142.0	108.0	120.0		4606	2.8	0.7	2	dbSNP_100	120	6875,1725	737.2+/-407.0	2785,1305,210	no	coding-synonymous	LCT	NM_002299.2		3321,2405,777	AA,AG,GG		20.0581,49.2964,30.4398		1536/1928	136561557	9047,3959	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon11			CATTCAGCGTGAT	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4606C>T	2.37:g.136561557G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.327;A|0.673	0.673	strong		0.522	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
HAGH	3029	hgsc.bcm.edu	37	16	1869147	1869147	+	Silent	SNP	G	G	A	rs56316151	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1869147G>A	ENST00000397356.3	-	5	916	c.510C>T	c.(508-510)ccC>ccT	p.P170P	HAGH_ENST00000455446.2_Intron|HAGH_ENST00000566709.1_Silent_p.P122P|HAGH_ENST00000397353.2_Silent_p.P122P	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	170					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)	CCGAGCCTCCGGGCTTGCTCA	0.627													G|||	53	0.0105831	0.0023	0.0173	5008	,	,		14613	0.0		0.0278	False		,,,				2504	0.0102				p.P170P	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C510T						PASS	.	G	,	40,4356	42.3+/-75.8	0,40,2158	44.0	44.0	44.0		366,510	-6.6	0.0	16	dbSNP_129	44	332,8268	112.9+/-173.0	6,320,3974	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	6,360,6132	AA,AG,GG		3.8605,0.9099,2.8624	,	122/261,170/309	1869147	372,12624	2198	4300	6498	SO:0001819	synonymous_variant	3029	exon5			GCCTCCGGGCTTG	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.510C>T	16.37:g.1869147G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.975;A|0.025	0.025	strong		0.627	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326	
CCDC65	85478	hgsc.bcm.edu	37	12	49308284	49308284	+	Missense_Mutation	SNP	A	A	G	rs10747556	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49308284A>G	ENST00000320516.4	+	3	586	c.398A>G	c.(397-399)cAc>cGc	p.H133R	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Missense_Mutation_p.H133R	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	133			H -> R (in dbSNP:rs10747556).							breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						CTGCAGAGGCACCGGCTCAGT	0.547													G|||	1552	0.309904	0.1067	0.4971	5008	,	,		16937	0.4444		0.4095	False		,,,				2504	0.2106				p.H133R		Atlas-SNP	.											.	CCDC65	41	.	0			c.A398G						PASS	.	G	ARG/HIS	711,3695	760.3+/-413.0	77,557,1569	77.0	67.0	70.0		398	0.9	0.0	12	dbSNP_120	70	3288,5312	646.6+/-400.3	618,2052,1630	yes	missense	CCDC65	NM_033124.4	29	695,2609,3199	GG,GA,AA		38.2326,16.1371,30.7473	benign	133/485	49308284	3999,9007	2203	4300	6503	SO:0001583	missense	85478	exon3			AGAGGCACCGGCT		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.398A>G	12.37:g.49308284A>G	ENSP00000312706:p.His133Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	780	0.35714285714285715	51	0.10365853658536585	161	0.4447513812154696	265	0.4632867132867133	303	0.3997361477572559	G	0.013	-1.610638	0.00835	0.161371	0.382326	ENSG00000139537	ENST00000266984;ENST00000320516	T;T	0.28069	1.63;1.64	4.78	0.867	0.19085	.	0.765819	0.12896	N	0.430158	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	0.48525	-0.9028	9	0.15952	T	0.53	6.4696	11.2745	0.49159	0.4129:0.0:0.5871:0.0	rs10747556;rs52811535;rs58420544;rs10747556	133	Q8IXS2	CCD65_HUMAN	R	133	ENSP00000266984:H133R;ENSP00000312706:H133R	ENSP00000266984:H133R	H	+	2	0	CCDC65	47594551	0.998000	0.40836	0.042000	0.18584	0.208000	0.24298	3.153000	0.50685	-0.378000	0.07918	-3.123000	0.00061	CAC	A|0.685;G|0.315	0.315	strong		0.547	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
MYO3A	53904	hgsc.bcm.edu	37	10	26310470	26310470	+	Silent	SNP	C	C	T	rs35010955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:26310470C>T	ENST00000265944.5	+	8	790	c.624C>T	c.(622-624)gaC>gaT	p.D208D	MYO3A_ENST00000543632.1_Silent_p.D208D|MYO3A_ENST00000376302.1_Silent_p.D208D	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	208	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CCACTTATGACGCCAGATGTG	0.438													T|||	243	0.0485224	0.0628	0.0533	5008	,	,		19555	0.001		0.0974	False		,,,				2504	0.0245				p.D208D		Atlas-SNP	.											.	MYO3A	371	.	0			c.C624T						PASS	.	T		293,4113	799.6+/-415.5	7,279,1917	194.0	164.0	174.0		624	4.9	1.0	10	dbSNP_126	174	862,7738	780.4+/-407.7	47,768,3485	no	coding-synonymous	MYO3A	NM_017433.4		54,1047,5402	TT,TC,CC		10.0233,6.65,8.8805		208/1617	26310470	1155,11851	2203	4300	6503	SO:0001819	synonymous_variant	53904	exon8			TTATGACGCCAGA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.624C>T	10.37:g.26310470C>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Silent	SNP	ENST00000265944.5	37	CCDS7148.1																																																																																			C|0.923;T|0.077	0.077	strong		0.438	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
INPP4A	3631	hgsc.bcm.edu	37	2	99149946	99149946	+	Silent	SNP	G	G	A	rs2278211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:99149946G>A	ENST00000523221.1	+	3	258	c.258G>A	c.(256-258)acG>acA	p.T86T	INPP4A_ENST00000074304.5_Silent_p.T86T|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409540.3_Silent_p.T86T|INPP4A_ENST00000545415.1_Silent_p.T86T|INPP4A_ENST00000409851.3_Silent_p.T86T|INPP4A_ENST00000409016.4_Silent_p.T86T			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	86	C2.				inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(1)|endometrium(9)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(4)|upper_aerodigestive_tract(4)	43						ATGCACAGACGGAGATCATTG	0.522													G|||	1154	0.230431	0.0749	0.304	5008	,	,		18892	0.2956		0.2674	False		,,,				2504	0.2832				p.T86T		Atlas-SNP	.											.	INPP4A	205	.	0			c.G258A						PASS	.	G	,,,	479,3711		32,415,1648	112.0	112.0	112.0		258,258,258,258	-2.2	1.0	2	dbSNP_100	112	2216,6242		296,1624,2309	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	,,,	328,2039,3957	AA,AG,GG		26.2,11.432,21.3077	,,,	86/978,86/973,86/955,86/939	99149946	2695,9953	2095	4229	6324	SO:0001819	synonymous_variant	3631	exon5			ACAGACGGAGATC	U26398	CCDS46369.1, CCDS46370.1, CCDS46371.1, CCDS46372.1	2q11.2	2008-05-27	2002-08-29		ENSG00000040933	ENSG00000040933			6074	protein-coding gene	gene with protein product		600916	"""inositol polyphosphate-4-phosphatase, type I, 107kD"""	INPP4		7608176, 9295334	Standard	NM_004027		Approved		uc002syy.3	Q96PE3	OTTHUMG00000153106	ENST00000523221.1:c.258G>A	2.37:g.99149946G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	83	0.976471	NM_004027	O15326|Q13187|Q53TD8|Q8TC02	Silent	SNP	ENST00000523221.1	37	CCDS46369.1																																																																																			G|0.779;N|0.000	.	strong		0.522	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
GALNT6	11226	hgsc.bcm.edu	37	12	51771040	51771040	+	Silent	SNP	T	T	C	rs2277379	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51771040T>C	ENST00000543196.2	-	3	808	c.603A>G	c.(601-603)ctA>ctG	p.L201L	GALNT6_ENST00000356317.3_Silent_p.L201L|GALNT6_ENST00000603203.1_5'Flank			Q8NCL4	GALT6_HUMAN	polypeptide N-acetylgalactosaminyltransferase 6	201	Catalytic subdomain A.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(2)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GGGTGGTGTGTAGGACGCTGT	0.617													T|||	538	0.107428	0.0469	0.1585	5008	,	,		19747	0.1726		0.0497	False		,,,				2504	0.1452				p.L201L		Atlas-SNP	.											.	GALNT6	63	.	0			c.A603G						PASS	.	T		208,4198	127.4+/-164.3	7,194,2002	139.0	108.0	118.0		603	-7.9	0.5	12	dbSNP_100	118	338,8262	116.8+/-176.5	5,328,3967	no	coding-synonymous	GALNT6	NM_007210.3		12,522,5969	CC,CT,TT		3.9302,4.7208,4.1981		201/623	51771040	546,12460	2203	4300	6503	SO:0001819	synonymous_variant	11226	exon4			GGTGTGTAGGACG	Y08565	CCDS8813.1	12q13	2014-03-13	2014-03-13		ENSG00000139629	ENSG00000139629		"""Glycosyltransferase family 2 domain containing"""	4128	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 6"""	605148	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 6 (GalNAc-T6)"""			10464263	Standard	NM_007210		Approved	GalNAc-T6	uc001ryl.1	Q8NCL4		ENST00000543196.2:c.603A>G	12.37:g.51771040T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	193	97	0.502591	NM_007210	Q8IYH4|Q9H6G2|Q9UIV5	Silent	SNP	ENST00000543196.2	37	CCDS8813.1																																																																																			T|0.930;C|0.070	0.070	strong		0.617	GALNT6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469735.1	NM_007210	
FCGBP	8857	hgsc.bcm.edu	37	19	40389741	40389741	+	Missense_Mutation	SNP	A	A	G	rs141158749		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40389741A>G	ENST00000221347.6	-	18	8448	c.8441T>C	c.(8440-8442)gTg>gCg	p.V2814A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2814	Cys-rich.		V -> A (in dbSNP:rs3746009). {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)			GACTTTACCCACATGGCACGT	0.637																																					p.V2814A		Atlas-SNP	.											FCGBP,NS,neuroblastoma,0,3	FCGBP	416	3	0			c.T8441C						scavenged	.						13.0	11.0	12.0					19																	40389741		2055	3702	5757	SO:0001583	missense	8857	exon18			TTACCCACATGGC	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.8441T>C	19.37:g.40389741A>G	ENSP00000221347:p.Val2814Ala	Somatic	1136	5	0.00440141		WXS	Illumina HiSeq	Phase_I	783	325	0.41507	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	N	0.031	-1.331696	0.01298	.	.	ENSG00000090920	ENST00000221347	T	0.04603	3.59	2.94	-1.02	0.10135	von Willebrand factor, type C (1);	0.713318	0.11461	N	0.561738	T	0.01222	0.0040	N	0.00760	-1.21	0.80722	P	0.0	B	0.16603	0.018	B	0.18871	0.023	T	0.45760	-0.9239	9	0.07990	T	0.79	.	3.5552	0.07862	0.3816:0.1953:0.4231:0.0	.	2814	Q9Y6R7	FCGBP_HUMAN	A	2814	ENSP00000221347:V2814A	ENSP00000221347:V2814A	V	-	2	0	FCGBP	45081581	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.449000	0.21744	-0.587000	0.05890	-1.994000	0.00447	GTG	A|0.200;G|0.800	0.800	strong		0.637	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
HOXC4	3221	hgsc.bcm.edu	37	12	54448106	54448106	+	Missense_Mutation	SNP	A	A	G	rs75256744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:54448106A>G	ENST00000430889.2	+	1	446	c.400A>G	c.(400-402)Ata>Gta	p.I134V	HOXC4_ENST00000303406.4_Missense_Mutation_p.I134V|HOXC4_ENST00000609810.1_Missense_Mutation_p.I134V	NM_153633.2	NP_705897.1	P09017	HXC4_HUMAN	homeobox C4	134					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	13						CAAGCAACCCATAGTCTACCC	0.647													A|||	554	0.110623	0.0174	0.0908	5008	,	,		8955	0.0337		0.1769	False		,,,				2504	0.2618				p.I134V		Atlas-SNP	.											.	HOXC4	29	.	0			c.A400G						PASS	.	A	VAL/ILE,VAL/ILE	184,4222		6,172,2025	25.0	25.0	25.0		400,400	4.3	1.0	12	dbSNP_131	25	1507,7091		132,1243,2924	yes	missense,missense	HOXC4	NM_014620.4,NM_153633.2	29,29	138,1415,4949	GG,GA,AA		17.5273,4.1761,13.0037	benign,benign	134/265,134/265	54448106	1691,11313	2203	4299	6502	SO:0001583	missense	3221	exon3			CAACCCATAGTCT		CCDS8873.1	12q13.13	2011-06-20	2005-12-22		ENSG00000198353	ENSG00000198353		"""Homeoboxes / ANTP class : HOXL subclass"""	5126	protein-coding gene	gene with protein product		142974	"""homeo box C4"""	HOX3, HOX3E		1973146, 1358459	Standard	NM_014620		Approved		uc001sex.3	P09017	OTTHUMG00000160036	ENST00000430889.2:c.400A>G	12.37:g.54448106A>G	ENSP00000399808:p.Ile134Val	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	91	32	0.351648	NM_014620		Missense_Mutation	SNP	ENST00000430889.2	37	CCDS8873.1	217	0.09935897435897435	24	0.04878048780487805	38	0.10497237569060773	19	0.033216783216783216	136	0.17941952506596306	A	0.226	-1.024613	0.02061	0.041761	0.175273	ENSG00000198353	ENST00000303406;ENST00000430889	D;D	0.88354	-2.37;-2.37	4.26	4.26	0.50523	.	0.062472	0.64402	D	0.000007	T	0.00210	0.0006	N	0.00258	-1.755	0.26297	P	0.9780349	B	0.06786	0.001	B	0.08055	0.003	T	0.42032	-0.9475	9	0.02654	T	1	.	12.7918	0.57539	1.0:0.0:0.0:0.0	.	134	P09017	HXC4_HUMAN	V	134	ENSP00000305973:I134V;ENSP00000399808:I134V	ENSP00000305973:I134V	I	+	1	0	HOXC4	52734373	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.533000	0.45667	1.918000	0.55548	0.379000	0.24179	ATA	A|0.880;G|0.120	0.120	strong		0.647	HOXC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358963.1		
SQSTM1	8878	hgsc.bcm.edu	37	5	179260153	179260153	+	Silent	SNP	C	C	T	rs4935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179260153C>T	ENST00000389805.4	+	6	1054	c.876C>T	c.(874-876)gaC>gaT	p.D292D	SQSTM1_ENST00000360718.5_Silent_p.D208D|SQSTM1_ENST00000376929.3_Silent_p.D208D|SQSTM1_ENST00000402874.3_Silent_p.D208D|SQSTM1_ENST00000510187.1_Silent_p.D292D	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	292	Interaction with NTRK1. {ECO:0000250}.|Ser-rich.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCTGCTCTGACCCCAGCAAGC	0.637													C|||	3474	0.69369	0.7284	0.7349	5008	,	,		18222	0.8442		0.5099	False		,,,				2504	0.6513				p.D292D		Atlas-SNP	.											.	SQSTM1	30	.	0			c.C876T						PASS	.	C	,,	3214,1192	700.6+/-406.6	1174,866,163	32.0	34.0	33.0		624,624,876	-4.4	0.0	5	dbSNP_52	33	4553,4047	588.8+/-392.4	1218,2117,965	no	coding-synonymous,coding-synonymous,coding-synonymous	SQSTM1	NM_001142298.1,NM_001142299.1,NM_003900.4	,,	2392,2983,1128	TT,TC,CC		47.0581,27.054,40.2814	,,	208/357,208/357,292/441	179260153	7767,5239	2203	4300	6503	SO:0001819	synonymous_variant	8878	exon6			CTCTGACCCCAGC	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"""Paget disease of bone 3"", ""oxidative stress induced like"""	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.876C>T	5.37:g.179260153C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	43	0.614286	NM_003900	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Silent	SNP	ENST00000389805.4	37	CCDS34317.1																																																																																			C|0.358;T|0.642	0.642	strong		0.637	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1		
PARP4	143	hgsc.bcm.edu	37	13	25016008	25016008	+	Silent	SNP	C	C	T	rs59195808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25016008C>T	ENST00000381989.3	-	30	3747	c.3642G>A	c.(3640-3642)gaG>gaA	p.E1214E		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1214					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CTTCTTGGGGCTCCCCCTGCC	0.433																																					p.E1214E		Atlas-SNP	.											.	PARP4	142	.	0			c.G3642A						PASS	.						50.0	52.0	52.0					13																	25016008		2203	4298	6501	SO:0001819	synonymous_variant	143	exon30			TTGGGGCTCCCCC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3642G>A	13.37:g.25016008C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			.	.	weak		0.433	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
TUBA3E	112714	hgsc.bcm.edu	37	2	130949491	130949491	+	Silent	SNP	G	G	A	rs60154251	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130949491G>A	ENST00000312988.7	-	5	1366	c.1266C>T	c.(1264-1266)cgC>cgT	p.R422R		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	422					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					CCAGGTCCTCGCGGGCCTCAG	0.582																																					p.R422R		Atlas-SNP	.											TUBA3E,colon,carcinoma,-2,1	TUBA3E	73	1	0			c.C1266T						PASS	.	G		1579,2827	492.0+/-362.3	286,1007,910	126.0	130.0	129.0		1266	-5.0	0.8	2	dbSNP_129	129	3354,5246	497.4+/-374.5	654,2046,1600	no	coding-synonymous	TUBA3E	NM_207312.2		940,3053,2510	AA,AG,GG		39.0,35.8375,37.9286		422/451	130949491	4933,8073	2203	4300	6503	SO:0001819	synonymous_variant	112714	exon5			GTCCTCGCGGGCC	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.1266C>T	2.37:g.130949491G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	221	100	0.452489	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			G|0.612;A|0.388	0.388	strong		0.582	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
AVL9	23080	hgsc.bcm.edu	37	7	32623477	32623477	+	Silent	SNP	C	C	G	rs34778959	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:32623477C>G	ENST00000318709.4	+	16	2126	c.1905C>G	c.(1903-1905)tcC>tcG	p.S635S	AVL9_ENST00000409301.1_Silent_p.S617S|AVL9_ENST00000404479.1_Intron	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	635					cell migration (GO:0016477)	integral component of membrane (GO:0016021)|recycling endosome (GO:0055037)				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCACCACTTCCACCTCCCAAA	0.502													C|||	1083	0.216254	0.2489	0.1599	5008	,	,		16265	0.1319		0.162	False		,,,				2504	0.3548				p.S635S		Atlas-SNP	.											.	AVL9	66	.	0			c.C1905G						PASS	.	C		1095,3311	394.4+/-329.3	139,817,1247	98.0	87.0	91.0		1905	0.4	0.0	7	dbSNP_126	91	1400,7200	270.1+/-288.8	112,1176,3012	no	coding-synonymous	AVL9	NM_015060.1		251,1993,4259	GG,GC,CC		16.2791,24.8525,19.1835		635/649	32623477	2495,10511	2203	4300	6503	SO:0001819	synonymous_variant	23080	exon16			CACTTCCACCTCC	D87682	CCDS34613.1	7p14.3	2013-05-01	2008-10-03	2008-10-03	ENSG00000105778	ENSG00000105778			28994	protein-coding gene	gene with protein product		612927	"""KIAA0241"""	KIAA0241		17229886, 22595670	Standard	XM_005249668		Approved		uc003tcv.1	Q8NBF6	OTTHUMG00000152929	ENST00000318709.4:c.1905C>G	7.37:g.32623477C>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	213	115	0.539906	NM_015060	Q92573	Silent	SNP	ENST00000318709.4	37	CCDS34613.1	396	0.1813186813186813	122	0.24796747967479674	59	0.16298342541436464	93	0.16258741258741258	122	0.16094986807387862	C	3.851	-0.031861	0.07543	0.248525	0.162791	ENSG00000105778	ENST00000446718	T	0.51325	0.71	5.7	0.43	0.16515	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.30742	P	0.746033	.	.	.	.	.	.	T	0.31081	-0.9956	5	0.17369	T	0.5	-1.3255	4.7324	0.12972	0.1139:0.5423:0.2237:0.1202	rs34778959	.	.	.	R	509	ENSP00000395134:P509R	ENSP00000395134:P509R	P	+	2	0	AVL9	32590002	0.000000	0.05858	0.009000	0.14445	0.396000	0.30629	-0.093000	0.11111	0.336000	0.23639	0.561000	0.74099	CCA	C|0.811;G|0.189	0.189	strong		0.502	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060	
FAM53A	152877	hgsc.bcm.edu	37	4	1657281	1657281	+	Silent	SNP	G	G	A	rs79735962	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1657281G>A	ENST00000308132.6	-	4	498	c.306C>T	c.(304-306)acC>acT	p.T102T	FAM53A_ENST00000461064.1_Silent_p.T102T|FAM53A_ENST00000472884.2_Silent_p.T102T|FAM53A_ENST00000489363.1_Silent_p.T102T	NM_001174070.1	NP_001167541.1	Q6NSI3	FA53A_HUMAN	family with sequence similarity 53, member A	102						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)			TGGGGTCCACGGTGCTGGCTG	0.687													G|||	1123	0.224241	0.0991	0.2291	5008	,	,		13181	0.0595		0.3678	False		,,,				2504	0.4121				p.T102T		Atlas-SNP	.											.	FAM53A	25	.	0			c.C306T						PASS	.	G	,	492,3574		43,406,1584	7.0	8.0	8.0		306,306	-3.3	0.0	4	dbSNP_131	8	2517,5567		409,1699,1934	no	coding-synonymous,coding-synonymous	FAM53A	NM_001013622.3,NM_001174070.1	,	452,2105,3518	AA,AG,GG		31.1356,12.1003,24.7654	,	102/399,102/399	1657281	3009,9141	2033	4042	6075	SO:0001819	synonymous_variant	152877	exon4			GTCCACGGTGCTG	BC070112	CCDS33939.1, CCDS75091.1	4p16.3	2005-08-09			ENSG00000174137	ENSG00000174137			31860	protein-coding gene	gene with protein product							Standard	NM_001013622		Approved	DNTNP	uc021xkl.1	Q6NSI3	OTTHUMG00000159855	ENST00000308132.6:c.306C>T	4.37:g.1657281G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_001013622	Q6ZUL5	Silent	SNP	ENST00000308132.6	37	CCDS33939.1																																																																																			G|0.787;A|0.213	0.213	strong		0.687	FAM53A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359224.1	NM_001013622	
HABP2	3026	hgsc.bcm.edu	37	10	115341753	115341753	+	Silent	SNP	G	G	A	rs2245056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115341753G>A	ENST00000351270.3	+	9	1053	c.957G>A	c.(955-957)aaG>aaA	p.K319K	HABP2_ENST00000542051.1_Silent_p.K293K|HABP2_ENST00000541666.1_Intron	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2	319	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	GAGGCTTTAAGAGCACGGCGG	0.582													G|||	1888	0.376997	0.416	0.4914	5008	,	,		18948	0.2996		0.3917	False		,,,				2504	0.3078				p.K319K		Atlas-SNP	.											.	HABP2	52	.	0			c.G957A						PASS	.	G	,	1833,2573	533.7+/-373.8	356,1121,726	77.0	82.0	81.0		879,957	5.3	1.0	10	dbSNP_100	81	3618,4982	521.8+/-380.0	721,2176,1403	no	coding-synonymous,coding-synonymous	HABP2	NM_001177660.1,NM_004132.3	,	1077,3297,2129	AA,AG,GG		42.0698,41.6024,41.9114	,	293/535,319/561	115341753	5451,7555	2203	4300	6503	SO:0001819	synonymous_variant	3026	exon9			CTTTAAGAGCACG		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.957G>A	10.37:g.115341753G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	62	27	0.435484	NM_004132	A8K467|B7Z8U5|F5H5M6|O00663	Silent	SNP	ENST00000351270.3	37	CCDS7577.1																																																																																			G|0.601;A|0.399	0.399	strong		0.582	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
SPG7	6687	hgsc.bcm.edu	37	16	89620328	89620328	+	Missense_Mutation	SNP	G	G	A	rs12960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:89620328G>A	ENST00000268704.2	+	15	2078	c.2063G>A	c.(2062-2064)cGg>cAg	p.R688Q		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	688			R -> Q (neutral polymorphism; dbSNP:rs12960). {ECO:0000269|PubMed:16534102, ECO:0000269|PubMed:20186691}.		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		GGCATCGGGCGGCGCCCCTTC	0.667													G|||	530	0.105831	0.0098	0.1124	5008	,	,		14832	0.131		0.166	False		,,,				2504	0.1431				p.R688Q		Atlas-SNP	.											.	SPG7	75	.	0			c.G2063A						PASS	.	G	GLN/ARG	165,4231	108.6+/-147.0	3,159,2036	71.0	63.0	65.0		2063	5.2	1.0	16	dbSNP_52	65	1667,6931	299.4+/-304.4	149,1369,2781	yes	missense	SPG7	NM_003119.2	43	152,1528,4817	AA,AG,GG		19.3882,3.7534,14.0988	probably-damaging	688/796	89620328	1832,11162	2198	4299	6497	SO:0001583	missense	6687	exon15			TCGGGCGGCGCCC	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.2063G>A	16.37:g.89620328G>A	ENSP00000268704:p.Arg688Gln	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	257	0.11767399267399267	8	0.016260162601626018	43	0.11878453038674033	76	0.13286713286713286	130	0.17150395778364116	G	22.2	4.264034	0.80358	0.037534	0.193882	ENSG00000197912	ENST00000268704	D	0.83163	-1.69	5.21	5.21	0.72293	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	T	0.00241	0.0007	N	0.17631	0.505	0.09310	P	1.0	P	0.43826	0.818	B	0.37780	0.258	T	0.13469	-1.0508	9	0.21014	T	0.42	-17.3655	17.776	0.88508	0.0:0.0:1.0:0.0	rs12960;rs730263;rs1801445;rs16965809;rs17354997;rs12960	688	Q9UQ90	SPG7_HUMAN	Q	688	ENSP00000268704:R688Q	ENSP00000268704:R688Q	R	+	2	0	SPG7	88147829	1.000000	0.71417	0.985000	0.45067	0.586000	0.36452	9.423000	0.97461	2.423000	0.82170	0.563000	0.77884	CGG	G|0.871;A|0.129	0.129	strong		0.667	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
MPDZ	8777	hgsc.bcm.edu	37	9	13190163	13190163	+	Missense_Mutation	SNP	C	C	T	rs4741289	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:13190163C>T	ENST00000319217.7	-	16	2351	c.2104G>A	c.(2104-2106)Gag>Aag	p.E702K	MPDZ_ENST00000381015.4_Missense_Mutation_p.E702K|MPDZ_ENST00000541718.1_Missense_Mutation_p.E702K|MPDZ_ENST00000536827.1_Missense_Mutation_p.E702K|MPDZ_ENST00000381022.2_Missense_Mutation_p.E702K|MPDZ_ENST00000546205.1_Missense_Mutation_p.E702K|MPDZ_ENST00000447879.1_Missense_Mutation_p.E702K	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	702	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.		E -> K (in dbSNP:rs4741289).|E -> V (in dbSNP:rs4740548).		cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TTCTCCAGCTCTATGTGCTGA	0.438													C|||	155	0.0309505	0.034	0.0173	5008	,	,		17107	0.004		0.002	False		,,,				2504	0.0941				p.E702K		Atlas-SNP	.											.	MPDZ	324	.	0			c.G2104A						PASS	.						73.0	70.0	71.0					9																	13190163		2003	4182	6185	SO:0001583	missense	8777	exon16			CCAGCTCTATGTG	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2104G>A	9.37:g.13190163C>T	ENSP00000320006:p.Glu702Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		21	0.009615384615384616	12	0.024390243902439025	7	0.019337016574585635	2	0.0034965034965034965	0	0.0	C	27.0	4.789896	0.90367	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72;1.72;1.72	5.83	5.83	0.93111	.	0.000000	0.44285	D	0.000475	T	0.25827	0.0629	L	0.60012	1.86	0.80722	D	1	P;P;D	0.61697	0.951;0.94;0.99	P;P;P	0.57057	0.812;0.714;0.779	T	0.01301	-1.1391	10	0.44086	T	0.13	.	15.2561	0.73585	0.0:0.8601:0.1399:0.0	rs4741289;rs4741289	702;702;702	B7ZMI4;O75970-3;O75970-2	.;.;.	K	702;702;702;702;702;702;652;702	ENSP00000320006:E702K;ENSP00000439807:E702K;ENSP00000370410:E702K;ENSP00000444151:E702K;ENSP00000415208:E702K;ENSP00000370403:E702K;ENSP00000446358:E702K	ENSP00000320006:E702K	E	-	1	0	MPDZ	13180163	1.000000	0.71417	0.992000	0.48379	0.944000	0.59088	5.676000	0.68131	2.770000	0.95276	0.655000	0.94253	GAG	C|0.983;T|0.017	0.017	strong		0.438	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
TOP2B	7155	hgsc.bcm.edu	37	3	25639828	25639828	+	Missense_Mutation	SNP	T	T	A	rs61739570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:25639828T>A	ENST00000264331.4	-	36	4850	c.4851A>T	c.(4849-4851)gaA>gaT	p.E1617D	TOP2B_ENST00000542520.1_Missense_Mutation_p.E469D|TOP2B_ENST00000540199.1_Missense_Mutation_p.E469D|TOP2B_ENST00000435706.2_Missense_Mutation_p.E1612D	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	1617					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)	CAACATCATCTTCTTCTTCAT	0.408													t|||	115	0.0229633	0.0439	0.0331	5008	,	,		18342	0.002		0.0219	False		,,,				2504	0.0102				p.E1612D		Atlas-SNP	.											.	TOP2B	98	.	0			c.A4836T						PASS	.	A	ASP/GLU	169,3577		3,163,1707	162.0	160.0	161.0		4836	-2.8	1.0	3	dbSNP_129	161	212,7986		1,210,3888	yes	missense	TOP2B	NM_001068.2	45	4,373,5595	AA,AT,TT		2.586,4.5115,3.1899	benign	1612/1622	25639828	381,11563	1873	4099	5972	SO:0001583	missense	7155	exon36			ATCATCTTCTTCT	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.4851A>T	3.37:g.25639828T>A	ENSP00000264331:p.Glu1617Asp	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	111	52	0.468468	NM_001068	Q13600|Q9UMG8|Q9UQP8	Missense_Mutation	SNP	ENST00000264331.4	37		42	0.019230769230769232	15	0.03048780487804878	14	0.03867403314917127	0	0.0	13	0.017150395778364115	t	0	-2.802343	0.00075	0.045115	0.02586	ENSG00000077097	ENST00000542520;ENST00000435706;ENST00000264331;ENST00000540199	T;T;T;T	0.42513	1.0;0.97;0.97;1.0	4.4	-2.82	0.05787	.	0.392577	0.26911	N	0.021874	T	0.02193	0.0068	N	0.08118	0	0.29900	N	0.82451	B;B	0.09022	0.0;0.002	B;B	0.08055	0.0;0.003	T	0.29336	-1.0015	10	0.02654	T	1	.	9.8882	0.41274	0.7115:0.0:0.104:0.1844	rs61739570	1617;1612	Q02880;Q02880-2	TOP2B_HUMAN;.	D	469;1612;1617;469	ENSP00000446023:E469D;ENSP00000396704:E1612D;ENSP00000264331:E1617D;ENSP00000437352:E469D	ENSP00000264331:E1617D	E	-	3	2	TOP2B	25614832	0.178000	0.23122	0.987000	0.45799	0.313000	0.28021	-0.483000	0.06536	-0.452000	0.07087	-1.488000	0.00978	GAA	T|0.952;A|0.048	0.048	strong		0.408	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
FYCO1	79443	hgsc.bcm.edu	37	3	46008790	46008790	+	Missense_Mutation	SNP	G	G	A	rs3796375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46008790G>A	ENST00000296137.2	-	8	2241	c.2036C>T	c.(2035-2037)gCg>gTg	p.A679V	FYCO1_ENST00000535325.1_Missense_Mutation_p.A679V	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	679			A -> V (in dbSNP:rs3796375). {ECO:0000269|PubMed:17974005}.		plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CAGCAAGCTCGCCTCCATCTG	0.617													G|||	1979	0.395168	0.093	0.5648	5008	,	,		18181	0.6607		0.4314	False		,,,				2504	0.3722				p.A679V		Atlas-SNP	.											.	FYCO1	115	.	0			c.C2036T						PASS	.	G	VAL/ALA	626,3780	268.6+/-268.5	47,532,1624	67.0	72.0	71.0		2036	3.5	0.9	3	dbSNP_107	71	3706,4892	521.8+/-380.0	808,2090,1401	yes	missense	FYCO1	NM_024513.2	64	855,2622,3025	AA,AG,GG		43.103,14.2079,33.3128	possibly-damaging	679/1479	46008790	4332,8672	2203	4299	6502	SO:0001583	missense	79443	exon8			AAGCTCGCCTCCA	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.2036C>T	3.37:g.46008790G>A	ENSP00000296137:p.Ala679Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	80	42	0.525	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	933	0.4271978021978022	45	0.09146341463414634	198	0.5469613259668509	363	0.6346153846153846	327	0.4313984168865435	G	15.03	2.711650	0.48517	0.142079	0.43103	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.21031	2.03;2.03	5.53	3.55	0.40652	.	0.182612	0.45867	N	0.000338	T	0.00012	0.0000	L	0.57536	1.79	0.37551	P	0.08129600000000003	D;D	0.60160	0.984;0.987	B;B	0.43155	0.41;0.356	T	0.35475	-0.9787	9	0.33141	T	0.24	-16.3376	6.1101	0.20096	0.0989:0.0:0.5877:0.3134	rs3796375;rs57674943;rs3796375	679;679	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	V	679	ENSP00000296137:A679V;ENSP00000441178:A679V	ENSP00000296137:A679V	A	-	2	0	FYCO1	45983794	0.998000	0.40836	0.871000	0.34182	0.819000	0.46315	2.820000	0.48057	1.331000	0.45412	0.655000	0.94253	GCG	G|0.650;A|0.350	0.350	strong		0.617	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
ZSCAN29	146050	hgsc.bcm.edu	37	15	43658935	43658935	+	Missense_Mutation	SNP	C	C	T	rs3917221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43658935C>T	ENST00000396976.2	-	3	729	c.595G>A	c.(595-597)Ggc>Agc	p.G199S	ZSCAN29_ENST00000396972.1_Intron|ZSCAN29_ENST00000562072.1_Missense_Mutation_p.G198S|ZSCAN29_ENST00000568898.1_Intron	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	199			G -> S (in dbSNP:rs12912744). {ECO:0000269|PubMed:14702039}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		TCCTTAGAGCCCAGCAGATCT	0.493													C|||	676	0.134984	0.1891	0.1037	5008	,	,		18985	0.001		0.1958	False		,,,				2504	0.1595				p.G199S		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.G595A						PASS	.	C	SER/GLY	845,3557	333.1+/-302.8	81,683,1437	80.0	79.0	79.0		595	3.2	1.0	15	dbSNP_121	79	1622,6976	301.2+/-305.3	145,1332,2822	yes	missense	ZSCAN29	NM_152455.3	56	226,2015,4259	TT,TC,CC		18.8649,19.1958,18.9769	benign	199/853	43658935	2467,10533	2201	4299	6500	SO:0001583	missense	146050	exon3			TAGAGCCCAGCAG	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.595G>A	15.37:g.43658935C>T	ENSP00000380174:p.Gly199Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	131	76	0.580153	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	37	CCDS10095.2	298	0.13644688644688643	98	0.1991869918699187	44	0.12154696132596685	0	0.0	156	0.20580474934036938	C	21.3	4.131907	0.77662	0.191958	0.188649	ENSG00000140265	ENST00000396976	T	0.08102	3.13	4.17	3.24	0.37175	.	0.134994	0.34067	N	0.004287	T	0.00012	0.0000	N	0.13327	0.33	0.09310	P	0.9999999999999998	B;B;B	0.27997	0.021;0.197;0.006	B;B;B	0.25140	0.015;0.058;0.003	T	0.46679	-0.9174	9	0.11182	T	0.66	-0.6465	7.1511	0.25612	0.0:0.8737:0.0:0.1263	rs3917221	198;199;199	C9K0J8;Q8IWY8-3;Q8IWY8	.;.;ZSC29_HUMAN	S	199	ENSP00000380174:G199S	ENSP00000380174:G199S	G	-	1	0	ZSCAN29	41446227	0.000000	0.05858	1.000000	0.80357	0.976000	0.68499	0.137000	0.15995	1.062000	0.40625	0.655000	0.94253	GGC	C|0.817;T|0.183	0.183	strong		0.493	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
CFAP46	54777	hgsc.bcm.edu	37	10	134691427	134691427	+	Missense_Mutation	SNP	G	G	C	rs527530176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691427G>C	ENST00000368586.5	-	30	4270	c.4170C>G	c.(4168-4170)gaC>gaG	p.D1390E	TTC40_ENST00000368582.2_Missense_Mutation_p.D1390E	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						ccttctccttgtccttctctt	0.507													-|||	23	0.00459265	0.0008	0.0029	5008	,	,		17437	0.002		0.007	False		,,,				2504	0.0112				p.D1390E		Atlas-SNP	.											.	TTC40	100	.	0			c.C4170G						PASS	.																																			SO:0001583	missense	54777	exon30			CTCCTTGTCCTTC																												ENST00000368586.5:c.4170C>G	10.37:g.134691427G>C	ENSP00000357575:p.Asp1390Glu	Somatic	314	0	0		WXS	Illumina HiSeq	Phase_I	298	23	0.0771812	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	-	0.018	-1.468881	0.01053	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.10860	2.83;2.83	2.3	-4.61	0.03380	.	.	.	.	.	T	0.02494	0.0076	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35549	-0.9784	6	0.02654	T	1	.	2.0591	0.03587	0.1265:0.1607:0.4006:0.3123	.	.	.	.	E	1390	ENSP00000357575:D1390E;ENSP00000357571:D1390E	ENSP00000357571:D1390E	D	-	3	2	C10orf93	134541417	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.253000	0.01184	-1.780000	0.01279	-1.213000	0.01624	GAC	.	.	none		0.507	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
PCDHB2	56133	hgsc.bcm.edu	37	5	140475980	140475980	+	Missense_Mutation	SNP	G	G	A	rs17844376	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140475980G>A	ENST00000194155.4	+	1	1754	c.1606G>A	c.(1606-1608)Gca>Aca	p.A536T		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	536	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTGGGCGCCGCAGACCGCGG	0.687													G|||	1390	0.277556	0.115	0.3228	5008	,	,		15803	0.4554		0.2336	False		,,,				2504	0.3272				p.A536T		Atlas-SNP	.											.	PCDHB2	163	.	0			c.G1606A						PASS	.	G	THR/ALA	562,3844	232.0+/-245.7	36,490,1677	51.0	56.0	54.0		1606	-9.0	0.0	5	dbSNP_123	54	1885,6715	304.2+/-306.8	205,1475,2620	no	missense	PCDHB2	NM_018936.2	58	241,1965,4297	AA,AG,GG		21.9186,12.7553,18.8144	benign	536/799	140475980	2447,10559	2203	4300	6503	SO:0001583	missense	56133	exon1			GGCGCCGCAGACC	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.1606G>A	5.37:g.140475980G>A	ENSP00000194155:p.Ala536Thr	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	63	39	0.619048	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	563	0.25778388278388276	52	0.10569105691056911	91	0.2513812154696133	260	0.45454545454545453	160	0.21108179419525067	G	0.009	-1.833531	0.00579	0.127553	0.219186	ENSG00000112852	ENST00000194155	T	0.01215	5.16	4.5	-9.0	0.00747	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.01146	-0.985	0.80722	P	0.0	B	0.09022	0.002	B	0.11329	0.006	T	0.41288	-0.9517	8	0.02654	T	1	.	13.4636	0.61241	0.6715:0.0:0.2511:0.0774	rs17844376	536	Q9Y5E7	PCDB2_HUMAN	T	536	ENSP00000194155:A536T	ENSP00000194155:A536T	A	+	1	0	PCDHB2	140456164	0.000000	0.05858	0.000000	0.03702	0.572000	0.35998	-4.652000	0.00203	-2.902000	0.00311	-2.500000	0.00191	GCA	G|0.783;A|0.217	0.217	strong		0.687	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
SMG8	55181	hgsc.bcm.edu	37	17	57287454	57287454	+	Silent	SNP	A	A	G	rs6503905	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:57287454A>G	ENST00000543872.2	+	2	306	c.42A>G	c.(40-42)gcA>gcG	p.A14A	SMG8_ENST00000580498.1_3'UTR|SMG8_ENST00000300917.5_Silent_p.A14A|CTD-2510F5.6_ENST00000577660.1_Intron|SMG8_ENST00000578922.1_Silent_p.A14A			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	14					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						TAATGGGAGCATCAGCCTGGA	0.617													G|||	3326	0.664137	0.9546	0.5562	5008	,	,		14640	0.4415		0.6183	False		,,,				2504	0.6247				p.A14A		Atlas-SNP	.											.	SMG8	79	.	0			c.A42G						PASS	.	G		3918,488	218.4+/-236.5	1743,432,28	34.0	38.0	37.0		42	-5.2	0.6	17	dbSNP_116	37	5457,3143	466.4+/-366.8	1740,1977,583	no	coding-synonymous	SMG8	NM_018149.6		3483,2409,611	GG,GA,AA		36.5465,11.0758,27.9179		14/992	57287454	9375,3631	2203	4300	6503	SO:0001819	synonymous_variant	55181	exon1			GGGAGCATCAGCC	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.42A>G	17.37:g.57287454A>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	24	23	0.958333	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Silent	SNP	ENST00000543872.2	37	CCDS11615.1																																																																																			A|0.301;G|0.699	0.699	strong		0.617	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149	
CARD14	79092	hgsc.bcm.edu	37	17	78178893	78178893	+	Missense_Mutation	SNP	C	C	T	rs11652075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:78178893C>T	ENST00000573882.1	+	20	2994	c.2458C>T	c.(2458-2460)Cgg>Tgg	p.R820W	RP11-334C17.5_ENST00000576824.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.R820W|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	820	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.		R -> W (in dbSNP:rs11652075). {ECO:0000269|PubMed:11278692, ECO:0000269|PubMed:11356195}.		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)			TACCCTGGTGCGGCCCCATCG	0.662													C|||	1768	0.353035	0.1914	0.2767	5008	,	,		14385	0.499		0.5099	False		,,,				2504	0.3139				p.R820W		Atlas-SNP	.											.	CARD14	98	.	0			c.C2458T						PASS	.	C	TRP/ARG	1095,3307	387.2+/-326.4	146,803,1252	43.0	40.0	41.0		2458	1.9	0.5	17	dbSNP_120	41	4227,4373	560.0+/-387.5	1054,2119,1127	yes	missense	CARD14	NM_024110.3	101	1200,2922,2379	TT,TC,CC		49.1512,24.8751,40.9322	benign	820/1005	78178893	5322,7680	2201	4300	6501	SO:0001583	missense	79092	exon18			CTGGTGCGGCCCC	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.2458C>T	17.37:g.78178893C>T	ENSP00000458715:p.Arg820Trp	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	922	0.42216117216117216	121	0.2459349593495935	121	0.3342541436464088	305	0.5332167832167832	375	0.4947229551451187	C	9.626	1.135215	0.21123	0.248751	0.491512	ENSG00000141527	ENST00000344227	T	0.05649	3.41	4.09	1.85	0.25348	.	0.424901	0.23754	N	0.044886	T	0.00012	0.0000	L	0.34521	1.04	0.29554	P	0.851119	P	0.48589	0.912	B	0.33799	0.17	T	0.41179	-0.9523	9	0.66056	D	0.02	-13.7883	4.3708	0.11246	0.3814:0.4907:0.0:0.128	rs11652075;rs59880441;rs11652075	820	Q9BXL6	CAR14_HUMAN	W	820	ENSP00000344549:R820W	ENSP00000344549:R820W	R	+	1	2	CARD14	75793488	0.981000	0.34729	0.544000	0.28141	0.008000	0.06430	3.132000	0.50523	0.706000	0.31912	-0.424000	0.05967	CGG	C|0.597;T|0.403	0.403	strong		0.662	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
UTRN	7402	hgsc.bcm.edu	37	6	145051594	145051594	+	Silent	SNP	G	G	A	rs4305737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:145051594G>A	ENST00000367545.3	+	53	7911	c.7911G>A	c.(7909-7911)gaG>gaA	p.E2637E	UTRN_ENST00000367526.4_Silent_p.E192E	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2637					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		CCCCTGAAGAGCCAAGAAGAA	0.443													A|||	3219	0.642772	0.9123	0.6225	5008	,	,		13715	0.8681		0.2286	False		,,,				2504	0.4867				p.E2637E		Atlas-SNP	.											.	UTRN	327	.	0			c.G7911A						PASS	.	A		3479,927	354.6+/-312.7	1376,727,100	67.0	73.0	71.0		7911	2.7	1.0	6	dbSNP_111	71	2174,6426	712.7+/-405.9	280,1614,2406	no	coding-synonymous	UTRN	NM_007124.2		1656,2341,2506	AA,AG,GG		25.2791,21.0395,43.4646		2637/3434	145051594	5653,7353	2203	4300	6503	SO:0001819	synonymous_variant	7402	exon53			TGAAGAGCCAAGA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.7911G>A	6.37:g.145051594G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																			G|0.490;A|0.510	0.510	strong		0.443	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
GLTSCR2	29997	hgsc.bcm.edu	37	19	48254799	48254799	+	Silent	SNP	T	T	C	rs11538669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48254799T>C	ENST00000246802.5	+	5	659	c.621T>C	c.(619-621)gtT>gtC	p.V207V	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	207				SDNPLDRPLVGQDEFFLE -> LNNPDKPVVWPGCLFPG (in Ref. 3; AAG30413). {ECO:0000305}.		intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GGCCGTTGGTTGGCCAGGATG	0.607													T|||	77	0.0153754	0.0053	0.0029	5008	,	,		18264	0.0069		0.0149	False		,,,				2504	0.047				p.V207V	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.T621C						PASS	.	T		46,4360	48.9+/-83.8	0,46,2157	84.0	76.0	79.0		621	-7.0	0.0	19	dbSNP_120	79	151,8449	73.2+/-135.9	0,151,4149	no	coding-synonymous	GLTSCR2	NM_015710.4		0,197,6306	CC,CT,TT		1.7558,1.044,1.5147		207/479	48254799	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon5			GTTGGTTGGCCAG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.621T>C	19.37:g.48254799T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	81	39	0.481481	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			T|0.987;C|0.013	0.013	strong		0.607	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
YDJC	150223	hgsc.bcm.edu	37	22	21984205	21984205	+	Silent	SNP	A	A	G	rs710177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:21984205A>G	ENST00000292778.6	-	1	148	c.99T>C	c.(97-99)gcT>gcC	p.A33A	CCDC116_ENST00000607942.1_5'Flank|YDJC_ENST00000398873.3_Silent_p.A33A|CCDC116_ENST00000292779.3_5'Flank	NM_001017964.1	NP_001017964.1	A8MPS7	YDJC_HUMAN	YdjC homolog (bacterial)	33					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)					Colorectal(54;0.105)					CGCTGGTCACAGCCCCGGCCA	0.706													-|||	2301	0.459465	0.3926	0.4986	5008	,	,		13664	0.5109		0.3887	False		,,,				2504	0.5419				p.A33A		Atlas-SNP	.											YDJC,rectum,carcinoma,0,1	YDJC	8	1	0			c.T99C						PASS	.			1688,2672		342,1004,834	18.0	17.0	17.0		99	-8.9	0.0	22	dbSNP_86	17	3196,5354		640,1916,1719	no	coding-synonymous	YDJC	NM_001017964.1		982,2920,2553	GG,GA,AA		37.3801,38.7156,37.8311		33/324	21984205	4884,8026	2180	4275	6455	SO:0001819	synonymous_variant	150223	exon1			GGTCACAGCCCCG		CCDS33613.1	22q11.21	2008-02-26			ENSG00000161179	ENSG00000161179			27158	protein-coding gene	gene with protein product						18177738	Standard	XM_005261347		Approved		uc002zvb.2	A8MPS7	OTTHUMG00000150822	ENST00000292778.6:c.99T>C	22.37:g.21984205A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	51	16	0.313726	NM_001017964	Q2YDT4|Q4V9R7	Silent	SNP	ENST00000292778.6	37	CCDS33613.1																																																																																			A|0.605;G|0.395	0.395	strong		0.706	YDJC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320213.1		
NACA2	342538	hgsc.bcm.edu	37	17	59667953	59667953	+	Nonsense_Mutation	SNP	G	G	A	rs17610181	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:59667953G>A	ENST00000521764.1	-	1	610	c.589C>T	c.(589-591)Cga>Tga	p.R197*		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	197	UBA.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					TTCAGAGCTCGGACTGCCTTT	0.403													G|||	741	0.147963	0.0575	0.1037	5008	,	,		22626	0.1667		0.1471	False		,,,				2504	0.2832				p.R197X		Atlas-SNP	.											.	NACA2	33	.	0			c.C589T						PASS	.	G	stop/ARG	329,4077	171.9+/-202.1	15,299,1889	257.0	228.0	238.0		589	-0.3	0.9	17	dbSNP_123	238	1249,7351	248.5+/-276.1	97,1055,3148	no	stop-gained	NACA2	NM_199290.3		112,1354,5037	AA,AG,GG		14.5233,7.4671,12.1329		197/216	59667953	1578,11428	2203	4300	6503	SO:0001587	stop_gained	342538	exon1			GAGCTCGGACTGC	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.589C>T	17.37:g.59667953G>A	ENSP00000427802:p.Arg197*	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	232	111	0.478448	NM_199290	Q2VIR9	Nonsense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	254	0.1163003663003663	26	0.052845528455284556	40	0.11049723756906077	73	0.12762237762237763	115	0.1517150395778364	G	18.41	3.617954	0.66787	0.074671	0.145233	ENSG00000253506	ENST00000521764	.	.	.	0.753	-0.349	0.12609	.	0.000000	0.64402	U	0.000002	.	.	.	.	.	.	0.09310	P	0.9999998989	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9511	0.14015	0.2556:0.0:0.7444:0.0	rs17610181;rs52809144;rs17610181	.	.	.	X	197	.	.	R	-	1	2	NACA2	57022735	1.000000	0.71417	0.903000	0.35520	0.781000	0.44180	4.753000	0.62183	-0.112000	0.11979	0.411000	0.27672	CGA	G|0.879;A|0.121	0.121	strong		0.403	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
DSPP	1834	hgsc.bcm.edu	37	4	88537115	88537115	+	Missense_Mutation	SNP	G	G	A	rs201186956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537115G>A	ENST00000282478.7	+	4	3334	c.3301G>A	c.(3301-3303)Gac>Aac	p.D1101N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1101N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1101	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		cgatagcagcgacagcagcga	0.542													G|||	7	0.00139776	0.0038	0.0	5008	,	,		12523	0.001		0.0	False		,,,				2504	0.001				p.D1101N		Atlas-SNP	.											.	DSPP	174	.	0			c.G3301A						PASS	.																																			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.3301G>A	4.37:g.88537115G>A	ENSP00000282478:p.Asp1101Asn	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	12	5	0.416667	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	5.679	0.309927	0.10733	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90004	-2.6;-2.6	1.51	0.638	0.17742	.	.	.	.	.	T	0.78698	0.4324	L	0.34521	1.04	0.09310	N	0.999993	B	0.14438	0.01	B	0.04013	0.001	T	0.60383	-0.7274	9	0.19147	T	0.46	.	4.1914	0.10422	0.2248:0.0:0.7752:0.0	.	1101	Q9NZW4	DSPP_HUMAN	N	1101	ENSP00000382213:D1101N;ENSP00000282478:D1101N	ENSP00000282478:D1101N	D	+	1	0	DSPP	88756139	0.671000	0.27521	0.311000	0.25182	0.002000	0.02628	0.881000	0.28173	0.216000	0.20781	-0.791000	0.03333	GAC	.	.	weak		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
METTL12	751071	hgsc.bcm.edu	37	11	62434173	62434173	+	Missense_Mutation	SNP	G	G	A	rs11231181	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62434173G>A	ENST00000532971.1	+	3	630	c.373G>A	c.(373-375)Ggc>Agc	p.G125S	C11orf48_ENST00000532208.1_Intron|C11orf48_ENST00000524958.1_5'Flank|SNORA57_ENST00000383870.1_RNA|C11orf48_ENST00000354588.3_Intron|C11orf48_ENST00000431002.2_Intron|METTL12_ENST00000398922.2_3'UTR|C11orf48_ENST00000525675.1_5'Flank|RP11-831H9.11_ENST00000528405.1_5'Flank	NM_001043229.1	NP_001036694.1	A8MUP2	MET12_HUMAN	methyltransferase like 12	125			G -> S (in dbSNP:rs11231181).			mitochondrion (GO:0005739)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	6						GGGTGGCCCAGGCCAAACACC	0.592													G|||	748	0.149361	0.0756	0.2161	5008	,	,		17989	0.0526		0.2604	False		,,,				2504	0.1871				p.G125S		Atlas-SNP	.											.	METTL12	11	.	0			c.G373A						PASS	.	G	SER/GLY,	467,3523		31,405,1559	42.0	46.0	45.0		373,	1.7	0.2	11	dbSNP_120	45	2405,5925		366,1673,2126	yes	missense,intron	C11orf48,METTL12	NM_001043229.1,NM_024099.3	56,	397,2078,3685	AA,AG,GG		28.8715,11.7043,23.3117	benign,	125/241,	62434173	2872,9448	1995	4165	6160	SO:0001583	missense	751071	exon3			GGCCCAGGCCAAA	BC041359	CCDS41657.1	11q12.3	2013-09-30			ENSG00000214756	ENSG00000214756			33113	protein-coding gene	gene with protein product							Standard	NM_001043229		Approved	U99HG	uc001nuh.3	A8MUP2	OTTHUMG00000167545	ENST00000532971.1:c.373G>A	11.37:g.62434173G>A	ENSP00000431287:p.Gly125Ser	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_001043229	B7Z4C1	Missense_Mutation	SNP	ENST00000532971.1	37	CCDS41657.1	371	0.16987179487179488	41	0.08333333333333333	95	0.26243093922651933	36	0.06293706293706294	199	0.262532981530343	G	9.658	1.143349	0.21205	0.117043	0.288715	ENSG00000214756	ENST00000532971	T	0.42513	0.97	4.87	1.72	0.24424	Methyltransferase type 11 (1);	1.077670	0.07388	U	0.888510	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.13145	0.007	B	0.15052	0.012	T	0.34179	-0.9839	9	0.38643	T	0.18	-25.8093	3.6963	0.08365	0.2209:0.0:0.5822:0.1969	rs11231181;rs11231181	125	A8MUP2	MTL12_HUMAN	S	125	ENSP00000431287:G125S	ENSP00000431287:G125S	G	+	1	0	METTL12	62190749	0.001000	0.12720	0.161000	0.22692	0.358000	0.29455	0.978000	0.29488	0.258000	0.21686	-0.355000	0.07637	GGC	G|0.803;A|0.197	0.197	strong		0.592	METTL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394990.1	NM_001043229	
TESPA1	9840	hgsc.bcm.edu	37	12	55368245	55368245	+	Silent	SNP	G	G	A	rs4758993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55368245G>A	ENST00000449076.1	-	2	234	c.102C>T	c.(100-102)gcC>gcT	p.A34A	TESPA1_ENST00000524959.1_5'Flank|TESPA1_ENST00000316577.8_Silent_p.A34A|TESPA1_ENST00000524622.1_5'Flank|TESPA1_ENST00000531122.1_5'Flank|TESPA1_ENST00000532804.1_5'Flank	NM_001136030.2	NP_001129502.1	A2RU30	TESP1_HUMAN	thymocyte expressed, positive selection associated 1	34					COP9 signalosome assembly (GO:0010387)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)											GCAGGGCGGCGGCAGCCTCCT	0.602													G|||	2058	0.410942	0.2451	0.2262	5008	,	,		16775	0.7044		0.2336	False		,,,				2504	0.6462				p.A34A		Atlas-SNP	.											.	.	.	.	0			c.C102T						PASS	.	G	,	943,2959		121,701,1129	19.0	22.0	21.0		102,102	-9.7	0.2	12	dbSNP_111	21	1651,6645		168,1315,2665	no	coding-synonymous,coding-synonymous	KIAA0748	NM_001098815.1,NM_001136030.1	,	289,2016,3794	AA,AG,GG		19.9012,24.1671,21.2658	,	34/522,34/522	55368245	2594,9604	1951	4148	6099	SO:0001819	synonymous_variant	9840	exon2			GGCGGCGGCAGCC	AB018291	CCDS44913.1, CCDS58240.1	12q13.2	2012-03-21	2012-03-21	2012-03-21	ENSG00000135426	ENSG00000135426			29109	protein-coding gene	gene with protein product		615664	"""KIAA0748"""	KIAA0748		9872452	Standard	NM_001136030		Approved		uc001sgn.4	A2RU30	OTTHUMG00000165407	ENST00000449076.1:c.102C>T	12.37:g.55368245G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	116	54	0.465517	NM_001098815	B4DPM3|B4E048|B7Z9K7|O94849|Q4G0P2|Q9P0C4	Silent	SNP	ENST00000449076.1	37	CCDS44913.1																																																																																			G|0.625;A|0.375	0.375	strong		0.602	TESPA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000383822.1	NM_001098815	
MMS19	64210	hgsc.bcm.edu	37	10	99225645	99225645	+	Missense_Mutation	SNP	G	G	A	rs12360068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99225645G>A	ENST00000438925.2	-	18	2008	c.1673C>T	c.(1672-1674)gCc>gTc	p.A558V	MMS19_ENST00000327238.10_Missense_Mutation_p.A460V|MMS19_ENST00000355839.6_Missense_Mutation_p.A515V|MMS19_ENST00000327277.7_Missense_Mutation_p.A194V|MMS19_ENST00000370782.2_Missense_Mutation_p.A558V	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	558			A -> V (in dbSNP:rs12360068). {ECO:0000269|Ref.5}.		cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		AGCTGACAAGGCTTGCAGACA	0.502								Direct reversal of damage					G|||	79	0.0157748	0.0038	0.0331	5008	,	,		20802	0.0		0.0467	False		,,,				2504	0.0041				p.A558V		Atlas-SNP	.											.	MMS19	36	.	0			c.C1673T						PASS	.	G	VAL/ALA	33,4373	39.2+/-71.8	0,33,2170	180.0	166.0	171.0		1673	4.6	1.0	10	dbSNP_120	171	370,8230	123.1+/-182.0	7,356,3937	yes	missense	MMS19	NM_022362.4	64	7,389,6107	AA,AG,GG		4.3023,0.749,3.0986	benign	558/1031	99225645	403,12603	2203	4300	6503	SO:0001583	missense	64210	exon18			GACAAGGCTTGCA	AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.1673C>T	10.37:g.99225645G>A	ENSP00000412698:p.Ala558Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	33	0.52381	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	37	CCDS7464.1	54|54	0.024725274725274724|0.024725274725274724	6|6	0.012195121951219513|0.012195121951219513	14|14	0.03867403314917127|0.03867403314917127	0|0	0.0|0.0	34|34	0.044854881266490766|0.044854881266490766	G|G	20.5|20.5	3.995419|3.995419	0.74703|0.74703	0.00749|0.00749	0.043023|0.043023	ENSG00000155229|ENSG00000155229	ENST00000438925;ENST00000370782;ENST00000327238;ENST00000422291;ENST00000327277;ENST00000327253;ENST00000355839|ENST00000434538	T;T;T;T;T|.	0.30981|.	1.51;1.51;1.51;1.51;1.51|.	5.54|5.54	4.64|4.64	0.57946|0.57946	Armadillo-like helical (1);Armadillo-type fold (1);|.	0.102590|.	0.64402|.	D|.	0.000003|.	T|T	0.43277|0.43277	0.1240|0.1240	M|M	0.74258|0.74258	2.255|2.255	0.46131|0.46131	D|D	0.998881|0.998881	D;D;D;P;D|.	0.89917|.	0.994;1.0;1.0;0.584;0.994|.	D;D;D;B;D|.	0.91635|.	0.917;0.999;0.999;0.213;0.917|.	T|T	0.63097|0.63097	-0.6713|-0.6713	10|5	0.23891|.	T|.	0.37|.	.|.	14.2368|14.2368	0.65932|0.65932	0.0723:0.0:0.9277:0.0|0.0723:0.0:0.9277:0.0	rs12360068;rs52809901;rs12360068|rs12360068;rs52809901;rs12360068	579;460;515;558;515|.	B4DQX2;Q96T76-5;F8W9Y2;Q96T76;B4E2I3|.	.;.;.;MMS19_HUMAN;.|.	V|S	558;558;460;537;194;143;515|133	ENSP00000412698:A558V;ENSP00000359818:A558V;ENSP00000320059:A460V;ENSP00000322236:A194V;ENSP00000348097:A515V|.	ENSP00000320059:A460V|.	A|P	-|-	2|1	0|0	MMS19|MMS19	99215635|99215635	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.638000|4.638000	0.61353|0.61353	1.330000|1.330000	0.45394|0.45394	0.561000|0.561000	0.74099|0.74099	GCC|CCT	G|0.974;A|0.026	0.026	strong		0.502	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
PTPRO	5800	hgsc.bcm.edu	37	12	15733669	15733669	+	Silent	SNP	G	G	A	rs3748299	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:15733669G>A	ENST00000281171.4	+	22	3366	c.3036G>A	c.(3034-3036)ggG>ggA	p.G1012G	PTPRO_ENST00000445537.2_Silent_p.G201G|PTPRO_ENST00000542557.1_Silent_p.G173G|PTPRO_ENST00000442921.2_Silent_p.G201G|PTPRO_ENST00000544244.1_Silent_p.G173G|PTPRO_ENST00000348962.2_Silent_p.G984G	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	1012	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				CCACCCAGGGGCCACTGCCTG	0.448													G|||	664	0.132588	0.0681	0.049	5008	,	,		18038	0.2986		0.0706	False		,,,				2504	0.1718				p.G1012G		Atlas-SNP	.											.	PTPRO	148	.	0			c.G3036A						PASS	.	G	,,,,,	309,4097	166.2+/-197.5	13,283,1907	106.0	97.0	100.0		2952,3036,519,603,519,603	-2.6	0.8	12	dbSNP_107	100	745,7855	179.3+/-228.5	38,669,3593	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRO	NM_002848.3,NM_030667.2,NM_030668.2,NM_030669.2,NM_030670.2,NM_030671.2	,,,,,	51,952,5500	AA,AG,GG		8.6628,7.0132,8.104	,,,,,	984/1189,1012/1217,173/378,201/406,173/378,201/406	15733669	1054,11952	2203	4300	6503	SO:0001819	synonymous_variant	5800	exon22			CCAGGGGCCACTG	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.3036G>A	12.37:g.15733669G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_030667	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																			G|0.893;A|0.107	0.107	strong		0.448	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
TNMD	64102	hgsc.bcm.edu	37	X	99849017	99849017	+	Silent	SNP	G	G	A	rs2073162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:99849017G>A	ENST00000373031.4	+	3	523	c.306G>A	c.(304-306)gtG>gtA	p.V102V	TNMD_ENST00000485971.1_3'UTR	NM_022144.2	NP_071427.2	Q9H2S6	TNMD_HUMAN	tenomodulin	102	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				cellular response to BMP stimulus (GO:0071773)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|tendon cell differentiation (GO:0035990)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(7)|skin(1)	16						CATTGGAAGTGCACGACTTTA	0.368													A|||	1788	0.473642	0.329	0.3631	3775	,	,		14013	0.5139		0.3052	False		,,,				2504	0.2822				p.V102V		Atlas-SNP	.											.	TNMD	40	.	0			c.G306A						PASS	.	A		1640,2195		290,802,258,540,313	106.0	98.0	101.0		306	-1.5	1.0	X	dbSNP_96	101	2455,4273		343,1089,680,996,1192	no	coding-synonymous	TNMD	NM_022144.2		633,1891,938,1536,1505	AA,AG,A,GG,G		36.4893,42.764,38.7674		102/318	99849017	4095,6468	2203	4300	6503	SO:0001819	synonymous_variant	64102	exon3			GGAAGTGCACGAC	AF191770	CCDS14469.1	Xq21.33-q23	2012-10-10			ENSG00000000005	ENSG00000000005		"""BRICHOS domain containing"""	17757	protein-coding gene	gene with protein product	"""BRICHOS domain containing 4"""	300459					Standard	NM_022144		Approved	myodulin, ChM1L, tendin, TEM, BRICD4	uc004efy.4	Q9H2S6	OTTHUMG00000022001	ENST00000373031.4:c.306G>A	X.37:g.99849017G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	136	133	0.977941	NM_022144	Q9HBX0|Q9UJG0	Silent	SNP	ENST00000373031.4	37	CCDS14469.1																																																																																			0|0.015;A|0.433	0.433	strong		0.368	TNMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057481.1	NM_022144	
GLO1	2739	hgsc.bcm.edu	37	6	38650628	38650628	+	Missense_Mutation	SNP	T	T	G	rs4746	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:38650628T>G	ENST00000373365.4	-	4	418	c.332A>C	c.(331-333)gAg>gCg	p.E111A	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	111			E -> A (in dbSNP:rs4746). {ECO:0000269|PubMed:10564821, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7684374, ECO:0000269|PubMed:8449929}.		carbohydrate metabolic process (GO:0005975)|glutathione metabolic process (GO:0006749)|methylglyoxal metabolic process (GO:0009438)|negative regulation of apoptotic process (GO:0043066)|osteoclast differentiation (GO:0030316)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	lactoylglutathione lyase activity (GO:0004462)|zinc ion binding (GO:0008270)			lung(2)|ovary(2)|prostate(1)|urinary_tract(1)	6					Glutathione(DB00143)|Indomethacin(DB00328)	ACTCTGGGTCTCATCATCTTC	0.373													T|||	1439	0.28734	0.3132	0.3818	5008	,	,		16728	0.1002		0.4185	False		,,,				2504	0.2434				p.E111A		Atlas-SNP	.											.	GLO1	12	.	0			c.A332C	GRCh37	CM042995	GLO1	M	rs4746	PASS	.	T	ALA/GLU	1539,2867	485.8+/-360.4	258,1023,922	160.0	131.0	140.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	332	3.5	0.9	6	dbSNP_52	140	3800,4800	538.3+/-383.4	854,2092,1354	yes	missense	GLO1	NM_006708.2	107	1112,3115,2276	GG,GT,TT		44.186,34.9296,41.0503	benign	111/185	38650628	5339,7667	2203	4300	6503	SO:0001583	missense	2739	exon4			TGGGTCTCATCAT	L07837	CCDS4837.1	6p21.3-p21.1	2012-10-02			ENSG00000124767	ENSG00000124767	4.4.1.5		4323	protein-coding gene	gene with protein product	"""glyoxalase domain containing 1"""	138750				8449929, 7684374	Standard	NM_006708		Approved	GLOD1	uc003ooc.3	Q04760	OTTHUMG00000014636	ENST00000373365.4:c.332A>C	6.37:g.38650628T>G	ENSP00000362463:p.Glu111Ala	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Missense_Mutation	SNP	ENST00000373365.4	37	CCDS4837.1	661	0.30265567765567764	160	0.3252032520325203	135	0.3729281767955801	49	0.08566433566433566	317	0.4182058047493404	T	11.51	1.659204	0.29515	0.349296	0.44186	ENSG00000124767	ENST00000373365	T	0.27256	1.68	5.95	3.5	0.40072	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.237043	0.49305	N	0.000147	T	0.06826	0.0174	N	0.17723	0.515	0.20307	P	0.9999123594	B	0.02656	0.0	B	0.06405	0.002	T	0.13980	-1.0489	9	0.21540	T	0.41	-4.0688	14.9417	0.70997	0.0:0.0:0.1352:0.8648	rs4746;rs1130533;rs2736654;rs3189496;rs17295902;rs17350302;rs17551405;rs17851360;rs52837965;rs2736654	111	Q04760	LGUL_HUMAN	A	111	ENSP00000362463:E111A	ENSP00000362463:E111A	E	-	2	0	GLO1	38758606	1.000000	0.71417	0.942000	0.38095	0.991000	0.79684	4.247000	0.58750	0.518000	0.28383	0.533000	0.62120	GAG	T|0.638;G|0.362	0.362	strong		0.373	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708	
KRT83	3889	hgsc.bcm.edu	37	12	52709880	52709880	+	Silent	SNP	A	A	G	rs2852468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52709880A>G	ENST00000293670.3	-	7	1121	c.1059T>C	c.(1057-1059)gcT>gcC	p.A353A		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	353	Coil 2.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.A353A(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGGCCACCGCAGCTTCCAGCT	0.567													N|||	1882	0.375799	0.5008	0.317	5008	,	,		16607	0.1885		0.4095	False		,,,				2504	0.407				p.A353A	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,0,1	KRT83	64	1	1	Substitution - coding silent(1)	stomach(1)	c.T1059C						PASS	.	A		2100,2306		554,992,657	24.0	27.0	26.0		1059	-7.7	0.2	12	dbSNP_100	26	3442,5158		717,2008,1575	no	coding-synonymous	KRT83	NM_002282.3		1271,3000,2232	GG,GA,AA		40.0233,47.6623,42.6111		353/494	52709880	5542,7464	2203	4300	6503	SO:0001819	synonymous_variant	3889	exon7			CACCGCAGCTTCC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.1059T>C	12.37:g.52709880A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	72	26	0.361111	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			A|0.630;G|0.370	0.370	strong		0.567	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
RRP12	23223	hgsc.bcm.edu	37	10	99130282	99130282	+	Silent	SNP	T	T	G	rs11189170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99130282T>G	ENST00000370992.4	-	23	2730	c.2619A>C	c.(2617-2619)gcA>gcC	p.A873A	RRP12_ENST00000536831.1_Silent_p.A591A|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000315563.6_Silent_p.A773A|RRP12_ENST00000414986.1_Silent_p.A812A	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	873						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CGTTCTTCCGTGCGCCCACCG	0.607													T|||	201	0.0401358	0.059	0.0548	5008	,	,		19934	0.0		0.0716	False		,,,				2504	0.0133				p.A873A		Atlas-SNP	.											RRP12,NS,carcinoma,-2,1	RRP12	97	1	0			c.A2619C						scavenged	.	T	,	254,4152	147.3+/-181.8	9,236,1958	118.0	90.0	99.0		2436,2619	-9.4	0.4	10	dbSNP_120	99	503,8097	144.7+/-200.5	17,469,3814	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,705,5772	GG,GT,TT		5.8488,5.7649,5.8204	,	812/1237,873/1298	99130282	757,12249	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon23			CTTCCGTGCGCCC		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.2619A>C	10.37:g.99130282T>G		Somatic	109	2	0.0183486		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			T|0.952;G|0.048	0.048	strong		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
BBX	56987	hgsc.bcm.edu	37	3	107491892	107491892	+	Missense_Mutation	SNP	G	G	A	rs138961599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:107491892G>A	ENST00000325805.8	+	11	1611	c.1324G>A	c.(1324-1326)Gca>Aca	p.A442T	BBX_ENST00000402543.1_Missense_Mutation_p.A442T|BBX_ENST00000416476.2_Intron|BBX_ENST00000406780.1_Missense_Mutation_p.A442T|BBX_ENST00000415149.2_Missense_Mutation_p.A442T			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	442					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)			TGAGGATCCCGCAGCATTAAA	0.358													G|||	9	0.00179712	0.0	0.0014	5008	,	,		18346	0.0		0.006	False		,,,				2504	0.002				p.A442T		Atlas-SNP	.											.	BBX	156	.	0			c.G1324A						PASS	.	G	THR/ALA,THR/ALA	9,4397	15.5+/-35.6	0,9,2194	67.0	73.0	71.0		1324,1324	0.5	1.0	3	dbSNP_134	71	84,8516	47.6+/-106.9	2,80,4218	yes	missense,missense	BBX	NM_001142568.1,NM_020235.5	58,58	2,89,6412	AA,AG,GG		0.9767,0.2043,0.7151	benign,benign	442/942,442/912	107491892	93,12913	2203	4300	6503	SO:0001583	missense	56987	exon11			GATCCCGCAGCAT	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.1324G>A	3.37:g.107491892G>A	ENSP00000319974:p.Ala442Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	0.656	-0.807550	0.02819	0.002043	0.009767	ENSG00000114439	ENST00000415149;ENST00000325767;ENST00000402543;ENST00000325805;ENST00000402163;ENST00000406780	D;D;D;D;D	0.98192	-4.39;-4.38;-4.39;-4.78;-4.39	6.07	0.455	0.16649	.	0.817289	0.11680	N	0.539909	D	0.84584	0.5504	N	0.01874	-0.695	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	0.82059	-0.0645	10	0.02654	T	1	-1.6382	0.4743	0.00537	0.3839:0.1217:0.2416:0.2529	.	442;442;442	C9JA69;Q8WY36;Q8WY36-2	.;BBX_HUMAN;.	T	442;293;442;442;442;442	ENSP00000408358:A442T;ENSP00000385317:A442T;ENSP00000319974:A442T;ENSP00000385518:A442T;ENSP00000385530:A442T	ENSP00000319742:A293T	A	+	1	0	BBX	108974582	0.002000	0.14202	0.974000	0.42286	0.699000	0.40488	0.163000	0.16520	0.528000	0.28580	-0.438000	0.05819	GCA	G|0.993;A|0.007	0.007	strong		0.358	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
TBC1D15	64786	hgsc.bcm.edu	37	12	72312268	72312268	+	Silent	SNP	G	G	A	rs11178985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:72312268G>A	ENST00000550746.1	+	15	1654	c.1590G>A	c.(1588-1590)agG>agA	p.R530R	TBC1D15_ENST00000319106.8_Silent_p.R521R|TBC1D15_ENST00000485960.2_Silent_p.R513R|TBC1D15_ENST00000393309.3_Silent_p.R284R|TBC1D15_ENST00000548679.1_3'UTR	NM_001146213.1|NM_022771.4	NP_001139685.2|NP_073608.4	Q8TC07	TBC15_HUMAN	TBC1 domain family, member 15	530	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						TTTGCTTCAGGTGGCTTTTAA	0.303													A|||	828	0.165335	0.3926	0.0764	5008	,	,		17736	0.0377		0.0755	False		,,,				2504	0.1452				p.R530R		Atlas-SNP	.											.	TBC1D15	99	.	0			c.G1590A						PASS	.	A	,,	1660,2746	655.8+/-400.0	309,1042,852	185.0	195.0	192.0		1539,1563,1590	-3.6	1.0	12	dbSNP_120	192	854,7746	779.3+/-407.7	50,754,3496	no	coding-synonymous,coding-synonymous,coding-synonymous	TBC1D15	NM_001146213.1,NM_001146214.1,NM_022771.4	,,	359,1796,4348	AA,AG,GG		9.9302,37.6759,19.3295	,,	513/675,521/683,530/692	72312268	2514,10492	2203	4300	6503	SO:0001819	synonymous_variant	64786	exon15			CTTCAGGTGGCTT	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.1590G>A	12.37:g.72312268G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_022771	B4DMT9|B9A6L6|J3KNI9|Q9HA83	Silent	SNP	ENST00000550746.1	37	CCDS31858.1																																																																																			G|0.829;A|0.171	0.171	strong		0.303	TBC1D15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351266.2	NM_022771	
XIRP2	129446	hgsc.bcm.edu	37	2	168115769	168115769	+	Missense_Mutation	SNP	G	G	C	rs16853344	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168115769G>C	ENST00000409728.1	+	11	2901	c.2812G>C	c.(2812-2814)Gaa>Caa	p.E938Q	XIRP2_ENST00000409043.1_Missense_Mutation_p.E905Q|XIRP2_ENST00000409605.1_Missense_Mutation_p.E683Q|XIRP2_ENST00000420519.1_Missense_Mutation_p.E938Q|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.E905Q	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TCTGAGCCATGAATGTACAGC	0.438													G|||	904	0.180511	0.3154	0.1239	5008	,	,		19064	0.12		0.1123	False		,,,				2504	0.1708				p.E938Q		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2812C						PASS	.	G	GLN/GLU,GLN/GLU,,GLN/GLU,	1076,2764		155,766,999	91.0	84.0	86.0		2713,2812,,2047,	4.0	0.0	2	dbSNP_123	86	808,7474		43,722,3376	yes	missense,missense,utr-3,missense,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	29,29,,29,	198,1488,4375	CC,CG,GG		9.7561,28.0208,15.542	,,,,	905/939,938/972,,683/717,	168115769	1884,10238	1920	4141	6061	SO:0001583	missense	129446	exon11			AGCCATGAATGTA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2812G>C	2.37:g.168115769G>C	ENSP00000386619:p.Glu938Gln	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	378	0.17307692307692307	175	0.3556910569105691	43	0.11878453038674033	72	0.1258741258741259	88	0.11609498680738786	G	15.51	2.855789	0.51376	0.280208	0.097561	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.78707	-1.19;-1.2;-1.19;-1.2;-1.19	5.91	3.97	0.46021	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P;P	0.43287	0.454;0.802	B;B	0.36719	0.117;0.231	T	0.22521	-1.0214	7	0.25751	T	0.34	.	5.0051	0.14284	0.0883:0.16:0.6078:0.1439	rs16853344;rs52807647;rs57534200;rs16853344	905;938	A4UGR9-4;A4UGR9-6	.;.	Q	905;938;905;938;683	ENSP00000386454:E905Q;ENSP00000386619:E938Q;ENSP00000386724:E905Q;ENSP00000415541:E938Q;ENSP00000386981:E683Q	ENSP00000386454:E905Q	E	+	1	0	XIRP2	167824015	0.033000	0.19621	0.004000	0.12327	0.148000	0.21650	1.778000	0.38614	1.466000	0.48025	0.650000	0.86243	GAA	G|0.841;C|0.159	0.159	strong		0.438	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
FRMD4B	23150	hgsc.bcm.edu	37	3	69299233	69299233	+	Missense_Mutation	SNP	C	C	G	rs4361282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:69299233C>G	ENST00000398540.3	-	6	602	c.519G>C	c.(517-519)gaG>gaC	p.E173D	FRMD4B_ENST00000542259.1_Missense_Mutation_p.E119D	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	173	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		TGGTTTCGCTCTCTACTTCGA	0.433													G|||	1237	0.247005	0.3457	0.2133	5008	,	,		18600	0.2649		0.2237	False		,,,				2504	0.1431				p.E173D		Atlas-SNP	.											.	FRMD4B	90	.	0			c.G519C						PASS	.	G	ASP/GLU	1174,2712		165,844,934	279.0	271.0	273.0		519	4.3	1.0	3	dbSNP_111	273	1816,6458		195,1426,2516	yes	missense	FRMD4B	NM_015123.1	45	360,2270,3450	GG,GC,CC		21.9483,30.211,24.5888	benign	173/1035	69299233	2990,9170	1943	4137	6080	SO:0001583	missense	23150	exon6			TTCGCTCTCTACT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.519G>C	3.37:g.69299233C>G	ENSP00000381549:p.Glu173Asp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	577	0.2641941391941392	176	0.35772357723577236	73	0.20165745856353592	143	0.25	185	0.24406332453825857	G	1.525	-0.545949	0.04024	0.30211	0.219483	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000493880;ENST00000473029;ENST00000460709	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.33	4.33	0.51752	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.106811	0.64402	N	0.000007	T	0.00012	0.0000	N	0.11560	0.145	0.51233	P	8.60000000000305E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10474	-1.0628	9	0.02654	T	1	-15.1785	7.5424	0.27746	0.0:0.1412:0.5798:0.279	rs4361282;rs52807668;rs4361282	17;173	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	D	173;119;64;119;119	ENSP00000381549:E173D;ENSP00000437658:E119D;ENSP00000418962:E64D;ENSP00000418373:E119D;ENSP00000418023:E119D	ENSP00000381549:E173D	E	-	3	2	FRMD4B	69381923	1.000000	0.71417	0.999000	0.59377	0.706000	0.40770	1.131000	0.31406	1.400000	0.46741	-0.187000	0.12897	GAG	C|0.742;G|0.258	0.258	strong		0.433	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
ATR	545	hgsc.bcm.edu	37	3	142281612	142281612	+	Missense_Mutation	SNP	A	A	G	rs2227928	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142281612A>G	ENST00000350721.4	-	4	753	c.632T>C	c.(631-633)aTg>aCg	p.M211T	ATR_ENST00000383101.3_Missense_Mutation_p.M211T	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	211			M -> T (in dbSNP:rs2227928).		cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.M211T(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						AGTAAGAACCATTAATAAAGT	0.318								Other conserved DNA damage response genes					G|||	2992	0.597444	0.8517	0.5058	5008	,	,		19058	0.4732		0.5865	False		,,,				2504	0.4581				p.M211T		Atlas-SNP	.											ATR,NS,carcinoma,0,1	ATR	285	1	1	Substitution - Missense(1)	stomach(1)	c.T632C						scavenged	.	G	THR/MET	3493,913	341.8+/-306.9	1387,719,97	55.0	56.0	56.0		632	4.6	0.8	3	dbSNP_98	56	5121,3479	506.7+/-376.7	1501,2119,680	yes	missense	ATR	NM_001184.3	81	2888,2838,777	GG,GA,AA		40.4535,20.7217,33.769	benign	211/2645	142281612	8614,4392	2203	4300	6503	SO:0001583	missense	545	exon4			AGAACCATTAATA	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.632T>C	3.37:g.142281612A>G	ENSP00000343741:p.Met211Thr	Somatic	66	1	0.0151515		WXS	Illumina HiSeq	Phase_I	86	42	0.488372	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	1348	0.6172161172161172	416	0.8455284552845529	198	0.5469613259668509	291	0.5087412587412588	443	0.5844327176781002	G	0.013	-1.635725	0.00806	0.792783	0.595465	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.65178	-0.14;-0.14	5.56	4.6	0.57074	Armadillo-type fold (1);	0.682857	0.14770	N	0.299410	T	0.00012	0.0000	N	0.08118	0	0.58432	P	9.99999999995449E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44907	-0.9297	9	0.02654	T	1	-1.8968	4.0735	0.09892	0.322:0.1719:0.5061:0.0	rs2227928;rs52801743;rs59723696;rs2227928	211	Q13535	ATR_HUMAN	T	211	ENSP00000343741:M211T;ENSP00000372581:M211T	ENSP00000343741:M211T	M	-	2	0	ATR	143764302	0.877000	0.30153	0.839000	0.33178	0.943000	0.58893	1.273000	0.33121	0.547000	0.28938	-0.186000	0.12905	ATG	A|0.361;G|0.639	0.639	strong		0.318	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
DEFB127	140850	hgsc.bcm.edu	37	20	139456	139456	+	Missense_Mutation	SNP	G	G	A	rs12624954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:139456G>A	ENST00000382388.3	+	2	166	c.91G>A	c.(91-93)Gga>Aga	p.G31R		NM_139074.3	NP_620713.1	Q9H1M4	DB127_HUMAN	defensin, beta 127	31			G -> R (in dbSNP:rs12624954). {ECO:0000269|PubMed:11854508}.		defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)	extracellular region (GO:0005576)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)	9		all_cancers(10;7.65e-05)|Lung NSC(37;0.0417)|all_epithelial(17;0.0676)|all_lung(30;0.0713)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.122)			CTATGTACAAGGACATTGCAG	0.403													G|||	1624	0.324281	0.0424	0.3487	5008	,	,		22136	0.5446		0.3419	False		,,,				2504	0.4427				p.G31R		Atlas-SNP	.											DEFB127,NS,carcinoma,-1,1	DEFB127	15	1	0			c.G91A						PASS	.	G	ARG/GLY	395,4011	195.3+/-220.0	18,359,1826	92.0	82.0	85.0		91	3.1	0.1	20	dbSNP_120	85	3023,5577	463.2+/-365.9	518,1987,1795	yes	missense	DEFB127	NM_139074.2	125	536,2346,3621	AA,AG,GG		35.1512,8.965,26.2802	probably-damaging	31/100	139456	3418,9588	2203	4300	6503	SO:0001583	missense	140850	exon2			GTACAAGGACATT	AY358796	CCDS12991.1	20p13	2008-02-01	2002-05-09	2002-05-10	ENSG00000088782	ENSG00000088782		"""Defensins, beta"""	16206	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 73"""	C20orf73		11854508	Standard	NM_139074		Approved	bA530N10.2, DEF-27	uc002wcy.2	Q9H1M4	OTTHUMG00000031617	ENST00000382388.3:c.91G>A	20.37:g.139456G>A	ENSP00000371825:p.Gly31Arg	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	157	71	0.452229	NM_139074	Q14DW7	Missense_Mutation	SNP	ENST00000382388.3	37	CCDS12991.1	702	0.32142857142857145	19	0.03861788617886179	135	0.3729281767955801	287	0.5017482517482518	261	0.34432717678100266	G	10.22	1.289992	0.23478	0.08965	0.351512	ENSG00000088782	ENST00000382388	T	0.62639	0.01	3.12	3.12	0.35913	.	0.000000	0.33834	N	0.004506	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	D	0.89917	1.0	D	0.97110	1.0	T	0.47849	-0.9085	8	0.56958	D	0.05	-21.6232	9.9776	0.41793	0.0:0.0:1.0:0.0	rs12624954;rs52796717;rs61481484;rs12624954	31	Q9H1M4	DB127_HUMAN	R	31	ENSP00000371825:G31R	ENSP00000371825:G31R	G	+	1	0	DEFB127	87456	0.951000	0.32395	0.140000	0.22221	0.028000	0.11728	3.236000	0.51336	2.059000	0.61396	0.305000	0.20034	GGA	G|0.719;A|0.281	0.281	strong		0.403	DEFB127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077429.1	NM_139074	
LRFN5	145581	hgsc.bcm.edu	37	14	42360633	42360633	+	Silent	SNP	T	T	C	rs6572117	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:42360633T>C	ENST00000298119.4	+	4	2755	c.1566T>C	c.(1564-1566)tcT>tcC	p.S522S	LRFN5_ENST00000554171.1_Intron|LRFN5_ENST00000554120.1_Intron	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	522						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TCATGCAGTCTCAGTTTTTGG	0.423										HNSCC(30;0.082)			C|||	3532	0.705272	0.6634	0.6398	5008	,	,		20147	0.745		0.7117	False		,,,				2504	0.7607				p.S522S		Atlas-SNP	.											.	LRFN5	269	.	0			c.T1566C						PASS	.	C		3019,1387	458.0+/-351.8	1021,977,205	231.0	219.0	223.0		1566	3.8	1.0	14	dbSNP_116	223	6089,2511	412.5+/-350.8	2188,1713,399	no	coding-synonymous	LRFN5	NM_152447.3		3209,2690,604	CC,CT,TT		29.1977,31.4798,29.9708		522/720	42360633	9108,3898	2203	4300	6503	SO:0001819	synonymous_variant	145581	exon4			GCAGTCTCAGTTT	AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	20360	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 8"""	612811	"""chromosome 14 open reading frame 146"""	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1566T>C	14.37:g.42360633T>C		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_152447	B3KU78|Q86XL2	Silent	SNP	ENST00000298119.4	37	CCDS9678.1																																																																																			T|0.301;C|0.699	0.699	strong		0.423	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447	
CRACR2A	84766	hgsc.bcm.edu	37	12	3788260	3788260	+	Silent	SNP	G	G	A	rs242016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:3788260G>A	ENST00000252322.1	-	6	813	c.345C>T	c.(343-345)caC>caT	p.H115H	EFCAB4B_ENST00000440314.2_Silent_p.H115H|EFCAB4B_ENST00000444507.1_Silent_p.H115H	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		115	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TGAAGAAGAAGTGACCTGGGG	0.527													G|||	359	0.0716853	0.0461	0.111	5008	,	,		20406	0.004		0.1531	False		,,,				2504	0.0644				p.H115H		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.C345T						PASS	.	G	,	265,4141	151.0+/-185.0	10,245,1948	108.0	93.0	98.0		345,345	3.6	1.0	12	dbSNP_79	98	1471,7129	278.9+/-293.6	120,1231,2949	no	coding-synonymous,coding-synonymous	EFCAB4B	NM_001144958.1,NM_032680.3	,	130,1476,4897	AA,AG,GG		17.1047,6.0145,13.3477	,	115/732,115/396	3788260	1736,11270	2203	4300	6503	SO:0001819	synonymous_variant	84766	exon6			GAAGAAGTGACCT																												ENST00000252322.1:c.345C>T	12.37:g.3788260G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	74	28	0.378378	NM_001144958	B4E1X0|B9EK63	Silent	SNP	ENST00000252322.1	37	CCDS8522.1																																																																																			G|0.885;A|0.115	0.115	strong		0.527	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
SLX4	84464	hgsc.bcm.edu	37	16	3647692	3647692	+	Missense_Mutation	SNP	A	A	C	rs74319927	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3647692A>C	ENST00000294008.3	-	7	2011	c.1371T>G	c.(1369-1371)aaT>aaG	p.N457K		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	457	Interaction with SLX4IP, ERCC4 and MSH2.		N -> K (in dbSNP:rs74319927). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TGCGACTTTTATTCTCTAGAG	0.552								Direct reversal of damage					C|||	275	0.0549121	0.0507	0.0706	5008	,	,		16428	0.0506		0.0656	False		,,,				2504	0.0429				p.N457K		Atlas-SNP	.											.	SLX4	173	.	0			c.T1371G						PASS	.	C	LYS/ASN	264,4124		8,248,1938	42.0	51.0	48.0		1371	5.2	1.0	16	dbSNP_131	48	581,8017		16,549,3734	yes	missense	SLX4	NM_032444.2	94	24,797,5672	CC,CA,AA		6.7574,6.0164,6.507	benign	457/1835	3647692	845,12141	2194	4299	6493	SO:0001583	missense	84464	exon7			ACTTTTATTCTCT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.1371T>G	16.37:g.3647692A>C	ENSP00000294008:p.Asn457Lys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	69	42	0.608696	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	124	0.056776556776556776	26	0.052845528455284556	24	0.06629834254143646	24	0.04195804195804196	50	0.06596306068601583	C	5.789	0.329828	0.10956	0.060164	0.067574	ENSG00000188827	ENST00000294008	T	0.16324	2.35	5.19	5.19	0.71726	.	0.000000	0.64402	N	0.000011	T	0.00300	0.0009	N	0.00399	-1.545	0.20489	N	0.999898	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	10	0.02654	T	1	.	8.0402	0.30517	0.1615:0.7518:0.0:0.0867	.	457	Q8IY92	SLX4_HUMAN	K	457	ENSP00000294008:N457K	ENSP00000294008:N457K	N	-	3	2	SLX4	3587693	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	0.674000	0.25218	1.195000	0.43115	-0.121000	0.15023	AAT	A|0.941;C|0.059	0.059	strong		0.552	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
ZCCHC7	84186	hgsc.bcm.edu	37	9	37305550	37305550	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37305550C>G	ENST00000336755.5	+	5	896	c.790C>G	c.(790-792)Cgc>Ggc	p.R264G	ZCCHC7_ENST00000534928.1_5'UTR|ZCCHC7_ENST00000461038.1_3'UTR	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	264						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		GAAAGTTCGTCGCTGCTTCCT	0.408																																					p.R264G		Atlas-SNP	.											ZCCHC7,NS,carcinoma,0,1	ZCCHC7	56	1	0			c.C790G						scavenged	.						144.0	136.0	139.0					9																	37305550		2203	4300	6503	SO:0001583	missense	84186	exon5			GTTCGTCGCTGCT	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"""Zinc fingers, CCHC domain containing"""	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.790C>G	9.37:g.37305550C>G	ENSP00000337839:p.Arg264Gly	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	109	3	0.0275229	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Missense_Mutation	SNP	ENST00000336755.5	37	CCDS6608.2	.	.	.	.	.	.	.	.	.	.	C	1.980	-0.434309	0.04669	.	.	ENSG00000147905	ENST00000336755	T	0.31247	1.5	5.48	-11.0	0.00169	Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (2);	1.766550	0.02644	N	0.105642	T	0.14917	0.0360	N	0.10916	0.065	0.39025	D	0.959814	B	0.10296	0.003	B	0.10450	0.005	T	0.24693	-1.0153	10	0.22706	T	0.39	-11.5487	13.3193	0.60424	0.144:0.1792:0.6197:0.0571	.	264	Q8N3Z6	ZCHC7_HUMAN	G	264	ENSP00000337839:R264G	ENSP00000337839:R264G	R	+	1	0	ZCCHC7	37295550	0.000000	0.05858	0.003000	0.11579	0.137000	0.21094	-2.050000	0.01404	-1.446000	0.01945	-0.152000	0.13540	CGC	.	.	none		0.408	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226	
GFPT2	9945	hgsc.bcm.edu	37	5	179740827	179740827	+	Missense_Mutation	SNP	T	T	C	rs2303007	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179740827T>C	ENST00000253778.8	-	14	1580	c.1411A>G	c.(1411-1413)Atc>Gtc	p.I471V	GFPT2_ENST00000520165.1_5'Flank	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	471	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.		I -> V (in dbSNP:rs2303007). {ECO:0000269|Ref.2}.		carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-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)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	GCCACGCCGATCTCCGGCCCT	0.711													T|||	1174	0.234425	0.062	0.2176	5008	,	,		8734	0.4028		0.2256	False		,,,				2504	0.3149				p.I471V		Atlas-SNP	.											GFPT2,NS,carcinoma,0,1	GFPT2	74	1	0			c.A1411G	GRCh37	CM040423	GFPT2	M	rs2303007	PASS	.	T	VAL/ILE	320,4048		14,292,1878	12.0	15.0	14.0		1411	2.2	1.0	5	dbSNP_100	14	1641,6917		163,1315,2801	yes	missense	GFPT2	NM_005110.2	29	177,1607,4679	CC,CT,TT		19.175,7.326,15.171	benign	471/683	179740827	1961,10965	2184	4279	6463	SO:0001583	missense	9945	exon14			CGCCGATCTCCGG	AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"""glutamine: fructose-6-phosphate aminotransferase 2"""	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1411A>G	5.37:g.179740827T>C	ENSP00000253778:p.Ile471Val	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	34	33	0.970588	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	37	CCDS43411.1	497	0.22756410256410256	26	0.052845528455284556	75	0.20718232044198895	218	0.3811188811188811	178	0.23482849604221637	T	12.31	1.900188	0.33535	0.07326	0.19175	ENSG00000131459	ENST00000253778	T	0.62788	-0.0	5.8	2.15	0.27550	Sugar isomerase (SIS) (2);	0.139878	0.64402	N	0.000007	T	0.00012	0.0000	L	0.42744	1.35	0.20703	P	0.999866909	B	0.06786	0.001	B	0.13407	0.009	T	0.36529	-0.9744	8	.	.	.	-20.4654	11.429	0.50029	0.0:0.1875:0.0:0.8125	rs2303007;rs17855340;rs2303007	471	O94808	GFPT2_HUMAN	V	471	ENSP00000253778:I471V	.	I	-	1	0	GFPT2	179673433	1.000000	0.71417	0.983000	0.44433	0.689000	0.40095	3.092000	0.50207	-0.084000	0.12595	-1.162000	0.01777	ATC	T|0.789;C|0.211	0.211	strong		0.711	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	
PCNT	5116	hgsc.bcm.edu	37	21	47836216	47836216	+	Silent	SNP	A	A	G	rs60444527	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47836216A>G	ENST00000359568.5	+	30	6491	c.6384A>G	c.(6382-6384)acA>acG	p.T2128T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2128					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)					ACATAGACACATGTGATGCCA	0.517													G|||	891	0.177915	0.4856	0.0922	5008	,	,		18403	0.004		0.0924	False		,,,				2504	0.09				p.T2128T		Atlas-SNP	.											.	PCNT	283	.	0			c.A6384G	GRCh37	CD080881	PCNT	D	rs60444527	PASS	.	G		1912,2494	626.3+/-394.7	414,1084,705	89.0	89.0	89.0		6384	-3.6	0.0	21	dbSNP_129	89	652,7948	789.7+/-407.6	15,622,3663	no	coding-synonymous	PCNT	NM_006031.5		429,1706,4368	GG,GA,AA		7.5814,43.3954,19.714		2128/3337	47836216	2564,10442	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon30			AGACACATGTGAT	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.6384A>G	21.37:g.47836216A>G		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	132	56	0.424242	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			A|0.818;G|0.182	0.182	strong		0.517	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
NPAP1	23742	hgsc.bcm.edu	37	15	24923129	24923129	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:24923129T>C	ENST00000329468.2	+	1	2589	c.2115T>C	c.(2113-2115)ccT>ccC	p.P705P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	705					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCACTCCTCCTTCCAAGGCTG	0.507																																					p.P705P		Atlas-SNP	.											.	.	.	.	0			c.T2115C						PASS	.						176.0	163.0	168.0					15																	24923129		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TCCTCCTTCCAAG	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.2115T>C	15.37:g.24923129T>C		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	271	110	0.405904	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			.	.	none		0.507	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
RPS15	6209	hgsc.bcm.edu	37	19	1440068	1440068	+	Missense_Mutation	SNP	G	G	C	rs201657403		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1440068G>C	ENST00000586686.2	+	3	179	c.140G>C	c.(139-141)cGg>cCg	p.R47P	RPS15_ENST00000591804.2_Missense_Mutation_p.R14P|RPS15_ENST00000591032.1_Missense_Mutation_p.R14P|RPS15_ENST00000589656.2_Missense_Mutation_p.R47P|AC027307.3_ENST00000594262.1_5'Flank|RPS15_ENST00000233609.4_Missense_Mutation_p.R20P|RPS15_ENST00000585665.1_Missense_Mutation_p.R14P|RPS15_ENST00000593052.1_Missense_Mutation_p.R54P|RPS15_ENST00000586096.2_Missense_Mutation_p.R47P			P62841	RS15_HUMAN	ribosomal protein S15	47					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)	p.R47P(1)		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)		CGGCTGAACCGGGGCCTGCGG	0.687																																					p.R47P	Ovarian(170;79 2680 5719 44260)	Atlas-SNP	.											RPS15,extremity,malignant_melanoma,0,1	RPS15	11	1	1	Substitution - Missense(1)	skin(1)	c.G140C						scavenged	.						3.0	5.0	4.0					19																	1440068		2019	3993	6012	SO:0001583	missense	6209	exon3			TGAACCGGGGCCT		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.140G>C	19.37:g.1440068G>C	ENSP00000467676:p.Arg47Pro	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	40	3	0.075	NM_001018	A5D8V9|P11174|Q3KRA1|Q9UDC2	Missense_Mutation	SNP	ENST00000586686.2	37	CCDS12067.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.516509	0.27123	.	.	ENSG00000115268	ENST00000233609	.	.	.	4.26	3.21	0.36854	Ribosomal protein S19, superfamily (2);	0.000000	0.64402	U	0.000002	T	0.79452	0.4448	H	0.96489	3.83	0.80722	D	1	B	0.17465	0.022	B	0.26310	0.068	T	0.78595	-0.2143	9	0.51188	T	0.08	-26.4524	11.4241	0.50001	0.0902:0.0:0.9098:0.0	.	47	P62841	RS15_HUMAN	P	47	.	ENSP00000233609:R47P	R	+	2	0	RPS15	1391068	1.000000	0.71417	0.710000	0.30468	0.007000	0.05969	9.198000	0.94994	0.908000	0.36671	-0.192000	0.12808	CGG	G|0.442;C|0.558	0.558	strong		0.687	RPS15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449609.4	NM_001018	
MTIF3	219402	hgsc.bcm.edu	37	13	28009851	28009851	+	Silent	SNP	G	G	A	rs7669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:28009851G>A	ENST00000381116.1	-	7	1032	c.798C>T	c.(796-798)gaC>gaT	p.D266D	MTIF3_ENST00000431572.2_Silent_p.D266D|MTIF3_ENST00000381120.3_Silent_p.D266D|MTIF3_ENST00000461838.1_5'UTR|MTIF3_ENST00000405591.2_Silent_p.D266D			Q9H2K0	IF3M_HUMAN	mitochondrial translational initiation factor 3	266					formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)		CATTTCCATGGTCTTTGTTCA	0.378													G|||	585	0.116813	0.0635	0.0922	5008	,	,		21270	0.1488		0.1938	False		,,,				2504	0.0941				p.D266D		Atlas-SNP	.											.	MTIF3	21	.	0			c.C798T						PASS	.	G	,,,	389,4017	193.0+/-218.2	17,355,1831	208.0	207.0	207.0		798,798,798,798	-1.9	0.0	13	dbSNP_52	207	1555,7045	290.9+/-300.1	148,1259,2893	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MTIF3	NM_001166261.1,NM_001166262.1,NM_001166263.1,NM_152912.4	,,,	165,1614,4724	AA,AG,GG		18.0814,8.8289,14.9469	,,,	266/279,266/279,266/279,266/279	28009851	1944,11062	2203	4300	6503	SO:0001819	synonymous_variant	219402	exon6			TCCATGGTCTTTG	BC046166	CCDS9322.1	13q12.2	2007-05-03			ENSG00000122033	ENSG00000122033			29788	protein-coding gene	gene with protein product						12095986	Standard	NM_152912		Approved	IF-3mt, IF3(mt)	uc001uri.3	Q9H2K0	OTTHUMG00000016633	ENST00000381116.1:c.798C>T	13.37:g.28009851G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	144	71	0.493056	NM_001166263	Q05BL8|Q5W0V0|Q86X68	Silent	SNP	ENST00000381116.1	37	CCDS9322.1																																																																																			A|0.137;C|0.000;G|0.863	0.137	strong		0.378	MTIF3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044300.1	NM_152912	
EVPL	2125	hgsc.bcm.edu	37	17	74003846	74003846	+	Missense_Mutation	SNP	G	G	A	rs7342883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74003846G>A	ENST00000301607.3	-	22	5693	c.5440C>T	c.(5440-5442)Ccc>Tcc	p.P1814S	EVPL_ENST00000586740.1_Missense_Mutation_p.P1836S|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1814	Globular 2.		P -> S (in dbSNP:rs7342883). {ECO:0000269|PubMed:15489334}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						GAGAAGCTGGGAGAGAAGAAA	0.597													G|||	878	0.175319	0.5484	0.085	5008	,	,		17116	0.0089		0.0577	False		,,,				2504	0.0276				p.P1814S		Atlas-SNP	.											.	EVPL	155	.	0			c.C5440T						PASS	.	G	SER/PRO	2086,2320	570.4+/-382.8	514,1058,631	100.0	113.0	108.0		5440	4.2	0.3	17	dbSNP_116	108	468,8132	138.3+/-195.1	17,434,3849	yes	missense	EVPL	NM_001988.2	74	531,1492,4480	AA,AG,GG		5.4419,47.3445,19.6371	probably-damaging	1814/2034	74003846	2554,10452	2203	4300	6503	SO:0001583	missense	2125	exon22			AGCTGGGAGAGAA	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.5440C>T	17.37:g.74003846G>A	ENSP00000301607:p.Pro1814Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	330	0.1510989010989011	259	0.5264227642276422	30	0.08287292817679558	4	0.006993006993006993	37	0.048812664907651716	G	6.011	0.370374	0.11352	0.473445	0.054419	ENSG00000167880	ENST00000301607	T	0.62498	0.02	5.15	4.19	0.49359	.	0.446063	0.19314	N	0.117330	T	0.00012	0.0000	L	0.28274	0.84	0.41226	P	0.013457000000000052	B	0.16166	0.016	B	0.14578	0.011	T	0.45116	-0.9283	9	0.23891	T	0.37	-13.1638	13.6074	0.62056	0.0751:0.0:0.9249:0.0	rs7342883;rs52809318;rs61613567;rs7342883	1814	Q92817	EVPL_HUMAN	S	1814	ENSP00000301607:P1814S	ENSP00000301607:P1814S	P	-	1	0	EVPL	71515441	0.861000	0.29849	0.268000	0.24571	0.439000	0.31926	0.562000	0.23531	1.161000	0.42604	0.549000	0.68633	CCC	G|0.803;A|0.197	0.197	strong		0.597	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
ABCA13	154664	hgsc.bcm.edu	37	7	48318242	48318242	+	Missense_Mutation	SNP	G	G	A	rs79834369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48318242G>A	ENST00000435803.1	+	18	7475	c.7451G>A	c.(7450-7452)aGa>aAa	p.R2484K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2484					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						GCTATTTCAAGAGCAAGTGAA	0.393													G|||	10	0.00199681	0.0	0.0	5008	,	,		18633	0.0		0.0099	False		,,,				2504	0.0				p.R2484K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G7451A						PASS	.	G	LYS/ARG	10,3654		0,10,1822	149.0	150.0	150.0		7451	-0.0	0.0	7	dbSNP_132	150	73,8097		0,73,4012	yes	missense	ABCA13	NM_152701.3	26	0,83,5834	AA,AG,GG		0.8935,0.2729,0.7014	benign	2484/5059	48318242	83,11751	1832	4085	5917	SO:0001583	missense	154664	exon18			TTTCAAGAGCAAG	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.7451G>A	7.37:g.48318242G>A	ENSP00000411096:p.Arg2484Lys	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	100	54	0.54	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	9.467	1.094712	0.20471	0.002729	0.008935	ENSG00000179869	ENST00000435803	T	0.56611	0.45	4.11	-0.0121	0.13989	.	0.877287	0.09429	N	0.803261	T	0.24431	0.0592	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.16158	-1.0412	10	0.27082	T	0.32	.	3.6594	0.08233	0.3281:0.191:0.4809:0.0	.	2484	Q86UQ4	ABCAD_HUMAN	K	2484	ENSP00000411096:R2484K	ENSP00000411096:R2484K	R	+	2	0	ABCA13	48288788	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	0.015000	0.13355	0.085000	0.17107	0.655000	0.94253	AGA	G|0.996;A|0.004	0.004	strong		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
RAD17	5884	hgsc.bcm.edu	37	5	68695940	68695940	+	Missense_Mutation	SNP	T	T	G	rs1045051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:68695940T>G	ENST00000509734.1	+	16	2348	c.1670T>G	c.(1669-1671)cTc>cGc	p.L557R	RAD17_ENST00000521422.1_Missense_Mutation_p.L381R|RAD17_ENST00000354868.5_Missense_Mutation_p.L546R|RAD17_ENST00000358030.2_Missense_Mutation_p.L381R|RAD17_ENST00000354312.3_Missense_Mutation_p.L546R|RAD17_ENST00000504177.1_Intron|RAD17_ENST00000361732.2_Missense_Mutation_p.L546R|RAD17_ENST00000305138.4_Missense_Mutation_p.L546R|RAD17_ENST00000282891.6_Missense_Mutation_p.L460R|RAD17_ENST00000345306.6_Missense_Mutation_p.L546R|RAD17_ENST00000380774.3_Missense_Mutation_p.L557R			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	557	Interaction with MCM7.		L -> R (in dbSNP:rs1045051). {ECO:0000269|PubMed:10232579, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.13}.		cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		GCTTTATGCCTCCAAACTCAG	0.358								Other conserved DNA damage response genes					T|||	1276	0.254792	0.0446	0.3012	5008	,	,		12165	0.3155		0.3231	False		,,,				2504	0.3732				p.L557R		Atlas-SNP	.											.	RAD17	49	.	0			c.T1670G						PASS	.	T	ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU,ARG/LEU	370,4036	189.2+/-215.4	14,342,1847	65.0	57.0	59.0		1637,1637,1670,1142,1379,1637,1637,1637	5.7	1.0	5	dbSNP_86	59	2767,5833	436.2+/-358.2	464,1839,1997	yes	missense,missense,missense,missense,missense,missense,missense,missense	RAD17	NM_002873.1,NM_133338.1,NM_133339.1,NM_133340.1,NM_133341.1,NM_133342.1,NM_133343.1,NM_133344.1	102,102,102,102,102,102,102,102	478,2181,3844	GG,GT,TT		32.1744,8.3976,24.1196	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	546/671,546/671,557/682,381/506,460/585,546/671,546/671,546/671	68695940	3137,9869	2203	4300	6503	SO:0001583	missense	5884	exon14			TATGCCTCCAAAC	AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1670T>G	5.37:g.68695940T>G	ENSP00000426191:p.Leu557Arg	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	384	384	1	NM_133339	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Missense_Mutation	SNP	ENST00000509734.1	37	CCDS4003.1	559	0.25595238095238093	28	0.056910569105691054	96	0.26519337016574585	197	0.34440559440559443	238	0.31398416886543534	T	22.4	4.291210	0.80914	0.083976	0.321744	ENSG00000152942	ENST00000361732;ENST00000509734;ENST00000354868;ENST00000521422;ENST00000354312;ENST00000345306;ENST00000305138;ENST00000282891;ENST00000358030;ENST00000380774;ENST00000513214	T;T;T;T;T;T;T;T;T;T;T	0.25579	1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79;1.79	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.67397	2.05	0.09310	P	0.9999999042773	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.16808	-1.0390	9	0.87932	D	0	0.0332	15.0598	0.71944	0.0:0.0:0.0:1.0	rs1045051;rs3184869;rs11542279;rs17236548;rs1045051	557;460;546	O75943;O75943-4;O75943-2	RAD17_HUMAN;.;.	R	546;557;546;381;546;546;546;460;381;557;165	ENSP00000355226:L546R;ENSP00000426191:L557R;ENSP00000346938:L546R;ENSP00000427743:L381R;ENSP00000346271:L546R;ENSP00000311227:L546R;ENSP00000303134:L546R;ENSP00000282891:L460R;ENSP00000350725:L381R;ENSP00000370151:L557R;ENSP00000425005:L165R	ENSP00000282891:L460R	L	+	2	0	RAD17	68731696	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	7.248000	0.78268	2.203000	0.70933	0.473000	0.43528	CTC	T|0.763;G|0.237	0.237	strong		0.358	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344	
HSPA1L	3305	hgsc.bcm.edu	37	6	31777946	31777946	+	Missense_Mutation	SNP	C	C	T	rs2075800	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31777946C>T	ENST00000375654.4	-	2	1993	c.1804G>A	c.(1804-1806)Gag>Aag	p.E602K	HSPA1L_ENST00000417199.3_Missense_Mutation_p.E602K	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	602			E -> K (in dbSNP:rs2075800). {ECO:0000269|Ref.5}.		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						CACATCTGCTCCAATTCCTTT	0.473													C|||	1278	0.255192	0.0204	0.3372	5008	,	,		20025	0.3681		0.3489	False		,,,				2504	0.3016				p.E602K		Atlas-SNP	.											HSPA1L,NS,carcinoma,+2,1	HSPA1L	185	1	0			c.G1804A						PASS	.	C	LYS/GLU	287,4119	158.1+/-190.9	13,261,1929	137.0	122.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1804	5.9	1.0	6	dbSNP_96	127	2826,5774	447.9+/-361.7	465,1896,1939	yes	missense	HSPA1L	NM_005527.3	56	478,2157,3868	TT,TC,CC		32.8605,6.5138,23.9351	possibly-damaging	602/642	31777946	3113,9893	2203	4300	6503	SO:0001583	missense	3305	exon2			TCTGCTCCAATTC	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.1804G>A	6.37:g.31777946C>T	ENSP00000364805:p.Glu602Lys	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	206	97	0.470874	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	37	CCDS34413.1	634	0.2902930402930403	15	0.03048780487804878	132	0.36464088397790057	234	0.4090909090909091	253	0.3337730870712401	C	20.3	3.968810	0.74131	0.065138	0.328605	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653	T;T	0.15834	2.39;2.39	5.94	5.94	0.96194	.	0.000000	0.35067	N	0.003477	T	0.29355	0.0731	L	0.58925	1.835	0.09310	P	0.9999999366136	D	0.54047	0.964	P	0.61328	0.887	T	0.00726	-1.1592	9	0.87932	D	0	-23.9259	17.8531	0.88754	0.0:1.0:0.0:0.0	rs2075800;rs35486322;rs60193164;rs2075800	602	P34931	HS71L_HUMAN	K	602;602;547	ENSP00000364805:E602K;ENSP00000387691:E602K	ENSP00000364804:E547K	E	-	1	0	HSPA1L	31885925	1.000000	0.71417	0.989000	0.46669	0.340000	0.28889	7.818000	0.86416	2.807000	0.96579	0.591000	0.81541	GAG	C|0.741;T|0.259	0.259	strong		0.473	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2		
ALCAM	214	hgsc.bcm.edu	37	3	105266274	105266274	+	Silent	SNP	T	T	C	rs16851279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:105266274T>C	ENST00000306107.5	+	11	1781	c.1281T>C	c.(1279-1281)agT>agC	p.S427S	ALCAM_ENST00000486979.2_Silent_p.S376S|ALCAM_ENST00000472644.2_Silent_p.S427S|ALCAM_ENST00000389927.4_Silent_p.S149S	NM_001627.3	NP_001618.2	Q13740	CD166_HUMAN	activated leukocyte cell adhesion molecule	427	Ig-like C2-type 3.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|motor neuron axon guidance (GO:0008045)|signal transduction (GO:0007165)	axon (GO:0030424)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CTGATCCCAGTGGACTATCTA	0.353													T|||	701	0.139976	0.0696	0.2334	5008	,	,		18341	0.1716		0.0954	False		,,,				2504	0.182				p.S427S		Atlas-SNP	.											.	ALCAM	71	.	0			c.T1281C						PASS	.	T		374,4030	185.0+/-212.2	15,344,1843	62.0	59.0	60.0		1281	2.2	1.0	3	dbSNP_123	60	883,7713	198.0+/-242.5	64,755,3479	no	coding-synonymous	ALCAM	NM_001627.3		79,1099,5322	CC,CT,TT		10.2722,8.4923,9.6692		427/584	105266274	1257,11743	2202	4298	6500	SO:0001819	synonymous_variant	214	exon11			TCCCAGTGGACTA	AK054632	CCDS33810.1, CCDS58841.1	3q13.1	2013-01-29	2002-08-08		ENSG00000170017	ENSG00000170017		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	400	protein-coding gene	gene with protein product		601662	"""activated leucocyte cell adhesion molecule"""			7760007	Standard	NM_001627		Approved	CD166, MEMD	uc003dvx.3	Q13740	OTTHUMG00000159192	ENST00000306107.5:c.1281T>C	3.37:g.105266274T>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	174	72	0.413793	NM_001627	B2RNS3|B4DTU0|O60892|Q1HGM8|Q1HGM9|Q6PEY4|Q6ZS95	Silent	SNP	ENST00000306107.5	37	CCDS33810.1	281	0.12866300366300365	32	0.06504065040650407	67	0.1850828729281768	108	0.1888111888111888	74	0.09762532981530343	T	9.545	1.114307	0.20795	0.084923	0.102722	ENSG00000170017	ENST00000465413	.	.	.	5.76	2.15	0.27550	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999819279	.	.	.	.	.	.	T	0.09975	-1.0650	3	.	.	.	-6.6805	6.7058	0.23250	0.1207:0.1126:0.0:0.7667	rs16851279;rs60994031;rs16851279	.	.	.	R	188	.	.	W	+	1	0	ALCAM	106748964	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.238000	0.43070	0.978000	0.38470	0.477000	0.44152	TGG	T|0.886;C|0.114	0.114	strong		0.353	ALCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353764.1	NM_001627	
JAG1	182	hgsc.bcm.edu	37	20	10620275	10620275	+	Silent	SNP	G	G	A	rs1051421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:10620275G>A	ENST00000254958.5	-	26	4043	c.3528C>T	c.(3526-3528)taC>taT	p.Y1176Y	JAG1_ENST00000423891.2_Silent_p.Y1017Y	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	1176					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.Y1176Y(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						CTACCAGCGTGTACGCCGGCT	0.502									Alagille Syndrome				G|||	902	0.180112	0.0681	0.2565	5008	,	,		17189	0.1667		0.2833	False		,,,				2504	0.1851				p.Y1176Y		Atlas-SNP	.											JAG1_ENST00000254958,NS,carcinoma,0,1	JAG1	213	1	1	Substitution - coding silent(1)	stomach(1)	c.C3528T						PASS	.	G		528,3878	240.3+/-251.1	40,448,1715	192.0	185.0	188.0		3528	4.6	1.0	20	dbSNP_86	188	2439,6161	403.9+/-348.0	361,1717,2222	no	coding-synonymous	JAG1	NM_000214.2		401,2165,3937	AA,AG,GG		28.3605,11.9837,22.8125		1176/1219	10620275	2967,10039	2203	4300	6503	SO:0001819	synonymous_variant	182	exon26	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CAGCGTGTACGCC	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.3528C>T	20.37:g.10620275G>A		Somatic	338	0	0		WXS	Illumina HiSeq	Phase_I	353	179	0.507082	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			G|0.785;A|0.215	0.215	strong		0.502	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
PIGZ	80235	hgsc.bcm.edu	37	3	196675397	196675397	+	Missense_Mutation	SNP	G	G	A	rs144088027	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196675397G>A	ENST00000412723.1	-	3	517	c.371C>T	c.(370-372)gCg>gTg	p.A124V	PIGZ_ENST00000443835.1_Intron	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	124					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)		CACCAGCAGCGCATAGCCGCT	0.682													g|||	12	0.00239617	0.0023	0.0	5008	,	,		14442	0.0		0.007	False		,,,				2504	0.002				p.A124V		Atlas-SNP	.											.	PIGZ	34	.	0			c.C371T						PASS	.		VAL/ALA	5,4389		0,5,2192	21.0	19.0	20.0		371	-10.5	0.0	3	dbSNP_134	20	30,8560		0,30,4265	yes	missense	PIGZ	NM_025163.2	64	0,35,6457	AA,AG,GG		0.3492,0.1138,0.2696	benign	124/580	196675397	35,12949	2197	4295	6492	SO:0001583	missense	80235	exon3			AGCAGCGCATAGC	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.371C>T	3.37:g.196675397G>A	ENSP00000413405:p.Ala124Val	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	37	CCDS3324.1	9	0.004120879120879121	2	0.0040650406504065045	0	0.0	0	0.0	7	0.009234828496042216	g	1.154	-0.645692	0.03531	0.001138	0.003492	ENSG00000119227	ENST00000412723	T	0.11495	2.77	5.25	-10.5	0.00291	.	2.309490	0.01740	N	0.029334	T	0.03608	0.0103	N	0.11341	0.13	0.18873	N	0.999989	B	0.09022	0.002	B	0.06405	0.002	T	0.28996	-1.0026	10	0.08381	T	0.77	3.9812	15.9089	0.79456	0.0966:0.0:0.8226:0.0808	.	124	Q86VD9	PIGZ_HUMAN	V	124	ENSP00000413405:A124V	ENSP00000413405:A124V	A	-	2	0	PIGZ	198159794	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.517000	0.06275	-3.012000	0.00272	-1.122000	0.02009	GCG	G|0.997;A|0.003	0.003	strong		0.682	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
WDR4	10785	hgsc.bcm.edu	37	21	44270229	44270229	+	Missense_Mutation	SNP	C	C	T	rs6586250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:44270229C>T	ENST00000398208.2	-	11	1228	c.1169G>A	c.(1168-1170)cGg>cAg	p.R390Q	WDR4_ENST00000492742.1_5'UTR|WDR4_ENST00000330317.2_Missense_Mutation_p.R390Q	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)		CGGGGGACTCCGGCGCCGCTG	0.602													C|||	1169	0.233427	0.4811	0.1513	5008	,	,		16852	0.0734		0.1779	False		,,,				2504	0.1789				p.R390Q		Atlas-SNP	.											.	WDR4	35	.	0			c.G1169A						PASS	.	C	GLN/ARG,GLN/ARG	1921,2485	544.3+/-376.5	442,1037,724	77.0	85.0	82.0		1169,1169	-1.8	0.0	21	dbSNP_116	82	1626,6974	299.3+/-304.4	144,1338,2818	yes	missense,missense	WDR4	NM_018669.4,NM_033661.3	43,43	586,2375,3542	TT,TC,CC		18.907,43.5996,27.272	benign,benign	390/413,390/413	44270229	3547,9459	2203	4300	6503	SO:0001583	missense	10785	exon11			GGACTCCGGCGCC	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.1169G>A	21.37:g.44270229C>T	ENSP00000381266:p.Arg390Gln	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_018669		Missense_Mutation	SNP	ENST00000398208.2	37	CCDS13691.1	475	0.2174908424908425	238	0.483739837398374	62	0.1712707182320442	45	0.07867132867132867	130	0.17150395778364116	C	2.150	-0.394655	0.04899	0.435996	0.18907	ENSG00000160193	ENST00000330317;ENST00000398208	T;T	0.62788	-0.0;-0.0	2.7	-1.78	0.07957	.	1.424290	0.04586	N	0.395909	T	0.00012	0.0000	N	0.04018	-0.295	0.80722	P	0.0	B;B	0.17268	0.021;0.012	B;B	0.06405	0.002;0.001	T	0.28996	-1.0026	9	0.09590	T	0.72	-3.2097	6.1533	0.20324	0.0:0.4154:0.0:0.5846	rs6586250;rs58274587;rs6586250	389;390	P57081-2;P57081	.;WDR4_HUMAN	Q	390	ENSP00000328671:R390Q;ENSP00000381266:R390Q	ENSP00000328671:R390Q	R	-	2	0	WDR4	43143298	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	-0.223000	0.09177	-0.438000	0.07232	-1.012000	0.02466	CGG	C|0.748;T|0.252	0.252	strong		0.602	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
DZANK1	55184	hgsc.bcm.edu	37	20	18393312	18393312	+	Silent	SNP	C	C	G	rs6075337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:18393312C>G	ENST00000358866.6	-	12	1432	c.1410G>C	c.(1408-1410)ctG>ctC	p.L470L	DZANK1_ENST00000487128.1_5'UTR|DZANK1_ENST00000357236.4_Silent_p.L356L|DZANK1_ENST00000262547.5_Silent_p.L470L|DZANK1_ENST00000329494.5_Silent_p.L472L			Q9NVP4	DZAN1_HUMAN	double zinc ribbon and ankyrin repeat domains 1	470							zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(10)	19						TGATGGCTGTCAGGAGGGGTT	0.493													G|||	3153	0.629593	0.6029	0.6441	5008	,	,		16810	0.3095		0.7992	False		,,,				2504	0.8108				p.L470L		Atlas-SNP	.											.	DZANK1	65	.	0			c.G1410C						PASS	.	G		2473,1325		825,823,251	209.0	196.0	200.0		1410	4.7	1.0	20	dbSNP_114	200	6491,1759		2515,1461,149	no	coding-synonymous	DZANK1	NM_001099407.1		3340,2284,400	GG,GC,CC		21.3212,34.8868,25.5976		470/753	18393312	8964,3084	1899	4125	6024	SO:0001819	synonymous_variant	55184	exon13			GGCTGTCAGGAGG	AK001462	CCDS46582.1	20p11.23	2013-01-11	2011-10-03	2011-10-03	ENSG00000089091	ENSG00000089091		"""Ankyrin repeat domain containing"""	15858	protein-coding gene	gene with protein product	"""ankyrin repeat domain 64"""		"""chromosome 20 open reading frame 12"""	C20orf84, C20orf12			Standard	NM_001099407		Approved	FLJ10600, dJ568F9.2, FLJ30892, bA189K21.8, ANKRD64	uc002wqq.4	Q9NVP4	OTTHUMG00000031968	ENST00000358866.6:c.1410G>C	20.37:g.18393312C>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	169	169	1	NM_001099407	B7ZLZ4|Q4F7X1|Q5QPD9|Q5QPE0|Q68DN8|Q6ZMX9|Q96NF0|Q9H1E0|Q9H442	Silent	SNP	ENST00000358866.6	37	CCDS46582.1	1291	0.5911172161172161	269	0.5467479674796748	232	0.6408839779005525	194	0.33916083916083917	596	0.7862796833773087	G	1.772	-0.484086	0.04383	0.651132	0.786788	ENSG00000089091	ENST00000358866	.	.	.	5.67	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.2918	11.1108	0.48232	0.0678:0.2562:0.676:0.0	rs6075337;rs59648532;rs6075337	.	.	.	S	269	.	.	X	-	2	2	C20orf12	18341312	1.000000	0.71417	0.987000	0.45799	0.236000	0.25371	0.831000	0.27476	0.770000	0.33336	-0.120000	0.15030	TGA	C|0.389;G|0.611	0.611	strong		0.493	DZANK1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471926.1	NM_001099407	
SBF1	6305	hgsc.bcm.edu	37	22	50885658	50885658	+	Silent	SNP	C	C	T	rs371139013		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50885658C>T	ENST00000390679.3	-	40	5701	c.5517G>A	c.(5515-5517)acG>acA	p.T1839T	SBF1_ENST00000380817.3_Silent_p.T1865T|SBF1_ENST00000348911.6_Silent_p.T1840T			O95248	MTMR5_HUMAN	SET binding factor 1	1839	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		AAACGCGACGCGTTGTCTTCA	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		12737	0.0		0.0	False		,,,				2504	0.001				p.T1865T		Atlas-SNP	.											.	SBF1	211	.	0			c.G5595A						PASS	.	C		0,4186		0,0,2093	47.0	57.0	53.0		5595	-0.8	1.0	22		53	2,8400		0,2,4199	no	coding-synonymous	SBF1	NM_002972.2		0,2,6292	TT,TC,CC		0.0238,0.0,0.0159		1865/1894	50885658	2,12586	2093	4201	6294	SO:0001819	synonymous_variant	6305	exon41			GCGACGCGTTGTC	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.5517G>A	22.37:g.50885658C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	178	80	0.449438	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	7.644	0.681479	0.14907	0.0	2.38E-4	ENSG00000100241	ENST00000418590	.	.	.	3.51	-0.837	0.10766	.	.	.	.	.	T	0.39886	0.1095	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	.	1.2292	0.01940	0.1426:0.3402:0.2736:0.2437	.	.	.	.	T	387	.	.	A	-	1	0	SBF1	49232524	0.061000	0.20836	0.996000	0.52242	0.814000	0.46013	-0.957000	0.03861	-0.171000	0.10797	0.462000	0.41574	GCG	.	.	weak		0.667	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
C12orf71	728858	hgsc.bcm.edu	37	12	27234999	27234999	+	Missense_Mutation	SNP	T	T	C	rs708167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:27234999T>C	ENST00000429849.2	-	1	448	c.418A>G	c.(418-420)Ata>Gta	p.I140V		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	140			I -> V (in dbSNP:rs708167).							endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						TCTAGAAATATCTGAAACTCT	0.418													T|||	894	0.178514	0.053	0.2118	5008	,	,		22542	0.0357		0.4423	False		,,,				2504	0.2004				p.I140V		Atlas-SNP	.											.	C12orf71	20	.	0			c.A418G						PASS	.	T	VAL/ILE	421,3263		26,369,1447	60.0	56.0	58.0		418	2.0	0.0	12	dbSNP_86	58	3670,4514		817,2036,1239	yes	missense	C12orf71	NM_001080406.1	29	843,2405,2686	CC,CT,TT		44.8436,11.4278,34.4708	benign	140/270	27234999	4091,7777	1842	4092	5934	SO:0001583	missense	728858	exon1			GAAATATCTGAAA		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.418A>G	12.37:g.27234999T>C	ENSP00000413728:p.Ile140Val	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	278	147	0.528777	NM_001080406		Missense_Mutation	SNP	ENST00000429849.2	37	CCDS44851.1	473	0.21657509157509158	28	0.056910569105691054	84	0.23204419889502761	22	0.038461538461538464	339	0.4472295514511873	T	6.227	0.409973	0.11812	0.114278	0.448436	ENSG00000214700	ENST00000398815;ENST00000429849	T	0.40756	1.02	3.22	2.05	0.26809	.	0.260386	0.19682	U	0.108493	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	0.46233	-0.9206	9	0.39692	T	0.17	-0.5574	5.1545	0.15027	0.0:0.1429:0.0:0.8571	rs708167;rs61061734;rs708167	140	A8MTZ7	CL071_HUMAN	V	140	ENSP00000413728:I140V	ENSP00000381796:I140V	I	-	1	0	C12orf71	27126266	0.001000	0.12720	0.030000	0.17652	0.021000	0.10359	-0.196000	0.09532	0.443000	0.26582	0.418000	0.28097	ATA	T|0.788;C|0.212	0.212	strong		0.418	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
RD3	343035	hgsc.bcm.edu	37	1	211654619	211654619	+	Missense_Mutation	SNP	G	G	A	rs34049451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:211654619G>A	ENST00000367002.4	-	2	1302	c.139C>T	c.(139-141)Cgc>Tgc	p.R47C	RD3_ENST00000484910.1_Intron	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	47			R -> C (in dbSNP:rs34049451). {ECO:0000269|PubMed:12914764, ECO:0000269|PubMed:17186464}.		response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)					central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		GCATTGCTGCGCTCCCGCTGC	0.632													G|||	21	0.00419329	0.0	0.0086	5008	,	,		19526	0.0		0.0109	False		,,,				2504	0.0041				p.R47C		Atlas-SNP	.											.	RD3	26	.	0			c.C139T						PASS	.	G	CYS/ARG,CYS/ARG	12,4394	19.1+/-41.9	0,12,2191	84.0	81.0	82.0		139,139	3.8	1.0	1	dbSNP_126	82	119,8481	61.3+/-123.2	1,117,4182	yes	missense,missense	RD3	NM_001164688.1,NM_183059.2	180,180	1,129,6373	AA,AG,GG		1.3837,0.2724,1.0072	probably-damaging,probably-damaging	47/196,47/196	211654619	131,12875	2203	4300	6503	SO:0001583	missense	343035	exon2			TGCTGCGCTCCCG	AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"""chromosome 1 open reading frame 36"""	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.139C>T	1.37:g.211654619G>A	ENSP00000355969:p.Arg47Cys	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	185	94	0.508108	NM_183059	A8K595	Missense_Mutation	SNP	ENST00000367002.4	37	CCDS1498.1	14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	G	19.17	3.775122	0.70107	0.002724	0.013837	ENSG00000198570	ENST00000367002	T	0.16897	2.31	4.85	3.8	0.43715	.	0.144576	0.56097	D	0.000023	T	0.31513	0.0799	M	0.74881	2.28	0.46131	D	0.998881	D	0.89917	1.0	D	0.69824	0.966	T	0.24048	-1.0171	10	0.87932	D	0	-29.8403	13.3021	0.60332	0.0:0.0:0.7348:0.2652	rs34049451	47	Q7Z3Z2	RD3_HUMAN	C	47	ENSP00000355969:R47C	ENSP00000355969:R47C	R	-	1	0	RD3	209721242	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	2.422000	0.44696	2.395000	0.81488	0.561000	0.74099	CGC	G|0.990;A|0.010	0.010	strong		0.632	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059	
COL22A1	169044	hgsc.bcm.edu	37	8	139749799	139749799	+	Missense_Mutation	SNP	G	G	T	rs10111520	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:139749799G>T	ENST00000303045.6	-	23	2553	c.2107C>A	c.(2107-2109)Cca>Aca	p.P703T	COL22A1_ENST00000435777.1_Missense_Mutation_p.P703T	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	703	Collagen-like 4.|Gly-rich.|Pro-rich.		P -> T (in dbSNP:rs10111520).		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)			ATTCCAGGTGGTCCCATGTCA	0.448										HNSCC(7;0.00092)			G|||	240	0.0479233	0.0083	0.1066	5008	,	,		19565	0.0526		0.0507	False		,,,				2504	0.0521				p.P703T		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2107A						PASS	.	G	THR/PRO	107,4299	85.3+/-124.0	0,107,2096	95.0	93.0	93.0		2107	-1.2	0.0	8	dbSNP_119	93	576,8024	155.1+/-209.2	25,526,3749	yes	missense	COL22A1	NM_152888.1	38	25,633,5845	TT,TG,GG		6.6977,2.4285,5.2514	benign	703/1627	139749799	683,12323	2203	4300	6503	SO:0001583	missense	169044	exon23			CAGGTGGTCCCAT	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.2107C>A	8.37:g.139749799G>T	ENSP00000303153:p.Pro703Thr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	108	0.04945054945054945	9	0.018292682926829267	35	0.09668508287292818	27	0.0472027972027972	37	0.048812664907651716	G	7.365	0.625676	0.14257	0.024285	0.066977	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.97710	-4.5;-4.5	3.16	-1.25	0.09405	.	0.628214	0.12886	U	0.431056	T	0.43233	0.1238	L	0.54863	1.705	0.09310	N	1	B;B	0.23650	0.073;0.089	B;B	0.22880	0.025;0.042	T	0.70992	-0.4721	10	0.14252	T	0.57	.	7.1842	0.25791	0.1183:0.5885:0.2932:0.0	rs10111520;rs52810650;rs10111520	703;703	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	T	703;703;416	ENSP00000303153:P703T;ENSP00000387655:P703T	ENSP00000303153:P703T	P	-	1	0	COL22A1	139818981	0.004000	0.15560	0.001000	0.08648	0.715000	0.41141	-0.750000	0.04808	-0.287000	0.09064	0.561000	0.74099	CCA	G|0.948;T|0.052	0.052	strong		0.448	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
CSPG4	1464	hgsc.bcm.edu	37	15	75969335	75969335	+	Missense_Mutation	SNP	C	C	T	rs77237106	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75969335C>T	ENST00000308508.5	-	10	5617	c.5525G>A	c.(5524-5526)cGg>cAg	p.R1842Q	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1842	Cysteine-containing.|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						TCGGGTGAGCCGGAGTGGGAC	0.662													C|||	274	0.0547125	0.0076	0.0821	5008	,	,		17011	0.0		0.1759	False		,,,				2504	0.0307				p.R1842Q		Atlas-SNP	.											.	CSPG4	175	.	0			c.G5525A						PASS	.	C	GLN/ARG	123,4079		2,119,1980	14.0	15.0	15.0		5525	3.2	0.1	15	dbSNP_131	15	1331,7005		123,1085,2960	yes	missense	CSPG4	NM_001897.4	43	125,1204,4940	TT,TC,CC		15.9669,2.9272,11.5967	possibly-damaging	1842/2323	75969335	1454,11084	2101	4168	6269	SO:0001583	missense	1464	exon10			GTGAGCCGGAGTG	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.5525G>A	15.37:g.75969335C>T	ENSP00000312506:p.Arg1842Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	162	0.07417582417582418	4	0.008130081300813009	34	0.09392265193370165	0	0.0	124	0.16358839050131926	C	10.22	1.288895	0.23478	0.029272	0.159669	ENSG00000173546	ENST00000308508	T	0.19250	2.16	5.29	3.16	0.36331	.	0.295925	0.29087	N	0.013188	T	0.00039	0.0001	N	0.25647	0.755	0.31038	P	0.7166239999999999	B	0.15719	0.014	B	0.06405	0.002	T	0.30563	-0.9974	9	0.11182	T	0.66	.	6.6071	0.22731	0.0:0.6128:0.0:0.3872	.	1842	Q6UVK1	CSPG4_HUMAN	Q	1842	ENSP00000312506:R1842Q	ENSP00000312506:R1842Q	R	-	2	0	CSPG4	73756390	0.015000	0.18098	0.125000	0.21846	0.776000	0.43924	-0.059000	0.11731	1.222000	0.43521	0.561000	0.74099	CGG	C|0.919;T|0.081	0.081	strong		0.662	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
COL6A2	1292	hgsc.bcm.edu	37	21	47538960	47538960	+	Missense_Mutation	SNP	G	G	A	rs2839110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47538960G>A	ENST00000300527.4	+	14	1300	c.1196G>A	c.(1195-1197)aGt>aAt	p.S399N	COL6A2_ENST00000409416.1_Missense_Mutation_p.S399N|COL6A2_ENST00000397763.1_Missense_Mutation_p.S399N|COL6A2_ENST00000310645.5_Missense_Mutation_p.S399N|COL6A2_ENST00000357838.4_Missense_Mutation_p.S399N	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	399	Triple-helical region.		S -> N (in dbSNP:rs2839110). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15563506, ECO:0000269|PubMed:15689448, ECO:0000269|PubMed:1765372, ECO:0000269|PubMed:17886299, ECO:0000269|Ref.1}.		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		CAAGGCAACAGTGGAGCCCCA	0.667													A|||	3532	0.705272	0.5045	0.8804	5008	,	,		16538	0.874		0.83	False		,,,				2504	0.5501				p.S399N		Atlas-SNP	.											.	COL6A2	351	.	0			c.G1196A						PASS	.	A	ASN/SER,ASN/SER,ASN/SER	2362,2040	558.7+/-380.1	637,1088,476	47.0	41.0	43.0		1196,1196,1196	0.7	0.7	21	dbSNP_100	43	7118,1480	280.5+/-294.5	2951,1216,132	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	46,46,46	3588,2304,608	AA,AG,GG		17.2133,46.3426,27.0769	benign,benign,benign	399/1020,399/919,399/829	47538960	9480,3520	2201	4299	6500	SO:0001583	missense	1292	exon14			GCAACAGTGGAGC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.1196G>A	21.37:g.47538960G>A	ENSP00000300527:p.Ser399Asn	Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	231	227	0.982684	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	1728	0.7912087912087912	266	0.540650406504065	315	0.8701657458563536	517	0.9038461538461539	630	0.8311345646437994	A	4.669	0.124319	0.08931	0.536574	0.827867	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24;-3.24	4.57	0.703	0.18116	.	0.475810	0.23245	N	0.050308	T	0.00012	0.0000	N	0.16862	0.45	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	0.38178	-0.9673	9	0.14656	T	0.56	-5.2478	5.8733	0.18814	0.3381:0.4045:0.2573:0.0	rs2839110;rs11554665;rs17855968;rs59285155;rs2839110	399;399;399	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	N	399	ENSP00000300527:S399N;ENSP00000350497:S399N;ENSP00000312529:S399N;ENSP00000387115:S399N;ENSP00000380870:S399N	ENSP00000300527:S399N	S	+	2	0	COL6A2	46363388	0.027000	0.19231	0.683000	0.30040	0.203000	0.24098	0.361000	0.20267	-0.153000	0.11137	-0.332000	0.08345	AGT	G|0.256;A|0.744	0.744	strong		0.667	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
DDX31	64794	hgsc.bcm.edu	37	9	135521303	135521303	+	Silent	SNP	C	C	T	rs306537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135521303C>T	ENST00000372159.3	-	13	1825	c.1674G>A	c.(1672-1674)ctG>ctA	p.L558L	DDX31_ENST00000310532.2_Silent_p.L558L|DDX31_ENST00000438527.3_Silent_p.L429L|DDX31_ENST00000372153.1_Silent_p.L558L	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	558	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		TGCCGCCATGCAGCCGTAGGA	0.612													C|||	455	0.0908546	0.1324	0.121	5008	,	,		18566	0.1171		0.0417	False		,,,				2504	0.0368				p.L558L		Atlas-SNP	.											.	DDX31	76	.	0			c.G1674A						PASS	.	C	,	477,3929	222.6+/-239.4	28,421,1754	32.0	31.0	31.0		1674,1674	3.7	1.0	9	dbSNP_79	31	366,8234	121.7+/-180.7	3,360,3937	no	coding-synonymous,coding-synonymous	DDX31	NM_022779.7,NM_138620.1	,	31,781,5691	TT,TC,CC		4.2558,10.8261,6.4816	,	558/852,558/586	135521303	843,12163	2203	4300	6503	SO:0001819	synonymous_variant	64794	exon13			GCCATGCAGCCGT	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"""DEAD-boxes"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16715	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 25"""		"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"""				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.1674G>A	9.37:g.135521303C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Silent	SNP	ENST00000372159.3	37	CCDS6951.1																																																																																			C|0.927;T|0.073	0.073	strong		0.612	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806812	33806812	+	Silent	SNP	C	C	T	rs12451876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33806812C>T	ENST00000260908.7	-	2	534	c.417G>A	c.(415-417)acG>acA	p.T139T	SLFN12L_ENST00000361112.4_Silent_p.T168T|SLFN12L_ENST00000449046.1_Silent_p.T170T|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	139						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)	p.T170T(2)|p.T168T(1)		breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						TGGAGCTCAACGTGGCAATCT	0.433													C|||	641	0.127995	0.0968	0.1023	5008	,	,		19931	0.0149		0.1561	False		,,,				2504	0.2761				p.T139T		Atlas-SNP	.											SLFN12L_ENST00000449046,NS,carcinoma,0,3	SLFN12L	140	3	3	Substitution - coding silent(3)	endometrium(3)	c.G417A						scavenged	.	C		139,1245		5,129,558	74.0	63.0	66.0		417	1.5	0.0	17	dbSNP_120	66	456,2726		39,378,1174	no	coding-synonymous	SLFN12L	NM_001195790.1		44,507,1732	TT,TC,CC		14.3306,10.0434,13.0311		139/589	33806812	595,3971	692	1591	2283	SO:0001819	synonymous_variant	100506736	exon2			GCTCAACGTGGCA	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.417G>A	17.37:g.33806812C>T		Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	139	71	0.510791	NM_001195790	F5H6G3	Silent	SNP	ENST00000260908.7	37	CCDS56026.1																																																																																			A|0.000;C|0.891;T|0.109	0.109	strong		0.433	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
EPC1	80314	hgsc.bcm.edu	37	10	32580205	32580205	+	Missense_Mutation	SNP	C	C	T	rs72789797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:32580205C>T	ENST00000263062.8	-	6	1130	c.861G>A	c.(859-861)atG>atA	p.M287I	EPC1_ENST00000375110.2_Missense_Mutation_p.M237I|EPC1_ENST00000319778.6_Missense_Mutation_p.M287I	NM_025209.2	NP_079485.1	Q9H2F5	EPC1_HUMAN	enhancer of polycomb homolog 1 (Drosophila)	287					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(5)|urinary_tract(1)	24		Prostate(175;0.0199)				GTCTCTGTGCCATAACCTCAG	0.353													C|||	148	0.0295527	0.0053	0.0418	5008	,	,		15126	0.0		0.0805	False		,,,				2504	0.0317				p.M287I		Atlas-SNP	.											.	EPC1	74	.	0			c.G861A						PASS	.	C	ILE/MET	51,4355	51.6+/-87.1	0,51,2152	119.0	113.0	115.0		861	5.5	1.0	10	dbSNP_130	115	589,8011	157.0+/-210.8	27,535,3738	yes	missense	EPC1	NM_025209.2	10	27,586,5890	TT,TC,CC		6.8488,1.1575,4.9208	benign	287/837	32580205	640,12366	2203	4300	6503	SO:0001583	missense	80314	exon6			CTGTGCCATAACC	AF277374	CCDS7172.1, CCDS60511.1, CCDS73083.1	10p11	2005-12-12			ENSG00000120616	ENSG00000120616			19876	protein-coding gene	gene with protein product		610999				10976108	Standard	NM_025209		Approved	Epl1	uc001iwg.2	Q9H2F5	OTTHUMG00000017925	ENST00000263062.8:c.861G>A	10.37:g.32580205C>T	ENSP00000263062:p.Met287Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	57	0.612903	NM_025209	B4DSC3|D3DRX7|Q5VW54|Q5VW56|Q5VW58|Q8NAQ4|Q8NE21|Q96LF4|Q96RR6|Q9H7T7	Missense_Mutation	SNP	ENST00000263062.8	37	CCDS7172.1	86	0.039377289377289376	5	0.01016260162601626	21	0.058011049723756904	0	0.0	60	0.079155672823219	C	13.69	2.311444	0.40895	0.011575	0.068488	ENSG00000120616	ENST00000375110;ENST00000319778;ENST00000263062	T;T;T	0.66638	-0.22;-0.22;-0.22	5.46	5.46	0.80206	.	0.039922	0.85682	D	0.000000	T	0.05731	0.0150	N	0.22421	0.69	0.44175	D	0.996987	B;B;B;B	0.30146	0.086;0.27;0.061;0.086	B;B;B;B	0.28385	0.07;0.036;0.089;0.07	T	0.08680	-1.0710	10	0.30078	T	0.28	-7.6163	19.6573	0.95847	0.0:1.0:0.0:0.0	.	287;237;287;287	B8XCX7;Q9H2F5-3;Q9H2F5-2;Q9H2F5	.;.;.;EPC1_HUMAN	I	237;287;287	ENSP00000364251:M237I;ENSP00000318559:M287I;ENSP00000263062:M287I	ENSP00000263062:M287I	M	-	3	0	EPC1	32620211	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.935000	0.48963	2.728000	0.93425	0.467000	0.42956	ATG	C|0.956;T|0.044	0.044	strong		0.353	EPC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047484.1		
USP6NL	9712	hgsc.bcm.edu	37	10	11505175	11505175	+	Silent	SNP	A	A	G	rs3740204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:11505175A>G	ENST00000609104.1	-	15	2146	c.1752T>C	c.(1750-1752)ccT>ccC	p.P584P	USP6NL_ENST00000379237.2_Silent_p.P607P|USP6NL_ENST00000277575.5_Silent_p.P601P	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	584					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						TTCTCGGGCTAGGAGGGTAAA	0.567													G|||	2501	0.499401	0.5772	0.2997	5008	,	,		18328	0.7351		0.3042	False		,,,				2504	0.4939				p.P601P		Atlas-SNP	.											.	USP6NL	57	.	0			c.T1803C						PASS	.	G	,	2008,1898		504,1000,449	47.0	49.0	48.0		1803,1752	-1.2	0.0	10	dbSNP_107	48	2613,5693		402,1809,1942	no	coding-synonymous,coding-synonymous	USP6NL	NM_001080491.2,NM_014688.2	,	906,2809,2391	GG,GA,AA		31.4592,48.5919,37.8398	,	601/846,584/829	11505175	4621,7591	1953	4153	6106	SO:0001819	synonymous_variant	9712	exon14			CGGGCTAGGAGGG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.1752T>C	10.37:g.11505175A>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	32	15	0.46875	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Silent	SNP	ENST00000609104.1	37	CCDS53492.1																																																																																			A|0.502;G|0.498	0.498	strong		0.567	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
CFAP46	54777	hgsc.bcm.edu	37	10	134659626	134659626	+	Missense_Mutation	SNP	A	A	G	rs10870341	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134659626A>G	ENST00000368586.5	-	44	6473	c.6373T>C	c.(6373-6375)Tgc>Cgc	p.C2125R	TTC40_ENST00000263170.5_Missense_Mutation_p.C286R	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTGTCTTGGCACCGGAGCTGG	0.672													G|||	845	0.16873	0.2867	0.1167	5008	,	,		14135	0.0744		0.1352	False		,,,				2504	0.1779				p.C2125R		Atlas-SNP	.											.	TTC40	100	.	0			c.T6373C						PASS	.	G	ARG/CYS	1111,3287	684.6+/-404.4	154,803,1242	36.0	37.0	36.0		1309	-1.5	0.0	10	dbSNP_120	36	1057,7543	747.6+/-407.3	67,923,3310	yes	missense	C10orf92	NM_001200049.1	180	221,1726,4552	GG,GA,AA		12.2907,25.2615,16.6795	benign	437/1028	134659626	2168,10830	2199	4300	6499	SO:0001583	missense	54777	exon44			CTTGGCACCGGAG																												ENST00000368586.5:c.6373T>C	10.37:g.134659626A>G	ENSP00000357575:p.Cys2125Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	310	0.14194139194139194	125	0.2540650406504065	51	0.1408839779005525	39	0.06818181818181818	95	0.12532981530343007	G	0.001	-2.939895	0.00052	0.252615	0.122907	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.11063	3.04;2.81	4.38	-1.49	0.08718	.	1.969230	0.02798	N	0.122830	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43228	-0.9404	9	0.11485	T	0.65	.	6.2058	0.20602	0.307:0.2289:0.4641:0.0	rs10870341;rs61193559;rs10870341	286	Q8IYW2	CJ092_HUMAN	R	2125;286	ENSP00000357575:C2125R;ENSP00000263170:C286R	ENSP00000263170:C286R	C	-	1	0	C10orf93	134509616	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.032000	0.13732	-0.729000	0.04875	-3.198000	0.00054	TGC	A|0.840;G|0.160	0.160	strong		0.672	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
CBX2	84733	hgsc.bcm.edu	37	17	77758691	77758691	+	Silent	SNP	G	G	A	rs3751957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:77758691G>A	ENST00000310942.4	+	5	1553	c.1449G>A	c.(1447-1449)ccG>ccA	p.P483P		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	483					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GACAGAACCCGTCAGTGTCCG	0.637													g|||	2119	0.423123	0.6694	0.3458	5008	,	,		16653	0.4058		0.2087	False		,,,				2504	0.3834				p.P483P		Atlas-SNP	.											CBX2,mucosal,malignant_melanoma,+2,1	CBX2	50	1	0			c.G1449A						PASS	.	A		2594,1812	634.6+/-396.2	771,1052,380	59.0	53.0	55.0		1449	-3.2	0.0	17	dbSNP_107	55	2071,6529	358.1+/-331.0	263,1545,2492	no	coding-synonymous	CBX2	NM_005189.2		1034,2597,2872	AA,AG,GG		24.0814,41.1257,35.8681		483/533	77758691	4665,8341	2203	4300	6503	SO:0001819	synonymous_variant	84733	exon5			GAACCCGTCAGTG	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.1449G>A	17.37:g.77758691G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	31	0.462687	NM_005189	Q0VDA5|Q9BTB1	Silent	SNP	ENST00000310942.4	37	CCDS32757.1																																																																																			G|0.630;A|0.370	0.370	strong		0.637	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
XIRP2	129446	hgsc.bcm.edu	37	2	168106085	168106085	+	Missense_Mutation	SNP	G	G	A	rs16853328	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168106085G>A	ENST00000409195.1	+	9	8272	c.8183G>A	c.(8182-8184)aGc>aAc	p.S2728N	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.S2506N|XIRP2_ENST00000295237.9_Missense_Mutation_p.S2728N|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2553			G -> D (in dbSNP:rs3749002).		actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						ACAGACCACAGCTATGAAAGT	0.353													G|||	865	0.172724	0.2882	0.1196	5008	,	,		20459	0.12		0.1123	False		,,,				2504	0.1708				p.S2728N		Atlas-SNP	.											.	XIRP2	914	.	0			c.G8183A						PASS	.	G	,,,ASN/SER,ASN/SER	959,2729		131,697,1016	83.0	80.0	81.0		,,,8183,7517	0.5	0.0	2	dbSNP_123	81	796,7374		42,712,3331	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,46,46	173,1409,4347	AA,AG,GG		9.743,26.0033,14.8001	,,,benign,benign	,,,2728/3550,2506/3328	168106085	1755,10103	1844	4085	5929	SO:0001583	missense	129446	exon9			ACCACAGCTATGA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8183G>A	2.37:g.168106085G>A	ENSP00000386840:p.Ser2728Asn	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	55	0.514019	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	353	0.16163003663003664	151	0.30691056910569103	42	0.11602209944751381	72	0.1258741258741259	88	0.11609498680738786	G	4.989	0.183668	0.09495	0.260033	0.09743	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02812	4.16;4.16;4.15	6.07	0.503	0.16940	.	1.274170	0.04825	N	0.437620	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B;B;B	0.10296	0.001;0.003;0.003	B;B;B	0.09377	0.002;0.004;0.004	T	0.48186	-0.9057	9	0.16420	T	0.52	0.7895	1.5737	0.02620	0.3016:0.1424:0.4114:0.1447	rs16853328;rs52831947;rs59277562;rs16853328	2553;2553;2506	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	N	2728;2728;2506;142	ENSP00000386840:S2728N;ENSP00000295237:S2728N;ENSP00000387255:S2506N	ENSP00000295237:S2728N	S	+	2	0	XIRP2	167814331	0.000000	0.05858	0.000000	0.03702	0.139000	0.21198	0.218000	0.17622	0.145000	0.18977	-0.182000	0.12963	AGC	G|0.837;A|0.163	0.163	strong		0.353	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
CNTN5	53942	hgsc.bcm.edu	37	11	99690450	99690450	+	Silent	SNP	T	T	C	rs12222337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:99690450T>C	ENST00000524871.1	+	4	521	c.231T>C	c.(229-231)taT>taC	p.Y77Y	CNTN5_ENST00000279463.3_Silent_p.Y77Y|CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000527185.1_Silent_p.Y77Y|CNTN5_ENST00000528682.1_Silent_p.Y77Y	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	77					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)		AGAATTATTATTCCCCCATCA	0.443																																					p.Y77Y		Atlas-SNP	.											.	CNTN5	324	.	0			c.T231C						PASS	.						61.0	61.0	61.0					11																	99690450		1892	4090	5982	SO:0001819	synonymous_variant	53942	exon3			TTATTATTCCCCC	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.231T>C	11.37:g.99690450T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	128	18	0.140625	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																			C|0.101;T|0.899	0.101	strong		0.443	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
BCAM	4059	hgsc.bcm.edu	37	19	45315445	45315445	+	Missense_Mutation	SNP	G	G	A	rs28399653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45315445G>A	ENST00000270233.6	+	3	252	c.230G>A	c.(229-231)cGc>cAc	p.R77H	BCAM_ENST00000589651.1_Missense_Mutation_p.R77H	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	77	Ig-like V-type 1.		R -> H (defines the Lu(a) antigen; dbSNP:rs28399653). {ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GCTCGCCCCCGCCTAGCCTCG	0.692													G|||	84	0.0167732	0.0295	0.0216	5008	,	,		13249	0.0		0.0288	False		,,,				2504	0.001				p.R77H		Atlas-SNP	.											.	BCAM	53	.	0			c.G230A	GRCh37	CM973375	BCAM	M	rs28399653	PASS	.	G	HIS/ARG,HIS/ARG	124,4242		0,124,2059	11.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	230,230	-0.1	1.0	19	dbSNP_125	13	277,8273		7,263,4005	yes	missense,missense	BCAM	NM_001013257.1,NM_005581.3	29,29	7,387,6064	AA,AG,GG		3.2398,2.8401,3.1047	probably-damaging,probably-damaging	77/589,77/629	45315445	401,12515	2183	4275	6458	SO:0001583	missense	4059	exon3			GCCCCCGCCTAGC	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.230G>A	19.37:g.45315445G>A	ENSP00000270233:p.Arg77His	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	40	0.018315018315018316	8	0.016260162601626018	10	0.027624309392265192	0	0.0	22	0.029023746701846966	.	15.79	2.936247	0.52972	0.028401	0.032398	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.27890	1.64;1.64	3.58	-0.142	0.13448	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.06005	0.0156	L	0.29908	0.895	0.34224	D	0.675761	B	0.22346	0.068	B	0.12156	0.007	T	0.14839	-1.0458	9	0.35671	T	0.21	-11.2605	5.2337	0.15436	0.0:0.1786:0.3627:0.4587	rs28399653	77	P50895	BCAM_HUMAN	H	77	ENSP00000270233:R77H;ENSP00000375817:R77H	ENSP00000270233:R77H	R	+	2	0	BCAM	50007285	0.000000	0.05858	0.993000	0.49108	0.406000	0.30931	-1.971000	0.01503	0.232000	0.21100	0.313000	0.20887	CGC	G|0.977;A|0.023	0.023	strong		0.692	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
WDR72	256764	hgsc.bcm.edu	37	15	54003091	54003091	+	Missense_Mutation	SNP	G	G	A	rs551225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:54003091G>A	ENST00000396328.1	-	9	1156	c.917C>T	c.(916-918)cCt>cTt	p.P306L	WDR72_ENST00000557913.1_Missense_Mutation_p.P305L|WDR72_ENST00000360509.5_Missense_Mutation_p.P306L|WDR72_ENST00000559418.1_Missense_Mutation_p.P318L	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	306				P -> L (in Ref. 1; CAD97880 and 3; AAI01617/AAI01615). {ECO:0000305}.						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)		CAGTAAATGAGGATAAATGGT	0.398													G|||	1607	0.320887	0.1626	0.3156	5008	,	,		16888	0.2014		0.494	False		,,,				2504	0.4836				p.P306L		Atlas-SNP	.											.	WDR72	177	.	0			c.C917T						PASS	.	G	LEU/PRO	949,3439	359.6+/-314.9	114,721,1359	142.0	127.0	132.0		917	5.6	1.0	15	dbSNP_83	132	4304,4282	576.9+/-390.5	1067,2170,1056	yes	missense	WDR72	NM_182758.2	98	1181,2891,2415	AA,AG,GG		49.8719,21.6272,40.4887	probably-damaging	306/1103	54003091	5253,7721	2194	4293	6487	SO:0001583	missense	256764	exon9			AAATGAGGATAAA	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.917C>T	15.37:g.54003091G>A	ENSP00000379619:p.Pro306Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	690	0.3159340659340659	67	0.13617886178861788	132	0.36464088397790057	119	0.20804195804195805	372	0.49076517150395776	G	20.7	4.027819	0.75390	0.216272	0.501281	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.18016	2.24;2.24	5.58	5.58	0.84498	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.45137	1.4	0.09310	P	0.999999221283	D	0.89917	1.0	D	0.74674	0.984	T	0.51647	-0.8679	9	0.59425	D	0.04	.	18.919	0.92518	0.0:0.0:1.0:0.0	rs551225;rs52834404;rs59983782;rs551225	306	Q3MJ13	WDR72_HUMAN	L	306	ENSP00000379619:P306L;ENSP00000353699:P306L	ENSP00000353699:P306L	P	-	2	0	WDR72	51790383	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.344000	0.72991	2.778000	0.95560	0.655000	0.94253	CCT	G|0.619;A|0.381	0.381	strong		0.398	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
CASD1	64921	hgsc.bcm.edu	37	7	94173803	94173803	+	Silent	SNP	T	T	C	rs13242090	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:94173803T>C	ENST00000297273.4	+	11	1724	c.1437T>C	c.(1435-1437)ttT>ttC	p.F479F		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	479						integral component of membrane (GO:0016021)				NS(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|ovary(3)|stomach(2)|upper_aerodigestive_tract(1)	31	all_cancers(62;6.71e-10)|all_epithelial(64;5e-09)|Lung NSC(181;0.188)|all_lung(186;0.215)		STAD - Stomach adenocarcinoma(171;0.0031)			TCTCATACTTTTGGATAAAAG	0.358													T|||	599	0.119609	0.0038	0.1297	5008	,	,		16417	0.2103		0.0944	False		,,,				2504	0.2014				p.F479F		Atlas-SNP	.											.	CASD1	70	.	0			c.T1437C						PASS	.	T		77,4329	68.1+/-105.8	1,75,2127	124.0	119.0	120.0		1437	-0.4	1.0	7	dbSNP_121	120	703,7895	173.6+/-224.1	27,649,3623	no	coding-synonymous	CASD1	NM_022900.4		28,724,5750	CC,CT,TT		8.1763,1.7476,5.9982		479/798	94173803	780,12224	2203	4299	6502	SO:0001819	synonymous_variant	64921	exon11			ATACTTTTGGATA	AF355594	CCDS5636.1	7q22	2006-03-09			ENSG00000127995	ENSG00000127995			16014	protein-coding gene	gene with protein product	"""chromosome 7 open reading frame 12"""	611686				11703667, 11528394	Standard	NM_022900		Approved	FLJ21213, FLJ21879, C7orf12	uc003uni.4	Q96PB1	OTTHUMG00000023356	ENST00000297273.4:c.1437T>C	7.37:g.94173803T>C		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	222	112	0.504505	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Silent	SNP	ENST00000297273.4	37	CCDS5636.1																																																																																			T|0.913;C|0.087	0.087	strong		0.358	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900	
TAF10	6881	hgsc.bcm.edu	37	11	6632450	6632450	+	Silent	SNP	C	C	T	rs12451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6632450C>T	ENST00000299424.4	-	4	1014	c.537G>A	c.(535-537)acG>acA	p.T179T	RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'UTR	NM_006284.3	NP_006275.1	Q12962	TAF10_HUMAN	TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa	179					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|perinuclear region of cytoplasm (GO:0048471)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|RNA polymerase binding (GO:0070063)|transcription coactivator activity (GO:0003713)						Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.0481)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGCCGGAGGCCGTGCCCTTCA	0.498													T|||	708	0.141374	0.0825	0.1974	5008	,	,		21101	0.0833		0.2406	False		,,,				2504	0.1391				p.T179T		Atlas-SNP	.											.	TAF10	9	.	0			c.G537A						PASS	.	T		553,3849	771.8+/-413.8	34,485,1682	69.0	72.0	71.0		537	2.5	1.0	11	dbSNP_52	71	2054,6538	717.7+/-406.2	246,1562,2488	no	coding-synonymous	TAF10	NM_006284.3		280,2047,4170	TT,TC,CC		23.906,12.5625,20.0631		179/219	6632450	2607,10387	2201	4296	6497	SO:0001819	synonymous_variant	6881	exon4			GGAGGCCGTGCCC	U13991, U25816	CCDS7769.1	11p15.5-p15.2	2006-11-14	2002-08-29	2001-12-07	ENSG00000166337	ENSG00000166337			11543	protein-coding gene	gene with protein product		600475	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, H, 30kD"""	TAF2H, TAF2A		7923369	Standard	NM_006284		Approved	TAFII30	uc001mej.2	Q12962	OTTHUMG00000133402	ENST00000299424.4:c.537G>A	11.37:g.6632450C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	152	92	0.605263	NM_006284	O00703|Q13175|Q6FH13	Silent	SNP	ENST00000299424.4	37	CCDS7769.1																																																																																			C|0.817;T|0.183	0.183	strong		0.498	TAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257259.2	NM_006284	
NPBWR2	2832	hgsc.bcm.edu	37	20	62737537	62737537	+	Silent	SNP	C	C	A	rs4809400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62737537C>A	ENST00000369768.1	-	1	987	c.648G>T	c.(646-648)acG>acT	p.T216T		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	216					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					CCAGGACCAACGTGTAGACAC	0.652													C|||	425	0.0848642	0.0189	0.0893	5008	,	,		20635	0.0823		0.1362	False		,,,				2504	0.1207				p.T216T		Atlas-SNP	.											.	NPBWR2	36	.	0			c.G648T						PASS	.	C		148,4256	100.3+/-138.9	2,144,2056	58.0	50.0	52.0		648	-7.8	0.0	20	dbSNP_111	52	1022,7558	214.3+/-254.0	60,902,3328	no	coding-synonymous	NPBWR2	NM_005286.2		62,1046,5384	AA,AC,CC		11.9114,3.3606,9.0111		216/334	62737537	1170,11814	2202	4290	6492	SO:0001819	synonymous_variant	2832	exon1			GACCAACGTGTAG	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.648G>T	20.37:g.62737537C>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_005286	Q6NWQ6|Q9H4K3	Silent	SNP	ENST00000369768.1	37	CCDS13557.1																																																																																			C|0.908;A|0.092	0.092	strong		0.652	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
NLRP4	147945	hgsc.bcm.edu	37	19	56392920	56392920	+	Silent	SNP	C	C	T	rs12975929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56392920C>T	ENST00000301295.6	+	10	3374	c.2952C>T	c.(2950-2952)gaC>gaT	p.D984D	NLRP4_ENST00000346986.5_Silent_p.D928D|NLRP4_ENST00000587891.1_Silent_p.D909D	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	984					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		CCATCACAGACGACTGTGACA	0.473													C|||	1111	0.221845	0.0151	0.3256	5008	,	,		17030	0.2589		0.2376	False		,,,				2504	0.3732				p.D984D		Atlas-SNP	.											.	NLRP4	331	.	0			c.C2952T						PASS	.	C		231,4175	137.3+/-173.1	3,225,1975	92.0	75.0	81.0		2952	-3.2	0.0	19	dbSNP_121	81	1961,6639	345.9+/-325.9	222,1517,2561	no	coding-synonymous	NLRP4	NM_134444.4		225,1742,4536	TT,TC,CC		22.8023,5.2429,16.8538		984/995	56392920	2192,10814	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon10			CACAGACGACTGT	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2952C>T	19.37:g.56392920C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.817;T|0.183	0.183	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
KRT6B	3854	hgsc.bcm.edu	37	12	52843581	52843581	+	Silent	SNP	A	A	G	rs382894		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52843581A>G	ENST00000252252.3	-	4	920	c.873T>C	c.(871-873)ctT>ctC	p.L291L		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	291	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)	p.L291L(1)		NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		TCTCATCTGTAAGAGTGTCTG	0.488																																					p.L291L		Atlas-SNP	.											KRT6B,NS,carcinoma,0,5	KRT6B	90	5	1	Substitution - coding silent(1)	prostate(1)	c.T873C						scavenged	.						186.0	173.0	177.0					12																	52843581		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon4			ATCTGTAAGAGTG	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.873T>C	12.37:g.52843581A>G		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	244	27	0.110656	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			A|1.000;|0.000	.	weak		0.488	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
CHD9	80205	hgsc.bcm.edu	37	16	53326860	53326860	+	Silent	SNP	G	G	A	rs2287078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:53326860G>A	ENST00000398510.3	+	28	5493	c.5406G>A	c.(5404-5406)caG>caA	p.Q1802Q	CHD9_ENST00000564845.1_Silent_p.Q1802Q|CHD9_ENST00000566029.1_Silent_p.Q1802Q|CHD9_ENST00000447540.1_Silent_p.Q1802Q			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	1802					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q1802Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				GACAAATTCAGCAGATACAAC	0.428													A|||	1497	0.298922	0.3729	0.1902	5008	,	,		16272	0.247		0.2962	False		,,,				2504	0.3323				p.Q1802Q		Atlas-SNP	.											CHD9,NS,carcinoma,0,1	CHD9	203	1	1	Substitution - coding silent(1)	stomach(1)	c.G5406A						PASS	.	A		1258,2540		201,856,842	106.0	98.0	100.0		5406	1.1	1.0	16	dbSNP_100	100	2575,5677		402,1771,1953	no	coding-synonymous	CHD9	NM_025134.4		603,2627,2795	AA,AG,GG		31.2046,33.1227,31.8091		1802/2882	53326860	3833,8217	1899	4126	6025	SO:0001819	synonymous_variant	80205	exon29			AATTCAGCAGATA	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.5406G>A	16.37:g.53326860G>A		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	70	0.48951	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Silent	SNP	ENST00000398510.3	37																																																																																				G|0.692;A|0.308	0.308	strong		0.428	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
COG1	9382	hgsc.bcm.edu	37	17	71197439	71197439	+	Silent	SNP	C	C	T	rs1551036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:71197439C>T	ENST00000299886.4	+	7	1553	c.1473C>T	c.(1471-1473)agC>agT	p.S491S		NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	491					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18			LUSC - Lung squamous cell carcinoma(166;0.197)			CCTGGGTCAGCGTGGCAAACC	0.532													C|||	660	0.131789	0.0083	0.1225	5008	,	,		20222	0.1746		0.1958	False		,,,				2504	0.1953				p.S491S		Atlas-SNP	.											.	COG1	46	.	0			c.C1473T						PASS	.	C		172,4234	112.5+/-150.6	5,162,2036	139.0	129.0	132.0		1473	-2.5	0.0	17	dbSNP_88	132	1661,6939	304.5+/-307.0	178,1305,2817	no	coding-synonymous	COG1	NM_018714.2		183,1467,4853	TT,TC,CC		19.314,3.9038,14.0935		491/981	71197439	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	9382	exon7			GGTCAGCGTGGCA		CCDS11692.1	17q25.1	2008-05-14	2002-05-28	2002-05-31		ENSG00000166685		"""Components of oligomeric golgi complex"""	6545	protein-coding gene	gene with protein product		606973	"""low density lipoprotein receptor defect B complementing"""	LDLB		9927668	Standard	NM_018714		Approved	KIAA1381	uc002jjg.3	Q8WTW3		ENST00000299886.4:c.1473C>T	17.37:g.71197439C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_018714	Q9NPV9|Q9P2G6	Silent	SNP	ENST00000299886.4	37	CCDS11692.1																																																																																			C|0.867;N|0.001	.	strong		0.532	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1		
RPS6KC1	26750	hgsc.bcm.edu	37	1	213414948	213414948	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:213414948C>T	ENST00000366960.3	+	11	2279	c.2129C>T	c.(2128-2130)cCt>cTt	p.P710L	RPS6KC1_ENST00000543354.1_Missense_Mutation_p.P413L|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.P498L|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.P698L	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	710					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GCAATGGGACCTACTAAGTTT	0.398																																					p.P710L		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.C2129T						PASS	.						65.0	68.0	67.0					1																	213414948		2203	4300	6503	SO:0001583	missense	26750	exon11			TGGGACCTACTAA	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.2129C>T	1.37:g.213414948C>T	ENSP00000355927:p.Pro710Leu	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	C	9.247	1.039788	0.19669	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.39997	1.46;1.49;1.5;1.05	5.44	4.52	0.55395	.	0.244148	0.42821	D	0.000641	T	0.31606	0.0802	L	0.38838	1.175	0.38907	D	0.957457	B;B;B	0.21753	0.06;0.016;0.016	B;B;B	0.20955	0.032;0.01;0.01	T	0.23013	-1.0200	10	0.56958	D	0.05	-40.1504	8.6494	0.34025	0.1519:0.7721:0.0:0.076	.	498;710;698	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	L	498;710;698;413	ENSP00000442306:P498L;ENSP00000355927:P710L;ENSP00000355926:P698L;ENSP00000439282:P413L	ENSP00000355926:P698L	P	+	2	0	RPS6KC1	211481571	0.936000	0.31750	0.931000	0.37212	0.967000	0.64934	1.929000	0.40114	2.541000	0.85698	0.650000	0.86243	CCT	.	.	none		0.398	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
CUEDC1	404093	hgsc.bcm.edu	37	17	55951037	55951037	+	Missense_Mutation	SNP	C	C	T	rs17762338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:55951037C>T	ENST00000577830.1	-	4	919	c.506G>A	c.(505-507)cGc>cAc	p.R169H	CUEDC1_ENST00000577840.1_Missense_Mutation_p.R32H|CUEDC1_ENST00000407144.2_Missense_Mutation_p.R169H|CUEDC1_ENST00000360238.2_Missense_Mutation_p.R169H	NM_001271875.1	NP_001258804.1	Q9NWM3	CUED1_HUMAN	CUE domain containing 1	169			R -> H (in dbSNP:rs17762338).							endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(3)	12						GTTCCGATAGCGTCTCTGGCT	0.607													C|||	325	0.0648962	0.0076	0.0893	5008	,	,		19752	0.006		0.169	False		,,,				2504	0.0787				p.R169H		Atlas-SNP	.											.	CUEDC1	37	.	0			c.G506A						PASS	.	C	HIS/ARG	148,4258	103.0+/-141.5	1,146,2056	102.0	85.0	91.0		506	3.6	1.0	17	dbSNP_123	91	1588,7012	297.0+/-303.2	145,1298,2857	yes	missense	CUEDC1	NM_017949.1	29	146,1444,4913	TT,TC,CC		18.4651,3.3591,13.3477	benign	169/387	55951037	1736,11270	2203	4300	6503	SO:0001583	missense	404093	exon4			CGATAGCGTCTCT	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.506G>A	17.37:g.55951037C>T	ENSP00000462717:p.Arg169His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_001271875	D3DTZ2|Q9NWD0	Missense_Mutation	SNP	ENST00000577830.1	37	CCDS11599.1	169	0.07738095238095238	2	0.0040650406504065045	37	0.10220994475138122	3	0.005244755244755245	127	0.16754617414248021	C	17.13	3.311349	0.60414	0.033591	0.184651	ENSG00000180891	ENST00000407144;ENST00000360238	T;T	0.24350	1.86;1.86	5.62	3.63	0.41609	.	0.257661	0.46145	N	0.000310	T	0.00039	0.0001	N	0.19112	0.55	0.23916	P	0.99647388	B	0.16166	0.016	B	0.12156	0.007	T	0.11591	-1.0581	9	0.56958	D	0.05	.	9.5761	0.39459	0.0:0.7801:0.0:0.2199	rs17762338;rs52838158;rs57194209;rs17762338	169	Q9NWM3	CUED1_HUMAN	H	169	ENSP00000384712:R169H;ENSP00000353373:R169H	ENSP00000353373:R169H	R	-	2	0	CUEDC1	53306036	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	2.208000	0.42797	1.381000	0.46364	0.655000	0.94253	CGC	C|0.897;T|0.103	0.103	strong		0.607	CUEDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443305.1	NM_017949	
PUS7L	83448	hgsc.bcm.edu	37	12	44130330	44130330	+	Missense_Mutation	SNP	G	G	A	rs116948464	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:44130330G>A	ENST00000416848.2	-	7	2067	c.1579C>T	c.(1579-1581)Cgc>Tgc	p.R527C	PUS7L_ENST00000431332.3_Missense_Mutation_p.R214C|PUS7L_ENST00000344862.5_Missense_Mutation_p.R527C|PUS7L_ENST00000551923.1_Missense_Mutation_p.R527C	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	527	TRUD. {ECO:0000255|PROSITE- ProRule:PRU00342}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TAGAATATGCGCATGGAATGG	0.458													G|||	9	0.00179712	0.0008	0.0	5008	,	,		20268	0.001		0.006	False		,,,				2504	0.001				p.R527C		Atlas-SNP	.											PUS7L,NS,carcinoma,+1,1	PUS7L	73	1	0			c.C1579T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	179.0	145.0	157.0		1579,1579,1579	5.0	1.0	12	dbSNP_132	157	53,8547	33.3+/-86.6	1,51,4248	yes	missense,missense,missense	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	180,180,180	1,53,6449	AA,AG,GG		0.6163,0.0454,0.4229	probably-damaging,probably-damaging,probably-damaging	527/702,527/702,527/702	44130330	55,12951	2203	4300	6503	SO:0001583	missense	83448	exon7			ATATGCGCATGGA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1579C>T	12.37:g.44130330G>A	ENSP00000415899:p.Arg527Cys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	168	74	0.440476	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	7	0.003205128205128205	0	0.0	0	0.0	1	0.0017482517482517483	6	0.0079155672823219	G	22.0	4.231553	0.79688	4.54E-4	0.006163	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000431332	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.02	5.02	0.67125	Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase, TruD, insertion domain (1);	0.000000	0.85682	D	0.000000	T	0.72684	0.3491	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83148	-0.0105	10	0.87932	D	0	-10.4718	19.2216	0.93799	0.0:0.0:1.0:0.0	.	527	Q9H0K6	PUS7L_HUMAN	C	527;527;527;214	ENSP00000415899:R527C;ENSP00000343081:R527C;ENSP00000447706:R527C;ENSP00000398497:R214C	ENSP00000343081:R527C	R	-	1	0	PUS7L	42416597	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.921000	0.70028	2.723000	0.93209	0.591000	0.81541	CGC	G|0.996;A|0.004	0.004	strong		0.458	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
DENND1C	79958	hgsc.bcm.edu	37	19	6472930	6472930	+	Silent	SNP	C	C	A	rs74800876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6472930C>A	ENST00000381480.2	-	15	1240	c.1128G>T	c.(1126-1128)cgG>cgT	p.R376R	DENND1C_ENST00000543576.1_Silent_p.R332R	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	376	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				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						GCACAGCCCGCCGGTGGAAGG	0.617													c|||	58	0.0115815	0.0008	0.0231	5008	,	,		16112	0.0		0.0258	False		,,,				2504	0.0153				p.R376R		Atlas-SNP	.											DENND1C_ENST00000381480,NS,haematopoietic_neoplasm,0,2	DENND1C	93	2	0			c.G1128T						PASS	.	C		23,3837		0,23,1907	22.0	26.0	25.0		1128	0.4	0.0	19	dbSNP_132	25	198,8066		3,192,3937	no	coding-synonymous	DENND1C	NM_024898.2		3,215,5844	AA,AC,CC		2.3959,0.5959,1.8228		376/802	6472930	221,11903	1930	4132	6062	SO:0001819	synonymous_variant	79958	exon15			AGCCCGCCGGTGG	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.1128G>T	19.37:g.6472930C>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Silent	SNP	ENST00000381480.2	37	CCDS45938.1																																																																																			C|0.984;A|0.016	0.016	strong		0.617	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
CFAP46	54777	hgsc.bcm.edu	37	10	134694526	134694526	+	Missense_Mutation	SNP	A	A	G	rs148582169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134694526A>G	ENST00000368586.5	-	28	3738	c.3638T>C	c.(3637-3639)aTg>aCg	p.M1213T	TTC40_ENST00000368582.2_Missense_Mutation_p.M1213T	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTGCCACTCCATCTCAGGCTT	0.542													G|||	47	0.00938498	0.0	0.0072	5008	,	,		18461	0.002		0.0129	False		,,,				2504	0.0276				p.M1213T		Atlas-SNP	.											.	TTC40	100	.	0			c.T3638C						PASS	.																																			SO:0001583	missense	54777	exon28			CACTCCATCTCAG																												ENST00000368586.5:c.3638T>C	10.37:g.134694526A>G	ENSP00000357575:p.Met1213Thr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	0	-2.644992	0.00111	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.38722	3.1;1.12	3.63	-0.816	0.10839	.	.	.	.	.	T	0.08268	0.0206	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21724	-1.0237	6	0.02654	T	1	.	0.3205	0.00302	0.2416:0.1795:0.2888:0.2901	.	.	.	.	T	1213	ENSP00000357575:M1213T;ENSP00000357571:M1213T	ENSP00000357571:M1213T	M	-	2	0	C10orf93	134544516	0.000000	0.05858	0.015000	0.15790	0.007000	0.05969	-0.688000	0.05150	-0.490000	0.06707	-0.320000	0.08662	ATG	A|0.993;G|0.007	0.007	strong		0.542	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
SLC46A2	57864	hgsc.bcm.edu	37	9	115652836	115652836	+	Silent	SNP	G	G	A	rs3802492	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115652836G>A	ENST00000374228.4	-	1	357	c.126C>T	c.(124-126)ctC>ctT	p.L42L		NM_033051.3	NP_149040.3	Q9BY10	TSCOT_HUMAN	solute carrier family 46, member 2	42					negative regulation of T cell apoptotic process (GO:0070233)|regulation of T cell differentiation (GO:0045580)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(11)|pancreas(1)|skin(1)	18						CCTTCACCACGAGGAGTAGCC	0.677													G|||	1408	0.28115	0.3986	0.2363	5008	,	,		15844	0.0982		0.3191	False		,,,				2504	0.3037				p.L42L		Atlas-SNP	.											.	SLC46A2	30	.	0			c.C126T						PASS	.	G		1716,2690	514.7+/-368.7	349,1018,836	57.0	60.0	59.0		126	-1.1	1.0	9	dbSNP_107	59	2750,5850	437.4+/-358.6	472,1806,2022	no	coding-synonymous	SLC46A2	NM_033051.3		821,2824,2858	AA,AG,GG		31.9767,38.9469,34.338		42/476	115652836	4466,8540	2203	4300	6503	SO:0001819	synonymous_variant	57864	exon1			CACCACGAGGAGT	AF242557	CCDS6786.1	9q32	2013-05-22	2007-03-29	2007-03-29	ENSG00000119457	ENSG00000119457		"""Solute carriers"""	16055	protein-coding gene	gene with protein product		608956	"""thymic stromal co-transporter"""	TSCOT		10978518, 12826694	Standard	NM_033051		Approved	Ly110	uc004bgk.3	Q9BY10	OTTHUMG00000020513	ENST00000374228.4:c.126C>T	9.37:g.115652836G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_033051	B1ALK1|Q86VT0|Q96NE2	Silent	SNP	ENST00000374228.4	37	CCDS6786.1																																																																																			G|0.682;A|0.318	0.318	strong		0.677	SLC46A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053702.1	NM_033051	
ASB18	401036	hgsc.bcm.edu	37	2	237103697	237103697	+	Missense_Mutation	SNP	G	G	T	rs10177957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:237103697G>T	ENST00000409749.3	-	6	1218	c.1219C>A	c.(1219-1221)Cac>Aac	p.H407N	AC079135.1_ENST00000415226.1_RNA|ASB18_ENST00000330842.6_Missense_Mutation_p.H378N|AC079135.1_ENST00000483218.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	407	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.		H -> N (in dbSNP:rs10177957).		intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		AACGGCTTGTGCATCTGGAAG	0.537													G|||	543	0.108427	0.1732	0.0735	5008	,	,		17656	0.002		0.1352	False		,,,				2504	0.1278				p.H407N		Atlas-SNP	.											.	ASB18	34	.	0			c.C1219A						PASS	.	G	ASN/HIS	660,3554		49,562,1496	54.0	66.0	62.0		1219	3.7	1.0	2	dbSNP_119	62	970,7516		61,848,3334	yes	missense	ASB18	NM_212556.2	68	110,1410,4830	TT,TG,GG		11.4306,15.6621,12.8346	possibly-damaging	407/467	237103697	1630,11070	2107	4243	6350	SO:0001583	missense	401036	exon6			GCTTGTGCATCTG	AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"""Ankyrin repeat domain containing"""	19770	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 18"""			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.1219C>A	2.37:g.237103697G>T	ENSP00000386532:p.His407Asn	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_212556	B6ZDL7	Missense_Mutation	SNP	ENST00000409749.3	37	CCDS46548.1	206	0.09432234432234432	65	0.13211382113821138	33	0.09116022099447514	0	0.0	108	0.1424802110817942	G	18.15	3.561021	0.65538	0.156621	0.114306	ENSG00000182177	ENST00000330842;ENST00000409749	T;T	0.39056	1.1;1.15	4.64	3.73	0.42828	SOCS protein, C-terminal (1);	.	.	.	.	T	0.00328	0.0010	M	0.83223	2.63	0.20638	P	0.999874701	D	0.54047	0.964	P	0.52823	0.71	T	0.20174	-1.0283	8	0.62326	D	0.03	.	11.276	0.49168	0.088:0.0:0.912:0.0	rs10177957;rs58809580;rs10177957	407	Q6ZVZ8	ASB18_HUMAN	N	378;407	ENSP00000329970:H378N;ENSP00000386532:H407N	ENSP00000329970:H378N	H	-	1	0	ASB18	236768436	1.000000	0.71417	0.975000	0.42487	0.858000	0.48976	3.588000	0.53964	2.411000	0.81874	0.561000	0.74099	CAC	G|0.894;T|0.106	0.106	strong		0.537	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
REPIN1	29803	hgsc.bcm.edu	37	7	150068371	150068371	+	Missense_Mutation	SNP	T	T	C	rs3735165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150068371T>C	ENST00000425389.2	+	1	119	c.41T>C	c.(40-42)cTg>cCg	p.L14P	RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000397281.2_Missense_Mutation_p.L14P|REPIN1_ENST00000482680.1_Missense_Mutation_p.W113R|REPIN1_ENST00000479668.1_Missense_Mutation_p.W113R|REPIN1_ENST00000518462.1_3'UTR|REPIN1_ENST00000444957.1_Missense_Mutation_p.L14P|REPIN1_ENST00000540729.1_Missense_Mutation_p.L14P|REPIN1_ENST00000518514.1_Silent_p.P62P|REPIN1_ENST00000489432.2_Missense_Mutation_p.L71P|REPIN1_ENST00000466559.1_Missense_Mutation_p.W32R	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	14			L -> P (in dbSNP:rs3735165). {ECO:0000269|Ref.2}.		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			GCCATGGGCCTGGCCCAGCCC	0.652													C|||	2164	0.432109	0.5484	0.2248	5008	,	,		17092	0.4673		0.3171	False		,,,				2504	0.5041				p.L71P		Atlas-SNP	.											REPIN1_ENST00000489432,NS,carcinoma,0,2	REPIN1	74	2	0			c.T212C						PASS	.	C	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	1918,1844		507,904,470	11.0	15.0	14.0		212,41,41,41	3.4	0.3	7	dbSNP_107	14	2545,5649		428,1689,1980	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	98,98,98,98	935,2593,2450	CC,CT,TT		31.0593,49.0165,37.3285	benign,benign,benign,benign	71/625,14/568,14/568,14/568	150068371	4463,7493	1881	4097	5978	SO:0001583	missense	29803	exon3			TGGGCCTGGCCCA	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.41T>C	7.37:g.150068371T>C	ENSP00000388287:p.Leu14Pro	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	904|904	0.4139194139194139|0.4139194139194139	272|272	0.5528455284552846|0.5528455284552846	88|88	0.2430939226519337|0.2430939226519337	281|281	0.49125874125874125|0.49125874125874125	263|263	0.3469656992084433|0.3469656992084433	C|C	1.773|1.773	-0.483945|-0.483945	0.04383|0.04383	0.509835|0.509835	0.310593|0.310593	ENSG00000214022|ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389|ENST00000479668;ENST00000466559;ENST00000482680	T;T;T;T;T;T;T;T|.	0.06687|.	5.54;3.29;3.29;3.29;3.27;3.53;3.43;3.29|.	5.2|5.2	3.4|3.4	0.38934|0.38934	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.21579|0.21579	P|P	0.999634327|0.999634327	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.01281|.	0.0;0.0|.	T|T	0.42068|0.42068	-0.9473|-0.9473	8|5	0.48119|0.87932	T|D	0.1|0	-3.7114|-3.7114	7.7378|7.7378	0.28825|0.28825	0.0:0.7341:0.0:0.2659|0.0:0.7341:0.0:0.2659	rs3735165;rs11553625;rs59736478|rs3735165;rs11553625;rs59736478	71;14|.	C9J3L7;Q9BWE0|.	.;REPI1_HUMAN|.	P|R	14;14;14;14;71;73;74;71;14|113;32;113	ENSP00000428562:L14P;ENSP00000445016:L14P;ENSP00000380451:L14P;ENSP00000407714:L14P;ENSP00000417291:L71P;ENSP00000419789:L73P;ENSP00000419872:L74P;ENSP00000388287:L14P|.	ENSP00000380451:L14P|ENSP00000418507:W32R	L|W	+|+	2|1	0|0	REPIN1|REPIN1	149699304|149699304	0.040000|0.040000	0.19996|0.19996	0.294000|0.294000	0.24946|0.24946	0.559000|0.559000	0.35586|0.35586	0.888000|0.888000	0.28268|0.28268	0.217000|0.217000	0.20800|0.20800	-1.403000|-1.403000	0.01137|0.01137	CTG|TGG	T|0.578;C|0.422	0.422	strong		0.652	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
SP100	6672	hgsc.bcm.edu	37	2	231333763	231333763	+	Missense_Mutation	SNP	A	A	G	rs12724|rs57377576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231333763A>G	ENST00000264052.5	+	14	1652	c.1297A>G	c.(1297-1299)Atg>Gtg	p.M433V	SP100_ENST00000409341.1_Missense_Mutation_p.M433V|SP100_ENST00000341950.4_Missense_Mutation_p.M433V|SP100_ENST00000427101.2_Missense_Mutation_p.M405V|SP100_ENST00000409112.1_Missense_Mutation_p.M433V|SP100_ENST00000409824.1_Missense_Mutation_p.M408V|SP100_ENST00000409897.1_Missense_Mutation_p.M398V|SP100_ENST00000340126.4_Missense_Mutation_p.M433V	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	433	Sufficient to mediate interaction with ETS1.		M -> V (in HeLa cells; dbSNP:rs12724).		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)		TCTAGCTCCTATGACTTCTAG	0.323													A|||	901	0.179912	0.0688	0.1729	5008	,	,		15981	0.0635		0.3221	False		,,,				2504	0.3088				p.M433V		Atlas-SNP	.											.	SP100	167	.	0			c.A1297G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET,VAL/MET	440,3966	214.8+/-234.0	19,402,1782	110.0	107.0	108.0		1297,1297,1297,1213,1192,1297	-4.2	0.0	2	dbSNP_52	108	2764,5834	437.2+/-358.5	452,1860,1987	yes	missense,missense,missense,missense,missense,missense	SP100	NM_001080391.1,NM_001206701.1,NM_001206702.1,NM_001206703.1,NM_001206704.1,NM_003113.3	21,21,21,21,21,21	471,2262,3769	GG,GA,AA		32.147,9.9864,24.6386	benign,benign,benign,benign,benign,benign	433/886,433/689,433/481,405/453,398/446,433/880	231333763	3204,9800	2203	4299	6502	SO:0001583	missense	6672	exon14			GCTCCTATGACTT	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.1297A>G	2.37:g.231333763A>G	ENSP00000264052:p.Met433Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	102	41	0.401961	NM_001206702	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	390	0.17857142857142858	50	0.1016260162601626	69	0.19060773480662985	34	0.05944055944055944	237	0.31266490765171506	A	0.003	-2.414046	0.00191	0.099864	0.32147	ENSG00000067066	ENST00000264052;ENST00000427101;ENST00000409824;ENST00000409341;ENST00000409112;ENST00000340126;ENST00000341950;ENST00000409897;ENST00000452345	T;T;T;T;T;T;T;T;T	0.78364	2.48;2.37;2.37;2.37;-1.17;0.41;2.38;2.37;1.04	3.33	-4.21	0.03812	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	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	0.16689	-1.0394	8	0.18276	T	0.48	.	0.2456	0.00198	0.3195:0.1348:0.2204:0.3253	rs12724;rs1131025;rs1678160;rs3190536;rs3731730;rs11555637;rs17274178;rs17296406;rs17357235;rs52837394;rs1678160	405;398;433;433;433;408;433	F8WFE2;B8ZZD8;P23497-4;P23497;E7EUA7;E9PHV6;P23497-2	.;.;.;SP100_HUMAN;.;.;.	V	433;405;408;433;433;433;433;398;98	ENSP00000264052:M433V;ENSP00000399389:M405V;ENSP00000387311:M408V;ENSP00000386404:M433V;ENSP00000386427:M433V;ENSP00000343023:M433V;ENSP00000342729:M433V;ENSP00000386998:M398V;ENSP00000416563:M98V	ENSP00000264052:M433V	M	+	1	0	SP100	231042007	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-0.538000	0.06120	-1.007000	0.03408	-1.032000	0.02404	ATG	A|0.778;G|0.221;N|0.000;T|0.000	0.221	strong		0.323	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
VCAN	1462	hgsc.bcm.edu	37	5	82833145	82833145	+	Silent	SNP	G	G	A	rs2548541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:82833145G>A	ENST00000265077.3	+	8	4888	c.4323G>A	c.(4321-4323)caG>caA	p.Q1441Q	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Silent_p.Q454Q|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1441	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CACCTTCTCAGAATTTCTCGG	0.453																																					p.Q1441Q		Atlas-SNP	.											.	VCAN	498	.	0			c.G4323A						PASS	.	A	,,,	3493,913	350.5+/-310.9	1395,703,105	77.0	80.0	79.0		,1362,,4323	-7.8	0.2	5	dbSNP_100	79	5248,3352	497.6+/-374.5	1577,2094,629	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	2972,2797,734	AA,AG,GG		38.9767,20.7217,32.7926	,,,	,454/2410,,1441/3397	82833145	8741,4265	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			TTCTCAGAATTTC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4323G>A	5.37:g.82833145G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			G|0.316;A|0.684	0.684	strong		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
KCNK12	56660	hgsc.bcm.edu	37	2	47797123	47797123	+	Silent	SNP	G	G	A	rs139772114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:47797123G>A	ENST00000327876.4	-	1	955	c.348C>T	c.(346-348)ttC>ttT	p.F116F	KCNK12_ENST00000493527.1_5'UTR|AC138655.1_ENST00000601243.1_5'Flank	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	116						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(1)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGGCGCCGGGGAAGTCCCAGC	0.721													G|||	65	0.0129792	0.0015	0.0231	5008	,	,		9123	0.0		0.0368	False		,,,				2504	0.0102				p.F116F		Atlas-SNP	.											.	KCNK12	11	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(2)|prostate(1)	c.C348T						PASS	.	G		16,3302		0,16,1643	3.0	4.0	4.0		348	1.4	1.0	2	dbSNP_134	4	161,6537		2,157,3190	no	coding-synonymous	KCNK12	NM_022055.1		2,173,4833	AA,AG,GG		2.4037,0.4822,1.7672		116/431	47797123	177,9839	1659	3349	5008	SO:0001819	synonymous_variant	56660	exon1			GCCGGGGAAGTCC	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.348C>T	2.37:g.47797123G>A		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	12	7	0.583333	NM_022055		Silent	SNP	ENST00000327876.4	37	CCDS1835.1																																																																																			G|0.979;A|0.021	0.021	strong		0.721	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274416	39274416	+	Missense_Mutation	SNP	C	C	T	rs408579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39274416C>T	ENST00000391413.2	-	1	190	c.152G>A	c.(151-153)aGg>aAg	p.R51K		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.R51K(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)			GCACTGGGGCCTGCAGCAGCT	0.672													t|||	242	0.0483227	0.1248	0.0202	5008	,	,		19066	0.005		0.0219	False		,,,				2504	0.0368				p.R51K		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,11	KRTAP4-11	94	11	1	Substitution - Missense(1)	endometrium(1)	c.G152A						scavenged	.						9.0	15.0	13.0					17																	39274416		682	1579	2261	SO:0001583	missense	653240	exon1			TGGGGCCTGCAGC	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.152G>A	17.37:g.39274416C>T	ENSP00000375232:p.Arg51Lys	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	108	8	0.0740741	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	4.205	0.036712	0.08148	.	.	ENSG00000212721	ENST00000391413	T	0.01455	4.87	3.47	-1.13	0.09775	.	2.855670	0.02563	U	0.096976	T	0.02610	0.0079	M	0.72118	2.19	0.09310	N	1	B	0.25441	0.126	B	0.28916	0.096	T	0.52283	-0.8596	10	0.05959	T	0.93	.	3.7627	0.08610	0.1684:0.4051:0.0:0.4265	rs408579	51	Q9BYQ6	KR411_HUMAN	K	51	ENSP00000375232:R51K	ENSP00000375232:R51K	R	-	2	0	KRTAP4-11	36527942	0.000000	0.05858	0.002000	0.10522	0.072000	0.16883	-0.738000	0.04871	-0.091000	0.12440	-0.208000	0.12717	AGG	.	.	weak		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
FOXF2	2295	hgsc.bcm.edu	37	6	1395043	1395043	+	Silent	SNP	T	T	C	rs2293783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:1395043T>C	ENST00000259806.1	+	2	1398	c.1284T>C	c.(1282-1284)taT>taC	p.Y428Y		NM_001452.1	NP_001443.1	Q12947	FOXF2_HUMAN	forkhead box F2	428					embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|establishment of planar polarity of embryonic epithelium (GO:0042249)|extracellular matrix organization (GO:0030198)|genitalia development (GO:0048806)|negative regulation of transcription, DNA-templated (GO:0045892)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			large_intestine(2)|lung(5)|prostate(1)	8	Ovarian(93;0.0733)	all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.095)		GGTCGTATTATCACCATCACC	0.512													T|||	1088	0.217252	0.1649	0.2291	5008	,	,		20398	0.2698		0.2336	False		,,,				2504	0.2086				p.Y428Y		Atlas-SNP	.											.	FOXF2	28	.	0			c.T1284C						PASS	.	T		654,3752	281.4+/-275.9	40,574,1589	220.0	186.0	197.0		1284	2.1	1.0	6	dbSNP_100	197	1920,6680	339.9+/-323.4	224,1472,2604	no	coding-synonymous	FOXF2	NM_001452.1		264,2046,4193	CC,CT,TT		22.3256,14.8434,19.7909		428/445	1395043	2574,10432	2203	4300	6503	SO:0001819	synonymous_variant	2295	exon2			GTATTATCACCAT	U13220	CCDS4472.1	6p25.3	2008-04-10			ENSG00000137273	ENSG00000137273		"""Forkhead boxes"""	3810	protein-coding gene	gene with protein product		603250		FKHL6		9799607, 7957066	Standard	NM_001452		Approved	FREAC2	uc003mtm.3	Q12947	OTTHUMG00000016243	ENST00000259806.1:c.1284T>C	6.37:g.1395043T>C		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	177	82	0.463277	NM_001452	Q5TGJ1|Q9UQ85	Silent	SNP	ENST00000259806.1	37	CCDS4472.1																																																																																			T|0.783;C|0.217	0.217	strong		0.512	FOXF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043558.1		
TEX14	56155	hgsc.bcm.edu	37	17	56643109	56643109	+	Splice_Site	SNP	A	A	G	rs34818467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56643109A>G	ENST00000240361.8	-	28	4186	c.4101T>C	c.(4099-4101)aaT>aaC	p.N1367N	TEX14_ENST00000584699.1_5'Flank|TEX14_ENST00000389934.3_Splice_Site_p.N1361N|TEX14_ENST00000349033.5_Splice_Site_p.N1321N			Q8IWB6	TEX14_HUMAN	testis expressed 14	1367					attachment of spindle microtubules to kinetochore (GO:0008608)|intercellular bridge organization (GO:0043063)|male meiosis (GO:0007140)|mitotic sister chromatid separation (GO:0051306)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)	cell (GO:0005623)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|kinetochore (GO:0000776)|midbody (GO:0030496)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)			breast(6)|endometrium(5)|kidney(3)|large_intestine(22)|liver(1)|lung(24)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	81	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TTCACTTACCATTTGCAGTGC	0.478													A|||	694	0.138578	0.0514	0.1455	5008	,	,		21585	0.1766		0.1809	False		,,,				2504	0.1687				p.N1367N		Atlas-SNP	.											.	TEX14	343	.	0			c.T4101C						PASS	.	A	,,	286,4120	156.3+/-189.4	7,272,1924	146.0	91.0	109.0		4101,3963,4083	-1.6	0.0	17	dbSNP_126	109	1709,6891	298.6+/-304.0	180,1349,2771	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	TEX14	NM_001201457.1,NM_031272.4,NM_198393.3	,,	187,1621,4695	GG,GA,AA		19.8721,6.4911,15.3391	,,	1367/1498,1321/1452,1361/1492	56643109	1995,11011	2203	4300	6503	SO:0001630	splice_region_variant	56155	exon28			CTTACCATTTGCA	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.4102+1T>C	17.37:g.56643109A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	148	71	0.47973	NM_001201457	A6NH19|Q7RTP3|Q8ND97|Q9BXT9	Silent	SNP	ENST00000240361.8	37	CCDS56042.1																																																																																			A|0.851;G|0.149	0.149	strong		0.478	TEX14-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445446.1		Silent
PEAK1	79834	hgsc.bcm.edu	37	15	77407114	77407114	+	Missense_Mutation	SNP	C	C	G	rs1867780	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:77407114C>G	ENST00000560626.2	-	7	5100	c.4625G>C	c.(4624-4626)aGc>aCc	p.S1542T	PEAK1_ENST00000312493.4_Missense_Mutation_p.S1542T			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1542	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		S -> T (in dbSNP:rs1867780). {ECO:0000269|PubMed:17344846}.		cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGAGGTGGGGCTGGGCTCTGC	0.582													C|||	989	0.197484	0.0696	0.2536	5008	,	,		18231	0.2153		0.2873	False		,,,				2504	0.2198				p.S1542T		Atlas-SNP	.											.	.	.	.	0			c.G4625C						PASS	.	C	THR/SER	416,3388		29,358,1515	54.0	55.0	55.0		4625	3.5	0.7	15	dbSNP_92	55	2356,5898		355,1646,2126	no	missense	PEAK1	NM_024776.3	58	384,2004,3641	GG,GC,CC		28.5437,10.9359,22.9889	benign	1542/1747	77407114	2772,9286	1902	4127	6029	SO:0001583	missense	0	exon8			GTGGGGCTGGGCT		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.4625G>C	15.37:g.77407114C>G	ENSP00000452796:p.Ser1542Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	480	0.21978021978021978	41	0.08333333333333333	90	0.24861878453038674	130	0.22727272727272727	219	0.28891820580474936	C	9.359	1.067504	0.20067	0.109359	0.285437	ENSG00000173517	ENST00000312493	T	0.68479	-0.33	5.47	3.49	0.39957	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.647154	0.14457	U	0.318453	T	0.00012	0.0000	N	0.08118	0	0.50632	P	1.1700000000003374E-4	B	0.10296	0.003	B	0.10450	0.005	T	0.18335	-1.0340	9	0.21540	T	0.41	-1.0031	7.1818	0.25776	0.0:0.6645:0.1217:0.2138	rs1867780;rs3743480;rs52820530;rs59760970;rs1867780	1542	Q9H792	PEAK1_HUMAN	T	1542	ENSP00000309230:S1542T	ENSP00000309230:S1542T	S	-	2	0	AC087465.1	75194169	1.000000	0.71417	0.689000	0.30133	0.860000	0.49131	1.665000	0.37449	0.596000	0.29794	0.561000	0.74099	AGC	C|0.750;G|0.250	0.250	strong		0.582	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
KRT5	3852	hgsc.bcm.edu	37	12	52912906	52912906	+	Silent	SNP	G	G	T	rs641621	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52912906G>T	ENST00000252242.4	-	2	984	c.594C>A	c.(592-594)acC>acA	p.T198T		NM_000424.3	NP_000415.2	P13647	K2C5_HUMAN	keratin 5	198	Coil 1A.|Rod.				cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|hemidesmosome assembly (GO:0031581)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			endometrium(5)|kidney(1)|large_intestine(8)|lung(15)|prostate(4)|skin(2)	35				BRCA - Breast invasive adenocarcinoma(357;0.189)		GGGTCCACTTGGTGTCCAGAA	0.537													G|||	1077	0.215056	0.1089	0.2233	5008	,	,		19699	0.3393		0.2823	False		,,,				2504	0.1554				p.T198T		Atlas-SNP	.											.	KRT5	88	.	0			c.C594A						PASS	.						59.0	52.0	55.0					12																	52912906		2203	4298	6501	SO:0001819	synonymous_variant	3852	exon2			CCACTTGGTGTCC		CCDS8830.1	12q13.13	2013-01-16	2008-08-01		ENSG00000186081	ENSG00000186081		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6442	protein-coding gene	gene with protein product		148040	"""epidermolysis bullosa simplex 2 Dowling-Meara/Kobner/Weber-Cockayne types"", ""keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types)"""	EBS2		1713141, 16831889	Standard	NM_000424		Approved	KRT5A	uc001san.3	P13647	OTTHUMG00000169657	ENST00000252242.4:c.594C>A	12.37:g.52912906G>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	120	37	0.308333	NM_000424	Q6PI71|Q6UBJ0|Q8TA91	Silent	SNP	ENST00000252242.4	37	CCDS8830.1																																																																																			T|0.177;G|0.823	0.177	strong		0.537	KRT5-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405312.1		
NLRC3	197358	hgsc.bcm.edu	37	16	3613904	3613904	+	RNA	SNP	C	C	G	rs117213971	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3613904C>G	ENST00000301749.7	-	0	1439				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000359128.5_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCCCGTCCTGCTGCGCCACAG	0.662													C|||	212	0.0423323	0.0038	0.0677	5008	,	,		17153	0.0546		0.0636	False		,,,				2504	0.0419				p.S345T		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1034C						PASS	.	C	THR/SER	51,3935		0,51,1942	30.0	34.0	33.0		1034	-4.9	0.0	16	dbSNP_132	33	552,7744		14,524,3610	yes	missense	NLRC3	NM_178844.2	58	14,575,5552	GG,GC,CC		6.6538,1.2795,4.9096	benign	345/1066	3613904	603,11679	1993	4148	6141			197358	exon5			GTCCTGCTGCGCC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613904C>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		103	0.04716117216117216	5	0.01016260162601626	22	0.06077348066298342	28	0.04895104895104895	48	0.0633245382585752	C	0.013	-1.635514	0.00806	0.012795	0.066538	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79	5.15	-4.9	0.03094	.	0.759465	0.12896	N	0.430187	T	0.11623	0.0283	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.26677	-1.0096	9	0.13853	T	0.58	.	9.0719	0.36497	0.0:0.5558:0.115:0.3292	.	392	C9JLH9	.	T	345;345;345;392;327	ENSP00000301749:S345T;ENSP00000352039:S345T;ENSP00000414415:S392T;ENSP00000323897:S327T	ENSP00000301749:S345T	S	-	2	0	NLRC3	3553905	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.419000	0.07071	-0.607000	0.05738	-0.345000	0.07892	AGC	C|0.956;G|0.044	0.044	strong		0.662	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
OR2T34	127068	hgsc.bcm.edu	37	1	248737329	248737329	+	Missense_Mutation	SNP	C	C	T	rs75095367	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248737329C>T	ENST00000328782.2	-	1	751	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAGCAGGTGGCCAAGGCCTTC	0.562																																					p.A244T		Atlas-SNP	.											.	OR2T34	72	.	0			c.G730A						PASS	.	C	THR/ALA	894,3456		168,558,1449	101.0	114.0	110.0		730	0.0	0.4	1	dbSNP_131	110	734,7866		28,678,3594	no	missense	OR2T34	NM_001001821.1	58	196,1236,5043	TT,TC,CC		8.5349,20.5517,12.5714	benign	244/319	248737329	1628,11322	2175	4300	6475	SO:0001583	missense	127068	exon1			AGGTGGCCAAGGC	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.730G>A	1.37:g.248737329C>T	ENSP00000330904:p.Ala244Thr	Somatic	304	1	0.00328947		WXS	Illumina HiSeq	Phase_I	324	141	0.435185	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	526	0.24084249084249085	133	0.2703252032520325	54	0.14917127071823205	259	0.4527972027972028	80	0.10554089709762533	.	2.736	-0.263225	0.05754	0.205517	0.085349	ENSG00000183310	ENST00000328782	T	0.00063	8.78	2.37	0.0258	0.14147	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.21583	0.68	0.80722	P	0.0	B	0.26672	0.156	B	0.30943	0.122	T	0.00171	-1.1960	8	0.27082	T	0.32	.	4.2667	0.10766	0.453:0.4117:0.0:0.1352	.	244	Q8NGX1	O2T34_HUMAN	T	244	ENSP00000330904:A244T	ENSP00000330904:A244T	A	-	1	0	OR2T34	246803952	0.008000	0.16893	0.422000	0.26621	0.327000	0.28475	0.078000	0.14761	0.208000	0.20626	0.123000	0.15791	GCC	C|0.816;T|0.184	0.184	strong		0.562	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
FAM208B	54906	hgsc.bcm.edu	37	10	5799613	5799613	+	Missense_Mutation	SNP	A	A	G	rs2275774	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5799613A>G	ENST00000328090.5	+	17	7488	c.6863A>G	c.(6862-6864)aAg>aGg	p.K2288R		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2288			K -> R (in dbSNP:rs2275774).														TCAGATGACAAGATACTAGAA	0.418													A|||	416	0.0830671	0.0212	0.0994	5008	,	,		21518	0.0595		0.1759	False		,,,				2504	0.0838				p.K2288R		Atlas-SNP	.											.	.	.	.	0			c.A6863G						PASS	.	A	ARG/LYS	156,3632		2,152,1740	243.0	230.0	234.0		6863	-3.2	0.0	10	dbSNP_100	234	1587,6647		160,1267,2690	yes	missense	FAM208B	NM_017782.4	26	162,1419,4430	GG,GA,AA		19.2737,4.1183,14.4984	benign	2288/2431	5799613	1743,10279	1894	4117	6011	SO:0001583	missense	54906	exon17			ATGACAAGATACT	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.6863A>G	10.37:g.5799613A>G	ENSP00000328426:p.Lys2288Arg	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	180	95	0.527778	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	226	0.10347985347985347	14	0.028455284552845527	42	0.11602209944751381	35	0.06118881118881119	135	0.17810026385224276	A	7.930	0.740551	0.15642	0.041183	0.192737	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.42900	0.96	5.59	-3.17	0.05202	.	0.622148	0.15979	N	0.235401	T	0.00039	0.0001	L	0.36672	1.1	0.80722	P	0.0	B	0.19200	0.034	B	0.14023	0.01	T	0.15983	-1.0418	9	0.27082	T	0.32	.	1.7479	0.02966	0.4115:0.2225:0.2581:0.1079	rs2275774;rs56581575;rs58161058;rs2275774	2288	Q5VWN6	F208B_HUMAN	R	2288;1483	ENSP00000328426:K2288R	ENSP00000328426:K2288R	K	+	2	0	C10orf18	5839619	0.000000	0.05858	0.005000	0.12908	0.046000	0.14306	-0.019000	0.12546	-0.495000	0.06659	0.533000	0.62120	AAG	A|0.887;G|0.113	0.113	strong		0.418	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
SMOC1	64093	hgsc.bcm.edu	37	14	70477508	70477508	+	Silent	SNP	C	C	T	rs3825739	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:70477508C>T	ENST00000381280.4	+	8	955	c.702C>T	c.(700-702)gcC>gcT	p.A234A	SMOC1_ENST00000361956.3_Silent_p.A234A	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	234	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GGCAGAGTGCCCTGGAAGAGG	0.537													C|||	1030	0.205671	0.0061	0.3213	5008	,	,		19744	0.4196		0.173	False		,,,				2504	0.2065				p.A234A		Atlas-SNP	.											SMOC1,colon,carcinoma,+1,1	SMOC1	61	1	0			c.C702T						PASS	.	C	,	212,4194	131.0+/-167.6	10,192,2001	111.0	118.0	116.0		702,702	4.6	1.0	14	dbSNP_107	116	1567,7033	295.1+/-302.2	143,1281,2876	no	coding-synonymous,coding-synonymous	SMOC1	NM_001034852.2,NM_022137.5	,	153,1473,4877	TT,TC,CC		18.2209,4.8116,13.6783	,	234/436,234/435	70477508	1779,11227	2203	4300	6503	SO:0001819	synonymous_variant	64093	exon8			GAGTGCCCTGGAA	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.702C>T	14.37:g.70477508C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	96	41	0.427083	NM_001034852	A8K1S3|B2R7P5|Q96F78	Silent	SNP	ENST00000381280.4	37	CCDS9798.1																																																																																			C|0.825;T|0.175	0.175	strong		0.537	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1		
SLIT3	6586	hgsc.bcm.edu	37	5	168180081	168180081	+	Missense_Mutation	SNP	C	C	T	rs10036727	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:168180081C>T	ENST00000519560.1	-	18	2271	c.1852G>A	c.(1852-1854)Ggc>Agc	p.G618S	SLIT3_ENST00000404867.3_Missense_Mutation_p.G618S|SLIT3_ENST00000332966.8_Missense_Mutation_p.G618S	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	618			G -> S (in dbSNP:rs10036727). {ECO:0000269|PubMed:12975309}.		apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTCACACAGCCGATCAAGTTA	0.557													T|||	2859	0.570887	0.705	0.5072	5008	,	,		22384	0.5258		0.5258	False		,,,				2504	0.5276				p.G618S	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.G1852A						PASS	.	T	SER/GLY	3059,1347	449.0+/-348.9	1069,921,213	111.0	79.0	90.0		1852	5.3	1.0	5	dbSNP_119	90	4411,4189	568.4+/-389.0	1155,2101,1044	yes	missense	SLIT3	NM_003062.2	56	2224,3022,1257	TT,TC,CC		48.7093,30.5719,42.565	benign	618/1524	168180081	7470,5536	2203	4300	6503	SO:0001583	missense	6586	exon18			CACAGCCGATCAA	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.1852G>A	5.37:g.168180081C>T	ENSP00000430333:p.Gly618Ser	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	1229	0.5627289377289377	328	0.6666666666666666	185	0.511049723756906	325	0.5681818181818182	391	0.5158311345646438	T	10.40	1.339436	0.24339	0.694281	0.512907	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	T;T;T	0.56103	0.48;0.48;0.48	5.34	5.34	0.76211	.	0.157308	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00793	-1.18	0.47214	P	6.439999999999779E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.44159	-0.9346	9	0.02654	T	1	.	11.2503	0.49022	0.0:0.0718:0.0:0.9282	rs10036727;rs17634699;rs52808264;rs58822677;rs10036727	618	O75094	SLIT3_HUMAN	S	618	ENSP00000430333:G618S;ENSP00000332164:G618S;ENSP00000384890:G618S	ENSP00000332164:G618S	G	-	1	0	SLIT3	168112659	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.302000	0.72788	0.879000	0.35944	-0.254000	0.11334	GGC	C|0.423;N|0.000	.	strong		0.557	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
C9orf50	375759	hgsc.bcm.edu	37	9	132377900	132377900	+	Missense_Mutation	SNP	C	C	T	rs918165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:132377900C>T	ENST00000372478.4	-	4	944	c.743G>A	c.(742-744)aGg>aAg	p.R248K	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	248			R -> K (in dbSNP:rs918165).							central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				AGCCTTGAGCCTGGGGACCTG	0.687													N|||	2788	0.556709	0.711	0.5216	5008	,	,		17511	0.498		0.4513	False		,,,				2504	0.5419				p.R248K		Atlas-SNP	.											.	C9orf50	25	.	0			c.G743A						PASS	.		LYS/ARG	2947,1459		975,997,231	51.0	50.0	50.0		743	-0.7	0.0	9	dbSNP_86	50	3357,5243		648,2061,1591	yes	missense	C9orf50	NM_199350.3	26	1623,3058,1822	TT,TC,CC		39.0349,33.1139,48.4699	benign	248/432	132377900	6304,6702	2203	4300	6503	SO:0001583	missense	375759	exon4			TTGAGCCTGGGGA	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.743G>A	9.37:g.132377900C>T	ENSP00000361556:p.Arg248Lys	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	1162	0.532051282051282	356	0.7235772357723578	184	0.5082872928176796	288	0.5034965034965035	334	0.44063324538258575	N	0.201	-1.044468	0.01997	0.668861	0.390349	ENSG00000179058	ENST00000372478	T	0.15139	2.45	3.1	-0.718	0.11205	.	1.402030	0.05197	N	0.504289	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	0.36962	-0.9726	9	0.06099	T	0.92	-0.0034	3.8899	0.09114	0.0:0.3712:0.2074:0.4215	rs918165;rs17507612;rs59121984	248	Q5SZB4	CI050_HUMAN	K	248	ENSP00000361556:R248K	ENSP00000361556:R248K	R	-	2	0	C9orf50	131417721	0.002000	0.14202	0.001000	0.08648	0.040000	0.13550	-0.826000	0.04429	-0.455000	0.07054	-0.867000	0.03001	AGG	C|0.491;T|0.509	0.509	strong		0.687	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
IFI44	10561	hgsc.bcm.edu	37	1	79115905	79115905	+	Missense_Mutation	SNP	T	T	C	rs2070123	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:79115905T>C	ENST00000370747.4	+	2	110	c.25T>C	c.(25-27)Tgg>Cgg	p.W9R	IFI44_ENST00000545124.1_Intron|IFI44_ENST00000495254.1_Intron	NM_006417.4	NP_006408.3	Q8TCB0	IFI44_HUMAN	interferon-induced protein 44	9			W -> R (in dbSNP:rs2070123). {ECO:0000269|PubMed:15489334}.		response to virus (GO:0009615)	cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21						TCGTTTGACATGGTTGCACGA	0.353													T|||	610	0.121805	0.1346	0.1138	5008	,	,		17255	0.131		0.0775	False		,,,				2504	0.1462				p.W9R		Atlas-SNP	.											IFI44,NS,carcinoma,-1,1	IFI44	55	1	0			c.T25C						PASS	.	T	ARG/TRP	590,3816	261.9+/-264.6	40,510,1653	102.0	96.0	98.0		25	-0.7	0.0	1	dbSNP_96	98	703,7897	172.7+/-223.4	27,649,3624	yes	missense	IFI44	NM_006417.4	101	67,1159,5277	CC,CT,TT		8.1744,13.3908,9.9416	possibly-damaging	9/445	79115905	1293,11713	2203	4300	6503	SO:0001583	missense	10561	exon2			TTGACATGGTTGC	D28915	CCDS688.1	1p31.1	2013-03-14			ENSG00000137965	ENSG00000137965			16938	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 5"""	610468				7925411	Standard	NM_006417		Approved	MTAP44, p44, TLDC5	uc001dip.4	Q8TCB0	OTTHUMG00000009723	ENST00000370747.4:c.25T>C	1.37:g.79115905T>C	ENSP00000359783:p.Trp9Arg	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	141	77	0.546099	NM_006417	B7ZAG3|D3DQ80|Q14496	Missense_Mutation	SNP	ENST00000370747.4	37	CCDS688.1	237	0.10851648351648352	58	0.11788617886178862	48	0.13259668508287292	73	0.12762237762237763	58	0.07651715039577836	T	4.491	0.091066	0.08632	0.133908	0.081744	ENSG00000137965	ENST00000370747	T	0.08193	3.12	3.32	-0.723	0.11181	.	0.879816	0.09828	N	0.750596	T	0.04272	0.0118	M	0.68952	2.095	0.80722	P	0.0	P;P	0.50272	0.933;0.933	P;P	0.45881	0.496;0.496	T	0.30966	-0.9960	9	0.40728	T	0.16	-0.3873	4.5869	0.12287	0.1923:0.0:0.3963:0.4114	rs2070123;rs2070602;rs17852121;rs52832822;rs2070123	9;9	B7ZB11;Q8TCB0	.;IFI44_HUMAN	R	9	ENSP00000359783:W9R	ENSP00000359783:W9R	W	+	1	0	IFI44	78888493	0.078000	0.21339	0.004000	0.12327	0.003000	0.03518	0.111000	0.15458	-0.137000	0.11455	-0.661000	0.03856	TGG	T|0.891;C|0.109	0.109	strong		0.353	IFI44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026825.1	NM_006417	
ZNF155	7711	hgsc.bcm.edu	37	19	44501518	44501518	+	Silent	SNP	G	G	A	rs446016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44501518G>A	ENST00000270014.2	+	5	1637	c.1509G>A	c.(1507-1509)ccG>ccA	p.P503P	ZNF155_ENST00000590615.1_Silent_p.P503P|RP11-15A1.7_ENST00000589021.1_RNA|ZNF155_ENST00000407951.2_Silent_p.P514P|RP11-15A1.7_ENST00000586860.1_RNA	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	503					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				AAGACCAGCCGAGAGACTATA	0.418													G|||	1989	0.397165	0.3328	0.5086	5008	,	,		17839	0.6081		0.2763	False		,,,				2504	0.3119				p.P514P	NSCLC(61;554 1277 20909 42067 42312)	Atlas-SNP	.											.	ZNF155	30	.	0			c.G1542A						PASS	.	G	,	1382,3024	454.9+/-350.8	193,996,1014	92.0	95.0	94.0		1509,1509	-4.1	0.0	19	dbSNP_80	94	2406,6194	397.3+/-345.7	312,1782,2206	no	coding-synonymous,coding-synonymous	ZNF155	NM_003445.2,NM_198089.1	,	505,2778,3220	AA,AG,GG		27.9767,31.3663,29.125	,	503/539,503/539	44501518	3788,9218	2203	4300	6503	SO:0001819	synonymous_variant	7711	exon6			CCAGCCGAGAGAC	U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"""Zinc fingers, C2H2-type"", ""-"""	12940	protein-coding gene	gene with protein product		604086	"""zinc finger protein 155 (pHZ-96)"""			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.1509G>A	19.37:g.44501518G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	43	19	0.44186	NM_001260488	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Silent	SNP	ENST00000270014.2	37	CCDS12634.1																																																																																			G|0.668;A|0.332	0.332	strong		0.418	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445	
IGLL1	3543	hgsc.bcm.edu	37	22	23915516	23915516	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:23915516G>A	ENST00000330377.2	-	3	696	c.579C>T	c.(577-579)agC>agT	p.S193S	IGLL1_ENST00000249053.3_3'UTR|AP000345.2_ENST00000454863.1_RNA|AP000345.2_ENST00000458318.1_RNA	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	193	C region (By similarity to lambda light- chain).|Ig-like C1-type.				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						TGACCTGGCAGCTGTAGCTTC	0.627																																					p.S193S		Atlas-SNP	.											IGLL1,NS,carcinoma,0,1	IGLL1	27	1	0			c.C579T						scavenged	.						73.0	70.0	71.0					22																	23915516		2203	4300	6503	SO:0001819	synonymous_variant	3543	exon3			CTGGCAGCTGTAG	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.579C>T	22.37:g.23915516G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	124	3	0.0241935	NM_020070	Q0P681	Silent	SNP	ENST00000330377.2	37	CCDS13809.1																																																																																			.	.	none		0.627	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070	
TRMT6	51605	hgsc.bcm.edu	37	20	5924828	5924828	+	Silent	SNP	A	A	G	rs35861347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5924828A>G	ENST00000203001.2	-	4	568	c.438T>C	c.(436-438)taT>taC	p.Y146Y	TRMT6_ENST00000453074.2_5'UTR|TRMT6_ENST00000473131.1_5'UTR	NM_015939.3	NP_057023.2	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6 homolog (S. cerevisiae)	146					regulation of translational initiation (GO:0006446)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	15						TCTTTTTAATATATTTATCTT	0.239													A|||	284	0.0567093	0.1127	0.098	5008	,	,		12906	0.001		0.0199	False		,,,				2504	0.047				p.Y146Y		Atlas-SNP	.											.	TRMT6	28	.	0			c.T438C						PASS	.	A		424,3858		22,380,1739	16.0	17.0	17.0		438	3.3	1.0	20	dbSNP_126	17	178,8304		2,174,4065	no	coding-synonymous	TRMT6	NM_015939.3		24,554,5804	GG,GA,AA		2.0986,9.9019,4.7164		146/498	5924828	602,12162	2141	4241	6382	SO:0001819	synonymous_variant	51605	exon4			TTTAATATATTTA	AK000613	CCDS13093.1, CCDS63225.1	20p12.3	2009-01-12			ENSG00000089195	ENSG00000089195			20900	protein-coding gene	gene with protein product						16043508	Standard	NM_001281467		Approved	GCD10, MGC5029, Gcd10p, CGI-09	uc002wmh.1	Q9UJA5	OTTHUMG00000031816	ENST00000203001.2:c.438T>C	20.37:g.5924828A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_015939	B4DUV6|Q76P92|Q9BQV5|Q9ULR7|Q9Y2Z8	Silent	SNP	ENST00000203001.2	37	CCDS13093.1																																																																																			A|0.958;G|0.042	0.042	strong		0.239	TRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077889.2		
CPOX	1371	hgsc.bcm.edu	37	3	98307696	98307696	+	Missense_Mutation	SNP	T	T	G	rs1131857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:98307696T>G	ENST00000264193.2	-	4	1032	c.814A>C	c.(814-816)Aac>Cac	p.N272H		NM_000097.5	NP_000088.3	P36551	HEM6_HUMAN	coproporphyrinogen oxidase	272			N -> H (in dbSNP:rs1131857). {ECO:0000269|PubMed:7849704, ECO:0000269|PubMed:8159699}.		heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to arsenic-containing substance (GO:0046685)|response to insecticide (GO:0017085)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to methylmercury (GO:0051597)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)	coproporphyrinogen oxidase activity (GO:0004109)|protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)	p.N272H(1)		endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CACTGCTTGTTGCCTACCAAA	0.413													T|||	1231	0.245807	0.4902	0.1571	5008	,	,		16660	0.2252		0.1511	False		,,,				2504	0.0971				p.N272H	Esophageal Squamous(75;7 1223 22300 43648 48951)	Atlas-SNP	.											CPOX,NS,carcinoma,0,1	CPOX	34	1	1	Substitution - Missense(1)	stomach(1)	c.A814C	GRCh37	CM056569	CPOX	M	rs1131857	PASS	.	T	HIS/ASN	1959,2447	551.2+/-378.2	429,1101,673	82.0	72.0	76.0		814	4.8	1.0	3	dbSNP_86	76	1141,7459	233.5+/-266.7	82,977,3241	yes	missense	CPOX	NM_000097.5	68	511,2078,3914	GG,GT,TT		13.2674,44.4621,23.8352	benign	272/455	98307696	3100,9906	2203	4300	6503	SO:0001583	missense	1371	exon4			GCTTGTTGCCTAC	BC017210	CCDS2932.1	3q12	2012-10-02		2004-01-30		ENSG00000080819	1.3.3.3		2321	protein-coding gene	gene with protein product	"""coproporphyria"""	612732	"""coproporphyrinogen oxidase (coproporphyria, harderoporphyria)"""	CPO		7757079, 8407975	Standard	NM_000097		Approved	CPX, HCP	uc003dsx.3	P36551		ENST00000264193.2:c.814A>C	3.37:g.98307696T>G	ENSP00000264193:p.Asn272His	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	109	46	0.422018	NM_000097	A8K275|B4DSD5|Q14060|Q53F08|Q8IZ45|Q96AF3	Missense_Mutation	SNP	ENST00000264193.2	37	CCDS2932.1	521	0.23855311355311357	220	0.44715447154471544	58	0.16022099447513813	117	0.20454545454545456	126	0.1662269129287599	T	17.87	3.494742	0.64186	0.444621	0.132674	ENSG00000080819	ENST00000264193	D	0.93247	-3.19	5.93	4.76	0.60689	.	0.420058	0.28659	N	0.014576	T	0.00012	0.0000	L	0.47716	1.5	0.32184	P	0.580047	P	0.41673	0.759	B	0.43155	0.41	T	0.00038	-1.2246	9	0.52906	T	0.07	-10.0918	11.5194	0.50543	0.0:0.0:0.1504:0.8496	rs1131857;rs1675514;rs1803297;rs2229122;rs3192093;rs11541766;rs17417460;rs17845531;rs17858427;rs52809922;rs57270840;rs1131857	272	P36551	HEM6_HUMAN	H	272	ENSP00000264193:N272H	ENSP00000264193:N272H	N	-	1	0	CPOX	99790386	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.829000	0.39121	1.050000	0.40346	-0.460000	0.05396	AAC	T|0.760;G|0.235	0.235	strong		0.413	CPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358900.1	NM_000097	
HLA-A	3105	hgsc.bcm.edu	37	6	29910716	29910716	+	Missense_Mutation	SNP	C	C	G	rs386698551|rs386698552|rs200082950|rs1059455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910716C>G	ENST00000396634.1	+	4	597	c.256C>G	c.(256-258)Cag>Gag	p.Q86E	HLA-A_ENST00000376809.5_Missense_Mutation_p.Q86E|HLA-A_ENST00000376806.5_Missense_Mutation_p.Q86E|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q86E			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	86	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						GTATTGGGACCAGGAGACACG	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)			c|||	1965	0.392372	0.3048	0.4986	5008	,	,		11305	0.4851		0.4175	False		,,,				2504	0.3139				p.Q86E		Atlas-SNP	.											.	HLA-A	89	.	0			c.C256G						PASS	.						73.0	78.0	76.0					6																	29910716		2201	4293	6494	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TGGGACCAGGAGA	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.256C>G	6.37:g.29910716C>G	ENSP00000379873:p.Gln86Glu	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	103	88	0.854369	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	5.115	0.206908	0.09704	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00695	5.83;5.83;5.83;5.83	3.57	-7.15	0.01521	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	10.635600	0.01145	N	0.006290	T	0.00271	0.0008	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.40496	-0.9560	9	0.29301	T	0.29	.	15.7686	0.78146	0.0827:0.7593:0.158:0.0	rs1059455;rs2230989;rs3179180;rs3200131;rs28749146;rs41548918	86;86;86;86;86	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	E	86	ENSP00000379873:Q86E;ENSP00000366002:Q86E;ENSP00000366005:Q86E;ENSP00000365998:Q86E	ENSP00000348012:Q86E	Q	+	1	0	HLA-A	30018695	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-3.953000	0.00326	-2.903000	0.00311	-0.589000	0.04120	CAG	G|1.000	.	weak		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
RPE65	6121	hgsc.bcm.edu	37	1	68903942	68903942	+	Silent	SNP	C	C	T	rs12145904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:68903942C>T	ENST00000262340.5	-	10	1109	c.1056G>A	c.(1054-1056)gaG>gaA	p.E352E		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	352					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						TTTTTTTCACCTCTTCCCAGT	0.353													C|||	1121	0.223842	0.2315	0.1729	5008	,	,		17522	0.3641		0.1272	False		,,,				2504	0.2045				p.E352E		Atlas-SNP	.											RPE65,NS,carcinoma,-2,1	RPE65	87	1	0			c.G1056A						PASS	.	C		1017,3389	374.9+/-321.4	122,773,1308	90.0	92.0	91.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1056	-0.7	1.0	1	dbSNP_120	91	1012,7588	215.5+/-254.8	55,902,3343	no	coding-synonymous	RPE65	NM_000329.2		177,1675,4651	TT,TC,CC		11.7674,23.0822,15.6005		352/534	68903942	2029,10977	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon10			TTTCACCTCTTCC	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.1056G>A	1.37:g.68903942C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	66	18	0.272727	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			C|0.815;T|0.185	0.185	strong		0.353	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
TEDDM1	127670	hgsc.bcm.edu	37	1	182369233	182369233	+	Missense_Mutation	SNP	A	A	G	rs6674281	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:182369233A>G	ENST00000367565.1	-	1	518	c.388T>C	c.(388-390)Tat>Cat	p.Y130H		NM_172000.3	NP_741997.3	Q5T9Z0	TEDM1_HUMAN	transmembrane epididymal protein 1	130			Y -> H (in dbSNP:rs6674281).			integral component of membrane (GO:0016021)				haematopoietic_and_lymphoid_tissue(1)|lung(4)|ovary(2)	7						AGCAGAGAATAAACGTGCAGC	0.512													G|||	3396	0.678115	0.761	0.6124	5008	,	,		22039	0.8294		0.5417	False		,,,				2504	0.5971				p.Y130H		Atlas-SNP	.											.	TEDDM1	32	.	0			c.T388C						PASS	.	G	HIS/TYR	3281,1125	402.8+/-332.5	1230,821,152	147.0	146.0	147.0		388	5.1	0.0	1	dbSNP_116	147	4445,4155	566.7+/-388.7	1151,2143,1006	yes	missense	TEDDM1	NM_172000.3	83	2381,2964,1158	GG,GA,AA		48.314,25.5334,40.5966	benign	130/274	182369233	7726,5280	2203	4300	6503	SO:0001583	missense	127670	exon1			GAGAATAAACGTG	AJ515384	CCDS30953.1	1q25.3	2009-09-17		2005-08-09	ENSG00000203730	ENSG00000203730			30233	protein-coding gene	gene with protein product	"""putative membrane protein HE9"", ""transmembrane protein 45C"", ""epididymal protein 9"""						Standard	NM_172000		Approved	HE9, Epdd1, TMEM45C, EDDM9	uc001gpe.3	Q5T9Z0	OTTHUMG00000037398	ENST00000367565.1:c.388T>C	1.37:g.182369233A>G	ENSP00000356536:p.Tyr130His	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_172000	Q8IVJ0	Missense_Mutation	SNP	ENST00000367565.1	37	CCDS30953.1	1442	0.6602564102564102	362	0.7357723577235772	222	0.6132596685082873	461	0.8059440559440559	397	0.5237467018469657	G	0.012	-1.684426	0.00745	0.744666	0.51686	ENSG00000203730	ENST00000367565	T	0.31769	1.48	5.05	5.05	0.67936	.	0.000000	0.64402	N	0.000002	T	0.00012	0.0000	N	0.00017	-2.845	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40136	-0.9579	9	0.02654	T	1	-45.4785	11.5331	0.50622	0.0864:0.0:0.9136:0.0	rs6674281;rs17463348;rs58719880;rs6674281	130	Q5T9Z0	TEDM1_HUMAN	H	130	ENSP00000356536:Y130H	ENSP00000356536:Y130H	Y	-	1	0	TEDDM1	180635856	0.922000	0.31269	0.020000	0.16555	0.001000	0.01503	3.052000	0.49893	1.368000	0.46115	-0.119000	0.15052	TAT	A|0.364;G|0.636	0.636	strong		0.512	TEDDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091029.1	NM_172000	
DGKI	9162	hgsc.bcm.edu	37	7	137263068	137263068	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:137263068G>T	ENST00000288490.5	-	16	1646	c.1646C>A	c.(1645-1647)gCa>gAa	p.A549E	DGKI_ENST00000453654.2_Missense_Mutation_p.A249E|DGKI_ENST00000424189.2_Missense_Mutation_p.A549E|DGKI_ENST00000446122.1_Missense_Mutation_p.A549E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	549					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CTCTGGATTTGCTTCTGTGAA	0.373																																					p.A549E		Atlas-SNP	.											DGKI_ENST00000288490,NS,carcinoma,-1,2	DGKI	335	2	0			c.C1646A						PASS	.						67.0	68.0	67.0					7																	137263068		2202	4299	6501	SO:0001583	missense	9162	exon16			GGATTTGCTTCTG	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.1646C>A	7.37:g.137263068G>T	ENSP00000288490:p.Ala549Glu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.920853	0.92249	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.27890	1.64;1.64;1.64	5.15	5.15	0.70609	Diacylglycerol kinase, accessory domain (2);	0.000000	0.85682	D	0.000000	T	0.45256	0.1333	L	0.28694	0.88	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.987;0.995	T	0.31998	-0.9923	10	0.42905	T	0.14	.	18.6041	0.91261	0.0:0.0:1.0:0.0	.	249;549	E9PFX6;O75912	.;DGKI_HUMAN	E	249;497;549;549;549	ENSP00000392161:A249E;ENSP00000288490:A549E;ENSP00000399131:A549E	ENSP00000288490:A549E	A	-	2	0	DGKI	136913608	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.610000	0.98337	2.573000	0.86826	0.462000	0.41574	GCA	.	.	none		0.373	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
HTR1F	3355	hgsc.bcm.edu	37	3	88040545	88040545	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:88040545C>A	ENST00000319595.4	+	1	700	c.646C>A	c.(646-648)Caa>Aaa	p.Q216K		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	216					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(8;0.147)	Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00664)	Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Ketamine(DB01221)|Methysergide(DB00247)|Mianserin(DB06148)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Zolmitriptan(DB00315)	CCACAAGAGACAAGCAAGTAG	0.388																																					p.Q216K		Atlas-SNP	.											HTR1F,NS,carcinoma,-2,1	HTR1F	66	1	0			c.C646A						scavenged	.						72.0	74.0	74.0					3																	88040545		2203	4300	6503	SO:0001583	missense	3355	exon2			AAGAGACAAGCAA	L05597	CCDS2920.1	3p12	2012-08-08	2012-02-03		ENSG00000179097	ENSG00000179097		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5292	protein-coding gene	gene with protein product		182134	"""5-hydroxytryptamine (serotonin) receptor 1F"""			8384716, 8380639	Standard	NM_000866		Approved	HTR1EL, 5-HT1F	uc003dqr.2	P30939	OTTHUMG00000159008	ENST00000319595.4:c.646C>A	3.37:g.88040545C>A	ENSP00000322924:p.Gln216Lys	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	123	3	0.0243902	NM_000866		Missense_Mutation	SNP	ENST00000319595.4	37	CCDS2920.1	.	.	.	.	.	.	.	.	.	.	C	0.843	-0.741256	0.03088	.	.	ENSG00000179097	ENST00000319595	T	0.35973	1.28	5.01	4.04	0.47022	GPCR, rhodopsin-like superfamily (1);	0.381590	0.28908	N	0.013744	T	0.20047	0.0482	N	0.26042	0.785	0.29509	N	0.854314	B	0.09022	0.002	B	0.12156	0.007	T	0.20505	-1.0273	10	0.02654	T	1	.	9.4331	0.38622	0.361:0.639:0.0:0.0	.	216	P30939	5HT1F_HUMAN	K	216	ENSP00000322924:Q216K	ENSP00000322924:Q216K	Q	+	1	0	HTR1F	88123235	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	4.188000	0.58351	2.338000	0.79540	0.460000	0.39030	CAA	.	.	none		0.388	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1	NM_000866	
ZNF154	7710	hgsc.bcm.edu	37	19	58213743	58213743	+	Nonsense_Mutation	SNP	G	G	A	rs74939505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58213743G>A	ENST00000512439.2	-	3	770	c.574C>T	c.(574-576)Cga>Tga	p.R192*	ZNF154_ENST00000426889.1_Nonsense_Mutation_p.R192*|ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	192					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CCACACTCTCGACATTCATAA	0.428													G|||	26	0.00519169	0.0008	0.0029	5008	,	,		23939	0.001		0.0179	False		,,,				2504	0.0041				p.R192X		Atlas-SNP	.											.	ZNF154	34	.	0			c.C574T						PASS	.	G	stop/ARG	9,4345	12.9+/-30.5	0,9,2168	129.0	128.0	128.0		574	-2.7	0.0	19	dbSNP_132	128	114,8456	59.5+/-121.1	0,114,4171	yes	stop-gained	ZNF154	NM_001085384.1		0,123,6339	AA,AG,GG		1.3302,0.2067,0.9517		192/438	58213743	123,12801	2177	4285	6462	SO:0001587	stop_gained	7710	exon3			ACTCTCGACATTC	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.574C>T	19.37:g.58213743G>A	ENSP00000421258:p.Arg192*	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	207	101	0.487923	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Nonsense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	G	14.30	2.495078	0.44352	0.002067	0.013302	ENSG00000179909	ENST00000512439;ENST00000426889	.	.	.	2.82	-2.67	0.06059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	2.8458	0.05542	0.2637:0.2107:0.4239:0.1018	.	.	.	.	X	192	.	ENSP00000442370:R192X	R	-	1	2	ZNF154	62905555	0.000000	0.05858	0.001000	0.08648	0.112000	0.19704	-8.748000	0.00017	-0.786000	0.04516	-1.268000	0.01426	CGA	G|0.993;A|0.007	0.007	strong		0.428	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
PRSS53	339105	hgsc.bcm.edu	37	16	31095999	31095999	+	Silent	SNP	G	G	A	rs138417092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31095999G>A	ENST00000280606.6	-	9	1458	c.1305C>T	c.(1303-1305)ccC>ccT	p.P435P		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	435	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						GGAGGGTCACGGGCACTGTCT	0.667													G|||	43	0.00858626	0.0008	0.0187	5008	,	,		17066	0.0		0.0268	False		,,,				2504	0.002				p.P435P		Atlas-SNP	.											PRSS53,NS,haematopoietic_neoplasm,0,1	PRSS53	29	1	0			c.C1305T						scavenged	.	G		9,4091		0,9,2041	15.0	19.0	18.0		1305	0.3	1.0	16	dbSNP_134	18	95,8309		0,95,4107	no	coding-synonymous	PRSS53	NM_001039503.2		0,104,6148	AA,AG,GG		1.1304,0.2195,0.8317		435/554	31095999	104,12400	2050	4202	6252	SO:0001819	synonymous_variant	339105	exon9			GGTCACGGGCACT		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.1305C>T	16.37:g.31095999G>A		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	177	65	0.367232	NM_001039503		Silent	SNP	ENST00000280606.6	37	CCDS42153.1																																																																																			G|0.988;A|0.012	0.012	strong		0.667	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
PTK2B	2185	hgsc.bcm.edu	37	8	27255146	27255146	+	Silent	SNP	G	G	A	rs1045511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27255146G>A	ENST00000397501.1	+	7	853	c.45G>A	c.(43-45)acG>acA	p.T15T	PTK2B_ENST00000420218.2_Silent_p.T15T|PTK2B_ENST00000346049.5_Silent_p.T15T|PTK2B_ENST00000517339.1_Silent_p.T15T|PTK2B_ENST00000544172.1_Silent_p.T15T|PTK2B_ENST00000338238.4_Silent_p.T15T	NM_173174.2	NP_775266.1	Q14289	FAK2_HUMAN	protein tyrosine kinase 2 beta	15					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)	AGTTGGGCACGTTACGCCGGC	0.572													G|||	1560	0.311502	0.1823	0.3818	5008	,	,		19285	0.2748		0.4304	False		,,,				2504	0.3517				p.T15T		Atlas-SNP	.											.	PTK2B	304	.	0			c.G45A						PASS	.	G	,,,	939,3467	357.1+/-313.8	113,713,1377	138.0	116.0	123.0		45,45,45,45	-8.1	0.5	8	dbSNP_86	123	3839,4761	540.9+/-383.9	867,2105,1328	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK2B	NM_004103.4,NM_173174.2,NM_173175.2,NM_173176.2	,,,	980,2818,2705	AA,AG,GG		44.6395,21.3118,36.7369	,,,	15/1010,15/1010,15/968,15/1010	27255146	4778,8228	2203	4300	6503	SO:0001819	synonymous_variant	2185	exon7			GGGCACGTTACGC	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.45G>A	8.37:g.27255146G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	97	54	0.556701	NM_173174	D3DST0|Q13475|Q14290|Q16709|Q6PID4	Silent	SNP	ENST00000397501.1	37	CCDS6057.1																																																																																			G|0.645;A|0.355	0.355	strong		0.572	PTK2B-009	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219916.1	NM_004103	
ACER1	125981	hgsc.bcm.edu	37	19	6333476	6333476	+	Silent	SNP	G	G	A	rs16993553	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6333476G>A	ENST00000301452.4	-	1	164	c.87C>T	c.(85-87)taC>taT	p.Y29Y		NM_133492.2	NP_597999.1	Q8TDN7	ACER1_HUMAN	alkaline ceramidase 1	29					cell differentiation (GO:0030154)|cellular response to calcium ion (GO:0071277)|ceramide catabolic process (GO:0046514)|epidermis development (GO:0008544)|keratinocyte differentiation (GO:0030216)|regulation of lipid metabolic process (GO:0019216)|response to alkaline pH (GO:0010446)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(4)|pancreas(1)	15						TCACCGTGTTGTAGAACTCGG	0.572													G|||	451	0.0900559	0.0393	0.0634	5008	,	,		18511	0.0129		0.0855	False		,,,				2504	0.2618				p.Y29Y		Atlas-SNP	.											ACER1,NS,carcinoma,-2,1	ACER1	38	1	0			c.C87T						PASS	.	G		201,4203		4,193,2005	70.0	44.0	53.0		87	4.9	1.0	19	dbSNP_123	53	705,7893		37,631,3631	no	coding-synonymous	ACER1	NM_133492.2		41,824,5636	AA,AG,GG		8.1996,4.564,6.9682		29/265	6333476	906,12096	2202	4299	6501	SO:0001819	synonymous_variant	125981	exon1			CGTGTTGTAGAAC	AF347024	CCDS12161.1	19p13.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000167769	ENSG00000167769	3.5.1.23	"""Alkaline ceramidase"""	18356	protein-coding gene	gene with protein product		613491	"""N-acylsphingosine amidohydrolase (alkaline ceramidase) 3"""	ASAH3		12783875	Standard	NM_133492		Approved		uc002mel.2	Q8TDN7		ENST00000301452.4:c.87C>T	19.37:g.6333476G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	89	52	0.58427	NM_133492		Silent	SNP	ENST00000301452.4	37	CCDS12161.1																																																																																			G|0.938;A|0.062	0.062	strong		0.572	ACER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452982.1	NM_133492	
IFNB1	3456	hgsc.bcm.edu	37	9	21077716	21077716	+	Silent	SNP	G	G	A	rs1051922	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:21077716G>A	ENST00000380232.2	-	1	227	c.153C>T	c.(151-153)taC>taT	p.Y51Y		NM_002176.2	NP_002167.1	P01574	IFNB_HUMAN	interferon, beta 1, fibroblast	51					adaptive immune response (GO:0002250)|B cell activation involved in immune response (GO:0002312)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|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 (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of T cell differentiation (GO:0045581)|negative regulation of T-helper 2 cell cytokine production (GO:2000552)|negative regulation of viral genome replication (GO:0045071)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of innate immune response (GO:0045089)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	12				GBM - Glioblastoma multiforme(5;7.45e-142)|Lung(24;2.42e-17)|LUSC - Lung squamous cell carcinoma(38;7.17e-11)		CCTTGAGGCAGTATTCAAGCC	0.483													A|||	1644	0.328275	0.3979	0.2608	5008	,	,		20472	0.3204		0.3579	False		,,,				2504	0.2597				p.Y51Y		Atlas-SNP	.											.	IFNB1	33	.	0			c.C153T						PASS	.	A		1651,2755	657.8+/-400.3	300,1051,852	69.0	68.0	68.0		153	-8.9	0.0	9	dbSNP_86	68	2819,5781	674.9+/-403.2	472,1875,1953	no	coding-synonymous	IFNB1	NM_002176.2		772,2926,2805	AA,AG,GG		32.7791,37.4716,34.3688		51/188	21077716	4470,8536	2203	4300	6503	SO:0001819	synonymous_variant	3456	exon1			GAGGCAGTATTCA		CCDS6495.1	9p22	2008-07-21			ENSG00000171855	ENSG00000171855		"""Interferons"""	5434	protein-coding gene	gene with protein product		147640		IFNB			Standard	NM_002176		Approved	IFB, IFF	uc003zok.3	P01574	OTTHUMG00000019652	ENST00000380232.2:c.153C>T	9.37:g.21077716G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	118	61	0.516949	NM_002176	Q5VWC9	Silent	SNP	ENST00000380232.2	37	CCDS6495.1																																																																																			G|0.656;N|0.000	.	strong		0.483	IFNB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051881.1	NM_002176	
FAM162B	221303	hgsc.bcm.edu	37	6	117083182	117083182	+	Silent	SNP	G	G	A	rs41305290	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:117083182G>A	ENST00000368557.4	-	3	494	c.348C>T	c.(346-348)ctC>ctT	p.L116L		NM_001085480.2	NP_001078949.1	Q5T6X4	F162B_HUMAN	family with sequence similarity 162, member B	116						integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)	6						CGATAATTGTGAGTCCAATCA	0.373													G|||	26	0.00519169	0.0008	0.0072	5008	,	,		15559	0.0		0.0199	False		,,,				2504	0.0				p.L116L		Atlas-SNP	.											.	FAM162B	19	.	0			c.C348T						PASS	.	G		9,3799		0,9,1895	195.0	188.0	190.0		348	2.4	1.0	6	dbSNP_127	190	115,8139		1,113,4013	no	coding-synonymous	FAM162B	NM_001085480.2		1,122,5908	AA,AG,GG		1.3933,0.2363,1.028		116/163	117083182	124,11938	1904	4127	6031	SO:0001819	synonymous_variant	221303	exon3			AATTGTGAGTCCA	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.348C>T	6.37:g.117083182G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	123	15	0.121951	NM_001085480	Q8IXW8	Silent	SNP	ENST00000368557.4	37	CCDS43497.1																																																																																			G|0.990;A|0.010	0.010	strong		0.373	FAM162B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041965.1	XM_927381	
DGCR6L	85359	hgsc.bcm.edu	37	22	20302276	20302276	+	Missense_Mutation	SNP	A	A	T	rs1056804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20302276A>T	ENST00000248879.3	-	5	676	c.585T>A	c.(583-585)aaT>aaA	p.N195K	DGCR6L_ENST00000405465.3_Missense_Mutation_p.N157K	NM_033257.3	NP_150282.2	Q9BY27	DGC6L_HUMAN	DiGeorge syndrome critical region gene 6-like	195			N -> K (in dbSNP:rs1056804).			nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(2)|stomach(1)	5	Colorectal(54;0.0993)					CCAGGGCTGCATTCCCTGCCC	0.637													.|||	209	0.0417332	0.0	0.0692	5008	,	,		17992	0.13		0.0249	False		,,,				2504	0.0051				p.N195K		Atlas-SNP	.											.	DGCR6L	9	.	0			c.T585A						PASS	.	A	LYS/ASN	10,4396		0,10,2193	40.0	38.0	39.0		585	-1.5	0.0	22	dbSNP_86	39	166,8434		1,164,4135	no	missense	DGCR6L	NM_033257.3	94	1,174,6328	TT,TA,AA		1.9302,0.227,1.3532	benign	195/221	20302276	176,12830	2203	4300	6503	SO:0001583	missense	85359	exon5			GGCTGCATTCCCT	AF228708	CCDS13778.1	22q11.21	2013-02-19			ENSG00000128185	ENSG00000128185			18551	protein-coding gene	gene with protein product		609459				11157784	Standard	NM_033257		Approved	FLJ10666	uc002zrx.3	Q9BY27	OTTHUMG00000150583	ENST00000248879.3:c.585T>A	22.37:g.20302276A>T	ENSP00000248879:p.Asn195Lys	Somatic	473	1	0.00211416		WXS	Illumina HiSeq	Phase_I	452	230	0.50885	NM_033257	A8K1N7|B3KMC0|D3DX29|Q9BW33	Missense_Mutation	SNP	ENST00000248879.3	37	CCDS13778.1	116	0.05311355311355311	0	0.0	14	0.03867403314917127	84	0.14685314685314685	18	0.023746701846965697	C	0.010	-1.797115	0.00617	0.00227	0.019302	ENSG00000128185	ENST00000248879;ENST00000405465	T;T	0.28454	2.14;1.61	2.04	-1.54	0.08584	.	0.381500	0.28677	N	0.014509	T	0.00039	0.0001	N	0.01800	-0.715	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25882	-1.0119	9	0.02654	T	1	-26.6997	4.2486	0.10684	0.5802:0.2873:0.0:0.1326	.	195	Q9BY27	DGC6L_HUMAN	K	195;157	ENSP00000248879:N195K;ENSP00000386052:N157K	ENSP00000248879:N195K	N	-	3	2	DGCR6L	18682276	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.013000	0.13310	-0.283000	0.09115	-1.262000	0.01453	AAT	A|0.975;T|0.025	0.025	strong		0.637	DGCR6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318970.3	NM_033257	
SSPO	23145	hgsc.bcm.edu	37	7	149511985	149511985	+	RNA	SNP	A	A	G	rs10952230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149511985A>G	ENST00000378016.2	+	0	10535							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGCCCTGGGAACCACACGCAG	0.672													G|||	4361	0.870807	0.9962	0.8213	5008	,	,		16421	0.7212		0.825	False		,,,				2504	0.9376				p.N3512S		Atlas-SNP	.											.	.	.	.	0			c.A10535G						PASS	.	G		4103,129		1991,121,4	8.0	11.0	10.0		10545	-0.1	0.1	7	dbSNP_120	10	6984,1340		2940,1104,118	no	coding-notMod3	SSPO	NM_198455.2		4931,1225,122	GG,GA,AA		16.098,3.0482,11.6996			149511985	11087,1469	2116	4162	6278			23145	exon74			CTGGGAACCACAC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149511985A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				A|0.139;G|0.861	0.861	strong		0.672	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SLC7A14	57709	hgsc.bcm.edu	37	3	170198898	170198898	+	Silent	SNP	C	C	T	rs3732449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:170198898C>T	ENST00000231706.5	-	7	1488	c.1173G>A	c.(1171-1173)tcG>tcA	p.S391S	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	391			S -> L (in RP68; uncertain pathological significance). {ECO:0000269|PubMed:24670872}.		negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			CCAGGAACCCCGACACGATGC	0.587													c|||	1690	0.33746	0.5212	0.2608	5008	,	,		18123	0.3849		0.1968	False		,,,				2504	0.2393				p.S391S		Atlas-SNP	.											.	SLC7A14	110	.	0			c.G1173A						PASS	.	T		2131,2275	578.2+/-384.6	503,1125,575	54.0	47.0	50.0		1173	-10.6	0.1	3	dbSNP_107	50	1557,7043	293.4+/-301.3	134,1289,2877	no	coding-synonymous	SLC7A14	NM_020949.2		637,2414,3452	TT,TC,CC		18.1047,48.3659,28.3561		391/772	170198898	3688,9318	2203	4300	6503	SO:0001819	synonymous_variant	57709	exon7			GAACCCCGACACG	BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1173G>A	3.37:g.170198898C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_020949	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	37	CCDS33892.1																																																																																			C|0.688;T|0.312	0.312	strong		0.587	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949	
MUC4	4585	hgsc.bcm.edu	37	3	195516305	195516305	+	Missense_Mutation	SNP	C	C	T	rs3749331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195516305C>T	ENST00000463781.3	-	2	2605	c.2146G>A	c.(2146-2148)Gca>Aca	p.A716T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A716T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	721					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)		CTGCTGGGTGCTGCCTGCAGT	0.612													.|||	569	0.113618	0.1195	0.0922	5008	,	,		17928	0.0456		0.173	False		,,,				2504	0.1299				p.A716T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G2146A						PASS	.		,,THR/ALA	481,3785		30,421,1682	92.0	104.0	100.0		,,2146	-5.2	0.0	3	dbSNP_107	100	1436,7066		130,1176,2945	no	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,58	160,1597,4627	TT,TC,CC		16.8901,11.2752,15.0141	,,benign	,,716/5413	195516305	1917,10851	2133	4251	6384	SO:0001583	missense	4585	exon2			TGGGTGCTGCCTG	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.2146G>A	3.37:g.195516305C>T	ENSP00000417498:p.Ala716Thr	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	129	62	0.48062	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	257	0.11767399267399267	49	0.09959349593495935	34	0.09392265193370165	34	0.05944055944055944	140	0.18469656992084432	-	2.509	-0.313408	0.05422	0.112752	0.168901	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.49139	0.79;0.8	2.61	-5.21	0.02815	.	2.628920	0.01614	N	0.022697	T	0.00073	0.0002	L	0.38175	1.15	0.80722	P	0.0	B;B	0.22080	0.064;0.0	B;B	0.13407	0.009;0.001	T	0.32079	-0.9920	9	0.06757	T	0.87	-1.837	1.2702	0.02019	0.4386:0.1336:0.1094:0.3183	rs3749331;rs17455375;rs3749331	716;721	E7ESK3;Q99102	.;MUC4_HUMAN	T	716;716;690	ENSP00000417498:A716T;ENSP00000420243:A716T	ENSP00000376209:A690T	A	-	1	0	MUC4	197000700	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.260000	0.00536	-3.912000	0.00092	-0.273000	0.10243	GCA	C|0.881;T|0.119	0.119	strong		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PCDHGA3	56112	hgsc.bcm.edu	37	5	140725828	140725828	+	Missense_Mutation	SNP	C	C	T	rs7736541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140725828C>T	ENST00000253812.6	+	1	2228	c.2228C>T	c.(2227-2229)gCg>gTg	p.A743V	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	743			A -> V (in dbSNP:rs7736541).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTGTGGGCGCGGACGGGGTT	0.667													.|||	2709	0.540935	0.8495	0.6297	5008	,	,		13856	0.3264		0.4274	False		,,,				2504	0.3988				p.A743V		Atlas-SNP	.											.	PCDHGA3	246	.	0			c.C2228T						PASS	.	T	,,VAL/ALA,VAL/ALA	3497,909		1397,703,103	49.0	60.0	56.0		,,2228,2228	4.1	1.0	5	dbSNP_116	56	3761,4839		808,2145,1347	no	intron,intron,missense,missense	PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_032011.1	,,64,64	2205,2848,1450	TT,TC,CC		43.7326,20.631,44.195	,,,	,,743/933,743/830	140725828	7258,5748	2203	4300	6503	SO:0001583	missense	56112	exon1			TGGGCGCGGACGG	AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.2228C>T	5.37:g.140725828C>T	ENSP00000253812:p.Ala743Val	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	161	161	1	NM_032011	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	1148	0.5256410256410257	394	0.8008130081300813	220	0.6077348066298343	193	0.3374125874125874	341	0.449868073878628	.	4.381	0.070226	0.08436	0.79369	0.437326	ENSG00000254245	ENST00000253812	T	0.41400	1.0	5.33	4.14	0.48551	.	0.467918	0.13384	N	0.391917	T	0.00012	0.0000	N	0.00006	-3.215	0.48762	P	2.9599999999996296E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.42498	-0.9448	9	0.02654	T	1	.	5.5632	0.17157	0.2648:0.0722:0.0:0.663	rs7736541;rs59073584	743;743	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	V	743	ENSP00000253812:A743V	ENSP00000253812:A743V	A	+	2	0	PCDHGA3	140706012	0.003000	0.15002	0.983000	0.44433	0.605000	0.37080	0.472000	0.22116	0.399000	0.25367	-0.360000	0.07572	GCG	C|0.492;T|0.508	0.508	strong		0.667	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1	NM_018916	
AXDND1	126859	hgsc.bcm.edu	37	1	179414105	179414105	+	Splice_Site	SNP	A	A	C	rs11577579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:179414105A>C	ENST00000367618.3	+	16	1951	c.1564A>C	c.(1564-1566)Atc>Ctc	p.I522L	AXDND1_ENST00000457238.2_Splice_Site_p.I522L|AXDND1_ENST00000461179.2_3'UTR	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	522			I -> L (in dbSNP:rs11577579).					p.I522L(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						CACTCTTTAGATCCTGAATGA	0.363													A|||	1066	0.212859	0.2882	0.2435	5008	,	,		14591	0.0526		0.2783	False		,,,				2504	0.1871				p.I522L		Atlas-SNP	.											AXDND1,NS,carcinoma,0,1	AXDND1	142	1	1	Substitution - Missense(1)	stomach(1)	c.A1564C						PASS	.	A	LEU/ILE	1234,3168	407.5+/-334.3	161,912,1128	56.0	58.0	57.0		1564	0.6	0.1	1	dbSNP_120	57	2638,5960	419.7+/-353.2	419,1800,2080	yes	missense-near-splice	AXDND1	NM_144696.4	5	580,2712,3208	CC,CA,AA		30.6816,28.0327,29.7846	benign	522/1013	179414105	3872,9128	2201	4299	6500	SO:0001630	splice_region_variant	126859	exon16			CTTTAGATCCTGA	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.1564-1A>C	1.37:g.179414105A>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	457	0.20924908424908426	122	0.24796747967479674	87	0.24033149171270718	30	0.05244755244755245	218	0.287598944591029	A	11.39	1.624894	0.28889	0.280327	0.306816	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000457238;ENST00000434088	T;T;T	0.42900	2.27;0.96;2.27	5.65	0.62	0.17637	.	0.593638	0.20303	N	0.094986	T	0.00012	0.0000	N	0.14661	0.345	0.48236	P	3.8199999999999346E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.43877	-0.9364	8	.	.	.	-10.7028	7.962	0.30076	0.6445:0.0:0.3555:0.0	rs11577579;rs52791405;rs57477380;rs11577579	480;522;522	E9PCJ4;Q5T1B0;F5GWM2	.;AXDN1_HUMAN;.	L	522;480;522;456	ENSP00000356590:I522L;ENSP00000416712:I522L;ENSP00000391716:I456L	.	I	+	1	0	AXDND1	177680728	0.053000	0.20554	0.102000	0.21198	0.008000	0.06430	-0.036000	0.12185	-0.068000	0.12953	-0.384000	0.06662	ATC	A|0.748;C|0.252	0.252	strong		0.363	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	Missense_Mutation
DOPEY2	9980	hgsc.bcm.edu	37	21	37617724	37617724	+	Missense_Mutation	SNP	C	C	A	rs3746866	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:37617724C>A	ENST00000399151.3	+	19	3531	c.3446C>A	c.(3445-3447)cCc>cAc	p.P1149H		NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	1149			P -> H (in dbSNP:rs3746866). {ECO:0000269|PubMed:10950924}.		cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GCACCCATCCCCATGGGGGGC	0.642													C|||	859	0.171526	0.112	0.1383	5008	,	,		11419	0.2262		0.1372	False		,,,				2504	0.2546				p.P1149H		Atlas-SNP	.											DOPEY2,NS,carcinoma,0,1	DOPEY2	184	1	0			c.C3446A						PASS	.	C	HIS/PRO	477,3929	217.8+/-236.0	26,425,1752	80.0	64.0	70.0		3446	3.8	0.7	21	dbSNP_107	70	1126,7474	227.2+/-262.7	80,966,3254	yes	missense	DOPEY2	NM_005128.2	77	106,1391,5006	AA,AC,CC		13.093,10.8261,12.3251	benign	1149/2299	37617724	1603,11403	2203	4300	6503	SO:0001583	missense	9980	exon19			CCATCCCCATGGG	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.3446C>A	21.37:g.37617724C>A	ENSP00000382104:p.Pro1149His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Missense_Mutation	SNP	ENST00000399151.3	37	CCDS13643.1	356	0.163003663003663	62	0.12601626016260162	47	0.1298342541436464	138	0.24125874125874125	109	0.1437994722955145	C	9.478	1.097311	0.20552	0.108261	0.13093	ENSG00000142197	ENST00000399151	T	0.39406	1.08	4.7	3.81	0.43845	.	0.546294	0.18501	N	0.139358	T	0.00012	0.0000	L	0.43152	1.355	0.31879	P	0.6187	D;B	0.53885	0.963;0.001	P;B	0.46479	0.518;0.001	T	0.11203	-1.0597	9	0.51188	T	0.08	.	10.9834	0.47508	0.0:0.9128:0.0:0.0872	rs3746866;rs61483860;rs3746866	1149;1149	Q9Y3R5-2;Q9Y3R5	.;DOP2_HUMAN	H	1149	ENSP00000382104:P1149H	ENSP00000382104:P1149H	P	+	2	0	DOPEY2	36539594	0.447000	0.25673	0.739000	0.30968	0.295000	0.27426	4.235000	0.58666	1.341000	0.45600	0.650000	0.86243	CCC	C|0.859;A|0.141	0.141	strong		0.642	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
SCIN	85477	hgsc.bcm.edu	37	7	12610451	12610451	+	Silent	SNP	G	G	A	rs76096341	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:12610451G>A	ENST00000297029.5	+	1	140	c.39G>A	c.(37-39)gcG>gcA	p.A13A	AC005281.2_ENST00000433040.1_RNA	NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	13	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)		TCGCCCGGGCGGGCAAGCAGG	0.652													G|||	115	0.0229633	0.0045	0.0317	5008	,	,		15575	0.0		0.0696	False		,,,				2504	0.0174				p.A13A		Atlas-SNP	.											.	SCIN	105	.	0			c.G39A						PASS	.	G		22,1360		0,22,669	17.0	27.0	24.0		39	-7.9	0.1	7	dbSNP_132	24	149,3031		5,139,1446	no	coding-synonymous	SCIN	NM_001112706.2		5,161,2115	AA,AG,GG		4.6855,1.5919,3.7484		13/716	12610451	171,4391	691	1590	2281	SO:0001819	synonymous_variant	85477	exon1			CCGGGCGGGCAAG	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.39G>A	7.37:g.12610451G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Silent	SNP	ENST00000297029.5	37	CCDS47545.1																																																																																			G|0.970;A|0.030	0.030	strong		0.652	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128	
FLNC	2318	hgsc.bcm.edu	37	7	128488734	128488734	+	Missense_Mutation	SNP	G	G	A	rs2291569	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128488734G>A	ENST00000325888.8	+	27	4961	c.4700G>A	c.(4699-4701)cGg>cAg	p.R1567Q	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Missense_Mutation_p.R1567Q	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1567			R -> Q (in dbSNP:rs2291569).		cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						ATCGACGCACGGGACGCGGGC	0.662													G|||	313	0.0625	0.0106	0.0447	5008	,	,		15225	0.1111		0.0765	False		,,,				2504	0.0808				p.R1567Q		Atlas-SNP	.											.	FLNC	339	.	0			c.G4700A						PASS	.	G	GLN/ARG,GLN/ARG	102,4070		1,100,1985	105.0	116.0	112.0		4700,4700	5.1	1.0	7	dbSNP_100	112	716,7706		28,660,3523	yes	missense,missense	FLNC	NM_001127487.1,NM_001458.4	43,43	29,760,5508	AA,AG,GG		8.5015,2.4449,6.4952	possibly-damaging,possibly-damaging	1567/2693,1567/2726	128488734	818,11776	2086	4211	6297	SO:0001583	missense	2318	exon27			ACGCACGGGACGC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.4700G>A	7.37:g.128488734G>A	ENSP00000327145:p.Arg1567Gln	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	154	0.07051282051282051	7	0.014227642276422764	19	0.052486187845303865	64	0.11188811188811189	64	0.08443271767810026	G	16.99	3.273010	0.59649	0.024449	0.085015	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.86164	-2.08;-2.08	5.09	5.09	0.68999	Immunoglobulin E-set (1);Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.33904	0.0879	M	0.89968	3.075	0.22066	P	0.999382205	D;P	0.89917	1.0;0.907	D;P	0.85130	0.997;0.547	T	0.71185	-0.4667	9	0.51188	T	0.08	.	12.7242	0.57162	0.0868:0.0:0.9132:0.0	rs2291569;rs17477492	1567;1567	Q14315-2;Q14315	.;FLNC_HUMAN	Q	1567	ENSP00000327145:R1567Q;ENSP00000344002:R1567Q	ENSP00000327145:R1567Q	R	+	2	0	FLNC	128275970	0.436000	0.25586	0.995000	0.50966	0.033000	0.12548	3.398000	0.52579	2.513000	0.84729	0.655000	0.94253	CGG	G|0.921;A|0.079	0.079	strong		0.662	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
ACSS3	79611	hgsc.bcm.edu	37	12	81627238	81627238	+	Silent	SNP	C	C	T	rs1921038	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:81627238C>T	ENST00000548058.1	+	13	2617	c.1707C>T	c.(1705-1707)ggC>ggT	p.G569G	ACSS3_ENST00000548324.1_Silent_p.G251G|ACSS3_ENST00000261206.3_Silent_p.G568G			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	569						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						TTTCTGCAGGCGCCATTGAAG	0.393													T|||	886	0.176917	0.1029	0.1801	5008	,	,		18410	0.2321		0.2207	False		,,,				2504	0.1728				p.G569G		Atlas-SNP	.											.	ACSS3	118	.	0			c.C1707T						PASS	.	T		539,3867	776.8+/-414.2	35,469,1699	199.0	195.0	197.0		1707	-1.2	1.0	12	dbSNP_92	197	1833,6767	731.2+/-406.8	207,1419,2674	no	coding-synonymous	ACSS3	NM_024560.2		242,1888,4373	TT,TC,CC		21.314,12.2333,18.2377		569/687	81627238	2372,10634	2203	4300	6503	SO:0001819	synonymous_variant	79611	exon13			TGCAGGCGCCATT		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1707C>T	12.37:g.81627238C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	132	49	0.371212	NM_024560	Q8NC66	Silent	SNP	ENST00000548058.1	37	CCDS9022.1																																																																																			C|0.811;T|0.189	0.189	strong		0.393	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	
MUC7	4589	hgsc.bcm.edu	37	4	71346978	71346978	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71346978T>C	ENST00000304887.5	+	3	707	c.517T>C	c.(517-519)Tct>Cct	p.S173P	MUC7_ENST00000413702.1_Missense_Mutation_p.S173P|MUC7_ENST00000456088.1_Missense_Mutation_p.S173P|MUC7_ENST00000514512.1_3'UTR	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	173	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.S173P(3)		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	0.522																																					p.S173P		Atlas-SNP	.											MUC7,NS,carcinoma,0,5	MUC7	91	5	3	Substitution - Missense(3)	lung(2)|kidney(1)	c.T517C						scavenged	.						341.0	284.0	303.0					4																	71346978		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.517T>C	4.37:g.71346978T>C	ENSP00000302021:p.Ser173Pro	Somatic	314	4	0.0127389		WXS	Illumina HiSeq	Phase_I	359	4	0.0111421	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	T	8.294	0.818323	0.16607	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.52754	0.65;0.65;0.65	2.59	-1.83	0.07833	.	.	.	.	.	T	0.22360	0.0539	N	0.12182	0.205	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.19451	-1.0305	8	.	.	.	-1.8981	3.858	0.08984	0.0:0.2646:0.3931:0.3423	.	173	Q8TAX7	MUC7_HUMAN	P	173	ENSP00000407422:S173P;ENSP00000400585:S173P;ENSP00000302021:S173P	.	S	+	1	0	MUC7	71381567	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.097000	0.01348	-0.350000	0.08262	-0.605000	0.04089	TCT	.	.	none		0.522	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
KRT6B	3854	hgsc.bcm.edu	37	12	52845801	52845801	+	Missense_Mutation	SNP	T	T	C	rs428894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52845801T>C	ENST00000252252.3	-	1	109	c.62A>G	c.(61-63)aAc>aGc	p.N21S		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	21	Head.		N -> S (in dbSNP:rs428894). {ECO:0000269|PubMed:2410904, ECO:0000269|PubMed:7543104}.		ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CCTGGCTGAGTTGGCACTGAA	0.647																																					p.N21S		Atlas-SNP	.											.	KRT6B	90	.	0			c.A62G						PASS	.						14.0	16.0	15.0					12																	52845801		2180	4233	6413	SO:0001583	missense	3854	exon1			GCTGAGTTGGCAC	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.62A>G	12.37:g.52845801T>C	ENSP00000252252:p.Asn21Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	179	68	0.379888	NM_005555	P48669	Missense_Mutation	SNP	ENST00000252252.3	37	CCDS8828.1	1323	0.6057692307692307	240	0.4878048780487805	233	0.643646408839779	413	0.722027972027972	437	0.5765171503957783	C	5.203	0.222893	0.09863	.	.	ENSG00000185479	ENST00000252252;ENST00000544607	T	0.74947	-0.89	2.98	2.98	0.34508	.	0.755412	0.12892	N	0.430493	T	0.00012	0.0000	N	0.01761	-0.735	0.54753	P	1.4999999999987246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.44003	-0.9356	9	0.12430	T	0.62	.	6.1872	0.20503	0.0:0.5101:0.3697:0.1202	rs428894;rs1053681;rs3809177;rs4083307;rs4761915;rs17099820;rs59601513	21	P04259	K2C6B_HUMAN	S	21	ENSP00000252252:N21S	ENSP00000252252:N21S	N	-	2	0	KRT6B	51132068	0.065000	0.20965	0.911000	0.35937	0.615000	0.37417	0.318000	0.19504	0.849000	0.35215	-0.711000	0.03637	AAC	T|0.417;C|0.583	0.583	strong		0.647	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
PRG3	10394	hgsc.bcm.edu	37	11	57146202	57146202	+	Silent	SNP	G	G	A	rs1940145	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57146202G>A	ENST00000287143.2	-	4	568	c.459C>T	c.(457-459)agC>agT	p.S153S		NM_006093.3	NP_006084.2	Q8TBJ4	LPPR1_HUMAN	proteoglycan 3	0					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)			large_intestine(3)|lung(5)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	13						GGTTGACTGTGCTAGTGCAGC	0.493													G|||	94	0.01877	0.0023	0.0288	5008	,	,		19071	0.0		0.0497	False		,,,				2504	0.0215				p.S153S	Melanoma(154;1456 2519 19358 45229)	Atlas-SNP	.											.	PRG3	35	.	0			c.C459T						PASS	.	G		44,4358	46.7+/-81.2	1,42,2158	262.0	248.0	253.0		459	-10.5	0.0	11	dbSNP_92	253	434,8158	133.3+/-190.8	7,420,3869	no	coding-synonymous	PRG3	NM_006093.3		8,462,6027	AA,AG,GG		5.0512,0.9995,3.6786		153/226	57146202	478,12516	2201	4296	6497	SO:0001819	synonymous_variant	10394	exon4			GACTGTGCTAGTG	AF132209	CCDS7954.1	11q12.1	2008-02-05			ENSG00000156575	ENSG00000156575			9363	protein-coding gene	gene with protein product		606814				10318872, 11170744	Standard	NM_006093		Approved	MBPH	uc001njv.2	Q9Y2Y8	OTTHUMG00000167026	ENST00000287143.2:c.459C>T	11.37:g.57146202G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	52	0.641975	NM_006093	Q5VX23|Q9NXE2	Silent	SNP	ENST00000287143.2	37	CCDS7954.1																																																																																			G|0.966;A|0.034	0.034	strong		0.493	PRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392467.1	NM_006093	
UBQLN1	29979	hgsc.bcm.edu	37	9	86278913	86278913	+	Silent	SNP	C	C	T	rs2781004	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:86278913C>T	ENST00000376395.4	-	10	2017	c.1494G>A	c.(1492-1494)tcG>tcA	p.S498S	UBQLN1_ENST00000257468.7_Silent_p.S470S	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	498					cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)			breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						CATTAGTTCCCGAAGAGCCTC	0.488													C|||	481	0.0960463	0.0189	0.1239	5008	,	,		17736	0.0337		0.1869	False		,,,				2504	0.1513				p.S498S	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.G1494A						PASS	.	C	,	181,4225	116.7+/-154.6	7,167,2029	185.0	166.0	173.0		1494,1410	-3.4	1.0	9	dbSNP_100	173	1590,7010	296.9+/-303.1	138,1314,2848	no	coding-synonymous,coding-synonymous	UBQLN1	NM_013438.4,NM_053067.2	,	145,1481,4877	TT,TC,CC		18.4884,4.108,13.6168	,	498/590,470/562	86278913	1771,11235	2203	4300	6503	SO:0001819	synonymous_variant	29979	exon10			AGTTCCCGAAGAG	AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1494G>A	9.37:g.86278913C>T		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	156	77	0.49359	NM_013438	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	37	CCDS6663.1	207	0.09478021978021978	10	0.02032520325203252	56	0.15469613259668508	12	0.02097902097902098	129	0.17018469656992086	C	9.772	1.173046	0.21704	0.04108	0.184884	ENSG00000135018	ENST00000526134	.	.	.	5.93	-3.42	0.04825	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.28364	-1.0046	3	.	.	.	.	0.809	0.01089	0.3018:0.1198:0.2074:0.371	rs2781004	.	.	.	Q	105	.	.	R	-	2	0	UBQLN1	85468733	0.999000	0.42202	0.954000	0.39281	0.857000	0.48899	0.386000	0.20702	-0.444000	0.07170	-0.238000	0.12139	CGG	C|0.873;T|0.127	0.127	strong		0.488	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438	
FAM109B	150368	hgsc.bcm.edu	37	22	42473860	42473860	+	Missense_Mutation	SNP	C	C	G	rs1807493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:42473860C>G	ENST00000321753.3	+	3	750	c.563C>G	c.(562-564)gCg>gGg	p.A188G	SMDT1_ENST00000331479.3_5'Flank|snoU13_ENST00000458891.1_RNA	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	188			A -> G (in dbSNP:rs1807493). {ECO:0000269|PubMed:15489334}.		endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						GTTGAAGAAGCGGGCAGCAGG	0.667													C|||	808	0.161342	0.0484	0.2363	5008	,	,		17874	0.1101		0.2396	False		,,,				2504	0.2331				p.A188G		Atlas-SNP	.											.	FAM109B	22	.	0			c.C563G						PASS	.	C	GLY/ALA	308,4096		14,280,1908	28.0	29.0	29.0		563	-2.4	0.0	22	dbSNP_92	29	1915,6685		246,1423,2631	yes	missense	FAM109B	NM_001002034.2	60	260,1703,4539	GG,GC,CC		22.2674,6.9936,17.0947	benign	188/260	42473860	2223,10781	2202	4300	6502	SO:0001583	missense	150368	exon3			AAGAAGCGGGCAG	BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"""Pleckstrin homology (PH) domain containing"""	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.563C>G	22.37:g.42473860C>G	ENSP00000312753:p.Ala188Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	50	26	0.52	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	367	0.16804029304029305	28	0.056910569105691054	78	0.2154696132596685	78	0.13636363636363635	183	0.24142480211081793	C	0.005	-2.164310	0.00318	0.069936	0.222674	ENSG00000177096	ENST00000321753	T	0.42513	0.97	4.37	-2.38	0.06622	.	1.543610	0.05328	N	0.527815	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	0.23226	-1.0194	9	0.17369	T	0.5	-8.7261	2.597	0.04856	0.1219:0.3229:0.3358:0.2193	rs1807493;rs17845905;rs17858880	188	Q6ICB4	SESQ2_HUMAN	G	188	ENSP00000312753:A188G	ENSP00000312753:A188G	A	+	2	0	FAM109B	40803806	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.591000	0.05753	-0.397000	0.07691	-4.145000	0.00010	GCG	C|0.837;G|0.163	0.163	strong		0.667	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
BRSK1	84446	hgsc.bcm.edu	37	19	55817694	55817694	+	Silent	SNP	C	C	T	rs200320831		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55817694C>T	ENST00000309383.1	+	17	2242	c.1965C>T	c.(1963-1965)tcC>tcT	p.S655S	BRSK1_ENST00000326848.7_Silent_p.S350S|BRSK1_ENST00000590333.1_Silent_p.S671S	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	655					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.S655S(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		GCGGCCCCTCCGTCTTCCAAA	0.637																																					p.S655S		Atlas-SNP	.											BRSK1_ENST00000309383,NS,carcinoma,0,2	BRSK1	192	2	2	Substitution - coding silent(2)	endometrium(2)	c.C1965T						PASS	.						59.0	58.0	58.0					19																	55817694		2203	4300	6503	SO:0001819	synonymous_variant	84446	exon17			CCCCTCCGTCTTC	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1965C>T	19.37:g.55817694C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.999;T|0.001	0.001	weak		0.637	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
TNRC18	84629	hgsc.bcm.edu	37	7	5353253	5353253	+	Silent	SNP	G	G	T	rs140781391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5353253G>T	ENST00000430969.1	-	27	7617	c.7269C>A	c.(7267-7269)gcC>gcA	p.A2423A	TNRC18_ENST00000399537.4_Silent_p.A2423A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2423	Pro-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGGGTGCTGGGGCCAGGGAGG	0.731													G|||	449	0.0896565	0.062	0.1758	5008	,	,		12013	0.0605		0.1034	False		,,,				2504	0.0818				p.A2423A		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7269A						PASS	.	G		203,2919		10,183,1368	11.0	12.0	11.0		7269	2.4	0.3	7	dbSNP_134	11	767,6389		35,697,2846	no	coding-synonymous	TNRC18	NM_001080495.2		45,880,4214	TT,TG,GG		10.7183,6.5022,9.4376		2423/2969	5353253	970,9308	1561	3578	5139	SO:0001819	synonymous_variant	84629	exon27			TGCTGGGGCCAGG	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.7269C>A	7.37:g.5353253G>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1	203	0.09294871794871795	34	0.06910569105691057	51	0.1408839779005525	33	0.057692307692307696	85	0.11213720316622691	g	0.025	-1.377010	0.01214	0.065022	0.107183	ENSG00000182095	ENST00000328270	.	.	.	3.33	2.43	0.29744	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.46185	P	0.0010879999999999779	.	.	.	.	.	.	T	0.09357	-1.0678	3	.	.	.	.	5.1903	0.15207	0.1266:0.2132:0.6602:0.0	.	.	.	.	T	237	.	.	P	-	1	0	TNRC18	5319779	0.770000	0.28543	0.332000	0.25469	0.057000	0.15508	0.143000	0.16115	0.682000	0.31407	0.313000	0.20887	CCC	G|0.907;T|0.093	0.093	strong		0.731	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
GABBR1	2550	hgsc.bcm.edu	37	6	29581113	29581113	+	Silent	SNP	A	A	G	rs17854216	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29581113A>G	ENST00000377034.4	-	12	1808	c.1473T>C	c.(1471-1473)tcT>tcC	p.S491S	GABBR1_ENST00000355973.3_Silent_p.S374S|GABBR1_ENST00000377012.4_Silent_p.S374S|GABBR1_ENST00000377016.4_Silent_p.S429S|GABBR1_ENST00000376977.3_Silent_p.S491S	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	491					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	GGCGCACACCAGAACGGCCGC	0.567													G|||	545	0.108826	0.0946	0.0807	5008	,	,		17576	0.122		0.0974	False		,,,				2504	0.1462				p.S491S		Atlas-SNP	.											.	GABBR1	95	.	0			c.T1473C						PASS	.	G	,,	272,2750		10,252,1249	106.0	116.0	112.0		1473,1122,1287	-11.7	0.0	6	dbSNP_123	112	561,4855		35,491,2182	no	coding-synonymous,coding-synonymous,coding-synonymous	GABBR1	NM_001470.2,NM_021903.2,NM_021904.2	,,	45,743,3431	GG,GA,AA		10.3582,9.0007,9.872	,,	491/962,374/845,429/900	29581113	833,7605	1511	2708	4219	SO:0001819	synonymous_variant	2550	exon12			CACACCAGAACGG	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4070	protein-coding gene	gene with protein product	"""GABA-B receptor"""	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1473T>C	6.37:g.29581113A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1																																																																																			A|0.900;G|0.100	0.100	strong		0.567	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3		
GGNBP2	79893	hgsc.bcm.edu	37	17	34942595	34942595	+	Silent	SNP	G	G	A	rs376057009|rs1106908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:34942595G>A	ENST00000304718.4	+	12	1924	c.1608G>A	c.(1606-1608)aaG>aaA	p.K536K		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	536					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)		p.K536K(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)	38		Breast(25;0.00957)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0193)		AAAAGAAGAAGAAGAAAAGCA	0.358													A|||	1704	0.340256	0.2451	0.3357	5008	,	,		21411	0.372		0.4453	False		,,,				2504	0.3313				p.K536K		Atlas-SNP	.											GGNBP2,NS,carcinoma,0,1	GGNBP2	72	1	1	Substitution - coding silent(1)	stomach(1)	c.G1608A						scavenged	.	A		1214,3192	705.6+/-407.3	174,866,1163	76.0	79.0	78.0		1608	5.6	1.0	17	dbSNP_86	78	3893,4707	605.7+/-395.0	880,2133,1287	no	coding-synonymous	GGNBP2	NM_024835.3		1054,2999,2450	AA,AG,GG		45.2674,27.5533,39.2665		536/698	34942595	5107,7899	2203	4300	6503	SO:0001819	synonymous_variant	79893	exon12			GAAGAAGAAGAAA	AF126964	CCDS11314.1	17q21.1	2014-05-06	2007-08-20	2007-08-20	ENSG00000005955	ENSG00000278311			19357	protein-coding gene	gene with protein product		612275	"""zinc finger protein 403"""	ZNF403		11728448	Standard	NM_024835		Approved	ZFP403, LZK1, FLJ22561, FLJ21230, DIF-3, DIF3	uc002hnb.3	Q9H3C7	OTTHUMG00000188440	ENST00000304718.4:c.1608G>A	17.37:g.34942595G>A		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Silent	SNP	ENST00000304718.4	37	CCDS11314.1																																																																																			G|0.613;A|0.387	0.387	strong		0.358	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835	
KRT35	3886	hgsc.bcm.edu	37	17	39637244	39637244	+	Missense_Mutation	SNP	A	A	G	rs743686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39637244A>G	ENST00000393989.1	-	1	148	c.106T>C	c.(106-108)Tct>Cct	p.S36P	KRT35_ENST00000246639.2_Missense_Mutation_p.S6P	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	36	Head.|Poly-Ser.		S -> P (in dbSNP:rs743686). {ECO:0000269|PubMed:8823373}.		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)				AGCTTGCAAGAGCTGCTGGAG	0.607													A|||	2877	0.574481	0.7352	0.5591	5008	,	,		14411	0.3333		0.5398	False		,,,				2504	0.6524				p.S36P		Atlas-SNP	.											KRT35,colon,carcinoma,+1,1	KRT35	58	1	0			c.T106C						PASS	.	A	PRO/SER	2867,1177		1002,863,157	54.0	63.0	60.0		106	5.3	1.0	17	dbSNP_86	60	4604,3794		1250,2104,845	yes	missense	KRT35	NM_002280.4	74	2252,2967,1002	GG,GA,AA		45.1774,29.1048,39.9534	probably-damaging	36/456	39637244	7471,4971	2022	4199	6221	SO:0001583	missense	3886	exon1			TGCAAGAGCTGCT	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.106T>C	17.37:g.39637244A>G	ENSP00000377558:p.Ser36Pro	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	31	0.596154	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	CCDS11394.2	1163	0.5325091575091575	363	0.7378048780487805	222	0.6132596685082873	170	0.2972027972027972	408	0.5382585751978892	A	16.84	3.234991	0.58886	0.708952	0.548226	ENSG00000197079	ENST00000246639;ENST00000393989	D;D	0.82255	-1.58;-1.59	5.31	5.31	0.75309	.	0.338199	0.26058	N	0.026597	T	0.00012	0.0000	M	0.69358	2.11	0.33048	P	0.46760599999999997	D	0.76494	0.999	D	0.65233	0.933	T	0.52793	-0.8528	9	0.52906	T	0.07	.	9.1168	0.36762	0.9196:0.0:0.0804:0.0	rs743686;rs17495901;rs52830500;rs57843904;rs743686	36	Q92764	KRT35_HUMAN	P	6;36	ENSP00000246639:S6P;ENSP00000377558:S36P	ENSP00000246639:S6P	S	-	1	0	KRT35	36890770	0.119000	0.22226	0.998000	0.56505	0.628000	0.37860	0.577000	0.23758	2.231000	0.72958	0.460000	0.39030	TCT	A|0.450;G|0.549	0.549	strong		0.607	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
MRPL44	65080	hgsc.bcm.edu	37	2	224824617	224824617	+	Silent	SNP	A	A	G	rs11546405	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:224824617A>G	ENST00000258383.3	+	2	615	c.546A>G	c.(544-546)gaA>gaG	p.E182E		NM_022915.3	NP_075066.1	Q9H9J2	RM44_HUMAN	mitochondrial ribosomal protein L44	182	RNase III.				mitochondrial translational elongation (GO:0070125)|RNA processing (GO:0006396)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		all_lung(227;0.00679)|Lung NSC(271;0.00855)|Renal(207;0.0112)|all_hematologic(139;0.189)		Epithelial(121;2.51e-10)|all cancers(144;7.89e-08)|Lung(261;0.00705)|LUSC - Lung squamous cell carcinoma(224;0.008)		CACTGAGTGAAGAATTCCCAG	0.478													G|||	243	0.0485224	0.0038	0.0634	5008	,	,		18001	0.002		0.1521	False		,,,				2504	0.0399				p.E182E		Atlas-SNP	.											.	MRPL44	31	.	0			c.A546G						PASS	.	G		116,4290	814.6+/-416.2	0,116,2087	117.0	114.0	115.0		546	-7.3	0.5	2	dbSNP_120	115	1184,7416	763.8+/-407.6	76,1032,3192	yes	coding-synonymous	MRPL44	NM_022915.3		76,1148,5279	GG,GA,AA		13.7674,2.6328,9.9954		182/333	224824617	1300,11706	2203	4300	6503	SO:0001819	synonymous_variant	65080	exon2			GAGTGAAGAATTC	AK022763	CCDS2459.1	2p24.3-p24.1	2012-09-13			ENSG00000135900	ENSG00000135900		"""Mitochondrial ribosomal proteins / large subunits"""	16650	protein-coding gene	gene with protein product	"""39S ribosomal protein L44, mitochondrial"""	611849					Standard	NM_022915		Approved	FLJ12701, FLJ13990	uc002vnr.4	Q9H9J2	OTTHUMG00000133164	ENST00000258383.3:c.546A>G	2.37:g.224824617A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	154	91	0.590909	NM_022915	Q53S16|Q6IA62|Q9H821	Silent	SNP	ENST00000258383.3	37	CCDS2459.1																																																																																			A|0.912;G|0.088	0.088	strong		0.478	MRPL44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256866.2	NM_022915	
OR11H6	122748	hgsc.bcm.edu	37	14	20692188	20692188	+	Missense_Mutation	SNP	T	T	C	rs12891553	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20692188T>C	ENST00000315519.2	+	1	398	c.320T>C	c.(319-321)aTt>aCt	p.I107T		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	107			I -> T (in dbSNP:rs12891553).			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)		CTCTCTGAGATTAAAACCATC	0.408													N|||	1958	0.390974	0.4735	0.3516	5008	,	,		22554	0.2371		0.4781	False		,,,				2504	0.3763				p.I107T		Atlas-SNP	.											.	OR11H6	60	.	0			c.T320C						PASS	.	C	THR/ILE	2256,2150	581.7+/-385.4	610,1036,557	133.0	126.0	129.0		320	2.9	1.0	14	dbSNP_121	129	4158,4442	588.1+/-392.3	997,2164,1139	yes	missense	OR11H6	NM_001004480.1	89	1607,3200,1696	CC,CT,TT		48.3488,48.7971,49.3157	benign	107/331	20692188	6414,6592	2203	4300	6503	SO:0001583	missense	122748	exon1			CTGAGATTAAAAC		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.320T>C	14.37:g.20692188T>C	ENSP00000319071:p.Ile107Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	42	0.446809	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	870	0.3983516483516483	237	0.4817073170731707	135	0.3729281767955801	123	0.21503496503496503	375	0.4947229551451187	C	0.008	-1.933307	0.00488	0.512029	0.483488	ENSG00000176219	ENST00000315519	T	0.01279	5.06	4.77	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.255939	0.27375	N	0.019648	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.27297	-1.0078	9	0.02654	T	1	.	4.8554	0.13557	0.1516:0.6167:0.1467:0.085	rs12891553;rs17211278;rs52838142;rs58124063;rs12891553	107	Q8NGC7	O11H6_HUMAN	T	107	ENSP00000319071:I107T	ENSP00000319071:I107T	I	+	2	0	OR11H6	19762028	0.000000	0.05858	0.991000	0.47740	0.832000	0.47134	-1.010000	0.03656	0.214000	0.20742	-0.432000	0.05891	ATT	T|0.554;C|0.446	0.446	strong		0.408	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
TP53BP1	7158	hgsc.bcm.edu	37	15	43767774	43767774	+	Missense_Mutation	SNP	G	G	C	rs560191	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43767774G>C	ENST00000263801.3	-	9	1311	c.1059C>G	c.(1057-1059)gaC>gaG	p.D353E	TP53BP1_ENST00000450115.2_Missense_Mutation_p.D358E|TP53BP1_ENST00000382039.3_Missense_Mutation_p.D358E|TP53BP1_ENST00000382044.4_Missense_Mutation_p.D358E	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	353			D -> E (in dbSNP:rs560191). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.		cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		TGGAAAGACTGTCCTGAACAA	0.498								Other conserved DNA damage response genes					C|||	2633	0.525759	0.9728	0.3285	5008	,	,		18423	0.3869		0.3032	False		,,,				2504	0.4335				p.D358E		Atlas-SNP	.											.	TP53BP1	157	.	0			c.C1074G	GRCh37	CM067475	TP53BP1	M	rs560191	PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	3740,662	282.5+/-276.6	1594,552,55	98.0	103.0	101.0		1074,1074,1059	2.0	1.0	15	dbSNP_83	101	2604,5992	687.9+/-404.2	385,1834,2079	yes	missense,missense,missense	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	45,45,45	1979,2386,2134	CC,CG,GG		30.2932,15.0386,48.8075	benign,benign,benign	358/1976,358/1978,353/1973	43767774	6344,6654	2201	4298	6499	SO:0001583	missense	7158	exon9			AAGACTGTCCTGA	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.1059C>G	15.37:g.43767774G>C	ENSP00000263801:p.Asp353Glu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	1080	0.4945054945054945	473	0.9613821138211383	124	0.3425414364640884	253	0.4423076923076923	230	0.3034300791556728	C	4.734	0.136511	0.09032	0.849614	0.302932	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115;ENST00000413546	T;T;T;T;T	0.04406	4.33;4.33;4.36;4.33;3.63	5.94	1.95	0.26073	.	0.062172	0.64402	N	0.000007	T	0.00012	0.0000	N	0.00890	-1.11	0.46096	P	0.0011339999999999684	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;0.002	T	0.25710	-1.0124	9	0.02654	T	1	-3.2994	1.3447	0.02161	0.1618:0.4569:0.1413:0.2401	rs560191;rs52834994;rs560191	358;353;358;358	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	E	353;358;358;358;358	ENSP00000263801:D353E;ENSP00000371475:D358E;ENSP00000371470:D358E;ENSP00000393497:D358E;ENSP00000388028:D358E	ENSP00000263801:D353E	D	-	3	2	TP53BP1	41555066	0.998000	0.40836	0.999000	0.59377	0.982000	0.71751	0.226000	0.17776	0.118000	0.18165	-0.127000	0.14921	GAC	G|0.501;C|0.499	0.499	strong		0.498	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
NDFIP2	54602	hgsc.bcm.edu	37	13	80095030	80095030	+	Missense_Mutation	SNP	C	C	T	rs11549502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:80095030C>T	ENST00000218652.7	+	2	459	c.407C>T	c.(406-408)gCg>gTg	p.A136V	NDFIP2_ENST00000494647.1_3'UTR	NM_001161407.1|NM_019080.2	NP_001154879.1|NP_061953.2	Q9NV92	NFIP2_HUMAN	Nedd4 family interacting protein 2	136			A -> V (in dbSNP:rs11549502). {ECO:0000269|PubMed:10574461, ECO:0000269|PubMed:12761501, ECO:0000269|PubMed:15489334}.		negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of transporter activity (GO:0032410)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			NS(1)|breast(1)|endometrium(2)|kidney(3)|lung(3)|ovary(2)|prostate(1)|skin(1)	14		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)		GTGCAGGCTGCGTCTTCAGCA	0.443													C|||	307	0.0613019	0.0287	0.0749	5008	,	,		15400	0.0		0.1223	False		,,,				2504	0.0961				p.A136V		Atlas-SNP	.											NDFIP2,NS,carcinoma,-1,1	NDFIP2	23	1	0			c.C407T						PASS	.	C	VAL/ALA,VAL/ALA	211,4195	130.2+/-166.9	7,197,1999	102.0	92.0	95.0		407,407	1.9	0.0	13	dbSNP_120	95	1175,7425	239.6+/-270.6	80,1015,3205	yes	missense,missense	NDFIP2	NM_001161407.1,NM_019080.2	64,64	87,1212,5204	TT,TC,CC		13.6628,4.7889,10.6566	benign,benign	136/317,136/337	80095030	1386,11620	2203	4300	6503	SO:0001583	missense	54602	exon2			AGGCTGCGTCTTC	AB032991	CCDS31998.1	13q22.1	2011-05-18			ENSG00000102471	ENSG00000102471			18537	protein-coding gene	gene with protein product		610041				10574461, 12050153	Standard	NM_019080		Approved	KIAA1165, N4wbp5a	uc001vlf.3	Q9NV92	OTTHUMG00000017136	ENST00000218652.7:c.407C>T	13.37:g.80095030C>T	ENSP00000218652:p.Ala136Val	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	131	65	0.496183	NM_019080	Q7Z2H3|Q7Z428|Q8TAR3|Q9ULQ5	Missense_Mutation	SNP	ENST00000218652.7	37	CCDS31998.1	149	0.06822344322344322	17	0.034552845528455285	35	0.09668508287292818	0	0.0	97	0.1279683377308707	C	9.329	1.059920	0.19987	0.047889	0.136628	ENSG00000102471	ENST00000218652;ENST00000487865	T;T	0.33654	1.4;1.46	5.75	1.86	0.25419	.	0.719210	0.14146	N	0.338351	T	0.00178	0.0005	L	0.43152	1.355	0.80722	P	0.0	B;P	0.34892	0.24;0.474	B;B	0.23716	0.048;0.038	T	0.07597	-1.0764	9	0.35671	T	0.21	4.0E-4	7.5368	0.27714	0.0:0.5994:0.2558:0.1448	rs11549502;rs17852355;rs52798056;rs11549502	42;136	B4DGY6;Q9NV92	.;NFIP2_HUMAN	V	136;53	ENSP00000218652:A136V;ENSP00000419200:A53V	ENSP00000218652:A136V	A	+	2	0	NDFIP2	78993031	0.087000	0.21565	0.001000	0.08648	0.012000	0.07955	2.041000	0.41213	0.335000	0.23614	0.655000	0.94253	GCG	C|0.910;G|0.000;T|0.090	0.090	strong		0.443	NDFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045380.2		
DNAJC25	548645	hgsc.bcm.edu	37	9	114411945	114411945	+	Silent	SNP	G	G	T	rs7019332	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:114411945G>T	ENST00000313525.3	+	3	758	c.702G>T	c.(700-702)ggG>ggT	p.G234G	DNAJC25_ENST00000556107.1_Intron|DNAJC25-GNG10_ENST00000374294.3_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	234						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						ATATAAAGGGGGGCTATCAGA	0.353													G|||	1563	0.312101	0.3517	0.4251	5008	,	,		18464	0.4127		0.2306	False		,,,				2504	0.1585				p.G234G		Atlas-SNP	.											.	DNAJC25	20	.	0			c.G702T						PASS	.	G	,	1147,2465		194,759,853	41.0	42.0	42.0		702,	-0.3	1.0	9	dbSNP_116	42	1718,6410		175,1368,2521	no	coding-synonymous,intron	DNAJC25,DNAJC25-GNG10	NM_001015882.2,NM_004125.3	,	369,2127,3374	TT,TG,GG		21.1368,31.7553,24.4037	,	234/361,	114411945	2865,8875	1806	4064	5870	SO:0001819	synonymous_variant	548645	exon3			AAAGGGGGGCTAT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"""Heat shock proteins / DNAJ (HSP40)"""	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.702G>T	9.37:g.114411945G>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	71	33	0.464789	NM_001015882	Q5QTD8|Q96BN9	Silent	SNP	ENST00000313525.3	37	CCDS43862.1																																																																																			G|0.691;T|0.309	0.309	strong		0.353	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882	
OR6V1	346517	hgsc.bcm.edu	37	7	142749919	142749919	+	Missense_Mutation	SNP	G	G	A	rs28563993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:142749919G>A	ENST00000418316.1	+	1	503	c.482G>A	c.(481-483)cGa>cAa	p.R161Q		NM_001001667.1	NP_001001667.1	Q8N148	OR6V1_HUMAN	olfactory receptor, family 6, subfamily V, member 1	161						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(13)|ovary(1)|upper_aerodigestive_tract(1)	20	Melanoma(164;0.059)					GTCCTCTCCCGAGCTCATCTT	0.562													G|||	263	0.052516	0.1203	0.0418	5008	,	,		21123	0.0		0.0646	False		,,,				2504	0.0102				p.R161Q		Atlas-SNP	.											OR6V1_ENST00000418316,NS,carcinoma,-1,2	OR6V1	77	2	0			c.G482A						PASS	.	G	GLN/ARG	365,3809		15,335,1737	102.0	108.0	106.0		482	-1.8	0.0	7	dbSNP_125	106	485,8011		10,465,3773	yes	missense	OR6V1	NM_001001667.1	43	25,800,5510	AA,AG,GG		5.7086,8.7446,6.7088	possibly-damaging	161/314	142749919	850,11820	2087	4248	6335	SO:0001583	missense	346517	exon1			TCTCCCGAGCTCA		CCDS47728.1	7q34	2014-05-06			ENSG00000225781	ENSG00000225781		"""GPCR / Class A : Olfactory receptors"""	15090	protein-coding gene	gene with protein product						12732197	Standard	NM_001001667		Approved	GPR138	uc011ksv.2	Q8N148	OTTHUMG00000158385	ENST00000418316.1:c.482G>A	7.37:g.142749919G>A	ENSP00000396085:p.Arg161Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	122	67	0.54918	NM_001001667	A4D2I0|B9EH48|Q6IF70	Missense_Mutation	SNP	ENST00000418316.1	37	CCDS47728.1	122	0.055860805860805864	58	0.11788617886178862	17	0.04696132596685083	0	0.0	47	0.06200527704485488	G	11.24	1.580503	0.28180	0.087446	0.057086	ENSG00000225781	ENST00000418316	T	0.00115	8.71	4.72	-1.81	0.07882	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.50943	0.94	B	0.42738	0.396	T	0.03514	-1.1029	8	0.28530	T	0.3	.	5.1535	0.15023	0.523:0.0:0.332:0.145	rs28563993	161	Q8N148	OR6V1_HUMAN	Q	161	ENSP00000396085:R161Q	ENSP00000396085:R161Q	R	+	2	0	OR6V1	142460041	0.000000	0.05858	0.000000	0.03702	0.591000	0.36615	-0.368000	0.07543	-0.105000	0.12132	0.655000	0.94253	CGA	G|0.941;A|0.059	0.059	strong		0.562	OR6V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350860.1		
CYP4F3	4051	hgsc.bcm.edu	37	19	15763721	15763721	+	Silent	SNP	G	G	A	rs1805042	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15763721G>A	ENST00000221307.8	+	9	1121	c.1074G>A	c.(1072-1074)gtG>gtA	p.V358V	CYP4F3_ENST00000585846.1_Silent_p.V358V|CYP4F3_ENST00000591058.1_Silent_p.V358V|CYP4F3_ENST00000586182.2_Silent_p.V358V	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	358					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)	p.V358V(1)		endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						GGCAGGAGGTGCAAGAGCTTC	0.597													.|||	2580	0.515176	0.643	0.5663	5008	,	,		18400	0.6577		0.3509	False		,,,				2504	0.3282				p.V358V		Atlas-SNP	.											CYP4F3,NS,carcinoma,0,1	CYP4F3	69	1	1	Substitution - coding silent(1)	stomach(1)	c.G1074A						PASS	.	G	,,	2626,1780		800,1026,377	110.0	90.0	97.0		1074,1074,1074	0.2	0.6	19	dbSNP_111	97	3046,5554		551,1944,1805	no	coding-synonymous,coding-synonymous,coding-synonymous	CYP4F3	NM_000896.2,NM_001199208.1,NM_001199209.1	,,	1351,2970,2182	AA,AG,GG		35.4186,40.3995,43.6106	,,	358/521,358/521,358/521	15763721	5672,7334	2203	4300	6503	SO:0001819	synonymous_variant	4051	exon9			GGAGGTGCAAGAG	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.1074G>A	19.37:g.15763721G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_001199209	B7Z8Z3|O60634|Q5U740	Silent	SNP	ENST00000221307.8	37	CCDS12332.1																																																																																			G|0.523;A|0.477	0.477	strong		0.597	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896	
C6orf15	29113	hgsc.bcm.edu	37	6	31079371	31079371	+	Silent	SNP	C	C	G	rs2233983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31079371C>G	ENST00000259870.3	-	2	768	c.765G>C	c.(763-765)cgG>cgC	p.R255R		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	255	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						CTCCTGGATACCGATTAATAT	0.527													C|||	521	0.104034	0.0068	0.0994	5008	,	,		16226	0.2361		0.0785	False		,,,				2504	0.1288				p.R255R		Atlas-SNP	.											.	C6orf15	29	.	0			c.G765C						PASS	.	C		52,3420		0,52,1684	56.0	66.0	62.0		765	-4.2	0.0	6	dbSNP_98	62	449,6123		19,411,2856	no	coding-synonymous	C6orf15	NM_014070.2		19,463,4540	GG,GC,CC		6.832,1.4977,4.9881		255/326	31079371	501,9543	1736	3286	5022	SO:0001819	synonymous_variant	29113	exon2			TGGATACCGATTA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.765G>C	6.37:g.31079371C>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	142	63	0.443662	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			C|0.932;G|0.068	0.068	strong		0.527	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
PRB3	5544	hgsc.bcm.edu	37	12	11420563	11420563	+	Missense_Mutation	SNP	G	G	T	rs200902635		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:11420563G>T	ENST00000279573.7	-	3	755	c.620C>A	c.(619-621)cCa>cAa	p.P207Q	PRB3_ENST00000538488.1_Missense_Mutation_p.P186Q|PRB3_ENST00000440870.3_Intron|PRB3_ENST00000381842.3_Intron			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	207	10 X 21 AA tandem repeats of [RH]-P-G-K- P-[EQ]-G-[PQS]-P-[PS]-Q-[GE]-G-N-[QK]- [SP]-[QR]-[GR]-P-P-P.|Pro-rich.		Missing (in allele S).		defense response to Gram-negative bacterium (GO:0050829)	extracellular region (GO:0005576)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(1)|skin(5)	25			OV - Ovarian serous cystadenocarcinoma(49;0.201)			TTGTGGGGGTGGTCCTTCTGG	0.632																																					p.P207Q		Atlas-SNP	.											PRB3_ENST00000538488,NS,carcinoma,0,1	PRB3	84	1	0			c.C620A						scavenged	.						67.0	93.0	85.0					12																	11420563		1603	3645	5248	SO:0001583	missense	5544	exon3			GGGGGTGGTCCTT			12p13.2	2012-10-02				ENSG00000197870			9339	protein-coding gene	gene with protein product		168840				1894623	Standard	NM_006249		Approved	PRG	uc001qzs.3	Q04118		ENST00000279573.7:c.620C>A	12.37:g.11420563G>T	ENSP00000279573:p.Pro207Gln	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	0.001	-3.098522	0.00033	.	.	ENSG00000197870	ENST00000538488	T	0.09445	2.98	1.25	-2.5	0.06384	.	0.000000	0.30302	U	0.009922	T	0.07279	0.0184	.	.	.	0.09310	N	1	B	0.27166	0.17	B	0.17979	0.02	T	0.18335	-1.0340	9	0.59425	D	0.04	.	6.227	0.20714	0.0:0.1573:0.2128:0.6299	.	207	Q04118	PRB3_HUMAN	Q	186	ENSP00000442626:P186Q	ENSP00000279573:P207Q	P	-	2	0	PRB3	11311830	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.685000	0.00834	-3.567000	0.00140	-2.957000	0.00083	CCA	.	.	weak		0.632	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249	
OR1S1	219959	hgsc.bcm.edu	37	11	57982635	57982635	+	Missense_Mutation	SNP	G	G	A	rs143246332	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57982635G>A	ENST00000309433.6	+	1	419	c.419G>A	c.(418-420)tGc>tAc	p.C140Y		NM_001004458.1	NP_001004458.1	Q8NH92	OR1S1_HUMAN	olfactory receptor, family 1, subfamily S, member 1	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)				GTGGCGATCTGCCACCCTCTG	0.453													G|||	33	0.00658946	0.0008	0.0187	5008	,	,		21441	0.0		0.0189	False		,,,				2504	0.0				p.C140Y		Atlas-SNP	.											OR1S1,NS,carcinoma,-1,1	OR1S1	139	1	0			c.G419A						PASS	.	G	TYR/CYS	8,4394	14.3+/-33.2	0,8,2193	178.0	170.0	173.0		419	3.5	1.0	11	dbSNP_134	173	114,8478	60.6+/-122.4	0,114,4182	yes	missense	OR1S1	NM_001004458.1	194	0,122,6375	AA,AG,GG		1.3268,0.1817,0.9389	probably-damaging	140/326	57982635	122,12872	2201	4296	6497	SO:0001583	missense	219959	exon1			CGATCTGCCACCC	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.419G>A	11.37:g.57982635G>A	ENSP00000311688:p.Cys140Tyr	Somatic	269	1	0.00371747		WXS	Illumina HiSeq	Phase_I	287	138	0.480836	NM_001004458	Q6IFG3	Missense_Mutation	SNP	ENST00000309433.6	37	CCDS31546.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	G	17.16	3.318872	0.60524	0.001817	0.013268	ENSG00000172774	ENST00000309433	T	0.34667	1.35	3.45	3.45	0.39498	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000053	T	0.51601	0.1684	M	0.92507	3.315	0.43399	D	0.99552	D	0.89917	1.0	D	0.91635	0.999	T	0.73455	-0.3977	10	0.87932	D	0	.	14.1	0.65049	0.0:0.0:1.0:0.0	.	140	Q8NH92	OR1S1_HUMAN	Y	140	ENSP00000311688:C140Y	ENSP00000311688:C140Y	C	+	2	0	OR1S1	57739211	1.000000	0.71417	1.000000	0.80357	0.598000	0.36846	5.968000	0.70413	1.770000	0.52166	0.479000	0.44913	TGC	G|0.989;A|0.011	0.011	strong		0.453	OR1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394705.1	NM_001004458	
CTSB	1508	hgsc.bcm.edu	37	8	11710888	11710888	+	Missense_Mutation	SNP	G	G	C	rs12338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:11710888G>C	ENST00000353047.6	-	2	329	c.76C>G	c.(76-78)Ctg>Gtg	p.L26V	CTSB_ENST00000530640.2_Missense_Mutation_p.L26V|CTSB_ENST00000534510.1_Missense_Mutation_p.L26V|CTSB_ENST00000453527.2_Missense_Mutation_p.L26V|CTSB_ENST00000533455.1_Missense_Mutation_p.L26V|CTSB_ENST00000531089.1_Missense_Mutation_p.L26V|CTSB_ENST00000415599.2_Missense_Mutation_p.L26V|CTSB_ENST00000434271.1_Missense_Mutation_p.L26V|CTSB_ENST00000525076.1_5'UTR|CTSB_ENST00000345125.3_Missense_Mutation_p.L26V	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	26			L -> V (in dbSNP:rs12338). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3463996}.		cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		TCATCCGACAGGGGATGGAAA	0.597													G|||	1983	0.395966	0.3298	0.3905	5008	,	,		20207	0.5149		0.3827	False		,,,				2504	0.3804				p.L26V		Atlas-SNP	.											.	CTSB	24	.	0			c.C76G	GRCh37	CM066015	CTSB	M	rs12338	PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	1491,2915	476.4+/-357.6	249,993,961	126.0	99.0	108.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	76,76,76,76,76	2.4	0.2	8	dbSNP_52	108	3222,5378	485.5+/-371.6	593,2036,1671	yes	missense,missense,missense,missense,missense	CTSB	NM_001908.3,NM_147780.2,NM_147781.2,NM_147782.2,NM_147783.2	32,32,32,32,32	842,3029,2632	CC,CG,GG		37.4651,33.8402,36.2371	benign,benign,benign,benign,benign	26/340,26/340,26/340,26/340,26/340	11710888	4713,8293	2203	4300	6503	SO:0001583	missense	1508	exon4			CCGACAGGGGATG	M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"""Cathepsins"""	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.76C>G	8.37:g.11710888G>C	ENSP00000345672:p.Leu26Val	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_147780	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	884	0.40476190476190477	163	0.3313008130081301	139	0.3839779005524862	285	0.4982517482517482	297	0.391820580474934	G	13.16	2.154838	0.38021	0.338402	0.374651	ENSG00000164733	ENST00000434271;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000415599;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000534636;ENST00000533572;ENST00000530296;ENST00000526195;ENST00000527243;ENST00000534149;ENST00000526645;ENST00000530573;ENST00000505496;ENST00000524500;ENST00000531502;ENST00000527215;ENST00000532656;ENST00000534382;ENST00000528965;ENST00000524654	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.77489	-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-0.15;-1.1	5.16	2.39	0.29439	Peptidase C1A, propeptide (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.95151	3.63	0.21064	P	0.999794298	B	0.14438	0.01	B	0.17098	0.017	T	0.28364	-1.0046	9	0.72032	D	0.01	.	4.8161	0.13367	0.233:0.0:0.617:0.15	rs12338;rs17572;rs1059863;rs1122181;rs3200720;rs4292649;rs17855419;rs52795645;rs12338	26	P07858	CATB_HUMAN	V	26	ENSP00000415889:L26V;ENSP00000345672:L26V;ENSP00000435105:L26V;ENSP00000433215:L26V;ENSP00000409917:L26V;ENSP00000411254:L26V;ENSP00000342070:L26V;ENSP00000432244:L26V;ENSP00000434217:L26V;ENSP00000436159:L26V;ENSP00000433995:L26V;ENSP00000435074:L26V;ENSP00000436627:L26V;ENSP00000434725:L26V;ENSP00000436122:L26V;ENSP00000431518:L26V;ENSP00000435650:L26V;ENSP00000436074:L26V;ENSP00000435886:L26V;ENSP00000431143:L26V;ENSP00000435260:L26V;ENSP00000433929:L26V;ENSP00000432077:L26V	ENSP00000342070:L26V	L	-	1	2	CTSB	11748297	0.941000	0.31946	0.212000	0.23672	0.642000	0.38348	1.474000	0.35398	0.192000	0.20272	0.462000	0.41574	CTG	G|0.625;C|0.375	0.375	strong		0.597	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780	
EGFR	1956	hgsc.bcm.edu	37	7	55259450	55259450	+	Silent	SNP	C	C	T	rs2229066	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55259450C>T	ENST00000275493.2	+	21	2685	c.2508C>T	c.(2506-2508)cgC>cgT	p.R836R	EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000455089.1_Silent_p.R791R|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Silent_p.R783R	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	836	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	p.R836R(1)		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)	TGGTGCACCGCGACCTGGCAG	0.542		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	27	0.00539137	0.0008	0.0058	5008	,	,		20375	0.0		0.0169	False		,,,				2504	0.0051				p.R836R		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,NS,carcinoma,0,8	EGFR	20426	8	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C2508T						scavenged	.	C		25,4381	31.7+/-61.6	0,25,2178	112.0	97.0	102.0		2508	-11.6	0.0	7	dbSNP_123	102	196,8404	86.9+/-149.2	3,190,4107	no	coding-synonymous	EGFR	NM_005228.3		3,215,6285	TT,TC,CC		2.2791,0.5674,1.6992		836/1211	55259450	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon21	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GCACCGCGACCTG		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.2508C>T	7.37:g.55259450C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	19	3	0.157895	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.986;T|0.014	0.014	strong		0.542	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
OR4K15	81127	hgsc.bcm.edu	37	14	20444026	20444026	+	Missense_Mutation	SNP	T	T	G	rs3861513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20444026T>G	ENST00000305051.5	+	1	424	c.349T>G	c.(349-351)Tct>Gct	p.S117A		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	117			S -> A (in dbSNP:rs3861513). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CAAGACTATTTCTTTTGATGC	0.433													T|||	1093	0.218251	0.2141	0.1715	5008	,	,		22872	0.123		0.2227	False		,,,				2504	0.3507				p.S117A		Atlas-SNP	.											.	OR4K15	82	.	0			c.T349G						PASS	.	T	ALA/SER	1058,3348		122,814,1267	134.0	137.0	136.0		349	3.8	0.8	14	dbSNP_108	136	2283,6313		291,1701,2306	no	missense	OR4K15	NM_001005486.1	99	413,2515,3573	GG,GT,TT		26.5589,24.0127,25.696	probably-damaging	117/349	20444026	3341,9661	2203	4298	6501	SO:0001583	missense	81127	exon1			ACTATTTCTTTTG		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.349T>G	14.37:g.20444026T>G	ENSP00000304077:p.Ser117Ala	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	179	82	0.458101	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	400	0.18315018315018314	95	0.19308943089430894	65	0.17955801104972377	66	0.11538461538461539	174	0.22955145118733508	.	15.40	2.823282	0.50739	0.240127	0.265589	ENSG00000169488	ENST00000305051	T	0.00700	5.82	3.8	3.8	0.43715	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000117	T	0.00012	0.0000	M	0.92459	3.31	0.40068	P	0.024025999999999992	D	0.71674	0.998	P	0.60286	0.872	T	0.31971	-0.9924	9	0.72032	D	0.01	.	10.5358	0.45002	0.0:0.0:0.0:1.0	rs3861513;rs58615739;rs3861513	117	Q8NH41	OR4KF_HUMAN	A	117	ENSP00000304077:S117A	ENSP00000304077:S117A	S	+	1	0	OR4K15	19513866	0.833000	0.29383	0.755000	0.31263	0.388000	0.30384	1.743000	0.38258	1.578000	0.49821	0.477000	0.44152	TCT	T|0.767;G|0.233	0.233	strong		0.433	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
CCDC57	284001	hgsc.bcm.edu	37	17	80159665	80159665	+	Silent	SNP	G	G	A	rs11653797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80159665G>A	ENST00000389641.4	-	2	192	c.156C>T	c.(154-156)tgC>tgT	p.C52C	CCDC57_ENST00000392347.1_Silent_p.C52C|CCDC57_ENST00000392343.3_Silent_p.C52C			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	52										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)			CCTCCTGCAGGCACCGCAGTT	0.672													G|||	556	0.111022	0.0552	0.1268	5008	,	,		17085	0.0565		0.1998	False		,,,				2504	0.1401				p.C52C		Atlas-SNP	.											.	CCDC57	102	.	0			c.C156T						PASS	.	G		406,3868		19,368,1750	50.0	57.0	55.0		156	-0.8	0.5	17	dbSNP_120	55	1893,6617		204,1485,2566	no	coding-synonymous	CCDC57	NM_198082.2		223,1853,4316	AA,AG,GG		22.2444,9.4993,17.9834		52/916	80159665	2299,10485	2137	4255	6392	SO:0001819	synonymous_variant	284001	exon2			CTGCAGGCACCGC	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.156C>T	17.37:g.80159665G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	189	99	0.52381	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				G|0.859;A|0.141	0.141	strong		0.672	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
SPATA17	128153	hgsc.bcm.edu	37	1	217915324	217915324	+	Silent	SNP	C	C	T	rs34347452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:217915324C>T	ENST00000366933.4	+	6	458	c.403C>T	c.(403-405)Ctg>Ttg	p.L135L		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	135						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)		CAGGAAGGCACTGGAGGAGTT	0.383													C|||	632	0.126198	0.0817	0.0951	5008	,	,		21411	0.1419		0.174	False		,,,				2504	0.1431				p.L135L		Atlas-SNP	.											.	SPATA17	59	.	0			c.C403T						PASS	.	C		464,3942	220.4+/-237.8	18,428,1757	99.0	93.0	95.0		403	2.8	0.7	1	dbSNP_126	95	1306,7294	258.1+/-281.9	109,1088,3103	no	coding-synonymous	SPATA17	NM_138796.2		127,1516,4860	TT,TC,CC		15.186,10.5311,13.6091		135/362	217915324	1770,11236	2203	4300	6503	SO:0001819	synonymous_variant	128153	exon6			AAGGCACTGGAGG	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.403C>T	1.37:g.217915324C>T		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	54	34	0.62963	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			C|0.870;T|0.130	0.130	strong		0.383	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
APOBEC3F	200316	hgsc.bcm.edu	37	22	39441197	39441197	+	Silent	SNP	G	G	A	rs200983508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	138	3	0.0217391		WXS	Illumina HiSeq	Phase_I	156	7	0.0448718	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	
FAM205A	259308	hgsc.bcm.edu	37	9	34724796	34724796	+	Missense_Mutation	SNP	T	T	A	rs150496452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34724796T>A	ENST00000378788.3	-	4	2480	c.2441A>T	c.(2440-2442)gAg>gTg	p.E814V		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	814				E -> V (in Ref. 1; BAC86357). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GGGACTAGGCTCCATCTCTGT	0.552													A|||	2018	0.402955	0.0696	0.4049	5008	,	,		19637	0.6181		0.4871	False		,,,				2504	0.544				p.E814V		Atlas-SNP	.											.	FAM205A	45	.	0			c.A2441T						PASS	.	A	VAL/GLU	176,1208		8,160,524	22.0	20.0	21.0		2441	2.2	0.0	9	dbSNP_134	21	1527,1655		357,813,421	no	missense	FAM205A	NM_001141917.1	121	365,973,945	AA,AT,TT		47.9887,12.7168,37.2974	benign	814/1336	34724796	1703,2863	692	1591	2283	SO:0001583	missense	259308	exon4			CTAGGCTCCATCT		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.2441A>T	9.37:g.34724796T>A	ENSP00000417711:p.Glu814Val	Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	206	94	0.456311	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	910	0.4166666666666667	45	0.09146341463414634	151	0.4171270718232044	334	0.583916083916084	380	0.5013192612137203	A	0.136	-1.107839	0.01813	0.127168	0.479887	ENSG00000205108	ENST00000378788	T	0.37584	1.19	4.7	2.24	0.28232	.	.	.	.	.	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	0.47142	-0.9140	8	0.02654	T	1	.	4.3631	0.11211	0.4712:0.1804:0.0:0.3484	.	814	Q6ZU69	F205A_HUMAN	V	814	ENSP00000417711:E814V	ENSP00000417711:E814V	E	-	2	0	RP11-195F19.10	34714796	0.000000	0.05858	0.004000	0.12327	0.027000	0.11550	-0.281000	0.08456	0.758000	0.33059	-0.265000	0.10407	GAG	T|1.000;|0.000	.	weak		0.552	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
MYO3B	140469	hgsc.bcm.edu	37	2	171240249	171240249	+	Silent	SNP	C	C	T	rs11675394	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:171240249C>T	ENST00000408978.4	+	12	1358	c.1215C>T	c.(1213-1215)cgC>cgT	p.R405R	MYO3B_ENST00000334231.6_Silent_p.R414R|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Silent_p.R405R	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	405	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)	p.S397_A406del(1)		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						GGGTGAAACGCGCCTCCAATC	0.453													C|||	1079	0.215455	0.0303	0.2493	5008	,	,		20601	0.2887		0.325	False		,,,				2504	0.2536				p.R405R		Atlas-SNP	.											MYO3B_ENST00000408978,rectum,carcinoma,0,6	MYO3B	320	6	1	Deletion - In frame(1)	ovary(1)	c.C1215T						PASS	.	C	,,	327,3487		13,301,1593	120.0	112.0	114.0		1215,1215,1215	-2.5	1.0	2	dbSNP_120	114	2679,5543		437,1805,1869	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	,,	450,2106,3462	TT,TC,CC		32.5833,8.5737,24.9751	,,	405/1315,405/1276,405/1342	171240249	3006,9030	1907	4111	6018	SO:0001819	synonymous_variant	140469	exon12			GAAACGCGCCTCC		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.1215C>T	2.37:g.171240249C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Silent	SNP	ENST00000408978.4	37	CCDS42773.1																																																																																			C|0.732;T|0.268	0.268	strong		0.453	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
FRG1	2483	hgsc.bcm.edu	37	4	190876268	190876268	+	Missense_Mutation	SNP	A	A	G	rs528665769		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:190876268A>G	ENST00000226798.4	+	5	616	c.394A>G	c.(394-396)Att>Gtt	p.I132V	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	132					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		TTCAGATGCAATTGGACCAAG	0.358																																					p.I132V		Atlas-SNP	.											FRG1,trunk,malignant_melanoma,-1,1	FRG1	76	1	0			c.A394G						scavenged	.						91.0	91.0	91.0					4																	190876268		2203	4300	6503	SO:0001583	missense	2483	exon5			GATGCAATTGGAC	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.394A>G	4.37:g.190876268A>G	ENSP00000226798:p.Ile132Val	Somatic	247	2	0.00809717		WXS	Illumina HiSeq	Phase_I	278	4	0.0143885	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	11.81	1.749824	0.30955	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.44083	2.0;0.93	4.04	4.04	0.47022	Actin cross-linking (1);	0.133249	0.64402	D	0.000004	T	0.31918	0.0812	L	0.42686	1.345	0.80722	D	1	B	0.18741	0.03	B	0.26693	0.072	T	0.07009	-1.0795	10	0.06891	T	0.86	2.1537	11.3071	0.49342	1.0:0.0:0.0:0.0	.	132	Q14331	FRG1_HUMAN	V	132;69	ENSP00000226798:I132V;ENSP00000435943:I69V	ENSP00000226798:I132V	I	+	1	0	FRG1	191113262	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.941000	0.75922	1.599000	0.50093	0.462000	0.41574	ATT	.	.	none		0.358	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
CACNA1I	8911	hgsc.bcm.edu	37	22	40054948	40054948	+	Silent	SNP	T	T	C	rs5757761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:40054948T>C	ENST00000402142.3	+	12	2157	c.2157T>C	c.(2155-2157)atT>atC	p.I719I	CACNA1I_ENST00000401624.1_Silent_p.I719I|CACNA1I_ENST00000400164.3_Silent_p.I684I|CACNA1I_ENST00000404898.1_Silent_p.I684I|CACNA1I_ENST00000336649.4_Silent_p.I725I|CACNA1I_ENST00000407673.1_Silent_p.I684I	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	719					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)	p.I684I(1)		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)	TCTGGGAGATTGTGGGGCAGG	0.672													C|||	3748	0.748403	0.8328	0.7392	5008	,	,		18304	0.994		0.5567	False		,,,				2504	0.5849				p.I719I		Atlas-SNP	.											CACNA1I,NS,carcinoma,0,1	CACNA1I	264	1	1	Substitution - coding silent(1)	prostate(1)	c.T2157C						PASS	.	C	,	3391,899		1349,693,103	17.0	21.0	20.0		2052,2157	-2.8	0.8	22	dbSNP_114	20	4616,3876		1278,2060,908	no	coding-synonymous,coding-synonymous	CACNA1I	NM_001003406.1,NM_021096.3	,	2627,2753,1011	CC,CT,TT		45.643,20.9557,37.3572	,	684/2189,719/2224	40054948	8007,4775	2145	4246	6391	SO:0001819	synonymous_variant	8911	exon12			GGAGATTGTGGGG	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.2157T>C	22.37:g.40054948T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	37	CCDS46710.1																																																																																			T|0.245;C|0.755	0.755	strong		0.672	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
HK2	3099	hgsc.bcm.edu	37	2	75113789	75113789	+	Silent	SNP	C	C	G	rs2229627	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75113789C>G	ENST00000290573.2	+	15	2808	c.2208C>G	c.(2206-2208)ccC>ccG	p.P736P	HK2_ENST00000409174.1_Silent_p.P708P	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	736	Catalytic.|Hexokinase type-2 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CACTCAACCCCGGCAAGCAGA	0.542													C|||	2592	0.517572	0.4175	0.4928	5008	,	,		17288	0.4554		0.6203	False		,,,				2504	0.6288				p.P736P		Atlas-SNP	.											HK2,colon,carcinoma,+1,1	HK2	85	1	0			c.C2208G						PASS	.	C		1971,2435	540.4+/-375.5	453,1065,685	64.0	67.0	66.0		2208	-11.0	0.6	2	dbSNP_98	66	5172,3428	624.7+/-397.6	1578,2016,706	no	coding-synonymous	HK2	NM_000189.4		2031,3081,1391	GG,GC,CC		39.8605,44.7345,45.0792		736/918	75113789	7143,5863	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon15			CAACCCCGGCAAG		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.2208C>G	2.37:g.75113789C>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	67	29	0.432836	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																			C|0.457;0|0.000	.	strong		0.542	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
ACO1	48	hgsc.bcm.edu	37	9	32425910	32425910	+	Silent	SNP	A	A	G	rs3780473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:32425910A>G	ENST00000309951.6	+	11	1401	c.1263A>G	c.(1261-1263)gaA>gaG	p.E421E	ACO1_ENST00000379923.1_Silent_p.E421E|ACO1_ENST00000541043.1_Silent_p.E322E	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	421					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		ATAACACTGAATTCACCCTTG	0.393													A|||	1772	0.353834	0.2632	0.3386	5008	,	,		17408	0.5516		0.336	False		,,,				2504	0.3016				p.E421E		Atlas-SNP	.											.	ACO1	149	.	0			c.A1263G						PASS	.	A		1204,3202	417.8+/-338.1	167,870,1166	142.0	110.0	121.0		1263	0.7	1.0	9	dbSNP_107	121	3048,5552	468.5+/-367.3	566,1916,1818	no	coding-synonymous	ACO1	NM_002197.2		733,2786,2984	GG,GA,AA		35.4419,27.3264,32.6926		421/890	32425910	4252,8754	2203	4300	6503	SO:0001819	synonymous_variant	48	exon11			CACTGAATTCACC	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1263A>G	9.37:g.32425910A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	53	0.519608	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	37	CCDS6525.1																																																																																			G|0.346;N|0.000	0.346	strong		0.393	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
MICAL2	9645	hgsc.bcm.edu	37	11	12265542	12265542	+	Silent	SNP	A	A	G	rs2270511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12265542A>G	ENST00000256194.4	+	21	2955	c.2667A>G	c.(2665-2667)ctA>ctG	p.L889L	MICAL2_ENST00000379612.3_Intron|MICAL2_ENST00000342902.5_Silent_p.L889L|MICAL2_ENST00000537344.1_Intron|MICAL2_ENST00000527546.1_Intron	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	889					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)		AGAATAAACTACTCTCTAAAG	0.483													A|||	1047	0.209065	0.1551	0.2651	5008	,	,		20969	0.2103		0.168	False		,,,				2504	0.2832				p.L889L		Atlas-SNP	.											.	MICAL2	114	.	0			c.A2667G						PASS	.	A		794,3608	317.7+/-295.3	73,648,1480	316.0	275.0	289.0		2667	-10.5	0.4	11	dbSNP_100	289	1318,7270	259.5+/-282.7	98,1122,3074	no	coding-synonymous	MICAL2	NM_014632.2		171,1770,4554	GG,GA,AA		15.347,18.0373,16.2587		889/1125	12265542	2112,10878	2201	4294	6495	SO:0001819	synonymous_variant	9645	exon21			TAAACTACTCTCT	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.2667A>G	11.37:g.12265542A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	191	97	0.507853	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Silent	SNP	ENST00000256194.4	37	CCDS7809.1																																																																																			A|0.826;G|0.173	0.173	strong		0.483	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
KRTAP5-7	440050	hgsc.bcm.edu	37	11	71238705	71238705	+	Missense_Mutation	SNP	G	G	A	rs536797652		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71238705G>A	ENST00000398536.4	+	1	393	c.359G>A	c.(358-360)tGc>tAc	p.C120Y		NM_001012503.1	NP_001012521.1	Q6L8G8	KRA57_HUMAN	keratin associated protein 5-7	120	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.C120Y(2)		breast(1)|endometrium(1)|kidney(3)|lung(6)|ovary(1)	12						tgtaagccctgctgctgccag	0.607													g|||	1	0.000199681	0.0008	0.0	5008	,	,		20154	0.0		0.0	False		,,,				2504	0.0				p.C120Y		Atlas-SNP	.											KRTAP5-7,NS,carcinoma,0,3	KRTAP5-7	23	3	2	Substitution - Missense(2)	kidney(2)	c.G359A						scavenged	.						129.0	139.0	136.0					11																	71238705		2200	4294	6494	SO:0001583	missense	440050	exon1			AGCCCTGCTGCTG	AB126076	CCDS41682.1	11q13.4	2008-02-05			ENSG00000244411	ENSG00000244411		"""Keratin associated proteins"""	23602	protein-coding gene	gene with protein product						15144888	Standard	NM_001012503		Approved	KRTAP5.7, KRTAP5-3	uc001oqq.1	Q6L8G8	OTTHUMG00000057570	ENST00000398536.4:c.359G>A	11.37:g.71238705G>A	ENSP00000417330:p.Cys120Tyr	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	142	4	0.028169	NM_001012503	B2RNM3|Q701N5	Missense_Mutation	SNP	ENST00000398536.4	37	CCDS41682.1	.	.	.	.	.	.	.	.	.	.	N	4.462	0.085611	0.08583	.	.	ENSG00000244411	ENST00000398536	T	0.01304	5.03	1.87	1.87	0.25490	.	.	.	.	.	T	0.01421	0.0046	L	0.60455	1.87	0.26143	N	0.980242	B	0.12630	0.006	B	0.08055	0.003	T	0.51733	-0.8668	9	0.02654	T	1	.	4.3831	0.11304	0.201:0.0:0.799:0.0	.	120	Q6L8G8	KRA57_HUMAN	Y	120	ENSP00000417330:C120Y	ENSP00000417330:C120Y	C	+	2	0	KRTAP5-7	70916353	0.718000	0.27976	0.999000	0.59377	0.075000	0.17131	2.143000	0.42187	1.367000	0.46095	0.289000	0.19496	TGC	.	.	none		0.607	KRTAP5-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127953.1		
LIPA	3988	hgsc.bcm.edu	37	10	91007360	91007360	+	Missense_Mutation	SNP	T	T	G	rs1051338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:91007360T>G	ENST00000336233.5	-	2	368	c.46A>C	c.(46-48)Acc>Ccc	p.T16P	LIPA_ENST00000371837.1_Intron|LIPA_ENST00000456827.1_Missense_Mutation_p.T16P			P38571	LICH_HUMAN	lipase A, lysosomal acid, cholesterol esterase	16			T -> P (in dbSNP:rs1051338). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1718995}.		cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cytokine production (GO:0001816)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|lung development (GO:0030324)|tissue remodeling (GO:0048771)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	lipase activity (GO:0016298)|sterol esterase activity (GO:0004771)			endometrium(1)|large_intestine(2)|lung(3)	6		Colorectal(252;0.0162)		GBM - Glioblastoma multiforme(2;0.00406)		GAATGCAGGGTCCAGAGAACC	0.373													T|||	1433	0.286142	0.1082	0.3545	5008	,	,		11907	0.3085		0.327	False		,,,				2504	0.4131				p.T16P		Atlas-SNP	.											.	LIPA	29	.	0			c.A46C						PASS	.	T	PRO/THR,PRO/THR	568,3838	254.6+/-260.1	41,486,1676	109.0	106.0	107.0		46,46	3.7	1.0	10	dbSNP_86	107	2566,6034	416.2+/-352.0	393,1780,2127	yes	missense,missense	LIPA	NM_000235.2,NM_001127605.1	38,38	434,2266,3803	GG,GT,TT		29.8372,12.8915,24.0966	benign,benign	16/400,16/400	91007360	3134,9872	2203	4300	6503	SO:0001583	missense	3988	exon2			GCAGGGTCCAGAG	M74775	CCDS7401.1, CCDS73160.1	10q23.2-q23.3	2012-07-13	2008-08-01		ENSG00000107798	ENSG00000107798	3.1.1.13		6617	protein-coding gene	gene with protein product	"""Wolman disease"""	613497				8432549	Standard	NM_000235		Approved	LAL, CESD	uc009xtq.3	P38571	OTTHUMG00000018716	ENST00000336233.5:c.46A>C	10.37:g.91007360T>G	ENSP00000337354:p.Thr16Pro	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_000235	B2RBH5|D3DR29|Q16529|Q53H21|Q5T074|Q5T771|Q96EJ0	Missense_Mutation	SNP	ENST00000336233.5	37	CCDS7401.1	599	0.2742673992673993	54	0.10975609756097561	118	0.3259668508287293	166	0.2902097902097902	261	0.34432717678100266	T	11.49	1.652821	0.29336	0.128915	0.298372	ENSG00000107798	ENST00000336233;ENST00000371829;ENST00000541980;ENST00000456827;ENST00000542307;ENST00000428800;ENST00000282673	T;T;T;T	0.77750	-0.51;-0.51;-0.39;-1.12	4.93	3.72	0.42706	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.47153	P	6.650000000000267E-4	B	0.09022	0.002	B	0.06405	0.002	T	0.06391	-1.0829	8	0.35671	T	0.21	-1.309	7.5127	0.27583	0.1911:0.0:0.0:0.8089	rs1051338;rs2229254;rs3191715;rs17845330;rs17858173;rs52817712;rs1051338	16	P38571	LICH_HUMAN	P	16	ENSP00000337354:T16P;ENSP00000413019:T16P;ENSP00000388415:T16P;ENSP00000282673:T16P	ENSP00000282673:T16P	T	-	1	0	LIPA	90997340	0.000000	0.05858	0.997000	0.53966	0.146000	0.21551	-0.090000	0.11163	2.216000	0.71823	0.454000	0.30748	ACC	T|0.740;G|0.254	0.254	strong		0.373	LIPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049308.1	NM_000235	
CEP70	80321	hgsc.bcm.edu	37	3	138218994	138218994	+	Missense_Mutation	SNP	T	T	C	rs35340237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:138218994T>C	ENST00000264982.3	-	16	1876	c.1610A>G	c.(1609-1611)aAt>aGt	p.N537S	CEP70_ENST00000484888.1_Missense_Mutation_p.N537S|CEP70_ENST00000481834.1_Missense_Mutation_p.N537S|CEP70_ENST00000542237.1_Missense_Mutation_p.N517S|CEP70_ENST00000489254.1_Missense_Mutation_p.N385S	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	537			N -> S (in dbSNP:rs35340237).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						AACCTGCTCATTCACATCTTC	0.393													T|||	979	0.195487	0.3048	0.0548	5008	,	,		16557	0.3978		0.0298	False		,,,				2504	0.1094				p.N537S		Atlas-SNP	.											.	CEP70	51	.	0			c.A1610G						PASS	.	T	SER/ASN	1248,3158	424.5+/-340.5	181,886,1136	111.0	122.0	118.0		1610	-2.8	0.0	3	dbSNP_126	118	201,8399	87.6+/-150.0	1,199,4100	yes	missense	CEP70	NM_024491.2	46	182,1085,5236	CC,CT,TT		2.3372,28.325,11.141	benign	537/598	138218994	1449,11557	2203	4300	6503	SO:0001583	missense	80321	exon16			TGCTCATTCACAT	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.1610A>G	3.37:g.138218994T>C	ENSP00000264982:p.Asn537Ser	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	258	126	0.488372	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	37	CCDS3102.1	395	0.18086080586080586	140	0.2845528455284553	21	0.058011049723756904	210	0.36713286713286714	24	0.0316622691292876	T	0.010	-1.751701	0.00663	0.28325	0.023372	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000459695;ENST00000481834	T;T;T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12;2.12;2.12	5.21	-2.81	0.05805	.	0.698418	0.14368	N	0.323957	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.09377	0.003;0.003;0.004;0.003	T	0.39761	-0.9598	9	0.02654	T	1	-1.876	6.634	0.22874	0.0:0.4933:0.1665:0.3402	rs35340237;rs61380838	385;517;537;537	B7Z2D2;F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;.;CEP70_HUMAN	S	537;517;385;537;519;10;537	ENSP00000264982:N537S;ENSP00000444128:N517S;ENSP00000417821:N385S;ENSP00000419231:N537S;ENSP00000419833:N519S;ENSP00000418552:N10S;ENSP00000417465:N537S	ENSP00000264982:N537S	N	-	2	0	CEP70	139701684	0.001000	0.12720	0.022000	0.16811	0.636000	0.38137	-0.881000	0.04179	-0.355000	0.08199	-1.119000	0.02030	AAT	T|0.869;C|0.131	0.131	strong		0.393	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
MYH11	4629	hgsc.bcm.edu	37	16	15811023	15811023	+	Silent	SNP	C	C	T	rs587781067|rs1050163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15811023C>T	ENST00000300036.5	-	38	5587	c.5478G>A	c.(5476-5478)ctG>ctA	p.L1826L	NDE1_ENST00000396355.1_Intron|MYH11_ENST00000576790.2_Silent_p.L1826L|MYH11_ENST00000396324.3_Silent_p.L1833L|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000452625.2_Silent_p.L1833L	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1826					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CCTGCTCCTCCAGCTGTGCAA	0.602			T	CBFB	AML								C|||	1984	0.396166	0.2549	0.5029	5008	,	,		20047	0.3313		0.4811	False		,,,				2504	0.4908				p.L1833L		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G5499A						PASS	.	C	,,,,,	1343,3051	448.3+/-348.6	209,925,1063	134.0	111.0	119.0		5499,5499,,5478,,5478	0.2	1.0	16	dbSNP_86	119	4361,4239	582.1+/-391.3	1128,2105,1067	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	1337,3030,2130	TT,TC,CC		49.2907,30.5644,43.8972	,,,,,	1833/1946,1833/1980,,1826/1973,,1826/1939	15811023	5704,7290	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon39			CTCCTCCAGCTGT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5478G>A	16.37:g.15811023C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			C|0.592;T|0.408	0.408	strong		0.602	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
GABRB1	2560	hgsc.bcm.edu	37	4	47322219	47322219	+	Silent	SNP	C	C	A	rs6284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:47322219C>A	ENST00000295454.3	+	5	829	c.537C>A	c.(535-537)atC>atA	p.I179I	GABRB1_ENST00000538619.1_Silent_p.I109I	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	179					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCCTGGAGATCGAAAGTTGTG	0.423													C|||	634	0.126597	0.1074	0.1282	5008	,	,		17941	0.1101		0.1968	False		,,,				2504	0.0961				p.I179I		Atlas-SNP	.											.	GABRB1	107	.	0			c.C537A						PASS	.	C		553,3853	247.8+/-255.9	39,475,1689	111.0	96.0	101.0		537	-2.5	1.0	4	dbSNP_52	101	1727,6873	313.1+/-311.2	146,1435,2719	no	coding-synonymous	GABRB1	NM_000812.3		185,1910,4408	AA,AC,CC		20.0814,12.5511,17.5304		179/475	47322219	2280,10726	2203	4300	6503	SO:0001819	synonymous_variant	2560	exon5			GGAGATCGAAAGT		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4081	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 1"""	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.537C>A	4.37:g.47322219C>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	37	CCDS3474.1																																																																																			C|0.849;A|0.151	0.151	strong		0.423	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1		
INPP5A	3632	hgsc.bcm.edu	37	10	134459388	134459388	+	Missense_Mutation	SNP	A	A	G	rs1133400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134459388A>G	ENST00000368594.3	+	3	411	c.134A>G	c.(133-135)aAg>aGg	p.K45R	INPP5A_ENST00000368593.3_Missense_Mutation_p.K45R	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	45			K -> R (in dbSNP:rs1133400).		inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	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)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		CACACACACAAGCCGCACTTC	0.607													A|||	1063	0.21226	0.1014	0.2565	5008	,	,		17008	0.3016		0.2137	False		,,,				2504	0.2372				p.K45R	Pancreas(63;823 1267 11107 20380 51626)	Atlas-SNP	.											.	INPP5A	77	.	0			c.A134G						PASS	.	A	ARG/LYS	475,3931	221.0+/-238.3	27,421,1755	139.0	84.0	103.0		134	-0.9	1.0	10	dbSNP_86	103	1745,6855	311.6+/-310.4	176,1393,2731	yes	missense	INPP5A	NM_005539.3	26	203,1814,4486	GG,GA,AA		20.2907,10.7808,17.069	benign	45/413	134459388	2220,10786	2203	4300	6503	SO:0001583	missense	3632	exon3			CACACAAGCCGCA	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"""CTCL tumor antigen HD-CL-02"", ""43 kDa inositol polyphosphate 5-phophatase"", ""inositol polyphosphate 5-phophatase, 40kDa"", ""InsP3 5-phosphatase"", ""type I inositol-1,4,5-trisphosphate 5-phosphatase"""	600106	"""inositol polyphosphate-5-phosphatase, 40kD"""			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.134A>G	10.37:g.134459388A>G	ENSP00000357583:p.Lys45Arg	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_005539	D3DXI3|Q14640|Q5JSF1	Missense_Mutation	SNP	ENST00000368594.3	37	CCDS7669.2	505	0.23122710622710624	58	0.11788617886178862	98	0.27071823204419887	180	0.3146853146853147	169	0.22295514511873352	A	10.69	1.422128	0.25639	0.107808	0.202907	ENSG00000068383	ENST00000368594;ENST00000368593;ENST00000416326;ENST00000368595;ENST00000451873	T;T	0.42900	0.96;0.96	4.31	-0.882	0.10604	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.284900	0.37053	N	0.002266	T	0.00012	0.0000	N	0.25201	0.72	0.25964	P	0.9825875	B;B	0.09022	0.0;0.002	B;B	0.06405	0.001;0.002	T	0.43393	-0.9394	9	0.17832	T	0.49	-17.8059	8.6704	0.34147	0.6762:0.0:0.3238:0.0	rs1133400;rs3195167;rs3818511;rs11545720;rs59704452;rs1133400	45;45	Q14642;Q5T1B5	I5P1_HUMAN;.	R	45;45;45;45;41	ENSP00000357583:K45R;ENSP00000357582:K45R	ENSP00000357582:K45R	K	+	2	0	INPP5A	134309378	1.000000	0.71417	0.988000	0.46212	0.976000	0.68499	1.210000	0.32370	-0.258000	0.09446	0.533000	0.62120	AAG	A|0.804;G|0.196	0.196	strong		0.607	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539	
EHMT1	79813	hgsc.bcm.edu	37	9	140611436	140611436	+	Silent	SNP	T	T	C	rs3812497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140611436T>C	ENST00000460843.1	+	3	471	c.444T>C	c.(442-444)ccT>ccC	p.P148P	EHMT1_ENST00000334856.6_Silent_p.P117P|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.P148P	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	148					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		CTTCGCTGCCTGGCCATGCTG	0.607													t|||	1141	0.227835	0.0893	0.4539	5008	,	,		16940	0.1429		0.2634	False		,,,				2504	0.3057				p.P148P		Atlas-SNP	.											.	EHMT1	196	.	0			c.T444C						PASS	.		,	507,3899	229.4+/-244.0	29,449,1725	54.0	56.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	444,444	-0.9	1.0	9	dbSNP_107	56	2364,6234	387.7+/-342.3	321,1722,2256	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	350,2171,3981	CC,CT,TT		27.4948,11.507,22.0778	,	148/809,148/1299	140611436	2871,10133	2203	4299	6502	SO:0001819	synonymous_variant	79813	exon3			GCTGCCTGGCCAT	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.444T>C	9.37:g.140611436T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			T|0.785;C|0.215	0.215	strong		0.607	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
CROCC	9696	hgsc.bcm.edu	37	1	17270751	17270751	+	Silent	SNP	G	G	A	rs12025984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17270751G>A	ENST00000375541.5	+	14	2034	c.1965G>A	c.(1963-1965)gcG>gcA	p.A655A	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		AGGATGGCGCGCGGGTGCGCC	0.711													g|||	1190	0.23762	0.0182	0.3242	5008	,	,		21546	0.4643		0.2495	False		,,,				2504	0.227				p.A655A		Atlas-SNP	.											.	CROCC	185	.	0			c.G1965A						PASS	.						8.0	6.0	7.0					1																	17270751		2084	4087	6171	SO:0001819	synonymous_variant	9696	exon14			TGGCGCGCGGGTG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1965G>A	1.37:g.17270751G>A		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			G|0.762;A|0.238	0.238	strong		0.711	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
CLEC7A	64581	hgsc.bcm.edu	37	12	10271087	10271087	+	Nonsense_Mutation	SNP	A	A	C	rs16910526	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:10271087A>C	ENST00000304084.8	-	6	868	c.714T>G	c.(712-714)taT>taG	p.Y238*	CLEC7A_ENST00000298523.5_3'UTR|CLEC7A_ENST00000533022.1_3'UTR|CLEC7A_ENST00000353231.5_Nonsense_Mutation_p.Y192*|CLEC7A_ENST00000396484.2_Nonsense_Mutation_p.Y159*	NM_197947.2	NP_922938.1	Q9BXN2	CLC7A_HUMAN	C-type lectin domain family 7, member A	238	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				carbohydrate mediated signaling (GO:0009756)|cell recognition (GO:0008037)|defense response to protozoan (GO:0042832)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|pattern recognition receptor signaling pathway (GO:0002221)|phagocytosis, recognition (GO:0006910)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|MHC protein binding (GO:0042287)|signaling pattern recognition receptor activity (GO:0008329)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	7						CACAAATACTATATGAGGGCA	0.408													A|||	205	0.0409345	0.0113	0.0375	5008	,	,		18575	0.004		0.0706	False		,,,				2504	0.091				p.Y238X		Atlas-SNP	.											.	CLEC7A	55	.	0			c.T714G						PASS	.	A	stop/TYR,stop/TYR,,,stop/TYR	116,4290	87.8+/-126.4	2,112,2089	147.0	139.0	141.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	576,714,,,477	-2.3	0.2	12	dbSNP_123	141	679,7921	170.1+/-221.3	34,611,3655	yes	stop-gained,stop-gained,utr-3,utr-3,stop-gained	CLEC7A	NM_022570.4,NM_197947.2,NM_197948.2,NM_197949.2,NM_197950.2	,,,,	36,723,5744	CC,CA,AA		7.8953,2.6328,6.1126	,,,,	192/202,238/248,,,159/169	10271087	795,12211	2203	4300	6503	SO:0001587	stop_gained	64581	exon6			AATACTATATGAG	AY009090	CCDS8613.1, CCDS8614.1, CCDS8617.1, CCDS41753.1, CCDS41754.1, CCDS53744.1	12p13.2-p12.3	2014-09-17		2005-02-09	ENSG00000172243	ENSG00000172243		"""C-type lectin domain containing"""	14558	protein-coding gene	gene with protein product		606264	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 12"""	CLECSF12			Standard	XM_005253468		Approved	dectin-1, hDectin-1	uc001qxg.2	Q9BXN2	OTTHUMG00000133597	ENST00000304084.8:c.714T>G	12.37:g.10271087A>C	ENSP00000302569:p.Tyr238*	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	173	75	0.433526	NM_197947	B2R861|B7Z494|B7Z5A9|B7Z5B9|Q6IPS7|Q96D32|Q96DR9|Q96LD3|Q96PA4|Q96PA5|Q96PA6|Q96PA7|Q96PA8|Q9H1K3	Nonsense_Mutation	SNP	ENST00000304084.8	37	CCDS41753.1	74	0.03388278388278388	7	0.014227642276422764	16	0.04419889502762431	0	0.0	51	0.06728232189973615	A	14.03	2.413294	0.42817	0.026328	0.078953	ENSG00000172243	ENST00000353231;ENST00000396484;ENST00000304084	.	.	.	3.84	-2.33	0.06724	.	0.596133	0.14071	N	0.343371	.	.	.	.	.	.	0.26769	A	0.0301528	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.8263	0.35057	0.6592:0.0:0.3408:0.0	rs16910526;rs52822212;rs16910526	.	.	.	X	192;159;238	.	ENSP00000302569:Y238X	Y	-	3	2	CLEC7A	10162354	0.965000	0.33210	0.166000	0.22797	0.674000	0.39518	-0.075000	0.11431	-0.549000	0.06191	-0.248000	0.11899	TAT	A|0.950;C|0.050	0.050	strong		0.408	CLEC7A-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390772.1	NM_197954	
SMPD3	55512	hgsc.bcm.edu	37	16	68398924	68398924	+	Silent	SNP	C	C	T	rs1868158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68398924C>T	ENST00000219334.5	-	4	1998	c.1395G>A	c.(1393-1395)ccG>ccA	p.P465P	SMPD3_ENST00000566009.1_5'UTR|SMPD3_ENST00000568373.1_Silent_p.P465P|SMPD3_ENST00000563226.1_Silent_p.P465P	NM_018667.3	NP_061137.1	Q9NY59	NSMA2_HUMAN	sphingomyelin phosphodiesterase 3, neutral membrane (neutral sphingomyelinase II)	465					cell cycle (GO:0007049)|glycosphingolipid metabolic process (GO:0006687)|hematopoietic progenitor cell differentiation (GO:0002244)|peptide hormone secretion (GO:0030072)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	Golgi cis cisterna (GO:0000137)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0184)|Epithelial(162;0.0785)	Phosphatidylserine(DB00144)	CCCTACCTTGCGGGGCATGCA	0.607													C|||	3167	0.632388	0.6679	0.6671	5008	,	,		18917	0.7698		0.5308	False		,,,				2504	0.5225				p.P465P		Atlas-SNP	.											.	SMPD3	52	.	0			c.G1395A						PASS	.	C		2877,1519	673.2+/-402.8	948,981,269	111.0	79.0	90.0		1395	-3.5	0.0	16	dbSNP_92	90	4964,3636	624.1+/-397.5	1427,2110,763	no	coding-synonymous	SMPD3	NM_018667.3		2375,3091,1032	TT,TC,CC		42.2791,34.5541,39.6661		465/656	68398924	7841,5155	2198	4300	6498	SO:0001819	synonymous_variant	55512	exon4			ACCTTGCGGGGCA	AJ250460	CCDS10867.1	16q22.1	2008-02-05			ENSG00000103056	ENSG00000103056			14240	protein-coding gene	gene with protein product		605777				10823942	Standard	NM_018667		Approved	NSMASE2	uc002ewa.3	Q9NY59	OTTHUMG00000137559	ENST00000219334.5:c.1395G>A	16.37:g.68398924C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_018667	B7ZL82|Q2M1S8	Silent	SNP	ENST00000219334.5	37	CCDS10867.1																																																																																			C|0.368;T|0.632	0.632	strong		0.607	SMPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268895.3	NM_018667	
MAPK15	225689	hgsc.bcm.edu	37	8	144804000	144804000	+	Missense_Mutation	SNP	C	C	T	rs536928468		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144804000C>T	ENST00000338033.4	+	13	1527	c.1408C>T	c.(1408-1410)Cgg>Tgg	p.R470W	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	470					MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	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)			GGCCCTGATCCGGGGTGACTG	0.687													c|||	1	0.000199681	0.0008	0.0	5008	,	,		13081	0.0		0.0	False		,,,				2504	0.0				p.R470W		Atlas-SNP	.											.	MAPK15	32	.	0			c.C1408T						PASS	.						30.0	39.0	36.0					8																	144804000		1960	4118	6078	SO:0001583	missense	225689	exon13			CTGATCCGGGGTG	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"""Mitogen-activated protein kinase cascade / Kinases"""	24667	protein-coding gene	gene with protein product	"""extracellular signal regulated kinase 8"""					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.1408C>T	8.37:g.144804000C>T	ENSP00000337691:p.Arg470Trp	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	69	22	0.318841	NM_139021	Q2TCF9|Q8N362	Missense_Mutation	SNP	ENST00000338033.4	37	CCDS6409.2	.	.	.	.	.	.	.	.	.	.	c	12.80	2.045324	0.36085	.	.	ENSG00000181085	ENST00000338033	T	0.81330	-1.48	3.23	2.31	0.28768	.	0.000000	0.85682	U	0.000000	T	0.81884	0.4917	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.80761	-0.1238	10	0.87932	D	0	-20.9811	9.0646	0.36455	0.2217:0.7783:0.0:0.0	.	470	Q8TD08	MK15_HUMAN	W	470	ENSP00000337691:R470W	ENSP00000337691:R470W	R	+	1	2	MAPK15	144875988	0.017000	0.18338	0.486000	0.27416	0.049000	0.14656	1.449000	0.35123	0.519000	0.28406	0.306000	0.20318	CGG	.	.	none		0.687	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	
XIRP2	129446	hgsc.bcm.edu	37	2	168103304	168103304	+	Missense_Mutation	SNP	G	G	A	rs16853309	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168103304G>A	ENST00000409195.1	+	9	5491	c.5402G>A	c.(5401-5403)cGt>cAt	p.R1801H	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R1579H|XIRP2_ENST00000295237.9_Missense_Mutation_p.R1801H|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1626					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CTGGTTGAACGTACTGTTAGT	0.403													G|||	989	0.197484	0.3245	0.1311	5008	,	,		21072	0.12		0.1233	False		,,,				2504	0.229				p.R1801H		Atlas-SNP	.											.	XIRP2	914	.	0			c.G5402A						PASS	.	G	HIS/ARG,HIS/ARG,,,	1080,2776		156,768,1004	180.0	168.0	172.0		4736,5402,,,	2.8	1.0	2	dbSNP_123	172	921,7361		55,811,3275	yes	missense,missense,intron,intron,intron	XIRP2	NM_001199144.1,NM_152381.5,NM_001079810.3,NM_001199143.1,NM_001199145.1	29,29,,,	211,1579,4279	AA,AG,GG		11.1205,28.0083,16.4854	possibly-damaging,possibly-damaging,,,	1579/3328,1801/3550,,,	168103304	2001,10137	1928	4141	6069	SO:0001583	missense	129446	exon9			TTGAACGTACTGT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5402G>A	2.37:g.168103304G>A	ENSP00000386840:p.Arg1801His	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	155	73	0.470968	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	384	0.17582417582417584	170	0.34552845528455284	47	0.1298342541436464	72	0.1258741258741259	95	0.12532981530343007	G	10.60	1.396329	0.25205	0.280083	0.111205	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.04502	3.61;3.61;3.61	5.59	2.84	0.33178	.	0.053822	0.85682	D	0.000000	T	0.00012	0.0000	M	0.74258	2.255	0.18873	P	0.999981003	P;P;P	0.41947	0.655;0.766;0.477	B;B;B	0.33121	0.076;0.158;0.081	T	0.49634	-0.8919	9	0.49607	T	0.09	-5.9326	9.9833	0.41826	0.2251:0.0:0.7749:0.0	rs16853309;rs52829936;rs16853309	1626;1626;1579	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	H	1801;1801;1579	ENSP00000386840:R1801H;ENSP00000295237:R1801H;ENSP00000387255:R1579H	ENSP00000295237:R1801H	R	+	2	0	XIRP2	167811550	1.000000	0.71417	1.000000	0.80357	0.350000	0.29205	2.750000	0.47500	0.740000	0.32651	-0.133000	0.14855	CGT	G|0.820;A|0.180	0.180	strong		0.403	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
MAGEB10	139422	hgsc.bcm.edu	37	X	27839617	27839617	+	Missense_Mutation	SNP	G	G	A	rs12557898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:27839617G>A	ENST00000356790.2	+	3	439	c.194G>A	c.(193-195)cGg>cAg	p.R65Q		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	65			R -> Q (in dbSNP:rs12557898). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						CATGGACTTCGGGAAGCCCAA	0.498													G|||	792	0.209801	0.1112	0.1873	3775	,	,		13898	0.0357		0.3559	False		,,,				2504	0.1237				p.R65Q		Atlas-SNP	.											.	MAGEB10	107	.	0			c.G194A						PASS	.	G	GLN/ARG	678,3155		54,465,105,1112,466	58.0	45.0	49.0		194	-5.0	0.0	X	dbSNP_120	49	3376,3351		620,1200,936,608,935	yes	missense	MAGEB10	NM_182506.3	43	674,1665,1041,1720,1401	AA,AG,A,GG,G		49.8142,17.6885,38.3902	benign	65/348	27839617	4054,6506	2202	4299	6501	SO:0001583	missense	139422	exon3			GACTTCGGGAAGC		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.194G>A	X.37:g.27839617G>A	ENSP00000368304:p.Arg65Gln	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	37	CCDS35221.1	407	0.24532851115129597	35	0.07608695652173914	52	0.16666666666666666	13	0.022887323943661973	184	0.3076923076923077	g	0.010	-1.757108	0.00657	0.176885	0.501858	ENSG00000177689	ENST00000356790	T	0.02737	4.18	2.52	-5.04	0.02964	Melanoma associated antigen, MAGE, N-terminal (1);	14.954800	0.00166	N	0.000004	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.15141	0.012	B	0.09377	0.004	T	0.43940	-0.9360	9	0.02654	T	1	.	4.2766	0.10811	0.4058:0.3297:0.2645:0.0	rs12557898;rs52801205;rs58263199;rs12557898	65	Q96LZ2	MAGBA_HUMAN	Q	65	ENSP00000368304:R65Q	ENSP00000368304:R65Q	R	+	2	0	MAGEB10	27749538	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.569000	0.05902	-1.585000	0.01634	-2.735000	0.00129	CGG	0|0.012;A|0.299	0.299	strong		0.498	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
TEX35	84066	hgsc.bcm.edu	37	1	178492447	178492447	+	Silent	SNP	T	T	A	rs7527160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:178492447T>A	ENST00000367639.1	+	9	666	c.621T>A	c.(619-621)gcT>gcA	p.A207A	TEX35_ENST00000258298.2_Intron	NM_001170722.1|NM_001170724.1	NP_001164193.1|NP_001164195.1			testis expressed 35																		gtatatacgctgcagtgggac	0.403													A|||	2880	0.57508	0.7239	0.5937	5008	,	,		21495	0.503		0.5547	False		,,,				2504	0.456				p.A207A		Atlas-SNP	.											.	TEX35	15	.	0			c.T621A						PASS	.	A	,	962,422		329,304,59	100.0	93.0	95.0		621,597	0.1	0.3	1	dbSNP_116	95	1648,1534		420,808,363	no	coding-synonymous,coding-synonymous	C1orf49	NM_001170722.1,NM_001170724.1	,	749,1112,422	AA,AT,TT		48.2087,30.4913,42.8384	,	207/216,199/208	178492447	2610,1956	692	1591	2283	SO:0001819	synonymous_variant	84066	exon9			ATACGCTGCAGTG	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"""Testis-Specific Conserved gene 24kDa"""		"""chromosome 1 open reading frame 49"""	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000367639.1:c.621T>A	1.37:g.178492447T>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	11	7	0.636364	NM_001170722		Silent	SNP	ENST00000367639.1	37	CCDS53434.1																																																																																			T|0.409;A|0.591	0.591	strong		0.403	TEX35-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098170.1	NM_032126	
NRF1	4899	hgsc.bcm.edu	37	7	129297332	129297332	+	Silent	SNP	T	T	G	rs1882094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129297332T>G	ENST00000393232.1	+	2	258	c.141T>G	c.(139-141)tcT>tcG	p.S47S	NRF1_ENST00000223190.4_Silent_p.S47S|NRF1_ENST00000539636.1_5'UTR|NRF1_ENST00000393230.2_Silent_p.S47S|NRF1_ENST00000353868.4_Silent_p.S47S|NRF1_ENST00000393231.3_Silent_p.S47S|NRF1_ENST00000311967.2_Silent_p.S47S	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	47	Asp/Glu-rich (acidic).|Dimerization.				cellular lipid metabolic process (GO:0044255)|generation of precursor metabolites and energy (GO:0006091)|mitochondrion organization (GO:0007005)|organ regeneration (GO:0031100)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)	24						CGCCTTCTTCTCCCGAGGACA	0.512																																					p.S47S		Atlas-SNP	.											NRF1,NS,adenoma,0,1	NRF1	40	1	0			c.T141G						scavenged	.	T	,	2992,1414	686.2+/-404.7	1016,960,227	127.0	108.0	114.0		141,141	-0.5	1.0	7	dbSNP_92	114	2533,6067	412.5+/-350.8	383,1767,2150	no	coding-synonymous,coding-synonymous	NRF1	NM_001040110.1,NM_005011.3	,	1399,2727,2377	GG,GT,TT		29.4535,32.0926,42.4804	,	47/504,47/504	129297332	5525,7481	2203	4300	6503	SO:0001819	synonymous_variant	4899	exon2			TTCTTCTCCCGAG	L22454	CCDS5813.2	7q32	2008-07-18			ENSG00000106459	ENSG00000106459			7996	protein-coding gene	gene with protein product	"""alpha palindromic-binding protein"""	600879				2584221	Standard	NM_005011		Approved	EWG, ALPHA-PAL	uc003voz.3	Q16656	OTTHUMG00000143736	ENST00000393232.1:c.141T>G	7.37:g.129297332T>G		Somatic	66	3	0.0454545		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_005011	A8K4C6|B4DDV6|Q15305|Q96AN2	Silent	SNP	ENST00000393232.1	37	CCDS5813.2																																																																																			T|0.531;G|0.469	0.469	strong		0.512	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110	
COL4A4	1286	hgsc.bcm.edu	37	2	227886773	227886773	+	Missense_Mutation	SNP	A	A	G	rs1800518|rs3752895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227886773A>G	ENST00000396625.3	-	44	4414	c.4207T>C	c.(4207-4209)Tca>Cca	p.S1403P	COL4A4_ENST00000329662.7_Missense_Mutation_p.S1400P	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1403	Triple-helical region.		S -> P (in dbSNP:rs3752895). {ECO:0000269|PubMed:7523402, ECO:0000269|PubMed:8365481, ECO:0000269|PubMed:9792860}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CCTGGTCCTGAGGGGCCTCTC	0.483													G|||	2635	0.526158	0.6891	0.4841	5008	,	,		15580	0.4058		0.4334	False		,,,				2504	0.5552				p.S1403P		Atlas-SNP	.											.	COL4A4	215	.	0			c.T4207C						PASS	.	G	PRO/SER	2276,1470		695,886,292	108.0	116.0	113.0		4207	5.6	1.0	2	dbSNP_107	113	3440,4766		723,1994,1386	yes	missense	COL4A4	NM_000092.4	74	1418,2880,1678	GG,GA,AA		41.9205,39.2419,47.8246	benign	1403/1691	227886773	5716,6236	1873	4103	5976	SO:0001583	missense	1286	exon44			GTCCTGAGGGGCC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4207T>C	2.37:g.227886773A>G	ENSP00000379866:p.Ser1403Pro	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	1045	0.4784798534798535	317	0.6443089430894309	172	0.47513812154696133	226	0.3951048951048951	330	0.43535620052770446	G	3.071	-0.191210	0.06299	0.607581	0.419205	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.90133	-2.62;-2.57	5.63	5.63	0.86233	.	.	.	.	.	T	0.00012	0.0000	N	0.01493	-0.835	0.51233	P	8.799999999997699E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41680	-0.9495	8	0.12766	T	0.61	.	11.0766	0.48036	0.0856:0.0:0.9144:0.0	rs3752895;rs52823297;rs58171427;rs3752895	1403	P53420	CO4A4_HUMAN	P	1403;1400	ENSP00000379866:S1403P;ENSP00000328553:S1400P	ENSP00000328553:S1400P	S	-	1	0	COL4A4	227595017	0.996000	0.38824	0.977000	0.42913	0.387000	0.30353	3.419000	0.52728	1.525000	0.49052	-0.215000	0.12644	TCA	A|0.523;G|0.477	0.477	strong		0.483	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449037	89449037	+	Missense_Mutation	SNP	C	C	A	rs200081893		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449037C>A	ENST00000321792.5	-	2	900	c.473G>T	c.(472-474)gGg>gTg	p.G158V	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.G158V	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	158					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										AGAAGGACCCCCACTTCTTGG	0.493																																					p.G158V		Atlas-SNP	.											.	.	.	.	0			c.G473T						PASS	.						146.0	153.0	151.0					1																	89449037		2203	4300	6503	SO:0001583	missense	494115	exon3			GGACCCCCACTTC	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.473G>T	1.37:g.89449037C>A	ENSP00000318415:p.Gly158Val	Somatic	473	0	0		WXS	Illumina HiSeq	Phase_I	486	23	0.0473251	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.995423	0.54147	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.78924	-1.22;-1.22	1.76	0.711	0.18162	.	0.000000	0.85682	U	0.000000	T	0.57888	0.2084	M	0.72894	2.215	0.80722	D	1	B	0.23316	0.083	B	0.19391	0.025	T	0.55483	-0.8134	10	0.51188	T	0.08	-9.2612	6.8205	0.23855	0.2788:0.7212:0.0:0.0	.	158	Q96E39	RBMXL_HUMAN	V	158	ENSP00000318415:G158V;ENSP00000446099:G158V	ENSP00000318415:G158V	G	-	2	0	RBMXL1	89221625	0.997000	0.39634	0.791000	0.31998	0.903000	0.53119	2.436000	0.44819	0.049000	0.15920	0.306000	0.20318	GGG	C|0.997;A|0.003	0.003	weak		0.493	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
NQO2	4835	hgsc.bcm.edu	37	6	3015790	3015790	+	Silent	SNP	A	A	G	rs1049115	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:3015790A>G	ENST00000338130.2	+	8	1042	c.330A>G	c.(328-330)ccA>ccG	p.P110P	NQO2_ENST00000380430.1_Silent_p.P110P|NQO2_ENST00000380455.4_Silent_p.P110P|NQO2_ENST00000380454.4_Intron|NQO2_ENST00000380441.1_Intron			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	110					memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	TCAGCGTGCCAGCCATCCTGA	0.547													G|||	3793	0.757388	0.9312	0.7334	5008	,	,		20068	0.6538		0.7147	False		,,,				2504	0.6902				p.P110P		Atlas-SNP	.											.	NQO2	21	.	0			c.A330G						PASS	.	G		3961,445	213.8+/-233.3	1781,399,23	86.0	81.0	83.0		330	-6.9	0.1	6	dbSNP_86	83	6178,2422	402.2+/-347.4	2209,1760,331	no	coding-synonymous	NQO2	NM_000904.3		3990,2159,354	GG,GA,AA		28.1628,10.0999,22.0437		110/232	3015790	10139,2867	2203	4300	6503	SO:0001819	synonymous_variant	4835	exon5			CGTGCCAGCCATC	U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"""NAD(P)H menadione oxidoreductase 2, dioxin-inducible"""	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.330A>G	6.37:g.3015790A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_000904	B2R492|Q5TD04	Silent	SNP	ENST00000338130.2	37	CCDS4481.1																																																																																			A|0.232;G|0.768	0.768	strong		0.547	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107533175	107533175	+	Missense_Mutation	SNP	C	C	G	rs3739741	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107533175C>G	ENST00000374762.3	+	4	547	c.476C>G	c.(475-477)gCt>gGt	p.A159G	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	159			A -> G (in dbSNP:rs3739741). {ECO:0000269|PubMed:14702039}.					p.A159G(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						GGTGGGCCAGCTCTGTGGGGT	0.383													C|||	882	0.176118	0.0257	0.1427	5008	,	,		17296	0.2847		0.1769	False		,,,				2504	0.2904				p.A159G		Atlas-SNP	.											NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	1	Substitution - Missense(1)	stomach(1)	c.C476G						PASS	.	C	GLY/ALA	199,4207	126.1+/-163.2	6,187,2010	136.0	129.0	131.0		476	2.4	1.0	9	dbSNP_107	131	1631,6969	302.9+/-306.2	172,1287,2841	yes	missense	NIPSNAP3B	NM_018376.2	60	178,1474,4851	GG,GC,CC		18.9651,4.5166,14.0704	benign	159/248	107533175	1830,11176	2203	4300	6503	SO:0001583	missense	55335	exon4			GGCCAGCTCTGTG	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.476C>G	9.37:g.107533175C>G	ENSP00000363894:p.Ala159Gly	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	177	80	0.451977	NM_018376	Q5VX30|Q9NUM2	Missense_Mutation	SNP	ENST00000374762.3	37	CCDS6761.1	356	0.163003663003663	15	0.03048780487804878	59	0.16298342541436464	146	0.25524475524475526	136	0.17941952506596306	C	19.13	3.767716	0.69878	0.045166	0.189651	ENSG00000165028	ENST00000374762	T	0.70986	-0.53	4.3	2.44	0.29823	Dimeric alpha-beta barrel (1);	0.177687	0.47852	D	0.000203	T	0.00039	0.0001	M	0.67625	2.065	0.24750	P	0.99298667	D	0.76494	0.999	D	0.74023	0.982	T	0.07271	-1.0781	9	0.22706	T	0.39	-9.1353	10.6947	0.45892	0.0:0.8331:0.0:0.1669	rs3739741;rs3739741	159	Q9BS92	NPS3B_HUMAN	G	159	ENSP00000363894:A159G	ENSP00000363894:A159G	A	+	2	0	NIPSNAP3B	106572996	0.974000	0.33945	1.000000	0.80357	0.980000	0.70556	1.528000	0.35985	1.148000	0.42385	0.655000	0.94253	GCT	C|0.851;G|0.149	0.149	strong		0.383	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376	
GPR153	387509	hgsc.bcm.edu	37	1	6314758	6314758	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:6314758G>A	ENST00000377893.2	-	2	467	c.208C>T	c.(208-210)Cgg>Tgg	p.R70W		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		CGCTGCCGCCGCAGCTGCACC	0.607																																					p.R70W		Atlas-SNP	.											.	GPR153	44	.	0			c.C208T						PASS	.						119.0	107.0	111.0					1																	6314758		2203	4300	6503	SO:0001583	missense	387509	exon2			GCCGCCGCAGCTG	AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"""GPCR / Class A : Orphans"""	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.208C>T	1.37:g.6314758G>A	ENSP00000367125:p.Arg70Trp	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	115	9	0.0782609	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	37	CCDS64.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546288	0.86022	.	.	ENSG00000158292	ENST00000377893	T	0.37584	1.19	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48447	0.1500	L	0.32530	0.975	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.48625	-0.9019	10	0.87932	D	0	-53.1149	12.8394	0.57793	0.0:0.0:0.8368:0.1632	.	70	Q6NV75	GP153_HUMAN	W	70	ENSP00000367125:R70W	ENSP00000367125:R70W	R	-	1	2	GPR153	6237345	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.795000	0.85887	2.534000	0.85438	0.557000	0.71058	CGG	.	.	none		0.607	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2		
PTCH2	8643	hgsc.bcm.edu	37	1	45293518	45293518	+	Silent	SNP	A	A	G	rs7525308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:45293518A>G	ENST00000372192.3	-	14	2185	c.2055T>C	c.(2053-2055)gcT>gcC	p.A685A	PTCH2_ENST00000447098.2_Silent_p.A685A	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	685					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					GTCTTACCTTAGCATGTGACT	0.617									Basal Cell Nevus syndrome				G|||	2231	0.445487	0.6021	0.4409	5008	,	,		21976	0.4911		0.3191	False		,,,				2504	0.32				p.A685A		Atlas-SNP	.											.	PTCH2	96	.	0			c.T2055C						PASS	.	G	,	2576,1830	533.1+/-373.6	765,1046,392	57.0	55.0	56.0		2055,2055	2.6	0.8	1	dbSNP_116	56	2944,5656	667.7+/-402.5	524,1896,1880	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	1289,2942,2272	GG,GA,AA		34.2326,41.5343,42.4419	,	685/1147,685/1204	45293518	5520,7486	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon14	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	TACCTTAGCATGT	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.2055T>C	1.37:g.45293518A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			A|0.574;G|0.426	0.426	strong		0.617	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
DUSP22	56940	hgsc.bcm.edu	37	6	311938	311938	+	Silent	SNP	C	C	T	rs11242786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:311938C>T	ENST00000344450.5	+	3	557	c.114C>T	c.(112-114)caC>caT	p.H38H	DUSP22_ENST00000605035.1_5'UTR|DUSP22_ENST00000605315.1_Intron|DUSP22_ENST00000605863.1_Intron|DUSP22_ENST00000419235.2_Silent_p.H38H|DUSP22_ENST00000603453.1_Intron	NM_020185.3	NP_064570.1	Q9NRW4	DUS22_HUMAN	dual specificity phosphatase 22	38					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of JNK cascade (GO:0046330)|protein dephosphorylation (GO:0006470)|regulation of cell proliferation (GO:0042127)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(2)	26	all_hematologic(77;0.228)	Breast(5;0.0249)|all_hematologic(90;0.0489)		OV - Ovarian serous cystadenocarcinoma(45;0.0277)|BRCA - Breast invasive adenocarcinoma(62;0.0669)		TGTCTGTCCACGATAGTGCCA	0.493													C|||	184	0.0367412	0.0045	0.0807	5008	,	,		35647	0.0		0.1093	False		,,,				2504	0.0123				p.H38H		Atlas-SNP	.											DUSP22,right_upper_lobe,carcinoma,+2,1	DUSP22	55	1	0			c.C114T						PASS	.	C		111,4295		0,111,2092	168.0	129.0	142.0		114	-3.4	0.8	6	dbSNP_120	142	986,7614		4,978,3318	no	coding-synonymous	DUSP22	NM_020185.3		4,1089,5410	TT,TC,CC		11.4651,2.5193,8.4346		38/185	311938	1097,11909	2203	4300	6503	SO:0001819	synonymous_variant	56940	exon3			TGTCCACGATAGT	AF165519	CCDS4468.1, CCDS69035.1	6p25.3	2013-09-19			ENSG00000112679	ENSG00000112679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	16077	protein-coding gene	gene with protein product						9205128, 11717427	Standard	NM_001286555		Approved	MKPX, JSP1, JKAP, VHX	uc003msx.3	Q9NRW4	OTTHUMG00000014113	ENST00000344450.5:c.114C>T	6.37:g.311938C>T		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	292	91	0.311644	NM_020185	B4DK56|Q59GW2|Q5VWR2|Q96AR1	Silent	SNP	ENST00000344450.5	37	CCDS4468.1																																																																																			C|0.938;T|0.062	0.062	strong		0.493	DUSP22-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000039621.1	NM_020185	
C12orf49	79794	hgsc.bcm.edu	37	12	117175608	117175608	+	Missense_Mutation	SNP	C	C	T	rs73220422	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117175608C>T	ENST00000261318.3	-	1	258	c.98G>A	c.(97-99)aGc>aAc	p.S33N	RNFT2_ENST00000392549.2_5'Flank|RNFT2_ENST00000257575.4_5'Flank|C12orf49_ENST00000536380.1_Silent_p.Q55Q|RNFT2_ENST00000407967.3_5'Flank|RNFT2_ENST00000319176.7_5'Flank	NM_024738.1	NP_079014.1	Q9H741	CL049_HUMAN	chromosome 12 open reading frame 49	33						extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)|skin(1)	4	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0281)		CTTGAAGGTGCTGCTGAGGAA	0.612													C|||	46	0.0091853	0.0008	0.0115	5008	,	,		12967	0.0		0.0328	False		,,,				2504	0.0041				p.S33N		Atlas-SNP	.											.	C12orf49	17	.	0			c.G98A						PASS	.	C	ASN/SER	25,4379	30.8+/-60.4	0,25,2177	74.0	49.0	57.0		98	3.9	1.0	12	dbSNP_130	57	245,8355	94.2+/-156.2	4,237,4059	yes	missense	C12orf49	NM_024738.1	46	4,262,6236	TT,TC,CC		2.8488,0.5677,2.0763	probably-damaging	33/206	117175608	270,12734	2202	4300	6502	SO:0001583	missense	79794	exon1			AAGGTGCTGCTGA	AK025068	CCDS9179.1	12q24.22	2012-05-30			ENSG00000111412	ENSG00000111412			26128	protein-coding gene	gene with protein product						12477932	Standard	NM_024738		Approved	FLJ21415	uc001tvz.1	Q9H741	OTTHUMG00000169392	ENST00000261318.3:c.98G>A	12.37:g.117175608C>T	ENSP00000261318:p.Ser33Asn	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	112	44	0.392857	NM_024738	Q53GE8	Missense_Mutation	SNP	ENST00000261318.3	37	CCDS9179.1	27|27	0.012362637362637362|0.012362637362637362	1|1	0.0020325203252032522|0.0020325203252032522	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	18|18	0.023746701846965697|0.023746701846965697	C|C	18.63|18.63	3.664426|3.664426	0.67700|0.67700	0.005677|0.005677	0.028488|0.028488	ENSG00000111412|ENSG00000111412	ENST00000547606|ENST00000261318	.|T	.|0.47177	.|0.85	4.75|4.75	3.86|3.86	0.44501|0.44501	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.20088|0.20088	0.0483|0.0483	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	.|D	.|0.60160	.|0.987	.|P	.|0.52793	.|0.709	T|T	0.04467|0.04467	-1.0949|-1.0949	5|10	.|0.37606	.|T	.|0.19	-21.1467|-21.1467	10.4099|10.4099	0.44287|0.44287	0.0:0.9099:0.0:0.0901|0.0:0.9099:0.0:0.0901	.|.	.|33	.|Q9H741	.|CL049_HUMAN	T|N	12|33	.|ENSP00000261318:S33N	.|ENSP00000261318:S33N	A|S	-|-	1|2	0|0	C12orf49|C12orf49	115659991|115659991	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	5.142000|5.142000	0.64820|0.64820	1.221000|1.221000	0.43506|0.43506	0.655000|0.655000	0.94253|0.94253	GCA|AGC	C|0.983;T|0.017	0.017	strong		0.612	C12orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403847.1	NM_024738	
NUTM2G	441457	hgsc.bcm.edu	37	9	99700212	99700212	+	Missense_Mutation	SNP	C	C	T	rs202040012	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:99700212C>T	ENST00000372322.3	+	6	1390	c.1369C>T	c.(1369-1371)Cca>Tca	p.P457S	NUTM2G_ENST00000354649.3_Missense_Mutation_p.P457S|HIATL2_ENST00000506067.1_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	457								p.P457T(2)									ATTGCTTTCCCCAGATCCACA	0.577													.|||	56	0.0111821	0.0008	0.0115	5008	,	,		17560	0.0		0.0427	False		,,,				2504	0.0041				p.P457S		Atlas-SNP	.											.	FAM22G	66	.	2	Substitution - Missense(2)	lung(2)	c.C1369T						PASS	.	C	SER/PRO,SER/PRO	19,3583		0,19,1782	39.0	42.0	41.0		1369,1369	-1.7	0.0	9		41	231,7839		1,229,3805	no	missense,missense	FAM22G	NM_001045477.2,NM_001170741.1	74,74	1,248,5587	TT,TC,CC		2.8625,0.5275,2.1419	probably-damaging,probably-damaging	457/493,457/742	99700212	250,11422	1801	4035	5836	SO:0001583	missense	441457	exon6			CTTTCCCCAGATC		CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152			23449	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member G"""	FAM22G			Standard	NM_001045477		Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.1369C>T	9.37:g.99700212C>T	ENSP00000361397:p.Pro457Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_001045477	A6NNI5|Q5VZR3	Missense_Mutation	SNP	ENST00000372322.3	37	CCDS55329.1	.	.	.	.	.	.	.	.	.	.	.	13.33	2.204886	0.38905	0.005275	0.028625	ENSG00000188152	ENST00000354649;ENST00000372322;ENST00000417159;ENST00000375230	T;T	0.24151	1.87;2.68	1.01	-1.74	0.08056	.	0.617073	0.14991	N	0.286692	T	0.10723	0.0262	M	0.62266	1.93	0.09310	N	1	D	0.57899	0.981	P	0.52031	0.688	T	0.07065	-1.0792	10	0.59425	D	0.04	.	2.4279	0.04464	0.0:0.4197:0.3238:0.2565	.	457	Q5VZR2-2	.	S	457;457;306;338	ENSP00000346670:P457S;ENSP00000361397:P457S	ENSP00000346670:P457S	P	+	1	0	FAM22G	98740033	0.002000	0.14202	0.014000	0.15608	0.656000	0.38851	-1.139000	0.03213	-0.528000	0.06366	0.473000	0.43528	CCA	C|0.977;T|0.023	0.023	strong		0.577	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053291.2	NM_001170741	
PCDHB14	56122	hgsc.bcm.edu	37	5	140605069	140605069	+	Silent	SNP	C	C	T	rs145919831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140605069C>T	ENST00000239449.4	+	1	1992	c.1992C>T	c.(1990-1992)gaC>gaT	p.D664D	PCDHB14_ENST00000515856.2_Silent_p.D511D	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	664	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCTGGTGGACGGCTTCTCCC	0.711													c|||	11	0.00219649	0.0	0.0014	5008	,	,		12076	0.0		0.006	False		,,,				2504	0.0041				p.D664D	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C1992T						PASS	.	C		4,4176		0,4,2086	31.0	36.0	34.0		1992	-0.4	1.0	5	dbSNP_134	34	21,8289		0,21,4134	no	coding-synonymous	PCDHB14	NM_018934.2		0,25,6220	TT,TC,CC		0.2527,0.0957,0.2002		664/799	140605069	25,12465	2090	4155	6245	SO:0001819	synonymous_variant	56122	exon1			GGTGGACGGCTTC	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.1992C>T	5.37:g.140605069C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	15	12	0.8	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.998;T|0.002	0.002	strong		0.711	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
CD109	135228	hgsc.bcm.edu	37	6	74521947	74521947	+	Missense_Mutation	SNP	C	C	T	rs2917862	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:74521947C>T	ENST00000287097.5	+	29	3834	c.3722C>T	c.(3721-3723)aCg>aTg	p.T1241M	CD109_ENST00000437994.2_Missense_Mutation_p.T1224M|CD109_ENST00000422508.2_Missense_Mutation_p.T1164M			Q6YHK3	CD109_HUMAN	CD109 molecule	1241			T -> M (in dbSNP:rs2917862). {ECO:0000269|PubMed:11861284, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GTACAGCCAACGGCAGTTAAT	0.328													C|||	2045	0.408347	0.202	0.4669	5008	,	,		20547	0.4583		0.4901	False		,,,				2504	0.5102				p.T1241M		Atlas-SNP	.											.	CD109	170	.	0			c.C3722T						PASS	.	C	MET/THR,MET/THR,MET/THR	1141,3265	406.6+/-333.9	144,853,1206	149.0	141.0	144.0		3671,3491,3722	-2.0	0.0	6	dbSNP_101	144	4056,4544	558.9+/-387.3	977,2102,1221	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	81,81,81	1121,2955,2427	TT,TC,CC		47.1628,25.8965,39.9585	benign,benign,benign	1224/1429,1164/1369,1241/1446	74521947	5197,7809	2203	4300	6503	SO:0001583	missense	135228	exon29			AGCCAACGGCAGT	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.3722C>T	6.37:g.74521947C>T	ENSP00000287097:p.Thr1241Met	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	118	16	0.135593	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	920	0.42124542124542125	112	0.22764227642276422	159	0.43922651933701656	265	0.4632867132867133	384	0.5065963060686016	C	4.096	0.015803	0.07959	0.258965	0.471628	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.25579	1.79;2.02;1.8	5.25	-1.95	0.07548	.	0.901547	0.09940	N	0.736070	T	0.10035	0.0246	L	0.50333	1.59	0.80722	P	0.0	B;P;P	0.43542	0.177;0.81;0.607	B;B;B	0.37550	0.03;0.253;0.107	T	0.19321	-1.0309	9	0.44086	T	0.13	.	12.6268	0.56634	0.0:0.2844:0.0:0.7156	rs2917862;rs58804669;rs2917862	1164;1224;1241	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	M	1224;1164;1241	ENSP00000388062:T1224M;ENSP00000404475:T1164M;ENSP00000287097:T1241M	ENSP00000287097:T1241M	T	+	2	0	CD109	74578668	0.000000	0.05858	0.001000	0.08648	0.536000	0.34869	-0.978000	0.03778	-0.333000	0.08476	-0.251000	0.11542	ACG	C|0.593;T|0.407	0.407	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
MUC16	94025	hgsc.bcm.edu	37	19	9020154	9020154	+	Silent	SNP	A	A	G	rs11882881|rs386806634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9020154A>G	ENST00000397910.4	-	21	37544	c.37341T>C	c.(37339-37341)tcT>tcC	p.S12447S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12449	SEA 3. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATCCTTCTCAGACCTGGGGA	0.502													-|||	2236	0.446486	0.4138	0.5418	5008	,	,		19846	0.4623		0.3966	False		,,,				2504	0.4581				p.S12447S		Atlas-SNP	.											.	MUC16	4315	.	0			c.T37341C						PASS	.	T		1475,2351		288,899,726	93.0	81.0	85.0		37341	-6.4	0.0	19	dbSNP_120	85	3138,5116		570,1998,1559	no	coding-synonymous	MUC16	NM_024690.2		858,2897,2285	GG,GA,AA		38.0179,38.552,38.1871		12447/14508	9020154	4613,7467	1913	4127	6040	SO:0001819	synonymous_variant	94025	exon21			CTTCTCAGACCTG	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.37341T>C	19.37:g.9020154A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			A|0.580;G|0.420	0.420	strong		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
FAM160A2	84067	hgsc.bcm.edu	37	11	6238960	6238960	+	Missense_Mutation	SNP	C	C	A	rs3750943	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6238960C>A	ENST00000449352.2	-	9	2119	c.1856G>T	c.(1855-1857)cGg>cTg	p.R619L	FAM160A2_ENST00000265978.4_Missense_Mutation_p.R633L|FAM160A2_ENST00000524416.1_Missense_Mutation_p.R619L|FAM160A2_ENST00000529360.1_5'Flank			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	619			R -> L (in dbSNP:rs3750943).		early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						acccccagcccgccccctcct	0.652													A|||	654	0.130591	0.059	0.0778	5008	,	,		8807	0.2431		0.1461	False		,,,				2504	0.1329				p.R633L		Atlas-SNP	.											.	FAM160A2	100	.	0			c.G1898T						PASS	.	A	LEU/ARG,LEU/ARG	318,4002		17,284,1859	9.0	10.0	10.0		1856,1898	4.0	0.9	11	dbSNP_107	10	1364,7104		122,1120,2992	no	missense,missense	FAM160A2	NM_001098794.1,NM_032127.3	102,102	139,1404,4851	AA,AC,CC		16.1077,7.3611,13.153	benign,benign	619/973,633/987	6238960	1682,11106	2160	4234	6394	SO:0001583	missense	84067	exon9			CCAGCCCGCCCCC		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.1856G>T	11.37:g.6238960C>A	ENSP00000416918:p.Arg619Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	320	0.14652014652014653	37	0.07520325203252033	36	0.09944751381215469	125	0.21853146853146854	122	0.16094986807387862	A	1.787	-0.480378	0.04383	0.073611	0.161077	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.46819	0.86;0.86;0.86	5.16	3.97	0.46021	.	0.645966	0.14866	N	0.293783	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.24764	-1.0151	9	0.09084	T	0.74	-18.0925	5.0671	0.14587	0.6113:0.1554:0.0:0.2333	rs3750943	619;619;633	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	L	619;544;633;619	ENSP00000416918:R619L;ENSP00000265978:R633L;ENSP00000431773:R619L	ENSP00000265978:R633L	R	-	2	0	FAM160A2	6195536	0.534000	0.26362	0.881000	0.34555	0.135000	0.20990	1.447000	0.35101	0.994000	0.38892	-0.363000	0.07495	CGG	C|0.853;A|0.147	0.147	strong		0.652	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
CPM	1368	hgsc.bcm.edu	37	12	69252715	69252715	+	Silent	SNP	A	A	G	rs1143653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:69252715A>G	ENST00000551568.1	-	8	1137	c.1077T>C	c.(1075-1077)tcT>tcC	p.S359S	CPM_ENST00000546373.1_Silent_p.S359S|CPM_ENST00000338356.3_Silent_p.S359S	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	359					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			TTATTATATAAGACCCAGGCA	0.328													G|||	907	0.18111	0.323	0.2075	5008	,	,		12922	0.0139		0.2117	False		,,,				2504	0.1115				p.S359S		Atlas-SNP	.											.	CPM	30	.	0			c.T1077C						PASS	.	G	,,	1311,3095	692.4+/-405.5	193,925,1085	79.0	78.0	78.0		1077,1077,1077	0.9	0.7	12	dbSNP_86	78	1780,6818	729.6+/-406.7	194,1392,2713	no	coding-synonymous,coding-synonymous,coding-synonymous	CPM	NM_001005502.2,NM_001874.4,NM_198320.3	,,	387,2317,3798	GG,GA,AA		20.7025,29.7549,23.7696	,,	359/444,359/444,359/444	69252715	3091,9913	2203	4299	6502	SO:0001819	synonymous_variant	1368	exon8			TATATAAGACCCA	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"""renal carboxypeptidase"", ""urinary carboxypeptidase B"""	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.1077T>C	12.37:g.69252715A>G		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_001005502	B2R800|Q9H2K9	Silent	SNP	ENST00000551568.1	37	CCDS8987.1	369	0.16895604395604397	135	0.27439024390243905	69	0.19060773480662985	8	0.013986013986013986	157	0.20712401055408972	G	7.668	0.686302	0.14973	0.297549	0.207025	ENSG00000135678	ENST00000551897	.	.	.	5.38	0.945	0.19543	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999906543	.	.	.	.	.	.	T	0.36212	-0.9757	3	.	.	.	-6.6564	1.4215	0.02313	0.2953:0.1051:0.3859:0.2137	rs1143653;rs17225048;rs17362456;rs60210122;rs17225048	.	.	.	P	162	.	.	L	-	2	0	CPM	67538982	0.910000	0.30920	0.683000	0.30040	0.966000	0.64601	-0.043000	0.12043	0.023000	0.15187	-0.374000	0.07098	CTT	T|0.153;G|0.175;C|0.041;A|0.631	0.175	strong		0.328	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
PKHD1	5314	hgsc.bcm.edu	37	6	51524403	51524403	+	Silent	SNP	G	G	A	rs34460237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:51524403G>A	ENST00000371117.3	-	61	10796	c.10521C>T	c.(10519-10521)caC>caT	p.H3507H		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3507					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)					CTAAGAAGACGTGGGGGCTCT	0.433													G|||	329	0.0656949	0.003	0.098	5008	,	,		19840	0.1339		0.0517	False		,,,				2504	0.0716				p.H3507H		Atlas-SNP	.											.	PKHD1	927	.	0			c.C10521T						PASS	.	G		44,4362	46.0+/-80.4	0,44,2159	64.0	64.0	64.0		10521	-9.8	0.0	6	dbSNP_126	64	371,8229	121.5+/-180.6	11,349,3940	no	coding-synonymous	PKHD1	NM_138694.3		11,393,6099	AA,AG,GG		4.314,0.9986,3.1908		3507/4075	51524403	415,12591	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon61			GAAGACGTGGGGG	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.10521C>T	6.37:g.51524403G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			G|0.955;A|0.045	0.045	strong		0.433	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PRR21	643905	hgsc.bcm.edu	37	2	240982052	240982052	+	Silent	SNP	C	C	G	rs77588089		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:240982052C>G	ENST00000408934.1	-	1	347	c.348G>C	c.(346-348)tcG>tcC	p.S116S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	116	Pro-rich.							p.S116S(2)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GAGGCATGGACGAAGGGCCGT	0.627																																					p.S116S		Atlas-SNP	.											PRR21,pharynx,carcinoma,0,4	PRR21	53	4	2	Substitution - coding silent(2)	upper_aerodigestive_tract(2)	c.G348C						PASS	.						5.0	6.0	6.0					2																	240982052		1363	2884	4247	SO:0001819	synonymous_variant	643905	exon1			CATGGACGAAGGG	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.348G>C	2.37:g.240982052C>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	49	26	0.530612	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			C|0.250;G|0.750	0.750	weak		0.627	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
PSG6	5675	hgsc.bcm.edu	37	19	43420451	43420451	+	Missense_Mutation	SNP	G	G	C	rs386809477|rs3198831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:43420451G>C	ENST00000292125.2	-	2	297	c.253C>G	c.(253-255)Cac>Gac	p.H85D	PSG6_ENST00000601833.1_Missense_Mutation_p.H14D|PSG6_ENST00000402603.4_Missense_Mutation_p.H85D|PSG6_ENST00000187910.2_Missense_Mutation_p.H85D	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	85	Ig-like V-type.		H -> D (in dbSNP:rs3198831). {ECO:0000269|PubMed:2271648, ECO:0000269|PubMed:2346748}.		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				ATTTGACCGTGTACTACATAT	0.443													.|||	2271	0.453474	0.5991	0.4265	5008	,	,		21337	0.4325		0.2525	False		,,,				2504	0.5041				p.H85D		Atlas-SNP	.											.	PSG6	89	.	0			c.C253G						PASS	.	C	ASP/HIS,ASP/HIS	2533,1869		767,999,435	312.0	293.0	300.0		253,253	-4.2	0.0	19	dbSNP_105	300	2232,6366		347,1538,2414	yes	missense,missense	PSG6	NM_001031850.2,NM_002782.3	81,81	1114,2537,2849	CC,CG,GG		25.9595,42.458,36.6538	,	85/425,85/436	43420451	4765,8235	2201	4299	6500	SO:0001583	missense	5675	exon2			GACCGTGTACTAC		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.253C>G	19.37:g.43420451G>C	ENSP00000292125:p.His85Asp	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	196	97	0.494898	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	850	0.3891941391941392	293	0.5955284552845529	130	0.35911602209944754	231	0.40384615384615385	196	0.25857519788918204	N	0.005	-2.167004	0.00318	0.57542	0.259595	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.63744	-0.06;-0.06;-0.06	2.24	-4.23	0.03789	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00033	-2.575	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34153	-0.9840	8	0.02654	T	1	.	5.3567	0.16065	0.2634:0.2385:0.4981:0.0	rs3198831;rs52810447;rs3198831	85;85;85	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	D	85	ENSP00000187910:H85D;ENSP00000385736:H85D;ENSP00000292125:H85D	ENSP00000187910:H85D	H	-	1	0	PSG6	48112291	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.739000	0.01840	-1.078000	0.03117	-1.041000	0.02371	CAC	G|0.625;C|0.375	0.375	strong		0.443	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
BOC	91653	hgsc.bcm.edu	37	3	112989763	112989763	+	Silent	SNP	C	C	T	rs9819129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112989763C>T	ENST00000495514.1	+	6	1343	c.639C>T	c.(637-639)tcC>tcT	p.S213S	BOC_ENST00000273395.4_Silent_p.S213S|BOC_ENST00000355385.3_Silent_p.S213S			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	213	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGAAAACCTCCGGCTCCAGCG	0.607													C|||	113	0.0225639	0.0484	0.0173	5008	,	,		20556	0.0		0.0258	False		,,,				2504	0.0112				p.S213S		Atlas-SNP	.											.	BOC	139	.	0			c.C639T						PASS	.	C		167,4239	110.4+/-148.6	2,163,2038	126.0	126.0	126.0		639	-11.6	0.5	3	dbSNP_119	126	209,8391	89.7+/-151.9	2,205,4093	no	coding-synonymous	BOC	NM_033254.2		4,368,6131	TT,TC,CC		2.4302,3.7903,2.891		213/1115	112989763	376,12630	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon6			AACCTCCGGCTCC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.639C>T	3.37:g.112989763C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	65	21	0.323077	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.974;T|0.026	0.026	strong		0.607	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918963	12918963	+	Missense_Mutation	SNP	G	G	T	rs9661554	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12918963G>T	ENST00000240189.2	+	2	186	c.99G>T	c.(97-99)agG>agT	p.R33S		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	33			R -> S (in dbSNP:rs9661554).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGCTGCCCAGGGTGCTCTATC	0.627													.|||	523	0.104433	0.1127	0.0965	5008	,	,		19696	0.128		0.1064	False		,,,				2504	0.0726				p.R33S		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G99T						PASS	.	G	SER/ARG	576,3826	254.9+/-260.3	62,452,1687	100.0	109.0	106.0		99	-1.7	0.0	1	dbSNP_119	106	975,7617	211.0+/-251.7	75,825,3396	no	missense	PRAMEF2	NM_023014.1	110	137,1277,5083	TT,TG,GG		11.3478,13.085,11.9363	probably-damaging	33/475	12918963	1551,11443	2201	4296	6497	SO:0001583	missense	65122	exon2			GCCCAGGGTGCTC		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.99G>T	1.37:g.12918963G>T	ENSP00000240189:p.Arg33Ser	Somatic	325	0	0		WXS	Illumina HiSeq	Phase_I	337	23	0.0682493	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	218	0.09981684981684982	38	0.07723577235772358	34	0.09392265193370165	60	0.1048951048951049	86	0.11345646437994723	G	4.074	0.011518	0.07912	0.13085	0.113478	ENSG00000120952	ENST00000240189	T	0.04551	3.6	0.842	-1.68	0.08212	.	1.537720	0.04347	N	0.355072	T	0.00073	0.0002	M	0.70275	2.135	0.80722	P	0.0	P	0.44776	0.843	P	0.45610	0.487	T	0.31696	-0.9934	9	0.20519	T	0.43	.	4.1361	0.10170	0.5271:0.0:0.4729:0.0	rs9661554	33	O60811	PRAM2_HUMAN	S	33	ENSP00000240189:R33S	ENSP00000240189:R33S	R	+	3	2	PRAMEF2	12841550	0.017000	0.18338	0.000000	0.03702	0.002000	0.02628	-0.372000	0.07504	-0.705000	0.05035	-1.038000	0.02383	AGG	G|0.891;T|0.109	0.109	strong		0.627	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549443	32549443	+	Silent	SNP	G	G	A	rs557962729	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32549443G>A	ENST00000360004.5	-	3	648	c.543C>T	c.(541-543)gaC>gaT	p.D181D		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	181	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						GGAAGGTCCAGTCTCCATTCT	0.552										Multiple Myeloma(14;0.17)			G|||	324	0.0646965	0.0575	0.1052	5008	,	,		26939	0.0208		0.1282	False		,,,				2504	0.0256				p.D181D		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C543T						PASS	.	G		136,2886		11,114,1386	143.0	160.0	154.0		543	3.9	1.0	6	dbSNP_134	154	344,5074		27,290,2392	no	coding-synonymous	HLA-DRB1	NM_002124.3		38,404,3778	AA,AG,GG		6.3492,4.5003,5.6872		181/267	32549443	480,7960	1511	2709	4220	SO:0001819	synonymous_variant	3123	exon3			GGTCCAGTCTCCA	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.543C>T	6.37:g.32549443G>A		Somatic	385	1	0.0025974		WXS	Illumina HiSeq	Phase_I	247	82	0.331984	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.980;A|0.020	0.020	strong		0.552	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
FOCAD	54914	hgsc.bcm.edu	37	9	20953049	20953049	+	Missense_Mutation	SNP	A	A	G	rs3206852	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:20953049A>G	ENST00000380249.1	+	37	4481	c.4117A>G	c.(4117-4119)Aca>Gca	p.T1373A	FOCAD_ENST00000605086.1_Missense_Mutation_p.T809A|FOCAD_ENST00000338382.6_Missense_Mutation_p.T1373A	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1373			T -> A (in dbSNP:rs3206852). {ECO:0000269|PubMed:14702039}.|T -> P (in dbSNP:rs3206852).|T -> S (in dbSNP:rs3206852).			focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)		p.T1373A(1)									CTTCTTCATTACAGGAGGAAA	0.373													A|||	1681	0.335663	0.2405	0.2695	5008	,	,		19170	0.4355		0.4006	False		,,,				2504	0.3415				p.T1373A		Atlas-SNP	.											KIAA1797,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A4117G						PASS	.	A	ALA/THR	1256,3150	428.9+/-342.0	163,930,1110	111.0	108.0	109.0		4117	3.7	1.0	9	dbSNP_105	109	3578,5022	516.7+/-378.9	753,2072,1475	yes	missense	KIAA1797	NM_017794.3	58	916,3002,2585	GG,GA,AA		41.6047,28.5066,37.1675	benign	1373/1802	20953049	4834,8172	2203	4300	6503	SO:0001583	missense	54914	exon37			TTCATTACAGGAG	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.4117A>G	9.37:g.20953049A>G	ENSP00000369599:p.Thr1373Ala	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	64	20	0.3125	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	772	0.3534798534798535	136	0.2764227642276423	101	0.27900552486187846	227	0.3968531468531469	308	0.40633245382585753	A	10.14	1.267734	0.23136	0.285066	0.416047	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.21932	1.98;1.98	6.07	3.73	0.42828	.	0.342483	0.31145	N	0.008168	T	0.00012	0.0000	L	0.44542	1.39	0.43740	P	0.0037679999999999936	B	0.02656	0.0	B	0.04013	0.001	T	0.47497	-0.9113	9	0.28530	T	0.3	-2.0043	2.4306	0.04470	0.5373:0.0:0.2603:0.2024	rs3206852;rs3739935;rs17759648;rs58774393;rs3206852	1373	Q5VW36	K1797_HUMAN	A	1373	ENSP00000369599:T1373A;ENSP00000344307:T1373A	ENSP00000344307:T1373A	T	+	1	0	KIAA1797	20943049	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	1.718000	0.38001	1.107000	0.41642	0.533000	0.62120	ACA	G|0.351;A|0.649	0.351	strong		0.373	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79065483	79065483	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79065483G>A	ENST00000388820.4	-	14	2283	c.2073C>T	c.(2071-2073)caC>caT	p.H691H	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	691	Cys-rich.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						AGCCGTTGCCGTGGCACACAC	0.652																																					p.H691H		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C2073T						PASS	.						10.0	10.0	10.0					15																	79065483		2113	4023	6136	SO:0001819	synonymous_variant	11173	exon14			GTTGCCGTGGCAC	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.2073C>T	15.37:g.79065483G>A		Somatic	610	0	0		WXS	Illumina HiSeq	Phase_I	709	69	0.0973202	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			.	.	none		0.652	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
VARS2	57176	hgsc.bcm.edu	37	6	30892322	30892322	+	Silent	SNP	C	C	T	rs2532942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30892322C>T	ENST00000321897.5	+	25	3290	c.2658C>T	c.(2656-2658)ccC>ccT	p.P886P	VARS2_ENST00000541562.1_Silent_p.P916P|VARS2_ENST00000542001.1_Silent_p.P746P|VARS2_ENST00000416670.2_Silent_p.P886P|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	886					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CCCCCTACCCCAGCGCCTGCA	0.662													C|||	1112	0.222045	0.0983	0.2075	5008	,	,		12561	0.247		0.3559	False		,,,				2504	0.2362				p.P916P		Atlas-SNP	.											.	VARS2	60	.	0			c.C2748T						PASS	.	C	,,	442,2570		36,370,1100	15.0	19.0	17.0		2238,2748,2658	2.4	0.9	6	dbSNP_100	17	2048,3366		372,1304,1031	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	408,1674,2131	TT,TC,CC		37.8279,14.6746,29.5514	,,	746/924,916/1094,886/1064	30892322	2490,5936	1506	2707	4213	SO:0001819	synonymous_variant	57176	exon26			CTACCCCAGCGCC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.2658C>T	6.37:g.30892322C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			C|0.739;T|0.261	0.261	strong		0.662	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
SLC11A2	4891	hgsc.bcm.edu	37	12	51390685	51390685	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51390685C>T	ENST00000262051.7	-	9	833	c.746G>A	c.(745-747)cGc>cAc	p.R249H	SLC11A2_ENST00000545993.2_Missense_Mutation_p.R245H|SLC11A2_ENST00000547198.1_Missense_Mutation_p.R249H|SLC11A2_ENST00000394904.3_Missense_Mutation_p.R278H|SLC11A2_ENST00000541174.2_Missense_Mutation_p.R249H|SLC11A2_ENST00000262052.5_Missense_Mutation_p.R249H|SLC11A2_ENST00000546743.1_Missense_Mutation_p.R170H|SLC11A2_ENST00000547688.1_Missense_Mutation_p.R278H	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	249					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						CTGTGGAGTGCGACAGCCTGA	0.498																																					p.R278H		Atlas-SNP	.											SLC11A2,caecum,carcinoma,0,1	SLC11A2	51	1	0			c.G833A						PASS	.						233.0	148.0	177.0					12																	51390685		2203	4300	6503	SO:0001583	missense	4891	exon9			GGAGTGCGACAGC	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.746G>A	12.37:g.51390685C>T	ENSP00000262051:p.Arg249His	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	148	63	0.425676	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170540	0.38315	.	.	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.30714	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.52	5.79	-5.03	0.02973	.	1.323470	0.04699	N	0.415517	T	0.18964	0.0455	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B	0.10450	0.003;0.003;0.005;0.003;0.003;0.003	T	0.34453	-0.9828	10	0.48119	T	0.1	8.703	8.5091	0.33206	0.0:0.402:0.0991:0.4989	.	212;245;278;249;98;249	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	H	249;249;249;278;278;249;245;170	ENSP00000262051:R249H;ENSP00000446769:R249H;ENSP00000262052:R249H;ENSP00000378364:R278H;ENSP00000449200:R278H;ENSP00000444542:R249H;ENSP00000442810:R245H;ENSP00000446914:R170H	ENSP00000262051:R249H	R	-	2	0	SLC11A2	49676952	0.000000	0.05858	0.001000	0.08648	0.493000	0.33554	0.566000	0.23593	-0.836000	0.04229	-0.140000	0.14226	CGC	.	.	none		0.498	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
MMP8	4317	hgsc.bcm.edu	37	11	102587062	102587062	+	Silent	SNP	G	G	A	rs3740938	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102587062G>A	ENST00000236826.3	-	6	971	c.873C>T	c.(871-873)ctC>ctT	p.L291L		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	291					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)	p.L291L(1)		autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	TTTCTCCACGGAGTGTGGTGA	0.378													G|||	588	0.117412	0.0038	0.1282	5008	,	,		16940	0.2778		0.0626	False		,,,				2504	0.1544				p.L291L		Atlas-SNP	.											MMP8,colon,carcinoma,0,5	MMP8	68	5	1	Substitution - coding silent(1)	stomach(1)	c.C873T						scavenged	.	G		86,4320	71.4+/-109.4	3,80,2120	117.0	122.0	120.0		873	4.1	1.0	11	dbSNP_107	120	547,8051	151.0+/-205.8	15,517,3767	no	coding-synonymous	MMP8	NM_002424.2		18,597,5887	AA,AG,GG		6.3619,1.9519,4.8677		291/468	102587062	633,12371	2203	4299	6502	SO:0001819	synonymous_variant	4317	exon6			TCCACGGAGTGTG	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.873C>T	11.37:g.102587062G>A		Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_002424	Q45F99	Silent	SNP	ENST00000236826.3	37	CCDS8320.1	241	0.11034798534798534	1	0.0020325203252032522	40	0.11049723756906077	155	0.270979020979021	45	0.059366754617414245	G	8.669	0.902281	0.17760	0.019519	0.063619	ENSG00000118113	ENST00000438475	.	.	.	5.03	4.11	0.48088	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999495	.	.	.	.	.	.	T	0.17258	-1.0375	3	.	.	.	.	8.5229	0.33287	0.0:0.1684:0.6573:0.1743	rs3740938;rs60162198;rs3740938	.	.	.	S	267	.	.	P	-	1	0	MMP8	102092272	0.632000	0.27172	0.990000	0.47175	0.986000	0.74619	-0.270000	0.08584	1.092000	0.41356	0.563000	0.77884	CCG	G|0.920;A|0.080	0.080	strong		0.378	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
KIF27	55582	hgsc.bcm.edu	37	9	86504005	86504005	+	Missense_Mutation	SNP	C	C	T	rs13289566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:86504005C>T	ENST00000297814.2	-	7	2116	c.1973G>A	c.(1972-1974)gGa>gAa	p.G658E	KIF27_ENST00000376347.1_Missense_Mutation_p.G49E|KIF27_ENST00000334204.2_Missense_Mutation_p.G658E|KIF27_ENST00000413982.1_Missense_Mutation_p.G658E	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	658					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						ATACCTAGTTCCAGATTTCTC	0.328													C|||	875	0.17472	0.2451	0.1657	5008	,	,		17277	0.002		0.2336	False		,,,				2504	0.2035				p.G658E		Atlas-SNP	.											.	KIF27	103	.	0			c.G1973A						PASS	.	C	GLU/GLY	1101,3303	368.1+/-318.5	137,827,1238	52.0	51.0	51.0		1973	0.4	0.7	9	dbSNP_121	51	1869,6725	310.1+/-309.7	191,1487,2619	no	missense	KIF27	NM_017576.1	98	328,2314,3857	TT,TC,CC		21.7477,25.0,22.8497	benign	658/1402	86504005	2970,10028	2202	4297	6499	SO:0001583	missense	55582	exon7			CTAGTTCCAGATT	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.1973G>A	9.37:g.86504005C>T	ENSP00000297814:p.Gly658Glu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	99	39	0.393939	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	346	0.15842490842490842	110	0.22357723577235772	62	0.1712707182320442	0	0.0	174	0.22955145118733508	C	7.059	0.565938	0.13560	0.25	0.217477	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204;ENST00000376347	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	4.95	0.394	0.16299	.	1.657160	0.04144	N	0.320083	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.16571	-1.0398	9	0.02654	T	1	.	1.4027	0.02274	0.1283:0.2012:0.2611:0.4094	rs13289566;rs57559061	658;658;658	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	E	658;658;658;49	ENSP00000297814:G658E;ENSP00000401688:G658E;ENSP00000333928:G658E;ENSP00000365525:G49E	ENSP00000297814:G658E	G	-	2	0	KIF27	85693825	0.638000	0.27225	0.703000	0.30354	0.951000	0.60555	0.075000	0.14686	0.094000	0.17404	0.557000	0.71058	GGA	C|0.798;T|0.202	0.202	strong		0.328	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
OBSCN	84033	hgsc.bcm.edu	37	1	228496014	228496014	+	Silent	SNP	G	G	A	rs876180	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228496014G>A	ENST00000422127.1	+	47	12713	c.12669G>A	c.(12667-12669)acG>acA	p.T4223T	OBSCN_ENST00000366707.4_Silent_p.T1857T|OBSCN_ENST00000366709.4_Silent_p.T1342T|OBSCN_ENST00000284548.11_Silent_p.T4223T|OBSCN_ENST00000570156.2_Silent_p.T5180T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4223	Ig-like 43.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGGCGTGACGCCCGAGGACG	0.637													G|||	1067	0.213059	0.32	0.2781	5008	,	,		18436	0.1825		0.161	False		,,,				2504	0.1074				p.T5180T		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,0,3	OBSCN	2142	3	0			c.G15540A						PASS	.	G	,	1355,2893		229,897,998	36.0	40.0	39.0		12669,12669	-12.1	0.0	1	dbSNP_86	39	1498,6956		141,1216,2870	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	370,2113,3868	AA,AG,GG		17.7194,31.8974,22.461	,	4223/7969,4223/6621	228496014	2853,9849	2124	4227	6351	SO:0001819	synonymous_variant	84033	exon58			CGTGACGCCCGAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12669G>A	1.37:g.228496014G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.776;A|0.224	0.224	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
HTR3D	200909	hgsc.bcm.edu	37	3	183755822	183755822	+	Missense_Mutation	SNP	G	G	A	rs1000952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183755822G>A	ENST00000382489.3	+	6	674	c.674G>A	c.(673-675)cGc>cAc	p.R225H	HTR3D_ENST00000334128.2_Missense_Mutation_p.R52H|HTR3D_ENST00000428798.2_Missense_Mutation_p.R177H|HTR3D_ENST00000453435.1_Missense_Mutation_p.R6H	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	225			R -> H (in dbSNP:rs1000952). {ECO:0000269|PubMed:15489334}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	GCCATCAGGCGCAGGTGCAGG	0.572													G|||	3826	0.763978	0.8623	0.7061	5008	,	,		18146	0.9167		0.6531	False		,,,				2504	0.6288				p.R225H		Atlas-SNP	.											.	HTR3D	65	.	0			c.G674A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	3626,780	752.0+/-412.2	1489,648,66	49.0	42.0	44.0		530,674,155	0.2	1.0	3	dbSNP_86	44	5462,3138	655.2+/-401.2	1734,1994,572	yes	missense,missense,missense	HTR3D	NM_001145143.1,NM_001163646.1,NM_182537.2	29,29,29	3223,2642,638	AA,AG,GG		36.4884,17.7031,30.1246	possibly-damaging,possibly-damaging,possibly-damaging	177/405,225/455,52/280	183755822	9088,3918	2203	4300	6503	SO:0001583	missense	200909	exon6			TCAGGCGCAGGTG	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	ENST00000382489.3:c.674G>A	3.37:g.183755822G>A	ENSP00000371929:p.Arg225His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Missense_Mutation	SNP	ENST00000382489.3	37	CCDS54685.1	1660	0.76007326007326	407	0.8272357723577236	243	0.6712707182320442	527	0.9213286713286714	483	0.637203166226913	G	3.556	-0.090615	0.07053	0.822969	0.635116	ENSG00000186090	ENST00000334128;ENST00000428798;ENST00000382489;ENST00000453435	T;D;D;T	0.93133	-1.05;-2.0;-3.17;-0.94	0.149	0.149	0.14863	Neurotransmitter-gated ion-channel ligand-binding (1);	0.145914	0.46145	N	0.000310	T	0.00012	0.0000	L	0.55213	1.73	0.51767	P	6.799999999995698E-5	D;B;B;B	0.71674	0.998;0.228;0.114;0.45	P;B;B;B	0.54460	0.753;0.171;0.071;0.249	T	0.42699	-0.9436	8	0.66056	D	0.02	-7.3849	.	.	.	rs1000952;rs17671237;rs1000952	225;52;6;52	Q70Z44;Q70Z44-2;Q70Z44-3;F6WC43	5HT3D_HUMAN;.;.;.	H	52;177;225;6	ENSP00000334315:R52H;ENSP00000405409:R177H;ENSP00000371929:R225H;ENSP00000389268:R6H	ENSP00000334315:R52H	R	+	2	0	HTR3D	185238516	0.602000	0.26916	0.962000	0.40283	0.012000	0.07955	0.251000	0.18257	0.192000	0.20272	0.195000	0.17529	CGC	G|0.272;A|0.728	0.728	strong		0.572	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	
CCDC171	203238	hgsc.bcm.edu	37	9	15874585	15874585	+	Missense_Mutation	SNP	T	T	G	rs149814894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:15874585T>G	ENST00000380701.3	+	24	3852	c.3524T>G	c.(3523-3525)cTa>cGa	p.L1175R	CCDC171_ENST00000486641.2_3'UTR|CCDC171_ENST00000297641.3_Missense_Mutation_p.L1175R	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1175																	GACTTCACCCTACAGCTACCC	0.493													T|||	34	0.00678914	0.0	0.0058	5008	,	,		17965	0.0		0.0109	False		,,,				2504	0.0194				p.L1175R		Atlas-SNP	.											C9orf93_ENST00000380689,NS,lymphoid_neoplasm,0,2	.	.	2	0			c.T3524G						PASS	.	T	ARG/LEU	5,4401	9.9+/-24.2	0,5,2198	139.0	125.0	130.0		3524	5.7	1.0	9	dbSNP_134	130	61,8539	37.8+/-93.5	0,61,4239	yes	missense	C9orf93	NM_173550.2	102	0,66,6437	GG,GT,TT		0.7093,0.1135,0.5075	probably-damaging	1175/1327	15874585	66,12940	2203	4300	6503	SO:0001583	missense	203238	exon24			TCACCCTACAGCT	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.3524T>G	9.37:g.15874585T>G	ENSP00000370077:p.Leu1175Arg	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	196	92	0.469388	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	T|T	18.34|18.34	3.602189|3.602189	0.66445|0.66445	0.001135|0.001135	0.007093|0.007093	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701;ENST00000359391|ENST00000449575;ENST00000432954	T;T|.	0.19938|.	2.14;2.11|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.64402|.	D|.	0.000020|.	T|T	0.46889|0.46889	0.1416|0.1416	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.998;0.999|.	T|T	0.48031|0.48031	-0.9070|-0.9070	10|5	0.45353|.	T|.	0.12|.	-5.9924|-5.9924	16.1053|16.1053	0.81216|0.81216	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1183;442;1175|.	B7ZM22;A6NK04;Q6TFL3|.	.;.;CI093_HUMAN|.	R|D	1175;442;1175;29|415;229	ENSP00000297641:L1175R;ENSP00000370077:L1175R|.	ENSP00000297641:L1175R|.	L|Y	+|+	2|1	0|0	C9orf93|C9orf93	15864585|15864585	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	5.172000|5.172000	0.65003|0.65003	2.205000|2.205000	0.71048|0.71048	0.524000|0.524000	0.50904|0.50904	CTA|TAC	T|0.993;G|0.007	0.007	strong		0.493	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
OR9G4	283189	hgsc.bcm.edu	37	11	56511160	56511160	+	Missense_Mutation	SNP	A	A	G	rs11228763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56511160A>G	ENST00000302957.3	-	1	127	c.128T>C	c.(127-129)tTt>tCt	p.F43S		NM_001005284.1	NP_001005284.1	Q8NGQ1	OR9G4_HUMAN	olfactory receptor, family 9, subfamily G, member 4	43			F -> S (in dbSNP:rs11228763).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F43S(1)		NS(1)|autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						AAACACTCCAAATAGAATCGG	0.438													A|||	504	0.100639	0.084	0.0994	5008	,	,		18457	0.119		0.1004	False		,,,				2504	0.1053				p.F43S		Atlas-SNP	.											OR9G4,NS,carcinoma,0,1	OR9G4	73	1	1	Substitution - Missense(1)	stomach(1)	c.T128C						PASS	.	A	SER/PHE	403,3999	199.4+/-223.0	16,371,1814	76.0	70.0	72.0		128	4.0	0.9	11	dbSNP_120	72	729,7863	177.5+/-227.1	34,661,3601	yes	missense	OR9G4	NM_001005284.1	155	50,1032,5415	GG,GA,AA		8.4846,9.1549,8.7117	probably-damaging	43/328	56511160	1132,11862	2201	4296	6497	SO:0001583	missense	283189	exon1			ACTCCAAATAGAA	BK004400	CCDS31537.1	11q11	2012-08-09			ENSG00000172457	ENSG00000172457		"""GPCR / Class A : Olfactory receptors"""	15322	protein-coding gene	gene with protein product							Standard	NM_001005284		Approved		uc010rjo.2	Q8NGQ1	OTTHUMG00000166932	ENST00000302957.3:c.128T>C	11.37:g.56511160A>G	ENSP00000307515:p.Phe43Ser	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_001005284	Q6IF62|Q96RA9	Missense_Mutation	SNP	ENST00000302957.3	37	CCDS31537.1	234	0.10714285714285714	47	0.09552845528455285	34	0.09392265193370165	69	0.12062937062937062	84	0.11081794195250659	A	11.63	1.696822	0.30142	0.091549	0.084846	ENSG00000172457	ENST00000302957	T	0.04551	3.6	5.16	4.03	0.46877	.	0.000000	0.40385	N	0.001114	T	0.00271	0.0008	M	0.81497	2.545	0.48395	P	3.5799999999996945E-4	D	0.76494	0.999	D	0.80764	0.994	T	0.02070	-1.1219	9	0.87932	D	0	-25.4032	10.0006	0.41927	0.9198:0.0:0.0802:0.0	rs11228763;rs11228763	43	Q8NGQ1	OR9G4_HUMAN	S	43	ENSP00000307515:F43S	ENSP00000307515:F43S	F	-	2	0	OR9G4	56267736	0.010000	0.17322	0.852000	0.33557	0.080000	0.17528	1.752000	0.38349	0.980000	0.38523	0.448000	0.29417	TTT	A|0.905;G|0.095	0.095	strong		0.438	OR9G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391945.1	NM_001005284	
LRRC31	79782	hgsc.bcm.edu	37	3	169558025	169558025	+	Silent	SNP	C	C	T	rs3732451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:169558025C>T	ENST00000316428.5	-	9	1461	c.1404G>A	c.(1402-1404)gcG>gcA	p.A468A	LRRC31_ENST00000523069.1_3'UTR|LRRC31_ENST00000264676.5_Silent_p.A412A	NM_001277127.1|NM_024727.2	NP_001264056.1|NP_079003.2	Q6UY01	LRC31_HUMAN	leucine rich repeat containing 31	468										cervix(3)|endometrium(3)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	31	all_cancers(22;2.76e-22)|all_epithelial(15;4.73e-27)|all_lung(20;9.24e-17)|Lung NSC(18;3.85e-16)|Ovarian(172;0.000223)|Breast(254;0.197)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.00943)			TGGTCCACCCCGCATCACAGA	0.473													c|||	2799	0.558906	0.5499	0.6037	5008	,	,		2259	0.754		0.3897	False		,,,				2504	0.5123				p.S468R		Atlas-SNP	.											.	LRRC31	66	.	0			c.C1404A						PASS	.	C		2004,2028		476,1052,488	116.0	110.0	112.0		1404	0.6	0.2	3	dbSNP_107	112	3076,5282		583,1910,1686	no	coding-synonymous	LRRC31	NM_024727.2		1059,2962,2174	TT,TC,CC		36.8031,49.7024,41.0008		468/553	169558025	5080,7310	2016	4179	6195	SO:0001819	synonymous_variant	79782	exon9			CCACCCCGCATCA	AK026912	CCDS43167.1, CCDS63832.1, CCDS63833.1	3q26.2	2005-01-24			ENSG00000114248	ENSG00000114248			26261	protein-coding gene	gene with protein product						12975309	Standard	NM_001277127		Approved	FLJ23259	uc003fgc.2	Q6UY01	OTTHUMG00000164421	ENST00000316428.5:c.1404G>A	3.37:g.169558025C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	158	156	0.987342	NM_024727	B7ZL44|E5RJA9|Q17RA3|Q8N848|Q9H5N5|V9HW14	Missense_Mutation	SNP	ENST00000316428.5	37	CCDS43167.1																																																																																			C|0.485;T|0.515	0.515	strong		0.473	LRRC31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378699.1	NM_024727	
HNF1A	6927	hgsc.bcm.edu	37	12	121416650	121416650	+	Missense_Mutation	SNP	A	A	C	rs1169288	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121416650A>C	ENST00000257555.6	+	1	305	c.79A>C	c.(79-81)Atc>Ctc	p.I27L	HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000538626.1_Intron|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000544413.1_Missense_Mutation_p.I27L|HNF1A_ENST00000402929.1_Missense_Mutation_p.I27L|HNF1A_ENST00000400024.2_Missense_Mutation_p.I27L|HNF1A_ENST00000541395.1_Missense_Mutation_p.I27L|HNF1A-AS1_ENST00000537361.1_RNA			P20823	HNF1A_HUMAN	HNF1 homeobox A	27	Dimerization.		I -> L (in dbSNP:rs1169288). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9112026, ECO:0000269|PubMed:9133564, ECO:0000269|PubMed:9287055, ECO:0000269|PubMed:9604876, ECO:0000269|PubMed:9621514, ECO:0000269|Ref.6}.		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.I27_L30delIQAL(1)|p.A25_Q28del(1)|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)					AGAGGCACTGATCCAGGCACT	0.677									Hepatic Adenoma, Familial Clustering of				A|||	1495	0.298522	0.0832	0.33	5008	,	,		12439	0.3889		0.339	False		,,,				2504	0.4325				p.I27L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	3	Deletion - In frame(2)|Unknown(1)	liver(2)|endometrium(1)	c.A79C	GRCh37	CM001349	HNF1A	M	rs1169288	PASS	.	A	LEU/ILE	532,3874		43,446,1714	25.0	28.0	27.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	79	4.4	1.0	12	dbSNP_87	27	2881,5715		500,1881,1917	yes	missense	HNF1A	NM_000545.5	5	543,2327,3631	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	33.5156,12.0744,26.2498	benign	27/632	121416650	3413,9589	2203	4298	6501	SO:0001583	missense	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	GCACTGATCCAGG	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.79A>C	12.37:g.121416650A>C	ENSP00000257555:p.Ile27Leu	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	654	0.29945054945054944	35	0.07113821138211382	123	0.3397790055248619	243	0.42482517482517484	253	0.3337730870712401	A	14.27	2.485259	0.44147	0.120744	0.335156	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000543536;ENST00000544680;ENST00000537424;ENST00000543027;ENST00000545458;ENST00000541395;ENST00000340577;ENST00000344370;ENST00000544413	D;D;D	0.98550	-4.99;-4.99;-4.99	4.45	4.45	0.53987	Hepatocyte nuclear factor 1, dimerisation domain (1);Hepatocyte nuclear factor 1, N-terminal (1);	0.102545	0.43260	D	0.000599	T	0.00012	0.0000	L	0.46157	1.445	0.09310	P	0.9999999999999999	B;B;B;B	0.18013	0.02;0.025;0.015;0.006	B;B;B;B	0.23574	0.013;0.022;0.047;0.012	T	0.00149	-1.1988	9	0.26408	T	0.33	-28.5113	12.8999	0.58119	1.0:0.0:0.0:0.0	rs1169288;rs3751160;rs16950605;rs17847506;rs1169288	27;27;27;27	F5H0K0;P20823;E7EUQ4;E7EMR0	.;HNF1A_HUMAN;.;.	L	27	ENSP00000257555:I27L;ENSP00000443112:I27L;ENSP00000438804:I27L	ENSP00000257555:I27L	I	+	1	0	HNF1A	119901033	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.135000	0.50546	1.637000	0.50538	0.482000	0.46254	ATC	T|0.002;G|0.007	.	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
MGAM	8972	hgsc.bcm.edu	37	7	141724852	141724852	+	Silent	SNP	C	C	T	rs10255702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141724852C>T	ENST00000549489.2	+	8	980	c.885C>T	c.(883-885)aaC>aaT	p.N295N	MGAM_ENST00000475668.2_Silent_p.N295N	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	295	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTCTGCAGAACGGAACTAATT	0.403													C|||	352	0.0702875	0.1452	0.0231	5008	,	,		19260	0.1161		0.0129	False		,,,				2504	0.0143				p.N295N		Atlas-SNP	.											.	MGAM	767	.	0			c.C885T						PASS	.	C		444,3288		23,398,1445	125.0	118.0	120.0		885	-4.9	1.0	7	dbSNP_119	120	89,8129		0,89,4020	no	coding-synonymous	MGAM	NM_004668.2		23,487,5465	TT,TC,CC		1.083,11.8971,4.4603		295/1858	141724852	533,11417	1866	4109	5975	SO:0001819	synonymous_variant	8972	exon8			GCAGAACGGAACT	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.885C>T	7.37:g.141724852C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	102	37	0.362745	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			C|0.922;T|0.078	0.078	strong		0.403	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
MAP3K19	80122	hgsc.bcm.edu	37	2	135745722	135745722	+	Silent	SNP	A	A	G	rs10928526	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:135745722A>G	ENST00000375845.3	-	7	750	c.720T>C	c.(718-720)agT>agC	p.S240S	MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Silent_p.S127S|MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Silent_p.S257S	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	240							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										AAGATGTGAGACTTGGAATGT	0.478													G|||	1817	0.362819	0.3306	0.232	5008	,	,		19049	0.5417		0.2704	False		,,,				2504	0.41				p.S240S		Atlas-SNP	.											.	.	.	.	0			c.T720C						PASS	.	G	,	1393,3013	685.6+/-404.6	222,949,1032	97.0	108.0	105.0		,720	-0.5	0.0	2	dbSNP_120	105	1980,6620	721.7+/-406.4	259,1462,2579	no	intron,coding-synonymous	YSK4	NM_001018046.1,NM_025052.3	,	481,2411,3611	GG,GA,AA		23.0233,31.616,25.9342	,	,240/1329	135745722	3373,9633	2203	4300	6503	SO:0001819	synonymous_variant	80122	exon7			TGTGAGACTTGGA	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.720T>C	2.37:g.135745722A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Silent	SNP	ENST00000375845.3	37	CCDS2176.2																																																																																			A|0.687;G|0.313	0.313	strong		0.478	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
COL4A4	1286	hgsc.bcm.edu	37	2	227915832	227915832	+	Missense_Mutation	SNP	G	G	A	rs1800517	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227915832G>A	ENST00000396625.3	-	33	3218	c.3011C>T	c.(3010-3012)cCg>cTg	p.P1004L	COL4A4_ENST00000329662.7_Missense_Mutation_p.P1004L	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1004	Triple-helical region.		P -> L (in dbSNP:rs1800517). {ECO:0000269|PubMed:7523402, ECO:0000269|PubMed:9792860}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GTATCTTCCCGGCTCTCCTCT	0.532													G|||	2741	0.547324	0.587	0.5173	5008	,	,		17359	0.4821		0.494	False		,,,				2504	0.637				p.P1004L		Atlas-SNP	.											.	COL4A4	215	.	0			c.C3011T						PASS	.	G	LEU/PRO	2198,1576		629,940,318	113.0	110.0	111.0		3011	4.6	0.9	2	dbSNP_89	111	4022,4198		980,2062,1068	yes	missense	COL4A4	NM_000092.4	98	1609,3002,1386	AA,AG,GG		48.9294,41.7594,48.1407	possibly-damaging	1004/1691	227915832	6220,5774	1887	4110	5997	SO:0001583	missense	1286	exon33			CTTCCCGGCTCTC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3011C>T	2.37:g.227915832G>A	ENSP00000379866:p.Pro1004Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	128	49	0.382812	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	1117	0.5114468864468864	275	0.5589430894308943	186	0.5138121546961326	274	0.479020979020979	382	0.503957783641161	G	12.13	1.845210	0.32606	0.582406	0.489294	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.96685	-4.09;-4.09	5.52	4.64	0.57946	.	.	.	.	.	T	0.00012	0.0000	M	0.81179	2.53	0.09310	P	0.99999999685141	P	0.38504	0.634	B	0.35312	0.2	T	0.00673	-1.1616	8	0.56958	D	0.05	.	12.4796	0.55833	0.0781:0.0:0.9219:0.0	rs1800517;rs2229816;rs4675141;rs17643696;rs52806160;rs57381214;rs4675141	1004	P53420	CO4A4_HUMAN	L	1004	ENSP00000379866:P1004L;ENSP00000328553:P1004L	ENSP00000328553:P1004L	P	-	2	0	COL4A4	227624076	1.000000	0.71417	0.871000	0.34182	0.152000	0.21847	4.358000	0.59442	1.336000	0.45506	-0.150000	0.13652	CCG	T|0.180;G|0.324;C|0.162;N|0.000;A|0.334	0.334	strong		0.532	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
ZNF45	7596	hgsc.bcm.edu	37	19	44418693	44418693	+	Missense_Mutation	SNP	T	T	C	rs388706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44418693T>C	ENST00000269973.5	-	10	1985	c.895A>G	c.(895-897)Act>Gct	p.T299A	ZNF45_ENST00000589703.1_Missense_Mutation_p.T299A|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	299			T -> A (in dbSNP:rs388706). {ECO:0000269|PubMed:15057824}.		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						TTCTTTCCAGTGTGAACTTTC	0.463													C|||	2631	0.525359	0.3336	0.6499	5008	,	,		21442	0.7996		0.5169	False		,,,				2504	0.4223				p.T299A		Atlas-SNP	.											.	ZNF45	51	.	0			c.A895G						PASS	.	C	ALA/THR	1578,2828	666.6+/-401.7	293,992,918	92.0	78.0	83.0		895	-2.2	0.0	19	dbSNP_80	83	4351,4249	573.5+/-389.9	1118,2115,1067	yes	missense	ZNF45	NM_003425.3	58	1411,3107,1985	CC,CT,TT		49.407,35.8148,45.5867	benign	299/683	44418693	5929,7077	2203	4300	6503	SO:0001583	missense	7596	exon10			TTCCAGTGTGAAC	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.895A>G	19.37:g.44418693T>C	ENSP00000269973:p.Thr299Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	126	126	1	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	1255	0.5746336996336996	187	0.3800813008130081	209	0.5773480662983426	470	0.8216783216783217	389	0.5131926121372031	C	2.197	-0.383998	0.04966	0.358148	0.50593	ENSG00000124459	ENST00000269973;ENST00000328762	T	0.26518	1.73	3.07	-2.16	0.07080	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	2.708020	0.01708	N	0.027547	T	0.00012	0.0000	L	0.47078	1.49	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.48490	-0.9031	9	0.52906	T	0.07	5.6738	6.2967	0.21089	0.1154:0.2785:0.0:0.6061	rs388706;rs17712977;rs52790068;rs61572009;rs388706	299	Q02386	ZNF45_HUMAN	A	299	ENSP00000269973:T299A	ENSP00000269973:T299A	T	-	1	0	ZNF45	49110533	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-0.211000	0.09332	-1.254000	0.02485	-2.985000	0.00079	ACT	T|0.488;C|0.512	0.512	strong		0.463	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
RBMX	27316	hgsc.bcm.edu	37	X	135956506	135956506	+	Missense_Mutation	SNP	C	C	G	rs77794331		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135956506C>G	ENST00000320676.7	-	9	1125	c.971G>C	c.(970-972)cGa>cCa	p.R324P	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Missense_Mutation_p.R196P|RBMX_ENST00000570135.1_Missense_Mutation_p.R189P|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	324					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GTAACTGTCTCGACTTCCACC	0.537																																					p.R324P		Atlas-SNP	.											.	RBMX	149	.	0			c.G971C						PASS	.						126.0	116.0	119.0					X																	135956506		2203	4297	6500	SO:0001583	missense	27316	exon9			CTGTCTCGACTTC		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.971G>C	X.37:g.135956506C>G	ENSP00000359645:p.Arg324Pro	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	319	130	0.407524	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	17.04	3.287583	0.59976	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.78481	-1.18	5.4	5.4	0.78164	.	0.000000	0.64402	U	0.000002	D	0.86151	0.5864	L	0.59436	1.845	0.80722	D	1	D	0.67145	0.996	D	0.70487	0.969	D	0.86574	0.1849	10	0.54805	T	0.06	.	18.4308	0.90624	0.0:1.0:0.0:0.0	.	324	P38159	HNRPG_HUMAN	P	324;311	ENSP00000359645:R324P	ENSP00000359645:R324P	R	-	2	0	RBMX	135784172	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.717000	0.84732	2.380000	0.81148	0.600000	0.82982	CGA	C|0.333;G|0.667	0.667	weak		0.537	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
ZNF782	158431	hgsc.bcm.edu	37	9	99581343	99581343	+	Missense_Mutation	SNP	C	C	T	rs146058964	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:99581343C>T	ENST00000481138.1	-	6	1623	c.962G>A	c.(961-963)cGt>cAt	p.R321H	ZNF782_ENST00000535338.1_Missense_Mutation_p.R189H|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				GGTTGAATTACGGTTGAAACT	0.408													C|||	10	0.00199681	0.0	0.0086	5008	,	,		19795	0.0		0.003	False		,,,				2504	0.001				p.R321H		Atlas-SNP	.											.	ZNF782	64	.	0			c.G962A						PASS	.	C	HIS/ARG	7,4399	12.9+/-30.5	0,7,2196	125.0	121.0	122.0		962	-0.2	0.0	9	dbSNP_134	122	68,8532	41.2+/-98.3	0,68,4232	yes	missense	ZNF782	NM_001001662.1	29	0,75,6428	TT,TC,CC		0.7907,0.1589,0.5767	benign	321/700	99581343	75,12931	2203	4300	6503	SO:0001583	missense	158431	exon6			GAATTACGGTTGA	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.962G>A	9.37:g.99581343C>T	ENSP00000419397:p.Arg321His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	2.340	-0.351334	0.05173	0.001589	0.007907	ENSG00000196597	ENST00000481138;ENST00000535338	T;T	0.15718	2.4;2.4	3.52	-0.249	0.13011	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.483182	0.15497	N	0.259259	T	0.04272	0.0118	N	0.10629	0.01	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35871	-0.9771	10	0.23302	T	0.38	.	4.2727	0.10794	0.0:0.2038:0.1748:0.6214	.	321	Q6ZMW2	ZN782_HUMAN	H	321;189	ENSP00000419397:R321H;ENSP00000440624:R189H	ENSP00000419397:R321H	R	-	2	0	ZNF782	98621164	0.000000	0.05858	0.009000	0.14445	0.018000	0.09664	-2.399000	0.01050	-0.034000	0.13713	-0.259000	0.10710	CGT	C|0.995;T|0.005	0.005	strong		0.408	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
OR5H15	403274	hgsc.bcm.edu	37	3	97888337	97888337	+	Missense_Mutation	SNP	C	C	T	rs13082608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:97888337C>T	ENST00000356526.2	+	1	794	c.794C>T	c.(793-795)cCg>cTg	p.P265L		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	265						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						CCTGCATCTCCGCAAGCAGAT	0.438													C|||	1563	0.312101	0.2534	0.3444	5008	,	,		15123	0.4782		0.1819	False		,,,				2504	0.3313				p.P265L		Atlas-SNP	.											.	OR5H15	70	.	0			c.C794T						PASS	.	C	LEU/PRO	1035,3371		113,809,1281	86.0	90.0	88.0		794	0.3	0.0	3	dbSNP_121	88	1565,7035		140,1285,2875	yes	missense	OR5H15	NM_001005515.1	98	253,2094,4156	TT,TC,CC		18.1977,23.4907,19.9908	benign	265/314	97888337	2600,10406	2203	4300	6503	SO:0001583	missense	403274	exon1			CATCTCCGCAAGC		CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"""GPCR / Class A : Olfactory receptors"""	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.794C>T	3.37:g.97888337C>T	ENSP00000373195:p.Pro265Leu	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	217	103	0.474654	NM_001005515		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	675	0.3090659340659341	127	0.258130081300813	93	0.2569060773480663	309	0.5402097902097902	146	0.19261213720316622	-	3.880	-0.026185	0.07589	0.234907	0.181977	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.00069	8.77	2.48	0.278	0.15673	GPCR, rhodopsin-like superfamily (1);	1.334550	0.05193	N	0.503515	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.18166	0.026	B	0.13407	0.009	T	0.01675	-1.1298	9	0.42905	T	0.14	.	5.1938	0.15225	0.0:0.6419:0.2131:0.1451	rs13082608	265	A6NDH6	O5H15_HUMAN	L	265	ENSP00000373195:P265L	ENSP00000373195:P265L	P	+	2	0	OR5H15	99371027	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.925000	0.00691	0.370000	0.24538	0.184000	0.17185	CCG	C|0.771;T|0.229	0.229	strong		0.438	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1		
TMEM8A	58986	hgsc.bcm.edu	37	16	427516	427516	+	Silent	SNP	T	T	C	rs11649031	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:427516T>C	ENST00000431232.2	-	3	529	c.369A>G	c.(367-369)gtA>gtG	p.V123V	TMEM8A_ENST00000250930.3_5'UTR|TMEM8A_ENST00000476735.1_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	123					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AGGAGGGCTGTACCGCGGTGT	0.692											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2859	0.570887	0.736	0.4885	5008	,	,		15299	0.3036		0.5437	False		,,,				2504	0.7096				p.V123V		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,2	TMEM8A	49	2	0			c.A369G						PASS	.	C		3129,1243		1125,879,182	19.0	19.0	19.0		369	-0.5	0.0	16	dbSNP_120	19	4870,3712		1419,2032,840	no	coding-synonymous	TMEM8A	NM_021259.2		2544,2911,1022	CC,CT,TT		43.2533,28.4309,38.2507		123/772	427516	7999,4955	2186	4291	6477	SO:0001819	synonymous_variant	58986	exon3			GGGCTGTACCGCG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.369A>G	16.37:g.427516T>C		Somatic	96	0	0	588	WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			T|0.429;C|0.571	0.571	strong		0.692	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
SAMSN1	64092	hgsc.bcm.edu	37	21	15918577	15918577	+	Silent	SNP	G	G	C	rs7281104	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:15918577G>C	ENST00000400566.1	-	1	87	c.6C>G	c.(4-6)ctC>ctG	p.L2L	SAMSN1_ENST00000400564.1_Silent_p.L2L|SAMSN1_ENST00000285670.2_Intron	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	2					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		GCTTTCTCTTGAGCATTTTGA	0.358													G|||	1520	0.303514	0.3722	0.1931	5008	,	,		18584	0.2946		0.2475	False		,,,				2504	0.3558				p.L2L		Atlas-SNP	.											.	SAMSN1	112	.	0			c.C6G						PASS	.	G		1359,2387		260,839,774	149.0	138.0	142.0		6	1.4	1.0	21	dbSNP_116	142	1939,6275		236,1467,2404	no	coding-synonymous	SAMSN1	NM_022136.3		496,2306,3178	CC,CG,GG		23.606,36.2787,27.5753		2/374	15918577	3298,8662	1873	4107	5980	SO:0001819	synonymous_variant	64092	exon1			TCTCTTGAGCATT	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000400566.1:c.6C>G	21.37:g.15918577G>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_022136	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Silent	SNP	ENST00000400566.1	37	CCDS42906.1																																																																																			G|0.725;C|0.275	0.275	strong		0.358	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1		
USP31	57478	hgsc.bcm.edu	37	16	23079408	23079408	+	Missense_Mutation	SNP	T	T	C	rs114976439	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:23079408T>C	ENST00000219689.7	-	16	4017	c.4018A>G	c.(4018-4020)Agc>Ggc	p.S1340G	USP31_ENST00000567975.1_Missense_Mutation_p.S633G	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		GTTTGCATGCTAGAAGATAAC	0.448													T|||	4	0.000798722	0.0	0.0029	5008	,	,		19237	0.0		0.002	False		,,,				2504	0.0				p.S1340G		Atlas-SNP	.											.	USP31	122	.	0			c.A4018G						PASS	.	T	GLY/SER	2,4392	4.2+/-10.8	0,2,2195	66.0	70.0	69.0		4018	4.6	1.0	16	dbSNP_132	69	30,8570	19.8+/-62.0	0,30,4270	yes	missense	USP31	NM_020718.3	56	0,32,6465	CC,CT,TT		0.3488,0.0455,0.2463	possibly-damaging	1340/1353	23079408	32,12962	2197	4300	6497	SO:0001583	missense	57478	exon16			GCATGCTAGAAGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.4018A>G	16.37:g.23079408T>C	ENSP00000219689:p.Ser1340Gly	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	17.73	3.460859	0.63513	4.55E-4	0.003488	ENSG00000103404	ENST00000219689	T	0.13420	2.59	5.68	4.6	0.57074	.	0.381647	0.25164	N	0.032643	T	0.15912	0.0383	L	0.60455	1.87	0.48135	D	0.999591	B;B	0.19583	0.012;0.037	B;B	0.19148	0.006;0.024	T	0.01966	-1.1238	10	0.72032	D	0.01	-9.5109	10.6397	0.45586	0.0:0.0746:0.0:0.9253	.	1340;633	Q70CQ4;B3KS48	UBP31_HUMAN;.	G	1340	ENSP00000219689:S1340G	ENSP00000219689:S1340G	S	-	1	0	USP31	22986909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.848000	0.55903	0.989000	0.38761	0.533000	0.62120	AGC	T|0.997;C|0.003	0.003	strong		0.448	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
VCAN	1462	hgsc.bcm.edu	37	5	82835545	82835545	+	Silent	SNP	A	A	G	rs160279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:82835545A>G	ENST00000265077.3	+	8	7288	c.6723A>G	c.(6721-6723)agA>agG	p.R2241R	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Silent_p.R1254R|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2241	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AAGGCATGAGACCAACAATTC	0.388													A|||	2356	0.470447	0.5091	0.5288	5008	,	,		21131	0.3919		0.5249	False		,,,				2504	0.4018				p.R2241R		Atlas-SNP	.											VCAN,NS,carcinoma,+2,1	VCAN	498	1	0			c.A6723G						PASS	.	A	,,,	2201,2205	586.2+/-386.4	547,1107,549	67.0	66.0	66.0		,3762,,6723	-5.1	0.0	5	dbSNP_79	66	4263,4337	572.8+/-389.8	1066,2131,1103	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	1613,3238,1652	GG,GA,AA		49.5698,49.9546,49.7001	,,,	,1254/2410,,2241/3397	82835545	6464,6542	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			CATGAGACCAACA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.6723A>G	5.37:g.82835545A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			G|0.496;N|0.000	0.496	strong		0.388	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
KLHL3	26249	hgsc.bcm.edu	37	5	136975604	136975604	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:136975604G>A	ENST00000309755.4	-	9	1409	c.966C>T	c.(964-966)ttC>ttT	p.F322F	KLHL3_ENST00000508657.1_Silent_p.F290F|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000506491.1_Silent_p.F240F|KLHL3_ENST00000541417.1_Intron	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	322			F -> C (in PHA2D). {ECO:0000269|PubMed:22266938}.		distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GGTCCTCCTCGAAATCATAGC	0.577																																					p.F322F		Atlas-SNP	.											.	KLHL3	54	.	0			c.C966T						PASS	.						104.0	90.0	95.0					5																	136975604		2203	4300	6503	SO:0001819	synonymous_variant	26249	exon9			CTCCTCGAAATCA	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"""Kelch-like"", ""BTB/POZ domain containing"""	6354	protein-coding gene	gene with protein product		605775	"""kelch (Drosophila)-like 3"", ""kelch-like 3 (Drosophila)"""			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.966C>T	5.37:g.136975604G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	139	58	0.417266	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																			.	.	none		0.577	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		
DMD	1756	hgsc.bcm.edu	37	X	32380996	32380996	+	Missense_Mutation	SNP	C	C	T	rs1801187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:32380996C>T	ENST00000357033.4	-	37	5440	c.5234G>A	c.(5233-5235)cGc>cAc	p.R1745H	DMD_ENST00000378677.2_Missense_Mutation_p.R1741H	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1745	Interaction with SYNM. {ECO:0000250}.		R -> H (in dbSNP:rs1801187). {ECO:0000269|PubMed:2668885}.		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTGGTCACCGCGGTTTGCCAT	0.463													C|||	1756	0.465166	0.0219	0.4914	3775	,	,		14430	0.5288		0.3529	False		,,,				2504	0.5092				p.R1745H		Atlas-SNP	.											.	DMD	2127	.	0			c.G5234A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	309,3524		16,230,47,1385,524	208.0	158.0	175.0		5210,5234,4865,5222,4865,1211,1202	5.2	1.0	X	dbSNP_89	175	3209,3519		537,1205,930,686,942	yes	missense,missense,missense,missense,missense,missense,missense	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3,NM_004011.3,NM_004012.3	29,29,29,29,29,29,29	553,1435,977,2071,1466	TT,TC,T,CC,C		47.6962,8.0616,33.3112	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1737/3678,1745/3686,1622/3563,1741/3682,1622/3563,404/2345,401/2342	32380996	3518,7043	2202	4300	6502	SO:0001583	missense	1756	exon37			TCACCGCGGTTTG	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.5234G>A	X.37:g.32380996C>T	ENSP00000354923:p.Arg1745His	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	743	0.4478601567209162	13	0.026859504132231406	116	0.44274809160305345	194	0.5052083333333334	190	0.31986531986531985	C	27.0	4.789998	0.90367	0.080616	0.476962	ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.50548	0.74;0.74	5.24	5.24	0.73138	.	0.000000	0.35903	U	0.002916	T	0.00012	0.0000	M	0.73962	2.25	0.09310	P	1.0	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.85130	0.994;0.984;0.997;0.997;0.997	T	0.48375	-0.9041	9	0.29301	T	0.29	.	17.9202	0.88964	0.0:1.0:0.0:0.0	rs1801187;rs52833754;rs60102213;rs1801187	1737;1745;1741;404;401	P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6	.;DMD_HUMAN;.;.;.	H	1737;404;401;1741;1745;1745;1622	ENSP00000367948:R1741H;ENSP00000354923:R1745H	ENSP00000354923:R1745H	R	-	2	0	DMD	32290917	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	4.005000	0.57075	2.164000	0.68074	0.538000	0.68166	CGC	0|0.010;T|0.376	0.376	strong		0.463	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
MUC5B	727897	hgsc.bcm.edu	37	11	1269627	1269627	+	Silent	SNP	C	C	T	rs4963056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1269627C>T	ENST00000529681.1	+	31	11575	c.11517C>T	c.(11515-11517)acC>acT	p.T3839T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.T3842T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3839	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TGCTTACCACCACGGCCACCA	0.637													C|||	1690	0.33746	0.2126	0.3199	5008	,	,		16897	0.5962		0.2853	False		,,,				2504	0.3057				p.T3839T		Atlas-SNP	.											.	MUC5B	473	.	0			c.C11517T						PASS	.	C		831,3419		75,681,1369	156.0	183.0	174.0		11517	2.0	0.0	11	dbSNP_111	174	2509,5905		399,1711,2097	no	coding-synonymous	MUC5B	NM_002458.2		474,2392,3466	TT,TC,CC		29.8193,19.5529,26.374		3839/5763	1269627	3340,9324	2125	4207	6332	SO:0001819	synonymous_variant	727897	exon31			TACCACCACGGCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.11517C>T	11.37:g.1269627C>T		Somatic	334	1	0.00299401		WXS	Illumina HiSeq	Phase_I	313	132	0.421725	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.749;T|0.251	0.251	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MMP8	4317	hgsc.bcm.edu	37	11	102593248	102593248	+	Missense_Mutation	SNP	T	T	C	rs1940475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102593248T>C	ENST00000236826.3	-	2	357	c.259A>G	c.(259-261)Aaa>Gaa	p.K87E		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	87			K -> E (in dbSNP:rs1940475). {ECO:0000269|Ref.2}.		collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	CGAGGCTTTTTCATCATGTCC	0.453													T|||	3005	0.60004	0.7095	0.5173	5008	,	,		21446	0.5685		0.5467	False		,,,				2504	0.5982				p.K87E		Atlas-SNP	.											MMP8,face,malignant_melanoma,+2,1	MMP8	68	1	0			c.A259G						PASS	.	T	GLU/LYS	2849,1557	669.7+/-402.2	919,1011,273	166.0	158.0	161.0		259	-6.1	0.0	11	dbSNP_92	161	4348,4250	579.6+/-390.9	1099,2150,1050	yes	missense	MMP8	NM_002424.2	56	2018,3161,1323	CC,CT,TT		49.4301,35.3382,44.6555	benign	87/468	102593248	7197,5807	2203	4299	6502	SO:0001583	missense	4317	exon2			GCTTTTTCATCAT	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"""matrix metalloproteinase 8 (neutrophil collagenase)"""	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.259A>G	11.37:g.102593248T>C	ENSP00000236826:p.Lys87Glu	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	320	153	0.478125	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	1288|1288	0.5897435897435898|0.5897435897435898	355|355	0.7215447154471545|0.7215447154471545	195|195	0.5386740331491713|0.5386740331491713	340|340	0.5944055944055944|0.5944055944055944	398|398	0.525065963060686|0.525065963060686	T|T	14.71|14.71	2.615422|2.615422	0.46631|0.46631	0.646618|0.646618	0.505699|0.505699	ENSG00000118113|ENSG00000118113	ENST00000438475|ENST00000236826;ENST00000544383;ENST00000534942	.|T	.|0.30714	.|1.52	5.73|5.73	-6.06|-6.06	0.02165|0.02165	.|Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	.|1.456970	.|0.04177	.|N	.|0.325809	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43701|0.43701	1.375|1.375	0.53688|0.53688	P|P	2.4000000000024002E-5|2.4000000000024002E-5	.|B;B	.|0.14438	.|0.001;0.01	.|B;B	.|0.17098	.|0.017;0.009	T|T	0.40664|0.40664	-0.9551|-0.9551	4|9	.|0.40728	.|T	.|0.16	.|.	12.0951|12.0951	0.53750|0.53750	0.0:0.2066:0.0998:0.6936|0.0:0.2066:0.0998:0.6936	rs1940475;rs52827903;rs59499834;rs1940475|rs1940475;rs52827903;rs59499834;rs1940475	.|22;87	.|F5GXB5;P22894	.|.;MMP8_HUMAN	G|E	62|87;64;22	.|ENSP00000236826:K87E	.|ENSP00000236826:K87E	E|K	-|-	2|1	0|0	MMP8|MMP8	102098458|102098458	0.003000|0.003000	0.15002|0.15002	0.001000|0.001000	0.08648|0.08648	0.763000|0.763000	0.43281|0.43281	-0.023000|-0.023000	0.12456|0.12456	-1.123000|-1.123000	0.02940|0.02940	-0.242000|-0.242000	0.12053|0.12053	GAA|AAA	T|0.417;C|0.583	0.583	strong		0.453	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424	
FILIP1L	11259	hgsc.bcm.edu	37	3	99643176	99643176	+	Missense_Mutation	SNP	C	C	T	rs793440	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:99643176C>T	ENST00000354552.3	-	4	973	c.503G>A	c.(502-504)cGt>cAt	p.R168H	CMSS1_ENST00000496116.1_Intron|FILIP1L_ENST00000331335.5_Missense_Mutation_p.R168H|CMSS1_ENST00000421999.2_Intron|FILIP1L_ENST00000398326.2_Missense_Mutation_p.R168H	NM_182909.2	NP_878913.2	Q4L180	FIL1L_HUMAN	filamin A interacting protein 1-like	168			R -> H (in dbSNP:rs793440). {ECO:0000269|Ref.3, ECO:0000269|Ref.4}.			cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	35						GGTTTGCCTACGGGATTTTTC	0.373													T|||	1269	0.253395	0.1558	0.3545	5008	,	,		19145	0.1954		0.3111	False		,,,				2504	0.3139				p.R168H		Atlas-SNP	.											.	FILIP1L	154	.	0			c.G503A						PASS	.	T	HIS/ARG,,HIS/ARG	713,2967		61,591,1188	248.0	227.0	233.0		503,,503	5.5	0.9	3	dbSNP_86	233	2720,5448		463,1794,1827	yes	missense,intron,missense	FILIP1L,C3orf26	NM_001042459.1,NM_032359.3,NM_182909.2	29,,29	524,2385,3015	TT,TC,CC		33.3007,19.375,28.9754	benign,,benign	168/1134,,168/1136	99643176	3433,8415	1840	4084	5924	SO:0001583	missense	11259	exon4			TGCCTACGGGATT		CCDS43117.1, CCDS43118.1, CCDS43119.1, CCDS63700.1, CCDS74969.1	3q12.1	2011-10-21			ENSG00000168386	ENSG00000168386			24589	protein-coding gene	gene with protein product	"""downregulated in ovarian cancer 1"", ""GPBP-interacting protein of 130 kDa"""	612993				8314147, 15935955, 21832087	Standard	NM_001282793		Approved	DOC-1, GIP130	uc003dtm.3	Q4L180	OTTHUMG00000159055	ENST00000354552.3:c.503G>A	3.37:g.99643176C>T	ENSP00000346560:p.Arg168His	Somatic	344	0	0		WXS	Illumina HiSeq	Phase_I	359	184	0.512535	NM_182909	B2CNV7|B2CNV8|Q13597|Q2YDY5|Q6KFX5|Q6KFX6|Q6KFX7|Q8IUM3|Q8N6Z0	Missense_Mutation	SNP	ENST00000354552.3	37	CCDS43117.1	527	0.2413003663003663	80	0.16260162601626016	120	0.3314917127071823	80	0.13986013986013987	247	0.3258575197889182	T	4.956	0.177581	0.09443	0.19375	0.333007	ENSG00000168386	ENST00000354552;ENST00000331335;ENST00000398326	T;T;T	0.41400	1.0;1.0;1.0	5.5	5.5	0.81552	Cortactin-binding protein-2, N-terminal (1);	0.277746	0.25073	N	0.033358	T	0.00012	0.0000	N	0.00030	-2.605	0.09310	P	1.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38112	-0.9676	9	0.02654	T	1	-5.2185	11.5161	0.50522	0.0:0.0703:0.0:0.9297	rs793440;rs1680276;rs17379418;rs52794044;rs60414686;rs793440	168;168	Q4L180-2;Q4L180	.;FIL1L_HUMAN	H	168	ENSP00000346560:R168H;ENSP00000327880:R168H;ENSP00000381371:R168H	ENSP00000327880:R168H	R	-	2	0	FILIP1L	101125866	1.000000	0.71417	0.927000	0.36925	0.478000	0.33099	5.664000	0.68045	0.931000	0.37242	-0.352000	0.07741	CGT	C|0.763;T|0.237	0.237	strong		0.373	FILIP1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353069.1	NM_014890	
OR7G1	125962	hgsc.bcm.edu	37	19	9225685	9225685	+	Missense_Mutation	SNP	T	T	C	rs2195951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9225685T>C	ENST00000541538.1	-	1	754	c.755A>G	c.(754-756)tAt>tGt	p.Y252C	OR7G1_ENST00000293614.1_Missense_Mutation_p.Y252C	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	252			Y -> C (in dbSNP:rs2195951).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						AGCTGTCCCATAGAACAAGGA	0.453													T|||	1690	0.33746	0.5953	0.1354	5008	,	,		18925	0.3254		0.1918	False		,,,				2504	0.2945				p.Y252C		Atlas-SNP	.											.	OR7G1	53	.	0			c.A755G						PASS	.	T	CYS/TYR	2314,2092	603.3+/-390.1	591,1132,480	99.0	95.0	97.0		755	2.6	0.6	19	dbSNP_96	97	1490,7110	281.7+/-295.2	125,1240,2935	yes	missense	OR7G1	NM_001005192.2	194	716,2372,3415	CC,CT,TT		17.3256,47.4807,29.248	probably-damaging	252/312	9225685	3804,9202	2203	4300	6503	SO:0001583	missense	125962	exon1			GTCCCATAGAACA		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"""GPCR / Class A : Olfactory receptors"""	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.755A>G	19.37:g.9225685T>C	ENSP00000444134:p.Tyr252Cys	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	23	0.377049	NM_001005192	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	647	0.29624542124542125	286	0.5813008130081301	44	0.12154696132596685	180	0.3146853146853147	137	0.18073878627968337	t	9.824	1.186540	0.21870	0.525193	0.173256	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.41758	0.99;0.99	3.78	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	0.227928	0.22228	U	0.062851	T	0.00012	0.0000	M	0.93016	3.37	0.80722	P	0.0	P	0.35944	0.529	B	0.40477	0.33	T	0.47774	-0.9091	9	0.72032	D	0.01	.	7.687	0.28546	0.2556:0.0:0.0:0.7444	rs2195951;rs52813886;rs61268819;rs2195951	252	Q8NGA0	OR7G1_HUMAN	C	252	ENSP00000293614:Y252C;ENSP00000444134:Y252C	ENSP00000293614:Y252C	Y	-	2	0	OR7G1	9086685	0.000000	0.05858	0.570000	0.28473	0.291000	0.27294	-0.114000	0.10757	1.700000	0.51204	0.410000	0.27636	TAT	T|0.690;C|0.310	0.310	strong		0.453	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1		
UNC13C	440279	hgsc.bcm.edu	37	15	54838957	54838957	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:54838957C>A	ENST00000260323.11	+	26	5734	c.5734C>A	c.(5734-5736)Cta>Ata	p.L1912I	UNC13C_ENST00000537900.1_Missense_Mutation_p.L1910I|UNC13C_ENST00000545554.1_Missense_Mutation_p.L1912I	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1912	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GAAAACAGTCCTAAAGCGAGT	0.294																																					p.L1912I		Atlas-SNP	.											.	UNC13C	674	.	0			c.C5734A						PASS	.						37.0	32.0	33.0					15																	54838957		1748	4012	5760	SO:0001583	missense	440279	exon25			ACAGTCCTAAAGC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5734C>A	15.37:g.54838957C>A	ENSP00000260323:p.Leu1912Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	133	54	0.406015	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509347	0.44660	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.81996	-1.56;-1.56;-1.56	5.59	4.68	0.58851	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.000000	0.64402	D	0.000002	D	0.90830	0.7120	M	0.87682	2.9	0.42046	D	0.991092	D	0.76494	0.999	D	0.87578	0.998	D	0.91027	0.4861	10	0.54805	T	0.06	.	9.6213	0.39723	0.0:0.8427:0.0:0.1573	.	1912	Q8NB66	UN13C_HUMAN	I	1912;1912;1910	ENSP00000260323:L1912I;ENSP00000438156:L1912I;ENSP00000442569:L1910I	ENSP00000260323:L1912I	L	+	1	2	UNC13C	52626249	0.999000	0.42202	0.571000	0.28486	0.201000	0.24016	2.469000	0.45110	1.364000	0.46038	0.561000	0.74099	CTA	.	.	none		0.294	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
ZNF10	7556	hgsc.bcm.edu	37	12	133732512	133732512	+	Missense_Mutation	SNP	A	A	G	rs11147259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133732512A>G	ENST00000248211.6	+	5	902	c.680A>G	c.(679-681)cAg>cGg	p.Q227R	ZNF268_ENST00000416488.1_Intron|ZNF10_ENST00000402932.2_Intron|ZNF10_ENST00000426665.2_Missense_Mutation_p.Q227R|CTD-2140B24.4_ENST00000540096.2_Intron	NM_015394.4	NP_056209.2	P21506	ZNF10_HUMAN	zinc finger protein 10	227			Q -> R (in dbSNP:rs11147259).	Missing (in Ref. 1). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(1)|skin(5)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;1.28e-06)|all_epithelial(31;0.0051)|Lung NSC(355;0.00948)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		CACCTTATTCAGTTTGCAAGA	0.358													A|||	337	0.0672923	0.1944	0.0303	5008	,	,		22500	0.002		0.0398	False		,,,				2504	0.0174				p.Q227R		Atlas-SNP	.											ZNF10,bladder,carcinoma,+1,1	ZNF10	58	1	0			c.A680G						PASS	.	A	ARG/GLN	711,3695	295.6+/-283.7	54,603,1546	111.0	102.0	105.0		680	4.2	0.9	12	dbSNP_120	105	366,8234	121.8+/-180.9	6,354,3940	yes	missense	ZNF10	NM_015394.4	43	60,957,5486	GG,GA,AA		4.2558,16.1371,8.2808	possibly-damaging	227/574	133732512	1077,11929	2203	4300	6503	SO:0001583	missense	7556	exon5			TTATTCAGTTTGC	X52332, BC024182	CCDS9283.1	12q24.33	2013-01-08	2005-05-22		ENSG00000256223	ENSG00000256223		"""Zinc fingers, C2H2-type"", ""-"""	12879	protein-coding gene	gene with protein product		194538	"""zinc finger protein 10 (KOX 1)"""			7865130, 8262519	Standard	NM_015394		Approved	KOX1	uc001ulq.3	P21506	OTTHUMG00000167944	ENST00000248211.6:c.680A>G	12.37:g.133732512A>G	ENSP00000248211:p.Gln227Arg	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	60	0.535714	NM_015394	B2RBS1|Q8TC91	Missense_Mutation	SNP	ENST00000248211.6	37	CCDS9283.1	137	0.06272893772893773	98	0.1991869918699187	8	0.022099447513812154	0	0.0	31	0.040897097625329816	A	6.062	0.379830	0.11466	0.161371	0.042558	ENSG00000256223	ENST00000248211;ENST00000426665;ENST00000537119	T;T;T	0.59364	0.27;0.27;4.7	4.22	4.22	0.49857	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36234	N	0.002714	T	0.00039	0.0001	N	0.05574	-0.02	0.09310	P	0.99999835466	B	0.30326	0.276	B	0.27796	0.083	T	0.09930	-1.0652	8	.	.	.	.	9.4701	0.38837	0.8219:0.1781:0.0:0.0	rs11147259;rs58328991;rs11147259	227	P21506	ZNF10_HUMAN	R	227;227;185	ENSP00000248211:Q227R;ENSP00000393814:Q227R;ENSP00000437397:Q185R	.	Q	+	2	0	ZNF10	132242585	0.000000	0.05858	0.916000	0.36221	0.450000	0.32258	0.710000	0.25748	1.896000	0.54893	0.533000	0.62120	CAG	A|0.918;G|0.082	0.082	strong		0.358	ZNF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397182.1	NM_015394	
FRRS1	391059	hgsc.bcm.edu	37	1	100203693	100203693	+	Silent	SNP	G	G	A	rs7514021	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:100203693G>A	ENST00000414213.1	-	7	1309	c.708C>T	c.(706-708)agC>agT	p.S236S	FRRS1_ENST00000287474.5_Silent_p.S236S			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	236	DOMON. {ECO:0000255|PROSITE- ProRule:PRU00246}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		TACTGGGGCCGCTCATTTCAA	0.453													A|||	2796	0.558307	0.9402	0.4928	5008	,	,		18333	0.3909		0.3082	False		,,,				2504	0.5184				p.S236S		Atlas-SNP	.											.	FRRS1	50	.	0			c.C708T						PASS	.	A		3680,726	302.1+/-287.2	1536,608,59	117.0	119.0	119.0		708	-7.1	0.5	1	dbSNP_116	119	2915,5685	671.2+/-402.8	505,1905,1890	no	coding-synonymous	FRRS1	NM_001013660.2		2041,2513,1949	AA,AG,GG		33.8953,16.4775,49.2926		236/627	100203693	6595,6411	2203	4300	6503	SO:0001819	synonymous_variant	391059	exon7			GGGGCCGCTCATT	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.708C>T	1.37:g.100203693G>A		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	213	112	0.525822	NM_001013660	A6NLN7	Silent	SNP	ENST00000414213.1	37																																																																																				G|0.486;A|0.514	0.514	strong		0.453	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
PRKCA	5578	hgsc.bcm.edu	37	17	64685078	64685078	+	Silent	SNP	G	G	A	rs2227857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:64685078G>A	ENST00000413366.3	+	8	857	c.831G>A	c.(829-831)ttG>ttA	p.L277L		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	277					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	GGTACAAGTTGCTTAACCAAG	0.478													G|||	1150	0.229633	0.0908	0.3473	5008	,	,		17492	0.1081		0.3658	False		,,,				2504	0.319				p.L277L		Atlas-SNP	.											.	PRKCA	82	.	0			c.G831A						PASS	.	G		599,3807	260.1+/-263.5	50,499,1654	89.0	70.0	76.0		831	4.5	1.0	17	dbSNP_98	76	3146,5454	475.0+/-369.0	559,2028,1713	no	coding-synonymous	PRKCA	NM_002737.2		609,2527,3367	AA,AG,GG		36.5814,13.5951,28.7944		277/673	64685078	3745,9261	2203	4300	6503	SO:0001819	synonymous_variant	5578	exon8			CAAGTTGCTTAAC		CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.831G>A	17.37:g.64685078G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_002737	B5BU22|Q15137|Q32M72|Q96RE4	Silent	SNP	ENST00000413366.3	37	CCDS11664.1																																																																																			G|0.741;A|0.259	0.259	strong		0.478	PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1		
MGAM	8972	hgsc.bcm.edu	37	7	141727526	141727526	+	Missense_Mutation	SNP	G	G	T	rs2272330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141727526G>T	ENST00000549489.2	+	10	1307	c.1212G>T	c.(1210-1212)caG>caT	p.Q404H	MGAM_ENST00000475668.2_Missense_Mutation_p.Q404H	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	404	Maltase.		Q -> H (in dbSNP:rs2272330).		carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GCGCAGCACAGCTCCCTTATG	0.423													G|||	354	0.0706869	0.1467	0.0231	5008	,	,		15747	0.1151		0.0139	False		,,,				2504	0.0143				p.Q404H		Atlas-SNP	.											MGAM_ENST00000549489,NS,carcinoma,+2,3	MGAM	767	3	0			c.G1212T						PASS	.	G	HIS/GLN	445,3267		22,401,1433	46.0	46.0	46.0		1212	-0.3	0.2	7	dbSNP_100	46	85,8127		0,85,4021	yes	missense	MGAM	NM_004668.2	24	22,486,5454	TT,TG,GG		1.0351,11.9881,4.4448	benign	404/1858	141727526	530,11394	1856	4106	5962	SO:0001583	missense	8972	exon10			AGCACAGCTCCCT	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.1212G>T	7.37:g.141727526G>T	ENSP00000447378:p.Gln404His	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	148	0.06776556776556776	73	0.1483739837398374	8	0.022099447513812154	61	0.10664335664335664	6	0.0079155672823219	G	12.02	1.812666	0.32053	0.119881	0.010351	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.92752	-3.1	5.55	-0.291	0.12843	Glycoside hydrolase, superfamily (1);	0.516985	0.17896	N	0.158361	T	0.02848	0.0085	L	0.37630	1.12	0.80722	P	0.0	P	0.36378	0.55	B	0.39840	0.311	T	0.50642	-0.8804	9	0.38643	T	0.18	.	9.3604	0.38192	0.5394:0.0:0.4606:0.0	rs2272330;rs10345129;rs17741014;rs52833576;rs2272330	404	O43451	MGA_HUMAN	H	404;404;281	ENSP00000447378:Q404H	ENSP00000316431:Q281H	Q	+	3	2	MGAM	141373995	0.000000	0.05858	0.237000	0.24090	0.833000	0.47200	-1.221000	0.02968	0.051000	0.15978	-0.982000	0.02568	CAG	G|0.921;T|0.079	0.079	strong		0.423	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
ALMS1	7840	hgsc.bcm.edu	37	2	73679866	73679866	+	Missense_Mutation	SNP	T	T	C	rs10496192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73679866T>C	ENST00000264448.6	+	8	6320	c.6209T>C	c.(6208-6210)aTt>aCt	p.I2070T	ALMS1_ENST00000409009.1_Missense_Mutation_p.I2028T|ALMS1_ENST00000377715.1_Missense_Mutation_p.I2070T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2070	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AGTAAAGGTATTCTAAAGATT	0.358													T|||	519	0.103634	0.0787	0.1772	5008	,	,		21501	0.004		0.161	False		,,,				2504	0.1288				p.I2070T		Atlas-SNP	.											.	ALMS1	384	.	0			c.T6209C						PASS	.	T	THR/ILE	292,3342		13,266,1538	49.0	49.0	49.0		6209	-5.1	0.0	2	dbSNP_119	49	1356,6750		100,1156,2797	yes	missense	ALMS1	NM_015120.4	89	113,1422,4335	CC,CT,TT		16.7283,8.0352,14.0375	benign	2070/4168	73679866	1648,10092	1817	4053	5870	SO:0001583	missense	7840	exon8			AAGGTATTCTAAA	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.6209T>C	2.37:g.73679866T>C	ENSP00000264448:p.Ile2070Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	100	51	0.51	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	227	0.10393772893772894	40	0.08130081300813008	59	0.16298342541436464	4	0.006993006993006993	124	0.16358839050131926	T	0.001	-3.029968	0.00041	0.080352	0.167283	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.19532	2.99;2.99;2.14	4.38	-5.09	0.02920	.	0.621363	0.14407	N	0.321532	T	0.00039	0.0001	L	0.39898	1.24	0.80722	P	0.0	B;B;B	0.20261	0.019;0.043;0.034	B;B;B	0.20184	0.013;0.028;0.013	T	0.28554	-1.0040	9	0.34782	T	0.22	.	2.7425	0.05257	0.145:0.4915:0.1234:0.2402	rs10496192;rs17349559;rs52826651;rs10496192	2070;2028;2070	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	T	2028;2070;2070	ENSP00000386627:I2028T;ENSP00000264448:I2070T;ENSP00000366944:I2070T	ENSP00000264448:I2070T	I	+	2	0	ALMS1	73533374	0.324000	0.24652	0.000000	0.03702	0.023000	0.10783	-0.190000	0.09615	-0.965000	0.03591	-0.299000	0.09455	ATT	T|0.882;C|0.118	0.118	strong		0.358	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SLC25A32	81034	hgsc.bcm.edu	37	8	104427578	104427578	+	5'Flank	SNP	T	T	C	rs3134297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:104427578T>C	ENST00000297578.4	-	0	0				DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'Flank|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000297579.5_Silent_p.S120S	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	TGACTGGAAGTAGTCTGGGAA	0.632													T|||	1270	0.253594	0.202	0.268	5008	,	,		18261	0.3333		0.2306	False		,,,				2504	0.2546				p.S120S		Atlas-SNP	.											DCAF13,NS,carcinoma,0,1	DCAF13	66	1	0			c.T360C						PASS	.	T		949,3453		103,743,1355	37.0	45.0	43.0		360	1.9	0.7	8	dbSNP_103	43	1809,6783		189,1431,2676	no	coding-synonymous	DCAF13	NM_015420.6		292,2174,4031	CC,CT,TT		21.0545,21.5584,21.2252		120/598	104427578	2758,10236	2201	4296	6497	SO:0001631	upstream_gene_variant	25879	exon1			TGGAAGTAGTCTG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		8.37:g.104427578T>C	Exception_encountered	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_015420	Q96JZ6|Q96SU7	Silent	SNP	ENST00000297578.4	37	CCDS6300.1																																																																																			T|0.764;C|0.236	0.236	strong		0.632	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340906	55340906	+	Missense_Mutation	SNP	G	G	A	rs45542639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55340906G>A	ENST00000391728.4	+	7	1124	c.1091G>A	c.(1090-1092)tGc>tAc	p.C364Y	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.C347Y|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.C347Y|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.C269Y|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.C364Y	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	364					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		catctcTGGTGCTCCAACAAA	0.537													g|||	525	0.104832	0.093	0.1427	5008	,	,		14730	0.001		0.2475	False		,,,				2504	0.0542				p.C364Y		Atlas-SNP	.											KIR3DL1_ENST00000391728,NS,carcinoma,+1,1	KIR3DL1	174	1	0			c.G1091A						PASS	.	G	TYR/CYS	488,3852		82,324,1764	178.0	138.0	152.0		1091	-0.4	0.0	19	dbSNP_127	152	1718,6576		424,870,2853	no	missense	KIR3DL1	NM_013289.2	194	506,1194,4617	AA,AG,GG		20.7138,11.2442,17.4608		364/445	55340906	2206,10428	2170	4147	6317	SO:0001583	missense	3811	exon7			TCTGGTGCTCCAA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1091G>A	19.37:g.55340906G>A	ENSP00000375608:p.Cys364Tyr	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	265	0.12133699633699634	35	0.07113821138211382	46	0.1270718232044199	2	0.0034965034965034965	182	0.24010554089709762	-	7.282	0.609265	0.14066	0.112442	0.207138	ENSG00000167633	ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T	0.00483	7.09;7.16;7.09;7.16;7.09	0.743	-0.445	0.12242	.	4.446860	0.01420	U	0.014336	T	0.00012	0.0000	M	0.93062	3.375	0.80722	P	0.0	D;D;D	0.76494	0.963;0.999;0.992	P;D;D	0.74674	0.776;0.984;0.954	T	0.46857	-0.9161	9	0.62326	D	0.03	.	3.1214	0.06392	0.3487:0.0:0.6513:0.0	rs45542639	347;269;364	Q15702;Q14946;P43629	.;.;KI3L1_HUMAN	Y	364;347;342;364;347;269	ENSP00000443350:C364Y;ENSP00000442355:C347Y;ENSP00000375608:C364Y;ENSP00000326868:C347Y;ENSP00000350901:C269Y	ENSP00000326868:C347Y	C	+	2	0	KIR3DL1	60032718	0.022000	0.18835	0.001000	0.08648	0.031000	0.12232	-0.184000	0.09698	-0.103000	0.12175	0.184000	0.17185	TGC	G|0.875;A|0.125	0.125	strong		0.537	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
VARS2	57176	hgsc.bcm.edu	37	6	30888161	30888161	+	Missense_Mutation	SNP	T	T	C	rs2249464	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30888161T>C	ENST00000321897.5	+	13	1977	c.1345T>C	c.(1345-1347)Tgg>Cgg	p.W449R	VARS2_ENST00000541562.1_Missense_Mutation_p.W479R|VARS2_ENST00000542001.1_Missense_Mutation_p.W309R|VARS2_ENST00000416670.2_Missense_Mutation_p.W449R|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	449			W -> R (in dbSNP:rs2249464). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						GCTGAGTGAATGGGGCCTGTT	0.507													C|||	3086	0.616214	0.3593	0.6297	5008	,	,		16650	0.8413		0.5596	False		,,,				2504	0.7802				p.W479R		Atlas-SNP	.											.	VARS2	60	.	0			c.T1435C						PASS	.	C	ARG/TRP,ARG/TRP,ARG/TRP	1639,2767	657.5+/-400.2	284,1071,848	47.0	50.0	49.0		925,1435,1345	4.3	1.0	6	dbSNP_100	49	4645,3955	549.6+/-385.6	1242,2161,897	yes	missense,missense,missense	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	101,101,101	1526,3232,1745	CC,CT,TT		45.9884,37.1993,48.3162	benign,benign,benign	309/924,479/1094,449/1064	30888161	6284,6722	2203	4300	6503	SO:0001583	missense	57176	exon14			AGTGAATGGGGCC	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1345T>C	6.37:g.30888161T>C	ENSP00000316092:p.Trp449Arg	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	92	35	0.380435	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	1260	0.5769230769230769	149	0.30284552845528456	217	0.5994475138121547	458	0.8006993006993007	436	0.575197889182058	C	0.043	-1.278043	0.01410	0.371993	0.540116	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.33216	1.42;1.42;1.42;1.42	4.27	4.27	0.50696	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class Ia, editing domain (2);Aminoacyl-tRNA synthetase, class Ia (1);	0.262247	0.36002	N	0.002851	T	0.01092	0.0036	N	0.00039	-2.505	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40869	-0.9540	9	0.07175	T	0.84	-15.0648	5.8387	0.18621	0.1888:0.7098:0.0:0.1013	rs2249464;rs17195977;rs52836674;rs58710343;rs2249464	479;449	F5GXJ0;Q5ST30	.;SYVM_HUMAN	R	449;449;309;479	ENSP00000316092:W449R;ENSP00000394802:W449R;ENSP00000438200:W309R;ENSP00000441000:W479R	ENSP00000316092:W449R	W	+	1	0	VARS2	30996140	0.844000	0.29557	0.999000	0.59377	0.258000	0.26162	1.299000	0.33424	0.943000	0.37553	-0.355000	0.07637	TGG	T|0.471;C|0.529	0.529	strong		0.507	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
EYS	346007	hgsc.bcm.edu	37	6	65301211	65301211	+	Missense_Mutation	SNP	T	T	C	rs62415826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301211T>C	ENST00000370621.3	-	26	5075	c.4549A>G	c.(4549-4551)Agt>Ggt	p.S1517G	EYS_ENST00000370616.2_Missense_Mutation_p.S1517G|EYS_ENST00000503581.1_Missense_Mutation_p.S1517G			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1517			S -> G (in dbSNP:rs62415826). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GCTTTTGTACTGAACCGGTGC	0.433													C|||	470	0.0938498	0.0151	0.1182	5008	,	,		19137	0.1567		0.0984	False		,,,				2504	0.1135				p.S1517G		Atlas-SNP	.											.	EYS	527	.	0			c.A4549G						PASS	.	C	GLY/SER	49,1335		1,47,644	48.0	40.0	43.0		4549	2.0	0.0	6	dbSNP_129	43	446,2734		41,364,1185	yes	missense	EYS	NM_001142800.1	56	42,411,1829	CC,CT,TT		14.0252,3.5405,10.8457	benign	1517/3145	65301211	495,4069	692	1590	2282	SO:0001583	missense	346007	exon26			TTGTACTGAACCG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4549A>G	6.37:g.65301211T>C	ENSP00000359655:p.Ser1517Gly	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		214	0.09798534798534798	5	0.01016260162601626	44	0.12154696132596685	86	0.15034965034965034	79	0.10422163588390501	C	0.001	-3.258870	0.00021	0.035405	0.140252	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84070	-1.8;-1.78;-1.78	5.84	2.04	0.26737	.	.	.	.	.	T	0.42517	0.1206	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.01675	-1.1298	8	0.23302	T	0.38	.	7.0495	0.25065	0.0:0.137:0.2282:0.6348	rs62415826	1517;1517	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	G	1517	ENSP00000424243:S1517G;ENSP00000359655:S1517G;ENSP00000359650:S1517G	ENSP00000359650:S1517G	S	-	1	0	EYS	65357932	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.336000	0.07863	-0.104000	0.12154	-1.290000	0.01357	AGT	T|0.902;C|0.098	0.098	strong		0.433	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
ZACN	353174	hgsc.bcm.edu	37	17	74077797	74077797	+	Nonsense_Mutation	SNP	C	C	T	rs1043149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74077797C>T	ENST00000334586.5	+	7	924	c.841C>T	c.(841-843)Cag>Tag	p.Q281*	EXOC7_ENST00000591724.1_Intron|EXOC7_ENST00000332065.5_3'UTR|EXOC7_ENST00000589210.1_3'UTR|EXOC7_ENST00000607838.1_3'UTR	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	281	Leu-rich.				ion transmembrane transport (GO:0034220)|response to zinc ion (GO:0010043)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)|ligand-gated ion channel activity (GO:0015276)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	11						CTCCCTGGTGCAGGCCCTGCC	0.632													C|||	946	0.188898	0.0658	0.3184	5008	,	,		19188	0.3065		0.1899	False		,,,				2504	0.1411				p.Q281X		Atlas-SNP	.											.	ZACN	29	.	0			c.C841T						PASS	.	C	,,,,,stop/GLN	436,3970	207.8+/-229.1	28,380,1795	106.0	100.0	102.0		,,,,,841	2.8	1.0	17	dbSNP_86	102	1515,7085	286.2+/-297.6	137,1241,2922	yes	utr-3,utr-3,utr-3,utr-3,utr-3,stop-gained	EXOC7,ZACN	NM_001013839.2,NM_001145297.2,NM_001145298.2,NM_001145299.2,NM_015219.3,NM_180990.3	,,,,,	165,1621,4717	TT,TC,CC		17.6163,9.8956,15.0008	,,,,,	,,,,,281/413	74077797	1951,11055	2203	4300	6503	SO:0001587	stop_gained	353174	exon7			CTGGTGCAGGCCC	AK122638	CCDS11740.2	17q25.3	2012-01-18	2008-04-17	2008-04-17	ENSG00000186919	ENSG00000186919		"""Ligand-gated ion channels / Zinc activated channels"""	29504	protein-coding gene	gene with protein product		610935	"""ligand-gated ion channel, zinc activated 1"""	LGICZ1		12381728, 16083862	Standard	NM_180990		Approved	LGICZ, L2, ZAC, ZAC1	uc002jqn.2	Q401N2	OTTHUMG00000157186	ENST00000334586.5:c.841C>T	17.37:g.74077797C>T	ENSP00000334854:p.Gln281*	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	115	43	0.373913	NM_180990	Q2TB29|Q6ZWK3|Q86YW4	Nonsense_Mutation	SNP	ENST00000334586.5	37	CCDS11740.2	477	0.2184065934065934	31	0.06300813008130081	111	0.30662983425414364	189	0.3304195804195804	146	0.19261213720316622	C	21.1	4.093899	0.76870	0.098956	0.176163	ENSG00000186919	ENST00000334586	.	.	.	4.85	2.78	0.32641	.	0.373083	0.25250	N	0.032031	.	.	.	.	.	.	0.09310	P	0.999999999886038	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.1912	8.2332	0.31610	0.1691:0.5031:0.3279:0.0	rs1043149;rs52825779;rs61081835;rs1043149	.	.	.	X	281	.	ENSP00000334854:Q281X	Q	+	1	0	ZACN	71589392	0.980000	0.34600	0.978000	0.43139	0.580000	0.36256	0.222000	0.17699	0.602000	0.29896	0.505000	0.49811	CAG	C|0.826;T|0.174	0.174	strong		0.632	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990	
ZNF501	115560	hgsc.bcm.edu	37	3	44775962	44775962	+	Missense_Mutation	SNP	A	A	G	rs4682752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:44775962A>G	ENST00000396048.2	+	3	486	c.49A>G	c.(49-51)Atg>Gtg	p.M17V		NM_001258280.1|NM_145044.3	NP_001245209.1|NP_659481.2	Q96CX3	ZN501_HUMAN	zinc finger protein 501	17			M -> V (in dbSNP:rs4682752). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00843)|KIRC - Kidney renal clear cell carcinoma(197;0.0463)|Kidney(197;0.0579)		GAGAGTTAACATGCAGAAGAA	0.403													A|||	3482	0.695288	0.6112	0.6643	5008	,	,		21877	0.881		0.5954	False		,,,				2504	0.7423				p.M17V		Atlas-SNP	.											.	ZNF501	27	.	0			c.A49G						PASS	.	A	VAL/MET	2638,1528		844,950,289	97.0	97.0	97.0		49	2.4	0.0	3	dbSNP_111	97	4720,3776		1303,2114,831	yes	missense	ZNF501	NM_145044.2	21	2147,3064,1120	GG,GA,AA		44.4444,36.6779,41.8891	benign	17/272	44775962	7358,5304	2083	4248	6331	SO:0001583	missense	115560	exon3			GTTAACATGCAGA	BC013762	CCDS2720.2	3p21.32	2013-01-08			ENSG00000186446	ENSG00000186446		"""Zinc fingers, C2H2-type"""	23717	protein-coding gene	gene with protein product			"""zinc finger protein 52"""	ZNF52		1505991	Standard	NM_145044		Approved	MGC21738	uc003cnu.2	Q96CX3	OTTHUMG00000133048	ENST00000396048.2:c.49A>G	3.37:g.44775962A>G	ENSP00000379363:p.Met17Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_001258280	B4DLY7|Q96NU9	Missense_Mutation	SNP	ENST00000396048.2	37	CCDS2720.2	1501	0.6872710622710623	288	0.5853658536585366	247	0.6823204419889503	514	0.8986013986013986	452	0.5963060686015831	A	12.92	2.082127	0.36758	0.633221	0.555556	ENSG00000186446	ENST00000396048;ENST00000332489	T	0.38401	1.14	2.39	2.39	0.29439	.	.	.	.	.	T	0.00012	0.0000	L	0.35854	1.095	0.37504	P	0.08313000000000004	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.28933	-1.0028	8	0.72032	D	0.01	.	9.9914	0.41874	1.0:0.0:0.0:0.0	rs4682752;rs17624679;rs61047958;rs4682752	17;17	Q96CX3-2;Q96CX3	.;ZN501_HUMAN	V	17	ENSP00000379363:M17V	ENSP00000330388:M17V	M	+	1	0	ZNF501	44750966	0.001000	0.12720	0.009000	0.14445	0.251000	0.25915	1.006000	0.29847	1.351000	0.45789	0.455000	0.32223	ATG	A|0.329;G|0.671	0.671	strong		0.403	ZNF501-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256654.4	NM_145044	
OR51B6	390058	hgsc.bcm.edu	37	11	5373129	5373129	+	Missense_Mutation	SNP	C	C	T	rs5006887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373129C>T	ENST00000380219.1	+	1	392	c.392C>T	c.(391-393)aCc>aTc	p.T131I	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	131			T -> I (in dbSNP:rs5006887). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTAAGATATACCTCTATCCTG	0.463													C|||	1173	0.234225	0.326	0.2349	5008	,	,		23502	0.0863		0.2644	False		,,,				2504	0.2311				p.T131I		Atlas-SNP	.											.	OR51B6	53	.	0			c.C392T						PASS	.	C	ILE/THR	1240,3162	424.2+/-340.4	174,892,1135	128.0	116.0	120.0		392	4.1	0.7	11	dbSNP_113	120	2214,6380	370.8+/-336.0	308,1598,2391	yes	missense	OR51B6	NM_001004750.1	89	482,2490,3526	TT,TC,CC		25.7622,28.169,26.5774	benign	131/313	5373129	3454,9542	2201	4297	6498	SO:0001583	missense	390058	exon1			GATATACCTCTAT		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.392C>T	11.37:g.5373129C>T	ENSP00000369568:p.Thr131Ile	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	198	65	0.328283	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	C	6.898	0.535295	0.13188	0.28169	0.257622	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.19938	2.11	5.01	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.238996	0.29444	N	0.012131	T	0.00012	0.0000	M	0.87097	2.86	0.80722	P	0.0	B	0.23442	0.085	B	0.20955	0.032	T	0.17107	-1.0380	9	0.66056	D	0.02	.	13.5332	0.61633	0.0:0.7017:0.2983:0.0	rs5006887;rs5006887	131	Q9H340	O51B6_HUMAN	I	130;131	ENSP00000369568:T131I	ENSP00000369568:T131I	T	+	2	0	OR51B6	5329705	0.000000	0.05858	0.714000	0.30535	0.382000	0.30200	-0.232000	0.09055	1.315000	0.45114	0.455000	0.32223	ACC	C|0.760;T|0.240	0.240	strong		0.463	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
KRT83	3889	hgsc.bcm.edu	37	12	52710309	52710309	+	Silent	SNP	G	G	A	rs2257286	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52710309G>A	ENST00000293670.3	-	6	1046	c.984C>T	c.(982-984)aaC>aaT	p.N328N		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	328	Coil 2.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.N328N(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGTTCAGCTCGTTGATCTCCT	0.602													g|||	1882	0.375799	0.5008	0.317	5008	,	,		19119	0.1885		0.4095	False		,,,				2504	0.407				p.N328N	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,0,1	KRT83	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C984T						PASS	.	G		2156,2250	582.3+/-385.5	551,1054,598	127.0	101.0	110.0		984	-1.3	1.0	12	dbSNP_100	110	3529,5067	514.6+/-378.4	722,2085,1491	no	coding-synonymous	KRT83	NM_002282.3		1273,3139,2089	AA,AG,GG		41.054,48.9333,43.724		328/494	52710309	5685,7317	2203	4298	6501	SO:0001819	synonymous_variant	3889	exon6			CAGCTCGTTGATC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.984C>T	12.37:g.52710309G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			.	.	weak		0.602	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
PRAM1	84106	hgsc.bcm.edu	37	19	8564466	8564466	+	Missense_Mutation	SNP	C	C	A	rs371461475|rs4239540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8564466C>A	ENST00000423345.4	-	2	746	c.226G>T	c.(226-228)Gtc>Ttc	p.V76F	PRAM1_ENST00000255612.3_Missense_Mutation_p.V76F			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	124	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.		F -> V (in dbSNP:rs4239540).		integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						AGGTCAGTGACCTCAGGCGGC	0.647													G|||	1793	0.358027	0.6203	0.2954	5008	,	,		12427	0.1577		0.3072	False		,,,				2504	0.3067				p.V76F		Atlas-SNP	.											.	PRAM1	53	.	0			c.G226T						PASS	.						38.0	50.0	46.0					19																	8564466		1845	4081	5926	SO:0001583	missense	84106	exon2			CAGTGACCTCAGG	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.226G>T	19.37:g.8564466C>A	ENSP00000408342:p.Val76Phe	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	61	20	0.327869	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	823	0.3768315018315018	380	0.7723577235772358	110	0.30386740331491713	82	0.14335664335664336	251	0.3311345646437995	c	0.069	-1.205606	0.01568	.	.	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.13307	2.6;2.6	4.36	-8.73	0.00841	.	1.188040	0.06658	N	0.763976	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37820	-0.9689	9	0.09338	T	0.73	.	11.7718	0.51962	0.3799:0.5451:0.0749:0.0	rs4239540;rs4239540	76;124	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	F	76	ENSP00000255612:V76F;ENSP00000408342:V76F	ENSP00000255612:V76F	V	-	1	0	PRAM1	8470466	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.770000	0.01791	-1.430000	0.01985	-4.114000	0.00011	GTC	C|0.601;A|0.399	0.399	strong		0.647	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
LZTS1	11178	hgsc.bcm.edu	37	8	20110641	20110641	+	Silent	SNP	C	C	T	rs2645386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:20110641C>T	ENST00000381569.1	-	3	1158	c.801G>A	c.(799-801)gaG>gaA	p.E267E	LZTS1_ENST00000265801.6_Silent_p.E267E|LZTS1_ENST00000522290.1_Silent_p.E267E			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	267					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		ACAGCTTCTGCTCCAGCTCCT	0.657													C|||	1796	0.358626	0.3843	0.2205	5008	,	,		17260	0.4623		0.3231	False		,,,				2504	0.3517				p.E267E		Atlas-SNP	.											.	LZTS1	72	.	0			c.G801A						PASS	.	C		1774,2626		384,1006,810	49.0	45.0	46.0		801	5.6	1.0	8	dbSNP_100	46	2966,5612		546,1874,1869	no	coding-synonymous	LZTS1	NM_021020.2		930,2880,2679	TT,TC,CC		34.5768,40.3182,36.5233		267/597	20110641	4740,8238	2200	4289	6489	SO:0001819	synonymous_variant	11178	exon2			CTTCTGCTCCAGC	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"""F37/Esophageal cancer-related gene-coding leucine-zipper motif"""			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.801G>A	8.37:g.20110641C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Silent	SNP	ENST00000381569.1	37	CCDS6015.1																																																																																			C|0.631;T|0.369	0.369	strong		0.657	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020	
PCNXL3	399909	hgsc.bcm.edu	37	11	65386206	65386206	+	Missense_Mutation	SNP	C	C	G	rs1193851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:65386206C>G	ENST00000355703.3	+	6	1912	c.1373C>G	c.(1372-1374)tCc>tGc	p.S458C		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	458	Ser-rich.		S -> C (in dbSNP:rs1193851).			integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCTGAGAGCTCCCGGGGTGCA	0.672													C|||	1189	0.23742	0.3336	0.245	5008	,	,		14635	0.1329		0.336	False		,,,				2504	0.1084				p.S458C		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C1373G						PASS	.	C	CYS/SER	1233,2513		195,843,835	28.0	29.0	29.0		1373	4.1	1.0	11	dbSNP_87	29	2830,5362		493,1844,1759	yes	missense	PCNXL3	NM_032223.2	112	688,2687,2594	GG,GC,CC		34.5459,32.9151,34.0342	probably-damaging	458/2035	65386206	4063,7875	1873	4096	5969	SO:0001583	missense	399909	exon6			AGAGCTCCCGGGG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.1373C>G	11.37:g.65386206C>G	ENSP00000347931:p.Ser458Cys	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	44	0.578947	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	566	0.2591575091575092	150	0.3048780487804878	93	0.2569060773480663	66	0.11538461538461539	257	0.3390501319261214	C	15.99	2.995718	0.54147	0.329151	0.345459	ENSG00000197136	ENST00000355703	T	0.01068	5.38	5.1	4.13	0.48395	.	0.000000	0.38959	N	0.001516	T	0.00012	0.0000	N	0.14661	0.345	0.43275	P	0.0047639999999999905	D	0.58620	0.983	B	0.43783	0.431	T	0.55490	-0.8133	9	0.66056	D	0.02	.	10.0494	0.42205	0.2006:0.7994:0.0:0.0	rs1193851;rs1194079;rs1679083;rs3814750;rs1193851	458	Q9H6A9	PCX3_HUMAN	C	458	ENSP00000347931:S458C	ENSP00000347931:S458C	S	+	2	0	PCNXL3	65142782	0.855000	0.29742	1.000000	0.80357	0.997000	0.91878	0.682000	0.25335	2.384000	0.81235	0.462000	0.41574	TCC	C|0.734;G|0.266	0.266	strong		0.672	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
NUP54	53371	hgsc.bcm.edu	37	4	77055474	77055474	+	Silent	SNP	A	A	G	rs11097244	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77055474A>G	ENST00000264883.3	-	5	704	c.564T>C	c.(562-564)gaT>gaC	p.D188D	NUP54_ENST00000514987.1_Silent_p.D140D|NUP54_ENST00000342467.6_Silent_p.D8D|NUP54_ENST00000458189.2_Silent_p.D8D|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	188	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						CCACTAGCCCATCTTCATCTT	0.343													A|||	777	0.155152	0.0567	0.1297	5008	,	,		16365	0.3512		0.1312	False		,,,				2504	0.1288				p.D188D		Atlas-SNP	.											NUP54,colon,carcinoma,-2,1	NUP54	48	1	0			c.T564C						PASS	.	A		308,4098	165.8+/-197.2	15,278,1910	69.0	60.0	63.0		564	4.7	1.0	4	dbSNP_120	63	1300,7300	256.2+/-280.8	101,1098,3101	no	coding-synonymous	NUP54	NM_017426.2		116,1376,5011	GG,GA,AA		15.1163,6.9905,12.3635		188/508	77055474	1608,11398	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon5			TAGCCCATCTTCA	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.564T>C	4.37:g.77055474A>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	29	0.381579	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			A|0.865;G|0.135	0.135	strong		0.343	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
PRAM1	84106	hgsc.bcm.edu	37	19	8564523	8564523	+	Missense_Mutation	SNP	T	T	G	rs4804305	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8564523T>G	ENST00000423345.4	-	2	689	c.169A>C	c.(169-171)Aag>Cag	p.K57Q	PRAM1_ENST00000255612.3_Missense_Mutation_p.K57Q			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	57	Pro-rich.		K -> Q (in dbSNP:rs4804305). {ECO:0000269|PubMed:11301322}.		integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						GGGGCCTTCTTGGGGTGCTCG	0.622													-|||	1161	0.231829	0.0877	0.2896	5008	,	,		12472	0.1736		0.336	False		,,,				2504	0.3384				p.K57Q		Atlas-SNP	.											.	PRAM1	53	.	0			c.A169C						PASS	.	T	GLN/LYS	371,3547		22,327,1610	57.0	66.0	63.0		169	-1.1	0.0	19	dbSNP_111	63	2368,5908		362,1644,2132	yes	missense	PRAM1	NM_032152.4	53	384,1971,3742	GG,GT,TT		28.6129,9.4691,22.4619	probably-damaging	57/671	8564523	2739,9455	1959	4138	6097	SO:0001583	missense	84106	exon2			CCTTCTTGGGGTG	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.169A>C	19.37:g.8564523T>G	ENSP00000408342:p.Lys57Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	488	0.22344322344322345	50	0.1016260162601626	94	0.2596685082872928	89	0.1555944055944056	255	0.33641160949868076	T	13.93	2.383623	0.42207	0.094691	0.286129	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.18657	2.2;2.2	4.28	-1.1	0.09872	.	.	.	.	.	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	D;D	0.76494	0.997;0.999	D;D	0.69479	0.913;0.964	T	0.34204	-0.9838	8	0.45353	T	0.12	.	6.29	0.21054	0.1667:0.0:0.5122:0.3211	rs4804305;rs4804305	57;57	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	Q	57	ENSP00000255612:K57Q;ENSP00000408342:K57Q	ENSP00000255612:K57Q	K	-	1	0	PRAM1	8470523	0.466000	0.25823	0.002000	0.10522	0.001000	0.01503	0.883000	0.28200	-0.059000	0.13154	-0.468000	0.05107	AAG	T|0.793;G|0.207	0.207	strong		0.622	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
GBE1	2632	hgsc.bcm.edu	37	3	81627175	81627175	+	Missense_Mutation	SNP	T	T	C	rs2228389	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:81627175T>C	ENST00000429644.2	-	12	2162	c.1519A>G	c.(1519-1521)Act>Gct	p.T507A	GBE1_ENST00000489715.1_Missense_Mutation_p.T466A	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	507			T -> A (in dbSNP:rs2228389).		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)		GTAAAAGGAGTCAGGACACTC	0.408									Glycogen Storage Disease, type IV				T|||	381	0.0760783	0.1536	0.0735	5008	,	,		16809	0.0575		0.0278	False		,,,				2504	0.0419				p.T507A		Atlas-SNP	.											.	GBE1	111	.	0			c.A1519G						PASS	.	T	ALA/THR	467,3431		30,407,1512	90.0	87.0	88.0		1519	-5.5	0.0	3	dbSNP_98	88	190,8116		1,188,3964	yes	missense	GBE1	NM_000158.3	58	31,595,5476	CC,CT,TT		2.2875,11.9805,5.3835	benign	507/703	81627175	657,11547	1949	4153	6102	SO:0001583	missense	2632	exon12	Familial Cancer Database	Andersen Disease, Brancher deficiency	AAGGAGTCAGGAC		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.1519A>G	3.37:g.81627175T>C	ENSP00000410833:p.Thr507Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	112	43	0.383929	NM_000158	B3KWV3|Q96EN0	Missense_Mutation	SNP	ENST00000429644.2	37	CCDS54612.1	159	0.07280219780219781	58	0.11788617886178862	26	0.0718232044198895	48	0.08391608391608392	27	0.03562005277044855	T	10.69	1.420445	0.25639	0.119805	0.022875	ENSG00000114480	ENST00000429644;ENST00000264326;ENST00000489715;ENST00000536832	D;D	0.85861	-2.04;-2.04	5.68	-5.52	0.02560	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.751547	0.13110	N	0.413060	T	0.04998	0.0134	M	0.83384	2.64	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.001;0.003	T	0.49978	-0.8881	9	0.29301	T	0.29	-0.0928	5.7202	0.17982	0.4209:0.122:0.0:0.4571	rs2228389;rs7633228;rs52833052;rs56699531;rs7633228	466;507	E9PGM4;Q04446	.;GLGB_HUMAN	A	507;558;466;270	ENSP00000410833:T507A;ENSP00000419638:T466A	ENSP00000264326:T558A	T	-	1	0	GBE1	81709865	0.096000	0.21769	0.007000	0.13788	0.611000	0.37282	0.051000	0.14141	-0.561000	0.06094	0.477000	0.44152	ACT	T|0.604;G|0.030;C|0.042;A|0.325	0.042	strong		0.408	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
RASSF4	83937	hgsc.bcm.edu	37	10	45488738	45488738	+	Silent	SNP	G	G	A	rs145503557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45488738G>A	ENST00000340258.5	+	11	1040	c.927G>A	c.(925-927)acG>acA	p.T309T	RASSF4_ENST00000374417.2_3'UTR|RASSF4_ENST00000334940.6_Silent_p.T318T|RASSF4_ENST00000472561.1_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0	Poly-Pro.				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)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGCGTCTGACGATGCTGCAGC	0.627													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19979	0.0		0.0	False		,,,				2504	0.0				p.T309T		Atlas-SNP	.											.	RASSF4	33	.	0			c.G927A						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	67.0	51.0	56.0		927	-8.1	1.0	10	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RASSF4	NM_032023.3		0,12,6491	AA,AG,GG		0.0116,0.2497,0.0923		309/322	45488738	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	83937	exon11			TCTGACGATGCTG	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.927G>A	10.37:g.45488738G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000340258.5	37	CCDS7208.1																																																																																			G|0.999;A|0.001	0.001	strong		0.627	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023	
TBC1D4	9882	hgsc.bcm.edu	37	13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	rs557337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:75861001A>G	ENST00000377636.3	-	21	4170	c.3824T>C	c.(3823-3825)gTc>gCc	p.V1275A	TBC1D4_ENST00000425511.1_Missense_Mutation_p.V439A|TBC1D4_ENST00000377625.2_Missense_Mutation_p.V1212A|TBC1D4_ENST00000431480.2_Missense_Mutation_p.V1267A	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1275			V -> A (in dbSNP:rs557337). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19077034, ECO:0000269|PubMed:9628581}.		cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GTCACAATTGACTAGAGCATC	0.463													G|||	873	0.174321	0.556	0.0778	5008	,	,		16760	0.0		0.0666	False		,,,				2504	0.0174				p.V1275A		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T3824C						PASS	.	G	ALA/VAL	1770,2058		428,914,572	104.0	107.0	106.0		3824	3.9	0.0	13	dbSNP_83	106	484,7778		13,458,3660	yes	missense	TBC1D4	NM_014832.2	64	441,1372,4232	GG,GA,AA		5.8581,46.2382,18.6435	benign	1275/1299	75861001	2254,9836	1914	4131	6045	SO:0001583	missense	9882	exon21			CAATTGACTAGAG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3824T>C	13.37:g.75861001A>G	ENSP00000366863:p.Val1275Ala	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	305	163	0.534426	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	333	0.15247252747252749	256	0.5203252032520326	32	0.08839779005524862	0	0.0	45	0.059366754617414245	G	0.218	-1.030972	0.02029	0.462382	0.058581	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.03358	4.23;4.23;4.23;3.96	5.63	3.87	0.44632	.	0.297360	0.28841	N	0.013979	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.38329	-0.9666	9	0.02654	T	1	-5.6523	10.4567	0.44555	0.2148:0.0:0.7852:0.0	rs557337;rs52811417;rs60191388;rs557337	439;1212;1267;1275	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	A	1275;1267;1212;439	ENSP00000366863:V1275A;ENSP00000395986:V1267A;ENSP00000366852:V1212A;ENSP00000390654:V439A	ENSP00000366852:V1212A	V	-	2	0	TBC1D4	74759002	1.000000	0.71417	0.008000	0.14137	0.004000	0.04260	4.134000	0.57990	0.847000	0.35167	-0.119000	0.15052	GTC	A|0.827;G|0.173	0.173	strong		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
FANCD2	2177	hgsc.bcm.edu	37	3	10088308	10088308	+	Silent	SNP	T	T	C	rs72492998		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:10088308T>C	ENST00000419585.1	+	15	1340	c.1179T>C	c.(1177-1179)acT>acC	p.T393T	FANCD2_ENST00000383807.1_Silent_p.T393T|FANCD2_ENST00000383806.1_Silent_p.T393T|FANCD2_ENST00000287647.3_Silent_p.T393T			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	393					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		GCACCAATACTCAGACAAAGA	0.373			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T393T		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253	.	0			c.T1179C						PASS	.						117.0	107.0	111.0					3																	10088308		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon15	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAATACTCAGACA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1179T>C	3.37:g.10088308T>C		Somatic	398	0	0		WXS	Illumina HiSeq	Phase_I	482	129	0.267635	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			T|0.500;C|0.500	0.500	weak		0.373	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43816735	43816735	+	Missense_Mutation	SNP	G	G	C	rs200986004	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:43816735G>C	ENST00000377564.3	+	6	1234	c.841G>C	c.(841-843)Gac>Cac	p.D281H	CNTNAP3B_ENST00000276974.6_Missense_Mutation_p.D281H	NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	281	Laminin G-like 1. {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						CGAGCTCCTCGACACGCAGGT	0.488													g|||	100	0.0199681	0.0166	0.0101	5008	,	,		22562	0.0466		0.008	False		,,,				2504	0.0164				p.D281H		Atlas-SNP	.											CNTNAP3B,right_lower_lobe,carcinoma,-2,1	CNTNAP3B	37	1	0			c.G841C						scavenged	.																																			SO:0001583	missense	728577	exon6			CTCCTCGACACGC	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.841G>C	9.37:g.43816735G>C	ENSP00000366787:p.Asp281His	Somatic	1106	1	0.000904159		WXS	Illumina HiSeq	Phase_I	837	84	0.100358	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.	.	.	.	.	.	.	.	.	.	g	14.89	2.671567	0.47781	.	.	ENSG00000154529	ENST00000377564;ENST00000276974;ENST00000341990;ENST00000403166	T;T	0.78246	-1.16;-1.16	2.77	-4.35	0.03656	.	.	.	.	.	T	0.60907	0.2305	N	0.14661	0.345	0.09310	N	1	.	.	.	.	.	.	T	0.56492	-0.7970	7	0.62326	D	0.03	.	8.1029	0.30868	0.5769:0.0:0.4231:0.0	.	.	.	.	H	281	ENSP00000366787:D281H;ENSP00000276974:D281H	ENSP00000276974:D281H	D	+	1	0	CNTNAP3B	43756731	0.000000	0.05858	0.000000	0.03702	0.466000	0.32739	0.894000	0.28350	-0.920000	0.03799	-0.506000	0.04501	GAC	A|0.002;C|0.002;G|0.995	0.002	strong		0.488	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
CNDP2	55748	hgsc.bcm.edu	37	18	72168608	72168608	+	Silent	SNP	G	G	A	rs2303463	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:72168608G>A	ENST00000324262.4	+	3	421	c.105G>A	c.(103-105)ccG>ccA	p.P35P	CNDP2_ENST00000324301.8_Silent_p.P35P|CNDP2_ENST00000579847.1_Silent_p.P35P	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	35					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.P35P(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		CTGCGTGGCCGGAGAAGAGAG	0.507													G|||	1233	0.246206	0.2231	0.3127	5008	,	,		19326	0.2956		0.164	False		,,,				2504	0.2638				p.P35P		Atlas-SNP	.											CNDP2,caecum,carcinoma,0,2	CNDP2	55	2	1	Substitution - coding silent(1)	stomach(1)	c.G105A						PASS	.	G	,	937,3469	358.4+/-314.3	119,699,1385	173.0	152.0	159.0		105,105	-11.6	0.3	18	dbSNP_100	159	1623,6977	301.7+/-305.6	134,1355,2811	no	coding-synonymous,coding-synonymous	CNDP2	NM_001168499.1,NM_018235.2	,	253,2054,4196	AA,AG,GG		18.8721,21.2665,19.6832	,	35/392,35/476	72168608	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	55748	exon2			GTGGCCGGAGAAG	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.105G>A	18.37:g.72168608G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_001168499	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Silent	SNP	ENST00000324262.4	37	CCDS12006.1																																																																																			G|0.791;A|0.209	0.209	strong		0.507	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609806	32609806	+	Missense_Mutation	SNP	C	C	T	rs707952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32609806C>T	ENST00000343139.5	+	3	491	c.389C>T	c.(388-390)aCc>aTc	p.T130I	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.T130I|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.T130I	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	129	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CAGCCCAACACCCTCATTTGT	0.507													.|||	937	0.187101	0.2209	0.2392	5008	,	,		18850	0.12		0.2286	False		,,,				2504	0.1309				p.T130I		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.C389T						PASS	.	C	ILE/THR	680,2342		130,420,961	156.0	115.0	130.0		389	2.1	1.0	6	dbSNP_86	130	1340,4078		191,958,1560	yes	missense	HLA-DQA1	NM_002122.3	89	321,1378,2521	TT,TC,CC		24.7324,22.5017,23.9336	benign	130/256	32609806	2020,6420	1511	2709	4220	SO:0001583	missense	3117	exon3			CCAACACCCTCAT		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.389C>T	6.37:g.32609806C>T	ENSP00000339398:p.Thr130Ile	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	292	134	0.458904	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	444|444	0.2032967032967033|0.2032967032967033	103|103	0.20934959349593496|0.20934959349593496	96|96	0.26519337016574585|0.26519337016574585	87|87	0.1520979020979021|0.1520979020979021	158|158	0.20844327176781002|0.20844327176781002	.|.	7.950|7.950	0.744573|0.744573	0.15710|0.15710	0.225017|0.225017	0.247324|0.247324	ENSG00000196735|ENSG00000196735	ENST00000486548|ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	.|T;T;T;T	.|0.00646	.|6.0;6.0;6.0;6.0	4.1|4.1	2.07|2.07	0.26955|0.26955	.|.	.|0.503713	.|0.18451	.|N	.|0.140840	T|T	0.00271|0.00271	0.0008|0.0008	L|L	0.49640|0.49640	1.575|1.575	0.34178|0.34178	P|P	0.32944399999999996|0.32944399999999996	.|B;B	.|0.14012	.|0.009;0.001	.|B;B	.|0.16722	.|0.016;0.016	T|T	0.41124|0.41124	-0.9526|-0.9526	4|9	.|0.26408	.|T	.|0.33	.|.	4.8377|4.8377	0.13473|0.13473	0.0:0.5171:0.0:0.4829|0.0:0.5171:0.0:0.4829	rs707952;rs2308879;rs3176021;rs9272745;rs16870410;rs707952|rs707952;rs2308879;rs3176021;rs9272745;rs16870410;rs707952	.|136;130	.|Q59F33;G4XQK2	.|.;.	S|I	103|130	.|ENSP00000339398:T130I;ENSP00000378767:T130I;ENSP00000437302:T130I;ENSP00000364087:T130I	.|ENSP00000339398:T130I	P|T	+|+	1|2	0|0	HLA-DQA1|HLA-DQA1	32717784|32717784	0.879000|0.879000	0.30193|0.30193	0.999000|0.999000	0.59377|0.59377	0.311000|0.311000	0.27955|0.27955	0.300000|0.300000	0.19156|0.19156	0.410000|0.410000	0.25675|0.25675	0.655000|0.655000	0.94253|0.94253	CCC|ACC	C|0.785;T|0.215	0.215	strong		0.507	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
ARL2	402	hgsc.bcm.edu	37	11	64789194	64789194	+	Splice_Site	SNP	T	T	C	rs664226	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64789194T>C	ENST00000246747.4	+	5	517	c.422T>C	c.(421-423)gTc>gCc	p.V141A	RP11-399J13.3_ENST00000301886.3_Intron|ARL2_ENST00000533729.1_Splice_Site_p.V114A|ARL2_ENST00000529384.1_Splice_Site_p.V141A	NM_001667.3	NP_001658.2	P36404	ARL2_HUMAN	ADP-ribosylation factor-like 2	141			V -> A (in dbSNP:rs664226). {ECO:0000269|PubMed:15146197, ECO:0000269|PubMed:8415637, ECO:0000269|Ref.3}.		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)	p.V141A(1)|p.?(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	5						TCCTCCCAGGTCCTGGAGCTG	0.667													C|||	2292	0.457668	0.7088	0.3905	5008	,	,		16560	0.1806		0.6064	False		,,,				2504	0.2986				p.V141A		Atlas-SNP	.											ARL2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ARL2	11	1	2	Substitution - Missense(1)|Unknown(1)	central_nervous_system(2)	c.T422C						PASS	.	C	ALA/VAL,ALA/VAL	3111,1291	423.4+/-340.1	1097,917,187	43.0	35.0	38.0		341,422	3.5	1.0	11	dbSNP_83	38	5392,3200	467.6+/-367.1	1685,2022,589	yes	missense-near-splice,missense-near-splice	ARL2	NM_001199745.1,NM_001667.3	64,64	2782,2939,776	CC,CT,TT		37.2439,29.3276,34.5621	benign,benign	114/158,141/185	64789194	8503,4491	2201	4296	6497	SO:0001630	splice_region_variant	402	exon5			CCCAGGTCCTGGA	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.421-1T>C	11.37:g.64789194T>C		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_001667	G3V184|Q9BUK8	Missense_Mutation	SNP	ENST00000246747.4	37	CCDS8088.1	1041	0.4766483516483517	331	0.6727642276422764	163	0.45027624309392267	92	0.16083916083916083	455	0.600263852242744	C	2.707	-0.269614	0.05716	0.706724	0.627561	ENSG00000213465	ENST00000246747;ENST00000529384;ENST00000533729	D;D;D	0.81908	-1.55;-1.55;-1.55	4.5	3.5	0.40072	Small GTP-binding protein domain (1);	0.315868	0.28082	N	0.016667	T	0.00012	0.0000	N	0.00666	-1.275	0.09310	P	0.9999999999922409	B	0.02656	0.0	B	0.06405	0.002	T	0.45891	-0.9230	9	0.27785	T	0.31	-11.8565	8.1549	0.31162	0.0:0.7835:0.0:0.2165	rs664226;rs947902;rs2070187;rs2230868;rs11540367;rs61323596;rs664226	141	P36404	ARL2_HUMAN	A	141;141;114	ENSP00000246747:V141A;ENSP00000436021:V141A;ENSP00000432971:V114A	ENSP00000246747:V141A	V	+	2	0	ARL2	64545770	0.998000	0.40836	1.000000	0.80357	0.768000	0.43524	2.192000	0.42649	1.136000	0.42199	-0.338000	0.08134	GTC	T|0.439;C|0.561	0.561	strong		0.667	ARL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385963.1	NM_001667	Missense_Mutation
CAPN2	824	hgsc.bcm.edu	37	1	223949900	223949900	+	Missense_Mutation	SNP	G	G	A	rs145816861		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:223949900G>A	ENST00000295006.5	+	14	1888	c.1579G>A	c.(1579-1581)Gag>Aag	p.E527K	CAPN2_ENST00000433674.2_Missense_Mutation_p.E449K|CAPN2_ENST00000474026.1_3'UTR	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	527	Linker.				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)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CGACATCAGCGAGGATGACAT	0.517																																					p.E527K		Atlas-SNP	.											.	CAPN2	69	.	0			c.G1579A						PASS	.	G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	174.0	128.0	143.0		1345,1579	4.7	0.9	1	dbSNP_134	143	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	CAPN2	NM_001146068.1,NM_001748.4	56,56	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging	449/623,527/701	223949900	3,13003	2203	4300	6503	SO:0001583	missense	824	exon14			ATCAGCGAGGATG	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.1579G>A	1.37:g.223949900G>A	ENSP00000295006:p.Glu527Lys	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	36	0.433735	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339343	0.41398	2.27E-4	2.33E-4	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	T;T	0.30714	1.52;1.52	5.63	4.71	0.59529	.	0.442904	0.27284	N	0.020073	T	0.30448	0.0765	L	0.57536	1.79	0.80722	D	1	B;B;B	0.28128	0.003;0.201;0.036	B;B;B	0.20184	0.005;0.028;0.007	T	0.04946	-1.0916	10	0.33141	T	0.24	.	14.7507	0.69522	0.0:0.0:0.8544:0.1456	.	449;110;527	B7ZA96;B3KUH9;P17655	.;.;CAN2_HUMAN	K	449;527;556	ENSP00000413158:E449K;ENSP00000295006:E527K	ENSP00000295006:E527K	E	+	1	0	CAPN2	222016523	1.000000	0.71417	0.853000	0.33588	0.071000	0.16799	9.176000	0.94839	1.364000	0.46038	0.655000	0.94253	GAG	G|1.000;A|0.000	0.000	weak		0.517	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748	
KIF20B	9585	hgsc.bcm.edu	37	10	91488979	91488979	+	Missense_Mutation	SNP	A	A	T	rs3758388	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:91488979A>T	ENST00000371728.3	+	18	2431	c.2366A>T	c.(2365-2367)cAt>cTt	p.H789L	KIF20B_ENST00000416354.1_Missense_Mutation_p.H789L|KIF20B_ENST00000394289.2_Missense_Mutation_p.H789L|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.H749L	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	789			H -> L (in dbSNP:rs3758388). {ECO:0000269|PubMed:11470801, ECO:0000269|PubMed:12740395}.		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						CTAAAGTCTCATATGGAAAAC	0.229													A|||	1047	0.209065	0.0492	0.2133	5008	,	,		15884	0.3621		0.2416	False		,,,				2504	0.2311				p.H749L		Atlas-SNP	.											.	KIF20B	191	.	0			c.A2246T						PASS	.	A	LEU/HIS	306,3992		9,288,1852	34.0	37.0	36.0		2246	0.7	0.0	10	dbSNP_107	36	1686,6778		179,1328,2725	yes	missense	KIF20B	NM_016195.2	99	188,1616,4577	TT,TA,AA		19.9197,7.1196,15.6088	benign	749/1781	91488979	1992,10770	2149	4232	6381	SO:0001583	missense	9585	exon18			AGTCTCATATGGA	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.2366A>T	10.37:g.91488979A>T	ENSP00000360793:p.His789Leu	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	217	86	0.396313	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		502	0.22985347985347984	27	0.054878048780487805	76	0.20994475138121546	215	0.3758741258741259	184	0.24274406332453827	A	2.315	-0.356936	0.05138	0.071196	0.199197	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.68331	-0.18;-0.26;-0.32;-0.26	3.1	0.696	0.18075	.	1.156200	0.06706	N	0.772258	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B;B	0.22414	0.041;0.069	B;B	0.21917	0.017;0.037	T	0.23762	-1.0179	9	0.20519	T	0.43	.	6.0179	0.19613	0.7562:0.0:0.2438:0.0	rs3758388;rs52791862;rs59884640;rs3758388	789;749	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	L	749;789;789;789	ENSP00000260753:H749L;ENSP00000411545:H789L;ENSP00000377830:H789L;ENSP00000360793:H789L	ENSP00000260753:H749L	H	+	2	0	KIF20B	91478959	0.016000	0.18221	0.001000	0.08648	0.002000	0.02628	0.719000	0.25881	-0.052000	0.13311	-0.274000	0.10170	CAT	A|0.807;T|0.193	0.193	strong		0.229	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
SPCS1	28972	hgsc.bcm.edu	37	3	52740182	52740182	+	5'UTR	SNP	C	C	G	rs6617	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52740182C>G	ENST00000602728.1	+	0	89				GLT8D1_ENST00000394783.3_5'Flank|GLT8D1_ENST00000407584.3_5'Flank|GLT8D1_ENST00000478968.2_5'Flank|SPCS1_ENST00000423431.1_Intron|GLT8D1_ENST00000266014.5_5'Flank|GLT8D1_ENST00000491606.1_5'Flank|SPCS1_ENST00000233025.7_Missense_Mutation_p.P41A			Q9Y6A9	SPCS1_HUMAN	signal peptidase complex subunit 1 homolog (S. cerevisiae)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6				BRCA - Breast invasive adenocarcinoma(193;6.51e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)|OV - Ovarian serous cystadenocarcinoma(275;0.0469)		CCAGACCTTACCCCTCACGGT	0.697													G|||	2230	0.445288	0.5575	0.5144	5008	,	,		13167	0.4286		0.4304	False		,,,				2504	0.2771				p.P41A		Atlas-SNP	.											SPCS1_ENST00000233025,rectum,carcinoma,0,1	SPCS1	20	1	0			c.C121G						PASS	.						10.0	15.0	14.0					3																	52740182		687	1590	2277	SO:0001623	5_prime_UTR_variant	28972	exon1			ACCTTACCCCTCA	AF092138	CCDS33769.2	3p21.31	2005-01-05			ENSG00000114902	ENSG00000114902			23401	protein-coding gene	gene with protein product		610358				8632014	Standard	NM_014041		Approved	SPC12, HSPC033, YJR010C-A, SPC1	uc011bei.2	Q9Y6A9	OTTHUMG00000154930	ENST00000602728.1:c.-81C>G	3.37:g.52740182C>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	16	7	0.4375	NM_014041	B3KNF8|Q9BVW1	Missense_Mutation	SNP	ENST00000602728.1	37		1074	0.49175824175824173	273	0.5548780487804879	192	0.5303867403314917	280	0.48951048951048953	329	0.4340369393139842	G	1.062	-0.672572	0.03403	.	.	ENSG00000114902	ENST00000233025	.	.	.	3.96	-4.39	0.03611	.	.	.	.	.	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	0.41716	-0.9493	7	0.02654	T	1	.	3.0659	0.06214	0.2759:0.4525:0.1602:0.1114	rs6617;rs1139798;rs3184127;rs17548630;rs6617	41	Q9Y6A9	SPCS1_HUMAN	A	41	.	ENSP00000233025:P41A	P	+	1	0	SPCS1	52715222	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.407000	0.02488	-1.177000	0.02744	-0.127000	0.14921	CCC	C|0.512;G|0.488	0.488	strong		0.697	SPCS1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467759.1	NM_014041	
SLC17A9	63910	hgsc.bcm.edu	37	20	61595636	61595636	+	Silent	SNP	C	C	T	rs2248900	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:61595636C>T	ENST00000370351.4	+	8	1010	c.879C>T	c.(877-879)agC>agT	p.S293S	SLC17A9_ENST00000370349.3_Silent_p.S287S|SLC17A9_ENST00000488738.1_3'UTR	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	293					exocytosis (GO:0006887)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	23						GTCTATTCAGCGGGTTTCTCT	0.617													C|||	771	0.153954	0.0832	0.2118	5008	,	,		18199	0.1974		0.1958	False		,,,				2504	0.1207				p.S293S		Atlas-SNP	.											SLC17A9,caecum,carcinoma,0,1	SLC17A9	54	1	0			c.C879T						PASS	.	C		432,3608		21,390,1609	201.0	215.0	210.0		879	-10.1	0.0	20	dbSNP_100	210	1838,6506		208,1422,2542	yes	coding-synonymous	SLC17A9	NM_022082.3		229,1812,4151	TT,TC,CC		22.0278,10.6931,18.3301		293/437	61595636	2270,10114	2020	4172	6192	SO:0001819	synonymous_variant	63910	exon8			ATTCAGCGGGTTT	AK027065	CCDS42901.1	20q13.33	2013-07-18	2013-07-18	2009-01-22	ENSG00000101194	ENSG00000101194		"""Solute carriers"""	16192	protein-coding gene	gene with protein product		612107	"""chromosome 20 open reading frame 59"", ""solute carrier family 17, member 9"""	C20orf59		18375752	Standard	NM_022082		Approved	FLJ23412, VNUT	uc002yea.4	Q9BYT1	OTTHUMG00000032951	ENST00000370351.4:c.879C>T	20.37:g.61595636C>T		Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	196	106	0.540816	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Silent	SNP	ENST00000370351.4	37	CCDS42901.1																																																																																			C|0.831;T|0.169	0.169	strong		0.617	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082	
KNTC1	9735	hgsc.bcm.edu	37	12	123032478	123032478	+	Missense_Mutation	SNP	C	C	T	rs61751321	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:123032478C>T	ENST00000333479.7	+	12	1126	c.949C>T	c.(949-951)Ctc>Ttc	p.L317F	KNTC1_ENST00000450485.2_Missense_Mutation_p.L280F	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	317					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AATTACAAATCTCAAATTAAT	0.259													C|||	5	0.000998403	0.0	0.0	5008	,	,		15154	0.0		0.001	False		,,,				2504	0.0041				p.L317F		Atlas-SNP	.											.	KNTC1	182	.	0			c.C949T						PASS	.	C	PHE/LEU	1,3563		0,1,1781	43.0	40.0	41.0		949	5.3	1.0	12	dbSNP_129	41	27,8073		0,27,4023	yes	missense	KNTC1	NM_014708.4	22	0,28,5804	TT,TC,CC		0.3333,0.0281,0.2401	possibly-damaging	317/2210	123032478	28,11636	1782	4050	5832	SO:0001583	missense	9735	exon12			ACAAATCTCAAAT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.949C>T	12.37:g.123032478C>T	ENSP00000328236:p.Leu317Phe	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	C	12.64	2.000039	0.35320	2.81E-4	0.003333	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.17054	2.3;2.3	5.35	5.35	0.76521	.	0.201753	0.44483	D	0.000444	T	0.32285	0.0824	L	0.56769	1.78	0.80722	D	1	D;D	0.63880	0.983;0.993	P;P	0.59288	0.799;0.855	T	0.00722	-1.1594	10	0.46703	T	0.11	-12.1835	12.9217	0.58237	0.0:0.8244:0.1756:0.0	rs61751321	280;317	E7ES84;P50748	.;KNTC1_HUMAN	F	280;317	ENSP00000397992:L280F;ENSP00000328236:L317F	ENSP00000328236:L317F	L	+	1	0	KNTC1	121598431	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	3.241000	0.51376	2.668000	0.90789	0.573000	0.79308	CTC	C|0.991;T|0.008	0.008	strong		0.259	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K2182fs*61(1)|p.S2163_T2283del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AGCCCTTGCCGTCCTGGGACT	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47.0	54.0	52.0		6555	-0.8	1.0	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6555C>T	9.37:g.139391636G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	107	107	1	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
WWOX	51741	hgsc.bcm.edu	37	16	78466437	78466437	+	Missense_Mutation	SNP	C	C	G	rs3764340	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:78466437C>G	ENST00000566780.1	+	8	1210	c.844C>G	c.(844-846)Cca>Gca	p.P282A	WWOX_ENST00000408984.3_Missense_Mutation_p.P282A|WWOX_ENST00000406884.2_Intron|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000539474.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	282	Interaction with MAPT. {ECO:0000250}.		P -> A (in dbSNP:rs3764340). {ECO:0000269|PubMed:11572989}.		cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		TCGCCTCTCTCCAACAAAAAA	0.473													C|||	459	0.0916534	0.1044	0.085	5008	,	,		18591	0.1012		0.0537	False		,,,				2504	0.1084				p.P282A		Atlas-SNP	.											.	WWOX	98	.	0			c.C844G						PASS	.	C	ALA/PRO	340,3592		20,300,1646	110.0	113.0	112.0		844	5.9	1.0	16	dbSNP_107	112	491,7797		14,463,3667	yes	missense	WWOX	NM_016373.2	27	34,763,5313	GG,GC,CC		5.9242,8.647,6.8003	possibly-damaging	282/415	78466437	831,11389	1966	4144	6110	SO:0001583	missense	51741	exon8			CTCTCTCCAACAA	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.844C>G	16.37:g.78466437C>G	ENSP00000457230:p.Pro282Ala	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_016373	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	169	0.07738095238095238	50	0.1016260162601626	19	0.052486187845303865	54	0.0944055944055944	46	0.06068601583113457	C	17.32	3.360412	0.61403	0.08647	0.059242	ENSG00000186153	ENST00000408984	D	0.85955	-2.05	5.93	5.93	0.95920	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.27205	0.0667	L	0.58669	1.825	0.09310	P	0.99999999878347	D	0.64830	0.994	P	0.61533	0.89	T	0.65298	-0.6202	9	0.23302	T	0.38	.	20.3261	0.98701	0.0:1.0:0.0:0.0	rs3764340;rs52831312;rs3764340	282	Q9NZC7	WWOX_HUMAN	A	282	ENSP00000386161:P282A	ENSP00000386161:P282A	P	+	1	0	WWOX	77023938	1.000000	0.71417	0.994000	0.49952	0.019000	0.09904	7.487000	0.81328	2.814000	0.96858	0.655000	0.94253	CCA	C|0.921;G|0.079	0.079	strong		0.473	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1		
RIC3	79608	hgsc.bcm.edu	37	11	8159892	8159892	+	Silent	SNP	G	G	T	rs10839976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:8159892G>T	ENST00000309737.6	-	3	353	c.354C>A	c.(352-354)ctC>ctA	p.L118L	RIC3_ENST00000343202.4_Silent_p.L118L|RIC3_ENST00000425599.2_Silent_p.L118L|RIC3_ENST00000335425.7_Intron|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000539720.1_Silent_p.L69L			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	118					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TCCCCTTTGAGAGCTGAGAAT	0.433													G|||	1520	0.303514	0.2799	0.3444	5008	,	,		16372	0.4196		0.2197	False		,,,				2504	0.273				p.L118L		Atlas-SNP	.											.	RIC3	42	.	0			c.C354A						PASS	.	G	,,,	1189,3213	415.7+/-337.3	155,879,1167	203.0	196.0	198.0		,354,354,354	-1.8	1.0	11	dbSNP_120	198	2007,6585	351.5+/-328.3	234,1539,2523	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	,,,	389,2418,3690	TT,TG,GG		23.3589,27.0104,24.596	,,,	,118/370,118/289,118/369	8159892	3196,9798	2201	4296	6497	SO:0001819	synonymous_variant	79608	exon3			CTTTGAGAGCTGA		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"""resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"""			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.354C>A	11.37:g.8159892G>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Silent	SNP	ENST00000309737.6	37	CCDS55742.1																																																																																			G|0.727;T|0.273	0.273	strong		0.433	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
PCK1	5105	hgsc.bcm.edu	37	20	56136536	56136536	+	Silent	SNP	A	A	G	rs1042521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:56136536A>G	ENST00000319441.4	+	2	233	c.69A>G	c.(67-69)ctA>ctG	p.L23L	PCK1_ENST00000543666.1_5'UTR|PCK1_ENST00000535860.1_5'Flank	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	23					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)			TGGACAGCCTACCCCAGGCAG	0.567													G|||	1988	0.396965	0.3064	0.3761	5008	,	,		18025	0.377		0.5278	False		,,,				2504	0.4202				p.L23L		Atlas-SNP	.											.	PCK1	95	.	0			c.A69G						PASS	.	G		1471,2935	678.0+/-403.5	221,1029,953	96.0	92.0	93.0		69	4.5	1.0	20	dbSNP_86	93	4355,4245	572.9+/-389.8	1091,2173,1036	no	coding-synonymous	PCK1	NM_002591.3		1312,3202,1989	GG,GA,AA		49.3605,33.3863,44.7947		23/623	56136536	5826,7180	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon2			CAGCCTACCCCAG		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.69A>G	20.37:g.56136536A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			A|0.555;G|0.445	0.445	strong		0.567	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
ZGRF1	55345	hgsc.bcm.edu	37	4	113482146	113482146	+	Missense_Mutation	SNP	G	G	A	rs17605622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:113482146G>A	ENST00000505019.1	-	19	4828	c.4703C>T	c.(4702-4704)tCg>tTg	p.S1568L		NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		1568			S -> L (in dbSNP:rs17605622).			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)		TATAGTTGGCGAAGACCTAAT	0.328													G|||	187	0.0373403	0.0083	0.0648	5008	,	,		18185	0.0		0.1183	False		,,,				2504	0.0123				p.S1568L		Atlas-SNP	.											.	C4orf21	223	.	0			c.C4703T						PASS	.	G	LEU/SER	84,4318	65.8+/-103.3	1,82,2118	66.0	61.0	63.0		4703	4.2	0.3	4	dbSNP_123	63	859,7735	184.5+/-232.4	44,771,3482	yes	missense	C4orf21	NM_018392.4	145	45,853,5600	AA,AG,GG		9.9953,1.9082,7.2561	benign	1568/2105	113482146	943,12053	2201	4297	6498	SO:0001583	missense	55345	exon19			GTTGGCGAAGACC																												ENST00000505019.1:c.4703C>T	4.37:g.113482146G>A	ENSP00000424737:p.Ser1568Leu	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	137	68	0.49635	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		117	0.05357142857142857	2	0.0040650406504065045	22	0.06077348066298342	0	0.0	93	0.12269129287598944	G	4.932	0.173215	0.09391	0.019082	0.099953	ENSG00000138658	ENST00000505019	T	0.26373	1.74	5.95	4.19	0.49359	.	0.749772	0.12630	N	0.452224	T	0.00271	0.0008	M	0.65975	2.015	0.35547	P	0.19647499999999996	B;P	0.37997	0.202;0.614	B;B	0.19666	0.012;0.026	T	0.16247	-1.0409	9	0.26408	T	0.33	-0.0499	3.9261	0.09263	0.1428:0.1254:0.5945:0.1373	rs17605622;rs17605622	1568;26	G5EA02;B3KQX2	.;.	L	1568	ENSP00000424737:S1568L	ENSP00000404365:S466L	S	-	2	0	C4orf21	113701595	0.008000	0.16893	0.326000	0.25389	0.257000	0.26127	0.359000	0.20233	0.807000	0.34208	-0.145000	0.13849	TCG	G|0.939;A|0.061	0.061	strong		0.328	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
MAD2L1	4085	hgsc.bcm.edu	37	4	120982045	120982045	+	Silent	SNP	T	T	C	rs61752609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:120982045T>C	ENST00000296509.6	-	4	768	c.429A>G	c.(427-429)ccA>ccG	p.P143P		NM_002358.3	NP_002349.1	Q13257	MD2L1_HUMAN	MAD2 mitotic arrest deficient-like 1 (yeast)	143	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(2)|kidney(2)|large_intestine(2)|lung(3)	9						CTTCCAACAGTGGCAGAAATG	0.373													T|||	116	0.0231629	0.003	0.0447	5008	,	,		16877	0.003		0.0726	False		,,,				2504	0.0051				p.P143P		Atlas-SNP	.											.	MAD2L1	17	.	0			c.A429G						PASS	.	T		54,4352	54.9+/-90.9	0,54,2149	52.0	52.0	52.0		429	-2.8	0.9	4	dbSNP_129	52	593,8007	156.4+/-210.3	18,557,3725	no	coding-synonymous	MAD2L1	NM_002358.3		18,611,5874	CC,CT,TT		6.8953,1.2256,4.9746		143/206	120982045	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	4085	exon4			CAACAGTGGCAGA	U65410	CCDS3715.1	4q27	2013-01-17	2001-11-28		ENSG00000164109	ENSG00000164109			6763	protein-coding gene	gene with protein product		601467	"""MAD2 (mitotic arrest deficient, yeast, homolog)-like 1"""			8824189, 9345911	Standard	NM_002358		Approved	MAD2, HSMAD2	uc003idl.2	Q13257	OTTHUMG00000132967	ENST00000296509.6:c.429A>G	4.37:g.120982045T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	150	64	0.426667	NM_002358	Q53F56|Q548X9|Q6IRW7|Q8IZX3	Silent	SNP	ENST00000296509.6	37	CCDS3715.1																																																																																			T|0.955;C|0.045	0.045	strong		0.373	MAD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256525.2		
DDRGK1	65992	hgsc.bcm.edu	37	20	3171337	3171337	+	Missense_Mutation	SNP	C	C	T	rs11591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3171337C>T	ENST00000354488.3	-	9	964	c.907G>A	c.(907-909)Gcc>Acc	p.A303T	DDRGK1_ENST00000496781.1_5'UTR	NM_023935.1	NP_076424.1	Q96HY6	DDRGK_HUMAN	DDRGK domain containing 1	303			A -> T (in dbSNP:rs11591). {ECO:0000269|PubMed:15489334}.			endoplasmic reticulum (GO:0005783)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7						CGGCCCCAGGCGATGAGGGAG	0.637													C|||	351	0.0700879	0.0061	0.0994	5008	,	,		17224	0.001		0.1968	False		,,,				2504	0.0767				p.A303T		Atlas-SNP	.											.	DDRGK1	21	.	0			c.G907A						PASS	.	C	THR/ALA	181,4225	115.9+/-153.8	7,167,2029	47.0	55.0	52.0		907	-2.3	0.9	20	dbSNP_52	52	1581,7019	294.3+/-301.8	140,1301,2859	yes	missense	DDRGK1	NM_023935.1	58	147,1468,4888	TT,TC,CC		18.3837,4.108,13.5476	benign	303/315	3171337	1762,11244	2203	4300	6503	SO:0001583	missense	65992	exon9			CCCAGGCGATGAG	AL121891	CCDS13050.1	20p13	2011-08-18	2008-10-03	2008-10-03	ENSG00000198171	ENSG00000198171			16110	protein-coding gene	gene with protein product	"""Dashurin"""		"""chromosome 20 open reading frame 116"""	C20orf116		20036718, 20228063, 21494687	Standard	NM_023935		Approved	dJ1187M17.3	uc002wic.3	Q96HY6	OTTHUMG00000031732	ENST00000354488.3:c.907G>A	20.37:g.3171337C>T	ENSP00000346483:p.Ala303Thr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_023935	A6NIU5|C9JSZ5|Q9BW47	Missense_Mutation	SNP	ENST00000354488.3	37	CCDS13050.1	190	0.08699633699633699	7	0.014227642276422764	42	0.11602209944751381	0	0.0	141	0.18601583113456466	C	9.251	1.040633	0.19669	0.04108	0.183837	ENSG00000198171	ENST00000354488;ENST00000380213	T	0.43688	0.94	4.98	-2.27	0.06846	.	0.347908	0.30869	N	0.008703	T	0.00039	0.0001	N	0.08118	0	0.09310	P	0.99999999739718	B	0.11235	0.004	B	0.08055	0.003	T	0.17018	-1.0383	9	0.31617	T	0.26	-0.4349	3.4261	0.07412	0.4458:0.2276:0.0:0.3266	rs11591;rs3171338;rs17256431;rs17845142;rs17857945;rs59952895;rs11591	303	Q96HY6	DDRGK_HUMAN	T	303;302	ENSP00000346483:A303T	ENSP00000346483:A303T	A	-	1	0	DDRGK1	3119337	1.000000	0.71417	0.942000	0.38095	0.997000	0.91878	1.072000	0.30678	-0.223000	0.09943	0.561000	0.74099	GCC	C|0.885;T|0.115	0.115	strong		0.637	DDRGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077709.2	NM_023935	
SEC14L1	6397	hgsc.bcm.edu	37	17	75190962	75190962	+	Silent	SNP	C	C	T	rs674402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:75190962C>T	ENST00000413679.2	+	7	981	c.678C>T	c.(676-678)agC>agT	p.S226S	SEC14L1_ENST00000443798.4_Silent_p.S226S|SEC14L1_ENST00000585618.1_Silent_p.S226S|SEC14L1_ENST00000430767.4_Silent_p.S226S|SEC14L1_ENST00000431431.2_Silent_p.S192S|SEC14L1_ENST00000591437.1_Silent_p.S192S|SEC14L1_ENST00000436233.4_Silent_p.S226S|SEC14L1_ENST00000392476.2_Silent_p.S226S	NM_001143998.1|NM_001143999.1|NM_003003.3	NP_001137470|NP_001137471|NP_002994	Q92503	S14L1_HUMAN	SEC14-like 1 (S. cerevisiae)	226					transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(2)	31						GCAGCCCCAGCGCACCTGAGC	0.622													C|||	1794	0.358227	0.3064	0.3329	5008	,	,		15446	0.3433		0.3559	False		,,,				2504	0.4642				p.S226S		Atlas-SNP	.											.	SEC14L1	81	.	0			c.C678T						PASS	.	C	,,,,,,	1390,3016	456.7+/-351.4	232,926,1045	65.0	64.0	64.0		678,678,678,576,678,678,678	-11.2	0.0	17	dbSNP_83	64	3214,5386	476.3+/-369.4	585,2044,1671	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEC14L1	NM_001039573.2,NM_001143998.1,NM_001143999.1,NM_001144001.1,NM_001204408.1,NM_001204410.1,NM_003003.3	,,,,,,	817,2970,2716	TT,TC,CC		37.3721,31.5479,35.399	,,,,,,	226/720,226/716,226/716,192/682,226/720,226/716,226/716	75190962	4604,8402	2203	4300	6503	SO:0001819	synonymous_variant	6397	exon9			CCCCAGCGCACCT	D67029	CCDS11752.1, CCDS42385.1, CCDS45789.1	17q25.2	2008-02-01	2001-11-28			ENSG00000129657			10698	protein-coding gene	gene with protein product		601504	"""SEC14 (S. cerevisiae)-like 1"""	SEC14L		8697811	Standard	NM_001143998		Approved	PRELID4A	uc002jto.3	Q92503		ENST00000413679.2:c.678C>T	17.37:g.75190962C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	162	81	0.5	NM_001204408	A8K4E8|B4DDI5|D5G3K1|Q99780	Silent	SNP	ENST00000413679.2	37	CCDS11752.1																																																																																			C|0.643;T|0.357	0.357	strong		0.622	SEC14L1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000436240.1	NM_003003	
SERPINA4	5267	hgsc.bcm.edu	37	14	95033356	95033356	+	Silent	SNP	C	C	T	rs5510	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:95033356C>T	ENST00000557004.1	+	3	1120	c.699C>T	c.(697-699)ttC>ttT	p.F233F	SERPINA4_ENST00000555095.1_Silent_p.F233F|SERPINA5_ENST00000553780.1_Intron|SERPINA4_ENST00000298841.5_Silent_p.F233F			P29622	KAIN_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4	233					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(1)|large_intestine(9)|lung(28)|ovary(3)|skin(1)|urinary_tract(1)	46				COAD - Colon adenocarcinoma(157;0.211)		CCAAAGACTTCTATGTTGATG	0.507													C|||	1505	0.300519	0.3434	0.1787	5008	,	,		20522	0.2867		0.2565	False		,,,				2504	0.3885				p.F233F		Atlas-SNP	.											.	SERPINA4	81	.	0			c.C699T						PASS	.	C		1375,3031	455.7+/-351.1	222,931,1050	112.0	103.0	106.0		699	2.6	0.4	14	dbSNP_52	106	2131,6469	366.6+/-334.4	260,1611,2429	no	coding-synonymous	SERPINA4	NM_006215.2		482,2542,3479	TT,TC,CC		24.7791,31.2074,26.9568		233/428	95033356	3506,9500	2203	4300	6503	SO:0001819	synonymous_variant	5267	exon3			AGACTTCTATGTT	L19684	CCDS9927.1	14q32.13	2014-02-18	2005-08-18		ENSG00000100665	ENSG00000100665		"""Serine (or cysteine) peptidase inhibitors"""	8948	protein-coding gene	gene with protein product		147935	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 4"""	PI4		8227002, 24172014	Standard	NM_001289032		Approved	KST, KAL, KLST, kallistatin	uc001ydk.3	P29622	OTTHUMG00000170859	ENST00000557004.1:c.699C>T	14.37:g.95033356C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_006215	Q53XB5|Q86TR9|Q96BZ5	Silent	SNP	ENST00000557004.1	37	CCDS9927.1																																																																																			C|0.718;T|0.282	0.282	strong		0.507	SERPINA4-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410718.1	NM_006215	
C9orf66	157983	hgsc.bcm.edu	37	9	215269	215269	+	Missense_Mutation	SNP	A	A	C	rs636922	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:215269A>C	ENST00000382387.2	-	1	624	c.128T>G	c.(127-129)cTg>cGg	p.L43R	DOCK8_ENST00000432829.2_Intron|DOCK8_ENST00000453981.1_Intron	NM_152569.2	NP_689782.2	Q5T8R8	CI066_HUMAN	chromosome 9 open reading frame 66	43			L -> R (in dbSNP:rs636922).							central_nervous_system(1)|cervix(1)|kidney(1)|skin(1)	4	all_lung(41;0.218)	all_cancers(5;2.09e-12)|all_epithelial(5;6.16e-09)|all_lung(10;1.15e-08)|Lung NSC(10;1.91e-08)|Acute lymphoblastic leukemia(5;0.00457)|all_hematologic(5;0.0332)|Breast(48;0.0646)|Prostate(43;0.137)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GGATGTCCTCAGCCGCCGGGG	0.706													A|||	899	0.179513	0.0083	0.2104	5008	,	,		12428	0.3185		0.2634	False		,,,				2504	0.1595				p.L43R		Atlas-SNP	.											.	C9orf66	16	.	0			c.T128G						PASS	.	A	,ARG/LEU	240,4156		11,218,1969	13.0	13.0	13.0		,128	-6.2	0.0	9	dbSNP_83	13	2130,6466		267,1596,2435	yes	intron,missense	DOCK8,C9orf66	NM_203447.3,NM_152569.2	,102	278,1814,4404	CC,CA,AA		24.779,5.4595,18.242	,benign	,43/296	215269	2370,10622	2198	4298	6496	SO:0001583	missense	157983	exon1			GTCCTCAGCCGCC	AK055720	CCDS6439.1	9p24.3	2008-02-05			ENSG00000183784	ENSG00000183784			26436	protein-coding gene	gene with protein product							Standard	NM_152569		Approved	FLJ31158	uc003zge.4	Q5T8R8	OTTHUMG00000021017	ENST00000382387.2:c.128T>G	9.37:g.215269A>C	ENSP00000371824:p.Leu43Arg	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	36	21	0.583333	NM_152569	Q96NB0	Missense_Mutation	SNP	ENST00000382387.2	37	CCDS6439.1	458	0.2097069597069597	7	0.014227642276422764	77	0.212707182320442	182	0.3181818181818182	192	0.2532981530343008	A	11.77	1.737391	0.30774	0.054595	0.24779	ENSG00000183784	ENST00000382387	T	0.21031	2.03	3.1	-6.2	0.02072	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.0999999999983245E-5	B	0.23650	0.089	B	0.18871	0.023	T	0.44682	-0.9312	8	0.87932	D	0	.	1.2171	0.01916	0.198:0.2815:0.3296:0.1908	rs636922;rs61367171;rs636922	43	Q5T8R8	CI066_HUMAN	R	43	ENSP00000371824:L43R	ENSP00000371824:L43R	L	-	2	0	C9orf66	205269	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.285000	0.00526	-1.934000	0.01051	-0.464000	0.05259	CTG	A|0.824;C|0.176	0.176	strong		0.706	C9orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055436.1	NM_152569	
NWD2	57495	hgsc.bcm.edu	37	4	37445315	37445315	+	Missense_Mutation	SNP	C	C	A	rs4634233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:37445315C>A	ENST00000309447.5	+	7	2553	c.1705C>A	c.(1705-1707)Ctg>Atg	p.L569M		NM_001144990.1	NP_001138462.1	Q9ULI1	NWD2_HUMAN		569	NACHT.		L -> M (in dbSNP:rs4634233).							breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(2)|skin(2)	16						CTACATCGAGCTGATTCCCCG	0.512													C|||	757	0.151158	0.1218	0.1715	5008	,	,		22977	0.0625		0.2773	False		,,,				2504	0.138				p.L569M		Atlas-SNP	.											.	KIAA1239	79	.	0			c.C1705A						PASS	.	C	MET/LEU	182,1202		7,168,517	94.0	75.0	81.0		1705	4.4	1.0	4	dbSNP_111	81	854,2328		105,644,842	yes	missense	KIAA1239	NM_001144990.1	15	112,812,1359	AA,AC,CC		26.8385,13.1503,22.6894	probably-damaging	569/1743	37445315	1036,3530	692	1591	2283	SO:0001583	missense	57495	exon7			ATCGAGCTGATTC																												ENST00000309447.5:c.1705C>A	4.37:g.37445315C>A	ENSP00000309501:p.Leu569Met	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001144990	A8MRU1	Missense_Mutation	SNP	ENST00000309447.5	37	CCDS47040.1	389	0.17811355311355312	70	0.14227642276422764	67	0.1850828729281768	44	0.07692307692307693	208	0.27440633245382584	C	14.30	2.494469	0.44352	0.131503	0.268385	ENSG00000174145	ENST00000309447	D	0.84146	-1.81	6.07	4.36	0.52297	.	.	.	.	.	T	0.00073	0.0002	L	0.58101	1.795	0.22489	P	0.999053227	D	0.76494	0.999	D	0.87578	0.998	T	0.01048	-1.1469	8	0.87932	D	0	.	9.2091	0.37306	0.0:0.732:0.0:0.268	rs4634233;rs52808878;rs4634233	569	Q9ULI1	K1239_HUMAN	M	569	ENSP00000309501:L569M	ENSP00000309501:L569M	L	+	1	2	KIAA1239	37121710	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.952000	0.29149	0.911000	0.36747	0.650000	0.86243	CTG	C|0.819;A|0.181	0.181	strong		0.512	KIAA1239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347551.2		
ERCC2	2068	hgsc.bcm.edu	37	19	45854919	45854919	+	Missense_Mutation	SNP	T	T	G	rs13181	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45854919T>G	ENST00000391945.4	-	23	2328	c.2251A>C	c.(2251-2253)Aag>Cag	p.K751Q	ERCC2_ENST00000391944.3_Missense_Mutation_p.K673Q	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	751			K -> Q (may be linked to a reduced activity; dbSNP:rs13181). {ECO:0000269|PubMed:11245433, ECO:0000269|PubMed:11470747, ECO:0000269|PubMed:11709541, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TCTATCCTCTTCAGCGTCTCC	0.607			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1185	0.236621	0.1921	0.2147	5008	,	,		16775	0.0764		0.3638	False		,,,				2504	0.3466				p.K751Q		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	ERCC2	78	.	0			c.A2251C	GRCh37	CM004814	ERCC2	M	rs13181	PASS	.	G	GLN/LYS	1037,3369	724.9+/-409.6	119,799,1285	125.0	129.0	128.0		2251	4.3	0.9	19	dbSNP_52	128	3203,5397	651.5+/-400.8	642,1919,1739	yes	missense	ERCC2	NM_000400.3	53	761,2718,3024	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	37.2442,23.5361,32.6003	benign	751/761	45854919	4240,8766	2203	4300	6503	SO:0001583	missense	2068	exon23	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TCCTCTTCAGCGT		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.2251A>C	19.37:g.45854919T>G	ENSP00000375809:p.Lys751Gln	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	517	0.2367216117216117	102	0.2073170731707317	77	0.212707182320442	51	0.08916083916083917	287	0.3786279683377309	G	1.232	-0.623727	0.03636	0.235361	0.372442	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	T;D	0.82711	-1.42;-1.64	4.29	4.29	0.51040	.	0.612831	0.16775	N	0.200058	T	0.00012	0.0000	N	0.20881	0.62	0.09310	P	0.9999999999999628	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.05733	-1.0867	9	0.06494	T	0.89	-14.1137	11.3922	0.49822	0.0:0.0:0.8176:0.1824	rs13181;rs1052559;rs3170171;rs3859422;rs17285142;rs17355147;rs17359310;rs60606175;rs13181	673;751	E7EVE9;P18074	.;ERCC2_HUMAN	Q	701;727;751;673	ENSP00000375809:K751Q;ENSP00000375808:K673Q	ENSP00000375805:K701Q	K	-	1	0	ERCC2	50546759	0.991000	0.36638	0.917000	0.36280	0.036000	0.12997	1.198000	0.32223	1.046000	0.40249	-0.217000	0.12591	AAG	A|0.006;C|0.001	.	strong		0.607	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
B3GNTL1	146712	hgsc.bcm.edu	37	17	81006387	81006387	+	Silent	SNP	G	G	A	rs1143006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:81006387G>A	ENST00000320865.3	-	3	250	c.237C>T	c.(235-237)caC>caT	p.H79H	B3GNTL1_ENST00000571954.1_5'UTR|B3GNTL1_ENST00000576599.1_De_novo_Start_InFrame	NM_001009905.1	NP_001009905.1	Q67FW5	B3GNL_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase-like 1	79							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)			CAATGATCACGTGGACACCAG	0.453													G|||	1430	0.285543	0.2542	0.2709	5008	,	,		20205	0.3661		0.2962	False		,,,				2504	0.2444				p.H79H		Atlas-SNP	.											.	B3GNTL1	40	.	0			c.C237T						PASS	.	G		1083,3323	390.3+/-327.6	151,781,1271	112.0	90.0	98.0		237	-7.2	0.3	17	dbSNP_86	98	2370,6230	396.6+/-345.4	343,1684,2273	no	coding-synonymous	B3GNTL1	NM_001009905.1		494,2465,3544	AA,AG,GG		27.5581,24.5801,26.5493		79/362	81006387	3453,9553	2203	4300	6503	SO:0001819	synonymous_variant	146712	exon3			GATCACGTGGACA	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.237C>T	17.37:g.81006387G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	176	84	0.477273	NM_001009905	Q6GV30|Q8WUT3	Silent	SNP	ENST00000320865.3	37	CCDS32778.1																																																																																			G|0.721;A|0.279	0.279	strong		0.453	B3GNTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438949.1	NM_001009905	
C3orf20	84077	hgsc.bcm.edu	37	3	14769980	14769980	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14769980G>A	ENST00000253697.3	+	12	2177	c.1725G>A	c.(1723-1725)gaG>gaA	p.E575E	C3orf20_ENST00000435614.1_Silent_p.E453E|C3orf20_ENST00000412910.1_Silent_p.E453E	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	575	Poly-Glu.					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						CCAAAAAGGAGGAGGAAGAAT	0.473																																					p.E575E		Atlas-SNP	.											.	C3orf20	109	.	0			c.G1725A						PASS	.						81.0	82.0	82.0					3																	14769980		2203	4300	6503	SO:0001819	synonymous_variant	84077	exon12			AAAGGAGGAGGAA	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.1725G>A	3.37:g.14769980G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	150	49	0.326667	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	37	CCDS33706.1																																																																																			.	.	none		0.473	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
WDYHV1	55093	hgsc.bcm.edu	37	8	124449466	124449466	+	Missense_Mutation	SNP	C	C	T	rs3824250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124449466C>T	ENST00000287387.2	+	5	525	c.400C>T	c.(400-402)Cgt>Tgt	p.R134C	WDYHV1_ENST00000518125.1_5'UTR|WDYHV1_ENST00000523356.1_Missense_Mutation_p.R134C|WDYHV1_ENST00000517609.1_3'UTR|WDYHV1_ENST00000523984.1_Missense_Mutation_p.R74C	NM_018024.1	NP_060494.1	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	134			R -> C (in dbSNP:rs3824250). {ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						TAGAGTGATCCGTGCAGATTC	0.403													C|||	2055	0.410343	0.3427	0.3919	5008	,	,		18563	0.5863		0.3121	False		,,,				2504	0.4346				p.R134C		Atlas-SNP	.											.	WDYHV1	30	.	0			c.C400T						PASS	.	C	CYS/ARG	1600,2806	493.1+/-362.6	293,1014,896	76.0	76.0	76.0		400	5.5	1.0	8	dbSNP_107	76	3027,5573	465.8+/-366.6	540,1947,1813	yes	missense	WDYHV1	NM_018024.1	180	833,2961,2709	TT,TC,CC		35.1977,36.3141,35.5759	possibly-damaging	134/206	124449466	4627,8379	2203	4300	6503	SO:0001583	missense	55093	exon5			GTGATCCGTGCAG	AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795			25490	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 32"""	C8orf32		12477932	Standard	NM_018024		Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000287387.2:c.400C>T	8.37:g.124449466C>T	ENSP00000287387:p.Arg134Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	97	0.989796	NM_018024	B4DE68|Q9NW95	Missense_Mutation	SNP	ENST00000287387.2	37	CCDS6344.1	841	0.3850732600732601	140	0.2845528455284553	136	0.3756906077348066	327	0.5716783216783217	238	0.31398416886543534	C	17.67	3.447205	0.63178	0.363141	0.351977	ENSG00000156795	ENST00000287387;ENST00000523984;ENST00000523356	T;T;T	0.18016	2.24;2.24;2.24	5.48	5.48	0.80851	Protein N-terminal glutamine amidohydrolase, alpha beta roll (1);Protein N-terminal glutamine amidohydrolase (1);	0.125087	0.56097	D	0.000032	T	0.00012	0.0000	L	0.47716	1.5	0.09310	P	1.0	D	0.61697	0.99	P	0.51101	0.659	T	0.46428	-0.9192	9	0.59425	D	0.04	-11.8085	13.822	0.63329	0.0:0.8464:0.1536:0.0	rs3824250;rs17850383;rs52821731;rs59927018;rs3824250	134	Q96HA8	NTAQ1_HUMAN	C	134;74;134	ENSP00000287387:R134C;ENSP00000430427:R74C;ENSP00000428615:R134C	ENSP00000287387:R134C	R	+	1	0	WDYHV1	124518647	0.998000	0.40836	1.000000	0.80357	0.517000	0.34286	2.593000	0.46180	2.567000	0.86603	0.591000	0.81541	CGT	C|0.628;N|0.000	.	strong		0.403	WDYHV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381772.1	NM_018024	
ABHD4	63874	hgsc.bcm.edu	37	14	23078810	23078810	+	Silent	SNP	A	A	T	rs72677597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23078810A>T	ENST00000428304.2	+	6	1003	c.933A>T	c.(931-933)cgA>cgT	p.R311R		NM_022060.2	NP_071343.2	Q8TB40	ABHD4_HUMAN	abhydrolase domain containing 4	311					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(3)|prostate(1)	14	all_cancers(95;5.49e-05)			GBM - Glioblastoma multiforme(265;0.0153)		CCTATGTCCGAGACATGGTAT	0.493													A|||	537	0.107228	0.267	0.0519	5008	,	,		18707	0.003		0.0636	False		,,,				2504	0.0828				p.R311R		Atlas-SNP	.											ABHD4,NS,carcinoma,+2,1	ABHD4	30	1	0			c.A933T						PASS	.	A		1137,3269	405.3+/-333.4	148,841,1214	69.0	62.0	64.0		933	-0.7	1.0	14	dbSNP_130	64	469,8131	138.3+/-195.1	13,443,3844	no	coding-synonymous	ABHD4	NM_022060.2		161,1284,5058	TT,TA,AA		5.4535,25.8057,12.3481		311/343	23078810	1606,11400	2203	4300	6503	SO:0001819	synonymous_variant	63874	exon6			TGTCCGAGACATG	AK022878	CCDS9572.1	14q11.1	2006-10-06			ENSG00000100439	ENSG00000100439		"""Abhydrolase domain containing"""	20154	protein-coding gene	gene with protein product							Standard	NM_022060		Approved	FLJ12816	uc001wgm.3	Q8TB40	OTTHUMG00000028686	ENST00000428304.2:c.933A>T	14.37:g.23078810A>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	52	33	0.634615	NM_022060	B4DDH7|Q9H9E0	Silent	SNP	ENST00000428304.2	37	CCDS9572.1																																																																																			A|0.885;T|0.115	0.115	strong		0.493	ABHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071623.3		
FRY	10129	hgsc.bcm.edu	37	13	32768428	32768428	+	Missense_Mutation	SNP	G	G	A	rs41292163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32768428G>A	ENST00000380250.3	+	29	4236	c.3740G>A	c.(3739-3741)gGa>gAa	p.G1247E		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1247						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ACTGTGTGTGGAAGCAGGTAC	0.413													G|||	6	0.00119808	0.0	0.0014	5008	,	,		19625	0.0		0.005	False		,,,				2504	0.0				p.G1247E		Atlas-SNP	.											.	FRY	312	.	0			c.G3740A						PASS	.	G	GLU/GLY	7,3831		0,7,1912	97.0	92.0	93.0		3740	5.2	1.0	13	dbSNP_127	93	45,8251		0,45,4103	yes	missense	FRY	NM_023037.2	98	0,52,6015	AA,AG,GG		0.5424,0.1824,0.4285	benign	1247/3014	32768428	52,12082	1919	4148	6067	SO:0001583	missense	10129	exon29			TGTGTGGAAGCAG	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3740G>A	13.37:g.32768428G>A	ENSP00000369600:p.Gly1247Glu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	106	58	0.54717	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	21.1	4.104845	0.77096	0.001824	0.005424	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.65549	-0.16	5.2	5.2	0.72013	.	0.112550	0.64402	D	0.000008	T	0.53206	0.1782	L	0.50333	1.59	0.80722	D	1	P	0.41848	0.763	P	0.46208	0.507	T	0.56341	-0.7995	10	0.05436	T	0.98	.	19.0865	0.93204	0.0:0.0:1.0:0.0	rs41292163	1247	Q5TBA9	FRY_HUMAN	E	1247;86	ENSP00000369600:G1247E	ENSP00000369600:G1247E	G	+	2	0	FRY	31666428	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.659000	0.83766	2.567000	0.86603	0.563000	0.77884	GGA	G|0.996;A|0.004	0.004	strong		0.413	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
PCF11	51585	hgsc.bcm.edu	37	11	82879825	82879825	+	Silent	SNP	G	G	A	rs75717911	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:82879825G>A	ENST00000298281.4	+	8	2900	c.2448G>A	c.(2446-2448)ggG>ggA	p.G816G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	816	Gly-rich.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						TAGGAGGTGGGTGTCCTTTGA	0.562													G|||	19	0.00379393	0.0	0.0	5008	,	,		18518	0.0		0.0129	False		,,,				2504	0.0061				p.G816G		Atlas-SNP	.											.	PCF11	220	.	0			c.G2448A						PASS	.	G		5,3839		0,5,1917	60.0	63.0	62.0		2448	-1.9	1.0	11	dbSNP_133	62	102,8136		0,102,4017	no	coding-synonymous	PCF11	NM_015885.3		0,107,5934	AA,AG,GG		1.2382,0.1301,0.8856		816/1556	82879825	107,11975	1922	4119	6041	SO:0001819	synonymous_variant	51585	exon8			AGGTGGGTGTCCT	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.2448G>A	11.37:g.82879825G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	156	79	0.50641	NM_015885	A6H8W7|O43671|Q6P0X8	Silent	SNP	ENST00000298281.4	37	CCDS44689.1																																																																																			G|0.995;A|0.005	0.005	strong		0.562	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
CACHD1	57685	hgsc.bcm.edu	37	1	65142686	65142686	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:65142686G>A	ENST00000371073.2	+	22	3084	c.3084G>A	c.(3082-3084)ctG>ctA	p.L1028L	CACHD1_ENST00000290039.5_Silent_p.L977L|CACHD1_ENST00000495994.1_3'UTR			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1028					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						GTCAGAGGCTGGAAAGTGGGT	0.453																																					p.L977L		Atlas-SNP	.											.	CACHD1	125	.	0			c.G2931A						PASS	.						74.0	69.0	71.0					1																	65142686		2203	4300	6503	SO:0001819	synonymous_variant	57685	exon22			GAGGCTGGAAAGT	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.3084G>A	1.37:g.65142686G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	169	67	0.39645	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																				.	.	none		0.453	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
LRFN2	57497	hgsc.bcm.edu	37	6	40360492	40360492	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:40360492C>T	ENST00000338305.6	-	3	2102	c.1560G>A	c.(1558-1560)ccG>ccA	p.P520P		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	520						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)					ACTGGCACTGCGGGTAGTCAG	0.602																																					p.P520P		Atlas-SNP	.											.	LRFN2	133	.	0			c.G1560A						PASS	.						78.0	55.0	63.0					6																	40360492		2203	4300	6503	SO:0001819	synonymous_variant	57497	exon3			GCACTGCGGGTAG	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.1560G>A	6.37:g.40360492C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	119	67	0.563025	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	37	CCDS34443.1																																																																																			.	.	none		0.602	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
RSBN1L	222194	hgsc.bcm.edu	37	7	77365770	77365770	+	Silent	SNP	A	A	G	rs3764824	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:77365770A>G	ENST00000334955.8	+	2	657	c.630A>G	c.(628-630)gaA>gaG	p.E210E	RSBN1L_ENST00000445288.1_5'UTR	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	210	Lys-rich.					nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						aagaaaaagaaagagaaaaaa	0.249													G|||	2892	0.577476	0.8979	0.4481	5008	,	,		15634	0.3095		0.5219	False		,,,				2504	0.5695				p.E210E		Atlas-SNP	.											.	RSBN1L	74	.	0			c.A630G						PASS	.	G		2886,600		1200,486,57	51.0	53.0	53.0		630	2.8	1.0	7	dbSNP_107	53	4049,3933		1084,1881,1026	no	coding-synonymous	RSBN1L	NM_198467.2		2284,2367,1083	GG,GA,AA		49.2734,17.2117,39.5274		210/847	77365770	6935,4533	1743	3991	5734	SO:0001819	synonymous_variant	222194	exon2			AAAAGAAAGAGAA	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.630A>G	7.37:g.77365770A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Silent	SNP	ENST00000334955.8	37	CCDS43607.1																																																																																			A|0.466;G|0.534	0.534	strong		0.249	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467	
BICD1	636	hgsc.bcm.edu	37	12	32481093	32481093	+	Silent	SNP	G	G	C	rs3748275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:32481093G>C	ENST00000281474.5	+	5	1807	c.1704G>C	c.(1702-1704)gtG>gtC	p.V568V	BICD1_ENST00000548411.1_Silent_p.V568V	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	568					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			GGCGGGGTGTGTCATCCCCGG	0.537													G|||	1325	0.264577	0.1377	0.2118	5008	,	,		18566	0.5764		0.2296	False		,,,				2504	0.1881				p.V568V		Atlas-SNP	.											BICD1,rectum,carcinoma,0,1	BICD1	89	1	0			c.G1704C						PASS	.	G	,	651,3755	278.7+/-274.4	63,525,1615	112.0	110.0	111.0		1704,1704	3.2	1.0	12	dbSNP_107	111	1802,6798	324.1+/-316.3	192,1418,2690	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	255,1943,4305	CC,CG,GG		20.9535,14.7753,18.8605	,	568/836,568/976	32481093	2453,10553	2203	4300	6503	SO:0001819	synonymous_variant	636	exon5			GGGTGTGTCATCC	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1704G>C	12.37:g.32481093G>C		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	124	60	0.483871	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			G|0.767;C|0.233	0.233	strong		0.537	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
EVC	2121	hgsc.bcm.edu	37	4	5721021	5721021	+	Missense_Mutation	SNP	A	A	C	rs2291157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5721021A>C	ENST00000264956.6	+	2	405	c.221A>C	c.(220-222)cAg>cCg	p.Q74P	EVC_ENST00000509451.1_Missense_Mutation_p.Q74P|EVC_ENST00000382674.2_Missense_Mutation_p.Q74P	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	74			Q -> P (in dbSNP:rs2291157). {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)				TCTAATGCGCAGACCCCCTCG	0.478													A|||	522	0.104233	0.031	0.1254	5008	,	,		19446	0.1597		0.0954	False		,,,				2504	0.1401				p.Q74P		Atlas-SNP	.											.	EVC	90	.	0			c.A221C						PASS	.	A	PRO/GLN	223,4183	134.9+/-171.1	6,211,1986	198.0	198.0	198.0		221	-0.1	0.0	4	dbSNP_100	198	792,7808	185.5+/-233.2	36,720,3544	yes	missense	EVC	NM_153717.2	76	42,931,5530	CC,CA,AA		9.2093,5.0613,7.8041	probably-damaging	74/993	5721021	1015,11991	2203	4300	6503	SO:0001583	missense	2121	exon2			ATGCGCAGACCCC	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.221A>C	4.37:g.5721021A>C	ENSP00000264956:p.Gln74Pro	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	113	47	0.415929	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	252	0.11538461538461539	23	0.046747967479674794	55	0.15193370165745856	105	0.18356643356643357	69	0.09102902374670185	A	13.15	2.150749	0.37923	0.050613	0.092093	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.54479	0.57;0.57;0.65	3.99	-0.0931	0.13652	.	0.500397	0.20474	N	0.091627	T	0.00109	0.0003	L	0.57536	1.79	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.03773	-1.1005	9	0.45353	T	0.12	.	4.6228	0.12463	0.4996:0.3919:0.1085:0.0	rs2291157;rs61234179;rs2291157	74	P57679	EVC_HUMAN	P	74	ENSP00000264956:Q74P;ENSP00000372120:Q74P;ENSP00000426774:Q74P	ENSP00000264956:Q74P	Q	+	2	0	EVC	5771922	0.290000	0.24343	0.006000	0.13384	0.016000	0.09150	1.862000	0.39448	-0.072000	0.12864	-0.460000	0.05396	CAG	A|0.908;C|0.092	0.092	strong		0.478	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
MYO9B	4650	hgsc.bcm.edu	37	19	17303774	17303774	+	Missense_Mutation	SNP	T	T	G	rs1545620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17303774T>G	ENST00000594824.1	+	21	3178	c.3031T>G	c.(3031-3033)Tca>Gca	p.S1011A	MYO9B_ENST00000397274.2_Missense_Mutation_p.S1011A|MYO9B_ENST00000595618.1_Missense_Mutation_p.S1011A			Q13459	MYO9B_HUMAN	myosin IXB	1011	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.			S -> A (in Ref. 1; AAC50402). {ECO:0000305}.	actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						CCTCCAGGCCTCATGGAGGGG	0.677													G|||	3227	0.644369	0.7905	0.7032	5008	,	,		14650	0.7391		0.3897	False		,,,				2504	0.5695				p.S1011A		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.T3031G	GRCh37	CM066145	MYO9B	M	rs1545620	PASS	.	G	ALA/SER,ALA/SER	2939,1003		1112,715,144	12.0	17.0	15.0		3031,3031	-1.5	0.0	19	dbSNP_88	15	3377,4719		787,1803,1458	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	99,99	1899,2518,1602	GG,GT,TT		41.712,25.4439,47.5328	benign,benign	1011/2023,1011/2158	17303774	6316,5722	1971	4048	6019	SO:0001583	missense	4650	exon21			CAGGCCTCATGGA		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.3031T>G	19.37:g.17303774T>G	ENSP00000471367:p.Ser1011Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		1361	0.6231684981684982	382	0.7764227642276422	239	0.6602209944751382	440	0.7692307692307693	300	0.39577836411609496	G	0.005	-2.214157	0.00289	0.745561	0.41712	ENSG00000099331	ENST00000397274	T	0.21361	2.01	4.88	-1.46	0.08800	.	1.199970	0.06003	N	0.648098	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.43909	-0.9362	9	0.02654	T	1	.	0.9756	0.01425	0.2544:0.1088:0.337:0.2998	rs1545620;rs57113186;rs1545620	1011;1011;1017	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	A	1011	ENSP00000380444:S1011A	ENSP00000380444:S1011A	S	+	1	0	MYO9B	17164774	0.000000	0.05858	0.043000	0.18650	0.020000	0.10135	0.668000	0.25127	0.092000	0.17331	-0.721000	0.03606	TCA	T|0.363;G|0.637	0.637	strong		0.677	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
ZNF302	55900	hgsc.bcm.edu	37	19	35175208	35175208	+	Missense_Mutation	SNP	A	A	G	rs2290652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35175208A>G	ENST00000446502.2	+	6	606	c.398A>G	c.(397-399)tAt>tGt	p.Y133C	ZNF302_ENST00000457781.2_Missense_Mutation_p.Y89C|ZNF302_ENST00000505242.1_Missense_Mutation_p.Y89C|ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000509528.1_Missense_Mutation_p.M21V|ZNF302_ENST00000423823.2_Missense_Mutation_p.Y89C|ZNF302_ENST00000507959.1_3'UTR			Q9NR11	ZN302_HUMAN	zinc finger protein 302	73					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			AAGGATATTTATGATGAAGAT	0.289													A|||	1255	0.250599	0.1369	0.2075	5008	,	,		15422	0.3006		0.3767	False		,,,				2504	0.2536				p.Y89C		Atlas-SNP	.											.	ZNF302	27	.	0			c.A266G						PASS	.	A	CYS/TYR,CYS/TYR	726,3476		68,590,1443	47.0	51.0	50.0		266,266	1.0	0.7	19	dbSNP_100	50	3012,5452		533,1946,1753	no	missense,missense	ZNF302	NM_001012320.1,NM_018443.2	194,194	601,2536,3196	GG,GA,AA		35.586,17.2775,29.5121	probably-damaging,probably-damaging	89/400,89/400	35175208	3738,8928	2101	4232	6333	SO:0001583	missense	55900	exon5			ATATTTATGATGA	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.398A>G	19.37:g.35175208A>G	ENSP00000396379:p.Tyr133Cys	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	251	150	0.59761	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		615	0.2815934065934066	74	0.15040650406504066	83	0.2292817679558011	174	0.3041958041958042	284	0.37467018469656993	A	10.21	1.288432	0.23478	0.172775	0.35586	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000505163;ENST00000423823;ENST00000446502	T;T;T;T;T	0.04654	3.59;3.59;6.05;3.59;3.58	0.967	0.967	0.19674	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.41825	P	0.009959999999999969	D;D	0.89917	0.999;1.0	D;D	0.87578	0.99;0.998	T	0.48410	-0.9038	7	0.45353	T	0.12	.	4.1694	0.10322	1.0:0.0:0.0:0.0	rs2290652;rs17649399;rs52790156;rs60043199;rs2290652	133;89	E7EVR1;Q9NR11-2	.;.	C	89;89;89;89;133	ENSP00000391067:Y89C;ENSP00000421028:Y89C;ENSP00000421696:Y89C;ENSP00000405219:Y89C;ENSP00000396379:Y133C	ENSP00000405219:Y89C	Y	+	2	0	ZNF302	39867048	0.989000	0.36119	0.678000	0.29963	0.054000	0.15201	0.223000	0.17719	0.686000	0.31488	0.383000	0.25322	TAT	A|0.726;G|0.274	0.274	strong		0.289	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
APBB1	322	hgsc.bcm.edu	37	11	6415690	6415690	+	IGR	SNP	G	G	A	rs35098198	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6415690G>A	ENST00000609360.1	-	0	2642				SMPD1_ENST00000527275.1_Silent_p.S582S|APBB1_ENST00000526240.1_5'Flank|SMPD1_ENST00000299397.3_Silent_p.S539S|SMPD1_ENST00000356761.2_Silent_p.S527S|SMPD1_ENST00000342245.4_Silent_p.S583S	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)						apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)			breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		ACCCACCCTCGGAGCCCTGTG	0.617													G|||	61	0.0121805	0.0	0.0173	5008	,	,		17836	0.0		0.0288	False		,,,				2504	0.0204				p.S583S	GBM(147;1810 2556 5672 39622)	Atlas-SNP	.											.	SMPD1	108	.	0			c.G1749A						PASS	.	G	,	18,4384	25.3+/-52.1	0,18,2183	108.0	110.0	109.0		1749,1746	-10.8	0.3	11	dbSNP_126	109	197,8395	86.6+/-149.0	2,193,4101	no	coding-synonymous,coding-synonymous	SMPD1	NM_000543.4,NM_001007593.2	,	2,211,6284	AA,AG,GG		2.2928,0.4089,1.6546	,	583/632,582/631	6415690	215,12779	2201	4296	6497	SO:0001628	intergenic_variant	6609	exon6			ACCCTCGGAGCCC	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213			11.37:g.6415690G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	109	63	0.577982	NM_000543	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Silent	SNP	ENST00000609360.1	37		34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	G	7.094	0.572716	0.13623	0.004089	0.022928	ENSG00000166311	ENST00000526280	.	.	.	5.41	-10.8	0.00216	.	.	.	.	.	T	0.13713	0.0332	.	.	.	0.37312	D	0.909181	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	-41.8479	3.5651	0.07897	0.4056:0.2383:0.2762:0.0799	rs35098198	.	.	.	Q	269	.	.	R	+	2	0	SMPD1	6372266	0.000000	0.05858	0.310000	0.25168	0.873000	0.50193	-3.606000	0.00416	-2.420000	0.00564	-1.871000	0.00553	CGG	G|0.985;A|0.015	0.015	strong		0.617	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
ATP6V1B1	525	hgsc.bcm.edu	37	2	71163173	71163173	+	Missense_Mutation	SNP	C	C	T	rs17720303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:71163173C>T	ENST00000234396.4	+	1	162	c.89C>T	c.(88-90)aCc>aTc	p.T30I	ATP6V1B1_ENST00000412314.1_Missense_Mutation_p.T30I	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	30			T -> I (in dbSNP:rs17720303). {ECO:0000269|PubMed:12414817, ECO:0000269|Ref.3}.		ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						CAGGCGGTCACCCGAAACTAC	0.667													C|||	794	0.158546	0.115	0.2147	5008	,	,		12234	0.1865		0.1531	False		,,,				2504	0.1544				p.T30I		Atlas-SNP	.											.	ATP6V1B1	66	.	0			c.C89T						PASS	.	C	ILE/THR	619,3787	267.4+/-267.8	42,535,1626	63.0	67.0	66.0		89	4.9	1.0	2	dbSNP_123	66	1443,7157	275.6+/-291.8	135,1173,2992	yes	missense	ATP6V1B1	NM_001692.3	89	177,1708,4618	TT,TC,CC		16.7791,14.049,15.8542	benign	30/514	71163173	2062,10944	2203	4300	6503	SO:0001583	missense	525	exon1			CGGTCACCCGAAA	AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"""ATPases / V-type"""	853	protein-coding gene	gene with protein product	"""Renal tubular acidosis with deafness"""	192132	"""vacuolar proton pump 3"""	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.89C>T	2.37:g.71163173C>T	ENSP00000234396:p.Thr30Ile	Somatic	263	1	0.00380228		WXS	Illumina HiSeq	Phase_I	312	310	0.99359	NM_001692	Q53FY0|Q6P4H6	Missense_Mutation	SNP	ENST00000234396.4	37	CCDS1912.1	363	0.1662087912087912	54	0.10975609756097561	87	0.24033149171270718	116	0.20279720279720279	106	0.13984168865435356	C	15.23	2.772100	0.49680	0.14049	0.167791	ENSG00000116039	ENST00000234396;ENST00000483246;ENST00000412314	D;D	0.82803	-1.64;-1.65	4.89	4.89	0.63831	.	0.000000	0.51477	D	0.000095	T	0.00073	0.0002	L	0.27053	0.805	0.20489	P	0.999899324	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.04029	-1.0983	9	0.41790	T	0.15	-1.64	15.5589	0.76223	0.0:1.0:0.0:0.0	rs17720303;rs17720303	30;30	C9JL73;P15313	.;VATB1_HUMAN	I	30;5;30	ENSP00000234396:T30I;ENSP00000388353:T30I	ENSP00000234396:T30I	T	+	2	0	ATP6V1B1	71016681	0.997000	0.39634	0.998000	0.56505	0.896000	0.52359	2.279000	0.43435	2.256000	0.74724	0.467000	0.42956	ACC	C|0.839;N|0.001	.	strong		0.667	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692	
KIAA0825	285600	hgsc.bcm.edu	37	5	93722050	93722050	+	Silent	SNP	G	G	T	rs29913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:93722050G>T	ENST00000513200.3	-	18	3588	c.3516C>A	c.(3514-3516)atC>atA	p.I1172I	KIAA0825_ENST00000427991.2_Silent_p.I1172I	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	1172										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						TTAAAGGTCGGATGGGTAATG	0.388													G|||	581	0.116014	0.1157	0.1066	5008	,	,		17135	0.004		0.1471	False		,,,				2504	0.2065				p.I1172I		Atlas-SNP	.											.	KIAA0825	172	.	0			c.C3516A						PASS	.						157.0	136.0	142.0					5																	93722050		692	1591	2283	SO:0001819	synonymous_variant	285600	exon19			AGGTCGGATGGGT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.3516C>A	5.37:g.93722050G>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	158	70	0.443038	NM_001145678	O94914|Q6ZNN2	Silent	SNP	ENST00000513200.3	37																																																																																				G|0.892;T|0.108	0.108	strong		0.388	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
DHX57	90957	hgsc.bcm.edu	37	2	39025555	39025555	+	Silent	SNP	G	G	A	rs1530853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:39025555G>A	ENST00000295373.6	-	24	4173	c.4047C>T	c.(4045-4047)tgC>tgT	p.C1349C		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1349							ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(20)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	62		all_hematologic(82;0.248)				GATCAAGTTCGCAACGAAGCT	0.443													G|||	2945	0.588059	0.3139	0.5821	5008	,	,		19068	0.7857		0.6441	False		,,,				2504	0.7014				p.C1349C	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.C4047T						PASS	.	G		1603,2803	496.0+/-363.4	289,1025,889	113.0	103.0	106.0		4047	-10.8	0.0	2	dbSNP_88	106	5436,3164	655.0+/-401.2	1716,2004,580	no	coding-synonymous	DHX57	NM_198963.1		2005,3029,1469	AA,AG,GG		36.7907,36.3822,45.8788		1349/1387	39025555	7039,5967	2203	4300	6503	SO:0001819	synonymous_variant	90957	exon24			AAGTTCGCAACGA	AF070590	CCDS1800.1	2p22.3	2008-02-05			ENSG00000163214	ENSG00000163214		"""DEAH-boxes"""	20086	protein-coding gene	gene with protein product							Standard	NM_198963		Approved	DDX57	uc002rrf.3	Q6P158	OTTHUMG00000102103	ENST00000295373.6:c.4047C>T	2.37:g.39025555G>A		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	140	66	0.471429	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Silent	SNP	ENST00000295373.6	37	CCDS1800.1	1326	0.6071428571428571	154	0.3130081300813008	214	0.5911602209944752	456	0.7972027972027972	502	0.662269129287599	G	6.637	0.485909	0.12641	0.363822	0.632093	ENSG00000163214	ENST00000452978	.	.	.	5.42	-10.8	0.00216	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999143102	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9687	0.79995	0.744:0.0:0.1799:0.0761	rs1530853;rs17174676;rs57997508;rs1530853	.	.	.	X	628	.	.	R	-	1	2	DHX57	38879059	0.003000	0.15002	0.000000	0.03702	0.808000	0.45660	-1.137000	0.03219	-2.701000	0.00398	-0.312000	0.09012	CGA	G|0.437;A|0.563	0.563	strong		0.443	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646	
KIAA1429	25962	hgsc.bcm.edu	37	8	95531419	95531419	+	Silent	SNP	T	T	C	rs1866844	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95531419T>C	ENST00000297591.5	-	9	2382	c.2307A>G	c.(2305-2307)caA>caG	p.Q769Q	KIAA1429_ENST00000421249.2_Silent_p.Q769Q|KIAA1429_ENST00000437199.1_Silent_p.Q769Q	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	769					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			CTGTAATACATTGCAATGTCT	0.413													T|||	1590	0.317492	0.3283	0.2608	5008	,	,		17876	0.3194		0.2247	False		,,,				2504	0.4366				p.Q769Q		Atlas-SNP	.											KIAA1429,caecum,carcinoma,0,1	KIAA1429	176	1	0			c.A2307G						PASS	.	T	,	1289,3117	438.0+/-345.2	194,901,1108	113.0	97.0	103.0		2307,2307	1.8	1.0	8	dbSNP_92	103	2209,6391	376.1+/-338.0	258,1693,2349	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	452,2594,3457	CC,CT,TT		25.686,29.2556,26.8953	,	769/1813,769/1148	95531419	3498,9508	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon9			AATACATTGCAAT	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2307A>G	8.37:g.95531419T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			T|0.715;C|0.285	0.285	strong		0.413	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
OBSCN	84033	hgsc.bcm.edu	37	1	228506661	228506661	+	Silent	SNP	G	G	A	rs41305126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228506661G>A	ENST00000422127.1	+	54	14252	c.14208G>A	c.(14206-14208)ctG>ctA	p.L4736L	OBSCN_ENST00000366707.4_Silent_p.L2370L|OBSCN_ENST00000366709.4_Silent_p.L1855L|OBSCN_ENST00000284548.11_Silent_p.L4736L|OBSCN_ENST00000570156.2_Silent_p.L5693L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4736					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)				AGGGTGACCTGCACCTACTGT	0.657													G|||	54	0.0107827	0.0015	0.0216	5008	,	,		18553	0.001		0.0288	False		,,,				2504	0.0072				p.L5693L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G17079A						PASS	.	G	,	21,4305		0,21,2142	14.0	17.0	16.0		14208,14208	2.2	1.0	1	dbSNP_127	16	196,8330		1,194,4068	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1,215,6210	AA,AG,GG		2.2989,0.4854,1.6885	,	4736/7969,4736/6621	228506661	217,12635	2163	4263	6426	SO:0001819	synonymous_variant	84033	exon65			TGACCTGCACCTA	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.14208G>A	1.37:g.228506661G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	143	50	0.34965	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.986;A|0.014	0.014	strong		0.657	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
DHX34	9704	hgsc.bcm.edu	37	19	47858424	47858424	+	Silent	SNP	G	G	A	rs2245046	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:47858424G>A	ENST00000328771.4	+	3	1183	c.834G>A	c.(832-834)gtG>gtA	p.V278V		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	278	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		TCCTGATTGTGGATGAAGTCC	0.602													G|||	547	0.109225	0.2012	0.121	5008	,	,		16411	0.0942		0.0577	False		,,,				2504	0.045				p.V278V		Atlas-SNP	.											.	DHX34	98	.	0			c.G834A						PASS	.	G		804,3602	321.5+/-297.2	80,644,1479	108.0	89.0	96.0		834	2.4	1.0	19	dbSNP_100	96	447,8153	135.4+/-192.6	9,429,3862	no	coding-synonymous	DHX34	NM_014681.5		89,1073,5341	AA,AG,GG		5.1977,18.2478,9.6186		278/1144	47858424	1251,11755	2203	4300	6503	SO:0001819	synonymous_variant	9704	exon3			GATTGTGGATGAA	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.834G>A	19.37:g.47858424G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	37	CCDS12700.1																																																																																			G|0.897;A|0.103	0.103	strong		0.602	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274364	39274364	+	Missense_Mutation	SNP	T	T	G	rs425784		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39274364T>G	ENST00000391413.2	-	1	242	c.204A>C	c.(202-204)agA>agC	p.R68S		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	68	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)			AGATGCAGCATCTGGGGCGGC	0.667																																					p.R68S		Atlas-SNP	.											KRTAP4-11,caecum,carcinoma,0,2	KRTAP4-11	94	2	0			c.A204C						scavenged	.						8.0	12.0	11.0					17																	39274364		676	1581	2257	SO:0001583	missense	653240	exon1			GCAGCATCTGGGG	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.204A>C	17.37:g.39274364T>G	ENSP00000375232:p.Arg68Ser	Somatic	66	4	0.0606061		WXS	Illumina HiSeq	Phase_I	97	15	0.154639	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.572	-0.840659	0.02692	.	.	ENSG00000212721	ENST00000391413	T	0.01139	5.28	3.77	-0.689	0.11313	.	91.536500	0.00963	N	0.003131	T	0.00271	0.0008	N	0.00022	-2.74	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.53429	-0.8440	10	0.02654	T	1	.	0.7939	0.01062	0.2891:0.1622:0.3809:0.1678	rs425784	68	Q9BYQ6	KR411_HUMAN	S	68	ENSP00000375232:R68S	ENSP00000375232:R68S	R	-	3	2	KRTAP4-11	36527890	0.005000	0.15991	0.041000	0.18516	0.133000	0.20885	-0.083000	0.11286	-0.156000	0.11079	-0.875000	0.02981	AGA	.	.	weak		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
C10orf54	64115	hgsc.bcm.edu	37	10	73521578	73521578	+	Silent	SNP	G	G	A	rs3747866	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:73521578G>A	ENST00000394957.3	-	2	346	c.288C>T	c.(286-288)gaC>gaT	p.D96D	C10orf54_ENST00000481568.2_5'UTR|CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	96	Ig-like.				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						GCAGGTGAAGGTCCTGGAACG	0.652													G|||	1053	0.210264	0.5734	0.0965	5008	,	,		20753	0.0645		0.0765	False		,,,				2504	0.0879				p.D96D		Atlas-SNP	.											.	C10orf54	29	.	0			c.C288T						PASS	.	G	,	2087,2319	569.1+/-382.5	521,1045,637	100.0	101.0	101.0		,288	3.8	1.0	10	dbSNP_107	101	648,7952	165.8+/-217.9	31,586,3683	no	intron,coding-synonymous	CDH23,C10orf54	NM_022124.5,NM_022153.1	,	552,1631,4320	AA,AG,GG		7.5349,47.3672,21.0288	,	,96/312	73521578	2735,10271	2203	4300	6503	SO:0001819	synonymous_variant	64115	exon2			GTGAAGGTCCTGG	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.288C>T	10.37:g.73521578G>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Silent	SNP	ENST00000394957.3	37	CCDS31218.1																																																																																			G|0.790;A|0.210	0.210	strong		0.652	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153	
UBXN11	91544	hgsc.bcm.edu	37	1	26608853	26608853	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608853G>A	ENST00000374222.1	-	16	1964	c.1500C>T	c.(1498-1500)ggC>ggT	p.G500G	UBXN11_ENST00000314675.7_Silent_p.G380G|UBXN11_ENST00000374217.2_Silent_p.G467G|UBXN11_ENST00000357089.4_Silent_p.G467G|UBXN11_ENST00000374223.1_Silent_p.G257G|UBXN11_ENST00000374221.3_Silent_p.G500G			Q5T124	UBX11_HUMAN	UBX domain protein 11	500	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						cgggactggggccgggaccgg	0.731																																					p.G500G		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.C1500T						PASS	.						20.0	23.0	22.0					1																	26608853		1694	3910	5604	SO:0001819	synonymous_variant	91544	exon16			ACTGGGGCCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1500C>T	1.37:g.26608853G>A		Somatic	24	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	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			.	.	none		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
LAMB2	3913	hgsc.bcm.edu	37	3	49159152	49159152	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49159152C>A	ENST00000418109.1	-	31	5229	c.5065G>T	c.(5065-5067)Ggc>Tgc	p.G1689C	USP19_ENST00000417901.1_5'Flank|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank|USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.G1689C|USP19_ENST00000398892.3_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1689	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGGGCACTGCCTGCCGTTTCT	0.597																																					p.G1689C		Atlas-SNP	.											.	LAMB2	156	.	0			c.G5065T						PASS	.						71.0	74.0	73.0					3																	49159152		2203	4300	6503	SO:0001583	missense	3913	exon30			CACTGCCTGCCGT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.5065G>T	3.37:g.49159152C>A	ENSP00000388325:p.Gly1689Cys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	103	36	0.349515	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.378244	0.61735	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34859	1.34;1.34	5.79	1.37	0.22104	.	0.448886	0.23889	N	0.043563	T	0.36413	0.0966	L	0.40543	1.245	0.37970	D	0.93324	D	0.69078	0.997	P	0.55667	0.781	T	0.29305	-1.0016	10	0.59425	D	0.04	.	5.0677	0.14591	0.0:0.4547:0.1499:0.3954	.	1689	P55268	LAMB2_HUMAN	C	1689	ENSP00000388325:G1689C;ENSP00000307156:G1689C	ENSP00000307156:G1689C	G	-	1	0	LAMB2	49134156	0.288000	0.24324	0.990000	0.47175	0.978000	0.69477	0.697000	0.25556	0.342000	0.23796	0.655000	0.94253	GGC	.	.	none		0.597	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
RAPSN	5913	hgsc.bcm.edu	37	11	47463220	47463220	+	Silent	SNP	C	C	T	rs45603036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:47463220C>T	ENST00000298854.2	-	5	1068	c.855G>A	c.(853-855)caG>caA	p.Q285Q	RAPSN_ENST00000528356.1_5'UTR|RNU6-1302P_ENST00000516518.1_RNA|RAPSN_ENST00000529341.1_Intron|RAPSN_ENST00000352508.3_Intron|RAPSN_ENST00000524487.1_Silent_p.Q232Q	NM_005055.4	NP_005046.2	Q13702	RAPSN_HUMAN	receptor-associated protein of the synapse	285					positive regulation of neuron apoptotic process (GO:0043525)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)	acetylcholine receptor binding (GO:0033130)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(6)|ovary(2)	12						GCGCCTGCACCTGCCCCAGGC	0.647													C|||	358	0.0714856	0.0446	0.0951	5008	,	,		13668	0.0466		0.1501	False		,,,				2504	0.0358				p.Q285Q		Atlas-SNP	.											.	RAPSN	27	.	0			c.G855A						PASS	.	C	,	294,4108	152.2+/-185.9	7,280,1914	32.0	32.0	32.0		855,	2.8	1.0	11	dbSNP_127	32	1229,7367	238.2+/-269.8	97,1035,3166	no	coding-synonymous,intron	RAPSN	NM_005055.4,NM_032645.4	,	104,1315,5080	TT,TC,CC		14.2973,6.6788,11.7172	,	285/413,	47463220	1523,11475	2201	4298	6499	SO:0001819	synonymous_variant	5913	exon5			CTGCACCTGCCCC		CCDS7936.1, CCDS7937.1	11p11.2	2009-04-28	2007-02-23		ENSG00000165917	ENSG00000165917		"""RING-type (C3HC4) zinc fingers"""	9863	protein-coding gene	gene with protein product	"""rapsyn"""	601592	"""receptor-associated protein of the synapse, 43kD"""			8812503	Standard	NM_005055		Approved	RNF205, CMS1D, CMS1E	uc001nfi.2	Q13702	OTTHUMG00000166891	ENST00000298854.2:c.855G>A	11.37:g.47463220C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	206	92	0.446602	NM_005055	Q8TDF3|Q9BTD9	Silent	SNP	ENST00000298854.2	37	CCDS7936.1																																																																																			C|0.891;T|0.109	0.109	strong		0.647	RAPSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391726.1		
FAHD1	81889	hgsc.bcm.edu	37	16	1877558	1877558	+	Missense_Mutation	SNP	G	G	A	rs3743853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1877558G>A	ENST00000427358.2	+	1	334	c.328G>A	c.(328-330)Gac>Aac	p.D110N	HAGH_ENST00000455446.2_5'Flank|FAHD1_ENST00000382668.4_Missense_Mutation_p.D110N|HAGH_ENST00000566709.1_5'Flank|HAGH_ENST00000397356.3_5'Flank|HAGH_ENST00000397353.2_5'Flank|FAHD1_ENST00000382666.4_Missense_Mutation_p.D110N	NM_031208.3	NP_112485.1	Q6P587	FAHD1_HUMAN	fumarylacetoacetate hydrolase domain containing 1	110			D -> N (in dbSNP:rs3743853).			cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetylpyruvate hydrolase activity (GO:0018773)|acylpyruvate hydrolase activity (GO:0047621)|fumarylpyruvate hydrolase activity (GO:0034545)|metal ion binding (GO:0046872)			NS(1)|large_intestine(1)|liver(1)|ovary(2)|urinary_tract(1)	6						GGACGTGCAGGACGAGTGCAA	0.672													G|||	683	0.136382	0.0106	0.2075	5008	,	,		19134	0.1667		0.1769	False		,,,				2504	0.183				p.D110N		Atlas-SNP	.											.	FAHD1	18	.	0			c.G328A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP	134,4264	88.2+/-126.9	1,132,2066	33.0	32.0	32.0		328,328,328	1.5	1.0	16	dbSNP_107	32	1320,7280	243.5+/-273.1	109,1102,3089	yes	missense,missense,missense	FAHD1	NM_001018104.2,NM_001142398.1,NM_031208.3	23,23,23	110,1234,5155	AA,AG,GG		15.3488,3.0468,11.1863	benign,benign,benign	110/249,110/227,110/225	1877558	1454,11544	2199	4300	6499	SO:0001583	missense	81889	exon1			GTGCAGGACGAGT	BC063017	CCDS10448.1, CCDS32367.1, CCDS45380.1	16p13.3	2011-10-21	2004-08-19	2004-08-26	ENSG00000180185	ENSG00000180185			14169	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 36"""	C16orf36		21878618	Standard	NM_001018104		Approved	DKFZP566J2046	uc002cnd.3	Q6P587	OTTHUMG00000128663	ENST00000427358.2:c.328G>A	16.37:g.1877558G>A	ENSP00000398053:p.Asp110Asn	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_031208	B1AK40|B1AK41|Q6FIC7|Q96RY1|Q9H0N6	Missense_Mutation	SNP	ENST00000427358.2	37	CCDS10448.1	306	0.1401098901098901	8	0.016260162601626018	57	0.1574585635359116	100	0.17482517482517482	141	0.18601583113456466	G	16.09	3.024726	0.54683	0.030468	0.153488	ENSG00000180185	ENST00000382668;ENST00000382666;ENST00000427358	D;D;D	0.94687	-3.49;-3.49;-3.49	4.53	1.46	0.22682	Fumarylacetoacetase, C-terminal-related (2);Fumarylacetoacetase, C-terminal (1);	0.262703	0.36519	N	0.002558	T	0.00608	0.0020	N	0.16790	0.44	0.19300	P	0.9999759796	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.10450	0.002;0.005;0.005	T	0.34875	-0.9811	9	0.22706	T	0.39	.	6.3111	0.21164	0.2373:0.1348:0.6279:0.0	rs3743853;rs3743853	110;110;110	Q6P587-2;B1AK40;Q6P587	.;.;FAHD1_HUMAN	N	110	ENSP00000372114:D110N;ENSP00000372112:D110N;ENSP00000398053:D110N	ENSP00000372112:D110N	D	+	1	0	FAHD1	1817559	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	2.652000	0.46682	0.166000	0.19597	0.655000	0.94253	GAC	G|0.882;A|0.118	0.118	strong		0.672	FAHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250550.2	NM_001018104	
TTC7B	145567	hgsc.bcm.edu	37	14	91123575	91123575	+	Silent	SNP	T	T	C	rs3742660	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:91123575T>C	ENST00000328459.6	-	11	1405	c.1284A>G	c.(1282-1284)ccA>ccG	p.P428P	TTC7B_ENST00000357056.2_Silent_p.P428P	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	428										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				TGGCATCGTCTGGCTTCAGGC	0.582													C|||	4466	0.891773	0.8419	0.8545	5008	,	,		18820	0.9812		0.8588	False		,,,				2504	0.9274				p.P428P		Atlas-SNP	.											TTC7B,NS,carcinoma,-2,1	TTC7B	93	1	0			c.A1284G						PASS	.	C		3752,654	278.7+/-274.4	1605,542,56	82.0	79.0	80.0		1284	-10.7	0.0	14	dbSNP_107	80	7456,1144	234.9+/-267.6	3226,1004,70	no	coding-synonymous	TTC7B	NM_001010854.1		4831,1546,126	CC,CT,TT		13.3023,14.8434,13.8244		428/844	91123575	11208,1798	2203	4300	6503	SO:0001819	synonymous_variant	145567	exon11			ATCGTCTGGCTTC	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"""Tetratricopeptide (TTC) repeat domain containing"""	19858	protein-coding gene	gene with protein product			"""tetratricopeptide repeat domain 7 like 1"""	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.1284A>G	14.37:g.91123575T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	67	67	1	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	37	CCDS32140.1	1944	0.8901098901098901	428	0.8699186991869918	306	0.8453038674033149	557	0.9737762237762237	653	0.8614775725593667	C	0.399	-0.919400	0.02396	0.851566	0.866977	ENSG00000165914	ENST00000554462	.	.	.	5.35	-10.7	0.00240	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999999	.	.	.	.	.	.	T	0.09773	-1.0659	3	.	.	.	-25.7517	3.9977	0.09566	0.153:0.3654:0.1104:0.3712	rs3742660;rs17224131;rs59960459;rs3742660	.	.	.	G	98	.	.	R	-	1	2	TTC7B	90193328	0.000000	0.05858	0.006000	0.13384	0.015000	0.08874	-3.998000	0.00317	-3.663000	0.00124	-3.368000	0.00041	AGA	T|0.123;G|0.000;C|0.877	0.877	strong		0.582	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
NFATC1	4772	hgsc.bcm.edu	37	18	77227554	77227554	+	Silent	SNP	C	C	T	rs35099556	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:77227554C>T	ENST00000427363.2	+	8	2064	c.2064C>T	c.(2062-2064)taC>taT	p.Y688Y	NFATC1_ENST00000587635.1_3'UTR|NFATC1_ENST00000253506.5_Silent_p.Y688Y|NFATC1_ENST00000318065.5_Silent_p.Y675Y|NFATC1_ENST00000586434.1_Silent_p.Y675Y|NFATC1_ENST00000329101.4_Silent_p.Y675Y|NFATC1_ENST00000591814.1_Silent_p.Y688Y|NFATC1_ENST00000397790.2_Silent_p.Y216Y|NFATC1_ENST00000592223.1_Silent_p.Y675Y|NFATC1_ENST00000542384.1_Silent_p.Y688Y|NFATC1_ENST00000545796.1_Silent_p.Y216Y			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	688					calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	GAAGCCAGTACCAGCGTTTCA	0.532													C|||	35	0.00698882	0.0015	0.0101	5008	,	,		17163	0.0		0.0219	False		,,,				2504	0.0041				p.Y688Y	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C2064T						PASS	.	C	,,,,	11,4393	19.1+/-41.9	0,11,2191	126.0	94.0	105.0		2064,2025,648,2025,2064	3.4	1.0	18	dbSNP_126	105	135,8465	68.0+/-130.5	2,131,4167	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	,,,,	2,142,6358	TT,TC,CC		1.5698,0.2498,1.1227	,,,,	688/826,675/931,216/354,675/813,688/717	77227554	146,12858	2202	4300	6502	SO:0001819	synonymous_variant	4772	exon8			CCAGTACCAGCGT	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.2064C>T	18.37:g.77227554C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Silent	SNP	ENST00000427363.2	37																																																																																				C|0.988;T|0.012	0.012	strong		0.532	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
SCRN3	79634	hgsc.bcm.edu	37	2	175289259	175289259	+	Missense_Mutation	SNP	G	G	T	rs41270195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:175289259G>T	ENST00000272732.6	+	7	1056	c.974G>T	c.(973-975)aGt>aTt	p.S325I	SCRN3_ENST00000409673.3_Missense_Mutation_p.S318I|SCRN3_ENST00000548921.1_3'UTR	NM_001193528.1|NM_024583.4	NP_001180457.1|NP_078859.2	Q0VDG4	SCRN3_HUMAN	secernin 3	325							dipeptidase activity (GO:0016805)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|urinary_tract(3)	13			OV - Ovarian serous cystadenocarcinoma(117;0.229)			TTGGATACCAGTTCACCAACA	0.313													G|||	53	0.0105831	0.0	0.0115	5008	,	,		19014	0.0		0.0408	False		,,,				2504	0.0041				p.S325I		Atlas-SNP	.											.	SCRN3	76	.	0			c.G974T						PASS	.	G	ILE/SER,ILE/SER	42,4364	46.7+/-81.2	0,42,2161	71.0	67.0	68.0		953,974	-0.7	0.3	2	dbSNP_127	68	376,8224	122.7+/-181.7	8,360,3932	yes	missense,missense	SCRN3	NM_001193528.1,NM_024583.4	142,142	8,402,6093	TT,TG,GG		4.3721,0.9532,3.2139	benign,benign	318/418,325/425	175289259	418,12588	2203	4300	6503	SO:0001583	missense	79634	exon7			ATACCAGTTCACC	AF279776	CCDS2258.1, CCDS54420.1	2q31	2008-02-05			ENSG00000144306	ENSG00000144306			30382	protein-coding gene	gene with protein product		614967				12221138	Standard	NM_024583		Approved	FLJ23142	uc002uiq.3	Q0VDG4	OTTHUMG00000132332	ENST00000272732.6:c.974G>T	2.37:g.175289259G>T	ENSP00000272732:p.Ser325Ile	Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	226	117	0.517699	NM_024583	B4DI11|C9JPC1|D3DPE0|Q7L1C5|Q9H5R5	Missense_Mutation	SNP	ENST00000272732.6	37	CCDS2258.1	34	0.015567765567765568	0	0.0	5	0.013812154696132596	0	0.0	29	0.03825857519788918	G	3.398	-0.122847	0.06795	0.009532	0.043721	ENSG00000144306	ENST00000409673;ENST00000272732	T;T	0.08546	3.08;3.08	4.91	-0.677	0.11357	.	0.409489	0.27253	N	0.020212	T	0.00936	0.0031	L	0.31294	0.92	0.09310	N	1	B;B	0.12013	0.005;0.004	B;B	0.12156	0.007;0.002	T	0.34650	-0.9820	10	0.35671	T	0.21	-2.0764	1.0261	0.01528	0.2119:0.2024:0.3628:0.2229	rs41270195	318;325	B4DI11;Q0VDG4	.;SCRN3_HUMAN	I	318;325	ENSP00000387142:S318I;ENSP00000272732:S325I	ENSP00000272732:S325I	S	+	2	0	SCRN3	174997505	0.000000	0.05858	0.267000	0.24556	0.187000	0.23431	0.068000	0.14531	0.103000	0.17682	-0.266000	0.10368	AGT	G|0.971;T|0.029	0.029	strong		0.313	SCRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255451.2	NM_024583	
LRP4	4038	hgsc.bcm.edu	37	11	46890197	46890197	+	Silent	SNP	G	G	A	rs2290883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:46890197G>A	ENST00000378623.1	-	33	5147	c.4905C>T	c.(4903-4905)ttC>ttT	p.F1635F	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1635					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		AGGCACATACGAAGTCCGAGG	0.582													.|||	1098	0.219249	0.0045	0.2781	5008	,	,		18416	0.6101		0.1193	False		,,,				2504	0.1677				p.F1635F		Atlas-SNP	.											.	LRP4	160	.	0			c.C4905T						PASS	.	G		148,4254		3,142,2056	87.0	79.0	82.0		4905	-2.5	1.0	11	dbSNP_100	82	1052,7546		55,942,3302	no	coding-synonymous	LRP4	NM_002334.3		58,1084,5358	AA,AG,GG		12.2354,3.3621,9.2308		1635/1906	46890197	1200,11800	2201	4299	6500	SO:0001819	synonymous_variant	4038	exon33			ACATACGAAGTCC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4905C>T	11.37:g.46890197G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																			G|0.841;A|0.159	0.159	strong		0.582	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
TAAR1	134864	hgsc.bcm.edu	37	6	132967002	132967002	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:132967002A>G	ENST00000275216.1	-	1	140	c.141T>C	c.(139-141)tcT>tcC	p.S47S		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	47					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	AGTGTGATATAGAAACAATAA	0.418																																					p.S47S		Atlas-SNP	.											TAAR1,NS,carcinoma,-1,1	TAAR1	41	1	0			c.T141C						scavenged	.						147.0	144.0	145.0					6																	132967002		2203	4300	6503	SO:0001819	synonymous_variant	134864	exon1			TGATATAGAAACA	AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"""GPCR / Class A : Trace amine associated receptors"""	17734	protein-coding gene	gene with protein product		609333	"""trace amine receptor 1"""	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.141T>C	6.37:g.132967002A>G		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Silent	SNP	ENST00000275216.1	37	CCDS5158.1																																																																																			.	.	none		0.418	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382792	24382792	+	IGR	SNP	G	G	A	rs5944420		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:24382792G>A								AC004552.1 (15769 upstream) : PDK3 (100545 downstream)																							GGGTGCCCCCGCTCCTGCAGG	0.627													G|||	516	0.136689	0.0265	0.121	3775	,	,		10257	0.124		0.0915	False		,,,				2504	0.184				p.A639T		Atlas-SNP	.											.	.	.	.	0			c.G1915A						PASS	.	G	THR/ALA	163,2464		5,118,35,936,474	28.0	27.0	27.0		1915	2.7	0.0	X	dbSNP_114	27	667,4830		34,400,199,1482,1466	no	missense	FAM48B1	NM_001136234.1	58	39,518,234,2418,1940	AA,AG,A,GG,G		12.1339,6.2048,10.2166	possibly-damaging	639/888	24382792	830,7294	1568	3581	5149	SO:0001628	intergenic_variant	100130302	exon1			GCCCCCGCTCCTG																													X.37:g.24382792G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	120	0.96	NM_001136234		Missense_Mutation	SNP		37																																																																																				G|0.882;A|0.118	0.118	strong	0	0.627								
OPTN	10133	hgsc.bcm.edu	37	10	13168025	13168025	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13168025C>A	ENST00000378748.3	+	12	1590	c.1228C>A	c.(1228-1230)Cta>Ata	p.L410I	OPTN_ENST00000378764.2_Missense_Mutation_p.L404I|OPTN_ENST00000378757.2_Missense_Mutation_p.L410I|OPTN_ENST00000263036.5_Missense_Mutation_p.L410I|OPTN_ENST00000378747.3_Missense_Mutation_p.L410I|OPTN_ENST00000378752.3_Missense_Mutation_p.L404I	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	410					cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						AATTGAGGAACTAACAAGAAA	0.294																																					p.L410I		Atlas-SNP	.											.	OPTN	57	.	0			c.C1228A						PASS	.						75.0	74.0	74.0					10																	13168025		2203	4298	6501	SO:0001583	missense	10133	exon11			GAGGAACTAACAA	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"""glaucoma 1, open angle, E (adult-onset)"""	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.1228C>A	10.37:g.13168025C>A	ENSP00000368022:p.Leu410Ile	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	37	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141179	0.37825	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	D;D;D;D;D;D	0.87809	-2.28;-2.3;-2.28;-2.3;-2.28;-2.28	5.57	4.67	0.58626	.	0.427472	0.25981	N	0.027066	D	0.87896	0.6293	L	0.59436	1.845	0.27698	N	0.945886	P;P	0.46457	0.878;0.807	P;P	0.52481	0.7;0.504	T	0.81267	-0.1010	10	0.40728	T	0.16	-2.6754	8.8732	0.35330	0.0:0.83:0.0:0.17	.	404;410	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	I	410;404;410;404;410;410	ENSP00000263036:L410I;ENSP00000368040:L404I;ENSP00000368032:L410I;ENSP00000368027:L404I;ENSP00000368022:L410I;ENSP00000368021:L410I	ENSP00000263036:L410I	L	+	1	2	OPTN	13208031	1.000000	0.71417	0.730000	0.30809	0.374000	0.29953	1.614000	0.36911	1.490000	0.48466	0.650000	0.86243	CTA	.	.	none		0.294	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919079	12919079	+	Missense_Mutation	SNP	C	C	G	rs9659529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12919079C>G	ENST00000240189.2	+	2	302	c.215C>G	c.(214-216)aCg>aGg	p.T72R		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	72			T -> R (in dbSNP:rs9659529).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGATGAAGACGCTTCATCTG	0.557													.|||	540	0.107827	0.1263	0.098	5008	,	,		22731	0.127		0.1064	False		,,,				2504	0.0716				p.T72R		Atlas-SNP	.											PRAMEF2,caecum,carcinoma,-1,2	PRAMEF2	85	2	0			c.C215G						PASS	.	T	ARG/THR	623,3779	268.6+/-268.5	67,489,1645	153.0	163.0	160.0		215	-1.7	0.1	1	dbSNP_119	160	960,7632	209.4+/-250.6	62,836,3398	no	missense	PRAMEF2	NM_023014.1	71	129,1325,5043	GG,GC,CC		11.1732,14.1527,12.1825	possibly-damaging	72/475	12919079	1583,11411	2201	4296	6497	SO:0001583	missense	65122	exon2			TGAAGACGCTTCA		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.215C>G	1.37:g.12919079C>G	ENSP00000240189:p.Thr72Arg	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	199	17	0.0854271	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	230	0.10531135531135531	46	0.09349593495934959	35	0.09668508287292818	62	0.10839160839160839	87	0.11477572559366754	c	1.758	-0.487598	0.04352	0.141527	0.111732	ENSG00000120952	ENST00000240189	T	0.11277	2.79	0.842	-1.68	0.08212	.	4.218360	0.00582	N	0.000330	T	0.00178	0.0005	L	0.50919	1.6	0.80722	P	0.0	P	0.41643	0.758	D	0.64237	0.923	T	0.14476	-1.0471	9	0.25106	T	0.35	.	4.1359	0.10170	0.0:0.4732:0.0:0.5268	rs9659529;rs9659529	72	O60811	PRAM2_HUMAN	R	72	ENSP00000240189:T72R	ENSP00000240189:T72R	T	+	2	0	PRAMEF2	12841666	0.000000	0.05858	0.064000	0.19789	0.045000	0.14185	-0.129000	0.10515	-0.704000	0.05042	-1.031000	0.02408	ACG	C|0.887;G|0.113	0.113	strong		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
KDF1	126695	hgsc.bcm.edu	37	1	27278553	27278553	+	Missense_Mutation	SNP	G	G	A	rs3010109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:27278553G>A	ENST00000320567.5	-	2	407	c.319C>T	c.(319-321)Cgg>Tgg	p.R107W		NM_152365.2	NP_689578.2	Q8NAX2	KDF1_HUMAN		107	Cys-rich.		R -> W (in dbSNP:rs3010109).		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)		CTGCATCCCCGCACACAGGCT	0.672													G|||	470	0.0938498	0.0068	0.085	5008	,	,		14326	0.0288		0.173	False		,,,				2504	0.2035				p.R107W		Atlas-SNP	.											.	C1orf172	38	.	0			c.C319T						PASS	.	G	TRP/ARG	138,4262		1,136,2063	15.0	19.0	18.0		319	4.9	1.0	1	dbSNP_101	18	1527,7067		125,1277,2895	yes	missense	C1orf172	NM_152365.2	101	126,1413,4958	AA,AG,GG		17.7682,3.1364,12.8136	possibly-damaging	107/399	27278553	1665,11329	2200	4297	6497	SO:0001583	missense	126695	exon2			ATCCCCGCACACA																												ENST00000320567.5:c.319C>T	1.37:g.27278553G>A	ENSP00000319179:p.Arg107Trp	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	151	20	0.13245	NM_152365	Q5QP32|Q8N0S7	Missense_Mutation	SNP	ENST00000320567.5	37	CCDS293.1	229	0.10485347985347986	21	0.042682926829268296	40	0.11049723756906077	25	0.043706293706293704	143	0.18865435356200527	G	18.11	3.549805	0.65311	0.031364	0.177682	ENSG00000175707	ENST00000320567	T	0.28255	1.62	4.92	4.92	0.64577	.	0.566641	0.18788	N	0.131151	T	0.00039	0.0001	N	0.24115	0.695	0.34882	P	0.255348	D	0.59767	0.986	B	0.39876	0.312	T	0.10660	-1.0620	9	0.62326	D	0.03	.	13.491	0.61395	0.0:0.0:1.0:0.0	rs3010109;rs3010109	107	Q8NAX2	CA172_HUMAN	W	107	ENSP00000319179:R107W	ENSP00000319179:R107W	R	-	1	2	C1orf172	27151140	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	3.282000	0.51693	2.547000	0.85894	0.557000	0.71058	CGG	G|0.894;A|0.106	0.106	strong		0.672	C1orf172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012340.1		
SERPINA3	12	hgsc.bcm.edu	37	14	95080803	95080803	+	Missense_Mutation	SNP	G	G	A	rs4934	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:95080803G>A	ENST00000467132.1	+	2	1173	c.25G>A	c.(25-27)Gct>Act	p.A9T	SERPINA3_ENST00000393078.3_Missense_Mutation_p.A9T|SERPINA3_ENST00000393080.4_Missense_Mutation_p.A9T|RP11-986E7.7_ENST00000553947.1_3'UTR			P01011	AACT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3	9			A -> T (in dbSNP:rs4934). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of endopeptidase activity (GO:0010951)|regulation of lipid metabolic process (GO:0019216)|regulation of proteolysis (GO:0030162)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	DNA binding (GO:0003677)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(17)|ovary(2)|pancreas(1)|skin(3)|stomach(1)	40		all_cancers(154;0.0525)|all_epithelial(191;0.179)		COAD - Colon adenocarcinoma(157;0.212)|Epithelial(152;0.228)		ACCTCTCCTGGCTCTGGGGCT	0.582													G|||	2000	0.399361	0.2133	0.2781	5008	,	,		18889	0.62		0.4871	False		,,,				2504	0.4192				p.A9T		Atlas-SNP	.											.	SERPINA3	78	.	0			c.G25A	GRCh37	CM950001	SERPINA3	M	rs4934	PASS	.	G	THR/ALA	1129,3277	400.6+/-331.6	146,837,1220	66.0	65.0	65.0		25	-0.7	0.0	14	dbSNP_52	65	4102,4498	560.5+/-387.6	1007,2088,1205	yes	missense	SERPINA3	NM_001085.4	58	1153,2925,2425	AA,AG,GG		47.6977,25.6241,40.2199	possibly-damaging	9/424	95080803	5231,7775	2203	4300	6503	SO:0001583	missense	12	exon2			CTCCTGGCTCTGG	K01500	CCDS32150.1	14q32.1	2014-06-03	2005-08-18		ENSG00000196136	ENSG00000196136		"""Serine (or cysteine) peptidase inhibitors"""	16	protein-coding gene	gene with protein product		107280	"""alpha-1-antichymotrypsin"", ""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3"""	AACT		3260956, 24172014	Standard	NM_001085		Approved	ACT, alpha-1-antichymotrypsin	uc001ydp.3	P01011	OTTHUMG00000029851	ENST00000467132.1:c.25G>A	14.37:g.95080803G>A	ENSP00000450540:p.Ala9Thr	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_001085	B3KVQ7|Q13703|Q2TU87|Q2TU88|Q59GP9|Q6LBY8|Q6LDT7|Q6NSC9|Q8N177|Q96DW8|Q9UC47|Q9UNU9	Missense_Mutation	SNP	ENST00000467132.1	37	CCDS32150.1	952	0.4358974358974359	100	0.2032520325203252	108	0.2983425414364641	371	0.6486013986013986	373	0.4920844327176781	G	14.13	2.443510	0.43429	0.256241	0.476977	ENSG00000196136	ENST00000553947;ENST00000393078;ENST00000393080;ENST00000555820;ENST00000467132;ENST00000380354	D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26	4.61	-0.687	0.11320	Serpin domain (1);	1.376250	0.04847	N	0.441646	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.30851	0.121;0.297	B;B	0.31751	0.019;0.135	T	0.37430	-0.9706	9	0.23891	T	0.37	.	0.7578	0.01001	0.3256:0.1603:0.3502:0.1639	rs4934;rs7399;rs1065214;rs1065661;rs3168981;rs17753472;rs52816435;rs59552549;rs4934	9;34	P01011;G3V5I3	AACT_HUMAN;.	T	34;9;9;9;9;9	ENSP00000452367:A34T;ENSP00000376793:A9T;ENSP00000376795:A9T;ENSP00000450540:A9T	ENSP00000369712:A9T	A	+	1	0	SERPINA3	94150556	0.002000	0.14202	0.006000	0.13384	0.579000	0.36224	-0.060000	0.11712	-0.020000	0.14032	-0.258000	0.10820	GCT	G|0.587;A|0.413	0.413	strong		0.582	SERPINA3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268080.3	NM_001085	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12V	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,NS,adenocarcinoma,0,25136	KRAS	30930	25136	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35T						PASS	.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	211	89	0.421801	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
FAM209B	388799	hgsc.bcm.edu	37	20	55108589	55108589	+	Missense_Mutation	SNP	G	G	T	rs386815439		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:55108589G>T	ENST00000371325.1	+	1	288	c.192G>T	c.(190-192)ttG>ttT	p.L64F		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	64						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TCTGGCTTTTGTTTGCTGTTG	0.483																																					p.L64F		Atlas-SNP	.											.	.	.	.	0			c.G192T						PASS	.						168.0	146.0	153.0					20																	55108589		2203	4300	6503	SO:0001583	missense	388799	exon1			GCTTTTGTTTGCT	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.192G>T	20.37:g.55108589G>T	ENSP00000360376:p.Leu64Phe	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	260	19	0.0730769	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	G	0.325	-0.959853	0.02267	.	.	ENSG00000213714	ENST00000371325	T	0.08896	3.04	2.8	-3.7	0.04437	.	1.580090	0.04046	N	0.303922	T	0.04137	0.0115	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38090	-0.9677	10	0.07990	T	0.79	0.1847	4.0099	0.09618	0.0:0.2385:0.3799:0.3817	.	64	Q5JX69	CT107_HUMAN	F	64	ENSP00000360376:L64F	ENSP00000360376:L64F	L	+	3	2	C20orf107	54541996	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-1.684000	0.01932	-1.037000	0.03283	-0.782000	0.03352	TTG	.	.	none		0.483	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
PLA2G4D	283748	hgsc.bcm.edu	37	15	42371752	42371752	+	Missense_Mutation	SNP	A	A	T	rs4924618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:42371752A>T	ENST00000290472.3	-	13	1394	c.1300T>A	c.(1300-1302)Tcc>Acc	p.S434T		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	434	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		S -> T (in dbSNP:rs4924618).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		TGCAGCATGGACTCCAGCACT	0.711													A|||	1502	0.29992	0.1634	0.4726	5008	,	,		15047	0.3958		0.3429	False		,,,				2504	0.2188				p.S434T		Atlas-SNP	.											PLA2G4D,NS,carcinoma,0,1	PLA2G4D	72	1	0			c.T1300A						PASS	.	A	THR/SER	864,3540		81,702,1419	22.0	24.0	23.0		1300	1.3	0.2	15	dbSNP_111	23	2980,5614		521,1938,1838	yes	missense	PLA2G4D	NM_178034.3	58	602,2640,3257	TT,TA,AA		34.6754,19.6185,29.5738	benign	434/819	42371752	3844,9154	2202	4297	6499	SO:0001583	missense	283748	exon13			GCATGGACTCCAG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1300T>A	15.37:g.42371752A>T	ENSP00000290472:p.Ser434Thr	Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	12	12	1	NM_178034	Q8N176	Missense_Mutation	SNP	ENST00000290472.3	37	CCDS32203.1	710	0.3250915750915751	67	0.13617886178861788	160	0.4419889502762431	215	0.3758741258741259	268	0.35356200527704484	A	13.24	2.179065	0.38511	0.196185	0.346754	ENSG00000159337	ENST00000290472	T	0.04502	3.61	5.0	1.28	0.21552	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.813383	0.11149	N	0.594335	T	0.00012	0.0000	L	0.33485	1.01	0.40941	P	0.015539999999999998	B	0.27264	0.173	B	0.21151	0.033	T	0.41413	-0.9510	9	0.23891	T	0.37	-1.1751	3.7273	0.08480	0.6594:0.1369:0.0728:0.1309	rs4924618	434	Q86XP0	PA24D_HUMAN	T	434	ENSP00000290472:S434T	ENSP00000290472:S434T	S	-	1	0	PLA2G4D	40159044	0.086000	0.21541	0.183000	0.23137	0.987000	0.75469	0.628000	0.24522	-0.029000	0.13827	0.459000	0.35465	TCC	A|0.716;T|0.284	0.284	strong		0.711	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
SCNN1D	6339	hgsc.bcm.edu	37	1	1222622	1222622	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1222622G>A	ENST00000338555.2	+	6	1905	c.761G>A	c.(760-762)aGc>aAc	p.S254N	SCNN1D_ENST00000400928.3_Missense_Mutation_p.S254N|SCNN1D_ENST00000379116.5_Missense_Mutation_p.S418N|SCNN1D_ENST00000325425.8_Missense_Mutation_p.S320N			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	254					ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	AGCCACGGGAGCCAGGACGGC	0.677																																					p.S418N		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G1253A						PASS	.						22.0	20.0	21.0					1																	1222622		2169	4249	6418	SO:0001583	missense	6339	exon9			ACGGGAGCCAGGA	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.761G>A	1.37:g.1222622G>A	ENSP00000339504:p.Ser254Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	79	75	0.949367	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	37		.	.	.	.	.	.	.	.	.	.	G	8.390	0.839506	0.16891	.	.	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928;ENST00000379099	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	4.4	-0.589	0.11683	.	8.235220	0.00166	N	0.000001	T	0.53286	0.1787	L	0.51422	1.61	0.09310	N	1	B;B	0.32968	0.392;0.003	B;B	0.33960	0.173;0.001	T	0.26360	-1.0105	10	0.27785	T	0.31	.	2.8715	0.05618	0.2348:0.1198:0.5233:0.1222	.	254;418	P51172;A6NNF7	SCNND_HUMAN;.	N	285;418;254;320;254;45	ENSP00000368411:S418N;ENSP00000339504:S254N;ENSP00000321594:S320N;ENSP00000383717:S254N	ENSP00000321594:S320N	S	+	2	0	SCNN1D	1212485	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.212000	0.09319	0.280000	0.22209	0.313000	0.20887	AGC	.	.	none		0.677	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
SLC44A5	204962	hgsc.bcm.edu	37	1	75702674	75702674	+	Silent	SNP	G	G	A	rs17096508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:75702674G>A	ENST00000370855.5	-	11	851	c.738C>T	c.(736-738)ctC>ctT	p.L246L	SLC44A5_ENST00000535611.1_Silent_p.L116L|SLC44A5_ENST00000370859.3_Silent_p.L246L	NM_152697.4	NP_689910.2	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	246					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						TCACTTACATGAGAATCCAAT	0.318													G|||	582	0.116214	0.1172	0.0821	5008	,	,		18032	0.0397		0.2008	False		,,,				2504	0.1309				p.L246L		Atlas-SNP	.											.	SLC44A5	231	.	0			c.C738T						PASS	.	G	,	531,3875	238.7+/-250.0	36,459,1708	64.0	58.0	60.0		738,738	3.5	1.0	1	dbSNP_123	60	1819,6781	322.9+/-315.8	194,1431,2675	no	coding-synonymous,coding-synonymous	SLC44A5	NM_001130058.1,NM_152697.4	,	230,1890,4383	AA,AG,GG		21.1512,12.0517,18.0686	,	246/718,246/720	75702674	2350,10656	2203	4300	6503	SO:0001819	synonymous_variant	204962	exon11			TTACATGAGAATC	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370855.5:c.738C>T	1.37:g.75702674G>A		Somatic	322	1	0.00310559		WXS	Illumina HiSeq	Phase_I	366	161	0.439891	NM_152697	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Silent	SNP	ENST00000370855.5	37	CCDS667.1																																																																																			G|0.845;A|0.155	0.155	strong		0.318	SLC44A5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026921.1	NM_152697	
CD79B	974	hgsc.bcm.edu	37	17	62007498	62007498	+	Silent	SNP	A	A	G	rs2070776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:62007498A>G	ENST00000006750.3	-	3	458	c.366T>C	c.(364-366)tgT>tgC	p.C122C	CD79B_ENST00000349817.2_Intron|CD79B_ENST00000392795.3_Silent_p.C123C	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	122	Ig-like V-type.				B cell receptor signaling pathway (GO:0050853)|immune response (GO:0006955)|signal transduction (GO:0007165)	B cell receptor complex (GO:0019815)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.C122C(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						ACTTCTGCTGACAGAAGTAGA	0.577			"""Mis, O"""		DLBCL								G|||	2813	0.561701	0.6974	0.4841	5008	,	,		21845	0.4881		0.6531	False		,,,				2504	0.4151				p.C123C		Atlas-SNP	.		Dom	yes		17	17q23	974	"""CD79b molecule, immunoglobulin-associated beta"""		L	CD79B,NS,carcinoma,0,1	CD79B	38	1	1	Substitution - coding silent(1)	stomach(1)	c.T369C						PASS	.	G	,,	2967,1439	466.2+/-354.4	996,975,232	127.0	102.0	111.0		366,369,	0.6	0.1	17	dbSNP_96	111	5612,2988	462.5+/-365.7	1846,1920,534	no	coding-synonymous,coding-synonymous,intron	CD79B	NM_000626.2,NM_001039933.1,NM_021602.2	,,	2842,2895,766	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	34.7442,32.66,34.0381	,,	122/230,123/231,	62007498	8579,4427	2203	4300	6503	SO:0001819	synonymous_variant	974	exon3			CTGCTGACAGAAG	L27587	CCDS11655.1, CCDS11656.1, CCDS42372.1	17q23	2014-09-17	2006-03-28			ENSG00000007312		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1699	protein-coding gene	gene with protein product		147245	"""CD79B antigen (immunoglobulin-associated beta)"""	IGB		9545642	Standard	XM_005257858		Approved	B29	uc002jdp.1	P40259		ENST00000006750.3:c.366T>C	17.37:g.62007498A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	107	105	0.981308	NM_001039933	Q53FS2|Q9BU06	Silent	SNP	ENST00000006750.3	37	CCDS11655.1																																																																																			A|0.371;G|0.629	0.629	strong		0.577	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1		
FAM189A1	23359	hgsc.bcm.edu	37	15	29544656	29544656	+	Silent	SNP	T	T	C	rs4583203	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:29544656T>C	ENST00000261275.4	-	3	302	c.303A>G	c.(301-303)gcA>gcG	p.A101A		NM_015307.1	NP_056122.1	O60320	F1891_HUMAN	family with sequence similarity 189, member A1	101						integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(2)|kidney(1)|lung(1)|stomach(1)	7						TTACACACACTGCAGAAAGCA	0.398													T|||	2500	0.499201	0.2231	0.4885	5008	,	,		17356	0.6339		0.5835	False		,,,				2504	0.6544				p.A101A		Atlas-SNP	.											FAM189A1,NS,carcinoma,-1,1	FAM189A1	20	1	0			c.A303G						PASS	.	T		379,1005		53,273,366	143.0	112.0	121.0		303	-5.2	0.6	15	dbSNP_111	121	1907,1275		566,775,250	no	coding-synonymous	FAM189A1	NM_015307.1		619,1048,616	CC,CT,TT		40.0691,27.3844,49.9343		101/540	29544656	2286,2280	692	1591	2283	SO:0001819	synonymous_variant	23359	exon3			ACACACTGCAGAA		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.303A>G	15.37:g.29544656T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	191	93	0.486911	NM_015307	A0PK09	Silent	SNP	ENST00000261275.4	37	CCDS45198.1																																																																																			T|0.529;C|0.471	0.471	strong		0.398	FAM189A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417254.1	NM_015307	
MMEL1	79258	hgsc.bcm.edu	37	1	2526746	2526746	+	Missense_Mutation	SNP	A	A	G	rs3748816	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2526746A>G	ENST00000378412.3	-	16	1714	c.1553T>C	c.(1552-1554)aTg>aCg	p.M518T	MMEL1_ENST00000502556.1_Missense_Mutation_p.M361T|MMEL1_ENST00000288709.6_Missense_Mutation_p.M509T			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	518			M -> T (in dbSNP:rs3748816). {ECO:0000269|PubMed:15489334}.			endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		GCGCCTGTTCATCTCCTCCAG	0.647													G|||	2711	0.541334	0.7284	0.487	5008	,	,		15245	0.5407		0.332	False		,,,				2504	0.5429				p.M518T		Atlas-SNP	.											.	MMEL1	64	.	0			c.T1553C						PASS	.	G	THR/MET	3002,1404	459.8+/-352.4	1022,958,223	70.0	66.0	67.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1553	-5.5	0.0	1	dbSNP_107	67	2892,5708	671.0+/-402.8	487,1918,1895	yes	missense	MMEL1	NM_033467.3	81	1509,2876,2118	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	33.6279,31.8656,45.3175	benign	518/780	2526746	5894,7112	2203	4300	6503	SO:0001583	missense	79258	exon16			CTGTTCATCTCCT	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.1553T>C	1.37:g.2526746A>G	ENSP00000367668:p.Met518Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	152	151	0.993421	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	37	CCDS30569.2	1043	0.4775641025641026	347	0.7052845528455285	165	0.4558011049723757	278	0.486013986013986	253	0.3337730870712401	G	0	-2.755514	0.00085	0.681344	0.336279	ENSG00000142606	ENST00000378411;ENST00000288709;ENST00000378412;ENST00000502556	D;D;D	0.81579	-1.51;-1.51;-1.51	4.89	-5.48	0.02592	.	1.727810	0.02496	N	0.089927	T	0.00012	0.0000	N	0.00446	-1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	9	0.08381	T	0.77	-0.0773	2.1612	0.03825	0.1136:0.2449:0.3589:0.2826	rs3748816;rs61663127;rs3748816	518	Q495T6	MMEL1_HUMAN	T	361;509;518;361	ENSP00000288709:M509T;ENSP00000367668:M518T;ENSP00000422492:M361T	ENSP00000288709:M509T	M	-	2	0	MMEL1	2516606	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.199000	0.00561	-1.671000	0.01466	-2.367000	0.00236	ATG	A|0.529;G|0.471	0.471	strong		0.647	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
GPR126	57211	hgsc.bcm.edu	37	6	142737048	142737048	+	Missense_Mutation	SNP	C	C	T	rs186655757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:142737048C>T	ENST00000230173.6	+	20	3261	c.2785C>T	c.(2785-2787)Ctt>Ttt	p.L929F	GPR126_ENST00000367609.3_Missense_Mutation_p.L929F|GPR126_ENST00000367608.2_Missense_Mutation_p.L901F|GPR126_ENST00000296932.8_Missense_Mutation_p.L901F	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	929					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)		TGTGGATGGACTTTGCATTGC	0.463													C|||	22	0.00439297	0.0	0.0043	5008	,	,		16398	0.0		0.002	False		,,,				2504	0.0174				p.L929F		Atlas-SNP	.											.	GPR126	192	.	0			c.C2785T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	0,3976		0,0,1988	208.0	201.0	203.0		2701,2701,2785,2785	5.4	0.7	6		203	16,8336		0,16,4160	yes	missense,missense,missense,missense	GPR126	NM_001032394.2,NM_001032395.2,NM_020455.5,NM_198569.2	22,22,22,22	0,16,6148	TT,TC,CC		0.1916,0.0,0.1298	probably-damaging,probably-damaging,probably-damaging,probably-damaging	901/1194,901/1223,929/1222,929/1251	142737048	16,12312	1988	4176	6164	SO:0001583	missense	57211	exon20			GATGGACTTTGCA	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.2785C>T	6.37:g.142737048C>T	ENSP00000230173:p.Leu929Phe	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	55	11	0.2	NM_198569	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	19.84	3.902673	0.72754	0.0	0.001916	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609	T;T;T;T	0.39592	1.07;1.07;1.07;1.07	5.4	5.4	0.78164	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000014	T	0.63462	0.2513	M	0.81341	2.54	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	T	0.65623	-0.6123	10	0.56958	D	0.05	.	19.5245	0.95199	0.0:1.0:0.0:0.0	.	901;929;901;929	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4	.;.;.;GP126_HUMAN	F	929;901;901;929	ENSP00000230173:L929F;ENSP00000356580:L901F;ENSP00000296932:L901F;ENSP00000356581:L929F	ENSP00000230173:L929F	L	+	1	0	GPR126	142778741	1.000000	0.71417	0.687000	0.30102	0.309000	0.27889	4.661000	0.61518	2.694000	0.91930	0.650000	0.86243	CTT	C|0.998;T|0.002	0.002	strong		0.463	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
C17orf98	388381	hgsc.bcm.edu	37	17	36997461	36997461	+	Missense_Mutation	SNP	G	G	A	rs7210156	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36997461G>A	ENST00000398575.4	-	1	247	c.182C>T	c.(181-183)cCg>cTg	p.P61L		NM_001080465.2	NP_001073934.1	A8MV24	CQ098_HUMAN	chromosome 17 open reading frame 98	61			P -> L (in dbSNP:rs7210156).							endometrium(5)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(3)	14						CAAAAGGGGCGGAACCACGTG	0.582													G|||	375	0.0748802	0.1195	0.0432	5008	,	,		12441	0.0496		0.0646	False		,,,				2504	0.0736				p.P61L		Atlas-SNP	.											.	C17orf98	34	.	0			c.C182T						PASS	.	G	LEU/PRO	348,3522		13,322,1600	56.0	56.0	56.0		182	4.1	1.0	17	dbSNP_116	56	597,7665		19,559,3553	yes	missense	C17orf98	NM_001080465.2	98	32,881,5153	AA,AG,GG		7.2259,8.9922,7.7893	benign	61/155	36997461	945,11187	1935	4131	6066	SO:0001583	missense	388381	exon1			AGGGGCGGAACCA	AC006449, DY654789	CCDS42310.1	17q12	2014-05-06			ENSG00000214556	ENSG00000275489			34492	protein-coding gene	gene with protein product						16625196	Standard	NM_001080465		Approved	LOC388381	uc002hqv.2	A8MV24	OTTHUMG00000188506	ENST00000398575.4:c.182C>T	17.37:g.36997461G>A	ENSP00000381580:p.Pro61Leu	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_001080465		Missense_Mutation	SNP	ENST00000398575.4	37	CCDS42310.1	149	0.06822344322344322	50	0.1016260162601626	20	0.055248618784530384	33	0.057692307692307696	46	0.06068601583113457	G	15.64	2.893532	0.52121	0.089922	0.072259	ENSG00000214556	ENST00000398575	T	0.45276	0.9	5.16	4.14	0.48551	.	0.554257	0.13184	U	0.407254	T	0.00936	0.0031	L	0.50333	1.59	0.23180	P	0.99816711	P	0.50710	0.938	B	0.39419	0.299	T	0.10894	-1.0610	9	0.49607	T	0.09	-20.2728	7.7622	0.28959	0.0:0.1629:0.6462:0.1909	rs7210156;rs52804942;rs59176984;rs7210156	61	A8MV24	CQ098_HUMAN	L	61	ENSP00000381580:P61L	ENSP00000381580:P61L	P	-	2	0	C17orf98	34250987	0.979000	0.34478	0.999000	0.59377	0.938000	0.57974	1.436000	0.34980	2.687000	0.91594	0.462000	0.41574	CCG	G|0.926;A|0.074	0.074	strong		0.582	C17orf98-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255469.2	NM_001080465	
RBM5	10181	hgsc.bcm.edu	37	3	50153356	50153356	+	Silent	SNP	T	T	C	rs1138536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50153356T>C	ENST00000347869.3	+	22	2212	c.2037T>C	c.(2035-2037)taT>taC	p.Y679Y	RP11-493K19.3_ENST00000437204.1_RNA|RP11-493K19.3_ENST00000425674.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	679	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGGACATCTATCGACGATCCA	0.438													C|||	3743	0.747404	0.7458	0.6945	5008	,	,		22551	0.8819		0.5686	False		,,,				2504	0.8323				p.Y679Y		Atlas-SNP	.											.	RBM5	76	.	0			c.T2037C						PASS	.	C		3176,1230	424.0+/-340.3	1145,886,172	108.0	110.0	109.0		2037	2.0	1.0	3	dbSNP_86	109	4904,3696	529.7+/-381.6	1370,2164,766	no	coding-synonymous	RBM5	NM_005778.2		2515,3050,938	CC,CT,TT		42.9767,27.9165,37.8748		679/816	50153356	8080,4926	2203	4300	6503	SO:0001819	synonymous_variant	10181	exon22			CATCTATCGACGA	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.2037T>C	3.37:g.50153356T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			T|0.328;C|0.672	0.672	strong		0.438	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
HERC2	8924	hgsc.bcm.edu	37	15	28420676	28420676	+	Silent	SNP	C	C	T	rs139728053	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28420676C>T	ENST00000261609.7	-	64	9921	c.9813G>A	c.(9811-9813)gcG>gcA	p.A3271A		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)		AGTCCGTGACCGCCAGGCAGT	0.662													C|||	5	0.000998403	0.0	0.0	5008	,	,		16999	0.005		0.0	False		,,,				2504	0.0				p.A3271A		Atlas-SNP	.											.	HERC2	501	.	0			c.G9813A						PASS	.	C		0,4406		0,0,2203	38.0	30.0	33.0		9813	-7.9	0.9	15	dbSNP_134	33	1,8587		0,1,4293	no	coding-synonymous	HERC2	NM_004667.4		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		3271/4835	28420676	1,12993	2203	4294	6497	SO:0001819	synonymous_variant	8924	exon64			CGTGACCGCCAGG	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.9813G>A	15.37:g.28420676C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|1.000;T|0.000	0.000	weak		0.662	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
PCDHGB7	56099	hgsc.bcm.edu	37	5	140797630	140797630	+	Silent	SNP	G	G	T	rs2015825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140797630G>T	ENST00000398594.2	+	1	204	c.204G>T	c.(202-204)gtG>gtT	p.V68V	PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	68	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCTGCGAGTGAGCGCGGAGA	0.572													t|||	2709	0.540935	0.8419	0.6182	5008	,	,		14025	0.3244		0.4225	False		,,,				2504	0.4243				p.V68V		Atlas-SNP	.											.	PCDHGB7	117	.	0			c.G204T						PASS	.	T	,,,,,,,,,,,,,,,,,	3121,775		1265,591,92	70.0	77.0	75.0		,,,,,,,,,,,,,,,204,,204	-4.5	0.9	5	dbSNP_92	75	3568,4730		755,2058,1336	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032101.2	,,,,,,,,,,,,,,,,,	2020,2649,1428	TT,TG,GG		42.9983,19.8922,45.1452	,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,68/930,,68/809	140797630	6689,5505	1948	4149	6097	SO:0001819	synonymous_variant	56099	exon1			GCGAGTGAGCGCG	AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.204G>T	5.37:g.140797630G>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	144	142	0.986111	NM_018927	Q9UN63	Silent	SNP	ENST00000398594.2	37	CCDS47293.1																																																																																			G|0.500;T|0.500	0.500	strong		0.572	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
GTDC1	79712	hgsc.bcm.edu	37	2	144899559	144899559	+	Missense_Mutation	SNP	C	C	A	rs3731958	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:144899559C>A	ENST00000392869.2	-	5	563	c.411G>T	c.(409-411)atG>atT	p.M137I	GTDC1_ENST00000409214.1_Missense_Mutation_p.M137I|GTDC1_ENST00000392867.3_Missense_Mutation_p.M137I|GTDC1_ENST00000463875.2_Missense_Mutation_p.M8I|GTDC1_ENST00000344850.4_Missense_Mutation_p.M137I|GTDC1_ENST00000241391.5_Missense_Mutation_p.M137I|GTDC1_ENST00000542155.1_Missense_Mutation_p.M137I|GTDC1_ENST00000409298.1_Missense_Mutation_p.M137I	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	137			M -> I (in dbSNP:rs3731958). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15068588}.		biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		TAAATTTTCCCATGGAAGTGA	0.408													A|||	3424	0.683706	0.7443	0.7104	5008	,	,		18668	0.8413		0.5447	False		,,,				2504	0.5634				p.M137I		Atlas-SNP	.											.	GTDC1	61	.	0			c.G411T						PASS	.	A	ILE/MET,ILE/MET,ILE/MET	3209,1197	415.0+/-337.0	1146,917,140	69.0	72.0	71.0		411,411,411	4.9	1.0	2	dbSNP_107	71	4206,4392	582.1+/-391.3	1036,2134,1129	yes	missense,missense,missense	GTDC1	NM_001006636.3,NM_001164629.2,NM_024659.4	10,10,10	2182,3051,1269	AA,AC,CC		48.9184,27.1675,42.9791	benign,benign,benign	137/459,137/459,137/374	144899559	7415,5589	2203	4299	6502	SO:0001583	missense	79712	exon6			TTTTCCCATGGAA	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.411G>T	2.37:g.144899559C>A	ENSP00000376608:p.Met137Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	123	59	0.479675	NM_001006636	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Missense_Mutation	SNP	ENST00000392869.2	37	CCDS33300.1	1487	0.6808608058608059	364	0.7398373983739838	234	0.6464088397790055	473	0.8269230769230769	416	0.5488126649076517	A	5.380	0.255412	0.10185	0.728325	0.489184	ENSG00000121964	ENST00000392869;ENST00000409214;ENST00000392867;ENST00000409298;ENST00000542155;ENST00000241391;ENST00000344850;ENST00000463875;ENST00000437114	T;T;T;T;T;T;T;T;T	0.78707	1.15;1.15;1.15;-1.2;1.15;1.15;1.15;1.78;1.15	6.11	4.9	0.64082	Glycosyltransferase family 1, N-terminal (1);	0.046782	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00193	-1.875	0.50467	P	1.24000000000013E-4	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.42832	-0.9428	9	0.02654	T	1	-19.5844	13.0113	0.58733	0.7461:0.2539:0.0:0.0	rs3731958;rs17690312;rs52829764;rs61347201;rs3731958	137;137;137;137;137	G1UFN1;Q4AE62-2;B8ZZ45;Q4AE62;Q4AE62-3	.;.;.;GTDC1_HUMAN;.	I	137;137;137;137;137;137;137;8;137	ENSP00000376608:M137I;ENSP00000386581:M137I;ENSP00000376606:M137I;ENSP00000386691:M137I;ENSP00000438323:M137I;ENSP00000241391:M137I;ENSP00000339750:M137I;ENSP00000437964:M8I;ENSP00000403869:M137I	ENSP00000241391:M137I	M	-	3	0	GTDC1	144616029	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	1.888000	0.39708	1.134000	0.42165	-0.256000	0.11100	ATG	C|0.374;A|0.625	0.625	strong		0.408	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659	
GRID2IP	392862	hgsc.bcm.edu	37	7	6547902	6547902	+	Missense_Mutation	SNP	G	G	A	rs112305062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6547902G>A	ENST00000457091.2	-	13	2257	c.2258C>T	c.(2257-2259)cCg>cTg	p.P753L	GRID2IP_ENST00000452113.1_Missense_Mutation_p.P562L|GRID2IP_ENST00000435185.1_Missense_Mutation_p.P569L	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	753	Pro-rich.				long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						GGGGCTGAGCGGGGGTGGGGG	0.657													G|||	401	0.0800719	0.0098	0.196	5008	,	,		4499	0.0685		0.1054	False		,,,				2504	0.0787				p.P753L		Atlas-SNP	.											.	GRID2IP	82	.	0			c.C2258T						PASS	.						6.0	6.0	6.0					7																	6547902		684	1570	2254	SO:0001583	missense	392862	exon13			CTGAGCGGGGGTG		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.2258C>T	7.37:g.6547902G>A	ENSP00000397351:p.Pro753Leu	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	107	51	0.476636	NM_001145118		Missense_Mutation	SNP	ENST00000457091.2	37	CCDS47537.1	210	0.09615384615384616	19	0.03861788617886179	78	0.2154696132596685	37	0.06468531468531469	76	0.10026385224274406	g	15.29	2.789692	0.50102	.	.	ENSG00000215045	ENST00000452113;ENST00000435185;ENST00000457091	T;T;T	0.57107	0.46;0.45;0.42	3.75	3.75	0.43078	.	0.000000	0.85682	U	0.000000	T	0.00073	0.0002	L	0.61218	1.895	0.09310	P	0.99999281359	D	0.89917	1.0	D	0.74023	0.982	T	0.02885	-1.1098	9	0.54805	T	0.06	.	13.4078	0.60924	0.0:0.0:1.0:0.0	.	753	A4D2P6	GRD2I_HUMAN	L	562;569;753	ENSP00000397887:P562L;ENSP00000408364:P569L;ENSP00000397351:P753L	ENSP00000408364:P569L	P	-	2	0	GRID2IP	6514427	1.000000	0.71417	0.614000	0.29051	0.845000	0.48019	5.766000	0.68843	1.814000	0.52955	0.558000	0.71614	CCG	G|0.908;A|0.092	0.092	strong		0.657	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
B4GALT2	8704	hgsc.bcm.edu	37	1	44451234	44451234	+	Silent	SNP	C	C	T	rs1061781	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:44451234C>T	ENST00000356836.6	+	6	1699	c.909C>T	c.(907-909)atC>atT	p.I303I	B4GALT2_ENST00000372324.1_Silent_p.I303I|B4GALT2_ENST00000481924.1_3'UTR|B4GALT2_ENST00000309519.7_Silent_p.I332I|B4GALT2_ENST00000434555.2_Silent_p.I237I	NM_001005417.2|NM_030587.2	NP_001005417.1|NP_085076.2	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	303					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)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)	p.I303I(1)		endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)	ACATCCGAATCGGCCGCTACC	0.587													c|||	468	0.0934505	0.0477	0.0778	5008	,	,		10726	0.1528		0.1004	False		,,,				2504	0.0982				p.I332I		Atlas-SNP	.											B4GALT2,NS,carcinoma,0,1	B4GALT2	35	1	1	Substitution - coding silent(1)	stomach(1)	c.C996T						PASS	.	C	,,	278,4128	156.6+/-189.7	15,248,1940	149.0	129.0	136.0		909,909,996	0.3	1.0	1	dbSNP_86	136	880,7720	199.0+/-243.2	40,800,3460	no	coding-synonymous,coding-synonymous,coding-synonymous	B4GALT2	NM_001005417.2,NM_003780.4,NM_030587.2	,,	55,1048,5400	TT,TC,CC		10.2326,6.3096,8.9036	,,	303/373,303/373,332/402	44451234	1158,11848	2203	4300	6503	SO:0001819	synonymous_variant	8704	exon6			CCGAATCGGCCGC	AF038660	CCDS506.1, CCDS55596.1	1p34-p33	2013-02-19			ENSG00000117411	ENSG00000117411		"""Beta 4-glycosyltransferases"""	925	protein-coding gene	gene with protein product		604013				9405390, 9597550	Standard	NM_003780		Approved	beta4Gal-T2	uc010okl.2	O60909	OTTHUMG00000008296	ENST00000356836.6:c.909C>T	1.37:g.44451234C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_030587	B3KTP0|B4DE14|D3DPY6|D3DPY7|O60511|Q4V9L9|Q5T4X5|Q5T4Y5|Q9BUP6|Q9NSY7	Silent	SNP	ENST00000356836.6	37	CCDS506.1																																																																																			C|0.910;T|0.090	0.090	strong		0.587	B4GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022840.1	NM_003780	
NRDE2	55051	hgsc.bcm.edu	37	14	90756760	90756760	+	Silent	SNP	A	A	T	rs3742671	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:90756760A>T	ENST00000354366.3	-	10	2266	c.2034T>A	c.(2032-2034)acT>acA	p.T678T	NRDE2_ENST00000357904.3_Silent_p.T447T	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	678																	GGTTGAAAAAAGTCAAGGGCT	0.507													A|||	594	0.11861	0.0272	0.1916	5008	,	,		18696	0.0774		0.167	False		,,,				2504	0.183				p.T678T		Atlas-SNP	.											.	.	.	.	0			c.T2034A						PASS	.	A	,	235,4171	138.0+/-173.8	8,219,1976	49.0	52.0	51.0		2034,1341	-1.0	0.0	14	dbSNP_107	51	1710,6890	309.7+/-309.5	169,1372,2759	no	coding-synonymous,coding-synonymous	C14orf102	NM_017970.3,NM_199043.1	,	177,1591,4735	TT,TA,AA		19.8837,5.3336,14.9546	,	678/1165,447/934	90756760	1945,11061	2203	4300	6503	SO:0001819	synonymous_variant	55051	exon10			GAAAAAAGTCAAG	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 102"""	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.2034T>A	14.37:g.90756760A>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	113	68	0.60177	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Silent	SNP	ENST00000354366.3	37	CCDS9890.1																																																																																			A|0.861;T|0.139	0.139	strong		0.507	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970	
NUP133	55746	hgsc.bcm.edu	37	1	229635521	229635521	+	Silent	SNP	A	A	G	rs10916495	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:229635521A>G	ENST00000261396.3	-	5	649	c.558T>C	c.(556-558)taT>taC	p.Y186Y	NUP133_ENST00000366678.3_Silent_p.Y186Y|NUP133_ENST00000537506.1_Silent_p.Y170Y	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	186					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.Y186Y(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GGCTTGGCCAATAGCGGATAG	0.453													A|||	883	0.176318	0.1369	0.2896	5008	,	,		17612	0.1577		0.2028	False		,,,				2504	0.1411				p.Y186Y		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - coding silent(1)	stomach(1)	c.T558C						PASS	.	A		650,3756	276.0+/-272.9	50,550,1603	94.0	91.0	92.0		558	-2.6	1.0	1	dbSNP_120	92	1811,6789	325.4+/-316.9	190,1431,2679	no	coding-synonymous	NUP133	NM_018230.2		240,1981,4282	GG,GA,AA		21.0581,14.7526,18.922		186/1157	229635521	2461,10545	2203	4300	6503	SO:0001819	synonymous_variant	55746	exon5			TGGCCAATAGCGG		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.558T>C	1.37:g.229635521A>G		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	37	CCDS1579.1																																																																																			A|0.813;G|0.187	0.187	strong		0.453	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
INTS4	92105	hgsc.bcm.edu	37	11	77635882	77635882	+	Silent	SNP	A	A	C	rs7119720	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:77635882A>C	ENST00000534064.1	-	12	1462	c.1428T>G	c.(1426-1428)gtT>gtG	p.V476V	INTS4_ENST00000529807.1_Silent_p.V476V|INTS4_ENST00000525931.1_5'UTR	NM_033547.3	NP_291025.3	Q96HW7	INT4_HUMAN	integrator complex subunit 4	476					snRNA processing (GO:0016180)	integrator complex (GO:0032039)			INTS4/GAB2(2)	NS(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(5)|upper_aerodigestive_tract(1)	32	all_cancers(14;4.53e-19)|all_epithelial(13;1.73e-21)|Breast(9;2.71e-16)|Ovarian(111;0.152)		Epithelial(5;1.13e-46)|all cancers(3;8.92e-44)|BRCA - Breast invasive adenocarcinoma(5;8.4e-26)|OV - Ovarian serous cystadenocarcinoma(8;1.05e-23)			CTTTGGTTGAAACATTAGTAC	0.353													A|||	871	0.173922	0.1687	0.1427	5008	,	,		20915	0.1478		0.2068	False		,,,				2504	0.1963				p.V476V		Atlas-SNP	.											.	INTS4	89	.	0			c.T1428G						PASS	.	A		763,3625		57,649,1488	25.0	25.0	25.0		1428	0.7	1.0	11	dbSNP_116	25	1735,6825		166,1403,2711	no	coding-synonymous	INTS4	NM_033547.3		223,2052,4199	CC,CA,AA		20.2687,17.3883,19.2926		476/964	77635882	2498,10450	2194	4280	6474	SO:0001819	synonymous_variant	92105	exon12			GGTTGAAACATTA	BC015664	CCDS31644.1	11q14.1	2006-04-26			ENSG00000149262	ENSG00000149262			25048	protein-coding gene	gene with protein product		611348				16239144	Standard	NM_033547		Approved	INT4, MGC16733, MST093	uc001oys.3	Q96HW7	OTTHUMG00000166629	ENST00000534064.1:c.1428T>G	11.37:g.77635882A>C		Somatic	348	0	0		WXS	Illumina HiSeq	Phase_I	348	154	0.442529	NM_033547	Q2YD62|Q6PJG4|Q7Z4E7|Q96G32|Q96GA1|Q9BRC0	Silent	SNP	ENST00000534064.1	37	CCDS31644.1																																																																																			A|0.818;C|0.182	0.182	strong		0.353	INTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390927.1	NM_033547	
WDR63	126820	hgsc.bcm.edu	37	1	85594466	85594466	+	Missense_Mutation	SNP	G	G	A	rs709783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:85594466G>A	ENST00000294664.6	+	21	2573	c.2393G>A	c.(2392-2394)cGc>cAc	p.R798H	WDR63_ENST00000370596.1_Missense_Mutation_p.R759H|WDR63_ENST00000326813.8_Missense_Mutation_p.R759H	NM_145172.3	NP_660155.2	Q8IWG1	WDR63_HUMAN	WD repeat domain 63	798			R -> H (in dbSNP:rs709783).							NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)	36				all cancers(265;0.00391)|Epithelial(280;0.00922)|Colorectal(170;0.166)		ACATTAAGTCGCCCTTCCACC	0.323													G|||	1090	0.217652	0.3245	0.2406	5008	,	,		18925	0.2133		0.1829	False		,,,				2504	0.0971				p.R798H		Atlas-SNP	.											WDR63,colon,carcinoma,0,1	WDR63	91	1	0			c.G2393A						PASS	.	G	HIS/ARG	1338,3068	427.6+/-341.6	215,908,1080	76.0	78.0	78.0		2393	3.5	1.0	1	dbSNP_86	78	1448,7152	274.5+/-291.2	132,1184,2984	yes	missense	WDR63	NM_145172.3	29	347,2092,4064	AA,AG,GG		16.8372,30.3677,21.4209	benign	798/892	85594466	2786,10220	2203	4300	6503	SO:0001583	missense	126820	exon21			TAAGTCGCCCTTC		CCDS702.1, CCDS72818.1	1p22.3	2014-02-21	2013-02-19	2013-02-19	ENSG00000162643	ENSG00000162643		"""WD repeat domain containing"""	30711	protein-coding gene	gene with protein product						21953912	Standard	XM_005270438		Approved	DIC3, FLJ30067, NYD-SP29	uc001dkt.3	Q8IWG1	OTTHUMG00000009953	ENST00000294664.6:c.2393G>A	1.37:g.85594466G>A	ENSP00000294664:p.Arg798His	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_145172	A8K988|Q96L72|Q96NU4	Missense_Mutation	SNP	ENST00000294664.6	37	CCDS702.1	520	0.23809523809523808	160	0.3252032520325203	93	0.2569060773480663	134	0.23426573426573427	133	0.17546174142480211	G	1.362	-0.588500	0.03799	0.303677	0.168372	ENSG00000162643	ENST00000370596;ENST00000326813;ENST00000294664;ENST00000484007	T;T;T;T	0.39406	1.08;1.08;1.08;1.08	5.81	3.49	0.39957	.	0.394740	0.30686	N	0.009081	T	0.06050	0.0157	N	0.01529	-0.815	0.37425	P	0.08620499999999998	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.20773	-1.0265	9	0.30078	T	0.28	-11.261	9.9147	0.41427	0.8588:0.0:0.1412:0.0	rs709783;rs11564847;rs17121817;rs57576192;rs709783	759;798	Q8IWG1-2;Q8IWG1	.;WDR63_HUMAN	H	759;759;798;80	ENSP00000359628:R759H;ENSP00000317463:R759H;ENSP00000294664:R798H;ENSP00000435544:R80H	ENSP00000294664:R798H	R	+	2	0	WDR63	85367054	0.925000	0.31364	1.000000	0.80357	0.760000	0.43138	1.110000	0.31147	0.466000	0.27193	-0.384000	0.06662	CGC	G|0.780;A|0.220	0.220	strong		0.323	WDR63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027565.2	NM_145172	
RALGAPA1	253959	hgsc.bcm.edu	37	14	36191030	36191030	+	Silent	SNP	A	A	G	rs2296168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:36191030A>G	ENST00000389698.3	-	16	2520	c.2130T>C	c.(2128-2130)gtT>gtC	p.V710V	RALGAPA1_ENST00000554704.1_5'UTR|RALGAPA1_ENST00000258840.6_Silent_p.V710V|RALGAPA1_ENST00000307138.6_Silent_p.V710V|RALGAPA1_ENST00000382366.3_Silent_p.V710V	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	710					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGTCAACTGAAACTTTCTGAA	0.423													A|||	793	0.158347	0.1392	0.0677	5008	,	,		18289	0.3978		0.0408	False		,,,				2504	0.1227				p.V710V		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.T2130C						PASS	.	A	,	625,3781	268.6+/-268.5	43,539,1621	82.0	79.0	80.0		2130,2130	-0.2	1.0	14	dbSNP_100	80	384,8216	125.0+/-183.6	13,358,3929	no	coding-synonymous,coding-synonymous	RALGAPA1	NM_014990.1,NM_194301.2	,	56,897,5550	GG,GA,AA		4.4651,14.1852,7.758	,	710/2037,710/2084	36191030	1009,11997	2203	4300	6503	SO:0001819	synonymous_variant	253959	exon16			AACTGAAACTTTC	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2130T>C	14.37:g.36191030A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Silent	SNP	ENST00000389698.3	37	CCDS32065.1																																																																																			A|0.890;G|0.110	0.110	strong		0.423	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
ZNF469	84627	hgsc.bcm.edu	37	16	88502208	88502208	+	Missense_Mutation	SNP	A	A	T	rs3812954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88502208A>T	ENST00000437464.1	+	2	8246	c.8246A>T	c.(8245-8247)gAc>gTc	p.D2749V	ZNF469_ENST00000565624.1_Missense_Mutation_p.D2777V	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2749			D -> V (in dbSNP:rs3812954).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						CCTGCGGAGGACAGCAGCAGG	0.652													A|||	218	0.0435304	0.0068	0.0432	5008	,	,		16230	0.0427		0.0984	False		,,,				2504	0.0378				p.D2749V		Atlas-SNP	.											.	ZNF469	121	.	0			c.A8246T						PASS	.	A	VAL/ASP	16,1368		1,14,677	45.0	62.0	57.0		8246	2.2	0.0	16	dbSNP_107	57	239,2943		7,225,1359	yes	missense	ZNF469	NM_001127464.1	152	8,239,2036	TT,TA,AA		7.511,1.1561,5.5848	possibly-damaging	2749/3926	88502208	255,4311	692	1591	2283	SO:0001583	missense	84627	exon2			CGGAGGACAGCAG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.8246A>T	16.37:g.88502208A>T	ENSP00000402343:p.Asp2749Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	123	0.05631868131868132	6	0.012195121951219513	23	0.06353591160220995	27	0.0472027972027972	67	0.08839050131926121	A	11.24	1.580640	0.28180	0.011561	0.07511	ENSG00000225614	ENST00000437464	T	0.07567	3.18	4.56	2.24	0.28232	.	.	.	.	.	T	0.00210	0.0006	N	0.19112	0.55	0.80722	P	0.0	P	0.46512	0.879	B	0.37943	0.261	T	0.38887	-0.9640	8	0.62326	D	0.03	.	5.1164	0.14836	0.544:0.3576:0.0984:0.0	rs3812954	2749	Q96JG9	ZN469_HUMAN	V	2749	ENSP00000402343:D2749V	ENSP00000402343:D2749V	D	+	2	0	ZNF469	87029709	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.155000	0.10115	0.136000	0.18733	0.459000	0.35465	GAC	A|0.944;T|0.056	0.056	strong		0.652	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
GRID2	2895	hgsc.bcm.edu	37	4	94137954	94137954	+	Silent	SNP	G	G	A	rs75225211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:94137954G>A	ENST00000282020.4	+	6	1113	c.855G>A	c.(853-855)cgG>cgA	p.R285R	GRID2_ENST00000510992.1_Silent_p.R190R|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	285					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		CGATTATTCGGCAGACATTTC	0.408													G|||	20	0.00399361	0.0008	0.0014	5008	,	,		16944	0.0		0.0179	False		,,,				2504	0.0				p.R285R		Atlas-SNP	.											GRID2,NS,malignant_melanoma,+2,1	GRID2	233	1	0			c.G855A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	157.0	150.0	152.0		855	-2.1	1.0	4	dbSNP_131	152	105,8495	57.2+/-118.5	0,105,4195	no	coding-synonymous	GRID2	NM_001510.2		0,117,6386	AA,AG,GG		1.2209,0.2724,0.8996		285/1008	94137954	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	2895	exon6			TATTCGGCAGACA	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.855G>A	4.37:g.94137954G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Silent	SNP	ENST00000282020.4	37	CCDS3637.1																																																																																			G|0.990;A|0.010	0.010	strong		0.408	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2		
NOTCH3	4854	hgsc.bcm.edu	37	19	15291576	15291576	+	Missense_Mutation	SNP	C	C	G	rs35769976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15291576C>G	ENST00000263388.2	-	19	3133	c.3058G>C	c.(3058-3060)Gcc>Ccc	p.A1020P		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1020	EGF-like 26. {ECO:0000255|PROSITE- ProRule:PRU00076}.		A -> P (in dbSNP:rs35769976).		forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			AGGCAATAGGCCCCAGTCTGG	0.632													C|||	552	0.110224	0.3669	0.0375	5008	,	,		17984	0.001		0.0129	False		,,,				2504	0.0276				p.A1020P		Atlas-SNP	.											.	NOTCH3	340	.	0			c.G3058C	GRCh37	CM085589	NOTCH3	M	rs35769976	PASS	.	C	PRO/ALA	1294,3106		226,842,1132	39.0	35.0	37.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3058	1.4	0.0	19	dbSNP_126	37	122,8478		0,122,4178	yes	missense	NOTCH3	NM_000435.2	27	226,964,5310	GG,GC,CC		1.4186,29.4091,10.8923	benign	1020/2322	15291576	1416,11584	2200	4300	6500	SO:0001583	missense	4854	exon19			AATAGGCCCCAGT	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.3058G>C	19.37:g.15291576C>G	ENSP00000263388:p.Ala1020Pro	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	183	0.08379120879120878	149	0.30284552845528456	22	0.06077348066298342	0	0.0	12	0.0158311345646438	C	9.463	1.093538	0.20471	0.294091	0.014186	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.91792	-2.91	5.13	1.44	0.22558	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.32190	N	0.006458	T	0.00012	0.0000	N	0.26130	0.795	0.43965	P	0.003354999999999997	B;B	0.21309	0.054;0.027	B;B	0.28638	0.092;0.075	T	0.04128	-1.0975	9	0.37606	T	0.19	.	7.3526	0.26700	0.0:0.6162:0.1375:0.2462	rs35769976;rs60155197	971;1020	Q59FL3;Q9UM47	.;NOTC3_HUMAN	P	1020;970	ENSP00000263388:A1020P	ENSP00000263388:A1020P	A	-	1	0	NOTCH3	15152576	0.000000	0.05858	0.018000	0.16275	0.401000	0.30781	-1.039000	0.03550	0.569000	0.29329	0.563000	0.77884	GCC	C|0.886;G|0.114	0.114	strong		0.632	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
HSD17B14	51171	hgsc.bcm.edu	37	19	49334991	49334991	+	Silent	SNP	C	C	T	rs62127966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49334991C>T	ENST00000263278.4	-	5	569	c.303G>A	c.(301-303)gaG>gaA	p.E101E	HSD17B14_ENST00000599157.1_Intron	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	101					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GGGCAGAGGTCTCCTCAGGCC	0.642													C|||	329	0.0656949	0.0076	0.0951	5008	,	,		14585	0.0		0.2048	False		,,,				2504	0.0481				p.E101E		Atlas-SNP	.											.	HSD17B14	25	.	0			c.G303A						PASS	.	C		191,4215	116.3+/-154.2	8,175,2020	51.0	54.0	53.0		303	2.0	1.0	19	dbSNP_129	53	1740,6860	307.2+/-308.3	163,1414,2723	no	coding-synonymous	HSD17B14	NM_016246.2		171,1589,4743	TT,TC,CC		20.2326,4.335,14.847		101/271	49334991	1931,11075	2203	4300	6503	SO:0001819	synonymous_variant	51171	exon5			AGAGGTCTCCTCA	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.303G>A	19.37:g.49334991C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	144	55	0.381944	NM_016246	Q9UKU3	Silent	SNP	ENST00000263278.4	37	CCDS12736.1																																																																																			C|0.873;T|0.127	0.127	strong		0.642	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
TSSK2	23617	hgsc.bcm.edu	37	22	19119938	19119938	+	Silent	SNP	G	G	A	rs1052773	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19119938G>A	ENST00000399635.2	+	1	1618	c.1026G>A	c.(1024-1026)agG>agA	p.R342R	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	342					multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					AGACCTCCAGGGCCAAAGACC	0.632													G|||	1081	0.215855	0.2867	0.1527	5008	,	,		16419	0.1448		0.1809	False		,,,				2504	0.274				p.R342R		Atlas-SNP	.											.	TSSK2	29	.	0			c.G1026A						PASS	.	G	,	1081,3317		132,817,1250	36.0	37.0	37.0		,1026	2.2	0.2	22	dbSNP_86	37	1559,7015		173,1213,2901	no	utr-3,coding-synonymous	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,	305,2030,4151	AA,AG,GG		18.1829,24.5794,20.3515	,	,342/359	19119938	2640,10332	2199	4287	6486	SO:0001819	synonymous_variant	23617	exon1			CTCCAGGGCCAAA	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.1026G>A	22.37:g.19119938G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_053006	Q8IY55	Silent	SNP	ENST00000399635.2	37	CCDS13755.1																																																																																			A|0.201;C|0.006	0.201	strong		0.632	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
GPR133	283383	hgsc.bcm.edu	37	12	131471699	131471699	+	Missense_Mutation	SNP	G	G	A	rs61732860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:131471699G>A	ENST00000261654.5	+	6	1109	c.550G>A	c.(550-552)Gtc>Atc	p.V184I	RP11-76C10.5_ENST00000542980.1_lincRNA|GPR133_ENST00000535015.1_Missense_Mutation_p.V216I	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	184					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V184I(1)		NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GAAAGTCTACGTCAACGGGAC	0.517													G|||	44	0.00878594	0.0008	0.0202	5008	,	,		20919	0.0		0.0209	False		,,,				2504	0.0082				p.V184I		Atlas-SNP	.											GPR133,NS,carcinoma,0,1	GPR133	136	1	1	Substitution - Missense(1)	prostate(1)	c.G550A						PASS	.	G	ILE/VAL	15,4391	22.3+/-47.3	0,15,2188	115.0	107.0	110.0		550	3.7	1.0	12	dbSNP_129	110	173,8427	79.5+/-142.1	3,167,4130	yes	missense	GPR133	NM_198827.3	29	3,182,6318	AA,AG,GG		2.0116,0.3404,1.4455	possibly-damaging	184/875	131471699	188,12818	2203	4300	6503	SO:0001583	missense	283383	exon6			GTCTACGTCAACG	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.550G>A	12.37:g.131471699G>A	ENSP00000261654:p.Val184Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	9.840	1.190859	0.21954	0.003404	0.020116	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015	T;T;T	0.74526	-0.85;-0.85;-0.85	4.55	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.146844	0.46442	N	0.000283	T	0.43478	0.1249	L	0.28014	0.82	0.80722	D	1	B;B	0.28512	0.003;0.214	B;B	0.24006	0.01;0.05	T	0.48917	-0.8992	10	0.33141	T	0.24	.	11.9058	0.52711	0.0852:0.0:0.9148:0.0	rs61732860	216;184	B7ZLF7;Q6QNK2	.;GP133_HUMAN	I	184;124;216	ENSP00000261654:V184I;ENSP00000442501:V124I;ENSP00000444425:V216I	ENSP00000261654:V184I	V	+	1	0	GPR133	130037652	0.991000	0.36638	0.999000	0.59377	0.690000	0.40134	2.351000	0.44071	0.912000	0.36772	-0.126000	0.14955	GTC	G|0.985;A|0.015	0.015	strong		0.517	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
AK8	158067	hgsc.bcm.edu	37	9	135753629	135753629	+	Missense_Mutation	SNP	A	A	G	rs2231400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135753629A>G	ENST00000298545.3	-	1	535	c.14T>C	c.(13-15)aTc>aCc	p.I5T	AK8_ENST00000477396.1_5'UTR|C9orf9_ENST00000372136.3_5'UTR|C9orf9_ENST00000350499.6_5'Flank|C9orf9_ENST00000356311.5_5'Flank	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	5			I -> T (in dbSNP:rs2231400).		nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						GTGCGGGGCGATAGTGGCGTC	0.701													G|||	587	0.117212	0.3555	0.0605	5008	,	,		12654	0.002		0.0427	False		,,,				2504	0.0307				p.I5T		Atlas-SNP	.											.	AK8	45	.	0			c.T14C						PASS	.	G	THR/ILE	1329,3077		228,873,1102	37.0	33.0	35.0		14	1.5	0.0	9	dbSNP_98	35	382,8216		14,354,3931	yes	missense	AK8	NM_152572.2	89	242,1227,5033	GG,GA,AA		4.4429,30.1634,13.1575	benign	5/480	135753629	1711,11293	2203	4299	6502	SO:0001583	missense	158067	exon1			GGGGCGATAGTGG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"""Adenylate kinases"""	26526	protein-coding gene	gene with protein product		615365	"""chromosome 9 open reading frame 98"""	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.14T>C	9.37:g.135753629A>G	ENSP00000298545:p.Ile5Thr	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_152572	A8K821|Q8N9W9	Missense_Mutation	SNP	ENST00000298545.3	37	CCDS6954.1	209	0.09569597069597069	153	0.31097560975609756	21	0.058011049723756904	0	0.0	35	0.04617414248021108	G	0.022	-1.414199	0.01145	0.301634	0.044429	ENSG00000165695	ENST00000298545	T	0.65178	-0.14	4.62	1.49	0.22878	.	0.932048	0.09057	N	0.854846	T	0.00012	0.0000	N	0.00538	-1.39	0.58432	P	4.000000000004E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29518	-1.0009	9	0.10111	T	0.7	-4.0202	11.827	0.52273	0.0741:0.4465:0.4795:0.0	rs2231400;rs2231400	5;5	Q8N9Z7;Q96MA6	.;KAD8_HUMAN	T	5	ENSP00000298545:I5T	ENSP00000298545:I5T	I	-	2	0	AK8	134743450	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.520000	0.22878	-0.182000	0.10602	-3.955000	0.00015	ATC	A|0.871;G|0.129	0.129	strong		0.701	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572	
RIPK3	11035	hgsc.bcm.edu	37	14	24805463	24805463	+	Missense_Mutation	SNP	G	G	T	rs3212254	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24805463G>T	ENST00000216274.5	-	10	1693	c.1475C>A	c.(1474-1476)cCa>cAa	p.P492Q	ADCY4_ENST00000554068.2_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000396747.3_5'Flank|RP11-934B9.3_ENST00000555591.1_Intron	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	492			P -> Q (in dbSNP:rs3212254). {ECO:0000269|PubMed:17344846}.		activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		ACCTACTGGTGGGGGGTGCTG	0.547													G|||	602	0.120208	0.239	0.036	5008	,	,		15712	0.1339		0.0537	False		,,,				2504	0.0736				p.P492Q	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C1475A						PASS	.	G	GLN/PRO	886,3520	343.1+/-307.5	92,702,1409	74.0	77.0	76.0		1475	1.9	0.0	14	dbSNP_105	76	486,8114	141.1+/-197.5	13,460,3827	yes	missense	RIPK3	NM_006871.3	76	105,1162,5236	TT,TG,GG		5.6512,20.1089,10.549	benign	492/519	24805463	1372,11634	2203	4300	6503	SO:0001583	missense	11035	exon10			ACTGGTGGGGGGT	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1475C>A	14.37:g.24805463G>T	ENSP00000216274:p.Pro492Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Missense_Mutation	SNP	ENST00000216274.5	37	CCDS9628.1	233	0.10668498168498168	108	0.21951219512195122	15	0.04143646408839779	67	0.11713286713286714	43	0.05672823218997362	G	7.107	0.575327	0.13623	0.201089	0.056512	ENSG00000129465	ENST00000216274	T	0.77620	-1.11	2.77	1.86	0.25419	.	0.903075	0.09280	N	0.823841	T	0.00109	0.0003	N	0.12182	0.205	0.80722	P	0.0	D	0.76494	0.999	D	0.65010	0.931	T	0.12116	-1.0560	9	0.52906	T	0.07	-0.7917	7.7066	0.28653	0.0:0.2611:0.7389:0.0	rs3212254;rs3212254	492	Q9Y572	RIPK3_HUMAN	Q	492	ENSP00000216274:P492Q	ENSP00000216274:P492Q	P	-	2	0	RIPK3	23875303	0.009000	0.17119	0.002000	0.10522	0.078000	0.17371	1.803000	0.38863	0.719000	0.32188	-0.304000	0.09214	CCA	G|0.896;T|0.104	0.104	strong		0.547	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
FHDC1	85462	hgsc.bcm.edu	37	4	153874666	153874666	+	Missense_Mutation	SNP	G	G	A	rs61753649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:153874666G>A	ENST00000511601.1	+	3	702	c.514G>A	c.(514-516)Gca>Aca	p.A172T	FHDC1_ENST00000260008.3_Missense_Mutation_p.A172T			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	172	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.								ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					TATTTTGGATGCAAAACGGAG	0.303													G|||	389	0.0776757	0.0946	0.0807	5008	,	,		19369	0.121		0.0229	False		,,,				2504	0.0644				p.A172T		Atlas-SNP	.											.	FHDC1	102	.	0			c.G514A						PASS	.	G	THR/ALA	361,4043	182.2+/-210.1	25,311,1866	127.0	130.0	129.0		514	5.1	1.0	4	dbSNP_129	129	132,8468	66.3+/-128.7	1,130,4169	yes	missense	FHDC1	NM_033393.2	58	26,441,6035	AA,AG,GG		1.5349,8.1971,3.7911	probably-damaging	172/1144	153874666	493,12511	2202	4300	6502	SO:0001583	missense	85462	exon2			TTGGATGCAAAAC	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.514G>A	4.37:g.153874666G>A	ENSP00000427567:p.Ala172Thr	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	65	32	0.492308	NM_033393		Missense_Mutation	SNP	ENST00000511601.1	37	CCDS34081.1	176	0.08058608058608059	49	0.09959349593495935	23	0.06353591160220995	85	0.1486013986013986	19	0.025065963060686015	G	22.2	4.258580	0.80246	0.081971	0.015349	ENSG00000137460	ENST00000511601;ENST00000260008	T;T	0.63255	-0.03;-0.03	5.91	5.05	0.67936	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.227351	0.46145	D	0.000309	T	0.01061	0.0035	L	0.60845	1.875	0.24711	P	0.99320252	D	0.76494	0.999	D	0.70716	0.97	T	0.32161	-0.9917	9	0.59425	D	0.04	.	14.0088	0.64483	0.0:0.0:0.7249:0.2751	rs61753649	172	Q9C0D6	FHDC1_HUMAN	T	172	ENSP00000427567:A172T;ENSP00000260008:A172T	ENSP00000260008:A172T	A	+	1	0	FHDC1	154094116	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.609000	0.54117	1.456000	0.47831	0.655000	0.94253	GCA	G|0.954;A|0.046	0.046	strong		0.303	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393	
SLC26A3	1811	hgsc.bcm.edu	37	7	107423254	107423254	+	Silent	SNP	C	C	T	rs3735605	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:107423254C>T	ENST00000340010.5	-	11	1483	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	SLC26A3_ENST00000422236.2_Silent_p.A398A	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	433					anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						TTTGTAGAGGCGCCAGGAGAA	0.413													C|||	756	0.150958	0.0552	0.1369	5008	,	,		18734	0.2758		0.175	False		,,,				2504	0.137				p.A433A		Atlas-SNP	.											SLC26A3,caecum,carcinoma,0,1	SLC26A3	120	1	0			c.G1299A						scavenged	.	C		328,4078	174.4+/-204.0	16,296,1891	86.0	85.0	85.0		1299	-0.1	0.1	7	dbSNP_107	85	1523,7077	287.5+/-298.3	148,1227,2925	no	coding-synonymous	SLC26A3	NM_000111.2		164,1523,4816	TT,TC,CC		17.7093,7.4444,14.2319		433/765	107423254	1851,11155	2203	4300	6503	SO:0001819	synonymous_variant	1811	exon11			TAGAGGCGCCAGG	L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"""Solute carriers"""	3018	protein-coding gene	gene with protein product		126650	"""congenital chloride diarrhea"", ""solute carrier family 26, member 3"""	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.1299G>A	7.37:g.107423254C>T		Somatic	77	1	0.012987		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_000111		Silent	SNP	ENST00000340010.5	37	CCDS5748.1																																																																																			C|0.847;T|0.153	0.153	strong		0.413	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111	
CEP170	9859	hgsc.bcm.edu	37	1	243328887	243328887	+	Nonsense_Mutation	SNP	G	G	T	rs2728433		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:243328887G>T	ENST00000366542.1	-	13	2426	c.2375C>A	c.(2374-2376)tCa>tAa	p.S792*	CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366544.1_Nonsense_Mutation_p.S694*|RP11-261C10.4_ENST00000422938.1_RNA|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Nonsense_Mutation_p.S694*	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	792						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.S792*(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			AGAATGTCCTGAATTTTTTTC	0.398																																					p.S792X		Atlas-SNP	.											CEP170,extremity,malignant_melanoma,0,1	CEP170	153	1	1	Substitution - Nonsense(1)	skin(1)	c.C2375A						scavenged	.						85.0	80.0	81.0					1																	243328887		1846	4111	5957	SO:0001587	stop_gained	9859	exon13			TGTCCTGAATTTT	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2375C>A	1.37:g.243328887G>T	ENSP00000355500:p.Ser792*	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	148	3	0.0202703	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Nonsense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.986185|3.986185	0.74589|0.74589	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543	.|.	.|.	.|.	5.34|5.34	0.747|0.747	0.18371|0.18371	.|.	.|0.921055	.|0.09339	.|N	.|0.815762	T|.	0.31263|.	0.0791|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.31779|.	-0.9931|.	4|.	.|.	.|.	.|.	1.7324|1.7324	6.9628|6.9628	0.24608|0.24608	0.2357:0.0:0.6372:0.1271|0.2357:0.0:0.6372:0.1271	.|.	.|.	.|.	.|.	K|X	756|792;694;694	.|.	.|.	Q|S	-|-	1|2	0|0	CEP170|CEP170	241395510|241395510	0.785000|0.785000	0.28726|0.28726	0.030000|0.030000	0.17652|0.17652	0.547000|0.547000	0.35210|0.35210	1.683000|1.683000	0.37638|0.37638	0.240000|0.240000	0.21263|0.21263	0.555000|0.555000	0.69702|0.69702	CAG|TCA	T|0.500;G|0.500	0.500	weak		0.398	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
PARM1	25849	hgsc.bcm.edu	37	4	75938179	75938179	+	Silent	SNP	G	G	A	rs3775527	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:75938179G>A	ENST00000307428.7	+	2	800	c.588G>A	c.(586-588)ccG>ccA	p.P196P	RP11-44F21.2_ENST00000513770.1_RNA|PARM1_ENST00000513238.1_Intron	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	196					positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)		p.P196P(1)		cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						CAGAGTCCCCGACAGAGGAGT	0.567													G|||	1599	0.319289	0.2542	0.2637	5008	,	,		19672	0.1627		0.4523	False		,,,				2504	0.4714				p.P196P		Atlas-SNP	.											PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	1	Substitution - coding silent(1)	stomach(1)	c.G588A						PASS	.	G		1183,3093		180,823,1135	161.0	175.0	171.0		588	-5.0	0.0	4	dbSNP_107	171	3600,4922		772,2056,1433	no	coding-synonymous	PARM1	NM_015393.3		952,2879,2568	AA,AG,GG		42.2436,27.666,37.373		196/311	75938179	4783,8015	2138	4261	6399	SO:0001819	synonymous_variant	25849	exon2			GTCCCCGACAGAG	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"""Prostatic androgen-repressed message 1"", ""Castration-induced prostatic apoptosis-related protein 1"", ""WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"""					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.588G>A	4.37:g.75938179G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	124	123	0.991935	NM_015393	B3KMQ9|Q96DV8|Q9Y4S1	Silent	SNP	ENST00000307428.7	37	CCDS47077.1																																																																																			G|0.698;A|0.302	0.302	strong		0.567	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393	
STEAP2	261729	hgsc.bcm.edu	37	7	89861832	89861832	+	Missense_Mutation	SNP	G	G	A	rs194524	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:89861832G>A	ENST00000287908.3	+	5	1760	c.1367G>A	c.(1366-1368)cGa>cAa	p.R456Q	STEAP2_ENST00000394621.2_Missense_Mutation_p.R456Q|STEAP2_ENST00000394626.1_Intron|STEAP2_ENST00000394622.2_Missense_Mutation_p.R456Q|STEAP2_ENST00000394632.1_Intron|STEAP2_ENST00000394629.2_Intron|STEAP2_ENST00000402625.2_Intron	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	456			R -> Q (in dbSNP:rs194524). {ECO:0000269|PubMed:12429817}.		copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					TGTATAAGCCGAAAGCTAAAA	0.393													G|||	1652	0.329872	0.2685	0.3862	5008	,	,		16904	0.1825		0.5119	False		,,,				2504	0.3374				p.R456Q		Atlas-SNP	.											.	STEAP2	78	.	0			c.G1367A						PASS	.	G	GLN/ARG,,GLN/ARG	1434,2972	456.5+/-351.3	242,950,1011	80.0	79.0	79.0		1367,,1367	1.9	1.0	7	dbSNP_79	79	4542,4056	589.2+/-392.5	1217,2108,974	yes	missense,intron,missense	STEAP2	NM_001040665.1,NM_001040666.1,NM_152999.3	43,,43	1459,3058,1985	AA,AG,GG		47.1738,32.5465,45.9551	benign,,benign	456/491,,456/491	89861832	5976,7028	2203	4299	6502	SO:0001583	missense	261729	exon6			TAAGCCGAAAGCT	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"""prostate cancer associated protein 1"", ""six transmembrane epithelial antigen of the prostate 2"""	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.1367G>A	7.37:g.89861832G>A	ENSP00000287908:p.Arg456Gln	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	122	121	0.991803	NM_001040665	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Missense_Mutation	SNP	ENST00000287908.3	37	CCDS5615.1	791	0.36217948717948717	143	0.29065040650406504	146	0.40331491712707185	108	0.1888111888111888	394	0.5197889182058048	G	16.10	3.026150	0.54683	0.325465	0.528262	ENSG00000157214	ENST00000287908;ENST00000394622;ENST00000394621	T;T;T	0.05258	3.47;3.47;3.47	5.67	1.91	0.25777	.	0.231260	0.40640	N	0.001049	T	0.00012	0.0000	M	0.70595	2.14	0.34633	P	0.280215	B	0.10296	0.003	B	0.11329	0.006	T	0.36792	-0.9733	9	0.48119	T	0.1	-0.1413	8.8654	0.35282	0.3459:0.0:0.654:0.0	rs194524;rs11563933;rs17688661;rs194524	456	Q8NFT2	STEA2_HUMAN	Q	456	ENSP00000287908:R456Q;ENSP00000378120:R456Q;ENSP00000378119:R456Q	ENSP00000287908:R456Q	R	+	2	0	STEAP2	89699768	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	1.918000	0.40006	0.080000	0.16959	0.644000	0.83932	CGA	G|0.606;A|0.394	0.394	strong		0.393	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999	
LENG9	94059	hgsc.bcm.edu	37	19	54973307	54973307	+	Missense_Mutation	SNP	C	C	T	rs115799049	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54973307C>T	ENST00000333834.4	-	1	1587	c.1469G>A	c.(1468-1470)gGg>gAg	p.G490E		NM_198988.1	NP_945339.2	Q96B70	LENG9_HUMAN	leukocyte receptor cluster (LRC) member 9	490							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)		CTGGAAAGGCCCCCCTGTCCT	0.622													C|||	80	0.0159744	0.003	0.0274	5008	,	,		15399	0.001		0.0457	False		,,,				2504	0.0102				p.G490E		Atlas-SNP	.											.	LENG9	46	.	0			c.G1469A						PASS	.	C	GLU/GLY	32,4374	39.2+/-71.8	0,32,2171	51.0	59.0	57.0		1469	-5.9	0.0	19	dbSNP_132	57	309,8291	107.4+/-168.2	1,307,3992	yes	missense	LENG9	NM_198988.1	98	1,339,6163	TT,TC,CC		3.593,0.7263,2.6219	benign	490/502	54973307	341,12665	2203	4300	6503	SO:0001583	missense	94059	exon1			AAAGGCCCCCCTG	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.1469G>A	19.37:g.54973307C>T	ENSP00000331647:p.Gly490Glu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_198988	B2VAM3	Missense_Mutation	SNP	ENST00000333834.4	37	CCDS12895.2	41	0.018772893772893772	2	0.0040650406504065045	11	0.03038674033149171	1	0.0017482517482517483	27	0.03562005277044855	C	11.54	1.669688	0.29693	0.007263	0.03593	ENSG00000182909	ENST00000333834	T	0.46451	0.87	4.98	-5.94	0.02247	RNA ligase/cyclic nucleotide phosphodiesterase (1);	0.274738	0.33916	U	0.004426	T	0.07369	0.0186	L	0.50333	1.59	0.09310	N	1	B	0.20052	0.041	B	0.25614	0.062	T	0.12041	-1.0563	10	0.33141	T	0.24	-0.0382	7.5113	0.27575	0.0:0.2166:0.1344:0.649	.	490	Q96B70	LENG9_HUMAN	E	490	ENSP00000331647:G490E	ENSP00000331647:G490E	G	-	2	0	LENG9	59665119	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.447000	0.02396	-0.793000	0.04475	0.655000	0.94253	GGG	C|0.977;T|0.023	0.023	strong		0.622	LENG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140806.3	NM_198988	
ERCC6	2074	hgsc.bcm.edu	37	10	50678369	50678369	+	Missense_Mutation	SNP	T	T	C	rs2228527	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50678369T>C	ENST00000355832.5	-	18	3715	c.3637A>G	c.(3637-3639)Aga>Gga	p.R1213G	ERCC6_ENST00000542458.1_Missense_Mutation_p.R583G|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1213			R -> G (in dbSNP:rs2228527). {ECO:0000269|PubMed:19894250, 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						TTGGCGTCTCTGCAATGCTTA	0.443								Direct reversal of damage;Nucleotide excision repair (NER)					T|||	925	0.184704	0.1452	0.2104	5008	,	,		19648	0.0437		0.2087	False		,,,				2504	0.3405				p.L1213V		Atlas-SNP	.											.	ERCC6	162	.	0			c.C3637G	GRCh37	CM980633	ERCC6	M	rs2228527	PASS	.	T	GLY/ARG	688,3718	288.1+/-279.7	70,548,1585	337.0	321.0	326.0		3637	1.9	0.0	10	dbSNP_98	326	1870,6730	333.3+/-320.5	198,1474,2628	yes	missense	ERCC6	NM_000124.2	125	268,2022,4213	CC,CT,TT		21.7442,15.6151,19.6678	possibly-damaging	1213/1494	50678369	2558,10448	2203	4300	6503	SO:0001583	missense	2074	exon18			CGTCTCTGCAATG	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.3637A>G	10.37:g.50678369T>C	ENSP00000348089:p.Arg1213Gly	Somatic	405	1	0.00246914		WXS	Illumina HiSeq	Phase_I	403	401	0.995037	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	356	0.163003663003663	75	0.1524390243902439	83	0.2292817679558011	30	0.05244755244755245	168	0.22163588390501318	T	11.21	1.572105	0.28092	0.156151	0.217442	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.83591	-1.74;-1.48	5.65	1.87	0.25490	.	.	.	.	.	T	0.00109	0.0003	M	0.72118	2.19	0.80722	P	0.0	P	0.38922	0.651	B	0.32677	0.15	T	0.01071	-1.1461	8	0.27785	T	0.31	-8.3756	8.6269	0.33895	0.0:0.0653:0.3698:0.5649	rs2228527;rs17702436;rs56512951;rs60642826;rs2228527	1213	Q03468	ERCC6_HUMAN	G	1213;590;583	ENSP00000348089:R1213G;ENSP00000445134:R583G	ENSP00000348089:R1213G	R	-	1	2	ERCC6	50348375	0.572000	0.26668	0.042000	0.18584	0.716000	0.41182	1.716000	0.37981	0.122000	0.18314	-0.316000	0.08728	AGA	T|0.820;C|0.180	0.180	strong		0.443	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
MUC2	4583	hgsc.bcm.edu	37	11	1093274	1093274	+	Missense_Mutation	SNP	C	C	T	rs11245949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1093274C>T	ENST00000441003.2	+	30	5120	c.5093C>T	c.(5092-5094)tCg>tTg	p.S1698L	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.S1665L|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)	accccaacatcgacacccatc	0.637													N|||	2435	0.486222	0.4826	0.4899	5008	,	,		22392	0.631		0.3608	False		,,,				2504	0.4683				p.S1698L		Atlas-SNP	.											.	MUC2	614	.	0			c.C5093T						PASS	.						129.0	167.0	154.0					11																	1093274		1842	3364	5206	SO:0001583	missense	4583	exon30			CAACATCGACACC	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.5093C>T	11.37:g.1093274C>T	ENSP00000415183:p.Ser1698Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	47	14	0.297872	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	T	1.748	-0.490089	0.04322	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.08370	3.13;3.1	0.851	-1.7	0.08159	.	227.466000	0.04577	U	0.394340	T	0.06005	0.0156	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40979	-0.9534	9	0.30854	T	0.27	.	5.5277	0.16967	0.0:0.5285:0.0:0.4715	rs11245949;rs59265712	1698	E7EUV1	.	L	1698;1665	ENSP00000415183:S1698L;ENSP00000351956:S1665L	ENSP00000351956:S1665L	S	+	2	0	MUC2	1083274	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.256000	0.18351	-1.248000	0.02503	-2.819000	0.00109	TCG	C|1.000;|0.000	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
CCDC108	255101	hgsc.bcm.edu	37	2	219895548	219895548	+	Missense_Mutation	SNP	C	C	A	rs56411706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219895548C>A	ENST00000341552.5	-	9	1107	c.1024G>T	c.(1024-1026)Gcc>Tcc	p.A342S	CCDC108_ENST00000441968.1_Missense_Mutation_p.A342S|CCDC108_ENST00000409865.3_Missense_Mutation_p.A331S|CCDC108_ENST00000453220.1_Missense_Mutation_p.A342S|CCDC108_ENST00000410037.1_Missense_Mutation_p.A277S	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	342						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCAGCTGGGCGCACTTGGCT	0.637													C|||	858	0.171326	0.3222	0.1066	5008	,	,		15229	0.1726		0.0964	False		,,,				2504	0.089				p.A342S		Atlas-SNP	.											.	CCDC108	208	.	0			c.G1024T						PASS	.	C	SER/ALA	1234,3172	418.3+/-338.2	173,888,1142	38.0	40.0	39.0		1024	2.0	0.9	2	dbSNP_129	39	849,7751	193.2+/-239.0	37,775,3488	yes	missense	CCDC108	NM_194302.2	99	210,1663,4630	AA,AC,CC		9.8721,28.0073,16.0157	possibly-damaging	342/1926	219895548	2083,10923	2203	4300	6503	SO:0001583	missense	255101	exon9			GCTGGGCGCACTT	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.1024G>T	2.37:g.219895548C>A	ENSP00000340776:p.Ala342Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	358	0.16391941391941392	149	0.30284552845528456	37	0.10220994475138122	99	0.17307692307692307	73	0.09630606860158311	C	11.61	1.689268	0.29962	0.280073	0.098721	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220;ENST00000409865;ENST00000410037;ENST00000441164	T;T;T;T;T	0.06449	3.57;3.57;3.57;3.3;3.31	4.97	1.99	0.26369	.	0.318910	0.22850	N	0.054861	T	0.00012	0.0000	L	0.55481	1.735	0.09310	P	1.0	P;P	0.39535	0.677;0.677	B;B	0.41374	0.355;0.355	T	0.51371	-0.8714	9	0.23302	T	0.38	-17.5074	9.2326	0.37446	0.0:0.3853:0.5221:0.0925	rs56411706	331;342	E9PG25;Q6ZU64	.;CC108_HUMAN	S	342;342;342;331;277;276	ENSP00000340776:A342S;ENSP00000413377:A342S;ENSP00000409117:A342S;ENSP00000386945:A331S;ENSP00000386258:A277S	ENSP00000340776:A342S	A	-	1	0	CCDC108	219603792	0.118000	0.22208	0.898000	0.35279	0.492000	0.33523	0.250000	0.18235	0.654000	0.30846	-0.259000	0.10710	GCC	C|0.847;A|0.153	0.153	strong		0.637	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
HKR1	284459	hgsc.bcm.edu	37	19	37854580	37854580	+	Missense_Mutation	SNP	C	C	T	rs3745764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37854580C>T	ENST00000324411.4	+	6	2152	c.1883C>T	c.(1882-1884)aCa>aTa	p.T628I	HKR1_ENST00000392153.3_Missense_Mutation_p.T609I|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000544914.1_Missense_Mutation_p.T355I|HKR1_ENST00000589392.1_Missense_Mutation_p.T610I|HKR1_ENST00000591471.1_Missense_Mutation_p.T355I|HKR1_ENST00000541583.2_Missense_Mutation_p.T567I	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	628			T -> I (in dbSNP:rs3745764).		multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CACCAGAGGACACATTCAGGA	0.507													C|||	943	0.188299	0.1067	0.1801	5008	,	,		21232	0.1627		0.2614	False		,,,				2504	0.2556				p.T628I		Atlas-SNP	.											.	HKR1	74	.	0			c.C1883T						PASS	.	C	ILE/THR	628,3778	273.1+/-271.2	54,520,1629	73.0	74.0	73.0		1883	-0.5	1.0	19	dbSNP_107	73	2192,6408	374.0+/-337.2	287,1618,2395	yes	missense	HKR1	NM_181786.2	89	341,2138,4024	TT,TC,CC		25.4884,14.2533,21.6823	benign	628/660	37854580	2820,10186	2203	4300	6503	SO:0001583	missense	284459	exon6			AGAGGACACATTC	M20675	CCDS12502.1	19q13.13	2013-01-08	2010-05-04			ENSG00000181666		"""Zinc fingers, C2H2-type"", ""-"""	4928	protein-coding gene	gene with protein product	"""oncogene HKR1"""	165250	"""GLI-Kruppel family member HKR1"""			2850480, 9813242	Standard	NM_181786		Approved	ZNF875	uc002ogb.3	P10072		ENST00000324411.4:c.1883C>T	19.37:g.37854580C>T	ENSP00000315505:p.Thr628Ile	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Missense_Mutation	SNP	ENST00000324411.4	37	CCDS12502.1	399|399	0.18269230769230768|0.18269230769230768	61|61	0.12398373983739837|0.12398373983739837	69|69	0.19060773480662985|0.19060773480662985	77|77	0.1346153846153846|0.1346153846153846	192|192	0.2532981530343008|0.2532981530343008	C|C	8.511|8.511	0.866564|0.866564	0.17250|0.17250	0.142533|0.142533	0.254884|0.254884	ENSG00000181666|ENSG00000181666	ENST00000542144|ENST00000544914;ENST00000414402;ENST00000392153;ENST00000324411;ENST00000541583	.|T;T;T;T	.|0.53640	.|0.61;0.61;0.61;0.61	2.96|2.96	-0.455|-0.455	0.12193|0.12193	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04636|0.04636	-0.2|-0.2	0.09310|0.09310	P|P	0.999999121925|0.999999121925	.|B;B;B;B	.|0.11235	.|0.0;0.004;0.001;0.001	.|B;B;B;B	.|0.19148	.|0.003;0.024;0.005;0.001	T|T	0.33828|0.33828	-0.9853|-0.9853	5|8	0.87932|0.09590	D|T	0|0.72	.|.	4.441|4.441	0.11573|0.11573	0.177:0.5389:0.0:0.284|0.177:0.5389:0.0:0.284	rs3745764;rs17585173;rs52828567;rs3745764|rs3745764;rs17585173;rs52828567;rs3745764	.|567;609;628;610	.|Q7Z6E1;P10072-2;P10072;B4DSY3	.|.;.;HKR1_HUMAN;.	Y|I	663|355;407;609;628;567	.|ENSP00000437774:T355I;ENSP00000375994:T609I;ENSP00000315505:T628I;ENSP00000438261:T567I	ENSP00000440633:H663Y|ENSP00000315505:T628I	H|T	+|+	1|2	0|0	HKR1|HKR1	42546420|42546420	0.000000|0.000000	0.05858|0.05858	0.979000|0.979000	0.43373|0.43373	0.992000|0.992000	0.81027|0.81027	-0.735000|-0.735000	0.04888|0.04888	0.077000|0.077000	0.16863|0.16863	0.650000|0.650000	0.86243|0.86243	CAC|ACA	C|0.794;T|0.206	0.206	strong		0.507	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786	
ZNF628	89887	hgsc.bcm.edu	37	19	55995272	55995272	+	Silent	SNP	G	G	A	rs11550705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55995272G>A	ENST00000598519.1	+	3	3265	c.2712G>A	c.(2710-2712)ccG>ccA	p.P904P	NAT14_ENST00000587400.1_5'Flank|NAT14_ENST00000591590.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.P900P|NAT14_ENST00000205194.4_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	904					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TCACTGGCCCGGGCCCCGGGG	0.662													g|||	1181	0.235823	0.0825	0.2781	5008	,	,		13382	0.0149		0.4404	False		,,,				2504	0.4305				p.P904P		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2712A						PASS	.	G		544,3850		32,480,1685	17.0	19.0	18.0		2700	-7.0	0.0	19	dbSNP_120	18	3972,4614		924,2124,1245	no	coding-synonymous	ZNF628	NM_033113.2		956,2604,2930	AA,AG,GG		46.2614,12.3805,34.792		900/1056	55995272	4516,8464	2197	4293	6490	SO:0001819	synonymous_variant	89887	exon3			TGGCCCGGGCCCC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2712G>A	19.37:g.55995272G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																			G|0.723;A|0.277	0.277	strong		0.662	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
ENPP5	59084	hgsc.bcm.edu	37	6	46135489	46135489	+	Missense_Mutation	SNP	T	T	C	rs6926570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46135489T>C	ENST00000371383.2	-	3	771	c.511A>G	c.(511-513)Att>Gtt	p.I171V	ENPP5_ENST00000492313.1_5'Flank|ENPP5_ENST00000230565.3_Missense_Mutation_p.I171V					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						AACCATTCAATAATTTTGGCA	0.423													T|||	2226	0.444489	0.1899	0.4467	5008	,	,		20698	0.4494		0.5308	False		,,,				2504	0.6933				p.I171V		Atlas-SNP	.											.	ENPP5	44	.	0			c.A511G						PASS	.	T	VAL/ILE	1041,3365	374.9+/-321.4	125,791,1287	89.0	98.0	95.0		511	5.3	1.0	6	dbSNP_116	95	4556,4044	593.5+/-393.2	1205,2146,949	yes	missense	ENPP5	NM_021572.4	29	1330,2937,2236	CC,CT,TT		47.0233,23.6269,43.034	benign	171/478	46135489	5597,7409	2203	4300	6503	SO:0001583	missense	59084	exon2			ATTCAATAATTTT	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.511A>G	6.37:g.46135489T>C	ENSP00000360436:p.Ile171Val	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_021572		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	908	0.4157509157509158	95	0.19308943089430894	178	0.49171270718232046	231	0.40384615384615385	404	0.5329815303430079	T	15.67	2.903331	0.52333	0.236269	0.529767	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.72505	-0.66;-0.66	5.33	5.33	0.75918	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.49558	0.1564	L	0.35644	1.08	0.23681	P	0.99712777	B	0.32653	0.379	B	0.37091	0.241	T	0.52268	-0.8598	9	0.19147	T	0.46	-26.7479	15.6241	0.76840	0.0:0.0:0.0:1.0	rs6926570;rs57037284;rs6926570	171	Q9UJA9	ENPP5_HUMAN	V	171	ENSP00000360436:I171V;ENSP00000230565:I171V	ENSP00000230565:I171V	I	-	1	0	ENPP5	46243448	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.618000	0.83043	2.145000	0.66743	0.533000	0.62120	ATT	C|0.421;N|0.000	0.421	strong		0.423	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2		
PODXL	5420	hgsc.bcm.edu	37	7	131196062	131196062	+	Silent	SNP	C	C	T	rs17744792	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:131196062C>T	ENST00000378555.3	-	2	478	c.231G>A	c.(229-231)tcG>tcA	p.S77S	PODXL_ENST00000322985.9_Silent_p.S77S|PODXL_ENST00000537928.1_Silent_p.S77S|PODXL_ENST00000465001.1_5'UTR|PODXL_ENST00000541194.1_Silent_p.S79S			O00592	PODXL_HUMAN	podocalyxin-like	77	Thr-rich.				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)					TCGCCTTGACCGAGGCCAAGA	0.572													C|||	502	0.10024	0.0567	0.1369	5008	,	,		18838	0.0099		0.1849	False		,,,				2504	0.1391				p.S77S		Atlas-SNP	.											.	PODXL	53	.	0			c.G231A						PASS	.	C	,	334,4072	175.5+/-204.9	14,306,1883	174.0	167.0	169.0		231,231	-5.2	0.0	7	dbSNP_123	169	1477,7123	280.6+/-294.6	129,1219,2952	no	coding-synonymous,coding-synonymous	PODXL	NM_001018111.2,NM_005397.3	,	143,1525,4835	TT,TC,CC		17.1744,7.5806,13.9243	,	77/559,77/527	131196062	1811,11195	2203	4300	6503	SO:0001819	synonymous_variant	5420	exon2			CTTGACCGAGGCC		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.231G>A	7.37:g.131196062C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	37	CCDS34755.1																																																																																			C|0.871;T|0.129	0.129	strong		0.572	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
XIRP2	129446	hgsc.bcm.edu	37	2	168102774	168102774	+	Missense_Mutation	SNP	G	G	T	rs72884678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168102774G>T	ENST00000409195.1	+	9	4961	c.4872G>T	c.(4870-4872)ttG>ttT	p.L1624F	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.L1402F|XIRP2_ENST00000295237.9_Missense_Mutation_p.L1624F|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1449					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAGAGATTTTGATTAGTGAAG	0.338													G|||	66	0.0131789	0.0008	0.0216	5008	,	,		19376	0.002		0.0398	False		,,,				2504	0.0082				p.L1624F		Atlas-SNP	.											.	XIRP2	914	.	0			c.G4872T						PASS	.	G	,,,PHE/LEU,PHE/LEU	41,3601		0,41,1780	44.0	41.0	42.0		,,,4872,4206	-0.8	0.1	2	dbSNP_130	42	440,7694		12,416,3639	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,22,22	12,457,5419	TT,TG,GG		5.4094,1.1258,4.0846	,,,benign,benign	,,,1624/3550,1402/3328	168102774	481,11295	1821	4067	5888	SO:0001583	missense	129446	exon9			GATTTTGATTAGT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4872G>T	2.37:g.168102774G>T	ENSP00000386840:p.Leu1624Phe	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	32	0.014652014652014652	0	0.0	8	0.022099447513812154	0	0.0	24	0.0316622691292876	G	3.186	-0.166882	0.06461	0.011258	0.054094	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.03386	3.95;3.95;3.95	5.45	-0.802	0.10889	.	0.968430	0.08577	N	0.925178	T	0.00496	0.0016	L	0.39147	1.195	0.09310	N	1	B;B;B	0.12013	0.001;0.005;0.002	B;B;B	0.09377	0.002;0.004;0.004	T	0.48151	-0.9060	10	0.27785	T	0.31	0.5804	1.3678	0.02205	0.2297:0.2809:0.3385:0.1509	.	1449;1449;1402	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	F	1624;1624;1402	ENSP00000386840:L1624F;ENSP00000295237:L1624F;ENSP00000387255:L1402F	ENSP00000295237:L1624F	L	+	3	2	XIRP2	167811020	0.000000	0.05858	0.060000	0.19600	0.810000	0.45777	-0.604000	0.05667	-0.035000	0.13691	0.557000	0.71058	TTG	G|0.968;T|0.032	0.032	strong		0.338	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
MUC4	4585	hgsc.bcm.edu	37	3	195510146	195510146	+	Missense_Mutation	SNP	G	G	C	rs199750921		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195510146G>C	ENST00000463781.3	-	2	8764	c.8305C>G	c.(8305-8307)Ctt>Gtt	p.L2769V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L2769V	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.L2769V(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)		GTGACAGGAAGAGGGGTGGCG	0.577																																					p.L2769V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	kidney(1)	c.C8305G						scavenged	.						35.0	21.0	25.0					3																	195510146		686	1538	2224	SO:0001583	missense	4585	exon2			CAGGAAGAGGGGT	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.8305C>G	3.37:g.195510146G>C	ENSP00000417498:p.Leu2769Val	Somatic	212	2	0.00943396		WXS	Illumina HiSeq	Phase_I	106	4	0.0377358	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	2.836	-0.241610	0.05906	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.38722	1.12;1.16	1.02	-1.7	0.08159	.	.	.	.	.	T	0.20007	0.0481	N	0.19112	0.55	0.09310	N	1	B	0.24426	0.103	B	0.20384	0.029	T	0.19160	-1.0314	8	.	.	.	.	1.6641	0.02798	0.4545:0.0:0.2536:0.2919	.	2641	E7ESK3	.	V	2769	ENSP00000417498:L2769V;ENSP00000420243:L2769V	.	L	-	1	0	MUC4	196994925	0.000000	0.05858	0.002000	0.10522	0.103000	0.19146	-1.498000	0.02287	-0.413000	0.07507	0.074000	0.15403	CTT	.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SCAF8	22828	hgsc.bcm.edu	37	6	155152262	155152262	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:155152262A>G	ENST00000367178.3	+	19	2923	c.2347A>G	c.(2347-2349)Aac>Gac	p.N783D	TIAM2_ENST00000461783.3_5'Flank|SCAF8_ENST00000367186.4_Missense_Mutation_p.N849D|SCAF8_ENST00000417268.1_Missense_Mutation_p.N783D	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	783	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						TTCTGGTGAAAACACCAGATC	0.383																																					p.N783D		Atlas-SNP	.											.	SCAF8	122	.	0			c.A2347G						PASS	.						28.0	27.0	28.0					6																	155152262		2203	4300	6503	SO:0001583	missense	22828	exon19			GGTGAAAACACCA	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.2347A>G	6.37:g.155152262A>G	ENSP00000356146:p.Asn783Asp	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	21	20	0.952381	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.731115	0.48939	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.47528	0.87;0.87;0.84	5.32	4.08	0.47627	.	0.189894	0.24940	U	0.034400	T	0.20047	0.0482	L	0.44542	1.39	0.29468	N	0.857268	B;B;P;P	0.37864	0.094;0.094;0.61;0.61	B;B;B;B	0.35510	0.016;0.016;0.204;0.145	T	0.04579	-1.0941	10	0.26408	T	0.33	.	10.1615	0.42855	0.8517:0.0:0.0:0.1483	.	828;849;861;783	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	D	783;783;849	ENSP00000356146:N783D;ENSP00000413098:N783D;ENSP00000356154:N849D	ENSP00000356146:N783D	N	+	1	0	SCAF8	155193954	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	3.825000	0.55730	2.136000	0.66102	0.533000	0.62120	AAC	.	.	none		0.383	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892	
MROH9	80133	hgsc.bcm.edu	37	1	170952652	170952652	+	Missense_Mutation	SNP	C	C	A	rs112394419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:170952652C>A	ENST00000367758.3	+	9	805	c.706C>A	c.(706-708)Caa>Aaa	p.Q236K	MROH9_ENST00000367759.4_Missense_Mutation_p.Q236K	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	236																	GGAGTTTCAACAAGACGAAAG	0.358													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		16447	0.0		0.0099	False		,,,				2504	0.002				p.Q236K		Atlas-SNP	.											.	.	.	.	0			c.C706A						PASS	.	C	LYS/GLN,LYS/GLN	8,3616		0,8,1804	80.0	73.0	76.0		706,706	-5.2	0.0	1	dbSNP_132	76	71,8085		0,71,4007	yes	missense,missense	C1orf129	NM_001163629.1,NM_025063.2	53,53	0,79,5811	AA,AC,CC		0.8705,0.2208,0.6706	benign,benign	236/862,236/574	170952652	79,11701	1812	4078	5890	SO:0001583	missense	80133	exon9			TTTCAACAAGACG	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.706C>A	1.37:g.170952652C>A	ENSP00000356732:p.Gln236Lys	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	0.018	-1.467182	0.01053	0.002208	0.008705	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.31769	4.08;1.48	3.86	-5.21	0.02815	.	2.159800	0.02223	N	0.064196	T	0.05227	0.0139	L	0.34521	1.04	0.09310	N	1	B;B	0.13594	0.008;0.008	B;B	0.11329	0.006;0.006	T	0.10337	-1.0634	10	0.02654	T	1	6.0798	7.38	0.26849	0.4342:0.1874:0.3784:0.0	.	236;236	F5GWX6;Q5TGP6	.;CA129_HUMAN	K	236	ENSP00000356733:Q236K;ENSP00000356732:Q236K	ENSP00000356732:Q236K	Q	+	1	0	C1orf129	169219276	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.168000	0.09925	-0.676000	0.05238	-0.499000	0.04595	CAA	C|0.996;A|0.004	0.004	strong		0.358	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
FAM63B	54629	hgsc.bcm.edu	37	15	59064214	59064214	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:59064214G>A	ENST00000559228.1	+	1	702	c.620G>A	c.(619-621)gGc>gAc	p.G207D	FAM63B_ENST00000450403.2_Missense_Mutation_p.G207D|RP11-30K9.6_ENST00000500929.2_lincRNA			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	207										central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						GAGGAGGAGGGCGCGGCGGTG	0.622																																					p.G207D		Atlas-SNP	.											.	FAM63B	33	.	0			c.G620A						PASS	.						31.0	35.0	34.0					15																	59064214		1929	4117	6046	SO:0001583	missense	54629	exon1			AGGAGGGCGCGGC	AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09							26954	protein-coding gene	gene with protein product						10574461	Standard	NM_001040450		Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.620G>A	15.37:g.59064214G>A	ENSP00000452885:p.Gly207Asp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_001040450	B2RTT8|Q9ULQ6	Missense_Mutation	SNP	ENST00000559228.1	37	CCDS42046.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603459	0.46423	.	.	ENSG00000128923	ENST00000316848;ENST00000450403	T	0.51574	0.7	3.92	2.95	0.34219	.	0.870346	0.10083	N	0.718159	T	0.36331	0.0963	N	0.22421	0.69	0.41810	D	0.989967	P;P	0.41131	0.483;0.739	B;B	0.43082	0.084;0.407	T	0.06789	-1.0807	10	0.12430	T	0.62	-14.985	12.3052	0.54898	0.0:0.2553:0.7447:0.0	.	207;207	Q8NBR6;Q8NBR6-2	FA63B_HUMAN;.	D	207	ENSP00000393231:G207D	ENSP00000326194:G207D	G	+	2	0	FAM63B	56851506	0.985000	0.35326	0.961000	0.40146	0.496000	0.33645	0.082000	0.14847	2.024000	0.59613	0.543000	0.68304	GGC	.	.	none		0.622	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1	NM_019092	
CLOCK	9575	hgsc.bcm.edu	37	4	56325365	56325365	+	Missense_Mutation	SNP	G	G	C	rs34897046	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:56325365G>C	ENST00000309964.4	-	9	873	c.623C>G	c.(622-624)tCt>tGt	p.S208C	CLOCK_ENST00000513440.1_Missense_Mutation_p.S208C|CLOCK_ENST00000381322.1_Missense_Mutation_p.S208C	NM_004898.3	NP_004889.1	O15516	CLOCK_HUMAN	clock circadian regulator	208			S -> C (in dbSNP:rs34897046).		cellular response to ionizing radiation (GO:0071479)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|circadian rhythm (GO:0007623)|DNA damage checkpoint (GO:0000077)|histone acetylation (GO:0016573)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of transcription, DNA-templated (GO:0045892)|photoperiodism (GO:0009648)|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)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of hair cycle (GO:0042634)|regulation of insulin secretion (GO:0050796)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of type B pancreatic cell development (GO:2000074)|response to redox state (GO:0051775)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|chromosome (GO:0005694)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|histone acetyltransferase activity (GO:0004402)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(8)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(11;0.00335)|Glioma(25;0.08)|all_epithelial(27;0.0992)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(4;1.62e-07)|Lung(4;1.34e-06)|Epithelial(7;0.0107)			TTCATAGGTAGATGGCTCCTT	0.303													G|||	97	0.019369	0.0038	0.0245	5008	,	,		18720	0.001		0.0447	False		,,,				2504	0.0297				p.S208C		Atlas-SNP	.											.	CLOCK	81	.	0			c.C623G						PASS	.	G	CYS/SER	49,4355	49.6+/-84.7	0,49,2153	53.0	53.0	53.0		623	5.9	1.0	4	dbSNP_126	53	445,8147	133.8+/-191.2	14,417,3865	yes	missense	CLOCK	NM_004898.2	112	14,466,6018	CC,CG,GG		5.1792,1.1126,3.8012	benign	208/847	56325365	494,12502	2202	4296	6498	SO:0001583	missense	9575	exon10			TAGGTAGATGGCT	AF011568	CCDS3500.1	4q12	2012-12-07	2012-12-07		ENSG00000134852	ENSG00000134852		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	2082	protein-coding gene	gene with protein product		601851	"""clock (mouse) homolog"", ""clock homolog (mouse)"""			10198158	Standard	NM_001267843		Approved	KIAA0334, KAT13D, bHLHe8	uc003hba.2	O15516	OTTHUMG00000102141	ENST00000309964.4:c.623C>G	4.37:g.56325365G>C	ENSP00000308741:p.Ser208Cys	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	175	65	0.371429	NM_004898	A0AV01|A2I2N9|O14516|Q9UIT8	Missense_Mutation	SNP	ENST00000309964.4	37	CCDS3500.1	54	0.024725274725274724	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	40	0.052770448548812667	G	21.2	4.116404	0.77323	0.011126	0.051792	ENSG00000134852	ENST00000309964;ENST00000381322;ENST00000513440	T;T;T	0.04454	3.62;3.62;3.62	5.87	5.87	0.94306	.	0.259104	0.46442	D	0.000289	T	0.01124	0.0037	L	0.32530	0.975	0.48571	D	0.999677	P	0.40250	0.709	B	0.42087	0.375	T	0.21586	-1.0241	10	0.72032	D	0.01	.	20.2147	0.98293	0.0:0.0:1.0:0.0	rs34897046	208	O15516	CLOCK_HUMAN	C	208	ENSP00000308741:S208C;ENSP00000370723:S208C;ENSP00000426983:S208C	ENSP00000308741:S208C	S	-	2	0	CLOCK	56020122	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.388000	0.97237	2.785000	0.95823	0.591000	0.81541	TCT	G|0.964;C|0.036	0.036	strong		0.303	CLOCK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361993.2	NM_004898	
PCDHB6	56130	hgsc.bcm.edu	37	5	140531545	140531545	+	Silent	SNP	C	C	T	rs138345434	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140531545C>T	ENST00000231136.1	+	1	1707	c.1707C>T	c.(1705-1707)ccC>ccT	p.P569P	PCDHB6_ENST00000543635.1_Silent_p.P433P	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	569	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTCCGCGCCCTGCACCGAGC	0.711													C|||	10	0.00199681	0.0	0.0014	5008	,	,		13508	0.0		0.005	False		,,,				2504	0.0041				p.P569P		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C1707T						PASS	.	C		2,4258		0,2,2128	13.0	18.0	16.0		1707	3.3	1.0	5	dbSNP_134	16	27,8431		0,27,4202	no	coding-synonymous	PCDHB6	NM_018939.2		0,29,6330	TT,TC,CC		0.3192,0.0469,0.228		569/795	140531545	29,12689	2130	4229	6359	SO:0001819	synonymous_variant	56130	exon1			CGCGCCCTGCACC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1707C>T	5.37:g.140531545C>T		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	10	5	0.5	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1	.	.	.	.	.	.	.	.	.	.	C	7.815	0.716486	0.15306	4.69E-4	0.003192	ENSG00000113211	ENST00000542861	.	.	.	4.19	3.32	0.38043	.	.	.	.	.	T	0.36026	0.0952	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06058	-1.0848	5	0.10636	T	0.68	.	5.8998	0.18960	0.0:0.661:0.1593:0.1797	.	.	.	.	L	354	.	ENSP00000438850:P354L	P	+	2	0	PCDHB6	140511729	0.000000	0.05858	1.000000	0.80357	0.971000	0.66376	-0.322000	0.08007	0.884000	0.36064	-0.265000	0.10407	CCT	C|0.997;T|0.003	0.003	strong		0.711	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
AIFM2	84883	hgsc.bcm.edu	37	10	71874048	71874048	+	Silent	SNP	G	G	A	rs1053495	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:71874048G>A	ENST00000307864.1	-	9	1221	c.1008C>T	c.(1006-1008)gaC>gaT	p.D336D	AIFM2_ENST00000482166.1_5'Flank|AIFM2_ENST00000373248.1_Silent_p.D336D	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	336					apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						GGCCCACACCGTCATTTCTCC	0.582													G|||	949	0.189497	0.2859	0.0735	5008	,	,		17271	0.1835		0.1024	False		,,,				2504	0.2372				p.D336D		Atlas-SNP	.											.	AIFM2	33	.	0			c.C1008T						PASS	.	G	,	1052,3354	385.1+/-325.6	122,808,1273	75.0	70.0	72.0		1008,1008	-2.6	1.0	10	dbSNP_86	72	714,7886	174.6+/-224.8	30,654,3616	no	coding-synonymous,coding-synonymous	AIFM2	NM_001198696.1,NM_032797.5	,	152,1462,4889	AA,AG,GG		8.3023,23.8765,13.5783	,	336/374,336/374	71874048	1766,11240	2203	4300	6503	SO:0001819	synonymous_variant	84883	exon9			CACACCGTCATTT	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"""apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"""	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.1008C>T	10.37:g.71874048G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_001198696	B3KXI0|Q63Z39	Silent	SNP	ENST00000307864.1	37	CCDS7297.1																																																																																			G|0.845;A|0.155	0.155	strong		0.582	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797	
ZCCHC2	54877	hgsc.bcm.edu	37	18	60227833	60227833	+	Silent	SNP	T	T	C	rs17070100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:60227833T>C	ENST00000269499.5	+	8	1924	c.1506T>C	c.(1504-1506)caT>caC	p.H502H	ZCCHC2_ENST00000586834.1_Silent_p.H181H	NM_017742.4	NP_060212.4	Q9C0B9	ZCHC2_HUMAN	zinc finger, CCHC domain containing 2	502						cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25						TGTTGCAGCATGCCATAATCC	0.353													t|||	566	0.113019	0.2322	0.0908	5008	,	,		18793	0.003		0.1103	False		,,,				2504	0.0838				p.H502H		Atlas-SNP	.											.	ZCCHC2	64	.	0			c.T1506C						PASS	.	T		822,2894		95,632,1131	196.0	168.0	177.0		1506	-1.0	0.8	18	dbSNP_123	177	939,7267		59,821,3223	no	coding-synonymous	ZCCHC2	NM_017742.4		154,1453,4354	CC,CT,TT		11.4428,22.1206,14.771		502/1179	60227833	1761,10161	1858	4103	5961	SO:0001819	synonymous_variant	54877	exon8			GCAGCATGCCATA	AB051531	CCDS45880.1	18q21.33	2012-04-19			ENSG00000141664	ENSG00000141664		"""Zinc fingers, CCHC domain containing"""	22916	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 49"""	C18orf49		11214970	Standard	NM_017742		Approved	FLJ20281, KIAA1744, FLJ20222	uc002lip.4	Q9C0B9		ENST00000269499.5:c.1506T>C	18.37:g.60227833T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	137	1	NM_017742	B2RPG6|Q8N3S1|Q9NXF6	Silent	SNP	ENST00000269499.5	37	CCDS45880.1																																																																																			T|0.893;C|0.107	0.107	strong		0.353	ZCCHC2-005	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450083.1	NM_017742	
LRP2	4036	hgsc.bcm.edu	37	2	170115672	170115672	+	Silent	SNP	A	A	G	rs33954745	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:170115672A>G	ENST00000263816.3	-	17	2661	c.2376T>C	c.(2374-2376)gaT>gaC	p.D792D	LRP2_ENST00000443831.1_Silent_p.D655D	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	792					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TTGAAATCCAATCAAAAGCCA	0.343													A|||	382	0.076278	0.1589	0.072	5008	,	,		16692	0.0		0.0845	False		,,,				2504	0.0378				p.D792D		Atlas-SNP	.											.	LRP2	751	.	0			c.T2376C						PASS	.	A		574,3832	256.1+/-261.0	40,494,1669	118.0	121.0	120.0		2376	1.2	1.0	2	dbSNP_126	120	733,7867	177.2+/-226.9	37,659,3604	no	coding-synonymous	LRP2	NM_004525.2		77,1153,5273	GG,GA,AA		8.5233,13.0277,10.0492		792/4656	170115672	1307,11699	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon17			AATCCAATCAAAA		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.2376T>C	2.37:g.170115672A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			A|0.909;G|0.091	0.091	strong		0.343	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
SBNO1	55206	hgsc.bcm.edu	37	12	123825559	123825559	+	Silent	SNP	C	C	T	rs12322888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:123825559C>T	ENST00000602398.1	-	5	754	c.627G>A	c.(625-627)aaG>aaA	p.K209K	SBNO1_ENST00000602750.1_Silent_p.K208K|SBNO1_ENST00000420886.2_Silent_p.K209K|SBNO1_ENST00000267176.4_Silent_p.K208K			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	209					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)		AACTCCTCATCTTCATGTCGT	0.358													C|||	1229	0.245407	0.4887	0.2233	5008	,	,		20344	0.003		0.2247	False		,,,				2504	0.2035				p.K209K		Atlas-SNP	.											.	SBNO1	138	.	0			c.G627A						PASS	.	C	,	1989,2417	557.3+/-379.7	435,1119,649	150.0	140.0	143.0		627,624	-3.2	1.0	12	dbSNP_120	143	1727,6873	313.5+/-311.4	163,1401,2736	no	coding-synonymous,coding-synonymous	SBNO1	NM_001167856.1,NM_018183.3	,	598,2520,3385	TT,TC,CC		20.0814,45.143,28.5714	,	209/1394,208/1393	123825559	3716,9290	2203	4300	6503	SO:0001819	synonymous_variant	55206	exon4			CCTCATCTTCATG	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.627G>A	12.37:g.123825559C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	37	CCDS53844.1																																																																																			C|0.728;T|0.272	0.272	strong		0.358	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
GH1	2688	hgsc.bcm.edu	37	17	61995241	61995241	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61995241C>T	ENST00000323322.5	-	4	377	c.335G>A	c.(334-336)tGg>tAg	p.W112*	CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Nonsense_Mutation_p.W72*|GH1_ENST00000458650.2_Nonsense_Mutation_p.W97*|GH1_ENST00000342364.4_Intron	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	112					bone maturation (GO:0070977)|glucose transport (GO:0015758)|growth hormone receptor signaling pathway (GO:0060396)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)|growth hormone receptor binding (GO:0005131)|metal ion binding (GO:0046872)|prolactin receptor binding (GO:0005148)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)	19						GGGCTCCAGCCACGACTGGAT	0.607																																					p.W112X		Atlas-SNP	.											GH1,NS,carcinoma,0,1	GH1	39	1	0			c.G335A						scavenged	.						62.0	65.0	64.0					17																	61995241		2203	4300	6503	SO:0001587	stop_gained	2688	exon4			TCCAGCCACGACT	M13438	CCDS11653.1, CCDS11654.1, CCDS45760.1	17q22-q24	2014-01-30				ENSG00000259384		"""Endogenous ligands"""	4261	protein-coding gene	gene with protein product	"""pituitary growth hormone"", ""somatotropin"""	139250				6306568	Standard	XM_005257218		Approved	GH-N, GHN, GH, hGH-N	uc002jdj.3	P01241		ENST00000323322.5:c.335G>A	17.37:g.61995241C>T	ENSP00000312673:p.Trp112*	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	140	2	0.0142857	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Nonsense_Mutation	SNP	ENST00000323322.5	37	CCDS11653.1	.	.	.	.	.	.	.	.	.	.	c	9.035	0.988316	0.18966	.	.	ENSG00000204414	ENST00000323322;ENST00000458650;ENST00000351388	.	.	.	2.86	2.86	0.33363	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.5437	0.50681	0.0:1.0:0.0:0.0	.	.	.	.	X	112;97;72	.	ENSP00000312673:W112X	W	-	2	0	GH1	59348973	1.000000	0.71417	0.995000	0.50966	0.056000	0.15407	5.123000	0.64703	1.594000	0.50039	0.298000	0.19748	TGG	.	.	none		0.607	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515	
GOT2	2806	hgsc.bcm.edu	37	16	58752466	58752466	+	Missense_Mutation	SNP	C	C	T	rs11076256	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58752466C>T	ENST00000245206.5	-	5	690	c.562G>A	c.(562-564)Ggt>Agt	p.G188S	GOT2_ENST00000434819.2_Missense_Mutation_p.G145S|GOT2_ENST00000564400.1_5'UTR	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	188			G -> S (in dbSNP:rs11076256).		2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	AAGTCAAAACCGCAAGTCTTG	0.488													C|||	231	0.0461262	0.0197	0.0375	5008	,	,		19560	0.0099		0.0855	False		,,,				2504	0.0849				p.G188S		Atlas-SNP	.											.	GOT2	42	.	0			c.G562A						PASS	.	C	SER/GLY	139,4257	98.0+/-136.7	4,131,2063	118.0	115.0	116.0		562	5.7	0.9	16	dbSNP_120	116	680,7920	170.6+/-221.7	22,636,3642	yes	missense	GOT2	NM_002080.2	56	26,767,5705	TT,TC,CC		7.907,3.162,6.3019	possibly-damaging	188/431	58752466	819,12177	2198	4300	6498	SO:0001583	missense	2806	exon5			CAAAACCGCAAGT		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.562G>A	16.37:g.58752466C>T	ENSP00000245206:p.Gly188Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Missense_Mutation	SNP	ENST00000245206.5	37	CCDS10801.1	86	0.039377289377289376	8	0.016260162601626018	14	0.03867403314917127	3	0.005244755244755245	61	0.08047493403693931	C	28.7	4.942779	0.92526	0.03162	0.07907	ENSG00000125166	ENST00000245206;ENST00000434819	D;D	0.90444	-2.67;-2.67	5.73	5.73	0.89815	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.044096	0.85682	D	0.000000	T	0.34454	0.0898	L	0.51422	1.61	0.80722	D	1	P;P	0.40681	0.559;0.727	B;B	0.38106	0.202;0.265	T	0.66440	-0.5923	9	.	.	.	-4.6434	12.1616	0.54107	0.0:0.9142:0.0:0.0858	rs11076256;rs11076256	145;188	E7ERW2;P00505	.;AATM_HUMAN	S	188;145	ENSP00000245206:G188S;ENSP00000394100:G145S	.	G	-	1	0	GOT2	57309967	1.000000	0.71417	0.876000	0.34364	0.961000	0.63080	5.964000	0.70379	2.723000	0.93209	0.561000	0.74099	GGT	C|0.948;T|0.052	0.052	strong		0.488	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
MT-CYB	4519	hgsc.bcm.edu	37	M	14766	14766	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:14766C>T	ENST00000361789.2	+	1	20	c.20C>T	c.(19-21)aCt>aTt	p.T7I	MT-TH_ENST00000387441.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND6_ENST00000361681.2_5'Flank			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	7			T -> I (in dbSNP:rs3135031). {ECO:0000269|PubMed:10453733, ECO:0000269|PubMed:11130070, ECO:0000269|PubMed:11553319, ECO:0000269|PubMed:12022039, ECO:0000269|PubMed:1757091, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:7530363, ECO:0000269|PubMed:7623448}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						AATACGCAAAATTAACCCCCT	0.433																																					p.T7I		Atlas-SNP	.											.	.	.	.	0			c.C20T						PASS	.																																			SO:0001583	missense	0	exon1			GCAAAACTAACCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.20C>T	M.37:g.14766C>T	ENSP00000354554:p.Thr7Ile	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.433	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
PIK3R5	23533	hgsc.bcm.edu	37	17	8792029	8792029	+	Silent	SNP	A	A	G	rs381309	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8792029A>G	ENST00000447110.1	-	10	1199	c.1075T>C	c.(1075-1077)Ttg>Ctg	p.L359L	PIK3R5_ENST00000581552.1_Silent_p.L359L|PIK3R5_ENST00000584803.1_Silent_p.L359L	NM_001142633.2|NM_001251851.1|NM_001251852.1|NM_001251853.1|NM_001251855.1	NP_001136105.1|NP_001238780.1|NP_001238781.1|NP_001238782.1|NP_001238784.1	Q8WYR1	PI3R5_HUMAN	phosphoinositide-3-kinase, regulatory subunit 5	359				DILQEILLKEQELLQPGILGDDEEEEEEEEEVEEDLETDGH CAERDSLLSTSSLASHDSTLSLASSQASG -> GNIEGDPG PRRPDSAGLASLQTSCRKSCSRNRSYSSQGSWEMMKRRERR RRRWRRTWKLTGTVPREIPCS (in Ref. 6; AAW63121). {ECO:0000305}.	blood coagulation (GO:0007596)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|G-protein beta/gamma-subunit complex binding (GO:0031683)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(14)|prostate(3)|skin(4)|urinary_tract(1)	34						GCAAGGGACAAGGTGGAGTCA	0.622													G|||	2221	0.44349	0.7262	0.4049	5008	,	,		18663	0.1786		0.3907	False		,,,				2504	0.4162				p.L359L	NSCLC(18;589 615 7696 20311 50332)	Atlas-SNP	.											.	PIK3R5	79	.	0			c.T1075C						PASS	.	G	,	2907,1499	473.5+/-356.7	965,977,261	101.0	97.0	98.0		1075,1075	-1.2	0.1	17	dbSNP_80	98	3624,4976	621.7+/-397.2	752,2120,1428	no	coding-synonymous,coding-synonymous	PIK3R5	NM_001142633.1,NM_014308.3	,	1717,3097,1689	GG,GA,AA		42.1395,34.0218,49.7847	,	359/881,359/881	8792029	6531,6475	2203	4300	6503	SO:0001819	synonymous_variant	23533	exon10			GGGACAAGGTGGA	AF128881	CCDS11147.1, CCDS73986.1	17p13.1	2011-10-13	2008-02-04		ENSG00000141506	ENSG00000141506			30035	protein-coding gene	gene with protein product		611317				12507995	Standard	NM_014308		Approved	P101-PI3K, p101	uc002glt.3	Q8WYR1	OTTHUMG00000108197	ENST00000447110.1:c.1075T>C	17.37:g.8792029A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	55	19	0.345455	NM_001142633	B0LPH4|D3DTS3|Q5G936|Q5G938|Q5G939|Q8IZ23|Q9Y2Y2	Silent	SNP	ENST00000447110.1	37	CCDS11147.1																																																																																			A|0.524;C|0.002	.	strong		0.622	PIK3R5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000227003.2	NM_014308	
PSAPL1	768239	hgsc.bcm.edu	37	4	7435194	7435194	+	Silent	SNP	G	G	A	rs12498567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:7435194G>A	ENST00000319098.4	-	1	1506	c.1413C>T	c.(1411-1413)ggC>ggT	p.G471G	SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000511199.1_Intron|SORCS2_ENST00000507866.2_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	471	Saposin B-type 4. {ECO:0000255|PROSITE- ProRule:PRU00415}.				sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						GGGTCCTGGGGCCGTGGCAGG	0.642													G|||	577	0.115216	0.1036	0.1138	5008	,	,		17473	0.1111		0.1839	False		,,,				2504	0.0654				p.G471G		Atlas-SNP	.											PSAPL1_ENST00000319098,NS,carcinoma,-1,2	PSAPL1	51	2	0			c.C1413T						PASS	.	G	,	490,3460		32,426,1517	19.0	22.0	21.0		1413,	-1.3	0.0	4	dbSNP_120	21	1450,6834		121,1208,2813	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	153,1634,4330	AA,AG,GG		17.5036,12.4051,15.8574	,	471/522,	7435194	1940,10294	1975	4142	6117	SO:0001819	synonymous_variant	768239	exon1			CCTGGGGCCGTGG	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.1413C>T	4.37:g.7435194G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			G|0.868;A|0.132	0.132	strong		0.642	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
DRC1	92749	hgsc.bcm.edu	37	2	26667130	26667130	+	Missense_Mutation	SNP	A	A	G	rs3795958	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26667130A>G	ENST00000288710.2	+	9	1143	c.1069A>G	c.(1069-1071)Aag>Gag	p.K357E	DRC1_ENST00000483675.1_3'UTR	NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	357			K -> E (in dbSNP:rs3795958). {ECO:0000269|PubMed:17974005}.		axonemal dynein complex assembly (GO:0070286)|bacterial-type flagellum-dependent cell motility (GO:0071973)|cilium-dependent cell motility (GO:0060285)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)											AAAATATGCCAAGCAAATAAA	0.408													A|||	807	0.161142	0.0053	0.1931	5008	,	,		23665	0.2421		0.1918	False		,,,				2504	0.2342				p.K357E		Atlas-SNP	.											.	CCDC164	84	.	0			c.A1069G						PASS	.	A	GLU/LYS	156,4250	106.0+/-144.5	1,154,2048	110.0	100.0	104.0		1069	4.2	0.7	2	dbSNP_107	104	1473,7127	280.9+/-294.7	133,1207,2960	yes	missense	CCDC164	NM_145038.2	56	134,1361,5008	GG,GA,AA		17.1279,3.5406,12.525	possibly-damaging	357/741	26667130	1629,11377	2203	4300	6503	SO:0001583	missense	92749	exon9			TATGCCAAGCAAA	AL833892	CCDS1723.1	2p23.3	2014-07-18	2014-07-18	2013-03-14	ENSG00000157856	ENSG00000157856			24245	protein-coding gene	gene with protein product		615288	"""chromosome 2 open reading frame 39"", ""coiled-coil domain containing 164"", ""dynein regulatory complex subunit 1 homolog (Chlamydomonas)"""	C2orf39, CCDC164		23354437	Standard	NM_145038		Approved	MGC16372, FLJ32660, CILD21	uc002rhg.2	Q96MC2	OTTHUMG00000125531	ENST00000288710.2:c.1069A>G	2.37:g.26667130A>G	ENSP00000288710:p.Lys357Glu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	135	73	0.540741	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	345	0.15796703296703296	3	0.006097560975609756	76	0.20994475138121546	114	0.1993006993006993	152	0.20052770448548812	A	22.0	4.225716	0.79576	0.035406	0.171279	ENSG00000157856	ENST00000288710	T	0.15952	2.38	5.39	4.2	0.49525	.	0.367187	0.32093	N	0.006596	T	0.00012	0.0000	L	0.49699	1.58	0.32998	P	0.474106	P	0.49253	0.921	P	0.48524	0.58	T	0.35001	-0.9806	9	0.20046	T	0.44	-22.0796	10.739	0.46141	0.8399:0.1601:0.0:0.0	rs3795958;rs52806794;rs61481502;rs3795958	357	Q96MC2	CC164_HUMAN	E	357	ENSP00000288710:K357E	ENSP00000288710:K357E	K	+	1	0	CCDC164	26520634	1.000000	0.71417	0.711000	0.30485	0.997000	0.91878	3.392000	0.52537	0.943000	0.37553	0.528000	0.53228	AAG	A|0.858;G|0.142	0.142	strong		0.408	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038	
C9orf72	203228	hgsc.bcm.edu	37	9	27561628	27561628	+	Missense_Mutation	SNP	T	T	C	rs113299382|rs17769294	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:27561628T>C	ENST00000380003.3	-	5	683	c.620A>G	c.(619-621)aAt>aGt	p.N207S	C9orf72_ENST00000379997.3_Missense_Mutation_p.N207S|C9orf72_ENST00000488117.1_5'UTR	NM_001256054.1|NM_018325.3	NP_001242983.1|NP_060795.1	Q96LT7	CI072_HUMAN	chromosome 9 open reading frame 72	207			N -> S (in dbSNP:rs17769294).		autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|extracellular space (GO:0005615)|lysosome (GO:0005764)|nucleus (GO:0005634)	Rab GTPase binding (GO:0017137)	p.N207I(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(4)|pancreas(1)	23		all_neural(11;7.57e-10)		LUSC - Lung squamous cell carcinoma(38;0.0001)|Lung(218;0.00016)		ATCATCATCATTGAGTACTGT	0.318													T|||	246	0.0491214	0.0189	0.0735	5008	,	,		18348	0.001		0.1083	False		,,,				2504	0.0613				p.N207S		Atlas-SNP	.											.	C9orf72	48	.	1	Substitution - Missense(1)	lung(1)	c.A620G						PASS	.	T	SER/ASN,SER/ASN	150,4256	101.6+/-140.2	0,150,2053	60.0	57.0	58.0		620,620	4.9	1.0	9	dbSNP_123	58	1085,7513	225.1+/-261.3	74,937,3288	yes	missense,missense	C9orf72	NM_018325.2,NM_145005.4	46,46	74,1087,5341	CC,CT,TT		12.6192,3.4044,9.4971	possibly-damaging,possibly-damaging	207/482,207/223	27561628	1235,11769	2203	4299	6502	SO:0001583	missense	203228	exon5			TCATCATTGAGTA	AL832467	CCDS6522.1, CCDS6523.1	9p21.1	2014-09-17			ENSG00000147894	ENSG00000147894			28337	protein-coding gene	gene with protein product		614260				21944778, 24549040	Standard	NM_145005		Approved	MGC23980	uc003zqq.3	Q96LT7	OTTHUMG00000019716	ENST00000380003.3:c.620A>G	9.37:g.27561628T>C	ENSP00000369339:p.Asn207Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_018325	A8K5W0|D3DRK6|G8I0B6|Q6NUS9	Missense_Mutation	SNP	ENST00000380003.3	37	CCDS6522.1	113	0.051739926739926737	9	0.018292682926829267	24	0.06629834254143646	0	0.0	80	0.10554089709762533	T	14.66	2.602228	0.46423	0.034044	0.126192	ENSG00000147894	ENST00000380003;ENST00000379997;ENST00000379995	T;T;T	0.42900	0.96;0.96;0.96	6.07	4.95	0.65309	.	0.042329	0.85682	D	0.000000	T	0.00384	0.0012	L	0.54323	1.7	0.09310	P	0.99999873259	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.06409	-1.0828	8	.	.	.	.	9.7079	0.40227	0.0:0.1306:0.0:0.8694	rs17769294;rs52789634;rs17769294	207;207	Q96LT7-2;Q96LT7	.;CI072_HUMAN	S	207	ENSP00000369339:N207S;ENSP00000369333:N207S;ENSP00000369331:N207S	.	N	-	2	0	C9orf72	27551628	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	1.986000	0.40677	2.330000	0.79161	0.477000	0.44152	AAT	T|0.919;C|0.081	0.081	strong		0.318	C9orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051969.1	NM_018325	
GRIN3A	116443	hgsc.bcm.edu	37	9	104433034	104433034	+	Silent	SNP	A	A	G	rs10512285	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104433034A>G	ENST00000361820.3	-	3	2260	c.1660T>C	c.(1660-1662)Ttg>Ctg	p.L554L		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	554					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)	AGGCTGTCCAATGTGGAAGAG	0.448													A|||	1340	0.267572	0.1241	0.3617	5008	,	,		21313	0.2173		0.4056	False		,,,				2504	0.3047				p.L554L		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T1660C						PASS	.	A		789,3617	316.1+/-294.4	73,643,1487	114.0	105.0	108.0		1660	-2.4	0.0	9	dbSNP_119	108	3551,5049	515.9+/-378.7	726,2099,1475	no	coding-synonymous	GRIN3A	NM_133445.2		799,2742,2962	GG,GA,AA		41.2907,17.9074,33.3692		554/1116	104433034	4340,8666	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			TGTCCAATGTGGA		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.1660T>C	9.37:g.104433034A>G		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|0.698;G|0.302	0.302	strong		0.448	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
OR10A7	121364	hgsc.bcm.edu	37	12	55615229	55615229	+	Missense_Mutation	SNP	T	T	C	rs151030005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55615229T>C	ENST00000326258.1	+	1	421	c.421T>C	c.(421-423)Tgc>Cgc	p.C141R		NM_001005280.1	NP_001005280.1	Q8NGE5	O10A7_HUMAN	olfactory receptor, family 10, subfamily A, member 7	141						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)|lung(11)|ovary(4)|prostate(2)|skin(3)	24						CAGGTCCCTATGCTTGTGGAT	0.483													t|||	34	0.00678914	0.0008	0.0101	5008	,	,		19385	0.0		0.0249	False		,,,				2504	0.001				p.C141R		Atlas-SNP	.											.	OR10A7	53	.	0			c.T421C						PASS	.	T	ARG/CYS	14,4392	22.3+/-47.3	0,14,2189	140.0	122.0	128.0		421	3.2	0.0	12	dbSNP_134	128	150,8450	72.6+/-135.2	1,148,4151	yes	missense	OR10A7	NM_001005280.1	180	1,162,6340	CC,CT,TT		1.7442,0.3177,1.261	benign	141/317	55615229	164,12842	2203	4300	6503	SO:0001583	missense	121364	exon1			TCCCTATGCTTGT	BK004327	CCDS31815.1	12q13.13	2012-08-09				ENSG00000179919		"""GPCR / Class A : Olfactory receptors"""	15329	protein-coding gene	gene with protein product							Standard	NM_001005280		Approved		uc010spf.2	Q8NGE5	OTTHUMG00000169860	ENST00000326258.1:c.421T>C	12.37:g.55615229T>C	ENSP00000326718:p.Cys141Arg	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	236	114	0.483051	NM_001005280	Q6IFD5|Q96R19	Missense_Mutation	SNP	ENST00000326258.1	37	CCDS31815.1	20	0.009157509157509158	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.01978891820580475	t	8.121	0.780903	0.16120	0.003177	0.017442	ENSG00000179919	ENST00000326258	T	0.00241	8.46	3.25	3.25	0.37280	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42821	D	0.000643	T	0.00241	0.0007	M	0.72118	2.19	0.22787	N	0.998736	D	0.76494	0.999	D	0.72625	0.978	T	0.49862	-0.8894	10	0.49607	T	0.09	.	11.7185	0.51668	0.0:0.0:0.0:1.0	.	141	Q8NGE5	O10A7_HUMAN	R	141	ENSP00000326718:C141R	ENSP00000326718:C141R	C	+	1	0	OR10A7	53901496	0.018000	0.18449	0.032000	0.17829	0.123000	0.20343	1.073000	0.30691	1.502000	0.48669	0.519000	0.50382	TGC	T|0.988;C|0.012	0.012	strong		0.483	OR10A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406308.1		
JRK	8629	hgsc.bcm.edu	37	8	143746069	143746069	+	RNA	SNP	T	T	C	rs3735999	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143746069T>C	ENST00000507178.2	-	0	1741							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ggtcagcttttggagtctttt	0.672													C|||	2666	0.532348	0.7171	0.3213	5008	,	,		16647	0.5188		0.3926	False		,,,				2504	0.59				p.P469P		Atlas-SNP	.											.	.	.	.	0			c.A1407G						PASS	.	C	,	2527,1527		799,929,299	19.0	22.0	21.0		1409,1409	-2.2	0.0	8	dbSNP_107	21	3154,5166		626,1902,1632	yes	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	1425,2831,1931	CC,CT,TT		37.9087,37.6665,45.9108	,	469/557,469/569	143746069	5681,6693	2027	4160	6187			8629	exon3			AGCTTTTGGAGTC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746069T>C		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	24	11	0.458333	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				T|0.479;C|0.521	0.521	strong		0.672	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
TLR8	51311	hgsc.bcm.edu	37	X	12924826	12924826	+	Start_Codon_SNP	SNP	A	A	G	rs3764880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:12924826A>G	ENST00000218032.6	+	1	88	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	TLR8-AS1_ENST00000451564.1_RNA|TLR8_ENST00000311912.5_5'UTR	NM_138636.4	NP_619542.1	Q9NR97	TLR8_HUMAN	toll-like receptor 8	1					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|regulation of cytokine secretion (GO:0050707)|response to virus (GO:0009615)|toll-like receptor 8 signaling pathway (GO:0034158)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)			breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(21)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	50					Imiquimod(DB00724)	CAACAGAAACATGGTAAGCCA	0.453													G|||	1751	0.463841	0.2201	0.317	3775	,	,		14224	0.6121		0.2048	False		,,,				2504	0.4264				p.M1V		Atlas-SNP	.											.	TLR8	134	.	0			c.A1G	GRCh37	CM083186	TLR8	M	rs3764880	PASS	.	G	VAL/MET	1013,2822		133,601,146,898,425	67.0	58.0	61.0		1	-3.6	0.0	X	dbSNP_107	61	1664,5064		141,936,446,1351,1426	yes	missense	TLR8	NM_138636.4	21	274,1537,592,2249,1851	GG,GA,G,AA,A		24.7325,26.4146,25.3432	benign	1/1042	12924826	2677,7886	2203	4300	6503	SO:0001582	initiator_codon_variant	51311	exon1			AGAAACATGGTAA	AF246971	CCDS14152.1, CCDS14153.1	Xp22	2009-11-23			ENSG00000101916	ENSG00000101916		"""CD molecules"""	15632	protein-coding gene	gene with protein product		300366				11022119	Standard	NM_138636		Approved	CD288	uc004cve.3	Q9NR97	OTTHUMG00000021145	ENST00000218032.6:c.1A>G	X.37:g.12924826A>G	ENSP00000218032:p.Met1Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	142	140	0.985915	NM_138636	B3Y654|D1CS70|D1CS76|Q495P4|Q6UXL6|Q9NYG9	Missense_Mutation	SNP	ENST00000218032.6	37	CCDS14152.1	728	0.4388185654008439	85	0.1985981308411215	77	0.2711267605633803	221	0.65	100	0.1557632398753894	G	0.369	-0.934864	0.02340	0.264146	0.247325	ENSG00000101916	ENST00000218032	T	0.27890	1.64	4.56	-3.64	0.04515	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46798	P	7.909999999999862E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.43278	-0.9401	7	0.87932	D	0	.	1.7067	0.02883	0.3541:0.2228:0.3092:0.1138	rs3764880;rs52808745;rs58935011;rs3764880	1	Q9NR97	TLR8_HUMAN	V	1	ENSP00000218032:M1V	ENSP00000218032:M1V	M	+	1	0	TLR8	12834747	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.626000	0.05527	-1.451000	0.01933	-3.568000	0.00029	ATG	A|0.639;0|0.017	.	strong		0.453	TLR8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055784.2	NM_016610	Missense_Mutation
MLPH	79083	hgsc.bcm.edu	37	2	238434434	238434434	+	Missense_Mutation	SNP	C	C	T	rs11883500	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238434434C>T	ENST00000264605.3	+	7	1160	c.866C>T	c.(865-867)aCt>aTt	p.T289I	MLPH_ENST00000409373.1_Missense_Mutation_p.T249I|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.T289I|MLPH_ENST00000410032.1_Intron|MLPH_ENST00000338530.4_Missense_Mutation_p.T289I	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	289			T -> I (in dbSNP:rs11883500).		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)		GCCCTGGGGACTGCTGCTGCA	0.657													C|||	657	0.13119	0.2352	0.0778	5008	,	,		17959	0.0675		0.1421	False		,,,				2504	0.0828				p.T289I		Atlas-SNP	.											.	MLPH	41	.	0			c.C866T						PASS	.	C	ILE/THR,ILE/THR	1044,3360	350.3+/-310.7	122,800,1280	28.0	29.0	29.0		866,866	-4.4	0.0	2	dbSNP_120	29	1434,7166	257.9+/-281.7	118,1198,2984	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	89,89	240,1998,4264	TT,TC,CC		16.6744,23.7057,19.0557	benign,benign	289/573,289/601	238434434	2478,10526	2202	4300	6502	SO:0001583	missense	79083	exon7			TGGGGACTGCTGC	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.866C>T	2.37:g.238434434C>T	ENSP00000264605:p.Thr289Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	293	0.13415750915750915	108	0.21951219512195122	30	0.08287292817679558	43	0.07517482517482517	112	0.14775725593667546	C	5.026	0.190481	0.09547	0.237057	0.166744	ENSG00000115648	ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T;T;T;T	0.26810	2.07;2.06;1.92;1.71	3.09	-4.43	0.03568	.	3.607730	0.00757	N	0.001103	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B;B;B	0.15719	0.014;0.011;0.004;0.004;0.007;0.004	B;B;B;B;B;B	0.19391	0.007;0.005;0.011;0.007;0.025;0.007	T	0.27839	-1.0062	9	0.24483	T	0.36	5.367	5.7615	0.18203	0.1637:0.6192:0.0:0.2171	rs11883500;rs52823878;rs57325617;rs11883500	289;173;289;249;289;289	B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36	.;.;.;.;.;MELPH_HUMAN	I	289;289;289;249	ENSP00000264605:T289I;ENSP00000414849:T289I;ENSP00000341845:T289I;ENSP00000386780:T249I	ENSP00000264605:T289I	T	+	2	0	MLPH	238099173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.252000	0.01185	-1.022000	0.03346	-0.471000	0.05019	ACT	C|0.832;T|0.168	0.168	strong		0.657	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
SLC4A11	83959	hgsc.bcm.edu	37	20	3208967	3208967	+	Missense_Mutation	SNP	C	C	T	rs34224785	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3208967C>T	ENST00000380056.3	-	18	2591	c.2544G>A	c.(2542-2544)atG>atA	p.M848I	SLC4A11_ENST00000539553.2_Missense_Mutation_p.M832I|SLC4A11_ENST00000488544.1_5'Flank|SLC4A11_ENST00000380059.3_Missense_Mutation_p.M875I	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	848	Membrane (bicarbonate transporter).		M -> I (in dbSNP:rs34224785).		bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						GCAGGGAGCTCATGCCGAAGG	0.617													C|||	57	0.0113818	0.0386	0.0058	5008	,	,		13939	0.0		0.002	False		,,,				2504	0.0				p.M875I	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G2625A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET	120,4286	90.2+/-128.9	2,116,2085	106.0	94.0	98.0		2496,2625,2544	4.4	1.0	20	dbSNP_126	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	10,10,10	2,117,6384	TT,TC,CC		0.0116,2.7236,0.9303	probably-damaging,probably-damaging,probably-damaging	832/876,875/919,848/892	3208967	121,12885	2203	4300	6503	SO:0001583	missense	83959	exon19			GGAGCTCATGCCG	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.2544G>A	20.37:g.3208967C>T	ENSP00000369396:p.Met848Ile	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	156	64	0.410256	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	30	0.013736263736263736	23	0.046747967479674794	5	0.013812154696132596	0	0.0	2	0.002638522427440633	C	14.38	2.517442	0.44763	0.027236	1.16E-4	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553	T;T;T	0.79454	-1.27;-1.27;-1.26	5.37	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	M	0.81682	2.555	0.58432	D	0.999999	B;B;B	0.29766	0.122;0.256;0.043	B;B;B	0.31614	0.133;0.063;0.035	T	0.65372	-0.6184	10	0.24483	T	0.36	.	15.9593	0.79914	0.0:0.8646:0.1354:0.0	rs34224785	832;875;848	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	I	875;848;832	ENSP00000369399:M875I;ENSP00000369396:M848I;ENSP00000441370:M832I	ENSP00000369396:M848I	M	-	3	0	SLC4A11	3156967	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	3.253000	0.51469	1.239000	0.43787	0.455000	0.32223	ATG	C|0.988;T|0.012	0.012	strong		0.617	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
SPTLC3	55304	hgsc.bcm.edu	37	20	13071816	13071816	+	Silent	SNP	C	C	T	rs6109692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:13071816C>T	ENST00000399002.2	+	5	967	c.693C>T	c.(691-693)ttC>ttT	p.F231F	SPTLC3_ENST00000378194.4_Silent_p.F231F	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	231					small molecule metabolic process (GO:0044281)|sphingoid biosynthetic process (GO:0046520)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|serine C-palmitoyltransferase complex (GO:0017059)	pyridoxal phosphate binding (GO:0030170)|serine C-palmitoyltransferase activity (GO:0004758)			breast(1)|endometrium(1)|large_intestine(7)|lung(14)|skin(1)|urinary_tract(1)	25						GGATGGGATTCGCAACTAACT	0.413													C|||	371	0.0740815	0.0567	0.0836	5008	,	,		20998	0.0694		0.1054	False		,,,				2504	0.0634				p.F231F		Atlas-SNP	.											.	SPTLC3	78	.	0			c.C693T						PASS	.	C		250,3606		4,242,1682	140.0	140.0	140.0		693	0.8	1.0	20	dbSNP_114	140	888,7366		44,800,3283	no	coding-synonymous	SPTLC3	NM_018327.2		48,1042,4965	TT,TC,CC		10.7584,6.4834,9.3972		231/553	13071816	1138,10972	1928	4127	6055	SO:0001819	synonymous_variant	55304	exon5			GGGATTCGCAACT	AL109983	CCDS13115.2	20p12.1	2011-07-05	2006-12-21	2006-12-21	ENSG00000172296	ENSG00000172296	2.3.1.50		16253	protein-coding gene	gene with protein product		611120	"""chromosome 20 open reading frame 38"", ""serine palmitoyltransferase, long chain base subunit 2-like (aminotransferase 2)"""	C20orf38, SPTLC2L		17023427	Standard	NM_018327		Approved	LCB2B, FLJ11112, hLCB2b	uc002wod.1	Q9NUV7	OTTHUMG00000031899	ENST00000399002.2:c.693C>T	20.37:g.13071816C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	180	83	0.461111	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Silent	SNP	ENST00000399002.2	37	CCDS13115.2																																																																																			C|0.913;T|0.087	0.087	strong		0.413	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327	
LRP2	4036	hgsc.bcm.edu	37	2	170070348	170070348	+	Silent	SNP	T	T	C	rs11886219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:170070348T>C	ENST00000263816.3	-	36	6144	c.5859A>G	c.(5857-5859)cgA>cgG	p.R1953R		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1953					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CCAGGATCATTCGATCTGTTC	0.368													T|||	806	0.160942	0.4947	0.0965	5008	,	,		19502	0.0		0.0527	False		,,,				2504	0.0327				p.R1953R		Atlas-SNP	.											.	LRP2	751	.	0			c.A5859G						PASS	.	T		1814,2592	527.0+/-372.0	381,1052,770	76.0	74.0	75.0		5859	-2.4	1.0	2	dbSNP_120	75	485,8115	138.4+/-195.2	21,443,3836	no	coding-synonymous	LRP2	NM_004525.2		402,1495,4606	CC,CT,TT		5.6395,41.1711,17.6765		1953/4656	170070348	2299,10707	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon36			GATCATTCGATCT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.5859A>G	2.37:g.170070348T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	130	68	0.523077	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			T|0.827;C|0.173	0.173	strong		0.368	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
CD82	3732	hgsc.bcm.edu	37	11	44636848	44636848	+	Silent	SNP	G	G	A	rs2303864	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:44636848G>A	ENST00000227155.4	+	7	611	c.363G>A	c.(361-363)gtG>gtA	p.V121V	CD82_ENST00000342935.3_Silent_p.V96V|CD82_ENST00000530931.1_3'UTR	NM_002231.3	NP_002222.1	P27701	CD82_HUMAN	CD82 molecule	121						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				large_intestine(1)|ovary(1)	2						GCGGCATCGTGACTGAGCTCA	0.607													G|||	49	0.00978435	0.0	0.0	5008	,	,		19683	0.0446		0.003	False		,,,				2504	0.001				p.V121V		Atlas-SNP	.											.	CD82	27	.	0			c.G363A						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	78.0	64.0	68.0		288,363	0.2	0.0	11	dbSNP_100	68	10,8588	7.7+/-29.5	0,10,4289	no	coding-synonymous,coding-synonymous	CD82	NM_001024844.1,NM_002231.3	,	0,12,6490	AA,AG,GG		0.1163,0.0454,0.0923	,	96/243,121/268	44636848	12,12992	2203	4299	6502	SO:0001819	synonymous_variant	3732	exon7			CATCGTGACTGAG	U20770	CCDS7909.1, CCDS31469.1	11p11.2	2013-02-14	2006-03-28	2005-03-03		ENSG00000085117		"""CD molecules"", ""Tetraspanins"""	6210	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 6"", ""R2 leukocyte antigen"""	600623	"""kangai 1 (suppression of tumorigenicity 6, prostate; CD82 antigen (R2 leukocyte antigen, antigen detected by monoclonal and antibody IA4))"", ""CD82 antigen"""	ST6, KAI1			Standard	XM_006718222		Approved	R2, IA4, TSPAN27	uc001myc.3	P27701		ENST00000227155.4:c.363G>A	11.37:g.44636848G>A		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	183	85	0.464481	NM_002231	D3DQN6|E9PC70|Q7Z2D4|Q7Z5N2	Silent	SNP	ENST00000227155.4	37	CCDS7909.1																																																																																			G|0.994;A|0.006	0.006	strong		0.607	CD82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389886.1		
CMC2	56942	hgsc.bcm.edu	37	16	81010073	81010073	+	Missense_Mutation	SNP	C	C	T	rs1127390	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81010073C>T	ENST00000219400.3	-	4	572	c.157G>A	c.(157-159)Gta>Ata	p.V53I	CMC2_ENST00000565925.1_3'UTR|CMC2_ENST00000566231.1_5'UTR|CMC2_ENST00000564249.1_Missense_Mutation_p.V53I|CMC2_ENST00000565914.1_Missense_Mutation_p.V53I|CMC2_ENST00000486645.1_3'UTR|CMC2_ENST00000562713.1_3'UTR|CMC2_ENST00000565108.1_Missense_Mutation_p.V29I|CMC2_ENST00000564174.1_Missense_Mutation_p.V29I|CMC2_ENST00000570195.1_3'UTR	NM_020188.3	NP_064573.1	Q9NRP2	COXM2_HUMAN	C-x(9)-C motif containing 2	53						mitochondrion (GO:0005739)											CTGTTTTCTACGTACTGAAAA	0.343													T|||	1994	0.398163	0.6694	0.366	5008	,	,		16380	0.4454		0.2296	False		,,,				2504	0.1789				p.V53I		Atlas-SNP	.											.	.	.	.	0			c.G157A						PASS	.	T	ILE/VAL	2534,1872	527.8+/-372.2	739,1056,408	42.0	45.0	44.0		157	-4.7	0.0	16	dbSNP_86	44	1847,6753	725.8+/-406.6	212,1423,2665	yes	missense	C16orf61	NM_020188.3	29	951,2479,3073	TT,TC,CC		21.4767,42.4875,33.6845	benign	53/80	81010073	4381,8625	2203	4300	6503	SO:0001583	missense	56942	exon4			TTTCTACGTACTG	BC032631	CCDS10930.1	16q23.2	2013-10-18	2013-10-18	2012-02-14	ENSG00000103121	ENSG00000103121			24447	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 61"", ""COX assembly mitochondrial protein 2 homolog (S. cerevisiae)"""	C16orf61		20220131	Standard	NM_020188		Approved	DC13, MGC45036	uc002ffu.3	Q9NRP2	OTTHUMG00000137625	ENST00000219400.3:c.157G>A	16.37:g.81010073C>T	ENSP00000219400:p.Val53Ile	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_020188	D3DUK6	Missense_Mutation	SNP	ENST00000219400.3	37	CCDS10930.1	882	0.40384615384615385	327	0.6646341463414634	132	0.36464088397790057	251	0.4388111888111888	172	0.22691292875989447	T	2.211	-0.380614	0.05000	0.575125	0.214767	ENSG00000103121	ENST00000219400	T	0.42131	0.98	4.68	-4.67	0.03319	.	1.480890	0.03549	N	0.225217	T	0.00012	0.0000	.	.	.	0.50313	P	1.32000000000021E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.39722	-0.9600	8	0.28530	T	0.3	.	4.4894	0.11806	0.1311:0.5137:0.1334:0.2218	rs9304	53	Q9NRP2	CP061_HUMAN	I	53	ENSP00000219400:V53I	ENSP00000219400:V53I	V	-	1	0	C16orf61	79567574	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.722000	0.04958	-1.468000	0.01892	-0.321000	0.08615	GTA	.	.	weak		0.343	CMC2-001	KNOWN	upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269047.1	NM_020188	
ANKRD50	57182	hgsc.bcm.edu	37	4	125631261	125631261	+	Missense_Mutation	SNP	G	G	A	rs79454313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:125631261G>A	ENST00000504087.1	-	2	1443	c.406C>T	c.(406-408)Cgc>Tgc	p.R136C	ANKRD50_ENST00000515641.1_Intron	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	136										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						AGTCCACTGCGGCAGATCTGG	0.502													G|||	24	0.00479233	0.0174	0.0014	5008	,	,		16679	0.0		0.0	False		,,,				2504	0.0				p.R136C		Atlas-SNP	.											.	ANKRD50	136	.	0			c.C406T						PASS	.	G	,CYS/ARG	53,4353	53.6+/-89.4	0,53,2150	77.0	76.0	76.0		,406	5.2	1.0	4	dbSNP_132	76	13,8587	11.2+/-40.8	0,13,4287	yes	intron,missense	ANKRD50	NM_001167882.1,NM_020337.2	,180	0,66,6437	AA,AG,GG		0.1512,1.2029,0.5075	,probably-damaging	,136/1430	125631261	66,12940	2203	4300	6503	SO:0001583	missense	57182	exon2			CACTGCGGCAGAT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.406C>T	4.37:g.125631261G>A	ENSP00000425658:p.Arg136Cys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	47	22	0.468085	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	G	19.24	3.790420	0.70337	0.012029	0.001512	ENSG00000151458	ENST00000504087	T	0.18502	2.21	5.16	5.16	0.70880	.	0.437689	0.23477	N	0.047758	T	0.20007	0.0481	L	0.60455	1.87	0.80722	D	1	D	0.67145	0.996	P	0.46885	0.53	T	0.02844	-1.1103	10	0.87932	D	0	.	18.6344	0.91371	0.0:0.0:1.0:0.0	.	136	Q9ULJ7	ANR50_HUMAN	C	136	ENSP00000425658:R136C	ENSP00000425658:R136C	R	-	1	0	ANKRD50	125850711	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.102000	0.64572	2.394000	0.81467	0.462000	0.41574	CGC	G|0.996;A|0.004	0.004	strong		0.502	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
CDNF	441549	hgsc.bcm.edu	37	10	14867557	14867557	+	5'UTR	SNP	T	T	G	rs61843027	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:14867557T>G	ENST00000378442.1	-	0	503				CDNF_ENST00000378441.2_Intron			Q49AH0	CDNF_HUMAN	cerebral dopamine neurotrophic factor							extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(1)	5						GCACACTCATTGGGCGAGTGA	0.433													T|||	44	0.00878594	0.0008	0.0187	5008	,	,		21682	0.0		0.0239	False		,,,				2504	0.0061				p.P102P		Atlas-SNP	.											.	CDNF	19	.	0			c.A306C						PASS	.	T		15,4391	23.3+/-48.9	0,15,2188	191.0	179.0	183.0		306	-8.2	0.8	10	dbSNP_129	183	228,8372	94.2+/-156.2	3,222,4075	no	coding-synonymous	CDNF	NM_001029954.2		3,237,6263	GG,GT,TT		2.6512,0.3404,1.8684		102/188	14867557	243,12763	2203	4300	6503	SO:0001623	5_prime_UTR_variant	441549	exon3			ACTCATTGGGCGA	BC037872	CCDS31148.1	10p13	2009-06-04	2009-06-04	2009-06-04	ENSG00000185267	ENSG00000185267			24913	protein-coding gene	gene with protein product	"""conserved dopamine neurotrophic factor"""	611233	"""arginine-rich, mutated in early stage tumors-like 1"""	ARMETL1		17611540	Standard	NM_001029954		Approved		uc001inb.1	Q49AH0	OTTHUMG00000017713	ENST00000378442.1:c.-1A>C	10.37:g.14867557T>G		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	181	85	0.469613	NM_001029954	A2RUU0|B4DVW3	Silent	SNP	ENST00000378442.1	37																																																																																				T|0.983;G|0.017	0.017	strong		0.433	CDNF-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000046919.1	NM_001029954	
PYGB	5834	hgsc.bcm.edu	37	20	25260931	25260931	+	Silent	SNP	A	A	G	rs2227890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25260931A>G	ENST00000216962.4	+	10	1232	c.1122A>G	c.(1120-1122)gcA>gcG	p.A374A		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	374					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						AGACCTGTGCATACACCAACC	0.537													G|||	2690	0.537141	0.4523	0.3473	5008	,	,		21077	0.9107		0.4334	False		,,,				2504	0.5082				p.A374A		Atlas-SNP	.											PYGB,NS,carcinoma,0,1	PYGB	84	1	0			c.A1122G						scavenged	.	G		1903,2503	628.7+/-395.1	401,1101,701	136.0	122.0	126.0		1122	-7.7	0.6	20	dbSNP_98	126	3754,4846	616.5+/-396.5	813,2128,1359	no	coding-synonymous	PYGB	NM_002862.3		1214,3229,2060	GG,GA,AA		43.6512,43.1911,43.4953		374/844	25260931	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon10			CTGTGCATACACC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1122A>G	20.37:g.25260931A>G		Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	156	65	0.416667	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			A|0.513;G|0.487	0.487	strong		0.537	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
GYLTL1B	120071	hgsc.bcm.edu	37	11	45949746	45949746	+	Silent	SNP	A	A	C	rs11038714	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:45949746A>C	ENST00000531526.1	+	13	1884	c.1773A>C	c.(1771-1773)cgA>cgC	p.R591R	GYLTL1B_ENST00000325468.5_Silent_p.R591R|GYLTL1B_ENST00000536139.1_Silent_p.R560R|GYLTL1B_ENST00000401752.1_Silent_p.R591R|GYLTL1B_ENST00000529052.1_Silent_p.R560R	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	591					muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		AGTGGCCCCGAGGCCACGCAC	0.672													G|||	127	0.0253594	0.003	0.0476	5008	,	,		17859	0.0		0.0636	False		,,,				2504	0.0266				p.R591R		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.A1773C						PASS	.	G		48,4358		0,48,2155	65.0	69.0	67.0		1773	1.0	0.4	11	dbSNP_120	67	463,8133		16,431,3851	no	coding-synonymous	GYLTL1B	NM_152312.3		16,479,6006	CC,CA,AA		5.3862,1.0894,3.9302		591/722	45949746	511,12491	2203	4298	6501	SO:0001819	synonymous_variant	120071	exon13			GCCCCGAGGCCAC		CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"""Glycosyltransferase family 8 domain containing"""	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1773A>C	11.37:g.45949746A>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Silent	SNP	ENST00000531526.1	37	CCDS31473.1																																																																																			A|0.961;C|0.039	0.039	strong		0.672	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312	
LMBR1	64327	hgsc.bcm.edu	37	7	156556385	156556385	+	Silent	SNP	G	G	C	rs138255184	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:156556385G>C	ENST00000353442.5	-	6	764	c.528C>G	c.(526-528)gcC>gcG	p.A176A	LMBR1_ENST00000540390.1_Silent_p.A155A|LMBR1_ENST00000354505.4_Silent_p.A176A|LMBR1_ENST00000359422.4_Silent_p.A24A	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	176					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		CCATGCTTGCGGCATCGTTGT	0.398													G|||	43	0.00858626	0.0061	0.0072	5008	,	,		14242	0.0		0.0109	False		,,,				2504	0.0194				p.A176A		Atlas-SNP	.											.	LMBR1	35	.	0			c.C528G						PASS	.	G		21,4385	28.1+/-56.4	0,21,2182	109.0	103.0	105.0		528	-4.0	0.3	7	dbSNP_134	105	67,8533	41.2+/-98.3	1,65,4234	no	coding-synonymous	LMBR1	NM_022458.3		1,86,6416	CC,CG,GG		0.7791,0.4766,0.6766		176/491	156556385	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	64327	exon6			GCTTGCGGCATCG	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.528C>G	7.37:g.156556385G>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Silent	SNP	ENST00000353442.5	37	CCDS5945.1																																																																																			G|0.994;C|0.006	0.006	strong		0.398	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
CCDC94	55702	hgsc.bcm.edu	37	19	4267681	4267681	+	Missense_Mutation	SNP	C	C	T	rs149224144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4267681C>T	ENST00000262962.7	+	7	837	c.769C>T	c.(769-771)Cgg>Tgg	p.R257W		NM_018074.4	NP_060544.2	Q9BW85	CCD94_HUMAN	coiled-coil domain containing 94	257										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)		CCTGGGCAGCCGGCCCCCGCT	0.682											OREG0025164	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	12	0.00239617	0.0	0.0072	5008	,	,		14361	0.0		0.007	False		,,,				2504	0.0				p.R257W		Atlas-SNP	.											.	CCDC94	28	.	0			c.C769T						PASS	.	C	TRP/ARG	3,4401		0,3,2199	25.0	28.0	27.0		769	1.5	0.0	19	dbSNP_134	27	47,8553		0,47,4253	yes	missense	CCDC94	NM_018074.4	101	0,50,6452	TT,TC,CC		0.5465,0.0681,0.3845	probably-damaging	257/324	4267681	50,12954	2202	4300	6502	SO:0001583	missense	55702	exon7			GGCAGCCGGCCCC	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.769C>T	19.37:g.4267681C>T	ENSP00000262962:p.Arg257Trp	Somatic	126	0	0	617	WXS	Illumina HiSeq	Phase_I	166	87	0.524096	NM_018074	O75270|Q9H862|Q9NW16	Missense_Mutation	SNP	ENST00000262962.7	37	CCDS12124.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	14.33	2.502075	0.44455	6.81E-4	0.005465	ENSG00000105248	ENST00000262962	T	0.38722	1.12	4.96	1.53	0.23141	.	0.331465	0.31177	N	0.008110	T	0.45736	0.1357	M	0.63428	1.95	0.09310	N	1	D	0.76494	0.999	D	0.70487	0.969	T	0.39603	-0.9606	10	0.87932	D	0	-32.1111	6.2754	0.20977	0.5208:0.3319:0.0:0.1474	.	257	Q9BW85	CCD94_HUMAN	W	257	ENSP00000262962:R257W	ENSP00000262962:R257W	R	+	1	2	CCDC94	4218681	0.929000	0.31497	0.000000	0.03702	0.477000	0.33069	2.133000	0.42093	-0.051000	0.13334	0.306000	0.20318	CGG	C|0.996;T|0.004	0.004	strong		0.682	CCDC94-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458007.2	NM_018074	
RBP1	5947	hgsc.bcm.edu	37	3	139258411	139258411	+	Silent	SNP	G	G	A	rs11549984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:139258411G>A	ENST00000483943.2	-	1	150	c.150C>T	c.(148-150)cgC>cgT	p.R50R	RP11-319G6.1_ENST00000515247.1_RNA|RP11-319G6.1_ENST00000381790.3_RNA|RBP1_ENST00000492918.1_Silent_p.R50R|RBP1_ENST00000232219.2_Silent_p.R50R	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN	retinol binding protein 1, cellular	0					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	CCACAAGCGGGCGGGACGGCT	0.662													G|||	431	0.0860623	0.0537	0.121	5008	,	,		13021	0.0843		0.1183	False		,,,				2504	0.0736				p.R50R		Atlas-SNP	.											.	RBP1	39	.	0			c.C150T						PASS	.	G	,,	261,4141		3,255,1943	22.0	17.0	19.0		150,150,150	2.2	0.7	3	dbSNP_120	19	992,7606		64,864,3371	no	coding-synonymous,coding-synonymous,coding-synonymous	RBP1	NM_001130992.1,NM_001130993.1,NM_002899.3	,,	67,1119,5314	AA,AG,GG		11.5376,5.9291,9.6385	,,	50/158,50/154,50/198	139258411	1253,11747	2201	4299	6500	SO:0001819	synonymous_variant	5947	exon1			AAGCGGGCGGGAC		CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"""Fatty acid binding protein family"""	9919	protein-coding gene	gene with protein product		180260	"""retinol-binding protein 1, cellular"""			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000483943.2:c.150C>T	3.37:g.139258411G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	84	44	0.52381	NM_002899	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Silent	SNP	ENST00000483943.2	37	CCDS46925.1																																																																																			G|0.910;A|0.090	0.090	strong		0.662	RBP1-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341497.2	NM_002899	
MYOM2	9172	hgsc.bcm.edu	37	8	2092803	2092803	+	Silent	SNP	A	A	G	rs1063523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:2092803A>G	ENST00000262113.4	+	37	4437	c.4296A>G	c.(4294-4296)acA>acG	p.T1432T	MYOM2_ENST00000520298.1_3'UTR|MYOM2_ENST00000523438.1_Silent_p.T857T	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1432	Ig-like C2-type 5.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TCGACGTGACAGTGAGCGTGT	0.587													G|||	1206	0.240815	0.2481	0.2435	5008	,	,		13751	0.2292		0.2883	False		,,,				2504	0.1922				p.T1432T		Atlas-SNP	.											.	MYOM2	251	.	0			c.A4296G						PASS	.	G		1137,3269	716.8+/-408.6	130,877,1196	108.0	92.0	98.0		4296	-9.3	0.1	8	dbSNP_86	98	2274,6326	707.3+/-405.6	301,1672,2327	no	coding-synonymous	MYOM2	NM_003970.2		431,2549,3523	GG,GA,AA		26.4419,25.8057,26.2264		1432/1466	2092803	3411,9595	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon37			CGTGACAGTGAGC		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.4296A>G	8.37:g.2092803A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	63	30	0.47619	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			A|0.741;G|0.259	0.259	strong		0.587	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
TMIGD2	126259	hgsc.bcm.edu	37	19	4292597	4292597	+	Silent	SNP	C	C	T	rs888932	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4292597C>T	ENST00000301272.2	-	5	893	c.848G>A	c.(847-849)tGa>tAa	p.*283*	TMIGD2_ENST00000600114.1_Silent_p.*163*|TMIGD2_ENST00000600349.1_Silent_p.*111*|TMIGD2_ENST00000595645.1_Silent_p.*279*	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	0					positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGATCTCTCACTCCTCTCC	0.617													T|||	2306	0.460463	0.7905	0.3818	5008	,	,		14645	0.3552		0.2803	False		,,,				2504	0.364				p.X283X		Atlas-SNP	.											.	TMIGD2	38	.	0			c.G848A						PASS	.	T	,	3084,1322	444.7+/-347.4	1086,912,205	94.0	106.0	102.0		836,848	-3.6	0.0	19	dbSNP_86	102	2376,6224	700.7+/-405.2	370,1636,2294	no	coding-synonymous,coding-synonymous	TMIGD2	NM_001169126.1,NM_144615.2	,	1456,2548,2499	TT,TC,CC		27.6279,30.0045,41.9806	,	279/279,283/283	4292597	5460,7546	2203	4300	6503	SO:0001819	synonymous_variant	126259	exon5			ATCTCTCACTCCT	BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.848G>A	19.37:g.4292597C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_144615	Q6UW59	Silent	SNP	ENST00000301272.2	37	CCDS12126.1																																																																																			C|0.569;T|0.431	0.431	strong		0.617	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1	NM_144615	
MMP3	4314	hgsc.bcm.edu	37	11	102713465	102713465	+	Silent	SNP	A	A	G	rs602128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102713465A>G	ENST00000299855.5	-	2	544	c.288T>C	c.(286-288)gaT>gaC	p.D96D		NM_002422.3	NP_002413.1	P08254	MMP3_HUMAN	matrix metallopeptidase 3 (stromelysin 1, progelatinase)	96					cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|positive regulation of oxidative stress-induced cell death (GO:1903209)|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)|endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0142)	Marimastat(DB00786)	AGTGACCAACATCAGGAACTC	0.498													G|||	3098	0.61861	0.5499	0.6643	5008	,	,		16797	0.6667		0.5278	False		,,,				2504	0.7229				p.D96D		Atlas-SNP	.											MMP3,NS,carcinoma,0,1	MMP3	60	1	0			c.T288C						PASS	.	G		2375,2031	563.8+/-381.3	636,1103,464	73.0	66.0	68.0		288	-12.1	0.0	11	dbSNP_83	68	4301,4297	577.9+/-390.6	1066,2169,1064	no	coding-synonymous	MMP3	NM_002422.3		1702,3272,1528	GG,GA,AA		49.9767,46.0962,48.662		96/478	102713465	6676,6328	2203	4299	6502	SO:0001819	synonymous_variant	4314	exon2			ACCAACATCAGGA	X05232	CCDS8323.1	11q22.3	2012-10-02	2005-08-08		ENSG00000149968	ENSG00000149968	3.4.24.17		7173	protein-coding gene	gene with protein product		185250	"""matrix metalloproteinase 3 (stromelysin 1, progelatinase)"""	STMY1, STMY			Standard	NM_002422		Approved		uc001phj.1	P08254	OTTHUMG00000048254	ENST00000299855.5:c.288T>C	11.37:g.102713465A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	159	77	0.484277	NM_002422	B2R8B8|Q3B7S0|Q6GRF8	Silent	SNP	ENST00000299855.5	37	CCDS8323.1																																																																																			A|0.461;G|0.539	0.539	strong		0.498	MMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109758.2	NM_002422	
ACSM5	54988	hgsc.bcm.edu	37	16	20441053	20441053	+	Missense_Mutation	SNP	C	C	G	rs8062344	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:20441053C>G	ENST00000331849.4	+	8	1202	c.1055C>G	c.(1054-1056)cCt>cGt	p.P352R		NM_017888.2	NP_060358.2	Q6NUN0	ACSM5_HUMAN	acyl-CoA synthetase medium-chain family member 5	352			P -> R (in dbSNP:rs8062344). {ECO:0000269|PubMed:12654705}.		fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(3)|urinary_tract(1)	51						GCCCTCAACCCTGACGTGAGG	0.557													C|||	2199	0.439097	0.6846	0.2046	5008	,	,		17393	0.5774		0.2813	False		,,,				2504	0.2935				p.P352R		Atlas-SNP	.											ACSM5,NS,carcinoma,-1,1	ACSM5	101	1	0			c.C1055G						PASS	.	C	ARG/PRO	2687,1719	644.0+/-397.9	850,987,366	91.0	92.0	92.0		1055	4.4	1.0	16	dbSNP_116	92	2533,6067	411.2+/-350.4	370,1793,2137	no	missense	ACSM5	NM_017888.2	103	1220,2780,2503	GG,GC,CC		29.4535,39.015,40.1353	probably-damaging	352/580	20441053	5220,7786	2203	4300	6503	SO:0001583	missense	54988	exon8			TCAACCCTGACGT		CCDS10585.1	16p12.3	2007-10-17			ENSG00000183549	ENSG00000183549		"""Acyl-CoA synthetase family"""	26060	protein-coding gene	gene with protein product		614361				17762044	Standard	NM_017888		Approved	FLJ20581	uc002dhe.3	Q6NUN0	OTTHUMG00000131551	ENST00000331849.4:c.1055C>G	16.37:g.20441053C>G	ENSP00000327916:p.Pro352Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_017888	Q96AV1|Q96CX8|Q9NWV3	Missense_Mutation	SNP	ENST00000331849.4	37	CCDS10585.1	966	0.4423076923076923	328	0.6666666666666666	82	0.2265193370165746	331	0.5786713286713286	225	0.29683377308707126	C	16.35	3.098109	0.56183	0.60985	0.294535	ENSG00000183549	ENST00000331849	T	0.46451	0.87	4.44	4.44	0.53790	AMP-dependent synthetase/ligase (1);	0.113343	0.39834	N	0.001244	T	0.00012	0.0000	M	0.70842	2.15	0.21697	P	0.999586955	D	0.64830	0.994	D	0.65987	0.94	T	0.48127	-0.9062	9	0.87932	D	0	-6.3652	16.2059	0.82131	0.0:1.0:0.0:0.0	rs8062344;rs56850377	352	Q6NUN0	ACSM5_HUMAN	R	352	ENSP00000327916:P352R	ENSP00000327916:P352R	P	+	2	0	ACSM5	20348554	0.969000	0.33509	0.999000	0.59377	0.317000	0.28152	6.068000	0.71201	2.149000	0.67028	0.557000	0.71058	CCT	C|0.598;G|0.402	0.402	strong		0.557	ACSM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254413.1	NM_017888	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482964	54482964	+	Missense_Mutation	SNP	C	C	T	rs843704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:54482964C>T	ENST00000317802.7	-	1	445	c.325G>A	c.(325-327)Ggc>Agc	p.G109S	ACYP2_ENST00000607452.1_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000394666.3_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	109			G -> S (in dbSNP:rs843704). {ECO:0000269|PubMed:15489334}.		nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.G109S(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						TTGAGGCTGCCGTCAGTTGTC	0.617													C|||	1353	0.270168	0.2171	0.1902	5008	,	,		16934	0.2966		0.2624	False		,,,				2504	0.3793				p.G109S		Atlas-SNP	.											TSPYL6,NS,carcinoma,0,1	TSPYL6	54	1	1	Substitution - Missense(1)	stomach(1)	c.G325A						PASS	.	C	SER/GLY,	906,3210		98,710,1250	41.0	44.0	43.0		325,	-2.3	0.0	2	dbSNP_86	43	2146,6242		277,1592,2325	yes	missense,intron	ACYP2,TSPYL6	NM_001003937.2,NM_138448.3	56,	375,2302,3575	TT,TC,CC		25.5842,22.0117,24.4082	benign,	109/411,	54482964	3052,9452	2058	4194	6252	SO:0001583	missense	388951	exon1			GGCTGCCGTCAGT	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.325G>A	2.37:g.54482964C>T	ENSP00000417919:p.Gly109Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	35	0.486111	NM_001003937	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	37	CCDS42682.1	523	0.23946886446886448	110	0.22357723577235772	72	0.19889502762430938	140	0.24475524475524477	201	0.26517150395778366	C	5.023	0.189912	0.09547	0.220117	0.255842	ENSG00000178021	ENST00000317802	T	0.19250	2.16	1.15	-2.31	0.06765	.	.	.	.	.	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.22146	0.065	B	0.12156	0.007	T	0.44003	-0.9356	8	0.20519	T	0.43	.	2.5356	0.04713	0.3989:0.3414:0.0:0.2597	rs843704;rs1616842;rs17189750;rs56646920;rs60727366;rs843704	109	Q8N831	TSYL6_HUMAN	S	109	ENSP00000417919:G109S	ENSP00000417919:G109S	G	-	1	0	TSPYL6	54336468	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.965000	0.03829	-1.916000	0.01075	-0.366000	0.07423	GGC	C|0.746;T|0.253	0.253	strong		0.617	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
ADAM7	8756	hgsc.bcm.edu	37	8	24350715	24350715	+	Silent	SNP	G	G	A	rs12547971	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:24350715G>A	ENST00000175238.6	+	16	1898	c.1815G>A	c.(1813-1815)gcG>gcA	p.A605A	RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000380789.1_Silent_p.A605A|RP11-624C23.1_ENST00000519689.1_RNA|RP11-561E1.1_ENST00000519364.1_RNA|ADAM7_ENST00000520720.1_Silent_p.A377A	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	605	Cys-rich.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		GCCTGGTGGCGTCAGGAACAA	0.358													G|||	270	0.0539137	0.0416	0.121	5008	,	,		18897	0.001		0.0855	False		,,,				2504	0.045				p.A605A		Atlas-SNP	.											.	ADAM7	165	.	0			c.G1815A						PASS	.	G		200,4206	126.1+/-163.2	3,194,2006	80.0	79.0	79.0		1815	0.3	0.0	8	dbSNP_120	79	719,7879	174.6+/-224.8	25,669,3605	no	coding-synonymous	ADAM7	NM_003817.2		28,863,5611	AA,AG,GG		8.3624,4.5393,7.0671		605/755	24350715	919,12085	2203	4299	6502	SO:0001819	synonymous_variant	8756	exon16			GGTGGCGTCAGGA	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1815G>A	8.37:g.24350715G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	42	0.482759	NM_003817	A8K8X7|O75959|Q6PEJ6	Silent	SNP	ENST00000175238.6	37	CCDS6045.1																																																																																			G|0.925;A|0.075	0.075	strong		0.358	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
SYNRG	11276	hgsc.bcm.edu	37	17	35937637	35937637	+	Missense_Mutation	SNP	T	T	C	rs12602536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:35937637T>C	ENST00000339208.6	-	7	804	c.664A>G	c.(664-666)Act>Gct	p.T222A	SYNRG_ENST00000346661.4_Missense_Mutation_p.T222A|SYNRG_ENST00000345615.4_Intron|SYNRG_ENST00000591288.1_Intron|SYNRG_ENST00000585472.1_Intron|SYNRG_ENST00000588194.1_Intron|SYNRG_ENST00000502449.2_Intron|SYNRG_ENST00000394378.2_Intron	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	222			T -> A (in dbSNP:rs12602536).		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)	p.T222A(1)		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						ACTTCAGAAGTATTTAATTTA	0.428													T|||	849	0.169529	0.0877	0.2176	5008	,	,		16631	0.1389		0.2097	False		,,,				2504	0.2362				p.T222A		Atlas-SNP	.											SYNRG,NS,carcinoma,0,1	SYNRG	101	1	1	Substitution - Missense(1)	prostate(1)	c.A664G						PASS	.	T	,,,,ALA/THR,,	442,3964	213.5+/-233.1	19,404,1780	154.0	161.0	159.0		,,,,664,,	2.0	0.9	17	dbSNP_120	159	1525,7075	288.1+/-298.6	127,1271,2902	yes	intron,intron,intron,intron,missense,intron,intron	SYNRG	NM_001163544.1,NM_001163545.1,NM_001163546.1,NM_001163547.1,NM_007247.4,NM_080550.3,NM_198882.1	,,,,58,,	146,1675,4682	CC,CT,TT		17.7326,10.0318,15.1238	,,,,benign,,	,,,,222/1315,,	35937637	1967,11039	2203	4300	6503	SO:0001583	missense	11276	exon7			CAGAAGTATTTAA	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.664A>G	17.37:g.35937637T>C	ENSP00000343610:p.Thr222Ala	Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	153	150	0.980392	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	353	0.16163003663003664	40	0.08130081300813008	72	0.19889502762430938	77	0.1346153846153846	164	0.21635883905013192	T	11.99	1.802382	0.31869	0.100318	0.177326	ENSG00000006114	ENST00000346661;ENST00000345615;ENST00000394379	T	0.30182	1.54	5.46	1.97	0.26223	.	0.346213	0.30302	N	0.009933	T	0.00012	0.0000	L	0.41236	1.265	0.35584	P	0.193465	P;B;B	0.37207	0.587;0.004;0.004	B;B;B	0.32724	0.151;0.006;0.006	T	0.28996	-1.0026	9	0.09590	T	0.72	-9.3107	4.795	0.13269	0.291:0.0787:0.0:0.6303	rs12602536;rs52810147;rs59102053;rs12602536	323;222;222	A8MYE0;Q9UMZ2-5;Q9UMZ2	.;.;SYNRG_HUMAN	A	222;222;323	ENSP00000005279:T222A	ENSP00000315722:T222A	T	-	1	0	SYNRG	33011750	0.997000	0.39634	0.931000	0.37212	0.899000	0.52679	0.400000	0.20932	0.320000	0.23234	0.482000	0.46254	ACT	C|0.151;T|0.849	0.151	strong		0.428	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
FAM47C	442444	hgsc.bcm.edu	37	X	37029254	37029254	+	Missense_Mutation	SNP	A	A	C	rs1995914	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:37029254A>C	ENST00000358047.3	+	1	2823	c.2771A>C	c.(2770-2772)aAt>aCt	p.N924T		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	924			N -> T (in dbSNP:rs1995914).							breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						AAAATCCAGAATGCACCAAAT	0.453													N|||	1396	0.369801	0.6445	0.2392	3775	,	,		15358	0.0982		0.0785	False		,,,				2504	0.2045				p.N924T		Atlas-SNP	.											.	FAM47C	267	.	0			c.A2771C						PASS	.	C	THR/ASN	2991,842		1003,538,447,90,124	85.0	87.0	86.0		2771	-1.7	0.0	X	dbSNP_92	86	783,5945		26,499,232,1903,1640	yes	missense	FAM47C	NM_001013736.2	65	1029,1037,679,1993,1764	CC,CA,C,AA,A		11.6379,21.9671,35.7353	benign	924/1036	37029254	3774,6787	2202	4300	6502	SO:0001583	missense	442444	exon1			TCCAGAATGCACC	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2771A>C	X.37:g.37029254A>C	ENSP00000367913:p.Asn924Thr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	495	0.298372513562387	216	0.7058823529411765	54	0.16981132075471697	37	0.06801470588235294	43	0.05922865013774105	C	0.001	-3.759422	0.00005	0.780329	0.116379	ENSG00000198173	ENST00000358047	T	0.42131	0.98	0.829	-1.66	0.08265	.	.	.	.	.	T	0.00012	0.0000	N	0.00823	-1.155	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.45789	-0.9237	7	0.14252	T	0.57	.	.	.	.	rs1995914;rs52815039;rs59553201;rs1995914	924	Q5HY64	FA47C_HUMAN	T	924	ENSP00000367913:N924T	ENSP00000367913:N924T	N	+	2	0	FAM47C	36939175	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.842000	0.04354	-4.876000	0.00028	-4.602000	0.00004	AAT	A|0.631;C|0.369	0.369	strong		0.453	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
MUC4	4585	hgsc.bcm.edu	37	3	195517124	195517124	+	Silent	SNP	G	G	A	rs1806440	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195517124G>A	ENST00000463781.3	-	2	1786	c.1327C>T	c.(1327-1329)Cta>Tta	p.L443L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.L443L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	448					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TTTGGAGGTAGAGAACTGGGG	0.493													N|||	637	0.127196	0.1679	0.0951	5008	,	,		19914	0.0456		0.173	False		,,,				2504	0.1319				p.L443L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C1327T						PASS	.		,,	554,3356		46,462,1447	218.0	214.0	215.0		,1327,	-0.1	0.0	3	dbSNP_92	215	1424,6882		124,1176,2853	yes	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	170,1638,4300	AA,AG,GG		17.1442,14.1688,16.1919	,,	,443/5413,	195517124	1978,10238	1955	4153	6108	SO:0001819	synonymous_variant	4585	exon2			GAGGTAGAGAACT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.1327C>T	3.37:g.195517124G>A		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.871;A|0.129	0.129	strong		0.493	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CXorf36	79742	hgsc.bcm.edu	37	X	45051111	45051111	+	Missense_Mutation	SNP	C	C	T	rs1132201	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:45051111C>T	ENST00000398000.2	-	2	457	c.383G>A	c.(382-384)aGa>aAa	p.R128K	CXorf36_ENST00000477281.1_5'UTR|RP11-342D14.1_ENST00000438181.1_RNA|RP11-342D14.1_ENST00000450527.1_RNA|CXorf36_ENST00000377934.4_Missense_Mutation_p.R128K	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	128			R -> K (in dbSNP:rs1132201). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						GGCACAGATTCTCCTGTCTGA	0.498													C|||	1659	0.43947	0.1324	0.3775	3775	,	,		13466	0.5724		0.2525	False		,,,				2504	0.3998				p.R128K		Atlas-SNP	.											.	CXorf36	53	.	0			c.G383A						PASS	.	C	LYS/ARG,LYS/ARG	774,3061		62,538,112,1032,459	89.0	84.0	86.0		383,383	2.9	1.0	X	dbSNP_86	86	2185,4543		261,1067,596,1100,1276	yes	missense,missense	CXorf36	NM_024689.2,NM_176819.3	26,26	323,1605,708,2132,1735	TT,TC,T,CC,C		32.4762,20.1825,28.0129	benign,benign	128/183,128/434	45051111	2959,7604	2203	4300	6503	SO:0001583	missense	79742	exon2			CAGATTCTCCTGT	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.383G>A	X.37:g.45051111C>T	ENSP00000381086:p.Arg128Lys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	37	CCDS48096.1	717	0.4321880650994575	48	0.10714285714285714	80	0.29411764705882354	220	0.625	133	0.2078125	C	12.98	2.101528	0.37048	0.201825	0.324762	ENSG00000147113	ENST00000398000;ENST00000377934	T;T	0.30448	1.62;1.53	5.63	2.92	0.33932	.	0.225472	0.38897	N	0.001527	T	0.00012	0.0000	N	0.26042	0.785	0.40769	P	0.016925999999999997	B;B	0.20052	0.005;0.041	B;B	0.14578	0.006;0.011	T	0.40887	-0.9539	9	0.08599	T	0.76	.	8.5812	0.33630	0.0:0.6796:0.0:0.3204	rs1132201;rs3192766;rs17261166;rs52822123;rs56729282;rs1132201	128;128	Q9H7Y0-2;Q9H7Y0	.;CX036_HUMAN	K	128	ENSP00000381086:R128K;ENSP00000367168:R128K	ENSP00000367168:R128K	R	-	2	0	CXorf36	44936055	1.000000	0.71417	0.992000	0.48379	0.972000	0.66771	1.172000	0.31908	0.553000	0.29044	-0.191000	0.12829	AGA	0|0.013;T|0.348	0.348	strong		0.498	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449383	89449383	+	Missense_Mutation	SNP	G	G	A	rs147771633	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449383G>A	ENST00000321792.5	-	2	554	c.127C>T	c.(127-129)Cgt>Tgt	p.R43C	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.R43C	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	43	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										TTGGTTTCACGGTCTTTTATC	0.413											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R43C		Atlas-SNP	.											CCBL2,NS,carcinoma,0,1	.	.	1	0			c.C127T						PASS	.	G	,,CYS/ARG,CYS/ARG	2,4404	2.1+/-5.4	0,2,2201	208.0	196.0	200.0		,,127,127	-0.9	1.0	1	dbSNP_134	200	13,8587	6.4+/-24.3	0,13,4287	no	intron,intron,missense,missense	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,180,180	0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153	,,probably-damaging,probably-damaging	,,43/391,43/391	89449383	15,12991	2203	4300	6503	SO:0001583	missense	494115	exon3			TTTCACGGTCTTT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.127C>T	1.37:g.89449383G>A	ENSP00000318415:p.Arg43Cys	Somatic	249	0	0	1267	WXS	Illumina HiSeq	Phase_I	381	66	0.173228	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.008797	0.75046	4.54E-4	0.001512	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.85702	-2.02;-2.02	1.59	-0.931	0.10438	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	U	0.000000	D	0.84938	0.5583	M	0.80616	2.505	0.49687	D	0.999813	D	0.71674	0.998	D	0.65987	0.94	T	0.81988	-0.0680	10	0.87932	D	0	-3.8545	4.2107	0.10510	0.4537:0.0:0.5463:0.0	.	43	Q96E39	RBMXL_HUMAN	C	43	ENSP00000318415:R43C;ENSP00000446099:R43C	ENSP00000318415:R43C	R	-	1	0	RBMXL1	89221971	1.000000	0.71417	0.976000	0.42696	0.893000	0.52053	3.231000	0.51294	-0.417000	0.07461	0.306000	0.20318	CGT	G|0.500;A|0.500	0.500	weak		0.413	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
ATP8A2	51761	hgsc.bcm.edu	37	13	26273403	26273403	+	Silent	SNP	C	C	A	rs7335858	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:26273403C>A	ENST00000381655.2	+	25	2446	c.2304C>A	c.(2302-2304)acC>acA	p.T768T	ATP8A2_ENST00000255283.8_Silent_p.T728T|ATP8A2_ENST00000491840.1_3'UTR	NM_016529.4	NP_057613.4	Q9NTI2	AT8A2_HUMAN	ATPase, aminophospholipid transporter, class I, type 8A, member 2	728					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)		ATGGCCACACCCTGAAGTACG	0.552													C|||	365	0.0728834	0.1324	0.0562	5008	,	,		16412	0.0208		0.0994	False		,,,				2504	0.0307				p.T768T		Atlas-SNP	.											ATP8A2,middle_lobe,carcinoma,+1,1	ATP8A2	181	1	0			c.C2304A						PASS	.	C		453,3529		22,409,1560	87.0	83.0	85.0		2304	-6.6	0.7	13	dbSNP_116	85	876,7450		53,770,3340	no	coding-synonymous	ATP8A2	NM_016529.4		75,1179,4900	AA,AC,CC		10.5213,11.3762,10.7979		768/1189	26273403	1329,10979	1991	4163	6154	SO:0001819	synonymous_variant	51761	exon25			CCACACCCTGAAG	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.2304C>A	13.37:g.26273403C>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	97	50	0.515464	NM_016529	Q9H527|Q9NPU6|Q9NTL2|Q9NYM3	Silent	SNP	ENST00000381655.2	37	CCDS41873.1																																																																																			C|0.913;A|0.087	0.087	strong		0.552	ATP8A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044236.2	NM_016529	
ANKMY2	57037	hgsc.bcm.edu	37	7	16655387	16655387	+	Silent	SNP	C	C	T	rs11540037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:16655387C>T	ENST00000306999.2	-	5	756	c.513G>A	c.(511-513)acG>acA	p.T171T		NM_020319.2	NP_064715.1	Q8IV38	ANKY2_HUMAN	ankyrin repeat and MYND domain containing 2	171						cilium (GO:0005929)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|urinary_tract(1)	23	Lung NSC(10;0.103)|all_lung(11;0.204)			UCEC - Uterine corpus endometrioid carcinoma (126;0.195)		GATGAAGATTCGTTGTGGTGA	0.413													C|||	883	0.176318	0.0681	0.1657	5008	,	,		16455	0.2173		0.1948	False		,,,				2504	0.2689				p.T171T		Atlas-SNP	.											.	ANKMY2	46	.	0			c.G513A						PASS	.	C		420,3986	203.5+/-225.9	16,388,1799	95.0	92.0	93.0		513	-1.6	1.0	7	dbSNP_120	93	1795,6805	323.0+/-315.8	178,1439,2683	no	coding-synonymous	ANKMY2	NM_020319.2		194,1827,4482	TT,TC,CC		20.8721,9.5325,17.0306		171/442	16655387	2215,10791	2203	4300	6503	SO:0001819	synonymous_variant	57037	exon5			AAGATTCGTTGTG	AK001740	CCDS5361.1	7p21	2013-01-10			ENSG00000106524	ENSG00000106524		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	25370	protein-coding gene	gene with protein product						12477932	Standard	NM_020319		Approved	DKFZP564O043, ZMYND20	uc003sti.3	Q8IV38	OTTHUMG00000090806	ENST00000306999.2:c.513G>A	7.37:g.16655387C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_020319	A4D124|Q659G1|Q96BL3	Silent	SNP	ENST00000306999.2	37	CCDS5361.1																																																																																			T|0.144;G|0.146;C|0.687;A|0.024	0.144	strong		0.413	ANKMY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207600.2	NM_020319	
MICA	100507436	hgsc.bcm.edu	37	6	31378387	31378387	+	Silent	SNP	T	T	C	rs1063631|rs386699190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31378387T>C	ENST00000449934.2	+	2	192	c.138T>C	c.(136-138)ctT>ctC	p.L46L	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CAGGGTTTCTTGCTGAGGTAC	0.532													c|||	1829	0.365216	0.4788	0.4078	5008	,	,		19543	0.3016		0.3141	False		,,,				2504	0.2996				p.L46L		Atlas-SNP	.											MICA,bladder,carcinoma,0,1	MICA	21	1	0			c.T138C						PASS	.	C		573,811		132,309,251	19.0	21.0	21.0		138	-5.8	0.0	6	dbSNP_86	21	881,2301		126,629,836	no	coding-synonymous	MICA	NM_001177519.1		258,938,1087	CC,CT,TT		27.687,41.4017,31.8441		46/333	31378387	1454,3112	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon2			GTTTCTTGCTGAG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.138T>C	6.37:g.31378387T>C		Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	238	234	0.983193	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			T|0.642;C|0.358	0.358	strong		0.532	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
THOC5	8563	hgsc.bcm.edu	37	22	29908072	29908072	+	Missense_Mutation	SNP	C	C	T	rs1049534	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:29908072C>T	ENST00000490103.1	-	18	1857	c.1735G>A	c.(1735-1737)Gtt>Att	p.V579I	CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.V579I|THOC5_ENST00000397873.2_Missense_Mutation_p.V579I|THOC5_ENST00000397872.1_Missense_Mutation_p.V579I	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	579			V -> I (in dbSNP:rs1049534). {ECO:0000269|PubMed:15461802, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8242058}.		blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AGCTGGAAAACAGGTGGGATG	0.542													T|||	1112	0.222045	0.0983	0.1988	5008	,	,		21300	0.4167		0.2425	False		,,,				2504	0.184				p.V579I		Atlas-SNP	.											.	THOC5	58	.	0			c.G1735A						PASS	.	T	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	559,3847	774.1+/-414.0	35,489,1679	128.0	99.0	109.0		1735,1735,1735,1735	1.1	0.1	22	dbSNP_86	109	1957,6643	725.1+/-406.5	224,1509,2567	yes	missense,missense,missense,missense	THOC5	NM_001002877.1,NM_001002878.1,NM_001002879.1,NM_003678.4	29,29,29,29	259,1998,4246	TT,TC,CC		22.7558,12.6872,19.3449	benign,benign,benign,benign	579/684,579/684,579/684,579/684	29908072	2516,10490	2203	4300	6503	SO:0001583	missense	8563	exon19			GGAAAACAGGTGG	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1735G>A	22.37:g.29908072C>T	ENSP00000420306:p.Val579Ile	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	194	193	0.994845	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	589	0.2696886446886447	58	0.11788617886178862	66	0.18232044198895028	273	0.4772727272727273	192	0.2532981530343008	T	0.010	-1.780653	0.00634	0.126872	0.227558	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.20598	2.06;2.06;2.06;2.06	6.06	1.09	0.20402	.	0.352841	0.34338	N	0.004059	T	0.00012	0.0000	N	0.01188	-0.97	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.48007	-0.9072	9	0.18710	T	0.47	-21.0443	13.851	0.63496	0.0:0.467:0.0:0.533	rs1049534;rs17844989;rs17857748;rs52805826;rs58951214;rs1049534	579	Q13769	THOC5_HUMAN	I	579	ENSP00000420306:V579I;ENSP00000380970:V579I;ENSP00000380969:V579I;ENSP00000380971:V579I	ENSP00000380969:V579I	V	-	1	0	THOC5	28238072	0.001000	0.12720	0.139000	0.22197	0.186000	0.23388	-0.307000	0.08167	-0.692000	0.05128	-2.276000	0.00273	GTT	C|0.771;T|0.229	0.229	strong		0.542	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
PRMT2	3275	hgsc.bcm.edu	37	21	48071901	48071901	+	Intron	SNP	C	C	T	rs77776707	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:48071901C>T	ENST00000397637.1	+	6	1608				PRMT2_ENST00000291705.6_Intron|PRMT2_ENST00000355680.3_Intron|PRMT2_ENST00000334494.4_Missense_Mutation_p.P280S|PRMT2_ENST00000451211.2_Intron|PRMT2_ENST00000440086.1_Intron|PRMT2_ENST00000458387.2_Intron|PRMT2_ENST00000397638.2_Intron			P55345	ANM2_HUMAN	protein arginine methyltransferase 2						developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		TCTCTCCTGGCCCATCTTCCT	0.552													C|||	41	0.0081869	0.0008	0.0072	5008	,	,		20121	0.0159		0.007	False		,,,				2504	0.0123				p.P280S		Atlas-SNP	.											.	PRMT2	48	.	0			c.C838T						PASS	.	C	,SER/PRO,,,	2,1750		0,2,874	75.0	68.0	70.0		,838,,,	-1.7	0.0	21	dbSNP_131	70	11,3971		0,11,1980	no	intron,missense,intron,intron,intron	PRMT2	NM_001242864.1,NM_001242865.1,NM_001242866.1,NM_001535.3,NM_206962.2	,74,,,	0,13,2854	TT,TC,CC		0.2762,0.1142,0.2267	,,,,	,280/285,,,	48071901	13,5721	876	1991	2867	SO:0001627	intron_variant	3275	exon7			TCCTGGCCCATCT	U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"""Protein arginine methyltransferases"""	5186	protein-coding gene	gene with protein product		601961	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1"", ""HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"""	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.654+2250C>T	21.37:g.48071901C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	154	70	0.454545	NM_001242865	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	11	0.019230769230769232	7	0.009234828496042216	.	8.123	0.781437	0.16120	0.001142	0.002762	ENSG00000160310	ENST00000334494	T	0.66280	-0.2	0.852	-1.7	0.08159	.	.	.	.	.	T	0.40839	0.1133	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.50118	-0.8865	6	0.87932	D	0	.	6.4147	0.21710	0.0:0.6399:0.0:0.3601	.	.	.	.	S	280	ENSP00000335490:P280S	ENSP00000335490:P280S	P	+	1	0	PRMT2	46896329	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	-0.364000	0.07583	-1.587000	0.01630	-1.786000	0.00637	CCC	C|0.992;T|0.008	0.008	strong		0.552	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535	
RSPH4A	345895	hgsc.bcm.edu	37	6	116951678	116951678	+	Missense_Mutation	SNP	A	A	C	rs9488991	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:116951678A>C	ENST00000229554.5	+	5	2016	c.1879A>C	c.(1879-1881)Aac>Cac	p.N627H	RSPH4A_ENST00000368581.4_Silent_p.P581P|RSPH4A_ENST00000368580.4_Missense_Mutation_p.N380H	NM_001010892.2	NP_001010892.1	Q5TD94	RSH4A_HUMAN	radial spoke head 4 homolog A (Chlamydomonas)	627			N -> H (in dbSNP:rs9488991).		axoneme assembly (GO:0035082)|cilium movement (GO:0003341)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|radial spoke (GO:0001534)				breast(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27						CCTTCAATCCAACCTTTGGCC	0.408									Kartagener syndrome				A|||	678	0.135383	0.2655	0.1988	5008	,	,		17640	0.0188		0.0437	False		,,,				2504	0.1288				p.N627H		Atlas-SNP	.											.	RSPH4A	54	.	0			c.A1879C						PASS	.	A	HIS/ASN,	999,3407	374.6+/-321.3	113,773,1317	153.0	128.0	136.0		1879,1743	5.5	1.0	6	dbSNP_119	136	448,8152	135.2+/-192.5	13,422,3865	yes	missense,coding-synonymous	RSPH4A	NM_001010892.2,NM_001161664.1	68,	126,1195,5182	CC,CA,AA		5.2093,22.6736,11.1256	probably-damaging,	627/717,581/601	116951678	1447,11559	2203	4300	6503	SO:0001583	missense	345895	exon5	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAATCCAACCTTT		CCDS34521.1, CCDS55051.1	6q22.1	2012-05-03	2009-02-17	2009-02-17	ENSG00000111834	ENSG00000111834			21558	protein-coding gene	gene with protein product		612647	"""radial spokehead-like 3"""	RSHL3		19200523	Standard	NM_001010892		Approved	dJ412I7.1, FLJ37974, RSPH6B, CILD11	uc003pxe.2	Q5TD94	OTTHUMG00000015444	ENST00000229554.5:c.1879A>C	6.37:g.116951678A>C	ENSP00000229554:p.Asn627His	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	116	102	0.87931	NM_001010892	B4DSI1|Q3KP24|Q5TD95	Missense_Mutation	SNP	ENST00000229554.5	37	CCDS34521.1	234	0.10714285714285714	124	0.25203252032520324	69	0.19060773480662985	6	0.01048951048951049	35	0.04617414248021108	A	24.4	4.527986	0.85706	0.226736	0.052093	ENSG00000111834	ENST00000229554;ENST00000447842;ENST00000368580	T;T	0.20069	2.1;2.1	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.26231	0.0640	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.97110	1.0	T	0.07290	-1.0780	8	0.15952	T	0.53	-17.9881	13.5445	0.61695	1.0:0.0:0.0:0.0	rs9488991;rs56447201;rs59132035;rs9488991	627	Q5TD94	RSH4A_HUMAN	H	627;422;380	ENSP00000229554:N627H;ENSP00000357569:N380H	ENSP00000229554:N627H	N	+	1	0	RSPH4A	117058371	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.954000	0.93051	2.094000	0.63399	0.482000	0.46254	AAC	A|0.888;C|0.112	0.112	strong		0.408	RSPH4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041960.1	NM_001010892	
GGT1	2678	hgsc.bcm.edu	37	22	25023444	25023444	+	Missense_Mutation	SNP	G	G	T	rs201546887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:25023444G>T	ENST00000400382.1	+	12	1821	c.1066G>T	c.(1066-1068)Gcc>Tcc	p.A356S	GGT1_ENST00000400383.1_Missense_Mutation_p.A356S|GGT1_ENST00000248923.4_Missense_Mutation_p.A356S|GGT1_ENST00000404532.1_Missense_Mutation_p.A12S|GGT1_ENST00000404920.1_Missense_Mutation_p.A12S|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Missense_Mutation_p.A12S|GGT1_ENST00000403838.1_Missense_Mutation_p.A12S|GGT1_ENST00000401885.1_Missense_Mutation_p.A12S|GGT1_ENST00000406383.2_Missense_Mutation_p.A356S|GGT1_ENST00000400380.1_Missense_Mutation_p.A356S			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	356				A -> S (in Ref. 10; AAI28240). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.A356S(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	CCAGCTCCGGGCCCAGATCTC	0.652													g|||	27	0.00539137	0.0023	0.0058	5008	,	,		10309	0.0		0.0109	False		,,,				2504	0.0092				p.A356S		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	prostate(1)	c.G1066T						scavenged	.						45.0	46.0	45.0					22																	25023444		2201	4297	6498	SO:0001583	missense	2678	exon12			CTCCGGGCCCAGA	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.1066G>T	22.37:g.25023444G>T	ENSP00000383232:p.Ala356Ser	Somatic	237	1	0.00421941		WXS	Illumina HiSeq	Phase_I	312	51	0.163462	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	0.717	-0.784921	0.02907	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23	3.4	2.37	0.29283	.	0.683912	0.14246	N	0.331733	T	0.03695	0.0105	N	0.16066	0.365	0.21527	N	0.999659	B	0.02656	0.0	B	0.09377	0.004	T	0.45789	-0.9237	10	0.09084	T	0.74	-4.876	3.5096	0.07703	0.2536:0.2162:0.5302:0.0	.	356	P19440	GGT1_HUMAN	S	356;356;356;356;356;356;12;12;12;12;12	ENSP00000248923:A356S;ENSP00000393537:A356S;ENSP00000383232:A356S;ENSP00000383233:A356S;ENSP00000383231:A356S;ENSP00000385975:A356S;ENSP00000384381:A12S;ENSP00000385445:A12S;ENSP00000384820:A12S;ENSP00000385016:A12S;ENSP00000385001:A12S	ENSP00000248923:A356S	A	+	1	0	GGT1	23353444	0.490000	0.26012	0.009000	0.14445	0.418000	0.31294	1.292000	0.33342	0.762000	0.33152	0.298000	0.19748	GCC	.	.	weak		0.652	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
ZNF195	7748	hgsc.bcm.edu	37	11	3381369	3381369	+	Missense_Mutation	SNP	G	G	C	rs62619253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:3381369G>C	ENST00000399602.4	-	6	995	c.869C>G	c.(868-870)cCt>cGt	p.P290R	ZNF195_ENST00000526601.1_Missense_Mutation_p.P271R|ZNF195_ENST00000005082.9_Missense_Mutation_p.P267R|ZNF195_ENST00000343338.7_Missense_Mutation_p.P222R|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000354599.6_Missense_Mutation_p.P218R|ZNF195_ENST00000429541.2_Missense_Mutation_p.P222R|ZNF195_ENST00000438262.2_3'UTR	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	290				P -> R (in Ref. 2; BAG53114). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		AATGTTCTCAGGTTCAGTAAA	0.363													t|||	1121	0.223842	0.1808	0.1167	5008	,	,		19200	0.4067		0.1093	False		,,,				2504	0.2873				p.P290R		Atlas-SNP	.											.	ZNF195	77	.	0			c.C869G						PASS	.	T	ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO,ARG/PRO	624,3186		53,518,1334	96.0	92.0	93.0		800,869,812,734,665,653	1.1	0.0	11	dbSNP_129	93	944,7368		57,830,3269	no	missense,missense,missense,missense,missense,missense	ZNF195	NM_001130519.2,NM_001130520.2,NM_001242841.1,NM_001242842.1,NM_001242843.1,NM_007152.4	103,103,103,103,103,103	110,1348,4603	CC,CG,GG		11.3571,16.378,12.9352	benign,benign,benign,benign,benign,benign	267/607,290/630,271/611,245/585,222/562,218/558	3381369	1568,10554	1905	4156	6061	SO:0001583	missense	7748	exon6			TTCTCAGGTTCAG		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"""Zinc fingers, C2H2-type"", ""-"""	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.869C>G	11.37:g.3381369G>C	ENSP00000382511:p.Pro290Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_001130520	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	37	CCDS44522.1	470	0.21520146520146521	82	0.16666666666666666	48	0.13259668508287292	256	0.44755244755244755	84	0.11081794195250659	t	0.319	-0.963046	0.02249	0.16378	0.113571	ENSG00000005801	ENST00000354599;ENST00000399602;ENST00000343338;ENST00000429541;ENST00000005082;ENST00000526601;ENST00000528410	T;T;T;T;T;T;T	0.14640	3.39;3.41;3.37;3.37;3.41;3.41;2.49	1.11	1.11	0.20524	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.11364	0.135	0.53688	P	2.8999999999945736E-5	B;B;B;B;B;B	0.20780	0.048;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.18871	0.023;0.0;0.0;0.0;0.0;0.0	T	0.45629	-0.9248	8	0.87932	D	0	.	5.0372	0.14440	0.0:0.0:0.3092:0.6908	rs62619253	271;149;267;222;290;218	O14628-6;Q59EZ7;O14628-5;O14628-7;O14628;O14628-4	.;.;.;.;ZN195_HUMAN;.	R	218;290;222;222;267;271;245	ENSP00000346613:P218R;ENSP00000382511:P290R;ENSP00000344483:P222R;ENSP00000387998:P222R;ENSP00000005082:P267R;ENSP00000435828:P271R;ENSP00000431937:P245R	ENSP00000005082:P267R	P	-	2	0	ZNF195	3337945	0.996000	0.38824	0.001000	0.08648	0.021000	0.10359	2.870000	0.48451	-0.436000	0.07254	-0.824000	0.03097	CCT	G|0.817;C|0.183	0.183	strong		0.363	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2		
RSAD1	55316	hgsc.bcm.edu	37	17	48559559	48559559	+	Silent	SNP	A	A	G	rs7210579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48559559A>G	ENST00000258955.2	+	4	667	c.582A>G	c.(580-582)gtA>gtG	p.V194V		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	194					porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GCGTGTCTGTAGACTTGATGC	0.667											OREG0024567	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1429	0.285343	0.4909	0.2723	5008	,	,		13876	0.0804		0.2594	False		,,,				2504	0.2546				p.V194V		Atlas-SNP	.											RSAD1,colon,carcinoma,0,1	RSAD1	36	1	0			c.A582G						PASS	.	G		1952,2454	593.0+/-387.9	460,1032,711	34.0	39.0	37.0		582	3.4	1.0	17	dbSNP_116	37	2150,6448	680.1+/-403.6	296,1558,2445	no	coding-synonymous	RSAD1	NM_018346.1		756,2590,3156	GG,GA,AA		25.0058,44.3032,31.5441		194/443	48559559	4102,8902	2203	4299	6502	SO:0001819	synonymous_variant	55316	exon4			GTCTGTAGACTTG	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.582A>G	17.37:g.48559559A>G		Somatic	71	0	0	955	WXS	Illumina HiSeq	Phase_I	83	83	1	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Silent	SNP	ENST00000258955.2	37	CCDS11569.1																																																																																			A|0.693;G|0.307	0.307	strong		0.667	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346	
ISX	91464	hgsc.bcm.edu	37	22	35463249	35463249	+	Missense_Mutation	SNP	C	C	T	rs362090	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:35463249C>T	ENST00000308700.6	+	1	1121	c.169C>T	c.(169-171)Ccc>Tcc	p.P57S	RP1-272J12.1_ENST00000448318.4_RNA|ISX_ENST00000404699.2_Missense_Mutation_p.P57S	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	57			P -> S (in dbSNP:rs362090). {ECO:0000269|PubMed:15489334}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						TGAAGAGGGCCCCGGAGAAGC	0.567													C|||	2880	0.57508	0.4448	0.5432	5008	,	,		17652	0.7827		0.507	False		,,,				2504	0.6299				p.P57S		Atlas-SNP	.											.	ISX	62	.	0			c.C169T						PASS	.	C	SER/PRO	2090,2314		491,1108,603	31.0	34.0	33.0		169	-6.2	0.0	22	dbSNP_79	33	4250,4350		1051,2148,1101	yes	missense	ISX	NM_001008494.1	74	1542,3256,1704	TT,TC,CC		49.4186,47.4569,48.7542	benign	57/246	35463249	6340,6664	2202	4300	6502	SO:0001583	missense	91464	exon1			GAGGGCCCCGGAG	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.169C>T	22.37:g.35463249C>T	ENSP00000311492:p.Pro57Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	1262	0.5778388278388278	204	0.4146341463414634	210	0.580110497237569	452	0.7902097902097902	396	0.5224274406332454	C	8.515	0.867336	0.17250	0.474569	0.494186	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.90732	-2.72;-2.72	4.9	-6.22	0.02058	.	1.523810	0.04048	N	0.304336	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	0.36432	-0.9748	9	0.08599	T	0.76	.	1.7971	0.03063	0.2911:0.389:0.1379:0.182	rs362090;rs362090	57	Q2M1V0	ISX_HUMAN	S	57	ENSP00000311492:P57S;ENSP00000386037:P57S	ENSP00000311492:P57S	P	+	1	0	ISX	33793249	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.951000	0.00678	-0.993000	0.03467	-0.140000	0.14226	CCC	C|0.453;T|0.547	0.547	strong		0.567	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951754	130951754	+	Missense_Mutation	SNP	G	G	T	rs13000249	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130951754G>T	ENST00000312988.7	-	4	761	c.661C>A	c.(661-663)Cgt>Agt	p.R221S		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	221					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					TACGTGGGACGTTCAATGTCC	0.542																																					p.R221S		Atlas-SNP	.											.	TUBA3E	73	.	0			c.C661A						PASS	.						144.0	99.0	114.0					2																	130951754		2203	4296	6499	SO:0001583	missense	112714	exon4			TGGGACGTTCAAT	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.661C>A	2.37:g.130951754G>T	ENSP00000318197:p.Arg221Ser	Somatic	409	1	0.00244499		WXS	Illumina HiSeq	Phase_I	401	116	0.289277	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	748	0.3424908424908425	105	0.21341463414634146	144	0.39779005524861877	245	0.42832167832167833	254	0.33509234828496043	g	5.322	0.244819	0.10077	.	.	ENSG00000152086	ENST00000312988	T	0.68903	-0.36	2.92	2.03	0.26663	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.47852	U	0.000204	T	0.00012	0.0000	L	0.52759	1.655	0.22866	P	0.99863671	P	0.37731	0.607	P	0.49683	0.619	T	0.38972	-0.9636	9	0.87932	D	0	.	7.8744	0.29584	0.1321:0.0:0.8679:0.0	rs13000249;rs36038899	221	Q6PEY2	TBA3E_HUMAN	S	221	ENSP00000318197:R221S	ENSP00000318197:R221S	R	-	1	0	TUBA3E	130668224	1.000000	0.71417	0.999000	0.59377	0.183000	0.23260	2.977000	0.49297	0.584000	0.29591	0.449000	0.29647	CGT	G|0.500;T|0.500	0.500	weak		0.542	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
CASP9	842	hgsc.bcm.edu	37	1	15850603	15850603	+	Silent	SNP	G	G	A	rs4645983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15850603G>A	ENST00000333868.5	-	1	187	c.93C>T	c.(91-93)agC>agT	p.S31S	CASP9_ENST00000375890.4_Intron|DNAJC16_ENST00000375838.1_5'Flank|DNAJC16_ENST00000375847.3_5'Flank|CASP9_ENST00000348549.5_Silent_p.S31S|DNAJC16_ENST00000375849.1_5'Flank|CASP9_ENST00000546424.1_Silent_p.S31S|CASP9_ENST00000469637.1_Intron	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	31	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		ACAGCTCGCGGCTCAGCAGGG	0.721													G|||	1180	0.235623	0.4425	0.1873	5008	,	,		6140	0.0565		0.2177	False		,,,				2504	0.1933				p.S31S		Atlas-SNP	.											.	CASP9	40	.	0			c.C93T						PASS	.	G	,	1542,2670		284,974,848	8.0	11.0	10.0		93,	1.2	0.3	1	dbSNP_111	10	1607,6705		156,1295,2705	no	coding-synonymous,intron	CASP9	NM_001229.3,NM_032996.2	,	440,2269,3553	AA,AG,GG		19.3335,36.6097,25.1437	,	31/417,	15850603	3149,9375	2106	4156	6262	SO:0001819	synonymous_variant	842	exon1			CTCGCGGCTCAGC	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.93C>T	1.37:g.15850603G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	26	18	0.692308	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Silent	SNP	ENST00000333868.5	37	CCDS158.1																																																																																			G|0.777;A|0.223	0.223	strong		0.721	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
OR6C74	254783	hgsc.bcm.edu	37	12	55641255	55641255	+	Nonsense_Mutation	SNP	C	C	T	rs4522268	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55641255C>T	ENST00000343870.4	+	1	274	c.184C>T	c.(184-186)Cga>Tga	p.R62*		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						TTTCTTCCTCCGAAATTTCTC	0.388													C|||	1180	0.235623	0.1483	0.2334	5008	,	,		18707	0.1171		0.333	False		,,,				2504	0.3773				p.R62X		Atlas-SNP	.											OR6C74,colon,carcinoma,0,6	OR6C74	52	6	0			c.C184T						PASS	.	C	stop/ARG	818,3588	324.8+/-298.8	65,688,1450	156.0	155.0	155.0		184	1.7	0.6	12	dbSNP_111	155	2719,5881	434.5+/-357.7	426,1867,2007	no	stop-gained	OR6C74	NM_001005490.1		491,2555,3457	TT,TC,CC		31.6163,18.5656,27.1951		62/313	55641255	3537,9469	2203	4300	6503	SO:0001587	stop_gained	254783	exon1			TTCCTCCGAAATT		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"""GPCR / Class A : Olfactory receptors"""	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.184C>T	12.37:g.55641255C>T	ENSP00000342836:p.Arg62*	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	214	92	0.429907	NM_001005490		Nonsense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	495	0.22664835164835165	76	0.15447154471544716	98	0.27071823204419887	74	0.12937062937062938	247	0.3258575197889182	c	23.3	4.402942	0.83230	0.185656	0.316163	ENSG00000197706	ENST00000343870	.	.	.	4.83	1.73	0.24493	.	0.000000	0.43919	D	0.000516	.	.	.	.	.	.	0.09310	P	0.9999999999999993	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.628	0.17492	0.2419:0.5656:0.1184:0.0742	rs4522268;rs17382945;rs52829092;rs58701179;rs4522268	.	.	.	X	62	.	ENSP00000342836:R62X	R	+	1	2	OR6C74	53927522	0.000000	0.05858	0.611000	0.29010	0.940000	0.58332	-1.308000	0.02730	0.706000	0.31912	-0.234000	0.12200	CGA	C|0.743;N|0.000	.	strong		0.388	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
CMYA5	202333	hgsc.bcm.edu	37	5	79041057	79041057	+	Missense_Mutation	SNP	A	A	G	rs12514461	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:79041057A>G	ENST00000446378.2	+	4	10778	c.10747A>G	c.(10747-10749)Aaa>Gaa	p.K3583E		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3583	B-box coiled-coil; BBC.		K -> E (in dbSNP:rs12514461). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AAACTGTAGTAAAAATGAGAA	0.353													A|||	499	0.0996406	0.0393	0.1744	5008	,	,		18473	0.0833		0.1252	False		,,,				2504	0.1186				p.K3583E		Atlas-SNP	.											.	CMYA5	643	.	0			c.A10747G						PASS	.	A	GLU/LYS	176,3482		8,160,1661	30.0	30.0	30.0		10747	5.4	1.0	5	dbSNP_120	30	903,7257		57,789,3234	yes	missense	CMYA5	NM_153610.3	56	65,949,4895	GG,GA,AA		11.0662,4.8114,9.1301	benign	3583/4070	79041057	1079,10739	1829	4080	5909	SO:0001583	missense	202333	exon4			TGTAGTAAAAATG	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.10747A>G	5.37:g.79041057A>G	ENSP00000394770:p.Lys3583Glu	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	222	0.10164835164835165	20	0.04065040650406504	58	0.16022099447513813	45	0.07867132867132867	99	0.13060686015831136	A	14.25	2.478239	0.44044	0.048114	0.110662	ENSG00000164309	ENST00000446378	T	0.26518	1.73	5.43	5.43	0.79202	.	0.000000	0.53938	D	0.000044	T	0.00144	0.0004	L	0.61036	1.89	0.28591	P	0.9096466	D	0.57899	0.981	P	0.53490	0.727	T	0.13202	-1.0518	9	0.59425	D	0.04	.	8.2949	0.31980	0.8513:0.0:0.1487:0.0	rs12514461;rs52825873;rs58659811;rs12514461	3583	Q8N3K9	CMYA5_HUMAN	E	3583	ENSP00000394770:K3583E	ENSP00000394770:K3583E	K	+	1	0	CMYA5	79076813	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.280000	0.58959	2.179000	0.69175	0.533000	0.62120	AAA	A|0.904;G|0.096	0.096	strong		0.353	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
FAM53A	152877	hgsc.bcm.edu	37	4	1656801	1656801	+	Silent	SNP	A	A	C	rs62287700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1656801A>C	ENST00000308132.6	-	4	978	c.786T>G	c.(784-786)ccT>ccG	p.P262P	FAM53A_ENST00000461064.1_Silent_p.P262P|FAM53A_ENST00000472884.2_Silent_p.P262P|FAM53A_ENST00000489363.1_Silent_p.P262P	NM_001174070.1	NP_001167541.1	Q6NSI3	FA53A_HUMAN	family with sequence similarity 53, member A	262						nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10		all_epithelial(65;0.206)|Breast(71;0.212)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)			TGAGCACGCAAGGCTGTGAGC	0.701													C|||	1165	0.232628	0.1271	0.2305	5008	,	,		12141	0.0615		0.3698	False		,,,				2504	0.4121				p.P262P		Atlas-SNP	.											FAM53A,NS,carcinoma,0,1	FAM53A	25	1	0			c.T786G						PASS	.	C	,	668,3736		60,548,1594	23.0	20.0	21.0		786,786	-9.0	0.0	4	dbSNP_129	21	2920,5672		503,1914,1879	no	coding-synonymous,coding-synonymous	FAM53A	NM_001013622.3,NM_001174070.1	,	563,2462,3473	CC,CA,AA		33.9851,15.168,27.6085	,	262/399,262/399	1656801	3588,9408	2202	4296	6498	SO:0001819	synonymous_variant	152877	exon4			CACGCAAGGCTGT	BC070112	CCDS33939.1, CCDS75091.1	4p16.3	2005-08-09			ENSG00000174137	ENSG00000174137			31860	protein-coding gene	gene with protein product							Standard	NM_001013622		Approved	DNTNP	uc021xkl.1	Q6NSI3	OTTHUMG00000159855	ENST00000308132.6:c.786T>G	4.37:g.1656801A>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_001013622	Q6ZUL5	Silent	SNP	ENST00000308132.6	37	CCDS33939.1	481	0.22023809523809523	67	0.13617886178861788	102	0.281767955801105	30	0.05244755244755245	282	0.3720316622691293	C	0.053	-1.245306	0.01481	0.15168	0.339851	ENSG00000174137	ENST00000489029	.	.	.	4.51	-9.02	0.00741	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999996236	.	.	.	.	.	.	T	0.07443	-1.0772	3	.	.	.	3.862	1.6068	0.02685	0.2264:0.1615:0.3607:0.2513	rs62287700	.	.	.	R	112	.	.	L	-	2	0	FAM53A	1626598	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-3.903000	0.00338	-6.035000	0.00007	-6.070000	0.00000	CTT	A|0.738;C|0.262	0.262	strong		0.701	FAM53A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359224.1	NM_001013622	
SBK1	388228	hgsc.bcm.edu	37	16	28328916	28328916	+	Silent	SNP	C	C	T	rs113394773	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:28328916C>T	ENST00000341901.4	+	2	993	c.204C>T	c.(202-204)gaC>gaT	p.D68D		NM_001024401.2	NP_001019572.1	Q52WX2	SBK1_HUMAN	SH3 domain binding kinase 1	68	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(3)|ovary(1)	5						GGAAGGTTGACCTGGTGGTCT	0.627											OREG0023701	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	147	0.029353	0.0015	0.0605	5008	,	,		15668	0.001		0.0924	False		,,,				2504	0.0092				p.D68D		Atlas-SNP	.											.	SBK1	36	.	0			c.C204T						PASS	.	C		73,4321	62.9+/-100.1	0,73,2124	67.0	57.0	60.0		204	1.2	1.0	16	dbSNP_132	60	720,7880	173.5+/-223.9	25,670,3605	no	coding-synonymous	SBK1	NM_001024401.2		25,743,5729	TT,TC,CC		8.3721,1.6614,6.1028		68/425	28328916	793,12201	2197	4300	6497	SO:0001819	synonymous_variant	388228	exon2			GGTTGACCTGGTG		CCDS32416.1	16p11.2	2013-09-27	2013-09-27			ENSG00000188322			17699	protein-coding gene	gene with protein product			"""SH3-binding domain kinase 1"""				Standard	XM_005255315		Approved	Sbk	uc002dpd.3	Q52WX2		ENST00000341901.4:c.204C>T	16.37:g.28328916C>T		Somatic	142	0	0	801	WXS	Illumina HiSeq	Phase_I	204	89	0.436274	NM_001024401		Silent	SNP	ENST00000341901.4	37	CCDS32416.1																																																																																			C|0.945;T|0.055	0.055	strong		0.627	SBK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387677.1	XM_370948	
RTN4	57142	hgsc.bcm.edu	37	2	55253973	55253973	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:55253973T>G	ENST00000337526.6	-	3	1505	c.1262A>C	c.(1261-1263)gAt>gCt	p.D421A	RTN4_ENST00000394611.2_Missense_Mutation_p.D215A|RTN4_ENST00000357376.3_Missense_Mutation_p.D215A|RTN4_ENST00000404909.1_Missense_Mutation_p.D215A|RTN4_ENST00000354474.6_Missense_Mutation_p.D189A|RTN4_ENST00000357732.4_Intron|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.D215A	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	421					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)			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						ACATTTTTTATCCACTTTACT	0.383																																					p.D421A		Atlas-SNP	.											.	RTN4	189	.	0			c.A1262C						PASS	.						236.0	233.0	234.0					2																	55253973		2202	4300	6502	SO:0001583	missense	57142	exon3			TTTTTATCCACTT	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.1262A>C	2.37:g.55253973T>G	ENSP00000337838:p.Asp421Ala	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	227	120	0.528634	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	t	10.97	1.500459	0.26861	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.27557	1.66;1.66;2.34;1.66;1.66;1.72	6.06	0.962	0.19643	.	0.933951	0.09057	N	0.854885	T	0.33876	0.0878	M	0.66939	2.045	0.33241	D	0.557225	P	0.48294	0.908	P	0.44422	0.449	T	0.48139	-0.9061	10	0.87932	D	0	-1.8717	6.2376	0.20772	0.0:0.1944:0.148:0.6577	.	421	Q9NQC3	RTN4_HUMAN	A	215;215;421;215;215;189	ENSP00000384471:D215A;ENSP00000349944:D215A;ENSP00000337838:D421A;ENSP00000378109:D215A;ENSP00000385650:D215A;ENSP00000346465:D189A	ENSP00000337838:D421A	D	-	2	0	RTN4	55107477	0.005000	0.15991	0.153000	0.22517	0.300000	0.27592	0.122000	0.15687	-0.072000	0.12864	-0.266000	0.10368	GAT	.	.	none		0.383	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388724	1388724	+	Missense_Mutation	SNP	C	C	G	rs76728908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388724C>G	ENST00000324803.4	+	1	3385	c.425C>G	c.(424-426)cCa>cGa	p.P142R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	142					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P142R(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CACACGTGCCCATGCGGAGTG	0.697													N|||	556	0.111022	0.0658	0.1657	5008	,	,		14551	0.0238		0.1968	False		,,,				2504	0.135				p.P142R		Atlas-SNP	.											CRIPAK,NS,other,0,1	CRIPAK	185	1	1	Substitution - Missense(1)	pancreas(1)	c.C425G						scavenged	.						38.0	36.0	36.0					4																	1388724		1907	3680	5587	SO:0001583	missense	285464	exon1			CGTGCCCATGCGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.425C>G	4.37:g.1388724C>G	ENSP00000323978:p.Pro142Arg	Somatic	24	2	0.0833333		WXS	Illumina HiSeq	Phase_I	39	12	0.307692	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	0.221	-1.028683	0.02045	.	.	ENSG00000179979	ENST00000324803	T	0.19250	2.16	0.948	-1.9	0.07665	Post-SET domain (1);	.	.	.	.	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.28364	-1.0046	9	0.09843	T	0.71	.	0.6802	0.00873	0.2336:0.357:0.2313:0.1781	.	142	Q8N1N5	CRPAK_HUMAN	R	142	ENSP00000323978:P142R	ENSP00000323978:P142R	P	+	2	0	CRIPAK	1378724	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.476000	0.02333	-2.809000	0.00348	-3.729000	0.00022	CCA	C|0.500;G|0.500	0.500	weak		0.697	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
FCGBP	8857	hgsc.bcm.edu	37	19	40383905	40383905	+	Silent	SNP	G	G	A	rs145218790		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40383905G>A	ENST00000221347.6	-	21	9712	c.9705C>T	c.(9703-9705)tgC>tgT	p.C3235C		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3235						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)			CCCCAGGCCCGCAGCGACACC	0.677																																					p.C3235C		Atlas-SNP	.											FCGBP,NS,carcinoma,0,6	FCGBP	416	6	0			c.C9705T						scavenged	.						1.0	1.0	1.0					19																	40383905		234	700	934	SO:0001819	synonymous_variant	8857	exon21			AGGCCCGCAGCGA	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.9705C>T	19.37:g.40383905G>A		Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	409	75	0.183374	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.667;A|0.333	0.333	strong		0.677	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56703248	56703248	+	Missense_Mutation	SNP	G	G	A	rs527025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56703248G>A	ENST00000586855.2	-	3	872	c.559C>T	c.(559-561)Ccc>Tcc	p.P187S	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.P187S			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	187			P -> S (in dbSNP:rs527025).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GCGACCCTGGGCAGGATCTGC	0.622													G|||	1232	0.246006	0.1936	0.2032	5008	,	,		14284	0.2798		0.2932	False		,,,				2504	0.2638				p.P187S		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.C559T						PASS	.	G	SER/PRO	899,3507	327.2+/-299.9	90,719,1394	35.0	36.0	35.0		559	-2.5	0.0	19	dbSNP_83	35	2700,5900	402.8+/-347.6	427,1846,2027	yes	missense	ZSCAN5B	NM_001080456.2	74	517,2565,3421	AA,AG,GG		31.3953,20.404,27.6718	probably-damaging	187/496	56703248	3599,9407	2203	4300	6503	SO:0001583	missense	342933	exon2			CCCTGGGCAGGAT		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"""-"", ""Zinc fingers, C2H2-type"""	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.559C>T	19.37:g.56703248G>A	ENSP00000466072:p.Pro187Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_001080456		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	556	0.25457875457875456	95	0.19308943089430894	78	0.2154696132596685	160	0.27972027972027974	223	0.2941952506596306	G	11.85	1.762444	0.31228	0.20404	0.313953	ENSG00000197213	ENST00000358992	T	0.06449	3.3	1.9	-2.51	0.06365	.	.	.	.	.	T	0.00012	0.0000	M	0.82517	2.595	0.80722	P	0.0	D	0.89917	1.0	D	0.83275	0.996	T	0.20140	-1.0284	8	0.32370	T	0.25	.	3.8942	0.09131	0.1953:0.4955:0.3092:0.0	rs527025;rs527025	187	A6NJL1	ZSA5B_HUMAN	S	187	ENSP00000351883:P187S	ENSP00000351883:P187S	P	-	1	0	ZSCAN5B	61395060	0.001000	0.12720	0.000000	0.03702	0.041000	0.13682	-0.393000	0.07305	-0.516000	0.06470	0.306000	0.20318	CCC	G|0.725;A|0.275	0.275	strong		0.622	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
CEP63	80254	hgsc.bcm.edu	37	3	134278270	134278270	+	Splice_Site	SNP	C	C	T	rs1127826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:134278270C>T	ENST00000337090.3	+	14	2125	c.1952C>T	c.(1951-1953)tCg>tTg	p.S651L	CEP63_ENST00000354446.3_Intron|CEP63_ENST00000606977.1_Splice_Site_p.S651L|CEP63_ENST00000383229.3_Intron|CEP63_ENST00000332047.5_Intron|CEP63_ENST00000513612.2_Splice_Site_p.S651L			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	651			S -> L (in dbSNP:rs1127826).		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						TTTATATCTTCGGTATGGAAA	0.313													C|||	1638	0.327077	0.0219	0.5288	5008	,	,		19506	0.6002		0.3668	False		,,,				2504	0.274				p.S651L		Atlas-SNP	.											.	CEP63	56	.	0			c.C1952T						PASS	.	C	,,,LEU/SER	402,4004	187.4+/-214.1	17,368,1818	47.0	46.0	47.0		,,,1952	-2.9	0.8	3	dbSNP_86	47	3075,5525	463.1+/-365.9	531,2013,1756	yes	intron,intron,intron,missense-near-splice	CEP63	NM_001042383.1,NM_001042384.1,NM_001042400.1,NM_025180.3	,,,145	548,2381,3574	TT,TC,CC		35.7558,9.1239,26.7338	,,,possibly-damaging	,,,651/704	134278270	3477,9529	2203	4300	6503	SO:0001630	splice_region_variant	80254	exon15			TATCTTCGGTATG	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.1953+1C>T	3.37:g.134278270C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_025180	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	796	0.36446886446886445	20	0.04065040650406504	166	0.4585635359116022	341	0.5961538461538461	269	0.3548812664907652	C	12.56	1.975602	0.34848	0.091239	0.357558	ENSG00000182923	ENST00000337090;ENST00000513612	T;T	0.18016	2.24;2.24	5.35	-2.93	0.05598	.	0.948307	0.08789	N	0.893552	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	0.9999999403245	B	0.06786	0.001	B	0.06405	0.002	T	0.42616	-0.9441	9	0.26408	T	0.33	1.3872	6.7487	0.23475	0.1413:0.1855:0.0:0.6732	rs1127826;rs9868985;rs17352684;rs52808223;rs57512520;rs9868985	651	Q96MT8	CEP63_HUMAN	L	651	ENSP00000336524:S651L;ENSP00000426129:S651L	ENSP00000336524:S651L	S	+	2	0	CEP63	135760960	0.998000	0.40836	0.840000	0.33206	0.950000	0.60333	0.235000	0.17948	-0.737000	0.04824	-0.142000	0.14014	TCG	C|0.695;T|0.305	0.305	strong		0.313	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	Missense_Mutation
GTF2A1L	11036	hgsc.bcm.edu	37	2	48896897	48896897	+	Missense_Mutation	SNP	A	A	G	rs33987892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:48896897A>G	ENST00000403751.3	+	7	1052	c.1015A>G	c.(1015-1017)Act>Gct	p.T339A	STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.T1043A|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.T1043A|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.T1043A|GTF2A1L_ENST00000430487.2_Missense_Mutation_p.T305A|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.T1043A|LHCGR_ENST00000420913.3_5'Flank|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.T996A	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	339					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)			CATTCGGGTTACTGATGATGA	0.313													A|||	37	0.00738818	0.0008	0.0115	5008	,	,		17076	0.0		0.0249	False		,,,				2504	0.0031				p.T1043A		Atlas-SNP	.											.	STON1-GTF2A1L	180	.	0			c.A3127G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	18,4386	25.3+/-52.1	0,18,2184	108.0	118.0	115.0		913,3127,2986,1015,3127	-2.5	0.0	2	dbSNP_126	115	161,8439	76.6+/-139.3	1,159,4140	yes	missense,missense,missense,missense,missense	GTF2A1L,STON1-GTF2A1L	NM_001193487.1,NM_001198593.1,NM_001198594.1,NM_006872.3,NM_172311.2	58,58,58,58,58	1,177,6324	GG,GA,AA		1.8721,0.4087,1.3765	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	305/445,1043/1159,996/1136,339/479,1043/1183	48896897	179,12825	2202	4300	6502	SO:0001583	missense	286749	exon9			CGGGTTACTGATG	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.1015A>G	2.37:g.48896897A>G	ENSP00000384597:p.Thr339Ala	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	123	47	0.382114	NM_001198593	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	A	7.999	0.754993	0.15846	0.004087	0.018721	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000430487;ENST00000403751	T;T;T;T;T	0.09723	2.95;2.97;2.95;2.95;3.15	4.94	-2.52	0.06346	.	1.480890	0.03742	N	0.255152	T	0.02610	0.0079	L	0.41356	1.27	0.09310	N	1	P;B;B;B;B	0.47841	0.901;0.0;0.019;0.363;0.001	B;B;B;B;B	0.42030	0.373;0.001;0.042;0.183;0.002	T	0.14008	-1.0488	10	0.51188	T	0.08	.	0.4944	0.00569	0.2275:0.2515:0.2749:0.2461	rs33987892	305;996;1043;339;1043	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	A	1043;1043;1043;1043;996;338;305;339	ENSP00000385499:T1043A;ENSP00000385701:T1043A;ENSP00000378236:T1043A;ENSP00000311493:T1043A;ENSP00000378234:T996A	ENSP00000384597:T339A	T	+	1	0	STON1-GTF2A1L;GTF2A1L	48750401	0.000000	0.05858	0.003000	0.11579	0.171000	0.22731	-0.188000	0.09642	-0.620000	0.05641	0.459000	0.35465	ACT	A|0.985;G|0.015	0.015	strong		0.313	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872	
OR13C5	138799	hgsc.bcm.edu	37	9	107361452	107361452	+	Silent	SNP	C	C	G	rs376107801|rs377523807|rs199665292	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107361452C>G	ENST00000374779.2	-	1	336	c.243G>C	c.(241-243)acG>acC	p.T81T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						AGCTCACTAGCGTGGAGGGAA	0.512													G|||	1377	0.27496	0.3116	0.2133	5008	,	,		19807	0.4504		0.1163	False		,,,				2504	0.2515				p.T81T		Atlas-SNP	.											OR13C5,NS,carcinoma,-2,1	OR13C5	60	1	0			c.G243C						PASS	.						15.0	28.0	23.0					9																	107361452		2059	4256	6315	SO:0001819	synonymous_variant	138799	exon1			CACTAGCGTGGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.243G>C	9.37:g.107361452C>G		Somatic	607	0	0		WXS	Illumina HiSeq	Phase_I	390	76	0.194872	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			.	.	weak		0.512	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
TEC	7006	hgsc.bcm.edu	37	4	48165757	48165757	+	Silent	SNP	G	G	A	rs16861083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:48165757G>A	ENST00000381501.3	-	8	856	c.699C>T	c.(697-699)taC>taT	p.Y233Y		NM_003215.2	NP_003206.2	P42680	TEC_HUMAN	tec protein tyrosine kinase	233	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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						TTCCCGTTACGTAATTACTTG	0.284													g|||	250	0.0499201	0.0764	0.0403	5008	,	,		18367	0.0		0.0497	False		,,,				2504	0.0726				p.Y233Y		Atlas-SNP	.											TEC,NS,carcinoma,0,1	TEC	81	1	0			c.C699T						PASS	.	G		333,4043		16,301,1871	68.0	61.0	64.0		699	-1.2	1.0	4	dbSNP_123	64	472,8068		24,424,3822	no	coding-synonymous	TEC	NM_003215.2		40,725,5693	AA,AG,GG		5.5269,7.6097,6.2326		233/632	48165757	805,12111	2188	4270	6458	SO:0001819	synonymous_variant	7006	exon8			CGTTACGTAATTA	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.699C>T	4.37:g.48165757G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	129	53	0.410853	NM_003215	B7ZKZ6|Q3MIS5	Silent	SNP	ENST00000381501.3	37	CCDS3481.1																																																																																			G|0.950;A|0.050	0.050	strong		0.284	TEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250492.3		
PDGFA	5154	hgsc.bcm.edu	37	7	552046	552046	+	Silent	SNP	A	A	G	rs1129401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:552046A>G	ENST00000354513.5	-	3	599	c.207T>C	c.(205-207)caT>caC	p.H69H	PDGFA_ENST00000402802.3_Silent_p.H69H|PDGFA_ENST00000426681.2_5'Flank	NM_002607.5	NP_002598.4	P04085	PDGFA_HUMAN	platelet-derived growth factor alpha polypeptide	69					actin cytoskeleton organization (GO:0030036)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell activation (GO:0001775)|cell projection assembly (GO:0030031)|cell-cell signaling (GO:0007267)|embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|lung alveolus development (GO:0048286)|negative chemotaxis (GO:0050919)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of branching involved in salivary gland morphogenesis by epithelial-mesenchymal signaling (GO:0060683)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of smooth muscle cell migration (GO:0014910)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to retinoic acid (GO:0032526)|response to wounding (GO:0009611)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|microvillus (GO:0005902)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|growth factor activity (GO:0008083)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	16		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|Epithelial(4;1.1e-17)|OV - Ovarian serous cystadenocarcinoma(56;1.7e-17)|all cancers(6;4.89e-15)		GCTTAGTGGCATGGACCCCGT	0.652													G|||	1244	0.248403	0.1271	0.2133	5008	,	,		16261	0.3234		0.2535	False		,,,				2504	0.3548				p.H69H		Atlas-SNP	.											.	PDGFA	34	.	0			c.T207C						PASS	.	G	,	710,3696	759.4+/-412.9	58,594,1551	65.0	62.0	63.0		207,207	-6.8	0.0	7	dbSNP_86	63	2246,6346	707.6+/-405.6	300,1646,2350	no	coding-synonymous,coding-synonymous	PDGFA	NM_002607.5,NM_033023.4	,	358,2240,3901	GG,GA,AA		26.1406,16.1144,22.742	,	69/212,69/197	552046	2956,10042	2203	4296	6499	SO:0001819	synonymous_variant	5154	exon3			AGTGGCATGGACC		CCDS34578.1, CCDS47524.1	7p22	2008-07-18			ENSG00000197461	ENSG00000197461			8799	protein-coding gene	gene with protein product	"""PDGF A-chain"", ""platelet-derived growth factor alpha chain"""	173430				1505216, 2536956	Standard	NM_002607		Approved	PDGF1, PDGF-A	uc003sir.3	P04085	OTTHUMG00000151412	ENST00000354513.5:c.207T>C	7.37:g.552046A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	130	67	0.515385	NM_002607	B5BU73	Silent	SNP	ENST00000354513.5	37	CCDS34578.1	536	0.2454212454212454	59	0.11991869918699187	84	0.23204419889502761	199	0.3479020979020979	194	0.2559366754617414	G	0.412	-0.912876	0.02415	0.161144	0.261406	ENSG00000197461	ENST00000400761	.	.	.	5.03	-6.84	0.01687	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.06197	-1.0840	3	.	.	.	-5.3505	17.1287	0.86721	0.6784:0.0:0.3216:0.0	rs1129401;rs1800816;rs2228457;rs3187241;rs17415666;rs61732882	.	.	.	R	76	.	.	C	-	1	0	PDGFA	518572	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.539000	0.06113	-1.968000	0.01006	-0.374000	0.07098	TGC	A|0.769;G|0.231	0.231	strong		0.652	PDGFA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322534.1		
LRRC61	65999	hgsc.bcm.edu	37	7	150034378	150034378	+	Missense_Mutation	SNP	A	A	G	rs3735169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150034378A>G	ENST00000359623.4	+	3	1016	c.428A>G	c.(427-429)aAc>aGc	p.N143S	LRRC61_ENST00000493307.1_Missense_Mutation_p.N143S|LRRC61_ENST00000323078.7_Missense_Mutation_p.N143S	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	143	LRRCT.		N -> S (in dbSNP:rs3735169). {ECO:0000269|PubMed:14702039}.							endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			CTCTGTGCCAACCCCTCCTAC	0.657													G|||	1294	0.258387	0.2625	0.1571	5008	,	,		18703	0.2897		0.2455	False		,,,				2504	0.3057				p.N143S		Atlas-SNP	.											.	LRRC61	17	.	0			c.A428G						PASS	.	G	SER/ASN,SER/ASN	1076,3330	719.7+/-409.0	128,820,1255	57.0	57.0	57.0		428,428	0.7	0.1	7	dbSNP_107	57	2198,6402	709.9+/-405.7	286,1626,2388	yes	missense,missense	LRRC61	NM_001142928.1,NM_023942.2	46,46	414,2446,3643	GG,GA,AA		25.5581,24.4212,25.173	benign,benign	143/260,143/260	150034378	3274,9732	2203	4300	6503	SO:0001583	missense	65999	exon2			GTGCCAACCCCTC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.428A>G	7.37:g.150034378A>G	ENSP00000352642:p.Asn143Ser	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_023942	B3KUW0|D3DWY8	Missense_Mutation	SNP	ENST00000359623.4	37	CCDS5901.1	572	0.2619047619047619	118	0.23983739837398374	66	0.18232044198895028	182	0.3181818181818182	206	0.2717678100263852	G	0.012	-1.649709	0.00785	0.244212	0.255581	ENSG00000127399	ENST00000323078;ENST00000359623;ENST00000493307	T;T;T	0.22945	1.93;1.93;1.93	3.82	0.741	0.18336	.	0.276635	0.36591	N	0.002504	T	0.00012	0.0000	N	0.02158	-0.66	0.48452	P	3.429999999999822E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.48352	-0.9043	9	0.18710	T	0.47	-7.5883	7.2278	0.26026	0.4766:0.0:0.5234:0.0	rs3735169;rs57401595;rs3735169	143	Q9BV99	LRC61_HUMAN	S	143	ENSP00000339047:N143S;ENSP00000352642:N143S;ENSP00000420560:N143S	ENSP00000339047:N143S	N	+	2	0	LRRC61	149665311	0.000000	0.05858	0.095000	0.20976	0.498000	0.33706	-0.123000	0.10611	-0.314000	0.08716	-0.665000	0.03846	AAC	A|0.744;G|0.256	0.256	strong		0.657	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557486	32557486	+	Missense_Mutation	SNP	T	T	A	rs201540428	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32557486T>A	ENST00000360004.5	-	1	139	c.34A>T	c.(34-36)Atg>Ttg	p.M12L		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	12					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGCGCTGTCATGCAGGAGCCT	0.577										Multiple Myeloma(14;0.17)			T|||	371	0.0740815	0.1225	0.0389	5008	,	,		26616	0.0585		0.0417	False		,,,				2504	0.0828				p.M12L		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	0			c.A34T						PASS	.						86.0	104.0	97.0					6																	32557486		1511	2709	4220	SO:0001583	missense	3123	exon1			CTGTCATGCAGGA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.34A>T	6.37:g.32557486T>A	ENSP00000353099:p.Met12Leu	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	247	22	0.0890688	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.35	1.912089	0.33721	.	.	ENSG00000196126	ENST00000360004	T	0.00211	8.54	4.4	-0.756	0.11057	MHC classes I/II-like antigen recognition protein (1);	3.037640	0.01196	N	0.007449	T	0.00039	0.0001	L	0.39898	1.24	0.09310	N	1	B	0.31435	0.323	B	0.23716	0.048	T	0.30563	-0.9974	10	0.62326	D	0.03	.	0.4245	0.00461	0.1798:0.2114:0.1864:0.4224	rs3179205	12	P01911	2B1F_HUMAN	L	12	ENSP00000353099:M12L	ENSP00000353099:M12L	M	-	1	0	HLA-DRB1	32665464	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-0.388000	0.07352	-0.281000	0.09141	-0.530000	0.04314	ATG	T|0.848;A|0.152	0.152	strong		0.577	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
AXIN1	8312	hgsc.bcm.edu	37	16	396264	396264	+	Silent	SNP	A	A	G	rs1805105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:396264A>G	ENST00000262320.3	-	2	1133	c.762T>C	c.(760-762)gaT>gaC	p.D254D	AXIN1_ENST00000354866.3_Silent_p.D254D|AXIN1_ENST00000481769.1_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	254	Interaction with TP53. {ECO:0000250}.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CATCGTCCTCATCCATGTCCT	0.582													G|||	3200	0.638978	0.9024	0.5375	5008	,	,		17364	0.2897		0.6173	False		,,,				2504	0.7372				p.D254D		Atlas-SNP	.											.	AXIN1	290	.	0			c.T762C						PASS	.	G	,	3738,668	283.4+/-277.1	1581,576,46	123.0	116.0	119.0		762,762	-9.6	0.0	16	dbSNP_89	119	5550,3050	469.4+/-367.6	1788,1974,538	no	coding-synonymous,coding-synonymous	AXIN1	NM_003502.3,NM_181050.2	,	3369,2550,584	GG,GA,AA		35.4651,15.1611,28.5868	,	254/863,254/827	396264	9288,3718	2203	4300	6503	SO:0001819	synonymous_variant	8312	exon2			GTCCTCATCCATG	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.762T>C	16.37:g.396264A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	51	0.573034	NM_181050	Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	CCDS10405.1																																																																																			A|0.335;G|0.665	0.665	strong		0.582	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3		
PLIN3	10226	hgsc.bcm.edu	37	19	4847868	4847868	+	Silent	SNP	G	G	A	rs10406652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4847868G>A	ENST00000221957.4	-	6	845	c.669C>T	c.(667-669)gtC>gtT	p.V223V	PLIN3_ENST00000592528.1_Silent_p.V211V|PLIN3_ENST00000585479.1_Silent_p.V223V	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	223					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GCACGGACGCGACGTCAAAGC	0.617													G|||	581	0.116014	0.1604	0.1484	5008	,	,		17332	0.0685		0.1312	False		,,,				2504	0.0665				p.V223V		Atlas-SNP	.											.	PLIN3	36	.	0			c.C669T						PASS	.	G	,,	696,3710	277.2+/-273.6	47,602,1554	44.0	35.0	38.0		669,633,669	0.9	0.2	19	dbSNP_119	38	1163,7437	226.6+/-262.3	74,1015,3211	no	coding-synonymous,coding-synonymous,coding-synonymous	PLIN3	NM_001164189.1,NM_001164194.1,NM_005817.4	,,	121,1617,4765	AA,AG,GG		13.5233,15.7966,14.2934	,,	223/434,211/423,223/435	4847868	1859,11147	2203	4300	6503	SO:0001819	synonymous_variant	10226	exon6			GGACGCGACGTCA	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"""Perilipins"""	16893	protein-coding gene	gene with protein product	"""cargo selection protein (mannose 6 phosphate receptor binding protein)"", ""placental protein 17"", ""MPR-BINDING PROTEIN, 47-KD"""	602702	"""mannose-6-phosphate receptor binding protein 1"""	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.669C>T	19.37:g.4847868G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	125	59	0.472	NM_001164189	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Silent	SNP	ENST00000221957.4	37	CCDS12137.1																																																																																			G|0.867;A|0.132	0.132	strong		0.617	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817	
OR4M2	390538	hgsc.bcm.edu	37	15	22369290	22369290	+	Missense_Mutation	SNP	A	A	G	rs12593418	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:22369290A>G	ENST00000332663.2	+	1	813	c.715A>G	c.(715-717)Atg>Gtg	p.M239V	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	239			M -> V (in dbSNP:rs12593418).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M239V(1)		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)		CAACAGGGCCATGTCCACCTG	0.453																																					p.M239V		Atlas-SNP	.											OR4M2,NS,carcinoma,0,1	OR4M2	140	1	1	Substitution - Missense(1)	stomach(1)	c.A715G						PASS	.						288.0	199.0	229.0					15																	22369290		2203	4300	6503	SO:0001583	missense	390538	exon1			AGGGCCATGTCCA	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.715A>G	15.37:g.22369290A>G	ENSP00000329467:p.Met239Val	Somatic	408	0	0		WXS	Illumina HiSeq	Phase_I	498	162	0.325301	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	37	CCDS32172.1	566	0.2591575091575092	57	0.11585365853658537	114	0.3149171270718232	177	0.3094405594405594	218	0.287598944591029	.	6.608	0.480486	0.12581	.	.	ENSG00000182974	ENST00000332663	T	0.00044	8.83	2.28	-0.1	0.13621	GPCR, rhodopsin-like superfamily (1);	0.309717	0.27139	N	0.020757	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.31806	-0.9930	9	0.72032	D	0.01	-4.5993	5.3649	0.16107	0.6814:0.0:0.3186:0.0	rs12593418	239	Q8NGB6	OR4M2_HUMAN	V	239	ENSP00000329467:M239V	ENSP00000329467:M239V	M	+	1	0	OR4M2	19870654	0.000000	0.05858	0.993000	0.49108	0.973000	0.67179	-1.357000	0.02607	0.160000	0.19432	0.368000	0.22195	ATG	.	.	weak		0.453	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
T	6862	hgsc.bcm.edu	37	6	166571935	166571935	+	Silent	SNP	C	C	T	rs35819705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:166571935C>T	ENST00000296946.2	-	9	1644	c.1176G>A	c.(1174-1176)gcG>gcA	p.A392A	T_ENST00000366871.3_Silent_p.A334A	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	392					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		AGGAAGAGGGCGCCGAGACCG	0.711									Chordoma, Familial Clustering of				C|||	1194	0.238419	0.0499	0.3213	5008	,	,		15354	0.3095		0.2783	False		,,,				2504	0.32				p.A392A		Atlas-SNP	.											.	T	77	.	0			c.G1176A						PASS	.	C		362,4042	183.3+/-210.9	15,332,1855	52.0	61.0	58.0		1176	-6.6	0.0	6	dbSNP_126	58	2610,5986	418.2+/-352.7	403,1804,2091	no	coding-synonymous	T	NM_003181.2		418,2136,3946	TT,TC,CC		30.363,8.2198,22.8615		392/436	166571935	2972,10028	2202	4298	6500	SO:0001819	synonymous_variant	6862	exon9	Familial Cancer Database		AGAGGGCGCCGAG	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.1176G>A	6.37:g.166571935C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	60	46	0.766667	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																			C|0.771;T|0.229	0.229	strong		0.711	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
NOV	4856	hgsc.bcm.edu	37	8	120431506	120431506	+	Missense_Mutation	SNP	G	G	A	rs11538929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:120431506G>A	ENST00000259526.3	+	4	925	c.698G>A	c.(697-699)cGt>cAt	p.R233H	RP11-775B15.2_ENST00000519786.1_RNA	NM_002514.3	NP_002505.1	Q9UIW2	PLXA1_HUMAN	nephroblastoma overexpressed	1554	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|multicellular organismal development (GO:0007275)|regulation of smooth muscle cell migration (GO:0014910)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	receptor activity (GO:0004872)|semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(3)	21	all_cancers(13;3.84e-26)|Lung NSC(37;1.19e-08)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000507)			AATAGGAACCGTCAATGTGAG	0.537													G|||	234	0.0467252	0.0159	0.0432	5008	,	,		17698	0.0		0.1133	False		,,,				2504	0.0706				p.R233H		Atlas-SNP	.											.	NOV	51	.	0			c.G698A						PASS	.	G	HIS/ARG	136,4270	98.5+/-137.1	2,132,2069	144.0	136.0	139.0		698	-0.4	0.0	8	dbSNP_120	139	963,7637	210.4+/-251.3	58,847,3395	yes	missense	NOV	NM_002514.3	29	60,979,5464	AA,AG,GG		11.1977,3.0867,8.4499	benign	233/358	120431506	1099,11907	2203	4300	6503	SO:0001583	missense	4856	exon4			GGAACCGTCAATG	X96584	CCDS6328.1	8q24.12	2012-02-27	2012-02-27		ENSG00000136999	ENSG00000136999			7885	protein-coding gene	gene with protein product		164958	"""nephroblastoma overexpressed gene"""			1334251	Standard	NM_002514		Approved	IGFBP9, CCN3	uc003yoq.2	P48745	OTTHUMG00000164984	ENST00000259526.3:c.698G>A	8.37:g.120431506G>A	ENSP00000259526:p.Arg233His	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	24	0.342857	NM_002514		Missense_Mutation	SNP	ENST00000259526.3	37	CCDS6328.1	113	0.051739926739926737	6	0.012195121951219513	20	0.055248618784530384	0	0.0	87	0.11477572559366754	G	13.52	2.260816	0.39995	0.030867	0.111977	ENSG00000136999	ENST00000259526	T	0.51071	0.72	5.96	-0.365	0.12549	.	0.451639	0.25792	N	0.028266	T	0.00815	0.0027	M	0.76170	2.325	0.20074	N	0.999931	B	0.20780	0.048	B	0.17979	0.02	T	0.13072	-1.0523	10	0.51188	T	0.08	-1.1254	1.42	0.02310	0.2749:0.3509:0.1991:0.1751	rs11538929;rs52810677;rs59594770;rs11538929	233	P48745	NOV_HUMAN	H	233	ENSP00000259526:R233H	ENSP00000259526:R233H	R	+	2	0	NOV	120500687	0.000000	0.05858	0.010000	0.14722	0.988000	0.76386	-0.219000	0.09228	-0.379000	0.07906	0.655000	0.94253	CGT	G|0.931;A|0.069	0.069	strong		0.537	NOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381301.1	NM_002514	
TSSK2	23617	hgsc.bcm.edu	37	22	19119751	19119751	+	Missense_Mutation	SNP	C	C	T	rs1052763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19119751C>T	ENST00000399635.2	+	1	1431	c.839C>T	c.(838-840)aCg>aTg	p.T280M	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	280			T -> M (in dbSNP:rs1052763). {ECO:0000269|PubMed:17344846}.		multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					CCCAAAGCCACGTCTTCTGCC	0.642													T|||	1388	0.277157	0.3631	0.2233	5008	,	,		18784	0.2133		0.1948	False		,,,				2504	0.3497				p.T280M		Atlas-SNP	.											TSSK2,NS,carcinoma,-1,1	TSSK2	29	1	0			c.C839T						scavenged	.	T	,MET/THR	1402,3004	674.8+/-403.0	210,982,1011	50.0	46.0	47.0		,839	4.7	1.0	22	dbSNP_86	47	1615,6985	729.7+/-406.7	170,1275,2855	yes	utr-3,missense	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,81	380,2257,3866	TT,TC,CC		18.7791,31.8202,23.197	,benign	,280/359	19119751	3017,9989	2203	4300	6503	SO:0001583	missense	23617	exon1			AAGCCACGTCTTC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.839C>T	22.37:g.19119751C>T	ENSP00000382544:p.Thr280Met	Somatic	41	1	0.0243902		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_053006	Q8IY55	Missense_Mutation	SNP	ENST00000399635.2	37	CCDS13755.1	535	0.24496336996336995	178	0.3617886178861789	85	0.23480662983425415	121	0.21153846153846154	151	0.19920844327176782	T	6.138	0.393751	0.11638	0.318202	0.187791	ENSG00000206203	ENST00000399635	T	0.70516	-0.49	5.7	4.67	0.58626	.	0.328506	0.26549	N	0.023741	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	4.000000000004E-6	B	0.09022	0.002	B	0.06405	0.002	T	0.23833	-1.0177	9	0.32370	T	0.25	.	7.8473	0.29433	0.0:0.1641:0.0:0.8359	rs1052763;rs3171566;rs17743850;rs1052763	280	Q96PF2	TSSK2_HUMAN	M	280	ENSP00000382544:T280M	ENSP00000382544:T280M	T	+	2	0	TSSK2	17499751	.	.	1.000000	0.80357	0.977000	0.68977	.	.	0.993000	0.38866	-0.254000	0.11334	ACG	C|0.762;T|0.238	0.238	strong		0.642	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
IGHMBP2	3508	hgsc.bcm.edu	37	11	68671477	68671477	+	Silent	SNP	T	T	C	rs1249463	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68671477T>C	ENST00000255078.3	+	1	168	c.57T>C	c.(55-57)ctT>ctC	p.L19L	IGHMBP2_ENST00000539224.1_Silent_p.L19L|MRPL21_ENST00000450904.2_5'Flank|MRPL21_ENST00000567045.1_5'Flank|MRPL21_ENST00000362034.2_5'Flank	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	19					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			TGCTGGAGCTTGAGAGAGACG	0.721													C|||	3381	0.67512	0.5825	0.8156	5008	,	,		13450	0.4653		0.8509	False		,,,				2504	0.7362				p.L19L		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.T57C						PASS	.	C		2604,1354		892,820,267	12.0	12.0	12.0		57	-0.5	1.0	11	dbSNP_87	12	6600,1128		2838,924,102	no	coding-synonymous	IGHMBP2	NM_002180.2		3730,1744,369	CC,CT,TT		14.5963,34.2092,21.2391		19/994	68671477	9204,2482	1979	3864	5843	SO:0001819	synonymous_variant	3508	exon1			GGAGCTTGAGAGA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.57T>C	11.37:g.68671477T>C		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_002180	A0PJD2|Q00443|Q14177	Silent	SNP	ENST00000255078.3	37	CCDS8187.1																																																																																			T|0.304;C|0.696	0.696	strong		0.721	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
C8B	732	hgsc.bcm.edu	37	1	57409459	57409459	+	Missense_Mutation	SNP	C	C	A	rs139498867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:57409459C>A	ENST00000371237.4	-	8	1210	c.1144G>T	c.(1144-1146)Gat>Tat	p.D382Y	C8B_ENST00000543257.1_Missense_Mutation_p.D330Y|C8B_ENST00000535057.1_Missense_Mutation_p.D320Y	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	382	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ATTTTAAAATCATTTTTGGCA	0.403													C|||	14	0.00279553	0.0	0.0058	5008	,	,		21667	0.0		0.0099	False		,,,				2504	0.0				p.D382Y		Atlas-SNP	.											.	C8B	107	.	0			c.G1144T						PASS	.	C	TYR/ASP	4,4402	8.1+/-20.4	0,4,2199	187.0	166.0	173.0		1144	3.7	0.0	1	dbSNP_134	173	73,8527	44.5+/-102.8	0,73,4227	yes	missense	C8B	NM_000066.2	160	0,77,6426	AA,AC,CC		0.8488,0.0908,0.592	possibly-damaging	382/592	57409459	77,12929	2203	4300	6503	SO:0001583	missense	732	exon8			TAAAATCATTTTT	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1144G>T	1.37:g.57409459C>A	ENSP00000360281:p.Asp382Tyr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	173	74	0.427746	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	26.5	4.741358	0.89573	9.08E-4	0.008488	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.84146	-1.81;-1.81;-1.81	4.59	3.66	0.41972	Membrane attack complex component/perforin (MACPF) domain (3);	0.458353	0.25651	N	0.029202	D	0.83977	0.5371	L	0.51422	1.61	0.29294	N	0.869162	P;D;D	0.61080	0.874;0.974;0.989	P;P;P	0.58331	0.568;0.66;0.837	T	0.81992	-0.0678	10	0.72032	D	0.01	-3.603	12.8556	0.57884	0.0:0.9173:0.0:0.0827	.	330;320;382	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	Y	382;330;320	ENSP00000360281:D382Y;ENSP00000442548:D330Y;ENSP00000440113:D320Y	ENSP00000360281:D382Y	D	-	1	0	C8B	57182047	0.013000	0.17824	0.013000	0.15412	0.915000	0.54546	2.152000	0.42272	1.507000	0.48752	0.655000	0.94253	GAT	C|0.994;A|0.006	0.006	strong		0.403	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
LILRB1	10859	hgsc.bcm.edu	37	19	55143156	55143156	+	Silent	SNP	T	T	C	rs12462774|rs34880987|rs200526666	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55143156T>C	ENST00000396331.1	+	5	633	c.276T>C	c.(274-276)caT>caC	p.H92H	LILRB1_ENST00000434867.2_Silent_p.H92H|LILRB1_ENST00000396321.2_Silent_p.H92H|LILRB1_ENST00000396315.1_Silent_p.H92H|LILRB1_ENST00000418536.2_Silent_p.H92H|LILRB1_ENST00000427581.2_Silent_p.H128H|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Silent_p.H92H|LILRB1_ENST00000396317.1_Silent_p.H92H|LILRB1_ENST00000448689.1_Silent_p.H92H|LILRB1_ENST00000396327.3_Silent_p.H92H|LILRB1_ENST00000324602.7_Silent_p.H92H	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	92	Ig-like C2-type 1.				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)		CCTGGGAACATGCAGGGCGGT	0.552										HNSCC(37;0.09)			N|||	1071	0.213858	0.0575	0.232	5008	,	,		17947	0.505		0.1312	False		,,,				2504	0.1973				p.H92H		Atlas-SNP	.											.	LILRB1	140	.	0			c.T276C						PASS	.	C	,,,	143,4263		8,127,2068	162.0	148.0	153.0		276,276,276,276	-0.2	0.0	19	dbSNP_120	153	608,7992		74,460,3766	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	,,,	82,587,5834	CC,CT,TT		7.0698,3.2456,5.7743	,,,	92/653,92/652,92/652,92/651	55143156	751,12255	2203	4300	6503	SO:0001819	synonymous_variant	10859	exon4			GGAACATGCAGGG	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.276T>C	19.37:g.55143156T>C		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	230	117	0.508696	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1																																																																																			.	.	alt		0.552	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
KIR3DL1	3811	hgsc.bcm.edu	37	19	55331308	55331308	+	Missense_Mutation	SNP	C	C	A	rs1065331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55331308C>A	ENST00000391728.4	+	4	529	c.496C>A	c.(496-498)Cgc>Agc	p.R166S	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.R166S|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.R166S|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.R166S|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.R71S|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.R166S	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	166	Ig-like C2-type 2.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		GGACCCCTCACGCCTCGTTGG	0.512													c|||	155	0.0309505	0.0658	0.0144	5008	,	,		16338	0.0377		0.0199	False		,,,				2504	0.0				p.R166S		Atlas-SNP	.											KIR3DL1_ENST00000402254,NS,carcinoma,-1,2	KIR3DL1	174	2	0			c.C496A						PASS	.	C	SER/ARG	288,4084		37,214,1935	177.0	164.0	168.0		496	-1.4	0.0	19	dbSNP_86	168	224,8156		36,152,4002	no	missense	KIR3DL1	NM_013289.2	110	73,366,5937	AA,AC,CC		2.673,6.5874,4.0151		166/445	55331308	512,12240	2186	4190	6376	SO:0001583	missense	3811	exon4			CCCTCACGCCTCG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.496C>A	19.37:g.55331308C>A	ENSP00000375608:p.Arg166Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	228	111	0.486842	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	69	0.03159340659340659	31	0.06300813008130081	5	0.013812154696132596	18	0.03146853146853147	15	0.01978891820580475	-	4.242	0.043933	0.08196	0.065874	0.02673	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T;T	0.02863	4.13;4.13;4.13;4.13;4.13;4.13	1.44	-1.44	0.08856	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00300	0.0009	L	0.45581	1.43	0.09310	N	1	B;B;P;B	0.35923	0.03;0.068;0.528;0.014	B;B;B;B	0.40534	0.037;0.093;0.332;0.037	T	0.41928	-0.9481	9	0.46703	T	0.11	.	2.6762	0.05082	0.2622:0.5429:0.0:0.1949	rs1065331;rs3206366	166;71;166;166	Q15702;Q14946;F6QF33;P43629	.;.;.;KI3L1_HUMAN	S	166;166;166;144;166;166;71	ENSP00000384528:R166S;ENSP00000443350:R166S;ENSP00000442355:R166S;ENSP00000375608:R166S;ENSP00000326868:R166S;ENSP00000350901:R71S	ENSP00000326868:R166S	R	+	1	0	KIR3DL1	60023120	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.597000	0.05713	-0.374000	0.07967	-1.109000	0.02080	CGC	C|0.968;A|0.032	0.032	strong		0.512	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
GLB1L	79411	hgsc.bcm.edu	37	2	220107997	220107997	+	Missense_Mutation	SNP	G	G	A	rs147143842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220107997G>A	ENST00000295759.7	-	3	425	c.112C>T	c.(112-114)Cgg>Tgg	p.R38W	STK16_ENST00000409516.3_5'Flank|GLB1L_ENST00000409640.1_Missense_Mutation_p.R38W|GLB1L_ENST00000356283.3_Missense_Mutation_p.R38W|STK16_ENST00000409260.1_5'Flank|GLB1L_ENST00000392089.2_Missense_Mutation_p.R38W|STK16_ENST00000396738.2_5'Flank|STK16_ENST00000409638.3_5'Flank|STK16_ENST00000409743.1_5'Flank			Q6UWU2	GLB1L_HUMAN	galactosidase, beta 1-like	38					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22		all_lung(227;1.19e-05)|Lung NSC(271;2.76e-05)|Medulloblastoma(418;0.0208)|Esophageal squamous(248;0.0559)		Epithelial(149;1.3e-11)|all cancers(144;2.07e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGGAGAAACCGGTCATGACCC	0.607													G|||	13	0.00259585	0.0	0.0058	5008	,	,		15458	0.0		0.0089	False		,,,				2504	0.0				p.R38W		Atlas-SNP	.											.	GLB1L	52	.	0			c.C112T						PASS	.	G	TRP/ARG	4,4402	6.2+/-15.9	0,4,2199	53.0	59.0	57.0		112	-3.5	0.1	2	dbSNP_134	57	109,8491	57.2+/-118.5	1,107,4192	yes	missense	GLB1L	NM_024506.3	101	1,111,6391	AA,AG,GG		1.2674,0.0908,0.8688	probably-damaging	38/655	220107997	113,12893	2203	4300	6503	SO:0001583	missense	79411	exon3			GAAACCGGTCATG		CCDS2437.1, CCDS74657.1	2q36.1	2008-02-05			ENSG00000163521	ENSG00000163521			28129	protein-coding gene	gene with protein product						12975309	Standard	XM_005246850		Approved	MGC10771	uc002vkm.3	Q6UWU2	OTTHUMG00000133133	ENST00000295759.7:c.112C>T	2.37:g.220107997G>A	ENSP00000295759:p.Arg38Trp	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	97	40	0.412371	NM_024506	Q96DR0	Missense_Mutation	SNP	ENST00000295759.7	37	CCDS2437.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	20.4	3.976618	0.74360	9.08E-4	0.012674	ENSG00000163521	ENST00000295759;ENST00000409640;ENST00000392089;ENST00000356283;ENST00000428427	D;D;D;D;D	0.98012	-4.66;-4.66;-4.66;-4.66;-4.66	5.49	-3.5	0.04710	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.202993	0.49916	D	0.000137	D	0.96043	0.8711	M	0.62723	1.935	0.22911	N	0.998573	D;D	0.89917	0.997;1.0	P;D	0.70716	0.533;0.97	D	0.91099	0.4913	10	0.66056	D	0.02	-5.1762	5.2728	0.15634	0.1871:0.0688:0.5034:0.2407	.	38;38	Q6UWU2-2;Q6UWU2	.;GLB1L_HUMAN	W	38	ENSP00000295759:R38W;ENSP00000386354:R38W;ENSP00000375939:R38W;ENSP00000348628:R38W;ENSP00000400738:R38W	ENSP00000295759:R38W	R	-	1	2	GLB1L	219816241	0.997000	0.39634	0.082000	0.20525	0.852000	0.48524	1.463000	0.35277	-0.399000	0.07668	-0.256000	0.11100	CGG	G|0.991;A|0.009	0.009	strong		0.607	GLB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256822.2	NM_024506	
PLIN4	729359	hgsc.bcm.edu	37	19	4512945	4512945	+	Missense_Mutation	SNP	C	C	T	rs75031432	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4512945C>T	ENST00000301286.3	-	3	984	c.985G>A	c.(985-987)Ggt>Agt	p.G329S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	329	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TTCATGGCACCAGTCACCCCA	0.567													C|||	840	0.167732	0.4539	0.1037	5008	,	,		18994	0.0119		0.0934	False		,,,				2504	0.0634				p.G329S		Atlas-SNP	.											PLIN4_ENST00000301286,NS,carcinoma,0,2	PLIN4	191	2	0			c.G985A						scavenged	.						39.0	40.0	39.0					19																	4512945		1862	4105	5967	SO:0001583	missense	729359	exon3			TGGCACCAGTCAC	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.985G>A	19.37:g.4512945C>T	ENSP00000301286:p.Gly329Ser	Somatic	324	3	0.00925926		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.776204	0.49786	.	.	ENSG00000167676	ENST00000301286	T	0.13901	2.55	4.53	1.21	0.21127	.	0.420915	0.19796	N	0.105865	T	0.13543	0.0328	L	0.46157	1.445	0.80722	P	0.0	D	0.54397	0.966	P	0.45794	0.493	T	0.19353	-1.0308	9	0.87932	D	0	-15.096	7.3812	0.26856	0.0:0.7112:0.0:0.2888	rs56366613	329	Q96Q06	PLIN4_HUMAN	S	329	ENSP00000301286:G329S	ENSP00000301286:G329S	G	-	1	0	PLIN4	4463945	0.091000	0.21658	0.003000	0.11579	0.001000	0.01503	0.810000	0.27183	0.906000	0.36621	0.407000	0.27541	GGT	C|0.826;T|0.174	0.174	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
OR2T3	343173	hgsc.bcm.edu	37	1	248637381	248637381	+	Missense_Mutation	SNP	G	G	A	rs139789199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248637381G>A	ENST00000359594.2	+	1	755	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	244						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAAGGCCTTGGCCACCTGCTC	0.562																																					p.A244T		Atlas-SNP	.											OR2T3,NS,carcinoma,0,3	OR2T3	79	3	0			c.G730A						scavenged	.	G	THR/ALA	108,4298	63.5+/-100.7	4,100,2099	200.0	168.0	179.0		730	-4.7	0.0	1	dbSNP_134	179	4,8596	3.0+/-9.4	0,4,4296	no	missense	OR2T3	NM_001005495.1	58	4,104,6395	AA,AG,GG		0.0465,2.4512,0.8611	benign	244/319	248637381	112,12894	2203	4300	6503	SO:0001583	missense	343173	exon1			GCCTTGGCCACCT		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.730G>A	1.37:g.248637381G>A	ENSP00000352604:p.Ala244Thr	Somatic	555	1	0.0018018		WXS	Illumina HiSeq	Phase_I	561	73	0.130125	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	56	0.02564102564102564	16	0.032520325203252036	7	0.019337016574585635	21	0.03671328671328671	12	0.0158311345646438	g	8.134	0.783767	0.16189	0.024512	4.65E-4	ENSG00000196539	ENST00000359594	T	0.00063	8.78	2.37	-4.74	0.03249	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	L	0.32530	0.975	0.09310	N	1	B	0.29531	0.247	B	0.37888	0.26	T	0.02167	-1.1202	9	0.27082	T	0.32	.	3.8534	0.08965	0.2803:0.0:0.43:0.2897	.	244	Q8NH03	OR2T3_HUMAN	T	244	ENSP00000352604:A244T	ENSP00000352604:A244T	A	+	1	0	OR2T3	246704004	0.000000	0.05858	0.001000	0.08648	0.247000	0.25773	-1.692000	0.01918	-1.238000	0.02535	0.186000	0.17326	GCC	G|0.987;A|0.013	0.013	strong		0.562	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
SLFN14	342618	hgsc.bcm.edu	37	17	33875262	33875262	+	Missense_Mutation	SNP	T	T	A	rs8073060	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33875262T>A	ENST00000415846.3	-	4	2770	c.2735A>T	c.(2734-2736)tAc>tTc	p.Y912F		NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	912			Y -> F (in dbSNP:rs8073060).				ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						TAATTTTCAGTAGGCTGCCCT	0.398													A|||	1755	0.350439	0.4766	0.3069	5008	,	,		20366	0.1815		0.3201	False		,,,				2504	0.4162				p.Y912F		Atlas-SNP	.											.	SLFN14	43	.	0			c.A2735T						PASS	.	A	PHE/TYR	626,758		145,336,211	89.0	84.0	86.0		2735	2.8	0.3	17	dbSNP_116	86	958,2224		147,664,780	yes	missense	SLFN14	NM_001129820.1	22	292,1000,991	AA,AT,TT		30.1069,45.2312,34.6912	benign	912/913	33875262	1584,2982	692	1591	2283	SO:0001583	missense	342618	exon4			TTTCAGTAGGCTG		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.2735A>T	17.37:g.33875262T>A	ENSP00000391101:p.Tyr912Phe	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_001129820	B2RTW9	Missense_Mutation	SNP	ENST00000415846.3	37	CCDS45650.1	688	0.315018315018315	226	0.45934959349593496	110	0.30386740331491713	109	0.19055944055944055	243	0.32058047493403696	A	0.005	-2.218174	0.00286	0.452312	0.301069	ENSG00000236320	ENST00000415846	T	0.01745	4.66	4.97	2.75	0.32379	.	.	.	.	.	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	0.38067	-0.9678	8	0.02654	T	1	.	3.6425	0.08172	0.6653:0.0:0.1751:0.1597	rs8073060;rs52819255;rs8073060	912	P0C7P3	SLN14_HUMAN	F	912	ENSP00000391101:Y912F	ENSP00000391101:Y912F	Y	-	2	0	SLFN14	30899375	0.392000	0.25229	0.343000	0.25615	0.080000	0.17528	0.507000	0.22675	0.132000	0.18615	-0.364000	0.07487	TAC	T|0.694;A|0.306	0.306	strong		0.398	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
OR6K3	391114	hgsc.bcm.edu	37	1	158687224	158687224	+	Missense_Mutation	SNP	G	G	A	rs857703	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158687224G>A	ENST00000368146.1	-	1	729	c.730C>T	c.(730-732)Ccc>Tcc	p.P244S	OR6K3_ENST00000368145.1_Missense_Mutation_p.P228S			Q8NGY3	OR6K3_HUMAN	olfactory receptor, family 6, subfamily K, member 3	244			P -> S (in dbSNP:rs857703). {ECO:0000269|PubMed:14983052}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P244S(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(2)|stomach(1)	41	all_hematologic(112;0.0378)					TCAGAAGAGGGAATCCTCAAT	0.438													G|||	1404	0.280351	0.09	0.389	5008	,	,		23447	0.4474		0.3946	False		,,,				2504	0.1708				p.P228S		Atlas-SNP	.											OR6K3,NS,carcinoma,0,1	OR6K3	101	1	1	Substitution - Missense(1)	stomach(1)	c.C682T						PASS	.	G	SER/PRO	589,3817	259.5+/-263.1	47,495,1661	107.0	96.0	100.0		682	0.8	0.0	1	dbSNP_86	100	3247,5353	487.5+/-372.1	610,2027,1663	yes	missense	OR6K3	NM_001005327.2	74	657,2522,3324	AA,AG,GG		37.7558,13.3681,29.4941	benign	228/316	158687224	3836,9170	2203	4300	6503	SO:0001583	missense	391114	exon1			AAGAGGGAATCCT	AB065633	CCDS30903.1, CCDS30903.2	1q23.1	2012-08-09			ENSG00000203757	ENSG00000203757		"""GPCR / Class A : Olfactory receptors"""	15030	protein-coding gene	gene with protein product							Standard	NM_001005327		Approved		uc021pbn.1	Q8NGY3	OTTHUMG00000022770	ENST00000368146.1:c.730C>T	1.37:g.158687224G>A	ENSP00000357128:p.Pro244Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_001005327	Q5VUV0|Q6IFR5	Missense_Mutation	SNP	ENST00000368146.1	37		732	0.33516483516483514	56	0.11382113821138211	140	0.3867403314917127	238	0.4160839160839161	298	0.39313984168865435	G	13.46	2.243764	0.39697	0.133681	0.377558	ENSG00000203757	ENST00000368145;ENST00000368146	T;T	0.36878	1.23;1.23	3.77	0.813	0.18749	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.12987	0.0315	L	0.45137	1.4	0.80722	P	0.0	B	0.23128	0.08	B	0.24006	0.05	T	0.10776	-1.0615	8	0.48119	T	0.1	.	7.9959	0.30267	0.2855:0.0:0.7145:0.0	rs857703;rs52791601;rs56909898;rs857703	244	Q8NGY3	OR6K3_HUMAN	S	228;244	ENSP00000357127:P228S;ENSP00000357128:P244S	ENSP00000357127:P228S	P	-	1	0	OR6K3	156953848	0.000000	0.05858	0.001000	0.08648	0.627000	0.37826	-0.113000	0.10774	0.055000	0.16094	0.467000	0.42956	CCC	G|0.696;A|0.304	0.304	strong		0.438	OR6K3-201	KNOWN	basic	protein_coding	protein_coding			
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383027	39383027	+	Missense_Mutation	SNP	G	G	T	rs71371478	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39383027G>T	ENST00000377721.3	+	1	128	c.121G>T	c.(121-123)Gcc>Tcc	p.A41S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.A41S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	41	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.A41S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CTGCCAGCCCGCCTGCTGTGT	0.637																																					p.A41S		Atlas-SNP	.											KRTAP9-2,extremity,malignant_melanoma,0,1	KRTAP9-2	24	1	1	Substitution - Missense(1)	skin(1)	c.G121T						scavenged	.						59.0	53.0	55.0					17																	39383027		2203	4300	6503	SO:0001583	missense	83899	exon1			CAGCCCGCCTGCT	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.121G>T	17.37:g.39383027G>T	ENSP00000366950:p.Ala41Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	8	0.117647	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.020245	0.00418	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01192	5.2;5.4	2.86	-2.81	0.05805	.	.	.	.	.	T	0.00328	0.0010	N	0.00368	-1.59	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.39742	-0.9599	9	0.02654	T	1	.	5.0512	0.14508	0.3642:0.0:0.0934:0.5425	.	41	Q9BYQ4	KRA92_HUMAN	S	41	ENSP00000366950:A41S;ENSP00000398325:A41S	ENSP00000366950:A41S	A	+	1	0	KRTAP9-2	36636553	0.000000	0.05858	0.088000	0.20740	0.203000	0.24098	-1.973000	0.01500	-1.243000	0.02519	-4.519000	0.00005	GCC	G|0.997;T|0.003	0.003	strong		0.637	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
HGS	9146	hgsc.bcm.edu	37	17	79663931	79663931	+	Silent	SNP	T	T	C	rs8070488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79663931T>C	ENST00000329138.4	+	18	1920	c.1785T>C	c.(1783-1785)ccT>ccC	p.P595P		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	595	Gln-rich.|Interaction with NF2.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CCTTCAGCCCTGCCGGCTCGG	0.692													t|||	1271	0.253794	0.3729	0.1556	5008	,	,		13726	0.2252		0.2714	False		,,,				2504	0.1738				p.P595P		Atlas-SNP	.											.	HGS	54	.	0			c.T1785C						PASS	.	T		1581,2823		310,961,931	34.0	42.0	40.0		1785	-8.4	0.0	17	dbSNP_116	40	1881,6705		218,1445,2630	no	coding-synonymous	HGS	NM_004712.4		528,2406,3561	CC,CT,TT		21.9078,35.8992,26.6513		595/778	79663931	3462,9528	2202	4293	6495	SO:0001819	synonymous_variant	9146	exon18			CAGCCCTGCCGGC	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.1785T>C	17.37:g.79663931T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	37	CCDS11784.1																																																																																			T|0.742;C|0.258	0.258	strong		0.692	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
SPTA1	6708	hgsc.bcm.edu	37	1	158582646	158582646	+	Silent	SNP	T	T	C	rs2251969	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158582646T>C	ENST00000368147.4	-	51	7275	c.7095A>G	c.(7093-7095)gcA>gcG	p.A2365A	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2365	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ACTTGCCCTCTGCCAGGGCTT	0.443													C|||	2528	0.504792	0.4183	0.5202	5008	,	,		19129	0.6319		0.5626	False		,,,				2504	0.4202				p.A2365A		Atlas-SNP	.											SPTA1,NS,carcinoma,-2,2	SPTA1	720	2	0			c.A7095G						PASS	.	C		1681,2167		361,959,604	130.0	125.0	126.0		7095	0.2	1.0	1	dbSNP_100	126	4498,3782		1247,2004,889	no	coding-synonymous	SPTA1	NM_003126.2		1608,2963,1493	CC,CT,TT		45.6763,43.685,49.0518		2365/2420	158582646	6179,5949	1924	4140	6064	SO:0001819	synonymous_variant	6708	exon51			GCCCTCTGCCAGG	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.7095A>G	1.37:g.158582646T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			T|0.458;C|0.542	0.542	strong		0.443	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
ITPR1	3708	hgsc.bcm.edu	37	3	4829732	4829732	+	Silent	SNP	A	A	G	rs13079522	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:4829732A>G	ENST00000443694.2	+	49	6672	c.6672A>G	c.(6670-6672)acA>acG	p.T2224T	ITPR1_ENST00000423119.2_Silent_p.T2191T|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Silent_p.T2224T|ITPR1_ENST00000354582.6_Silent_p.T2224T|ITPR1_ENST00000357086.4_Silent_p.T2191T|ITPR1_ENST00000456211.2_Silent_p.T2176T			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2239					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)	ACTATACTACAGAGAGAGACG	0.418													A|||	1230	0.245607	0.2716	0.2133	5008	,	,		17866	0.0923		0.3191	False		,,,				2504	0.316				p.T2224T		Atlas-SNP	.											.	ITPR1	659	.	0			c.A6672G						PASS	.	A	,,	1005,2755		133,739,1008	65.0	59.0	61.0		6573,6672,6528	-8.4	0.6	3	dbSNP_121	61	2645,5567		404,1837,1865	no	coding-synonymous,coding-synonymous,coding-synonymous	ITPR1	NM_001099952.2,NM_001168272.1,NM_002222.5	,,	537,2576,2873	GG,GA,AA		32.209,26.7287,30.4878	,,	2191/2711,2224/2744,2176/2696	4829732	3650,8322	1880	4106	5986	SO:0001819	synonymous_variant	3708	exon51			TACTACAGAGAGA	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.6672A>G	3.37:g.4829732A>G		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	197	112	0.568528	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Silent	SNP	ENST00000443694.2	37	CCDS54551.1																																																																																			A|0.754;G|0.246	0.246	strong		0.418	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632820	32632820	+	Missense_Mutation	SNP	C	C	G	rs1130375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32632820C>G	ENST00000399084.1	-	3	312	c.134G>C	c.(133-135)gGc>gCc	p.G45A	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.G45A|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.G45A|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.G45A|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	45	Beta-1.		A -> G (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:05, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:15, allele DQB1*03:17, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*04:03, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:23, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; dbSNP:rs1130375). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GTAGCACATGCCCTTAAACTG	0.652									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				c|||	1300	0.259585	0.2216	0.2147	5008	,	,		7556	0.3234		0.1998	False		,,,				2504	0.3384				p.G45A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G134C						PASS	.	C	ALA/GLY	656,3586		71,514,1536	24.0	24.0	24.0		134	2.3	0.0	6	dbSNP_86	24	1516,6910		184,1148,2881	yes	missense	HLA-DQB1	NM_002123.4	60	255,1662,4417	GG,GC,CC		17.9919,15.4644,17.1456	benign	45/262	32632820	2172,10496	2121	4213	6334	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CACATGCCCTTAA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.134G>C	6.37:g.32632820C>G	ENSP00000382034:p.Gly45Ala	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	484	0.2216117216117216	93	0.18902439024390244	72	0.19889502762430938	191	0.3339160839160839	128	0.16886543535620052	.	4.079	0.012574	0.07912	0.154644	0.179919	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00235	8.48;8.48;8.48;8.48	4.13	2.26	0.28386	.	0.340862	0.12493	N	0.464088	T	0.00039	0.0001	.	.	.	0.39429	P	0.03294699999999995	B;B;B;B	0.26775	0.159;0.005;0.001;0.001	B;B;B;B	0.32149	0.141;0.012;0.009;0.009	T	0.00000	-1.3101	8	0.12103	T	0.63	.	11.998	0.53214	0.0:0.5934:0.4066:0.0	rs1130375;rs3189158;rs12722109;rs17416204	55;45;45;45	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	A	45	ENSP00000382029:G45A;ENSP00000364080:G45A;ENSP00000407332:G45A;ENSP00000382034:G45A	ENSP00000364080:G45A	G	-	2	0	HLA-DQB1	32740798	0.000000	0.05858	0.040000	0.18447	0.076000	0.17211	-4.545000	0.00218	0.344000	0.23847	0.305000	0.20034	GGC	G|0.228;C|0.772	0.228	strong		0.652	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
GNL3	26354	hgsc.bcm.edu	37	3	52727257	52727257	+	Missense_Mutation	SNP	G	G	A	rs2289247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52727257G>A	ENST00000418458.1	+	11	1272	c.1099G>A	c.(1099-1101)Gtg>Atg	p.V367M	GLT8D1_ENST00000463827.1_5'Flank|SNORD69_ENST00000391150.1_RNA|SNORD19B_ENST00000459623.1_RNA|GNL3_ENST00000394799.2_Missense_Mutation_p.V355M|SNORD19_ENST00000410413.1_RNA	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	367	Intermediate. {ECO:0000250}.		V -> M (in dbSNP:rs2289247). {ECO:0000269|PubMed:11085516, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16012751, ECO:0000269|PubMed:21269460}.		cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		ATTTTTTACTGTGCTTGCTCA	0.428													A|||	2229	0.445088	0.5575	0.513	5008	,	,		18562	0.4276		0.4294	False		,,,				2504	0.2791				p.V367M		Atlas-SNP	.											GNL3,caecum,carcinoma,-1,1	GNL3	37	1	0			c.G1099A						PASS	.	A	MET/VAL,MET/VAL,MET/VAL	2282,2124	571.5+/-383.1	602,1078,523	117.0	125.0	122.0		1099,1063,1063	0.5	0.0	3	dbSNP_100	122	3704,4896	620.0+/-397.0	795,2114,1391	yes	missense,missense,missense	GNL3	NM_014366.4,NM_206825.1,NM_206826.1	21,21,21	1397,3192,1914	AA,AG,GG		43.0698,48.207,46.0249	benign,benign,benign	367/550,355/538,355/538	52727257	5986,7020	2203	4300	6503	SO:0001583	missense	26354	exon11			TTTACTGTGCTTG	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.1099G>A	3.37:g.52727257G>A	ENSP00000395772:p.Val367Met	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	188	87	0.462766	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Missense_Mutation	SNP	ENST00000418458.1	37	CCDS2861.1	1075	0.49221611721611724	273	0.5548780487804879	191	0.5276243093922652	280	0.48951048951048953	331	0.4366754617414248	A	9.162	1.018908	0.19355	0.51793	0.430698	ENSG00000163938	ENST00000418458;ENST00000394799	T;T	0.32272	1.46;1.46	6.0	0.476	0.16779	.	1.319570	0.04466	N	0.375284	T	0.00012	0.0000	N	0.00446	-1.495	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44251	-0.9340	9	0.25106	T	0.35	.	0.787	0.01050	0.1596:0.2371:0.1896:0.4137	rs2289247;rs17856028;rs58107261;rs2289247	367	Q9BVP2	GNL3_HUMAN	M	367;355	ENSP00000395772:V367M;ENSP00000378278:V355M	ENSP00000378278:V355M	V	+	1	0	GNL3	52702297	0.002000	0.14202	0.003000	0.11579	0.864000	0.49448	0.261000	0.18442	-0.059000	0.13154	-0.254000	0.11334	GTG	G|0.533;A|0.467	0.467	strong		0.428	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366	
NDUFS1	4719	hgsc.bcm.edu	37	2	207008763	207008763	+	Silent	SNP	C	C	A	rs1127566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:207008763C>A	ENST00000233190.6	-	10	1232	c.966G>T	c.(964-966)gcG>gcT	p.A322A	NDUFS1_ENST00000455934.2_Silent_p.A336A|NDUFS1_ENST00000440274.1_Silent_p.A286A|NDUFS1_ENST00000423725.1_Silent_p.A265A|NDUFS1_ENST00000432169.1_Silent_p.A211A|NDUFS1_ENST00000449699.1_Silent_p.A322A|NDUFS1_ENST00000457011.1_Silent_p.A206A	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	322					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.A322A(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CGCGAGAGAGCGCATCCTCCC	0.388													C|||	2315	0.46226	0.6475	0.5778	5008	,	,		18330	0.2609		0.4831	False		,,,				2504	0.316				p.A336A		Atlas-SNP	.											NDUFS1,NS,carcinoma,0,1	NDUFS1	82	1	1	Substitution - coding silent(1)	prostate(1)	c.G1008T						scavenged	.	C	,,,,	2800,1606	664.4+/-401.4	896,1008,299	104.0	100.0	102.0		858,633,795,1008,966	-1.0	1.0	2	dbSNP_86	102	3828,4772	538.9+/-383.5	857,2114,1329	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDUFS1	NM_001199981.1,NM_001199982.1,NM_001199983.1,NM_001199984.1,NM_005006.6	,,,,	1753,3122,1628	AA,AC,CC		44.5116,36.4503,49.0389	,,,,	286/692,211/617,265/671,336/742,322/728	207008763	6628,6378	2203	4300	6503	SO:0001819	synonymous_variant	4719	exon10			AGAGAGCGCATCC		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.966G>T	2.37:g.207008763C>A		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Silent	SNP	ENST00000233190.6	37	CCDS2366.1																																																																																			C|0.495;A|0.505	0.505	strong		0.388	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006	
MAML3	55534	hgsc.bcm.edu	37	4	140811117	140811117	+	Silent	SNP	C	C	T	rs62344938		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:140811117C>T	ENST00000509479.2	-	2	2329	c.1473G>A	c.(1471-1473)caG>caA	p.Q491Q	MAML3_ENST00000398940.1_Silent_p.Q30Q|MAML3_ENST00000327122.5_Silent_p.Q335Q	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)					gctgctgctgctgctgttgct	0.547																																					p.Q491Q		Atlas-SNP	.											.	MAML3	192	.	0			c.G1473A						PASS	.						16.0	20.0	18.0					4																	140811117		2191	4287	6478	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGT	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.1473G>A	4.37:g.140811117C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	55	14	0.254545	NM_018717		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.	.	weak		0.547	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
C19orf71	100128569	hgsc.bcm.edu	37	19	3543397	3543397	+	Missense_Mutation	SNP	C	C	T	rs12608919	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:3543397C>T	ENST00000329493.5	+	2	272	c.248C>T	c.(247-249)cCg>cTg	p.P83L	MFSD12_ENST00000398558.4_Intron|AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000389395.3_Intron	NM_001135580.1	NP_001129052.1	A6NCJ1	CS071_HUMAN	chromosome 19 open reading frame 71	83			P -> L (in dbSNP:rs12608919).							endometrium(2)	2						CCACGGGCCCCGGCCAGCCCC	0.692													C|||	1839	0.367212	0.0159	0.4986	5008	,	,		12289	0.7986		0.334	False		,,,				2504	0.3384				p.P83L		Atlas-SNP	.											C19orf71,colon,carcinoma,0,1	C19orf71	12	1	0			c.C248T						PASS	.						10.0	23.0	19.0					19																	3543397		678	1557	2235	SO:0001583	missense	100128569	exon2			GGGCCCCGGCCAG		CCDS45918.1	19p13.3	2012-10-26			ENSG00000183397	ENSG00000183397			34496	protein-coding gene	gene with protein product							Standard	NM_001135580		Approved	LOC100128569	uc010xhm.2	A6NCJ1		ENST00000329493.5:c.248C>T	19.37:g.3543397C>T	ENSP00000327950:p.Pro83Leu	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_001135580		Missense_Mutation	SNP	ENST00000329493.5	37	CCDS45918.1	904	0.4139194139194139	18	0.036585365853658534	162	0.44751381215469616	464	0.8111888111888111	260	0.34300791556728233	C	1.241	-0.621326	0.03636	.	.	ENSG00000183397	ENST00000329493	T	0.25085	1.82	4.51	-6.94	0.01633	.	0.989975	0.08196	N	0.983046	T	0.00012	0.0000	N	0.05031	-0.125	0.80722	P	0.0	B	0.14805	0.011	B	0.10450	0.005	T	0.38222	-0.9671	9	0.02654	T	1	.	13.7342	0.62807	0.0:0.7188:0.0:0.2812	rs12608919;rs12608919	83	A6NCJ1	CS071_HUMAN	L	83	ENSP00000327950:P83L	ENSP00000327950:P83L	P	+	2	0	C19orf71	3494397	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.787000	0.00769	-1.520000	0.01773	-0.657000	0.03884	CCG	C|0.611;T|0.389	0.389	strong		0.692	C19orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452943.1	NM_001135580	
POGK	57645	hgsc.bcm.edu	37	1	166818566	166818566	+	Silent	SNP	A	A	G	rs2075946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:166818566A>G	ENST00000367875.1	+	5	1110	c.750A>G	c.(748-750)gcA>gcG	p.A250A	POGK_ENST00000537173.1_Silent_p.A132A|POGK_ENST00000536514.1_Silent_p.A165A|POGK_ENST00000367876.4_Silent_p.A250A			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	250	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	22						TGCGGCGGGCATTCCGAGGCC	0.577													A|||	1386	0.276757	0.152	0.17	5008	,	,		19070	0.5565		0.162	False		,,,				2504	0.3507				p.A250A	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											.	POGK	54	.	0			c.A750G						PASS	.	A		769,3637	285.5+/-278.2	61,647,1495	38.0	41.0	40.0		750	-11.0	0.0	1	dbSNP_96	40	1593,7007	271.9+/-289.8	144,1305,2851	no	coding-synonymous	POGK	NM_017542.3		205,1952,4346	GG,GA,AA		18.5233,17.4535,18.1608		250/610	166818566	2362,10644	2203	4300	6503	SO:0001819	synonymous_variant	57645	exon5			GCGGGCATTCCGA	AB040946	CCDS1254.1	1q23.2	2013-01-08			ENSG00000143157	ENSG00000143157		"""-"""	18800	protein-coding gene	gene with protein product	"""KRAB box domain containing 2"""						Standard	NM_017542		Approved	KIAA15131, LST003, BASS2, KRBOX2	uc001gdt.1	Q9P215	OTTHUMG00000034325	ENST00000367875.1:c.750A>G	1.37:g.166818566A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_017542	Q5TIJ1|Q8TE07	Silent	SNP	ENST00000367875.1	37	CCDS1254.1																																																																																			A|0.786;G|0.214	0.214	strong		0.577	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542	
LILRA1	11024	hgsc.bcm.edu	37	19	55106288	55106288	+	Missense_Mutation	SNP	A	A	C	rs147848714	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55106288A>C	ENST00000251372.3	+	4	411	c.229A>C	c.(229-231)Att>Ctt	p.I77L	LILRA1_ENST00000453777.1_Missense_Mutation_p.I77L|LILRB1_ENST00000396321.2_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA1_ENST00000473156.1_3'UTR	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	77	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.I77L(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CCCACAGGAGATTGTGAAGAA	0.562																																					p.I77L		Atlas-SNP	.											LILRA1,colon,carcinoma,0,1	LILRA1	105	1	1	Substitution - Missense(1)	large_intestine(1)	c.A229C						scavenged	.						162.0	152.0	155.0					19																	55106288		2203	4300	6503	SO:0001583	missense	11024	exon4			CAGGAGATTGTGA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.229A>C	19.37:g.55106288A>C	ENSP00000251372:p.Ile77Leu	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	297	11	0.037037	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	C	4.547	0.101544	0.08731	.	.	ENSG00000104974	ENST00000251372;ENST00000453777	T;T	0.00695	5.83;5.83	1.62	-1.94	0.07571	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.576540	0.03526	N	0.221733	T	0.00300	0.0009	N	0.00224	-1.81	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.46693	-0.9173	10	0.25106	T	0.35	.	4.3965	0.11365	0.55:0.2547:0.1953:0.0	.	77;77	O75019-2;O75019	.;LIRA1_HUMAN	L	77	ENSP00000251372:I77L;ENSP00000413715:I77L	ENSP00000251372:I77L	I	+	1	0	LILRA1	59798100	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.742000	0.00191	-0.999000	0.03442	-0.982000	0.02568	ATT	A|0.996;C|0.004	0.004	strong		0.562	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
RNF180	285671	hgsc.bcm.edu	37	5	63665448	63665448	+	Missense_Mutation	SNP	G	G	A	rs76090587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:63665448G>A	ENST00000389100.4	+	8	1658	c.1586G>A	c.(1585-1587)cGc>cAc	p.R529H		NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	529					adult behavior (GO:0030534)|norepinephrine metabolic process (GO:0042415)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein polyubiquitination (GO:0000209)|regulation of catalytic activity (GO:0050790)|serotonin metabolic process (GO:0042428)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	20		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0848)|Colorectal(97;0.234)		Lung(70;0.114)		CTAGGTTTCCGCAGACATGCA	0.438													G|||	431	0.0860623	0.0787	0.1052	5008	,	,		15836	0.002		0.1074	False		,,,				2504	0.1472				p.R529H		Atlas-SNP	.											.	RNF180	94	.	0			c.G1586A						PASS	.	G	HIS/ARG	118,1266		7,104,581	249.0	199.0	214.0		1586	-0.1	1.0	5	dbSNP_132	214	357,2825		20,317,1254	yes	missense	RNF180	NM_001113561.1	29	27,421,1835	AA,AG,GG		11.2194,8.526,10.403	benign	529/593	63665448	475,4091	692	1591	2283	SO:0001583	missense	285671	exon8			GTTTCCGCAGACA	AK090756	CCDS34169.1, CCDS47219.1	5q12.3	2013-01-09			ENSG00000164197	ENSG00000164197		"""RING-type (C3HC4) zinc fingers"""	27752	protein-coding gene	gene with protein product							Standard	NM_178532		Approved		uc003jti.3	Q86T96	OTTHUMG00000162278	ENST00000389100.4:c.1586G>A	5.37:g.63665448G>A	ENSP00000373752:p.Arg529His	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	173	86	0.49711	NM_001113561	Q0JSU3|Q495A8|Q8NBD1	Missense_Mutation	SNP	ENST00000389100.4	37	CCDS47219.1	142	0.06501831501831502	39	0.07926829268292683	27	0.07458563535911603	1	0.0017482517482517483	75	0.09894459102902374	G	1.632	-0.518749	0.04171	0.08526	0.112194	ENSG00000164197	ENST00000389100	T	0.42513	0.97	5.45	-0.0956	0.13640	.	0.416882	0.26394	N	0.024622	T	0.00271	0.0008	N	0.08118	0	0.09310	P	0.9999999999985018	B	0.06786	0.001	B	0.01281	0.0	T	0.19943	-1.0290	9	0.02654	T	1	-1.2505	4.0138	0.09634	0.3146:0.3932:0.2921:0.0	.	529	Q86T96	RN180_HUMAN	H	529	ENSP00000373752:R529H	ENSP00000373752:R529H	R	+	2	0	RNF180	63701204	0.608000	0.26966	0.978000	0.43139	0.746000	0.42486	0.291000	0.18994	0.341000	0.23771	-0.605000	0.04089	CGC	G|0.925;A|0.075	0.075	strong		0.438	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1	NM_178532	
DNAH9	1770	hgsc.bcm.edu	37	17	11809063	11809063	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:11809063G>A	ENST00000262442.4	+	61	11754	c.11686G>A	c.(11686-11688)Gcc>Acc	p.A3896T	DNAH9_ENST00000608377.1_Missense_Mutation_p.A208T|DNAH9_ENST00000454412.2_Missense_Mutation_p.A3896T|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3896	AAA 6. {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)	p.A3896T(1)		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)		ATCGGGACCAGCCACTCCTAT	0.473																																					p.A3896T		Atlas-SNP	.											DNAH9,mouth,carcinoma,0,1	DNAH9	695	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G11686A						scavenged	.						69.0	69.0	69.0					17																	11809063		2203	4300	6503	SO:0001583	missense	1770	exon61			GGACCAGCCACTC	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.11686G>A	17.37:g.11809063G>A	ENSP00000262442:p.Ala3896Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	165	3	0.0181818	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.922710	0.52653	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001;ENST00000361801	T;T;T	0.08102	3.13;3.13;3.13	4.81	3.78	0.43462	Dynein heavy chain (1);	0.053373	0.85682	D	0.000000	T	0.04815	0.0130	N	0.11724	0.165	0.53688	D	0.999975	B;B	0.23540	0.036;0.087	B;B	0.27608	0.05;0.081	T	0.44892	-0.9298	10	0.22109	T	0.4	.	8.4451	0.32836	0.0788:0.0:0.7336:0.1876	.	249;3896	B7Z7H0;Q9NYC9	.;DYH9_HUMAN	T	3896;3896;2478;208;249	ENSP00000262442:A3896T;ENSP00000414874:A3896T;ENSP00000379323:A208T	ENSP00000262442:A3896T	A	+	1	0	DNAH9	11749788	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	3.194000	0.51005	1.214000	0.43395	0.655000	0.94253	GCC	.	.	none		0.473	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ECD	11319	hgsc.bcm.edu	37	10	74897816	74897816	+	Silent	SNP	C	C	T	rs2271905	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:74897816C>T	ENST00000372979.4	-	12	1640	c.1434G>A	c.(1432-1434)gaG>gaA	p.E478E	ECD_ENST00000430082.2_Silent_p.E511E|ECD_ENST00000454759.2_Silent_p.E435E	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	478					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)	p.E478E(1)		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)					TGATTGGAGCCTCAGAAGGTT	0.308													T|||	1180	0.235623	0.3676	0.1239	5008	,	,		17095	0.3145		0.0596	False		,,,				2504	0.2362				p.E511E		Atlas-SNP	.											ECD,NS,carcinoma,0,1	ECD	50	1	1	Substitution - coding silent(1)	stomach(1)	c.G1533A						PASS	.	T	,,	1422,2984	667.3+/-401.8	226,970,1007	53.0	52.0	52.0		1533,1305,1434	-0.3	0.9	10	dbSNP_100	52	613,7987	784.4+/-407.6	30,553,3717	no	coding-synonymous,coding-synonymous,coding-synonymous	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	,,	256,1523,4724	TT,TC,CC		7.1279,32.2742,15.6466	,,	511/678,435/602,478/645	74897816	2035,10971	2203	4300	6503	SO:0001819	synonymous_variant	11319	exon13			TGGAGCCTCAGAA	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		ENST00000372979.4:c.1434G>A	10.37:g.74897816C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	37	CCDS7321.1																																																																																			C|0.809;T|0.191	0.191	strong		0.308	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
SPATA4	132851	hgsc.bcm.edu	37	4	177113956	177113956	+	Silent	SNP	A	A	G	rs2291244	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:177113956A>G	ENST00000280191.2	-	4	618	c.510T>C	c.(508-510)taT>taC	p.Y170Y	SPATA4_ENST00000515234.1_5'UTR	NM_144644.2	NP_653245.2	Q8NEY3	SPAT4_HUMAN	spermatogenesis associated 4	170						cytoplasm (GO:0005737)				NS(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)	22		Breast(14;0.0011)|Prostate(90;0.0129)|Melanoma(52;0.0133)|Renal(120;0.0376)|all_hematologic(60;0.124)		all cancers(43;2.9e-20)|Epithelial(43;1.99e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.58e-09)|GBM - Glioblastoma multiforme(59;0.000162)|STAD - Stomach adenocarcinoma(60;0.000543)|LUSC - Lung squamous cell carcinoma(193;0.096)		TCTGGTAGCTATAGTCCGTGA	0.338													A|||	1133	0.226238	0.1573	0.1614	5008	,	,		18209	0.381		0.1769	False		,,,				2504	0.2566				p.Y170Y		Atlas-SNP	.											.	SPATA4	44	.	0			c.T510C						PASS	.	A		727,3679	299.6+/-285.9	67,593,1543	61.0	61.0	61.0		510	-7.6	0.4	4	dbSNP_100	61	1497,7103	282.9+/-295.8	138,1221,2941	no	coding-synonymous	SPATA4	NM_144644.2		205,1814,4484	GG,GA,AA		17.407,16.5002,17.0998		170/306	177113956	2224,10782	2203	4300	6503	SO:0001819	synonymous_variant	132851	exon4			GTAGCTATAGTCC	AY040204	CCDS3826.1	4q34.2	2008-02-05			ENSG00000150628	ENSG00000150628			17333	protein-coding gene	gene with protein product		609879					Standard	NM_144644		Approved	TSARG2, SPEF1B	uc003iuo.1	Q8NEY3	OTTHUMG00000160788	ENST00000280191.2:c.510T>C	4.37:g.177113956A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	70	42	0.6	NM_144644	Q8NCS5|Q8WW15	Silent	SNP	ENST00000280191.2	37	CCDS3826.1																																																																																			A|0.801;G|0.199	0.199	strong		0.338	SPATA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362326.1	NM_144644	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248925	48248925	+	Silent	SNP	C	C	A	rs144346550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48248925C>A	ENST00000246802.5	+	1	147	c.109C>A	c.(109-111)Cgg>Agg	p.R37R	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	37						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GCTGAGGCGGCGGCGGCGAGG	0.662													C|||	61	0.0121805	0.0008	0.0216	5008	,	,		9582	0.0		0.0338	False		,,,				2504	0.0112				p.R37R	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.C109A						PASS	.	C		13,4393		0,13,2190	34.0	43.0	40.0		109	2.2	1.0	19	dbSNP_134	40	179,8417		5,169,4124	no	coding-synonymous	GLTSCR2	NM_015710.4		5,182,6314	AA,AC,CC		2.0824,0.2951,1.4767		37/479	48248925	192,12810	2203	4298	6501	SO:0001819	synonymous_variant	29997	exon1			AGGCGGCGGCGGC	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.109C>A	19.37:g.48248925C>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	157	71	0.452229	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			C|0.981;A|0.019	0.019	strong		0.662	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
SYNE1	23345	hgsc.bcm.edu	37	6	152772264	152772264	+	Missense_Mutation	SNP	A	A	G	rs214976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:152772264A>G	ENST00000367255.5	-	26	3705	c.3104T>C	c.(3103-3105)gTa>gCa	p.V1035A	SYNE1_ENST00000448038.1_Missense_Mutation_p.V1042A|SYNE1_ENST00000423061.1_Missense_Mutation_p.V1042A|SYNE1_ENST00000367248.3_Missense_Mutation_p.V1025A|SYNE1_ENST00000265368.4_Missense_Mutation_p.V1035A|SYNE1_ENST00000413186.2_Missense_Mutation_p.V1035A|SYNE1_ENST00000341594.5_Missense_Mutation_p.V1101A|SYNE1_ENST00000367253.4_Missense_Mutation_p.V1035A	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1035			V -> A (in dbSNP:rs214976).		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)		GCATTCTTCTACAGAGGCTAA	0.453										HNSCC(10;0.0054)			a|||	3041	0.607228	0.8086	0.3732	5008	,	,		17297	0.749		0.4473	False		,,,				2504	0.5194				p.V1042A		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T3125C						PASS	.		ALA/VAL,ALA/VAL	3232,1174	711.6+/-408.0	1188,856,159	177.0	159.0	165.0		3125,3104	5.8	0.0	6	dbSNP_79	165	3694,4906	529.1+/-381.5	807,2080,1413	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	64,64	1995,2936,1572	GG,GA,AA		42.9535,26.6455,46.7477	possibly-damaging,possibly-damaging	1042/8750,1035/8798	152772264	6926,6080	2203	4300	6503	SO:0001583	missense	23345	exon26			TCTTCTACAGAGG	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.3104T>C	6.37:g.152772264A>G	ENSP00000356224:p.Val1035Ala	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	1279	0.5856227106227107	380	0.7723577235772358	143	0.39502762430939226	425	0.743006993006993	331	0.4366754617414248	A	19.02	3.745785	0.69418	0.733545	0.429535	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;D;D;D	0.88896	0.55;0.54;0.46;0.54;0.63;-2.29;-2.44;-2.43	5.84	5.84	0.93424	.	0.636632	0.14357	N	0.324693	D	0.83917	0.5358	M	0.63843	1.955	0.09310	P	1.0	B;B;B;B;B;P	0.35033	0.033;0.009;0.11;0.18;0.009;0.481	B;B;B;B;B;B	0.33454	0.045;0.011;0.157;0.157;0.011;0.164	D	0.85312	0.1079	9	0.54805	T	0.06	.	16.5601	0.84551	1.0:0.0:0.0:0.0	rs214976;rs530857;rs17463800;rs58629854;rs214976	1018;1035;1025;1035;1035;1042	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	A	1035;1042;1035;1042;1101;1035;1025;1035	ENSP00000356224:V1035A;ENSP00000396024:V1042A;ENSP00000265368:V1035A;ENSP00000390975:V1042A;ENSP00000341887:V1101A;ENSP00000356222:V1035A;ENSP00000356217:V1025A;ENSP00000414510:V1035A	ENSP00000265368:V1035A	V	-	2	0	SYNE1	152813957	0.985000	0.35326	0.005000	0.12908	0.991000	0.79684	8.644000	0.91044	2.367000	0.80283	0.529000	0.55759	GTA	G|0.567;N|0.000	0.567	strong		0.453	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
CYP4V2	285440	hgsc.bcm.edu	37	4	187122332	187122332	+	Missense_Mutation	SNP	G	G	A	rs34745240	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187122332G>A	ENST00000378802.4	+	7	1127	c.823G>A	c.(823-825)Gaa>Aaa	p.E275K		NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	275			E -> K (in dbSNP:rs34745240). {ECO:0000269|Ref.3}.		fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|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)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		ACGGGCCAATGAAATGAACGC	0.428													G|||	168	0.0335463	0.084	0.0346	5008	,	,		16116	0.0		0.0288	False		,,,				2504	0.0041				p.E275K		Atlas-SNP	.											.	CYP4V2	49	.	0			c.G823A						PASS	.	G	LYS/GLU	253,4153	146.1+/-180.8	13,227,1963	76.0	77.0	76.0		823	3.8	0.0	4	dbSNP_126	76	248,8352	97.9+/-159.5	5,238,4057	yes	missense	CYP4V2	NM_207352.3	56	18,465,6020	AA,AG,GG		2.8837,5.7422,3.8521	benign	275/526	187122332	501,12505	2203	4300	6503	SO:0001583	missense	285440	exon7			GCCAATGAAATGA	AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"""Cytochrome P450s"""	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.823G>A	4.37:g.187122332G>A	ENSP00000368079:p.Glu275Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	87	49	0.563218	NM_207352	B7U6W2|Q6ZTM4	Missense_Mutation	SNP	ENST00000378802.4	37	CCDS34119.1	65	0.02976190476190476	33	0.06707317073170732	13	0.03591160220994475	0	0.0	19	0.025065963060686015	G	13.49	2.253322	0.39797	0.057422	0.028837	ENSG00000145476	ENST00000378802;ENST00000274118	T	0.68331	-0.32	5.5	3.75	0.43078	.	0.453863	0.26362	N	0.024810	T	0.09686	0.0238	L	0.58669	1.825	0.09310	N	0.999999	B	0.23128	0.08	B	0.24848	0.056	T	0.09596	-1.0667	10	0.29301	T	0.29	.	7.6797	0.28507	0.1432:0.1428:0.7141:0.0	rs34745240;rs61745842	275	Q6ZWL3	CP4V2_HUMAN	K	275;253	ENSP00000368079:E275K	ENSP00000274118:E253K	E	+	1	0	CYP4V2	187359326	0.185000	0.23213	0.011000	0.14972	0.687000	0.40016	1.037000	0.30241	1.309000	0.44985	0.655000	0.94253	GAA	G|0.961;A|0.039	0.039	strong		0.428	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612	
FRMD4B	23150	hgsc.bcm.edu	37	3	69271032	69271032	+	Silent	SNP	G	G	A	rs62254461	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:69271032G>A	ENST00000398540.3	-	9	791	c.708C>T	c.(706-708)ctC>ctT	p.L236L	FRMD4B_ENST00000542259.1_Silent_p.L182L	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	236	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				establishment of epithelial cell polarity (GO:0090162)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|ruffle (GO:0001726)				NS(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(2)	19		Lung NSC(201;0.0138)|Prostate(884;0.11)		BRCA - Breast invasive adenocarcinoma(55;0.000201)|Epithelial(33;0.00141)|LUSC - Lung squamous cell carcinoma(21;0.00999)|Lung(16;0.0182)		GACCTCGAGTGAGACCTTTGA	0.358													G|||	198	0.0395367	0.0068	0.0663	5008	,	,		18997	0.001		0.1183	False		,,,				2504	0.0235				p.L236L		Atlas-SNP	.											.	FRMD4B	90	.	0			c.C708T						PASS	.	G		74,3708		0,74,1817	82.0	77.0	79.0		708	2.5	1.0	3	dbSNP_129	79	967,7249		63,841,3204	no	coding-synonymous	FRMD4B	NM_015123.1		63,915,5021	AA,AG,GG		11.7697,1.9566,8.6764		236/1035	69271032	1041,10957	1891	4108	5999	SO:0001819	synonymous_variant	23150	exon9			TCGAGTGAGACCT	AL832231	CCDS46863.1	3p14.2	2006-04-12			ENSG00000114541	ENSG00000114541			24886	protein-coding gene	gene with protein product						10231032, 11445584	Standard	XM_005264720		Approved	KIAA1013, GRSP1	uc003dnv.2	Q9Y2L6	OTTHUMG00000158772	ENST00000398540.3:c.708C>T	3.37:g.69271032G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	88	40	0.454545	NM_015123	Q8TAI3	Silent	SNP	ENST00000398540.3	37	CCDS46863.1																																																																																			G|0.928;A|0.072	0.072	strong		0.358	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1		
HMGCS1	3157	hgsc.bcm.edu	37	5	43297144	43297144	+	Silent	SNP	A	A	G	rs3733769	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:43297144A>G	ENST00000325110.6	-	5	905	c.699T>C	c.(697-699)taT>taC	p.Y233Y	HMGCS1_ENST00000433297.2_Silent_p.Y233Y	NM_001098272.2	NP_001091742.1	Q01581	HMCS1_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)	233					brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|lipid metabolic process (GO:0006629)|liver development (GO:0001889)|male gonad development (GO:0008584)|response to acid chemical (GO:0001101)|response to drug (GO:0042493)|response to lipoprotein particle (GO:0055094)|response to low light intensity stimulus (GO:0009645)|response to purine-containing compound (GO:0014074)|response to tellurium ion (GO:0046690)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hydroxymethylglutaryl-CoA synthase activity (GO:0004421)|isomerase activity (GO:0016853)|organic acid binding (GO:0043177)			NS(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|stomach(1)|urinary_tract(1)	15						AGTAGACAGAATAGCAGCGGT	0.408													A|||	1773	0.354034	0.3124	0.4582	5008	,	,		20749	0.125		0.5308	False		,,,				2504	0.3906				p.Y233Y		Atlas-SNP	.											.	HMGCS1	33	.	0			c.T699C						PASS	.	A	,	1507,2899	480.3+/-358.8	233,1041,929	159.0	157.0	158.0		699,699	2.3	1.0	5	dbSNP_107	158	4478,4122	590.9+/-392.8	1149,2180,971	no	coding-synonymous,coding-synonymous	HMGCS1	NM_001098272.1,NM_002130.6	,	1382,3221,1900	GG,GA,AA		47.9302,34.2034,46.0172	,	233/521,233/521	43297144	5985,7021	2203	4300	6503	SO:0001819	synonymous_variant	3157	exon5			GACAGAATAGCAG		CCDS34154.1	5p14-p13	2012-10-02	2010-04-30			ENSG00000112972	2.3.3.10		5007	protein-coding gene	gene with protein product	"""3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase"""	142940	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)"""	HMGCS			Standard	NM_001098272		Approved		uc003jnq.5	Q01581		ENST00000325110.6:c.699T>C	5.37:g.43297144A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	161	92	0.571429	NM_001098272	B2RDL8	Silent	SNP	ENST00000325110.6	37	CCDS34154.1																																																																																			A|0.589;G|0.411	0.411	strong		0.408	HMGCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368022.1		
PRR27	401137	hgsc.bcm.edu	37	4	71024240	71024240	+	Missense_Mutation	SNP	C	C	T	rs1613461	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71024240C>T	ENST00000344526.5	+	3	460	c.271C>T	c.(271-273)Cgt>Tgt	p.R91C	C4orf40_ENST00000502294.1_Missense_Mutation_p.R91C|C4orf40_ENST00000502441.2_Intron	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		91	Ala/Pro-rich.		R -> C (in dbSNP:rs1613461).			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						CTATCACATCCGTGGTTTTCC	0.493													C|||	210	0.0419329	0.056	0.0202	5008	,	,		20996	0.001		0.0149	False		,,,				2504	0.1084				p.R91C		Atlas-SNP	.											.	C4orf40	19	.	0			c.C271T						PASS	.	C	CYS/ARG	199,4207	124.5+/-161.8	3,193,2007	267.0	251.0	257.0		271	0.6	0.0	4	dbSNP_89	257	149,8451	72.6+/-135.2	0,149,4151	yes	missense	C4orf40	NM_214711.3	180	3,342,6158	TT,TC,CC		1.7326,4.5166,2.6757	possibly-damaging	91/220	71024240	348,12658	2203	4300	6503	SO:0001583	missense	401137	exon3			CACATCCGTGGTT																												ENST00000344526.5:c.271C>T	4.37:g.71024240C>T	ENSP00000343172:p.Arg91Cys	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	208	106	0.509615	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	49	0.022435897435897436	24	0.04878048780487805	10	0.027624309392265192	1	0.0017482517482517483	14	0.018469656992084433	C	14.43	2.532322	0.45073	0.045166	0.017326	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.32023	1.47;1.47	4.45	0.609	0.17575	.	.	.	.	.	T	0.01870	0.0059	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.19811	-1.0294	9	0.42905	T	0.14	4.2071	3.2743	0.06893	0.1834:0.5114:0.0:0.3052	rs1613461;rs52791776;rs1613461	91	Q6MZM9	CD040_HUMAN	C	91	ENSP00000426249:R91C;ENSP00000343172:R91C	ENSP00000343172:R91C	R	+	1	0	C4orf40	71058829	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.074000	0.11450	0.178000	0.19917	-0.241000	0.12123	CGT	C|0.971;T|0.029	0.029	strong		0.493	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1264795	1264795	+	Missense_Mutation	SNP	G	G	C	rs200138247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1264795G>C	ENST00000529681.1	+	31	6743	c.6685G>C	c.(6685-6687)Gag>Cag	p.E2229Q	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.E2232Q	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2229	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)		CCACATCACAGAGCCTTCCAC	0.652													g|||	19	0.00379393	0.0008	0.0058	5008	,	,		13832	0.0		0.0119	False		,,,				2504	0.002				p.E2229Q		Atlas-SNP	.											.	MUC5B	473	.	0			c.G6685C						PASS	.	G	GLN/GLU	5,4165		0,5,2080	95.0	120.0	112.0		6685	-1.5	0.0	11		112	55,8297		0,55,4121	no	missense	MUC5B	NM_002458.2	29	0,60,6201	CC,CG,GG		0.6585,0.1199,0.4792	possibly-damaging	2229/5763	1264795	60,12462	2085	4176	6261	SO:0001583	missense	727897	exon31			ATCACAGAGCCTT	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.6685G>C	11.37:g.1264795G>C	ENSP00000436812:p.Glu2229Gln	Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	322	117	0.363354	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	4.475	0.088061	0.08583	0.001199	0.006585	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21031	2.03;2.21	1.87	-1.45	0.08828	.	.	.	.	.	T	0.06280	0.0162	L	0.36672	1.1	0.09310	N	1	P;P	0.47604	0.813;0.898	B;B	0.28784	0.053;0.094	T	0.24512	-1.0158	9	0.87932	D	0	.	0.5061	0.00588	0.4066:0.1743:0.2245:0.1945	.	2867;2232	A7Y9J9;E9PBJ0	.;.	Q	2229;2232;2230;2244	ENSP00000436812:E2229Q;ENSP00000415793:E2232Q	ENSP00000343037:E2230Q	E	+	1	0	MUC5B	1221371	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.475000	0.06599	-0.394000	0.07727	0.305000	0.20034	GAG	.	.	weak		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
NIPSNAP3B	55335	hgsc.bcm.edu	37	9	107531152	107531152	+	Missense_Mutation	SNP	G	G	C	rs10761084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107531152G>C	ENST00000374762.3	+	3	351	c.280G>C	c.(280-282)Gct>Cct	p.A94P	NIPSNAP3B_ENST00000461177.1_3'UTR	NM_018376.2	NP_060846.2	Q9BS92	NPS3B_HUMAN	nipsnap homolog 3B (C. elegans)	94			A -> P (in dbSNP:rs10761084). {ECO:0000269|PubMed:14702039}.					p.A94P(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	11						AGATAATTTTGCTCATCGAGC	0.358													.|||	890	0.177716	0.0257	0.1455	5008	,	,		15655	0.2857		0.1769	False		,,,				2504	0.2955				p.A94P		Atlas-SNP	.											NIPSNAP3B,NS,carcinoma,0,1	NIPSNAP3B	22	1	1	Substitution - Missense(1)	stomach(1)	c.G280C						scavenged	.	G	PRO/ALA	199,4207	124.5+/-161.8	6,187,2010	62.0	59.0	60.0		280	3.8	1.0	9	dbSNP_120	60	1633,6967	301.6+/-305.5	171,1291,2838	yes	missense	NIPSNAP3B	NM_018376.2	27	177,1478,4848	CC,CG,GG		18.9884,4.5166,14.0858	possibly-damaging	94/248	107531152	1832,11174	2203	4300	6503	SO:0001583	missense	55335	exon3			AATTTTGCTCATC	BC017914	CCDS6761.1	9q31.3	2003-11-27			ENSG00000165028	ENSG00000165028			23641	protein-coding gene	gene with protein product		608872				12477932	Standard	NM_018376		Approved	FLJ11275	uc004bci.3	Q9BS92	OTTHUMG00000020414	ENST00000374762.3:c.280G>C	9.37:g.107531152G>C	ENSP00000363894:p.Ala94Pro	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	130	66	0.507692	NM_018376	Q5VX30|Q9NUM2	Missense_Mutation	SNP	ENST00000374762.3	37	CCDS6761.1	357	0.16346153846153846	15	0.03048780487804878	60	0.16574585635359115	146	0.25524475524475526	136	0.17941952506596306	G	17.64	3.439372	0.63067	0.045166	0.189884	ENSG00000165028	ENST00000374762	T	0.50813	0.73	3.77	3.77	0.43336	Dimeric alpha-beta barrel (1);	0.060953	0.64402	U	0.000004	T	0.00039	0.0001	M	0.81239	2.535	0.20821	P	0.999845625	D	0.63880	0.993	D	0.70487	0.969	T	0.04281	-1.0963	9	0.30854	T	0.27	-6.9526	12.9916	0.58622	0.0:0.0:1.0:0.0	rs10761084;rs56447258;rs10761084	94	Q9BS92	NPS3B_HUMAN	P	94	ENSP00000363894:A94P	ENSP00000363894:A94P	A	+	1	0	NIPSNAP3B	106570973	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.087000	0.50167	2.088000	0.63022	0.650000	0.86243	GCT	G|0.846;C|0.154	0.154	strong		0.358	NIPSNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053486.1	NM_018376	
ATP8B3	148229	hgsc.bcm.edu	37	19	1783027	1783027	+	Nonstop_Mutation	SNP	T	T	C	rs60482625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1783027T>C	ENST00000310127.6	-	29	4141	c.3903A>G	c.(3901-3903)tgA>tgG	p.*1301W	ATP8B3_ENST00000539485.1_Nonstop_Mutation_p.*1311W|ATP8B3_ENST00000525591.1_Nonstop_Mutation_p.*1264W	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	0					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)		TCCTGAGGTGTCACTGTGACT	0.557													.|||	449	0.0896565	0.2231	0.0432	5008	,	,		18819	0.002		0.0437	False		,,,				2504	0.0798				p.X1301W		Atlas-SNP	.											.	ATP8B3	108	.	0			c.A3903G						PASS	.	C	TRP/stop,TRP/stop	750,3296		72,606,1345	61.0	60.0	60.0		3792,3903	-1.0	0.0	19	dbSNP_129	60	397,7975		11,375,3800	yes	stop-lost,stop-lost	ATP8B3	NM_001178002.1,NM_138813.2	,	83,981,5145	CC,CT,TT		4.742,18.5368,9.2366	,	1264/1264,1301/1301	1783027	1147,11271	2023	4186	6209	SO:0001578	stop_lost	148229	exon29			GAGGTGTCACTGT	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.3903A>G	19.37:g.1783027T>C	ENSP00000311336:p.*1301Cysext*245	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	154	0.07051282051282051	96	0.1951219512195122	19	0.052486187845303865	1	0.0017482517482517483	38	0.05013192612137203	C	8.836	0.941090	0.18281	0.185368	0.04742	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	.	.	.	3.46	-0.957	0.10350	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.1953	0.00139	0.2142:0.2675:0.1944:0.3238	rs60482625	.	.	.	W	1301;1311;1264	.	.	X	-	3	0	ATP8B3	1734027	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.165000	0.03132	-0.210000	0.10140	-1.147000	0.01851	TGA	T|0.934;C|0.066	0.066	strong		0.557	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
ANKUB1	389161	hgsc.bcm.edu	37	3	149484970	149484970	+	Intron	SNP	G	G	A	rs75077284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:149484970G>A	ENST00000383050.3	-	5	1687				ANKUB1_ENST00000446160.1_Silent_p.N493N|ANKUB1_ENST00000462519.2_Silent_p.N493N			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1											breast(1)|kidney(1)|lung(1)|skin(1)	4						AGTAGATTGCGTTCTCCCATG	0.438													G|||	84	0.0167732	0.0083	0.0159	5008	,	,		18826	0.001		0.0517	False		,,,				2504	0.0092				p.N493N		Atlas-SNP	.											.	ANKUB1	27	.	0			c.C1479T						PASS	.	G		18,1366		1,16,675	126.0	107.0	113.0		1479	-10.3	0.2	3	dbSNP_132	113	175,3007		8,159,1424	no	coding-synonymous	ANKUB1	NM_001144960.1		9,175,2099	AA,AG,GG		5.4997,1.3006,4.2269		493/545	149484970	193,4373	692	1591	2283	SO:0001627	intron_variant	389161	exon5			GATTGCGTTCTCC	AK027233		3q25.1	2013-01-11	2011-05-10	2011-05-10	ENSG00000206199	ENSG00000206199		"""Ankyrin repeat domain containing"""	29642	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 16"""	C3orf16			Standard	NM_001144960		Approved		uc003exl.3	A6NFN9	OTTHUMG00000159615	ENST00000383050.3:c.1230+248C>T	3.37:g.149484970G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_001144960	B4E2N8	Silent	SNP	ENST00000383050.3	37																																																																																				G|0.975;A|0.025	0.025	strong		0.438	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
TACC3	10460	hgsc.bcm.edu	37	4	1729953	1729953	+	Missense_Mutation	SNP	G	G	A	rs17132047	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1729953G>A	ENST00000313288.4	+	4	930	c.824G>A	c.(823-825)tGc>tAc	p.C275Y		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	275			C -> Y (in dbSNP:rs17132047). {ECO:0000269|PubMed:11298601}.		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)			GCCCTGGGCTGCCCTGCGGGT	0.662													G|||	747	0.149161	0.059	0.1873	5008	,	,		15585	0.1478		0.2634	False		,,,				2504	0.1278				p.C275Y	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											TACC3,NS,carcinoma,0,1	TACC3	69	1	0			c.G824A						PASS	.	G	TYR/CYS	414,3974		23,368,1803	15.0	17.0	16.0		824	-0.3	0.0	4	dbSNP_123	16	2073,6513		245,1583,2465	yes	missense	TACC3	NM_006342.1	194	268,1951,4268	AA,AG,GG		24.144,9.4348,19.1691	benign	275/839	1729953	2487,10487	2194	4293	6487	SO:0001583	missense	10460	exon4			TGGGCTGCCCTGC	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.824G>A	4.37:g.1729953G>A	ENSP00000326550:p.Cys275Tyr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	28	0.482759	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	394	0.1804029304029304	32	0.06504065040650407	64	0.17679558011049723	95	0.1660839160839161	203	0.2678100263852243	G	5.376	0.254644	0.10185	0.094348	0.24144	ENSG00000013810	ENST00000313288	T	0.09817	2.94	3.71	-0.35	0.12606	.	2.209180	0.02893	U	0.134360	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B	0.22414	0.069;0.007	B;B	0.15052	0.012;0.002	T	0.42982	-0.9419	9	0.46703	T	0.11	0.8318	4.8608	0.13583	0.2962:0.158:0.5457:0.0	rs17132047	275;275	B4DYJ1;Q9Y6A5	.;TACC3_HUMAN	Y	275	ENSP00000326550:C275Y	ENSP00000326550:C275Y	C	+	2	0	TACC3	1699751	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.074000	0.14662	-0.095000	0.12351	-0.300000	0.09419	TGC	G|0.827;A|0.173	0.173	strong		0.662	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
MCF2L2	23101	hgsc.bcm.edu	37	3	183027542	183027542	+	Missense_Mutation	SNP	T	T	G	rs7639705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183027542T>G	ENST00000328913.3	-	10	1372	c.1075A>C	c.(1075-1077)Att>Ctt	p.I359L	MCF2L2_ENST00000447025.2_Missense_Mutation_p.I359L|MCF2L2_ENST00000473233.1_Missense_Mutation_p.I359L|MCF2L2_ENST00000414362.2_Missense_Mutation_p.I359L	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	359			I -> L (in dbSNP:rs7639705). {ECO:0000269|PubMed:14702039}.				Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I359L(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TCCTTAAGAATCTGCTCCACG	0.448													G|||	1675	0.334465	0.4244	0.2363	5008	,	,		17356	0.3562		0.2167	False		,,,				2504	0.3814				p.I359L		Atlas-SNP	.											MCF2L2,NS,carcinoma,0,1	MCF2L2	164	1	1	Substitution - Missense(1)	stomach(1)	c.A1075C						PASS	.	G	LEU/ILE	1762,2644	645.6+/-398.2	377,1008,818	160.0	148.0	152.0		1075	3.8	0.0	3	dbSNP_116	152	1689,6911	738.6+/-407.1	170,1349,2781	yes	missense	MCF2L2	NM_015078.2	5	547,2357,3599	GG,GT,TT		19.6395,39.9909,26.5339	benign	359/1115	183027542	3451,9555	2203	4300	6503	SO:0001583	missense	23101	exon10			TAAGAATCTGCTC	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.1075A>C	3.37:g.183027542T>G	ENSP00000328118:p.Ile359Leu	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	145	73	0.503448	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	637	0.2916666666666667	181	0.3678861788617886	96	0.26519337016574585	192	0.3356643356643357	168	0.22163588390501318	G	0.349	-0.945787	0.02304	0.399909	0.196395	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	4.73	3.84	0.44239	.	0.066665	0.64402	N	0.000009	T	0.00012	0.0000	N	0.00456	-1.48	0.49483	P	2.0600000000003948E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44862	-0.9300	9	0.02654	T	1	.	14.0032	0.64446	0.0:0.0:0.7235:0.2765	rs7639705;rs17749805;rs52825331;rs61011857;rs7639705	359;359	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	L	359	ENSP00000328118:I359L;ENSP00000420070:I359L;ENSP00000388190:I359L;ENSP00000414131:I359L	ENSP00000328118:I359L	I	-	1	0	MCF2L2	184510236	1.000000	0.71417	0.037000	0.18230	0.074000	0.17049	3.804000	0.55568	0.706000	0.31912	-0.121000	0.15023	ATT	T|0.718;G|0.282	0.282	strong		0.448	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
MANBA	4126	hgsc.bcm.edu	37	4	103611845	103611845	+	Missense_Mutation	SNP	C	C	T	rs227368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:103611845C>T	ENST00000226578.4	-	6	856	c.757G>A	c.(757-759)Gta>Ata	p.V253I	MANBA_ENST00000505239.1_Missense_Mutation_p.V196I	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	253			V -> I (in dbSNP:rs227368). {ECO:0000269|PubMed:9384606}.|V -> L (in dbSNP:rs227368).		cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		GGGATGGCTACGATCACTTGA	0.393													C|||	1886	0.376597	0.1195	0.3545	5008	,	,		12527	0.4732		0.497	False		,,,				2504	0.5164				p.V253I		Atlas-SNP	.											.	MANBA	78	.	0			c.G757A						PASS	.	C	ILE/VAL	929,3477	354.1+/-312.5	107,715,1381	271.0	229.0	243.0		757	1.3	0.0	4	dbSNP_79	243	4081,4519	560.9+/-387.7	967,2147,1186	yes	missense	MANBA	NM_005908.3	29	1074,2862,2567	TT,TC,CC		47.4535,21.0849,38.5207	benign	253/880	103611845	5010,7996	2203	4300	6503	SO:0001583	missense	4126	exon6			TGGCTACGATCAC		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.757G>A	4.37:g.103611845C>T	ENSP00000226578:p.Val253Ile	Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	865	0.39606227106227104	58	0.11788617886178862	137	0.3784530386740331	288	0.5034965034965035	382	0.503957783641161	C	7.365	0.625609	0.14257	0.210849	0.474535	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.55760	0.5;0.5	4.93	1.29	0.21616	.	0.358272	0.29342	N	0.012434	T	0.00012	0.0000	L	0.37800	1.135	0.48830	P	2.8799999999995496E-4	B;B	0.19583	0.037;0.016	B;B	0.08055	0.003;0.003	T	0.48536	-0.9027	9	0.25751	T	0.34	-10.9971	8.9216	0.35615	0.0:0.702:0.0:0.298	rs227368;rs3912789;rs52818263;rs58634559;rs227368	196;253	E9PFW2;O00462	.;MANBA_HUMAN	I	253;196	ENSP00000226578:V253I;ENSP00000427322:V196I	ENSP00000226578:V253I	V	-	1	0	MANBA	103830893	0.000000	0.05858	0.007000	0.13788	0.915000	0.54546	-0.243000	0.08915	0.016000	0.14998	-0.143000	0.13931	GTA	T|0.377;G|0.002;C|0.617;A|0.004	0.377	strong		0.393	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
TMEM198	130612	hgsc.bcm.edu	37	2	220414019	220414019	+	Silent	SNP	T	T	C	rs13023533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220414019T>C	ENST00000344458.2	+	5	1473	c.888T>C	c.(886-888)ccT>ccC	p.P296P	RP11-256I23.1_ENST00000596829.1_RNA|TMEM198_ENST00000373883.3_Silent_p.P296P|MIR3132_ENST00000581997.1_RNA			Q66K66	TM198_HUMAN	transmembrane protein 198	296	Arg-rich.				multicellular organismal development (GO:0007275)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	16		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		CACCAGACCCTGCTTATCGGC	0.622													T|||	1965	0.392372	0.4077	0.5231	5008	,	,		11770	0.38		0.4592	False		,,,				2504	0.2229				p.P296P		Atlas-SNP	.											TMEM198,NS,carcinoma,0,2	TMEM198	36	2	0			c.T888C						scavenged	.	T		716,3690		295,126,1782	41.0	45.0	44.0		888	-1.4	1.0	2	dbSNP_121	44	1537,7063		640,257,3403	no	coding-synonymous	TMEM198	NM_001005209.1		935,383,5185	CC,CT,TT		17.8721,16.2506,17.3228		296/361	220414019	2253,10753	2203	4300	6503	SO:0001819	synonymous_variant	130612	exon4			AGACCCTGCTTAT	BC068567	CCDS33385.1	2q35	2011-12-06			ENSG00000188760	ENSG00000188760			33704	protein-coding gene	gene with protein product							Standard	NM_001005209		Approved	MGC99813, TMEM198A	uc002vmf.3	Q66K66	OTTHUMG00000059156	ENST00000344458.2:c.888T>C	2.37:g.220414019T>C		Somatic	201	2	0.00995025		WXS	Illumina HiSeq	Phase_I	175	94	0.537143	NM_001005209		Silent	SNP	ENST00000344458.2	37	CCDS33385.1																																																																																			T|0.559;C|0.441	0.441	strong		0.622	TMEM198-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131063.1	NM_001005209	
SERPINB8	5271	hgsc.bcm.edu	37	18	61654297	61654297	+	Missense_Mutation	SNP	A	A	G	rs3169983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:61654297A>G	ENST00000397985.2	+	7	1166	c.910A>G	c.(910-912)Act>Gct	p.T304A	SERPINB8_ENST00000542677.1_Missense_Mutation_p.T122A|SERPINB8_ENST00000493661.1_Intron|SERPINB8_ENST00000353706.2_Missense_Mutation_p.T304A	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	304			T -> A (in dbSNP:rs3169983). {ECO:0000269|PubMed:17974005}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				TGGAATGTCAACTGAGAAGAA	0.498													A|||	889	0.177516	0.2648	0.0663	5008	,	,		19756	0.1756		0.0716	False		,,,				2504	0.2495				p.T304A		Atlas-SNP	.											.	SERPINB8	42	.	0			c.A910G						PASS	.	A	ALA/THR,ALA/THR	941,3465	358.6+/-314.5	109,723,1371	116.0	98.0	104.0		910,910	-1.0	0.0	18	dbSNP_105	104	785,7815	185.3+/-233.1	45,695,3560	yes	missense,missense	SERPINB8	NM_002640.3,NM_198833.1	58,58	154,1418,4931	GG,GA,AA		9.1279,21.3572,13.2708	benign,benign	304/375,304/375	61654297	1726,11280	2203	4300	6503	SO:0001583	missense	5271	exon7			ATGTCAACTGAGA	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"""Serine (or cysteine) peptidase inhibitors"""	8952	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase 2"""	601697	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"""	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.910A>G	18.37:g.61654297A>G	ENSP00000381072:p.Thr304Ala	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_198833	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	37	CCDS11991.1	314	0.14377289377289376	109	0.22154471544715448	26	0.0718232044198895	127	0.22202797202797203	52	0.06860158311345646	A	5.544	0.285312	0.10513	0.213572	0.091279	ENSG00000166401	ENST00000397985;ENST00000353706;ENST00000542677	D;D;T	0.82255	-1.59;-1.59;2.81	5.65	-1.01	0.10169	Serpin domain (3);	0.744591	0.13300	N	0.398299	T	0.00039	0.0001	N	0.05199	-0.095	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.02821	-1.1106	9	0.09338	T	0.73	.	1.3588	0.02187	0.323:0.1099:0.3293:0.2378	rs3169983;rs3744957;rs3169983	304	P50452	SPB8_HUMAN	A	304;304;122	ENSP00000381072:T304A;ENSP00000331368:T304A;ENSP00000438328:T122A	ENSP00000331368:T304A	T	+	1	0	SERPINB8	59805277	0.000000	0.05858	0.001000	0.08648	0.870000	0.49936	0.113000	0.15499	-0.053000	0.13289	0.533000	0.62120	ACT	A|0.851;G|0.149	0.149	strong		0.498	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	
SIRPB1	10326	hgsc.bcm.edu	37	20	1546911	1546911	+	Missense_Mutation	SNP	C	C	G	rs2243603	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1546911C>G	ENST00000381605.4	-	5	1151	c.1087G>C	c.(1087-1089)Gca>Cca	p.A363P	SIRPB1_ENST00000262929.5_Missense_Mutation_p.A145P|SIRPB1_ENST00000381603.3_Missense_Mutation_p.A146P|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	363			A -> P (in dbSNP:rs2243603). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191}.		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						GCCAGCGCTGCTTCTGGAAAT	0.602													.|||	4047	0.808107	0.9448	0.6369	5008	,	,		16125	0.7887		0.7724	False		,,,				2504	0.8016				p.A363P		Atlas-SNP	.											.	SIRPB1	83	.	0			c.G1087C						PASS	.	G	PRO/ALA,PRO/ALA	3979,425		1805,369,28	35.0	30.0	32.0		436,1087	-3.1	0.0	20	dbSNP_100	32	6645,1949		2558,1529,210	yes	missense,missense	SIRPB1	NM_001083910.2,NM_006065.3	27,27	4363,1898,238	GG,GC,CC		22.6786,9.6503,18.2643	benign,benign	146/182,363/399	1546911	10624,2374	2202	4297	6499	SO:0001583	missense	10326	exon5			GCGCTGCTTCTGG	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.1087G>C	20.37:g.1546911C>G	ENSP00000371018:p.Ala363Pro	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	1643	0.7522893772893773	430	0.8739837398373984	242	0.6685082872928176	430	0.7517482517482518	541	0.7137203166226913	.	7.626	0.677848	0.14841	0.903497	0.773214	ENSG00000101307	ENST00000381605;ENST00000381603;ENST00000262929	T;T;T	0.02345	4.33;4.4;4.4	3.66	-3.08	0.05347	.	2746.850000	0.00166	N	0.000000	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	0.13469	-1.0508	9	0.21014	T	0.42	.	3.0474	0.06158	0.0946:0.3967:0.2381:0.2706	rs2243603;rs60927301;rs2243603	363;146	O00241;O00241-2	SIRB1_HUMAN;.	P	363;146;145	ENSP00000371018:A363P;ENSP00000371016:A146P;ENSP00000262929:A145P	ENSP00000262929:A145P	A	-	1	0	SIRPB1	1494911	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.036000	0.12185	-0.783000	0.04534	-0.975000	0.02590	GCA	C|0.188;G|0.812	0.812	strong		0.602	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
GLRX5	51218	hgsc.bcm.edu	37	14	96010424	96010424	+	Missense_Mutation	SNP	G	G	A	rs11628901	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:96010424G>A	ENST00000331334.4	+	2	933	c.436G>A	c.(436-438)Gcc>Acc	p.A146T	GLRX5_ENST00000553672.1_3'UTR	NM_016417.2	NP_057501.2	Q86SX6	GLRX5_HUMAN	glutaredoxin 5	146			A -> T (in dbSNP:rs11628901). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16110529}.		cell redox homeostasis (GO:0045454)|hemopoiesis (GO:0030097)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|protein disulfide oxidoreductase activity (GO:0015035)			large_intestine(1)|lung(1)	2		all_cancers(154;0.135)		Epithelial(152;0.133)|COAD - Colon adenocarcinoma(157;0.21)|all cancers(159;0.212)		GATCCACTCCGCCCTTTTAGA	0.527													G|||	416	0.0830671	0.0431	0.1153	5008	,	,		16548	0.0218		0.1362	False		,,,				2504	0.1227				p.A146T		Atlas-SNP	.											.	GLRX5	7	.	0			c.G436A						PASS	.	G	THR/ALA	255,4151	146.5+/-181.1	10,235,1958	45.0	48.0	47.0		436	4.1	1.0	14	dbSNP_120	47	1261,7339	250.7+/-277.5	84,1093,3123	yes	missense	GLRX5	NM_016417.2	58	94,1328,5081	AA,AG,GG		14.6628,5.7876,11.6562	benign	146/158	96010424	1516,11490	2203	4300	6503	SO:0001583	missense	51218	exon2			CACTCCGCCCTTT	AF113691	CCDS9936.1	14q32.2	2007-08-16	2007-08-16	2005-11-11		ENSG00000182512			20134	protein-coding gene	gene with protein product		609588	"""chromosome 14 open reading frame 87"", ""glutaredoxin 5 homolog (S. cerevisiae)"""	C14orf87			Standard	NM_016417		Approved	PR01238, GRX5	uc001yem.1	Q86SX6		ENST00000331334.4:c.436G>A	14.37:g.96010424G>A	ENSP00000328570:p.Ala146Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	92	42	0.456522	NM_016417	Q0X088|Q3YML0|Q86WY3|Q8IZ54	Missense_Mutation	SNP	ENST00000331334.4	37	CCDS9936.1	174	0.07967032967032966	23	0.046747967479674794	34	0.09392265193370165	14	0.024475524475524476	103	0.1358839050131926	G	19.41	3.822386	0.71028	0.057876	0.146628	ENSG00000182512	ENST00000331334	T	0.36157	1.27	5.02	4.11	0.48088	Thioredoxin-like fold (1);	0.160491	0.56097	D	0.000037	T	0.00109	0.0003	L	0.41824	1.3	0.09310	P	0.9999999495891	P	0.45768	0.866	B	0.27715	0.082	T	0.11084	-1.0602	9	0.38643	T	0.18	-7.2558	12.8273	0.57726	0.0801:0.0:0.9199:0.0	rs11628901;rs17092662;rs17852142	146	Q86SX6	GLRX5_HUMAN	T	146	ENSP00000328570:A146T	ENSP00000328570:A146T	A	+	1	0	GLRX5	95080177	1.000000	0.71417	0.989000	0.46669	0.931000	0.56810	7.191000	0.77763	1.079000	0.41038	0.491000	0.48974	GCC	G|0.897;A|0.103	0.103	strong		0.527	GLRX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414550.1		
PEBP4	157310	hgsc.bcm.edu	37	8	22570905	22570905	+	Missense_Mutation	SNP	T	T	G	rs386723487|rs79936857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22570905T>G	ENST00000256404.6	-	7	753	c.662A>C	c.(661-663)cAg>cCg	p.Q221P	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	221						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		TATCTCCGCCTGGTTTTTGTG	0.592													T|||	374	0.0746805	0.2428	0.0231	5008	,	,		16389	0.004		0.0199	False		,,,				2504	0.0133				p.Q221P		Atlas-SNP	.											.	PEBP4	23	.	0			c.A662C						PASS	.						72.0	79.0	77.0					8																	22570905		1953	4151	6104	SO:0001583	missense	157310	exon7			TCCGCCTGGTTTT	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"""cousin-of-RKIP 1 protein"""	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.662A>C	8.37:g.22570905T>G	ENSP00000256404:p.Gln221Pro	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	108	59	0.546296	NM_144962	Q5EVA1|Q8WW74	Missense_Mutation	SNP	ENST00000256404.6	37	CCDS43724.1	114	0.0521978021978022	96	0.1951219512195122	6	0.016574585635359115	5	0.008741258741258742	7	0.009234828496042216	T	11.07	1.531292	0.27387	.	.	ENSG00000134020	ENST00000256404	T	0.33438	1.41	5.01	-1.92	0.07618	.	47.664200	0.00166	N	0.000000	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	D	0.65815	0.995	P	0.56278	0.795	T	0.02539	-1.1144	9	0.59425	D	0.04	8.4188	4.2246	0.10574	0.1617:0.3762:0.0:0.4621	.	221	Q96S96	PEBP4_HUMAN	P	221	ENSP00000256404:Q221P	ENSP00000256404:Q221P	Q	-	2	0	PEBP4	22626850	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.839000	0.04368	-0.336000	0.08438	0.459000	0.35465	CAG	T|0.962;G|0.038	0.038	strong		0.592	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
VSIG10	54621	hgsc.bcm.edu	37	12	118506186	118506186	+	Silent	SNP	A	A	T	rs67405503	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:118506186A>T	ENST00000359236.5	-	8	1839	c.1563T>A	c.(1561-1563)ctT>ctA	p.L521L		NM_019086.5	NP_061959.2	Q8N0Z9	VSI10_HUMAN	V-set and immunoglobulin domain containing 10	521						integral component of membrane (GO:0016021)				endometrium(5)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|urinary_tract(1)	17						GCTTACCTTGAAGATCCTGGA	0.448													T|||	2110	0.421326	0.4516	0.4582	5008	,	,		18101	0.372		0.4036	False		,,,				2504	0.4233				p.L521L		Atlas-SNP	.											.	VSIG10	41	.	0			c.T1563A						PASS	.	T		1649,2181		344,961,610	187.0	183.0	184.0		1563	-8.2	0.3	12	dbSNP_130	184	3170,5072		618,1934,1569	no	coding-synonymous	VSIG10	NM_019086.5		962,2895,2179	TT,TA,AA		38.4615,43.0548,39.9188		521/541	118506186	4819,7253	1915	4121	6036	SO:0001819	synonymous_variant	54621	exon8			ACCTTGAAGATCC		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.1563T>A	12.37:g.118506186A>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	220	115	0.522727	NM_019086	Q9NWQ7	Silent	SNP	ENST00000359236.5	37	CCDS44992.1																																																																																			A|0.602;T|0.398	0.398	strong		0.448	VSIG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401273.2	NM_019086	
TAF1C	9013	hgsc.bcm.edu	37	16	84213114	84213114	+	Silent	SNP	C	C	T	rs2230130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84213114C>T	ENST00000567759.1	-	14	2225	c.2043G>A	c.(2041-2043)gtG>gtA	p.V681V	TAF1C_ENST00000341690.6_Silent_p.V587V|TAF1C_ENST00000566732.1_Silent_p.V655V|TAF1C_ENST00000378541.4_Silent_p.V681V|TAF1C_ENST00000541676.1_Silent_p.V588V|TAF1C_ENST00000570117.1_Silent_p.V349V	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	681					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						CCTTGCGGAGCACACCCAGCC	0.687													C|||	1436	0.286741	0.1256	0.4135	5008	,	,		15010	0.371		0.3469	False		,,,				2504	0.2658				p.V681V		Atlas-SNP	.											.	TAF1C	60	.	0			c.G2043A						PASS	.	C	,	749,3647		65,619,1514	24.0	25.0	24.0		2043,1761	-2.0	0.0	16	dbSNP_98	24	3086,5510		583,1920,1795	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	648,2539,3309	TT,TC,CC		35.9004,17.0382,29.5182	,	681/870,587/776	84213114	3835,9157	2198	4298	6496	SO:0001819	synonymous_variant	9013	exon14			GCGGAGCACACCC	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.2043G>A	16.37:g.84213114C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			C|0.709;T|0.291	0.291	strong		0.687	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
ZNF443	10224	hgsc.bcm.edu	37	19	12542654	12542654	+	Missense_Mutation	SNP	T	T	A	rs28599549|rs369138475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12542654T>A	ENST00000301547.5	-	4	529	c.332A>T	c.(331-333)aAa>aTa	p.K111I	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	111			K -> I (in dbSNP:rs28599549).|K -> N (in dbSNP:rs4239550).		apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						ACCCATGACTTTTTCTCCTCT	0.423													.|||	1954	0.390176	0.4773	0.3084	5008	,	,		20719	0.3452		0.2793	False		,,,				2504	0.4908				p.K111I		Atlas-SNP	.											.	ZNF443	63	.	0			c.A332T						PASS	.	A	ILE/LYS	1935,2471		412,1111,680	138.0	117.0	124.0		332	-1.3	0.0	19	dbSNP_125	124	2441,6159		371,1699,2230	yes	missense	ZNF443	NM_005815.4	102	783,2810,2910	AA,AT,TT		28.3837,43.9174,33.646	benign	111/672	12542654	4376,8630	2203	4300	6503	SO:0001583	missense	10224	exon4			ATGACTTTTTCTC	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.332A>T	19.37:g.12542654T>A	ENSP00000301547:p.Lys111Ile	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	197	96	0.48731	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	603	0.2760989010989011	175	0.3556910569105691	96	0.26519337016574585	174	0.3041958041958042	158	0.20844327176781002	A	3.143	-0.175794	0.06421	0.439174	0.283837	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.08370	3.1	1.19	-1.34	0.09143	.	.	.	.	.	T	0.00012	0.0000	N	0.01656	-0.775	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43278	-0.9401	8	0.33940	T	0.23	.	0.462	0.00518	0.1943:0.1757:0.2812:0.3487	rs28599549;rs59078636	111	Q9Y2A4	ZN443_HUMAN	I	111	ENSP00000301547:K111I	ENSP00000301547:K111I	K	-	2	0	ZNF443	12403654	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.061000	0.01391	-1.214000	0.02614	-1.921000	0.00515	AAA	.	.	alt		0.423	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
ASCC2	84164	hgsc.bcm.edu	37	22	30189642	30189642	+	Missense_Mutation	SNP	C	C	T	rs61736786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30189642C>T	ENST00000397771.2	-	17	1889	c.1712G>A	c.(1711-1713)cGg>cAg	p.R571Q	ASCC2_ENST00000307790.3_Missense_Mutation_p.R571Q|ASCC2_ENST00000542393.1_Missense_Mutation_p.R495Q			Q9H1I8	ASCC2_HUMAN	activating signal cointegrator 1 complex subunit 2	571					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)			CAGCAAACTCCGCGTGTTTTC	0.597													C|||	156	0.0311502	0.0	0.062	5008	,	,		20424	0.0675		0.0249	False		,,,				2504	0.0204				p.R571Q		Atlas-SNP	.											.	ASCC2	53	.	0			c.G1712A						PASS	.	C	GLN/ARG,GLN/ARG	19,4385		0,19,2183	39.0	25.0	30.0		1484,1712	5.3	1.0	22	dbSNP_129	30	236,8362		3,230,4066	yes	missense,missense	ASCC2	NM_001242906.1,NM_032204.4	43,43	3,249,6249	TT,TC,CC		2.7448,0.4314,1.9612	possibly-damaging,possibly-damaging	495/682,571/758	30189642	255,12747	2202	4299	6501	SO:0001583	missense	84164	exon16			AAACTCCGCGTGT	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.1712G>A	22.37:g.30189642C>T	ENSP00000380877:p.Arg571Gln	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_032204	B7Z8E0|F5H6J9|Q4TT54|Q8TAZ0|Q9H711|Q9H9D6	Missense_Mutation	SNP	ENST00000397771.2	37	CCDS13869.1	86	0.039377289377289376	0	0.0	18	0.049723756906077346	48	0.08391608391608392	20	0.026385224274406333	C	12.76	2.034215	0.35893	0.004314	0.027448	ENSG00000100325	ENST00000307790;ENST00000397771;ENST00000542393;ENST00000411532	T;T;T;T	0.32753	3.05;3.05;3.05;1.44	5.26	5.26	0.73747	.	0.131042	0.52532	D	0.000071	T	0.01092	0.0036	L	0.45228	1.405	0.46927	D	0.999252	B;B	0.31485	0.325;0.181	B;B	0.22601	0.04;0.018	T	0.03473	-1.1033	10	0.15066	T	0.55	-23.8892	11.4524	0.50160	0.0:0.9188:0.0:0.0812	.	495;571	F5H6J9;Q9H1I8	.;ASCC2_HUMAN	Q	571;571;495;62	ENSP00000305502:R571Q;ENSP00000380877:R571Q;ENSP00000437570:R495Q;ENSP00000414545:R62Q	ENSP00000305502:R571Q	R	-	2	0	ASCC2	28519642	0.011000	0.17503	0.995000	0.50966	0.148000	0.21650	1.492000	0.35594	2.735000	0.93741	0.561000	0.74099	CGG	C|0.974;T|0.026	0.026	strong		0.597	ASCC2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322127.1	NM_032204	
PJA1	64219	hgsc.bcm.edu	37	X	68382422	68382422	+	Silent	SNP	C	C	T	rs149179614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:68382422C>T	ENST00000361478.1	-	2	1037	c.660G>A	c.(658-660)tcG>tcA	p.S220S	PJA1_ENST00000374583.1_Silent_p.S220S|PJA1_ENST00000477231.1_5'UTR|PJA1_ENST00000374571.4_Silent_p.S165S|PJA1_ENST00000374584.3_Intron	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	220					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						TCTCCCTCTCCGAGCTGTCAC	0.532													c|||	6	0.0015894	0.0	0.0	3775	,	,		14255	0.0		0.0	False		,,,				2504	0.0061				p.S220S		Atlas-SNP	.											.	PJA1	106	.	0			c.G660A						PASS	.		,,	1,3834		0,1,0,1631,571	47.0	38.0	41.0		495,,660	1.0	0.0	X	dbSNP_134	41	4,6724		0,3,1,2425,1871	no	coding-synonymous,intron,coding-synonymous	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	,,	0,4,1,4056,2442	TT,TC,T,CC,C		0.0595,0.0261,0.0473	,,	165/589,,220/644	68382422	5,10558	2203	4300	6503	SO:0001819	synonymous_variant	64219	exon2			CCTCTCCGAGCTG	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.660G>A	X.37:g.68382422C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	37	CCDS14393.1																																																																																			C|0.999;T|0.001	0.001	strong		0.532	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
HLA-A	3105	hgsc.bcm.edu	37	6	29911064	29911064	+	Missense_Mutation	SNP	A	A	G	rs386698553|rs1136695	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911064A>G	ENST00000396634.1	+	5	704	c.363A>G	c.(361-363)atA>atG	p.I121M	HLA-A_ENST00000376809.5_Missense_Mutation_p.I121M|HLA-A_ENST00000376806.5_Missense_Mutation_p.I121M|HLA-A_ENST00000376802.2_Missense_Mutation_p.I121M			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	121	Alpha-2.		M -> I (in allele A*31:03 and allele A*31:04).		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						CCATCCAGATAATGTATGGCT	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)			a|||	3311	0.661142	0.6467	0.768	5008	,	,		10662	0.6865		0.6292	False		,,,				2504	0.6115				p.I121M		Atlas-SNP	.											.	HLA-A	89	.	0			c.A363G						PASS	.	A	MET/ILE	1609,1361		568,473,444	22.0	17.0	19.0		363	-7.4	0.0	6	dbSNP_86	19	2393,2865		826,741,1062	no	missense	HLA-A	NM_002116.7	10	1394,1214,1506	GG,GA,AA		45.5116,45.8249,48.6388	benign	121/366	29911064	4002,4226	1485	2629	4114	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCAGATAATGTAT	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.363A>G	6.37:g.29911064A>G	ENSP00000379873:p.Ile121Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	1385	0.6341575091575091	295	0.5995934959349594	254	0.7016574585635359	402	0.7027972027972028	434	0.5725593667546174	.	7.067	0.567560	0.13560	0.541751	0.455116	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00010	9.45;9.45;9.45;9.45	3.77	-7.42	0.01388	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	7739.210000	0.00447	U	0.000092	T	0.00039	0.0001	M	0.80982	2.52	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	0.15484	0.006;0.005;0.006;0.013;0.006	T	0.26052	-1.0114	9	0.35671	T	0.21	.	5.1467	0.14989	0.242:0.5204:0.1325:0.1051	rs1136695;rs3179187;rs3200170;rs17366347;rs17433772;rs41546614	121;121;121;121;121	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	M	121	ENSP00000379873:I121M;ENSP00000366002:I121M;ENSP00000366005:I121M;ENSP00000365998:I121M	ENSP00000348012:I121M	I	+	3	3	HLA-A	30019043	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-5.084000	0.00153	-1.641000	0.01523	-0.389000	0.06534	ATA	A|0.399;G|0.601	0.601	strong		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
HLA-A	3105	hgsc.bcm.edu	37	6	29911154	29911154	+	Missense_Mutation	SNP	C	C	A	rs1059509	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911154C>A	ENST00000396634.1	+	5	794	c.453C>A	c.(451-453)aaC>aaA	p.N151K	HLA-A_ENST00000376809.5_Missense_Mutation_p.N151K|HLA-A_ENST00000376806.5_Missense_Mutation_p.N151K|HLA-A_ENST00000376802.2_Missense_Mutation_p.N151K			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	151	Alpha-2.		N -> K (in dbSNP:rs1059509).		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						TCGCCCTGAACGAGGACCTGC	0.652									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	2296	0.458466	0.4009	0.5922	5008	,	,		13225	0.502		0.4672	False		,,,				2504	0.3875				p.N151K		Atlas-SNP	.											.	HLA-A	89	.	0			c.C453A						PASS	.						46.0	32.0	37.0					6																	29911154		1507	2707	4214	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCTGAACGAGGAC	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.453C>A	6.37:g.29911154C>A	ENSP00000379873:p.Asn151Lys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	142	139	0.978873	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	1029	0.47115384615384615	198	0.4024390243902439	194	0.5359116022099447	301	0.5262237762237763	336	0.44327176781002636	.	6.064	0.380138	0.11466	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.00012	9.3;9.3;9.3;9.3	3.78	0.727	0.18254	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	0.504521	0.14187	U	0.335654	T	0.00039	0.0001	.	.	.	0.48236	P	3.809999999999647E-4	B;B;B;B;B;B;B	0.14012	0.007;0.003;0.0;0.003;0.003;0.009;0.003	B;B;B;B;B;B;B	0.21917	0.005;0.02;0.008;0.037;0.037;0.02;0.02	T	0.00458	-1.1727	8	0.26408	T	0.33	.	6.843	0.23973	0.0:0.5587:0.3392:0.102	rs1059509;rs3173416;rs16896617;rs28749153;rs41542815	30;151;151;151;151;151;151	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	K	151	ENSP00000379873:N151K;ENSP00000366002:N151K;ENSP00000366005:N151K;ENSP00000365998:N151K	ENSP00000365998:N151K	N	+	3	2	HLA-A	30019133	0.072000	0.21174	0.866000	0.34008	0.213000	0.24496	0.176000	0.16782	0.021000	0.15133	0.485000	0.47835	AAC	A|0.451;C|0.549	0.451	strong		0.652	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
EYS	346007	hgsc.bcm.edu	37	6	65622420	65622420	+	Silent	SNP	G	G	A	rs183814213		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65622420G>A	ENST00000370621.3	-	16	3124	c.2598C>T	c.(2596-2598)tgC>tgT	p.C866C	EYS_ENST00000370616.2_Silent_p.C866C|EYS_ENST00000503581.1_Silent_p.C866C			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	866	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCAAAGCTAAGCATGTTGAGT	0.353													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17718	0.0		0.0	False		,,,				2504	0.0				p.C866C		Atlas-SNP	.											.	EYS	527	.	0			c.C2598T						PASS	.	G		0,1384		0,0,692	156.0	129.0	137.0		2598	2.6	0.0	6		137	1,3181		0,1,1590	no	coding-synonymous	EYS	NM_001142800.1		0,1,2282	AA,AG,GG		0.0314,0.0,0.0219		866/3145	65622420	1,4565	692	1591	2283	SO:0001819	synonymous_variant	346007	exon16			AGCTAAGCATGTT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2598C>T	6.37:g.65622420G>A		Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	167	19	0.113772	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				G|1.000;A|0.000	0.000	strong		0.353	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
KALRN	8997	hgsc.bcm.edu	37	3	124114068	124114068	+	Silent	SNP	G	G	A	rs9841322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124114068G>A	ENST00000240874.3	+	12	2200	c.2043G>A	c.(2041-2043)aaG>aaA	p.K681K	KALRN_ENST00000460856.1_Silent_p.K681K|KALRN_ENST00000360013.3_Silent_p.K681K	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	681					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						AACTGATCAAGCAGTTCCAGC	0.532													G|||	417	0.0832668	0.0197	0.1254	5008	,	,		21040	0.0208		0.1809	False		,,,				2504	0.1033				p.K681K		Atlas-SNP	.											.	KALRN	556	.	0			c.G2043A						PASS	.	G	,	173,4233	113.8+/-151.8	6,161,2036	84.0	73.0	77.0		2043,2043	2.6	1.0	3	dbSNP_119	77	1412,7188	272.2+/-289.9	104,1204,2992	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	110,1365,5028	AA,AG,GG		16.4186,3.9265,12.1867	,	681/2987,681/1664	124114068	1585,11421	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon12			GATCAAGCAGTTC	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.2043G>A	3.37:g.124114068G>A		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	177	175	0.988701	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	202	0.0924908424908425	15	0.03048780487804878	40	0.11049723756906077	8	0.013986013986013986	139	0.18337730870712401	G	8.877	0.950664	0.18431	0.039265	0.164186	ENSG00000160145	ENST00000354186	.	.	.	5.28	2.59	0.31030	.	.	.	.	.	T	0.00144	0.0004	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06625	-1.0816	3	.	.	.	.	8.7283	0.34483	0.2859:0.0:0.7141:0.0	rs9841322;rs9841322	.	.	.	N	659	.	.	S	+	2	0	KALRN	125596758	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.858000	0.27845	0.406000	0.25560	-0.126000	0.14955	AGC	G|0.886;A|0.114	0.114	strong		0.532	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
KRT6C	286887	hgsc.bcm.edu	37	12	52867190	52867190	+	Missense_Mutation	SNP	C	C	T	rs394598	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52867190C>T	ENST00000252250.6	-	1	379	c.332G>A	c.(331-333)gGt>gAt	p.G111D		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	111	Head.			G -> D (in Ref. 1; AAC41770/AAC41769). {ECO:0000305}.	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)		ACCACCCAGACCAAAGCCAAT	0.647																																					p.G111D		Atlas-SNP	.											KRT6C,brain,glioma,0,1	KRT6C	55	1	0			c.G332A						scavenged	.						4.0	4.0	4.0					12																	52867190		1761	2940	4701	SO:0001583	missense	286887	exon1			CCCAGACCAAAGC	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.332G>A	12.37:g.52867190C>T	ENSP00000252250:p.Gly111Asp	Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	350	35	0.1	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Missense_Mutation	SNP	ENST00000252250.6	37	CCDS8829.1	.	.	.	.	.	.	.	.	.	.	c	9.356	1.066808	0.20067	.	.	ENSG00000170465	ENST00000252250;ENST00000411979	D	0.97941	-4.62	2.61	2.61	0.31194	.	0.000000	0.50627	D	0.000103	D	0.98121	0.9380	M	0.93328	3.405	0.28954	P	0.890213	D	0.64830	0.994	P	0.51516	0.672	D	0.99897	1.1151	9	0.52906	T	0.07	.	10.5791	0.45244	0.193:0.807:0.0:0.0	rs394598;rs1707772;rs2885244	111	P48668	K2C6C_HUMAN	D	111;96	ENSP00000252250:G111D	ENSP00000252250:G111D	G	-	2	0	KRT6C	51153457	.	.	0.999000	0.59377	0.138000	0.21146	.	.	1.770000	0.52166	0.508000	0.49915	GGT	C|0.500;T|0.500	0.500	weak		0.647	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
DIMT1	27292	hgsc.bcm.edu	37	5	61694379	61694379	+	Silent	SNP	T	T	C	rs247264	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:61694379T>C	ENST00000199320.4	-	6	565	c.405A>G	c.(403-405)tcA>tcG	p.S135S	KIF2A_ENST00000509663.2_Intron|DIMT1_ENST00000506390.1_Silent_p.S135S	NM_014473.2	NP_055288.1	Q9UNQ2	DIM1_HUMAN	DIM1 dimethyladenosine transferase 1 homolog (S. cerevisiae)	135						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase activity (GO:0052909)|poly(A) RNA binding (GO:0044822)|rRNA (adenine-N6,N6-)-dimethyltransferase activity (GO:0000179)										AGACAAAAGGTGAAGAGATCT	0.378													C|||	2924	0.583866	0.7179	0.5029	5008	,	,		19644	0.6806		0.4771	False		,,,				2504	0.4703				p.S135S		Atlas-SNP	.											.	.	.	.	0			c.A405G						PASS	.	C		3070,1336	443.7+/-347.1	1075,920,208	128.0	134.0	132.0		405	-0.3	1.0	5	dbSNP_79	132	4059,4541	594.3+/-393.3	960,2139,1201	no	coding-synonymous	DIMT1	NM_014473.2		2035,3059,1409	CC,CT,TT		47.1977,30.3223,45.1868		135/314	61694379	7129,5877	2203	4300	6503	SO:0001819	synonymous_variant	27292	exon6			AAAAGGTGAAGAG	AF102147	CCDS3981.1	5q12.1	2011-08-11	2011-08-11	2011-08-11	ENSG00000086189	ENSG00000086189			30217	protein-coding gene	gene with protein product		612499	"""DIM1 dimethyladenosine transferase 1-like (S. cerevisiae)"""	DIMT1L		11124703	Standard	NM_014473		Approved	HSA9761	uc003jta.3	Q9UNQ2	OTTHUMG00000131223	ENST00000199320.4:c.405A>G	5.37:g.61694379T>C		Somatic	198	1	0.00505051		WXS	Illumina HiSeq	Phase_I	203	201	0.990148	NM_014473	O76025|Q9BU77|Q9UES1	Silent	SNP	ENST00000199320.4	37	CCDS3981.1																																																																																			T|0.437;C|0.563	0.563	strong		0.378	DIMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253967.1	NM_014473	
OR51B6	390058	hgsc.bcm.edu	37	11	5373111	5373111	+	Missense_Mutation	SNP	G	G	A	rs7479477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373111G>A	ENST00000380219.1	+	1	374	c.374G>A	c.(373-375)cGc>cAc	p.R125H	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	125			R -> H (in dbSNP:rs7479477).	TIRS -> AIHN (in Ref. 1; AAG41682). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATTACCATCCGCAGCCCCTTA	0.468													G|||	1188	0.23722	0.3389	0.2363	5008	,	,		23005	0.0863		0.2644	False		,,,				2504	0.228				p.R125H		Atlas-SNP	.											.	OR51B6	53	.	0			c.G374A						PASS	.	G	HIS/ARG	1273,3129	430.1+/-342.5	189,895,1117	126.0	116.0	119.0		374	1.1	0.0	11	dbSNP_116	119	2202,6392	370.3+/-335.8	307,1588,2402	yes	missense	OR51B6	NM_001004750.1	29	496,2483,3519	AA,AG,GG		25.6225,28.9187,26.739	benign	125/313	5373111	3475,9521	2201	4297	6498	SO:0001583	missense	390058	exon1			CCATCCGCAGCCC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.374G>A	11.37:g.5373111G>A	ENSP00000369568:p.Arg125His	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	177	62	0.350282	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	475	0.2174908424908425	161	0.32723577235772355	92	0.2541436464088398	30	0.05244755244755245	192	0.2532981530343008	G	3.536	-0.094754	0.07053	0.289187	0.256225	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.19806	2.12	5.01	1.1	0.20463	GPCR, rhodopsin-like superfamily (1);	0.488989	0.19156	N	0.121339	T	0.00012	0.0000	L	0.49455	1.56	0.09310	N	0.999999	B	0.12630	0.006	B	0.11329	0.006	T	0.44726	-0.9309	10	0.49607	T	0.09	.	9.4751	0.38867	0.2976:0.0:0.7024:0.0	rs7479477;rs52815192;rs7479477	125	Q9H340	O51B6_HUMAN	H	124;125	ENSP00000369568:R125H	ENSP00000369568:R125H	R	+	2	0	OR51B6	5329687	0.000000	0.05858	0.044000	0.18714	0.012000	0.07955	0.546000	0.23284	0.050000	0.15949	-1.505000	0.00955	CGC	G|0.768;A|0.232	0.232	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
SDCBP2	27111	hgsc.bcm.edu	37	20	1293046	1293046	+	Missense_Mutation	SNP	G	G	A	rs1048621	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1293046G>A	ENST00000360779.3	-	7	840	c.667C>T	c.(667-669)Cgc>Tgc	p.R223C	SDCBP2_ENST00000381812.1_Missense_Mutation_p.R223C|SDCBP2_ENST00000339987.3_Missense_Mutation_p.R223C|SDCBP2_ENST00000467129.1_5'Flank|SDCBP2_ENST00000381808.3_Missense_Mutation_p.R138C	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	223	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.		R -> C (in dbSNP:rs1048621).		intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						AGCCCGTTGCGGGCCGCAGAA	0.612													G|||	680	0.135783	0.149	0.1974	5008	,	,		19368	0.0208		0.2247	False		,,,				2504	0.1012				p.R223C		Atlas-SNP	.											.	SDCBP2	78	.	0			c.C667T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	737,3669	300.4+/-286.3	59,619,1525	77.0	62.0	67.0		667,412,667	2.8	1.0	20	dbSNP_86	67	2320,6280	380.0+/-339.5	312,1696,2292	yes	missense,missense,missense	SDCBP2	NM_001199784.1,NM_015685.5,NM_080489.4	180,180,180	371,2315,3817	AA,AG,GG		26.9767,16.7272,23.5045	probably-damaging,probably-damaging,probably-damaging	223/293,138/208,223/293	1293046	3057,9949	2203	4300	6503	SO:0001583	missense	27111	exon7			CGTTGCGGGCCGC	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.667C>T	20.37:g.1293046G>A	ENSP00000354013:p.Arg223Cys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	83	30	0.361446	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	37	CCDS42848.1	310	0.14194139194139194	61	0.12398373983739837	77	0.212707182320442	12	0.02097902097902098	160	0.21108179419525067	g	19.83	3.900364	0.72754	0.167272	0.269767	ENSG00000125775	ENST00000381812;ENST00000381808;ENST00000360779;ENST00000339987	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	4.7	2.75	0.32379	PDZ/DHR/GLGF (4);	0.133760	0.51477	N	0.000093	T	0.00012	0.0000	M	0.93197	3.39	0.09310	P	0.999999283908	D	0.62365	0.991	P	0.55508	0.777	T	0.05068	-1.0908	9	0.87932	D	0	-22.5959	5.8309	0.18581	0.163:0.0:0.6836:0.1534	rs1048621;rs3188641;rs17718154;rs52811665;rs59907914;rs1048621	223	Q9H190	SDCB2_HUMAN	C	223;138;223;223	ENSP00000371233:R223C;ENSP00000371229:R138C;ENSP00000354013:R223C;ENSP00000342935:R223C	ENSP00000342935:R223C	R	-	1	0	SDCBP2	1241046	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.735000	0.55044	0.582000	0.29556	-0.291000	0.09656	CGC	G|0.816;A|0.184	0.184	strong		0.612	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232568041	232568041	+	Missense_Mutation	SNP	G	G	A	rs1547742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:232568041G>A	ENST00000366630.1	-	15	4566	c.4208C>T	c.(4207-4209)tCg>tTg	p.S1403L	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.S477L|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.S1403L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1403			S -> L (in dbSNP:rs1547742).		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)				GCTGCCCTCCGATTTCTTCCA	0.557													G|||	311	0.0621006	0.0129	0.1311	5008	,	,		13952	0.0397		0.0994	False		,,,				2504	0.0644				p.S1403L		Atlas-SNP	.											SIPA1L2,colon,carcinoma,0,1	SIPA1L2	218	1	0			c.C4208T						PASS	.	G	LEU/SER	118,3750		3,112,1819	75.0	73.0	74.0		4208	5.0	0.5	1	dbSNP_88	74	804,7472		33,738,3367	yes	missense	SIPA1L2	NM_020808.3	145	36,850,5186	AA,AG,GG		9.7148,3.0507,7.5922	possibly-damaging	1403/1723	232568041	922,11222	1934	4138	6072	SO:0001583	missense	57568	exon14			CCCTCCGATTTCT	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.4208C>T	1.37:g.232568041G>A	ENSP00000355589:p.Ser1403Leu	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	119	58	0.487395	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	150	0.06868131868131869	9	0.018292682926829267	47	0.1298342541436464	21	0.03671328671328671	73	0.09630606860158311	G	16.74	3.206872	0.58343	0.030507	0.097148	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.79247	-1.25;-1.25;2.66	5.92	5.01	0.66863	.	0.599107	0.17520	N	0.171294	T	0.02380	0.0073	L	0.51422	1.61	0.30094	P	0.808038	P;D	0.62365	0.93;0.991	B;P	0.44518	0.101;0.452	T	0.52230	-0.8603	9	0.72032	D	0.01	-3.5084	14.9542	0.71098	0.0681:0.0:0.9319:0.0	rs1547742;rs52825369;rs58546657;rs1547742	1403;477	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	L	1403;1403;477	ENSP00000355589:S1403L;ENSP00000262861:S1403L;ENSP00000309102:S477L	ENSP00000262861:S1403L	S	-	2	0	SIPA1L2	230634664	0.996000	0.38824	0.540000	0.28089	0.891000	0.51852	4.530000	0.60595	1.515000	0.48885	0.655000	0.94253	TCG	G|0.931;A|0.069	0.069	strong		0.557	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
ZNF45	7596	hgsc.bcm.edu	37	19	44418824	44418824	+	Missense_Mutation	SNP	C	C	T	rs399098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44418824C>T	ENST00000269973.5	-	10	1854	c.764G>A	c.(763-765)aGg>aAg	p.R255K	ZNF45_ENST00000589703.1_Missense_Mutation_p.R255K|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	255			R -> K (in dbSNP:rs399098). {ECO:0000269|PubMed:15057824}.		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						CCCAACATTCCTCCCACACTC	0.453													C|||	2075	0.414337	0.174	0.5764	5008	,	,		20551	0.5486		0.5119	False		,,,				2504	0.3855				p.R255K		Atlas-SNP	.											ZNF45,NS,adenoma,0,1	ZNF45	51	1	0			c.G764A						PASS	.	C	LYS/ARG	994,3412	372.7+/-320.5	131,732,1340	113.0	109.0	110.0		764	0.5	0.4	19	dbSNP_80	110	4306,4294	577.2+/-390.5	1095,2116,1089	yes	missense	ZNF45	NM_003425.3	26	1226,2848,2429	TT,TC,CC		49.9302,22.5601,40.7504	benign	255/683	44418824	5300,7706	2203	4300	6503	SO:0001583	missense	7596	exon10			ACATTCCTCCCAC	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.764G>A	19.37:g.44418824C>T	ENSP00000269973:p.Arg255Lys	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	1018	0.4661172161172161	125	0.2540650406504065	183	0.505524861878453	324	0.5664335664335665	386	0.5092348284960422	C	5.834	0.338167	0.11069	0.225601	0.500698	ENSG00000124459	ENST00000269973;ENST00000328762	T	0.09163	3.01	3.51	0.479	0.16796	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.183360	0.26734	N	0.022776	T	0.00012	0.0000	N	0.05383	-0.06	0.39528	P	0.03137100000000004	B	0.02656	0.0	B	0.01281	0.0	T	0.43909	-0.9362	9	0.02654	T	1	-10.8166	5.5663	0.17173	0.0:0.3903:0.0:0.6097	rs399098;rs3170387;rs17799099;rs52819763;rs60343668;rs399098	255	Q02386	ZNF45_HUMAN	K	255	ENSP00000269973:R255K	ENSP00000269973:R255K	R	-	2	0	ZNF45	49110664	0.705000	0.27846	0.367000	0.25926	0.426000	0.31534	-0.022000	0.12480	0.402000	0.25451	0.462000	0.41574	AGG	C|0.566;T|0.434	0.434	strong		0.453	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
GGCX	2677	hgsc.bcm.edu	37	2	85780536	85780536	+	Missense_Mutation	SNP	C	C	T	rs699664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:85780536C>T	ENST00000233838.4	-	8	1054	c.974G>A	c.(973-975)cGa>cAa	p.R325Q	GGCX_ENST00000473665.1_5'UTR|GGCX_ENST00000430215.3_Missense_Mutation_p.R268Q	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	325			R -> Q (in dbSNP:rs699664). {ECO:0000269|PubMed:1749935}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	TTGCAACCTTCGGGGGCAGTA	0.597													T|||	1892	0.377796	0.6626	0.2695	5008	,	,		17272	0.3095		0.3668	False		,,,				2504	0.1513				p.R325Q		Atlas-SNP	.											.	GGCX	44	.	0			c.G974A	GRCh37	CM073086	GGCX	M	rs699664	PASS	.	T	GLN/ARG,GLN/ARG	2648,1758	516.2+/-369.1	807,1034,362	62.0	70.0	67.0		974,803	-0.8	0.1	2	dbSNP_86	67	2804,5796	672.2+/-402.9	469,1866,1965	yes	missense,missense	GGCX	NM_000821.5,NM_001142269.2	43,43	1276,2900,2327	TT,TC,CC		32.6047,39.9001,41.9191	benign,benign	325/759,268/702	85780536	5452,7554	2203	4300	6503	SO:0001583	missense	2677	exon8			AACCTTCGGGGGC		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.974G>A	2.37:g.85780536C>T	ENSP00000233838:p.Arg325Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	100	44	0.44	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Missense_Mutation	SNP	ENST00000233838.4	37	CCDS1978.1	906	0.41483516483516486	340	0.6910569105691057	106	0.292817679558011	188	0.32867132867132864	272	0.35883905013192613	T	0.271	-0.992796	0.02162	0.600999	0.326047	ENSG00000115486	ENST00000233838;ENST00000430215	D;D	0.92249	-3.0;-3.0	5.64	-0.842	0.10748	.	1.025530	0.07686	N	0.937884	T	0.00012	0.0000	N	0.20685	0.6	0.80722	P	0.0	B;B	0.13145	0.007;0.003	B;B	0.09377	0.004;0.002	T	0.40251	-0.9573	9	0.10902	T	0.67	0.4177	1.9336	0.03332	0.1363:0.3536:0.1402:0.3698	rs699664;rs17617541;rs52835631;rs699664	268;325	E9PEE1;P38435	.;VKGC_HUMAN	Q	325;268	ENSP00000233838:R325Q;ENSP00000408045:R268Q	ENSP00000233838:R325Q	R	-	2	0	GGCX	85634047	0.000000	0.05858	0.123000	0.21794	0.094000	0.18550	-0.117000	0.10708	-0.152000	0.11156	-1.170000	0.01741	CGA	C|0.580;T|0.420	0.420	strong		0.597	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
PRSS50	29122	hgsc.bcm.edu	37	3	46755937	46755937	+	Silent	SNP	C	C	T	rs12492868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46755937C>T	ENST00000460241.1	-	9	2195	c.525G>A	c.(523-525)acG>acA	p.T175T	PRSS50_ENST00000315170.7_Silent_p.T175T			Q9UI38	TSP50_HUMAN	protease, serine, 50	175	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						AGGCGGTCTGCGTCATCTGGT	0.647													C|||	1920	0.383387	0.705	0.2939	5008	,	,		17590	0.2708		0.162	False		,,,				2504	0.3558				p.T175T	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS50	35	.	0			c.G525A						PASS	.	C		2535,1871	592.2+/-387.7	742,1051,410	68.0	51.0	57.0		525	-6.3	0.0	3	dbSNP_120	57	1258,7342	234.3+/-267.3	88,1082,3130	no	coding-synonymous	PRSS50	NM_013270.4		830,2133,3540	TT,TC,CC		14.6279,42.4648,29.1635		175/386	46755937	3793,9213	2203	4300	6503	SO:0001819	synonymous_variant	29122	exon4			GGTCTGCGTCATC	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"""Serine peptidases / Serine peptidases"""	17910	protein-coding gene	gene with protein product	"""cancer/testis antigen 20"", ""testes specific protease 50"""	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.525G>A	3.37:g.46755937C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_013270		Silent	SNP	ENST00000460241.1	37	CCDS2745.1																																																																																			A|0.000;C|0.703;T|0.296	0.296	strong		0.647	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1		
GPR179	440435	hgsc.bcm.edu	37	17	36486802	36486802	+	Missense_Mutation	SNP	G	G	A	rs72832277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36486802G>A	ENST00000342292.4	-	11	2670	c.2650C>T	c.(2650-2652)Cgg>Tgg	p.R884W	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	884					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GATGGCCTCCGCACCAGGCTG	0.672													G|||	168	0.0335463	0.028	0.062	5008	,	,		14960	0.0		0.0726	False		,,,				2504	0.0153				p.R884W		Atlas-SNP	.											.	GPR179	170	.	0			c.C2650T						PASS	.	G	TRP/ARG	94,4018		1,92,1963	14.0	16.0	15.0		2650	2.9	0.8	17	dbSNP_130	15	412,7982		10,392,3795	yes	missense	GPR179	NM_001004334.2	101	11,484,5758	AA,AG,GG		4.9083,2.286,4.0461	probably-damaging	884/2368	36486802	506,12000	2056	4197	6253	SO:0001583	missense	440435	exon11			GCCTCCGCACCAG		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2650C>T	17.37:g.36486802G>A	ENSP00000345060:p.Arg884Trp	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	81	0.03708791208791209	13	0.026422764227642278	25	0.06906077348066299	0	0.0	43	0.05672823218997362	G	8.253	0.809460	0.16537	0.02286	0.049083	ENSG00000188888	ENST00000342292	T	0.54479	0.57	5.04	2.89	0.33648	.	0.604659	0.15459	N	0.261207	T	0.04227	0.0117	L	0.32530	0.975	0.24481	N	0.99434	B	0.22541	0.071	B	0.12156	0.007	T	0.11275	-1.0594	10	0.87932	D	0	-7.649	11.843	0.52366	0.0:0.0:0.6549:0.3451	.	884	Q6PRD1	GP179_HUMAN	W	884	ENSP00000345060:R884W	ENSP00000345060:R884W	R	-	1	2	GPR179	33740328	0.000000	0.05858	0.793000	0.32043	0.443000	0.32047	-0.459000	0.06728	1.301000	0.44836	0.561000	0.74099	CGG	G|0.964;A|0.036	0.036	strong		0.672	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
KIF20B	9585	hgsc.bcm.edu	37	10	91487649	91487649	+	Missense_Mutation	SNP	A	A	T	rs12572012	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:91487649A>T	ENST00000371728.3	+	17	2332	c.2267A>T	c.(2266-2268)aAt>aTt	p.N756I	KIF20B_ENST00000416354.1_Missense_Mutation_p.N756I|KIF20B_ENST00000394289.2_Missense_Mutation_p.N756I|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.N716I	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	756			N -> I (in dbSNP:rs12572012). {ECO:0000269|PubMed:11470801, ECO:0000269|PubMed:12740395}.		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						GAGACATCTAATAAGGTAATG	0.229													A|||	1047	0.209065	0.0492	0.2133	5008	,	,		17463	0.3621		0.2416	False		,,,				2504	0.2311				p.N716I		Atlas-SNP	.											.	KIF20B	191	.	0			c.A2147T						PASS	.	A	ILE/ASN	316,4054	159.2+/-191.8	10,296,1879	56.0	56.0	56.0		2147	1.1	0.9	10	dbSNP_120	56	1737,6829	301.8+/-305.6	192,1353,2738	yes	missense	KIF20B	NM_016195.2	149	202,1649,4617	TT,TA,AA		20.2778,7.2311,15.8704	possibly-damaging	716/1781	91487649	2053,10883	2185	4283	6468	SO:0001583	missense	9585	exon17			CATCTAATAAGGT	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.2267A>T	10.37:g.91487649A>T	ENSP00000360793:p.Asn756Ile	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	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		502	0.22985347985347984	27	0.054878048780487805	76	0.20994475138121546	215	0.3758741258741259	184	0.24274406332453827	A	11.59	1.683508	0.29872	0.072311	0.202778	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728;ENST00000439656	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	4.77	1.09	0.20402	.	0.325397	0.23105	N	0.051870	T	0.00012	0.0000	L	0.41236	1.265	0.44207	P	0.0029609999999999914	D;B	0.67145	0.996;0.003	P;B	0.53649	0.731;0.011	T	0.45804	-0.9236	9	0.36615	T	0.2	-1.011	2.5768	0.04808	0.5609:0.0:0.2415:0.1976	rs12572012;rs52825579;rs12572012	756;716	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	I	716;756;756;756;323	ENSP00000260753:N716I;ENSP00000411545:N756I;ENSP00000377830:N756I;ENSP00000360793:N756I	ENSP00000260753:N716I	N	+	2	0	KIF20B	91477629	0.999000	0.42202	0.894000	0.35097	0.471000	0.32888	0.333000	0.19768	0.024000	0.15214	0.254000	0.18369	AAT	A|0.813;T|0.187	0.187	strong		0.229	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
ZNF227	7770	hgsc.bcm.edu	37	19	44739303	44739303	+	Silent	SNP	T	T	C	rs2279073	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44739303T>C	ENST00000313040.7	+	6	925	c.720T>C	c.(718-720)aaT>aaC	p.N240N	ZNF227_ENST00000589005.1_Silent_p.N189N|ZNF227_ENST00000391961.2_Silent_p.N189N	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	240					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				ATGGCTCCAATCAGAAATTAC	0.423													T|||	2095	0.418331	0.115	0.4841	5008	,	,		18758	0.4286		0.5417	False		,,,				2504	0.6442				p.N240N		Atlas-SNP	.											.	ZNF227	62	.	0			c.T720C						PASS	.	T		887,3519	339.4+/-305.8	108,671,1424	55.0	56.0	56.0		720	-0.8	0.0	19	dbSNP_100	56	4712,3888	603.4+/-394.7	1309,2094,897	no	coding-synonymous	ZNF227	NM_182490.1		1417,2765,2321	CC,CT,TT		45.2093,20.1316,43.0494		240/800	44739303	5599,7407	2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			CTCCAATCAGAAA	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.720T>C	19.37:g.44739303T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	37	CCDS12636.1																																																																																			T|0.587;C|0.413	0.413	strong		0.423	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
RTP2	344892	hgsc.bcm.edu	37	3	187416666	187416666	+	Missense_Mutation	SNP	C	C	T	rs11927120	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:187416666C>T	ENST00000358241.1	-	2	726	c.298G>A	c.(298-300)Ggc>Agc	p.G100S		NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	100					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)		CGCGCCGTGCCGCACTCATAG	0.647													C|||	912	0.182109	0.1725	0.1081	5008	,	,		16063	0.1339		0.1958	False		,,,				2504	0.2832				p.G100S		Atlas-SNP	.											RTP2,NS,carcinoma,0,1	RTP2	38	1	0			c.G298A						PASS	.	C	SER/GLY	708,3694		54,600,1547	25.0	23.0	24.0		298	4.2	1.0	3	dbSNP_120	24	1668,6876		142,1384,2746	no	missense	RTP2	NM_001004312.2	56	196,1984,4293	TT,TC,CC		19.5225,16.0836,18.3532	probably-damaging	100/226	187416666	2376,10570	2201	4272	6473	SO:0001583	missense	344892	exon2			CCGTGCCGCACTC	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.298G>A	3.37:g.187416666C>T	ENSP00000350976:p.Gly100Ser	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	215	127	0.590698	NM_001004312	Q6NVH4	Missense_Mutation	SNP	ENST00000358241.1	37	CCDS33911.1	329	0.15064102564102563	81	0.16463414634146342	37	0.10220994475138122	57	0.09965034965034965	154	0.20316622691292877	C	12.86	2.063669	0.36373	0.160836	0.195225	ENSG00000198471	ENST00000358241	T	0.13196	2.61	4.17	4.17	0.49024	.	0.485095	0.23842	N	0.044031	T	0.00012	0.0000	N	0.11154	0.105	0.29340	P	0.866106	D	0.55172	0.97	P	0.48425	0.577	T	0.25187	-1.0139	9	0.07325	T	0.83	-51.3596	12.2956	0.54844	0.0:1.0:0.0:0.0	rs11927120	100	Q5QGT7	RTP2_HUMAN	S	100	ENSP00000350976:G100S	ENSP00000350976:G100S	G	-	1	0	RTP2	188899360	0.966000	0.33281	1.000000	0.80357	0.466000	0.32739	2.796000	0.47869	2.621000	0.88768	0.563000	0.77884	GGC	C|0.839;T|0.161	0.161	strong		0.647	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312	
HNF1A	6927	hgsc.bcm.edu	37	12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	rs2464196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121435427G>A	ENST00000257555.6	+	7	1686	c.1460G>A	c.(1459-1461)aGc>aAc	p.S487N	HNF1A_ENST00000538626.1_Missense_Mutation_p.S69N|HNF1A_ENST00000544413.1_Missense_Mutation_p.S487N|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000400024.2_Missense_Mutation_p.S487N|HNF1A_ENST00000541395.1_Missense_Mutation_p.S487N			P20823	HNF1A_HUMAN	HNF1 homeobox A	487			S -> N (in dbSNP:rs2464196). {ECO:0000269|PubMed:9112026, ECO:0000269|PubMed:9133564, ECO:0000269|PubMed:9287055, ECO:0000269|PubMed:9604876, ECO:0000269|PubMed:9621514, ECO:0000269|Ref.6}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGACCCAGAGCCCCTTCATG	0.637									Hepatic Adenoma, Familial Clustering of				g|||	1591	0.317692	0.112	0.3501	5008	,	,		18114	0.4732		0.3161	False		,,,				2504	0.4141				p.S487N		Atlas-SNP	.											.	HNF1A	302	.	0			c.G1460A	GRCh37	CM067474	HNF1A	M	rs2464196	PASS	.	G	ASN/SER	541,3865	230.4+/-244.6	42,457,1704	29.0	28.0	29.0		1460	3.5	1.0	12	dbSNP_100	29	2676,5924	411.0+/-350.3	431,1814,2055	yes	missense	HNF1A	NM_000545.5	46	473,2271,3759	AA,AG,GG		31.1163,12.2787,24.7347	possibly-damaging	487/632	121435427	3217,9789	2203	4300	6503	SO:0001583	missense	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCCAGAGCCCCTT	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.1460G>A	12.37:g.121435427G>A	ENSP00000257555:p.Ser487Asn	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	715	0.3273809523809524	54	0.10975609756097561	132	0.36464088397790057	296	0.5174825174825175	233	0.3073878627968338	G	12.39	1.924644	0.34002	0.122787	0.311163	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000340577;ENST00000544413	D;D;D	0.97455	-4.39;-4.39;-4.39	4.49	3.53	0.40419	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.068781	0.64402	N	0.000014	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.99999999123403	B;B;B	0.24576	0.0;0.014;0.106	B;B;B	0.32533	0.005;0.085;0.147	T	0.04153	-1.0973	9	0.42905	T	0.14	-9.2011	10.4952	0.44772	0.104:0.0:0.896:0.0	rs2464196;rs2708085;rs16950667;rs17847503;rs56962510;rs2464196	487;487;487	F5H0K0;P20823;E7EUQ4	.;HNF1A_HUMAN;.	N	487;379;487;308;487;487;487	ENSP00000257555:S487N;ENSP00000443112:S487N;ENSP00000438804:S487N	ENSP00000257555:S487N	S	+	2	0	HNF1A	119919810	0.950000	0.32346	0.992000	0.48379	0.944000	0.59088	1.527000	0.35975	0.976000	0.38417	0.655000	0.94253	AGC	G|0.725;A|0.275	0.275	strong		0.637	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
TMCO3	55002	hgsc.bcm.edu	37	13	114175038	114175038	+	Missense_Mutation	SNP	G	G	A	rs7319493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:114175038G>A	ENST00000434316.2	+	8	1692	c.1333G>A	c.(1333-1335)Gca>Aca	p.A445T	TMCO3_ENST00000474393.1_3'UTR|TMCO3_ENST00000375391.1_Intron	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	445			A -> T (in dbSNP:rs7319493). {ECO:0000269|PubMed:14702039}.			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)			GGGCGCCAGTGCATCTTCTAG	0.473													G|||	960	0.191693	0.205	0.3199	5008	,	,		16465	0.123		0.1302	False		,,,				2504	0.2168				p.A445T		Atlas-SNP	.											.	TMCO3	77	.	0			c.G1333A						PASS	.	G	THR/ALA	929,3477	354.9+/-312.8	100,729,1374	78.0	71.0	73.0		1333	-9.9	0.0	13	dbSNP_116	73	1256,7344	251.8+/-278.1	84,1088,3128	yes	missense	TMCO3	NM_017905.4	58	184,1817,4502	AA,AG,GG		14.6047,21.0849,16.7999	benign	445/678	114175038	2185,10821	2203	4300	6503	SO:0001583	missense	55002	exon8			GCCAGTGCATCTT	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.1333G>A	13.37:g.114175038G>A	ENSP00000389399:p.Ala445Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	CCDS9537.1	349	0.15979853479853479	101	0.20528455284552846	95	0.26243093922651933	62	0.10839160839160839	91	0.12005277044854881	G	5.097	0.203455	0.09704	0.210849	0.146047	ENSG00000150403	ENST00000434316	T	0.15372	2.43	4.94	-9.87	0.00470	Cation/H+ exchanger (1);	0.637765	0.16438	N	0.214420	T	0.00012	0.0000	N	0.11818	0.18	0.46028	P	0.0011799999999999589	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.26430	-1.0103	9	0.13108	T	0.6	-11.3682	2.3263	0.04223	0.244:0.0853:0.3363:0.3343	rs7319493;rs60291985;rs7319493	445;445	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	T	445	ENSP00000389399:A445T	ENSP00000389399:A445T	A	+	1	0	TMCO3	113223039	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.505000	0.06367	-5.105000	0.00021	-2.375000	0.00234	GCA	G|0.835;A|0.165	0.165	strong		0.473	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
UNC5C	8633	hgsc.bcm.edu	37	4	96127799	96127799	+	Missense_Mutation	SNP	C	C	T	rs146123204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:96127799C>T	ENST00000453304.1	-	11	2230	c.1882G>A	c.(1882-1884)Gca>Aca	p.A628T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	628	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		CCCTGTGCTGCCTGGTTCTTG	0.537													C|||	3	0.000599042	0.0	0.0014	5008	,	,		15911	0.0		0.002	False		,,,				2504	0.0				p.A628T		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1882A						PASS	.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	106.0	94.0	98.0		1882	-2.4	0.8	4	dbSNP_134	98	17,8583	10.5+/-38.8	0,17,4283	yes	missense	UNC5C	NM_003728.3	58	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign	628/932	96127799	18,12988	2203	4300	6503	SO:0001583	missense	8633	exon11			GTGCTGCCTGGTT	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1882G>A	4.37:g.96127799C>T	ENSP00000406022:p.Ala628Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	118	51	0.432203	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	7.398	0.632177	0.14322	2.27E-4	0.001977	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.41400	1.0;1.0	5.28	-2.41	0.06562	ZU5 (3);	0.761342	0.12964	N	0.424732	T	0.13628	0.0330	N	0.02225	-0.63	0.35230	D	0.776799	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38779	-0.9645	10	0.09338	T	0.73	.	8.1752	0.31278	0.1126:0.2927:0.0:0.5947	.	628;628	A8K385;O95185	.;UNC5C_HUMAN	T	628;587;647	ENSP00000406022:A628T;ENSP00000426924:A647T	ENSP00000328673:A587T	A	-	1	0	UNC5C	96346822	0.002000	0.14202	0.791000	0.31998	0.797000	0.45037	-0.626000	0.05527	-0.391000	0.07763	-0.251000	0.11542	GCA	C|0.998;T|0.002	0.002	strong		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
PSG1	5669	hgsc.bcm.edu	37	19	43382374	43382374	+	Missense_Mutation	SNP	C	C	G	rs707744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:43382374C>G	ENST00000436291.2	-	2	237	c.121G>C	c.(121-123)Gag>Cag	p.E41Q	PSG1_ENST00000244296.2_Missense_Mutation_p.E41Q|PSG1_ENST00000403380.3_Missense_Mutation_p.E41Q|PSG1_ENST00000595124.1_Missense_Mutation_p.E41Q|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000312439.6_Missense_Mutation_p.E41Q|PSG1_ENST00000595356.1_Missense_Mutation_p.E41Q	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	41	Ig-like V-type.		E -> Q (in dbSNP:rs707744).	EPT -> QPP (in Ref. 4, 5 and 6). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TTGGTTGGCTCGGCTTCAATC	0.473													.|||	2124	0.424121	0.503	0.4207	5008	,	,		18131	0.4276		0.2505	False		,,,				2504	0.4949				p.E41Q		Atlas-SNP	.											.	PSG1	196	.	0			c.G121C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	2154,2252		582,990,631	147.0	166.0	160.0		121,121,121	-1.2	0.0	19	dbSNP_86	160	2121,6477		320,1481,2498	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	29,29,29	902,2471,3129	GG,GC,CC		24.6685,48.8879,32.8745	,,	41/420,41/418,41/427	43382374	4275,8729	2203	4299	6502	SO:0001583	missense	5669	exon2			TTGGCTCGGCTTC		CCDS12612.1, CCDS54275.1, CCDS59392.1, CCDS74380.1	19q13.2	2013-01-29			ENSG00000231924	ENSG00000231924		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9514	protein-coding gene	gene with protein product		176390		PSBG1			Standard	NM_006905		Approved	PSGGA, CD66f, PBG1		P11464	OTTHUMG00000151123	ENST00000436291.2:c.121G>C	19.37:g.43382374C>G	ENSP00000413041:p.Glu41Gln	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	217	94	0.43318	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	.	.	.	.	.	.	.	.	.	.	N	0.484	-0.878652	0.02550	0.488879	0.246685	ENSG00000231924	ENST00000270059;ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	1.46	-1.17	0.09648	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00061	-2.33	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.11235	0.004;0.0;0.0;0.0;0.0;0.001;0.003;0.0	B;B;B;B;B;B;B;B	0.13407	0.008;0.003;0.001;0.004;0.003;0.007;0.009;0.004	T	0.43988	-0.9357	8	0.22706	T	0.39	.	4.7175	0.12903	0.0:0.5961:0.2282:0.1757	rs707744;rs3205494;rs16976238;rs61289360	41;41;41;41;41;41;41;41	O75238;P11464-4;G5E9F7;P11464;P11464-3;Q9UPK8;O75237;P11464-2	.;.;.;PSG1_HUMAN;.;.;.;.	Q	41	ENSP00000413041:E41Q;ENSP00000385386:E41Q;ENSP00000308970:E41Q;ENSP00000244296:E41Q	ENSP00000244296:E41Q	E	-	1	0	PSG1	48074214	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.330000	0.07925	-0.696000	0.05098	-1.122000	0.02009	GAG	C|0.695;G|0.305	0.305	strong		0.473	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
TCTE1	202500	hgsc.bcm.edu	37	6	44253765	44253765	+	Missense_Mutation	SNP	A	A	G	rs2297336	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:44253765A>G	ENST00000371505.4	-	3	904	c.782T>C	c.(781-783)tTc>tCc	p.F261S	TMEM151B_ENST00000438774.2_Intron|TCTE1_ENST00000371503.3_Missense_Mutation_p.F108S|RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_Missense_Mutation_p.F108S	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	261			F -> S (in dbSNP:rs2297336).							breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGTGAAGAGGAAGAGATTCCA	0.587													A|||	998	0.199281	0.0242	0.134	5008	,	,		18717	0.3998		0.1769	False		,,,				2504	0.2986				p.F261S		Atlas-SNP	.											.	TCTE1	77	.	0			c.T782C						PASS	.	A	SER/PHE	237,4169	137.7+/-173.5	8,221,1974	118.0	104.0	109.0		782	4.9	1.0	6	dbSNP_100	109	1351,7249	265.2+/-286.0	115,1121,3064	yes	missense	TCTE1	NM_182539.3	155	123,1342,5038	GG,GA,AA		15.7093,5.379,12.2097	probably-damaging	261/502	44253765	1588,11418	2203	4300	6503	SO:0001583	missense	202500	exon3			AAGAGGAAGAGAT	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.782T>C	6.37:g.44253765A>G	ENSP00000360560:p.Phe261Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_182539	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	37	CCDS4910.1	424	0.19413919413919414	18	0.036585365853658534	47	0.1298342541436464	223	0.38986013986013984	136	0.17941952506596306	A	19.76	3.888394	0.72524	0.05379	0.157093	ENSG00000146221	ENST00000371505;ENST00000371503;ENST00000371504	T;T;T	0.54479	1.79;0.57;0.57	4.89	4.89	0.63831	.	0.094392	0.85682	D	0.000000	T	0.65417	0.2689	M	0.78456	2.415	0.20074	P	0.9999334244	D	0.89917	1.0	D	0.71414	0.973	T	0.73119	-0.4083	9	0.72032	D	0.01	-35.9923	14.4897	0.67642	1.0:0.0:0.0:0.0	rs2297336;rs52795123;rs59287625;rs2297336	261	Q5JU00	TCTE1_HUMAN	S	261;108;108	ENSP00000360560:F261S;ENSP00000360558:F108S;ENSP00000360559:F108S	ENSP00000360558:F108S	F	-	2	0	TCTE1	44361743	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.054000	0.76649	1.832000	0.53329	0.379000	0.24179	TTC	A|0.842;G|0.158	0.158	strong		0.587	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
PI4K2A	55361	hgsc.bcm.edu	37	10	99410790	99410790	+	Silent	SNP	T	T	C	rs7915721	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99410790T>C	ENST00000370631.3	+	2	585	c.528T>C	c.(526-528)ccT>ccC	p.P176P	PI4K2A_ENST00000555577.1_Silent_p.P146P|PI4K2A_ENST00000370649.3_Silent_p.P146P	NM_018425.2	NP_060895.1	Q9BTU6	P4K2A_HUMAN	phosphatidylinositol 4-kinase type 2 alpha	176	PI3K/PI4K.				basophil degranulation (GO:0002561)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|early endosome membrane (GO:0031901)|endosome (GO:0005768)|exocytic vesicle (GO:0070382)|Golgi apparatus (GO:0005794)|growing cell tip (GO:0035838)|host cell presynaptic membrane (GO:0044231)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|AP-3 adaptor complex binding (GO:0035651)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)	p.P176P(2)|p.P146P(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12		Colorectal(252;0.162)		Epithelial(162;1.24e-10)|all cancers(201;1.2e-08)		TGTGCTGTCCTTGCTGCTTTG	0.517													C|||	1715	0.342452	0.6233	0.2666	5008	,	,		20300	0.3006		0.2028	False		,,,				2504	0.2035				p.P176P		Atlas-SNP	.											PI4K2A_ENST00000555577,NS,carcinoma,0,2	PI4K2A	57	2	3	Substitution - coding silent(3)	prostate(3)	c.T528C						PASS	.	C		2425,1981	556.8+/-379.6	676,1073,454	92.0	79.0	83.0		528	3.1	1.0	10	dbSNP_116	83	1911,6689	726.6+/-406.6	192,1527,2581	no	coding-synonymous	PI4K2A	NM_018425.2		868,2600,3035	CC,CT,TT		22.2209,44.9614,33.3385		176/480	99410790	4336,8670	2203	4300	6503	SO:0001819	synonymous_variant	55361	exon2			CTGTCCTTGCTGC	AF070611	CCDS7469.1	10q24	2011-02-09			ENSG00000155252	ENSG00000155252			30031	protein-coding gene	gene with protein product		609763				11244087, 11279162	Standard	NM_018425		Approved	PI4KII, DKFZP761G1923, PIK42A	uc001kog.1	Q9BTU6	OTTHUMG00000018863	ENST00000370631.3:c.528T>C	10.37:g.99410790T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_018425	D3DR59|Q9NSG8	Silent	SNP	ENST00000370631.3	37	CCDS7469.1																																																																																			T|0.663;C|0.337	0.337	strong		0.517	PI4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049735.1	NM_018425	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1876631	1876631	+	Silent	SNP	C	C	T	rs2272611	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:1876631C>T	ENST00000398564.1	+	24	2811	c.2811C>T	c.(2809-2811)atC>atT	p.I937I	ARHGEF10_ENST00000518288.1_Silent_p.I936I|ARHGEF10_ENST00000520359.1_Silent_p.I874I|ARHGEF10_ENST00000349830.3_Silent_p.I912I|ARHGEF10_ENST00000262112.6_Silent_p.I908I			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	937					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)		AGATTGCCATCGTCTCGTTTC	0.488													C|||	723	0.144369	0.1437	0.1758	5008	,	,		16389	0.1617		0.1143	False		,,,				2504	0.136				p.I912I		Atlas-SNP	.											ARHGEF10_ENST00000398564,colon,carcinoma,0,2	ARHGEF10	255	2	0			c.C2736T						PASS	.	C		533,3873	240.9+/-251.5	41,451,1711	175.0	170.0	172.0		2736	-1.3	0.5	8	dbSNP_100	172	1243,7357	249.2+/-276.5	101,1041,3158	no	coding-synonymous	ARHGEF10	NM_014629.2		142,1492,4869	TT,TC,CC		14.4535,12.0971,13.6552		912/1345	1876631	1776,11230	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon24			TGCCATCGTCTCG	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.2811C>T	8.37:g.1876631C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	99	45	0.454545	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				C|0.861;T|0.139	0.139	strong		0.488	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
CLSPN	63967	hgsc.bcm.edu	37	1	36202125	36202125	+	Missense_Mutation	SNP	C	C	T	rs115320551		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:36202125C>T	ENST00000318121.3	-	25	4049	c.3992G>A	c.(3991-3993)cGa>cAa	p.R1331Q	CLSPN_ENST00000373220.3_Missense_Mutation_p.R1267Q|RP11-435D7.3_ENST00000373226.2_RNA|CLSPN_ENST00000520551.1_Missense_Mutation_p.R1278Q|CLSPN_ENST00000251195.5_Intron|CLSPN_ENST00000466308.1_5'UTR	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1331					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)	p.R1331Q(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GAAGATGCTTCGCGTCAATCC	0.423													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18800	0.0		0.0	False		,,,				2504	0.0				p.R1331Q		Atlas-SNP	.											CLSPN,colon,carcinoma,-1,4	CLSPN	248	4	1	Substitution - Missense(1)	ovary(1)	c.G3992A						PASS	.						150.0	141.0	144.0					1																	36202125		2203	4300	6503	SO:0001583	missense	63967	exon25			ATGCTTCGCGTCA	AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.3992G>A	1.37:g.36202125C>T	ENSP00000312995:p.Arg1331Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	144	132	0.916667	NM_022111	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.64	2.298942	0.40694	.	.	ENSG00000092853	ENST00000318121;ENST00000373220;ENST00000520551	T;T;T	0.27557	1.66;1.71;1.72	5.29	-1.26	0.09376	.	0.312008	0.29046	N	0.013319	T	0.14960	0.0361	N	0.12746	0.255	0.24776	N	0.992842	B;B	0.25007	0.116;0.068	B;B	0.15052	0.012;0.012	T	0.13176	-1.0519	10	0.32370	T	0.25	0.0185	13.1085	0.59261	0.0:0.8736:0.0:0.1264	.	1267;1331	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	Q	1331;1267;1278	ENSP00000312995:R1331Q;ENSP00000362317:R1267Q;ENSP00000428848:R1278Q	ENSP00000312995:R1331Q	R	-	2	0	CLSPN	35974712	0.998000	0.40836	0.974000	0.42286	0.967000	0.64934	0.428000	0.21395	-0.357000	0.08175	-0.290000	0.09829	CGA	C|0.999;T|0.001	0.001	strong		0.423	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
KRT14	3861	hgsc.bcm.edu	37	17	39742807	39742807	+	Missense_Mutation	SNP	C	C	T	rs3826550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39742807C>T	ENST00000167586.6	-	1	366	c.280G>A	c.(280-282)Gct>Act	p.A94T		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	94	Head.		A -> T (in dbSNP:rs3826550). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9989794, ECO:0000269|Ref.3}.		aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				cccaagccagcaccaaggcca	0.632													C|||	1456	0.290735	0.4153	0.2709	5008	,	,		15358	0.0575		0.4145	False		,,,				2504	0.2495				p.A94T		Atlas-SNP	.											.	KRT14	65	.	0			c.G280A						PASS	.						125.0	126.0	126.0					17																	39742807		2203	4300	6503	SO:0001583	missense	3861	exon1			AGCCAGCACCAAG	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.280G>A	17.37:g.39742807C>T	ENSP00000167586:p.Ala94Thr	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	654	0.29945054945054944	202	0.4105691056910569	110	0.30386740331491713	27	0.0472027972027972	315	0.4155672823218997	C	6.698	0.497409	0.12762	.	.	ENSG00000186847	ENST00000167586	D	0.89415	-2.51	5.11	5.11	0.69529	.	0.845655	0.10115	N	0.714173	T	0.00012	0.0000	L	0.58101	1.795	0.46654	P	8.550000000000502E-4	B	0.20780	0.048	B	0.27500	0.08	T	0.08289	-1.0729	9	0.22706	T	0.39	.	14.2293	0.65879	0.0:0.9257:0.0:0.0743	rs3826550;rs17497944;rs17855365;rs17855479;rs3826550	94	P02533	K1C14_HUMAN	T	94	ENSP00000167586:A94T	ENSP00000167586:A94T	A	-	1	0	KRT14	36996333	0.000000	0.05858	0.725000	0.30721	0.013000	0.08279	0.065000	0.14466	2.541000	0.85698	0.549000	0.68633	GCT	C|0.705;T|0.295	0.295	strong		0.632	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
INPP4B	8821	hgsc.bcm.edu	37	4	143067054	143067054	+	Silent	SNP	G	G	A	rs35390852	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:143067054G>A	ENST00000513000.1	-	19	2092	c.1659C>T	c.(1657-1659)ggC>ggT	p.G553G	INPP4B_ENST00000509777.1_Silent_p.G553G|INPP4B_ENST00000508116.1_Silent_p.G553G|INPP4B_ENST00000308502.4_Silent_p.G553G|INPP4B_ENST00000262992.4_Silent_p.G553G	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	553					cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					CATTGTTGCCGCCACTGCCTT	0.443													G|||	480	0.0958466	0.0083	0.1052	5008	,	,		17327	0.0615		0.1163	False		,,,				2504	0.2219				p.G553G		Atlas-SNP	.											.	INPP4B	132	.	0			c.C1659T						PASS	.	G	,	149,4257	102.1+/-140.7	2,145,2056	194.0	162.0	173.0		1659,1659	-1.8	0.0	4	dbSNP_126	173	1038,7562	221.0+/-258.6	58,922,3320	yes	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	60,1067,5376	AA,AG,GG		12.0698,3.3818,9.1266	,	553/925,553/925	143067054	1187,11819	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon19			GTTGCCGCCACTG	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.1659C>T	4.37:g.143067054G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	209	99	0.473684	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			G|0.911;A|0.089	0.089	strong		0.443	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
PKP1	5317	hgsc.bcm.edu	37	1	201285712	201285712	+	Silent	SNP	C	C	T	rs7514146	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201285712C>T	ENST00000352845.3	+	4	733	c.733C>T	c.(733-735)Ctg>Ttg	p.L245L	PKP1_ENST00000367324.3_Silent_p.L245L|PKP1_ENST00000263946.3_Silent_p.L245L|PKP1_ENST00000475988.1_3'UTR			Q13835	PKP1_HUMAN	plakophilin 1	245					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						GTGCAGTGGGCTGACCATCCC	0.572													C|||	756	0.150958	0.3064	0.0821	5008	,	,		19582	0.0099		0.0994	False		,,,				2504	0.1881				p.L245L		Atlas-SNP	.											.	PKP1	127	.	0			c.C733T						PASS	.	C	,	1172,3234	408.2+/-334.5	174,824,1205	74.0	57.0	63.0		733,733	3.9	1.0	1	dbSNP_116	63	808,7792	186.2+/-233.7	33,742,3525	no	coding-synonymous,coding-synonymous	PKP1	NM_000299.3,NM_001005337.2	,	207,1566,4730	TT,TC,CC		9.3953,26.6001,15.2237	,	245/748,245/727	201285712	1980,11026	2203	4300	6503	SO:0001819	synonymous_variant	5317	exon4			AGTGGGCTGACCA	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.733C>T	1.37:g.201285712C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	170	87	0.511765	NM_001005337	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																			C|0.863;T|0.137	0.137	strong		0.572	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
C6orf15	29113	hgsc.bcm.edu	37	6	31079242	31079242	+	Silent	SNP	A	A	G	rs2233985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31079242A>G	ENST00000259870.3	-	2	897	c.894T>C	c.(892-894)ccT>ccC	p.P298P		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	298	Pro-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GGAGGACTCCAGGAGGAAATG	0.537													G|||	524	0.104633	0.0091	0.0994	5008	,	,		16642	0.2361		0.0785	False		,,,				2504	0.1288				p.P298P		Atlas-SNP	.											.	C6orf15	29	.	0			c.T894C						PASS	.	G		65,3431		0,65,1683	43.0	43.0	43.0		894	-4.6	0.0	6	dbSNP_98	43	458,6512		21,416,3048	no	coding-synonymous	C6orf15	NM_014070.2		21,481,4731	GG,GA,AA		6.571,1.8593,4.9971		298/326	31079242	523,9943	1748	3485	5233	SO:0001819	synonymous_variant	29113	exon2			GACTCCAGGAGGA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.894T>C	6.37:g.31079242A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			A|0.923;G|0.077	0.077	strong		0.537	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
SIRPA	140885	hgsc.bcm.edu	37	20	1895965	1895965	+	Missense_Mutation	SNP	C	C	A	rs17855614|rs373583167|rs386811662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1895965C>A	ENST00000358771.4	+	2	452	c.300C>A	c.(298-300)aaC>aaA	p.N100K	SIRPA_ENST00000356025.3_Missense_Mutation_p.N100K|SIRPA_ENST00000400068.3_Missense_Mutation_p.N100K	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	100	Ig-like V-type.		N -> E (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CAAAGAGAAACAACATGGACT	0.517													C|||	480	0.0958466	0.0386	0.1095	5008	,	,		14804	0.1835		0.0537	False		,,,				2504	0.1166				p.N100K	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,brain,glioma,0,4	SIRPA	83	4	0			c.C300A						scavenged	.																																			SO:0001583	missense	140885	exon3			GAGAAACAACATG	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.300C>A	20.37:g.1895965C>A	ENSP00000351621:p.Asn100Lys	Somatic	543	0	0		WXS	Illumina HiSeq	Phase_I	279	22	0.078853	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.533326	0.27387	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02158	4.42;4.42;4.42	5.11	0.771	0.18504	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.743450	0.02696	N	0.111247	T	0.04634	0.0126	M	0.65975	2.015	0.09310	N	1	B;B;B	0.33299	0.003;0.407;0.039	B;B;B	0.31812	0.056;0.136;0.082	T	0.44345	-0.9334	10	0.72032	D	0.01	.	8.1767	0.31285	0.0:0.4423:0.4696:0.0881	rs17855614	80;100;100	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	K	100	ENSP00000382941:N100K;ENSP00000348307:N100K;ENSP00000351621:N100K	ENSP00000348307:N100K	N	+	3	2	SIRPA	1843965	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.328000	0.07945	0.028000	0.15324	-0.315000	0.08773	AAC	.	.	weak		0.517	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
ZNF283	284349	hgsc.bcm.edu	37	19	44352665	44352665	+	Missense_Mutation	SNP	T	T	C	rs2356437|rs386809609|rs371852581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44352665T>C	ENST00000324461.7	+	7	2209	c.1912T>C	c.(1912-1914)Tgt>Cgt	p.C638R	ZNF283_ENST00000588797.1_Missense_Mutation_p.C499R	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	638			C -> R (in dbSNP:rs2356437).|C -> Y (in dbSNP:rs1061769).	C -> H (in Ref. 1; BAC05251/BAG57956 and 4; AAS55109). {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)			endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				GACCTTTACTTGTGGCTCAAA	0.398													C|||	3417	0.682308	0.8533	0.536	5008	,	,		19701	0.374		0.7684	False		,,,				2504	0.7843				p.C638R		Atlas-SNP	.											ZNF283_ENST00000324461,colon,carcinoma,0,1	ZNF283	83	1	0			c.T1912C						PASS	.	C	ARG/CYS	3346,690		1429,488,101	98.0	106.0	103.0		1912	-1.7	0.0	19	dbSNP_100	103	6268,2114		2464,1340,387	yes	missense	ZNF283	NM_181845.1	180	3893,1828,488	CC,CT,TT		25.2207,17.0961,22.5801	benign	638/680	44352665	9614,2804	2018	4191	6209	SO:0001583	missense	284349	exon7			TTTACTTGTGGCT	AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"""Zinc fingers, C2H2-type"", ""-"""	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1912T>C	19.37:g.44352665T>C	ENSP00000327314:p.Cys638Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	1338	0.6126373626373627	387	0.7865853658536586	205	0.5662983425414365	191	0.3339160839160839	555	0.7321899736147758	C	2.444	-0.327973	0.05314	0.829039	0.747793	ENSG00000167637	ENST00000324461	T	0.06608	3.28	2.6	-1.72	0.08107	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.03194	-0.395	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.14783	-1.0460	8	0.08179	T	0.78	.	3.364	0.07197	0.3032:0.2499:0.0:0.4469	rs2356437;rs57860916;rs2356437	638	Q8N7M2	ZN283_HUMAN	R	638	ENSP00000327314:C638R	ENSP00000327314:C638R	C	+	1	0	ZNF283	49044505	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-4.778000	0.00187	-0.926000	0.03770	-0.226000	0.12346	TGT	T|0.341;C|0.659	0.659	strong		0.398	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
LILRA4	23547	hgsc.bcm.edu	37	19	54848275	54848275	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54848275C>T	ENST00000291759.4	-	6	1148	c.1092G>A	c.(1090-1092)ccG>ccA	p.P364P	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	364	Ig-like C2-type 4.				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)		TCAGACGCAACGGGGGATGGG	0.592																																					p.P364P		Atlas-SNP	.											LILRA4,NS,carcinoma,0,1	LILRA4	91	1	0			c.G1092A						scavenged	.						152.0	141.0	145.0					19																	54848275		2203	4300	6503	SO:0001819	synonymous_variant	23547	exon6			ACGCAACGGGGGA	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.1092G>A	19.37:g.54848275C>T		Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	244	3	0.0122951	NM_012276	Q32MC4	Silent	SNP	ENST00000291759.4	37	CCDS12890.1																																																																																			.	.	none		0.592	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276	
MCM8	84515	hgsc.bcm.edu	37	20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	rs16991638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5974265A>G	ENST00000378896.3	+	18	2731	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	MCM8_ENST00000265187.4_Missense_Mutation_p.N769S|MCM8_ENST00000378886.2_Missense_Mutation_p.N825S|MCM8_ENST00000378883.1_Missense_Mutation_p.N738S	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	785			N -> S (in dbSNP:rs16991638).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						GCTCTCAACAACGTTGCTGAA	0.358													A|||	378	0.0754792	0.1853	0.1009	5008	,	,		18096	0.001		0.0199	False		,,,				2504	0.0429				p.N785S		Atlas-SNP	.											.	MCM8	125	.	0			c.A2354G						PASS	.	A	SER/ASN,SER/ASN	703,3703	283.4+/-277.1	58,587,1558	57.0	62.0	61.0		2354,2306	0.4	1.0	20	dbSNP_123	61	181,8419	82.3+/-144.9	2,177,4121	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	46,46	60,764,5679	GG,GA,AA		2.1047,15.9555,6.7969	benign,benign	785/841,769/825	5974265	884,12122	2203	4300	6503	SO:0001583	missense	84515	exon18			TCAACAACGTTGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2354A>G	20.37:g.5974265A>G	ENSP00000368174:p.Asn785Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	128	0.05860805860805861	86	0.17479674796747968	26	0.0718232044198895	1	0.0017482517482517483	15	0.01978891820580475	A	9.100	1.003892	0.19199	0.159555	0.021047	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.02812	4.25;4.15;4.23;4.25	5.82	0.411	0.16392	.	0.769958	0.13000	N	0.421768	T	0.00012	0.0000	N	0.01576	-0.805	0.54753	P	1.3000000000040757E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.45056	-0.9287	9	0.17832	T	0.49	-3.3433	6.6121	0.22757	0.2319:0.3374:0.4307:0.0	rs16991638;rs56419414;rs16991638	738;825;769;785	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	S	785;738;825;769	ENSP00000368174:N785S;ENSP00000368161:N738S;ENSP00000368164:N825S;ENSP00000265187:N769S	ENSP00000265187:N769S	N	+	2	0	MCM8	5922265	0.001000	0.12720	0.997000	0.53966	0.995000	0.86356	-0.073000	0.11468	0.055000	0.16094	0.533000	0.62120	AAC	A|0.934;G|0.066	0.066	strong		0.358	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919934	12919934	+	Missense_Mutation	SNP	A	A	G	rs3204805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12919934A>G	ENST00000240189.2	+	3	761	c.674A>G	c.(673-675)tAt>tGt	p.Y225C		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	225			Y -> C (in dbSNP:rs3204805).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGAAAGCTTTATTGTTACCTG	0.383													.|||	849	0.169529	0.1437	0.1095	5008	,	,		22588	0.3125		0.1352	False		,,,				2504	0.135				p.Y225C		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.A674G						PASS	.	G	CYS/TYR	714,3690	758.0+/-412.8	77,560,1565	101.0	106.0	104.0		674	-1.7	0.0	1	dbSNP_105	104	1254,7330	756.9+/-407.5	112,1030,3150	no	missense	PRAMEF2	NM_023014.1	194	189,1590,4715	GG,GA,AA		14.6086,16.2125,15.1524	benign	225/475	12919934	1968,11020	2202	4292	6494	SO:0001583	missense	65122	exon3			AGCTTTATTGTTA		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.674A>G	1.37:g.12919934A>G	ENSP00000240189:p.Tyr225Cys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	119	9	0.0756303	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	372	0.17032967032967034	50	0.1016260162601626	46	0.1270718232044199	165	0.28846153846153844	111	0.14643799472295516	G	1.447	-0.566127	0.03910	0.162125	0.146086	ENSG00000120952	ENST00000240189	T	0.14766	2.48	0.842	-1.68	0.08212	.	0.335847	0.28688	N	0.014461	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.17465	0.022	B	0.26202	0.067	T	0.48103	-0.9064	9	0.66056	D	0.02	.	3.4172	0.07380	0.4582:0.2964:0.2453:0.0	rs3204805;rs17038687;rs52806752;rs3204805	225	O60811	PRAM2_HUMAN	C	225	ENSP00000240189:Y225C	ENSP00000240189:Y225C	Y	+	2	0	PRAMEF2	12842521	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.549000	0.02182	-2.688000	0.00405	-2.828000	0.00107	TAT	A|0.846;G|0.154	0.154	strong		0.383	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
FAM129B	64855	hgsc.bcm.edu	37	9	130270782	130270782	+	Silent	SNP	G	G	A	rs11545937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130270782G>A	ENST00000373312.3	-	11	1566	c.1353C>T	c.(1351-1353)ctC>ctT	p.L451L	FAM129B_ENST00000468379.1_Intron|FAM129B_ENST00000373314.3_Silent_p.L438L	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	451					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CCTGGTGCAGGAGGGTCTCGA	0.652													G|||	118	0.0235623	0.0045	0.0389	5008	,	,		17611	0.0		0.0596	False		,,,				2504	0.0256				p.L451L		Atlas-SNP	.											.	FAM129B	84	.	0			c.C1353T						PASS	.	G	,	56,4350	55.5+/-91.7	0,56,2147	137.0	133.0	135.0		1314,1353	-1.5	1.0	9	dbSNP_120	135	570,8030	153.9+/-208.2	20,530,3750	no	coding-synonymous,coding-synonymous	FAM129B	NM_001035534.1,NM_022833.2	,	20,586,5897	AA,AG,GG		6.6279,1.271,4.8132	,	438/734,451/747	130270782	626,12380	2203	4300	6503	SO:0001819	synonymous_variant	64855	exon11			GTGCAGGAGGGTC	AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"""chromosome 9 open reading frame 88"""	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.1353C>T	9.37:g.130270782G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	37	12	0.324324	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Silent	SNP	ENST00000373312.3	37	CCDS35145.1																																																																																			G|0.957;C|0.000;A|0.043	0.043	strong		0.652	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833	
DNAJC15	29103	hgsc.bcm.edu	37	13	43597865	43597865	+	Missense_Mutation	SNP	A	A	G	rs12015	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:43597865A>G	ENST00000379221.2	+	1	527	c.103A>G	c.(103-105)Aga>Gga	p.R35G	DNAJC15_ENST00000474320.1_3'UTR	NM_013238.2	NP_037370.2	Q9Y5T4	DJC15_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 15	35			R -> G (in dbSNP:rs11617079). {ECO:0000269|PubMed:11358853, ECO:0000269|PubMed:15489334}.		cellular response to starvation (GO:0009267)|negative regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902957)|negative regulation of protein complex assembly (GO:0031333)|protein transport (GO:0015031)|regulation of lipid metabolic process (GO:0019216)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(1)|urinary_tract(1)	4		Lung NSC(96;4.3e-06)|Breast(139;0.00869)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		GBM - Glioblastoma multiforme(144;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0737)		CGACCAGCAGAGACTGGTGAG	0.632													G|||	1181	0.235823	0.4281	0.2219	5008	,	,		8065	0.1002		0.2535	False		,,,				2504	0.1074				p.R35G		Atlas-SNP	.											DNAJC15_ENST00000379221,NS,carcinoma,0,2	DNAJC15	16	2	0			c.A103G						PASS	.	G	GLY/ARG	1795,2609		375,1045,782	19.0	20.0	20.0		103	0.6	0.0	13	dbSNP_120	20	2062,6538		279,1504,2517	yes	missense	DNAJC15	NM_013238.2	125	654,2549,3299	GG,GA,AA		23.9767,40.7584,29.6601	benign	35/151	43597865	3857,9147	2202	4300	6502	SO:0001583	missense	29103	exon1			CAGCAGAGACTGG	AF126743	CCDS9388.1	13q14.1	2011-09-02	2005-06-30	2005-06-30	ENSG00000120675	ENSG00000120675		"""Heat shock proteins / DNAJ (HSP40)"""	20325	protein-coding gene	gene with protein product		615339	"""DnaJ (Hsp40) homolog, subfamily D, member 1"""	DNAJD1		11358853	Standard	NM_013238		Approved	MCJ	uc001uyy.3	Q9Y5T4	OTTHUMG00000016813	ENST00000379221.2:c.103A>G	13.37:g.43597865A>G	ENSP00000368523:p.Arg35Gly	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_013238	B2R4L0|Q5T219|Q6X963	Missense_Mutation	SNP	ENST00000379221.2	37	CCDS9388.1	521	0.23855311355311357	180	0.36585365853658536	79	0.21823204419889503	65	0.11363636363636363	197	0.2598944591029024	G	5.877	0.345947	0.11126	0.407584	0.239767	ENSG00000120675	ENST00000379221	T	0.44881	0.91	4.56	0.561	0.17285	.	0.816791	0.11028	N	0.607571	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.46582	-0.9181	9	0.19590	T	0.45	-19.9861	4.356	0.11178	0.4233:0.1645:0.4122:0.0	rs11617079;rs17856341;rs59811457;rs11617079	35	Q9Y5T4	DJC15_HUMAN	G	35	ENSP00000368523:R35G	ENSP00000368523:R35G	R	+	1	2	DNAJC15	42495865	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.682000	0.05185	-0.381000	0.07882	-0.166000	0.13349	AGA	A|0.735;G|0.265	0.265	strong		0.632	DNAJC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044709.2	NM_013238	
SFSWAP	6433	hgsc.bcm.edu	37	12	132237750	132237750	+	Silent	SNP	C	C	T	rs1051219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:132237750C>T	ENST00000261674.4	+	8	1305	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	SFSWAP_ENST00000541286.1_Silent_p.D388D	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	388					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						CCGGAATCGACGTGACTACTT	0.612													C|||	515	0.102835	0.0091	0.2147	5008	,	,		17969	0.001		0.2565	False		,,,				2504	0.0971				p.D388D		Atlas-SNP	.											.	SFSWAP	69	.	0			c.C1164T						PASS	.	C		211,4195	129.0+/-165.8	6,199,1998	160.0	140.0	147.0		1164	-4.4	0.1	12	dbSNP_86	147	2395,6205	399.4+/-346.4	321,1753,2226	no	coding-synonymous	SFSWAP	NM_004592.2		327,1952,4224	TT,TC,CC		27.8488,4.7889,20.0369		388/952	132237750	2606,10400	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon8			AATCGACGTGACT	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1164C>T	12.37:g.132237750C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	162	68	0.419753	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	293	0.13415750915750915	6	0.012195121951219513	94	0.2596685082872928	0	0.0	193	0.2546174142480211	C	3.164	-0.171526	0.06421	0.047889	0.278488	ENSG00000061936	ENST00000537164	.	.	.	5.28	-4.44	0.03557	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999777251	.	.	.	.	.	.	T	0.28427	-1.0044	3	.	.	.	-26.8037	8.7176	0.34421	0.0:0.2818:0.1823:0.5358	rs1051219;rs17678035;rs60659244;rs1051219	.	.	.	M	28	.	.	T	+	2	0	SFSWAP	130803703	0.016000	0.18221	0.112000	0.21494	0.302000	0.27658	-0.993000	0.03720	-0.865000	0.04073	-0.369000	0.07265	ACG	C|0.832;T|0.168	0.168	strong		0.612	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
ZNF45	7596	hgsc.bcm.edu	37	19	44418680	44418680	+	Missense_Mutation	SNP	G	G	C	rs388685	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44418680G>C	ENST00000269973.5	-	10	1998	c.908C>G	c.(907-909)cCa>cGa	p.P303R	ZNF45_ENST00000589703.1_Missense_Mutation_p.P303R|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	303			P -> R (in dbSNP:rs388685). {ECO:0000269|PubMed:15057824}.		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						ACACTTATATGGTTTCTTTCC	0.463													G|||	2075	0.414337	0.174	0.5764	5008	,	,		21910	0.5486		0.5119	False		,,,				2504	0.3855				p.P303R		Atlas-SNP	.											.	ZNF45	51	.	0			c.C908G						PASS	.	G	ARG/PRO	994,3412	372.7+/-320.5	131,732,1340	87.0	73.0	78.0		908	3.4	0.2	19	dbSNP_80	78	4306,4294	577.4+/-390.6	1094,2118,1088	yes	missense	ZNF45	NM_003425.3	103	1225,2850,2428	CC,CG,GG		49.9302,22.5601,40.7504	possibly-damaging	303/683	44418680	5300,7706	2203	4300	6503	SO:0001583	missense	7596	exon10			TTATATGGTTTCT	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.908C>G	19.37:g.44418680G>C	ENSP00000269973:p.Pro303Arg	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	120	120	1	NM_003425	P17016|P78472|Q9P1U9	Missense_Mutation	SNP	ENST00000269973.5	37	CCDS12632.1	1018	0.4661172161172161	125	0.2540650406504065	183	0.505524861878453	324	0.5664335664335665	386	0.5092348284960422	G	12.18	1.860140	0.32884	0.225601	0.500698	ENSG00000124459	ENST00000269973;ENST00000328762	T	0.17213	2.29	3.39	3.39	0.38822	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36134	N	0.002777	T	0.00012	0.0000	M	0.77486	2.375	0.20821	P	0.999846303	D	0.89917	1.0	D	0.91635	0.999	T	0.49523	-0.8931	9	0.72032	D	0.01	-5.3101	14.0503	0.64732	0.0:0.0:1.0:0.0	rs388685;rs17173169;rs17712965;rs56609263;rs60039409;rs388685	303	Q02386	ZNF45_HUMAN	R	303	ENSP00000269973:P303R	ENSP00000269973:P303R	P	-	2	0	ZNF45	49110520	0.999000	0.42202	0.248000	0.24265	0.125000	0.20455	2.850000	0.48294	1.915000	0.55452	0.462000	0.41574	CCA	G|0.566;C|0.433	0.433	strong		0.463	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1900911	1900911	+	Silent	SNP	C	C	T	rs2272608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:1900911C>T	ENST00000398564.1	+	28	3513	c.3513C>T	c.(3511-3513)caC>caT	p.H1171H	ARHGEF10_ENST00000518288.1_Silent_p.H1170H|ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000520359.1_Silent_p.H1108H|ARHGEF10_ENST00000349830.3_Silent_p.H1146H|ARHGEF10_ENST00000262112.6_Silent_p.H1142H			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1171					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)		TCGTCTGCCACGGATTGCTGA	0.642													C|||	1077	0.215056	0.3555	0.2075	5008	,	,		14241	0.2123		0.0954	False		,,,				2504	0.1564				p.H1146H		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C3438T						PASS	.	C		1315,3091	430.8+/-342.7	215,885,1103	49.0	49.0	49.0		3438	-7.9	0.4	8	dbSNP_100	49	1077,7523	220.8+/-258.4	71,935,3294	no	coding-synonymous	ARHGEF10	NM_014629.2		286,1820,4397	TT,TC,CC		12.5233,29.8457,18.3915		1146/1345	1900911	2392,10614	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon28			CTGCCACGGATTG	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.3513C>T	8.37:g.1900911C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				C|0.809;T|0.191	0.191	strong		0.642	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
HLA-A	3105	hgsc.bcm.edu	37	6	29910607	29910607	+	Silent	SNP	G	G	C	rs72555397		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910607G>C	ENST00000396634.1	+	4	488	c.147G>C	c.(145-147)gtG>gtC	p.V49V	HLA-A_ENST00000376809.5_Silent_p.V49V|HLA-A_ENST00000376806.5_Silent_p.V49V|HLA-A_ENST00000376802.2_Silent_p.V49V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	49	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.V49V(2)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TCATCGCCGTGGGCTACGTGG	0.692									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.V49V		Atlas-SNP	.											HLA-A,NS,carcinoma,0,5	HLA-A	89	5	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G147C						PASS	.																																			SO:0001819	synonymous_variant	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGCCGTGGGCTAC	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.147G>C	6.37:g.29910607G>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	91	14	0.153846	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	weak		0.692	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
IDI2	91734	hgsc.bcm.edu	37	10	1065710	1065710	+	Nonsense_Mutation	SNP	C	C	T	rs1044261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:1065710C>T	ENST00000277517.1	-	5	495	c.431G>A	c.(430-432)tGg>tAg	p.W144*	IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|GTPBP4_ENST00000360803.4_3'UTR|IDI2-AS1_ENST00000420381.1_RNA|IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000437374.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	144	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)		ATGCTCTCCCCAAATTCTGTC	0.438													C|||	153	0.0305511	0.0378	0.0432	5008	,	,		20211	0.0		0.0656	False		,,,				2504	0.0072				p.W144X		Atlas-SNP	.											.	IDI2	20	.	0			c.G431A						PASS	.	C	stop/TRP	209,4197	126.1+/-163.2	6,197,2000	139.0	120.0	127.0		431	3.5	0.7	10	dbSNP_86	127	658,7942	167.1+/-218.9	29,600,3671	yes	stop-gained	IDI2	NM_033261.2		35,797,5671	TT,TC,CC		7.6512,4.7435,6.6662		144/228	1065710	867,12139	2203	4300	6503	SO:0001587	stop_gained	91734	exon5			TCTCCCCAAATTC	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.431G>A	10.37:g.1065710C>T	ENSP00000277517:p.Trp144*	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	207	100	0.483092	NM_033261		Nonsense_Mutation	SNP	ENST00000277517.1	37	CCDS7055.1	89	0.04075091575091575	18	0.036585365853658534	19	0.052486187845303865	0	0.0	52	0.06860158311345646	C	20.2	3.949034	0.73787	0.047435	0.076512	ENSG00000148377	ENST00000277517	.	.	.	3.55	3.55	0.40652	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.5525	13.7851	0.63105	0.0:1.0:0.0:0.0	rs1044261;rs3167827;rs17221498;rs52825068;rs61475337;rs1044261	.	.	.	X	144	.	ENSP00000277517:W144X	W	-	2	0	IDI2	1055710	1.000000	0.71417	0.702000	0.30337	0.498000	0.33706	4.671000	0.61590	1.982000	0.57802	0.185000	0.17295	TGG	C|0.949;T|0.051	0.051	strong		0.438	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261	
HLA-A	3105	hgsc.bcm.edu	37	6	29912297	29912297	+	Missense_Mutation	SNP	A	A	G	rs1136949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29912297A>G	ENST00000396634.1	+	7	1257	c.916A>G	c.(916-918)Atc>Gtc	p.I306V	HLA-A_ENST00000376809.5_Missense_Mutation_p.I306V|HLA-A_ENST00000376806.5_Missense_Mutation_p.I306V|HLA-A_ENST00000376802.2_Intron			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	306	Connecting peptide.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	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						CCAGCCCACCATCCCCATCGT	0.592									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	759	0.151558	0.1241	0.1744	5008	,	,		19702	0.2034		0.1113	False		,,,				2504	0.1605				p.I306V		Atlas-SNP	.											.	HLA-A	89	.	0			c.A916G						PASS	.	A	VAL/ILE	402,2618		28,346,1136	93.0	88.0	89.0		916	-2.9	0.0	6	dbSNP_86	89	582,4836		37,508,2164	no	missense	HLA-A	NM_002116.7	29	65,854,3300	GG,GA,AA		10.742,13.3113,11.6615	benign	306/366	29912297	984,7454	1510	2709	4219	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCCACCATCCCCA	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.916A>G	6.37:g.29912297A>G	ENSP00000379873:p.Ile306Val	Somatic	378	0	0		WXS	Illumina HiSeq	Phase_I	271	150	0.553506	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	323	0.1478937728937729	45	0.09146341463414634	70	0.19337016574585636	133	0.23251748251748253	75	0.09894459102902374	.	6.056	0.378690	0.11466	0.133113	0.10742	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00644	6.02;6.01;6.02	3.69	-2.88	0.05682	Immunoglobulin-like fold (3);	2.223100	0.02747	U	0.116991	T	0.00356	0.0011	M	0.70787	2.145	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.47222	-0.9134	9	0.87932	D	0	.	3.396	0.07305	0.3235:0.0:0.13:0.5465	rs1136949;rs1804981;rs2231103;rs3179261;rs12721765;rs41560218	185;306;306;306;306	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	V	306	ENSP00000379873:I306V;ENSP00000366002:I306V;ENSP00000366005:I306V	ENSP00000366002:I306V	I	+	1	0	HLA-A	30020276	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.325000	0.07976	-0.192000	0.10432	0.397000	0.26171	ATC	A|0.875;G|0.125	0.125	strong		0.592	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
DTX2	113878	hgsc.bcm.edu	37	7	76112299	76112299	+	Missense_Mutation	SNP	A	A	G	rs145151450	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:76112299A>G	ENST00000324432.5	+	5	1253	c.743A>G	c.(742-744)aAc>aGc	p.N248S	DTX2_ENST00000430490.2_Missense_Mutation_p.N248S|DTX2_ENST00000446600.1_Missense_Mutation_p.N157S|DTX2_ENST00000413936.2_Missense_Mutation_p.N248S|DTX2_ENST00000307569.8_Missense_Mutation_p.N248S|DTX2_ENST00000446820.2_Missense_Mutation_p.N248S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	248					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						GCACCGTACAACAAACCCTCA	0.672													.|||	11	0.00219649	0.0	0.0029	5008	,	,		18951	0.001		0.008	False		,,,				2504	0.0				p.N248S		Atlas-SNP	.											.	DTX2	64	.	0			c.A743G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	3,4403		0,3,2200	151.0	159.0	157.0		743,743,743,743	1.4	1.0	7	dbSNP_134	157	46,8554		0,46,4254	yes	missense,missense,missense,missense	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	46,46,46,46	0,49,6454	GG,GA,AA		0.5349,0.0681,0.3767	benign,benign,benign,benign	248/623,248/623,248/576,248/623	76112299	49,12957	2203	4300	6503	SO:0001583	missense	113878	exon2			CGTACAACAAACC		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.743A>G	7.37:g.76112299A>G	ENSP00000322885:p.Asn248Ser	Somatic	329	1	0.00303951		WXS	Illumina HiSeq	Phase_I	266	116	0.43609	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	37	CCDS5587.1	4	0.0018315018315018315	0	0.0	0	0.0	2	0.0034965034965034965	2	0.002638522427440633	.	0.016	-1.528964	0.00951	6.81E-4	0.005349	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490;ENST00000446820	T;T;T;T;T;T	0.10668	2.85;2.86;2.85;2.85;2.85;2.86	5.18	1.39	0.22231	.	0.598456	0.18389	N	0.142736	T	0.02688	0.0081	N	0.08118	0	0.24585	N	0.993856	B;B;B	0.11235	0.004;0.001;0.0	B;B;B	0.12837	0.006;0.008;0.002	T	0.45716	-0.9242	10	0.08381	T	0.77	-14.9182	6.4167	0.21719	0.5953:0.1273:0.2774:0.0	.	157;248;248	F5GX89;Q86UW9-2;Q86UW9	.;.;DTX2_HUMAN	S	248;248;157;157;248;248;248	ENSP00000322885:N248S;ENSP00000305242:N248S;ENSP00000397648:N157S;ENSP00000390218:N248S;ENSP00000411986:N248S;ENSP00000392545:N248S	ENSP00000305242:N248S	N	+	2	0	AC005522.1	75950235	0.994000	0.37717	0.993000	0.49108	0.282000	0.26991	0.532000	0.23067	0.005000	0.14708	-1.447000	0.01057	AAC	A|0.997;G|0.003	0.003	strong		0.672	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
KIAA1549L	25758	hgsc.bcm.edu	37	11	33631423	33631423	+	Silent	SNP	G	G	A	rs2076622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:33631423G>A	ENST00000321505.4	+	14	4479	c.4299G>A	c.(4297-4299)aaG>aaA	p.K1433K	KIAA1549L_ENST00000389726.3_Silent_p.K1439K			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1433						integral component of membrane (GO:0016021)											CCGAAAGAAAGAAGATGTATG	0.483													A|||	2262	0.451677	0.5605	0.3818	5008	,	,		21178	0.3839		0.3857	False		,,,				2504	0.4918				p.K1433K		Atlas-SNP	.											.	.	.	.	0			c.G4299A						PASS	.	A		2033,1827		550,933,447	71.0	76.0	75.0		4299	-6.6	0.1	11	dbSNP_96	75	3205,5051		631,1943,1554	no	coding-synonymous	C11orf41	NM_012194.2		1181,2876,2001	AA,AG,GG		38.8203,47.3316,43.2321		1433/1850	33631423	5238,6878	1930	4128	6058	SO:0001819	synonymous_variant	25758	exon14			AAGAAAGAAGATG	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.4299G>A	11.37:g.33631423G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	927	0.42445054945054944	265	0.5386178861788617	148	0.4088397790055249	212	0.3706293706293706	302	0.39841688654353563	A	0.057	-1.234862	0.01505	0.526684	0.388203	ENSG00000110427	ENST00000526400	.	.	.	5.54	-6.56	0.01848	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.23101	P	0.99829438	.	.	.	.	.	.	T	0.12967	-1.0527	3	.	.	.	-16.3549	13.6844	0.62506	0.3434:0.0948:0.5619:0.0	rs2076622;rs59056818;rs2076622	.	.	.	K	831	.	.	R	+	2	0	C11orf41	33587999	0.507000	0.26146	0.126000	0.21872	0.003000	0.03518	-0.097000	0.11042	-1.233000	0.02551	-0.972000	0.02603	AGA	G|0.561;A|0.439	0.439	strong		0.483	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
PCNT	5116	hgsc.bcm.edu	37	21	47831509	47831509	+	Missense_Mutation	SNP	A	A	G	rs35940413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47831509A>G	ENST00000359568.5	+	28	5629	c.5522A>G	c.(5521-5523)aAt>aGt	p.N1841S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1841			N -> S (in dbSNP:rs35940413).		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)					CTGGAGCGCAATGTAGCCCTC	0.647													A|||	1016	0.202875	0.5113	0.1369	5008	,	,		15822	0.004		0.1322	False		,,,				2504	0.1104				p.N1841S		Atlas-SNP	.											.	PCNT	283	.	0			c.A5522G						PASS	.	A	SER/ASN	2018,2384		478,1062,661	23.0	27.0	26.0		5522	2.6	0.0	21	dbSNP_126	26	1114,7486		86,942,3272	yes	missense	PCNT	NM_006031.5	46	564,2004,3933	GG,GA,AA		12.9535,45.8428,24.0886	benign	1841/3337	47831509	3132,9870	2201	4300	6501	SO:0001583	missense	5116	exon28			AGCGCAATGTAGC	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.5522A>G	21.37:g.47831509A>G	ENSP00000352572:p.Asn1841Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	405	0.18543956043956045	246	0.5	53	0.1464088397790055	2	0.0034965034965034965	104	0.13720316622691292	A	0.006	-2.021430	0.00414	0.458428	0.129535	ENSG00000160299	ENST00000359568	T	0.01414	4.92	5.47	2.58	0.30949	.	0.854162	0.09792	N	0.755339	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09574	-1.0668	9	0.08179	T	0.78	.	7.4807	0.27404	0.1565:0.0:0.7053:0.1382	rs35940413	1723;1841	O95613-2;O95613	.;PCNT_HUMAN	S	1841	ENSP00000352572:N1841S	ENSP00000352572:N1841S	N	+	2	0	PCNT	46655937	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	0.260000	0.18424	0.770000	0.33336	-0.146000	0.13790	AAT	A|0.789;G|0.211	0.211	strong		0.647	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
ZBTB1	22890	hgsc.bcm.edu	37	14	64988279	64988279	+	Silent	SNP	A	A	G	rs28626711	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:64988279A>G	ENST00000554015.1	+	4	488	c.57A>G	c.(55-57)gaA>gaG	p.E19E	ZBTB1_ENST00000394712.2_Silent_p.E19E|RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000358738.3_Silent_p.E19E			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	19					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		ACCAAAGAGAATGGGGTTTTC	0.393													A|||	812	0.162141	0.0401	0.1254	5008	,	,		19165	0.2083		0.2326	False		,,,				2504	0.2331				p.E19E		Atlas-SNP	.											.	ZBTB1	93	.	0			c.A57G						PASS	.	A	,	347,4059	179.7+/-208.2	16,315,1872	102.0	97.0	99.0		57,57	-0.4	1.0	14	dbSNP_125	99	1884,6716	336.2+/-321.7	212,1460,2628	no	coding-synonymous,coding-synonymous	ZBTB1	NM_001123329.1,NM_014950.2	,	228,1775,4500	GG,GA,AA		21.907,7.8756,17.1536	,	19/714,19/645	64988279	2231,10775	2203	4300	6503	SO:0001819	synonymous_variant	22890	exon2			AAGAGAATGGGGT	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.57A>G	14.37:g.64988279A>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_014950	A8K6S8|Q86SW8	Silent	SNP	ENST00000554015.1	37	CCDS45126.1																																																																																			A|0.827;G|0.173	0.173	strong		0.393	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1		
TRAPPC9	83696	hgsc.bcm.edu	37	8	141263015	141263015	+	Silent	SNP	G	G	A	rs11166965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:141263015G>A	ENST00000438773.2	-	16	2425	c.2292C>T	c.(2290-2292)ggC>ggT	p.G764G	TRAPPC9_ENST00000389327.3_Silent_p.G755G|TRAPPC9_ENST00000389328.4_Silent_p.G862G	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	764					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						TCAAGAAGTCGCCATACAATT	0.448													G|||	357	0.0712859	0.0212	0.1945	5008	,	,		19943	0.004		0.1183	False		,,,				2504	0.0726				p.G862G		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C2586T						PASS	.	G	,	174,4232	114.2+/-152.2	9,156,2038	57.0	57.0	57.0		2292,2586	-10.2	0.1	8	dbSNP_120	57	1123,7477	233.7+/-266.9	56,1011,3233	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	65,1167,5271	AA,AG,GG		13.0581,3.9492,9.9723	,	764/1149,862/1247	141263015	1297,11709	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon16			GAAGTCGCCATAC	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.2292C>T	8.37:g.141263015G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	162	0.07417582417582418	9	0.018292682926829267	62	0.1712707182320442	2	0.0034965034965034965	89	0.11741424802110818	G	1.263	-0.615166	0.03663	0.039492	0.130581	ENSG00000167632	ENST00000520857	.	.	.	5.08	-10.2	0.00374	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999998579	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9976	0.14247	0.2589:0.0872:0.489:0.1649	rs11166965;rs11166965	.	.	.	X	608	.	.	R	-	1	2	TRAPPC9	141332197	0.000000	0.05858	0.071000	0.20095	0.269000	0.26545	-3.343000	0.00504	-2.610000	0.00446	-1.027000	0.02421	CGA	G|0.914;A|0.086	0.086	strong		0.448	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362287	105362287	+	Silent	SNP	C	C	G	rs3740472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105362287C>G	ENST00000369774.4	-	15	2964	c.2688G>C	c.(2686-2688)ctG>ctC	p.L896L	SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000355946.2_Silent_p.L868L|SH3PXD2A_ENST00000540321.1_Silent_p.L763L|SH3PXD2A_ENST00000538130.1_Silent_p.L731L|SH3PXD2A_ENST00000427662.2_Intron			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	896	SH3 4. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)		CGTTCTCATCCAGCACCAAAT	0.612													C|||	443	0.0884585	0.0227	0.0879	5008	,	,		18634	0.1994		0.1014	False		,,,				2504	0.0501				p.L868L		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.G2604C						PASS	.	C		125,4281	91.1+/-129.8	1,123,2079	76.0	74.0	75.0		2604	-7.8	0.0	10	dbSNP_107	75	777,7823	184.2+/-232.2	31,715,3554	yes	coding-synonymous	SH3PXD2A	NM_014631.2		32,838,5633	GG,GC,CC		9.0349,2.837,6.9353		868/1106	105362287	902,12104	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			CTCATCCAGCACC	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.2688G>C	10.37:g.105362287C>G		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	42	0.396226	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		240	0.10989010989010989	13	0.026422764227642278	33	0.09116022099447514	114	0.1993006993006993	80	0.10554089709762533	C	0.005	-2.124565	0.00342	0.02837	0.090349	ENSG00000107957	ENST00000420222	.	.	.	4.59	-7.79	0.01218	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.31943	P	0.6106469999999999	.	.	.	.	.	.	T	0.21930	-1.0231	3	.	.	.	-2.1339	3.2667	0.06868	0.4117:0.1947:0.3079:0.0857	rs3740472;rs3740472	.	.	.	R	823	.	.	G	-	1	0	SH3PXD2A	105352277	0.000000	0.05858	0.005000	0.12908	0.228000	0.25075	-3.344000	0.00504	-1.616000	0.01572	-0.397000	0.06425	GGA	C|0.914;G|0.086	0.086	strong		0.612	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
FUS	2521	hgsc.bcm.edu	37	16	31193942	31193942	+	Silent	SNP	C	C	A	rs741810	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31193942C>A	ENST00000254108.7	+	3	252	c.147C>A	c.(145-147)ggC>ggA	p.G49G	RP11-388M20.6_ENST00000564743.1_RNA|FUS_ENST00000568685.1_Silent_p.G49G|FUS_ENST00000380244.3_Silent_p.G49G	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	49	Gln/Gly/Ser/Tyr-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		ACACTTCAGGCTATGGCCAGA	0.532			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""								C|||	1397	0.278954	0.028	0.3617	5008	,	,		19513	0.253		0.3062	False		,,,				2504	0.5583				p.G49G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	FUS,caecum,carcinoma,0,1	FUS	52	1	0			c.C147A						scavenged	.	C	,,	321,4073	169.4+/-200.1	16,289,1892	101.0	95.0	97.0		147,147,147	4.1	1.0	16	dbSNP_86	97	2495,6105	410.1+/-350.0	357,1781,2162	no	coding-synonymous,coding-synonymous,coding-synonymous	FUS	NM_001170634.1,NM_001170937.1,NM_004960.3	,,	373,2070,4054	AA,AC,CC		29.0116,7.3054,21.6715	,,	49/526,49/523,49/527	31193942	2816,10178	2197	4300	6497	SO:0001819	synonymous_variant	2521	exon3			TTCAGGCTATGGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.147C>A	16.37:g.31193942C>A		Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	174	83	0.477012	NM_001170634	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			C|0.783;A|0.217	0.217	strong		0.532	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
CIDEC	63924	hgsc.bcm.edu	37	3	9920138	9920138	+	Silent	SNP	G	G	C	rs17851444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9920138G>C	ENST00000336832.2	-	2	172	c.33C>G	c.(31-33)ctC>ctG	p.L11L	CIDEC_ENST00000443115.1_Silent_p.L11L|CIDEC_ENST00000383817.1_Silent_p.L11L|CIDEC_ENST00000455015.1_5'UTR|CIDEC_ENST00000423850.1_5'UTR|CIDEC_ENST00000430427.1_Silent_p.L11L	NM_001199552.1|NM_001199623.1|NM_022094.3	NP_001186481.1|NP_001186552.1|NP_071377.2	Q96AQ7	CIDEC_HUMAN	cell death-inducing DFFA-like effector c	11					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|lipid particle organization (GO:0034389)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|lipid particle (GO:0005811)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)|skin(1)	8	Medulloblastoma(99;0.227)					ACTTGGGGTAGAGAAGGCTAA	0.498													G|||	426	0.0850639	0.0484	0.0605	5008	,	,		21255	0.0437		0.1292	False		,,,				2504	0.1493				p.L24L		Atlas-SNP	.											.	CIDEC	22	.	0			c.C72G						PASS	.	G	,,,	242,4164	141.9+/-177.2	10,222,1971	179.0	142.0	154.0		33,33,72,33	0.7	1.0	3	dbSNP_123	154	1135,7465	233.3+/-266.6	78,979,3243	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIDEC	NM_001199551.1,NM_001199552.1,NM_001199623.1,NM_022094.3	,,,	88,1201,5214	CC,CG,GG		13.1977,5.4925,10.5874	,,,	11/249,11/239,24/252,11/239	9920138	1377,11629	2203	4300	6503	SO:0001819	synonymous_variant	63924	exon2			GGGGTAGAGAAGG		CCDS2587.1, CCDS56239.1, CCDS74897.1	3p25	2004-07-26			ENSG00000187288	ENSG00000187288			24229	protein-coding gene	gene with protein product		612120				12429024	Standard	NM_001199623		Approved	CIDE-3, FLJ20871, Fsp27	uc021wsw.1	Q96AQ7	OTTHUMG00000128522	ENST00000336832.2:c.33C>G	3.37:g.9920138G>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	157	74	0.471338	NM_001199623	C9JMN7|Q67DW9|Q9GZY9	Silent	SNP	ENST00000336832.2	37	CCDS2587.1																																																																																			G|0.895;C|0.105	0.105	strong		0.498	CIDEC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250334.1	NM_022094	
LAMP2	3920	hgsc.bcm.edu	37	X	119576455	119576455	+	Splice_Site	SNP	G	G	A	rs73219144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:119576455G>A	ENST00000200639.4	-	7	1063	c.927C>T	c.(925-927)tcC>tcT	p.S309S	LAMP2_ENST00000538785.1_Splice_Site_p.S198S|LAMP2_ENST00000371335.4_Splice_Site_p.S309S|LAMP2_ENST00000434600.2_Splice_Site_p.S309S|LAMP2_ENST00000540603.1_Splice_Site_p.S262S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	309	Second lumenal domain.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						TTTGCTTACCGGAGCCATTAA	0.358													G|||	50	0.013245	0.0	0.0072	3775	,	,		13506	0.0		0.0398	False		,,,				2504	0.0051				p.S309S		Atlas-SNP	.											.	LAMP2	101	.	0			c.C927T						PASS	.	G	,,	29,3806		0,24,5,1608,566	254.0	242.0	246.0		927,927,927	0.9	1.0	X	dbSNP_130	246	274,6454		6,187,75,2235,1797	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	LAMP2	NM_001122606.1,NM_002294.2,NM_013995.2	,,	6,211,80,3843,2363	AA,AG,A,GG,G		4.0725,0.7562,2.8685	,,	309/412,309/411,309/411	119576455	303,10260	2203	4300	6503	SO:0001630	splice_region_variant	3920	exon7			CTTACCGGAGCCA	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"""CD molecules"""	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.928+1C>T	X.37:g.119576455G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_013995	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Silent	SNP	ENST00000200639.4	37	CCDS14599.1																																																																																			G|0.975;A|0.025	0.025	strong		0.358	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1		Silent
GALNT15	117248	hgsc.bcm.edu	37	3	16254172	16254172	+	Missense_Mutation	SNP	G	G	A	rs17851238	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:16254172G>A	ENST00000339732.5	+	6	1797	c.1294G>A	c.(1294-1296)Gcc>Acc	p.A432T	GALNT15_ENST00000437509.1_Missense_Mutation_p.A432T	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	432			A -> T (in dbSNP:rs17851238). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.7}.		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										CGACCAGGAGGCCACCCTGAG	0.557													G|||	768	0.153355	0.3396	0.1599	5008	,	,		19930	0.002		0.1133	False		,,,				2504	0.0941				p.A432T		Atlas-SNP	.											GALNTL2,colon,carcinoma,0,1	.	.	1	0			c.G1294A						scavenged	.	G	THR/ALA	1272,3134	432.6+/-343.3	198,876,1129	105.0	98.0	100.0		1294	4.5	1.0	3	dbSNP_123	100	1011,7589	216.6+/-255.6	73,865,3362	yes	missense	GALNTL2	NM_054110.4	58	271,1741,4491	AA,AG,GG		11.7558,28.8697,17.5534	benign	432/640	16254172	2283,10723	2203	4300	6503	SO:0001583	missense	117248	exon6			CAGGAGGCCACCC	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1294G>A	3.37:g.16254172G>A	ENSP00000344260:p.Ala432Thr	Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Missense_Mutation	SNP	ENST00000339732.5	37	CCDS33711.1	317	0.14514652014652016	173	0.3516260162601626	54	0.14917127071823205	1	0.0017482517482517483	89	0.11741424802110818	G	12.11	1.838866	0.32513	0.288697	0.117558	ENSG00000131386	ENST00000339732;ENST00000437509	T;T	0.59224	0.28;0.28	5.38	4.47	0.54385	.	0.970203	0.08511	N	0.934923	T	0.00012	0.0000	N	0.25426	0.745	0.34732	P	0.270134	P	0.38922	0.651	B	0.32864	0.154	T	0.22765	-1.0207	9	0.35671	T	0.21	.	15.5033	0.75716	0.0:0.0:0.8613:0.1387	rs17851238;rs61690896	432	Q8N3T1	GLTL2_HUMAN	T	432	ENSP00000344260:A432T;ENSP00000395873:A432T	ENSP00000344260:A432T	A	+	1	0	GALNTL2	16229176	1.000000	0.71417	0.956000	0.39512	0.141000	0.21300	2.581000	0.46077	2.524000	0.85096	0.561000	0.74099	GCC	G|0.837;A|0.163	0.163	strong		0.557	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
HLA-B	3106	hgsc.bcm.edu	37	6	31324603	31324603	+	Missense_Mutation	SNP	C	C	T	rs9266178|rs200186034	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31324603C>T	ENST00000412585.2	-	2	233	c.205G>A	c.(205-207)Gag>Aag	p.E69K		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	69	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGCGGCTCCTCTCTCGGACTC	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	2428	0.484824	0.4644	0.5058	5008	,	,		7573	0.4256		0.4354	False		,,,				2504	0.6094				p.E69K		Atlas-SNP	.											.	HLA-B	54	.	0			c.G205A						PASS	.						34.0	34.0	34.0					6																	31324603		2066	4050	6116	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	GCTCCTCTCTCGG	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.205G>A	6.37:g.31324603C>T	ENSP00000399168:p.Glu69Lys	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	81	40	0.493827	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	367	0.16804029304029305	64	0.13008130081300814	56	0.15469613259668508	115	0.20104895104895104	132	0.1741424802110818	N	1.204	-0.631712	0.03584	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00009	9.48;9.48	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	4.848800	0.01913	U	0.040001	T	0.00012	0.0000	N	0.20483	0.58	0.80722	P	0.0	B;B;P	0.41673	0.0;0.0;0.759	B;B;P	0.50136	0.0;0.0;0.632	T	0.54662	-0.8260	9	0.02654	T	1	.	7.8979	0.29717	0.1052:0.3562:0.0:0.5386	rs9266178	69;69;44	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	K	69;80	ENSP00000399168:E69K;ENSP00000405931:E80K	ENSP00000399168:E69K	E	-	1	0	HLA-B	31432582	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-4.600000	0.00210	-3.012000	0.00272	-0.833000	0.03075	GAG	C|0.719;T|0.281	0.281	strong		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ANKRD22	118932	hgsc.bcm.edu	37	10	90583092	90583092	+	Missense_Mutation	SNP	T	T	G	rs2304804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90583092T>G	ENST00000371930.4	-	5	653	c.443A>C	c.(442-444)cAg>cCg	p.Q148P	ANKRD22_ENST00000476963.1_5'UTR	NM_144590.2	NP_653191.2	Q5VYY1	ANR22_HUMAN	ankyrin repeat domain 22	148			Q -> P (in dbSNP:rs2304804). {ECO:0000269|PubMed:15489334}.							NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10		Colorectal(252;0.0163)		Colorectal(12;6.29e-05)|COAD - Colon adenocarcinoma(12;7.69e-05)		GATAAGAGACTGGTTTTTCAT	0.498													T|||	421	0.0840655	0.2428	0.0447	5008	,	,		16301	0.004		0.0328	False		,,,				2504	0.0327				p.Q148P		Atlas-SNP	.											.	ANKRD22	23	.	0			c.A443C						PASS	.	T	PRO/GLN	844,3562	333.6+/-303.0	81,682,1440	123.0	125.0	124.0		443	3.3	1.0	10	dbSNP_100	124	349,8251	118.5+/-177.9	8,333,3959	yes	missense	ANKRD22	NM_144590.2	76	89,1015,5399	GG,GT,TT		4.0581,19.1557,9.1727	possibly-damaging	148/192	90583092	1193,11813	2203	4300	6503	SO:0001583	missense	118932	exon5			AGAGACTGGTTTT	BC021671	CCDS7390.1	10q23.31	2013-09-20			ENSG00000152766	ENSG00000152766		"""Ankyrin repeat domain containing"""	28321	protein-coding gene	gene with protein product						12477932	Standard	NM_144590		Approved	MGC22805	uc001kfj.4	Q5VYY1	OTTHUMG00000018699	ENST00000371930.4:c.443A>C	10.37:g.90583092T>G	ENSP00000360998:p.Gln148Pro	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_144590	B2R9Y7|Q8WU06	Missense_Mutation	SNP	ENST00000371930.4	37	CCDS7390.1	166	0.076007326007326	112	0.22764227642276422	21	0.058011049723756904	4	0.006993006993006993	29	0.03825857519788918	T	17.05	3.290814	0.59976	0.191557	0.040581	ENSG00000152766	ENST00000371930	T	0.51574	0.7	5.74	3.3	0.37823	Ankyrin repeat-containing domain (4);	0.322779	0.35040	N	0.003498	T	0.00012	0.0000	N	0.11560	0.145	0.24357	P	0.9948926	P	0.41366	0.747	B	0.41440	0.357	T	0.17349	-1.0372	9	0.37606	T	0.19	-4.7633	9.9863	0.41843	0.27:0.0:0.0:0.73	rs2304804;rs2304804	148	Q5VYY1	ANR22_HUMAN	P	148	ENSP00000360998:Q148P	ENSP00000360998:Q148P	Q	-	2	0	ANKRD22	90573072	1.000000	0.71417	0.989000	0.46669	0.925000	0.55904	1.990000	0.40717	0.385000	0.24970	0.533000	0.62120	CAG	T|0.911;G|0.089	0.089	strong		0.498	ANKRD22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049262.1	NM_144590	
DUOX2	50506	hgsc.bcm.edu	37	15	45398797	45398797	+	Missense_Mutation	SNP	C	C	T	rs373620034		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:45398797C>T	ENST00000603300.1	-	16	2076	c.1874G>A	c.(1873-1875)cGa>cAa	p.R625Q	DUOX2_ENST00000389039.6_Missense_Mutation_p.R625Q	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	625					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTTGTGTTCTCGGCCCCGGAA	0.557																																					p.R625Q		Atlas-SNP	.											DUOX2,NS,carcinoma,-1,1	DUOX2	137	1	0			c.G1874A						PASS	.	C	GLN/ARG	0,4396		0,0,2198	154.0	150.0	151.0		1874	-1.0	1.0	15		151	1,8595	1.2+/-3.3	0,1,4297	no	missense	DUOX2	NM_014080.4	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	625/1549	45398797	1,12991	2198	4298	6496	SO:0001583	missense	50506	exon16			TGTTCTCGGCCCC	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1874G>A	15.37:g.45398797C>T	ENSP00000475084:p.Arg625Gln	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	154	72	0.467532	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357373	0.41801	0.0	1.16E-4	ENSG00000140279	ENST00000389039	.	.	.	5.42	-1.02	0.10135	.	0.584816	0.18081	N	0.152290	T	0.49287	0.1548	M	0.72894	2.215	0.40470	D	0.980336	B;B	0.31931	0.188;0.347	B;B	0.24701	0.023;0.055	T	0.44467	-0.9326	9	0.42905	T	0.14	-3.1592	9.9682	0.41738	0.0:0.6012:0.0:0.3988	.	625;187	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	Q	625	.	ENSP00000373691:R625Q	R	-	2	0	DUOX2	43186089	0.024000	0.19004	0.990000	0.47175	0.648000	0.38561	-0.235000	0.09016	-0.185000	0.10550	0.455000	0.32223	CGA	.	.	weak		0.557	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48259787	48259787	+	Silent	SNP	C	C	T	rs11538664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48259787C>T	ENST00000246802.5	+	11	1337	c.1299C>T	c.(1297-1299)ccC>ccT	p.P433P	SNORD23_ENST00000408876.1_RNA|CTD-2571L23.6_ENST00000602048.1_RNA|GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	433				PEGNILRDRFKSFQRRNMIEPRERAKFKRKYKVKLVEKRAF REIQ -> VLTVSCRGAPCPVMTPSLLPVPPRGYGRHHGCP WAGPVGPMPRG (in Ref. 5). {ECO:0000305}.		intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		TCCTGTAGCCCGAGGGCAACA	0.642													C|||	80	0.0159744	0.0053	0.0043	5008	,	,		17005	0.0069		0.0149	False		,,,				2504	0.0491				p.P433P	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.C1299T						PASS	.	C		49,4357	49.6+/-84.7	0,49,2154	32.0	34.0	33.0		1299	-7.4	0.9	19	dbSNP_120	33	168,8432	77.2+/-139.8	0,168,4132	no	coding-synonymous	GLTSCR2	NM_015710.4		0,217,6286	TT,TC,CC		1.9535,1.1121,1.6685		433/479	48259787	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon11			GTAGCCCGAGGGC	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.1299C>T	19.37:g.48259787C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
GLRX	2745	hgsc.bcm.edu	37	5	95152313	95152313	+	Silent	SNP	A	A	G	rs4561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:95152313A>G	ENST00000379979.4	-	2	276	c.225T>C	c.(223-225)atT>atC	p.I75I	GLRX_ENST00000505427.1_Silent_p.I75I|GLRX_ENST00000512469.2_Silent_p.I75I|GLRX_ENST00000508780.1_Silent_p.I75I|GLRX_ENST00000237858.6_Silent_p.I75I|GLRX_ENST00000507605.1_5'UTR	NM_002064.2	NP_002055.1	P35754	GLRX1_HUMAN	glutaredoxin (thioltransferase)	75	Glutaredoxin. {ECO:0000255|PROSITE- ProRule:PRU00686}.				cell redox homeostasis (GO:0045454)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of membrane potential (GO:0045838)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein deglutathionylation (GO:0080058)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|glutathione disulfide oxidoreductase activity (GO:0015038)|glutathione oxidoreductase activity (GO:0097573)|protein N-terminus binding (GO:0047485)			endometrium(3)|large_intestine(1)|lung(1)	5		all_cancers(142;3.38e-06)|all_epithelial(76;5.66e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;2.62e-16)	Glutathione(DB00143)	AATCTTTACCAATAAAGACTC	0.443													G|||	1509	0.301318	0.3169	0.2752	5008	,	,		19925	0.1716		0.4135	False		,,,				2504	0.317				p.I75I		Atlas-SNP	.											GLRX,NS,carcinoma,-1,1	GLRX	11	1	0			c.T225C						PASS	.	G	,	1469,2937	680.1+/-403.8	248,973,982	71.0	67.0	68.0		225,225	-6.0	0.0	5	dbSNP_52	68	3697,4903	620.4+/-397.1	811,2075,1414	no	coding-synonymous,coding-synonymous	GLRX	NM_001118890.1,NM_002064.2	,	1059,3048,2396	GG,GA,AA		42.9884,33.3409,39.7201	,	75/107,75/107	95152313	5166,7840	2203	4300	6503	SO:0001819	synonymous_variant	2745	exon2			TTTACCAATAAAG		CCDS4078.1	5q14	2008-02-05			ENSG00000173221	ENSG00000173221			4330	protein-coding gene	gene with protein product		600443				8838810	Standard	NM_002064		Approved	GRX, GRX1	uc021ybo.1	P35754	OTTHUMG00000121167	ENST00000379979.4:c.225T>C	5.37:g.95152313A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	145	76	0.524138	NM_001243659	B2R4L2|Q3KQS1|Q6ICT1	Silent	SNP	ENST00000379979.4	37	CCDS4078.1																																																																																			T|0.018;G|0.347	0.347	strong		0.443	GLRX-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370267.1	NM_002064	
ZNF512B	57473	hgsc.bcm.edu	37	20	62641575	62641575	+	Intron	SNP	G	G	A	rs2427588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62641575G>A	ENST00000450537.1	-	1	56				ZNF512B_ENST00000217130.3_Intron|PRPF6_ENST00000535781.1_Silent_p.S403S			Q96KM6	Z512B_HUMAN	zinc finger protein 512B						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)					TTCCAAACTCGGTTCGCTTGT	0.532													G|||	181	0.0361422	0.0507	0.0548	5008	,	,		22873	0.001		0.0716	False		,,,				2504	0.0031				p.S403S		Atlas-SNP	.											PRPF6,NS,carcinoma,+1,1	PRPF6	88	1	0			c.G1209A						PASS	.	G		244,4162	141.5+/-176.9	6,232,1965	130.0	119.0	122.0		1209	-11.4	0.1	20	dbSNP_100	122	551,8049	151.5+/-206.2	17,517,3766	no	coding-synonymous	PRPF6	NM_012469.3		23,749,5731	AA,AG,GG		6.407,5.5379,6.1126		403/942	62641575	795,12211	2203	4300	6503	SO:0001627	intron_variant	24148	exon10			AAACTCGGTTCGC	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.4+38482C>T	20.37:g.62641575G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	37	0.393617	NM_012469	Q08AK9|Q9ULM4	Silent	SNP	ENST00000450537.1	37	CCDS13548.1																																																																																			A|0.057;C|0.007	0.057	strong		0.532	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713	
ZNF587	84914	hgsc.bcm.edu	37	19	58371212	58371212	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58371212A>T	ENST00000339656.5	+	3	1614	c.1432A>T	c.(1432-1434)Agc>Tgc	p.S478C	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF587_ENST00000419854.1_Missense_Mutation_p.S435C|ZNF587_ENST00000423137.1_Missense_Mutation_p.S477C|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		CAATAAGCACAGCGTGACTAT	0.423																																					p.S478C	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.A1432T						PASS	.						156.0	149.0	152.0					19																	58371212		2203	4300	6503	SO:0001583	missense	84914	exon3			AAGCACAGCGTGA	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1432A>T	19.37:g.58371212A>T	ENSP00000345479:p.Ser478Cys	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	250	17	0.068	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	.	.	.	.	.	.	.	.	.	.	.	7.068	0.567735	0.13560	.	.	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.08008	3.14;3.14;3.14	0.882	-0.521	0.11931	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08980	0.0222	M	0.64630	1.985	0.24750	N	0.992985	B;B	0.27140	0.169;0.025	B;B	0.29598	0.104;0.033	T	0.20773	-1.0265	8	0.38643	T	0.18	.	4.8451	0.13510	0.7267:0.0:0.0:0.2733	.	477;478	G3V0H5;Q96SQ5	.;ZN587_HUMAN	C	435;477;478;478;435	ENSP00000393865:S477C;ENSP00000345479:S478C;ENSP00000406999:S435C	ENSP00000345479:S478C	S	+	1	0	ZNF587	63063024	0.000000	0.05858	0.000000	0.03702	0.344000	0.29017	-2.794000	0.00765	-0.256000	0.09473	0.164000	0.16699	AGC	.	.	none		0.423	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
OR8J3	81168	hgsc.bcm.edu	37	11	55904828	55904828	+	Missense_Mutation	SNP	A	A	G	rs11227321	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55904828A>G	ENST00000301529.1	-	1	366	c.367T>C	c.(367-369)Tat>Cat	p.Y123H		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y123H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					ATGGCCACATAGCGGTCATAG	0.507													A|||	517	0.103235	0.0499	0.098	5008	,	,		17549	0.1429		0.1213	False		,,,				2504	0.1196				p.Y123H		Atlas-SNP	.											OR8J3,NS,carcinoma,0,1	OR8J3	112	1	1	Substitution - Missense(1)	stomach(1)	c.T367C						PASS	.	A	HIS/TYR	240,4162	140.8+/-176.2	7,226,1968	150.0	137.0	141.0		367	3.3	1.0	11	dbSNP_120	141	1007,7585	216.6+/-255.6	54,899,3343	no	missense	OR8J3	NM_001004064.1	83	61,1125,5311	GG,GA,AA		11.7202,5.4521,9.5967	possibly-damaging	123/316	55904828	1247,11747	2201	4296	6497	SO:0001583	missense	81168	exon1			CCACATAGCGGTC		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.367T>C	11.37:g.55904828A>G	ENSP00000301529:p.Tyr123His	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	173	98	0.566474	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	253	0.11584249084249085	32	0.06504065040650407	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	A	16.07	3.019022	0.54576	0.054521	0.117202	ENSG00000167822	ENST00000301529	T	0.57273	0.41	3.26	3.26	0.37387	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000031	T	0.00580	0.0019	M	0.90759	3.145	0.30023	P	0.814203	B	0.34226	0.443	B	0.40285	0.325	T	0.39418	-0.9615	9	0.46703	T	0.11	.	11.5522	0.50726	1.0:0.0:0.0:0.0	rs11227321	123	Q8NGG0	OR8J3_HUMAN	H	123	ENSP00000301529:Y123H	ENSP00000301529:Y123H	Y	-	1	0	OR8J3	55661404	0.998000	0.40836	0.952000	0.39060	0.818000	0.46254	3.920000	0.56446	1.268000	0.44264	0.240000	0.17902	TAT	A|0.901;G|0.099	0.099	strong		0.507	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
PCSK1	5122	hgsc.bcm.edu	37	5	95733112	95733112	+	Silent	SNP	A	A	G	rs6233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:95733112A>G	ENST00000311106.3	-	12	1887	c.1650T>C	c.(1648-1650)aaT>aaC	p.N550N	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000513085.1_5'UTR|PCSK1_ENST00000508626.1_Silent_p.N503N	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	550					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TGAAGTCCCAATTCTTAAAGC	0.398													A|||	1717	0.342851	0.4092	0.4078	5008	,	,		18310	0.2401		0.3678	False		,,,				2504	0.2873				p.N550N		Atlas-SNP	.											.	PCSK1	93	.	0			c.T1650C						PASS	.	A	,,	1822,2584	533.9+/-373.8	356,1110,737	118.0	103.0	108.0		1650,1509,720	-6.4	0.9	5	dbSNP_52	108	3230,5370	485.6+/-371.7	590,2050,1660	no	coding-synonymous,coding-synonymous,coding-synonymous	PCSK1	NM_000439.4,NM_001177875.1,NM_001177876.1	,,	946,3160,2397	GG,GA,AA		37.5581,41.3527,38.8436	,,	550/754,503/707,240/444	95733112	5052,7954	2203	4300	6503	SO:0001819	synonymous_variant	5122	exon12			GTCCCAATTCTTA		CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1650T>C	5.37:g.95733112A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	129	60	0.465116	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Silent	SNP	ENST00000311106.3	37	CCDS4081.1																																																																																			A|0.628;G|0.372	0.372	strong		0.398	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
RGPD2	729857	hgsc.bcm.edu	37	2	88125212	88125212	+	Missense_Mutation	SNP	C	C	G	rs192443832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:88125212C>G	ENST00000398146.3	-	1	259	c.37G>C	c.(37-39)Gcc>Ccc	p.A13P	RGPD2_ENST00000327544.6_5'UTR|RGPD2_ENST00000420840.2_Intron			P0DJD1	RGPD2_HUMAN	RANBP2-like and GRIP domain containing 2	13					protein targeting to Golgi (GO:0000042)					breast(1)|pancreas(1)	2						TGCACCGAGGCGAGGTACCGC	0.706													.|||	128	0.0255591	0.003	0.0288	5008	,	,		9675	0.0		0.0577	False		,,,				2504	0.047				p.A13P		Atlas-SNP	.											.	RGPD2	14	.	0			c.G37C						PASS	.	C	PRO/ALA	13,1371		0,13,679	23.0	38.0	33.0		37	1.6	1.0	2		33	170,3012		10,150,1431	no	missense	RGPD2	NM_001078170.2	27	10,163,2110	GG,GC,CC		5.3426,0.9393,4.0079	benign	13/1757	88125212	183,4383	692	1591	2283	SO:0001583	missense	729857	exon1			CCGAGGCGAGGTA		CCDS42710.1, CCDS42710.2	2p11.2	2013-01-10			ENSG00000185304	ENSG00000185304		"""Tetratricopeptide (TTC) repeat domain containing"""	32415	protein-coding gene	gene with protein product		612705				15710750, 15815621	Standard	NM_001078170		Approved	RGP2, RANBP2L2		P0DJD1	OTTHUMG00000153276	ENST00000398146.3:c.37G>C	2.37:g.88125212C>G	ENSP00000381214:p.Ala13Pro	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	276	121	0.438406	NM_001078170	P0C839|Q68DN6|Q6V1X0	Missense_Mutation	SNP	ENST00000398146.3	37	CCDS42710.2	39	0.017857142857142856	3	0.006097560975609756	9	0.024861878453038673	1	0.0017482517482517483	26	0.03430079155672823	.	9.609	1.130713	0.21041	0.009393	0.053426	ENSG00000185304	ENST00000398146	T	0.43294	0.95	1.6	1.6	0.23607	.	.	.	.	.	T	0.11879	0.0289	L	0.40543	1.245	0.80722	D	1	D	0.71674	0.998	D	0.67103	0.949	T	0.04005	-1.0985	9	0.44086	T	0.13	-0.2647	6.5949	0.22667	0.0:1.0:0.0:0.0	.	13	B4DYH0	.	P	13	ENSP00000381214:A13P	ENSP00000381214:A13P	A	-	1	0	RGPD2	87906327	1.000000	0.71417	0.998000	0.56505	0.113000	0.19764	1.187000	0.32090	0.871000	0.35750	0.175000	0.17021	GCC	C|0.975;G|0.025	0.025	strong		0.706	RGPD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330534.2	NM_001078170	
SGOL2	151246	hgsc.bcm.edu	37	2	201437214	201437214	+	Silent	SNP	A	A	G	rs17532679	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:201437214A>G	ENST00000357799.4	+	7	2243	c.2145A>G	c.(2143-2145)aaA>aaG	p.K715K		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	715					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)		p.K715K(1)		NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						TTAGGCAGAAAGTAAATCGGA	0.338													A|||	620	0.123802	0.0711	0.1138	5008	,	,		18421	0.0794		0.2207	False		,,,				2504	0.1483				p.K715K		Atlas-SNP	.											SGOL2,NS,carcinoma,0,1	SGOL2	126	1	1	Substitution - coding silent(1)	stomach(1)	c.A2145G						scavenged	.	A	,,	353,3271		16,321,1475	58.0	52.0	54.0		2145,2145,2145	-0.0	0.1	2	dbSNP_123	54	1629,6511		156,1317,2597	no	coding-synonymous,coding-synonymous,coding-synonymous	SGOL2	NM_001160033.1,NM_001160046.1,NM_152524.5	,,	172,1638,4072	GG,GA,AA		20.0123,9.7406,16.848	,,	715/1261,715/1262,715/1266	201437214	1982,9782	1812	4070	5882	SO:0001819	synonymous_variant	151246	exon7			GCAGAAAGTAAAT	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2145A>G	2.37:g.201437214A>G		Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	150	60	0.4	NM_001160046	Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Silent	SNP	ENST00000357799.4	37	CCDS42796.1																																																																																			A|0.865;G|0.135	0.135	strong		0.338	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
DCHS2	54798	hgsc.bcm.edu	37	4	155312411	155312411	+	Silent	SNP	G	G	A	rs62331900	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155312411G>A	ENST00000357232.4	-	1	38	c.39C>T	c.(37-39)gaC>gaT	p.D13D	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	13					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)		tcttttctccgtcttcattct	0.373													G|||	1610	0.321486	0.4607	0.1311	5008	,	,		19449	0.3403		0.1948	False		,,,				2504	0.3793				p.D13D		Atlas-SNP	.											DCHS2,right_upper_lobe,carcinoma,-2,1	DCHS2	594	1	0			c.C39T						PASS	.	G	,	1711,2693	508.3+/-366.9	348,1015,839	181.0	154.0	163.0		,39	-6.3	0.0	4	dbSNP_129	163	1529,7069	287.3+/-298.2	135,1259,2905	yes	intron,coding-synonymous	DCHS2	NM_001142552.1,NM_017639.3	,	483,2274,3744	AA,AG,GG		17.7832,38.851,24.9192	,	,13/2917	155312411	3240,9762	2202	4299	6501	SO:0001819	synonymous_variant	54798	exon1			TTCTCCGTCTTCA	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.39C>T	4.37:g.155312411G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	53	0.445378	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			G|0.723;A|0.277	0.277	strong		0.373	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
HYI	81888	hgsc.bcm.edu	37	1	43917637	43917637	+	Silent	SNP	G	G	A	rs2251802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43917637G>A	ENST00000372425.4	-	4	669	c.474C>T	c.(472-474)gaC>gaT	p.D158D	HYI-AS1_ENST00000444386.1_RNA|HYI_ENST00000583037.1_Silent_p.D85D|SZT2_ENST00000372442.1_3'UTR|HYI_ENST00000372432.1_Silent_p.D158D|HYI_ENST00000486909.1_Silent_p.D158D|HYI_ENST00000372426.1_Silent_p.D110D|SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372434.1_Silent_p.D183D			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	158							hydroxypyruvate isomerase activity (GO:0008903)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				AGTACTGGGGGTCAGTGATGC	0.597													G|||	1117	0.223043	0.1884	0.389	5008	,	,		18026	0.0784		0.4215	False		,,,				2504	0.0971				p.D183D		Atlas-SNP	.											.	HYI	23	.	0			c.C549T						PASS	.	G	,,	1028,3378	378.5+/-322.9	108,812,1283	106.0	111.0	109.0		474,,474	2.5	1.0	1	dbSNP_100	109	3560,5040	516.2+/-378.8	760,2040,1500	no	coding-synonymous,utr-3,coding-synonymous	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	,,	868,2852,2783	AA,AG,GG		41.3953,23.3318,35.276	,,	158/278,,158/248	43917637	4588,8418	2203	4300	6503	SO:0001819	synonymous_variant	81888	exon5			CTGGGGGTCAGTG		CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"""hydroxypyruvate isomerase homolog (E. coli)"""			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502	ENST00000372425.4:c.474C>T	1.37:g.43917637G>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	NM_001243526	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Silent	SNP	ENST00000372425.4	37	CCDS53309.1	622	0.2847985347985348	103	0.20934959349593496	153	0.42265193370165743	46	0.08041958041958042	320	0.42216358839050133	G	9.510	1.105568	0.20632	0.233318	0.413953	ENSG00000178922	ENST00000470662;ENST00000487366	.	.	.	5.38	2.46	0.29980	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.45948	-0.9226	3	.	.	.	.	4.5099	0.11906	0.2125:0.0:0.5195:0.268	rs2251802;rs3184210;rs17400088;rs17404673;rs17851702;rs2251802	.	.	.	I	77;82	.	.	T	-	2	0	HYI	43690224	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	0.684000	0.25364	0.334000	0.23590	0.462000	0.41574	ACC	G|0.679;A|0.321	0.321	strong		0.597	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207	
TRAF7	84231	hgsc.bcm.edu	37	16	2222286	2222286	+	Silent	SNP	C	C	T	rs11547311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2222286C>T	ENST00000326181.6	+	8	702	c.570C>T	c.(568-570)caC>caT	p.H190H		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	190					activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of MAPK cascade (GO:0043410)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasmic vesicle (GO:0031410)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	23						ACTGCCGGCACGGCTGCCGGG	0.647													C|||	152	0.0303514	0.0038	0.0663	5008	,	,		13645	0.0		0.0795	False		,,,				2504	0.0215				p.H190H		Atlas-SNP	.											.	TRAF7	158	.	0			c.C570T						PASS	.	C		68,4324	57.4+/-93.9	1,66,2129	36.0	38.0	37.0		570	-0.6	1.0	16	dbSNP_120	37	659,7939	164.9+/-217.2	21,617,3661	no	coding-synonymous	TRAF7	NM_032271.2		22,683,5790	TT,TC,CC		7.6646,1.5483,5.5966		190/671	2222286	727,12263	2196	4299	6495	SO:0001819	synonymous_variant	84231	exon8			CCGGCACGGCTGC	AL136921	CCDS10461.1	16p13.3	2013-01-10	2012-02-23	2004-06-04	ENSG00000131653	ENSG00000131653		"""RING-type (C3HC4) zinc fingers"", ""WD repeat domain containing"""	20456	protein-coding gene	gene with protein product		606692	"""ring finger and WD repeat domain 1"", ""TNF receptor-associated factor 7"""	RFWD1		11230166, 15001576	Standard	NM_032271		Approved	RNF119, DKFZp586I021, MGC7807	uc002cow.3	Q6Q0C0	OTTHUMG00000128826	ENST00000326181.6:c.570C>T	16.37:g.2222286C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_032271	Q9H073	Silent	SNP	ENST00000326181.6	37	CCDS10461.1																																																																																			C|0.945;T|0.055	0.055	strong		0.647	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271	
FBXO17	115290	hgsc.bcm.edu	37	19	39440966	39440966	+	5'UTR	SNP	T	T	C	rs2304118	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39440966T>C	ENST00000292852.4	-	0	335				FBXO17_ENST00000595329.1_5'UTR|CTC-360G5.8_ENST00000599996.1_5'Flank|SARS2_ENST00000448145.2_5'Flank	NM_024907.5	NP_079183.4	Q96EF6	FBX17_HUMAN	F-box protein 17							SCF ubiquitin ligase complex (GO:0019005)	glycoprotein binding (GO:0001948)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	7	all_cancers(60;8.37e-07)|all_lung(34;3.71e-07)|Lung NSC(34;4.17e-07)|all_epithelial(25;1.13e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CCATCTCCAGTAGCCAGAGTC	0.731													c|||	2379	0.47504	0.3343	0.3746	5008	,	,		13822	0.6796		0.4195	False		,,,				2504	0.5828				p.L7L		Atlas-SNP	.											.	FBXO17	42	.	0			c.A21G						PASS	.		,	912,2398		186,540,929	2.0	3.0	3.0		,21	-0.3	0.0	19	dbSNP_100	3	2149,4473		479,1191,1641	no	utr-5,coding-synonymous	FBXO17	NM_024907.5,NM_148169.1	,	665,1731,2570	CC,CT,TT		32.4524,27.5529,30.8196	,	,7/288	39440966	3061,6871	1655	3311	4966	SO:0001623	5_prime_UTR_variant	115290	exon2			CTCCAGTAGCCAG	AF386743	CCDS12526.1	19q13.2	2010-07-02	2004-06-15	2004-06-16		ENSG00000269190		"""F-boxes /  ""other"""""	18754	protein-coding gene	gene with protein product	"""F-box only protein 26"""	609094	"""F-box only protein 17"""	FBXO26			Standard	NM_148169		Approved	FBG4, FLJ25205, MGC9379, FLJ11798, Fbx17		Q96EF6		ENST00000292852.4:c.-7A>G	19.37:g.39440966T>C		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	11	4	0.363636	NM_148169	Q96LQ4	Silent	SNP	ENST00000292852.4	37	CCDS12526.1																																																																																			T|0.453;C|0.547	0.547	strong		0.731	FBXO17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463273.1	NM_024907	
PRIMPOL	201973	hgsc.bcm.edu	37	4	185578337	185578337	+	Nonsense_Mutation	SNP	C	C	T	rs145651098		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:185578337C>T	ENST00000314970.6	+	3	476	c.43C>T	c.(43-45)Cga>Tga	p.R15*	PRIMPOL_ENST00000515774.1_Intron|PRIMPOL_ENST00000503752.1_Nonsense_Mutation_p.R15*|PRIMPOL_ENST00000512834.1_Nonsense_Mutation_p.R15*	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	15					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										AATTGAAGAACGAGCATCTCA	0.398																																					p.R15X		Atlas-SNP	.											.	CCDC111	43	.	0			c.C43T						PASS	.	C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	118.0	109.0	112.0		43	5.6	0.9	4	dbSNP_134	112	0,8600		0,0,4300	no	stop-gained	CCDC111	NM_152683.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		15/561	185578337	1,13005	2203	4300	6503	SO:0001587	stop_gained	201973	exon3			GAAGAACGAGCAT	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.43C>T	4.37:g.185578337C>T	ENSP00000313816:p.Arg15*	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Nonsense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	C	37	6.625279	0.97714	2.27E-4	0.0	ENSG00000164306	ENST00000314970;ENST00000503752;ENST00000512834	.	.	.	5.64	5.64	0.86602	.	0.353602	0.27362	N	0.019716	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-2.1277	19.7127	0.96102	0.0:1.0:0.0:0.0	.	.	.	.	X	15	.	ENSP00000313816:R15X	R	+	1	2	CCDC111	185815331	0.999000	0.42202	0.894000	0.35097	0.999000	0.98932	3.362000	0.52314	2.652000	0.90054	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	weak		0.398	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
HIST1H4E	8367	hgsc.bcm.edu	37	6	26205052	26205052	+	Silent	SNP	G	G	A	rs61910695	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26205052G>A	ENST00000360441.4	+	1	195	c.180G>A	c.(178-180)aaG>aaA	p.K60K		NM_003545.3	NP_003536.1	P62805	H4_HUMAN	histone cluster 1, H4e	60					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)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	18		all_hematologic(11;0.196)				GGGTTCTGAAGGTGTTTCTGG	0.567													G|||	338	0.067492	0.0772	0.0548	5008	,	,		17081	0.0615		0.0517	False		,,,				2504	0.0859				p.K60K		Atlas-SNP	.											.	HIST1H4E	22	.	0			c.G180A						PASS	.	G		300,4106		9,282,1912	127.0	117.0	120.0		180	-0.8	0.5	6	dbSNP_129	120	417,8183		11,395,3894	no	coding-synonymous	HIST1H4E	NM_003545.3		20,677,5806	AA,AG,GG		4.8488,6.8089,5.5128		60/104	26205052	717,12289	2203	4300	6503	SO:0001819	synonymous_variant	8367	exon1			TCTGAAGGTGTTT	Z80787	CCDS4593.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198518	ENSG00000276966		"""Histones / Replication-dependent"""	4790	protein-coding gene	gene with protein product		602830	"""H4 histone family, member J"", ""histone 1, H4e"""	H4FJ		9119399, 12408966	Standard	NM_003545		Approved	H4/j	uc003ngy.3	P62805	OTTHUMG00000014441	ENST00000360441.4:c.180G>A	6.37:g.26205052G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	110	64	0.581818	NM_003545	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000360441.4	37	CCDS4593.1																																																																																			G|0.946;A|0.054	0.054	strong		0.567	HIST1H4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040104.1	NM_003545	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110476993	110476993	+	Silent	SNP	A	A	G	rs1673398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110476993A>G	ENST00000378402.5	+	49	8036	c.7932A>G	c.(7930-7932)gcA>gcG	p.A2644A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2644					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CAGTGCCTGCACCTGCAATAT	0.403										HNSCC(38;0.096)			G|||	2582	0.515575	0.3918	0.634	5008	,	,		20498	0.4147		0.504	False		,,,				2504	0.7147				p.A2644A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A7932G						PASS	.	G		1533,2239		321,891,674	131.0	127.0	128.0		7932	-0.9	0.0	8	dbSNP_89	128	4282,3952		1134,2014,969	no	coding-synonymous	PKHD1L1	NM_177531.4		1455,2905,1643	GG,GA,AA		47.9961,40.6416,48.4341		2644/4244	110476993	5815,6191	1886	4117	6003	SO:0001819	synonymous_variant	93035	exon49			GCCTGCACCTGCA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.7932A>G	8.37:g.110476993A>G		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			A|0.525;G|0.475	0.475	strong		0.403	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
PON1	5444	hgsc.bcm.edu	37	7	94937446	94937446	+	Missense_Mutation	SNP	T	T	C	rs662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:94937446T>C	ENST00000222381.3	-	6	806	c.575A>G	c.(574-576)cAa>cGa	p.Q192R	PON1_ENST00000542556.1_Missense_Mutation_p.Q192R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	192			Q -> R (polymorphism important for activity; dbSNP:rs662). {ECO:0000269|PubMed:1657140, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:7916578, ECO:0000269|PubMed:8098250, ECO:0000269|PubMed:8393742, ECO:0000269|PubMed:8393745, ECO:0000269|Ref.8}.		aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)	p.Q192R(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	CTCCCAGGATTGTAAGTAGGG	0.398													C|||	2719	0.542931	0.7526	0.4986	5008	,	,		16184	0.6657		0.2903	False		,,,				2504	0.4243				p.Q192R	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											PON1,NS,carcinoma,0,1	PON1	55	1	1	Substitution - Missense(1)	stomach(1)	c.A575G	GRCh37	CM930596	PON1	M	rs662	PASS	.	C	ARG/GLN	2910,1496	475.5+/-357.3	958,994,251	130.0	108.0	116.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	575	-1.0	0.0	7	dbSNP_36	116	2451,6149	698.1+/-405.0	360,1731,2209	yes	missense	PON1	NM_000446.5	43	1318,2725,2460	CC,CT,TT		28.5,33.9537,41.2194	benign	192/356	94937446	5361,7645	2203	4300	6503	SO:0001583	missense	5444	exon6			CAGGATTGTAAGT	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.575A>G	7.37:g.94937446T>C	ENSP00000222381:p.Gln192Arg	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	105	44	0.419048	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	1127	0.5160256410256411	368	0.7479674796747967	172	0.47513812154696133	367	0.6416083916083916	220	0.29023746701846964	C	0.090	-1.168995	0.01660	0.660463	0.285	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.45276	0.9;0.9	5.04	-1.02	0.10135	Six-bladed beta-propeller, TolB-like (1);	0.663414	0.14660	N	0.306026	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33189	-0.9878	9	0.09084	T	0.74	-0.0356	8.8215	0.35030	0.1205:0.2374:0.0:0.6421	rs662;rs11567868;rs13306697;rs17773773;rs60480675;rs662	192;192	F5H4W9;P27169	.;PON1_HUMAN	R	192	ENSP00000222381:Q192R;ENSP00000444854:Q192R	ENSP00000222381:Q192R	Q	-	2	0	PON1	94775382	0.000000	0.05858	0.001000	0.08648	0.185000	0.23345	-1.304000	0.02741	-0.587000	0.05890	-0.215000	0.12644	CAA	T|0.544;C|0.456	0.456	strong		0.398	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
SPAG17	200162	hgsc.bcm.edu	37	1	118537074	118537074	+	Silent	SNP	A	A	G	rs12031260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:118537074A>G	ENST00000336338.5	-	35	5198	c.5133T>C	c.(5131-5133)ccT>ccC	p.P1711P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1711						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GGAGATTAGGAGGGACAATTG	0.418													A|||	643	0.128395	0.034	0.0418	5008	,	,		19044	0.3204		0.0616	False		,,,				2504	0.1881				p.P1711P		Atlas-SNP	.											.	SPAG17	263	.	0			c.T5133C						PASS	.	A		182,4224	115.0+/-153.0	4,174,2025	189.0	165.0	173.0		5133	2.0	1.0	1	dbSNP_120	173	491,8107	143.0+/-199.1	16,459,3824	no	coding-synonymous	SPAG17	NM_206996.2		20,633,5849	GG,GA,AA		5.7106,4.1307,5.1753		1711/2224	118537074	673,12331	2203	4299	6502	SO:0001819	synonymous_variant	200162	exon35			ATTAGGAGGGACA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5133T>C	1.37:g.118537074A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			A|0.919;G|0.081	0.081	strong		0.418	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
COG8	84342	hgsc.bcm.edu	37	16	69373414	69373414	+	Silent	SNP	T	T	C	rs11542583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:69373414T>C	ENST00000306875.4	-	1	156	c.42A>G	c.(40-42)acA>acG	p.T14T	RP11-343C2.9_ENST00000563634.1_Intron|NIP7_ENST00000569637.2_5'Flank|NIP7_ENST00000254940.5_5'UTR|COG8_ENST00000562081.1_Silent_p.T14T|RP11-343C2.7_ENST00000564737.1_Intron|NIP7_ENST00000254941.6_5'Flank	NM_032382.4	NP_115758.3	Q96MW5	COG8_HUMAN	component of oligomeric golgi complex 8	14					protein transport (GO:0015031)	Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|kidney(1)|large_intestine(2)|ovary(2)|skin(1)	9						GAGCCGCTGCTGTGGCCGTGG	0.677													C|||	1290	0.257588	0.3192	0.2161	5008	,	,		14793	0.0833		0.2853	False		,,,				2504	0.3548				p.T14T		Atlas-SNP	.											.	COG8	32	.	0			c.A42G						PASS	.	C		1459,2839		233,993,923	15.0	15.0	15.0		42	-1.1	0.0	16	dbSNP_120	15	2691,5805		446,1799,2003	no	coding-synonymous	COG8	NM_032382.4		679,2792,2926	CC,CT,TT		31.6737,33.946,32.4371		14/613	69373414	4150,8644	2149	4248	6397	SO:0001819	synonymous_variant	84342	exon1			CGCTGCTGTGGCC	AK025968	CCDS10876.1	16q22.1	2011-05-31			ENSG00000213380	ENSG00000213380		"""Components of oligomeric golgi complex"""	18623	protein-coding gene	gene with protein product		606979				11980916	Standard	NM_032382		Approved	FLJ22315, DOR1	uc002ewy.2	Q96MW5	OTTHUMG00000154277	ENST00000306875.4:c.42A>G	16.37:g.69373414T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	33	15	0.454545	NM_032382	Q0VAK2|Q8WVV6|Q9H6F8	Silent	SNP	ENST00000306875.4	37	CCDS10876.1																																																																																			T|0.711;C|0.289	0.289	strong		0.677	COG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268948.2	NM_032382	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383012	39383012	+	Missense_Mutation	SNP	C	C	T	rs9903833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39383012C>T	ENST00000377721.3	+	1	113	c.106C>T	c.(106-108)Ccc>Tcc	p.P36S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.P36S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	36	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].		P -> S (in dbSNP:rs9903833). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CAGCAGCACACCCTGCTGCCA	0.642																																					p.P36S		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.C106T						PASS	.						51.0	47.0	48.0					17																	39383012		2202	4298	6500	SO:0001583	missense	83899	exon1			AGCACACCCTGCT	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.106C>T	17.37:g.39383012C>T	ENSP00000366950:p.Pro36Ser	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	1204	0.5512820512820513	262	0.532520325203252	227	0.6270718232044199	298	0.5209790209790209	417	0.5501319261213721	.	7.176	0.588686	0.13812	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01159	5.57;5.25	2.85	0.535	0.17133	.	.	.	.	.	T	0.00012	0.0000	N	0.01751	-0.74	0.44221	P	0.002942	B	0.22604	0.072	B	0.19666	0.026	T	0.11966	-1.0566	8	0.02654	T	1	.	7.7358	0.28812	0.5744:0.4256:0.0:0.0	rs9903833;rs60053887	36	Q9BYQ4	KRA92_HUMAN	S	36	ENSP00000366950:P36S;ENSP00000398325:P36S	ENSP00000366950:P36S	P	+	1	0	KRTAP9-2	36636538	0.000000	0.05858	0.320000	0.25306	0.991000	0.79684	-2.240000	0.01197	0.134000	0.18681	0.552000	0.68991	CCC	C|0.448;T|0.552	0.552	strong		0.642	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
MUC16	94025	hgsc.bcm.edu	37	19	9069892	9069892	+	Missense_Mutation	SNP	A	A	C	rs1862460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9069892A>C	ENST00000397910.4	-	3	17757	c.17554T>G	c.(17554-17556)Ttt>Gtt	p.F5852V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5854	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						CCTGTTACAAAAGGAAAAGTG	0.478													C|||	1275	0.254593	0.2905	0.2911	5008	,	,		21340	0.3264		0.169	False		,,,				2504	0.1943				p.F5852V		Atlas-SNP	.											.	MUC16	4315	.	0			c.T17554G						PASS	.	C	VAL/PHE	1008,2846		132,744,1051	207.0	193.0	198.0		17554	-0.7	0.0	19	dbSNP_92	198	1514,6724		138,1238,2743	yes	missense	MUC16	NM_024690.2	50	270,1982,3794	CC,CA,AA		18.3782,26.1546,20.8568	benign	5852/14508	9069892	2522,9570	1927	4119	6046	SO:0001583	missense	94025	exon3			TTACAAAAGGAAA	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.17554T>G	19.37:g.9069892A>C	ENSP00000381008:p.Phe5852Val	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	244	123	0.504098	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	549	0.25137362637362637	125	0.2540650406504065	93	0.2569060773480663	205	0.3583916083916084	126	0.1662269129287599	c	3.417	-0.118983	0.06838	0.261546	0.183782	ENSG00000181143	ENST00000397910	T	0.02682	4.2	1.74	-0.715	0.11215	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.44997	-0.9291	8	0.87932	D	0	.	2.8277	0.05490	0.4787:0.3557:0.0:0.1656	rs1862460;rs52808057;rs57945851;rs1862460	5852	B5ME49	.	V	5852	ENSP00000381008:F5852V	ENSP00000381008:F5852V	F	-	1	0	MUC16	8930892	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.147000	0.01293	-0.452000	0.07087	-0.729000	0.03580	TTT	A|0.755;C|0.245	0.245	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZRANB3	84083	hgsc.bcm.edu	37	2	135965376	135965376	+	Silent	SNP	T	T	C	rs7578111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:135965376T>C	ENST00000264159.6	-	19	2753	c.2637A>G	c.(2635-2637)ccA>ccG	p.P879P	ZRANB3_ENST00000401392.1_Silent_p.P877P|ZRANB3_ENST00000536680.1_Silent_p.P877P|ZRANB3_ENST00000412849.1_5'UTR	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	879					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		GATTTAGAAATGGGACACAGG	0.378													T|||	1365	0.272564	0.3472	0.2666	5008	,	,		21232	0.2173		0.1352	False		,,,				2504	0.3742				p.P879P		Atlas-SNP	.											.	ZRANB3	109	.	0			c.A2637G						PASS	.	T		1200,2594		199,802,896	73.0	68.0	69.0		2637	-1.2	0.4	2	dbSNP_116	69	828,7430		49,730,3350	no	coding-synonymous	ZRANB3	NM_032143.2		248,1532,4246	CC,CT,TT		10.0266,31.6289,16.8271		879/1080	135965376	2028,10024	1897	4129	6026	SO:0001819	synonymous_variant	84083	exon19			TAGAAATGGGACA	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.2637A>G	2.37:g.135965376T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Silent	SNP	ENST00000264159.6	37	CCDS46419.1																																																																																			T|0.792;C|0.208	0.208	strong		0.378	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
GOT2	2806	hgsc.bcm.edu	37	16	58757683	58757683	+	Silent	SNP	A	A	G	rs257636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58757683A>G	ENST00000245206.5	-	2	341	c.213T>C	c.(211-213)aaT>aaC	p.N71N	GOT2_ENST00000434819.2_Silent_p.N71N|GOT2_ENST00000564400.1_5'UTR	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	71					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	AAGGCTTTCCATTATCATCCC	0.498													G|||	3453	0.689497	0.8238	0.7594	5008	,	,		20246	0.6032		0.661	False		,,,				2504	0.5767				p.N71N		Atlas-SNP	.											.	GOT2	42	.	0			c.T213C						PASS	.	G		3474,922	353.1+/-312.0	1360,754,84	209.0	211.0	210.0		213	-2.0	1.0	16	dbSNP_79	210	5580,3020	466.1+/-366.7	1808,1964,528	yes	coding-synonymous	GOT2	NM_002080.2		3168,2718,612	GG,GA,AA		35.1163,20.9736,30.3324		71/431	58757683	9054,3942	2198	4300	6498	SO:0001819	synonymous_variant	2806	exon2			CTTTCCATTATCA		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.213T>C	16.37:g.58757683A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	200	196	0.98	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1																																																																																			A|0.308;G|0.692	0.692	strong		0.498	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
DTWD1	56986	hgsc.bcm.edu	37	15	49917401	49917401	+	Missense_Mutation	SNP	G	G	A	rs11539519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:49917401G>A	ENST00000251250.6	+	3	244	c.37G>A	c.(37-39)Gaa>Aaa	p.E13K	DTWD1_ENST00000559223.1_3'UTR|DTWD1_ENST00000403028.3_Missense_Mutation_p.E13K|DTWD1_ENST00000558653.1_Missense_Mutation_p.E13K|DTWD1_ENST00000329873.5_Missense_Mutation_p.E13K	NM_020234.5	NP_064619.2	Q8N5C7	DTWD1_HUMAN	DTW domain containing 1	13			E -> K (in dbSNP:rs11539519).							endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;0.0384)		all cancers(107;3.27e-08)|GBM - Glioblastoma multiforme(94;7.6e-05)		CAAACGAAGTGAAGAAAATAG	0.333													G|||	72	0.014377	0.0363	0.0144	5008	,	,		17721	0.001		0.0119	False		,,,				2504	0.001				p.E13K		Atlas-SNP	.											.	DTWD1	22	.	0			c.G37A						PASS	.	G	LYS/GLU,LYS/GLU	126,4266	87.8+/-126.4	2,122,2072	43.0	43.0	43.0		37,37	1.9	1.0	15	dbSNP_120	43	144,8442	67.7+/-130.1	0,144,4149	no	missense,missense	DTWD1	NM_001144955.1,NM_020234.5	56,56	2,266,6221	AA,AG,GG		1.6771,2.8689,2.0804	benign,benign	13/305,13/305	49917401	270,12708	2196	4293	6489	SO:0001583	missense	56986	exon2			CGAAGTGAAGAAA	BC032535	CCDS10132.1	15q21.2	2005-08-09			ENSG00000104047	ENSG00000104047			30926	protein-coding gene	gene with protein product							Standard	NM_020234		Approved	MDS009, MGC111207	uc001zxs.3	Q8N5C7	OTTHUMG00000131567	ENST00000251250.6:c.37G>A	15.37:g.49917401G>A	ENSP00000251250:p.Glu13Lys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_001144955	Q567Q3|Q8WVG9|Q9NRU6	Missense_Mutation	SNP	ENST00000251250.6	37	CCDS10132.1	34	0.015567765567765568	22	0.044715447154471545	5	0.013812154696132596	0	0.0	7	0.009234828496042216	G	10.29	1.309848	0.23821	0.028689	0.016771	ENSG00000104047	ENST00000403028;ENST00000329873;ENST00000251250	T;T;T	0.24350	1.96;1.86;1.96	5.09	1.92	0.25849	.	0.685348	0.15354	N	0.266812	T	0.02888	0.0086	N	0.17674	0.51	0.32329	N	0.561328	B	0.09022	0.002	B	0.08055	0.003	T	0.15178	-1.0446	9	.	.	.	-17.9555	7.332	0.26588	0.2145:0.14:0.6455:0.0	rs11539519;rs52801911;rs11539519	13	Q8N5C7	DTWD1_HUMAN	K	13	ENSP00000385399:E13K;ENSP00000329313:E13K;ENSP00000251250:E13K	.	E	+	1	0	DTWD1	47704693	0.090000	0.21635	0.978000	0.43139	0.407000	0.30961	0.075000	0.14686	1.223000	0.43536	0.591000	0.81541	GAA	G|0.982;A|0.018	0.018	strong		0.333	DTWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254431.2	NM_020234	
COL5A1	1289	hgsc.bcm.edu	37	9	137619195	137619195	+	Silent	SNP	C	C	T	rs3124299	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:137619195C>T	ENST00000371817.3	+	5	1152	c.738C>T	c.(736-738)acC>acT	p.T246T		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	246	Nonhelical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		ACTGTGACACCGCAGTACCTG	0.537													C|||	1716	0.342652	0.0424	0.5519	5008	,	,		18306	0.4077		0.4652	False		,,,				2504	0.407				p.T246T		Atlas-SNP	.											.	COL5A1	323	.	0			c.C738T						PASS	.	C		427,3979	204.8+/-226.9	33,361,1809	107.0	94.0	98.0		738	-8.4	0.0	9	dbSNP_103	98	3893,4707	545.0+/-384.7	895,2103,1302	yes	coding-synonymous	COL5A1	NM_000093.3		928,2464,3111	TT,TC,CC		45.2674,9.6913,33.2154		246/1839	137619195	4320,8686	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon5			TGACACCGCAGTA	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.738C>T	9.37:g.137619195C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	48	0.470588	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			C|0.665;T|0.335	0.335	strong		0.537	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
NDOR1	27158	hgsc.bcm.edu	37	9	140108857	140108857	+	Silent	SNP	T	T	C	rs73563696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140108857T>C	ENST00000344894.5	+	6	797	c.714T>C	c.(712-714)tcT>tcC	p.S238S	NDOR1_ENST00000458322.2_Silent_p.S238S|NDOR1_ENST00000371521.4_Silent_p.S238S|NDOR1_ENST00000427047.2_Silent_p.S204S	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		TCTTGGGCTCTGGCATCAGGT	0.632													C|||	705	0.140775	0.0817	0.1282	5008	,	,		16006	0.2014		0.1362	False		,,,				2504	0.1718				p.S238S		Atlas-SNP	.											.	NDOR1	71	.	0			c.T714C						PASS	.	C	,,,	439,3967	785.4+/-414.7	28,383,1792	80.0	82.0	81.0		714,612,714,714	-9.1	0.0	9	dbSNP_130	81	1083,7517	769.2+/-407.6	81,921,3298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDOR1	NM_001144026.1,NM_001144027.1,NM_001144028.1,NM_014434.2	,,,	109,1304,5090	CC,CT,TT		12.593,9.9637,11.7023	,,,	238/607,204/522,238/591,238/598	140108857	1522,11484	2203	4300	6503	SO:0001819	synonymous_variant	27158	exon6			GGGCTCTGGCATC	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"""NADPH dependent FMN and FAD containing oxidoreductase"""	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.714T>C	9.37:g.140108857T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	50	0.45045	NM_001144026		Silent	SNP	ENST00000344894.5	37	CCDS7036.1																																																																																			T|0.875;C|0.125	0.125	strong		0.632	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434	
DSPP	1834	hgsc.bcm.edu	37	4	88535869	88535869	+	Silent	SNP	C	C	T	rs200233307		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88535869C>T	ENST00000282478.7	+	4	2088	c.2055C>T	c.(2053-2055)aaC>aaT	p.N685N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.N685N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	685	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		acagcagcaacagcagtgata	0.478																																					p.N685N		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	0			c.C2055T						PASS	.						116.0	132.0	126.0					4																	88535869		1685	3089	4774	SO:0001819	synonymous_variant	1834	exon5			CAGCAACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2055C>T	4.37:g.88535869C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	194	20	0.103093	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.478	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254064	30254064	+	Missense_Mutation	SNP	C	C	T	rs201131077		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:30254064C>T	ENST00000361644.2	+	5	760	c.23C>T	c.(22-24)aCg>aTg	p.T8M		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	8										NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						CAGAAGAGTACGCTCCATGCA	0.542																																					p.T8M		Atlas-SNP	.											.	MAGEB3	54	.	0			c.C23T						PASS	.	A	MET/THR	0,3833		0,0,1631,571	61.0	51.0	55.0		23	-1.8	0.0	X		55	1,6727		0,1,2427,1872	yes	missense	MAGEB3	NM_002365.4	81	0,1,4058,2443	TT,TC,CC,C		0.0149,0.0,0.0095	possibly-damaging	8/347	30254064	1,10560	2202	4300	6502	SO:0001583	missense	4114	exon5			AGAGTACGCTCCA	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.23C>T	X.37:g.30254064C>T	ENSP00000355198:p.Thr8Met	Somatic	122	1	0.00819672		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_002365	A0AVE4|B3KQ52|O75861	Missense_Mutation	SNP	ENST00000361644.2	37	CCDS14220.1	.	.	.	.	.	.	.	.	.	.	c	13.20	2.166490	0.38217	0.0	1.49E-4	ENSG00000198798	ENST00000378986;ENST00000361644	T;T	0.04360	3.64;3.64	3.77	-1.77	0.07982	Melanoma associated antigen, MAGE, N-terminal (1);	11.449600	0.01612	U	0.022560	T	0.07052	0.0179	N	0.22421	0.69	0.09310	N	1	D	0.54397	0.966	P	0.51701	0.677	T	0.22591	-1.0212	10	0.87932	D	0	.	5.614	0.17420	0.5656:0.3294:0.1051:0.0	.	8	O15480	MAGB3_HUMAN	M	8	ENSP00000368271:T8M;ENSP00000355198:T8M	ENSP00000355198:T8M	T	+	2	0	MAGEB3	30163985	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.113000	0.15499	-0.461000	0.06993	-1.548000	0.00902	ACG	.	.	weak		0.542	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
TP53BP1	7158	hgsc.bcm.edu	37	15	43724646	43724646	+	Missense_Mutation	SNP	T	T	G	rs2602141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43724646T>G	ENST00000263801.3	-	17	3658	c.3406A>C	c.(3406-3408)Aag>Cag	p.K1136Q	TP53BP1_ENST00000450115.2_Missense_Mutation_p.K1141Q|TP53BP1_ENST00000382039.3_Missense_Mutation_p.K1141Q|TP53BP1_ENST00000382044.4_Missense_Mutation_p.K1141Q	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1136			K -> Q (in dbSNP:rs2602141). {ECO:0000269|PubMed:17974005, ECO:0000269|Ref.4}.		cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|replication fork (GO:0005657)	damaged DNA binding (GO:0003684)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription cofactor activity (GO:0001104)|telomeric DNA binding (GO:0042162)			breast(4)|endometrium(5)|kidney(7)|large_intestine(22)|lung(13)|ovary(4)|pancreas(2)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(3)	72		all_cancers(109;6.94e-11)|all_epithelial(112;2.69e-09)|Lung NSC(122;7.86e-07)|all_lung(180;7.84e-06)|Melanoma(134;0.0728)		GBM - Glioblastoma multiforme(94;1.59e-06)		GGATTTTCCTTATTAGTACTC	0.468								Other conserved DNA damage response genes					G|||	2636	0.526358	0.9584	0.3285	5008	,	,		20922	0.3869		0.3032	False		,,,				2504	0.456				p.K1141Q		Atlas-SNP	.											.	TP53BP1	157	.	0			c.A3421C	GRCh37	CM067476	TP53BP1	M	rs2602141	PASS	.	G	GLN/LYS,GLN/LYS,GLN/LYS	3676,726	301.8+/-287.1	1539,598,64	134.0	125.0	128.0		3421,3421,3406	4.4	1.0	15	dbSNP_100	128	2610,5986	687.4+/-404.2	389,1832,2077	yes	missense,missense,missense	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	53,53,53	1928,2430,2141	GG,GT,TT		30.363,16.4925,48.3613	benign,benign,benign	1141/1976,1141/1978,1136/1973	43724646	6286,6712	2201	4298	6499	SO:0001583	missense	7158	exon17			TTTCCTTATTAGT	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.3406A>C	15.37:g.43724646T>G	ENSP00000263801:p.Lys1136Gln	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	212	98	0.462264	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	1066	0.4880952380952381	460	0.9349593495934959	124	0.3425414364640884	252	0.4405594405594406	230	0.3034300791556728	G	5.579	0.291690	0.10567	0.835075	0.30363	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.03635	3.86;3.86;3.88;3.86	5.42	4.45	0.53987	.	0.106561	0.42420	N	0.000707	T	0.00012	0.0000	N	0.00128	-2.045	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	0.29941	-0.9995	9	0.02654	T	1	-0.3537	11.308	0.49347	0.0:0.1372:0.7204:0.1424	rs2602141;rs3803338;rs58179572;rs2602141	1141;1136;1141;1141	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	Q	1136;1141;1141;1141	ENSP00000263801:K1136Q;ENSP00000371475:K1141Q;ENSP00000371470:K1141Q;ENSP00000393497:K1141Q	ENSP00000263801:K1136Q	K	-	1	0	TP53BP1	41511938	0.998000	0.40836	0.984000	0.44739	0.860000	0.49131	3.261000	0.51530	1.452000	0.47756	-0.121000	0.15023	AAG	G|0.508;N|0.000	0.508	strong		0.468	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
GAK	2580	hgsc.bcm.edu	37	4	843720	843720	+	Missense_Mutation	SNP	T	T	C	rs2306242	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:843720T>C	ENST00000314167.4	-	27	3904	c.3794A>G	c.(3793-3795)aAg>aGg	p.K1265R	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Missense_Mutation_p.K1186R	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1265	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.		K -> R (in dbSNP:rs2306242). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		GCGATAGTGCTTCTTCACTTG	0.721													T|||	177	0.0353435	0.0061	0.0346	5008	,	,		13707	0.0863		0.0368	False		,,,				2504	0.0215				p.K1265R		Atlas-SNP	.											.	GAK	104	.	0			c.A3794G						PASS	.	T	ARG/LYS	43,4361	38.4+/-70.7	0,43,2159	24.0	24.0	24.0		3794	4.6	1.0	4	dbSNP_100	24	327,8271	102.3+/-163.5	3,321,3975	yes	missense	GAK	NM_005255.2	26	3,364,6134	CC,CT,TT		3.8032,0.9764,2.8457	benign	1265/1312	843720	370,12632	2202	4299	6501	SO:0001583	missense	2580	exon27			TAGTGCTTCTTCA	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.3794A>G	4.37:g.843720T>C	ENSP00000314499:p.Lys1265Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	109|109	0.04990842490842491|0.04990842490842491	3|3	0.006097560975609756|0.006097560975609756	16|16	0.04419889502762431|0.04419889502762431	61|61	0.10664335664335664|0.10664335664335664	29|29	0.03825857519788918|0.03825857519788918	T|T	12.58|12.58	1.980464|1.980464	0.34942|0.34942	0.009764|0.009764	0.038032|0.038032	ENSG00000178950|ENSG00000178950	ENST00000398567;ENST00000314167;ENST00000511163|ENST00000511980	T;T|.	0.27890|.	1.64;1.64|.	4.55|4.55	4.55|4.55	0.56014|0.56014	Heat shock protein DnaJ, N-terminal (5);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.01523|0.01523	0.0049|0.0049	L|L	0.42581|0.42581	1.335|1.335	0.19575|0.19575	P|P	0.9999673675|0.9999673675	B;B;B;B|.	0.19073|.	0.005;0.005;0.005;0.033|.	B;B;B;B|.	0.32465|.	0.096;0.031;0.096;0.146|.	T|T	0.26573|0.26573	-1.0099|-1.0099	9|4	0.66056|.	D|.	0.02|.	-23.9045|-23.9045	12.1453|12.1453	0.54020|0.54020	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs2306242;rs2306242|rs2306242;rs2306242	1167;1186;1265;1150|.	B4DS37;E9PGR2;O14976;Q59HA5|.	.;.;GAK_HUMAN;.|.	R|G	541;1265;1186|421	ENSP00000314499:K1265R;ENSP00000421361:K1186R|.	ENSP00000314499:K1265R|.	K|S	-|-	2|1	0|0	GAK|GAK	833720|833720	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.290000|0.290000	0.27261|0.27261	4.000000|4.000000	0.57039|0.57039	1.807000|1.807000	0.52817|0.52817	0.519000|0.519000	0.50382|0.50382	AAG|AGC	T|0.963;C|0.037	0.037	strong		0.721	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
FOXN4	121643	hgsc.bcm.edu	37	12	109717697	109717697	+	Silent	SNP	A	A	G	rs10774641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109717697A>G	ENST00000299162.5	-	10	1437	c.1333T>C	c.(1333-1335)Ttg>Ctg	p.L445L	FOXN4_ENST00000355216.1_Silent_p.L265L	NM_213596.2	NP_998761.2	Q96NZ1	FOXN4_HUMAN	forkhead box N4	445					amacrine cell differentiation (GO:0035881)|atrioventricular canal development (GO:0036302)|heart looping (GO:0001947)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of heart contraction (GO:0008016)|regulation of transcription, DNA-templated (GO:0006355)|retina layer formation (GO:0010842)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(5)|lung(9)|ovary(2)	16						AGTGTGTCCAAGCTGAATCCC	0.577													A|||	1505	0.300519	0.1467	0.3401	5008	,	,		17925	0.2857		0.4901	False		,,,				2504	0.3006				p.L445L		Atlas-SNP	.											.	FOXN4	74	.	0			c.T1333C						PASS	.	A		797,3609	319.1+/-295.9	77,643,1483	96.0	74.0	82.0		1333	3.0	1.0	12	dbSNP_120	82	3984,4616	550.4+/-385.7	909,2166,1225	no	coding-synonymous	FOXN4	NM_213596.2		986,2809,2708	GG,GA,AA		46.3256,18.089,36.76		445/518	109717697	4781,8225	2203	4300	6503	SO:0001819	synonymous_variant	121643	exon10			TGTCCAAGCTGAA	AF425596	CCDS9126.2	12q24.12	2008-02-05			ENSG00000139445	ENSG00000139445		"""Forkhead boxes"""	21399	protein-coding gene	gene with protein product		609429					Standard	NM_213596		Approved		uc001toe.4	Q96NZ1	OTTHUMG00000152868	ENST00000299162.5:c.1333T>C	12.37:g.109717697A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_213596	Q6ZMR4|Q96NZ0	Silent	SNP	ENST00000299162.5	37	CCDS9126.2																																																																																			A|0.660;G|0.340	0.340	strong		0.577	FOXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328306.1	XM_062735	
ITIH1	3697	hgsc.bcm.edu	37	3	52821011	52821011	+	Missense_Mutation	SNP	A	A	G	rs1042779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52821011A>G	ENST00000273283.2	+	14	1808	c.1784A>G	c.(1783-1785)cAg>cGg	p.Q595R	ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000537050.1_Missense_Mutation_p.Q307R|ITIH1_ENST00000542827.1_Missense_Mutation_p.Q595R|ITIH1_ENST00000540715.1_Missense_Mutation_p.Q453R	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	595	Hyaluronan-binding.		Q -> R (in allele ITIH1*2 and allele ITIH1*3; dbSNP:rs1042779). {ECO:0000269|PubMed:1380832, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7535743}.		hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		CAGGCCCTGCAGATGTCGCTG	0.617													G|||	2127	0.42472	0.5393	0.487	5008	,	,		17314	0.379		0.3986	False		,,,				2504	0.2996				p.Q595R		Atlas-SNP	.											.	ITIH1	108	.	0			c.A1784G						PASS	.	G	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	2127,2279	597.4+/-388.9	508,1111,584	91.0	84.0	86.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1358,920,920,1784	3.0	0.4	3	dbSNP_86	86	3330,5270	645.1+/-400.1	670,1990,1640	yes	missense,missense,missense,missense	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	43,43,43,43	1178,3101,2224	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	38.7209,48.2751,41.9576	benign,benign,benign,benign	453/770,307/624,307/624,595/912	52821011	5457,7549	2203	4300	6503	SO:0001583	missense	3697	exon14			CCCTGCAGATGTC		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.1784A>G	3.37:g.52821011A>G	ENSP00000273283:p.Gln595Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	138	54	0.391304	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	1006	0.4606227106227106	271	0.5508130081300813	176	0.4861878453038674	254	0.44405594405594406	305	0.4023746701846966	G	4.384	0.070936	0.08436	0.482751	0.387209	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.44	2.96	0.34315	.	0.733154	0.14237	N	0.332314	T	0.00012	0.0000	M	0.68593	2.085	0.80722	P	0.0	B;B;B	0.24882	0.008;0.113;0.0	B;B;B	0.22880	0.042;0.033;0.002	T	0.41998	-0.9477	9	0.27082	T	0.32	-3.4004	7.1456	0.25581	0.7294:0.1253:0.1452:0.0	rs1042779;rs3182234;rs17418937;rs52791326;rs57378468;rs1042779	453;196;595	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	R	595;595;453;307;148	ENSP00000442584:Q595R;ENSP00000273283:Q595R;ENSP00000443973:Q453R;ENSP00000443847:Q307R;ENSP00000395836:Q148R	ENSP00000273283:Q595R	Q	+	2	0	ITIH1	52796051	1.000000	0.71417	0.438000	0.26821	0.003000	0.03518	2.813000	0.48002	0.165000	0.19558	-1.088000	0.02184	CAG	A|0.564;G|0.436	0.436	strong		0.617	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
KRT26	353288	hgsc.bcm.edu	37	17	38927462	38927462	+	Silent	SNP	G	G	A	rs113285472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38927462G>A	ENST00000335552.4	-	2	516	c.468C>T	c.(466-468)gcC>gcT	p.A156A		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				GAACAATGCTGGCATTGCAGA	0.348													G|||	6	0.00119808	0.0	0.0014	5008	,	,		15657	0.0		0.005	False		,,,				2504	0.0				p.A156A		Atlas-SNP	.											.	KRT26	49	.	0			c.C468T						PASS	.	G		7,4399	11.4+/-27.6	0,7,2196	43.0	43.0	43.0		468	5.3	1.0	17	dbSNP_132	43	41,8559	25.7+/-73.6	0,41,4259	no	coding-synonymous	KRT26	NM_181539.4		0,48,6455	AA,AG,GG		0.4767,0.1589,0.3691		156/469	38927462	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	353288	exon2			AATGCTGGCATTG	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30840	protein-coding gene	gene with protein product			"""keratin 25B"""	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.468C>T	17.37:g.38927462G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_181539		Silent	SNP	ENST00000335552.4	37	CCDS11374.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539	
OR7G1	125962	hgsc.bcm.edu	37	19	9226017	9226017	+	Missense_Mutation	SNP	C	C	G	rs2217657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9226017C>G	ENST00000541538.1	-	1	422	c.423G>C	c.(421-423)tgG>tgC	p.W141C	OR7G1_ENST00000293614.1_Missense_Mutation_p.W141C	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	141			W -> C (in dbSNP:rs2217657).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						TCAGCAAGCCCCAGAAATGGA	0.493													G|||	2538	0.506789	0.8896	0.2781	5008	,	,		20452	0.3562		0.328	False		,,,				2504	0.4908				p.W141C		Atlas-SNP	.											OR7G1,NS,carcinoma,0,3	OR7G1	53	3	0			c.G423C						PASS	.	G	CYS/TRP	3479,927		1391,697,115	82.0	86.0	85.0		423	1.6	0.0	19	dbSNP_96	85	2756,5844		462,1832,2006	yes	missense	OR7G1	NM_001005192.2	215	1853,2529,2121	GG,GC,CC		32.0465,21.0395,47.9394	benign	141/312	9226017	6235,6771	2203	4300	6503	SO:0001583	missense	125962	exon1			CAAGCCCCAGAAA		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"""GPCR / Class A : Olfactory receptors"""	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.423G>C	19.37:g.9226017C>G	ENSP00000444134:p.Trp141Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_001005192	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	969	0.44368131868131866	436	0.8861788617886179	98	0.27071823204419887	194	0.33916083916083917	241	0.3179419525065963	a	0	-2.659280	0.00108	0.789605	0.320465	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.33865	1.39;1.39	3.78	1.58	0.23477	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41938	N	0.000781	T	0.00012	0.0000	N	0.00016	-2.855	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32666	-0.9898	9	0.02654	T	1	.	5.2712	0.15627	0.6745:0.1497:0.1759:0.0	rs2217657;rs17238774;rs52793601;rs59648625;rs2217657	141	Q8NGA0	OR7G1_HUMAN	C	141	ENSP00000293614:W141C;ENSP00000444134:W141C	ENSP00000293614:W141C	W	-	3	0	OR7G1	9087017	0.000000	0.05858	0.008000	0.14137	0.003000	0.03518	-0.383000	0.07398	-0.132000	0.11557	-2.681000	0.00142	TGG	G|0.476;C|0.522;A|0.002	0.476	strong		0.493	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1		
PKD1	5310	hgsc.bcm.edu	37	16	2156021	2156021	+	Silent	SNP	A	A	G	rs28575767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2156021A>G	ENST00000262304.4	-	20	7916	c.7708T>C	c.(7708-7710)Ttg>Ctg	p.L2570L	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Silent_p.L2570L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2570	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GTGATGGCCAAAGACCTACGA	0.701													g|||	890	0.177716	0.5212	0.1383	5008	,	,		15830	0.0		0.0905	False		,,,				2504	0.0143				p.L2570L		Atlas-SNP	.											PKD1,right_upper_lobe,carcinoma,+2,1	PKD1	184	1	0			c.T7708C						scavenged	.						23.0	36.0	31.0					16																	2156021		1407	2607	4014	SO:0001819	synonymous_variant	5310	exon20			TGGCCAAAGACCT	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.7708T>C	16.37:g.2156021A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.873;G|0.127	0.127	strong		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
TESC	54997	hgsc.bcm.edu	37	12	117486947	117486947	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117486947G>T	ENST00000335209.7	-	4	412	c.226C>A	c.(226-228)Ccc>Acc	p.P76T	TESC_ENST00000535198.1_5'UTR|TESC_ENST00000541210.1_Missense_Mutation_p.P49T|TESC_ENST00000392545.4_Missense_Mutation_p.P129T			Q96BS2	CHP3_HUMAN	tescalcin	76					cell differentiation (GO:0030154)|cellular response to retinoic acid (GO:0071300)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell proliferation (GO:0008285)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of sodium:proton antiporter activity (GO:0032417)|positive regulation of transcription, DNA-templated (GO:0045893)|protein maturation (GO:0051604)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of cell adhesion mediated by integrin (GO:0033628)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphatase inhibitor activity (GO:0019212)|protein homodimerization activity (GO:0042803)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0297)		AGGCCACTGGGTCCCTTGCGC	0.537																																					p.P76T		Atlas-SNP	.											.	TESC	16	.	0			c.C226A						PASS	.						131.0	119.0	123.0					12																	117486947		2203	4300	6503	SO:0001583	missense	54997	exon4			CACTGGGTCCCTT	AF443207	CCDS9183.2, CCDS9183.3, CCDS53835.1	12q24.22	2013-01-10			ENSG00000088992	ENSG00000088992		"""EF-hand domain containing"""	26065	protein-coding gene	gene with protein product	"""calcineurin-like EF hand protein 3"""	611585				11145610, 11696366, 12809501, 14661968	Standard	NM_017899		Approved	TSC, FLJ20607, CHP3	uc001twh.3	Q96BS2	OTTHUMG00000144168	ENST00000335209.7:c.226C>A	12.37:g.117486947G>T	ENSP00000334785:p.Pro76Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	73	31	0.424658	NM_017899	F5H1Y5|Q9NWT9	Missense_Mutation	SNP	ENST00000335209.7	37	CCDS9183.3	.	.	.	.	.	.	.	.	.	.	G	7.196	0.592551	0.13875	.	.	ENSG00000088992	ENST00000335209;ENST00000392545;ENST00000541210	T;T;T	0.39997	1.05;1.05;1.13	5.92	0.671	0.17929	EF-hand-like domain (1);	0.691593	0.14781	N	0.298762	T	0.18635	0.0447	N	0.13043	0.29	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22243	-1.0222	10	0.14252	T	0.57	-11.9903	2.8483	0.05550	0.3475:0.109:0.4322:0.1112	.	76	Q96BS2	TESC_HUMAN	T	76;129;49	ENSP00000334785:P76T;ENSP00000376328:P129T;ENSP00000445689:P49T	ENSP00000334785:P76T	P	-	1	0	TESC	115971330	0.000000	0.05858	0.478000	0.27316	0.638000	0.38207	-0.280000	0.08468	-0.381000	0.07882	-1.164000	0.01763	CCC	.	.	none		0.537	TESC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291363.2	NM_017899	
VRK1	7443	hgsc.bcm.edu	37	14	97321689	97321689	+	Silent	SNP	C	C	T	rs2230532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:97321689C>T	ENST00000216639.3	+	8	854	c.705C>T	c.(703-705)ggC>ggT	p.G235G		NM_003384.2	NP_003375.1	Q99986	VRK1_HUMAN	vaccinia related kinase 1	235	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Golgi disassembly (GO:0090166)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-T3 phosphorylation (GO:0072355)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi stack (GO:0005795)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H3-S10 specific) (GO:0035175)|histone kinase activity (H3-T3 specific) (GO:0072354)|nucleosomal histone binding (GO:0031493)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(5)|lung(3)|skin(1)|stomach(1)	12		Melanoma(154;0.155)		COAD - Colon adenocarcinoma(157;0.234)		CACACAATGGCGTGGGTATGT	0.393													C|||	2087	0.416733	0.1649	0.4928	5008	,	,		19633	0.8442		0.3698	False		,,,				2504	0.3108				p.G235G		Atlas-SNP	.											.	VRK1	34	.	0			c.C705T						PASS	.	C		753,3653	309.1+/-290.9	67,619,1517	116.0	103.0	108.0		705	-6.1	0.6	14	dbSNP_98	108	3022,5578	465.1+/-366.4	560,1902,1838	yes	coding-synonymous	VRK1	NM_003384.2		627,2521,3355	TT,TC,CC		35.1395,17.0903,29.0251		235/397	97321689	3775,9231	2203	4300	6503	SO:0001819	synonymous_variant	7443	exon8			CAATGGCGTGGGT	AB000449	CCDS9947.1	14q32.2	2012-07-05			ENSG00000100749	ENSG00000100749			12718	protein-coding gene	gene with protein product		602168				9344656	Standard	XM_006720247		Approved		uc001yft.3	Q99986	OTTHUMG00000171459	ENST00000216639.3:c.705C>T	14.37:g.97321689C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_003384	Q3SYL2	Silent	SNP	ENST00000216639.3	37	CCDS9947.1	1001	0.4583333333333333	81	0.16463414634146342	159	0.43922651933701656	486	0.8496503496503497	275	0.3627968337730871	C	9.288	1.049864	0.19827	0.170903	0.351395	ENSG00000100749	ENST00000557222;ENST00000557352	.	.	.	6.05	-6.05	0.02172	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11084	-1.0602	3	.	.	.	-22.2293	9.1188	0.36775	0.1465:0.5561:0.0:0.2974	rs2230532;rs11160370;rs11557224;rs57291592;rs2230532	.	.	.	C	92;17	.	.	R	+	1	0	VRK1	96391442	0.127000	0.22367	0.628000	0.29241	0.800000	0.45204	-0.690000	0.05138	-1.420000	0.02009	-0.813000	0.03139	CGT	C|0.650;T|0.350	0.350	strong		0.393	VRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413520.1	NM_003384	
NLRP5	126206	hgsc.bcm.edu	37	19	56538976	56538976	+	Missense_Mutation	SNP	G	G	C	rs471979	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56538976G>C	ENST00000390649.3	+	7	1377	c.1377G>C	c.(1375-1377)atG>atC	p.M459I		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	459	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		M -> I (in dbSNP:rs471979). {ECO:0000269|PubMed:11925379}.		cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			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)		GTGCGATCATGAACAACCGTG	0.602													G|||	626	0.125	0.0567	0.0908	5008	,	,		18103	0.1369		0.1213	False		,,,				2504	0.2331				p.M459I		Atlas-SNP	.											.	NLRP5	217	.	0			c.G1377C						PASS	.	G	ILE/MET	241,3969		4,233,1868	43.0	47.0	46.0		1377	-0.7	0.0	19	dbSNP_83	46	944,7514		50,844,3335	yes	missense	NLRP5	NM_153447.4	10	54,1077,5203	CC,CG,GG		11.161,5.7245,9.3543	benign	459/1201	56538976	1185,11483	2105	4229	6334	SO:0001583	missense	126206	exon7			GATCATGAACAAC	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.1377G>C	19.37:g.56538976G>C	ENSP00000375063:p.Met459Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	240	0.10989010989010989	20	0.04065040650406504	38	0.10497237569060773	87	0.1520979020979021	95	0.12532981530343007	G	1.003	-0.690390	0.03303	0.057245	0.11161	ENSG00000171487	ENST00000390649	T	0.71222	-0.55	2.72	-0.707	0.11245	.	1.448660	0.04827	N	0.438036	T	0.00328	0.0010	N	0.11255	0.115	0.80722	P	0.0	B	0.10296	0.003	B	0.12837	0.008	T	0.02257	-1.1187	9	0.34782	T	0.22	.	2.9776	0.05942	0.2901:0.2393:0.4706:0.0	rs471979;rs17646093;rs471979	459	P59047	NALP5_HUMAN	I	459	ENSP00000375063:M459I	ENSP00000375063:M459I	M	+	3	0	NLRP5	61230788	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.516000	0.06282	-0.074000	0.12820	0.655000	0.94253	ATG	G|0.894;C|0.106	0.106	strong		0.602	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
OR11H6	122748	hgsc.bcm.edu	37	14	20692643	20692643	+	Missense_Mutation	SNP	T	T	C	rs17277228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20692643T>C	ENST00000315519.2	+	1	853	c.775T>C	c.(775-777)Tgt>Cgt	p.C259R		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	259			C -> R (in dbSNP:rs17277228).			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)		TTTCTCCACATGTGGGTCCCA	0.493													t|||	1958	0.390974	0.4735	0.3516	5008	,	,		21989	0.2371		0.4781	False		,,,				2504	0.3763				p.C259R		Atlas-SNP	.											.	OR11H6	60	.	0			c.T775C						PASS	.	T	ARG/CYS	2257,2149	595.8+/-388.5	611,1035,557	110.0	93.0	99.0		775	4.8	1.0	14	dbSNP_123	99	4157,4443	566.4+/-388.7	997,2163,1140	yes	missense	OR11H6	NM_001004480.1	180	1608,3198,1697	CC,CT,TT		48.3372,48.7744,49.3157	probably-damaging	259/331	20692643	6414,6592	2203	4300	6503	SO:0001583	missense	122748	exon1			TCCACATGTGGGT		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.775T>C	14.37:g.20692643T>C	ENSP00000319071:p.Cys259Arg	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	169	70	0.414201	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	870	0.3983516483516483	237	0.4817073170731707	135	0.3729281767955801	123	0.21503496503496503	375	0.4947229551451187	T	16.90	3.250844	0.59212	0.512256	0.483372	ENSG00000176219	ENST00000315519	T	0.00372	7.73	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000045	T	0.00012	0.0000	H	0.96970	3.915	0.09310	P	0.999999854784	D	0.89917	1.0	D	0.97110	1.0	T	0.12734	-1.0536	9	0.87932	D	0	.	12.2972	0.54854	0.0:0.0:0.0:1.0	rs17277228;rs52820021;rs60871786;rs17277228	259	Q8NGC7	O11H6_HUMAN	R	259	ENSP00000319071:C259R	ENSP00000319071:C259R	C	+	1	0	OR11H6	19762483	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.410000	0.80065	2.000000	0.58554	0.386000	0.25728	TGT	C|0.445;N|0.001	0.445	strong		0.493	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
MUC16	94025	hgsc.bcm.edu	37	19	9048320	9048320	+	Missense_Mutation	SNP	C	C	T	rs56334501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9048320C>T	ENST00000397910.4	-	5	33514	c.33311G>A	c.(33310-33312)aGt>aAt	p.S11104N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11106	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						TGCCCTGGAACTAGTGACCAG	0.527													C|||	927	0.185104	0.062	0.2752	5008	,	,		22994	0.3363		0.167	False		,,,				2504	0.1503				p.S11104N		Atlas-SNP	.											.	MUC16	4315	.	0			c.G33311A						PASS	.		ASN/SER	306,3534		15,276,1629	76.0	69.0	71.0		33311	0.3	0.0	19	dbSNP_129	71	1502,6772		137,1228,2772	yes	missense	MUC16	NM_024690.2	46	152,1504,4401	TT,TC,CC		18.1533,7.9687,14.9249	benign	11104/14508	9048320	1808,10306	1920	4137	6057	SO:0001583	missense	94025	exon5			CTGGAACTAGTGA	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.33311G>A	19.37:g.9048320C>T	ENSP00000381008:p.Ser11104Asn	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	52	0.460177	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	464	0.21245421245421245	34	0.06910569105691057	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	c	12.98	2.099153	0.37048	0.079687	0.181533	ENSG00000181143	ENST00000397910	T	0.02656	4.21	2.94	0.273	0.15650	.	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	.	.	.	B	0.34226	0.443	B	0.37888	0.26	T	0.45469	-0.9259	8	0.87932	D	0	.	7.801	0.29174	0.5775:0.4225:0.0:0.0	rs56334501;rs61745162	11104	B5ME49	.	N	11104	ENSP00000381008:S11104N	ENSP00000381008:S11104N	S	-	2	0	MUC16	8909320	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.768000	0.01794	0.105000	0.17753	-0.345000	0.07892	AGT	C|0.795;T|0.205	0.205	strong		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRAMEF11	440560	hgsc.bcm.edu	37	1	12885088	12885088	+	Silent	SNP	G	G	A	rs201576084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12885088G>A	ENST00000535591.1	-	4	1218	c.1023C>T	c.(1021-1023)aaC>aaT	p.N341N	RP5-845O24.8_ENST00000438401.1_lincRNA	NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	341					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						AGCTGAAGGTGTTGAGCTCAA	0.522													.|||	2	0.000399361	0.0	0.0	5008	,	,		19269	0.002		0.0	False		,,,				2504	0.0				p.N341N		Atlas-SNP	.											PRAMEF11,NS,carcinoma,-2,2	PRAMEF11	72	2	0			c.C1023T						scavenged	.						25.0	19.0	21.0					1																	12885088		692	1577	2269	SO:0001819	synonymous_variant	440560	exon4			GAAGGTGTTGAGC	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.1023C>T	1.37:g.12885088G>A		Somatic	160	2	0.0125		WXS	Illumina HiSeq	Phase_I	175	3	0.0171429	NM_001146344		Silent	SNP	ENST00000535591.1	37	CCDS53268.1																																																																																			G|0.500;A|0.500	0.500	weak		0.522	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341	
EBF4	57593	hgsc.bcm.edu	37	20	2739583	2739583	+	Silent	SNP	T	T	C	rs2073125	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:2739583T>C	ENST00000609451.1	+	16	1839	c.1767T>C	c.(1765-1767)ttT>ttC	p.F589F	EBF4_ENST00000477287.1_3'UTR|EBF4_ENST00000380648.4_Silent_p.F585F			Q9BQW3	COE4_HUMAN	early B-cell factor 4	589					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)										CTGACAAGTTTCACTCTCCAG	0.582													C|||	1929	0.385184	0.3404	0.2565	5008	,	,		17183	0.5417		0.2982	False		,,,				2504	0.4652				p.F585F		Atlas-SNP	.											.	.	.	.	0			c.T1755C						PASS	.	C		544,840		104,336,252	122.0	105.0	110.0		1755	3.8	1.0	20	dbSNP_96	110	973,2209		153,667,771	no	coding-synonymous	EBF4	NM_001110514.1		257,1003,1023	CC,CT,TT		30.5783,39.3064,33.2238		585/599	2739583	1517,3049	692	1591	2283	SO:0001819	synonymous_variant	57593	exon17			CAAGTTTCACTCT	BC019106	CCDS46573.1	20p13	2008-10-23			ENSG00000088881	ENSG00000088881			29278	protein-coding gene	gene with protein product		609935				10718198	Standard	NM_001110514		Approved	KIAA1442, COE4, RP5-860F19.3, O/E-4	uc002wgt.4	Q9BQW3	OTTHUMG00000031709	ENST00000609451.1:c.1767T>C	20.37:g.2739583T>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	108	44	0.407407	NM_001110514	Q1MTP7|Q5JY53|Q9NUB6|Q9P2A6	Silent	SNP	ENST00000609451.1	37																																																																																				T|0.647;C|0.353	0.353	strong		0.582	EBF4-011	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471930.1	XM_938882	
CYP24A1	1591	hgsc.bcm.edu	37	20	52786219	52786219	+	Silent	SNP	G	G	A	rs2296241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:52786219G>A	ENST00000216862.3	-	4	945	c.552C>T	c.(550-552)gcC>gcT	p.A184A	CYP24A1_ENST00000395954.3_Silent_p.A42A|CYP24A1_ENST00000395955.3_Silent_p.A184A	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	184					osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|response to vitamin D (GO:0033280)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D catabolic process (GO:0042369)|vitamin D metabolic process (GO:0042359)|vitamin D receptor signaling pathway (GO:0070561)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)	1-alpha,25-dihydroxyvitamin D3 24-hydroxylase activity (GO:0030342)|25-hydroxycholecalciferol-24-hydroxylase activity (GO:0008403)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity (GO:0016491)			breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(4;1.08e-05)|all_lung(4;2.7e-05)		STAD - Stomach adenocarcinoma(23;0.206)		Calcidiol(DB00146)|Calcipotriol(DB02300)|Calcitriol(DB00136)|Corticotropin(DB01285)|Ergocalciferol(DB00153)|Paricalcitol(DB00910)	CCATAAAATCGGCCAAGACCT	0.408													A|||	2294	0.458067	0.4917	0.4222	5008	,	,		21649	0.4058		0.5328	False		,,,				2504	0.4151				p.A184A		Atlas-SNP	.											CYP24A1,trunk,malignant_melanoma,-1,1	CYP24A1	75	1	0			c.C552T						PASS	.	A	,	2184,2222	590.7+/-387.4	515,1154,534	106.0	92.0	97.0		552,552	-3.5	1.0	20	dbSNP_100	97	4635,3965	551.3+/-385.9	1236,2163,901	yes	coding-synonymous,coding-synonymous	CYP24A1	NM_000782.4,NM_001128915.1	,	1751,3317,1435	AA,AG,GG		46.1047,49.5688,47.5704	,	184/515,184/449	52786219	6819,6187	2203	4300	6503	SO:0001819	synonymous_variant	1591	exon4			AAAATCGGCCAAG	U60669	CCDS33491.1, CCDS46616.1	20q13.2-q13.3	2003-02-28	2003-02-14	2003-02-28	ENSG00000019186	ENSG00000019186		"""Cytochrome P450s"""	2602	protein-coding gene	gene with protein product		126065	"""cytochrome P450, subfamily XXIV (vitamin D 24-hydroxylase)"""	CYP24			Standard	NM_000782		Approved	CP24, P450-CC24	uc002xwv.2	Q07973	OTTHUMG00000032773	ENST00000216862.3:c.552C>T	20.37:g.52786219G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_000782	Q15807|Q32ML3|Q5I2W7	Silent	SNP	ENST00000216862.3	37	CCDS33491.1																																																																																			G|0.500;A|0.500	0.500	strong		0.408	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2		
AMT	275	hgsc.bcm.edu	37	3	49459683	49459683	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49459683G>A	ENST00000273588.3	-	2	414	c.112C>T	c.(112-114)Ctc>Ttc	p.L38F	AMT_ENST00000546031.1_Intron|AMT_ENST00000458307.2_Missense_Mutation_p.L38F|NICN1-AS1_ENST00000424915.1_RNA|AMT_ENST00000395338.2_Missense_Mutation_p.L38F|AMT_ENST00000538581.1_Intron|NICN1_ENST00000422593.1_5'Flank|AMT_ENST00000476226.1_5'UTR	NM_000481.3	NP_000472.2	P48728	GCST_HUMAN	aminomethyltransferase	38					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|transaminase activity (GO:0008483)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Tetrahydrofolic acid(DB00116)	AAGTCATAGAGCGGTGTCCTG	0.657																																					p.L38F		Atlas-SNP	.											.	AMT	22	.	0			c.C112T						PASS	.						101.0	105.0	103.0					3																	49459683		2203	4300	6503	SO:0001583	missense	275	exon2			CATAGAGCGGTGT	D13811	CCDS2797.1, CCDS54583.1, CCDS54584.1, CCDS54585.1	3p21.2-p21.1	2014-09-17	2006-05-22		ENSG00000145020	ENSG00000145020	2.1.2.10		473	protein-coding gene	gene with protein product	"""glycine cleavage system protein T"""	238310	"""aminomethyltransferase (glycine cleavage system protein T)"""			1993704, 8188235	Standard	NM_000481		Approved	GCST, NKH	uc003cww.3	P48728	OTTHUMG00000156847	ENST00000273588.3:c.112C>T	3.37:g.49459683G>A	ENSP00000273588:p.Leu38Phe	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	23	0.242105	NM_001164712	A8K3I5|B4DE61|B4DJQ0|E9PBG1|Q96IG6	Missense_Mutation	SNP	ENST00000273588.3	37	CCDS2797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.53|15.53	2.861431|2.861431	0.51482|0.51482	.|.	.|.	ENSG00000145020|ENSG00000145020	ENST00000427987|ENST00000395338;ENST00000458307;ENST00000273588	.|D;D;D	.|0.86097	.|-2.07;-2.07;-2.07	5.22|5.22	4.33|4.33	0.51752|0.51752	.|.	.|0.148983	.|0.46145	.|D	.|0.000309	D|D	0.90089|0.90089	0.6904|0.6904	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;1.0	D|D	0.90373|0.90373	0.4382|0.4382	5|10	.|0.59425	.|D	.|0.04	-14.4114|-14.4114	13.1666|13.1666	0.59575|0.59575	0.0:0.0:0.8386:0.1614|0.0:0.0:0.8386:0.1614	.|.	.|38;38;38	.|B4DJQ0;E9PBG1;P48728	.|.;.;GCST_HUMAN	V|F	35|38	.|ENSP00000378747:L38F;ENSP00000415619:L38F;ENSP00000273588:L38F	.|ENSP00000273588:L38F	A|L	-|-	2|1	0|0	AMT|AMT	49434687|49434687	1.000000|1.000000	0.71417|0.71417	0.034000|0.034000	0.17996|0.17996	0.003000|0.003000	0.03518|0.03518	9.009000|9.009000	0.93606|0.93606	1.299000|1.299000	0.44798|0.44798	-0.181000|-0.181000	0.13052|0.13052	GCT|CTC	.	.	none		0.657	AMT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346216.2	NM_000481	
PSG7	5676	hgsc.bcm.edu	37	19	43433805	43433805	+	RNA	SNP	A	A	G	rs1065178	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:43433805A>G	ENST00000406070.2	-	0	594				PSG7_ENST00000446844.3_RNA	NM_002783.2	NP_002774.2	Q13046	PSG7_HUMAN	pregnancy specific beta-1-glycoprotein 7 (gene/pseudogene)						female pregnancy (GO:0007565)	extracellular region (GO:0005576)							Prostate(69;0.00682)				CACAGGTTAAAATCACAGCCT	0.527													.|||	2229	0.445088	0.5666	0.4294	5008	,	,		18641	0.4216		0.2704	False		,,,				2504	0.4959				p.I44I		Atlas-SNP	.											.	.	.	.	0			c.T132C						PASS	.	G	,	2464,1938		733,998,470	220.0	217.0	218.0		132,498	-2.7	0.0	19	dbSNP_86	218	2421,6179		400,1621,2279	no	coding-synonymous,coding-synonymous	PSG7	NM_001206650.1,NM_002783.2	,	1133,2619,2749	GG,GA,AA		28.1512,44.0254,37.5711	,	44/298,166/420	43433805	4885,8117	2201	4300	6501			5676	exon2			GGTTAAAATCACA			19q13.2	2013-01-29	2010-02-26		ENSG00000221878	ENSG00000221878		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9524	protein-coding gene	gene with protein product		176396	"""pregnancy specific beta-1-glycoprotein 7"""				Standard	NM_002783		Approved		uc010xwl.2	Q13046	OTTHUMG00000151125		19.37:g.43433805A>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_001206650	Q15232	Silent	SNP	ENST00000406070.2	37																																																																																				A|0.622;G|0.378	0.378	strong		0.527	PSG7-001	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000321431.2	NM_001206650	
CD2BP2	10421	hgsc.bcm.edu	37	16	30364805	30364805	+	Missense_Mutation	SNP	C	C	T	rs13330462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30364805C>T	ENST00000305596.3	-	5	867	c.692G>A	c.(691-693)gGt>gAt	p.G231D	CD2BP2_ENST00000569466.1_Missense_Mutation_p.G231D|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_006110.2	NP_006101.1	O95400	CD2B2_HUMAN	CD2 (cytoplasmic tail) binding protein 2	231			G -> D (in dbSNP:rs13330462).		gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of phosphatase activity (GO:0010923)|RNA splicing (GO:0008380)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	ribonucleoprotein complex binding (GO:0043021)			breast(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	15						ACACCCCAAACCCTTCAGACG	0.632													c|||	517	0.103235	0.3359	0.0432	5008	,	,		16256	0.001		0.0119	False		,,,				2504	0.0307				p.G231D		Atlas-SNP	.											.	CD2BP2	30	.	0			c.G692A						PASS	.	C	ASP/GLY	1197,3197	418.5+/-338.3	163,871,1163	65.0	64.0	65.0		692	3.4	1.0	16	dbSNP_121	65	119,8481	61.7+/-123.6	1,117,4182	yes	missense	CD2BP2	NM_006110.2	94	164,988,5345	TT,TC,CC		1.3837,27.2417,10.1278	benign	231/342	30364805	1316,11678	2197	4300	6497	SO:0001583	missense	10421	exon5			CCCAAACCCTTCA	AF104222	CCDS10675.1	16p11.2	2012-04-17	2006-03-28		ENSG00000169217	ENSG00000169217		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 59"""	604470	"""CD2 antigen (cytoplasmic tail)-binding protein 2"""			9843987	Standard	NM_006110		Approved	LIN1, Snu40, PPP1R59	uc002dxs.3	O95400	OTTHUMG00000132397	ENST00000305596.3:c.692G>A	16.37:g.30364805C>T	ENSP00000304903:p.Gly231Asp	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_006110	B2RDX2|Q9ULP2	Missense_Mutation	SNP	ENST00000305596.3	37	CCDS10675.1	184	0.08424908424908426	154	0.3130081300813008	20	0.055248618784530384	1	0.0017482517482517483	9	0.011873350923482849	c	10.63	1.405572	0.25378	0.272417	0.013837	ENSG00000169217	ENST00000305596	T	0.28666	1.6	5.51	3.4	0.38934	.	0.446171	0.27631	N	0.018511	T	0.00012	0.0000	L	0.27053	0.805	0.31159	P	0.704604	B	0.27559	0.181	B	0.18561	0.022	T	0.39961	-0.9588	9	0.13108	T	0.6	-0.0537	14.0925	0.65000	0.0:0.6336:0.3664:0.0	rs13330462;rs13330462	231	O95400	CD2B2_HUMAN	D	231	ENSP00000304903:G231D	ENSP00000304903:G231D	G	-	2	0	CD2BP2	30272306	0.332000	0.24722	0.977000	0.42913	0.887000	0.51463	0.830000	0.27462	1.314000	0.45095	0.643000	0.83706	GGT	C|0.892;T|0.108	0.108	strong		0.632	CD2BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255528.1	NM_006110	
AHSG	197	hgsc.bcm.edu	37	3	186330969	186330969	+	Silent	SNP	C	C	G	rs4831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:186330969C>G	ENST00000273784.5	+	1	115	c.39C>G	c.(37-39)ctC>ctG	p.L13L	AHSG_ENST00000411641.2_Silent_p.L13L	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	13					acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)	p.L13L(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		TTGCTCAGCTCTGGGGCTGCC	0.597													.|||	1089	0.217452	0.3797	0.1542	5008	,	,		16331	0.126		0.1581	False		,,,				2504	0.1984				p.L13L		Atlas-SNP	.											AHSG,NS,carcinoma,0,1	AHSG	40	1	1	Substitution - coding silent(1)	stomach(1)	c.C39G						PASS	.	C		1418,2988	459.0+/-352.1	221,976,1006	39.0	41.0	40.0		39	2.9	1.0	3	dbSNP_52	40	1266,7334	251.1+/-277.7	96,1074,3130	no	coding-synonymous	AHSG	NM_001622.2		317,2050,4136	GG,GC,CC		14.7209,32.1834,20.6366		13/368	186330969	2684,10322	2203	4300	6503	SO:0001819	synonymous_variant	197	exon1			TCAGCTCTGGGGC	D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.39C>G	3.37:g.186330969C>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	96	39	0.40625	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Silent	SNP	ENST00000273784.5	37																																																																																				C|0.798;G|0.202	0.202	strong		0.597	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622	
PARVB	29780	hgsc.bcm.edu	37	22	44395451	44395451	+	Missense_Mutation	SNP	T	T	C	rs1007863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:44395451T>C	ENST00000406477.3	+	2	239	c.109T>C	c.(109-111)Tgg>Cgg	p.W37R		NM_001003828.2	NP_001003828.1	Q9HBI1	PARVB_HUMAN	parvin, beta	0					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)		p.W37R(1)		NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				ttcctgcagctggggcctgtg	0.517													t|||	2664	0.531949	0.674	0.5014	5008	,	,		16851	0.4623		0.4344	False		,,,				2504	0.5337				p.W37R		Atlas-SNP	.											PARVB,NS,carcinoma,0,1	PARVB	44	1	1	Substitution - Missense(1)	stomach(1)	c.T109C						PASS	.	C	ARG/TRP	2375,1695		712,951,372	91.0	98.0	96.0		109	-3.8	0.0	22	dbSNP_86	96	3171,5173		631,1909,1632	yes	missense	PARVB	NM_001003828.2	101	1343,2860,2004	CC,CT,TT		38.0034,41.6462,44.6754		37/398	44395451	5546,6868	2035	4172	6207	SO:0001583	missense	29780	exon2			TGCAGCTGGGGCC	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000406477.3:c.109T>C	22.37:g.44395451T>C	ENSP00000384515:p.Trp37Arg	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	145	78	0.537931	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000406477.3	37	CCDS46724.1	1113	0.5096153846153846	313	0.6361788617886179	178	0.49171270718232046	291	0.5087412587412588	331	0.4366754617414248	C	0.014	-1.586745	0.00872	0.583538	0.380034	ENSG00000188677	ENST00000406477	T	0.35048	1.33	1.91	-3.83	0.04269	.	1.001040	0.08064	N	0.998800	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.41520	-0.9504	9	0.06891	T	0.86	-4.2361	7.888	0.29661	0.0:0.5695:0.0:0.4305	rs1007863;rs52789429;rs1007863	37	Q9HBI1-2	.	R	37	ENSP00000384515:W37R	ENSP00000384515:W37R	W	+	1	0	PARVB	42726784	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.505000	0.00963	-1.311000	0.02309	-1.645000	0.00762	TGG	T|0.506;C|0.494	0.494	strong		0.517	PARVB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319517.1	NM_001003828	
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1814440	1814440	+	Missense_Mutation	SNP	A	A	G	rs2294619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1814440A>G	ENST00000250894.4	+	19	2414	c.2257A>G	c.(2257-2259)Acg>Gcg	p.T753A	MAPK8IP3_ENST00000356010.5_Missense_Mutation_p.T747A	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	753			T -> A (in dbSNP:rs2294619).		activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						GAGCGCCCACACGTCTCCCGA	0.657													A|||	1482	0.295927	0.382	0.3386	5008	,	,		16930	0.2639		0.1988	False		,,,				2504	0.2822				p.T753A		Atlas-SNP	.											MAPK8IP3_ENST00000250894,NS,carcinoma,0,2	MAPK8IP3	164	2	0			c.A2257G						PASS	.	A	ALA/THR,ALA/THR	1365,2797		237,891,953	20.0	26.0	24.0		2239,2257	-3.8	0.2	16	dbSNP_100	24	1544,6870		144,1256,2807	yes	missense,missense	MAPK8IP3	NM_001040439.1,NM_015133.3	58,58	381,2147,3760	GG,GA,AA		18.3504,32.7967,23.1314	benign,benign	747/1331,753/1337	1814440	2909,9667	2081	4207	6288	SO:0001583	missense	23162	exon19			GCCCACACGTCTC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.2257A>G	16.37:g.1814440A>G	ENSP00000250894:p.Thr753Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Missense_Mutation	SNP	ENST00000250894.4	37	CCDS10442.2	569	0.26053113553113555	167	0.3394308943089431	103	0.2845303867403315	144	0.2517482517482518	155	0.20448548812664907	a	7.199	0.593035	0.13875	0.327967	0.183504	ENSG00000138834	ENST00000250894;ENST00000356010	T;T	0.29917	1.55;1.55	4.99	-3.85	0.04243	.	0.438582	0.25978	N	0.027089	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	6.999999999979245E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.0;0.001;0.002	T	0.43228	-0.9404	9	0.10377	T	0.69	-0.7791	2.6217	0.04918	0.5542:0.1115:0.2229:0.1114	rs2294619;rs58067579;rs2294619	754;747;753	B7ZMF3;E9PFH7;Q9UPT6	.;.;JIP3_HUMAN	A	753;747	ENSP00000250894:T753A;ENSP00000348290:T747A	ENSP00000250894:T753A	T	+	1	0	MAPK8IP3	1754441	0.714000	0.27936	0.175000	0.22980	0.007000	0.05969	0.880000	0.28159	-1.163000	0.02793	-1.345000	0.01243	ACG	A|0.741;G|0.259	0.259	strong		0.657	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
TMPRSS6	164656	hgsc.bcm.edu	37	22	37471290	37471290	+	Silent	SNP	G	G	A	rs881144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37471290G>A	ENST00000346753.3	-	11	1370	c.1254C>T	c.(1252-1254)taC>taT	p.Y418Y	TMPRSS6_ENST00000381792.2_Silent_p.Y409Y|TMPRSS6_ENST00000406725.1_Silent_p.Y409Y|TMPRSS6_ENST00000406856.1_Silent_p.Y409Y	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	418	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.		Y -> C (in IRIDA; does not undergo proteolytic processing; loss of activity). {ECO:0000269|PubMed:22581667}.		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						TCCTCTCGGCGTAGGGCTGCA	0.652													G|||	227	0.0453275	0.0045	0.0663	5008	,	,		16713	0.0367		0.1143	False		,,,				2504	0.0235				p.Y418Y		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.C1254T						PASS	.	G		107,4299	82.9+/-121.4	1,105,2097	45.0	47.0	46.0		1254	-8.8	0.2	22	dbSNP_86	46	1024,7576	213.6+/-253.5	59,906,3335	no	coding-synonymous	TMPRSS6	NM_153609.2		60,1011,5432	AA,AG,GG		11.907,2.4285,8.696		418/812	37471290	1131,11875	2203	4300	6503	SO:0001819	synonymous_variant	164656	exon11			CTCGGCGTAGGGC	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.1254C>T	22.37:g.37471290G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	74	39	0.527027	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			G|0.926;A|0.074	0.074	strong		0.652	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
OTOF	9381	hgsc.bcm.edu	37	2	26689997	26689997	+	Silent	SNP	G	G	A	rs149236286	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26689997G>A	ENST00000272371.2	-	35	4458	c.4332C>T	c.(4330-4332)acC>acT	p.T1444T	OTOF_ENST00000339598.3_Silent_p.T677T|OTOF_ENST00000403946.3_Silent_p.T1444T|OTOF_ENST00000338581.6_Silent_p.T677T|OTOF_ENST00000402415.3_Silent_p.T754T	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1444					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTCCTCCTCGGTGGAGCCAT	0.622													G|||	33	0.00658946	0.0045	0.0115	5008	,	,		14631	0.001		0.0159	False		,,,				2504	0.002				p.T1444T	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.C4332T						PASS	.	G	,,,	44,4362	46.7+/-81.2	0,44,2159	60.0	54.0	56.0		2031,4332,2262,2031	-9.4	0.1	2	dbSNP_134	56	200,8400	86.3+/-148.7	3,194,4103	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	3,238,6262	AA,AG,GG		2.3256,0.9986,1.8761	,,,	677/1231,1444/1998,754/1308,677/1231	26689997	244,12762	2203	4300	6503	SO:0001819	synonymous_variant	9381	exon35			CTCCTCGGTGGAG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4332C>T	2.37:g.26689997G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.984;A|0.016	0.016	strong		0.622	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
ACOXL	55289	hgsc.bcm.edu	37	2	111551725	111551725	+	Missense_Mutation	SNP	G	G	A	rs150003283	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:111551725G>A	ENST00000389811.4	+	5	543	c.319G>A	c.(319-321)Gaa>Aaa	p.E107K	ACOXL_ENST00000340561.4_Missense_Mutation_p.E107K|ACOXL_ENST00000439055.1_Missense_Mutation_p.E107K			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	107					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						GATCCAGACCGAAGCCACCTT	0.537													G|||	43	0.00858626	0.0	0.0043	5008	,	,		19322	0.001		0.007	False		,,,				2504	0.0327				p.E107K		Atlas-SNP	.											ACOXL_ENST00000439055,colon,carcinoma,0,2	ACOXL	93	2	0			c.G319A						PASS	.	G	LYS/GLU	1,3935		0,1,1967	88.0	96.0	94.0		319	3.5	0.1	2	dbSNP_134	94	37,8249		0,37,4106	yes	missense	ACOXL	NM_001142807.1	56	0,38,6073	AA,AG,GG		0.4465,0.0254,0.3109	probably-damaging	107/581	111551725	38,12184	1968	4143	6111	SO:0001583	missense	55289	exon5			CAGACCGAAGCCA		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.319G>A	2.37:g.111551725G>A	ENSP00000374461:p.Glu107Lys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	109	57	0.522936	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		11	0.005036630036630037	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	7	0.009234828496042216	G	22.8	4.335963	0.81801	2.54E-4	0.004465	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000340561	D;D;D	0.94862	-3.54;-3.54;-3.54	5.33	3.53	0.40419	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.269326	0.27787	N	0.017858	D	0.87529	0.6200	N	0.04162	-0.26	0.33945	D	0.643766	D;D;D	0.71674	0.998;0.997;0.963	P;P;P	0.58130	0.833;0.742;0.49	D	0.90091	0.4177	10	0.59425	D	0.04	-7.9556	9.0146	0.36161	0.0824:0.1491:0.7686:0.0	.	107;107;107	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	K	107	ENSP00000374461:E107K;ENSP00000407761:E107K;ENSP00000343717:E107K	ENSP00000343717:E107K	E	+	1	0	ACOXL	111268196	0.988000	0.35896	0.122000	0.21767	0.936000	0.57629	2.001000	0.40825	0.615000	0.30124	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.537	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110465060	110465060	+	Silent	SNP	G	G	C	rs1673404	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110465060G>C	ENST00000378402.5	+	43	6725	c.6621G>C	c.(6619-6621)ctG>ctC	p.L2207L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	2207	G8 1. {ECO:0000255|PROSITE- ProRule:PRU00817}.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AGACCATTCTGCTGGATCAAA	0.393										HNSCC(38;0.096)			G|||	2507	0.500599	0.3858	0.6196	5008	,	,		11314	0.4028		0.503	False		,,,				2504	0.6697				p.L2207L		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	0			c.G6621C						PASS	.	G		1554,2088		330,894,597	60.0	56.0	57.0		6621	0.6	0.9	8	dbSNP_89	57	4233,3913		1125,1983,965	no	coding-synonymous	PKHD1L1	NM_177531.4		1455,2877,1562	CC,CG,GG		48.0358,42.6689,49.0923		2207/4244	110465060	5787,6001	1821	4073	5894	SO:0001819	synonymous_variant	93035	exon43			CATTCTGCTGGAT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.6621G>C	8.37:g.110465060G>C		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|0.517;C|0.483	0.483	strong		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
ADAMTS19	171019	hgsc.bcm.edu	37	5	129001247	129001247	+	Silent	SNP	G	G	A	rs77945368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:129001247G>A	ENST00000274487.4	+	16	2608	c.2463G>A	c.(2461-2463)gaG>gaA	p.E821E	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	821	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AAGTTGTGGAGGAAAAGCCGG	0.428													G|||	18	0.00359425	0.0136	0.0	5008	,	,		13404	0.0		0.0	False		,,,				2504	0.0				p.E821E		Atlas-SNP	.											ADAMTS19,NS,carcinoma,0,1	ADAMTS19	216	1	0			c.G2463A						PASS	.	G		79,4327	68.1+/-105.8	0,79,2124	119.0	107.0	111.0		2463	0.8	1.0	5	dbSNP_132	111	0,8600		0,0,4300	no	coding-synonymous	ADAMTS19	NM_133638.3		0,79,6424	AA,AG,GG		0.0,1.793,0.6074		821/1208	129001247	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	171019	exon16			TGTGGAGGAAAAG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2463G>A	5.37:g.129001247G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	62	25	0.403226	NM_133638		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			G|0.993;A|0.007	0.007	strong		0.428	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
TM4SF20	79853	hgsc.bcm.edu	37	2	228228462	228228462	+	Missense_Mutation	SNP	T	T	G	rs137891000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:228228462T>G	ENST00000304568.3	-	4	705	c.668A>C	c.(667-669)aAg>aCg	p.K223T		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		ACTTCTTCGCTTAGAGACTCC	0.373													T|||	27	0.00539137	0.0008	0.0072	5008	,	,		19702	0.0		0.006	False		,,,				2504	0.0153				p.K223T		Atlas-SNP	.											.	TM4SF20	24	.	0			c.A668C						PASS	.	T	THR/LYS	5,4401	9.9+/-24.2	0,5,2198	104.0	107.0	106.0		668	2.0	0.0	2	dbSNP_134	106	41,8559	27.9+/-77.7	0,41,4259	yes	missense	TM4SF20	NM_024795.3	78	0,46,6457	GG,GT,TT		0.4767,0.1135,0.3537	possibly-damaging	223/230	228228462	46,12960	2203	4300	6503	SO:0001583	missense	79853	exon4			CTTCGCTTAGAGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.668A>C	2.37:g.228228462T>G	ENSP00000303028:p.Lys223Thr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	9	0.004120879120879121	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	3	0.00395778364116095	T	16.53	3.150382	0.57151	0.001135	0.004767	ENSG00000168955	ENST00000304568	T	0.30448	1.53	5.62	1.98	0.26296	.	0.601254	0.17265	N	0.180637	T	0.33177	0.0854	M	0.72118	2.19	0.09310	N	1	P	0.52577	0.954	P	0.57057	0.812	T	0.19484	-1.0304	10	0.20519	T	0.43	-6.6529	7.0811	0.25231	0.0:0.2599:0.0:0.7401	.	223	Q53R12	T4S20_HUMAN	T	223	ENSP00000303028:K223T	ENSP00000303028:K223T	K	-	2	0	TM4SF20	227936706	0.000000	0.05858	0.004000	0.12327	0.576000	0.36127	-0.112000	0.10791	0.109000	0.17891	0.533000	0.62120	AAG	T|0.995;G|0.005	0.005	strong		0.373	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
KCNQ4	9132	hgsc.bcm.edu	37	1	41285591	41285591	+	Silent	SNP	A	A	G	rs12143503	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41285591A>G	ENST00000347132.5	+	6	961	c.879A>G	c.(877-879)acA>acG	p.T293T	KCNQ4_ENST00000509682.2_Silent_p.T293T|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	293					inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	CACCGCACACATGGCTGGGCA	0.592													A|||	582	0.116214	0.0159	0.0994	5008	,	,		19120	0.25		0.1014	False		,,,				2504	0.1411				p.T293T		Atlas-SNP	.											.	KCNQ4	58	.	0			c.A879G						PASS	.	A	,	123,4283	85.3+/-124.0	3,117,2083	145.0	145.0	145.0		879,879	-11.1	0.7	1	dbSNP_120	145	709,7891	156.4+/-210.3	41,627,3632	no	coding-synonymous,coding-synonymous	KCNQ4	NM_004700.3,NM_172163.2	,	44,744,5715	GG,GA,AA		8.2442,2.7916,6.397	,	293/696,293/642	41285591	832,12174	2203	4300	6503	SO:0001819	synonymous_variant	9132	exon6			GCACACATGGCTG	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.879A>G	1.37:g.41285591A>G		Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	166	155	0.933735	NM_004700	O96025	Silent	SNP	ENST00000347132.5	37	CCDS456.1	257	0.11767399267399267	6	0.012195121951219513	38	0.10497237569060773	135	0.23601398601398602	78	0.10290237467018469	A	10.93	1.490197	0.26686	0.027916	0.082442	ENSG00000117013	ENST00000443478	.	.	.	5.71	-11.1	0.00147	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999997826	.	.	.	.	.	.	T	0.12372	-1.0550	3	.	.	.	-12.452	3.3727	0.07227	0.4441:0.2558:0.2148:0.0853	rs12143503	.	.	.	V	189	.	.	M	+	1	0	KCNQ4	41058178	0.000000	0.05858	0.659000	0.29680	0.982000	0.71751	-2.655000	0.00854	-1.529000	0.01754	-0.333000	0.08304	ATG	A|0.918;G|0.082	0.082	strong		0.592	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
TIMP1	7076	hgsc.bcm.edu	37	X	47444985	47444985	+	Silent	SNP	T	T	C	rs4898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:47444985T>C	ENST00000218388.4	+	5	542	c.372T>C	c.(370-372)ttT>ttC	p.F124F	TIMP1_ENST00000377018.2_Silent_p.F118F|TIMP1_ENST00000456754.2_3'UTR|SYN1_ENST00000340666.4_Intron|SYN1_ENST00000295987.7_Intron|MIR4769_ENST00000584126.1_RNA|TIMP1_ENST00000377017.1_Silent_p.F60F	NM_003254.2	NP_003245.1	P01033	TIMP1_HUMAN	TIMP metallopeptidase inhibitor 1	124	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				aging (GO:0007568)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of trophoblast cell migration (GO:1901164)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell proliferation (GO:0008284)|regulation of integrin-mediated signaling pathway (GO:2001044)|response to cytokine (GO:0034097)|response to peptide hormone (GO:0043434)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	cytokine activity (GO:0005125)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			endometrium(1)|large_intestine(2)	3						CCTGCAGTTTTGTGGCTCCCT	0.572													c|||	1772	0.469404	0.3676	0.3184	3775	,	,		10671	0.3472		0.3539	False		,,,				2504	0.3671				p.F124F		Atlas-SNP	.											.	TIMP1	12	.	0			c.T372C	GRCh37	CM991177	TIMP1	M	rs4898	PASS	.		,,	1814,2021		368,820,258,444,313	44.0	36.0	39.0		372,,	0.4	0.3	X	dbSNP_52	39	3078,3650		522,1211,823,695,1049	no	coding-synonymous,intron,intron	SYN1,TIMP1	NM_003254.2,NM_006950.3,NM_133499.2	,,	890,2031,1081,1139,1362	CC,CT,C,TT,T		45.7491,47.3012,46.3126	,,	124/208,,	47444985	4892,5671	2203	4300	6503	SO:0001819	synonymous_variant	7076	exon5			CAGTTTTGTGGCT		CCDS14281.1	Xp11.3-p11.23	2008-07-29	2005-08-08		ENSG00000102265	ENSG00000102265			11820	protein-coding gene	gene with protein product		305370	"""tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor)"""	TIMP, CLGI			Standard	XM_005272645		Approved	EPO	uc004dif.3	P01033	OTTHUMG00000021447	ENST00000218388.4:c.372T>C	X.37:g.47444985T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	57	56	0.982456	NM_003254	Q14252|Q9UCU1	Silent	SNP	ENST00000218388.4	37	CCDS14281.1	748	0.45087402049427366	101	0.27595628415300544	79	0.2762237762237762	124	0.2818181818181818	199	0.33166666666666667	c	3.324	-0.138159	0.06669	0.473012	0.457491	ENSG00000102265	ENST00000445623	.	.	.	5.29	0.454	0.16644	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.39430	P	0.03293199999999996	.	.	.	.	.	.	T	0.47381	-0.9122	3	.	.	.	.	9.163	0.37035	0.0:0.4676:0.0:0.5324	rs4898;rs1043945;rs6520277;rs17849372;rs57987733;rs4898	.	.	.	S	82	.	.	L	+	2	0	TIMP1	47329929	0.052000	0.20516	0.290000	0.24890	0.402000	0.30811	-1.200000	0.03029	-0.352000	0.08237	-1.181000	0.01715	TTG	T|0.536;C|0.464	0.464	strong		0.572	TIMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056423.1	NM_003254	
MCEMP1	199675	hgsc.bcm.edu	37	19	7743821	7743821	+	Missense_Mutation	SNP	A	A	G	rs72996468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7743821A>G	ENST00000333598.3	+	6	953	c.499A>G	c.(499-501)Att>Gtt	p.I167V	C19orf59_ENST00000597445.1_Missense_Mutation_p.I124V|TRAPPC5_ENST00000426877.2_5'Flank|TRAPPC5_ENST00000596148.1_5'Flank|TRAPPC5_ENST00000317378.5_5'Flank|CTD-3214H19.16_ENST00000597959.1_Missense_Mutation_p.H39R	NM_174918.2	NP_777578.2	Q8IX19	MCEM1_HUMAN		167			I -> V (in dbSNP:rs72996468). {ECO:0000269|PubMed:15953541}.			integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|skin(1)|stomach(1)	5						CATAAAAAACATTGACACAAA	0.557											OREG0025208	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	463	0.0924521	0.0832	0.0821	5008	,	,		12957	0.1052		0.1431	False		,,,				2504	0.047				p.I167V		Atlas-SNP	.											.	C19orf59	15	.	0			c.A499G						PASS	.	A	VAL/ILE	398,4006		23,352,1827	22.0	24.0	23.0		499	-0.2	0.0	19	dbSNP_130	23	1207,7391		92,1023,3184	yes	missense	C19orf59	NM_174918.2	29	115,1375,5011	GG,GA,AA		14.0381,9.0372,12.3443	benign	167/188	7743821	1605,11397	2202	4299	6501	SO:0001583	missense	199675	exon6			AAAAACATTGACA																												ENST00000333598.3:c.499A>G	19.37:g.7743821A>G	ENSP00000329920:p.Ile167Val	Somatic	168	0	0	644	WXS	Illumina HiSeq	Phase_I	205	93	0.453659	NM_174918	Q8IX20	Missense_Mutation	SNP	ENST00000333598.3	37	CCDS12183.1	234	0.10714285714285714	35	0.07113821138211382	33	0.09116022099447514	50	0.08741258741258741	116	0.15303430079155672	A	4.490	0.090819	0.08632	0.090372	0.140381	ENSG00000183019	ENST00000333598	T	0.20881	2.04	3.23	-0.146	0.13432	.	0.504904	0.15100	N	0.280569	T	0.00073	0.0002	N	0.19112	0.55	0.80722	P	0.0	B	0.13594	0.008	B	0.12156	0.007	T	0.31806	-0.9930	9	0.32370	T	0.25	-8.7911	6.0971	0.20027	0.6369:0.0:0.3631:0.0	.	167	Q8IX19	MCEM1_HUMAN	V	167	ENSP00000329920:I167V	ENSP00000329920:I167V	I	+	1	0	C19orf59	7649821	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.106000	0.10890	-0.129000	0.11620	-0.537000	0.04273	ATT	A|0.897;G|0.103	0.103	strong		0.557	C19orf59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461248.1		
MUC16	94025	hgsc.bcm.edu	37	19	9072975	9072975	+	Missense_Mutation	SNP	G	G	A	rs17000816	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9072975G>A	ENST00000397910.4	-	3	14674	c.14471C>T	c.(14470-14472)aCg>aTg	p.T4824M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4826	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						GGAAGGATGCGTTGTCTCTAT	0.448													G|||	936	0.186901	0.0923	0.2536	5008	,	,		23617	0.3254		0.1322	False		,,,				2504	0.181				p.T4824M		Atlas-SNP	.											MUC16_ENST00000397910,rectum,carcinoma,0,3	MUC16	4315	3	0			c.C14471T						PASS	.		MET/THR	399,3763		17,365,1699	165.0	153.0	157.0		14471	-1.5	0.0	19	dbSNP_123	157	1164,7258		73,1018,3120	yes	missense	MUC16	NM_024690.2	81	90,1383,4819	AA,AG,GG		13.8209,9.5867,12.4205	benign	4824/14508	9072975	1563,11021	2081	4211	6292	SO:0001583	missense	94025	exon3			GGATGCGTTGTCT	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.14471C>T	19.37:g.9072975G>A	ENSP00000381008:p.Thr4824Met	Somatic	350	1	0.00285714		WXS	Illumina HiSeq	Phase_I	357	174	0.487395	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	439	0.20100732600732601	56	0.11382113821138211	80	0.22099447513812154	205	0.3583916083916084	98	0.12928759894459102	g	1.725	-0.495688	0.04291	0.095867	0.138209	ENSG00000181143	ENST00000397910	T	0.20332	2.08	2.02	-1.54	0.08584	.	.	.	.	.	T	0.00012	0.0000	N	0.02011	-0.69	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.46005	-0.9222	8	0.87932	D	0	.	5.65	0.17610	0.644:0.0:0.356:0.0	rs17000816;rs56515928;rs17000816	4824	B5ME49	.	M	4824	ENSP00000381008:T4824M	ENSP00000381008:T4824M	T	-	2	0	MUC16	8933975	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.495000	0.02294	-0.474000	0.06862	-0.692000	0.03713	ACG	G|0.810;A|0.190	0.190	strong		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CARD6	84674	hgsc.bcm.edu	37	5	40841741	40841741	+	Missense_Mutation	SNP	C	C	T	rs10512747	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:40841741C>T	ENST00000254691.5	+	1	456	c.257C>T	c.(256-258)tCa>tTa	p.S86L	CARD6_ENST00000381677.3_Missense_Mutation_p.S86L	NM_032587.3	NP_115976.2	Q9BX69	CARD6_HUMAN	caspase recruitment domain family, member 6	86	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		S -> L (in dbSNP:rs10512747). {ECO:0000269|Ref.1}.		apoptotic process (GO:0006915)|regulation of apoptotic process (GO:0042981)					NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(2)|lung(29)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	62						TTTCCACAGTCAGCTGCCATT	0.413													C|||	241	0.048123	0.0068	0.0605	5008	,	,		17389	0.005		0.1272	False		,,,				2504	0.0583				p.S86L		Atlas-SNP	.											.	CARD6	141	.	0			c.C257T						PASS	.	C	LEU/SER	108,4298	80.4+/-118.8	2,104,2097	100.0	105.0	103.0		257	4.0	0.8	5	dbSNP_119	103	1036,7564	218.0+/-256.5	53,930,3317	yes	missense	CARD6	NM_032587.3	145	55,1034,5414	TT,TC,CC		12.0465,2.4512,8.7959	probably-damaging	86/1038	40841741	1144,11862	2203	4300	6503	SO:0001583	missense	84674	exon1			CACAGTCAGCTGC	AF356193	CCDS3935.1	5p13.1	2008-05-23			ENSG00000132357	ENSG00000132357			16394	protein-coding gene	gene with protein product		609986				12775719	Standard	NM_032587		Approved	CINCIN1	uc003jmg.3	Q9BX69	OTTHUMG00000094775	ENST00000254691.5:c.257C>T	5.37:g.40841741C>T	ENSP00000254691:p.Ser86Leu	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	117	44	0.376068	NM_032587	Q52LR2	Missense_Mutation	SNP	ENST00000254691.5	37	CCDS3935.1	127	0.05815018315018315	3	0.006097560975609756	24	0.06629834254143646	1	0.0017482517482517483	99	0.13060686015831136	C	19.51	3.840641	0.71488	0.024512	0.120465	ENSG00000132357	ENST00000254691;ENST00000381677;ENST00000444789;ENST00000509771	T;T	0.11604	2.76;2.76	4.88	4.01	0.46588	DEATH-like (2);Caspase Recruitment (2);	0.404992	0.18636	N	0.135436	T	0.00241	0.0007	M	0.62723	1.935	0.36453	P	0.133811	D	0.61080	0.989	P	0.58780	0.845	T	0.04991	-1.0913	9	0.87932	D	0	-2.8394	8.5439	0.33410	0.0:0.8962:0.0:0.1038	rs10512747;rs17240044;rs52789341;rs60928010;rs10512747	86	Q9BX69	CARD6_HUMAN	L	86	ENSP00000254691:S86L;ENSP00000371093:S86L	ENSP00000254691:S86L	S	+	2	0	CARD6	40877498	0.026000	0.19158	0.805000	0.32314	0.858000	0.48976	0.479000	0.22228	1.275000	0.44379	0.563000	0.77884	TCA	C|0.922;T|0.078	0.078	strong		0.413	CARD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211584.3		
TRIM5	85363	hgsc.bcm.edu	37	11	5701001	5701001	+	Missense_Mutation	SNP	C	C	T	rs10838525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5701001C>T	ENST00000380034.3	-	2	663	c.407G>A	c.(406-408)cGg>cAg	p.R136Q	TRIM5_ENST00000483835.1_5'UTR|TRIM5_ENST00000396853.4_Missense_Mutation_p.R136Q|TRIM5_ENST00000305836.5_Missense_Mutation_p.R136Q|TRIM5_ENST00000380027.1_Missense_Mutation_p.R136Q|TRIM5_ENST00000396855.3_Missense_Mutation_p.R136Q|TRIM5_ENST00000396847.3_Missense_Mutation_p.R136Q	NM_033034.2|NM_033092.2	NP_149023.2|NP_149083.2	Q9C035	TRIM5_HUMAN	tripartite motif containing 5	136			R -> Q (in dbSNP:rs10838525). {ECO:0000269|PubMed:11331580, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18312418, ECO:0000269|Ref.9}.		activation of innate immune response (GO:0002218)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein K63-linked ubiquitination (GO:0070534)|protein trimerization (GO:0070206)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|signaling pattern recognition receptor activity (GO:0008329)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R136Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)|Lung NSC(207;0.138)|all_lung(207;0.221)		Epithelial(150;7.21e-09)|BRCA - Breast invasive adenocarcinoma(625;0.139)		TTGGTACTCCCGGGCAACCTC	0.512													T|||	926	0.184904	0.1029	0.2349	5008	,	,		18833	0.0784		0.3847	False		,,,				2504	0.1646				p.R136Q		Atlas-SNP	.											TRIM5_ENST00000380034,NS,carcinoma,0,1	TRIM5	111	1	1	Substitution - Missense(1)	stomach(1)	c.G407A	GRCh37	CM068300	TRIM5	M	rs10838525	PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	633,3769	271.0+/-269.9	49,535,1617	105.0	92.0	97.0		407,407,407	0.2	0.0	11	dbSNP_120	97	3012,5582	465.6+/-366.6	554,1904,1839	yes	missense,missense,missense	TRIM5	NM_033034.2,NM_033092.2,NM_033093.2	43,43,43	603,2439,3456	TT,TC,CC		35.0477,14.3798,28.0471	benign,benign,benign	136/494,136/348,136/327	5701001	3645,9351	2201	4297	6498	SO:0001583	missense	85363	exon2			TACTCCCGGGCAA	AF220025	CCDS31392.1, CCDS31393.1, CCDS31394.1	11p15	2014-06-03	2011-01-25		ENSG00000132256	ENSG00000132256		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16276	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM5"", ""tripartite motif protein TRIM"""	608487	"""tripartite motif-containing 5"""			11331580	Standard	NM_033034		Approved	RNF88, TRIM5alpha	uc001mbm.2	Q9C035	OTTHUMG00000066893	ENST00000380034.3:c.407G>A	11.37:g.5701001C>T	ENSP00000369373:p.Arg136Gln	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_033093	A6NGQ1|A8WFA8|D3DQS8|D3DQS9|G3GJY1|Q2MLV4|Q2MLV8|Q2MLV9|Q2MLW1|Q2MLW3|Q2MLW4|Q2MLW6|Q2MLW7|Q2MLX1|Q2MLX2|Q2MLX3|Q2MLX5|Q2MLY3|Q2MLY4|Q2V6Q6|Q6GX26|Q8WU46|Q96SR5|Q9C031|Q9C032|Q9C033|Q9C034	Missense_Mutation	SNP	ENST00000380034.3	37	CCDS31393.1	462|462	0.21153846153846154|0.21153846153846154	49|49	0.09959349593495935|0.09959349593495935	91|91	0.2513812154696133|0.2513812154696133	30|30	0.05244755244755245|0.05244755244755245	292|292	0.38522427440633245|0.38522427440633245	c|c	0.006|0.006	-2.061954|-2.061954	0.00386|0.00386	0.143798|0.143798	0.350477|0.350477	ENSG00000132256|ENSG00000132256	ENST00000438025|ENST00000396855;ENST00000305836;ENST00000380034;ENST00000380027;ENST00000396847;ENST00000396853;ENST00000412903	.|T;T;T;T;T;T;T	.|0.55413	.|0.52;0.52;0.52;0.52;0.52;0.52;0.52	4.07|4.07	0.203|0.203	0.15195|0.15195	.|.	.|0.418264	.|0.20632	.|N	.|0.088573	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00252|0.00252	-1.77|-1.77	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B	.|0.13145	.|0.007;0.0;0.0	.|B;B;B	.|0.06405	.|0.002;0.002;0.0	T|T	0.36841|0.36841	-0.9731|-0.9731	4|9	.|0.02654	.|T	.|1	.|.	4.1195|4.1195	0.10099|0.10099	0.0:0.2902:0.1754:0.5344|0.0:0.2902:0.1754:0.5344	rs10838525;rs52810416;rs57044514;rs10838525|rs10838525;rs52810416;rs57044514;rs10838525	.|136;136;136	.|Q9C035-3;Q9C035-4;Q9C035	.|.;.;TRIM5_HUMAN	R|Q	13|136	.|ENSP00000380064:R136Q;ENSP00000307031:R136Q;ENSP00000369373:R136Q;ENSP00000369366:R136Q;ENSP00000380058:R136Q;ENSP00000380062:R136Q;ENSP00000388031:R136Q	.|ENSP00000307031:R136Q	G|R	-|-	1|2	0|0	TRIM5|TRIM5	5657577|5657577	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.761000|0.761000	0.26489|0.26489	0.015000|0.015000	0.14971|0.14971	-0.295000|-0.295000	0.09555|0.09555	GGG|CGG	C|0.763;T|0.237	0.237	strong		0.512	TRIM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143360.3	NM_033034	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152257	151152257	+	Silent	SNP	A	A	G	rs926624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151152257A>G	ENST00000358517.2	+	15	2221	c.2010A>G	c.(2008-2010)aaA>aaG	p.K670K	PLEKHG1_ENST00000367328.1_Silent_p.K670K			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	670							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		AGGACTTAAAACTAATGGTTG	0.473													A|||	1351	0.269768	0.1195	0.3329	5008	,	,		21898	0.381		0.3082	False		,,,				2504	0.274				p.K670K		Atlas-SNP	.											PLEKHG1,NS,carcinoma,0,2	PLEKHG1	97	2	0			c.A2010G						PASS	.	A		641,3765	272.5+/-270.8	42,557,1604	44.0	45.0	45.0		2010	-0.4	0.2	6	dbSNP_86	45	2533,6067	407.9+/-349.3	344,1845,2111	no	coding-synonymous	PLEKHG1	NM_001029884.1		386,2402,3715	GG,GA,AA		29.4535,14.5483,24.4041		670/1386	151152257	3174,9832	2203	4300	6503	SO:0001819	synonymous_variant	57480	exon16			CTTAAAACTAATG	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.2010A>G	6.37:g.151152257A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	53	8	0.150943	NM_001029884	Q5T1F2	Silent	SNP	ENST00000358517.2	37	CCDS34552.1																																																																																			A|0.733;G|0.267	0.267	strong		0.473	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
SGK223	157285	hgsc.bcm.edu	37	8	8234218	8234218	+	Silent	SNP	C	C	T	rs4840954|rs373458829	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:8234218C>T	ENST00000520004.1	-	3	1965	c.1701G>A	c.(1699-1701)ccG>ccA	p.P567P	SGK223_ENST00000330777.4_Silent_p.P567P			Q86YV5	SG223_HUMAN		569							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GGTCAGCCAGCGGTGACACTG	0.662													C|||	2272	0.453674	0.3896	0.4323	5008	,	,		16883	0.6409		0.3002	False		,,,				2504	0.5204				p.P567P	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G1701A						PASS	.	C		1303,2737		237,829,954	24.0	29.0	27.0		1701	-9.8	0.0	8	dbSNP_127	27	2269,6033		341,1587,2223	no	coding-synonymous	SGK223	NM_001080826.1		578,2416,3177	TT,TC,CC		27.3308,32.2525,28.9418		567/1403	8234218	3572,8770	2020	4151	6171	SO:0001819	synonymous_variant	0	exon2			AGCCAGCGGTGAC																												ENST00000520004.1:c.1701G>A	8.37:g.8234218C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	14	0.341463	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.631;T|0.369	0.369	strong		0.662	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
PCDHB12	56124	hgsc.bcm.edu	37	5	140590641	140590641	+	Missense_Mutation	SNP	C	C	G	rs150562956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140590641C>G	ENST00000239450.2	+	1	2351	c.2162C>G	c.(2161-2163)cCg>cGg	p.P721R	PCDHB13_ENST00000341948.4_5'Flank|PCDHB12_ENST00000541609.1_Missense_Mutation_p.P384R	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	721					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGGCGGCCCCGGTCGGTCGC	0.657													C|||	36	0.0071885	0.0	0.0014	5008	,	,		14069	0.001		0.005	False		,,,				2504	0.0297				p.P721R		Atlas-SNP	.											PCDHB12,colon,carcinoma,0,1	PCDHB12	179	1	0			c.C2162G						PASS	.	C	ARG/PRO	2,4404		0,2,2201	70.0	79.0	76.0		2162	1.7	0.0	5	dbSNP_134	76	47,8553		0,47,4253	no	missense	PCDHB12	NM_018932.3	103	0,49,6454	GG,GC,CC		0.5465,0.0454,0.3767	benign	721/796	140590641	49,12957	2203	4300	6503	SO:0001583	missense	56124	exon1			CGGCCCCGGTCGG	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.2162C>G	5.37:g.140590641C>G	ENSP00000239450:p.Pro721Arg	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	90	46	0.511111	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	C	8.354	0.831566	0.16820	4.54E-4	0.005465	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.52295	0.67;0.85	3.67	1.7	0.24286	.	.	.	.	.	T	0.27384	0.0672	L	0.38838	1.175	0.09310	N	1	B	0.21821	0.061	B	0.21360	0.034	T	0.18745	-1.0327	9	0.38643	T	0.18	.	7.7474	0.28877	0.2725:0.3123:0.4152:0.0	.	721	Q9Y5F1	PCDBC_HUMAN	R	384;721;341	ENSP00000440199:P384R;ENSP00000239450:P721R	ENSP00000239450:P721R	P	+	2	0	PCDHB12	140570825	0.006000	0.16342	0.002000	0.10522	0.053000	0.15095	0.784000	0.26816	0.128000	0.18479	0.479000	0.44913	CCG	C|0.998;G|0.002;T|0.000	0.002	strong		0.657	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
NEK1	4750	hgsc.bcm.edu	37	4	170506525	170506525	+	Missense_Mutation	SNP	C	C	T	rs200161705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:170506525C>T	ENST00000439128.2	-	9	1422	c.782G>A	c.(781-783)cGc>cAc	p.R261H	NEK1_ENST00000510533.1_Missense_Mutation_p.R261H|NEK1_ENST00000511633.1_Missense_Mutation_p.R261H|NEK1_ENST00000512193.1_Missense_Mutation_p.R261H|NEK1_ENST00000507142.1_Missense_Mutation_p.R261H	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	261					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)	p.R261L(2)		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)		CTTTTCAATGCGTTTGGCTAT	0.388													C|||	4	0.000798722	0.0	0.0029	5008	,	,		18346	0.0		0.001	False		,,,				2504	0.001				p.R261H		Atlas-SNP	.											NEK1_ENST00000507142,NS,carcinoma,0,2	NEK1	203	2	2	Substitution - Missense(2)	breast(2)	c.G782A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	3,3653		0,3,1825	72.0	68.0	69.0		782,782,782,782,782	5.8	1.0	4		69	31,8137		0,31,4053	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	29,29,29,29,29	0,34,5878	TT,TC,CC		0.3795,0.0821,0.2876	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	261/1287,261/1243,261/1190,261/1215,261/1259	170506525	34,11790	1828	4084	5912	SO:0001583	missense	4750	exon10			TCAATGCGTTTGG	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.782G>A	4.37:g.170506525C>T	ENSP00000408020:p.Arg261His	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_001199399	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	33	5.219726	0.95139	8.21E-4	0.003795	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	5.82	5.82	0.92795	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000004	T	0.42471	0.1204	M	0.62016	1.91	0.80722	D	1	D;D;D;D;D;D	0.89917	0.972;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.97110	0.55;0.999;1.0;1.0;0.997;0.999	T	0.11108	-1.0601	10	0.30078	T	0.28	.	20.0909	0.97817	0.0:1.0:0.0:0.0	.	261;261;261;261;261;261	Q96PY6-5;Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;.;NEK1_HUMAN	H	261	ENSP00000408020:R261H;ENSP00000423332:R261H;ENSP00000427653:R261H;ENSP00000424757:R261H;ENSP00000424938:R261H	ENSP00000408020:R261H	R	-	2	0	NEK1	170743100	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.709000	0.84645	2.756000	0.94617	0.591000	0.81541	CGC	C|0.999;T|0.001	0.001	strong		0.388	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
ZNF770	54989	hgsc.bcm.edu	37	15	35273620	35273620	+	Silent	SNP	C	C	T	rs4923849	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:35273620C>T	ENST00000356321.4	-	3	2360	c.2016G>A	c.(2014-2016)caG>caA	p.Q672Q		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	672					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		AGTGAGTAAGCTGATGTCTCT	0.428													T|||	2350	0.469249	0.879	0.4611	5008	,	,		18734	0.376		0.2684	False		,,,				2504	0.2239				p.Q672Q		Atlas-SNP	.											.	ZNF770	64	.	0			c.G2016A						PASS	.	T		3489,911	348.0+/-309.7	1379,731,90	68.0	62.0	64.0		2016	0.8	1.0	15	dbSNP_111	64	2446,6150	695.3+/-404.8	347,1752,2199	no	coding-synonymous	ZNF770	NM_014106.3		1726,2483,2289	TT,TC,CC		28.4551,20.7045,45.6679		672/692	35273620	5935,7061	2200	4298	6498	SO:0001819	synonymous_variant	54989	exon3			AGTAAGCTGATGT	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.2016G>A	15.37:g.35273620C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	82	45	0.548781	NM_014106	Q6ZMZ6|Q9NWV2	Silent	SNP	ENST00000356321.4	37	CCDS10042.1																																																																																			C|0.523;T|0.477	0.477	strong		0.428	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
CHRNA3	1136	hgsc.bcm.edu	37	15	78894339	78894339	+	Silent	SNP	G	G	A	rs1051730	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78894339G>A	ENST00000326828.5	-	5	1029	c.645C>T	c.(643-645)taC>taT	p.Y215Y	CHRNA3_ENST00000348639.3_Silent_p.Y215Y	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	215					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|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)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	TGTCGTGTTTGTAGCCTGGGG	0.532													G|||	842	0.168131	0.087	0.2161	5008	,	,		17692	0.0268		0.3688	False		,,,				2504	0.183				p.Y215Y		Atlas-SNP	.											.	CHRNA3	56	.	0			c.C645T	GRCh37	CM078027	CHRNA3	M	rs1051730	PASS	.	G	,	529,3863	240.6+/-251.3	28,473,1695	163.0	139.0	147.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	645,645	5.3	1.0	15	dbSNP_86	147	3000,5586	463.5+/-366.0	555,1890,1848	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	583,2363,3543	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	34.9406,12.0446,27.1922	,	215/506,215/490	78894339	3529,9449	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GTGTTTGTAGCCT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.645C>T	15.37:g.78894339G>A		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	231	229	0.991342	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			G|0.754;A|0.246	0.246	strong		0.532	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
CNTN1	1272	hgsc.bcm.edu	37	12	41330611	41330611	+	Silent	SNP	T	T	C	rs935105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:41330611T>C	ENST00000551295.2	+	10	1131	c.1014T>C	c.(1012-1014)aaT>aaC	p.N338N	CNTN1_ENST00000360099.3_Silent_p.N338N|CNTN1_ENST00000547702.1_Silent_p.N338N|CNTN1_ENST00000348761.2_Silent_p.N327N|CNTN1_ENST00000347616.1_Silent_p.N338N|CNTN1_ENST00000547849.1_Silent_p.N338N	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	338	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				AACACATCAATGACACAGAGG	0.423													T|||	541	0.108027	0.1785	0.0706	5008	,	,		20140	0.0784		0.1203	False		,,,				2504	0.0573				p.N338N		Atlas-SNP	.											.	CNTN1	207	.	0			c.T1014C						PASS	.	T	,	711,3695	298.4+/-285.3	54,603,1546	185.0	153.0	164.0		1014,981	2.9	1.0	12	dbSNP_86	164	1078,7522	227.2+/-262.7	71,936,3293	no	coding-synonymous,coding-synonymous	CNTN1	NM_001843.2,NM_175038.1	,	125,1539,4839	CC,CT,TT		12.5349,16.1371,13.7552	,	338/1019,327/1008	41330611	1789,11217	2203	4300	6503	SO:0001819	synonymous_variant	1272	exon10			CATCAATGACACA	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.1014T>C	12.37:g.41330611T>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	97	34	0.350515	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Silent	SNP	ENST00000551295.2	37	CCDS8737.1																																																																																			T|0.868;C|0.132	0.132	strong		0.423	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843	
MUC16	94025	hgsc.bcm.edu	37	19	9049910	9049910	+	Missense_Mutation	SNP	C	C	T	rs56307190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9049910C>T	ENST00000397910.4	-	5	31924	c.31721G>A	c.(31720-31722)cGt>cAt	p.R10574H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	10576	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						TGCCCCAGAACGAGAGACCAG	0.498													C|||	928	0.185304	0.0628	0.2752	5008	,	,		20093	0.3363		0.167	False		,,,				2504	0.1503				p.R10574H		Atlas-SNP	.											.	MUC16	4315	.	0			c.G31721A						PASS	.		HIS/ARG	303,3471		14,275,1598	134.0	124.0	127.0		31721	-0.1	0.0	19	dbSNP_129	127	1499,6711		137,1225,2743	yes	missense	MUC16	NM_024690.2	29	151,1500,4341	TT,TC,CC		18.2582,8.0286,15.0367	benign	10574/14508	9049910	1802,10182	1887	4105	5992	SO:0001583	missense	94025	exon5			CCAGAACGAGAGA	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.31721G>A	19.37:g.9049910C>T	ENSP00000381008:p.Arg10574His	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	298	163	0.54698	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	462	0.21153846153846154	32	0.06504065040650407	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	c	6.957	0.546438	0.13312	0.080286	0.182582	ENSG00000181143	ENST00000397910	T	0.02916	4.11	3.2	-0.111	0.13576	.	.	.	.	.	T	0.00012	0.0000	N	0.01874	-0.695	.	.	.	B	0.14012	0.009	B	0.09377	0.004	T	0.42849	-0.9427	8	0.87932	D	0	.	5.6847	0.17797	0.0:0.6388:0.0:0.3612	rs56307190;rs61748894	10574	B5ME49	.	H	10574	ENSP00000381008:R10574H	ENSP00000381008:R10574H	R	-	2	0	MUC16	8910910	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.183000	0.16919	0.055000	0.16094	-0.711000	0.03637	CGT	C|0.794;T|0.206	0.206	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF585A	199704	hgsc.bcm.edu	37	19	37642917	37642917	+	Silent	SNP	G	G	A	rs77675231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37642917G>A	ENST00000356958.4	-	5	2142	c.1884C>T	c.(1882-1884)caC>caT	p.H628H	ZNF585A_ENST00000392157.2_Silent_p.H573H|ZNF585A_ENST00000355533.2_Intron|ZNF585A_ENST00000588723.1_Intron|ZNF585A_ENST00000292841.5_Silent_p.H573H			Q6P3V2	Z585A_HUMAN	zinc finger protein 585A	628					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|central_nervous_system(1)|endometrium(2)|large_intestine(17)|lung(11)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TCTCTCCTGTGTGAACTGGCT	0.493													G|||	2519	0.502995	0.8086	0.5778	5008	,	,		19421	0.1944		0.497	False		,,,				2504	0.3609				p.H573H		Atlas-SNP	.											.	ZNF585A	117	.	0			c.C1719T						PASS	.						38.0	37.0	37.0					19																	37642917		2203	4300	6503	SO:0001819	synonymous_variant	199704	exon6			TCCTGTGTGAACT	AK074345	CCDS12499.1, CCDS74353.1	19q13.13	2013-01-08				ENSG00000196967		"""Zinc fingers, C2H2-type"", ""-"""	26305	protein-coding gene	gene with protein product						12477932	Standard	NM_199126		Approved	FLJ23765	uc002ofn.1	Q6P3V2		ENST00000356958.4:c.1884C>T	19.37:g.37642917G>A		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	237	89	0.375527	NM_199126	Q8TE95|Q96MV3	Silent	SNP	ENST00000356958.4	37																																																																																				G|0.497;A|0.503	0.503	strong		0.493	ZNF585A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000457980.2	NM_152655	
OR2G3	81469	hgsc.bcm.edu	37	1	247769752	247769752	+	Missense_Mutation	SNP	A	A	G	rs61730407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:247769752A>G	ENST00000320002.2	+	1	897	c.865A>G	c.(865-867)Atc>Gtc	p.I289V	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA|RNU6-691P_ENST00000516585.1_RNA	NM_001001914.1	NP_001001914.1	Q8NGZ4	OR2G3_HUMAN	olfactory receptor, family 2, subfamily G, member 3	289						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(31)|skin(5)	50	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			AAATCCTATCATCTATACTTT	0.418													A|||	1693	0.338059	0.2307	0.3127	5008	,	,		19391	0.4325		0.4394	False		,,,				2504	0.2996				p.I289V		Atlas-SNP	.											.	OR2G3	108	.	0			c.A865G						PASS	.	A	VAL/ILE	1057,3349	385.1+/-325.6	140,777,1286	85.0	82.0	83.0		865	3.7	0.5	1	dbSNP_129	83	3646,4954	524.7+/-380.6	790,2066,1444	yes	missense	OR2G3	NM_001001914.1	29	930,2843,2730	GG,GA,AA		42.3953,23.99,36.1602	probably-damaging	289/310	247769752	4703,8303	2203	4300	6503	SO:0001583	missense	81469	exon1			CCTATCATCTATA	BK004417	CCDS31093.1	1q44	2012-08-09			ENSG00000177476	ENSG00000177476		"""GPCR / Class A : Olfactory receptors"""	15008	protein-coding gene	gene with protein product							Standard	NM_001001914		Approved		uc010pyz.2	Q8NGZ4	OTTHUMG00000040576	ENST00000320002.2:c.865A>G	1.37:g.247769752A>G	ENSP00000326301:p.Ile289Val	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_001001914	B2RN64|Q5JQT1|Q6IF45	Missense_Mutation	SNP	ENST00000320002.2	37	CCDS31093.1	814	0.3727106227106227	104	0.21138211382113822	134	0.3701657458563536	247	0.4318181818181818	329	0.4340369393139842	A	14.76	2.630914	0.46944	0.2399	0.423953	ENSG00000177476	ENST00000320002	T	0.52057	0.68	3.65	3.65	0.41850	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37178	U	0.002213	T	0.00012	0.0000	M	0.86651	2.83	0.49130	P	2.4500000000005073E-4	D	0.63046	0.992	D	0.80764	0.994	T	0.37731	-0.9693	9	0.66056	D	0.02	.	10.5906	0.45308	1.0:0.0:0.0:0.0	rs61730407	289	Q8NGZ4	OR2G3_HUMAN	V	289	ENSP00000326301:I289V	ENSP00000326301:I289V	I	+	1	0	OR2G3	245836375	0.445000	0.25657	0.531000	0.27976	0.988000	0.76386	0.983000	0.29552	1.648000	0.50643	0.403000	0.27427	ATC	A|0.629;G|0.371	0.371	strong		0.418	OR2G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097624.1		
MYO7A	4647	hgsc.bcm.edu	37	11	76922946	76922946	+	Silent	SNP	G	G	A	rs11237123	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76922946G>A	ENST00000409709.3	+	46	6590	c.6318G>A	c.(6316-6318)aaG>aaA	p.K2106K	MYO7A_ENST00000458637.2_Silent_p.K2068K|MYO7A_ENST00000409619.2_Silent_p.K2057K|MYO7A_ENST00000605744.1_3'UTR	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2106	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TCATCTTCAAGTGGCCCACCT	0.562													G|||	980	0.195687	0.3994	0.147	5008	,	,		15615	0.0635		0.2227	False		,,,				2504	0.0634				p.K2106K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6318A						PASS	.	G	,	1490,2892		279,932,980	57.0	60.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6318,6204	4.6	1.0	11	dbSNP_120	59	1705,6857		175,1355,2751	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	454,2287,3731	AA,AG,GG		19.9136,34.0027,24.6833	,	2106/2216,2068/2176	76922946	3195,9749	2191	4281	6472	SO:0001819	synonymous_variant	4647	exon46			CTTCAAGTGGCCC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6318G>A	11.37:g.76922946G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			G|0.785;A|0.215	0.215	strong		0.562	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
PBRM1	55193	hgsc.bcm.edu	37	3	52643685	52643685	+	Silent	SNP	T	T	C	rs3755806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52643685T>C	ENST00000296302.7	-	16	2212	c.2211A>G	c.(2209-2211)acA>acG	p.T737T	PBRM1_ENST00000394830.3_Silent_p.T737T|PBRM1_ENST00000410007.1_Silent_p.T737T|PBRM1_ENST00000409114.3_Silent_p.T752T|PBRM1_ENST00000409057.1_Silent_p.T737T|PBRM1_ENST00000356770.4_Silent_p.T705T|PBRM1_ENST00000337303.4_Silent_p.T737T|PBRM1_ENST00000409767.1_Silent_p.T752T			Q86U86	PB1_HUMAN	polybromo 1	737	Bromo 5. {ECO:0000255|PROSITE- ProRule:PRU00035}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.A735fs*7(2)|p.A703fs*7(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GCTCATTGTATGTACAGGCAT	0.423			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	1615	0.322484	0.1483	0.4611	5008	,	,		22548	0.4276		0.4215	False		,,,				2504	0.2495				p.T737T		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	PBRM1_ENST00000356770,rectum,carcinoma,0,3	PBRM1	1252	3	3	Deletion - Frameshift(3)	kidney(3)	c.A2211G						PASS	.	T	,,	771,3635	314.4+/-293.6	64,643,1496	141.0	135.0	137.0		2115,2211,2211	-2.2	1.0	3	dbSNP_107	137	3516,5084	512.1+/-377.9	737,2042,1521	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	801,2685,3017	CC,CT,TT		40.8837,17.4989,32.9617	,,	705/1603,737/1583,737/1583	52643685	4287,8719	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon17			ATTGTATGTACAG	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.2211A>G	3.37:g.52643685T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	163	75	0.460123	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.658;C|0.342	0.342	strong		0.423	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
LRRC8E	80131	hgsc.bcm.edu	37	19	7963976	7963976	+	Missense_Mutation	SNP	T	T	C	rs2115108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7963976T>C	ENST00000306708.6	+	3	670	c.569T>C	c.(568-570)aTg>aCg	p.M190T	AC010336.1_ENST00000539278.1_3'UTR	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	190			M -> T (in dbSNP:rs2115108). {ECO:0000269|PubMed:17974005}.		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						ATAGTGGCCATGGCAGGGACC	0.652													C|||	1407	0.28095	0.3563	0.2046	5008	,	,		17043	0.2629		0.325	False		,,,				2504	0.2065				p.M190T		Atlas-SNP	.											.	LRRC8E	67	.	0			c.T569C						PASS	.	C	THR/MET	1520,2864		277,966,949	28.0	36.0	33.0		569	-0.7	0.0	19	dbSNP_96	33	2638,5940		427,1784,2078	no	missense	LRRC8E	NM_025061.3	81	704,2750,3027	CC,CT,TT		30.7531,34.6715,32.0784	benign	190/797	7963976	4158,8804	2192	4289	6481	SO:0001583	missense	80131	exon4			TGGCCATGGCAGG		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.569T>C	19.37:g.7963976T>C	ENSP00000306524:p.Met190Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Missense_Mutation	SNP	ENST00000306708.6	37	CCDS12189.1	659	0.3017399267399267	195	0.39634146341463417	73	0.20165745856353592	155	0.270979020979021	236	0.3113456464379947	C	0.004	-2.370692	0.00209	0.346715	0.307531	ENSG00000171017	ENST00000306708	T	0.24908	1.83	5.19	-0.706	0.11249	.	1.138340	0.06349	N	0.709546	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47368	-0.9123	9	0.13108	T	0.6	.	1.9981	0.03461	0.1299:0.4175:0.1272:0.3253	rs2115108;rs3745381;rs60796256	190	Q6NSJ5	LRC8E_HUMAN	T	190	ENSP00000306524:M190T	ENSP00000306524:M190T	M	+	2	0	LRRC8E	7869976	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.295000	0.19065	-0.101000	0.12219	-0.735000	0.03563	ATG	T|0.676;C|0.324	0.324	strong		0.652	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
ANKIB1	54467	hgsc.bcm.edu	37	7	92027537	92027537	+	Silent	SNP	C	C	G	rs1861635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92027537C>G	ENST00000265742.3	+	20	2920	c.2544C>G	c.(2542-2544)tcC>tcG	p.S848S		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	848							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CTCTGAGTTCCTTGGATGAAG	0.398													C|||	775	0.154752	0.0643	0.1167	5008	,	,		16849	0.3413		0.0845	False		,,,				2504	0.184				p.S848S		Atlas-SNP	.											.	ANKIB1	92	.	0			c.C2544G						PASS	.	C		219,3475		1,217,1629	66.0	60.0	61.0		2544	5.0	1.0	7	dbSNP_92	61	788,7438		46,696,3371	no	coding-synonymous	ANKIB1	NM_019004.1		47,913,5000	GG,GC,CC		9.5794,5.9285,8.448		848/1090	92027537	1007,10913	1847	4113	5960	SO:0001819	synonymous_variant	54467	exon20			GAGTTCCTTGGAT	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2544C>G	7.37:g.92027537C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	47	0.479592	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	37	CCDS47639.1																																																																																			C|0.845;G|0.155	0.155	strong		0.398	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
ZNF681	148213	hgsc.bcm.edu	37	19	23927345	23927345	+	Missense_Mutation	SNP	T	T	C	rs7245561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:23927345T>C	ENST00000402377.3	-	4	1148	c.1007A>G	c.(1006-1008)aAa>aGa	p.K336R	ZNF681_ENST00000395385.3_Missense_Mutation_p.K267R	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	336					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				TTTGTAGGGTTTCTCTCCAGT	0.398													T|||	777	0.155152	0.1157	0.0764	5008	,	,		21266	0.2133		0.1789	False		,,,				2504	0.18				p.K336R		Atlas-SNP	.											ZNF681,NS,carcinoma,+1,2	ZNF681	76	2	0			c.A1007G						scavenged	.	T	ARG/LYS	533,3873		27,479,1697	87.0	90.0	89.0		1007	0.9	0.0	19	dbSNP_116	89	1403,7193		109,1185,3004	no	missense	ZNF681	NM_138286.2	26	136,1664,4701	CC,CT,TT		16.3215,12.0971,14.89	possibly-damaging	336/646	23927345	1936,11066	2203	4298	6501	SO:0001583	missense	148213	exon4			TAGGGTTTCTCTC	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.1007A>G	19.37:g.23927345T>C	ENSP00000384000:p.Lys336Arg	Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	53	16	0.301887	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	350	0.16025641025641027	57	0.11585365853658537	35	0.09668508287292818	120	0.2097902097902098	138	0.1820580474934037	.	12.74	2.029063	0.35797	0.120971	0.163215	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.24908	1.83;1.83	0.946	0.946	0.19549	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04669	-0.19	0.40659	P	0.017888000000000015	D	0.59767	0.986	P	0.54401	0.751	T	0.25047	-1.0143	8	0.66056	D	0.02	.	6.0099	0.19569	0.0:0.0:0.0:1.0	rs7245561;rs60666232	336	Q96N22	ZN681_HUMAN	R	336;267	ENSP00000384000:K336R;ENSP00000378783:K267R	ENSP00000378783:K267R	K	-	2	0	ZNF681	23719185	0.015000	0.18098	0.029000	0.17559	0.010000	0.07245	-0.904000	0.04080	0.663000	0.31027	0.260000	0.18958	AAA	T|0.849;C|0.151	0.151	strong		0.398	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
PRDM14	63978	hgsc.bcm.edu	37	8	70981451	70981451	+	Silent	SNP	G	G	A	rs9969435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:70981451G>A	ENST00000276594.2	-	2	846	c.645C>T	c.(643-645)caC>caT	p.H215H		NM_024504.3	NP_078780.1	Q9GZV8	PRD14_HUMAN	PR domain containing 14	215					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)			GGCTGGCTGGGTGCTCCAGGC	0.592													G|||	198	0.0395367	0.0817	0.0144	5008	,	,		19372	0.001		0.0437	False		,,,				2504	0.0358				p.H215H	NSCLC(129;99 1813 5906 40656 46114)	Atlas-SNP	.											.	PRDM14	102	.	0			c.C645T						PASS	.	G		335,4071	175.5+/-204.9	9,317,1877	77.0	81.0	80.0		645	0.4	0.0	8	dbSNP_119	80	415,8185	129.7+/-187.7	6,403,3891	no	coding-synonymous	PRDM14	NM_024504.2		15,720,5768	AA,AG,GG		4.8256,7.6033,5.7666		215/572	70981451	750,12256	2203	4300	6503	SO:0001819	synonymous_variant	63978	exon2			GGCTGGGTGCTCC	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.645C>T	8.37:g.70981451G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_024504	Q86UX9	Silent	SNP	ENST00000276594.2	37	CCDS6206.1																																																																																			G|0.951;A|0.049	0.049	strong		0.592	PRDM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318505.1		
NACAD	23148	hgsc.bcm.edu	37	7	45122464	45122464	+	Missense_Mutation	SNP	A	A	C	rs10243185	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45122464A>C	ENST00000490531.2	-	2	3334	c.3315T>G	c.(3313-3315)gaT>gaG	p.D1105E		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	1105			D -> E (in dbSNP:rs10243185).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						CAGGAGGCGCATCGGGGACCT	0.662													C|||	2432	0.485623	0.6755	0.464	5008	,	,		17039	0.3026		0.3877	False		,,,				2504	0.5337				p.D1105E		Atlas-SNP	.											.	NACAD	44	.	0			c.T3315G						PASS	.	C	GLU/ASP	907,477		295,317,80	55.0	58.0	57.0		3315	0.3	0.0	7	dbSNP_119	57	1299,1883		260,779,552	yes	missense	NACAD	NM_001146334.1	45	555,1096,632	CC,CA,AA		40.8234,34.4653,48.3136	benign	1105/1563	45122464	2206,2360	692	1591	2283	SO:0001583	missense	23148	exon2			AGGCGCATCGGGG	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.3315T>G	7.37:g.45122464A>C	ENSP00000420477:p.Asp1105Glu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	47	23	0.489362	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	953	0.43635531135531136	343	0.6971544715447154	164	0.4530386740331492	152	0.26573426573426573	294	0.38786279683377306	c	0.055	-1.239931	0.01493	0.655347	0.408234	ENSG00000136274	ENST00000490531	T	0.09255	3.0	3.42	0.273	0.15650	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34204	-0.9838	8	0.02654	T	1	0.9154	5.8426	0.18643	0.543:0.3569:0.0:0.1001	rs10243185	1105	O15069	NACAD_HUMAN	E	1105	ENSP00000420477:D1105E	ENSP00000420477:D1105E	D	-	3	2	NACAD	45088989	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.091000	0.03369	-0.358000	0.08162	-0.757000	0.03467	GAT	A|0.565;C|0.435	0.435	strong		0.662	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
PLIN4	729359	hgsc.bcm.edu	37	19	4511890	4511890	+	Silent	SNP	G	G	A	rs200897749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4511890G>A	ENST00000301286.3	-	3	2039	c.2040C>T	c.(2038-2040)acC>acT	p.T680T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	680	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CCTTGGTGCCGGTCAGCACGG	0.577																																					p.T680T		Atlas-SNP	.											.	PLIN4	191	.	0			c.C2040T						PASS	.	G		109,4179		0,109,2035	193.0	206.0	201.0		2040	-10.6	0.0	19	dbSNP_132	201	121,8343		0,121,4111	no	coding-synonymous	PLIN4	NM_001080400.1		0,230,6146	AA,AG,GG		1.4296,2.542,1.8036		680/1358	4511890	230,12522	2144	4232	6376	SO:0001819	synonymous_variant	729359	exon3			GGTGCCGGTCAGC	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.2040C>T	19.37:g.4511890G>A		Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	307	61	0.198697	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.982;A|0.018	0.018	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
DDX60	55601	hgsc.bcm.edu	37	4	169158489	169158489	+	Silent	SNP	G	G	C	rs3828560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169158489G>C	ENST00000393743.3	-	32	4650	c.4359C>G	c.(4357-4359)gtC>gtG	p.V1453V		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1453					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)		CAAGAAAACTGACAAAAACAA	0.353													G|||	378	0.0754792	0.003	0.2003	5008	,	,		12745	0.1319		0.0646	False		,,,				2504	0.0378				p.V1453V		Atlas-SNP	.											.	DDX60	304	.	0			c.C4359G						PASS	.	G		47,4359	49.6+/-84.7	0,47,2156	54.0	52.0	52.0		4359	1.7	0.9	4	dbSNP_107	52	474,8124	137.8+/-194.7	12,450,3837	no	coding-synonymous	DDX60	NM_017631.5		12,497,5993	CC,CG,GG		5.5129,1.0667,4.0065		1453/1713	169158489	521,12483	2203	4299	6502	SO:0001819	synonymous_variant	55601	exon32			AAAACTGACAAAA	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.4359C>G	4.37:g.169158489G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	123	61	0.495935	NM_017631	Q6PK35|Q9NVE3	Silent	SNP	ENST00000393743.3	37	CCDS34097.1																																																																																			G|0.938;C|0.062	0.062	strong		0.353	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
PRLR	5618	hgsc.bcm.edu	37	5	35084647	35084647	+	Missense_Mutation	SNP	T	T	C	rs2228482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:35084647T>C	ENST00000382002.5	-	5	724	c.298A>G	c.(298-300)Atc>Gtc	p.I100V	PRLR_ENST00000513753.1_Missense_Mutation_p.I100V|PRLR_ENST00000397391.3_Missense_Mutation_p.I29V|PRLR_ENST00000542609.1_Missense_Mutation_p.I100V|PRLR_ENST00000348262.3_Missense_Mutation_p.I100V|PRLR_ENST00000511486.1_Intron|PRLR_ENST00000310101.5_Missense_Mutation_p.I100V|PRLR_ENST00000231423.3_Missense_Mutation_p.I100V|PRLR_ENST00000342362.5_Intron|PRLR_ENST00000509934.1_5'UTR	NM_000949.5	NP_000940.1	P16471	PRLR_HUMAN	prolactin receptor	100	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		I -> V (in dbSNP:rs2228482).		activation of JAK2 kinase activity (GO:0042977)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cell surface receptor signaling pathway (GO:0007166)|embryo implantation (GO:0007566)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|prolactin signaling pathway (GO:0038161)|steroid biosynthetic process (GO:0006694)|T cell activation (GO:0042110)	cell surface (GO:0009986)|endosome lumen (GO:0031904)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|ornithine decarboxylase activator activity (GO:0042978)|peptide hormone binding (GO:0017046)|prolactin receptor activity (GO:0004925)|protein homodimerization activity (GO:0042803)			central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48	all_lung(31;3.83e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)		Fluoxymesterone(DB01185)|Somatropin recombinant(DB00052)	ACCATCATGATGTATGTCCTC	0.493													T|||	358	0.0714856	0.1392	0.0461	5008	,	,		20071	0.0327		0.0229	False		,,,				2504	0.0879				p.I100V		Atlas-SNP	.											.	PRLR	90	.	0			c.A298G						PASS	.	T	VAL/ILE,,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	548,3858	248.1+/-256.1	34,480,1689	238.0	222.0	227.0		298,,298,298,298,298	3.4	0.6	5	dbSNP_131	227	250,8350	97.7+/-159.3	6,238,4056	yes	missense,intron,missense,missense,missense,missense	PRLR	NM_000949.5,NM_001204314.1,NM_001204315.1,NM_001204316.1,NM_001204317.1,NM_001204318.1	29,,29,29,29,29	40,718,5745	CC,CT,TT		2.907,12.4376,6.1356	benign,,benign,benign,benign,benign	100/623,,100/350,100/377,100/289,100/269	35084647	798,12208	2203	4300	6503	SO:0001583	missense	5618	exon5			TCATGATGTATGT		CCDS3909.1, CCDS56358.1, CCDS56359.1, CCDS56360.1, CCDS56361.1, CCDS56362.1	5p14-p13	2013-02-27			ENSG00000113494	ENSG00000113494			9446	protein-coding gene	gene with protein product		176761					Standard	NM_001204315		Approved		uc003jjm.3	P16471	OTTHUMG00000090789	ENST00000382002.5:c.298A>G	5.37:g.35084647T>C	ENSP00000371432:p.Ile100Val	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	164	75	0.457317	NM_000949	B2R882|D1MDP1|Q16354|Q8TD75|Q8TD78|Q96P35|Q96P36|Q9BX87|Q9UHJ5	Missense_Mutation	SNP	ENST00000382002.5	37	CCDS3909.1	111	0.050824175824175824	62	0.12601626016260162	15	0.04143646408839779	22	0.038461538461538464	12	0.0158311345646438	T	2.194	-0.384548	0.04966	0.124376	0.02907	ENSG00000113494	ENST00000231423;ENST00000513753;ENST00000348262;ENST00000397391;ENST00000542609;ENST00000382002;ENST00000310101;ENST00000514206;ENST00000509839;ENST00000503330	T;T;T;T;T;T;T;D;D;D	0.82803	1.6;1.6;1.6;1.6;1.6;1.6;1.6;-1.65;-1.65;-1.65	5.78	3.4	0.38934	Fibronectin, type III (3);Growth hormone/erythropoietin receptor, ligand binding (1);Immunoglobulin-like fold (1);	0.271201	0.45867	N	0.000324	T	0.01627	0.0052	L	0.33093	0.98	0.09310	P	0.999999999588892	B;B;B;B;B;B	0.13145	0.0;0.001;0.007;0.002;0.0;0.0	B;B;B;B;B;B	0.15484	0.002;0.003;0.009;0.013;0.001;0.002	T	0.21793	-1.0235	9	0.16896	T	0.51	-5.4043	5.7888	0.18349	0.0:0.1471:0.1408:0.7121	rs2228482;rs16871473;rs52811179;rs16871473	100;100;29;100;100;100	P16471-3;P16471;Q8TD76;P16471-7;P16471-6;P16471-4	.;PRLR_HUMAN;.;.;.;.	V	100;100;100;29;100;100;100;100;100;100	ENSP00000231423:I100V;ENSP00000424841:I100V;ENSP00000311613:I100V;ENSP00000380546:I29V;ENSP00000441813:I100V;ENSP00000371432:I100V;ENSP00000309008:I100V;ENSP00000423493:I100V;ENSP00000427060:I100V;ENSP00000422385:I100V	ENSP00000231423:I100V	I	-	1	0	PRLR	35120404	0.339000	0.24784	0.616000	0.29078	0.019000	0.09904	0.201000	0.17276	0.473000	0.27368	-0.261000	0.10672	ATC	T|0.899;G|0.003	.	strong		0.493	PRLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207575.2		
GRAMD3	65983	hgsc.bcm.edu	37	5	125802027	125802027	+	Intron	SNP	G	G	A	rs62394179	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:125802027G>A	ENST00000285689.3	+	2	664				RP11-517I3.1_ENST00000515808.1_RNA|RP11-517I3.1_ENST00000512779.1_RNA|GRAMD3_ENST00000502348.1_Intron|GRAMD3_ENST00000544396.1_Intron|GRAMD3_ENST00000511134.1_Intron|GRAMD3_ENST00000542322.1_Splice_Site_p.E76K|GRAMD3_ENST00000515200.1_Splice_Site_p.R82K|GRAMD3_ENST00000513040.1_Intron|GRAMD3_ENST00000514932.1_Intron|GRAMD3_ENST00000543198.1_Splice_Site_p.R82K	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3							cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		TCAGGACCAAGAGTAAGTCTT	0.408													G|||	932	0.186102	0.2436	0.1772	5008	,	,		19851	0.1399		0.2664	False		,,,				2504	0.0798				p.E76K		Atlas-SNP	.											.	GRAMD3	30	.	0			c.G226A						PASS	.	G	,,LYS/GLU,,	334,1050		37,260,395	222.0	168.0	185.0		,,226,,	2.5	0.0	5	dbSNP_129	185	819,2363		93,633,865	yes	intron,intron,missense-near-splice,intron,intron	GRAMD3	NM_001146319.1,NM_001146320.1,NM_001146321.1,NM_001146322.1,NM_023927.2	,,56,,	130,893,1260	AA,AG,GG		25.7385,24.1329,25.2519	,,,,	,,76/441,,	125802027	1153,3413	692	1591	2283	SO:0001627	intron_variant	65983	exon3			GACCAAGAGTAAG	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000285689.3:c.203+790G>A	5.37:g.125802027G>A		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	131	73	0.557252	NM_001146321	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000285689.3	37	CCDS4136.1	462|462	0.21153846153846154|0.21153846153846154	107|107	0.21747967479674796|0.21747967479674796	81|81	0.22375690607734808|0.22375690607734808	83|83	0.1451048951048951|0.1451048951048951	191|191	0.2519788918205805|0.2519788918205805	G|G	3.980|3.980	-0.006697|-0.006697	0.07773|0.07773	0.241329|0.241329	0.257385|0.257385	ENSG00000155324|ENSG00000155324	ENST00000542322|ENST00000515200;ENST00000543198	T|T;T	0.32272|0.28454	1.46|1.61;1.61	3.42|3.42	2.54|2.54	0.30619|0.30619	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.58432|0.58432	P|P	1.999999999946489E-6|1.999999999946489E-6	B|.	0.16166|.	0.016|.	B|.	0.10450|.	0.005|.	T|T	0.36456|0.36456	-0.9747|-0.9747	6|5	.|0.07482	.|T	.|0.82	.|.	6.5573|6.5573	0.22468|0.22468	0.1315:0.0:0.8685:0.0|0.1315:0.0:0.8685:0.0	rs62394179|rs62394179	76|.	B7Z3R1|.	.|.	K|K	76|82	ENSP00000441876:E76K|ENSP00000426143:R82K;ENSP00000442902:R82K	.|ENSP00000421494:R82K	E|R	+|+	1|2	0|0	GRAMD3|GRAMD3	125829926|125829926	0.224000|0.224000	0.23674|0.23674	0.006000|0.006000	0.13384|0.13384	0.588000|0.588000	0.36517|0.36517	0.739000|0.739000	0.26173|0.26173	1.027000|1.027000	0.39758|0.39758	0.609000|0.609000	0.83330|0.83330	GAG|AGA	G|0.787;A|0.213	0.213	strong		0.408	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927	
KRTAP15-1	254950	hgsc.bcm.edu	37	21	31812828	31812828	+	Silent	SNP	C	C	T	rs35857034	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:31812828C>T	ENST00000334067.3	+	1	232	c.183C>T	c.(181-183)tgC>tgT	p.C61C		NM_181623.1	NP_853654.1	Q3LI76	KR151_HUMAN	keratin associated protein 15-1	61						intermediate filament (GO:0005882)				kidney(1)|large_intestine(3)|lung(6)|skin(1)	11						CCACCAGCTGCCAGACATCCT	0.512													C|||	85	0.0169728	0.0023	0.0375	5008	,	,		20639	0.0		0.0477	False		,,,				2504	0.0082				p.C61C		Atlas-SNP	.											.	KRTAP15-1	35	.	0			c.C183T						PASS	.	C		39,4367	43.8+/-77.6	0,39,2164	107.0	102.0	104.0		183	-0.2	0.0	21	dbSNP_126	104	470,8130	140.0+/-196.6	12,446,3842	no	coding-synonymous	KRTAP15-1	NM_181623.1		12,485,6006	TT,TC,CC		5.4651,0.8852,3.9136		61/138	31812828	509,12497	2203	4300	6503	SO:0001819	synonymous_variant	254950	exon1			CAGCTGCCAGACA	AP001708	CCDS13593.1	21q22.1	2008-05-21			ENSG00000186970	ENSG00000186970		"""Keratin associated proteins"""	18927	protein-coding gene	gene with protein product						12359730	Standard	NM_181623		Approved	KAP15.1	uc002yod.3	Q3LI76	OTTHUMG00000057784	ENST00000334067.3:c.183C>T	21.37:g.31812828C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_181623	Q2M3F4	Silent	SNP	ENST00000334067.3	37	CCDS13593.1																																																																																			C|0.967;T|0.033	0.033	strong		0.512	KRTAP15-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128236.1		
PARP4	143	hgsc.bcm.edu	37	13	25052321	25052321	+	Silent	SNP	A	A	G	rs149727830		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25052321A>G	ENST00000381989.3	-	13	1647	c.1542T>C	c.(1540-1542)caT>caC	p.H514H		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	514	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		AGTCCTTCTCATGTAAGTCCA	0.473																																					p.H514H		Atlas-SNP	.											PARP4,rectum,carcinoma,0,1	PARP4	142	1	0			c.T1542C						scavenged	.						113.0	91.0	98.0					13																	25052321		2203	4300	6503	SO:0001819	synonymous_variant	143	exon13			CTTCTCATGTAAG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1542T>C	13.37:g.25052321A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	11	0.112245	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			A|1.000;C|0.000	.	alt		0.473	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
TMEM38B	55151	hgsc.bcm.edu	37	9	108536246	108536246	+	Missense_Mutation	SNP	G	G	C	rs35232724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:108536246G>C	ENST00000374692.3	+	6	878	c.761G>C	c.(760-762)tGt>tCt	p.C254S	TMEM38B_ENST00000374688.1_Missense_Mutation_p.C200S	NM_018112.1	NP_060582.1	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	254			C -> S (in dbSNP:rs35232724).			integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13						TTTTCATCATGTGAGAAGAAA	0.418													G|||	142	0.0283546	0.0968	0.0101	5008	,	,		16874	0.0		0.005	False		,,,				2504	0.002				p.C254S		Atlas-SNP	.											.	TMEM38B	31	.	0			c.G761C						PASS	.	G	SER/CYS	488,3918	227.8+/-242.9	29,430,1744	105.0	101.0	103.0		761	1.3	0.0	9	dbSNP_126	103	80,8520	46.3+/-105.2	0,80,4220	yes	missense	TMEM38B	NM_018112.1	112	29,510,5964	CC,CG,GG		0.9302,11.0758,4.3672	benign	254/292	108536246	568,12438	2203	4300	6503	SO:0001583	missense	55151	exon6			CATCATGTGAGAA	BC031938	CCDS6768.1	9q31.3	2013-05-23	2004-12-21	2004-12-22	ENSG00000095209	ENSG00000095209			25535	protein-coding gene	gene with protein product		611236	"""chromosome 9 open reading frame 87"""	C9orf87		17611541, 23316006	Standard	NM_018112		Approved	FLJ10493, bA219P18.1, D4Ertd89e, TRIC-B	uc004bcu.2	Q9NVV0	OTTHUMG00000020429	ENST00000374692.3:c.761G>C	9.37:g.108536246G>C	ENSP00000363824:p.Cys254Ser	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_018112	Q5JR63|Q5SVN5|Q5SVN6|Q5VTE2|Q6IA97	Missense_Mutation	SNP	ENST00000374692.3	37	CCDS6768.1	62	0.028388278388278388	54	0.10975609756097561	3	0.008287292817679558	0	0.0	5	0.006596306068601583	G	0.255	-1.003554	0.02128	0.110758	0.009302	ENSG00000095209	ENST00000374692;ENST00000374688	T;T	0.39056	1.1;1.1	4.25	1.3	0.21679	.	0.987695	0.08274	N	0.970939	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12502	-1.0545	10	0.07990	T	0.79	-3.46	7.6203	0.28181	0.0:0.3465:0.4746:0.1789	rs35232724	254	Q9NVV0	TM38B_HUMAN	S	254;200	ENSP00000363824:C254S;ENSP00000363820:C200S	ENSP00000363820:C200S	C	+	2	0	TMEM38B	107576067	0.178000	0.23122	0.014000	0.15608	0.185000	0.23345	0.189000	0.17037	0.289000	0.22422	-0.234000	0.12200	TGT	G|0.960;C|0.040	0.040	strong		0.418	TMEM38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053517.1	NM_018112	
SIRPA	140885	hgsc.bcm.edu	37	20	1895951	1895951	+	Missense_Mutation	SNP	C	C	T	rs149634649|rs386811661	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1895951C>T	ENST00000358771.4	+	2	438	c.286C>T	c.(286-288)Ctc>Ttc	p.L96F	SIRPA_ENST00000356025.3_Missense_Mutation_p.L96F|SIRPA_ENST00000400068.3_Missense_Mutation_p.L96F	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	96	Ig-like V-type.		L -> S. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		TGTTTCAGACCTCACAAAGAG	0.527													C|||	1881	0.375599	0.2368	0.402	5008	,	,		13930	0.5883		0.2942	False		,,,				2504	0.409				p.L96F	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											.	SIRPA	83	.	0			c.C286T						PASS	.						129.0	106.0	114.0					20																	1895951		2202	4284	6486	SO:0001583	missense	140885	exon3			TCAGACCTCACAA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.286C>T	20.37:g.1895951C>T	ENSP00000351621:p.Leu96Phe	Somatic	502	0	0		WXS	Illumina HiSeq	Phase_I	262	25	0.0954198	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	C	3.243	-0.155011	0.06544	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02421	4.3;4.3;4.3	4.78	-8.38	0.00973	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	5.957210	0.00166	N	0.000001	T	0.02083	0.0065	L	0.34521	1.04	0.09310	N	1	B;P;B	0.45176	0.001;0.852;0.002	B;B;B	0.41723	0.017;0.365;0.017	T	0.47935	-0.9078	10	0.10111	T	0.7	.	3.4	0.07320	0.2096:0.3771:0.3116:0.1017	.	76;96;96	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	F	96	ENSP00000382941:L96F;ENSP00000348307:L96F;ENSP00000351621:L96F	ENSP00000348307:L96F	L	+	1	0	SIRPA	1843951	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.951000	0.00166	-1.729000	0.01364	-0.410000	0.06199	CTC	C|0.697;T|0.304	0.304	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
MFSD1	64747	hgsc.bcm.edu	37	3	158538056	158538056	+	Silent	SNP	T	T	C	rs4680469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:158538056T>C	ENST00000264266.8	+	9	866	c.804T>C	c.(802-804)ctT>ctC	p.L268L	MFSD1_ENST00000415822.2_Silent_p.L317L|MFSD1_ENST00000392813.4_Silent_p.L278L			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1	268					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			CCCTGTGGCTTATATTTATCA	0.343													C|||	767	0.153155	0.0492	0.2176	5008	,	,		16270	0.1389		0.2296	False		,,,				2504	0.184				p.L317L	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.T951C						PASS	.	C	,	385,4021	790.9+/-415.1	19,347,1837	207.0	187.0	194.0		834,951	-2.7	0.2	3	dbSNP_111	194	1973,6625	721.9+/-406.4	229,1515,2555	no	coding-synonymous,coding-synonymous	MFSD1	NM_001167903.1,NM_022736.2	,	248,1862,4392	CC,CT,TT		22.9472,8.7381,18.1329	,	278/476,317/515	158538056	2358,10646	2203	4299	6502	SO:0001819	synonymous_variant	64747	exon9			GTGGCTTATATTT	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.804T>C	3.37:g.158538056T>C		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	190	75	0.394737	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Silent	SNP	ENST00000264266.8	37																																																																																				T|0.820;C|0.180	0.180	strong		0.343	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
PSMD3	5709	hgsc.bcm.edu	37	17	38146154	38146154	+	Silent	SNP	T	T	C	rs9916279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38146154T>C	ENST00000264639.4	+	5	1023	c.849T>C	c.(847-849)aaT>aaC	p.N283N	PSMD3_ENST00000541736.1_Silent_p.N145N	NM_002809.3	NP_002800.2	O43242	PSMD3_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 3	283					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)					CCAACAACAATGAGTGGGCCA	0.537													T|||	844	0.16853	0.3805	0.1398	5008	,	,		18840	0.0069		0.165	False		,,,				2504	0.0726				p.N283N	Ovarian(186;531 2051 6385 19668 48409)	Atlas-SNP	.											.	PSMD3	56	.	0			c.T849C						PASS	.	T		1483,2923	476.4+/-357.6	248,987,968	71.0	57.0	62.0		849	-8.4	0.5	17	dbSNP_119	62	1416,7184	272.8+/-290.3	116,1184,3000	no	coding-synonymous	PSMD3	NM_002809.2		364,2171,3968	CC,CT,TT		16.4651,33.6586,22.2897		283/535	38146154	2899,10107	2203	4300	6503	SO:0001819	synonymous_variant	5709	exon5			CAACAATGAGTGG	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.849T>C	17.37:g.38146154T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_002809	B3KMW9|B4DT72|Q96EI2|Q9BQA4	Silent	SNP	ENST00000264639.4	37	CCDS11356.1																																																																																			T|0.798;C|0.202	0.202	strong		0.537	PSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257018.1	NM_002809	
DNAJB11	51726	hgsc.bcm.edu	37	3	186301703	186301703	+	Missense_Mutation	SNP	A	A	G	rs8147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:186301703A>G	ENST00000439351.1	+	9	1719	c.790A>G	c.(790-792)Atc>Gtc	p.I264V	DNAJB11_ENST00000265028.3_Missense_Mutation_p.I264V			Q9UBS4	DJB11_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 11	264			I -> V (in dbSNP:rs8147). {ECO:0000269|PubMed:16303743, 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)|mRNA modification (GO:0016556)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|urinary_tract(2)	15	all_cancers(143;2.84e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.44e-20)	GBM - Glioblastoma multiforme(93;0.0476)		AAATGTGACAATCTCATTAGT	0.348													A|||	1484	0.296326	0.5461	0.2378	5008	,	,		22257	0.1498		0.1859	False		,,,				2504	0.2648				p.I264V		Atlas-SNP	.											.	DNAJB11	42	.	0			c.A790G						PASS	.	A	VAL/ILE	2043,2363	566.3+/-381.9	471,1101,631	190.0	170.0	177.0		790	-0.8	0.2	3	dbSNP_52	177	1448,7152	277.6+/-293.0	113,1222,2965	yes	missense	DNAJB11	NM_016306.4	29	584,2323,3596	GG,GA,AA		16.8372,46.3686,26.8415	possibly-damaging	264/359	186301703	3491,9515	2203	4300	6503	SO:0001583	missense	51726	exon8			GTGACAATCTCAT	AB028859	CCDS3277.1	3q27	2011-09-02			ENSG00000090520	ENSG00000090520		"""Heat shock proteins / DNAJ (HSP40)"""	14889	protein-coding gene	gene with protein product		611341				10827079, 11147971	Standard	NM_016306		Approved	EDJ, HEDJ, ERdj3	uc003fqi.3	Q9UBS4	OTTHUMG00000156614	ENST00000439351.1:c.790A>G	3.37:g.186301703A>G	ENSP00000414398:p.Ile264Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_016306	Q542Y5|Q542Y9|Q6IAQ8|Q96JC6	Missense_Mutation	SNP	ENST00000439351.1	37	CCDS3277.1	578|578	0.26465201465201466|0.26465201465201466	257|257	0.5223577235772358|0.5223577235772358	101|101	0.27900552486187846|0.27900552486187846	82|82	0.14335664335664336|0.14335664335664336	138|138	0.1820580474934037|0.1820580474934037	A|A	16.71|16.71	3.199267|3.199267	0.58126|0.58126	0.463686|0.463686	0.168372|0.168372	ENSG00000090520|ENSG00000090520	ENST00000439351;ENST00000265028|ENST00000418776	T;T|.	0.53640|.	0.61;0.61|.	5.79|5.79	-0.818|-0.818	0.10833|0.10833	Chaperone DnaJ, C-terminal (1);HSP40/DnaJ peptide-binding (1);|.	0.192343|.	0.56097|.	N|.	0.000040|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.78285|0.78285	2.405|2.405	0.09310|0.09310	P|P	1.0|1.0	P|.	0.48589|.	0.912|.	P|.	0.51297|.	0.665|.	T|T	0.45862|0.45862	-0.9232|-0.9232	9|4	0.54805|.	T|.	0.06|.	-1.9249|-1.9249	9.7291|9.7291	0.40350|0.40350	0.583:0.0:0.417:0.0|0.583:0.0:0.417:0.0	rs8147;rs3193237;rs52831972;rs59580631;rs8147|rs8147;rs3193237;rs52831972;rs59580631;rs8147	264|.	Q9UBS4|.	DJB11_HUMAN|.	V|S	264|64	ENSP00000414398:I264V;ENSP00000265028:I264V|.	ENSP00000265028:I264V|.	I|N	+|+	1|2	0|0	DNAJB11|DNAJB11	187784397|187784397	0.978000|0.978000	0.34361|0.34361	0.220000|0.220000	0.23810|0.23810	0.973000|0.973000	0.67179|0.67179	2.653000|2.653000	0.46691|0.46691	-0.361000|-0.361000	0.08125|0.08125	-0.256000|-0.256000	0.11100|0.11100	ATC|AAT	A|0.723;G|0.277	0.277	strong		0.348	DNAJB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344779.1		
ICAM3	3385	hgsc.bcm.edu	37	19	10450285	10450285	+	Silent	SNP	G	G	A	rs281414	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10450285G>A	ENST00000160262.5	-	1	214	c.6C>T	c.(4-6)gcC>gcT	p.A2A	ICAM3_ENST00000589261.1_5'UTR	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	2					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)			GTACCATGGTGGCCATTCTGA	0.632													G|||	759	0.151558	0.2632	0.121	5008	,	,		17884	0.0744		0.166	False		,,,				2504	0.0869				p.A2A		Atlas-SNP	.											.	ICAM3	29	.	0			c.C6T						PASS	.	G		1021,3385	368.3+/-318.6	102,817,1284	50.0	46.0	48.0		6	-0.1	0.3	19	dbSNP_79	48	1497,7103	275.7+/-291.9	137,1223,2940	no	coding-synonymous	ICAM3	NM_002162.3		239,2040,4224	AA,AG,GG		17.407,23.1729,19.3603		2/548	10450285	2518,10488	2203	4300	6503	SO:0001819	synonymous_variant	3385	exon1			CATGGTGGCCATT		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.6C>T	19.37:g.10450285G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	42	41	0.97619	NM_002162	Q6PD68	Silent	SNP	ENST00000160262.5	37	CCDS12235.1																																																																																			G|0.827;A|0.173	0.173	strong		0.632	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1		
CEP85	64793	hgsc.bcm.edu	37	1	26582091	26582091	+	Missense_Mutation	SNP	G	G	A	rs3795686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26582091G>A	ENST00000252992.4	+	4	769	c.638G>A	c.(637-639)aGc>aAc	p.S213N	CEP85_ENST00000451429.2_Missense_Mutation_p.S162N	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	213			S -> N (in dbSNP:rs3795686).			centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						CCAAGAACCAGCACAAGTAAG	0.517													G|||	933	0.186302	0.0575	0.2363	5008	,	,		21145	0.2599		0.3022	False		,,,				2504	0.1299				p.S213N		Atlas-SNP	.											.	CEP85	61	.	0			c.G638A						PASS	.	G	ASN/SER	418,3988	203.8+/-226.2	23,372,1808	94.0	87.0	89.0		638	4.2	0.2	1	dbSNP_107	89	2645,5955	428.0+/-355.8	406,1833,2061	yes	missense	CEP85	NM_022778.2	46	429,2205,3869	AA,AG,GG		30.7558,9.4871,23.5507	benign	213/763	26582091	3063,9943	2203	4300	6503	SO:0001583	missense	64793	exon4			GAACCAGCACAAG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.638G>A	1.37:g.26582091G>A	ENSP00000252992:p.Ser213Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	132	7	0.0530303	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	495	0.22664835164835165	36	0.07317073170731707	86	0.23756906077348067	142	0.24825174825174826	231	0.30474934036939316	G	0.115	-1.133765	0.01756	0.094871	0.307558	ENSG00000130695	ENST00000451429;ENST00000252992	T;T	0.11385	2.78;2.78	5.43	4.24	0.50183	.	0.254552	0.46145	D	0.000320	T	0.00012	0.0000	N	0.04508	-0.205	0.43351	P	0.004585999999999979	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.44360	-0.9333	9	0.02654	T	1	-6.4603	9.9193	0.41455	0.9227:0.0:0.0773:0.0	rs3795686;rs52795730;rs58466682;rs3795686	162;213;213	F8W7K4;Q6P2H3;Q6P2H3-2	.;CEP85_HUMAN;.	N	162;213	ENSP00000417002:S162N;ENSP00000252992:S213N	ENSP00000252992:S213N	S	+	2	0	CEP85	26454678	0.005000	0.15991	0.241000	0.24154	0.019000	0.09904	1.327000	0.33746	1.069000	0.40788	-0.290000	0.09829	AGC	G|0.777;A|0.223	0.223	strong		0.517	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
BAIAP3	8938	hgsc.bcm.edu	37	16	1388909	1388909	+	Silent	SNP	C	C	T	rs77633104	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1388909C>T	ENST00000324385.5	+	3	401	c.243C>T	c.(241-243)ccC>ccT	p.P81P	BAIAP3_ENST00000426824.3_Silent_p.P46P|BAIAP3_ENST00000562208.1_Silent_p.P46P|BAIAP3_ENST00000397489.1_Silent_p.P46P|BAIAP3_ENST00000397488.2_Silent_p.P46P|BAIAP3_ENST00000421665.2_Silent_p.P46P|BAIAP3_ENST00000568887.1_Silent_p.P46P	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	81					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)				CCAGGAAACCCGGGGATGGCG	0.647													C|||	207	0.0413339	0.0908	0.0259	5008	,	,		17156	0.0		0.0179	False		,,,				2504	0.0521				p.P81P		Atlas-SNP	.											BAIAP3,NS,carcinoma,0,1	BAIAP3	88	1	0			c.C243T						PASS	.	C	,,,,	417,3981	202.8+/-225.5	15,387,1797	81.0	87.0	85.0		138,138,138,138,243	-8.1	0.1	16	dbSNP_132	85	131,8469	67.0+/-129.4	0,131,4169	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	,,,,	15,518,5966	TT,TC,CC		1.5233,9.4816,4.216	,,,,	46/1117,46/1153,46/1130,46/1125,81/1188	1388909	548,12450	2199	4300	6499	SO:0001819	synonymous_variant	8938	exon3			GAAACCCGGGGAT	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.243C>T	16.37:g.1388909C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	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|0.962;T|0.038	0.038	strong		0.647	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
GPC1	2817	hgsc.bcm.edu	37	2	241401741	241401741	+	Silent	SNP	C	C	T	rs1042829	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:241401741C>T	ENST00000264039.2	+	3	707	c.459C>T	c.(457-459)cgC>cgT	p.R153R		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	153					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)		TGTACTACCGCGGTGCCAACC	0.677													c|||	760	0.151757	0.2088	0.1412	5008	,	,		14261	0.0238		0.2018	False		,,,				2504	0.1626				p.R153R		Atlas-SNP	.											GPC1,NS,carcinoma,0,1	GPC1	32	1	0			c.C459T						PASS	.			786,3584		67,652,1466	20.0	21.0	20.0		459	-4.0	0.6	2	dbSNP_86	20	1823,6763		180,1463,2650	no	coding-synonymous	GPC1	NM_002081.2		247,2115,4116	TT,TC,CC		21.2322,17.9863,20.1374		153/559	241401741	2609,10347	2185	4293	6478	SO:0001819	synonymous_variant	2817	exon3			CTACCGCGGTGCC	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.459C>T	2.37:g.241401741C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	316|316	0.1446886446886447|0.1446886446886447	95|95	0.19308943089430894|0.19308943089430894	59|59	0.16298342541436464|0.16298342541436464	5|5	0.008741258741258742|0.008741258741258742	157|157	0.20712401055408972|0.20712401055408972	c|c	9.646|9.646	1.140218|1.140218	0.21205|0.21205	0.179863|0.179863	0.212322|0.212322	ENSG00000063660|ENSG00000063660	ENST00000427506;ENST00000425056|ENST00000420138	.|T	.|0.51071	.|0.72	3.1|3.1	-4.02|-4.02	0.04034|0.04034	.|.	.|0.181348	.|0.43919	.|D	.|0.000501	T|T	0.00039|0.00039	0.0001|0.0001	.|.	.|.	.|.	0.09310|0.09310	P|P	0.999999999524217|0.999999999524217	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.09079|0.09079	-1.0691|-1.0691	3|6	.|0.66056	.|D	.|0.02	-12.5012|-12.5012	0.4616|0.4616	0.00517|0.00517	0.3075:0.1766:0.3071:0.2088|0.3075:0.1766:0.3071:0.2088	rs1042829;rs3182269|rs1042829;rs3182269	.|.	.|.	.|.	V|W	110;149|193	.|ENSP00000415077:R193W	.|ENSP00000415077:R193W	A|R	+|+	2|1	0|2	GPC1|GPC1	241050414|241050414	0.000000|0.000000	0.05858|0.05858	0.640000|0.640000	0.29408|0.29408	0.840000|0.840000	0.47671|0.47671	-1.650000|-1.650000	0.01991|0.01991	-0.567000|-0.567000	0.06046|0.06046	-0.281000|-0.281000	0.10026|0.10026	GCG|CGG	C|0.820;T|0.180	0.180	strong		0.677	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592215	1592215	+	Intron	SNP	C	C	G	rs41289057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1592215C>G	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Missense_Mutation_p.G74A|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Missense_Mutation_p.G74A|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TAATTCCCGGCCTGGTCCAGC	0.522													c|||	3213	0.641573	0.7254	0.5029	5008	,	,		7138	0.7351		0.4781	False		,,,				2504	0.6984				p.G74A		Atlas-SNP	.											.	SIRPB1	83	.	0			c.G221C						PASS	.						66.0	79.0	75.0					20																	1592215		452	1342	1794	SO:0001627	intron_variant	10326	exon2			TCCCGGCCTGGTC	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8299G>C	20.37:g.1592215C>G		Somatic	379	0	0		WXS	Illumina HiSeq	Phase_I	28	27	0.964286	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	821	0.3759157509157509	204	0.4146341463414634	117	0.32320441988950277	293	0.5122377622377622	207	0.27308707124010556	.	5.490	0.275498	0.10403	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.66995	-0.24	2.75	-5.49	0.02584	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.52905	1.665	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.35151	-0.9800	8	0.36615	T	0.2	.	9.7994	0.40755	0.0:0.6565:0.0:0.3435	rs41289057	74	Q5TFQ8	SIRBL_HUMAN	A	74	ENSP00000279477:G74A	ENSP00000279477:G74A	G	-	2	0	SIRPB1	1540215	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.679000	0.01940	-1.538000	0.01734	-0.474000	0.04947	GGC	C|0.624;G|0.376	0.376	strong		0.522	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
OTOF	9381	hgsc.bcm.edu	37	2	26697422	26697422	+	Missense_Mutation	SNP	C	C	G	rs80356574	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26697422C>G	ENST00000272371.2	-	26	3373	c.3247G>C	c.(3247-3249)Gcc>Ccc	p.A1083P	OTOF_ENST00000339598.3_Missense_Mutation_p.A336P|OTOF_ENST00000403946.3_Missense_Mutation_p.A1083P|OTOF_ENST00000338581.6_Missense_Mutation_p.A336P|OTOF_ENST00000402415.3_Missense_Mutation_p.A393P	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1083			A -> P (in dbSNP:rs80356574). {ECO:0000269|PubMed:16371502}.		membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGCTGTGGCGTTGCCACGG	0.657													c|||	31	0.0061901	0.0038	0.0115	5008	,	,		11790	0.0		0.0159	False		,,,				2504	0.002				p.A1083P	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G3247C						PASS	.		PRO/ALA,PRO/ALA,PRO/ALA,PRO/ALA	46,4356	46.7+/-81.2	0,46,2155	52.0	44.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1006,3247,1177,1006	4.9	0.9	2	dbSNP_131	47	200,8400	83.1+/-145.7	3,194,4103	yes	missense,missense,missense,missense	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	27,27,27,27	3,240,6258	GG,GC,CC		2.3256,1.045,1.892	benign,benign,benign,benign	336/1231,1083/1998,393/1308,336/1231	26697422	246,12756	2201	4300	6501	SO:0001583	missense	9381	exon26			CTGTGGCGTTGCC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3247G>C	2.37:g.26697422C>G	ENSP00000272371:p.Ala1083Pro	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	20	0.009157509157509158	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	15	0.01978891820580475	c	15.50	2.851923	0.51270	0.01045	0.023256	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3	5.76	4.89	0.63831	C2 calcium/lipid-binding domain, CaLB (1);	0.301620	0.40728	N	0.001024	T	0.31040	0.0784	N	0.19112	0.55	0.33584	D	0.600252	P;P;P;B	0.45569	0.622;0.676;0.861;0.282	B;B;B;B	0.39805	0.208;0.265;0.31;0.265	T	0.55095	-0.8194	10	0.31617	T	0.26	-26.8138	8.1628	0.31209	0.2464:0.6761:0.0:0.0775	.	1083;336;393;336	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	P	336;336;393;1083;1083	ENSP00000345137:A336P;ENSP00000344521:A336P;ENSP00000383906:A393P;ENSP00000272371:A1083P;ENSP00000385255:A1083P	ENSP00000272371:A1083P	A	-	1	0	OTOF	26550926	0.219000	0.23619	0.924000	0.36721	0.893000	0.52053	0.698000	0.25571	1.453000	0.47775	0.556000	0.70494	GCC	C|0.983;G|0.017	0.017	strong		0.657	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784427	140784427	+	Silent	SNP	T	T	C	rs3749769	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140784427T>C	ENST00000573521.1	+	1	1908	c.1908T>C	c.(1906-1908)gaT>gaC	p.D636D	PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	636	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAGATAGAGATGCGCTCAAAC	0.612													.|||	644	0.128594	0.177	0.1527	5008	,	,		20005	0.1181		0.0586	False		,,,				2504	0.1288				p.D636D		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.T1908C						PASS	.	T	,,,,,,,,,,,,,,	784,3586		74,636,1475	40.0	47.0	45.0		,,,,,,,,1908,,,,,,1908	-10.6	0.0	5	dbSNP_107	45	644,7946		26,592,3677	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,,,,,,,	100,1228,5152	CC,CT,TT		7.4971,17.9405,11.0185	,,,,,,,,,,,,,,	,,,,,,,,636/933,,,,,,636/829	140784427	1428,11532	2185	4295	6480	SO:0001819	synonymous_variant	56107	exon1			TAGAGATGCGCTC	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1908T>C	5.37:g.140784427T>C		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			T|0.875;C|0.125	0.125	strong		0.612	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
RFPL3	10738	hgsc.bcm.edu	37	22	32754306	32754306	+	Missense_Mutation	SNP	T	T	C	rs16987625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:32754306T>C	ENST00000249007.4	+	1	453	c.248T>C	c.(247-249)aTg>aCg	p.M83T	RFPL3_ENST00000397468.1_Missense_Mutation_p.M54T|RFPL3_ENST00000382088.3_Missense_Mutation_p.M54T|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	83			M -> T (in dbSNP:rs16987625).				zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TGCTGTTCCATGGTCTCTCAG	0.532													t|||	730	0.145767	0.0303	0.0908	5008	,	,		19526	0.4583		0.0408	False		,,,				2504	0.1268				p.M83T		Atlas-SNP	.											.	RFPL3	91	.	0			c.T248C						PASS	.	T	THR/MET,THR/MET	203,4203	127.0+/-164.0	9,185,2009	130.0	121.0	124.0		248,161	-1.7	0.0	22	dbSNP_123	124	474,8126	139.5+/-196.2	11,452,3837	no	missense,missense	RFPL3	NM_001098535.1,NM_006604.2	81,81	20,637,5846	CC,CT,TT		5.5116,4.6074,5.2053	benign,benign	83/318,54/289	32754306	677,12329	2203	4300	6503	SO:0001583	missense	10738	exon1			GTTCCATGGTCTC	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.248T>C	22.37:g.32754306T>C	ENSP00000249007:p.Met83Thr	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	273	143	0.52381	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	341	0.15613553113553114	10	0.02032520325203252	37	0.10220994475138122	260	0.45454545454545453	34	0.044854881266490766	T	0.005	-2.141191	0.00332	0.046074	0.055116	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.21932	1.98;1.98;1.98	0.851	-1.7	0.08159	Zinc finger, RING/FYVE/PHD-type (1);RDM domain, Ret finger protein-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45745	-0.9240	8	0.20519	T	0.43	.	2.4356	0.04482	0.2332:0.2312:0.0:0.5355	rs16987625;rs52810165;rs56897624;rs16987625	83	O75679	RFPL3_HUMAN	T	54;83;54	ENSP00000380609:M54T;ENSP00000249007:M83T;ENSP00000371520:M54T	ENSP00000249007:M83T	M	+	2	0	RFPL3	31084306	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.115000	0.10741	-2.354000	0.00614	-1.366000	0.01203	ATG	T|0.910;C|0.090	0.090	strong		0.532	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
FAM179A	165186	hgsc.bcm.edu	37	2	29274720	29274720	+	Missense_Mutation	SNP	A	A	G	rs895591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29274720A>G	ENST00000379558.4	+	20	3172	c.2821A>G	c.(2821-2823)Acc>Gcc	p.T941A	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.T886A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	941			T -> A (in dbSNP:rs895591). {ECO:0000269|PubMed:14702039}.							breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						CAGGAATGGCACCCTGCCTGG	0.652													A|||	2940	0.587061	0.5582	0.6513	5008	,	,		15944	0.6905		0.5149	False		,,,				2504	0.5481				p.T941A		Atlas-SNP	.											FAM179A,NS,carcinoma,0,1	FAM179A	106	1	0			c.A2821G						PASS	.	A	ALA/THR	2245,1759		665,915,422	15.0	17.0	16.0		2821	-3.7	0.0	2	dbSNP_86	16	4393,3919		1205,1983,968	yes	missense	FAM179A	NM_199280.2	58	1870,2898,1390	GG,GA,AA		47.1487,43.9311,46.1026	benign	941/1020	29274720	6638,5678	2002	4156	6158	SO:0001583	missense	165186	exon20			AATGGCACCCTGC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2821A>G	2.37:g.29274720A>G	ENSP00000368876:p.Thr941Ala	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	1302	0.5961538461538461	285	0.5792682926829268	222	0.6132596685082873	406	0.7097902097902098	389	0.5131926121372031	A	11.47	1.648166	0.29336	0.560689	0.528513	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.13420	2.59;2.59	5.67	-3.68	0.04463	Armadillo-like helical (1);Armadillo-type fold (1);	1.042290	0.07582	N	0.920405	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.19706	0.038;0.0	B;B	0.21708	0.036;0.0	T	0.29181	-1.0020	9	0.15066	T	0.55	.	7.9756	0.30153	0.5491:0.0:0.3454:0.1055	rs895591;rs60473165	886;941	F8W8E4;Q6ZUX3	.;F179A_HUMAN	A	941;886	ENSP00000368876:T941A;ENSP00000384699:T886A	ENSP00000368876:T941A	T	+	1	0	FAM179A	29128224	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.082000	0.14847	-1.246000	0.02510	0.528000	0.53228	ACC	A|0.416;G|0.584	0.584	strong		0.652	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
SLC39A14	23516	hgsc.bcm.edu	37	8	22262418	22262418	+	Silent	SNP	A	A	G	rs2293144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22262418A>G	ENST00000381237.1	+	2	314	c.195A>G	c.(193-195)ctA>ctG	p.L65L	SLC39A14_ENST00000289952.5_Silent_p.L65L|SLC39A14_ENST00000240095.6_Silent_p.L65L|SLC39A14_ENST00000359741.5_Silent_p.L65L	NM_001128431.2	NP_001121903.1	Q15043	S39AE_HUMAN	solute carrier family 39 (zinc transporter), member 14	65					cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)|zinc ion transmembrane import (GO:0071578)|zinc ion transmembrane transport (GO:0071577)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ferrous iron transmembrane transporter activity (GO:0015093)|zinc ion transmembrane transporter activity (GO:0005385)			NS(1)|endometrium(4)|large_intestine(2)|lung(4)|prostate(1)	12				Colorectal(74;0.019)|COAD - Colon adenocarcinoma(73;0.0731)		TGAAGGCCCTACTCAACCACC	0.607													G|||	3379	0.67472	0.8298	0.5576	5008	,	,		19822	0.7798		0.505	False		,,,				2504	0.6145				p.L65L		Atlas-SNP	.											.	SLC39A14	59	.	0			c.A195G						PASS	.	G	,,,	3387,1019	377.3+/-322.4	1302,783,118	68.0	64.0	65.0		195,195,195,195	0.6	0.9	8	dbSNP_100	65	4079,4521	593.1+/-393.1	961,2157,1182	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A14	NM_001128431.2,NM_001135153.1,NM_001135154.1,NM_015359.4	,,,	2263,2940,1300	GG,GA,AA		47.4302,23.1276,42.5957	,,,	65/493,65/493,65/482,65/493	22262418	7466,5540	2203	4300	6503	SO:0001819	synonymous_variant	23516	exon2			GGCCCTACTCAAC	D31887	CCDS6030.1, CCDS47822.1, CCDS47823.1	8p21.2	2013-05-22			ENSG00000104635	ENSG00000104635		"""Solute carriers"""	20858	protein-coding gene	gene with protein product		608736	"""solute carrier family 39 (metal ion transporter), member 14"""			12659941	Standard	NM_015359		Approved	KIAA0062, NET34, ZIP14	uc011kzh.2	Q15043	OTTHUMG00000097791	ENST00000381237.1:c.195A>G	8.37:g.22262418A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001135153	A6NH98|B4DIW3|B6EU88|D3DSR4|Q6ZME8|Q96BB3	Silent	SNP	ENST00000381237.1	37	CCDS47823.1																																																																																			A|0.386;G|0.614	0.614	strong		0.607	SLC39A14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215039.2	XM_046677	
SLC9A3	6550	hgsc.bcm.edu	37	5	476353	476353	+	Silent	SNP	C	C	T	rs2230437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:476353C>T	ENST00000264938.3	-	13	2040	c.2031G>A	c.(2029-2031)gcG>gcA	p.A677A	SLC9A3_ENST00000514375.1_Silent_p.A668A|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.7_ENST00000606319.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	677					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)	p.A677A(1)		NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			ACAGCTTGGCCGCCTTCTTGT	0.642													C|||	1062	0.212061	0.1377	0.3112	5008	,	,		16387	0.0347		0.4115	False		,,,				2504	0.2198				p.A677A		Atlas-SNP	.											SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	1	Substitution - coding silent(1)	prostate(1)	c.G2031A						PASS	.	C		788,3616	316.3+/-294.6	73,642,1487	61.0	60.0	61.0		2031	-9.5	0.0	5	dbSNP_98	61	3384,5216	499.2+/-374.9	689,2006,1605	no	coding-synonymous	SLC9A3	NM_004174.2		762,2648,3092	TT,TC,CC		39.3488,17.8928,32.0824		677/835	476353	4172,8832	2202	4300	6502	SO:0001819	synonymous_variant	6550	exon13			CTTGGCCGCCTTC		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.2031G>A	5.37:g.476353C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	44	0.517647	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			C|0.706;T|0.294	0.294	strong		0.642	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
ANKRD27	84079	hgsc.bcm.edu	37	19	33117666	33117666	+	Silent	SNP	T	T	C	rs6510271	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33117666T>C	ENST00000306065.4	-	16	1646	c.1488A>G	c.(1486-1488)ggA>ggG	p.G496G		NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	496					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					GCGGAGTGGCTCCATGGTAGT	0.607													C|||	3265	0.651957	0.7179	0.536	5008	,	,		17706	0.6528		0.6451	False		,,,				2504	0.6513				p.G496G		Atlas-SNP	.											ANKRD27,NS,carcinoma,-1,1	ANKRD27	86	1	0			c.A1488G						PASS	.	C		3084,1322	438.6+/-345.4	1055,974,174	92.0	72.0	79.0		1488	0.5	0.1	19	dbSNP_116	79	5489,3111	461.8+/-365.5	1749,1991,560	no	coding-synonymous	ANKRD27	NM_032139.2		2804,2965,734	CC,CT,TT		36.1744,30.0045,34.0843		496/1051	33117666	8573,4433	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon16			AGTGGCTCCATGG	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.1488A>G	19.37:g.33117666T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			T|0.335;C|0.665	0.665	strong		0.607	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
HSF5	124535	hgsc.bcm.edu	37	17	56540267	56540267	+	Missense_Mutation	SNP	C	C	T	rs3803752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56540267C>T	ENST00000323777.3	-	4	1527	c.1418G>A	c.(1417-1419)aGc>aAc	p.S473N		NM_001080439.1	NP_001073908.1	Q4G112	HSF5_HUMAN	heat shock transcription factor family member 5	473			S -> N (in dbSNP:rs3803752).		transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	16	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CTGTATTGTGCTATTTTCAAC	0.443													C|||	666	0.132987	0.0424	0.1628	5008	,	,		21970	0.1786		0.1849	False		,,,				2504	0.1339				p.S473N		Atlas-SNP	.											.	HSF5	51	.	0			c.G1418A						PASS	.	C	ASN/SER	276,4130	154.8+/-188.1	5,266,1932	251.0	221.0	231.0		1418	3.1	1.0	17	dbSNP_107	231	1740,6860	316.8+/-312.9	186,1368,2746	yes	missense	HSF5	NM_001080439.1	46	191,1634,4678	TT,TC,CC		20.2326,6.2642,15.5005	benign	473/597	56540267	2016,10990	2203	4300	6503	SO:0001583	missense	124535	exon4			ATTGTGCTATTTT	BC033020	CCDS32690.1	17q23.2	2006-04-25				ENSG00000176160			26862	protein-coding gene	gene with protein product							Standard	NM_001080439		Approved	FLJ40311	uc002iwi.1	Q4G112		ENST00000323777.3:c.1418G>A	17.37:g.56540267C>T	ENSP00000313243:p.Ser473Asn	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	237	114	0.481013	NM_001080439	Q08EH7|Q8N7V2	Missense_Mutation	SNP	ENST00000323777.3	37	CCDS32690.1	362	0.16575091575091574	38	0.07723577235772358	52	0.143646408839779	117	0.20454545454545456	155	0.20448548812664907	C	11.19	1.565724	0.27915	0.062642	0.202326	ENSG00000176160	ENST00000412540;ENST00000323777	T	0.73258	-0.73	5.04	3.07	0.35406	.	0.215770	0.35585	N	0.003101	T	0.00073	0.0002	N	0.08118	0	0.43896	P	0.0034729999999999484	B	0.02656	0.0	B	0.04013	0.001	T	0.04115	-1.0976	9	0.72032	D	0.01	.	7.3237	0.26542	0.0:0.3027:0.5601:0.1372	rs3803752;rs12950319;rs16943060;rs52825805;rs59225401;rs3803752	473	Q4G112	HSF5_HUMAN	N	373;473	ENSP00000313243:S473N	ENSP00000313243:S473N	S	-	2	0	HSF5	53895266	0.846000	0.29590	0.989000	0.46669	0.641000	0.38312	1.017000	0.29989	0.739000	0.32628	-0.145000	0.13849	AGC	C|0.850;T|0.150	0.150	strong		0.443	HSF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444719.1	XM_064190	
MARCH1	55016	hgsc.bcm.edu	37	4	165118652	165118652	+	Intron	SNP	C	C	T	rs2288675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:165118652C>T	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				CCCTGAGACTCTTAGTTCAAG	0.403													C|||	1463	0.292133	0.1067	0.3112	5008	,	,		18350	0.2163		0.4732	False		,,,				2504	0.4213				p.R71K		Atlas-SNP	.											.	ANP32C	59	.	0			c.G212A						PASS	.	C	,LYS/ARG	714,3692	295.3+/-283.6	68,578,1557	120.0	121.0	121.0		,212	0.5	0.7	4	dbSNP_100	121	4249,4351	572.9+/-389.8	1049,2151,1100	yes	intron,missense	ANP32C,MARCH1	NM_001166373.1,NM_012403.1	,26	1117,2729,2657	TT,TC,CC		49.407,16.2052,38.1593	,benign	,71/235	165118652	4963,8043	2203	4300	6503	SO:0001627	intron_variant	23520	exon1			GAGACTCTTAGTT	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-85838G>A	4.37:g.165118652C>T		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	201	90	0.447761	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			C|0.676;T|0.324	0.324	strong		0.403	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
ASTN1	460	hgsc.bcm.edu	37	1	176833427	176833427	+	Missense_Mutation	SNP	T	T	C	rs61756323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:176833427T>C	ENST00000367654.3	-	23	4113	c.3902A>G	c.(3901-3903)gAg>gGg	p.E1301G	ASTN1_ENST00000367657.3_Intron|ASTN1_ENST00000361833.2_Missense_Mutation_p.E1293G	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	1301					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						GTGCTAGATCTCTTTGCTGTC	0.522													T|||	4	0.000798722	0.0	0.0014	5008	,	,		18259	0.0		0.002	False		,,,				2504	0.001				p.E1293G		Atlas-SNP	.											.	ASTN1	314	.	0			c.A3878G						PASS	.	T	GLY/GLU	2,4404	4.2+/-10.8	0,2,2201	132.0	129.0	130.0		3878	4.6	1.0	1	dbSNP_129	130	40,8560	27.4+/-76.7	0,40,4260	yes	missense	ASTN1	NM_004319.1	98	0,42,6461	CC,CT,TT		0.4651,0.0454,0.3229	benign	1293/1295	176833427	42,12964	2203	4300	6503	SO:0001583	missense	460	exon23			TAGATCTCTTTGC	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.3902A>G	1.37:g.176833427T>C	ENSP00000356626:p.Glu1301Gly	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	15.80	2.939460	0.52972	4.54E-4	0.004651	ENSG00000152092	ENST00000361833;ENST00000367654	T;T	0.11385	2.78;2.78	4.61	4.61	0.57282	.	0.144733	0.64402	D	0.000010	T	0.06508	0.0167	N	0.08118	0	0.80722	D	1	B	0.29301	0.241	B	0.23419	0.046	T	0.33420	-0.9869	10	0.72032	D	0.01	-18.084	13.9805	0.64301	0.0:0.0:0.0:1.0	rs61756323	1293	O14525-2	.	G	1293;1301	ENSP00000354536:E1293G;ENSP00000356626:E1301G	ENSP00000354536:E1293G	E	-	2	0	ASTN1	175100050	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	3.364000	0.52328	1.852000	0.53769	0.454000	0.30748	GAG	T|0.998;C|0.002	0.002	strong		0.522	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68257352	68257352	+	Missense_Mutation	SNP	T	T	A	rs17192170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68257352T>A	ENST00000347230.4	-	15	2830	c.2692A>T	c.(2692-2694)Acc>Tcc	p.T898S	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.T898S	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	898			T -> S (in dbSNP:rs17192170).		cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CTCCGAATGGTGCTGCTACCC	0.547													T|||	215	0.0429313	0.0061	0.0648	5008	,	,		20189	0.0		0.1153	False		,,,				2504	0.047				p.T898S		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A2692T						PASS	.	T	SER/THR	122,4284	91.6+/-130.3	4,114,2085	149.0	118.0	128.0		2692	2.4	1.0	14	dbSNP_123	128	1032,7568	219.9+/-257.8	61,910,3329	yes	missense	ZFYVE26	NM_015346.3	58	65,1024,5414	AA,AT,TT		12.0,2.769,8.8728	benign	898/2540	68257352	1154,11852	2203	4300	6503	SO:0001583	missense	23503	exon15			GAATGGTGCTGCT	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.2692A>T	14.37:g.68257352T>A	ENSP00000251119:p.Thr898Ser	Somatic	249	1	0.00401606		WXS	Illumina HiSeq	Phase_I	215	94	0.437209	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	102	0.046703296703296704	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	74	0.09762532981530343	T	12.54	1.967920	0.34754	0.02769	0.12	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.28895	1.73;1.59	5.95	2.38	0.29361	.	0.540708	0.19473	N	0.113394	T	0.00300	0.0009	M	0.65975	2.015	0.34490	P	0.29508900000000005	B;B	0.23128	0.041;0.08	B;B	0.19946	0.027;0.023	T	0.18461	-1.0336	9	0.06494	T	0.89	-15.8916	2.4765	0.04577	0.1242:0.1348:0.1296:0.6114	rs17192170;rs52807491;rs17192170	898;898	G3V2D8;Q68DK2	.;ZFY26_HUMAN	S	898;877;898	ENSP00000251119:T898S;ENSP00000450603:T898S	ENSP00000251119:T898S	T	-	1	0	ZFYVE26	67327105	1.000000	0.71417	0.991000	0.47740	0.836000	0.47400	1.256000	0.32921	0.504000	0.28082	-0.336000	0.08194	ACC	T|0.932;A|0.068	0.068	strong		0.547	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
MUC2	4583	hgsc.bcm.edu	37	11	1082605	1082605	+	Silent	SNP	G	G	A	rs41480348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1082605G>A	ENST00000441003.2	+	15	1881	c.1854G>A	c.(1852-1854)acG>acA	p.T618T	MUC2_ENST00000359061.5_Silent_p.T618T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	618					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)	AATATGACACGTGTAACTGTC	0.647													G|||	159	0.0317492	0.0038	0.0605	5008	,	,		17089	0.001		0.0875	False		,,,				2504	0.0235				p.T618T		Atlas-SNP	.											.	MUC2	614	.	0			c.G1854A						PASS	.	G		86,4258		0,86,2086	55.0	59.0	58.0		1854	-5.2	0.8	11	dbSNP_127	58	724,7794		32,660,3567	no	coding-synonymous	MUC2	NM_002457.2		32,746,5653	AA,AG,GG		8.4996,1.9797,6.2976		618/2813	1082605	810,12052	2172	4259	6431	SO:0001819	synonymous_variant	4583	exon15			TGACACGTGTAAC	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.1854G>A	11.37:g.1082605G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				G|0.952;A|0.048	0.048	strong		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
KMT2E	55904	hgsc.bcm.edu	37	7	104717517	104717517	+	Silent	SNP	C	C	T	rs2240455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:104717517C>T	ENST00000311117.3	+	10	1421	c.876C>T	c.(874-876)taC>taT	p.Y292Y	KMT2E_ENST00000334914.7_5'UTR|KMT2E_ENST00000257745.4_Silent_p.Y292Y|KMT2E_ENST00000334877.4_Silent_p.Y292Y|KMT2E_ENST00000476671.1_Silent_p.Y292Y	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	292					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)										ACAACCAGTACAGTGAGGGTG	0.388													T|||	1919	0.383187	0.59	0.2435	5008	,	,		17085	0.6319		0.1342	False		,,,				2504	0.2025				p.Y292Y		Atlas-SNP	.											.	MLL5	173	.	0			c.C876T						PASS	.	T	,	2304,2102	574.8+/-383.8	606,1092,505	127.0	118.0	121.0		876,876	-2.9	1.0	7	dbSNP_98	121	1057,7543	770.7+/-407.7	69,919,3312	no	coding-synonymous,coding-synonymous	MLL5	NM_018682.3,NM_182931.2	,	675,2011,3817	TT,TC,CC		12.2907,47.7077,25.8419	,	292/1859,292/1859	104717517	3361,9645	2203	4300	6503	SO:0001819	synonymous_variant	55904	exon9			CCAGTACAGTGAG	AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.876C>T	7.37:g.104717517C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	171	170	0.994152	NM_018682	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Silent	SNP	ENST00000311117.3	37	CCDS34723.1																																																																																			C|0.620;T|0.380	0.380	strong		0.388	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
GSTO2	119391	hgsc.bcm.edu	37	10	106058901	106058901	+	Silent	SNP	G	G	T	rs3758572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:106058901G>T	ENST00000338595.2	+	7	911	c.591G>T	c.(589-591)acG>acT	p.T197T	GSTO2_ENST00000369707.2_Silent_p.T169T|GSTO2_ENST00000450629.2_Silent_p.T163T|GSTO2_ENST00000429569.2_Missense_Mutation_p.A100S	NM_183239.1	NP_899062.1	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	197	GST C-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)	TGAGCCACACGCCAGCCCTGC	0.512													G|||	385	0.076877	0.1392	0.0288	5008	,	,		16780	0.126		0.0209	False		,,,				2504	0.0337				p.T197T		Atlas-SNP	.											.	GSTO2	23	.	0			c.G591T						PASS	.	G	,,,	568,3838	252.1+/-258.6	46,476,1681	80.0	79.0	79.0		489,507,405,591	2.1	1.0	10	dbSNP_107	79	163,8437	76.3+/-139.0	2,159,4139	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GSTO2	NM_001191013.1,NM_001191014.1,NM_001191015.1,NM_183239.1	,,,	48,635,5820	TT,TG,GG		1.8953,12.8915,5.6205	,,,	163/210,169/216,135/182,197/244	106058901	731,12275	2203	4300	6503	SO:0001819	synonymous_variant	119391	exon7			CCACACGCCAGCC	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.591G>T	10.37:g.106058901G>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_183239	A8K771|B4DJW6|E7ESD6|Q49TW5|Q5GM70|Q5JU15|Q86WP3	Silent	SNP	ENST00000338595.2	37	CCDS7556.1	163	0.07463369963369963	65	0.13211382113821138	11	0.03038674033149171	71	0.12412587412587413	16	0.021108179419525065	G	12.41	1.928928	0.34002	0.128915	0.018953	ENSG00000065621	ENST00000429569	T	0.14391	2.51	6.04	2.08	0.27032	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.58432	P	1.999999999946489E-6	B	0.15141	0.012	B	0.09377	0.004	T	0.33854	-0.9852	7	0.33141	T	0.24	-25.3486	4.6308	0.12500	0.1396:0.4602:0.32:0.0803	rs3758572	100	B4DML4	.	S	100	ENSP00000407381:A100S	ENSP00000407381:A100S	A	+	1	0	GSTO2	106048891	0.989000	0.36119	0.995000	0.50966	0.852000	0.48524	-0.001000	0.12947	0.122000	0.18314	-0.344000	0.07964	GCC	G|0.938;T|0.062	0.062	strong		0.512	GSTO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050210.2	NM_183239	
SDHA	6389	hgsc.bcm.edu	37	5	251469	251469	+	Silent	SNP	G	G	A	rs10039029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:251469G>A	ENST00000264932.6	+	13	1795	c.1680G>A	c.(1678-1680)acG>acA	p.T560T	SDHA_ENST00000510361.1_Silent_p.T512T|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Intron	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	560					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)	TCTGGAACACGGACCTGGTGG	0.632									Familial Paragangliomas				G|||	1244	0.248403	0.6271	0.2406	5008	,	,		21830	0.0585		0.1113	False		,,,				2504	0.0787				p.T560T		Atlas-SNP	.											SDHA,NS,malignant_melanoma,+1,1	SDHA	80	1	0			c.G1680A						scavenged	.						18.0	24.0	22.0					5																	251469		2202	4292	6494	SO:0001819	synonymous_variant	6389	exon13	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	GAACACGGACCTG	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.1680G>A	5.37:g.251469G>A		Somatic	361	4	0.0110803		WXS	Illumina HiSeq	Phase_I	348	81	0.232759	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			A|1.000;|0.000	1.000	weak		0.632	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
C19orf53	28974	hgsc.bcm.edu	37	19	13885309	13885309	+	Silent	SNP	C	C	T	rs1128749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:13885309C>T	ENST00000588234.1	+	1	328	c.18C>T	c.(16-18)cgC>cgT	p.R6R	CTB-5E10.3_ENST00000586894.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA|CTB-5E10.3_ENST00000586297.1_RNA|C19orf53_ENST00000593274.1_5'Flank	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53	6										breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			AGGGGCAGCGCAAGTTTCAGG	0.642													C|||	1884	0.376198	0.4032	0.317	5008	,	,		16423	0.4256		0.2505	False		,,,				2504	0.4601				p.R6R		Atlas-SNP	.											C19orf53,NS,carcinoma,0,1	C19orf53	14	1	0			c.C18T						PASS	.	C		1733,2661		341,1051,805	16.0	19.0	18.0		18	0.3	1.0	19	dbSNP_86	18	2204,6384		303,1598,2393	no	coding-synonymous	C19orf53	NM_014047.2		644,2649,3198	TT,TC,CC		25.6637,39.4401,30.3266		6/100	13885309	3937,9045	2197	4294	6491	SO:0001819	synonymous_variant	28974	exon1			GCAGCGCAAGTTT	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"""leydig cell tumor 10 kDa protein homolog"""					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5		ENST00000588234.1:c.18C>T	19.37:g.13885309C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	70	42	0.6	NM_014047	B2R4J9	Silent	SNP	ENST00000588234.1	37	CCDS12298.1																																																																																			A|0.000;C|0.661;G|0.000;T|0.338	0.338	strong		0.642	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047	
BARD1	580	hgsc.bcm.edu	37	2	215645545	215645545	+	Silent	SNP	C	C	G	rs2070096	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:215645545C>G	ENST00000260947.4	-	4	1187	c.1053G>C	c.(1051-1053)acG>acC	p.T351T	BARD1_ENST00000471787.1_5'Flank|BARD1_ENST00000449967.2_Silent_p.T207T	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	351					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTGAGGGCACCGTTTGCTTAA	0.428									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				C|||	953	0.190296	0.1611	0.1916	5008	,	,		20817	0.1815		0.1839	False		,,,				2504	0.2444				p.T351T		Atlas-SNP	.											.	BARD1	138	.	0			c.G1053C						PASS	.	C		748,3658	305.5+/-289.0	57,634,1512	105.0	101.0	103.0		1053	-11.3	0.0	2	dbSNP_96	103	1898,6702	336.9+/-322.1	207,1484,2609	no	coding-synonymous	BARD1	NM_000465.2		264,2118,4121	GG,GC,CC		22.0698,16.9768,20.3445		351/778	215645545	2646,10360	2203	4300	6503	SO:0001819	synonymous_variant	580	exon4	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGGCACCGTTTGC		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"""Ankyrin repeat domain containing"""	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.1053G>C	2.37:g.215645545C>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	103	51	0.495146	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Silent	SNP	ENST00000260947.4	37	CCDS2397.1																																																																																			C|0.803;G|0.197	0.197	strong		0.428	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465	
SLC23A2	9962	hgsc.bcm.edu	37	20	4855309	4855309	+	Silent	SNP	G	G	A	rs41282100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4855309G>A	ENST00000379333.1	-	10	1250	c.858C>T	c.(856-858)taC>taT	p.Y286Y	SLC23A2_ENST00000338244.1_Silent_p.Y286Y|SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Silent_p.Y172Y	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	286					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CATTTCTGGCGTATTGAGAAA	0.368													A|||	32	0.00638978	0.0129	0.0101	5008	,	,		20889	0.0		0.008	False		,,,				2504	0.0				p.Y286Y		Atlas-SNP	.											.	SLC23A2	62	.	0			c.C858T						PASS	.	A	,	55,4351	821.2+/-416.4	0,55,2148	119.0	122.0	121.0		858,858	3.7	1.0	20	dbSNP_127	121	107,8493	814.5+/-407.0	1,105,4194	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1,160,6342	AA,AG,GG		1.2442,1.2483,1.2456	,	286/651,286/651	4855309	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon10			TCTGGCGTATTGA	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.858C>T	20.37:g.4855309G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1	11	0.005036630036630037	3	0.006097560975609756	5	0.013812154696132596	0	0.0	3	0.00395778364116095	A	0.141	-1.102585	0.01828	0.012483	0.012442	ENSG00000089057	ENST00000423430	.	.	.	5.9	3.67	0.42095	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44772	-0.9306	4	.	.	.	-10.7793	8.3011	0.32014	0.7051:0.0:0.2949:0.0	rs41282100	.	.	.	C	43	.	.	R	-	1	0	SLC23A2	4803309	1.000000	0.71417	0.982000	0.44146	0.006000	0.05464	2.001000	0.40825	0.161000	0.19458	-0.982000	0.02568	CGC	G|0.990;A|0.010	0.010	strong		0.368	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
ENPP3	5169	hgsc.bcm.edu	37	6	132061420	132061420	+	Missense_Mutation	SNP	G	G	A	rs17601580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:132061420G>A	ENST00000414305.1	+	25	2685	c.2357G>A	c.(2356-2358)aGt>aAt	p.S786N	ENPP3_ENST00000358229.5_3'UTR|ENPP3_ENST00000357639.3_Missense_Mutation_p.S786N			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	786	Nuclease.		S -> N (in dbSNP:rs17601580).		immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		GTGCTGACCAGTTGTAAAAAC	0.443													G|||	447	0.0892572	0.0106	0.0879	5008	,	,		15569	0.0129		0.1998	False		,,,				2504	0.1616				p.S786N		Atlas-SNP	.											.	ENPP3	117	.	0			c.G2357A						PASS	.	G	ASN/SER	126,4280	92.0+/-130.7	1,124,2078	111.0	97.0	102.0		2357	5.4	0.3	6	dbSNP_123	102	1403,7197	270.4+/-288.9	106,1191,3003	yes	missense	ENPP3	NM_005021.3	46	107,1315,5081	AA,AG,GG		16.314,2.8597,11.7561	possibly-damaging	786/876	132061420	1529,11477	2203	4300	6503	SO:0001583	missense	5169	exon24			TGACCAGTTGTAA	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.2357G>A	6.37:g.132061420G>A	ENSP00000406261:p.Ser786Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	47	40	0.851064	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	37	CCDS5148.1	213	0.09752747252747253	8	0.016260162601626018	40	0.11049723756906077	5	0.008741258741258742	160	0.21108179419525067	G	24.4	4.527897	0.85706	0.028597	0.16314	ENSG00000154269	ENST00000414305;ENST00000357639	T;T	0.70399	-0.48;-0.48	5.45	5.45	0.79879	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.061286	0.64402	D	0.000002	T	0.81264	0.4786	M	0.82823	2.61	0.09310	P	1.0	D	0.54207	0.965	P	0.57371	0.819	T	0.82874	-0.0241	9	0.62326	D	0.03	-22.9283	19.6632	0.95882	0.0:0.0:1.0:0.0	rs17601580;rs52796056;rs58865025;rs17601580	786	O14638	ENPP3_HUMAN	N	786	ENSP00000406261:S786N;ENSP00000350265:S786N	ENSP00000350265:S786N	S	+	2	0	ENPP3	132103113	1.000000	0.71417	0.332000	0.25469	0.987000	0.75469	8.015000	0.88690	2.716000	0.92895	0.655000	0.94253	AGT	G|0.897;A|0.103	0.103	strong		0.443	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		
CRACR2A	84766	hgsc.bcm.edu	37	12	3805977	3805977	+	Missense_Mutation	SNP	A	A	C	rs144314920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:3805977A>C	ENST00000252322.1	-	4	657	c.189T>G	c.(187-189)gaT>gaG	p.D63E	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.D63E|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.D63E	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		63	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TGCCTTCAGCATCACAGGTCT	0.567													A|||	2	0.000399361	0.0	0.0014	5008	,	,		20268	0.0		0.001	False		,,,				2504	0.0				p.D63E		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.T189G						PASS	.	A	GLU/ASP,GLU/ASP	0,4406		0,0,2203	133.0	96.0	108.0		189,189	-4.5	0.0	12	dbSNP_134	108	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	45,45	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	probably-damaging,probably-damaging	63/732,63/396	3805977	5,13001	2203	4300	6503	SO:0001583	missense	84766	exon4			TTCAGCATCACAG																												ENST00000252322.1:c.189T>G	12.37:g.3805977A>C	ENSP00000252322:p.Asp63Glu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.653645	0.67472	0.0	5.81E-4	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;D;T	0.95821	-0.03;-3.82;-0.03	5.57	-4.47	0.03525	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.97430	0.9159	M	0.89904	3.07	0.21553	N	0.999645	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.996;0.991	D	0.94659	0.7846	10	0.87932	D	0	-24.417	15.1484	0.72677	0.2367:0.0:0.7633:0.0	.	63;63;63	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	E	63	ENSP00000409382:D63E;ENSP00000412496:D63E;ENSP00000252322:D63E	ENSP00000252322:D63E	D	-	3	2	EFCAB4B	3676238	0.001000	0.12720	0.009000	0.14445	0.854000	0.48673	-0.320000	0.08028	-0.748000	0.04753	-0.263000	0.10527	GAT	A|1.000;C|0.000	0.000	strong		0.567	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
UNC79	57578	hgsc.bcm.edu	37	14	94088369	94088369	+	Missense_Mutation	SNP	T	T	C	rs28670114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:94088369T>C	ENST00000393151.2	+	30	4790	c.4790T>C	c.(4789-4791)gTa>gCa	p.V1597A	UNC79_ENST00000555664.1_Missense_Mutation_p.V1597A|UNC79_ENST00000256339.4_Missense_Mutation_p.V1420A|UNC79_ENST00000553484.1_Missense_Mutation_p.V1619A			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	1597			V -> A (in dbSNP:rs28670114).		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						GACTCGCCGGTAAAGCCTGCT	0.478													T|||	594	0.11861	0.1634	0.134	5008	,	,		19307	0.004		0.2038	False		,,,				2504	0.0777				p.V1420A		Atlas-SNP	.											.	UNC79	366	.	0			c.T4259C						PASS	.	T	ALA/VAL	675,3731	284.6+/-277.7	54,567,1582	69.0	73.0	72.0		4259	-10.5	0.0	14	dbSNP_125	72	1535,7065	288.0+/-298.5	140,1255,2905	yes	missense	UNC79	NM_020818.3	64	194,1822,4487	CC,CT,TT		17.8488,15.32,16.9922	benign	1420/2459	94088369	2210,10796	2203	4300	6503	SO:0001583	missense	57578	exon30			CGCCGGTAAAGCC	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.4790T>C	14.37:g.94088369T>C	ENSP00000376858:p.Val1597Ala	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		296	0.13553113553113552	77	0.1565040650406504	55	0.15193370165745856	1	0.0017482517482517483	163	0.21503957783641162	T	1.765	-0.485748	0.04352	0.1532	0.178488	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.17054	2.3;2.31;2.3;2.3	5.85	-10.5	0.00291	.	1.244990	0.05238	N	0.511633	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	0.36311	-0.9753	9	0.07990	T	0.79	1.8056	7.1867	0.25803	0.0888:0.115:0.523:0.2731	rs28670114	1619	C9JQL1	.	A	1420;1597;1619;1597;1619	ENSP00000256339:V1420A;ENSP00000450868:V1597A;ENSP00000451360:V1619A;ENSP00000376858:V1597A	ENSP00000256339:V1420A	V	+	2	0	KIAA1409	93158122	0.000000	0.05858	0.000000	0.03702	0.230000	0.25150	-0.415000	0.07106	-1.287000	0.02381	-0.680000	0.03767	GTA	T|0.833;C|0.167	0.167	strong		0.478	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
NFATC2	4773	hgsc.bcm.edu	37	20	50140627	50140627	+	Silent	SNP	G	G	C	rs3746420	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:50140627G>C	ENST00000396009.3	-	2	372	c.153C>G	c.(151-153)gtC>gtG	p.V51V	NFATC2_ENST00000609507.1_Intron|NFATC2_ENST00000371564.3_Silent_p.V51V|NFATC2_ENST00000610033.1_Intron|NFATC2_ENST00000609943.1_Silent_p.V31V|NFATC2_ENST00000414705.1_Silent_p.V31V	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	51					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GTGGGCTGGCGACCTTATGTG	0.587													G|||	299	0.0597045	0.0507	0.0447	5008	,	,		13783	0.0734		0.0606	False		,,,				2504	0.0675				p.V51V		Atlas-SNP	.											.	NFATC2	112	.	0			c.C153G						PASS	.	G	,,	177,4227	106.0+/-144.5	5,167,2030	46.0	54.0	51.0		93,153,153	2.1	0.9	20	dbSNP_107	51	493,8105	137.8+/-194.7	17,459,3823	no	coding-synonymous,coding-synonymous,coding-synonymous	NFATC2	NM_001136021.1,NM_012340.3,NM_173091.2	,,	22,626,5853	CC,CG,GG		5.7339,4.0191,5.1531	,,	31/902,51/922,51/926	50140627	670,12332	2202	4299	6501	SO:0001819	synonymous_variant	4773	exon2			GCTGGCGACCTTA	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.153C>G	20.37:g.50140627G>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Silent	SNP	ENST00000396009.3	37	CCDS13437.1																																																																																			G|0.939;C|0.061	0.061	strong		0.587	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
ABCD4	5826	hgsc.bcm.edu	37	14	74759006	74759006	+	Missense_Mutation	SNP	C	C	T	rs3742801	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:74759006C>T	ENST00000356924.4	-	11	1245	c.1102G>A	c.(1102-1104)Gag>Aag	p.E368K	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000298816.7_Missense_Mutation_p.E264K	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	368			E -> K (in dbSNP:rs3742801). {ECO:0000269|PubMed:12111378, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.6}.		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)		AAGCCCCACTCGCTCTCGCCC	0.572													C|||	1354	0.270367	0.1475	0.2723	5008	,	,		20469	0.247		0.3857	False		,,,				2504	0.3405				p.E368K		Atlas-SNP	.											.	ABCD4	54	.	0			c.G1102A						PASS	.	C	LYS/GLU	868,3538	339.4+/-305.8	83,702,1418	91.0	82.0	85.0		1102	1.5	0.5	14	dbSNP_107	85	3128,5472	476.2+/-369.3	553,2022,1725	yes	missense	ABCD4	NM_005050.3	56	636,2724,3143	TT,TC,CC		36.3721,19.7004,30.7243	benign	368/607	74759006	3996,9010	2203	4300	6503	SO:0001583	missense	5826	exon11			CCCACTCGCTCTC	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.1102G>A	14.37:g.74759006C>T	ENSP00000349396:p.Glu368Lys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	590	0.27014652014652013	65	0.13211382113821138	104	0.287292817679558	138	0.24125874125874125	283	0.3733509234828496	C	13.35	2.210747	0.39102	0.197004	0.363721	ENSG00000119688	ENST00000356924;ENST00000298816	D;D	0.94376	-3.41;-3.14	5.48	1.48	0.22813	ABC transporter, transmembrane domain, type 1 (1);	0.596993	0.19358	N	0.116227	T	0.00012	0.0000	N	0.08118	0	0.49051	P	2.5799999999998047E-4	B;B;B;B	0.14805	0.011;0.001;0.006;0.002	B;B;B;B	0.11329	0.006;0.001;0.001;0.001	T	0.07195	-1.0785	9	0.08381	T	0.77	.	5.2873	0.15708	0.0:0.4646:0.3032:0.2322	rs3742801;rs17782478;rs17850966;rs52835914;rs56756083;rs3742801	264;264;368;368	F8W7M4;B7Z4V6;A8K5L7;O14678	.;.;.;ABCD4_HUMAN	K	368;264	ENSP00000349396:E368K;ENSP00000298816:E264K	ENSP00000298816:E264K	E	-	1	0	ABCD4	73828759	0.003000	0.15002	0.542000	0.28115	0.947000	0.59692	0.007000	0.13174	0.337000	0.23665	0.655000	0.94253	GAG	C|0.710;T|0.290	0.290	strong		0.572	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
ZNF480	147657	hgsc.bcm.edu	37	19	52825032	52825032	+	Missense_Mutation	SNP	C	C	T	rs13343641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52825032C>T	ENST00000595962.1	+	5	595	c.529C>T	c.(529-531)Ccc>Tcc	p.P177S	CTD-2525I3.6_ENST00000594379.1_RNA|ZNF480_ENST00000335090.6_Missense_Mutation_p.P100S|ZNF480_ENST00000490272.1_3'UTR|ZNF480_ENST00000334564.7_Missense_Mutation_p.P134S	NM_144684.2	NP_653285.2	Q8WV37	ZN480_HUMAN	zinc finger protein 480	177			P -> S (in dbSNP:rs13343641).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(134;0.00212)|OV - Ovarian serous cystadenocarcinoma(262;0.00369)		TGTCAAAACCCCCATTTTTAA	0.343													C|||	841	0.167931	0.1203	0.1513	5008	,	,		19266	0.2292		0.2177	False		,,,				2504	0.1299				p.P177S		Atlas-SNP	.											.	ZNF480	123	.	0			c.C529T						PASS	.	C	SER/PRO	610,3796	265.0+/-266.4	47,516,1640	84.0	82.0	83.0		529	-2.5	0.0	19	dbSNP_121	83	1736,6864	313.7+/-311.4	167,1402,2731	yes	missense	ZNF480	NM_144684.2	74	214,1918,4371	TT,TC,CC		20.186,13.8448,18.0378	benign	177/536	52825032	2346,10660	2203	4300	6503	SO:0001583	missense	147657	exon5			AAAACCCCCATTT	AY512662	CCDS12850.2, CCDS74437.1	19q13.41	2013-01-08			ENSG00000198464	ENSG00000198464		"""Zinc fingers, C2H2-type"", ""-"""	23305	protein-coding gene	gene with protein product		613910				15219843	Standard	XM_005258525		Approved	MGC32104	uc010ydl.2	Q8WV37	OTTHUMG00000157507	ENST00000595962.1:c.529C>T	19.37:g.52825032C>T	ENSP00000471754:p.Pro177Ser	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	240	121	0.504167	NM_144684	Q5JPG9|Q6P0Q4|Q8N1M5	Missense_Mutation	SNP	ENST00000595962.1	37	CCDS12850.2	401	0.18360805860805862	57	0.11585365853658537	60	0.16574585635359115	124	0.21678321678321677	160	0.21108179419525067	C	8.368	0.834575	0.16820	0.138448	0.20186	ENSG00000198464	ENST00000468240;ENST00000334564;ENST00000335090	T;T;T	0.06142	3.48;3.43;3.34	2.02	-2.54	0.06307	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.29716	0.026;0.255	B;B	0.26614	0.005;0.071	T	0.47774	-0.9091	8	0.72032	D	0.01	.	0.1334	0.00076	0.3098:0.2659:0.1932:0.2311	rs13343641;rs52836994;rs58264265;rs13343641	134;177	F8WEZ9;Q8WV37	.;ZN480_HUMAN	S	177;134;100	ENSP00000417424:P177S;ENSP00000334164:P134S;ENSP00000335670:P100S	ENSP00000334164:P134S	P	+	1	0	ZNF480	57516844	0.000000	0.05858	0.006000	0.13384	0.571000	0.35966	-0.315000	0.08081	-0.333000	0.08476	0.313000	0.20887	CCC	C|0.820;T|0.180	0.180	strong		0.343	ZNF480-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349001.3	NM_144684	
CENPN	55839	hgsc.bcm.edu	37	16	81056441	81056441	+	Intron	SNP	T	T	G	rs3743503	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81056441T>G	ENST00000305850.5	+	7	1423				RP11-303E16.3_ENST00000566390.1_RNA|RP11-303E16.3_ENST00000562315.1_RNA|CENPN_ENST00000393335.3_Intron|RP11-303E16.3_ENST00000561808.1_RNA|CENPN_ENST00000299572.5_Nonstop_Mutation_p.*205E|CMC2_ENST00000565914.1_5'Flank|CENPN_ENST00000428963.2_Intron|CENPN_ENST00000439957.3_Intron	NM_001100624.2|NM_001270474.1	NP_001094094.2|NP_001257403.1	Q96H22	CENPN_HUMAN	centromere protein N						CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|large_intestine(5)|lung(4)	10						AGCTTGCAATTAGTGAACATG	0.338													t|||	664	0.132588	0.0658	0.1369	5008	,	,		17491	0.2063		0.1262	False		,,,				2504	0.1503				p.X205E		Atlas-SNP	.											.	CENPN	84	.	0			c.T613G						PASS	.	T	,,GLU/stop	295,4109	149.9+/-184.0	8,279,1915	54.0	58.0	56.0		,,613	-8.3	0.0	16	dbSNP_107	56	1003,7597	211.8+/-252.3	66,871,3363	yes	intron,intron,stop-lost	CENPN	NM_001100624.1,NM_001100625.1,NM_018455.4	,,	74,1150,5278	GG,GT,TT		11.6628,6.6985,9.9815	,,	,,205/205	81056441	1298,11706	2202	4300	6502	SO:0001627	intron_variant	55839	exon7			TGCAATTAGTGAA	AK026313	CCDS10931.1, CCDS42199.1, CCDS42200.1, CCDS58482.1, CCDS58483.1	16q23.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000166451	ENSG00000166451			30873	protein-coding gene	gene with protein product		611509	"""chromosome 16 open reading frame 60"""	C16orf60		16622419	Standard	NM_001100625		Approved	FLJ13607, FLJ22660, BM039	uc002ffy.4	Q96H22	OTTHUMG00000137628	ENST00000305850.5:c.633+138T>G	16.37:g.81056441T>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	76	30	0.394737	NM_018455	A8MZE6|B3KN53|B4DJD1|B4DPY7|C9JJM5|D3DUK8|E7ES30|E7ETS3|Q9NZ83	Missense_Mutation	SNP	ENST00000305850.5	37	CCDS42200.1	312	0.14285714285714285	36	0.07317073170731707	54	0.14917127071823205	121	0.21153846153846154	101	0.13324538258575197	T	0.869	-0.732616	0.03135	0.066985	0.116628	ENSG00000166451	ENST00000299572	.	.	.	4.16	-8.33	0.00992	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.2879	0.04131	0.4934:0.2626:0.0955:0.1485	rs3743503;rs52826364;rs61114085;rs3743503	.	.	.	E	205	.	.	X	+	1	0	CENPN	79613942	0.006000	0.16342	0.000000	0.03702	0.000000	0.00434	0.047000	0.14056	-1.710000	0.01397	-1.133000	0.01973	TAG	T|0.878;G|0.122	0.122	strong		0.338	CENPN-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269051.1	NM_018455	
CKAP2L	150468	hgsc.bcm.edu	37	2	113498566	113498566	+	Missense_Mutation	SNP	A	A	G	rs3811040	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113498566A>G	ENST00000302450.6	-	8	1919	c.1841T>C	c.(1840-1842)tTa>tCa	p.L614S	CKAP2L_ENST00000541405.1_Missense_Mutation_p.L449S|NT5DC4_ENST00000327581.4_Intron	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	614			L -> S (in dbSNP:rs3811040).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						TTCAGCAACTAAAGAGTCAGA	0.368													A|||	2116	0.422524	0.056	0.5519	5008	,	,		22421	0.6895		0.508	False		,,,				2504	0.4632				p.L614S		Atlas-SNP	.											.	CKAP2L	54	.	0			c.T1841C						PASS	.	A	SER/LEU	551,3855	244.7+/-253.9	35,481,1687	149.0	137.0	141.0		1841	-0.5	0.0	2	dbSNP_107	141	4338,4262	579.4+/-390.9	1127,2084,1089	yes	missense	CKAP2L	NM_152515.3	145	1162,2565,2776	GG,GA,AA		49.5581,12.5057,37.5903	benign	614/746	113498566	4889,8117	2203	4300	6503	SO:0001583	missense	150468	exon8			GCAACTAAAGAGT	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.1841T>C	2.37:g.113498566A>G	ENSP00000305204:p.Leu614Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	152	64	0.421053	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	1006	0.4606227106227106	30	0.06097560975609756	197	0.5441988950276243	400	0.6993006993006993	379	0.5	A	0.014	-1.597170	0.00857	0.125057	0.504419	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.20598	2.06;2.06	4.43	-0.529	0.11901	.	1.678030	0.02972	N	0.144541	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.19331	0.009;0.035	B;B	0.21360	0.007;0.034	T	0.36187	-0.9758	9	0.09338	T	0.73	0.421	7.2134	0.25947	0.5654:0.0:0.4346:0.0	rs3811040;rs17649870;rs56445792;rs58162560;rs3811040	203;614	Q8IYA6-2;Q8IYA6	.;CKP2L_HUMAN	S	449;614	ENSP00000438763:L449S;ENSP00000305204:L614S	ENSP00000305204:L614S	L	-	2	0	CKAP2L	113215037	0.000000	0.05858	0.000000	0.03702	0.368000	0.29767	-0.101000	0.10973	-0.079000	0.12707	0.533000	0.62120	TTA	A|0.592;G|0.408	0.408	strong		0.368	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
ITGBL1	9358	hgsc.bcm.edu	37	13	102366825	102366825	+	Silent	SNP	A	A	G	rs2281991	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:102366825A>G	ENST00000376180.3	+	10	1536	c.1317A>G	c.(1315-1317)gaA>gaG	p.E439E	RP11-397O8.7_ENST00000606869.1_lincRNA|ITGBL1_ENST00000376162.3_Silent_p.E346E|ITGBL1_ENST00000545560.2_Silent_p.E298E	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	439	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					GTTCTGCTGAAGAGTGGTATA	0.393													A|||	1071	0.213858	0.0847	0.1614	5008	,	,		21448	0.4058		0.1521	False		,,,				2504	0.2914				p.E439E		Atlas-SNP	.											.	ITGBL1	83	.	0			c.A1317G						PASS	.	A		416,3990	205.5+/-227.4	23,370,1810	424.0	393.0	403.0		1317	1.7	0.2	13	dbSNP_100	403	1183,7417	241.3+/-271.7	84,1015,3201	no	coding-synonymous	ITGBL1	NM_004791.1		107,1385,5011	GG,GA,AA		13.7558,9.4417,12.2943		439/495	102366825	1599,11407	2203	4300	6503	SO:0001819	synonymous_variant	9358	exon10			TGCTGAAGAGTGG	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"""ten integrin EGF-like repeat domains protein"", ""ITGBL1, integrin beta-like 1"""	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.1317A>G	13.37:g.102366825A>G		Somatic	241	1	0.00414938		WXS	Illumina HiSeq	Phase_I	221	112	0.506787	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Silent	SNP	ENST00000376180.3	37	CCDS9499.1																																																																																			A|0.829;G|0.171	0.171	strong		0.393	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791	
PCDHB6	56130	hgsc.bcm.edu	37	5	140531193	140531193	+	Missense_Mutation	SNP	C	C	T	rs149392351	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140531193C>T	ENST00000231136.1	+	1	1355	c.1355C>T	c.(1354-1356)aCc>aTc	p.T452I	PCDHB6_ENST00000543635.1_Missense_Mutation_p.T316I	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	452					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTCACCCAAACCTCCTACACC	0.592													C|||	7	0.00139776	0.0023	0.0014	5008	,	,		15610	0.0		0.003	False		,,,				2504	0.0				p.T452I		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C1355T						PASS	.	C	ILE/THR	3,4403	6.2+/-15.9	0,3,2200	91.0	98.0	95.0		1355	3.3	0.9	5	dbSNP_134	95	24,8570	16.0+/-53.3	0,24,4273	no	missense	PCDHB6	NM_018939.2	89	0,27,6473	TT,TC,CC		0.2793,0.0681,0.2077	benign	452/795	140531193	27,12973	2203	4297	6500	SO:0001583	missense	56130	exon1			CCCAAACCTCCTA	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1355C>T	5.37:g.140531193C>T	ENSP00000231136:p.Thr452Ile	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	113	49	0.433628	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	3	0.00395778364116095	C	11.45	1.642518	0.29246	6.81E-4	0.002793	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01767	4.65;4.65	4.18	3.28	0.37604	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.08133	0.0203	M	0.69823	2.125	0.09310	N	1	D	0.59357	0.985	P	0.61070	0.883	T	0.05869	-1.0859	9	0.66056	D	0.02	.	13.947	0.64091	0.0:0.8464:0.1536:0.0	.	452	Q9Y5E3	PCDB6_HUMAN	I	316;452;237	ENSP00000438466:T316I;ENSP00000231136:T452I	ENSP00000231136:T452I	T	+	2	0	PCDHB6	140511377	0.000000	0.05858	0.926000	0.36857	0.978000	0.69477	-0.227000	0.09126	0.840000	0.34995	0.485000	0.47835	ACC	C|0.997;T|0.003	0.003	strong		0.592	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
NUTM1	256646	hgsc.bcm.edu	37	15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	rs149177074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:34649336G>A	ENST00000333756.4	+	7	3198	c.3043G>A	c.(3043-3045)Gag>Aag	p.E1015K	NUTM1_ENST00000438749.3_Missense_Mutation_p.E1033K|NUTM1_ENST00000537011.1_Missense_Mutation_p.E1043K	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1015						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GGAAGAGGATGAGGAACTCTC	0.498													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20984	0.0		0.006	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	0			c.G3043A						PASS	.	G	LYS/GLU	4,4398	9.9+/-24.2	0,4,2197	76.0	61.0	66.0		3043	4.3	1.0	15	dbSNP_134	66	31,8565	22.8+/-68.1	0,31,4267	yes	missense	C15orf55	NM_175741.1	56	0,35,6464	AA,AG,GG		0.3606,0.0909,0.2693	benign	1015/1133	34649336	35,12963	2201	4298	6499	SO:0001583	missense	256646	exon7			GAGGATGAGGAAC	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3043G>A	15.37:g.34649336G>A	ENSP00000329448:p.Glu1015Lys	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	15.74	2.923315	0.52653	9.09E-4	0.003606	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.13307	2.62;2.6;2.61	5.2	4.28	0.50868	.	0.557345	0.16563	N	0.208980	T	0.11324	0.0276	L	0.61387	1.9	0.33479	D	0.58722	B;B;B	0.29085	0.232;0.154;0.192	B;B;B	0.27076	0.059;0.076;0.031	T	0.10222	-1.0639	10	0.66056	D	0.02	.	9.6167	0.39696	0.0944:0.0:0.9056:0.0	.	1033;1043;1015	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	K	1043;1033;1015	ENSP00000444896:E1043K;ENSP00000407031:E1033K;ENSP00000329448:E1015K	ENSP00000329448:E1015K	E	+	1	0	C15orf55	32436628	0.965000	0.33210	0.991000	0.47740	0.842000	0.47809	1.928000	0.40104	1.422000	0.47177	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.498	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
EPS8L2	64787	hgsc.bcm.edu	37	11	709567	709567	+	Missense_Mutation	SNP	G	G	A	rs12283031	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:709567G>A	ENST00000533256.1	+	4	434	c.59G>A	c.(58-60)cGg>cAg	p.R20Q	AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000526198.1_Missense_Mutation_p.R20Q|EPS8L2_ENST00000318562.8_Missense_Mutation_p.R20Q|EPS8L2_ENST00000530636.1_Missense_Mutation_p.R20Q			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	20					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)		AGCCTGGGCCGGTCCGACGGT	0.637													G|||	117	0.0233626	0.0552	0.0173	5008	,	,		14306	0.0		0.0189	False		,,,				2504	0.0133				p.R20Q		Atlas-SNP	.											.	EPS8L2	42	.	0			c.G59A						PASS	.	G	GLN/ARG	239,4153	132.1+/-168.6	5,229,1962	42.0	37.0	39.0		59	2.7	1.0	11	dbSNP_120	39	190,8406	82.0+/-144.6	5,180,4113	yes	missense	EPS8L2	NM_022772.3	43	10,409,6075	AA,AG,GG		2.2103,5.4417,3.303	possibly-damaging	20/716	709567	429,12559	2196	4298	6494	SO:0001583	missense	64787	exon3			TGGGCCGGTCCGA	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.59G>A	11.37:g.709567G>A	ENSP00000435585:p.Arg20Gln	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Missense_Mutation	SNP	ENST00000533256.1	37	CCDS31328.1	75	0.034340659340659344	32	0.06504065040650407	13	0.03591160220994475	5	0.008741258741258742	25	0.032981530343007916	G	12.81	2.048644	0.36181	0.054417	0.022103	ENSG00000177106	ENST00000524763;ENST00000527199;ENST00000318562;ENST00000533256;ENST00000534755;ENST00000533500;ENST00000531348;ENST00000530636;ENST00000526198	T;T;T;T;T;T	0.42131	0.98;2.08;2.08;0.98;2.08;2.08	2.74	2.74	0.32292	.	0.462105	0.17420	N	0.174879	T	0.07052	0.0179	L	0.60455	1.87	0.32699	N	0.513111	D;D;P	0.76494	0.968;0.999;0.913	B;P;B	0.58970	0.161;0.849;0.161	T	0.41822	-0.9487	10	0.56958	D	0.05	-41.8667	9.1549	0.36988	0.0:0.0:1.0:0.0	rs12283031	20;48;20	B7ZKL3;B4DFD2;Q9H6S3	.;.;ES8L2_HUMAN	Q	20	ENSP00000435128:R20Q;ENSP00000320828:R20Q;ENSP00000435585:R20Q;ENSP00000432765:R20Q;ENSP00000436035:R20Q;ENSP00000436230:R20Q	ENSP00000320828:R20Q	R	+	2	0	EPS8L2	699567	0.035000	0.19736	0.969000	0.41365	0.596000	0.36781	1.342000	0.33919	1.842000	0.53543	0.555000	0.69702	CGG	G|0.963;A|0.037	0.037	strong		0.637	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
ANAPC1	64682	hgsc.bcm.edu	37	2	112619981	112619981	+	Missense_Mutation	SNP	G	G	A	rs201128090	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:112619981G>A	ENST00000341068.3	-	10	2019	c.1247C>T	c.(1246-1248)aCg>aTg	p.T416M		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	416					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.T416M(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						ATTAGTAATCGTTTCTGTCCA	0.313																																					p.T416M		Atlas-SNP	.											ANAPC1,NS,carcinoma,0,2	ANAPC1	116	2	1	Substitution - Missense(1)	skin(1)	c.C1247T						scavenged	.						6.0	7.0	7.0					2																	112619981		2139	4197	6336	SO:0001583	missense	64682	exon10			GTAATCGTTTCTG	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.1247C>T	2.37:g.112619981G>A	ENSP00000339109:p.Thr416Met	Somatic	145	1	0.00689655		WXS	Illumina HiSeq	Phase_I	182	33	0.181319	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.172314	0.38315	.	.	ENSG00000153107	ENST00000341068	.	.	.	5.64	4.75	0.60458	.	0.837001	0.09499	N	0.793841	T	0.39886	0.1095	L	0.50333	1.59	0.09310	N	1	B	0.33904	0.431	B	0.29785	0.107	T	0.32824	-0.9892	9	0.59425	D	0.04	-0.0065	13.163	0.59554	0.0752:0.0:0.9248:0.0	.	416	Q9H1A4	APC1_HUMAN	M	416	.	ENSP00000339109:T416M	T	-	2	0	ANAPC1	112336452	0.983000	0.35010	0.049000	0.19019	0.939000	0.58152	6.428000	0.73383	2.645000	0.89757	0.655000	0.94253	ACG	G|0.940;A|0.060	0.060	strong		0.313	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
KRT6B	3854	hgsc.bcm.edu	37	12	52841765	52841765	+	Silent	SNP	G	G	A	rs388626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52841765G>A	ENST00000252252.3	-	7	1268	c.1221C>T	c.(1219-1221)gcC>gcT	p.A407A		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	407	Coil 2.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CAGCAATGGCGGCCTGTAGGT	0.537													G|||	2592	0.517572	0.4781	0.572	5008	,	,		21821	0.6825		0.505	False		,,,				2504	0.3753				p.A407A		Atlas-SNP	.											.	KRT6B	90	.	0			c.C1221T						PASS	.	G		1978,2428	558.4+/-380.0	438,1102,663	74.0	68.0	70.0		1221	-4.8	0.0	12	dbSNP_80	70	4228,4372	571.5+/-389.6	1031,2166,1103	no	coding-synonymous	KRT6B	NM_005555.3		1469,3268,1766	AA,AG,GG		49.1628,44.8933,47.7164		407/565	52841765	6206,6800	2203	4300	6503	SO:0001819	synonymous_variant	3854	exon7			AATGGCGGCCTGT	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.1221C>T	12.37:g.52841765G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			G|0.488;A|0.512	0.512	strong		0.537	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
PGAM1	5223	hgsc.bcm.edu	37	10	99190185	99190185	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99190185G>A	ENST00000334828.5	+	2	337	c.189G>A	c.(187-189)gcG>gcA	p.A63A	PGAM1_ENST00000467867.1_3'UTR	NM_002629.2	NP_002620.1	P18669	PGAM1_HUMAN	phosphoglycerate mutase 1 (brain)	63					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|regulation of glycolytic process (GO:0006110)|regulation of pentose-phosphate shunt (GO:0043456)|respiratory burst (GO:0045730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)|protein kinase binding (GO:0019901)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(252;0.162)		Epithelial(162;8.36e-10)|all cancers(201;5.62e-08)		AGAAGAGAGCGATCCGGACCC	0.522																																					p.A63A		Atlas-SNP	.											PGAM1,caecum,carcinoma,+1,1	PGAM1	11	1	0			c.G189A						PASS	.						101.0	105.0	104.0					10																	99190185		2203	4297	6500	SO:0001819	synonymous_variant	5223	exon2			GAGAGCGATCCGG	BC010038	CCDS7458.1	10q25.3	2012-10-02			ENSG00000171314	ENSG00000171314	5.4.2.1		8888	protein-coding gene	gene with protein product	"""Phosphoglycerate mutase A, nonmuscle form"""	172250		PGAMA		2846553	Standard	NM_002629		Approved	PGAM-B	uc001knh.3	P18669	OTTHUMG00000018846	ENST00000334828.5:c.189G>A	10.37:g.99190185G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_002629	Q9BWC0	Silent	SNP	ENST00000334828.5	37	CCDS7458.1																																																																																			.	.	none		0.522	PGAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049652.1	NM_002629	
DOT1L	84444	hgsc.bcm.edu	37	19	2226676	2226676	+	Missense_Mutation	SNP	G	G	A	rs3815308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	4	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	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	
CCHCR1	54535	hgsc.bcm.edu	37	6	31122330	31122330	+	Silent	SNP	G	G	A	rs130077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31122330G>A	ENST00000376266.5	-	4	599	c.477C>T	c.(475-477)aaC>aaT	p.N159N	CCHCR1_ENST00000451521.2_Silent_p.N212N|CCHCR1_ENST00000396263.2_Silent_p.N159N|CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000396268.3_Silent_p.N248N	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	159					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						CCTCTTCCAAGTTCTTCCGGA	0.607													G|||	573	0.114417	0.1528	0.1254	5008	,	,		17351	0.0625		0.168	False		,,,				2504	0.0532				p.N248N		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C744T						PASS	.	G	,,	509,2511		34,441,1035	255.0	323.0	298.0		636,744,477	1.2	1.0	6	dbSNP_78	298	846,4572		69,708,1932	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	103,1149,2967	AA,AG,GG		15.6146,16.8543,16.0583	,,	212/836,248/872,159/783	31122330	1355,7083	1510	2709	4219	SO:0001819	synonymous_variant	54535	exon4			TTCCAAGTTCTTC	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.477C>T	6.37:g.31122330G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	138	138	1	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			G|0.860;A|0.140	0.140	strong		0.607	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
DNHD1	144132	hgsc.bcm.edu	37	11	6549995	6549995	+	Missense_Mutation	SNP	A	A	G	rs7480644	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6549995A>G	ENST00000527990.2	+	9	2081	c.2081A>G	c.(2080-2082)aAt>aGt	p.N694S	DNHD1_ENST00000254579.6_Missense_Mutation_p.N694S			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	694					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CAGGCACTGAATATACAACAG	0.537													A|||	3633	0.725439	0.6831	0.6571	5008	,	,		20488	0.87		0.6302	False		,,,				2504	0.7802				p.N694S		Atlas-SNP	.											DNHD1,colon,carcinoma,0,1	DNHD1	198	1	0			c.A2081G						PASS	.	A	SER/ASN	937,447		321,295,76	55.0	47.0	49.0		2081	-0.9	0.0	11	dbSNP_116	49	2141,1041		726,689,176	yes	missense	DNHD1	NM_144666.2	46	1047,984,252	GG,GA,AA		32.7153,32.2977,32.5887	benign	694/4754	6549995	3078,1488	692	1591	2283	SO:0001583	missense	144132	exon11			CACTGAATATACA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.2081A>G	11.37:g.6549995A>G	ENSP00000436180:p.Asn694Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1547	0.7083333333333334	342	0.6951219512195121	235	0.649171270718232	484	0.8461538461538461	486	0.6411609498680739	A	2.474	-0.321286	0.05386	0.677023	0.672847	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.26223	1.75;1.75	5.6	-0.949	0.10376	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.14012	0.009	B	0.10450	0.005	T	0.27739	-1.0065	8	0.09338	T	0.73	.	1.8355	0.03139	0.4088:0.3113:0.1243:0.1556	rs7480644;rs58671974;rs7480644	694	Q96M86	DNHD1_HUMAN	S	694	ENSP00000254579:N694S;ENSP00000436180:N694S	ENSP00000254579:N694S	N	+	2	0	DNHD1	6506571	0.001000	0.12720	0.006000	0.13384	0.022000	0.10575	-0.181000	0.09740	-0.478000	0.06823	-1.017000	0.02453	AAT	A|0.284;G|0.716	0.716	strong		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
ABI3BP	25890	hgsc.bcm.edu	37	3	100617668	100617668	+	Silent	SNP	G	G	T	rs34999788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:100617668G>T	ENST00000284322.5	-	4	529	c.420C>A	c.(418-420)tcC>tcA	p.S140S	ABI3BP_ENST00000532144.1_5'Flank|ABI3BP_ENST00000471714.1_Silent_p.S140S|ABI3BP_ENST00000495063.1_Silent_p.S140S	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	140	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						GGAAACCCCAGGACAGGAAGA	0.478													G|||	270	0.0539137	0.0076	0.072	5008	,	,		20097	0.002		0.1541	False		,,,				2504	0.0542				p.S140S		Atlas-SNP	.											.	ABI3BP	305	.	0			c.C420A						PASS	.	G		126,4102		4,118,1992	88.0	97.0	94.0		420	4.6	1.0	3	dbSNP_126	94	1250,7252		93,1064,3094	no	coding-synonymous	ABI3BP	NM_015429.3		97,1182,5086	TT,TG,GG		14.7024,2.9801,10.8091		140/1076	100617668	1376,11354	2114	4251	6365	SO:0001819	synonymous_variant	25890	exon4			ACCCCAGGACAGG	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.420C>A	3.37:g.100617668G>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	78	45	0.576923	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Silent	SNP	ENST00000284322.5	37	CCDS46880.1																																																																																			G|0.913;T|0.087	0.087	strong		0.478	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
PINK1	65018	hgsc.bcm.edu	37	1	20977000	20977000	+	Missense_Mutation	SNP	A	A	C	rs1043424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:20977000A>C	ENST00000321556.4	+	8	1656	c.1562A>C	c.(1561-1563)aAt>aCt	p.N521T	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	521			N -> T (in dbSNP:rs1043424). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15349860, ECO:0000269|PubMed:15596610, ECO:0000269|PubMed:16009891, ECO:0000269|PubMed:16257123, ECO:0000269|PubMed:16482571, ECO:0000269|PubMed:17344846}.		activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCCCTGAAGAATCTGAAGTTA	0.498													A|||	1505	0.300519	0.2458	0.1931	5008	,	,		21372	0.3571		0.2922	False		,,,				2504	0.4008				p.N521T	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.A1562C						PASS	.	A	THR/ASN	1179,3227	413.9+/-336.6	167,845,1191	74.0	66.0	69.0		1562	1.5	0.2	1	dbSNP_86	69	2333,6267	390.2+/-343.2	309,1715,2276	yes	missense	PINK1	NM_032409.2	65	476,2560,3467	CC,CA,AA		27.1279,26.759,27.0029	benign	521/582	20977000	3512,9494	2203	4300	6503	SO:0001583	missense	65018	exon8			TGAAGAATCTGAA	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1562A>C	1.37:g.20977000A>C	ENSP00000364204:p.Asn521Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	87	0.87	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	37	CCDS211.1	614	0.28113553113553114	109	0.22154471544715448	80	0.22099447513812154	208	0.36363636363636365	217	0.2862796833773087	A	13.74	2.327369	0.41197	0.26759	0.271279	ENSG00000158828	ENST00000321556	T	0.74106	-0.81	5.83	1.55	0.23275	.	0.653207	0.17574	N	0.169362	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.17465	0.004;0.022	B;B	0.11329	0.005;0.006	T	0.18681	-1.0329	9	0.33141	T	0.24	-7.6155	7.3998	0.26956	0.6411:0.0:0.3589:0.0	rs1043424;rs60071348;rs1043424	214;521	Q9BXM7-2;Q9BXM7	.;PINK1_HUMAN	T	521	ENSP00000364204:N521T	ENSP00000364204:N521T	N	+	2	0	PINK1	20849587	0.208000	0.23494	0.242000	0.24170	0.980000	0.70556	0.601000	0.24119	0.382000	0.24878	0.402000	0.26972	AAT	A|0.725;C|0.275	0.275	strong		0.498	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
NLRP14	338323	hgsc.bcm.edu	37	11	7091569	7091569	+	Missense_Mutation	SNP	C	C	T	rs17280682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7091569C>T	ENST00000299481.4	+	11	3374	c.3028C>T	c.(3028-3030)Ctt>Ttt	p.L1010F		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	1010			L -> F (in dbSNP:rs17280682). {ECO:0000269|PubMed:16931801}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		CTCCTCTGCTCTTATCTGCAA	0.358													C|||	481	0.0960463	0.0666	0.1297	5008	,	,		19436	0.0169		0.2147	False		,,,				2504	0.0716				p.L1010F		Atlas-SNP	.											.	NLRP14	187	.	0			c.C3028T						PASS	.	C	PHE/LEU	368,4034	189.9+/-215.9	10,348,1843	108.0	103.0	105.0		3028	4.1	0.1	11	dbSNP_123	105	1848,6744	330.3+/-319.2	205,1438,2653	yes	missense	NLRP14	NM_176822.3	22	215,1786,4496	TT,TC,CC		21.5084,8.3598,17.054	probably-damaging	1010/1094	7091569	2216,10778	2201	4296	6497	SO:0001583	missense	338323	exon11			TCTGCTCTTATCT	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.3028C>T	11.37:g.7091569C>T	ENSP00000299481:p.Leu1010Phe	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	147	70	0.47619	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	246	0.11263736263736264	24	0.04878048780487805	48	0.13259668508287292	13	0.022727272727272728	161	0.21240105540897097	C	14.57	2.575489	0.45902	0.083598	0.215084	ENSG00000158077	ENST00000299481	T	0.61859	0.07	4.13	4.13	0.48395	.	0.000000	0.37095	N	0.002246	T	0.00073	0.0002	M	0.74881	2.28	0.47547	P	5.450000000000177E-4	P	0.40197	0.706	B	0.43838	0.433	T	0.07539	-1.0767	9	0.51188	T	0.08	.	12.1948	0.54290	0.0:1.0:0.0:0.0	rs17280682;rs58608223;rs17280682	1010	Q86W24	NAL14_HUMAN	F	1010	ENSP00000299481:L1010F	ENSP00000299481:L1010F	L	+	1	0	NLRP14	7048145	0.901000	0.30685	0.091000	0.20842	0.027000	0.11550	2.377000	0.44300	2.602000	0.87976	0.557000	0.71058	CTT	C|0.850;T|0.150	0.150	strong		0.358	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
ZSCAN29	146050	hgsc.bcm.edu	37	15	43661802	43661802	+	Missense_Mutation	SNP	T	T	C	rs3809482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43661802T>C	ENST00000396976.2	-	1	444	c.310A>G	c.(310-312)Aga>Gga	p.R104G	ZSCAN29_ENST00000396972.1_Missense_Mutation_p.R104G|TUBGCP4_ENST00000260383.7_5'Flank|ZSCAN29_ENST00000562072.1_Missense_Mutation_p.R103G|ZSCAN29_ENST00000568898.1_Missense_Mutation_p.R103G|TUBGCP4_ENST00000570081.1_3'UTR|TUBGCP4_ENST00000564079.1_5'Flank|ZSCAN29_ENST00000563508.1_5'Flank	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	104			R -> G (in dbSNP:rs3809482). {ECO:0000269|PubMed:14702039}.		regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		ACCGAAGATCTAGGTCTTCCA	0.463													C|||	2734	0.545927	0.9728	0.3357	5008	,	,		20870	0.4692		0.3082	False		,,,				2504	0.4417				p.R104G		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.A310G						PASS	.	C	GLY/ARG	3743,659	281.1+/-275.7	1596,551,54	96.0	107.0	103.0		310	3.9	1.0	15	dbSNP_107	103	2625,5973	686.6+/-404.1	393,1839,2067	yes	missense	ZSCAN29	NM_152455.3	125	1989,2390,2121	CC,CT,TT		30.5304,14.9705,48.9846	benign	104/853	43661802	6368,6632	2201	4299	6500	SO:0001583	missense	146050	exon1			AAGATCTAGGTCT	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.310A>G	15.37:g.43661802T>C	ENSP00000380174:p.Arg104Gly	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	180	67	0.372222	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Missense_Mutation	SNP	ENST00000396976.2	37	CCDS10095.2	1120	0.5128205128205128	473	0.9613821138211383	126	0.34806629834254144	287	0.5017482517482518	234	0.3087071240105541	C	12.58	1.979660	0.34942	0.850295	0.305304	ENSG00000140265	ENST00000396976;ENST00000396972	T;T	0.04049	3.72;3.72	4.79	3.87	0.44632	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (2);	0.138436	0.33161	N	0.005210	T	0.00012	0.0000	N	0.13140	0.3	0.09310	P	0.999999999179701	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.002;0.001;0.0	T	0.42189	-0.9466	9	0.02654	T	1	-9.2469	9.3264	0.37995	0.0:0.8239:0.0:0.1761	rs3809482;rs52793500;rs61337793;rs3809482	104;103;104;104	Q8IWY8-4;C9K0J8;Q8IWY8-3;Q8IWY8	.;.;.;ZSC29_HUMAN	G	104	ENSP00000380174:R104G;ENSP00000380170:R104G	ENSP00000380170:R104G	R	-	1	2	ZSCAN29	41449094	0.933000	0.31639	0.995000	0.50966	0.861000	0.49209	1.320000	0.33666	0.739000	0.32628	-0.119000	0.15052	AGA	T|0.485;C|0.515	0.515	strong		0.463	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
CTBP2	1488	hgsc.bcm.edu	37	10	126714966	126714966	+	Intron	SNP	A	A	G	rs3012075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:126714966A>G	ENST00000337195.5	-	3	458				CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.Y455H|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000494626.2_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)		TGCAGGGGGTACGTGGGGCTC	0.672													A|||	2243	0.447883	0.298	0.3343	5008	,	,		14085	0.6597		0.4811	False		,,,				2504	0.4785				p.Y455H		Atlas-SNP	.											.	CTBP2	100	.	0			c.T1363C						PASS	.	A	,,HIS/TYR	1449,2953		226,997,978	35.0	40.0	38.0		,,1363	4.0	0.0	10	dbSNP_101	38	4276,4324		1059,2158,1083	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,83	1285,3155,2061	GG,GA,AA		49.7209,32.9169,44.0317	,,possibly-damaging	,,455/986	126714966	5725,7277	2201	4300	6501	SO:0001627	intron_variant	1488	exon1			GGGGGTACGTGGG	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+12599T>C	10.37:g.126714966A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	93	42	0.451613	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	1004	0.4597069597069597	160	0.3252032520325203	124	0.3425414364640884	353	0.6171328671328671	367	0.4841688654353562	A	14.35	2.507941	0.44558	0.329169	0.497209	ENSG00000175029	ENST00000309035	D	0.83250	-1.7	4.04	4.04	0.47022	.	1.938270	0.02364	N	0.077162	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999341817	B	0.06786	0.001	B	0.08055	0.003	T	0.42582	-0.9443	8	0.62326	D	0.03	.	12.024	0.53360	1.0:0.0:0.0:0.0	rs3012075;rs3781414;rs17710513;rs60363956;rs3012075	455	P56545-2	.	H	455	ENSP00000311825:Y455H	ENSP00000311825:Y455H	Y	-	1	0	CTBP2	126704956	0.534000	0.26362	0.003000	0.11579	0.562000	0.35680	4.895000	0.63214	1.829000	0.53265	0.383000	0.25322	TAC	A|0.547;G|0.453	0.453	strong		0.672	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
HIST1H2BG	8339	hgsc.bcm.edu	37	6	26216584	26216584	+	Silent	SNP	C	C	T	rs16891427	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26216584C>T	ENST00000244601.3	-	1	288	c.288G>A	c.(286-288)caG>caA	p.Q96Q	HIST1H2AE_ENST00000303910.2_5'Flank	NM_003518.3	NP_003509.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bg	96					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(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	8		all_hematologic(11;0.196)				GCACGGCGGTCTGGATCTCCC	0.562													C|||	329	0.0656949	0.0719	0.0548	5008	,	,		18517	0.0615		0.0507	False		,,,				2504	0.0849				p.Q96Q		Atlas-SNP	.											.	HIST1H2BG	25	.	0			c.G288A						PASS	.	C		265,4141		6,253,1944	93.0	93.0	93.0		288	3.0	1.0	6	dbSNP_123	93	417,8183		11,395,3894	no	coding-synonymous	HIST1H2BG	NM_003518.3		17,648,5838	TT,TC,CC		4.8488,6.0145,5.2437		96/127	26216584	682,12324	2203	4300	6503	SO:0001819	synonymous_variant	8339	exon1			GGCGGTCTGGATC	M60750	CCDS4594.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000187990	ENSG00000273802		"""Histones / Replication-dependent"""	4746	protein-coding gene	gene with protein product		602798	"""H2B histone family, member A"", ""histone 1, H2bg"""	H2BFA		1916825, 12408966	Standard	NM_003518		Approved	H2B/a, H2B.1A	uc003ngz.2	P62807	OTTHUMG00000014446	ENST00000244601.3:c.288G>A	6.37:g.26216584C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	104	61	0.586538	NM_003518	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000244601.3	37	CCDS4594.1																																																																																			C|0.948;T|0.052	0.052	strong		0.562	HIST1H2BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040109.2	NM_003518	
ZNF853	54753	hgsc.bcm.edu	37	7	6661256	6661256	+	Missense_Mutation	SNP	C	C	G	rs11971880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6661256C>G	ENST00000457543.3	+	3	1192	c.634C>G	c.(634-636)Cag>Gag	p.Q212E		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	212	Gln-rich.		Q -> E (in dbSNP:rs11971880).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						ggaacagttacagcagcagca	0.512													C|||	493	0.0984425	0.1558	0.0994	5008	,	,		25510	0.0546		0.0855	False		,,,				2504	0.0787				p.Q212E		Atlas-SNP	.											.	ZNF853	32	.	0			c.C634G						PASS	.	C	GLU/GLN	212,1172		17,178,497	85.0	95.0	92.0		634	3.0	0.0	7	dbSNP_120	92	322,2860		12,298,1281	yes	missense	ZNF853	NM_017560.1	29	29,476,1778	GG,GC,CC		10.1194,15.3179,11.6951	probably-damaging	212/660	6661256	534,4032	692	1591	2283	SO:0001583	missense	54753	exon3			CAGTTACAGCAGC	AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.634C>G	7.37:g.6661256C>G	ENSP00000455585:p.Gln212Glu	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	213	209	0.981221	NM_017560		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																			C|0.905;G|0.095	0.095	strong		0.512	ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
MUC17	140453	hgsc.bcm.edu	37	7	100686291	100686291	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100686291G>A	ENST00000306151.4	+	3	11658	c.11594G>A	c.(11593-11595)cGt>cAt	p.R3865H		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3865					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)					ACTACCATACGTATTTCAATT	0.488																																					p.R3865H		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.G11594A						PASS	.						143.0	130.0	135.0					7																	100686291		2203	4300	6503	SO:0001583	missense	140453	exon3			CCATACGTATTTC	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.11594G>A	7.37:g.100686291G>A	ENSP00000302716:p.Arg3865His	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	3.518	-0.098385	0.07010	.	.	ENSG00000169876	ENST00000306151	T	0.02140	4.43	0.558	-1.12	0.09808	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	D	0.65443	0.935	T	0.40001	-0.9586	8	0.38643	T	0.18	.	.	.	.	.	3865	Q685J3	MUC17_HUMAN	H	3865	ENSP00000302716:R3865H	ENSP00000302716:R3865H	R	+	2	0	MUC17	100473011	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.161000	0.03144	-1.475000	0.01876	-1.089000	0.02181	CGT	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CLCN7	1186	hgsc.bcm.edu	37	16	1509123	1509123	+	Silent	SNP	G	G	A	rs12923538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1509123G>A	ENST00000382745.4	-	7	1265	c.660C>T	c.(658-660)caC>caT	p.H220H	CLCN7_ENST00000262318.8_Silent_p.H196H|CLCN7_ENST00000448525.1_Silent_p.H196H	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	220					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				GCCGCACCACGTGGGGGATCT	0.662													G|||	611	0.122005	0.2352	0.1225	5008	,	,		18275	0.0099		0.1113	False		,,,				2504	0.0951				p.H220H		Atlas-SNP	.											CLCN7,colon,carcinoma,-1,1	CLCN7	53	1	0			c.C660T						PASS	.	G	,	880,3516	332.0+/-302.3	101,678,1419	42.0	45.0	44.0		588,660	-1.5	1.0	16	dbSNP_121	44	1124,7476	228.4+/-263.5	77,970,3253	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	178,1648,4672	AA,AG,GG		13.0698,20.0182,15.4201	,	196/782,220/806	1509123	2004,10992	2198	4300	6498	SO:0001819	synonymous_variant	1186	exon7			CACCACGTGGGGG	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.660C>T	16.37:g.1509123G>A		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	190	74	0.389474	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			G|0.854;A|0.146	0.146	strong		0.662	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
TRIM22	10346	hgsc.bcm.edu	37	11	5718517	5718517	+	Missense_Mutation	SNP	G	G	A	rs7935564	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5718517G>A	ENST00000379965.3	+	3	740	c.463G>A	c.(463-465)Gat>Aat	p.D155N	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	155			D -> N (in dbSNP:rs7935564). {ECO:0000269|PubMed:15489334}.		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)		GATAAAGGAGGATCAAGAGGC	0.463											OREG0003730	type=REGULATORY REGION|Gene=TRIM22|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	2289	0.457069	0.4728	0.4928	5008	,	,		18237	0.1766		0.6372	False		,,,				2504	0.5143				p.D155N	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.G463A						PASS	.	G	ASN/ASP,ASN/ASP	1890,1908		463,964,472	46.0	50.0	48.0		463,463	-4.5	0.0	11	dbSNP_116	48	4965,3357		1482,2001,678	yes	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	23,23	1945,2965,1150	AA,AG,GG		40.3389,49.763,43.4406	benign,benign	155/495,155/499	5718517	6855,5265	1899	4161	6060	SO:0001583	missense	10346	exon3			AAGGAGGATCAAG	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.463G>A	11.37:g.5718517G>A	ENSP00000369299:p.Asp155Asn	Somatic	85	0	0	628	WXS	Illumina HiSeq	Phase_I	92	54	0.586957	NM_001199573	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	994	0.4551282051282051	233	0.4735772357723577	179	0.494475138121547	104	0.18181818181818182	478	0.6306068601583114	G	13.40	2.227061	0.39399	0.49763	0.596611	ENSG00000132274	ENST00000379965;ENST00000425490;ENST00000414641	T;T;T	0.71103	-0.08;-0.36;-0.54	4.07	-4.48	0.03515	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.26147	0.143;0.139	B;B	0.28011	0.085;0.03	T	0.44329	-0.9335	8	0.72032	D	0.01	.	2.2631	0.04072	0.3158:0.3428:0.2409:0.1004	rs7935564;rs52804308;rs60125811;rs7935564	155;155	Q8IYM9-2;Q8IYM9	.;TRI22_HUMAN	N	155	ENSP00000369299:D155N;ENSP00000400417:D155N;ENSP00000396849:D155N	ENSP00000369299:D155N	D	+	1	0	TRIM22	5675093	0.000000	0.05858	0.000000	0.03702	0.218000	0.24690	-2.582000	0.00905	-0.659000	0.05359	0.313000	0.20887	GAT	G|0.528;A|0.472	0.472	strong		0.463	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
ANXA7	310	hgsc.bcm.edu	37	10	75148116	75148116	+	Silent	SNP	A	A	G	rs2234965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75148116A>G	ENST00000372921.5	-	6	548	c.492T>C	c.(490-492)gaT>gaC	p.D164D	ANXA7_ENST00000492380.1_5'UTR|ANXA7_ENST00000535178.1_Silent_p.D34D	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	186					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)	p.D186D(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					CTCTTATAGCATCGAAGTTGG	0.378													A|||	884	0.176518	0.1785	0.0994	5008	,	,		20815	0.3026		0.0557	False		,,,				2504	0.2229				p.D186D		Atlas-SNP	.											ANXA7,NS,carcinoma,-2,2	ANXA7	50	2	1	Substitution - coding silent(1)	stomach(1)	c.T558C						PASS	.	A	,	659,3747	281.4+/-275.9	56,547,1600	110.0	107.0	108.0		492,558	3.5	0.9	10	dbSNP_98	108	564,8036	153.0+/-207.5	25,514,3761	no	coding-synonymous,coding-synonymous	ANXA7	NM_001156.3,NM_004034.2	,	81,1061,5361	GG,GA,AA		6.5581,14.9569,9.4034	,	164/467,186/489	75148116	1223,11783	2203	4300	6503	SO:0001819	synonymous_variant	310	exon7			TATAGCATCGAAG	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"""Annexins"""	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.492T>C	10.37:g.75148116A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	123	51	0.414634	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Silent	SNP	ENST00000372921.5	37	CCDS7325.1																																																																																			A|0.871;G|0.129	0.129	strong		0.378	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156	
C7	730	hgsc.bcm.edu	37	5	40964852	40964852	+	Missense_Mutation	SNP	A	A	C	rs13157656	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:40964852A>C	ENST00000313164.9	+	14	2118	c.1759A>C	c.(1759-1761)Aca>Cca	p.T587P		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	587	CCP 1.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		T -> P (polymorphism confirmed at protein level; dbSNP:rs13157656). {ECO:0000269|PubMed:22028381, ECO:0000269|PubMed:3335508}.		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)				GGATGAAGGTACAATGTTTCC	0.353													A|||	965	0.192692	0.0265	0.2089	5008	,	,		18703	0.2133		0.2207	False		,,,				2504	0.3558				p.T587P		Atlas-SNP	.											.	C7	136	.	0			c.A1759C						PASS	.	A	PRO/THR	239,3489		6,227,1631	143.0	141.0	142.0		1759	-4.7	0.0	5	dbSNP_121	142	1927,6279		231,1465,2407	yes	missense	C7	NM_000587.2	38	237,1692,4038	CC,CA,AA		23.4828,6.4109,18.1498	benign	587/844	40964852	2166,9768	1864	4103	5967	SO:0001583	missense	730	exon14			GAAGGTACAATGT	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.1759A>C	5.37:g.40964852A>C	ENSP00000322061:p.Thr587Pro	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	169	94	0.556213	NM_000587	Q6P3T5|Q92489	Missense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	395	0.18086080586080586	21	0.042682926829268296	81	0.22375690607734808	123	0.21503496503496503	170	0.22427440633245382	A	13.95	2.391395	0.42410	0.064109	0.234828	ENSG00000112936	ENST00000313164;ENST00000440677	T	0.63913	-0.07	6.17	-4.69	0.03299	Complement control module (2);Sushi/SCR/CCP (3);	0.765086	0.12472	N	0.465951	T	0.00012	0.0000	L	0.28192	0.835	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.14420	-1.0473	9	0.37606	T	0.19	0.0778	0.5007	0.00579	0.3586:0.1501:0.2454:0.2459	rs13157656;rs17176312;rs52828491;rs13157656	587	P10643	CO7_HUMAN	P	587;427	ENSP00000322061:T587P	ENSP00000322061:T587P	T	+	1	0	C7	41000609	0.000000	0.05858	0.040000	0.18447	0.625000	0.37756	-1.442000	0.02407	-0.366000	0.08064	-0.327000	0.08410	ACA	A|0.817;C|0.182	0.182	strong		0.353	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1		
CRK	1398	hgsc.bcm.edu	37	17	1359363	1359363	+	Silent	SNP	T	T	G	rs2229075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1359363T>G	ENST00000300574.2	-	1	189	c.49A>C	c.(49-51)Agg>Cgg	p.R17R	CRK_ENST00000574295.1_Silent_p.R17R|CRK_ENST00000398970.5_Silent_p.R17R|CRK_ENST00000572145.1_Intron	NM_016823.3	NP_058431.2	P46108	CRK_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog	17	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPKK activity (GO:0000186)|blood coagulation (GO:0007596)|ephrin receptor signaling pathway (GO:0048013)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of signal transduction (GO:0009967)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Rho GTPase activity (GO:0032319)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|SH2 domain binding (GO:0042169)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(2)	9				UCEC - Uterine corpus endometrioid carcinoma (25;0.083)		CGACTCAACCTCCCCCAGTAC	0.721													G|||	3645	0.727835	0.9213	0.7104	5008	,	,		9691	0.5149		0.7018	False		,,,				2504	0.7249				p.R17R		Atlas-SNP	.											.	CRK	14	.	0			c.A49C						PASS	.	G	,	3740,508		1659,422,43	17.0	17.0	17.0		49,49	5.1	1.0	17	dbSNP_98	17	6091,2317		2224,1643,337	no	coding-synonymous,coding-synonymous	CRK	NM_005206.3,NM_016823.2	,	3883,2065,380	GG,GT,TT		27.5571,11.9586,22.3214	,	17/205,17/305	1359363	9831,2825	2124	4204	6328	SO:0001819	synonymous_variant	1398	exon1			TCAACCTCCCCCA	D10656	CCDS11002.1, CCDS45561.1	17p13	2013-07-09	2013-07-09		ENSG00000167193	ENSG00000167193		"""SH2 domain containing"""	2362	protein-coding gene	gene with protein product		164762				1690891	Standard	NM_005206		Approved		uc002fsl.3	P46108	OTTHUMG00000090317	ENST00000300574.2:c.49A>C	17.37:g.1359363T>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_016823	A8MWE8|B0LPE8|D3DTH6|Q96GA9|Q96HJ0	Silent	SNP	ENST00000300574.2	37	CCDS11002.1																																																																																			T|0.252;G|0.748;C|0.000	0.748	strong		0.721	CRK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206679.1	NM_016823	
SLC6A11	6538	hgsc.bcm.edu	37	3	10976876	10976876	+	Silent	SNP	A	A	G	rs2245532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:10976876A>G	ENST00000254488.2	+	13	1803	c.1737A>G	c.(1735-1737)acA>acG	p.T579T		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	579					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	CGGAGGGGACACTGCCCGAGG	0.642													G|||	1677	0.334864	0.5363	0.2954	5008	,	,		18258	0.1012		0.4254	False		,,,				2504	0.2382				p.T579T		Atlas-SNP	.											.	SLC6A11	87	.	0			c.A1737G						PASS	.	G		2318,2088	573.2+/-383.5	592,1134,477	104.0	100.0	101.0		1737	-8.4	0.0	3	dbSNP_100	101	3523,5077	632.1+/-398.6	741,2041,1518	no	coding-synonymous	SLC6A11	NM_014229.1		1333,3175,1995	GG,GA,AA		40.9651,47.3899,44.91		579/633	10976876	5841,7165	2203	4300	6503	SO:0001819	synonymous_variant	6538	exon13			GGGGACACTGCCC	S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1737A>G	3.37:g.10976876A>G		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	140	63	0.45	NM_014229	B2R6U6|Q8IYC9	Silent	SNP	ENST00000254488.2	37	CCDS2602.1																																																																																			A|0.595;G|0.405	0.405	strong		0.642	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
CAPN12	147968	hgsc.bcm.edu	37	19	39229089	39229089	+	Missense_Mutation	SNP	A	A	G	rs12983010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39229089A>G	ENST00000328867.4	-	7	1167	c.859T>C	c.(859-861)Tgc>Cgc	p.C287R	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Missense_Mutation_p.C138R	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	287	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		C -> R (in dbSNP:rs12983010).		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)			CACTCCACGCAGCCCCATGGG	0.692													G|||	567	0.113219	0.1483	0.1326	5008	,	,		15035	0.0982		0.0646	False		,,,				2504	0.1176				p.C287R		Atlas-SNP	.											.	CAPN12	43	.	0			c.T859C						PASS	.	G	ARG/CYS	487,3911	751.0+/-412.2	34,419,1746	33.0	34.0	34.0		859	5.0	1.0	19	dbSNP_121	34	550,8048	772.5+/-407.7	12,526,3761	yes	missense	CAPN12	NM_144691.3	180	46,945,5507	GG,GA,AA		6.3968,11.0732,7.9794	benign	287/720	39229089	1037,11959	2199	4299	6498	SO:0001583	missense	147968	exon7			CCACGCAGCCCCA	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.859T>C	19.37:g.39229089A>G	ENSP00000331636:p.Cys287Arg	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	223	0.1021062271062271	67	0.13617886178861788	38	0.10497237569060773	68	0.11888111888111888	50	0.06596306068601583	G	9.575	1.122059	0.20877	0.110732	0.063968	ENSG00000182472	ENST00000328867	D	0.86627	-2.15	5.02	5.02	0.67125	Peptidase C2, calpain, catalytic domain (3);	0.458584	0.25329	N	0.031451	T	0.00580	0.0019	N	0.00101	-2.135	0.36573	P	0.12689300000000003	B	0.02656	0.0	B	0.01281	0.0	T	0.25676	-1.0125	9	0.20046	T	0.44	.	7.6556	0.28373	0.0897:0.1645:0.7458:0.0	rs12983010;rs12983010	287	Q6ZSI9	CAN12_HUMAN	R	287	ENSP00000331636:C287R	ENSP00000331636:C287R	C	-	1	0	CAPN12	43920929	0.002000	0.14202	0.996000	0.52242	0.688000	0.40055	0.179000	0.16840	1.272000	0.44329	-0.355000	0.07637	TGC	A|0.915;G|0.085	0.085	strong		0.692	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
RMND1	55005	hgsc.bcm.edu	37	6	151766822	151766822	+	Missense_Mutation	SNP	C	C	A	rs11550103	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151766822C>A	ENST00000367303.4	-	2	247	c.125G>T	c.(124-126)aGc>aTc	p.S42I	RMND1_ENST00000491268.1_5'UTR|RMND1_ENST00000336451.3_5'Flank	NM_017909.2	NP_060379.2	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog (S. cerevisiae)	42			S -> I (in dbSNP:rs11550103).		translation (GO:0006412)	mitochondrion (GO:0005739)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		TGTCAGTGTGCTGCATGTTGT	0.373													C|||	362	0.0722843	0.0454	0.0764	5008	,	,		17906	0.0159		0.1193	False		,,,				2504	0.1155				p.S42I		Atlas-SNP	.											RMND1,lymph_node,lymphoid_neoplasm,0,1	RMND1	32	1	0			c.G125T						PASS	.	C	ILE/SER	254,4152	146.1+/-180.8	7,240,1956	118.0	108.0	112.0		125	-3.4	0.0	6	dbSNP_120	112	1083,7517	227.2+/-262.7	62,959,3279	no	missense	RMND1	NM_017909.2	142	69,1199,5235	AA,AC,CC		12.593,5.7649,10.2799	benign	42/450	151766822	1337,11669	2203	4300	6503	SO:0001583	missense	55005	exon2			AGTGTGCTGCATG	AK000634	CCDS5232.1, CCDS75539.1	6q25.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000155906	ENSG00000155906			21176	protein-coding gene	gene with protein product		614917	"""chromosome 6 open reading frame 96"""	C6orf96			Standard	NM_001271937		Approved	bA351K16.3, FLJ20627, RMD1	uc003qoi.3	Q9NWS8	OTTHUMG00000015837	ENST00000367303.4:c.125G>T	6.37:g.151766822C>A	ENSP00000356272:p.Ser42Ile	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_017909	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Missense_Mutation	SNP	ENST00000367303.4	37	CCDS5232.1	167	0.07646520146520147	28	0.056910569105691054	34	0.09392265193370165	10	0.017482517482517484	95	0.12532981530343007	C	10.21	1.288088	0.23478	0.057649	0.12593	ENSG00000155906	ENST00000367303	T	0.44881	0.91	5.46	-3.36	0.04913	.	1.251530	0.05252	N	0.514092	T	0.06416	0.0165	N	0.08118	0	0.80722	P	0.0	B;B	0.16396	0.017;0.0	B;B	0.16289	0.015;0.001	T	0.22906	-1.0203	9	0.34782	T	0.22	1.0502	2.8012	0.05415	0.1159:0.2957:0.1144:0.474	rs11550103;rs52812057;rs11550103	42;42	Q9NWS8-3;Q9NWS8	.;RMND1_HUMAN	I	42	ENSP00000356272:S42I	ENSP00000356272:S42I	S	-	2	0	RMND1	151808515	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-0.509000	0.06336	-0.325000	0.08577	0.563000	0.77884	AGC	C|0.912;A|0.088	0.088	strong		0.373	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	
FKBP15	23307	hgsc.bcm.edu	37	9	115933885	115933885	+	Silent	SNP	A	A	C	rs1128118	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115933885A>C	ENST00000238256.3	-	24	2751	c.2634T>G	c.(2632-2634)gcT>gcG	p.A878A		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	878					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						CAGATGCAGCAGCTTCAACCC	0.458													A|||	417	0.0832668	0.112	0.0403	5008	,	,		16027	0.0387		0.0477	False		,,,				2504	0.1575				p.A878A		Atlas-SNP	.											.	FKBP15	128	.	0			c.T2634G						PASS	.	A		431,3379		14,403,1488	78.0	84.0	82.0		2634	-2.8	0.0	9	dbSNP_86	82	520,7738		15,490,3624	no	coding-synonymous	FKBP15	NM_015258.1		29,893,5112	CC,CA,AA		6.2969,11.3123,7.8803		878/1220	115933885	951,11117	1905	4129	6034	SO:0001819	synonymous_variant	23307	exon24			TGCAGCAGCTTCA	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2634T>G	9.37:g.115933885A>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	147	75	0.510204	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			A|0.938;C|0.062	0.062	strong		0.458	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
ADAM28	10863	hgsc.bcm.edu	37	8	24171051	24171051	+	Silent	SNP	C	C	T	rs6996616	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:24171051C>T	ENST00000265769.4	+	6	644	c.534C>T	c.(532-534)caC>caT	p.H178H	RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000437154.2_Silent_p.H178H|ADAM28_ENST00000540823.1_Intron|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	178					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TGTGGGCCCACGATTTGCAGC	0.448													T|||	932	0.186102	0.152	0.0965	5008	,	,		16774	0.3621		0.1571	False		,,,				2504	0.1442				p.H178H	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.C534T						PASS	.	T	,	754,3652	755.8+/-412.6	65,624,1514	208.0	181.0	190.0		534,534	0.0	0.0	8	dbSNP_116	190	1315,7285	758.0+/-407.5	104,1107,3089	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	169,1731,4603	TT,TC,CC		15.2907,17.113,15.908	,	178/776,178/541	24171051	2069,10937	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon6			GGCCCACGATTTG	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.534C>T	8.37:g.24171051C>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	208	93	0.447115	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			C|0.809;T|0.191	0.191	strong		0.448	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
METTL3	56339	hgsc.bcm.edu	37	14	21967916	21967916	+	Silent	SNP	A	A	G	rs1139130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21967916A>G	ENST00000298717.4	-	7	1486	c.1335T>C	c.(1333-1335)aaT>aaC	p.N445N		NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	445					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		ACCCCCAGAGATTTAGACATT	0.388													G|||	2564	0.511981	0.5749	0.6282	5008	,	,		19002	0.3542		0.5	False		,,,				2504	0.5194				p.N445N		Atlas-SNP	.											.	METTL3	48	.	0			c.T1335C						PASS	.	G		2340,2066	570.8+/-382.9	614,1112,477	162.0	150.0	154.0		1335	1.0	1.0	14	dbSNP_86	154	4327,4273	575.6+/-390.3	1130,2067,1103	no	coding-synonymous	METTL3	NM_019852.3		1744,3179,1580	GG,GA,AA		49.686,46.8906,48.739		445/581	21967916	6667,6339	2203	4300	6503	SO:0001819	synonymous_variant	56339	exon7			CCAGAGATTTAGA	AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"""N6-adenosine-methyltransferase 70 kDa subunit"""	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.1335T>C	14.37:g.21967916A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	124	124	1	NM_019852	O14736|Q86V05|Q9HB32	Silent	SNP	ENST00000298717.4	37	CCDS32044.1																																																																																			A|0.488;G|0.512	0.512	strong		0.388	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852	
FDXR	2232	hgsc.bcm.edu	37	17	72863030	72863030	+	Intron	SNP	T	T	C	rs1688149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72863030T>C	ENST00000293195.5	-	3	256				FDXR_ENST00000583917.1_Intron|FDXR_ENST00000582944.1_Intron|FDXR_ENST00000413947.2_Intron|FDXR_ENST00000442102.2_Missense_Mutation_p.D92G|FDXR_ENST00000455107.2_Intron|FDXR_ENST00000544854.1_Intron|FDXR_ENST00000581530.1_Intron|FDXR_ENST00000581969.1_Intron|FDXR_ENST00000420580.2_Intron	NM_001258014.1|NM_004110.3|NM_024417.2	NP_001244943.1|NP_004101.2|NP_077728.2	P22570	ADRO_HUMAN	ferredoxin reductase						cholesterol metabolic process (GO:0008203)|generation of precursor metabolites and energy (GO:0006091)|NADPH oxidation (GO:0070995)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ferredoxin-NADP+ reductase activity (GO:0004324)|NADPH binding (GO:0070402)|NADPH-adrenodoxin reductase activity (GO:0015039)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16	all_lung(278;0.172)|Lung NSC(278;0.207)				Flavin adenine dinucleotide(DB03147)	GCTGGTGGGGTCGAGAGAGAG	0.642													C|||	939	0.1875	0.0333	0.1614	5008	,	,		16471	0.38		0.2187	False		,,,				2504	0.184				p.D92G		Atlas-SNP	.											.	FDXR	68	.	0			c.A275G						PASS	.	C	,	285,4119		8,269,1925	34.0	31.0	32.0		,	-5.6	0.0	17	dbSNP_89	32	1903,6693		199,1505,2594	no	intron,intron	FDXR	NM_004110.3,NM_024417.2	,	207,1774,4519	CC,CT,TT		22.1382,6.4714,16.8308	,	,	72863030	2188,10812	2202	4298	6500	SO:0001627	intron_variant	2232	exon3			GTGGGGTCGAGAG	J03826	CCDS11707.1, CCDS58591.1, CCDS58592.1, CCDS58593.1, CCDS58594.1, CCDS58595.1, CCDS58596.1	17q25.1	2013-06-18			ENSG00000161513	ENSG00000161513	1.18.1.6		3642	protein-coding gene	gene with protein product	"""adrenodoxin-NADP(+) reductase"", ""adrenodoxin reductase"""	103270		ADXR		2969697	Standard	NM_001258014		Approved		uc010wrl.2	P22570	OTTHUMG00000179026	ENST00000293195.5:c.178-32A>G	17.37:g.72863030T>C		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_001258012	B4DDI7|B4DHX5|B4DQQ4|B4DX24|B7Z7G2|E7EQC1|Q13716|Q4PJI0|Q9BU12	Missense_Mutation	SNP	ENST00000293195.5	37	CCDS58593.1	471	0.21565934065934067	16	0.032520325203252036	60	0.16574585635359115	226	0.3951048951048951	169	0.22295514511873352	C	8.864	0.947610	0.18356	0.064714	0.221382	ENSG00000161513	ENST00000442102	T	0.05996	3.36	4.38	-5.56	0.02529	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48399	-0.9039	6	.	.	.	.	8.8315	0.35087	0.0:0.1833:0.1639:0.6529	rs1688149	92	B4DHX5	.	G	92	ENSP00000416515:D92G	.	D	-	2	0	FDXR	70374625	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.266000	0.02842	-1.270000	0.02433	-1.163000	0.01768	GAC	T|0.781;C|0.219	0.219	strong		0.642	FDXR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000444449.1	NM_004110	
ABCC6	368	hgsc.bcm.edu	37	16	16278863	16278863	+	Missense_Mutation	SNP	G	G	T	rs8058694	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:16278863G>T	ENST00000205557.7	-	15	1925	c.1896C>A	c.(1894-1896)caC>caA	p.H632Q	ABCC6_ENST00000574094.1_5'UTR	NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	632	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		H -> Q (in dbSNP:rs8058694). {ECO:0000269|PubMed:10954200, ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:11776382, ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	AGGTGGCACTGTGTATGGTGA	0.597													G|||	1666	0.332668	0.3245	0.4769	5008	,	,		17607	0.1627		0.4861	False		,,,				2504	0.2587				p.H632Q		Atlas-SNP	.											.	ABCC6	110	.	0			c.C1896A						PASS	.	G	GLN/HIS	1574,2820	492.2+/-362.3	287,1000,910	169.0	129.0	142.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1896	-9.0	0.0	16	dbSNP_116	142	4313,4287	578.7+/-390.8	1084,2145,1071	yes	missense	ABCC6	NM_001171.5	24	1371,3145,1981	TT,TG,GG		49.8488,35.8216,45.3055	benign	632/1504	16278863	5887,7107	2197	4300	6497	SO:0001583	missense	368	exon15			GGCACTGTGTATG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.1896C>A	16.37:g.16278863G>T	ENSP00000205557:p.His632Gln	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	127	126	0.992126	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	782	0.35805860805860806	156	0.3170731707317073	162	0.44751381215469616	95	0.1660839160839161	369	0.4868073878627968	G	9.447	1.089665	0.20390	0.358216	0.501512	ENSG00000091262	ENST00000205557;ENST00000456970;ENST00000546056	D;D	0.90004	-2.6;-2.6	5.13	-8.99	0.00751	ABC transporter-like (1);	0.857990	0.09944	N	0.735553	T	0.00012	0.0000	N	0.01446	-0.86	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.28681	-1.0036	9	0.26408	T	0.33	.	4.3691	0.11239	0.0798:0.3838:0.1417:0.3947	rs8058694;rs52827050;rs56728784;rs8058694	644;632	F5GWQ0;O95255	.;MRP6_HUMAN	Q	632;632;644	ENSP00000205557:H632Q;ENSP00000405002:H632Q	ENSP00000205557:H632Q	H	-	3	2	ABCC6	16186364	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.090000	0.03372	-1.176000	0.02747	-0.182000	0.12963	CAC	G|0.607;T|0.393	0.393	strong		0.597	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
PRR15	222171	hgsc.bcm.edu	37	7	29606316	29606316	+	Missense_Mutation	SNP	C	C	A	rs112093295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:29606316C>A	ENST00000319694.2	+	2	1083	c.371C>A	c.(370-372)cCc>cAc	p.P124H		NM_175887.2	NP_787083.1	Q8IV56	PRR15_HUMAN	proline rich 15	124					multicellular organismal development (GO:0007275)					endometrium(1)|lung(1)|skin(1)	3						CCTGGTGACCCCCACGAGGAC	0.657													C|||	270	0.0539137	0.003	0.0476	5008	,	,		11674	0.002		0.0815	False		,,,				2504	0.1524				p.P124H		Atlas-SNP	.											PRR15,NS,carcinoma,0,3	PRR15	6	3	0			c.C371A						PASS	.	C	HIS/PRO	47,4289		0,47,2121	6.0	7.0	7.0		371	4.5	0.0	7	dbSNP_132	7	584,7910		14,556,3677	yes	missense	PRR15	NM_175887.2	77	14,603,5798	AA,AC,CC		6.8754,1.0839,4.9182	probably-damaging	124/130	29606316	631,12199	2168	4247	6415	SO:0001583	missense	222171	exon2			GTGACCCCCACGA	BC029131	CCDS5421.1	7p15.1	2006-08-21			ENSG00000176532	ENSG00000176532			22310	protein-coding gene	gene with protein product						12477932	Standard	NM_175887		Approved		uc003tac.1	Q8IV56	OTTHUMG00000128555	ENST00000319694.2:c.371C>A	7.37:g.29606316C>A	ENSP00000317836:p.Pro124His	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_175887		Missense_Mutation	SNP	ENST00000319694.2	37	CCDS5421.1	79	0.036172161172161175	2	0.0040650406504065045	16	0.04419889502762431	1	0.0017482517482517483	60	0.079155672823219	C	19.68	3.872544	0.72180	0.010839	0.068754	ENSG00000176532	ENST00000319694	T	0.51817	0.69	5.43	4.54	0.55810	.	0.553031	0.18142	N	0.150373	T	0.06600	0.0169	L	0.60455	1.87	0.22389	N	0.999143	D	0.65815	0.995	P	0.60415	0.874	T	0.02437	-1.1159	10	0.44086	T	0.13	-2.6431	10.0131	0.41999	0.0:0.9066:0.0:0.0934	.	124	Q8IV56	PRR15_HUMAN	H	124	ENSP00000317836:P124H	ENSP00000317836:P124H	P	+	2	0	PRR15	29572841	0.783000	0.28701	0.036000	0.18154	0.299000	0.27559	3.047000	0.49854	1.292000	0.44672	0.491000	0.48974	CCC	A|0.036;C|0.963;G|0.000	0.036	strong		0.657	PRR15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250402.2	NM_175887	
MANEAL	149175	hgsc.bcm.edu	37	1	38265653	38265653	+	Silent	SNP	T	T	C	rs41267339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:38265653T>C	ENST00000373045.6	+	4	1533	c.1152T>C	c.(1150-1152)taT>taC	p.Y384Y	MANEAL_ENST00000329006.5_Silent_p.Y162Y|RP11-109P14.9_ENST00000433474.1_RNA|MANEAL_ENST00000397631.3_3'UTR|MANEAL_ENST00000525897.1_Silent_p.Y190Y	NM_001113482.1	NP_001106954.1	Q5VSG8	MANEL_HUMAN	mannosidase, endo-alpha-like	384						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|liver(1)|lung(1)|prostate(3)	7	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GCAAGTACTATGAGACGGCCC	0.567													T|||	28	0.00559105	0.0	0.0115	5008	,	,		19471	0.0		0.0189	False		,,,				2504	0.001				p.Y384Y		Atlas-SNP	.											.	MANEAL	43	.	0			c.T1152C						PASS	.	T	,,	30,4376	35.2+/-66.4	0,30,2173	79.0	86.0	83.0		,1152,486	-0.6	1.0	1	dbSNP_127	83	232,8368	94.5+/-156.4	3,226,4071	no	utr-3,coding-synonymous,coding-synonymous	MANEAL	NM_001031740.2,NM_001113482.1,NM_152496.2	,,	3,256,6244	CC,CT,TT		2.6977,0.6809,2.0145	,,	,384/458,162/236	38265653	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	149175	exon4			GTACTATGAGACG	AK055996	CCDS426.1, CCDS44110.1, CCDS44111.1	1p34.3	2008-02-05			ENSG00000185090	ENSG00000185090			26452	protein-coding gene	gene with protein product							Standard	NM_152496		Approved	FLJ31434	uc001cby.2	Q5VSG8	OTTHUMG00000004317	ENST00000373045.6:c.1152T>C	1.37:g.38265653T>C		Somatic	128	1	0.0078125		WXS	Illumina HiSeq	Phase_I	125	118	0.944	NM_001113482	Q6DD86|Q6P497|Q8N5P8|Q96G55|Q96N42	Silent	SNP	ENST00000373045.6	37	CCDS44110.1																																																																																			T|0.982;C|0.018	0.018	strong		0.567	MANEAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012469.2	NM_152496	
NLRP1	22861	hgsc.bcm.edu	37	17	5462240	5462240	+	Silent	SNP	C	C	T	rs61753142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5462240C>T	ENST00000572272.1	-	4	1775	c.1776G>A	c.(1774-1776)agG>agA	p.R592R	NLRP1_ENST00000354411.3_Silent_p.R592R|NLRP1_ENST00000269280.4_Silent_p.R592R|NLRP1_ENST00000262467.5_Silent_p.R592R|NLRP1_ENST00000345221.3_Silent_p.R592R|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000577119.1_Silent_p.R592R			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	592	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				ACCCATGCTTCCTGAGGTCAT	0.522													C|||	140	0.0279553	0.003	0.049	5008	,	,		20705	0.001		0.0855	False		,,,				2504	0.0153				p.R592R		Atlas-SNP	.											.	NLRP1	358	.	0			c.G1776A						PASS	.	C	,,,,	82,4324	68.1+/-105.8	1,80,2122	58.0	60.0	59.0		1776,1776,1776,1776,1776	-0.2	0.0	17	dbSNP_129	59	821,7779	188.9+/-235.7	37,747,3516	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	,,,,	38,827,5638	TT,TC,CC		9.5465,1.8611,6.9429	,,,,	592/1376,592/1430,592/1474,592/1444,592/1400	5462240	903,12103	2203	4300	6503	SO:0001819	synonymous_variant	22861	exon4			ATGCTTCCTGAGG	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.1776G>A	17.37:g.5462240C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	103	60	0.582524	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Silent	SNP	ENST00000572272.1	37	CCDS42246.1																																																																																			C|0.937;T|0.063	0.063	strong		0.522	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
ELF3	1999	hgsc.bcm.edu	37	1	201981218	201981218	+	Silent	SNP	C	C	G	rs11543979	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201981218C>G	ENST00000359651.3	+	2	3489	c.297C>G	c.(295-297)ggC>ggG	p.G99G	RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000495848.1_3'UTR|RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Silent_p.G99G|ELF3_ENST00000367284.5_Silent_p.G99G					E74-like factor 3 (ets domain transcription factor, epithelial-specific )									p.G99G(1)		breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						ACATGGATGGCGCCACCCTCT	0.577													G|||	1694	0.338259	0.5424	0.2363	5008	,	,		20658	0.3363		0.2396	False		,,,				2504	0.2382				p.G99G		Atlas-SNP	.											ELF3,NS,carcinoma,0,1	ELF3	92	1	1	Substitution - coding silent(1)	stomach(1)	c.C297G						PASS	.	G	,	1965,2441	620.6+/-393.6	423,1119,661	88.0	80.0	83.0		297,297	-1.9	1.0	1	dbSNP_120	83	1879,6721	728.9+/-406.7	194,1491,2615	no	coding-synonymous,coding-synonymous	ELF3	NM_001114309.1,NM_004433.4	,	617,2610,3276	GG,GC,CC		21.8488,44.5983,29.5556	,	99/372,99/372	201981218	3844,9162	2203	4300	6503	SO:0001819	synonymous_variant	1999	exon3			GGATGGCGCCACC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.297C>G	1.37:g.201981218C>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	137	66	0.481752	NM_001114309		Silent	SNP	ENST00000359651.3	37	CCDS1419.1																																																																																			C|0.695;G|0.305	0.305	strong		0.577	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433	
SHROOM2	357	hgsc.bcm.edu	37	X	9859098	9859098	+	Silent	SNP	A	A	G	rs6640543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:9859098A>G	ENST00000380913.3	+	3	489	c.399A>G	c.(397-399)ccA>ccG	p.P133P		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	133					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)				CGGCCTCCCCATTCACCTCCA	0.637													A|||	3254	0.861987	0.4713	0.6844	3775	,	,		12174	0.754		0.7038	False		,,,				2504	0.7035				p.P133P		Atlas-SNP	.											.	SHROOM2	139	.	0			c.A399G						PASS	.	A		2571,1264		742,707,380,183,191	64.0	41.0	49.0		399	-3.6	0.0	X	dbSNP_116	49	6319,407		2146,270,1757,12,113	no	coding-synonymous	SHROOM2	NM_001649.2		2888,977,2137,195,304	GG,GA,G,AA,A		6.0511,32.9596,15.8224		133/1617	9859098	8890,1671	2203	4298	6501	SO:0001819	synonymous_variant	357	exon3			CTCCCCATTCACC	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.399A>G	X.37:g.9859098A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	150	149	0.993333	NM_001649	B9EIQ7	Silent	SNP	ENST00000380913.3	37	CCDS14135.1																																																																																			A|0.147;G|0.853	0.853	strong		0.637	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
USP26	83844	hgsc.bcm.edu	37	X	132161673	132161673	+	Silent	SNP	C	C	T	rs41304540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:132161673C>T	ENST00000511190.1	-	6	1045	c.576G>A	c.(574-576)gaG>gaA	p.E192E	USP26_ENST00000370832.1_Silent_p.E192E|USP26_ENST00000406273.1_Silent_p.E192E	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	192					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					TCAAGAATTCCTCATTCATCT	0.353													C|||	1148	0.304106	0.0386	0.1816	3775	,	,		14974	0.2867		0.4026	False		,,,				2504	0.2832				p.E192E	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.G576A						PASS	.	C		391,3443		17,300,57,1315,513	85.0	70.0	75.0		576	0.6	0.0	X	dbSNP_127	75	3339,3386		605,1182,947,640,924	no	coding-synonymous	USP26	NM_031907.1		622,1482,1004,1955,1437	TT,TC,T,CC,C		49.6506,10.1982,35.3253		192/914	132161673	3730,6829	2202	4298	6500	SO:0001819	synonymous_variant	83844	exon1			GAATTCCTCATTC	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.576G>A	X.37:g.132161673C>T		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	132	130	0.984848	NM_031907	B9WRT6|Q5H9H4	Silent	SNP	ENST00000511190.1	37	CCDS14635.1																																																																																			C|0.677;T|0.323	0.323	strong		0.353	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907	
SSH2	85464	hgsc.bcm.edu	37	17	27963141	27963141	+	Missense_Mutation	SNP	T	T	C	rs61737983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:27963141T>C	ENST00000269033.3	-	14	2177	c.2026A>G	c.(2026-2028)Atg>Gtg	p.M676V	SSH2_ENST00000540801.1_Missense_Mutation_p.M703V|RP11-68I3.2_ENST00000581474.1_RNA	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	676					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGTTCCTCCATCCTTGAATGG	0.483													T|||	53	0.0105831	0.0008	0.0274	5008	,	,		17570	0.001		0.0239	False		,,,				2504	0.0082				p.M676V		Atlas-SNP	.											SSH2,NS,carcinoma,+2,1	SSH2	107	1	0			c.A2026G						PASS	.	T	VAL/MET	21,4385	28.1+/-56.4	0,21,2182	134.0	132.0	133.0		2026	3.8	1.0	17	dbSNP_129	133	193,8407	85.6+/-148.0	2,189,4109	yes	missense	SSH2	NM_033389.2	21	2,210,6291	CC,CT,TT		2.2442,0.4766,1.6454	benign	676/1424	27963141	214,12792	2203	4300	6503	SO:0001583	missense	85464	exon14			CCTCCATCCTTGA	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.2026A>G	17.37:g.27963141T>C	ENSP00000269033:p.Met676Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	162	97	0.598765	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	31	0.014194139194139194	0	0.0	10	0.027624309392265192	0	0.0	21	0.027704485488126648	T	10.19	1.281463	0.23392	0.004766	0.022442	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.34667	1.35;1.35	6.17	3.78	0.43462	.	0.891618	0.10161	N	0.708375	T	0.09113	0.0225	L	0.51422	1.61	0.80722	D	1	B;B	0.10296	0.003;0.002	B;B	0.10450	0.005;0.002	T	0.31752	-0.9932	10	0.02654	T	1	-5.5851	3.3358	0.07101	0.1826:0.0699:0.1227:0.6248	rs61737983	703;676	F5H527;Q76I76	.;SSH2_HUMAN	V	676;703	ENSP00000269033:M676V;ENSP00000444743:M703V	ENSP00000269033:M676V	M	-	1	0	SSH2	24987267	0.766000	0.28496	1.000000	0.80357	0.985000	0.73830	0.103000	0.15292	2.371000	0.80710	0.533000	0.62120	ATG	T|0.984;C|0.016	0.016	strong		0.483	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449483	89449483	+	Missense_Mutation	SNP	C	C	G	rs74100106	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449483C>G	ENST00000321792.5	-	2	454	c.27G>C	c.(25-27)aaG>aaC	p.K9N	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.K9N	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	9	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CAATGAAGAGCTTTCCTGGGC	0.463											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K9N		Atlas-SNP	.											.	.	.	.	0			c.G27C						PASS	.						160.0	160.0	160.0					1																	89449483		2203	4300	6503	SO:0001583	missense	494115	exon3			GAAGAGCTTTCCT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.27G>C	1.37:g.89449483C>G	ENSP00000318415:p.Lys9Asn	Somatic	319	0	0	1267	WXS	Illumina HiSeq	Phase_I	440	58	0.131818	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	17.28	3.348677	0.61183	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.89050	-2.46;-2.46	1.28	0.26	0.15588	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.062453	0.64402	U	0.000007	D	0.83008	0.5161	M	0.66506	2.035	0.38488	D	0.947901	P	0.47841	0.901	P	0.50490	0.642	T	0.79794	-0.1653	10	0.66056	D	0.02	4.7301	4.4037	0.11399	0.0:0.5845:0.0:0.4155	.	9	Q96E39	RBMXL_HUMAN	N	9	ENSP00000318415:K9N;ENSP00000446099:K9N	ENSP00000318415:K9N	K	-	3	2	RBMXL1	89222071	1.000000	0.71417	0.958000	0.39756	0.727000	0.41649	0.334000	0.19787	-0.169000	0.10834	-1.206000	0.01644	AAG	C|0.904;G|0.096	0.096	strong		0.463	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
CHRNA2	1135	hgsc.bcm.edu	37	8	27324844	27324844	+	Silent	SNP	G	G	A	rs2565061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27324844G>A	ENST00000520933.2	-	4	504	c.351C>T	c.(349-351)gaC>gaT	p.D117D	CHRNA2_ENST00000240132.2_Silent_p.D102D|CHRNA2_ENST00000407991.1_Silent_p.D117D			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	117					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GCAGTTTGTAGTCGCTCCACT	0.547													G|||	1191	0.237819	0.2579	0.2017	5008	,	,		18862	0.4177		0.1402	False		,,,				2504	0.1513				p.D117D		Atlas-SNP	.											.	CHRNA2	48	.	0			c.C351T						PASS	.	G		1047,3359	384.4+/-325.3	116,815,1272	102.0	100.0	101.0		351	4.7	1.0	8	dbSNP_100	101	1127,7473	233.0+/-266.5	77,973,3250	no	coding-synonymous	CHRNA2	NM_000742.3		193,1788,4522	AA,AG,GG		13.1047,23.7631,16.7154		117/530	27324844	2174,10832	2203	4300	6503	SO:0001819	synonymous_variant	1135	exon5			TTTGTAGTCGCTC	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.351C>T	8.37:g.27324844G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	130	63	0.484615	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Silent	SNP	ENST00000520933.2	37	CCDS6059.1																																																																																			G|0.788;A|0.212	0.212	strong		0.547	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
GLI2	2736	hgsc.bcm.edu	37	2	121747406	121747406	+	Missense_Mutation	SNP	G	G	A	rs12711538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:121747406G>A	ENST00000452319.1	+	14	3976	c.3916G>A	c.(3916-3918)Gat>Aat	p.D1306N	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Missense_Mutation_p.D1306N					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				TGGGGTCCCCGATTCAGCCCT	0.642													A|||	2840	0.567093	0.5681	0.5951	5008	,	,		18427	0.4712		0.7247	False		,,,				2504	0.4826				p.D1306N		Atlas-SNP	.											.	GLI2	187	.	0			c.G3916A						PASS	.	A	ASN/ASP	2536,1864		740,1056,404	23.0	23.0	23.0		3916	2.1	0.0	2	dbSNP_121	23	6262,2336		2289,1684,326	yes	missense	GLI2	NM_005270.4	23	3029,2740,730	AA,AG,GG		27.1691,42.3636,32.3127	benign	1306/1587	121747406	8798,4200	2200	4299	6499	SO:0001583	missense	2736	exon13			GTCCCCGATTCAG		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3916G>A	2.37:g.121747406G>A	ENSP00000390436:p.Asp1306Asn	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	187	77	0.411765	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	1298	0.5943223443223443	257	0.5223577235772358	217	0.5994475138121547	283	0.49475524475524474	541	0.7137203166226913	A	0.017	-1.502030	0.00992	0.576364	0.728309	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.13307	2.6;2.6	4.5	2.13	0.27403	.	0.742484	0.12604	N	0.454393	T	0.00012	0.0000	N	0.00170	-1.935	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.20207	-1.0282	8	.	.	.	.	9.0523	0.36383	0.699:0.0:0.301:0.0	rs12711538;rs12711538	1306;961	P10070;P10070-2	GLI2_HUMAN;.	N	1306	ENSP00000390436:D1306N;ENSP00000354586:D1306N	.	D	+	1	0	GLI2	121463876	0.006000	0.16342	0.000000	0.03702	0.685000	0.39939	2.156000	0.42310	-0.006000	0.14370	-0.556000	0.04195	GAT	G|0.360;A|0.640	0.640	strong		0.642	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
ENTPD6	955	hgsc.bcm.edu	37	20	25193949	25193949	+	Silent	SNP	G	G	A	rs2076561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25193949G>A	ENST00000376652.4	+	5	667	c.504G>A	c.(502-504)ccG>ccA	p.P168P	ENTPD6_ENST00000354989.5_Silent_p.P151P|Y_RNA_ENST00000365544.1_RNA|ENTPD6_ENST00000360031.2_Silent_p.P167P|ENTPD6_ENST00000433259.2_Silent_p.P168P			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	168					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						AGGACATTCCGTTCGACTTCT	0.547													G|||	1553	0.310104	0.0983	0.2262	5008	,	,		20740	0.5913		0.3459	False		,,,				2504	0.3292				p.P168P		Atlas-SNP	.											ENTPD6,face,carcinoma,+2,1	ENTPD6	57	1	0			c.G504A						PASS	.	G	,	619,3787	269.2+/-268.9	42,535,1626	169.0	127.0	141.0		453,504	-11.6	0.0	20	dbSNP_96	141	2765,5835	439.7+/-359.3	431,1903,1966	no	coding-synonymous,coding-synonymous	ENTPD6	NM_001114089.1,NM_001247.2	,	473,2438,3592	AA,AG,GG		32.1512,14.049,26.0188	,	151/468,168/485	25193949	3384,9622	2203	4300	6503	SO:0001819	synonymous_variant	955	exon5			CATTCCGTTCGAC	AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.504G>A	20.37:g.25193949G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_001247	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Silent	SNP	ENST00000376652.4	37	CCDS13170.1	755	0.3456959706959707	59	0.11991869918699187	92	0.2541436464088398	346	0.6048951048951049	258	0.3403693931398417	G	0.470	-0.885057	0.02511	0.14049	0.321512	ENSG00000197586	ENST00000433417;ENST00000447877	.	.	.	5.79	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999861442	.	.	.	.	.	.	T	0.26608	-1.0098	3	.	.	.	-1.1705	1.9584	0.03381	0.1245:0.3117:0.2786:0.2853	rs2076561;rs17250460;rs58880188;rs2076561	.	.	.	H	89;61	.	.	R	+	2	0	ENTPD6	25141949	0.000000	0.05858	0.008000	0.14137	0.056000	0.15407	-2.000000	0.01466	-3.712000	0.00117	-2.589000	0.00165	CGT	G|0.708;A|0.292	0.292	strong		0.547	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
ESYT2	57488	hgsc.bcm.edu	37	7	158536345	158536345	+	Missense_Mutation	SNP	A	A	G	rs2305475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158536345A>G	ENST00000251527.5	-	16	1815	c.1750T>C	c.(1750-1752)Tcc>Ccc	p.S584P	ESYT2_ENST00000435514.2_Missense_Mutation_p.S19P	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	612	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						TTCCCCAGGGAACACTGGTGC	0.552													A|||	1682	0.335863	0.3994	0.1801	5008	,	,		17966	0.5843		0.17	False		,,,				2504	0.2751				p.S584P		Atlas-SNP	.											.	ESYT2	70	.	0			c.T1750C						PASS	.		PRO/SER	1486,2920	455.7+/-351.1	265,956,982	74.0	60.0	65.0		1750	4.1	0.2	7	dbSNP_100	65	1421,7179	248.6+/-276.2	125,1171,3004	yes	missense	ESYT2	NM_020728.2	74	390,2127,3986	GG,GA,AA		16.5233,33.7267,22.3512	probably-damaging	584/894	158536345	2907,10099	2203	4300	6503	SO:0001583	missense	57488	exon16			CCAGGGAACACTG	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.1750T>C	7.37:g.158536345A>G	ENSP00000251527:p.Ser584Pro	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	68	30	0.441176	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Missense_Mutation	SNP	ENST00000251527.5	37	CCDS34791.1	701	0.320970695970696	187	0.3800813008130081	63	0.17403314917127072	323	0.5646853146853147	128	0.16886543535620052	A	17.00	3.277386	0.59758	0.337267	0.165233	ENSG00000117868	ENST00000251527;ENST00000421679;ENST00000275418;ENST00000435514;ENST00000377650;ENST00000429474	T;T;T	0.25749	1.78;1.78;1.78	5.28	4.09	0.47781	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.305484	0.36815	N	0.002395	T	0.00012	0.0000	L	0.61387	1.9	0.24527	P	0.994134	D;B	0.62365	0.991;0.089	P;B	0.56700	0.804;0.178	T	0.46830	-0.9163	9	0.66056	D	0.02	-16.699	10.6259	0.45508	0.8561:0.0:0.0:0.1439	rs2305475;rs61453775;rs2305475	584;612	A0FGR8-2;A0FGR8	.;ESYT2_HUMAN	P	584;633;575;19;19;408	ENSP00000251527:S584P;ENSP00000275418:S575P;ENSP00000411488:S19P	ENSP00000251527:S584P	S	-	1	0	ESYT2	158229106	1.000000	0.71417	0.191000	0.23289	0.556000	0.35491	3.699000	0.54778	0.812000	0.34326	0.455000	0.32223	TCC	A|0.737;C|0.000;G|0.262;T|0.000	0.262	strong		0.552	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
BPTF	2186	hgsc.bcm.edu	37	17	65955758	65955758	+	Silent	SNP	T	T	C	rs139709271|rs202116659		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:65955758T>C	ENST00000321892.4	+	26	8467	c.8406T>C	c.(8404-8406)gcT>gcC	p.A2802A	BPTF_ENST00000335221.5_Silent_p.A2659A|BPTF_ENST00000306378.6_Silent_p.A2676A|BPTF_ENST00000424123.3_Silent_p.A2520A			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2802	Pro-rich.			AP -> VL (in Ref. 1; BAA89208). {ECO:0000305}.	anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.A2676A(1)|p.A2659A(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGACAccagctcctccagccc	0.582																																					p.A2676A		Atlas-SNP	.											BPTF_ENST00000335221,rectum,carcinoma,0,2	BPTF	415	2	2	Substitution - coding silent(2)	large_intestine(2)	c.T8028C						scavenged	.						40.0	33.0	36.0					17																	65955758		2203	4300	6503	SO:0001819	synonymous_variant	2186	exon24			ACCAGCTCCTCCA	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.8406T>C	17.37:g.65955758T>C		Somatic	143	5	0.034965		WXS	Illumina HiSeq	Phase_I	125	20	0.16	NM_182641	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																				.	.	weak		0.582	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
SF3A1	10291	hgsc.bcm.edu	37	22	30733111	30733111	+	Silent	SNP	C	C	A	rs2229807	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30733111C>A	ENST00000215793.8	-	13	2164	c.2010G>T	c.(2008-2010)gtG>gtT	p.V670V	SF3A1_ENST00000439242.1_Silent_p.V605V	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	670					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						GTGGGGGATGCACAGGGGGCA	0.572													A|||	769	0.153554	0.1331	0.1556	5008	,	,		17096	0.1448		0.2535	False		,,,				2504	0.0859				p.V670V		Atlas-SNP	.											.	SF3A1	61	.	0			c.G2010T						PASS	.	A	,	667,3739	763.8+/-413.2	56,555,1592	55.0	55.0	55.0		1815,2010	-2.6	0.9	22	dbSNP_98	55	2193,6407	711.1+/-405.8	284,1625,2391	no	coding-synonymous,coding-synonymous	SF3A1	NM_001005409.1,NM_005877.4	,	340,2180,3983	AA,AC,CC		25.5,15.1384,21.9899	,	605/729,670/794	30733111	2860,10146	2203	4300	6503	SO:0001819	synonymous_variant	10291	exon13			GGGATGCACAGGG	X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.2010G>T	22.37:g.30733111C>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	92	0.968421	NM_005877	E9PAW1	Silent	SNP	ENST00000215793.8	37	CCDS13875.1																																																																																			C|0.795;A|0.205	0.205	strong		0.572	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877	
SOGA3	387104	hgsc.bcm.edu	37	6	127797179	127797179	+	Silent	SNP	G	G	A	rs3734448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:127797179G>A	ENST00000525778.1	-	6	2737	c.1992C>T	c.(1990-1992)gcC>gcT	p.A664A	SOGA3_ENST00000481848.2_Silent_p.A664A|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000556132.1_Silent_p.A664A|SOGA3_ENST00000368268.2_Silent_p.A664A|SOGA3_ENST00000465909.2_Silent_p.A664A			Q5TF21	SOGA3_HUMAN	SOGA family member 3	664					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CCTCCAGGTCGGCCACGTTCC	0.642													G|||	1875	0.374401	0.2035	0.4467	5008	,	,		17874	0.7351		0.2406	False		,,,				2504	0.32				p.A664A		Atlas-SNP	.											.	.	.	.	0			c.C1992T						PASS	.	G		931,3445	314.4+/-293.6	115,701,1372	55.0	60.0	58.0		1992	-3.4	1.0	6	dbSNP_107	58	2110,6462	351.3+/-328.2	278,1554,2454	no	coding-synonymous	C6orf174	NM_001012279.2		393,2255,3826	AA,AG,GG		24.615,21.2751,23.4863		664/948	127797179	3041,9907	2188	4286	6474	SO:0001819	synonymous_variant	387104	exon6			CAGGTCGGCCACG	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1992C>T	6.37:g.127797179G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	35	7	0.2	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																			G|0.657;A|0.343	0.343	strong		0.642	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
KRTAP11-1	337880	hgsc.bcm.edu	37	21	32253629	32253629	+	Missense_Mutation	SNP	C	C	T	rs71321355	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:32253629C>T	ENST00000332378.4	-	1	245	c.215G>A	c.(214-216)cGg>cAg	p.R72Q		NM_175858.2	NP_787054.1	Q8IUC1	KR111_HUMAN	keratin associated protein 11-1	72						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|pancreas(1)	18						TGAAGTTCGCCGGTAACAGGT	0.567													T|||	723	0.144369	0.0492	0.1455	5008	,	,		20581	0.0526		0.1978	False		,,,				2504	0.3119				p.R72Q		Atlas-SNP	.											.	KRTAP11-1	46	.	0			c.G215A						PASS	.	T	GLN/ARG	354,4052	794.6+/-415.3	16,322,1865	82.0	76.0	78.0		215	2.1	0.3	21	dbSNP_130	78	1862,6738	729.6+/-406.7	212,1438,2650	yes	missense	KRTAP11-1	NM_175858.2	43	228,1760,4515	TT,TC,CC		21.6512,8.0345,17.0383	benign	72/164	32253629	2216,10790	2203	4300	6503	SO:0001583	missense	337880	exon1			GTTCGCCGGTAAC	AJ457065	CCDS13608.1	21q22.1	2003-03-11			ENSG00000182591	ENSG00000182591		"""Keratin associated proteins"""	18922	protein-coding gene	gene with protein product		600064				12359730	Standard	NM_175858		Approved	KAP11.1	uc002yov.3	Q8IUC1	OTTHUMG00000057773	ENST00000332378.4:c.215G>A	21.37:g.32253629C>T	ENSP00000330720:p.Arg72Gln	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_175858	A1L4I8	Missense_Mutation	SNP	ENST00000332378.4	37	CCDS13608.1	265	0.12133699633699634	20	0.04065040650406504	60	0.16574585635359115	35	0.06118881118881119	150	0.19788918205804748	T	0.788	-0.759997	0.03019	0.080345	0.216512	ENSG00000182591	ENST00000332378	T	0.02812	4.15	4.72	2.11	0.27256	.	0.390240	0.24185	N	0.040779	T	0.00012	0.0000	N	0.00605	-1.335	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44283	-0.9338	9	0.02654	T	1	0.8325	6.5317	0.22330	0.0:0.0884:0.3544:0.5572	.	72	Q8IUC1	KR111_HUMAN	Q	72	ENSP00000330720:R72Q	ENSP00000330720:R72Q	R	-	2	0	KRTAP11-1	31175500	0.982000	0.34865	0.251000	0.24312	0.934000	0.57294	0.755000	0.26405	0.365000	0.24400	-0.260000	0.10688	CGG	C|0.841;T|0.159	0.159	strong		0.567	KRTAP11-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128225.1		
ATAD3B	83858	hgsc.bcm.edu	37	1	1431048	1431048	+	Missense_Mutation	SNP	A	A	G	rs201429000		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1431048A>G	ENST00000308647.7	+	16	1914	c.1798A>G	c.(1798-1800)Acg>Gcg	p.T600A		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	600						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GAGCCTGGCCACGGACCCCTC	0.672																																					p.T600A		Atlas-SNP	.											ATAD3B,NS,neuroblastoma,0,1	ATAD3B	68	1	0			c.A1798G						scavenged	.																																			SO:0001583	missense	83858	exon16			CTGGCCACGGACC	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1798A>G	1.37:g.1431048A>G	ENSP00000311766:p.Thr600Ala	Somatic	119	2	0.0168067		WXS	Illumina HiSeq	Phase_I	147	9	0.0612245	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	g	0.005	-2.129716	0.00338	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.93189	-3.18	1.2	-1.67	0.08238	.	0.186138	0.20546	N	0.090207	T	0.78220	0.4249	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.65792	-0.6082	10	0.12766	T	0.61	.	2.0444	0.03557	0.4037:0.0:0.3428:0.2535	.	554;600	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	A	434;600	ENSP00000311766:T600A	ENSP00000311766:T600A	T	+	1	0	ATAD3B	1420911	0.007000	0.16637	0.000000	0.03702	0.003000	0.03518	0.259000	0.18405	-1.264000	0.02452	-1.032000	0.02404	ACG	.	.	weak		0.672	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
SLC12A8	84561	hgsc.bcm.edu	37	3	124896668	124896668	+	Missense_Mutation	SNP	G	G	A	rs2993631	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124896668G>A	ENST00000393469.4	-	4	590	c.541C>T	c.(541-543)Cgc>Tgc	p.R181C	SLC12A8_ENST00000423114.2_Missense_Mutation_p.R210C|SLC12A8_ENST00000469902.1_Missense_Mutation_p.R181C|SLC12A8_ENST00000314584.7_5'UTR	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	181			R -> C (in dbSNP:rs2993631). {ECO:0000269|PubMed:11863360}.		potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						AGCTGGAGGCGGATTATCCAT	0.557													G|||	168	0.0335463	0.0008	0.0807	5008	,	,		14908	0.0099		0.0447	False		,,,				2504	0.0573				p.R181C		Atlas-SNP	.											.	SLC12A8	81	.	0			c.C541T						PASS	.	G	CYS/ARG,CYS/ARG	46,4110		0,46,2032	71.0	83.0	79.0		541,541	5.5	1.0	3	dbSNP_101	79	403,8051		11,381,3835	yes	missense,missense	SLC12A8	NM_001195483.1,NM_024628.5	180,180	11,427,5867	AA,AG,GG		4.767,1.1068,3.5607	probably-damaging,probably-damaging	181/715,181/715	124896668	449,12161	2078	4227	6305	SO:0001583	missense	84561	exon5			GGAGGCGGATTAT		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.541C>T	3.37:g.124896668G>A	ENSP00000377112:p.Arg181Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	40	0.408163	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	CCDS43143.1	67	0.030677655677655676	3	0.006097560975609756	25	0.06906077348066299	5	0.008741258741258742	34	0.044854881266490766	g	21.0	4.077054	0.76415	0.011068	0.04767	ENSG00000221955	ENST00000393469;ENST00000423114;ENST00000469902	D;D;D	0.98807	-5.15;-5.15;-5.15	5.5	5.5	0.81552	Amino acid permease domain (1);	.	.	.	.	D	0.92277	0.7550	M	0.88181	2.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.81339	-0.0977	9	0.66056	D	0.02	.	14.1094	0.65113	0.0:0.0:0.8505:0.1495	rs2993631;rs60764229;rs2993631	73;210;181	B5MDT1;A0AV02-2;A0AV02	.;.;S12A8_HUMAN	C	181;210;181	ENSP00000377112:R181C;ENSP00000404243:R210C;ENSP00000418783:R181C	ENSP00000377112:R181C	R	-	1	0	SLC12A8	126379358	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.895000	0.63214	2.599000	0.87857	0.448000	0.29417	CGC	G|0.964;A|0.036	0.036	strong		0.557	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
AHSG	197	hgsc.bcm.edu	37	3	186337713	186337713	+	Missense_Mutation	SNP	T	T	C	rs4917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:186337713T>C	ENST00000273784.5	+	6	822	c.746T>C	c.(745-747)aTg>aCg	p.M249T	AHSG_ENST00000411641.2_Missense_Mutation_p.M248T	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	248	Cystatin fetuin-A-type 2. {ECO:0000255|PROSITE-ProRule:PRU00861}.				acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		GTGACCTGCATGGTGTTCCAA	0.453													.|||	3683	0.735423	0.7867	0.5965	5008	,	,		18189	0.745		0.6759	False		,,,				2504	0.816				p.M248T		Atlas-SNP	.											.	AHSG	40	.	0			c.T743C	GRCh37	CM052829	AHSG	M	rs4917	PASS	.	C	THR/MET	3303,1103		1224,855,124	90.0	90.0	90.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	743	-0.9	0.0	3	dbSNP_52	90	5607,2993		1822,1963,515	yes	missense	AHSG	NM_001622.2	81	3046,2818,639	CC,CT,TT		34.8023,25.034,31.4932	benign	248/368	186337713	8910,4096	2203	4300	6503	SO:0001583	missense	197	exon6			CCTGCATGGTGTT	D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.746T>C	3.37:g.186337713T>C	ENSP00000273784:p.Met249Thr	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	66	64	0.969697	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	37		1542	0.7060439560439561	371	0.7540650406504065	242	0.6685082872928176	434	0.7587412587412588	495	0.6530343007915568	N	0.020	-1.446053	0.01089	0.74966	0.651977	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.04119	3.7;3.7	5.45	-0.913	0.10500	.	0.842078	0.10916	N	0.620018	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	0.29852	-0.9998	8	0.02654	T	1	-1.1123	3.8259	0.08853	0.4207:0.2696:0.0:0.3097	rs4917;rs1130657;rs2518135;rs3189766;rs17403330;rs17433992;rs17846428;rs17857413;rs17859476;rs52793906;rs59454784;rs4917	314;249	F5H0Q5;C9JV77	.;.	T	248;314;249	ENSP00000393887:M248T;ENSP00000273784:M249T	ENSP00000273784:M249T	M	+	2	0	AHSG	187820407	0.002000	0.14202	0.013000	0.15412	0.092000	0.18411	-0.507000	0.06352	-0.293000	0.08986	-0.119000	0.15052	ATG	T|0.293;C|0.707	0.707	strong		0.453	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622	
GLI2	2736	hgsc.bcm.edu	37	2	121747429	121747429	+	Silent	SNP	A	A	G	rs10167980	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:121747429A>G	ENST00000452319.1	+	14	3999	c.3939A>G	c.(3937-3939)ccA>ccG	p.P1313P	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Silent_p.P1313P					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CTGGAGTGCCACCACCTCACC	0.652													A|||	2566	0.51238	0.3593	0.5865	5008	,	,		17670	0.4762		0.7286	False		,,,				2504	0.4816				p.P1313P		Atlas-SNP	.											.	GLI2	187	.	0			c.A3939G						PASS	.	A		1802,2600		376,1050,775	22.0	22.0	22.0		3939	-2.4	0.0	2	dbSNP_119	22	6311,2287		2324,1663,312	no	coding-synonymous	GLI2	NM_005270.4		2700,2713,1087	GG,GA,AA		26.5992,40.9359,37.5923		1313/1587	121747429	8113,4887	2201	4299	6500	SO:0001819	synonymous_variant	2736	exon13			AGTGCCACCACCT		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3939A>G	2.37:g.121747429A>G		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	185	84	0.454054	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			A|0.400;G|0.600	0.600	strong		0.652	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
OR2H1	26716	hgsc.bcm.edu	37	6	29429766	29429766	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29429766A>G	ENST00000377136.1	+	4	685	c.220A>G	c.(220-222)Agt>Ggt	p.S74G	OR2H1_ENST00000377132.1_Missense_Mutation_p.S74G|OR2H1_ENST00000473369.1_Splice_Site|OR2H1_ENST00000377133.1_Missense_Mutation_p.S74G|OR2H1_ENST00000442615.1_Missense_Mutation_p.S74G|OR2H1_ENST00000396792.2_Missense_Mutation_p.S74G			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	74						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						CTTTACCACAAGTTGTGTCCC	0.537																																					p.S74G		Atlas-SNP	.											.	OR2H1	38	.	0			c.A220G						PASS	.						108.0	107.0	107.0					6																	29429766		1511	2709	4220	SO:0001583	missense	26716	exon3			ACCACAAGTTGTG	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.220A>G	6.37:g.29429766A>G	ENSP00000366340:p.Ser74Gly	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	203	93	0.458128	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	A	0.142	-1.100996	0.01843	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.01933	4.55;4.55;4.55;4.55;4.55	2.92	2.92	0.33932	GPCR, rhodopsin-like superfamily (1);	0.149339	0.31257	N	0.007964	T	0.02012	0.0063	M	0.90977	3.165	0.09310	N	1	P	0.47962	0.903	B	0.39876	0.312	T	0.31752	-0.9932	10	0.56958	D	0.05	.	6.2425	0.20800	0.8763:0.0:0.1237:0.0	.	74	Q9GZK4	OR2H1_HUMAN	G	74	ENSP00000366340:S74G;ENSP00000366337:S74G;ENSP00000393254:S74G;ENSP00000366336:S74G;ENSP00000380010:S74G	ENSP00000366336:S74G	S	+	1	0	OR2H1	29537745	0.000000	0.05858	0.013000	0.15412	0.048000	0.14542	-0.288000	0.08377	1.582000	0.49881	0.491000	0.48974	AGT	.	.	none		0.537	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
CUL9	23113	hgsc.bcm.edu	37	6	43193877	43193877	+	IGR	SNP	G	G	A	rs7832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43193877G>A	ENST00000252050.4	+	0	7780				DNPH1_ENST00000230431.6_Silent_p.V90V|RP3-330M21.5_ENST00000500590.1_RNA|DNPH1_ENST00000393987.2_Silent_p.V90V	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						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						CTTCTGCCACGACCACTGGGA	0.592													G|||	208	0.0415335	0.0023	0.0908	5008	,	,		21379	0.003		0.0706	False		,,,				2504	0.0695				p.V90V		Atlas-SNP	.											C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	0			c.C270T						PASS	.	G	,	85,4303		1,83,2110	30.0	24.0	26.0		270,270	-9.2	0.0	6	dbSNP_52	26	882,7688		43,796,3446	no	coding-synonymous,coding-synonymous	C6orf108	NM_006443.2,NM_199184.1	,	44,879,5556	AA,AG,GG		10.2917,1.9371,7.4626	,	90/175,90/149	43193877	967,11991	2194	4285	6479	SO:0001628	intergenic_variant	10591	exon3			TGCCACGACCACT	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		6.37:g.43193877G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	31	16	0.516129	NM_006443	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			G|0.942;A|0.058	0.058	strong		0.592	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
LAMA5	3911	hgsc.bcm.edu	37	20	60897488	60897488	+	Silent	SNP	G	G	A	rs2274933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60897488G>A	ENST00000252999.3	-	47	6249	c.6183C>T	c.(6181-6183)ttC>ttT	p.F2061F		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2061	Laminin EGF-like 20. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			CGCAGCCATCGAAACCAAAAT	0.677													.|||	848	0.169329	0.1059	0.2061	5008	,	,		11140	0.1885		0.2187	False		,,,				2504	0.1585				p.F2061F		Atlas-SNP	.											.	LAMA5	268	.	0			c.C6183T						PASS	.	A		539,3757		30,479,1639	9.0	11.0	11.0		6183	-4.8	0.1	20	dbSNP_100	11	1731,6767		193,1345,2711	no	coding-synonymous	LAMA5	NM_005560.3		223,1824,4350	AA,AG,GG		20.3695,12.5466,17.7427		2061/3696	60897488	2270,10524	2148	4249	6397	SO:0001819	synonymous_variant	3911	exon47			GCCATCGAAACCA	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.6183C>T	20.37:g.60897488G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.817;C|0.000;A|0.183	0.183	strong		0.677	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
MTUS1	57509	hgsc.bcm.edu	37	8	17513484	17513484	+	Missense_Mutation	SNP	T	T	C	rs61733708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17513484T>C	ENST00000262102.6	-	9	3220	c.2996A>G	c.(2995-2997)gAa>gGa	p.E999G	MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000400046.1_Missense_Mutation_p.E71G|MTUS1_ENST00000381869.3_Missense_Mutation_p.E945G|MTUS1_ENST00000297488.6_Missense_Mutation_p.E165G|MTUS1_ENST00000519263.1_Missense_Mutation_p.E945G|MTUS1_ENST00000381861.3_Missense_Mutation_p.E246G|MTUS1_ENST00000544260.1_Missense_Mutation_p.E144G	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	999				E -> G (in Ref. 5; CAH56128). {ECO:0000305}.	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)		TTCTGTTTTTTCAGCCTGGTG	0.418													T|||	15	0.00299521	0.0	0.0029	5008	,	,		19675	0.0		0.0129	False		,,,				2504	0.0				p.E999G		Atlas-SNP	.											.	MTUS1	144	.	0			c.A2996G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	8,3748		0,8,1870	190.0	173.0	178.0		2996,2834,737,431,494	5.1	0.1	8	dbSNP_129	178	76,8168		1,74,4047	yes	missense,missense,missense,missense,missense	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	98,98,98,98,98	1,82,5917	CC,CT,TT		0.9219,0.213,0.7	benign,benign,benign,benign,benign	999/1271,945/1217,246/518,144/416,165/437	17513484	84,11916	1878	4122	6000	SO:0001583	missense	57509	exon9			GTTTTTTCAGCCT	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.2996A>G	8.37:g.17513484T>C	ENSP00000262102:p.Glu999Gly	Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	209	110	0.526316	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	18.28	3.589263	0.66105	0.00213	0.009219	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T;T;T;T	0.39056	1.1;1.1;1.6;1.1;1.1;1.1;1.1	5.13	5.13	0.70059	.	0.199759	0.51477	D	0.000098	T	0.45337	0.1337	M	0.79258	2.445	0.80722	D	1	P;P;B;B	0.40970	0.734;0.734;0.411;0.246	B;P;B;B	0.44946	0.302;0.465;0.281;0.157	T	0.58504	-0.7625	10	0.87932	D	0	-18.4737	15.2621	0.73631	0.0:0.0:0.0:1.0	rs61733708	945;999;246;165	Q9ULD2-2;Q9ULD2;Q9ULD2-6;Q9ULD2-3	.;MTUS1_HUMAN;.;.	G	945;144;71;165;246;999;945	ENSP00000371293:E945G;ENSP00000445738:E144G;ENSP00000382921:E71G;ENSP00000297488:E165G;ENSP00000371285:E246G;ENSP00000262102:E999G;ENSP00000430167:E945G	ENSP00000262102:E999G	E	-	2	0	MTUS1	17557764	1.000000	0.71417	0.086000	0.20670	0.802000	0.45316	7.411000	0.80078	2.079000	0.62486	0.482000	0.46254	GAA	T|0.992;C|0.008	0.008	strong		0.418	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
E2F7	144455	hgsc.bcm.edu	37	12	77419593	77419593	+	Silent	SNP	A	A	G	rs310830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:77419593A>G	ENST00000322886.7	-	12	2545	c.2310T>C	c.(2308-2310)tcT>tcC	p.S770S	E2F7_ENST00000416496.2_Intron	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	770					chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						CACCAAGAGTAGAAGAAACCG	0.542													A|||	212	0.0423323	0.0045	0.0677	5008	,	,		17686	0.0		0.1402	False		,,,				2504	0.0184				p.S770S		Atlas-SNP	.											.	E2F7	201	.	0			c.T2310C						PASS	.	A		104,4302	79.9+/-118.3	2,100,2101	50.0	52.0	51.0		2310	-1.6	0.1	12	dbSNP_79	51	1051,7549	222.4+/-259.5	67,917,3316	no	coding-synonymous	E2F7	NM_203394.2		69,1017,5417	GG,GA,AA		12.2209,2.3604,8.8805		770/912	77419593	1155,11851	2203	4300	6503	SO:0001819	synonymous_variant	144455	exon12			AAGAGTAGAAGAA	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.2310T>C	12.37:g.77419593A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	74	45	0.608108	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Silent	SNP	ENST00000322886.7	37	CCDS9016.1																																																																																			A|0.919;G|0.081	0.081	strong		0.542	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
LOXHD1	125336	hgsc.bcm.edu	37	18	44157746	44157746	+	Missense_Mutation	SNP	C	C	A	rs35088381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:44157746C>A	ENST00000398722.4	-	7	1059	c.1060G>T	c.(1060-1062)Ggc>Tgc	p.G354C	LOXHD1_ENST00000441551.2_Missense_Mutation_p.G632C|LOXHD1_ENST00000536736.1_Missense_Mutation_p.G632C			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	354	PLAT 3. {ECO:0000255|PROSITE- ProRule:PRU00152}.		G -> C (in dbSNP:rs35088381).		calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						AGGTACCAGCCGCTGCCGGAG	0.602													C|||	62	0.0123802	0.0113	0.013	5008	,	,		18925	0.0		0.0129	False		,,,				2504	0.0256				p.G632C		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G1894T						PASS	.	C	CYS/GLY	21,1363		0,21,671	36.0	49.0	45.0		1894	4.8	0.9	18	dbSNP_126	45	45,3137		0,45,1546	yes	missense	LOXHD1	NM_144612.6	159	0,66,2217	AA,AC,CC		1.4142,1.5173,1.4455	probably-damaging	632/2212	44157746	66,4500	692	1591	2283	SO:0001583	missense	125336	exon14			ACCAGCCGCTGCC	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1060G>T	18.37:g.44157746C>A	ENSP00000381707:p.Gly354Cys	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		29|29	0.013278388278388278|0.013278388278388278	13|13	0.026422764227642278|0.026422764227642278	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	11.42|11.42	1.634805|1.634805	0.29068|0.29068	0.015173|0.015173	0.014142|0.014142	ENSG00000167210|ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000335730|ENST00000441551	T;T|.	0.65732|.	-0.17;-0.17|.	5.66|5.66	4.79|4.79	0.61399|0.61399	.|.	0.107620|.	0.64402|.	D|.	0.000008|.	T|T	0.70894|0.70894	0.3276|0.3276	H|H	0.94658|0.94658	3.565|3.565	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.991;0.996|.	D|D	0.84597|0.84597	0.0670|0.0670	10|5	0.45353|.	T|.	0.12|.	.|.	14.4404|14.4404	0.67311|0.67311	0.0:0.9295:0.0:0.0705|0.0:0.9295:0.0:0.0705	rs35088381|rs35088381	632;354|.	F5GZB4;Q8IVV2-2|.	.;.|.	C|L	354;632;354|612	ENSP00000381707:G354C;ENSP00000444586:G632C|.	ENSP00000338222:G354C|.	G|R	-|-	1|2	0|0	LOXHD1|LOXHD1	42411744|42411744	1.000000|1.000000	0.71417|0.71417	0.894000|0.894000	0.35097|0.35097	0.335000|0.335000	0.28730|0.28730	7.701000|7.701000	0.84566|0.84566	1.391000|1.391000	0.46566|0.46566	0.561000|0.561000	0.74099|0.74099	GGC|CGG	C|0.984;A|0.016	0.016	strong		0.602	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
OXTR	5021	hgsc.bcm.edu	37	3	8809703	8809703	+	Silent	SNP	G	G	A	rs2228485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:8809703G>A	ENST00000316793.3	-	3	795	c.171C>T	c.(169-171)aaC>aaT	p.N57N	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	57					cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	GCACACACGCGTTCCCGCTCA	0.682													A|||	3595	0.717851	0.6377	0.5937	5008	,	,		13066	0.7272		0.7604	False		,,,				2504	0.8609				p.N57N		Atlas-SNP	.											.	OXTR	31	.	0			c.C171T						PASS	.	A		2850,1540		932,986,277	25.0	24.0	24.0		171	3.8	1.0	3	dbSNP_98	24	6500,2078		2452,1596,241	no	coding-synonymous	OXTR	NM_000916.3		3384,2582,518	AA,AG,GG		24.2248,35.0797,27.8994		57/390	8809703	9350,3618	2195	4289	6484	SO:0001819	synonymous_variant	5021	exon3			ACACGCGTTCCCG		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.171C>T	3.37:g.8809703G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_000916	Q15071	Silent	SNP	ENST00000316793.3	37	CCDS2570.1																																																																																			G|0.297;A|0.703	0.703	strong		0.682	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2		
RNASE11	122651	hgsc.bcm.edu	37	14	21052414	21052414	+	Missense_Mutation	SNP	T	T	A	rs35818240	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21052414T>A	ENST00000610205.1	-	3	403	c.220A>T	c.(220-222)Aca>Tca	p.T74S	RNASE11_ENST00000555841.1_Missense_Mutation_p.T74S|RNASE11_ENST00000398008.2_Missense_Mutation_p.T74S|RNASE11_ENST00000398009.2_Missense_Mutation_p.T74S|RNASE11_ENST00000553849.1_Missense_Mutation_p.T74S|RNASE11_ENST00000432835.2_Missense_Mutation_p.T74S	NM_145250.3	NP_660293.1	Q8TAA1	RNS11_HUMAN	ribonuclease, RNase A family, 11 (non-active)	74			T -> S (in dbSNP:rs35818240).			extracellular region (GO:0005576)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(6)|lung(7)|ovary(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	21	all_cancers(95;0.00238)	all_lung(585;0.235)	Epithelial(56;1.85e-06)|all cancers(55;1.46e-05)	GBM - Glioblastoma multiforme(265;0.0139)		GTCAGTAATGTGGAAGACATA	0.388													A|||	351	0.0700879	0.1747	0.0331	5008	,	,		20783	0.0		0.0596	False		,,,				2504	0.0378				p.T74S		Atlas-SNP	.											.	RNASE11	44	.	0			c.A220T						PASS	.	A	SER/THR	595,3811	770.9+/-413.8	38,519,1646	207.0	196.0	200.0		220	0.1	0.0	14	dbSNP_126	200	512,8088	796.7+/-407.5	16,480,3804	yes	missense	RNASE11	NM_145250.3	58	54,999,5450	AA,AT,TT		5.9535,13.5043,8.5115	benign	74/200	21052414	1107,11899	2203	4300	6503	SO:0001583	missense	122651	exon3			GTAATGTGGAAGA	BC025410	CCDS9553.1	14q11.1	2013-08-05	2004-11-18	2004-11-18	ENSG00000173464	ENSG00000173464		"""Ribonucleases, RNase A"""	19269	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 6"""	C14orf6			Standard	NM_145250		Approved		uc001vxs.3	Q8TAA1	OTTHUMG00000170990	ENST00000610205.1:c.220A>T	14.37:g.21052414T>A	ENSP00000476537:p.Thr74Ser	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	219	120	0.547945	NM_145250		Missense_Mutation	SNP	ENST00000610205.1	37	CCDS9553.1	116	0.05311355311355311	58	0.11788617886178862	16	0.04419889502762431	0	0.0	42	0.055408970976253295	A	0.037	-1.302353	0.01353	0.135043	0.059535	ENSG00000173464	ENST00000335950;ENST00000553849;ENST00000555841;ENST00000398009;ENST00000398008;ENST00000432835;ENST00000443456;ENST00000557503;ENST00000557105;ENST00000413502;ENST00000554842	T;T;T;T;T;T;T;T;T;T;T	0.71341	-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56;-0.56	3.8	0.0823	0.14428	Ribonuclease A, domain (1);	1.252050	0.05754	N	0.603655	T	0.00328	0.0010	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.03184	-1.1063	10	0.02654	T	1	-16.6805	2.4174	0.04439	0.4323:0.0:0.2098:0.3579	rs35818240	74	Q8TAA1	RNS11_HUMAN	S	74	ENSP00000338288:T74S;ENSP00000451318:T74S;ENSP00000451563:T74S;ENSP00000381093:T74S;ENSP00000381092:T74S;ENSP00000395210:T74S;ENSP00000401398:T74S;ENSP00000451839:T74S;ENSP00000452412:T74S;ENSP00000415954:T74S;ENSP00000451466:T74S	ENSP00000338288:T74S	T	-	1	0	RNASE11	20122254	0.374000	0.25081	0.001000	0.08648	0.012000	0.07955	0.060000	0.14342	-0.246000	0.09611	-0.448000	0.05591	ACA	T|0.926;A|0.074	0.074	strong		0.388	RNASE11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073662.3	NM_145250	
GALNT16	57452	hgsc.bcm.edu	37	14	69727121	69727121	+	Silent	SNP	G	G	A	rs150774678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:69727121G>A	ENST00000337827.4	+	1	441	c.114G>A	c.(112-114)cgG>cgA	p.R38R	GALNT16_ENST00000553669.1_Silent_p.R38R|GALNT16_ENST00000448469.3_Silent_p.R38R|RP11-363J20.2_ENST00000556316.1_lincRNA	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	38					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|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)										CCGGCGGCCGGGGCGCGCAGA	0.682													G|||	118	0.0235623	0.003	0.0259	5008	,	,		7435	0.0		0.0736	False		,,,				2504	0.0225				p.R38R		Atlas-SNP	.											.	GALNT16	8	.	0			c.G114A						PASS	.	G	,	47,4353		1,45,2154	45.0	34.0	38.0		114,114	3.2	1.0	14	dbSNP_134	38	518,8076		14,490,3793	no	coding-synonymous,coding-synonymous	GALNTL1	NM_001168368.1,NM_020692.2	,	15,535,5947	AA,AG,GG		6.0275,1.0682,4.3482	,	38/559,38/559	69727121	565,12429	2200	4297	6497	SO:0001819	synonymous_variant	57452	exon1			CGGCCGGGGCGCG	AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23233	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 16"""	615132	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"""	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.114G>A	14.37:g.69727121G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_001168368	Q4KMG3|Q58A55|Q9ULT9	Silent	SNP	ENST00000337827.4	37	CCDS32107.1																																																																																			G|0.960;A|0.040	0.040	strong		0.682	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549548	32549548	+	Silent	SNP	G	G	A	rs2308764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32549548G>A	ENST00000360004.5	-	3	543	c.438C>T	c.(436-438)tgC>tgT	p.C146C		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	146	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						CACTCACAGAGCAGACCAGGA	0.522										Multiple Myeloma(14;0.17)																											p.C146C		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C438T						PASS	.						107.0	128.0	120.0					6																	32549548		1511	2709	4220	SO:0001819	synonymous_variant	3123	exon3			CACAGAGCAGACC	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.438C>T	6.37:g.32549548G>A		Somatic	431	0	0		WXS	Illumina HiSeq	Phase_I	177	54	0.305085	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			G|0.500;A|0.500	0.500	strong		0.522	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	140788	140788	+	Silent	SNP	A	A	G	rs12516245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140788A>G	ENST00000283426.6	+	1	416	c.366A>G	c.(364-366)ccA>ccG	p.P122P	CTD-2231H16.1_ENST00000512035.1_lincRNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	122							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)		TGGGGACCCCAAACTGTGTCC	0.657													A|||	739	0.147564	0.3767	0.0951	5008	,	,		9959	0.0129		0.1243	False		,,,				2504	0.0378				p.P122P		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.A366G						PASS	.			1505,2859		277,951,954	19.0	24.0	22.0		366	1.3	0.0	5	dbSNP_120	22	1034,7516		61,912,3302	no	coding-synonymous	PLEKHG4B	NM_052909.3		338,1863,4256	GG,GA,AA		12.0936,34.4867,19.6608		122/1272	140788	2539,10375	2182	4275	6457	SO:0001819	synonymous_variant	153478	exon1			GACCCCAAACTGT	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.366A>G	5.37:g.140788A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_052909		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			A|0.830;G|0.170	0.170	strong		0.657	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
ATP2B2	491	hgsc.bcm.edu	37	3	10379923	10379923	+	Silent	SNP	C	C	T	rs35678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:10379923C>T	ENST00000352432.4	-	21	3426	c.3357G>A	c.(3355-3357)gcG>gcA	p.A1119A	ATP2B2_ENST00000467702.2_5'Flank|ATP2B2_ENST00000397077.1_Silent_p.A1074A|ATP2B2_ENST00000383800.4_Silent_p.A1074A|ATP2B2_ENST00000343816.4_Silent_p.A1105A|ATP2B2_ENST00000360273.2_Silent_p.A1119A			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	1119					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						GCTCCCGCTCCGCGTGGTCGA	0.652													C|||	2844	0.567891	0.5953	0.6455	5008	,	,		17377	0.5407		0.4274	False		,,,				2504	0.6483				p.A1119A	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.G3357A						PASS	.	C	,	2365,2041	610.9+/-391.7	649,1067,487	73.0	71.0	72.0		3357,3222	-9.2	0.0	3	dbSNP_76	72	3570,5030	516.8+/-378.9	755,2060,1485	no	coding-synonymous,coding-synonymous	ATP2B2	NM_001001331.2,NM_001683.3	,	1404,3127,1972	TT,TC,CC		41.5116,46.3232,45.6328	,	1119/1244,1074/1199	10379923	5935,7071	2203	4300	6503	SO:0001819	synonymous_variant	491	exon22			CCGCTCCGCGTGG	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.3357G>A	3.37:g.10379923C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	40	0.57971	NM_001001331	O00766|Q12994|Q16818	Silent	SNP	ENST00000352432.4	37	CCDS33701.1																																																																																			C|0.505;T|0.495	0.495	strong		0.652	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
RGS22	26166	hgsc.bcm.edu	37	8	100990177	100990177	+	Silent	SNP	A	A	G	rs7841915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:100990177A>G	ENST00000360863.6	-	23	3681	c.3487T>C	c.(3487-3489)Ttg>Ctg	p.L1163L	RGS22_ENST00000523287.1_Silent_p.L982L|RGS22_ENST00000523437.1_Silent_p.L1151L	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	1163					positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			AGGACTGCCAATTTTTTTTTC	0.313													A|||	375	0.0748802	0.1483	0.0461	5008	,	,		17076	0.0456		0.0477	False		,,,				2504	0.0542				p.L1163L		Atlas-SNP	.											.	RGS22	319	.	0			c.T3487C						PASS	.	A		408,3172		25,358,1407	94.0	86.0	89.0		3487	-10.1	0.0	8	dbSNP_116	89	296,7840		5,286,3777	no	coding-synonymous	RGS22	NM_015668.3		30,644,5184	GG,GA,AA		3.6382,11.3966,6.0089		1163/1265	100990177	704,11012	1790	4068	5858	SO:0001819	synonymous_variant	26166	exon23			CTGCCAATTTTTT	AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554		"""Regulators of G-protein signaling"""	24499	protein-coding gene	gene with protein product		615650	"""regulator of G-protein signalling 22"""				Standard	XM_005250856		Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000360863.6:c.3487T>C	8.37:g.100990177A>G		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	245	119	0.485714	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Silent	SNP	ENST00000360863.6	37	CCDS43758.1																																																																																			A|0.924;G|0.076	0.076	strong		0.313	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668	
PCDH1	5097	hgsc.bcm.edu	37	5	141244356	141244356	+	Missense_Mutation	SNP	C	C	T	rs3822357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:141244356C>T	ENST00000394536.3	-	3	1679	c.1540G>A	c.(1540-1542)Gcc>Acc	p.A514T	PCDH1_ENST00000511044.1_5'UTR|PCDH1_ENST00000287008.3_Missense_Mutation_p.A514T|PCDH1_ENST00000456271.1_Missense_Mutation_p.A502T|PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000536585.1_Missense_Mutation_p.A492T	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	514	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in dbSNP:rs3822357).		cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		TCCGGGAAGGCGACCTCAGTG	0.547													C|||	441	0.0880591	0.025	0.147	5008	,	,		20523	0.1379		0.0656	False		,,,				2504	0.1033				p.A514T	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.G1540A						PASS	.	C	THR/ALA,THR/ALA	158,4248	106.9+/-145.3	4,150,2049	119.0	106.0	111.0		1540,1540	3.9	0.8	5	dbSNP_107	111	521,8079	146.2+/-201.8	18,485,3797	yes	missense,missense	PCDH1	NM_002587.3,NM_032420.2	58,58	22,635,5846	TT,TC,CC		6.0581,3.586,5.2207	benign,benign	514/1061,514/1238	141244356	679,12327	2203	4300	6503	SO:0001583	missense	5097	exon3			GGAAGGCGACCTC	AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.1540G>A	5.37:g.141244356C>T	ENSP00000378043:p.Ala514Thr	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	177	96	0.542373	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	37	CCDS43375.1	199	0.09111721611721611	8	0.016260162601626018	46	0.1270718232044199	96	0.16783216783216784	49	0.06464379947229551	c	12.12	1.843432	0.32606	0.03586	0.060581	ENSG00000156453	ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585	T;T;T;T;T	0.50001	0.76;4.03;4.03;4.03;4.03	5.75	3.87	0.44632	Cadherin (4);Cadherin-like (1);	0.122851	0.36374	N	0.002625	T	0.00073	0.0002	N	0.03999	-0.3	0.27759	P	0.9438906	P;P	0.50710	0.869;0.938	B;B	0.40285	0.322;0.325	T	0.07868	-1.0750	9	0.22706	T	0.39	.	9.5319	0.39198	0.0:0.8162:0.0:0.1838	rs3822357;rs52808216;rs57120458;rs3822357	514;514	Q08174;Q08174-2	PCDH1_HUMAN;.	T	514;514;502;525;492	ENSP00000287008:A514T;ENSP00000378043:A514T;ENSP00000403497:A502T;ENSP00000350122:A525T;ENSP00000438825:A492T	ENSP00000287008:A514T	A	-	1	0	PCDH1	141224540	0.567000	0.26626	0.847000	0.33407	0.967000	0.64934	1.269000	0.33074	0.696000	0.31696	0.550000	0.68814	GCC	C|0.935;T|0.065	0.065	strong		0.547	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420	
CCDC137	339230	hgsc.bcm.edu	37	17	79639708	79639708	+	Missense_Mutation	SNP	C	C	T	rs11546631	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79639708C>T	ENST00000329214.8	+	6	1247	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	282			R -> W (in dbSNP:rs11546631).				poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CCTCACTTCCCGGAAGAAGCC	0.662													c|||	659	0.131589	0.1997	0.0519	5008	,	,		16851	0.2232		0.0596	False		,,,				2504	0.0757				p.R282W		Atlas-SNP	.											.	CCDC137	27	.	0			c.C844T						PASS	.	A	TRP/ARG	557,3433		29,499,1467	13.0	18.0	16.0		844	-7.8	0.0	17	dbSNP_120	16	378,7986		8,362,3812	no	missense	CCDC137	NM_199287.2	101	37,861,5279	TT,TC,CC		4.5194,13.9599,7.5684	benign	282/290	79639708	935,11419	1995	4182	6177	SO:0001583	missense	339230	exon6			ACTTCCCGGAAGA	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.844C>T	17.37:g.79639708C>T	ENSP00000329360:p.Arg282Trp	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	88	49	0.556818	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	302	0.1382783882783883	114	0.23170731707317074	18	0.049723756906077346	124	0.21678321678321677	46	0.06068601583113457	C	9.192	1.026261	0.19512	0.139599	0.045194	ENSG00000185298	ENST00000329214	D	0.92299	-3.01	3.92	-7.84	0.01196	.	4.564520	0.00397	N	0.000056	T	0.00144	0.0004	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.48536	-0.9027	9	0.54805	T	0.06	-8.7547	1.2414	0.01964	0.3899:0.2314:0.216:0.1627	rs11546631;rs59897550	282	Q6PK04	CC137_HUMAN	W	282	ENSP00000329360:R282W	ENSP00000329360:R282W	R	+	1	2	CCDC137	77250113	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.437000	0.00471	-2.470000	0.00530	-1.984000	0.00453	CGG	C|0.877;T|0.123	0.123	strong		0.662	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
RECK	8434	hgsc.bcm.edu	37	9	36107981	36107981	+	Missense_Mutation	SNP	C	C	G	rs148296262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:36107981C>G	ENST00000377966.3	+	14	2151	c.1585C>G	c.(1585-1587)Ctg>Gtg	p.L529V		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	529					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			AGGTTGCAAACTGGGAGAAGC	0.383													C|||	2	0.000399361	0.0	0.0	5008	,	,		17308	0.0		0.002	False		,,,				2504	0.0				p.L529V		Atlas-SNP	.											.	RECK	73	.	0			c.C1585G						PASS	.	C	VAL/LEU	6,4400	9.9+/-24.2	0,6,2197	92.0	84.0	87.0		1585	0.6	1.0	9	dbSNP_134	87	22,8578	16.0+/-53.3	0,22,4278	yes	missense	RECK	NM_021111.2	32	0,28,6475	GG,GC,CC		0.2558,0.1362,0.2153	possibly-damaging	529/972	36107981	28,12978	2203	4300	6503	SO:0001583	missense	8434	exon14			TGCAAACTGGGAG	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1585C>G	9.37:g.36107981C>G	ENSP00000367202:p.Leu529Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	37	CCDS6597.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.95	3.264660	0.59431	0.001362	0.002558	ENSG00000122707	ENST00000377966	T	0.56941	0.43	5.45	0.56	0.17279	.	0.000000	0.64402	D	0.000002	T	0.41282	0.1152	L	0.53561	1.675	0.39944	D	0.974446	P;P	0.48407	0.91;0.91	B;B	0.39217	0.294;0.294	T	0.34950	-0.9808	10	0.52906	T	0.07	-9.0488	8.2357	0.31625	0.0:0.3492:0.0:0.6508	.	529;529	A8K9D8;O95980	.;RECK_HUMAN	V	529	ENSP00000367202:L529V	ENSP00000367202:L529V	L	+	1	2	RECK	36097981	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	0.655000	0.24933	0.125000	0.18397	-0.302000	0.09304	CTG	C|0.997;G|0.003	0.003	strong		0.383	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
ATP8B3	148229	hgsc.bcm.edu	37	19	1789721	1789721	+	Silent	SNP	T	T	C	rs56335545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1789721T>C	ENST00000310127.6	-	23	2722	c.2484A>G	c.(2482-2484)aaA>aaG	p.K828K	ATP8B3_ENST00000539485.1_Silent_p.K838K|ATP8B3_ENST00000525591.1_Silent_p.K791K	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	828					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.K838K(1)		central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACACCAGCAGTTTGTCCTGGC	0.716													.|||	526	0.105032	0.2398	0.0605	5008	,	,		9595	0.002		0.0815	False		,,,				2504	0.0849				p.K828K		Atlas-SNP	.											ATP8B3,NS,lymphoid_neoplasm,0,1	ATP8B3	108	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.A2484G						PASS	.	C	,	617,3103		40,537,1283	9.0	10.0	10.0		2373,2484	1.9	1.0	19	dbSNP_129	10	499,7457		16,467,3495	no	coding-synonymous,coding-synonymous	ATP8B3	NM_001178002.1,NM_138813.2	,	56,1004,4778	CC,CT,TT		6.272,16.586,9.5581	,	791/1264,828/1301	1789721	1116,10560	1860	3978	5838	SO:0001819	synonymous_variant	148229	exon23			CAGCAGTTTGTCC	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.2484A>G	19.37:g.1789721T>C		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Silent	SNP	ENST00000310127.6	37	CCDS45901.1																																																																																			T|0.914;C|0.086	0.086	strong		0.716	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
FBN3	84467	hgsc.bcm.edu	37	19	8145921	8145921	+	Silent	SNP	C	C	T	rs2303168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8145921C>T	ENST00000600128.1	-	59	7833	c.7419G>A	c.(7417-7419)ccG>ccA	p.P2473P	FBN3_ENST00000601739.1_Silent_p.P2473P|FBN3_ENST00000270509.2_Silent_p.P2473P			Q75N90	FBN3_HUMAN	fibrillin 3	2473	EGF-like 40; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGAAGCCGGGCGGACAGCGGC	0.617													C|||	2821	0.563299	0.8389	0.6354	5008	,	,		17531	0.3581		0.5636	False		,,,				2504	0.3507				p.P2473P		Atlas-SNP	.											.	FBN3	300	.	0			c.G7419A						PASS	.	C		3503,903	729.3+/-410.0	1386,731,86	59.0	54.0	56.0		7419	-4.9	1.0	19	dbSNP_100	56	4633,3967	594.7+/-393.3	1261,2111,928	no	coding-synonymous	FBN3	NM_032447.3		2647,2842,1014	TT,TC,CC		46.1279,20.4948,37.4443		2473/2810	8145921	8136,4870	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon58			GCCGGGCGGACAG		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.7419G>A	19.37:g.8145921C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	39	39	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			C|0.386;T|0.614	0.614	strong		0.617	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
ZNF91	7644	hgsc.bcm.edu	37	19	23542290	23542290	+	Missense_Mutation	SNP	A	A	G	rs368101335|rs386808073|rs428549	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:23542290A>G	ENST00000300619.7	-	4	3696	c.3491T>C	c.(3490-3492)cTa>cCa	p.L1164P	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.L1132P|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1164			L -> P (in dbSNP:rs428549).|L -> V (in dbSNP:rs385750).	L -> A (in Ref. 2; BAF83945). {ECO:0000305}.	transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				ctcccaaagtagtgggattac	0.428													G|||	1832	0.365815	0.5915	0.1787	5008	,	,		16607	0.369		0.2505	False		,,,				2504	0.3088				p.L1164P		Atlas-SNP	.											.	ZNF91	349	.	0			c.T3491C						PASS	.	G	PRO/LEU	55,4071		4,47,2012	29.0	35.0	33.0		3491		0.0	19	dbSNP_80	33	24,8410		1,22,4194	no	missense	ZNF91	NM_003430.2	98	5,69,6206	GG,GA,AA		0.2846,1.333,0.629	benign	1164/1192	23542290	79,12481	2063	4217	6280	SO:0001583	missense	7644	exon4			CAAAGTAGTGGGA	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3491T>C	19.37:g.23542290A>G	ENSP00000300619:p.Leu1164Pro	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	624	0.2857142857142857	231	0.4695121951219512	69	0.19060773480662985	181	0.31643356643356646	143	0.18865435356200527	G	2.172	-0.389649	0.04932	0.01333	0.002846	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.05925	3.41;3.37	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.17667	0.023;0.0	B;B	0.04013	0.001;0.0	T	0.46569	-0.9182	7	0.66056	D	0.02	.	1.4642	0.02402	0.3314:0.0:0.3362:0.3323	rs428549	1132;1164	Q05481-2;Q05481	.;ZNF91_HUMAN	P	1164;1132	ENSP00000300619:L1164P;ENSP00000380272:L1132P	ENSP00000300619:L1164P	L	-	2	0	ZNF91	23334130	0.224000	0.23674	0.006000	0.13384	0.007000	0.05969	-0.260000	0.08708	-1.871000	0.01138	-1.895000	0.00532	CTA	A|0.713;G|0.287	0.287	strong		0.428	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
ZNF677	342926	hgsc.bcm.edu	37	19	53741068	53741068	+	Silent	SNP	C	C	T	rs12984188	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53741068C>T	ENST00000598513.1	-	5	1062	c.912G>A	c.(910-912)tcG>tcA	p.S304S	CTD-2245F17.6_ENST00000596041.1_RNA|ZNF677_ENST00000333952.4_Silent_p.S304S	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	304					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.S304S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		TAGTGAGGTTCGAACACTGGT	0.403													C|||	2328	0.464856	0.2148	0.4294	5008	,	,		20469	0.752		0.4324	False		,,,				2504	0.5654				p.S304S		Atlas-SNP	.											ZNF677,rectum,carcinoma,-1,3	ZNF677	94	3	1	Substitution - coding silent(1)	stomach(1)	c.G912A						PASS	.	C		1072,3334	388.4+/-326.9	106,860,1237	123.0	112.0	116.0		912	-3.1	0.0	19	dbSNP_121	116	3609,4991	521.4+/-379.9	748,2113,1439	no	coding-synonymous	ZNF677	NM_182609.2		854,2973,2676	TT,TC,CC		41.9651,24.3305,35.9911		304/585	53741068	4681,8325	2203	4300	6503	SO:0001819	synonymous_variant	342926	exon5			GAGGTTCGAACAC	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.912G>A	19.37:g.53741068C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_182609		Silent	SNP	ENST00000598513.1	37	CCDS12861.1																																																																																			C|0.591;T|0.409	0.409	strong		0.403	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
MSLN	10232	hgsc.bcm.edu	37	16	818559	818559	+	Missense_Mutation	SNP	A	A	G	rs1135210	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:818559A>G	ENST00000382862.3	+	16	1896	c.1801A>G	c.(1801-1803)Atg>Gtg	p.M601V	MIR662_ENST00000384847.1_RNA|MSLN_ENST00000545450.2_Missense_Mutation_p.M593V|MSLN_ENST00000566549.1_Missense_Mutation_p.M593V|MSLN_ENST00000563941.1_Missense_Mutation_p.M593V	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	601			M -> V (in dbSNP:rs1135210). {ECO:0000269|PubMed:10500211, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15616553, ECO:0000269|PubMed:15897581, ECO:0000269|PubMed:7665620, ECO:0000269|PubMed:8552591}.		cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				AGACCTCAGCATGCAAGGTGG	0.706													G|||	1770	0.353435	0.6059	0.2968	5008	,	,		10967	0.3115		0.1978	False		,,,				2504	0.2556				p.M601V		Atlas-SNP	.											MSLN_ENST00000446427,NS,carcinoma,0,2	MSLN	109	2	0			c.A1801G						scavenged	.	G	VAL/MET,VAL/MET,VAL/MET	2203,2121		564,1075,523	15.0	16.0	16.0		1777,1777,1801	-6.5	0.0	16	dbSNP_86	16	1921,6613		222,1477,2568	no	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	21,21,21	786,2552,3091	GG,GA,AA		22.51,49.0518,32.0734	benign,benign,benign	593/623,593/623,601/631	818559	4124,8734	2162	4267	6429	SO:0001583	missense	10232	exon16			CTCAGCATGCAAG	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.1801A>G	16.37:g.818559A>G	ENSP00000372313:p.Met601Val	Somatic	58	2	0.0344828		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	719	0.3292124542124542	305	0.6199186991869918	92	0.2541436464088398	174	0.3041958041958042	148	0.19525065963060687	G	0.008	-1.869221	0.00547	0.509482	0.2251	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.08896	3.04;3.04	3.27	-6.54	0.01860	.	1.419940	0.04960	N	0.461970	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42207	-0.9465	9	0.10111	T	0.7	0.374	3.2179	0.06705	0.2108:0.0953:0.5431:0.1508	rs1135210;rs1803988;rs2272906;rs3178838;rs3197756;rs11558321;rs17143768;rs17855368;rs60036829;rs1135210	592;601;593	Q13421-4;Q13421;Q13421-3	.;MSLN_HUMAN;.	V	601;593;593;601	ENSP00000442965:M593V;ENSP00000372313:M601V	ENSP00000372313:M601V	M	+	1	0	MSLN	758560	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.235000	0.09016	-1.745000	0.01337	-2.568000	0.00172	ATG	A|0.678;G|0.322	0.322	strong		0.706	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
C17orf97	400566	hgsc.bcm.edu	37	17	260142	260142	+	Silent	SNP	G	G	T	rs7503725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:260142G>T	ENST00000571106.1	+	1	15	c.9G>T	c.(7-9)acG>acT	p.T3T	AC108004.3_ENST00000466740.2_RNA|AC108004.3_ENST00000599026.1_RNA|C17orf97_ENST00000360127.6_Silent_p.T3T			Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	3										breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						CCATGGAGACGCGTGGCCCTG	0.741													g|||	1931	0.385583	0.6293	0.2666	5008	,	,		15082	0.3115		0.2406	False		,,,				2504	0.3661				p.T3T		Atlas-SNP	.											.	C17orf97	76	.	0			c.G9T						PASS	.			1838,1922		489,860,531	4.0	4.0	4.0		9	3.5	1.0	17	dbSNP_116	4	1734,5886		294,1146,2370	no	coding-synonymous	C17orf97	NM_001013672.4		783,2006,2901	TT,TG,GG		22.7559,48.883,31.3884		3/424	260142	3572,7808	1880	3810	5690	SO:0001819	synonymous_variant	400566	exon1			GGAGACGCGTGGC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000571106.1:c.9G>T	17.37:g.260142G>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Silent	SNP	ENST00000571106.1	37																																																																																				G|0.658;T|0.342	0.342	strong		0.741	C17orf97-003	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000436874.1	NM_001013672	
CLCA4	22802	hgsc.bcm.edu	37	1	87045902	87045902	+	Silent	SNP	A	A	T	rs1932809|rs4001061|rs77067122|rs56040873|rs574759485|rs368263974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	2	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	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	
CAPN1	823	hgsc.bcm.edu	37	11	64981818	64981818	+	IGR	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64981818C>T	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		GTGTGAGGCCCGCACTCTCCG	0.662																																					p.R135C		Atlas-SNP	.											.	SLC22A20	36	.	0			c.C403T						PASS	.						35.0	39.0	38.0					11																	64981818		2065	4197	6262	SO:0001628	intergenic_variant	440044	exon2			GAGGCCCGCACTC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981818C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	45	0.625	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			.	.	none		0.662	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
RDH5	5959	hgsc.bcm.edu	37	12	56115585	56115585	+	Silent	SNP	C	C	T	rs3138142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56115585C>T	ENST00000257895.5	+	3	575	c.423C>T	c.(421-423)atC>atT	p.I141I	RDH5_ENST00000553160.1_Intron|RDH5_ENST00000547072.1_Silent_p.I44I|RP11-644F5.10_ENST00000550412.1_3'UTR|RDH5_ENST00000548082.1_Silent_p.I141I	NM_001199771.1|NM_002905.3	NP_001186700.1|NP_002896.2	Q92781	RDH1_HUMAN	retinol dehydrogenase 5 (11-cis/9-cis)	141					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	cell body (GO:0044297)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	retinol dehydrogenase activity (GO:0004745)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|skin(1)	12					Vitamin A(DB00162)	TGGGTCCCATCGGGGTCACCC	0.622													C|||	765	0.152756	0.0098	0.1023	5008	,	,		17734	0.12		0.1899	False		,,,				2504	0.3773				p.I141I		Atlas-SNP	.											.	RDH5	25	.	0			c.C423T						PASS	.	C	,	219,4187	131.0+/-167.6	8,203,1992	46.0	43.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	423,423	-2.2	0.8	12	dbSNP_104	44	1828,6772	323.7+/-316.1	214,1400,2686	no	coding-synonymous,coding-synonymous	RDH5	NM_001199771.1,NM_002905.3	,	222,1603,4678	TT,TC,CC		21.2558,4.9705,15.7389	,	141/319,141/319	56115585	2047,10959	2203	4300	6503	SO:0001819	synonymous_variant	5959	exon3			TCCCATCGGGGTC	U89717	CCDS31829.1	12q13-q14	2013-06-03	2006-05-09			ENSG00000135437	1.1.1.105	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	9940	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 9C, member 5"""	601617	"""retinol dehydrogenase 5 (11-cis and 9-cis)"""	RDH1		9115228, 8884265, 19027726	Standard	NM_002905		Approved	HSD17B9, SDR9C5	uc001shl.3	Q92781	OTTHUMG00000170126	ENST00000257895.5:c.423C>T	12.37:g.56115585C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	39	17	0.435897	NM_001199771	O00179|Q8TAI2	Silent	SNP	ENST00000257895.5	37	CCDS31829.1																																																																																			C|0.865;T|0.135	0.135	strong		0.622	RDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407493.1	NM_002905	
OR5D18	219438	hgsc.bcm.edu	37	11	55587914	55587914	+	Missense_Mutation	SNP	A	A	G	rs55832853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55587914A>G	ENST00000333976.4	+	1	829	c.809A>G	c.(808-810)cAc>cGc	p.H270R		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	270			H -> R (in dbSNP:rs55832853).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				AACTCCAGGCACACAGTCAAA	0.498													N|||	1167	0.233027	0.0204	0.3228	5008	,	,		18084	0.3889		0.2903	False		,,,				2504	0.2372				p.H270R		Atlas-SNP	.											OR5D18,NS,carcinoma,-1,1	OR5D18	121	1	0			c.A809G						PASS	.	A	ARG/HIS	288,4112		11,266,1923	89.0	86.0	87.0		809	2.4	1.0	11	dbSNP_129	87	2368,6224		350,1668,2278	no	missense	OR5D18	NM_001001952.1	29	361,1934,4201	GG,GA,AA		27.5605,6.5455,20.4433	benign	270/314	55587914	2656,10336	2200	4296	6496	SO:0001583	missense	219438	exon1			CCAGGCACACAGT	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.809A>G	11.37:g.55587914A>G	ENSP00000335025:p.His270Arg	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	125	76	0.608	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	CCDS31510.1	576	0.26373626373626374	15	0.03048780487804878	126	0.34806629834254144	212	0.3706293706293706	223	0.2941952506596306	.	0.046	-1.267286	0.01433	0.065455	0.275605	ENSG00000186119	ENST00000333976	T	0.00044	8.83	5.03	2.44	0.29823	GPCR, rhodopsin-like superfamily (1);	0.181667	0.26939	N	0.021727	T	0.00012	0.0000	N	0.13098	0.295	0.80722	P	0.0	B	0.11235	0.004	B	0.18263	0.021	T	0.25676	-1.0125	9	0.62326	D	0.03	-11.8734	5.983	0.19417	0.5245:0.1337:0.0:0.3418	rs55832853;rs61896324	270	Q8NGL1	OR5DI_HUMAN	R	270	ENSP00000335025:H270R	ENSP00000335025:H270R	H	+	2	0	OR5D18	55344490	0.000000	0.05858	0.973000	0.42090	0.199000	0.23934	0.454000	0.21827	0.236000	0.21180	-0.508000	0.04489	CAC	A|0.774;G|0.226	0.226	strong		0.498	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
ZNF644	84146	hgsc.bcm.edu	37	1	91404256	91404256	+	Missense_Mutation	SNP	C	C	A	rs41286761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91404256C>A	ENST00000370440.1	-	3	2872	c.2655G>T	c.(2653-2655)gaG>gaT	p.E885D	ZNF644_ENST00000337393.5_Missense_Mutation_p.E885D|ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	885					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)		AATTTACATGCTCTTGATTAA	0.363													C|||	51	0.0101837	0.0008	0.0173	5008	,	,		18538	0.0		0.0328	False		,,,				2504	0.0051				p.E885D		Atlas-SNP	.											.	ZNF644	120	.	0			c.G2655T						PASS	.	C	,,ASP/GLU	34,4372	39.2+/-71.8	0,34,2169	83.0	85.0	85.0		,,2655	0.5	1.0	1	dbSNP_127	85	267,8331	103.6+/-164.7	4,259,4036	yes	intron,intron,missense	ZNF644	NM_016620.3,NM_032186.4,NM_201269.2	,,45	4,293,6205	AA,AC,CC		3.1054,0.7717,2.3147	,,benign	,,885/1328	91404256	301,12703	2203	4299	6502	SO:0001583	missense	84146	exon3			TACATGCTCTTGA	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.2655G>T	1.37:g.91404256C>A	ENSP00000359469:p.Glu885Asp	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	30	0.013736263736263736	0	0.0	5	0.013812154696132596	0	0.0	25	0.032981530343007916	C	7.879	0.729812	0.15507	0.007717	0.031054	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	T;T	0.00601	6.29;6.29	5.59	0.468	0.16732	.	0.166763	0.52532	N	0.000065	T	0.00178	0.0005	L	0.32530	0.975	0.36658	D	0.877789	B	0.02656	0.0	B	0.04013	0.001	T	0.50224	-0.8853	10	0.33141	T	0.24	-9.8039	1.1211	0.01725	0.162:0.3136:0.1455:0.379	rs41286761	885	Q9H582	ZN644_HUMAN	D	885;885;457	ENSP00000359469:E885D;ENSP00000337008:E885D	ENSP00000337008:E885D	E	-	3	2	ZNF644	91176844	0.302000	0.24454	1.000000	0.80357	0.988000	0.76386	-0.251000	0.08818	0.035000	0.15519	-0.383000	0.06682	GAG	C|0.981;A|0.019	0.019	strong		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186	
ETV3	2117	hgsc.bcm.edu	37	1	157095470	157095470	+	Silent	SNP	A	A	G	rs2231856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:157095470A>G	ENST00000368192.4	-	5	766	c.702T>C	c.(700-702)ttT>ttC	p.F234F		NM_001145312.1	NP_001138784.1	P41162	ETV3_HUMAN	ets variant 3	234					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	9	Hepatocellular(266;0.158)	Prostate(1639;0.174)				CTGGCCTAGCAAACAGAGGAA	0.587													A|||	1212	0.242013	0.0129	0.2882	5008	,	,		20596	0.5565		0.1123	False		,,,				2504	0.3282				p.F234F		Atlas-SNP	.											.	ETV3	50	.	0			c.T702C						PASS	.	A		38,1346		1,36,655	100.0	97.0	98.0		702	4.1	0.9	1	dbSNP_98	98	302,2880		12,278,1301	no	coding-synonymous	ETV3	NM_001145312.1		13,314,1956	GG,GA,AA		9.4909,2.7457,7.4463		234/513	157095470	340,4226	692	1591	2283	SO:0001819	synonymous_variant	2117	exon5			CCTAGCAAACAGA	BC022868	CCDS1164.1, CCDS44250.1	1q21-q23	2008-09-12	2008-09-12		ENSG00000117036	ENSG00000117036			3492	protein-coding gene	gene with protein product		164873	"""ets variant gene 3, ETS family transcriptional repressor"", ""ets variant gene 3"""			8020980	Standard	NM_005240		Approved	PE-1	uc001fqr.2	P41162	OTTHUMG00000034298	ENST00000368192.4:c.702T>C	1.37:g.157095470A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_001145312	B4E3M7|Q8TAC8|Q9BX30	Silent	SNP	ENST00000368192.4	37	CCDS44250.1																																																																																			A|0.792;G|0.208	0.208	strong		0.587	ETV3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082843.2	NM_005240	
KCNH4	23415	hgsc.bcm.edu	37	17	40312349	40312349	+	Silent	SNP	G	G	A	rs138917401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:40312349G>A	ENST00000264661.3	-	16	3095	c.2763C>T	c.(2761-2763)tcC>tcT	p.S921S	KCNH4_ENST00000607371.1_Silent_p.S921S	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	921					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGGTCCAAGCGGAGCCTGCTG	0.647													G|||	11	0.00219649	0.0008	0.0043	5008	,	,		16423	0.0		0.004	False		,,,				2504	0.0031				p.S921S	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.C2763T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	53.0	48.0	49.0		2763	-9.9	0.0	17	dbSNP_134	49	60,8540	36.9+/-92.0	1,58,4241	no	coding-synonymous	KCNH4	NM_012285.2		1,65,6437	AA,AG,GG		0.6977,0.1589,0.5151		921/1018	40312349	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	23415	exon16			CCAAGCGGAGCCT	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.2763C>T	17.37:g.40312349G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	110	50	0.454545	NM_012285		Silent	SNP	ENST00000264661.3	37	CCDS11420.1																																																																																			G|0.996;A|0.004	0.004	strong		0.647	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285	
DNAH5	1767	hgsc.bcm.edu	37	5	13811775	13811775	+	Missense_Mutation	SNP	T	T	C	rs10078391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13811775T>C	ENST00000265104.4	-	44	7492	c.7388A>G	c.(7387-7389)cAa>cGa	p.Q2463R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2463			Q -> R (in dbSNP:rs10078391).		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AATCAGGCCTTGAAGCATGTT	0.413									Kartagener syndrome				T|||	1313	0.262181	0.1884	0.1758	5008	,	,		11862	0.5585		0.2147	False		,,,				2504	0.1667				p.Q2463R		Atlas-SNP	.											DNAH5,right_upper_lobe,carcinoma,-1,1	DNAH5	868	1	0			c.A7388G						PASS	.	T	ARG/GLN	888,3518	344.9+/-308.3	101,686,1416	94.0	93.0	93.0		7388	5.8	0.5	5	dbSNP_119	93	1761,6839	320.9+/-314.9	172,1417,2711	yes	missense	DNAH5	NM_001369.2	43	273,2103,4127	CC,CT,TT		20.4767,20.1543,20.3675	possibly-damaging	2463/4625	13811775	2649,10357	2203	4300	6503	SO:0001583	missense	1767	exon44	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGCCTTGAAGCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.7388A>G	5.37:g.13811775T>C	ENSP00000265104:p.Gln2463Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	91	54	0.593407	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	622	0.2847985347985348	99	0.20121951219512196	63	0.17403314917127072	293	0.5122377622377622	167	0.22031662269129287	T	15.09	2.730316	0.48939	0.201543	0.204767	ENSG00000039139	ENST00000265104	T	0.25579	1.79	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.83603	2.65	0.09310	P	0.999999792992	B	0.32893	0.389	B	0.35039	0.194	T	0.46020	-0.9221	9	0.66056	D	0.02	.	16.1193	0.81336	0.0:0.0:0.0:1.0	rs10078391;rs52804450;rs10078391	2463	Q8TE73	DYH5_HUMAN	R	2463	ENSP00000265104:Q2463R	ENSP00000265104:Q2463R	Q	-	2	0	DNAH5	13864775	1.000000	0.71417	0.547000	0.28179	0.422000	0.31414	7.977000	0.88081	2.204000	0.70986	0.528000	0.53228	CAA	T|0.764;C|0.236	0.236	strong		0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
USP42	84132	hgsc.bcm.edu	37	7	6193752	6193752	+	Missense_Mutation	SNP	G	G	A	rs61753119	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6193752G>A	ENST00000306177.5	+	15	2725	c.2567G>A	c.(2566-2568)aGt>aAt	p.S856N		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	856	Pro-rich.				cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		GAAGGGTTGAGTCCGGCTCCG	0.701													G|||	342	0.0682907	0.0484	0.1225	5008	,	,		11334	0.0089		0.1382	False		,,,				2504	0.046				p.S856N		Atlas-SNP	.											USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	0			c.G2567A						PASS	.	G	ASN/SER	214,3498		2,210,1644	19.0	25.0	23.0		2567	3.4	0.1	7	dbSNP_129	23	941,7121		45,851,3135	no	missense	USP42	NM_032172.2	46	47,1061,4779	AA,AG,GG		11.672,5.7651,9.8098	probably-damaging	856/1317	6193752	1155,10619	1856	4031	5887	SO:0001583	missense	84132	exon15			GGTTGAGTCCGGC	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.2567G>A	7.37:g.6193752G>A	ENSP00000301962:p.Ser856Asn	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	17	10	0.588235	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	165	0.07554945054945054	26	0.052845528455284556	42	0.11602209944751381	2	0.0034965034965034965	95	0.12532981530343007	G	18.30	3.593525	0.66219	0.057651	0.11672	ENSG00000106346	ENST00000306177;ENST00000426246	T;T	0.17854	2.25;2.67	5.2	3.37	0.38596	.	0.312951	0.33670	N	0.004665	T	0.00144	0.0004	L	0.29908	0.895	0.53688	P	2.199999999996649E-5	P;B	0.36909	0.573;0.437	B;B	0.39217	0.294;0.154	T	0.22906	-1.0203	9	0.39692	T	0.17	.	7.3813	0.26858	0.0973:0.2021:0.7005:0.0	rs61753119	856;856	Q9H9J4-2;Q9H9J4	.;UBP42_HUMAN	N	856;702	ENSP00000301962:S856N;ENSP00000408217:S702N	ENSP00000301962:S856N	S	+	2	0	USP42	6160277	0.129000	0.22400	0.053000	0.19242	0.001000	0.01503	3.032000	0.49736	0.786000	0.33708	-0.136000	0.14681	AGT	G|0.919;A|0.081	0.081	strong		0.701	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
USP42	84132	hgsc.bcm.edu	37	7	6194383	6194383	+	Silent	SNP	C	C	T	rs73058659	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6194383C>T	ENST00000306177.5	+	15	3356	c.3198C>T	c.(3196-3198)taC>taT	p.Y1066Y		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	1066	Arg-rich.				cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		ATGACAGGTACGCCCTGTACG	0.706													C|||	227	0.0453275	0.0068	0.0865	5008	,	,		7457	0.0		0.1392	False		,,,				2504	0.0184				p.Y1066Y		Atlas-SNP	.											USP42_ENST00000306177,NS,carcinoma,0,2	USP42	138	2	0			c.C3198T						PASS	.	C		96,3946		1,94,1926	8.0	10.0	10.0		3198	2.5	0.4	7	dbSNP_132	10	973,7321		38,897,3212	no	coding-synonymous	USP42	NM_032172.2		39,991,5138	TT,TC,CC		11.7314,2.3751,8.6657		1066/1317	6194383	1069,11267	2021	4147	6168	SO:0001819	synonymous_variant	84132	exon15			CAGGTACGCCCTG	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.3198C>T	7.37:g.6194383C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	19	9	0.473684	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Silent	SNP	ENST00000306177.5	37	CCDS47535.1																																																																																			C|0.929;T|0.071	0.071	strong		0.706	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
UNC13A	23025	hgsc.bcm.edu	37	19	17746940	17746940	+	Silent	SNP	C	C	T	rs77267738	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17746940C>T	ENST00000519716.2	-	26	3107	c.3108G>A	c.(3106-3108)gaG>gaA	p.E1036E	UNC13A_ENST00000252773.7_Silent_p.E1036E|UNC13A_ENST00000552293.1_Silent_p.E1036E|UNC13A_ENST00000550896.1_Silent_p.E1034E|UNC13A_ENST00000428389.2_Silent_p.E1124E|UNC13A_ENST00000551649.1_Silent_p.E1036E	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1036					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GCCCCTGTTCCTCTGGGAGAA	0.517													c|||	116	0.0231629	0.0061	0.0504	5008	,	,		19614	0.001		0.0656	False		,,,				2504	0.0061				p.E1036E		Atlas-SNP	.											.	UNC13A	299	.	0			c.G3108A						PASS	.	C		56,3772		0,56,1858	64.0	61.0	62.0		3108	3.5	1.0	19	dbSNP_132	62	498,7780		16,466,3657	no	coding-synonymous	UNC13A	NM_001080421.2		16,522,5515	TT,TC,CC		6.0159,1.4629,4.5762		1036/1704	17746940	554,11552	1914	4139	6053	SO:0001819	synonymous_variant	23025	exon25			CTGTTCCTCTGGG	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.3108G>A	19.37:g.17746940C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	182	94	0.516484	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			C|0.958;T|0.042	0.042	strong		0.517	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
ZNF587B	100293516	hgsc.bcm.edu	37	19	58353003	58353003	+	Missense_Mutation	SNP	G	G	A	rs34871842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58353003G>A	ENST00000442832.4	+	3	1195	c.961G>A	c.(961-963)Gct>Act	p.A321T	CTD-2583A14.10_ENST00000598031.1_Intron|ZNF587B_ENST00000316462.4_Intron|ZNF587B_ENST00000594901.1_Missense_Mutation_p.A321T	NM_001204818.1	NP_001191747.1	E7ETH6	Z587B_HUMAN	zinc finger protein 587B	321					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AAAAGTTCACGCTGGAAAAGG	0.418													.|||	148	0.0295527	0.0068	0.049	5008	,	,		20383	0.001		0.0885	False		,,,				2504	0.0153				p.A321T		Atlas-SNP	.											.	.	.	.	0			c.G961A						PASS	.																																			SO:0001583	missense	100293516	exon3			GTTCACGCTGGAA	AK299091	CCDS56109.1	19q13.43	2013-01-08				ENSG00000269343		"""Zinc fingers, C2H2-type"", ""-"""	37142	protein-coding gene	gene with protein product							Standard	NM_001204818		Approved		uc021vcp.1	E7ETH6		ENST00000442832.4:c.961G>A	19.37:g.58353003G>A	ENSP00000392410:p.Ala321Thr	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	18	12	0.666667	NM_001204818	B4DR41	Missense_Mutation	SNP	ENST00000442832.4	37	CCDS56109.1	90	0.04120879120879121	3	0.006097560975609756	20	0.055248618784530384	0	0.0	67	0.08839050131926121	.	0.011	-1.719340	0.00700	.	.	ENSG00000198466	ENST00000442832	T	0.11277	2.79	1.95	-0.711	0.11230	.	.	.	.	.	T	0.00178	0.0005	N	0.02391	-0.57	.	.	.	B;B	0.11235	0.004;0.0	B;B	0.06405	0.002;0.0	T	0.47497	-0.9113	7	.	.	.	.	8.043	0.30532	0.8648:0.0:0.1352:0.0	rs34871842;rs34871842	321;270	E7ETH6;Q92967	.;.	T	321	ENSP00000392410:A321T	.	A	+	1	0	ZNF587	63044815	0.000000	0.05858	0.012000	0.15200	0.001000	0.01503	-0.072000	0.11486	-0.455000	0.07054	-1.873000	0.00551	GCT	G|0.956;A|0.044	0.044	strong		0.418	ZNF587B-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466834.2	NM_001204818	
MT-ND4	4538	hgsc.bcm.edu	37	M	11719	11719	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:11719G>A	ENST00000361381.2	+	1	960	c.960G>A	c.(958-960)ggG>ggA	p.G320G	MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	320					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ATCGCCCACGGACTCACATCC	0.483																																					p.G320G		Atlas-SNP	.											.	.	.	.	0			c.G960A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CCACGGGCTTACA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.960G>A	M.37:g.11719G>A		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.483	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
PCDHB6	56130	hgsc.bcm.edu	37	5	140530852	140530852	+	Silent	SNP	G	G	C	rs246708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140530852G>C	ENST00000231136.1	+	1	1014	c.1014G>C	c.(1012-1014)gtG>gtC	p.V338V	PCDHB6_ENST00000543635.1_Silent_p.V202V	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	338	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCTGGACGTGAATGACAATG	0.468													G|||	1122	0.224042	0.4909	0.2406	5008	,	,		18488	0.0407		0.169	False		,,,				2504	0.0971				p.V338V		Atlas-SNP	.											PCDHB6,NS,carcinoma,+2,1	PCDHB6	161	1	0			c.G1014C						PASS	.	G		1871,2535	542.4+/-376.0	393,1085,725	102.0	98.0	99.0		1014	0.0	0.9	5	dbSNP_79	99	1580,7020	295.5+/-302.4	152,1276,2872	no	coding-synonymous	PCDHB6	NM_018939.2		545,2361,3597	CC,CG,GG		18.3721,42.4648,26.5339		338/795	140530852	3451,9555	2203	4300	6503	SO:0001819	synonymous_variant	56130	exon1			GGACGTGAATGAC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1014G>C	5.37:g.140530852G>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	195	83	0.425641	NM_018939	B2R8R9	Silent	SNP	ENST00000231136.1	37	CCDS4248.1																																																																																			G|0.747;C|0.253	0.253	strong		0.468	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
SGK223	157285	hgsc.bcm.edu	37	8	8234219	8234219	+	Missense_Mutation	SNP	G	G	A	rs4840955|rs373458829	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:8234219G>A	ENST00000520004.1	-	3	1964	c.1700C>T	c.(1699-1701)cCg>cTg	p.P567L	SGK223_ENST00000330777.4_Missense_Mutation_p.P567L			Q86YV5	SG223_HUMAN		569							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GTCAGCCAGCGGTGACACTGG	0.657													G|||	2270	0.453275	0.388	0.4323	5008	,	,		16798	0.6409		0.3002	False		,,,				2504	0.5204				p.P567L	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1700T						PASS	.	G	LEU/PRO	1293,2749		229,835,957	24.0	29.0	27.0		1700	4.9	0.0	8	dbSNP_111	27	2275,6025		338,1599,2213	yes	missense	SGK223	NM_001080826.1	98	567,2434,3170	AA,AG,GG		27.4096,31.9891,28.9094	probably-damaging	567/1403	8234219	3568,8774	2021	4150	6171	SO:0001583	missense	0	exon2			GCCAGCGGTGACA																												ENST00000520004.1:c.1700C>T	8.37:g.8234219G>A	ENSP00000428054:p.Pro567Leu	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	39	14	0.358974	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	906	0.41483516483516486	193	0.39227642276422764	131	0.36187845303867405	367	0.6416083916083916	215	0.2836411609498681	G	14.12	2.440334	0.43326	0.319891	0.274096	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59906	0.23;0.23	4.91	4.91	0.64330	.	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	M	0.62723	1.935	0.32196	P	0.578445	B	0.25312	0.123	B	0.18871	0.023	T	0.48969	-0.8987	9	0.56958	D	0.05	.	7.8195	0.29280	0.0832:0.0:0.7549:0.1619	rs4840955;rs61637687	567	Q86YV5	SG223_HUMAN	L	567	ENSP00000330930:P567L;ENSP00000428054:P567L	ENSP00000330930:P567L	P	-	2	0	AC068353.1	8271629	1.000000	0.71417	0.040000	0.18447	0.002000	0.02628	4.250000	0.58772	2.446000	0.82766	0.563000	0.77884	CCG	G|0.631;A|0.369	0.369	strong		0.657	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
MYO1E	4643	hgsc.bcm.edu	37	15	59500970	59500970	+	Silent	SNP	C	C	T	rs117265950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:59500970C>T	ENST00000288235.4	-	14	1839	c.1440G>A	c.(1438-1440)acG>acA	p.T480T		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	480	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)		TCTGGAGCAGCGTCTGATCTG	0.532													c|||	47	0.00938498	0.0015	0.0086	5008	,	,		19011	0.0		0.0149	False		,,,				2504	0.0245				p.T480T		Atlas-SNP	.											.	MYO1E	99	.	0			c.G1440A						PASS	.	T		10,4372	16.8+/-37.8	0,10,2181	176.0	148.0	157.0		1440	-10.7	0.2	15	dbSNP_132	157	116,8464	61.0+/-122.8	2,112,4176	no	coding-synonymous	MYO1E	NM_004998.2		2,122,6357	TT,TC,CC		1.352,0.2282,0.9721		480/1109	59500970	126,12836	2191	4290	6481	SO:0001819	synonymous_variant	4643	exon14			GAGCAGCGTCTGA	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.1440G>A	15.37:g.59500970C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	158	63	0.398734	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			C|0.991;T|0.009	0.009	strong		0.532	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998	
SFSWAP	6433	hgsc.bcm.edu	37	12	132250712	132250712	+	Silent	SNP	G	G	C	rs1051233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:132250712G>C	ENST00000261674.4	+	13	2142	c.2001G>C	c.(1999-2001)ctG>ctC	p.L667L	SFSWAP_ENST00000541286.1_Silent_p.L667L	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	667					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						GGGAAAAGCTGGCCCAGGCGT	0.443													G|||	508	0.101438	0.0091	0.2291	5008	,	,		18099	0.0		0.2366	False		,,,				2504	0.1012				p.L667L		Atlas-SNP	.											.	SFSWAP	69	.	0			c.G2001C						PASS	.	G		206,4200	127.0+/-164.0	7,192,2004	104.0	119.0	114.0		2001	-9.3	0.5	12	dbSNP_86	114	2198,6402	375.7+/-337.9	275,1648,2377	no	coding-synonymous	SFSWAP	NM_004592.2		282,1840,4381	CC,CG,GG		25.5581,4.6754,18.4838		667/952	132250712	2404,10602	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon13			AAAGCTGGCCCAG	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.2001G>C	12.37:g.132250712G>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	50	20	0.4	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	284	0.13003663003663005	8	0.016260162601626018	98	0.27071823204419887	0	0.0	178	0.23482849604221637	G	9.674	1.147491	0.21288	0.046754	0.255581	ENSG00000061936	ENST00000537164	.	.	.	5.73	-9.28	0.00656	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999998	.	.	.	.	.	.	T	0.30650	-0.9971	3	.	.	.	-17.2187	1.6034	0.02679	0.2261:0.1231:0.2084:0.4424	rs1051233;rs3191598;rs17678095;rs1051233	.	.	.	S	230	.	.	W	+	2	0	SFSWAP	130816665	0.879000	0.30193	0.539000	0.28077	0.987000	0.75469	-0.165000	0.09968	-1.785000	0.01271	0.591000	0.81541	TGG	G|0.840;C|0.160	0.160	strong		0.443	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
PIGX	54965	hgsc.bcm.edu	37	3	196460680	196460680	+	Silent	SNP	C	C	T	rs34830136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196460680C>T	ENST00000314118.4	+	6	843	c.561C>T	c.(559-561)acC>acT	p.T187T	PIGX_ENST00000541663.1_Silent_p.T138T	NM_017861.3	NP_060331.3	Q8TBF5	PIGX_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class X	228					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(5)|lung(4)|stomach(1)	11	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;1.08e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00322)		CTGTACATACCTCTCTAGTAT	0.388													C|||	652	0.130192	0.1241	0.1599	5008	,	,		19508	0.001		0.2286	False		,,,				2504	0.1493				p.T246T		Atlas-SNP	.											.	PIGX	16	.	0			c.C738T						PASS	.	C	,	712,3694	297.6+/-284.8	57,598,1548	219.0	185.0	196.0		738,684	5.0	1.0	3	dbSNP_126	196	1927,6673	340.9+/-323.8	179,1569,2552	no	coding-synonymous,coding-synonymous	PIGX	NM_001166304.1,NM_017861.3	,	236,2167,4100	TT,TC,CC		22.407,16.1598,20.2906	,	246/277,228/259	196460680	2639,10367	2203	4300	6503	SO:0001819	synonymous_variant	54965	exon7			ACATACCTCTCTA	AK000529	CCDS3320.1, CCDS3320.2, CCDS54701.1	3q29	2013-02-26	2006-06-28		ENSG00000163964	ENSG00000163964		"""Phosphatidylinositol glycan anchor biosynthesis"""	26046	protein-coding gene	gene with protein product		610276	"""phosphatidylinositol glycan, class X"""			15635094	Standard	NM_017861		Approved	FLJ20522	uc010iaj.3	Q8TBF5	OTTHUMG00000155535	ENST00000314118.4:c.561C>T	3.37:g.196460680C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	139	49	0.352518	NM_001166304	Q9NWZ2	Silent	SNP	ENST00000314118.4	37																																																																																				C|0.811;T|0.189	0.189	strong		0.388	PIGX-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017861	
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20740129	20740129	+	Missense_Mutation	SNP	G	G	A	rs199932545		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:20740129G>A	ENST00000427390.2	-	8	1711	c.1621C>T	c.(1621-1623)Cgg>Tgg	p.R541W		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	541	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						tcctgctcccgtatcttctcc	0.562																																					p.R541W		Atlas-SNP	.											.	GOLGA6L6	37	.	0			c.C1621T						PASS	.						31.0	46.0	41.0					15																	20740129		669	1543	2212	SO:0001583	missense	727832	exon8			GCTCCCGTATCTT	AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1621C>T	15.37:g.20740129G>A	ENSP00000398615:p.Arg541Trp	Somatic	816	0	0		WXS	Illumina HiSeq	Phase_I	422	209	0.495261	NM_001145004	D3YTC0	Missense_Mutation	SNP	ENST00000427390.2	37	CCDS45184.1	.	.	.	.	.	.	.	.	.	.	g	3.863	-0.029474	0.07589	.	.	ENSG00000215405	ENST00000427390	T	0.10763	2.84	.	.	.	.	.	.	.	.	T	0.15219	0.0367	L	0.39898	1.24	0.09310	N	0.999999	D	0.76494	0.999	P	0.56216	0.794	T	0.15665	-1.0429	7	0.66056	D	0.02	.	.	.	.	.	541	A8MZA4	GG6L6_HUMAN	W	541	ENSP00000398615:R541W	ENSP00000398615:R541W	R	-	1	2	GOLGA6L6	19000143	0.172000	0.23043	0.017000	0.16124	0.018000	0.09664	0.641000	0.24720	0.159000	0.19401	0.162000	0.16502	CGG	.	.	weak		0.562	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3	NM_001145004	
CTNNA2	1496	hgsc.bcm.edu	37	2	80801346	80801346	+	Silent	SNP	T	T	C	rs2228460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:80801346T>C	ENST00000402739.4	+	12	1805	c.1800T>C	c.(1798-1800)gtT>gtC	p.V600V	CTNNA2_ENST00000466387.1_Silent_p.V600V|CTNNA2_ENST00000540488.1_Silent_p.V600V|AC008067.2_ENST00000430876.1_RNA|CTNNA2_ENST00000541047.1_Silent_p.V600V|CTNNA2_ENST00000496558.1_Silent_p.V600V|CTNNA2_ENST00000361291.4_Silent_p.V634V|AC008067.2_ENST00000609950.1_RNA|CTNNA2_ENST00000343114.3_Silent_p.V279V	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	600					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						GTGCCAACGTTCCTCAACCGT	0.488													T|||	1187	0.237021	0.0477	0.4236	5008	,	,		19540	0.3403		0.3519	False		,,,				2504	0.136				p.V600V		Atlas-SNP	.											.	CTNNA2	462	.	0			c.T1800C						PASS	.	T	,	373,3891		23,327,1782	188.0	181.0	183.0		1800,1800	1.6	1.0	2	dbSNP_123	183	2879,5647		465,1949,1849	no	coding-synonymous,coding-synonymous	CTNNA2	NM_001164883.1,NM_004389.3	,	488,2276,3631	CC,CT,TT		33.7673,8.7477,25.4261	,	600/861,600/906	80801346	3252,9538	2132	4263	6395	SO:0001819	synonymous_variant	1496	exon13			CAACGTTCCTCAA		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1800T>C	2.37:g.80801346T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	185	182	0.983784	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																				T|0.724;C|0.276	0.276	strong		0.488	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
PGS1	9489	hgsc.bcm.edu	37	17	76423151	76423151	+	IGR	SNP	C	C	T	rs3209030	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76423151C>T	ENST00000262764.6	+	0	2201				DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.P4232P|DNAH17_ENST00000585328.1_Silent_p.P4204P	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)			cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TGAAAGTCTCCGGAATCTTCT	0.562													C|||	416	0.0830671	0.1127	0.0605	5008	,	,		18579	0.0317		0.0895	False		,,,				2504	0.1053				p.P4209P	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.G12627A						PASS	.	C		352,4054		15,322,1866	44.0	35.0	38.0		12627	-9.9	0.3	17	dbSNP_105	38	787,7809		45,697,3556	no	coding-synonymous	DNAH17	NM_173628.3		60,1019,5422	TT,TC,CC		9.1554,7.9891,8.7602		4209/4463	76423151	1139,11863	2203	4298	6501	SO:0001628	intergenic_variant	8632	exon78			AGTCTCCGGAATC		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76423151C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	37	CCDS42391.1																																																																																			C|0.914;T|0.086	0.086	strong		0.562	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
SIRPA	140885	hgsc.bcm.edu	37	20	1896060	1896060	+	Missense_Mutation	SNP	T	T	C	rs114499682|rs386811663	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1896060T>C	ENST00000358771.4	+	2	547	c.395T>C	c.(394-396)gTg>gCg	p.V132A	SIRPA_ENST00000356025.3_Missense_Mutation_p.V132A|SIRPA_ENST00000400068.3_Missense_Mutation_p.V132A	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	132	Ig-like V-type.		V -> T (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CCCGATGACGTGGAGTTTAAG	0.527													T|||	2050	0.409345	0.2761	0.4222	5008	,	,		15517	0.625		0.3171	False		,,,				2504	0.453				p.V132A	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,caecum,carcinoma,+1,2	SIRPA	83	2	0			c.T395C						scavenged	.						110.0	94.0	99.0					20																	1896060		2199	4290	6489	SO:0001583	missense	140885	exon3			ATGACGTGGAGTT	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.395T>C	20.37:g.1896060T>C	ENSP00000351621:p.Val132Ala	Somatic	360	1	0.00277778		WXS	Illumina HiSeq	Phase_I	209	32	0.15311	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.858225	0.32791	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.63913	-0.07;-0.07;-0.07	5.11	-4.1	0.03940	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	2.497550	0.01234	N	0.008420	T	0.55257	0.1909	L	0.47190	1.495	0.09310	N	1	B;B;B	0.18741	0.028;0.011;0.03	B;B;B	0.33295	0.113;0.125;0.161	T	0.39165	-0.9627	10	0.33141	T	0.24	.	4.5618	0.12163	0.5656:0.1906:0.0:0.2438	.	112;132;132	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	A	132	ENSP00000382941:V132A;ENSP00000348307:V132A;ENSP00000351621:V132A	ENSP00000348307:V132A	V	+	2	0	SIRPA	1844060	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-1.908000	0.01587	-0.575000	0.05982	-0.530000	0.04314	GTG	T|0.684;C|0.317	0.317	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
EPB41L2	2037	hgsc.bcm.edu	37	6	131186718	131186718	+	Silent	SNP	T	T	A	rs149001048		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:131186718T>A	ENST00000337057.3	-	17	2968	c.2787A>T	c.(2785-2787)acA>acT	p.T929T	EPB41L2_ENST00000525193.1_Silent_p.T630T|EPB41L2_ENST00000528282.1_Silent_p.T671T|EPB41L2_ENST00000445890.2_Silent_p.T671T|EPB41L2_ENST00000368128.2_Silent_p.T929T|EPB41L2_ENST00000527411.1_Silent_p.T859T|EPB41L2_ENST00000524581.1_Silent_p.T307T|EPB41L2_ENST00000530481.1_Silent_p.T776T|EPB41L2_ENST00000529208.1_Silent_p.T859T|EPB41L2_ENST00000525271.1_Intron|EPB41L2_ENST00000531410.1_Silent_p.T50T|EPB41L2_ENST00000530757.1_Intron|EPB41L2_ENST00000392427.3_Intron|EPB41L2_ENST00000527659.1_Silent_p.T735T	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	929	C-terminal (CTD).				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)		CGGACTCAGATGTGATGGTTT	0.458													T|||	1	0.000199681	0.0	0.0	5008	,	,		5461	0.0		0.001	False		,,,				2504	0.0				p.T929T		Atlas-SNP	.											.	EPB41L2	96	.	0			c.A2787T						PASS	.						357.0	260.0	293.0					6																	131186718		2203	4300	6503	SO:0001819	synonymous_variant	2037	exon17			CTCAGATGTGATG	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.2787A>T	6.37:g.131186718T>A		Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	154	19	0.123377	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Silent	SNP	ENST00000337057.3	37	CCDS5141.1																																																																																			T|1.000;A|0.000	0.000	strong		0.458	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3		
LILRB1	10859	hgsc.bcm.edu	37	19	55143491	55143491	+	Missense_Mutation	SNP	G	G	T	rs1061681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55143491G>T	ENST00000396331.1	+	6	821	c.464G>T	c.(463-465)aGt>aTt	p.S155I	LILRB1_ENST00000434867.2_Missense_Mutation_p.S155I|LILRB1_ENST00000396321.2_Missense_Mutation_p.S155I|LILRB1_ENST00000396315.1_Missense_Mutation_p.S155I|LILRB1_ENST00000418536.2_Missense_Mutation_p.S155I|LILRB1_ENST00000427581.2_Missense_Mutation_p.S191I|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Missense_Mutation_p.S155I|LILRB1_ENST00000396317.1_Missense_Mutation_p.S155I|LILRB1_ENST00000448689.1_Missense_Mutation_p.S155I|LILRB1_ENST00000396327.3_Missense_Mutation_p.S155I|LILRB1_ENST00000324602.7_Missense_Mutation_p.S155I	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	155	Ig-like C2-type 2.		S -> I (in dbSNP:rs1061681). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:20600445, ECO:0000269|PubMed:9285411}.		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)		GATGGCTTCAGTCTGTGTAAG	0.587										HNSCC(37;0.09)			t|||	2254	0.45008	0.5862	0.4755	5008	,	,		18369	0.5952		0.2783	False		,,,				2504	0.2751				p.S155I		Atlas-SNP	.											LILRB1,colon,carcinoma,0,1	LILRB1	140	1	0			c.G464T						scavenged	.	T	ILE/SER,ILE/SER,ILE/SER,ILE/SER	2425,1981		682,1061,460	118.0	118.0	118.0		464,464,464,464	0.3	0.0	19	dbSNP_86	118	2847,5753		457,1933,1910	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	142,142,142,142	1139,2994,2370	TT,TG,GG		33.1047,44.9614,40.5351	benign,benign,benign,benign	155/653,155/652,155/652,155/651	55143491	5272,7734	2203	4300	6503	SO:0001583	missense	10859	exon5			GCTTCAGTCTGTG	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.464G>T	19.37:g.55143491G>T	ENSP00000379622:p.Ser155Ile	Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	174	93	0.534483	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	872	0.3992673992673993	240	0.4878048780487805	145	0.4005524861878453	305	0.5332167832167832	182	0.24010554089709762	C	0.004	-2.381260	0.00205	0.550386	0.331047	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.03772	3.81;3.81;3.81;3.81;3.81;3.81;3.81;3.81;3.81;3.81;3.81	1.57	0.317	0.15861	Immunoglobulin-like fold (1);	1.784900	0.02843	N	0.128185	T	0.00012	0.0000	N	0.00132	-2.035	0.80722	P	0.0	B;B;B;B;B	0.06786	0.001;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	0.48547	-0.9026	9	0.02654	T	1	.	2.4378	0.04487	0.0:0.1948:0.2954:0.5098	rs1061681;rs3202771;rs3945748;rs17845473;rs17858352;rs59526154	155;155;155;155;155	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	I	155;155;155;155;155;155;155;155;191;155;155	ENSP00000379614:S155I;ENSP00000391514:S155I;ENSP00000409968:S155I;ENSP00000379622:S155I;ENSP00000379618:S155I;ENSP00000315997:S155I;ENSP00000405243:S155I;ENSP00000379623:S155I;ENSP00000395004:S191I;ENSP00000379610:S155I;ENSP00000379608:S155I	ENSP00000315997:S155I	S	+	2	0	LILRB1	59835303	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.921000	0.04008	-0.293000	0.08986	-2.970000	0.00081	AGT	G|0.602;T|0.398	0.398	strong		0.587	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
HEG1	57493	hgsc.bcm.edu	37	3	124746237	124746237	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124746237A>T	ENST00000311127.4	-	3	792	c.725T>A	c.(724-726)cTg>cAg	p.L242Q		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	242					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						TTCTTCTGACAGCCCCATCGC	0.547																																					p.L242Q		Atlas-SNP	.											.	HEG1	109	.	0			c.T725A						PASS	.						66.0	67.0	66.0					3																	124746237		1989	4156	6145	SO:0001583	missense	57493	exon3			TCTGACAGCCCCA	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.725T>A	3.37:g.124746237A>T	ENSP00000311502:p.Leu242Gln	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	213	106	0.497653	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.626598	0.66901	.	.	ENSG00000173706	ENST00000311127	T	0.42513	0.97	4.69	3.54	0.40534	.	.	.	.	.	T	0.53334	0.1790	L	0.60455	1.87	0.26084	N	0.981056	D;D	0.67145	0.996;0.994	D;D	0.69479	0.964;0.922	T	0.37267	-0.9713	9	0.27785	T	0.31	.	6.9296	0.24434	0.8966:0.0:0.1034:0.0	.	242;242	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	Q	242	ENSP00000311502:L242Q	ENSP00000311502:L242Q	L	-	2	0	HEG1	126228927	0.000000	0.05858	0.750000	0.31169	0.261000	0.26267	0.557000	0.23454	0.931000	0.37242	0.528000	0.53228	CTG	.	.	none		0.547	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
BRINP2	57795	hgsc.bcm.edu	37	1	177247854	177247854	+	Missense_Mutation	SNP	C	C	G	rs3176443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:177247854C>G	ENST00000361539.4	+	7	1480	c.1168C>G	c.(1168-1170)Cta>Gta	p.L390V	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	390			L -> V (in dbSNP:rs3176443).		cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											CCATCGGATCCTACGCCGGCT	0.612													G|||	1325	0.264577	0.4017	0.2061	5008	,	,		15428	0.2113		0.2187	False		,,,				2504	0.2229				p.L390V		Atlas-SNP	.											.	FAM5B	191	.	0			c.C1168G						PASS	.	G	VAL/LEU	1680,2726	654.9+/-399.8	289,1102,812	84.0	88.0	87.0		1168	3.2	0.6	1	dbSNP_105	87	1779,6821	734.2+/-406.9	199,1381,2720	yes	missense	FAM5B	NM_021165.2	32	488,2483,3532	GG,GC,CC		20.686,38.1298,26.5954	benign	390/784	177247854	3459,9547	2203	4300	6503	SO:0001583	missense	57795	exon7			CGGATCCTACGCC		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.1168C>G	1.37:g.177247854C>G	ENSP00000354481:p.Leu390Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	576	0.26373626373626374	217	0.4410569105691057	72	0.19889502762430938	123	0.21503496503496503	164	0.21635883905013192	G	0.863	-0.734660	0.03111	0.381298	0.20686	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.11821	2.74	5.39	3.17	0.36434	.	0.246637	0.40064	N	0.001185	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.47573	-0.9107	9	0.02654	T	1	-19.594	8.7092	0.34374	0.1994:0.1281:0.6726:0.0	rs3176443;rs3736682;rs56601222;rs3176443	140;285;390	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	V	140;390	ENSP00000354481:L390V	ENSP00000354481:L390V	L	+	1	2	FAM5B	175514477	0.934000	0.31675	0.602000	0.28890	0.977000	0.68977	1.390000	0.34464	0.670000	0.31165	-0.120000	0.15030	CTA	C|0.730;G|0.270	0.270	strong		0.612	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
PCNX	22990	hgsc.bcm.edu	37	14	71444788	71444788	+	Silent	SNP	G	G	A	rs3814871	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:71444788G>A	ENST00000304743.2	+	6	2180	c.1734G>A	c.(1732-1734)agG>agA	p.R578R	PCNX_ENST00000439984.3_Silent_p.R578R|PCNX_ENST00000238570.5_Silent_p.R578R	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	578						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GCCGGCATAGGGACTATGTTT	0.468													G|||	2035	0.40635	0.4009	0.4164	5008	,	,		21529	0.6131		0.3539	False		,,,				2504	0.2474				p.R578R		Atlas-SNP	.											PCNX,NS,carcinoma,0,1	PCNX	198	1	0			c.G1734A						PASS	.	G		1680,2726	508.3+/-366.9	334,1012,857	109.0	107.0	107.0		1734	5.0	1.0	14	dbSNP_107	107	3002,5598	463.4+/-366.0	544,1914,1842	no	coding-synonymous	PCNX	NM_014982.2		878,2926,2699	AA,AG,GG		34.907,38.1298,35.9988		578/2342	71444788	4682,8324	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon6			GCATAGGGACTAT	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.1734G>A	14.37:g.71444788G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1																																																																																			G|0.604;A|0.396	0.396	strong		0.468	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
DNHD1	144132	hgsc.bcm.edu	37	11	6550004	6550004	+	Missense_Mutation	SNP	A	A	G	rs2344828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6550004A>G	ENST00000527990.2	+	9	2090	c.2090A>G	c.(2089-2091)cAg>cGg	p.Q697R	DNHD1_ENST00000254579.6_Missense_Mutation_p.Q697R			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	697					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		AATATACAACAGGTGCTGCTG	0.537													A|||	3656	0.730032	0.6944	0.6585	5008	,	,		20172	0.874		0.6302	False		,,,				2504	0.7832				p.Q697R		Atlas-SNP	.											DNHD1,colon,carcinoma,0,1	DNHD1	198	1	0			c.A2090G						PASS	.	A	ARG/GLN	955,429		327,301,64	54.0	45.0	48.0		2090	4.5	0.0	11	dbSNP_100	48	2141,1041		726,689,176	yes	missense	DNHD1	NM_144666.2	43	1053,990,240	GG,GA,AA		32.7153,30.9971,32.1945	possibly-damaging	697/4754	6550004	3096,1470	692	1591	2283	SO:0001583	missense	144132	exon11			TACAACAGGTGCT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.2090A>G	11.37:g.6550004A>G	ENSP00000436180:p.Gln697Arg	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1562	0.7152014652014652	353	0.717479674796748	236	0.6519337016574586	487	0.8513986013986014	486	0.6411609498680739	A	5.599	0.295334	0.10622	0.690029	0.672847	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.27104	1.69;1.69	5.6	4.48	0.54585	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.20052	0.041	B	0.21917	0.037	T	0.12708	-1.0537	8	0.24483	T	0.36	.	8.4785	0.33027	0.9121:0.0:0.0879:0.0	rs2344828;rs52806435;rs58180413;rs2344828	697	Q96M86	DNHD1_HUMAN	R	697	ENSP00000254579:Q697R;ENSP00000436180:Q697R	ENSP00000254579:Q697R	Q	+	2	0	DNHD1	6506580	0.741000	0.28217	0.007000	0.13788	0.001000	0.01503	1.937000	0.40193	0.951000	0.37770	-0.280000	0.10049	CAG	A|0.275;G|0.725	0.725	strong		0.537	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
CMYA5	202333	hgsc.bcm.edu	37	5	79031558	79031558	+	Missense_Mutation	SNP	G	G	A	rs62621912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:79031558G>A	ENST00000446378.2	+	2	7001	c.6970G>A	c.(6970-6972)Ggt>Agt	p.G2324S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2324					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TTCACTAATCGGTGAGAAATT	0.378													G|||	835	0.166733	0.0696	0.2003	5008	,	,		18940	0.2639		0.1451	False		,,,				2504	0.1963				p.G2324S		Atlas-SNP	.											.	CMYA5	643	.	0			c.G6970A						PASS	.	G	SER/GLY	292,3394		11,270,1562	71.0	68.0	69.0		6970	-1.7	0.0	5	dbSNP_129	69	1160,7012		95,970,3021	yes	missense	CMYA5	NM_153610.3	56	106,1240,4583	AA,AG,GG		14.1948,7.9219,12.2449	probably-damaging	2324/4070	79031558	1452,10406	1843	4086	5929	SO:0001583	missense	202333	exon2			CTAATCGGTGAGA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6970G>A	5.37:g.79031558G>A	ENSP00000394770:p.Gly2324Ser	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	358	0.16391941391941392	36	0.07317073170731707	70	0.19337016574585636	141	0.2465034965034965	111	0.14643799472295516	G	11.17	1.559197	0.27827	0.079219	0.141948	ENSG00000164309	ENST00000446378	T	0.21734	1.99	5.65	-1.67	0.08238	.	0.967888	0.08507	N	0.935481	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	B	0.25312	0.123	B	0.16289	0.015	T	0.40534	-0.9558	9	0.21540	T	0.41	.	0.4092	0.00438	0.311:0.1292:0.2954:0.2644	rs62621912	2324	Q8N3K9	CMYA5_HUMAN	S	2324	ENSP00000394770:G2324S	ENSP00000394770:G2324S	G	+	1	0	CMYA5	79067314	0.000000	0.05858	0.000000	0.03702	0.458000	0.32498	-0.308000	0.08156	-0.312000	0.08741	0.655000	0.94253	GGT	A|0.166;C|0.000;G|0.834	0.166	strong		0.378	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
ISOC1	51015	hgsc.bcm.edu	37	5	128430757	128430757	+	Silent	SNP	T	T	C	rs1127827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:128430757T>C	ENST00000173527.5	+	1	314	c.298T>C	c.(298-300)Ttg>Ctg	p.L100L	MIR4633_ENST00000584064.1_RNA	NM_016048.2	NP_057132.2	Q96CN7	ISOC1_HUMAN	isochorismatase domain containing 1	100						extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	catalytic activity (GO:0003824)			kidney(2)|lung(7)	9		all_cancers(142;0.0813)|Prostate(80;0.0865)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.138)|OV - Ovarian serous cystadenocarcinoma(64;0.164)		CCTCGTGCCGTTGCAGATCCA	0.692													C|||	4039	0.80651	0.9682	0.7464	5008	,	,		11507	0.8661		0.6004	False		,,,				2504	0.7812				p.L100L		Atlas-SNP	.											.	ISOC1	26	.	0			c.T298C						PASS	.	C		3754,388		1706,342,23	17.0	21.0	20.0		298	3.4	1.0	5	dbSNP_86	20	5111,3281		1551,2009,636	no	coding-synonymous	ISOC1	NM_016048.2		3257,2351,659	CC,CT,TT		39.0968,9.3675,29.2724		100/299	128430757	8865,3669	2071	4196	6267	SO:0001819	synonymous_variant	51015	exon1			GTGCCGTTGCAGA	AF151869	CCDS43357.1	5q22.1-q33.3	2010-03-19			ENSG00000066583	ENSG00000066583			24254	protein-coding gene	gene with protein product						10810093, 18566572	Standard	NM_016048		Approved	CGI-111	uc003kva.3	Q96CN7	OTTHUMG00000163144	ENST00000173527.5:c.298T>C	5.37:g.128430757T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	NM_016048	Q7Z770	Silent	SNP	ENST00000173527.5	37	CCDS43357.1																																																																																			T|0.232;C|0.768	0.768	strong		0.692	ISOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371826.1	NM_016048	
MRPL40	64976	hgsc.bcm.edu	37	22	19423257	19423257	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19423257G>A	ENST00000333130.3	+	4	1046	c.393G>A	c.(391-393)atG>atA	p.M131I	MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000541063.1_Intron|HIRA_ENST00000546308.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	131					anatomical structure morphogenesis (GO:0009653)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					AGCGTAAGATGGAGAGGGACA	0.567																																					p.M131I		Atlas-SNP	.											.	MRPL40	13	.	0			c.G393A						PASS	.						145.0	147.0	146.0					22																	19423257		2203	4300	6503	SO:0001583	missense	64976	exon4			TAAGATGGAGAGG	AB051624	CCDS13760.1	22q11.2	2012-09-13	2002-11-13		ENSG00000185608	ENSG00000185608		"""Mitochondrial ribosomal proteins / large subunits"""	14491	protein-coding gene	gene with protein product		605089	"""nuclear localization signal deleted in velocardiofacial syndrome"""	NLVCF		9790763, 11543634	Standard	NM_003776		Approved	MRP-L22	uc002zpg.3	Q9NQ50	OTTHUMG00000150136	ENST00000333130.3:c.393G>A	22.37:g.19423257G>A	ENSP00000333401:p.Met131Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	120	5	0.0416667	NM_003776	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	37	CCDS13760.1	.	.	.	.	.	.	.	.	.	.	G	8.714	0.912730	0.17907	.	.	ENSG00000185608	ENST00000333130	T	0.43294	0.95	5.22	-0.486	0.12064	.	0.620008	0.17767	N	0.162711	T	0.28433	0.0703	L	0.56769	1.78	0.35764	D	0.820406	B	0.14012	0.009	B	0.17098	0.017	T	0.11941	-1.0567	10	0.17832	T	0.49	-1.0103	1.306	0.02088	0.445:0.1498:0.2525:0.1527	.	131	Q9NQ50	RM40_HUMAN	I	131	ENSP00000333401:M131I	ENSP00000333401:M131I	M	+	3	0	MRPL40	17803257	0.988000	0.35896	0.439000	0.26833	0.259000	0.26198	0.659000	0.24994	0.366000	0.24427	-0.251000	0.11542	ATG	.	.	none		0.567	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776	
PIGB	9488	hgsc.bcm.edu	37	15	55647492	55647492	+	Silent	SNP	C	C	T	rs8043415	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:55647492C>T	ENST00000164305.5	+	12	1818	c.1527C>T	c.(1525-1527)agC>agT	p.S509S	CCPG1_ENST00000310958.6_3'UTR|CCPG1_ENST00000442196.3_3'UTR|PIGB_ENST00000539642.1_Silent_p.S314S|DYX1C1-CCPG1_ENST00000565113.1_RNA	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	509					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		AGGAAATAAGCGCTTTCCTAA	0.348													C|||	488	0.0974441	0.2254	0.0519	5008	,	,		17133	0.001		0.0696	False		,,,				2504	0.0849				p.S509S		Atlas-SNP	.											PIGB,NS,carcinoma,+1,1	PIGB	36	1	0			c.C1527T						PASS	.	C	,,,,	728,2880		68,592,1144	46.0	45.0	45.0		,,,1527,	1.0	0.2	15	dbSNP_116	45	603,7529		17,569,3480	no	utr-3,utr-3,utr-3,coding-synonymous,utr-3	CCPG1,PIGB	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_004855.4,NM_020739.3	,,,,	85,1161,4624	TT,TC,CC		7.4152,20.1774,11.3373	,,,,	,,,509/555,	55647492	1331,10409	1804	4066	5870	SO:0001819	synonymous_variant	9488	exon12			AATAAGCGCTTTC	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8959	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 3"", ""dol-P-Man dependent GPI mannosyltransferase"""	604122	"""phosphatidylinositol glycan, class B"""			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.1527C>T	15.37:g.55647492C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	125	64	0.512	NM_004855	Q53FF9|Q8WVN7	Silent	SNP	ENST00000164305.5	37																																																																																				C|0.909;T|0.091	0.091	strong		0.348	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
WDFY4	57705	hgsc.bcm.edu	37	10	50098740	50098740	+	Silent	SNP	T	T	A	rs41283285	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50098740T>A	ENST00000325239.5	+	43	7311	c.7284T>A	c.(7282-7284)ggT>ggA	p.G2428G	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						CTCCCACGGGTGATGTCTACT	0.547													T|||	97	0.019369	0.0	0.0202	5008	,	,		22918	0.0		0.0437	False		,,,				2504	0.0399				p.G2428G		Atlas-SNP	.											.	WDFY4	205	.	0			c.T7284A						PASS	.	T		12,1372		0,12,680	116.0	90.0	98.0		7284	-3.4	0.9	10	dbSNP_127	98	128,3054		2,124,1465	no	coding-synonymous	WDFY4	NM_020945.1		2,136,2145	AA,AT,TT		4.0226,0.8671,3.0661		2428/3185	50098740	140,4426	692	1591	2283	SO:0001819	synonymous_variant	57705	exon44			CACGGGTGATGTC	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.7284T>A	10.37:g.50098740T>A		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	183	110	0.601093	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	42|42	0.019230769230769232|0.019230769230769232	0|0	0.0|0.0	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	34|34	0.044854881266490766|0.044854881266490766	T|T	10.56|10.56	1.385533|1.385533	0.25031|0.25031	0.008671|0.008671	0.040226|0.040226	ENSG00000128815|ENSG00000128815	ENST00000265453|ENST00000312002	.|.	.|.	.|.	4.83|4.83	-3.42|-3.42	0.04825|0.04825	.|.	.|.	.|.	.|.	.|.	T|.	0.17023|.	0.0409|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.33879|.	-0.9851|.	4|.	.|.	.|.	.|.	.|.	5.0627|5.0627	0.14566|0.14566	0.1564:0.2558:0.0:0.5878|0.1564:0.2558:0.0:0.5878	rs41283285;rs61733231|rs41283285;rs61733231	.|.	.|.	.|.	E|R	515|1519	.|.	.|.	V|X	+|+	2|1	0|0	WDFY4|WDFY4	49768746|49768746	0.000000|0.000000	0.05858|0.05858	0.940000|0.940000	0.37924|0.37924	0.932000|0.932000	0.56968|0.56968	-4.707000|-4.707000	0.00196|0.00196	-0.164000|-0.164000	0.10927|0.10927	-0.337000|-0.337000	0.08149|0.08149	GTG|TGA	T|0.974;A|0.026	0.026	strong		0.547	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
LIPK	643414	hgsc.bcm.edu	37	10	90503075	90503075	+	Silent	SNP	T	T	C	rs390152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90503075T>C	ENST00000404190.1	+	8	957	c.957T>C	c.(955-957)caT>caC	p.H319H		NM_001080518.1	NP_001073987.1	Q5VXJ0	LIPK_HUMAN	lipase, family member K	319					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)	12		Colorectal(252;0.0381)		Colorectal(12;7.03e-05)|COAD - Colon adenocarcinoma(12;8.33e-05)		TGCACTTCCATCAGGTACAAA	0.363													C|||	1291	0.257788	0.1959	0.2911	5008	,	,		17658	0.3502		0.2207	False		,,,				2504	0.2607				p.H319H		Atlas-SNP	.											LIPK_ENST00000404190,colon,carcinoma,0,2	LIPK	50	2	0			c.T957C						PASS	.	C		767,2963		81,605,1179	76.0	71.0	72.0		957	-3.8	0.0	10	dbSNP_80	72	1837,6373		244,1349,2512	no	coding-synonymous	LIPK	NM_001080518.1		325,1954,3691	CC,CT,TT		22.3752,20.563,21.809		319/400	90503075	2604,9336	1865	4105	5970	SO:0001819	synonymous_variant	643414	exon8			CTTCCATCAGGTA		CCDS44455.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000204021	ENSG00000204021			23444	protein-coding gene	gene with protein product		613922	"""lipase-like, ab-hydrolase domain containing 2"""	LIPL2			Standard	NM_001080518		Approved	bA186O14.2	uc010qmv.2	Q5VXJ0	OTTHUMG00000018693	ENST00000404190.1:c.957T>C	10.37:g.90503075T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_001080518	A7KIH8	Silent	SNP	ENST00000404190.1	37	CCDS44455.1																																																																																			T|0.754;C|0.246	0.246	strong		0.363	LIPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049253.2	XM_061222	
VEGFB	7423	hgsc.bcm.edu	37	11	64004692	64004692	+	Silent	SNP	C	C	T	rs11558381|rs12366035	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64004692C>T	ENST00000309422.2	+	5	704	c.408C>T	c.(406-408)gaC>gaT	p.D136D	RP11-783K16.14_ENST00000539963.1_RNA|RP11-783K16.14_ENST00000534988.1_RNA|VEGFB_ENST00000426086.2_Silent_p.D136D	NM_001243733.1|NM_003377.4	NP_001230662.1|NP_003368.1	P49765	VEGFB_HUMAN	vascular endothelial growth factor B	136					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|coronary vasculature development (GO:0060976)|induction of positive chemotaxis (GO:0050930)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular wound healing (GO:0035470)|protein O-linked glycosylation (GO:0006493)|response to drug (GO:0042493)|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)|heparin binding (GO:0008201)|vascular endothelial growth factor receptor 1 binding (GO:0043183)	p.D136D(1)		endometrium(2)|large_intestine(2)|prostate(1)|stomach(1)	6					Aflibercept(DB08885)	TGAAGCCAGACAGGTGAGTCT	0.488													C|||	862	0.172125	0.0151	0.134	5008	,	,		14845	0.1478		0.2952	False		,,,				2504	0.3098				p.D136D		Atlas-SNP	.											VEGFB,NS,carcinoma,0,1	VEGFB	18	1	1	Substitution - coding silent(1)	stomach(1)	c.C408T						PASS	.	C		242,4160	139.6+/-175.2	7,228,1966	134.0	123.0	127.0		408	4.5	1.0	11	dbSNP_120	127	2673,5921	430.0+/-356.4	414,1845,2038	no	coding-synonymous	VEGFB	NM_003377.4		421,2073,4004	TT,TC,CC		31.1031,5.4975,22.43		136/208	64004692	2915,10081	2201	4297	6498	SO:0001819	synonymous_variant	7423	exon5			GCCAGACAGGTGA	BC008818	CCDS8062.1, CCDS58144.1	11q13	2005-09-29				ENSG00000173511			12681	protein-coding gene	gene with protein product		601398		VRF		8637916, 8919691	Standard	NM_001243733		Approved	VEGFL	uc001nyw.3	P49765		ENST00000309422.2:c.408C>T	11.37:g.64004692C>T		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	112	41	0.366071	NM_003377	Q16528	Silent	SNP	ENST00000309422.2	37	CCDS8062.1																																																																																			C|0.792;T|0.208	0.208	strong		0.488	VEGFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396393.2	NM_003377	
OTOP3	347741	hgsc.bcm.edu	37	17	72943184	72943184	+	Missense_Mutation	SNP	C	C	T	rs142183564	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72943184C>T	ENST00000328801.4	+	6	1234	c.1234C>T	c.(1234-1236)Cgc>Tgc	p.R412C		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	412						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)					GAACCCTACCCGCAGCCTGGA	0.622																																					p.R412C		Atlas-SNP	.											.	OTOP3	64	.	0			c.C1234T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	94.0	92.0	93.0		1234	4.5	1.0	17	dbSNP_134	93	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OTOP3	NM_178233.1	180	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	probably-damaging	412/597	72943184	5,13001	2203	4300	6503	SO:0001583	missense	347741	exon6			CCTACCCGCAGCC	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.1234C>T	17.37:g.72943184C>T	ENSP00000328090:p.Arg412Cys	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_178233		Missense_Mutation	SNP	ENST00000328801.4	37	CCDS11709.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508979	0.64410	2.27E-4	4.65E-4	ENSG00000182938	ENST00000328801	T	0.22743	1.94	4.54	4.54	0.55810	.	0.000000	0.64402	D	0.000001	T	0.52208	0.1720	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.62793	-0.6779	10	0.87932	D	0	-16.6297	17.2793	0.87124	0.0:1.0:0.0:0.0	.	412	Q7RTS5	OTOP3_HUMAN	C	412	ENSP00000328090:R412C	ENSP00000328090:R412C	R	+	1	0	OTOP3	70454779	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	4.414000	0.59802	2.073000	0.62155	0.462000	0.41574	CGC	C|0.999;T|0.001	0.001	strong		0.622	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
ESPL1	9700	hgsc.bcm.edu	37	12	53670545	53670545	+	Missense_Mutation	SNP	C	C	A	rs1318648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:53670545C>A	ENST00000257934.4	+	8	1933	c.1842C>A	c.(1840-1842)agC>agA	p.S614R	ESPL1_ENST00000552462.1_Missense_Mutation_p.S614R	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	614			S -> R (in dbSNP:rs1318648).		apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TGGAGCTGAGCCCCGAGGAGA	0.637													C|||	3171	0.633187	0.4024	0.5994	5008	,	,		19167	0.8194		0.6372	False		,,,				2504	0.773				p.S614R	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C1842A						PASS	.	C	ARG/SER	1887,2519		394,1099,710	50.0	54.0	53.0		1842	1.2	1.0	12	dbSNP_88	53	5491,3105		1770,1951,577	yes	missense	ESPL1	NM_012291.4	110	2164,3050,1287	AA,AC,CC		36.1215,42.828,43.2549	probably-damaging	614/2121	53670545	7378,5624	2203	4298	6501	SO:0001583	missense	9700	exon8			GCTGAGCCCCGAG	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.1842C>A	12.37:g.53670545C>A	ENSP00000257934:p.Ser614Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	1355	0.6204212454212454	203	0.41260162601626016	221	0.6104972375690608	462	0.8076923076923077	469	0.6187335092348285	C	16.80	3.223939	0.58668	0.42828	0.638785	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.14144	2.53;2.53	5.11	1.25	0.21368	.	0.144838	0.64402	D	0.000007	T	0.00012	0.0000	M	0.68317	2.08	0.38397	P	0.054444999999999966	D	0.71674	0.998	P	0.61940	0.896	T	0.10567	-1.0624	9	0.46703	T	0.11	.	8.7053	0.34351	0.0:0.6008:0.0:0.3992	rs1318648;rs3817539;rs52811463;rs59896279;rs1318648	614	Q14674	ESPL1_HUMAN	R	614;289;614	ENSP00000257934:S614R;ENSP00000449831:S614R	ENSP00000257934:S614R	S	+	3	2	ESPL1	51956812	0.553000	0.26513	0.996000	0.52242	0.994000	0.84299	-0.161000	0.10026	0.341000	0.23771	0.650000	0.86243	AGC	C|0.400;N|0.000	.	strong		0.637	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
ABLIM3	22885	hgsc.bcm.edu	37	5	148596547	148596547	+	Missense_Mutation	SNP	C	C	T	rs116226381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:148596547C>T	ENST00000506113.1	+	7	1177	c.695C>T	c.(694-696)aCc>aTc	p.T232I	RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000508983.1_Missense_Mutation_p.T232I|RP11-331K21.1_ENST00000522685.1_RNA|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000326685.7_Missense_Mutation_p.T232I|ABLIM3_ENST00000504238.1_Missense_Mutation_p.T232I|ABLIM3_ENST00000309868.7_Missense_Mutation_p.T232I|ABLIM3_ENST00000356541.3_Missense_Mutation_p.T232I			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	232	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACCACCCAACCTGTGCCAGG	0.522													C|||	10	0.00199681	0.0008	0.0	5008	,	,		21664	0.0		0.005	False		,,,				2504	0.0041				p.T232I		Atlas-SNP	.											.	ABLIM3	91	.	0			c.C695T						PASS	.	C	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	94.0	81.0	85.0		695	2.6	1.0	5	dbSNP_132	85	46,8554	30.1+/-81.4	0,46,4254	yes	missense	ABLIM3	NM_014945.2	89	0,48,6455	TT,TC,CC		0.5349,0.0454,0.3691	benign	232/684	148596547	48,12958	2203	4300	6503	SO:0001583	missense	22885	exon8			ACCCAACCTGTGC	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.695C>T	5.37:g.148596547C>T	ENSP00000425394:p.Thr232Ile	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	15.76	2.928929	0.52759	4.54E-4	0.005349	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983	D;D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26;-2.26	5.49	2.56	0.30785	Zinc finger, LIM-type (5);	0.416904	0.28192	N	0.016242	T	0.81851	0.4910	M	0.77820	2.39	0.28363	N	0.920359	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.13407	0.001;0.001;0.009	T	0.79105	-0.1940	10	0.72032	D	0.01	.	10.4399	0.44460	0.0:0.6783:0.2521:0.0696	.	232;232;232	O94929-3;O94929-2;O94929	.;.;ABLM3_HUMAN	I	232	ENSP00000315841:T232I;ENSP00000348938:T232I;ENSP00000310309:T232I;ENSP00000425394:T232I;ENSP00000421183:T232I;ENSP00000420855:T232I	ENSP00000310309:T232I	T	+	2	0	ABLIM3	148576740	0.957000	0.32711	0.991000	0.47740	0.991000	0.79684	3.543000	0.53633	0.790000	0.33803	0.655000	0.94253	ACC	C|0.997;T|0.003	0.003	strong		0.522	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
NACAD	23148	hgsc.bcm.edu	37	7	45125466	45125466	+	Missense_Mutation	SNP	G	G	C	rs11760885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45125466G>C	ENST00000490531.2	-	2	332	c.313C>G	c.(313-315)Ctg>Gtg	p.L105V		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	105					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						TCCGTGGACAGAGCCTGGGAA	0.716													G|||	137	0.0273562	0.0008	0.0317	5008	,	,		13992	0.0139		0.0487	False		,,,				2504	0.0521				p.L105V		Atlas-SNP	.											.	NACAD	44	.	0			c.C313G						PASS	.	G	VAL/LEU	12,1366		0,12,677	11.0	18.0	16.0		313	-1.2	0.0	7	dbSNP_120	16	121,3049		3,115,1467	yes	missense	NACAD	NM_001146334.1	32	3,127,2144	CC,CG,GG		3.817,0.8708,2.9244	benign	105/1563	45125466	133,4415	689	1585	2274	SO:0001583	missense	23148	exon2			TGGACAGAGCCTG	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.313C>G	7.37:g.45125466G>C	ENSP00000420477:p.Leu105Val	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	67	0.030677655677655676	2	0.0040650406504065045	17	0.04696132596685083	9	0.015734265734265736	39	0.051451187335092345	G	0.013	-1.634074	0.00806	0.008708	0.03817	ENSG00000136274	ENST00000490531	T	0.12361	2.69	2.02	-1.22	0.09494	.	3.164540	0.01272	N	0.009468	T	0.00998	0.0033	N	0.12182	0.205	0.09310	N	1	B	0.19331	0.035	B	0.15870	0.014	T	0.23726	-1.0180	10	0.19590	T	0.45	.	2.9053	0.05719	0.3478:0.2615:0.3907:0.0	rs11760885	105	O15069	NACAD_HUMAN	V	105	ENSP00000420477:L105V	ENSP00000420477:L105V	L	-	1	2	NACAD	45091991	0.000000	0.05858	0.005000	0.12908	0.006000	0.05464	0.009000	0.13219	-0.346000	0.08312	-0.258000	0.10820	CTG	G|0.970;C|0.030	0.030	strong		0.716	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
USP6	9098	hgsc.bcm.edu	37	17	5039138	5039138	+	Silent	SNP	C	C	T	rs3213878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5039138C>T	ENST00000574788.1	+	17	2809	c.579C>T	c.(577-579)acC>acT	p.T193T	USP6_ENST00000332776.4_Silent_p.T193T|USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Silent_p.T193T			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	193	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GCCACATCACCGCCTTGTTCC	0.607			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	490	0.0978435	0.1853	0.0375	5008	,	,		20475	0.0774		0.1143	False		,,,				2504	0.0266				p.T193T		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C579T						PASS	.	C		682,3724	287.2+/-279.2	60,562,1581	126.0	110.0	115.0		579	-1.7	0.2	17	dbSNP_106	115	949,7651	208.0+/-249.6	52,845,3403	no	coding-synonymous	USP6	NM_004505.2		112,1407,4984	TT,TC,CC		11.0349,15.4789,12.5404		193/1407	5039138	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	9098	exon9			CATCACCGCCTTG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.579C>T	17.37:g.5039138C>T		Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	14	7	0.5	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			C|0.883;T|0.117	0.117	strong		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
ART3	419	hgsc.bcm.edu	37	4	77003484	77003484	+	Missense_Mutation	SNP	G	G	A	rs142545952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77003484G>A	ENST00000355810.4	+	3	696	c.577G>A	c.(577-579)Gct>Act	p.A193T	ART3_ENST00000349321.3_Missense_Mutation_p.A193T|ART3_ENST00000341029.5_Missense_Mutation_p.A193T|ART3_ENST00000513494.1_3'UTR	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	193					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)	p.A193T(1)		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)			CAAACCTCAGGCTGCTAATGA	0.403																																					p.A193T		Atlas-SNP	.											ART3,NS,carcinoma,0,1	ART3	34	1	1	Substitution - Missense(1)	lung(1)	c.G577A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	46.0	43.0	44.0		577,577,577	1.0	0.0	4	dbSNP_134	44	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	ART3	NM_001130016.1,NM_001130017.1,NM_001179.4	58,58,58	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign,benign,benign	193/390,193/368,193/379	77003484	4,13002	2203	4300	6503	SO:0001583	missense	419	exon3			CCTCAGGCTGCTA	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.577G>A	4.37:g.77003484G>A	ENSP00000348064:p.Ala193Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_001130017	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	37	CCDS47079.1	.	.	.	.	.	.	.	.	.	.	G	3.557	-0.090400	0.07053	0.0	4.65E-4	ENSG00000156219	ENST00000341029;ENST00000513122;ENST00000355810;ENST00000349321	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	6.04	1.03	0.20045	.	0.443020	0.25575	N	0.029735	T	0.10121	0.0248	L	0.46157	1.445	0.09310	N	1	B;B;P;B;B;B	0.34977	0.007;0.003;0.478;0.015;0.023;0.254	B;B;B;B;B;B	0.31390	0.019;0.007;0.129;0.038;0.016;0.098	T	0.21518	-1.0243	9	.	.	.	-6.6012	7.7094	0.28669	0.2965:0.1213:0.5823:0.0	.	163;193;193;193;193;193	D6RBN3;E7ESB3;B4DHX3;Q13508;Q13508-3;Q13508-2	.;.;.;NAR3_HUMAN;.;.	T	193	ENSP00000343843:A193T;ENSP00000422287:A193T;ENSP00000348064:A193T;ENSP00000304313:A193T	.	A	+	1	0	ART3	77222508	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	0.959000	0.29240	0.154000	0.19237	-0.251000	0.11542	GCT	G|1.000;A|0.000	0.000	strong		0.403	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179	
OR2B11	127623	hgsc.bcm.edu	37	1	247614896	247614896	+	Missense_Mutation	SNP	A	A	C	rs11583410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:247614896A>C	ENST00000318749.6	-	1	412	c.389T>G	c.(388-390)aTc>aGc	p.I130S		NM_001004492.1	NP_001004492.1	Q5JQS5	OR2BB_HUMAN	olfactory receptor, family 2, subfamily B, member 11	130			I -> S (in dbSNP:rs11583410).			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)			GGGCTTGCAGATGGCCACGTA	0.617													A|||	1851	0.369609	0.1165	0.3401	5008	,	,		20141	0.4474		0.4742	False		,,,				2504	0.545				p.I130S		Atlas-SNP	.											.	OR2B11	102	.	0			c.T389G						PASS	.	A	SER/ILE	729,3677	302.1+/-287.2	70,589,1544	84.0	69.0	74.0		389	5.0	1.0	1	dbSNP_120	74	3974,4626	551.3+/-385.9	928,2118,1254	yes	missense	OR2B11	NM_001004492.1	142	998,2707,2798	CC,CA,AA		46.2093,16.5456,36.1602	possibly-damaging	130/318	247614896	4703,8303	2203	4300	6503	SO:0001583	missense	127623	exon1			TTGCAGATGGCCA		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.389T>G	1.37:g.247614896A>C	ENSP00000325682:p.Ile130Ser	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	69	27	0.391304	NM_001004492	B2RP03	Missense_Mutation	SNP	ENST00000318749.6	37	CCDS31090.1	807	0.3695054945054945	58	0.11788617886178862	119	0.3287292817679558	278	0.486013986013986	352	0.46437994722955145	A	19.21	3.783249	0.70222	0.165456	0.462093	ENSG00000177535	ENST00000318749	T	0.59502	0.26	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000040	T	0.00012	0.0000	H	0.99336	4.52	0.25226	P	0.9898656	D	0.71674	0.998	P	0.62649	0.905	T	0.39981	-0.9587	9	0.87932	D	0	.	12.9237	0.58247	1.0:0.0:0.0:0.0	rs11583410	130	Q5JQS5	OR2BB_HUMAN	S	130	ENSP00000325682:I130S	ENSP00000325682:I130S	I	-	2	0	OR2B11	245681519	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	6.292000	0.72725	2.219000	0.72066	0.450000	0.29827	ATC	A|0.630;C|0.370	0.370	strong		0.617	OR2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097620.1	NM_001004492	
MCM3	4172	hgsc.bcm.edu	37	6	52129484	52129484	+	Missense_Mutation	SNP	C	C	T	rs2230240	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:52129484C>T	ENST00000229854.7	-	17	2405	c.2329G>A	c.(2329-2331)Gaa>Aaa	p.E777K	MCM3_ENST00000596288.1_Missense_Mutation_p.E822K|MCM3_ENST00000419835.2_Missense_Mutation_p.E731K			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	777			E -> K (in dbSNP:rs2230240). {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)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					AAGGGCTCTTCGCTGTCCCGG	0.532													C|||	573	0.114417	0.0151	0.1686	5008	,	,		21520	0.002		0.2883	False		,,,				2504	0.1472				p.E822K		Atlas-SNP	.											.	MCM3	63	.	0			c.G2464A						PASS	.	C	LYS/GLU	205,4201	126.1+/-163.2	5,195,2003	212.0	184.0	193.0		2329	4.5	0.9	6	dbSNP_98	193	2223,6377	376.9+/-338.3	264,1695,2341	yes	missense	MCM3	NM_002388.3	56	269,1890,4344	TT,TC,CC		25.8488,4.6527,18.6683	benign	777/809	52129484	2428,10578	2203	4300	6503	SO:0001583	missense	4172	exon17			GCTCTTCGCTGTC	X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"""minichromosome maintenance deficient (S. cerevisiae) 3"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"""			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.2329G>A	6.37:g.52129484C>T	ENSP00000229854:p.Glu777Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Missense_Mutation	SNP	ENST00000229854.7	37		301|301	0.13782051282051283|0.13782051282051283	11|11	0.022357723577235773|0.022357723577235773	68|68	0.1878453038674033|0.1878453038674033	1|1	0.0017482517482517483|0.0017482517482517483	221|221	0.29155672823219|0.29155672823219	C|C	9.414|9.414	1.081380|1.081380	0.20309|0.20309	0.046527|0.046527	0.258488|0.258488	ENSG00000112118|ENSG00000112118	ENST00000229854;ENST00000419835|ENST00000340349;ENST00000421471	T;T|T	0.60040|0.34667	0.22;0.22|1.35	5.39|5.39	4.53|4.53	0.55603|0.55603	.|.	0.546643|.	0.21374|.	N|.	0.075591|.	T|T	0.28366|0.28366	0.0701|0.0701	L|L	0.46157|0.46157	1.445|1.445	0.51767|0.51767	P|P	6.300000000003525E-5|6.300000000003525E-5	B;B|.	0.23591|.	0.082;0.088|.	B;B|.	0.18871|.	0.005;0.023|.	T|T	0.22417|0.22417	-1.0217|-1.0217	9|6	0.08837|0.87932	T|D	0.75|0	-14.6083|-14.6083	10.3857|10.3857	0.44138|0.44138	0.0:0.7525:0.1704:0.0771|0.0:0.7525:0.1704:0.0771	rs2230240;rs3208353;rs17240266;rs17581678;rs52808543;rs61476086;rs2230240|rs2230240;rs3208353;rs17240266;rs17581678;rs52808543;rs61476086;rs2230240	731;777|.	B4DUQ9;P25205|.	.;MCM3_HUMAN|.	K|Q	777;731|324;322	ENSP00000229854:E777K;ENSP00000388647:E731K|ENSP00000407651:R322Q	ENSP00000229854:E777K|ENSP00000340566:R324Q	E|R	-|-	1|2	0|0	MCM3|MCM3	52237443|52237443	0.894000|0.894000	0.30519|0.30519	0.895000|0.895000	0.35142|0.35142	0.239000|0.239000	0.25481|0.25481	1.996000|1.996000	0.40776|0.40776	1.515000|1.515000	0.48885|0.48885	-0.137000|-0.137000	0.14449|0.14449	GAA|CGA	C|0.841;T|0.159	0.159	strong		0.532	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		
TBC1D16	125058	hgsc.bcm.edu	37	17	77925393	77925393	+	Silent	SNP	G	G	A	rs35286723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:77925393G>A	ENST00000310924.2	-	5	1060	c.945C>T	c.(943-945)gaC>gaT	p.D315D	TBC1D16_ENST00000570373.1_5'Flank|TBC1D16_ENST00000572862.1_5'Flank|TBC1D16_ENST00000340848.7_5'Flank|TBC1D16_ENST00000576768.1_5'Flank	NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	315							Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			TGCAGGCCTCGTCGCTGAAGG	0.572													G|||	756	0.150958	0.0514	0.2968	5008	,	,		15158	0.1885		0.1233	False		,,,				2504	0.1718				p.D315D	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.C945T						PASS	.	G		308,4098	164.7+/-196.3	9,290,1904	52.0	48.0	50.0		945	-3.7	1.0	17	dbSNP_126	50	997,7603	214.3+/-254.0	62,873,3365	no	coding-synonymous	TBC1D16	NM_019020.2		71,1163,5269	AA,AG,GG		11.593,6.9905,10.0338		315/768	77925393	1305,11701	2203	4300	6503	SO:0001819	synonymous_variant	125058	exon5			GGCCTCGTCGCTG	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.945C>T	17.37:g.77925393G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	78	38	0.487179	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	37	CCDS11766.1																																																																																			G|0.883;A|0.117	0.117	strong		0.572	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887546	9887546	+	Missense_Mutation	SNP	G	G	A	rs2240906	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9887546G>A	ENST00000306084.6	+	2	1269	c.1070G>A	c.(1069-1071)gGt>gAt	p.G357D	TXNDC2_ENST00000357775.5_Missense_Mutation_p.G290D|TXNDC2_ENST00000536353.2_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	357	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.		G -> D (in dbSNP:rs2240906). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						CCCAAGAAGGGTGACATCCCC	0.572													g|||	2412	0.481629	0.3548	0.4481	5008	,	,		22318	0.8155		0.4185	False		,,,				2504	0.3978				p.G357D		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,0,2	TXNDC2	168	2	0			c.G1070A						PASS	.	G	ASP/GLY,ASP/GLY	1660,2746		314,1032,857	151.0	142.0	145.0		1070,869	0.9	0.0	18	dbSNP_98	145	3635,4965		796,2043,1461	no	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	94,94	1110,3075,2318	AA,AG,GG		42.2674,37.6759,40.712	benign,benign	357/554,290/487	9887546	5295,7711	2203	4300	6503	SO:0001583	missense	84203	exon2			AGAAGGGTGACAT	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.1070G>A	18.37:g.9887546G>A	ENSP00000304908:p.Gly357Asp	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	1104	0.5054945054945055	165	0.3353658536585366	156	0.430939226519337	458	0.8006993006993007	325	0.4287598944591029	-	3.140	-0.176442	0.06380	0.376759	0.422674	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.32988	1.43;1.43	3.74	0.852	0.18995	.	.	.	.	.	T	0.00012	0.0000	N	0.25485	0.75	0.80722	P	0.0	B	0.17667	0.023	B	0.24155	0.051	T	0.16928	-1.0386	7	.	.	.	-0.4401	6.3628	0.21437	0.1838:0.2762:0.54:0.0	rs2240906;rs60707091;rs2240906	357	Q86VQ3	TXND2_HUMAN	D	155;290;357;342	ENSP00000350419:G290D;ENSP00000304908:G357D	.	G	+	2	0	TXNDC2	9877546	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.783000	0.01770	-0.049000	0.13379	-0.813000	0.03139	GGT	G|0.562;A|0.438	0.438	strong		0.572	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
C5orf52	100190949	hgsc.bcm.edu	37	5	157102159	157102159	+	Missense_Mutation	SNP	G	G	A	rs10051838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:157102159G>A	ENST00000409999.3	+	2	334	c.272G>A	c.(271-273)cGg>cAg	p.R91Q		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	91										endometrium(2)|lung(1)	3						CATTTATCTCGGGTGATTATT	0.448													.|||	913	0.182308	0.3071	0.111	5008	,	,		19662	0.119		0.1252	False		,,,				2504	0.1881				p.R91Q		Atlas-SNP	.											C5orf52,NS,carcinoma,+1,1	C5orf52	17	1	0			c.G272A						PASS	.	G	GLN/ARG	412,972		53,306,333	123.0	111.0	115.0		272	2.2	1.0	5	dbSNP_119	115	431,2751		32,367,1192	yes	missense	C5orf52	NM_001145132.1	43	85,673,1525	AA,AG,GG		13.5449,29.7688,18.4625	probably-damaging	91/160	157102159	843,3723	692	1591	2283	SO:0001583	missense	100190949	exon2			TATCTCGGGTGAT	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.272G>A	5.37:g.157102159G>A	ENSP00000387027:p.Arg91Gln	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	97	95	0.979381	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	37	CCDS47329.1	355	0.16254578754578755	148	0.3008130081300813	39	0.10773480662983426	74	0.12937062937062938	94	0.12401055408970976	G	11.63	1.697086	0.30142	0.297688	0.135449	ENSG00000187658	ENST00000409999	T	0.36878	1.23	2.22	2.22	0.28083	.	.	.	.	.	T	0.00012	0.0000	L	0.32530	0.975	0.39575	P	0.030656000000000017	P	0.46952	0.887	B	0.32211	0.142	T	0.37753	-0.9692	8	0.66056	D	0.02	-17.8701	7.8836	0.29637	0.0:0.0:1.0:0.0	rs10051838;rs52825189;rs61469151;rs10051838	91	A6NGY3	CE052_HUMAN	Q	91	ENSP00000387027:R91Q	ENSP00000387027:R91Q	R	+	2	0	C5orf52	157034737	0.989000	0.36119	0.998000	0.56505	0.581000	0.36288	0.228000	0.17814	1.235000	0.43724	0.313000	0.20887	CGG	G|0.823;A|0.177	0.177	strong		0.448	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
ZUFSP	221302	hgsc.bcm.edu	37	6	116973182	116973182	+	Missense_Mutation	SNP	T	T	C	rs4946188	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:116973182T>C	ENST00000368576.3	-	6	1378	c.1135A>G	c.(1135-1137)Aac>Gac	p.N379D	ZUFSP_ENST00000368573.1_3'UTR|ZUFSP_ENST00000471919.1_5'UTR	NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	379			N -> D (in dbSNP:rs4946188). {ECO:0000269|PubMed:14702039}.				metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		AAGCAATCGTTGTAAGCATCA	0.323													C|||	2030	0.405351	0.5076	0.4928	5008	,	,		19570	0.3056		0.2932	False		,,,				2504	0.4233				p.N379D		Atlas-SNP	.											ZUFSP,NS,carcinoma,0,1	ZUFSP	46	1	0			c.A1135G						PASS	.	C	ASP/ASN	2088,2318	603.5+/-390.1	475,1138,590	117.0	121.0	120.0		1135	1.5	0.4	6	dbSNP_111	120	2404,6196	699.1+/-405.1	321,1762,2217	yes	missense	ZUFSP	NM_145062.2	23	796,2900,2807	CC,CT,TT		27.9535,47.3899,34.5379	benign	379/579	116973182	4492,8514	2203	4300	6503	SO:0001583	missense	221302	exon6			AATCGTTGTAAGC	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"""Zinc fingers, C2H2-type"""	21224	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 113"""	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.1135A>G	6.37:g.116973182T>C	ENSP00000357565:p.Asn379Asp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	41	34	0.829268	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	37	CCDS5110.1	807	0.3695054945054945	242	0.491869918699187	164	0.4530386740331492	172	0.3006993006993007	229	0.3021108179419525	C	3.231	-0.157533	0.06544	0.473899	0.279535	ENSG00000153975	ENST00000368576	T	0.41400	1.0	5.83	1.52	0.23074	.	0.579616	0.20593	N	0.089307	T	0.07098	0.0180	N	0.19112	0.55	0.43304	P	0.004693999999999976	B	0.02656	0.0	B	0.06405	0.002	T	0.32798	-0.9893	9	0.08837	T	0.75	6.0687	5.3231	0.15891	0.0:0.2902:0.1594:0.5504	rs4946188;rs52824326;rs57266096;rs4946188	379	Q96AP4	ZUFSP_HUMAN	D	379	ENSP00000357565:N379D	ENSP00000357565:N379D	N	-	1	0	ZUFSP	117079875	0.957000	0.32711	0.356000	0.25785	0.915000	0.54546	0.628000	0.24522	0.108000	0.17862	-0.757000	0.03467	AAC	T|0.640;C|0.360	0.360	strong		0.323	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062	
CA9	768	hgsc.bcm.edu	37	9	35674053	35674053	+	Missense_Mutation	SNP	G	G	A	rs2071676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35674053G>A	ENST00000378357.4	+	1	201	c.97G>A	c.(97-99)Gtg>Atg	p.V33M	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	33			V -> M (in dbSNP:rs2071676). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8084592}.		bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GCTGCTTCTGGTGCCTGTCCA	0.657													G|||	1619	0.323283	0.0764	0.4078	5008	,	,		17771	0.4444		0.3569	False		,,,				2504	0.4376				p.V33M		Atlas-SNP	.											.	CA9	48	.	0			c.G97A						PASS	.	G	MET/VAL	507,3899	236.1+/-248.4	28,451,1724	62.0	56.0	58.0		97	3.1	1.0	9	dbSNP_96	58	2993,5607	462.1+/-365.6	527,1939,1834	yes	missense	CA9	NM_001216.2	21	555,2390,3558	AA,AG,GG		34.8023,11.507,26.9107	possibly-damaging	33/460	35674053	3500,9506	2203	4300	6503	SO:0001583	missense	768	exon1			CTTCTGGTGCCTG	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.97G>A	9.37:g.35674053G>A	ENSP00000367608:p.Val33Met	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_001216	Q5T4R1	Missense_Mutation	SNP	ENST00000378357.4	37	CCDS6585.1	705	0.3228021978021978	54	0.10975609756097561	133	0.3674033149171271	264	0.46153846153846156	254	0.33509234828496043	G	11.61	1.688594	0.29962	0.11507	0.348023	ENSG00000107159	ENST00000378357;ENST00000544074	T	0.72505	-0.66	5.01	3.11	0.35812	.	1.392810	0.04640	N	0.405154	T	0.00012	0.0000	L	0.34521	1.04	0.39357	P	0.034143000000000034	P;P	0.43701	0.815;0.718	P;B	0.46389	0.515;0.316	T	0.22836	-1.0205	9	0.87932	D	0	.	8.0091	0.30342	0.0:0.1758:0.6418:0.1824	rs2071676;rs17855453;rs2071676	33;33	F5H404;Q16790	.;CAH9_HUMAN	M	33	ENSP00000367608:V33M	ENSP00000367608:V33M	V	+	1	0	CA9	35664053	0.004000	0.15560	0.989000	0.46669	0.478000	0.33099	0.359000	0.20233	0.654000	0.30846	0.655000	0.94253	GTG	G|0.707;A|0.293	0.293	strong		0.657	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
PRB2	653247	hgsc.bcm.edu	37	12	11546495	11546495	+	Missense_Mutation	SNP	A	A	G	rs567948307	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:11546495A>G	ENST00000389362.4	-	3	552	c.517T>C	c.(517-519)Tct>Cct	p.S173P	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	173	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GGAGATCGAGAACTTCGGGAC	0.607													N|||	10	0.00199681	0.003	0.0	5008	,	,		20119	0.001		0.001	False		,,,				2504	0.0041				p.S173P		Atlas-SNP	.											PRB2_ENST00000389362,colon,carcinoma,+1,2	PRB2	168	2	0			c.T517C						scavenged	.						276.0	256.0	263.0					12																	11546495		2200	4299	6499	SO:0001583	missense	653247	exon3			ATCGAGAACTTCG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.517T>C	12.37:g.11546495A>G	ENSP00000374013:p.Ser173Pro	Somatic	213	8	0.0375587		WXS	Illumina HiSeq	Phase_I	226	17	0.0752212	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	0.009	-1.840215	0.00573	.	.	ENSG00000121335	ENST00000389362	T	0.03831	3.79	1.07	-1.34	0.09143	.	0.224686	0.18466	N	0.140380	T	0.00967	0.0032	N	0.00237	-1.79	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.46005	-0.9222	10	0.11485	T	0.65	.	5.5822	0.17256	0.2598:0.0:0.7402:0.0	.	173	P02812	PRB2_HUMAN	P	173	ENSP00000374013:S173P	ENSP00000374013:S173P	S	-	1	0	PRB2	11437762	0.000000	0.05858	0.002000	0.10522	0.154000	0.21943	-5.737000	0.00101	-0.425000	0.07371	0.092000	0.15492	TCT	.	.	none		0.607	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
ZFP91	80829	hgsc.bcm.edu	37	11	58378424	58378424	+	Splice_Site	SNP	A	A	G	rs8373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58378424A>G	ENST00000316059.6	+	5	790	c.619A>G	c.(619-621)Agt>Ggt	p.S207G	ZFP91-CNTF_ENST00000389919.4_Splice_Site_p.S207G	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	207	Glu-rich.		S -> G (in dbSNP:rs8373). {ECO:0000269|Ref.6}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				TATTTTTAGTAGTGAAGAGGA	0.373													A|||	1075	0.214657	0.1626	0.2176	5008	,	,		17003	0.1835		0.2505	False		,,,				2504	0.2781				p.S207G		Atlas-SNP	.											.	ZFP91	66	.	0			c.A619G						PASS	.	A	,GLY/SER	631,3771	270.4+/-269.6	44,543,1614	73.0	65.0	68.0		,619	5.8	1.0	11	dbSNP_52	68	2108,6482	361.1+/-332.2	264,1580,2451	no	splice-3,missense-near-splice	ZFP91	NM_001197051.1,NM_053023.4	,56	308,2123,4065	GG,GA,AA		24.5402,14.3344,21.0822	,probably-damaging	,207/571	58378424	2739,10253	2201	4295	6496	SO:0001630	splice_region_variant	80829	exon5			TTTAGTAGTGAAG	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"""Zinc fingers, C2H2-type"""	14983	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp91 in mouse"", ""zinc finger protein 91 homolog (mouse)"""			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.618-1A>G	11.37:g.58378424A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_053023	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	37	CCDS31553.1	488	0.22344322344322345	109	0.22154471544715448	69	0.19060773480662985	114	0.1993006993006993	196	0.25857519788918204	A	17.02	3.282804	0.59867	0.143344	0.245402	ENSG00000186660	ENST00000316059;ENST00000389918	T	0.11930	2.73	5.76	5.76	0.90799	.	2.285560	0.01956	N	0.042984	T	0.00012	0.0000	N	0.24115	0.695	0.30548	P	0.765736	P	0.48764	0.915	B	0.40940	0.344	T	0.17440	-1.0369	9	0.15499	T	0.54	-3.059	8.6083	0.33786	0.9147:0.0:0.0853:0.0	rs8373;rs1129269;rs2275992;rs3177502;rs11541681;rs17016487;rs17489327;rs52827541;rs57129919;rs8373	207	Q96JP5	ZFP91_HUMAN	G	207	ENSP00000339030:S207G	ENSP00000374569:S207G	S	+	1	0	ZFP91	58135000	1.000000	0.71417	1.000000	0.80357	0.671000	0.39405	4.471000	0.60182	2.199000	0.70637	0.528000	0.53228	AGT	A|0.780;G|0.220	0.220	strong		0.373	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023	Missense_Mutation
SLC12A9	56996	hgsc.bcm.edu	37	7	100464053	100464053	+	Silent	SNP	G	G	A	rs199582669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100464053G>A	ENST00000354161.3	+	14	2696	c.2571G>A	c.(2569-2571)gaG>gaA	p.E857E	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	857				E -> K (in Ref. 3; BAB40456). {ECO:0000305}.	chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					GTGGGCCGGAGGGTGGGGATG	0.736													G|||	19	0.00379393	0.0	0.0058	5008	,	,		9921	0.001		0.0089	False		,,,				2504	0.0051				p.E857E		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2571A						PASS	.	G		7,4113		0,7,2053	11.0	12.0	12.0		2571	-0.8	0.0	7		12	77,7943		0,77,3933	no	coding-synonymous	SLC12A9	NM_020246.2		0,84,5986	AA,AG,GG		0.9601,0.1699,0.6919		857/915	100464053	84,12056	2060	4010	6070	SO:0001819	synonymous_variant	56996	exon14			GCCGGAGGGTGGG	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.2571G>A	7.37:g.100464053G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	6	0.0079155672823219	G	2.646	-0.283100	0.05642	0.001699	0.009601	ENSG00000146828	ENST00000539308	.	.	.	4.7	-0.816	0.10839	.	.	.	.	.	T	0.50086	0.1595	.	.	.	0.40595	D	0.981521	.	.	.	.	.	.	T	0.57195	-0.7853	5	0.87932	D	0	.	5.1517	0.15013	0.2797:0.2866:0.4337:0.0	.	.	.	.	R	483	.	ENSP00000442859:G483R	G	+	1	0	SLC12A9	100301989	0.977000	0.34250	0.023000	0.16930	0.499000	0.33736	0.261000	0.18442	-0.044000	0.13491	0.555000	0.69702	GGG	G|0.995;A|0.005	0.005	strong		0.736	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
NRN1L	123904	hgsc.bcm.edu	37	16	67920049	67920049	+	Missense_Mutation	SNP	G	G	A	rs73594554	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67920049G>A	ENST00000339176.3	+	3	484	c.385G>A	c.(385-387)Gaa>Aaa	p.E129K	NRN1L_ENST00000576147.1_Silent_p.P55P|CTC-479C5.10_ENST00000572067.1_lincRNA	NM_198443.1	NP_940845.1	Q496H8	NRN1L_HUMAN	neuritin 1-like	129					nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)	7		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00415)|Epithelial(162;0.0182)|all cancers(182;0.119)		CACAGGCTCCGAAACCAACCA	0.667													G|||	759	0.151558	0.2458	0.1556	5008	,	,		15590	0.0258		0.1332	False		,,,				2504	0.1697				p.E129K		Atlas-SNP	.											NRN1L,colon,carcinoma,0,1	NRN1L	13	1	0			c.G385A						PASS	.	G	LYS/GLU	941,3455		106,729,1363	30.0	32.0	31.0		385	4.9	0.6	16	dbSNP_130	31	1054,7546		81,892,3327	yes	missense	NRN1L	NM_198443.1	56	187,1621,4690	AA,AG,GG		12.2558,21.4058,15.3509	probably-damaging	129/166	67920049	1995,11001	2198	4300	6498	SO:0001583	missense	123904	exon3			GGCTCCGAAACCA	AY358782	CCDS10850.1	16q22.1	2008-02-05			ENSG00000188038	ENSG00000188038			29811	protein-coding gene	gene with protein product						12975309	Standard	NM_198443		Approved	UNQ2446, MRCC2446	uc002euu.3	Q496H8	OTTHUMG00000137541	ENST00000339176.3:c.385G>A	16.37:g.67920049G>A	ENSP00000342411:p.Glu129Lys	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	36	19	0.527778	NM_198443	Q6UWH7	Missense_Mutation	SNP	ENST00000339176.3	37	CCDS10850.1	286	0.13095238095238096	113	0.22967479674796748	59	0.16298342541436464	15	0.026223776223776224	99	0.13060686015831136	G	18.05	3.536400	0.65085	0.214058	0.122558	ENSG00000188038	ENST00000339176	.	.	.	4.86	4.86	0.63082	.	0.233899	0.33916	N	0.004424	T	0.00039	0.0001	M	0.71581	2.175	0.09310	P	0.9999999999999861	D	0.61697	0.99	P	0.50791	0.65	T	0.00865	-1.1535	8	0.46703	T	0.11	.	16.1255	0.81392	0.0:0.0:1.0:0.0	.	129	Q496H8	NRN1L_HUMAN	K	129	.	ENSP00000342411:E129K	E	+	1	0	NRN1L	66477550	1.000000	0.71417	0.604000	0.28916	0.138000	0.21146	5.744000	0.68664	2.411000	0.81874	0.462000	0.41574	GAA	G|0.854;A|0.146	0.146	strong		0.667	NRN1L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268872.2	NM_198443	
MT-ND6	4541	hgsc.bcm.edu	37	M	14311	14311	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:14311T>C	ENST00000361681.2	-	1	362	c.363A>G	c.(361-363)gtA>gtG	p.V121V	MT-TH_ENST00000387441.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	121					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						ATTCAGCTTCCTACACTATTA	0.468																																					p.V121V		Atlas-SNP	.											.	.	.	.	0			c.A363G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			GCTTCCTACACTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.363A>G	M.37:g.14311T>C		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.468	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
PPP1R21	129285	hgsc.bcm.edu	37	2	48713777	48713777	+	Silent	SNP	C	C	T	rs33994624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:48713777C>T	ENST00000294952.8	+	14	1483	c.1326C>T	c.(1324-1326)tcC>tcT	p.S442S	PPP1R21_ENST00000281394.4_Silent_p.S442S|PPP1R21_ENST00000449090.2_Silent_p.S442S	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	442						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						TAGATATTTCCAAACATTATA	0.328													C|||	450	0.0898562	0.0113	0.0965	5008	,	,		16802	0.0248		0.1203	False		,,,				2504	0.227				p.S442S		Atlas-SNP	.											.	PPP1R21	47	.	0			c.C1326T						PASS	.	C	,,	109,4297	78.3+/-116.7	0,109,2094	44.0	43.0	43.0		1326,1326,1326	1.5	1.0	2	dbSNP_126	43	1091,7509	221.5+/-258.9	61,969,3270	no	coding-synonymous,coding-synonymous,coding-synonymous	KLRAQ1	NM_001135629.2,NM_001193475.1,NM_152994.4	,,	61,1078,5364	TT,TC,CC		12.686,2.4739,9.2265	,,	442/781,442/739,442/770	48713777	1200,11806	2203	4300	6503	SO:0001819	synonymous_variant	129285	exon14			TATTTCCAAACAT	AY134855	CCDS1839.1, CCDS46278.1, CCDS54358.1	2p16.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000162869	ENSG00000162869		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	30595	protein-coding gene	gene with protein product			"""coiled-coil domain containing 128"", ""KLRAQ motif containing 1"""	CCDC128, KLRAQ1		12477932	Standard	NM_001135629		Approved	FLJ16566	uc002rwm.3	Q6ZMI0	OTTHUMG00000129167	ENST00000294952.8:c.1326C>T	2.37:g.48713777C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Silent	SNP	ENST00000294952.8	37	CCDS46278.1																																																																																			C|0.914;T|0.086	0.086	strong		0.328	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994	
SERPINH1	871	hgsc.bcm.edu	37	11	75279846	75279846	+	Silent	SNP	C	C	T	rs649257	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:75279846C>T	ENST00000524558.1	+	3	2128	c.693C>T	c.(691-693)acC>acT	p.T231T	SERPINH1_ENST00000533603.1_Silent_p.T231T|SERPINH1_ENST00000525876.1_Silent_p.T14T|SERPINH1_ENST00000530284.1_Silent_p.T231T|SERPINH1_ENST00000358171.3_Silent_p.T231T			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	231					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.T231T(1)		endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					GGTCCTATACCGTGGGTGTCA	0.567													C|||	1888	0.376997	0.4766	0.379	5008	,	,		19111	0.2103		0.2972	False		,,,				2504	0.4949				p.T231T		Atlas-SNP	.											SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	1	Substitution - coding silent(1)	stomach(1)	c.C693T						PASS	.	C	,	1954,2446	553.2+/-378.7	444,1066,690	149.0	113.0	125.0		693,693	-11.4	0.2	11	dbSNP_83	125	2616,5970	422.8+/-354.1	383,1850,2060	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	827,2916,2750	TT,TC,CC		30.4682,44.4091,35.1917	,	231/419,231/419	75279846	4570,8416	2200	4293	6493	SO:0001819	synonymous_variant	871	exon3			CTATACCGTGGGT	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.693C>T	11.37:g.75279846C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			C|0.660;T|0.340	0.340	strong		0.567	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
PRDM16	63976	hgsc.bcm.edu	37	1	3329037	3329037	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:3329037G>A	ENST00000270722.5	+	9	2325	c.2276G>A	c.(2275-2277)cGg>cAg	p.R759Q	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000378391.2_Missense_Mutation_p.R759Q|PRDM16_ENST00000442529.2_Missense_Mutation_p.R759Q|PRDM16_ENST00000511072.1_Missense_Mutation_p.R760Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.R760Q|PRDM16_ENST00000441472.2_Missense_Mutation_p.R759Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.R760Q			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	759	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				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)		AAGTCACCCCGGGACGCCCTC	0.652			T	EVI1	"""MDS, AML"""																																p.R759Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	PRDM16,NS,lymphoid_neoplasm,+1,1	PRDM16	147	1	0			c.G2276A						PASS	.						53.0	61.0	58.0					1																	3329037		2015	4158	6173	SO:0001583	missense	63976	exon9			CACCCCGGGACGC	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.2276G>A	1.37:g.3329037G>A	ENSP00000270722:p.Arg759Gln	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	85	77	0.905882	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	G	14.09	2.433145	0.43224	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.05649	3.41;3.44;3.46;3.44;3.43;3.44;3.46;3.41;3.41	4.41	4.41	0.53225	.	0.000000	0.46758	U	0.000280	T	0.19208	0.0461	M	0.67953	2.075	0.51012	D	0.999903	D;D;D;D	0.76494	0.999;0.998;0.999;0.997	P;P;P;P	0.62184	0.75;0.821;0.899;0.667	T	0.10382	-1.0632	10	0.16420	T	0.52	.	17.3359	0.87281	0.0:0.0:1.0:0.0	.	759;759;759;759	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	760;760;759;759;759;760;759;575;575;568	ENSP00000426975:R760Q;ENSP00000367651:R760Q;ENSP00000407968:R759Q;ENSP00000405253:R759Q;ENSP00000367643:R759Q;ENSP00000421400:R760Q;ENSP00000270722:R759Q;ENSP00000422504:R575Q;ENSP00000425796:R568Q	ENSP00000270722:R759Q	R	+	2	0	PRDM16	3318897	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	4.285000	0.58989	2.169000	0.68431	0.453000	0.30009	CGG	.	.	none		0.652	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
ZNF835	90485	hgsc.bcm.edu	37	19	57176304	57176304	+	Missense_Mutation	SNP	T	T	G	rs12460400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57176304T>G	ENST00000537055.2	-	2	494	c.263A>C	c.(262-264)gAg>gCg	p.E88A		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	88			E -> A (in dbSNP:rs12460400). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						CTTCGGGCTCTCCCCAGGCGC	0.637													.|||	2007	0.400759	0.4123	0.3732	5008	,	,		15470	0.4702		0.3121	False		,,,				2504	0.4243				p.E88A		Atlas-SNP	.											.	ZNF835	106	.	0			c.A263C						PASS	.	T	ALA/GLU	1630,2550		347,936,807	54.0	59.0	57.0		263	-1.0	0.0	19	dbSNP_120	57	2524,5938		380,1764,2087	no	missense	ZNF835	NM_001005850.2	107	727,2700,2894	GG,GT,TT		29.8275,38.9952,32.8587	benign	88/538	57176304	4154,8488	2090	4231	6321	SO:0001583	missense	90485	exon2			GGGCTCTCCCCAG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.263A>C	19.37:g.57176304T>G	ENSP00000444747:p.Glu88Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	68	38	0.558824	NM_001005850	B7Z5Y0|G3V1S0	Missense_Mutation	SNP	ENST00000537055.2	37	CCDS56105.1	847	0.38782051282051283	215	0.4369918699186992	127	0.35082872928176795	264	0.46153846153846156	241	0.3179419525065963	T	6.640	0.486634	0.12641	0.389952	0.298275	ENSG00000127903	ENST00000342088;ENST00000537055	T	0.06849	3.25	2.58	-1.04	0.10068	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.12837	0.008	T	0.44605	-0.9317	8	0.72032	D	0.01	.	2.9659	0.05908	0.0:0.2978:0.2397:0.4625	rs12460400	110	Q9Y2P0	ZN835_HUMAN	A	110;88	ENSP00000444747:E88A	ENSP00000341756:E110A	E	-	2	0	ZNF835	61868116	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.149000	0.10204	-0.483000	0.06772	0.459000	0.35465	GAG	T|0.628;G|0.372	0.372	strong		0.637	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
CPO	130749	hgsc.bcm.edu	37	2	207827220	207827220	+	Missense_Mutation	SNP	G	G	A	rs62617140	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:207827220G>A	ENST00000272852.3	+	7	705	c.659G>A	c.(658-660)aGc>aAc	p.S220N		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	220						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		GCTGTTGCCAGCTTCATAGAG	0.433													G|||	103	0.0205671	0.0008	0.0274	5008	,	,		21599	0.001		0.0716	False		,,,				2504	0.0102				p.S220N		Atlas-SNP	.											.	CPO	42	.	0			c.G659A						PASS	.	G	ASN/SER	62,4344	58.1+/-94.6	0,62,2141	206.0	196.0	199.0		659	3.7	0.3	2	dbSNP_129	199	408,8192	129.3+/-187.4	9,390,3901	yes	missense	CPO	NM_173077.2	46	9,452,6042	AA,AG,GG		4.7442,1.4072,3.6137	benign	220/375	207827220	470,12536	2203	4300	6503	SO:0001583	missense	130749	exon7			TTGCCAGCTTCAT		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.659G>A	2.37:g.207827220G>A	ENSP00000272852:p.Ser220Asn	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_173077	Q2M277|Q7RTW7	Missense_Mutation	SNP	ENST00000272852.3	37	CCDS2372.1	61	0.027930402930402932	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	53	0.06992084432717678	G	0.429	-0.904539	0.02453	0.014072	0.047442	ENSG00000144410	ENST00000272852	T	0.27720	1.65	5.5	3.72	0.42706	Peptidase M14, carboxypeptidase A (2);	0.443249	0.28665	N	0.014547	T	0.00815	0.0027	N	0.03000	-0.44	0.22050	N	0.99939	B	0.12630	0.006	B	0.10450	0.005	T	0.22452	-1.0216	10	0.23302	T	0.38	.	7.3163	0.26503	0.2513:0.0:0.7487:0.0	rs62617140	220	Q8IVL8	CBPO_HUMAN	N	220	ENSP00000272852:S220N	ENSP00000272852:S220N	S	+	2	0	CPO	207535465	0.286000	0.24305	0.292000	0.24919	0.419000	0.31324	2.790000	0.47821	0.893000	0.36288	0.555000	0.69702	AGC	G|0.965;A|0.035	0.035	strong		0.433	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
RRN3	54700	hgsc.bcm.edu	37	16	15185186	15185186	+	Missense_Mutation	SNP	C	C	T	rs151006368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15185186C>T	ENST00000198767.6	-	3	321	c.238G>A	c.(238-240)Gat>Aat	p.D80N	PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000563559.1_Missense_Mutation_p.D80N|RRN3_ENST00000564131.1_Missense_Mutation_p.D80N|RRN3_ENST00000327307.7_Missense_Mutation_p.D47N|RRN3_ENST00000429751.2_Missense_Mutation_p.D80N	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	80					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						ATGTCTGGATCTAACAGCTGG	0.358													.|||	48	0.00958466	0.0008	0.0173	5008	,	,		21424	0.0		0.0249	False		,,,				2504	0.0102				p.D80N		Atlas-SNP	.											.	RRN3	36	.	0			c.G238A						PASS	.	C	ASN/ASP	15,4367		0,15,2176	33.0	30.0	31.0		238	4.1	1.0	16	dbSNP_134	31	210,8364		1,208,4078	no	missense	RRN3	NM_018427.3	23	1,223,6254	TT,TC,CC		2.4493,0.3423,1.7366	probably-damaging	80/652	15185186	225,12731	2191	4287	6478	SO:0001583	missense	54700	exon3			CTGGATCTAACAG	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.238G>A	16.37:g.15185186C>T	ENSP00000198767:p.Asp80Asn	Somatic	551	1	0.00181488		WXS	Illumina HiSeq	Phase_I	737	557	0.755767	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	37	CCDS10559.1	31	0.014194139194139194	4	0.008130081300813009	8	0.022099447513812154	0	0.0	19	0.025065963060686015	.	17.96	3.516475	0.64634	0.003423	0.024493	ENSG00000085721	ENST00000198767;ENST00000429751;ENST00000327307	T;T;T	0.51817	0.97;0.69;0.97	4.14	4.14	0.48551	.	0.000000	0.64402	U	0.000001	T	0.40767	0.1130	M	0.73319	2.225	0.80722	D	1	D;P;D	0.69078	0.997;0.566;0.991	D;B;D	0.67725	0.952;0.338;0.953	T	0.55958	-0.8058	10	0.29301	T	0.29	.	15.7787	0.78243	0.0:1.0:0.0:0.0	.	80;80;80	F5H148;Q3MHU9;Q9NYV6	.;.;RRN3_HUMAN	N	80;80;47	ENSP00000198767:D80N;ENSP00000402027:D80N;ENSP00000318484:D47N	ENSP00000198767:D80N	D	-	1	0	RRN3	15092687	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	6.612000	0.74187	2.017000	0.59298	0.455000	0.32223	GAT	C|0.988;T|0.012	0.012	strong		0.358	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	
TTC7B	145567	hgsc.bcm.edu	37	14	91084338	91084338	+	Silent	SNP	C	C	T	rs754247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:91084338C>T	ENST00000328459.6	-	16	1924	c.1803G>A	c.(1801-1803)gaG>gaA	p.E601E	TTC7B_ENST00000357056.2_Silent_p.E601E|TTC7B_ENST00000554654.1_5'UTR	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	601										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				TCAGCAGTGCCTCGTCCGGGC	0.547													C|||	2334	0.466054	0.7186	0.3862	5008	,	,		21540	0.4157		0.2694	False		,,,				2504	0.4356				p.E601E		Atlas-SNP	.											.	TTC7B	93	.	0			c.G1803A						PASS	.	C		2835,1571	667.7+/-401.9	910,1015,278	115.0	108.0	110.0		1803	4.7	1.0	14	dbSNP_86	110	2349,6251	392.1+/-343.9	339,1671,2290	no	coding-synonymous	TTC7B	NM_001010854.1		1249,2686,2568	TT,TC,CC		27.314,35.6559,39.8585		601/844	91084338	5184,7822	2203	4300	6503	SO:0001819	synonymous_variant	145567	exon16			CAGTGCCTCGTCC	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"""Tetratricopeptide (TTC) repeat domain containing"""	19858	protein-coding gene	gene with protein product			"""tetratricopeptide repeat domain 7 like 1"""	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.1803G>A	14.37:g.91084338C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	82	80	0.97561	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	37	CCDS32140.1																																																																																			C|0.578;T|0.422	0.422	strong		0.547	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
LILRB3	11025	hgsc.bcm.edu	37	19	54726237	54726237	+	Missense_Mutation	SNP	C	C	G	rs138323850		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54726237C>G	ENST00000391750.1	-	4	404	c.268G>C	c.(268-270)Gag>Cag	p.E90Q	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000469273.1_5'Flank|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRA6_ENST00000440558.2_Intron|LILRB3_ENST00000407860.2_Intron|LILRB3_ENST00000424807.1_Missense_Mutation_p.E90Q|LILRB3_ENST00000346401.6_Missense_Mutation_p.E90Q|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.E90Q|LILRA6_ENST00000270464.5_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	90	Ig-like C2-type 1.		E -> Q (in dbSNP:rs1052963). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.E90Q(1)		endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GCATGGTGCTCTGTCATGGAT	0.557																																					p.E90Q		Atlas-SNP	.											LILRB3,NS,carcinoma,0,1	LILRB3	67	1	1	Substitution - Missense(1)	prostate(1)	c.G268C						scavenged	.						87.0	123.0	111.0					19																	54726237		2019	4025	6044	SO:0001583	missense	11025	exon3			GGTGCTCTGTCAT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.268G>C	19.37:g.54726237C>G	ENSP00000375630:p.Glu90Gln	Somatic	635	0	0		WXS	Illumina HiSeq	Phase_I	240	6	0.025	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	G	0.767	-0.767250	0.02974	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000445347	T;T;T;T;T	0.13196	2.61;2.61;2.61;2.61;2.61	3.08	-6.17	0.02091	Immunoglobulin-like fold (1);	2.768340	0.01040	N	0.004297	T	0.09818	0.0241	L	0.39245	1.2	0.09310	N	1	B;B	0.22800	0.037;0.075	B;B	0.27608	0.002;0.081	T	0.31806	-0.9930	10	0.12103	T	0.63	.	3.0186	0.06067	0.1961:0.2034:0.4352:0.1653	.	90;90	O75022;O75022-3	LIRB3_HUMAN;.	Q	90	ENSP00000375630:E90Q;ENSP00000412771:E90Q;ENSP00000345184:E90Q;ENSP00000245620:E90Q;ENSP00000388199:E90Q	ENSP00000245620:E90Q	E	-	1	0	LILRB3	59418049	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-5.048000	0.00156	-2.865000	0.00325	-0.957000	0.02645	GAG	C|0.333;G|0.667	0.667	strong		0.557	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
MATN2	4147	hgsc.bcm.edu	37	8	98954108	98954108	+	Silent	SNP	G	G	T	rs35407519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:98954108G>T	ENST00000520016.1	+	3	940	c.816G>T	c.(814-816)tcG>tcT	p.S272S	MATN2_ENST00000521689.1_Silent_p.S272S|MATN2_ENST00000522025.2_5'UTR|MATN2_ENST00000254898.5_Silent_p.S272S|MATN2_ENST00000524308.1_Silent_p.S272S			O00339	MATN2_HUMAN	matrilin 2	272	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TTCTCAACTCGGATCAGACGA	0.463													G|||	557	0.111222	0.0098	0.2493	5008	,	,		22830	0.1042		0.0915	False		,,,				2504	0.1779				p.S272S		Atlas-SNP	.											.	MATN2	165	.	0			c.G816T						PASS	.	G	,	112,4018		3,106,1956	116.0	116.0	116.0		816,816	-1.0	0.9	8	dbSNP_126	116	884,7548		61,762,3393	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	64,868,5349	TT,TG,GG		10.4839,2.7119,7.9287	,	272/957,272/938	98954108	996,11566	2065	4216	6281	SO:0001819	synonymous_variant	4147	exon4			CAACTCGGATCAG	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.816G>T	8.37:g.98954108G>T		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	256	114	0.445312	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	209	0.09569597069597069	6	0.012195121951219513	64	0.17679558011049723	60	0.1048951048951049	79	0.10422163588390501	G	7.339	0.620463	0.14193	0.027119	0.104839	ENSG00000132561	ENST00000518154	.	.	.	5.24	-0.969	0.10310	.	.	.	.	.	.	.	.	.	.	.	0.20638	P	0.999873685	.	.	.	.	.	.	.	.	.	.	.	.	.	-1.3583	3.0914	0.06295	0.3844:0.1066:0.4007:0.1083	rs35407519	.	.	.	X	96	.	.	G	+	1	0	MATN2	99023284	0.797000	0.28877	0.927000	0.36925	0.908000	0.53690	0.050000	0.14120	-0.244000	0.09639	-1.134000	0.01955	GGA	G|0.905;T|0.095	0.095	strong		0.463	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
KRTAP10-5	386680	hgsc.bcm.edu	37	21	46000367	46000367	+	Missense_Mutation	SNP	G	G	T	rs149326833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46000367G>T	ENST00000400372.1	-	1	114	c.89C>A	c.(88-90)cCc>cAc	p.P30H	TSPEAR_ENST00000323084.4_Intron	NM_198694.2	NP_941967.2	P60370	KR105_HUMAN	keratin associated protein 10-5	30	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(2)|kidney(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	14						GGTGCCGCAGGGGGGCTCACA	0.697													.|||	68	0.0135783	0.0023	0.0159	5008	,	,		17922	0.0		0.0427	False		,,,				2504	0.0112				p.P30H		Atlas-SNP	.											KRTAP10-5,NS,carcinoma,-1,1	KRTAP10-5	43	1	0			c.C89A						PASS	.	G	HIS/PRO,	32,4370	34.3+/-65.2	1,30,2170	55.0	61.0	59.0		89,	1.0	0.6	21	dbSNP_134	59	369,8227	120.2+/-179.5	6,357,3935	no	missense,intron	TSPEAR,KRTAP10-5	NM_198694.2,NM_144991.2	77,	7,387,6105	TT,TG,GG		4.2927,0.7269,3.0851	probably-damaging,	30/272,	46000367	401,12597	2201	4298	6499	SO:0001583	missense	386680	exon1			CCGCAGGGGGGCT	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.89C>A	21.37:g.46000367G>T	ENSP00000383223:p.Pro30His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	121	67	0.553719	NM_198694	Q0VAR7|Q0VAR8|Q70LJ3	Missense_Mutation	SNP	ENST00000400372.1	37	CCDS42958.1	45	0.020604395604395604	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	34	0.044854881266490766	g	5.751	0.323011	0.10900	0.007269	0.042927	ENSG00000241123	ENST00000400372	T	0.08102	3.13	3.39	1.05	0.20165	.	.	.	.	.	T	0.03305	0.0096	L	0.59436	1.845	0.09310	N	0.999998	D	0.69078	0.997	P	0.52881	0.712	T	0.09796	-1.0658	9	0.59425	D	0.04	.	9.6006	0.39601	0.0:0.5751:0.4248:0.0	.	30	P60370	KR105_HUMAN	H	30	ENSP00000383223:P30H	ENSP00000383223:P30H	P	-	2	0	KRTAP10-5	44824795	0.165000	0.22948	0.556000	0.28293	0.176000	0.22953	0.123000	0.15708	0.610000	0.30035	0.298000	0.19748	CCC	G|0.971;T|0.029	0.029	strong		0.697	KRTAP10-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128042.1		
IKBIP	121457	hgsc.bcm.edu	37	12	99007411	99007411	+	Silent	SNP	C	C	T	rs201283576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:99007411C>T	ENST00000342502.2	-	3	1416	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	IKBIP_ENST00000420861.1_Silent_p.E229E|IKBIP_ENST00000393042.3_3'UTR	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	335					response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						TATCCTTAATCTCAGCTTGGA	0.308																																					p.E335E		Atlas-SNP	.											.	IKBIP	46	.	0			c.G1005A						PASS	.						52.0	58.0	56.0					12																	99007411		2199	4297	6496	SO:0001819	synonymous_variant	121457	exon3			CTTAATCTCAGCT	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"""I kappa B kinase interacting protein"""	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.1005G>A	12.37:g.99007411C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	15	0.319149	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Silent	SNP	ENST00000342502.2	37	CCDS9067.1																																																																																			C|0.999;A|0.001	.	alt		0.308	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687	
QPRT	23475	hgsc.bcm.edu	37	16	29706444	29706444	+	Missense_Mutation	SNP	C	C	T	rs2303255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:29706444C>T	ENST00000395384.4	+	2	634	c.473C>T	c.(472-474)gCc>gTc	p.A158V	QPRT_ENST00000562473.1_Intron|QPRT_ENST00000219771.7_Intron	NM_014298.3	NP_055113.2	Q15274	NADC_HUMAN	quinolinate phosphoribosyltransferase	158			A -> V (in dbSNP:rs2303255).		NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|protein oligomerization (GO:0051259)|quinolinate catabolic process (GO:0034213)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	nicotinate-nucleotide diphosphorylase (carboxylating) activity (GO:0004514)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)	9					Niacin(DB00627)	GGCGGGGCCGCCTCGCACCGC	0.692													c|||	492	0.0982428	0.0144	0.1052	5008	,	,		11992	0.0546		0.17	False		,,,				2504	0.1779				p.A158V		Atlas-SNP	.											.	QPRT	19	.	0			c.C473T						PASS	.		VAL/ALA	189,4125		5,179,1973	24.0	38.0	33.0		473	1.9	0.0	16	dbSNP_100	33	1591,6907		156,1279,2814	yes	missense	QPRT	NM_014298.3	64	161,1458,4787	TT,TC,CC		18.7221,4.3811,13.8932	possibly-damaging	158/298	29706444	1780,11032	2157	4249	6406	SO:0001583	missense	23475	exon2			GGGCCGCCTCGCA	D78177	CCDS10651.1	16p11.2	2008-07-31	2008-07-31		ENSG00000103485	ENSG00000103485	2.4.2.19		9755	protein-coding gene	gene with protein product	"""nicotinate-nucleotide pyrophosphorylase (carboxylating)"""	606248				9473669	Standard	NM_014298		Approved	QPRTase	uc002dto.3	Q15274	OTTHUMG00000097770	ENST00000395384.4:c.473C>T	16.37:g.29706444C>T	ENSP00000378782:p.Ala158Val	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_014298	Q53XW7|Q96G22|Q9BSG6	Missense_Mutation	SNP	ENST00000395384.4	37	CCDS10651.1	223	0.1021062271062271	9	0.018292682926829267	42	0.11602209944751381	39	0.06818181818181818	133	0.17546174142480211	.	11.61	1.691437	0.30052	0.043811	0.187221	ENSG00000103485	ENST00000449759;ENST00000395384	T	0.30714	1.52	3.88	1.86	0.25419	Aldolase-type TIM barrel (1);Quinolinate phosphoribosyl transferase, C-terminal (2);	0.237069	0.35096	N	0.003458	T	0.00012	0.0000	N	0.05608	-0.01	0.42134	P	0.008518000000000026	B	0.14438	0.01	B	0.12837	0.008	T	0.28427	-1.0044	9	0.24483	T	0.36	-11.1753	2.3129	0.04191	0.2005:0.4953:0.1941:0.1102	rs2303255;rs17640184;rs2303255	158	Q15274	NADC_HUMAN	V	158	ENSP00000378782:A158V	ENSP00000378782:A158V	A	+	2	0	QPRT	29613945	0.000000	0.05858	0.042000	0.18584	0.450000	0.32258	0.655000	0.24933	0.949000	0.37715	0.461000	0.40582	GCC	C|0.895;T|0.105	0.105	strong		0.692	QPRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215011.2	NM_014298	
TMEM72	643236	hgsc.bcm.edu	37	10	45430462	45430462	+	Silent	SNP	C	C	T	rs17417442	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45430462C>T	ENST00000544540.1	+	4	838	c.354C>T	c.(352-354)gcC>gcT	p.A118A	TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.9_ENST00000425541.2_lincRNA			A0PK05	TMM72_HUMAN	transmembrane protein 72	236						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						CCTCCCTCGCCGAAGGTCTGG	0.592													c|||	1670	0.333466	0.3086	0.4438	5008	,	,		18282	0.3274		0.3986	False		,,,				2504	0.228				p.A236A		Atlas-SNP	.											.	TMEM72	25	.	0			c.C708T						PASS	.	G		1040,2096		167,706,695	111.0	113.0	113.0		708	-10.8	0.0	10	dbSNP_123	113	3019,4145		625,1769,1188	no	coding-synonymous	TMEM72	NM_001123376.1		792,2475,1883	TT,TC,CC		42.1413,33.1633,39.4078		236/276	45430462	4059,6241	1568	3582	5150	SO:0001819	synonymous_variant	643236	exon5			CCTCGCCGAAGGT	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 127"""	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.354C>T	10.37:g.45430462C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	106	60	0.566038	NM_001123376	A1L181|Q5T740	Silent	SNP	ENST00000544540.1	37																																																																																				C|0.634;T|0.366	0.366	strong		0.592	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	
LMTK3	114783	hgsc.bcm.edu	37	19	49003060	49003060	+	Silent	SNP	C	C	A	rs201659713	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49003060C>A	ENST00000600059.1	-	11	1493	c.1266G>T	c.(1264-1266)ccG>ccT	p.P422P	LMTK3_ENST00000270238.3_Silent_p.P451P			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	422	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GTGGGGGTGGCGGCGGTGGGG	0.716													C|||	34	0.00678914	0.0015	0.0159	5008	,	,		7177	0.0		0.0119	False		,,,				2504	0.0092				p.P451P		Atlas-SNP	.											.	LMTK3	125	.	0			c.G1353T						PASS	.	C		6,2534		0,6,1264	2.0	3.0	3.0		1353	-3.7	0.1	19		3	75,5831		0,75,2878	no	coding-synonymous	LMTK3	NM_001080434.1		0,81,4142	AA,AC,CC		1.2699,0.2362,0.959		451/1490	49003060	81,8365	1270	2953	4223	SO:0001819	synonymous_variant	114783	exon12			GGGTGGCGGCGGT	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.1266G>T	19.37:g.49003060C>A		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	20	15	0.75	NM_001080434	Q4G0U1	Silent	SNP	ENST00000600059.1	37																																																																																				C|0.987;A|0.013	0.013	strong		0.716	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	
EID3	493861	hgsc.bcm.edu	37	12	104698208	104698208	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:104698208G>A	ENST00000527879.1	+	1	692	c.496G>A	c.(496-498)Gag>Aag	p.E166K	TXNRD1_ENST00000503506.2_Intron|TXNRD1_ENST00000525566.1_Intron|TXNRD1_ENST00000529546.1_Intron|TXNRD1_ENST00000524698.1_Intron|TXNRD1_ENST00000378070.4_Intron|TXNRD1_ENST00000388854.3_Intron|TXNRD1_ENST00000542918.1_Intron|TXNRD1_ENST00000429002.2_Intron|TXNRD1_ENST00000526691.1_Intron|TXNRD1_ENST00000397736.2_Intron|TXNRD1_ENST00000526390.1_Intron|TXNRD1_ENST00000354940.6_Intron|TXNRD1_ENST00000540716.1_Intron	NM_001008394.2	NP_001008395.1			EP300 interacting inhibitor of differentiation 3											large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						GGTAAAAGCTGAGACATTCCA	0.428																																					p.E166K		Atlas-SNP	.											EID3,NS,carcinoma,0,2	EID3	28	2	0			c.G496A						scavenged	.						200.0	197.0	198.0					12																	104698208		1937	4145	6082	SO:0001583	missense	493861	exon1			AAAGCTGAGACAT	BC027612	CCDS53822.1	12q23.3	2006-11-24				ENSG00000255150			32961	protein-coding gene	gene with protein product		612986				15987788, 15752197	Standard	NM_001008394		Approved	FLJ25832, NSMCE4B, NSE4B	uc001tkw.3	Q8N140		ENST00000527879.1:c.496G>A	12.37:g.104698208G>A	ENSP00000435619:p.Glu166Lys	Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_001008394		Missense_Mutation	SNP	ENST00000527879.1	37	CCDS53822.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827581	0.50845	.	.	ENSG00000255150	ENST00000527879	T	0.42900	0.96	4.82	1.75	0.24633	.	.	.	.	.	T	0.42765	0.1217	L	0.51422	1.61	0.09310	N	1	P	0.46621	0.881	P	0.50270	0.636	T	0.18335	-1.0340	9	0.36615	T	0.2	.	6.4222	0.21750	0.0982:0.3601:0.5417:0.0	.	166	Q8N140	EID3_HUMAN	K	166	ENSP00000435619:E166K	ENSP00000435619:E166K	E	+	1	0	EID3	103222338	0.045000	0.20229	0.012000	0.15200	0.023000	0.10783	0.972000	0.29409	0.739000	0.32628	0.555000	0.69702	GAG	.	.	none		0.428	EID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387034.1	NM_001008394	
PDCD4	27250	hgsc.bcm.edu	37	10	112647433	112647433	+	Missense_Mutation	SNP	G	G	A	rs41292600	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:112647433G>A	ENST00000280154.7	+	6	840	c.566G>A	c.(565-567)aGa>aAa	p.R189K	PDCD4_ENST00000481353.1_3'UTR|PDCD4_ENST00000393104.2_Missense_Mutation_p.R178K	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	189	MI 1. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		GAAATGTTAAGAGATTTAAAT	0.299													G|||	11	0.00219649	0.0	0.0014	5008	,	,		18117	0.0		0.005	False		,,,				2504	0.0051				p.R189K	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.G566A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	7,4399	12.9+/-30.5	0,7,2196	87.0	85.0	86.0		524,566,533	3.9	1.0	10	dbSNP_127	86	88,8512	43.6+/-101.6	1,86,4213	no	missense,missense,missense	PDCD4	NM_001199492.1,NM_014456.4,NM_145341.3	26,26,26	1,93,6409	AA,AG,GG		1.0233,0.1589,0.7304	benign,benign,benign	175/456,189/470,178/459	112647433	95,12911	2203	4300	6503	SO:0001583	missense	27250	exon6			TGTTAAGAGATTT	U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"""nuclear antigen H731"""	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.566G>A	10.37:g.112647433G>A	ENSP00000280154:p.Arg189Lys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	36	0.467532	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Missense_Mutation	SNP	ENST00000280154.7	37	CCDS7567.1	17	0.007783882783882784	4	0.008130081300813009	5	0.013812154696132596	1	0.0017482517482517483	7	0.009234828496042216	G	5.092	0.202557	0.09652	0.001589	0.010233	ENSG00000150593	ENST00000280154;ENST00000393104;ENST00000444997	T;T;T	0.38887	1.11;1.11;1.11	5.72	3.87	0.44632	Initiation factor eIF-4 gamma, MA3 (3);Armadillo-type fold (1);	0.306707	0.41396	N	0.000893	T	0.10766	0.0263	N	0.03071	-0.42	0.31940	N	0.611103	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.20273	-1.0280	10	0.07482	T	0.82	-16.6869	7.2204	0.25983	0.3582:0.0:0.6418:0.0	rs41292600;rs61753065	175;189;178	B4DKX4;Q53EL6;B5ME91	.;PDCD4_HUMAN;.	K	189;178;175	ENSP00000280154:R189K;ENSP00000376816:R178K;ENSP00000394668:R175K	ENSP00000280154:R189K	R	+	2	0	PDCD4	112637423	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.509000	0.35780	0.884000	0.36064	0.650000	0.86243	AGA	G|0.993;A|0.007	0.007	strong		0.299	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456	
MDN1	23195	hgsc.bcm.edu	37	6	90418262	90418262	+	Silent	SNP	C	C	T	rs2026634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90418262C>T	ENST00000369393.3	-	51	7966	c.7851G>A	c.(7849-7851)acG>acA	p.T2617T	MDN1_ENST00000428876.1_Silent_p.T2617T			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2617					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CAGGCTGGTCCGTTTGTGGGT	0.463													C|||	4415	0.881589	0.8048	0.902	5008	,	,		18386	0.997		0.838	False		,,,				2504	0.8967				p.T2617T		Atlas-SNP	.											.	MDN1	478	.	0			c.G7851A						PASS	.	C		3539,867	744.0+/-411.5	1432,675,96	176.0	177.0	176.0		7851	-11.1	0.0	6	dbSNP_94	176	7147,1453	751.2+/-407.4	2978,1191,131	no	coding-synonymous	MDN1	NM_014611.1		4410,1866,227	TT,TC,CC		16.8953,19.6777,17.8379		2617/5597	90418262	10686,2320	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon51			CTGGTCCGTTTGT	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.7851G>A	6.37:g.90418262C>T		Somatic	102	1	0.00980392		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			C|0.152;T|0.848	0.848	strong		0.463	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
DDHD1	80821	hgsc.bcm.edu	37	14	53619500	53619500	+	Missense_Mutation	SNP	C	C	G	rs117525276	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:53619500C>G	ENST00000323669.5	-	1	316	c.317G>C	c.(316-318)gGt>gCt	p.G106A	DDHD1_ENST00000357758.3_Missense_Mutation_p.G106A|RP11-547D23.1_ENST00000554235.1_RNA|AL356020.1_ENST00000584587.1_RNA|DDHD1_ENST00000395606.1_Missense_Mutation_p.G106A	NM_001160148.1	NP_001153620.1	Q8NEL9	DDHD1_HUMAN	DDHD domain containing 1	106					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)	25	Breast(41;0.037)					GCCGCTCTCACCCTCGCTGTA	0.706													C|||	362	0.0722843	0.031	0.1412	5008	,	,		10844	0.123		0.0318	False		,,,				2504	0.0685				p.G106A		Atlas-SNP	.											.	DDHD1	202	.	0			c.G317C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	91,4233		1,89,2072	13.0	15.0	14.0		317,317,317	3.8	1.0	14	dbSNP_132	14	261,8247		6,249,3999	yes	missense,missense,missense	DDHD1	NM_001160147.1,NM_001160148.1,NM_030637.2	60,60,60	7,338,6071	GG,GC,CC		3.0677,2.1045,2.7431	probably-damaging,probably-damaging,probably-damaging	106/880,106/901,106/873	53619500	352,12480	2162	4254	6416	SO:0001583	missense	80821	exon1			CTCTCACCCTCGC	AB051492	CCDS9714.1, CCDS53895.1, CCDS53896.1	14q21	2012-11-23			ENSG00000100523	ENSG00000100523			19714	protein-coding gene	gene with protein product	"""phosphatidic acid-preferring phospholipase A1"""	614603	"""spastic paraplegia 28 (autosomal recessive)"""	SPG28		11214970, 20359546	Standard	NM_030637		Approved	KIAA1705, PA-PLA1	uc001xai.3	Q8NEL9	OTTHUMG00000140305	ENST00000323669.5:c.317G>C	14.37:g.53619500C>G	ENSP00000327104:p.Gly106Ala	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	87	47	0.54023	NM_001160147	G5E9D1|Q8WVH3|Q96LL2|Q9C0F8	Missense_Mutation	SNP	ENST00000323669.5	37	CCDS53895.1	157	0.07188644688644688	13	0.026422764227642278	48	0.13259668508287292	71	0.12412587412587413	25	0.032981530343007916	C	15.52	2.857904	0.51376	0.021045	0.030677	ENSG00000100523	ENST00000323669;ENST00000395606;ENST00000357758;ENST00000395610	.	.	.	3.77	3.77	0.43336	.	0.705587	0.12871	N	0.432287	T	0.00695	0.0023	N	0.22421	0.69	0.34392	P	0.30570699999999995	D;P;D	0.89917	1.0;0.802;0.999	D;B;D	0.83275	0.996;0.206;0.994	T	0.06991	-1.0796	8	0.26408	T	0.33	-9.3925	10.7584	0.46251	0.1902:0.8098:0.0:0.0	.	106;106;106	G5E9D1;Q8NEL9;Q8NEL9-2	.;DDHD1_HUMAN;.	A	106	.	ENSP00000327104:G106A	G	-	2	0	DDHD1	52689250	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.008000	0.40893	1.914000	0.55421	0.455000	0.32223	GGT	C|0.928;G|0.072	0.072	strong		0.706	DDHD1-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276901.1		
CFHR5	81494	hgsc.bcm.edu	37	1	196952092	196952092	+	Missense_Mutation	SNP	C	C	T	rs12097550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:196952092C>T	ENST00000256785.4	+	2	245	c.136C>T	c.(136-138)Cct>Tct	p.P46S	CFHR5_ENST00000367414.5_Missense_Mutation_p.P70S			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	46	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		P -> S (in dbSNP:rs12097550).		complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						TTCCCAAGTTCCTACAGGGGA	0.368													C|||	45	0.00898562	0.0234	0.0072	5008	,	,		5095	0.0		0.008	False		,,,				2504	0.001				p.P46S		Atlas-SNP	.											.	CFHR5	150	.	0			c.C136T	GRCh37	CM062506	CFHR5	M	rs12097550	PASS	.	C	SER/PRO	79,4327		1,77,2125	109.0	109.0	109.0		136	-4.4	0.0	1	dbSNP_120	109	68,8532		0,68,4232	yes	missense	CFHR5	NM_030787.3	74	1,145,6357	TT,TC,CC		0.7907,1.793,1.1302	benign	46/570	196952092	147,12859	2203	4300	6503	SO:0001583	missense	81494	exon2			CAAGTTCCTACAG	AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"""Complement system"""	24668	protein-coding gene	gene with protein product	"""factor H related protein 5"""	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.136C>T	1.37:g.196952092C>T	ENSP00000256785:p.Pro46Ser	Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	260	103	0.396154	NM_030787	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	23	0.010531135531135532	15	0.03048780487804878	3	0.008287292817679558	0	0.0	5	0.006596306068601583	.	9.935	1.215822	0.22373	0.01793	0.007907	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.62941	-0.01;-0.01	2.45	-4.39	0.03611	Complement control module (2);Sushi/SCR/CCP (2);	.	.	.	.	T	0.13670	0.0331	N	0.12182	0.205	0.09310	N	1	B	0.20368	0.044	B	0.29353	0.101	T	0.24764	-1.0151	9	0.07030	T	0.85	.	4.5807	0.12257	0.0:0.337:0.3968:0.2663	rs12097550;rs52820460;rs12097550	46	Q9BXR6	FHR5_HUMAN	S	70;46	ENSP00000356384:P70S;ENSP00000256785:P46S	ENSP00000256785:P46S	P	+	1	0	CFHR5	195218715	0.000000	0.05858	0.001000	0.08648	0.417000	0.31264	-2.774000	0.00777	-0.970000	0.03569	0.305000	0.20034	CCT	C|0.986;T|0.014	0.014	strong		0.368	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787	
LAMA5	3911	hgsc.bcm.edu	37	20	60913127	60913127	+	Silent	SNP	A	A	G	rs8124907	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60913127A>G	ENST00000252999.3	-	14	1902	c.1836T>C	c.(1834-1836)gcT>gcC	p.A612A		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	612	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			AATGAGGTCCAGCAAACTCAG	0.652													G|||	1177	0.235024	0.3427	0.1686	5008	,	,		19473	0.2054		0.2455	False		,,,				2504	0.1564				p.A612A		Atlas-SNP	.											LAMA5,NS,carcinoma,0,3	LAMA5	268	3	0			c.T1836C						scavenged	.	G		1436,2966	650.5+/-399.1	230,976,995	38.0	37.0	37.0		1836	-10.1	0.0	20	dbSNP_116	37	1971,6617	699.9+/-405.1	236,1499,2559	no	coding-synonymous	LAMA5	NM_005560.3		466,2475,3554	GG,GA,AA		22.9506,32.6215,26.2279		612/3696	60913127	3407,9583	2201	4294	6495	SO:0001819	synonymous_variant	3911	exon14			AGGTCCAGCAAAC	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.1836T>C	20.37:g.60913127A>G		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			A|0.749;G|0.251	0.251	strong		0.652	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
DSPP	1834	hgsc.bcm.edu	37	4	88537035	88537035	+	Missense_Mutation	SNP	A	A	G	rs202210195		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537035A>G	ENST00000282478.7	+	4	3254	c.3221A>G	c.(3220-3222)gAc>gGc	p.D1074G	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1074G			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1074	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)		gacagcagtgacagcagcgac	0.542																																					p.D1074G		Atlas-SNP	.											DSPP,NS,carcinoma,-1,1	DSPP	174	1	0			c.A3221G						scavenged	.						58.0	65.0	62.0					4																	88537035		1567	2848	4415	SO:0001583	missense	1834	exon5			GCAGTGACAGCAG	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.3221A>G	4.37:g.88537035A>G	ENSP00000282478:p.Asp1074Gly	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	109	38	0.348624	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	a	3.083	-0.188481	0.06299	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.88741	-2.42;-2.42	1.51	1.51	0.23008	.	.	.	.	.	D	0.83468	0.5261	L	0.34521	1.04	0.58432	P	4.000000000004E-6	D	0.58620	0.983	P	0.48598	0.583	T	0.81771	-0.0780	8	0.48119	T	0.1	.	5.1866	0.15187	1.0:0.0:0.0:0.0	.	1074	Q9NZW4	DSPP_HUMAN	G	1074	ENSP00000382213:D1074G;ENSP00000282478:D1074G	ENSP00000282478:D1074G	D	+	2	0	DSPP	88756059	0.407000	0.25352	0.138000	0.22173	0.004000	0.04260	1.380000	0.34351	0.963000	0.38082	0.242000	0.17961	GAC	.	.	weak		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
TG	7038	hgsc.bcm.edu	37	8	133899575	133899575	+	Missense_Mutation	SNP	G	G	A	rs2069548	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:133899575G>A	ENST00000220616.4	+	9	1998	c.1958G>A	c.(1957-1959)gGt>gAt	p.G653D	TG_ENST00000377869.1_Missense_Mutation_p.G653D	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	653	Thyroglobulin type-1 5. {ECO:0000255|PROSITE-ProRule:PRU00500}.		G -> D (in dbSNP:rs2069548). {ECO:0000269|PubMed:10199792, ECO:0000269|PubMed:3595599, ECO:0000269|PubMed:3971976}.		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)		AGAGTCAGAGGTGGACAGCCA	0.557													G|||	18	0.00359425	0.0	0.0043	5008	,	,		19138	0.0		0.0089	False		,,,				2504	0.0061				p.G653D		Atlas-SNP	.											.	TG	416	.	0			c.G1958A						PASS	.	G	ASP/GLY	16,4390	23.3+/-48.9	0,16,2187	73.0	63.0	66.0		1958	5.6	0.5	8	dbSNP_96	66	118,8482	62.1+/-124.0	3,112,4185	yes	missense	TG	NM_003235.4	94	3,128,6372	AA,AG,GG		1.3721,0.3631,1.0303	probably-damaging	653/2769	133899575	134,12872	2203	4300	6503	SO:0001583	missense	7038	exon9			TCAGAGGTGGACA	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.1958G>A	8.37:g.133899575G>A	ENSP00000220616:p.Gly653Asp	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	151	60	0.397351	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	15.37	2.813148	0.50527	0.003631	0.013721	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	T;T	0.62941	-0.01;-0.01	5.56	5.56	0.83823	Thyroglobulin type-1 (5);	0.000000	0.64402	D	0.000011	T	0.73713	0.3622	M	0.71871	2.18	0.47862	D	0.999538	D	0.89917	1.0	D	0.91635	0.999	T	0.78814	-0.2056	10	0.72032	D	0.01	.	18.5144	0.90930	0.0:0.0:1.0:0.0	rs2069548;rs2069548	653	P01266	THYG_HUMAN	D	653	ENSP00000367100:G653D;ENSP00000220616:G653D	ENSP00000220616:G653D	G	+	2	0	TG	133968757	1.000000	0.71417	0.520000	0.27837	0.138000	0.21146	5.765000	0.68834	2.613000	0.88420	0.655000	0.94253	GGT	G|0.991;A|0.009	0.009	strong		0.557	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
CTBP2	1488	hgsc.bcm.edu	37	10	126715075	126715075	+	Intron	SNP	T	T	C	rs3781413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:126715075T>C	ENST00000337195.5	-	3	458				CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000309035.6_Silent_p.A418A|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000494626.2_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		AATAGGTGGCTGCCGTCTCCA	0.687													C|||	609	0.121605	0.1074	0.2896	5008	,	,		13999	0.0456		0.1352	False		,,,				2504	0.0859				p.A418A		Atlas-SNP	.											CTBP2,NS,carcinoma,0,1	CTBP2	100	1	0			c.A1254G						PASS	.	C	,,	411,3985		17,377,1804	28.0	26.0	27.0		,,1254	-6.0	0.0	10	dbSNP_107	27	1080,7510		61,958,3276	no	intron,intron,coding-synonymous	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,	78,1335,5080	CC,CT,TT		12.5728,9.3494,11.4816	,,	,,418/986	126715075	1491,11495	2198	4295	6493	SO:0001627	intron_variant	1488	exon1			GGTGGCTGCCGTC	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12490A>G	10.37:g.126715075T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	37	CCDS7643.1																																																																																			T|0.892;C|0.108	0.108	strong		0.687	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
SCN4A	6329	hgsc.bcm.edu	37	17	62020348	62020348	+	Missense_Mutation	SNP	T	T	C	rs2058194	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:62020348T>C	ENST00000435607.1	-	23	4202	c.4126A>G	c.(4126-4128)Aac>Gac	p.N1376D	SCN4A_ENST00000578147.1_Missense_Mutation_p.N1376D	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1376			N -> D (in dbSNP:rs2058194). {ECO:0000269|PubMed:1315496}.		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)	p.N1376D(1)		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)	TGGCTCTGGTTGTCTGTCTCC	0.532													C|||	2812	0.561502	0.7837	0.4697	5008	,	,		24608	0.5377		0.5557	False		,,,				2504	0.3569				p.N1376D		Atlas-SNP	.											SCN4A,NS,carcinoma,0,1	SCN4A	205	1	1	Substitution - Missense(1)	stomach(1)	c.A4126G						PASS	.	C	ASP/ASN	3221,1185	414.6+/-336.9	1193,835,175	224.0	209.0	214.0		4126	3.9	1.0	17	dbSNP_94	214	4574,4026	556.3+/-386.8	1265,2044,991	yes	missense	SCN4A	NM_000334.4	23	2458,2879,1166	CC,CT,TT		46.814,26.8951,40.0661	benign	1376/1837	62020348	7795,5211	2203	4300	6503	SO:0001583	missense	6329	exon23			TCTGGTTGTCTGT	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.4126A>G	17.37:g.62020348T>C	ENSP00000396320:p.Asn1376Asp	Somatic	240	1	0.00416667		WXS	Illumina HiSeq	Phase_I	220	218	0.990909	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	1282	0.586996336996337	387	0.7865853658536586	184	0.5082872928176796	289	0.5052447552447552	422	0.5567282321899736	C	8.322	0.824528	0.16678	0.731049	0.53186	ENSG00000007314	ENST00000435607	D	0.97328	-4.34	3.87	3.87	0.44632	.	0.050633	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00045	-2.445	0.48288	P	3.769999999999607E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47100	-0.9143	9	0.02654	T	1	.	11.0601	0.47942	0.0:0.9087:0.0:0.0913	rs2058194;rs52833416;rs56720134;rs2058194	1376	P35499	SCN4A_HUMAN	D	1376	ENSP00000396320:N1376D	ENSP00000396320:N1376D	N	-	1	0	SCN4A	59374080	1.000000	0.71417	0.988000	0.46212	0.969000	0.65631	4.799000	0.62517	0.993000	0.38866	-0.355000	0.07637	AAC	T|0.407;C|0.593	0.593	strong		0.532	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
OR8H1	219469	hgsc.bcm.edu	37	11	56058197	56058197	+	Silent	SNP	G	G	A	rs1842674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56058197G>A	ENST00000313022.2	-	1	369	c.342C>T	c.(340-342)ctC>ctT	p.L114L		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	114						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					CCATTGATGAGAGAAGAAAAC	0.458													g|||	2150	0.429313	0.1861	0.5072	5008	,	,		21350	0.6151		0.3708	False		,,,				2504	0.5716				p.L114L		Atlas-SNP	.											OR8H1,NS,carcinoma,-1,1	OR8H1	89	1	0			c.C342T						PASS	.	G		942,3460	359.4+/-314.8	104,734,1363	162.0	158.0	160.0		342	-2.2	0.2	11	dbSNP_92	160	3194,5398	483.8+/-371.2	611,1972,1713	no	coding-synonymous	OR8H1	NM_001005199.1		715,2706,3076	AA,AG,GG		37.1741,21.3994,31.8301		114/312	56058197	4136,8858	2201	4296	6497	SO:0001819	synonymous_variant	219469	exon1			TGATGAGAGAAGA	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"""GPCR / Class A : Olfactory receptors"""	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.342C>T	11.37:g.56058197G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_001005199	B2RNI7|Q6IFC5	Silent	SNP	ENST00000313022.2	37	CCDS31526.1																																																																																			G|0.650;A|0.350	0.350	strong		0.458	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199	
MTMR1	8776	hgsc.bcm.edu	37	X	149931106	149931106	+	Silent	SNP	C	C	T	rs16995747	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:149931106C>T	ENST00000370390.3	+	15	2059	c.1902C>T	c.(1900-1902)ggC>ggT	p.G634G	MTMR1_ENST00000541925.1_Silent_p.G540G|MTMR1_ENST00000445323.2_Silent_p.G642G|MTMR1_ENST00000544228.1_Silent_p.G634G|MTMR1_ENST00000538506.1_Intron	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	634					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GTGTGGAGGGCCTACAGCGGG	0.642													c|||	3120	0.82649	0.4781	0.696	3775	,	,		13399	0.752		0.672	False		,,,				2504	0.5838				p.G634G		Atlas-SNP	.											.	MTMR1	82	.	0			c.C1902T						PASS	.			2620,1215		776,687,381,169,190	73.0	63.0	67.0		1902	-1.2	1.0	X	dbSNP_123	67	5918,810		1880,518,1640,30,232	no	coding-synonymous	MTMR1	NM_003828.2		2656,1205,2021,199,422	TT,TC,T,CC,C		12.0392,31.6819,19.1707		634/666	149931106	8538,2025	2203	4300	6503	SO:0001819	synonymous_variant	8776	exon15			GGAGGGCCTACAG	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.1902C>T	X.37:g.149931106C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	167	163	0.976048	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Silent	SNP	ENST00000370390.3	37	CCDS14695.1																																																																																			C|0.180;0|0.003	.	strong		0.642	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789	
LCE1C	353133	hgsc.bcm.edu	37	1	152777868	152777868	+	Silent	SNP	A	A	G	rs36107483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152777868A>G	ENST00000607093.1	-	1	86	c.87T>C	c.(85-87)tgT>tgC	p.C29C	LCE1C_ENST00000368768.1_Silent_p.C29C			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	29	Pro-rich.				keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			actttgggggacactttgggg	0.647													a|||	936	0.186901	0.1672	0.2262	5008	,	,		12066	0.0347		0.3608	False		,,,				2504	0.1636				p.C29C		Atlas-SNP	.											.	LCE1C	40	.	0			c.T87C						PASS	.	A		832,3574	314.1+/-293.5	74,684,1445	48.0	49.0	49.0		87	-4.9	0.0	1	dbSNP_126	49	2897,5703	436.4+/-358.3	492,1913,1895	no	coding-synonymous	LCE1C	NM_178351.3		566,2597,3340	GG,GA,AA		33.686,18.8833,28.6714		29/119	152777868	3729,9277	2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			TGGGGGACACTTT		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"""Late cornified envelopes"""	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.87T>C	1.37:g.152777868A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	202	201	0.995049	NM_178351		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			A|0.738;G|0.262	0.262	strong		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351	
FNBP4	23360	hgsc.bcm.edu	37	11	47745696	47745696	+	Missense_Mutation	SNP	G	G	C	rs138653244	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:47745696G>C	ENST00000263773.5	-	14	2360	c.2348C>G	c.(2347-2349)tCt>tGt	p.S783C	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	783						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						AGTGGAAGAAGAACTAGAGAT	0.438													G|||	16	0.00319489	0.0	0.0014	5008	,	,		17458	0.0		0.0139	False		,,,				2504	0.001				p.S783C		Atlas-SNP	.											.	FNBP4	99	.	0			c.C2348G						PASS	.	G	CYS/SER	3,3737		0,3,1867	115.0	114.0	115.0		2348	5.3	1.0	11	dbSNP_134	115	35,8187		1,33,4077	yes	missense	FNBP4	NM_015308.2	112	1,36,5944	CC,CG,GG		0.4257,0.0802,0.3177	benign	783/1018	47745696	38,11924	1870	4111	5981	SO:0001583	missense	23360	exon14			GAAGAAGAACTAG	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.2348C>G	11.37:g.47745696G>C	ENSP00000263773:p.Ser783Cys	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	76	41	0.539474	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Missense_Mutation	SNP	ENST00000263773.5	37	CCDS41644.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	13.01	2.110675	0.37242	8.02E-4	0.004257	ENSG00000109920	ENST00000263773	T	0.50813	0.73	5.28	5.28	0.74379	.	0.535484	0.20786	N	0.085712	T	0.29190	0.0726	L	0.36672	1.1	0.20821	N	0.999849	P	0.47034	0.889	B	0.40101	0.319	T	0.31752	-0.9932	10	0.46703	T	0.11	-6.1082	10.9719	0.47444	0.0942:0.0:0.9058:0.0	.	783	Q8N3X1	FNBP4_HUMAN	C	783	ENSP00000263773:S783C	ENSP00000263773:S783C	S	-	2	0	FNBP4	47702272	1.000000	0.71417	1.000000	0.80357	0.357000	0.29423	6.483000	0.73617	2.483000	0.83821	0.561000	0.74099	TCT	G|0.995;C|0.005	0.005	strong		0.438	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
FBN2	2201	hgsc.bcm.edu	37	5	127597518	127597518	+	Silent	SNP	G	G	A	rs10070365	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:127597518G>A	ENST00000508053.1	-	70	9248	c.8274C>T	c.(8272-8274)tcC>tcT	p.S2758S	FBN2_ENST00000262464.4_Silent_p.S2758S			P35556	FBN2_HUMAN	fibrillin 2	2758					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)		ATGCTTCTGGGGACAGAGCAT	0.453													G|||	565	0.112819	0.1952	0.0865	5008	,	,		20024	0.0476		0.1243	False		,,,				2504	0.0757				p.S2758S		Atlas-SNP	.											.	FBN2	858	.	0			c.C8274T						PASS	.	G		764,3642	310.5+/-291.6	61,642,1500	233.0	198.0	210.0		8274	0.3	1.0	5	dbSNP_119	210	1038,7562	220.2+/-258.0	62,914,3324	no	coding-synonymous	FBN2	NM_001999.3		123,1556,4824	AA,AG,GG		12.0698,17.34,13.8551		2758/2913	127597518	1802,11204	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon64			TTCTGGGGACAGA	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.8274C>T	5.37:g.127597518G>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	179	79	0.441341	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			G|0.871;A|0.129	0.129	strong		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
ATIC	471	hgsc.bcm.edu	37	2	216190020	216190020	+	Missense_Mutation	SNP	C	C	G	rs2372536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:216190020C>G	ENST00000236959.9	+	5	673	c.347C>G	c.(346-348)aCt>aGt	p.T116S	ATIC_ENST00000540518.1_Missense_Mutation_p.T57S|ATIC_ENST00000435675.1_Missense_Mutation_p.T115S	NM_004044.6	NP_004035.2	P31939	PUR9_HUMAN	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase	116			T -> S (in dbSNP:rs2372536). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.7}.		'de novo' IMP biosynthetic process (GO:0006189)|brainstem development (GO:0003360)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|dihydrofolate metabolic process (GO:0046452)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|organ regeneration (GO:0031100)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to inorganic substance (GO:0010035)|small molecule metabolic process (GO:0044281)|tetrahydrofolate biosynthetic process (GO:0046654)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	IMP cyclohydrolase activity (GO:0003937)|phosphoribosylaminoimidazolecarboxamide formyltransferase activity (GO:0004643)|protein homodimerization activity (GO:0042803)		ATIC/ALK(24)	large_intestine(2)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	8		Renal(323;0.229)		Epithelial(149;2.02e-06)|all cancers(144;0.000316)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.0097)	Methotrexate(DB00563)|Pemetrexed(DB00642)|Tetrahydrofolic acid(DB00116)	CCAGGTGTAACTGTTGAGGAG	0.383			T	ALK	ALCL								C|||	1391	0.277756	0.062	0.3084	5008	,	,		13991	0.2927		0.3161	False		,,,				2504	0.4928				p.T116S		Atlas-SNP	.		Dom	yes		2	2q35	471	5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase		L	.	ATIC	84	.	0			c.C347G						PASS	.	C	SER/THR	424,3982	205.2+/-227.1	26,372,1805	111.0	111.0	111.0		347	5.9	0.9	2	dbSNP_100	111	2786,5814	441.9+/-359.9	462,1862,1976	yes	missense	ATIC	NM_004044.6	58	488,2234,3781	GG,GC,CC		32.3953,9.6232,24.6809	benign	116/593	216190020	3210,9796	2203	4300	6503	SO:0001583	missense	471	exon5			GTGTAACTGTTGA		CCDS2398.1	2q35	2010-04-27			ENSG00000138363	ENSG00000138363	2.1.2.3, 3.5.4.10		794	protein-coding gene	gene with protein product	"""phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase"""	601731				8567683, 9378707	Standard	NM_004044		Approved	PURH, AICARFT, IMPCHASE	uc002vex.4	P31939	OTTHUMG00000133023	ENST00000236959.9:c.347C>G	2.37:g.216190020C>G	ENSP00000236959:p.Thr116Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	144	77	0.534722	NM_004044	A8K202|E9PBU3|Q13856|Q53S28	Missense_Mutation	SNP	ENST00000236959.9	37	CCDS2398.1	493	0.22573260073260074	34	0.06910569105691057	103	0.2845303867403315	116	0.20279720279720279	240	0.316622691292876	C	16.25	3.070943	0.55646	0.096232	0.323953	ENSG00000138363	ENST00000236959;ENST00000540518;ENST00000435675;ENST00000413174	T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45	5.87	5.87	0.94306	Methylglyoxal synthase-like domain (4);	0.044548	0.85682	N	0.000000	T	0.00012	0.0000	L	0.49640	1.575	0.09310	P	0.99999999840034	B;B	0.06786	0.001;0.001	B;B	0.09377	0.004;0.004	T	0.04165	-1.0972	9	0.25106	T	0.35	3.42	20.1777	0.98189	0.0:1.0:0.0:0.0	rs2372536;rs3821352;rs52824931;rs2372536	115;116	E9PBU3;P31939	.;PUR9_HUMAN	S	116;57;115;57	ENSP00000236959:T116S;ENSP00000440523:T57S;ENSP00000415935:T115S;ENSP00000402393:T57S	ENSP00000236959:T116S	T	+	2	0	ATIC	215898265	1.000000	0.71417	0.921000	0.36526	0.451000	0.32288	5.856000	0.69518	2.941000	0.99782	0.655000	0.94253	ACT	C|0.763;G|0.237	0.237	strong		0.383	ATIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256610.1	NM_004044	
KIF17	57576	hgsc.bcm.edu	37	1	21031046	21031046	+	Silent	SNP	C	C	T	rs2296226	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:21031046C>T	ENST00000247986.2	-	5	1327	c.1017G>A	c.(1015-1017)ccG>ccA	p.P339P	KIF17_ENST00000400463.3_Silent_p.P339P|KIF17_ENST00000375044.1_Silent_p.P239P			Q9P2E2	KIF17_HUMAN	kinesin family member 17	339					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.P339P(1)		NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		CATTGATGCGCGGCTTGTTCC	0.602													C|||	930	0.185703	0.23	0.1354	5008	,	,		17402	0.3998		0.0507	False		,,,				2504	0.0798				p.P339P		Atlas-SNP	.											KIF17,colon,carcinoma,0,1	KIF17	130	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1017A						PASS	.	C	,	886,3520	346.2+/-308.9	103,680,1420	158.0	119.0	132.0		1017,1017	-10.5	0.1	1	dbSNP_100	132	415,8185	130.2+/-188.1	10,395,3895	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	113,1075,5315	TT,TC,CC		4.8256,20.1089,10.0031	,	339/1029,339/1030	21031046	1301,11705	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon5			GATGCGCGGCTTG	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1017G>A	1.37:g.21031046C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	240	223	0.929167	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			C|0.878;T|0.122	0.122	strong		0.602	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
NBPF15	284565	hgsc.bcm.edu	37	1	148594455	148594455	+	Missense_Mutation	SNP	A	A	G	rs1043751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:148594455A>G	ENST00000369187.3	+	19	2317	c.1828A>G	c.(1828-1830)Aga>Gga	p.R610G	NBPF15_ENST00000442702.2_Missense_Mutation_p.R610G	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	610	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					CTCACTGGATAGATGTTATTC	0.453																																					p.R610G		Atlas-SNP	.											NBPF15,NS,carcinoma,-1,1	NBPF15	20	1	0			c.A1828G						scavenged	.						193.0	250.0	231.0					1																	148594455		2203	4299	6502	SO:0001583	missense	284565	exon19			CTGGATAGATGTT	BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"""neuroblastoma breakpoint family"""	28791	protein-coding gene	gene with protein product		610414, 614005	"""neuroblastoma breakpoint family, member 16"""	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1828A>G	1.37:g.148594455A>G	ENSP00000358188:p.Arg610Gly	Somatic	297	30	0.10101		WXS	Illumina HiSeq	Phase_I	318	39	0.122642	NM_173638	Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	3.941	-0.014253	0.07681	.	.	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.07908	3.15;3.15	0.502	-0.965	0.10323	DUF1220 (2);	.	.	.	.	T	0.02083	0.0065	L	0.45470	1.425	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.44544	-0.9321	8	0.38643	T	0.18	.	.	.	.	rs1043751;rs3183409	610	Q8N660	NBPFF_HUMAN	G	610	ENSP00000416864:R610G;ENSP00000358188:R610G	ENSP00000358188:R610G	R	+	1	2	NBPF15	146861079	0.958000	0.32768	0.000000	0.03702	0.002000	0.02628	-0.245000	0.08890	-0.355000	0.08199	0.310000	0.20435	AGA	A|0.996;G|0.004	0.004	strong		0.453	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638	
TCF20	6942	hgsc.bcm.edu	37	22	42606257	42606257	+	Silent	SNP	C	C	T	rs2070116	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:42606257C>T	ENST00000359486.3	-	1	5191	c.5055G>A	c.(5053-5055)tcG>tcA	p.S1685S	TCF20_ENST00000335626.4_Silent_p.S1685S|TCF20_ENST00000404876.1_5'Flank	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1685					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						GCATAAAGGACGAGGCCGGGA	0.567													C|||	1138	0.227236	0.115	0.3228	5008	,	,		17784	0.3006		0.2286	False		,,,				2504	0.2342				p.S1685S		Atlas-SNP	.											.	TCF20	164	.	0			c.G5055A						PASS	.	C	,	589,3817	258.9+/-262.7	31,527,1645	71.0	71.0	71.0		5055,5055	-11.9	0.1	22	dbSNP_96	71	1906,6694	337.8+/-322.5	201,1504,2595	no	coding-synonymous,coding-synonymous	TCF20	NM_005650.1,NM_181492.1	,	232,2031,4240	TT,TC,CC		22.1628,13.3681,19.1835	,	1685/1961,1685/1939	42606257	2495,10511	2203	4300	6503	SO:0001819	synonymous_variant	6942	exon1			AAAGGACGAGGCC	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.5055G>A	22.37:g.42606257C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	150	76	0.506667	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Silent	SNP	ENST00000359486.3	37	CCDS14033.1																																																																																			C|0.788;T|0.212	0.212	strong		0.567	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604721	140604721	+	Silent	SNP	C	C	A	rs2910003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140604721C>A	ENST00000239449.4	+	1	1644	c.1644C>A	c.(1642-1644)cgC>cgA	p.R548R	PCDHB14_ENST00000515856.2_Silent_p.R395R	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	548	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCTGGTGCGCGTGCTGGTGC	0.711													c|||	1818	0.363019	0.6543	0.3329	5008	,	,		16379	0.1359		0.3211	False		,,,				2504	0.2679				p.R548R	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											PCDHB14,NS,carcinoma,+2,1	PCDHB14	132	1	0			c.C1644A						PASS	.						35.0	39.0	37.0					5																	140604721		2202	4297	6499	SO:0001819	synonymous_variant	56122	exon1			GGTGCGCGTGCTG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1644C>A	5.37:g.140604721C>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	124	76	0.612903	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.642;A|0.358	0.358	strong		0.711	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
POLR2B	5431	hgsc.bcm.edu	37	4	57889677	57889677	+	Silent	SNP	C	C	T	rs1056364	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:57889677C>T	ENST00000381227.1	+	20	3110	c.2697C>T	c.(2695-2697)agC>agT	p.S899S	POLR2B_ENST00000314595.5_Silent_p.S899S|POLR2B_ENST00000431623.2_Silent_p.S824S|POLR2B_ENST00000441246.2_Silent_p.S892S			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	899					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonucleoside binding (GO:0032549)	p.S899S(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(10)|large_intestine(9)|lung(17)|ovary(2)|prostate(4)|skin(1)	52	Glioma(25;0.08)|all_neural(26;0.181)					TCAGAACTAGCGAGACGGGCA	0.393													C|||	2764	0.551917	0.4637	0.6412	5008	,	,		19700	0.6786		0.5845	False		,,,				2504	0.4438				p.S899S		Atlas-SNP	.											POLR2B,NS,carcinoma,0,1	POLR2B	108	1	1	Substitution - coding silent(1)	prostate(1)	c.C2697T						PASS	.	C		2143,2263	580.5+/-385.1	518,1107,578	106.0	104.0	105.0		2697	0.9	1.0	4	dbSNP_86	105	4946,3654	622.5+/-397.3	1418,2110,772	no	coding-synonymous	POLR2B	NM_000938.1		1936,3217,1350	TT,TC,CC		42.4884,48.6382,45.4944		899/1175	57889677	7089,5917	2203	4300	6503	SO:0001819	synonymous_variant	5431	exon19			AACTAGCGAGACG		CCDS3511.1	4q12	2013-01-21	2002-08-29		ENSG00000047315	ENSG00000047315		"""RNA polymerase subunits"""	9188	protein-coding gene	gene with protein product		180661	"""polymerase (RNA) II (DNA directed) polypeptide B (140kD)"""			1518060, 8034326	Standard	NM_000938		Approved	RPB2	uc003hcl.1	P30876	OTTHUMG00000128771	ENST00000381227.1:c.2697C>T	4.37:g.57889677C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_000938	A8K1A8|Q8IZ61	Silent	SNP	ENST00000381227.1	37	CCDS3511.1																																																																																			C|0.436;T|0.564	0.564	strong		0.393	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938	
KRT40	125115	hgsc.bcm.edu	37	17	39137297	39137297	+	Missense_Mutation	SNP	C	C	T	rs721957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39137297C>T	ENST00000398486.2	-	6	954	c.794G>A	c.(793-795)tGt>tAt	p.C265Y	KRT40_ENST00000377755.4_Missense_Mutation_p.C265Y	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	265	Coil 2.|Rod.		C -> Y (in dbSNP:rs721957). {ECO:0000269|PubMed:15617563}.			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CACCGTTTCACACTGACAGCG	0.532													T|||	3475	0.69389	0.9047	0.6744	5008	,	,		21098	0.5843		0.5358	False		,,,				2504	0.6984				p.C265Y		Atlas-SNP	.											.	KRT40	27	.	0			c.G794A						PASS	.	T	TYR/CYS	3403,701		1413,577,62	173.0	180.0	178.0		794	5.4	1.0	17	dbSNP_86	178	4438,3972		1146,2146,913	yes	missense	KRT40	NM_182497.3	194	2559,2723,975	TT,TC,CC		47.2295,17.0809,37.3422	benign	265/432	39137297	7841,4673	2052	4205	6257	SO:0001583	missense	125115	exon6			GTTTCACACTGAC	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.794G>A	17.37:g.39137297C>T	ENSP00000381500:p.Cys265Tyr	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	190	90	0.473684	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	1429	0.6543040293040293	450	0.9146341463414634	233	0.643646408839779	330	0.5769230769230769	416	0.5488126649076517	T	6.643	0.487147	0.12641	0.829191	0.527705	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.81499	-1.5;-1.5	5.4	5.4	0.78164	Filament (1);	0.000000	0.30850	N	0.008758	T	0.00012	0.0000	N	0.00001	-3.685	0.40311	P	0.021287999999999974	B	0.02656	0.0	B	0.01281	0.0	T	0.46456	-0.9190	9	0.02654	T	1	.	10.8983	0.47036	0.0:0.0739:0.0:0.9261	rs721957;rs17714337	265	Q6A162	K1C40_HUMAN	Y	265	ENSP00000366984:C265Y;ENSP00000381500:C265Y	ENSP00000366984:C265Y	C	-	2	0	KRT40	36390823	1.000000	0.71417	0.977000	0.42913	0.938000	0.57974	6.219000	0.72231	0.993000	0.38866	-0.254000	0.11334	TGT	T|0.613;G|0.022	0.613	strong		0.532	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
ILVBL	10994	hgsc.bcm.edu	37	19	15227030	15227030	+	Silent	SNP	G	G	A	rs2074263	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15227030G>A	ENST00000263383.3	-	12	1543	c.1404C>T	c.(1402-1404)ggC>ggT	p.G468G	ILVBL_ENST00000534378.1_Silent_p.G361G	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	468						integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CGAAGTCCCCGCCATCCACCA	0.657													G|||	3164	0.631789	0.7269	0.6427	5008	,	,		17892	0.5417		0.7147	False		,,,				2504	0.5031				p.G468G		Atlas-SNP	.											.	ILVBL	54	.	0			c.C1404T						PASS	.	G		3097,1307	695.0+/-405.9	1089,919,194	117.0	99.0	105.0		1404	-10.4	0.2	19	dbSNP_96	105	6174,2426	697.0+/-404.9	2208,1758,334	no	coding-synonymous	ILVBL	NM_006844.3		3297,2677,528	AA,AG,GG		28.2093,29.6776,28.7066		468/633	15227030	9271,3733	2202	4300	6502	SO:0001819	synonymous_variant	10994	exon12			GTCCCCGCCATCC	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"""acetolactate synthase homolog"""	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1404C>T	19.37:g.15227030G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	82	47	0.573171	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Silent	SNP	ENST00000263383.3	37	CCDS12325.1																																																																																			G|0.293;A|0.707	0.707	strong		0.657	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844	
NLRP5	126206	hgsc.bcm.edu	37	19	56539240	56539240	+	Silent	SNP	C	C	T	rs397977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56539240C>T	ENST00000390649.3	+	7	1641	c.1641C>T	c.(1639-1641)gaC>gaT	p.D547D		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	547	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.D547D(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		CAGTGTTTGACGGTGACGACC	0.547													C|||	1740	0.347444	0.1316	0.4366	5008	,	,		18759	0.3571		0.4235	False		,,,				2504	0.4877				p.D547D		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - coding silent(1)	stomach(1)	c.C1641T						PASS	.	C		816,3442		98,620,1411	59.0	62.0	61.0		1641	-4.4	0.0	19	dbSNP_80	61	3833,4665		889,2055,1305	no	coding-synonymous	NLRP5	NM_153447.4		987,2675,2716	TT,TC,CC		45.1047,19.1639,36.4456		547/1201	56539240	4649,8107	2129	4249	6378	SO:0001819	synonymous_variant	126206	exon7			GTTTGACGGTGAC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1641C>T	19.37:g.56539240C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	136	74	0.544118	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			C|0.671;N|0.000	.	strong		0.547	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
KPRP	448834	hgsc.bcm.edu	37	1	152732436	152732436	+	Silent	SNP	G	G	C	rs4845480	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152732436G>C	ENST00000606109.1	+	1	400	c.372G>C	c.(370-372)gcG>gcC	p.A124A	KPRP_ENST00000368773.1_Silent_p.A124A			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	124	Gln-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGTGCGAAGCGTCACAACCTG	0.502													C|||	2456	0.490415	0.5787	0.4914	5008	,	,		23278	0.4187		0.5159	False		,,,				2504	0.4182				p.A124A		Atlas-SNP	.											KPRP,NS,carcinoma,+1,1	KPRP	152	1	0			c.G372C						PASS	.	C		2439,1967	554.9+/-379.1	676,1087,440	259.0	245.0	250.0		372	-0.8	0.0	1	dbSNP_111	250	4322,4278	575.7+/-390.3	1096,2130,1074	no	coding-synonymous	KPRP	NM_001025231.1		1772,3217,1514	CC,CG,GG		49.7442,44.6437,48.0163		124/580	152732436	6761,6245	2203	4300	6503	SO:0001819	synonymous_variant	448834	exon2			CGAAGCGTCACAA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.372G>C	1.37:g.152732436G>C		Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	241	237	0.983402	NM_001025231		Silent	SNP	ENST00000606109.1	37	CCDS30862.1																																																																																			G|0.490;C|0.510	0.510	strong		0.502	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
SCAF4	57466	hgsc.bcm.edu	37	21	33068962	33068962	+	Silent	SNP	T	T	C	rs7280330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33068962T>C	ENST00000286835.7	-	8	1261	c.879A>G	c.(877-879)gcA>gcG	p.A293A	SCAF4_ENST00000399804.1_Silent_p.A293A|SCAF4_ENST00000434667.3_Silent_p.A278A	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	293						nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A293A(1)		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						CAGGGGGTACTGCGGCAGCAG	0.532													t|||	721	0.14397	0.1785	0.1167	5008	,	,		13024	0.0784		0.1839	False		,,,				2504	0.1431				p.A293A		Atlas-SNP	.											SCAF4,NS,carcinoma,0,2	SCAF4	142	2	1	Substitution - coding silent(1)	stomach(1)	c.A879G						PASS	.	T	,,	745,3661	306.0+/-289.3	61,623,1519	92.0	92.0	92.0		834,879,879	-7.6	0.0	21	dbSNP_116	92	1636,6964	302.2+/-305.8	162,1312,2826	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAF4	NM_001145444.1,NM_001145445.1,NM_020706.2	,,	223,1935,4345	CC,CT,TT		19.0233,16.9088,18.3069	,,	278/1133,293/1126,293/1148	33068962	2381,10625	2203	4300	6503	SO:0001819	synonymous_variant	57466	exon8			GGGTACTGCGGCA	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.879A>G	21.37:g.33068962T>C		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	36	0.356436	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																			T|0.831;C|0.169	0.169	strong		0.532	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
CPM	1368	hgsc.bcm.edu	37	12	69265578	69265578	+	Silent	SNP	A	A	G	rs2228654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:69265578A>G	ENST00000551568.1	-	4	477	c.417T>C	c.(415-417)taT>taC	p.Y139Y	CPM_ENST00000546373.1_Silent_p.Y139Y|CPM_ENST00000338356.3_Silent_p.Y139Y	NM_001005502.2|NM_198320.3	NP_001005502.1|NP_938079.1	P14384	CBPM_HUMAN	carboxypeptidase M	139					anatomical structure morphogenesis (GO:0009653)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)|prostate(2)	9	all_epithelial(5;1.09e-35)|Lung NSC(4;1.47e-33)|all_lung(4;1.02e-31)|Breast(13;1.59e-06)		all cancers(2;2.69e-50)|GBM - Glioblastoma multiforme(2;7.34e-41)|BRCA - Breast invasive adenocarcinoma(5;5.38e-10)|Lung(24;4.61e-05)|LUAD - Lung adenocarcinoma(15;0.000376)|STAD - Stomach adenocarcinoma(21;0.00372)|Kidney(9;0.143)			CGATGCTGTAATAACAGTCAG	0.463													A|||	2459	0.491014	0.3124	0.5879	5008	,	,		23224	0.5179		0.5825	False		,,,				2504	0.5419				p.Y139Y		Atlas-SNP	.											.	CPM	30	.	0			c.T417C						PASS	.	A	,,	1504,2902	480.6+/-358.9	254,996,953	160.0	146.0	151.0		417,417,417	1.5	0.8	12	dbSNP_98	151	4972,3628	625.1+/-397.7	1430,2112,758	no	coding-synonymous,coding-synonymous,coding-synonymous	CPM	NM_001005502.2,NM_001874.4,NM_198320.3	,,	1684,3108,1711	GG,GA,AA		42.186,34.1353,49.7924	,,	139/444,139/444,139/444	69265578	6476,6530	2203	4300	6503	SO:0001819	synonymous_variant	1368	exon4			GCTGTAATAACAG	AF368463	CCDS8987.1	12q15	2012-02-10			ENSG00000135678	ENSG00000135678	3.4.17.12		2311	protein-coding gene	gene with protein product	"""renal carboxypeptidase"", ""urinary carboxypeptidase B"""	114860				8586455	Standard	NM_001874		Approved		uc001suq.3	P14384	OTTHUMG00000169300	ENST00000551568.1:c.417T>C	12.37:g.69265578A>G		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	182	79	0.434066	NM_001005502	B2R800|Q9H2K9	Silent	SNP	ENST00000551568.1	37	CCDS8987.1																																																																																			T|0.108;G|0.403	0.403	strong		0.463	CPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403355.1	NM_198320	
NUP133	55746	hgsc.bcm.edu	37	1	229631734	229631734	+	Missense_Mutation	SNP	T	T	C	rs11805194	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:229631734T>C	ENST00000261396.3	-	7	971	c.880A>G	c.(880-882)Atc>Gtc	p.I294V	NUP133_ENST00000537506.1_Missense_Mutation_p.I278V	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	294			I -> V (in dbSNP:rs11805194).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.I294V(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				CATTTACTGATGTTTGAACTC	0.368													T|||	1062	0.212061	0.2617	0.3012	5008	,	,		18607	0.1577		0.2068	False		,,,				2504	0.1431				p.I294V		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - Missense(1)	stomach(1)	c.A880G						PASS	.	T	VAL/ILE	1097,3309	392.1+/-328.4	134,829,1240	104.0	100.0	101.0		880	1.7	1.0	1	dbSNP_120	101	1818,6782	324.6+/-316.5	191,1436,2673	yes	missense	NUP133	NM_018230.2	29	325,2265,3913	CC,CT,TT		21.1395,24.8979,22.4127	benign	294/1157	229631734	2915,10091	2203	4300	6503	SO:0001583	missense	55746	exon7			TACTGATGTTTGA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.880A>G	1.37:g.229631734T>C	ENSP00000261396:p.Ile294Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	451	0.2065018315018315	122	0.24796747967479674	93	0.2569060773480663	80	0.13986013986013987	156	0.20580474934036938	T	12.64	1.999786	0.35320	0.248979	0.211395	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.60424	0.19;0.19;0.19	5.57	1.67	0.24075	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.164275	0.52532	D	0.000067	T	0.00012	0.0000	L	0.41236	1.265	0.31397	P	0.677155	B	0.06786	0.001	B	0.06405	0.002	T	0.11155	-1.0599	9	0.30854	T	0.27	-22.3481	3.4333	0.07436	0.0942:0.1504:0.1651:0.5903	rs11805194;rs17756650;rs52814082;rs61334161;rs11805194	294	Q8WUM0	NU133_HUMAN	V	294;294;294;278	ENSP00000261396:I294V;ENSP00000355640:I294V;ENSP00000443496:I278V	ENSP00000261396:I294V	I	-	1	0	NUP133	227698357	0.960000	0.32886	0.982000	0.44146	0.917000	0.54804	0.306000	0.19279	0.408000	0.25621	0.528000	0.53228	ATC	C|0.213;N|0.000	0.213	strong		0.368	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110397780	110397780	+	Missense_Mutation	SNP	A	A	G	rs62508075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110397780A>G	ENST00000378402.5	+	6	594	c.490A>G	c.(490-492)Atc>Gtc	p.I164V		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	164	IPT/TIG 2.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ACTAATAACAATCCAAGGCAG	0.323										HNSCC(38;0.096)			A|||	65	0.0129792	0.0038	0.0202	5008	,	,		15871	0.0		0.0378	False		,,,				2504	0.0082				p.I164V		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A490G						PASS	.	A	VAL/ILE	44,3558		1,42,1758	58.0	56.0	57.0		490	5.6	1.0	8	dbSNP_129	57	389,7739		13,363,3688	yes	missense	PKHD1L1	NM_177531.4	29	14,405,5446	GG,GA,AA		4.7859,1.2215,3.6914	benign	164/4244	110397780	433,11297	1801	4064	5865	SO:0001583	missense	93035	exon6			ATAACAATCCAAG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.490A>G	8.37:g.110397780A>G	ENSP00000367655:p.Ile164Val	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	43	0.019688644688644688	4	0.008130081300813009	8	0.022099447513812154	0	0.0	31	0.040897097625329816	A	9.419	1.082586	0.20309	0.012215	0.047859	ENSG00000205038	ENST00000378402	T	0.64260	-0.09	5.58	5.58	0.84498	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.234810	0.37906	N	0.001891	T	0.16471	0.0396	N	0.20483	0.58	0.27144	N	0.961579	D	0.53462	0.96	P	0.50570	0.644	T	0.19844	-1.0293	10	0.22706	T	0.39	.	13.699	0.62597	1.0:0.0:0.0:0.0	rs62508075	164	Q86WI1	PKHL1_HUMAN	V	164	ENSP00000367655:I164V	ENSP00000367655:I164V	I	+	1	0	PKHD1L1	110466956	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.483000	0.45233	2.129000	0.65627	0.454000	0.30748	ATC	A|0.975;G|0.025	0.025	strong		0.323	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
SUGCT	79783	hgsc.bcm.edu	37	7	40899967	40899967	+	Silent	SNP	G	G	C	rs2010706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:40899967G>C	ENST00000335693.4	+	14	1250	c.1227G>C	c.(1225-1227)ccG>ccC	p.P409P	C7orf10_ENST00000401647.2_Silent_p.P361P|C7orf10_ENST00000309930.5_Silent_p.P435P|C7orf10_ENST00000464028.1_3'UTR	NM_001193313.1	NP_001180242.1	Q9HAC7	SUCHY_HUMAN		409					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						GGCCGCCCCCGCTGCTCGGGC	0.577																																					p.P435P		Atlas-SNP	.											.	C7orf10	99	.	0			c.G1305C						PASS	.	C	,,,	903,3287		119,665,1311	99.0	109.0	106.0		1305,1083,1227,1194	2.2	1.0	7	dbSNP_92	106	2887,5565		519,1849,1858	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C7orf10	NM_001193311.1,NM_001193312.1,NM_001193313.1,NM_024728.2	,,,	638,2514,3169	CC,CG,GG		34.1576,21.5513,29.9794	,,,	435/472,361/398,409/446,398/435	40899967	3790,8852	2095	4226	6321	SO:0001819	synonymous_variant	79783	exon15			GCCCCCGCTGCTC																												ENST00000335693.4:c.1227G>C	7.37:g.40899967G>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	136	135	0.992647	NM_001193311	A4D1W5|B4DR73|Q4KMW4|Q4KMW8|Q4KMZ0|Q8TE00|Q8TEY1	Silent	SNP	ENST00000335693.4	37	CCDS55105.1																																																																																			G|0.556;C|0.444	0.444	strong		0.577	C7orf10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338388.1		
APOL2	23780	hgsc.bcm.edu	37	22	36624231	36624231	+	Missense_Mutation	SNP	C	C	T	rs118097350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:36624231C>T	ENST00000249066.6	-	6	709	c.233G>A	c.(232-234)aGg>aAg	p.R78K	APOL2_ENST00000358502.5_Missense_Mutation_p.R78K|APOL2_ENST00000451256.2_Missense_Mutation_p.R190K	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	78					acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						AAACCACTGCCTGTGCTGCTG	0.507													N|||	15	0.00299521	0.0	0.0101	5008	,	,		21603	0.0		0.007	False		,,,				2504	0.001				p.R78K		Atlas-SNP	.											APOL2,NS,carcinoma,0,1	APOL2	20	1	0			c.G233A						PASS	.	C	LYS/ARG,LYS/ARG	14,4360	19.1+/-41.9	0,14,2173	145.0	156.0	152.0		233,233	-4.6	0.0	22	dbSNP_132	152	76,8504	42.6+/-100.3	0,76,4214	yes	missense,missense	APOL2	NM_030882.2,NM_145637.1	26,26	0,90,6387	TT,TC,CC		0.8858,0.3201,0.6948	probably-damaging,probably-damaging	78/338,78/338	36624231	90,12864	2187	4290	6477	SO:0001583	missense	23780	exon5			CACTGCCTGTGCT	AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"""Apolipoproteins"""	619	protein-coding gene	gene with protein product	"""apolipoprotein L-II"""	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.233G>A	22.37:g.36624231C>T	ENSP00000249066:p.Arg78Lys	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	48	0.551724	NM_030882	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Missense_Mutation	SNP	ENST00000249066.6	37	CCDS43014.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	14.98	2.697046	0.48202	0.003201	0.008858	ENSG00000128335	ENST00000358502;ENST00000249066;ENST00000451256;ENST00000529194	T;T;T;T	0.03181	4.02;4.02;4.02;4.02	3.66	-4.57	0.03421	.	1.131670	0.06466	N	0.730265	T	0.03220	0.0094	L	0.38692	1.165	0.09310	N	1	D;D	0.57571	0.98;0.966	P;P	0.58928	0.814;0.848	T	0.37079	-0.9721	10	0.11182	T	0.66	.	1.0007	0.01476	0.1629:0.2418:0.161:0.4343	.	190;78	B4E1T5;Q9BQE5	.;APOL2_HUMAN	K	78;78;190;78	ENSP00000351292:R78K;ENSP00000249066:R78K;ENSP00000403153:R190K;ENSP00000431231:R78K	ENSP00000249066:R78K	R	-	2	0	APOL2	34954177	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.584000	0.02114	-0.497000	0.06641	0.411000	0.27672	AGG	C|0.994;T|0.006	0.006	strong		0.507	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637	
OR6S1	341799	hgsc.bcm.edu	37	14	21108909	21108909	+	Silent	SNP	G	G	A	rs17277515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21108909G>A	ENST00000320704.3	-	1	941	c.942C>T	c.(940-942)ggC>ggT	p.G314G		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, member 1	314						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)		TCCCTAAAACGCCTGCCACTA	0.353													G|||	480	0.0958466	0.0545	0.1585	5008	,	,		20731	0.0704		0.0785	False		,,,				2504	0.1513				p.G314G		Atlas-SNP	.											.	OR6S1	49	.	0			c.C942T						PASS	.	G		240,4166	140.8+/-176.2	6,228,1969	145.0	144.0	145.0		942	-0.9	0.0	14	dbSNP_123	145	867,7733	197.3+/-242.0	42,783,3475	no	coding-synonymous	OR6S1	NM_001001968.1		48,1011,5444	AA,AG,GG		10.0814,5.4471,8.5115		314/332	21108909	1107,11899	2203	4300	6503	SO:0001819	synonymous_variant	341799	exon1			TAAAACGCCTGCC	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.942C>T	14.37:g.21108909G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	179	64	0.357542	NM_001001968	Q6IFJ9	Silent	SNP	ENST00000320704.3	37	CCDS32038.1																																																																																			A|0.090;C|0.000;G|0.910	0.090	strong		0.353	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1		
CES3	23491	hgsc.bcm.edu	37	16	67006838	67006838	+	Silent	SNP	G	G	A	rs3848289	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67006838G>A	ENST00000303334.4	+	13	1673	c.1602G>A	c.(1600-1602)cgG>cgA	p.R534R	CES3_ENST00000394037.1_Silent_p.R531R|CES3_ENST00000543856.1_Silent_p.R173R	NM_024922.5	NP_079198.2	Q6UWW8	EST3_HUMAN	carboxylesterase 3	534						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	carboxylic ester hydrolase activity (GO:0052689)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(3)|skin(1)	24		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0488)|Epithelial(162;0.127)		CAGTGCCACGGGCCGGACAGA	0.572													G|||	216	0.043131	0.0015	0.0836	5008	,	,		19260	0.0675		0.0527	False		,,,				2504	0.0358				p.R534R		Atlas-SNP	.											.	CES3	56	.	0			c.G1602A						PASS	.	G	,,	54,4346	52.9+/-88.7	0,54,2146	89.0	88.0	88.0		519,1593,1602	-7.4	0.0	16	dbSNP_108	88	419,8181	130.8+/-188.7	11,397,3892	no	coding-synonymous,coding-synonymous,coding-synonymous	CES3	NM_001185176.1,NM_001185177.1,NM_024922.5	,,	11,451,6038	AA,AG,GG		4.8721,1.2273,3.6385	,,	173/211,531/569,534/572	67006838	473,12527	2200	4300	6500	SO:0001819	synonymous_variant	23491	exon13			GCCACGGGCCGGA	AK025389	CCDS10826.1, CCDS54022.1, CCDS54023.1	16q22.1	2014-05-13	2008-07-25		ENSG00000172828	ENSG00000172828		"""Carboxylesterases"""	1865	protein-coding gene	gene with protein product	"""esterase 31"", ""brain carboxylesterase BR3"""	605279	"""carboxylesterase 3 (brain)"""			10518925, 14581373, 15100172, 20931200	Standard	NM_001185176		Approved	FLJ21736, ES31	uc002eqt.3	Q6UWW8	OTTHUMG00000137525	ENST00000303334.4:c.1602G>A	16.37:g.67006838G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	152	79	0.519737	NM_024922	B2Z3W9|F5H242|Q7Z6J1|Q9H6X7	Silent	SNP	ENST00000303334.4	37	CCDS10826.1																																																																																			G|0.955;A|0.045	0.045	strong		0.572	CES3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268848.1	NM_024922	
RAVER1	125950	hgsc.bcm.edu	37	19	10431799	10431799	+	Silent	SNP	G	G	T	rs281425	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10431799G>T	ENST00000293677.6	-	8	1530	c.1449C>A	c.(1447-1449)ccC>ccA	p.P483P	CTD-2369P2.12_ENST00000586529.1_5'Flank	NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	466						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			CCACAGGGGCGGGGGGAGGAG	0.736													G|||	1073	0.214257	0.3086	0.1801	5008	,	,		12960	0.1012		0.2256	False		,,,				2504	0.2157				p.P483P		Atlas-SNP	.											.	RAVER1	67	.	0			c.C1449A						PASS	.	G		462,2062		41,380,841	2.0	2.0	2.0		1449	-7.2	0.3	19	dbSNP_79	2	1100,4946		110,880,2033	no	coding-synonymous	RAVER1	NM_133452.2		151,1260,2874	TT,TG,GG		18.1938,18.3043,18.2264		483/757	10431799	1562,7008	1262	3023	4285	SO:0001819	synonymous_variant	125950	exon8			AGGGGCGGGGGGA		CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"""RNA binding motif (RRM) containing"""	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.1449C>A	19.37:g.10431799G>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	12	11	0.916667	NM_133452	A6NMU4|Q8IY60|Q8TF24	Silent	SNP	ENST00000293677.6	37	CCDS45960.1																																																																																			G|0.798;T|0.202	0.202	strong		0.736	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	
PTPRB	5787	hgsc.bcm.edu	37	12	71002893	71002893	+	Missense_Mutation	SNP	C	C	T	rs2252784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:71002893C>T	ENST00000261266.5	-	2	310	c.281G>A	c.(280-282)aGg>aAg	p.R94K	PTPRB_ENST00000551525.1_Missense_Mutation_p.R311K|PTPRB_ENST00000334414.6_Missense_Mutation_p.R312K|PTPRB_ENST00000451516.2_Missense_Mutation_p.R94K|PTPRB_ENST00000550358.1_Missense_Mutation_p.R312K|PTPRB_ENST00000538708.1_Missense_Mutation_p.R94K|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550857.1_Missense_Mutation_p.R94K	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	94	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> K (in dbSNP:rs2252784). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2170109}.		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)			AGAAATAATCCTGAAGTTATA	0.502													T|||	2961	0.591254	0.7663	0.5173	5008	,	,		19491	0.5982		0.4085	False		,,,				2504	0.5879				p.R312K		Atlas-SNP	.											.	PTPRB	676	.	0			c.G935A						PASS	.	T	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	2537,1261		857,823,219	140.0	150.0	146.0		935,281,281,281	-1.7	0.9	12	dbSNP_100	146	3259,4973		626,2007,1483	yes	missense,missense,missense,missense	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	26,26,26,26	1483,2830,1702	TT,TC,CC		39.5894,33.2017,48.1796	benign,benign,benign,benign	312/2216,94/1908,94/1908,94/1998	71002893	5796,6234	1899	4116	6015	SO:0001583	missense	5787	exon4			ATAATCCTGAAGT	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.281G>A	12.37:g.71002893C>T	ENSP00000261266:p.Arg94Lys	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	254	106	0.417323	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	1209	0.5535714285714286	375	0.7621951219512195	166	0.4585635359116022	353	0.6171328671328671	315	0.4155672823218997	T	5.326	0.245474	0.10077	0.667983	0.395894	ENSG00000127329	ENST00000334414;ENST00000451516;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000550857;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T;T;T	0.59364	0.27;0.27;0.27;0.27;0.27;0.27;0.27;0.27	4.75	-1.74	0.08056	Fibronectin, type III (3);	0.345695	0.25601	N	0.029557	T	0.00012	0.0000	M	0.67953	2.075	0.58432	P	2.9999999999752447E-6	B;B;B;B;B;B;B;B	0.19073	0.0;0.0;0.002;0.033;0.004;0.005;0.002;0.002	B;B;B;B;B;B;B;B	0.28553	0.002;0.004;0.007;0.091;0.005;0.011;0.011;0.012	T	0.46456	-0.9190	9	0.06494	T	0.89	.	7.8294	0.29334	0.0:0.478:0.314:0.208	rs2252784;rs17846472;rs17859530;rs52826132;rs60646468;rs2252784	94;94;191;312;311;312;94;312	P23467-2;F5H3G6;Q6ZR19;Q6ZTX7;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;.;.;PTPRB_HUMAN;.	K	312;94;312;312;94;94;94;311;191	ENSP00000334928:R312K;ENSP00000393028:R94K;ENSP00000448058:R312K;ENSP00000438927:R94K;ENSP00000447302:R94K;ENSP00000261266:R94K;ENSP00000448349:R311K;ENSP00000446982:R191K	ENSP00000261266:R94K	R	-	2	0	PTPRB	69289160	0.781000	0.28676	0.917000	0.36280	0.930000	0.56654	0.019000	0.13444	-0.540000	0.06265	-0.889000	0.02933	AGG	C|0.424;T|0.576	0.576	strong		0.502	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
NALCN	259232	hgsc.bcm.edu	37	13	101747984	101747984	+	Silent	SNP	G	G	A	rs9513851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:101747984G>A	ENST00000251127.6	-	28	3291	c.3210C>T	c.(3208-3210)aaC>aaT	p.N1070N		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1070					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)					TTAAATTTAAGTTCTTTGACA	0.363													G|||	311	0.0621006	0.0681	0.0418	5008	,	,		16207	0.0347		0.0447	False		,,,				2504	0.1145				p.N1070N		Atlas-SNP	.											.	NALCN	431	.	0			c.C3210T						PASS	.	G		313,4093	166.5+/-197.7	9,295,1899	77.0	82.0	80.0		3210	1.1	1.0	13	dbSNP_119	80	549,8049	150.4+/-205.3	18,513,3768	no	coding-synonymous	NALCN	NM_052867.2		27,808,5667	AA,AG,GG		6.3852,7.1039,6.6287		1070/1739	101747984	862,12142	2203	4299	6502	SO:0001819	synonymous_variant	259232	exon28			ATTTAAGTTCTTT	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.3210C>T	13.37:g.101747984G>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	52	21	0.403846	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			G|0.939;A|0.061	0.061	strong		0.363	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
LAMA5	3911	hgsc.bcm.edu	37	20	60903419	60903419	+	Silent	SNP	C	C	T	rs7262393	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60903419C>T	ENST00000252999.3	-	35	4596	c.4530G>A	c.(4528-4530)ctG>ctA	p.L1510L		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1510	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCTGGCACAGCAGGCAGTCGG	0.682													C|||	924	0.184505	0.2458	0.1542	5008	,	,		15666	0.1062		0.2306	False		,,,				2504	0.1564				p.L1510L		Atlas-SNP	.											LAMA5,colon,carcinoma,0,1	LAMA5	268	1	0			c.G4530A						PASS	.	C		1187,3181		154,879,1151	20.0	21.0	21.0		4530	0.2	0.0	20	dbSNP_116	21	1850,6724		196,1458,2633	no	coding-synonymous	LAMA5	NM_005560.3		350,2337,3784	TT,TC,CC		21.5769,27.1749,23.4662		1510/3696	60903419	3037,9905	2184	4287	6471	SO:0001819	synonymous_variant	3911	exon35			GCACAGCAGGCAG	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.4530G>A	20.37:g.60903419C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	76	42	0.552632	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.782;T|0.218	0.218	strong		0.682	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
BRCA2	675	hgsc.bcm.edu	37	13	32914126	32914126	+	Missense_Mutation	SNP	C	C	G	rs80358784		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32914126C>G	ENST00000380152.3	+	11	5867	c.5634C>G	c.(5632-5634)aaC>aaG	p.N1878K	BRCA2_ENST00000544455.1_Missense_Mutation_p.N1878K			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1878					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)		AGGAAAACAACGAGAATAAAT	0.323			"""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)																											p.N1878K	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.C5634G						PASS	.						44.0	43.0	43.0					13																	32914126		2203	4300	6503	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AAACAACGAGAAT	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.5634C>G	13.37:g.32914126C>G	ENSP00000369497:p.Asn1878Lys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	4.413	0.076344	0.08485	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.68181	-0.31;-0.31	5.71	-5.99	0.02213	.	0.505217	0.19599	N	0.110421	T	0.29588	0.0738	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.14578	0.011	T	0.32903	-0.9889	10	0.12766	T	0.61	.	0.9378	0.01348	0.3907:0.1216:0.2013:0.2864	.	1878	P51587	BRCA2_HUMAN	K	1878	ENSP00000369497:N1878K;ENSP00000439902:N1878K	ENSP00000369497:N1878K	N	+	3	2	BRCA2	31812126	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.132000	0.10467	-1.353000	0.02191	-0.295000	0.09555	AAC	C|0.999;T|0.001	.	weak		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
PFAS	5198	hgsc.bcm.edu	37	17	8166458	8166458	+	Missense_Mutation	SNP	T	T	A	rs35217368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8166458T>A	ENST00000314666.6	+	13	1575	c.1442T>A	c.(1441-1443)tTt>tAt	p.F481Y	PFAS_ENST00000545834.1_Missense_Mutation_p.F57Y|PFAS_ENST00000585319.1_3'UTR	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	481			F -> Y (in dbSNP:rs35217368).		'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	GACCTGGACTTTGGGGCTGTG	0.582													T|||	154	0.0307508	0.0023	0.0548	5008	,	,		18309	0.0		0.1034	False		,,,				2504	0.0092				p.F481Y		Atlas-SNP	.											.	PFAS	91	.	0			c.T1442A						PASS	.	T	TYR/PHE	60,4346	57.4+/-93.9	2,56,2145	114.0	114.0	114.0		1442	4.8	0.8	17	dbSNP_126	114	617,7983	161.0+/-214.0	25,567,3708	yes	missense	PFAS	NM_012393.2	22	27,623,5853	AA,AT,TT		7.1744,1.3618,5.2053	benign	481/1339	8166458	677,12329	2203	4300	6503	SO:0001583	missense	5198	exon13			TGGACTTTGGGGC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.1442T>A	17.37:g.8166458T>A	ENSP00000313490:p.Phe481Tyr	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	51	25	0.490196	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	103	0.04716117216117216	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	79	0.10422163588390501	T	14.99	2.699938	0.48307	0.013618	0.071744	ENSG00000178921	ENST00000545834;ENST00000314666	T;T	0.32272	1.46;1.46	5.91	4.82	0.62117	AIR synthase-related protein, C-terminal (2);	0.184978	0.48286	N	0.000195	T	0.01320	0.0043	M	0.86953	2.85	0.44302	D	0.997172	B;B	0.21309	0.003;0.054	B;B	0.28638	0.007;0.092	T	0.01468	-1.1347	10	0.66056	D	0.02	-8.494	10.2394	0.43303	0.1602:0.0:0.0:0.8398	rs35217368	57;481	F5GWT9;O15067	.;PUR4_HUMAN	Y	57;481	ENSP00000441706:F57Y;ENSP00000313490:F481Y	ENSP00000313490:F481Y	F	+	2	0	PFAS	8107183	1.000000	0.71417	0.813000	0.32504	0.921000	0.55340	3.439000	0.52878	1.022000	0.39626	0.533000	0.62120	TTT	T|0.955;A|0.045	0.045	strong		0.582	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
CLSTN2	64084	hgsc.bcm.edu	37	3	140178485	140178485	+	Missense_Mutation	SNP	G	G	A	rs7632885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:140178485G>A	ENST00000458420.3	+	7	1286	c.1096G>A	c.(1096-1098)Gtc>Atc	p.V366I	RP11-68L1.2_ENST00000503357.1_RNA|RP11-68L1.1_ENST00000483759.2_RNA	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	366			V -> I (in dbSNP:rs7632885). {ECO:0000269|PubMed:12498782, ECO:0000269|PubMed:12972431, ECO:0000269|Ref.5}.		homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GGGTGCCAAAGTCCCCGATGG	0.577										HNSCC(16;0.037)			A|||	2666	0.532348	0.6112	0.4265	5008	,	,		19051	0.502		0.5944	False		,,,				2504	0.4683				p.V366I	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G1096A						PASS	.	A	ILE/VAL	2582,1824	533.3+/-373.7	744,1094,365	82.0	70.0	74.0		1096	4.2	1.0	3	dbSNP_116	74	5209,3391	501.9+/-375.6	1606,1997,697	yes	missense	CLSTN2	NM_022131.2	29	2350,3091,1062	AA,AG,GG		39.4302,41.3981,40.0969	benign	366/956	140178485	7791,5215	2203	4300	6503	SO:0001583	missense	64084	exon7			GCCAAAGTCCCCG	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.1096G>A	3.37:g.140178485G>A	ENSP00000402460:p.Val366Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	1202	0.5503663003663004	295	0.5995934959349594	162	0.44751381215469616	293	0.5122377622377622	452	0.5963060686015831	A	2.739	-0.262611	0.05754	0.586019	0.605698	ENSG00000158258	ENST00000458420	T	0.74209	-0.82	5.4	4.25	0.50352	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.178921	0.47852	N	0.000210	T	0.00012	0.0000	N	0.03917	-0.325	0.48040	P	4.210000000000047E-4	B	0.02656	0.0	B	0.04013	0.001	T	0.47018	-0.9149	9	0.10902	T	0.67	-15.312	8.393	0.32540	0.8373:0.0:0.1627:0.0	rs7632885;rs13090511;rs16850312;rs52798163;rs60628243;rs7632885	366	Q9H4D0	CSTN2_HUMAN	I	366	ENSP00000402460:V366I	ENSP00000402460:V366I	V	+	1	0	CLSTN2	141661175	1.000000	0.71417	0.999000	0.59377	0.739000	0.42172	2.225000	0.42954	0.369000	0.24510	-0.269000	0.10298	GTC	G|0.425;A|0.574	0.574	strong		0.577	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
SMYD3	64754	hgsc.bcm.edu	37	1	246078851	246078851	+	Missense_Mutation	SNP	C	C	T	rs61762672	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:246078851C>T	ENST00000388985.4	-	8	793	c.794G>A	c.(793-795)cGt>cAt	p.R265H	SMYD3_ENST00000490107.1_Missense_Mutation_p.R206H|SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000541742.1_Missense_Mutation_p.R206H			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	265					cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		GGTTTGGCAACGGAAACAGTC	0.488													C|||	5	0.000998403	0.0	0.0029	5008	,	,		17129	0.0		0.003	False		,,,				2504	0.0				p.R265H		Atlas-SNP	.											.	SMYD3	77	.	0			c.G794A						PASS	.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	145.0	120.0	128.0		794,617	5.0	0.2	1	dbSNP_129	128	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense	SMYD3	NM_001167740.1,NM_022743.2	29,29	0,13,6490	TT,TC,CC		0.1395,0.0227,0.1	probably-damaging,probably-damaging	265/429,206/370	246078851	13,12993	2203	4300	6503	SO:0001583	missense	64754	exon8			TGGCAACGGAAAC	AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	15513	protein-coding gene	gene with protein product		608783	"""zinc finger, MYND domain containing 1"""	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.794G>A	1.37:g.246078851C>T	ENSP00000373637:p.Arg265His	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	103	43	0.417476	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	16.78	3.217791	0.58560	2.27E-4	0.001395	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000544586;ENST00000388985;ENST00000391836	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.97	5.03	0.67393	.	0.287715	0.33438	N	0.004906	T	0.31765	0.0807	L	0.28400	0.85	0.20489	N	0.999892	D;D	0.89917	1.0;1.0	P;D	0.69142	0.865;0.962	T	0.09796	-1.0658	10	0.37606	T	0.19	-18.4741	12.7104	0.57086	0.1631:0.8369:0.0:0.0	rs61762672	265;76	Q9H7B4;B3KN46	SMYD3_HUMAN;.	H	206;206;95;265;76	ENSP00000444184:R206H;ENSP00000419184:R206H;ENSP00000373637:R265H;ENSP00000375712:R76H	ENSP00000373637:R265H	R	-	2	0	SMYD3	244145474	0.032000	0.19561	0.156000	0.22583	0.785000	0.44390	0.472000	0.22116	2.836000	0.97738	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.488	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743	
NCAPH	23397	hgsc.bcm.edu	37	2	97030247	97030247	+	Missense_Mutation	SNP	T	T	C	rs2305935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:97030247T>C	ENST00000240423.4	+	13	1659	c.1616T>C	c.(1615-1617)gTa>gCa	p.V539A	NCAPH_ENST00000427946.1_Missense_Mutation_p.V403A|NCAPH_ENST00000455200.1_Missense_Mutation_p.V528A	NM_001281710.1|NM_001281711.1|NM_015341.3	NP_001268639.1|NP_001268640.1|NP_056156.2	Q15003	CND2_HUMAN	non-SMC condensin I complex, subunit H	539			V -> A (in dbSNP:rs2305935). {ECO:0000269|PubMed:15489334}.		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.V539A(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(717;0.0221)				GGCCATAGGGTAGAGACTGAG	0.398													C|||	1908	0.38099	0.2806	0.3184	5008	,	,		21877	0.2758		0.3221	False		,,,				2504	0.7301				p.V539A		Atlas-SNP	.											NCAPH,NS,carcinoma,0,1	NCAPH	67	1	1	Substitution - Missense(1)	stomach(1)	c.T1616C						PASS	.	C	ALA/VAL	1249,3157	704.7+/-407.2	179,891,1133	85.0	78.0	80.0		1616	4.2	0.0	2	dbSNP_100	80	2881,5719	672.7+/-403.0	508,1865,1927	yes	missense	NCAPH	NM_015341.3	64	687,2756,3060	CC,CT,TT		33.5,28.3477,31.7546	benign	539/742	97030247	4130,8876	2203	4300	6503	SO:0001583	missense	23397	exon13			ATAGGGTAGAGAC	BC024211	CCDS2021.1, CCDS62960.1	2q11.2	2008-02-05	2006-09-04	2006-09-04	ENSG00000121152	ENSG00000121152			1112	protein-coding gene	gene with protein product		602332	"""barren (Drosophila) homolog"", ""barren homolog (Drosophila)"", ""barren homolog 1 (Drosophila)"""	BRRN1		9417923	Standard	NM_015341		Approved	CAP-H, hCAP-H	uc002svz.1	Q15003	OTTHUMG00000130451	ENST00000240423.4:c.1616T>C	2.37:g.97030247T>C	ENSP00000240423:p.Val539Ala	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_015341	B4E189|Q8TB87	Missense_Mutation	SNP	ENST00000240423.4	37	CCDS2021.1	633	0.28983516483516486	129	0.2621951219512195	113	0.31215469613259667	147	0.256993006993007	244	0.32189973614775724	C	0.833	-0.744640	0.03065	0.283477	0.335	ENSG00000121152	ENST00000240423;ENST00000427946;ENST00000435975;ENST00000455200	T;T;T;T	0.38722	1.12;1.12;1.12;1.12	5.03	4.16	0.48862	.	0.414407	0.26828	N	0.022283	T	0.00012	0.0000	N	0.01410	-0.885	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38222	-0.9671	9	0.07990	T	0.79	-1.1494	9.5907	0.39543	0.0:0.8296:0.0:0.1704	rs2305935;rs17856718;rs56707886;rs2305935	528;539	E9PHA2;Q15003	.;CND2_HUMAN	A	539;403;528;528	ENSP00000240423:V539A;ENSP00000400774:V403A;ENSP00000405237:V528A;ENSP00000407308:V528A	ENSP00000240423:V539A	V	+	2	0	NCAPH	96393974	0.336000	0.24757	0.001000	0.08648	0.125000	0.20455	2.566000	0.45948	0.742000	0.32697	-0.733000	0.03571	GTA	T|0.688;C|0.312	0.312	strong		0.398	NCAPH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252842.2	NM_015341	
ZNF407	55628	hgsc.bcm.edu	37	18	72346701	72346701	+	Silent	SNP	T	T	C	rs146635665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:72346701T>C	ENST00000299687.5	+	1	3726	c.3726T>C	c.(3724-3726)ggT>ggC	p.G1242G	ZNF407_ENST00000577538.1_Silent_p.G1242G|ZNF407_ENST00000582337.1_Silent_p.G1242G|ZNF407_ENST00000309902.6_Silent_p.G1242G	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1242					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)		ACGGTGGAGGTGTTGTCCCCC	0.537													T|||	15	0.00299521	0.0	0.0058	5008	,	,		17029	0.0		0.007	False		,,,				2504	0.0041				p.G1242G		Atlas-SNP	.											.	ZNF407	231	.	0			c.T3726C						PASS	.	T	,,	5,4097		0,5,2046	53.0	61.0	58.0		3726,3726,3726	-6.3	0.0	18	dbSNP_134	58	48,8320		0,48,4136	yes	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	0,53,6182	CC,CT,TT		0.5736,0.1219,0.425	,,	1242/1816,1242/1661,1242/2249	72346701	53,12417	2051	4184	6235	SO:0001819	synonymous_variant	55628	exon1			TGGAGGTGTTGTC	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.3726T>C	18.37:g.72346701T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	58	27	0.465517	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			T|0.997;C|0.003	0.003	strong		0.537	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
MAP1A	4130	hgsc.bcm.edu	37	15	43817404	43817404	+	Missense_Mutation	SNP	G	G	A	rs71471869|rs12912505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43817404G>A	ENST00000300231.5	+	4	4183	c.3733G>A	c.(3733-3735)Gat>Aat	p.D1245N	MAP1A_ENST00000382031.1_Missense_Mutation_p.D1483N|MAP1A_ENST00000399453.1_Missense_Mutation_p.D1245N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1245			D -> N (in dbSNP:rs12912505).		microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GCAGGCCGAGGATACCTCTCA	0.547													G|||	520	0.103834	0.0764	0.1037	5008	,	,		18864	0.001		0.1918	False		,,,				2504	0.1564				p.D1245N		Atlas-SNP	.											.	MAP1A	189	.	0			c.G3733A						PASS	.	G	ASN/ASP	332,3964		13,306,1829	95.0	110.0	105.0		3733	4.0	1.0	15	dbSNP_121	105	1600,6872		144,1312,2780	yes	missense	MAP1A	NM_002373.5	23	157,1618,4609	AA,AG,GG		18.8857,7.7281,15.1316	probably-damaging	1245/2804	43817404	1932,10836	2148	4236	6384	SO:0001583	missense	4130	exon4			GCCGAGGATACCT	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3733G>A	15.37:g.43817404G>A	ENSP00000300231:p.Asp1245Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	127	55	0.433071	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	237	0.10851648351648352	44	0.08943089430894309	43	0.11878453038674033	0	0.0	150	0.19788918205804748	G	7.442	0.640845	0.14386	0.077281	0.188857	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01584	4.75;4.75;4.75	4.98	4.03	0.46877	.	.	.	.	.	T	0.00012	0.0000	M	0.76574	2.34	0.38761	P	0.04566999999999999	P	0.44139	0.827	P	0.46758	0.526	T	0.59936	-0.7360	8	0.24483	T	0.36	-19.2726	15.0151	0.71578	0.0:0.1543:0.8457:0.0	rs12912505;rs60405560;rs12912505	1245	P78559	MAP1A_HUMAN	N	1483;1245;1245	ENSP00000371462:D1483N;ENSP00000382380:D1245N;ENSP00000300231:D1245N	ENSP00000300231:D1245N	D	+	1	0	MAP1A	41604696	0.251000	0.23961	0.972000	0.41901	0.023000	0.10783	0.564000	0.23563	2.605000	0.88082	0.563000	0.77884	GAT	GAT|0.500;AAC|0.500	.	alt		0.547	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
GDF9	2661	hgsc.bcm.edu	37	5	132198199	132198199	+	Silent	SNP	G	G	A	rs254286	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:132198199G>A	ENST00000378673.2	-	3	1313	c.447C>T	c.(445-447)acC>acT	p.T149T	GDF9_ENST00000296875.2_Silent_p.T149T|GDF9_ENST00000464378.1_5'UTR			O60383	GDF9_HUMAN	growth differentiation factor 9	149					female gamete generation (GO:0007292)|negative regulation of cell growth (GO:0030308)|oocyte growth (GO:0001555)|positive regulation of cell proliferation (GO:0008284)|regulation of progesterone secretion (GO:2000870)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(1)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	22		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGTGTTCAACGGTAGTAATGC	0.383													G|||	2283	0.455871	0.3313	0.4885	5008	,	,		19646	0.2897		0.5994	False		,,,				2504	0.6247				p.T149T		Atlas-SNP	.											.	GDF9	50	.	0			c.C447T	GRCh37	CM056327	GDF9	M	rs254286	PASS	.	G		1582,2820	454.2+/-350.6	287,1008,906	76.0	79.0	78.0		447	-4.7	0.0	5	dbSNP_79	78	4988,3612	615.5+/-396.4	1439,2110,751	no	coding-synonymous	GDF9	NM_005260.3		1726,3118,1657	AA,AG,GG		42.0,35.9382,49.4693		149/455	132198199	6570,6432	2201	4300	6501	SO:0001819	synonymous_variant	2661	exon2			TTCAACGGTAGTA		CCDS4162.1, CCDS75299.1	5q31.1	2014-01-30			ENSG00000164404	ENSG00000164404		"""Endogenous ligands"""	4224	protein-coding gene	gene with protein product		601918				7760846	Standard	NM_005260		Approved		uc003kxz.1	O60383	OTTHUMG00000059842	ENST00000378673.2:c.447C>T	5.37:g.132198199G>A		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_005260	Q4VAW5	Silent	SNP	ENST00000378673.2	37	CCDS4162.1																																																																																			G|0.516;A|0.484	0.484	strong		0.383	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260	
CELA1	1990	hgsc.bcm.edu	37	12	51737562	51737562	+	Missense_Mutation	SNP	T	T	C	rs17860300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51737562T>C	ENST00000293636.1	-	3	215	c.175A>G	c.(175-177)Atg>Gtg	p.M59V		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	59	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		M -> V (in dbSNP:rs17860300).		exocrine pancreas development (GO:0031017)|inflammatory response (GO:0006954)|multicellular organism growth (GO:0035264)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas morphogenesis (GO:0061113)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15						GCAGCTGTCATCACCCAGTTC	0.507													T|||	720	0.14377	0.0809	0.1772	5008	,	,		19403	0.0417		0.2873	False		,,,				2504	0.1626				p.M59V		Atlas-SNP	.											CELA1,NS,carcinoma,+2,1	CELA1	39	1	0			c.A175G						PASS	.	T	VAL/MET	524,3882	237.1+/-249.0	26,472,1705	59.0	50.0	53.0		175	-0.8	1.0	12	dbSNP_123	53	2666,5934	425.1+/-354.9	418,1830,2052	yes	missense	CELA1	NM_001971.5	21	444,2302,3757	CC,CT,TT		31.0,11.8929,24.5271	benign	59/259	51737562	3190,9816	2203	4300	6503	SO:0001583	missense	1990	exon3			CTGTCATCACCCA		CCDS8812.1	12q13	2012-10-02	2009-05-05	2009-05-05	ENSG00000139610	ENSG00000139610			3308	protein-coding gene	gene with protein product		130120	"""elastase 1, pancreatic"""	ELA1			Standard	NM_001971		Approved		uc001ryi.1	Q9UNI1	OTTHUMG00000167523	ENST00000293636.1:c.175A>G	12.37:g.51737562T>C	ENSP00000293636:p.Met59Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	37	CCDS8812.1	328	0.15018315018315018	42	0.08536585365853659	69	0.19060773480662985	19	0.033216783216783216	198	0.2612137203166227	T	12.72	2.021611	0.35701	0.118929	0.31	ENSG00000139610	ENST00000293636	D	0.91945	-2.94	5.03	-0.799	0.10901	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.246105	0.43260	N	0.000592	T	0.00012	0.0000	N	0.01686	-0.76	0.26678	P	0.9715944	B	0.14805	0.011	B	0.19148	0.024	T	0.15723	-1.0427	9	0.15066	T	0.55	-12.8783	3.4045	0.07336	0.1286:0.0785:0.3914:0.4014	rs17860300	59	Q9UNI1	CELA1_HUMAN	V	59	ENSP00000293636:M59V	ENSP00000293636:M59V	M	-	1	0	CELA1	50023829	0.027000	0.19231	0.998000	0.56505	0.995000	0.86356	-0.007000	0.12810	0.013000	0.14918	0.523000	0.50628	ATG	T|0.788;C|0.212	0.212	strong		0.507	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971	
MICA	100507436	hgsc.bcm.edu	37	6	31379931	31379931	+	Missense_Mutation	SNP	G	G	A	rs1063635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31379931G>A	ENST00000449934.2	+	4	875	c.821G>A	c.(820-822)cGa>cAa	p.R274Q	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				AGGATTTGCCGAGGAGAGGAG	0.602													a|||	2921	0.583267	0.7519	0.6196	5008	,	,		19002	0.4226		0.5089	False		,,,				2504	0.5716				p.R274Q		Atlas-SNP	.											.	MICA	21	.	0			c.G821A						PASS	.						20.0	19.0	19.0					6																	31379931		692	1591	2283	SO:0001583	missense	100507436	exon4			TTTGCCGAGGAGA	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.821G>A	6.37:g.31379931G>A	ENSP00000413079:p.Arg274Gln	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	N	0.751	-0.772915	0.02951	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.02763	4.17;4.17	2.72	-0.104	0.13605	.	0.817674	0.09786	N	0.756012	T	0.00496	0.0016	.	.	.	0.80722	P	0.0	B;B	0.18610	0.029;0.009	B;B	0.14023	0.01;0.003	T	0.46911	-0.9157	8	0.21540	T	0.41	.	1.3364	0.02145	0.2905:0.4047:0.1327:0.1721	rs1063635;rs16899611;rs17794659;rs17845523;rs17858413;rs17884605;rs1063635	136;274	Q5SS58;Q96QC4	.;.	Q	136;274;231;274;165	ENSP00000413079:R274Q;ENSP00000402410:R165Q	ENSP00000365394:R274Q	R	+	2	0	MICA	31487910	0.000000	0.05858	0.012000	0.15200	0.088000	0.18126	-0.399000	0.07250	-0.066000	0.12998	-0.621000	0.04028	CGA	G|0.488;A|0.512	0.512	strong		0.602	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CUBN	8029	hgsc.bcm.edu	37	10	17113563	17113563	+	Silent	SNP	C	C	T	rs1801225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:17113563C>T	ENST00000377833.4	-	19	2552	c.2487G>A	c.(2485-2487)tcG>tcA	p.S829S		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	829	CUB 4. {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)	GAAAAAAAGGCGAGCGAATGA	0.408													c|||	1783	0.35603	0.0552	0.4827	5008	,	,		13947	0.5407		0.3966	False		,,,				2504	0.4407				p.S829S		Atlas-SNP	.											.	CUBN	515	.	0			c.G2487A						PASS	.	T		477,3929	223.9+/-240.3	24,429,1750	70.0	72.0	72.0		2487	-10.9	0.0	10	dbSNP_89	72	3889,4711	543.6+/-384.4	871,2147,1282	no	coding-synonymous	CUBN	NM_001081.3		895,2576,3032	TT,TC,CC		45.2209,10.8261,33.5691		829/3624	17113563	4366,8640	2203	4300	6503	SO:0001819	synonymous_variant	8029	exon19			AAAAGGCGAGCGA	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.2487G>A	10.37:g.17113563C>T		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	27	18	0.666667	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			C|0.657;T|0.343	0.343	strong		0.408	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MARCH10	162333	hgsc.bcm.edu	37	17	60813627	60813627	+	Silent	SNP	G	G	A	rs2041283	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:60813627G>A	ENST00000311269.5	-	6	1876	c.1602C>T	c.(1600-1602)aaC>aaT	p.N534N	RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000583600.1_Silent_p.N572N|RP11-156L14.1_ENST00000577270.1_RNA|RP11-156L14.1_ENST00000579201.1_RNA|MARCH10_ENST00000456609.2_Silent_p.N534N|RP11-156L14.1_ENST00000582564.1_RNA|MARCH10_ENST00000544856.2_Silent_p.N533N	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	534					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						CGTGTGCACTGTTTACTGGGA	0.448													G|||	1359	0.271366	0.1309	0.3876	5008	,	,		18880	0.2083		0.4215	False		,,,				2504	0.2894				p.N534N		Atlas-SNP	.											.	MARCH10	102	.	0			c.C1602T						PASS	.	G	,	821,3585	324.2+/-298.5	86,649,1468	91.0	95.0	93.0		1602,1602	0.6	0.0	17	dbSNP_94	93	3387,5213	498.5+/-374.8	714,1959,1627	no	coding-synonymous,coding-synonymous	MARCH10	NM_001100875.1,NM_152598.2	,	800,2608,3095	AA,AG,GG		39.3837,18.6337,32.3543	,	534/809,534/809	60813627	4208,8798	2203	4300	6503	SO:0001819	synonymous_variant	162333	exon6			TGCACTGTTTACT	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.1602C>T	17.37:g.60813627G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	103	65	0.631068	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Silent	SNP	ENST00000311269.5	37	CCDS11635.1																																																																																			G|0.692;A|0.308	0.308	strong		0.448	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
GRM7	2917	hgsc.bcm.edu	37	3	7620168	7620168	+	Silent	SNP	A	A	G	rs34373930	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:7620168A>G	ENST00000357716.4	+	8	1849	c.1575A>G	c.(1573-1575)ctA>ctG	p.L525L	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000486284.1_Silent_p.L525L|GRM7_ENST00000403881.1_Silent_p.L525L|GRM7_ENST00000402647.2_Silent_p.L525L|GRM7_ENST00000389336.4_Silent_p.L525L	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	525					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TGTGCACACTACCATGTAAGC	0.463													A|||	854	0.170527	0.0552	0.2565	5008	,	,		19770	0.1379		0.2932	False		,,,				2504	0.1728				p.L525L		Atlas-SNP	.											.	GRM7	223	.	0			c.A1575G						PASS	.	A	,	371,4035	187.1+/-213.8	16,339,1848	104.0	100.0	102.0		1575,1575	0.8	0.2	3	dbSNP_126	102	2397,6203	399.2+/-346.4	339,1719,2242	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	355,2058,4090	GG,GA,AA		27.8721,8.4203,21.2825	,	525/916,525/923	7620168	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			CACACTACCATGT	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1575A>G	3.37:g.7620168A>G		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	209	107	0.511962	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			A|0.788;G|0.212	0.212	strong		0.463	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
CRYL1	51084	hgsc.bcm.edu	37	13	21063524	21063524	+	Silent	SNP	A	A	G	rs14236	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:21063524A>G	ENST00000298248.7	-	3	323	c.261T>C	c.(259-261)ggT>ggC	p.G87G	CRYL1_ENST00000480748.1_5'UTR|CRYL1_ENST00000382812.1_Silent_p.G65G	NM_015974.2	NP_057058.2	Q9Y2S2	CRYL1_HUMAN	crystallin, lambda 1	87					fatty acid metabolic process (GO:0006631)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|L-gulonate 3-dehydrogenase activity (GO:0050104)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)			NS(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(29;2.27e-23)|all_epithelial(30;1.69e-19)|all_lung(29;8.29e-18)|Lung SC(185;0.0262)|Ovarian(182;0.0827)|Hepatocellular(188;0.244)		all cancers(112;6.6e-05)|Epithelial(112;0.00178)|OV - Ovarian serous cystadenocarcinoma(117;0.0169)|Lung(94;0.0215)|GBM - Glioblastoma multiforme(144;0.0402)|LUSC - Lung squamous cell carcinoma(192;0.061)		TGTGCATGGCACCCTCTACTG	0.562											OREG0022283	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1354	0.270367	0.5008	0.1988	5008	,	,		18630	0.1389		0.2217	False		,,,				2504	0.1953				p.G87G		Atlas-SNP	.											CRYL1,mouth,carcinoma,-1,1	CRYL1	28	1	0			c.T261C						PASS	.	G		1698,2352		341,1016,668	81.0	88.0	86.0		261	3.8	1.0	13	dbSNP_107	86	1906,6462		215,1476,2493	no	coding-synonymous	CRYL1	NM_015974.2		556,2492,3161	GG,GA,AA		22.7772,41.9259,29.0224		87/320	21063524	3604,8814	2025	4184	6209	SO:0001819	synonymous_variant	51084	exon3			CATGGCACCCTCT	AF077049	CCDS41871.1	13q11	2008-07-18			ENSG00000165475	ENSG00000165475			18246	protein-coding gene	gene with protein product	"""crystallin, lamda 1"", ""L-gulonate 3-dehydrogenase"", ""lambda-crystallin homolog"""	609877				12527201	Standard	NM_015974		Approved	GDH, lambda-CRY, MGC149525, MGC149526	uc001une.3	Q9Y2S2	OTTHUMG00000016516	ENST00000298248.7:c.261T>C	13.37:g.21063524A>G		Somatic	58	0	0	745	WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_015974	A0PJ43|B3KN92|Q0VDI1|Q7Z4Z9|Q9P0G7	Silent	SNP	ENST00000298248.7	37	CCDS41871.1																																																																																			A|0.737;G|0.263	0.263	strong		0.562	CRYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044071.1	NM_015974	
CFAP46	54777	hgsc.bcm.edu	37	10	134680921	134680921	+	Silent	SNP	A	A	G	rs141926275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134680921A>G	ENST00000368586.5	-	34	4801	c.4701T>C	c.(4699-4701)ccT>ccC	p.P1567P		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CAGGCTGGACAGGAAGTGTCT	0.537													a|||	145	0.0289537	0.0703	0.0144	5008	,	,		16426	0.002		0.0139	False		,,,				2504	0.0266				p.P1567P		Atlas-SNP	.											.	TTC40	100	.	0			c.T4701C						PASS	.																																			SO:0001819	synonymous_variant	54777	exon34			CTGGACAGGAAGT																												ENST00000368586.5:c.4701T>C	10.37:g.134680921A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	152	71	0.467105	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			A|0.985;G|0.015	0.015	strong		0.537	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
KCNA5	3741	hgsc.bcm.edu	37	12	5155046	5155046	+	Missense_Mutation	SNP	G	G	A	rs12720445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:5155046G>A	ENST00000252321.3	+	1	1962	c.1733G>A	c.(1732-1734)aGg>aAg	p.R578K		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	578			R -> K (in dbSNP:rs12720445).		atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|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 membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	AGTGCCCGAAGGGGCAGCTGC	0.637													G|||	16	0.00319489	0.0	0.0043	5008	,	,		18223	0.0		0.0119	False		,,,				2504	0.001				p.R578K		Atlas-SNP	.											.	KCNA5	138	.	0			c.G1733A						PASS	.	G	LYS/ARG	15,4391	17.9+/-39.9	0,15,2188	32.0	35.0	34.0		1733	4.8	1.0	12	dbSNP_126	34	80,8520	40.8+/-97.7	0,80,4220	yes	missense	KCNA5	NM_002234.2	26	0,95,6408	AA,AG,GG		0.9302,0.3404,0.7304	benign	578/614	5155046	95,12911	2203	4300	6503	SO:0001583	missense	3741	exon1			CCCGAAGGGGCAG	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.1733G>A	12.37:g.5155046G>A	ENSP00000252321:p.Arg578Lys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	37	CCDS8536.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	G	7.570	0.666578	0.14710	0.003404	0.009302	ENSG00000130037	ENST00000252321	D	0.97404	-4.37	4.76	4.76	0.60689	.	0.285392	0.25830	U	0.028022	D	0.91088	0.7195	L	0.42245	1.32	0.23095	N	0.998303	B	0.06786	0.001	B	0.06405	0.002	T	0.79619	-0.1728	10	0.15066	T	0.55	.	8.84	0.35135	0.1699:0.0:0.8301:0.0	rs12720445;rs45438698	578	P22460	KCNA5_HUMAN	K	578	ENSP00000252321:R578K	ENSP00000252321:R578K	R	+	2	0	KCNA5	5025307	0.859000	0.29813	0.980000	0.43619	0.141000	0.21300	1.243000	0.32767	2.486000	0.83907	0.561000	0.74099	AGG	G|0.993;A|0.007	0.007	strong		0.637	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
IL22RA1	58985	hgsc.bcm.edu	37	1	24447468	24447468	+	Missense_Mutation	SNP	G	G	C	rs3795299	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:24447468G>C	ENST00000270800.1	-	7	1590	c.1552C>G	c.(1552-1554)Cgt>Ggt	p.R518G		NM_021258.3	NP_067081.2	Q8N6P7	I22R1_HUMAN	interleukin 22 receptor, alpha 1	518			R -> G (in dbSNP:rs3795299). {ECO:0000269|PubMed:10875937, ECO:0000269|PubMed:14702039}.		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)		GAACATGGACGGGAAGGAGGT	0.627													G|||	2335	0.466254	0.2874	0.4035	5008	,	,		19250	0.7252		0.3996	False		,,,				2504	0.5542				p.R518G		Atlas-SNP	.											.	IL22RA1	62	.	0			c.C1552G						PASS	.	G	GLY/ARG	1339,3067	446.7+/-348.1	218,903,1082	82.0	71.0	75.0		1552	4.2	0.2	1	dbSNP_107	75	3507,5093	511.1+/-377.6	723,2061,1516	yes	missense	IL22RA1	NM_021258.3	125	941,2964,2598	CC,CG,GG		40.7791,30.3904,37.2597	benign	518/575	24447468	4846,8160	2203	4300	6503	SO:0001583	missense	58985	exon7			ATGGACGGGAAGG	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.1552C>G	1.37:g.24447468G>C	ENSP00000270800:p.Arg518Gly	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	165	16	0.0969697	NM_021258	A8K839|B2R9Y9|Q9HB22	Missense_Mutation	SNP	ENST00000270800.1	37	CCDS247.1	961	0.440018315018315	140	0.2845528455284553	127	0.35082872928176795	407	0.7115384615384616	287	0.3786279683377309	G	7.672	0.687230	0.14973	0.303904	0.407791	ENSG00000142677	ENST00000270800	T	0.08282	3.11	5.17	4.24	0.50183	.	1.536800	0.03697	N	0.248041	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.27416	0.178	B	0.22386	0.039	T	0.36578	-0.9742	9	0.27082	T	0.32	-1.3849	11.3002	0.49300	0.0:0.1921:0.8079:0.0	rs3795299;rs17256862;rs3795299	518	Q8N6P7	I22R1_HUMAN	G	518	ENSP00000270800:R518G	ENSP00000270800:R518G	R	-	1	0	IL22RA1	24320055	0.973000	0.33851	0.173000	0.22940	0.006000	0.05464	1.837000	0.39201	1.394000	0.46624	0.650000	0.86243	CGT	G|0.599;C|0.401	0.401	strong		0.627	IL22RA1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008412.1		
ATXN1	6310	hgsc.bcm.edu	37	6	16327330	16327330	+	Silent	SNP	T	T	C	rs2075974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:16327330T>C	ENST00000244769.4	-	8	2148	c.1212A>G	c.(1210-1212)gaA>gaG	p.E404E	ATXN1_ENST00000436367.1_Silent_p.E404E	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	404					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)				AAGGGGAGGCTTCACGATGAG	0.617													C|||	1849	0.369209	0.4569	0.2075	5008	,	,		17432	0.4772		0.2147	False		,,,				2504	0.4131				p.E404E		Atlas-SNP	.											.	ATXN1	117	.	0			c.A1212G						PASS	.	C	,	1908,2498	627.3+/-394.9	401,1106,696	163.0	180.0	174.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1212,1212	0.5	0.9	6	dbSNP_96	174	1746,6854	735.8+/-407.0	165,1416,2719	no	coding-synonymous,coding-synonymous	ATXN1	NM_000332.3,NM_001128164.1	,	566,2522,3415	CC,CT,TT		20.3023,43.3046,28.0947	,	404/816,404/816	16327330	3654,9352	2203	4300	6503	SO:0001819	synonymous_variant	6310	exon7			GGAGGCTTCACGA	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.1212A>G	6.37:g.16327330T>C		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Silent	SNP	ENST00000244769.4	37	CCDS34342.1																																																																																			T|0.695;C|0.305	0.305	strong		0.617	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
ABCA3	21	hgsc.bcm.edu	37	16	2348528	2348528	+	Silent	SNP	G	G	C	rs323043	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2348528G>C	ENST00000301732.5	-	15	2455	c.1755C>G	c.(1753-1755)ccC>ccG	p.P585P	ABCA3_ENST00000382381.3_Silent_p.P527P	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	585	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	GTCCACTGGTGGGGGGAAAGA	0.602													G|||	409	0.0816693	0.0507	0.1124	5008	,	,		16245	0.0198		0.1819	False		,,,				2504	0.0624				p.P585P		Atlas-SNP	.											.	ABCA3	176	.	0			c.C1755G						PASS	.	G		329,4067	173.4+/-203.2	10,309,1879	60.0	59.0	60.0		1755	-12.3	0.0	16	dbSNP_79	60	1702,6898	309.0+/-309.2	173,1356,2771	no	coding-synonymous	ABCA3	NM_001089.2		183,1665,4650	CC,CG,GG		19.7907,7.4841,15.6279		585/1705	2348528	2031,10965	2198	4300	6498	SO:0001819	synonymous_variant	21	exon15			ACTGGTGGGGGGA	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.1755C>G	16.37:g.2348528G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	91	49	0.538462	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			G|0.858;C|0.142	0.142	strong		0.602	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
DNAH7	56171	hgsc.bcm.edu	37	2	196825256	196825256	+	Silent	SNP	G	G	C	rs115124743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:196825256G>C	ENST00000312428.6	-	18	2719	c.2619C>G	c.(2617-2619)gtC>gtG	p.V873V		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	873	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						AAAAAGAGGAGACTGTGGAGT	0.448													G|||	94	0.01877	0.0045	0.0389	5008	,	,		19851	0.0		0.0507	False		,,,				2504	0.0102				p.V873V		Atlas-SNP	.											.	DNAH7	512	.	0			c.C2619G						PASS	.	G		30,3736		0,30,1853	105.0	103.0	104.0		2619	2.4	0.8	2	dbSNP_132	104	347,7895		8,331,3782	no	coding-synonymous	DNAH7	NM_018897.2		8,361,5635	CC,CG,GG		4.2101,0.7966,3.1396		873/4025	196825256	377,11631	1883	4121	6004	SO:0001819	synonymous_variant	56171	exon18			AGAGGAGACTGTG	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.2619C>G	2.37:g.196825256G>C		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	163	74	0.453988	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			G|0.969;C|0.031	0.031	strong		0.448	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
OR51B6	390058	hgsc.bcm.edu	37	11	5373646	5373646	+	Silent	SNP	T	T	C	rs5024041	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373646T>C	ENST00000380219.1	+	1	909	c.909T>C	c.(907-909)cgT>cgC	p.R303R	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	303					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GCATACTTCGTTTATTCTCTC	0.413													C|||	3023	0.603634	0.5764	0.5692	5008	,	,		20475	0.5466		0.6054	False		,,,				2504	0.7219				p.R303R		Atlas-SNP	.											OR51B6,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	OR51B6	53	1	0			c.T909C						PASS	.	C		2551,1849	483.7+/-359.8	736,1079,385	87.0	88.0	88.0		909	-1.1	0.0	11	dbSNP_113	88	5122,3468	490.7+/-372.9	1520,2082,693	no	coding-synonymous	OR51B6	NM_001004750.1		2256,3161,1078	CC,CT,TT		40.3725,42.0227,40.9315		303/313	5373646	7673,5317	2200	4295	6495	SO:0001819	synonymous_variant	390058	exon1			ACTTCGTTTATTC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.909T>C	11.37:g.5373646T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			T|0.407;C|0.593	0.593	strong		0.413	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
DNAJC5B	85479	hgsc.bcm.edu	37	8	66992737	66992737	+	Silent	SNP	G	G	A	rs7006209	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:66992737G>A	ENST00000276570.5	+	5	746	c.459G>A	c.(457-459)gtG>gtA	p.V153V	DNAJC5B_ENST00000519330.1_3'UTR	NM_033105.4	NP_149096.2	Q9UF47	DNJ5B_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5 beta	153						membrane (GO:0016020)				endometrium(3)|large_intestine(6)|liver(1)|lung(6)|prostate(1)|skin(3)	20		Lung NSC(129;0.114)|all_lung(136;0.188)	Epithelial(68;0.0213)|all cancers(69;0.0839)|BRCA - Breast invasive adenocarcinoma(89;0.0886)|OV - Ovarian serous cystadenocarcinoma(28;0.112)			ACTTCTATGTGTCCCCAGAGG	0.552													G|||	357	0.0712859	0.1944	0.0375	5008	,	,		20135	0.0		0.0487	False		,,,				2504	0.0256				p.V153V		Atlas-SNP	.											.	DNAJC5B	42	.	0			c.G459A						PASS	.	G		783,3623	310.2+/-291.5	70,643,1490	65.0	54.0	58.0		459	5.1	1.0	8	dbSNP_116	58	408,8192	128.5+/-186.7	11,386,3903	no	coding-synonymous	DNAJC5B	NM_033105.4		81,1029,5393	AA,AG,GG		4.7442,17.7712,9.1573		153/200	66992737	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	85479	exon5			CTATGTGTCCCCA	AF368276	CCDS6183.1	8q13.1	2012-10-02			ENSG00000147570	ENSG00000147570		"""Heat shock proteins / DNAJ (HSP40)"""	24138	protein-coding gene	gene with protein product		613945				12477932	Standard	NM_033105		Approved	MGC26226, CSP-beta	uc003xvs.1	Q9UF47	OTTHUMG00000164470	ENST00000276570.5:c.459G>A	8.37:g.66992737G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	48	0.413793	NM_033105	Q969Y8	Silent	SNP	ENST00000276570.5	37	CCDS6183.1																																																																																			G|0.909;A|0.091	0.091	strong		0.552	DNAJC5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378915.1	NM_033105	
GOLT1A	127845	hgsc.bcm.edu	37	1	204172090	204172090	+	Silent	SNP	G	G	A	rs13334	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204172090G>A	ENST00000308302.3	-	2	236	c.51C>T	c.(49-51)ttC>ttT	p.F17F	GOLT1A_ENST00000475517.1_5'Flank	NM_198447.1	NP_940849.1			golgi transport 1A											kidney(1)|lung(2)|urinary_tract(1)	4	all_cancers(21;0.0165)|Breast(84;0.179)|all_epithelial(62;0.242)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.244)			AGAAGATGCCGAAACCGGTGA	0.572													G|||	48	0.00958466	0.0	0.0115	5008	,	,		19018	0.0109		0.0199	False		,,,				2504	0.0092				p.F17F		Atlas-SNP	.											.	GOLT1A	15	.	0			c.C51T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	110.0	96.0	101.0		51	-2.8	1.0	1	dbSNP_52	101	185,8415	83.4+/-145.9	2,181,4117	no	coding-synonymous	GOLT1A	NM_198447.1		2,195,6306	AA,AG,GG		2.1512,0.3177,1.5301		17/133	204172090	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	127845	exon2			GATGCCGAAACCG	BC058832	CCDS1443.1	1q32.1	2010-06-24	2010-06-24		ENSG00000174567	ENSG00000174567			24766	protein-coding gene	gene with protein product			"""golgi transport 1 homolog A (S. cerevisiae)"""			12477932	Standard	NM_198447		Approved	FLJ42654, CGI-141, YMR292W, GOT1, MGC62027	uc001has.1	Q6ZVE7	OTTHUMG00000036056	ENST00000308302.3:c.51C>T	1.37:g.204172090G>A		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	212	100	0.471698	NM_198447		Silent	SNP	ENST00000308302.3	37	CCDS1443.1																																																																																			A|0.016;G|0.984	0.016	strong		0.572	GOLT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087887.1	NM_198447	
CSTL1	128817	hgsc.bcm.edu	37	20	23421101	23421101	+	Missense_Mutation	SNP	G	G	A	rs17757442	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:23421101G>A	ENST00000246020.2	+	1	217	c.197G>A	c.(196-198)aGg>aAg	p.R66K	CSTL1_ENST00000472140.1_3'UTR|CSTL1_ENST00000347397.1_Missense_Mutation_p.R66K			Q9H114	CST1L_HUMAN	cystatin-like 1	66			R -> K (in dbSNP:rs17757442).			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(2)|endometrium(2)|large_intestine(3)|lung(4)|skin(2)|stomach(1)	14	Colorectal(13;0.0993)|Lung NSC(19;0.235)					CGAGTCCAGAGGCTAATTCGA	0.463													A|||	609	0.121605	0.0197	0.1499	5008	,	,		22513	0.2996		0.0785	False		,,,				2504	0.1002				p.R66K		Atlas-SNP	.											.	CSTL1	30	.	0			c.G197A						PASS	.	A	LYS/ARG	126,4280	815.2+/-416.2	2,122,2079	181.0	167.0	172.0		197	3.6	0.7	20	dbSNP_123	172	677,7923	788.9+/-407.6	32,613,3655	yes	missense	CSTL1	NM_138283.1	26	34,735,5734	AA,AG,GG		7.8721,2.8597,6.1741	benign	66/146	23421101	803,12203	2203	4300	6503	SO:0001583	missense	128817	exon2			TCCAGAGGCTAAT	AL096677	CCDS13153.1	20p11.21	2012-08-14			ENSG00000125823	ENSG00000125823			15958	protein-coding gene	gene with protein product						20565543	Standard	NM_138283		Approved	dJ322G13.4, CTES1	uc002wte.3	Q9H114	OTTHUMG00000032068	ENST00000246020.2:c.197G>A	20.37:g.23421101G>A	ENSP00000246020:p.Arg66Lys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	138	60	0.434783	NM_138283	Q17RA8|Q64FF7	Missense_Mutation	SNP	ENST00000246020.2	37	CCDS13153.1	282	0.12912087912087913	16	0.032520325203252036	52	0.143646408839779	159	0.27797202797202797	55	0.07255936675461741	A	0.015	-1.548507	0.00926	0.028597	0.078721	ENSG00000125823	ENST00000347397;ENST00000538508;ENST00000246020	T;T	0.23552	1.9;1.9	4.68	3.59	0.41128	Proteinase inhibitor I25, cystatin (2);	0.125021	0.36740	N	0.002425	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	0.41910	-0.9482	9	0.08179	T	0.78	-8.296	6.3146	0.21184	0.8077:0.0:0.1923:0.0	rs17757442;rs17757442	66	Q9H114	CST1L_HUMAN	K	66;26;66	ENSP00000344907:R66K;ENSP00000246020:R66K	ENSP00000246020:R66K	R	+	2	0	CSTL1	23369101	0.995000	0.38212	0.711000	0.30485	0.011000	0.07611	1.899000	0.39818	0.545000	0.28902	-0.254000	0.11334	AGG	G|0.906;A|0.094	0.094	strong		0.463	CSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078328.1		
CDH13	1012	hgsc.bcm.edu	37	16	83065664	83065664	+	Silent	SNP	G	G	A	rs6565105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:83065664G>A	ENST00000566620.1	+	3	497	c.207G>A	c.(205-207)tcG>tcA	p.S69S	CDH13_ENST00000446376.2_Silent_p.S69S|CDH13_ENST00000428848.3_Silent_p.S69S|CDH13_ENST00000565636.1_Silent_p.S69S|CDH13_ENST00000431540.3_Silent_p.S69S|CDH13_ENST00000569454.1_3'UTR|CDH13_ENST00000268613.10_Silent_p.S116S	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	69					adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		ATGAGGTCTCGAGCCCATACT	0.507													G|||	2675	0.534145	0.559	0.5821	5008	,	,		21576	0.4573		0.5298	False		,,,				2504	0.5501				p.S116S		Atlas-SNP	.											.	CDH13	97	.	0			c.G348A						PASS	.	G	,,,,,	2229,1811		639,951,430	71.0	69.0	70.0		348,207,,207,207,207	-2.0	1.0	16	dbSNP_116	70	4635,3727		1288,2059,834	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001220491.1,NM_001220492.1,NM_001257.4	,,,,,	1927,3010,1264	AA,AG,GG		44.5707,44.8267,44.6541	,,,,,	116/761,69/675,,69/191,69/176,69/714	83065664	6864,5538	2020	4181	6201	SO:0001819	synonymous_variant	1012	exon4			GGTCTCGAGCCCA	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.207G>A	16.37:g.83065664G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	107	42	0.392523	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			A|0.532;C|0.000;G|0.467	0.532	strong		0.507	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
ERC2	26059	hgsc.bcm.edu	37	3	55922561	55922561	+	Missense_Mutation	SNP	T	T	G	rs61745935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:55922561T>G	ENST00000288221.6	-	14	2675	c.2420A>C	c.(2419-2421)aAt>aCt	p.N807T		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	807						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CTCCAGTGCATTCATCAGTTC	0.502													T|||	2	0.000399361	0.0	0.0	5008	,	,		18713	0.0		0.002	False		,,,				2504	0.0				p.N805T		Atlas-SNP	.											ERC2_ENST00000288221,NS,carcinoma,+1,2	ERC2	221	2	0			c.A2414C						PASS	.	T	THR/ASN	2,4176		0,2,2087	220.0	226.0	224.0		2420	4.8	0.9	3	dbSNP_129	224	18,8410		0,18,4196	yes	missense	ERC2	NM_015576.1	65	0,20,6283	GG,GT,TT		0.2136,0.0479,0.1587	benign	807/958	55922561	20,12586	2089	4214	6303	SO:0001583	missense	26059	exon13			AGTGCATTCATCA	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2420A>C	3.37:g.55922561T>G	ENSP00000288221:p.Asn807Thr	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	226	117	0.517699	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	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	T|T	3.251|3.251	-0.153272|-0.153272	0.06585|0.06585	4.79E-4|4.79E-4	0.002136|0.002136	ENSG00000187672|ENSG00000187672	ENST00000492584|ENST00000288221	.|T	.|0.42131	.|0.98	5.93|5.93	4.76|4.76	0.60689|0.60689	.|.	.|0.171337	.|0.51477	.|N	.|0.000089	T|T	0.30198|0.30198	0.0757|0.0757	L|L	0.34521|0.34521	1.04|1.04	0.35402|0.35402	D|D	0.791684|0.791684	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.28073|0.28073	-1.0055|-1.0055	5|10	.|0.14252	.|T	.|0.57	-14.0227|-14.0227	12.0725|12.0725	0.53624|0.53624	0.0:0.0:0.2732:0.7268|0.0:0.0:0.2732:0.7268	.|.	.|807	.|O15083	.|ERC2_HUMAN	L|T	454|807	.|ENSP00000288221:N807T	.|ENSP00000288221:N807T	M|N	-|-	1|2	0|0	ERC2|ERC2	55897601|55897601	0.378000|0.378000	0.25114|0.25114	0.875000|0.875000	0.34327|0.34327	0.574000|0.574000	0.36063|0.36063	0.622000|0.622000	0.24433|0.24433	1.037000|1.037000	0.40024|0.40024	-0.316000|-0.316000	0.08728|0.08728	ATG|AAT	T|0.999;G|0.001	0.001	strong		0.502	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
IL31RA	133396	hgsc.bcm.edu	37	5	55147405	55147405	+	Missense_Mutation	SNP	A	A	C	rs75528518		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:55147405A>C	ENST00000447346.2	+	1	72	c.7A>C	c.(7-9)Atc>Ctc	p.I3L	IL31RA_ENST00000396836.2_Missense_Mutation_p.I3L|IL31RA_ENST00000490985.1_5'Flank|IL31RA_ENST00000354961.4_5'Flank|IL31RA_ENST00000359040.5_Missense_Mutation_p.I3L|IL31RA_ENST00000297015.3_5'Flank|IL31RA_ENST00000396834.1_5'UTR	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	0					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				gggaatgtgcatcaggcaact	0.438																																					p.I3L		Atlas-SNP	.											.	IL31RA	84	.	0			c.A7C						PASS	.						133.0	138.0	136.0					5																	55147405		2024	4184	6208	SO:0001583	missense	133396	exon1			ATGTGCATCAGGC	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.7A>C	5.37:g.55147405A>C	ENSP00000415900:p.Ile3Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	160	69	0.43125	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	.	4.977	0.181530	0.09495	.	.	ENSG00000164509	ENST00000396836;ENST00000447346;ENST00000359040	T;T;T	0.37915	1.33;1.2;1.17	2.33	-2.34	0.06704	.	1.884850	0.02918	N	0.137637	T	0.25865	0.0630	.	.	.	0.09310	N	1	B;B;B	0.19583	0.037;0.037;0.037	B;B;B	0.24541	0.036;0.054;0.054	T	0.28713	-1.0035	9	0.87932	D	0	.	2.59	0.04840	0.4946:0.0:0.1516:0.3539	.	3;3;3	Q8NI17-5;Q8NI17-2;Q8NI17-8	.;.;.	L	3	ENSP00000380048:I3L;ENSP00000415900:I3L;ENSP00000351935:I3L	ENSP00000351935:I3L	I	+	1	0	IL31RA	55183162	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.332000	0.07904	-0.487000	0.06735	-0.415000	0.06103	ATC	.	.	alt		0.438	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
FLNC	2318	hgsc.bcm.edu	37	7	128495338	128495338	+	Silent	SNP	C	C	T	rs3816885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128495338C>T	ENST00000325888.8	+	43	7482	c.7221C>T	c.(7219-7221)gaC>gaT	p.D2407D	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.D2374D	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	2407	Interaction with INPPL1.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCTCGGATGACGCTCGCCGTC	0.587													C|||	1296	0.258786	0.4244	0.1571	5008	,	,		18935	0.378		0.0378	False		,,,				2504	0.2117				p.D2407D		Atlas-SNP	.											.	FLNC	339	.	0			c.C7221T						PASS	.	C	,	1551,2783		286,979,902	59.0	66.0	64.0		7122,7221	-10.6	0.1	7	dbSNP_107	64	374,8202		7,360,3921	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	293,1339,4823	TT,TC,CC		4.361,35.7868,14.9109	,	2374/2693,2407/2726	128495338	1925,10985	2167	4288	6455	SO:0001819	synonymous_variant	2318	exon43			GGATGACGCTCGC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.7221C>T	7.37:g.128495338C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			C|0.813;T|0.187	0.187	strong		0.587	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
RDH8	50700	hgsc.bcm.edu	37	19	10124257	10124257	+	Silent	SNP	C	C	T	rs150712129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10124257C>T	ENST00000171214.1	+	1	333	c.84C>T	c.(82-84)gaC>gaT	p.D28D	RDH8_ENST00000591589.1_Silent_p.D48D	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	28					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)	TGGCCCATGACCCCAAGAAGC	0.612																																					p.D48D		Atlas-SNP	.											.	RDH8	51	.	0			c.C144T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	83.0	76.0	78.0		84	1.5	0.9	19	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RDH8	NM_015725.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		28/312	10124257	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	50700	exon1			CCATGACCCCAAG	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.84C>T	19.37:g.10124257C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	37																																																																																				C|1.000;T|0.000	0.000	strong		0.612	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
PKHD1L1	93035	hgsc.bcm.edu	37	8	110460488	110460488	+	Missense_Mutation	SNP	G	G	T	rs1673407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110460488G>T	ENST00000378402.5	+	39	5997	c.5893G>T	c.(5893-5895)Gtg>Ttg	p.V1965L		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1965	IPT/TIG 12.		V -> L (in dbSNP:rs1673407). {ECO:0000269|PubMed:12620974}.		immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TGATAGTGTGGTGCAGTGCAT	0.433										HNSCC(38;0.096)			T|||	3077	0.614417	0.7474	0.6671	5008	,	,		13927	0.4048		0.5119	False		,,,				2504	0.7188				p.V1965L		Atlas-SNP	.											PKHD1L1,colon,carcinoma,0,1	PKHD1L1	522	1	0			c.G5893T						PASS	.	T	LEU/VAL	2958,1114		1086,786,164	95.0	97.0	96.0		5893	-3.2	0.0	8	dbSNP_89	96	4512,3902		1234,2044,929	yes	missense	PKHD1L1	NM_177531.4	32	2320,2830,1093	TT,TG,GG		46.3751,27.3576,40.173	benign	1965/4244	110460488	7470,5016	2036	4207	6243	SO:0001583	missense	93035	exon39			AGTGTGGTGCAGT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.5893G>T	8.37:g.110460488G>T	ENSP00000367655:p.Val1965Leu	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	1220	0.5586080586080586	356	0.7235772357723578	235	0.649171270718232	245	0.42832167832167833	384	0.5065963060686016	T	0.432	-0.902887	0.02453	0.726424	0.536249	ENSG00000205038	ENST00000378402	D	0.81499	-1.5	5.49	-3.17	0.05202	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.224078	0.28933	N	0.013661	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.11329	0.006	T	0.29458	-1.0011	9	0.07813	T	0.8	.	2.4839	0.04594	0.1127:0.3488:0.2314:0.3071	rs1673407;rs13264278;rs16879586;rs52798906;rs61398933;rs1673407	1965	Q86WI1	PKHL1_HUMAN	L	1965	ENSP00000367655:V1965L	ENSP00000367655:V1965L	V	+	1	0	PKHD1L1	110529664	0.000000	0.05858	0.001000	0.08648	0.617000	0.37484	-1.884000	0.01622	-1.308000	0.02318	-0.346000	0.07831	GTG	G|0.427;T|0.573	0.573	strong		0.433	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
MEIOB	254528	hgsc.bcm.edu	37	16	1894961	1894961	+	Missense_Mutation	SNP	A	A	G	rs9806945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1894961A>G	ENST00000397344.3	-	10	976	c.782T>C	c.(781-783)aTa>aCa	p.I261T	MEIOB_ENST00000452149.2_Missense_Mutation_p.I261T|MEIOB_ENST00000470044.1_Missense_Mutation_p.I54T|LA16c-429E7.1_ENST00000570247.1_RNA|MEIOB_ENST00000412554.2_Missense_Mutation_p.I261T|MEIOB_ENST00000325962.3_Missense_Mutation_p.I261T	NM_152764.2	NP_689977.2	Q8N635	MEIOB_HUMAN	meiosis specific with OB domains	261			I -> T (in dbSNP:rs9806945).		double-strand break repair via homologous recombination (GO:0000724)|female meiosis I (GO:0007144)|fertilization (GO:0009566)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|resolution of meiotic recombination intermediates (GO:0000712)|synapsis (GO:0007129)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA binding (GO:0003697)										AGCTTCTGGTATATCTTAAAT	0.249													G|||	1010	0.201677	0.1831	0.2262	5008	,	,		16259	0.1736		0.1819	False		,,,				2504	0.2587				p.I261T		Atlas-SNP	.											.	.	.	.	0			c.T782C						PASS	.	G	THR/ILE,THR/ILE	789,3597	726.1+/-409.7	80,629,1484	38.0	38.0	38.0		782,782	4.9	1.0	16	dbSNP_119	38	1319,7251	738.4+/-407.1	109,1101,3075	yes	missense,missense	C16orf73	NM_001163560.2,NM_152764.2	89,89	189,1730,4559	GG,GA,AA		15.3909,17.9891,16.2705	benign,benign	261/472,261/443	1894961	2108,10848	2193	4285	6478	SO:0001583	missense	254528	exon10			TCTGGTATATCTT	BC029829	CCDS10449.2, CCDS53983.1	16p13.3	2012-08-13	2012-08-13	2012-08-13	ENSG00000162039	ENSG00000162039			28569	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 73"""	C16orf73		12477932	Standard	NM_152764		Approved	MGC35212	uc010uvq.1	Q8N635	OTTHUMG00000128683	ENST00000397344.3:c.782T>C	16.37:g.1894961A>G	ENSP00000380504:p.Ile261Thr	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	131	52	0.396947	NM_001163560	B1AK39|C9J0S1|Q96RY0	Missense_Mutation	SNP	ENST00000397344.3	37	CCDS10449.2	396	0.1813186813186813	91	0.18495934959349594	62	0.1712707182320442	101	0.17657342657342656	142	0.18733509234828497	G	0.037	-1.303042	0.01353	0.179891	0.153909	ENSG00000162039	ENST00000412554;ENST00000452149;ENST00000325962;ENST00000397344	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	5.98	4.91	0.64330	Nucleic acid-binding, OB-fold-like (1);Nucleic acid-binding, OB-fold (1);	0.166727	0.53938	N	0.000054	T	0.00012	0.0000	N	0.00069	-2.28	0.53005	P	3.2999999999949736E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34527	-0.9825	9	0.10377	T	0.69	.	10.2088	0.43128	0.1842:0.0:0.8158:0.0	rs9806945;rs52797208;rs59366262;rs9806945	261;261	C9J0S1;Q8N635	.;CP073_HUMAN	T	261	ENSP00000390778:I261T;ENSP00000391033:I261T;ENSP00000314484:I261T;ENSP00000380504:I261T	ENSP00000314484:I261T	I	-	2	0	C16orf73	1834962	1.000000	0.71417	0.972000	0.41901	0.134000	0.20937	2.440000	0.44855	0.686000	0.31488	-0.186000	0.12905	ATA	A|0.839;G|0.161	0.161	strong		0.249	MEIOB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250580.1	NM_152764	
CFAP46	54777	hgsc.bcm.edu	37	10	134671154	134671154	+	Silent	SNP	G	G	A	rs189775198	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134671154G>A	ENST00000368586.5	-	39	5614	c.5514C>T	c.(5512-5514)ggC>ggT	p.G1838G	TTC40_ENST00000263170.5_5'UTR	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CAGCCATGGCGCCCTGGGCCA	0.587													G|||	46	0.0091853	0.0	0.0072	5008	,	,		16138	0.002		0.0129	False		,,,				2504	0.0266				p.G1838G		Atlas-SNP	.											.	TTC40	100	.	0			c.C5514T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	125.0	83.0	97.0		450	-1.4	0.0	10		97	82,8518	46.3+/-105.2	0,82,4218	no	coding-synonymous	C10orf92	NM_001200049.1		0,91,6412	AA,AG,GG		0.9535,0.2043,0.6997		150/1028	134671154	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	54777	exon39			CATGGCGCCCTGG																												ENST00000368586.5:c.5514C>T	10.37:g.134671154G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	132	60	0.454545	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.991;A|0.009	0.009	strong		0.587	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
XIRP2	129446	hgsc.bcm.edu	37	2	168104679	168104679	+	Silent	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168104679T>G	ENST00000409195.1	+	9	6866	c.6777T>G	c.(6775-6777)acT>acG	p.T2259T	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.T2037T|XIRP2_ENST00000295237.9_Silent_p.T2259T|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2084					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAACAAATACTTCCACAGGCT	0.388																																					p.T2259T		Atlas-SNP	.											.	XIRP2	914	.	0			c.T6777G						PASS	.						68.0	64.0	65.0					2																	168104679		1834	4085	5919	SO:0001819	synonymous_variant	129446	exon9			AAATACTTCCACA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6777T>G	2.37:g.168104679T>G		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	176	60	0.340909	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			.	.	none		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
MFSD3	113655	hgsc.bcm.edu	37	8	145737123	145737123	+	IGR	SNP	G	G	A	rs35346077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145737123G>A	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Missense_Mutation_p.S1148F|RECQL4_ENST00000532237.1_5'UTR|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGGCCTCAGGGACAGGAACTG	0.662													G|||	4	0.000798722	0.0	0.0	5008	,	,		18429	0.0		0.002	False		,,,				2504	0.002				p.S1148F		Atlas-SNP	.											.	RECQL4	75	.	0			c.C3443T						PASS	.	G	PHE/SER	1,4329		0,1,2164	66.0	79.0	75.0		3444	5.0	1.0	8	dbSNP_126	75	13,8505		0,13,4246	no	missense	RECQL4	NM_004260.3	155	0,14,6410	AA,AG,GG		0.1526,0.0231,0.109	possibly-damaging	1148/1209	145737123	14,12834	2165	4259	6424	SO:0001628	intergenic_variant	9401	exon21			CTCAGGGACAGGA		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		8.37:g.145737123G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	79	50	0.632911	NM_004260		Missense_Mutation	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																			G|0.995;A|0.005	0.005	weak		0.662	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
ARHGEF38	54848	hgsc.bcm.edu	37	4	106474078	106474078	+	Silent	SNP	G	G	A	rs10032241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:106474078G>A	ENST00000420470.2	+	1	300	c.156G>A	c.(154-156)agG>agA	p.R52R	AC004066.3_ENST00000514879.1_RNA|ARHGEF38_ENST00000265154.2_Silent_p.R52R	NM_001242729.1	NP_001229658.1	Q9NXL2	ARH38_HUMAN	Rho guanine nucleotide exchange factor (GEF) 38	52						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(3)	11						CCTTGAGGAGGAGCCAATCTG	0.473													G|||	756	0.150958	0.4493	0.072	5008	,	,		19274	0.0		0.0616	False		,,,				2504	0.0511				p.R52R		Atlas-SNP	.											.	ARHGEF38	52	.	0			c.G156A						PASS	.	G	,	1665,2741	506.2+/-366.3	301,1063,839	71.0	67.0	68.0		156,156	3.2	1.0	4	dbSNP_119	68	594,8006	157.6+/-211.2	17,560,3723	no	coding-synonymous,coding-synonymous	ARHGEF38	NM_001242729.1,NM_017700.1	,	318,1623,4562	AA,AG,GG		6.907,37.7894,17.3689	,	52/778,52/220	106474078	2259,10747	2203	4300	6503	SO:0001819	synonymous_variant	54848	exon1			GAGGAGGAGCCAA	AK000191	CCDS3670.1, CCDS56338.1	4q24	2012-07-24			ENSG00000236699	ENSG00000236699		"""Rho guanine nucleotide exchange factors"""	25968	protein-coding gene	gene with protein product							Standard	NM_001242729		Approved	FLJ20184	uc003hxv.2	Q9NXL2	OTTHUMG00000154752	ENST00000420470.2:c.156G>A	4.37:g.106474078G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_001242729	C9JIB4	Silent	SNP	ENST00000420470.2	37	CCDS56338.1																																																																																			G|0.830;A|0.170	0.170	strong		0.473	ARHGEF38-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000336934.3	NM_017700	
OR5T1	390155	hgsc.bcm.edu	37	11	56044050	56044050	+	Silent	SNP	A	A	G	rs148135770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56044050A>G	ENST00000313033.2	+	1	1022	c.936A>G	c.(934-936)gcA>gcG	p.A312A		NM_001004745.1	NP_001004745.1	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T, member 1	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(27)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	43	Esophageal squamous(21;0.00448)					TAAAGGAGGCAATCAAAAGAT	0.343													a|||	4	0.000798722	0.0	0.0029	5008	,	,		20481	0.0		0.0	False		,,,				2504	0.002				p.A312A		Atlas-SNP	.											OR5T1,right_upper_lobe,carcinoma,+1,1	OR5T1	95	1	0			c.A936G						PASS	.	A		0,4402		0,0,2201	72.0	70.0	71.0		936	-2.9	0.1	11	dbSNP_134	71	8,8584	6.4+/-24.3	0,8,4288	no	coding-synonymous	OR5T1	NM_001004745.1		0,8,6489	GG,GA,AA		0.0931,0.0,0.0616		312/327	56044050	8,12986	2201	4296	6497	SO:0001819	synonymous_variant	390155	exon1			GGAGGCAATCAAA	AB065962	CCDS31525.1	11q11	2012-08-09		2004-03-10	ENSG00000181698	ENSG00000181698		"""GPCR / Class A : Olfactory receptors"""	14821	protein-coding gene	gene with protein product				OR5T1P			Standard	NM_001004745		Approved		uc001nio.1	Q8NG75	OTTHUMG00000166853	ENST00000313033.2:c.936A>G	11.37:g.56044050A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_001004745	B2RNM9	Silent	SNP	ENST00000313033.2	37	CCDS31525.1																																																																																			A|0.999;G|0.001	0.001	strong		0.343	OR5T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391600.1	NM_001004745	
AQP11	282679	hgsc.bcm.edu	37	11	77301385	77301385	+	Silent	SNP	G	G	A	rs145642525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:77301385G>A	ENST00000313578.3	+	1	706	c.348G>A	c.(346-348)acG>acA	p.T116T	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	116					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)			CCCCCGAGACGGGTGCGGTGA	0.612													G|||	6	0.00119808	0.0015	0.0014	5008	,	,		19669	0.0		0.003	False		,,,				2504	0.0				p.T116T		Atlas-SNP	.											.	AQP11	14	.	0			c.G348A						PASS	.	G		1,4399	2.1+/-5.4	0,1,2199	88.0	70.0	76.0		348	0.2	0.0	11	dbSNP_134	76	12,8572	9.1+/-34.3	0,12,4280	no	coding-synonymous	AQP11	NM_173039.2		0,13,6479	AA,AG,GG		0.1398,0.0227,0.1001		116/272	77301385	13,12971	2200	4292	6492	SO:0001819	synonymous_variant	282679	exon1			CGAGACGGGTGCG	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.348G>A	11.37:g.77301385G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_173039		Silent	SNP	ENST00000313578.3	37	CCDS8251.1																																																																																			G|0.998;A|0.002	0.002	strong		0.612	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039	
CYFIP1	23191	hgsc.bcm.edu	37	15	22925851	22925851	+	Silent	SNP	C	C	T	rs4134802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:22925851C>T	ENST00000313077.7	+	2	194	c.69C>T	c.(67-69)ccC>ccT	p.P23P	CYFIP1_ENST00000560848.1_Silent_p.P23P	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		TGCCCCTGCCCGACCAGCAGC	0.667													C|||	886	0.176917	0.3427	0.1412	5008	,	,		15649	0.003		0.2207	False		,,,				2504	0.1125				p.P23P		Atlas-SNP	.											.	CYFIP1	159	.	0			c.C69T						PASS	.	C		1456,2950	467.2+/-354.7	231,994,978	42.0	41.0	41.0		69	-10.9	0.0	15	dbSNP_108	41	1820,6780	325.8+/-317.1	185,1450,2665	no	coding-synonymous	CYFIP1	NM_014608.2		416,2444,3643	TT,TC,CC		21.1628,33.0458,25.1884		23/1254	22925851	3276,9730	2203	4300	6503	SO:0001819	synonymous_variant	23191	exon2			CCTGCCCGACCAG	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.69C>T	15.37:g.22925851C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_014608		Silent	SNP	ENST00000313077.7	37	CCDS10009.1																																																																																			C|0.769;T|0.231	0.231	strong		0.667	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64606840	64606840	+	Silent	SNP	C	C	A	rs149253049	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:64606840C>A	ENST00000498707.1	-	19	3105	c.2763G>T	c.(2761-2763)ctG>ctT	p.L921L	ADAMTS9_ENST00000295903.4_Silent_p.L893L	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	921	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		CAGGCTGGGGCAGCCGATCGC	0.463													C|||	5	0.000998403	0.0023	0.0014	5008	,	,		16289	0.0		0.001	False		,,,				2504	0.0				p.L921L		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G2763T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	70.0	71.0	71.0		2763	3.0	1.0	3	dbSNP_134	71	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ADAMTS9	NM_182920.1		0,10,6493	AA,AC,CC		0.0349,0.1589,0.0769		921/1936	64606840	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	56999	exon19			CTGGGGCAGCCGA	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.2763G>T	3.37:g.64606840C>A		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	208	98	0.471154	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	37	CCDS2903.1																																																																																			A|0.001;C|0.999;G|0.000	0.001	strong		0.463	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
GOLGB1	2804	hgsc.bcm.edu	37	3	121416623	121416623	+	Missense_Mutation	SNP	G	G	C	rs3732407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:121416623G>C	ENST00000340645.5	-	13	2857	c.2732C>G	c.(2731-2733)aCt>aGt	p.T911S	GOLGB1_ENST00000393667.3_Missense_Mutation_p.T916S	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	911			T -> S (in dbSNP:rs3732407). {ECO:0000269|PubMed:18487259}.		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CATTTTCTCAGTCATACTAAA	0.383													G|||	528	0.105431	0.0121	0.147	5008	,	,		20713	0.0476		0.2435	False		,,,				2504	0.1196				p.T916S		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C2747G						PASS	.	G	SER/THR	181,4225	116.7+/-154.6	3,175,2025	143.0	148.0	146.0		2732	4.5	1.0	3	dbSNP_107	146	2073,6525	359.6+/-331.6	263,1547,2489	yes	missense	GOLGB1	NM_004487.3	58	266,1722,4514	CC,CG,GG		24.1103,4.108,17.3331	benign	911/3260	121416623	2254,10750	2203	4299	6502	SO:0001583	missense	2804	exon13			TTCTCAGTCATAC	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.2732C>G	3.37:g.121416623G>C	ENSP00000341848:p.Thr911Ser	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	303|303	0.13873626373626374|0.13873626373626374	10|10	0.02032520325203252|0.02032520325203252	70|70	0.19337016574585636|0.19337016574585636	34|34	0.05944055944055944|0.05944055944055944	189|189	0.24934036939313983|0.24934036939313983	G|G	7.435|7.435	0.639547|0.639547	0.14386|0.14386	0.04108|0.04108	0.241103|0.241103	ENSG00000173230|ENSG00000173230	ENST00000489400|ENST00000340645;ENST00000393667;ENST00000494517;ENST00000426235	.|T;T;T	.|0.13089	.|3.16;3.16;2.62	5.35|5.35	4.48|4.48	0.54585|0.54585	.|.	.|0.198851	.|0.35495	.|N	.|0.003174	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.13043|0.13043	0.29|0.29	0.43545|0.43545	P|P	0.004153999999999991|0.004153999999999991	.|B;B;B;B	.|0.15141	.|0.012;0.005;0.012;0.002	.|B;B;B;B	.|0.19946	.|0.027;0.013;0.027;0.012	T|T	0.42481|0.42481	-0.9449|-0.9449	4|9	.|0.09843	.|T	.|0.71	.|.	12.0937|12.0937	0.53742|0.53742	0.0827:0.0:0.9173:0.0|0.0827:0.0:0.9173:0.0	rs3732407;rs17549959;rs52791658;rs3732407|rs3732407;rs17549959;rs52791658;rs3732407	.|836;875;916;911	.|F1T0J2;E7EU81;E7EP74;Q14789	.|.;.;.;GOGB1_HUMAN	V|S	782|911;916;875;723	.|ENSP00000341848:T911S;ENSP00000377275:T916S;ENSP00000418231:T875S	.|ENSP00000341848:T911S	L|T	-|-	1|2	2|0	GOLGB1|GOLGB1	122899313|122899313	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.999000|0.999000	0.98932|0.98932	3.941000|3.941000	0.56607|0.56607	1.493000|1.493000	0.48517|0.48517	0.655000|0.655000	0.94253|0.94253	CTG|ACT	G|0.843;C|0.157	0.157	strong		0.383	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
ELOVL5	60481	hgsc.bcm.edu	37	6	53159090	53159090	+	Intron	SNP	G	G	T	rs2294857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:53159090G>T	ENST00000542638.1	-	2	506				ELOVL5_ENST00000541407.1_Intron|ELOVL5_ENST00000304434.6_Intron|ELOVL5_ENST00000370913.5_Silent_p.A86A|ELOVL5_ENST00000370918.4_Intron|ELOVL5_ENST00000486973.1_Intron			Q9NYP7	ELOV5_HUMAN	ELOVL fatty acid elongase 5						alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7	Lung NSC(77;0.116)					ttcaggcaggggcatgtgaag	0.517													G|||	331	0.0660942	0.0061	0.2579	5008	,	,		17072	0.0407		0.0765	False		,,,				2504	0.0266				p.A86A		Atlas-SNP	.											.	ELOVL5	25	.	0			c.C258A						PASS	.	G	,,,	24,1720		0,24,848	10.0	9.0	9.0		,,258,	-2.7	0.0	6	dbSNP_100	9	213,3759		4,205,1777	no	intron,intron,coding-synonymous,intron	ELOVL5	NM_001242828.1,NM_001242830.1,NM_001242831.1,NM_021814.4	,,,	4,229,2625	TT,TG,GG		5.3625,1.3761,4.1463	,,,	,,86/89,	53159090	237,5479	872	1986	2858	SO:0001627	intron_variant	60481	exon3			GGCAGGGGCATGT	AF052129	CCDS4951.1, CCDS56433.1, CCDS56434.1, CCDS75470.1	6p21.1-p12.1	2014-07-30	2011-05-25		ENSG00000012660	ENSG00000012660			21308	protein-coding gene	gene with protein product		611805	"""ELOVL family member 5, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"", ""spinocerebellar ataxia 38"""	SCA38		10970790, 25065913	Standard	NM_021814		Approved	HELO1, dJ483K16.1	uc011dwx.2	Q9NYP7	OTTHUMG00000016249	ENST00000542638.1:c.58+1349C>A	6.37:g.53159090G>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_001242831	B4DZJ2|F6SH78|Q59EL3|Q5TGH5|Q6NXE7|Q7L2S5|Q8NCG4|Q9UI22	Silent	SNP	ENST00000542638.1	37	CCDS4951.1																																																																																			G|0.922;T|0.078	0.078	strong		0.517	ELOVL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043566.1	NM_021814	
LGR6	59352	hgsc.bcm.edu	37	1	202287156	202287156	+	Silent	SNP	C	C	T	rs12123010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:202287156C>T	ENST00000367278.3	+	18	1814	c.1725C>T	c.(1723-1725)tcC>tcT	p.S575S	LGR6_ENST00000439764.2_Silent_p.S436S|LGR6_ENST00000255432.7_Silent_p.S523S	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	575					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						TGTTGCTCTCCGTGCTCTGCA	0.607													C|||	408	0.0814696	0.059	0.1037	5008	,	,		19252	0.0496		0.1113	False		,,,				2504	0.0982				p.S575S		Atlas-SNP	.											.	LGR6	102	.	0			c.C1725T						PASS	.	C	,,	235,4171	138.4+/-174.2	8,219,1976	119.0	107.0	111.0		1725,1308,1569	-5.6	0.5	1	dbSNP_120	111	1127,7473	234.6+/-267.5	79,969,3252	no	coding-synonymous,coding-synonymous,coding-synonymous	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,,	87,1188,5228	TT,TC,CC		13.1047,5.3336,10.4721	,,	575/968,436/829,523/916	202287156	1362,11644	2203	4300	6503	SO:0001819	synonymous_variant	59352	exon18			GCTCTCCGTGCTC	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.1725C>T	1.37:g.202287156C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	176	95	0.539773	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																			C|0.899;T|0.101	0.101	strong		0.607	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
KIAA1755	85449	hgsc.bcm.edu	37	20	36841756	36841756	+	Silent	SNP	T	T	C	rs1534967	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36841756T>C	ENST00000279024.4	-	14	3562	c.3291A>G	c.(3289-3291)tcA>tcG	p.S1097S		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1097								p.S1097S(1)		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)				CCATGCCCAGTGAGTCTAGTG	0.607													C|||	1970	0.393371	0.2436	0.4424	5008	,	,		18755	0.5238		0.4344	False		,,,				2504	0.3845				p.S1097S		Atlas-SNP	.											KIAA1755,NS,carcinoma,0,1	KIAA1755	145	1	1	Substitution - coding silent(1)	stomach(1)	c.A3291G						scavenged	.	C		1169,3237	690.7+/-405.3	162,845,1196	41.0	30.0	34.0		3291	-10.6	0.0	20	dbSNP_88	34	3941,4657	580.1+/-391.0	907,2127,1265	no	coding-synonymous	KIAA1755	NM_001029864.1		1069,2972,2461	CC,CT,TT		45.8362,26.532,39.2956		1097/1201	36841756	5110,7894	2203	4299	6502	SO:0001819	synonymous_variant	85449	exon14			GCCCAGTGAGTCT	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.3291A>G	20.37:g.36841756T>C		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	70	68	0.971429	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			T|0.603;C|0.397	0.397	strong		0.607	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
GAB4	128954	hgsc.bcm.edu	37	22	17446991	17446991	+	Splice_Site	SNP	C	C	T	rs4819925	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:17446991C>T	ENST00000400588.1	-	6	1394	c.1287G>A	c.(1285-1287)aaG>aaA	p.K429K	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	429										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)				AAGACTTACCCTTCTGGTTAG	0.532													T|||	4133	0.82528	0.9773	0.8444	5008	,	,		21489	0.8353		0.7396	False		,,,				2504	0.684				p.K429K		Atlas-SNP	.											GAB4,NS,carcinoma,0,1	GAB4	95	1	0			c.G1287A						PASS	.	T		3849,227		1820,209,9	94.0	102.0	99.0		1287	1.2	1.0	22	dbSNP_111	99	6337,2071		2412,1513,279	yes	coding-synonymous-near-splice	GAB4	NM_001037814.1		4232,1722,288	TT,TC,CC		24.6313,5.5692,18.4076		429/575	17446991	10186,2298	2038	4204	6242	SO:0001630	splice_region_variant	128954	exon6			CTTACCCTTCTGG	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.1288+1G>A	22.37:g.17446991C>T		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	131	61	0.465649	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.190;T|0.810	0.810	strong		0.532	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	Silent
ZNF568	374900	hgsc.bcm.edu	37	19	37441365	37441365	+	Missense_Mutation	SNP	T	T	C	rs547483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37441365T>C	ENST00000333987.7	+	7	1816	c.1310T>C	c.(1309-1311)aTg>aCg	p.M437T	ZNF568_ENST00000415168.1_Missense_Mutation_p.M373T|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	437			M -> T (in dbSNP:rs547483).		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACCGTACATATGCGAAATCAT	0.388													T|||	1519	0.303315	0.3911	0.3718	5008	,	,		20049	0.0913		0.3618	False		,,,				2504	0.2945				p.M437T		Atlas-SNP	.											.	ZNF568	106	.	0			c.T1310C						PASS	.	T	THR/MET,THR/MET,THR/MET,,,THR/MET	1788,2618	480.6+/-358.9	367,1054,782	72.0	80.0	77.0		1307,1118,1118,,,1310	0.4	0.1	19	dbSNP_83	77	3108,5488	458.6+/-364.7	560,1988,1750	yes	missense,missense,missense,intron,intron,missense	ZNF568	NM_001204835.1,NM_001204836.1,NM_001204837.1,NM_001204838.1,NM_001204839.1,NM_198539.3	81,81,81,,,81	927,3042,2532	CC,CT,TT		36.1564,40.581,37.6557	possibly-damaging,possibly-damaging,possibly-damaging,,,possibly-damaging	436/644,373/581,373/581,,,437/645	37441365	4896,8106	2203	4298	6501	SO:0001583	missense	374900	exon7			TACATATGCGAAA	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1310T>C	19.37:g.37441365T>C	ENSP00000334685:p.Met437Thr	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	31	14	0.451613	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Missense_Mutation	SNP	ENST00000333987.7	37	CCDS42558.1	645	0.29532967032967034	185	0.37601626016260165	124	0.3425414364640884	47	0.08216783216783216	289	0.3812664907651715	T	6.400	0.442011	0.12164	0.40581	0.361564	ENSG00000198453	ENST00000333987;ENST00000415168	T;T	0.19669	2.13;2.13	4.09	0.406	0.16366	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.173251	0.27966	N	0.017136	T	0.00012	0.0000	L	0.47078	1.49	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.44832	-0.9302	9	0.72032	D	0.01	.	8.2689	0.31831	0.6252:0.0:0.0:0.3748	rs547483;rs826302;rs1080456;rs16971821;rs56512048;rs60790821;rs547483	437	Q3ZCX4	ZN568_HUMAN	T	437;373	ENSP00000334685:M437T;ENSP00000394514:M373T	ENSP00000334685:M437T	M	+	2	0	ZNF568	42133205	0.000000	0.05858	0.073000	0.20177	0.791000	0.44710	-1.420000	0.02457	0.203000	0.20529	0.460000	0.39030	ATG	T|0.698;C|0.302	0.302	strong		0.388	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
MUC4	4585	hgsc.bcm.edu	37	3	195509353	195509353	+	Missense_Mutation	SNP	G	G	A	rs200052949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195509353G>A	ENST00000463781.3	-	2	9557	c.9098C>T	c.(9097-9099)gCa>gTa	p.A3033V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3033V	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)		ACCGGTGGATGCTGAGGAAGG	0.587													.|||	649	0.129593	0.1657	0.0893	5008	,	,		11728	0.0407		0.1899	False		,,,				2504	0.1391				p.A3033V		Atlas-SNP	.											MUC4_ENST00000463781,uveal_tract,malignant_melanoma,-1,4	MUC4	1505	4	0			c.C9098T						scavenged	.						16.0	11.0	13.0					3																	195509353		652	1528	2180	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9098C>T	3.37:g.195509353G>A	ENSP00000417498:p.Ala3033Val	Somatic	160	4	0.025		WXS	Illumina HiSeq	Phase_I	105	11	0.104762	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	8.873	0.949658	0.18431	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.58;1.52	1.18	-0.252	0.12999	.	.	.	.	.	T	0.13884	0.0336	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.04013	0.001	T	0.29731	-1.0002	8	.	.	.	.	0.0707	0.00022	0.2431:0.2098:0.2446:0.3025	.	2905	E7ESK3	.	V	3033	ENSP00000417498:A3033V;ENSP00000420243:A3033V	.	A	-	2	0	MUC4	196994132	0.001000	0.12720	0.020000	0.16555	0.000000	0.00434	0.695000	0.25527	-0.846000	0.04174	0.000000	0.15137	GCA	.	.	weak		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR10AD1	121275	hgsc.bcm.edu	37	12	48597064	48597064	+	Silent	SNP	A	A	G	rs17224828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48597064A>G	ENST00000310248.2	-	1	106	c.12T>C	c.(10-12)aaT>aaC	p.N4N		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						CTATGCTGCCATTCCTTAGCA	0.517													G|||	212	0.0423323	0.059	0.036	5008	,	,		22556	0.006		0.0915	False		,,,				2504	0.0112				p.N4N		Atlas-SNP	.											.	OR10AD1	24	.	0			c.T12C						PASS	.	G		271,4135	767.2+/-413.5	7,257,1939	44.0	42.0	43.0		12	-5.8	0.0	12	dbSNP_123	43	761,7839	754.1+/-407.5	28,705,3567	no	coding-synonymous	OR10AD1	NM_001004134.1		35,962,5506	GG,GA,AA		8.8488,6.1507,7.9348		4/318	48597064	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	121275	exon1			GCTGCCATTCCTT		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.12T>C	12.37:g.48597064A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_001004134	B9EGT9|Q6IFA8	Silent	SNP	ENST00000310248.2	37	CCDS31787.1																																																																																			A|0.939;G|0.061	0.061	strong		0.517	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
PPFIA4	8497	hgsc.bcm.edu	37	1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	rs12130501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:203044777G>A	ENST00000447715.2	+	34	3841	c.3400G>A	c.(3400-3402)Ggc>Agc	p.G1134S	PPFIA4_ENST00000367240.2_Missense_Mutation_p.G1135S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.G641S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.G650S|PPFIA4_ENST00000599966.1_Missense_Mutation_p.G641S|PPFIA4_ENST00000414050.2_Missense_Mutation_p.G863S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1134				G -> A (in Ref. 5; AAC26102). {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						CCACGGTCGCGGCGGCATGCT	0.716													g|||	32	0.00638978	0.0	0.0115	5008	,	,		11140	0.0		0.0189	False		,,,				2504	0.0051				p.G650S		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	0			c.G1948A						PASS	.		SER/GLY	15,3733		0,15,1859	11.0	14.0	13.0		1948	-0.2	0.0	1	dbSNP_120	13	228,7910		2,224,3843	no	missense	PPFIA4	NM_015053.1	56	2,239,5702	AA,AG,GG		2.8017,0.4002,2.0444	benign	650/702	203044777	243,11643	1874	4069	5943	SO:0001583	missense	8497	exon16			GGTCGCGGCGGCA	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.3400G>A	1.37:g.203044777G>A	ENSP00000402576:p.Gly1134Ser	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	11	6	0.545455	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	g	12.32	1.901775	0.33535	0.004002	0.028017	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.21734	2.32;2.0;1.99;2.0;1.99	4.58	-0.158	0.13383	.	1.035160	0.07805	U	0.957214	T	0.03564	0.0102	N	0.17474	0.49	0.09310	N	1	B;B;B;B;B	0.17038	0.0;0.0;0.005;0.02;0.012	B;B;B;B;B	0.16722	0.0;0.0;0.002;0.016;0.007	T	0.34875	-0.9811	10	0.32370	T	0.25	-0.3686	4.4121	0.11438	0.4118:0.2651:0.3231:0.0	rs12130501	863;1134;336;641;650	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	S	1135;1134;641;863;650	ENSP00000356209:G1135S;ENSP00000402576:G1134S;ENSP00000295706:G641S;ENSP00000400379:G863S;ENSP00000272198:G650S	ENSP00000272198:G650S	G	+	1	0	PPFIA4	201311400	0.948000	0.32251	0.014000	0.15608	0.413000	0.31143	1.380000	0.34351	-0.369000	0.08028	0.298000	0.19748	GGC	G|0.992;A|0.008	0.008	strong		0.716	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48151822	48151822	+	Missense_Mutation	SNP	C	C	G	rs11168230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48151822C>G	ENST00000449771.2	-	2	134	c.46G>C	c.(46-48)Gct>Cct	p.A16P	SLC48A1_ENST00000547002.1_5'Flank|RAPGEF3_ENST00000171000.4_5'UTR|RAPGEF3_ENST00000548919.1_5'UTR|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.A16P|RAPGEF3_ENST00000405493.2_5'UTR|RAPGEF3_ENST00000549151.1_5'UTR|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.A16P|RAPGEF3_ENST00000549347.1_5'UTR			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	16			A -> P (in dbSNP:rs11168230). {ECO:0000269|PubMed:15489334}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		TCCTCCACAGCCAGGCCCACC	0.657													C|||	1487	0.296925	0.2988	0.2709	5008	,	,		16982	0.2004		0.335	False		,,,				2504	0.3732				p.A16P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.G46C						PASS	.	C	PRO/ALA,,	1187,3177		185,817,1180	13.0	14.0	14.0		46,,	2.0	0.9	12	dbSNP_120	14	2586,5970		408,1770,2100	no	missense,utr-5,utr-5	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	27,,	593,2587,3280	GG,GC,CC		30.2244,27.1998,29.2028	possibly-damaging,,	16/924,,	48151822	3773,9147	2182	4278	6460	SO:0001583	missense	10411	exon2			CCACAGCCAGGCC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.46G>C	12.37:g.48151822C>G	ENSP00000395708:p.Ala16Pro	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	116	44	0.37931	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	611	0.27976190476190477	138	0.2804878048780488	103	0.2845303867403315	122	0.21328671328671328	248	0.32717678100263853	C	16.11	3.029273	0.54790	0.271998	0.302244	ENSG00000079337	ENST00000449771;ENST00000389212;ENST00000397089;ENST00000395358	T;T;T	0.62498	0.02;0.02;0.02	5.12	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.22240	P	0.999267639	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.0;0.004;0.001	T	0.26430	-1.0103	8	0.30078	T	0.28	.	4.294	0.10892	0.0:0.5898:0.1857:0.2245	rs11168230;rs11168230	28;16;16	B7Z5J6;O95398-2;O95398	.;.;RPGF3_HUMAN	P	16;16;28;16	ENSP00000395708:A16P;ENSP00000373864:A16P;ENSP00000378764:A16P	ENSP00000373864:A16P	A	-	1	0	RAPGEF3	46438089	0.037000	0.19845	0.918000	0.36340	0.989000	0.77384	0.843000	0.27640	0.540000	0.28808	0.591000	0.81541	GCT	C|0.721;G|0.279	0.279	strong		0.657	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
OR10H3	26532	hgsc.bcm.edu	37	19	15852872	15852872	+	Missense_Mutation	SNP	G	G	A	rs2240228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15852872G>A	ENST00000305892.1	+	1	670	c.670G>A	c.(670-672)Gtg>Atg	p.V224M		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	224			V -> M (in dbSNP:rs2240228). {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.V224M(1)		cervix(2)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						TGTCTTCATTGTGGCTGCCAT	0.502													g|||	998	0.199281	0.0832	0.2061	5008	,	,		21910	0.1984		0.2793	False		,,,				2504	0.2699				p.V224M		Atlas-SNP	.											OR10H3,NS,carcinoma,0,1	OR10H3	53	1	1	Substitution - Missense(1)	stomach(1)	c.G670A						PASS	.	G	MET/VAL	458,3948		28,402,1773	279.0	249.0	259.0		670	2.4	0.9	19	dbSNP_98	259	2228,6372		293,1642,2365	yes	missense	OR10H3	NM_013938.1	21	321,2044,4138	AA,AG,GG		25.907,10.3949,20.652	benign	224/317	15852872	2686,10320	2203	4300	6503	SO:0001583	missense	26532	exon1			TTCATTGTGGCTG		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.670G>A	19.37:g.15852872G>A	ENSP00000307130:p.Val224Met	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	279	147	0.526882	NM_013938	Q2HIZ3|Q6IFQ0	Missense_Mutation	SNP	ENST00000305892.1	37	CCDS12334.1	465	0.2129120879120879	60	0.12195121951219512	81	0.22375690607734808	112	0.1958041958041958	212	0.2796833773087071	.	5.213	0.224752	0.09916	0.103949	0.25907	ENSG00000171936	ENST00000305892	T	0.00164	8.64	2.37	2.37	0.29283	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	U	0.002428	T	0.00012	0.0000	M	0.62154	1.92	0.39635	P	0.029761999999999955	P	0.37083	0.581	B	0.42343	0.384	T	0.04128	-1.0975	9	0.56958	D	0.05	.	7.0644	0.25143	0.0:0.2853:0.7147:0.0	rs2240228;rs17749836;rs57020354;rs2240228	224	O60404	O10H3_HUMAN	M	224	ENSP00000307130:V224M	ENSP00000307130:V224M	V	+	1	0	OR10H3	15713872	0.000000	0.05858	0.928000	0.36995	0.049000	0.14656	-1.721000	0.01870	1.330000	0.45394	0.205000	0.17691	GTG	G|0.797;A|0.203	0.203	strong		0.502	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1		
ZNF804A	91752	hgsc.bcm.edu	37	2	185801103	185801103	+	Missense_Mutation	SNP	A	A	C	rs61739291	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:185801103A>C	ENST00000302277.6	+	4	1574	c.980A>C	c.(979-981)aAt>aCt	p.N327T		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	327							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						AATTGTCAAAATTCAGTCCCA	0.323													A|||	47	0.00938498	0.0	0.0058	5008	,	,		20581	0.0		0.0288	False		,,,				2504	0.0143				p.N327T		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A980C						PASS	.	A	THR/ASN	30,4376	35.2+/-66.4	0,30,2173	40.0	39.0	39.0		980	3.1	0.1	2	dbSNP_129	39	233,8361	88.1+/-150.5	3,227,4067	yes	missense	ZNF804A	NM_194250.1	65	3,257,6240	CC,CA,AA		2.7112,0.6809,2.0231	benign	327/1210	185801103	263,12737	2203	4297	6500	SO:0001583	missense	91752	exon4			GTCAAAATTCAGT	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.980A>C	2.37:g.185801103A>C	ENSP00000303252:p.Asn327Thr	Somatic	271	1	0.00369004		WXS	Illumina HiSeq	Phase_I	292	128	0.438356	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	26	0.011904761904761904	0	0.0	3	0.008287292817679558	0	0.0	23	0.030343007915567283	A	8.043	0.764214	0.15914	0.006809	0.027112	ENSG00000170396	ENST00000302277	T	0.47528	0.84	5.57	3.09	0.35607	.	0.309791	0.28011	N	0.016949	T	0.12689	0.0308	L	0.47716	1.5	0.18873	N	0.999985	B	0.26195	0.144	B	0.18561	0.022	T	0.10989	-1.0606	10	0.23891	T	0.37	-10.372	3.017	0.06063	0.6278:0.1486:0.0811:0.1425	rs61739291	327	Q7Z570	Z804A_HUMAN	T	327	ENSP00000303252:N327T	ENSP00000303252:N327T	N	+	2	0	ZNF804A	185509348	0.000000	0.05858	0.099000	0.21106	0.677000	0.39632	0.214000	0.17541	0.356000	0.24157	0.482000	0.46254	AAT	A|0.984;C|0.016	0.016	strong		0.323	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250	
DNAAF3	352909	hgsc.bcm.edu	37	19	55672470	55672470	+	Missense_Mutation	SNP	T	T	C	rs2365725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55672470T>C	ENST00000524407.2	-	8	908	c.875A>G	c.(874-876)gAg>gGg	p.E292G	DNAAF3_ENST00000527223.2_Missense_Mutation_p.E360G|DNAAF3_ENST00000587789.2_5'Flank|DNAAF3_ENST00000391720.4_Missense_Mutation_p.E339G|CTD-2587H24.5_ENST00000591665.1_RNA|CTD-2587H24.4_ENST00000587871.1_5'Flank|DNAAF3_ENST00000455045.1_Missense_Mutation_p.E238G			Q8N9W5	DAAF3_HUMAN	dynein, axonemal, assembly factor 3	292			E -> G (in dbSNP:rs2365725).		axonemal dynein complex assembly (GO:0070286)|motile cilium assembly (GO:0044458)	cytoplasm (GO:0005737)											CAGGAGGCTCTCGTCGTCCGC	0.716													t|||	1140	0.227636	0.5234	0.1455	5008	,	,		9834	0.0913		0.1421	False		,,,				2504	0.1145				p.E360G		Atlas-SNP	.											C19orf51,rectum,carcinoma,0,3	.	.	3	0			c.A1079G						PASS	.	T	GLY/GLU	1334,2304		255,824,740	4.0	7.0	6.0		1016	3.2	0.7	19	dbSNP_100	6	922,6602		75,772,2915	yes	missense	C19orf51	NM_178837.3	98	330,1596,3655	CC,CT,TT		12.2541,36.6685,20.2114	possibly-damaging	339/589	55672470	2256,8906	1819	3762	5581	SO:0001583	missense	352909	exon8			AGGCTCTCGTCGT	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.875A>G	19.37:g.55672470T>C	ENSP00000432046:p.Glu292Gly	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	55	0.964912	NM_001256714	A8MUY0|E3W9A1|E9PAX5|Q6P4F6|Q8N9W0|Q96AR2	Missense_Mutation	SNP	ENST00000524407.2	37	CCDS59422.1	457	0.20924908424908426	260	0.5284552845528455	56	0.15469613259668508	45	0.07867132867132867	96	0.1266490765171504	T	13.36	2.213980	0.39102	0.366685	0.122541	ENSG00000167646	ENST00000301249;ENST00000455045;ENST00000391720	T;T	0.22336	1.96;1.96	4.24	3.18	0.36537	.	0.812692	0.10927	N	0.618852	T	0.00012	0.0000	M	0.77486	2.375	0.51767	P	6.700000000003925E-5	P;P;B;P	0.41848	0.557;0.763;0.187;0.763	B;B;B;B	0.36845	0.234;0.229;0.073;0.229	T	0.43956	-0.9359	9	0.59425	D	0.04	-4.1385	8.5773	0.33605	0.0:0.0:0.3813:0.6186	rs2365725;rs2365725	360;238;313;292	E9PAX5;E3W9A1;Q8N9W5-3;Q8N9W5	.;.;.;CS051_HUMAN	G	360;238;339	ENSP00000394343:E238G;ENSP00000375600:E339G	ENSP00000301249:E360G	E	-	2	0	C19orf51	60364282	0.356000	0.24930	0.735000	0.30896	0.448000	0.32197	1.240000	0.32731	0.585000	0.29608	0.454000	0.30748	GAG	T|0.756;C|0.244	0.244	strong		0.716	DNAAF3-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250388.5	NM_178837	
OR13C2	392376	hgsc.bcm.edu	37	9	107367008	107367008	+	Missense_Mutation	SNP	T	T	C	rs10156474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107367008T>C	ENST00000542196.1	-	1	943	c.901A>G	c.(901-903)Aag>Gag	p.K301E		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	301			K -> E (in dbSNP:rs10156474).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						TTCACATCCTTGTTTCTAAGA	0.373													T|||	2155	0.430312	0.6256	0.2248	5008	,	,		20518	0.5774		0.1789	False		,,,				2504	0.4192				p.K301E		Atlas-SNP	.											.	OR13C2	46	.	0			c.A901G						PASS	.	T	GLU/LYS	2508,1894	629.6+/-395.3	759,990,452	163.0	161.0	162.0		901	3.5	1.0	9	dbSNP_119	162	1668,6932	307.4+/-308.4	183,1302,2815	no	missense	OR13C2	NM_001004481.1	56	942,2292,3267	CC,CT,TT		19.3953,43.0259,32.1181	probably-damaging	301/319	107367008	4176,8826	2201	4300	6501	SO:0001583	missense	392376	exon1			CATCCTTGTTTCT		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.901A>G	9.37:g.107367008T>C	ENSP00000438815:p.Lys301Glu	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	210	112	0.533333	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	826	0.3782051282051282	284	0.5772357723577236	79	0.21823204419889503	331	0.5786713286713286	132	0.1741424802110818	T	13.90	2.373626	0.42105	0.569741	0.193953	ENSG00000257019	ENST00000542196	T	0.44083	0.93	3.53	3.53	0.40419	.	0.000000	0.38436	U	0.001685	T	0.00012	0.0000	M	0.87038	2.855	0.39415	P	0.03319000000000005	P	0.39883	0.693	B	0.38500	0.275	T	0.48433	-0.9036	9	0.87932	D	0	.	6.7989	0.23740	0.0:0.0:0.2401:0.7599	rs10156474;rs59534843	301	Q8NGS9	O13C2_HUMAN	E	301	ENSP00000438815:K301E	ENSP00000438815:K301E	K	-	1	0	OR13C2	106406829	0.437000	0.25593	0.996000	0.52242	0.867000	0.49689	1.835000	0.39181	1.475000	0.48197	0.379000	0.24179	AAG	T|0.639;C|0.361	0.361	strong		0.373	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
FABP2	2169	hgsc.bcm.edu	37	4	120240238	120240238	+	Silent	SNP	T	T	C	rs1511025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:120240238T>C	ENST00000274024.3	-	4	644	c.357A>G	c.(355-357)gtA>gtG	p.V119V		NM_000134.3	NP_000125.2	P12104	FABPI_HUMAN	fatty acid binding protein 2, intestinal	119					digestion (GO:0007586)	cytoplasm (GO:0005737)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			breast(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	8					Estradiol(DB00783)|Ibuprofen(DB01050)|Sulfinpyrazone(DB01138)	CTCCTTCATATACATAAGTCT	0.299													T|||	1668	0.333067	0.4017	0.33	5008	,	,		11767	0.3948		0.3121	False		,,,				2504	0.2004				p.V119V		Atlas-SNP	.											FABP2,NS,carcinoma,-1,1	FABP2	21	1	0			c.A357G						PASS	.	T		1656,2750	503.4+/-365.5	308,1040,855	107.0	108.0	108.0		357	-10.1	0.0	4	dbSNP_88	108	2817,5775	443.7+/-360.5	465,1887,1944	no	coding-synonymous	FABP2	NM_000134.3		773,2927,2799	CC,CT,TT		32.7863,37.5851,34.413		119/133	120240238	4473,8525	2203	4296	6499	SO:0001819	synonymous_variant	2169	exon4			TTCATATACATAA	J03465	CCDS3712.1	4q28-q31	2013-03-01			ENSG00000145384	ENSG00000145384		"""Fatty acid binding protein family"""	3556	protein-coding gene	gene with protein product		134640					Standard	NM_000134		Approved	I-FABP	uc003icw.3	P12104	OTTHUMG00000132972	ENST00000274024.3:c.357A>G	4.37:g.120240238T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	174	87	0.5	NM_000134	Q2NKJ1	Silent	SNP	ENST00000274024.3	37	CCDS3712.1																																																																																			T|0.654;C|0.346	0.346	strong		0.299	FABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256531.1	NM_000134	
PTGDR	5729	hgsc.bcm.edu	37	14	52735108	52735108	+	Silent	SNP	C	C	T	rs34968651	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:52735108C>T	ENST00000306051.2	+	1	678	c.576C>T	c.(574-576)ggC>ggT	p.G192G	PTGDR_ENST00000553372.1_Silent_p.G192G	NM_000953.2	NP_000944.1	Q13258	PD2R_HUMAN	prostaglandin D2 receptor (DP)	192					adenosine metabolic process (GO:0046085)|cellular response to prostaglandin D stimulus (GO:0071799)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|male sex determination (GO:0030238)|sleep (GO:0030431)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	prostaglandin D receptor activity (GO:0004956)|prostaglandin J receptor activity (GO:0001785)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Breast(41;0.0639)|all_epithelial(31;0.0887)				Nedocromil(DB00716)	ACGAGGAGGGCTCGCTGTCGG	0.627													C|||	406	0.0810703	0.0068	0.0519	5008	,	,		17584	0.123		0.0905	False		,,,				2504	0.1493				p.G192G		Atlas-SNP	.											.	PTGDR	58	.	0			c.C576T						PASS	.	C		95,4311	77.3+/-115.6	0,95,2108	98.0	85.0	89.0		576	-1.4	0.9	14	dbSNP_126	89	742,7858	179.9+/-228.9	26,690,3584	no	coding-synonymous	PTGDR	NM_000953.2		26,785,5692	TT,TC,CC		8.6279,2.1562,6.4355		192/360	52735108	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	5729	exon1			GGAGGGCTCGCTG	U31332	CCDS9707.1, CCDS61454.1	14q22.1	2012-08-08			ENSG00000168229	ENSG00000168229		"""GPCR / Class A : Prostanoid receptors"""	9591	protein-coding gene	gene with protein product		604687				7642548	Standard	NM_000953		Approved	DP, DP1, PTGDR1	uc001wzq.3	Q13258	OTTHUMG00000140299	ENST00000306051.2:c.576C>T	14.37:g.52735108C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_000953	G3V5L3|Q13250|Q13251|Q1ZZ52	Silent	SNP	ENST00000306051.2	37	CCDS9707.1																																																																																			C|0.932;T|0.068	0.068	strong		0.627	PTGDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276889.1	NM_000953	
NCOA3	8202	hgsc.bcm.edu	37	20	46279866	46279866	+	Silent	SNP	A	A	G	rs578139784|rs112826888|rs1132443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:46279866A>G	ENST00000371998.3	+	20	3983	c.3792A>G	c.(3790-3792)caA>caG	p.Q1264Q	NCOA3_ENST00000371997.3_Silent_p.Q1255Q|NCOA3_ENST00000341724.6_Silent_p.Q1190Q|NCOA3_ENST00000372004.3_Silent_p.Q1260Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1264	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcagcaacagcaacagc	0.567													G|||	599	0.119609	0.2186	0.0663	5008	,	,		14499	0.0873		0.0726	False		,,,				2504	0.1053				p.Q1264Q		Atlas-SNP	.											NCOA3,colon,carcinoma,0,1	NCOA3	156	1	0			c.A3792G						PASS	.	G	,,,	561,3841		126,309,1766	56.0	66.0	62.0		3789,3765,3780,3792	0.0	0.2	20	dbSNP_86	62	436,8164		30,376,3894	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	156,685,5660	GG,GA,AA		5.0698,12.7442,7.6681	,,,	1263/1424,1255/1416,1260/1421,1264/1425	46279866	997,12005	2201	4300	6501	SO:0001819	synonymous_variant	8202	exon20			GCAGCAACAGCAA	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3792A>G	20.37:g.46279866A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	86	45	0.523256	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			A|0.870;G|0.130	0.130	strong		0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
MYO16	23026	hgsc.bcm.edu	37	13	109613929	109613929	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:109613929C>T	ENST00000357550.2	+	17	2055	c.2014C>T	c.(2014-2016)Ctt>Ttt	p.L672F	MYO16_ENST00000251041.5_Missense_Mutation_p.L672F|MYO16_ENST00000457511.2_Missense_Mutation_p.L184F|MYO16_ENST00000356711.2_Missense_Mutation_p.L672F	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)			AATATTGCACCTTGGAGACAT	0.453																																					p.L694F		Atlas-SNP	.											.	MYO16	285	.	0			c.C2080T						PASS	.						191.0	153.0	166.0					13																	109613929		2203	4300	6503	SO:0001583	missense	23026	exon18			TTGCACCTTGGAG		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.2014C>T	13.37:g.109613929C>T	ENSP00000350160:p.Leu672Phe	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	99	4	0.040404	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.743813	0.30865	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857;ENST00000457511	D;D;D;D	0.97959	-4.63;-4.63;-4.63;-4.63	5.07	-8.68	0.00859	Myosin head, motor domain (2);	0.760287	0.10614	U	0.654105	D	0.96253	0.8778	M	0.74389	2.26	0.23913	N	0.996482	P;P;P	0.46987	0.888;0.888;0.733	P;P;B	0.46885	0.474;0.53;0.375	D	0.93439	0.6792	9	.	.	.	.	11.4832	0.50337	0.2328:0.5853:0.182:0.0	.	184;672;672	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	F	672;672;672;672;460;184	ENSP00000349145:L672F;ENSP00000350160:L672F;ENSP00000251041:L672F;ENSP00000401633:L184F	.	L	+	1	0	MYO16	108411930	0.881000	0.30235	0.010000	0.14722	0.052000	0.14988	-0.121000	0.10643	-1.924000	0.01064	-1.513000	0.00942	CTT	.	.	none		0.453	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
CEP83	51134	hgsc.bcm.edu	37	12	94772742	94772742	+	Missense_Mutation	SNP	C	C	T	rs2271979	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:94772742C>T	ENST00000397809.5	-	7	1175	c.626G>A	c.(625-627)cGa>cAa	p.R209Q	CCDC41_ENST00000547575.1_Missense_Mutation_p.R209Q|CCDC41_ENST00000339839.5_Missense_Mutation_p.R209Q|CCDC41_ENST00000397807.2_Missense_Mutation_p.R176Q|CCDC41_ENST00000549352.1_5'UTR	NM_016122.2	NP_057206.2	Q9Y592	CEP83_HUMAN		201					cilium assembly (GO:0042384)|protein localization to centrosome (GO:0071539)|vesicle docking (GO:0048278)	centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|Golgi apparatus (GO:0005794)				breast(1)|central_nervous_system(3)|kidney(3)|large_intestine(8)|lung(8)|prostate(2)|skin(2)	27						TTGTTCCACTCGTTTGCTGTC	0.358													C|||	657	0.13119	0.0053	0.1369	5008	,	,		19135	0.3224		0.0746	False		,,,				2504	0.1585				p.R209Q		Atlas-SNP	.											CCDC41,caecum,carcinoma,0,1	CCDC41	59	1	0			c.G626A						PASS	.	C	GLN/ARG,GLN/ARG	76,3588		2,72,1758	122.0	114.0	116.0		626,626	3.8	1.0	12	dbSNP_100	116	575,7593		15,545,3524	yes	missense,missense	CCDC41	NM_016122.2,NM_001042399.1	43,43	17,617,5282	TT,TC,CC		7.0397,2.0742,5.502	benign,benign	209/702,209/702	94772742	651,11181	1832	4084	5916	SO:0001583	missense	51134	exon7			TCCACTCGTTTGC																												ENST00000397809.5:c.626G>A	12.37:g.94772742C>T	ENSP00000380911:p.Arg209Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_016122	A4FVB1|Q08AP1	Missense_Mutation	SNP	ENST00000397809.5	37	CCDS41820.1	310	0.14194139194139194	4	0.008130081300813009	52	0.143646408839779	187	0.3269230769230769	67	0.08839050131926121	C	13.37	2.216616	0.39201	0.020742	0.070397	ENSG00000173588	ENST00000339839;ENST00000397809;ENST00000397807;ENST00000547575	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.59	3.75	0.43078	.	.	.	.	.	T	0.00012	0.0000	M	0.63843	1.955	0.24721	P	0.99314158	P;P;B	0.41748	0.641;0.761;0.392	B;B;B	0.30029	0.11;0.11;0.03	T	0.46219	-0.9207	8	0.18710	T	0.47	-2.4485	12.3709	0.55254	0.0:0.861:0.0:0.139	rs2271979;rs58671937;rs2271979	209;176;201	F8VYN8;Q9Y592-2;Q9Y592	.;.;CCD41_HUMAN	Q	209;209;176;209	ENSP00000344655:R209Q;ENSP00000380911:R209Q;ENSP00000380909:R176Q;ENSP00000448913:R209Q	ENSP00000344655:R209Q	R	-	2	0	CCDC41	93296873	0.994000	0.37717	0.992000	0.48379	0.399000	0.30720	3.159000	0.50731	0.708000	0.31955	0.585000	0.79938	CGA	C|0.864;T|0.136	0.136	strong		0.358	CCDC41-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408147.3		
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920196	51920196	+	Missense_Mutation	SNP	G	G	T	rs73049612	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51920196G>T	ENST00000339313.5	-	3	546	c.430C>A	c.(430-432)Cag>Aag	p.Q144K	CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Intron|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.Q144K|SIGLEC10_ENST00000439889.2_Intron|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.Q144K|SIGLEC10_ENST00000525998.1_Missense_Mutation_p.Q144K|SIGLEC10_ENST00000436984.2_Intron|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.Q144K			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	144					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)		TCAGGCTTCTGAGTCAGGGCT	0.617																																					p.Q144K		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C430A						PASS	.						70.0	81.0	77.0					19																	51920196		2203	4300	6503	SO:0001583	missense	89790	exon3			GCTTCTGAGTCAG	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.430C>A	19.37:g.51920196G>T	ENSP00000345243:p.Gln144Lys	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	180	37	0.205556	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	11.57	1.677583	0.29783	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000525998;ENST00000339313;ENST00000530476	T;T;T;T;T;T	0.18810	3.96;2.19;3.96;3.96;3.96;3.96	4.85	2.57	0.30868	Immunoglobulin-like fold (1);	0.404011	0.21813	N	0.068733	T	0.21468	0.0517	M	0.79343	2.45	0.20638	N	0.999877	P;B;B	0.41929	0.765;0.095;0.243	B;B;B	0.35899	0.213;0.094;0.032	T	0.16837	-1.0389	10	0.18710	T	0.47	.	11.5078	0.50476	0.0:0.3473:0.6527:0.0	.	144;144;144	E9PL79;Q96LC7-2;Q96LC7	.;.;SIG10_HUMAN	K	144;144;144;144;144;111	ENSP00000342389:Q144K;ENSP00000396742:Q144K;ENSP00000348646:Q144K;ENSP00000431444:Q144K;ENSP00000345243:Q144K;ENSP00000433838:Q111K	ENSP00000345243:Q144K	Q	-	1	0	SIGLEC10	56612008	0.002000	0.14202	0.320000	0.25306	0.554000	0.35429	0.861000	0.27885	1.019000	0.39547	0.313000	0.20887	CAG	.	.	weak		0.617	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
SIRPB1	10326	hgsc.bcm.edu	37	20	1552430	1552430	+	Missense_Mutation	SNP	T	T	C	rs386811627|rs2253427	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1552430T>C	ENST00000381605.4	-	3	751	c.687A>G	c.(685-687)atA>atG	p.I229M	SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	229	Ig-like C1-type 1.		I -> M (in dbSNP:rs2253427). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9062191}.		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)		p.I229M(1)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TGATGTGGGCTATCTCGCAGA	0.607													.|||	4127	0.824081	0.9448	0.6427	5008	,	,		19977	0.7937		0.7893	False		,,,				2504	0.8569				p.I229M		Atlas-SNP	.											SIRPB1,NS,carcinoma,0,1	SIRPB1	83	1	1	Substitution - Missense(1)	prostate(1)	c.A687G						PASS	.	C	,MET/ILE	4001,405		1823,355,25	144.0	126.0	132.0		,687	2.5	1.0	20	dbSNP_100	132	6748,1852		2633,1482,185	yes	intron,missense	SIRPB1	NM_001083910.2,NM_006065.3	,10	4456,1837,210	CC,CT,TT		21.5349,9.192,17.3535	,benign	,229/399	1552430	10749,2257	2203	4300	6503	SO:0001583	missense	10326	exon3			GTGGGCTATCTCG	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.687A>G	20.37:g.1552430T>C	ENSP00000371018:p.Ile229Met	Somatic	446	1	0.00224215		WXS	Illumina HiSeq	Phase_I	413	409	0.990315	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	1756	0.8040293040293041	460	0.9349593495934959	248	0.6850828729281768	450	0.7867132867132867	598	0.7889182058047494	.	5.965	0.362082	0.11296	0.90808	0.784651	ENSG00000101307	ENST00000381605	T	0.03212	4.01	2.47	2.47	0.30058	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.237664	0.29410	N	0.012233	T	0.00012	0.0000	N	0.12182	0.205	0.09310	P	0.99999999356862	B	0.02656	0.0	B	0.06405	0.002	T	0.10917	-1.0609	9	0.66056	D	0.02	.	5.4584	0.16604	0.0:0.8325:0.0:0.1675	rs2253427;rs17721307;rs52793924;rs56602251;rs60761561;rs2253427	229	O00241	SIRB1_HUMAN	M	229	ENSP00000371018:I229M	ENSP00000371018:I229M	I	-	3	3	SIRPB1	1500430	0.606000	0.26949	0.996000	0.52242	0.027000	0.11550	-0.012000	0.12699	0.391000	0.25143	-0.365000	0.07479	ATA	C|0.824;N|0.000	0.824	strong		0.607	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
ANO3	63982	hgsc.bcm.edu	37	11	26621117	26621117	+	Silent	SNP	A	A	C	rs11604868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:26621117A>C	ENST00000256737.3	+	17	2544	c.1692A>C	c.(1690-1692)gcA>gcC	p.A564A	ANO3_ENST00000537978.1_Silent_p.A548A|ANO3_ENST00000531568.1_Silent_p.A418A|ANO3_ENST00000525139.1_Silent_p.A548A	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	564					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	phospholipid scramblase activity (GO:0017128)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68						TGATCACTGCAGTGTTTGGAG	0.388													A|||	816	0.162939	0.0794	0.1268	5008	,	,		18447	0.3224		0.2058	False		,,,				2504	0.093				p.A564A		Atlas-SNP	.											.	ANO3	145	.	0			c.A1692C						PASS	.	A		387,4019	193.0+/-218.2	18,351,1834	306.0	266.0	280.0		1692	-2.6	1.0	11	dbSNP_120	280	1528,7070	289.3+/-299.2	127,1274,2898	no	coding-synonymous	ANO3	NM_031418.2		145,1625,4732	CC,CA,AA		17.7716,8.7835,14.7262		564/982	26621117	1915,11089	2203	4299	6502	SO:0001819	synonymous_variant	63982	exon17			CACTGCAGTGTTT	AJ300461	CCDS31447.1	11p14.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000134343	ENSG00000134343		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	14004	protein-coding gene	gene with protein product	"""transmembrane protein 16C (eight membrane-spanning domains)"""	610110	"""chromosome 11 open reading frame 25"", ""transmembrane protein 16C"""	C11orf25, TMEM16C		12739008, 15067359, 23200863, 24692353	Standard	NM_031418		Approved	GENX-3947, DYT23	uc001mqt.4	Q9BYT9	OTTHUMG00000166096	ENST00000256737.3:c.1692A>C	11.37:g.26621117A>C		Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	226	110	0.486726	NM_031418	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																			A|0.835;C|0.165	0.165	strong		0.388	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418	
PCDHGB2	56103	hgsc.bcm.edu	37	5	140739779	140739779	+	Missense_Mutation	SNP	C	C	G	rs17097231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140739779C>G	ENST00000522605.1	+	1	77	c.77C>G	c.(76-78)cCc>cGc	p.P26R	PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	26			P -> R (in dbSNP:rs17097231).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTTTGTTCCCCGGGGCTCTC	0.592											OREG0016857	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	653	0.130391	0.1573	0.1671	5008	,	,		14680	0.119		0.0706	False		,,,				2504	0.1411				p.P26R		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.C77G						PASS	.	C	,,,,,ARG/PRO,ARG/PRO	565,3303		41,483,1410	37.0	43.0	41.0		,,,,,77,77	2.5	0.3	5	dbSNP_123	41	742,7522		38,666,3428	yes	intron,intron,intron,intron,intron,missense,missense	PCDHGB2,PCDHGB1,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018922.2,NM_018923.2,NM_032096.1	,,,,,103,103	79,1149,4838	GG,GC,CC		8.9787,14.607,10.7732	,,,,,,	,,,,,26/932,26/812	140739779	1307,10825	1934	4132	6066	SO:0001583	missense	56103	exon1			TGTTCCCCGGGGC	AF152331	CCDS54924.1, CCDS75332.1	5q31	2010-01-26				ENSG00000253910		"""Cadherins / Protocadherins : Clustered"""	8709	other	protocadherin		606300				10380929	Standard	NM_018923		Approved	PCDH-GAMMA-B2		Q9Y5G2		ENST00000522605.1:c.77C>G	5.37:g.140739779C>G	ENSP00000429018:p.Pro26Arg	Somatic	132	0	0	1658	WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_018923	Q3MIJ3|Q9UN65	Missense_Mutation	SNP	ENST00000522605.1	37	CCDS54924.1	254	0.1163003663003663	69	0.1402439024390244	55	0.15193370165745856	70	0.12237762237762238	60	0.079155672823219	.	0.087	-1.173915	0.01646	0.14607	0.089787	ENSG00000253910	ENST00000522605	T	0.49720	0.77	5.3	2.45	0.29901	Cadherin-like (1);	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12293	-1.0553	8	0.24483	T	0.36	.	8.4831	0.33054	0.1542:0.1344:0.7114:0.0	rs17097231;rs52831211;rs58908268;rs17097231	26;26	Q9Y5G2-2;Q9Y5G2	.;PCDGE_HUMAN	R	26	ENSP00000429018:P26R	ENSP00000429018:P26R	P	+	2	0	PCDHGB2	140719963	0.001000	0.12720	0.286000	0.24833	0.249000	0.25844	0.942000	0.29017	0.694000	0.31654	-0.344000	0.07964	CCC	C|0.880;G|0.120	0.120	strong		0.592	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923	
KL	9365	hgsc.bcm.edu	37	13	33628239	33628239	+	Silent	SNP	G	G	A	rs9527026	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:33628239G>A	ENST00000380099.3	+	2	1163	c.1155G>A	c.(1153-1155)aaG>aaA	p.K385K	KL_ENST00000426690.2_Silent_p.K78K|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	385	Glycosyl hydrolase-1 1.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		CTCACATGAAGTTCCGCCAAT	0.408													A|||	651	0.129992	0.2005	0.0821	5008	,	,		18159	0.0		0.1938	False		,,,				2504	0.137				p.K385K		Atlas-SNP	.											.	KL	106	.	0			c.G1155A						PASS	.	A		815,3591	748.9+/-412.0	74,667,1462	174.0	180.0	178.0		1155	3.2	1.0	13	dbSNP_119	178	1411,7189	752.1+/-407.4	116,1179,3005	no	coding-synonymous	KL	NM_004795.3		190,1846,4467	AA,AG,GG		16.407,18.4975,17.1152		385/1013	33628239	2226,10780	2203	4300	6503	SO:0001819	synonymous_variant	9365	exon2			CATGAAGTTCCGC	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1155G>A	13.37:g.33628239G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	119	46	0.386555	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																			G|0.844;A|0.156	0.156	strong		0.408	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
EPS8L2	64787	hgsc.bcm.edu	37	11	721570	721570	+	Silent	SNP	C	C	T	rs7635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:721570C>T	ENST00000533256.1	+	11	1149	c.774C>T	c.(772-774)atC>atT	p.I258I	AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000526198.1_Silent_p.I274I|EPS8L2_ENST00000318562.8_Silent_p.I258I|EPS8L2_ENST00000530636.1_Silent_p.I258I			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	258					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)		CCCAGCAAATCCTCAACTGCG	0.637													c|||	1401	0.279752	0.1884	0.5648	5008	,	,		14025	0.1746		0.4155	False		,,,				2504	0.1697				p.I258I		Atlas-SNP	.											EPS8L2,colon,carcinoma,0,1	EPS8L2	42	1	0			c.C774T						PASS	.			970,3408		127,716,1346	22.0	27.0	26.0		774	3.8	1.0	11	dbSNP_52	26	3854,4700		888,2078,1311	no	coding-synonymous	EPS8L2	NM_022772.3		1015,2794,2657	TT,TC,CC		45.0549,22.1562,37.3028		258/716	721570	4824,8108	2189	4277	6466	SO:0001819	synonymous_variant	64787	exon10			GCAAATCCTCAAC	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.774C>T	11.37:g.721570C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Silent	SNP	ENST00000533256.1	37	CCDS31328.1																																																																																			C|0.687;T|0.313	0.313	strong		0.637	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772	
GNB2	2783	hgsc.bcm.edu	37	7	100276355	100276355	+	Silent	SNP	C	C	T	rs17850902	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100276355C>T	ENST00000303210.4	+	10	1436	c.954C>T	c.(952-954)ctC>ctT	p.L318L	GNB2_ENST00000419828.1_Silent_p.L218L|GNB2_ENST00000436220.1_Silent_p.L274L|GNB2_ENST00000393924.1_Silent_p.L318L|GNB2_ENST00000424361.1_Silent_p.L274L|GNB2_ENST00000427895.1_Silent_p.L218L|GNB2_ENST00000393926.1_Silent_p.L318L	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	318					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)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|lung(3)|ovary(2)|prostate(1)	7	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				TGAGCTGCCTCGGGGTCACCG	0.652													C|||	17	0.00339457	0.0008	0.0029	5008	,	,		16180	0.001		0.005	False		,,,				2504	0.0082				p.L318L		Atlas-SNP	.											.	GNB2	29	.	0			c.C954T						PASS	.	C		7,4399		0,7,2196	60.0	63.0	62.0		954	-6.0	0.9	7	dbSNP_123	62	76,8524		0,76,4224	no	coding-synonymous	GNB2	NM_005273.3		0,83,6420	TT,TC,CC		0.8837,0.1589,0.6382		318/341	100276355	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	2783	exon10			CTGCCTCGGGGTC	M16514	CCDS5703.1	7q21.3-q22.1	2013-01-10			ENSG00000172354	ENSG00000172354		"""WD repeat domain containing"""	4398	protein-coding gene	gene with protein product	"""G protein, beta-2 subunit"", ""guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2"", ""signal-transducing guanine nucleotide-binding regulatory protein beta subunit"", ""transducin beta chain 2"""	139390				9799793	Standard	NM_005273		Approved		uc003uwb.3	P62879	OTTHUMG00000137419	ENST00000303210.4:c.954C>T	7.37:g.100276355C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	147	83	0.564626	NM_005273	B3KPU1|P11016|P54312	Silent	SNP	ENST00000303210.4	37	CCDS5703.1																																																																																			C|0.995;T|0.005	0.005	strong		0.652	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273	
MICA	100507436	hgsc.bcm.edu	37	6	31379795	31379795	+	Missense_Mutation	SNP	A	A	G	rs1131898|rs386699191	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31379795A>G	ENST00000449934.2	+	4	739	c.685A>G	c.(685-687)Agc>Ggc	p.S229G	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				CAGGGCTTCCAGCTTCTATCC	0.587													g|||	1823	0.364018	0.4773	0.4063	5008	,	,		19594	0.2996		0.3141	False		,,,				2504	0.2986				p.S229G		Atlas-SNP	.											.	MICA	21	.	0			c.A685G						PASS	.						20.0	24.0	23.0					6																	31379795		692	1591	2283	SO:0001583	missense	100507436	exon4			GCTTCCAGCTTCT	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.685A>G	6.37:g.31379795A>G	ENSP00000413079:p.Ser229Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	664	0.304029304029304	188	0.3821138211382114	147	0.40607734806629836	134	0.23426573426573427	195	0.25725593667546176	N	0.013	-1.630927	0.00813	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.09163	3.01;3.01	2.52	-1.92	0.07618	.	1.300610	0.05734	N	0.600057	T	0.00967	0.0032	.	.	.	0.80722	P	0.0	B;B	0.14012	0.009;0.003	B;B	0.08055	0.003;0.001	T	0.43310	-0.9399	8	0.02654	T	1	.	8.8893	0.35423	0.6127:0.0:0.3873:0.0	rs1131898;rs3192173;rs17206701;rs17883642	91;229	Q5SS58;Q96QC4	.;.	G	91;229;186;229;120	ENSP00000413079:S229G;ENSP00000402410:S120G	ENSP00000365394:S229G	S	+	1	0	MICA	31487774	0.015000	0.18098	0.001000	0.08648	0.014000	0.08584	0.171000	0.16685	-0.782000	0.04541	-1.366000	0.01203	AGC	A|0.700;G|0.300	0.300	strong		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
POU2F2	5452	hgsc.bcm.edu	37	19	42600030	42600030	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:42600030T>C	ENST00000526816.2	-	9	730	c.715A>G	c.(715-717)Acg>Gcg	p.T239A	POU2F2_ENST00000560398.1_Missense_Mutation_p.T245A|POU2F2_ENST00000342301.4_Missense_Mutation_p.T239A|POU2F2_ENST00000389341.5_Missense_Mutation_p.T223A|POU2F2_ENST00000533720.1_Missense_Mutation_p.T223A|POU2F2_ENST00000529067.1_Missense_Mutation_p.T223A|POU2F2_ENST00000529952.1_Missense_Mutation_p.T239A|POU2F2_ENST00000560558.1_Missense_Mutation_p.T184A			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	239	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	GAAATGGTCGTCTGGCTGAAG	0.627																																					p.T239A		Atlas-SNP	.											POU2F2_ENST00000292077,NS,lymphoid_neoplasm,0,8	POU2F2	106	8	0			c.A715G						PASS	.						119.0	118.0	118.0					19																	42600030		2203	4300	6503	SO:0001583	missense	5452	exon9			TGGTCGTCTGGCT		CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9213	protein-coding gene	gene with protein product		164176	"""POU domain class 2, transcription factor 2"""	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.715A>G	19.37:g.42600030T>C	ENSP00000431603:p.Thr239Ala	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	79	31	0.392405	NM_001207025	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957613	0.73902	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	4.38	2.18	0.27775	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.247967	0.39834	N	0.001250	D	0.91492	0.7314	M	0.88310	2.945	0.52501	D	0.999956	D;P;B	0.76494	0.999;0.953;0.262	D;D;B	0.79784	0.993;0.938;0.37	D	0.89325	0.3643	10	0.87932	D	0	.	6.8485	0.24003	0.15:0.0:0.1568:0.6932	.	223;239;223	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	A	223;239;239;223;238;223;239	ENSP00000373992:T223A;ENSP00000339369:T239A;ENSP00000437221:T223A;ENSP00000437224:T223A;ENSP00000436988:T239A	ENSP00000292077:T239A	T	-	1	0	POU2F2	47291870	1.000000	0.71417	0.972000	0.41901	0.994000	0.84299	7.819000	0.86621	0.269000	0.21961	0.454000	0.30748	ACG	.	.	none		0.627	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3		
LAMA1	284217	hgsc.bcm.edu	37	18	7012123	7012123	+	Silent	SNP	A	A	G	rs9946794	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:7012123A>G	ENST00000389658.3	-	24	3471	c.3378T>C	c.(3376-3378)ggT>ggC	p.G1126G		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1126	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TGCACTGAGGACCAAAGACAT	0.512													G|||	2104	0.420128	0.851	0.3833	5008	,	,		15427	0.0536		0.3648	False		,,,				2504	0.2986				p.G1126G		Atlas-SNP	.											LAMA1,NS,carcinoma,0,1	LAMA1	458	1	0			c.T3378C						PASS	.	G		3346,1060	383.0+/-324.7	1264,818,121	42.0	42.0	42.0		3378	-0.9	0.8	18	dbSNP_119	42	3349,5251	640.8+/-399.6	663,2023,1614	no	coding-synonymous	LAMA1	NM_005559.3		1927,2841,1735	GG,GA,AA		38.9419,24.0581,48.5238		1126/3076	7012123	6695,6311	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon24			CTGAGGACCAAAG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3378T>C	18.37:g.7012123A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	42	27	0.642857	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			A|0.528;G|0.472	0.472	strong		0.512	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026491	176026491	+	Silent	SNP	G	G	A	rs35847475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176026491G>A	ENST00000303991.4	-	2	522	c.345C>T	c.(343-345)gcC>gcT	p.A115A		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	115					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTGAGATGGAGGCTCCATGTG	0.602													G|||	40	0.00798722	0.0	0.0072	5008	,	,		18716	0.0		0.0278	False		,,,				2504	0.0072				p.A115A		Atlas-SNP	.											.	GPRIN1	77	.	0			c.C345T						PASS	.	G		21,4385	28.1+/-56.4	0,21,2182	78.0	82.0	81.0		345	1.0	0.0	5	dbSNP_126	81	221,8379	92.1+/-154.2	2,217,4081	no	coding-synonymous	GPRIN1	NM_052899.2		2,238,6263	AA,AG,GG		2.5698,0.4766,1.8607		115/1009	176026491	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	114787	exon2			GATGGAGGCTCCA	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.345C>T	5.37:g.176026491G>A		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_052899	C9JM70|Q8ND74|Q96PZ4	Silent	SNP	ENST00000303991.4	37	CCDS4405.1																																																																																			G|0.984;A|0.016	0.016	strong		0.602	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
ACADL	33	hgsc.bcm.edu	37	2	211085491	211085491	+	Missense_Mutation	SNP	G	G	A	rs61731470	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211085491G>A	ENST00000233710.3	-	2	340	c.113C>T	c.(112-114)aCt>aTt	p.T38I	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	38					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		AGCAGAAGGAGTTTCTAGACG	0.333													G|||	78	0.0155751	0.0015	0.0274	5008	,	,		18116	0.001		0.0358	False		,,,				2504	0.0204				p.T38I		Atlas-SNP	.											.	ACADL	38	.	0			c.C113T						PASS	.	G	ILE/THR	25,4381	29.0+/-57.7	0,25,2178	60.0	59.0	60.0		113	1.5	0.3	2	dbSNP_129	60	310,8290	108.0+/-168.7	2,306,3992	yes	missense	ACADL	NM_001608.3	89	2,331,6170	AA,AG,GG		3.6047,0.5674,2.5757	benign	38/431	211085491	335,12671	2203	4300	6503	SO:0001583	missense	33	exon2			GAAGGAGTTTCTA	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"""acyl-Coenzyme A dehydrogenase, long chain"""			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.113C>T	2.37:g.211085491G>A	ENSP00000233710:p.Thr38Ile	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	39	25	0.641026	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	39	0.017857142857142856	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	27	0.03562005277044855	G	12.72	2.022726	0.35701	0.005674	0.036047	ENSG00000115361	ENST00000233710	D	0.97553	-4.43	5.69	1.46	0.22682	.	0.233058	0.42294	D	0.000738	T	0.76147	0.3947	N	0.08118	0	0.34426	D	0.697969	B	0.15141	0.012	B	0.12156	0.007	T	0.81678	-0.0824	10	0.48119	T	0.1	.	13.294	0.60286	0.0639:0.3386:0.5975:0.0	rs61731470	38	P28330	ACADL_HUMAN	I	38	ENSP00000233710:T38I	ENSP00000233710:T38I	T	-	2	0	ACADL	210793736	0.999000	0.42202	0.338000	0.25549	0.833000	0.47200	1.967000	0.40491	0.319000	0.23209	-0.126000	0.14955	ACT	G|0.976;A|0.024	0.024	strong		0.333	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204399061	204399061	+	Silent	SNP	A	A	G	rs2271419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204399061A>G	ENST00000367187.3	-	30	4942	c.4386T>C	c.(4384-4386)ccT>ccC	p.P1462P	PIK3C2B_ENST00000424712.2_Silent_p.P1434P|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1462	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CGGCCACCTCAGGGGGTGCGT	0.667													G|||	690	0.13778	0.2784	0.1037	5008	,	,		17000	0.0774		0.1113	False		,,,				2504	0.0613				p.P1462P		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.T4386C						PASS	.	G		130,4276		55,20,2128	83.0	75.0	78.0		4386	-10.9	0.0	1	dbSNP_100	78	34,8566		11,12,4277	no	coding-synonymous	PIK3C2B	NM_002646.3		66,32,6405	GG,GA,AA		0.3953,2.9505,1.261		1462/1635	204399061	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon30			CACCTCAGGGGGT	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4386T>C	1.37:g.204399061A>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			A|0.866;G|0.134	0.134	strong		0.667	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
DNMT3B	1789	hgsc.bcm.edu	37	20	31367948	31367948	+	Intron	SNP	C	C	T	rs6058885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:31367948C>T	ENST00000328111.2	+	2	315				DNMT3B_ENST00000456297.2_Intron|DNMT3B_ENST00000344505.4_Intron|DNMT3B_ENST00000443239.3_Intron|DNMT3B_ENST00000348286.2_Intron|DNMT3B_ENST00000353855.2_Intron|DNMT3B_ENST00000201963.3_Silent_p.S9S|DNMT3B_ENST00000375623.4_Intron	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta						C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						AGCCTCCAAGCTTGGTGAGGG	0.632													c|||	478	0.0954473	0.1687	0.0519	5008	,	,		12424	0.0754		0.0606	False		,,,				2504	0.0838				p.S9S		Atlas-SNP	.											.	DNMT3B	196	.	0			c.C27T						PASS	.		,,,,,	609,3793		53,503,1645	19.0	21.0	20.0		,,,,,27	0.4	0.7	20	dbSNP_114	20	519,8077		11,497,3790	no	intron,intron,intron,intron,intron,coding-synonymous	DNMT3B	NM_001207055.1,NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,NM_175850.2	,,,,,	64,1000,5435	TT,TC,CC		6.0377,13.8346,8.6783	,,,,,	,,,,,9/846	31367948	1128,11870	2201	4298	6499	SO:0001627	intron_variant	1789	exon1			TCCAAGCTTGGTG		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.-6-176C>T	20.37:g.31367948C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_175850	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1																																																																																			C|0.921;T|0.079	0.079	strong		0.632	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	
GALC	2581	hgsc.bcm.edu	37	14	88459434	88459434	+	Silent	SNP	G	G	T	rs111976362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:88459434G>T	ENST00000261304.2	-	1	181	c.75C>A	c.(73-75)ggC>ggA	p.G25G	GALC_ENST00000393569.2_Intron|GALC_ENST00000393568.4_Silent_p.G25G|GALC_ENST00000544807.2_5'Flank	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	25					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)	p.G25G(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CCGCGGCGCGGCCCGCCGAAC	0.711													G|||	393	0.0784744	0.0174	0.1657	5008	,	,		9796	0.005		0.1561	False		,,,				2504	0.0951				p.G25G		Atlas-SNP	.											GALC,NS,carcinoma,0,1	GALC	48	1	1	Substitution - coding silent(1)	prostate(1)	c.C75A						PASS	.	G	,,	106,2730		1,104,1313	4.0	5.0	5.0		75,75,	3.1	1.0	14	dbSNP_132	5	768,5808		21,726,2541	yes	coding-synonymous,coding-synonymous,intron	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	,,	22,830,3854	TT,TG,GG		11.6788,3.7377,9.286	,,	25/686,25/663,	88459434	874,8538	1418	3288	4706	SO:0001819	synonymous_variant	2581	exon1			GGCGCGGCCCGCC	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.75C>A	14.37:g.88459434G>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Silent	SNP	ENST00000261304.2	37	CCDS9878.2																																																																																			G|0.907;T|0.093	0.093	strong		0.711	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
TLN1	7094	hgsc.bcm.edu	37	9	35705759	35705759	+	Silent	SNP	G	G	A	rs11541908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35705759G>A	ENST00000314888.9	-	42	5954	c.5601C>T	c.(5599-5601)acC>acT	p.T1867T	TLN1_ENST00000464379.1_Intron|TLN1_ENST00000540444.1_Silent_p.T1801T	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1867	Interaction with SYNM.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCTCCTGAACGGTCACTGCAA	0.522													G|||	847	0.169129	0.0197	0.2305	5008	,	,		21120	0.253		0.2515	False		,,,				2504	0.1564				p.T1867T		Atlas-SNP	.											.	TLN1	185	.	0			c.C5601T						PASS	.	G		265,4141	150.3+/-184.3	14,237,1952	105.0	104.0	104.0		5601	-4.3	1.0	9	dbSNP_120	104	2295,6305	386.7+/-342.0	293,1709,2298	no	coding-synonymous	TLN1	NM_006289.3		307,1946,4250	AA,AG,GG		26.686,6.0145,19.6832		1867/2542	35705759	2560,10446	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon42			CTGAACGGTCACT	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.5601C>T	9.37:g.35705759G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			G|0.806;A|0.194	0.194	strong		0.522	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
TRIM64C	646754	hgsc.bcm.edu	37	11	49080565	49080565	+	Missense_Mutation	SNP	A	A	C	rs7932738	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:49080565A>C	ENST00000530230.1	-	1	99	c.100T>G	c.(100-102)Ttt>Gtt	p.F34V		NM_001206631.1	NP_001193560.1	A6NLI5	TR64C_HUMAN	tripartite motif containing 64C	34						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.F34V(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						GGCCTGCAAAAGCTGTGCACA	0.517													A|||	904	0.180511	0.3185	0.1268	5008	,	,		17437	0.1607		0.1352	False		,,,				2504	0.0992				p.F34V		Atlas-SNP	.											TRIM64C,NS,carcinoma,0,1	TRIM64C	18	1	1	Substitution - Missense(1)	stomach(1)	c.T100G						PASS	.																																			SO:0001583	missense	646754	exon1			TGCAAAAGCTGTG		CCDS73287.1	11p11.12	2014-04-02	2011-01-25		ENSG00000214891	ENSG00000214891		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	37148	protein-coding gene	gene with protein product			"""tripartite motif-containing 64C"""				Standard	NM_001206631		Approved		uc021qiy.1	A6NLI5	OTTHUMG00000166752	ENST00000530230.1:c.100T>G	11.37:g.49080565A>C	ENSP00000431987:p.Phe34Val	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	226	112	0.495575	NM_001206631		Missense_Mutation	SNP	ENST00000530230.1	37		382	0.1749084249084249	142	0.2886178861788618	45	0.12430939226519337	90	0.15734265734265734	105	0.13852242744063326	A	14.70	2.612876	0.46631	.	.	ENSG00000214891	ENST00000530230	T	0.32753	1.44	1.55	1.55	0.23275	.	.	.	.	.	T	0.00012	0.0000	M	0.77103	2.36	0.44149	P	0.0030569999999999764	.	.	.	.	.	.	T	0.17048	-1.0382	6	0.66056	D	0.02	.	5.2593	0.15563	1.0:0.0:0.0:0.0	rs7932738;rs52833221;rs57539737;rs7932738	.	.	.	V	34	ENSP00000431987:F34V	ENSP00000431987:F34V	F	-	1	0	TRIM64C	49037141	1.000000	0.71417	0.054000	0.19295	0.026000	0.11368	4.322000	0.59215	0.994000	0.38892	0.155000	0.16302	TTT	A|0.844;C|0.156	0.156	strong		0.517	TRIM64C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391366.1		
CRIPAK	285464	hgsc.bcm.edu	37	4	1388324	1388324	+	Missense_Mutation	SNP	A	A	C	rs74377230		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388324A>C	ENST00000324803.4	+	1	2985	c.25A>C	c.(25-27)Aat>Cat	p.N9H		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	9					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCTTTGTGCCAATGTGGAGTG	0.537																																					p.N9H		Atlas-SNP	.											CRIPAK,caecum,carcinoma,0,1	CRIPAK	185	1	0			c.A25C						PASS	.						124.0	130.0	128.0					4																	1388324		2203	4300	6503	SO:0001583	missense	285464	exon1			TGTGCCAATGTGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.25A>C	4.37:g.1388324A>C	ENSP00000323978:p.Asn9His	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	166	11	0.0662651	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	G	0.580	-0.837604	0.02692	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.23348	1.91	.	.	.	.	.	.	.	.	T	0.09598	0.0236	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	7	0.49607	T	0.09	.	.	.	.	.	9	Q8N1N5	CRPAK_HUMAN	H	9;2	ENSP00000323978:N9H	ENSP00000323978:N9H	N	+	1	0	CRIPAK	1378324	0.752000	0.28338	0.019000	0.16419	0.027000	0.11550	-1.046000	0.03525	-1.644000	0.01517	-1.639000	0.00775	AAT	A|0.833;C|0.167	0.167	weak		0.537	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
ZNF844	284391	hgsc.bcm.edu	37	19	12187861	12187861	+	Missense_Mutation	SNP	T	T	G	rs10426017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187861T>G	ENST00000439326.3	+	4	2101	c.1926T>G	c.(1924-1926)atT>atG	p.I642M	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	642			I -> M (in dbSNP:rs10426017).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GAAACCATATTAATGTAAGGA	0.408													.|||	1456	0.290735	0.73	0.1455	5008	,	,		23398	0.0863		0.161	False		,,,				2504	0.1442				p.I642M		Atlas-SNP	.											.	ZNF844	69	.	0			c.T1926G						PASS	.	G	MET/ILE	887,497		287,313,92	78.0	83.0	82.0		1926	-1.4	0.0	19	dbSNP_119	82	416,2766		25,366,1200	yes	missense	ZNF844	NM_001136501.1	10	312,679,1292	GG,GT,TT		13.0735,35.9104,28.537	possibly-damaging	642/667	12187861	1303,3263	692	1591	2283	SO:0001583	missense	284391	exon4			CCATATTAATGTA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1926T>G	19.37:g.12187861T>G	ENSP00000392024:p.Ile642Met	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	573	0.2623626373626374	339	0.6890243902439024	53	0.1464088397790055	54	0.0944055944055944	127	0.16754617414248021	t	0.011	-1.726840	0.00694	0.640896	0.130735	ENSG00000223547	ENST00000439326	T	0.05580	3.42	2.32	-1.43	0.08884	.	.	.	.	.	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	0.18871	-1.0323	8	0.49607	T	0.09	.	0.0881	0.00037	0.3078:0.1659:0.1916:0.3347	rs10426017;rs52790788;rs61089424;rs10426017	642	Q08AG5	ZN844_HUMAN	M	642	ENSP00000392024:I642M	ENSP00000392024:I642M	I	+	3	3	ZNF844	12048861	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-11.239000	0.00004	-0.471000	0.06891	-0.982000	0.02568	ATT	T|0.746;G|0.254	0.254	strong		0.408	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
TSHR	7253	hgsc.bcm.edu	37	14	81610504	81610504	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:81610504G>A	ENST00000541158.2	+	11	2424	c.2102G>A	c.(2101-2103)cGc>cAc	p.R701H	TSHR_ENST00000298171.2_Missense_Mutation_p.R701H|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	701					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)	ATCTGTAAACGCCAGGCTCAG	0.507			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.R701H		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR,colon,carcinoma,+1,1	TSHR	462	1	0			c.G2102A						scavenged	.						131.0	125.0	127.0					14																	81610504		2203	4300	6503	SO:0001583	missense	7253	exon10			GTAAACGCCAGGC	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.2102G>A	14.37:g.81610504G>A	ENSP00000441235:p.Arg701His	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	G	2.064	-0.414578	0.04766	.	.	ENSG00000165409	ENST00000541158;ENST00000412429;ENST00000298171	T;T	0.38240	1.15;1.15	5.4	0.898	0.19264	.	0.317238	0.38605	N	0.001626	T	0.17789	0.0427	N	0.22421	0.69	0.32374	N	0.555383	B	0.12013	0.005	B	0.06405	0.002	T	0.28933	-1.0028	10	0.09338	T	0.73	.	6.9538	0.24560	0.633:0.0:0.367:0.0	.	701	F5GYU5	.	H	701;348;701	ENSP00000441235:R701H;ENSP00000298171:R701H	ENSP00000298171:R701H	R	+	2	0	TSHR	80680257	0.879000	0.30193	0.858000	0.33744	0.915000	0.54546	1.379000	0.34340	0.258000	0.21686	0.561000	0.74099	CGC	.	.	none		0.507	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369	
KRTAP25-1	100131902	hgsc.bcm.edu	37	21	31661691	31661691	+	Missense_Mutation	SNP	A	A	G	rs8127420	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:31661691A>G	ENST00000416044.1	-	1	141	c.118T>C	c.(118-120)Tcc>Ccc	p.S40P		NM_001128598.1	NP_001122070.1	Q3LHN0	KR251_HUMAN	keratin associated protein 25-1	40			S -> P (in dbSNP:rs8127420).			intermediate filament (GO:0005882)				breast(1)	1						CAGGTCCTGGACACAAAATTC	0.403													A|||	2591	0.517372	0.6392	0.5014	5008	,	,		19139	0.5853		0.327	False		,,,				2504	0.4898				p.S40P		Atlas-SNP	.											.	KRTAP25-1	13	.	0			c.T118C						PASS	.	A	PRO/SER	837,547		251,335,106	131.0	124.0	126.0		118	-2.9	0.0	21	dbSNP_116	126	926,2256		137,652,802	yes	missense	KRTAP25-1	NM_001128598.1	74	388,987,908	GG,GA,AA		29.1012,39.5231,38.6115	possibly-damaging	40/103	31661691	1763,2803	692	1591	2283	SO:0001583	missense	100131902	exon1			TCCTGGACACAAA		CCDS46640.1	21q22.1	2010-10-18	2008-02-26	2008-04-22	ENSG00000232263	ENSG00000232263		"""Keratin associated proteins"""	34003	protein-coding gene	gene with protein product							Standard	NM_001128598		Approved	KAP25.1	uc010glr.1	Q3LHN0	OTTHUMG00000125482	ENST00000416044.1:c.118T>C	21.37:g.31661691A>G	ENSP00000398619:p.Ser40Pro	Somatic	245	1	0.00408163		WXS	Illumina HiSeq	Phase_I	200	105	0.525	NM_001128598		Missense_Mutation	SNP	ENST00000416044.1	37	CCDS46640.1	1092	0.5	327	0.6646341463414634	175	0.48342541436464087	341	0.5961538461538461	249	0.32849604221635886	A	11.25	1.583312	0.28268	0.604769	0.291012	ENSG00000232263	ENST00000416044	T	0.05081	3.5	3.54	-2.86	0.05717	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.29378	0.243	B	0.32393	0.145	T	0.24835	-1.0149	8	0.87932	D	0	.	0.5677	0.00690	0.4339:0.1749:0.2209:0.1703	rs8127420	40	Q3LHN0	KR251_HUMAN	P	40	ENSP00000398619:S40P	ENSP00000398619:S40P	S	-	1	0	KRTAP25-1	30583562	0.000000	0.05858	0.000000	0.03702	0.161000	0.22273	-0.077000	0.11394	-0.665000	0.05317	0.346000	0.21813	TCC	A|0.520;G|0.480	0.480	strong		0.403	KRTAP25-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246805.1	NM_001128598	
RAET1E	135250	hgsc.bcm.edu	37	6	150212003	150212003	+	Missense_Mutation	SNP	C	C	T	rs9383583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:150212003C>T	ENST00000357183.4	-	1	167	c.35G>A	c.(34-36)cGc>cAc	p.R12H	RAET1E-AS1_ENST00000605899.1_RNA|RAET1E_ENST00000529948.1_Missense_Mutation_p.R12H|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA|RAET1E_ENST00000532335.1_Missense_Mutation_p.R12H|RAET1E_ENST00000367363.3_Missense_Mutation_p.R12H	NM_139165.2	NP_631904.1	Q8TD07	N2DL4_HUMAN	retinoic acid early transcript 1E	12			R -> H (in dbSNP:rs9383583).		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)		CAAAAGAAGGCGCACAGGGCT	0.498													c|||	1341	0.267772	0.2209	0.1182	5008	,	,		20195	0.5526		0.1581	False		,,,				2504	0.2566				p.R12H		Atlas-SNP	.											.	RAET1E	20	.	0			c.G35A						PASS	.	C	HIS/ARG	979,3427	368.1+/-318.5	103,773,1327	128.0	108.0	115.0		35	-4.4	0.0	6	dbSNP_119	115	1200,7400	243.3+/-273.0	92,1016,3192	yes	missense	RAET1E	NM_139165.2	29	195,1789,4519	TT,TC,CC		13.9535,22.2197,16.7538	benign	12/264	150212003	2179,10827	2203	4300	6503	SO:0001583	missense	135250	exon1			AGAAGGCGCACAG	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.35G>A	6.37:g.150212003C>T	ENSP00000349709:p.Arg12His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	34	31	0.911765	NM_139165	A6YF59|Q5VYB7|Q5VYB8|Q8TEZ2|Q96L41	Missense_Mutation	SNP	ENST00000357183.4	37	CCDS5221.1	568	0.2600732600732601	94	0.1910569105691057	49	0.13535911602209943	316	0.5524475524475524	109	0.1437994722955145	C	5.780	0.328267	0.10956	0.222197	0.139535	ENSG00000164520	ENST00000532335;ENST00000357183;ENST00000367363;ENST00000529948;ENST00000531073	T;T;T;T;T	0.23147	4.87;5.18;3.95;4.81;1.92	2.19	-4.39	0.03611	.	.	.	.	.	T	0.02230	0.0069	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.04013	0.0;0.001;0.0	T	0.38693	-0.9649	8	0.22706	T	0.39	3.5103	7.0463	0.25048	0.0:0.18:0.1453:0.6748	rs9383583;rs52793456;rs60046247;rs9383583	12;12;12	Q8TD07;Q8TD07-2;Q8TD07-3	N2DL4_HUMAN;.;.	H	12	ENSP00000437067:R12H;ENSP00000349709:R12H;ENSP00000356332:R12H;ENSP00000432366:R12H;ENSP00000433489:R12H	ENSP00000349709:R12H	R	-	2	0	RAET1E	150253696	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.057000	0.01395	-2.414000	0.00569	-0.967000	0.02615	CGC	C|0.783;T|0.217	0.217	strong		0.498	RAET1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042659.1	NM_139165	
TMEM175	84286	hgsc.bcm.edu	37	4	946226	946226	+	Silent	SNP	T	T	C	rs11552301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:946226T>C	ENST00000264771.4	+	7	635	c.450T>C	c.(448-450)atT>atC	p.I150I	TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000508204.1_Silent_p.I68I|TMEM175_ENST00000515740.1_Silent_p.I34I	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	150						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TGATCGCCATTGGGGTCGTGC	0.527													C|||	3243	0.647564	0.7466	0.4769	5008	,	,		16953	0.7222		0.5765	False		,,,				2504	0.6309				p.I150I		Atlas-SNP	.											.	TMEM175	44	.	0			c.T450C						PASS	.	C		3178,1228	425.1+/-340.7	1146,886,171	182.0	161.0	168.0		450	-4.8	0.1	4	dbSNP_120	168	5169,3431	506.4+/-376.6	1543,2083,674	no	coding-synonymous	TMEM175	NM_032326.2		2689,2969,845	CC,CT,TT		39.8953,27.8711,35.8219		150/505	946226	8347,4659	2203	4300	6503	SO:0001819	synonymous_variant	84286	exon7			CGCCATTGGGGTC	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.450T>C	4.37:g.946226T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_032326	D3DVN4|Q8ND13	Silent	SNP	ENST00000264771.4	37	CCDS3341.1	1353	0.6195054945054945	352	0.7154471544715447	191	0.5276243093922652	390	0.6818181818181818	420	0.554089709762533	c	1.280	-0.610490	0.03690	0.721289	0.601047	ENSG00000127419	ENST00000505148	.	.	.	4.77	-4.77	0.03219	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999859422	.	.	.	.	.	.	T	0.28106	-1.0054	3	.	.	.	-1.4655	8.9801	0.35959	0.0:0.1893:0.1227:0.6879	rs11552301;rs17849924	.	.	.	R	42	.	.	W	+	1	0	TMEM175	936226	0.337000	0.24766	0.125000	0.21846	0.067000	0.16453	-0.585000	0.05794	-1.024000	0.03338	-0.343000	0.07986	TGG	T|0.369;C|0.631	0.631	strong		0.527	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326	
PTPRN2	5799	hgsc.bcm.edu	37	7	157369324	157369324	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:157369324A>G	ENST00000389418.4	-	19	2773	c.2764T>C	c.(2764-2766)Tcc>Ccc	p.S922P	MIR153-2_ENST00000385225.1_RNA|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S945P|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S893P|PTPRN2_ENST00000409483.1_Missense_Mutation_p.S884P|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S905P	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	922	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCCAGGAGGGACCTTGAGGAG	0.647																																					p.S922P		Atlas-SNP	.											.	PTPRN2	243	.	0			c.T2764C						PASS	.						62.0	49.0	54.0					7																	157369324		2203	4300	6503	SO:0001583	missense	5799	exon19			GGAGGGACCTTGA	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2764T>C	7.37:g.157369324A>G	ENSP00000374069:p.Ser922Pro	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	57	20	0.350877	NM_002847	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	A	8.190	0.795727	0.16327	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83	5.44	1.67	0.24075	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.066743	0.64402	D	0.000012	T	0.57814	0.2079	N	0.02266	-0.62	0.80722	D	1	B;B;B;B;B	0.29301	0.203;0.241;0.203;0.208;0.241	B;B;B;B;B	0.30495	0.071;0.116;0.071;0.044;0.116	T	0.55224	-0.8174	10	0.02654	T	1	.	5.9778	0.19391	0.7094:0.1376:0.153:0.0	.	945;884;893;905;922	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	P	884;893;905;922;945	ENSP00000387114:S884P;ENSP00000374064:S893P;ENSP00000374067:S905P;ENSP00000374069:S922P;ENSP00000385464:S945P	ENSP00000374064:S893P	S	-	1	0	PTPRN2	157062085	1.000000	0.71417	0.100000	0.21137	0.015000	0.08874	2.455000	0.44988	0.041000	0.15688	0.528000	0.53228	TCC	.	.	none		0.647	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
GOLGB1	2804	hgsc.bcm.edu	37	3	121415720	121415720	+	Missense_Mutation	SNP	T	T	C	rs3732410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:121415720T>C	ENST00000340645.5	-	13	3760	c.3635A>G	c.(3634-3636)tAt>tGt	p.Y1212C	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Y1217C	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1212			Y -> C (in dbSNP:rs3732410). {ECO:0000269|PubMed:18487259}.		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		CAAGCGATTATAGTCATCTTT	0.428													T|||	1101	0.219848	0.0522	0.1585	5008	,	,		22709	0.4841		0.2505	False		,,,				2504	0.1861				p.Y1217C		Atlas-SNP	.											GOLGB1,NS,carcinoma,0,1	GOLGB1	319	1	0			c.A3650G						PASS	.	T	CYS/TYR	327,4079	171.9+/-202.1	11,305,1887	221.0	217.0	219.0		3635	4.6	0.9	3	dbSNP_107	219	2113,6487	365.1+/-333.8	277,1559,2464	yes	missense	GOLGB1	NM_004487.3	194	288,1864,4351	CC,CT,TT		24.5698,7.4217,18.7606	probably-damaging	1212/3260	121415720	2440,10566	2203	4300	6503	SO:0001583	missense	2804	exon13			CGATTATAGTCAT	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.3635A>G	3.37:g.121415720T>C	ENSP00000341848:p.Tyr1212Cys	Somatic	305	0	0		WXS	Illumina HiSeq	Phase_I	382	185	0.484293	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	563	0.25778388278388276	33	0.06707317073170732	70	0.19337016574585636	267	0.46678321678321677	193	0.2546174142480211	T	10.43	1.349415	0.24426	0.074217	0.245698	ENSG00000173230	ENST00000340645;ENST00000393667;ENST00000494517	T;T;T	0.32515	2.09;2.09;1.45	5.81	4.59	0.56863	.	0.000000	0.56097	D	0.000036	T	0.00012	0.0000	L	0.32530	0.975	0.29624	P	0.845993	D;P;P;D	0.76494	0.999;0.936;0.936;0.999	D;P;P;D	0.70487	0.912;0.609;0.609;0.969	T	0.49113	-0.8973	9	0.39692	T	0.17	.	10.852	0.46775	0.0:0.0:0.1579:0.8421	rs3732410;rs52794344;rs61628092;rs3732410	1137;1176;1217;1212	F1T0J2;E7EU81;E7EP74;Q14789	.;.;.;GOGB1_HUMAN	C	1212;1217;1176	ENSP00000341848:Y1212C;ENSP00000377275:Y1217C;ENSP00000418231:Y1176C	ENSP00000341848:Y1212C	Y	-	2	0	GOLGB1	122898410	1.000000	0.71417	0.911000	0.35937	0.780000	0.44128	1.966000	0.40481	2.210000	0.71456	0.533000	0.62120	TAT	T|0.787;C|0.213	0.213	strong		0.428	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
SPEG	10290	hgsc.bcm.edu	37	2	220331911	220331911	+	Missense_Mutation	SNP	G	G	A	rs34861443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220331911G>A	ENST00000312358.7	+	10	3029	c.2897G>A	c.(2896-2898)cGg>cAg	p.R966Q	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	966	Ig-like 4.		R -> Q (in dbSNP:rs34861443). {ECO:0000269|PubMed:17344846}.		cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CCTGAAAGCCGGTCCCTGGCC	0.677											OREG0004000	type=REGULATORY REGION|Gene=APEG1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	25	0.00499201	0.0008	0.0043	5008	,	,		15110	0.0		0.0209	False		,,,				2504	0.0				p.R966Q		Atlas-SNP	.											.	SPEG	272	.	0			c.G2897A						PASS	.	G	GLN/ARG	28,4056		0,28,2014	40.0	49.0	46.0		2897	4.8	1.0	2	dbSNP_126	46	203,8143		4,195,3974	yes	missense	SPEG	NM_005876.4	43	4,223,5988	AA,AG,GG		2.4323,0.6856,1.8584	probably-damaging	966/3268	220331911	231,12199	2042	4173	6215	SO:0001583	missense	10290	exon10			AAAGCCGGTCCCT	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2897G>A	2.37:g.220331911G>A	ENSP00000311684:p.Arg966Gln	Somatic	59	0	0	2265	WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	18	0.008241758241758242	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	13	0.017150395778364115	G	11.23	1.576809	0.28092	0.006856	0.024323	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.65732	-0.17	4.75	4.75	0.60458	Immunoglobulin-like (1);	0.000000	0.36628	N	0.002490	T	0.23370	0.0565	L	0.27053	0.805	0.80722	D	1	B	0.31077	0.307	B	0.17722	0.019	T	0.16928	-1.0386	10	0.19590	T	0.45	.	5.3131	0.15841	0.1326:0.2:0.6674:0.0	rs34861443	966	Q15772	SPEG_HUMAN	Q	966	ENSP00000311684:R966Q	ENSP00000265327:R966Q	R	+	2	0	SPEG	220040155	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	0.907000	0.28531	2.465000	0.83290	0.655000	0.94253	CGG	G|0.988;A|0.012	0.012	strong		0.677	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
SLFN13	146857	hgsc.bcm.edu	37	17	33772658	33772658	+	Nonsense_Mutation	SNP	G	G	T	rs8072510	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33772658G>T	ENST00000285013.6	-	3	317	c.42C>A	c.(40-42)taC>taA	p.Y14*	SLFN13_ENST00000360502.2_Intron|SLFN13_ENST00000526861.1_Nonsense_Mutation_p.Y14*|SLFN13_ENST00000542635.1_Nonsense_Mutation_p.Y14*|SLFN13_ENST00000533791.1_Nonsense_Mutation_p.Y14*|SLFN13_ENST00000534689.1_Intron	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	14						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)		CCAGGTCTGGGTAAGATGGAT	0.403													G|||	464	0.0926518	0.1135	0.0519	5008	,	,		18203	0.1329		0.1024	False		,,,				2504	0.0419				p.Y14X		Atlas-SNP	.											.	SLFN13	79	.	0			c.C42A						PASS	.	G	stop/TYR	438,3968	201.8+/-224.7	25,388,1790	50.0	49.0	49.0		42	-1.4	0.0	17	dbSNP_116	49	864,7736	188.3+/-235.3	46,772,3482	yes	stop-gained	SLFN13	NM_144682.5		71,1160,5272	TT,TG,GG		10.0465,9.941,10.0108		14/898	33772658	1302,11704	2203	4300	6503	SO:0001587	stop_gained	146857	exon3			GTCTGGGTAAGAT	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.42C>A	17.37:g.33772658G>T	ENSP00000285013:p.Tyr14*	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	48	0.384	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Nonsense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	239	0.10943223443223443	59	0.11991869918699187	19	0.052486187845303865	93	0.16258741258741258	68	0.08970976253298153	G	25.1	4.607662	0.87157	0.09941	0.100465	ENSG00000154760	ENST00000285013;ENST00000526861;ENST00000542635;ENST00000524511	.	.	.	3.08	-1.42	0.08913	.	2.034220	0.03005	U	0.148710	.	.	.	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.0689	0.19877	0.5763:0.0:0.4237:0.0	rs8072510;rs59942021;rs8072510	.	.	.	X	14	.	ENSP00000285013:Y14X	Y	-	3	2	SLFN13	30796771	0.003000	0.15002	0.001000	0.08648	0.297000	0.27493	0.203000	0.17315	-0.124000	0.11724	0.205000	0.17691	TAC	G|0.896;T|0.104	0.104	strong		0.403	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
OR4C16	219428	hgsc.bcm.edu	37	11	55339798	55339798	+	Silent	SNP	C	C	T	rs557667	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55339798C>T	ENST00000314634.3	+	1	195	c.195C>T	c.(193-195)tcC>tcT	p.S65S		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	65						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)				TCTACTTATCCTTATCTGATA	0.413													c|||	1288	0.257188	0.1188	0.3242	5008	,	,		19752	0.3909		0.2843	False		,,,				2504	0.2311				p.S65S		Atlas-SNP	.											.	OR4C16	104	.	0			c.C195T						PASS	.	C		621,3781	270.1+/-269.4	36,549,1616	274.0	249.0	257.0		195	0.8	0.3	11	dbSNP_83	257	2289,6303	385.8+/-341.6	329,1631,2336	no	coding-synonymous	OR4C16	NM_001004701.2		365,2180,3952	TT,TC,CC		26.6411,14.1072,22.395		65/311	55339798	2910,10084	2201	4296	6497	SO:0001819	synonymous_variant	219428	exon1			CTTATCCTTATCT	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.195C>T	11.37:g.55339798C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	152	61	0.401316	NM_001004701	Q6IEV8	Silent	SNP	ENST00000314634.3	37	CCDS31502.1																																																																																			C|0.755;T|0.245	0.245	strong		0.413	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
ZNF70	7621	hgsc.bcm.edu	37	22	24087319	24087319	+	Silent	SNP	A	A	C	rs2070451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:24087319A>C	ENST00000341976.3	-	2	469	c.9T>G	c.(7-9)gtT>gtG	p.V3V		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	3					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TTGCTGGGGGAACCTCCATTG	0.443													A|||	832	0.166134	0.1732	0.1225	5008	,	,		19789	0.2966		0.1034	False		,,,				2504	0.1176				p.V3V		Atlas-SNP	.											.	ZNF70	49	.	0			c.T9G						PASS	.	A		794,3612	306.9+/-289.7	71,652,1480	77.0	77.0	77.0		9	1.1	0.7	22	dbSNP_96	77	802,7798	181.8+/-230.4	46,710,3544	no	coding-synonymous	ZNF70	NM_021916.2		117,1362,5024	CC,CA,AA		9.3256,18.0209,12.2713		3/447	24087319	1596,11410	2203	4300	6503	SO:0001819	synonymous_variant	7621	exon2			TGGGGGAACCTCC	X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"""Zinc fingers, C2H2-type"""	13140	protein-coding gene	gene with protein product		194544	"""zinc finger protein 70 (Cos17)"""			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.9T>G	22.37:g.24087319A>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	104	58	0.557692	NM_021916		Silent	SNP	ENST00000341976.3	37	CCDS13812.1																																																																																			A|0.865;C|0.135	0.135	strong		0.443	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916	
GOLGA3	2802	hgsc.bcm.edu	37	12	133384864	133384864	+	Missense_Mutation	SNP	G	G	A	rs3741486	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133384864G>A	ENST00000450791.2	-	4	974	c.791C>T	c.(790-792)cCg>cTg	p.P264L	GOLGA3_ENST00000204726.3_Missense_Mutation_p.P264L|GOLGA3_ENST00000456883.2_Missense_Mutation_p.P264L|GOLGA3_ENST00000545875.1_Missense_Mutation_p.P264L|GOLGA3_ENST00000537452.1_Missense_Mutation_p.P264L			Q08378	GOGA3_HUMAN	golgin A3	264			P -> L (in dbSNP:rs3741486).		intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		ATCGGGAGCCGGGACATTTCC	0.527													G|||	711	0.141973	0.0106	0.1571	5008	,	,		15064	0.1736		0.2813	False		,,,				2504	0.1329				p.P264L		Atlas-SNP	.											.	GOLGA3	234	.	0			c.C791T						PASS	.	G	LEU/PRO,LEU/PRO	225,4181	138.0+/-173.8	9,207,1987	134.0	148.0	143.0		791,791	0.8	0.0	12	dbSNP_107	143	2559,6041	416.7+/-352.2	385,1789,2126	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	98,98	394,1996,4113	AA,AG,GG		29.7558,5.1067,21.4055	benign,benign	264/1135,264/1499	133384864	2784,10222	2203	4300	6503	SO:0001583	missense	2802	exon5			GGAGCCGGGACAT	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.791C>T	12.37:g.133384864G>A	ENSP00000410378:p.Pro264Leu	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	181	82	0.453039	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	394	0.1804029304029304	8	0.016260162601626018	59	0.16298342541436464	105	0.18356643356643357	222	0.2928759894459103	G	1.008	-0.688716	0.03328	0.051067	0.297558	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.23	0.791	0.18619	.	1.119980	0.06397	N	0.718094	T	0.00012	0.0000	L	0.38531	1.155	0.80722	P	0.0	B;B;B	0.14805	0.011;0.006;0.006	B;B;B	0.06405	0.002;0.002;0.001	T	0.35919	-0.9769	9	0.66056	D	0.02	.	9.7493	0.40466	0.4088:0.0:0.5912:0.0	rs3741486;rs52796197;rs60613371;rs3741486	264;264;264	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	L	264	ENSP00000204726:P264L;ENSP00000410378:P264L;ENSP00000409303:P264L;ENSP00000442143:P264L;ENSP00000442603:P264L	ENSP00000204726:P264L	P	-	2	0	GOLGA3	131894937	0.000000	0.05858	0.002000	0.10522	0.034000	0.12701	0.439000	0.21575	0.310000	0.22990	0.585000	0.79938	CCG	G|0.802;A|0.198	0.198	strong		0.527	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
PPP1R3A	5506	hgsc.bcm.edu	37	7	113518434	113518434	+	Missense_Mutation	SNP	C	C	A	rs1799999	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:113518434C>A	ENST00000284601.3	-	4	2781	c.2713G>T	c.(2713-2715)Gac>Tac	p.D905Y		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	905			D -> Y (common polymorphism; can be associated with insulin resistance; dbSNP:rs1799999). {ECO:0000269|PubMed:7581368, ECO:0000269|PubMed:9726244}.		glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						CTATTAGTGTCTGAGTTAAAA	0.378													C|||	1546	0.308706	0.1793	0.2046	5008	,	,		18875	0.6409		0.1153	False		,,,				2504	0.4141				p.D905Y		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G2713T	GRCh37	CM950973	PPP1R3A	M	rs1799999	PASS	.	C	TYR/ASP	858,3548	336.5+/-304.4	77,704,1422	89.0	87.0	88.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2713	5.6	1.0	7	dbSNP_89	88	902,7696	201.7+/-245.1	56,790,3453	yes	missense	PPP1R3A	NM_002711.3	160	133,1494,4875	AA,AC,CC		10.4908,19.4734,13.5343	probably-damaging	905/1123	113518434	1760,11244	2203	4299	6502	SO:0001583	missense	5506	exon4			TAGTGTCTGAGTT	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.2713G>T	7.37:g.113518434C>A	ENSP00000284601:p.Asp905Tyr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	637	0.2916666666666667	75	0.1524390243902439	78	0.2154696132596685	392	0.6853146853146853	92	0.12137203166226913	C	12.29	1.893032	0.33442	0.194734	0.104908	ENSG00000154415	ENST00000284601	T	0.20738	2.05	5.64	5.64	0.86602	.	0.367148	0.26414	N	0.024511	T	0.00012	0.0000	L	0.56769	1.78	0.35982	P	0.16393800000000003	D	0.56521	0.976	P	0.53185	0.72	T	0.30504	-0.9976	9	0.72032	D	0.01	-3.5799	11.6403	0.51228	0.0:0.9117:0.0:0.0883	rs1799999;rs8192685;rs17847379;rs59907640;rs1799999	905	Q16821	PPR3A_HUMAN	Y	905	ENSP00000284601:D905Y	ENSP00000284601:D905Y	D	-	1	0	PPP1R3A	113305670	1.000000	0.71417	0.997000	0.53966	0.368000	0.29767	3.209000	0.51122	2.646000	0.89796	0.603000	0.83216	GAC	C|0.769;N|0.000	.	strong		0.378	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
EFCAB6	64800	hgsc.bcm.edu	37	22	44083442	44083442	+	Missense_Mutation	SNP	T	T	C	rs5764214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:44083442T>C	ENST00000262726.7	-	11	1304	c.1051A>G	c.(1051-1053)Act>Gct	p.T351A	EFCAB6_ENST00000358439.4_Intron|EFCAB6_ENST00000396231.2_Missense_Mutation_p.T199A	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	351			T -> A (in dbSNP:rs5764214). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TTGATTTTAGTGGTGGCTTTA	0.328													T|||	2082	0.415735	0.5053	0.2867	5008	,	,		14884	0.2669		0.4573	False		,,,				2504	0.4969				p.T351A		Atlas-SNP	.											.	EFCAB6	177	.	0			c.A1051G						PASS	.	T	ALA/THR,ALA/THR	2205,2201	587.5+/-386.7	547,1111,545	59.0	59.0	59.0		1051,595	-3.8	0.0	22	dbSNP_114	59	4081,4519	559.1+/-387.3	944,2193,1163	yes	missense,missense	EFCAB6	NM_022785.3,NM_198856.2	58,58	1491,3304,1708	CC,CT,TT		47.4535,49.9546,48.3315	benign,benign	351/1502,199/1350	44083442	6286,6720	2203	4300	6503	SO:0001583	missense	64800	exon11			TTTTAGTGGTGGC	Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.1051A>G	22.37:g.44083442T>C	ENSP00000262726:p.Thr351Ala	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_022785	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	830	0.38003663003663	237	0.4817073170731707	118	0.3259668508287293	136	0.23776223776223776	339	0.4472295514511873	T	6.692	0.496279	0.12762	0.500454	0.474535	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.07688	3.17;3.17	4.68	-3.84	0.04256	.	1.984030	0.02128	N	0.056195	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.46190	-0.9209	9	0.18710	T	0.47	0.2565	13.2868	0.60247	0.0:0.6849:0.0:0.3151	rs5764214;rs7284270;rs52791933;rs5764214	351;351	Q5THR3-6;Q5THR3	.;EFCB6_HUMAN	A	199;351	ENSP00000379533:T199A;ENSP00000262726:T351A	ENSP00000262726:T351A	T	-	1	0	EFCAB6	42414775	0.000000	0.05858	0.001000	0.08648	0.958000	0.62258	-1.233000	0.02934	-0.759000	0.04684	0.533000	0.62120	ACT	T|0.603;C|0.397	0.397	strong		0.328	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
ZNF761	388561	hgsc.bcm.edu	37	19	53959568	53959568	+	RNA	SNP	G	G	C	rs2617726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53959568G>C	ENST00000454407.1	+	0	2260							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)			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)		TCATACTGAAGAGAATCCTTA	0.393													g|||	1936	0.386581	0.3964	0.5346	5008	,	,		24330	0.2401		0.3986	False		,,,				2504	0.407				p.E603Q		Atlas-SNP	.											ZNF761,rectum,carcinoma,0,1	ZNF761	104	1	0			c.G1807C						PASS	.	G	GLN/GLU	1775,2631	521.7+/-370.6	392,991,820	116.0	121.0	119.0		1808	1.1	0.2	19	dbSNP_100	119	3494,5102	510.5+/-377.5	706,2082,1510	no	missense	ZNF761	NM_001008401.3	29	1098,3073,2330	CC,CG,GG		40.6468,40.286,40.5245	benign	603/747	53959568	5269,7733	2203	4298	6501			388561	exon7			ACTGAAGAGAATC	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.53959568G>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	37	0.560606	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				.	.	weak		0.393	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
SLC4A4	8671	hgsc.bcm.edu	37	4	72433545	72433545	+	3'UTR	SNP	A	A	C	rs1062677	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:72433545A>C	ENST00000264485.5	+	0	3434				SLC4A4_ENST00000425175.1_Missense_Mutation_p.I1074L|SLC4A4_ENST00000351898.6_3'UTR|SLC4A4_ENST00000340595.3_3'UTR	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4						bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TCAAATTAGAATAGAACTTGA	0.338													A|||	860	0.171725	0.0998	0.3487	5008	,	,		17638	0.1181		0.1849	False		,,,				2504	0.1851				p.I1074L		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A3220C						PASS	.	A	,LEU/ILE,	393,2721		31,331,1195	75.0	66.0	69.0		,3220,	4.4	1.0	4	dbSNP_86	69	1332,5804		132,1068,2368	yes	utr-3,missense,utr-3	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	,5,	163,1399,3563	CC,CA,AA		18.6659,12.6204,16.8293	,benign,	,1074/1095,	72433545	1725,8525	1557	3568	5125	SO:0001624	3_prime_UTR_variant	8671	exon25			ATTAGAATAGAAC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.*77A>C	4.37:g.72433545A>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	171	90	0.526316	NM_001134742	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	346	0.15842490842490842	56	0.11382113821138211	107	0.2955801104972376	54	0.0944055944055944	129	0.17018469656992086	A	13.89	2.371522	0.42003	0.126204	0.186659	ENSG00000080493	ENST00000425175	T	0.78816	-1.21	5.62	4.42	0.53409	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.41340	P	0.012705999999999995	B	0.02656	0.0	B	0.01281	0.0	T	0.05209	-1.0899	8	0.66056	D	0.02	.	13.1225	0.59336	0.8661:0.1339:0.0:0.0	rs1062677;rs1453454;rs3203670;rs17400075;rs59241443;rs1062677	1074	A5JJ20	.	L	1074	ENSP00000393557:I1074L	ENSP00000393557:I1074L	I	+	1	0	SLC4A4	72652409	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.445000	0.52921	1.053000	0.40415	0.477000	0.44152	ATA	A|0.847;C|0.153	0.153	strong		0.338	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
OCEL1	79629	hgsc.bcm.edu	37	19	17337928	17337928	+	Silent	SNP	C	C	T	rs1045201	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17337928C>T	ENST00000215061.4	+	3	416	c.372C>T	c.(370-372)gcC>gcT	p.A124A	OCEL1_ENST00000601576.1_3'UTR|OCEL1_ENST00000601529.1_Silent_p.A124A|OCEL1_ENST00000597836.1_Silent_p.A68A	NM_024578.1	NP_078854.1	Q9H607	OCEL1_HUMAN	occludin/ELL domain containing 1	124										central_nervous_system(2)|endometrium(2)|kidney(1)|lung(2)	7						TCTCCCAGGCCCTCCTGGGCG	0.612													C|||	397	0.0792732	0.1203	0.0879	5008	,	,		14459	0.001		0.0775	False		,,,				2504	0.1002				p.A124A		Atlas-SNP	.											OCEL1,colon,carcinoma,0,1	OCEL1	20	1	0			c.C372T						PASS	.	C		484,3922	224.6+/-240.7	27,430,1746	68.0	79.0	75.0		372	-5.0	0.0	19	dbSNP_86	75	674,7926	168.3+/-219.8	22,630,3648	no	coding-synonymous	OCEL1	NM_024578.1		49,1060,5394	TT,TC,CC		7.8372,10.985,8.9036		124/265	17337928	1158,11848	2203	4300	6503	SO:0001819	synonymous_variant	79629	exon3			CCAGGCCCTCCTG	BC029361	CCDS12351.1	19p13.11	2008-02-05				ENSG00000099330			26221	protein-coding gene	gene with protein product						12477932	Standard	NM_024578		Approved	FLJ22709	uc002nfp.3	Q9H607		ENST00000215061.4:c.372C>T	19.37:g.17337928C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_024578		Silent	SNP	ENST00000215061.4	37	CCDS12351.1																																																																																			C|0.914;T|0.086	0.086	strong		0.612	OCEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463307.1	NM_024578	
TMEM161A	54929	hgsc.bcm.edu	37	19	19230816	19230816	+	Missense_Mutation	SNP	T	T	C	rs45467802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19230816T>C	ENST00000162044.9	-	12	1427	c.1363A>G	c.(1363-1365)Atc>Gtc	p.I455V	TMEM161A_ENST00000587583.2_Missense_Mutation_p.I430V|TMEM161A_ENST00000450333.2_Missense_Mutation_p.I352V	NM_017814.2	NP_060284.1	Q9NX61	T161A_HUMAN	transmembrane protein 161A	455				I -> V (in Ref. 2; BAG53402). {ECO:0000305}.	cellular response to oxidative stress (GO:0034599)|cellular response to UV (GO:0034644)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of DNA repair (GO:0045739)|response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(5;1.19e-05)|Epithelial(12;0.0011)			GTCCACCAGATGAGGTAGGCC	0.662													T|||	243	0.0485224	0.0477	0.0331	5008	,	,		15175	0.0446		0.0437	False		,,,				2504	0.0695				p.I455V		Atlas-SNP	.											.	TMEM161A	37	.	0			c.A1363G						PASS	.	T	VAL/ILE	231,4151		4,223,1964	20.0	21.0	20.0		1363	3.5	1.0	19	dbSNP_127	20	406,8160		11,384,3888	yes	missense	TMEM161A	NM_017814.1	29	15,607,5852	CC,CT,TT		4.7397,5.2716,4.9197	benign	455/480	19230816	637,12311	2191	4283	6474	SO:0001583	missense	54929	exon12			ACCAGATGAGGTA	BC005210	CCDS12393.1, CCDS58656.1	19p13.11	2008-02-05				ENSG00000064545			26020	protein-coding gene	gene with protein product						12975309	Standard	NM_017814		Approved	FLJ39645, FLJ20422	uc002nlg.4	Q9NX61		ENST00000162044.9:c.1363A>G	19.37:g.19230816T>C	ENSP00000162044:p.Ile455Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	141	72	0.510638	NM_017814	B3KUE0|G5E9M6|Q7L2Y1	Missense_Mutation	SNP	ENST00000162044.9	37	CCDS12393.1	319	0.14606227106227107	104	0.21138211382113822	37	0.10220994475138122	65	0.11363636363636363	113	0.14907651715039577	T	11.76	1.735741	0.30774	0.052716	0.047397	ENSG00000064545	ENST00000450333;ENST00000162044	.	.	.	4.53	3.48	0.39840	.	0.051611	0.85682	D	0.000000	T	0.00039	0.0001	N	0.22421	0.69	0.33292	P	0.436354	B;B	0.14012	0.009;0.0	B;B	0.11329	0.006;0.002	T	0.10917	-1.0609	8	0.36615	T	0.2	-15.4835	7.5498	0.27790	0.0:0.1139:0.0:0.8861	rs45467802;rs61739370	352;455	G5E9M6;Q9NX61	.;T161A_HUMAN	V	352;455	.	ENSP00000162044:I455V	I	-	1	0	TMEM161A	19091816	1.000000	0.71417	0.998000	0.56505	0.343000	0.28985	1.729000	0.38115	0.602000	0.29896	0.260000	0.18958	ATC	T|0.911;C|0.089	0.089	strong		0.662	TMEM161A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460089.2	NM_017814	
C5orf45	51149	hgsc.bcm.edu	37	5	179264731	179264731	+	Missense_Mutation	SNP	T	T	C	rs10277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179264731T>C	ENST00000292586.6	-	7	782	c.692A>G	c.(691-693)cAa>cGa	p.Q231R	C5orf45_ENST00000518235.1_Intron|C5orf45_ENST00000523084.1_Missense_Mutation_p.Q97R|SQSTM1_ENST00000376929.3_3'UTR|C5orf45_ENST00000523267.1_5'UTR|SQSTM1_ENST00000389805.4_3'UTR|C5orf45_ENST00000518219.1_3'UTR|C5orf45_ENST00000403396.2_Intron|C5orf45_ENST00000520698.1_Intron|C5orf45_ENST00000521333.1_3'UTR|C5orf45_ENST00000376931.2_Missense_Mutation_p.Q176R	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	231			Q -> R (in dbSNP:rs10277). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.					p.Q231R(1)		breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						CAGGACAAATTGCGCCCATTT	0.567													C|||	3445	0.687899	0.7837	0.7291	5008	,	,		20832	0.7629		0.5189	False		,,,				2504	0.6258				p.Q231R		Atlas-SNP	.											C5orf45,NS,carcinoma,0,1	C5orf45	23	1	1	Substitution - Missense(1)	prostate(1)	c.A692G						scavenged	.	C	ARG/GLN,,,,ARG/GLN	3376,1030	381.6+/-324.1	1286,804,113	79.0	84.0	82.0		527,,,,692	-5.1	0.0	5	dbSNP_52	82	4685,3915	546.9+/-385.1	1299,2087,914	yes	missense,utr-3,utr-3,utr-3,missense	SQSTM1,C5orf45	NM_001017987.2,NM_001142298.1,NM_001142299.1,NM_003900.4,NM_016175.3	43,,,,43	2585,2891,1027	CC,CT,TT		45.5233,23.3772,38.0209	benign,,,,benign	176/289,,,,231/344	179264731	8061,4945	2203	4300	6503	SO:0001583	missense	51149	exon7			ACAAATTGCGCCC		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.692A>G	5.37:g.179264731T>C	ENSP00000292586:p.Gln231Arg	Somatic	178	2	0.011236		WXS	Illumina HiSeq	Phase_I	157	68	0.433121	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	37	CCDS34319.1	1461	0.6689560439560439	387	0.7865853658536586	237	0.6546961325966851	455	0.7954545454545454	382	0.503957783641161	C	0.097	-1.158248	0.01686	0.766228	0.544767	ENSG00000161010	ENST00000376931;ENST00000523084;ENST00000292586	T;T;T	0.06687	3.27;3.27;3.27	4.67	-5.13	0.02884	.	0.785759	0.10746	N	0.638897	T	0.00012	0.0000	N	0.25647	0.755	0.47994	P	4.309999999999592E-4	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	-0.5185	7.9671	0.30104	0.1099:0.3011:0.0:0.5891	rs10277;rs248243;rs3206175;rs3734006;rs17680466;rs60625205;rs10277	176;231	E9PAK6;Q6NTE8	.;CE045_HUMAN	R	176;97;231	ENSP00000366130:Q176R;ENSP00000429107:Q97R;ENSP00000292586:Q231R	ENSP00000292586:Q231R	Q	-	2	0	C5orf45	179197337	0.000000	0.05858	0.009000	0.14445	0.045000	0.14185	-4.992000	0.00162	-1.779000	0.01280	-2.286000	0.00268	CAA	T|0.352;C|0.648	0.648	strong		0.567	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
DGCR6L	85359	hgsc.bcm.edu	37	22	20303664	20303664	+	Missense_Mutation	SNP	G	G	A	rs113468394	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20303664G>A	ENST00000248879.3	-	3	441	c.350C>T	c.(349-351)gCg>gTg	p.A117V	DGCR6L_ENST00000405465.3_Intron|XXbac-B444P24.13_ENST00000608275.1_RNA	NM_033257.3	NP_150282.2	Q9BY27	DGC6L_HUMAN	DiGeorge syndrome critical region gene 6-like	117						nucleus (GO:0005634)				endometrium(1)|kidney(1)|lung(2)|stomach(1)	5	Colorectal(54;0.0993)					CTGCTGAGCCGCCTGAACCAC	0.687													.|||	208	0.0415335	0.0	0.0677	5008	,	,		16391	0.13		0.0249	False		,,,				2504	0.0051				p.A117V		Atlas-SNP	.											.	DGCR6L	9	.	0			c.C350T						PASS	.	G	VAL/ALA	9,4391	15.5+/-35.6	0,9,2191	23.0	25.0	25.0		350	0.9	1.0	22	dbSNP_132	25	166,8430	72.9+/-135.5	1,164,4133	no	missense	DGCR6L	NM_033257.3	64	1,173,6324	AA,AG,GG		1.9311,0.2045,1.3466	benign	117/221	20303664	175,12821	2200	4298	6498	SO:0001583	missense	85359	exon3			TGAGCCGCCTGAA	AF228708	CCDS13778.1	22q11.21	2013-02-19			ENSG00000128185	ENSG00000128185			18551	protein-coding gene	gene with protein product		609459				11157784	Standard	NM_033257		Approved	FLJ10666	uc002zrx.3	Q9BY27	OTTHUMG00000150583	ENST00000248879.3:c.350C>T	22.37:g.20303664G>A	ENSP00000248879:p.Ala117Val	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	183	86	0.469945	NM_033257	A8K1N7|B3KMC0|D3DX29|Q9BW33	Missense_Mutation	SNP	ENST00000248879.3	37	CCDS13778.1	116	0.05311355311355311	0	0.0	14	0.03867403314917127	84	0.14685314685314685	18	0.023746701846965697	G	7.241	0.601233	0.13939	0.002045	0.019311	ENSG00000128185	ENST00000248879	T	0.30714	1.52	1.98	0.943	0.19531	.	0.145239	0.48286	D	0.000184	T	0.00109	0.0003	L	0.34521	1.04	0.09310	P	0.9999999999999988	B;B	0.13145	0.004;0.007	B;B	0.09377	0.004;0.003	T	0.21280	-1.0250	9	0.21014	T	0.42	-3.599	6.8902	0.24224	0.1585:0.0:0.8414:0.0	.	117;117	B3KMC0;Q9BY27	.;DGC6L_HUMAN	V	117	ENSP00000248879:A117V	ENSP00000248879:A117V	A	-	2	0	DGCR6L	18683664	0.997000	0.39634	0.964000	0.40570	0.473000	0.32948	3.821000	0.55700	0.410000	0.25675	-0.683000	0.03753	GCG	G|0.974;A|0.026	0.026	strong		0.687	DGCR6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318970.3	NM_033257	
ZNF799	90576	hgsc.bcm.edu	37	19	12501852	12501852	+	Missense_Mutation	SNP	C	C	T	rs200077318		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12501852C>T	ENST00000430385.3	-	4	1560	c.1360G>A	c.(1360-1362)Ggg>Agg	p.G454R	ZNF799_ENST00000419318.1_Missense_Mutation_p.G422R|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	454					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						AAGGCTTTCCCACATTTGCAT	0.383																																					p.G454R		Atlas-SNP	.											ZNF799_ENST00000430385,head_neck,carcinoma,0,2	ZNF799	111	2	0			c.G1360A						scavenged	.						75.0	80.0	78.0					19																	12501852		2202	4299	6501	SO:0001583	missense	90576	exon4			CTTTCCCACATTT	BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.1360G>A	19.37:g.12501852C>T	ENSP00000411084:p.Gly454Arg	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	102	3	0.0294118	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	C	16.12	3.033438	0.54896	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.21361	2.01;2.01	1.31	-1.12	0.09808	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27349	0.0671	M	0.86097	2.795	0.31959	N	0.608702	B	0.19200	0.034	B	0.28849	0.095	T	0.34179	-0.9839	9	0.72032	D	0.01	.	5.5527	0.17099	0.0:0.6435:0.0:0.3565	.	454	Q96GE5	ZN799_HUMAN	R	422;454	ENSP00000415278:G422R;ENSP00000411084:G454R	ENSP00000415278:G422R	G	-	1	0	ZNF799	12362852	0.004000	0.15560	0.000000	0.03702	0.966000	0.64601	1.363000	0.34159	-0.271000	0.09272	0.430000	0.28490	GGG	.	.	weak		0.383	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
CFAP70	118491	hgsc.bcm.edu	37	10	75095253	75095253	+	Silent	SNP	G	G	A	rs7910541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75095253G>A	ENST00000310715.3	-	8	942	c.822C>T	c.(820-822)tgC>tgT	p.C274C	TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000401621.2_Silent_p.C274C|TTC18_ENST00000355577.3_5'UTR|TTC18_ENST00000394865.1_Silent_p.C274C	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		274						extracellular vesicular exosome (GO:0070062)		p.C274C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					TTTTCTTTATGCACTCTGCTT	0.418													G|||	892	0.178115	0.177	0.0994	5008	,	,		15691	0.3105		0.0547	False		,,,				2504	0.226				p.C274C		Atlas-SNP	.											TTC18,NS,carcinoma,0,1	TTC18	106	1	1	Substitution - coding silent(1)	stomach(1)	c.C822T						PASS	.	G		659,3747	281.4+/-275.9	56,547,1600	122.0	110.0	114.0		822	1.3	0.7	10	dbSNP_116	114	573,8027	154.3+/-208.6	27,519,3754	no	coding-synonymous	TTC18	NM_145170.3		83,1066,5354	AA,AG,GG		6.6628,14.9569,9.4726		274/1122	75095253	1232,11774	2203	4300	6503	SO:0001819	synonymous_variant	118491	exon8			CTTTATGCACTCT																												ENST00000310715.3:c.822C>T	10.37:g.75095253G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	145	62	0.427586	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Silent	SNP	ENST00000310715.3	37	CCDS7324.3																																																																																			G|0.871;A|0.129	0.129	strong		0.418	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
COL9A1	1297	hgsc.bcm.edu	37	6	70963124	70963124	+	Silent	SNP	A	A	C	rs9346373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:70963124A>C	ENST00000357250.6	-	26	1886	c.1728T>G	c.(1726-1728)ccT>ccG	p.P576P	COL9A1_ENST00000370499.4_Silent_p.P333P|COL9A1_ENST00000320755.7_Silent_p.P333P|COL9A1_ENST00000489611.1_5'UTR	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	576	Triple-helical region (COL2).				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						CAGGAATTCCAGGTACACCCT	0.373													A|||	950	0.189696	0.2927	0.196	5008	,	,		17309	0.0952		0.0974	False		,,,				2504	0.2382				p.P576P		Atlas-SNP	.											.	COL9A1	228	.	0			c.T1728G						PASS	.	A	,	1210,3196	421.3+/-339.3	164,882,1157	112.0	107.0	109.0		1728,999	0.9	1.0	6	dbSNP_119	109	900,7700	201.1+/-244.7	52,796,3452	no	coding-synonymous,coding-synonymous	COL9A1	NM_001851.4,NM_078485.3	,	216,1678,4609	CC,CA,AA		10.4651,27.4626,16.2233	,	576/922,333/679	70963124	2110,10896	2203	4300	6503	SO:0001819	synonymous_variant	1297	exon26			AATTCCAGGTACA		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.1728T>G	6.37:g.70963124A>C		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	129	21	0.162791	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Silent	SNP	ENST00000357250.6	37	CCDS4971.1																																																																																			A|0.831;C|0.169	0.169	strong		0.373	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2		
ZNF419	79744	hgsc.bcm.edu	37	19	58002964	58002964	+	Splice_Site	SNP	G	G	C	rs1135692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58002964G>C	ENST00000221735.7	+	3	384	c.198G>C	c.(196-198)ctG>ctC	p.L66L	ZNF419_ENST00000415379.2_Splice_Site_p.L53L|ZNF419_ENST00000518999.1_Splice_Site_p.L67L|ZNF419_ENST00000424930.2_Splice_Site_p.L67L|ZNF419_ENST00000347466.6_Splice_Site_p.L67L|ZNF419_ENST00000442920.2_Splice_Site_p.L53L|ZNF419_ENST00000426954.2_Splice_Site_p.L54L|AC003005.4_ENST00000601674.1_Splice_Site_p.L53L|ZNF419_ENST00000354197.4_Splice_Site_p.L54L|ZNF419_ENST00000520540.1_Splice_Site_p.L54L			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	66	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)		TGGCCTCTCTGGGTAAGGTTC	0.542													G|||	1310	0.261581	0.2761	0.2608	5008	,	,		20364	0.1181		0.3638	False		,,,				2504	0.2853				p.L67L		Atlas-SNP	.											.	ZNF419	134	.	0			c.G201C						PASS	.	G	,,,,,,	1262,3144	428.7+/-342.0	179,904,1120	67.0	69.0	69.0		201,162,159,201,162,159,198	-0.9	0.2	19	dbSNP_116	69	3010,5588	464.4+/-366.2	498,2014,1787	no	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	ZNF419	NM_001098491.1,NM_001098492.1,NM_001098493.1,NM_001098494.1,NM_001098495.1,NM_001098496.1,NM_024691.3	,,,,,,	677,2918,2907	CC,CG,GG		35.0081,28.6428,32.8514	,,,,,,	67/512,54/499,53/498,67/479,54/466,53/465,66/511	58002964	4272,8732	2203	4299	6502	SO:0001630	splice_region_variant	79744	exon3			CTCTCTGGGTAAG	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.199+1G>C	19.37:g.58002964G>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	182	175	0.961538	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																			G|0.730;C|0.270	0.270	strong		0.542	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	Silent
SLFN12L	100506736	hgsc.bcm.edu	37	17	33805180	33805180	+	Missense_Mutation	SNP	G	G	C	rs2304967	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33805180G>C	ENST00000260908.7	-	3	1235	c.1118C>G	c.(1117-1119)gCa>gGa	p.A373G	SLFN12L_ENST00000361112.4_Missense_Mutation_p.A402G|SLFN12L_ENST00000449046.1_Missense_Mutation_p.A404G|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	373			A -> G (in dbSNP:rs2304967).			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)	p.A404G(2)|p.A402G(1)		breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						TGATGTACTTGCTGGAGAGGG	0.393													G|||	1145	0.228634	0.3245	0.1239	5008	,	,		20242	0.1577		0.164	False		,,,				2504	0.3129				p.A373G		Atlas-SNP	.											SLFN12L_ENST00000449046,NS,carcinoma,0,3	SLFN12L	140	3	3	Substitution - Missense(3)	kidney(3)	c.C1118G						PASS	.						135.0	120.0	125.0					17																	33805180		692	1591	2283	SO:0001583	missense	100506736	exon3			GTACTTGCTGGAG	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.1118C>G	17.37:g.33805180G>C	ENSP00000437635:p.Ala373Gly	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	37	CCDS56026.1	427	0.1955128205128205	161	0.32723577235772355	51	0.1408839779005525	95	0.1660839160839161	120	0.158311345646438	G	1.121	-0.655425	0.03480	.	.	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.03831	3.8;3.9;3.79	1.27	-2.55	0.06288	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.25904	0.137	B	0.20767	0.031	T	0.46898	-0.9158	8	0.52906	T	0.07	.	0.4961	0.00572	0.2076:0.2871:0.2924:0.2128	rs2304967;rs52790215;rs2304967	402	Q6IEE8-2	.	G	373;402;404	ENSP00000437635:A373G;ENSP00000354412:A402G;ENSP00000389348:A404G	ENSP00000437635:A373G	A	-	2	0	SLFN12L	30829293	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-2.608000	0.00887	-1.584000	0.01636	0.205000	0.17691	GCA	G|0.810;C|0.190	0.190	strong		0.393	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
CHRNE	1145	hgsc.bcm.edu	37	17	4802329	4802329	+	Silent	SNP	G	G	A	rs33978919	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4802329G>A	ENST00000293780.4	-	11	1303	c.1293C>T	c.(1291-1293)gcC>gcT	p.A431A	C17orf107_ENST00000521575.1_5'Flank|C17orf107_ENST00000381365.3_5'Flank|CHRNE_ENST00000575637.1_5'Flank	NM_000080.3	NP_000071.1	Q04844	ACHE_HUMAN	cholinergic receptor, nicotinic, epsilon (muscle)	431			A -> P (in FCCMS; causes an increase in distributions of rates for channel opening and closing increasing the range of activation kinetics). {ECO:0000269|PubMed:10962020}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)	12					Galantamine(DB00674)	TCGTGCTCTCGGCCACGAAGT	0.706													g|||	958	0.191294	0.3298	0.2176	5008	,	,		14907	0.0655		0.1461	False		,,,				2504	0.1616				p.A431A		Atlas-SNP	.											.	CHRNE	25	.	0			c.C1293T						PASS	.	G		1231,3173		154,923,1125	14.0	15.0	15.0		1293	-10.9	0.2	17	dbSNP_126	15	1203,7387		98,1007,3190	no	coding-synonymous	CHRNE	NM_000080.3		252,1930,4315	AA,AG,GG		14.0047,27.9519,18.7317		431/494	4802329	2434,10560	2202	4295	6497	SO:0001819	synonymous_variant	1145	exon11			GCTCTCGGCCACG	X66403	CCDS11058.1	17p13.2	2012-02-11	2012-02-07		ENSG00000108556	ENSG00000108556		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1966	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, epsilon (muscle)"""	100725	"""cholinergic receptor, nicotinic, epsilon"""			7688301	Standard	NM_000080		Approved	ACHRE	uc002fzk.1	Q04844	OTTHUMG00000090778	ENST00000293780.4:c.1293C>T	17.37:g.4802329G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_000080	D3DTK6	Silent	SNP	ENST00000293780.4	37	CCDS11058.1																																																																																			G|0.820;A|0.180	0.180	strong		0.706	CHRNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207560.3		
ACSF2	80221	hgsc.bcm.edu	37	17	48539035	48539035	+	Silent	SNP	T	T	C	rs9674937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48539035T>C	ENST00000300441.4	+	4	599	c.495T>C	c.(493-495)taT>taC	p.Y165Y	ACSF2_ENST00000541920.1_Silent_p.Y5Y|ACSF2_ENST00000504392.1_Silent_p.Y122Y|ACSF2_ENST00000427954.2_Silent_p.Y190Y|ACSF2_ENST00000502667.1_Silent_p.Y152Y	NM_025149.4	NP_079425.3	Q96CM8	ACSF2_HUMAN	acyl-CoA synthetase family member 2	165					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ligase activity (GO:0016874)			endometrium(7)|kidney(3)|large_intestine(1)|lung(1)|stomach(1)	13	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			AACTGGAGTATGTCCTCAAGA	0.607													T|||	1723	0.34405	0.705	0.2824	5008	,	,		18866	0.0863		0.2545	False		,,,				2504	0.2577				p.Y165Y		Atlas-SNP	.											.	ACSF2	46	.	0			c.T495C						PASS	.	T		2719,1687	653.9+/-399.7	849,1021,333	83.0	79.0	80.0		495	-0.4	1.0	17	dbSNP_119	80	2180,6420	373.2+/-336.9	300,1580,2420	no	coding-synonymous	ACSF2	NM_025149.4		1149,2601,2753	CC,CT,TT		25.3488,38.2887,37.6672		165/616	48539035	4899,8107	2203	4300	6503	SO:0001819	synonymous_variant	80221	exon4			GGAGTATGTCCTC	AK024573, BC012053	CCDS11567.1, CCDS74103.1, CCDS74104.1, CCDS74105.1	17q21.33	2007-10-17			ENSG00000167107	ENSG00000167107		"""Acyl-CoA synthetase family"""	26101	protein-coding gene	gene with protein product		610465				17762044	Standard	NM_001288968		Approved	FLJ20920, ACSMW	uc002iqu.2	Q96CM8	OTTHUMG00000162128	ENST00000300441.4:c.495T>C	17.37:g.48539035T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	173	170	0.982659	NM_025149	B4DFQ6|B4DHT5|B4DUF5|Q9H7G2	Silent	SNP	ENST00000300441.4	37	CCDS11567.1	664	0.304029304029304	324	0.6585365853658537	103	0.2845303867403315	47	0.08216783216783216	190	0.25065963060686014	T	11.10	1.538263	0.27475	0.617113	0.253488	ENSG00000167107	ENST00000506582	T	0.55760	0.5	5.49	-0.363	0.12556	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999525967	.	.	.	.	.	.	T	0.47156	-0.9139	5	0.87932	D	0	-3.9033	10.1911	0.43028	0.0:0.4557:0.0:0.5443	rs9674937;rs11546317;rs56922985;rs9674937	.	.	.	R	138	ENSP00000424842:C138R	ENSP00000424842:C138R	C	+	1	0	ACSF2	45894034	1.000000	0.71417	0.994000	0.49952	0.985000	0.73830	1.020000	0.30027	-0.127000	0.11661	0.533000	0.62120	TGT	T|0.644;C|0.356	0.356	strong		0.607	ACSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367423.3	NM_025149	
CARD8	22900	hgsc.bcm.edu	37	19	48722180	48722180	+	Silent	SNP	C	C	T	rs10500299	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48722180C>T	ENST00000359009.4	-	8	1245	c.933G>A	c.(931-933)gaG>gaA	p.E311E	CARD8_ENST00000520015.1_Intron|CARD8_ENST00000519940.1_Silent_p.E417E|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000391898.3_Silent_p.E417E|CARD8_ENST00000520753.1_Intron|CARD8_ENST00000357778.5_Silent_p.E142E|CARD8_ENST00000520153.1_Silent_p.E367E|CARD8_ENST00000447740.2_Silent_p.E367E|CARD8_ENST00000521613.1_Silent_p.E367E			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8	311					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		TTTCAGTAATCTCAAGTTGAA	0.463													T|||	1300	0.259585	0.2042	0.3487	5008	,	,		17821	0.1766		0.2465	False		,,,				2504	0.3701				p.E417E		Atlas-SNP	.											.	CARD8	53	.	0			c.G1251A						PASS	.	T	,,,,	920,3486	739.1+/-411.0	92,736,1375	157.0	149.0	151.0		1251,1101,,,1101	1.2	0.0	19	dbSNP_119	151	2429,6171	699.2+/-405.1	379,1671,2250	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	,,,,	471,2407,3625	TT,TC,CC		28.2442,20.8806,25.7497	,,,,	417/538,367/488,,,367/488	48722180	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	22900	exon9			AGTAATCTCAAGT	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.933G>A	19.37:g.48722180C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	163	163	1	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	37																																																																																				C|0.758;T|0.242	0.242	strong		0.463	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
ATP8B4	79895	hgsc.bcm.edu	37	15	50212572	50212572	+	Silent	SNP	G	G	T	rs72733094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:50212572G>T	ENST00000284509.6	-	18	1935	c.1794C>A	c.(1792-1794)atC>atA	p.I598I	ATP8B4_ENST00000559829.1_Silent_p.I598I	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	598						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(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		CTCTGTATGCGATGGCCAAGG	0.458													G|||	7	0.00139776	0.0	0.0	5008	,	,		20424	0.0		0.007	False		,,,				2504	0.0				p.I598I		Atlas-SNP	.											.	ATP8B4	173	.	0			c.C1794A						PASS	.	G		6,4386	9.9+/-24.2	0,6,2190	84.0	76.0	79.0		1794	-11.3	0.0	15	dbSNP_130	79	85,8505	48.5+/-108.0	0,85,4210	no	coding-synonymous	ATP8B4	NM_024837.2		0,91,6400	TT,TG,GG		0.9895,0.1366,0.701		598/1193	50212572	91,12891	2196	4295	6491	SO:0001819	synonymous_variant	79895	exon18			GTATGCGATGGCC	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"""ATPases / P-type"""	13536	protein-coding gene	gene with protein product		609123	"""ATPase, Class I, type 8B, member 4"""			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1794C>A	15.37:g.50212572G>T		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	174	92	0.528736	NM_024837	Q9H727	Silent	SNP	ENST00000284509.6	37	CCDS32238.1																																																																																			G|0.994;T|0.006	0.006	strong		0.458	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837	
MMRN1	22915	hgsc.bcm.edu	37	4	90857479	90857479	+	Missense_Mutation	SNP	G	G	A	rs12646270	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:90857479G>A	ENST00000394980.1	+	7	2967	c.2648G>A	c.(2647-2649)gGc>gAc	p.G883D	MMRN1_ENST00000264790.2_Missense_Mutation_p.G883D|MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000508372.1_Missense_Mutation_p.G625D			Q13201	MMRN1_HUMAN	multimerin 1	883			G -> D (in dbSNP:rs12646270).		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)		p.G883D(1)		breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GTTAAAAAAGGCAGTGTAGTT	0.348													G|||	434	0.0866613	0.0008	0.0115	5008	,	,		18484	0.2728		0.0477	False		,,,				2504	0.1043				p.G883D		Atlas-SNP	.											MMRN1,NS,carcinoma,0,2	MMRN1	174	2	1	Substitution - Missense(1)	stomach(1)	c.G2648A						PASS	.	G	ASP/GLY	49,4345	39.2+/-71.8	0,49,2148	46.0	49.0	48.0		2648	-0.5	0.0	4	dbSNP_120	48	372,8216	121.7+/-180.7	7,358,3929	yes	missense	MMRN1	NM_007351.2	94	7,407,6077	AA,AG,GG		4.3316,1.1152,3.243	benign	883/1229	90857479	421,12561	2197	4294	6491	SO:0001583	missense	22915	exon6			AAAAAGGCAGTGT	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2648G>A	4.37:g.90857479G>A	ENSP00000378431:p.Gly883Asp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	212	0.09706959706959707	0	0.0	5	0.013812154696132596	167	0.291958041958042	40	0.052770448548812667	G	1.871	-0.460202	0.04508	0.011152	0.043316	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.64438	0.25;0.25;-0.1	5.3	-0.489	0.12052	.	0.759983	0.12411	N	0.471241	T	0.00012	0.0000	L	0.28740	0.885	0.80722	P	0.0	B	0.15141	0.012	B	0.13407	0.009	T	0.19289	-1.0310	9	0.11485	T	0.65	.	2.1337	0.03756	0.3386:0.2176:0.3419:0.1019	rs12646270;rs52807437;rs12646270	883	Q13201	MMRN1_HUMAN	D	883;883;625	ENSP00000378431:G883D;ENSP00000264790:G883D;ENSP00000426461:G625D	ENSP00000264790:G883D	G	+	2	0	MMRN1	91076502	0.011000	0.17503	0.004000	0.12327	0.477000	0.33069	-0.077000	0.11394	-0.054000	0.13266	-0.140000	0.14226	GGC	G|0.939;A|0.061	0.061	strong		0.348	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
CNOT1	23019	hgsc.bcm.edu	37	16	58577421	58577421	+	Intron	SNP	C	C	T	rs41260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58577421C>T	ENST00000317147.5	-	31	4767				CNOT1_ENST00000569240.1_Intron|CNOT1_ENST00000441024.2_Silent_p.A1508A|CNOT1_ENST00000245138.4_Intron	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1						gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		taagtggtaacgcccagtgcc	0.343													T|||	4038	0.80631	0.9062	0.7392	5008	,	,		20105	0.9712		0.5726	False		,,,				2504	0.7894				p.A1508A		Atlas-SNP	.											CNOT1_ENST00000441024,colon,carcinoma,-1,1	CNOT1	359	1	0			c.G4524A						PASS	.	T	,	2224,396		955,314,41	48.0	54.0	52.0		,4524	-6.4	0.0	16	dbSNP_76	52	2544,2074		737,1070,502	no	intron,coding-synonymous	CNOT1	NM_016284.3,NM_206999.1	,	1692,1384,543	TT,TC,CC		44.9112,15.1145,34.1254	,	,1508/1552	58577421	4768,2470	1310	2309	3619	SO:0001627	intron_variant	23019	exon31			TGGTAACGCCCAG	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4434+89G>A	16.37:g.58577421C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			C|0.186;T|0.814	0.814	strong		0.343	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
B4GALNT3	283358	hgsc.bcm.edu	37	12	662838	662838	+	Silent	SNP	T	T	C	rs1056008	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:662838T>C	ENST00000266383.5	+	14	1762	c.1749T>C	c.(1747-1749)ccT>ccC	p.P583P		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	583					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)			CTCAGGCCCCTGGAAGGGGCT	0.652													C|||	1424	0.284345	0.3805	0.1945	5008	,	,		17522	0.1974		0.2942	False		,,,				2504	0.2975				p.P583P		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.T1749C						PASS	.	C		1649,2757		302,1045,856	32.0	34.0	33.0		1749	-0.4	0.0	12	dbSNP_86	33	2267,6327		310,1647,2340	no	coding-synonymous	B4GALNT3	NM_173593.3		612,2692,3196	CC,CT,TT		26.3789,37.4262,30.1231		583/999	662838	3916,9084	2203	4297	6500	SO:0001819	synonymous_variant	283358	exon14			GGCCCCTGGAAGG	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.1749T>C	12.37:g.662838T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			.	.	weak		0.652	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
C7orf66	154907	hgsc.bcm.edu	37	7	108524494	108524494	+	Missense_Mutation	SNP	C	C	T	rs141228190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:108524494C>T	ENST00000379007.2	-	1	150	c.96G>A	c.(94-96)atG>atA	p.M32I		NM_001024607.1	NP_001019778.1	A4D0T2	CG066_HUMAN	chromosome 7 open reading frame 66	32						integral component of membrane (GO:0016021)				breast(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	15						CCTGAAACAGCATTGCAAGGC	0.403													C|||	2	0.000399361	0.0	0.0	5008	,	,		17511	0.0		0.002	False		,,,				2504	0.0				p.M32I		Atlas-SNP	.											.	C7orf66	29	.	0			c.G96A						PASS	.	C	ILE/MET	2,4404	4.2+/-10.8	0,2,2201	133.0	114.0	121.0		96	0.5	0.0	7	dbSNP_134	121	12,8588	9.1+/-34.3	0,12,4288	yes	missense	C7orf66	NM_001024607.1	10	0,14,6489	TT,TC,CC		0.1395,0.0454,0.1076	benign	32/116	108524494	14,12992	2203	4300	6503	SO:0001583	missense	154907	exon1			AAACAGCATTGCA	AF103078	CCDS34735.1	7q31.1	2009-03-06			ENSG00000205174	ENSG00000205174			33712	protein-coding gene	gene with protein product							Standard	NM_001024607		Approved		uc003vfo.3	A4D0T2	OTTHUMG00000154867	ENST00000379007.2:c.96G>A	7.37:g.108524494C>T	ENSP00000368292:p.Met32Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_001024607		Missense_Mutation	SNP	ENST00000379007.2	37	CCDS34735.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	2.215	-0.379825	0.05000	4.54E-4	0.001395	ENSG00000205174	ENST00000379007	.	.	.	2.81	0.526	0.17078	.	.	.	.	.	T	0.14917	0.0360	N	0.08118	0	0.09310	N	1	B	0.21606	0.058	B	0.14023	0.01	T	0.27571	-1.0070	7	.	.	.	.	4.4233	0.11492	0.0:0.5684:0.0:0.4316	.	32	A4D0T2	CG066_HUMAN	I	32	.	.	M	-	3	0	C7orf66	108311730	0.000000	0.05858	0.000000	0.03702	0.049000	0.14656	0.027000	0.13621	0.098000	0.17522	0.455000	0.32223	ATG	C|0.999;T|0.001	0.001	strong		0.403	C7orf66-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337420.1	NM_001024607	
NUAK2	81788	hgsc.bcm.edu	37	1	205273142	205273142	+	Silent	SNP	G	G	C	rs41264881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:205273142G>C	ENST00000367157.3	-	7	1449	c.1323C>G	c.(1321-1323)ccC>ccG	p.P441P		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			TGGGGAGCAGGGGGGCAGCCT	0.627													G|||	382	0.076278	0.0461	0.1571	5008	,	,		16405	0.001		0.1501	False		,,,				2504	0.0613				p.P441P		Atlas-SNP	.											NUAK2_ENST00000367157,NS,carcinoma,0,2	NUAK2	107	2	0			c.C1323G						scavenged	.	G		321,4085	160.3+/-192.7	10,301,1892	39.0	39.0	39.0		1323	3.1	0.5	1	dbSNP_127	39	1318,7282	246.1+/-274.7	97,1124,3079	no	coding-synonymous	NUAK2	NM_030952.1		107,1425,4971	CC,CG,GG		15.3256,7.2855,12.6019		441/629	205273142	1639,11367	2203	4300	6503	SO:0001819	synonymous_variant	81788	exon7			GAGCAGGGGGGCA	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1323C>G	1.37:g.205273142G>C		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_030952		Silent	SNP	ENST00000367157.3	37	CCDS1453.1																																																																																			G|0.874;C|0.126	0.126	strong		0.627	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45971299	45971299	+	Missense_Mutation	SNP	T	T	C	rs233240	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45971299T>C	ENST00000391621.1	-	1	89	c.43A>G	c.(43-45)Aac>Gac	p.N15D	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron|KRTAP10-2_ENST00000498210.1_5'UTR	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	15			N -> D (in dbSNP:rs233240). {ECO:0000269|PubMed:15028290}.			keratin filament (GO:0045095)		p.N15D(1)		large_intestine(1)|lung(4)|skin(1)	6						TGCCAGGAGTTGGTGCAGGCG	0.667													T|||	1085	0.216653	0.1725	0.1527	5008	,	,		17203	0.371		0.2068	False		,,,				2504	0.1728				p.N15D		Atlas-SNP	.											KRTAP10-2,bladder,carcinoma,0,3	KRTAP10-2	21	3	1	Substitution - Missense(1)	large_intestine(1)	c.A43G						PASS	.	T	,ASP/ASN	761,3645	309.4+/-291.0	65,631,1507	81.0	86.0	84.0		,43	-1.0	0.0	21	dbSNP_79	84	1692,6908	310.1+/-309.7	158,1376,2766	no	intron,missense	TSPEAR,KRTAP10-2	NM_144991.2,NM_198693.2	,23	223,2007,4273	CC,CT,TT		19.6744,17.2719,18.8605	,benign	,15/256	45971299	2453,10553	2203	4300	6503	SO:0001583	missense	386679	exon1			AGGAGTTGGTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.43A>G	21.37:g.45971299T>C	ENSP00000375479:p.Asn15Asp	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	124	71	0.572581	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	531	0.24313186813186813	81	0.16463414634146342	60	0.16574585635359115	218	0.3811188811188811	172	0.22691292875989447	t	0.005	-2.231254	0.00280	0.172719	0.196744	ENSG00000205445	ENST00000391621	T	0.14640	2.49	3.46	-1.05	0.10036	.	.	.	.	.	T	0.00012	0.0000	N	0.00355	-1.605	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38457	-0.9660	8	0.02654	T	1	.	3.6264	0.08114	0.0:0.4225:0.1919:0.3855	rs233240;rs620443;rs59814995	15	P60368	KR102_HUMAN	D	15	ENSP00000375479:N15D	ENSP00000375479:N15D	N	-	1	0	KRTAP10-2	44795727	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.100000	0.15231	-0.801000	0.04427	-0.814000	0.03130	AAC	T|0.767;C|0.233	0.233	strong		0.667	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
PLCD1	5333	hgsc.bcm.edu	37	3	38052725	38052725	+	Missense_Mutation	SNP	C	C	T	rs933135	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38052725C>T	ENST00000334661.4	-	5	992	c.770G>A	c.(769-771)cGc>cAc	p.R257H	PLCD1_ENST00000463876.1_Missense_Mutation_p.R278H|PLCD1_ENST00000479619.1_5'Flank	NM_006225.3	NP_006216.2	P51178	PLCD1_HUMAN	phospholipase C, delta 1	257			R -> H (in dbSNP:rs933135).		angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|GTPase activating protein binding (GO:0032794)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol phosphate binding (GO:1901981)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylserine binding (GO:0001786)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(6)|prostate(1)|skin(1)	24				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		GGGCTCGTAGCGCTCAATGAG	0.672													C|||	316	0.063099	0.0	0.0303	5008	,	,		16535	0.1825		0.0149	False		,,,				2504	0.0982				p.R278H		Atlas-SNP	.											.	PLCD1	87	.	0			c.G833A	GRCh37	CM067709	PLCD1	M	rs933135	PASS	.	C	HIS/ARG,HIS/ARG	16,4390		0,16,2187	28.0	29.0	29.0		833,770	4.9	1.0	3	dbSNP_86	29	152,8444		0,152,4146	yes	missense,missense	PLCD1	NM_001130964.1,NM_006225.3	29,29	0,168,6333	TT,TC,CC		1.7683,0.3631,1.2921	possibly-damaging,possibly-damaging	278/778,257/757	38052725	168,12834	2203	4298	6501	SO:0001583	missense	5333	exon5			TCGTAGCGCTCAA		CCDS2671.1, CCDS46793.1	3p22-p21.3	2013-01-10			ENSG00000187091	ENSG00000187091	3.1.4.11	"""EF-hand domain containing"""	9060	protein-coding gene	gene with protein product		602142				9345909	Standard	NM_001130964		Approved		uc003chm.3	P51178	OTTHUMG00000130813	ENST00000334661.4:c.770G>A	3.37:g.38052725C>T	ENSP00000335600:p.Arg257His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_001130964	B3KR14|Q86VN8	Missense_Mutation	SNP	ENST00000334661.4	37	CCDS2671.1	124	0.056776556776556776	1	0.0020325203252032522	8	0.022099447513812154	100	0.17482517482517482	15	0.01978891820580475	C	18.23	3.577339	0.65878	0.003631	0.017683	ENSG00000187091	ENST00000463876;ENST00000334661	T;T	0.46451	0.87;0.87	4.95	4.95	0.65309	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);EF-hand-like domain (1);	0.102292	0.64402	D	0.000003	T	0.00271	0.0008	M	0.75615	2.305	0.26759	P	0.9700436	D;P	0.62365	0.991;0.792	P;B	0.61201	0.885;0.132	T	0.15723	-1.0427	9	0.62326	D	0.03	.	9.8655	0.41140	0.0:0.8434:0.0:0.1566	rs933135;rs52803102;rs933135	257;278	P51178;B3KR14	PLCD1_HUMAN;.	H	278;257	ENSP00000430344:R278H;ENSP00000335600:R257H	ENSP00000335600:R257H	R	-	2	0	PLCD1	38027729	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.560000	0.36331	2.677000	0.91161	0.655000	0.94253	CGC	C|0.958;A|0.000	.	strong		0.672	PLCD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253359.2		
TMEM99	147184	hgsc.bcm.edu	37	17	38991052	38991052	+	Missense_Mutation	SNP	T	T	G	rs1044806|rs386796999	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38991052T>G	ENST00000301665.3	+	3	588	c.284T>G	c.(283-285)cTt>cGt	p.L95R		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	95			L -> R (in dbSNP:rs1044806). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				AGAGAAGGACTTCTTCTTCCT	0.468													T|||	544	0.108626	0.1248	0.1182	5008	,	,		19701	0.004		0.1928	False		,,,				2504	0.1012				p.L95R		Atlas-SNP	.											.	TMEM99	21	.	0			c.T284G						PASS	.	T	ARG/LEU,ARG/LEU,ARG/LEU	429,3453		27,375,1539	202.0	199.0	200.0		284,284,284	0.2	0.1	17	dbSNP_86	200	1612,6682		151,1310,2686	yes	missense,missense,missense	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	102,102,102	178,1685,4225	GG,GT,TT		19.4357,11.051,16.7625	possibly-damaging,possibly-damaging,possibly-damaging	95/259,95/259,95/259	38991052	2041,10135	1941	4147	6088	SO:0001583	missense	147184	exon3			AAGGACTTCTTCT	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.284T>G	17.37:g.38991052T>G	ENSP00000301665:p.Leu95Arg	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	173	83	0.479769	NM_001195386	B4DQ34|Q96BP9	Missense_Mutation	SNP	ENST00000301665.3	37	CCDS42319.1	190	0.08699633699633699	48	0.0975609756097561	39	0.10773480662983426	0	0.0	103	0.1358839050131926	T	7.070	0.568095	0.13560	0.11051	0.194357	ENSG00000167920	ENST00000436612;ENST00000301665	T;T	0.33654	1.4;1.4	0.158	0.158	0.14942	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	D	0.54397	0.966	P	0.61070	0.883	T	0.17623	-1.0363	7	0.87932	D	0	.	.	.	.	rs1044806;rs3169916;rs1044806	95	Q8N816	TMM99_HUMAN	R	95	ENSP00000390036:L95R;ENSP00000301665:L95R	ENSP00000301665:L95R	L	+	2	0	TMEM99	36244578	0.051000	0.20477	0.089000	0.20774	0.090000	0.18270	0.215000	0.17562	0.175000	0.19841	0.172000	0.16884	CTT	T|0.907;G|0.093	0.093	strong		0.468	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
MYH11	4629	hgsc.bcm.edu	37	16	15811062	15811062	+	Silent	SNP	C	C	T	rs587781066|rs1050162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15811062C>T	ENST00000300036.5	-	38	5548	c.5439G>A	c.(5437-5439)aaG>aaA	p.K1813K	NDE1_ENST00000396355.1_Intron|MYH11_ENST00000576790.2_Silent_p.K1813K|MYH11_ENST00000396324.3_Silent_p.K1820K|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000452625.2_Silent_p.K1820K	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1813					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CGATGGTGGACTTGAACTTGG	0.622			T	CBFB	AML								C|||	1987	0.396765	0.2542	0.5029	5008	,	,		19368	0.3323		0.4841	False		,,,				2504	0.4908				p.K1820K		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	MYH11_ENST00000396324,NS,neuroblastoma,-1,2	MYH11	520	2	0			c.G5460A						PASS	.	C	,,,,,	1339,3055	447.5+/-348.4	208,923,1066	123.0	103.0	110.0		5460,5460,,5439,,5439	3.4	1.0	16	dbSNP_86	110	4371,4229	582.5+/-391.4	1133,2105,1062	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	1341,3028,2128	TT,TC,CC		49.1744,30.4734,43.9434	,,,,,	1820/1946,1820/1980,,1813/1973,,1813/1939	15811062	5710,7284	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon39			GGTGGACTTGAAC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5439G>A	16.37:g.15811062C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			C|0.596;T|0.404	0.404	strong		0.622	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
GLIS3	169792	hgsc.bcm.edu	37	9	4118111	4118111	+	Missense_Mutation	SNP	G	G	T	rs6415788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:4118111G>T	ENST00000324333.10	-	3	1095	c.902C>A	c.(901-903)cCa>cAa	p.P301Q	GLIS3_ENST00000381971.3_Missense_Mutation_p.P456Q	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	301	Pro-rich.		P -> Q (in dbSNP:rs6415788). {ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		tggggggcctgggggcggcgg	0.731													T|||	3386	0.676118	0.6006	0.7622	5008	,	,		9673	0.874		0.6302	False		,,,				2504	0.5603				p.P456Q		Atlas-SNP	.											.	GLIS3	152	.	0			c.C1367A						PASS	.	T	GLN/PRO,GLN/PRO	2499,1143		894,711,216	8.0	11.0	10.0		1367,902	5.4	1.0	9	dbSNP_116	10	4958,2542		1716,1526,508	yes	missense,missense	GLIS3	NM_001042413.1,NM_152629.3	76,76	2610,2237,724	TT,TG,GG		33.8933,31.3839,33.0731	benign,benign	456/931,301/776	4118111	7457,3685	1821	3750	5571	SO:0001583	missense	169792	exon4			GGGCCTGGGGGCG	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.902C>A	9.37:g.4118111G>T	ENSP00000325494:p.Pro301Gln	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	14	14	1	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	1503	0.6881868131868132	289	0.5873983739837398	261	0.7209944751381215	500	0.8741258741258742	453	0.5976253298153035	T	1.187	-0.636435	0.03557	0.686161	0.661067	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.10192	2.92;2.9	5.37	5.37	0.77165	.	0.000000	0.47852	N	0.000210	T	0.00012	0.0000	N	0.01048	-1.04	0.42193	P	0.008264000000000049	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34576	-0.9823	9	0.02654	T	1	.	12.6151	0.56571	0.0:0.0:0.1388:0.8612	rs6415788;rs13294473;rs59237658;rs6415788	456;301	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	Q	301;456	ENSP00000325494:P301Q;ENSP00000371398:P456Q	ENSP00000325494:P301Q	P	-	2	0	GLIS3	4108111	1.000000	0.71417	0.971000	0.41717	0.160000	0.22226	4.123000	0.57917	0.872000	0.35775	-0.256000	0.11100	CCA	G|0.313;T|0.687	0.687	strong		0.731	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
TRAPPC5	126003	hgsc.bcm.edu	37	19	7747293	7747293	+	Missense_Mutation	SNP	T	T	G	rs6952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7747293T>G	ENST00000317378.5	+	2	341	c.154T>G	c.(154-156)Tcg>Gcg	p.S52A	TRAPPC5_ENST00000426877.2_Missense_Mutation_p.S52A|TRAPPC5_ENST00000595985.1_Intron|TRAPPC5_ENST00000596148.1_Missense_Mutation_p.S52A|CTD-3214H19.16_ENST00000597959.1_Missense_Mutation_p.S110R	NM_174894.2	NP_777554.1	Q8IUR0	TPPC5_HUMAN	trafficking protein particle complex 5	52			S -> A (in dbSNP:rs6952).		vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|TRAPP complex (GO:0030008)				NS(1)|lung(2)	3						CGAGCTGCAGTCGCGCCTGGC	0.726													G|||	1793	0.358027	0.5726	0.2089	5008	,	,		12182	0.2669		0.3231	False		,,,				2504	0.3037				p.S52A		Atlas-SNP	.											TRAPPC5,NS,carcinoma,0,1	TRAPPC5	11	1	0			c.T154G						PASS	.	G	ALA/SER,ALA/SER,ALA/SER	1566,1884		395,776,554	9.0	11.0	11.0		154,154,154	3.0	1.0	19	dbSNP_52	11	1982,5366		327,1328,2019	yes	missense,missense,missense	TRAPPC5	NM_001042461.1,NM_001042462.1,NM_174894.1	99,99,99	722,2104,2573	GG,GT,TT		26.9733,45.3913,32.8579	benign,benign,benign	52/189,52/189,52/189	7747293	3548,7250	1725	3674	5399	SO:0001583	missense	126003	exon2			CTGCAGTCGCGCC	BC042161	CCDS42490.1	19p13.3	2011-10-10				ENSG00000181029		"""Trafficking protein particle complex"""	23067	protein-coding gene	gene with protein product							Standard	NM_001042462		Approved	MGC52424, TRS31	uc002mhj.2	Q8IUR0		ENST00000317378.5:c.154T>G	19.37:g.7747293T>G	ENSP00000316990:p.Ser52Ala	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001042461	A8K7I6	Missense_Mutation	SNP	ENST00000317378.5	37	CCDS42490.1	740	0.33882783882783885	272	0.5528455284552846	83	0.2292817679558011	137	0.2395104895104895	248	0.32717678100263853	G	9.250	1.040448	0.19669	0.453913	0.269733	ENSG00000181029	ENST00000317378;ENST00000426877	T;T	0.40225	1.04;1.04	4.09	3.04	0.35103	NO signalling/Golgi transport  ligand-binding domain (1);	0.150646	0.43416	N	0.000567	T	0.00012	0.0000	N	0.03194	-0.395	0.58432	P	9.000000000036756E-6	B	0.02656	0.0	B	0.06405	0.002	T	0.46400	-0.9194	9	0.11794	T	0.64	-5.7203	6.0462	0.19762	0.1047:0.0:0.7046:0.1907	rs6952;rs3170248	52	Q8IUR0	TPPC5_HUMAN	A	52	ENSP00000316990:S52A;ENSP00000399025:S52A	ENSP00000316990:S52A	S	+	1	0	TRAPPC5	7653293	0.919000	0.31177	1.000000	0.80357	0.606000	0.37113	1.119000	0.31258	0.725000	0.32318	-0.224000	0.12420	TCG	T|0.657;G|0.343	0.343	strong		0.726	TRAPPC5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461252.1	XM_058961	
ZIM3	114026	hgsc.bcm.edu	37	19	57649900	57649900	+	Missense_Mutation	SNP	C	C	T	rs2370134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57649900C>T	ENST00000269834.1	-	3	467	c.82G>A	c.(82-84)Gaa>Aaa	p.E28K		NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	28	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		E -> K (in dbSNP:rs2370134).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(27)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	52		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.243)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTTCTCTGTTCGGGATTCAGC	0.512													C|||	696	0.138978	0.0144	0.2161	5008	,	,		16919	0.247		0.161	False		,,,				2504	0.1186				p.E28K		Atlas-SNP	.											.	ZIM3	107	.	0			c.G82A						PASS	.	C	LYS/GLU	214,4192	129.4+/-166.1	9,196,1998	98.0	87.0	91.0		82	-1.3	0.0	19	dbSNP_100	91	1569,7031	294.3+/-301.8	153,1263,2884	no	missense	ZIM3	NM_052882.1	56	162,1459,4882	TT,TC,CC		18.2442,4.857,13.7091	benign	28/473	57649900	1783,11223	2203	4300	6503	SO:0001583	missense	114026	exon3			TCTGTTCGGGATT	AF365931	CCDS33125.1	19q13.4	2013-01-08				ENSG00000141946		"""Zinc fingers, C2H2-type"", ""-"""	16366	protein-coding gene	gene with protein product							Standard	NM_052882		Approved	ZNF657	uc002qnz.1	Q96PE6		ENST00000269834.1:c.82G>A	19.37:g.57649900C>T	ENSP00000269834:p.Glu28Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	111	60	0.540541	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	346	0.15842490842490842	15	0.03048780487804878	67	0.1850828729281768	152	0.26573426573426573	112	0.14775725593667546	C	10.87	1.473521	0.26423	0.04857	0.182442	ENSG00000141946	ENST00000269834	T	0.01705	4.68	2.72	-1.33	0.09172	Krueppel-associated box (4);	.	.	.	.	T	0.00012	0.0000	L	0.53249	1.67	0.80722	P	0.0	P	0.37914	0.611	B	0.23716	0.048	T	0.47971	-0.9075	8	0.72032	D	0.01	.	0.2325	0.00182	0.2046:0.2664:0.2019:0.3271	rs2370134;rs17207663;rs52794544;rs61460479;rs2370134	28	Q96PE6	ZIM3_HUMAN	K	28	ENSP00000269834:E28K	ENSP00000269834:E28K	E	-	1	0	ZIM3	62341712	0.000000	0.05858	0.000000	0.03702	0.309000	0.27889	-2.790000	0.00767	0.277000	0.22141	0.205000	0.17691	GAA	C|0.856;T|0.143	0.143	strong		0.512	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1		
GOLGA5	9950	hgsc.bcm.edu	37	14	93275841	93275841	+	Silent	SNP	A	A	G	rs17128583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93275841A>G	ENST00000163416.2	+	4	1225	c.969A>G	c.(967-969)gaA>gaG	p.E323E	GOLGA5_ENST00000355976.2_Silent_p.E323E	NM_005113.2	NP_005104	Q8TBA6	GOGA5_HUMAN	golgin A5	323					Golgi organization (GO:0007030)|Golgi vesicle transport (GO:0048193)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)			large_intestine(6)|lung(1)|ovary(2)	9		all_cancers(154;0.0934)		COAD - Colon adenocarcinoma(157;0.222)		AAGCATTAGAAGCCTTACAGA	0.418			T	RET	papillary thyroid								A|||	685	0.136781	0.0333	0.1628	5008	,	,		17200	0.1796		0.0905	False		,,,				2504	0.2618				p.E323E		Atlas-SNP	.		Dom	yes		14	14q	9950	"""golgi autoantigen, golgin subfamily a, 5  (PTC5)"""		E	.	GOLGA5	84	.	0			c.A969G						PASS	.	A		192,4214	118.4+/-156.1	3,186,2014	43.0	44.0	43.0		969	2.1	0.9	14	dbSNP_123	43	534,8066	145.9+/-201.5	14,506,3780	no	coding-synonymous	GOLGA5	NM_005113.2		17,692,5794	GG,GA,AA		6.2093,4.3577,5.582		323/732	93275841	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	9950	exon4			ATTAGAAGCCTTA	AF085199	CCDS9905.1	14q32.12	2012-05-04	2010-02-12		ENSG00000066455	ENSG00000066455			4428	protein-coding gene	gene with protein product	"""golgi integral membrane protein 5"""	606918	"""golgi autoantigen, golgin subfamily a, 5"""			2734021, 9443391, 15004235	Standard	NM_005113		Approved	ret-II, golgin-84, rfg5, GOLIM5	uc001yaz.1	Q8TBA6	OTTHUMG00000171217	ENST00000163416.2:c.969A>G	14.37:g.93275841A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	74	33	0.445946	NM_005113	C9JRU1|O95287|Q03962|Q2TS49|Q9UQQ7	Silent	SNP	ENST00000163416.2	37	CCDS9905.1																																																																																			A|0.925;G|0.075	0.075	strong		0.418	GOLGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412365.1		
DCSTAMP	81501	hgsc.bcm.edu	37	8	105361354	105361354	+	Missense_Mutation	SNP	G	G	C	rs67114147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:105361354G>C	ENST00000297581.2	+	2	623	c.574G>C	c.(574-576)Gaa>Caa	p.E192Q	DPYS_ENST00000521601.1_Intron|DCSTAMP_ENST00000517991.1_Missense_Mutation_p.E192Q	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	192					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)											CAGCAAAGGGGAAGTCCTGAG	0.522													G|||	583	0.116414	0.0605	0.1859	5008	,	,		18345	0.1319		0.1272	False		,,,				2504	0.1155				p.E192Q		Atlas-SNP	.											.	.	.	.	0			c.G574C						PASS	.	G	GLN/GLU	350,4056	178.3+/-207.1	18,314,1871	104.0	96.0	99.0		574	-1.9	0.0	8	dbSNP_130	99	1136,7464	231.0+/-265.1	82,972,3246	yes	missense	TM7SF4	NM_030788.2	29	100,1286,5117	CC,CG,GG		13.2093,7.9437,11.4255	benign	192/471	105361354	1486,11520	2203	4300	6503	SO:0001583	missense	81501	exon2			AAAGGGGAAGTCC	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.574G>C	8.37:g.105361354G>C	ENSP00000297581:p.Glu192Gln	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	259	0.11858974358974358	34	0.06910569105691057	72	0.19889502762430938	56	0.0979020979020979	97	0.1279683377308707	G	9.109	1.006175	0.19199	0.079437	0.132093	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.33216	1.42	5.53	-1.86	0.07760	.	0.517494	0.23175	N	0.051088	T	0.00039	0.0001	L	0.34521	1.04	0.54753	P	1.2000000000012001E-5	B	0.21071	0.051	B	0.16722	0.016	T	0.33727	-0.9857	8	.	.	.	-1.1699	11.861	0.52465	0.0768:0.5286:0.3946:0.0	.	192	Q9H295	TM7S4_HUMAN	Q	192	ENSP00000297581:E192Q	.	E	+	1	0	TM7SF4	105430530	0.138000	0.22547	0.010000	0.14722	0.873000	0.50193	-0.341000	0.07811	-0.817000	0.04335	0.561000	0.74099	GAA	G|0.883;C|0.117	0.117	strong		0.522	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788	
SDHA	6389	hgsc.bcm.edu	37	5	233734	233734	+	Silent	SNP	C	C	G	rs1041949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:233734C>G	ENST00000264932.6	+	8	1153	c.1038C>G	c.(1036-1038)tcC>tcG	p.S346S	SDHA_ENST00000510361.1_Silent_p.S298S|SDHA_ENST00000504309.1_Silent_p.S346S	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	346					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)	TGTCTCGGTCCATGACTCTGG	0.567									Familial Paragangliomas				G|||	1291	0.257788	0.6589	0.2478	5008	,	,		18679	0.0585		0.1113	False		,,,				2504	0.0787				p.S346S		Atlas-SNP	.											.	SDHA	80	.	0			c.C1038G						PASS	.	G		2492,1914		703,1086,414	137.0	129.0	132.0		1038	-3.9	0.8	5	dbSNP_86	132	1181,7419		81,1019,3200	no	coding-synonymous	SDHA	NM_004168.2		784,2105,3614	GG,GC,CC		13.7326,43.4408,28.2408		346/665	233734	3673,9333	2203	4300	6503	SO:0001819	synonymous_variant	6389	exon8	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	TCGGTCCATGACT	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.1038C>G	5.37:g.233734C>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	88	36	0.409091	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			C|0.725;G|0.275	0.275	strong		0.567	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558326	140558326	+	Silent	SNP	T	T	C	rs2910317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140558326T>C	ENST00000239444.2	+	1	956	c.711T>C	c.(709-711)aaT>aaC	p.N237N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	237	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCGATGTCAATGATAATGCCC	0.502													C|||	2283	0.455871	0.5061	0.4971	5008	,	,		25181	0.5327		0.3559	False		,,,				2504	0.3824				p.N237N		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T711C						PASS	.	C		1947,2459		482,983,738	196.0	247.0	230.0		711	-5.5	0.0	5	dbSNP_101	230	2460,6138		703,1054,2542	no	coding-synonymous	PCDHB8	NM_019120.3		1185,2037,3280	CC,CT,TT		28.6113,44.1897,33.8896		237/802	140558326	4407,8597	2203	4299	6502	SO:0001819	synonymous_variant	56128	exon1			TGTCAATGATAAT	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.711T>C	5.37:g.140558326T>C		Somatic	924	2	0.0021645		WXS	Illumina HiSeq	Phase_I	205	198	0.965854	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			T|0.573;C|0.427	0.427	strong		0.502	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
RIN3	79890	hgsc.bcm.edu	37	14	93118790	93118790	+	Missense_Mutation	SNP	A	A	C	rs139248637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93118790A>C	ENST00000216487.7	+	6	1555	c.1396A>C	c.(1396-1398)Atc>Ctc	p.I466L	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	466	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				GAAAAAACGGATCTCTCGACA	0.627													A|||	15	0.00299521	0.0	0.0014	5008	,	,		16397	0.0		0.007	False		,,,				2504	0.0072				p.I466L		Atlas-SNP	.											.	RIN3	81	.	0			c.A1396C						PASS	.	A	LEU/ILE	0,4406		0,0,2203	94.0	118.0	110.0		1396	-3.2	0.7	14	dbSNP_134	110	32,8568	22.2+/-67.0	0,32,4268	yes	missense	RIN3	NM_024832.3	5	0,32,6471	CC,CA,AA		0.3721,0.0,0.246	benign	466/986	93118790	32,12974	2203	4300	6503	SO:0001583	missense	79890	exon6			AAACGGATCTCTC	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.1396A>C	14.37:g.93118790A>C	ENSP00000216487:p.Ile466Leu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	6.565	0.472587	0.12461	0.0	0.003721	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.05199	3.48	4.22	-3.16	0.05217	.	1.726180	0.03309	N	0.190221	T	0.03263	0.0095	L	0.38531	1.155	0.22591	N	0.99896	P;B;B;B	0.42518	0.782;0.0;0.001;0.001	B;B;B;B	0.41813	0.367;0.001;0.001;0.001	T	0.35126	-0.9801	10	0.02654	T	1	-7.5443	4.3078	0.10956	0.1825:0.2771:0.438:0.1024	.	466;512;391;466	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	L	466;390	ENSP00000216487:I466L	ENSP00000216487:I466L	I	+	1	0	RIN3	92188543	0.047000	0.20315	0.692000	0.30179	0.814000	0.46013	-0.512000	0.06313	-1.044000	0.03254	0.260000	0.18958	ATC	A|0.998;C|0.002	0.002	strong		0.627	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
ATP6V1B1	525	hgsc.bcm.edu	37	2	71190384	71190384	+	Silent	SNP	C	C	T	rs2072462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:71190384C>T	ENST00000234396.4	+	10	1075	c.1002C>T	c.(1000-1002)cgC>cgT	p.R334R	AC007040.11_ENST00000606025.1_Intron|RN7SL160P_ENST00000468558.2_RNA|ATP6V1B1_ENST00000412314.1_Silent_p.R334R	NM_001692.3	NP_001683.2	P15313	VATB1_HUMAN	ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B1	334					ATP hydrolysis coupled proton transport (GO:0015991)|ATP metabolic process (GO:0046034)|calcium ion homeostasis (GO:0055074)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|pH reduction (GO:0045851)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATP binding (GO:0005524)|hydrogen ion transmembrane transporter activity (GO:0015078)|hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances (GO:0016820)			endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(5)|prostate(1)|skin(1)	19						GGGCGGGCCGCGTGGAGGGTC	0.622													C|||	2191	0.4375	0.146	0.4928	5008	,	,		17308	0.6548		0.4622	False		,,,				2504	0.5429				p.R334R		Atlas-SNP	.											.	ATP6V1B1	66	.	0			c.C1002T						PASS	.	C		795,3611	318.2+/-295.5	74,647,1482	69.0	63.0	65.0		1002	-9.8	0.4	2	dbSNP_96	65	3865,4735	541.8+/-384.1	865,2135,1300	no	coding-synonymous	ATP6V1B1	NM_001692.3		939,2782,2782	TT,TC,CC		44.9419,18.0436,35.8296		334/514	71190384	4660,8346	2203	4300	6503	SO:0001819	synonymous_variant	525	exon10			GGGCCGCGTGGAG	AF107466	CCDS1912.1	2p13	2010-04-21	2008-07-31	2002-05-10	ENSG00000116039	ENSG00000116039	3.6.3.14	"""ATPases / V-type"""	853	protein-coding gene	gene with protein product	"""Renal tubular acidosis with deafness"""	192132	"""vacuolar proton pump 3"""	VPP3, ATP6B1		9916796, 2527371	Standard	XM_005264368		Approved	VATB, RTA1B, Vma2	uc002shj.3	P15313	OTTHUMG00000129711	ENST00000234396.4:c.1002C>T	2.37:g.71190384C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001692	Q53FY0|Q6P4H6	Silent	SNP	ENST00000234396.4	37	CCDS1912.1																																																																																			C|0.602;T|0.398	0.398	strong		0.622	ATP6V1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251920.2	NM_001692	
HLA-C	3107	hgsc.bcm.edu	37	6	31239622	31239622	+	Missense_Mutation	SNP	C	C	G	rs9264668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31239622C>G	ENST00000376228.5	-	2	111	c.97G>C	c.(97-99)Gac>Cac	p.D33H	HLA-C_ENST00000383329.3_Missense_Mutation_p.D33H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	33	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGGCGGTGTCGAAATACCTC	0.726													a|||	20	0.00399361	0.0113	0.0	5008	,	,		11654	0.001		0.003	False		,,,				2504	0.001				p.D33H		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	0			c.G97C						scavenged	.						16.0	17.0	17.0					6																	31239622		1477	2676	4153	SO:0001583	missense	3107	exon2			CGGTGTCGAAATA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.97G>C	6.37:g.31239622C>G	ENSP00000365402:p.Asp33His	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	58	11	0.189655	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.003|0.003	-2.468672|-2.468672	0.00169|0.00169	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.5;9.5|.	2.16|2.16	-4.32|-4.32	0.03688|0.03688	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	10.311600|.	0.00879|.	N|.	0.002109|.	T|T	0.03390|0.03390	0.0098|0.0098	L|L	0.31578|0.31578	0.945|0.945	0.09310|0.09310	N|N	1|1	P;P;P;P|.	0.51351|.	0.944;0.822;0.822;0.888|.	P;P;P;D|.	0.68483|.	0.904;0.904;0.829;0.958|.	T|T	0.58504|0.58504	-0.7625|-0.7625	10|5	0.42905|.	T|.	0.14|.	.|.	0.4543|0.4543	0.00506|0.00506	0.2454:0.267:0.2544:0.2332|0.2454:0.267:0.2544:0.2332	.|.	33;33;33;33|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	H|P	33;33;33;70|32	ENSP00000365402:D33H;ENSP00000372819:D33H|.	ENSP00000365402:D33H|.	D|R	-|-	1|2	0|0	HLA-C|HLA-C	31347601|31347601	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-13.217000|-13.217000	0.00001|0.00001	-7.736000|-7.736000	0.00000|0.00000	-4.008000|-4.008000	0.00013|0.00013	GAC|CGA	A|0.575;C|0.423;G|0.002	0.002	strong		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
MEP1A	4224	hgsc.bcm.edu	37	6	46803102	46803102	+	Missense_Mutation	SNP	A	A	G	rs2297019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46803102A>G	ENST00000230588.4	+	13	1909	c.1900A>G	c.(1900-1902)Atg>Gtg	p.M634V		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	634			M -> V (in dbSNP:rs2297019).		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)			GGGAAAGGCCATGTTAGAGGA	0.602													A|||	1701	0.339657	0.4818	0.3069	5008	,	,		18214	0.2688		0.2515	False		,,,				2504	0.3344				p.M634V		Atlas-SNP	.											.	MEP1A	93	.	0			c.A1900G						PASS	.	A	VAL/MET	1942,2464	517.5+/-369.5	438,1066,699	23.0	22.0	22.0		1900	-6.7	0.0	6	dbSNP_100	22	2152,6448	348.8+/-327.2	267,1618,2415	no	missense	MEP1A	NM_005588.2	21	705,2684,3114	GG,GA,AA		25.0233,44.0763,31.4778	benign	634/747	46803102	4094,8912	2203	4300	6503	SO:0001583	missense	4224	exon13			AAGGCCATGTTAG		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.1900A>G	6.37:g.46803102A>G	ENSP00000230588:p.Met634Val	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	127	66	0.519685	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Missense_Mutation	SNP	ENST00000230588.4	37	CCDS4918.1	736	0.336996336996337	261	0.5304878048780488	108	0.2983425414364641	165	0.28846153846153844	202	0.26649076517150394	A	1.588	-0.529944	0.04112	0.440763	0.250233	ENSG00000112818	ENST00000230588	T	0.21932	1.98	3.64	-6.73	0.01749	.	2.950380	0.00725	N	0.000908	T	0.01353	0.0044	N	0.04959	-0.14	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19063	-1.0317	9	0.02654	T	1	4.2207	0.9823	0.01439	0.4172:0.1069:0.1713:0.3046	rs2297019;rs52801887;rs2297019	662;634	B7ZL91;Q16819	.;MEP1A_HUMAN	V	634	ENSP00000230588:M634V	ENSP00000230588:M634V	M	+	1	0	MEP1A	46911061	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.022000	0.00642	-1.344000	0.02216	-0.917000	0.02746	ATG	A|0.676;G|0.324	0.324	strong		0.602	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588	
SCUBE1	80274	hgsc.bcm.edu	37	22	43619200	43619200	+	Silent	SNP	G	G	A	rs6003114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:43619200G>A	ENST00000360835.4	-	11	1356	c.1230C>T	c.(1228-1230)cgC>cgT	p.R410R		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	410					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)				AGGTCTTGGCGCGAGAAAGAC	0.632													G|||	1120	0.223642	0.236	0.2939	5008	,	,		17723	0.0327		0.2505	False		,,,				2504	0.3262				p.R410R		Atlas-SNP	.											.	SCUBE1	105	.	0			c.C1230T						PASS	.	G		1165,3241	402.4+/-332.3	165,835,1203	80.0	88.0	85.0		1230	-2.4	0.0	22	dbSNP_114	85	2440,6160	391.6+/-343.7	356,1728,2216	no	coding-synonymous	SCUBE1	NM_173050.3		521,2563,3419	AA,AG,GG		28.3721,26.4412,27.718		410/989	43619200	3605,9401	2203	4300	6503	SO:0001819	synonymous_variant	80274	exon11			CTTGGCGCGAGAA		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.1230C>T	22.37:g.43619200G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_173050	Q5R336	Silent	SNP	ENST00000360835.4	37	CCDS14048.1																																																																																			G|0.765;A|0.235	0.235	strong		0.632	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
CCDC108	255101	hgsc.bcm.edu	37	2	219900068	219900068	+	Intron	SNP	C	C	T	rs17852959	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219900068C>T	ENST00000341552.5	-	5	626				CCDC108_ENST00000324264.6_Missense_Mutation_p.V161M|CCDC108_ENST00000441968.1_Intron|CCDC108_ENST00000409865.3_Intron|CCDC108_ENST00000453220.1_Intron|CCDC108_ENST00000295729.2_Missense_Mutation_p.V161M|CCDC108_ENST00000410037.1_Intron	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108							integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)	p.V161M(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATACTGCACGTATTTTAAA	0.363													C|||	457	0.091254	0.0439	0.0893	5008	,	,		21263	0.1597		0.0885	False		,,,				2504	0.089				p.V161M		Atlas-SNP	.											CCDC108_ENST00000295729,NS,carcinoma,0,1	CCDC108	208	1	1	Substitution - Missense(1)	stomach(1)	c.G481A						PASS	.	C	MET/VAL,	202,4150		7,188,1981	28.0	30.0	29.0		481,	2.7	0.0	2	dbSNP_123	29	764,7720		25,714,3503	yes	missense,intron	CCDC108	NM_152389.2,NM_194302.2	21,	32,902,5484	TT,TC,CC		9.0052,4.6415,7.5257	,	161/165,	219900068	966,11870	2176	4242	6418	SO:0001627	intron_variant	255101	exon4			ACTGCACGTATTT	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.542+133G>A	2.37:g.219900068C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	98	33	0.336735	NM_152389	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	210	0.09615384615384616	24	0.04878048780487805	29	0.08011049723756906	90	0.15734265734265734	67	0.08839050131926121	C	1.176	-0.639592	0.03557	0.046415	0.090052	ENSG00000181378	ENST00000295729;ENST00000324264	T;T	0.53640	0.61;0.61	2.72	2.72	0.32119	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	D	0.89917	1.0	D	0.67900	0.954	T	0.01993	-1.1233	8	0.17369	T	0.5	.	9.1072	0.36705	0.0:1.0:0.0:0.0	rs17852959;rs59675281	161	E9PCR1	.	M	161	ENSP00000295729:V161M;ENSP00000313807:V161M	ENSP00000295729:V161M	V	-	1	0	CCDC108	219608312	0.000000	0.05858	0.021000	0.16686	0.024000	0.10985	-0.214000	0.09292	1.828000	0.53243	0.561000	0.74099	GTG	C|0.904;T|0.096	0.096	strong		0.363	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50658698	50658698	+	Missense_Mutation	SNP	T	T	A	rs5771107	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50658698T>A	ENST00000248846.5	-	16	4194	c.4090A>T	c.(4090-4092)Agt>Tgt	p.S1364C	TUBGCP6_ENST00000439308.2_Missense_Mutation_p.S1364C|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1364			S -> C (in dbSNP:rs5771107).		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)		TCAGAGACACTGTCTCCCGGG	0.657													T|||	809	0.161542	0.0885	0.1354	5008	,	,		20207	0.255		0.164	False		,,,				2504	0.18				p.S1364C		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.A4090T						PASS	.	T	CYS/SER	372,4034	185.3+/-212.5	9,354,1840	49.0	48.0	48.0		4090	-10.2	0.0	22	dbSNP_114	48	1283,7317	253.3+/-279.0	92,1099,3109	yes	missense	TUBGCP6	NM_020461.3	112	101,1453,4949	AA,AT,TT		14.9186,8.443,12.7249	probably-damaging	1364/1820	50658698	1655,11351	2203	4300	6503	SO:0001583	missense	85378	exon16			AGACACTGTCTCC	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.4090A>T	22.37:g.50658698T>A	ENSP00000248846:p.Ser1364Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	83	42	0.506024	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	380	0.17399267399267399	43	0.08739837398373984	72	0.19889502762430938	139	0.243006993006993	126	0.1662269129287599	T	13.58	2.279751	0.40294	0.08443	0.149186	ENSG00000128159	ENST00000248846;ENST00000425018;ENST00000439308	T;T;T	0.24538	3.04;1.85;2.58	5.11	-10.2	0.00374	.	2.621510	0.02256	U	0.067092	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	D;D;D	0.63880	0.993;0.98;0.992	P;P;P	0.59595	0.815;0.86;0.719	T	0.37957	-0.9683	9	0.36615	T	0.2	.	6.016	0.19603	0.0769:0.1928:0.1688:0.5615	rs5771107;rs5771107	1356;1364;1364	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	C	1364;50;1364	ENSP00000248846:S1364C;ENSP00000405979:S50C;ENSP00000397387:S1364C	ENSP00000248846:S1364C	S	-	1	0	TUBGCP6	49000825	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.043000	0.00157	-2.434000	0.00554	-1.044000	0.02363	AGT	T|0.857;A|0.143	0.143	strong		0.657	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
PPIAL4G	644591	hgsc.bcm.edu	37	1	143767466	143767466	+	Missense_Mutation	SNP	G	G	A	rs77641628|rs61824237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:143767466G>A	ENST00000419275.1	-	1	415	c.383C>T	c.(382-384)gCc>gTc	p.A128V		NM_001123068.1	NP_001116540.1	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like 4G	128	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(2)|kidney(1)|lung(8)|ovary(1)|skin(1)	14						CTTGCCAAAGGCCACATGCTT	0.483																																					p.A128V		Atlas-SNP	.											PPIAL4G,NS,carcinoma,0,2	PPIAL4G	22	2	0			c.C383T						PASS	.	G	VAL/ALA	12,3098		0,12,1543	143.0	125.0	130.0		383	-1.0	0.9	1	dbSNP_131	130	196,6914		0,196,3359	no	missense	PPIAL4G	NM_001123068.1	64	0,208,4902	AA,AG,GG		2.7567,0.3859,2.0352	benign	128/165	143767466	208,10012	1555	3555	5110	SO:0001583	missense	644591	exon1			CCAAAGGCCACAT		CCDS41375.1, CCDS41375.2	1q21.1	2010-06-03			ENSG00000236334	ENSG00000236334			33996	protein-coding gene	gene with protein product							Standard	NM_001123068		Approved		uc001ejt.3	A2BFH1	OTTHUMG00000013629	ENST00000419275.1:c.383C>T	1.37:g.143767466G>A	ENSP00000393845:p.Ala128Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	55	8	0.145455	NM_001123068	A1L431	Missense_Mutation	SNP	ENST00000419275.1	37	CCDS41375.1	.	.	.	.	.	.	.	.	.	.	.	0.335	-0.954069	0.02285	0.003859	0.027567	ENSG00000236334	ENST00000419275	T	0.15372	2.43	0.523	-1.05	0.10036	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (4);Cyclophilin-like (1);	0.075217	0.52532	N	0.000073	T	0.00412	0.0013	N	0.00043	-2.465	0.22940	N	0.99853	B	0.06786	0.001	B	0.04013	0.001	T	0.16928	-1.0386	10	0.02654	T	1	.	2.6455	0.04983	0.4777:0.27:0.2523:0.0	.	128	A2BFH1	PAL4G_HUMAN	V	128	ENSP00000393845:A128V	ENSP00000393845:A128V	A	-	2	0	PPIAL4G	142558989	1.000000	0.71417	0.929000	0.37066	0.709000	0.40893	3.502000	0.53332	-1.226000	0.02574	-0.817000	0.03123	GCC	G|0.982;A|0.018	0.018	strong		0.483	PPIAL4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037969.1	NM_001123068	
CREBZF	58487	hgsc.bcm.edu	37	11	85374993	85374993	+	Silent	SNP	C	C	T	rs1192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:85374993C>T	ENST00000527447.1	-	1	1153	c.927G>A	c.(925-927)ccG>ccA	p.P309P	CREBZF_ENST00000398294.2_Silent_p.P227P|CREBZF_ENST00000534224.1_Intron|CREBZF_ENST00000531515.1_Intron	NM_001039618.2	NP_001034707.1	Q9NS37	ZHANG_HUMAN	CREB/ATF bZIP transcription factor	309					negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)				GCTTTCCCACCGGCAGAGCGT	0.642											OREG0021274	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1041	0.207867	0.118	0.2867	5008	,	,		15506	0.2847		0.0984	False		,,,				2504	0.3067				p.P309P	NSCLC(172;674 2044 9050 18334 41735)	Atlas-SNP	.											.	CREBZF	26	.	0			c.G927A						PASS	.	C		477,3473		23,431,1521	59.0	63.0	62.0		927	-6.4	0.4	11	dbSNP_36	62	782,7516		39,704,3406	no	coding-synonymous	CREBZF	NM_001039618.2		62,1135,4927	TT,TC,CC		9.424,12.0759,10.2792		309/355	85374993	1259,10989	1975	4149	6124	SO:0001819	synonymous_variant	58487	exon1			TCCCACCGGCAGA	AF039942	CCDS41697.1	11q14.1	2013-01-10			ENSG00000137504	ENSG00000137504		"""basic leucine zipper proteins"""	24905	protein-coding gene	gene with protein product	"""Zhangfei"""	606444				10871379	Standard	NM_001039618		Approved	ZF	uc001pas.2	Q9NS37	OTTHUMG00000133648	ENST00000527447.1:c.927G>A	11.37:g.85374993C>T		Somatic	74	0	0	1236	WXS	Illumina HiSeq	Phase_I	105	48	0.457143	NM_001039618	B2R8Q9|Q0P5U9|Q52LT3	Silent	SNP	ENST00000527447.1	37	CCDS41697.1																																																																																			C|0.837;T|0.163	0.163	strong		0.642	CREBZF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390191.2	NM_001039618	
AP5Z1	9907	hgsc.bcm.edu	37	7	4830971	4830971	+	Silent	SNP	G	G	T	rs77393809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4830971G>T	ENST00000348624.4	+	17	2473	c.2379G>T	c.(2377-2379)acG>acT	p.T793T	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000490487.1_3'UTR	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	793					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGCGCACGGTCAGCCGGC	0.677													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		17357	0.0		0.0239	False		,,,				2504	0.0235				p.T793T		Atlas-SNP	.											.	.	.	.	0			c.G2379T						PASS	.	G		12,4080		0,12,2034	15.0	20.0	18.0		2379	-9.4	0.0	7	dbSNP_133	18	204,8148		4,196,3976	no	coding-synonymous	KIAA0415	NM_014855.2		4,208,6010	TT,TG,GG		2.4425,0.2933,1.7358		793/808	4830971	216,12228	2046	4176	6222	SO:0001819	synonymous_variant	9907	exon17			GCGCACGGTCAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.2379G>T	7.37:g.4830971G>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			G|0.985;T|0.015	0.015	strong		0.677	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
NCK1	4690	hgsc.bcm.edu	37	3	136646930	136646930	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:136646930A>G	ENST00000481752.1	+	2	251	c.87A>G	c.(85-87)ttA>ttG	p.L29L	NCK1_ENST00000288986.2_Silent_p.L29L|NCK1_ENST00000469404.1_5'Flank			P16333	NCK1_HUMAN	NCK adaptor protein 1	29	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)	p.L29L(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						ATGAGAGATTATGGCTTCTGG	0.418																																					p.L29L		Atlas-SNP	.											NCK1,colon,carcinoma,0,1	NCK1	26	1	1	Substitution - coding silent(1)	large_intestine(1)	c.A87G						scavenged	.						128.0	118.0	121.0					3																	136646930		2203	4300	6503	SO:0001819	synonymous_variant	4690	exon2			GAGATTATGGCTT	X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"""SH2 domain containing"""	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.87A>G	3.37:g.136646930A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	189	3	0.015873	NM_006153	B7Z751|D3DNE3	Silent	SNP	ENST00000481752.1	37	CCDS3092.1	.	.	.	.	.	.	.	.	.	.	A	10.05	1.244189	0.22796	.	.	ENSG00000158092	ENST00000496489	.	.	.	5.98	-1.93	0.07594	.	.	.	.	.	T	0.48169	0.1485	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41342	-0.9514	4	.	.	.	-7.3615	4.7785	0.13190	0.4073:0.0:0.3859:0.2068	.	.	.	.	C	17	.	.	Y	+	2	0	NCK1	138129620	0.948000	0.32251	1.000000	0.80357	0.988000	0.76386	0.110000	0.15437	0.059000	0.16252	0.533000	0.62120	TAT	.	.	none		0.418	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153	
CACNA1S	779	hgsc.bcm.edu	37	1	201046058	201046058	+	Missense_Mutation	SNP	C	C	T	rs142356235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201046058C>T	ENST00000362061.3	-	12	2043	c.1817G>A	c.(1816-1818)aGc>aAc	p.S606N	CACNA1S_ENST00000367338.3_Missense_Mutation_p.S606N	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	606					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)	ctggaagacgctgatgagggC	0.547													C|||	24	0.00479233	0.0008	0.0043	5008	,	,		23085	0.001		0.0139	False		,,,				2504	0.0051				p.S606N		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G1817A						PASS	.	C	ASN/SER	14,4392	22.3+/-47.3	0,14,2189	178.0	153.0	161.0		1817	3.6	1.0	1	dbSNP_134	161	99,8501	54.4+/-115.2	3,93,4204	yes	missense	CACNA1S	NM_000069.2	46	3,107,6393	TT,TC,CC		1.1512,0.3177,0.8688	possibly-damaging	606/1874	201046058	113,12893	2203	4300	6503	SO:0001583	missense	779	exon12			AAGACGCTGATGA	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.1817G>A	1.37:g.201046058C>T	ENSP00000355192:p.Ser606Asn	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	260	123	0.473077	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	11	0.014511873350923483	C	17.52	3.409920	0.62399	0.003177	0.011512	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.97480	-4.4;-4.4	4.55	3.63	0.41609	Ion transport (1);	0.088945	0.85682	D	0.000000	D	0.96137	0.8741	L	0.50993	1.605	0.35083	D	0.76358	P	0.49862	0.929	P	0.59546	0.859	D	0.97166	0.9841	10	0.87932	D	0	.	14.0837	0.64942	0.0:0.5698:0.4302:0.0	.	606	Q13698	CAC1S_HUMAN	N	606	ENSP00000355192:S606N;ENSP00000356307:S606N	ENSP00000355192:S606N	S	-	2	0	CACNA1S	199312681	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	1.498000	0.35660	1.033000	0.39918	0.549000	0.68633	AGC	C|0.993;T|0.007	0.007	strong		0.547	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
GPR111	222611	hgsc.bcm.edu	37	6	47649265	47649265	+	Missense_Mutation	SNP	T	T	A	rs17541107	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:47649265T>A	ENST00000296862.1	+	6	970	c.970T>A	c.(970-972)Ttg>Atg	p.L324M	GPR111_ENST00000398742.2_Missense_Mutation_p.L256M|GPR111_ENST00000507065.1_Missense_Mutation_p.L256M			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	324					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						TGGGAGAGTGTTGATCAGCAG	0.418													T|||	1991	0.397564	0.236	0.5331	5008	,	,		22240	0.6915		0.3678	False		,,,				2504	0.2474				p.L256M		Atlas-SNP	.											.	GPR111	123	.	0			c.T766A						PASS	.	T	MET/LEU	1062,2724		134,794,965	154.0	144.0	147.0		766	-6.7	0.0	6	dbSNP_123	147	2868,5372		508,1852,1760	yes	missense	GPR111	NM_153839.6	15	642,2646,2725	AA,AT,TT		34.8058,28.0507,32.6792	possibly-damaging	256/643	47649265	3930,8096	1893	4120	6013	SO:0001583	missense	222611	exon7			AGAGTGTTGATCA	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.970T>A	6.37:g.47649265T>A	ENSP00000296862:p.Leu324Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_153839	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		969	0.44368131868131866	110	0.22357723577235772	172	0.47513812154696133	401	0.701048951048951	286	0.37730870712401055	T	13.60	2.286730	0.40494	0.280507	0.348058	ENSG00000164393	ENST00000507065;ENST00000296862;ENST00000398742	T;T;T	0.44881	0.91;0.91;0.91	5.37	-6.69	0.01772	.	0.636305	0.13081	N	0.415293	T	0.33411	0.0862	M	0.74881	2.28	0.80722	P	0.0	D;P	0.55800	0.973;0.954	P;P	0.56823	0.807;0.646	T	0.32188	-0.9916	9	0.38643	T	0.18	.	9.618	0.39704	0.0852:0.7102:0.0927:0.1119	rs17541107;rs52808586;rs61436836;rs17541107	256;324	Q8IZF7-2;Q8IZF7	.;GP111_HUMAN	M	256;324;256	ENSP00000422934:L256M;ENSP00000296862:L324M;ENSP00000381727:L256M	ENSP00000296862:L324M	L	+	1	2	GPR111	47757224	0.000000	0.05858	0.000000	0.03702	0.822000	0.46500	-1.302000	0.02746	-1.925000	0.01063	-0.472000	0.04984	TTG	T|0.577;A|0.423	0.423	strong		0.418	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
GABBR2	9568	hgsc.bcm.edu	37	9	101056122	101056122	+	Missense_Mutation	SNP	T	T	C	rs10985765	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:101056122T>C	ENST00000259455.2	-	18	3064	c.2605A>G	c.(2605-2607)Aca>Gca	p.T869A		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	869			T -> A (in dbSNP:rs10985765). {ECO:0000269|PubMed:10328880}.		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)	GAGGGCTCTGTTGTGTTCCAC	0.388													T|||	1175	0.234625	0.3835	0.2219	5008	,	,		19724	0.1587		0.1859	False		,,,				2504	0.1708				p.T869A		Atlas-SNP	.											.	GABBR2	126	.	0			c.A2605G						PASS	.	T	ALA/THR	1689,2717	511.1+/-367.7	328,1033,842	243.0	237.0	239.0		2605	1.5	1.0	9	dbSNP_120	239	1485,7115	282.4+/-295.5	119,1247,2934	yes	missense	GABBR2	NM_005458.7	58	447,2280,3776	CC,CT,TT		17.2674,38.3341,24.4041	benign	869/942	101056122	3174,9832	2203	4300	6503	SO:0001583	missense	9568	exon18			GCTCTGTTGTGTT	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.2605A>G	9.37:g.101056122T>C	ENSP00000259455:p.Thr869Ala	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	179	82	0.458101	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	496	0.2271062271062271	173	0.3516260162601626	82	0.2265193370165746	96	0.16783216783216784	145	0.19129287598944592	T	11.98	1.801580	0.31869	0.383341	0.172674	ENSG00000136928	ENST00000259455	T	0.77620	-1.11	5.1	1.54	0.23209	.	0.308380	0.40469	N	0.001090	T	0.00012	0.0000	N	0.14661	0.345	0.44155	P	0.003049999999999997	B	0.02656	0.0	B	0.01281	0.0	T	0.19095	-1.0316	9	0.08837	T	0.75	-1.9476	7.6266	0.28216	0.0:0.2503:0.0:0.7497	rs10985765;rs52804588;rs59128016;rs10985765	869	O75899	GABR2_HUMAN	A	869	ENSP00000259455:T869A	ENSP00000259455:T869A	T	-	1	0	GABBR2	100095943	1.000000	0.71417	0.972000	0.41901	0.998000	0.95712	1.132000	0.31418	0.104000	0.17725	0.528000	0.53228	ACA	T|0.756;C|0.244	0.244	strong		0.388	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
STAC	6769	hgsc.bcm.edu	37	3	36422216	36422216	+	Silent	SNP	T	T	C	rs73052248	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:36422216T>C	ENST00000273183.3	+	1	381	c.81T>C	c.(79-81)tcT>tcC	p.S27S	STAC_ENST00000457375.2_Silent_p.S27S|STAC_ENST00000476388.1_3'UTR	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	27					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)	p.S27S(1)		endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						AACCGCCCTCTCCTGCATCCA	0.662													T|||	867	0.173123	0.031	0.2579	5008	,	,		14453	0.1994		0.2475	False		,,,				2504	0.2014				p.S27S		Atlas-SNP	.											STAC,caecum,carcinoma,0,1	STAC	78	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T81C						PASS	.	T		266,4128		12,242,1943	26.0	21.0	23.0		81	-0.7	1.0	3	dbSNP_130	23	1974,6604		238,1498,2553	no	coding-synonymous	STAC	NM_003149.1		250,1740,4496	CC,CT,TT		23.0124,6.0537,17.268		27/403	36422216	2240,10732	2197	4289	6486	SO:0001819	synonymous_variant	6769	exon1			GCCCTCTCCTGCA	D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"""src homology three (SH3) and cysteine rich domain"""			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.81T>C	3.37:g.36422216T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_003149	B2R8S8	Silent	SNP	ENST00000273183.3	37	CCDS2662.1																																																																																			T|0.823;C|0.177	0.177	strong		0.662	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149	
CARS	833	hgsc.bcm.edu	37	11	3028140	3028140	+	Silent	SNP	G	G	A	rs729662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:3028140G>A	ENST00000397111.5	-	18	2114	c.1869C>T	c.(1867-1869)ccC>ccT	p.P623P	CARS_ENST00000401769.3_Silent_p.P636P|CARS_ENST00000397114.3_Silent_p.P613P|CARS_ENST00000278224.9_Silent_p.P623P|CARS_ENST00000380525.4_Silent_p.P706P|CARS_ENST00000470221.2_5'UTR			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	623					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)		CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		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;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	CCCCAAGCTCGGGCAGGATGT	0.587			T	ALK	ALCL								G|||	1757	0.350839	0.0303	0.4957	5008	,	,		20311	0.6627		0.2922	False		,,,				2504	0.4202				p.P706P	Ovarian(61;932 1157 5961 20446 52152)	Atlas-SNP	.		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	CARS	114	.	0			c.C2118T						PASS	.	G	,,,	333,4071	174.4+/-204.0	12,309,1881	177.0	169.0	172.0		2118,2118,1869,1869	-4.1	1.0	11	dbSNP_86	172	2504,6092	409.7+/-349.9	363,1778,2157	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CARS	NM_001014437.2,NM_001194997.1,NM_001751.5,NM_139273.3	,,,	375,2087,4038	AA,AG,GG		29.1298,7.5613,21.8231	,,,	706/832,706/810,623/749,623/727	3028140	2837,10163	2202	4298	6500	SO:0001819	synonymous_variant	833	exon19			AAGCTCGGGCAGG	AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	1493	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 1, cytoplasmic"""	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1869C>T	11.37:g.3028140G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	60	25	0.416667	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Silent	SNP	ENST00000397111.5	37	CCDS7742.1																																																																																			G|0.727;A|0.273	0.273	strong		0.587	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751	
KIAA1549L	25758	hgsc.bcm.edu	37	11	33680371	33680371	+	Silent	SNP	C	C	T	rs12280103	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:33680371C>T	ENST00000321505.4	+	18	5223	c.5043C>T	c.(5041-5043)agC>agT	p.S1681S	KIAA1549L_ENST00000389726.3_Silent_p.S1687S			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1681						integral component of membrane (GO:0016021)											TGCACGACAGCGCCTCCTTCA	0.597													C|||	1484	0.296326	0.2436	0.2824	5008	,	,		18049	0.3343		0.2654	False		,,,				2504	0.3701				p.S1681S		Atlas-SNP	.											.	.	.	.	0			c.C5043T						PASS	.	C		907,3113		109,689,1212	20.0	27.0	25.0		5043	0.1	1.0	11	dbSNP_120	25	2169,6097		302,1565,2266	no	coding-synonymous	C11orf41	NM_012194.2		411,2254,3478	TT,TC,CC		26.24,22.5622,25.0366		1681/1850	33680371	3076,9210	2010	4133	6143	SO:0001819	synonymous_variant	25758	exon18			CGACAGCGCCTCC	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.5043C>T	11.37:g.33680371C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	102	99	0.970588	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																			C|0.716;T|0.284	0.284	strong		0.597	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
CXorf22	170063	hgsc.bcm.edu	37	X	35938045	35938045	+	Silent	SNP	C	C	T	rs6629019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:35938045C>T	ENST00000297866.5	+	1	195	c.129C>T	c.(127-129)atC>atT	p.I43I		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	43										breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(3)	44						TGCGGGTGATCCCGGCTGAGG	0.562													C|||	801	0.212185	0.1505	0.219	3775	,	,		11836	0.1627		0.1064	False		,,,				2504	0.183				p.I43I		Atlas-SNP	.											.	CXorf22	272	.	0			c.C129T						PASS	.	C		732,3100		64,498,106,1069,464	53.0	44.0	47.0		129	2.9	0.1	X	dbSNP_116	47	768,5960		28,497,215,1903,1657	no	coding-synonymous	CXorf22	NM_152632.3		92,995,321,2972,2121	TT,TC,T,CC,C		11.415,19.1023,14.2045		43/977	35938045	1500,9060	2201	4300	6501	SO:0001819	synonymous_variant	170063	exon1			GGTGATCCCGGCT	BC027936	CCDS14237.2	Xp21.1	2014-08-07			ENSG00000165164	ENSG00000165164			28546	protein-coding gene	gene with protein product						12477932	Standard	NM_152632		Approved	MGC34831	uc004ddj.3	Q6ZTR5	OTTHUMG00000021350	ENST00000297866.5:c.129C>T	X.37:g.35938045C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_152632	Q5JRM8|Q8N6X8	Silent	SNP	ENST00000297866.5	37	CCDS14237.2																																																																																			C|0.834;T|0.166	0.166	strong		0.562	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632	
FBN3	84467	hgsc.bcm.edu	37	19	8160897	8160897	+	Missense_Mutation	SNP	G	G	C	rs12150963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8160897G>C	ENST00000600128.1	-	45	6021	c.5607C>G	c.(5605-5607)aaC>aaG	p.N1869K	FBN3_ENST00000601739.1_Missense_Mutation_p.N1869K|FBN3_ENST00000270509.2_Missense_Mutation_p.N1869K			Q75N90	FBN3_HUMAN	fibrillin 3	1869	EGF-like 29; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		N -> K (in dbSNP:rs12150963). {ECO:0000269|PubMed:15221638}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AGCAGAGGCAGTTGTAGGAGC	0.552													G|||	662	0.132188	0.0159	0.2594	5008	,	,		17917	0.245		0.1153	False		,,,				2504	0.1002				p.N1869K		Atlas-SNP	.											.	FBN3	300	.	0			c.C5607G						PASS	.	G	LYS/ASN	159,4247	108.2+/-146.6	1,157,2045	120.0	87.0	98.0		5607	3.7	1.0	19	dbSNP_120	98	1141,7459	236.0+/-268.3	82,977,3241	yes	missense	FBN3	NM_032447.3	94	83,1134,5286	CC,CG,GG		13.2674,3.6087,9.9954	benign	1869/2810	8160897	1300,11706	2203	4300	6503	SO:0001583	missense	84467	exon44			GAGGCAGTTGTAG		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.5607C>G	19.37:g.8160897G>C	ENSP00000470498:p.Asn1869Lys	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	149	72	0.483221	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	331	0.15155677655677655	12	0.024390243902439025	83	0.2292817679558011	147	0.256993006993007	89	0.11741424802110818	G	12.26	1.885399	0.33255	0.036087	0.132674	ENSG00000142449	ENST00000270509	D	0.91631	-2.88	3.71	3.71	0.42584	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.105878	0.64402	U	0.000007	T	0.00073	0.0002	N	0.12637	0.245	0.09310	P	0.9999999383616	B	0.31655	0.334	B	0.31946	0.138	T	0.05068	-1.0908	9	0.27785	T	0.31	.	15.8328	0.78769	0.0:0.0:1.0:0.0	rs12150963;rs12150963	1869	Q75N90	FBN3_HUMAN	K	1869	ENSP00000270509:N1869K	ENSP00000270509:N1869K	N	-	3	2	FBN3	8066897	1.000000	0.71417	0.980000	0.43619	0.258000	0.26162	6.946000	0.75953	1.748000	0.51833	0.655000	0.94253	AAC	G|0.880;C|0.120	0.120	strong		0.552	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
KLK3	354	hgsc.bcm.edu	37	19	51359497	51359497	+	Splice_Site	SNP	T	T	C	rs17849961|rs11573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51359497T>C	ENST00000326003.2	+	2	89	c.48T>C	c.(46-48)ggT>ggC	p.G16G	KLK3_ENST00000593997.1_Splice_Site_p.G16G|KLK3_ENST00000360617.3_Splice_Site_p.G16G|KLK3_ENST00000597483.1_Splice_Site_p.G16G|KLK3_ENST00000595952.1_Splice_Site_p.G16G	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	16					cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		CCTCTGCAGGTGCTGCACCCC	0.582													C|||	1702	0.339856	0.1921	0.4914	5008	,	,		19205	0.4851		0.4195	False		,,,				2504	0.2004				p.G16G	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.T48C						PASS	.	C	,,,	1066,3340	722.5+/-409.3	139,788,1276	92.0	82.0	85.0		48,48,48,48	-1.4	0.0	19	dbSNP_52	85	3589,5011	627.5+/-398.0	767,2055,1478	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	KLK3	NM_001030047.1,NM_001030048.1,NM_001030050.1,NM_001648.2	,,,	906,2843,2754	CC,CT,TT		41.7326,24.1943,35.7912	,,,	16/239,16/219,16/70,16/262	51359497	4655,8351	2203	4300	6503	SO:0001630	splice_region_variant	354	exon2			TGCAGGTGCTGCA	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.47-1T>C	19.37:g.51359497T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_001030050	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			T|0.629;C|0.371	0.371	strong		0.582	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	Silent
RSF1	51773	hgsc.bcm.edu	37	11	77412851	77412851	+	Missense_Mutation	SNP	A	A	G	rs7950873	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:77412851A>G	ENST00000308488.6	-	6	1725	c.1423T>C	c.(1423-1425)Tct>Cct	p.S475P	RSF1_ENST00000360355.2_Missense_Mutation_p.S444P|RSF1_ENST00000480887.1_Missense_Mutation_p.S223P			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	475			S -> P (in dbSNP:rs7950873).		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)			CTGTCCTTAGAGGGGCTATAG	0.398													A|||	622	0.124201	0.0272	0.1599	5008	,	,		19309	0.0675		0.2316	False		,,,				2504	0.1779				p.S475P		Atlas-SNP	.											.	RSF1	105	.	0			c.T1423C						PASS	.	A	PRO/SER	278,4122	148.0+/-182.4	7,264,1929	119.0	117.0	117.0		1423	2.5	1.0	11	dbSNP_116	117	2049,6535	350.7+/-328.0	229,1591,2472	yes	missense	RSF1	NM_016578.3	74	236,1855,4401	GG,GA,AA		23.87,6.3182,17.9221	possibly-damaging	475/1442	77412851	2327,10657	2200	4292	6492	SO:0001583	missense	51773	exon6			CCTTAGAGGGGCT	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.1423T>C	11.37:g.77412851A>G	ENSP00000311513:p.Ser475Pro	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	150	89	0.593333	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	294	0.1346153846153846	14	0.028455284552845527	68	0.1878453038674033	43	0.07517482517482517	169	0.22295514511873352	A	10.72	1.430536	0.25726	0.063182	0.2387	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324;ENST00000528095	D;D;D;D;T	0.86297	-2.07;-2.08;-2.07;-2.1;1.38	5.01	2.51	0.30379	.	0.402164	0.21569	N	0.072430	T	0.00073	0.0002	L	0.27053	0.805	0.35569	P	0.19467999999999996	B	0.33448	0.412	B	0.25759	0.063	T	0.02705	-1.1121	9	0.33141	T	0.24	-2.1915	7.0521	0.25079	0.5645:0.2996:0.0:0.1358	rs7950873;rs17836030;rs52834634;rs59192724;rs7950873	475	Q96T23	RSF1_HUMAN	P	475;223;444;276;474	ENSP00000311513:S475P;ENSP00000434509:S223P;ENSP00000353511:S444P;ENSP00000432022:S276P;ENSP00000436408:S474P	ENSP00000311513:S475P	S	-	1	0	RSF1	77090499	0.726000	0.28059	0.983000	0.44433	0.950000	0.60333	0.838000	0.27572	0.917000	0.36895	0.533000	0.62120	TCT	A|0.846;G|0.154	0.154	strong		0.398	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
OBSCN	84033	hgsc.bcm.edu	37	1	228494696	228494696	+	Silent	SNP	G	G	A	rs4653939	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228494696G>A	ENST00000422127.1	+	45	12065	c.12021G>A	c.(12019-12021)gcG>gcA	p.A4007A	OBSCN_ENST00000366707.4_Silent_p.A1641A|OBSCN_ENST00000366709.4_Silent_p.A1126A|OBSCN_ENST00000284548.11_Silent_p.A4007A|OBSCN_ENST00000570156.2_Silent_p.A4964A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4007	Ig-like 41.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGGCGGGTGCGAGCGTGGAGT	0.652													G|||	1545	0.308506	0.3714	0.2925	5008	,	,		20661	0.497		0.1869	False		,,,				2504	0.1656				p.A4964A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G14892A						PASS	.	G	,	1627,2743		313,1001,871	40.0	48.0	45.0		12021,12021	-5.7	0.0	1	dbSNP_111	45	1661,6879		162,1337,2771	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	475,2338,3642	AA,AG,GG		19.4496,37.2311,25.4686	,	4007/7969,4007/6621	228494696	3288,9622	2185	4270	6455	SO:0001819	synonymous_variant	84033	exon56			GGGTGCGAGCGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12021G>A	1.37:g.228494696G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	235	126	0.53617	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.667;A|0.333	0.333	strong		0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OR1B1	347169	hgsc.bcm.edu	37	9	125391369	125391369	+	Missense_Mutation	SNP	A	A	G	rs1536929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:125391369A>G	ENST00000304833.3	-	1	483	c.446T>C	c.(445-447)tTg>tCg	p.L149S	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	149			L -> S (in dbSNP:rs1536929).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						CACCCAGCTCAAGGCTAGTAA	0.552													A|||	3212	0.641374	0.4357	0.5965	5008	,	,		20260	0.6409		0.7207	False		,,,				2504	0.8701				p.L149S		Atlas-SNP	.											.	OR1B1	48	.	0			c.T446C						PASS	.	A	SER/LEU	2239,2167	593.7+/-388.1	573,1093,537	98.0	74.0	82.0		446	2.0	0.0	9	dbSNP_88	82	6300,2300	705.7+/-405.5	2306,1688,306	yes	missense	OR1B1	NM_001004450.1	145	2879,2781,843	GG,GA,AA		26.7442,49.1829,34.3457	benign	149/319	125391369	8539,4467	2203	4300	6503	SO:0001583	missense	347169	exon1			CAGCTCAAGGCTA	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.446T>C	9.37:g.125391369A>G	ENSP00000303151:p.Leu149Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_001004450	Q6IFN3	Missense_Mutation	SNP	ENST00000304833.3	37	CCDS35126.1	1381	0.6323260073260073	214	0.4349593495934959	217	0.5994475138121547	393	0.6870629370629371	557	0.7348284960422163	A	0.018	-1.475677	0.01035	0.508171	0.732558	ENSG00000171484	ENST00000304833	T	0.39592	1.07	4.26	1.96	0.26148	GPCR, rhodopsin-like superfamily (1);	0.494819	0.15426	N	0.262921	T	0.00012	0.0000	N	0.20610	0.595	0.80722	P	0.0	B	0.06786	0.001	B	0.11329	0.006	T	0.27536	-1.0071	9	0.51188	T	0.08	-3.8081	6.8619	0.24072	0.7973:0.0:0.2027:0.0	rs1536929;rs61313001;rs1536929	149	Q8NGR6	OR1B1_HUMAN	S	149	ENSP00000303151:L149S	ENSP00000303151:L149S	L	-	2	0	OR1B1	124431190	0.000000	0.05858	0.007000	0.13788	0.038000	0.13279	0.040000	0.13905	0.787000	0.33731	-0.262000	0.10625	TTG	G|0.645;N|0.000	0.645	strong		0.552	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
MROH9	80133	hgsc.bcm.edu	37	1	170959029	170959029	+	Silent	SNP	C	C	T	rs16863922	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:170959029C>T	ENST00000367758.3	+	11	1012	c.913C>T	c.(913-915)Ctg>Ttg	p.L305L	MROH9_ENST00000367759.4_Silent_p.L305L	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	305																	TTACAGGCAACTGTGTGATAA	0.413													T|||	1032	0.20607	0.4047	0.1873	5008	,	,		20225	0.001		0.2227	False		,,,				2504	0.1452				p.L305L		Atlas-SNP	.											.	.	.	.	0			c.C913T						PASS	.	T	,	1362,2426		259,844,791	198.0	186.0	189.0		913,913	-4.3	0.0	1	dbSNP_123	189	1707,6533		185,1337,2598	no	coding-synonymous,coding-synonymous	C1orf129	NM_001163629.1,NM_025063.2	,	444,2181,3389	TT,TC,CC		20.716,35.9556,25.5155	,	305/862,305/574	170959029	3069,8959	1894	4120	6014	SO:0001819	synonymous_variant	80133	exon11			AGGCAACTGTGTG	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.913C>T	1.37:g.170959029C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	131	53	0.40458	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	37	CCDS41436.1																																																																																			C|0.806;T|0.194	0.194	strong		0.413	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262122	39262122	+	Missense_Mutation	SNP	G	G	A	rs200757692|rs188946528	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39262122G>A	ENST00000391415.1	+	1	539	c.482G>A	c.(481-483)cGc>cAc	p.R161H		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	161	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						agctgctgccgcccctcttgc	0.652													g|||	92	0.0183706	0.0038	0.0331	5008	,	,		17570	0.001		0.0616	False		,,,				2504	0.001				p.R161H		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-9	110	2	0			c.G482A						PASS	.						8.0	13.0	11.0					17																	39262122		684	1580	2264	SO:0001583	missense	100132386	exon1			GCTGCCGCCCCTC	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.482G>A	17.37:g.39262122G>A	ENSP00000375234:p.Arg161His	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	61	0.027930402930402932	3	0.006097560975609756	12	0.03314917127071823	1	0.0017482517482517483	45	0.059366754617414245	.	12.11	1.839141	0.32513	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00599	6.3	2.87	-2.78	0.05859	.	0.000000	0.40640	U	0.001042	T	0.00109	0.0003	M	0.74881	2.28	0.09310	N	1	B	0.22080	0.064	B	0.12837	0.008	T	0.47598	-0.9105	10	0.56958	D	0.05	.	4.4035	0.11399	0.3381:0.1654:0.4965:0.0	.	161	Q9BYQ8	KRA49_HUMAN	H	149;161;152	ENSP00000375234:R161H	ENSP00000334461:R152H	R	+	2	0	KRTAP4-9	36515648	0.000000	0.05858	0.312000	0.25196	0.222000	0.24845	-0.253000	0.08794	-0.966000	0.03587	-1.073000	0.02249	CGC	G|0.972;A|0.028	0.028	strong		0.652	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
VAMP8	8673	hgsc.bcm.edu	37	2	85808737	85808737	+	Silent	SNP	A	A	G	rs1009	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:85808737A>G	ENST00000263864.5	+	3	357	c.201A>G	c.(199-201)cgA>cgG	p.R67R	VAMP8_ENST00000432071.1_Silent_p.R41R|VAMP8_ENST00000409760.1_3'UTR|VAMP5_ENST00000306384.4_5'Flank	NM_003761.4	NP_003752.2	Q9BV40	VAMP8_HUMAN	vesicle-associated membrane protein 8	67	v-SNARE coiled-coil homology. {ECO:0000255|PROSITE-ProRule:PRU00290}.				autophagic vacuole fusion (GO:0000046)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|regulation of endocytosis (GO:0030100)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|secretory granule membrane (GO:0030667)|SNARE complex (GO:0031201)		p.R67R(1)		breast(1)|endometrium(2)|large_intestine(1)|stomach(2)	6						AGGTGGCTCGAAAATTCTGGT	0.468													G|||	2201	0.439497	0.5976	0.3473	5008	,	,		21409	0.3859		0.4314	False		,,,				2504	0.3548				p.R67R		Atlas-SNP	.											VAMP8,NS,carcinoma,0,1	VAMP8	10	1	1	Substitution - coding silent(1)	stomach(1)	c.A201G						PASS	.	G		2423,1983	557.4+/-379.7	672,1079,452	378.0	321.0	340.0		201	0.4	1.0	2	dbSNP_36	340	3554,5046	629.9+/-398.3	734,2086,1480	no	coding-synonymous	VAMP8	NM_003761.4		1406,3165,1932	GG,GA,AA		41.3256,45.0068,45.9557		67/101	85808737	5977,7029	2203	4300	6503	SO:0001819	synonymous_variant	8673	exon3			GGCTCGAAAATTC	AF053233	CCDS1979.1	2p12-p11.2	2013-02-13	2012-10-17		ENSG00000118640	ENSG00000118640		"""Vesicle-associated membrane proteins"""	12647	protein-coding gene	gene with protein product	"""endobrevin"""	603177				9878266, 9614193	Standard	NM_003761		Approved	EDB	uc002spt.4	Q9BV40	OTTHUMG00000130180	ENST00000263864.5:c.201A>G	2.37:g.85808737A>G		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	230	110	0.478261	NM_003761	O60625|Q53SP9|Q6IB09	Silent	SNP	ENST00000263864.5	37	CCDS1979.1																																																																																			A|0.547;G|0.453	0.453	strong		0.468	VAMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252498.3	NM_003761	
LRRC8C	84230	hgsc.bcm.edu	37	1	90179532	90179532	+	Missense_Mutation	SNP	A	A	G	rs12032393	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:90179532A>G	ENST00000370454.4	+	3	1658	c.1403A>G	c.(1402-1404)aAt>aGt	p.N468S	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	468			N -> S (in dbSNP:rs12032393).		fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CAGCTAGACAATCTTCAAGAG	0.438													A|||	754	0.150559	0.0325	0.2089	5008	,	,		20196	0.25		0.1531	False		,,,				2504	0.1636				p.N468S		Atlas-SNP	.											.	LRRC8C	73	.	0			c.A1403G						PASS	.	A	SER/ASN	203,4203	127.0+/-164.0	7,189,2007	94.0	89.0	91.0		1403	4.8	1.0	1	dbSNP_120	91	1235,7365	248.7+/-276.3	71,1093,3136	yes	missense	LRRC8C	NM_032270.4	46	78,1282,5143	GG,GA,AA		14.3605,4.6074,11.0564	benign	468/804	90179532	1438,11568	2203	4300	6503	SO:0001583	missense	84230	exon3			TAGACAATCTTCA		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"""hypothetical protein AD158"""	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1403A>G	1.37:g.90179532A>G	ENSP00000359483:p.Asn468Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_032270	B3KXS9|Q29RV6|Q9H075	Missense_Mutation	SNP	ENST00000370454.4	37	CCDS725.1	358	0.16391941391941392	22	0.044715447154471545	64	0.17679558011049723	152	0.26573426573426573	120	0.158311345646438	A	8.862	0.947264	0.18356	0.046074	0.143605	ENSG00000171488	ENST00000370454	T	0.17213	2.29	5.95	4.83	0.62350	.	0.085066	0.85682	D	0.000000	T	0.06188	0.0160	L	0.35793	1.09	0.26258	P	0.9786276	B	0.24483	0.104	B	0.21708	0.036	T	0.12863	-1.0531	9	0.39692	T	0.17	.	12.0658	0.53588	0.933:0.0:0.067:0.0	rs12032393;rs52828026;rs56419062;rs57211627;rs12032393	468	Q8TDW0	LRC8C_HUMAN	S	468	ENSP00000359483:N468S	ENSP00000359483:N468S	N	+	2	0	LRRC8C	89952120	0.997000	0.39634	0.979000	0.43373	0.989000	0.77384	3.287000	0.51732	1.078000	0.41014	0.528000	0.53228	AAT	A|0.869;G|0.131	0.131	strong		0.438	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270	
ERCC8	1161	hgsc.bcm.edu	37	5	60200665	60200665	+	Silent	SNP	A	A	G	rs4647100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:60200665A>G	ENST00000265038.5	-	5	477	c.435T>C	c.(433-435)taT>taC	p.Y145Y	ERCC8_ENST00000426742.2_Silent_p.Y87Y|ERCC8_ENST00000462279.1_5'UTR|ERCC8_ENST00000543101.1_Intron	NM_000082.3	NP_000073.1	Q13216	ERCC8_HUMAN	excision repair cross-complementation group 8	145					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|positive regulation of DNA repair (GO:0045739)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|response to X-ray (GO:0010165)|transcription-coupled nucleotide-excision repair (GO:0006283)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|protein complex (GO:0043234)	protein complex binding (GO:0032403)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14		Lung NSC(810;1.51e-06)|Prostate(74;0.0322)|Ovarian(174;0.0481)|Breast(144;0.077)				TATGATGACTATAAACTGTTT	0.308													A|||	680	0.135783	0.0666	0.1686	5008	,	,		8590	0.002		0.2704	False		,,,				2504	0.2055				p.Y145Y		Atlas-SNP	.											.	ERCC8	31	.	0			c.T435C						PASS	.	A		397,4009	197.1+/-221.3	15,367,1821	110.0	111.0	111.0		435	3.5	1.0	5	dbSNP_111	111	2258,6338	381.7+/-340.1	282,1694,2322	no	coding-synonymous	ERCC8	NM_000082.3		297,2061,4143	GG,GA,AA		26.268,9.0104,20.4199		145/397	60200665	2655,10347	2203	4298	6501	SO:0001819	synonymous_variant	1161	exon5			ATGACTATAAACT	U28413	CCDS3978.1	5q12.1	2014-09-17	2014-03-07		ENSG00000049167	ENSG00000049167		"""WD repeat domain containing"""	3439	protein-coding gene	gene with protein product		609412	"""Cockayne syndrome 1 (classical)"", ""excision repair cross-complementing rodent repair deficiency, complementation group 8"""	CKN1		8596535	Standard	NM_000082		Approved	CSA	uc003jsm.3	Q13216	OTTHUMG00000097741	ENST00000265038.5:c.435T>C	5.37:g.60200665A>G		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	197	100	0.507614	NM_000082	B2RB64|Q6FHX5|Q96GB9	Silent	SNP	ENST00000265038.5	37	CCDS3978.1																																																																																			A|0.820;G|0.180	0.180	strong		0.308	ERCC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214971.2	NM_000082	
FAM187B	148109	hgsc.bcm.edu	37	19	35719020	35719020	+	Nonsense_Mutation	SNP	C	C	T	rs541169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35719020C>T	ENST00000324675.3	-	1	612	c.564G>A	c.(562-564)tgG>tgA	p.W188*		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	188						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						AGCGGCTAGACCACACCAGCA	0.572													C|||	1594	0.318291	0.3124	0.3487	5008	,	,		17240	0.1746		0.3221	False		,,,				2504	0.4489				p.W188X		Atlas-SNP	.											.	FAM187B	28	.	0			c.G564A						PASS	.	C	stop/TRP	1409,2997	460.0+/-352.4	232,945,1026	66.0	60.0	62.0		564	1.2	0.0	19	dbSNP_83	62	2823,5777	444.3+/-360.6	452,1919,1929	yes	stop-gained	FAM187B	NM_152481.1		684,2864,2955	TT,TC,CC		32.8256,31.9791,32.5388		188/370	35719020	4232,8774	2203	4300	6503	SO:0001587	stop_gained	148109	exon1			GCTAGACCACACC	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"""transmembrane protein 162"""	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.564G>A	19.37:g.35719020C>T	ENSP00000323355:p.Trp188*	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_152481	Q8N7G6	Nonsense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	606	0.2774725274725275	146	0.2967479674796748	132	0.36464088397790057	90	0.15734265734265734	238	0.31398416886543534	C	17.24	3.338827	0.60963	0.319791	0.328256	ENSG00000177558	ENST00000324675	.	.	.	4.65	1.22	0.21188	.	1.033650	0.07717	N	0.942959	.	.	.	.	.	.	0.09310	P	0.9999999999887824	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-1.6996	3.618	0.08085	0.1706:0.5689:0.1652:0.0953	rs541169;rs3746246;rs17614052;rs60899247;rs541169	.	.	.	X	188	.	ENSP00000323355:W188X	W	-	3	0	FAM187B	40410860	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	0.391000	0.20784	0.236000	0.21180	0.655000	0.94253	TGG	C|0.697;T|0.303	0.303	strong		0.572	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
NBPF10	100132406	hgsc.bcm.edu	37	1	145368461	145368461	+	Missense_Mutation	SNP	A	A	C	rs12128680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145368461A>C	ENST00000369339.3	+	17	2046	c.1793A>C	c.(1792-1794)gAa>gCa	p.E598A	NBPF10_ENST00000369338.1_Missense_Mutation_p.E596A|NBPF10_ENST00000342960.5_Missense_Mutation_p.E3480A			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	775	NBPF 3. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GTGCTGATGGAAGTGGAAGAG	0.468																																					p.E3480A		Atlas-SNP	.											.	NBPF10	221	.	0			c.A10439C						PASS	.																																			SO:0001583	missense	100132406	exon84			TGATGGAAGTGGA	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	ENST00000369339.3:c.1793A>C	1.37:g.145368461A>C	ENSP00000358345:p.Glu598Ala	Somatic	288	0	0		WXS	Illumina HiSeq	Phase_I	302	123	0.407285	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	6.133	0.392687	0.11638	.	.	ENSG00000163386	ENST00000369339;ENST00000369338;ENST00000342960	T;T	0.09817	2.94;2.94	0.732	-1.11	0.09840	.	.	.	.	.	T	0.04679	0.0127	M	0.83603	2.65	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.38178	-0.9673	9	0.66056	D	0.02	.	2.7049	0.05159	0.5769:0.0:0.0:0.4231	rs12128680;rs57717963;rs12128680	544	Q4VC10	.	A	600;596;3480	ENSP00000358344:E596A;ENSP00000345684:E3480A	ENSP00000345684:E3480A	E	+	2	0	NBPF10	144079818	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.155000	0.16362	-0.323000	0.08602	0.316000	0.21350	GAA	A|0.899;C|0.101	0.101	strong		0.468	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
KCNH2	3757	hgsc.bcm.edu	37	7	150645534	150645534	+	Missense_Mutation	SNP	T	T	G	rs1805123	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150645534T>G	ENST00000262186.5	-	11	3091	c.2690A>C	c.(2689-2691)aAg>aCg	p.K897T	KCNH2_ENST00000330883.4_Missense_Mutation_p.K557T|KCNH2_ENST00000392968.2_Missense_Mutation_p.K801T	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	897			K -> T (in dbSNP:rs1805123). {ECO:0000269|PubMed:10862094, ECO:0000269|PubMed:11997281}.		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)	cgcctcacccTTGTCCGTGCG	0.667													T|||	682	0.136182	0.0068	0.17	5008	,	,		7620	0.0536		0.2535	False		,,,				2504	0.2515				p.K897T	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											KCNH2,colon,carcinoma,0,1	KCNH2	157	1	0			c.A2690C	GRCh37	CM004877	KCNH2	M	rs1805123	PASS	.	T	THR/LYS,THR/LYS	199,4207	116.7+/-154.6	8,183,2012	27.0	27.0	27.0		2690,1670	-0.0	1.0	7	dbSNP_89	27	2000,6600	322.6+/-315.6	248,1504,2548	yes	missense,missense	KCNH2	NM_000238.3,NM_172057.2	78,78	256,1687,4560	GG,GT,TT		23.2558,4.5166,16.9076	benign,benign	897/1160,557/820	150645534	2199,10807	2203	4300	6503	SO:0001583	missense	3757	exon11			TCACCCTTGTCCG	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.2690A>C	7.37:g.150645534T>G	ENSP00000262186:p.Lys897Thr	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	282	0.12912087912087913	8	0.016260162601626018	72	0.19889502762430938	20	0.03496503496503497	182	0.24010554089709762	T	14.87	2.663067	0.47572	0.045166	0.232558	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186	D;D;D	0.98747	-4.79;-4.89;-5.11	3.87	-0.036	0.13890	.	0.265285	0.34223	N	0.004151	T	0.00552	0.0018	M	0.62723	1.935	0.09310	P	0.9999999999999913	P;B;B	0.52316	0.952;0.0;0.248	B;B;B	0.39617	0.305;0.001;0.067	T	0.07616	-1.0763	9	0.46703	T	0.11	.	7.2061	0.25907	0.0:0.2987:0.0:0.7013	rs1805123;rs2968861;rs8179016;rs1805123	801;897;557	C4PFH9;Q12809;Q12809-2	.;KCNH2_HUMAN;.	T	557;801;897	ENSP00000328531:K557T;ENSP00000376695:K801T;ENSP00000262186:K897T	ENSP00000262186:K897T	K	-	2	0	KCNH2	150276467	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	2.069000	0.41481	-0.079000	0.12707	0.402000	0.26972	AAG	T|0.855;G|0.145	0.145	strong		0.667	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
IVL	3713	hgsc.bcm.edu	37	1	152882952	152882952	+	Missense_Mutation	SNP	G	G	C	rs11807064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152882952G>C	ENST00000368764.3	+	2	743	c.679G>C	c.(679-681)Gag>Cag	p.E227Q	IVL_ENST00000392667.2_Missense_Mutation_p.E81Q			P07476	INVO_HUMAN	involucrin	227	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		E -> Q (in dbSNP:rs11807064). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggagctcccagagcagcagga	0.687																																					p.E227Q		Atlas-SNP	.											IVL,caecum,carcinoma,0,3	IVL	100	3	0			c.G679C						scavenged	.						1.0	2.0	2.0					1																	152882952		1226	2796	4022	SO:0001583	missense	3713	exon2			CTCCCAGAGCAGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.679G>C	1.37:g.152882952G>C	ENSP00000357753:p.Glu227Gln	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	83	9	0.108434	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	9	0.004120879120879121	8	0.016260162601626018	0	0.0	0	0.0	1	0.0013192612137203166	G	10.99	1.507992	0.27036	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10288	3.09;2.89	3.65	-6.24	0.02046	.	.	.	.	.	T	0.01976	0.0062	L	0.36672	1.1	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.47114	-0.9142	9	0.24483	T	0.36	.	7.2256	0.26014	0.4858:0.2031:0.3111:0.0	rs62652338	227	P07476	INVO_HUMAN	Q	227;81	ENSP00000357753:E227Q;ENSP00000376435:E81Q	ENSP00000357753:E227Q	E	+	1	0	IVL	151149576	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.094000	0.15107	-0.793000	0.04475	0.414000	0.27820	GAG	G|0.995;C|0.005	0.005	strong		0.687	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
NLRP13	126204	hgsc.bcm.edu	37	19	56424532	56424532	+	Silent	SNP	G	G	A	rs731338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56424532G>A	ENST00000342929.3	-	5	650	c.651C>T	c.(649-651)cgC>cgT	p.R217R	NLRP13_ENST00000588751.1_Silent_p.R217R	NM_176810.2	NP_789780.2	Q86W25	NAL13_HUMAN	NLR family, pyrin domain containing 13	217							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)		GATCCAGTAGGCGCTGCAGTT	0.522													G|||	540	0.107827	0.0091	0.1412	5008	,	,		17897	0.1746		0.1342	False		,,,				2504	0.1217				p.R217R		Atlas-SNP	.											.	NLRP13	220	.	0			c.C651T						PASS	.	G		118,4288	88.2+/-126.9	3,112,2088	152.0	156.0	155.0		651	-3.1	0.0	19	dbSNP_86	155	1271,7329	253.4+/-279.1	90,1091,3119	no	coding-synonymous	NLRP13	NM_176810.2		93,1203,5207	AA,AG,GG		14.7791,2.6782,10.6797		217/1044	56424532	1389,11617	2203	4300	6503	SO:0001819	synonymous_variant	126204	exon5			CAGTAGGCGCTGC	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.651C>T	19.37:g.56424532G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_176810	Q7RTR5	Silent	SNP	ENST00000342929.3	37	CCDS33119.1																																																																																			G|0.891;A|0.109	0.109	strong		0.522	NLRP13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396560.1	NM_176810	
PLCG2	5336	hgsc.bcm.edu	37	16	81922813	81922813	+	Missense_Mutation	SNP	C	C	T	rs1143687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81922813C>T	ENST00000359376.3	+	10	1016	c.802C>T	c.(802-804)Cgg>Tgg	p.R268W		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	268			R -> W (in dbSNP:rs17537869).		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						AGTCCGTGAGCGGATGACAAA	0.458													C|||	120	0.0239617	0.0015	0.0403	5008	,	,		22254	0.0		0.0736	False		,,,				2504	0.0164				p.R268W		Atlas-SNP	.											.	PLCG2	276	.	0			c.C802T						PASS	.	C	TRP/ARG	46,3964		0,46,1959	166.0	157.0	160.0		802	2.8	1.0	16	dbSNP_123	160	580,7772		23,534,3619	yes	missense	PLCG2	NM_002661.3	101	23,580,5578	TT,TC,CC		6.9444,1.1471,5.0639	probably-damaging	268/1266	81922813	626,11736	2005	4176	6181	SO:0001583	missense	5336	exon10			CGTGAGCGGATGA		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.802C>T	16.37:g.81922813C>T	ENSP00000352336:p.Arg268Trp	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	154	86	0.558442	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	79	0.036172161172161175	2	0.0040650406504065045	18	0.049723756906077346	0	0.0	59	0.07783641160949868	C	20.7	4.032193	0.75504	0.011471	0.069444	ENSG00000197943	ENST00000359376	T	0.16897	2.31	4.94	2.81	0.32909	Phospholipase C, phosphoinositol-specific, EF-hand-like (1);	0.062968	0.64402	D	0.000005	T	0.00967	0.0032	N	0.22421	0.69	0.47547	D	0.999458	D	0.61697	0.99	P	0.54210	0.745	T	0.02269	-1.1185	10	0.66056	D	0.02	.	13.8546	0.63519	0.2748:0.7252:0.0:0.0	rs17537869;rs17537869	268	P16885	PLCG2_HUMAN	W	268	ENSP00000352336:R268W	ENSP00000352336:R268W	R	+	1	2	PLCG2	80480314	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.138000	0.42140	1.179000	0.42884	0.563000	0.77884	CGG	C|0.959;T|0.041	0.041	strong		0.458	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
DES	1674	hgsc.bcm.edu	37	2	220285666	220285666	+	Silent	SNP	G	G	C	rs12920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220285666G>C	ENST00000373960.3	+	5	1100	c.1014G>C	c.(1012-1014)ctG>ctC	p.L338L		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	338	Coil 2B.|Rod.		L -> R (in MFM1; results in the formation of a filamentous network disrupted by multiple breaks and clumps or large aggregates). {ECO:0000269|PubMed:16865695}.		cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		TTGACGCCCTGAAGGGCACTG	0.592													C|||	1691	0.33766	0.475	0.3444	5008	,	,		19718	0.1835		0.3648	False		,,,				2504	0.2781				p.L338L		Atlas-SNP	.											.	DES	53	.	0			c.G1014C						PASS	.	C		1974,2432	614.6+/-392.4	454,1066,683	77.0	66.0	70.0		1014	2.1	1.0	2	dbSNP_52	70	3054,5546	658.0+/-401.5	564,1926,1810	no	coding-synonymous	DES	NM_001927.3		1018,2992,2493	CC,CG,GG		35.5116,44.8025,38.6591		338/471	220285666	5028,7978	2203	4300	6503	SO:0001819	synonymous_variant	1674	exon5			CGCCCTGAAGGGC	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1014G>C	2.37:g.220285666G>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent	SNP	ENST00000373960.3	37	CCDS33383.1																																																																																			G|0.635;C|0.365	0.365	strong		0.592	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
XYLT2	64132	hgsc.bcm.edu	37	17	48437456	48437456	+	Missense_Mutation	SNP	C	C	G	rs6504649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48437456C>G	ENST00000017003.2	+	11	2451	c.2402C>G	c.(2401-2403)aCa>aGa	p.T801R	XYLT2_ENST00000507602.1_Intron	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	801			T -> R (acts as a disease modifier of severity of Pseudoxanthoma elasticum disease; dbSNP:rs6504649). {ECO:0000269|PubMed:16571645}.		chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					CAGCGGCACACACAGCTCACA	0.652													C|||	1257	0.250998	0.1989	0.2767	5008	,	,		18346	0.0962		0.4006	False		,,,				2504	0.3088				p.T801R		Atlas-SNP	.											XYLT2,colon,carcinoma,0,1	XYLT2	51	1	0			c.C2402G	GRCh37	CM064361	XYLT2	M	rs6504649	PASS	.	C	ARG/THR	1064,3342	382.1+/-324.3	142,780,1281	56.0	45.0	48.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2402	1.9	0.0	17	dbSNP_116	48	3418,5180	500.9+/-375.3	664,2090,1545	yes	missense	XYLT2	NM_022167.2	71	806,2870,2826	GG,GC,CC		39.7534,24.1489,34.4663	benign	801/866	48437456	4482,8522	2203	4299	6502	SO:0001583	missense	64132	exon11			GGCACACACAGCT	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.2402C>G	17.37:g.48437456C>G	ENSP00000017003:p.Thr801Arg	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	159	157	0.987421	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	594	0.27197802197802196	113	0.22967479674796748	116	0.32044198895027626	54	0.0944055944055944	311	0.4102902374670185	C	5.524	0.281686	0.10458	0.241489	0.397534	ENSG00000015532	ENST00000017003	T	0.04156	3.69	4.99	1.87	0.25490	.	0.423563	0.27861	N	0.017549	T	0.00012	0.0000	N	0.14661	0.345	0.44927	P	0.0020529999999999715	B	0.18013	0.025	B	0.21708	0.036	T	0.47935	-0.9078	9	0.87932	D	0	-0.0353	5.8296	0.18572	0.1367:0.6439:0.0:0.2194	rs6504649;rs17703474;rs6504649	801	Q9H1B5	XYLT2_HUMAN	R	801	ENSP00000017003:T801R	ENSP00000017003:T801R	T	+	2	0	XYLT2	45792455	0.027000	0.19231	0.000000	0.03702	0.004000	0.04260	3.021000	0.49651	0.273000	0.22049	0.655000	0.94253	ACA	C|0.688;G|0.312	0.312	strong		0.652	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
LRRC61	65999	hgsc.bcm.edu	37	7	150034184	150034184	+	Silent	SNP	T	T	C	rs3735170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150034184T>C	ENST00000359623.4	+	3	822	c.234T>C	c.(232-234)gcT>gcC	p.A78A	LRRC61_ENST00000493307.1_Silent_p.A78A|LRRC61_ENST00000323078.7_Silent_p.A78A	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	78										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			GCCAGCTAGCTGTGCTCAATG	0.647													C|||	1295	0.258586	0.2625	0.1571	5008	,	,		17325	0.2907		0.2455	False		,,,				2504	0.3057				p.A78A		Atlas-SNP	.											LRRC61,rectum,carcinoma,0,1	LRRC61	17	1	0			c.T234C						PASS	.	C	,	1062,3342	697.3+/-406.2	129,804,1269	49.0	46.0	47.0		234,234	-7.1	0.0	7	dbSNP_107	47	2188,6412	681.9+/-403.8	286,1616,2398	no	coding-synonymous,coding-synonymous	LRRC61	NM_001142928.1,NM_023942.2	,	415,2420,3667	CC,CT,TT		25.4419,24.1144,24.9923	,	78/260,78/260	150034184	3250,9754	2202	4300	6502	SO:0001819	synonymous_variant	65999	exon2			GCTAGCTGTGCTC	BC001354	CCDS5901.1	7q31-q35	2006-02-07			ENSG00000127399	ENSG00000127399			21704	protein-coding gene	gene with protein product							Standard	NM_023942		Approved	MGC3036, FLJ31392, HSPC295	uc003wgv.4	Q9BV99	OTTHUMG00000158326	ENST00000359623.4:c.234T>C	7.37:g.150034184T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_023942	B3KUW0|D3DWY8	Silent	SNP	ENST00000359623.4	37	CCDS5901.1																																																																																			T|0.745;C|0.255	0.255	strong		0.647	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942	
PACS2	23241	hgsc.bcm.edu	37	14	105833623	105833623	+	Missense_Mutation	SNP	C	C	T	rs111376436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:105833623C>T	ENST00000325438.8	+	5	1001	c.497C>T	c.(496-498)gCg>gTg	p.A166V	PACS2_ENST00000547217.1_Missense_Mutation_p.A136V|PACS2_ENST00000458164.2_Missense_Mutation_p.A166V|PACS2_ENST00000447393.1_Missense_Mutation_p.A166V|PACS2_ENST00000430725.2_Missense_Mutation_p.A99V			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	166					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)		CCCGTCAAGGCGGCCGAGATC	0.642													C|||	35	0.00698882	0.0	0.0086	5008	,	,		17115	0.0		0.0239	False		,,,				2504	0.0051				p.A166V		Atlas-SNP	.											.	PACS2	75	.	0			c.C497T						PASS	.	C	VAL/ALA,VAL/ALA	15,4391	22.3+/-47.3	0,15,2188	61.0	69.0	66.0		497,497	3.4	0.9	14	dbSNP_132	66	218,8380	91.6+/-153.7	6,206,4087	yes	missense,missense	PACS2	NM_001100913.2,NM_015197.3	64,64	6,221,6275	TT,TC,CC		2.5355,0.3404,1.7918	benign,benign	166/894,166/890	105833623	233,12771	2203	4299	6502	SO:0001583	missense	23241	exon5			TCAAGGCGGCCGA	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.497C>T	14.37:g.105833623C>T	ENSP00000321834:p.Ala166Val	Somatic	228	1	0.00438596		WXS	Illumina HiSeq	Phase_I	223	111	0.497758	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Missense_Mutation	SNP	ENST00000325438.8	37	CCDS32168.1	18	0.008241758241758242	0	0.0	1	0.0027624309392265192	0	0.0	17	0.022427440633245383	C	2.320	-0.355880	0.05138	0.003404	0.025355	ENSG00000179364	ENST00000430725;ENST00000325438;ENST00000458164;ENST00000447393;ENST00000547217	T;T;T;T;T	0.17370	2.28;2.28;2.28;2.28;2.28	4.5	3.36	0.38483	.	0.073243	0.53938	N	0.000049	T	0.01061	0.0035	N	0.00468	-1.46	0.28640	N	0.907204	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.0;0.002;0.0;0.001	T	0.40136	-0.9579	10	0.02654	T	1	-20.905	8.277	0.31879	0.0:0.1005:0.0:0.8995	.	166;166;166;175	E9PB38;Q86VP3-2;Q86VP3;Q86VP3-3	.;.;PACS2_HUMAN;.	V	99;166;166;166;136	ENSP00000393524:A99V;ENSP00000321834:A166V;ENSP00000399732:A166V;ENSP00000393559:A166V;ENSP00000449525:A136V	ENSP00000321834:A166V	A	+	2	0	PACS2	104904668	1.000000	0.71417	0.923000	0.36655	0.514000	0.34195	5.933000	0.70130	0.591000	0.29711	-0.469000	0.05056	GCG	C|0.985;T|0.015	0.015	strong		0.642	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
JMJD1C	221037	hgsc.bcm.edu	37	10	64974537	64974537	+	Missense_Mutation	SNP	A	A	T	rs10761725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:64974537A>T	ENST00000399262.2	-	8	1608	c.1390T>A	c.(1390-1392)Tcg>Acg	p.S464T	JMJD1C_ENST00000489372.2_5'Flank|JMJD1C_ENST00000399251.1_Missense_Mutation_p.S245T|JMJD1C_ENST00000402544.1_Missense_Mutation_p.S245T|JMJD1C_ENST00000542921.1_Missense_Mutation_p.S282T	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	464			S -> T (in dbSNP:rs10761725). {ECO:0000269|PubMed:17974005}.		blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TGTTCTGACGAATGAATAATC	0.388													A|||	2561	0.511382	0.3154	0.4669	5008	,	,		19020	0.377		0.7783	False		,,,				2504	0.6718				p.S464T		Atlas-SNP	.											JMJD1C_ENST00000399262,NS,carcinoma,+2,2	JMJD1C	347	2	0			c.T1390A						PASS	.	A	THR/SER,THR/SER	1527,2181		311,905,638	164.0	148.0	153.0		733,1390	3.2	1.0	10	dbSNP_120	153	6382,1810		2482,1418,196	yes	missense,missense	JMJD1C	NM_004241.2,NM_032776.1	58,58	2793,2323,834	TT,TA,AA		22.0947,41.1812,33.5378	benign,benign	245/2304,464/2541	64974537	7909,3991	1854	4096	5950	SO:0001583	missense	221037	exon8			CTGACGAATGAAT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.1390T>A	10.37:g.64974537A>T	ENSP00000382204:p.Ser464Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	105	103	0.980952	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	1162	0.532051282051282	149	0.30284552845528456	190	0.5248618784530387	231	0.40384615384615385	592	0.7810026385224275	A	7.754	0.703933	0.15172	0.411812	0.779053	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.14266	2.52;2.52;2.52;2.52	5.71	3.24	0.37175	.	0.365789	0.26967	N	0.021583	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B;B	0.25007	0.116;0.094	B;B	0.21708	0.036;0.026	T	0.05582	-1.0876	9	0.30078	T	0.28	-4.5093	8.7222	0.34447	0.5488:0.3828:0.0684:0.0	rs10761725;rs52823266;rs10761725	464;282	Q15652;A0T124	JHD2C_HUMAN;.	T	464;245;245;282	ENSP00000382204:S464T;ENSP00000384990:S245T;ENSP00000382195:S245T;ENSP00000444682:S282T	ENSP00000382195:S245T	S	-	1	0	JMJD1C	64644543	0.631000	0.27164	0.958000	0.39756	0.721000	0.41392	0.761000	0.26489	0.951000	0.37770	0.459000	0.35465	TCG	A|0.395;T|0.605	0.605	strong		0.388	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
MYO9B	4650	hgsc.bcm.edu	37	19	17317955	17317955	+	Silent	SNP	A	A	G	rs8110964	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17317955A>G	ENST00000594824.1	+	35	5673	c.5526A>G	c.(5524-5526)tcA>tcG	p.S1842S	MYO9B_ENST00000397274.2_Silent_p.S1842S|MYO9B_ENST00000595618.1_Silent_p.S1842S|CTD-3032J10.3_ENST00000601929.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	1842	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.|Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						ACCGCATGTCACCTGGGGCGC	0.637													G|||	3162	0.63139	0.7073	0.6772	5008	,	,		14431	0.746		0.3926	False		,,,				2504	0.6237				p.S1842S		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.A5526G						scavenged	.	G	,	2827,1549		936,955,297	33.0	38.0	37.0		5526,5526	-8.3	0.1	19	dbSNP_116	37	3377,5189		705,1967,1611	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1641,2922,1908	GG,GA,AA		39.4233,35.3976,47.9369	,	1842/2023,1842/2158	17317955	6204,6738	2188	4283	6471	SO:0001819	synonymous_variant	4650	exon35			CATGTCACCTGGG		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.5526A>G	19.37:g.17317955A>G		Somatic	202	2	0.00990099		WXS	Illumina HiSeq	Phase_I	171	169	0.988304	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				A|0.384;G|0.616	0.616	strong		0.637	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
PALLD	23022	hgsc.bcm.edu	37	4	169433327	169433327	+	Missense_Mutation	SNP	G	G	A	rs397718410|rs373066707|rs7671781	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169433327G>A	ENST00000505667.1	+	2	845	c.672G>A	c.(670-672)atG>atA	p.M224I	PALLD_ENST00000261509.6_Missense_Mutation_p.M224I|PALLD_ENST00000333488.4_Missense_Mutation_p.M101I|PALLD_ENST00000335742.7_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	224			M -> I (in dbSNP:rs7671781).|M -> T (in dbSNP:rs7655494). {ECO:0000269|PubMed:14702039}.		cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		AGAGCCCTATGGAAGACCAAG	0.582									Pancreatic Cancer, Familial Clustering of				G|||	1200	0.239617	0.2368	0.1844	5008	,	,		17181	0.1935		0.33	False		,,,				2504	0.2372				p.M224I	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.G672A						PASS	.	G	ILE/MET,ILE/MET	1065,3341		151,763,1289	101.0	105.0	104.0		672,672	-10.8	0.0	4	dbSNP_116	104	2624,5976		460,1704,2136	yes	missense,missense	PALLD	NM_001166108.1,NM_016081.3	10,10	611,2467,3425	AA,AG,GG		30.5116,24.1716,28.3638	benign,benign	224/1124,224/1107	169433327	3689,9317	2203	4300	6503	SO:0001583	missense	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	CCCTATGGAAGAC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.672G>A	4.37:g.169433327G>A	ENSP00000425556:p.Met224Ile	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	447	0.20467032967032966	89	0.18089430894308944	68	0.1878453038674033	84	0.14685314685314685	206	0.2717678100263852	G	10.73	1.433994	0.25813	0.241716	0.305116	ENSG00000129116	ENST00000261509;ENST00000505667;ENST00000508898;ENST00000333488	T;T;T;T	0.61742	0.18;0.46;0.08;0.18	5.41	-10.8	0.00216	.	0.307711	0.17926	N	0.157333	T	0.00012	0.0000	N	0.08118	0	0.53688	P	2.6999999999999247E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08576	-1.0715	9	0.13853	T	0.58	.	2.9803	0.05951	0.2733:0.4205:0.1616:0.1446	rs7671781	224;224	B7ZMM5;B2RTX2	.;.	I	224;224;203;101	ENSP00000261509:M224I;ENSP00000425556:M224I;ENSP00000423063:M203I;ENSP00000328945:M101I	ENSP00000261509:M224I	M	+	3	0	PALLD	169669902	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.466000	0.00229	-4.316000	0.00057	-0.918000	0.02743	ATG	G|0.733;A|0.267	0.267	strong		0.582	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
NPW	283869	hgsc.bcm.edu	37	16	2070568	2070568	+	Missense_Mutation	SNP	A	A	C	rs2286472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2070568A>C	ENST00000566435.1	+	2	803	c.290A>C	c.(289-291)gAc>gCc	p.D97A	NPW_ENST00000329610.4_Missense_Mutation_p.D149A			Q8N729	NPW_HUMAN	neuropeptide W	149					feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				kidney(1)	1						CCAGCGGTGGACCCCGCAGCA	0.726													C|||	1810	0.361422	0.6218	0.2579	5008	,	,		11024	0.3313		0.329	False		,,,				2504	0.1472				p.D149A		Atlas-SNP	.											NPW,NS,carcinoma,0,2	NPW	4	2	0			c.A446C						PASS	.	C	ALA/ASP	2209,1627		693,823,402	17.0	23.0	21.0		446	-0.2	0.0	16	dbSNP_100	21	2599,5625		402,1795,1915	yes	missense	NPW	NM_001099456.2	126	1095,2618,2317	CC,CA,AA		31.6026,42.414,39.8673	benign	149/166	2070568	4808,7252	1918	4112	6030	SO:0001583	missense	283869	exon2			CGGTGGACCCCGC	AB084276	CCDS42102.1	16p13.3	2013-02-26			ENSG00000183971	ENSG00000183971		"""Endogenous ligands"""	30509	protein-coding gene	gene with protein product	"""prepro-neuropeptide W"""	607997				12118011, 12401809	Standard	NM_001099456		Approved	PPL8	uc002coh.4	Q8N729	OTTHUMG00000176914	ENST00000566435.1:c.290A>C	16.37:g.2070568A>C	ENSP00000456974:p.Asp97Ala	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001099456		Missense_Mutation	SNP	ENST00000566435.1	37		820	0.37545787545787546	303	0.6158536585365854	105	0.2900552486187845	173	0.30244755244755245	239	0.3153034300791557	N	0.008	-1.886957	0.00527	0.57586	0.316026	ENSG00000183971	ENST00000329610	T	0.54071	0.59	2.21	-0.235	0.13071	.	0.833798	0.10009	N	0.727475	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	0.45338	-0.9268	9	0.09590	T	0.72	.	2.1559	0.03811	0.2384:0.3075:0.0:0.4541	rs2286472;rs56777272;rs2286472	149	Q8N729	NPW_HUMAN	A	149	ENSP00000330070:D149A	ENSP00000330070:D149A	D	+	2	0	NPW	2010569	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	-0.827000	0.04424	-0.424000	0.07382	-2.803000	0.00113	GAC	A|0.624;C|0.376	0.376	strong		0.726	NPW-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000434312.1	NM_001099456	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138738204	138738204	+	Silent	SNP	G	G	A	rs11977775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:138738204G>A	ENST00000242351.5	-	12	2758	c.2442C>T	c.(2440-2442)taC>taT	p.Y814Y	ZC3HAV1_ENST00000464606.1_Silent_p.Y936Y	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	814	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						AACCTTTTCCGTATTTGTTTT	0.363													A|||	517	0.103235	0.2897	0.0504	5008	,	,		20828	0.0248		0.0338	False		,,,				2504	0.0409				p.Y814Y		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.C2442T						PASS	.	A		1173,3233	711.4+/-408.0	153,867,1183	119.0	123.0	121.0		2442	0.2	1.0	7	dbSNP_120	121	231,8369	808.7+/-407.2	1,229,4070	no	coding-synonymous	ZC3HAV1	NM_020119.3		154,1096,5253	AA,AG,GG		2.686,26.6228,10.795		814/903	138738204	1404,11602	2203	4300	6503	SO:0001819	synonymous_variant	56829	exon12			TTTTCCGTATTTG	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2442C>T	7.37:g.138738204G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_020119	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	37	CCDS5851.1																																																																																			G|0.898;A|0.102	0.102	strong		0.363	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
AOC1	26	hgsc.bcm.edu	37	7	150556002	150556002	+	Silent	SNP	T	T	C	rs1049748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150556002T>C	ENST00000493429.1	+	5	2306	c.1722T>C	c.(1720-1722)ccT>ccC	p.P574P	AOC1_ENST00000416793.2_Silent_p.P574P|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000360937.4_Silent_p.P574P|AOC1_ENST00000467291.1_Silent_p.P574P			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	574	Heparin-binding. {ECO:0000250}.				amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	GGAAGCTGCCTAAGTACCTGC	0.647													C|||	2583	0.515775	0.59	0.4611	5008	,	,		17985	0.5605		0.3877	False		,,,				2504	0.5399				p.P574P		Atlas-SNP	.											.	ABP1	92	.	0			c.T1722C						PASS	.	C		2097,1717		574,949,384	20.0	23.0	22.0		1722	5.6	1.0	7	dbSNP_86	22	3254,4984		652,1950,1517	no	coding-synonymous	ABP1	NM_001091.2		1226,2899,1901	CC,CT,TT		39.4999,45.0184,44.3993		574/752	150556002	5351,6701	1907	4119	6026	SO:0001819	synonymous_variant	26	exon3			GCTGCCTAAGTAC	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1722T>C	7.37:g.150556002T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	135	71	0.525926	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1																																																																																			T|0.510;C|0.490	0.490	strong		0.647	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
CYFIP1	23191	hgsc.bcm.edu	37	15	22960868	22960868	+	Silent	SNP	G	G	C	rs2289818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:22960868G>C	ENST00000313077.7	+	18	2186	c.2061G>C	c.(2059-2061)ctG>ctC	p.L687L	CYFIP1_ENST00000435939.2_Silent_p.L256L|CYFIP1_ENST00000560848.1_Silent_p.L687L	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)		AGCAGTTCCTGTACGACGAAA	0.502													C|||	2286	0.45647	0.6573	0.5202	5008	,	,		20127	0.4385		0.3201	False		,,,				2504	0.2986				p.L687L		Atlas-SNP	.											.	CYFIP1	159	.	0			c.G2061C						PASS	.	C	,	2761,1645	503.9+/-365.7	858,1045,300	78.0	66.0	70.0		768,2061	3.6	1.0	15	dbSNP_100	70	2872,5728	673.0+/-403.0	495,1882,1923	no	coding-synonymous,coding-synonymous	CYFIP1	NM_001033028.1,NM_014608.2	,	1353,2927,2223	CC,CG,GG		33.3953,37.3355,43.3108	,	256/823,687/1254	22960868	5633,7373	2203	4300	6503	SO:0001819	synonymous_variant	23191	exon18			GTTCCTGTACGAC	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.2061G>C	15.37:g.22960868G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	105	105	1	NM_014608		Silent	SNP	ENST00000313077.7	37	CCDS10009.1																																																																																			G|0.543;C|0.457	0.457	strong		0.502	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
PLXND1	23129	hgsc.bcm.edu	37	3	129303236	129303236	+	Missense_Mutation	SNP	G	G	C	rs201334507	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:129303236G>C	ENST00000324093.4	-	6	2199	c.2021C>G	c.(2020-2022)cCc>cGc	p.P674R	PLXND1_ENST00000393239.1_Missense_Mutation_p.P674R	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	674					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						ACCCTGGTTGGGGGGGAAGGG	0.637													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19988	0.001		0.0	False		,,,				2504	0.0				p.P674R	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C2021G						PASS	.	G	ARG/PRO	0,4406		0,0,2203	53.0	53.0	53.0		2021	2.9	0.0	3		53	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PLXND1	NM_015103.2	103	0,3,6500	CC,CG,GG		0.0349,0.0,0.0231	benign	674/1926	129303236	3,13003	2203	4300	6503	SO:0001583	missense	23129	exon6			TGGTTGGGGGGGA	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.2021C>G	3.37:g.129303236G>C	ENSP00000317128:p.Pro674Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	70	40	0.571429	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	G	1.556	-0.538035	0.04082	0.0	3.49E-4	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.34275	1.42;1.37	4.77	2.94	0.34122	.	0.473004	0.19301	N	0.117635	T	0.33644	0.0870	M	0.65975	2.015	0.09310	N	1	B	0.21688	0.059	B	0.26310	0.068	T	0.31530	-0.9940	10	0.12103	T	0.63	.	10.1176	0.42601	0.0:0.1326:0.593:0.2744	.	674	Q9Y4D7	PLXD1_HUMAN	R	674	ENSP00000317128:P674R;ENSP00000376931:P674R	ENSP00000317128:P674R	P	-	2	0	PLXND1	130785926	0.013000	0.17824	0.002000	0.10522	0.049000	0.14656	1.150000	0.31639	0.528000	0.28580	-0.218000	0.12543	CCC	.	.	weak		0.637	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
MYH11	4629	hgsc.bcm.edu	37	16	15818141	15818141	+	Silent	SNP	A	A	C	rs587781059|rs2075511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15818141A>C	ENST00000300036.5	-	31	4351	c.4242T>G	c.(4240-4242)gcT>gcG	p.A1414A	NDE1_ENST00000396355.1_3'UTR|MYH11_ENST00000576790.2_Silent_p.A1414A|MYH11_ENST00000396324.3_Silent_p.A1421A|NDE1_ENST00000571896.1_3'UTR|AF001548.5_ENST00000574212.1_RNA|NDE1_ENST00000342673.5_3'UTR|NDE1_ENST00000396354.1_3'UTR|MYH11_ENST00000452625.2_Silent_p.A1421A	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1414					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GTTTATCATAAGCGGCCGCCT	0.537			T	CBFB	AML								A|||	2054	0.410144	0.2564	0.5317	5008	,	,		18915	0.3155		0.496	False		,,,				2504	0.5409				p.A1421A		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.T4263G						PASS	.	A	,,,,,	1354,3040	450.2+/-349.3	215,924,1058	85.0	79.0	81.0		4263,4263,,4242,,4242	1.7	1.0	16	dbSNP_96	81	4610,3990	600.0+/-394.1	1233,2144,923	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous,utr-3,coding-synonymous	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	,,,,,	1448,3068,1981	CC,CA,AA		46.3953,30.8147,45.8981	,,,,,	1421/1946,1421/1980,,1414/1973,,1414/1939	15818141	5964,7030	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon32			ATCATAAGCGGCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.4242T>G	16.37:g.15818141A>C		Somatic	173	1	0.00578035		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			A|0.589;C|0.411	0.411	strong		0.537	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
GLI2	2736	hgsc.bcm.edu	37	2	121746956	121746956	+	Missense_Mutation	SNP	G	G	T	rs3738880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:121746956G>T	ENST00000452319.1	+	14	3526	c.3466G>T	c.(3466-3468)Gcc>Tcc	p.A1156S	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Missense_Mutation_p.A1156S					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				CACCGTAGACGCCCTGGCCAG	0.612													G|||	2549	0.508986	0.3578	0.5836	5008	,	,		17208	0.4722		0.7247	False		,,,				2504	0.4765				p.A1156S		Atlas-SNP	.											.	GLI2	187	.	0			c.G3466T						PASS	.	G	SER/ALA	1801,2555		392,1017,769	27.0	25.0	26.0		3466	0.0	0.2	2	dbSNP_107	26	6231,2297		2304,1623,337	yes	missense	GLI2	NM_005270.4	99	2696,2640,1106	TT,TG,GG		26.9348,41.3453,37.6591	benign	1156/1587	121746956	8032,4852	2178	4264	6442	SO:0001583	missense	2736	exon13			GTAGACGCCCTGG		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.3466G>T	2.37:g.121746956G>T	ENSP00000390436:p.Ala1156Ser	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	1224	0.5604395604395604	180	0.36585365853658536	215	0.5939226519337016	285	0.4982517482517482	544	0.7176781002638523	G	2.076	-0.411771	0.04799	0.413453	0.730652	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.14144	2.53;2.53	4.87	0.0393	0.14204	.	0.833216	0.11014	N	0.609104	T	0.00012	0.0000	L	0.39633	1.23	0.80722	P	0.0	B;B	0.29341	0.156;0.242	B;B	0.25140	0.018;0.058	T	0.16188	-1.0411	8	.	.	.	.	6.8098	0.23799	0.4893:0.1217:0.389:0.0	rs3738880;rs3738880	1156;811	P10070;P10070-2	GLI2_HUMAN;.	S	1156	ENSP00000390436:A1156S;ENSP00000354586:A1156S	.	A	+	1	0	GLI2	121463426	0.000000	0.05858	0.182000	0.23118	0.760000	0.43138	-0.368000	0.07543	-0.176000	0.10707	0.449000	0.29647	GCC	G|0.411;T|0.589	0.589	strong		0.612	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
ZNF142	7701	hgsc.bcm.edu	37	2	219508372	219508372	+	Missense_Mutation	SNP	A	A	T	rs3770213	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219508372A>T	ENST00000449707.1	-	8	3288	c.2867T>A	c.(2866-2868)cTt>cAt	p.L956H	ZNF142_ENST00000411696.2_Missense_Mutation_p.L956H	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	956			L -> H (in dbSNP:rs3770213).		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)		GACTGTGGCAAGAGGCTCTTC	0.562													A|||	959	0.191494	0.028	0.3271	5008	,	,		18398	0.0556		0.3757	False		,,,				2504	0.2669				p.L956H	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.T2867A						PASS	.	A	HIS/LEU	298,3464		9,280,1592	199.0	203.0	202.0		2867	-1.6	0.0	2	dbSNP_107	202	3128,5106		625,1878,1614	yes	missense	ZNF142	NM_001105537.1	99	634,2158,3206	TT,TA,AA		37.9888,7.9213,28.5595	possibly-damaging	956/1688	219508372	3426,8570	1881	4117	5998	SO:0001583	missense	7701	exon8			GTGGCAAGAGGCT	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.2867T>A	2.37:g.219508372A>T	ENSP00000408643:p.Leu956His	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	57	0.483051	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	459	0.21016483516483517	26	0.052845528455284556	114	0.3149171270718232	36	0.06293706293706294	283	0.3733509234828496	A	15.87	2.960372	0.53400	0.079213	0.379888	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.14144	2.53;2.53	3.93	-1.58	0.08479	.	2.400410	0.01281	N	0.009736	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D;D	0.57257	0.979;0.979	P;P	0.46975	0.533;0.533	T	0.39396	-0.9616	9	0.15499	T	0.54	-14.8295	5.5057	0.16852	0.4894:0.1476:0.363:0.0	rs3770213;rs17463262;rs52792951;rs3770213	956;793	P52746;A8MWU9	ZN142_HUMAN;.	H	956	ENSP00000408643:L956H;ENSP00000398798:L956H	ENSP00000398798:L956H	L	-	2	0	ZNF142	219216616	0.000000	0.05858	0.000000	0.03702	0.484000	0.33280	0.104000	0.15313	-0.052000	0.13311	0.459000	0.35465	CTT	A|0.741;N|0.000	.	strong		0.562	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
GPR20	2843	hgsc.bcm.edu	37	8	142367400	142367400	+	Silent	SNP	G	G	A	rs11167054	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:142367400G>A	ENST00000377741.3	-	2	714	c.624C>T	c.(622-624)ccC>ccT	p.P208P	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	208					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)			TGACCAGCAGGGGCAGCAGGA	0.701													A|||	3770	0.752796	0.8533	0.8573	5008	,	,		17946	0.5099		0.8171	False		,,,				2504	0.727				p.P208P		Atlas-SNP	.											GPR20,NS,carcinoma,0,2	GPR20	43	2	0			c.C624T						scavenged	.	A		3616,550		1570,476,37	10.0	11.0	11.0		624	-8.4	0.7	8	dbSNP_120	11	6656,1574		2708,1240,167	no	coding-synonymous	GPR20	NM_005293.2		4278,1716,204	AA,AG,GG		19.1252,13.2021,17.1346		208/359	142367400	10272,2124	2083	4115	6198	SO:0001819	synonymous_variant	2843	exon2			CAGCAGGGGCAGC	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.624C>T	8.37:g.142367400G>A		Somatic	5	1	0.2		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_005293	Q17R96	Silent	SNP	ENST00000377741.3	37	CCDS34949.1																																																																																			G|0.248;A|0.752	0.752	strong		0.701	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293	
ACOXL	55289	hgsc.bcm.edu	37	2	111598958	111598958	+	Missense_Mutation	SNP	C	C	T	rs1554005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:111598958C>T	ENST00000389811.4	+	10	988	c.764C>T	c.(763-765)aCg>aTg	p.T255M	ACOXL_ENST00000340561.4_Missense_Mutation_p.T255M|ACOXL_ENST00000439055.1_Missense_Mutation_p.T255M			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	255			T -> M (in dbSNP:rs1554005).		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						CTTGGGTTGACGATAGCCATT	0.328													C|||	916	0.182907	0.1467	0.2349	5008	,	,		19499	0.1567		0.1809	False		,,,				2504	0.2239				p.T255M		Atlas-SNP	.											.	ACOXL	93	.	0			c.C764T						PASS	.	C	MET/THR	705,3699	289.8+/-280.6	66,573,1563	154.0	145.0	148.0		764	3.4	1.0	2	dbSNP_88	148	1618,6978	297.0+/-303.2	162,1294,2842	yes	missense	ACOXL	NM_001142807.1	81	228,1867,4405	TT,TC,CC		18.8227,16.0082,17.8692	benign	255/581	111598958	2323,10677	2202	4298	6500	SO:0001583	missense	55289	exon10			GGTTGACGATAGC		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.764C>T	2.37:g.111598958C>T	ENSP00000374461:p.Thr255Met	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		407|407	0.18635531135531136|0.18635531135531136	93|93	0.18902439024390244|0.18902439024390244	89|89	0.24585635359116023|0.24585635359116023	87|87	0.1520979020979021|0.1520979020979021	138|138	0.1820580474934037|0.1820580474934037	C|C	8.885|8.885	0.952660|0.952660	0.18431|0.18431	0.160082|0.160082	0.188227|0.188227	ENSG00000153093|ENSG00000153093	ENST00000433706|ENST00000389811;ENST00000439055;ENST00000422487;ENST00000340561;ENST00000417074	.|D;D;T;D	.|0.96011	.|-3.88;-3.88;-0.63;-3.88	5.2|5.2	3.38|3.38	0.38709|0.38709	.|Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	.|0.377447	.|0.25768	.|N	.|0.028432	.|T	.|0.00210	.|0.0006	L|L	0.57130|0.57130	1.785|1.785	0.41383|0.41383	P|P	0.012433000000000027|0.012433000000000027	.|P;P;P	.|0.39404	.|0.672;0.621;0.615	.|B;B;B	.|0.39379	.|0.084;0.05;0.298	.|T	.|0.00146	.|-1.1992	.|9	.|0.51188	.|T	.|0.08	-30.5644|-30.5644	7.5501|7.5501	0.27790|0.27790	0.0:0.7982:0.0:0.2018|0.0:0.7982:0.0:0.2018	rs1554005;rs17464711;rs59445452;rs1554005|rs1554005;rs17464711;rs59445452;rs1554005	.|255;255;255	.|E9PB20;Q9NUZ1-2;Q9NUZ1	.|.;.;ACOXL_HUMAN	X|M	30|255;255;106;255;93	.|ENSP00000374461:T255M;ENSP00000407761:T255M;ENSP00000343717:T255M;ENSP00000387832:T93M	.|ENSP00000343717:T255M	R|T	+|+	1|2	2|0	ACOXL|ACOXL	111315429|111315429	0.757000|0.757000	0.28394|0.28394	1.000000|1.000000	0.80357|0.80357	0.311000|0.311000	0.27955|0.27955	0.153000|0.153000	0.16323|0.16323	0.685000|0.685000	0.31468|0.31468	0.655000|0.655000	0.94253|0.94253	CGA|ACG	C|0.823;N|0.000	.	strong		0.328	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
CYBRD1	79901	hgsc.bcm.edu	37	2	172411273	172411273	+	Missense_Mutation	SNP	G	G	A	rs10455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:172411273G>A	ENST00000321348.4	+	4	995	c.797G>A	c.(796-798)aGt>aAt	p.S266N	CYBRD1_ENST00000409484.1_Missense_Mutation_p.S208N|CYBRD1_ENST00000375252.3_3'UTR	NM_024843.3	NP_079119.3	Q53TN4	CYBR1_HUMAN	cytochrome b reductase 1	266			S -> N (in dbSNP:rs10455). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.		cellular iron ion homeostasis (GO:0006879)|response to iron ion (GO:0010039)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|oxidoreductase activity, oxidizing metal ions (GO:0016722)			endometrium(1)|kidney(1)|large_intestine(3)|liver(2)|lung(3)	10						GAGTTAAACAGTGAAGTAGCA	0.443													A|||	3421	0.683107	0.9327	0.6009	5008	,	,		21456	0.3958		0.666	False		,,,				2504	0.7178				p.S266N		Atlas-SNP	.											.	CYBRD1	16	.	0			c.G797A						PASS	.	A	,ASN/SER	3875,531	239.9+/-250.9	1704,467,32	74.0	71.0	72.0		,797	-3.3	0.3	2	dbSNP_52	72	5670,2930	458.4+/-364.6	1889,1892,519	yes	utr-3,missense	CYBRD1	NM_001127383.1,NM_024843.3	,46	3593,2359,551	AA,AG,GG		34.0698,12.0517,26.6108	,benign	,266/287	172411273	9545,3461	2203	4300	6503	SO:0001583	missense	79901	exon4			TAAACAGTGAAGT	AK027115	CCDS2244.1, CCDS46449.1, CCDS58736.1	2q31	2013-03-14			ENSG00000071967	ENSG00000071967		"""Cytochrome b genes"""	20797	protein-coding gene	gene with protein product	"""ferric-chelate reductase 3"", ""cytochrome b561 family, member A2"""	605745				11230685	Standard	NM_001127383		Approved	DCYTB, FLJ23462, FRRS3, CYB561A2	uc002ugy.4	Q53TN4	OTTHUMG00000132260	ENST00000321348.4:c.797G>A	2.37:g.172411273G>A	ENSP00000319141:p.Ser266Asn	Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	148	148	1	NM_024843	B2RE79|B4DWD7|Q6KC16|Q6KC17|Q6P147|Q6ZR51|Q9H0Q8|Q9H5G5	Missense_Mutation	SNP	ENST00000321348.4	37	CCDS2244.1	1417	0.6488095238095238	448	0.9105691056910569	233	0.643646408839779	215	0.3758741258741259	521	0.6873350923482849	A	5.162	0.215404	0.09810	0.879483	0.659302	ENSG00000071967	ENST00000409484;ENST00000321348	T;T	0.57595	0.39;0.4	5.16	-3.33	0.04958	.	0.669254	0.14511	N	0.315126	T	0.00012	0.0000	N	0.12961	0.28	0.29769	P	0.834894	B	0.02656	0.0	B	0.04013	0.001	T	0.45440	-0.9261	9	0.11794	T	0.64	0.0168	20.0263	0.97523	0.0846:0.0866:0.8288:0.0	rs10455;rs3172057;rs16859492;rs17846696;rs17859796;rs52827505;rs58982019;rs10455	266	Q53TN4	CYBR1_HUMAN	N	208;266	ENSP00000386739:S208N;ENSP00000319141:S266N	ENSP00000319141:S266N	S	+	2	0	CYBRD1	172119519	0.000000	0.05858	0.269000	0.24586	0.822000	0.46500	-1.717000	0.01876	-1.628000	0.01548	-0.972000	0.02603	AGT	A|0.688;C|0.004	0.688	strong		0.443	CYBRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255344.2	NM_024843	
UNC5C	8633	hgsc.bcm.edu	37	4	96127798	96127798	+	Missense_Mutation	SNP	G	G	T	rs141976218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:96127798G>T	ENST00000453304.1	-	11	2231	c.1883C>A	c.(1882-1884)gCa>gAa	p.A628E		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	628	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		TCCCTGTGCTGCCTGGTTCTT	0.537													G|||	3	0.000599042	0.0	0.0014	5008	,	,		15925	0.0		0.002	False		,,,				2504	0.0				p.A628E		Atlas-SNP	.											.	UNC5C	141	.	0			c.C1883A						PASS	.	G	GLU/ALA	1,4405	2.1+/-5.4	0,1,2202	106.0	94.0	98.0		1883	3.5	0.8	4	dbSNP_134	98	19,8581	10.5+/-38.8	0,19,4281	yes	missense	UNC5C	NM_003728.3	107	0,20,6483	TT,TG,GG		0.2209,0.0227,0.1538	benign	628/932	96127798	20,12986	2203	4300	6503	SO:0001583	missense	8633	exon11			TGTGCTGCCTGGT	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1883C>A	4.37:g.96127798G>T	ENSP00000406022:p.Ala628Glu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	117	50	0.42735	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	10.51	1.369746	0.24771	2.27E-4	0.002209	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.40476	1.03;1.03	5.28	3.45	0.39498	ZU5 (3);	0.761342	0.12964	N	0.424732	T	0.28433	0.0703	N	0.19112	0.55	0.28023	N	0.934452	B;B	0.17852	0.004;0.024	B;B	0.19391	0.01;0.025	T	0.19844	-1.0293	10	0.34782	T	0.22	.	9.8179	0.40865	0.0805:0.1393:0.7802:0.0	.	628;628	A8K385;O95185	.;UNC5C_HUMAN	E	628;587;647	ENSP00000406022:A628E;ENSP00000426924:A647E	ENSP00000328673:A587E	A	-	2	0	UNC5C	96346821	0.714000	0.27936	0.807000	0.32361	0.801000	0.45260	3.981000	0.56902	0.633000	0.30452	-0.300000	0.09419	GCA	G|0.998;T|0.002	0.002	strong		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
OR2L5	81466	hgsc.bcm.edu	37	1	248185883	248185883	+	Missense_Mutation	SNP	G	G	A	rs55982561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248185883G>A	ENST00000355281.1	+	1	634	c.634G>A	c.(634-636)Ggc>Agc	p.G212S	OR2L13_ENST00000366478.2_Intron	NM_001258284.1	NP_001245213.1	Q8NG80	OR2L5_HUMAN	olfactory receptor, family 2, subfamily L, member 5	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										TCCCTTCACTGGCATTGCGTG	0.502													g|||	68	0.0135783	0.0015	0.0202	5008	,	,		23093	0.0		0.0388	False		,,,				2504	0.0133				p.G212S		Atlas-SNP	.											.	.	.	.	0			c.G634A						PASS	.																																			SO:0001583	missense	81466	exon1			TTCACTGGCATTG		CCDS58068.1	1q44	2012-08-09		2004-03-10	ENSG00000197454	ENSG00000197454		"""GPCR / Class A : Olfactory receptors"""	15011	protein-coding gene	gene with protein product				OR2L11, OR2L5P			Standard	NM_001258284		Approved		uc031psy.1	Q8NG80	OTTHUMG00000040194	ENST00000355281.1:c.634G>A	1.37:g.248185883G>A	ENSP00000347428:p.Gly212Ser	Somatic	324	0	0		WXS	Illumina HiSeq	Phase_I	396	185	0.467172	NM_001258284	Q6IF04	Missense_Mutation	SNP	ENST00000355281.1	37	CCDS58068.1	39	0.017857142857142856	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	28	0.036939313984168866	.	9.956	1.221364	0.22457	.	.	ENSG00000197454	ENST00000355281	T	0.36878	1.23	2.17	-2.09	0.07232	.	0.592589	0.12695	U	0.446832	T	0.07098	0.0180	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21690	-1.0238	7	0.72032	D	0.01	.	1.3934	0.02255	0.129:0.172:0.3518:0.3472	rs55982561;rs61856392	.	.	.	S	212	ENSP00000347428:G212S	ENSP00000347428:G212S	G	+	1	0	OR2L5	246252506	0.000000	0.05858	0.000000	0.03702	0.185000	0.23345	-3.641000	0.00406	-0.407000	0.07576	0.184000	0.17185	GGC	G|0.977;A|0.023	0.023	strong		0.502	OR2L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096851.1		
PAPPA	5069	hgsc.bcm.edu	37	9	119106881	119106881	+	Missense_Mutation	SNP	C	C	A	rs7020782	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:119106881C>A	ENST00000328252.3	+	14	4040	c.3671C>A	c.(3670-3672)tCt>tAt	p.S1224Y	PAPPA_ENST00000534838.1_Missense_Mutation_p.S262Y	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1224	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.		S -> Y (in dbSNP:rs7020782). {ECO:0000269|PubMed:11822024, ECO:0000269|PubMed:15489334}.		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						GAGAATGCTTCTCTCAATTGC	0.572													C|||	2863	0.571685	0.2632	0.6412	5008	,	,		19905	0.6984		0.6918	False		,,,				2504	0.6851				p.S1224Y		Atlas-SNP	.											.	PAPPA	243	.	0			c.C3671A						PASS	.	C	TYR/SER	1489,2917	477.4+/-357.9	245,999,959	117.0	105.0	109.0		3671	2.5	0.7	9	dbSNP_116	109	6011,2589	690.1+/-404.4	2101,1809,390	yes	missense	PAPPA	NM_002581.3	144	2346,2808,1349	AA,AC,CC		30.1047,33.7948,42.3343	possibly-damaging	1224/1628	119106881	7500,5506	2203	4300	6503	SO:0001583	missense	5069	exon14			ATGCTTCTCTCAA		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.3671C>A	9.37:g.119106881C>A	ENSP00000330658:p.Ser1224Tyr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	1328	0.608058608058608	140	0.2845528455284553	236	0.6519337016574586	430	0.7517482517482518	522	0.6886543535620053	C	12.40	1.926786	0.34002	0.337948	0.698953	ENSG00000182752	ENST00000328252;ENST00000534838	T;T	0.76448	-1.02;-1.02	5.36	2.54	0.30619	Complement control module (2);Sushi/SCR/CCP (2);	0.880932	0.10291	N	0.692356	T	0.00012	0.0000	L	0.43152	1.355	0.58432	P	8.000000000008E-6	B;B	0.32188	0.023;0.359	B;B	0.27500	0.029;0.08	T	0.41324	-0.9515	9	0.72032	D	0.01	-2.5374	3.5502	0.07843	0.2668:0.4166:0.0:0.3166	rs7020782;rs52831117;rs56898212;rs7020782	262;1224	F5GZ19;Q13219	.;PAPP1_HUMAN	Y	1224;262	ENSP00000330658:S1224Y;ENSP00000441461:S262Y	ENSP00000330658:S1224Y	S	+	2	0	PAPPA	118146702	0.666000	0.27475	0.654000	0.29608	0.951000	0.60555	0.762000	0.26503	0.348000	0.23949	0.655000	0.94253	TCT	C|0.420;A|0.580	0.580	strong		0.572	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
OR56A3	390083	hgsc.bcm.edu	37	11	5969185	5969185	+	Silent	SNP	A	A	G	rs10769378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5969185A>G	ENST00000329564.6	+	1	616	c.609A>G	c.(607-609)caA>caG	p.Q203Q	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCTTTACCAATTTGCTGGAG	0.478													A|||	981	0.195887	0.0598	0.281	5008	,	,		23928	0.3016		0.2624	False		,,,				2504	0.1421				p.Q203Q		Atlas-SNP	.											OR56A3,NS,carcinoma,+2,1	OR56A3	81	1	0			c.A609G						PASS	.	A		444,3824		23,398,1713	146.0	143.0	144.0		609	-5.8	0.6	11	dbSNP_120	144	2485,6069		347,1791,2139	no	coding-synonymous	OR56A3	NM_001003443.2		370,2189,3852	GG,GA,AA		29.0507,10.403,22.8436		203/316	5969185	2929,9893	2134	4277	6411	SO:0001819	synonymous_variant	390083	exon1			TTACCAATTTGCT		CCDS41614.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184478	ENSG00000184478		"""GPCR / Class A : Olfactory receptors"""	14786	protein-coding gene	gene with protein product				OR56A6, OR56A3P			Standard	NM_001003443		Approved		uc010qzt.2	Q8NH54	OTTHUMG00000165373	ENST00000329564.6:c.609A>G	11.37:g.5969185A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	87	38	0.436782	NM_001003443	A6NN77|Q6IFF7	Silent	SNP	ENST00000329564.6	37	CCDS41614.1																																																																																			A|0.777;G|0.223	0.223	strong		0.478	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1	NM_001003443	
EP300	2033	hgsc.bcm.edu	37	22	41548008	41548008	+	Missense_Mutation	SNP	A	A	G	rs20551	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:41548008A>G	ENST00000263253.7	+	15	4208	c.2989A>G	c.(2989-2991)Att>Gtt	p.I997V		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	997			I -> V (in dbSNP:rs20551).		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						GCCGGAGGATATTTCAGAGGT	0.418			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	1119	0.223442	0.0227	0.513	5008	,	,		17915	0.0536		0.3032	False		,,,				2504	0.3824				p.I997V		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A2989G						PASS	.	A	VAL/ILE	266,4140	151.0+/-185.0	8,250,1945	100.0	105.0	103.0		2989	3.6	0.2	22	dbSNP_67	103	2411,6189	399.6+/-346.5	341,1729,2230	yes	missense	EP300	NM_001429.3	29	349,1979,4175	GG,GA,AA		28.0349,6.0372,20.5828	benign	997/2415	41548008	2677,10329	2203	4300	6503	SO:0001583	missense	2033	exon15	Familial Cancer Database	Broad Thumb-Hallux syndrome	GAGGATATTTCAG	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.2989A>G	22.37:g.41548008A>G	ENSP00000263253:p.Ile997Val	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	165	71	0.430303	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	460	0.21062271062271062	15	0.03048780487804878	181	0.5	32	0.055944055944055944	232	0.30606860158311344	A	7.139	0.581359	0.13686	0.060372	0.280349	ENSG00000100393	ENST00000263253	D	0.81996	-1.56	5.77	3.62	0.41486	.	0.552881	0.14785	N	0.298584	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	0.42649	-0.9439	9	0.27082	T	0.32	-4.794	10.2891	0.43586	0.8649:0.0:0.1351:0.0	rs20551;rs2413638;rs17349228;rs17398623;rs20551	997	Q09472	EP300_HUMAN	V	997	ENSP00000263253:I997V	ENSP00000263253:I997V	I	+	1	0	EP300	39877954	0.717000	0.27966	0.250000	0.24296	0.132000	0.20833	2.165000	0.42396	0.432000	0.26286	0.460000	0.39030	ATT	A|0.802;G|0.198	0.198	strong		0.418	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
STAB2	55576	hgsc.bcm.edu	37	12	104153004	104153004	+	Missense_Mutation	SNP	C	C	G	rs2271637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:104153004C>G	ENST00000388887.2	+	65	7405	c.7201C>G	c.(7201-7203)Ctg>Gtg	p.L2401V	RP11-341G23.4_ENST00000551299.1_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						GCAAACGAGGCTGGGAAGCAA	0.537													C|||	1629	0.32528	0.1286	0.317	5008	,	,		19970	0.5238		0.2535	False		,,,				2504	0.4663				p.L2401V		Atlas-SNP	.											.	STAB2	370	.	0			c.C7201G						PASS	.	C	VAL/LEU	641,3765	275.2+/-272.4	47,547,1609	123.0	100.0	108.0		7201	3.8	1.0	12	dbSNP_100	108	2301,6299	388.9+/-342.7	280,1741,2279	yes	missense	STAB2	NM_017564.9	32	327,2288,3888	GG,GC,CC		26.7558,14.5483,22.6203	benign	2401/2552	104153004	2942,10064	2203	4300	6503	SO:0001583	missense	55576	exon65			ACGAGGCTGGGAA	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.7201C>G	12.37:g.104153004C>G	ENSP00000373539:p.Leu2401Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	637	0.2916666666666667	53	0.10772357723577236	109	0.3011049723756906	283	0.49475524475524474	192	0.2532981530343008	C	12.05	1.822038	0.32237	0.145483	0.267558	ENSG00000136011	ENST00000388887	D	0.90620	-2.7	4.77	3.8	0.43715	FAS1 domain (4);	0.273443	0.30093	N	0.010439	T	0.00012	0.0000	M	0.78916	2.43	0.28695	P	0.9043705	P	0.47604	0.898	P	0.45167	0.472	T	0.11717	-1.0576	9	0.31617	T	0.26	.	11.0836	0.48074	0.311:0.689:0.0:0.0	rs2271637;rs52828564;rs2271637	2401	Q8WWQ8	STAB2_HUMAN	V	2401	ENSP00000373539:L2401V	ENSP00000373539:L2401V	L	+	1	2	STAB2	102677134	1.000000	0.71417	0.992000	0.48379	0.390000	0.30446	2.061000	0.41403	2.340000	0.79590	0.655000	0.94253	CTG	C|0.734;G|0.266	0.266	strong		0.537	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
PCDHB13	56123	hgsc.bcm.edu	37	5	140594466	140594466	+	Silent	SNP	G	G	A	rs17844608		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140594466G>A	ENST00000341948.4	+	1	958	c.771G>A	c.(769-771)ccG>ccA	p.P257P		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	257	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGACAGTCCGGTAGGCTTCC	0.493																																					p.P257P		Atlas-SNP	.											PCDHB13,rectum,carcinoma,+1,1	PCDHB13	142	1	0			c.G771A						scavenged	.						174.0	172.0	173.0					5																	140594466		2203	4300	6503	SO:0001819	synonymous_variant	56123	exon1			CAGTCCGGTAGGC	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.771G>A	5.37:g.140594466G>A		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	242	19	0.0785124	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			.	.	weak		0.493	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
ANKRD50	57182	hgsc.bcm.edu	37	4	125591423	125591423	+	Silent	SNP	A	A	T	rs3822116	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:125591423A>T	ENST00000504087.1	-	4	4046	c.3009T>A	c.(3007-3009)gcT>gcA	p.A1003A	ANKRD50_ENST00000515641.1_Silent_p.A824A	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1003										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						CATTGACGTCAGCATGGTATG	0.498													A|||	219	0.04373	0.0204	0.036	5008	,	,		22515	0.0129		0.0924	False		,,,				2504	0.0624				p.A1003A		Atlas-SNP	.											.	ANKRD50	136	.	0			c.T3009A						PASS	.	A	,	130,4276	94.4+/-133.1	0,130,2073	86.0	70.0	76.0		2472,3009	-8.8	0.2	4	dbSNP_107	76	662,7938	167.7+/-219.4	30,602,3668	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	30,732,5741	TT,TA,AA		7.6977,2.9505,6.0895	,	824/1251,1003/1430	125591423	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			GACGTCAGCATGG	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.3009T>A	4.37:g.125591423A>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	111	57	0.513514	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			A|0.940;T|0.060	0.060	strong		0.498	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
Unknown	0	hgsc.bcm.edu	37	17	17326363	17326363	+	IGR	SNP	G	G	A	rs35590625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:17326363G>A								NT5M (75388 upstream) : Y_RNA (37394 downstream)																							AGCTTTGAGTGTTCTTCGAAG	0.458													G|||	1288	0.257188	0.354	0.1744	5008	,	,		24040	0.1647		0.2555	False		,,,				2504	0.2822				p.V60I		Atlas-SNP	.											.	.	.	.	0			c.G178A						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			TTGAGTGTTCTTC																													17.37:g.17326363G>A		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	27	11	0.407407	NM_001243312		Missense_Mutation	SNP		37																																																																																				G|0.747;A|0.253	0.253	strong	0	0.458								
TGM3	7053	hgsc.bcm.edu	37	20	2297790	2297790	+	Missense_Mutation	SNP	G	G	A	rs214814	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:2297790G>A	ENST00000381458.5	+	6	809	c.746G>A	c.(745-747)aGc>aAc	p.S249N	TGM3_ENST00000463090.1_3'UTR	NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	249			S -> N (in dbSNP:rs214814). {ECO:0000269|Ref.3}.		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	GACCCAAGGAGCTGGAACGGC	0.547													A|||	560	0.111821	0.2126	0.0778	5008	,	,		19822	0.0685		0.1103	False		,,,				2504	0.046				p.S249N		Atlas-SNP	.											.	TGM3	105	.	0			c.G746A						PASS	.	A	ASN/SER	881,3525	742.4+/-411.4	84,713,1406	86.0	94.0	92.0		746	-0.4	1.0	20	dbSNP_79	92	992,7608	773.7+/-407.7	59,874,3367	yes	missense	TGM3	NM_003245.3	46	143,1587,4773	AA,AG,GG		11.5349,19.9955,14.401	benign	249/694	2297790	1873,11133	2203	4300	6503	SO:0001583	missense	7053	exon6			CAAGGAGCTGGAA	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"""Transglutaminases"""	11779	protein-coding gene	gene with protein product	"""E polypeptide, protein-glutamine-gamma-glutamyltransferase"""	600238	"""transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.746G>A	20.37:g.2297790G>A	ENSP00000370867:p.Ser249Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	49	23	0.469388	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	278	0.12728937728937728	114	0.23170731707317074	32	0.08839779005524862	47	0.08216783216783216	85	0.11213720316622691	A	1.560	-0.537040	0.04082	0.199955	0.115349	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.88818	-2.43	5.6	-0.391	0.12446	.	0.775169	0.12745	N	0.442732	T	0.00073	0.0002	N	0.16266	0.395	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.03278	-1.1053	9	0.17832	T	0.49	.	1.7939	0.03057	0.3242:0.3407:0.2191:0.116	rs214814;rs57982162;rs214814	249	Q08188	TGM3_HUMAN	N	249	ENSP00000370867:S249N	ENSP00000370867:S249N	S	+	2	0	TGM3	2245790	0.000000	0.05858	0.991000	0.47740	0.616000	0.37450	0.122000	0.15687	-0.342000	0.08363	-0.332000	0.08345	AGC	G|0.863;A|0.136	0.136	strong		0.547	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245	
MDN1	23195	hgsc.bcm.edu	37	6	90482397	90482397	+	Missense_Mutation	SNP	T	T	C	rs12110451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90482397T>C	ENST00000369393.3	-	14	2093	c.1978A>G	c.(1978-1980)Atc>Gtc	p.I660V	MDN1_ENST00000428876.1_Missense_Mutation_p.I660V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	660			I -> V (in dbSNP:rs12110451).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGCTGCTCGATGAGAACAGAG	0.512													T|||	822	0.164137	0.1793	0.1398	5008	,	,		16706	0.2163		0.1809	False		,,,				2504	0.09				p.I660V		Atlas-SNP	.											.	MDN1	478	.	0			c.A1978G						PASS	.	T	VAL/ILE	848,3558	333.3+/-302.9	87,674,1442	107.0	110.0	109.0		1978	4.5	1.0	6	dbSNP_120	109	1539,7061	290.5+/-299.9	142,1255,2903	yes	missense	MDN1	NM_014611.1	29	229,1929,4345	CC,CT,TT		17.8953,19.2465,18.3531	benign	660/5597	90482397	2387,10619	2203	4300	6503	SO:0001583	missense	23195	exon14			GCTCGATGAGAAC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1978A>G	6.37:g.90482397T>C	ENSP00000358400:p.Ile660Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	65	50	0.769231	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	410	0.18772893772893773	93	0.18902439024390244	46	0.1270718232044199	127	0.22202797202797203	144	0.18997361477572558	T	11.71	1.718341	0.30503	0.192465	0.178953	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.40476	1.03;1.03;1.03	5.65	4.47	0.54385	.	0.212692	0.41605	D	0.000848	T	0.12135	0.0295	N	0.11201	0.11	0.35477	P	0.20219200000000004	B;B	0.18610	0.007;0.029	B;B	0.20384	0.011;0.029	T	0.04855	-1.0922	9	0.62326	D	0.03	.	11.8001	0.52122	0.0:0.0:0.2879:0.7121	rs12110451;rs52821586;rs60532094;rs12110451	587;660	Q5T795;Q9NU22	.;MDN1_HUMAN	V	660;660;587	ENSP00000358400:I660V;ENSP00000413970:I660V;ENSP00000409664:I587V	ENSP00000358400:I660V	I	-	1	0	MDN1	90539118	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.720000	0.47252	0.953000	0.37825	0.528000	0.53228	ATC	T|0.817;C|0.183	0.183	strong		0.512	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
PLIN4	729359	hgsc.bcm.edu	37	19	4511746	4511746	+	Missense_Mutation	SNP	A	A	T	rs62115192		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4511746A>T	ENST00000301286.3	-	3	2183	c.2184T>A	c.(2182-2184)aaT>aaA	p.N728K		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	728	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CTTTGGCCACATTCGCAGCAC	0.577																																					p.N728K		Atlas-SNP	.											.	PLIN4	191	.	0			c.T2184A						PASS	.						148.0	134.0	138.0					19																	4511746		2024	4170	6194	SO:0001583	missense	729359	exon3			GGCCACATTCGCA	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2184T>A	19.37:g.4511746A>T	ENSP00000301286:p.Asn728Lys	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	227	42	0.185022	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	a	14.30	2.495348	0.44352	.	.	ENSG00000167676	ENST00000301286	T	0.05382	3.45	4.56	-9.13	0.00704	.	0.915443	0.08968	N	0.867615	T	0.13415	0.0325	M	0.82323	2.585	0.80722	P	0.0	P	0.52316	0.952	P	0.53649	0.731	T	0.00557	-1.1672	9	0.36615	T	0.2	-4.9999	8.1871	0.31346	0.2655:0.0976:0.541:0.0959	rs62115192	728	Q96Q06	PLIN4_HUMAN	K	728	ENSP00000301286:N728K	ENSP00000301286:N728K	N	-	3	2	PLIN4	4462746	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.931000	0.00169	-2.908000	0.00309	-1.193000	0.01689	AAT	A|0.333;T|0.667	0.667	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
ZNF155	7711	hgsc.bcm.edu	37	19	44496070	44496070	+	Silent	SNP	A	A	G	rs431509	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44496070A>G	ENST00000270014.2	+	4	347	c.219A>G	c.(217-219)caA>caG	p.Q73Q	ZNF155_ENST00000590615.1_Silent_p.Q73Q|ZNF155_ENST00000407951.2_Silent_p.Q84Q	NM_001260487.1|NM_198089.2	NP_001247416|NP_932355	Q12901	ZN155_HUMAN	zinc finger protein 155	73	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	15		Prostate(69;0.0352)				CAGCAACCCAAAGAGAAGGGA	0.478													A|||	2257	0.450679	0.5575	0.4942	5008	,	,		21633	0.5466		0.2893	False		,,,				2504	0.3425				p.Q84Q	NSCLC(61;554 1277 20909 42067 42312)	Atlas-SNP	.											.	ZNF155	30	.	0			c.A252G						PASS	.	A	,	2295,2111	601.2+/-389.7	607,1081,515	149.0	149.0	149.0		219,219	-2.0	0.1	19	dbSNP_80	149	2443,6157	403.2+/-347.7	355,1733,2212	no	coding-synonymous,coding-synonymous	ZNF155	NM_003445.2,NM_198089.1	,	962,2814,2727	GG,GA,AA		28.407,47.9119,36.4293	,	73/539,73/539	44496070	4738,8268	2203	4300	6503	SO:0001819	synonymous_variant	7711	exon5			AACCCAAAGAGAA	U09852	CCDS12634.1, CCDS58668.1	19q13.2-q13.32	2013-01-08	2006-08-22			ENSG00000204920		"""Zinc fingers, C2H2-type"", ""-"""	12940	protein-coding gene	gene with protein product		604086	"""zinc finger protein 155 (pHZ-96)"""			7557990	Standard	NM_001260486		Approved	pHZ-96	uc010xwt.2	Q12901		ENST00000270014.2:c.219A>G	19.37:g.44496070A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_001260488	A2BDE6|B2RB63|B4DM95|J3KQ08|Q6AZZ8|Q9UIE1|Q9UK14	Silent	SNP	ENST00000270014.2	37	CCDS12634.1																																																																																			A|0.624;G|0.376	0.376	strong		0.478	ZNF155-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460074.1	NM_003445	
ARHGEF39	84904	hgsc.bcm.edu	37	9	35662251	35662251	+	Missense_Mutation	SNP	T	T	C	rs2297879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35662251T>C	ENST00000378387.3	-	8	1034	c.917A>G	c.(916-918)cAt>cGt	p.H306R	ARHGEF39_ENST00000490970.1_5'UTR|ARHGEF39_ENST00000343259.3_Silent_p.S186S|ARHGEF39_ENST00000378395.2_Missense_Mutation_p.H270R	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	306	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		H -> R (in dbSNP:rs2297879).		positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)										TAGCTTCTCATGAGGGAAGGA	0.527													T|||	1531	0.305711	0.0628	0.3545	5008	,	,		20777	0.503		0.325	False		,,,				2504	0.3763				p.H306R		Atlas-SNP	.											.	.	.	.	0			c.A917G						PASS	.	T	ARG/HIS	531,3875	240.9+/-251.5	36,459,1708	112.0	98.0	103.0		917	2.4	0.2	9	dbSNP_100	103	2729,5871	436.5+/-358.3	426,1877,1997	yes	missense	C9orf100	NM_032818.2	29	462,2336,3705	CC,CT,TT		31.7326,12.0517,25.0654	benign	306/336	35662251	3260,9746	2203	4300	6503	SO:0001583	missense	84904	exon8			TTCTCATGAGGGA	AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135			25909	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 100"""	C9orf100		22327280	Standard	XR_242516		Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.917A>G	9.37:g.35662251T>C	ENSP00000367638:p.His306Arg	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	117	61	0.521368	NM_032818	Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation	SNP	ENST00000378387.3	37	CCDS6584.2	724	0.3315018315018315	49	0.09959349593495935	136	0.3756906077348066	285	0.4982517482517482	254	0.33509234828496043	T	5.983	0.365374	0.11352	0.120517	0.317326	ENSG00000137135	ENST00000378387;ENST00000378395	T;T	0.41065	1.01;1.01	5.97	2.39	0.29439	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.34399	P	0.304968	B	0.02656	0.0	B	0.01281	0.0	T	0.47971	-0.9075	8	0.13853	T	0.58	-7.3161	7.5244	0.27647	0.0:0.2434:0.0:0.7566	rs2297879;rs58265228;rs2297879	306	Q8N4T4	CI100_HUMAN	R	306;270	ENSP00000367638:H306R;ENSP00000367648:H270R	ENSP00000367638:H306R	H	-	2	0	C9orf100	35652251	0.163000	0.22920	0.163000	0.22734	0.974000	0.67602	0.418000	0.21230	0.169000	0.19679	-0.250000	0.11733	CAT	T|0.720;C|0.280	0.280	strong		0.527	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818	
ING3	54556	hgsc.bcm.edu	37	7	120610901	120610901	+	Silent	SNP	C	C	T	rs2525725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:120610901C>T	ENST00000315870.5	+	10	1216	c.1068C>T	c.(1066-1068)gaC>gaT	p.D356D	ING3_ENST00000431467.1_Silent_p.D341D	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	356					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					GGACTTACGACCCAAATGAAC	0.338													C|||	699	0.139577	0.2118	0.1095	5008	,	,		17479	0.0337		0.2127	False		,,,				2504	0.0971				p.D356D		Atlas-SNP	.											.	ING3	36	.	0			c.C1068T						PASS	.	C		930,3476	353.8+/-312.3	90,750,1363	86.0	75.0	78.0		1068	5.2	1.0	7	dbSNP_100	78	1718,6882	312.9+/-311.0	165,1388,2747	no	coding-synonymous	ING3	NM_019071.2		255,2138,4110	TT,TC,CC		19.9767,21.1076,20.3598		356/419	120610901	2648,10358	2203	4300	6503	SO:0001819	synonymous_variant	54556	exon10			TTACGACCCAAAT	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"""Zinc fingers, PHD-type"""	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.1068C>T	7.37:g.120610901C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	Silent	SNP	ENST00000315870.5	37	CCDS5778.1																																																																																			C|0.812;A|0.001	.	strong		0.338	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071	
FLG	2312	hgsc.bcm.edu	37	1	152281142	152281142	+	Missense_Mutation	SNP	C	C	G	rs141120727	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152281142C>G	ENST00000368799.1	-	3	6255	c.6220G>C	c.(6220-6222)Gag>Cag	p.E2074Q	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2074	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CGTGCGGACTCTTTGTGGCTC	0.557									Ichthyosis				-|||	13	0.00259585	0.0	0.0014	5008	,	,		29807	0.0		0.0089	False		,,,				2504	0.0031				p.E2074Q		Atlas-SNP	.											FLG,NS,lymphoid_neoplasm,0,1	FLG	900	1	0			c.G6220C						PASS	.	C	GLN/GLU	13,4393	20.2+/-43.8	0,13,2190	328.0	270.0	290.0		6220	-4.2	0.0	1	dbSNP_134	290	101,8499	57.2+/-118.5	2,97,4201	no	missense	FLG	NM_002016.1	29	2,110,6391	GG,GC,CC		1.1744,0.2951,0.8765	benign	2074/4062	152281142	114,12892	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGGACTCTTTGTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6220G>C	1.37:g.152281142C>G	ENSP00000357789:p.Glu2074Gln	Somatic	388	0	0		WXS	Illumina HiSeq	Phase_I	297	150	0.50505	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	c	4.095	0.015596	0.07959	0.002951	0.011744	ENSG00000143631	ENST00000368799	T	0.01685	4.69	2.33	-4.18	0.03846	.	.	.	.	.	T	0.00724	0.0024	M	0.75447	2.3	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.42155	-0.9468	9	0.18276	T	0.48	.	7.3479	0.26674	0.0:0.2262:0.6352:0.1386	.	2074	P20930	FILA_HUMAN	Q	2074	ENSP00000357789:E2074Q	ENSP00000357789:E2074Q	E	-	1	0	FLG	150547766	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.212000	0.09319	-0.825000	0.04290	-0.494000	0.04653	GAG	C|0.993;G|0.007	0.007	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
BOC	91653	hgsc.bcm.edu	37	3	112991959	112991959	+	Silent	SNP	C	C	T	rs11710894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112991959C>T	ENST00000495514.1	+	8	1709	c.1005C>T	c.(1003-1005)ccC>ccT	p.P335P	BOC_ENST00000273395.4_Silent_p.P335P|BOC_ENST00000355385.3_Silent_p.P335P			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	335	Ig-like C2-type 4.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGGTCATCCCCTGGGGCCAGA	0.637													C|||	1496	0.298722	0.2231	0.3948	5008	,	,		18599	0.4107		0.1998	False		,,,				2504	0.319				p.P335P		Atlas-SNP	.											.	BOC	139	.	0			c.C1005T						PASS	.	C		976,3430	367.1+/-318.1	110,756,1337	73.0	72.0	73.0		1005	-8.1	0.5	3	dbSNP_120	73	1488,7112	281.8+/-295.3	138,1212,2950	no	coding-synonymous	BOC	NM_033254.2		248,1968,4287	TT,TC,CC		17.3023,22.1516,18.9451		335/1115	112991959	2464,10542	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon8			CATCCCCTGGGGC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1005C>T	3.37:g.112991959C>T		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.773;T|0.227	0.227	strong		0.637	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
SAMSN1	64092	hgsc.bcm.edu	37	21	15954593	15954593	+	Missense_Mutation	SNP	G	G	A	rs2822786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:15954593G>A	ENST00000285670.2	-	2	299	c.125C>T	c.(124-126)cCt>cTt	p.P42L	SAMSN1-AS1_ENST00000449214.1_RNA	NM_001256370.1	NP_001243299.1	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	0					negative regulation of adaptive immune response (GO:0002820)|negative regulation of B cell activation (GO:0050869)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)	cell projection (GO:0042995)|cytosol (GO:0005829)|nucleus (GO:0005634)	phosphotyrosine binding (GO:0001784)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	24				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.00118)|Colorectal(24;0.00961)|Lung(58;0.164)		TTCAGGAAAAGGCTTCCAGTG	0.453													G|||	1159	0.23143	0.0212	0.3156	5008	,	,		18614	0.2679		0.341	False		,,,				2504	0.3057				p.P42L		Atlas-SNP	.											.	SAMSN1	112	.	0			c.C125T						PASS	.																																			SO:0001583	missense	64092	exon2			GGAAAAGGCTTCC	AF222927	CCDS42906.1, CCDS58786.1, CCDS74774.1	21q11	2013-01-10	2006-12-13		ENSG00000155307	ENSG00000155307		"""SAM and SH3 domain containing"", ""Sterile alpha motif (SAM) domain containing"""	10528	protein-coding gene	gene with protein product	"""nuclear localization signals, SAM and SH3 domain containing 1"", ""SAM and SH3 domain containing 2"", ""hematopoietic adapter-containing SH3 and sterile &#945;-motif (SAM) domains 1"", ""Src homology domain 3 (SH3)-containing adapter protein SH3 lymphocyte protein 2"""	607978				11536050, 11594764	Standard	NM_022136		Approved	NASH1, SASH2, SH3D6B, HACS1, SLy2	uc002yjv.1	Q9NSI8	OTTHUMG00000074317	ENST00000285670.2:c.125C>T	21.37:g.15954593G>A	ENSP00000285670:p.Pro42Leu	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000285670.2	37	CCDS58786.1	544	0.2490842490842491	22	0.044715447154471545	100	0.27624309392265195	168	0.2937062937062937	254	0.33509234828496043	G	12.34	1.908162	0.33721	.	.	ENSG00000155307	ENST00000285670	T	0.43688	0.94	5.87	1.88	0.25563	.	0.804248	0.10751	N	0.638314	T	0.00012	0.0000	.	.	.	0.51767	P	6.499999999998174E-5	B	0.12013	0.005	B	0.12156	0.007	T	0.29336	-1.0015	8	0.87932	D	0	.	10.0958	0.42475	0.0612:0.0:0.5892:0.3496	rs2822786;rs17274360;rs52820672;rs58195465;rs2822786	42	F8WAA1	.	L	42	ENSP00000285670:P42L	ENSP00000285670:P42L	P	-	2	0	SAMSN1	14876464	0.000000	0.05858	0.013000	0.15412	0.514000	0.34195	0.579000	0.23788	0.125000	0.18397	0.655000	0.94253	CCT	G|0.766;A|0.234	0.234	strong		0.453	SAMSN1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157913.1		
RNF6	6049	hgsc.bcm.edu	37	13	26788114	26788114	+	Silent	SNP	A	A	G	rs301047	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:26788114A>G	ENST00000381588.4	-	5	2657	c.1905T>C	c.(1903-1905)tgT>tgC	p.C635C	RNF6_ENST00000346166.3_Silent_p.C635C|RNF6_ENST00000381570.3_Silent_p.C635C|RNF6_ENST00000468480.1_Intron|RNF6_ENST00000399762.2_Silent_p.C279C	NM_005977.3	NP_005968.1	Q9Y252	RNF6_HUMAN	ring finger protein (C3H2C3 type) 6	635	Required for polyubiquitination. {ECO:0000250}.				negative regulation of axon extension (GO:0030517)|positive regulation of transcription, DNA-templated (GO:0045893)|protein K27-linked ubiquitination (GO:0044314)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(9)|lung(3)|ovary(2)|prostate(2)|skin(2)	23	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.00893)|Epithelial(112;0.0481)|OV - Ovarian serous cystadenocarcinoma(117;0.148)|GBM - Glioblastoma multiforme(144;0.23)|Lung(94;0.245)		AGTCACTAATACAAACACTAC	0.383													A|||	950	0.189696	0.3003	0.0951	5008	,	,		19386	0.1141		0.164	False		,,,				2504	0.2117				p.C635C		Atlas-SNP	.											.	RNF6	68	.	0			c.T1905C						PASS	.	A	,,	1235,3171	427.6+/-341.6	188,859,1156	156.0	145.0	149.0		1905,1905,1905	-7.7	0.7	13	dbSNP_79	149	1545,7055	291.2+/-300.2	137,1271,2892	no	coding-synonymous,coding-synonymous,coding-synonymous	RNF6	NM_005977.3,NM_183043.2,NM_183044.2	,,	325,2130,4048	GG,GA,AA		17.9651,28.03,21.3748	,,	635/686,635/686,635/686	26788114	2780,10226	2203	4300	6503	SO:0001819	synonymous_variant	6049	exon5			ACTAATACAAACA	AJ010346	CCDS9316.1	13q12.2	2013-01-09			ENSG00000127870	ENSG00000127870		"""RING-type (C3HC4) zinc fingers"""	10069	protein-coding gene	gene with protein product	"""RING-H2 protein RNF-6"""	604242				10331950	Standard	NM_005977		Approved	DKFZp686P0776	uc001uqq.3	Q9Y252	OTTHUMG00000016614	ENST00000381588.4:c.1905T>C	13.37:g.26788114A>G		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	163	81	0.496933	NM_183043	B4DDP0|Q5W0H0|Q9BZP5|Q9UF41	Silent	SNP	ENST00000381588.4	37	CCDS9316.1																																																																																			A|0.796;G|0.204	0.204	strong		0.383	RNF6-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044246.2	NM_005977	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592284	1592284	+	Intron	SNP	G	G	A	rs1135196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1592284G>A	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Missense_Mutation_p.T51I|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Missense_Mutation_p.T51I|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GCAGTGCAGAGTGGCCGACTC	0.552													g|||	3350	0.66893	0.739	0.5331	5008	,	,		8196	0.7669		0.5318	False		,,,				2504	0.7106				p.T51I		Atlas-SNP	.											.	SIRPB1	83	.	0			c.C152T						PASS	.						59.0	67.0	65.0					20																	1592284		446	1337	1783	SO:0001627	intron_variant	10326	exon2			TGCAGAGTGGCCG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8230C>T	20.37:g.1592284G>A		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	39	38	0.974359	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	1306	0.597985347985348	353	0.717479674796748	188	0.5193370165745856	406	0.7097902097902098	359	0.4736147757255937	.	14.38	2.519337	0.44866	.	.	ENSG00000101307	ENST00000279477;ENST00000381596	T	0.02890	4.12	2.61	1.63	0.23807	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	M	0.70275	2.135	0.09310	P	0.99999999105145	P	0.49862	0.929	P	0.58077	0.832	T	0.10177	-1.0641	8	0.59425	D	0.04	.	5.1542	0.15027	0.1762:0.0:0.8238:0.0	rs1135196;rs3197727	51	Q5TFQ8	SIRBL_HUMAN	I	51	ENSP00000279477:T51I	ENSP00000279477:T51I	T	-	2	0	SIRPB1	1540284	0.961000	0.32948	0.830000	0.32933	0.019000	0.09904	0.679000	0.25291	0.406000	0.25560	0.205000	0.17691	ACT	G|0.420;A|0.580	0.580	strong		0.552	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
EEF2	1938	hgsc.bcm.edu	37	19	3983184	3983184	+	Silent	SNP	A	A	G	rs2230560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:3983184A>G	ENST00000309311.6	-	3	412	c.324T>C	c.(322-324)caT>caC	p.H108H	SNORD37_ENST00000384048.1_RNA|EEF2_ENST00000600720.1_5'Flank	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	108	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)	p.H108H(1)		endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		AGAAGTCGACATGCCCGGGGG	0.592													G|||	1280	0.255591	0.6566	0.1009	5008	,	,		19536	0.0615		0.1034	False		,,,				2504	0.18				p.H108H	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											EEF2,NS,carcinoma,0,2	EEF2	57	2	1	Substitution - coding silent(1)	stomach(1)	c.T324C						scavenged	.	G		2482,1924	546.6+/-377.1	709,1064,430	109.0	108.0	109.0		324	-2.8	0.1	19	dbSNP_98	109	846,7754	780.5+/-407.7	37,772,3491	no	coding-synonymous	EEF2	NM_001961.3		746,1836,3921	GG,GA,AA		9.8372,43.6677,25.5882		108/859	3983184	3328,9678	2203	4300	6503	SO:0001819	synonymous_variant	1938	exon3			GTCGACATGCCCG	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.324T>C	19.37:g.3983184A>G		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_001961	B2RMP5|D6W618|Q58J86	Silent	SNP	ENST00000309311.6	37	CCDS12117.1																																																																																			T|0.000;G|0.239;C|0.000;A|0.760	0.239	strong		0.592	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
OTOF	9381	hgsc.bcm.edu	37	2	26739423	26739423	+	Silent	SNP	T	T	C	rs11687696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26739423T>C	ENST00000272371.2	-	5	498	c.372A>G	c.(370-372)acA>acG	p.T124T	OTOF_ENST00000403946.3_Silent_p.T124T	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	124					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGAGCCCACTGTGCCGTCAG	0.627													T|||	1279	0.255391	0.0272	0.2536	5008	,	,		18921	0.5248		0.3012	False		,,,				2504	0.2403				p.T124T	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.A372G						PASS	.	T		337,4069	176.6+/-205.7	16,305,1882	70.0	67.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	372	-9.7	0.0	2	dbSNP_120	68	2429,6171	399.4+/-346.4	318,1793,2189	no	coding-synonymous	OTOF	NM_194248.2		334,2098,4071	CC,CT,TT		28.2442,7.6487,21.2671		124/1998	26739423	2766,10240	2203	4300	6503	SO:0001819	synonymous_variant	9381	exon5			GCCCACTGTGCCG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.372A>G	2.37:g.26739423T>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	28	14	0.5	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			T|0.761;C|0.239	0.239	strong		0.627	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
OR13C9	286362	hgsc.bcm.edu	37	9	107380414	107380414	+	Missense_Mutation	SNP	C	C	A	rs2900373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107380414C>A	ENST00000259362.1	-	1	71	c.72G>T	c.(70-72)gaG>gaT	p.E24D		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	24			E -> D (in dbSNP:rs2900373).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAAAGAGTAACTCAAGCCTTG	0.403													C|||	2138	0.426917	0.6142	0.2262	5008	,	,		18141	0.5754		0.1779	False		,,,				2504	0.4192				p.E24D		Atlas-SNP	.											.	OR13C9	42	.	0			c.G72T						PASS	.	C	ASP/GLU	2419,1987	617.9+/-393.1	668,1083,452	127.0	125.0	125.0		72	3.9	1.0	9	dbSNP_101	125	1664,6936	306.9+/-308.1	183,1298,2819	no	missense	OR13C9	NM_001001956.1	45	851,2381,3271	AA,AC,CC		19.3488,45.0976,31.3932	possibly-damaging	24/319	107380414	4083,8923	2203	4300	6503	SO:0001583	missense	286362	exon1			GAGTAACTCAAGC		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.72G>T	9.37:g.107380414C>A	ENSP00000259362:p.Glu24Asp	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	264	123	0.465909	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	826	0.3782051282051282	284	0.5772357723577236	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	C	11.21	1.571963	0.28092	0.549024	0.193488	ENSG00000136839	ENST00000259362	T	0.01092	5.35	4.79	3.89	0.44902	.	0.134094	0.33753	N	0.004592	T	0.00012	0.0000	M	0.69358	2.11	0.58432	P	1.0000000000287557E-6	B	0.28971	0.229	B	0.25614	0.062	T	0.10941	-1.0608	9	0.87932	D	0	.	10.9252	0.47187	0.0:0.9082:0.0:0.0918	rs2900373;rs56843910;rs2900373	24	Q8NGT0	O13C9_HUMAN	D	24	ENSP00000259362:E24D	ENSP00000259362:E24D	E	-	3	2	OR13C9	106420235	0.557000	0.26546	0.982000	0.44146	0.622000	0.37654	1.318000	0.33643	1.236000	0.43740	0.573000	0.79308	GAG	A|0.365;C|0.635	0.365	strong		0.403	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
NSA2	10412	hgsc.bcm.edu	37	5	74069863	74069863	+	Silent	SNP	A	A	G	rs6874609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:74069863A>G	ENST00000296802.5	+	5	1062	c.693A>G	c.(691-693)acA>acG	p.T231T		NM_014886.3	NP_055701.1	O95478	NSA2_HUMAN	NSA2 ribosome biogenesis homolog (S. cerevisiae)	231					rRNA processing (GO:0006364)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|skin(1)	7						GCCTTGTGACACAAGGAGGCA	0.378													G|||	1907	0.380791	0.7481	0.3357	5008	,	,		16898	0.2063		0.2416	False		,,,				2504	0.2393				p.T231T		Atlas-SNP	.											NSA2,NS,carcinoma,+1,1	NSA2	18	1	0			c.A693G						scavenged	.	G		2961,1445	466.6+/-354.6	1000,961,242	96.0	92.0	94.0		693	-3.0	1.0	5	dbSNP_116	94	1912,6688	726.4+/-406.6	204,1504,2592	yes	coding-synonymous	NSA2	NM_014886.3		1204,2465,2834	GG,GA,AA		22.2326,32.7962,37.4673		231/261	74069863	4873,8133	2203	4300	6503	SO:0001819	synonymous_variant	10412	exon5			TGTGACACAAGGA	AF077615	CCDS4025.1, CCDS75260.1	5q13.3	2010-01-18			ENSG00000164346	ENSG00000164346			30728	protein-coding gene	gene with protein product	"""hairy cell leukemia protein 1"", ""TGF beta-inducible nuclear protein 1"""	612497				11124703, 10486207	Standard	NM_014886		Approved	HUSSY-29, HCLG1, FLJ94393, TINP1	uc003kdk.2	O95478	OTTHUMG00000131273	ENST00000296802.5:c.693A>G	5.37:g.74069863A>G		Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_014886		Silent	SNP	ENST00000296802.5	37	CCDS4025.1																																																																																			A|0.624;G|0.376	0.376	strong		0.378	NSA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254041.3	NM_014886	
BTN1A1	696	hgsc.bcm.edu	37	6	26501897	26501897	+	Silent	SNP	T	T	C	rs1321479	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26501897T>C	ENST00000244513.6	+	2	225	c.159T>C	c.(157-159)tcT>tcC	p.S53S		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	53	Ig-like V-type 1.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						GTCGCCTGTCTCCGAACGCGA	0.657													C|||	2834	0.565895	0.5136	0.5879	5008	,	,		14855	0.7312		0.4423	False		,,,				2504	0.5777				p.S53S		Atlas-SNP	.											BTN1A1,colon,carcinoma,0,1	BTN1A1	68	1	0			c.T159C						PASS	.	C		2285,2117		600,1085,516	34.0	36.0	35.0		159	1.6	0.0	6	dbSNP_88	35	4004,4584		990,2024,1280	no	coding-synonymous	BTN1A1	NM_001732.2		1590,3109,1796	CC,CT,TT		46.6232,48.0918,48.4142		53/527	26501897	6289,6701	2201	4294	6495	SO:0001819	synonymous_variant	696	exon2			CCTGTCTCCGAAC	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.159T>C	6.37:g.26501897T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Silent	SNP	ENST00000244513.6	37	CCDS4614.1																																																																																			T|0.485;C|0.515	0.515	strong		0.657	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67242087	67242087	+	Splice_Site	SNP	G	G	A	rs3816989	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:67242087G>A	ENST00000282670.2	+	4	464		c.e4+1			NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1											large_intestine(2)|lung(10)|skin(1)	13						CATTTCTGAGGTACGTGTGTG	0.368													G|||	654	0.130591	0.0794	0.1009	5008	,	,		17193	0.1488		0.1511	False		,,,				2504	0.181				.		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.336+1G>A						PASS	.	G		366,4040	185.7+/-212.7	18,330,1855	94.0	93.0	94.0			5.9	1.0	1	dbSNP_107	94	1187,7413	241.5+/-271.8	84,1019,3197	yes	splice-5	TCTEX1D1	NM_152665.2		102,1349,5052	AA,AG,GG		13.8023,8.3069,11.9406			67242087	1553,11453	2203	4300	6503	SO:0001630	splice_region_variant	200132	exon4			TCTGAGGTACGTG	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.336+1G>A	1.37:g.67242087G>A		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	184	94	0.51087	NM_152665	Q06YR9|Q5VYE1	Splice_Site	SNP	ENST00000282670.2	37	CCDS633.1	264	0.12087912087912088	35	0.07113821138211382	42	0.11602209944751381	82	0.14335664335664336	105	0.13852242744063326	G	18.01	3.528188	0.64860	0.083069	0.138023	ENSG00000152760	ENST00000282670	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.0921	0.93231	0.0:0.0:1.0:0.0	rs3816989;rs12748193;rs3816989	.	.	.	.	-1	.	.	.	+	.	.	TCTEX1D1	67014675	1.000000	0.71417	0.999000	0.59377	0.672000	0.39443	8.439000	0.90308	2.809000	0.96659	0.655000	0.94253	.	G|0.879;A|0.121	0.121	strong		0.368	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665	Intron
CTBP2	1488	hgsc.bcm.edu	37	10	126714714	126714714	+	Intron	SNP	G	G	C	rs2946994	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:126714714G>C	ENST00000337195.5	-	3	458				CTBP2_ENST00000531469.1_Intron|CTBP2_ENST00000309035.6_Missense_Mutation_p.Q539E|CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000494626.2_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)		GCCACCTTCTGGTACGGTGAG	0.672													G|||	2342	0.467652	0.3744	0.3357	5008	,	,		13550	0.6607		0.4761	False		,,,				2504	0.4796				p.Q539E		Atlas-SNP	.											CTBP2,colon,carcinoma,0,1	CTBP2	100	1	0			c.C1615G						scavenged	.	G	,,GLU/GLN	1695,2711	500.0+/-364.6	309,1077,817	83.0	84.0	84.0		,,1615	5.3	1.0	10	dbSNP_101	84	4263,4337	562.6+/-388.0	1050,2163,1087	yes	intron,intron,missense	CTBP2	NM_001083914.1,NM_001329.2,NM_022802.2	,,29	1359,3240,1904	CC,CG,GG		49.5698,38.4703,45.8096	,,benign	,,539/986	126714714	5958,7048	2203	4300	6503	SO:0001627	intron_variant	1488	exon1			CCTTCTGGTACGG	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+12851C>G	10.37:g.126714714G>C		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	129	63	0.488372	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Missense_Mutation	SNP	ENST00000337195.5	37	CCDS7643.1	1030	0.4716117216117216	192	0.3902439024390244	124	0.3425414364640884	353	0.6171328671328671	361	0.4762532981530343	G	17.74	3.464348	0.63513	0.384703	0.495698	ENSG00000175029	ENST00000309035	D	0.83419	-1.72	5.29	5.29	0.74685	.	0.768853	0.11608	N	0.547098	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	P	0.49559	0.925	P	0.46339	0.513	T	0.48559	-0.9025	8	0.49607	T	0.09	.	19.3229	0.94250	0.0:0.0:1.0:0.0	rs2946994;rs17710501;rs58027090;rs2946994	539	P56545-2	.	E	539	ENSP00000311825:Q539E	ENSP00000311825:Q539E	Q	-	1	0	CTBP2	126704704	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.729000	0.98795	2.642000	0.89623	0.591000	0.81541	CAG	G|0.533;C|0.467	0.467	strong		0.672	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
TMC4	147798	hgsc.bcm.edu	37	19	54675643	54675643	+	Missense_Mutation	SNP	G	G	A	rs77215230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54675643G>A	ENST00000376591.4	-	2	438	c.307C>T	c.(307-309)Cac>Tac	p.H103Y	TMC4_ENST00000476013.2_5'UTR|TMC4_ENST00000301187.4_Missense_Mutation_p.H97Y	NM_001145303.1|NM_144686.2	NP_001138775|NP_653287.2	Q7Z404	TMC4_HUMAN	transmembrane channel-like 4	103					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)					CCTCACCTGTGTGCCCGTCTG	0.667													G|||	628	0.125399	0.1437	0.1037	5008	,	,		14679	0.0367		0.1183	False		,,,				2504	0.2147				p.H103Y		Atlas-SNP	.											.	TMC4	89	.	0			c.C307T						PASS	.	G	TYR/HIS,TYR/HIS	733,3673	300.1+/-286.2	57,619,1527	82.0	82.0	82.0		307,289	2.7	1.0	19	dbSNP_131	82	1016,7584	218.7+/-257.0	60,896,3344	no	missense,missense	TMC4	NM_001145303.1,NM_144686.2	83,83	117,1515,4871	AA,AG,GG		11.814,16.6364,13.4476	possibly-damaging,possibly-damaging	103/713,97/707	54675643	1749,11257	2203	4300	6503	SO:0001583	missense	147798	exon2			ACCTGTGTGCCCG	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.307C>T	19.37:g.54675643G>A	ENSP00000365776:p.His103Tyr	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	89	48	0.539326	NM_001145303	Q7Z5M3|Q8N5E4|Q8TBS7	Missense_Mutation	SNP	ENST00000376591.4	37	CCDS46174.1	229	0.10485347985347986	73	0.1483739837398374	43	0.11878453038674033	23	0.04020979020979021	90	0.11873350923482849	G	2.669	-0.278009	0.05679	0.166364	0.11814	ENSG00000167608	ENST00000301187;ENST00000376591;ENST00000446291	T;T;T	0.76709	0.78;0.78;-1.04	3.8	2.74	0.32292	.	2.664940	0.01530	U	0.018756	T	0.00496	0.0016	M	0.62723	1.935	0.09310	P	0.999999670532	P;B	0.36199	0.543;0.27	B;B	0.36186	0.096;0.219	T	0.34279	-0.9835	9	0.07990	T	0.79	.	6.7276	0.23365	0.1323:0.0:0.8677:0.0	rs11538074	103;97	Q7Z404;Q7Z404-1	TMC4_HUMAN;.	Y	97;103;7	ENSP00000301187:H97Y;ENSP00000365776:H103Y;ENSP00000416444:H7Y	ENSP00000301187:H97Y	H	-	1	0	TMC4	59367455	0.956000	0.32656	0.997000	0.53966	0.954000	0.61252	1.583000	0.36579	1.908000	0.55244	0.435000	0.28638	CAC	G|0.876;A|0.124	0.124	strong		0.667	TMC4-011	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000156164.2		
NACAD	23148	hgsc.bcm.edu	37	7	45123859	45123859	+	Silent	SNP	G	G	A	rs72497819	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45123859G>A	ENST00000490531.2	-	2	1939	c.1920C>T	c.(1918-1920)tcC>tcT	p.S640S		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	640					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						GTGTCATAACGGAGTCCTGGG	0.602													G|||	1213	0.242212	0.1505	0.3415	5008	,	,		16852	0.2391		0.2853	False		,,,				2504	0.2546				p.S640S		Atlas-SNP	.											.	NACAD	44	.	0			c.C1920T						PASS	.						5.0	6.0	5.0					7																	45123859		630	1536	2166	SO:0001819	synonymous_variant	23148	exon2			CATAACGGAGTCC	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1920C>T	7.37:g.45123859G>A		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	19	6	0.315789	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			G|0.792;A|0.208	0.208	strong		0.602	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
ZNF835	90485	hgsc.bcm.edu	37	19	57176198	57176198	+	Silent	SNP	T	T	G	rs8108756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57176198T>G	ENST00000537055.2	-	2	600	c.369A>C	c.(367-369)tcA>tcC	p.S123S		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	123					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						AGATGAACGCTGAACAGTAGC	0.627													.|||	2330	0.465256	0.6377	0.4078	5008	,	,		14934	0.4692		0.3131	False		,,,				2504	0.4254				p.S123S		Atlas-SNP	.											.	ZNF835	106	.	0			c.A369C						PASS	.	G		2827,1579	461.1+/-352.8	919,989,295	73.0	86.0	82.0		369	-5.6	0.0	19	dbSNP_116	82	2609,5991	675.7+/-403.2	396,1817,2087	no	coding-synonymous	ZNF835	NM_001005850.2		1315,2806,2382	GG,GT,TT		30.3372,35.8375,41.7961		123/538	57176198	5436,7570	2203	4300	6503	SO:0001819	synonymous_variant	90485	exon2			GAACGCTGAACAG	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.369A>C	19.37:g.57176198T>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	37	CCDS56105.1																																																																																			T|0.587;G|0.413	0.413	strong		0.627	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
OR8S1	341568	hgsc.bcm.edu	37	12	48920073	48920073	+	Missense_Mutation	SNP	G	G	A	rs61941963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48920073G>A	ENST00000310194.1	+	1	659	c.659G>A	c.(658-660)cGt>cAt	p.R220H	OR8S1_ENST00000551654.1_Intron	NM_001005203.2	NP_001005203.2	Q8NH09	OR8S1_HUMAN	olfactory receptor, family 8, subfamily S, member 1	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|skin(4)	22						TCCTACACCCGTATAATCTCT	0.522													G|||	347	0.0692891	0.0106	0.1066	5008	,	,		20009	0.0288		0.2018	False		,,,				2504	0.0276				p.R220H		Atlas-SNP	.											.	OR8S1	47	.	0			c.G659A						PASS	.	G	HIS/ARG	184,4222	119.6+/-157.3	7,170,2026	147.0	119.0	128.0		659	-0.6	0.0	12	dbSNP_129	128	1678,6922	308.8+/-309.1	169,1340,2791	yes	missense	OR8S1	NM_001005203.2	29	176,1510,4817	AA,AG,GG		19.5116,4.1761,14.3165	possibly-damaging	220/360	48920073	1862,11144	2203	4300	6503	SO:0001583	missense	341568	exon1			ACACCCGTATAAT		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.659G>A	12.37:g.48920073G>A	ENSP00000310632:p.Arg220His	Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	251	136	0.541833	NM_001005203		Missense_Mutation	SNP	ENST00000310194.1	37	CCDS31789.1	206	0.09432234432234432	8	0.016260162601626018	36	0.09944751381215469	20	0.03496503496503497	142	0.18733509234828497	G	0.263	-0.998124	0.02145	0.041761	0.195116	ENSG00000197376	ENST00000310194	T	0.00107	8.72	5.03	-0.583	0.11706	GPCR, rhodopsin-like superfamily (1);	0.838313	0.10032	N	0.724611	T	0.00012	0.0000	N	0.25094	0.71	0.80722	P	0.0	B	0.21147	0.052	B	0.24269	0.052	T	0.14587	-1.0467	9	0.48119	T	0.1	-2.9994	0.1795	0.00122	0.2864:0.1485:0.2623:0.3028	rs61941963	220	Q8NH09	OR8S1_HUMAN	H	220	ENSP00000310632:R220H	ENSP00000310632:R220H	R	+	2	0	OR8S1	47206340	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.918000	0.04021	-0.298000	0.08921	0.655000	0.94253	CGT	G|0.873;A|0.127	0.127	strong		0.522	OR8S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406881.1		
HGFAC	3083	hgsc.bcm.edu	37	4	3444503	3444503	+	Silent	SNP	G	G	A	rs2073505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3444503G>A	ENST00000382774.3	+	2	277	c.162G>A	c.(160-162)gcG>gcA	p.A54A	HGFAC_ENST00000511533.1_Silent_p.A54A	NM_001528.2	NP_001519.1	Q04756	HGFA_HUMAN	HGF activator	54					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)		CGACCCCTGCGATCCCCACTA	0.627													G|||	550	0.109824	0.1195	0.1066	5008	,	,		17503	0.0873		0.0775	False		,,,				2504	0.1554				p.A54A		Atlas-SNP	.											HGFAC,caecum,adenoma,+1,1	HGFAC	69	1	0			c.G162A						PASS	.	G		476,3930	223.3+/-239.8	32,412,1759	138.0	148.0	145.0		162	2.2	0.0	4	dbSNP_96	145	710,7890	173.6+/-224.1	32,646,3622	no	coding-synonymous	HGFAC	NM_001528.2		64,1058,5381	AA,AG,GG		8.2558,10.8034,9.1189		54/656	3444503	1186,11820	2203	4300	6503	SO:0001819	synonymous_variant	3083	exon2			CCCTGCGATCCCC	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.162G>A	4.37:g.3444503G>A		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	222	107	0.481982	NM_001528	Q14726|Q2M1W7|Q53X47	Silent	SNP	ENST00000382774.3	37	CCDS3369.1																																																																																			G|0.898;A|0.102	0.102	strong		0.627	HGFAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206607.3		
FRAS1	80144	hgsc.bcm.edu	37	4	79432455	79432455	+	Silent	SNP	A	A	C	rs3749488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:79432455A>C	ENST00000264895.6	+	64	10248	c.9808A>C	c.(9808-9810)Agg>Cgg	p.R3270R		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3266					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTTCAGCCGGAGGTTCCATGT	0.488													A|||	2026	0.404553	0.4455	0.2925	5008	,	,		20972	0.4554		0.2674	False		,,,				2504	0.5174				p.R3270R		Atlas-SNP	.											.	FRAS1	779	.	0			c.A9808C						PASS	.	A		1642,2560		339,964,798	127.0	126.0	126.0		9808	-0.3	1.0	4	dbSNP_107	126	2109,6351		266,1577,2387	no	coding-synonymous	FRAS1	NM_025074.6		605,2541,3185	CC,CA,AA		24.9291,39.0766,29.6241		3270/4013	79432455	3751,8911	2101	4230	6331	SO:0001819	synonymous_variant	80144	exon64			AGCCGGAGGTTCC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.9808A>C	4.37:g.79432455A>C		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	258	123	0.476744	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	805	0.3685897435897436	219	0.4451219512195122	99	0.27348066298342544	277	0.48426573426573427	210	0.2770448548812665	A	10.70	1.425249	0.25639	0.390766	0.249291	ENSG00000138759	ENST00000512123	.	.	.	5.7	-0.309	0.12769	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.50566	-0.8813	3	.	.	.	.	15.3355	0.74250	0.3525:0.6475:0.0:0.0	rs3749488;rs60064328;rs3749488	.	.	.	A	1498	.	.	E	+	2	0	FRAS1	79651479	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.791000	0.38744	0.387000	0.25024	0.383000	0.25322	GAG	A|0.628;C|0.372	0.372	strong		0.488	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SCN3A	6328	hgsc.bcm.edu	37	2	165987772	165987772	+	Silent	SNP	T	T	G	rs62174900	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:165987772T>G	ENST00000360093.3	-	16	3038	c.2547A>C	c.(2545-2547)gtA>gtC	p.V849V	SCN3A_ENST00000283254.7_Silent_p.V849V|SCN3A_ENST00000409101.3_Silent_p.V800V	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	849					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)	ATGATCGCAGTACAGACAATC	0.333													T|||	910	0.181709	0.0234	0.1787	5008	,	,		11002	0.2728		0.1968	False		,,,				2504	0.2883				p.V849V		Atlas-SNP	.											.	SCN3A	544	.	0			c.A2547C						PASS	.	T	,,	284,4122	155.9+/-189.0	13,258,1932	103.0	100.0	101.0		2400,2400,2547	-1.7	1.0	2	dbSNP_129	101	1835,6765	328.5+/-318.3	208,1419,2673	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN3A	NM_001081676.1,NM_001081677.1,NM_006922.3	,,	221,1677,4605	GG,GT,TT		21.3372,6.4458,16.2925	,,	800/1952,800/1952,849/2001	165987772	2119,10887	2203	4300	6503	SO:0001819	synonymous_variant	6328	exon16			TCGCAGTACAGAC	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.2547A>C	2.37:g.165987772T>G		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																				T|0.828;G|0.172	0.172	strong		0.333	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
OR7A5	26659	hgsc.bcm.edu	37	19	14938184	14938184	+	Silent	SNP	A	A	G	rs200531878		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14938184A>G	ENST00000322301.3	-	2	957	c.870T>C	c.(868-870)taT>taC	p.Y290Y	OR7A5_ENST00000601611.1_Intron|OR7A5_ENST00000594432.1_Silent_p.Y290Y			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	290					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.Y290Y(2)		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						TCCTCAGACTATAGATAAAGG	0.478																																					p.Y290Y		Atlas-SNP	.											OR7A5,NS,carcinoma,0,1	OR7A5	43	1	2	Substitution - coding silent(2)	kidney(2)	c.T870C						PASS	.						74.0	72.0	72.0					19																	14938184		2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			CAGACTATAGATA	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.870T>C	19.37:g.14938184A>G		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	113	8	0.0707965	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			A|0.999;G|0.001	0.001	weak		0.478	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
CCDC61	729440	hgsc.bcm.edu	37	19	46518682	46518682	+	Missense_Mutation	SNP	G	G	A	rs7271	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46518682G>A	ENST00000595358.1	+	7	891	c.842G>A	c.(841-843)aGg>aAg	p.R281K	CCDC61_ENST00000536603.1_Intron|CCDC61_ENST00000594087.1_Intron|CCDC61_ENST00000263284.2_Missense_Mutation_p.R338K	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	281						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		TTGTACAAGAGGGGGTGAGAG	0.731													G|||	577	0.115216	0.0545	0.0663	5008	,	,		6255	0.1081		0.1392	False		,,,				2504	0.2147				p.R281K		Atlas-SNP	.											.	CCDC61	32	.	0			c.G842A						PASS	.						13.0	15.0	14.0					19																	46518682		1883	3970	5853	SO:0001583	missense	729440	exon7			ACAAGAGGGGGTG		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.842G>A	19.37:g.46518682G>A	ENSP00000471454:p.Arg281Lys	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001267723	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	221	0.10119047619047619	24	0.04878048780487805	28	0.07734806629834254	71	0.12412587412587413	98	0.12928759894459102	G	8.736	0.917912	0.17982	.	.	ENSG00000104983	ENST00000263284	.	.	.	3.86	1.66	0.24008	.	0.491827	0.21716	N	0.070186	T	0.00384	0.0012	L	0.54323	1.7	0.22446	P	0.999091975	B	0.31817	0.341	B	0.25140	0.058	T	0.06356	-1.0831	8	0.59425	D	0.04	-6.385	6.3339	0.21285	0.2413:0.0:0.7587:0.0	rs7271;rs17294786;rs17353314	281	Q9Y6R9	CCD61_HUMAN	K	338	.	ENSP00000263284:R338K	R	+	2	0	CCDC61	51210522	0.017000	0.18338	0.052000	0.19188	0.089000	0.18198	0.580000	0.23803	0.700000	0.31782	-1.267000	0.01435	AGG	G|0.900;A|0.100	0.100	strong		0.731	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	
MYH8	4626	hgsc.bcm.edu	37	17	10312472	10312472	+	Missense_Mutation	SNP	G	G	A	rs34693726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:10312472G>A	ENST00000403437.2	-	17	2001	c.1907C>T	c.(1906-1908)gCg>gTg	p.A636V	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	636	Myosin motor.		A -> V (in dbSNP:rs34693726).		ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						ACCTTTCTTCGCGCTGCTATC	0.343									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				G|||	299	0.0597045	0.0408	0.0375	5008	,	,		18253	0.0427		0.0517	False		,,,				2504	0.1268				p.A636V		Atlas-SNP	.											MYH8,NS,carcinoma,+1,1	MYH8	346	1	0			c.C1907T						PASS	.	G	VAL/ALA	199,4207	121.3+/-158.8	4,191,2008	52.0	55.0	54.0		1907	5.2	0.9	17	dbSNP_126	54	525,8075	146.5+/-202.0	16,493,3791	yes	missense	MYH8	NM_002472.2	64	20,684,5799	AA,AG,GG		6.1047,4.5166,5.5667	benign	636/1938	10312472	724,12282	2203	4300	6503	SO:0001583	missense	4626	exon17	Familial Cancer Database	Carney Complex Variant	TTCTTCGCGCTGC		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1907C>T	17.37:g.10312472G>A	ENSP00000384330:p.Ala636Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	158	64	0.405063	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	110	0.05036630036630037	21	0.042682926829268296	17	0.04696132596685083	26	0.045454545454545456	46	0.06068601583113457	G	9.307	1.054554	0.19907	0.045166	0.061047	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.72394	-0.65	5.23	5.23	0.72850	Myosin head, motor domain (2);	0.657409	0.11973	U	0.511511	T	0.17746	0.0426	L	0.39147	1.195	0.30323	N	0.787406	B	0.02656	0.0	B	0.08055	0.003	T	0.48019	-0.9071	10	0.66056	D	0.02	.	13.1246	0.59346	0.0:0.2884:0.7116:0.0	rs34693726	636	P13535	MYH8_HUMAN	V	636	ENSP00000384330:A636V	ENSP00000252173:A636V	A	-	2	0	MYH8	10253197	0.018000	0.18449	0.876000	0.34364	0.006000	0.05464	0.660000	0.25009	2.736000	0.93811	0.655000	0.94253	GCG	G|0.944;A|0.056	0.056	strong		0.343	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
MXRA5	25878	hgsc.bcm.edu	37	X	3241791	3241791	+	Silent	SNP	G	G	A	rs1635250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3241791G>A	ENST00000217939.6	-	5	2089	c.1935C>T	c.(1933-1935)gaC>gaT	p.D645D		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	645	Ig-like C2-type 2.					extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AGTAACCACTGTCACTGACTT	0.443													A|||	1750	0.463576	0.298	0.3991	3775	,	,		16554	0.2728		0.4573	False		,,,				2504	0.3517				p.D645D		Atlas-SNP	.											.	MXRA5	815	.	0			c.C1935T						PASS	.	A		1535,2300		246,806,237,580,334	109.0	96.0	101.0		1935	-1.8	0.0	X	dbSNP_89	101	3837,2891		791,1190,1065,447,807	no	coding-synonymous	MXRA5	NM_015419.3		1037,1996,1302,1027,1141	AA,AG,A,GG,G		42.9697,40.0261,49.1432		645/2829	3241791	5372,5191	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			ACCACTGTCACTG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.1935C>T	X.37:g.3241791G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	147	147	1	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			0|0.003;A|0.487	0.487	strong		0.443	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
OR51B6	390058	hgsc.bcm.edu	37	11	5373114	5373114	+	Missense_Mutation	SNP	G	G	A	rs5006888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373114G>A	ENST00000380219.1	+	1	377	c.377G>A	c.(376-378)aGc>aAc	p.S126N	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	126			S -> N (in dbSNP:rs5006888).	TIRS -> AIHN (in Ref. 1; AAG41682). {ECO:0000305}.	detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCATCCGCAGCCCCTTAAGA	0.468													A|||	3037	0.60643	0.587	0.5692	5008	,	,		23218	0.5446		0.6054	False		,,,				2504	0.7239				p.S126N		Atlas-SNP	.											.	OR51B6	53	.	0			c.G377A						PASS	.	A	ASN/SER	2560,1842	534.4+/-373.9	757,1046,398	127.0	116.0	120.0		377	2.7	0.0	11	dbSNP_113	120	5070,3524	511.0+/-377.6	1515,2040,742	yes	missense	OR51B6	NM_001004750.1	46	2272,3086,1140	AA,AG,GG		41.0054,41.8446,41.2896	benign	126/313	5373114	7630,5366	2201	4297	6498	SO:0001583	missense	390058	exon1			TCCGCAGCCCCTT		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.377G>A	11.37:g.5373114G>A	ENSP00000369568:p.Ser126Asn	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	176	60	0.340909	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	1268	0.5805860805860806	288	0.5853658536585366	218	0.6022099447513812	315	0.5506993006993007	447	0.5897097625329816	A	0	-2.607379	0.00121	0.581554	0.589946	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00532	6.75	5.01	2.67	0.31697	GPCR, rhodopsin-like superfamily (1);	0.101582	0.42964	N	0.000623	T	0.00012	0.0000	N	0.00217	-1.83	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.13980	-1.0489	9	0.02654	T	1	.	4.9735	0.14129	0.5439:0.2965:0.1596:0.0	rs5006888;rs59241671	126	Q9H340	O51B6_HUMAN	N	125;126	ENSP00000369568:S126N	ENSP00000369568:S126N	S	+	2	0	OR51B6	5329690	0.008000	0.16893	0.040000	0.18447	0.030000	0.12068	2.394000	0.44450	0.070000	0.16634	-0.556000	0.04195	AGC	G|0.408;A|0.592	0.592	strong		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
MTMR7	9108	hgsc.bcm.edu	37	8	17157677	17157677	+	Missense_Mutation	SNP	T	T	G	rs3764796	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17157677T>G	ENST00000180173.5	-	14	1711	c.1677A>C	c.(1675-1677)caA>caC	p.Q559H	MTMR7_ENST00000398099.3_Missense_Mutation_p.Q150H	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	559			Q -> H (in dbSNP:rs3764796). {ECO:0000269|PubMed:14702039}.		inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		TGGGCTCACTTTGCTTACTCT	0.403													T|||	529	0.105631	0.0091	0.0951	5008	,	,		18052	0.1062		0.1203	False		,,,				2504	0.228				p.Q559H		Atlas-SNP	.											.	MTMR7	75	.	0			c.A1677C						PASS	.	T	HIS/GLN	102,4304	80.4+/-118.8	1,100,2102	157.0	163.0	161.0		1677	-4.0	0.2	8	dbSNP_107	161	978,7622	210.7+/-251.5	68,842,3390	yes	missense	MTMR7	NM_004686.4	24	69,942,5492	GG,GT,TT		11.3721,2.315,8.3039	possibly-damaging	559/661	17157677	1080,11926	2203	4300	6503	SO:0001583	missense	9108	exon14			CTCACTTTGCTTA	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1677A>C	8.37:g.17157677T>G	ENSP00000180173:p.Gln559His	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	145	70	0.482759	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	214	0.09798534798534798	8	0.016260162601626018	38	0.10497237569060773	75	0.13111888111888112	93	0.12269129287598944	T	11.96	1.795621	0.31777	0.02315	0.113721	ENSG00000003987	ENST00000180173;ENST00000398099	T;T	0.77229	0.63;-1.08	4.76	-3.96	0.04106	.	1.050740	0.07301	N	0.874089	T	0.01061	0.0035	N	0.22421	0.69	0.80722	P	0.0	B	0.32365	0.367	B	0.31751	0.135	T	0.09552	-1.0669	9	0.42905	T	0.14	.	8.4294	0.32748	0.0:0.4513:0.191:0.3577	rs3764796;rs17625520;rs56575510;rs57964925;rs3764796	559	Q9Y216	MTMR7_HUMAN	H	559;150	ENSP00000180173:Q559H;ENSP00000381171:Q150H	ENSP00000180173:Q559H	Q	-	3	2	MTMR7	17202048	0.000000	0.05858	0.210000	0.23637	0.994000	0.84299	-1.732000	0.01851	-0.409000	0.07553	0.482000	0.46254	CAA	T|0.909;G|0.091	0.091	strong		0.403	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
GRHL3	57822	hgsc.bcm.edu	37	1	24680915	24680915	+	Intron	SNP	C	C	T	rs12030057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:24680915C>T	ENST00000350501.5	+	15	1821				GRHL3_ENST00000361548.4_Silent_p.V582V|STPG1_ENST00000468303.1_5'Flank|GRHL3_ENST00000356046.2_Silent_p.V536V|GRHL3_ENST00000236255.4_Silent_p.V587V|GRHL3_ENST00000342072.4_Silent_p.V489V	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)						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)		GCAACCACGTCGCCTTCCTGC	0.517													C|||	1352	0.269968	0.0703	0.3818	5008	,	,		22287	0.4127		0.2982	False		,,,				2504	0.2843				p.V587V		Atlas-SNP	.											.	GRHL3	69	.	0			c.C1761T						PASS	.	C	,,,	480,3926	224.6+/-240.7	26,428,1749	162.0	132.0	142.0		1608,1761,1746,	-10.4	0.3	1	dbSNP_120	142	2320,6280	389.1+/-342.8	311,1698,2291	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	GRHL3	NM_001195010.1,NM_021180.3,NM_198173.2,NM_198174.2	,,,	337,2126,4040	TT,TC,CC		26.9767,10.8942,21.5285	,,,	536/557,587/608,582/603,	24680915	2800,10206	2203	4300	6503	SO:0001627	intron_variant	57822	exon16			CCACGTCGCCTTC	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.1694+4303C>T	1.37:g.24680915C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	63	57	0.904762	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Silent	SNP	ENST00000350501.5	37	CCDS252.2																																																																																			C|0.754;T|0.246	0.246	strong		0.517	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
GGCX	2677	hgsc.bcm.edu	37	2	85780131	85780131	+	Silent	SNP	G	G	A	rs2592551	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:85780131G>A	ENST00000233838.4	-	9	1298	c.1218C>T	c.(1216-1218)cgC>cgT	p.R406R	GGCX_ENST00000473665.1_5'UTR|GGCX_ENST00000430215.3_Silent_p.R349R	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	406					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)	p.R406R(1)		endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	GCTGGTGGGAGCGGGAGTGCA	0.537													G|||	1432	0.285942	0.3903	0.2219	5008	,	,		19279	0.3095		0.3111	False		,,,				2504	0.1401				p.R406R		Atlas-SNP	.											GGCX,NS,carcinoma,0,1	GGCX	44	1	1	Substitution - coding silent(1)	stomach(1)	c.C1218T						PASS	.	G	,	1547,2859	486.9+/-360.8	280,987,936	188.0	165.0	173.0		1218,1047	4.7	1.0	2	dbSNP_100	173	2388,6212	396.6+/-345.4	334,1720,2246	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	614,2707,3182	AA,AG,GG		27.7674,35.1112,30.2553	,	406/759,349/702	85780131	3935,9071	2203	4300	6503	SO:0001819	synonymous_variant	2677	exon9			GTGGGAGCGGGAG		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.1218C>T	2.37:g.85780131G>A		Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	182	83	0.456044	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			G|0.693;A|0.307	0.307	strong		0.537	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
VDAC3	7419	hgsc.bcm.edu	37	8	42259418	42259418	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:42259418T>C	ENST00000022615.4	+	7	504	c.436T>C	c.(436-438)Ttc>Ctc	p.F146L	VDAC3_ENST00000521158.1_Missense_Mutation_p.F147L|VDAC3_ENST00000392935.3_Missense_Mutation_p.F147L|VDAC3_ENST00000522572.1_Intron			Q9Y277	VDAC3_HUMAN	voltage-dependent anion channel 3	146					adenine transport (GO:0015853)	extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|pore complex (GO:0046930)	nucleotide binding (GO:0000166)|porin activity (GO:0015288)|voltage-gated anion channel activity (GO:0008308)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	7	all_cancers(6;3.86e-23)|all_lung(13;6.47e-12)|Lung NSC(13;1.08e-10)|Ovarian(28;0.00769)|Prostate(17;0.0119)|Lung SC(25;0.211)	all_lung(54;0.00671)|Lung NSC(58;0.0184)|Esophageal squamous(32;0.131)|Hepatocellular(245;0.133)|Renal(179;0.151)	BRCA - Breast invasive adenocarcinoma(8;3.48e-10)|OV - Ovarian serous cystadenocarcinoma(14;0.00266)|Lung(22;0.00849)|LUSC - Lung squamous cell carcinoma(45;0.024)		Dihydroxyaluminium(DB01375)	TGTGTTGGCCTTCGAAGGGTG	0.458																																					p.F147L		Atlas-SNP	.											VDAC3,NS,carcinoma,-2,1	VDAC3	17	1	0			c.T439C						scavenged	.						116.0	115.0	115.0					8																	42259418		2203	4300	6503	SO:0001583	missense	7419	exon7			TTGGCCTTCGAAG	AF038962	CCDS6131.1, CCDS47850.1	8p11.21	2011-11-15			ENSG00000078668	ENSG00000078668		"""Voltage-dependent anion channels"""	12674	protein-coding gene	gene with protein product		610029				9653160, 9781040	Standard	NM_001135694		Approved	HD-VDAC3	uc003xpc.3	Q9Y277	OTTHUMG00000164168	ENST00000022615.4:c.436T>C	8.37:g.42259418T>C	ENSP00000022615:p.Phe146Leu	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	200	5	0.025	NM_001135694	Q9UIS0	Missense_Mutation	SNP	ENST00000022615.4	37	CCDS6131.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.139761	0.56936	.	.	ENSG00000078668	ENST00000392935;ENST00000520115;ENST00000522069;ENST00000521158;ENST00000022615	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	5.64	0.363	0.16118	.	0.270733	0.43919	N	0.000517	T	0.14570	0.0352	N	0.03608	-0.345	0.30742	N	0.746015	B	0.02656	0.0	B	0.06405	0.002	T	0.15896	-1.0421	9	.	.	.	0.2973	4.7613	0.13110	0.1286:0.2335:0.0:0.6379	.	146	Q9Y277	VDAC3_HUMAN	L	147;146;146;147;146	ENSP00000442811:F147L;ENSP00000428519:F146L;ENSP00000429006:F146L;ENSP00000428845:F147L;ENSP00000022615:F146L	.	F	+	1	0	VDAC3	42378575	0.994000	0.37717	0.902000	0.35471	0.821000	0.46438	2.347000	0.44036	-0.086000	0.12550	-0.296000	0.09543	TTC	.	.	none		0.458	VDAC3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377574.1		
FAM154B	283726	hgsc.bcm.edu	37	15	82574461	82574461	+	Splice_Site	SNP	C	C	T	rs76375505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:82574461C>T	ENST00000339465.5	+	3	324	c.255C>T	c.(253-255)gaC>gaT	p.D85D	FAM154B_ENST00000427381.2_Splice_Site_p.D70D|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	85										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						ATTTTCAAGACGATTATAGAG	0.333													C|||	132	0.0263578	0.003	0.0144	5008	,	,		19292	0.0605		0.0229	False		,,,				2504	0.0348				p.D85D		Atlas-SNP	.											.	FAM154B	50	.	0			c.C255T						PASS	.	C		15,4379		0,15,2182	53.0	58.0	56.0		255	2.4	1.0	15	dbSNP_131	56	192,8404		4,184,4110	no	coding-synonymous-near-splice	FAM154B	NM_001008226.1		4,199,6292	TT,TC,CC		2.2336,0.3414,1.5935		85/399	82574461	207,12783	2197	4298	6495	SO:0001630	splice_region_variant	283726	exon3			TCAAGACGATTAT	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.254-1C>T	15.37:g.82574461C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	115	69	0.6	NM_001008226	B4E2M2	Silent	SNP	ENST00000339465.5	37	CCDS32310.1																																																																																			C|0.977;T|0.023	0.023	strong		0.333	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226	Silent
NTAN1	123803	hgsc.bcm.edu	37	16	15131974	15131974	+	Missense_Mutation	SNP	G	G	T	rs1136001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15131974G>T	ENST00000287706.3	-	10	939	c.847C>A	c.(847-849)Cac>Aac	p.H283N	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	283			H -> N (in dbSNP:rs1136001).		adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						AACAGTGTGTGAGCTGGAGAT	0.383													T|||	1719	0.343251	0.1838	0.5331	5008	,	,		17380	0.3661		0.3072	False		,,,				2504	0.4376				p.H283N		Atlas-SNP	.											.	NTAN1	21	.	0			c.C847A						PASS	.	T	ASN/HIS	992,3402	725.7+/-409.6	118,756,1323	79.0	80.0	80.0	http://www.ncbi.nlm.nih.gov/pubmed?term	847	1.8	0.0	16	dbSNP_86	80	2583,6017	688.7+/-404.3	358,1867,2075	yes	missense	NTAN1	NM_173474.2	68	476,2623,3398	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	30.0349,22.5762,27.5127	benign	283/311	15131974	3575,9419	2197	4300	6497	SO:0001583	missense	123803	exon10			GTGTGTGAGCTGG	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.847C>A	16.37:g.15131974G>T	ENSP00000287706:p.His283Asn	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	NM_173474	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	37	CCDS10558.1	727	0.33287545787545786	94	0.1910569105691057	174	0.48066298342541436	216	0.3776223776223776	243	0.32058047493403696	T	1.619	-0.522108	0.04171	0.225762	0.300349	ENSG00000157045	ENST00000287706	T	0.27720	1.65	5.35	1.84	0.25277	.	0.385250	0.30565	N	0.009345	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	0.47355	-0.9124	9	0.17369	T	0.5	-18.7544	6.9113	0.24336	0.0:0.1394:0.3861:0.4745	rs1136001;rs3199049;rs16966957;rs52834819;rs58508909;rs1136001	283	Q96AB6	NTAN1_HUMAN	N	283	ENSP00000287706:H283N	ENSP00000287706:H283N	H	-	1	0	NTAN1	15039475	0.000000	0.05858	0.000000	0.03702	0.756000	0.42949	0.598000	0.24074	-0.026000	0.13895	-1.131000	0.01979	CAC	G|0.706;T|0.294	0.294	strong		0.383	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
LRRC56	115399	hgsc.bcm.edu	37	11	551235	551235	+	Silent	SNP	G	G	A	rs35537971	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:551235G>A	ENST00000270115.7	+	9	1229	c.729G>A	c.(727-729)ccG>ccA	p.P243P		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	243	LRRCT.									kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGGCCCCCCCGCGGCTGAGCC	0.687													G|||	758	0.151358	0.2277	0.2435	5008	,	,		10391	0.0188		0.1879	False		,,,				2504	0.0818				p.P243P		Atlas-SNP	.											.	LRRC56	23	.	0			c.G729A						PASS	.	G		817,3135		88,641,1247	21.0	17.0	19.0		729	3.6	0.0	11	dbSNP_126	19	1473,6373		141,1191,2591	no	coding-synonymous	LRRC56	NM_198075.3		229,1832,3838	AA,AG,GG		18.7739,20.6731,19.4101		243/543	551235	2290,9508	1976	3923	5899	SO:0001819	synonymous_variant	115399	exon9			CCCCCCGCGGCTG		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.729G>A	11.37:g.551235G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	161	84	0.521739	NM_198075	Q8N3Q4	Silent	SNP	ENST00000270115.7	37	CCDS7700.1																																																																																			G|0.835;A|0.165	0.165	strong		0.687	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
PSG2	5670	hgsc.bcm.edu	37	19	43585334	43585334	+	Silent	SNP	T	T	G	rs79582550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:43585334T>G	ENST00000406487.1	-	2	227	c.129A>C	c.(127-129)ccA>ccC	p.P43P	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	43	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.P43P(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CGGAAACTTTTGGTGGCTGGG	0.488																																					p.P43P		Atlas-SNP	.											PSG2,NS,carcinoma,-1,2	PSG2	84	2	2	Substitution - coding silent(2)	lung(2)	c.A129C						scavenged	.						171.0	168.0	169.0					19																	43585334		2203	4299	6502	SO:0001819	synonymous_variant	5670	exon2			AACTTTTGGTGGC		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.129A>C	19.37:g.43585334T>G		Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	291	23	0.0790378	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			T|0.944;G|0.056	0.056	strong		0.488	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
BRSK1	84446	hgsc.bcm.edu	37	19	55815159	55815159	+	Silent	SNP	C	C	A	rs17851415	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55815159C>A	ENST00000309383.1	+	12	1528	c.1251C>A	c.(1249-1251)acC>acA	p.T417T	BRSK1_ENST00000326848.7_Silent_p.T112T|BRSK1_ENST00000590333.1_Silent_p.T433T	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	417					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CTGTACCCACCCGACGGGCCT	0.637													C|||	420	0.0838658	0.1452	0.0576	5008	,	,		15128	0.0883		0.0268	False		,,,				2504	0.0736				p.T417T		Atlas-SNP	.											.	BRSK1	192	.	0			c.C1251A						PASS	.	C		529,3877		37,455,1711	39.0	45.0	43.0		1251	-1.2	1.0	19	dbSNP_123	43	311,8289		8,295,3997	no	coding-synonymous	BRSK1	NM_032430.1		45,750,5708	AA,AC,CC		3.6163,12.0064,6.4586		417/779	55815159	840,12166	2203	4300	6503	SO:0001819	synonymous_variant	84446	exon12			ACCCACCCGACGG	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1251C>A	19.37:g.55815159C>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.936;A|0.064	0.064	strong		0.637	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
SLC52A3	113278	hgsc.bcm.edu	37	20	744570	744570	+	Silent	SNP	G	G	A	rs6054605	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:744570G>A	ENST00000217254.7	-	3	886	c.645C>T	c.(643-645)ccC>ccT	p.P215P	SLC52A3_ENST00000381944.3_Silent_p.P215P|SLC52A3_ENST00000473664.1_Intron	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	215					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										AGAAGTGGGCGGGAAGGTAGC	0.607													G|||	692	0.138179	0.0522	0.072	5008	,	,		18546	0.4534		0.0497	False		,,,				2504	0.0675				p.P215P		Atlas-SNP	.											.	.	.	.	0			c.C645T						PASS	.	G		199,4207	121.3+/-158.8	4,191,2008	57.0	49.0	52.0		645	-9.9	0.0	20	dbSNP_114	52	437,8163	131.5+/-189.3	7,423,3870	no	coding-synonymous	C20orf54	NM_033409.3		11,614,5878	AA,AG,GG		5.0814,4.5166,4.8901		215/470	744570	636,12370	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon3			GTGGGCGGGAAGG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.645C>T	20.37:g.744570G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			G|0.908;A|0.092	0.092	strong		0.607	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
MYO18B	84700	hgsc.bcm.edu	37	22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	rs7284177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26423477G>A	ENST00000407587.2	+	43	7709	c.7540G>A	c.(7540-7542)Ggc>Agc	p.G2514S	MYO18B_ENST00000335473.7_Missense_Mutation_p.G2513S|MYO18B_ENST00000536101.1_Missense_Mutation_p.G2513S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2513	Poly-Ser.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTCATCCTCCGGCTCCATCGT	0.587													A|||	352	0.0702875	0.2005	0.0259	5008	,	,		18932	0.004		0.0179	False		,,,				2504	0.0481				p.G2513S		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7537A						PASS	.	A	SER/GLY	695,3407		58,579,1414	53.0	55.0	55.0		7537	1.8	1.0	22	dbSNP_116	55	146,8242		1,144,4049	yes	missense	MYO18B	NM_032608.5	56	59,723,5463	AA,AG,GG		1.7406,16.943,6.7334	benign	2513/2568	26423477	841,11649	2051	4194	6245	SO:0001583	missense	84700	exon43			TCCTCCGGCTCCA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7540G>A	22.37:g.26423477G>A	ENSP00000386096:p.Gly2514Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		123	0.05631868131868132	92	0.18699186991869918	13	0.03591160220994475	4	0.006993006993006993	14	0.018469656992084433	A	4.656	0.121893	0.08931	0.16943	0.017406	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.85088	-1.92;-1.92;-1.94	5.17	1.8	0.24995	.	0.170297	0.37437	N	0.002083	T	0.00109	0.0003	N	0.00729	-1.24	0.54753	P	1.0999999999983245E-5	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.002;0.002	T	0.12426	-1.0548	9	0.02654	T	1	.	4.0444	0.09766	0.4128:0.0:0.4136:0.1736	rs7284177;rs52837742;rs59696890;rs7284177	2026;2515;2513;2514;2513	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2513;2513;2514	ENSP00000441229:G2513S;ENSP00000334563:G2513S;ENSP00000386096:G2514S	ENSP00000334563:G2513S	G	+	1	0	MYO18B	24753477	0.459000	0.25768	0.958000	0.39756	0.893000	0.52053	0.694000	0.25512	-0.007000	0.14345	-0.361000	0.07541	GGC	G|0.931;A|0.069	0.069	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604475	140604475	+	Silent	SNP	C	C	T	rs149933809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140604475C>T	ENST00000239449.4	+	1	1398	c.1398C>T	c.(1396-1398)ccC>ccT	p.P466P	PCDHB14_ENST00000515856.2_Silent_p.P313P	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	466	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACAACAGCCCCGCCCTGCACA	0.632													c|||	10	0.00199681	0.0	0.0014	5008	,	,		17658	0.0		0.005	False		,,,				2504	0.0041				p.P466P	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C1398T						PASS	.	C		3,4403		0,3,2200	109.0	115.0	113.0		1398	2.6	1.0	5	dbSNP_134	113	34,8556		0,34,4261	no	coding-synonymous	PCDHB14	NM_018934.2		0,37,6461	TT,TC,CC		0.3958,0.0681,0.2847		466/799	140604475	37,12959	2203	4295	6498	SO:0001819	synonymous_variant	56122	exon1			CAGCCCCGCCCTG	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.1398C>T	5.37:g.140604475C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	137	77	0.562044	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.997;T|0.003	0.003	strong		0.632	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
FLNC	2318	hgsc.bcm.edu	37	7	128484816	128484816	+	Silent	SNP	A	A	G	rs3734973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128484816A>G	ENST00000325888.8	+	21	3558	c.3297A>G	c.(3295-3297)gtA>gtG	p.V1099V	FLNC_ENST00000346177.6_Silent_p.V1099V	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1099					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGCTGACCGTAGAGGGCCCCT	0.637													G|||	1903	0.379992	0.6082	0.2248	5008	,	,		19215	0.4891		0.1551	False		,,,				2504	0.3006				p.V1099V		Atlas-SNP	.											FLNC,caecum,carcinoma,+2,1	FLNC	339	1	0			c.A3297G						scavenged	.	G	,	2140,1996		574,992,502	57.0	66.0	63.0		3297,3297	2.7	1.0	7	dbSNP_107	63	1392,7054		94,1204,2925	yes	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	668,2196,3427	GG,GA,AA		16.4812,48.2592,28.0718	,	1099/2693,1099/2726	128484816	3532,9050	2068	4223	6291	SO:0001819	synonymous_variant	2318	exon21			GACCGTAGAGGGC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3297A>G	7.37:g.128484816A>G		Somatic	74	1	0.0135135		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			A|0.663;G|0.337	0.337	strong		0.637	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
B4GALT2	8704	hgsc.bcm.edu	37	1	44447413	44447413	+	Missense_Mutation	SNP	G	G	C	rs1859728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:44447413G>C	ENST00000356836.6	+	3	1156	c.366G>C	c.(364-366)caG>caC	p.Q122H	B4GALT2_ENST00000372324.1_Missense_Mutation_p.Q122H|B4GALT2_ENST00000309519.7_Missense_Mutation_p.Q151H|B4GALT2_ENST00000434555.2_Missense_Mutation_p.Q56H	NM_001005417.2|NM_030587.2	NP_001005417.1|NP_085076.2	O60909	B4GT2_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 2	122			Q -> H (in dbSNP:rs1859728). {ECO:0000269|PubMed:15489334}.		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|lactose synthase activity (GO:0004461)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0511)			N-Acetyl-D-glucosamine(DB00141)	AGCGGGTGCAGAGGGAGAACC	0.627													g|||	399	0.0796725	0.0356	0.0461	5008	,	,		17706	0.1786		0.0527	False		,,,				2504	0.089				p.Q151H		Atlas-SNP	.											.	B4GALT2	35	.	0			c.G453C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN	236,4170	138.0+/-173.8	12,212,1979	61.0	64.0	63.0		366,366,453	3.1	1.0	1	dbSNP_92	63	476,8124	139.8+/-196.4	13,450,3837	yes	missense,missense,missense	B4GALT2	NM_001005417.2,NM_003780.4,NM_030587.2	24,24,24	25,662,5816	CC,CG,GG		5.5349,5.3563,5.4744	probably-damaging,probably-damaging,probably-damaging	122/373,122/373,151/402	44447413	712,12294	2203	4300	6503	SO:0001583	missense	8704	exon3			GGTGCAGAGGGAG	AF038660	CCDS506.1, CCDS55596.1	1p34-p33	2013-02-19			ENSG00000117411	ENSG00000117411		"""Beta 4-glycosyltransferases"""	925	protein-coding gene	gene with protein product		604013				9405390, 9597550	Standard	NM_003780		Approved	beta4Gal-T2	uc010okl.2	O60909	OTTHUMG00000008296	ENST00000356836.6:c.366G>C	1.37:g.44447413G>C	ENSP00000349293:p.Gln122His	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	149	67	0.449664	NM_030587	B3KTP0|B4DE14|D3DPY6|D3DPY7|O60511|Q4V9L9|Q5T4X5|Q5T4Y5|Q9BUP6|Q9NSY7	Missense_Mutation	SNP	ENST00000356836.6	37	CCDS506.1	176	0.08058608058608059	20	0.04065040650406504	17	0.04696132596685083	100	0.17482517482517482	39	0.051451187335092345	G	19.18	3.778503	0.70107	0.053563	0.055349	ENSG00000117411	ENST00000372324;ENST00000434555;ENST00000356836;ENST00000309519	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	4.94	3.06	0.35304	.	0.000000	0.85682	D	0.000000	T	0.00109	0.0003	L	0.49513	1.565	0.09310	P	0.99999784246	D;D;D	0.71674	0.998;0.994;0.995	D;D;D	0.71870	0.975;0.916;0.95	T	0.02789	-1.1110	9	0.38643	T	0.18	-17.6565	10.5628	0.45154	0.2194:0.0:0.7806:0.0	rs1859728;rs17849581;rs1859728	151;56;122	B4DE14;O60909-2;O60909	.;.;B4GT2_HUMAN	H	122;56;122;151	ENSP00000361399:Q122H;ENSP00000407468:Q56H;ENSP00000349293:Q122H;ENSP00000310696:Q151H	ENSP00000310696:Q151H	Q	+	3	2	B4GALT2	44220000	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.816000	0.48026	0.498000	0.27948	0.561000	0.74099	CAG	G|0.928;C|0.072	0.072	strong		0.627	B4GALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022840.1	NM_003780	
PEX16	9409	hgsc.bcm.edu	37	11	45937306	45937306	+	Missense_Mutation	SNP	C	C	T	rs11553094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:45937306C>T	ENST00000378750.5	-	4	550	c.307G>A	c.(307-309)Gtg>Atg	p.V103M	PEX16_ENST00000532554.1_Intron|PEX16_ENST00000241041.3_Missense_Mutation_p.V103M|PEX16_ENST00000532681.1_Missense_Mutation_p.V8M			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	103			V -> M (in dbSNP:rs11553094).		ER-dependent peroxisome organization (GO:0032581)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)|protein localization to endoplasmic reticulum (GO:0070972)|protein targeting to peroxisome (GO:0006625)|protein to membrane docking (GO:0022615)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)			large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		TCACCCCACACCTTGGCAGCT	0.627													C|||	66	0.0131789	0.0008	0.0259	5008	,	,		19489	0.0		0.0308	False		,,,				2504	0.0164				p.V103M		Atlas-SNP	.											.	PEX16	24	.	0			c.G307A						PASS	.	C	MET/VAL,MET/VAL	25,4381	30.8+/-60.4	0,25,2178	181.0	178.0	179.0		307,307	5.3	1.0	11	dbSNP_120	179	232,8366	95.6+/-157.4	7,218,4074	yes	missense,missense	PEX16	NM_004813.2,NM_057174.2	21,21	7,243,6252	TT,TC,CC		2.6983,0.5674,1.9763	benign,benign	103/337,103/347	45937306	257,12747	2203	4299	6502	SO:0001583	missense	9409	exon4			CCCACACCTTGGC	AF118240	CCDS7917.1, CCDS31472.1	11p	2007-12-14			ENSG00000121680	ENSG00000121680			8857	protein-coding gene	gene with protein product		603360				9922452	Standard	NM_057174		Approved		uc001nbt.3	Q9Y5Y5	OTTHUMG00000167005	ENST00000378750.5:c.307G>A	11.37:g.45937306C>T	ENSP00000368024:p.Val103Met	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	232	118	0.508621	NM_004813	Q9BWB9	Missense_Mutation	SNP	ENST00000378750.5	37	CCDS31472.1	38	0.0173992673992674	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	25	0.032981530343007916	C	15.44	2.833253	0.50951	0.005674	0.026983	ENSG00000121680	ENST00000241041;ENST00000378750;ENST00000532681;ENST00000525192	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.29	5.29	0.74685	.	0.191341	0.45606	D	0.000348	T	0.08133	0.0203	L	0.41236	1.265	0.38040	D	0.935427	P;P	0.40230	0.515;0.708	B;B	0.34242	0.163;0.178	T	0.03483	-1.1032	10	0.34782	T	0.22	-26.6048	18.5294	0.90986	0.0:1.0:0.0:0.0	rs11553094;rs52818272;rs11553094	103;103	Q9Y5Y5;Q9Y5Y5-2	PEX16_HUMAN;.	M	103;103;8;8	ENSP00000241041:V103M;ENSP00000368024:V103M;ENSP00000434654:V8M;ENSP00000431309:V8M	ENSP00000241041:V103M	V	-	1	0	PEX16	45893882	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.227000	0.42972	2.480000	0.83734	0.561000	0.74099	GTG	C|0.980;T|0.020	0.020	strong		0.627	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174	
ITIH1	3697	hgsc.bcm.edu	37	3	52825585	52825585	+	Silent	SNP	T	T	C	rs9324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52825585T>C	ENST00000273283.2	+	21	2571	c.2547T>C	c.(2545-2547)tcT>tcC	p.S849S	ITIH1_ENST00000405128.3_Silent_p.S215S|ITIH1_ENST00000537050.1_Silent_p.S561S|ITIH1_ENST00000542827.1_3'UTR|ITIH1_ENST00000540715.1_Silent_p.S707S	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	849	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		ACCCAGGCTCTGACCCCACAA	0.597													C|||	2063	0.411941	0.5825	0.4669	5008	,	,		19605	0.373		0.3926	False		,,,				2504	0.2025				p.S849S		Atlas-SNP	.											.	ITIH1	108	.	0			c.T2547C						PASS	.	C	,,,	2279,2127	577.5+/-384.5	573,1133,497	88.0	85.0	86.0		2121,1683,1683,2547	-7.7	0.4	3	dbSNP_52	86	3140,5460	657.0+/-401.4	594,1952,1754	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	,,,	1167,3085,2251	CC,CT,TT		36.5116,48.2751,41.6654	,,,	707/770,561/624,561/624,849/912	52825585	5419,7587	2203	4300	6503	SO:0001819	synonymous_variant	3697	exon21			AGGCTCTGACCCC		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2547T>C	3.37:g.52825585T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Silent	SNP	ENST00000273283.2	37	CCDS2864.1																																																																																			T|0.568;C|0.432	0.432	strong		0.597	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
ACPT	93650	hgsc.bcm.edu	37	19	51293955	51293955	+	Splice_Site	SNP	G	G	A	rs2162784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51293955G>A	ENST00000270593.1	+	2	216	c.216G>A	c.(214-216)acG>acA	p.T72T	CTD-2568A17.8_ENST00000594114.1_RNA|ACPT_ENST00000270594.3_Splice_Site_p.T72T	NM_033068.2	NP_149059.1	Q9BZG2	PPAT_HUMAN	acid phosphatase, testicular	72						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)		AGCTGACCACGGTGAGAAGCG	0.706													G|||	499	0.0996406	0.152	0.0706	5008	,	,		11090	0.126		0.0805	False		,,,				2504	0.0419				p.T72T		Atlas-SNP	.											.	ACPT	43	.	0			c.G216A						PASS	.			450,3752		22,406,1673	7.0	7.0	7.0		216	4.2	0.9	19	dbSNP_96	7	668,7602		23,622,3490	yes	coding-synonymous-near-splice	ACPT	NM_033068.2		45,1028,5163	AA,AG,GG		8.0774,10.7092,8.9641		72/427	51293955	1118,11354	2101	4135	6236	SO:0001630	splice_region_variant	93650	exon2			GACCACGGTGAGA	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.216+1G>A	19.37:g.51293955G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	51	26	0.509804	NM_033068	C0H3P7|Q9BZG3|Q9BZG4	Silent	SNP	ENST00000270593.1	37	CCDS12802.1																																																																																			G|0.892;A|0.108	0.108	strong		0.706	ACPT-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464434.1	NM_033068	Silent
SSRP1	6749	hgsc.bcm.edu	37	11	57102096	57102096	+	Silent	SNP	A	A	G	rs2230649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57102096A>G	ENST00000278412.2	-	3	347	c.81T>C	c.(79-81)cgT>cgC	p.R27R		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	27					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						TGATGCCCTGACGGCTCAACC	0.517													G|||	846	0.16893	0.3941	0.1326	5008	,	,		23311	0.0218		0.1451	False		,,,				2504	0.0665				p.R27R	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.T81C						PASS	.	G		1539,2863	670.1+/-402.3	248,1043,910	185.0	171.0	176.0		81	3.5	1.0	11	dbSNP_98	176	1434,7158	751.5+/-407.4	100,1234,2962	no	coding-synonymous	SSRP1	NM_003146.2		348,2277,3872	GG,GA,AA		16.6899,34.9614,22.8798		27/710	57102096	2973,10021	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon3			GCCCTGACGGCTC	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.81T>C	11.37:g.57102096A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	25	0.471698	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			A|0.799;G|0.201	0.201	strong		0.517	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
MMP27	64066	hgsc.bcm.edu	37	11	102576358	102576358	+	Missense_Mutation	SNP	T	T	C	rs2846707	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102576358T>C	ENST00000260229.4	-	1	179	c.88A>G	c.(88-90)Atg>Gtg	p.M30V		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	30			M -> V (in dbSNP:rs2846707). {ECO:0000269|Ref.1}.		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)	GCCAGTTGCATATTTTCTTCA	0.343													C|||	4086	0.815895	0.9213	0.7233	5008	,	,		19293	0.8839		0.6799	False		,,,				2504	0.8088				p.M30V		Atlas-SNP	.											.	MMP27	84	.	0			c.A88G						PASS	.	C	VAL/MET	3846,560	249.3+/-256.8	1677,492,34	96.0	102.0	100.0		88	0.2	0.0	11	dbSNP_100	100	5673,2925	457.4+/-364.3	1876,1921,502	yes	missense	MMP27	NM_022122.2	21	3553,2413,536	CC,CT,TT		34.0195,12.7099,26.7994	benign	30/514	102576358	9519,3485	2203	4299	6502	SO:0001583	missense	64066	exon1			GTTGCATATTTTC	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.88A>G	11.37:g.102576358T>C	ENSP00000260229:p.Met30Val	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	180	178	0.988889	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	1728	0.7912087912087912	455	0.9247967479674797	270	0.7458563535911602	510	0.8916083916083916	493	0.6503957783641161	C	0.010	-1.767913	0.00645	0.872901	0.659805	ENSG00000137675	ENST00000260229	T	0.18657	2.2	5.22	0.184	0.15086	Peptidoglycan binding-like (1);Metallopeptidase, catalytic domain (1);	2.099370	0.01609	N	0.022433	T	0.00012	0.0000	N	0.17278	0.47	0.80722	P	0.0	B	0.09022	0.002	B	0.15052	0.012	T	0.33189	-0.9878	9	0.06236	T	0.91	.	7.2012	0.25881	0.0:0.2001:0.1148:0.6851	rs2846707;rs17357793;rs61659932;rs2846707	30	Q9H306	MMP27_HUMAN	V	30	ENSP00000260229:M30V	ENSP00000260229:M30V	M	-	1	0	MMP27	102081568	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.323000	0.07997	-0.282000	0.09128	-1.881000	0.00545	ATG	T|0.229;C|0.771	0.771	strong		0.343	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
ITIH1	3697	hgsc.bcm.edu	37	3	52820981	52820981	+	Missense_Mutation	SNP	A	A	T	rs678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52820981A>T	ENST00000273283.2	+	14	1778	c.1754A>T	c.(1753-1755)gAg>gTg	p.E585V	ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000537050.1_Missense_Mutation_p.E297V|ITIH1_ENST00000542827.1_Missense_Mutation_p.E585V|ITIH1_ENST00000540715.1_Missense_Mutation_p.E443V	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	585	Hyaluronan-binding.		E -> V (in allele ITIH1*2; dbSNP:rs678). {ECO:0000269|PubMed:1380832, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7535743}.		hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GACAGGGAGGAGAGGGCCAAC	0.572													A|||	1437	0.286941	0.1293	0.4452	5008	,	,		17837	0.3621		0.3936	False		,,,				2504	0.2004				p.E585V		Atlas-SNP	.											.	ITIH1	108	.	0			c.A1754T						PASS	.	A	VAL/GLU,VAL/GLU,VAL/GLU,VAL/GLU	646,3760	276.6+/-273.2	53,540,1610	84.0	77.0	79.0		1328,890,890,1754	5.3	1.0	3	dbSNP_36	79	3261,5339	488.0+/-372.2	652,1957,1691	yes	missense,missense,missense,missense	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	121,121,121,121	705,2497,3301	TT,TA,AA		37.9186,14.6618,30.04	probably-damaging,probably-damaging,probably-damaging,probably-damaging	443/770,297/624,297/624,585/912	52820981	3907,9099	2203	4300	6503	SO:0001583	missense	3697	exon14			GGGAGGAGAGGGC		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.1754A>T	3.37:g.52820981A>T	ENSP00000273283:p.Glu585Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	140	56	0.4	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	779	0.3566849816849817	70	0.14227642276422764	165	0.4558011049723757	242	0.4230769230769231	302	0.39841688654353563	A	17.23	3.337296	0.60963	0.146618	0.379186	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04	5.31	5.31	0.75309	.	0.095165	0.64402	D	0.000001	T	0.00012	0.0000	M	0.84846	2.72	0.22858	P	0.99864774	D;D;D	0.89917	0.989;0.997;1.0	D;D;D	0.85130	0.928;0.938;0.997	T	0.46091	-0.9216	9	0.62326	D	0.03	-40.9172	13.6481	0.62294	1.0:0.0:0.0:0.0	rs678;rs1126898;rs3177009;rs3182233;rs17418916;rs52793076;rs678	443;186;585	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	V	585;585;443;297;138	ENSP00000442584:E585V;ENSP00000273283:E585V;ENSP00000443973:E443V;ENSP00000443847:E297V;ENSP00000395836:E138V	ENSP00000273283:E585V	E	+	2	0	ITIH1	52796021	1.000000	0.71417	0.983000	0.44433	0.153000	0.21895	5.954000	0.70298	2.234000	0.73211	0.459000	0.35465	GAG	A|0.681;T|0.319	0.319	strong		0.572	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
B4GALNT3	283358	hgsc.bcm.edu	37	12	661656	661656	+	Missense_Mutation	SNP	A	A	G	rs7298766	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:661656A>G	ENST00000266383.5	+	13	1245	c.1232A>G	c.(1231-1233)aAg>aGg	p.K411R		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	411			K -> R (in dbSNP:rs7298766). {ECO:0000269|PubMed:12966086}.		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)			GAGTACATCAAGATTGACCAG	0.597													A|||	1363	0.272165	0.3026	0.2349	5008	,	,		17742	0.1726		0.329	False		,,,				2504	0.3016				p.K411R		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A1232G						PASS	.	A	ARG/LYS	1459,2947	471.1+/-356.0	251,957,995	57.0	54.0	55.0		1232	4.3	1.0	12	dbSNP_116	55	2628,5972	422.4+/-354.0	392,1844,2064	yes	missense	B4GALNT3	NM_173593.3	26	643,2801,3059	GG,GA,AA		30.5581,33.1139,31.424	probably-damaging	411/999	661656	4087,8919	2203	4300	6503	SO:0001583	missense	283358	exon13			ACATCAAGATTGA	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.1232A>G	12.37:g.661656A>G	ENSP00000266383:p.Lys411Arg	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	292	145	0.496575	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	575	0.2632783882783883	153	0.31097560975609756	103	0.2845303867403315	86	0.15034965034965034	233	0.3073878627968338	A	16.60	3.168671	0.57584	0.331139	0.305581	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.46063	2.95;0.88	5.47	4.3	0.51218	.	0.416227	0.28946	N	0.013626	T	0.00012	0.0000	M	0.64997	1.995	0.31212	P	0.698553	P;P	0.48503	0.911;0.779	B;B	0.42282	0.382;0.251	T	0.28933	-1.0028	9	0.66056	D	0.02	-31.4663	9.5586	0.39355	0.8431:0.0:0.0:0.1569	rs7298766;rs60883111;rs7298766	313;411	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	R	411;313	ENSP00000266383:K411R;ENSP00000322953:K313R	ENSP00000266383:K411R	K	+	2	0	B4GALNT3	531917	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.437000	0.59955	0.885000	0.36088	0.533000	0.62120	AAG	A|0.704;G|0.296	0.296	strong		0.597	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
RND1	27289	hgsc.bcm.edu	37	12	49255798	49255798	+	Silent	SNP	G	G	C	rs1565933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49255798G>C	ENST00000309739.5	-	3	442	c.312C>G	c.(310-312)ctC>ctG	p.L104L		NM_014470.3	NP_055285.1	Q92730	RND1_HUMAN	Rho family GTPase 1	104					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|GTP catabolic process (GO:0006184)|negative regulation of cell adhesion (GO:0007162)|neuron remodeling (GO:0016322)|small GTPase mediated signal transduction (GO:0007264)	adherens junction (GO:0005912)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(2)|skin(1)|urinary_tract(1)	10						TTACCTTCTTGAGTGCGCTGT	0.468													G|||	2057	0.410743	0.2821	0.5432	5008	,	,		22196	0.3869		0.4722	False		,,,				2504	0.4519				p.L104L		Atlas-SNP	.											.	RND1	26	.	0			c.C312G						PASS	.	G		1467,2939	473.7+/-356.8	250,967,986	126.0	105.0	112.0		312	2.3	1.0	12	dbSNP_88	112	4041,4559	556.0+/-386.8	941,2159,1200	no	coding-synonymous	RND1	NM_014470.3		1191,3126,2186	CC,CG,GG		46.9884,33.2955,42.3497		104/233	49255798	5508,7498	2203	4300	6503	SO:0001819	synonymous_variant	27289	exon3			CTTCTTGAGTGCG	Y07923	CCDS8771.1	12q12	2008-01-23				ENSG00000172602			18314	protein-coding gene	gene with protein product	"""ras homolog gene family, member S"""	609038				9531558	Standard	NM_014470		Approved	Rho6, ARHS, RHOS	uc001rsn.3	Q92730	OTTHUMG00000170400	ENST00000309739.5:c.312C>G	12.37:g.49255798G>C		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_014470	A8K9P7	Silent	SNP	ENST00000309739.5	37	CCDS8771.1																																																																																			G|0.576;C|0.424	0.424	strong		0.468	RND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408915.1	NM_014470	
CNKSR3	154043	hgsc.bcm.edu	37	6	154763401	154763401	+	Silent	SNP	G	G	A	rs6557351	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:154763401G>A	ENST00000607772.1	-	3	784	c.240C>T	c.(238-240)aaC>aaT	p.N80N	CNKSR3_ENST00000479339.1_5'UTR	NM_173515.2	NP_775786.2	Q6P9H4	CNKR3_HUMAN	CNKSR family member 3	80	CRIC. {ECO:0000255|PROSITE- ProRule:PRU00621}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)	cytoplasm (GO:0005737)|membrane (GO:0016020)		p.N80N(1)		breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|stomach(1)|urinary_tract(1)	15		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;5.03e-11)|BRCA - Breast invasive adenocarcinoma(81;0.00627)		AGTTCTTCATGTTATCAGTTT	0.428													A|||	1879	0.3752	0.6203	0.3602	5008	,	,		20916	0.2857		0.2445	False		,,,				2504	0.2812				p.N80N		Atlas-SNP	.											CNKSR3,NS,carcinoma,0,1	CNKSR3	56	1	1	Substitution - coding silent(1)	stomach(1)	c.C240T						scavenged	.	A		2556,1850	535.8+/-374.3	725,1106,372	78.0	85.0	83.0		240	-11.1	0.0	6	dbSNP_116	83	1730,6870	736.2+/-407.0	175,1380,2745	no	coding-synonymous	CNKSR3	NM_173515.2		900,2486,3117	AA,AG,GG		20.1163,41.9882,32.954		80/556	154763401	4286,8720	2203	4300	6503	SO:0001819	synonymous_variant	154043	exon3			CTTCATGTTATCA	AK055911	CCDS5246.1	6q25.2	2013-01-10	2005-04-11	2005-04-11	ENSG00000153721	ENSG00000153721		"""Sterile alpha motif (SAM) domain containing"""	23034	protein-coding gene	gene with protein product			"""membrane associated guanylate kinase interacting protein-like 1"""	MAGI1			Standard	NM_173515		Approved	FLJ31349		Q6P9H4	OTTHUMG00000015873	ENST00000607772.1:c.240C>T	6.37:g.154763401G>A		Somatic	75	1	0.0133333		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_173515	Q5SGD5|Q96N65	Silent	SNP	ENST00000607772.1	37	CCDS5246.1																																																																																			G|0.660;A|0.340	0.340	strong		0.428	CNKSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042792.2	NM_173515	
ZNF587	84914	hgsc.bcm.edu	37	19	58371274	58371274	+	Silent	SNP	G	G	T	rs10405892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58371274G>T	ENST00000339656.5	+	3	1676	c.1494G>T	c.(1492-1494)ggG>ggT	p.G498G	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF587_ENST00000419854.1_Silent_p.G455G|ZNF587_ENST00000423137.1_Silent_p.G497G|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		GTGAATGTGGGAAATCATTTC	0.408																																					p.G498G	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											ZNF587,NS,carcinoma,+2,1	ZNF587	53	1	0			c.G1494T						PASS	.						132.0	136.0	134.0					19																	58371274		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			ATGTGGGAAATCA	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1494G>T	19.37:g.58371274G>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	390	82	0.210256	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			G|0.822;T|0.178	0.178	strong		0.408	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
VCX2	51480	hgsc.bcm.edu	37	X	8138171	8138171	+	Missense_Mutation	SNP	T	T	C	rs78723459		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:8138171T>C	ENST00000317103.4	-	3	628	c.322A>G	c.(322-324)Agc>Ggc	p.S108G		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	108	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.			S -> A (in Ref. 1; AAG41765, 2; AAF28172 and 4; AAH98113/AAH96715/AAH98163). {ECO:0000305}.						endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				TCCACCTCGCTCTCCTGACTC	0.647																																					p.S108G		Atlas-SNP	.											.	VCX2	16	.	0			c.A322G						PASS	.						30.0	39.0	36.0					X																	8138171		2142	4234	6376	SO:0001583	missense	51480	exon3			CCTCGCTCTCCTG	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.322A>G	X.37:g.8138171T>C	ENSP00000321309:p.Ser108Gly	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	81	72	0.888889	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	1054	0.6353224834237492	145	0.3835978835978836	132	0.5689655172413793	214	0.6331360946745562	228	0.41155234657039713	T	6.220	0.408758	0.11812	.	.	ENSG00000177504	ENST00000317103	T	0.19105	2.17	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.12013	0.005	B	0.04013	0.001	T	0.35992	-0.9766	7	0.72032	D	0.01	.	.	.	.	.	108	Q9H322	VCX2_HUMAN	G	108	ENSP00000321309:S108G	ENSP00000321309:S108G	S	-	1	0	VCX2	8098171	0.001000	0.12720	0.008000	0.14137	0.008000	0.06430	0.893000	0.28336	0.105000	0.17753	0.104000	0.15600	AGC	T|0.364;C|0.636	0.636	strong		0.647	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
COL8A2	1296	hgsc.bcm.edu	37	1	36563509	36563509	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:36563509G>A	ENST00000397799.1	-	4	1997	c.1773C>T	c.(1771-1773)ccC>ccT	p.P591P	COL8A2_ENST00000303143.4_Silent_p.P591P|COL8A2_ENST00000481785.1_Silent_p.P526P			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	591	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CAAATTTCACGGGCATGCCCG	0.632																																					p.P591P		Atlas-SNP	.											.	COL8A2	41	.	0			c.C1773T						PASS	.						39.0	36.0	37.0					1																	36563509		2202	4300	6502	SO:0001819	synonymous_variant	1296	exon2			TTTCACGGGCATG	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"""Collagens"""	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.1773C>T	1.37:g.36563509G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	69	67	0.971014	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	37	CCDS403.1																																																																																			.	.	none		0.632	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202	
PIGC	5279	hgsc.bcm.edu	37	1	172410967	172410967	+	Missense_Mutation	SNP	G	G	A	rs1063412	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:172410967G>A	ENST00000367728.1	-	1	2259	c.796C>T	c.(796-798)Cca>Tca	p.P266S	PIGC_ENST00000484368.1_Intron|PIGC_ENST00000344529.4_Missense_Mutation_p.P266S|C1orf105_ENST00000367727.4_Intron|PIGC_ENST00000258324.1_Missense_Mutation_p.P266S			Q92535	PIGC_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class C	266			P -> S (in dbSNP:rs1063412). {ECO:0000269|PubMed:9325057}.		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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)|phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			breast(1)|endometrium(1)|kidney(1)|lung(1)	4						AGGTAGAATGGACACAGACAT	0.458													G|||	2275	0.454273	0.0605	0.536	5008	,	,		20245	0.6597		0.5994	False		,,,				2504	0.5675				p.P266S		Atlas-SNP	.											.	PIGC	24	.	0			c.C796T						PASS	.	G	SER/PRO,,SER/PRO	665,3741	282.5+/-276.6	54,557,1592	102.0	98.0	99.0		796,,796	4.2	1.0	1	dbSNP_86	99	4793,3807	613.4+/-396.1	1315,2163,822	yes	missense,intron,missense	PIGC,C1orf105	NM_002642.3,NM_139240.3,NM_153747.1	74,,74	1369,2720,2414	AA,AG,GG		44.2674,15.0931,41.9652	probably-damaging,,probably-damaging	266/298,,266/298	172410967	5458,7548	2203	4300	6503	SO:0001583	missense	5279	exon2			AGAATGGACACAG	BC006539	CCDS1302.1	1q23-q25	2013-02-26	2006-06-28		ENSG00000135845	ENSG00000135845	2.4.1.198	"""Phosphatidylinositol glycan anchor biosynthesis"""	8960	protein-coding gene	gene with protein product	"""phosphatidylinositol N-acetylglucosaminyltransferase"""	601730	"""phosphatidylinositol glycan, class C"""			8806613, 9325057	Standard	NM_153747		Approved		uc001gio.3	Q92535	OTTHUMG00000034751	ENST00000367728.1:c.796C>T	1.37:g.172410967G>A	ENSP00000356702:p.Pro266Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_153747	O14491	Missense_Mutation	SNP	ENST00000367728.1	37	CCDS1302.1	1092	0.5	47	0.09552845528455285	205	0.5662983425414365	377	0.6590909090909091	463	0.6108179419525066	G	21.0	4.083615	0.76642	0.150931	0.557326	ENSG00000135845	ENST00000344529;ENST00000367728;ENST00000258324	T;T;T	0.58060	0.36;0.36;0.36	5.16	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.53400	0.1794	L	0.48260	1.515	0.09310	P	1.0	D	0.89917	1.0	D	0.97110	1.0	T	0.57946	-0.7723	9	0.44086	T	0.13	0.0129	12.3206	0.54983	0.0826:0.0:0.9174:0.0	rs1063412;rs3170727;rs16844444;rs57213706;rs1063412	266	Q92535	PIGC_HUMAN	S	266	ENSP00000356701:P266S;ENSP00000356702:P266S;ENSP00000258324:P266S	ENSP00000258324:P266S	P	-	1	0	PIGC	170677590	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.034000	0.93747	1.157000	0.42530	0.655000	0.94253	CCA	G|0.552;A|0.448	0.448	strong		0.458	PIGC-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084068.1	NM_153747	
USH2A	7399	hgsc.bcm.edu	37	1	216258213	216258213	+	Missense_Mutation	SNP	A	A	G	rs56222536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:216258213A>G	ENST00000307340.3	-	25	5380	c.4994T>C	c.(4993-4995)aTc>aCc	p.I1665T	USH2A_ENST00000366943.2_Missense_Mutation_p.I1665T|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1665	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.		I -> T (in dbSNP:rs56222536). {ECO:0000269|PubMed:17085681, ECO:0000269|PubMed:17296898, ECO:0000269|PubMed:18273898}.		hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACCTTTTTGGATTATCTCTGC	0.328										HNSCC(13;0.011)			A|||	314	0.0626997	0.003	0.0937	5008	,	,		16915	0.0248		0.163	False		,,,				2504	0.0573				p.I1665T		Atlas-SNP	.											.	USH2A	1168	.	0			c.T4994C						PASS	.	A	THR/ILE	124,4278	88.2+/-126.9	2,120,2079	62.0	65.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4994	2.6	0.3	1	dbSNP_129	64	1354,7246	258.8+/-282.3	113,1128,3059	yes	missense	USH2A	NM_206933.2	89	115,1248,5138	GG,GA,AA		15.7442,2.8169,11.3675	benign	1665/5203	216258213	1478,11524	2201	4300	6501	SO:0001583	missense	7399	exon25			TTTTGGATTATCT	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4994T>C	1.37:g.216258213A>G	ENSP00000305941:p.Ile1665Thr	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	176	0.08058608058608059	2	0.0040650406504065045	40	0.11049723756906077	13	0.022727272727272728	121	0.15963060686015831	A	10.62	1.400689	0.25291	0.028169	0.157442	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.79247	-1.25;-1.25	4.93	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.479810	0.17138	N	0.185577	T	0.00552	0.0018	L	0.56769	1.78	0.47511	P	5.549999999999722E-4	B	0.13145	0.007	B	0.12837	0.008	T	0.14337	-1.0476	9	0.31617	T	0.26	.	4.44	0.11570	0.7008:0.0:0.1555:0.1437	rs56222536	1665	O75445	USH2A_HUMAN	T	1665	ENSP00000305941:I1665T;ENSP00000355910:I1665T	ENSP00000305941:I1665T	I	-	2	0	USH2A	214324836	0.854000	0.29725	0.299000	0.25016	0.951000	0.60555	0.932000	0.28884	0.261000	0.21753	-0.262000	0.10625	ATC	A|0.892;G|0.108	0.108	strong		0.328	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
GALNT12	79695	hgsc.bcm.edu	37	9	101611335	101611335	+	Silent	SNP	G	G	C	rs2273846	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:101611335G>C	ENST00000375011.3	+	10	1707	c.1707G>C	c.(1705-1707)tcG>tcC	p.S569S	RP11-92C4.3_ENST00000433997.1_RNA|RP11-92C4.3_ENST00000589257.1_RNA|GALNT12_ENST00000470473.1_3'UTR	NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	569	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				GCACCAACTCGGATCATCAGA	0.488											OREG0019361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	709	0.141573	0.1725	0.0965	5008	,	,		19362	0.2391		0.0686	False		,,,				2504	0.1063				p.S569S		Atlas-SNP	.											.	GALNT12	37	.	0			c.G1707C						PASS	.	G		634,3772	272.5+/-270.8	40,554,1609	111.0	103.0	106.0		1707	-11.5	0.0	9	dbSNP_100	106	448,8152	136.7+/-193.7	12,424,3864	no	coding-synonymous	GALNT12	NM_024642.4		52,978,5473	CC,CG,GG		5.2093,14.3895,8.3192		569/582	101611335	1082,11924	2203	4300	6503	SO:0001819	synonymous_variant	79695	exon10			CAACTCGGATCAT	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19877	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 12"""	610290	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"""			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.1707G>C	9.37:g.101611335G>C		Somatic	94	0	0	1360	WXS	Illumina HiSeq	Phase_I	107	58	0.542056	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Silent	SNP	ENST00000375011.3	37	CCDS6737.1																																																																																			G|0.886;C|0.114	0.114	strong		0.488	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642	
ADAM15	8751	hgsc.bcm.edu	37	1	155033918	155033918	+	Missense_Mutation	SNP	C	C	T	rs41264285	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155033918C>T	ENST00000356955.2	+	20	2406	c.2305C>T	c.(2305-2307)Ccc>Tcc	p.P769S	ADAM15_ENST00000360674.4_Intron|EFNA3_ENST00000556931.1_5'Flank|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000449910.2_Missense_Mutation_p.P768S|EFNA4_ENST00000359751.4_5'Flank|ADAM15_ENST00000368412.3_Silent_p.P744P|ADAM15_ENST00000355956.2_Missense_Mutation_p.P769S|ADAM15_ENST00000368410.2_Intron|EFNA4_ENST00000427683.2_5'Flank|EFNA3_ENST00000505139.1_5'Flank|EFNA4_ENST00000368409.3_5'Flank|ADAM15_ENST00000368413.1_Intron|ADAM15_ENST00000359280.4_Intron|ADAM15_ENST00000271836.6_Intron|ADAM15_ENST00000531455.1_Intron	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	769					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)			CTTCCCGGCCCCCCCTTCCAG	0.657											OREG0013848	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	667	0.133187	0.1921	0.1254	5008	,	,		18432	0.002		0.1928	False		,,,				2504	0.1329				p.P769S		Atlas-SNP	.											.	ADAM15	92	.	0			c.C2305T						PASS	.	C	,,SER/PRO,,SER/PRO,SER/PRO	899,3507	337.8+/-305.0	104,691,1408	45.0	43.0	44.0		,,2305,,2302,2305	3.4	0.6	1	dbSNP_127	44	1824,6776	322.1+/-315.4	188,1448,2664	yes	intron,intron,missense,intron,missense,missense	ADAM15	NM_003815.3,NM_207191.1,NM_207194.1,NM_207195.1,NM_207196.1,NM_207197.1	,,74,,74,74	292,2139,4072	TT,TC,CC		21.2093,20.404,20.9365	,,possibly-damaging,,possibly-damaging,possibly-damaging	,,769/840,,768/863,769/864	155033918	2723,10283	2203	4300	6503	SO:0001583	missense	8751	exon20			CCGGCCCCCCCTT	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.2305C>T	1.37:g.155033918C>T	ENSP00000349436:p.Pro769Ser	Somatic	155	0	0	1767	WXS	Illumina HiSeq	Phase_I	118	62	0.525424	NM_207194	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	37	CCDS1087.1	292	0.1336996336996337	91	0.18495934959349594	45	0.12430939226519337	1	0.0017482517482517483	155	0.20448548812664907	c	15.68	2.904433	0.52333	0.20404	0.212093	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000355956	T;T;T	0.00737	5.81;5.78;5.76	5.37	3.41	0.39046	.	0.163861	0.29133	N	0.013043	T	0.00300	0.0009	N	0.14661	0.345	0.09310	P	0.9999999999999984	P;P;P;P;P	0.45531	0.86;0.86;0.86;0.78;0.78	P;P;P;B;B	0.44561	0.453;0.453;0.453;0.265;0.265	T	0.67734	-0.5594	9	0.15952	T	0.53	.	12.0856	0.53695	0.0:0.6678:0.3322:0.0	rs41264285;rs61811913	768;769;768;769;765	Q13444-7;Q13444-4;Q13444-3;Q13444;Q59GF2	.;.;.;ADA15_HUMAN;.	S	769;768;769	ENSP00000349436:P769S;ENSP00000403843:P768S;ENSP00000348227:P769S	ENSP00000348227:P769S	P	+	1	0	ADAM15	153300542	0.636000	0.27207	0.583000	0.28640	0.958000	0.62258	0.856000	0.27818	0.573000	0.29400	0.639000	0.83563	CCC	C|0.818;T|0.182	0.182	strong		0.657	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	
LTN1	26046	hgsc.bcm.edu	37	21	30339120	30339120	+	Missense_Mutation	SNP	C	C	A	rs34191159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:30339120C>A	ENST00000361371.5	-	10	1772	c.1693G>T	c.(1693-1695)Ggc>Tgc	p.G565C	LTN1_ENST00000389195.2_Missense_Mutation_p.G611C|LTN1_ENST00000389194.2_Missense_Mutation_p.G611C			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	565			G -> C (in dbSNP:rs34191159).		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						AATTCCCAGCCTTCAATCTTC	0.353													C|||	970	0.19369	0.087	0.255	5008	,	,		20229	0.3849		0.1779	False		,,,				2504	0.1135				p.G611C		Atlas-SNP	.											.	LTN1	141	.	0			c.G1831T						PASS	.	C	CYS/GLY	422,3984	205.8+/-227.6	20,382,1801	60.0	55.0	57.0		1831	2.0	0.0	21	dbSNP_126	57	1351,7249	262.1+/-284.2	110,1131,3059	yes	missense	LTN1	NM_015565.2	159	130,1513,4860	AA,AC,CC		15.7093,9.5778,13.6322	probably-damaging	611/1813	30339120	1773,11233	2203	4300	6503	SO:0001583	missense	26046	exon10			CCCAGCCTTCAAT	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.1693G>T	21.37:g.30339120C>A	ENSP00000354977:p.Gly565Cys	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	56	55	0.982143	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		505	0.23122710622710624	49	0.09959349593495935	86	0.23756906077348067	233	0.40734265734265734	137	0.18073878627968337	C	9.941	1.217596	0.22373	0.095778	0.157093	ENSG00000198862	ENST00000389194;ENST00000361371;ENST00000389195	T;T;T	0.25414	2.15;2.16;1.8	4.75	1.97	0.26223	.	0.980624	0.08386	N	0.953805	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.69078	0.997	P	0.55667	0.781	T	0.47812	-0.9088	9	0.48119	T	0.1	.	6.5089	0.22210	0.0:0.7009:0.0:0.2991	rs34191159	565	O94822	LTN1_HUMAN	C	611;565;611	ENSP00000373846:G611C;ENSP00000354977:G565C;ENSP00000373847:G611C	ENSP00000354977:G565C	G	-	1	0	LTN1	29260991	0.010000	0.17322	0.002000	0.10522	0.002000	0.02628	0.745000	0.26259	0.318000	0.23185	-0.145000	0.13849	GGC	C|0.836;A|0.164	0.164	strong		0.353	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565	
SCLY	51540	hgsc.bcm.edu	37	2	238990388	238990388	+	Missense_Mutation	SNP	G	G	A	rs3210400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238990388G>A	ENST00000555827.1	+	5	587	c.523G>A	c.(523-525)Gca>Aca	p.A175T	SCLY_ENST00000254663.6_Missense_Mutation_p.A183T|SCLY_ENST00000373332.3_Missense_Mutation_p.A93T|SCLY_ENST00000422984.2_Missense_Mutation_p.A81T|SCLY_ENST00000429612.2_Intron|SCLY_ENST00000409736.2_Missense_Mutation_p.A175T			Q96I15	SCLY_HUMAN	selenocysteine lyase	175			A -> T (in dbSNP:rs3210400). {ECO:0000269|PubMed:15489334}.		cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		GAGCGGGCAGGCAGAGGTGGA	0.572													G|||	1272	0.253994	0.0393	0.438	5008	,	,		18735	0.2321		0.4563	False		,,,				2504	0.228				p.A183T	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)	Atlas-SNP	.											.	SCLY	51	.	0			c.G547A						PASS	.	G	THR/ALA	415,3991	203.1+/-225.7	18,379,1806	109.0	95.0	99.0		547	5.0	0.0	2	dbSNP_105	99	3642,4958	523.6+/-380.4	794,2054,1452	yes	missense	SCLY	NM_016510.5	58	812,2433,3258	AA,AG,GG		42.3488,9.419,31.1933	benign	183/454	238990388	4057,8949	2203	4300	6503	SO:0001583	missense	51540	exon5			GGGCAGGCAGAGG	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.523G>A	2.37:g.238990388G>A	ENSP00000450613:p.Ala175Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	112	59	0.526786	NM_016510	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Missense_Mutation	SNP	ENST00000555827.1	37		647|647	0.29624542124542125|0.29624542124542125	21|21	0.042682926829268296|0.042682926829268296	156|156	0.430939226519337|0.430939226519337	122|122	0.21328671328671328|0.21328671328671328	348|348	0.45910290237467016|0.45910290237467016	G|G	13.64|13.64	2.296062|2.296062	0.40594|0.40594	0.09419|0.09419	0.423488|0.423488	ENSG00000132330|ENSG00000132330	ENST00000254663;ENST00000555827;ENST00000373332;ENST00000413463;ENST00000409736;ENST00000422984;ENST00000450965|ENST00000437134	T;T;T;D;T;T;T|.	0.86627|.	1.98;1.98;1.56;-2.15;1.56;1.98;1.56|.	5.84|5.84	4.96|4.96	0.65561|0.65561	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);|.	0.522273|.	0.21381|.	N|.	0.075472|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.43152|0.43152	1.355|1.355	0.24182|0.24182	P|P	0.9955825700000001|0.9955825700000001	P;B;P|.	0.42296|.	0.775;0.452;0.696|.	P;B;B|.	0.48873|.	0.593;0.314;0.281|.	T|T	0.50923|0.50923	-0.8770|-0.8770	9|4	0.87932|.	D|.	0|.	-21.4942|-21.4942	10.0151|10.0151	0.42010|0.42010	0.1556:0.0:0.8444:0.0|0.1556:0.0:0.8444:0.0	rs3210400;rs3739052;rs52837213;rs60128375;rs3210400|rs3210400;rs3739052;rs52837213;rs60128375;rs3210400	81;175;175|.	E7ESG3;Q96I15;Q96I15-2|.	.;SCLY_HUMAN;.|.	T|D	183;175;93;89;175;81;5|18	ENSP00000254663:A183T;ENSP00000450613:A175T;ENSP00000362429:A93T;ENSP00000414165:A89T;ENSP00000387162:A175T;ENSP00000416865:A81T;ENSP00000414053:A5T|.	ENSP00000254663:A175T|.	A|G	+|+	1|2	0|0	SCLY|SCLY	238655127|238655127	1.000000|1.000000	0.71417|0.71417	0.008000|0.008000	0.14137|0.14137	0.123000|0.123000	0.20343|0.20343	4.874000|4.874000	0.63064|0.63064	1.464000|1.464000	0.47987|0.47987	0.655000|0.655000	0.94253|0.94253	GCA|GGC	G|0.715;A|0.285	0.285	strong		0.572	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_016510	
OR7G3	390883	hgsc.bcm.edu	37	19	9237542	9237542	+	Missense_Mutation	SNP	T	T	C	rs10414255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9237542T>C	ENST00000305444.2	-	1	84	c.85A>G	c.(85-87)Atg>Gtg	p.M29V		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	29			M -> V (in dbSNP:rs10414255).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						AGGAACAGCATGAAGAGGATG	0.522													t|||	2126	0.424521	0.7141	0.245	5008	,	,		18940	0.3651		0.3141	False		,,,				2504	0.3354				p.M29V		Atlas-SNP	.											.	OR7G3	41	.	0			c.A85G						PASS	.	C	VAL/MET	2875,1531	669.6+/-402.2	950,975,278	90.0	83.0	85.0		85	-8.0	0.0	19	dbSNP_119	85	2675,5925	428.4+/-355.9	386,1903,2011	yes	missense	OR7G3	NM_001001958.1	21	1336,2878,2289	CC,CT,TT		31.1047,34.7481,42.6726	benign	29/313	9237542	5550,7456	2203	4300	6503	SO:0001583	missense	390883	exon1			ACAGCATGAAGAG		CCDS32899.1	19p13.2	2013-09-24			ENSG00000170920	ENSG00000170920		"""GPCR / Class A : Olfactory receptors"""	8467	protein-coding gene	gene with protein product							Standard	NM_001001958		Approved	OST085	uc010xkl.2	Q8NG95	OTTHUMG00000165520	ENST00000305444.2:c.85A>G	19.37:g.9237542T>C	ENSP00000302867:p.Met29Val	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	178	65	0.365169	NM_001001958	Q6IFJ6|Q96R99	Missense_Mutation	SNP	ENST00000305444.2	37	CCDS32899.1	882	0.40384615384615385	370	0.7520325203252033	80	0.22099447513812154	200	0.34965034965034963	232	0.30606860158311344	t	10.30	1.312765	0.23908	0.652519	0.311047	ENSG00000170920	ENST00000305444	T	0.00382	7.61	4.02	-8.03	0.01114	.	0.734757	0.10891	U	0.622752	T	0.00012	0.0000	N	0.00408	-1.53	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.43589	-0.9382	9	0.54805	T	0.06	.	6.0865	0.19970	0.375:0.3986:0.0:0.2264	rs10414255;rs52791633;rs61133744;rs10414255	29	Q8NG95	OR7G3_HUMAN	V	29	ENSP00000302867:M29V	ENSP00000302867:M29V	M	-	1	0	OR7G3	9098542	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.565000	0.02150	-1.594000	0.01615	-0.969000	0.02612	ATG	T|0.569;C|0.431	0.431	strong		0.522	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1		
COL5A3	50509	hgsc.bcm.edu	37	19	10116375	10116375	+	Silent	SNP	G	G	T	rs2303099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10116375G>T	ENST00000264828.3	-	4	538	c.453C>A	c.(451-453)gcC>gcA	p.A151A		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	151	Laminin G-like.				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)			CTATGCTGACGGCCACACGGT	0.632													T|||	2547	0.508586	0.4924	0.5303	5008	,	,		16537	0.2946		0.5149	False		,,,				2504	0.729				p.A151A		Atlas-SNP	.											.	COL5A3	243	.	0			c.C453A						PASS	.	T		2287,2119	575.7+/-384.1	590,1107,506	57.0	51.0	53.0		453	-9.2	0.3	19	dbSNP_100	53	4611,3989	551.2+/-385.9	1224,2163,913	no	coding-synonymous	COL5A3	NM_015719.3		1814,3270,1419	TT,TG,GG		46.3837,48.0935,46.9629		151/1746	10116375	6898,6108	2203	4300	6503	SO:0001819	synonymous_variant	50509	exon4			GCTGACGGCCACA	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.453C>A	19.37:g.10116375G>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			G|0.490;T|0.510	0.510	strong		0.632	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
FFAR3	2865	hgsc.bcm.edu	37	19	35849926	35849926	+	Missense_Mutation	SNP	G	G	A	rs62109581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35849926G>A	ENST00000327809.4	+	2	335	c.134G>A	c.(133-135)cGc>cAc	p.R45H	FFAR3_ENST00000594310.1_Missense_Mutation_p.R45H	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	45			R -> C (in dbSNP:rs423385). {ECO:0000269|PubMed:19630535}.		adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.R45H(1)		endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			AAGCTGCAGCGCCGCCCGGTG	0.647																																					p.R45H	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											FFAR3,NS,carcinoma,0,1	FFAR3	40	1	1	Substitution - Missense(1)	stomach(1)	c.G134A						PASS	.	G	HIS/ARG	631,3767		14,603,1582	188.0	172.0	178.0		134	0.4	0.6	19	dbSNP_131	178	1976,6614		53,1870,2372	no	missense	FFAR3	NM_005304.3	29	67,2473,3954	AA,AG,GG		23.0035,14.3474,20.0724	probably-damaging	45/347	35849926	2607,10381	2199	4295	6494	SO:0001583	missense	2865	exon2			TGCAGCGCCGCCC	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"""GPCR / Class A : Fatty acid receptors"""	4499	protein-coding gene	gene with protein product		603821	"""G protein-coupled receptor 41"""	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.134G>A	19.37:g.35849926G>A	ENSP00000328230:p.Arg45His	Somatic	579	2	0.00345423		WXS	Illumina HiSeq	Phase_I	656	245	0.373476	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	404	0.184981684981685	58	0.11788617886178862	62	0.1712707182320442	119	0.20804195804195805	165	0.21767810026385223	G	11.81	1.750715	0.31046	0.143474	0.230035	ENSG00000185897	ENST00000327809	T	0.39406	1.08	4.99	0.408	0.16377	GPCR, rhodopsin-like superfamily (1);	0.283555	0.33610	U	0.004728	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.6000000000016E-5	B	0.32425	0.371	B	0.28553	0.091	T	0.28902	-1.0029	9	0.45353	T	0.12	-13.598	4.4639	0.11680	0.3446:0.1552:0.5002:0.0	.	45	O14843	FFAR3_HUMAN	H	45	ENSP00000328230:R45H	ENSP00000328230:R45H	R	+	2	0	FFAR3	40541766	0.000000	0.05858	0.608000	0.28969	0.840000	0.47671	-0.177000	0.09796	0.033000	0.15463	0.455000	0.32223	CGC	G|0.800;A|0.200	0.200	strong		0.647	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304	
VCAN	1462	hgsc.bcm.edu	37	5	82835724	82835724	+	Missense_Mutation	SNP	T	T	A	rs160278	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:82835724T>A	ENST00000265077.3	+	8	7467	c.6902T>A	c.(6901-6903)tTt>tAt	p.F2301Y	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.F1314Y|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2301	GAG-beta.		F -> Y (in dbSNP:rs160278).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	ATTGAAGACTTTAACAGAATG	0.373													C|||	2346	0.46845	0.5091	0.5231	5008	,	,		21996	0.3919		0.5199	False		,,,				2504	0.4008				p.F2301Y		Atlas-SNP	.											.	VCAN	498	.	0			c.T6902A						PASS	.	C	,TYR/PHE,,TYR/PHE	2200,2206		547,1106,550	103.0	102.0	102.0		,3941,,6902	3.6	0.0	5	dbSNP_79	102	4244,4356		1065,2114,1121	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,22,,22	1612,3220,1671	AA,AT,TT		49.3488,49.9319,49.5464	,benign,,benign	,1314/2410,,2301/3397	82835724	6444,6562	2203	4300	6503	SO:0001583	missense	1462	exon8			AAGACTTTAACAG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.6902T>A	5.37:g.82835724T>A	ENSP00000265077:p.Phe2301Tyr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	92	49	0.532609	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	1058	0.48443223443223443	235	0.47764227642276424	192	0.5303867403314917	239	0.4178321678321678	392	0.5171503957783641	C	0.004	-2.279707	0.00254	0.499319	0.493488	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.16597	2.33;2.33	6.07	3.61	0.41365	.	1.149720	0.06303	N	0.701319	T	0.00012	0.0000	N	0.11427	0.14	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44406	-0.9330	9	0.02654	T	1	.	6.6224	0.22810	0.4935:0.1278:0.0:0.3787	rs160278;rs310483;rs568397;rs871868;rs3734095;rs3844744;rs52819818;rs160278	1314;2301	P13611-2;P13611	.;CSPG2_HUMAN	Y	2301;1314	ENSP00000265077:F2301Y;ENSP00000340062:F1314Y	ENSP00000265077:F2301Y	F	+	2	0	VCAN	82871480	0.002000	0.14202	0.001000	0.08648	0.003000	0.03518	0.374000	0.20501	0.527000	0.28560	-1.150000	0.01838	TTT	T|0.507;G|0.000;N|0.000;A|0.493	0.493	strong		0.373	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
AGRP	181	hgsc.bcm.edu	37	16	67516605	67516605	+	Silent	SNP	G	G	C	rs34730014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67516605G>C	ENST00000290953.2	-	4	632	c.333C>G	c.(331-333)cgC>cgG	p.R111R	RP11-297D21.4_ENST00000602596.1_RNA|ATP6V0D1_ENST00000540149.1_5'Flank|ATP6V0D1_ENST00000290949.3_5'Flank	NM_001138.1	NP_001129.1	O00253	AGRP_HUMAN	agouti related neuropeptide	111	Agouti. {ECO:0000255|PROSITE- ProRule:PRU00494}.|Interaction with melanocortin receptors.				adult feeding behavior (GO:0008343)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|hormone-mediated signaling pathway (GO:0009755)|maternal process involved in female pregnancy (GO:0060135)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of feeding behavior (GO:2000253)|regulation of feeding behavior (GO:0060259)|response to insulin (GO:0032868)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)	neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			endometrium(1)	1		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)		CATTGAAGAAGCGGCAGTAGC	0.637													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19478	0.0		0.003	False		,,,				2504	0.0				p.R111R		Atlas-SNP	.											.	AGRP	8	.	0			c.C333G						PASS	.	G		6,4390	9.9+/-24.2	0,6,2192	106.0	99.0	101.0		333	0.6	1.0	16	dbSNP_126	101	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous	AGRP	NM_001138.1		0,50,6448	CC,CG,GG		0.5116,0.1365,0.3847		111/133	67516605	50,12946	2198	4300	6498	SO:0001819	synonymous_variant	181	exon4			GAAGAAGCGGCAG	U88063	CCDS10839.1	16q22	2014-07-15	2014-07-15		ENSG00000159723	ENSG00000159723		"""Endogenous ligands"""	330	protein-coding gene	gene with protein product		602311	"""agouti (mouse) related protein"", ""agouti related protein homolog (mouse)"""			9119224, 9311920	Standard	NM_001138		Approved	Agrt, ART, ASIP2	uc002etg.1	O00253	OTTHUMG00000137509	ENST00000290953.2:c.333C>G	16.37:g.67516605G>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	147	63	0.428571	NM_001138	O15459|Q2TBD9	Silent	SNP	ENST00000290953.2	37	CCDS10839.1																																																																																			G|0.997;C|0.003	0.003	strong		0.637	AGRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268828.1		
VCX2	51480	hgsc.bcm.edu	37	X	8138160	8138160	+	Silent	SNP	T	T	C	rs1058238		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:8138160T>C	ENST00000317103.4	-	3	639	c.333A>G	c.(331-333)gaA>gaG	p.E111E		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	111	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.									endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				TCAGTGGTTCTTCCACCTCGC	0.637																																					p.E111E		Atlas-SNP	.											.	VCX2	16	.	0			c.A333G						PASS	.						49.0	57.0	54.0					X																	8138160		2191	4282	6473	SO:0001819	synonymous_variant	51480	exon3			TGGTTCTTCCACC	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.333A>G	X.37:g.8138160T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	104	98	0.942308	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Silent	SNP	ENST00000317103.4	37	CCDS35200.1																																																																																			T|0.239;C|0.761	0.761	strong		0.637	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75407887	75407887	+	Missense_Mutation	SNP	G	G	T	rs57006992	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75407887G>T	ENST00000394810.2	-	4	1672	c.1523C>A	c.(1522-1524)cCc>cAc	p.P508H	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.P284H	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	508	Pro-rich.		P -> H (in dbSNP:rs57006992).			cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					AGACAAGAAGGGGGGTGGGGC	0.667													G|||	383	0.0764776	0.2511	0.0346	5008	,	,		12697	0.0089		0.007	False		,,,				2504	0.0112				p.P508H		Atlas-SNP	.											.	SYNPO2L	118	.	0			c.C1523A						PASS	.	G	HIS/PRO,HIS/PRO	846,3216		60,726,1245	6.0	9.0	8.0		1523,851	4.4	0.7	10	dbSNP_129	8	51,7955		2,47,3954	yes	missense,missense	SYNPO2L	NM_001114133.1,NM_024875.3	77,77	62,773,5199	TT,TG,GG		0.637,20.8272,7.4329	probably-damaging,probably-damaging	508/978,284/754	75407887	897,11171	2031	4003	6034	SO:0001583	missense	79933	exon4			AAGAAGGGGGGTG	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.1523C>A	10.37:g.75407887G>T	ENSP00000378289:p.Pro508His	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	38	19	0.5	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	144	0.06593406593406594	115	0.23373983739837398	16	0.04419889502762431	7	0.012237762237762238	6	0.0079155672823219	G	12.87	2.067278	0.36470	0.208272	0.00637	ENSG00000166317	ENST00000372873;ENST00000372872;ENST00000394810	T;T;T	0.35048	1.85;1.33;2.16	5.31	4.41	0.53225	.	0.264551	0.37715	N	0.001977	T	0.00012	0.0000	L	0.40543	1.245	0.22066	P	0.999386352	B;B	0.33171	0.278;0.4	B;B	0.36464	0.07;0.225	T	0.15578	-1.0432	9	0.62326	D	0.03	-5.2926	15.6046	0.76652	0.0:0.0:0.8615:0.1385	rs57006992	508;284	Q9H987;Q9H987-2	SYP2L_HUMAN;.	H	284;508;508	ENSP00000361964:P284H;ENSP00000361963:P508H;ENSP00000378289:P508H	ENSP00000361963:P508H	P	-	2	0	SYNPO2L	75077893	0.994000	0.37717	0.666000	0.29783	0.768000	0.43524	2.544000	0.45761	1.474000	0.48178	-0.268000	0.10319	CCC	G|0.933;T|0.067	0.067	strong		0.667	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
USH2A	7399	hgsc.bcm.edu	37	1	215848587	215848587	+	Silent	SNP	T	T	C	rs2797234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:215848587T>C	ENST00000307340.3	-	63	13052	c.12666A>G	c.(12664-12666)acA>acG	p.T4222T	USH2A_ENST00000366943.2_Silent_p.T4222T	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4222	Fibronectin type-III 27. {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)	p.T4222T(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TATACATAAATGTATTCCTTT	0.413										HNSCC(13;0.011)			T|||	1518	0.303115	0.1793	0.4539	5008	,	,		20174	0.3155		0.3738	False		,,,				2504	0.2781				p.T4222T		Atlas-SNP	.											USH2A,NS,carcinoma,0,2	USH2A	1168	2	1	Substitution - coding silent(1)	stomach(1)	c.A12666G						PASS	.	T		983,3423	369.8+/-319.3	127,729,1347	114.0	112.0	113.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	12666	-0.2	0.0	1	dbSNP_100	113	3357,5243	498.4+/-374.7	670,2017,1613	no	coding-synonymous	USH2A	NM_206933.2		797,2746,2960	CC,CT,TT		39.0349,22.3105,33.3692		4222/5203	215848587	4340,8666	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon63			CATAAATGTATTC	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.12666A>G	1.37:g.215848587T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			T|0.680;C|0.320	0.320	strong		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
ZBED8	63920	hgsc.bcm.edu	37	5	159820931	159820931	+	Missense_Mutation	SNP	C	C	A	rs10515808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:159820931C>A	ENST00000408953.3	-	2	2074	c.1567G>T	c.(1567-1569)Gca>Tca	p.A523S	C5orf54_ENST00000523213.1_Missense_Mutation_p.A523S	NM_022090.3	NP_071373.2														breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	12						tttggaaatgctgtgaattgg	0.378													C|||	259	0.0517173	0.0242	0.0692	5008	,	,		18533	0.001		0.1143	False		,,,				2504	0.0644				p.A523S		Atlas-SNP	.											C5orf54,NS,carcinoma,+1,1	C5orf54	46	1	0			c.G1567T						PASS	.	C	SER/ALA	176,4230	112.9+/-151.0	1,174,2028	98.0	91.0	93.0		1567	1.0	1.0	5	dbSNP_119	93	881,7719	198.9+/-243.1	45,791,3464	yes	missense	C5orf54	NM_022090.3	99	46,965,5492	AA,AC,CC		10.2442,3.9946,8.127	benign	523/595	159820931	1057,11949	2203	4300	6503	SO:0001583	missense	63920	exon2			GAAATGCTGTGAA																												ENST00000408953.3:c.1567G>T	5.37:g.159820931C>A	ENSP00000386184:p.Ala523Ser	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_022090		Missense_Mutation	SNP	ENST00000408953.3	37	CCDS34283.1	123	0.05631868131868132	12	0.024390243902439025	25	0.06906077348066299	1	0.0017482517482517483	85	0.11213720316622691	C	0.955	-0.705164	0.03255	0.039946	0.102442	ENSG00000221886	ENST00000408953;ENST00000523213	T;T	0.20881	2.04;2.04	2.82	1.03	0.20045	.	.	.	.	.	T	0.00109	0.0003	N	0.01576	-0.805	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40384	-0.9566	8	0.02654	T	1	.	5.1216	0.14863	0.0:0.7156:0.0:0.2844	rs10515808;rs17475306;rs52822306;rs10515808	523	Q8IZ13	CE054_HUMAN	S	523	ENSP00000386184:A523S;ENSP00000428831:A523S	ENSP00000386184:A523S	A	-	1	0	C5orf54	159753509	0.924000	0.31332	0.959000	0.39883	0.725000	0.41563	0.468000	0.22051	0.261000	0.21753	-0.137000	0.14449	GCA	C|0.943;A|0.057	0.057	strong		0.378	C5orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374143.1		
TAF1A	9015	hgsc.bcm.edu	37	1	222734803	222734803	+	Silent	SNP	G	G	C	rs1134898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:222734803G>C	ENST00000352967.4	-	10	1331	c.1143C>G	c.(1141-1143)ggC>ggG	p.G381G	TAF1A_ENST00000391882.1_Silent_p.G267G|TAF1A_ENST00000350027.4_Silent_p.G381G|TAF1A_ENST00000366890.1_Silent_p.G267G	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	381					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA binding (GO:0003677)			kidney(3)|large_intestine(3)|lung(11)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(131;0.0186)		TGAAATGAAAGCCTGGCCACC	0.433													G|||	1565	0.3125	0.0234	0.353	5008	,	,		19439	0.3671		0.5119	False		,,,				2504	0.4131				p.G381G		Atlas-SNP	.											.	TAF1A	35	.	0			c.C1143G						PASS	.	G	,,	458,3948	216.1+/-234.9	29,400,1774	84.0	85.0	85.0		1143,1143,801	1.5	0.5	1	dbSNP_86	85	4170,4430	566.0+/-388.6	1027,2116,1157	no	coding-synonymous,coding-synonymous,coding-synonymous	TAF1A	NM_001201536.1,NM_005681.3,NM_139352.2	,,	1056,2516,2931	CC,CG,GG		48.4884,10.3949,35.5836	,,	381/451,381/451,267/337	222734803	4628,8378	2203	4300	6503	SO:0001819	synonymous_variant	9015	exon10			ATGAAAGCCTGGC	L39060	CCDS1531.1, CCDS1532.1	1q42	2008-02-05	2002-08-29		ENSG00000143498	ENSG00000143498			11532	protein-coding gene	gene with protein product		604903	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kD"""			7801123	Standard	NM_005681		Approved	TAFI48, SL1	uc009xdz.2	Q15573	OTTHUMG00000037544	ENST00000352967.4:c.1143C>G	1.37:g.222734803G>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	181	69	0.381215	NM_001201536	B2RDZ8|D3DTB7|Q9NWA1	Silent	SNP	ENST00000352967.4	37	CCDS1531.1																																																																																			G|0.637;C|0.363	0.363	strong		0.433	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681	
IGF1R	3480	hgsc.bcm.edu	37	15	99465473	99465473	+	Silent	SNP	C	C	T	rs3743262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:99465473C>T	ENST00000268035.6	+	11	2909	c.2298C>T	c.(2296-2298)acC>acT	p.T766T	IGF1R_ENST00000558762.1_Silent_p.T766T	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	766	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	ACAACATCACCGACCCGGAAG	0.527													C|||	672	0.134185	0.0068	0.1427	5008	,	,		19992	0.3661		0.0547	False		,,,				2504	0.1431				p.T766T		Atlas-SNP	.											.	IGF1R	147	.	0			c.C2298T						PASS	.	C		72,4322	64.7+/-102.0	1,70,2126	100.0	96.0	97.0		2298	1.9	1.0	15	dbSNP_107	97	377,8217	123.8+/-182.6	10,357,3930	no	coding-synonymous	IGF1R	NM_000875.3		11,427,6056	TT,TC,CC		4.3868,1.6386,3.457		766/1368	99465473	449,12539	2197	4297	6494	SO:0001819	synonymous_variant	3480	exon11			CATCACCGACCCG	M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.2298C>T	15.37:g.99465473C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																			C|0.921;T|0.079	0.079	strong		0.527	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
FTCD	10841	hgsc.bcm.edu	37	21	47557222	47557222	+	Silent	SNP	G	G	A	rs10432965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47557222G>A	ENST00000291670.5	-	13	1513	c.1470C>T	c.(1468-1470)ggC>ggT	p.G490G	FTCD_ENST00000397743.1_Missense_Mutation_p.R476C|FTCD_ENST00000397746.3_Silent_p.G490G|FTCD_ENST00000498355.2_5'UTR|FTCD_ENST00000397748.1_Silent_p.G490G|FTCD_ENST00000355384.2_Missense_Mutation_p.R476C|FTCD_ENST00000359679.2_Silent_p.G490G	NM_006657.2	NP_006648.1	O95954	FTCD_HUMAN	formimidoyltransferase cyclodeaminase	490	Cyclodeaminase/cyclohydrolase. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|cytoskeleton organization (GO:0007010)|folic acid-containing compound metabolic process (GO:0006760)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)|tetrahydrofolate interconversion (GO:0035999)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	folic acid binding (GO:0005542)|formimidoyltetrahydrofolate cyclodeaminase activity (GO:0030412)|glutamate formimidoyltransferase activity (GO:0030409)			endometrium(1)|large_intestine(2)|lung(9)|pancreas(1)|prostate(3)|skin(3)	19	Breast(49;0.214)			Colorectal(79;0.235)	Tetrahydrofolic acid(DB00116)	CGCCAAACACGCCCATCTCCA	0.602													G|||	839	0.167532	0.2103	0.0951	5008	,	,		18852	0.3512		0.0338	False		,,,				2504	0.1094				p.G490G		Atlas-SNP	.											.	FTCD	59	.	0			c.C1470T						PASS	.	G	,	840,3566	331.0+/-301.8	82,676,1445	142.0	132.0	135.0		1470,1470	-8.2	0.2	21	dbSNP_119	135	352,8248	118.1+/-177.6	1,350,3949	no	coding-synonymous,coding-synonymous	FTCD	NM_006657.2,NM_206965.1	,	83,1026,5394	AA,AG,GG		4.093,19.0649,9.165	,	490/542,490/542	47557222	1192,11814	2203	4300	6503	SO:0001819	synonymous_variant	10841	exon13			AAACACGCCCATC	U91541	CCDS13731.1	21q22.3	2013-06-10	2013-06-10		ENSG00000160282	ENSG00000160282	2.1.2.5, 4.3.1.4		3974	protein-coding gene	gene with protein product		606806	"""formiminotransferase cyclodeaminase"""			10029623, 10773664	Standard	NM_006657		Approved		uc002zif.3	O95954	OTTHUMG00000090488	ENST00000291670.5:c.1470C>T	21.37:g.47557222G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_206965	B9EGD0|Q86V03|Q9HCT4|Q9HCT5|Q9HCT6|Q9UHJ2	Silent	SNP	ENST00000291670.5	37	CCDS13731.1	377|377	0.17261904761904762|0.17261904761904762	97|97	0.19715447154471544|0.19715447154471544	27|27	0.07458563535911603|0.07458563535911603	227|227	0.3968531468531469|0.3968531468531469	26|26	0.03430079155672823|0.03430079155672823	G|G	0.542|0.542	-0.853002|-0.853002	0.02630|0.02630	0.190649|0.190649	0.04093|0.04093	ENSG00000160282|ENSG00000160282	ENST00000446405|ENST00000355384;ENST00000397743	.|D;D	.|0.84800	.|-1.9;-1.9	4.12|4.12	-8.25|-8.25	0.01025|0.01025	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.52501|0.52501	P|P	4.300000000001525E-5|4.300000000001525E-5	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.24621|0.24621	-1.0155|-1.0155	3|7	.|0.72032	.|D	.|0.01	.|.	2.3273|2.3273	0.04226|0.04226	0.2715:0.0919:0.3691:0.2676|0.2715:0.0919:0.3691:0.2676	rs10432965;rs10432965|rs10432965;rs10432965	.|476	.|B7WPK3	.|.	V|C	31|476	.|ENSP00000347545:R476C;ENSP00000380851:R476C	.|ENSP00000347545:R476C	A|R	-|-	2|1	0|0	FTCD|FTCD	46381650|46381650	0.000000|0.000000	0.05858|0.05858	0.210000|0.210000	0.23637|0.23637	0.100000|0.100000	0.18952|0.18952	-4.192000|-4.192000	0.00277|0.00277	-1.093000|-1.093000	0.03058|0.03058	-1.360000|-1.360000	0.01215|0.01215	GCG|CGT	G|0.872;A|0.128	0.128	strong		0.602	FTCD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206962.1	NM_006657	
RIOK2	55781	hgsc.bcm.edu	37	5	96513471	96513471	+	Missense_Mutation	SNP	G	G	C	rs2544773	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96513471G>C	ENST00000283109.3	-	3	355	c.287C>G	c.(286-288)tCt>tGt	p.S96C	CTD-2215E18.1_ENST00000509481.1_Intron|RNU1-73P_ENST00000383971.1_RNA|RIOK2_ENST00000508447.1_Missense_Mutation_p.S96C	NM_018343.2	NP_060813.2	Q9BVS4	RIOK2_HUMAN	RIO kinase 2	96			S -> C (in dbSNP:rs2544773). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|urinary_tract(2)	23		all_cancers(142;0.000125)|all_epithelial(76;8.48e-07)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0676)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0657)		GTTTCCAACAGACTCAACTAC	0.388													G|||	1709	0.341254	0.0749	0.4308	5008	,	,		19950	0.4782		0.4095	False		,,,				2504	0.4264				p.S96C		Atlas-SNP	.											.	RIOK2	82	.	0			c.C287G						PASS	.	G	CYS/SER,CYS/SER	584,3822	258.0+/-262.2	45,494,1664	119.0	109.0	113.0		287,287	5.7	1.0	5	dbSNP_100	113	3418,5182	505.0+/-376.3	680,2058,1562	yes	missense,missense	RIOK2	NM_001159749.1,NM_018343.2	112,112	725,2552,3226	CC,CG,GG		39.7442,13.2547,30.7704	probably-damaging,probably-damaging	96/475,96/553	96513471	4002,9004	2203	4300	6503	SO:0001583	missense	55781	exon3			CCAACAGACTCAA	AK002021	CCDS4089.1, CCDS54884.1	5q14	2012-12-10	2012-12-10		ENSG00000058729	ENSG00000058729			18999	protein-coding gene	gene with protein product			"""RIO kinase 2 (yeast)"""				Standard	NM_018343		Approved	FLJ11159	uc003kmz.3	Q9BVS4	OTTHUMG00000128723	ENST00000283109.3:c.287C>G	5.37:g.96513471G>C	ENSP00000283109:p.Ser96Cys	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	149	65	0.436242	NM_001159749	D6RDI3|Q9NUT0	Missense_Mutation	SNP	ENST00000283109.3	37	CCDS4089.1	781	0.3576007326007326	56	0.11382113821138211	151	0.4171270718232044	254	0.44405594405594406	320	0.42216358839050133	G	26.9	4.785840	0.90282	0.132547	0.397442	ENSG00000058729	ENST00000283109;ENST00000508447	T;T	0.05717	3.49;3.4	5.7	5.7	0.88788	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.92317	3.295	0.09310	P	0.9999999999536962	D;D	0.89917	1.0;1.0	D;D	0.74674	0.984;0.971	T	0.36016	-0.9765	9	0.87932	D	0	-15.9783	19.4334	0.94781	0.0:0.0:1.0:0.0	rs2544773;rs52835076;rs2544773	96;96	D6RDI3;Q9BVS4	.;RIOK2_HUMAN	C	96	ENSP00000283109:S96C;ENSP00000420932:S96C	ENSP00000283109:S96C	S	-	2	0	RIOK2	96539227	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.230000	0.95299	2.683000	0.91414	0.650000	0.86243	TCT	G|0.673;C|0.327	0.327	strong		0.388	RIOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250628.1	NM_018343	
CCDC136	64753	hgsc.bcm.edu	37	7	128455916	128455916	+	Silent	SNP	G	G	A	rs2270590	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128455916G>A	ENST00000297788.4	+	16	3661	c.3294G>A	c.(3292-3294)gaG>gaA	p.E1098E	CCDC136_ENST00000378685.4_Intron|CCDC136_ENST00000487361.1_Intron|CCDC136_ENST00000464832.1_Intron|CCDC136_ENST00000471729.1_3'UTR	NM_022742.4	NP_073579	Q96JN2	CC136_HUMAN	coiled-coil domain containing 136	1098	Glu-rich.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(3)	24						aagaggaggaggaTGACGCCG	0.488													A|||	2110	0.421326	0.6793	0.2824	5008	,	,		21280	0.5833		0.1471	False		,,,				2504	0.2863				p.E1098E		Atlas-SNP	.											.	CCDC136	170	.	0			c.G3294A						PASS	.	A	,	2382,1680		694,994,343	108.0	124.0	119.0		,3294	-2.2	0.0	7	dbSNP_100	119	1309,7045		93,1123,2961	no	intron,coding-synonymous	CCDC136	NM_001201372.1,NM_022742.4	,	787,2117,3304	AA,AG,GG		15.6691,41.3589,29.7278	,	,1098/1155	128455916	3691,8725	2031	4177	6208	SO:0001819	synonymous_variant	64753	exon16			GGAGGAGGATGAC		CCDS47704.1, CCDS56510.1	7q33	2007-08-01			ENSG00000128596	ENSG00000128596			22225	protein-coding gene	gene with protein product		611902				15112360	Standard	NM_022742		Approved	KIAA1793, NAG6, DKFZP434G156	uc003vnv.2	Q96JN2	OTTHUMG00000158310	ENST00000297788.4:c.3294G>A	7.37:g.128455916G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_022742	A4D1K1|A7MCY7|A8MYA7|Q6ZVK7|Q9H8M3|Q9UFE1	Silent	SNP	ENST00000297788.4	37	CCDS47704.1	853	0.39056776556776557	309	0.6280487804878049	93	0.2569060773480663	339	0.5926573426573427	112	0.14775725593667546	A	1.198	-0.633386	0.03584	0.586411	0.156691	ENSG00000128596	ENST00000494552	.	.	.	1.08	-2.17	0.07059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.42599	-0.9442	3	.	.	.	4.4954	3.2714	0.06883	0.2236:0.0:0.5398:0.2366	rs2270590;rs60406895;rs2270590	.	.	.	K	975	.	.	R	+	2	0	CCDC136	128243152	0.000000	0.05858	0.002000	0.10522	0.080000	0.17528	-2.626000	0.00874	-1.561000	0.01684	-1.361000	0.01213	AGG	G|0.609;A|0.391	0.391	strong		0.488	CCDC136-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350641.1	NM_022742	
OR8D2	283160	hgsc.bcm.edu	37	11	124189729	124189729	+	Missense_Mutation	SNP	C	C	T	rs2512219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124189729C>T	ENST00000357438.2	-	1	455	c.365G>A	c.(364-366)cGt>cAt	p.R122H		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	122			R -> H (in dbSNP:rs2512219).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		AGCAACATAACGGTCATATTC	0.413													C|||	1390	0.277556	0.4531	0.2003	5008	,	,		21904	0.1895		0.1292	False		,,,				2504	0.3384				p.R122H		Atlas-SNP	.											.	OR8D2	65	.	0			c.G365A						PASS	.	C	HIS/ARG	1863,2539	632.0+/-395.8	384,1095,722	93.0	88.0	90.0		365	1.6	0.3	11	dbSNP_100	90	1275,7323	759.9+/-407.6	112,1051,3136	yes	missense	OR8D2	NM_001002918.1	29	496,2146,3858	TT,TC,CC		14.829,42.3217,24.1385	benign	122/312	124189729	3138,9862	2201	4299	6500	SO:0001583	missense	283160	exon1			ACATAACGGTCAT	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"""GPCR / Class A : Olfactory receptors"""	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.365G>A	11.37:g.124189729C>T	ENSP00000350022:p.Arg122His	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	59	26	0.440678	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	520	0.23809523809523808	224	0.45528455284552843	71	0.19613259668508287	124	0.21678321678321677	101	0.13324538258575197	t	8.823	0.938032	0.18206	0.423217	0.14829	ENSG00000197263	ENST00000357438	T	0.77489	-1.1	3.59	1.61	0.23674	GPCR, rhodopsin-like superfamily (1);	0.277746	0.25817	N	0.028104	T	0.00012	0.0000	M	0.81179	2.53	0.31244	P	0.6948639999999999	B	0.06786	0.001	B	0.04013	0.001	T	0.27905	-1.0060	9	0.87932	D	0	.	9.5229	0.39147	0.0:0.8075:0.0:0.1925	rs2512219;rs52814690;rs56609149;rs61070044;rs2512219	122	Q9GZM6	OR8D2_HUMAN	H	122	ENSP00000350022:R122H	ENSP00000350022:R122H	R	-	2	0	OR8D2	123694939	0.978000	0.34361	0.318000	0.25279	0.021000	0.10359	5.273000	0.65564	0.473000	0.27368	-0.271000	0.10264	CGT	C|0.749;T|0.250	0.250	strong		0.413	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918	
ANAPC1	64682	hgsc.bcm.edu	37	2	112592265	112592265	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:112592265T>C	ENST00000341068.3	-	19	3072	c.2300A>G	c.(2299-2301)cAc>cGc	p.H767R		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	767					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)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						ATACACAAGGTGAAGAACGAA	0.378																																					p.H767R		Atlas-SNP	.											ANAPC1,NS,carcinoma,0,1	ANAPC1	116	1	0			c.A2300G						scavenged	.						83.0	80.0	81.0					2																	112592265		2203	4300	6503	SO:0001583	missense	64682	exon19			ACAAGGTGAAGAA	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.2300A>G	2.37:g.112592265T>C	ENSP00000339109:p.His767Arg	Somatic	319	2	0.00626959		WXS	Illumina HiSeq	Phase_I	448	52	0.116071	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.370389	0.82573	.	.	ENSG00000153107	ENST00000341068	T	0.30448	1.53	5.16	5.16	0.70880	.	0.000000	0.46758	U	0.000266	T	0.60907	0.2305	M	0.87097	2.86	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.68949	-0.5274	10	0.72032	D	0.01	-17.8092	15.0301	0.71698	0.0:0.0:0.0:1.0	.	767	Q9H1A4	APC1_HUMAN	R	767	ENSP00000339109:H767R	ENSP00000339109:H767R	H	-	2	0	ANAPC1	112308736	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.495000	0.81514	1.962000	0.57031	0.456000	0.33151	CAC	CGAAGAACG|0.500;TGAAGAACA|0.500	.	alt		0.378	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557479	32557479	+	Missense_Mutation	SNP	G	G	A	rs9270302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32557479G>A	ENST00000360004.5	-	1	146	c.41C>T	c.(40-42)gCg>gTg	p.A14V		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	14					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						CACTGTCAGCGCTGTCATGCA	0.597										Multiple Myeloma(14;0.17)			G|||	877	0.17512	0.2617	0.1095	5008	,	,		24567	0.1806		0.1332	False		,,,				2504	0.1421				p.A14V		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C41T						PASS	.						88.0	107.0	100.0					6																	32557479		1511	2709	4220	SO:0001583	missense	3123	exon1			GTCAGCGCTGTCA	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.41C>T	6.37:g.32557479G>A	ENSP00000353099:p.Ala14Val	Somatic	278	0	0		WXS	Illumina HiSeq	Phase_I	259	51	0.196911	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	10.85	1.467756	0.26335	.	.	ENSG00000196126	ENST00000360004	T	0.00274	8.35	4.4	-2.03	0.07365	MHC classes I/II-like antigen recognition protein (1);	0.965897	0.08531	N	0.932108	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.04522	-1.0945	8	0.42905	T	0.14	.	4.4141	0.11447	0.3802:0.3072:0.3126:0.0	rs9270302;rs16822884;rs17885220;rs35245858	14	P01911	2B1F_HUMAN	V	14	ENSP00000353099:A14V	ENSP00000353099:A14V	A	-	2	0	HLA-DRB1	32665457	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.896000	0.28377	-0.082000	0.12640	-0.448000	0.05591	GCG	A|0.267;C|0.015;G|0.718	0.267	strong		0.597	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
CYTL1	54360	hgsc.bcm.edu	37	4	5021086	5021086	+	Silent	SNP	G	G	T	rs10006676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5021086G>T	ENST00000307746.4	-	1	113	c.87C>A	c.(85-87)tcC>tcA	p.S29S		NM_018659.2	NP_061129.1	Q9NRR1	CYTL1_HUMAN	cytokine-like 1	29					cartilage homeostasis (GO:1990079)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|inner ear development (GO:0048839)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			breast(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	11				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		CCCGCATGCGGGAGTAGCAGG	0.726													G|||	569	0.113618	0.2829	0.0605	5008	,	,		10464	0.0317		0.0567	False		,,,				2504	0.0654				p.S29S	Colon(15;457 478 29696 43408 47165)	Atlas-SNP	.											.	CYTL1	20	.	0			c.C87A						PASS	.	G		941,3437		98,745,1346	11.0	14.0	13.0		87	-3.0	0.4	4	dbSNP_119	13	474,8102		10,454,3824	no	coding-synonymous	CYTL1	NM_018659.2		108,1199,5170	TT,TG,GG		5.5271,21.4938,10.9233		29/137	5021086	1415,11539	2189	4288	6477	SO:0001819	synonymous_variant	54360	exon1			CATGCGGGAGTAG	AF193766	CCDS3379.1	4p16-p15	2007-08-01			ENSG00000170891	ENSG00000170891			24435	protein-coding gene	gene with protein product		607930				10857752	Standard	NM_018659		Approved	C17, C4orf4	uc003gig.3	Q9NRR1	OTTHUMG00000125479	ENST00000307746.4:c.87C>A	4.37:g.5021086G>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_018659		Silent	SNP	ENST00000307746.4	37	CCDS3379.1	230|230	0.10531135531135531|0.10531135531135531	149|149	0.30284552845528456|0.30284552845528456	23|23	0.06353591160220995|0.06353591160220995	16|16	0.027972027972027972|0.027972027972027972	42|42	0.055408970976253295|0.055408970976253295	G|G	3.033|3.033	-0.199159|-0.199159	0.06219|0.06219	0.214938|0.214938	0.055271|0.055271	ENSG00000170891|ENSG00000170891	ENST00000509419|ENST00000506508	.|.	.|.	.|.	4.76|4.76	-2.95|-2.95	0.05564|0.05564	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999270158|0.99999270158	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.40887|0.40887	-0.9539|-0.9539	3|3	.|.	.|.	.|.	-50.0875|-50.0875	1.1774|1.1774	0.01838|0.01838	0.2526:0.1145:0.3785:0.2544|0.2526:0.1145:0.3785:0.2544	rs10006676|rs10006676	.|.	.|.	.|.	H|T	28|27	.|.	.|.	P|P	-|-	2|1	0|0	CYTL1|CYTL1	5071987|5071987	0.740000|0.740000	0.28207|0.28207	0.431000|0.431000	0.26735|0.26735	0.145000|0.145000	0.21501|0.21501	-0.214000|-0.214000	0.09292|0.09292	-0.457000|-0.457000	0.07033|0.07033	-0.466000|-0.466000	0.05196|0.05196	CCC|CCG	G|0.898;T|0.102	0.102	strong		0.726	CYTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246802.1	NM_018659	
DLK2	65989	hgsc.bcm.edu	37	6	43418733	43418733	+	Silent	SNP	G	G	A	rs1214749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43418733G>A	ENST00000357338.3	-	6	1396	c.696C>T	c.(694-696)caC>caT	p.H232H	DLK2_ENST00000372488.3_Silent_p.H232H|DLK2_ENST00000414245.1_Silent_p.H226H|DLK2_ENST00000372485.1_Silent_p.H226H	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	232	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			AGTCGAAGTCGTGGACACGGT	0.627													A|||	1397	0.278954	0.5424	0.2147	5008	,	,		18721	0.0804		0.2863	False		,,,				2504	0.1656				p.H232H		Atlas-SNP	.											.	DLK2	22	.	0			c.C696T						PASS	.	A	,	2216,2190	577.0+/-384.4	559,1098,546	60.0	64.0	62.0		696,696	-5.8	0.8	6	dbSNP_87	62	2675,5925	675.2+/-403.2	424,1827,2049	no	coding-synonymous,coding-synonymous	DLK2	NM_023932.2,NM_206539.1	,	983,2925,2595	AA,AG,GG		31.1047,49.7049,37.6057	,	232/384,232/384	43418733	4891,8115	2203	4300	6503	SO:0001819	synonymous_variant	65989	exon6			GAAGTCGTGGACA	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.696C>T	6.37:g.43418733G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Silent	SNP	ENST00000357338.3	37	CCDS4897.1	577	0.2641941391941392	247	0.5020325203252033	81	0.22375690607734808	41	0.07167832167832168	208	0.27440633245382584	A	4.262	0.047770	0.08243	0.502951	0.311047	ENSG00000171462	ENST00000430324	.	.	.	4.94	-5.77	0.02369	.	.	.	.	.	T	0.18002	0.0432	.	.	.	0.09310	P	0.9999999602075	.	.	.	.	.	.	T	0.18808	-1.0325	3	.	.	.	.	9.4542	0.38745	0.2896:0.2188:0.4916:0.0	rs1214749;rs1674841;rs1214749	.	.	.	M	138	.	.	T	-	2	0	DLK2	43526711	0.338000	0.24775	0.835000	0.33067	0.653000	0.38743	-0.286000	0.08399	-1.278000	0.02408	-1.390000	0.01156	ACG	G|0.662;A|0.338	0.338	strong		0.627	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
OGDHL	55753	hgsc.bcm.edu	37	10	50960209	50960209	+	Silent	SNP	G	G	A	rs1258184	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50960209G>A	ENST00000374103.4	-	5	649	c.564C>T	c.(562-564)ctC>ctT	p.L188L	OGDHL_ENST00000432695.1_5'UTR|OGDHL_ENST00000419399.1_Silent_p.L131L	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	188					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						CCCGCAGAGAGAGGGTGTTTT	0.592													G|||	2325	0.464257	0.1407	0.4798	5008	,	,		18974	0.9107		0.4642	False		,,,				2504	0.4305				p.L188L		Atlas-SNP	.											.	OGDHL	149	.	0			c.C564T						PASS	.	G	,,	875,3531	338.4+/-305.3	95,685,1423	55.0	55.0	55.0		393,,564	-9.7	0.7	10	dbSNP_87	55	4170,4430	565.4+/-388.5	1014,2142,1144	no	coding-synonymous,utr-5,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	1109,2827,2567	AA,AG,GG		48.4884,19.8593,38.7898	,,	131/954,,188/1011	50960209	5045,7961	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon5			CAGAGAGAGGGTG	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.564C>T	10.37:g.50960209G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			G|0.567;A|0.433	0.433	strong		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
KIF17	57576	hgsc.bcm.edu	37	1	21011346	21011346	+	Silent	SNP	A	A	G	rs12028811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:21011346A>G	ENST00000247986.2	-	10	2497	c.2187T>C	c.(2185-2187)acT>acC	p.T729T	KIF17_ENST00000400463.3_Silent_p.T729T|KIF17_ENST00000375044.1_Silent_p.T629T|KIF17_ENST00000490034.1_5'UTR			Q9P2E2	KIF17_HUMAN	kinesin family member 17	729					ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		GCGGGTCATCAGTCAGCACTG	0.697													G|||	1129	0.225439	0.3116	0.1455	5008	,	,		16866	0.3353		0.0855	False		,,,				2504	0.1963				p.T729T		Atlas-SNP	.											KIF17,caecum,carcinoma,-1,1	KIF17	130	1	0			c.T2187C						PASS	.	G	,	1193,3201		170,853,1174	53.0	43.0	46.0		2187,2187	-7.8	0.0	1	dbSNP_120	46	755,7827		35,685,3571	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	205,1538,4745	GG,GA,AA		8.7975,27.1507,15.0123	,	729/1029,729/1030	21011346	1948,11028	2197	4291	6488	SO:0001819	synonymous_variant	57576	exon10			GTCATCAGTCAGC	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.2187T>C	1.37:g.21011346A>G		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	172	162	0.94186	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			A|0.831;G|0.169	0.169	strong		0.697	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
CCDC39	339829	hgsc.bcm.edu	37	3	180334623	180334623	+	Silent	SNP	C	C	T	rs7612917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:180334623C>T	ENST00000442201.2	-	17	2516	c.2397G>A	c.(2395-2397)gtG>gtA	p.V799V	TTC14_ENST00000382584.4_Intron|CCDC39_ENST00000273654.4_3'UTR	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	799					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)				NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			CCTGTTTGGTCACTCTTTCTA	0.308													C|||	658	0.13139	0.1536	0.2061	5008	,	,		15917	0.002		0.2147	False		,,,				2504	0.0961				p.V799V		Atlas-SNP	.											CCDC39_ENST00000442201,NS,carcinoma,-2,1	CCDC39	242	1	0			c.G2397A						PASS	.	C		549,3081		37,475,1303	171.0	152.0	158.0		2397	-0.5	1.0	3	dbSNP_116	158	1589,6541		141,1307,2617	no	coding-synonymous	CCDC39	NM_181426.1		178,1782,3920	TT,TC,CC		19.5449,15.124,18.1803		799/942	180334623	2138,9622	1815	4065	5880	SO:0001819	synonymous_variant	339829	exon17			TTTGGTCACTCTT	BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.2397G>A	3.37:g.180334623C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_181426	B4E2H1	Silent	SNP	ENST00000442201.2	37	CCDS46964.1																																																																																			C|0.838;T|0.162	0.162	strong		0.308	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
KRT83	3889	hgsc.bcm.edu	37	12	52709883	52709883	+	Silent	SNP	T	T	C	rs2248473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52709883T>C	ENST00000293670.3	-	7	1118	c.1056A>G	c.(1054-1056)gaA>gaG	p.E352E		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	352	Coil 2.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.E352E(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCACCGCAGCTTCCAGCTTGG	0.567													N|||	1882	0.375799	0.5008	0.317	5008	,	,		16721	0.1885		0.4095	False		,,,				2504	0.407				p.E352E	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,0,1	KRT83	64	1	1	Substitution - coding silent(1)	stomach(1)	c.A1056G						scavenged	.	T		2084,2322		553,978,672	23.0	26.0	25.0		1056	3.0	0.9	12	dbSNP_100	25	3392,5208		718,1956,1626	no	coding-synonymous	KRT83	NM_002282.3		1271,2934,2298	CC,CT,TT		39.4419,47.2991,42.1036		352/494	52709883	5476,7530	2203	4300	6503	SO:0001819	synonymous_variant	3889	exon7			CGCAGCTTCCAGC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.1056A>G	12.37:g.52709883T>C		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			T|0.629;C|0.371	0.371	strong		0.567	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
TAF7L	54457	hgsc.bcm.edu	37	X	100547804	100547804	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547804G>C	ENST00000372907.3	-	1	241	c.230C>G	c.(229-231)gCc>gGc	p.A77G	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_5'UTR	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	77					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						GTTTTCTGGGGCCTGGGCAGC	0.557																																					p.A77G	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.C230G						PASS	.						69.0	70.0	70.0					X																	100547804		2203	4300	6503	SO:0001583	missense	54457	exon1			TCTGGGGCCTGGG	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.230C>G	X.37:g.100547804G>C	ENSP00000361998:p.Ala77Gly	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	47	45	0.957447	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	G	8.991	0.977721	0.18812	.	.	ENSG00000102387	ENST00000372907	T	0.15834	2.39	3.06	2.19	0.27852	.	2.099320	0.02710	N	0.112725	T	0.12305	0.0299	L	0.27053	0.805	0.09310	N	0.999996	B	0.33694	0.421	B	0.24006	0.05	T	0.24476	-1.0159	10	0.72032	D	0.01	-1.4147	5.2676	0.15607	0.165:0.0:0.8349:0.0	.	77	Q5H9L4	TAF7L_HUMAN	G	77	ENSP00000361998:A77G	ENSP00000361998:A77G	A	-	2	0	TAF7L	100434460	0.006000	0.16342	0.001000	0.08648	0.009000	0.06853	1.723000	0.38053	0.681000	0.31386	0.600000	0.82982	GCC	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
RAB36	9609	hgsc.bcm.edu	37	22	23503170	23503170	+	Missense_Mutation	SNP	A	A	G	rs5759612	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:23503170A>G	ENST00000263116.2	+	10	962	c.922A>G	c.(922-924)Aat>Gat	p.N308D	RAB36_ENST00000341989.4_Missense_Mutation_p.N286D	NM_004914.2	NP_004905.2	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family	308			N -> D (in dbSNP:rs5759612). {ECO:0000269|PubMed:9920784}.		protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		CCAGGTCGGCAATGGAGACCT	0.607													G|||	2781	0.555312	0.5265	0.4654	5008	,	,		21125	0.6448		0.5119	False		,,,				2504	0.6104				p.N308D		Atlas-SNP	.											.	RAB36	26	.	0			c.A922G						PASS	.	G	ASP/ASN	2404,2002	559.6+/-380.3	661,1082,460	85.0	69.0	74.0		922	3.6	1.0	22	dbSNP_114	74	4288,4312	578.0+/-390.6	1088,2112,1100	yes	missense	RAB36	NM_004914.2	23	1749,3194,1560	GG,GA,AA		49.8605,45.438,48.5468	benign	308/334	23503170	6692,6314	2203	4300	6503	SO:0001583	missense	9609	exon10			GTCGGCAATGGAG	AB023061	CCDS13805.1	22q11.22	2008-06-11			ENSG00000100228	ENSG00000100228		"""RAB, member RAS oncogene"""	9775	protein-coding gene	gene with protein product		605662				9920784, 10591208	Standard	NM_004914		Approved		uc002zwv.1	O95755	OTTHUMG00000150601	ENST00000263116.2:c.922A>G	22.37:g.23503170A>G	ENSP00000263116:p.Asn308Asp	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_004914	Q2M390|Q7Z4A9|Q9UHP5	Missense_Mutation	SNP	ENST00000263116.2	37	CCDS13805.1	1182	0.5412087912087912	261	0.5304878048780488	179	0.494475138121547	359	0.6276223776223776	383	0.5052770448548812	G	1.563	-0.536108	0.04082	0.54562	0.498605	ENSG00000100228	ENST00000263116;ENST00000341989	T;T	0.63096	-0.02;0.38	5.67	3.59	0.41128	.	0.419531	0.24851	N	0.035086	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47548	-0.9109	9	0.02654	T	1	-13.2367	9.9112	0.41406	0.2244:0.0:0.7756:0.0	rs5759612;rs58963192;rs5759612	286;308	O95755-2;O95755	.;RAB36_HUMAN	D	308;286	ENSP00000263116:N308D;ENSP00000343494:N286D	ENSP00000263116:N308D	N	+	1	0	RAB36	21833170	0.332000	0.24722	0.980000	0.43619	0.283000	0.27025	0.812000	0.27211	0.457000	0.26962	-0.119000	0.15052	AAT	A|0.466;G|0.534	0.534	strong		0.607	RAB36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319046.1	NM_004914	
LRRC7	57554	hgsc.bcm.edu	37	1	70504360	70504360	+	Silent	SNP	C	C	T	rs77157341	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:70504360C>T	ENST00000035383.5	+	19	2769	c.2739C>T	c.(2737-2739)caC>caT	p.H913H	LRRC7_ENST00000415775.2_Silent_p.H197H|LRRC7_ENST00000310961.5_Silent_p.H918H	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	913						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)				breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						CTCAAATCCACTGCCGCCCGG	0.393													C|||	27	0.00539137	0.0	0.0072	5008	,	,		19249	0.0		0.0199	False		,,,				2504	0.002				p.H913H		Atlas-SNP	.											.	LRRC7	400	.	0			c.C2739T						PASS	.	C		14,4392	22.3+/-47.3	0,14,2189	55.0	54.0	55.0		2739	5.8	1.0	1	dbSNP_132	55	127,8473	64.2+/-126.4	1,125,4174	no	coding-synonymous	LRRC7	NM_020794.2		1,139,6363	TT,TC,CC		1.4767,0.3177,1.0841		913/1538	70504360	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	57554	exon19			AATCCACTGCCGC		CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2739C>T	1.37:g.70504360C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	58	22	0.37931	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Silent	SNP	ENST00000035383.5	37	CCDS645.1																																																																																			C|0.990;T|0.010	0.010	strong		0.393	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794	
PRC1	9055	hgsc.bcm.edu	37	15	91525197	91525197	+	Silent	SNP	C	C	T	rs2301826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91525197C>T	ENST00000361188.5	-	4	1493	c.282G>A	c.(280-282)acG>acA	p.T94T	PRC1_ENST00000442656.2_Silent_p.T53T|PRC1_ENST00000394249.3_Silent_p.T94T|PRC1_ENST00000556129.1_5'Flank|PRC1_ENST00000361919.3_Silent_p.T94T|PRC1-AS1_ENST00000554388.1_RNA					protein regulator of cytokinesis 1											endometrium(1)|kidney(2)|large_intestine(7)|lung(9)|ovary(3)|prostate(1)|skin(2)	25	Lung NSC(78;0.0987)|all_lung(78;0.175)					GCAAGATGGTCGTCTCTCCTT	0.418													T|||	2357	0.470647	0.767	0.3271	5008	,	,		22656	0.5109		0.2147	False		,,,				2504	0.3937				p.T94T		Atlas-SNP	.											PRC1,NS,carcinoma,-1,1	PRC1	51	1	0			c.G282A						PASS	.	T	,,	3004,1392	457.1+/-351.5	1031,942,225	160.0	166.0	164.0		282,282,282	-10.8	0.0	15	dbSNP_100	164	1766,6830	734.0+/-406.9	180,1406,2712	no	coding-synonymous,coding-synonymous,coding-synonymous	PRC1	NM_003981.2,NM_199413.1,NM_199414.1	,,	1211,2348,2937	TT,TC,CC		20.5444,31.6652,36.7149	,,	94/621,94/607,94/567	91525197	4770,8222	2198	4298	6496	SO:0001819	synonymous_variant	9055	exon4			GATGGTCGTCTCT	AF044588	CCDS32334.1, CCDS45352.1, CCDS45353.1, CCDS45353.2	15q26.1	2013-05-29		2006-07-07	ENSG00000198901	ENSG00000198901			9341	protein-coding gene	gene with protein product	"""anaphase spindle elongation 1 homolog (S. cerevisiae)"""	603484				9885575	Standard	NM_003981		Approved	ASE1	uc002bqm.4	O43663	OTTHUMG00000171685	ENST00000361188.5:c.282G>A	15.37:g.91525197C>T		Somatic	186	1	0.00537634		WXS	Illumina HiSeq	Phase_I	158	158	1	NM_199413		Silent	SNP	ENST00000361188.5	37	CCDS45352.1																																																																																			C|0.592;T|0.408	0.408	strong		0.418	PRC1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414760.1	NM_003981	
BIN3	55909	hgsc.bcm.edu	37	8	22526559	22526559	+	Silent	SNP	G	G	A	rs11550509	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22526559G>A	ENST00000276416.6	-	1	74	c.6C>T	c.(4-6)agC>agT	p.S2S	BIN3_ENST00000519513.1_5'UTR|BIN3_ENST00000519335.1_5'UTR|BIN3_ENST00000522268.1_Silent_p.S2S|BIN3_ENST00000520292.1_Silent_p.S2S	NM_018688.4	NP_061158.1	Q9NQY0	BIN3_HUMAN	bridging integrator 3	2					actin filament organization (GO:0007015)|barrier septum assembly (GO:0000917)|cytokinesis (GO:0000910)|myoblast migration involved in skeletal muscle regeneration (GO:0014839)|protein localization (GO:0008104)|regulation of lamellipodium assembly (GO:0010591)|skeletal muscle fiber development (GO:0048741)|unidimensional cell growth (GO:0009826)	actin filament (GO:0005884)|cytoplasm (GO:0005737)	cytoskeletal adaptor activity (GO:0008093)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	9		Prostate(55;0.0424)|Breast(100;0.102)|all_epithelial(46;0.143)		BRCA - Breast invasive adenocarcinoma(99;0.00664)|Colorectal(74;0.0189)|COAD - Colon adenocarcinoma(73;0.0727)		TCACTCACCAGCTCATGGTCC	0.682													G|||	495	0.0988419	0.0106	0.1614	5008	,	,		13749	0.0069		0.2555	False		,,,				2504	0.1074				p.S2S		Atlas-SNP	.											.	BIN3	16	.	0			c.C6T						PASS	.	G		220,3746		6,208,1769	14.0	21.0	19.0		6	0.7	1.0	8	dbSNP_123	19	2085,6159		267,1551,2304	no	coding-synonymous	BIN3	NM_018688.4		273,1759,4073	AA,AG,GG		25.2911,5.5472,18.878		2/254	22526559	2305,9905	1983	4122	6105	SO:0001819	synonymous_variant	55909	exon1			TCACCAGCTCATG		CCDS47825.1	8p21.2	2008-07-04			ENSG00000147439	ENSG00000147439			1054	protein-coding gene	gene with protein product		606396				16524918	Standard	NM_018688		Approved		uc003xcl.3	Q9NQY0	OTTHUMG00000163844	ENST00000276416.6:c.6C>T	8.37:g.22526559G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_018688	Q9BVG2|Q9NVY9	Silent	SNP	ENST00000276416.6	37	CCDS47825.1																																																																																			G|0.877;A|0.123	0.123	strong		0.682	BIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375895.1		
TAS2R4	50832	hgsc.bcm.edu	37	7	141478800	141478800	+	Missense_Mutation	SNP	G	G	A	rs2234002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141478800G>A	ENST00000247881.2	+	1	559	c.512G>A	c.(511-513)aGt>aAt	p.S171N	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	171			S -> N (in dbSNP:rs2234002).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		TTTAATATCAGTGAGGGCATC	0.423													g|||	2461	0.491414	0.1929	0.5663	5008	,	,		22114	0.745		0.4722	False		,,,				2504	0.6002				p.S171N		Atlas-SNP	.											.	TAS2R4	25	.	0			c.G512A						PASS	.	A	ASN/SER	1106,3300	398.5+/-330.9	147,812,1244	263.0	256.0	259.0		512	-8.9	0.0	7	dbSNP_98	259	4271,4329	574.9+/-390.1	1053,2165,1082	yes	missense	TAS2R4	NM_016944.1	46	1200,2977,2326	AA,AG,GG		49.6628,25.1021,41.3425	benign	171/300	141478800	5377,7629	2203	4300	6503	SO:0001583	missense	50832	exon1			ATATCAGTGAGGG	AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.512G>A	7.37:g.141478800G>A	ENSP00000247881:p.Ser171Asn	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	187	87	0.465241	NM_016944	Q645W5|Q75MV8	Missense_Mutation	SNP	ENST00000247881.2	37	CCDS5868.1	1081	0.49496336996337	103	0.20934959349593496	198	0.5469613259668509	427	0.7465034965034965	353	0.4656992084432718	g	0.003	-2.486927	0.00161	0.251021	0.496628	ENSG00000127364	ENST00000247881	T	0.00768	5.72	5.06	-8.91	0.00778	.	1.458410	0.03642	N	0.239661	T	0.00012	0.0000	N	0.10760	0.04	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.43294	-0.9400	9	0.02654	T	1	.	10.909	0.47097	0.2401:0.2116:0.5482:0.0	rs2234002;rs3735277;rs17523587;rs52816893;rs60480904;rs2234002	171	Q9NYW5	TA2R4_HUMAN	N	171	ENSP00000247881:S171N	ENSP00000247881:S171N	S	+	2	0	TAS2R4	141125269	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.744000	0.04839	-1.732000	0.01359	-0.508000	0.04489	AGT	G|0.543;A|0.457	0.457	strong		0.423	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1		
FAM186A	121006	hgsc.bcm.edu	37	12	50744581	50744581	+	Missense_Mutation	SNP	A	A	T	rs73108300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:50744581A>T	ENST00000327337.5	-	4	6033	c.6034T>A	c.(6034-6036)Ttt>Att	p.F2012I	FAM186A_ENST00000543111.1_Missense_Mutation_p.F2012I|FAM186A_ENST00000543096.1_Missense_Mutation_p.F23I	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2012								p.F2012I(1)									AATGTTCTAAATGATTCTATA	0.428													A|||	49	0.00978435	0.0015	0.0187	5008	,	,		19782	0.0		0.0308	False		,,,				2504	0.0031				p.F2012I	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											FAM186A_ENST00000327337,NS,carcinoma,0,1	FAM186A	181	1	1	Substitution - Missense(1)	kidney(1)	c.T6034A						PASS	.	A	ILE/PHE	9,1375		0,9,683	262.0	237.0	245.0		6034	1.7	0.0	12	dbSNP_130	245	94,3088		2,90,1499	yes	missense	FAM186A	NM_001145475.1	21	2,99,2182	TT,TA,AA		2.9541,0.6503,2.2558	possibly-damaging	2012/2352	50744581	103,4463	692	1591	2283	SO:0001583	missense	121006	exon4			TTCTAAATGATTC		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.6034T>A	12.37:g.50744581A>T	ENSP00000329995:p.Phe2012Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	37	CCDS44878.1	30	0.013736263736263736	3	0.006097560975609756	7	0.019337016574585635	0	0.0	20	0.026385224274406333	A	16.29	3.080372	0.55753	0.006503	0.029541	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.18016	2.82;2.24;2.82	4.1	1.73	0.24493	.	.	.	.	.	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	P;P	0.38677	0.642;0.642	B;B	0.35353	0.201;0.201	T	0.31861	-0.9928	9	0.19147	T	0.46	.	5.3694	0.16131	0.7615:0.0:0.2385:0.0	.	2012;2012	F5GYN0;A6NE01	.;F186A_HUMAN	I	2012;23;2012	ENSP00000441337:F2012I;ENSP00000443703:F23I;ENSP00000329995:F2012I	ENSP00000329995:F2012I	F	-	1	0	FAM186A	49030848	0.000000	0.05858	0.010000	0.14722	0.116000	0.19942	0.009000	0.13219	0.258000	0.21686	0.459000	0.35465	TTT	A|0.986;T|0.014	0.014	strong		0.428	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
UMODL1	89766	hgsc.bcm.edu	37	21	43539293	43539293	+	Missense_Mutation	SNP	G	G	A	rs220146	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43539293G>A	ENST00000408910.2	+	15	2548	c.2548G>A	c.(2548-2550)Gtc>Atc	p.V850I	UMODL1_ENST00000400427.1_Missense_Mutation_p.V906I|UMODL1_ENST00000400424.2_Missense_Mutation_p.V778I|UMODL1_ENST00000408989.2_Missense_Mutation_p.V978I	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	850	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.		V -> I (in dbSNP:rs220146). {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						AGTCGTCAGCGTCACCAACGG	0.597													G|||	1097	0.21905	0.1543	0.33	5008	,	,		18810	0.2222		0.2227	False		,,,				2504	0.2209				p.V978I	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.G2932A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	667,3723	252.4+/-258.8	54,559,1582	223.0	234.0	231.0		2548,2716,2332,2932	-6.2	0.0	21	dbSNP_79	231	1813,6755	318.4+/-313.7	193,1427,2664	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	29,29,29,29	247,1986,4246	AA,AG,GG		21.1601,15.1936,19.1388	benign,benign,benign,benign	850/1319,906/1375,778/1247,978/1447	43539293	2480,10478	2195	4284	6479	SO:0001583	missense	89766	exon14			GTCAGCGTCACCA		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.2548G>A	21.37:g.43539293G>A	ENSP00000386147:p.Val850Ile	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	502	0.22985347985347984	80	0.16260162601626016	112	0.30939226519337015	131	0.229020979020979	179	0.23614775725593667	G	0.004	-2.333671	0.00227	0.151936	0.211601	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.37584	1.19;1.19;1.19;1.19	3.75	-6.16	0.02098	SEA (1);	0.301289	0.22945	N	0.053726	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.18310	0.027;0.001	B;B	0.12156	0.007;0.003	T	0.35624	-0.9781	8	.	.	.	-23.2709	14.5121	0.67794	0.348:0.0:0.652:0.0	rs220146;rs60151193;rs220146	978;850	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	I	906;778;978;850	ENSP00000383279:V906I;ENSP00000383276:V778I;ENSP00000386126:V978I;ENSP00000386147:V850I	.	V	+	1	0	UMODL1	42412362	0.000000	0.05858	0.004000	0.12327	0.019000	0.09904	-0.816000	0.04477	-1.273000	0.02424	0.462000	0.41574	GTC	G|0.780;A|0.220	0.220	strong		0.597	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
ABCD4	5826	hgsc.bcm.edu	37	14	74766352	74766352	+	Silent	SNP	A	A	G	rs2301345	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:74766352A>G	ENST00000356924.4	-	3	327	c.184T>C	c.(184-186)Ttg>Ctg	p.L62L	ABCD4_ENST00000557554.1_5'UTR|ABCD4_ENST00000557588.1_Silent_p.L62L|ABCD4_ENST00000298816.7_5'UTR	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	62	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)		CTGGGGATCAAGCCAACCTGG	0.478													A|||	1315	0.26258	0.1195	0.2695	5008	,	,		20179	0.247		0.3857	False		,,,				2504	0.3405				p.L62L		Atlas-SNP	.											.	ABCD4	54	.	0			c.T184C						PASS	.	A		766,3640	309.1+/-290.9	64,638,1501	103.0	84.0	90.0		184	-2.6	1.0	14	dbSNP_100	90	3123,5477	472.3+/-368.3	551,2021,1728	no	coding-synonymous	ABCD4	NM_005050.3		615,2659,3229	GG,GA,AA		36.314,17.3854,29.9016		62/607	74766352	3889,9117	2203	4300	6503	SO:0001819	synonymous_variant	5826	exon3			GGATCAAGCCAAC	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.184T>C	14.37:g.74766352A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	132	69	0.522727	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Silent	SNP	ENST00000356924.4	37	CCDS9828.1																																																																																			A|0.717;G|0.283	0.283	strong		0.478	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
SPATC1L	84221	hgsc.bcm.edu	37	21	47588427	47588427	+	Silent	SNP	G	G	A	rs74486947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47588427G>A	ENST00000291672.5	-	3	1400	c.339C>T	c.(337-339)ccC>ccT	p.P113P	SPATC1L_ENST00000330205.6_5'UTR	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	113			P -> L (in dbSNP:rs884134).														AGGCCTTGAAGGGTGCCTGGG	0.652													G|||	278	0.0555112	0.1982	0.0202	5008	,	,		15628	0.0		0.002	False		,,,				2504	0.0				p.P113P		Atlas-SNP	.											.	.	.	.	0			c.C339T						PASS	.	G	,	227,1157		18,191,483	41.0	43.0	42.0		339,	1.4	0.9	21	dbSNP_132	42	6,3176		0,6,1585	no	coding-synonymous,utr-5	C21orf56	NM_001142854.1,NM_032261.4	,	18,197,2068	AA,AG,GG		0.1886,16.4017,5.1029	,	113/341,	47588427	233,4333	692	1591	2283	SO:0001819	synonymous_variant	84221	exon3			CTTGAAGGGTGCC	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.339C>T	21.37:g.47588427G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Silent	SNP	ENST00000291672.5	37	CCDS46653.1																																																																																			G|0.966;A|0.034	0.034	strong		0.652	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806332	33806332	+	Silent	SNP	C	C	T	rs8066132	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33806332C>T	ENST00000260908.7	-	2	1014	c.897G>A	c.(895-897)ggG>ggA	p.G299G	SLFN12L_ENST00000361112.4_Silent_p.G328G|SLFN12L_ENST00000449046.1_Silent_p.G330G|RP11-686D22.9_ENST00000587076.1_RNA	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	299						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						AATTTATCGTCCCCTTCTCCA	0.398													C|||	787	0.157149	0.2012	0.1095	5008	,	,		20256	0.0149		0.1561	False		,,,				2504	0.2791				p.G299G		Atlas-SNP	.											.	SLFN12L	140	.	0			c.G897A						PASS	.	C		244,1140		20,204,468	127.0	102.0	109.0		897	-0.8	0.0	17	dbSNP_116	109	458,2724		40,378,1173	no	coding-synonymous	SLFN12L	NM_001195790.1		60,582,1641	TT,TC,CC		14.3935,17.6301,15.3745		299/589	33806332	702,3864	692	1591	2283	SO:0001819	synonymous_variant	100506736	exon2			TATCGTCCCCTTC	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.897G>A	17.37:g.33806332C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	170	85	0.5	NM_001195790	F5H6G3	Silent	SNP	ENST00000260908.7	37	CCDS56026.1																																																																																			C|0.865;T|0.135	0.135	strong		0.398	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
NSD1	64324	hgsc.bcm.edu	37	5	176721272	176721272	+	Silent	SNP	G	G	C	rs11740250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176721272G>C	ENST00000439151.2	+	23	6948	c.6903G>C	c.(6901-6903)ggG>ggC	p.G2301G	NSD1_ENST00000354179.4_Silent_p.G2032G|NSD1_ENST00000361032.4_Silent_p.G2198G|NSD1_ENST00000347982.4_Silent_p.G2032G	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2301	Pro-rich.				gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		ACCTCGCTGGGTCAGGGACCA	0.572			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	541	0.108027	0.0106	0.1455	5008	,	,		18881	0.0		0.2475	False		,,,				2504	0.181				p.G2301G		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G6903C						PASS	.	G	,	184,4222	115.4+/-153.4	7,170,2026	55.0	57.0	57.0		6903,6096	-1.2	1.0	5	dbSNP_120	57	2158,6442	349.2+/-327.3	281,1596,2423	no	coding-synonymous,coding-synonymous	NSD1	NM_022455.4,NM_172349.2	,	288,1766,4449	CC,CG,GG		25.093,4.1761,18.0071	,	2301/2697,2032/2428	176721272	2342,10664	2203	4300	6503	SO:0001819	synonymous_variant	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	CGCTGGGTCAGGG	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.6903G>C	5.37:g.176721272G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_022455	Q96PD8|Q96RN7	Silent	SNP	ENST00000439151.2	37	CCDS4412.1																																																																																			G|0.836;C|0.164	0.164	strong		0.572	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
FANCD2	2177	hgsc.bcm.edu	37	3	10088299	10088299	+	Silent	SNP	C	C	T	rs112887807		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:10088299C>T	ENST00000419585.1	+	15	1331	c.1170C>T	c.(1168-1170)agC>agT	p.S390S	FANCD2_ENST00000383807.1_Silent_p.S390S|FANCD2_ENST00000383806.1_Silent_p.S390S|FANCD2_ENST00000287647.3_Silent_p.S390S			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	390					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TCATCTATAGCACCAATACTC	0.373			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S390S		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253	.	0			c.C1170T						PASS	.						116.0	106.0	109.0					3																	10088299		2203	4300	6503	SO:0001819	synonymous_variant	2177	exon15	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTATAGCACCAAT	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1170C>T	3.37:g.10088299C>T		Somatic	375	0	0		WXS	Illumina HiSeq	Phase_I	471	120	0.254777	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			C|0.500;T|0.500	0.500	weak		0.373	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
HCFC1	3054	hgsc.bcm.edu	37	X	153222835	153222835	+	Silent	SNP	G	G	C	rs2071134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153222835G>C	ENST00000310441.7	-	13	3249	c.2283C>G	c.(2281-2283)acC>acG	p.T761T	HCFC1_ENST00000369984.4_Silent_p.T761T|HCFC1_ENST00000461098.1_5'Flank|HCFC1_ENST00000354233.3_Silent_p.T692T	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	761	Interaction with ZBTB17.				cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGCCGGGCTTGGTGGTACTGG	0.642													G|||	1450	0.384106	0.0461	0.3545	3775	,	,		13235	0.5784		0.1223	False		,,,				2504	0.4468				p.T761T		Atlas-SNP	.											.	HCFC1	284	.	0			c.C2283G						PASS	.	G		249,3481		9,186,45,1385,525	116.0	126.0	122.0		2283	4.1	1.0	X	dbSNP_96	122	947,5648		43,588,273,1757,1546	no	coding-synonymous	HCFC1	NM_005334.2		52,774,318,3142,2071	CC,CG,C,GG,G		14.3594,6.6756,11.5835		761/2036	153222835	1196,9129	2150	4207	6357	SO:0001819	synonymous_variant	3054	exon13			GGGCTTGGTGGTA		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.2283C>G	X.37:g.153222835G>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	98	95	0.969388	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1																																																																																			G|0.665;C|0.335	0.335	strong		0.642	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
CACNA1I	8911	hgsc.bcm.edu	37	22	40057273	40057273	+	Silent	SNP	T	T	C	rs136852	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:40057273T>C	ENST00000402142.3	+	16	2859	c.2859T>C	c.(2857-2859)agT>agC	p.S953S	CACNA1I_ENST00000401624.1_Silent_p.S953S|CACNA1I_ENST00000400164.3_Silent_p.S918S|CACNA1I_ENST00000404898.1_Silent_p.S918S|CACNA1I_ENST00000336649.4_Silent_p.S959S|CACNA1I_ENST00000407673.1_Silent_p.S918S	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	953					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)	GAAAGAGCAGTGTCATGTCTC	0.667													C|||	3690	0.736821	0.792	0.7363	5008	,	,		18175	0.994		0.5527	False		,,,				2504	0.5869				p.S953S		Atlas-SNP	.											.	CACNA1I	264	.	0			c.T2859C						PASS	.	C	,	3008,930		1153,702,114	32.0	37.0	35.0		2754,2859	-5.4	0.8	22	dbSNP_78	35	4417,3857		1187,2043,907	no	coding-synonymous,coding-synonymous	CACNA1I	NM_001003406.1,NM_021096.3	,	2340,2745,1021	CC,CT,TT		46.6159,23.616,39.1991	,	918/2189,953/2224	40057273	7425,4787	1969	4137	6106	SO:0001819	synonymous_variant	8911	exon16			GAGCAGTGTCATG	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.2859T>C	22.37:g.40057273T>C		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	29	0.467742	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Silent	SNP	ENST00000402142.3	37	CCDS46710.1																																																																																			T|0.284;C|0.716	0.716	strong		0.667	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
CORIN	10699	hgsc.bcm.edu	37	4	47605505	47605505	+	Silent	SNP	G	G	A	rs61759670	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:47605505G>A	ENST00000273857.4	-	20	2720	c.2721C>T	c.(2719-2721)taC>taT	p.Y907Y	CORIN_ENST00000502252.1_Silent_p.Y840Y|CORIN_ENST00000508498.1_Silent_p.Y768Y|CORIN_ENST00000505909.1_Silent_p.Y870Y	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	907	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						CAGGCCGGACGTAGCCAGTCT	0.547													G|||	104	0.0207668	0.0015	0.0216	5008	,	,		18783	0.0		0.0169	False		,,,				2504	0.0716				p.Y907Y		Atlas-SNP	.											.	CORIN	154	.	0			c.C2721T						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	128.0	105.0	113.0		2721	-6.1	0.3	4	dbSNP_129	113	200,8400	86.9+/-149.2	3,194,4103	no	coding-synonymous	CORIN	NM_006587.2		3,212,6288	AA,AG,GG		2.3256,0.4085,1.6761		907/1043	47605505	218,12788	2203	4300	6503	SO:0001819	synonymous_variant	10699	exon20			CCGGACGTAGCCA	AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"""Serine peptidases / Transmembrane"""	19012	protein-coding gene	gene with protein product		605236	"""corin, serine protease"""			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.2721C>T	4.37:g.47605505G>A		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	120	54	0.45	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Silent	SNP	ENST00000273857.4	37	CCDS3477.1																																																																																			G|0.986;A|0.014	0.014	strong		0.547	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2		
NLRP3	114548	hgsc.bcm.edu	37	1	247588053	247588053	+	Silent	SNP	C	C	T	rs34298354	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:247588053C>T	ENST00000336119.3	+	3	2054	c.1308C>T	c.(1306-1308)tcC>tcT	p.S436S	NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391828.3_Silent_p.S436S|NLRP3_ENST00000391827.2_Silent_p.S436S|NLRP3_ENST00000366497.2_Silent_p.S436S|NLRP3_ENST00000366496.2_Silent_p.S436S|NLRP3_ENST00000348069.2_Silent_p.S436S	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	436	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CCCAGACATCCAAGACCACCA	0.612													C|||	329	0.0656949	0.0053	0.062	5008	,	,		19956	0.0685		0.1143	False		,,,				2504	0.0971				p.S436S		Atlas-SNP	.											NLRP3,NS,carcinoma,+1,1	NLRP3	286	1	0			c.C1308T						PASS	.	C	,,,,	106,4300	81.9+/-120.4	1,104,2098	97.0	80.0	86.0		1308,1308,1308,1308,1308	1.3	1.0	1	dbSNP_126	86	1051,7549	223.1+/-260.0	59,933,3308	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	60,1037,5406	TT,TC,CC		12.2209,2.4058,8.8959	,,,,	436/1037,436/980,436/980,436/1037,436/923	247588053	1157,11849	2203	4300	6503	SO:0001819	synonymous_variant	114548	exon3			GACATCCAAGACC	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1308C>T	1.37:g.247588053C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																			C|0.912;T|0.088	0.088	strong		0.612	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
SYNPO2	171024	hgsc.bcm.edu	37	4	119952955	119952955	+	Missense_Mutation	SNP	C	C	T	rs61732241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:119952955C>T	ENST00000429713.2	+	4	3207	c.3025C>T	c.(3025-3027)Cgg>Tgg	p.R1009W	SYNPO2_ENST00000307142.4_Missense_Mutation_p.R1009W|SYNPO2_ENST00000434046.2_Missense_Mutation_p.R1009W|SYNPO2_ENST00000448416.2_Intron	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	1009						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						TCTTCCTCCCCGGCCAGTGAA	0.542													C|||	180	0.0359425	0.0023	0.0562	5008	,	,		21466	0.001		0.1113	False		,,,				2504	0.0256				p.R1009W		Atlas-SNP	.											.	SYNPO2	353	.	0			c.C3025T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	87,4319	74.7+/-112.8	1,85,2117	100.0	85.0	90.0		3025,3025,3025	3.4	0.1	4	dbSNP_129	90	873,7727	197.8+/-242.3	51,771,3478	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	101,101,101	52,856,5595	TT,TC,CC		10.1512,1.9746,7.3812	probably-damaging,probably-damaging,probably-damaging	1009/1094,1009/1110,1009/1262	119952955	960,12046	2203	4300	6503	SO:0001583	missense	171024	exon4			CCTCCCCGGCCAG	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.3025C>T	4.37:g.119952955C>T	ENSP00000395143:p.Arg1009Trp	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	181	91	0.502762	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	105|105	0.04807692307692308|0.04807692307692308	2|2	0.0040650406504065045|0.0040650406504065045	18|18	0.049723756906077346|0.049723756906077346	0|0	0.0|0.0	85|85	0.11213720316622691|0.11213720316622691	C|C	8.808|8.808	0.934621|0.934621	0.18206|0.18206	0.019746|0.019746	0.101512|0.101512	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	T|T;T;T	0.13420|0.09630	2.59|2.96;2.98;2.97	5.19|5.19	3.41|3.41	0.39046|0.39046	.|.	.|0.357560	.|0.23668	.|N	.|0.045759	T|T	0.00440|0.00440	0.0014|0.0014	L|L	0.57536|0.57536	1.79|1.79	0.58432|0.58432	P|P	5.000000000032756E-6|5.000000000032756E-6	.|D;P;D;D	.|0.89917	.|1.0;0.463;1.0;0.999	.|D;B;P;P	.|0.65573	.|0.936;0.067;0.893;0.821	T|T	0.03761|0.03761	-1.1006|-1.1006	5|8	.|.	.|.	.|.	-8.7573|-8.7573	8.2935|8.2935	0.31971|0.31971	0.2772:0.649:0.0:0.0738|0.2772:0.649:0.0:0.0738	rs61732241|rs61732241	.|1009;1009;1009;1009	.|B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;.;SYNP2_HUMAN	L|W	960|1009	ENSP00000425496:P960L|ENSP00000306015:R1009W;ENSP00000395143:R1009W;ENSP00000390965:R1009W	.|.	P|R	+|+	2|1	0|2	SYNPO2|SYNPO2	120172403|120172403	0.000000|0.000000	0.05858|0.05858	0.070000|0.070000	0.20053|0.20053	0.039000|0.039000	0.13416|0.13416	-2.009000|-2.009000	0.01455|0.01455	0.538000|0.538000	0.28769|0.28769	0.655000|0.655000	0.94253|0.94253	CCG|CGG	C|0.932;T|0.068	0.068	strong		0.542	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
OR4K15	81127	hgsc.bcm.edu	37	14	20444588	20444588	+	Missense_Mutation	SNP	T	T	C	rs2153466	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20444588T>C	ENST00000305051.5	+	1	986	c.911T>C	c.(910-912)cTt>cCt	p.L304P		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	304			L -> P (in dbSNP:rs2153466). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATCTTCACGCTTATTTTAAAC	0.408													C|||	1885	0.376398	0.7496	0.2017	5008	,	,		18141	0.1498		0.2435	False		,,,				2504	0.3661				p.L304P		Atlas-SNP	.											.	OR4K15	82	.	0			c.T911C						PASS	.	C	PRO/LEU	3041,1365		1040,961,202	107.0	108.0	108.0		911	4.0	0.7	14	dbSNP_96	108	2424,6176		332,1760,2208	no	missense	OR4K15	NM_001005486.1	98	1372,2721,2410	CC,CT,TT		28.186,30.9805,42.0191	benign	304/349	20444588	5465,7541	2203	4300	6503	SO:0001583	missense	81127	exon1			TCACGCTTATTTT		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.911T>C	14.37:g.20444588T>C	ENSP00000304077:p.Leu304Pro	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	215	114	0.530233	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	696	0.31868131868131866	353	0.717479674796748	70	0.19337016574585636	81	0.14160839160839161	192	0.2532981530343008	.	0.012	-1.649809	0.00785	0.690195	0.28186	ENSG00000169488	ENST00000305051	T	0.30714	1.52	3.99	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	N	0.000110	T	0.00012	0.0000	N	0.08118	0	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40572	-0.9556	9	0.02654	T	1	.	9.6002	0.39598	0.0:0.8945:0.0:0.1055	rs2153466;rs17276905;rs52807813;rs57272158;rs2153466	304	Q8NH41	OR4KF_HUMAN	P	304	ENSP00000304077:L304P	ENSP00000304077:L304P	L	+	2	0	OR4K15	19514428	0.958000	0.32768	0.749000	0.31150	0.194000	0.23727	4.153000	0.58118	0.895000	0.36342	-0.186000	0.12905	CTT	T|0.613;C|0.387	0.387	strong		0.408	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
TSPAN16	26526	hgsc.bcm.edu	37	19	11407019	11407019	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11407019T>C	ENST00000316737.1	+	1	196	c.46T>C	c.(46-48)Tct>Cct	p.S16P	TSPAN16_ENST00000590327.1_Missense_Mutation_p.S16P|TSPAN16_ENST00000592955.1_Missense_Mutation_p.S16P	NM_012466.2	NP_036598.1	Q9UKR8	TSN16_HUMAN	tetraspanin 16	16						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	12						GAAACTGTTATCTTTACTCAA	0.463																																					p.S16P		Atlas-SNP	.											.	TSPAN16	22	.	0			c.T46C						PASS	.						122.0	114.0	117.0					19																	11407019		2203	4300	6503	SO:0001583	missense	26526	exon1			CTGTTATCTTTAC	BC029908	CCDS12256.1, CCDS62549.1, CCDS62550.1	19p13.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000130167	ENSG00000130167		"""Tetraspanins"""	30725	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 16"""	TM4SF16		10500248	Standard	NM_012466		Approved	TM4-B, TM-8	uc002mqv.1	Q9UKR8	OTTHUMG00000180833	ENST00000316737.1:c.46T>C	19.37:g.11407019T>C	ENSP00000319486:p.Ser16Pro	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	121	57	0.471074	NM_012466	K7EN22|K7EPD8|Q8N6J7	Missense_Mutation	SNP	ENST00000316737.1	37	CCDS12256.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.630464	0.46944	.	.	ENSG00000130167	ENST00000316737;ENST00000337994	T;T	0.79554	-1.28;-1.28	3.78	-0.82	0.10826	.	2.367380	0.02315	N	0.072502	T	0.65260	0.2674	N	0.12182	0.205	0.09310	N	1	B	0.15719	0.014	B	0.18263	0.021	T	0.54410	-0.8298	10	0.66056	D	0.02	-0.0342	3.9199	0.09239	0.0:0.3253:0.192:0.4827	.	16	Q9UKR8	TSN16_HUMAN	P	16	ENSP00000319486:S16P;ENSP00000338759:S16P	ENSP00000319486:S16P	S	+	1	0	TSPAN16	11268019	0.000000	0.05858	0.000000	0.03702	0.298000	0.27526	0.403000	0.20982	-0.257000	0.09459	-0.379000	0.06801	TCT	.	.	none		0.463	TSPAN16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453204.1	NM_012466	
LSS	4047	hgsc.bcm.edu	37	21	47635686	47635686	+	Missense_Mutation	SNP	C	C	T	rs143692945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47635686C>T	ENST00000397728.3	-	8	883	c.805G>A	c.(805-807)Gcc>Acc	p.A269T	LSS_ENST00000464357.1_5'UTR|LSS_ENST00000356396.4_Missense_Mutation_p.A269T|LSS_ENST00000457828.2_Missense_Mutation_p.A189T|LSS_ENST00000522411.1_Missense_Mutation_p.A258T	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	269					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)					TCAATGCTGGCGAAGTCCTCC	0.652													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		15065	0.0		0.0	False		,,,				2504	0.0				p.A269T	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G805A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	40,4366	43.1+/-76.7	0,40,2163	28.0	33.0	31.0		805,772,565,805	0.9	0.2	21	dbSNP_134	31	1,8597		0,1,4298	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	58,58,58,58	0,41,6461	TT,TC,CC		0.0116,0.9079,0.3153	benign,benign,benign,benign	269/733,258/722,189/653,269/733	47635686	41,12963	2203	4299	6502	SO:0001583	missense	4047	exon8			TGCTGGCGAAGTC	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.805G>A	21.37:g.47635686C>T	ENSP00000380837:p.Ala269Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	118	64	0.542373	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	7.049	0.564068	0.13498	0.009079	1.16E-4	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.32	0.867	0.19085	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.573488	0.18205	N	0.148380	T	0.11410	0.0278	L	0.35542	1.07	0.20873	N	0.999835	B;B	0.31153	0.31;0.206	B;B	0.18561	0.022;0.01	T	0.12268	-1.0554	10	0.28530	T	0.3	.	5.0794	0.14649	0.3294:0.4293:0.0:0.2412	.	258;269	E9PEI9;P48449	.;ERG7_HUMAN	T	269;189;269;258	ENSP00000348762:A269T;ENSP00000409191:A189T;ENSP00000380837:A269T;ENSP00000429133:A258T	ENSP00000348762:A269T	A	-	1	0	LSS	46460114	0.011000	0.17503	0.155000	0.22561	0.080000	0.17528	0.200000	0.17257	0.226000	0.20979	-0.258000	0.10820	GCC	C|0.997;T|0.003	0.003	strong		0.652	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
NUP54	53371	hgsc.bcm.edu	37	4	77053834	77053834	+	Missense_Mutation	SNP	T	T	C	rs61750814	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77053834T>C	ENST00000264883.3	-	6	889	c.749A>G	c.(748-750)aAt>aGt	p.N250S	NUP54_ENST00000514987.1_Missense_Mutation_p.N202S|NUP54_ENST00000342467.6_Missense_Mutation_p.N70S|NUP54_ENST00000458189.2_Missense_Mutation_p.N70S|NUP54_ENST00000515460.1_5'Flank	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	250	9 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						TGAAGTACCATTTGGCGAACG	0.378													T|||	708	0.141374	0.2156	0.2248	5008	,	,		14987	0.0278		0.172	False		,,,				2504	0.0675				p.N250S		Atlas-SNP	.											.	NUP54	48	.	0			c.A749G						PASS	.	T	SER/ASN	900,3506	346.2+/-308.9	92,716,1395	137.0	126.0	130.0		749	5.5	1.0	4	dbSNP_129	130	1343,7257	262.8+/-284.6	114,1115,3071	yes	missense	NUP54	NM_017426.2	46	206,1831,4466	CC,CT,TT		15.6163,20.4267,17.2459	benign	250/508	77053834	2243,10763	2203	4300	6503	SO:0001583	missense	53371	exon6			GTACCATTTGGCG	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.749A>G	4.37:g.77053834T>C	ENSP00000264883:p.Asn250Ser	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	191	82	0.429319	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	318	0.14560439560439561	94	0.1910569105691057	86	0.23756906077348067	15	0.026223776223776224	123	0.16226912928759896	T	12.31	1.900725	0.33535	0.204267	0.156163	ENSG00000138750	ENST00000264883;ENST00000342467;ENST00000514987;ENST00000458189	.	.	.	5.46	5.46	0.80206	.	0.041245	0.85682	D	0.000000	T	0.00012	0.0000	L	0.41710	1.295	0.09310	P	0.999999830858	B;B;B	0.25955	0.085;0.138;0.085	B;B;B	0.21151	0.02;0.03;0.033	T	0.06716	-1.0811	8	0.22706	T	0.39	-13.6304	15.5414	0.76052	0.0:0.0:0.0:1.0	rs61750814	202;70;250	B4DT35;Q7Z3B4-2;Q7Z3B4	.;.;NUP54_HUMAN	S	250;70;202;70	.	ENSP00000264883:N250S	N	-	2	0	NUP54	77272858	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.857000	0.69525	2.087000	0.62958	0.528000	0.53228	AAT	T|0.836;C|0.164	0.164	strong		0.378	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
MAP1A	4130	hgsc.bcm.edu	37	15	43816917	43816917	+	Silent	SNP	G	G	A	rs1060939	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43816917G>A	ENST00000300231.5	+	4	3696	c.3246G>A	c.(3244-3246)ggG>ggA	p.G1082G	MAP1A_ENST00000382031.1_Silent_p.G1320G|MAP1A_ENST00000399453.1_Silent_p.G1082G			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1082					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TTGATGAGGGGCTTACAGGCT	0.542													A|||	2648	0.528754	0.972	0.3329	5008	,	,		20623	0.4177		0.2962	False		,,,				2504	0.4223				p.G1082G		Atlas-SNP	.											.	MAP1A	189	.	0			c.G3246A						PASS	.	A		3210,676		1336,538,69	77.0	81.0	80.0		3246	-0.4	0.0	15	dbSNP_86	80	2441,5843		346,1749,2047	yes	coding-synonymous	MAP1A	NM_002373.5		1682,2287,2116	AA,AG,GG		29.4664,17.3958,46.4339		1082/2804	43816917	5651,6519	1943	4142	6085	SO:0001819	synonymous_variant	4130	exon4			TGAGGGGCTTACA	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.3246G>A	15.37:g.43816917G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	117	58	0.495726	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	37	CCDS42031.1																																																																																			G|0.497;A|0.503	0.503	strong		0.542	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
PTBP1	5725	hgsc.bcm.edu	37	19	804142	804142	+	Silent	SNP	A	A	G	rs61757783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:804142A>G	ENST00000349038.4	+	4	295	c.222A>G	c.(220-222)gaA>gaG	p.E74E	PTBP1_ENST00000356948.6_Silent_p.E74E|PTBP1_ENST00000394601.4_Silent_p.E74E|MIR4745_ENST00000577608.1_RNA|PTBP1_ENST00000350092.4_Intron	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	74	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGAGGGGGAAGTCATCTCCC	0.582													A|||	26	0.00519169	0.0008	0.0043	5008	,	,		17005	0.0		0.0149	False		,,,				2504	0.0072				p.E74E		Atlas-SNP	.											.	PTBP1	43	.	0			c.A222G						PASS	.	A	,,,	12,4394	17.9+/-39.9	0,12,2191	76.0	67.0	70.0		222,222,222,	0.8	1.0	19	dbSNP_129	70	123,8477	63.5+/-125.6	0,123,4177	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	0,135,6368	GG,GA,AA		1.4302,0.2724,1.038	,,,	74/558,74/551,74/532,	804142	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	5725	exon4			GGGGGAAGTCATC	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.222A>G	19.37:g.804142A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_031990	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			A|0.989;G|0.011	0.011	strong		0.582	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
HIVEP1	3096	hgsc.bcm.edu	37	6	12124587	12124587	+	Missense_Mutation	SNP	C	C	G	rs2228212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:12124587C>G	ENST00000379388.2	+	4	4891	c.4559C>G	c.(4558-4560)gCa>gGa	p.A1520G	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1520			A -> G (in dbSNP:rs2228212). {ECO:0000269|PubMed:15489334}.		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				CAAATCCATGCACCGCCTAGC	0.438													C|||	1242	0.248003	0.1982	0.3141	5008	,	,		20407	0.1796		0.3439	False		,,,				2504	0.2403				p.A1520G		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C4559G						PASS	.	C	GLY/ALA	815,3079		93,629,1225	71.0	68.0	69.0		4559	-3.8	0.0	6	dbSNP_98	69	2947,5359		515,1917,1721	yes	missense	HIVEP1	NM_002114.2	60	608,2546,2946	GG,GC,CC		35.4804,20.9296,30.8361	benign	1520/2719	12124587	3762,8438	1947	4153	6100	SO:0001583	missense	3096	exon4			TCCATGCACCGCC	J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.4559C>G	6.37:g.12124587C>G	ENSP00000368698:p.Ala1520Gly	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	84	0.988235	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	584	0.2673992673992674	102	0.2073170731707317	117	0.32320441988950277	92	0.16083916083916083	273	0.36015831134564646	C	8.046	0.764953	0.15914	0.209296	0.354804	ENSG00000095951	ENST00000379388	T	0.08984	3.03	5.93	-3.84	0.04256	.	2.326850	0.02143	N	0.057348	T	0.01558	0.0050	N	0.22421	0.69	0.80722	P	0.0	B	0.23806	0.091	B	0.16722	0.016	T	0.43940	-0.9360	8	.	.	.	3.6801	7.1783	0.25757	0.1612:0.3873:0.0:0.4515	rs2228212;rs17677180;rs52809676;rs2228212	1520	P15822	ZEP1_HUMAN	G	1520	ENSP00000368698:A1520G	.	A	+	2	0	HIVEP1	12232573	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.720000	0.04969	-0.373000	0.07979	-0.218000	0.12543	GCA	C|0.714;G|0.286	0.286	strong		0.438	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
DDO	8528	hgsc.bcm.edu	37	6	110714205	110714205	+	Missense_Mutation	SNP	C	C	T	rs35697832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:110714205C>T	ENST00000368924.3	-	5	898	c.883G>A	c.(883-885)Gga>Aga	p.G295R	DDO_ENST00000368923.3_Missense_Mutation_p.G236R	NM_003649.2	NP_003640.2	Q99489	OXDD_HUMAN	D-aspartate oxidase	267					aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|D-amino acid catabolic process (GO:0019478)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insemination (GO:0007320)|oxidation-reduction process (GO:0055114)	peroxisome (GO:0005777)	cofactor binding (GO:0048037)|D-aspartate oxidase activity (GO:0008445)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|pancreas(1)|skin(3)	24		all_cancers(87;3.47e-21)|all_epithelial(87;9.03e-20)|Acute lymphoblastic leukemia(125;2.13e-07)|all_hematologic(75;5.28e-06)|all_lung(197;2.98e-05)|Lung NSC(302;3.25e-05)|Colorectal(196;3.46e-05)|Ovarian(999;0.00327)		all cancers(137;2.54e-48)|Epithelial(106;3.11e-44)|OV - Ovarian serous cystadenocarcinoma(136;2.08e-24)|BRCA - Breast invasive adenocarcinoma(108;0.000141)|GBM - Glioblastoma multiforme(226;0.00046)		TTGCAGGCTCCGTGGAGGGAG	0.587													c|||	213	0.0425319	0.0076	0.0793	5008	,	,		20379	0.001		0.1342	False		,,,				2504	0.0123				p.G295R		Atlas-SNP	.											.	DDO	51	.	0			c.G883A						PASS	.	T	ARG/GLY,ARG/GLY	134,4272	96.7+/-135.4	1,132,2070	139.0	139.0	139.0		883,706	-0.7	0.0	6	dbSNP_126	139	1135,7465	234.7+/-267.5	77,981,3242	yes	missense,missense	DDO	NM_003649.2,NM_004032.2	125,125	78,1113,5312	TT,TC,CC		13.1977,3.0413,9.757	benign,benign	295/370,236/311	110714205	1269,11737	2203	4300	6503	SO:0001583	missense	8528	exon5			AGGCTCCGTGGAG	D89858	CCDS5082.1, CCDS5083.1	6q22.1	2008-02-05			ENSG00000203797	ENSG00000203797	1.4.3.1		2727	protein-coding gene	gene with protein product		124450				9163533	Standard	NM_003649		Approved		uc003puc.3	Q99489	OTTHUMG00000015360	ENST00000368924.3:c.883G>A	6.37:g.110714205C>T	ENSP00000357920:p.Gly295Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	66	55	0.833333	NM_003649	A8KAG4|Q5JXM4|Q5JXM5|Q5JXM6|Q8N552	Missense_Mutation	SNP	ENST00000368924.3	37	CCDS5082.1	147	0.0673076923076923	6	0.012195121951219513	32	0.08839779005524862	1	0.0017482517482517483	108	0.1424802110817942	c	0.012	-1.655226	0.00779	0.030413	0.131977	ENSG00000203797	ENST00000368924;ENST00000368923;ENST00000368925	T;T;T	0.55052	0.54;0.54;0.54	5.84	-0.676	0.11361	.	0.620135	0.17427	N	0.174608	T	0.11623	0.0283	N	0.16066	0.365	0.80722	P	0.0	B;B	0.14012	0.001;0.009	B;B	0.08055	0.002;0.003	T	0.17715	-1.0360	9	0.21540	T	0.41	-1.9342	6.9337	0.24455	0.0:0.4035:0.1142:0.4823	rs35697832	236;295	Q99489-4;Q99489-3	.;.	R	295;236;267	ENSP00000357920:G295R;ENSP00000357919:G236R;ENSP00000357921:G267R	ENSP00000357919:G236R	G	-	1	0	DDO	110820898	0.000000	0.05858	0.047000	0.18901	0.003000	0.03518	-0.089000	0.11180	0.029000	0.15352	-0.213000	0.12676	GGA	C|0.907;T|0.093	0.093	strong		0.587	DDO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041796.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1258184	1258184	+	Silent	SNP	C	C	T	rs55703838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1258184C>T	ENST00000529681.1	+	25	3145	c.3087C>T	c.(3085-3087)ttC>ttT	p.F1029F	MUC5B_ENST00000447027.1_Silent_p.F1032F	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1029	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCGGGAACTTCGACGACAATG	0.672													c|||	25	0.00499201	0.0008	0.0058	5008	,	,		17982	0.0		0.0139	False		,,,				2504	0.0061				p.F1029F		Atlas-SNP	.											.	MUC5B	473	.	0			c.C3087T						PASS	.	C		11,4265		0,11,2127	26.0	34.0	32.0		3087	-4.5	0.8	11	dbSNP_129	32	107,8349		0,107,4121	no	coding-synonymous	MUC5B	NM_002458.2		0,118,6248	TT,TC,CC		1.2654,0.2572,0.9268		1029/5763	1258184	118,12614	2138	4228	6366	SO:0001819	synonymous_variant	727897	exon25			GAACTTCGACGAC	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.3087C>T	11.37:g.1258184C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.993;T|0.007	0.007	strong		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SIRPB1	10326	hgsc.bcm.edu	37	20	1559259	1559259	+	Missense_Mutation	SNP	C	C	T	rs2746603	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1559259C>T	ENST00000381605.4	-	2	222	c.158G>A	c.(157-159)cGc>cAc	p.R53H	SIRPB1_ENST00000262929.5_Missense_Mutation_p.R52H|SIRPB1_ENST00000381603.3_Missense_Mutation_p.R53H|RP4-576H24.4_ENST00000564763.1_Missense_Mutation_p.R53H	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	53	Ig-like V-type.		R -> H (in dbSNP:rs2746603).		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						CATAGCACAGCGCAGAGTGGC	0.547													T|||	140	0.0279553	0.003	0.0533	5008	,	,		16312	0.0		0.0855	False		,,,				2504	0.0133				p.R53H		Atlas-SNP	.											SIRPB1,NS,carcinoma,0,2	SIRPB1	83	2	0			c.G158A						PASS	.	T	HIS/ARG,HIS/ARG	83,4309		12,59,2125	109.0	99.0	103.0		158,158	-4.7	0.0	20	dbSNP_100	103	891,7571		130,631,3470	yes	missense,missense	SIRPB1	NM_001083910.2,NM_006065.3	29,29	142,690,5595	TT,TC,CC		10.5294,1.8898,7.5774	benign,benign	53/182,53/399	1559259	974,11880	2196	4231	6427	SO:0001583	missense	10326	exon2			GCACAGCGCAGAG	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.158G>A	20.37:g.1559259C>T	ENSP00000371018:p.Arg53His	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	169	167	0.988166	NM_001083910	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	79	0.036172161172161175	1	0.0020325203252032522	23	0.06353591160220995	0	0.0	55	0.07255936675461741	.	4.950	0.176424	0.09443	0.018898	0.105294	ENSG00000101307	ENST00000381605;ENST00000381603;ENST00000262929	T;T;T	0.65549	-0.16;-0.16;-0.16	2.36	-4.72	0.03269	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.873450	0.02321	N	0.072964	T	0.00967	0.0032	N	0.17872	0.535	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.15321	-1.0441	10	0.15499	T	0.54	.	7.8579	0.29493	0.0:0.595:0.158:0.247	rs2746603;rs58758134;rs2746603	53;53	O00241;O00241-2	SIRB1_HUMAN;.	H	53;53;52	ENSP00000371018:R53H;ENSP00000371016:R53H;ENSP00000262929:R52H	ENSP00000262929:R52H	R	-	2	0	SIRPB1	1507259	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.462000	0.00463	-2.799000	0.00353	-1.390000	0.01156	CGC	C|0.952;T|0.048	0.048	strong		0.547	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43826204	43826204	+	Missense_Mutation	SNP	C	C	T	rs7297737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:43826204C>T	ENST00000389420.3	-	21	2998	c.2999G>A	c.(2998-3000)cGt>cAt	p.R1000H	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.R154H|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.R1000H	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1000	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.		R -> H (in dbSNP:rs7297737).		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)		GTCAGCAAGACGATGGCCAAA	0.433													C|||	183	0.0365415	0.0015	0.0086	5008	,	,		16709	0.0694		0.0348	False		,,,				2504	0.0716				p.R1000H		Atlas-SNP	.											ADAMTS20_ENST00000389420,colon,carcinoma,-1,1	ADAMTS20	635	1	0			c.G2999A						PASS	.	C	HIS/ARG	26,4380	31.7+/-61.6	0,26,2177	128.0	125.0	126.0		2999	-1.3	0.1	12	dbSNP_116	126	243,8357	97.7+/-159.3	6,231,4063	yes	missense	ADAMTS20	NM_025003.3	29	6,257,6240	TT,TC,CC		2.8256,0.5901,2.0683	benign	1000/1911	43826204	269,12737	2203	4300	6503	SO:0001583	missense	80070	exon21			GCAAGACGATGGC	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.2999G>A	12.37:g.43826204C>T	ENSP00000374071:p.Arg1000His	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	152	66	0.434211	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	78	0.03571428571428571	0	0.0	5	0.013812154696132596	44	0.07692307692307693	29	0.03825857519788918	C	5.530	0.282795	0.10458	0.005901	0.028256	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.54279	0.58;0.58;0.58;0.58	4.89	-1.3	0.09259	.	0.364200	0.23662	N	0.045818	T	0.02610	0.0079	L	0.42529	1.33	0.27320	N	0.957055	B;B	0.30634	0.015;0.288	B;B	0.29176	0.009;0.099	T	0.03717	-1.1010	10	0.42905	T	0.14	.	11.5449	0.50688	0.0:0.5165:0.0:0.4835	rs7297737;rs52825347;rs59491718;rs7297737	1000;154	P59510;E9PBD5	ATS20_HUMAN;.	H	1000;166;154;1000;1000	ENSP00000374071:R1000H;ENSP00000447427:R166H;ENSP00000378911:R154H;ENSP00000448341:R1000H	ENSP00000374068:R1000H	R	-	2	0	ADAMTS20	42112471	0.859000	0.29813	0.064000	0.19789	0.839000	0.47603	1.193000	0.32162	-0.387000	0.07809	-0.794000	0.03295	CGT	C|0.968;T|0.032	0.032	strong		0.433	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
PLD2	5338	hgsc.bcm.edu	37	17	4722785	4722785	+	Silent	SNP	G	G	A	rs1052751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4722785G>A	ENST00000263088.6	+	23	2501	c.2370G>A	c.(2368-2370)ctG>ctA	p.L790L	PLD2_ENST00000572940.1_Silent_p.L790L	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	790					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)	TGGCCGTGCTGATCGAGGACA	0.602													G|||	605	0.120807	0.1293	0.1715	5008	,	,		18999	0.0427		0.1829	False		,,,				2504	0.09				p.L790L		Atlas-SNP	.											.	PLD2	138	.	0			c.G2370A						PASS	.	G		510,3896	234.9+/-247.6	33,444,1726	107.0	79.0	88.0		2370	3.4	1.0	17	dbSNP_86	88	1459,7141	278.7+/-293.6	136,1187,2977	no	coding-synonymous	PLD2	NM_002663.4		169,1631,4703	AA,AG,GG		16.9651,11.5751,15.1392		790/934	4722785	1969,11037	2203	4300	6503	SO:0001819	synonymous_variant	5338	exon23			CGTGCTGATCGAG	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.2370G>A	17.37:g.4722785G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	35	0.514706	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Silent	SNP	ENST00000263088.6	37	CCDS11057.1																																																																																			G|0.863;A|0.137	0.137	strong		0.602	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
SPHK1	8877	hgsc.bcm.edu	37	17	74381555	74381555	+	5'UTR	SNP	G	G	A	rs2247856|rs397843720	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74381555G>A	ENST00000545180.1	+	0	639				SPHK1_ENST00000392496.3_5'UTR|SPHK1_ENST00000592299.1_5'UTR|SPHK1_ENST00000323374.4_Missense_Mutation_p.A30T|SPHK1_ENST00000590959.1_5'UTR			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1						'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)	AGGGAATGACGCCGGTGCTCC	0.726													G|||	1272	0.253994	0.0378	0.3934	5008	,	,		11861	0.1935		0.4473	False		,,,				2504	0.3108				p.A30T	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											SPHK1,NS,carcinoma,0,1	SPHK1	24	1	0			c.G88A						scavenged	.	G	,,,THR/ALA	269,3005		34,201,1402	3.0	4.0	4.0		,,,88	1.8	0.9	17	dbSNP_100	4	2929,4191		699,1531,1330	yes	utr-5,utr-5,utr-5,missense	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	,,,58	733,1732,2732	AA,AG,GG		41.1376,8.2162,30.7678	,,,possibly-damaging	,,,30/471	74381555	3198,7196	1637	3560	5197	SO:0001623	5_prime_UTR_variant	8877	exon2			AATGACGCCGGTG	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.-171G>A	17.37:g.74381555G>A		Somatic	5	2	0.4		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	37	CCDS45785.1	602	0.27564102564102566	22	0.044715447154471545	135	0.3729281767955801	97	0.16958041958041958	348	0.45910290237467016	G	14.90	2.673696	0.47781	0.082162	0.411376	ENSG00000176170	ENST00000323374	T	0.25414	1.8	5.03	1.8	0.24995	.	0.452752	0.18713	N	0.133237	T	0.00012	0.0000	.	.	.	0.27913	P	0.9385538	B	0.18013	0.025	B	0.11329	0.006	T	0.48210	-0.9055	8	0.25751	T	0.34	-17.578	6.4808	0.22061	0.1692:0.1461:0.6847:0.0	rs2247856;rs8176327;rs11546888	30	Q9NYA1-2	.	T	30	ENSP00000313681:A30T	ENSP00000313681:A30T	A	+	1	0	SPHK1	71893150	0.003000	0.15002	0.944000	0.38274	0.366000	0.29705	0.087000	0.14958	0.499000	0.27970	0.462000	0.41574	GCC	G|0.716;A|0.284	0.284	strong		0.726	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972	
VWA3B	200403	hgsc.bcm.edu	37	2	98779439	98779439	+	Splice_Site	SNP	G	G	T	rs62154921	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:98779439G>T	ENST00000477737.1	+	8	1318	c.1114G>T	c.(1114-1116)Gag>Tag	p.E372*	VWA3B_ENST00000435344.1_Splice_Site_p.E372*|VWA3B_ENST00000451075.2_Splice_Site_p.E222*	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	372										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						TGTGGACTGCGGTTGGTGCTA	0.572													G|||	57	0.0113818	0.003	0.013	5008	,	,		16750	0.0		0.0408	False		,,,				2504	0.0031				p.E372X		Atlas-SNP	.											.	VWA3B	138	.	0			c.G1114T						PASS	.	G	stop/GLU	42,3974		0,42,1966	65.0	71.0	69.0		1114	2.9	0.4	2	dbSNP_129	69	352,8022		8,336,3843	yes	stop-gained-near-splice	VWA3B	NM_144992.4		8,378,5809	TT,TG,GG		4.2035,1.0458,3.18		372/1295	98779439	394,11996	2008	4187	6195	SO:0001630	splice_region_variant	200403	exon8			GACTGCGGTTGGT	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.1114+1G>T	2.37:g.98779439G>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Nonsense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	43	0.019688644688644688	2	0.0040650406504065045	5	0.013812154696132596	4	0.006993006993006993	32	0.04221635883905013	G	38	6.786140	0.97837	0.010458	0.042035	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	.	.	.	4.68	2.86	0.33363	.	0.552015	0.16503	N	0.211549	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	6.3932	0.21599	0.2249:0.0:0.7751:0.0	rs62154921	.	.	.	X	372;372;222	.	ENSP00000388158:E372X	E	+	1	0	VWA3B	98145871	0.993000	0.37304	0.445000	0.26908	0.294000	0.27393	2.734000	0.47368	0.569000	0.29329	0.650000	0.86243	GAG	G|0.971;T|0.029	0.029	strong		0.572	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	Nonsense_Mutation
STAT1	6772	hgsc.bcm.edu	37	2	191874667	191874667	+	Silent	SNP	A	A	G	rs2066802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:191874667A>G	ENST00000361099.3	-	3	450	c.63T>C	c.(61-63)ctT>ctC	p.L21L	STAT1_ENST00000392323.2_Silent_p.L23L|STAT1_ENST00000540176.1_Silent_p.L21L|STAT1_ENST00000409465.1_Silent_p.L21L|STAT1_ENST00000392322.3_Silent_p.L21L	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	21					apoptotic process (GO:0006915)|blood circulation (GO:0008015)|cellular response to insulin stimulus (GO:0032869)|cellular response to interferon-beta (GO:0035458)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of macrophage fusion (GO:0034240)|negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003340)|negative regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072308)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mesenchymal cell proliferation (GO:0002053)|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)|regulation of apoptotic process (GO:0042981)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|renal tubule development (GO:0061326)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to hydrogen peroxide (GO:0042542)|response to mechanical stimulus (GO:0009612)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|transcription from RNA polymerase II promoter (GO:0006366)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|tumor necrosis factor receptor binding (GO:0005164)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			OV - Ovarian serous cystadenocarcinoma(117;0.00434)|Epithelial(96;0.0555)|all cancers(119;0.141)			TGTCATCATAAAGCTGGTGAA	0.393													A|||	574	0.114617	0.0734	0.0504	5008	,	,		19108	0.2272		0.0696	False		,,,				2504	0.1462				p.L21L		Atlas-SNP	.											.	STAT1	93	.	0			c.T63C						PASS	.	A	,	320,4086	171.6+/-201.8	10,300,1893	157.0	149.0	152.0		63,63	-2.9	1.0	2	dbSNP_94	152	532,8068	147.7+/-203.1	17,498,3785	no	coding-synonymous,coding-synonymous	STAT1	NM_007315.3,NM_139266.2	,	27,798,5678	GG,GA,AA		6.186,7.2628,6.5508	,	21/751,21/713	191874667	852,12154	2203	4300	6503	SO:0001819	synonymous_variant	6772	exon3			ATCATAAAGCTGG		CCDS2309.1, CCDS42793.1	2q32.2-q32.3	2014-09-17	2002-08-29		ENSG00000115415	ENSG00000115415		"""SH2 domain containing"""	11362	protein-coding gene	gene with protein product	"""transcription factor ISGF-3 components p91/p84"""	600555	"""signal transducer and activator of transcription 1, 91kD"""			7885841	Standard	NM_139266		Approved	STAT91, ISGF-3	uc002usj.2	P42224	OTTHUMG00000132699	ENST00000361099.3:c.63T>C	2.37:g.191874667A>G		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	174	92	0.528736	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Silent	SNP	ENST00000361099.3	37	CCDS2309.1																																																																																			A|0.909;G|0.091	0.091	strong		0.393	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315	
PSMC4	5704	hgsc.bcm.edu	37	19	40478362	40478362	+	Silent	SNP	T	T	C	rs35555615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40478362T>C	ENST00000157812.2	+	3	420	c.222T>C	c.(220-222)caT>caC	p.H74H	PSMC4_ENST00000455878.2_Intron	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	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)|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)					AATTTCTCCATGCCCAGGAGG	0.517													T|||	93	0.0185703	0.0008	0.0115	5008	,	,		16447	0.0		0.0249	False		,,,				2504	0.0603				p.H74H	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.T222C						PASS	.	T	,	35,4371	40.0+/-72.8	0,35,2168	77.0	77.0	77.0		222,	-5.6	0.9	19	dbSNP_126	77	297,8303	108.6+/-169.2	10,277,4013	no	coding-synonymous,intron	PSMC4	NM_006503.2,NM_153001.1	,	10,312,6181	CC,CT,TT		3.4535,0.7944,2.5527	,	74/419,	40478362	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	5704	exon3			TCTCCATGCCCAG	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.222T>C	19.37:g.40478362T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																			T|0.976;C|0.024	0.024	strong		0.517	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084639	31084639	+	Intron	SNP	C	C	T	rs4713436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31084639C>T	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Silent_p.R251R|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						CCACCACAGGCCTCTGACCCC	0.652													C|||	981	0.195887	0.0893	0.2104	5008	,	,		16280	0.2054		0.1968	False		,,,				2504	0.319				p.R251R		Atlas-SNP	.											.	CDSN	48	.	0			c.G753A						PASS	.	C	,	509,3895		22,465,1715	24.0	26.0	25.0		753,	2.8	0.8	6	dbSNP_111	25	1548,7046		144,1260,2893	no	coding-synonymous,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	,	166,1725,4608	TT,TC,CC		18.0126,11.5577,15.8255	,	251/530,	31084639	2057,10941	2202	4297	6499	SO:0001627	intron_variant	1041	exon2			CACAGGCCTCTGA	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+1971C>T	6.37:g.31084639C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																			C|0.838;T|0.162	0.162	strong		0.652	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
SGK223	157285	hgsc.bcm.edu	37	8	8234192	8234192	+	Missense_Mutation	SNP	G	G	C	rs4840953	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:8234192G>C	ENST00000520004.1	-	3	1991	c.1727C>G	c.(1726-1728)tCt>tGt	p.S576C	SGK223_ENST00000330777.4_Missense_Mutation_p.S576C			Q86YV5	SG223_HUMAN		578							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCTGCCGCCAGAGCTCCCATC	0.652													G|||	2276	0.454473	0.3918	0.4323	5008	,	,		16373	0.6409		0.3022	False		,,,				2504	0.5194				p.S576C	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1727G						PASS	.	G	CYS/SER	1306,2738		222,862,938	21.0	25.0	24.0		1727	1.9	0.0	8	dbSNP_111	24	2304,5992		322,1660,2166	yes	missense	SGK223	NM_001080826.1	112	544,2522,3104	CC,CG,GG		27.7724,32.2948,29.2545	benign	576/1403	8234192	3610,8730	2022	4148	6170	SO:0001583	missense	0	exon2			CCGCCAGAGCTCC																												ENST00000520004.1:c.1727C>G	8.37:g.8234192G>C	ENSP00000428054:p.Ser576Cys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	950	0.434981684981685	201	0.40853658536585363	142	0.39226519337016574	389	0.6800699300699301	218	0.287598944591029	G	10.25	1.297067	0.23650	0.322948	0.277724	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.59083	0.29;0.29	4.92	1.93	0.25924	.	2.545670	0.01254	N	0.008962	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.47169	-0.9138	9	0.38643	T	0.18	.	4.1097	0.10053	0.0811:0.2388:0.4682:0.212	rs4840953;rs52796687;rs59893685;rs4840953	576	Q86YV5	SG223_HUMAN	C	576	ENSP00000330930:S576C;ENSP00000428054:S576C	ENSP00000330930:S576C	S	-	2	0	AC068353.1	8271602	0.000000	0.05858	0.016000	0.15963	0.045000	0.14185	0.024000	0.13555	1.199000	0.43173	0.655000	0.94253	TCT	G|0.602;C|0.398	0.398	strong		0.652	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969085	49969085	+	Silent	SNP	C	C	T	rs10853810	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49969085C>T	ENST00000293350.4	+	13	1822	c.1659C>T	c.(1657-1659)aaC>aaT	p.N553N	ALDH16A1_ENST00000455361.2_Silent_p.N502N|ALDH16A1_ENST00000433981.2_Silent_p.N388N|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000540132.1_Silent_p.N390N	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	553						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CGTCTGGCAACCTCCATGGCT	0.657													C|||	1048	0.209265	0.3427	0.2277	5008	,	,		15702	0.005		0.335	False		,,,				2504	0.0971				p.N553N		Atlas-SNP	.											ALDH16A1,colon,carcinoma,0,1	ALDH16A1	54	1	0			c.C1659T						scavenged	.	C	,	1393,3013	451.2+/-349.6	220,953,1030	40.0	42.0	41.0		1506,1659	-4.2	0.3	19	dbSNP_120	41	3014,5586	460.2+/-365.1	526,1962,1812	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	746,2915,2842	TT,TC,CC		35.0465,31.616,33.8844	,	502/752,553/803	49969085	4407,8599	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon13			TGGCAACCTCCAT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1659C>T	19.37:g.49969085C>T		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	94	38	0.404255	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			C|0.695;T|0.305	0.305	strong		0.657	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
DDX47	51202	hgsc.bcm.edu	37	12	12967127	12967127	+	Silent	SNP	C	C	T	rs1051374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:12967127C>T	ENST00000358007.3	+	2	172	c.150C>T	c.(148-150)atC>atT	p.I50I	DDX47_ENST00000352940.4_Silent_p.I50I	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	50					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16		Prostate(47;0.0526)		BRCA - Breast invasive adenocarcinoma(232;0.0354)		CCACCAAGATCCAGATTGAAG	0.398													C|||	1937	0.386781	0.2511	0.4121	5008	,	,		23125	0.5992		0.2734	False		,,,				2504	0.4499				p.I50I		Atlas-SNP	.											.	DDX47	37	.	0			c.C150T						PASS	.	C	,	1166,3240	412.4+/-336.1	168,830,1205	308.0	290.0	296.0		150,150	5.3	1.0	12	dbSNP_86	296	2385,6215	397.3+/-345.7	330,1725,2245	yes	coding-synonymous,coding-synonymous	DDX47	NM_016355.3,NM_201224.1	,	498,2555,3450	TT,TC,CC		27.7326,26.4639,27.3028	,	50/456,50/407	12967127	3551,9455	2203	4300	6503	SO:0001819	synonymous_variant	51202	exon2			CAAGATCCAGATT	AK127712	CCDS8655.1, CCDS8656.1	12p13.2	2010-07-06			ENSG00000213782	ENSG00000213782		"""DEAD-boxes"""	18682	protein-coding gene	gene with protein product		615428					Standard	NM_016355		Approved	DKFZp564O176, FLJ30012, HQ0256, RRP3	uc001rax.3	Q9H0S4	OTTHUMG00000168709	ENST00000358007.3:c.150C>T	12.37:g.12967127C>T		Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	212	105	0.495283	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Silent	SNP	ENST00000358007.3	37	CCDS8655.1																																																																																			C|0.686;T|0.314	0.314	strong		0.398	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
MUC4	4585	hgsc.bcm.edu	37	3	195506760	195506760	+	Silent	SNP	T	T	A	rs62282473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506760T>A	ENST00000463781.3	-	2	12150	c.11691A>T	c.(11689-11691)gcA>gcT	p.A3897A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.A3897A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GACGTGTGGATGCTGAGGAAG	0.592													.|||	492	0.0982428	0.0166	0.0994	5008	,	,		8412	0.0526		0.2008	False		,,,				2504	0.1493				p.A3897A		Atlas-SNP	.											.	MUC4	1505	.	0			c.A11691T						PASS	.						9.0	8.0	8.0					3																	195506760		534	1118	1652	SO:0001819	synonymous_variant	4585	exon2			TGTGGATGCTGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11691A>T	3.37:g.195506760T>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	68	49	0.720588	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			T|0.967;A|0.033	0.033	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
IMPG1	3617	hgsc.bcm.edu	37	6	76640781	76640781	+	Missense_Mutation	SNP	C	C	T	rs3734313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:76640781C>T	ENST00000369950.3	-	15	2321	c.2132G>A	c.(2131-2133)cGc>cAc	p.R711H	IMPG1_ENST00000369963.3_3'UTR|Y_RNA_ENST00000363170.1_RNA	NM_001282368.1|NM_001563.2	NP_001269297.1|NP_001554.2			interphotoreceptor matrix proteoglycan 1											breast(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(8)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	63		Acute lymphoblastic leukemia(125;0.0418)|all_hematologic(105;0.222)				TGGTTTGCAGCGACACTCCGC	0.567													C|||	962	0.192093	0.1293	0.2032	5008	,	,		18124	0.254		0.1809	False		,,,				2504	0.2168				p.R711H	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											IMPG1,NS,carcinoma,-1,1	IMPG1	143	1	0			c.G2132A						scavenged	.	C	HIS/ARG	553,3853	249.3+/-256.8	36,481,1686	119.0	95.0	103.0		2132	1.2	1.0	6	dbSNP_107	103	1460,7140	278.6+/-293.5	118,1224,2958	yes	missense	IMPG1	NM_001563.2	29	154,1705,4644	TT,TC,CC		16.9767,12.5511,15.4775	probably-damaging	711/798	76640781	2013,10993	2203	4300	6503	SO:0001583	missense	3617	exon15			TTGCAGCGACACT	AF017776	CCDS4985.1, CCDS75483.1	6q14.2-q15	2008-02-05	2004-05-25		ENSG00000112706	ENSG00000112706			6055	protein-coding gene	gene with protein product		602870	"""sialoprotein associated with cones and rods"""	SPACR			Standard	NM_001282368		Approved	IPM150, GP147	uc003pik.1	Q17R60	OTTHUMG00000015063	ENST00000369950.3:c.2132G>A	6.37:g.76640781C>T	ENSP00000358966:p.Arg711His	Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	73	10	0.136986	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	442	0.20238095238095238	66	0.13414634146341464	68	0.1878453038674033	165	0.28846153846153844	143	0.18865435356200527	C	13.01	2.108235	0.37242	0.125511	0.169767	ENSG00000112706	ENST00000369950;ENST00000369952	T;T	0.20463	2.07;2.15	5.45	1.18	0.20946	Epidermal growth factor-like, type 3 (1);	0.353536	0.24280	N	0.039906	T	0.04543	0.0124	L	0.46157	1.445	0.09310	P	0.9999999898373	P	0.52316	0.952	B	0.35770	0.21	T	0.33369	-0.9871	9	0.34782	T	0.22	.	3.7999	0.08754	0.2697:0.437:0.0:0.2933	rs3734313;rs52816738;rs61241500;rs3734313	711	Q17R60	IMPG1_HUMAN	H	711;72	ENSP00000358966:R711H;ENSP00000358968:R72H	ENSP00000358966:R711H	R	-	2	0	IMPG1	76697501	0.112000	0.22096	0.992000	0.48379	0.274000	0.26718	0.372000	0.20467	0.283000	0.22279	0.461000	0.40582	CGC	C|0.826;T|0.174	0.174	strong		0.567	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563	
PXDNL	137902	hgsc.bcm.edu	37	8	52325767	52325767	+	Missense_Mutation	SNP	T	T	G	rs16916207	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:52325767T>G	ENST00000356297.4	-	15	1947	c.1847A>C	c.(1846-1848)gAt>gCt	p.D616A	PXDNL_ENST00000543296.1_Missense_Mutation_p.D616A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	616			D -> A (in dbSNP:rs16916207).		hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CTGTACAGCATCAAGAATGGA	0.343													T|||	795	0.158746	0.1921	0.0793	5008	,	,		20248	0.2768		0.0865	False		,,,				2504	0.1227				p.D616A		Atlas-SNP	.											.	PXDNL	414	.	0			c.A1847C						PASS	.	T	ALA/ASP	683,3073		64,555,1259	140.0	137.0	138.0		1847	3.6	0.0	8	dbSNP_123	138	720,7538		31,658,3440	yes	missense	PXDNL	NM_144651.4	126	95,1213,4699	GG,GT,TT		8.7188,18.1842,11.678	possibly-damaging	616/1464	52325767	1403,10611	1878	4129	6007	SO:0001583	missense	137902	exon15			ACAGCATCAAGAA		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.1847A>C	8.37:g.52325767T>G	ENSP00000348645:p.Asp616Ala	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	341	0.15613553113553114	94	0.1910569105691057	29	0.08011049723756906	152	0.26573426573426573	66	0.0870712401055409	T	11.16	1.557645	0.27827	0.181842	0.087188	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.64085	-0.06;-0.08	4.78	3.61	0.41365	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.43321	P	0.004654999999999965	B	0.25563	0.129	B	0.23419	0.046	T	0.06320	-1.0833	8	0.72032	D	0.01	.	8.6127	0.33813	0.0:0.0935:0.0:0.9064	rs16916207;rs57038753;rs16916207	616	A1KZ92	PXDNL_HUMAN	A	616	ENSP00000348645:D616A;ENSP00000444865:D616A	ENSP00000348645:D616A	D	-	2	0	PXDNL	52488320	0.988000	0.35896	0.017000	0.16124	0.489000	0.33432	4.320000	0.59203	0.674000	0.31244	0.533000	0.62120	GAT	T|0.846;G|0.154	0.154	strong		0.343	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
ESYT2	57488	hgsc.bcm.edu	37	7	158534372	158534372	+	Silent	SNP	G	G	A	rs57686648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158534372G>A	ENST00000251527.5	-	17	2156	c.2091C>T	c.(2089-2091)gcC>gcT	p.A697A	ESYT2_ENST00000435514.2_Silent_p.A132A	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	725					endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CCTGAGGGCCGGCCTCAGGGG	0.657													G|||	1602	0.319888	0.3563	0.183	5008	,	,		15920	0.5774		0.166	False		,,,				2504	0.2607				p.A697A		Atlas-SNP	.											ESYT2,NS,malignant_melanoma,-1,1	ESYT2	70	1	0			c.C2091T						PASS	.			1358,3048	447.1+/-348.2	215,928,1060	34.0	37.0	36.0		2091	2.1	0.7	7	dbSNP_129	36	1344,7256	258.7+/-282.2	100,1144,3056	no	coding-synonymous	ESYT2	NM_020728.2		315,2072,4116	AA,AG,GG		15.6279,30.8216,20.775		697/894	158534372	2702,10304	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon17			AGGGCCGGCCTCA	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2091C>T	7.37:g.158534372G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			G|0.759;A|0.241	0.241	strong		0.657	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
DYDC1	143241	hgsc.bcm.edu	37	10	82098881	82098881	+	Missense_Mutation	SNP	A	A	T	rs35605779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:82098881A>T	ENST00000372204.3	-	6	535	c.371T>A	c.(370-372)gTt>gAt	p.V124D	DYDC1_ENST00000421924.2_Missense_Mutation_p.V124D|DYDC1_ENST00000372202.1_Missense_Mutation_p.V124D	NM_138812.3	NP_620167.1	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1	124										kidney(1)|large_intestine(3)|skin(1)	5			Colorectal(32;0.229)			TTCATTCCTAACTAGATTTTC	0.254													A|||	10	0.00199681	0.0	0.0014	5008	,	,		13230	0.0		0.008	False		,,,				2504	0.001				p.V124D		Atlas-SNP	.											.	DYDC1	15	.	0			c.T371A						PASS	.	A	ASP/VAL	9,4361		0,9,2176	59.0	53.0	55.0		371	-3.6	0.0	10	dbSNP_126	55	106,8454		0,106,4174	yes	missense	DYDC1	NM_138812.2	152	0,115,6350	TT,TA,AA		1.2383,0.2059,0.8894	benign	124/178	82098881	115,12815	2185	4280	6465	SO:0001583	missense	143241	exon5			TTCCTAACTAGAT	BC019250	CCDS7366.1	10q22.3	2006-02-01			ENSG00000170788	ENSG00000170788			23460	protein-coding gene	gene with protein product		615154					Standard	NM_138812		Approved	bA36D19.5, DPY30D1	uc031pwj.1	Q8WWB3	OTTHUMG00000018609	ENST00000372204.3:c.371T>A	10.37:g.82098881A>T	ENSP00000361278:p.Val124Asp	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	112	51	0.455357	NM_001269053	A8K927|Q5QP03|Q5QP04|Q6WNP4|Q6ZU87	Missense_Mutation	SNP	ENST00000372204.3	37	CCDS7366.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	A	3.197	-0.164454	0.06502	0.002059	0.012383	ENSG00000170788	ENST00000372204;ENST00000372202;ENST00000421924;ENST00000454362	.	.	.	4.56	-3.64	0.04515	.	2.257240	0.01811	N	0.033424	T	0.12646	0.0307	N	0.08118	0	0.09310	N	1	B;B	0.24092	0.097;0.057	B;B	0.18871	0.023;0.014	T	0.10405	-1.0631	9	0.30078	T	0.28	5.9472	5.9793	0.19399	0.3843:0.4372:0.1785:0.0	rs35605779	124;124	A8K927;Q8WWB3	.;DYDC1_HUMAN	D	124	.	ENSP00000361276:V124D	V	-	2	0	DYDC1	82088861	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.099000	0.15210	-0.644000	0.05465	-1.276000	0.01395	GTT	A|0.994;T|0.006	0.006	strong		0.254	DYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049059.1	NM_138812	
GIPR	2696	hgsc.bcm.edu	37	19	46177997	46177997	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46177997G>T	ENST00000590918.1	+	7	645	c.546G>T	c.(544-546)ctG>ctT	p.L182L	GIPR_ENST00000263281.3_Silent_p.L182L|MIR642A_ENST00000385039.1_RNA|GIPR_ENST00000304207.8_Silent_p.L146L	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	182					activation of adenylate cyclase activity (GO:0007190)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|endocrine pancreas development (GO:0031018)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|response to axon injury (GO:0048678)|response to calcium ion (GO:0051592)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gastric inhibitory peptide receptor activity (GO:0016519)|peptide hormone binding (GO:0017046)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|kidney(2)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	12		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		CTTTCATGCTGCGAGCTGCGG	0.597																																					p.L182L		Atlas-SNP	.											.	GIPR	36	.	0			c.G546T						PASS	.						76.0	67.0	70.0					19																	46177997		2203	4300	6503	SO:0001819	synonymous_variant	2696	exon7			CATGCTGCGAGCT		CCDS12671.1	19q13.2-q13.3	2012-08-10				ENSG00000010310		"""GPCR / Class B : Glucagon receptors"""	4271	protein-coding gene	gene with protein product		137241				7490109	Standard	NM_000164		Approved		uc002pcu.1	P48546		ENST00000590918.1:c.546G>T	19.37:g.46177997G>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_000164	B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Silent	SNP	ENST00000590918.1	37	CCDS12671.1																																																																																			.	.	none		0.597	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1		
OR2C1	4993	hgsc.bcm.edu	37	16	3406516	3406516	+	Silent	SNP	A	A	G	rs11643487	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3406516A>G	ENST00000304936.2	+	1	628	c.576A>G	c.(574-576)acA>acG	p.T192T		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	192					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)	cell cortex (GO:0005938)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						GTGGCGACACAAGTCTCAACC	0.557													G|||	1587	0.316893	0.4357	0.2882	5008	,	,		20982	0.1736		0.336	False		,,,				2504	0.3047				p.T192T		Atlas-SNP	.											.	OR2C1	38	.	0			c.A576G						PASS	.			1886,2508	629.1+/-395.2	395,1096,706	126.0	102.0	110.0		576	-9.7	0.0	16	dbSNP_120	110	2915,5685	670.0+/-402.7	485,1945,1870	no	coding-synonymous	OR2C1	NM_012368.2		880,3041,2576	GG,GA,AA		33.8953,42.9222,36.9478		192/313	3406516	4801,8193	2197	4300	6497	SO:0001819	synonymous_variant	4993	exon1			CGACACAAGTCTC	AF098664	CCDS10502.1	16p13.3	2012-08-09			ENSG00000168158	ENSG00000168158		"""GPCR / Class A : Olfactory receptors"""	8242	protein-coding gene	gene with protein product				OR2C2P		9847080	Standard	NM_012368		Approved	OLFmf3	uc002cuw.1	O95371	OTTHUMG00000090505	ENST00000304936.2:c.576A>G	16.37:g.3406516A>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	56	19	0.339286	NM_012368	A0AVA4|Q6IF34|Q6IF55	Silent	SNP	ENST00000304936.2	37	CCDS10502.1																																																																																			A|0.659;G|0.341	0.341	strong		0.557	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
NDST1	3340	hgsc.bcm.edu	37	5	149907533	149907533	+	Silent	SNP	T	T	G	rs2273235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149907533T>G	ENST00000261797.6	+	3	1183	c.681T>G	c.(679-681)gtT>gtG	p.V227V	NDST1_ENST00000523767.1_Silent_p.V227V	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	227	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)			ACTGGACGGTTTTCCAGTCAA	0.627													G|||	1832	0.365815	0.2421	0.5	5008	,	,		20605	0.2788		0.4742	False		,,,				2504	0.4162				p.V227V		Atlas-SNP	.											.	NDST1	79	.	0			c.T681G						PASS	.	G		1312,3094	692.8+/-405.6	211,890,1102	51.0	44.0	46.0		681	2.0	1.0	5	dbSNP_100	46	4025,4575	594.8+/-393.4	971,2083,1246	no	coding-synonymous	NDST1	NM_001543.4		1182,2973,2348	GG,GT,TT		46.8023,29.7776,41.0349		227/883	149907533	5337,7669	2203	4300	6503	SO:0001819	synonymous_variant	3340	exon3			GACGGTTTTCCAG	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.681T>G	5.37:g.149907533T>G		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	67	30	0.447761	NM_001543	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																			T|0.626;G|0.374	0.374	strong		0.627	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
ECD	11319	hgsc.bcm.edu	37	10	74923562	74923562	+	Missense_Mutation	SNP	C	C	T	rs3812619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:74923562C>T	ENST00000372979.4	-	2	340	c.134G>A	c.(133-135)cGg>cAg	p.R45Q	ECD_ENST00000610256.1_5'UTR|ECD_ENST00000430082.2_Missense_Mutation_p.R45Q|ECD_ENST00000454759.2_Missense_Mutation_p.R45Q	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	45			R -> Q (in dbSNP:rs3812619).		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)					AGGTGCAAACCGAGTGATTAT	0.413													T|||	1181	0.235823	0.3684	0.1239	5008	,	,		17190	0.3145		0.0596	False		,,,				2504	0.2362				p.R45Q		Atlas-SNP	.											.	ECD	50	.	0			c.G134A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG	1433,2973	682.9+/-404.2	229,975,999	145.0	136.0	139.0		134,134,134	3.1	1.0	10	dbSNP_107	139	617,7983	791.8+/-407.5	30,557,3713	yes	missense,missense,missense	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	43,43,43	259,1532,4712	TT,TC,CC		7.1744,32.5238,15.762	benign,benign,benign	45/678,45/602,45/645	74923562	2050,10956	2203	4300	6503	SO:0001583	missense	11319	exon2			GCAAACCGAGTGA	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		ENST00000372979.4:c.134G>A	10.37:g.74923562C>T	ENSP00000362070:p.Arg45Gln	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	204	97	0.47549	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	461	0.21108058608058608	195	0.39634146341463417	38	0.10497237569060773	183	0.31993006993006995	45	0.059366754617414245	T	3.193	-0.165349	0.06461	0.325238	0.071744	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759;ENST00000413026	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.49	3.11	0.35812	.	0.557525	0.21129	N	0.079681	T	0.00012	0.0000	N	0.03608	-0.345	0.37191	P	0.096047	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.49597	-0.8923	9	0.27082	T	0.32	-14.1415	6.7976	0.23734	0.1158:0.14:0.0:0.7442	rs3812619;rs52826741;rs61387101;rs3812619	45;45;45	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	Q	45	ENSP00000362070:R45Q;ENSP00000401566:R45Q;ENSP00000395786:R45Q;ENSP00000416288:R45Q	ENSP00000362070:R45Q	R	-	2	0	ECD	74593568	0.830000	0.29337	0.993000	0.49108	0.535000	0.34838	1.033000	0.30191	-0.198000	0.10333	-2.269000	0.00276	CGG	C|0.811;T|0.189	0.189	strong		0.413	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
ZNF45	7596	hgsc.bcm.edu	37	19	44418544	44418544	+	Silent	SNP	A	A	G	rs425221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44418544A>G	ENST00000269973.5	-	10	2134	c.1044T>C	c.(1042-1044)aaT>aaC	p.N348N	ZNF45_ENST00000589703.1_Silent_p.N348N|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	348					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						TACAATGAATATTAAGGTGTG	0.478													G|||	2632	0.525559	0.3343	0.6499	5008	,	,		22417	0.7996		0.5169	False		,,,				2504	0.4223				p.N348N		Atlas-SNP	.											.	ZNF45	51	.	0			c.T1044C						PASS	.	G		1580,2826	666.5+/-401.7	293,994,916	71.0	66.0	68.0		1044	1.4	0.3	19	dbSNP_80	68	4353,4247	573.4+/-389.9	1119,2115,1066	no	coding-synonymous	ZNF45	NM_003425.3		1412,3109,1982	GG,GA,AA		49.3837,35.8602,45.6174		348/683	44418544	5933,7073	2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			ATGAATATTAAGG	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.1044T>C	19.37:g.44418544A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	109	107	0.981651	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	37	CCDS12632.1																																																																																			A|0.488;G|0.512	0.512	strong		0.478	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
POM121C	100101267	hgsc.bcm.edu	37	7	75053499	75053499	+	Missense_Mutation	SNP	G	G	A	rs113744930	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:75053499G>A	ENST00000257665.5	-	10	1606	c.1607C>T	c.(1606-1608)tCg>tTg	p.S536L	POM121C_ENST00000473168.1_5'UTR|POM121C_ENST00000453279.2_Missense_Mutation_p.S294L			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	536	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						GACAGAGTTCGAGGCAGCATC	0.562													.|||	752	0.15016	0.3169	0.098	5008	,	,		19287	0.002		0.1183	False		,,,				2504	0.1472				p.S294L		Atlas-SNP	.											POM121C,NS,carcinoma,+1,1	POM121C	46	1	0			c.C881T						PASS	.	G	LEU/SER	1149,3257	409.5+/-335.0	165,819,1219	241.0	265.0	257.0		881	1.7	0.0	7	dbSNP_132	257	1073,7527	223.7+/-260.4	60,953,3287	no	missense	POM121C	NM_001099415.1	145	225,1772,4506	AA,AG,GG		12.4767,26.0781,17.0844	benign	294/988	75053499	2222,10784	2203	4300	6503	SO:0001583	missense	100101267	exon12			GAGTTCGAGGCAG		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.1607C>T	7.37:g.75053499G>A	ENSP00000257665:p.Ser536Leu	Somatic	401	0	0		WXS	Illumina HiSeq	Phase_I	468	228	0.487179	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000257665.5	37		270	0.12362637362637363	151	0.30691056910569103	39	0.10773480662983426	1	0.0017482517482517483	79	0.10422163588390501	G	9.798	1.179694	0.21787	0.260781	0.124767	ENSG00000135213	ENST00000257665;ENST00000453279	T;T	0.20069	3.62;2.1	3.57	1.71	0.24356	.	0.422937	0.17553	N	0.170085	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	B	0.15473	0.013	B	0.14023	0.01	T	0.21690	-1.0238	9	0.62326	D	0.03	.	7.0486	0.25061	0.2201:0.0:0.7799:0.0	.	536	A8CG34	P121C_HUMAN	L	536;294	ENSP00000257665:S536L;ENSP00000414208:S294L	ENSP00000257665:S536L	S	-	2	0	POM121C	74891435	0.139000	0.22563	0.015000	0.15790	0.411000	0.31082	2.461000	0.45040	0.161000	0.19458	0.195000	0.17529	TCG	G|0.881;A|0.119	0.119	strong		0.562	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
CDRT1	374286	hgsc.bcm.edu	37	17	15496730	15496730	+	Missense_Mutation	SNP	A	A	G	rs8078150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15496730A>G	ENST00000395906.3	-	11	1926	c.1927T>C	c.(1927-1929)Ttc>Ctc	p.F643L	CDRT1_ENST00000583965.1_Intron|RP11-385D13.1_ENST00000455584.2_Intron|CDRT1_ENST00000354433.3_Missense_Mutation_p.F143L	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	643			F -> L (in dbSNP:rs8078150). {ECO:0000269|PubMed:9403059}.							endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(2;1.36e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0541)		TTCCCATTGAAGAAATTGTAA	0.512													.|||	1806	0.360623	0.4675	0.33	5008	,	,		17454	0.3819		0.2346	False		,,,				2504	0.3456				p.F643L		Atlas-SNP	.											.	CDRT1	83	.	0			c.T1927C						PASS	.	G	LEU/PHE	1972,2434		457,1058,688	221.0	234.0	230.0		1927	2.5	1.0	17	dbSNP_116	230	2187,6413		277,1633,2390	no	missense	CDRT1	NM_006382.3	22	734,2691,3078	GG,GA,AA		25.4302,44.7571,31.9775	benign	643/753	15496730	4159,8847	2203	4300	6503	SO:0001583	missense	374286	exon11			CATTGAAGAAATT	U65652	CCDS45619.1, CCDS73996.1	17p11	2013-01-10			ENSG00000241322	ENSG00000241322		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	14379	protein-coding gene	gene with protein product		604596	"""F-box and WD repeat domain containing 10 pseudogene 1"", ""F-box and WD-40 domain protein 10 pseudogene 1"""	FBXW10P1		9787083, 11381029	Standard	NM_006382		Approved	HREP, SM25H2, FBXW10B		O95170	OTTHUMG00000059074	ENST00000395906.3:c.1927T>C	17.37:g.15496730A>G	ENSP00000379242:p.Phe643Leu	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	237	111	0.468354	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	744	0.34065934065934067	228	0.4634146341463415	114	0.3149171270718232	212	0.3706293706293706	190	0.25065963060686014	N	4.048	0.006554	0.07866	0.447571	0.254302	ENSG00000241322;ENSG00000251537;ENSG00000251537	ENST00000354433;ENST00000261644;ENST00000395906	T;T	0.17054	2.3;2.3	4.74	2.47	0.30058	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.00210	-1.845	0.09310	P	0.9999999999997713	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	7	.	.	.	.	4.2827	0.10839	0.3871:0.1734:0.4395:0.0	rs8078150	643	O95170	CDRT1_HUMAN	L	143;673;643	ENSP00000346416:F143L;ENSP00000379242:F643L	.	F	-	1	0	CDRT1;RP11-385D13.1	15437455	1.000000	0.71417	0.990000	0.47175	0.914000	0.54420	2.533000	0.45667	0.301000	0.22738	-0.128000	0.14901	TTC	A|0.688;G|0.312	0.312	strong		0.512	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382	
MICB	4277	hgsc.bcm.edu	37	6	31473561	31473561	+	Missense_Mutation	SNP	A	A	G	rs1065075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31473561A>G	ENST00000252229.6	+	2	317	c.238A>G	c.(238-240)Aag>Gag	p.K80E	MICB_ENST00000399150.3_Missense_Mutation_p.K80E|MICB_ENST00000538442.1_Missense_Mutation_p.K48E	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						CCTGGGAGCTAAGACCTGGGA	0.572													a|||	1417	0.282947	0.3835	0.1902	5008	,	,		20308	0.2748		0.2634	False		,,,				2504	0.2413				p.K80E		Atlas-SNP	.											.	MICB	26	.	0			c.A238G						PASS	.	G	GLU/LYS	926,1650		172,582,534	39.0	43.0	41.0		238	-5.3	0.0	6	dbSNP_86	41	1565,3539		242,1081,1229	yes	missense	MICB	NM_005931.3	56	414,1663,1763	GG,GA,AA		30.6622,35.9472,32.4349	benign	80/384	31473561	2491,5189	1288	2552	3840	SO:0001583	missense	4277	exon2			GGAGCTAAGACCT		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.238A>G	6.37:g.31473561A>G	ENSP00000252229:p.Lys80Glu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_005931		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	614	0.28113553113553114	198	0.4024390243902439	77	0.212707182320442	130	0.22727272727272727	209	0.2757255936675462	N	0.009	-1.797801	0.00617	0.359472	0.306622	ENSG00000204516	ENST00000538442;ENST00000399150;ENST00000252229	T;T;T	0.01335	5.0;5.0;5.0	2.64	-5.29	0.02747	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.673345	0.12089	N	0.500570	T	0.00109	0.0003	N	0.01152	-0.98	0.80722	P	0.0	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.13407	0.004;0.009;0.001	T	0.32771	-0.9894	9	0.02654	T	1	.	3.1138	0.06367	0.1191:0.3073:0.4311:0.1425	rs1065075;rs3175107;rs16897483;rs59872907	48;80;80	F5H7Q8;A2AC57;Q29980	.;.;MICB_HUMAN	E	48;80;80	ENSP00000442345:K48E;ENSP00000382103:K80E;ENSP00000252229:K80E	ENSP00000252229:K80E	K	+	1	0	MICB	31581540	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.679000	0.05203	-1.442000	0.01955	-2.116000	0.00351	AAG	A|0.712;G|0.288	0.288	strong		0.572	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	
HNF4A	3172	hgsc.bcm.edu	37	20	43048368	43048368	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43048368C>T	ENST00000316099.4	+	7	833	c.744C>T	c.(742-744)gaC>gaT	p.D248D	HNF4A_ENST00000457232.1_Silent_p.D226D|HNF4A_ENST00000415691.2_Silent_p.D248D|HNF4A_ENST00000443598.2_Silent_p.D248D|HNF4A_ENST00000609795.1_Silent_p.D226D|HNF4A_ENST00000316673.4_Silent_p.D226D	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	248					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CAGGCAATGACTACATTGTCC	0.582																																					p.D248D	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	0			c.C744T						PASS	.						89.0	79.0	83.0					20																	43048368		2203	4300	6503	SO:0001819	synonymous_variant	3172	exon7			CAATGACTACATT	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"""Nuclear hormone receptors"""	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.744C>T	20.37:g.43048368C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_178849	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Silent	SNP	ENST00000316099.4	37	CCDS13330.1																																																																																			.	.	none		0.582	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3		
NDUFA6	4700	hgsc.bcm.edu	37	22	42486723	42486723	+	Missense_Mutation	SNP	G	G	A	rs1801311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:42486723G>A	ENST00000498737.2	-	1	236	c.104C>T	c.(103-105)gCt>gTt	p.A35V	NDUFA6_ENST00000602404.1_Missense_Mutation_p.A9V|NDUFA6-AS1_ENST00000600968.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000536447.2_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|RP1-257I20.14_ENST00000602718.1_RNA|NDUFA6-AS1_ENST00000417327.1_RNA|NDUFA6-AS1_ENST00000595777.1_RNA|NDUFA6-AS1_ENST00000608974.1_RNA|NDUFA6-AS1_ENST00000434834.1_RNA	NM_002490.3	NP_002481.2	P56556	NDUA6_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa	35			A -> V (in dbSNP:rs1801311). {ECO:0000269|PubMed:14702039}.		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 membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			kidney(1)|lung(3)|upper_aerodigestive_tract(1)	5						GGTAGAAGTAGCTTGGCGGAC	0.632													G|||	1772	0.353834	0.5371	0.3271	5008	,	,		15164	0.1508		0.335	False		,,,				2504	0.3538				p.A35V		Atlas-SNP	.											.	NDUFA6	13	.	0			c.C104T						PASS	.	G	VAL/ALA	2174,2232	583.2+/-385.8	537,1100,566	88.0	90.0	90.0		104	2.4	0.1	22	dbSNP_89	90	2889,5711	453.3+/-363.2	506,1877,1917	yes	missense	NDUFA6	NM_002490.3	64	1043,2977,2483	AA,AG,GG		33.593,49.3418,38.9282	benign	35/155	42486723	5063,7943	2203	4300	6503	SO:0001583	missense	4700	exon1			GAAGTAGCTTGGC	AF047182	CCDS33656.1	22q13.2	2010-05-07	2002-08-29		ENSG00000184983	ENSG00000184983		"""LYR motif containing"", ""Mitochondrial respiratory chain complex / Complex I"""	7690	protein-coding gene	gene with protein product	"""complex I B14 subunit"""	602138	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6 (14kD, B14)"""			9763676, 9425316	Standard	NM_002490		Approved	B14, LYRM6, CI-B14, NADHB14	uc003bcb.3	P56556	OTTHUMG00000151287	ENST00000498737.2:c.104C>T	22.37:g.42486723G>A	ENSP00000418842:p.Ala35Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	102	51	0.5	NM_002490	B2RE54|O43675|Q6FGW0|Q6IBT8|Q6IC39	Missense_Mutation	SNP	ENST00000498737.2	37	CCDS33656.1	731	0.3347069597069597	270	0.5487804878048781	115	0.31767955801104975	95	0.1660839160839161	251	0.3311345646437995	G	16.70	3.196846	0.58126	0.493418	0.33593	ENSG00000184983	ENST00000498737	T	0.69685	-0.42	5.64	2.39	0.29439	.	0.213179	0.49916	D	0.000138	T	0.00012	0.0000	N	0.12569	0.235	0.25870	P	0.9837283	B	0.17852	0.024	B	0.10450	0.005	T	0.44967	-0.9293	9	0.48119	T	0.1	-3.0867	5.8599	0.18740	0.2233:0.1494:0.6273:0.0	rs1801311;rs57054953;rs1801311	35	P56556	NDUA6_HUMAN	V	35	ENSP00000418842:A35V	ENSP00000418842:A35V	A	-	2	0	NDUFA6	40816669	0.974000	0.33945	0.066000	0.19879	0.009000	0.06853	1.568000	0.36418	0.720000	0.32209	0.655000	0.94253	GCT	G|0.625;A|0.375	0.375	strong		0.632	NDUFA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322089.4	NM_002490	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458765	39458765	+	Silent	SNP	A	A	G	rs1005197	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39458765A>G	ENST00000391353.1	-	1	338	c.339T>C	c.(337-339)tcT>tcC	p.S113S		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	113	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											GACAACAAGTAGATTCCGAGC	0.542													A|||	3397	0.678315	0.5166	0.8012	5008	,	,		24206	0.629		0.7336	False		,,,				2504	0.8037				p.S113S		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.T339C						PASS	.																																			SO:0001819	synonymous_variant	100533177	exon1			ACAAGTAGATTCC		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.339T>C	17.37:g.39458765A>G		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	56	36	0.642857	NM_001257309		Silent	SNP	ENST00000391353.1	37																																																																																				A|0.331;G|0.669	0.669	strong		0.542	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
EHD2	30846	hgsc.bcm.edu	37	19	48229169	48229169	+	Silent	SNP	A	A	G	rs8111184	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48229169A>G	ENST00000263277.3	+	4	854	c.603A>G	c.(601-603)tcA>tcG	p.S201S	CTD-2571L23.8_ENST00000599924.1_lincRNA|EHD2_ENST00000538399.1_Silent_p.S65S	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	201	Dynamin-type G.				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)		ACGAGTTCTCAGAGGCCATCG	0.637													G|||	551	0.110024	0.1899	0.0836	5008	,	,		17763	0.0139		0.1402	False		,,,				2504	0.089				p.S201S		Atlas-SNP	.											.	EHD2	59	.	0			c.A603G						PASS	.	G		873,3533	738.7+/-411.0	89,695,1419	48.0	39.0	42.0		603	-7.3	0.5	19	dbSNP_116	42	1250,7350	758.1+/-407.5	89,1072,3139	no	coding-synonymous	EHD2	NM_014601.3		178,1767,4558	GG,GA,AA		14.5349,19.8139,16.3232		201/544	48229169	2123,10883	2203	4300	6503	SO:0001819	synonymous_variant	30846	exon4			GTTCTCAGAGGCC	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.603A>G	19.37:g.48229169A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_014601	B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	CCDS12704.1																																																																																			A|0.861;G|0.139	0.139	strong		0.637	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1		
PCDHB15	56121	hgsc.bcm.edu	37	5	140626117	140626117	+	Missense_Mutation	SNP	G	G	C	rs147373970	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140626117G>C	ENST00000231173.3	+	1	971	c.971G>C	c.(970-972)gGc>gCc	p.G324A		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	324	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCATCTGATGGCGGGGGACTT	0.413													G|||	10	0.00199681	0.0	0.0014	5008	,	,		19141	0.0		0.005	False		,,,				2504	0.0041				p.G324A		Atlas-SNP	.											.	PCDHB15	138	.	0			c.G971C						PASS	.	G	ALA/GLY	3,4403	6.2+/-15.9	0,3,2200	134.0	137.0	136.0		971	4.8	1.0	5	dbSNP_134	136	33,8567	23.4+/-69.3	0,33,4267	yes	missense	PCDHB15	NM_018935.2	60	0,36,6467	CC,CG,GG		0.3837,0.0681,0.2768	benign	324/788	140626117	36,12970	2203	4300	6503	SO:0001583	missense	56121	exon1			CTGATGGCGGGGG	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.971G>C	5.37:g.140626117G>C	ENSP00000231173:p.Gly324Ala	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	152	55	0.361842	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	13.07	2.128339	0.37533	6.81E-4	0.003837	ENSG00000113248	ENST00000231173	T	0.50277	0.75	4.83	4.83	0.62350	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.55529	0.1926	M	0.64997	1.995	0.34438	D	0.699261	P	0.45986	0.87	P	0.57057	0.812	T	0.71567	-0.4554	9	0.56958	D	0.05	.	17.8824	0.88844	0.0:0.0:1.0:0.0	.	324	Q9Y5E8	PCDBF_HUMAN	A	324	ENSP00000231173:G324A	ENSP00000231173:G324A	G	+	2	0	PCDHB15	140606301	0.073000	0.21202	0.974000	0.42286	0.478000	0.33099	0.879000	0.28146	2.406000	0.81754	0.491000	0.48974	GGC	G|0.997;C|0.003	0.003	strong		0.413	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
BNC2	54796	hgsc.bcm.edu	37	9	16419519	16419519	+	Missense_Mutation	SNP	G	G	A	rs117452684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:16419519G>A	ENST00000380672.4	-	7	2825	c.2768C>T	c.(2767-2769)gCc>gTc	p.A923V	BNC2_ENST00000545497.1_Missense_Mutation_p.A828V|BNC2_ENST00000380667.2_Missense_Mutation_p.A856V	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GGGGTGCTGGGCACCATATAT	0.572													G|||	45	0.00898562	0.0008	0.0086	5008	,	,		16876	0.0		0.0288	False		,,,				2504	0.0092				p.A923V		Atlas-SNP	.											.	BNC2	166	.	0			c.C2768T						PASS	.	G	VAL/ALA	30,4376	36.0+/-67.5	0,30,2173	83.0	87.0	86.0		2768	5.5	1.0	9	dbSNP_132	86	293,8307	107.0+/-167.8	3,287,4010	yes	missense	BNC2	NM_017637.5	64	3,317,6183	AA,AG,GG		3.407,0.6809,2.4835	benign	923/1100	16419519	323,12683	2203	4300	6503	SO:0001583	missense	54796	exon7			TGCTGGGCACCAT	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.2768C>T	9.37:g.16419519G>A	ENSP00000370047:p.Ala923Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	26	0.011904761904761904	0	0.0	3	0.008287292817679558	0	0.0	23	0.030343007915567283	G	13.60	2.286262	0.40494	0.006809	0.03407	ENSG00000173068	ENST00000380672;ENST00000380667;ENST00000545497	T;T;T	0.31510	1.49;1.5;1.5	5.5	5.5	0.81552	.	0.166180	0.51477	D	0.000083	T	0.07954	0.0199	N	0.22421	0.69	0.80722	D	1	P;P;B	0.41673	0.578;0.759;0.18	B;B;B	0.39027	0.158;0.288;0.051	T	0.01844	-1.1262	10	0.27082	T	0.32	-9.5452	14.94	0.70986	0.0:0.1426:0.8574:0.0	.	828;923;688	F5H586;Q6ZN30;D3DRJ1	.;BNC2_HUMAN;.	V	923;856;828	ENSP00000370047:A923V;ENSP00000370042:A856V;ENSP00000444640:A828V	ENSP00000370042:A856V	A	-	2	0	BNC2	16409519	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.336000	0.52113	2.586000	0.87340	0.591000	0.81541	GCC	G|0.979;A|0.021	0.021	strong		0.572	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7505147	7505147	+	Missense_Mutation	SNP	G	G	T	rs201598844		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7505147G>T	ENST00000359920.6	+	1	574	c.321G>T	c.(319-321)caG>caT	p.Q107H	ARHGEF18_ENST00000319670.9_Intron|CTD-2207O23.3_ENST00000593531.1_Intron	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	107					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				TGCGGCCGCAGTCGGAGCGGG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		13103	0.0		0.0	False		,,,				2504	0.001				p.Q107H		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.G321T						PASS	.						27.0	35.0	33.0					19																	7505147		692	1591	2283	SO:0001583	missense	23370	exon1			GCCGCAGTCGGAG	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.321G>T	19.37:g.7505147G>T	ENSP00000352995:p.Gln107His	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	G	7.449	0.642374	0.14451	.	.	ENSG00000104880	ENST00000359920	T	0.30182	1.54	5.23	4.17	0.49024	.	0.187822	0.25607	U	0.029507	T	0.15565	0.0375	N	0.11560	0.145	0.09310	N	0.999997	B	0.10296	0.003	B	0.08055	0.003	T	0.13791	-1.0496	10	0.16896	T	0.51	-7.5996	11.9999	0.53224	0.0:0.0:0.7921:0.2079	.	107	Q6ZSZ5	ARHGI_HUMAN	H	107	ENSP00000352995:Q107H	ENSP00000352995:Q107H	Q	+	3	2	ARHGEF18	7411147	0.006000	0.16342	0.034000	0.17996	0.874000	0.50279	0.359000	0.20233	2.442000	0.82660	0.561000	0.74099	CAG	G|0.999;T|0.001	0.001	weak		0.602	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
PKN1	5585	hgsc.bcm.edu	37	19	14580197	14580197	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14580197G>T	ENST00000242783.6	+	16	2186	c.2021G>T	c.(2020-2022)gGa>gTa	p.G674V	PKN1_ENST00000342216.4_Missense_Mutation_p.G680V	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	674	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						ACCAGTGCGGGACACCCCTTC	0.602																																					p.G680V	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.G2039T						PASS	.						106.0	120.0	116.0					19																	14580197		2123	4227	6350	SO:0001583	missense	5585	exon16			GTGCGGGACACCC	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.2021G>T	19.37:g.14580197G>T	ENSP00000242783:p.Gly674Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	142	82	0.577465	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	37	CCDS42513.1	.	.	.	.	.	.	.	.	.	.	G	4.532	0.098772	0.08681	.	.	ENSG00000123143	ENST00000242783;ENST00000342216	T;T	0.25912	1.77;1.77	3.45	3.45	0.39498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.356188	0.26407	U	0.024542	T	0.20170	0.0485	L	0.39514	1.22	0.28256	N	0.925049	B;B	0.26744	0.131;0.158	B;B	0.26310	0.04;0.068	T	0.13522	-1.0506	10	0.56958	D	0.05	-18.5356	8.9541	0.35807	0.0:0.2289:0.7711:0.0	.	680;674	Q16512-2;Q16512	.;PKN1_HUMAN	V	674;680	ENSP00000242783:G674V;ENSP00000343325:G680V	ENSP00000242783:G674V	G	+	2	0	PKN1	14441197	0.001000	0.12720	0.885000	0.34714	0.129000	0.20672	1.374000	0.34283	1.926000	0.55796	0.491000	0.48974	GGA	.	.	none		0.602	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560	
ZNF235	9310	hgsc.bcm.edu	37	19	44792701	44792701	+	Missense_Mutation	SNP	T	T	G	rs2125579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44792701T>G	ENST00000291182.4	-	5	989	c.887A>C	c.(886-888)cAt>cCt	p.H296P	ZNF235_ENST00000589248.1_Intron|ZNF235_ENST00000589799.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	296			H -> P (in dbSNP:rs2125579). {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)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	29		Prostate(69;0.0352)|all_neural(266;0.116)				GTCCTTCTCATGTGTACTACA	0.418													T|||	2207	0.440695	0.1263	0.4582	5008	,	,		21722	0.5169		0.5427	False		,,,				2504	0.6697				p.H296P		Atlas-SNP	.											.	ZNF235	60	.	0			c.A887C						PASS	.	T	PRO/HIS	959,3447	364.4+/-316.9	120,719,1364	128.0	116.0	120.0		887	-8.6	0.0	19	dbSNP_96	120	4734,3866	608.9+/-395.5	1315,2104,881	yes	missense	ZNF235	NM_004234.4	77	1435,2823,2245	GG,GT,TT		44.9535,21.7658,43.7721	benign	296/739	44792701	5693,7313	2203	4300	6503	SO:0001583	missense	9310	exon5			TTCTCATGTGTAC	X78929	CCDS33048.1	19q13.2	2013-01-08	2002-11-04	2002-11-08	ENSG00000159917	ENSG00000159917		"""Zinc fingers, C2H2-type"", ""-"""	12866	protein-coding gene	gene with protein product		604749	"""zinc finger protein homologous to Zfp93 in mouse"""	ZNF270, ZFP93		7865130, 9570955	Standard	NM_004234		Approved	HZF6, ANF270	uc002oza.4	Q14590		ENST00000291182.4:c.887A>C	19.37:g.44792701T>G	ENSP00000291182:p.His296Pro	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	955	0.43727106227106227	82	0.16666666666666666	159	0.43922651933701656	294	0.513986013986014	420	0.554089709762533	t	9.415	1.081627	0.20309	0.217658	0.550465	ENSG00000159917	ENST00000391957;ENST00000291182;ENST00000359844	T	0.14766	2.48	4.32	-8.64	0.00874	.	1.533750	0.04170	N	0.324715	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.39251	-0.9623	9	0.66056	D	0.02	.	8.9373	0.35708	0.0:0.3701:0.4061:0.2238	rs2125579;rs17246963;rs61574517;rs2125579	292;296	Q14590-2;Q14590	.;ZN235_HUMAN	P	296;296;218	ENSP00000291182:H296P	ENSP00000291182:H296P	H	-	2	0	ZNF235	49484541	0.166000	0.22962	0.000000	0.03702	0.002000	0.02628	0.852000	0.27764	-2.264000	0.00689	0.370000	0.22315	CAT	G|0.429;N|0.000	0.429	strong		0.418	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1		
FAM210A	125228	hgsc.bcm.edu	37	18	13681962	13681962	+	Missense_Mutation	SNP	A	A	T	rs35493157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:13681962A>T	ENST00000322247.3	-	3	502	c.115T>A	c.(115-117)Tac>Aac	p.Y39N	FAM210A_ENST00000402563.1_Missense_Mutation_p.Y39N|FAM210A_ENST00000588475.1_5'UTR	NM_001098801.1	NP_001092271.1	Q96ND0	F210A_HUMAN	family with sequence similarity 210, member A	39			Y -> N (in dbSNP:rs35493157).			integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)											TCAGCATTGTATAAAAGTAAA	0.453													A|||	83	0.0165735	0.0068	0.0288	5008	,	,		19131	0.0		0.0467	False		,,,				2504	0.0072				p.Y39N		Atlas-SNP	.											.	.	.	.	0			c.T115A						PASS	.	A	ASN/TYR,ASN/TYR	64,4342	59.9+/-96.7	1,62,2140	144.0	134.0	137.0		115,115	-4.7	0.0	18	dbSNP_126	137	355,8245	120.1+/-179.3	8,339,3953	yes	missense,missense	C18orf19	NM_001098801.1,NM_152352.3	143,143	9,401,6093	TT,TA,AA		4.1279,1.4526,3.2216	benign,benign	39/273,39/273	13681962	419,12587	2203	4300	6503	SO:0001583	missense	125228	exon3			CATTGTATAAAAG	AK055618	CCDS11866.1	18p11.21	2011-11-24	2011-11-24	2011-11-24	ENSG00000177150	ENSG00000177150			28346	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 19"""	C18orf19		14702039	Standard	NM_152352		Approved	MGC24180, HsT2329	uc010dli.3	Q96ND0	OTTHUMG00000131719	ENST00000322247.3:c.115T>A	18.37:g.13681962A>T	ENSP00000323635:p.Tyr39Asn	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_001098801	D3DUJ4	Missense_Mutation	SNP	ENST00000322247.3	37	CCDS11866.1	48	0.02197802197802198	2	0.0040650406504065045	13	0.03591160220994475	1	0.0017482517482517483	32	0.04221635883905013	A	2.837	-0.241379	0.05906	0.014526	0.041279	ENSG00000177150	ENST00000322247;ENST00000402563	T;T	0.44482	0.92;0.92	5.48	-4.74	0.03249	.	0.831997	0.10539	N	0.662943	T	0.06554	0.0168	L	0.44542	1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18053	-1.0349	10	0.30078	T	0.28	1.011	3.9829	0.09503	0.357:0.1154:0.4151:0.1125	rs35493157	39	Q96ND0	CR019_HUMAN	N	39	ENSP00000323635:Y39N;ENSP00000386115:Y39N	ENSP00000323635:Y39N	Y	-	1	0	C18orf19	13671962	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.021000	0.12504	-0.430000	0.07318	-0.290000	0.09829	TAC	A|0.971;T|0.029	0.029	strong		0.453	FAM210A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254637.1	NM_152352	
MCM3AP	8888	hgsc.bcm.edu	37	21	47695220	47695220	+	Silent	SNP	A	A	G	rs2839190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47695220A>G	ENST00000397708.1	-	7	2132	c.1878T>C	c.(1876-1878)gaT>gaC	p.D626D	MCM3AP_ENST00000291688.1_Silent_p.D626D			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	626					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)					CTTTGTCCAGATCGGTTCTCT	0.473													A|||	700	0.139776	0.4251	0.0591	5008	,	,		19284	0.004		0.0129	False		,,,				2504	0.0818				p.D626D		Atlas-SNP	.											.	MCM3AP	146	.	0			c.T1878C						PASS	.	A		1581,2825	492.9+/-362.5	271,1039,893	97.0	76.0	83.0		1878	-3.5	0.6	21	dbSNP_100	83	114,8486	59.5+/-121.1	1,112,4187	yes	coding-synonymous	MCM3AP	NM_003906.3		272,1151,5080	GG,GA,AA		1.3256,35.8829,13.0324		626/1981	47695220	1695,11311	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon6			GTCCAGATCGGTT	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.1878T>C	21.37:g.47695220A>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			A|0.864;G|0.136	0.136	strong		0.473	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
MCM8	84515	hgsc.bcm.edu	37	20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	rs6117014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5935303A>C	ENST00000378896.3	+	4	680	c.303A>C	c.(301-303)aaA>aaC	p.K101N	MCM8_ENST00000265187.4_Missense_Mutation_p.K101N|MCM8_ENST00000378886.2_Missense_Mutation_p.K101N|MCM8_ENST00000378883.1_Missense_Mutation_p.K101N	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	101			K -> N (in dbSNP:rs6117014).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CATTTGAAAAATTTTTCACAA	0.373													A|||	351	0.0700879	0.1626	0.1009	5008	,	,		19997	0.001		0.0199	False		,,,				2504	0.046				p.K101N		Atlas-SNP	.											.	MCM8	125	.	0			c.A303C						PASS	.	A	ASN/LYS,ASN/LYS	652,3750	276.0+/-272.9	51,550,1600	101.0	97.0	98.0		303,303	-10.4	0.5	20	dbSNP_114	98	183,8417	83.1+/-145.7	2,179,4119	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	94,94	53,729,5719	CC,CA,AA		2.1279,14.8114,6.4221	benign,benign	101/841,101/825	5935303	835,12167	2201	4300	6501	SO:0001583	missense	84515	exon4			TGAAAAATTTTTC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.303A>C	20.37:g.5935303A>C	ENSP00000368174:p.Lys101Asn	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	100	36	0.36	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	145	0.06639194139194139	92	0.18699186991869918	29	0.08011049723756906	2	0.0034965034965034965	22	0.029023746701846966	A	11.02	1.515159	0.27123	0.148114	0.021279	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.37	-10.4	0.00318	Nucleic acid-binding, OB-fold-like (1);	0.302307	0.39475	N	0.001357	T	0.00012	0.0000	L	0.29908	0.895	0.27511	P	0.9516967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.002;0.001	T	0.38265	-0.9669	9	0.11485	T	0.65	-1.2423	2.7834	0.05367	0.2356:0.137:0.3949:0.2325	rs6117014;rs52802444;rs6117014	101;101;101;101	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	N	101	ENSP00000368174:K101N;ENSP00000368161:K101N;ENSP00000368164:K101N;ENSP00000265187:K101N	ENSP00000265187:K101N	K	+	3	2	MCM8	5883303	0.041000	0.20044	0.522000	0.27862	0.993000	0.82548	-1.262000	0.02852	-1.754000	0.01321	-0.250000	0.11733	AAA	A|0.936;C|0.064	0.064	strong		0.373	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
IL6ST	3572	hgsc.bcm.edu	37	5	55272085	55272085	+	Missense_Mutation	SNP	G	G	C	rs1063560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:55272085G>C	ENST00000381298.2	-	3	334	c.22C>G	c.(22-24)Cta>Gta	p.L8V	IL6ST_ENST00000536319.1_Missense_Mutation_p.L8V|IL6ST_ENST00000396816.1_Missense_Mutation_p.L8V|IL6ST_ENST00000381294.3_Missense_Mutation_p.L8V|IL6ST_ENST00000502326.3_Missense_Mutation_p.L8V|IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000522633.2_Missense_Mutation_p.L8V|IL6ST_ENST00000381286.3_Missense_Mutation_p.L8V|IL6ST_ENST00000381293.2_Missense_Mutation_p.L8V|IL6ST_ENST00000381287.4_Missense_Mutation_p.L8V|IL6ST_ENST00000336909.5_Missense_Mutation_p.L8V	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	8			L -> V (in dbSNP:rs1063560). {ECO:0000269|PubMed:10880057, ECO:0000269|PubMed:2261637}.		ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				GCTTGCACTAGCCAAGTCTGC	0.323			O		hepatocellular ca								g|||	42	0.00838658	0.0015	0.0	5008	,	,		12985	0.001		0.0129	False		,,,				2504	0.0266				p.L8V		Atlas-SNP	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.C22G						PASS	.	A	VAL/LEU,VAL/LEU,VAL/LEU	5,4401	9.9+/-24.2	0,5,2198	70.0	64.0	66.0		22,22,22	-1.1	0.0	5	dbSNP_86	66	99,8501	54.4+/-115.2	1,97,4202	yes	missense,missense,missense	IL6ST	NM_001190981.1,NM_002184.3,NM_175767.2	32,32,32	1,102,6400	CC,CG,GG		1.1512,0.1135,0.7996	benign,benign,benign	8/858,8/919,8/330	55272085	104,12902	2203	4300	6503	SO:0001583	missense	3572	exon3			GCACTAGCCAAGT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.22C>G	5.37:g.55272085G>C	ENSP00000370698:p.Leu8Val	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	180	82	0.455556	NM_175767	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	0	0.0	11	0.014511873350923483	g	0.001	-3.108750	0.00033	0.001135	0.011512	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294;ENST00000381287;ENST00000536319;ENST00000381293;ENST00000381286;ENST00000522633;ENST00000542298	T;T;T;T;T;T;T;T	0.61980	1.52;1.52;1.27;1.49;1.49;1.88;0.06;1.49	4.85	-1.07	0.09968	.	0.996520	0.08132	N	0.993050	T	0.35451	0.0932	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.17289	-1.0374	10	0.20519	T	0.43	.	0.7244	0.00946	0.2881:0.1764:0.3444:0.1911	rs1063560;rs3204590;rs52794902;rs1063560	8;8;8;8	Q5FC05;Q5FC04;P40189-2;P40189	.;.;.;IL6RB_HUMAN	V	8	ENSP00000370698:L8V;ENSP00000338799:L8V;ENSP00000370694:L8V;ENSP00000370687:L8V;ENSP00000444456:L8V;ENSP00000370693:L8V;ENSP00000370686:L8V;ENSP00000435399:L8V	ENSP00000338799:L8V	L	-	1	2	IL6ST	55307842	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.516000	0.06282	-0.573000	0.05998	-3.277000	0.00047	CTA	G|0.989;C|0.011	0.011	strong		0.323	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
UEVLD	55293	hgsc.bcm.edu	37	11	18555949	18555949	+	Silent	SNP	T	T	C	rs55999230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18555949T>C	ENST00000396197.3	-	11	1204	c.1176A>G	c.(1174-1176)ctA>ctG	p.L392L	UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000535484.1_Intron|UEVLD_ENST00000379387.4_Silent_p.L370L|UEVLD_ENST00000543987.1_Intron|UEVLD_ENST00000320750.6_Intron|UEVLD_ENST00000541984.1_Intron	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						CAGCTACTGATAGTCCAACAG	0.348													T|||	1262	0.251997	0.0469	0.2363	5008	,	,		17841	0.4415		0.1958	False		,,,				2504	0.4029				p.L392L		Atlas-SNP	.											.	UEVLD	58	.	0			c.A1176G						PASS	.	T	,	256,3444		7,242,1601	116.0	106.0	109.0		1176,	-3.1	1.0	11	dbSNP_129	109	1273,6923		117,1039,2942	no	coding-synonymous,intron	UEVLD	NM_001040697.1,NM_018314.3	,	124,1281,4543	CC,CT,TT		15.532,6.9189,12.8531	,	392/472,	18555949	1529,10367	1850	4098	5948	SO:0001819	synonymous_variant	55293	exon11			TACTGATAGTCCA	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.1176A>G	11.37:g.18555949T>C		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001040697		Silent	SNP	ENST00000396197.3	37	CCDS41624.1																																																																																			T|0.793;C|0.207	0.207	strong		0.348	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314	
CPZ	8532	hgsc.bcm.edu	37	4	8621269	8621269	+	Silent	SNP	C	C	T	rs61734024	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:8621269C>T	ENST00000360986.4	+	11	2058	c.1884C>T	c.(1882-1884)gaC>gaT	p.D628D	CPZ_ENST00000429646.2_Silent_p.D236D|CPZ_ENST00000382480.2_Silent_p.D491D|CPZ_ENST00000315782.6_Silent_p.D617D	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	628					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						CCTCGGCCGACGGGAGTAAGC	0.706													C|||	42	0.00838658	0.0136	0.0043	5008	,	,		13474	0.0		0.0169	False		,,,				2504	0.0041				p.D628D		Atlas-SNP	.											.	CPZ	95	.	0			c.C1884T						PASS	.	C	,,	63,4341	54.9+/-90.9	0,63,2139	27.0	29.0	28.0		1884,1473,1851	-3.5	0.1	4	dbSNP_129	28	148,8448	67.7+/-130.1	3,142,4153	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	3,205,6292	TT,TC,CC		1.7217,1.4305,1.6231	,,	628/653,491/516,617/642	8621269	211,12789	2202	4298	6500	SO:0001819	synonymous_variant	8532	exon11			GGCCGACGGGAGT	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.1884C>T	4.37:g.8621269C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	28	18	0.642857	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			C|0.987;T|0.013	0.013	strong		0.706	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
ITSN2	50618	hgsc.bcm.edu	37	2	24439048	24439048	+	Missense_Mutation	SNP	A	A	G	rs3731625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:24439048A>G	ENST00000355123.4	-	32	4303	c.3860T>C	c.(3859-3861)aTt>aCt	p.I1287T	ITSN2_ENST00000361999.3_Missense_Mutation_p.I1260T|AC009228.1_ENST00000413989.1_RNA|AC009228.1_ENST00000430105.1_RNA|AC009228.1_ENST00000413254.1_RNA	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1287	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.		I -> T (in dbSNP:rs3731625).		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)	p.I1286T(1)		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)					GATGTCCCCAATCATCTGCAC	0.532													A|||	328	0.0654952	0.0401	0.0548	5008	,	,		17822	0.0784		0.0895	False		,,,				2504	0.0695				p.I1287T		Atlas-SNP	.											ITSN2,NS,carcinoma,0,1	ITSN2	224	1	1	Substitution - Missense(1)	stomach(1)	c.T3860C						PASS	.	A	THR/ILE,THR/ILE	210,4196	128.2+/-165.1	4,202,1997	99.0	93.0	95.0		3779,3860	5.4	0.9	2	dbSNP_107	95	720,7880	175.5+/-225.5	19,682,3599	yes	missense,missense	ITSN2	NM_019595.3,NM_006277.2	89,89	23,884,5596	GG,GA,AA		8.3721,4.7662,7.1505	benign,benign	1260/1671,1287/1698	24439048	930,12076	2203	4300	6503	SO:0001583	missense	50618	exon32			TCCCCAATCATCT	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.3860T>C	2.37:g.24439048A>G	ENSP00000347244:p.Ile1287Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	126	66	0.52381	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	162	0.07417582417582418	26	0.052845528455284556	24	0.06629834254143646	47	0.08216783216783216	65	0.08575197889182058	A	19.74	3.883479	0.72410	0.047662	0.083721	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.70164	-0.46;-0.46;-0.46	5.38	5.38	0.77491	Dbl homology (DH) domain (5);	0.232813	0.21136	U	0.079565	T	0.14056	0.0340	M	0.89840	3.065	0.49687	D	0.999819	B;B	0.33171	0.348;0.4	B;B	0.42282	0.264;0.382	T	0.61569	-0.7036	10	0.72032	D	0.01	.	15.7592	0.78063	1.0:0.0:0.0:0.0	rs3731625;rs52815979;rs56638172;rs3731625	1260;1287	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	T	1260;1287;1260	ENSP00000354561:I1260T;ENSP00000347244:I1287T;ENSP00000370250:I1260T	ENSP00000347244:I1287T	I	-	2	0	ITSN2	24292552	1.000000	0.71417	0.950000	0.38849	0.986000	0.74619	8.850000	0.92190	2.189000	0.69895	0.529000	0.55759	ATT	A|0.924;G|0.076	0.076	strong		0.532	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
CDH23	64072	hgsc.bcm.edu	37	10	73569749	73569749	+	Silent	SNP	C	C	T	rs11000009	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:73569749C>T	ENST00000224721.6	+	60	8915	c.8910C>T	c.(8908-8910)ccC>ccT	p.P2970P	CDH23_ENST00000398788.3_Silent_p.P725P|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2965	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						ACGAGATCCCCGACCGTGTGC	0.587													C|||	405	0.0808706	0.09	0.072	5008	,	,		21487	0.0079		0.1213	False		,,,				2504	0.1084				p.P2965P		Atlas-SNP	.											.	CDH23	365	.	0			c.C8895T						PASS	.	C	,,	395,3841		15,365,1738	99.0	100.0	99.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2175,2175,8895	-11.6	0.4	10	dbSNP_120	99	1074,7354		74,926,3214	no	coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171933.1,NM_001171934.1,NM_022124.5	,,	89,1291,4952	TT,TC,CC		12.7432,9.3248,11.5998	,,	725/1115,725/1080,2965/3355	73569749	1469,11195	2118	4214	6332	SO:0001819	synonymous_variant	64072	exon59			GATCCCCGACCGT	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.8910C>T	10.37:g.73569749C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	29	0.630435	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.909;T|0.091	0.091	strong		0.587	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
BAGE2	85319	hgsc.bcm.edu	37	21	11049616	11049616	+	RNA	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:11049616C>T	ENST00000470054.1	-	0	492							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TTTGCATCTTCCTTCGCTATA	0.368																																					p.R95R		Atlas-SNP	.											.	.	.	.	0			c.G285A						PASS	.						135.0	96.0	108.0					21																	11049616		692	1591	2283			85318	exon4			CATCTTCCTTCGC	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11049616C>T		Somatic	430	0	0		WXS	Illumina HiSeq	Phase_I	388	27	0.0695876	NM_182481	A8K925|Q08ER0	Silent	SNP	ENST00000470054.1	37																																																																																				.	.	none		0.368	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
MEFV	4210	hgsc.bcm.edu	37	16	3297181	3297181	+	Silent	SNP	C	C	T	rs224208	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3297181C>T	ENST00000219596.1	-	5	1461	c.1422G>A	c.(1420-1422)gaG>gaA	p.E474E	MEFV_ENST00000339854.4_Silent_p.E294E|MEFV_ENST00000536379.1_Silent_p.E263E|MEFV_ENST00000541159.1_Silent_p.E263E	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	474	Required for homotrimerization and induction of pyroptosomes.		E -> K (in arFMF). {ECO:0000269|PubMed:16378925}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						GCTCTTGCTGCTCCAGGAAGT	0.582													C|||	3200	0.638978	0.6407	0.6239	5008	,	,		20588	0.6062		0.5577	False		,,,				2504	0.7648				p.E474E		Atlas-SNP	.											.	MEFV	170	.	0			c.G1422A						PASS	.	C	,	2782,1612	660.9+/-400.8	869,1044,284	157.0	144.0	148.0		1422,789	2.3	0.8	16	dbSNP_79	148	4580,4020	597.8+/-393.8	1248,2084,968	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2117,3128,1252	TT,TC,CC		46.7442,36.6864,43.3431	,	474/782,263/446	3297181	7362,5632	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon5			TTGCTGCTCCAGG	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1422G>A	16.37:g.3297181C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	159	76	0.477987	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			C|0.414;T|0.586	0.586	strong		0.582	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
STK10	6793	hgsc.bcm.edu	37	5	171482633	171482633	+	Missense_Mutation	SNP	C	C	T	rs115040416	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:171482633C>T	ENST00000176763.5	-	16	2828	c.2485G>A	c.(2485-2487)Ggc>Agc	p.G829S		NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	829	Gln-rich.				cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)	p.G829S(1)		breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTGCCCCCGCCGTTGATGTGG	0.642													C|||	3	0.000599042	0.0	0.0	5008	,	,		15696	0.003		0.0	False		,,,				2504	0.0				p.G829S		Atlas-SNP	.											STK10,NS,carcinoma,0,1	STK10	100	1	1	Substitution - Missense(1)	lung(1)	c.G2485A						scavenged	.						36.0	30.0	32.0					5																	171482633		2203	4300	6503	SO:0001583	missense	6793	exon16			CCCCGCCGTTGAT	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.2485G>A	5.37:g.171482633C>T	ENSP00000176763:p.Gly829Ser	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	270	3	0.0111111	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	C	0.138	-1.105396	0.01828	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.27402	1.67	5.23	5.23	0.72850	.	0.196000	0.44097	D	0.000485	T	0.11623	0.0283	N	0.02368	-0.58	0.24492	N	0.99429	B	0.24186	0.099	B	0.27380	0.079	T	0.20672	-1.0268	10	0.02654	T	1	.	12.084	0.53688	0.0:0.8265:0.1735:0.0	.	829	O94804	STK10_HUMAN	S	829	ENSP00000176763:G829S	ENSP00000176763:G829S	G	-	1	0	STK10	171415238	0.409000	0.25368	0.167000	0.22817	0.109000	0.19521	1.104000	0.31074	2.455000	0.83008	0.561000	0.74099	GGC	C|0.990;T|0.010	0.010	strong		0.642	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
USP18	11274	hgsc.bcm.edu	37	22	18650682	18650682	+	Missense_Mutation	SNP	C	C	T	rs3180408	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18650682C>T	ENST00000215794.7	+	6	936	c.506C>T	c.(505-507)aCg>aTg	p.T169M		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	169	USP.		T -> M (in dbSNP:rs3180408). {ECO:0000269|Ref.7}.		cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)	p.T169M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GCCCTGTATACGATCCGGGTG	0.547													c|||	1489	0.297324	0.3979	0.2997	5008	,	,		16115	0.1637		0.3072	False		,,,				2504	0.2873				p.T169M		Atlas-SNP	.											USP18,NS,carcinoma,0,1	USP18	22	1	1	Substitution - Missense(1)	stomach(1)	c.C506T						scavenged	.	C	MET/THR	1709,2697		320,1069,814	121.0	94.0	103.0		506	-3.1	0.0	22	dbSNP_105	103	2965,5635		496,1973,1831	no	missense	USP18	NM_017414.3	81	816,3042,2645	TT,TC,CC		34.4767,38.788,35.9373	benign	169/373	18650682	4674,8332	2203	4300	6503	SO:0001583	missense	11274	exon6			TGTATACGATCCG	AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"""Ubiquitin-specific peptidases"""	12616	protein-coding gene	gene with protein product		607057	"""ubiquitin specific protease 18"""			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.506C>T	22.37:g.18650682C>T	ENSP00000215794:p.Thr169Met	Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	243	122	0.502058	NM_017414	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	614	0.28113553113553114	173	0.3516260162601626	107	0.2955801104972376	92	0.16083916083916083	242	0.31926121372031663	.	2.520	-0.311064	0.05458	0.38788	0.344767	ENSG00000184979	ENST00000215794;ENST00000441683	T	0.31769	1.48	5.62	-3.07	0.05363	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.540147	0.20380	N	0.093467	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P	0.36789	0.57	B	0.33521	0.165	T	0.40270	-0.9572	9	0.46703	T	0.11	.	7.1474	0.25591	0.0:0.5396:0.1135:0.347	rs3180408;rs3210451;rs3180408	169	Q9UMW8	UBP18_HUMAN	M	169;1	ENSP00000215794:T169M	ENSP00000215794:T169M	T	+	2	0	USP18	17030682	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.076000	0.11412	-0.757000	0.04697	-1.789000	0.00628	ACG	C|0.674;N|0.000	.	strong		0.547	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1		
SSRP1	6749	hgsc.bcm.edu	37	11	57099661	57099661	+	Silent	SNP	T	T	C	rs2230648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57099661T>C	ENST00000278412.2	-	8	1232	c.966A>G	c.(964-966)gtA>gtG	p.V322V		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	322					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						TCTTGCGGTTTACCAGTGCTT	0.542													C|||	110	0.0219649	0.0136	0.0389	5008	,	,		22838	0.001		0.0388	False		,,,				2504	0.0256				p.V322V	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.A966G						PASS	.	C		104,4298	816.5+/-416.3	1,102,2098	113.0	91.0	98.0		966	0.6	1.0	11	dbSNP_98	98	391,8201	801.2+/-407.4	8,375,3913	no	coding-synonymous	SSRP1	NM_003146.2		9,477,6011	CC,CT,TT		4.5507,2.3626,3.8095		322/710	57099661	495,12499	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon8			GCGGTTTACCAGT	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.966A>G	11.37:g.57099661T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			T|0.967;C|0.033;A|0.000	0.033	strong		0.542	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
SLX4	84464	hgsc.bcm.edu	37	16	3640784	3640784	+	Missense_Mutation	SNP	G	G	A	rs78637028	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3640784G>A	ENST00000294008.3	-	12	3495	c.2855C>T	c.(2854-2856)gCg>gTg	p.A952V		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	952	Interaction with PLK1 and TERF2-TERF2IP.		A -> M (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						ATGGCCAAGCGCCTCCTCTGG	0.647								Direct reversal of damage					G|||	206	0.0411342	0.0038	0.0648	5008	,	,		16698	0.0496		0.0646	False		,,,				2504	0.0419				p.A952V		Atlas-SNP	.											SLX4,NS,carcinoma,+1,1	SLX4	173	1	0			c.C2855T						PASS	.	G	VAL/ALA	64,4330	56.2+/-92.4	0,64,2133	46.0	50.0	49.0		2855	3.2	0.0	16	dbSNP_131	49	556,8044	136.8+/-193.9	14,528,3758	yes	missense	SLX4	NM_032444.2	64	14,592,5891	AA,AG,GG		6.4651,1.4565,4.7714	probably-damaging	952/1835	3640784	620,12374	2197	4300	6497	SO:0001583	missense	84464	exon12			CCAAGCGCCTCCT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2855C>T	16.37:g.3640784G>A	ENSP00000294008:p.Ala952Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	121	62	0.512397	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	98	0.04487179487179487	5	0.01016260162601626	22	0.06077348066298342	23	0.04020979020979021	48	0.0633245382585752	G	14.67	2.603371	0.46423	0.014565	0.064651	ENSG00000188827	ENST00000294008	T	0.01446	4.88	5.27	3.18	0.36537	.	1.163550	0.06146	N	0.673336	T	0.00328	0.0010	L	0.53249	1.67	0.09310	N	1	P	0.49635	0.926	B	0.39419	0.299	T	0.48896	-0.8994	10	0.48119	T	0.1	.	5.0782	0.14642	0.0778:0.1232:0.5753:0.2237	.	952	Q8IY92	SLX4_HUMAN	V	952	ENSP00000294008:A952V	ENSP00000294008:A952V	A	-	2	0	SLX4	3580785	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.216000	0.09266	1.359000	0.45940	0.561000	0.74099	GCG	G|0.955;A|0.045	0.045	strong		0.647	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
UBR2	23304	hgsc.bcm.edu	37	6	42571346	42571346	+	Silent	SNP	A	A	T	rs16895863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42571346A>T	ENST00000372899.1	+	5	810	c.552A>T	c.(550-552)tcA>tcT	p.S184S	UBR2_ENST00000372903.2_Silent_p.S184S|UBR2_ENST00000372901.1_Silent_p.S184S	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	184					cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TTCATTTATCAGAAGATGTGA	0.328													A|||	1006	0.200879	0.2352	0.183	5008	,	,		18936	0.0893		0.2366	False		,,,				2504	0.2454				p.S184S		Atlas-SNP	.											.	UBR2	134	.	0			c.A552T						PASS	.	A	,	1026,3380	375.4+/-321.6	116,794,1293	66.0	64.0	65.0		552,552	3.1	1.0	6	dbSNP_123	65	1828,6762	326.6+/-317.4	204,1420,2671	no	coding-synonymous,coding-synonymous	UBR2	NM_001184801.1,NM_015255.2	,	320,2214,3964	TT,TA,AA		21.2806,23.2864,21.9606	,	184/440,184/1756	42571346	2854,10142	2203	4295	6498	SO:0001819	synonymous_variant	23304	exon5			TTTATCAGAAGAT	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.552A>T	6.37:g.42571346A>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	52	24	0.461538	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			A|0.793;T|0.207	0.207	strong		0.328	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
ZNF280D	54816	hgsc.bcm.edu	37	15	56959028	56959028	+	Missense_Mutation	SNP	C	C	T	rs28620278	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:56959028C>T	ENST00000267807.7	-	15	1918	c.1702G>A	c.(1702-1704)Gtc>Atc	p.V568I	ZNF280D_ENST00000396245.1_Missense_Mutation_p.V272I|ZNF280D_ENST00000559000.1_Missense_Mutation_p.V555I|ZNF280D_ENST00000559237.1_Missense_Mutation_p.V555I	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	568			V -> I (in dbSNP:rs28620278). {ECO:0000269|PubMed:10997877, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		TTGGATTTGACTGTATTAGGT	0.333													T|||	2640	0.527157	0.7141	0.6225	5008	,	,		15602	0.3829		0.4066	False		,,,				2504	0.4796				p.V568I		Atlas-SNP	.											.	ZNF280D	82	.	0			c.G1702A						PASS	.	T	ILE/VAL,ILE/VAL	2803,1581	486.2+/-360.5	917,969,306	139.0	145.0	143.0		1663,1702	-0.9	0.0	15	dbSNP_125	143	3481,5103	631.5+/-398.5	697,2087,1508	yes	missense,missense	ZNF280D	NM_001002843.1,NM_017661.2	29,29	1614,3056,1814	TT,TC,CC		40.5522,36.063,48.4577	benign,benign	555/967,568/980	56959028	6284,6684	2192	4292	6484	SO:0001583	missense	54816	exon15			ATTTGACTGTATT	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.1702G>A	15.37:g.56959028C>T	ENSP00000267807:p.Val568Ile	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	243	112	0.460905	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Missense_Mutation	SNP	ENST00000267807.7	37	CCDS32245.1	1099	0.5032051282051282	370	0.7520325203252033	214	0.5911602209944752	225	0.39335664335664333	290	0.38258575197889183	T	1.441	-0.567698	0.03910	0.63937	0.405522	ENSG00000137871	ENST00000267807;ENST00000455329;ENST00000396245	T;T	0.03004	4.08;4.5	4.58	-0.931	0.10438	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.05305	-1.0893	8	0.17832	T	0.49	0.0847	6.768	0.23579	0.0:0.4082:0.1329:0.459	rs28620278;rs28620278	568	Q6N043	Z280D_HUMAN	I	568;555;272	ENSP00000267807:V568I;ENSP00000379545:V272I	ENSP00000267807:V568I	V	-	1	0	ZNF280D	54746320	0.059000	0.20769	0.018000	0.16275	0.511000	0.34104	-0.286000	0.08399	-0.282000	0.09128	-0.332000	0.08345	GTC	C|0.495;T|0.505	0.505	strong		0.333	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
CENPB	1059	hgsc.bcm.edu	37	20	3766885	3766885	+	Silent	SNP	G	G	A	rs140023764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3766885G>A	ENST00000379751.4	-	1	452	c.246C>T	c.(244-246)atC>atT	p.I82I	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	82	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						GGAACCAGGCGATGAGCAAGC	0.657													g|||	16	0.00319489	0.0121	0.0	5008	,	,		8145	0.0		0.0	False		,,,				2504	0.0				p.I82I		Atlas-SNP	.											.	CENPB	24	.	0			c.C246T						PASS	.	G		28,4378	33.5+/-64.1	0,28,2175	67.0	66.0	67.0		246	-0.4	1.0	20	dbSNP_134	67	4,8596	4.3+/-15.6	0,4,4296	no	coding-synonymous	CENPB	NM_001810.5		0,32,6471	AA,AG,GG		0.0465,0.6355,0.246		82/600	3766885	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	1059	exon1			CCAGGCGATGAGC	X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"""centromere protein B (80kD)"""			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.246C>T	20.37:g.3766885G>A		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	35	16	0.457143	NM_001810	Q96EI4	Silent	SNP	ENST00000379751.4	37	CCDS13064.1																																																																																			G|0.997;A|0.003	0.003	strong		0.657	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810	
MUC6	4588	hgsc.bcm.edu	37	11	1018316	1018316	+	Silent	SNP	G	G	A	rs201954368		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1018316G>A	ENST00000421673.2	-	31	4535	c.4485C>T	c.(4483-4485)tcC>tcT	p.S1495S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1495	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGTGTGGGTGGACCCTGTGG	0.572																																					p.S1495S		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,4	MUC6	408	4	0			c.C4485T						PASS	.						280.0	289.0	286.0					11																	1018316		2189	4268	6457	SO:0001819	synonymous_variant	4588	exon31			GTGGGTGGACCCT	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.4485C>T	11.37:g.1018316G>A		Somatic	340	0	0		WXS	Illumina HiSeq	Phase_I	420	22	0.052381	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	weak		0.572	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PARD6B	84612	hgsc.bcm.edu	37	20	49366879	49366879	+	Silent	SNP	C	C	T	rs41283606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:49366879C>T	ENST00000371610.2	+	3	1216	c.973C>T	c.(973-975)Cta>Tta	p.L325L	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	325					axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						ACAGATAGAGCTAAGCTTTGA	0.433													C|||	6	0.00119808	0.0	0.0	5008	,	,		20869	0.0		0.006	False		,,,				2504	0.0				p.L325L		Atlas-SNP	.											.	PARD6B	31	.	0			c.C973T						PASS	.	C		14,4392	20.2+/-43.8	0,14,2189	109.0	102.0	104.0		973	4.8	0.5	20	dbSNP_127	104	56,8544	35.9+/-90.5	1,54,4245	no	coding-synonymous	PARD6B	NM_032521.2		1,68,6434	TT,TC,CC		0.6512,0.3177,0.5382		325/373	49366879	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	84612	exon3			ATAGAGCTAAGCT	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"""par-6 (partitioning defective 6, C.elegans) homolog beta"", ""par-6 partitioning defective 6 homolog beta (C. elegans)"""			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.973C>T	20.37:g.49366879C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	194	98	0.505155	NM_032521	A2A2A7|Q9Y510	Silent	SNP	ENST00000371610.2	37	CCDS33485.1																																																																																			C|0.996;T|0.004	0.004	strong		0.433	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521	
SMPD4	55627	hgsc.bcm.edu	37	2	130925088	130925088	+	Silent	SNP	C	C	T	rs10909567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130925088C>T	ENST00000409031.1	-	9	2000	c.852G>A	c.(850-852)acG>acA	p.T284T	SMPD4_ENST00000453750.1_Intron|SMPD4_ENST00000351288.6_Silent_p.T284T|SMPD4_ENST00000473720.1_5'UTR|SMPD4_ENST00000443958.2_5'UTR|SMPD4_ENST00000426662.2_5'UTR|SMPD4_ENST00000431183.2_Silent_p.T211T|SMPD4_ENST00000339679.7_Silent_p.T171T|SMPD4_ENST00000452225.2_5'UTR	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	245					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	CATTCACAGACGTCTGATGAG	0.552													.|||	1802	0.359824	0.211	0.4366	5008	,	,		16090	0.4405		0.3429	False		,,,				2504	0.4407				p.T284T		Atlas-SNP	.											.	SMPD4	67	.	0			c.G852A						PASS	.	C	,,	1155,3251		150,855,1198	90.0	79.0	83.0		633,852,852	-6.9	1.0	2	dbSNP_120	83	3096,5504		561,1974,1765	no	coding-synonymous,coding-synonymous,coding-synonymous	SMPD4	NM_001171083.2,NM_017751.4,NM_017951.4	,,	711,2829,2963	TT,TC,CC		36.0,26.2143,32.6849	,,	211/765,284/838,284/867	130925088	4251,8755	2203	4300	6503	SO:0001819	synonymous_variant	55627	exon9			CACAGACGTCTGA	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.852G>A	2.37:g.130925088C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	73	38	0.520548	NM_017751	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	Silent	SNP	ENST00000409031.1	37	CCDS42751.1	798|798	0.36538461538461536|0.36538461538461536	121|121	0.2459349593495935|0.2459349593495935	148|148	0.4088397790055249|0.4088397790055249	267|267	0.46678321678321677|0.46678321678321677	262|262	0.34564643799472294|0.34564643799472294	.|.	10.18|10.18	1.280335|1.280335	0.23392|0.23392	0.262143|0.262143	0.36|0.36	ENSG00000136699|ENSG00000136699	ENST00000439886|ENST00000430682	.|.	.|.	.|.	3.87|3.87	-6.91|-6.91	0.01649|0.01649	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.99999999679821|0.99999999679821	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.41645|0.41645	-0.9497|-0.9497	3|3	.|.	.|.	.|.	.|.	7.5421|7.5421	0.27744|0.27744	0.0:0.5121:0.204:0.2839|0.0:0.5121:0.204:0.2839	rs10909567;rs17846682;rs17859781;rs58345261|rs10909567;rs17846682;rs17859781;rs58345261	.|.	.|.	.|.	H|I	113|74	.|.	.|.	R|V	-|-	2|1	0|0	SMPD4|SMPD4	130641558|130641558	0.000000|0.000000	0.05858|0.05858	0.989000|0.989000	0.46669|0.46669	0.950000|0.950000	0.60333|0.60333	-3.081000|-3.081000	0.00613|0.00613	-0.789000|-0.789000	0.04498|0.04498	-1.263000|-1.263000	0.01449|0.01449	CGT|GTC	C|0.662;T|0.338	0.338	strong		0.552	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	
ZBTB42	100128927	hgsc.bcm.edu	37	14	105267579	105267579	+	Silent	SNP	A	A	G	rs12878684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:105267579A>G	ENST00000342537.7	+	1	330	c.45A>G	c.(43-45)agA>agG	p.R15R	ZBTB42_ENST00000555360.1_Silent_p.R15R	NM_001137601.1	NP_001131073.1	B2RXF5	ZBT42_HUMAN	zinc finger and BTB domain containing 42	15					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)										GCCGCCTGAGACAGCAGCGCG	0.721													G|||	3378	0.674521	0.7678	0.755	5008	,	,		11040	0.3234		0.8966	False		,,,				2504	0.6247				p.R15R		Atlas-SNP	.											.	ZBTB42	10	.	0			c.A45G						PASS	.	G		1021,207		420,181,13	3.0	6.0	5.0		45	1.8	1.0	14	dbSNP_121	5	2698,210		1251,196,7	no	coding-synonymous	ZBTB42	NM_001137601.1		1671,377,20	GG,GA,AA		7.2215,16.8567,10.0822		15/423	105267579	3719,417	614	1454	2068	SO:0001819	synonymous_variant	100128927	exon2			CCTGAGACAGCAG	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.45A>G	14.37:g.105267579A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_001137601	B7ZW21	Silent	SNP	ENST00000342537.7	37	CCDS45174.1																																																																																			A|0.292;G|0.708	0.708	strong		0.721	ZBTB42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410372.1		
NIM1K	167359	hgsc.bcm.edu	37	5	43245922	43245922	+	Silent	SNP	C	C	T	rs13176855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:43245922C>T	ENST00000512796.1	+	2	1544	c.45C>T	c.(43-45)caC>caT	p.H15H	NIM1_ENST00000326035.2_Silent_p.H15H			Q8IY84	NIM1_HUMAN		15					protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										TGAACCCCCACTATGCCCGGT	0.617													C|||	1439	0.28734	0.2905	0.2622	5008	,	,		20469	0.1409		0.4344	False		,,,				2504	0.3006				p.H15H		Atlas-SNP	.											.	.	.	.	0			c.C45T						PASS	.	C		1291,3115	437.0+/-344.8	196,899,1108	128.0	121.0	123.0		45	3.8	0.8	5	dbSNP_121	123	3631,4969	523.2+/-380.3	774,2083,1443	no	coding-synonymous	NIM1	NM_153361.2		970,2982,2551	TT,TC,CC		42.2209,29.301,37.8441		15/437	43245922	4922,8084	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			CCCCCACTATGCC																												ENST00000512796.1:c.45C>T	5.37:g.43245922C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_153361	B3KVM1	Silent	SNP	ENST00000512796.1	37	CCDS3943.1																																																																																			C|0.645;T|0.355	0.355	strong		0.617	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1		
SGCD	6444	hgsc.bcm.edu	37	5	155935708	155935708	+	Missense_Mutation	SNP	G	G	A	rs45559835	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:155935708G>A	ENST00000435422.3	+	3	774	c.287G>A	c.(286-288)cGa>cAa	p.R96Q	SGCD_ENST00000517913.1_Missense_Mutation_p.R97Q|SGCD_ENST00000447401.1_Missense_Mutation_p.R97Q|SGCD_ENST00000337851.4_Missense_Mutation_p.R97Q	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	96			R -> Q (in dbSNP:rs1801194). {ECO:0000269|PubMed:8842738}.		muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATCCAGTCCCGACCAGTAAGT	0.438													G|||	95	0.0189696	0.003	0.0317	5008	,	,		17897	0.0		0.0517	False		,,,				2504	0.0174				p.R97Q		Atlas-SNP	.											SGCD,NS,carcinoma,+1,1	SGCD	52	1	0			c.G290A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	44,3666		0,44,1811	76.0	69.0	71.0		290,287,290	5.5	1.0	5	dbSNP_127	71	527,7677		14,499,3589	yes	missense,missense,missense	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	43,43,43	14,543,5400	AA,AG,GG		6.4237,1.186,4.7927	benign,benign,benign	97/291,96/290,97/257	155935708	571,11343	1855	4102	5957	SO:0001583	missense	6444	exon4			AGTCCCGACCAGT	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"""sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"""			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.287G>A	5.37:g.155935708G>A	ENSP00000403003:p.Arg96Gln	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_000337	A8K9S9|Q53XA5|Q99644	Missense_Mutation	SNP	ENST00000435422.3	37	CCDS47327.1	49	0.022435897435897436	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	34	0.044854881266490766	G	26.3	4.727809	0.89390	0.01186	0.064237	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	D;D;D;D	0.95656	-3.77;-3.77;-3.77;-3.77	5.49	5.49	0.81192	.	0.127312	0.53938	D	0.000051	T	0.71685	0.3369	M	0.78049	2.395	0.43559	D	0.99587	P;P;D	0.56287	0.826;0.792;0.975	B;B;B	0.39738	0.105;0.063;0.308	T	0.80774	-0.1232	10	0.27082	T	0.32	-2.0249	12.2832	0.54776	0.0783:0.0:0.9217:0.0	rs45559835;rs61742485	96;97;97	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	Q	97;96;97;97	ENSP00000429378:R97Q;ENSP00000403003:R96Q;ENSP00000338343:R97Q;ENSP00000408324:R97Q	ENSP00000338343:R97Q	R	+	2	0	SGCD	155868286	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.094000	0.57721	2.732000	0.93576	0.585000	0.79938	CGA	G|0.972;A|0.028	0.028	strong		0.438	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
OR7E24	26648	hgsc.bcm.edu	37	19	9362443	9362443	+	Missense_Mutation	SNP	C	C	T	rs2240928	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9362443C>T	ENST00000456448.1	+	1	838	c.724C>T	c.(724-726)Ccc>Tcc	p.P242S		NM_001079935.1	NP_001073404.1	Q6IFN5	O7E24_HUMAN	olfactory receptor, family 7, subfamily E, member 24	242			P -> S (in dbSNP:rs2240928).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)	16						AATTGTTTCCCCCATTCTGAG	0.428													t|||	2664	0.531949	0.8548	0.3847	5008	,	,		21004	0.5377		0.2823	False		,,,				2504	0.4509				p.P242S		Atlas-SNP	.											.	OR7E24	48	.	0			c.C724T						PASS	.	T	SER/PRO	2776,1112		994,788,162	30.0	31.0	31.0		724	1.1	0.0	19	dbSNP_98	31	2133,6195		269,1595,2300	no	missense	OR7E24	NM_001079935.1	74	1263,2383,2462	TT,TC,CC		25.6124,28.6008,40.185	benign	242/340	9362443	4909,7307	1944	4164	6108	SO:0001583	missense	26648	exon1			GTTTCCCCCATTC	Y10529	CCDS45955.1	19p13.2	2012-08-09	2004-03-04	2004-03-05		ENSG00000237521		"""GPCR / Class A : Olfactory receptors"""	8396	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily E, member 24 pseudogene"""	OR7E24P		9268701	Standard	NM_001079935		Approved	OR19-8, HSHT2, OR7E24Q	uc002mlb.1	Q6IFN5		ENST00000456448.1:c.724C>T	19.37:g.9362443C>T	ENSP00000387523:p.Pro242Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_001079935	B9EJD9|Q9UPJ1	Missense_Mutation	SNP	ENST00000456448.1	37	CCDS45955.1	1090	0.4990842490842491	421	0.8556910569105691	137	0.3784530386740331	316	0.5524475524475524	216	0.2849604221635884	N	0.004	-2.333451	0.00227	0.713992	0.256124	ENSG00000237521	ENST00000456448	T	0.00036	8.86	2.21	1.1	0.20463	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00003	-3.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41520	-0.9504	8	0.02654	T	1	.	5.3672	0.16121	0.0:0.1333:0.5351:0.3316	rs2240928;rs12981289;rs60793799	242	Q6IFN5	O7E24_HUMAN	S	242	ENSP00000387523:P242S	ENSP00000387523:P242S	P	+	1	0	OR7E24	9223443	0.001000	0.12720	0.001000	0.08648	0.040000	0.13550	0.561000	0.23515	-0.285000	0.09089	-2.030000	0.00424	CCC	C|0.537;T|0.463	0.463	strong		0.428	OR7E24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449006.1		
TRIM10	10107	hgsc.bcm.edu	37	6	30128442	30128442	+	Missense_Mutation	SNP	C	C	T	rs12212092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30128442C>T	ENST00000449742.2	-	1	269	c.194G>A	c.(193-195)cGt>cAt	p.R65H	TRIM15_ENST00000376694.4_5'Flank|TRIM10_ENST00000376704.3_Missense_Mutation_p.R65H	NM_006778.3	NP_006769.2	Q9UDY6	TRI10_HUMAN	tripartite motif containing 10	65			R -> H (in dbSNP:rs12212092).		erythrocyte differentiation (GO:0030218)|innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			ovary(1)	1						GCTCCCAGGACGGAAGGGTTC	0.612													C|||	455	0.0908546	0.2254	0.0677	5008	,	,		20638	0.002		0.0954	False		,,,				2504	0.0123				p.R65H		Atlas-SNP	.											.	TRIM10	65	.	0			c.G194A						PASS	.	C	HIS/ARG,HIS/ARG	928,3478	354.9+/-312.8	102,724,1377	158.0	166.0	163.0		194,194	2.6	0.6	6	dbSNP_120	163	591,8009	157.3+/-211.0	23,545,3732	yes	missense,missense	TRIM10	NM_006778.3,NM_052828.2	29,29	125,1269,5109	TT,TC,CC		6.8721,21.0622,11.6792	benign,benign	65/482,65/396	30128442	1519,11487	2203	4300	6503	SO:0001583	missense	10107	exon1			CCAGGACGGAAGG	Y07829	CCDS4676.1, CCDS34375.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000204613	ENSG00000204613		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10072	protein-coding gene	gene with protein product		605701	"""tripartite motif-containing 10"""	RNF9		9271628, 10207104	Standard	NM_052828		Approved	RFB30, HERF1	uc003npo.3	Q9UDY6	OTTHUMG00000031295	ENST00000449742.2:c.194G>A	6.37:g.30128442C>T	ENSP00000397073:p.Arg65His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	180	86	0.477778	NM_052828	A6NF84|Q5SRJ5|Q5SRK8|Q86Z08|Q96QB6|Q9C023|Q9C024	Missense_Mutation	SNP	ENST00000449742.2	37	CCDS34375.1	197	0.0902014652014652	107	0.21747967479674796	25	0.06906077348066299	3	0.005244755244755245	62	0.08179419525065963	C	6.115	0.389391	0.11581	0.210622	0.068721	ENSG00000204613	ENST00000449742;ENST00000376704;ENST00000376706	D;D	0.84223	-1.82;-1.82	5.37	2.61	0.31194	Zinc finger, RING/FYVE/PHD-type (1);	0.241027	0.29972	N	0.010731	T	0.60495	0.2273	L	0.37850	1.14	0.53688	P	2.999999999997449E-5	B;B	0.15719	0.014;0.011	B;B	0.12156	0.003;0.007	T	0.51764	-0.8664	9	0.49607	T	0.09	.	4.6385	0.12536	0.1569:0.5851:0.0:0.258	rs12212092;rs17188092;rs52799461;rs56746532;rs12212092	65;65	Q9UDY6;Q9UDY6-2	TRI10_HUMAN;.	H	65	ENSP00000397073:R65H;ENSP00000365894:R65H	ENSP00000365894:R65H	R	-	2	0	TRIM10	30236421	0.000000	0.05858	0.582000	0.28627	0.212000	0.24457	-0.827000	0.04424	0.776000	0.33473	0.549000	0.68633	CGT	C|0.895;T|0.105	0.105	strong		0.612	TRIM10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076634.1		
EYS	346007	hgsc.bcm.edu	37	6	65301217	65301217	+	Missense_Mutation	SNP	G	G	A	rs62415827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301217G>A	ENST00000370621.3	-	26	5069	c.4543C>T	c.(4543-4545)Cgg>Tgg	p.R1515W	EYS_ENST00000370616.2_Missense_Mutation_p.R1515W|EYS_ENST00000503581.1_Missense_Mutation_p.R1515W			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1515			R -> W (in dbSNP:rs62415827). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GTACTGAACCGGTGCAGAGCT	0.443													G|||	470	0.0938498	0.0151	0.1182	5008	,	,		18973	0.1567		0.0984	False		,,,				2504	0.1135				p.R1515W		Atlas-SNP	.											.	EYS	527	.	0			c.C4543T						PASS	.	G	TRP/ARG	49,1335		1,47,644	46.0	39.0	41.0		4543	0.1	0.0	6	dbSNP_129	41	446,2734		41,364,1185	yes	missense	EYS	NM_001142800.1	101	42,411,1829	AA,AG,GG		14.0252,3.5405,10.8457	probably-damaging	1515/3145	65301217	495,4069	692	1590	2282	SO:0001583	missense	346007	exon26			TGAACCGGTGCAG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4543C>T	6.37:g.65301217G>A	ENSP00000359655:p.Arg1515Trp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		214	0.09798534798534798	5	0.01016260162601626	44	0.12154696132596685	86	0.15034965034965034	79	0.10422163588390501	G	10.02	1.236237	0.22626	0.035405	0.140252	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.85013	-1.93;-1.91;-1.91	5.84	0.078	0.14410	.	.	.	.	.	T	0.63260	0.2496	N	0.08118	0	0.80722	P	0.0	D;D	0.71674	0.998;0.996	P;B	0.53649	0.731;0.424	T	0.59010	-0.7534	8	0.87932	D	0	.	4.5724	0.12216	0.0766:0.147:0.2286:0.5478	rs62415827	1515;1515	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	W	1515	ENSP00000424243:R1515W;ENSP00000359655:R1515W;ENSP00000359650:R1515W	ENSP00000359650:R1515W	R	-	1	2	EYS	65357938	0.001000	0.12720	0.000000	0.03702	0.102000	0.19082	0.330000	0.19715	0.053000	0.16036	0.591000	0.81541	CGG	G|0.902;A|0.098	0.098	strong		0.443	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
PCDHB15	56121	hgsc.bcm.edu	37	5	140627225	140627225	+	Silent	SNP	A	A	G	rs141485224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140627225A>G	ENST00000231173.3	+	1	2079	c.2079A>G	c.(2077-2079)gcA>gcG	p.A693A		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	693					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGTGGTGGCATTGGCCTCGG	0.672													G|||	10	0.00199681	0.0	0.0014	5008	,	,		16485	0.0		0.005	False		,,,				2504	0.0041				p.A693A		Atlas-SNP	.											.	PCDHB15	138	.	0			c.A2079G						PASS	.	G		3,4403		0,3,2200	94.0	97.0	96.0		2079	-8.9	0.0	5	dbSNP_134	96	32,8562		0,32,4265	no	coding-synonymous	PCDHB15	NM_018935.2		0,35,6465	GG,GA,AA		0.3724,0.0681,0.2692		693/788	140627225	35,12965	2203	4297	6500	SO:0001819	synonymous_variant	56121	exon1			GGTGGCATTGGCC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.2079A>G	5.37:g.140627225A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	54	18	0.333333	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			A|0.997;G|0.003	0.003	strong		0.672	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
PGM1	5236	hgsc.bcm.edu	37	1	64097432	64097432	+	Missense_Mutation	SNP	C	C	T	rs1126728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:64097432C>T	ENST00000371084.3	+	4	874	c.661C>T	c.(661-663)Cgt>Tgt	p.R221C	PGM1_ENST00000371083.4_Missense_Mutation_p.R239C|PGM1_ENST00000540265.1_Missense_Mutation_p.R24C	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	221			R -> C (in allele PGM1*2+, allele PGM1*2-, allele PGM1*3+ and allele PGM1*3-; dbSNP:rs1126728). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7902567, ECO:0000269|PubMed:7902568, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						ACTGAAGATCCGTATTGATGC	0.408													C|||	1209	0.241414	0.1876	0.2478	5008	,	,		19639	0.2688		0.2505	False		,,,				2504	0.272				p.R239C		Atlas-SNP	.											PGM1_ENST00000371083,NS,carcinoma,-1,2	PGM1	75	2	0			c.C715T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	886,3520	344.4+/-308.1	92,702,1409	198.0	171.0	180.0		715,70,661	5.8	1.0	1	dbSNP_86	180	2016,6584	352.6+/-328.8	238,1540,2522	yes	missense,missense,missense	PGM1	NM_001172818.1,NM_001172819.1,NM_002633.2	180,180,180	330,2242,3931	TT,TC,CC		23.4419,20.1089,22.3128	possibly-damaging,possibly-damaging,possibly-damaging	239/581,24/366,221/563	64097432	2902,10104	2203	4300	6503	SO:0001583	missense	5236	exon4			AAGATCCGTATTG	BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.661C>T	1.37:g.64097432C>T	ENSP00000360125:p.Arg221Cys	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	126	55	0.436508	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Missense_Mutation	SNP	ENST00000371084.3	37	CCDS625.1	528	0.24175824175824176	82	0.16666666666666666	90	0.24861878453038674	168	0.2937062937062937	188	0.24802110817941952	C	22.2	4.263036	0.80358	0.201089	0.234419	ENSG00000079739	ENST00000538673;ENST00000371084;ENST00000540265;ENST00000371083	T;T;T	0.62788	-0.0;-0.0;-0.0	5.75	5.75	0.90469	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain II (1);	0.000000	0.85682	D	0.000000	T	0.39145	0.1067	L	0.33624	1.015	0.09310	P	0.9999999861343	P;P	0.39576	0.465;0.679	B;B	0.32289	0.031;0.143	T	0.37596	-0.9699	9	0.31617	T	0.26	-0.1816	20.3271	0.98704	0.0:1.0:0.0:0.0	rs1126728;rs2230476;rs3181940;rs11557105;rs17415330;rs17844922;rs17857648;rs56727270	239;221	P36871-2;P36871	.;PGM1_HUMAN	C	197;221;24;239	ENSP00000360125:R221C;ENSP00000443449:R24C;ENSP00000360124:R239C	ENSP00000360124:R239C	R	+	1	0	PGM1	63870020	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	2.557000	0.45871	2.885000	0.99019	0.655000	0.94253	CGT	C|0.767;T|0.233	0.233	strong		0.408	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633	
FAM205A	259308	hgsc.bcm.edu	37	9	34723935	34723935	+	Missense_Mutation	SNP	C	C	T	rs2297134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34723935C>T	ENST00000378788.3	-	4	3341	c.3302G>A	c.(3301-3303)cGt>cAt	p.R1101H		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	1101				R -> H (in Ref. 1; BAC86357). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						ATGAAAGCTACGGCTCCATCG	0.592													C|||	2012	0.401757	0.0666	0.4006	5008	,	,		19132	0.6181		0.4851	False		,,,				2504	0.547				p.R1101H		Atlas-SNP	.											.	FAM205A	45	.	0			c.G3302A						PASS	.						26.0	23.0	24.0					9																	34723935		692	1590	2282	SO:0001583	missense	259308	exon4			AAGCTACGGCTCC		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.3302G>A	9.37:g.34723935C>T	ENSP00000417711:p.Arg1101His	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	45	0.412844	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	909	0.41620879120879123	45	0.09146341463414634	150	0.4143646408839779	334	0.583916083916084	380	0.5013192612137203	C	3.371	-0.128490	0.06753	.	.	ENSG00000205108	ENST00000378788	T	0.22539	1.95	4.13	-4.91	0.03085	.	.	.	.	.	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	0.45323	-0.9269	8	0.17369	T	0.5	.	5.6327	0.17520	0.0:0.4064:0.3212:0.2724	rs2297134;rs2297134	1101	Q6ZU69	F205A_HUMAN	H	1101	ENSP00000417711:R1101H	ENSP00000417711:R1101H	R	-	2	0	RP11-195F19.10	34713935	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.033000	0.03571	-0.710000	0.05001	-0.300000	0.09419	CGT	T|1.000;|0.000	1.000	weak		0.592	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
ACACB	32	hgsc.bcm.edu	37	12	109623516	109623516	+	Missense_Mutation	SNP	G	G	A	rs2300455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109623516G>A	ENST00000338432.7	+	12	2070	c.1951G>A	c.(1951-1953)Gcc>Acc	p.A651T	ACACB_ENST00000377848.3_Missense_Mutation_p.A651T|ACACB_ENST00000377854.5_Missense_Mutation_p.A651T			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	651	Biotin carboxylation.		A -> T (in dbSNP:rs2300455).		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)	CGTCATTGCCGCCAGAATCAC	0.572													G|||	799	0.159545	0.0159	0.1571	5008	,	,		14912	0.2639		0.1581	False		,,,				2504	0.2495				p.A651T		Atlas-SNP	.											ACACB,colon,carcinoma,0,1	ACACB	330	1	0			c.G1951A						PASS	.	G	THR/ALA	198,4208	122.5+/-159.9	7,184,2012	47.0	44.0	45.0		1951	4.4	1.0	12	dbSNP_100	45	1704,6896	311.2+/-310.2	176,1352,2772	yes	missense	ACACB	NM_001093.3	58	183,1536,4784	AA,AG,GG		19.814,4.4939,14.624	probably-damaging	651/2459	109623516	1902,11104	2203	4300	6503	SO:0001583	missense	32	exon11			ATTGCCGCCAGAA	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.1951G>A	12.37:g.109623516G>A	ENSP00000341044:p.Ala651Thr	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	359	0.16437728937728938	10	0.02032520325203252	68	0.1878453038674033	159	0.27797202797202797	122	0.16094986807387862	G	22.2	4.264058	0.80358	0.044939	0.19814	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.82984	-1.67;-1.67;-1.67	5.33	4.44	0.53790	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.099413	0.64402	N	0.000002	T	0.00039	0.0001	L	0.58302	1.8	0.09310	P	1.0	D	0.89917	1.0	D	0.91635	0.999	T	0.00004	-1.2561	9	0.52906	T	0.07	.	14.2525	0.66028	0.073:0.0:0.927:0.0	rs2300455;rs52806590;rs61539340;rs2300455	651	O00763	ACACB_HUMAN	T	651	ENSP00000341044:A651T;ENSP00000367079:A651T;ENSP00000367085:A651T	ENSP00000341044:A651T	A	+	1	0	ACACB	108107899	1.000000	0.71417	0.964000	0.40570	0.597000	0.36814	8.003000	0.88520	1.402000	0.46780	-0.224000	0.12420	GCC	G|0.846;A|0.154	0.154	strong		0.572	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
ZCCHC9	84240	hgsc.bcm.edu	37	5	80604430	80604430	+	Silent	SNP	C	C	T	rs1055383	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:80604430C>T	ENST00000254037.2	+	2	3590	c.435C>T	c.(433-435)gcC>gcT	p.A145A	ZCCHC9_ENST00000407610.3_Silent_p.A145A|ZCCHC9_ENST00000438268.2_Silent_p.A145A|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000380199.5_Silent_p.A145A			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	145					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		ATTGCCCCGCCGCCCTTGAAA	0.478													C|||	694	0.138578	0.0991	0.304	5008	,	,		14056	0.0149		0.1849	False		,,,				2504	0.1544				p.A145A		Atlas-SNP	.											ZCCHC9,caecum,carcinoma,+1,1	ZCCHC9	26	1	0			c.C435T						scavenged	.	C	,,	499,3907	230.7+/-244.8	30,439,1734	85.0	86.0	86.0		435,435,435	-7.0	0.6	5	dbSNP_86	86	1694,6906	310.6+/-310.0	180,1334,2786	no	coding-synonymous,coding-synonymous,coding-synonymous	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	,,	210,1773,4520	TT,TC,CC		19.6977,11.3255,16.8614	,,	145/272,145/272,145/272	80604430	2193,10813	2203	4300	6503	SO:0001819	synonymous_variant	84240	exon3			CCCCGCCGCCCTT	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.435C>T	5.37:g.80604430C>T		Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	159	59	0.371069	NM_001131036	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	37	CCDS4054.1																																																																																			C|0.842;T|0.158	0.158	strong		0.478	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	
TRPV1	7442	hgsc.bcm.edu	37	17	3480447	3480447	+	Missense_Mutation	SNP	T	T	C	rs8065080	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3480447T>C	ENST00000571088.1	-	12	1966	c.1753A>G	c.(1753-1755)Atc>Gtc	p.I585V	SHPK_ENST00000572705.1_Missense_Mutation_p.I585V|TRPV1_ENST00000576351.1_Missense_Mutation_p.I575V|TRPV1_ENST00000399756.4_Missense_Mutation_p.I585V|TRPV1_ENST00000425167.2_Missense_Mutation_p.I596V|TRPV1_ENST00000310522.5_Missense_Mutation_p.I525V|TRPV1_ENST00000399759.3_Missense_Mutation_p.I585V|TRPV1_ENST00000174621.6_Missense_Mutation_p.I583V|RP11-235E17.3_ENST00000573568.1_RNA	NM_018727.5	NP_061197.4	Q8NER1	TRPV1_HUMAN	transient receptor potential cation channel, subfamily V, member 1	585			I -> V (in dbSNP:rs8065080). {ECO:0000269|PubMed:11050376}.		calcium ion transmembrane transport (GO:0070588)|cell surface receptor signaling pathway (GO:0007166)|cellular response to alkaloid (GO:0071312)|cellular response to ATP (GO:0071318)|chemosensory behavior (GO:0007635)|ion transmembrane transport (GO:0034220)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|calcium-release channel activity (GO:0015278)|excitatory extracellular ligand-gated ion channel activity (GO:0005231)|phosphoprotein binding (GO:0051219)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	17				Lung(1;0.055)|COAD - Colon adenocarcinoma(5;0.0896)|LUAD - Lung adenocarcinoma(1115;0.131)	Alpha-Linolenic Acid(DB00132)|Aspartame(DB00168)|Icosapent(DB00159)	AAGAAGACGATGTAGACAAAC	0.582													C|||	1591	0.317692	0.1067	0.3343	5008	,	,		18230	0.5883		0.4085	False		,,,				2504	0.2188				p.I585V	Melanoma(38;962 1762 15789)	Atlas-SNP	.											.	TRPV1	99	.	0			c.A1753G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	616,3428		48,520,1454	43.0	42.0	42.0		1753,1753,1753,1753	-1.9	0.0	17	dbSNP_116	42	3103,5237		579,1945,1646	yes	missense,missense,missense,missense	TRPV1	NM_018727.5,NM_080704.3,NM_080705.3,NM_080706.3	29,29,29,29	627,2465,3100	CC,CT,TT		37.2062,15.2324,30.0307	benign,benign,benign,benign	585/840,585/840,585/840,585/840	3480447	3719,8665	2022	4170	6192	SO:0001583	missense	7442	exon12			AGACGATGTAGAC	AJ272063	CCDS45576.1	17p13.2	2014-08-12	2002-01-29	2002-02-01	ENSG00000196689	ENSG00000262304		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12716	protein-coding gene	gene with protein product		602076	"""vanilloid receptor subtype 1"""	VR1		9349813, 11549313, 16382100	Standard	NM_018727		Approved		uc010vrt.2	Q8NER1	OTTHUMG00000177649	ENST00000571088.1:c.1753A>G	17.37:g.3480447T>C	ENSP00000461007:p.Ile585Val	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	141	48	0.340426	NM_018727	A2RUA9|Q3LU47|Q9H0G9|Q9H303|Q9H304|Q9NQ74|Q9NY22	Missense_Mutation	SNP	ENST00000571088.1	37	CCDS45576.1	851	0.38965201465201466	54	0.10975609756097561	140	0.3867403314917127	341	0.5961538461538461	316	0.41688654353562005	C	1.501	-0.552161	0.03996	0.152324	0.372062	ENSG00000196689	ENST00000399759;ENST00000399756;ENST00000174621;ENST00000425167;ENST00000310522	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	5.14	-1.93	0.07594	Ion transport (1);	0.755076	0.13129	N	0.411637	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B;B	0.09022	0.0;0.002;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.47169	-0.9138	9	0.36615	T	0.2	-6.2838	10.1969	0.43060	0.0:0.2668:0.2895:0.4437	rs8065080;rs57404253;rs8065080	585;583;525;596	Q8NER1;E7EQ80;E7ESJ2;E7EQ78	TRPV1_HUMAN;.;.;.	V	585;585;583;596;525	ENSP00000382661:I585V;ENSP00000382659:I585V;ENSP00000174621:I583V;ENSP00000409627:I596V;ENSP00000311692:I525V	ENSP00000174621:I583V	I	-	1	0	TRPV1	3427196	0.195000	0.23338	0.017000	0.16124	0.004000	0.04260	-0.245000	0.08890	-0.324000	0.08589	-2.015000	0.00435	ATC	T|0.625;C|0.375	0.375	strong		0.582	TRPV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438254.1	NM_018727	
OBSCN	84033	hgsc.bcm.edu	37	1	228526011	228526011	+	Silent	SNP	C	C	T	rs11577699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228526011C>T	ENST00000422127.1	+	68	17066	c.17022C>T	c.(17020-17022)gcC>gcT	p.A5674A	OBSCN_ENST00000366707.4_Silent_p.A3308A|OBSCN_ENST00000366709.4_Silent_p.A2793A|OBSCN_ENST00000284548.11_Silent_p.A5674A|OBSCN_ENST00000570156.2_Silent_p.A6631A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5674					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGTGGGGGGCCGCTGAGGCCC	0.642													C|||	589	0.117612	0.1006	0.1916	5008	,	,		16460	0.1091		0.1372	False		,,,				2504	0.0767				p.A6631A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19893T						PASS	.	C	,	525,3273		33,459,1407	20.0	26.0	24.0		17022,17022	-2.2	0.0	1	dbSNP_120	24	1296,6918		99,1098,2910	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	132,1557,4317	TT,TC,CC		15.7779,13.8231,15.1598	,	5674/7969,5674/6621	228526011	1821,10191	1899	4107	6006	SO:0001819	synonymous_variant	84033	exon79			GGGGGCCGCTGAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.17022C>T	1.37:g.228526011C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	273	0.125	40	0.08130081300813008	71	0.19613259668508287	54	0.0944055944055944	108	0.1424802110817942	C	4.625	0.116119	0.08831	0.138231	0.157779	ENSG00000154358	ENST00000441106	.	.	.	4.59	-2.15	0.07102	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.53688	P	2.4000000000024002E-5	.	.	.	.	.	.	T	0.24083	-1.0170	3	.	.	.	.	5.2594	0.15565	0.3755:0.2927:0.0:0.3318	rs11577699	.	.	.	C	290	.	.	R	+	1	0	OBSCN	226592634	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.668000	0.05268	-1.045000	0.03250	-1.579000	0.00862	CGC	C|0.879;T|0.121	0.121	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SPICE1	152185	hgsc.bcm.edu	37	3	113175984	113175984	+	Splice_Site	SNP	G	G	A	rs146846950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113175984G>A	ENST00000295872.4	-	13	1915	c.1656C>T	c.(1654-1656)gaC>gaT	p.D552D		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	552					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						AAGACTTACCGTCCTGAAGAG	0.353													g|||	46	0.0091853	0.0008	0.0014	5008	,	,		19525	0.0		0.0119	False		,,,				2504	0.0327				p.D552D		Atlas-SNP	.											SPICE1_ENST00000295872,NS,carcinoma,0,2	SPICE1	130	2	0			c.C1656T						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	55.0	55.0	55.0		1656	-11.3	0.8	3	dbSNP_134	55	46,8554	30.7+/-82.3	0,46,4254	yes	coding-synonymous-near-splice	SPICE1	NM_144718.3		0,49,6454	AA,AG,GG		0.5349,0.0681,0.3767		552/856	113175984	49,12957	2203	4300	6503	SO:0001630	splice_region_variant	152185	exon13			CTTACCGTCCTGA	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.1657+1C>T	3.37:g.113175984G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			G|0.995;A|0.005	0.005	strong		0.353	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	Silent
POLR1D	51082	hgsc.bcm.edu	37	13	28240075	28240075	+	Silent	SNP	G	G	T	rs75314566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:28240075G>T	ENST00000399697.3	+	3	472	c.354G>T	c.(352-354)cgG>cgT	p.R118R	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)			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)		ACGAAAAGCGGTCCAACCGGC	0.652													G|||	78	0.0155751	0.0015	0.013	5008	,	,		14972	0.0		0.0577	False		,,,				2504	0.0092				p.R118R		Atlas-SNP	.											POLR1D,NS,carcinoma,+1,1	POLR1D	31	1	0			c.G354T						PASS	.	G	,	53,4347	50.9+/-86.3	2,49,2149	53.0	58.0	56.0		270,354	-7.6	0.0	13	dbSNP_132	56	478,8118	132.5+/-190.1	10,458,3830	no	coding-synonymous,coding-synonymous	POLR1D	NM_001206559.1,NM_152705.2	,	12,507,5979	TT,TG,GG		5.5607,1.2045,4.0859	,	90/95,118/123	28240075	531,12465	2200	4298	6498	SO:0001819	synonymous_variant	51082	exon3			AAAGCGGTCCAAC	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.354G>T	13.37:g.28240075G>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_152705	Q5TBX2|Q96BR3	Silent	SNP	ENST00000399697.3	37	CCDS9324.1																																																																																			G|0.967;T|0.033	0.033	strong		0.652	POLR1D-004	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044306.1	NM_015972, NM_152705	
ATP11A	23250	hgsc.bcm.edu	37	13	113479813	113479813	+	Silent	SNP	G	G	A	rs9549564	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113479813G>A	ENST00000487903.1	+	11	1030	c.942G>A	c.(940-942)ctG>ctA	p.L314L	ATP11A_ENST00000283558.8_Silent_p.L314L|ATP11A_ENST00000375630.2_Silent_p.L314L|ATP11A_ENST00000375645.3_Silent_p.L314L			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	314					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)				ACACTGTGCTGAAATACATGT	0.468													G|||	1074	0.214457	0.1225	0.317	5008	,	,		23383	0.1905		0.2903	False		,,,				2504	0.2127				p.L314L		Atlas-SNP	.											.	ATP11A	225	.	0			c.G942A						PASS	.	G	,	639,3767	273.7+/-271.5	55,529,1619	127.0	107.0	114.0		942,942	-2.8	0.2	13	dbSNP_119	114	2376,6224	395.0+/-344.9	319,1738,2243	yes	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	374,2267,3862	AA,AG,GG		27.6279,14.503,23.1816	,	314/1135,314/1192	113479813	3015,9991	2203	4300	6503	SO:0001819	synonymous_variant	23250	exon11			TGTGCTGAAATAC	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.942G>A	13.37:g.113479813G>A		Somatic	216	1	0.00462963		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1																																																																																			G|0.774;A|0.226	0.226	strong		0.468	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
SUN5	140732	hgsc.bcm.edu	37	20	31590686	31590686	+	Missense_Mutation	SNP	C	C	A	rs1133358	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:31590686C>A	ENST00000356173.3	-	2	209	c.117G>T	c.(115-117)gaG>gaT	p.E39D	SUN5_ENST00000375519.2_Missense_Mutation_p.E39D|SUN5_ENST00000375523.3_Missense_Mutation_p.E39D	NM_080675.3	NP_542406.2	Q8TC36	SUN5_HUMAN	Sad1 and UNC84 domain containing 5	39			E -> D (in dbSNP:rs1133358).		spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	25						GGGAGGTGTCCTCTGCCATCC	0.537													C|||	957	0.191094	0.2315	0.281	5008	,	,		22312	0.0169		0.2535	False		,,,				2504	0.1881				p.E39D		Atlas-SNP	.											.	SUN5	63	.	0			c.G117T						PASS	.	C	ASP/GLU	1051,3355	385.6+/-325.8	133,785,1285	131.0	118.0	122.0		117	2.0	0.0	20	dbSNP_86	122	2086,6514	361.4+/-332.3	263,1560,2477	yes	missense	SUN5	NM_080675.3	45	396,2345,3762	AA,AC,CC		24.2558,23.8538,24.1196	probably-damaging	39/380	31590686	3137,9869	2203	4300	6503	SO:0001583	missense	140732	exon2			GGTGTCCTCTGCC	AL121756	CCDS13209.1	20q11.21	2010-01-27	2010-01-27	2010-01-27	ENSG00000167098	ENSG00000167098			16252	protein-coding gene	gene with protein product	"""testis and spermatogenesis related gene 4"""	613942	"""sperm associated antigen 4-like"""	SPAG4L		9691178, 10373309	Standard	NM_080675		Approved	dJ726C3.1, TSARG4	uc002wyi.3	Q8TC36	OTTHUMG00000032239	ENST00000356173.3:c.117G>T	20.37:g.31590686C>A	ENSP00000348496:p.Glu39Asp	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	133	70	0.526316	NM_080675	A6NJ82|Q5T9R0	Missense_Mutation	SNP	ENST00000356173.3	37	CCDS13209.1	396	0.1813186813186813	100	0.2032520325203252	94	0.2596685082872928	14	0.024475524475524476	188	0.24802110817941952	C	11.17	1.561289	0.27915	0.238538	0.242558	ENSG00000167098	ENST00000356173;ENST00000375523;ENST00000420875;ENST00000375519	T;T;T;T	0.44881	2.27;2.14;0.91;1.0	4.01	2.04	0.26737	.	2.010710	0.02353	N	0.076177	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	P	0.36027	0.533	B	0.36959	0.237	T	0.14755	-1.0461	9	0.62326	D	0.03	-13.2072	10.482	0.44700	0.0:0.6165:0.3835:0.0	rs1133358;rs8118712;rs11549791;rs52793813;rs61634050;rs1133358	39	Q8TC36	SUN5_HUMAN	D	39;39;28;39	ENSP00000348496:E39D;ENSP00000364673:E39D;ENSP00000400089:E28D;ENSP00000364669:E39D	ENSP00000348496:E39D	E	-	3	2	SUN5	31054347	0.001000	0.12720	0.002000	0.10522	0.006000	0.05464	0.531000	0.23052	0.641000	0.30601	-0.172000	0.13284	GAG	T|0.002;G|0.005	.	strong		0.537	SUN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078659.1	NM_080675	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592606	167592606	+	Silent	SNP	T	T	A	rs201866116	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167592606T>A	ENST00000366832.2	+	6	896	c.765T>A	c.(763-765)gtT>gtA	p.V255V		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	255										endometrium(1)|kidney(2)|lung(3)	6						CAGCCGGAGTTGCTGGTGAGC	0.577																																					p.V255V		Atlas-SNP	.											.	TCP10L2	41	.	0			c.T765A						PASS	.																																			SO:0001819	synonymous_variant	401285	exon6			CGGAGTTGCTGGT		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.765T>A	6.37:g.167592606T>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	58	20	0.344828	NM_001145121		Silent	SNP	ENST00000366832.2	37	CCDS47514.1																																																																																			T|0.927;A|0.073	0.073	strong		0.577	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
ADAMTS4	9507	hgsc.bcm.edu	37	1	161168004	161168004	+	Silent	SNP	C	C	T	rs33941127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161168004C>T	ENST00000367996.5	-	1	842	c.414G>A	c.(412-414)tcG>tcA	p.S138S	ADAMTS4_ENST00000478394.1_5'Flank|ADAMTS4_ENST00000367995.3_Silent_p.S138S|NDUFS2_ENST00000367993.3_5'Flank	NM_005099.4	NP_005090.3	O75173	ATS4_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 4	138					defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(20)|ovary(4)|prostate(3)|skin(1)|urinary_tract(1)	43	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		Tinzaparin(DB06822)	GAGATGCCACCGACTCCGGAT	0.632													C|||	1828	0.365016	0.4145	0.3141	5008	,	,		17741	0.4494		0.2087	False		,,,				2504	0.408				p.S138S		Atlas-SNP	.											.	ADAMTS4	171	.	0			c.G414A						PASS	.	C		1587,2819	489.4+/-361.5	271,1045,887	62.0	62.0	62.0		414	-6.8	0.9	1	dbSNP_126	62	1776,6824	320.1+/-314.5	175,1426,2699	no	coding-synonymous	ADAMTS4	NM_005099.4		446,2471,3586	TT,TC,CC		20.6512,36.0191,25.8573		138/838	161168004	3363,9643	2203	4300	6503	SO:0001819	synonymous_variant	9507	exon1			TGCCACCGACTCC	AB014588	CCDS1223.1	1q31-q32	2008-02-05	2005-08-19		ENSG00000158859	ENSG00000158859		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	220	protein-coding gene	gene with protein product		603876	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 4"""			10094461	Standard	NM_005099		Approved	KIAA0688, ADAMTS-2, ADMP-1	uc001fyt.4	O75173	OTTHUMG00000034349	ENST00000367996.5:c.414G>A	1.37:g.161168004C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_005099	Q5VTW2|Q6P4Q8|Q6UWA8|Q9UN83	Silent	SNP	ENST00000367996.5	37	CCDS1223.1																																																																																			C|0.720;T|0.280	0.280	strong		0.632	ADAMTS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083066.2	NM_005099	
TEKT3	64518	hgsc.bcm.edu	37	17	15217437	15217437	+	Missense_Mutation	SNP	C	C	G	rs230898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15217437C>G	ENST00000395930.1	-	6	1031	c.845G>C	c.(844-846)gGc>gCc	p.G282A	RNU6-799P_ENST00000363567.1_RNA|TEKT3_ENST00000338696.2_Missense_Mutation_p.G282A	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	282			G -> A (in dbSNP:rs230898). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		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)		GCGGAAGTAGCCGACACCGTC	0.542													C|||	2141	0.427516	0.2927	0.3919	5008	,	,		20486	0.4732		0.4652	False		,,,				2504	0.5491				p.G282A		Atlas-SNP	.											.	TEKT3	64	.	0			c.G845C						PASS	.	C	ALA/GLY	1437,2969	465.9+/-354.3	234,969,1000	214.0	145.0	169.0		845	5.4	1.0	17	dbSNP_79	169	4137,4463	565.4+/-388.5	965,2207,1128	yes	missense	TEKT3	NM_031898.2	60	1199,3176,2128	GG,GC,CC		48.1047,32.6146,42.8571	benign	282/491	15217437	5574,7432	2203	4300	6503	SO:0001583	missense	64518	exon6			AAGTAGCCGACAC	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.845G>C	17.37:g.15217437C>G	ENSP00000379263:p.Gly282Ala	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	275	132	0.48	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Missense_Mutation	SNP	ENST00000395930.1	37	CCDS11169.1	907	0.4152930402930403	121	0.2459349593495935	141	0.38950276243093923	268	0.46853146853146854	377	0.4973614775725594	C	12.09	1.832668	0.32421	0.326146	0.481047	ENSG00000125409	ENST00000395930;ENST00000338696;ENST00000539245	T;T;T	0.02323	4.34;4.34;4.34	5.43	5.43	0.79202	.	0.220679	0.64402	D	0.000015	T	0.00012	0.0000	N	0.21282	0.65	0.29250	P	0.8720559999999999	B	0.06786	0.001	B	0.09377	0.004	T	0.43589	-0.9382	9	0.12766	T	0.61	-7.0731	14.451	0.67385	0.0:0.9273:0.0:0.0727	rs230898;rs3826381;rs17700580;rs52800340;rs230898	282	Q9BXF9	TEKT3_HUMAN	A	282;282;116	ENSP00000379263:G282A;ENSP00000343995:G282A;ENSP00000443280:G116A	ENSP00000343995:G282A	G	-	2	0	TEKT3	15158162	1.000000	0.71417	1.000000	0.80357	0.095000	0.18619	5.786000	0.69006	2.549000	0.85964	0.655000	0.94253	GGC	C|0.581;G|0.419	0.419	strong		0.542	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
DHX37	57647	hgsc.bcm.edu	37	12	125453115	125453115	+	Missense_Mutation	SNP	C	C	T	rs11057939	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:125453115C>T	ENST00000308736.2	-	10	1471	c.1373G>A	c.(1372-1374)cGg>cAg	p.R458Q	DHX37_ENST00000544745.1_Missense_Mutation_p.R245Q	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	458			R -> Q (in dbSNP:rs11057939).				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)		GCAGACCTTCCGGAAGCACTC	0.602													C|||	269	0.0537141	0.0076	0.0994	5008	,	,		18822	0.0		0.1581	False		,,,				2504	0.0317				p.R458Q		Atlas-SNP	.											.	DHX37	114	.	0			c.G1373A						PASS	.	C	GLN/ARG	117,4289	89.2+/-127.9	1,115,2087	131.0	133.0	132.0		1373	4.6	1.0	12	dbSNP_120	132	1353,7247	265.6+/-286.2	108,1137,3055	yes	missense	DHX37	NM_032656.3	43	109,1252,5142	TT,TC,CC		15.7326,2.6555,11.3025	possibly-damaging	458/1158	125453115	1470,11536	2203	4300	6503	SO:0001583	missense	57647	exon10			ACCTTCCGGAAGC	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.1373G>A	12.37:g.125453115C>T	ENSP00000311135:p.Arg458Gln	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_032656	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	178	0.0815018315018315	7	0.014227642276422764	48	0.13259668508287292	0	0.0	123	0.16226912928759896	C	18.17	3.565362	0.65651	0.026555	0.157326	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.13538	2.58;2.58	4.6	4.6	0.57074	.	0.122536	0.53938	D	0.000043	T	0.00039	0.0001	L	0.54908	1.71	0.19775	P	0.9999506386	P	0.42941	0.794	B	0.32864	0.154	T	0.27571	-1.0070	9	0.52906	T	0.07	-5.5669	17.3773	0.87396	0.0:1.0:0.0:0.0	rs11057939;rs52834302;rs11057939	458	Q8IY37	DHX37_HUMAN	Q	458;245	ENSP00000311135:R458Q;ENSP00000439009:R245Q	ENSP00000311135:R458Q	R	-	2	0	DHX37	124019068	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.311000	0.59147	2.263000	0.75096	0.561000	0.74099	CGG	C|0.906;T|0.094	0.094	strong		0.602	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
IGF2R	3482	hgsc.bcm.edu	37	6	160453978	160453978	+	Silent	SNP	A	A	G	rs1570070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:160453978A>G	ENST00000356956.1	+	9	1198	c.1050A>G	c.(1048-1050)tcA>tcG	p.S350S		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	350					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTTTAGGTTCATCCTATATTT	0.313													A|||	2123	0.423922	0.2405	0.3545	5008	,	,		20863	0.746		0.3489	False		,,,				2504	0.4663				p.S350S		Atlas-SNP	.											.	IGF2R	251	.	0			c.A1050G						PASS	.	A		1139,3265	378.0+/-322.7	132,875,1195	79.0	88.0	85.0		1050	-7.8	0.0	6	dbSNP_88	85	2790,5810	437.3+/-358.6	463,1864,1973	no	coding-synonymous	IGF2R	NM_000876.2		595,2739,3168	GG,GA,AA		32.4419,25.8629,30.2138		350/2492	160453978	3929,9075	2202	4300	6502	SO:0001819	synonymous_variant	3482	exon9			AGGTTCATCCTAT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.1050A>G	6.37:g.160453978A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	25	23	0.92	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.643;G|0.357	0.357	strong		0.313	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
FAM83G	644815	hgsc.bcm.edu	37	17	18874720	18874720	+	Silent	SNP	C	C	G	rs916823	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18874720C>G	ENST00000388995.6	-	6	2647	c.2424G>C	c.(2422-2424)tcG>tcC	p.S808S	SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000585154.2_Silent_p.S808S|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_Silent_p.S808S|SLC5A10_ENST00000395643.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	808					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						GTTTAGAATCCGATGAGGCCC	0.617													G|||	3377	0.674321	0.7587	0.6844	5008	,	,		17660	0.6329		0.5855	False		,,,				2504	0.6871				p.S808S		Atlas-SNP	.											.	FAM83G	51	.	0			c.G2424C						PASS	.	G	,,	3108,1144		1159,790,177	54.0	66.0	62.0		2424,,	-11.1	0.0	17	dbSNP_86	62	4850,3600		1419,2012,794	no	coding-synonymous,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	,,	2578,2802,971	GG,GC,CC		42.6036,26.905,37.3484	,,	808/824,,	18874720	7958,4744	2126	4225	6351	SO:0001819	synonymous_variant	644815	exon6			AGAATCCGATGAG	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.2424G>C	17.37:g.18874720C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	37	CCDS42276.1																																																																																			C|0.359;G|0.641	0.641	strong		0.617	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
PDK2	5164	hgsc.bcm.edu	37	17	48174908	48174908	+	Silent	SNP	C	C	T	rs9839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48174908C>T	ENST00000503176.1	+	2	401	c.240C>T	c.(238-240)tcC>tcT	p.S80S	PDK2_ENST00000007708.3_Silent_p.S16S	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	80				S -> T (in Ref. 1; AAC42010). {ECO:0000305}.	cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						GCACACCCTCCGTGCAGCTGG	0.607									Autosomal Dominant Polycystic Kidney Disease				T|||	2179	0.435104	0.4932	0.4395	5008	,	,		22189	0.38		0.2783	False		,,,				2504	0.5716				p.S80S		Atlas-SNP	.											PDK2,NS,carcinoma,0,1	PDK2	41	1	0			c.C240T						PASS	.	T	,,,	2092,2314	605.2+/-390.5	499,1094,610	78.0	65.0	69.0		48,48,240,240	-7.4	0.8	17	dbSNP_105	69	2532,6068	692.8+/-404.6	370,1792,2138	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDK2	NM_001199898.1,NM_001199899.1,NM_001199900.1,NM_002611.4	,,,	869,2886,2748	TT,TC,CC		29.4419,47.4807,35.5528	,,,	16/344,16/344,80/200,80/408	48174908	4624,8382	2203	4300	6503	SO:0001819	synonymous_variant	5164	exon2	Familial Cancer Database	ADPKD	ACCCTCCGTGCAG	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"""pyruvate dehydrogenase kinase, isoenzyme 2"""			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.240C>T	17.37:g.48174908C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Silent	SNP	ENST00000503176.1	37	CCDS11559.1																																																																																			C|0.639;T|0.361	0.361	strong		0.607	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611	
TRIT1	54802	hgsc.bcm.edu	37	1	40349131	40349131	+	Silent	SNP	G	G	A	rs3845570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:40349131G>A	ENST00000316891.5	-	1	47	c.33C>T	c.(31-33)ccC>ccT	p.P11P	Y_RNA_ENST00000365352.1_RNA|TRIT1_ENST00000491865.1_5'UTR|TRIT1_ENST00000537223.1_5'Flank|TRIT1_ENST00000541099.1_5'Flank|TRIT1_ENST00000372818.1_Silent_p.P11P|TRIT1_ENST00000537440.1_5'Flank|TRIT1_ENST00000545233.1_5'Flank|TRIT1_ENST00000544981.1_Silent_p.P11P|TRIT1_ENST00000441669.2_Silent_p.P11P	NM_017646.4	NP_060116.2	Q9H3H1	MOD5_HUMAN	tRNA isopentenyltransferase 1	11					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|tRNA dimethylallyltransferase activity (GO:0052381)			breast(1)|large_intestine(5)|liver(1)|lung(3)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(1)	15	all_cancers(7;4.55e-14)|all_lung(5;1.23e-16)|all_epithelial(6;2.17e-16)|Lung NSC(20;7.03e-07)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;3.29e-18)|Epithelial(16;3.07e-17)|all cancers(16;6.21e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			CACTGCCCACGGGAACTGCTC	0.662													A|||	2547	0.508586	0.6157	0.4107	5008	,	,		13891	0.5933		0.3946	False		,,,				2504	0.4632				p.P11P		Atlas-SNP	.											TRIT1,NS,carcinoma,0,2	TRIT1	40	2	0			c.C33T						PASS	.	A		2498,1908		718,1062,423	22.0	27.0	26.0		33	-1.0	0.0	1	dbSNP_108	26	3379,5219		654,2071,1574	no	coding-synonymous	TRIT1	NM_017646.4		1372,3133,1997	AA,AG,GG		39.2998,43.3046,45.1938		11/468	40349131	5877,7127	2203	4299	6502	SO:0001819	synonymous_variant	54802	exon1			GCCCACGGGAACT	AF074918	CCDS30681.1	1p34.2	2012-10-05			ENSG00000043514	ENSG00000043514	2.5.1.8		20286	protein-coding gene	gene with protein product						11111046, 15870694	Standard	NM_017646		Approved	FLJ20061, IPT	uc021olz.1	Q9H3H1	OTTHUMG00000009245	ENST00000316891.5:c.33C>T	1.37:g.40349131G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	79	7	0.0886076	NM_017646	A1A4X7|Q3T7B5|Q5QPK5|Q5QPK6|Q6IAC9|Q96FJ3|Q96L45|Q9NXT7	Silent	SNP	ENST00000316891.5	37	CCDS30681.1																																																																																			G|0.541;A|0.459	0.459	strong		0.662	TRIT1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025627.2	NM_017646	
EYS	346007	hgsc.bcm.edu	37	6	65301167	65301167	+	Silent	SNP	C	C	T	rs62415825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301167C>T	ENST00000370621.3	-	26	5119	c.4593G>A	c.(4591-4593)gaG>gaA	p.E1531E	EYS_ENST00000370616.2_Silent_p.E1531E|EYS_ENST00000503581.1_Silent_p.E1531E			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1531					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TGCTTGAAGCCTCAGTAATAG	0.388													T|||	470	0.0938498	0.0151	0.1182	5008	,	,		19886	0.1567		0.0984	False		,,,				2504	0.1135				p.E1531E		Atlas-SNP	.											.	EYS	527	.	0			c.G4593A						PASS	.	T		49,1335		1,47,644	53.0	45.0	47.0		4593	0.5	1.0	6	dbSNP_129	47	445,2735		41,363,1186	yes	coding-synonymous	EYS	NM_001142800.1		42,410,1830	TT,TC,CC		13.9937,3.5405,10.8238		1531/3145	65301167	494,4070	692	1590	2282	SO:0001819	synonymous_variant	346007	exon26			TGAAGCCTCAGTA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4593G>A	6.37:g.65301167C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	98	98	1	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				C|0.902;T|0.098	0.098	strong		0.388	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
ZNF154	7710	hgsc.bcm.edu	37	19	58213969	58213969	+	Silent	SNP	T	T	G	rs11878316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58213969T>G	ENST00000512439.2	-	3	544	c.348A>C	c.(346-348)tcA>tcC	p.S116S	ZNF154_ENST00000426889.1_Silent_p.S116S|ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	116					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TTTTGCTATTTGATTGCTCCC	0.498													T|||	708	0.141374	0.3767	0.0922	5008	,	,		19378	0.0585		0.0696	False		,,,				2504	0.0174				p.S116S		Atlas-SNP	.											.	ZNF154	34	.	0			c.A348C						PASS	.	T		1274,2616		216,842,887	137.0	132.0	134.0		348	0.9	0.0	19	dbSNP_120	134	518,7774		16,486,3644	no	coding-synonymous	ZNF154	NM_001085384.1		232,1328,4531	GG,GT,TT		6.247,32.7506,14.7102		116/438	58213969	1792,10390	1945	4146	6091	SO:0001819	synonymous_variant	7710	exon3			GCTATTTGATTGC	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.348A>C	19.37:g.58213969T>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	139	64	0.460432	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Silent	SNP	ENST00000512439.2	37	CCDS42639.1																																																																																			T|0.862;G|0.138	0.138	strong		0.498	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
PCDHGA9	56107	hgsc.bcm.edu	37	5	140784055	140784055	+	Silent	SNP	T	T	C	rs3749770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140784055T>C	ENST00000573521.1	+	1	1536	c.1536T>C	c.(1534-1536)ggT>ggC	p.G512G	PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	512	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAGACACTGGTGTGCTGTATG	0.463													.|||	1552	0.309904	0.528	0.2608	5008	,	,		21232	0.1954		0.2018	False		,,,				2504	0.2791				p.G512G		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.T1536C						PASS	.	C	,,,,,,,,,,,,,,	1992,2050		491,1010,520	50.0	52.0	51.0		,,,,,,,,1536,,,,,,1536	-10.1	0.0	5	dbSNP_107	51	1870,6554		206,1458,2548	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,,,,,,,	697,2468,3068	CC,CT,TT		22.1985,49.2825,30.9803	,,,,,,,,,,,,,,	,,,,,,,,512/933,,,,,,512/829	140784055	3862,8604	2021	4212	6233	SO:0001819	synonymous_variant	56107	exon1			CACTGGTGTGCTG	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1536T>C	5.37:g.140784055T>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	130	128	0.984615	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			T|0.697;C|0.303	0.303	strong		0.463	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
SLC39A8	64116	hgsc.bcm.edu	37	4	103228734	103228734	+	Silent	SNP	C	C	T	rs35411892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:103228734C>T	ENST00000394833.2	-	3	887	c.411G>A	c.(409-411)acG>acA	p.T137T	SLC39A8_ENST00000510255.1_5'UTR|SLC39A8_ENST00000356736.4_Silent_p.T137T|SLC39A8_ENST00000424970.2_Silent_p.T137T	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8	137					transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		GATTAATAATCGTCACTGACA	0.393													C|||	821	0.163938	0.1604	0.1844	5008	,	,		18210	0.1171		0.1551	False		,,,				2504	0.2117				p.T137T		Atlas-SNP	.											.	SLC39A8	24	.	0			c.G411A						PASS	.	C	,,,	688,3718	280.8+/-275.6	49,590,1564	97.0	106.0	103.0		411,411,210,411	-11.1	0.0	4	dbSNP_126	103	1514,7086	284.2+/-296.5	122,1270,2908	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC39A8	NM_001135146.1,NM_001135147.1,NM_001135148.1,NM_022154.5	,,,	171,1860,4472	TT,TC,CC		17.6047,15.6151,16.9306	,,,	137/461,137/445,70/394,137/461	103228734	2202,10804	2203	4300	6503	SO:0001819	synonymous_variant	64116	exon3			AATAATCGTCACT		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"""Solute carriers"""	20862	protein-coding gene	gene with protein product		608732	"""solute carrier family 39 (metal ion transporter), member 8"""			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.411G>A	4.37:g.103228734C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	270	142	0.525926	NM_022154	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Silent	SNP	ENST00000394833.2	37	CCDS3656.1																																																																																			C|0.841;T|0.159	0.159	strong		0.393	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
ADCY2	108	hgsc.bcm.edu	37	5	7520881	7520881	+	Missense_Mutation	SNP	G	G	T	rs13166360	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:7520881G>T	ENST00000338316.4	+	3	528	c.439G>T	c.(439-441)Gtg>Ttg	p.V147L		NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	147			V -> L (in dbSNP:rs13166360). {ECO:0000269|PubMed:15489334}.		activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CATCTTCGTGGTGTACACCAT	0.507													G|||	459	0.0916534	0.0545	0.0994	5008	,	,		21118	0.0		0.2117	False		,,,				2504	0.1074				p.V147L		Atlas-SNP	.											.	ADCY2	337	.	0			c.G439T						PASS	.	G	LEU/VAL	390,4016	194.7+/-219.5	22,346,1835	179.0	124.0	143.0		439	5.4	1.0	5	dbSNP_121	143	2139,6461	367.0+/-334.5	269,1601,2430	yes	missense	ADCY2	NM_020546.2	32	291,1947,4265	TT,TG,GG		24.8721,8.8516,19.4449	possibly-damaging	147/1092	7520881	2529,10477	2203	4300	6503	SO:0001583	missense	108	exon3			TTCGTGGTGTACA	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.439G>T	5.37:g.7520881G>T	ENSP00000342952:p.Val147Leu	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	163	65	0.398773	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	236	0.10805860805860806	30	0.06097560975609756	41	0.1132596685082873	0	0.0	165	0.21767810026385223	G	20.9	4.072518	0.76415	0.088516	0.248721	ENSG00000078295	ENST00000338316	T	0.76186	-1.0	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.64997	1.995	0.09310	P	1.0	P	0.37525	0.598	B	0.37888	0.26	T	0.01652	-1.1303	9	0.54805	T	0.06	.	16.4516	0.83993	0.0:0.0:1.0:0.0	rs13166360;rs17826984;rs60134556;rs13166360	147	Q08462	ADCY2_HUMAN	L	147	ENSP00000342952:V147L	ENSP00000342952:V147L	V	+	1	0	ADCY2	7573881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.996000	0.70639	2.545000	0.85829	0.650000	0.86243	GTG	G|0.850;T|0.150	0.150	strong		0.507	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
PTCRA	171558	hgsc.bcm.edu	37	6	42893254	42893254	+	Missense_Mutation	SNP	G	G	A	rs146531157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42893254G>A	ENST00000304672.1	+	4	761	c.680G>A	c.(679-681)cGg>cAg	p.R227Q	PTCRA_ENST00000441198.1_Missense_Mutation_p.R202Q|PTCRA_ENST00000446507.1_Missense_Mutation_p.R120Q	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	227					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			CCTCCGGGTCGGAAGCCCGGG	0.682													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14322	0.0		0.005	False		,,,				2504	0.0				p.R242Q		Atlas-SNP	.											.	PTCRA	24	.	0			c.G725A						PASS	.	G	GLN/ARG	1,4387		0,1,2193	15.0	14.0	14.0		680	-6.3	0.0	6	dbSNP_134	14	41,8511		0,41,4235	yes	missense	PTCRA	NM_138296.2	43	0,42,6428	AA,AG,GG		0.4794,0.0228,0.3246	benign	227/282	42893254	42,12898	2194	4276	6470	SO:0001583	missense	171558	exon4			CGGGTCGGAAGCC	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.680G>A	6.37:g.42893254G>A	ENSP00000304447:p.Arg227Gln	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001243168	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	7.257	0.604442	0.14002	2.28E-4	0.004794	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507;ENST00000418903	T;T;T	0.55234	1.21;1.18;0.53	3.14	-6.28	0.02020	.	1.969100	0.03135	N	0.165837	T	0.10423	0.0255	N	0.14661	0.345	0.09310	N	1	B;B;B	0.15930	0.015;0.006;0.002	B;B;B	0.08055	0.003;0.003;0.003	T	0.03315	-1.1049	10	0.59425	D	0.04	.	1.8301	0.03128	0.3078:0.3482:0.2246:0.1194	.	120;202;227	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	Q	227;202;120;73	ENSP00000304447:R227Q;ENSP00000409550:R202Q;ENSP00000392288:R120Q	ENSP00000304447:R227Q	R	+	2	0	PTCRA	43001232	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.350000	0.01092	-2.666000	0.00416	-0.175000	0.13238	CGG	G|0.999;A|0.001	0.001	strong		0.682	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
COL5A3	50509	hgsc.bcm.edu	37	19	10078589	10078589	+	Silent	SNP	T	T	C	rs3815748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10078589T>C	ENST00000264828.3	-	61	4480	c.4395A>G	c.(4393-4395)aaA>aaG	p.K1465K		NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	1465	Collagen-like 6.|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)			CCGGAGACCCTTTTGAGCCTT	0.572													C|||	1210	0.241613	0.093	0.2363	5008	,	,		15764	0.3105		0.1759	False		,,,				2504	0.4427				p.K1465K		Atlas-SNP	.											.	COL5A3	243	.	0			c.A4395G						PASS	.	C		449,3957	782.1+/-414.5	23,403,1777	116.0	113.0	114.0		4395	0.9	1.0	19	dbSNP_107	114	1420,7180	747.2+/-407.3	132,1156,3012	no	coding-synonymous	COL5A3	NM_015719.3		155,1559,4789	CC,CT,TT		16.5116,10.1906,14.3703		1465/1746	10078589	1869,11137	2203	4300	6503	SO:0001819	synonymous_variant	50509	exon61			AGACCCTTTTGAG	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.4395A>G	19.37:g.10078589T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_015719	Q9NZQ6	Silent	SNP	ENST00000264828.3	37	CCDS12222.1																																																																																			T|0.837;C|0.163	0.163	strong		0.572	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057666	46057666	+	Missense_Mutation	SNP	A	A	T	rs116100696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057666A>T	ENST00000380095.1	+	1	394	c.332A>T	c.(331-333)aAg>aTg	p.K111M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	111	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						gtctgtaacaagcctgtgtgc	0.632													A|||	91	0.0181709	0.0651	0.0072	5008	,	,		20883	0.0		0.0	False		,,,				2504	0.0				p.K111M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.A332T						PASS	.	A	,MET/LYS	231,4175	136.5+/-172.5	10,211,1982	222.0	189.0	200.0		,332	-6.2	0.0	21	dbSNP_132	200	0,8600		0,0,4300	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,95	10,211,6282	TT,TA,AA		0.0,5.2429,1.7761	,benign	,111/252	46057666	231,12775	2203	4300	6503	SO:0001583	missense	353333	exon1			GTAACAAGCCTGT	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.332A>T	21.37:g.46057666A>T	ENSP00000369438:p.Lys111Met	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	150	90	0.6	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	a	6.984	0.551656	0.13374	0.052429	0.0	ENSG00000221859	ENST00000380095	T	0.01438	4.89	3.13	-6.25	0.02039	.	.	.	.	.	T	0.00241	0.0007	M	0.84846	2.72	0.09310	N	1	P	0.47302	0.893	P	0.46543	0.52	T	0.00529	-1.1687	9	0.52906	T	0.07	.	0.1928	0.00136	0.2301:0.2328:0.1914:0.3458	.	111	P60014	KR10A_HUMAN	M	111	ENSP00000369438:K111M	ENSP00000369438:K111M	K	+	2	0	KRTAP10-10	44882094	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.719000	0.04974	-2.037000	0.00920	-0.711000	0.03637	AAG	A|0.982;T|0.018	0.018	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
SEC24C	9632	hgsc.bcm.edu	37	10	75527708	75527708	+	Silent	SNP	A	A	G	rs4746147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75527708A>G	ENST00000339365.2	+	16	2286	c.2124A>G	c.(2122-2124)acA>acG	p.T708T	SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_Silent_p.T589T|SEC24C_ENST00000345254.4_Silent_p.T708T|SEC24C_ENST00000496827.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	708					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					ATGTGGCCACACTCTCTGTTG	0.552													G|||	723	0.144369	0.1528	0.1167	5008	,	,		12439	0.1171		0.1332	False		,,,				2504	0.1922				p.T708T		Atlas-SNP	.											SEC24C,NS,carcinoma,0,1	SEC24C	86	1	0			c.A2124G						PASS	.	G	,	653,3753	765.4+/-413.4	55,543,1605	160.0	142.0	148.0		2124,2124	-11.8	0.2	10	dbSNP_111	148	1232,7368	762.1+/-407.6	85,1062,3153	no	coding-synonymous,coding-synonymous	SEC24C	NM_004922.3,NM_198597.2	,	140,1605,4758	GG,GA,AA		14.3256,14.8207,14.4933	,	708/1095,708/1095	75527708	1885,11121	2203	4300	6503	SO:0001819	synonymous_variant	9632	exon15			GGCCACACTCTCT	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.2124A>G	10.37:g.75527708A>G		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	216	129	0.597222	NM_198597	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	37	CCDS7332.1																																																																																			A|0.856;G|0.144	0.144	strong		0.552	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
MAP1A	4130	hgsc.bcm.edu	37	15	43815999	43815999	+	Silent	SNP	C	C	T	rs3862138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43815999C>T	ENST00000300231.5	+	4	2778	c.2328C>T	c.(2326-2328)ccC>ccT	p.P776P	MAP1A_ENST00000382031.1_Silent_p.P1014P|MAP1A_ENST00000399453.1_Silent_p.P776P			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	776					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	ATGACCTGCCCGGGCCTGAAG	0.552													C|||	657	0.13119	0.1778	0.1081	5008	,	,		18474	0.001		0.1918	False		,,,				2504	0.1564				p.P776P		Atlas-SNP	.											.	MAP1A	189	.	0			c.C2328T						PASS	.	C		638,3294		57,524,1385	34.0	36.0	36.0		2328	-2.7	1.0	15	dbSNP_108	36	1579,6747		144,1291,2728	no	coding-synonymous	MAP1A	NM_002373.5		201,1815,4113	TT,TC,CC		18.9647,16.2258,18.0861		776/2804	43815999	2217,10041	1966	4163	6129	SO:0001819	synonymous_variant	4130	exon4			CCTGCCCGGGCCT	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.2328C>T	15.37:g.43815999C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	37	CCDS42031.1																																																																																			C|0.837;T|0.163	0.163	strong		0.552	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
R3HDML	140902	hgsc.bcm.edu	37	20	42966025	42966025	+	Silent	SNP	T	T	C	rs1884612	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:42966025T>C	ENST00000217043.2	+	1	400	c.228T>C	c.(226-228)agT>agC	p.S76S		NM_178491.2	NP_848586.1	Q9H3Y0	CRSPL_HUMAN	R3H domain containing-like	76	SCP.					extracellular region (GO:0005576)	peptidase inhibitor activity (GO:0030414)			NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)	21		Myeloproliferative disorder(115;0.028)	COAD - Colon adenocarcinoma(18;0.00189)			TCCGGGCCAGTGTGTACCCAC	0.607													C|||	1236	0.246805	0.2519	0.3516	5008	,	,		17546	0.0982		0.2962	False		,,,				2504	0.2679				p.S76S		Atlas-SNP	.											.	R3HDML	33	.	0			c.T228C						PASS	.	C		1187,3219	708.5+/-407.6	176,835,1192	57.0	54.0	55.0		228	0.6	1.0	20	dbSNP_92	55	2476,6124	694.4+/-404.7	346,1784,2170	no	coding-synonymous	R3HDML	NM_178491.2		522,2619,3362	CC,CT,TT		28.7907,26.9405,28.1639		76/254	42966025	3663,9343	2203	4300	6503	SO:0001819	synonymous_variant	140902	exon1			GGCCAGTGTGTAC	BC107048	CCDS13329.1	20q13.12	2007-04-26	2005-09-02		ENSG00000101074	ENSG00000101074			16249	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing-like"""				Standard	NM_178491		Approved	dJ881L22.3	uc002xls.2	Q9H3Y0	OTTHUMG00000032524	ENST00000217043.2:c.228T>C	20.37:g.42966025T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_178491		Silent	SNP	ENST00000217043.2	37	CCDS13329.1																																																																																			T|0.730;C|0.270	0.270	strong		0.607	R3HDML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079344.1	NM_178491	
EPHB2	2048	hgsc.bcm.edu	37	1	23208925	23208925	+	Silent	SNP	G	G	A	rs2229872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:23208925G>A	ENST00000400191.3	+	6	1395	c.1377G>A	c.(1375-1377)ccG>ccA	p.P459P	EPHB2_ENST00000374630.3_Silent_p.P459P|EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000374632.3_Silent_p.P459P|EPHB2_ENST00000374627.1_Silent_p.P453P|EPHB2_ENST00000544305.1_Silent_p.P459P	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	459	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		GGTCCCAGCCGGACCAGCCCA	0.602													G|||	1074	0.214457	0.1989	0.1585	5008	,	,		22352	0.4901		0.0755	False		,,,				2504	0.1339				p.P459P		Atlas-SNP	.											EPHB2_ENST00000374632,NS,adenoma,0,1	EPHB2	257	1	0			c.G1377A						PASS	.	G	,	728,3678	299.8+/-286.0	63,602,1538	150.0	136.0	141.0		1377,1377	-8.2	0.8	1	dbSNP_126	141	807,7793	188.6+/-235.5	41,725,3534	no	coding-synonymous,coding-synonymous	EPHB2	NM_004442.6,NM_017449.3	,	104,1327,5072	AA,AG,GG		9.3837,16.5229,11.8022	,	459/988,459/987	23208925	1535,11471	2203	4300	6503	SO:0001819	synonymous_variant	2048	exon6			CCAGCCGGACCAG	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1377G>A	1.37:g.23208925G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	91	85	0.934066	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	37																																																																																				G|0.854;A|0.146	0.146	strong		0.602	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31083945	31083945	+	Intron	SNP	C	C	T	rs145583110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31083945C>T	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Missense_Mutation_p.A483T|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						CAGGGCTTGGCACCAGCGGAG	0.627													C|||	8	0.00159744	0.0	0.0029	5008	,	,		16020	0.0		0.006	False		,,,				2504	0.0				p.A483T		Atlas-SNP	.											.	CDSN	48	.	0			c.G1447A						PASS	.	C	THR/ALA,	3,4163		0,3,2080	31.0	33.0	32.0		1447,	4.1	1.0	6	dbSNP_134	32	60,8108		0,60,4024	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	58,	0,63,6104	TT,TC,CC		0.7346,0.072,0.5108	probably-damaging,	483/530,	31083945	63,12271	2083	4084	6167	SO:0001627	intron_variant	1041	exon2			GCTTGGCACCAGC	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+1277C>T	6.37:g.31083945C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	19.05	3.751699	0.69533	7.2E-4	0.007346	ENSG00000204539	ENST00000376288	T	0.07908	3.15	4.09	4.09	0.47781	.	0.161533	0.29139	N	0.013037	T	0.05914	0.0154	L	0.32530	0.975	0.29308	N	0.868241	D	0.56035	0.974	P	0.51615	0.675	T	0.05903	-1.0857	10	0.72032	D	0.01	-21.708	11.9619	0.53013	0.0:1.0:0.0:0.0	.	483	Q15517	CDSN_HUMAN	T	483	ENSP00000365465:A483T	ENSP00000365465:A483T	A	-	1	0	CDSN	31191924	0.875000	0.30112	0.998000	0.56505	0.785000	0.44390	1.930000	0.40124	2.260000	0.74910	0.471000	0.43371	GCC	C|0.995;T|0.005	0.005	strong		0.627	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
ALPP	250	hgsc.bcm.edu	37	2	233243586	233243586	+	Missense_Mutation	SNP	C	C	T	rs1130335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233243586C>T	ENST00000392027.2	+	1	343	c.74C>T	c.(73-75)cCa>cTa	p.P25L	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	25			P -> L (in dbSNP:rs1130335). {ECO:0000269|PubMed:3001717, ECO:0000269|PubMed:3461452}.		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)		GGCATCATCCCAGGTAATGAG	0.642													C|||	423	0.0844649	0.025	0.0533	5008	,	,		16904	0.2153		0.0726	False		,,,				2504	0.0644				p.P25L		Atlas-SNP	.											.	ALPP	53	.	0			c.C74T						PASS	.	C	LEU/PRO	183,4223		4,175,2024	71.0	79.0	76.0		74	1.8	0.9	2	dbSNP_86	76	698,7902		32,634,3634	yes	missense	ALPP	NM_001632.3	98	36,809,5658	TT,TC,CC		8.1163,4.1534,6.7738	probably-damaging	25/536	233243586	881,12125	2203	4300	6503	SO:0001583	missense	250	exon1			TCATCCCAGGTAA	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.74C>T	2.37:g.233243586C>T	ENSP00000375881:p.Pro25Leu	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	155	67	0.432258	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	208	0.09523809523809523	14	0.028455284552845527	16	0.04419889502762431	121	0.21153846153846154	57	0.07519788918205805	.	14.18	2.459635	0.43736	0.041534	0.081163	ENSG00000163283	ENST00000392027	D	0.83673	-1.75	1.8	1.8	0.24995	Alkaline-phosphatase-like, core domain (1);	0.185016	0.47093	D	0.000260	T	0.00496	0.0016	M	0.86420	2.815	0.29546	P	0.8517250000000001	D	0.89917	1.0	D	0.80764	0.994	T	0.18713	-1.0328	9	0.62326	D	0.03	.	7.5124	0.27581	0.2567:0.7433:0.0:0.0	rs1130335;rs3189045;rs3748968;rs1130335	25	P05187	PPB1_HUMAN	L	25	ENSP00000375881:P25L	ENSP00000375881:P25L	P	+	2	0	ALPP	232951830	0.007000	0.16637	0.863000	0.33907	0.082000	0.17680	-0.094000	0.11094	1.299000	0.44798	0.313000	0.20887	CCA	C|1.000;|0.000	.	weak		0.642	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
OR56A3	390083	hgsc.bcm.edu	37	11	5968728	5968728	+	Missense_Mutation	SNP	T	T	C	rs1840178	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5968728T>C	ENST00000329564.6	+	1	159	c.152T>C	c.(151-153)aTg>aCg	p.M51T	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	51			M -> T (in dbSNP:rs1840178).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(27)|stomach(1)|upper_aerodigestive_tract(1)	41		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;9.41e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCCTCCTGATGACCATCTGG	0.602													T|||	2809	0.560903	0.4871	0.6412	5008	,	,		20155	0.6548		0.5408	False		,,,				2504	0.5276				p.M51T		Atlas-SNP	.											.	OR56A3	81	.	0			c.T152C						PASS	.	T	THR/MET	2245,2157	593.7+/-388.1	571,1103,527	121.0	121.0	121.0		152	4.0	1.0	11	dbSNP_92	121	4817,3775	614.5+/-396.2	1355,2107,834	yes	missense	OR56A3	NM_001003443.2	81	1926,3210,1361	CC,CT,TT		43.9362,49.0005,45.6518	benign	51/316	5968728	7062,5932	2201	4296	6497	SO:0001583	missense	390083	exon1			TCCTGATGACCAT		CCDS41614.1	11p15.4	2012-08-09		2004-03-10	ENSG00000184478	ENSG00000184478		"""GPCR / Class A : Olfactory receptors"""	14786	protein-coding gene	gene with protein product				OR56A6, OR56A3P			Standard	NM_001003443		Approved		uc010qzt.2	Q8NH54	OTTHUMG00000165373	ENST00000329564.6:c.152T>C	11.37:g.5968728T>C	ENSP00000331572:p.Met51Thr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	174	77	0.442529	NM_001003443	A6NN77|Q6IFF7	Missense_Mutation	SNP	ENST00000329564.6	37	CCDS41614.1	1243	0.5691391941391941	233	0.4735772357723577	234	0.6464088397790055	369	0.6451048951048951	407	0.5369393139841688	T	4.229	0.041428	0.08196	0.509995	0.560638	ENSG00000184478	ENST00000329564	T	0.03065	4.06	5.12	3.99	0.46301	GPCR, rhodopsin-like superfamily (1);	0.660669	0.14262	N	0.330710	T	0.00012	0.0000	N	0.00966	-1.09	0.52099	P	5.999999999994898E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.10941	-1.0608	9	0.62326	D	0.03	-22.7094	8.9442	0.35749	0.0:0.0879:0.0:0.9121	rs1840178;rs16905785;rs52813463;rs60686444;rs1840178	51	Q8NH54	O56A3_HUMAN	T	51	ENSP00000331572:M51T	ENSP00000331572:M51T	M	+	2	0	OR56A3	5925304	0.001000	0.12720	0.951000	0.38953	0.014000	0.08584	1.113000	0.31184	0.980000	0.38523	0.524000	0.50904	ATG	T|0.447;C|0.553	0.553	strong		0.602	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1	NM_001003443	
DYSF	8291	hgsc.bcm.edu	37	2	71780215	71780215	+	Silent	SNP	T	T	C	rs2303596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:71780215T>C	ENST00000258104.3	+	20	2104	c.1827T>C	c.(1825-1827)gaT>gaC	p.D609D	DYSF_ENST00000409651.1_Silent_p.D641D|DYSF_ENST00000409744.1_Silent_p.D596D|DYSF_ENST00000409582.3_Silent_p.D626D|DYSF_ENST00000410041.1_Silent_p.D627D|DYSF_ENST00000413539.2_Silent_p.D640D|DYSF_ENST00000394120.2_Silent_p.D610D|DYSF_ENST00000409762.1_Silent_p.D626D|DYSF_ENST00000409366.1_Silent_p.D610D|DYSF_ENST00000410020.3_Silent_p.D627D|DYSF_ENST00000429174.2_Silent_p.D609D	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	609					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						ATGTGGATGATGCCATCCAGT	0.562													C|||	2882	0.575479	0.7753	0.6412	5008	,	,		19523	0.2222		0.7336	False		,,,				2504	0.4601				p.D641D		Atlas-SNP	.											.	DYSF	536	.	0			c.T1923C						PASS	.	C	,,,,,,,,,,,,,	3451,955	363.9+/-316.7	1351,749,103	120.0	97.0	105.0		1830,1785,1785,1827,1920,1878,1878,1923,1830,1788,1881,1788,1881,1827	-1.7	0.4	2	dbSNP_100	105	6107,2493	409.6+/-349.9	2178,1751,371	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	3529,2500,474	CC,CT,TT		28.9884,21.675,26.5108	,,,,,,,,,,,,,	610/2082,595/2067,595/2088,609/2102,640/2112,626/2098,626/2119,641/2113,610/2103,596/2089,627/2099,596/2068,627/2120,609/2081	71780215	9558,3448	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon21			GGATGATGCCATC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1827T>C	2.37:g.71780215T>C		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			T|0.328;C|0.672	0.672	strong		0.562	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
SEC14L4	284904	hgsc.bcm.edu	37	22	30888494	30888494	+	Missense_Mutation	SNP	C	C	T	rs17738527	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30888494C>T	ENST00000255858.7	-	8	714	c.631G>A	c.(631-633)Gag>Aag	p.E211K	RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000540456.1_Missense_Mutation_p.E196K|SEC14L4_ENST00000392772.2_Missense_Mutation_p.E157K|SEC14L4_ENST00000381982.3_Missense_Mutation_p.E211K|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	211	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		E -> K (in dbSNP:rs17738527).			integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CGTGTCTCCTCACTCATGAAC	0.537													C|||	721	0.14397	0.0923	0.281	5008	,	,		21333	0.0397		0.2296	False		,,,				2504	0.136				p.E211K		Atlas-SNP	.											.	SEC14L4	43	.	0			c.G631A						PASS	.	C	LYS/GLU,LYS/GLU	500,3906	231.7+/-245.5	22,456,1725	142.0	97.0	112.0		631,631	5.1	1.0	22	dbSNP_123	112	1936,6664	340.9+/-323.8	216,1504,2580	yes	missense,missense	SEC14L4	NM_001161368.1,NM_174977.3	56,56	238,1960,4305	TT,TC,CC		22.5116,11.3482,18.7298	probably-damaging,probably-damaging	211/361,211/407	30888494	2436,10570	2203	4300	6503	SO:0001583	missense	284904	exon8			TCTCCTCACTCAT	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.631G>A	22.37:g.30888494C>T	ENSP00000255858:p.Glu211Lys	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	60	0.451128	NM_001161368	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	37	CCDS13878.1	332	0.152014652014652	56	0.11382113821138211	84	0.23204419889502761	22	0.038461538461538464	170	0.22427440633245382	c	35	5.495305	0.96355	0.113482	0.225116	ENSG00000133488	ENST00000255858;ENST00000540456;ENST00000392772;ENST00000381982	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	5.09	5.09	0.68999	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.79258	2.445	0.09310	P	1.0	D;P;D	0.63046	0.992;0.948;0.992	P;P;D	0.63703	0.879;0.643;0.917	T	0.00129	-1.2016	9	0.54805	T	0.06	-3.1812	17.6016	0.88026	0.0:1.0:0.0:0.0	rs17738527;rs52815728;rs17738527	157;196;211	B3KSF0;G3V1L4;Q9UDX3	.;.;S14L4_HUMAN	K	211;196;157;211	ENSP00000255858:E211K;ENSP00000440848:E196K;ENSP00000376525:E157K;ENSP00000371412:E211K	ENSP00000255858:E211K	E	-	1	0	SEC14L4	29218494	1.000000	0.71417	0.984000	0.44739	0.993000	0.82548	5.662000	0.68032	2.527000	0.85204	0.591000	0.81541	GAG	C|0.841;T|0.159	0.159	strong		0.537	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
EVPL	2125	hgsc.bcm.edu	37	17	74005476	74005476	+	Silent	SNP	G	G	A	rs7225323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74005476G>A	ENST00000301607.3	-	22	4063	c.3810C>T	c.(3808-3810)atC>atT	p.I1270I	EVPL_ENST00000586740.1_Silent_p.I1292I	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1270	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TCAGGCGGTCGATCTCACGCA	0.672													G|||	879	0.175519	0.5484	0.0865	5008	,	,		14770	0.0089		0.0577	False		,,,				2504	0.0276				p.I1270I		Atlas-SNP	.											.	EVPL	155	.	0			c.C3810T						PASS	.	G		2087,2319	572.2+/-383.3	515,1057,631	95.0	82.0	86.0		3810	2.1	1.0	17	dbSNP_116	86	468,8132	138.6+/-195.4	17,434,3849	no	coding-synonymous	EVPL	NM_001988.2		532,1491,4480	AA,AG,GG		5.4419,47.3672,19.6448		1270/2034	74005476	2555,10451	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon22			GCGGTCGATCTCA	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3810C>T	17.37:g.74005476G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	84	39	0.464286	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.810;A|0.190	0.190	strong		0.672	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
TNFRSF10A	8797	hgsc.bcm.edu	37	8	23060256	23060256	+	Missense_Mutation	SNP	T	T	C	rs17620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:23060256T>C	ENST00000221132.3	-	3	486	c.422A>G	c.(421-423)cAt>cGt	p.H141R		NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	141			H -> R (in dbSNP:rs6557634). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9082980}.		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)		GGCTCCAGGATGTTCTGATCT	0.483													T|||	2863	0.571685	0.2458	0.6153	5008	,	,		20194	0.9742		0.4553	False		,,,				2504	0.6861				p.H141R		Atlas-SNP	.											.	TNFRSF10A	40	.	0			c.A422G						PASS	.	T	ARG/HIS	1253,3153	428.9+/-342.0	159,935,1109	150.0	136.0	141.0		422	-7.0	0.0	8	dbSNP_116	141	3950,4650	551.3+/-385.9	925,2100,1275	yes	missense	TNFRSF10A	NM_003844.3	29	1084,3035,2384	CC,CT,TT		45.9302,28.4385,40.0046	possibly-damaging	141/469	23060256	5203,7803	2203	4300	6503	SO:0001583	missense	8797	exon3			CCAGGATGTTCTG	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.422A>G	8.37:g.23060256T>C	ENSP00000221132:p.His141Arg	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	148	61	0.412162	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	1233	0.5645604395604396	114	0.23170731707317074	208	0.574585635359116	562	0.9825174825174825	349	0.4604221635883905	T	2.650	-0.282244	0.05642	0.284385	0.459302	ENSG00000104689	ENST00000221132	T	0.41758	0.99	3.48	-6.96	0.01622	.	1.045100	0.07583	U	0.920699	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.44006	0.824	B	0.34180	0.177	T	0.47611	-0.9104	9	0.44086	T	0.13	.	2.0798	0.03632	0.2808:0.3163:0.2827:0.1202	rs6557634;rs11550537;rs17687367;rs59866941;rs6557634	141	O00220	TR10A_HUMAN	R	141	ENSP00000221132:H141R	ENSP00000221132:H141R	H	-	2	0	TNFRSF10A	23116201	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.096000	0.01349	-4.586000	0.00041	-1.400000	0.01143	CAT	T|0.514;C|0.486	0.486	strong		0.483	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58345606	58345606	+	Silent	SNP	T	T	C	rs17120203	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:58345606T>C	ENST00000300145.3	+	4	506	c.381T>C	c.(379-381)ctT>ctC	p.L127L	XRCC6BP1_ENST00000546709.1_3'UTR	NM_033276.2	NP_150592.1	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	127					double-strand break repair via nonhomologous end joining (GO:0006303)|protein phosphorylation (GO:0006468)	DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)	DNA-dependent protein kinase activity (GO:0004677)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	11						CACACGAGCTTATTCATGCAT	0.403													C|||	884	0.176518	0.3169	0.1585	5008	,	,		18580	0.0873		0.0527	False		,,,				2504	0.2188				p.L127L		Atlas-SNP	.											.	XRCC6BP1	22	.	0			c.T381C						PASS	.	C		1127,2745		175,777,984	231.0	219.0	223.0		381	3.3	1.0	12	dbSNP_123	223	404,7864		11,382,3741	no	coding-synonymous	XRCC6BP1	NM_033276.2		186,1159,4725	CC,CT,TT		4.8863,29.1064,12.6112		127/247	58345606	1531,10609	1936	4134	6070	SO:0001819	synonymous_variant	91419	exon4			CGAGCTTATTCAT	AF078164	CCDS41802.1	12q14.1	2006-01-09				ENSG00000166896			29452	protein-coding gene	gene with protein product	"""Ku70 binding protein 3"""					10219089	Standard	XM_005269223		Approved	KUB3	uc001sqp.3	Q9Y6H3	OTTHUMG00000170493	ENST00000300145.3:c.381T>C	12.37:g.58345606T>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	187	84	0.449198	NM_033276	Q1RLM4|Q96E81	Silent	SNP	ENST00000300145.3	37	CCDS41802.1																																																																																			T|0.861;C|0.139	0.139	strong		0.403	XRCC6BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409390.1	NM_033276	
BAZ1A	11177	hgsc.bcm.edu	37	14	35231108	35231108	+	Missense_Mutation	SNP	A	A	T	rs1044140	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:35231108A>T	ENST00000382422.2	-	23	4425	c.4098T>A	c.(4096-4098)aaT>aaA	p.N1366K	BAZ1A_ENST00000358716.4_Missense_Mutation_p.N1334K|BAZ1A_ENST00000360310.1_Missense_Mutation_p.N1366K			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1366			N -> K (in dbSNP:rs1044140). {ECO:0000269|PubMed:10880450, ECO:0000269|PubMed:17974005}.		chromatin remodeling (GO:0006338)|DNA-dependent DNA replication (GO:0006261)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	ACF complex (GO:0016590)|CHRAC (GO:0008623)|nuclear chromosome (GO:0000228)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(2)|large_intestine(7)|lung(19)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	Breast(36;0.0388)|Hepatocellular(127;0.158)		LUAD - Lung adenocarcinoma(48;7.23e-05)|Lung(238;0.00019)|Epithelial(34;0.0793)|all cancers(34;0.175)	GBM - Glioblastoma multiforme(112;0.0659)		TTTCTGGTGTATTATTAGCAC	0.428													A|||	193	0.0385383	0.0023	0.049	5008	,	,		19230	0.0		0.0805	False		,,,				2504	0.0767				p.N1366K		Atlas-SNP	.											.	BAZ1A	128	.	0			c.T4098A						PASS	.	A	LYS/ASN,LYS/ASN	94,4312		2,90,2111	208.0	200.0	203.0		4098,4002	0.9	0.8	14	dbSNP_86	203	835,7765		42,751,3507	yes	missense,missense	BAZ1A	NM_013448.2,NM_182648.1	94,94	44,841,5618	TT,TA,AA		9.7093,2.1335,7.1429	possibly-damaging,possibly-damaging	1366/1557,1334/1525	35231108	929,12077	2203	4300	6503	SO:0001583	missense	11177	exon24			TGGTGTATTATTA	AB032252	CCDS9651.1, CCDS41943.1	14q13.2	2013-01-28			ENSG00000198604	ENSG00000198604		"""Zinc fingers, PHD-type"""	960	protein-coding gene	gene with protein product		605680				10662543	Standard	NM_013448		Approved	hACF1, ACF1, WALp1, WCRF180	uc001wsk.3	Q9NRL2	OTTHUMG00000140216	ENST00000382422.2:c.4098T>A	14.37:g.35231108A>T	ENSP00000371859:p.Asn1366Lys	Somatic	337	0	0		WXS	Illumina HiSeq	Phase_I	345	168	0.486957	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Missense_Mutation	SNP	ENST00000382422.2	37	CCDS9651.1	82	0.037545787545787544	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	61	0.08047493403693931	.	14.49	2.552387	0.45487	0.021335	0.097093	ENSG00000198604	ENST00000358716;ENST00000382422;ENST00000360310;ENST00000543083	T;T;T	0.51071	0.72;0.72;0.72	5.9	0.952	0.19584	.	0.449576	0.26944	N	0.021712	T	0.00754	0.0025	L	0.34521	1.04	0.33831	D	0.630271	B;B	0.12630	0.006;0.003	B;B	0.09377	0.004;0.002	T	0.11251	-1.0595	10	0.20519	T	0.43	.	6.1758	0.20442	0.4759:0.0:0.3996:0.1245	rs1044140;rs3183812;rs52809122;rs1044140	1334;1366	Q9NRL2-2;Q9NRL2	.;BAZ1A_HUMAN	K	1334;1366;1366;1018	ENSP00000351555:N1334K;ENSP00000371859:N1366K;ENSP00000353458:N1366K	ENSP00000351555:N1334K	N	-	3	2	BAZ1A	34300859	0.232000	0.23762	0.805000	0.32314	0.694000	0.40290	0.631000	0.24568	0.133000	0.18654	0.460000	0.39030	AAT	A|0.941;T|0.059	0.059	strong		0.428	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1		
PIK3C2B	5287	hgsc.bcm.edu	37	1	204399064	204399064	+	Silent	SNP	G	G	A	rs2271420	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204399064G>A	ENST00000367187.3	-	30	4939	c.4383C>T	c.(4381-4383)ccC>ccT	p.P1461P	PIK3C2B_ENST00000424712.2_Silent_p.P1433P|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1461	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			CCACCTCAGGGGGTGCGTGGA	0.667													G|||	690	0.13778	0.2784	0.1037	5008	,	,		16736	0.0774		0.1113	False		,,,				2504	0.0613				p.P1461P		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4383T						PASS	.	G		117,4289		49,19,2135	88.0	78.0	81.0		4383	1.9	1.0	1	dbSNP_100	81	33,8567		10,13,4277	no	coding-synonymous	PIK3C2B	NM_002646.3		59,32,6412	AA,AG,GG		0.3837,2.6555,1.1533		1461/1635	204399064	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon30			CTCAGGGGGTGCG	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4383C>T	1.37:g.204399064G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			G|0.866;A|0.134	0.134	strong		0.667	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
MUC5B	727897	hgsc.bcm.edu	37	11	1247458	1247458	+	Missense_Mutation	SNP	C	C	T	rs2075853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1247458C>T	ENST00000529681.1	+	3	209	c.151C>T	c.(151-153)Cgg>Tgg	p.R51W	MUC5B_ENST00000447027.1_Missense_Mutation_p.R51W	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	51			R -> W (in dbSNP:rs2075853).		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)		CTCGCCCACCCGGCGCGTGAG	0.677													c|||	954	0.190495	0.1876	0.1052	5008	,	,		16646	0.3849		0.0895	False		,,,				2504	0.1585				p.R51W		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C151T						PASS	.	C	TRP/ARG	551,3357		32,487,1435	21.0	27.0	25.0		151	-3.3	0.0	11	dbSNP_96	25	569,7567		29,511,3528	yes	missense	MUC5B	NM_002458.2	101	61,998,4963	TT,TC,CC		6.9936,14.0993,9.2992	possibly-damaging	51/5763	1247458	1120,10924	1954	4068	6022	SO:0001583	missense	727897	exon3			CCCACCCGGCGCG	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.151C>T	11.37:g.1247458C>T	ENSP00000436812:p.Arg51Trp	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	394	0.1804029304029304	89	0.18089430894308944	44	0.12154696132596685	203	0.3548951048951049	58	0.07651715039577836	C	7.503	0.653026	0.14580	0.140993	0.069936	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20332	2.08;2.27	3.24	-3.29	0.05017	.	.	.	.	.	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	B;B;B	0.22414	0.002;0.069;0.069	B;B;B	0.09377	0.001;0.004;0.004	T	0.46020	-0.9221	8	0.87932	D	0	.	0.4716	0.00533	0.3246:0.3014:0.1594:0.2147	rs2075853;rs58847616;rs2075853	51;677;51	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	W	51;51;51;54	ENSP00000436812:R51W;ENSP00000415793:R51W	ENSP00000343037:R51W	R	+	1	2	MUC5B	1204034	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.998000	0.03701	-0.898000	0.03906	-1.131000	0.01979	CGG	C|0.812;T|0.188	0.188	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TTF1	7270	hgsc.bcm.edu	37	9	135277007	135277007	+	Missense_Mutation	SNP	C	C	T	rs3739916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135277007C>T	ENST00000334270.2	-	2	1241	c.1202G>A	c.(1201-1203)cGa>cAa	p.R401Q		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	401			R -> Q (in dbSNP:rs3739916).		chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R401Q(1)		endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		ACCAGACACTCGTGCCCTTTT	0.453													C|||	175	0.0349441	0.0068	0.0576	5008	,	,		15554	0.0268		0.0527	False		,,,				2504	0.047				p.R401Q		Atlas-SNP	.											TTF1,NS,carcinoma,0,2	TTF1	82	2	1	Substitution - Missense(1)	stomach(1)	c.G1202A						PASS	.	C	,GLN/ARG	62,4344	58.7+/-95.3	0,62,2141	220.0	182.0	195.0		,1202	-4.4	0.0	9	dbSNP_107	195	588,8012	156.7+/-210.5	21,546,3733	yes	intron,missense	TTF1	NM_001205296.1,NM_007344.3	,43	21,608,5874	TT,TC,CC		6.8372,1.4072,4.9977	,benign	,401/906	135277007	650,12356	2203	4300	6503	SO:0001583	missense	7270	exon2			GACACTCGTGCCC	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.1202G>A	9.37:g.135277007C>T	ENSP00000333920:p.Arg401Gln	Somatic	265	0	0		WXS	Illumina HiSeq	Phase_I	243	107	0.440329	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	81	0.03708791208791209	5	0.01016260162601626	22	0.06077348066298342	17	0.02972027972027972	37	0.048812664907651716	C	6.059	0.379209	0.11466	0.014072	0.068372	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.08896	3.04	4.95	-4.44	0.03557	.	57.353600	0.00166	N	0.000004	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37033	-0.9723	10	0.14252	T	0.57	.	2.7151	0.05185	0.3232:0.132:0.4163:0.1286	rs3739916;rs52805927;rs56617899;rs56847901;rs3739916	401	Q15361	TTF1_HUMAN	Q	401	ENSP00000333920:R401Q	ENSP00000245588:R401Q	R	-	2	0	TTF1	134266828	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.320000	0.08028	-0.392000	0.07751	-0.264000	0.10439	CGA	C|0.959;T|0.041	0.041	strong		0.453	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344	
RTP4	64108	hgsc.bcm.edu	37	3	187088903	187088903	+	Silent	SNP	C	C	A	rs1533595	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:187088903C>A	ENST00000259030.2	+	2	593	c.483C>A	c.(481-483)atC>atA	p.I161I		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	161					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)		CTTTGGGCATCTGTGGACAGG	0.512													C|||	1926	0.384585	0.1407	0.4942	5008	,	,		1612	0.7351		0.3469	False		,,,				2504	0.3139				p.I161I		Atlas-SNP	.											.	RTP4	20	.	0			c.C483A						PASS	.	C		913,3493	349.3+/-310.3	94,725,1384	63.0	55.0	58.0		483	0.2	0.0	3	dbSNP_88	58	3018,5582	466.0+/-366.7	525,1968,1807	no	coding-synonymous	RTP4	NM_022147.2		619,2693,3191	AA,AC,CC		35.093,20.7217,30.2245		161/247	187088903	3931,9075	2203	4300	6503	SO:0001819	synonymous_variant	64108	exon2			GGGCATCTGTGGA	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.483C>A	3.37:g.187088903C>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_022147	Q9H4F3	Silent	SNP	ENST00000259030.2	37	CCDS33910.1																																																																																			C|0.669;A|0.331	0.331	strong		0.512	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
SEMA3C	10512	hgsc.bcm.edu	37	7	80387766	80387766	+	Silent	SNP	C	C	T	rs1058425	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:80387766C>T	ENST00000265361.3	-	15	2085	c.1524G>A	c.(1522-1524)caG>caA	p.Q508Q	SEMA3C_ENST00000544525.1_Silent_p.Q526Q|SEMA3C_ENST00000419255.2_Silent_p.Q508Q	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	508	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GCAGAGATACCTGGGAAACCC	0.483													T|||	2064	0.412141	0.6498	0.3285	5008	,	,		17783	0.4286		0.1928	False		,,,				2504	0.3589				p.Q508Q		Atlas-SNP	.											.	SEMA3C	106	.	0			c.G1524A						PASS	.	T		2650,1756	523.0+/-370.9	789,1072,342	103.0	106.0	105.0		1524	4.1	1.0	7	dbSNP_86	105	1672,6928	739.4+/-407.1	173,1326,2801	no	coding-synonymous	SEMA3C	NM_006379.3		962,2398,3143	TT,TC,CC		19.4419,39.8547,33.2308		508/752	80387766	4322,8684	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon15			AGATACCTGGGAA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1524G>A	7.37:g.80387766C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			C|0.633;T|0.367	0.367	strong		0.483	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16534523	16534523	+	Missense_Mutation	SNP	G	G	A	rs141036884	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16534523G>A	ENST00000270747.3	-	3	746	c.610C>T	c.(610-612)Cgg>Tgg	p.R204W	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	204					regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTGCAGCCGGGTCATCAGC	0.662																																					p.R204W		Atlas-SNP	.											ARHGEF19,NS,carcinoma,+1,1	ARHGEF19	49	1	0			c.C610T						PASS	.	G	TRP/ARG	2,4400	4.2+/-10.8	0,2,2199	41.0	45.0	43.0		610	1.6	1.0	1	dbSNP_134	43	20,8580	14.6+/-50.1	0,20,4280	yes	missense	ARHGEF19	NM_153213.3	101	0,22,6479	AA,AG,GG		0.2326,0.0454,0.1692	probably-damaging	204/803	16534523	22,12980	2201	4300	6501	SO:0001583	missense	128272	exon3			GCAGCCGGGTCAT	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.610C>T	1.37:g.16534523G>A	ENSP00000270747:p.Arg204Trp	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	134	126	0.940298	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.211109	0.79240	4.54E-4	0.002326	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.54675	0.56;0.56	4.96	1.62	0.23740	.	0.218913	0.31809	N	0.007025	T	0.59824	0.2222	L	0.50333	1.59	0.35625	D	0.809747	D	0.89917	1.0	D	0.73708	0.981	T	0.64045	-0.6499	10	0.72032	D	0.01	.	5.9437	0.19207	0.0934:0.0:0.4865:0.4201	.	204	Q8IW93	ARHGJ_HUMAN	W	204	ENSP00000270747:R204W;ENSP00000396001:R204W	ENSP00000270747:R204W	R	-	1	2	ARHGEF19	16407110	0.992000	0.36948	0.960000	0.40013	0.964000	0.63967	1.421000	0.34815	0.075000	0.16796	0.561000	0.74099	CGG	G|0.999;A|0.001	0.001	strong		0.662	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596890	48596890	+	Silent	SNP	G	G	A	rs17823193	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48596890G>A	ENST00000310248.2	-	1	280	c.186C>T	c.(184-186)ttC>ttT	p.F62F		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, 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)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GGCCGAGGAAGAAGTACATGG	0.537													G|||	213	0.0425319	0.059	0.036	5008	,	,		21794	0.006		0.0924	False		,,,				2504	0.0112				p.F62F		Atlas-SNP	.											.	OR10AD1	24	.	0			c.C186T						PASS	.	G		273,4133	154.4+/-187.8	8,257,1938	118.0	95.0	103.0		186	3.1	1.0	12	dbSNP_123	103	762,7838	181.3+/-230.0	29,704,3567	yes	coding-synonymous	OR10AD1	NM_001004134.1		37,961,5505	AA,AG,GG		8.8605,6.1961,7.9579		62/318	48596890	1035,11971	2203	4300	6503	SO:0001819	synonymous_variant	121275	exon1			GAGGAAGAAGTAC		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.186C>T	12.37:g.48596890G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	204	100	0.490196	NM_001004134	B9EGT9|Q6IFA8	Silent	SNP	ENST00000310248.2	37	CCDS31787.1																																																																																			G|0.939;A|0.061	0.061	strong		0.537	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4511365	4511365	+	Silent	SNP	C	C	G	rs116973517	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4511365C>G	ENST00000301286.3	-	3	2564	c.2565G>C	c.(2563-2565)gtG>gtC	p.V855V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	855	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CAGCACCGGTCACCCCACTGC	0.582													C|||	229	0.0457268	0.0522	0.0692	5008	,	,		25279	0.001		0.0954	False		,,,				2504	0.0153				p.V855V		Atlas-SNP	.											.	PLIN4	191	.	0			c.G2565C						PASS	.	C		186,3692		2,182,1755	66.0	77.0	74.0		2565	-6.5	0.0	19	dbSNP_132	74	762,7514		3,756,3379	no	coding-synonymous	PLIN4	NM_001080400.1		5,938,5134	GG,GC,CC		9.2073,4.7963,7.7999		855/1358	4511365	948,11206	1939	4138	6077	SO:0001819	synonymous_variant	729359	exon3			ACCGGTCACCCCA	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.2565G>C	19.37:g.4511365C>G		Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	234	97	0.41453	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			C|0.937;G|0.063	0.063	strong		0.582	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
COL6A3	1293	hgsc.bcm.edu	37	2	238249108	238249108	+	Silent	SNP	T	T	C	rs61729844	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238249108T>C	ENST00000295550.4	-	38	8903	c.8451A>G	c.(8449-8451)ccA>ccG	p.P2817P	COL6A3_ENST00000353578.4_Silent_p.P2611P|COL6A3_ENST00000346358.4_Silent_p.P2617P|COL6A3_ENST00000347401.3_Silent_p.P2616P|COL6A3_ENST00000409809.1_Silent_p.P2611P|COL6A3_ENST00000472056.1_Silent_p.P2210P	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2817	Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		TGACGAAGGATGGCAACAGCC	0.547													t|||	218	0.0435304	0.003	0.0432	5008	,	,		21534	0.0089		0.1133	False		,,,				2504	0.0624				p.P2817P		Atlas-SNP	.											.	COL6A3	608	.	0			c.A8451G						PASS	.	C	,,	79,4327	70.3+/-108.2	1,77,2125	68.0	62.0	64.0		8451,6630,7833	-11.3	0.0	2	dbSNP_129	64	855,7745	194.9+/-240.2	43,769,3488	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	44,846,5613	CC,CT,TT		9.9419,1.793,7.1813	,,	2817/3178,2210/2571,2611/2972	238249108	934,12072	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			GAAGGATGGCAAC	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.8451A>G	2.37:g.238249108T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			A|0.000;C|0.070;T|0.930	0.070	strong		0.547	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
ZNF417	147687	hgsc.bcm.edu	37	19	58420699	58420699	+	Missense_Mutation	SNP	C	C	A	rs3745133	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58420699C>A	ENST00000312026.5	-	3	1111	c.947G>T	c.(946-948)cGt>cTt	p.R316L	ZNF417_ENST00000536263.1_Missense_Mutation_p.R117L|ZNF417_ENST00000595559.1_Missense_Mutation_p.R315L|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	316				R -> L (in Ref. 3; AAH25783). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R316L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		AGTGTGAACACGCTGATGGCT	0.458													C|||	1690	0.33746	0.4153	0.2911	5008	,	,		25205	0.2817		0.3499	False		,,,				2504	0.3098				p.R316L		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - Missense(1)	stomach(1)	c.G947T						PASS	.						167.0	147.0	154.0					19																	58420699		2203	4300	6503	SO:0001583	missense	147687	exon3			TGAACACGCTGAT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.947G>T	19.37:g.58420699C>A	ENSP00000311319:p.Arg316Leu	Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	277	219	0.790614	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	645	0.29532967032967034	167	0.3394308943089431	107	0.2955801104972376	118	0.2062937062937063	253	0.3337730870712401	.	8.577	0.881369	0.17467	.	.	ENSG00000173480	ENST00000312026;ENST00000536263	T;T	0.25085	1.82;1.82	2.15	-2.01	0.07410	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	L	0.60012	1.86	0.80722	P	0.0	P	0.38335	0.627	B	0.36922	0.236	T	0.32981	-0.9886	8	0.66056	D	0.02	.	7.8865	0.29653	0.0:0.6777:0.0:0.3223	rs3745133;rs17856732	316	Q8TAU3	ZN417_HUMAN	L	316;117	ENSP00000311319:R316L;ENSP00000442760:R117L	ENSP00000311319:R316L	R	-	2	0	ZNF417	63112511	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-2.414000	0.01037	-0.691000	0.05135	-1.050000	0.02344	CGT	C|0.500;A|0.500	0.500	weak		0.458	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
CCDC168	643677	hgsc.bcm.edu	37	13	103388370	103388370	+	Missense_Mutation	SNP	C	C	T	rs9518825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:103388370C>T	ENST00000322527.2	-	1	789	c.790G>A	c.(790-792)Ggt>Agt	p.G264S		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	264			G -> S (in dbSNP:rs9518825).					p.G264S(2)									AGTATTCTACCTTCCCTGCCT	0.398													C|||	1172	0.234026	0.2769	0.1931	5008	,	,		22757	0.4097		0.1123	False		,,,				2504	0.1493				p.G4893S		Atlas-SNP	.											Q8N800_HUMAN,NS,carcinoma,0,2	.	.	2	2	Substitution - Missense(2)	kidney(2)	c.G14677A						scavenged	.	C	SER/GLY	398,986		59,280,353	217.0	183.0	193.0		14677	2.3	0.0	13	dbSNP_119	193	404,2778		24,356,1211	yes	missense	CCDC168	NM_001146197.1	56	83,636,1564	TT,TC,CC		12.6964,28.7572,17.5646	probably-damaging	4893/7082	103388370	802,3764	692	1591	2283	SO:0001583	missense	643677	exon4			TTCTACCTTCCCT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.790G>A	13.37:g.103388370C>T	ENSP00000320232:p.Gly264Ser	Somatic	225	2	0.00888889		WXS	Illumina HiSeq	Phase_I	217	109	0.502304	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		537	0.24587912087912087	127	0.258130081300813	73	0.20165745856353592	251	0.4388111888111888	86	0.11345646437994723	C	16.33	3.091642	0.55968	0.287572	0.126964	ENSG00000175820	ENST00000322527	T	0.05199	3.48	3.25	2.35	0.29111	.	0.246855	0.21252	N	0.077635	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D	0.71674	0.998	D	0.67725	0.953	T	0.06232	-1.0838	9	0.05620	T	0.96	.	7.5159	0.27600	0.2562:0.7438:0.0:0.0	rs9518825;rs17635161;rs52793883;rs61475030;rs9518825	264	Q8NDH2	CC168_HUMAN	S	264	ENSP00000320232:G264S	ENSP00000320232:G264S	G	-	1	0	CCDC168	102186371	0.000000	0.05858	0.006000	0.13384	0.433000	0.31745	-0.484000	0.06528	0.882000	0.36016	0.404000	0.27445	GGT	C|0.737;T|0.263	0.263	strong		0.398	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
CLIP4	79745	hgsc.bcm.edu	37	2	29356669	29356669	+	Silent	SNP	A	A	G	rs3100232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29356669A>G	ENST00000320081.5	+	5	771	c.516A>G	c.(514-516)acA>acG	p.T172T	CLIP4_ENST00000404424.1_Silent_p.T172T|CLIP4_ENST00000401617.2_Silent_p.T65T|CLIP4_ENST00000401605.1_Silent_p.T172T	NM_024692.4	NP_078968.3	Q8N3C7	CLIP4_HUMAN	CAP-GLY domain containing linker protein family, member 4	172										endometrium(4)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(1)	26	Acute lymphoblastic leukemia(172;0.155)					TTTTGAAAACATCGAAACCAA	0.333													A|||	2079	0.415136	0.6747	0.317	5008	,	,		17714	0.3204		0.4006	False		,,,				2504	0.2464				p.T172T		Atlas-SNP	.											.	CLIP4	69	.	0			c.A516G						PASS	.	A		2675,1731	649.3+/-398.9	829,1017,357	101.0	97.0	98.0		516	-2.0	1.0	2	dbSNP_103	98	3414,5186	503.0+/-375.8	688,2038,1574	no	coding-synonymous	CLIP4	NM_024692.4		1517,3055,1931	GG,GA,AA		39.6977,39.2873,46.8169		172/706	29356669	6089,6917	2203	4300	6503	SO:0001819	synonymous_variant	79745	exon5			GAAAACATCGAAA	AK024722	CCDS1770.1, CCDS74502.1	2p23	2013-01-10	2007-01-04	2007-01-04	ENSG00000115295	ENSG00000115295		"""Ankyrin repeat domain containing"""	26108	protein-coding gene	gene with protein product			"""restin-like 2"""	RSNL2			Standard	XM_005264562		Approved	FLJ21069	uc002rmv.3	Q8N3C7	OTTHUMG00000097837	ENST00000320081.5:c.516A>G	2.37:g.29356669A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_024692	A0AV10|B2RMQ3|B7Z7N8|Q7Z4U3|Q96BR7|Q96MA5|Q9H7C0	Silent	SNP	ENST00000320081.5	37	CCDS1770.1																																																																																			A|0.551;G|0.449	0.449	strong		0.333	CLIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215123.2	NM_024692	
NUP54	53371	hgsc.bcm.edu	37	4	77065580	77065580	+	Silent	SNP	T	T	C	rs11558469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77065580T>C	ENST00000264883.3	-	2	254	c.114A>G	c.(112-114)gcA>gcG	p.A38A	NUP54_ENST00000514987.1_Silent_p.A38A|NUP54_ENST00000342467.6_5'UTR|NUP54_ENST00000458189.2_5'UTR|NUP54_ENST00000515460.1_5'UTR	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	38	9 X 2 AA repeats of F-G.|Gly-rich.|Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)	p.A38A(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						AAAAGCTGAATGCAGAACCTG	0.358													t|||	776	0.154952	0.0567	0.1282	5008	,	,		16392	0.3512		0.1312	False		,,,				2504	0.1288				p.A38A		Atlas-SNP	.											NUP54,NS,carcinoma,0,1	NUP54	48	1	1	Substitution - coding silent(1)	stomach(1)	c.A114G						PASS	.	C		308,4098	166.2+/-197.5	15,278,1910	91.0	89.0	90.0		114	-8.4	0.8	4	dbSNP_120	90	1299,7301	257.2+/-281.3	101,1097,3102	no	coding-synonymous	NUP54	NM_017426.2		116,1375,5012	CC,CT,TT		15.1047,6.9905,12.3558		38/508	77065580	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	53371	exon2			GCTGAATGCAGAA	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"""nucleoporin 54kD"""			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.114A>G	4.37:g.77065580T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	128	70	0.546875	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Silent	SNP	ENST00000264883.3	37	CCDS3576.1																																																																																			T|0.865;C|0.135	0.135	strong		0.358	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3		
IFRD1	3475	hgsc.bcm.edu	37	7	112102355	112102355	+	Silent	SNP	T	T	G	rs2253962	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:112102355T>G	ENST00000403825.3	+	8	1089	c.828T>G	c.(826-828)tcT>tcG	p.S276S	IFRD1_ENST00000535603.1_Silent_p.S226S|IFRD1_ENST00000005558.4_Silent_p.S276S	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	276					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						GCCTCCTCTCTTGTGATGATG	0.368													T|||	1186	0.236821	0.3283	0.1571	5008	,	,		20790	0.1915		0.2535	False		,,,				2504	0.1994				p.S276S		Atlas-SNP	.											.	IFRD1	46	.	0			c.T828G						PASS	.	T	,,,	1408,2998	460.9+/-352.8	223,962,1018	84.0	81.0	82.0		828,678,678,828	0.4	1.0	7	dbSNP_100	82	2108,6492	362.1+/-332.6	266,1576,2458	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFRD1	NM_001007245.2,NM_001197079.1,NM_001197080.1,NM_001550.3	,,,	489,2538,3476	GG,GT,TT		24.5116,31.9564,27.0337	,,,	276/452,226/402,226/402,276/452	112102355	3516,9490	2203	4300	6503	SO:0001819	synonymous_variant	3475	exon9			CCTCTCTTGTGAT	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.828T>G	7.37:g.112102355T>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	115	59	0.513043	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Silent	SNP	ENST00000403825.3	37	CCDS34736.1																																																																																			T|0.746;G|0.254	0.254	strong		0.368	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	
GZMB	3002	hgsc.bcm.edu	37	14	25101589	25101589	+	Missense_Mutation	SNP	G	G	C	rs11539752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:25101589G>C	ENST00000216341.4	-	3	386	c.280C>G	c.(280-282)Ccc>Gcc	p.P94A	GZMB_ENST00000526004.1_Intron|RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Intron|GZMB_ENST00000415355.3_Missense_Mutation_p.P82A|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Missense_Mutation_p.P128A			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	94	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		P -> A (in dbSNP:rs11539752). {ECO:0000269|PubMed:2332171, ECO:0000269|PubMed:3258865}.		apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.P94A(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		TGGGGGATGGGTCTTTTCACA	0.512													g|||	1512	0.301917	0.3759	0.2118	5008	,	,		17810	0.2867		0.2475	False		,,,				2504	0.3374				p.P94A		Atlas-SNP	.											GZMB,NS,carcinoma,0,1	GZMB	73	1	1	Substitution - Missense(1)	stomach(1)	c.C280G	GRCh37	CM033776	GZMB	M	rs11539752	PASS	.						128.0	144.0	138.0					14																	25101589		2203	4300	6503	SO:0001583	missense	3002	exon3			GGATGGGTCTTTT	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.280C>G	14.37:g.25101589G>C	ENSP00000216341:p.Pro94Ala	Somatic	391	0	0		WXS	Illumina HiSeq	Phase_I	304	78	0.256579	NM_004131	Q8N1D2|Q9UCC1	Missense_Mutation	SNP	ENST00000216341.4	37	CCDS9633.1	608	0.2783882783882784	195	0.39634146341463417	83	0.2292817679558011	138	0.24125874125874125	192	0.2532981530343008	g	0.017	-1.508410	0.00984	.	.	ENSG00000100453	ENST00000415355;ENST00000216341;ENST00000382542	D;D;D	0.87491	-2.26;-2.26;-2.26	5.4	-0.755	0.11061	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.747530	0.03630	N	0.237718	T	0.00012	0.0000	N	0.00317	-1.655	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.26360	-1.0105	9	0.02654	T	1	.	1.3803	0.02229	0.138:0.3597:0.2697:0.2327	rs11539752	82;94	Q6XGZ4;P10144	.;GRAB_HUMAN	A	82;94;128	ENSP00000387385:P82A;ENSP00000216341:P94A;ENSP00000371982:P128A	ENSP00000216341:P94A	P	-	1	0	GZMB	24171429	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.100000	0.03339	-0.316000	0.08690	-0.745000	0.03516	CCC	G|0.724;C|0.276	0.276	strong		0.512	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319488	21319488	+	Silent	SNP	C	C	T	rs77176173	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:21319488C>T	ENST00000583088.1	+	3	1729	c.834C>T	c.(832-834)agC>agT	p.S278S	KCNJ12_ENST00000331718.5_Silent_p.S278S	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	278					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.S278S(1)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	ACGAGGCCAGCCCGCTCTTCG	0.607										Prostate(3;0.18)																											p.S278S		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C834T						scavenged	.						104.0	85.0	91.0					17																	21319488		2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			GGCCAGCCCGCTC	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.834C>T	17.37:g.21319488C>T		Somatic	218	40	0.183486		WXS	Illumina HiSeq	Phase_I	186	18	0.0967742	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			C|0.625;T|0.375	0.375	strong		0.607	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
ESPNL	339768	hgsc.bcm.edu	37	2	239039896	239039896	+	Silent	SNP	G	G	C	rs10182906	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:239039896G>C	ENST00000343063.3	+	9	2804	c.2541G>C	c.(2539-2541)ccG>ccC	p.P847P	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Silent_p.P479P|ESPNL_ENST00000409169.1_Silent_p.P803P	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	847										endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		ACGGGGCTCCGGTGCCCTACA	0.701													C|||	4321	0.862819	0.9773	0.7968	5008	,	,		14119	0.9276		0.7276	False		,,,				2504	0.8272				p.P847P		Atlas-SNP	.											.	ESPNL	63	.	0			c.G2541C						PASS	.	C		4108,224		1950,208,8	9.0	9.0	9.0		2541	-3.2	0.6	2	dbSNP_119	9	6439,2123		2448,1543,290	no	coding-synonymous	ESPNL	NM_194312.2		4398,1751,298	CC,CG,GG		24.7956,5.1708,18.2023		847/1006	239039896	10547,2347	2166	4281	6447	SO:0001819	synonymous_variant	339768	exon9			GGCTCCGGTGCCC	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.2541G>C	2.37:g.239039896G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	29	0.483333	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Silent	SNP	ENST00000343063.3	37	CCDS2525.1																																																																																			G|0.154;C|0.846	0.846	strong		0.701	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
MRPL39	54148	hgsc.bcm.edu	37	21	26965148	26965148	+	Silent	SNP	G	G	A	rs1135638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:26965148G>A	ENST00000352957.4	-	8	938	c.897C>T	c.(895-897)ggC>ggT	p.G299G	MRPL39_ENST00000307301.7_Silent_p.G299G	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	299						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						GTAAAGACACGCCCTGGAATC	0.393													A|||	3668	0.732428	0.7284	0.8199	5008	,	,		16394	0.7153		0.8121	False		,,,				2504	0.6115				p.G299G		Atlas-SNP	.											.	MRPL39	61	.	0			c.C897T						PASS	.	A	,	3307,1099	395.6+/-329.7	1229,849,125	79.0	73.0	75.0		897,897	3.0	1.0	21	dbSNP_86	75	7111,1489	283.7+/-296.3	2954,1203,143	no	coding-synonymous,coding-synonymous	MRPL39	NM_017446.3,NM_080794.3	,	4183,2052,268	AA,AG,GG		17.314,24.9433,19.8985	,	299/339,299/354	26965148	10418,2588	2203	4300	6503	SO:0001819	synonymous_variant	54148	exon8			AGACACGCCCTGG	AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"""Mitochondrial ribosomal proteins / large subunits"""	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.897C>T	21.37:g.26965148G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	75	21	0.28	NM_017446	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Silent	SNP	ENST00000352957.4	37	CCDS13573.1																																																																																			G|0.221;A|0.779	0.779	strong		0.393	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446	
ABCA7	10347	hgsc.bcm.edu	37	19	1047002	1047002	+	Silent	SNP	A	A	G	rs3752234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1047002A>G	ENST00000263094.6	+	14	2055	c.1824A>G	c.(1822-1824)gcA>gcG	p.A608A	ABCA7_ENST00000433129.1_Silent_p.A608A|ABCA7_ENST00000533574.1_Intron|ABCA7_ENST00000435683.2_Silent_p.A470A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	608					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCAGCGCCGCACTGCTGGTTC	0.726													G|||	2899	0.578874	0.4637	0.7104	5008	,	,		13766	0.75		0.5199	False		,,,				2504	0.5256				p.A608A		Atlas-SNP	.											ABCA7,NS,carcinoma,0,1	ABCA7	174	1	0			c.A1824G						PASS	.			2219,2141		606,1007,567	14.0	13.0	13.0		1824	-2.7	0.3	19	dbSNP_107	13	4663,3873		1348,1967,953	no	coding-synonymous	ABCA7	NM_019112.3		1954,2974,1520	GG,GA,AA		45.3725,49.1055,46.6346		608/2147	1047002	6882,6014	2180	4268	6448	SO:0001819	synonymous_variant	10347	exon14			CGCCGCACTGCTG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1824A>G	19.37:g.1047002A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			A|0.401;G|0.599	0.599	strong		0.726	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149200043	149200043	+	Silent	SNP	T	T	C	rs32588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149200043T>C	ENST00000309241.5	+	2	158	c.126T>C	c.(124-126)ctT>ctC	p.L42L	PPARGC1B_ENST00000360453.4_Silent_p.L42L|PPARGC1B_ENST00000403750.1_Silent_p.L17L|PPARGC1B_ENST00000394320.3_Silent_p.L42L	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	42	Abolishes DNA transcriptional activity when missing.				actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)	p.L42L(1)		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)			TTCCAGAACTTGACCTCTCCC	0.577													C|||	1013	0.202276	0.3843	0.0937	5008	,	,		17057	0.0873		0.1372	False		,,,				2504	0.2188				p.L42L		Atlas-SNP	.											PPARGC1B,NS,carcinoma,0,1	PPARGC1B	74	1	1	Substitution - coding silent(1)	stomach(1)	c.T126C						PASS	.	C	,,	1514,2892		278,958,967	103.0	105.0	104.0		126,51,126	-11.3	0.1	5	dbSNP_76	104	1165,7435		69,1027,3204	yes	coding-synonymous,coding-synonymous,coding-synonymous	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	,,	347,1985,4171	CC,CT,TT		13.5465,34.3622,20.5982	,,	42/985,17/960,42/1024	149200043	2679,10327	2203	4300	6503	SO:0001819	synonymous_variant	133522	exon2			AGAACTTGACCTC	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.126T>C	5.37:g.149200043T>C		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	37	CCDS4298.1																																																																																			T|0.802;C|0.198	0.198	strong		0.577	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
ATP10B	23120	hgsc.bcm.edu	37	5	159992697	159992697	+	Silent	SNP	C	C	T	rs4921302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:159992697C>T	ENST00000327245.5	-	26	4995	c.4149G>A	c.(4147-4149)aaG>aaA	p.K1383K		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1383					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGTTAGAGCTCTTTGGGGTGC	0.567													C|||	406	0.0810703	0.0998	0.0692	5008	,	,		17508	0.0119		0.0765	False		,,,				2504	0.1401				p.K1383K		Atlas-SNP	.											.	ATP10B	201	.	0			c.G4149A						PASS	.	C		360,3672		17,326,1673	130.0	140.0	137.0		4149	4.4	1.0	5	dbSNP_111	137	800,7568		37,726,3421	no	coding-synonymous	ATP10B	NM_025153.2		54,1052,5094	TT,TC,CC		9.5602,8.9286,9.3548		1383/1462	159992697	1160,11240	2016	4184	6200	SO:0001819	synonymous_variant	23120	exon26			AGAGCTCTTTGGG	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.4149G>A	5.37:g.159992697C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	37	CCDS43394.1																																																																																			C|0.920;T|0.080	0.080	strong		0.567	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
SERPINB13	5275	hgsc.bcm.edu	37	18	61264298	61264298	+	Missense_Mutation	SNP	G	G	A	rs1020694	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:61264298G>A	ENST00000344731.5	+	8	979	c.877G>A	c.(877-879)Ggt>Agt	p.G293S	SERPINB13_ENST00000269489.5_Missense_Mutation_p.G241S	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	293			G -> S (in dbSNP:rs1020694). {ECO:0000269|PubMed:10527881, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.6}.		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						GGTGGAGGACGGTTACGATCT	0.527													A|||	4308	0.860224	0.9554	0.7925	5008	,	,		17263	0.875		0.8072	False		,,,				2504	0.819				p.G293S		Atlas-SNP	.											.	SERPINB13	51	.	0			c.G877A						PASS	.	A	SER/GLY	4098,308	165.8+/-197.2	1908,282,13	94.0	90.0	92.0		877	2.8	0.0	18	dbSNP_86	92	6809,1791	323.5+/-316.1	2696,1417,187	yes	missense	SERPINB13	NM_012397.3	56	4604,1699,200	AA,AG,GG		20.8256,6.9905,16.1387	benign	293/392	61264298	10907,2099	2203	4300	6503	SO:0001583	missense	5275	exon8			GAGGACGGTTACG	AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"""Serine (or cysteine) peptidase inhibitors"""	8944	protein-coding gene	gene with protein product		604445	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"""	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.877G>A	18.37:g.61264298G>A	ENSP00000341584:p.Gly293Ser	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_012397	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	37	CCDS11985.1	1853	0.8484432234432234	461	0.9369918699186992	289	0.7983425414364641	494	0.8636363636363636	609	0.8034300791556728	A	1.358	-0.589537	0.03799	0.930095	0.791744	ENSG00000197641	ENST00000269489;ENST00000539341;ENST00000344731	D;D	0.82344	-1.6;-1.6	5.3	2.85	0.33270	Serpin domain (3);	0.746815	0.12308	N	0.480501	T	0.00012	0.0000	N	0.00783	-1.19	0.80722	P	0.0	B;B	0.10296	0.003;0.0	B;B	0.04013	0.001;0.001	T	0.40384	-0.9566	9	0.02654	T	1	.	4.7982	0.13282	0.6085:0.1495:0.242:0.0	rs1020694;rs3810032;rs17699007;rs52794843;rs57934472;rs1020694	211;293	F5GZ40;Q9UIV8	.;SPB13_HUMAN	S	241;211;293	ENSP00000269489:G241S;ENSP00000341584:G293S	ENSP00000269489:G241S	G	+	1	0	SERPINB13	59415278	0.001000	0.12720	0.000000	0.03702	0.017000	0.09413	1.672000	0.37523	0.022000	0.15160	-1.585000	0.00851	GGT	G|0.178;A|0.822	0.822	strong		0.527	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397	
ACSL3	2181	hgsc.bcm.edu	37	2	223799388	223799388	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:223799388C>T	ENST00000357430.3	+	16	2519	c.1988C>T	c.(1987-1989)tCc>tTc	p.S663F	ACSL3_ENST00000392066.3_Missense_Mutation_p.S663F|AC013476.1_ENST00000582868.1_RNA	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	663					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	AAAGTGCTTTCCGAAGCTGCT	0.398			T	ETV1	prostate																																p.S663F		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.C1988T						PASS	.						123.0	111.0	115.0					2																	223799388		2203	4300	6503	SO:0001583	missense	2181	exon15			TGCTTTCCGAAGC	D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"""Acyl-CoA synthetase family"""	3570	protein-coding gene	gene with protein product		602371	"""fatty-acid-Coenzyme A ligase, long-chain 3"""	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.1988C>T	2.37:g.223799388C>T	ENSP00000350012:p.Ser663Phe	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_203372	Q60I92|Q8IUM9	Missense_Mutation	SNP	ENST00000357430.3	37	CCDS2455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.26|19.26	3.793730|3.793730	0.70452|0.70452	.|.	.|.	ENSG00000123983|ENSG00000123983	ENST00000407441|ENST00000357430;ENST00000392066	.|T;T	.|0.11277	.|2.79;2.79	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.106594	.|0.64402	.|D	.|0.000004	T|T	0.15825|0.15825	0.0381|0.0381	L|L	0.43152|0.43152	1.355|1.355	0.58432|0.58432	D|D	0.999991|0.999991	.|B	.|0.27625	.|0.183	.|B	.|0.33392	.|0.163	T|T	0.02539|0.02539	-1.1144|-1.1144	5|10	.|0.56958	.|D	.|0.05	-17.9388|-17.9388	20.0411|20.0411	0.97590|0.97590	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|663	.|O95573	.|ACSL3_HUMAN	S|F	164|663	.|ENSP00000350012:S663F;ENSP00000375918:S663F	.|ENSP00000350012:S663F	P|S	+|+	1|2	0|0	ACSL3|ACSL3	223507632|223507632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	3.908000|3.908000	0.56355|0.56355	2.739000|2.739000	0.93911|0.93911	0.655000|0.655000	0.94253|0.94253	CCG|TCC	.	.	none		0.398	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457	
FAM154B	283726	hgsc.bcm.edu	37	15	82574879	82574879	+	Missense_Mutation	SNP	T	T	C	rs11630197	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:82574879T>C	ENST00000339465.5	+	3	742	c.673T>C	c.(673-675)Tgg>Cgg	p.W225R	FAM154B_ENST00000427381.2_Missense_Mutation_p.W210R|FAM154B_ENST00000565501.1_3'UTR	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	225			W -> R (in dbSNP:rs11630197).							autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						TTTTCAACCATGGGAAATCCC	0.458													T|||	1176	0.234824	0.146	0.17	5008	,	,		20570	0.1647		0.2873	False		,,,				2504	0.4192				p.W225R		Atlas-SNP	.											.	FAM154B	50	.	0			c.T673C						PASS	.	T	ARG/TRP	737,3669	302.4+/-287.4	73,591,1539	87.0	86.0	86.0		673	3.9	0.8	15	dbSNP_120	86	2199,6401	375.3+/-337.7	291,1617,2392	no	missense	FAM154B	NM_001008226.1	101	364,2208,3931	CC,CT,TT		25.5698,16.7272,22.5742	probably-damaging	225/399	82574879	2936,10070	2203	4300	6503	SO:0001583	missense	283726	exon3			CAACCATGGGAAA	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.673T>C	15.37:g.82574879T>C	ENSP00000340445:p.Trp225Arg	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	130	62	0.476923	NM_001008226	B4E2M2	Missense_Mutation	SNP	ENST00000339465.5	37	CCDS32310.1	454	0.2078754578754579	59	0.11991869918699187	70	0.19337016574585636	98	0.17132867132867133	227	0.2994722955145119	T	17.60	3.429838	0.62844	0.167272	0.255698	ENSG00000188659	ENST00000339465;ENST00000427381	T;T	0.19250	2.16;2.16	3.9	3.9	0.45041	.	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	M	0.83953	2.67	0.20489	P	0.999892806	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.26883	-1.0090	9	0.26408	T	0.33	-9.3148	13.1531	0.59500	0.0:0.0:0.0:1.0	rs11630197;rs52815083;rs11630197	210;225	B4E2M2;Q658L1	.;F154B_HUMAN	R	225;210	ENSP00000340445:W225R;ENSP00000403743:W210R	ENSP00000340445:W225R	W	+	1	0	FAM154B	80361934	1.000000	0.71417	0.817000	0.32601	0.817000	0.46193	6.255000	0.72466	1.751000	0.51876	0.438000	0.28831	TGG	T|0.779;C|0.221	0.221	strong		0.458	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226	
ZFP90	146198	hgsc.bcm.edu	37	16	68598007	68598007	+	Silent	SNP	A	A	G	rs1177648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68598007A>G	ENST00000570495.1	+	5	1609	c.1317A>G	c.(1315-1317)caA>caG	p.Q439Q	ZFP90_ENST00000398253.2_Silent_p.Q439Q|ZFP90_ENST00000563169.2_Silent_p.Q439Q			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	439					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		CTCTCACTCAAGATGAAAGCA	0.408													A|||	2648	0.528754	0.1884	0.6167	5008	,	,		23241	0.7659		0.5676	False		,,,				2504	0.6421				p.Q439Q		Atlas-SNP	.											ZFP90,NS,carcinoma,+1,1	ZFP90	67	1	0			c.A1317G						scavenged	.	A		1043,2963		157,729,1117	93.0	90.0	91.0		1317	2.1	0.1	16	dbSNP_87	91	4990,3378		1470,2050,664	no	coding-synonymous	ZFP90	NM_133458.2		1627,2779,1781	GG,GA,AA		40.3681,26.0359,48.7555		439/637	68598007	6033,6341	2003	4184	6187	SO:0001819	synonymous_variant	146198	exon4			CACTCAAGATGAA	AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"""Zinc fingers, C2H2-type"", ""-"""	23329	protein-coding gene	gene with protein product		609451	"""zinc finger protein 90 homolog (mouse)"""			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.1317A>G	16.37:g.68598007A>G		Somatic	97	1	0.0103093		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_133458	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Silent	SNP	ENST00000570495.1	37	CCDS42183.1																																																																																			A|0.462;G|0.538	0.538	strong		0.408	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375	
CAPN14	440854	hgsc.bcm.edu	37	2	31399988	31399988	+	Missense_Mutation	SNP	C	C	T	rs4592896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:31399988C>T	ENST00000403897.3	-	20	2017	c.1876G>A	c.(1876-1878)Gtc>Atc	p.V626I	CAPN14_ENST00000444918.2_Missense_Mutation_p.V626I	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	626	Domain IV.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						AGCTGACAGACGTCATCACTG	0.557													C|||	1826	0.364617	0.6278	0.4481	5008	,	,		17954	0.1736		0.2256	False		,,,				2504	0.2894				p.V626I		Atlas-SNP	.											.	CAPN14	36	.	0			c.G1876A						PASS	.	C	ILE/VAL	760,624		206,348,138	45.0	48.0	47.0		1876	2.4	0.0	2	dbSNP_111	47	711,2471		75,561,955	yes	missense	CAPN14	NM_001145122.1	29	281,909,1093	TT,TC,CC		22.3444,45.0867,32.2164	benign	626/685	31399988	1471,3095	692	1591	2283	SO:0001583	missense	440854	exon20			GACAGACGTCATC	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.1876G>A	2.37:g.31399988C>T	ENSP00000385247:p.Val626Ile	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	725	0.33195970695970695	293	0.5955284552845529	151	0.4171270718232044	104	0.18181818181818182	177	0.23350923482849603	C	8.452	0.853364	0.17106	0.549133	0.223444	ENSG00000214711	ENST00000444918;ENST00000403897	T;T	0.29655	1.56;1.56	5.29	2.38	0.29361	EF-hand-like domain (1);	0.385688	0.21440	U	0.074519	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	B;B	0.32350	0.251;0.366	B;B	0.21546	0.015;0.035	T	0.42498	-0.9448	9	0.30854	T	0.27	.	6.4197	0.21736	0.0:0.6626:0.0:0.3374	rs4592896;rs52814384;rs59685902;rs4592896	626;450	A8MX76;A8MX76-2	CAN14_HUMAN;.	I	626	ENSP00000398670:V626I;ENSP00000385247:V626I	ENSP00000385247:V626I	V	-	1	0	CAPN14	31253492	0.158000	0.22850	0.049000	0.19019	0.056000	0.15407	0.273000	0.18662	0.179000	0.19938	0.561000	0.74099	GTC	C|0.689;T|0.311	0.311	strong		0.557	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
TMC7	79905	hgsc.bcm.edu	37	16	19067933	19067933	+	Silent	SNP	G	G	A	rs17854511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:19067933G>A	ENST00000304381.5	+	14	2071	c.1941G>A	c.(1939-1941)acG>acA	p.T647T	TMC7_ENST00000569532.1_Silent_p.T647T|TMC7_ENST00000421369.3_Silent_p.T537T	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	647					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						TCCCCAAGACGGTGAGCACCT	0.547													G|||	2360	0.471246	0.0946	0.5	5008	,	,		17901	0.754		0.6193	False		,,,				2504	0.5164				p.T647T		Atlas-SNP	.											.	TMC7	75	.	0			c.G1941A						PASS	.	G	,	805,3589	321.5+/-297.2	66,673,1458	186.0	139.0	154.0		1611,1941	-11.6	0.0	16	dbSNP_123	154	5150,3450	637.3+/-399.2	1553,2044,703	no	coding-synonymous,coding-synonymous	TMC7	NM_001160364.1,NM_024847.3	,	1619,2717,2161	AA,AG,GG		40.1163,18.3204,45.8288	,	537/614,647/724	19067933	5955,7039	2197	4300	6497	SO:0001819	synonymous_variant	79905	exon14			CAAGACGGTGAGC	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1941G>A	16.37:g.19067933G>A		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	222	102	0.459459	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	37	CCDS10573.1																																																																																			G|0.511;A|0.489	0.489	strong		0.547	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	
SLU7	10569	hgsc.bcm.edu	37	5	159840980	159840980	+	Missense_Mutation	SNP	T	T	C	rs17856338	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:159840980T>C	ENST00000297151.4	-	4	718	c.331A>G	c.(331-333)Ata>Gta	p.I111V		NM_006425.4	NP_006416.3	O95391	SLU7_HUMAN	SLU7 splicing factor homolog (S. cerevisiae)	111			I -> V (in dbSNP:rs17856338). {ECO:0000269|PubMed:15489334}.		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)			TTAGTAATTATGGAATTCTAT	0.308													T|||	24	0.00479233	0.0	0.0101	5008	,	,		13104	0.0		0.0169	False		,,,				2504	0.0				p.I111V		Atlas-SNP	.											.	SLU7	35	.	0			c.A331G						PASS	.	T	VAL/ILE	6,4398	12.9+/-30.5	0,6,2196	45.0	47.0	46.0		331	2.0	1.0	5	dbSNP_123	46	70,8524	40.8+/-97.7	1,68,4228	yes	missense	SLU7	NM_006425.4	29	1,74,6424	CC,CT,TT		0.8145,0.1362,0.5847	benign	111/587	159840980	76,12922	2202	4297	6499	SO:0001583	missense	10569	exon4			TAATTATGGAATT	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.331A>G	5.37:g.159840980T>C	ENSP00000297151:p.Ile111Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_006425	D3DQK2|Q3LUJ0|Q3LUJ1|Q6RXQ5|Q96FM9	Missense_Mutation	SNP	ENST00000297151.4	37	CCDS4352.1	18	0.008241758241758242	0	0.0	3	0.008287292817679558	0	0.0	15	0.01978891820580475	T	1.221	-0.626964	0.03610	0.001362	0.008145	ENSG00000164609	ENST00000297151;ENST00000521826;ENST00000519349	T;T;T	0.40756	1.58;1.02;1.04	5.72	1.99	0.26369	.	0.483471	0.23543	N	0.047048	T	0.06416	0.0165	N	0.04132	-0.27	0.36809	D	0.88578	B	0.02656	0.0	B	0.01281	0.0	T	0.22765	-1.0207	10	0.02654	T	1	-14.2209	2.3172	0.04201	0.2125:0.2522:0.0:0.5353	rs17856338	111	O95391	SLU7_HUMAN	V	111	ENSP00000297151:I111V;ENSP00000428943:I111V;ENSP00000429990:I111V	ENSP00000297151:I111V	I	-	1	0	SLU7	159773558	0.585000	0.26774	1.000000	0.80357	0.890000	0.51754	0.082000	0.14847	0.418000	0.25898	0.533000	0.62120	ATA	T|0.995;C|0.005	0.005	strong		0.308	SLU7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252673.1	NM_006425	
ICAM1	3383	hgsc.bcm.edu	37	19	10385540	10385540	+	Missense_Mutation	SNP	A	A	T	rs5491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10385540A>T	ENST00000264832.3	+	2	492	c.167A>T	c.(166-168)aAg>aTg	p.K56M	CTD-2369P2.5_ENST00000592893.1_RNA|ICAM1_ENST00000423829.2_Intron	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	56	Ig-like C2-type 1.		K -> M (in Kilifi; at homozygosity it is associated with increased susceptibility to cerebral malaria; dbSNP:rs5491). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:9259284, ECO:0000269|Ref.6}.		adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	GACCAGCCCAAGTTGTTGGGC	0.562													a|||	423	0.0844649	0.2504	0.0173	5008	,	,		19414	0.0526		0.007	False		,,,				2504	0.0204				p.K56M		Atlas-SNP	.											.	ICAM1	32	.	0			c.A167T	GRCh37	CM970747	ICAM1	M	rs5491	PASS	.	A	MET/LYS	934,3472	357.6+/-314.0	103,728,1372	99.0	95.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	167	-5.4	0.0	19	dbSNP_52	96	26,8574	16.6+/-54.9	0,26,4274	yes	missense	ICAM1	NM_000201.2	95	103,754,5646	TT,TA,AA		0.3023,21.1984,7.3812	benign	56/533	10385540	960,12046	2203	4300	6503	SO:0001583	missense	3383	exon2			AGCCCAAGTTGTT		CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.167A>T	19.37:g.10385540A>T	ENSP00000264832:p.Lys56Met	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	98	51	0.520408	NM_000201	B2R6M3|Q5NKV7|Q96B50	Missense_Mutation	SNP	ENST00000264832.3	37	CCDS12231.1	164	0.07509157509157509	114	0.23170731707317074	7	0.019337016574585635	36	0.06293706293706294	7	0.009234828496042216	a	10.23	1.293021	0.23564	0.211984	0.003023	ENSG00000090339	ENST00000264832	T	0.15487	2.42	4.45	-5.4	0.02656	Intercellular adhesion molecule, N-terminal (1);Immunoglobulin-like fold (1);	8.976480	0.00166	N	0.000000	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	5.000000000032756E-6	B	0.22146	0.065	B	0.31442	0.13	T	0.30794	-0.9966	9	0.48119	T	0.1	1.2014	2.5057	0.04645	0.109:0.3535:0.3044:0.2331	rs5491;rs52822152;rs57463344;rs5491	56	P05362	ICAM1_HUMAN	M	56	ENSP00000264832:K56M	ENSP00000264832:K56M	K	+	2	0	ICAM1	10246540	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.205000	0.00559	-1.363000	0.02164	-1.831000	0.00592	AAG	A|0.924;T|0.076	0.076	strong		0.562	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1		
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549452	32549452	+	Missense_Mutation	SNP	C	C	G	rs77637983		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32549452C>G	ENST00000360004.5	-	3	639	c.534G>C	c.(532-534)caG>caC	p.Q178H		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	178	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						AGTCTCCATTCTGGATCAGGC	0.552										Multiple Myeloma(14;0.17)																											p.Q178H		Atlas-SNP	.											HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	0			c.G534C						PASS	.						141.0	159.0	152.0					6																	32549452		1511	2709	4220	SO:0001583	missense	3123	exon3			TCCATTCTGGATC	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.534G>C	6.37:g.32549452C>G	ENSP00000353099:p.Gln178His	Somatic	409	0	0		WXS	Illumina HiSeq	Phase_I	242	89	0.367769	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	9.019	0.984432	0.18889	.	.	ENSG00000196126	ENST00000360004	T	0.03181	4.02	3.87	-6.02	0.02192	Immunoglobulin-like (3);Immunoglobulin C1-set (6);Immunoglobulin-like fold (3);	1.094850	0.06883	N	0.802821	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	B;B;B	0.17038	0.02;0.003;0.003	B;B;B	0.15870	0.014;0.014;0.007	T	0.47711	-0.9096	8	0.34782	T	0.22	.	8.422	0.32707	0.401:0.5079:0.0:0.0911	rs2308771;rs9269801	178;178;178	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	H	178	ENSP00000353099:Q178H	ENSP00000353099:Q178H	Q	-	3	2	HLA-DRB1	32657430	0.000000	0.05858	0.048000	0.18961	0.990000	0.78478	-3.650000	0.00403	-1.028000	0.03321	0.453000	0.30009	CAG	C|0.500;G|0.500	0.500	weak		0.552	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SMEK1	55671	hgsc.bcm.edu	37	14	91948043	91948043	+	Silent	SNP	T	T	C	rs17127374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:91948043T>C	ENST00000554943.1	-	4	907	c.792A>G	c.(790-792)acA>acG	p.T264T	SMEK1_ENST00000555462.1_Intron|SMEK1_ENST00000337238.4_Silent_p.T264T|SMEK1_ENST00000428424.2_Intron|SMEK1_ENST00000554684.1_Silent_p.T264T			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	264					positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				NS(1)|endometrium(1)|kidney(1)|liver(1)|lung(1)|stomach(1)	6		all_cancers(154;0.0691)|all_epithelial(191;0.219)		COAD - Colon adenocarcinoma(157;0.221)		GAACTCTGTATGTCTGATGAA	0.348													T|||	233	0.0465256	0.0204	0.0605	5008	,	,		17946	0.003		0.1163	False		,,,				2504	0.045				p.T264T		Atlas-SNP	.											.	SMEK1	94	.	0			c.A792G						PASS	.	T		163,4243	109.5+/-147.8	6,151,2046	158.0	147.0	151.0		792	-2.8	1.0	14	dbSNP_123	151	896,7704	199.7+/-243.7	53,790,3457	yes	coding-synonymous	SMEK1	NM_032560.4		59,941,5503	CC,CT,TT		10.4186,3.6995,8.1424		264/821	91948043	1059,11947	2203	4300	6503	SO:0001819	synonymous_variant	55671	exon5			TCTGTATGTCTGA	AK000714	CCDS9895.1, CCDS61532.1	14q32.12	2008-09-15	2006-10-12	2006-10-12		ENSG00000100796			20219	protein-coding gene	gene with protein product		610351	"""KIAA2010"""	KIAA2010		16085932, 18487071	Standard	XM_005267842		Approved	FLJ20707, MSTP033, FLFL1, smk-1, smk1	uc001xzm.3	Q6IN85		ENST00000554943.1:c.792A>G	14.37:g.91948043T>C		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	264	125	0.473485	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Silent	SNP	ENST00000554943.1	37		113	0.051739926739926737	10	0.02032520325203252	24	0.06629834254143646	3	0.005244755244755245	76	0.10026385224274406	T	8.401	0.841920	0.16963	0.036995	0.104186	ENSG00000100796	ENST00000555470	.	.	.	6.03	-2.82	0.05787	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18840	-1.0324	4	.	.	.	-14.8432	1.3143	0.02104	0.1967:0.2318:0.1018:0.4697	rs17127374;rs52791686;rs59536884;rs17127374	.	.	.	V	59	.	.	I	-	1	0	SMEK1	91017796	0.980000	0.34600	0.992000	0.48379	0.977000	0.68977	0.101000	0.15251	-0.337000	0.08426	-0.313000	0.08912	ATA	T|0.932;C|0.068	0.068	strong		0.348	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383153	41383153	+	Missense_Mutation	SNP	A	A	G	rs2261144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41383153A>G	ENST00000301146.4	-	7	1644	c.1103T>C	c.(1102-1104)aTg>aCg	p.M368T	CYP2A7_ENST00000291764.3_Missense_Mutation_p.M317T|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	368			M -> T (in dbSNP:rs2261144).			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)			GGCCAAACTCATGGGGATCAC	0.547													.|||	1572	0.313898	0.1657	0.451	5008	,	,		19217	0.2569		0.3499	False		,,,				2504	0.4387				p.M368T		Atlas-SNP	.											CYP2A7,colon,carcinoma,0,1	CYP2A7	71	1	0			c.T1103C						scavenged	.	A	THR/MET,THR/MET	899,3507	346.4+/-309.0	103,693,1407	104.0	91.0	96.0		1103,950	1.2	0.0	19	dbSNP_100	96	2843,5755	447.3+/-361.5	502,1839,1958	no	missense,missense	CYP2A7	NM_000764.2,NM_030589.2	81,81	605,2532,3365	GG,GA,AA		33.0658,20.404,28.7758	possibly-damaging,possibly-damaging	368/495,317/444	41383153	3742,9262	2203	4299	6502	SO:0001583	missense	1549	exon7			AAACTCATGGGGA	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.1103T>C	19.37:g.41383153A>G	ENSP00000301146:p.Met368Thr	Somatic	225	2	0.00888889		WXS	Illumina HiSeq	Phase_I	246	138	0.560976	NM_000764	Q13121	Missense_Mutation	SNP	ENST00000301146.4	37	CCDS12569.1	667	0.30540293040293043	90	0.18292682926829268	163	0.45027624309392267	149	0.26048951048951047	265	0.3496042216358839	A	0.003	-2.412682	0.00191	0.20404	0.330658	ENSG00000198077	ENST00000301146;ENST00000291764	T;T	0.67865	-0.29;-0.29	2.29	1.19	0.21007	.	0.117868	0.56097	U	0.000024	T	0.00012	0.0000	L	0.35793	1.09	0.53688	P	2.8999999999945736E-5	B;B;B	0.28082	0.2;0.046;0.025	B;B;B	0.39094	0.29;0.049;0.097	T	0.31110	-0.9955	9	0.06757	T	0.87	.	7.4198	0.27065	0.7781:0.2219:0.0:0.0	rs2261144;rs4001949;rs2261144	368;317;368	B7ZKR0;F8W816;P20853	.;.;CP2A7_HUMAN	T	368;317	ENSP00000301146:M368T;ENSP00000291764:M317T	ENSP00000291764:M317T	M	-	2	0	CYP2A7	46074993	0.558000	0.26554	0.007000	0.13788	0.284000	0.27059	3.405000	0.52630	0.121000	0.18284	0.155000	0.16302	ATG	A|0.704;G|0.296	0.296	strong		0.547	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
PRKAG3	53632	hgsc.bcm.edu	37	2	219695487	219695487	+	Missense_Mutation	SNP	G	G	C	rs692243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219695487G>C	ENST00000529249.1	-	3	526	c.211C>G	c.(211-213)Cca>Gca	p.P71A	PRKAG3_ENST00000439262.2_Missense_Mutation_p.P46A|PRKAG3_ENST00000545803.1_5'UTR|PRKAG3_ENST00000392098.3_Missense_Mutation_p.P71A			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	71			P -> A (in dbSNP:rs692243). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17878938}.		cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	TGACCTGGTGGCTCCCCTTCC	0.612													G|||	908	0.18131	0.0605	0.1758	5008	,	,		18442	0.4018		0.1471	False		,,,				2504	0.1564				p.P71A		Atlas-SNP	.											PRKAG3,NS,carcinoma,+1,1	PRKAG3	47	1	0			c.C211G						scavenged	.	G	ALA/PRO	365,4041	186.0+/-213.0	15,335,1853	148.0	122.0	130.0		211	1.9	0.1	2	dbSNP_83	130	1532,7068	288.8+/-298.9	148,1236,2916	yes	missense	PRKAG3	NM_017431.2	27	163,1571,4769	CC,CG,GG		17.814,8.2842,14.5856	benign	71/490	219695487	1897,11109	2203	4300	6503	SO:0001583	missense	53632	exon3			CTGGTGGCTCCCC	AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.211C>G	2.37:g.219695487G>C	ENSP00000436068:p.Pro71Ala	Somatic	120	1	0.00833333		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	37	CCDS2424.1	448	0.20512820512820512	47	0.09552845528455285	55	0.15193370165745856	228	0.3986013986013986	118	0.15567282321899736	G	12.42	1.933641	0.34096	0.082842	0.17814	ENSG00000115592	ENST00000439262;ENST00000529249;ENST00000392098;ENST00000430489	D;D;T;T	0.83914	-1.66;-1.78;-0.05;0.79	4.78	1.91	0.25777	.	0.360067	0.23775	N	0.044685	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	D;B;B	0.63880	0.993;0.287;0.189	P;B;B	0.55545	0.778;0.124;0.058	T	0.22347	-1.0219	9	0.19147	T	0.46	-0.0387	5.0549	0.14527	0.167:0.1924:0.6406:0.0	rs692243;rs832678;rs17848621;rs52808491;rs59655878;rs692243	71;46;71	B4DUK8;Q9UGI9-2;Q9UGI9	.;.;AAKG3_HUMAN	A	46;71;71;71	ENSP00000397133:P46A;ENSP00000436068:P71A;ENSP00000375947:P71A;ENSP00000416100:P71A	ENSP00000233944:P71A	P	-	1	0	PRKAG3	219403731	0.446000	0.25665	0.091000	0.20842	0.449000	0.32228	1.419000	0.34793	0.992000	0.38840	0.655000	0.94253	CCA	G|0.835;C|0.165	0.165	strong		0.612	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1		
TMEM30A	55754	hgsc.bcm.edu	37	6	75965985	75965985	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:75965985G>A	ENST00000230461.6	-	7	1248	c.919C>T	c.(919-921)Cga>Tga	p.R307*	TMEM30A_ENST00000370050.5_Nonsense_Mutation_p.R188*|TMEM30A_ENST00000475111.2_Nonsense_Mutation_p.R271*	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	307					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATCCGTTTTCGTCCATCAAAA	0.378																																					p.R307X		Atlas-SNP	.											TMEM30A,NS,carcinoma,+1,3	TMEM30A	40	3	0			c.C919T						PASS	.						105.0	101.0	102.0					6																	75965985		2203	4300	6503	SO:0001587	stop_gained	55754	exon7			GTTTTCGTCCATC	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"""chromosome 6 open reading frame 67"""	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.919C>T	6.37:g.75965985G>A	ENSP00000230461:p.Arg307*	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	55	41	0.745455	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Nonsense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	G	39	7.619958	0.98393	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111	.	.	.	5.88	5.88	0.94601	.	0.055311	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	13.6255	0.62161	0.0:0.0:0.7294:0.2706	.	.	.	.	X	307;291;188;271	.	ENSP00000230461:R307X	R	-	1	2	TMEM30A	76022705	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.821000	0.55700	2.780000	0.95670	0.655000	0.94253	CGA	.	.	none		0.378	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247	
SLC47A2	146802	hgsc.bcm.edu	37	17	19617236	19617236	+	Silent	SNP	G	G	T	rs4924792	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:19617236G>T	ENST00000325411.5	-	4	395	c.345C>A	c.(343-345)ggC>ggA	p.G115G	SLC47A2_ENST00000350657.5_Silent_p.G115G|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	115					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)	GGACCAGCGCGCCCCGCTGCA	0.662													G|||	1811	0.361621	0.3169	0.3372	5008	,	,		15295	0.4514		0.2942	False		,,,				2504	0.4162				p.G115G		Atlas-SNP	.											SLC47A2_ENST00000350657,NS,carcinoma,-2,2	SLC47A2	61	2	0			c.C345A						PASS	.	G	,	1421,2985	461.7+/-353.0	223,975,1005	78.0	73.0	74.0		345,345	-6.4	0.0	17	dbSNP_111	74	2695,5905	431.5+/-356.8	415,1865,2020	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	638,2840,3025	TT,TG,GG		31.3372,32.2515,31.6469	,	115/567,115/603	19617236	4116,8890	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon4			CAGCGCGCCCCGC	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.345C>A	17.37:g.19617236G>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	114	112	0.982456	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			G|0.682;T|0.318	0.318	strong		0.662	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
MCM3AP	8888	hgsc.bcm.edu	37	21	47676711	47676711	+	Silent	SNP	G	G	A	rs2839173	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47676711G>A	ENST00000397708.1	-	18	4178	c.3924C>T	c.(3922-3924)tcC>tcT	p.S1308S	MCM3AP_ENST00000467026.1_5'UTR|AP001469.9_ENST00000430259.1_RNA|MCM3AP_ENST00000291688.1_Silent_p.S1308S|MCM3AP-AS1_ENST00000590829.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1308					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)					ACCTGGTGCAGGAGATGCCCA	0.632													G|||	2027	0.404752	0.4773	0.4942	5008	,	,		18504	0.3264		0.3598	False		,,,				2504	0.3701				p.S1308S		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C3924T						PASS	.	G		2047,2303		529,989,657	14.0	18.0	17.0		3924	2.8	1.0	21	dbSNP_100	17	3299,5205		735,1829,1688	no	coding-synonymous	MCM3AP	NM_003906.3		1264,2818,2345	AA,AG,GG		38.7935,47.0575,41.5902		1308/1981	47676711	5346,7508	2175	4252	6427	SO:0001819	synonymous_variant	8888	exon17			GGTGCAGGAGATG	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.3924C>T	21.37:g.47676711G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	146	85	0.582192	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			G|0.614;A|0.386	0.386	strong		0.632	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
OR8U1	219417	hgsc.bcm.edu	37	11	56143592	56143592	+	Missense_Mutation	SNP	C	C	T	rs17150411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56143592C>T	ENST00000302270.1	+	1	493	c.493C>T	c.(493-495)Cgc>Tgc	p.R165C		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	165			R -> C (in dbSNP:rs17150411).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					CCTCACCTTCCGCCTCTCCTA	0.448																																					p.R165C		Atlas-SNP	.											OR8U1,colon,carcinoma,0,1	OR8U1	59	1	0			c.C493T						PASS	.						217.0	209.0	211.0					11																	56143592		2105	4224	6329	SO:0001583	missense	219417	exon1			ACCTTCCGCCTCT	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.493C>T	11.37:g.56143592C>T	ENSP00000304188:p.Arg165Cys	Somatic	273	0	0		WXS	Illumina HiSeq	Phase_I	210	45	0.214286	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	696	0.31868131868131866	77	0.1565040650406504	152	0.4198895027624309	244	0.42657342657342656	223	0.2941952506596306	C	4.583	0.108223	0.08780	.	.	ENSG00000172199	ENST00000302270	T	0.00188	8.59	5.78	2.79	0.32731	GPCR, rhodopsin-like superfamily (1);	0.274133	0.26467	N	0.024205	T	0.00012	0.0000	L	0.41492	1.28	0.80722	P	0.0	B	0.18741	0.03	B	0.18561	0.022	T	0.13548	-1.0505	9	0.62326	D	0.03	.	7.7725	0.29017	0.1327:0.7267:0.0:0.1406	rs17150411;rs17150411	165	Q8NH10	OR8U1_HUMAN	C	165	ENSP00000304188:R165C	ENSP00000304188:R165C	R	+	1	0	OR8U1	55900168	0.000000	0.05858	0.590000	0.28732	0.002000	0.02628	-2.520000	0.00951	1.472000	0.48140	-0.135000	0.14842	CGC	C|0.653;N|0.000	.	strong		0.448	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
C2orf16	84226	hgsc.bcm.edu	37	2	27801493	27801493	+	Missense_Mutation	SNP	T	T	C	rs1919127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27801493T>C	ENST00000408964.2	+	1	2105	c.2054T>C	c.(2053-2055)gTg>gCg	p.V685A		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	685			V -> A (in dbSNP:rs1919127).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CTTCAGGCTGTGAAATCTACA	0.403													T|||	1539	0.307308	0.1732	0.5231	5008	,	,		21205	0.5079		0.2644	False		,,,				2504	0.1728				p.V685A		Atlas-SNP	.											.	C2orf16	357	.	0			c.T2054C						PASS	.	T	ALA/VAL	687,3047		60,567,1240	82.0	78.0	79.0		2054	1.8	0.0	2	dbSNP_92	79	2218,6008		299,1620,2194	yes	missense	C2orf16	NM_032266.3	64	359,2187,3434	CC,CT,TT		26.9633,18.3985,24.2893	possibly-damaging	685/1985	27801493	2905,9055	1867	4113	5980	SO:0001583	missense	84226	exon1			AGGCTGTGAAATC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.2054T>C	2.37:g.27801493T>C	ENSP00000386190:p.Val685Ala	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	156	69	0.442308	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	772	0.3534798534798535	72	0.14634146341463414	171	0.4723756906077348	322	0.5629370629370629	207	0.27308707124010556	T	12.13	1.845535	0.32606	0.183985	0.269633	ENSG00000221843	ENST00000408964	T	0.07021	3.23	4.27	1.81	0.25067	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.33318	0.408	B	0.28553	0.091	T	0.27706	-1.0066	8	0.30078	T	0.28	.	3.4217	0.07396	0.2069:0.1085:0.0:0.6846	rs1919127;rs17006144;rs57887820;rs1919127	685	Q68DN1	CB016_HUMAN	A	685	ENSP00000386190:V685A	ENSP00000386190:V685A	V	+	2	0	C2orf16	27654997	0.001000	0.12720	0.003000	0.11579	0.752000	0.42762	0.405000	0.21015	0.391000	0.25143	0.459000	0.35465	GTG	T|0.680;C|0.320	0.320	strong		0.403	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
KIF1C	10749	hgsc.bcm.edu	37	17	4904564	4904564	+	Silent	SNP	T	T	C	rs17707385	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4904564T>C	ENST00000320785.5	+	5	588	c.231T>C	c.(229-231)atT>atC	p.I77I		NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	77	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						ATCGGGACATTGGAGAAGAGA	0.532													T|||	236	0.0471246	0.0076	0.0591	5008	,	,		21465	0.0466		0.1133	False		,,,				2504	0.0245				p.I77I	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.T231C						PASS	.	T		84,4322	70.9+/-108.8	1,82,2120	107.0	97.0	101.0		231	-2.8	1.0	17	dbSNP_123	101	924,7676	204.2+/-247.0	42,840,3418	no	coding-synonymous	KIF1C	NM_006612.5		43,922,5538	CC,CT,TT		10.7442,1.9065,7.7503		77/1104	4904564	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	10749	exon5			GGACATTGGAGAA	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.231T>C	17.37:g.4904564T>C		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	221	96	0.434389	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			C|0.070;N|0.000	0.070	strong		0.532	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
ARHGEF40	55701	hgsc.bcm.edu	37	14	21551058	21551058	+	Silent	SNP	G	G	A	rs1958395	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21551058G>A	ENST00000298694.4	+	16	3682	c.3555G>A	c.(3553-3555)gcG>gcA	p.A1185A	ARHGEF40_ENST00000298693.3_Silent_p.A1185A			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1185	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GTCTGGCTGCGCTCAGTCCCT	0.498													G|||	2728	0.544728	0.5424	0.4942	5008	,	,		20403	0.5139		0.6193	False		,,,				2504	0.5389				p.A1185A		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.G3555A						PASS	.	G		2400,2006	615.8+/-392.6	668,1064,471	100.0	81.0	88.0		3555	-6.7	0.1	14	dbSNP_92	88	5289,3311	645.3+/-400.1	1664,1961,675	no	coding-synonymous	ARHGEF40	NM_018071.3		2332,3025,1146	AA,AG,GG		38.5,45.5288,40.8811		1185/1520	21551058	7689,5317	2203	4300	6503	SO:0001819	synonymous_variant	55701	exon16			GGCTGCGCTCAGT		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.3555G>A	14.37:g.21551058G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	37	CCDS32041.1																																																																																			G|0.422;A|0.578	0.578	strong		0.498	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
ZNF286A	57335	hgsc.bcm.edu	37	17	15611495	15611495	+	Missense_Mutation	SNP	T	T	C	rs3760299	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15611495T>C	ENST00000464847.2	+	4	821	c.268T>C	c.(268-270)Tac>Cac	p.Y90H	ZNF286A_ENST00000585194.1_Missense_Mutation_p.Y90H|ZNF286A_ENST00000472486.1_Missense_Mutation_p.Y80H|ZNF286A_ENST00000421016.1_Missense_Mutation_p.Y90H|ZNF286A_ENST00000395894.2_Missense_Mutation_p.Y90H|ZNF286A_ENST00000395893.2_Missense_Mutation_p.Y90H|ZNF286A_ENST00000580259.1_Silent_p.A51A|ZNF286A_ENST00000581529.1_Silent_p.A41A|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000413242.2_Missense_Mutation_p.Y90H|ZNF286A_ENST00000583566.1_Missense_Mutation_p.Y90H|ZNF286A_ENST00000593105.1_Missense_Mutation_p.Y80H			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	90	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		Y -> H (in dbSNP:rs3760299). {ECO:0000269|PubMed:11347906}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		ACCTGAGAGCTACAACTTGGA	0.378													T|||	2545	0.508187	0.5703	0.4207	5008	,	,		11126	0.626		0.3708	False		,,,				2504	0.5061				p.Y90H		Atlas-SNP	.											ZNF286A,NS,carcinoma,0,1	ZNF286A	58	1	0			c.T268C						PASS	.	T	HIS/TYR,HIS/TYR	2462,1944	615.4+/-392.6	698,1066,439	55.0	56.0	55.0		268,268	3.9	0.3	17	dbSNP_107	55	3159,5441	476.7+/-369.5	575,2009,1716	yes	missense,missense	ZNF286A	NM_001130842.1,NM_020652.2	83,83	1273,3075,2155	CC,CT,TT		36.7326,44.1217,43.2185	benign,benign	90/522,90/522	15611495	5621,7385	2203	4300	6503	SO:0001583	missense	57335	exon5			GAGAGCTACAACT	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.268T>C	17.37:g.15611495T>C	ENSP00000464218:p.Tyr90His	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	1057	0.483974358974359	287	0.5833333333333334	140	0.3867403314917127	344	0.6013986013986014	286	0.37730870712401055	t	9.566	1.119785	0.20877	0.558783	0.367326	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.00801	5.68;5.68;5.68;5.68	4.97	3.9	0.45041	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.04880	-0.145	0.47065	P	6.930000000000547E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.10730	-1.0617	8	0.62326	D	0.03	-3.2436	7.5099	0.27566	0.0:0.0964:0.0:0.9036	rs3760299;rs52804179;rs59667491;rs3760299	90	Q9HBT8	Z286A_HUMAN	H	90;80;90;90	ENSP00000397163:Y90H;ENSP00000408168:Y80H;ENSP00000379231:Y90H;ENSP00000379230:Y90H	ENSP00000435872:Y90H	Y	+	1	0	ZNF286A	15552220	0.129000	0.22400	0.340000	0.25575	0.402000	0.30811	1.340000	0.33896	1.029000	0.39812	0.533000	0.62120	TAC	T|0.541;C|0.459	0.459	strong		0.378	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
OR13C5	138799	hgsc.bcm.edu	37	9	107360851	107360851	+	Missense_Mutation	SNP	T	T	C	rs1523678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107360851T>C	ENST00000374779.2	-	1	937	c.844A>G	c.(844-846)Ata>Gta	p.I282V		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	282			I -> V (in dbSNP:rs1523678).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTGTAGAATATGAATATAAGT	0.393													T|||	2184	0.436102	0.6475	0.2277	5008	,	,		19814	0.5754		0.1789	False		,,,				2504	0.4192				p.I282V		Atlas-SNP	.											.	OR13C5	60	.	0			c.A844G						PASS	.	T	VAL/ILE	2577,1829	638.3+/-396.9	762,1053,388	123.0	118.0	120.0		844	-7.7	0.0	9	dbSNP_88	120	1669,6931	308.1+/-308.7	183,1303,2814	yes	missense	OR13C5	NM_001004482.1	29	945,2356,3202	CC,CT,TT		19.407,41.5116,32.6465	benign	282/319	107360851	4246,8760	2203	4300	6503	SO:0001583	missense	138799	exon1			AGAATATGAATAT		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.844A>G	9.37:g.107360851T>C	ENSP00000363911:p.Ile282Val	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	155	72	0.464516	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	839	0.3841575091575092	297	0.6036585365853658	80	0.22099447513812154	330	0.5769230769230769	132	0.1741424802110818	T	6.399	0.441735	0.12164	0.584884	0.19407	ENSG00000255800	ENST00000374779	T	0.00019	9.06	3.85	-7.7	0.01259	GPCR, rhodopsin-like superfamily (1);	0.893919	0.09140	N	0.843087	T	0.00012	0.0000	N	0.00879	-1.12	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40421	-0.9564	9	0.51188	T	0.08	.	3.554	0.07857	0.3832:0.0767:0.4015:0.1386	rs1523678;rs52800382;rs58776918;rs1523678	282	Q8NGS8	O13C5_HUMAN	V	282	ENSP00000363911:I282V	ENSP00000363911:I282V	I	-	1	0	OR13C5	106400672	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-6.926000	0.00049	-2.857000	0.00329	0.347000	0.21830	ATA	T|0.634;C|0.366	0.366	strong		0.393	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
HSPB7	27129	hgsc.bcm.edu	37	1	16344360	16344360	+	Silent	SNP	A	A	G	rs732286	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16344360A>G	ENST00000311890.9	-	1	925	c.99T>C	c.(97-99)gcT>gcC	p.A33A	HSPB7_ENST00000487046.1_Silent_p.A33A|HSPB7_ENST00000545268.1_Silent_p.A33A|HSPB7_ENST00000375718.4_Intron|HSPB7_ENST00000411503.1_Silent_p.A33A|HSPB7_ENST00000406363.2_Silent_p.A33A	NM_014424.4	NP_055239.1	Q9UBY9	HSPB7_HUMAN	heat shock 27kDa protein family, member 7 (cardiovascular)	33	Required for localization to SC35 splicing speckles.				regulation of heart contraction (GO:0008016)|response to unfolded protein (GO:0006986)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(1)|liver(1)|lung(6)|skin(1)	10		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;8.21e-08)|COAD - Colon adenocarcinoma(227;5.5e-06)|BRCA - Breast invasive adenocarcinoma(304;9.08e-05)|Kidney(64;0.000162)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GGGCCGGGAGAGCACGGGAGG	0.622													G|||	3250	0.648962	0.7103	0.4553	5008	,	,		17259	0.7639		0.5934	False		,,,				2504	0.6421				p.A33A		Atlas-SNP	.											.	HSPB7	17	.	0			c.T99C						PASS	.	G		3006,1398	447.5+/-348.4	1025,956,221	34.0	37.0	36.0		99	4.6	1.0	1	dbSNP_86	36	5031,3567	507.7+/-376.9	1489,2053,757	no	coding-synonymous	HSPB7	NM_014424.4		2514,3009,978	GG,GA,AA		41.4864,31.7439,38.1864		33/171	16344360	8037,4965	2202	4299	6501	SO:0001819	synonymous_variant	27129	exon1			CGGGAGAGCACGG	AF155908	CCDS30611.1	1p36.23-p34.3	2011-09-02	2002-08-29		ENSG00000173641	ENSG00000173641		"""Heat shock proteins / HSPB"""	5249	protein-coding gene	gene with protein product		610692	"""heat shock 27kD protein family, member 7 (cardiovascular)"""			10593960	Standard	NM_014424		Approved	cvHSP	uc001axo.2	Q9UBY9	OTTHUMG00000009531	ENST00000311890.9:c.99T>C	1.37:g.16344360A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_014424	B3KQ37|C9K0Y0|Q9NU17	Silent	SNP	ENST00000311890.9	37	CCDS30611.1																																																																																			A|0.366;G|0.634	0.634	strong		0.622	HSPB7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026334.2	NM_014424	
WDR17	116966	hgsc.bcm.edu	37	4	177089839	177089839	+	Missense_Mutation	SNP	C	C	G	rs375753370|rs140459637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:177089839C>G	ENST00000280190.4	+	25	3280	c.3124C>G	c.(3124-3126)Ctt>Gtt	p.L1042V	WDR17_ENST00000508596.1_Missense_Mutation_p.L1003V|WDR17_ENST00000393643.2_Missense_Mutation_p.L1018V|WDR17_ENST00000507824.2_Missense_Mutation_p.L1017V			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1042										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)		GGCAGCTGATCTTCTTCTGAT	0.348													C|||	16	0.00319489	0.0	0.0029	5008	,	,		17511	0.0		0.0129	False		,,,				2504	0.001				p.L1042V		Atlas-SNP	.											.	WDR17	198	.	0			c.C3124G						PASS	.	C	VAL/LEU,VAL/LEU	4,4402	8.1+/-20.4	0,4,2199	140.0	134.0	136.0		3124,3007	5.1	1.0	4	dbSNP_134	136	50,8550	33.3+/-86.6	0,50,4250	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	32,32	0,54,6449	GG,GC,CC		0.5814,0.0908,0.4152	possibly-damaging,possibly-damaging	1042/1323,1003/1284	177089839	54,12952	2203	4300	6503	SO:0001583	missense	116966	exon25			GCTGATCTTCTTC	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.3124C>G	4.37:g.177089839C>G	ENSP00000280190:p.Leu1042Val	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	131	51	0.389313	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	C|C	12.08|12.08	1.831352|1.831352	0.32329|0.32329	9.08E-4|9.08E-4	0.005814|0.005814	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.61392|.	0.31;0.18;0.11|.	5.1|5.1	5.1|5.1	0.69264|0.69264	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.68302|0.68302	0.2986|0.2986	M|M	0.68317|0.68317	2.08|2.08	0.53688|0.53688	D|D	0.999974|0.999974	D;D;D|.	0.76494|.	0.97;0.999;0.999|.	P;D;D|.	0.77557|.	0.591;0.99;0.99|.	T|T	0.70857|0.70857	-0.4758|-0.4758	10|5	0.56958|.	D|.	0.05|.	-22.4333|-22.4333	18.6954|18.6954	0.91599|0.91599	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1018;1003;1042|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	V|C	1003;1018;1042;1018|276	ENSP00000422763:L1003V;ENSP00000377258:L1018V;ENSP00000280190:L1042V|.	ENSP00000280190:L1042V|.	L|S	+|+	1|2	0|0	WDR17|WDR17	177326833|177326833	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.055000|0.055000	0.15305|0.15305	4.228000|4.228000	0.58619|0.58619	2.647000|2.647000	0.89833|0.89833	0.591000|0.591000	0.81541|0.81541	CTT|TCT	C|0.995;G|0.005	0.005	strong		0.348	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
CFB	629	hgsc.bcm.edu	37	6	31914179	31914179	+	Missense_Mutation	SNP	C	C	T	rs12614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31914179C>T	ENST00000425368.2	+	2	607	c.94C>T	c.(94-96)Cgg>Tgg	p.R32W	CFB_ENST00000477310.1_Intron|CFB_ENST00000556679.1_Missense_Mutation_p.R534W|CFB_ENST00000456570.1_Missense_Mutation_p.R534W	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	32			R -> Q (in allele S; dbSNP:rs641153). {ECO:0000269|PubMed:16518403, ECO:0000269|PubMed:2249879, ECO:0000269|PubMed:8181962, ECO:0000269|PubMed:8225386, ECO:0000269|PubMed:8247029, ECO:0000269|Ref.7}.|R -> W (in dbSNP:rs12614). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.10, ECO:0000269|Ref.7, ECO:0000269|Ref.8}.		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement binding (GO:0001848)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|urinary_tract(1)	21						GTCTTTGGCCCGGCCCCAGGG	0.597													C|||	952	0.190096	0.3835	0.1369	5008	,	,		18580	0.0645		0.1332	False		,,,				2504	0.1544				p.R32W		Atlas-SNP	.											.	CFB	33	.	0			c.C94T	GRCh37	CM087207	CFB	M	rs12614	PASS	.	C	TRP/ARG	964,2056		144,676,690	70.0	72.0	71.0		94	-4.9	0.0	6	dbSNP_132	71	530,4888		27,476,2206	yes	missense	CFB	NM_001710.5	101	171,1152,2896	TT,TC,CC		9.7822,31.9205,17.7056	probably-damaging	32/765	31914179	1494,6944	1510	2709	4219	SO:0001583	missense	629	exon2			TTGGCCCGGCCCC	L15702	CCDS4729.1	6p21.33	2014-09-17	2006-02-10	2006-02-10	ENSG00000243649	ENSG00000243649	3.4.21.47	"""Complement system"""	1037	protein-coding gene	gene with protein product		138470	"""B-factor, properdin"""	BFD, BF			Standard	NM_001710		Approved	H2-Bf	uc011dor.2	P00751	OTTHUMG00000031198	ENST00000425368.2:c.94C>T	6.37:g.31914179C>T	ENSP00000416561:p.Arg32Trp	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	132	61	0.462121	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Missense_Mutation	SNP	ENST00000425368.2	37	CCDS4729.1	365	0.1671245421245421	169	0.3434959349593496	53	0.1464088397790055	38	0.06643356643356643	105	0.13852242744063326	C	15.72	2.916647	0.52546	0.319205	0.097822	ENSG00000243649;ENSG00000243649;ENSG00000243649;ENSG00000244255	ENST00000556679;ENST00000475617;ENST00000425368;ENST00000456570	D;T;T;D	0.82255	-1.59;2.39;-1.49;-1.59	5.31	-4.9	0.03094	.	1.901760	0.02486	N	0.088946	T	0.64962	0.2646	N	0.08118	0	0.80722	P	0.0	D;D;D;D	0.76494	0.999;0.998;0.985;0.997	P;P;B;P	0.57679	0.825;0.613;0.332;0.627	T	0.58775	-0.7577	9	0.66056	D	0.02	2.7207	9.1884	0.37184	0.5401:0.1442:0.3156:0.0	rs12614;rs1130149;rs3188725;rs4151649;rs11541540;rs12614	32;534;32;32	B4E1Z1;B4E1Z4;P00751;P00751-2	.;.;CFAB_HUMAN;.	W	534;32;32;534	ENSP00000451848:R534W;ENSP00000420090:R32W;ENSP00000416561:R32W;ENSP00000410815:R534W	ENSP00000416561:R32W	R	+	1	2	CFB;XXbac-BPG116M5.17	32022158	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.851000	0.04313	-0.564000	0.06070	-0.518000	0.04402	CGG	C|0.824;T|0.176	0.176	strong		0.597	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305646	39305646	+	Missense_Mutation	SNP	C	C	T	rs1846044	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39305646C>T	ENST00000343246.4	-	1	408	c.374G>A	c.(373-375)tGc>tAc	p.C125Y		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	125	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		C -> Y (in dbSNP:rs1846044). {ECO:0000269|PubMed:11279113}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ggagatgcagcagctgggacg	0.662													C|||	218	0.0435304	0.0023	0.0533	5008	,	,		17499	0.0		0.0994	False		,,,				2504	0.0798				p.C125Y		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.G374A						PASS	.	C	TYR/CYS	74,4318		0,74,2122	24.0	24.0	24.0		374	4.0	1.0	17	dbSNP_92	24	592,7972		29,534,3719	no	missense	KRTAP4-5	NM_033188.3	194	29,608,5841	TT,TC,CC		6.9127,1.6849,5.1405	probably-damaging	125/182	39305646	666,12290	2196	4282	6478	SO:0001583	missense	85289	exon1			ATGCAGCAGCTGG	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.374G>A	17.37:g.39305646C>T	ENSP00000340546:p.Cys125Tyr	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	99	0.04532967032967033	1	0.0020325203252032522	22	0.06077348066298342	0	0.0	76	0.10026385224274406	.	20.8	4.054820	0.75960	0.016849	0.069127	ENSG00000198271	ENST00000343246	T	0.02812	4.15	3.96	3.96	0.45880	.	0.000000	0.40469	U	0.001083	T	0.00468	0.0015	M	0.92604	3.325	0.37904	D	0.931158	D	0.76494	0.999	D	0.70487	0.969	T	0.01195	-1.1422	10	0.51188	T	0.08	.	13.8753	0.63648	0.0:1.0:0.0:0.0	rs1846044;rs7504114	130	Q9BYR2	KRA45_HUMAN	Y	125	ENSP00000340546:C125Y	ENSP00000340546:C125Y	C	-	2	0	KRTAP4-5	36559172	0.989000	0.36119	0.990000	0.47175	0.756000	0.42949	1.410000	0.34691	2.195000	0.70347	0.514000	0.50259	TGC	C|0.949;T|0.051	0.051	strong		0.662	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
TLN1	7094	hgsc.bcm.edu	37	9	35712003	35712003	+	Splice_Site	SNP	G	G	A	rs2295795	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35712003G>A	ENST00000314888.9	-	28	4033	c.3680C>T	c.(3679-3681)tCg>tTg	p.S1227L	TLN1_ENST00000540444.1_Splice_Site_p.S1227L	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1227			S -> L (in dbSNP:rs2295795). {ECO:0000269|Ref.1}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TCCTCCTACCGAGTCACTCAG	0.597													G|||	1009	0.201478	0.0197	0.268	5008	,	,		18282	0.3383		0.2704	False		,,,				2504	0.1881				p.S1227L		Atlas-SNP	.											.	TLN1	185	.	0			c.C3680T						PASS	.	G	LEU/SER	280,4126	155.5+/-188.7	14,252,1937	54.0	49.0	51.0		3680	4.9	1.0	9	dbSNP_100	51	2408,6192	398.5+/-346.1	332,1744,2224	yes	missense-near-splice	TLN1	NM_006289.3	145	346,1996,4161	AA,AG,GG		28.0,6.355,20.6674	benign	1227/2542	35712003	2688,10318	2203	4300	6503	SO:0001630	splice_region_variant	7094	exon28			CCTACCGAGTCAC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.3681+1C>T	9.37:g.35712003G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	521	0.23855311355311357	12	0.024390243902439025	100	0.27624309392265195	213	0.3723776223776224	196	0.25857519788918204	G	16.00	2.999336	0.54147	0.06355	0.28	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.12147	2.71;2.71	5.82	4.92	0.64577	.	0.356696	0.30492	N	0.009506	T	0.00012	0.0000	L	0.54323	1.7	0.20403	P	0.9999095468	B	0.09022	0.002	B	0.04013	0.001	T	0.46978	-0.9152	9	0.32370	T	0.25	-0.5518	16.3893	0.83528	0.0:0.0:0.8673:0.1327	rs2295795;rs17260374;rs60567288;rs2295795	1227	Q9Y490	TLN1_HUMAN	L	1227	ENSP00000316029:S1227L;ENSP00000442981:S1227L	ENSP00000316029:S1227L	S	-	2	0	TLN1	35702003	1.000000	0.71417	1.000000	0.80357	0.682000	0.39822	7.695000	0.84257	1.466000	0.48025	-0.169000	0.13324	TCG	G|0.785;A|0.215	0.215	strong		0.597	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	Missense_Mutation
TNFRSF1A	7132	hgsc.bcm.edu	37	12	6450945	6450945	+	Silent	SNP	T	T	C	rs767455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:6450945T>C	ENST00000162749.2	-	1	335	c.36A>G	c.(34-36)ccA>ccG	p.P12P	RN7SL391P_ENST00000582559.1_RNA|TNFRSF1A_ENST00000540022.1_Silent_p.P12P|TNFRSF1A_ENST00000366159.4_Silent_p.P12P	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN	tumor necrosis factor receptor superfamily, member 1A	12					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of angiogenesis (GO:0045766)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|prostaglandin metabolic process (GO:0006693)|protein heterooligomerization (GO:0051291)|response to alkaloid (GO:0043279)|response to amino acid (GO:0043200)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|tetrapyrrole metabolic process (GO:0033013)|viral process (GO:0016032)	axon (GO:0030424)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	tumor necrosis factor-activated receptor activity (GO:0005031)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19						GTCTCACCAGTGGCAGCAGCA	0.687													T|||	1510	0.301518	0.3631	0.3012	5008	,	,		16699	0.122		0.4294	False		,,,				2504	0.272				p.P12P		Atlas-SNP	.											TNFRSF1A,NS,carcinoma,0,1	TNFRSF1A	39	1	0			c.A36G						PASS	.	T		1579,2827	479.0+/-358.4	283,1013,907	52.0	48.0	50.0		36	-0.3	1.0	12	dbSNP_86	50	3677,4923	505.5+/-376.4	796,2085,1419	no	coding-synonymous	TNFRSF1A	NM_001065.3		1079,3098,2326	CC,CT,TT		42.7558,35.8375,40.4121		12/456	6450945	5256,7750	2203	4300	6503	SO:0001819	synonymous_variant	7132	exon1			CACCAGTGGCAGC	M75866	CCDS8542.1	12p13.2	2014-09-17			ENSG00000067182	ENSG00000067182		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11916	protein-coding gene	gene with protein product		191190		TNFR1		1655358, 2158863	Standard	NM_001065		Approved	TNF-R, TNFAR, TNFR60, TNF-R-I, CD120a, TNF-R55	uc001qnu.3	P19438	OTTHUMG00000168267	ENST00000162749.2:c.36A>G	12.37:g.6450945T>C		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_001065	A8K4X3|B2RDE4|B3KPQ1|B4DQB7|B4E309|B5M0B5|D3DUR1|Q9UCA4	Silent	SNP	ENST00000162749.2	37	CCDS8542.1																																																																																			T|0.619;C|0.381	0.381	strong		0.687	TNFRSF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399038.1	NM_001065	
RASGEF1C	255426	hgsc.bcm.edu	37	5	179563435	179563435	+	Silent	SNP	T	T	C	rs11546322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179563435T>C	ENST00000393371.2	-	3	677	c.381A>G	c.(379-381)gaA>gaG	p.E127E	RASGEF1C_ENST00000522500.1_5'UTR|RASGEF1C_ENST00000519883.1_5'Flank|RASGEF1C_ENST00000361132.4_Silent_p.E127E			Q8N431	RGF1C_HUMAN	RasGEF domain family, member 1C	127	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				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)			TAGTCGACTCTTCCTGGAAGT	0.682													C|||	2335	0.466254	0.2595	0.5432	5008	,	,		13834	0.7113		0.3857	False		,,,				2504	0.5215				p.E127E		Atlas-SNP	.											RASGEF1C_ENST00000393371,NS,carcinoma,0,2	RASGEF1C	81	2	0			c.A381G						scavenged	.	C		1217,3105		198,821,1142	54.0	44.0	47.0		381	0.2	1.0	5	dbSNP_120	47	3063,5459		613,1837,1811	no	coding-synonymous	RASGEF1C	NM_175062.3		811,2658,2953	CC,CT,TT		35.9423,28.1583,33.323		127/467	179563435	4280,8564	2161	4261	6422	SO:0001819	synonymous_variant	255426	exon4			CGACTCTTCCTGG	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.381A>G	5.37:g.179563435T>C		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	203	79	0.389163	NM_175062	D3DWQ7|Q7Z4T0|Q8NA49	Silent	SNP	ENST00000393371.2	37	CCDS4452.1																																																																																			T|0.588;C|0.412	0.412	strong		0.682	RASGEF1C-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253506.2	NM_175062	
OR5W2	390148	hgsc.bcm.edu	37	11	55681865	55681865	+	Missense_Mutation	SNP	T	T	C	rs12419022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55681865T>C	ENST00000344514.1	-	1	193	c.194A>G	c.(193-195)cAt>cGt	p.H65R		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	65			H -> R (in dbSNP:rs12419022).			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						GAAAGACAGATGACTGAGGAA	0.393													T|||	512	0.102236	0.0477	0.0965	5008	,	,		21019	0.1448		0.1233	False		,,,				2504	0.1145				p.H65R	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.A194G						PASS	.	T	ARG/HIS	241,4161	141.1+/-176.5	7,227,1967	124.0	119.0	120.0		194	5.0	1.0	11	dbSNP_120	120	1022,7570	218.7+/-257.0	57,908,3331	yes	missense	OR5W2	NM_001001960.1	29	64,1135,5298	CC,CT,TT		11.8948,5.4748,9.7199	benign	65/311	55681865	1263,11731	2201	4296	6497	SO:0001583	missense	390148	exon1			GACAGATGACTGA	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.194A>G	11.37:g.55681865T>C	ENSP00000342448:p.His65Arg	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	153	82	0.535948	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	250	0.11446886446886446	29	0.05894308943089431	33	0.09116022099447514	87	0.1520979020979021	101	0.13324538258575197	T	11.80	1.745930	0.30955	0.054748	0.118948	ENSG00000187612	ENST00000344514	T	0.02916	4.11	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.172191	0.27816	N	0.017733	T	0.00039	0.0001	M	0.89214	3.015	0.29591	P	0.848406	B	0.13145	0.007	B	0.18263	0.021	T	0.03957	-1.0989	9	0.66056	D	0.02	.	12.6788	0.56910	0.0:0.0:0.0:1.0	rs12419022;rs52804851;rs59891570;rs12419022	65	Q8NH69	OR5W2_HUMAN	R	65	ENSP00000342448:H65R	ENSP00000342448:H65R	H	-	2	0	OR5W2	55438441	0.045000	0.20229	0.990000	0.47175	0.405000	0.30901	2.454000	0.44979	1.874000	0.54306	0.448000	0.29417	CAT	T|0.900;C|0.100	0.100	strong		0.393	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
ATG10	83734	hgsc.bcm.edu	37	5	81549216	81549216	+	Missense_Mutation	SNP	C	C	T	rs1864183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:81549216C>T	ENST00000282185.3	+	7	929	c.635C>T	c.(634-636)aCg>aTg	p.T212M	ATG10_ENST00000514253.2_Intron|ATG10_ENST00000458350.3_Missense_Mutation_p.T212M	NM_031482.4	NP_113670.1	Q9H0Y0	ATG10_HUMAN	autophagy related 10	212			T -> M (in dbSNP:rs1864183). {ECO:0000269|PubMed:15489334}.		autophagy (GO:0006914)|autophagy in response to ER overload (GO:0034263)|positive regulation of protein modification process (GO:0031401)|protein lipidation (GO:0006497)|protein modification by small protein conjugation (GO:0032446)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	Atg12 ligase activity (GO:0019777)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(2)	9		Lung NSC(167;0.0258)|all_lung(232;0.0294)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;9.94e-41)|Epithelial(54;6.3e-36)|all cancers(79;2.31e-30)		GCCAAAGCAACGTCTCAGGAT	0.408													C|||	2608	0.520767	0.1747	0.5692	5008	,	,		22191	0.8909		0.4632	False		,,,				2504	0.6319				p.T212M		Atlas-SNP	.											.	ATG10	23	.	0			c.C635T						PASS	.	C	MET/THR,MET/THR	913,3493	350.0+/-310.6	111,691,1401	167.0	143.0	151.0		635,635	1.6	0.0	5	dbSNP_92	151	3996,4604	553.5+/-386.3	891,2214,1195	yes	missense,missense	ATG10	NM_001131028.1,NM_031482.4	81,81	1002,2905,2596	TT,TC,CC		46.4651,20.7217,37.7441	benign,benign	212/221,212/221	81549216	4909,8097	2203	4300	6503	SO:0001583	missense	83734	exon8			AAGCAACGTCTCA	AK024016	CCDS4057.1	5q14.1	2014-02-12	2012-06-06	2005-09-11	ENSG00000152348	ENSG00000152348			20315	protein-coding gene	gene with protein product		610800	"""APG10 autophagy 10-like (S. cerevisiae)"", ""ATG10 autophagy related 10 homolog (S. cerevisiae)"""	APG10L			Standard	NM_031482		Approved	DKFZP586I0418, FLJ13954	uc003khr.3	Q9H0Y0	OTTHUMG00000119041	ENST00000282185.3:c.635C>T	5.37:g.81549216C>T	ENSP00000282185:p.Thr212Met	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	152	70	0.460526	NM_001131028	B2RE09|Q6PIX1|Q9H842	Missense_Mutation	SNP	ENST00000282185.3	37	CCDS4057.1	1177	0.5389194139194139	98	0.1991869918699187	191	0.5276243093922652	520	0.9090909090909091	368	0.48548812664907653	C	11.95	1.792911	0.31685	0.207217	0.464651	ENSG00000152348	ENST00000282185;ENST00000458350	T;T	0.22945	1.93;1.93	6.07	1.65	0.23941	.	1.104980	0.06687	N	0.768935	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.24882	0.113	B	0.11329	0.006	T	0.25467	-1.0131	9	0.39692	T	0.17	-20.7711	5.6695	0.17715	0.0:0.4901:0.2977:0.2122	rs1864183;rs17246167;rs17856117;rs17856773;rs57781122;rs1864183	212	Q9H0Y0	ATG10_HUMAN	M	212	ENSP00000282185:T212M;ENSP00000404938:T212M	ENSP00000282185:T212M	T	+	2	0	ATG10	81584972	0.000000	0.05858	0.000000	0.03702	0.132000	0.20833	-0.065000	0.11617	0.404000	0.25506	0.655000	0.94253	ACG	C|0.552;T|0.448	0.448	strong		0.408	ATG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239252.2	NM_001131028	
SV2B	9899	hgsc.bcm.edu	37	15	91811749	91811749	+	Silent	SNP	G	G	A	rs3743444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91811749G>A	ENST00000394232.1	+	9	1757	c.1287G>A	c.(1285-1287)gtG>gtA	p.V429V	SV2B_ENST00000330276.4_Silent_p.V429V|SV2B_ENST00000545111.2_Silent_p.V278V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	429					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			AAATGAAGGTGTTTTTTGGTG	0.413													A|||	697	0.139177	0.2595	0.0937	5008	,	,		21557	0.0893		0.1392	False		,,,				2504	0.0603				p.V429V		Atlas-SNP	.											.	SV2B	98	.	0			c.G1287A						PASS	.	A	,	899,3497	739.9+/-411.1	97,705,1396	172.0	164.0	166.0		834,1287	-7.5	0.7	15	dbSNP_107	166	982,7614	773.8+/-407.7	66,850,3382	no	coding-synonymous,coding-synonymous	SV2B	NM_001167580.1,NM_014848.4	,	163,1555,4778	AA,AG,GG		11.4239,20.4504,14.4781	,	278/533,429/684	91811749	1881,11111	2198	4298	6496	SO:0001819	synonymous_variant	9899	exon10			GAAGGTGTTTTTT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1287G>A	15.37:g.91811749G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	138	54	0.391304	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			G|0.848;A|0.152	0.152	strong		0.413	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
SBF1	6305	hgsc.bcm.edu	37	22	50894987	50894987	+	Silent	SNP	G	G	A	rs79468232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50894987G>A	ENST00000390679.3	-	29	4126	c.3942C>T	c.(3940-3942)ccC>ccT	p.P1314P	SBF1_ENST00000476293.1_5'Flank|SBF1_ENST00000380817.3_Silent_p.P1340P|SBF1_ENST00000348911.6_Silent_p.P1315P			O95248	MTMR5_HUMAN	SET binding factor 1	1314	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)		AGCCCGGGTCGGGAGGGCCCC	0.706													G|||	214	0.0427316	0.0598	0.0245	5008	,	,		9310	0.0		0.0517	False		,,,				2504	0.0675				p.P1340P		Atlas-SNP	.											.	SBF1	211	.	0			c.C4020T						PASS	.	G		195,3583		1,193,1695	7.0	8.0	8.0		4020	-9.3	0.0	22	dbSNP_131	8	397,7793		7,383,3705	no	coding-synonymous	SBF1	NM_002972.2		8,576,5400	AA,AG,GG		4.8474,5.1615,4.9465		1340/1894	50894987	592,11376	1889	4095	5984	SO:0001819	synonymous_variant	6305	exon30			CGGGTCGGGAGGG	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.3942C>T	22.37:g.50894987G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				G|0.963;A|0.037	0.037	strong		0.706	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
PCDHB15	56121	hgsc.bcm.edu	37	5	140626767	140626767	+	Silent	SNP	C	C	T	rs3096081	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140626767C>T	ENST00000231173.3	+	1	1621	c.1621C>T	c.(1621-1623)Ctg>Ttg	p.L541L		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	541	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTCCCGGCGCTGAGCAGCGA	0.687													C|||	1081	0.215855	0.4213	0.1499	5008	,	,		15746	0.0992		0.1571	False		,,,				2504	0.1656				p.L541L		Atlas-SNP	.											PCDHB15,NS,carcinoma,-2,1	PCDHB15	138	1	0			c.C1621T						scavenged	.	C		1704,2702	483.2+/-359.6	349,1006,848	42.0	53.0	49.0		1621	4.4	1.0	5	dbSNP_103	49	1523,7075	273.5+/-290.7	158,1207,2934	no	coding-synonymous	PCDHB15	NM_018935.2		507,2213,3782	TT,TC,CC		17.7134,38.6745,24.8154		541/788	140626767	3227,9777	2203	4299	6502	SO:0001819	synonymous_variant	56121	exon1			CCGGCGCTGAGCA	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1621C>T	5.37:g.140626767C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	195	3	0.0153846	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			C|0.770;T|0.230	0.230	strong		0.687	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
ATP11A	23250	hgsc.bcm.edu	37	13	113527967	113527967	+	Silent	SNP	G	G	A	rs1320525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113527967G>A	ENST00000487903.1	+	27	3226	c.3138G>A	c.(3136-3138)tcG>tcA	p.S1046S	ATP11A_ENST00000283558.8_Silent_p.S1046S|ATP11A_ENST00000375630.2_Silent_p.S1046S|ATP11A_ENST00000375645.3_Silent_p.S1046S			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	1046					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				TTGTCTTTTCGCTTCTCTGGG	0.393											OREG0003854	type=REGULATORY REGION|Gene=ATP11A|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	1877	0.3748	0.298	0.3761	5008	,	,		21339	0.4742		0.3658	False		,,,				2504	0.3845				p.S1046S		Atlas-SNP	.											.	ATP11A	225	.	0			c.G3138A						PASS	.	G	,	1360,3046	451.2+/-349.6	220,920,1063	205.0	169.0	181.0		3138,3138	2.5	1.0	13	dbSNP_88	181	3364,5236	499.4+/-375.0	674,2016,1610	no	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	894,2936,2673	AA,AG,GG		39.1163,30.867,36.3217	,	1046/1135,1046/1192	113527967	4724,8282	2203	4300	6503	SO:0001819	synonymous_variant	23250	exon27			CTTTTCGCTTCTC	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.3138G>A	13.37:g.113527967G>A		Somatic	193	0	0	1451	WXS	Illumina HiSeq	Phase_I	129	57	0.44186	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1																																																																																			G|0.623;A|0.377	0.377	strong		0.393	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
GALC	2581	hgsc.bcm.edu	37	14	88459467	88459467	+	Silent	SNP	C	C	G	rs112992946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:88459467C>G	ENST00000261304.2	-	1	148	c.42G>C	c.(40-42)gcG>gcC	p.A14A	GALC_ENST00000393569.2_Intron|GALC_ENST00000393568.4_Silent_p.A14A|GALC_ENST00000544807.2_5'Flank	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	14					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						TCATAGCTTTCGCTCGGCGTT	0.706													C|||	394	0.0786741	0.0174	0.1671	5008	,	,		10215	0.005		0.1561	False		,,,				2504	0.0951				p.A14A		Atlas-SNP	.											.	GALC	48	.	0			c.G42C						PASS	.	C	,,	122,3306		0,122,1592	4.0	5.0	4.0		42,42,	-3.8	0.0	14	dbSNP_132	4	868,6474		31,806,2834	no	coding-synonymous,coding-synonymous,intron	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	,,	31,928,4426	GG,GC,CC		11.8224,3.5589,9.1922	,,	14/686,14/663,	88459467	990,9780	1714	3671	5385	SO:0001819	synonymous_variant	2581	exon1			AGCTTTCGCTCGG	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.42G>C	14.37:g.88459467C>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Silent	SNP	ENST00000261304.2	37	CCDS9878.2																																																																																			C|0.909;G|0.091	0.091	strong		0.706	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
OR8J3	81168	hgsc.bcm.edu	37	11	55904382	55904382	+	Missense_Mutation	SNP	A	A	C	rs17150102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55904382A>C	ENST00000301529.1	-	1	812	c.813T>G	c.(811-813)gaT>gaG	p.D271E		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	271			D -> E (in dbSNP:rs17150102).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D271E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					AAGCCATCTTATCAGTATCCA	0.408													A|||	518	0.103435	0.0499	0.098	5008	,	,		18145	0.1438		0.1213	False		,,,				2504	0.1196				p.D271E		Atlas-SNP	.											OR8J3,NS,carcinoma,0,1	OR8J3	112	1	1	Substitution - Missense(1)	stomach(1)	c.T813G						scavenged	.	A	GLU/ASP	240,4162	140.8+/-176.2	7,226,1968	136.0	134.0	135.0		813	0.7	1.0	11	dbSNP_123	135	1007,7585	216.4+/-255.5	54,899,3343	yes	missense	OR8J3	NM_001004064.1	45	61,1125,5311	CC,CA,AA		11.7202,5.4521,9.5967	probably-damaging	271/316	55904382	1247,11747	2201	4296	6497	SO:0001583	missense	81168	exon1			CATCTTATCAGTA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.813T>G	11.37:g.55904382A>C	ENSP00000301529:p.Asp271Glu	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	214	103	0.481308	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	253	0.11584249084249085	32	0.06504065040650407	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	A	15.45	2.837998	0.50951	0.054521	0.117202	ENSG00000167822	ENST00000301529	T	0.00227	8.5	3.27	0.672	0.17935	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000003	T	0.00012	0.0000	L	0.52011	1.625	0.80722	P	0.0	D	0.69078	0.997	D	0.74348	0.983	T	0.53892	-0.8374	9	0.44086	T	0.13	.	1.7242	0.02918	0.3404:0.0:0.3678:0.2918	rs17150102;rs52801432;rs17150102	271	Q8NGG0	OR8J3_HUMAN	E	271	ENSP00000301529:D271E	ENSP00000301529:D271E	D	-	3	2	OR8J3	55660958	0.000000	0.05858	0.996000	0.52242	0.699000	0.40488	-0.398000	0.07259	1.272000	0.44329	0.247000	0.18012	GAT	A|0.900;C|0.100	0.100	strong		0.408	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
MMP20	9313	hgsc.bcm.edu	37	11	102477377	102477377	+	Missense_Mutation	SNP	G	G	T	rs1784424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102477377G>T	ENST00000260228.2	-	6	854	c.842C>A	c.(841-843)aCt>aAt	p.T281N	MMP20_ENST00000544938.1_5'UTR|RP11-817J15.2_ENST00000542119.1_RNA|RP11-817J15.2_ENST00000544115.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	300					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATGGGGCAGAGTGGGCTTCCC	0.532													G|||	2103	0.419928	0.2625	0.4424	5008	,	,		20032	0.4325		0.4364	False		,,,				2504	0.5869				p.T281N		Atlas-SNP	.											.	MMP20	52	.	0			c.C842A						PASS	.	G	ASN/THR	1360,3046	451.8+/-349.8	204,952,1047	113.0	109.0	110.0		842	2.3	0.2	11	dbSNP_89	110	3926,4672	547.7+/-385.2	867,2192,1240	yes	missense	MMP20	NM_004771.3	65	1071,3144,2287	TT,TG,GG		45.6618,30.867,40.649	benign	281/484	102477377	5286,7718	2203	4299	6502	SO:0001583	missense	9313	exon6			GGCAGAGTGGGCT	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.842C>A	11.37:g.102477377G>T	ENSP00000260228:p.Thr281Asn	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	143	142	0.993007	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	876	0.4010989010989011	129	0.2621951219512195	170	0.4696132596685083	248	0.43356643356643354	329	0.4340369393139842	G	0.027	-1.362562	0.01235	0.30867	0.456618	ENSG00000137674	ENST00000260228	T	0.14516	2.5	5.45	2.3	0.28687	.	0.506134	0.22203	N	0.063204	T	0.00012	0.0000	L	0.34521	1.04	0.53688	P	2.599999999997049E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.46317	-0.9200	9	0.16420	T	0.52	.	8.1778	0.31292	0.1424:0.0:0.6217:0.2359	rs1784424;rs52816330;rs1784424	281	O60882	MMP20_HUMAN	N	281	ENSP00000260228:T281N	ENSP00000260228:T281N	T	-	2	0	MMP20	101982587	0.576000	0.26700	0.164000	0.22755	0.001000	0.01503	0.646000	0.24797	0.417000	0.25871	-0.813000	0.03139	ACT	G|0.598;T|0.402	0.402	strong		0.532	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
SPDYE4	388333	hgsc.bcm.edu	37	17	8658901	8658901	+	Missense_Mutation	SNP	G	G	A	rs74844184	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8658901G>A	ENST00000328794.6	-	4	598	c.422C>T	c.(421-423)gCg>gTg	p.A141V		NM_001128076.1	NP_001121548.1	A6NLX3	SPDE4_HUMAN	speedy/RINGO cell cycle regulator family member E4	141										breast(1)|endometrium(2)|kidney(1)	4						GCTAAAATACGCTATGACCAT	0.483													G|||	124	0.0247604	0.0015	0.0548	5008	,	,		18390	0.0		0.0765	False		,,,				2504	0.0072				p.A141V		Atlas-SNP	.											.	SPDYE4	22	.	0			c.C422T						PASS	.	G	VAL/ALA	19,1365		1,17,674	69.0	59.0	62.0		422	3.0	0.2	17	dbSNP_131	62	273,2909		14,245,1332	yes	missense	SPDYE4	NM_001128076.1	64	15,262,2006	AA,AG,GG		8.5795,1.3728,6.3951	possibly-damaging	141/238	8658901	292,4274	692	1591	2283	SO:0001583	missense	388333	exon4			AAATACGCTATGA	BC146949	CCDS45609.1	17p13.1	2013-05-08	2013-05-08			ENSG00000183318		"""Speedy homologs"""	35463	protein-coding gene	gene with protein product			"""speedy homolog E4 (Xenopus laevis)"""				Standard	NM_001128076		Approved		uc010cnz.1	A6NLX3		ENST00000328794.6:c.422C>T	17.37:g.8658901G>A	ENSP00000329522:p.Ala141Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	97	36	0.371134	NM_001128076	B2RUZ6	Missense_Mutation	SNP	ENST00000328794.6	37	CCDS45609.1	90	0.04120879120879121	1	0.0020325203252032522	25	0.06906077348066299	0	0.0	64	0.08443271767810026	G	9.440	1.087856	0.20390	0.013728	0.085795	ENSG00000183318	ENST00000328794	.	.	.	2.98	2.98	0.34508	.	0.000000	0.64402	D	0.000014	T	0.01387	0.0045	L	0.45422	1.42	0.47819	P	4.769999999999497E-4	P	0.40931	0.733	B	0.38712	0.28	T	0.11108	-1.0601	8	0.15952	T	0.53	.	9.5264	0.39167	0.0:0.0:1.0:0.0	.	141	A6NLX3	SPDE4_HUMAN	V	141	.	ENSP00000329522:A141V	A	-	2	0	SPDYE4	8599626	0.002000	0.14202	0.209000	0.23619	0.006000	0.05464	0.068000	0.14531	1.663000	0.50791	0.411000	0.27672	GCG	G|0.952;A|0.048	0.048	strong		0.483	SPDYE4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442494.1	NM_001128076	
RGPD3	653489	hgsc.bcm.edu	37	2	107040572	107040572	+	Missense_Mutation	SNP	T	T	C	rs3870235		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:107040572T>C	ENST00000409886.3	-	20	3938	c.3851A>G	c.(3850-3852)cAc>cGc	p.H1284R	RGPD3_ENST00000304514.7_Missense_Mutation_p.H1284R	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	1284					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						CTCATCAAAGTGGAAAAGATT	0.403																																					p.H1284R		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,0,4	RGPD3	316	4	0			c.A3851G						scavenged	.						183.0	135.0	149.0					2																	107040572		659	1516	2175	SO:0001583	missense	653489	exon20			TCAAAGTGGAAAA		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.3851A>G	2.37:g.107040572T>C	ENSP00000386588:p.His1284Arg	Somatic	969	1	0.00103199		WXS	Illumina HiSeq	Phase_I	186	175	0.94086	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.926314	0.00054	.	.	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.34859	1.34;1.34	2.35	2.35	0.29111	.	.	.	.	.	T	0.10723	0.0262	N	0.00926	-1.1	0.45261	P	0.0017359999999999598	B	0.02656	0.0	B	0.01281	0.0	T	0.30937	-0.9961	8	0.10636	T	0.68	-3.2817	7.1563	0.25639	0.0:0.8506:0.0:0.1494	.	1284	A6NKT7	RGPD3_HUMAN	R	1284	ENSP00000386588:H1284R;ENSP00000303659:H1284R	ENSP00000303659:H1284R	H	-	2	0	RGPD3	106407004	1.000000	0.71417	0.999000	0.59377	0.042000	0.13812	4.693000	0.61753	0.328000	0.23435	-1.128000	0.01989	CAC	.	.	weak		0.403	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
AGAP1	116987	hgsc.bcm.edu	37	2	236708166	236708166	+	Splice_Site	SNP	C	C	T	rs2292708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:236708166C>T	ENST00000304032.8	+	8	1537	c.957C>T	c.(955-957)acC>acT	p.T319T	AGAP1_ENST00000336665.5_Splice_Site_p.T319T|AGAP1_ENST00000409538.1_Splice_Site_p.T584T|AGAP1_ENST00000428334.2_Splice_Site_p.T158T|AGAP1_ENST00000409457.1_Splice_Site_p.T319T	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	319					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)	p.T319T(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ACCTGTTCACCGTGAGTGTCA	0.542													C|||	960	0.191693	0.0295	0.4063	5008	,	,		18911	0.2708		0.2624	False		,,,				2504	0.1043				p.T319T		Atlas-SNP	.											AGAP1,NS,carcinoma,0,1	AGAP1	95	1	1	Substitution - coding silent(1)	prostate(1)	c.C957T						PASS	.	C	,	293,4113	159.6+/-192.1	14,265,1924	94.0	79.0	84.0		957,957	-2.0	1.0	2	dbSNP_100	84	2504,6096	412.1+/-350.7	374,1756,2170	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	AGAP1	NM_001037131.2,NM_014914.4	,	388,2021,4094	TT,TC,CC		29.1163,6.65,21.5055	,	319/858,319/805	236708166	2797,10209	2203	4300	6503	SO:0001630	splice_region_variant	116987	exon8			GTTCACCGTGAGT	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.957+1C>T	2.37:g.236708166C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Silent	SNP	ENST00000304032.8	37	CCDS33408.1																																																																																			C|0.787;T|0.213	0.213	strong		0.542	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	Silent
TMEM132E	124842	hgsc.bcm.edu	37	17	32957114	32957114	+	Missense_Mutation	SNP	G	G	A	rs56879769	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:32957114G>A	ENST00000321639.5	+	6	1484	c.1156G>A	c.(1156-1158)Gtc>Atc	p.V386I		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	386						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		GAATGGCCTCGTCCTGGACAT	0.587													G|||	194	0.038738	0.1021	0.0245	5008	,	,		19643	0.0		0.0358	False		,,,				2504	0.0061				p.V386I		Atlas-SNP	.											.	TMEM132E	122	.	0			c.G1156A						PASS	.	G	ILE/VAL	404,4002	200.4+/-223.7	20,364,1819	116.0	80.0	92.0		1156	5.0	1.0	17	dbSNP_129	92	273,8327	104.4+/-165.4	2,269,4029	yes	missense	TMEM132E	NM_207313.1	29	22,633,5848	AA,AG,GG		3.1744,9.1693,5.2053	benign	386/985	32957114	677,12329	2203	4300	6503	SO:0001583	missense	124842	exon6			GGCCTCGTCCTGG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1156G>A	17.37:g.32957114G>A	ENSP00000316532:p.Val386Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	162	84	0.518519	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	87	0.03983516483516483	52	0.10569105691056911	9	0.024861878453038673	0	0.0	26	0.03430079155672823	G	13.73	2.323321	0.41096	0.091693	0.031744	ENSG00000181291	ENST00000321639	T	0.32988	1.43	4.99	4.99	0.66335	.	0.231610	0.43747	D	0.000540	T	0.00356	0.0011	N	0.25647	0.755	0.51233	D	0.999914	B	0.27416	0.178	B	0.19391	0.025	T	0.05484	-1.0882	10	0.48119	T	0.1	-46.4222	7.1501	0.25606	0.1805:0.0:0.8195:0.0	rs56879769	386	Q6IEE7	T132E_HUMAN	I	386	ENSP00000316532:V386I	ENSP00000316532:V386I	V	+	1	0	TMEM132E	29981227	0.991000	0.36638	0.990000	0.47175	0.552000	0.35366	2.169000	0.42434	2.757000	0.94681	0.643000	0.83706	GTC	G|0.952;A|0.048	0.048	strong		0.587	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
MUC4	4585	hgsc.bcm.edu	37	3	195506627	195506627	+	Missense_Mutation	SNP	T	T	G	rs145875920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506627T>G	ENST00000463781.3	-	2	12283	c.11824A>C	c.(11824-11826)Act>Cct	p.T3942P	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3942P	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.T3942P(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGTGCTGGTGACA	0.582													.|||	144	0.028754	0.0658	0.0115	5008	,	,		10596	0.0179		0.0189	False		,,,				2504	0.0123				p.T3942P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	2	Substitution - Missense(2)	kidney(2)	c.A11824C						scavenged	.						16.0	15.0	15.0					3																	195506627		575	1239	1814	SO:0001583	missense	4585	exon2			AGGAAGTGCTGGT	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.11824A>C	3.37:g.195506627T>G	ENSP00000417498:p.Thr3942Pro	Somatic	23	8	0.347826		WXS	Illumina HiSeq	Phase_I	131	21	0.160305	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	418	0.19139194139194138	95	0.19308943089430894	73	0.20165745856353592	134	0.23426573426573427	116	0.15303430079155672	N	5.184	0.219525	0.09863	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35048	1.33;1.42	.	.	.	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.19945	N	0.999946	B	0.25521	0.128	B	0.28638	0.092	T	0.36456	-0.9747	7	.	.	.	.	2.6735	0.05075	0.0:0.409:0.0:0.591	.	3814	E7ESK3	.	P	3942	ENSP00000417498:T3942P;ENSP00000420243:T3942P	.	T	-	1	0	MUC4	196991406	0.000000	0.05858	0.044000	0.18714	0.027000	0.11550	-2.555000	0.00925	0.348000	0.23949	0.055000	0.15244	ACT	T|0.808;G|0.192	0.192	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CNOT6	57472	hgsc.bcm.edu	37	5	179996111	179996111	+	Splice_Site	SNP	C	C	T	rs6877400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179996111C>T	ENST00000393356.1	+	12	1453	c.1029C>T	c.(1027-1029)tcC>tcT	p.S343S	CNOT6_ENST00000261951.4_Splice_Site_p.S343S			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	343	Nuclease domain. {ECO:0000250}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		CTAATGTAGCCGGAAAGCCAC	0.418																																					p.S343S		Atlas-SNP	.											.	CNOT6	47	.	0			c.C1029T						PASS	.	T		3405,1001	369.5+/-319.1	1312,781,110	48.0	48.0	48.0		1029	-4.0	0.8	5	dbSNP_116	48	7696,904	200.6+/-244.3	3430,836,34	yes	coding-synonymous-near-splice	CNOT6	NM_015455.3		4742,1617,144	TT,TC,CC		10.5116,22.719,14.6471		343/558	179996111	11101,1905	2203	4300	6503	SO:0001630	splice_region_variant	57472	exon10			TGTAGCCGGAAAG	AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.1028-1C>T	5.37:g.179996111C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_015455	A7MD46|D3DWR0	Silent	SNP	ENST00000393356.1	37	CCDS4455.1																																																																																			C|0.128;T|0.872	0.872	strong		0.418	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1	NM_015455	Silent
TTC21B	79809	hgsc.bcm.edu	37	2	166773971	166773971	+	Silent	SNP	G	G	A	rs6750044	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:166773971G>A	ENST00000243344.7	-	14	1832	c.1695C>T	c.(1693-1695)taC>taT	p.Y565Y		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	565					forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						TTATCAAATGGTATAAAGGAT	0.313													A|||	1461	0.291733	0.3094	0.2291	5008	,	,		17512	0.2014		0.3668	False		,,,				2504	0.3282				p.Y565Y		Atlas-SNP	.											.	TTC21B	130	.	0			c.C1695T						PASS	.	A		1353,3053	688.4+/-405.0	210,933,1060	125.0	120.0	121.0		1695	3.5	1.0	2	dbSNP_116	121	3345,5253	642.6+/-399.8	636,2073,1590	no	coding-synonymous	TTC21B	NM_024753.3		846,3006,2650	AA,AG,GG		38.9044,30.7081,36.1273		565/1317	166773971	4698,8306	2203	4299	6502	SO:0001819	synonymous_variant	79809	exon14			CAAATGGTATAAA	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.1695C>T	2.37:g.166773971G>A		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	155	78	0.503226	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	37	CCDS33315.1																																																																																			G|0.668;A|0.332	0.332	strong		0.313	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
KTN1	3895	hgsc.bcm.edu	37	14	56096731	56096731	+	Silent	SNP	A	A	G	rs2274075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:56096731A>G	ENST00000395314.3	+	7	1205	c.1137A>G	c.(1135-1137)cgA>cgG	p.R379R	KTN1_ENST00000438792.2_Silent_p.R379R|KTN1_ENST00000395309.3_Silent_p.R379R|KTN1_ENST00000395311.1_Silent_p.R379R|KTN1_ENST00000413890.2_Silent_p.R379R|KTN1_ENST00000395308.1_Silent_p.R379R|KTN1_ENST00000416613.1_Silent_p.R379R	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	379					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						TGAAAGATCGAATTGGAACAT	0.289			T	RET	papillary thryoid								G|||	305	0.0609026	0.0484	0.072	5008	,	,		21066	0.0159		0.0626	False		,,,				2504	0.1145				p.R379R		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	KTN1_ENST00000416613,NS,carcinoma,+1,1	KTN1	147	1	0			c.A1137G						PASS	.	G	,,,	266,4140	800.9+/-415.6	8,250,1945	122.0	122.0	122.0		1137,1137,1137,1137	-0.8	1.0	14	dbSNP_100	122	845,7755	779.1+/-407.7	43,759,3498	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	51,1009,5443	GG,GA,AA		9.8256,6.0372,8.5422	,,,	379/1358,379/1307,379/1301,379/1358	56096731	1111,11895	2203	4300	6503	SO:0001819	synonymous_variant	3895	exon7			AGATCGAATTGGA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.1137A>G	14.37:g.56096731A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	141	70	0.496454	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																			A|0.925;G|0.075	0.075	strong		0.289	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
AK4	205	hgsc.bcm.edu	37	1	65690461	65690461	+	Silent	SNP	G	G	A	rs4915685	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:65690461G>A	ENST00000327299.7	+	4	670	c.465G>A	c.(463-465)ccG>ccA	p.P155P	AK4_ENST00000470888.2_3'UTR|AK4_ENST00000546702.1_Silent_p.P103P|AK4_ENST00000395334.2_Silent_p.P155P|AK4_ENST00000545314.1_Silent_p.P155P	NM_013410.3	NP_037542.1			adenylate kinase 4											breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	9						CTGGTGAACCGTTAGTCCAGC	0.413													A|||	1853	0.370008	0.3298	0.3314	5008	,	,		20813	0.6726		0.1769	False		,,,				2504	0.3384				p.P155P		Atlas-SNP	.											.	AK4	22	.	0			c.G465A						PASS	.	A	,,	1379,3027	689.8+/-405.2	220,939,1044	134.0	130.0	131.0		465,465,465	-9.7	0.0	1	dbSNP_111	131	1801,6799	732.9+/-406.9	187,1427,2686	no	coding-synonymous,coding-synonymous,coding-synonymous	AK4	NM_001005353.2,NM_013410.3,NM_203464.2	,,	407,2366,3730	AA,AG,GG		20.9419,31.2982,24.4503	,,	155/224,155/224,155/224	65690461	3180,9826	2203	4300	6503	SO:0001819	synonymous_variant	205	exon5			TGAACCGTTAGTC	AK025926	CCDS629.1	1p31.3	2012-10-02	2010-06-15	2010-06-15	ENSG00000162433	ENSG00000162433	2.7.4.3	"""Adenylate kinases"""	363	protein-coding gene	gene with protein product		103030	"""adenylate kinase 3"", ""adenylate kinase 3-like 1"""	AK3, AK3L1		11485571	Standard	NM_203464		Approved		uc001dby.3	P27144	OTTHUMG00000009033	ENST00000327299.7:c.465G>A	1.37:g.65690461G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	144	73	0.506944	NM_203464		Silent	SNP	ENST00000327299.7	37	CCDS629.1																																																																																			G|0.726;A|0.274	0.274	strong		0.413	AK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025040.2	NM_013410	
DUXA	503835	hgsc.bcm.edu	37	19	57669827	57669827	+	Missense_Mutation	SNP	G	G	A	rs140589597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57669827G>A	ENST00000554048.2	-	4	306	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W		NM_001012729.1	NP_001012747.1	A6NLW8	DUXA_HUMAN	double homeobox A	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)		GTACGACACCGTCTGGCTTCT	0.468																																					p.R103W		Atlas-SNP	.											DUXA,NS,carcinoma,+1,3	DUXA	46	3	0			c.C307T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	64.0	64.0	64.0		307	2.8	0.1	19	dbSNP_134	64	6,8594	4.3+/-15.6	0,6,4294	yes	missense	DUXA	NM_001012729.1	101	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	probably-damaging	103/205	57669827	6,13000	2203	4300	6503	SO:0001583	missense	503835	exon4			GACACCGTCTGGC		CCDS33126.1	19q13.43	2012-10-04			ENSG00000258873	ENSG00000258873		"""Homeoboxes / PRD class"""	32179	protein-coding gene	gene with protein product		611168					Standard	NM_001012729		Approved		uc002qoa.1	A6NLW8	OTTHUMG00000170714	ENST00000554048.2:c.307C>T	19.37:g.57669827G>A	ENSP00000452398:p.Arg103Trp	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_001012729		Missense_Mutation	SNP	ENST00000554048.2	37	CCDS33126.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.593578	0.46214	0.0	6.98E-4	ENSG00000258873	ENST00000554048	D	0.96940	-4.18	2.85	2.85	0.33270	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.281548	0.19295	N	0.117793	D	0.98213	0.9409	M	0.93507	3.425	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92627	0.6113	10	0.87932	D	0	-12.0051	9.41	0.38485	0.0:0.0:1.0:0.0	.	103	A6NLW8	DUXA_HUMAN	W	103	ENSP00000452398:R103W	ENSP00000365415:R103W	R	-	1	2	DUXA	62361639	0.030000	0.19436	0.064000	0.19789	0.033000	0.12548	0.925000	0.28791	1.900000	0.55004	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.468	DUXA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410075.3	NM_001012729	
BRCA2	675	hgsc.bcm.edu	37	13	32912299	32912299	+	Silent	SNP	T	T	C	rs543304	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32912299T>C	ENST00000380152.3	+	11	4040	c.3807T>C	c.(3805-3807)gtT>gtC	p.V1269V	BRCA2_ENST00000544455.1_Silent_p.V1269V			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1269					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		ATGATTCTGTTGTTTCAATGT	0.274			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)			T|||	842	0.168131	0.1846	0.1527	5008	,	,		19007	0.1726		0.1998	False		,,,				2504	0.1196				p.V1269V	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.T3807C						PASS	.	T		874,3532	313.0+/-292.9	86,702,1415	27.0	28.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3807	1.6	0.0	13	dbSNP_83	28	1610,6982	278.0+/-293.2	150,1310,2836	no	coding-synonymous	BRCA2	NM_000059.3		236,2012,4251	CC,CT,TT		18.7384,19.8366,19.1106		1269/3419	32912299	2484,10514	2203	4296	6499	SO:0001819	synonymous_variant	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	TTCTGTTGTTTCA	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.3807T>C	13.37:g.32912299T>C		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	55	27	0.490909	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			C|0.187;N|0.000;T|0.813	0.187	strong		0.274	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
MYOM1	8736	hgsc.bcm.edu	37	18	3176063	3176063	+	Silent	SNP	C	C	T	rs2230162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:3176063C>T	ENST00000356443.4	-	6	1332	c.999G>A	c.(997-999)ggG>ggA	p.G333G	MYOM1_ENST00000400569.3_Silent_p.G333G|MYOM1_ENST00000261606.7_Silent_p.G333G	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	333	Ig-like C2-type 1.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						GAGTGTGCATCCCATATCGAC	0.423													T|||	1368	0.273163	0.2436	0.2161	5008	,	,		22191	0.2659		0.3062	False		,,,				2504	0.3272				p.G333G		Atlas-SNP	.											.	MYOM1	192	.	0			c.G999A						PASS	.	T	,	1005,2911		130,745,1083	106.0	104.0	104.0		999,999	4.7	1.0	18	dbSNP_98	104	2585,5711		409,1767,1972	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	539,2512,3055	TT,TC,CC		31.1596,25.6639,29.3973	,	333/1686,333/1590	3176063	3590,8622	1958	4148	6106	SO:0001819	synonymous_variant	8736	exon6			GTGCATCCCATAT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.999G>A	18.37:g.3176063C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	115	115	1	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.164;G|0.282	0.164	strong		0.423	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
SLC22A18	5002	hgsc.bcm.edu	37	11	2929502	2929502	+	Missense_Mutation	SNP	G	G	T	rs143044180	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2929502G>T	ENST00000380574.1	+	3	615	c.184G>T	c.(184-186)Ggc>Tgc	p.G62C	SLC22A18_ENST00000347936.2_Missense_Mutation_p.G62C|SLC22A18_ENST00000312221.5_Missense_Mutation_p.G62C|SLC22A18_ENST00000449793.2_Missense_Mutation_p.G62C			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	62					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		CATTGCCTTCGGCTACCTGCA	0.617													G|||	5	0.000998403	0.0	0.0029	5008	,	,		15811	0.0		0.002	False		,,,				2504	0.001				p.G62C		Atlas-SNP	.											SLC22A18,NS,carcinoma,0,1	SLC22A18	20	1	0			c.G184T						PASS	.	G	CYS/GLY,CYS/GLY	2,4402	4.2+/-10.8	0,2,2200	86.0	82.0	84.0		184,184	3.3	0.9	11	dbSNP_134	84	33,8565	22.8+/-68.1	0,33,4266	yes	missense,missense	SLC22A18	NM_002555.5,NM_183233.2	159,159	0,35,6466	TT,TG,GG		0.3838,0.0454,0.2692	probably-damaging,probably-damaging	62/425,62/425	2929502	35,12967	2202	4299	6501	SO:0001583	missense	5002	exon3			GCCTTCGGCTACC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"""Solute carriers"""	10964	protein-coding gene	gene with protein product		602631	"""solute carrier family 22 (organic cation transporter), member 1-like"""	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.184G>T	11.37:g.2929502G>T	ENSP00000369948:p.Gly62Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	81	45	0.555556	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.97	2.395838	0.42512	4.54E-4	0.003838	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;D	0.86097	-0.21;-0.21;-0.21;-0.21;-2.07	4.27	3.34	0.38264	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	D	0.90861	0.7129	M	0.83953	2.67	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.986;1.0	D	0.90662	0.4591	10	0.87932	D	0	-1.8758	7.3817	0.26859	0.1199:0.0:0.8801:0.0	.	62;62	E9PRM7;Q96BI1	.;S22AI_HUMAN	C	62	ENSP00000307859:G62C;ENSP00000311139:G62C;ENSP00000392072:G62C;ENSP00000369948:G62C;ENSP00000433019:G62C	ENSP00000311139:G62C	G	+	1	0	SLC22A18	2886078	1.000000	0.71417	0.933000	0.37362	0.037000	0.13140	2.882000	0.48546	2.105000	0.64084	0.491000	0.48974	GGC	G|0.998;T|0.002	0.002	strong		0.617	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
UBB	7314	hgsc.bcm.edu	37	17	16285611	16285611	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:16285611C>T	ENST00000395837.1	+	2	571	c.390C>T	c.(388-390)cgC>cgT	p.R130R	UBB_ENST00000302182.3_Silent_p.R130R|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000578649.1_Intron|UBB_ENST00000535788.1_Intron|UBB_ENST00000395839.1_Silent_p.R130R	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	130	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AAGATGGCCGCACTCTTTCTG	0.542																																					p.R130R	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,rectum,carcinoma,+2,2	UBB	30	2	0			c.C390T						scavenged	.																																			SO:0001819	synonymous_variant	7314	exon2			TGGCCGCACTCTT		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.390C>T	17.37:g.16285611C>T		Somatic	125	2	0.016		WXS	Illumina HiSeq	Phase_I	126	4	0.031746	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			.	.	none		0.542	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
MTUS2	23281	hgsc.bcm.edu	37	13	29675049	29675049	+	Silent	SNP	A	A	T	rs140464903	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:29675049A>T	ENST00000431530.3	+	3	2674	c.2616A>T	c.(2614-2616)tcA>tcT	p.S872S		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	862	Localization to the growing distal tip of microtubules.|Mediates interaction with MAPRE1.|Sufficient for interaction with KIF2C.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GCGTCTCCTCAGTCTCCAGCA	0.632													A|||	114	0.0227636	0.0053	0.0259	5008	,	,		12307	0.002		0.0596	False		,,,				2504	0.0276				p.S872S		Atlas-SNP	.											MTUS2_ENST00000431530,NS,carcinoma,0,1	MTUS2	279	1	0			c.A2616T						PASS	.	A		41,4015		1,39,1988	8.0	9.0	9.0		2616	-10.5	0.0	13	dbSNP_134	9	361,8001		4,353,3824	no	coding-synonymous	MTUS2	NM_001033602.2		5,392,5812	TT,TA,AA		4.3171,1.0108,3.2372		872/1380	29675049	402,12016	2028	4181	6209	SO:0001819	synonymous_variant	23281	exon3			CTCCTCAGTCTCC	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2616A>T	13.37:g.29675049A>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000431530.3	37	CCDS45022.1																																																																																			A|0.965;T|0.035	0.035	strong		0.632	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
FGD6	55785	hgsc.bcm.edu	37	12	95602805	95602805	+	Missense_Mutation	SNP	C	C	A	rs117209224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:95602805C>A	ENST00000343958.4	-	2	2478	c.2255G>T	c.(2254-2256)cGc>cTc	p.R752L	FGD6_ENST00000546711.1_Missense_Mutation_p.R752L|FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.R752L	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	752					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CTCATAATGGCGTATATTTTC	0.458													C|||	24	0.00479233	0.0015	0.0115	5008	,	,		21324	0.0		0.0139	False		,,,				2504	0.0				p.R752L		Atlas-SNP	.											.	FGD6	127	.	0			c.G2255T						PASS	.	C	LEU/ARG	9,4397	15.5+/-35.6	0,9,2194	125.0	115.0	119.0		2255	4.8	0.9	12	dbSNP_132	119	94,8506	53.6+/-114.3	0,94,4206	yes	missense	FGD6	NM_018351.3	102	0,103,6400	AA,AC,CC		1.093,0.2043,0.7919	possibly-damaging	752/1431	95602805	103,12903	2203	4300	6503	SO:0001583	missense	55785	exon2			TAATGGCGTATAT	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.2255G>T	12.37:g.95602805C>A	ENSP00000344446:p.Arg752Leu	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	175	78	0.445714	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	CCDS31878.1	14	0.00641025641025641	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	13.21	2.168732	0.38315	0.002043	0.01093	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.69040	-0.27;-0.37;-0.3	5.77	4.79	0.61399	.	0.561745	0.16360	N	0.217829	T	0.53417	0.1795	M	0.62723	1.935	0.19300	N	0.999978	P	0.36616	0.561	B	0.29524	0.103	T	0.51172	-0.8739	10	0.39692	T	0.17	0.0757	14.3749	0.66867	0.0:0.9243:0.0:0.0757	.	752	Q6ZV73	FGD6_HUMAN	L	752	ENSP00000344446:R752L;ENSP00000450342:R752L;ENSP00000449005:R752L	ENSP00000344446:R752L	R	-	2	0	FGD6	94126936	0.160000	0.22878	0.871000	0.34182	0.985000	0.73830	1.317000	0.33631	1.280000	0.44463	0.561000	0.74099	CGC	C|0.993;A|0.007	0.007	strong		0.458	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42832683	42832683	+	Silent	SNP	G	G	A	rs10456519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42832683G>A	ENST00000314073.5	+	13	2915	c.2739G>A	c.(2737-2739)caG>caA	p.Q913Q	GLTSCR1L_ENST00000394168.1_Silent_p.Q913Q			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	913																	GCTTAGTGCAGTACCAGAGCA	0.517													G|||	36	0.0071885	0.0053	0.0101	5008	,	,		19729	0.001		0.0129	False		,,,				2504	0.0082				p.Q913Q		Atlas-SNP	.											.	.	.	.	0			c.G2739A						PASS	.	G		30,4376	36.8+/-68.6	0,30,2173	51.0	50.0	50.0		2739	-3.0	0.1	6	dbSNP_119	50	96,8504	52.7+/-113.3	3,90,4207	no	coding-synonymous	KIAA0240	NM_015349.1		3,120,6380	AA,AG,GG		1.1163,0.6809,0.9688		913/1080	42832683	126,12880	2203	4300	6503	SO:0001819	synonymous_variant	23506	exon12			AGTGCAGTACCAG	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"""KIAA0240"""	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.2739G>A	6.37:g.42832683G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	37	CCDS34451.1																																																																																			G|0.989;A|0.011	0.011	strong		0.517	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	
N4BP2	55728	hgsc.bcm.edu	37	4	40119501	40119501	+	Silent	SNP	T	T	C	rs1128372	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:40119501T>C	ENST00000261435.6	+	8	2093	c.1677T>C	c.(1675-1677)caT>caC	p.H559H		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	559					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						GTAACATTCATGGGGTAAGCA	0.313													T|||	569	0.113618	0.0106	0.255	5008	,	,		15891	0.0208		0.2207	False		,,,				2504	0.138				p.H559H		Atlas-SNP	.											.	N4BP2	166	.	0			c.T1677C						PASS	.	T		214,4192	129.4+/-166.1	10,194,1999	79.0	74.0	76.0		1677	4.1	1.0	4	dbSNP_86	76	1982,6618	345.4+/-325.7	235,1512,2553	no	coding-synonymous	N4BP2	NM_018177.4		245,1706,4552	CC,CT,TT		23.0465,4.857,16.8845		559/1771	40119501	2196,10810	2203	4300	6503	SO:0001819	synonymous_variant	55728	exon8			CATTCATGGGGTA	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.1677T>C	4.37:g.40119501T>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Silent	SNP	ENST00000261435.6	37	CCDS3457.1	286	0.13095238095238096	6	0.012195121951219513	97	0.26795580110497236	10	0.017482517482517484	173	0.22823218997361477	T	5.040	0.193016	0.09599	0.04857	0.230465	ENSG00000078177	ENST00000513269	.	.	.	5.3	4.11	0.48088	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999999	.	.	.	.	.	.	T	0.02081	-1.1217	3	.	.	.	-15.8173	12.6937	0.56990	0.0:0.0716:0.0:0.9284	rs1128372;rs16995561;rs17439970;rs1128372	.	.	.	R	206	.	.	W	+	1	0	N4BP2	39795896	1.000000	0.71417	0.998000	0.56505	0.740000	0.42216	2.177000	0.42509	0.322000	0.23283	-1.139000	0.01908	TGG	T|0.851;C|0.149	0.149	strong		0.313	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
ACTN4	81	hgsc.bcm.edu	37	19	39219780	39219780	+	Silent	SNP	T	T	C	rs1136956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39219780T>C	ENST00000252699.2	+	20	2639	c.2563T>C	c.(2563-2565)Tta>Cta	p.L855L	ACTN4_ENST00000497637.1_3'UTR|ACTN4_ENST00000424234.2_Silent_p.L465L|ACTN4_ENST00000390009.3_Silent_p.L636L	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	855	Mediates interaction with MICALL2. {ECO:0000250}.				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)			CTTCAAGGTCTTAGCAGGGGA	0.637													C|||	939	0.1875	0.1271	0.2378	5008	,	,		14127	0.0565		0.2913	False		,,,				2504	0.2618				p.L855L	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.T2563C						PASS	.	C		614,3792	766.5+/-413.4	46,522,1635	81.0	72.0	75.0		2563	2.6	1.0	19	dbSNP_86	75	2166,6434	709.9+/-405.7	283,1600,2417	no	coding-synonymous	ACTN4	NM_004924.4		329,2122,4052	CC,CT,TT		25.186,13.9355,21.3748		855/912	39219780	2780,10226	2203	4300	6503	SO:0001819	synonymous_variant	81	exon20			AAGGTCTTAGCAG	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.2563T>C	19.37:g.39219780T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_004924	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	37	CCDS12518.1																																																																																			T|0.788;C|0.212	0.212	strong		0.637	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
C10orf71	118461	hgsc.bcm.edu	37	10	50533841	50533841	+	Missense_Mutation	SNP	G	G	C	rs11101094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50533841G>C	ENST00000374144.3	+	3	3539	c.3251G>C	c.(3250-3252)gGa>gCa	p.G1084A	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1084			G -> A (in dbSNP:rs11101094).							endometrium(1)	1						CAGGCCCCTGGAGGACCAGAG	0.677													G|||	479	0.095647	0.053	0.0663	5008	,	,		14063	0.122		0.1203	False		,,,				2504	0.1217				p.G1084A		Atlas-SNP	.											.	C10orf71	179	.	0			c.G3251C						PASS	.						9.0	13.0	12.0					10																	50533841		689	1588	2277	SO:0001583	missense	118461	exon3			CCCCTGGAGGACC	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.3251G>C	10.37:g.50533841G>C	ENSP00000363259:p.Gly1084Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	69	33	0.478261	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	211	0.09661172161172162	32	0.06504065040650407	30	0.08287292817679558	60	0.1048951048951049	89	0.11741424802110818	G	0.004	-2.326711	0.00229	.	.	ENSG00000177354	ENST00000374144	T	0.04317	3.65	5.22	0.808	0.18719	.	0.766268	0.10833	N	0.629157	T	0.00039	0.0001	N	0.19112	0.55	0.80722	P	0.0	.	.	.	.	.	.	T	0.43032	-0.9416	7	0.07175	T	0.84	.	3.9484	0.09358	0.1554:0.122:0.5817:0.1409	rs11101094;rs11101094	.	.	.	A	1084	ENSP00000363259:G1084A	ENSP00000363259:G1084A	G	+	2	0	C10orf71	50203847	0.000000	0.05858	0.007000	0.13788	0.009000	0.06853	0.581000	0.23819	0.593000	0.29745	0.313000	0.20887	GGA	G|0.907;C|0.093	0.093	strong		0.677	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
PTBP1	5725	hgsc.bcm.edu	37	19	808577	808577	+	Silent	SNP	C	C	T	rs148751202	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:808577C>T	ENST00000349038.4	+	12	1273	c.1200C>T	c.(1198-1200)caC>caT	p.H400H	PTBP1_ENST00000356948.6_Silent_p.H426H|PTBP1_ENST00000394601.4_Silent_p.H419H|PTBP1_ENST00000350092.4_Silent_p.H66H	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	400	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACAAGCTGCACGGGAAGCCCA	0.697													C|||	69	0.013778	0.0008	0.0403	5008	,	,		9341	0.0119		0.0159	False		,,,				2504	0.0123				p.H426H		Atlas-SNP	.											.	PTBP1	43	.	0			c.C1278T						PASS	.	C	,,,	14,4370		0,14,2178	33.0	25.0	28.0		1278,1257,1200,198	-6.9	0.9	19	dbSNP_134	28	126,8468		0,126,4171	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTBP1	NM_002819.4,NM_031990.3,NM_031991.3,NM_175847.2	,,,	0,140,6349	TT,TC,CC		1.4661,0.3193,1.0787	,,,	426/558,419/551,400/532,66/198	808577	140,12838	2192	4297	6489	SO:0001819	synonymous_variant	5725	exon13			GCTGCACGGGAAG	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.1200C>T	19.37:g.808577C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_002819	Q9BUQ0	Silent	SNP	ENST00000349038.4	37	CCDS32859.1																																																																																			C|0.988;T|0.012	0.012	strong		0.697	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
FKBP15	23307	hgsc.bcm.edu	37	9	115933980	115933980	+	Missense_Mutation	SNP	C	C	A	rs1128116|rs386737766	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115933980C>A	ENST00000238256.3	-	24	2656	c.2539G>T	c.(2539-2541)Gcc>Tcc	p.A847S		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	847			A -> S (in dbSNP:rs1128116).		endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GCCTGGAGGGCTAAACACTGC	0.502													C|||	399	0.0796725	0.0991	0.0389	5008	,	,		11879	0.0387		0.0477	False		,,,				2504	0.1575				p.A847S		Atlas-SNP	.											.	FKBP15	128	.	0			c.G2539T						PASS	.	C	SER/ALA	387,3373		14,359,1507	80.0	82.0	81.0		2539	4.7	0.8	9	dbSNP_86	81	511,7709		15,481,3614	yes	missense	FKBP15	NM_015258.1	99	29,840,5121	AA,AC,CC		6.2165,10.2926,7.4958	probably-damaging	847/1220	115933980	898,11082	1880	4110	5990	SO:0001583	missense	23307	exon24			GGAGGGCTAAACA	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.2539G>T	9.37:g.115933980C>A	ENSP00000238256:p.Ala847Ser	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	115	0.052655677655677656	54	0.10975609756097561	15	0.04143646408839779	11	0.019230769230769232	35	0.04617414248021108	C	21.1	4.099307	0.76983	0.102926	0.062165	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.25749	1.78;1.79	5.62	4.71	0.59529	.	.	.	.	.	T	0.00784	0.0026	L	0.41824	1.3	0.22880	N	0.998611	D;D	0.69078	0.997;0.996	D;P	0.64042	0.921;0.787	T	0.01124	-1.1444	9	0.33141	T	0.24	-11.7822	11.9909	0.53173	0.1729:0.8271:0.0:0.0	rs1128116;rs3184696;rs17405802	428;847	B4DVS2;Q5T1M5	.;FKB15_HUMAN	S	872;847	ENSP00000416158:A872S;ENSP00000238256:A847S	ENSP00000238256:A847S	A	-	1	0	FKBP15	114973801	0.966000	0.33281	0.809000	0.32408	0.922000	0.55478	2.091000	0.41691	1.348000	0.45733	0.655000	0.94253	GCC	C|0.940;A|0.060	0.060	strong		0.502	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
CHRNA5	1138	hgsc.bcm.edu	37	15	78882925	78882925	+	Missense_Mutation	SNP	G	G	A	rs16969968	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78882925G>A	ENST00000299565.5	+	5	1392	c.1192G>A	c.(1192-1194)Gat>Aat	p.D398N	CHRNA5_ENST00000559554.1_Intron|RP11-650L12.2_ENST00000567141.1_RNA	NM_000745.3	NP_000736.2	P30532	ACHA5_HUMAN	cholinergic receptor, nicotinic, alpha 5 (neuronal)	398			D -> N (associated with susceptibility to lung cancer; dbSNP:rs16969968). {ECO:0000269|PubMed:8906617, ECO:0000269|Ref.4}.		behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|skin(3)	15					Galantamine(DB00674)|Nicotine(DB00184)	AGCTGCGCTCGATTCTATTCG	0.398													G|||	749	0.149561	0.0234	0.2089	5008	,	,		20833	0.0268		0.3658	False		,,,				2504	0.182				p.D398N		Atlas-SNP	.											.	CHRNA5	48	.	0			c.G1192A	GRCh37	CM081554	CHRNA5	M	rs16969968	PASS	.	G	ASN/ASP	274,4118	151.8+/-185.6	16,242,1938	71.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1192	3.9	0.0	15	dbSNP_123	69	2993,5593	459.1+/-364.8	550,1893,1850	yes	missense	CHRNA5	NM_000745.3	23	566,2135,3788	AA,AG,GG		34.8591,6.2386,25.1734	benign	398/469	78882925	3267,9711	2196	4293	6489	SO:0001583	missense	1138	exon5			GCGCTCGATTCTA		CCDS10304.1	15q24	2012-02-11	2012-02-07		ENSG00000169684	ENSG00000169684		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1959	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 5 (neuronal)"""	118505	"""cholinergic receptor, nicotinic, alpha polypeptide 5"""			2004777	Standard	NM_000745		Approved		uc002bdy.3	P30532	OTTHUMG00000143858	ENST00000299565.5:c.1192G>A	15.37:g.78882925G>A	ENSP00000299565:p.Asp398Asn	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	89	87	0.977528	NM_000745	Q15824|Q99554	Missense_Mutation	SNP	ENST00000299565.5	37	CCDS10304.1	383	0.17536630036630035	11	0.022357723577235773	85	0.23480662983425415	16	0.027972027972027972	271	0.3575197889182058	G	10.45	1.352305	0.24512	0.062386	0.348591	ENSG00000169684	ENST00000299565	T	0.69806	-0.43	4.79	3.88	0.44766	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.605324	0.18104	N	0.151590	T	0.00012	0.0000	L	0.60957	1.885	0.09310	P	1.0	B	0.20459	0.045	B	0.14578	0.011	T	0.15607	-1.0431	9	0.38643	T	0.18	.	10.8638	0.46842	0.1543:0.0:0.8457:0.0	rs16969968;rs17486705;rs52821477;rs16969968	398	P30532	ACHA5_HUMAN	N	398	ENSP00000299565:D398N	ENSP00000299565:D398N	D	+	1	0	CHRNA5	76669980	1.000000	0.71417	0.042000	0.18584	0.027000	0.11550	6.622000	0.74233	1.166000	0.42689	-0.229000	0.12294	GAT	G|0.771;A|0.229	0.229	strong		0.398	CHRNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290106.1		
ADCK1	57143	hgsc.bcm.edu	37	14	78374172	78374172	+	Silent	SNP	C	C	T	rs34272020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:78374172C>T	ENST00000238561.5	+	7	867	c.768C>T	c.(766-768)tcC>tcT	p.S256S	ADCK1_ENST00000341211.5_Silent_p.S188S	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	263	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(2)	25			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0376)		GGGACCTGTCCACGGAGCGGG	0.572													C|||	383	0.0764776	0.1014	0.0994	5008	,	,		21271	0.001		0.1322	False		,,,				2504	0.047				p.S256S		Atlas-SNP	.											.	ADCK1	81	.	0			c.C768T						PASS	.	C	,	531,3875	240.9+/-251.5	41,449,1713	83.0	70.0	74.0		564,768	1.9	1.0	14	dbSNP_126	74	992,7608	213.8+/-253.6	58,876,3366	no	coding-synonymous,coding-synonymous	ADCK1	NM_001142545.1,NM_020421.3	,	99,1325,5079	TT,TC,CC		11.5349,12.0517,11.71	,	188/456,256/524	78374172	1523,11483	2203	4300	6503	SO:0001819	synonymous_variant	57143	exon7			CCTGTCCACGGAG	AK096919	CCDS9869.1, CCDS45144.1	14q24	2005-10-30							19038	protein-coding gene	gene with protein product						12471243	Standard	NM_020421		Approved	FLJ39600	uc001xui.3	Q86TW2		ENST00000238561.5:c.768C>T	14.37:g.78374172C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Silent	SNP	ENST00000238561.5	37	CCDS9869.1																																																																																			C|0.893;T|0.107	0.107	strong		0.572	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421	
NSD1	64324	hgsc.bcm.edu	37	5	176721879	176721879	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176721879G>A	ENST00000439151.2	+	23	7555	c.7510G>A	c.(7510-7512)Gtt>Att	p.V2504I	NSD1_ENST00000354179.4_Missense_Mutation_p.V2235I|NSD1_ENST00000361032.4_Missense_Mutation_p.V2401I|NSD1_ENST00000347982.4_Missense_Mutation_p.V2235I	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2504					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		GCCGAGAGCTGTTGAGAAAGG	0.542			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.V2504I		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G7510A						PASS	.						125.0	121.0	123.0					5																	176721879		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AGAGCTGTTGAGA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7510G>A	5.37:g.176721879G>A	ENSP00000395929:p.Val2504Ile	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	42	17	0.404762	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	4.395	0.072998	0.08485	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93366	-3.11;-3.11;-3.11;-3.21	4.33	-0.92	0.10475	.	1.377650	0.04932	N	0.457076	D	0.84415	0.5467	N	0.14661	0.345	0.09310	N	1	B;B	0.23249	0.082;0.008	B;B	0.18561	0.022;0.006	T	0.71461	-0.4586	10	0.42905	T	0.14	.	2.489	0.04606	0.2231:0.3057:0.3602:0.111	.	2235;2504	Q96L73-2;Q96L73	.;NSD1_HUMAN	I	2235;2504;2235;2401	ENSP00000346111:V2235I;ENSP00000395929:V2504I;ENSP00000343209:V2235I;ENSP00000354310:V2401I	ENSP00000343209:V2235I	V	+	1	0	NSD1	176654485	0.000000	0.05858	0.008000	0.14137	0.469000	0.32828	-0.079000	0.11357	-0.438000	0.07232	0.462000	0.41574	GTT	.	.	none		0.542	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
CRAMP1L	57585	hgsc.bcm.edu	37	16	1706435	1706435	+	Silent	SNP	C	C	T	rs61739874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1706435C>T	ENST00000397412.3	+	10	1776	c.1677C>T	c.(1675-1677)gaC>gaT	p.D559D	CRAMP1L_ENST00000293925.5_Silent_p.D559D|CRAMP1L_ENST00000436138.3_Silent_p.D556D|LA16c-431H6.6_ENST00000454337.1_Intron|CRAMP1L_ENST00000262317.4_Intron			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	559						nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						CGCTTCTAGACCCCTTGCCCC	0.682													C|||	342	0.0682907	0.0083	0.1297	5008	,	,		15983	0.0		0.2058	False		,,,				2504	0.0348				p.D559D		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.C1677T						PASS	.	C		138,3844		1,136,1854	20.0	21.0	21.0		1677	2.9	1.0	16	dbSNP_129	21	1654,6526		187,1280,2623	no	coding-synonymous	CRAMP1L	NM_020825.3		188,1416,4477	TT,TC,CC		20.22,3.4656,14.7344		559/1270	1706435	1792,10370	1991	4090	6081	SO:0001819	synonymous_variant	57585	exon9			TCTAGACCCCTTG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.1677C>T	16.37:g.1706435C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	30	18	0.6	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			C|0.900;T|0.100	0.100	strong		0.682	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
ANO1	55107	hgsc.bcm.edu	37	11	69933891	69933891	+	Missense_Mutation	SNP	G	G	A	rs76718681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:69933891G>A	ENST00000355303.5	+	2	447	c.142G>A	c.(142-144)Gag>Aag	p.E48K	ANO1_ENST00000530676.1_5'UTR|ANO1_ENST00000398543.2_5'UTR|ANO1_ENST00000316296.5_Missense_Mutation_p.E20K|ANO1_ENST00000538023.1_Missense_Mutation_p.E48K	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	48					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CCCTGATGCCGAGTGCAAGTA	0.587													G|||	241	0.048123	0.0809	0.0432	5008	,	,		16531	0.0278		0.0457	False		,,,				2504	0.0307				p.E48K		Atlas-SNP	.											ANO1_ENST00000355303,NS,carcinoma,-2,2	ANO1	156	2	0			c.G142A						PASS	.	G	LYS/GLU	342,3830		17,308,1761	36.0	38.0	37.0		142	-4.0	0.4	11	dbSNP_131	37	419,8003		4,411,3796	yes	missense	ANO1	NM_018043.5	56	21,719,5557	AA,AG,GG		4.9751,8.1975,6.0426	benign	48/987	69933891	761,11833	2086	4211	6297	SO:0001583	missense	55107	exon2			GATGCCGAGTGCA	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.142G>A	11.37:g.69933891G>A	ENSP00000347454:p.Glu48Lys	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Missense_Mutation	SNP	ENST00000355303.5	37	CCDS44663.1	96	0.04395604395604396	31	0.06300813008130081	15	0.04143646408839779	11	0.019230769230769232	39	0.051451187335092345	G	6.646	0.487632	0.12641	0.081975	0.049751	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000531604;ENST00000316296	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	4.57	-3.99	0.04069	.	1.156430	0.06345	N	0.708854	T	0.01156	0.0038	L	0.48642	1.525	0.19300	N	0.99998	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25813	-1.0121	9	.	.	.	.	7.0704	0.25175	0.4248:0.1129:0.4624:0.0	.	20;48	Q5XXA6-3;Q5XXA6	.;ANO1_HUMAN	K	48;48;48;20	ENSP00000347454:E48K;ENSP00000444689:E48K;ENSP00000436392:E48K;ENSP00000319477:E20K	.	E	+	1	0	ANO1	69611539	0.005000	0.15991	0.369000	0.25952	0.465000	0.32709	-0.231000	0.09069	-0.471000	0.06891	-0.254000	0.11334	GAG	G|0.951;A|0.049	0.049	strong		0.587	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144857010	144857010	+	Missense_Mutation	SNP	T	T	C	rs3853916		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144857010T>C	ENST00000369354.3	-	40	6664	c.6475A>G	c.(6475-6477)Acc>Gcc	p.T2159A	RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T2295A|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.T2244A|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.T2159A|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T2053A			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2159					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.T2159A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTGGGAGGGGTCTTCATTACT	0.443			T	PDGFRB	MPD																																p.T2159A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP,NS,carcinoma,0,1	PDE4DIP	817	1	1	Substitution - Missense(1)	prostate(1)	c.A6475G						scavenged	.						76.0	72.0	74.0					1																	144857010		2203	4296	6499	SO:0001583	missense	9659	exon40			GAGGGGTCTTCAT	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.6475A>G	1.37:g.144857010T>C	ENSP00000358360:p.Thr2159Ala	Somatic	862	6	0.00696056		WXS	Illumina HiSeq	Phase_I	846	23	0.0271868	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	.	.	.	.	.	.	.	.	.	.	.	12.27	1.889088	0.33348	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01613	4.73;4.83;4.84;4.84;4.84	4.16	-0.82	0.10826	.	.	.	.	.	T	0.00637	0.0021	L	0.40543	1.245	0.09310	N	1	B;B	0.18461	0.015;0.028	B;B	0.12837	0.006;0.008	T	0.41893	-0.9483	9	0.49607	T	0.09	.	7.8317	0.29347	0.0:0.3889:0.0:0.6111	rs3853916;rs4067557	2053;2159	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	A	2053;2159;2159;2244;2295	ENSP00000327209:T2053A;ENSP00000358360:T2159A;ENSP00000358363:T2159A;ENSP00000435654:T2244A;ENSP00000358366:T2295A	ENSP00000327209:T2053A	T	-	1	0	PDE4DIP	143568367	0.002000	0.14202	0.005000	0.12908	0.631000	0.37964	-0.164000	0.09983	-0.097000	0.12307	0.369000	0.22263	ACC	.	.	weak		0.443	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
CPZ	8532	hgsc.bcm.edu	37	4	8616096	8616096	+	Silent	SNP	T	T	C	rs1131140	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:8616096T>C	ENST00000360986.4	+	9	1548	c.1374T>C	c.(1372-1374)gaT>gaC	p.D458D	CPZ_ENST00000429646.2_Silent_p.D66D|CPZ_ENST00000382480.2_Silent_p.D321D|CPZ_ENST00000315782.6_Silent_p.D447D	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	458					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						GCATGTCCGATTTCAACTACC	0.607													C|||	3089	0.616813	0.3782	0.6671	5008	,	,		16399	0.87		0.5517	False		,,,				2504	0.7096				p.D458D		Atlas-SNP	.											.	CPZ	95	.	0			c.T1374C						PASS	.	C	,,	1899,2507	627.0+/-394.8	397,1105,701	137.0	120.0	126.0		1374,963,1341	3.8	1.0	4	dbSNP_86	126	4569,4031	556.5+/-386.9	1196,2177,927	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	1593,3282,1628	CC,CT,TT		46.8721,43.1003,49.7309	,,	458/653,321/516,447/642	8616096	6468,6538	2203	4300	6503	SO:0001819	synonymous_variant	8532	exon9			GTCCGATTTCAAC	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.1374T>C	4.37:g.8616096T>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			T|0.457;C|0.543	0.543	strong		0.607	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
SCAF4	57466	hgsc.bcm.edu	37	21	33044378	33044378	+	Silent	SNP	G	G	A	rs73201505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33044378G>A	ENST00000286835.7	-	20	3160	c.2778C>T	c.(2776-2778)ggC>ggT	p.G926G	SCAF4_ENST00000399804.1_Silent_p.G904G|SCAF4_ENST00000434667.3_Silent_p.G911G	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	926						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						CTGGCCCTGGGCCCCCGAGCC	0.672													G|||	35	0.00698882	0.0	0.0173	5008	,	,		13262	0.0		0.0169	False		,,,				2504	0.0061				p.G926G		Atlas-SNP	.											.	SCAF4	142	.	0			c.C2778T						PASS	.	G	,,	16,4390		0,16,2187	21.0	23.0	22.0		2733,2712,2778	3.1	1.0	21	dbSNP_130	22	184,8412		4,176,4118	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAF4	NM_001145444.1,NM_001145445.1,NM_020706.2	,,	4,192,6305	AA,AG,GG		2.1405,0.3631,1.5382	,,	911/1133,904/1126,926/1148	33044378	200,12802	2203	4298	6501	SO:0001819	synonymous_variant	57466	exon20			CCCTGGGCCCCCG	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.2778C>T	21.37:g.33044378G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																			G|0.986;A|0.014	0.014	strong		0.672	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
MTR	4548	hgsc.bcm.edu	37	1	237058744	237058744	+	Silent	SNP	C	C	A	rs12070777	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:237058744C>A	ENST00000366577.5	+	31	3886	c.3492C>A	c.(3490-3492)cgC>cgA	p.R1164R	MTR_ENST00000470570.1_3'UTR|MTR_ENST00000535889.1_Silent_p.R1113R	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase	1164	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)	CAGACCTGCGCAGGCTGCGGT	0.622													C|||	1610	0.321486	0.1543	0.438	5008	,	,		16607	0.4196		0.3857	False		,,,				2504	0.2975				p.R1164R		Atlas-SNP	.											.	MTR	127	.	0			c.C3492A						PASS	.	C		913,3493		100,713,1390	30.0	24.0	26.0		3492	-9.2	0.3	1	dbSNP_120	26	3530,5068		744,2042,1513	yes	coding-synonymous	MTR	NM_000254.2		844,2755,2903	AA,AC,CC		41.0561,20.7217,34.1664		1164/1266	237058744	4443,8561	2203	4299	6502	SO:0001819	synonymous_variant	4548	exon31			CCTGCGCAGGCTG	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.3492C>A	1.37:g.237058744C>A		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	126	52	0.412698	NM_000254	A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Silent	SNP	ENST00000366577.5	37	CCDS1614.1																																																																																			C|0.658;A|0.342	0.342	strong		0.622	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	
SLC22A24	283238	hgsc.bcm.edu	37	11	62848445	62848445	+	Silent	SNP	A	A	G	rs11231340	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62848445A>G	ENST00000417740.1	-	9	1986	c.1545T>C	c.(1543-1545)ctT>ctC	p.L515L		NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	273					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.L515L(1)		kidney(1)|stomach(1)	2						TGGTTTCTGGAAGGAGGAGGA	0.507													A|||	2222	0.44369	0.3442	0.4914	5008	,	,		22919	0.4196		0.5109	False		,,,				2504	0.5				p.L515L		Atlas-SNP	.											SLC22A24_ENST00000417740,NS,carcinoma,0,1	SLC22A24	31	1	1	Substitution - coding silent(1)	kidney(1)	c.T1545C						PASS	.	A		491,893		86,319,287	155.0	133.0	139.0		1545	1.1	1.0	11	dbSNP_120	139	1692,1490		447,798,346	no	coding-synonymous	SLC22A24	NM_001136506.2		533,1117,633	GG,GA,AA		46.8259,35.4769,47.8099		515/553	62848445	2183,2383	692	1591	2283	SO:0001819	synonymous_variant	283238	exon9			TTCTGGAAGGAGG		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.1545T>C	11.37:g.62848445A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	131	59	0.450382	NM_001136506		Silent	SNP	ENST00000417740.1	37																																																																																				A|0.539;G|0.460	0.460	strong		0.507	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
CCNT1	904	hgsc.bcm.edu	37	12	49087656	49087656	+	Silent	SNP	G	G	C	rs3013	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49087656G>C	ENST00000261900.3	-	9	1563	c.1341C>G	c.(1339-1341)ccC>ccG	p.P447P		NM_001240.3	NP_001231.2	O60563	CCNT1_HUMAN	cyclin T1	447					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|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, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|skin(2)	27						AAGGCCGCTCGGGGTTTTCTG	0.443													G|||	617	0.123203	0.0794	0.121	5008	,	,		19212	0.004		0.2744	False		,,,				2504	0.1513				p.P447P		Atlas-SNP	.											.	CCNT1	55	.	0			c.C1341G						PASS	.	G		460,3946	196.4+/-220.7	25,410,1768	56.0	62.0	60.0		1341	-2.5	1.0	12	dbSNP_36	60	2794,5806	415.8+/-351.9	481,1832,1987	no	coding-synonymous	CCNT1	NM_001240.2		506,2242,3755	CC,CG,GG		32.4884,10.4403,25.0192		447/727	49087656	3254,9752	2203	4300	6503	SO:0001819	synonymous_variant	904	exon9			CCGCTCGGGGTTT	AF048730	CCDS8766.1, CCDS61109.1	12q13.11	2010-11-15			ENSG00000129315	ENSG00000129315			1599	protein-coding gene	gene with protein product		143055	"""human immunodeficiency virus type 1 (HIV-1) expression (elevated) 1"""	HIVE1		9491887, 9499409	Standard	NM_001240		Approved	CCNT, CYCT1	uc001rsd.4	O60563	OTTHUMG00000170393	ENST00000261900.3:c.1341C>G	12.37:g.49087656G>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	96	50	0.520833	NM_001240	A9XU13|E7EX76|O60581	Silent	SNP	ENST00000261900.3	37	CCDS8766.1																																																																																			G|0.788;C|0.212	0.212	strong		0.443	CCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408853.1	NM_001240	
WDFY4	57705	hgsc.bcm.edu	37	10	50040722	50040722	+	Silent	SNP	C	C	A	rs12761517	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50040722C>A	ENST00000325239.5	+	38	6658	c.6631C>A	c.(6631-6633)Cgg>Agg	p.R2211R	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2211						integral component of membrane (GO:0016021)		p.R2211W(2)		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						GATGCCCGGGCGGCAGGCCAA	0.522													C|||	408	0.0814696	0.0318	0.0836	5008	,	,		19204	0.002		0.1491	False		,,,				2504	0.1595				p.R2211R		Atlas-SNP	.											WDFY4,cerebellum,primitive_neuroectodermal_tumour-medulloblastoma,0,3	WDFY4	205	3	2	Substitution - Missense(2)	central_nervous_system(2)	c.C6631A						PASS	.	C		72,1312		3,66,623	60.0	59.0	59.0		6631	0.6	0.7	10	dbSNP_121	59	439,2743		35,369,1187	no	coding-synonymous	WDFY4	NM_020945.1		38,435,1810	AA,AC,CC		13.7964,5.2023,11.1914		2211/3185	50040722	511,4055	692	1591	2283	SO:0001819	synonymous_variant	57705	exon39			CCCGGGCGGCAGG	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.6631C>A	10.37:g.50040722C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	93	57	0.612903	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Silent	SNP	ENST00000325239.5	37	CCDS44385.1	179	0.08195970695970696	25	0.0508130081300813	38	0.10497237569060773	1	0.0017482517482517483	115	0.1517150395778364	C	9.268	1.044939	0.19748	0.052023	0.137964	ENSG00000128815	ENST00000312002	.	.	.	5.54	0.653	0.17828	.	.	.	.	.	T	0.00524	0.0017	.	.	.	0.20074	P	0.9999330134	.	.	.	.	.	.	T	0.32877	-0.9890	3	.	.	.	.	14.1056	0.65088	0.5696:0.4304:0.0:0.0	rs12761517;rs17772129;rs12761517	.	.	.	E	1301	.	.	A	+	2	0	WDFY4	49710728	0.101000	0.21875	0.745000	0.31077	0.989000	0.77384	-0.004000	0.12878	0.327000	0.23409	0.655000	0.94253	GCG	A|0.092;C|0.908;T|0.000	0.092	strong		0.522	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
ZNF142	7701	hgsc.bcm.edu	37	2	219513782	219513782	+	Silent	SNP	T	T	C	rs4674322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219513782T>C	ENST00000449707.1	-	6	1270	c.849A>G	c.(847-849)ccA>ccG	p.P283P	ZNF142_ENST00000411696.2_Silent_p.P283P	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	283					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)		GAAGGGGTAATGGCTCTGCTG	0.617											OREG0015202	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	434	0.0866613	0.0151	0.1441	5008	,	,		19362	0.0		0.2704	False		,,,				2504	0.0429				p.P283P	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A849G						PASS	.	C		185,3867		3,179,1844	29.0	32.0	31.0		849	-10.4	0.0	2	dbSNP_111	31	2169,6219		310,1549,2335	no	coding-synonymous	ZNF142	NM_001105537.1		313,1728,4179	CC,CT,TT		25.8584,4.5656,18.9228		283/1688	219513782	2354,10086	2026	4194	6220	SO:0001819	synonymous_variant	7701	exon6			GGGTAATGGCTCT	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.849A>G	2.37:g.219513782T>C		Somatic	61	0	0	2259	WXS	Illumina HiSeq	Phase_I	62	31	0.5	NM_001105537	Q92510	Silent	SNP	ENST00000449707.1	37	CCDS42817.1																																																																																			T|0.861;C|0.139	0.139	strong		0.617	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
TMEM106B	54664	hgsc.bcm.edu	37	7	12269417	12269417	+	Missense_Mutation	SNP	C	C	G	rs3173615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:12269417C>G	ENST00000396667.3	+	6	876	c.554C>G	c.(553-555)aCc>aGc	p.T185S	TMEM106B_ENST00000396668.3_Missense_Mutation_p.T185S	NM_018374.3	NP_060844.2	Q9NUM4	T106B_HUMAN	transmembrane protein 106B	185			T -> S (in dbSNP:rs3173615). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:23742080}.		cell death (GO:0008219)|dendrite morphogenesis (GO:0048813)|lysosome localization (GO:0032418)|transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(8)|large_intestine(2)|lung(7)	18				UCEC - Uterine corpus endometrioid carcinoma (126;0.185)		AACAACATAACCATTATTGGT	0.308													C|||	2980	0.595048	0.6808	0.5692	5008	,	,		18287	0.6508		0.4016	False		,,,				2504	0.6391				p.T185S		Atlas-SNP	.											TMEM106B,NS,adenoma,0,1	TMEM106B	34	1	0			c.C554G						PASS	.	C	SER/THR,SER/THR	2897,1509	673.6+/-402.8	965,967,271	69.0	70.0	69.0		554,554	5.4	1.0	7	dbSNP_105	69	3587,5009	516.1+/-378.7	780,2027,1491	yes	missense,missense	TMEM106B	NM_001134232.1,NM_018374.3	58,58	1745,2994,1762	GG,GC,CC		41.7287,34.2488,49.8693	possibly-damaging,possibly-damaging	185/275,185/275	12269417	6484,6518	2203	4298	6501	SO:0001583	missense	54664	exon5			ACATAACCATTAT	BC033901	CCDS5358.1	7p21.3	2012-06-06			ENSG00000106460	ENSG00000106460			22407	protein-coding gene	gene with protein product		613413				20154673, 22511793	Standard	NM_018374		Approved	MGC33727, FLJ11273	uc003ssh.3	Q9NUM4	OTTHUMG00000125537	ENST00000396667.3:c.554C>G	7.37:g.12269417C>G	ENSP00000379901:p.Thr185Ser	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	274	273	0.99635	NM_001134232	A4D108|Q53FL9|Q8N4L0	Missense_Mutation	SNP	ENST00000396667.3	37	CCDS5358.1	1198	0.5485347985347986	324	0.6585365853658537	184	0.5082872928176796	384	0.6713286713286714	306	0.40369393139841686	C	14.51	2.557596	0.45590	0.657512	0.417287	ENSG00000106460	ENST00000396668;ENST00000396667	T;T	0.22539	1.95;1.95	5.36	5.36	0.76844	.	0.048857	0.85682	D	0.000000	T	0.00012	0.0000	L	0.50333	1.59	0.22330	P	0.99919789	B	0.20261	0.043	B	0.17098	0.017	T	0.38178	-0.9673	9	0.54805	T	0.06	-15.6842	12.7762	0.57451	0.0:0.9247:0.0:0.0753	rs3173615;rs10348977;rs11546466;rs17149904;rs17853942;rs52789343;rs59821228;rs3173615	185	Q9NUM4	T106B_HUMAN	S	185	ENSP00000379902:T185S;ENSP00000379901:T185S	ENSP00000379901:T185S	T	+	2	0	TMEM106B	12235942	1.000000	0.71417	0.998000	0.56505	0.972000	0.66771	5.898000	0.69838	2.689000	0.91719	0.655000	0.94253	ACC	C|0.481;G|0.519	0.519	strong		0.308	TMEM106B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246870.3	NM_018374	
CEACAM3	1084	hgsc.bcm.edu	37	19	42312933	42312933	+	Silent	SNP	G	G	A	rs3752172	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:42312933G>A	ENST00000357396.3	+	3	748	c.507G>A	c.(505-507)gcG>gcA	p.A169A	CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Silent_p.A169A|CEACAM3_ENST00000344550.4_Silent_p.A169A	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	169						integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						TGGTGGCCGCGCTGGTGTGTT	0.602													N|||	948	0.189297	0.0318	0.2161	5008	,	,		16901	0.1964		0.1938	False		,,,				2504	0.3712				p.A169A		Atlas-SNP	.											.	CEACAM3	37	.	0			c.G507A						PASS	.	C		294,4112		11,272,1920	147.0	142.0	144.0		507	-1.2	0.0	19	dbSNP_107	144	1736,6864		184,1368,2748	no	coding-synonymous	CEACAM3	NM_001815.2		195,1640,4668	AA,AG,GG		20.186,6.6727,15.6082		169/253	42312933	2030,10976	2203	4300	6503	SO:0001819	synonymous_variant	1084	exon3			GGCCGCGCTGGTG	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.507G>A	19.37:g.42312933G>A		Somatic	244	1	0.00409836		WXS	Illumina HiSeq	Phase_I	209	110	0.526316	NM_001815	G5E978|Q3KPH9	Silent	SNP	ENST00000357396.3	37	CCDS12586.2																																																																																			G|0.840;A|0.160	0.160	strong		0.602	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815	
CELA2A	63036	hgsc.bcm.edu	37	1	15793913	15793913	+	Silent	SNP	G	G	A	rs1042010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15793913G>A	ENST00000359621.4	+	7	697	c.672G>A	c.(670-672)gcG>gcA	p.A224A	CELA2B_ENST00000494280.1_3'UTR	NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	224	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)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						ACTGTCAGGCGTCTGACGGCC	0.602													g|||	901	0.179912	0.2965	0.1556	5008	,	,		16915	0.0446		0.169	False		,,,				2504	0.1902				p.A224A		Atlas-SNP	.											.	CELA2A	32	.	0			c.G672A						PASS	.	A		1222,3184	424.5+/-340.5	190,842,1171	61.0	59.0	60.0		672	-6.2	0.0	1	dbSNP_86	60	1608,6992	299.0+/-304.2	128,1352,2820	no	coding-synonymous	CELA2A	NM_033440.2		318,2194,3991	AA,AG,GG		18.6977,27.7349,21.7592		224/270	15793913	2830,10176	2203	4300	6503	SO:0001819	synonymous_variant	63036	exon7			TCAGGCGTCTGAC		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.672G>A	1.37:g.15793913G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	64	61	0.953125	NM_033440	B2R5I4|Q14243	Silent	SNP	ENST00000359621.4	37	CCDS157.1																																																																																			G|0.799;A|0.201	0.201	strong		0.602	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440	
TNC	3371	hgsc.bcm.edu	37	9	117848201	117848201	+	Silent	SNP	T	T	C	rs3827815	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:117848201T>C	ENST00000350763.4	-	3	2220	c.1809A>G	c.(1807-1809)caA>caG	p.Q603Q	TNC_ENST00000542877.1_Silent_p.Q603Q|TNC_ENST00000345230.3_Silent_p.Q603Q|TNC_ENST00000423613.2_Silent_p.Q603Q|TNC_ENST00000537320.1_Silent_p.Q603Q|TNC_ENST00000340094.3_Silent_p.Q603Q|TNC_ENST00000341037.4_Silent_p.Q603Q|TNC_ENST00000346706.3_Silent_p.Q603Q|TNC_ENST00000535648.1_Silent_p.Q603Q	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	603	EGF-like 15. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.Q603Q(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						CCGAGACGCATTGTCCTAAGT	0.622													T|||	496	0.0990415	0.053	0.0937	5008	,	,		18901	0.119		0.1213	False		,,,				2504	0.1217				p.Q603Q		Atlas-SNP	.											TNC,NS,carcinoma,0,1	TNC	282	1	1	Substitution - coding silent(1)	stomach(1)	c.A1809G						PASS	.	T		223,4183	132.9+/-169.3	6,211,1986	64.0	54.0	57.0		1809	3.1	1.0	9	dbSNP_107	57	930,7670	203.7+/-246.6	46,838,3416	no	coding-synonymous	TNC	NM_002160.3		52,1049,5402	CC,CT,TT		10.814,5.0613,8.8651		603/2202	117848201	1153,11853	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon3			GACGCATTGTCCT		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.1809A>G	9.37:g.117848201T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	114	64	0.561404	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			T|0.907;C|0.093	0.093	strong		0.622	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
PDGFRB	5159	hgsc.bcm.edu	37	5	149499672	149499672	+	Silent	SNP	T	T	C	rs246395	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149499672T>C	ENST00000261799.4	-	19	3070	c.2601A>G	c.(2599-2601)ttA>ttG	p.L867L		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	867	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)	p.L867L(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCATCCACTTTAAAGGCAAAA	0.572			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								C|||	1184	0.236422	0.1528	0.2997	5008	,	,		21447	0.1538		0.2903	False		,,,				2504	0.3344				p.L867L		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	1	Substitution - coding silent(1)	stomach(1)	c.A2601G						PASS	.	C		822,3584	748.8+/-412.0	78,666,1459	84.0	76.0	79.0		2601	2.7	1.0	5	dbSNP_79	79	2833,5767	673.2+/-403.0	457,1919,1924	no	coding-synonymous	PDGFRB	NM_002609.3		535,2585,3383	CC,CT,TT		32.9419,18.6564,28.1024		867/1107	149499672	3655,9351	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon19			CCACTTTAAAGGC	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.2601A>G	5.37:g.149499672T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			T|0.745;C|0.255	0.255	strong		0.572	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
TMEM244	253582	hgsc.bcm.edu	37	6	130152479	130152479	+	Silent	SNP	T	T	C	rs7758540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:130152479T>C	ENST00000368143.1	-	5	454	c.372A>G	c.(370-372)tcA>tcG	p.S124S	TMEM244_ENST00000438392.1_Silent_p.S124S	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	124						integral component of membrane (GO:0016021)											CAAGCAATTTTGATATACCTA	0.269													C|||	2301	0.459465	0.6074	0.3934	5008	,	,		16994	0.1399		0.6193	False		,,,				2504	0.4714				p.S124S		Atlas-SNP	.											C6orf191,NS,carcinoma,-1,1	.	.	1	0			c.A372G						PASS	.	C		2708,1698	507.6+/-366.7	837,1034,332	61.0	59.0	59.0		372	-1.2	0.0	6	dbSNP_116	59	5563,3037	462.4+/-365.7	1802,1959,539	no	coding-synonymous	C6orf191	NM_001010876.1		2639,2993,871	CC,CT,TT		35.314,38.5384,36.4063		124/129	130152479	8271,4735	2203	4300	6503	SO:0001819	synonymous_variant	253582	exon5			CAATTTTGATATA		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.372A>G	6.37:g.130152479T>C		Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	123	121	0.98374	NM_001010876		Silent	SNP	ENST00000368143.1	37	CCDS34536.1																																																																																			T|0.428;C|0.572	0.572	strong		0.269	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
LRIF1	55791	hgsc.bcm.edu	37	1	111494194	111494194	+	Missense_Mutation	SNP	C	C	T	rs2232041	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:111494194C>T	ENST00000369763.4	-	2	1702	c.1312G>A	c.(1312-1314)Gcc>Acc	p.A438T	LRIF1_ENST00000485275.2_Intron|LRIF1_ENST00000494675.1_Intron|RP11-96K19.2_ENST00000440689.1_RNA	NM_018372.3	NP_060842.3	Q5T3J3	LRIF1_HUMAN	ligand dependent nuclear receptor interacting factor 1	438			A -> T (in dbSNP:rs2232041).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(2)|skin(1)|urinary_tract(2)	28						CTTAGATTGGCCATGGAAGCA	0.388													C|||	790	0.157748	0.1566	0.1081	5008	,	,		19439	0.0635		0.2714	False		,,,				2504	0.1748				p.A438T		Atlas-SNP	.											.	LRIF1	65	.	0			c.G1312A						PASS	.	C	,THR/ALA	702,3704	294.1+/-283.0	56,590,1557	174.0	175.0	175.0		,1312	1.2	1.0	1	dbSNP_98	175	2175,6425	372.5+/-336.7	265,1645,2390	yes	intron,missense	LRIF1	NM_001006945.1,NM_018372.3	,58	321,2235,3947	TT,TC,CC		25.2907,15.9328,22.1206	,benign	,438/770	111494194	2877,10129	2203	4300	6503	SO:0001583	missense	55791	exon2			GATTGGCCATGGA	AY190122	CCDS30800.1, CCDS41366.1	1p13.3	2011-04-15	2011-04-15	2011-04-15	ENSG00000121931	ENSG00000121931			30299	protein-coding gene	gene with protein product	"""receptor interacting factor 1"""	615354	"""chromosome 1 open reading frame 103"""	C1orf103		17455211	Standard	NM_018372		Approved	RIF1, FLJ11269	uc001eaa.3	Q5T3J3	OTTHUMG00000011913	ENST00000369763.4:c.1312G>A	1.37:g.111494194C>T	ENSP00000358778:p.Ala438Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_018372	Q86XS4|Q8N3B6|Q96HT4|Q9NUM5|Q9NV32	Missense_Mutation	SNP	ENST00000369763.4	37	CCDS30800.1	346	0.15842490842490842	71	0.1443089430894309	47	0.1298342541436464	26	0.045454545454545456	202	0.26649076517150394	C	8.548	0.874802	0.17395	0.159328	0.252907	ENSG00000121931	ENST00000369763	T	0.31247	1.5	5.3	1.19	0.21007	.	1.156850	0.06178	N	0.678975	T	0.10121	0.0248	L	0.44542	1.39	0.09310	P	0.999999485431	B	0.17852	0.024	B	0.17098	0.017	T	0.32161	-0.9917	9	0.48119	T	0.1	5.2568	4.2771	0.10815	0.0:0.5311:0.1832:0.2857	rs2232041;rs17639529;rs52799901;rs60246657;rs2232041	438	Q5T3J3	LRIF1_HUMAN	T	438	ENSP00000358778:A438T	ENSP00000358778:A438T	A	-	1	0	LRIF1	111295717	0.000000	0.05858	0.997000	0.53966	0.997000	0.91878	-0.526000	0.06207	0.393000	0.25203	0.591000	0.81541	GCC	C|0.813;T|0.187	0.187	strong		0.388	LRIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032932.2	NM_018372	
ITPR2	3709	hgsc.bcm.edu	37	12	26749831	26749831	+	Silent	SNP	G	G	A	rs2230377	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:26749831G>A	ENST00000381340.3	-	31	4655	c.4239C>T	c.(4237-4239)gaC>gaT	p.D1413D		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1413					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	GGATGCAGTCGTCATGGGTCA	0.458													G|||	898	0.179313	0.0938	0.1599	5008	,	,		18276	0.0476		0.3579	False		,,,				2504	0.2607				p.D1413D		Atlas-SNP	.											.	ITPR2	270	.	0			c.C4239T						PASS	.	G		521,3579		37,447,1566	82.0	82.0	82.0		4239	-5.6	1.0	12	dbSNP_98	82	2873,5519		500,1873,1823	no	coding-synonymous	ITPR2	NM_002223.2		537,2320,3389	AA,AG,GG		34.235,12.7073,27.1694		1413/2702	26749831	3394,9098	2050	4196	6246	SO:0001819	synonymous_variant	3709	exon31			GCAGTCGTCATGG	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.4239C>T	12.37:g.26749831G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.780;A|0.220	0.220	strong		0.458	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
POLRMT	5442	hgsc.bcm.edu	37	19	621148	621148	+	Silent	SNP	C	C	T	rs143192895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:621148C>T	ENST00000588649.2	-	10	2634	c.2550G>A	c.(2548-2550)ggG>ggA	p.G850G	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	850	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)		GCTTCTTCAACCCCGTGAGAT	0.687													C|||	15	0.00299521	0.0	0.0014	5008	,	,		5814	0.0		0.007	False		,,,				2504	0.0072				p.G850G		Atlas-SNP	.											.	POLRMT	91	.	0			c.G2550A						PASS	.	C		7,4399		0,7,2196	28.0	33.0	32.0		2550	-5.4	0.6	19	dbSNP_134	32	35,8555		1,33,4261	no	coding-synonymous	POLRMT	NM_005035.3		1,40,6457	TT,TC,CC		0.4075,0.1589,0.3232		850/1231	621148	42,12954	2203	4295	6498	SO:0001819	synonymous_variant	5442	exon10			CTTCAACCCCGTG		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.2550G>A	19.37:g.621148C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	26	0.302326	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			C|0.997;T|0.003	0.003	strong		0.687	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
ZFYVE9	9372	hgsc.bcm.edu	37	1	52803595	52803595	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:52803595C>T	ENST00000371591.1	+	15	3953	c.3822C>T	c.(3820-3822)aaC>aaT	p.N1274N	ZFYVE9_ENST00000287727.3_Silent_p.N1274N|ZFYVE9_ENST00000357206.2_Silent_p.N1215N	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1274					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						ATGACAAGAACGTTAGCAAGG	0.502																																					p.N1274N		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.C3822T						PASS	.						83.0	61.0	69.0					1																	52803595		2203	4300	6503	SO:0001819	synonymous_variant	9372	exon16			CAAGAACGTTAGC	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.3822C>T	1.37:g.52803595C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	128	73	0.570312	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	37	CCDS563.1																																																																																			.	.	none		0.502	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
CTNNA1	1495	hgsc.bcm.edu	37	5	138266546	138266546	+	Silent	SNP	G	G	A	rs1059110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:138266546G>A	ENST00000302763.7	+	16	2310	c.2220G>A	c.(2218-2220)tcG>tcA	p.S740S	CTNNA1_ENST00000540387.1_Silent_p.S370S|CTNNA1_ENST00000355078.5_Silent_p.S637S|CTNNA1_ENST00000518825.1_Silent_p.S740S	NM_001903.2	NP_001894.2	P35221	CTNA1_HUMAN	catenin (cadherin-associated protein), alpha 1, 102kDa	740					adherens junction organization (GO:0034332)|aging (GO:0007568)|apical junction assembly (GO:0043297)|axon regeneration (GO:0031103)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular protein localization (GO:0034613)|cellular response to indole-3-methanol (GO:0071681)|epithelial cell-cell adhesion (GO:0090136)|establishment or maintenance of cell polarity (GO:0007163)|gap junction assembly (GO:0016264)|male gonad development (GO:0008584)|muscle cell differentiation (GO:0042692)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell motility (GO:2000146)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|negative regulation of neuroblast proliferation (GO:0007406)|odontogenesis of dentin-containing tooth (GO:0042475)|ovarian follicle development (GO:0001541)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of smoothened signaling pathway (GO:0045880)|protein heterooligomerization (GO:0051291)|response to estrogen (GO:0043627)	acrosomal vesicle (GO:0001669)|actin cytoskeleton (GO:0015629)|catenin complex (GO:0016342)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|gamma-catenin binding (GO:0045295)|poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)|vinculin binding (GO:0017166)			NS(1)|breast(7)|cervix(2)|endometrium(4)|kidney(6)|large_intestine(16)|lung(9)|oesophagus(2)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	52			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AAAATACATCGGATGTCATCA	0.463													A|||	1247	0.249002	0.4259	0.2695	5008	,	,		20368	0.0079		0.2714	False		,,,				2504	0.2209				p.S740S		Atlas-SNP	.											.	CTNNA1	114	.	0			c.G2220A						PASS	.	A		1797,2609	641.3+/-397.4	345,1107,751	85.0	87.0	86.0		2220	-2.0	1.0	5	dbSNP_86	86	2557,6043	691.9+/-404.5	371,1815,2114	no	coding-synonymous	CTNNA1	NM_001903.2		716,2922,2865	AA,AG,GG		29.7326,40.7853,33.4769		740/907	138266546	4354,8652	2203	4300	6503	SO:0001819	synonymous_variant	1495	exon16			TACATCGGATGTC	D13866	CCDS34243.1, CCDS75315.1	5q31.2	2008-02-05	2002-08-29			ENSG00000044115			2509	protein-coding gene	gene with protein product		116805	"""catenin (cadherin-associated protein), alpha 1 (102kD)"""			1924379	Standard	XM_005271898		Approved	CAP102	uc003ldh.3	P35221		ENST00000302763.7:c.2220G>A	5.37:g.138266546G>A		Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	178	176	0.988764	NM_001903	Q12795|Q8N1C0	Silent	SNP	ENST00000302763.7	37	CCDS34243.1																																																																																			G|0.693;A|0.307	0.307	strong		0.463	CTNNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373868.1	NM_001903	
AP5Z1	9907	hgsc.bcm.edu	37	7	4821300	4821300	+	Missense_Mutation	SNP	C	C	G	rs11549839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4821300C>G	ENST00000348624.4	+	3	375	c.281C>G	c.(280-282)tCc>tGc	p.S94C	AP5Z1_ENST00000401897.1_Missense_Mutation_p.S94C	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	94			S -> C (in dbSNP:rs11549839).		cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CGAGAGATGTCCCCCTCTGAC	0.662													C|||	63	0.0125799	0.0015	0.0187	5008	,	,		18244	0.0		0.0249	False		,,,				2504	0.0235				p.S94C		Atlas-SNP	.											.	.	.	.	0			c.C281G						PASS	.	C	CYS/SER	12,4262		0,12,2125	25.0	30.0	28.0		281	5.1	0.6	7	dbSNP_120	28	208,8290		5,198,4046	yes	missense	KIAA0415	NM_014855.2	112	5,210,6171	GG,GC,CC		2.4476,0.2808,1.7225	benign	94/808	4821300	220,12552	2137	4249	6386	SO:0001583	missense	9907	exon3			AGATGTCCCCCTC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.281C>G	7.37:g.4821300C>G	ENSP00000297562:p.Ser94Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	126	70	0.555556	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	C	12.67	2.008321	0.35415	0.002808	0.024476	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.64085	-0.08;0.67	5.08	5.08	0.68730	.	0.645959	0.15127	N	0.279052	T	0.38585	0.1046	M	0.65975	2.015	0.18873	N	0.999984	B	0.22080	0.064	B	0.21917	0.037	T	0.46665	-0.9175	10	0.41790	T	0.15	.	15.7732	0.78187	0.0:1.0:0.0:0.0	rs11549839;rs11549839	94	O43299	K0415_HUMAN	C	94	ENSP00000297562:S94C;ENSP00000384980:S94C	ENSP00000297562:S94C	S	+	2	0	KIAA0415	4787826	0.990000	0.36364	0.650000	0.29550	0.856000	0.48823	3.089000	0.50183	2.640000	0.89533	0.655000	0.94253	TCC	C|0.987;G|0.013	0.013	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
XIRP2	129446	hgsc.bcm.edu	37	2	168103863	168103863	+	Silent	SNP	G	G	A	rs7581012	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168103863G>A	ENST00000409195.1	+	9	6050	c.5961G>A	c.(5959-5961)gcG>gcA	p.A1987A	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.A1765A|XIRP2_ENST00000295237.9_Silent_p.A1987A|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1812					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGAGCCAGCGGCCAAGTGGC	0.463													A|||	994	0.198482	0.3268	0.1326	5008	,	,		18638	0.12		0.1233	False		,,,				2504	0.2301				p.A1987A		Atlas-SNP	.											XIRP2,right_upper_lobe,carcinoma,+1,1	XIRP2	914	1	0			c.G5961A						PASS	.	A	,,,,	1074,2744		156,762,991	45.0	44.0	44.0		,,5295,,5961	1.8	0.1	2	dbSNP_116	44	923,7307		56,811,3248	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	212,1573,4239	AA,AG,GG		11.2151,28.1299,16.5754	,,,,	,,1765/3328,,1987/3550	168103863	1997,10051	1909	4115	6024	SO:0001819	synonymous_variant	129446	exon9			GCCAGCGGCCAAG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.5961G>A	2.37:g.168103863G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	133	79	0.593985	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			G|0.836;A|0.164	0.164	strong		0.463	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
OR5T2	219464	hgsc.bcm.edu	37	11	56000471	56000471	+	Missense_Mutation	SNP	G	G	A	rs11227599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56000471G>A	ENST00000313264.4	-	1	266	c.191C>T	c.(190-192)aCt>aTt	p.T64I		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	64			T -> I (in dbSNP:rs11227599).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T64I(1)		endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					GAAGAAGATAGTCTGCAGTTC	0.393													a|||	865	0.172724	0.1868	0.1585	5008	,	,		21467	0.124		0.2117	False		,,,				2504	0.1738				p.T64I		Atlas-SNP	.											OR5T2,NS,carcinoma,0,1	OR5T2	107	1	1	Substitution - Missense(1)	stomach(1)	c.C191T						PASS	.	A	ILE/THR	801,3601	749.1+/-412.0	76,649,1476	72.0	64.0	67.0		191	3.6	0.0	11	dbSNP_120	67	1699,6893	737.2+/-407.0	177,1345,2774	yes	missense	OR5T2	NM_001004746.1	89	253,1994,4250	AA,AG,GG		19.7742,18.1963,19.2396	benign	64/360	56000471	2500,10494	2201	4296	6497	SO:0001583	missense	219464	exon1			AAGATAGTCTGCA	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.191C>T	11.37:g.56000471G>A	ENSP00000323688:p.Thr64Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	381	0.17445054945054944	87	0.17682926829268292	54	0.14917127071823205	74	0.12937062937062938	166	0.21899736147757257	A	2.652	-0.281757	0.05642	0.181963	0.197742	ENSG00000181718	ENST00000313264	T	0.00231	8.49	4.77	3.64	0.41730	.	0.464406	0.15753	N	0.246309	T	0.00012	0.0000	N	0.00985	-1.075	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.00414	-1.1754	9	0.05959	T	0.93	.	8.8572	0.35236	0.839:0.0:0.161:0.0	rs11227599;rs52813445;rs11227599	64	Q8NGG2	OR5T2_HUMAN	I	64	ENSP00000323688:T64I	ENSP00000323688:T64I	T	-	2	0	OR5T2	55757047	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.030000	0.13688	0.284000	0.22305	-1.324000	0.01287	ACT	G|0.820;A|0.180	0.180	strong		0.393	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
DDX60L	91351	hgsc.bcm.edu	37	4	169362557	169362557	+	Missense_Mutation	SNP	C	C	G	rs13151700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169362557C>G	ENST00000511577.1	-	10	1472	c.1225G>C	c.(1225-1227)Gtt>Ctt	p.V409L	DDX60L_ENST00000505890.1_Missense_Mutation_p.V409L|DDX60L_ENST00000260184.7_Missense_Mutation_p.V409L			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	409			V -> L (in dbSNP:rs13151700).				ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GACTTTCCAACGTTAAATTCT	0.358													C|||	1674	0.334265	0.0469	0.5159	5008	,	,		17538	0.6141		0.3439	False		,,,				2504	0.2955				p.V409L		Atlas-SNP	.											.	DDX60L	116	.	0			c.G1225C						PASS	.	C	LEU/VAL	351,3307		31,289,1509	109.0	104.0	106.0		1225	3.1	0.8	4	dbSNP_121	106	2714,5446		435,1844,1801	yes	missense	DDX60L	NM_001012967.1	32	466,2133,3310	GG,GC,CC		33.2598,9.5954,25.935	benign	409/1707	169362557	3065,8753	1829	4080	5909	SO:0001583	missense	91351	exon10			TTCCAACGTTAAA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.1225G>C	4.37:g.169362557C>G	ENSP00000422423:p.Val409Leu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	155	69	0.445161	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		817	0.3740842490842491	27	0.054878048780487805	171	0.4723756906077348	365	0.6381118881118881	254	0.33509234828496043	C	11.22	1.574833	0.28092	0.095954	0.332598	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.18502	2.22;2.22;2.21;2.86	3.1	3.1	0.35709	.	0.263396	0.19176	U	0.120809	T	0.00012	0.0000	M	0.65975	2.015	0.46631	P	8.650000000000047E-4	B;B;B	0.32620	0.378;0.336;0.378	B;B;B	0.25987	0.065;0.048;0.065	T	0.20974	-1.0259	9	0.09084	T	0.74	.	9.9765	0.41786	0.0:1.0:0.0:0.0	rs13151700;rs17706604;rs52823633;rs13151700	409;409;409	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	L	409;409;409;137	ENSP00000260184:V409L;ENSP00000422423:V409L;ENSP00000422202:V409L;ENSP00000421026:V137L	ENSP00000260184:V409L	V	-	1	0	DDX60L	169599132	0.993000	0.37304	0.808000	0.32385	0.024000	0.10985	3.471000	0.53107	1.411000	0.46957	0.313000	0.20887	GTT	C|0.615;G|0.385	0.385	strong		0.358	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
COL6A2	1292	hgsc.bcm.edu	37	21	47545913	47545913	+	Silent	SNP	G	G	A	rs2839114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47545913G>A	ENST00000300527.4	+	26	2288	c.2184G>A	c.(2182-2184)gtG>gtA	p.V728V	COL6A2_ENST00000409416.1_Silent_p.V728V|COL6A2_ENST00000397763.1_Silent_p.V728V|COL6A2_ENST00000310645.5_Silent_p.V728V|COL6A2_ENST00000357838.4_Silent_p.V728V	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	728	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGTTTGCGGTGGTCATCACGG	0.652													G|||	1613	0.322085	0.1067	0.5548	5008	,	,		14926	0.4226		0.3837	False		,,,				2504	0.2812				p.V728V		Atlas-SNP	.											.	COL6A2	351	.	0			c.G2184A						PASS	.	G	,,	584,3822	256.7+/-261.4	47,490,1666	80.0	77.0	78.0		2184,2184,2184	3.1	1.0	21	dbSNP_100	78	3208,5392	483.3+/-371.1	614,1980,1706	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	661,2470,3372	AA,AG,GG		37.3023,13.2547,29.1558	,,	728/1020,728/919,728/829	47545913	3792,9214	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			TGCGGTGGTCATC	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2184G>A	21.37:g.47545913G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	106	59	0.556604	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			G|0.690;A|0.310	0.310	strong		0.652	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
LMOD1	25802	hgsc.bcm.edu	37	1	201869257	201869257	+	Missense_Mutation	SNP	G	G	A	rs2820312	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201869257G>A	ENST00000367288.4	-	2	1130	c.884C>T	c.(883-885)aCg>aTg	p.T295M	RP11-307B6.3_ENST00000414927.1_RNA|RP11-307B6.3_ENST00000458139.1_RNA	NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	295			T -> M (in dbSNP:rs2820312).		muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						GCCACTGGGCGTCTGTTTCTC	0.507													g|||	1091	0.217851	0.205	0.2219	5008	,	,		20434	0.1012		0.3032	False		,,,				2504	0.2648				p.T295M		Atlas-SNP	.											.	LMOD1	59	.	0			c.C884T						PASS	.	A	MET/THR	830,3194		66,698,1248	72.0	74.0	73.0		884	0.6	0.0	1	dbSNP_100	73	2618,5716		402,1814,1951	yes	missense	LMOD1	NM_012134.2	81	468,2512,3199	AA,AG,GG		31.4135,20.6262,27.901	possibly-damaging	295/601	201869257	3448,8910	2012	4167	6179	SO:0001583	missense	25802	exon2			CTGGGCGTCTGTT	X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.884C>T	1.37:g.201869257G>A	ENSP00000356257:p.Thr295Met	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	283	141	0.498233	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	37	CCDS53457.1	527	0.2413003663003663	132	0.2682926829268293	89	0.24585635359116023	64	0.11188811188811189	242	0.31926121372031663	g	10.27	1.305016	0.23736	0.206262	0.314135	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	D	0.92397	-3.03	5.32	0.581	0.17407	.	1.726880	0.03514	N	0.219988	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;P	0.51653	0.004;0.947	B;B	0.31547	0.002;0.132	T	0.14896	-1.0456	9	0.30078	T	0.28	-2.9137	8.7241	0.34458	0.1205:0.2326:0.6469:0.0	rs2820312;rs3820435;rs52806101;rs58496028;rs2820312	244;295	B4E3S9;P29536	.;LMOD1_HUMAN	M	295;295;244	ENSP00000356257:T295M	ENSP00000356257:T295M	T	-	2	0	LMOD1	200135880	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.111000	0.15458	-0.089000	0.12484	-2.465000	0.00204	ACG	G|0.763;A|0.237	0.237	strong		0.507	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2		
GNRH1	2796	hgsc.bcm.edu	37	8	25279148	25279148	+	Missense_Mutation	SNP	G	G	A	rs574867408		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:25279148G>A	ENST00000276414.4	-	2	1501	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C	GNRH1_ENST00000421054.2_Missense_Mutation_p.R60C	NM_000825.3	NP_000816.4	P01148	GON1_HUMAN	gonadotropin-releasing hormone 1 (luteinizing-releasing hormone)	60					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)		CATTCGAAGCGTTGGGTTTCT	0.448													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14545	0.0		0.0	False		,,,				2504	0.0				p.R64C		Atlas-SNP	.											.	GNRH1	8	.	0			c.C190T						PASS	.						102.0	110.0	107.0					8																	25279148		2033	4193	6226	SO:0001583	missense	2796	exon2			CGAAGCGTTGGGT	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.178C>T	8.37:g.25279148G>A	ENSP00000276414:p.Arg60Cys	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	150	67	0.446667	NM_000825	A0AVP0	Missense_Mutation	SNP	ENST00000276414.4	37	CCDS43725.1	.	.	.	.	.	.	.	.	.	.	G	5.063	0.197253	0.09599	.	.	ENSG00000147437	ENST00000421054;ENST00000276414	T;T	0.47528	0.84;0.84	4.91	2.09	0.27110	.	1.839800	0.02297	N	0.070879	T	0.38214	0.1032	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.25047	-1.0143	9	0.46703	T	0.11	0.5379	7.6257	0.28210	0.0774:0.0:0.5127:0.4099	.	60	P01148	GON1_HUMAN	C	60	ENSP00000391280:R60C;ENSP00000276414:R60C	ENSP00000276414:R60C	R	-	1	0	GNRH1	25335065	0.003000	0.15002	0.000000	0.03702	0.003000	0.03518	1.075000	0.30716	0.250000	0.21479	0.561000	0.74099	CGC	.	.	none		0.448	GNRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375982.1	NM_001083111	
FAM171B	165215	hgsc.bcm.edu	37	2	187615953	187615953	+	Missense_Mutation	SNP	G	G	A	rs201119796		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:187615953G>A	ENST00000304698.5	+	5	1020	c.817G>A	c.(817-819)Gtt>Att	p.V273I		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	273						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.V273F(1)		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						CTCTATTCAAGTTTCTCTTCC	0.363																																					p.V273I		Atlas-SNP	.											FAM171B,rectum,carcinoma,-1,2	FAM171B	146	2	1	Substitution - Missense(1)	breast(1)	c.G817A						PASS	.						108.0	115.0	113.0					2																	187615953		2203	4300	6503	SO:0001583	missense	165215	exon5			ATTCAAGTTTCTC	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.817G>A	2.37:g.187615953G>A	ENSP00000304108:p.Val273Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	29	0.376623	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	7.399	0.632436	0.14322	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.38401	1.14	5.53	-4.51	0.03483	.	0.550372	0.20261	N	0.095865	T	0.10208	0.0250	N	0.02202	-0.64	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.28554	-1.0040	10	0.05436	T	0.98	-0.8584	11.0846	0.48080	0.5502:0.0853:0.3645:0.0	.	273;274	Q6P995;A8K122	F171B_HUMAN;.	I	273	ENSP00000304108:V273I	ENSP00000272804:V273I	V	+	1	0	FAM171B	187324198	0.694000	0.27738	0.178000	0.23040	0.632000	0.37999	0.201000	0.17276	-1.197000	0.02673	-1.372000	0.01188	GTT	G|0.999;A|0.001	0.001	weak		0.363	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
FER1L6	654463	hgsc.bcm.edu	37	8	125115420	125115420	+	Missense_Mutation	SNP	G	G	A	rs56132579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:125115420G>A	ENST00000522917.1	+	39	5365	c.5159G>A	c.(5158-5160)cGa>cAa	p.R1720Q	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Missense_Mutation_p.R1720Q	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1720						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)			AGTTTCCCTCGAGCAGCTAAG	0.458													G|||	153	0.0305511	0.003	0.049	5008	,	,		20792	0.0		0.0755	False		,,,				2504	0.0399				p.R1720Q		Atlas-SNP	.											.	FER1L6	268	.	0			c.G5159A						PASS	.	G	GLN/ARG	65,3747		0,65,1841	161.0	160.0	160.0		5159	4.7	1.0	8	dbSNP_129	160	622,7618		20,582,3518	yes	missense	FER1L6	NM_001039112.2	43	20,647,5359	AA,AG,GG		7.5485,1.7051,5.7003	probably-damaging	1720/1858	125115420	687,11365	1906	4120	6026	SO:0001583	missense	654463	exon39			TCCCTCGAGCAGC	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.5159G>A	8.37:g.125115420G>A	ENSP00000428280:p.Arg1720Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	34	0.4	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	81	0.03708791208791209	1	0.0020325203252032522	20	0.055248618784530384	0	0.0	60	0.079155672823219	G	27.2	4.812589	0.90707	0.017051	0.075485	ENSG00000214814	ENST00000522917;ENST00000399018	D;D	0.95447	-3.71;-3.71	5.58	4.71	0.59529	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.071621	0.56097	U	0.000040	T	0.75598	0.3871	M	0.70842	2.15	0.58432	D	0.999997	D	0.89917	1.0	D	0.85130	0.997	T	0.78838	-0.2046	10	0.49607	T	0.09	-7.0267	14.8788	0.70516	0.0693:0.0:0.9307:0.0	rs56132579	1720	Q2WGJ9	FR1L6_HUMAN	Q	1720	ENSP00000428280:R1720Q;ENSP00000381982:R1720Q	ENSP00000381982:R1720Q	R	+	2	0	FER1L6	125184601	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.715000	0.74697	1.490000	0.48466	0.655000	0.94253	CGA	G|0.947;A|0.053	0.053	strong		0.458	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
ADORA3	140	hgsc.bcm.edu	37	1	112042787	112042787	+	Missense_Mutation	SNP	T	T	G	rs35511654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:112042787T>G	ENST00000241356.4	-	2	1147	c.742A>C	c.(742-744)Atc>Ctc	p.I248L	ADORA3_ENST00000486342.1_5'Flank|ADORA3_ENST00000369716.4_Intron|ADORA3_ENST00000369717.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	248			I -> L (in dbSNP:rs35511654). {ECO:0000269|Ref.3}.		activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	CAGTTGATGATAGATAAAGGC	0.463													T|||	298	0.0595048	0.0628	0.0836	5008	,	,		21916	0.001		0.1402	False		,,,				2504	0.0153				p.I248L		Atlas-SNP	.											ADORA3,caecum,carcinoma,0,1	ADORA3	104	1	0			c.A742C	GRCh37	CM077860	ADORA3	M	rs35511654	PASS	.	T	LEU/ILE,,	256,4150	147.6+/-182.1	13,230,1960	106.0	102.0	104.0		742,,	3.9	1.0	1	dbSNP_126	104	1175,7425	240.0+/-270.9	87,1001,3212	yes	missense,intron,intron	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	5,,	100,1231,5172	GG,GT,TT		13.6628,5.8103,11.0026	possibly-damaging,,	248/319,,	112042787	1431,11575	2203	4300	6503	SO:0001583	missense	140	exon2			TGATGATAGATAA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.742A>C	1.37:g.112042787T>G	ENSP00000241356:p.Ile248Leu	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	143	75	0.524476	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	169	0.07738095238095238	26	0.052845528455284556	31	0.0856353591160221	1	0.0017482517482517483	111	0.14643799472295516	T	18.52	3.642415	0.67244	0.058103	0.136628	ENSG00000121933	ENST00000241356	T	0.74421	-0.84	5.01	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.68531	0.3011	L	0.37850	1.14	0.30315	P	0.788123	D	0.63880	0.993	D	0.64687	0.928	T	0.70178	-0.4943	8	0.42905	T	0.14	.	10.9921	0.47555	0.1402:0.0:0.0:0.8598	rs35511654;rs62617132	248	P33765	AA3R_HUMAN	L	248	ENSP00000241356:I248L	ENSP00000241356:I248L	I	-	1	0	ADORA3	111844310	1.000000	0.71417	0.998000	0.56505	0.508000	0.34012	3.192000	0.50989	0.834000	0.34852	0.528000	0.53228	ATC	T|0.898;G|0.102	0.102	strong		0.463	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
ZNF568	374900	hgsc.bcm.edu	37	19	37441462	37441462	+	Silent	SNP	T	T	C	rs546589	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37441462T>C	ENST00000333987.7	+	7	1913	c.1407T>C	c.(1405-1407)acT>acC	p.T469T	ZNF568_ENST00000415168.1_Silent_p.T405T|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000427117.1_Intron	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	469					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(9)|ovary(1)	29	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			AAATTCACACTGGAGAGAAAC	0.393													C|||	2834	0.565895	0.761	0.5692	5008	,	,		20378	0.3105		0.5636	False		,,,				2504	0.5654				p.T469T		Atlas-SNP	.											.	ZNF568	106	.	0			c.T1407C						PASS	.	C	,,,,,	3269,1137	371.7+/-320.1	1196,877,130	52.0	58.0	56.0		1404,1215,1215,,,1407	-1.3	1.0	19	dbSNP_83	56	4919,3681	515.5+/-378.6	1428,2063,809	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	ZNF568	NM_001204835.1,NM_001204836.1,NM_001204837.1,NM_001204838.1,NM_001204839.1,NM_198539.3	,,,,,	2624,2940,939	CC,CT,TT		42.8023,25.8057,37.0444	,,,,,	468/644,405/581,405/581,,,469/645	37441462	8188,4818	2203	4300	6503	SO:0001819	synonymous_variant	374900	exon7			TCACACTGGAGAG	BX640681	CCDS42558.1, CCDS56092.1, CCDS56093.1, CCDS74351.1	19q13.12	2013-09-20			ENSG00000198453	ENSG00000198453		"""Zinc fingers, C2H2-type"", ""-"""	25392	protein-coding gene	gene with protein product							Standard	NM_198539		Approved	DKFZp686B0797	uc002ofc.3	Q3ZCX4	OTTHUMG00000048160	ENST00000333987.7:c.1407T>C	19.37:g.37441462T>C		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Silent	SNP	ENST00000333987.7	37	CCDS42558.1																																																																																			T|0.450;C|0.550	0.550	strong		0.393	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539	
KRT27	342574	hgsc.bcm.edu	37	17	38935812	38935812	+	Missense_Mutation	SNP	A	A	G	rs981684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38935812A>G	ENST00000301656.3	-	5	954	c.914T>C	c.(913-915)aTc>aCc	p.I305T	KRT27_ENST00000540723.1_5'Flank	NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TTTCATCTCGATAAGCTCATT	0.537													G|||	2783	0.555711	0.4531	0.6153	5008	,	,		16027	0.8254		0.5209	False		,,,				2504	0.41				p.I305T		Atlas-SNP	.											.	KRT27	41	.	0			c.T914C						PASS	.	G	THR/ILE	2021,2385	612.7+/-392.0	469,1083,651	66.0	60.0	62.0		914	5.5	0.1	17	dbSNP_86	62	4713,3887	544.9+/-384.7	1299,2115,886	yes	missense	KRT27	NM_181537.3	89	1768,3198,1537	GG,GA,AA		45.1977,45.8693,48.2239	benign	305/460	38935812	6734,6272	2203	4300	6503	SO:0001583	missense	342574	exon5			ATCTCGATAAGCT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.914T>C	17.37:g.38935812A>G	ENSP00000301656:p.Ile305Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	1302	0.5961538461538461	223	0.4532520325203252	210	0.580110497237569	474	0.8286713286713286	395	0.521108179419525	G	0.822	-0.748150	0.03065	0.458693	0.548023	ENSG00000171446	ENST00000301656	D	0.87491	-2.26	5.52	5.52	0.82312	Filament (1);	0.000000	0.64402	N	0.000012	T	0.00012	0.0000	N	0.00191	-1.88	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41822	-0.9487	9	0.02654	T	1	.	14.0101	0.64490	0.0729:0.0:0.9271:0.0	rs981684;rs17473670;rs60943463;rs981684	305	Q7Z3Y8	K1C27_HUMAN	T	305	ENSP00000301656:I305T	ENSP00000301656:I305T	I	-	2	0	KRT27	36189338	0.944000	0.32072	0.092000	0.20876	0.488000	0.33401	2.487000	0.45268	1.483000	0.48342	-0.186000	0.12905	ATC	A|0.443;G|0.557	0.557	strong		0.537	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
MYB	4602	hgsc.bcm.edu	37	6	135518402	135518402	+	Intron	SNP	G	G	A	rs547508696		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:135518402G>A	ENST00000367814.4	+	9	1389				MYB_ENST00000534121.1_Missense_Mutation_p.V487I|MYB_ENST00000534044.1_Intron|MYB_ENST00000442647.2_Intron|MYB_ENST00000531845.1_Intron|MYB_ENST00000525369.1_Intron|MYB_ENST00000341911.5_Missense_Mutation_p.V503I|MYB_ENST00000527615.1_Intron|MYB_ENST00000528774.1_Missense_Mutation_p.V500I|MYB_ENST00000533624.1_Intron|MYB_ENST00000316528.8_Intron|MYB-AS1_ENST00000455534.1_RNA	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|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)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		ATTTGCTGACGTCAGCAGTTC	0.507			T	NFIB	adenoid cystic carcinoma								G|||	1	0.000199681	0.0	0.0	5008	,	,		20039	0.001		0.0	False		,,,				2504	0.0				p.V503I		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.G1507A						PASS	.						77.0	72.0	73.0					6																	135518402		1568	3582	5150	SO:0001627	intron_variant	4602	exon10			GCTGACGTCAGCA		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1203+1262G>A	6.37:g.135518402G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_001130173	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.553390	0.27739	.	.	ENSG00000118513	ENST00000341911;ENST00000528774;ENST00000534121	T;T;T	0.11277	2.79;2.79;2.8	5.78	2.96	0.34315	.	0.514050	0.19050	N	0.124064	T	0.01976	0.0062	N	0.22421	0.69	0.80722	D	1	B;B;B	0.15719	0.004;0.005;0.014	B;B;B	0.11329	0.002;0.002;0.006	T	0.40683	-0.9550	10	0.17369	T	0.5	-0.0596	6.0033	0.19533	0.2267:0.1344:0.6389:0.0	.	500;487;503	E9PNL6;E9PNA4;P10242-4	.;.;.	I	503;500;487	ENSP00000339992:V503I;ENSP00000434723:V500I;ENSP00000432851:V487I	ENSP00000339992:V503I	V	+	1	0	MYB	135560095	0.999000	0.42202	0.999000	0.59377	0.999000	0.98932	0.652000	0.24888	0.337000	0.23665	0.655000	0.94253	GTC	.	.	none		0.507	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4		
ANK1	286	hgsc.bcm.edu	37	8	41585438	41585438	+	Silent	SNP	G	G	A	rs2304871	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:41585438G>A	ENST00000347528.4	-	4	398	c.315C>T	c.(313-315)aaC>aaT	p.N105N	ANK1_ENST00000265709.8_Silent_p.N138N|ANK1_ENST00000352337.4_Silent_p.N105N|ANK1_ENST00000289734.7_Silent_p.N105N|ANK1_ENST00000396942.1_Silent_p.N105N|ANK1_ENST00000379758.2_Silent_p.N105N|ANK1_ENST00000396945.1_Silent_p.N105N	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	105	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)			GTGACTGGGCGTTGACGTTGG	0.592													G|||	1144	0.228435	0.1778	0.219	5008	,	,		21163	0.2242		0.2684	False		,,,				2504	0.2669				p.N138N		Atlas-SNP	.											.	ANK1	497	.	0			c.C414T						PASS	.	G	,,,,	843,3563	334.7+/-303.5	71,701,1431	152.0	110.0	124.0		315,414,315,315,315	-9.0	0.3	8	dbSNP_100	124	2404,6196	399.9+/-346.6	329,1746,2225	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	,,,,	400,2447,3656	AA,AG,GG		27.9535,19.133,24.9654	,,,,	105/1881,138/1898,105/1857,105/1882,105/1720	41585438	3247,9759	2203	4300	6503	SO:0001819	synonymous_variant	286	exon4			CTGGGCGTTGACG	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.315C>T	8.37:g.41585438G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1																																																																																			G|0.763;A|0.237	0.237	strong		0.592	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
Unknown	0	hgsc.bcm.edu	37	11	5989282	5989282	+	IGR	SNP	G	G	A	rs116908319	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5989282G>A								OR56A3 (19691 upstream) : OR52L1 (17839 downstream)																							AACAAAGATGGCAGCCCTAGC	0.483													.|||	94	0.01877	0.0008	0.0216	5008	,	,		21911	0.001		0.0308	False		,,,				2504	0.047				p.A148V		Atlas-SNP	.											.	.	.	.	0			c.C443T						PASS	.	G	VAL/ALA	4,1380		0,4,688	84.0	73.0	77.0		443	1.5	0.1	11	dbSNP_132	77	83,3099		3,77,1511	yes	missense	OR56A5	NM_001146033.1	64	3,81,2199	AA,AG,GG		2.6084,0.289,1.9054	benign	148/314	5989282	87,4479	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			AAGATGGCAGCCC																													11.37:g.5989282G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	95	42	0.442105	NM_001146033		Missense_Mutation	SNP		37																																																																																				G|0.980;A|0.020	0.020	strong	0	0.483								
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105897003	105897003	+	Silent	SNP	G	G	A	rs2241799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:105897003G>A	ENST00000393359.2	-	6	1725	c.1299C>T	c.(1297-1299)aaC>aaT	p.N433N	TGFBRAP1_ENST00000258449.1_Silent_p.N433N			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	433					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						TGCGGACCTCGTTCAGGTAGC	0.572													G|||	778	0.155351	0.0098	0.2176	5008	,	,		21326	0.1508		0.2117	False		,,,				2504	0.2546				p.N433N	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C1299T						PASS	.	G	,	186,4220	118.4+/-156.1	2,182,2019	156.0	130.0	139.0		1299,1299	-5.1	0.8	2	dbSNP_98	139	1767,6833	320.5+/-314.7	197,1373,2730	no	coding-synonymous,coding-synonymous	TGFBRAP1	NM_001142621.1,NM_004257.4	,	199,1555,4749	AA,AG,GG		20.5465,4.2215,15.0161	,	433/861,433/861	105897003	1953,11053	2203	4300	6503	SO:0001819	synonymous_variant	9392	exon6			GACCTCGTTCAGG	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.1299C>T	2.37:g.105897003G>A		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	195	97	0.497436	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																			G|0.853;A|0.147	0.147	strong		0.572	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
ATF4	468	hgsc.bcm.edu	37	22	39917787	39917787	+	Missense_Mutation	SNP	T	T	G	rs141575018		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39917787T>G	ENST00000337304.2	+	2	1118	c.236T>G	c.(235-237)tTc>tGc	p.F79C	ATF4_ENST00000404241.2_Missense_Mutation_p.F79C|ATF4_ENST00000396680.1_Missense_Mutation_p.F79C	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	79					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	GAGGATGCCTTCTCCGGGACA	0.502																																					p.F79C		Atlas-SNP	.											.	ATF4	27	.	0			c.T236G						PASS	.	T	CYS/PHE,CYS/PHE	0,4406		0,0,2203	100.0	103.0	102.0		236,236	4.7	1.0	22	dbSNP_134	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ATF4	NM_001675.2,NM_182810.1	205,205	0,4,6499	GG,GT,TT		0.0465,0.0,0.0308	probably-damaging,probably-damaging	79/352,79/352	39917787	4,13002	2203	4300	6503	SO:0001583	missense	468	exon2			ATGCCTTCTCCGG	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.236T>G	22.37:g.39917787T>G	ENSP00000336790:p.Phe79Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	61	30	0.491803	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	T	19.58	3.853455	0.71719	0.0	4.65E-4	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.49432	0.78;0.78;0.78	4.74	4.74	0.60224	.	0.052105	0.85682	D	0.000000	T	0.68869	0.3048	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74144	-0.3760	10	0.87932	D	0	-24.7248	14.269	0.66140	0.0:0.0:0.0:1.0	.	79	P18848	ATF4_HUMAN	C	79	ENSP00000384587:F79C;ENSP00000336790:F79C;ENSP00000379912:F79C	ENSP00000336790:F79C	F	+	2	0	ATF4	38247733	1.000000	0.71417	0.998000	0.56505	0.902000	0.53008	7.654000	0.83653	1.770000	0.52166	0.459000	0.35465	TTC	T|1.000;G|0.000	0.000	weak		0.502	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
TOPAZ1	375337	hgsc.bcm.edu	37	3	44284584	44284584	+	Missense_Mutation	SNP	G	G	A	rs9284879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:44284584G>A	ENST00000309765.4	+	2	754	c.586G>A	c.(586-588)Gtt>Att	p.V196I		NM_001145030.1	NP_001138502.1	Q8N9V7	TOPZ1_HUMAN	testis and ovary specific PAZ domain containing 1	196			V -> I (in dbSNP:rs9284879).			cytoplasm (GO:0005737)	metal ion binding (GO:0046872)										AAATATTAAGGTTGAATTCCA	0.289													G|||	2822	0.563498	0.2587	0.5879	5008	,	,		18763	0.8085		0.5219	False		,,,				2504	0.7485				p.V196I		Atlas-SNP	.											C3orf77_ENST00000309765,NS,carcinoma,0,2	.	.	2	0			c.G586A						PASS	.	G	ILE/VAL	423,961		72,279,341	17.0	14.0	15.0		586	3.0	1.0	3	dbSNP_119	15	1488,1686		379,730,478	yes	missense	C3orf77	NM_001145030.1	29	451,1009,819	AA,AG,GG		46.8809,30.5636,41.9263	possibly-damaging	196/1693	44284584	1911,2647	692	1587	2279	SO:0001583	missense	375337	exon2			ATTAAGGTTGAAT	AK093476	CCDS46809.1	3p21.33	2012-10-08	2012-10-08	2012-10-08	ENSG00000173769	ENSG00000173769			24746	protein-coding gene	gene with protein product		614412	"""chromosome 3 open reading frame 77"""	C3orf77		22069478	Standard	NM_001145030		Approved	FLJ36157	uc003cna.4	Q8N9V7	OTTHUMG00000156172	ENST00000309765.4:c.586G>A	3.37:g.44284584G>A	ENSP00000310303:p.Val196Ile	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	41	0.506173	NM_001145030		Missense_Mutation	SNP	ENST00000309765.4	37	CCDS46809.1	1217	0.5572344322344323	148	0.3008130081300813	206	0.569060773480663	474	0.8286713286713286	389	0.5131926121372031	G	14.01	2.408794	0.42715	0.305636	0.468809	ENSG00000173769	ENST00000309765	T	0.12569	2.67	5.68	2.96	0.34315	.	0.309605	0.28790	N	0.014137	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.17268	0.021	B	0.15484	0.013	T	0.04767	-1.0928	9	0.49607	T	0.09	-3.0731	5.8722	0.18809	0.2192:0.0:0.6394:0.1413	rs9284879;rs17646493;rs60618729;rs9284879	196	Q8N9V7	CC077_HUMAN	I	196	ENSP00000310303:V196I	ENSP00000310303:V196I	V	+	1	0	C3orf77	44259588	0.904000	0.30761	0.993000	0.49108	0.983000	0.72400	1.317000	0.33631	0.364000	0.24374	-0.136000	0.14681	GTT	G|0.462;A|0.538	0.538	strong		0.289	TOPAZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343247.1	NM_001145030	
POU5F1B	5462	hgsc.bcm.edu	37	8	128428656	128428656	+	Missense_Mutation	SNP	A	A	C	rs13273814	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:128428656A>C	ENST00000465342.2	+	2	1702	c.545A>C	c.(544-546)aAg>aCg	p.K182T	POU5F1B_ENST00000391675.1_Missense_Mutation_p.K182T|CASC8_ENST00000523825.1_RNA|CASC8_ENST00000501396.1_RNA|CASC8_ENST00000502082.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	182	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.		K -> T (in dbSNP:rs13273814). {ECO:0000269|PubMed:21341266, ECO:0000269|Ref.3}.		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						TTCAGCCAAAAGACCATCTGC	0.527													c|||	1116	0.222843	0.5083	0.1268	5008	,	,		17607	0.0585		0.1958	False		,,,				2504	0.1022				p.K182T		Atlas-SNP	.											.	POU5F1B	32	.	0			c.A545C						PASS	.						64.0	81.0	76.0					8																	128428656		692	1591	2283	SO:0001583	missense	5462	exon1			GCCAAAAGACCAT	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.545A>C	8.37:g.128428656A>C	ENSP00000419298:p.Lys182Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	118	116	0.983051	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	369	0.16895604395604397	183	0.3719512195121951	48	0.13259668508287292	28	0.04895104895104895	110	0.14511873350923482	C	0.816	-0.750342	0.03041	.	.	ENSG00000212993	ENST00000465342;ENST00000391675	T;T	0.79454	-1.27;-1.27	1.14	-1.47	0.08772	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.53938	N	0.000055	T	0.00012	0.0000	N	0.00025	-2.685	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.18967	-1.0320	9	0.02654	T	1	.	1.4592	0.02392	0.2047:0.438:0.202:0.1552	rs13273814	182	Q06416	P5F1B_HUMAN	T	182	ENSP00000419298:K182T;ENSP00000375557:K182T	ENSP00000375557:K182T	K	+	2	0	POU5F1B	128497838	0.999000	0.42202	0.249000	0.24280	0.378000	0.30076	2.689000	0.46993	-1.120000	0.02953	-1.396000	0.01147	AAG	A|0.823;C|0.177	0.177	strong		0.527	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
GYLTL1B	120071	hgsc.bcm.edu	37	11	45948962	45948962	+	Silent	SNP	C	C	T	rs138897549		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:45948962C>T	ENST00000531526.1	+	11	1533	c.1422C>T	c.(1420-1422)ttC>ttT	p.F474F	GYLTL1B_ENST00000389968.3_Silent_p.F201F|GYLTL1B_ENST00000325468.5_Silent_p.F474F|GYLTL1B_ENST00000536139.1_Silent_p.F443F|GYLTL1B_ENST00000401752.1_Silent_p.F474F|GYLTL1B_ENST00000529052.1_Silent_p.F443F	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	474				HF -> IS (in Ref. 5; AAG23791). {ECO:0000305}.	muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		TCCTGCATTTCGTCGAGGCCT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20898	0.0		0.0	False		,,,				2504	0.0				p.F474F		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.C1422T						PASS	.	C		0,4406		0,0,2203	89.0	74.0	79.0		1422	-1.3	0.7	11	dbSNP_134	79	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	GYLTL1B	NM_152312.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		474/722	45948962	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	120071	exon11			GCATTTCGTCGAG		CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"""Glycosyltransferase family 8 domain containing"""	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1422C>T	11.37:g.45948962C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	32	0.385542	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Silent	SNP	ENST00000531526.1	37	CCDS31473.1																																																																																			C|1.000;T|0.000	0.000	strong		0.617	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312	
NLRP8	126205	hgsc.bcm.edu	37	19	56466227	56466227	+	Missense_Mutation	SNP	A	A	G	rs7259764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56466227A>G	ENST00000291971.3	+	3	874	c.803A>G	c.(802-804)cAg>cGg	p.Q268R	NLRP8_ENST00000590542.1_Missense_Mutation_p.Q268R	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	268	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.		Q -> R (in dbSNP:rs7259764).		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)		CCTGGATCTCAGGACCTCGTG	0.517													A|||	359	0.0716853	0.1241	0.062	5008	,	,		21128	0.005		0.0716	False		,,,				2504	0.0767				p.Q268R		Atlas-SNP	.											NLRP8_ENST00000291971,NS,carcinoma,+1,2	NLRP8	225	2	0			c.A803G						scavenged	.	A	ARG/GLN	559,3847	252.1+/-258.6	41,477,1685	181.0	179.0	179.0		803	-2.8	0.0	19	dbSNP_116	179	511,8089	145.3+/-201.0	18,475,3807	yes	missense	NLRP8	NM_176811.2	43	59,952,5492	GG,GA,AA		5.9419,12.6872,8.227	benign	268/1049	56466227	1070,11936	2203	4300	6503	SO:0001583	missense	126205	exon3			GATCTCAGGACCT	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.803A>G	19.37:g.56466227A>G	ENSP00000291971:p.Gln268Arg	Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	152	76	0.5	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	138	0.06318681318681318	59	0.11991869918699187	26	0.0718232044198895	1	0.0017482517482517483	52	0.06860158311345646	A	12.91	2.079765	0.36662	0.126872	0.059419	ENSG00000179709	ENST00000291971	T	0.18960	2.18	2.04	-2.85	0.05734	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.00300	0.0009	L	0.45470	1.425	0.80722	P	0.0	D;P	0.76494	0.999;0.885	D;P	0.65010	0.931;0.566	T	0.04885	-1.0920	8	0.44086	T	0.13	.	4.1677	0.10315	0.3214:0.2213:0.4573:0.0	rs7259764;rs52837562;rs58007135;rs7259764	268;268	Q86W28-2;Q86W28	.;NALP8_HUMAN	R	268	ENSP00000291971:Q268R	ENSP00000291971:Q268R	Q	+	2	0	NLRP8	61158039	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.332000	0.01109	-0.984000	0.03507	0.421000	0.28195	CAG	A|0.922;G|0.078	0.078	strong		0.517	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57076895	57076895	+	Missense_Mutation	SNP	T	T	C	rs35950335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57076895T>C	ENST00000532437.1	-	5	3601	c.3290A>G	c.(3289-3291)cAg>cGg	p.Q1097R	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.Q1097R			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1097	Acidic.|Gly-rich.				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)				TGCCTCTCGCTGGGGGCCAAC	0.617													C|||	101	0.0201677	0.0023	0.0389	5008	,	,		19520	0.002		0.0447	False		,,,				2504	0.0245				p.Q1097R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A3290G						PASS	.	C	ARG/GLN	46,4356	821.9+/-416.4	0,46,2155	76.0	66.0	69.0		3290	2.6	0.1	11	dbSNP_126	69	402,8190	800.7+/-407.4	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	43	8,432,6057	CC,CT,TT		4.6788,1.045,3.4477	benign	1097/1730	57076895	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon6			TCTCGCTGGGGGC	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.3290A>G	11.37:g.57076895T>C	ENSP00000437271:p.Gln1097Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	C	0.621	-0.821246	0.02755	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.31769	1.48;1.48	5.05	2.58	0.30949	.	0.438549	0.19467	N	0.113554	T	0.03220	0.0094	L	0.29908	0.895	0.09310	N	1	B	0.24576	0.106	B	0.29353	0.101	T	0.16512	-1.0400	10	0.25751	T	0.34	-6.1023	7.9512	0.30017	0.0:0.1873:0.0:0.8127	rs35950335	1097	Q9C0C2	TB182_HUMAN	R	1097	ENSP00000350990:Q1097R;ENSP00000437271:Q1097R	ENSP00000350990:Q1097R	Q	-	2	0	TNKS1BP1	56833471	0.125000	0.22332	0.082000	0.20525	0.005000	0.04900	0.530000	0.23036	0.270000	0.21984	-1.694000	0.00725	CAG	T|0.968;C|0.032	0.032	strong		0.617	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
TECTA	7007	hgsc.bcm.edu	37	11	121030874	121030874	+	Missense_Mutation	SNP	A	A	G	rs147354818		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:121030874A>G	ENST00000392793.1	+	15	4991	c.4720A>G	c.(4720-4722)Ata>Gta	p.I1574V	TECTA_ENST00000264037.2_Missense_Mutation_p.I1574V			O75443	TECTA_HUMAN	tectorin alpha	1574	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGTTCCATTTATAACTGGTTT	0.413													A|||	1	0.000199681	0.0	0.0014	5008	,	,		23199	0.0		0.0	False		,,,				2504	0.0				p.I1574V		Atlas-SNP	.											.	TECTA	329	.	0			c.A4720G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	88.0	91.0	90.0		4720	1.2	1.0	11	dbSNP_134	90	14,8584	10.5+/-38.8	0,14,4285	yes	missense	TECTA	NM_005422.2	29	0,14,6488	GG,GA,AA		0.1628,0.0,0.1077	benign	1574/2156	121030874	14,12990	2203	4299	6502	SO:0001583	missense	7007	exon14			CCATTTATAACTG	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.4720A>G	11.37:g.121030874A>G	ENSP00000376543:p.Ile1574Val	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	124	65	0.524194	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	1.012	-0.687529	0.03328	0.0	0.001628	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.58652	0.32;0.32	4.87	1.2	0.21068	von Willebrand factor, type D domain (3);	0.304381	0.32273	N	0.006326	T	0.23766	0.0575	N	0.02802	-0.49	0.27653	N	0.947345	B	0.06786	0.001	B	0.08055	0.003	T	0.31613	-0.9937	10	0.02654	T	1	.	8.3001	0.32008	0.4982:0.0:0.5018:0.0	.	1574	O75443	TECTA_HUMAN	V	1574	ENSP00000376543:I1574V;ENSP00000264037:I1574V	ENSP00000264037:I1574V	I	+	1	0	TECTA	120536084	0.926000	0.31397	0.991000	0.47740	0.997000	0.91878	1.014000	0.29950	0.033000	0.15463	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.413	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
TTC29	83894	hgsc.bcm.edu	37	4	147788709	147788709	+	Missense_Mutation	SNP	C	C	T	rs10013280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:147788709C>T	ENST00000325106.4	-	8	1052	c.826G>A	c.(826-828)Gcc>Acc	p.A276T	TTC29_ENST00000513335.1_Missense_Mutation_p.A302T|TTC29_ENST00000398886.4_Missense_Mutation_p.A302T	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	276			A -> T (in dbSNP:rs10013280). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.					p.A276T(1)		breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TAGTAAGAGGCTTCCGCTTCC	0.323													C|||	2045	0.408347	0.4478	0.3963	5008	,	,		14931	0.4067		0.3022	False		,,,				2504	0.4744				p.A276T		Atlas-SNP	.											TTC29,NS,carcinoma,0,1	TTC29	63	1	1	Substitution - Missense(1)	prostate(1)	c.G826A						PASS	.	C	THR/ALA	1461,2169		277,907,631	61.0	59.0	60.0		826	5.4	1.0	4	dbSNP_119	60	2499,5653		385,1729,1962	yes	missense	TTC29	NM_031956.2	58	662,2636,2593	TT,TC,CC		30.6551,40.2479,33.6106	possibly-damaging	276/476	147788709	3960,7822	1815	4076	5891	SO:0001583	missense	83894	exon8			AAGAGGCTTCCGC	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"""Tetratricopeptide (TTC) repeat domain containing"""	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.826G>A	4.37:g.147788709C>T	ENSP00000316740:p.Ala276Thr	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	207	204	0.985507	NM_031956	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	756	0.34615384615384615	187	0.3800813008130081	127	0.35082872928176795	221	0.38636363636363635	221	0.29155672823219	C	18.13	3.554978	0.65425	0.402479	0.306551	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000398883;ENST00000504425	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	5.45	5.45	0.79879	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.75777	2.31	0.21675	P	0.999592008	D;D;D	0.89917	0.999;1.0;0.999	P;D;P	0.80764	0.863;0.994;0.863	T	0.00717	-1.1596	9	0.49607	T	0.09	-12.7436	19.6493	0.95794	0.0:1.0:0.0:0.0	rs10013280;rs17852200;rs52832245;rs59208732;rs10013280	276;302;276	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	T	302;302;276;276;276	ENSP00000423505:A302T;ENSP00000381861:A302T;ENSP00000316740:A276T;ENSP00000425778:A276T	ENSP00000316740:A276T	A	-	1	0	TTC29	148008159	1.000000	0.71417	0.989000	0.46669	0.066000	0.16364	3.914000	0.56401	2.711000	0.92665	0.591000	0.81541	GCC	C|0.648;T|0.352	0.352	strong		0.323	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956	
LRRC15	131578	hgsc.bcm.edu	37	3	194080336	194080336	+	Silent	SNP	G	G	A	rs4974533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194080336G>A	ENST00000347624.3	-	2	1522	c.1437C>T	c.(1435-1437)ccC>ccT	p.P479P	LRRC15_ENST00000428839.1_Silent_p.P485P|LRRC15_ENST00000439944.2_Silent_p.P485P	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	479					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TAGGCACCTCGGGGACATGGA	0.547													G|||	750	0.14976	0.1657	0.1398	5008	,	,		22128	0.0685		0.2425	False		,,,				2504	0.1237				p.P485P		Atlas-SNP	.											LRRC15_ENST00000439944,NS,adenoma,0,1	LRRC15	137	1	0			c.C1455T						PASS	.	G	,	747,3659	303.8+/-288.1	53,641,1509	146.0	134.0	138.0		1455,1437	-8.7	0.0	3	dbSNP_111	138	2216,6384	375.4+/-337.8	282,1652,2366	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	335,2293,3875	AA,AG,GG		25.7674,16.9542,22.7818	,	485/588,479/582	194080336	2963,10043	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			CACCTCGGGGACA	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1437C>T	3.37:g.194080336G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	237	125	0.527426	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			G|0.792;A|0.208	0.208	strong		0.547	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
ZNF646	9726	hgsc.bcm.edu	37	16	31090094	31090094	+	Missense_Mutation	SNP	G	G	A	rs78522165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31090094G>A	ENST00000394979.2	+	1	2872	c.2449G>A	c.(2449-2451)Gct>Act	p.A817T	ZNF646_ENST00000300850.5_Missense_Mutation_p.A817T			O15015	ZN646_HUMAN	zinc finger protein 646	817					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						TGGCTGGCAGGCTGGGGCCGC	0.612													G|||	137	0.0273562	0.003	0.0504	5008	,	,		18187	0.0		0.0875	False		,,,				2504	0.0102				p.A817T		Atlas-SNP	.											.	ZNF646	133	.	0			c.G2449A						PASS	.	G	THR/ALA	58,4336	56.8+/-93.2	0,58,2139	70.0	71.0	71.0		2449	-0.9	0.4	16	dbSNP_131	71	619,7981	161.9+/-214.7	17,585,3698	yes	missense	ZNF646	NM_014699.3	58	17,643,5837	AA,AG,GG		7.1977,1.32,5.2101	benign	817/1833	31090094	677,12317	2197	4300	6497	SO:0001583	missense	9726	exon2			TGGCAGGCTGGGG	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.2449G>A	16.37:g.31090094G>A	ENSP00000378429:p.Ala817Thr	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	115	58	0.504348	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		88	0.040293040293040296	0	0.0	20	0.055248618784530384	0	0.0	68	0.08970976253298153	G	8.689	0.906916	0.17833	0.0132	0.071977	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.08193	3.12;3.18	5.25	-0.882	0.10604	.	.	.	.	.	T	0.00178	0.0005	N	0.11560	0.145	0.20926	N	0.999823	B	0.13145	0.007	B	0.14578	0.011	T	0.47459	-0.9116	9	0.21014	T	0.42	-0.3298	4.8583	0.13570	0.4322:0.0:0.4244:0.1434	.	817	O15015-2	.	T	817	ENSP00000300850:A817T;ENSP00000378429:A817T	ENSP00000300850:A817T	A	+	1	0	ZNF646	30997595	0.001000	0.12720	0.433000	0.26760	0.101000	0.19017	-0.216000	0.09266	-0.019000	0.14055	0.563000	0.77884	GCT	A|0.052;C|0.000;G|0.948	0.052	strong		0.612	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
OR2J2	26707	hgsc.bcm.edu	37	6	29142054	29142054	+	Silent	SNP	C	C	G	rs3129159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29142054C>G	ENST00000377167.2	+	1	744	c.642C>G	c.(640-642)ctC>ctG	p.L214L		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						CTCTCATTCTCATTCTCACTA	0.473													C|||	1893	0.377995	0.112	0.451	5008	,	,		20987	0.378		0.5477	False		,,,				2504	0.5112				p.L214L		Atlas-SNP	.											.	OR2J2	51	.	0			c.C642G						PASS	.	C		733,3157		72,589,1284	155.0	129.0	137.0		642	1.1	0.3	6	dbSNP_103	137	4502,3786		1240,2022,882	no	coding-synonymous	OR2J2	NM_030905.2		1312,2611,2166	GG,GC,CC		45.6805,18.8432,42.9874		214/313	29142054	5235,6943	1945	4144	6089	SO:0001819	synonymous_variant	26707	exon1			CATTCTCATTCTC		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.642C>G	6.37:g.29142054C>G		Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	314	155	0.493631	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Silent	SNP	ENST00000377167.2	37	CCDS43434.1																																																																																			C|0.567;G|0.433	0.433	strong		0.473	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2		
SPSB1	80176	hgsc.bcm.edu	37	1	9416151	9416151	+	Silent	SNP	G	G	A	rs9435243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:9416151G>A	ENST00000328089.6	+	2	542	c.201G>A	c.(199-201)gtG>gtA	p.V67V	SPSB1_ENST00000377399.2_Silent_p.V67V|SPSB1_ENST00000357898.3_Silent_p.V67V	NM_025106.3	NP_079382.2	Q96BD6	SPSB1_HUMAN	splA/ryanodine receptor domain and SOCS box containing 1	67	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(2)|lung(5)|prostate(2)	13	all_lung(157;0.194)	all_epithelial(116;4.38e-15)|all_lung(118;0.000156)|Lung NSC(185;0.000446)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;2.72e-07)|COAD - Colon adenocarcinoma(227;9.12e-05)|Kidney(185;0.000296)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00193)|BRCA - Breast invasive adenocarcinoma(304;0.00202)|READ - Rectum adenocarcinoma(331;0.0419)		ATGTCTTTGTGAAGGAGGACG	0.582													G|||	1299	0.259385	0.2368	0.3401	5008	,	,		20489	0.2748		0.1998	False		,,,				2504	0.2781				p.V67V		Atlas-SNP	.											.	SPSB1	22	.	0			c.G201A						PASS	.	G		1056,3350	387.7+/-326.6	147,762,1294	174.0	169.0	170.0		201	2.2	1.0	1	dbSNP_119	170	1998,6602	350.7+/-328.0	230,1538,2532	no	coding-synonymous	SPSB1	NM_025106.3		377,2300,3826	AA,AG,GG		23.2326,23.9673,23.4815		67/274	9416151	3054,9952	2203	4300	6503	SO:0001819	synonymous_variant	80176	exon2			CTTTGTGAAGGAG		CCDS102.1	1p36.22	2008-02-05			ENSG00000171621	ENSG00000171621			30628	protein-coding gene	gene with protein product		611657				15713673, 12076535	Standard	NM_025106		Approved	SSB-1	uc010oae.2	Q96BD6	OTTHUMG00000001279	ENST00000328089.6:c.201G>A	1.37:g.9416151G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	90	6	0.0666667	NM_025106	A2A275|Q59FA1|Q5TIH9|Q9BRY9|Q9H6C5	Silent	SNP	ENST00000328089.6	37	CCDS102.1																																																																																			G|0.765;A|0.235	0.235	strong		0.582	SPSB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003727.2	NM_025106	
DOCK6	57572	hgsc.bcm.edu	37	19	11347493	11347493	+	Silent	SNP	T	T	C	rs737337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11347493T>C	ENST00000294618.7	-	19	2147	c.2136A>G	c.(2134-2136)acA>acG	p.T712T	C19orf80_ENST00000591200.1_5'Flank|C19orf80_ENST00000252453.8_5'Flank|RN7SL298P_ENST00000581369.1_RNA|DOCK6_ENST00000319867.7_Silent_p.T16T	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	712	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						AGGACACGGCTGTGAGCTCCA	0.667													C|||	1244	0.248403	0.4887	0.1974	5008	,	,		18677	0.2401		0.0736	False		,,,				2504	0.1483				p.T712T		Atlas-SNP	.											.	DOCK6	104	.	0			c.A2136G						PASS	.	C		1432,2626		222,988,819	21.0	29.0	26.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2136	-9.3	0.0	19	dbSNP_86	26	595,7467		17,561,3453	yes	coding-synonymous	DOCK6	NM_020812.2		239,1549,4272	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	7.3803,35.2883,16.7244		712/2048	11347493	2027,10093	2029	4031	6060	SO:0001819	synonymous_variant	57572	exon19			CACGGCTGTGAGC		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.2136A>G	19.37:g.11347493T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			T|0.740;C|0.260	0.260	strong		0.667	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
APOBEC1	339	hgsc.bcm.edu	37	12	7805154	7805154	+	Missense_Mutation	SNP	G	G	A	rs61753204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7805154G>A	ENST00000229304.4	-	3	342	c.322C>T	c.(322-324)Cct>Tct	p.P108S		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	108					cellular response to insulin stimulus (GO:0032869)|cytidine deamination (GO:0009972)|cytidine to uridine editing (GO:0016554)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|gene expression (GO:0010467)|lipid metabolic process (GO:0006629)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein transport (GO:0042953)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to osmotic stress (GO:0006970)|response to zinc ion (GO:0010043)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	AU-rich element binding (GO:0017091)|cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						GTCACACCAGGGTGCCGACTC	0.498													G|||	45	0.00898562	0.0015	0.0072	5008	,	,		-128	0.002		0.0139	False		,,,				2504	0.0225				p.P108S	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											.	APOBEC1	43	.	0			c.C322T						PASS	.	G	SER/PRO	14,4392	21.2+/-45.6	1,12,2190	65.0	64.0	64.0		322	3.2	0.2	12	dbSNP_129	64	129,8471	66.7+/-129.0	1,127,4172	yes	missense	APOBEC1	NM_001644.3	74	2,139,6362	AA,AG,GG		1.5,0.3177,1.0995	probably-damaging	108/237	7805154	143,12863	2203	4300	6503	SO:0001583	missense	339	exon3			CACCAGGGTGCCG	U72891	CCDS8579.1	12p13.1	2007-02-01			ENSG00000111701	ENSG00000111701		"""Apolipoprotein B mRNA editing enzymes"""	604	protein-coding gene	gene with protein product		600130					Standard	XM_005253355		Approved	BEDP, CDAR1, APOBEC-1, HEPR	uc001qtb.3	P41238	OTTHUMG00000141288	ENST00000229304.4:c.322C>T	12.37:g.7805154G>A	ENSP00000229304:p.Pro108Ser	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	80	44	0.55	NM_001644	Q9UE64|Q9UM71	Missense_Mutation	SNP	ENST00000229304.4	37	CCDS8579.1	15	0.006868131868131868	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	10.29	1.309349	0.23821	0.003177	0.015	ENSG00000111701	ENST00000229304	T	0.64991	-0.13	4.12	3.23	0.37069	APOBEC-like, N-terminal (1);	0.000000	0.56097	D	0.000039	T	0.66934	0.2840	M	0.73319	2.225	0.26925	N	0.966593	D	0.89917	1.0	D	0.81914	0.995	T	0.60880	-0.7175	10	0.54805	T	0.06	-14.1848	7.9106	0.29789	0.1139:0.0:0.8861:0.0	rs61753204	108	P41238	ABEC1_HUMAN	S	108	ENSP00000229304:P108S	ENSP00000229304:P108S	P	-	1	0	APOBEC1	7696421	0.975000	0.34042	0.171000	0.22900	0.014000	0.08584	2.996000	0.49449	1.105000	0.41606	0.462000	0.41574	CCT	G|0.989;A|0.011	0.011	strong		0.498	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644	
FBN3	84467	hgsc.bcm.edu	37	19	8176919	8176919	+	Silent	SNP	C	C	T	rs4804264	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8176919C>T	ENST00000600128.1	-	31	4317	c.3903G>A	c.(3901-3903)ccG>ccA	p.P1301P	FBN3_ENST00000601739.1_Silent_p.P1301P|FBN3_ENST00000270509.2_Silent_p.P1301P			Q75N90	FBN3_HUMAN	fibrillin 3	1301	EGF-like 19; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TGAAACTCCCCGGGATGTTGA	0.597													C|||	3452	0.689297	0.6604	0.719	5008	,	,		12420	0.7847		0.5298	False		,,,				2504	0.773				p.P1301P		Atlas-SNP	.											.	FBN3	300	.	0			c.G3903A						PASS	.	C		2841,1565	668.8+/-402.1	923,995,285	142.0	121.0	128.0		3903	-8.7	0.1	19	dbSNP_111	128	4495,4105	591.7+/-392.9	1154,2187,959	no	coding-synonymous	FBN3	NM_032447.3		2077,3182,1244	TT,TC,CC		47.7326,35.5197,43.5953		1301/2810	8176919	7336,5670	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon30			ACTCCCCGGGATG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3903G>A	19.37:g.8176919C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	149	147	0.986577	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			C|0.388;N|0.000	.	strong		0.597	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
XIRP2	129446	hgsc.bcm.edu	37	2	168099775	168099775	+	Missense_Mutation	SNP	C	C	G	rs16853305	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168099775C>G	ENST00000409195.1	+	9	1962	c.1873C>G	c.(1873-1875)Ccc>Gcc	p.P625A	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.P403A|XIRP2_ENST00000295237.9_Missense_Mutation_p.P625A|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	450					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TGAAACCCAACCCATCGACAC	0.458													C|||	1165	0.232628	0.3828	0.1628	5008	,	,		19982	0.1855		0.1262	False		,,,				2504	0.2372				p.P625A		Atlas-SNP	.											.	XIRP2	914	.	0			c.C1873G						PASS	.	C	ALA/PRO,ALA/PRO,,,	1273,2641		211,851,895	83.0	87.0	86.0		1207,1873,,,	5.9	1.0	2	dbSNP_123	86	932,7326		55,822,3252	yes	missense,missense,intron,intron,intron	XIRP2	NM_001199144.1,NM_152381.5,NM_001079810.3,NM_001199143.1,NM_001199145.1	27,27,,,	266,1673,4147	GG,GC,CC		11.286,32.5243,18.1153	probably-damaging,probably-damaging,,,	403/3328,625/3550,,,	168099775	2205,9967	1957	4129	6086	SO:0001583	missense	129446	exon9			ACCCAACCCATCG	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.1873C>G	2.37:g.168099775C>G	ENSP00000386840:p.Pro625Ala	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	258	121	0.468992	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	466	0.21336996336996336	199	0.40447154471544716	52	0.143646408839779	117	0.20454545454545456	98	0.12928759894459102	C	22.4	4.282935	0.80692	0.325243	0.11286	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.55052	0.54;0.54;0.54	5.93	5.93	0.95920	.	0.106308	0.64402	D	0.000004	T	0.00012	0.0000	L	0.32530	0.975	0.09310	P	0.9999999890341	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.72338	0.977;0.961;0.961	T	0.30001	-0.9993	9	0.72032	D	0.01	-8.7118	19.9513	0.97200	0.0:1.0:0.0:0.0	rs16853305;rs52803621;rs56537632;rs58699025;rs16853305	450;450;403	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	A	625;625;403	ENSP00000386840:P625A;ENSP00000295237:P625A;ENSP00000387255:P403A	ENSP00000295237:P625A	P	+	1	0	XIRP2	167808021	0.998000	0.40836	0.997000	0.53966	0.834000	0.47266	1.729000	0.38115	2.814000	0.96858	0.655000	0.94253	CCC	C|0.784;G|0.216	0.216	strong		0.458	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
SRP14	6727	hgsc.bcm.edu	37	15	40330518	40330518	+	Silent	SNP	T	T	G	rs1059395	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:40330518T>G	ENST00000267884.6	-	3	246	c.175A>C	c.(175-177)Aga>Cga	p.R59R	SRP14_ENST00000559081.1_Silent_p.R59R|SRP14-AS1_ENST00000504245.1_lincRNA|SRP14_ENST00000560773.1_5'UTR|SRP14_ENST00000558720.1_5'UTR|SRP14_ENST00000558527.1_5'UTR	NM_003134.4	NP_003125.3	P37108	SRP14_HUMAN	signal recognition particle 14kDa (homologous Alu RNA binding protein)	59					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|protein targeting to ER (GO:0045047)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intercellular bridge (GO:0045171)|nucleolus (GO:0005730)|nucleus (GO:0005634)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|skin(1)|upper_aerodigestive_tract(1)	3		all_cancers(109;7.56e-18)|all_epithelial(112;4.02e-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;1.84e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0505)		TCGGTAGCTCTTAACAGACAC	0.463													T|||	489	0.0976438	0.0953	0.1023	5008	,	,		19815	0.0248		0.175	False		,,,				2504	0.093				p.R59R		Atlas-SNP	.											.	SRP14	11	.	0			c.A175C						PASS	.	T		430,3368		21,388,1490	122.0	115.0	117.0		175	3.7	1.0	15	dbSNP_86	117	1465,6767		122,1221,2773	no	coding-synonymous	SRP14	NM_003134.4		143,1609,4263	GG,GT,TT		17.7964,11.3217,15.7523		59/137	40330518	1895,10135	1899	4116	6015	SO:0001819	synonymous_variant	6727	exon3			TAGCTCTTAACAG		CCDS42017.1	15q22	2008-08-15	2002-08-29		ENSG00000140319	ENSG00000140319			11299	protein-coding gene	gene with protein product		600708	"""signal recognition particle 14kD (homologous Alu RNA-binding protein)"""			8196634	Standard	NM_003134		Approved	ALURBP, MGC14326	uc001zkq.2	P37108		ENST00000267884.6:c.175A>C	15.37:g.40330518T>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	91	47	0.516484	NM_003134	B5BUF5|Q6B0K5|Q96Q14	Silent	SNP	ENST00000267884.6	37	CCDS42017.1																																																																																			T|0.867;G|0.133	0.133	strong		0.463	SRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418262.2	NM_003134	
LRRC29	26231	hgsc.bcm.edu	37	16	67241930	67241930	+	Missense_Mutation	SNP	C	C	T	rs34595673	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67241930C>T	ENST00000409037.1	-	3	1245	c.349G>A	c.(349-351)Ggc>Agc	p.G117S	LRRC29_ENST00000462169.1_5'Flank|LRRC29_ENST00000341546.3_Missense_Mutation_p.G117S|LRRC29_ENST00000409509.1_Missense_Mutation_p.G117S|LRRC29_ENST00000393992.1_Missense_Mutation_p.G117S			Q8WV35	LRC29_HUMAN	leucine rich repeat containing 29	117			G -> S (in dbSNP:rs34595673).							autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		GCAACCAAGCCGTTGTCTGTG	0.612													C|||	455	0.0908546	0.2844	0.0288	5008	,	,		19362	0.0099		0.0278	False		,,,				2504	0.0215				p.G117S		Atlas-SNP	.											.	LRRC29	13	.	0			c.G349A						PASS	.	C	SER/GLY,SER/GLY	1023,3373		129,765,1304	22.0	20.0	21.0		349,349	5.6	0.5	16	dbSNP_126	21	273,8327		8,257,4035	yes	missense,missense	LRRC29	NM_001004055.1,NM_012163.2	56,56	137,1022,5339	TT,TC,CC		3.1744,23.2712,9.9723	possibly-damaging,possibly-damaging	117/224,117/224	67241930	1296,11700	2198	4300	6498	SO:0001583	missense	26231	exon5			CCAAGCCGTTGTC	AF176701	CCDS32465.1	16q22.1	2008-02-05	2004-08-23	2004-08-26	ENSG00000125122	ENSG00000125122			13605	protein-coding gene	gene with protein product			"""F-box and leucine-rich repeat protein 9"""	FBXL9		10531037	Standard	NM_012163		Approved	FBL9	uc002esf.3	Q8WV35	OTTHUMG00000154403	ENST00000409037.1:c.349G>A	16.37:g.67241930C>T	ENSP00000387318:p.Gly117Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	111	54	0.486486	NM_001004055	B2RE92|Q9UKA0	Missense_Mutation	SNP	ENST00000409037.1	37	CCDS32465.1	157	0.07188644688644688	124	0.25203252032520324	10	0.027624309392265192	4	0.006993006993006993	19	0.025065963060686015	C	19.59	3.855436	0.71719	0.232712	0.031744	ENSG00000125122	ENST00000409509;ENST00000393992;ENST00000409037;ENST00000341546;ENST00000433915;ENST00000424285	T;T;T;T;T;T	0.01172	5.23;5.23;5.23;5.23;5.23;5.23	5.57	5.57	0.84162	.	0.603229	0.17346	N	0.177597	T	0.00012	0.0000	L	0.55103	1.725	0.47584	P	5.309999999999482E-4	P	0.37824	0.609	B	0.21546	0.035	T	0.62751	-0.6788	9	0.35671	T	0.21	.	15.0432	0.71807	0.0:1.0:0.0:0.0	rs34595673	117	Q8WV35	LRC29_HUMAN	S	117;117;117;117;69;117	ENSP00000386622:G117S;ENSP00000377561:G117S;ENSP00000387318:G117S;ENSP00000344364:G117S;ENSP00000413129:G69S;ENSP00000409459:G117S	ENSP00000344364:G117S	G	-	1	0	LRRC29	65799431	0.968000	0.33430	0.482000	0.27366	0.824000	0.46624	2.258000	0.43249	2.617000	0.88574	0.655000	0.94253	GGC	C|0.909;T|0.091	0.091	strong		0.612	LRRC29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335073.1	NM_012163	
OBSCN	84033	hgsc.bcm.edu	37	1	228412227	228412227	+	Silent	SNP	T	T	C	rs386640006|rs1771480	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228412227T>C	ENST00000422127.1	+	9	2765	c.2721T>C	c.(2719-2721)agT>agC	p.S907S	OBSCN_ENST00000570156.2_Silent_p.S999S|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.S907S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	907	Ig-like 9.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGGAGCCAGTGCCACACTGA	0.612													T|||	2066	0.41254	0.5885	0.402	5008	,	,		17552	0.3849		0.3668	False		,,,				2504	0.2577				p.S999S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T2997C						PASS	.						41.0	43.0	42.0					1																	228412227		2110	4222	6332	SO:0001819	synonymous_variant	84033	exon10			AGCCAGTGCCACA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2721T>C	1.37:g.228412227T>C		Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	201	100	0.497512	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			T|0.612;C|0.388	0.388	strong		0.612	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37455583	37455583	+	Silent	SNP	G	G	A	rs41276132		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:37455583G>A	ENST00000374660.1	+	19	2046	c.1947G>A	c.(1945-1947)gcG>gcA	p.A649A	ANKRD30A_ENST00000602533.1_Intron|ANKRD30A_ENST00000361713.1_Silent_p.A649A			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	586					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						CCAAGGCTGCGCATCAAAAAG	0.299																																					p.A649A		Atlas-SNP	.											ANKRD30A,NS,haematopoietic_neoplasm,+1,1	ANKRD30A	448	1	0			c.G1947A						scavenged	.						3.0	3.0	3.0					10																	37455583		1398	3151	4549	SO:0001819	synonymous_variant	91074	exon19			GGCTGCGCATCAA	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	ENST00000374660.1:c.1947G>A	10.37:g.37455583G>A		Somatic	722	1	0.00138504		WXS	Illumina HiSeq	Phase_I	621	16	0.0257649	NM_052997	Q5W025	Silent	SNP	ENST00000374660.1	37																																																																																				A|1.000;|0.000	1.000	weak		0.299	ANKRD30A-002	PUTATIVE	NMD_exception|basic	protein_coding	protein_coding	OTTHUMT00000047589.2	NM_052997	
MACF1	23499	hgsc.bcm.edu	37	1	39549942	39549942	+	Missense_Mutation	SNP	C	C	T	rs369843705		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:39549942C>T	ENST00000372915.3	+	1	139	c.52C>T	c.(52-54)Cgg>Tgg	p.R18W	MACF1_ENST00000317713.7_Missense_Mutation_p.R18W|MACF1_ENST00000539005.1_Missense_Mutation_p.R18W|MACF1_ENST00000361689.2_Missense_Mutation_p.R18W|MACF1_ENST00000602421.1_Missense_Mutation_p.R18W|MACF1_ENST00000484793.1_Missense_Mutation_p.R18W|MACF1_ENST00000545844.1_Missense_Mutation_p.R18W|MACF1_ENST00000567887.1_Missense_Mutation_p.R18W			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	18	Actin-binding.				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)			TCGGAGTGAGCGGTCTTGTCG	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16833	0.0		0.0	False		,,,				2504	0.0				p.R18W		Atlas-SNP	.											MACF1_ENST00000361689,caecum,carcinoma,-1,1	MACF1	909	1	0			c.C52T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	68.0	61.0	64.0		52	0.7	1.0	1		64	1,8599	1.2+/-3.3	0,1,4299	no	missense	MACF1	NM_012090.4	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		18/5431	39549942	1,13005	2203	4300	6503	SO:0001583	missense	23499	exon3			AGTGAGCGGTCTT	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.52C>T	1.37:g.39549942C>T	ENSP00000362006:p.Arg18Trp	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	80	74	0.925	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	16.64	3.178377	0.57692	0.0	1.16E-4	ENSG00000127603	ENST00000484793;ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005	T;T;T;T;T	0.66099	-0.15;-0.13;-0.15;-0.19;0.0	5.35	0.69	0.18039	.	.	.	.	.	T	0.58466	0.2124	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.63598	-0.6601	9	0.62326	D	0.03	.	12.8938	0.58087	0.6321:0.3679:0.0:0.0	.	18	F8W8Q1	.	W	18;18;18;18;34;18;18	ENSP00000439537:R18W;ENSP00000362006:R18W;ENSP00000354573:R18W;ENSP00000313438:R18W;ENSP00000444364:R18W	ENSP00000313438:R18W	R	+	1	2	MACF1	39322529	0.998000	0.40836	0.998000	0.56505	0.963000	0.63663	0.510000	0.22723	0.559000	0.29153	0.655000	0.94253	CGG	.	.	none		0.642	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
OR2T8	343172	hgsc.bcm.edu	37	1	248084440	248084440	+	Missense_Mutation	SNP	T	T	G	rs111379878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248084440T>G	ENST00000319968.4	+	1	121	c.121T>G	c.(121-123)Tcc>Gcc	p.S41A		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S41A(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GTTTGGCAATTCCCTCATGAT	0.502													T|||	184	0.0367412	0.059	0.0274	5008	,	,		14500	0.0109		0.0249	False		,,,				2504	0.0521				p.S41A		Atlas-SNP	.											OR2T8,NS,other,0,1	OR2T8	67	1	1	Substitution - Missense(1)	pancreas(1)	c.T121G						scavenged	.						63.0	57.0	59.0					1																	248084440		2202	4280	6482	SO:0001583	missense	343172	exon1			GGCAATTCCCTCA		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.121T>G	1.37:g.248084440T>G	ENSP00000326225:p.Ser41Ala	Somatic	494	0	0		WXS	Illumina HiSeq	Phase_I	578	21	0.0363322	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	29	0.013278388278388278	20	0.04065040650406504	5	0.013812154696132596	0	0.0	4	0.005277044854881266	N	3.205	-0.162862	0.06502	.	.	ENSG00000177462	ENST00000319968	T	0.00012	9.33	3.65	-0.565	0.11771	GPCR, rhodopsin-like superfamily (1);	0.792834	0.10272	N	0.694616	T	0.00012	0.0000	N	0.10809	0.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13953	-1.0490	10	0.06891	T	0.86	.	0.9955	0.01465	0.2883:0.2491:0.3226:0.14	.	41	A6NH00	OR2T8_HUMAN	A	41	ENSP00000326225:S41A	ENSP00000326225:S41A	S	+	1	0	OR2T8	246151063	0.000000	0.05858	0.060000	0.19600	0.299000	0.27559	-3.158000	0.00579	-0.030000	0.13804	-0.186000	0.12905	TCC	T|0.988;G|0.012	0.012	strong		0.502	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
FHOD1	29109	hgsc.bcm.edu	37	16	67265360	67265360	+	Silent	SNP	C	C	A	rs6499118	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67265360C>A	ENST00000258201.4	-	16	2725	c.2478G>T	c.(2476-2478)gcG>gcT	p.A826A		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	826	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		AGTTGCCCACCGCTAGGAGGG	0.567													A|||	1312	0.261981	0.7368	0.0922	5008	,	,		20718	0.0238		0.0706	False		,,,				2504	0.183				p.A826A		Atlas-SNP	.											.	FHOD1	86	.	0			c.G2478T						PASS	.	A		2657,1739	520.2+/-370.2	812,1033,353	112.0	104.0	107.0		2478	4.3	1.0	16	dbSNP_116	107	604,7996	792.3+/-407.5	28,548,3724	no	coding-synonymous	FHOD1	NM_013241.2		840,1581,4077	AA,AC,CC		7.0233,39.5587,25.0923		826/1165	67265360	3261,9735	2198	4300	6498	SO:0001819	synonymous_variant	29109	exon16			GCCCACCGCTAGG	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.2478G>T	16.37:g.67265360C>A		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	119	63	0.529412	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	37	CCDS10834.1																																																																																			C|0.755;A|0.245	0.245	strong		0.567	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
ZCCHC14	23174	hgsc.bcm.edu	37	16	87446368	87446368	+	Silent	SNP	C	C	T	rs2241615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:87446368C>T	ENST00000268616.4	-	12	1765	c.1548G>A	c.(1546-1548)ccG>ccA	p.P516P		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	516							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		TCCCTCTTTCCGGCTTGTGCA	0.557													C|||	973	0.194289	0.1195	0.2392	5008	,	,		20712	0.4256		0.1193	False		,,,				2504	0.1022				p.P516P		Atlas-SNP	.											.	ZCCHC14	87	.	0			c.G1548A						PASS	.	C		514,3882	236.5+/-248.6	30,454,1714	72.0	73.0	73.0		1548	-5.2	0.0	16	dbSNP_98	73	973,7627	212.0+/-252.4	58,857,3385	no	coding-synonymous	ZCCHC14	NM_015144.2		88,1311,5099	TT,TC,CC		11.314,11.6924,11.442		516/950	87446368	1487,11509	2198	4300	6498	SO:0001819	synonymous_variant	23174	exon12			TCTTTCCGGCTTG	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.1548G>A	16.37:g.87446368C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	167	84	0.502994	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Silent	SNP	ENST00000268616.4	37	CCDS10961.1																																																																																			C|0.858;T|0.142	0.142	strong		0.557	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
TNRC18	84629	hgsc.bcm.edu	37	7	5352949	5352949	+	Missense_Mutation	SNP	G	G	C	rs76882791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5352949G>C	ENST00000430969.1	-	27	7921	c.7573C>G	c.(7573-7575)Ctc>Gtc	p.L2525V	TNRC18_ENST00000399537.4_Missense_Mutation_p.L2525V	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2525							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)		TCCTGGGCGAGGTCCCCGTCG	0.721													G|||	694	0.138578	0.0923	0.2752	5008	,	,		9519	0.1468		0.1133	False		,,,				2504	0.1217				p.L2525V		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7573G						PASS	.	G	VAL/LEU	182,2532		6,170,1181	3.0	3.0	3.0		7573	3.3	0.7	7	dbSNP_131	3	598,5770		19,560,2605	no	missense	TNRC18	NM_001080495.2	32	25,730,3786	CC,CG,GG		9.3907,6.706,8.5884	possibly-damaging	2525/2969	5352949	780,8302	1357	3184	4541	SO:0001583	missense	84629	exon27			GGGCGAGGTCCCC	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.7573C>G	7.37:g.5352949G>C	ENSP00000395538:p.Leu2525Val	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	33	13	0.393939	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	285|285	0.1304945054945055|0.1304945054945055	55|55	0.11178861788617886|0.11178861788617886	83|83	0.2292817679558011|0.2292817679558011	57|57	0.09965034965034965|0.09965034965034965	90|90	0.11873350923482849|0.11873350923482849	g|g	8.857|8.857	0.946106|0.946106	0.18356|0.18356	0.06706|0.06706	0.093907|0.093907	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.11712|.	2.75;2.75|.	4.24|4.24	3.34|3.34	0.38264|0.38264	.|.	0.552403|.	0.13692|.	N|.	0.369441|.	T|T	0.00039|0.00039	0.0001|0.0001	L|L	0.44542|0.44542	1.39|1.39	0.80722|0.80722	P|P	0.0|0.0	P|.	0.35328|.	0.495|.	B|.	0.31442|.	0.13|.	T|T	0.08932|0.08932	-1.0698|-1.0698	9|4	0.02654|.	T|.	1|.	.|.	8.8698|8.8698	0.35309|0.35309	0.087:0.1541:0.7588:0.0|0.087:0.1541:0.7588:0.0	.|.	2525|.	O15417|.	TNC18_HUMAN|.	V|R	2525|338	ENSP00000382452:L2525V;ENSP00000395538:L2525V|.	ENSP00000382452:L2525V|.	L|P	-|-	1|2	0|0	TNRC18|TNRC18	5319475|5319475	0.000000|0.000000	0.05858|0.05858	0.692000|0.692000	0.30179|0.30179	0.216000|0.216000	0.24613|0.24613	0.405000|0.405000	0.21015|0.21015	2.282000|2.282000	0.76494|0.76494	0.561000|0.561000	0.74099|0.74099	CTC|CCT	G|0.869;C|0.131	0.131	strong		0.721	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
SLC38A10	124565	hgsc.bcm.edu	37	17	79220224	79220224	+	Missense_Mutation	SNP	G	G	C	rs2725405	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79220224G>C	ENST00000374759.3	-	16	2875	c.2492C>G	c.(2491-2493)gCc>gGc	p.A831G		NM_001037984.1	NP_001033073.1	Q9HBR0	S38AA_HUMAN	solute carrier family 38, member 10	831			A -> G (in dbSNP:rs2725405). {ECO:0000269|PubMed:15498874}.		amino acid transport (GO:0006865)|bone development (GO:0060348)|sodium ion transport (GO:0006814)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			TCTCAGCTTGGCCTGGGCTGC	0.701													G|||	2146	0.428514	0.025	0.4784	5008	,	,		14012	0.7004		0.4374	False		,,,				2504	0.6493				p.A831G		Atlas-SNP	.											.	SLC38A10	133	.	0			c.C2492G						PASS	.	G	GLY/ALA	327,3373		26,275,1549	11.0	13.0	13.0		2492	0.7	0.0	17	dbSNP_100	13	3573,4591		819,1935,1328	yes	missense	SLC38A10	NM_001037984.1	60	845,2210,2877	CC,CG,GG		43.7653,8.8378,32.8726	benign	831/1120	79220224	3900,7964	1850	4082	5932	SO:0001583	missense	124565	exon16			AGCTTGGCCTGGG	BC014642	CCDS11780.1, CCDS42397.1	17q25.3	2013-05-22			ENSG00000157637	ENSG00000157637		"""Solute carriers"""	28237	protein-coding gene	gene with protein product							Standard	XM_005257019		Approved	MGC15523, PP1744	uc002jzz.1	Q9HBR0	OTTHUMG00000168049	ENST00000374759.3:c.2492C>G	17.37:g.79220224G>C	ENSP00000363891:p.Ala831Gly	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	62	41	0.66129	NM_001037984	Q6ZRC5|Q8NA99|Q96C66	Missense_Mutation	SNP	ENST00000374759.3	37	CCDS42397.1	946	0.43315018315018317	25	0.0508130081300813	175	0.48342541436464087	410	0.7167832167832168	336	0.44327176781002636	G	12.76	2.033367	0.35893	0.088378	0.437653	ENSG00000157637	ENST00000374759;ENST00000540966	T;T	0.53640	2.93;0.61	3.98	0.68	0.17980	.	4.052290	0.01250	N	0.008853	T	0.00012	0.0000	L	0.43923	1.385	0.80722	P	0.0	P	0.39282	0.666	B	0.33339	0.162	T	0.45411	-0.9263	9	0.37606	T	0.19	-0.9264	5.2532	0.15532	0.1956:0.1672:0.6372:0.0	rs2725405	831	Q9HBR0	S38AA_HUMAN	G	831;217	ENSP00000363891:A831G;ENSP00000437601:A217G	ENSP00000363891:A831G	A	-	2	0	SLC38A10	76834819	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	0.368000	0.20399	0.336000	0.23639	0.467000	0.42956	GCC	G|0.561;C|0.439	0.439	strong		0.701	SLC38A10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397747.1	NM_138570	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32605266	32605266	+	Missense_Mutation	SNP	G	G	A	rs1047992	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32605266G>A	ENST00000343139.5	+	1	133	c.31G>A	c.(31-33)Gcc>Acc	p.A11T	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.A11T|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.A11T	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	11			A -> T (in allele DQA1*05:05, allele DQA1*05:08 and allele DQA1*05:09; dbSNP:rs1047992).	A -> S (in Ref. 4; AAA59760). {ECO:0000305}.	antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						GCTGCTGGGGGCCCTCGCTCT	0.517																																					p.A11T		Atlas-SNP	.											.	HLA-DQA1	52	.	0			c.G31A						PASS	.	G	THR/ALA	316,4090		43,230,1930	75.0	68.0	70.0		31	0.0	0.0	6	dbSNP_86	70	564,8036		60,444,3796	no	missense	HLA-DQA1	NM_002122.3	58	103,674,5726	AA,AG,GG		6.5581,7.172,6.7661	benign	11/256	32605266	880,12126	2203	4300	6503	SO:0001583	missense	3117	exon1			CTGGGGGCCCTCG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.31G>A	6.37:g.32605266G>A	ENSP00000339398:p.Ala11Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	97	23	0.237113	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	255	0.11675824175824176	72	0.14634146341463414	46	0.1270718232044199	54	0.0944055944055944	83	0.10949868073878628	.	3.358	-0.131142	0.06753	0.07172	0.065581	ENSG00000196735	ENST00000422863;ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949	T;T;T;T;T	0.24723	1.84;4.7;4.7;4.39;4.7	4.15	0.00859	0.14075	.	0.954045	0.08671	N	0.910981	T	0.04363	0.0120	N	0.17838	0.53	0.80722	P	0.0	B;B	0.25609	0.13;0.004	B;B	0.22152	0.038;0.019	T	0.43972	-0.9358	9	0.18276	T	0.48	.	6.123	0.20164	0.4943:0.0:0.5057:0.0	rs1047992;rs2308822;rs9469203;rs16868253;rs35899717	17;11	Q59F33;G4XQK2	.;.	T	11	ENSP00000405797:A11T;ENSP00000339398:A11T;ENSP00000378767:A11T;ENSP00000437302:A11T;ENSP00000364087:A11T	ENSP00000339398:A11T	A	+	1	0	HLA-DQA1	32713244	0.000000	0.05858	0.006000	0.13384	0.168000	0.22595	-0.452000	0.06787	0.098000	0.17522	-0.275000	0.10095	GCC	G|0.879;A|0.121	0.121	strong		0.517	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
KDM8	79831	hgsc.bcm.edu	37	16	27231740	27231740	+	Silent	SNP	G	G	C	rs34577370	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:27231740G>C	ENST00000286096.4	+	7	1193	c.1020G>C	c.(1018-1020)ctG>ctC	p.L340L	KDM8_ENST00000380948.2_Intron|KDM8_ENST00000567785.1_3'UTR|KDM8_ENST00000568965.1_Intron|KDM8_ENST00000441782.2_Silent_p.L378L	NM_024773.2	NP_079049.2	Q8N371	KDM8_HUMAN	lysine (K)-specific demethylase 8	340	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				G2/M transition of mitotic cell cycle (GO:0000086)|histone H3-K36 demethylation (GO:0070544)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone demethylase activity (H3-K36 specific) (GO:0051864)|metal ion binding (GO:0046872)										ACATCCGGCTGTATTCCCCGC	0.622													G|||	396	0.0790735	0.0545	0.0893	5008	,	,		17903	0.0069		0.1332	False		,,,				2504	0.1237				p.L378L		Atlas-SNP	.											.	.	.	.	0			c.G1134C						PASS	.	G	,	376,4018	189.5+/-215.6	14,348,1835	152.0	150.0	151.0		1134,1020	4.3	1.0	16	dbSNP_126	151	1241,7359	250.0+/-277.0	86,1069,3145	no	coding-synonymous,coding-synonymous	JMJD5	NM_001145348.1,NM_024773.2	,	100,1417,4980	CC,CG,GG		14.4302,8.5571,12.4442	,	378/455,340/417	27231740	1617,11377	2197	4300	6497	SO:0001819	synonymous_variant	79831	exon7			CCGGCTGTATTCC	AK023860	CCDS10627.1, CCDS45448.1	16p12.1	2012-03-28	2012-03-28	2012-03-28	ENSG00000155666	ENSG00000155666		"""Chromatin-modifying enzymes / K-demethylases"""	25840	protein-coding gene	gene with protein product		611917	"""jumonji domain containing 5"""	JMJD5		20457893	Standard	NM_024773		Approved	FLJ13798	uc010vcn.1	Q8N371	OTTHUMG00000131677	ENST00000286096.4:c.1020G>C	16.37:g.27231740G>C		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_001145348	B4DLU9|Q6VAK5|Q9H8B1	Silent	SNP	ENST00000286096.4	37	CCDS10627.1																																																																																			G|0.891;C|0.109	0.109	strong		0.622	KDM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254580.3	NM_024773	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632781	32632781	+	Missense_Mutation	SNP	A	A	T	rs1049066	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32632781A>T	ENST00000399084.1	-	3	351	c.173T>A	c.(172-174)cTt>cAt	p.L58H	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.L58H|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.L58H|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.L58H|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	58	Beta-1.		Y -> G (in allele DQB1*03:05, allele DQB1*03:17, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:23; requires 2 nucleotide substitutions).|Y -> L (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:15, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TCTGGTCACAAGACGCACGCG	0.632									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.L58H	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.T173A						PASS	.						28.0	30.0	30.0					6																	32632781		2120	4206	6326	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GTCACAAGACGCA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.173T>A	6.37:g.32632781A>T	ENSP00000382034:p.Leu58His	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	33	22	0.666667	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	.	.	.	.	.	.	.	.	.	.	.	0.044	-1.273457	0.01421	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00357	7.89;7.89;7.89;7.89	3.91	-7.81	0.01210	.	1.484940	0.04916	U	0.454080	T	0.00073	0.0002	L	0.55213	1.73	0.09310	N	1	B;B;B;B;B	0.19200	0.034;0.002;0.001;0.002;0.0	B;B;B;B;B	0.17722	0.013;0.009;0.009;0.019;0.005	T	0.27434	-1.0074	10	0.54805	T	0.06	.	2.9111	0.05737	0.1916:0.3895:0.0766:0.3423	rs1049066;rs3189145;rs12722116	68;58;23;58;58	Q59F80;A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.;.	H	58	ENSP00000382029:L58H;ENSP00000364080:L58H;ENSP00000407332:L58H;ENSP00000382034:L58H	ENSP00000364080:L58H	L	-	2	0	HLA-DQB1	32740759	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.691000	0.00057	-2.933000	0.00300	-0.878000	0.02970	CTT	CCC|1.000;|0.000	.	alt		0.632	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
IDUA	3425	hgsc.bcm.edu	37	4	995868	995868	+	Silent	SNP	C	C	T	rs114806891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:995868C>T	ENST00000247933.4	+	7	979	c.891C>T	c.(889-891)aaC>aaT	p.N297N	IDUA_ENST00000453894.1_Nonsense_Mutation_p.R284*|IDUA_ENST00000514224.1_Silent_p.N165N	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	297					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCATTTACAACGACGAGGCGG	0.682													C|||	150	0.0299521	0.0076	0.0548	5008	,	,		13632	0.0208		0.0557	False		,,,				2504	0.0256				p.N297N		Atlas-SNP	.											.	IDUA	33	.	0			c.C891T						PASS	.	C		65,4275		0,65,2105	24.0	26.0	26.0		891	-1.2	1.0	4	dbSNP_132	26	549,7959		21,507,3726	no	coding-synonymous	IDUA	NM_000203.3		21,572,5831	TT,TC,CC		6.4528,1.4977,4.779		297/654	995868	614,12234	2170	4254	6424	SO:0001819	synonymous_variant	3425	exon7			TTACAACGACGAG	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.891C>T	4.37:g.995868C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	42	18	0.428571	NM_000203	B3KWK6	Silent	SNP	ENST00000247933.4	37	CCDS3343.1	73	0.033424908424908424	7	0.014227642276422764	21	0.058011049723756904	11	0.019230769230769232	34	0.044854881266490766	C	32	5.173413	0.94807	0.014977	0.064528	ENSG00000127415	ENST00000453894	.	.	.	4.91	-1.16	0.09678	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	0.484	10.2778	0.43521	0.0:0.3858:0.0:0.6142	.	.	.	.	X	284	.	ENSP00000396458:R284X	R	+	1	2	IDUA	985868	0.070000	0.21116	0.992000	0.48379	0.911000	0.54048	-0.575000	0.05861	-0.247000	0.09597	-0.254000	0.11334	CGA	C|0.965;T|0.035	0.035	strong		0.682	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
FABP2	2169	hgsc.bcm.edu	37	4	120241849	120241849	+	Silent	SNP	A	A	G	rs4834770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:120241849A>G	ENST00000274024.3	-	2	503	c.216T>C	c.(214-216)aaT>aaC	p.N72N		NM_000134.3	NP_000125.2	P12104	FABPI_HUMAN	fatty acid binding protein 2, intestinal	72					digestion (GO:0007586)	cytoplasm (GO:0005737)	fatty acid binding (GO:0005504)|transporter activity (GO:0005215)			breast(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	8					Estradiol(DB00783)|Ibuprofen(DB01050)|Sulfinpyrazone(DB01138)	CGTCTGCTAGATTGTAATTAA	0.313													G|||	2934	0.585863	0.5545	0.6499	5008	,	,		17574	0.6508		0.5676	False		,,,				2504	0.5348				p.N72N		Atlas-SNP	.											.	FABP2	21	.	0			c.T216C						PASS	.	G		2424,1978	554.0+/-378.9	677,1070,454	91.0	98.0	96.0		216	-0.2	0.0	4	dbSNP_111	96	4918,3680	525.3+/-380.7	1408,2102,789	no	coding-synonymous	FABP2	NM_000134.3		2085,3172,1243	GG,GA,AA		42.8007,44.9341,43.5231		72/133	120241849	7342,5658	2201	4299	6500	SO:0001819	synonymous_variant	2169	exon2			TGCTAGATTGTAA	J03465	CCDS3712.1	4q28-q31	2013-03-01			ENSG00000145384	ENSG00000145384		"""Fatty acid binding protein family"""	3556	protein-coding gene	gene with protein product		134640					Standard	NM_000134		Approved	I-FABP	uc003icw.3	P12104	OTTHUMG00000132972	ENST00000274024.3:c.216T>C	4.37:g.120241849A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_000134	Q2NKJ1	Silent	SNP	ENST00000274024.3	37	CCDS3712.1																																																																																			A|0.422;G|0.578	0.578	strong		0.313	FABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256531.1	NM_000134	
ANKRD6	22881	hgsc.bcm.edu	37	6	90340276	90340276	+	Silent	SNP	G	G	A	rs3210511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90340276G>A	ENST00000522441.1	+	16	2378	c.1737G>A	c.(1735-1737)tcG>tcA	p.S579S	ANKRD6_ENST00000369408.5_Silent_p.S544S|LYRM2_ENST00000520441.1_Intron|ANKRD6_ENST00000447838.2_Silent_p.S574S|ANKRD6_ENST00000520793.1_Silent_p.S515S|ANKRD6_ENST00000339746.4_Silent_p.S579S	NM_001242811.1	NP_001229740.1	Q9Y2G4	ANKR6_HUMAN	ankyrin repeat domain 6	579					negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of JNK cascade (GO:0046330)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|endometrium(3)|large_intestine(7)|lung(3)|ovary(3)|pancreas(1)|prostate(1)|stomach(2)	21		all_cancers(76;1.22e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.49e-10)|all_hematologic(105;7.79e-07)|all_epithelial(107;1.83e-05)|Lung NSC(302;0.239)		BRCA - Breast invasive adenocarcinoma(108;0.0209)		AGGAGCTGTCGTCTTCTGACT	0.587													G|||	3009	0.600839	0.5749	0.7003	5008	,	,		19233	0.9077		0.4662	False		,,,				2504	0.3875				p.S579S		Atlas-SNP	.											.	ANKRD6	51	.	0			c.G1737A						PASS	.	G	,,,,	2331,1589		714,903,343	31.0	33.0	32.0		1737,1737,1632,1545,1722	-3.7	1.0	6	dbSNP_105	32	3938,4334		969,2000,1167	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANKRD6	NM_001242809.1,NM_001242811.1,NM_001242813.1,NM_001242814.1,NM_014942.4	,,,,	1683,2903,1510	AA,AG,GG		47.6064,40.5357,48.581	,,,,	579/728,579/728,544/693,515/664,574/723	90340276	6269,5923	1960	4136	6096	SO:0001819	synonymous_variant	22881	exon16			GCTGTCGTCTTCT	AB023174	CCDS47460.1, CCDS56441.1, CCDS56442.1, CCDS56443.1	6q14.2-q16.1	2013-03-20			ENSG00000135299	ENSG00000135299		"""Ankyrin repeat domain containing"""	17280	protein-coding gene	gene with protein product		610583					Standard	NM_001242809		Approved	KIAA0957	uc003pni.4	Q9Y2G4	OTTHUMG00000015202	ENST00000522441.1:c.1737G>A	6.37:g.90340276G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_001242809	B3KUC3|Q5JUJ4|Q5JUJ5|Q8IUQ8|Q9NU24|Q9UFQ9	Silent	SNP	ENST00000522441.1	37	CCDS56441.1																																																																																			G|0.381;A|0.619	0.619	strong		0.587	ANKRD6-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376594.1		
CRB2	286204	hgsc.bcm.edu	37	9	126133497	126133497	+	Silent	SNP	C	C	T	rs13290763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:126133497C>T	ENST00000373631.3	+	8	2077	c.2076C>T	c.(2074-2076)tcC>tcT	p.S692S	CRB2_ENST00000359999.3_Silent_p.S692S|CRB2_ENST00000373629.2_Silent_p.S360S	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	692	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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						CCAATGACTCCGCAGCTGGCC	0.617													C|||	981	0.195887	0.053	0.1729	5008	,	,		20100	0.254		0.2734	False		,,,				2504	0.2658				p.S692S		Atlas-SNP	.											.	CRB2	86	.	0			c.C2076T						PASS	.	C		373,4033		16,341,1846	129.0	138.0	135.0		2076	-9.1	0.0	9	dbSNP_121	135	2696,5904		427,1842,2031	no	coding-synonymous	CRB2	NM_173689.5		443,2183,3877	TT,TC,CC		31.3488,8.4657,23.5968		692/1286	126133497	3069,9937	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon8			TGACTCCGCAGCT	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.2076C>T	9.37:g.126133497C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	199	97	0.487437	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.763;T|0.237	0.237	strong		0.617	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
GSTA4	2941	hgsc.bcm.edu	37	6	52849325	52849325	+	Silent	SNP	C	C	T	rs1802061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:52849325C>T	ENST00000370959.1	-	5	468	c.351G>A	c.(349-351)caG>caA	p.Q117Q	GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000370960.1_Silent_p.Q24Q|GSTA4_ENST00000541324.1_Silent_p.Q24Q			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	117	GST C-terminal.				glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	CTTCCTTTTGCTGATCATCTG	0.423													T|||	114	0.0227636	0.0023	0.0187	5008	,	,		19417	0.0		0.0557	False		,,,				2504	0.0429				p.Q117Q		Atlas-SNP	.											.	GSTA4	20	.	0			c.G351A						PASS	.	T		63,4343	820.5+/-416.4	0,63,2140	134.0	115.0	122.0		351	-8.1	0.3	6	dbSNP_89	122	588,8012	792.8+/-407.5	22,544,3734	no	coding-synonymous	GSTA4	NM_001512.3		22,607,5874	TT,TC,CC		6.8372,1.4299,5.0054		117/223	52849325	651,12355	2203	4300	6503	SO:0001819	synonymous_variant	2941	exon5			CTTTTGCTGATCA	AF020918	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4629	protein-coding gene	gene with protein product		605450	"""glutathione S-transferase A4"""			9480897	Standard	NM_001512		Approved		uc003pbf.3	O15217	OTTHUMG00000014868	ENST00000370959.1:c.351G>A	6.37:g.52849325C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	146	61	0.417808	NM_001512	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Silent	SNP	ENST00000370959.1	37	CCDS4948.1																																																																																			C|0.959;T|0.041	0.041	strong		0.423	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1	NM_001512	
FANCD2	2177	hgsc.bcm.edu	37	3	10088404	10088404	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:10088404C>T	ENST00000419585.1	+	15	1436	c.1275C>T	c.(1273-1275)taC>taT	p.Y425Y	FANCD2_ENST00000383807.1_Silent_p.Y425Y|FANCD2_ENST00000383806.1_Silent_p.Y425Y|FANCD2_ENST00000287647.3_Silent_p.Y425Y			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	425					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CTGTTCATTACTTAGTAAGTG	0.353			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Y425Y		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	FANCD2_ENST00000419585,caecum,carcinoma,0,2	FANCD2	253	2	0			c.C1275T						scavenged	.						39.0	36.0	37.0					3																	10088404		2203	4289	6492	SO:0001819	synonymous_variant	2177	exon15	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TCATTACTTAGTA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1275C>T	3.37:g.10088404C>T		Somatic	288	1	0.00347222		WXS	Illumina HiSeq	Phase_I	349	38	0.108883	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																			.	.	none		0.353	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
B4GALNT3	283358	hgsc.bcm.edu	37	12	657404	657404	+	Missense_Mutation	SNP	G	G	A	rs11063529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:657404G>A	ENST00000266383.5	+	9	807	c.794G>A	c.(793-795)cGg>cAg	p.R265Q	B4GALNT3_ENST00000544638.1_3'UTR	NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	265			R -> Q (in dbSNP:rs11063529).		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)			CAGTGGCGACGGAACGACCCT	0.582													G|||	899	0.179513	0.1467	0.1254	5008	,	,		19647	0.1706		0.2525	False		,,,				2504	0.1963				p.R265Q		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.G794A						PASS	.	G	GLN/ARG	750,3656	309.1+/-290.9	62,626,1515	134.0	103.0	114.0		794	1.8	0.8	12	dbSNP_120	114	2010,6590	351.3+/-328.2	235,1540,2525	yes	missense	B4GALNT3	NM_173593.3	43	297,2166,4040	AA,AG,GG		23.3721,17.0222,21.221	benign	265/999	657404	2760,10246	2203	4300	6503	SO:0001583	missense	283358	exon9			GGCGACGGAACGA	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.794G>A	12.37:g.657404G>A	ENSP00000266383:p.Arg265Gln	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	104	42	0.403846	NM_173593	Q6ZNC1|Q8N7T6	Missense_Mutation	SNP	ENST00000266383.5	37	CCDS8504.1	420	0.19230769230769232	89	0.18089430894308944	62	0.1712707182320442	85	0.1486013986013986	184	0.24274406332453827	G	11.78	1.740922	0.30865	0.170222	0.233721	ENSG00000139044	ENST00000266383;ENST00000322843	T;T	0.23950	1.88;1.88	4.97	1.81	0.25067	PA14 (2);	0.304442	0.31051	N	0.008359	T	0.00012	0.0000	L	0.31752	0.955	0.38672	P	0.047668000000000044	P;P	0.40398	0.716;0.469	B;B	0.25405	0.06;0.035	T	0.40942	-0.9536	9	0.17832	T	0.49	-18.8557	4.382	0.11299	0.2013:0.0:0.4489:0.3498	rs11063529;rs17800762;rs59340019;rs11063529	167;265	E9PHD9;Q6L9W6	.;B4GN3_HUMAN	Q	265;167	ENSP00000266383:R265Q;ENSP00000322953:R167Q	ENSP00000266383:R265Q	R	+	2	0	B4GALNT3	527665	1.000000	0.71417	0.764000	0.31436	0.285000	0.27093	2.952000	0.49097	1.075000	0.40932	-0.258000	0.10820	CGG	G|0.799;A|0.201	0.201	strong		0.582	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
TJP3	27134	hgsc.bcm.edu	37	19	3728609	3728609	+	Missense_Mutation	SNP	G	G	A	rs2067019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:3728609G>A	ENST00000541714.2	+	3	518	c.56G>A	c.(55-57)cGc>cAc	p.R19H	TJP3_ENST00000589378.1_Missense_Mutation_p.R28H|TJP3_ENST00000539908.2_5'UTR|TJP3_ENST00000587686.1_Missense_Mutation_p.R38H|TJP3_ENST00000262968.9_Missense_Mutation_p.R38H|TJP3_ENST00000382008.3_Missense_Mutation_p.R19H	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	19	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.			R -> H (in Ref. 4; AAI08907). {ECO:0000305}.	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)		CAGGACCCCCGCCGGGGCTTT	0.627													G|||	1440	0.28754	0.1626	0.3847	5008	,	,		16938	0.3482		0.1948	False		,,,				2504	0.4202				p.R28H		Atlas-SNP	.											TJP3,colon,carcinoma,0,1	TJP3	79	1	0			c.G83A						PASS	.	G	HIS/ARG	766,3638	282.2+/-276.4	73,620,1509	21.0	26.0	25.0		113	4.0	1.0	19	dbSNP_96	25	1634,6966	283.9+/-296.4	173,1288,2839	yes	missense	TJP3	NM_014428.1	29	246,1908,4348	AA,AG,GG		19.0,17.3933,18.4559	probably-damaging	38/953	3728609	2400,10604	2202	4300	6502	SO:0001583	missense	27134	exon3			ACCCCCGCCGGGG	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.56G>A	19.37:g.3728609G>A	ENSP00000439278:p.Arg19His	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	66	65	0.984848	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	572	0.2619047619047619	76	0.15447154471544716	123	0.3397790055248619	225	0.39335664335664333	148	0.19525065963060687	G	16.41	3.114745	0.56505	0.173933	0.19	ENSG00000105289	ENST00000541714;ENST00000382008;ENST00000262968	T;T;T	0.29917	1.55;1.55;2.28	4.02	4.02	0.46733	PDZ/DHR/GLGF (3);	0.147473	0.46758	D	0.000274	T	0.00012	0.0000	N	0.21545	0.675	0.28643	P	0.9070552000000001	D;D;D;D	0.89917	0.991;1.0;1.0;0.991	P;D;D;P	0.81914	0.72;0.995;0.984;0.72	T	0.40384	-0.9566	9	0.46703	T	0.11	.	9.3472	0.38115	0.1135:0.0:0.8865:0.0	rs2067019;rs59188659;rs2067019	38;38;19;19	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	H	19;19;38	ENSP00000439278:R19H;ENSP00000371438:R19H;ENSP00000262968:R38H	ENSP00000262968:R38H	R	+	2	0	TJP3	3679609	0.999000	0.42202	0.991000	0.47740	0.664000	0.39144	3.676000	0.54612	2.253000	0.74438	0.456000	0.33151	CGC	G|0.787;A|0.213	0.213	strong		0.627	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
DUS2	54920	hgsc.bcm.edu	37	16	68088485	68088485	+	Silent	SNP	A	A	G	rs11555011	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68088485A>G	ENST00000565263.1	+	6	767	c.273A>G	c.(271-273)tcA>tcG	p.S91S	AC130462.1_ENST00000408862.1_RNA|DUS2_ENST00000358896.6_Silent_p.S91S|DUS2_ENST00000432752.1_Intron	NM_017803.3	NP_060273.1	Q9NX74	DUS2L_HUMAN	dihydrouridine synthase 2	91					negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	double-stranded RNA binding (GO:0003725)|flavin adenine dinucleotide binding (GO:0050660)|protein kinase inhibitor activity (GO:0004860)|tRNA dihydrouridine synthase activity (GO:0017150)										AGGGGACTTCAGACGCAGAGC	0.522													A|||	609	0.121605	0.0635	0.1585	5008	,	,		21272	0.0992		0.1412	False		,,,				2504	0.1769				p.S91S		Atlas-SNP	.											.	DUS2L	39	.	0			c.A273G						PASS	.	A		422,3974	205.2+/-227.1	17,388,1793	238.0	190.0	206.0		273	3.4	1.0	16	dbSNP_120	206	1182,7418	241.0+/-271.5	100,982,3218	no	coding-synonymous	DUS2L	NM_017803.3		117,1370,5011	GG,GA,AA		13.7442,9.5996,12.3423		91/494	68088485	1604,11392	2198	4300	6498	SO:0001819	synonymous_variant	54920	exon5			GACTTCAGACGCA		CCDS10859.1, CCDS61970.1	16q22.1	2013-07-23	2013-07-23	2013-07-23	ENSG00000167264	ENSG00000167264			26014	protein-coding gene	gene with protein product	"""SMM1 homolog (S. cerevisiae)"""	609707	"""dihydrouridine synthase 2-like (SMM1, S. cerevisiae)"", ""dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)"", ""dihydrouridine synthase 2-like"""	DUS2L		15994936, 22741570	Standard	NM_017803		Approved	FLJ20399, SMM1	uc002evj.4	Q9NX74	OTTHUMG00000137538	ENST00000565263.1:c.273A>G	16.37:g.68088485A>G		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	299	132	0.441472	NM_001271762	A8K3G3|Q4H4D9	Silent	SNP	ENST00000565263.1	37	CCDS10859.1																																																																																			A|0.876;G|0.124	0.124	strong		0.522	DUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268869.2	NM_017803	
USP49	25862	hgsc.bcm.edu	37	6	41773735	41773735	+	Silent	SNP	G	G	A	rs6926173	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41773735G>A	ENST00000394253.3	-	3	1316	c.987C>T	c.(985-987)ggC>ggT	p.G329G	USP49_ENST00000373010.1_Silent_p.G329G|USP49_ENST00000373006.1_Silent_p.G329G|USP49_ENST00000297229.2_Silent_p.G329G|USP49_ENST00000373009.3_Silent_p.G329G			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	329	USP.				histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCCAGCAGAAGCCCTCCCGCT	0.587													G|||	1045	0.208666	0.3003	0.1614	5008	,	,		16774	0.1567		0.2326	False		,,,				2504	0.1472				p.G329G		Atlas-SNP	.											.	USP49	58	.	0			c.C987T						PASS	.	G		1231,3175	405.5+/-333.5	165,901,1137	32.0	37.0	35.0		987	3.3	1.0	6	dbSNP_116	35	2044,6556	340.4+/-323.6	241,1562,2497	no	coding-synonymous	USP49	NM_018561.3		406,2463,3634	AA,AG,GG		23.7674,27.9392,25.1807		329/641	41773735	3275,9731	2203	4300	6503	SO:0001819	synonymous_variant	25862	exon4			GCAGAAGCCCTCC	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"""Ubiquitin-specific peptidases"""	20078	protein-coding gene	gene with protein product			"""ubiquitin specific protease 49"""			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.987C>T	6.37:g.41773735G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Silent	SNP	ENST00000394253.3	37																																																																																				G|0.764;A|0.236	0.236	strong		0.587	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561	
SRRM5	100170229	hgsc.bcm.edu	37	19	44118191	44118191	+	Missense_Mutation	SNP	G	G	A	rs34163641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44118191G>A	ENST00000607544.1	+	3	2240	c.1918G>A	c.(1918-1920)Gac>Aac	p.D640N	SRRM5_ENST00000417606.1_Missense_Mutation_p.D640N|ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000526798.1_Missense_Mutation_p.D655N			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	640	Ser-rich.									endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						CAAGGAGAGCGACCCCAGTCA	0.512													G|||	1179	0.235423	0.2693	0.1628	5008	,	,		17199	0.1498		0.2565	False		,,,				2504	0.3078				p.D640N		Atlas-SNP	.											.	SRRM5	38	.	0			c.G1918A						PASS	.	G	ASN/ASP,	314,1070		32,250,410	78.0	80.0	79.0		1918,	-1.9	0.0	19	dbSNP_126	79	846,2336		112,622,857	yes	missense,intron	ZNF428,SRRM5	NM_001145641.1,NM_182498.3	23,	144,872,1267	AA,AG,GG		26.5871,22.6879,25.4052	possibly-damaging,	640/716,	44118191	1160,3406	692	1591	2283	SO:0001583	missense	100170229	exon1			GAGAGCGACCCCA	AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.1918G>A	19.37:g.44118191G>A	ENSP00000476253:p.Asp640Asn	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	37	CCDS46095.1	470	0.21520146520146521	129	0.2621951219512195	60	0.16574585635359115	86	0.15034965034965034	195	0.25725593667546176	G	10.30	1.312032	0.23821	0.226879	0.265871	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	4.28	-1.9	0.07665	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.24618	0.107	B	0.15484	0.013	T	0.37888	-0.9686	7	0.42905	T	0.14	.	5.2613	0.15576	0.4778:0.1513:0.3709:0.0	rs34163641	640	B3KS81	SRRM5_HUMAN	N	655;640	.	ENSP00000414512:D640N	D	+	1	0	SRRM5	48810031	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.560000	0.05964	-0.256000	0.09473	-0.258000	0.10820	GAC	G|0.784;A|0.216	0.216	strong		0.512	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
SERPINH1	871	hgsc.bcm.edu	37	11	75277757	75277757	+	Silent	SNP	C	C	G	rs650241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:75277757C>G	ENST00000524558.1	+	2	1798	c.363C>G	c.(361-363)tcC>tcG	p.S121S	SERPINH1_ENST00000533603.1_Silent_p.S121S|SERPINH1_ENST00000525876.1_5'Flank|SERPINH1_ENST00000530284.1_Silent_p.S121S|SERPINH1_ENST00000358171.3_Silent_p.S121S			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	121					chondrocyte development involved in endochondral bone morphogenesis (GO:0003433)|collagen biosynthetic process (GO:0032964)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|protein maturation (GO:0051604)|regulation of proteolysis (GO:0030162)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(4)|large_intestine(3)|liver(1)|lung(4)|ovary(2)|stomach(1)	15	Ovarian(111;0.11)					TCAGCAACTCCACGGCGCGCA	0.672													C|||	1868	0.373003	0.4614	0.3804	5008	,	,		16855	0.2103		0.2972	False		,,,				2504	0.4939				p.S121S		Atlas-SNP	.											SERPINH1,NS,carcinoma,0,1	SERPINH1	33	1	0			c.C363G						PASS	.	C	,	1898,2502		424,1050,726	20.0	18.0	18.0		363,363	4.1	0.9	11	dbSNP_83	18	2587,5991		381,1825,2083	no	coding-synonymous,coding-synonymous	SERPINH1	NM_001207014.1,NM_001235.3	,	805,2875,2809	GG,GC,CC		30.1585,43.1364,34.5585	,	121/419,121/419	75277757	4485,8493	2200	4289	6489	SO:0001819	synonymous_variant	871	exon2			CAACTCCACGGCG	X61598	CCDS8239.1	11q13.5	2014-02-18	2005-08-18		ENSG00000149257	ENSG00000149257		"""Serine (or cysteine) peptidase inhibitors"""	1546	protein-coding gene	gene with protein product		600943	"""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2"", ""serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)"""	CBP1, CBP2, SERPINH2		7656593, 9533029, 24172014	Standard	NM_001207014		Approved	HSP47, colligen	uc001owr.3	P50454	OTTHUMG00000165362	ENST00000524558.1:c.363C>G	11.37:g.75277757C>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	61	23	0.377049	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Silent	SNP	ENST00000524558.1	37	CCDS8239.1																																																																																			C|0.668;G|0.332	0.332	strong		0.672	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353	
ZNF77	58492	hgsc.bcm.edu	37	19	2936535	2936535	+	Nonsense_Mutation	SNP	G	G	A	rs35699176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:2936535G>A	ENST00000314531.4	-	3	390	c.298C>T	c.(298-300)Cag>Tag	p.Q100*	ZNF77_ENST00000588050.1_5'Flank	NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		AGATGCCTCTGTGGGATTTGG	0.463													G|||	101	0.0201677	0.0083	0.0288	5008	,	,		17364	0.0		0.0487	False		,,,				2504	0.0215				p.Q100X		Atlas-SNP	.											.	ZNF77	47	.	0			c.C298T						PASS	.	G	stop/GLN	90,4316	75.7+/-113.9	1,88,2114	72.0	76.0	75.0		298	-1.2	0.0	19	dbSNP_126	75	376,8224	122.9+/-181.8	6,364,3930	yes	stop-gained	ZNF77	NM_021217.2		7,452,6044	AA,AG,GG		4.3721,2.0427,3.583		100/546	2936535	466,12540	2203	4300	6503	SO:0001587	stop_gained	58492	exon3			GCCTCTGTGGGAT	X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"""Zinc fingers, C2H2-type"", ""-"""	13150	protein-coding gene	gene with protein product		194551	"""zinc finger protein 77 (pT1)"""			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.298C>T	19.37:g.2936535G>A	ENSP00000319053:p.Gln100*	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_021217	Q86XJ3|Q9NPP0	Nonsense_Mutation	SNP	ENST00000314531.4	37	CCDS12099.1	55	0.025183150183150184	8	0.016260162601626018	13	0.03591160220994475	0	0.0	34	0.044854881266490766	G	14.45	2.539818	0.45176	0.020427	0.043721	ENSG00000175691	ENST00000314531	.	.	.	2.52	-1.16	0.09678	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	4.928	0.13903	0.0:0.4403:0.4248:0.1349	rs35699176	.	.	.	X	100	.	ENSP00000319053:Q100X	Q	-	1	0	ZNF77	2887535	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.103000	0.15292	-0.133000	0.11537	-1.552000	0.00895	CAG	G|0.965;A|0.035	0.035	strong		0.463	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217	
OGFRL1	79627	hgsc.bcm.edu	37	6	72006512	72006512	+	Silent	SNP	T	T	C	rs2273888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:72006512T>C	ENST00000370435.4	+	6	818	c.684T>C	c.(682-684)caT>caC	p.H228H	RP11-154D6.1_ENST00000412751.1_RNA|RP11-154D6.1_ENST00000587253.1_RNA|RP11-154D6.1_ENST00000586030.1_RNA|RP11-154D6.1_ENST00000586232.1_RNA|RP11-154D6.1_ENST00000432050.1_RNA|RP11-154D6.1_ENST00000588612.1_RNA|RP11-154D6.1_ENST00000423255.1_RNA|RP3-331H24.5_ENST00000602823.1_lincRNA|RP11-154D6.1_ENST00000591156.1_RNA	NM_024576.3	NP_078852.3	Q5TC84	OGRL1_HUMAN	opioid growth factor receptor-like 1	228						membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|upper_aerodigestive_tract(1)	13						GATTTCAGCATCTGAATGAGT	0.408													C|||	1081	0.215855	0.323	0.2104	5008	,	,		16017	0.2708		0.1044	False		,,,				2504	0.1329				p.H228H		Atlas-SNP	.											.	OGFRL1	44	.	0			c.T684C						PASS	.	C		1178,3212	639.8+/-397.2	150,878,1167	54.0	60.0	58.0		684	1.6	1.0	6	dbSNP_100	58	873,7719	765.6+/-407.6	51,771,3474	no	coding-synonymous	OGFRL1	NM_024576.3		201,1649,4641	CC,CT,TT		10.1606,26.8337,15.7988		228/452	72006512	2051,10931	2195	4296	6491	SO:0001819	synonymous_variant	79627	exon6			TCAGCATCTGAAT		CCDS34482.1	6q13	2008-02-05			ENSG00000119900	ENSG00000119900			21378	protein-coding gene	gene with protein product							Standard	NM_024576		Approved	dJ331H24.1	uc003pfx.1	Q5TC84	OTTHUMG00000015000	ENST00000370435.4:c.684T>C	6.37:g.72006512T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	79	13	0.164557	NM_024576	Q2TAC1|Q8NEQ4|Q9H7B5	Silent	SNP	ENST00000370435.4	37	CCDS34482.1																																																																																			T|0.820;C|0.180	0.180	strong		0.408	OGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041153.2	NM_024576	
TCF7	6932	hgsc.bcm.edu	37	5	133451683	133451683	+	Missense_Mutation	SNP	C	C	A	rs5742913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:133451683C>A	ENST00000321584.4	+	3	596	c.400C>A	c.(400-402)Ccc>Acc	p.P134T	TCF7_ENST00000395029.1_Missense_Mutation_p.P134T|TCF7_ENST00000432532.2_Missense_Mutation_p.P19T|TCF7_ENST00000518915.1_Missense_Mutation_p.P19T|TCF7_ENST00000520958.1_Missense_Mutation_p.P19T|TCF7_ENST00000342854.5_Missense_Mutation_p.P134T|TCF7_ENST00000378560.4_Missense_Mutation_p.P19T|TCF7_ENST00000321603.6_Missense_Mutation_p.P134T|TCF7_ENST00000378564.1_Missense_Mutation_p.P134T|TCF7_ENST00000395023.1_Missense_Mutation_p.P19T			P36402	TCF7_HUMAN	transcription factor 7 (T-cell specific, HMG-box)	134					alpha-beta T cell differentiation (GO:0046632)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cellular response to interleukin-4 (GO:0071353)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|generation of neurons (GO:0048699)|immune response (GO:0006955)|neural tube development (GO:0021915)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor V(D)J recombination (GO:0033153)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			kidney(2)|large_intestine(7)|lung(2)|skin(1)	12		Breast(839;0.058)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTACCCACCCCCCTCGGGAGC	0.642													c|||	215	0.0429313	0.0061	0.0994	5008	,	,		13669	0.001		0.1203	False		,,,				2504	0.0164				p.P134T		Atlas-SNP	.											.	TCF7	81	.	0			c.C400A						PASS	.	C	THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO	105,4299	80.9+/-119.3	1,103,2098	50.0	49.0	49.0		55,400,55,55,55	-10.4	0.0	5	dbSNP_114	49	941,7659	203.5+/-246.5	53,835,3412	yes	missense,missense,missense,missense,missense	TCF7	NM_001134851.2,NM_003202.3,NM_201632.3,NM_201634.3,NM_213648.3	38,38,38,38,38	54,938,5510	AA,AC,CC		10.9419,2.3842,8.0437	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	19/270,134/385,19/270,19/269,19/270	133451683	1046,11958	2202	4300	6502	SO:0001583	missense	6932	exon3			CCACCCCCCTCGG	Z47362	CCDS4169.1, CCDS4170.1, CCDS43362.1, CCDS47263.1, CCDS47263.2	5q31	2008-02-05			ENSG00000081059	ENSG00000081059			11639	protein-coding gene	gene with protein product		189908					Standard	NM_003202		Approved	TCF-1	uc003kyt.3	P36402	OTTHUMG00000129124	ENST00000321584.4:c.400C>A	5.37:g.133451683C>A	ENSP00000326540:p.Pro134Thr	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	225	93	0.413333	NM_003202	B3KSH3|Q86WR9|Q9UKI4	Missense_Mutation	SNP	ENST00000321584.4	37		119	0.05448717948717949	5	0.01016260162601626	31	0.0856353591160221	1	0.0017482517482517483	82	0.10817941952506596	c	4.247	0.044851	0.08196	0.023842	0.109419	ENSG00000081059	ENST00000342854;ENST00000361590;ENST00000321603;ENST00000321584;ENST00000378564;ENST00000395029;ENST00000518887;ENST00000517851;ENST00000521639;ENST00000522375;ENST00000378560;ENST00000432532;ENST00000520958;ENST00000518915;ENST00000395023	D;D;D;D;D;D;D;D;D;D	0.99399	-5.62;-5.59;-5.6;-5.6;-5.6;-5.69;-5.83;-5.79;-5.82;-5.79	5.2	-10.4	0.00318	CTNNB1 binding, N-teminal (1);	1.151080	0.06305	N	0.701674	T	0.47116	0.1428	N	0.19112	0.55	0.09310	N	0.999996	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	D	0.85324	0.1086	10	0.25106	T	0.35	.	8.8966	0.35467	0.3351:0.0957:0.5064:0.0628	.	134;134;134;134	P36402-9;B7WNT5;P36402;P36402-5	.;.;TCF7_HUMAN;.	T	134;134;134;134;134;134;19;19;19;19;19;19;19;19;19	ENSP00000340347:P134T;ENSP00000326654:P134T;ENSP00000326540:P134T;ENSP00000367827:P134T;ENSP00000378472:P134T;ENSP00000367822:P19T;ENSP00000397946:P19T;ENSP00000429547:P19T;ENSP00000430179:P19T;ENSP00000378469:P19T	ENSP00000326540:P134T	P	+	1	0	TCF7	133479582	0.000000	0.05858	0.001000	0.08648	0.522000	0.34438	-1.994000	0.01474	-3.563000	0.00140	-4.958000	0.00002	CCC	A|0.060;C|0.931;T|0.009	0.060	strong		0.642	TCF7-201	KNOWN	basic	protein_coding	protein_coding		NM_201634	
CNOT1	23019	hgsc.bcm.edu	37	16	58579274	58579274	+	Silent	SNP	C	C	T	rs246258	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58579274C>T	ENST00000317147.5	-	30	4460	c.4128G>A	c.(4126-4128)ctG>ctA	p.L1376L	CNOT1_ENST00000569240.1_Silent_p.L1371L|CNOT1_ENST00000441024.2_Silent_p.L1376L|CNOT1_ENST00000245138.4_Silent_p.L227L	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1376	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		CTGTTGGATTCAGAGTAATGT	0.478													T|||	1424	0.284345	0.1339	0.4135	5008	,	,		19153	0.3839		0.2416	False		,,,				2504	0.3374				p.L1376L		Atlas-SNP	.											.	CNOT1	359	.	0			c.G4128A						PASS	.	T	,	668,3728	762.9+/-413.2	58,552,1588	246.0	201.0	216.0		4128,4128	1.9	1.0	16	dbSNP_79	216	2214,6386	710.5+/-405.8	289,1636,2375	no	coding-synonymous,coding-synonymous	CNOT1	NM_016284.3,NM_206999.1	,	347,2188,3963	TT,TC,CC		25.7442,15.1956,22.1761	,	1376/2377,1376/1552	58579274	2882,10114	2198	4300	6498	SO:0001819	synonymous_variant	23019	exon30			TGGATTCAGAGTA	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4128G>A	16.37:g.58579274C>T		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	222	96	0.432432	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																			C|0.754;T|0.246	0.246	strong		0.478	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68682402	68682402	+	Missense_Mutation	SNP	A	A	G	rs10896380	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68682402A>G	ENST00000255078.3	+	6	934	c.823A>G	c.(823-825)Att>Gtt	p.I275V	IGHMBP2_ENST00000539224.1_3'UTR	NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	275	Leu-rich.		I -> V (in dbSNP:rs10896380). {ECO:0000269|PubMed:8349627}.		ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CCTGGAGTCCATTCAGCAGCA	0.597													A|||	600	0.119808	0.1074	0.1888	5008	,	,		15618	0.0149		0.2674	False		,,,				2504	0.044				p.I275V		Atlas-SNP	.											IGHMBP2,NS,carcinoma,-1,2	IGHMBP2	83	2	0			c.A823G						scavenged	.	A	VAL/ILE	545,3855	246.8+/-255.3	37,471,1692	102.0	92.0	95.0		823	0.1	0.4	11	dbSNP_120	95	2127,6461	366.2+/-334.2	258,1611,2425	yes	missense	IGHMBP2	NM_002180.2	29	295,2082,4117	GG,GA,AA		24.7671,12.3864,20.5728	benign	275/994	68682402	2672,10316	2200	4294	6494	SO:0001583	missense	3508	exon6			GAGTCCATTCAGC	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.823A>G	11.37:g.68682402A>G	ENSP00000255078:p.Ile275Val	Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	343	0.15705128205128205	60	0.12195121951219512	73	0.20165745856353592	11	0.019230769230769232	199	0.262532981530343	A	5.864	0.343588	0.11126	0.123864	0.247671	ENSG00000132740	ENST00000255078	T	0.81078	-1.45	3.71	0.0501	0.14292	DEAD-like helicase (1);Helicase/UvrB domain (1);ATPase, AAA+ type, core (1);	0.262406	0.37012	N	0.002293	T	0.00012	0.0000	N	0.02854	-0.475	0.09310	P	1.0	B	0.10296	0.003	B	0.15870	0.014	T	0.04915	-1.0918	9	0.02654	T	1	-23.5642	3.4248	0.07406	0.5127:0.0:0.3163:0.171	rs10896380;rs17533010;rs60474416;rs10896380	275	P38935	SMBP2_HUMAN	V	275	ENSP00000255078:I275V	ENSP00000255078:I275V	I	+	1	0	IGHMBP2	68438978	0.869000	0.29996	0.423000	0.26634	0.699000	0.40488	1.576000	0.36504	-0.090000	0.12462	0.454000	0.30748	ATT	A|0.824;G|0.176	0.176	strong		0.597	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
MTUS2	23281	hgsc.bcm.edu	37	13	29933450	29933450	+	Missense_Mutation	SNP	C	C	T	rs114541586	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:29933450C>T	ENST00000431530.3	+	6	3045	c.2987C>T	c.(2986-2988)cCg>cTg	p.P996L		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	986	Localization to the growing distal tip of microtubules.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CCGCCCAAGCCGGACCCGCAG	0.612													C|||	39	0.00778754	0.0008	0.0231	5008	,	,		16222	0.0		0.0199	False		,,,				2504	0.002				p.P996L		Atlas-SNP	.											.	MTUS2	279	.	0			c.C2987T						PASS	.	C	LEU/PRO	14,3874		0,14,1930	13.0	15.0	14.0		2987	4.9	1.0	13	dbSNP_132	14	146,8138		1,144,3997	yes	missense	MTUS2	NM_001033602.2	98	1,158,5927	TT,TC,CC		1.7624,0.3601,1.3145	probably-damaging	996/1380	29933450	160,12012	1944	4142	6086	SO:0001583	missense	23281	exon6			CCAAGCCGGACCC	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2987C>T	13.37:g.29933450C>T	ENSP00000392057:p.Pro996Leu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	154	66	0.428571	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	CCDS45022.1	21	0.009615384615384616	0	0.0	7	0.019337016574585635	0	0.0	14	0.018469656992084433	C	20.3	3.966999	0.74131	0.003601	0.017624	ENSG00000132938	ENST00000431530	T	0.12984	2.63	4.91	4.91	0.64330	.	0.191509	0.35970	N	0.002876	T	0.15782	0.0380	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.00200	-1.1927	9	.	.	.	.	15.6341	0.76937	0.0:1.0:0.0:0.0	.	986	Q5JR59	MTUS2_HUMAN	L	996	ENSP00000392057:P996L	.	P	+	2	0	MTUS2	28831450	0.994000	0.37717	0.985000	0.45067	0.592000	0.36648	3.491000	0.53252	2.560000	0.86352	0.591000	0.81541	CCG	C|0.990;T|0.010	0.010	strong		0.612	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
EVC	2121	hgsc.bcm.edu	37	4	5743512	5743512	+	Missense_Mutation	SNP	T	T	C	rs6414624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5743512T>C	ENST00000264956.6	+	6	956	c.772T>C	c.(772-774)Tac>Cac	p.Y258H	EVC_ENST00000509451.1_Missense_Mutation_p.Y258H|EVC_ENST00000382674.2_Missense_Mutation_p.Y258H	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	258			Y -> H (in dbSNP:rs6414624). {ECO:0000269|PubMed:10700184}.		cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				TGATGAACTATACCAGAAGAT	0.289													T|||	3730	0.744808	0.5015	0.7839	5008	,	,		15627	0.9048		0.7932	False		,,,				2504	0.8313				p.Y258H		Atlas-SNP	.											.	EVC	90	.	0			c.T772C						PASS	.	T	HIS/TYR	2284,2120	571.5+/-383.1	597,1090,515	50.0	52.0	51.0		772	2.7	0.8	4	dbSNP_116	51	6902,1688	727.5+/-406.6	2770,1362,163	yes	missense	EVC	NM_153717.2	83	3367,2452,678	CC,CT,TT		19.6508,48.1381,29.3058	probably-damaging	258/993	5743512	9186,3808	2202	4295	6497	SO:0001583	missense	2121	exon6			GAACTATACCAGA	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.772T>C	4.37:g.5743512T>C	ENSP00000264956:p.Tyr258His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	108	108	1	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	1689	0.7733516483516484	263	0.5345528455284553	295	0.8149171270718232	523	0.9143356643356644	608	0.8021108179419525	T	5.677	0.309460	0.10733	0.518619	0.803492	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.55588	0.51;0.51;0.64	5.12	2.72	0.32119	.	0.735547	0.13245	N	0.402567	T	0.00012	0.0000	L	0.55481	1.735	0.80722	P	0.0	B	0.14012	0.009	B	0.16722	0.016	T	0.28073	-1.0055	9	0.20046	T	0.44	.	8.084	0.30760	0.0:0.1664:0.0:0.8336	rs6414624;rs57157110;rs6414624	258	P57679	EVC_HUMAN	H	258	ENSP00000264956:Y258H;ENSP00000372120:Y258H;ENSP00000426774:Y258H	ENSP00000264956:Y258H	Y	+	1	0	EVC	5794413	0.946000	0.32159	0.785000	0.31869	0.188000	0.23474	1.926000	0.40084	0.309000	0.22966	0.533000	0.62120	TAC	T|0.274;C|0.726	0.726	strong		0.289	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
RBM5	10181	hgsc.bcm.edu	37	3	50144951	50144951	+	Silent	SNP	T	T	C	rs1061474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50144951T>C	ENST00000347869.3	+	12	1165	c.990T>C	c.(988-990)gcT>gcC	p.A330A	RBM5_ENST00000441812.2_3'UTR	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	330	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GCGTCAGCGCTTTCTCTGTAG	0.488													C|||	3743	0.747404	0.7458	0.6945	5008	,	,		16513	0.881		0.5686	False		,,,				2504	0.8333				p.A330A		Atlas-SNP	.											.	RBM5	76	.	0			c.T990C						PASS	.	C		3175,1231	424.2+/-340.4	1144,887,172	169.0	147.0	154.0		990	5.0	1.0	3	dbSNP_86	154	4901,3699	529.7+/-381.6	1368,2165,767	no	coding-synonymous	RBM5	NM_005778.2		2512,3052,939	CC,CT,TT		43.0116,27.9392,37.9056		330/816	50144951	8076,4930	2203	4300	6503	SO:0001819	synonymous_variant	10181	exon12			CAGCGCTTTCTCT	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.990T>C	3.37:g.50144951T>C		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	196	100	0.510204	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			T|0.327;C|0.673	0.673	strong		0.488	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
KLHL7	55975	hgsc.bcm.edu	37	7	23164701	23164701	+	Silent	SNP	C	C	T	rs15775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:23164701C>T	ENST00000339077.5	+	4	595	c.352C>T	c.(352-354)Ctg>Ttg	p.L118L	KLHL7_ENST00000545443.1_Silent_p.L96L|KLHL7_ENST00000410047.1_Silent_p.L96L|KLHL7_ENST00000322275.5_Silent_p.L118L|KLHL7_ENST00000322231.7_Silent_p.L96L|KLHL7_ENST00000479288.1_Intron|KLHL7_ENST00000545771.1_Silent_p.L96L|KLHL7_ENST00000542558.1_Intron|KLHL7_ENST00000409689.1_Silent_p.L70L|KLHL7_ENST00000539124.1_Silent_p.L42L	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	118					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TCAGTCTTTGCTGGATGCAGC	0.318													T|||	2105	0.420327	0.711	0.3156	5008	,	,		17073	0.3462		0.3449	False		,,,				2504	0.2556				p.L118L		Atlas-SNP	.											.	KLHL7	102	.	0			c.C352T						PASS	.	T	,,	2781,1621	496.7+/-363.6	881,1019,301	91.0	94.0	93.0		352,352,208	4.6	1.0	7	dbSNP_52	93	3175,5423	653.2+/-401.0	601,1973,1725	no	coding-synonymous,coding-synonymous,coding-synonymous	KLHL7	NM_001031710.2,NM_001172428.1,NM_018846.4	,,	1482,2992,2026	TT,TC,CC		36.9272,36.8242,45.8154	,,	118/587,118/167,70/539	23164701	5956,7044	2201	4299	6500	SO:0001819	synonymous_variant	55975	exon4			TCTTTGCTGGATG		CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"""Kelch-like"", ""BTB/POZ domain containing"""	15646	protein-coding gene	gene with protein product	"""retinitis pigmentosa 42"""	611119	"""kelch-like 7 (Drosophila)"""			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.352C>T	7.37:g.23164701C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	132	65	0.492424	NM_001172428	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Silent	SNP	ENST00000339077.5	37	CCDS34609.1																																																																																			C|0.553;T|0.447	0.447	strong		0.318	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846	
ZNF491	126069	hgsc.bcm.edu	37	19	11916914	11916914	+	Missense_Mutation	SNP	A	A	G	rs141870350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11916914A>G	ENST00000323169.5	+	3	477	c.146A>G	c.(145-147)tAt>tGt	p.Y49C	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	49					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						TTCATGGGATATTCATCCTTT	0.383													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18120	0.0		0.002	False		,,,				2504	0.0				p.Y49C		Atlas-SNP	.											.	ZNF491	61	.	0			c.A146G						PASS	.	A	CYS/TYR	6,4400	9.9+/-24.2	0,6,2197	72.0	76.0	75.0		146	1.0	0.0	19	dbSNP_134	75	66,8534	41.2+/-98.3	1,64,4235	yes	missense	ZNF491	NM_152356.3	194	1,70,6432	GG,GA,AA		0.7674,0.1362,0.5536	benign	49/438	11916914	72,12934	2203	4300	6503	SO:0001583	missense	126069	exon3			TGGGATATTCATC	AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"""Zinc fingers, C2H2-type"""	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.146A>G	19.37:g.11916914A>G	ENSP00000313443:p.Tyr49Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_152356	Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	37	CCDS12267.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	a	9.874	1.199678	0.22121	0.001362	0.007674	ENSG00000177599	ENST00000323169;ENST00000455048;ENST00000450087	T;T	0.15256	2.44;2.44	1.01	1.01	0.19927	Zinc finger, C2H2 (1);	.	.	.	.	T	0.05273	0.0140	N	0.12831	0.26	0.09310	N	1	B	0.28900	0.227	B	0.19148	0.024	T	0.30851	-0.9964	9	0.37606	T	0.19	.	5.9285	0.19126	1.0:0.0:0.0:0.0	.	49	Q8N8L2	ZN491_HUMAN	C	49	ENSP00000313443:Y49C;ENSP00000392176:Y49C	ENSP00000313443:Y49C	Y	+	2	0	ZNF491	11777914	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-1.435000	0.02423	0.710000	0.31997	0.413000	0.27773	TAT	A|0.997;G|0.003	0.003	strong		0.383	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356	
KRT9	3857	hgsc.bcm.edu	37	17	39724810	39724810	+	Missense_Mutation	SNP	G	G	A	rs116216460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39724810G>A	ENST00000246662.4	-	5	1185	c.1120C>T	c.(1120-1122)Cgg>Tgg	p.R374W	KRT9_ENST00000588431.1_Missense_Mutation_p.R141W	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	374	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				ACACCGTGCCGGAGCTGGGTC	0.547																																					p.R374W		Atlas-SNP	.											.	KRT9	78	.	0			c.C1120T						PASS	.	G	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	287.0	271.0	277.0		1120	0.6	0.1	17	dbSNP_132	277	17,8583	12.6+/-44.7	0,17,4283	yes	missense	KRT9	NM_000226.3	101	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	probably-damaging	374/624	39724810	19,12987	2203	4300	6503	SO:0001583	missense	3857	exon5			CGTGCCGGAGCTG		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1120C>T	17.37:g.39724810G>A	ENSP00000246662:p.Arg374Trp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_000226	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	37	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.535278	0.64972	4.54E-4	0.001977	ENSG00000171403	ENST00000246662	D	0.92149	-2.98	5.15	0.585	0.17428	Filament (1);	0.304329	0.18190	N	0.148859	D	0.91202	0.7228	M	0.92649	3.33	0.09310	N	1	B	0.30236	0.274	B	0.26094	0.066	D	0.85544	0.1217	10	0.87932	D	0	.	4.1908	0.10419	0.2528:0.0:0.4257:0.3215	.	374	P35527	K1C9_HUMAN	W	374	ENSP00000246662:R374W	ENSP00000246662:R374W	R	-	1	2	KRT9	36978336	0.000000	0.05858	0.061000	0.19648	0.351000	0.29236	0.349000	0.20055	0.133000	0.18654	-0.224000	0.12420	CGG	G|0.998;A|0.002	0.002	strong		0.547	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
NUB1	51667	hgsc.bcm.edu	37	7	151074296	151074296	+	Silent	SNP	A	A	G	rs2159158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151074296A>G	ENST00000355851.4	+	15	1910	c.1833A>G	c.(1831-1833)gcA>gcG	p.A611A	NUB1_ENST00000568733.1_Silent_p.A635A|NUB1_ENST00000566856.1_Silent_p.A597A|NUB1_ENST00000413040.2_Silent_p.A621A|WDR86_ENST00000463000.1_Intron	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	611					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GGAAGTCAGCAACAAAGAAAA	0.333													A|||	1667	0.332867	0.1233	0.4035	5008	,	,		20987	0.4603		0.5249	False		,,,				2504	0.2372				p.A635A		Atlas-SNP	.											.	NUB1	31	.	0			c.A1905G						PASS	.	A		639,3053		58,523,1265	29.0	27.0	28.0		1791	1.1	0.1	7	dbSNP_96	28	4187,3983		1062,2063,960	no	coding-synonymous	NUB1	NM_016118.4		1120,2586,2225	GG,GA,AA		48.7515,17.3077,40.6845		597/602	151074296	4826,7036	1846	4085	5931	SO:0001819	synonymous_variant	51667	exon15			GTCAGCAACAAAG	AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.1833A>G	7.37:g.151074296A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	77	75	0.974026	NM_001243351	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37		932	0.4267399267399267	75	0.1524390243902439	164	0.4530386740331492	294	0.513986013986014	399	0.5263852242744064	A	0.352	-0.944139	0.02322	0.173077	0.512485	ENSG00000013374	ENST00000460712	.	.	.	5.11	1.06	0.20224	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.52501	P	4.8000000000048004E-5	.	.	.	.	.	.	T	0.48811	-0.9002	3	.	.	.	-18.3438	7.6126	0.28139	0.3371:0.5744:0.0885:0.0	rs2159158;rs3207510;rs10369514;rs11550340;rs2159158	.	.	.	R	198	.	.	Q	+	2	0	NUB1	150705229	0.005000	0.15991	0.118000	0.21660	0.142000	0.21351	0.018000	0.13422	0.019000	0.15079	0.482000	0.46254	CAA	A|0.597;G|0.403	0.403	strong		0.333	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
IHH	3549	hgsc.bcm.edu	37	2	219920565	219920565	+	Silent	SNP	C	C	T	rs3731878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219920565C>T	ENST00000295731.6	-	3	599	c.600G>A	c.(598-600)acG>acA	p.T200T	MIR3131_ENST00000583592.1_RNA	NM_002181.3	NP_002172.2	Q14623	IHH_HUMAN	indian hedgehog	200					bone resorption (GO:0045453)|camera-type eye photoreceptor cell fate commitment (GO:0060220)|cartilage development (GO:0051216)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|chondrocyte proliferation (GO:0035988)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint development (GO:0072498)|epithelial cell morphogenesis (GO:0003382)|epithelial cell-cell adhesion (GO:0090136)|head morphogenesis (GO:0060323)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intein-mediated protein splicing (GO:0016539)|maternal process involved in female pregnancy (GO:0060135)|multicellular organism growth (GO:0035264)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of eye pigmentation (GO:0048074)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell differentiation in thymus (GO:0033085)|neuron development (GO:0048666)|osteoblast differentiation (GO:0001649)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteoglycan metabolic process (GO:0006029)|regulation of growth (GO:0040008)|response to estradiol (GO:0032355)|retinal pigment epithelium development (GO:0003406)|skeletal system development (GO:0001501)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|somite development (GO:0061053)|vitelline membrane formation (GO:0030704)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|patched binding (GO:0005113)|peptidase activity (GO:0008233)			breast(1)|endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14		Renal(207;0.0915)		Epithelial(149;1.13e-06)|all cancers(144;0.000188)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCAGCCGCCCGTCTTGGCTG	0.672													C|||	551	0.110024	0.1104	0.0951	5008	,	,		16118	0.1617		0.0865	False		,,,				2504	0.091				p.T200T		Atlas-SNP	.											.	IHH	33	.	0			c.G600A						PASS	.	C		421,3975		30,361,1807	16.0	18.0	18.0		600	-5.4	1.0	2	dbSNP_107	18	670,7918		28,614,3652	no	coding-synonymous	IHH	NM_002181.3		58,975,5459	TT,TC,CC		7.8016,9.5769,8.4026		200/412	219920565	1091,11893	2198	4294	6492	SO:0001819	synonymous_variant	3549	exon3			GCCGCCCGTCTTG	L38517	CCDS33380.1	2q33-q35	2013-02-15	2013-02-15		ENSG00000163501	ENSG00000163501			5956	protein-coding gene	gene with protein product		600726	"""Indian hedgehog (Drosophila) homolog"", ""Indian hedgehog homolog (Drosophila)"""			7590746, 14770182	Standard	NM_002181		Approved	HHG2, BDA1	uc002vjo.2	Q14623	OTTHUMG00000154631	ENST00000295731.6:c.600G>A	2.37:g.219920565C>T		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	40	22	0.55	NM_002181	B9EGM5|O43322|Q8N4B9	Silent	SNP	ENST00000295731.6	37	CCDS33380.1																																																																																			C|0.902;T|0.098	0.098	strong		0.672	IHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336408.2	NM_002181	
RBM15	64783	hgsc.bcm.edu	37	1	110883569	110883569	+	Silent	SNP	A	A	T	rs3738752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110883569A>T	ENST00000369784.3	+	1	2442	c.1542A>T	c.(1540-1542)ccA>ccT	p.P514P	RP5-1074L1.1_ENST00000449169.1_RNA|RBM15_ENST00000602849.1_Silent_p.P514P|RBM15_ENST00000487146.2_Silent_p.P514P	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	514	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P514P(1)		ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		GGGGCTTCCCACTTGGTGGCC	0.532			T	MKL1	acute megakaryocytic leukemia								A|||	882	0.176118	0.0318	0.1614	5008	,	,		19788	0.2609		0.1889	False		,,,				2504	0.2812				p.P514P		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	RBM15_ENST00000369784,NS,carcinoma,0,1	RBM15	93	1	1	Substitution - coding silent(1)	stomach(1)	c.A1542T						PASS	.	A	,	246,4160	142.7+/-177.9	7,232,1964	69.0	72.0	71.0		1542,1542	-2.4	1.0	1	dbSNP_107	71	1595,7005	294.2+/-301.7	138,1319,2843	no	coding-synonymous,coding-synonymous	RBM15	NM_001201545.1,NM_022768.4	,	145,1551,4807	TT,TA,AA		18.5465,5.5833,14.155	,	514/970,514/978	110883569	1841,11165	2203	4300	6503	SO:0001819	synonymous_variant	64783	exon1			CTTCCCACTTGGT	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"""RNA binding motif (RRM) containing"""	14959	protein-coding gene	gene with protein product	"""one twenty-two"""	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.1542A>T	1.37:g.110883569A>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	89	36	0.404494	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Silent	SNP	ENST00000369784.3	37	CCDS822.1																																																																																			A|0.840;T|0.160	0.160	strong		0.532	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768	
KPNA4	3840	hgsc.bcm.edu	37	3	160227606	160227606	+	Silent	SNP	A	A	G	rs2305401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:160227606A>G	ENST00000334256.4	-	14	1496	c.1191T>C	c.(1189-1191)atT>atC	p.I397I		NM_002268.4	NP_002259.1	O00629	IMA3_HUMAN	karyopherin alpha 4 (importin alpha 3)	397					cytokine-mediated signaling pathway (GO:0019221)|NLS-bearing protein import into nucleus (GO:0006607)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)	22			Lung(72;0.00149)|LUSC - Lung squamous cell carcinoma(72;0.00216)			TCCTTCCACTAATTGTTAAGT	0.313													A|||	218	0.0435304	0.0454	0.0259	5008	,	,		15706	0.0288		0.0736	False		,,,				2504	0.0378				p.I397I		Atlas-SNP	.											.	KPNA4	50	.	0			c.T1191C						PASS	.	A		174,4232	112.9+/-151.0	5,164,2034	137.0	138.0	138.0		1191	0.6	1.0	3	dbSNP_100	138	424,8176	131.5+/-189.3	6,412,3882	no	coding-synonymous	KPNA4	NM_002268.4		11,576,5916	GG,GA,AA		4.9302,3.9492,4.5979		397/522	160227606	598,12408	2203	4300	6503	SO:0001819	synonymous_variant	3840	exon14			TCCACTAATTGTT	AB002533	CCDS3191.1	3q25.33	2013-02-14			ENSG00000186432	ENSG00000186432		"""Importins"", ""Armadillo repeat containing"""	6397	protein-coding gene	gene with protein product		602970				9168958, 9395085	Standard	NM_002268		Approved	QIP1, SRP3, IPOA3, MGC12217, MGC26703	uc003fdn.3	O00629	OTTHUMG00000159033	ENST00000334256.4:c.1191T>C	3.37:g.160227606A>G		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_002268	A8K4S6|D3DNM2|O00190	Silent	SNP	ENST00000334256.4	37	CCDS3191.1																																																																																			A|0.952;G|0.048	0.048	strong		0.313	KPNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352960.1	NM_002268	
SCN1B	6324	hgsc.bcm.edu	37	19	35524939	35524939	+	Intron	SNP	C	C	A	rs67701503	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35524939C>A	ENST00000262631.5	+	3	585				SCN1B_ENST00000415950.3_Missense_Mutation_p.S248R|CTD-2527I21.9_ENST00000601692.1_RNA|SCN1B_ENST00000595652.1_Intron|SCN1B_ENST00000596348.1_Intron	NM_001037.4	NP_001028.1	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta subunit						axon guidance (GO:0007411)|cardiac conduction (GO:0061337)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|corticospinal neuron axon guidance (GO:0021966)|locomotion (GO:0040011)|membrane depolarization (GO:0051899)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during Purkinje myocyte cell action potential (GO:0086047)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|intercalated disc (GO:0014704)|node of Ranvier (GO:0033268)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)|voltage-gated sodium channel activity involved in Purkinje myocyte action potential (GO:0086062)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	11	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Valproic Acid(DB00313)|Zonisamide(DB00909)	tgtctctgagccaaagggttg	0.552													C|||	638	0.127396	0.0885	0.1311	5008	,	,		21003	0.1825		0.1461	False		,,,				2504	0.1012				p.S248R		Atlas-SNP	.											.	SCN1B	32	.	0			c.C744A						PASS	.	C	,ARG/SER	190,2062		9,172,945	88.0	99.0	95.0		,744	1.9	0.1	19	dbSNP_130	95	640,3758		42,556,1601	yes	intron,missense	SCN1B	NM_001037.4,NM_199037.3	,110	51,728,2546	AA,AC,CC		14.5521,8.4369,12.4812	,benign	,248/269	35524939	830,5820	1126	2199	3325	SO:0001627	intron_variant	6324	exon3			TCTGAGCCAAAGG		CCDS12441.1, CCDS46047.1	19q13.12	2014-09-17	2012-02-28		ENSG00000105711	ENSG00000105711		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10586	protein-coding gene	gene with protein product		600235	"""sodium channel, voltage-gated, type I, beta polypeptide"", ""sodium channel, voltage-gated, type I, beta"""			8394762	Standard	NM_001037		Approved		uc002nxo.2	Q07699	OTTHUMG00000182472	ENST00000262631.5:c.448+296C>A	19.37:g.35524939C>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	231	117	0.506494	NM_199037	Q5TZZ4|Q6TN97	Missense_Mutation	SNP	ENST00000262631.5	37	CCDS12441.1	291	0.13324175824175824	33	0.06707317073170732	49	0.13535911602209943	93	0.16258741258741258	116	0.15303430079155672	C	14.15	2.449285	0.43531	0.084369	0.145521	ENSG00000105711	ENST00000415950	D	0.89617	-2.54	2.95	1.88	0.25563	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.31530	-0.9940	6	.	.	.	.	7.8587	0.29497	0.0:0.7425:0.2575:0.0	.	248	Q07699-2	.	R	248	ENSP00000396915:S248R	.	S	+	3	2	SCN1B	40216779	0.410000	0.25376	0.081000	0.20488	0.064000	0.16182	0.080000	0.14802	0.769000	0.33313	0.549000	0.68633	AGC	C|0.866;A|0.134	0.134	strong		0.552	SCN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461567.1		
DDX60L	91351	hgsc.bcm.edu	37	4	169369920	169369920	+	Missense_Mutation	SNP	C	C	T	rs12507582	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169369920C>T	ENST00000511577.1	-	9	1254	c.1007G>A	c.(1006-1008)tGt>tAt	p.C336Y	DDX60L_ENST00000505890.1_Missense_Mutation_p.C336Y|DDX60L_ENST00000260184.7_Missense_Mutation_p.C336Y			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	336			C -> Y (in dbSNP:rs12507582).				ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		GAAATATTCACACCACTTGTT	0.323													C|||	1645	0.328474	0.0212	0.5159	5008	,	,		17749	0.619		0.3429	False		,,,				2504	0.2965				p.C336Y		Atlas-SNP	.											.	DDX60L	116	.	0			c.G1007A						PASS	.	C	TYR/CYS	264,3362		20,224,1569	44.0	40.0	41.0		1007	2.5	1.0	4	dbSNP_120	41	2690,5432		431,1828,1802	yes	missense	DDX60L	NM_001012967.1	194	451,2052,3371	TT,TC,CC		33.1199,7.2808,25.1447	probably-damaging	336/1707	169369920	2954,8794	1813	4061	5874	SO:0001583	missense	91351	exon9			TATTCACACCACT	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.1007G>A	4.37:g.169369920C>T	ENSP00000422423:p.Cys336Tyr	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	190	97	0.510526	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		808	0.36996336996337	13	0.026422764227642278	171	0.4723756906077348	369	0.6451048951048951	255	0.33641160949868076	C	13.99	2.402486	0.42613	0.072808	0.331199	ENSG00000181381	ENST00000260184;ENST00000511577;ENST00000505890;ENST00000505863	T;T;T;T	0.26223	1.75;1.75;1.76;2.41	2.46	2.46	0.29980	.	0.000000	0.39759	U	0.001276	T	0.00012	0.0000	M	0.68317	2.08	0.41717	P	0.01051599999999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.40850	-0.9541	9	0.87932	D	0	.	9.9101	0.41399	0.0:1.0:0.0:0.0	rs12507582;rs52810781;rs12507582	336;336;336	E9PAP8;D6R906;Q5H9U9	.;.;DDX6L_HUMAN	Y	336;336;336;64	ENSP00000260184:C336Y;ENSP00000422423:C336Y;ENSP00000422202:C336Y;ENSP00000421026:C64Y	ENSP00000260184:C336Y	C	-	2	0	DDX60L	169606495	1.000000	0.71417	0.966000	0.40874	0.881000	0.50899	3.413000	0.52686	1.346000	0.45694	0.467000	0.42956	TGT	C|0.632;T|0.368	0.368	strong		0.323	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
LRRC15	131578	hgsc.bcm.edu	37	3	194080648	194080648	+	Silent	SNP	G	G	A	rs9682540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194080648G>A	ENST00000347624.3	-	2	1210	c.1125C>T	c.(1123-1125)aaC>aaT	p.N375N	LRRC15_ENST00000428839.1_Silent_p.N381N|LRRC15_ENST00000439944.2_Silent_p.N381N	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	375					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GTCTGAGGCGGTTGTTCTGCA	0.587													G|||	737	0.147165	0.1566	0.1398	5008	,	,		20370	0.0685		0.2416	False		,,,				2504	0.1237				p.N381N		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1143T						PASS	.	G	,	736,3670	302.4+/-287.4	50,636,1517	62.0	60.0	61.0		1143,1125	4.1	1.0	3	dbSNP_119	61	2214,6386	377.2+/-338.5	283,1648,2369	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	333,2284,3886	AA,AG,GG		25.7442,16.7045,22.6818	,	381/588,375/582	194080648	2950,10056	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			GAGGCGGTTGTTC	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1125C>T	3.37:g.194080648G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	120	66	0.55	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			G|0.808;A|0.192	0.192	strong		0.587	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
LMBRD1	55788	hgsc.bcm.edu	37	6	70407465	70407465	+	Missense_Mutation	SNP	A	A	T	rs12648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:70407465A>T	ENST00000370577.3	-	14	1636	c.1407T>A	c.(1405-1407)gaT>gaA	p.D469E	LMBRD1_ENST00000370570.1_Missense_Mutation_p.D396E	NM_018368.3	NP_060838.3	Q9NUN5	LMBD1_HUMAN	LMBR1 domain containing 1	469			D -> E (in dbSNP:rs9354880).		cobalamin metabolic process (GO:0009235)|insulin receptor internalization (GO:0038016)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase B signaling (GO:0051898)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	clathrin-coated endocytic vesicle (GO:0045334)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|upper_aerodigestive_tract(1)	31						CTTCAGGAGCATCTGCATCAC	0.303													A|||	1927	0.384784	0.1203	0.4337	5008	,	,		15161	0.5645		0.4324	False		,,,				2504	0.4734				p.D469E		Atlas-SNP	.											.	LMBRD1	61	.	0			c.T1407A						PASS	.	A	GLU/ASP	681,3725	285.2+/-278.0	55,571,1577	105.0	106.0	106.0		1407	2.0	1.0	6	dbSNP_119	106	3437,5163	502.4+/-375.7	683,2071,1546	yes	missense	LMBRD1	NM_018368.3	45	738,2642,3123	TT,TA,AA		39.9651,15.4562,31.6623	benign	469/541	70407465	4118,8888	2203	4300	6503	SO:0001583	missense	55788	exon14			AGGAGCATCTGCA	AF113224	CCDS4969.1	6q13	2011-05-12	2005-07-25	2005-07-25	ENSG00000168216	ENSG00000168216			23038	protein-coding gene	gene with protein product		612625	"""chromosome 6 open reading frame 209"""	C6orf209		19136951	Standard	NM_018368		Approved	FLJ11240, bA810I22.1, cblF	uc003pfa.3	Q9NUN5	OTTHUMG00000014985	ENST00000370577.3:c.1407T>A	6.37:g.70407465A>T	ENSP00000359609:p.Asp469Glu	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	29	25	0.862069	NM_018368	A8K204|E1P531|Q5VUN6|Q86Y70|Q96FW4|Q9BY56|Q9NZD6	Missense_Mutation	SNP	ENST00000370577.3	37	CCDS4969.1	860	0.39377289377289376	75	0.1524390243902439	143	0.39502762430939226	318	0.5559440559440559	324	0.42744063324538256	A	13.99	2.403229	0.42613	0.154562	0.399651	ENSG00000168216	ENST00000370577;ENST00000370570	T;T	0.16743	2.32;2.32	5.71	1.99	0.26369	.	0.138126	0.64402	D	0.000004	T	0.02083	0.0065	N	0.17723	0.515	0.23831	P	0.99672224	B	0.15473	0.013	B	0.13407	0.009	T	0.46105	-0.9215	9	0.05833	T	0.94	-15.4742	6.3237	0.21232	0.7224:0.1343:0.1434:0.0	rs9354880;rs52793334;rs9354880	469	Q9NUN5	LMBD1_HUMAN	E	469;396	ENSP00000359609:D469E;ENSP00000359602:D396E	ENSP00000359602:D396E	D	-	3	2	LMBRD1	70464186	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.360000	0.52299	0.111000	0.17947	-0.263000	0.10527	GAT	A|0.653;T|0.347	0.347	strong		0.303	LMBRD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041124.1	NM_018368	
PPM1N	147699	hgsc.bcm.edu	37	19	46002456	46002456	+	Silent	SNP	G	G	T	rs3745821	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46002456G>T	ENST00000451287.2	+	1	726	c.726G>T	c.(724-726)ccG>ccT	p.P242P	PPM1N_ENST00000456399.2_Intron|PPM1N_ENST00000401593.1_5'Flank|PPM1N_ENST00000396735.2_5'Flank|PPM1N_ENST00000401705.1_Intron|RTN2_ENST00000344680.4_5'Flank|RTN2_ENST00000590526.1_5'Flank|PPM1N_ENST00000324688.4_Silent_p.P164P|PPM1N_ENST00000396737.2_Intron|RTN2_ENST00000589384.1_5'Flank|PPM1N_ENST00000396736.2_5'Flank|RTN2_ENST00000245923.4_5'Flank	NM_001080401.1	NP_001073870.1	Q8N819	PPM1N_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1N (putative)	242	PP2C-like.						magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)	9						AGGAGGCTCCGGGGAGGCCCC	0.697													G|||	559	0.111621	0.0257	0.2075	5008	,	,		15593	0.2054		0.0755	False		,,,				2504	0.1002				p.P242P		Atlas-SNP	.											PPM1N,rectum,carcinoma,+1,1	PPM1N	25	1	0			c.G726T						scavenged	.			148,3678		2,144,1767	18.0	22.0	20.0		726	-3.2	0.5	19	dbSNP_107	20	621,7559		23,575,3492	no	coding-synonymous	PPM1N	NM_001080401.1		25,719,5259	TT,TG,GG		7.5917,3.8683,6.4051		242/431	46002456	769,11237	1913	4090	6003	SO:0001819	synonymous_variant	147699	exon1			GGCTCCGGGGAGG	AK097444	CCDS46115.1	19q13.32	2012-04-17			ENSG00000213889	ENSG00000213889		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	26845	protein-coding gene	gene with protein product							Standard	NM_001080401		Approved	FLJ40125	uc002pce.3	Q8N819	OTTHUMG00000140397	ENST00000451287.2:c.726G>T	19.37:g.46002456G>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	28	11	0.392857	NM_001080401	Q6P662	Silent	SNP	ENST00000451287.2	37	CCDS46115.1																																																																																			G|0.895;T|0.105	0.105	strong		0.697	PPM1N-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326517.2	NM_001080401	
HLA-A	3105	hgsc.bcm.edu	37	6	29912386	29912386	+	Missense_Mutation	SNP	G	G	C	rs1137160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29912386G>C	ENST00000396634.1	+	7	1346	c.1005G>C	c.(1003-1005)aaG>aaC	p.K335N	HLA-A_ENST00000376809.5_Missense_Mutation_p.K335N|HLA-A_ENST00000376806.5_Missense_Mutation_p.K335N|HLA-A_ENST00000376802.2_Intron			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	335					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						GGAGGAGGAAGAGCTCAGGTG	0.577									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|||	772	0.154153	0.1286	0.1758	5008	,	,		18081	0.2034		0.1153	False		,,,				2504	0.1626				p.K335N		Atlas-SNP	.											HLA-A,colon,carcinoma,0,1	HLA-A	89	1	0			c.G1005C						PASS	.	G	ASN/LYS	435,2585		58,319,1133	98.0	96.0	96.0		1005	1.2	0.0	6	dbSNP_86	96	608,4800		61,486,2157	no	missense	HLA-A	NM_002116.7	94	119,805,3290	CC,CG,GG		11.2426,14.404,12.3754	benign	335/366	29912386	1043,7385	1510	2704	4214	SO:0001583	missense	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGGAAGAGCTCA	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.1005G>C	6.37:g.29912386G>C	ENSP00000379873:p.Lys335Asn	Somatic	364	0	0		WXS	Illumina HiSeq	Phase_I	262	176	0.671756	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	341	0.15613553113553114	48	0.0975609756097561	72	0.19889502762430938	143	0.25	78	0.10290237467018469	.	9.448	1.089767	0.20390	0.14404	0.112426	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809	T;T;T	0.00792	5.71;5.69;5.71	3.69	1.25	0.21368	.	0.329884	0.20907	U	0.083532	T	0.00468	0.0015	M	0.70108	2.13	0.80722	P	0.0	B;B;B;B;B	0.23058	0.079;0.0;0.0;0.0;0.0	B;B;B;B;B	0.23716	0.048;0.003;0.002;0.001;0.001	T	0.40664	-0.9551	9	0.87932	D	0	.	6.8963	0.24257	0.2254:0.0:0.7746:0.0	rs1137160;rs2157680;rs2231116;rs3179297;rs41562615	214;335;335;335;335	B4DVB9;P16188;Q5SRN5;P30455;P04439	.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	N	335	ENSP00000379873:K335N;ENSP00000366002:K335N;ENSP00000366005:K335N	ENSP00000366002:K335N	K	+	3	2	HLA-A	30020365	0.004000	0.15560	0.001000	0.08648	0.642000	0.38348	0.648000	0.24828	0.132000	0.18615	0.485000	0.47835	AAG	G|0.868;C|0.132	0.132	strong		0.577	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
EYS	346007	hgsc.bcm.edu	37	6	66112409	66112409	+	Silent	SNP	A	A	G	rs974110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:66112409A>G	ENST00000370621.3	-	7	1672	c.1146T>C	c.(1144-1146)aaT>aaC	p.N382N	EYS_ENST00000370616.2_Silent_p.N382N|EYS_ENST00000503581.1_Silent_p.N382N|EYS_ENST00000393380.2_Silent_p.N382N|EYS_ENST00000342421.5_Silent_p.N382N|EYS_ENST00000370618.3_Silent_p.N382N			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	382	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TACATGTAGCATTATTCCTCA	0.299													G|||	2534	0.50599	0.5129	0.5072	5008	,	,		14830	0.4554		0.5388	False		,,,				2504	0.5143				p.N382N		Atlas-SNP	.											.	EYS	527	.	0			c.T1146C						PASS	.	G	,,	2353,2051	562.1+/-380.9	627,1099,476	61.0	61.0	61.0		1146,1146,1146	-1.5	0.0	6	dbSNP_86	61	4501,4071	554.1+/-386.4	1215,2071,1000	no	coding-synonymous,coding-synonymous,coding-synonymous	EYS	NM_001142800.1,NM_001142801.1,NM_198283.1	,,	1842,3170,1476	GG,GA,AA		47.4918,46.5713,47.1794	,,	382/3145,382/620,382/595	66112409	6854,6122	2202	4286	6488	SO:0001819	synonymous_variant	346007	exon7			TGTAGCATTATTC		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.1146T>C	6.37:g.66112409A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	94	18	0.191489	NM_001142801	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				A|0.498;G|0.502	0.502	strong		0.299	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
TUBA3C	7278	hgsc.bcm.edu	37	13	19748038	19748038	+	Missense_Mutation	SNP	C	C	T	rs1803092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19748038C>T	ENST00000400113.3	-	5	1422	c.1318G>A	c.(1318-1320)Gtg>Atg	p.V440M		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	440			V -> M (in dbSNP:rs1803092).		'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		TCGGCTTCCACGGAATCCACG	0.592													C|||	156	0.0311502	0.0038	0.0461	5008	,	,		16293	0.0129		0.0626	False		,,,				2504	0.044				p.V440M		Atlas-SNP	.											.	TUBA3C	166	.	0			c.G1318A						PASS	.	C	MET/VAL	73,4333	65.8+/-103.3	1,71,2131	111.0	116.0	115.0		1318	1.2	0.9	13	dbSNP_89	115	513,8087	145.6+/-201.3	20,473,3807	no	missense	TUBA3C	NM_006001.2	21	21,544,5938	TT,TC,CC		5.9651,1.6568,4.5056	benign	440/451	19748038	586,12420	2203	4300	6503	SO:0001583	missense	7278	exon5			CTTCCACGGAATC	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.1318G>A	13.37:g.19748038C>T	ENSP00000382982:p.Val440Met	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	132	68	0.515152	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000400113.3	37	CCDS9284.1	76	0.0347985347985348	6	0.012195121951219513	19	0.052486187845303865	5	0.008741258741258742	46	0.06068601583113457	c	2.915	-0.224469	0.06061	0.016568	0.059651	ENSG00000198033	ENST00000400113;ENST00000360801	T	0.77620	-1.11	1.22	1.22	0.21188	.	0.179635	0.24808	U	0.035425	T	0.23727	0.0574	.	.	.	0.26331	N	0.977515	.	.	.	.	.	.	T	0.44937	-0.9295	7	0.49607	T	0.09	.	4.5968	0.12334	0.3744:0.6255:0.0:0.0	rs1803092;rs3764136;rs9511894;rs17076692;rs17790596;rs36216909;rs52836735	.	.	.	M	440;408	ENSP00000382982:V440M	ENSP00000354037:V408M	V	-	1	0	TUBA3C	18646038	0.000000	0.05858	0.937000	0.37676	0.652000	0.38707	-0.838000	0.04372	0.982000	0.38575	0.194000	0.17425	GTG	C|0.957;T|0.043	0.043	strong		0.592	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
PLIN4	729359	hgsc.bcm.edu	37	19	4512886	4512886	+	Silent	SNP	G	G	A	rs112609940	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4512886G>A	ENST00000301286.3	-	3	1043	c.1044C>T	c.(1042-1044)gtC>gtT	p.V348V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	348	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TGCCAGTTAGGACAGTCTTGG	0.577													g|||	539	0.107628	0.3056	0.0605	5008	,	,		19341	0.001		0.0626	False		,,,				2504	0.0297				p.V348V		Atlas-SNP	.											.	PLIN4	191	.	0			c.C1044T						PASS	.	G		118,3114		4,110,1502	45.0	85.0	74.0		1044	-9.2	0.0	19	dbSNP_132	74	23,8265		1,21,4122	no	coding-synonymous	PLIN4	NM_001080400.1		5,131,5624	AA,AG,GG		0.2775,3.651,1.224		348/1358	4512886	141,11379	1616	4144	5760	SO:0001819	synonymous_variant	729359	exon3			AGTTAGGACAGTC	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.1044C>T	19.37:g.4512886G>A		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	57	55	0.964912	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.931;A|0.069	0.069	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
FPGS	2356	hgsc.bcm.edu	37	9	130566678	130566678	+	Missense_Mutation	SNP	C	C	T	rs41306702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130566678C>T	ENST00000373247.2	+	2	303	c.253C>T	c.(253-255)Cgg>Tgg	p.R85W	FPGS_ENST00000373245.1_Missense_Mutation_p.R85W|FPGS_ENST00000373225.3_Missense_Mutation_p.R35W|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000393706.2_Missense_Mutation_p.R85W	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	85					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GTACCTGGCACGGAGTGGGCT	0.607													C|||	7	0.00139776	0.0008	0.0	5008	,	,		19694	0.0		0.006	False		,,,				2504	0.0				p.R85W		Atlas-SNP	.											.	FPGS	30	.	0			c.C253T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	116.0	98.0	104.0		103,253	4.2	1.0	9	dbSNP_127	104	30,8570	21.0+/-64.5	0,30,4270	yes	missense,missense	FPGS	NM_001018078.1,NM_004957.4	101,101	0,32,6471	TT,TC,CC		0.3488,0.0454,0.246	probably-damaging,probably-damaging	35/538,85/588	130566678	32,12974	2203	4300	6503	SO:0001583	missense	2356	exon2			CTGGCACGGAGTG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.253C>T	9.37:g.130566678C>T	ENSP00000362344:p.Arg85Trp	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Missense_Mutation	SNP	ENST00000373247.2	37	CCDS35148.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	0	0.0	6	0.0079155672823219	C	18.11	3.550644	0.65311	4.54E-4	0.003488	ENSG00000136877	ENST00000373247;ENST00000373245;ENST00000393706;ENST00000373228;ENST00000373225;ENST00000431857;ENST00000423577	T;T;T;T;T	0.38722	2.53;1.12;2.57;1.12;2.15	5.17	4.25	0.50352	Mur ligase, central (2);	0.062573	0.64402	D	0.000005	T	0.64427	0.2597	H	0.94964	3.605	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.80764	0.992;0.994	T	0.75414	-0.3326	10	0.87932	D	0	-1.3396	10.6558	0.45673	0.3481:0.6519:0.0:0.0	rs41306702	85;85	Q05932-4;Q05932	.;FOLC_HUMAN	W	85;85;85;85;35;35;35	ENSP00000362344:R85W;ENSP00000362342:R85W;ENSP00000377309:R85W;ENSP00000362325:R85W;ENSP00000362322:R35W	ENSP00000362322:R35W	R	+	1	2	FPGS	129606499	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	1.130000	0.31393	1.124000	0.41980	0.563000	0.77884	CGG	C|0.997;T|0.003	0.003	strong		0.607	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1		
KIFAP3	22920	hgsc.bcm.edu	37	1	169951997	169951997	+	Silent	SNP	C	C	T	rs33943686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:169951997C>T	ENST00000361580.2	-	14	1745	c.1518G>A	c.(1516-1518)ggG>ggA	p.G506G	KIFAP3_ENST00000540905.1_Silent_p.G208G|KIFAP3_ENST00000367767.1_Silent_p.G462G|KIFAP3_ENST00000367765.1_Silent_p.G466G|KIFAP3_ENST00000538366.1_Silent_p.G428G	NM_014970.3	NP_055785.2	Q92845	KIFA3_HUMAN	kinesin-associated protein 3	506					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|membrane organization (GO:0061024)|microtubule-based movement (GO:0007018)|microtubule-based process (GO:0007017)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|plus-end-directed vesicle transport along microtubule (GO:0072383)|positive regulation of calcium-dependent cell-cell adhesion (GO:0046587)|protein complex assembly (GO:0006461)|protein localization (GO:0008104)|signal transduction (GO:0007165)	centrosome (GO:0005813)|condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intraciliary transport particle (GO:0030990)|kinesin II complex (GO:0016939)|microtubule cytoskeleton (GO:0015630)	kinesin binding (GO:0019894)			endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(18)|prostate(2)|skin(3)|urinary_tract(2)	35	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CTGCAAGGTCCCCAACATAAT	0.313													C|||	1372	0.273962	0.087	0.2867	5008	,	,		13409	0.503		0.326	False		,,,				2504	0.228				p.G506G		Atlas-SNP	.											.	KIFAP3	102	.	0			c.G1518A						PASS	.	C	,,,	484,3922	208.8+/-229.8	34,416,1753	52.0	50.0	51.0		1284,1386,1398,1518	1.3	1.0	1	dbSNP_126	51	2759,5837	424.4+/-354.6	484,1791,2023	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIFAP3	NM_001204514.1,NM_001204516.1,NM_001204517.1,NM_014970.3	,,,	518,2207,3776	TT,TC,CC		32.0963,10.985,24.9423	,,,	428/715,462/749,466/753,506/793	169951997	3243,9759	2203	4298	6501	SO:0001819	synonymous_variant	22920	exon14			AAGGTCCCCAACA	U59919	CCDS1288.1, CCDS55659.1, CCDS55660.1, CCDS55661.1	1q24.2	2012-09-20			ENSG00000075945	ENSG00000075945			17060	protein-coding gene	gene with protein product	"""Smg GDS"""	601836				8900189	Standard	NM_014970		Approved	SMAP, KAP3, FLA3, KAP-1	uc001ggv.3	Q92845	OTTHUMG00000035947	ENST00000361580.2:c.1518G>A	1.37:g.169951997C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_014970	B1AKU4|B1AKU5|B2RDL1|B7Z8A3|F5H591|Q8NHU7|Q9H416	Silent	SNP	ENST00000361580.2	37	CCDS1288.1																																																																																			C|0.728;T|0.272	0.272	strong		0.313	KIFAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087568.1	NM_014970	
KRT28	162605	hgsc.bcm.edu	37	17	38955961	38955961	+	Missense_Mutation	SNP	G	G	A	rs4624233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38955961G>A	ENST00000306658.7	-	1	250	c.185C>T	c.(184-186)gCt>gTt	p.A62V		NM_181535.3	NP_853513.2			keratin 28											NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30		Breast(137;0.000301)				GGCACCACCAGCATGGCTCCC	0.542													G|||	1465	0.292532	0.2958	0.134	5008	,	,		18308	0.4077		0.1938	False		,,,				2504	0.3834				p.A62V	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.C185T						PASS	.	G	VAL/ALA	1277,3129	433.5+/-343.6	192,893,1118	73.0	74.0	74.0		185	1.4	0.0	17	dbSNP_111	74	1596,7004	296.2+/-302.8	149,1298,2853	yes	missense	KRT28	NM_181535.3	64	341,2191,3971	AA,AG,GG		18.5581,28.9832,22.0898	benign	62/465	38955961	2873,10133	2203	4300	6503	SO:0001583	missense	162605	exon1			CCACCAGCATGGC	AK129827	CCDS11376.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000173908	ENSG00000173908		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30842	protein-coding gene	gene with protein product			"""keratin 25D"""	KRT25D		16831889	Standard	NM_181535		Approved		uc002hvh.1	Q7Z3Y7	OTTHUMG00000133365	ENST00000306658.7:c.185C>T	17.37:g.38955961G>A	ENSP00000305263:p.Ala62Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_181535		Missense_Mutation	SNP	ENST00000306658.7	37	CCDS11376.1	580	0.26556776556776557	148	0.3008130081300813	57	0.1574585635359116	231	0.40384615384615385	144	0.18997361477572558	G	5.492	0.275848	0.10403	0.289832	0.185581	ENSG00000173908	ENST00000306658	T	0.75821	-0.97	5.08	1.35	0.21983	.	0.852841	0.10182	N	0.705705	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.10450	0.005	T	0.31447	-0.9943	9	0.17369	T	0.5	.	5.8448	0.18659	0.2198:0.4563:0.3239:0.0	rs4624233;rs61130906;rs4624233	62	Q7Z3Y7	K1C28_HUMAN	V	62	ENSP00000305263:A62V	ENSP00000305263:A62V	A	-	2	0	KRT28	36209487	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.548000	0.06048	0.623000	0.30267	0.650000	0.86243	GCT	G|0.752;A|0.248	0.248	strong		0.542	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
TBC1D19	55296	hgsc.bcm.edu	37	4	26585881	26585881	+	Silent	SNP	C	C	T	rs4692549	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:26585881C>T	ENST00000264866.4	+	1	344	c.66C>T	c.(64-66)tcC>tcT	p.S22S	TBC1D19_ENST00000511789.1_Silent_p.S22S	NM_018317.2	NP_060787.2	Q8N5T2	TBC19_HUMAN	TBC1 domain family, member 19	22							Rab GTPase activator activity (GO:0005097)			breast(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	17		Breast(46;0.0503)				TCAAGGGCTCCAATTTGTACT	0.607													C|||	1568	0.313099	0.1672	0.2795	5008	,	,		15170	0.3601		0.3946	False		,,,				2504	0.4018				p.S22S		Atlas-SNP	.											.	TBC1D19	53	.	0			c.C66T						PASS	.	C		951,3455	349.5+/-310.4	118,715,1370	50.0	49.0	49.0		66	2.2	0.9	4	dbSNP_111	49	3513,5087	501.4+/-375.5	720,2073,1507	no	coding-synonymous	TBC1D19	NM_018317.2		838,2788,2877	TT,TC,CC		40.8488,21.5842,34.3226		22/527	26585881	4464,8542	2203	4300	6503	SO:0001819	synonymous_variant	55296	exon1			GGGCTCCAATTTG	AK001944	CCDS3439.1, CCDS75115.1	4p15.2	2008-02-05			ENSG00000109680	ENSG00000109680			25624	protein-coding gene	gene with protein product							Standard	XM_006713967		Approved	FLJ11082	uc003gsf.4	Q8N5T2	OTTHUMG00000097797	ENST00000264866.4:c.66C>T	4.37:g.26585881C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_018317	B9A6M0|Q9NUX1	Silent	SNP	ENST00000264866.4	37	CCDS3439.1																																																																																			C|0.679;T|0.321	0.321	strong		0.607	TBC1D19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215052.2	NM_018317	
ZSWIM8	23053	hgsc.bcm.edu	37	10	75552298	75552298	+	Silent	SNP	T	T	C	rs200674189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75552298T>C	ENST00000605216.1	+	10	2218	c.2001T>C	c.(1999-2001)taT>taC	p.Y667Y	ZSWIM8_ENST00000398706.2_Silent_p.Y667Y|ZSWIM8_ENST00000604524.1_Silent_p.Y667Y|ZSWIM8_ENST00000604729.1_Silent_p.Y667Y|ZSWIM8_ENST00000431225.1_3'UTR|ZSWIM8_ENST00000603114.1_Intron	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	667							zinc ion binding (GO:0008270)										CAGATACTTATGAAGAAGATG	0.622													T|||	7	0.00139776	0.003	0.0043	5008	,	,		16349	0.0		0.0	False		,,,				2504	0.0				p.Y667Y		Atlas-SNP	.											.	.	.	.	0			c.T2001C						PASS	.	T	,,	2,3828		0,2,1913	46.0	49.0	48.0		2001,2001,2001	1.6	1.0	10		48	5,8241		0,5,4118	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA0913	NM_001242487.1,NM_001242488.1,NM_015037.3	,,	0,7,6031	CC,CT,TT		0.0606,0.0522,0.058	,,	667/1838,667/1893,667/1843	75552298	7,12069	1915	4123	6038	SO:0001819	synonymous_variant	23053	exon10			TACTTATGAAGAA	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"""Zinc fingers, SWIM-type"""	23528	protein-coding gene	gene with protein product			"""KIAA0913"""	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.2001T>C	10.37:g.75552298T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	141	63	0.446809	NM_001242488	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	37		4|4	0.0018315018315018315|0.0018315018315018315	3|3	0.006097560975609756|0.006097560975609756	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	T|T	4.874|4.874	0.162425|0.162425	0.09287|0.09287	5.22E-4|5.22E-4	6.06E-4|6.06E-4	ENSG00000214655|ENSG00000214655	ENST00000431225|ENST00000433366	.|.	.|.	.|.	5.4|5.4	1.63|1.63	0.23807|0.23807	.|.	.|.	.|.	.|.	.|.	T|.	0.49389|.	0.1554|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.44620|.	-0.9316|.	4|.	.|.	.|.	.|.	-4.1973|-4.1973	9.2674|9.2674	0.37650|0.37650	0.0:0.2171:0.0:0.7829|0.0:0.2171:0.0:0.7829	.|.	.|.	.|.	.|.	T|R	164|390	.|.	.|.	M|X	+|+	2|1	0|0	KIAA0913|KIAA0913	75222304|75222304	0.236000|0.236000	0.23804|0.23804	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	-0.663000|-0.663000	0.05299|0.05299	0.112000|0.112000	0.17975|0.17975	-0.256000|-0.256000	0.11100|0.11100	ATG|TGA	T|0.997;C|0.003	0.003	strong		0.622	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487	
TNKS	8658	hgsc.bcm.edu	37	8	9609331	9609331	+	Silent	SNP	G	G	A	rs13265931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:9609331G>A	ENST00000310430.6	+	19	3071	c.3045G>A	c.(3043-3045)gcG>gcA	p.A1015A	TNKS_ENST00000518281.1_Silent_p.A778A	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	1015					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)			NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		ATGGCGCCGCGGGAACAGAAA	0.507													G|||	707	0.141174	0.1369	0.098	5008	,	,		16575	0.1994		0.1561	False		,,,				2504	0.1022				p.A1015A		Atlas-SNP	.											.	TNKS	198	.	0			c.G3045A						PASS	.	G		599,3807	255.2+/-260.5	42,515,1646	60.0	64.0	63.0		3045	-11.5	0.0	8	dbSNP_121	63	1403,7197	254.3+/-279.6	120,1163,3017	no	coding-synonymous	TNKS	NM_003747.2		162,1678,4663	AA,AG,GG		16.314,13.5951,15.3929		1015/1328	9609331	2002,11004	2203	4300	6503	SO:0001819	synonymous_variant	8658	exon19			CGCCGCGGGAACA	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.3045G>A	8.37:g.9609331G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	37	CCDS5974.1																																																																																			G|0.844;A|0.156	0.156	strong		0.507	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
DNAJC9	23234	hgsc.bcm.edu	37	10	75006932	75006932	+	Missense_Mutation	SNP	G	G	T	rs201308148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75006932G>T	ENST00000372950.4	-	1	1688	c.16C>A	c.(16-18)Ctt>Att	p.L6I	MRPS16_ENST00000416782.2_3'UTR|MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000513954.1_RNA|DNAJC9-AS1_ENST00000440197.2_RNA	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	6					social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					TCCTCGCAAAGGTCCAGCAGC	0.672													G|||	3	0.000599042	0.0	0.0043	5008	,	,		14564	0.0		0.0	False		,,,				2504	0.0				p.L6I		Atlas-SNP	.											.	DNAJC9	19	.	0			c.C16A						PASS	.	G	ILE/LEU	1,4373		0,1,2186	10.0	12.0	11.0		16	5.0	1.0	10		11	3,8543		0,3,4270	no	missense	DNAJC9	NM_015190.3	5	0,4,6456	TT,TG,GG		0.0351,0.0229,0.031	possibly-damaging	6/261	75006932	4,12916	2187	4273	6460	SO:0001583	missense	23234	exon1			CGCAAAGGTCCAG	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"""Heat shock proteins / DNAJ (HSP40)"""	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.16C>A	10.37:g.75006932G>T	ENSP00000362041:p.Leu6Ile	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_015190	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.980759	0.74474	2.29E-4	3.51E-4	ENSG00000213551	ENST00000372950	T	0.19250	2.16	5.93	5.02	0.67125	Heat shock protein DnaJ, N-terminal (1);	0.546225	0.18936	N	0.127072	T	0.18087	0.0434	L	0.39898	1.24	0.80722	D	1	B	0.25955	0.138	B	0.24541	0.054	T	0.03608	-1.1020	10	0.33141	T	0.24	-12.0946	11.1756	0.48596	0.0844:0.0:0.9156:0.0	.	6	Q8WXX5	DNJC9_HUMAN	I	6	ENSP00000362041:L6I	ENSP00000362041:L6I	L	-	1	0	DNAJC9	74676938	0.996000	0.38824	1.000000	0.80357	0.989000	0.77384	2.876000	0.48498	1.518000	0.48934	0.586000	0.80456	CTT	.	.	weak		0.672	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
OR8K1	390157	hgsc.bcm.edu	37	11	56113593	56113593	+	Missense_Mutation	SNP	C	C	A	rs10896272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56113593C>A	ENST00000279783.2	+	1	173	c.79C>A	c.(79-81)Cct>Act	p.P27T		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	27			P -> T (in dbSNP:rs10896272).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TACAGACAACCCTGGGCTGCA	0.453										HNSCC(65;0.19)			C|||	2282	0.455671	0.2133	0.598	5008	,	,		17747	0.6438		0.3708	False		,,,				2504	0.5757				p.P27T		Atlas-SNP	.											.	OR8K1	93	.	0			c.C79A						PASS	.	C	THR/PRO	1092,3310	395.1+/-329.5	141,810,1250	115.0	106.0	109.0		79	4.3	0.1	11	dbSNP_120	109	3194,5398	483.4+/-371.1	616,1962,1718	yes	missense	OR8K1	NM_001002907.1	38	757,2772,2968	AA,AC,CC		37.1741,24.8069,32.9845	benign	27/320	56113593	4286,8708	2201	4296	6497	SO:0001583	missense	390157	exon1			GACAACCCTGGGC	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.79C>A	11.37:g.56113593C>A	ENSP00000279783:p.Pro27Thr	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	946	0.43315018315018317	94	0.1910569105691057	215	0.5939226519337016	368	0.6433566433566433	269	0.3548812664907652	C	16.53	3.150464	0.57151	0.248069	0.371741	ENSG00000150261	ENST00000279783	T	0.00428	7.44	5.18	4.26	0.50523	.	0.135624	0.33834	N	0.004503	T	0.00012	0.0000	M	0.78637	2.42	0.80722	P	0.0	B	0.28820	0.224	B	0.28385	0.089	T	0.04153	-1.0973	9	0.66056	D	0.02	-9.85	8.9442	0.35749	0.1452:0.7789:0.0:0.0759	rs10896272;rs52806840;rs60301163;rs10896272	27	Q8NGG5	OR8K1_HUMAN	T	27	ENSP00000279783:P27T	ENSP00000279783:P27T	P	+	1	0	OR8K1	55870169	0.000000	0.05858	0.065000	0.19835	0.756000	0.42949	-0.062000	0.11674	2.387000	0.81309	0.549000	0.68633	CCT	C|0.621;A|0.379	0.379	strong		0.453	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
LRPAP1	4043	hgsc.bcm.edu	37	4	3520701	3520701	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3520701T>C	ENST00000500728.2	-	4	635	c.489A>G	c.(487-489)aaA>aaG	p.K163K	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	163					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)		CGCCGGAGAATTTCCCAGAGG	0.597																																					p.K163K		Atlas-SNP	.											.	LRPAP1	29	.	0			c.A489G						PASS	.						49.0	53.0	51.0					4																	3520701		2203	4300	6503	SO:0001819	synonymous_variant	4043	exon4			GGAGAATTTCCCA		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.489A>G	4.37:g.3520701T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			.	.	none		0.597	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
PPP6R2	9701	hgsc.bcm.edu	37	22	50878196	50878196	+	Missense_Mutation	SNP	G	G	A	rs13057311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50878196G>A	ENST00000216061.5	+	21	2565	c.2195G>A	c.(2194-2196)aGg>aAg	p.R732K	PPP6R2_ENST00000395741.3_Missense_Mutation_p.R706K|PPP6R2_ENST00000395744.3_Missense_Mutation_p.R705K|PPP6R2_ENST00000359139.3_Missense_Mutation_p.R706K			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	732			R -> K (in dbSNP:rs13057311).			cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						GGAGTGGTGAGGGACGTGGGT	0.602													G|||	970	0.19369	0.1059	0.2565	5008	,	,		20218	0.1419		0.2962	False		,,,				2504	0.2157				p.R732K		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G2195A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	567,3839	245.9+/-254.7	39,489,1675	69.0	58.0	62.0		2195,2117,2117,2114	1.5	0.0	22	dbSNP_121	62	2430,6170	398.7+/-346.2	358,1714,2228	no	missense,missense,missense,missense	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	26,26,26,26	397,2203,3903	AA,AG,GG		28.2558,12.8688,23.0432	benign,benign,benign,benign	732/960,706/934,706/928,705/933	50878196	2997,10009	2203	4300	6503	SO:0001583	missense	9701	exon20			TGGTGAGGGACGT	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.2195G>A	22.37:g.50878196G>A	ENSP00000216061:p.Arg732Lys	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	127	45	0.354331	NM_001242898	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Missense_Mutation	SNP	ENST00000216061.5	37		463	0.211996336996337	62	0.12601626016260162	96	0.26519337016574585	82	0.14335664335664336	223	0.2941952506596306	G	0.039	-1.293713	0.01375	0.128688	0.282558	ENSG00000100239	ENST00000359139;ENST00000395741;ENST00000395744;ENST00000216061	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.83	1.46	0.22682	.	0.800541	0.12348	N	0.476819	T	0.00012	0.0000	N	0.22421	0.69	0.51482	P	7.500000000004725E-5	P;B;B;B;B;B	0.35174	0.488;0.113;0.069;0.113;0.113;0.191	B;B;B;B;B;B	0.26416	0.05;0.048;0.021;0.048;0.048;0.069	T	0.28396	-1.0045	9	0.05959	T	0.93	-2.4742	7.137	0.25533	0.1152:0.0:0.4072:0.4776	rs13057311;rs17183769;rs13057311	265;732;732;706;705;706	F2Z3M7;O75170-5;O75170;O75170-3;O75170-4;O75170-2	.;.;PP6R2_HUMAN;.;.;.	K	706;706;705;732	ENSP00000352051:R706K;ENSP00000379090:R706K;ENSP00000379093:R705K;ENSP00000216061:R732K	ENSP00000216061:R732K	R	+	2	0	PPP6R2	49225062	.	.	0.023000	0.16930	0.201000	0.24016	.	.	0.071000	0.16664	-0.291000	0.09656	AGG	G|0.783;A|0.217	0.217	strong		0.602	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
SOCS4	122809	hgsc.bcm.edu	37	14	55510110	55510110	+	Silent	SNP	G	G	A	rs17128136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:55510110G>A	ENST00000395472.2	+	2	683	c.351G>A	c.(349-351)ccG>ccA	p.P117P	SOCS4_ENST00000339298.2_Silent_p.P117P|SOCS4_ENST00000555846.1_Silent_p.P117P	NM_080867.2|NM_199421.1	NP_543143.1|NP_955453.1	Q8WXH5	SOCS4_HUMAN	suppressor of cytokine signaling 4	117					intracellular signal transduction (GO:0035556)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)					central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	14						CAGGGCTTCCGTCTAAAAGGA	0.408													g|||	164	0.0327476	0.0045	0.0375	5008	,	,		21115	0.0		0.0954	False		,,,				2504	0.0368				p.P117P		Atlas-SNP	.											.	SOCS4	34	.	0			c.G351A						PASS	.	A	,	60,4346	54.2+/-90.2	0,60,2143	70.0	73.0	72.0		351,351	-6.7	0.8	14	dbSNP_123	72	677,7921	167.8+/-219.5	19,639,3641	no	coding-synonymous,coding-synonymous	SOCS4	NM_080867.2,NM_199421.1	,	19,699,5784	AA,AG,GG		7.8739,1.3618,5.6675	,	117/441,117/441	55510110	737,12267	2203	4299	6502	SO:0001819	synonymous_variant	122809	exon2			GCTTCCGTCTAAA	AF424815	CCDS9722.1	14q22.1	2013-02-14	2004-02-25	2004-02-27	ENSG00000180008	ENSG00000180008		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19392	protein-coding gene	gene with protein product			"""suppressor of cytokine signaling 7"""	SOCS7		12076535, 10500304	Standard	NM_080867		Approved		uc001xbp.3	Q8WXH5	OTTHUMG00000140311	ENST00000395472.2:c.351G>A	14.37:g.55510110G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	70	39	0.557143	NM_080867		Silent	SNP	ENST00000395472.2	37	CCDS9722.1																																																																																			G|0.944;A|0.056	0.056	strong		0.408	SOCS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276910.1		
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347053	140347053	+	Silent	SNP	C	C	T	rs155807	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140347053C>T	ENST00000289269.5	+	1	1234	c.702C>T	c.(700-702)atC>atT	p.I234I	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	234	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATGGGGGCATCCCAGCCCGCT	0.602													C|||	1777	0.354832	0.2239	0.3934	5008	,	,		21052	0.5456		0.332	False		,,,				2504	0.3313				p.I234I	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C702T						PASS	.	C	,,,,,,,,,,,,,,,,,,	1101,3305	394.0+/-329.1	144,813,1246	55.0	54.0	55.0		,702,,,,,,,,,,,,,,,,,702	3.0	1.0	5	dbSNP_79	55	2820,5780	441.0+/-359.7	446,1928,1926	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	590,2741,3172	TT,TC,CC		32.7907,24.9887,30.1476	,,,,,,,,,,,,,,,,,,	,234/1008,,,,,,,,,,,,,,,,,234/885	140347053	3921,9085	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			GGGCATCCCAGCC	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.702C>T	5.37:g.140347053C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			C|0.679;T|0.321	0.321	strong		0.602	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
POM121	9883	hgsc.bcm.edu	37	7	72418963	72418963	+	IGR	SNP	T	T	C	rs7056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:72418963T>C	ENST00000434423.2	+	0	3750				POM121_ENST00000395270.1_Missense_Mutation_p.L985P|POM121_ENST00000446813.1_Missense_Mutation_p.L985P|NSUN5P2_ENST00000388955.4_RNA			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin						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)				GCCCAGGGTCTTCCACGGAGA	0.582													.|||	2870	0.573083	0.6823	0.5403	5008	,	,		16694	0.4663		0.5408	False		,,,				2504	0.592				p.L985P		Atlas-SNP	.											.	POM121	131	.	0			c.T2954C						PASS	.	C		2658,1738		964,730,504	57.0	71.0	66.0			-0.5	0.0	7	dbSNP_52	66	4064,4528		1164,1736,1396	no	near-gene-3				2128,2466,1900	CC,CT,TT		47.2998,39.5359,48.2445			72418963	6722,6266	2198	4296	6494	SO:0001628	intergenic_variant	9883	exon16			AGGGTCTTCCACG	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		7.37:g.72418963T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	124	63	0.508065	NM_001257190	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		989	0.45283882783882784	235	0.47764227642276424	196	0.5414364640883977	225	0.39335664335664333	333	0.4393139841688654	C	4.789	0.146766	0.09134	0.604641	0.472998	ENSG00000196313	ENST00000446813;ENST00000395270	T;T	0.07688	3.17;3.17	0.792	-0.506	0.11989	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.36601	-0.9741	7	0.62326	D	0.03	.	4.7736	0.13167	0.0:0.275:0.0:0.725	rs7056;rs3890943;rs6423294;rs11266751;rs17145833;rs17339561	985	A8MXF9	.	P	985	ENSP00000393020:L985P;ENSP00000378687:L985P	ENSP00000378687:L985P	L	+	2	0	POM121	72056899	0.000000	0.05858	0.007000	0.13788	0.111000	0.19643	-1.592000	0.02098	-1.656000	0.01495	-1.687000	0.00730	CTT	T|0.473;C|0.527	0.527	strong		0.582	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
CLEC4A	50856	hgsc.bcm.edu	37	12	8278181	8278181	+	Missense_Mutation	SNP	A	A	T	rs2024301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:8278181A>T	ENST00000229332.5	+	2	354	c.107A>T	c.(106-108)cAc>cTc	p.H36L	CLEC4A_ENST00000352620.3_Missense_Mutation_p.H36L|CLEC4A_ENST00000345999.3_Intron|CLEC4A_ENST00000360500.3_Intron	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	36			H -> L (in dbSNP:rs2024301). {ECO:0000269|PubMed:11178971, ECO:0000269|PubMed:11994513, ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		ACTGCCCCTCACAAAAGTAAT	0.403													a|||	2552	0.509585	0.351	0.5216	5008	,	,		-128	0.5208		0.6789	False		,,,				2504	0.5297				p.H36L		Atlas-SNP	.											.	CLEC4A	28	.	0			c.A107T						PASS	.		LEU/HIS,,,LEU/HIS	1778,2628	524.9+/-371.5	376,1026,801	158.0	133.0	142.0		107,,,107	-1.3	0.0	12	dbSNP_94	142	5797,2803	676.8+/-403.3	1954,1889,457	yes	missense,intron,intron,missense	CLEC4A	NM_016184.3,NM_194447.2,NM_194448.2,NM_194450.2	99,,,99	2330,2915,1258	TT,TA,AA		32.593,40.3541,41.7577	probably-damaging,,,probably-damaging	36/238,,,36/205	8278181	7575,5431	2203	4300	6503	SO:0001583	missense	50856	exon2			CCCCTCACAAAAG	AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"""C-type lectin domain containing"""	13257	protein-coding gene	gene with protein product		605306	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"""	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.107A>T	12.37:g.8278181A>T	ENSP00000229332:p.His36Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_016184	Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Missense_Mutation	SNP	ENST00000229332.5	37	CCDS8590.1	1216	0.5567765567765568	198	0.4024390243902439	203	0.5607734806629834	301	0.5262237762237763	514	0.6781002638522428	A	7.474	0.647192	0.14516	0.403541	0.67407	ENSG00000111729	ENST00000229332;ENST00000352620;ENST00000546339	T;T;T	0.49432	5.47;5.26;0.78	3.89	-1.34	0.09143	.	.	.	.	.	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	D;D	0.55172	0.97;0.96	P;P	0.52957	0.714;0.602	T	0.44528	-0.9322	8	0.17832	T	0.49	.	3.8679	0.09024	0.4695:0.1969:0.3336:0.0	rs2024301;rs3741859;rs52836610;rs56916733;rs2024301	36;36	Q9UMR7-2;Q9UMR7	.;CLC4A_HUMAN	L	36;36;25	ENSP00000229332:H36L;ENSP00000247243:H36L;ENSP00000443082:H25L	ENSP00000229332:H36L	H	+	2	0	CLEC4A	8169448	0.005000	0.15991	0.000000	0.03702	0.093000	0.18481	0.306000	0.19279	-0.227000	0.09884	0.533000	0.62120	CAC	T|0.573;N|0.000	0.573	strong		0.403	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	NM_194450	
KIF13A	63971	hgsc.bcm.edu	37	6	17794494	17794494	+	Silent	SNP	G	G	A	rs3734234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:17794494G>A	ENST00000259711.6	-	25	3313	c.3208C>T	c.(3208-3210)Ctg>Ttg	p.L1070L	KIF13A_ENST00000378843.2_Silent_p.L1070L|KIF13A_ENST00000378826.2_Silent_p.L1070L|KIF13A_ENST00000378816.5_Silent_p.L1070L|KIF13A_ENST00000378814.5_Silent_p.L1070L	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1070					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)			TAACTGTCCAGCCCTCTTTGG	0.473													G|||	1878	0.375	0.146	0.4207	5008	,	,		17815	0.5823		0.4314	False		,,,				2504	0.3804				p.L1070L		Atlas-SNP	.											.	KIF13A	276	.	0			c.C3208T						PASS	.	G	,,,	683,3075		67,549,1263	107.0	99.0	101.0		3208,3208,3208,3208	3.6	1.0	6	dbSNP_107	101	3639,4613		806,2027,1293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	873,2576,2556	AA,AG,GG		44.0984,18.1746,35.9867	,,,	1070/1771,1070/1758,1070/1750,1070/1806	17794494	4322,7688	1879	4126	6005	SO:0001819	synonymous_variant	63971	exon25			TGTCCAGCCCTCT	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.3208C>T	6.37:g.17794494G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_001105567	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			G|0.609;A|0.391	0.391	strong		0.473	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
NID2	22795	hgsc.bcm.edu	37	14	52508842	52508842	+	Missense_Mutation	SNP	C	C	A	rs61747585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:52508842C>A	ENST00000216286.5	-	7	1805	c.1806G>T	c.(1804-1806)gaG>gaT	p.E602D	NID2_ENST00000541773.1_Missense_Mutation_p.E549D	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	602	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					TGAAGCCGTTCTCAGAGCCAG	0.577													c|||	161	0.0321486	0.062	0.0303	5008	,	,		19175	0.0		0.0517	False		,,,				2504	0.0061				p.E602D		Atlas-SNP	.											NID2,NS,carcinoma,-2,1	NID2	201	1	0			c.G1806T						scavenged	.	C	ASP/GLU	249,4157	142.3+/-177.5	9,231,1963	75.0	83.0	80.0		1806	4.1	0.8	14	dbSNP_129	80	371,8229	121.7+/-180.7	4,363,3933	yes	missense	NID2	NM_007361.3	45	13,594,5896	AA,AC,CC		4.314,5.6514,4.767	probably-damaging	602/1376	52508842	620,12386	2203	4300	6503	SO:0001583	missense	22795	exon7			GCCGTTCTCAGAG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1806G>T	14.37:g.52508842C>A	ENSP00000216286:p.Glu602Asp	Somatic	85	1	0.0117647		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	88	0.040293040293040296	33	0.06707317073170732	13	0.03591160220994475	0	0.0	42	0.055408970976253295	C	13.76	2.334393	0.41297	0.056514	0.04314	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.31247	1.5;1.5	5.93	4.11	0.48088	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.473992	0.25319	N	0.031528	T	0.03095	0.0091	M	0.68952	2.095	0.29539	N	0.85222	P;P;P;P	0.48998	0.542;0.799;0.918;0.741	B;B;P;P	0.49140	0.348;0.158;0.601;0.491	T	0.03103	-1.1072	10	0.25751	T	0.34	.	6.2035	0.20590	0.0:0.6512:0.1381:0.2107	.	196;549;604;602	E7EPP3;Q14112-2;Q5CZI2;Q14112	.;.;.;NID2_HUMAN	D	602;196;549;604	ENSP00000216286:E602D;ENSP00000443730:E549D	ENSP00000216286:E602D	E	-	3	2	NID2	51578592	0.990000	0.36364	0.769000	0.31535	0.920000	0.55202	0.896000	0.28377	0.853000	0.35312	0.655000	0.94253	GAG	C|0.953;A|0.047	0.047	strong		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
CA5B	11238	hgsc.bcm.edu	37	X	15800751	15800751	+	Silent	SNP	G	G	A	rs1808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:15800751G>A	ENST00000318636.3	+	8	1054	c.918G>A	c.(916-918)gcG>gcA	p.A306A	CA5B_ENST00000454127.2_Silent_p.A306A	NM_007220.3	NP_009151.1	Q8WTZ4	CA5BL_HUMAN	carbonic anhydrase VB, mitochondrial	0						mitochondrion (GO:0005739)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.A306A(1)		endometrium(1)|kidney(2)|lung(3)|prostate(1)|stomach(2)	9	Hepatocellular(33;0.183)					ATGTACAAGCGAAACCCAAGC	0.433													G|||	1313	0.347815	0.2383	0.3415	3775	,	,		13207	0.2996		0.2505	False		,,,				2504	0.2117				p.A306A		Atlas-SNP	.											.	CA5B	23	.	1	Substitution - coding silent(1)	stomach(1)	c.G918A						PASS	.	G		1072,2763		117,670,168,845,403	95.0	79.0	85.0		918	-8.9	0.0	X	dbSNP_36	85	2276,4452		266,1088,656,1074,1216	no	coding-synonymous	CA5B	NM_007220.3		383,1758,824,1919,1619	AA,AG,A,GG,G		33.8288,27.9531,31.6955		306/318	15800751	3348,7215	2203	4300	6503	SO:0001819	synonymous_variant	11238	exon8			ACAAGCGAAACCC	AB021660	CCDS14171.1	Xp22.1	2008-08-13			ENSG00000169239	ENSG00000169239		"""Carbonic anhydrases"""	1378	protein-coding gene	gene with protein product		300230				10409679	Standard	XM_005274442		Approved		uc004cxe.3	Q9Y2D0	OTTHUMG00000021183	ENST00000318636.3:c.918G>A	X.37:g.15800751G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_007220	A6NEZ4	Silent	SNP	ENST00000318636.3	37	CCDS14171.1																																																																																			G|0.655;0|0.003	.	strong		0.433	CA5B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354933.1	NM_007220	
DNHD1	144132	hgsc.bcm.edu	37	11	6585032	6585032	+	Missense_Mutation	SNP	G	G	A	rs11604232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6585032G>A	ENST00000527990.2	+	29	9962	c.9962G>A	c.(9961-9963)cGa>cAa	p.R3321Q	DNHD1_ENST00000254579.6_Missense_Mutation_p.R3321Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3321					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GCAGTGAGCCGACCTGCAGCC	0.587													G|||	80	0.0159744	0.0257	0.0101	5008	,	,		19997	0.005		0.0219	False		,,,				2504	0.0123				p.R3321Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.G9962A						PASS	.	G	GLN/ARG	48,1336		0,48,644	30.0	31.0	31.0		9962	-7.1	0.0	11	dbSNP_120	31	58,3124		1,56,1534	yes	missense	DNHD1	NM_144666.2	43	1,104,2178	AA,AG,GG		1.8228,3.4682,2.3215	benign	3321/4754	6585032	106,4460	692	1591	2283	SO:0001583	missense	144132	exon31			TGAGCCGACCTGC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.9962G>A	11.37:g.6585032G>A	ENSP00000436180:p.Arg3321Gln	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	59	27	0.457627	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	48	0.02197802197802198	18	0.036585365853658534	7	0.019337016574585635	5	0.008741258741258742	18	0.023746701846965697	G	9.627	1.135332	0.21123	0.034682	0.018228	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000526486	T;T	0.74106	-0.81;-0.81	4.76	-7.06	0.01568	Dynein heavy chain, coiled coil stalk (1);	.	.	.	.	T	0.15349	0.0370	N	0.14661	0.345	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.15150	-1.0447	9	0.22706	T	0.39	.	0.662	0.00844	0.2493:0.2588:0.1187:0.3732	rs11604232	3321	Q96M86	DNHD1_HUMAN	Q	3321;3321;233	ENSP00000254579:R3321Q;ENSP00000436180:R3321Q	ENSP00000254579:R3321Q	R	+	2	0	DNHD1	6541608	0.000000	0.05858	0.016000	0.15963	0.676000	0.39594	-0.520000	0.06252	-0.818000	0.04329	-0.823000	0.03104	CGA	G|0.978;A|0.022	0.022	strong		0.587	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
SGTA	6449	hgsc.bcm.edu	37	19	2761500	2761500	+	Silent	SNP	G	G	A	rs111283489	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:2761500G>A	ENST00000221566.2	-	8	818	c.657C>T	c.(655-657)ttC>ttT	p.F219F		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	219					viral process (GO:0016032)	cytoplasm (GO:0005737)				endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGCGATGTCGAAGCTGCCCA	0.637													G|||	15	0.00299521	0.0	0.0072	5008	,	,		16043	0.0		0.006	False		,,,				2504	0.0041				p.F219F		Atlas-SNP	.											.	SGTA	19	.	0			c.C657T						PASS	.	G		9,4073		0,9,2032	62.0	49.0	54.0		657	-2.6	0.9	19	dbSNP_132	54	32,7810		0,32,3889	no	coding-synonymous	SGTA	NM_003021.3		0,41,5921	AA,AG,GG		0.4081,0.2205,0.3438		219/314	2761500	41,11883	2041	3921	5962	SO:0001819	synonymous_variant	6449	exon8			GATGTCGAAGCTG	AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"""Tetratricopeptide (TTC) repeat domain containing"""	10819	protein-coding gene	gene with protein product		603419	"""small glutamine-rich tetratricopeptide repeat (TPR)-containing"""	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.657C>T	19.37:g.2761500G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	68	41	0.602941	NM_003021	D6W610|Q6FIA9|Q9BTZ9	Silent	SNP	ENST00000221566.2	37	CCDS12094.1																																																																																			G|0.997;A|0.003	0.003	strong		0.637	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2	NM_003021	
NEK11	79858	hgsc.bcm.edu	37	3	130947466	130947466	+	Silent	SNP	G	G	A	rs138864243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130947466G>A	ENST00000510769.1	+	11	1432	c.1179G>A	c.(1177-1179)gcG>gcA	p.A393A	NEK11_ENST00000383366.4_Silent_p.A498A|NEK11_ENST00000412440.2_Silent_p.A314A|NEK11_ENST00000510688.1_Silent_p.A498A|NEK11_ENST00000508196.1_Silent_p.A498A|NEK11_ENST00000429253.2_Silent_p.A498A					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						AAGAAATAGCGTTAGAAAGAC	0.453													G|||	5	0.000998403	0.0023	0.0014	5008	,	,		19611	0.0		0.001	False		,,,				2504	0.0				p.A498A		Atlas-SNP	.											.	NEK11	76	.	0			c.G1494A						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	117.0	109.0	112.0		1494,1494	1.6	0.0	3	dbSNP_134	112	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	NEK11	NM_001146003.1,NM_024800.4	,	0,16,6487	AA,AG,GG		0.1163,0.1362,0.123	,	498/600,498/646	130947466	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	79858	exon15			AATAGCGTTAGAA	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.1179G>A	3.37:g.130947466G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_024800		Silent	SNP	ENST00000510769.1	37																																																																																				G|0.998;A|0.002	0.002	strong		0.453	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
ZNF844	284391	hgsc.bcm.edu	37	19	12186611	12186611	+	Missense_Mutation	SNP	A	A	G	rs7259684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12186611A>G	ENST00000439326.3	+	4	851	c.676A>G	c.(676-678)Aaa>Gaa	p.K226E	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	226			K -> E (in dbSNP:rs7259684).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GAAACCATATAAATGTAAACA	0.373													.|||	825	0.164736	0.413	0.0663	5008	,	,		21878	0.0665		0.0825	False		,,,				2504	0.0849				p.K226E		Atlas-SNP	.											.	ZNF844	69	.	0			c.A676G						PASS	.	G	GLU/LYS	492,892		95,302,295	40.0	37.0	38.0		676	-1.7	0.0	19	dbSNP_116	38	236,2946		6,224,1361	no	missense	ZNF844	NM_001136501.1	56	101,526,1656	GG,GA,AA		7.4167,35.5491,15.9439	benign	226/667	12186611	728,3838	692	1591	2283	SO:0001583	missense	284391	exon4			CCATATAAATGTA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.676A>G	19.37:g.12186611A>G	ENSP00000392024:p.Lys226Glu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	323	0.1478937728937729	190	0.3861788617886179	27	0.07458563535911603	40	0.06993006993006994	66	0.0870712401055409	a	0.261	-0.999373	0.02128	0.355491	0.074167	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505;ENST00000550826	T;T	0.16196	3.1;2.36	2.31	-1.72	0.08107	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44452	-0.9327	8	0.02654	T	1	.	8.289	0.31946	0.5789:0.0:0.4211:0.0	rs7259684;rs7259684	226	Q08AG5	ZN844_HUMAN	E	226;226;201;69	ENSP00000392024:K226E;ENSP00000448588:K69E	ENSP00000392024:K226E	K	+	1	0	ZNF844	12047611	0.000000	0.05858	0.002000	0.10522	0.421000	0.31385	-5.762000	0.00100	-1.016000	0.03371	-0.971000	0.02607	AAA	A|0.854;G|0.146	0.146	strong		0.373	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ATAD3B	83858	hgsc.bcm.edu	37	1	1425700	1425700	+	Silent	SNP	T	T	C	rs819980	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1425700T>C	ENST00000308647.7	+	14	1517	c.1401T>C	c.(1399-1401)atT>atC	p.I467I		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	467						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		ACAGCCGCATTGACGTGATGG	0.577													N|||	2433	0.485823	0.8487	0.3357	5008	,	,		16643	0.623		0.0994	False		,,,				2504	0.3579				p.I467I		Atlas-SNP	.											ATAD3B,NS,carcinoma,0,2	ATAD3B	68	2	0			c.T1401C						PASS	.	C		3224,1180		1194,836,172	80.0	72.0	75.0		1401	-2.2	0.1	1	dbSNP_86	75	714,7884		45,624,3630	no	coding-synonymous	ATAD3B	NM_031921.4		1239,1460,3802	CC,CT,TT		8.3043,26.7938,30.2876		467/649	1425700	3938,9064	2202	4299	6501	SO:0001819	synonymous_variant	83858	exon14			CCGCATTGACGTG	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1401T>C	1.37:g.1425700T>C		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	146	128	0.876712	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Silent	SNP	ENST00000308647.7	37	CCDS30.1																																																																																			T|0.629;C|0.371	0.371	strong		0.577	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55331419	55331419	+	Missense_Mutation	SNP	C	C	T	rs143886704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55331419C>T	ENST00000391728.4	+	4	640	c.607C>T	c.(607-609)Ccc>Tcc	p.P203S	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.P203S|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.P203S|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.P203S|KIR3DL1_ENST00000358178.4_Missense_Mutation_p.P108S|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.P203S	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	203			P -> S (in dbSNP:rs2273731).		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TACTCACACCCCCTATCAGTT	0.517													c|||	1118	0.223243	0.1362	0.2824	5008	,	,		13667	0.1617		0.4284	False		,,,				2504	0.1513				p.P203S		Atlas-SNP	.											KIR3DL1_ENST00000402254,NS,neuroblastoma,0,2	KIR3DL1	174	2	0			c.C607T						PASS	.	C	SER/PRO	729,3637		118,493,1572	150.0	128.0	136.0		607	-2.9	0.0	19	dbSNP_100	136	3261,5035		995,1271,1882	no	missense	KIR3DL1	NM_013289.2	74	1113,1764,3454	TT,TC,CC		39.3081,16.6972,31.5116		203/445	55331419	3990,8672	2183	4148	6331	SO:0001583	missense	3811	exon4			CACACCCCCTATC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.607C>T	19.37:g.55331419C>T	ENSP00000375608:p.Pro203Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	560	0.2564102564102564	67	0.13617886178861788	98	0.27071823204419887	86	0.15034965034965034	309	0.4076517150395778	-	5.868	0.344314	0.11126	0.166972	0.393081	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542;ENST00000358178	T;T;T;T;T;T	0.00873	5.59;5.59;5.59;5.59;5.59;5.59	1.44	-2.88	0.05682	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.928050	0.04022	N	0.299910	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	P;P;B;P	0.44139	0.46;0.827;0.041;0.626	B;B;B;B	0.38985	0.058;0.287;0.03;0.036	T	0.28490	-1.0042	9	0.59425	D	0.04	.	1.9712	0.03406	0.2616:0.3423:0.0:0.3961	rs2273731;rs12971727	203;108;203;203	Q15702;Q14946;F6QF33;P43629	.;.;.;KI3L1_HUMAN	S	203;203;203;181;203;203;108	ENSP00000384528:P203S;ENSP00000443350:P203S;ENSP00000442355:P203S;ENSP00000375608:P203S;ENSP00000326868:P203S;ENSP00000350901:P108S	ENSP00000326868:P203S	P	+	1	0	KIR3DL1	60023231	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.035000	0.13797	-0.710000	0.05001	0.184000	0.17185	CCC	C|0.250;T|0.750	0.750	weak		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
SCN3A	6328	hgsc.bcm.edu	37	2	166003479	166003479	+	Silent	SNP	G	G	A	rs16850131	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:166003479G>A	ENST00000360093.3	-	12	1932	c.1441C>T	c.(1441-1443)Ctg>Ttg	p.L481L	SCN3A_ENST00000283254.7_Silent_p.L481L|RN7SL455P_ENST00000580629.1_RNA|SCN3A_ENST00000409101.3_Silent_p.L481L	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	481					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)	CTTTCCAACAGCTCTCCTAAC	0.448													A|||	1289	0.257388	0.267	0.2032	5008	,	,		15691	0.3065		0.2008	False		,,,				2504	0.2904				p.L481L		Atlas-SNP	.											.	SCN3A	544	.	0			c.C1441T						PASS	.	A	,,	1089,3317	722.2+/-409.3	138,813,1252	125.0	125.0	125.0		1441,1441,1441	3.7	0.9	2	dbSNP_123	125	1841,6759	730.9+/-406.8	211,1419,2670	no	coding-synonymous,coding-synonymous,coding-synonymous	SCN3A	NM_001081676.1,NM_001081677.1,NM_006922.3	,,	349,2232,3922	AA,AG,GG		21.407,24.7163,22.5281	,,	481/1952,481/1952,481/2001	166003479	2930,10076	2203	4300	6503	SO:0001819	synonymous_variant	6328	exon12			CCAACAGCTCTCC	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.1441C>T	2.37:g.166003479G>A		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	174	170	0.977012	NM_001081676	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Silent	SNP	ENST00000360093.3	37																																																																																				G|0.756;A|0.244	0.244	strong		0.448	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105363289	105363289	+	Silent	SNP	T	T	C	rs3740471	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105363289T>C	ENST00000369774.4	-	15	1962	c.1686A>G	c.(1684-1686)gcA>gcG	p.A562A	SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000355946.2_Silent_p.A534A|SH3PXD2A_ENST00000540321.1_Silent_p.A429A|SH3PXD2A_ENST00000538130.1_Silent_p.A397A|SH3PXD2A_ENST00000427662.2_Intron			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	562					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)		CAAAGCCGAATGCAGGGATGT	0.677													T|||	679	0.135583	0.0643	0.1628	5008	,	,		15829	0.1548		0.1998	False		,,,				2504	0.1268				p.A534A		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.A1602G						PASS	.	T		389,4017	191.9+/-217.4	21,347,1835	42.0	46.0	45.0		1602	1.3	1.0	10	dbSNP_107	45	1922,6678	333.3+/-320.5	216,1490,2594	yes	coding-synonymous	SH3PXD2A	NM_014631.2		237,1837,4429	CC,CT,TT		22.3488,8.8289,17.7687		534/1106	105363289	2311,10695	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			GCCGAATGCAGGG	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.1686A>G	10.37:g.105363289T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		333	0.15247252747252749	22	0.044715447154471545	53	0.1464088397790055	98	0.17132867132867133	160	0.21108179419525067	T	0.325	-0.959357	0.02267	0.088289	0.223488	ENSG00000107957	ENST00000420222	.	.	.	5.47	1.31	0.21738	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999847	.	.	.	.	.	.	T	0.22521	-1.0214	3	.	.	.	-30.7092	2.7623	0.05310	0.1377:0.114:0.4585:0.2898	rs3740471;rs17738234;rs56448553;rs3740471	.	.	.	V	489	.	.	I	-	1	0	SH3PXD2A	105353279	1.000000	0.71417	0.994000	0.49952	0.225000	0.24961	1.815000	0.38981	0.211000	0.20683	-0.441000	0.05720	ATT	T|0.835;C|0.165	0.165	strong		0.677	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
IL12RB1	3594	hgsc.bcm.edu	37	19	18180451	18180451	+	Missense_Mutation	SNP	A	A	G	rs375947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18180451A>G	ENST00000600835.2	-	11	1392	c.1094T>C	c.(1093-1095)aTg>aCg	p.M365T	IL12RB1_ENST00000593993.2_Missense_Mutation_p.M365T			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	365	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		M -> T (in dbSNP:rs375947). {ECO:0000269|Ref.3}.		cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GCAATACGTCATGCTCTGAGC	0.607													G|||	1345	0.26857	0.2368	0.1758	5008	,	,		18923	0.376		0.3131	False		,,,				2504	0.2209				p.M365T		Atlas-SNP	.											.	IL12RB1	92	.	0			c.T1094C	GRCh37	CM030470	IL12RB1	M	rs375947	PASS	.	G	THR/MET	1071,3079		140,791,1144	84.0	92.0	89.0		1094	-4.5	0.0	19	dbSNP_80	89	2613,5793		401,1811,1991	yes	missense	IL12RB1	NM_005535.1	81	541,2602,3135	GG,GA,AA		31.0849,25.8072,29.3406	benign	365/663	18180451	3684,8872	2075	4203	6278	SO:0001583	missense	3594	exon10			TACGTCATGCTCT	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.1094T>C	19.37:g.18180451A>G	ENSP00000470788:p.Met365Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	81	29	0.358025	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	630	0.28846153846153844	112	0.22764227642276422	75	0.20718232044198895	206	0.36013986013986016	237	0.31266490765171506	G	1.841	-0.467325	0.04476	0.258072	0.310849	ENSG00000096996	ENST00000430026	T	0.79352	-1.26	4.0	-4.51	0.03483	Long hematopoietin receptor, Gp130 family 2, conserved site (1);	0.655827	0.13905	N	0.354671	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09015	-1.0694	9	0.07325	T	0.83	-0.4671	5.8474	0.18673	0.5975:0.0:0.2565:0.1459	rs375947;rs2230366;rs17711020;rs17882709;rs52802164;rs58231425;rs375947	365;365	P42701-2;P42701	.;I12R1_HUMAN	T	365	ENSP00000403103:M365T	ENSP00000403103:M365T	M	-	2	0	IL12RB1	18041451	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.948000	0.03897	-0.781000	0.04548	-0.441000	0.05720	ATG	A|0.701;G|0.299	0.299	strong		0.607	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
AHDC1	27245	hgsc.bcm.edu	37	1	27875055	27875055	+	Missense_Mutation	SNP	C	C	T	rs146401682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:27875055C>T	ENST00000247087.5	-	5	4168	c.3572G>A	c.(3571-3573)aGt>aAt	p.S1191N	AHDC1_ENST00000374011.2_Missense_Mutation_p.S1191N			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	1191							DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		GCCCTCACTACTTGAGGCCTC	0.602																																					p.S1191N		Atlas-SNP	.											.	AHDC1	98	.	0			c.G3572A						PASS	.	C	ASN/SER	0,4406		0,0,2203	54.0	49.0	51.0		3572	4.9	1.0	1	dbSNP_134	51	10,8590	7.7+/-29.5	0,10,4290	yes	missense	AHDC1	NM_001029882.2	46	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	probably-damaging	1191/1604	27875055	10,12996	2203	4300	6503	SO:0001583	missense	27245	exon6			TCACTACTTGAGG	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.3572G>A	1.37:g.27875055C>T	ENSP00000247087:p.Ser1191Asn	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	56	50	0.892857	NM_001029882	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Missense_Mutation	SNP	ENST00000247087.5	37	CCDS30652.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181723	0.57800	0.0	0.001163	ENSG00000126705	ENST00000247087;ENST00000374011	T;T	0.53206	0.63;0.63	5.8	4.87	0.63330	.	0.275088	0.28104	N	0.016593	T	0.50377	0.1612	N	0.24115	0.695	0.36042	D	0.840185	D	0.56968	0.978	P	0.61722	0.893	T	0.59679	-0.7409	10	0.62326	D	0.03	-14.0945	12.5727	0.56347	0.0:0.6559:0.3441:0.0	.	1191	Q5TGY3	AHDC1_HUMAN	N	1191	ENSP00000247087:S1191N;ENSP00000363123:S1191N	ENSP00000247087:S1191N	S	-	2	0	AHDC1	27747642	1.000000	0.71417	0.997000	0.53966	0.858000	0.48976	5.146000	0.64845	2.746000	0.94184	0.591000	0.81541	AGT	C|0.999;T|0.001	0.001	strong		0.602	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009523.3		
FANCM	57697	hgsc.bcm.edu	37	14	45650900	45650900	+	Missense_Mutation	SNP	A	A	G	rs78211950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:45650900A>G	ENST00000267430.5	+	16	4463	c.4378A>G	c.(4378-4380)Ata>Gta	p.I1460V	FANCM_ENST00000542564.2_Missense_Mutation_p.I1434V|FANCM_ENST00000555013.1_3'UTR	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1460				I -> V (in Ref. 5; BAB13422). {ECO:0000305}.	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						CAGATTTCCTATAAACAGAGT	0.289								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				A|||	508	0.101438	0.0068	0.1081	5008	,	,		15094	0.1181		0.1153	False		,,,				2504	0.1933				p.I1460V		Atlas-SNP	.											.	FANCM	225	.	0			c.A4378G						PASS	.	A	VAL/ILE	101,4305	74.7+/-112.8	1,99,2103	50.0	50.0	50.0		4378	-1.2	0.7	14	dbSNP_131	50	887,7701	193.4+/-239.1	45,797,3452	yes	missense	FANCM	NM_020937.2	29	46,896,5555	GG,GA,AA		10.3284,2.2923,7.6035	benign	1460/2049	45650900	988,12006	2203	4294	6497	SO:0001583	missense	57697	exon16	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TTTCCTATAAACA	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.4378A>G	14.37:g.45650900A>G	ENSP00000267430:p.Ile1460Val	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	201|201	0.09203296703296704|0.09203296703296704	5|5	0.01016260162601626|0.01016260162601626	31|31	0.0856353591160221|0.0856353591160221	67|67	0.11713286713286714|0.11713286713286714	98|98	0.12928759894459102|0.12928759894459102	A|A	0.010|0.010	-1.782821|-1.782821	0.00634|0.00634	0.022923|0.022923	0.103284|0.103284	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.14893|.	3.07;3.07;2.47|.	4.25|4.25	-1.19|-1.19	0.09585|0.09585	.|.	0.707747|.	0.12458|.	N|.	0.467130|.	T|T	0.00144|0.00144	0.0004|0.0004	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.19817|.	0.039;0.015|.	B;B|.	0.14578|.	0.011;0.007|.	T|T	0.24333|0.24333	-1.0163|-1.0163	9|4	0.17369|.	T|.	0.5|.	.|.	0.8104|0.8104	0.01092|0.01092	0.2601:0.3721:0.1535:0.2143|0.2601:0.3721:0.1535:0.2143	.|.	1434;1460|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	V|C	1460;1434;976|392	ENSP00000267430:I1460V;ENSP00000442493:I1434V;ENSP00000452033:I976V|.	ENSP00000267430:I1460V|.	I|Y	+|+	1|2	0|0	FANCM|FANCM	44720650|44720650	0.000000|0.000000	0.05858|0.05858	0.698000|0.698000	0.30274|0.30274	0.546000|0.546000	0.35178|0.35178	-0.191000|-0.191000	0.09601|0.09601	-0.054000|-0.054000	0.13266|0.13266	-0.644000|-0.644000	0.03951|0.03951	ATA|TAT	A|0.918;G|0.082	0.082	strong		0.289	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
CD27	939	hgsc.bcm.edu	37	12	6554628	6554628	+	Missense_Mutation	SNP	G	G	A	rs25680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:6554628G>A	ENST00000266557.3	+	2	404	c.175G>A	c.(175-177)Gct>Act	p.A59T	CD27-AS1_ENST00000399492.2_RNA|CD27-AS1_ENST00000545339.1_RNA|CD27_ENST00000541233.1_3'UTR	NM_001242.4	NP_001233	P26842	CD27_HUMAN	CD27 molecule	59			A -> T (in dbSNP:rs25680). {ECO:0000269|PubMed:1334106, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		cell surface receptor signaling pathway (GO:0007166)|extrinsic apoptotic signaling pathway (GO:0097191)|immunoglobulin mediated immune response (GO:0016064)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of JNK cascade (GO:0046330)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|response to ethanol (GO:0045471)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|transmembrane signaling receptor activity (GO:0004888)			kidney(1)|large_intestine(5)|lung(1)|urinary_tract(3)	10						GCATAGAAAGGCTGCTCAGTG	0.572													G|||	839	0.167532	0.1505	0.1239	5008	,	,		19642	0.0536		0.1968	False		,,,				2504	0.3088				p.A59T		Atlas-SNP	.											.	CD27	17	.	0			c.G175A						PASS	.	G	THR/ALA	777,3629	314.4+/-293.6	77,623,1503	150.0	123.0	133.0		175	2.7	0.0	12	dbSNP_72	133	1977,6623	349.1+/-327.3	244,1489,2567	yes	missense	CD27	NM_001242.4	58	321,2112,4070	AA,AG,GG		22.9884,17.635,21.1748	benign	59/261	6554628	2754,10252	2203	4300	6503	SO:0001583	missense	939	exon2			AGAAAGGCTGCTC	M63928	CCDS8545.1	12p13	2014-09-17	2006-10-27	2006-10-27	ENSG00000139193	ENSG00000139193		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11922	protein-coding gene	gene with protein product		186711	"""tumor necrosis factor receptor superfamily, member 7"""	TNFRSF7		2442250, 8530100	Standard	NM_001242		Approved	S152, Tp55	uc001qod.3	P26842	OTTHUMG00000168316	ENST00000266557.3:c.175G>A	12.37:g.6554628G>A	ENSP00000266557:p.Ala59Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	78	37	0.474359	NM_001242	B2RDZ0	Missense_Mutation	SNP	ENST00000266557.3	37	CCDS8545.1	267	0.12225274725274725	58	0.11788617886178862	59	0.16298342541436464	13	0.022727272727272728	137	0.18073878627968337	G	13.38	2.219840	0.39201	0.17635	0.229884	ENSG00000139193	ENST00000266557	D	0.83591	-1.74	4.54	2.66	0.31614	TNFR/CD27/30/40/95 cysteine-rich region (2);	0.547236	0.15247	N	0.272531	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	P	0.34864	0.473	B	0.38106	0.265	T	0.03555	-1.1025	9	0.13470	T	0.59	-2.4359	6.0197	0.19623	0.104:0.1919:0.704:0.0	rs25680;rs758738;rs17787459;rs52809900;rs58117019;rs25680	59	P26842	CD27_HUMAN	T	59	ENSP00000266557:A59T	ENSP00000266557:A59T	A	+	1	0	CD27	6424889	0.001000	0.12720	0.002000	0.10522	0.812000	0.45895	0.839000	0.27586	0.513000	0.28278	0.563000	0.77884	GCT	G|0.844;A|0.156	0.156	strong		0.572	CD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399258.1		
PTCH1	5727	hgsc.bcm.edu	37	9	98238358	98238358	+	Silent	SNP	G	G	A	rs2066836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:98238358G>A	ENST00000331920.6	-	12	1985	c.1686C>T	c.(1684-1686)gcC>gcT	p.A562A	PTCH1_ENST00000437951.1_Silent_p.A496A|PTCH1_ENST00000429896.2_Silent_p.A411A|PTCH1_ENST00000375274.2_Silent_p.A561A|PTCH1_ENST00000418258.1_Silent_p.A411A|PTCH1_ENST00000430669.2_Silent_p.A496A|PTCH1_ENST00000421141.1_Silent_p.A411A	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	562	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)				GGATTAACGCGGCCATGAAGA	0.577													G|||	460	0.091853	0.0106	0.098	5008	,	,		17758	0.0833		0.1948	False		,,,				2504	0.1002				p.A562A		Atlas-SNP	.											.	PTCH1	1850	.	0			c.C1686T						PASS	.	G	,,,,,,	146,4260	99.8+/-138.5	3,140,2060	84.0	63.0	70.0		1686,1488,1683,1233,1233,1233,1233	-11.3	0.0	9	dbSNP_94	70	1903,6697	335.3+/-321.3	207,1489,2604	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	,,,,,,	210,1629,4664	AA,AG,GG		22.1279,3.3137,15.7543	,,,,,,	562/1448,496/1382,561/1447,411/1297,411/1297,411/1297,411/1297	98238358	2049,10957	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon12			TAACGCGGCCATG	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.1686C>T	9.37:g.98238358G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			G|0.865;A|0.135	0.135	strong		0.577	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
MATN4	8785	hgsc.bcm.edu	37	20	43933163	43933163	+	Silent	SNP	T	T	C	rs2233094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43933163T>C	ENST00000372754.1	-	2	356	c.348A>G	c.(346-348)gcA>gcG	p.A116A	MATN4_ENST00000342716.4_Silent_p.A116A|MATN4_ENST00000372751.4_Intron|MATN4_ENST00000372756.1_Silent_p.A116A|RBPJL_ENST00000372743.1_5'Flank|MATN4_ENST00000353917.5_Silent_p.A116A|MATN4_ENST00000360607.6_Silent_p.A116A|RBPJL_ENST00000372741.3_5'Flank|MATN4_ENST00000537548.1_Silent_p.A116A|RBPJL_ENST00000343694.3_5'Flank			O95460	MATN4_HUMAN	matrilin 4	116	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				extracellular matrix organization (GO:0030198)|response to axon injury (GO:0048678)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.0122)				CGTACTGGATTGCCAGTCCCG	0.687													T|||	2021	0.403554	0.2239	0.3444	5008	,	,		16128	0.755		0.2634	False		,,,				2504	0.4703				p.A116A		Atlas-SNP	.											MATN4,NS,carcinoma,0,1	MATN4	57	1	0			c.A348G						PASS	.	T	,,	985,3411		120,745,1333	19.0	16.0	17.0		348,348,348	-9.6	0.1	20	dbSNP_98	17	2373,6207		337,1699,2254	no	coding-synonymous,coding-synonymous,coding-synonymous	MATN4	NM_003833.3,NM_030590.2,NM_030592.2	,,	457,2444,3587	CC,CT,TT		27.6573,22.4067,25.8785	,,	116/582,116/541,116/500	43933163	3358,9618	2198	4290	6488	SO:0001819	synonymous_variant	8785	exon3			CTGGATTGCCAGT	AJ007581	CCDS13348.1, CCDS46607.1	20q13.1-q13.2	2008-07-07			ENSG00000124159	ENSG00000124159			6910	protein-coding gene	gene with protein product		603897				9827539, 9027493	Standard	NM_003833		Approved		uc002xnn.2	O95460	OTTHUMG00000033043	ENST00000372754.1:c.348A>G	20.37:g.43933163T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_030592	A6NH94|A6NKN5|Q5QPU2|Q5QPU3|Q5QPU4|Q8N2M5|Q8N2M7|Q9H1F8|Q9H1F9	Silent	SNP	ENST00000372754.1	37																																																																																				T|0.676;C|0.324	0.324	strong		0.687	MATN4-002	KNOWN	non_canonical_conserved|non_canonical_U12|not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000080335.1		
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274235	39274235	+	Silent	SNP	G	G	A	rs11654403	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39274235G>A	ENST00000391413.2	-	1	371	c.333C>T	c.(331-333)cgC>cgT	p.R111R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	111	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.R111R(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)			agcagctggggcgacagcagc	0.652													g|||	1468	0.293131	0.2852	0.2522	5008	,	,		17468	0.1042		0.4235	False		,,,				2504	0.3937				p.R111R		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	1	Substitution - coding silent(1)	kidney(1)	c.C333T						PASS	.						4.0	9.0	7.0					17																	39274235		652	1539	2191	SO:0001819	synonymous_variant	653240	exon1			GCTGGGGCGACAG	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.333C>T	17.37:g.39274235G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	82	29	0.353659	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			G|0.724;A|0.276	0.276	strong		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
LAMB2	3913	hgsc.bcm.edu	37	3	49166460	49166460	+	Missense_Mutation	SNP	C	C	T	rs61729152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49166460C>T	ENST00000418109.1	-	14	1888	c.1724G>A	c.(1723-1725)cGa>cAa	p.R575Q	LAMB2_ENST00000305544.4_Missense_Mutation_p.R575Q	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	575	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CACCTGCCCTCGGGTGTCCTC	0.622													C|||	32	0.00638978	0.0	0.013	5008	,	,		18383	0.0		0.0209	False		,,,				2504	0.002				p.R575Q		Atlas-SNP	.											LAMB2,NS,carcinoma,-1,1	LAMB2	156	1	0			c.G1724A						scavenged	.	C	GLN/ARG	17,4389	26.2+/-53.5	0,17,2186	52.0	55.0	54.0		1724	-1.9	0.0	3	dbSNP_129	54	139,8461	63.5+/-125.6	2,135,4163	yes	missense	LAMB2	NM_002292.3	43	2,152,6349	TT,TC,CC		1.6163,0.3858,1.1994	benign	575/1799	49166460	156,12850	2203	4300	6503	SO:0001583	missense	3913	exon13			TGCCCTCGGGTGT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1724G>A	3.37:g.49166460C>T	ENSP00000388325:p.Arg575Gln	Somatic	33	1	0.030303		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	22	0.010073260073260074	0	0.0	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	3.211	-0.161592	0.06502	0.003858	0.016163	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34275	1.37;1.37	5.18	-1.88	0.07713	Laminin IV (1);	0.609454	0.16134	N	0.228066	T	0.07052	0.0179	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.29027	-1.0025	10	0.10377	T	0.69	.	9.9192	0.41453	0.0:0.5495:0.0:0.4505	.	575	P55268	LAMB2_HUMAN	Q	575	ENSP00000388325:R575Q;ENSP00000307156:R575Q	ENSP00000307156:R575Q	R	-	2	0	LAMB2	49141464	0.000000	0.05858	0.014000	0.15608	0.012000	0.07955	-1.165000	0.03132	-0.448000	0.07128	-0.423000	0.05987	CGA	C|0.991;T|0.009	0.009	strong		0.622	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
NCOA7	135112	hgsc.bcm.edu	37	6	126249914	126249914	+	Missense_Mutation	SNP	T	T	G	rs1567|rs386705611	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:126249914T>G	ENST00000368357.3	+	17	3178	c.2826T>G	c.(2824-2826)gaT>gaG	p.D942E	NCOA7_ENST00000229634.9_Missense_Mutation_p.D827E|NCOA7_ENST00000392477.2_Missense_Mutation_p.D942E	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	942	TLD.		D -> E (in dbSNP:rs1567).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		GGGCATTTGATTGAAATTCAG	0.433													G|||	827	0.165136	0.2617	0.0764	5008	,	,		16628	0.2401		0.1153	False		,,,				2504	0.0716				p.D942E		Atlas-SNP	.											.	NCOA7	92	.	0			c.T2826G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	1109,3297	715.1+/-408.4	152,805,1246	76.0	78.0	77.0		2793,2826,2826,2481,657,2826	4.1	1.0	6	dbSNP_36	77	1106,7494	768.0+/-407.6	64,978,3258	yes	missense,missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_001199622.1,NM_181782.4	45,45,45,45,45,45	216,1783,4504	GG,GT,TT		12.8605,25.1702,17.0306	benign,benign,benign,benign,benign,benign	931/932,942/943,942/943,827/828,219/220,942/943	126249914	2215,10791	2203	4300	6503	SO:0001583	missense	135112	exon17			ATTTGATTGAAAT	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.2826T>G	6.37:g.126249914T>G	ENSP00000357341:p.Asp942Glu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	46	39	0.847826	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	343|343	0.15705128205128205|0.15705128205128205	116|116	0.23577235772357724|0.23577235772357724	24|24	0.06629834254143646|0.06629834254143646	115|115	0.20104895104895104|0.20104895104895104	88|88	0.11609498680738786|0.11609498680738786	G|G	1.772|1.772	-0.484123|-0.484123	0.04383|0.04383	0.251702|0.251702	0.128605|0.128605	ENSG00000111912|ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634|ENST00000438495	T;T;T|.	0.06933|.	3.26;3.26;3.24|.	6.17|6.17	4.1|4.1	0.47936|0.47936	TLDc (1);|.	0.000000|.	0.85682|.	N|.	0.000000|.	T|T	0.03305|0.03305	0.0096|0.0096	N|N	0.01202|0.01202	-0.96|-0.96	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.0;0.001;0.0;0.0|.	T|T	0.38265|0.38265	-0.9669|-0.9669	9|4	0.02654|.	T|.	1|.	.|.	6.2777|6.2777	0.20989|0.20989	0.2432:0.0:0.6121:0.1447|0.2432:0.0:0.6121:0.1447	rs1567;rs52814580;rs59469171;rs1567|rs1567;rs52814580;rs59469171;rs1567	931;236;931;942|.	B3KXK4;Q5JVL0;Q8NI08-2;Q8NI08|.	.;.;.;NCOA7_HUMAN|.	E|V	942;942;827|237	ENSP00000357341:D942E;ENSP00000376269:D942E;ENSP00000229634:D827E|.	ENSP00000229634:D827E|.	D|L	+|+	3|1	2|2	NCOA7|NCOA7	126291607|126291607	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.734000|0.734000	0.41952|0.41952	1.200000|1.200000	0.32247|0.32247	0.952000|0.952000	0.37798|0.37798	-0.121000|-0.121000	0.15023|0.15023	GAT|TTG	T|0.829;G|0.171	0.171	strong		0.433	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48918275	48918275	+	Silent	SNP	C	C	T	rs139049586	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48918275C>T	ENST00000311378.4	+	2	2154	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Silent_p.P449P	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	542	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				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)			TGCTGCGCCCCGATAGCTTTG	0.622													C|||	12	0.00239617	0.0008	0.0115	5008	,	,		16132	0.0		0.002	False		,,,				2504	0.001				p.P542P		Atlas-SNP	.											WFIKKN2,colon,carcinoma,0,1	WFIKKN2	69	1	0			c.C1626T						scavenged	.	C		3,4403	2.1+/-5.4	0,3,2200	50.0	42.0	45.0		1626	-10.2	0.2	17	dbSNP_134	45	42,8558	27.4+/-76.7	0,42,4258	no	coding-synonymous	WFIKKN2	NM_175575.5		0,45,6458	TT,TC,CC		0.4884,0.0681,0.346		542/577	48918275	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			GCGCCCCGATAGC	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.1626C>T	17.37:g.48918275C>T		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	116	56	0.482759	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
CCDC180	100499483	hgsc.bcm.edu	37	9	100139161	100139161	+	Silent	SNP	A	A	G	rs11581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100139161A>G	ENST00000357054.1	+	49	5861	c.4926A>G	c.(4924-4926)caA>caG	p.Q1642Q	CCDC180_ENST00000529487.1_Silent_p.Q1697Q|CCDC180_ENST00000375202.2_Silent_p.Q1697Q|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1642						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.Q1642Q(1)									ACACTATCCAAGGCCTGTATG	0.517													G|||	2100	0.419329	0.5726	0.4582	5008	,	,		21290	0.5248		0.1958	False		,,,				2504	0.3057				p.Q1697Q		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.A5091G						PASS	.	G		2343,2063	566.4+/-381.9	643,1057,503	127.0	104.0	112.0		5091	2.1	0.6	9	dbSNP_52	112	1624,6976	739.4+/-407.1	146,1332,2822	no	coding-synonymous	C9orf174	NM_020893.2		789,2389,3325	GG,GA,AA		18.8837,46.8225,30.5013		1697/1702	100139161	3967,9039	2203	4300	6503	SO:0001819	synonymous_variant	0	exon37			TATCCAAGGCCTG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.4926A>G	9.37:g.100139161A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	54	30	0.555556	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				A|0.654;G|0.346	0.346	strong		0.517	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
RADIL	55698	hgsc.bcm.edu	37	7	4874729	4874729	+	Missense_Mutation	SNP	C	C	G	rs144507770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4874729C>G	ENST00000399583.3	-	4	1112	c.925G>C	c.(925-927)Ggc>Cgc	p.G309R	RADIL_ENST00000536091.1_Missense_Mutation_p.G309R|RADIL_ENST00000538469.1_Missense_Mutation_p.G69R	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	309					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)		GCGGCCTGGCCGCTGTCCGGG	0.711													C|||	60	0.0119808	0.0015	0.0173	5008	,	,		10553	0.0		0.0249	False		,,,				2504	0.0215				p.G309R		Atlas-SNP	.											.	RADIL	110	.	0			c.G925C						PASS	.	C	ARG/GLY	8,3996		0,8,1994	9.0	13.0	12.0		925	-1.8	0.0	7	dbSNP_134	12	168,8110		4,160,3975	yes	missense	RADIL	NM_018059.4	125	4,168,5969	GG,GC,CC		2.0295,0.1998,1.433	possibly-damaging	309/1076	4874729	176,12106	2002	4139	6141	SO:0001583	missense	55698	exon4			CCTGGCCGCTGTC	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.925G>C	7.37:g.4874729C>G	ENSP00000382492:p.Gly309Arg	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	29	0.013278388278388278	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	18	0.023746701846965697	-	4.272	0.049630	0.08243	0.001998	0.020295	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091;ENST00000538469	T;T;T	0.06068	3.35;3.35;3.35	4.3	-1.83	0.07833	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	1.742530	0.03218	N	0.177080	T	0.02193	0.0068	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39643	-0.9604	10	0.18710	T	0.47	-0.7787	0.4916	0.00565	0.1804:0.2431:0.2692:0.3073	.	309	Q96JH8	RADIL_HUMAN	R	309;280;309;69	ENSP00000382492:G309R;ENSP00000442533:G309R;ENSP00000442966:G69R	ENSP00000320946:G280R	G	-	1	0	RADIL	4841255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.164000	0.16542	-0.261000	0.09405	-0.759000	0.03464	GGC	C|0.987;G|0.013	0.013	strong		0.711	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
COL5A1	1289	hgsc.bcm.edu	37	9	137642654	137642654	+	Missense_Mutation	SNP	G	G	A	rs61735045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:137642654G>A	ENST00000371817.3	+	13	2002	c.1588G>A	c.(1588-1590)Ggc>Agc	p.G530S		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	530	Interrupted collagenous region.		G -> S (in EDS1 and EDS2; dbSNP:rs61735045). {ECO:0000269|PubMed:10602121, ECO:0000269|PubMed:11992482, ECO:0000269|PubMed:15580559}.		axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		TGGAGGTGGCGGCGATGCGGG	0.637													G|||	118	0.0235623	0.0008	0.0403	5008	,	,		16043	0.001		0.0467	False		,,,				2504	0.0419				p.G530S		Atlas-SNP	.											COL5A1,NS,carcinoma,-2,2	COL5A1	323	2	0			c.G1588A	GRCh37	CM020927	COL5A1	M	rs61735045	PASS	.	G	SER/GLY	39,4367	42.3+/-75.8	0,39,2164	38.0	39.0	39.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1588	4.5	0.0	9	dbSNP_129	39	372,8228	121.1+/-180.3	9,354,3937	yes	missense	COL5A1	NM_000093.3	56	9,393,6101	AA,AG,GG		4.3256,0.8852,3.1601	probably-damaging	530/1839	137642654	411,12595	2203	4300	6503	SO:0001583	missense	1289	exon13			GGTGGCGGCGATG	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.1588G>A	9.37:g.137642654G>A	ENSP00000360882:p.Gly530Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	56	0.02564102564102564	1	0.0020325203252032522	22	0.06077348066298342	0	0.0	33	0.04353562005277045	G	14.49	2.550175	0.45383	0.008852	0.043256	ENSG00000130635	ENST00000371817	D	0.89415	-2.51	4.54	4.54	0.55810	.	0.000000	0.64402	U	0.000003	T	0.57858	0.2082	N	0.16656	0.425	0.80722	A	1	D	0.89917	1.0	D	0.87578	0.998	T	0.80638	-0.1293	9	0.42905	T	0.14	.	16.4173	0.83746	0.0:0.0:1.0:0.0	rs61735045	530	P20908	CO5A1_HUMAN	S	530	ENSP00000360882:G530S	ENSP00000360882:G530S	G	+	1	0	COL5A1	136782475	1.000000	0.71417	0.042000	0.18584	0.288000	0.27193	5.396000	0.66297	2.223000	0.72356	0.563000	0.77884	GGC	G|0.971;A|0.029	0.029	strong		0.637	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
ITGBL1	9358	hgsc.bcm.edu	37	13	102227872	102227872	+	Silent	SNP	C	C	T	rs3916912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:102227872C>T	ENST00000376180.3	+	4	780	c.561C>T	c.(559-561)gaC>gaT	p.D187D	ITGBL1_ENST00000376162.3_Silent_p.D94D|ITGBL1_ENST00000545560.2_Silent_p.D46D	NM_001271756.1|NM_004791.1	NP_001258685.1|NP_004782.1	O95965	ITGBL_HUMAN	integrin, beta-like 1 (with EGF-like repeat domains)	187	Cysteine-rich tandem repeats.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)				breast(1)|large_intestine(6)|lung(16)|ovary(1)|prostate(4)|skin(3)	31	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					AATGCATAGACGATGAAACAG	0.348													C|||	665	0.132788	0.2587	0.1081	5008	,	,		17994	0.001		0.1809	False		,,,				2504	0.0665				p.D187D		Atlas-SNP	.											.	ITGBL1	83	.	0			c.C561T						PASS	.	C		953,3453	363.1+/-316.4	102,749,1352	231.0	215.0	221.0		561	-0.7	1.0	13	dbSNP_108	221	1533,7067	289.7+/-299.4	149,1235,2916	no	coding-synonymous	ITGBL1	NM_004791.1		251,1984,4268	TT,TC,CC		17.8256,21.6296,19.1143		187/495	102227872	2486,10520	2203	4300	6503	SO:0001819	synonymous_variant	9358	exon4			CATAGACGATGAA	AF072752	CCDS9499.1, CCDS61361.1, CCDS61362.1, CCDS73594.1	13q33	2008-07-18			ENSG00000198542	ENSG00000198542			6164	protein-coding gene	gene with protein product	"""ten integrin EGF-like repeat domains protein"", ""ITGBL1, integrin beta-like 1"""	604234				10051402	Standard	NM_004791		Approved	TIED, OSCP	uc001vpb.4	O95965	OTTHUMG00000017296	ENST00000376180.3:c.561C>T	13.37:g.102227872C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	160	78	0.4875	NM_004791	A8K5M5|B3KTP1|B4DQ02|Q8N172|Q9NPR0	Silent	SNP	ENST00000376180.3	37	CCDS9499.1																																																																																			C|0.831;T|0.169	0.169	strong		0.348	ITGBL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045669.2	NM_004791	
KRT83	3889	hgsc.bcm.edu	37	12	52712975	52712975	+	Silent	SNP	G	G	A	rs3741715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52712975G>A	ENST00000293670.3	-	2	620	c.558C>T	c.(556-558)aaC>aaT	p.N186N		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	186	Coil 1B.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCTGCACGTGGTTGAGCTCTG	0.622													g|||	1816	0.36262	0.3654	0.3386	5008	,	,		16668	0.506		0.2823	False		,,,				2504	0.3108				p.N186N	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											.	KRT83	64	.	0			c.C558T						PASS	.	G		1606,2800	498.4+/-364.1	307,992,904	139.0	146.0	144.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	558	4.8	1.0	12	dbSNP_107	144	2547,6053	415.2+/-351.7	403,1741,2156	no	coding-synonymous	KRT83	NM_002282.3		710,2733,3060	AA,AG,GG		29.6163,36.4503,31.9314		186/494	52712975	4153,8853	2203	4300	6503	SO:0001819	synonymous_variant	3889	exon2			CACGTGGTTGAGC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.558C>T	12.37:g.52712975G>A		Somatic	283	0	0		WXS	Illumina HiSeq	Phase_I	281	143	0.508897	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			.	.	weak		0.622	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
CATSPERB	79820	hgsc.bcm.edu	37	14	92159558	92159558	+	Missense_Mutation	SNP	A	A	G	rs72629402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92159558A>G	ENST00000256343.3	-	9	899	c.743T>C	c.(742-744)gTt>gCt	p.V248A		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	248					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)|cilium (GO:0005929)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|kidney(3)|large_intestine(15)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(2)	54		all_cancers(154;0.0663)|all_epithelial(191;0.236)				ATTCGTTAAAACCATATCCAC	0.348													A|||	281	0.0561102	0.0113	0.0331	5008	,	,		19365	0.1409		0.0408	False		,,,				2504	0.0613				p.V248A		Atlas-SNP	.											.	CATSPERB	114	.	0			c.T743C						PASS	.	A	ALA/VAL	97,4309	79.3+/-117.8	2,93,2108	118.0	114.0	116.0		743	3.5	1.0	14	dbSNP_130	116	429,8171	131.7+/-189.4	16,397,3887	yes	missense	CATSPERB	NM_024764.2	64	18,490,5995	GG,GA,AA		4.9884,2.2015,4.0443	benign	248/1117	92159558	526,12480	2203	4300	6503	SO:0001583	missense	79820	exon9			GTTAAAACCATAT	AK024360	CCDS32142.1	14q32.12	2012-02-22	2012-02-22	2007-10-18	ENSG00000133962	ENSG00000133962			20500	protein-coding gene	gene with protein product		611169	"""chromosome 14 open reading frame 161"", ""cation channel, sperm-associated, beta"""	C14orf161		17478420	Standard	NM_024764		Approved	FLJ14298	uc001xzs.1	Q9H7T0	OTTHUMG00000171118	ENST00000256343.3:c.743T>C	14.37:g.92159558A>G	ENSP00000256343:p.Val248Ala	Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_024764	A0AV51	Missense_Mutation	SNP	ENST00000256343.3	37	CCDS32142.1	109	0.04990842490842491	5	0.01016260162601626	12	0.03314917127071823	69	0.12062937062937062	23	0.030343007915567283	A	14.02	2.411923	0.42817	0.022015	0.049884	ENSG00000133962	ENST00000256343	T	0.52754	0.65	5.88	3.48	0.39840	.	0.251868	0.28198	N	0.016227	T	0.00608	0.0020	L	0.55481	1.735	0.27884	N	0.939579	B	0.23249	0.082	B	0.25140	0.058	T	0.02705	-1.1121	10	0.25106	T	0.35	-24.0534	8.6627	0.34101	0.8457:0.0:0.1543:0.0	.	248	Q9H7T0	CTSRB_HUMAN	A	248	ENSP00000256343:V248A	ENSP00000256343:V248A	V	-	2	0	CATSPERB	91229311	0.999000	0.42202	1.000000	0.80357	0.697000	0.40408	3.255000	0.51484	0.464000	0.27142	0.459000	0.35465	GTT	A|0.955;G|0.045	0.045	strong		0.348	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764	
DHX37	57647	hgsc.bcm.edu	37	12	125434716	125434716	+	Silent	SNP	G	G	A	rs4078216	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:125434716G>A	ENST00000308736.2	-	24	3293	c.3195C>T	c.(3193-3195)gcC>gcT	p.A1065A	DHX37_ENST00000544745.1_Silent_p.A852A	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	1065							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)		GCAGGAACCGGGCAAAGTGCT	0.647													G|||	1296	0.258786	0.0537	0.268	5008	,	,		18264	0.5605		0.2197	False		,,,				2504	0.2587				p.A1065A		Atlas-SNP	.											DHX37,NS,carcinoma,0,1	DHX37	114	1	0			c.C3195T						PASS	.	G		346,4060	180.8+/-209.0	14,318,1871	61.0	59.0	59.0		3195	0.0	0.7	12	dbSNP_108	59	2001,6599	347.5+/-326.6	232,1537,2531	no	coding-synonymous	DHX37	NM_032656.3		246,1855,4402	AA,AG,GG		23.2674,7.8529,18.0455		1065/1158	125434716	2347,10659	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon24			GAACCGGGCAAAG	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.3195C>T	12.37:g.125434716G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			G|0.776;N|0.000	.	strong		0.647	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
MED12	9968	hgsc.bcm.edu	37	X	70349947	70349947	+	Silent	SNP	A	A	C	rs5030619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:70349947A>C	ENST00000374080.3	+	28	3962	c.3930A>C	c.(3928-3930)ccA>ccC	p.P1310P	MED12_ENST00000333646.6_Silent_p.P1310P|MED12_ENST00000374102.1_Silent_p.P1310P			Q93074	MED12_HUMAN	mediator complex subunit 12	1310					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					TGCAAGACCCAGTGTTGAGTA	0.552			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome						.|||	419	0.110993	0.0166	0.1326	3775	,	,		16117	0.001		0.2565	False		,,,				2504	0.047				p.P1310P		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A3930C						PASS	.	A		204,3369		12,145,35,1344,536	57.0	56.0	57.0		3930	-4.0	1.0	X	dbSNP_113	57	2089,4488		225,1046,593,1111,1220	no	coding-synonymous	MED12	NM_005120.2		237,1191,628,2455,1756	CC,CA,C,AA,A		31.7622,5.7095,22.5911		1310/2178	70349947	2293,7857	2072	4195	6267	SO:0001819	synonymous_variant	9968	exon28			AGACCCAGTGTTG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.3930A>C	X.37:g.70349947A>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	187	185	0.989305	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			A|0.853;0|0.007	.	strong		0.552	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
C6orf52	347744	hgsc.bcm.edu	37	6	10687746	10687746	+	Missense_Mutation	SNP	G	G	T	rs7749306	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:10687746G>T	ENST00000426700.2	-	1	37	c.38C>A	c.(37-39)gCt>gAt	p.A13D	C6orf52_ENST00000259983.3_Missense_Mutation_p.A13D|C6orf52_ENST00000460742.2_Intron|C6orf52_ENST00000379586.1_Intron|C6orf52_ENST00000467832.2_5'UTR|C6orf52_ENST00000503680.1_Intron			Q5T4I8	CF052_HUMAN	chromosome 6 open reading frame 52	13			A -> D (in dbSNP:rs7749306).							endometrium(1)|prostate(1)	2						ATTTTGTTGAGCTATGCCAAA	0.388													G|||	1215	0.242612	0.7829	0.0605	5008	,	,		18302	0.0397		0.0239	False		,,,				2504	0.0757				p.A13D		Atlas-SNP	.											.	C6orf52	9	.	0			c.C38A						PASS	.	G	ASP/ALA	897,487		304,289,99	118.0	111.0	113.0		38	2.2	0.0	6	dbSNP_116	113	68,3114		2,64,1525	yes	missense	C6orf52	NM_001145020.1	126	306,353,1624	TT,TG,GG		2.137,35.1879,21.1345	probably-damaging	13/153	10687746	965,3601	692	1591	2283	SO:0001583	missense	347744	exon2			TGTTGAGCTATGC	BC016820	CCDS47371.1	6p24.2	2009-09-22	2007-06-07	2007-06-07	ENSG00000137434	ENSG00000137434			20881	protein-coding gene	gene with protein product						12477932	Standard	NM_001145020		Approved		uc011dij.2	Q5T4I8	OTTHUMG00000014240	ENST00000426700.2:c.38C>A	6.37:g.10687746G>T	ENSP00000410749:p.Ala13Asp	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	71	32	0.450704	NM_001145020	Q5T4I7|Q96AS6	Missense_Mutation	SNP	ENST00000426700.2	37	CCDS47371.1	412	0.18864468864468864	355	0.7215447154471545	19	0.052486187845303865	19	0.033216783216783216	19	0.025065963060686015	G	14.42	2.529881	0.45073	0.648121	0.02137	ENSG00000137434	ENST00000259983;ENST00000426700	T;T	0.50001	0.76;0.76	5.02	2.19	0.27852	.	.	.	.	.	T	0.27731	0.0682	L	0.44542	1.39	0.80722	P	0.0	P	0.48016	0.904	P	0.48227	0.571	T	0.09997	-1.0649	8	0.87932	D	0	.	5.6412	0.17565	0.1876:0.167:0.6455:0.0	rs7749306;rs52792406;rs60049344;rs7749306	13	Q5T4I8	CF052_HUMAN	D	13	ENSP00000259983:A13D;ENSP00000410749:A13D	ENSP00000259983:A13D	A	-	2	0	C6orf52	10795732	0.258000	0.24033	0.001000	0.08648	0.044000	0.14063	1.563000	0.36364	0.626000	0.30322	-0.175000	0.13238	GCT	A|0.000;G|0.781;T|0.219	0.219	strong		0.388	C6orf52-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039825.2	NM_001145020	
COBL	23242	hgsc.bcm.edu	37	7	51094269	51094269	+	Missense_Mutation	SNP	G	G	A	rs61737954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:51094269G>A	ENST00000265136.7	-	11	3643	c.3478C>T	c.(3478-3480)Cac>Tac	p.H1160Y	COBL_ENST00000395542.2_Missense_Mutation_p.H1242Y	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1160	WH2 2. {ECO:0000255|PROSITE- ProRule:PRU00406}.				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)					GTGCCGCTGTGCCCGCGGATA	0.632													G|||	157	0.0313498	0.003	0.0245	5008	,	,		19629	0.001		0.0606	False		,,,				2504	0.0757				p.H1160Y	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C3478T						PASS	.	G	TYR/HIS	67,4339	62.3+/-99.4	0,67,2136	91.0	79.0	83.0		3478	5.0	0.9	7	dbSNP_129	83	681,7919	168.7+/-220.2	28,625,3647	yes	missense	COBL	NM_015198.3	83	28,692,5783	AA,AG,GG		7.9186,1.5207,5.7512	probably-damaging	1160/1262	51094269	748,12258	2203	4300	6503	SO:0001583	missense	23242	exon11			CGCTGTGCCCGCG	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.3478C>T	7.37:g.51094269G>A	ENSP00000265136:p.His1160Tyr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	43	0.452632	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	69	0.03159340659340659	3	0.006097560975609756	10	0.027624309392265192	1	0.0017482517482517483	55	0.07255936675461741	G	15.29	2.788493	0.49997	0.015207	0.079186	ENSG00000106078	ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.0	5.0	0.66597	Actin-binding WH2 (3);	0.000000	0.43747	D	0.000526	T	0.05135	0.0137	L	0.34521	1.04	0.38943	D	0.958182	D;D;D;D;D	0.89917	0.998;0.998;0.999;0.998;1.0	D;D;D;D;D	0.91635	0.994;0.994;0.984;0.994;0.999	T	0.08597	-1.0714	10	0.45353	T	0.12	.	15.0181	0.71605	0.0:0.0:1.0:0.0	.	1160;1217;1160;1242;702	O75128-3;O75128-7;O75128;O75128-2;O75128-6	.;.;COBL_HUMAN;.;.	Y	1160;1052;1045;1242	ENSP00000265136:H1160Y;ENSP00000401204:H1052Y;ENSP00000413498:H1045Y;ENSP00000378912:H1242Y	ENSP00000265136:H1160Y	H	-	1	0	COBL	51061763	1.000000	0.71417	0.891000	0.34965	0.033000	0.12548	7.524000	0.81866	2.294000	0.77228	0.563000	0.77884	CAC	G|0.947;A|0.053	0.053	strong		0.632	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
PLEKHG4	25894	hgsc.bcm.edu	37	16	67322414	67322414	+	Silent	SNP	G	G	A	rs11556908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67322414G>A	ENST00000360461.5	+	20	6012	c.3477G>A	c.(3475-3477)tcG>tcA	p.S1159S	PLEKHG4_ENST00000379344.3_Silent_p.S1159S|PLEKHG4_ENST00000450733.1_Silent_p.S1078S|PLEKHG4_ENST00000427155.2_Silent_p.S1159S	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	1159							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)		CAGAGATCTCGTCCCAATGCC	0.632													G|||	133	0.0265575	0.0204	0.0202	5008	,	,		18834	0.0228		0.0328	False		,,,				2504	0.0368				p.S1159S		Atlas-SNP	.											PLEKHG4,colon,carcinoma,+1,1	PLEKHG4	94	1	0			c.G3477A						PASS	.	G	,,,,	142,4254	98.9+/-137.6	0,142,2056	119.0	120.0	120.0		3477,3477,3477,3234,3477	-10.2	0.3	16	dbSNP_120	120	260,8340	101.2+/-162.5	6,248,4046	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	,,,,	6,390,6102	AA,AG,GG		3.0233,3.2302,3.0933	,,,,	1159/1192,1159/1192,1159/1192,1078/1111,1159/1192	67322414	402,12594	2198	4300	6498	SO:0001819	synonymous_variant	25894	exon21			GATCTCGTCCCAA	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.3477G>A	16.37:g.67322414G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_001129728	Q4G0J8|Q4H485|Q56A69|Q9H7K4|Q9UFW0	Silent	SNP	ENST00000360461.5	37	CCDS32466.1																																																																																			G|0.971;A|0.029	0.029	strong		0.632	PLEKHG4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421395.2	NM_015432	
WSCD1	23302	hgsc.bcm.edu	37	17	5991344	5991344	+	Silent	SNP	C	C	T	rs2302836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5991344C>T	ENST00000574946.1	+	3	852	c.462C>T	c.(460-462)caC>caT	p.H154H	WSCD1_ENST00000573634.1_Silent_p.H38H|WSCD1_ENST00000539421.1_Silent_p.H154H|WSCD1_ENST00000317744.5_Silent_p.H154H|WSCD1_ENST00000574232.1_Silent_p.H154H			Q658N2	WSCD1_HUMAN	WSC domain containing 1	154	WSC 1. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						ACGATGGCCACGAGAGGACTC	0.547													C|||	2638	0.526757	0.1611	0.5259	5008	,	,		19074	0.8204		0.5338	False		,,,				2504	0.7117				p.H154H		Atlas-SNP	.											.	WSCD1	84	.	0			c.C462T						PASS	.	C		978,3428	367.3+/-318.2	114,750,1339	157.0	134.0	142.0		462	2.8	1.0	17	dbSNP_100	142	4587,4013	599.1+/-394.0	1223,2141,936	no	coding-synonymous	WSCD1	NM_015253.1		1337,2891,2275	TT,TC,CC		46.6628,22.197,42.7879		154/576	5991344	5565,7441	2203	4300	6503	SO:0001819	synonymous_variant	23302	exon3			TGGCCACGAGAGG		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.462C>T	17.37:g.5991344C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Silent	SNP	ENST00000574946.1	37	CCDS32538.1																																																																																			C|0.529;T|0.471	0.471	strong		0.547	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
DST	667	hgsc.bcm.edu	37	6	56327849	56327849	+	Missense_Mutation	SNP	C	C	T	rs11758339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56327849C>T	ENST00000244364.6	-	82	15331	c.15124G>A	c.(15124-15126)Gca>Aca	p.A5042T	DST_ENST00000446842.2_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Intron	NM_001144769.2|NM_001144770.1|NM_015548.4|NM_183380.3	NP_001138241.1|NP_001138242.1|NP_056363.2|NP_899236.1	Q03001	DYST_HUMAN	dystonin	7442					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)			AATACCTCTGCAGATGGCACG	0.433													C|||	1095	0.21865	0.0802	0.2507	5008	,	,		19212	0.2401		0.2515	False		,,,				2504	0.3272				p.A5042T		Atlas-SNP	.											.	DST	1427	.	0			c.G15124A						PASS	.	C	THR/ALA	393,3485		16,361,1562	132.0	124.0	126.0		15124	1.9	1.0	6	dbSNP_120	126	2167,6149		295,1577,2286	yes	missense	DST	NM_015548.4	58	311,1938,3848	TT,TC,CC		26.0582,10.1341,20.9939	benign	5042/5172	56327849	2560,9634	1939	4158	6097	SO:0001583	missense	667	exon82			CCTCTGCAGATGG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000244364.6:c.15124G>A	6.37:g.56327849C>T	ENSP00000244364:p.Ala5042Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	63	0.492188	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	ENST00000244364.6	37	CCDS47443.1	446	0.2042124542124542	35	0.07113821138211382	103	0.2845303867403315	129	0.22552447552447552	179	0.23614775725593667	C	10.24	1.295014	0.23564	0.101341	0.260582	ENSG00000151914	ENST00000244364	T	0.39592	1.07	5.79	1.9	0.25705	.	.	.	.	.	T	0.05686	0.0149	N	0.11427	0.14	0.09310	P	0.999996	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.37244	-0.9714	8	0.02654	T	1	.	7.175	0.25738	0.0:0.4431:0.3626:0.1943	rs11758339;rs17234615;rs52794909;rs61232913;rs11758339	5042;129	Q03001-8;Q86T18	.;.	T	5042	ENSP00000244364:A5042T	ENSP00000244364:A5042T	A	-	1	0	DST	56435808	0.923000	0.31300	0.998000	0.56505	0.993000	0.82548	0.212000	0.17497	0.335000	0.23614	0.655000	0.94253	GCA	C|0.788;T|0.212	0.212	strong		0.433	DST-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041022.4	NM_001723	
TNN	63923	hgsc.bcm.edu	37	1	175097864	175097864	+	Silent	SNP	G	G	A	rs12022593	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:175097864G>A	ENST00000239462.4	+	15	3425	c.3312G>A	c.(3310-3312)acG>acA	p.T1104T		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	1104	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		ACATGGAAACGGACGGAGGTG	0.592													G|||	879	0.175519	0.1082	0.1643	5008	,	,		17883	0.2609		0.1948	False		,,,				2504	0.1667				p.T1104T		Atlas-SNP	.											TNN,right_upper_lobe,carcinoma,+1,1	TNN	297	1	0			c.G3312A						PASS	.	G		525,3881	240.6+/-251.3	24,477,1702	97.0	92.0	94.0		3312	-2.3	0.9	1	dbSNP_120	94	1856,6744	331.6+/-319.7	212,1432,2656	no	coding-synonymous	TNN	NM_022093.1		236,1909,4358	AA,AG,GG		21.5814,11.9156,18.3069		1104/1300	175097864	2381,10625	2203	4300	6503	SO:0001819	synonymous_variant	63923	exon15			GGAAACGGACGGA	AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.3312G>A	1.37:g.175097864G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	46	0.5	NM_022093	B9EGP3|Q5R360	Silent	SNP	ENST00000239462.4	37	CCDS30943.1																																																																																			G|0.813;A|0.187	0.187	strong		0.592	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
CXXC1	30827	hgsc.bcm.edu	37	18	47811374	47811374	+	Silent	SNP	G	G	A	rs17660776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:47811374G>A	ENST00000285106.6	-	7	1624	c.910C>T	c.(910-912)Ctg>Ttg	p.L304L	CXXC1_ENST00000589940.1_Silent_p.L304L|CXXC1_ENST00000412036.2_Silent_p.L304L|CXXC1_ENST00000587396.1_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	304	Asp/Glu-rich (acidic).				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						CTGCTCACCAGGCCATGGTCA	0.547													G|||	547	0.109225	0.0318	0.1052	5008	,	,		19404	0.0526		0.174	False		,,,				2504	0.2086				p.L304L		Atlas-SNP	.											.	CXXC1	50	.	0			c.C910T						PASS	.	G	,	258,4148	147.3+/-181.8	10,238,1955	71.0	76.0	74.0		910,910	2.2	1.0	18	dbSNP_123	74	1509,7091	284.4+/-296.6	129,1251,2920	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	139,1489,4875	AA,AG,GG		17.5465,5.8557,13.586	,	304/661,304/657	47811374	1767,11239	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon7			TCACCAGGCCATG	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.910C>T	18.37:g.47811374G>A		Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	148	146	0.986486	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			G|0.886;A|0.114	0.114	strong		0.547	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
GSG2	83903	hgsc.bcm.edu	37	17	3627840	3627840	+	Missense_Mutation	SNP	G	G	A	rs220462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3627840G>A	ENST00000325418.4	+	1	630	c.611G>A	c.(610-612)gGc>gAc	p.G204D	CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_5'UTR|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	204			G -> D (in dbSNP:rs220462). {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)										GTCCCGAGCGGCCTCCACCTC	0.662													G|||	1291	0.257788	0.0356	0.1556	5008	,	,		16159	0.3006		0.3101	False		,,,				2504	0.5327				p.G204D		Atlas-SNP	.											.	GSG2	48	.	0			c.G611A						PASS	.	G	,ASP/GLY	346,4060	179.7+/-208.2	21,304,1878	60.0	65.0	63.0		,611	-1.8	0.0	17	dbSNP_79	63	2761,5839	435.2+/-358.0	439,1883,1978	yes	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,94	460,2187,3856	AA,AG,GG		32.1047,7.8529,23.889	,benign	,204/799	3627840	3107,9899	2203	4300	6503	SO:0001583	missense	83903	exon1			CGAGCGGCCTCCA	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.611G>A	17.37:g.3627840G>A	ENSP00000325290:p.Gly204Asp	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	500	0.22893772893772893	20	0.04065040650406504	65	0.17955801104972377	177	0.3094405594405594	238	0.31398416886543534	G	13.17	2.158020	0.38119	0.078529	0.321047	ENSG00000177602	ENST00000325418	T	0.08458	3.09	4.02	-1.77	0.07982	.	1.355760	0.05475	N	0.553742	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.48433	-0.9036	9	0.87932	D	0	-26.5025	9.7666	0.40565	0.5364:0.0:0.4636:0.0	rs220462;rs220462	204	Q8TF76	HASP_HUMAN	D	204	ENSP00000325290:G204D	ENSP00000325290:G204D	G	+	2	0	GSG2	3574589	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.148000	0.10219	-0.416000	0.07473	-0.136000	0.14681	GGC	G|0.759;A|0.241	0.241	strong		0.662	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
GPR112	139378	hgsc.bcm.edu	37	X	135431358	135431358	+	Silent	SNP	C	C	T	rs5930933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135431358C>T	ENST00000394143.1	+	6	5784	c.5493C>T	c.(5491-5493)ccC>ccT	p.P1831P	GPR112_ENST00000370652.1_Silent_p.P1831P|GPR112_ENST00000412101.1_Silent_p.P1626P|GPR112_ENST00000287534.4_Silent_p.P1768P|GPR112_ENST00000394141.1_Silent_p.P1626P	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	1831					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CAACTCTACCCTCTTTGACAT	0.433													c|||	1787	0.473377	0.4236	0.3573	3775	,	,		16215	0.2778		0.3797	False		,,,				2504	0.3241				p.P1831P		Atlas-SNP	.											.	GPR112	459	.	0			c.C5493T						PASS	.			2112,1723		495,811,311,326,260	143.0	125.0	131.0		5493	0.4	0.0	X	dbSNP_114	131	3228,3500		567,1180,914,681,958	yes	coding-synonymous	GPR112	NM_153834.3		1062,1991,1225,1007,1218	TT,TC,T,CC,C		47.9786,44.9283,49.4462		1831/3081	135431358	5340,5223	2203	4300	6503	SO:0001819	synonymous_variant	139378	exon6			TCTACCCTCTTTG	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.5493C>T	X.37:g.135431358C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	CCDS35409.1																																																																																			C|0.507;0|0.003	.	strong		0.433	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
TNXB	7148	hgsc.bcm.edu	37	6	32024395	32024395	+	Missense_Mutation	SNP	C	C	T	rs10947230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32024395C>T	ENST00000375244.3	-	23	8312	c.8111G>A	c.(8110-8112)cGc>cAc	p.R2704H	TNXB_ENST00000375247.2_Missense_Mutation_p.R2704H			P22105	TENX_HUMAN	tenascin XB	2764	Fibronectin type-III 19. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGGGCCCACGCGCTGGCCACC	0.637													C|||	528	0.105431	0.202	0.0749	5008	,	,		18546	0.0823		0.0934	False		,,,				2504	0.0327				p.R2704H		Atlas-SNP	.											TNXB_ENST00000375247,caecum,carcinoma,+1,2	TNXB	553	2	0			c.G8111A						PASS	.	C	HIS/ARG	393,2097		27,339,879	34.0	38.0	37.0		8111	4.6	0.9	6	dbSNP_120	37	314,4752		6,302,2225	yes	missense	TNXB	NM_019105.6	29	33,641,3104	TT,TC,CC		6.1982,15.7831,9.3568	probably-damaging	2704/4243	32024395	707,6849	1245	2533	3778	SO:0001583	missense	7148	exon23			CCCACGCGCTGGC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.8111G>A	6.37:g.32024395C>T	ENSP00000364393:p.Arg2704His	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	249	118	0.473896	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		271	0.12408424908424909	101	0.20528455284552846	38	0.10497237569060773	59	0.10314685314685315	73	0.09630606860158311	C	15.54	2.864793	0.51482	0.157831	0.061982	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.05025	3.51;3.51	4.61	4.61	0.57282	.	0.000000	0.49305	D	0.000159	T	0.26376	0.0644	H	0.94886	3.595	0.33812	P	0.372008	D	0.89917	1.0	D	0.87578	0.998	T	0.42275	-0.9461	9	0.62326	D	0.03	.	14.4085	0.67099	0.0:1.0:0.0:0.0	rs10947230	2704	P22105-3	.	H	2704	ENSP00000364393:R2704H;ENSP00000364396:R2704H	ENSP00000364393:R2704H	R	-	2	0	TNXB	32132373	0.971000	0.33674	0.915000	0.36163	0.055000	0.15305	2.361000	0.44160	2.099000	0.63709	0.306000	0.20318	CGC	C|0.895;T|0.105	0.105	strong		0.637	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
DLGAP1	9229	hgsc.bcm.edu	37	18	3814148	3814148	+	Silent	SNP	C	C	G	rs3786431	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:3814148C>G	ENST00000315677.3	-	5	1678	c.1083G>C	c.(1081-1083)acG>acC	p.T361T	DLGAP1_ENST00000581699.1_Silent_p.T67T|DLGAP1_ENST00000534970.1_Silent_p.T73T|DLGAP1_ENST00000584874.1_Silent_p.T361T|DLGAP1_ENST00000478161.1_5'UTR|DLGAP1_ENST00000539435.1_Silent_p.T59T|DLGAP1_ENST00000581527.1_Silent_p.T361T|DLGAP1_ENST00000400150.3_Silent_p.T67T|DLGAP1_ENST00000400155.1_Silent_p.T67T|snoU13_ENST00000459060.1_RNA|DLGAP1_ENST00000400149.3_Silent_p.T69T|DLGAP1_ENST00000515196.2_Silent_p.T361T|DLGAP1_ENST00000400145.2_Silent_p.T59T|DLGAP1_ENST00000400147.2_Silent_p.T59T	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	361					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				GCTTAGGACTCGTGTCTGAGT	0.502													C|||	668	0.133387	0.3101	0.0576	5008	,	,		15513	0.0605		0.0358	False		,,,				2504	0.1237				p.T361T		Atlas-SNP	.											.	DLGAP1	201	.	0			c.G1083C						PASS	.	C	,,,,,,,	1133,3273	407.8+/-334.4	145,843,1215	157.0	142.0	147.0		177,1083,219,219,201,177,177,1083	-9.3	0.8	18	dbSNP_107	147	270,8330	102.7+/-163.9	2,266,4032	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLGAP1	NM_001003809.2,NM_001242761.1,NM_001242762.1,NM_001242763.1,NM_001242764.1,NM_001242765.1,NM_001242766.1,NM_004746.3	,,,,,,,	147,1109,5247	GG,GC,CC		3.1395,25.7149,10.7873	,,,,,,,	59/676,361/930,73/662,73/700,67/684,59/628,59/686,361/978	3814148	1403,11603	2203	4300	6503	SO:0001819	synonymous_variant	9229	exon5			AGGACTCGTGTCT	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"""discs, large (Drosophila) homolog-associated protein 1"""			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.1083G>C	18.37:g.3814148C>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Silent	SNP	ENST00000315677.3	37	CCDS11836.1																																																																																			C|0.896;G|0.104	0.104	strong		0.502	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		
LRRC69	100130742	hgsc.bcm.edu	37	8	92136728	92136728	+	Missense_Mutation	SNP	C	C	T	rs11785003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:92136728C>T	ENST00000448384.2	+	2	191	c.191C>T	c.(190-192)aCa>aTa	p.T64I	LRRC69_ENST00000343709.3_Intron	NM_001129890.1	NP_001123362.1	Q6ZNQ3	LRC69_HUMAN	leucine rich repeat containing 69	64			T -> I (in dbSNP:rs11785003).							endometrium(1)	1						CAGTTGACAACACTAAATCTG	0.333													C|||	2341	0.467452	0.205	0.3775	5008	,	,		15290	0.5804		0.5716	False		,,,				2504	0.6626				p.T64I		Atlas-SNP	.											.	LRRC69	24	.	0			c.C191T						PASS	.						79.0	66.0	70.0					8																	92136728		692	1588	2280	SO:0001583	missense	100130742	exon2			TGACAACACTAAA	AK130865		8q21.3	2010-07-14			ENSG00000214954	ENSG00000214954			34303	protein-coding gene	gene with protein product							Standard	NM_001129890		Approved		uc010mal.1	Q6ZNQ3	OTTHUMG00000164023	ENST00000448384.2:c.191C>T	8.37:g.92136728C>T	ENSP00000400803:p.Thr64Ile	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	28	9	0.321429	NM_001129890		Missense_Mutation	SNP	ENST00000448384.2	37		1010	0.4624542124542125	106	0.21544715447154472	145	0.4005524861878453	313	0.5472027972027972	446	0.5883905013192612	C	1.242	-0.620990	0.03636	.	.	ENSG00000214954	ENST00000448384	T	0.10382	2.88	5.53	-1.18	0.09617	.	.	.	.	.	T	0.00012	0.0000	N	0.04043	-0.29	0.80722	P	0.0	B	0.17667	0.023	B	0.13407	0.009	T	0.29397	-1.0013	8	0.20519	T	0.43	0.6915	7.042	0.25025	0.0:0.2244:0.1401:0.6354	rs11785003;rs52809669;rs60156813;rs11785003	64	Q6ZNQ3	LRC69_HUMAN	I	64	ENSP00000400803:T64I	ENSP00000400803:T64I	T	+	2	0	LRRC69	92205904	0.000000	0.05858	0.021000	0.16686	0.004000	0.04260	-0.811000	0.04500	-0.179000	0.10654	-0.882000	0.02950	ACA	C|0.555;T|0.445	0.445	strong		0.333	LRRC69-007	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000415207.1	NM_001129890	
OR2J3	442186	hgsc.bcm.edu	37	6	29079925	29079925	+	Silent	SNP	C	C	G	rs140877389	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29079925C>G	ENST00000377169.1	+	1	258	c.258C>G	c.(256-258)gtC>gtG	p.V86V		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	86						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						AGTTGCTGGTCAATCTCTGGG	0.493													c|||	29	0.00579073	0.003	0.0043	5008	,	,		20854	0.003		0.006	False		,,,				2504	0.0133				p.V86V		Atlas-SNP	.											OR2J3,NS,carcinoma,0,1	OR2J3	53	1	0			c.C258G						PASS	.	C		8,2526		0,8,1259	191.0	198.0	196.0		258	-5.2	0.0	6	dbSNP_134	196	53,5109		0,53,2528	no	coding-synonymous	OR2J3	NM_001005216.2		0,61,3787	GG,GC,CC		1.0267,0.3157,0.7926		86/312	29079925	61,7635	1267	2581	3848	SO:0001819	synonymous_variant	442186	exon1			GCTGGTCAATCTC		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.258C>G	6.37:g.29079925C>G		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	315	169	0.536508	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Silent	SNP	ENST00000377169.1	37	CCDS43433.1																																																																																			C|0.992;G|0.008	0.008	strong		0.493	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
SPRR1B	6699	hgsc.bcm.edu	37	1	153004853	153004853	+	Missense_Mutation	SNP	C	C	T	rs3795382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153004853C>T	ENST00000307098.4	+	2	97	c.32C>T	c.(31-33)aCc>aTc	p.T11I	SPRR1B_ENST00000392661.3_Missense_Mutation_p.T11I	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	11	2 X 12 AA approximate repeats.		T -> I (in dbSNP:rs3795382). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3133554, ECO:0000269|PubMed:8388378, ECO:0000269|Ref.4}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	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)			CAGCCTTGCACCCCACCCCCT	0.552													T|||	2474	0.49401	0.4402	0.4251	5008	,	,		16011	0.5913		0.5099	False		,,,				2504	0.499				p.T11I		Atlas-SNP	.											SPRR1B,head_neck,carcinoma,0,1	SPRR1B	18	1	0			c.C32T						PASS	.	T	ILE/THR	2068,2338	570.8+/-382.9	482,1104,617	142.0	138.0	139.0		32	-0.1	0.0	1	dbSNP_107	139	4392,4208	584.4+/-391.7	1128,2136,1036	no	missense	SPRR1B	NM_003125.2	89	1610,3240,1653	TT,TC,CC		48.9302,46.936,49.6694	benign	11/90	153004853	6460,6546	2203	4300	6503	SO:0001583	missense	6699	exon2			CTTGCACCCCACC	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"""cornifin"""	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.32C>T	1.37:g.153004853C>T	ENSP00000306461:p.Thr11Ile	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	201	98	0.487562	NM_003125	B2R5H7|P22529|P22530|Q5T524	Missense_Mutation	SNP	ENST00000307098.4	37	CCDS30863.1	1134	0.5192307692307693	228	0.4634146341463415	167	0.4613259668508287	355	0.6206293706293706	384	0.5065963060686016	c	1.477	-0.558376	0.03967	0.46936	0.510698	ENSG00000169469	ENST00000307098;ENST00000392661	T;T	0.14391	2.62;2.51	3.98	-0.059	0.13795	.	.	.	.	.	T	0.02418	0.0074	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47560	-0.9108	7	0.23891	T	0.37	-0.0032	8.0665	0.30663	0.0:0.5816:0.0:0.4184	rs3795382;rs17846538;rs17859612;rs17884771;rs52805231	11	P22528	SPR1B_HUMAN	I	11	ENSP00000306461:T11I;ENSP00000376429:T11I	ENSP00000306461:T11I	T	+	2	0	SPRR1B	151271477	0.005000	0.15991	0.000000	0.03702	0.408000	0.30992	-0.240000	0.08952	-0.338000	0.08413	-1.551000	0.00897	ACC	C|0.497;T|0.503	0.503	strong		0.552	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125	
NDUFV2	4729	hgsc.bcm.edu	37	18	9122591	9122591	+	Silent	SNP	T	T	C	rs76552443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9122591T>C	ENST00000318388.6	+	5	495	c.381T>C	c.(379-381)gtT>gtC	p.V127V	RP11-21J18.1_ENST00000579126.1_RNA|RP11-143J12.2_ENST00000582375.1_RNA|NDUFV2_ENST00000400033.1_Silent_p.V130V|NDUFV2_ENST00000465096.1_3'UTR|RP11-143J12.2_ENST00000583081.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	127					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.V127V(1)		breast(1)|lung(4)|ovary(1)|stomach(1)	7						GAAAGCCAGTTGGAAAGTATC	0.383																																					p.V127V		Atlas-SNP	.											NDUFV2,NS,carcinoma,0,1	NDUFV2	17	1	1	Substitution - coding silent(1)	lung(1)	c.T381C						scavenged	.						121.0	109.0	113.0					18																	9122591		2203	4300	6503	SO:0001819	synonymous_variant	4729	exon5			GCCAGTTGGAAAG	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7717	protein-coding gene	gene with protein product	"""complex I 24kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"""	600532	"""NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"""			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.381T>C	18.37:g.9122591T>C		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	249	36	0.144578	NM_021074	Q9BV41	Silent	SNP	ENST00000318388.6	37	CCDS11842.1																																																																																			T|0.879;C|0.121	0.121	strong		0.383	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074	
PRKCSH	5589	hgsc.bcm.edu	37	19	11558275	11558275	+	Missense_Mutation	SNP	G	G	A	rs11557488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11558275G>A	ENST00000589838.1	+	10	871	c.871G>A	c.(871-873)Gca>Aca	p.A291T	PRKCSH_ENST00000592741.1_Missense_Mutation_p.A291T|PRKCSH_ENST00000591462.1_Missense_Mutation_p.A291T|PRKCSH_ENST00000412601.1_Missense_Mutation_p.A291T|PRKCSH_ENST00000252455.2_Missense_Mutation_p.A291T|PRKCSH_ENST00000587327.1_Missense_Mutation_p.A291T			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	291			A -> T (in dbSNP:rs11557488). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		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						CGACCTTCCAGCACCTTCTGC	0.667													G|||	457	0.091254	0.0265	0.1182	5008	,	,		11468	0.0248		0.2256	False		,,,				2504	0.09				p.A291T		Atlas-SNP	.											.	PRKCSH	55	.	0			c.G871A						PASS	.	G	THR/ALA,THR/ALA	261,4145	145.7+/-180.5	7,247,1949	59.0	56.0	57.0		871,871	1.4	0.0	19	dbSNP_120	57	1855,6745	325.2+/-316.8	212,1431,2657	yes	missense,missense	PRKCSH	NM_001001329.1,NM_002743.2	58,58	219,1678,4606	AA,AG,GG		21.5698,5.9237,16.2694	benign,benign	291/526,291/529	11558275	2116,10890	2203	4300	6503	SO:0001583	missense	5589	exon11			CTTCCAGCACCTT		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.871G>A	19.37:g.11558275G>A	ENSP00000465461:p.Ala291Thr	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	147	64	0.435374	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Missense_Mutation	SNP	ENST00000589838.1	37	CCDS32911.1	273	0.125	17	0.034552845528455285	47	0.1298342541436464	18	0.03146853146853147	191	0.2519788918205805	G	12.20	1.867674	0.32977	0.059237	0.215698	ENSG00000130175	ENST00000252455;ENST00000412601	T;T	0.72505	-0.65;-0.66	3.67	1.41	0.22369	.	0.882793	0.09714	N	0.765357	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.28713	0.22;0.008;0.003	B;B;B	0.21708	0.036;0.012;0.002	T	0.04811	-1.0925	9	0.12430	T	0.62	-1.3026	7.7873	0.29099	0.0:0.1704:0.6359:0.1937	rs11557488;rs17855440	291;291;291	E7EQZ9;A8K318;P14314	.;.;GLU2B_HUMAN	T	291	ENSP00000252455:A291T;ENSP00000395616:A291T	ENSP00000252455:A291T	A	+	1	0	PRKCSH	11419275	0.004000	0.15560	0.000000	0.03702	0.140000	0.21249	1.332000	0.33805	0.480000	0.27534	0.491000	0.48974	GCA	A|0.141;C|0.000;G|0.859	0.141	strong		0.667	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
OR52R1	119695	hgsc.bcm.edu	37	11	4825349	4825349	+	Missense_Mutation	SNP	A	A	G	rs17327254	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4825349A>G	ENST00000356069.2	-	1	261	c.262T>C	c.(262-264)Ttc>Ctc	p.F88L	MMP26_ENST00000380390.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.F167L|MMP26_ENST00000477339.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	88			F -> L (in dbSNP:rs17327254).			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)		TGAAACCAGAATATGGCCAAC	0.517													A|||	157	0.0313498	0.0053	0.0548	5008	,	,		23740	0.0		0.0964	False		,,,				2504	0.0153				p.F88L		Atlas-SNP	.											.	OR52R1	81	.	0			c.T262C						PASS	.	A	LEU/PHE	107,4295	82.4+/-120.9	1,105,2095	143.0	127.0	133.0		262	-2.7	0.5	11	dbSNP_123	133	845,7751	194.8+/-240.1	47,751,3500	yes	missense	OR52R1	NM_001005177.3	22	48,856,5595	GG,GA,AA		9.8302,2.4307,7.3242	benign	88/316	4825349	952,12046	2201	4298	6499	SO:0001583	missense	119695	exon1			ACCAGAATATGGC	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.262T>C	11.37:g.4825349A>G	ENSP00000348368:p.Phe88Leu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	101	49	0.485149	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	101	0.04624542124542125	2	0.0040650406504065045	25	0.06906077348066299	0	0.0	74	0.09762532981530343	A	12.39	1.922678	0.33908	0.024307	0.098302	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00912	5.55;5.55	5.57	-2.66	0.06077	GPCR, rhodopsin-like superfamily (1);	0.443885	0.19125	N	0.122063	T	0.00039	0.0001	L	0.31845	0.965	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.38714	-0.9648	9	0.46703	T	0.11	.	13.3316	0.60490	0.8457:0.0:0.1543:0.0	rs17327254;rs52793345;rs17327254	88	Q8NGF1	O52R1_HUMAN	L	88;167	ENSP00000348368:F88L;ENSP00000369742:F167L	ENSP00000348368:F88L	F	-	1	0	OR52R1	4781925	0.013000	0.17824	0.458000	0.27068	0.944000	0.59088	0.193000	0.17116	-0.316000	0.08690	0.528000	0.53228	TTC	A|0.937;G|0.063	0.063	strong		0.517	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
RREB1	6239	hgsc.bcm.edu	37	6	7229346	7229346	+	Silent	SNP	T	T	C	rs2714315	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:7229346T>C	ENST00000349384.6	+	10	1328	c.1014T>C	c.(1012-1014)caT>caC	p.H338H	RREB1_ENST00000379938.2_Silent_p.H338H|RREB1_ENST00000334984.6_Silent_p.H338H|RREB1_ENST00000379933.3_Silent_p.H338H	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	338					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				AGCAGACCCATGTGGCGGCAG	0.627													C|||	2044	0.408147	0.792	0.2147	5008	,	,		16187	0.2718		0.3419	False		,,,				2504	0.2352				p.H338H		Atlas-SNP	.											.	RREB1	242	.	0			c.T1014C						PASS	.	C	,,,	3059,1347	448.5+/-348.7	1056,947,200	44.0	40.0	41.0		1014,1014,1014,1014	-0.2	0.2	6	dbSNP_100	41	2631,5969	685.0+/-404.0	408,1815,2077	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	,,,	1464,2762,2277	CC,CT,TT		30.593,30.5719,43.749	,,,	338/1688,338/1743,338/1477,338/1688	7229346	5690,7316	2203	4300	6503	SO:0001819	synonymous_variant	6239	exon10			GACCCATGTGGCG	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.1014T>C	6.37:g.7229346T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			T|0.555;C|0.445	0.445	strong		0.627	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
CHPF	79586	hgsc.bcm.edu	37	2	220405230	220405230	+	Silent	SNP	G	G	A	rs6436154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220405230G>A	ENST00000243776.6	-	4	1451	c.1203C>T	c.(1201-1203)caC>caT	p.H401H	CHPF_ENST00000535926.1_Silent_p.H239H	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	401					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		AGGAGAAAGCGTGCTGCTCCG	0.662													G|||	1558	0.311102	0.2065	0.4841	5008	,	,		17051	0.2748		0.4523	False		,,,				2504	0.2219				p.H401H		Atlas-SNP	.											.	CHPF	56	.	0			c.C1203T						PASS	.	G	,	1157,3247	387.2+/-326.4	135,887,1180	29.0	32.0	31.0		717,1203	-6.0	0.0	2	dbSNP_116	31	3978,4620	529.0+/-381.5	939,2100,1260	no	coding-synonymous,coding-synonymous	CHPF	NM_001195731.1,NM_024536.5	,	1074,2987,2440	AA,AG,GG		46.2666,26.2716,39.4939	,	239/614,401/776	220405230	5135,7867	2202	4299	6501	SO:0001819	synonymous_variant	79586	exon4			GAAAGCGTGCTGC	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24291	protein-coding gene	gene with protein product	"""chondroitin sulfate synthase 2"""	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1203C>T	2.37:g.220405230G>A		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																			G|0.613;A|0.387	0.387	strong		0.662	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549481	32549481	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32549481C>T	ENST00000360004.5	-	3	610	c.505G>A	c.(505-507)Gct>Act	p.A169T		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	169	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						ACCATCCCAGCCTTCTCTTCC	0.562										Multiple Myeloma(14;0.17)																											p.A169T		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G505A						PASS	.						88.0	106.0	100.0					6																	32549481		1511	2709	4220	SO:0001583	missense	3123	exon3			TCCCAGCCTTCTC	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.505G>A	6.37:g.32549481C>T	ENSP00000353099:p.Ala169Thr	Somatic	422	1	0.00236967		WXS	Illumina HiSeq	Phase_I	204	69	0.338235	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	4.123	0.021020	0.08006	.	.	ENSG00000196126	ENST00000360004	T	0.02812	4.15	3.87	2.02	0.26589	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.596257	0.17732	N	0.163842	T	0.04363	0.0120	.	.	.	0.80722	P	0.0	D	0.64830	0.994	D	0.79784	0.993	T	0.37291	-0.9712	8	0.32370	T	0.25	.	8.5729	0.33581	0.0:0.7959:0.0:0.2041	rs2308768;rs9269803;rs17841954;rs17856141	169	P01911	2B1F_HUMAN	T	169	ENSP00000353099:A169T	ENSP00000353099:A169T	A	-	1	0	HLA-DRB1	32657459	0.000000	0.05858	0.060000	0.19600	0.252000	0.25951	0.162000	0.16501	0.226000	0.20979	-0.476000	0.04901	GCT	.	.	none		0.562	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
KRT83	3889	hgsc.bcm.edu	37	12	52710721	52710721	+	Missense_Mutation	SNP	G	G	C	rs2852464	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52710721G>C	ENST00000293670.3	-	5	899	c.837C>G	c.(835-837)atC>atG	p.I279M		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	279	Coil 2.|Rod.		I -> M (in dbSNP:rs2852464). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9084137}.		aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.I279M(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTCGGCAACGATGCAGTCCA	0.592													g|||	1799	0.359225	0.4713	0.2997	5008	,	,		21137	0.1885		0.3877	False		,,,				2504	0.3967				p.I279M	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,-1,2	KRT83	64	2	1	Substitution - Missense(1)	stomach(1)	c.C837G						PASS	.	G	MET/ILE	2017,2389	562.7+/-381.0	485,1047,671	177.0	146.0	157.0		837	-0.3	0.0	12	dbSNP_100	157	3287,5313	492.7+/-373.4	635,2017,1648	yes	missense	KRT83	NM_002282.3	10	1120,3064,2319	CC,CG,GG		38.2209,45.7785,40.7812	benign	279/494	52710721	5304,7702	2203	4300	6503	SO:0001583	missense	3889	exon5			GGCAACGATGCAG	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.837C>G	12.37:g.52710721G>C	ENSP00000293670:p.Ile279Met	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	175	74	0.422857	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	37	CCDS8823.1	744	0.34065934065934067	236	0.4796747967479675	113	0.31215469613259667	108	0.1888111888111888	287	0.3786279683377309	G	12.79	2.043241	0.36085	0.457785	0.382209	ENSG00000170523	ENST00000293670	D	0.90504	-2.68	3.9	-0.295	0.12828	Filament (1);	0.648869	0.12705	U	0.446038	T	0.00012	0.0000	M	0.88704	2.975	0.43457	P	0.0043480000000000185	P	0.41929	0.765	P	0.58577	0.841	T	0.04191	-1.0970	9	0.72032	D	0.01	.	8.9219	0.35617	0.3216:0.0:0.6784:0.0	rs2852464;rs17368026;rs57859988;rs2852464	279	P78385	KRT83_HUMAN	M	279	ENSP00000293670:I279M	ENSP00000293670:I279M	I	-	3	3	KRT83	50996988	0.993000	0.37304	0.003000	0.11579	0.580000	0.36256	0.505000	0.22642	-0.327000	0.08551	0.561000	0.74099	ATC	G|0.638;C|0.362	0.362	strong		0.592	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138764233	138764233	+	Missense_Mutation	SNP	C	C	T	rs2236426	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:138764233C>T	ENST00000242351.5	-	4	1770	c.1454G>A	c.(1453-1455)aGa>aAa	p.R485K	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.R485K|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.R485K	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	485			R -> K (in dbSNP:rs2236426). {ECO:0000269|PubMed:14702039}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						AAGTGCTACTCTTGGGTCAGC	0.453													C|||	1163	0.232228	0.2201	0.3415	5008	,	,		21222	0.378		0.1243	False		,,,				2504	0.1319				p.R485K		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.G1454A						PASS	.	C	LYS/ARG,LYS/ARG	905,3501	348.7+/-310.1	94,717,1392	102.0	102.0	102.0		1454,1454	-3.2	0.0	7	dbSNP_98	102	1129,7471	234.0+/-267.1	70,989,3241	yes	missense,missense	ZC3HAV1	NM_020119.3,NM_024625.3	26,26	164,1706,4633	TT,TC,CC		13.1279,20.5402,15.6389	benign,benign	485/903,485/700	138764233	2034,10972	2203	4300	6503	SO:0001583	missense	56829	exon4			GCTACTCTTGGGT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1454G>A	7.37:g.138764233C>T	ENSP00000242351:p.Arg485Lys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	136	57	0.419118	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	557	0.25503663003663	118	0.23983739837398374	111	0.30662983425414364	232	0.40559440559440557	96	0.1266490765171504	C	6.963	0.547637	0.13312	0.205402	0.131279	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247	T;T;T	0.15952	3.38;3.36;2.38	4.64	-3.24	0.05094	.	1.407580	0.04463	N	0.374667	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.15141	0.012;0.007	B;B	0.20384	0.029;0.013	T	0.45469	-0.9259	9	0.07990	T	0.79	.	7.2643	0.26222	0.0:0.3384:0.4374:0.2242	rs2236426;rs58297788;rs2236426	485;485	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	K	485;485;485;245	ENSP00000242351:R485K;ENSP00000418385:R485K;ENSP00000419855:R485K	ENSP00000242351:R485K	R	-	2	0	ZC3HAV1	138414773	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.407000	0.07178	-0.834000	0.04239	-0.165000	0.13383	AGA	C|0.799;T|0.201	0.201	strong		0.453	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
UNC80	285175	hgsc.bcm.edu	37	2	210658517	210658517	+	Missense_Mutation	SNP	G	G	A	rs146565598		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:210658517G>A	ENST00000439458.1	+	7	952	c.872G>A	c.(871-873)cGa>cAa	p.R291Q	UNC80_ENST00000478701.1_3'UTR|UNC80_ENST00000272845.6_Missense_Mutation_p.R291Q	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	291					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						GGCTGTCACCGAGGAAACTCC	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		16682	0.0		0.001	False		,,,				2504	0.0				p.R291Q		Atlas-SNP	.											UNC80_ENST00000439458,NS,carcinoma,+1,2	UNC80	280	2	0			c.G872A						scavenged	.						114.0	103.0	107.0					2																	210658517		2203	4300	6503	SO:0001583	missense	285175	exon7			GTCACCGAGGAAA	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.872G>A	2.37:g.210658517G>A	ENSP00000391088:p.Arg291Gln	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	126	2	0.015873	NM_182587	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Missense_Mutation	SNP	ENST00000439458.1	37	CCDS46504.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.4	4.524775	0.85600	.	.	ENSG00000144406	ENST00000439458;ENST00000281753;ENST00000272845	T;T	0.32023	1.47;1.47	4.97	4.08	0.47627	.	0.275448	0.34156	N	0.004212	T	0.28732	0.0712	L	0.53249	1.67	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.001;0.002	T	0.05801	-1.0863	10	0.35671	T	0.21	.	11.6978	0.51553	0.0897:0.0:0.9103:0.0	.	291;291	Q8N2C7;Q8N2C7-3	UNC80_HUMAN;.	Q	291	ENSP00000391088:R291Q;ENSP00000272845:R291Q	ENSP00000272845:R291Q	R	+	2	0	UNC80	210366762	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.854000	0.62918	1.186000	0.42985	0.655000	0.94253	CGA	G|1.000;A|0.000	0.000	strong		0.488	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
LMO7	4008	hgsc.bcm.edu	37	13	76395464	76395464	+	Missense_Mutation	SNP	C	C	T	rs41286126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:76395464C>T	ENST00000321797.8	+	12	2381	c.1660C>T	c.(1660-1662)Cct>Tct	p.P554S	LMO7_ENST00000357063.3_Missense_Mutation_p.P839S|LMO7_ENST00000465261.2_Missense_Mutation_p.P554S|LMO7_ENST00000341547.4_Missense_Mutation_p.P505S|LMO7_ENST00000526202.1_Missense_Mutation_p.P404S|LMO7_ENST00000377534.3_Missense_Mutation_p.P839S			Q8WWI1	LMO7_HUMAN	LIM domain 7	839					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)		AGCAACTTATCCTTCAGAAAT	0.433													C|||	357	0.0712859	0.0764	0.0562	5008	,	,		20219	0.0407		0.0755	False		,,,				2504	0.1022				p.P554S		Atlas-SNP	.											.	LMO7	334	.	0			c.C1660T						PASS	.	C	SER/PRO,SER/PRO	271,4135	153.3+/-186.9	11,249,1943	89.0	87.0	87.0		1513,1660	2.0	0.0	13	dbSNP_127	87	597,8003	158.0+/-211.6	25,547,3728	yes	missense,missense	LMO7	NM_005358.5,NM_015842.2	74,74	36,796,5671	TT,TC,CC		6.9419,6.1507,6.6738	benign,benign	505/1350,554/1386	76395464	868,12138	2203	4300	6503	SO:0001583	missense	4008	exon11			ACTTATCCTTCAG	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.1660C>T	13.37:g.76395464C>T	ENSP00000317802:p.Pro554Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	50	0.609756	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		145|145	0.06639194139194139|0.06639194139194139	45|45	0.09146341463414634|0.09146341463414634	22|22	0.06077348066298342|0.06077348066298342	28|28	0.04895104895104895|0.04895104895104895	50|50	0.06596306068601583|0.06596306068601583	C|C	2.415|2.415	-0.334386|-0.334386	0.05278|0.05278	0.061507|0.061507	0.069419|0.069419	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000447038	T;T;T;T;T;T;T|.	0.41758|.	1.58;1.58;1.58;1.0;1.0;0.99;0.99|.	6.05|6.05	2.02|2.02	0.26589|0.26589	.|.	1.124490|.	0.06385|.	N|.	0.716019|.	T|T	0.01454|0.01454	0.0047|0.0047	N|N	0.25890|0.25890	0.77|0.77	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B;B|.	0.17667|.	0.008;0.023;0.005;0.008;0.012|.	B;B;B;B;B|.	0.14023|.	0.003;0.007;0.001;0.003;0.01|.	T|T	0.15206|0.15206	-1.0445|-1.0445	9|4	0.14252|.	T|.	0.57|.	-2.2781|-2.2781	8.1716|8.1716	0.31258|0.31258	0.0:0.4949:0.3371:0.168|0.0:0.4949:0.3371:0.168	rs41286126|rs41286126	404;505;839;554;787|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	S|F	505;839;839;453;554;404;554|462	ENSP00000342112:P505S;ENSP00000349571:P839S;ENSP00000366757:P839S;ENSP00000366719:P453S;ENSP00000317802:P554S;ENSP00000431129:P404S;ENSP00000433352:P554S|.	ENSP00000317802:P554S|.	P|S	+|+	1|2	0|0	LMO7|LMO7	75293465|75293465	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.048000|0.048000	0.14542|0.14542	0.059000|0.059000	0.14322|0.14322	0.403000|0.403000	0.25479|0.25479	-0.182000|-0.182000	0.12963|0.12963	CCT|TCC	C|0.935;T|0.065	0.065	strong		0.433	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
ZDHHC1	29800	hgsc.bcm.edu	37	16	67434917	67434917	+	Missense_Mutation	SNP	C	C	T	rs34229857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67434917C>T	ENST00000348579.2	-	4	712	c.371G>A	c.(370-372)cGa>cAa	p.R124Q		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	124			R -> Q (in dbSNP:rs34229857).		protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		GTGCTGGCTTCGGTTGAAGAT	0.602													C|||	51	0.0101837	0.0	0.0014	5008	,	,		20071	0.0089		0.0249	False		,,,				2504	0.0164				p.R124Q		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G371A						PASS	.	C	GLN/ARG	22,4374	28.1+/-56.4	0,22,2176	131.0	113.0	119.0		371	5.1	1.0	16	dbSNP_126	119	229,8371	93.5+/-155.5	5,219,4076	yes	missense	ZDHHC1	NM_013304.2	43	5,241,6252	TT,TC,CC		2.6628,0.5005,1.9314	probably-damaging	124/486	67434917	251,12745	2198	4300	6498	SO:0001583	missense	29800	exon4			TGGCTTCGGTTGA	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"""Zinc fingers, DHHC-type"""	17916	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 1"""	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.371G>A	16.37:g.67434917C>T	ENSP00000340299:p.Arg124Gln	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	164	89	0.542683	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	37	CCDS10836.1	20	0.009157509157509158	0	0.0	1	0.0027624309392265192	3	0.005244755244755245	16	0.021108179419525065	C	26.2	4.710737	0.89112	0.005005	0.026628	ENSG00000159714	ENST00000348579	T	0.37411	1.2	6.06	5.1	0.69264	.	0.081104	0.53938	D	0.000060	T	0.26011	0.0634	L	0.55834	1.745	0.51482	D	0.999921	D	0.89917	1.0	D	0.75484	0.986	T	0.21484	-1.0244	10	0.23302	T	0.38	.	9.8809	0.41233	0.0:0.7878:0.1405:0.0716	rs34229857	124	Q8WTX9	ZDHC1_HUMAN	Q	124	ENSP00000340299:R124Q	ENSP00000340299:R124Q	R	-	2	0	ZDHHC1	65992418	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.674000	0.61612	1.557000	0.49525	0.655000	0.94253	CGA	C|0.983;T|0.017	0.017	strong		0.602	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304	
RBM19	9904	hgsc.bcm.edu	37	12	114282496	114282496	+	Missense_Mutation	SNP	C	C	T	rs2075387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:114282496C>T	ENST00000545145.2	-	23	2840	c.2762G>A	c.(2761-2763)cGg>cAg	p.R921Q	RBM19_ENST00000261741.5_Missense_Mutation_p.R921Q|RBM19_ENST00000392561.3_Missense_Mutation_p.R921Q	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	921			R -> Q (in dbSNP:rs2075387). {ECO:0000269|PubMed:11230166}.		multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					GGCCGTCTTCCGCCGCAGGGC	0.647													C|||	1100	0.219649	0.1815	0.2032	5008	,	,		17432	0.131		0.3002	False		,,,				2504	0.2914				p.R921Q		Atlas-SNP	.											.	RBM19	117	.	0			c.G2762A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	776,3630	286.9+/-279.0	78,620,1505	35.0	32.0	33.0		2762,2762,2762	5.1	1.0	12	dbSNP_96	33	2321,6279	356.9+/-330.5	326,1669,2305	yes	missense,missense,missense	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	43,43,43	404,2289,3810	TT,TC,CC		26.9884,17.6123,23.8121	possibly-damaging,possibly-damaging,possibly-damaging	921/961,921/961,921/961	114282496	3097,9909	2203	4300	6503	SO:0001583	missense	9904	exon23			GTCTTCCGCCGCA	AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.2762G>A	12.37:g.114282496C>T	ENSP00000442053:p.Arg921Gln	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	486	0.22252747252747251	100	0.2032520325203252	74	0.20441988950276244	78	0.13636363636363635	234	0.3087071240105541	C	21.4	4.143675	0.77888	0.176123	0.269884	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05258	3.47;3.47;3.47	5.11	5.11	0.69529	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.99999854926	D	0.69078	0.997	P	0.59595	0.86	T	0.43475	-0.9389	9	0.56958	D	0.05	-9.4086	18.1548	0.89687	0.0:1.0:0.0:0.0	rs2075387;rs60062169;rs2075387	921	Q9Y4C8	RBM19_HUMAN	Q	921	ENSP00000442053:R921Q;ENSP00000376344:R921Q;ENSP00000261741:R921Q	ENSP00000261741:R921Q	R	-	2	0	RBM19	112766879	1.000000	0.71417	0.999000	0.59377	0.194000	0.23727	4.408000	0.59761	2.368000	0.80403	0.561000	0.74099	CGG	C|0.781;T|0.219	0.219	strong		0.647	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
CDAN1	146059	hgsc.bcm.edu	37	15	43023482	43023482	+	Missense_Mutation	SNP	T	T	C	rs12917189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43023482T>C	ENST00000356231.3	-	12	1810	c.1787A>G	c.(1786-1788)cAg>cGg	p.Q596R		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	596			Q -> R (in dbSNP:rs12917189).		chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		ATTGAGCTCCTGGATCTTCAA	0.517													C|||	2272	0.453674	0.9531	0.1729	5008	,	,		18714	0.2589		0.2068	False		,,,				2504	0.4325				p.Q596R		Atlas-SNP	.											.	CDAN1	70	.	0			c.A1787G						PASS	.	C	ARG/GLN	3608,798	320.7+/-296.8	1488,632,83	94.0	93.0	93.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1787	4.1	1.0	15	dbSNP_121	93	1805,6793	732.8+/-406.9	203,1399,2697	yes	missense	CDAN1	NM_138477.2	43	1691,2031,2780	CC,CT,TT		20.9933,18.1117,41.6257	benign	596/1228	43023482	5413,7591	2203	4299	6502	SO:0001583	missense	146059	exon12			AGCTCCTGGATCT	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.1787A>G	15.37:g.43023482T>C	ENSP00000348564:p.Gln596Arg	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	844	0.38644688644688646	465	0.9451219512195121	65	0.17955801104972377	144	0.2517482517482518	170	0.22427440633245382	C	5.952	0.359651	0.11239	0.818883	0.209933	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86297	-2.1	5.92	4.05	0.47172	.	0.271850	0.36815	N	0.002396	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	9	0.06365	T	0.9	-10.1082	4.6587	0.12632	0.1737:0.5317:0.0:0.2946	rs12917189;rs52826213;rs61456383;rs12917189	596	Q8IWY9	CDAN1_HUMAN	R	596;594	ENSP00000348564:Q596R	ENSP00000267892:Q594R	Q	-	2	0	CDAN1	40810774	0.988000	0.35896	0.992000	0.48379	0.979000	0.70002	2.077000	0.41557	0.421000	0.25980	-0.119000	0.15052	CAG	C|0.419;N|0.000	0.419	strong		0.517	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
OR2T34	127068	hgsc.bcm.edu	37	1	248737167	248737167	+	Missense_Mutation	SNP	G	G	A	rs148590921	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248737167G>A	ENST00000328782.2	-	1	913	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCTTTGTTGCGGAGACTGTAA	0.483																																					p.R298C		Atlas-SNP	.											OR2T34,NS,carcinoma,+2,1	OR2T34	72	1	0			c.C892T						scavenged	.						13.0	13.0	13.0					1																	248737167		1841	3755	5596	SO:0001583	missense	127068	exon1			TGTTGCGGAGACT	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.892C>T	1.37:g.248737167G>A	ENSP00000330904:p.Arg298Cys	Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	249	55	0.220884	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	418	0.19139194139194138	111	0.22560975609756098	65	0.17955801104972377	145	0.2534965034965035	97	0.1279683377308707	.	8.250	0.808823	0.16467	.	.	ENSG00000183310	ENST00000328782	T	0.40476	1.03	2.37	-4.74	0.03249	.	.	.	.	.	T	0.00012	0.0000	M	0.77820	2.39	0.80722	P	0.0	D	0.89917	1.0	D	0.74348	0.983	T	0.06588	-1.0818	8	0.72032	D	0.01	.	5.5241	0.16949	0.1475:0.0:0.2286:0.624	.	298	Q8NGX1	O2T34_HUMAN	C	298	ENSP00000330904:R298C	ENSP00000330904:R298C	R	-	1	0	OR2T34	246803790	0.000000	0.05858	0.003000	0.11579	0.341000	0.28922	-0.784000	0.04633	-1.176000	0.02747	0.123000	0.15791	CGC	G|0.500;A|0.500	0.500	strong		0.483	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
LMO7	4008	hgsc.bcm.edu	37	13	76409436	76409436	+	Silent	SNP	A	A	G	rs2273997	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:76409436A>G	ENST00000321797.8	+	16	3316	c.2595A>G	c.(2593-2595)ctA>ctG	p.L865L	LMO7_ENST00000357063.3_Silent_p.L1150L|LMO7_ENST00000465261.2_Silent_p.L865L|LMO7_ENST00000341547.4_Silent_p.L816L|LMO7_ENST00000526202.1_Silent_p.L742L|LMO7_ENST00000377534.3_Silent_p.L1150L			Q8WWI1	LMO7_HUMAN	LIM domain 7	1150					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L1150L(1)|p.L816L(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CTTCAAATCTATCTGTAACAA	0.378													A|||	1133	0.226238	0.1082	0.2349	5008	,	,		16249	0.0655		0.3598	False		,,,				2504	0.408				p.L865L		Atlas-SNP	.											LMO7_ENST00000465261,NS,carcinoma,0,3	LMO7	334	3	2	Substitution - coding silent(2)	prostate(2)	c.A2595G						PASS	.	A	,	577,3827	254.9+/-260.3	50,477,1675	90.0	91.0	91.0		2448,2595	-9.3	0.0	13	dbSNP_100	91	3120,5480	474.7+/-368.9	561,1998,1741	no	coding-synonymous,coding-synonymous	LMO7	NM_005358.5,NM_015842.2	,	611,2475,3416	GG,GA,AA		36.2791,13.1017,28.4297	,	816/1350,865/1386	76409436	3697,9307	2202	4300	6502	SO:0001819	synonymous_variant	4008	exon15			AAATCTATCTGTA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.2595A>G	13.37:g.76409436A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	ENST00000321797.8	37		454|454	0.2078754578754579|0.2078754578754579	62|62	0.12601626016260162|0.12601626016260162	91|91	0.2513812154696133|0.2513812154696133	41|41	0.07167832167832168|0.07167832167832168	260|260	0.34300791556728233|0.34300791556728233	A|A	0.352|0.352	-0.944115|-0.944115	0.02322|0.02322	0.131017|0.131017	0.362791|0.362791	ENSG00000136153|ENSG00000136153	ENST00000447038;ENST00000525914|ENST00000524651;ENST00000525107	.|.	.|.	.|.	5.78|5.78	-9.28|-9.28	0.00656|0.00656	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.19575|0.19575	P|P	0.9999632735|0.9999632735	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.35375|0.35375	-0.9791|-0.9791	3|3	.|.	.|.	.|.	-5.6978|-5.6978	4.2042|4.2042	0.10481|0.10481	0.2426:0.1679:0.4326:0.1569|0.2426:0.1679:0.4326:0.1569	rs2273997;rs17713708|rs2273997;rs17713708	.|.	.|.	.|.	V|C	774;53|197;104	.|.	.|.	I|Y	+|+	1|2	0|0	LMO7|LMO7	75307437|75307437	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.118000|0.118000	0.20060|0.20060	-1.837000|-1.837000	0.01689|0.01689	-1.404000|-1.404000	0.02050|0.02050	-1.039000|-1.039000	0.02377|0.02377	ATC|TAT	G|0.263;N|0.000	0.263	strong		0.378	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
MARVELD2	153562	hgsc.bcm.edu	37	5	68715310	68715310	+	Missense_Mutation	SNP	C	C	T	rs1185246	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:68715310C>T	ENST00000325631.5	+	2	172	c.98C>T	c.(97-99)aCt>aTt	p.T33I	MARVELD2_ENST00000413223.2_Missense_Mutation_p.T33I	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	33			T -> I (in dbSNP:rs1185246). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15372022, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16365161, ECO:0000269|PubMed:17186462}.		cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		ACCCACCCAACTCTTCATGAC	0.542													C|||	2419	0.483027	0.4153	0.5389	5008	,	,		16565	0.4881		0.494	False		,,,				2504	0.5184				p.T33I		Atlas-SNP	.											.	MARVELD2	49	.	0			c.C98T						PASS	.	C	ILE/THR	1870,2536	540.2+/-375.5	372,1126,705	108.0	96.0	100.0		98	0.2	0.0	5	dbSNP_87	100	4210,4390	570.2+/-389.3	1047,2116,1137	yes	missense	MARVELD2	NM_001038603.2	89	1419,3242,1842	TT,TC,CC		48.9535,42.4421,46.7477	possibly-damaging	33/559	68715310	6080,6926	2203	4300	6503	SO:0001583	missense	153562	exon2			ACCCAACTCTTCA	AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"""tricellulin"""	610572	"""MARVEL (membrane-associating) domain containing 2"", ""deafness, autosomal recessive 49"""	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.98C>T	5.37:g.68715310C>T	ENSP00000323264:p.Thr33Ile	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	155	155	1	NM_001244734	A1BQX0|A1BQX1|A8KA97|Q96NM9	Missense_Mutation	SNP	ENST00000325631.5	37	CCDS34175.1	1042	0.47710622710622713	207	0.42073170731707316	179	0.494475138121547	288	0.5034965034965035	368	0.48548812664907653	C	6.043	0.376219	0.11466	0.424421	0.489535	ENSG00000152939	ENST00000325631;ENST00000282886;ENST00000454295;ENST00000515844;ENST00000512803;ENST00000436532;ENST00000413223	T;T;T;T;T;T	0.45668	1.49;0.9;0.89;1.49;1.48;1.48	4.67	0.193	0.15139	.	1.536810	0.03786	N	0.262169	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B;P;B	0.42409	0.078;0.779;0.047	B;B;B	0.38616	0.054;0.277;0.024	T	0.42327	-0.9458	9	0.45353	T	0.12	-15.847	9.9384	0.41565	0.1222:0.4125:0.4653:0.0	rs1185246;rs52834471;rs56957476;rs1185246	33;33;33	Q8N4S9-3;Q8N4S9-2;Q8N4S9	.;.;MALD2_HUMAN	I	33	ENSP00000323264:T33I;ENSP00000396244:T33I;ENSP00000421902:T33I;ENSP00000423490:T33I;ENSP00000414776:T33I;ENSP00000398922:T33I	ENSP00000282886:T33I	T	+	2	0	MARVELD2	68751066	0.002000	0.14202	0.008000	0.14137	0.006000	0.05464	-0.490000	0.06482	0.017000	0.15025	0.563000	0.77884	ACT	C|0.528;A|0.003	.	strong		0.542	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724	
HMCN1	83872	hgsc.bcm.edu	37	1	186050417	186050417	+	Missense_Mutation	SNP	A	A	G	rs10798035	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186050417A>G	ENST00000271588.4	+	56	8907	c.8678A>G	c.(8677-8679)gAg>gGg	p.E2893G	HMCN1_ENST00000367492.2_Missense_Mutation_p.E2893G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2893	Ig-like C2-type 27.		E -> G (in dbSNP:rs10798035). {ECO:0000269|PubMed:14570714}.		response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCACTGATAGAGTGTTTATCC	0.463													A|||	2918	0.582668	0.6952	0.6311	5008	,	,		14601	0.5694		0.499	False		,,,				2504	0.4959				p.E2893G		Atlas-SNP	.											HMCN1,NS,carcinoma,0,2	HMCN1	797	2	0			c.A8678G						PASS	.	A	GLY/GLU	2939,1467	678.7+/-403.6	1003,933,267	159.0	152.0	155.0		8678	5.9	1.0	1	dbSNP_120	155	4279,4321	576.2+/-390.4	1079,2121,1100	yes	missense	HMCN1	NM_031935.2	98	2082,3054,1367	GG,GA,AA		49.7558,33.2955,44.5025	possibly-damaging	2893/5636	186050417	7218,5788	2203	4300	6503	SO:0001583	missense	83872	exon56			TGATAGAGTGTTT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8678A>G	1.37:g.186050417A>G	ENSP00000271588:p.Glu2893Gly	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	118	73	0.618644	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1286	0.5888278388278388	327	0.6646341463414634	228	0.6298342541436464	344	0.6013986013986014	387	0.5105540897097626	A	27.2	4.808057	0.90707	0.667045	0.497558	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.30182	1.54;1.54	5.86	5.86	0.93980	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188863	0.56097	D	0.000030	T	0.00012	0.0000	M	0.73598	2.24	0.09310	P	0.99999577304	D	0.76494	0.999	D	0.83275	0.996	T	0.46638	-0.9177	9	0.48119	T	0.1	.	14.8163	0.70036	1.0:0.0:0.0:0.0	rs10798035;rs52812505;rs56779083;rs10798035	2893	Q96RW7	HMCN1_HUMAN	G	2893	ENSP00000271588:E2893G;ENSP00000356462:E2893G	ENSP00000271588:E2893G	E	+	2	0	HMCN1	184317040	1.000000	0.71417	0.995000	0.50966	0.856000	0.48823	8.904000	0.92590	2.241000	0.73720	0.533000	0.62120	GAG	A|0.425;G|0.575	0.575	strong		0.463	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
RRP1	8568	hgsc.bcm.edu	37	21	45209559	45209559	+	Silent	SNP	C	C	T	rs78489660	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45209559C>T	ENST00000497547.1	+	1	166	c.49C>T	c.(49-51)Ctg>Ttg	p.L17L		NM_003683.5	NP_003674.1	P05386	RLA1_HUMAN	ribosomal RNA processing 1	0					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(1)|lung(4)|stomach(2)	8				COAD - Colon adenocarcinoma(84;0.00753)|Colorectal(79;0.0157)|STAD - Stomach adenocarcinoma(101;0.171)		GGCTCAGCGCCTGGCGGGGAA	0.697													C|||	331	0.0660942	0.0159	0.0259	5008	,	,		12101	0.0863		0.0457	False		,,,				2504	0.1626				p.L17L		Atlas-SNP	.											.	RRP1	23	.	0			c.C49T						PASS	.	C		90,3924		2,86,1919	10.0	16.0	14.0		49	4.4	0.9	21	dbSNP_131	14	467,7841		14,439,3701	yes	coding-synonymous	RRP1	NM_003683.5		16,525,5620	TT,TC,CC		5.6211,2.2422,4.5204		17/462	45209559	557,11765	2007	4154	6161	SO:0001819	synonymous_variant	8568	exon1			CAGCGCCTGGCGG	U79775	CCDS42951.1	21q22.3	2013-07-02	2013-07-02		ENSG00000160214	ENSG00000160214			18785	protein-coding gene	gene with protein product	"""DNA segment on chromosome 21 (unique) 2056 expressed sequence"", ""Nnp1 homolog, nucleolar protein (Drosophila)"""	610653	"""ribosomal RNA processing 1 homolog (S. cerevisiae)"""			10830953, 10341208	Standard	NM_003683		Approved	NNP-1, Nop52, NOP52, RRP1A, D21S2056E	uc002zds.2	P56182	OTTHUMG00000086884	ENST00000497547.1:c.49C>T	21.37:g.45209559C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	114	65	0.570175	NM_003683	A6NIB2	Silent	SNP	ENST00000497547.1	37	CCDS42951.1																																																																																			C|0.949;T|0.051	0.051	strong		0.697	RRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195680.1	NM_003683	
POFUT2	23275	hgsc.bcm.edu	37	21	46705621	46705621	+	Silent	SNP	G	G	A	rs2297285	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46705621G>A	ENST00000349485.5	-	2	380	c.354C>T	c.(352-354)ccC>ccT	p.P118P	POFUT2_ENST00000471540.1_5'Flank|POFUT2_ENST00000331343.7_Silent_p.P118P|BX322557.10_ENST00000454115.2_RNA	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	118					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		ACTCGATGACGGGGATGTTTT	0.547													G|||	818	0.163339	0.0159	0.1196	5008	,	,		21057	0.1776		0.2485	False		,,,				2504	0.2914				p.P118P		Atlas-SNP	.											POFUT2,NS,carcinoma,-1,1	POFUT2	77	1	0			c.C354T						scavenged	.	G	,	227,4179	135.7+/-171.8	3,221,1979	81.0	88.0	85.0		354,354	-9.3	0.3	21	dbSNP_100	85	2116,6484	363.6+/-333.2	267,1582,2451	no	coding-synonymous,coding-synonymous	POFUT2	NM_015227.4,NM_133635.4	,	270,1803,4430	AA,AG,GG		24.6047,5.1521,18.0148	,	118/425,118/430	46705621	2343,10663	2203	4300	6503	SO:0001819	synonymous_variant	23275	exon2			GATGACGGGGATG	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.354C>T	21.37:g.46705621G>A		Somatic	110	2	0.0181818		WXS	Illumina HiSeq	Phase_I	76	27	0.355263	NM_015227	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			G|0.821;A|0.179	0.179	strong		0.547	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	
CMYA5	202333	hgsc.bcm.edu	37	5	79048562	79048562	+	Silent	SNP	C	C	T	rs1366272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:79048562C>T	ENST00000446378.2	+	6	11086	c.11055C>T	c.(11053-11055)ttC>ttT	p.F3685F		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	3685					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)		p.F3685F(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		TTTCCCTTTTCGAACATTATG	0.378													T|||	1158	0.23123	0.2421	0.1945	5008	,	,		16948	0.4157		0.1044	False		,,,				2504	0.183				p.F3685F		Atlas-SNP	.											CMYA5,NS,carcinoma,0,1	CMYA5	643	1	1	Substitution - coding silent(1)	stomach(1)	c.C11055T						PASS	.	T		700,2976		74,552,1212	90.0	86.0	87.0		11055	3.8	1.0	5	dbSNP_88	87	805,7351		41,723,3314	no	coding-synonymous	CMYA5	NM_153610.3		115,1275,4526	TT,TC,CC		9.87,19.0424,12.7197		3685/4070	79048562	1505,10327	1838	4078	5916	SO:0001819	synonymous_variant	202333	exon6			CCTTTTCGAACAT	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.11055C>T	5.37:g.79048562C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			C|0.753;T|0.247	0.247	strong		0.378	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
C12orf54	121273	hgsc.bcm.edu	37	12	48888689	48888689	+	Silent	SNP	C	C	G	rs9268	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48888689C>G	ENST00000548364.1	+	7	408	c.351C>G	c.(349-351)ctC>ctG	p.L117L	RP11-722P11.4_ENST00000551847.1_RNA|C12orf54_ENST00000314014.2_Silent_p.L117L			Q6X4T0	CL054_HUMAN	chromosome 12 open reading frame 54	117										endometrium(1)|large_intestine(4)	5						AGACACAGCTCTTCAGTCAAT	0.512													C|||	1587	0.316893	0.1248	0.3689	5008	,	,		22147	0.1766		0.6421	False		,,,				2504	0.3497				p.L117L		Atlas-SNP	.											.	C12orf54	11	.	0			c.C351G						PASS	.			963,3443	363.1+/-316.4	124,715,1364	178.0	156.0	164.0		351	3.5	0.0	12	dbSNP_52	164	5654,2946	669.1+/-402.6	1846,1962,492	no	coding-synonymous	C12orf54	NM_152319.3		1970,2677,1856	GG,GC,CC		34.2558,21.8566,49.1235		117/128	48888689	6617,6389	2203	4300	6503	SO:0001819	synonymous_variant	121273	exon8			ACAGCTCTTCAGT	BC031670	CCDS8764.1	12q13.11	2011-01-31			ENSG00000177627	ENSG00000177627			28553	protein-coding gene	gene with protein product						12477932	Standard	NM_152319		Approved	MGC35033	uc001rrr.3	Q6X4T0	OTTHUMG00000170019	ENST00000548364.1:c.351C>G	12.37:g.48888689C>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_152319	Q6X4S9|Q8N5S2	Silent	SNP	ENST00000548364.1	37	CCDS8764.1																																																																																			C|0.533;G|0.467	0.467	strong		0.512	C12orf54-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406875.1	NM_152319	
XIRP2	129446	hgsc.bcm.edu	37	2	168115710	168115710	+	Missense_Mutation	SNP	T	T	G	rs3749006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168115710T>G	ENST00000409728.1	+	11	2842	c.2753T>G	c.(2752-2754)gTt>gGt	p.V918G	XIRP2_ENST00000409043.1_Missense_Mutation_p.V885G|XIRP2_ENST00000409605.1_Missense_Mutation_p.V663G|XIRP2_ENST00000420519.1_Missense_Mutation_p.V918G|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.V885G	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)		p.V918G(1)		NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CCTTGGCATGTTGAAACAACA	0.378													G|||	993	0.198283	0.3154	0.1297	5008	,	,		19526	0.1974		0.1143	False		,,,				2504	0.1759				p.V918G		Atlas-SNP	.											XIRP2_ENST00000409728,NS,carcinoma,0,1	XIRP2	914	1	1	Substitution - Missense(1)	stomach(1)	c.T2753G						PASS	.	G	GLY/VAL,GLY/VAL,,GLY/VAL,	1061,2691		155,751,970	94.0	86.0	88.0		2654,2753,,1988,	0.6	0.0	2	dbSNP_107	88	800,7418		42,716,3351	yes	missense,missense,utr-3,missense,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	109,109,,109,	197,1467,4321	GG,GT,TT		9.7347,28.2783,15.5472	,,,,	885/939,918/972,,663/717,	168115710	1861,10109	1876	4109	5985	SO:0001583	missense	129446	exon11			GGCATGTTGAAAC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2753T>G	2.37:g.168115710T>G	ENSP00000386619:p.Val918Gly	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	424	0.19413919413919414	175	0.3556910569105691	44	0.12154696132596685	115	0.20104895104895104	90	0.11873350923482849	G	1.293	-0.607143	0.03717	0.282783	0.097347	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.74526	-0.81;-0.85;-0.81;-0.85;-0.78	5.78	0.61	0.17580	.	.	.	.	.	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	0.13791	-1.0496	7	0.02654	T	1	.	6.9138	0.24349	0.4555:0.0:0.4348:0.1097	rs3749006;rs52810449;rs58687090;rs3749006	885;918	A4UGR9-4;A4UGR9-6	.;.	G	885;918;885;918;663	ENSP00000386454:V885G;ENSP00000386619:V918G;ENSP00000386724:V885G;ENSP00000415541:V918G;ENSP00000386981:V663G	ENSP00000386454:V885G	V	+	2	0	XIRP2	167823956	0.001000	0.12720	0.001000	0.08648	0.253000	0.25986	-0.469000	0.06648	-0.148000	0.11234	-0.225000	0.12378	GTT	T|0.808;G|0.192	0.192	strong		0.378	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
RAI1	10743	hgsc.bcm.edu	37	17	17700792	17700792	+	Silent	SNP	C	C	T	rs35686634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:17700792C>T	ENST00000353383.1	+	3	4999	c.4530C>T	c.(4528-4530)ccC>ccT	p.P1510P	RAI1_ENST00000261641.6_Silent_p.P1510P	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1510					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CCTCCCAGCCCCCGGAGGGCA	0.657													C|||	366	0.0730831	0.1906	0.0331	5008	,	,		13919	0.0069		0.0567	False		,,,				2504	0.0276				p.P1510P		Atlas-SNP	.											.	RAI1	121	.	0			c.C4530T						PASS	.	C		764,3640	272.5+/-270.8	67,630,1505	30.0	38.0	35.0		4530	0.6	0.0	17	dbSNP_126	35	510,8090	137.1+/-194.1	18,474,3808	no	coding-synonymous	RAI1	NM_030665.3		85,1104,5313	TT,TC,CC		5.9302,17.3479,9.797		1510/1907	17700792	1274,11730	2202	4300	6502	SO:0001819	synonymous_variant	10743	exon3			CCAGCCCCCGGAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.4530C>T	17.37:g.17700792C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			C|0.916;T|0.084	0.084	strong		0.657	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
AKR1E2	83592	hgsc.bcm.edu	37	10	4889403	4889403	+	Nonsense_Mutation	SNP	C	C	T	rs12240276	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:4889403C>T	ENST00000298375.7	+	9	972	c.901C>T	c.(901-903)Cga>Tga	p.R301*	AKR1E2_ENST00000334019.4_Nonsense_Mutation_p.R244*|AKR1E2_ENST00000345253.5_Nonsense_Mutation_p.R203*|AKR1E2_ENST00000532248.1_Nonsense_Mutation_p.R244*	NM_001040177.2	NP_001035267.1	Q96JD6	AKCL2_HUMAN	aldo-keto reductase family 1, member E2	301						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						CAGGAATCTCCGACTGGCCAT	0.363													C|||	393	0.0784744	0.1006	0.0879	5008	,	,		18282	0.0		0.1342	False		,,,				2504	0.0654				p.R301X	NSCLC(43;343 1097 20371 28813 45509)	Atlas-SNP	.											.	AKR1E2	30	.	0			c.C901T						PASS	.	C	stop/ARG	436,3970	209.2+/-230.0	16,404,1783	139.0	131.0	134.0		901	4.5	0.1	10	dbSNP_120	134	990,7610	214.8+/-254.3	62,866,3372	yes	stop-gained	AKR1E2	NM_001040177.1		78,1270,5155	TT,TC,CC		11.5116,9.8956,10.9642		301/321	4889403	1426,11580	2203	4300	6503	SO:0001587	stop_gained	83592	exon9			AATCTCCGACTGG	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.901C>T	10.37:g.4889403C>T	ENSP00000298375:p.Arg301*	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	181	97	0.535912	NM_001040177	Q86Z16|Q86Z17|Q86Z18|Q9BU71	Nonsense_Mutation	SNP	ENST00000298375.7	37	CCDS31134.1	169	0.07738095238095238	46	0.09349593495934959	31	0.0856353591160221	0	0.0	92	0.12137203166226913	C	10.97	1.502954	0.26949	0.098956	0.115116	ENSG00000165568	ENST00000298375;ENST00000532248;ENST00000334019;ENST00000345253	.	.	.	4.47	4.47	0.54385	.	0.061588	0.64402	D	0.000005	.	.	.	.	.	.	0.20975	P	0.99981642	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0518	0.71877	0.0:1.0:0.0:0.0	rs12240276;rs52824371;rs56813881;rs12240276	.	.	.	X	301;244;244;203	.	ENSP00000298375:R301X	R	+	1	2	AKR1E2	4879403	0.269000	0.24143	0.089000	0.20774	0.041000	0.13682	3.131000	0.50515	2.490000	0.84030	0.561000	0.74099	CGA	C|0.901;T|0.099	0.099	strong		0.363	AKR1E2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046520.4	NM_031436	
TTLL4	9654	hgsc.bcm.edu	37	2	219602819	219602819	+	Silent	SNP	G	G	A	rs3731876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219602819G>A	ENST00000392102.1	+	3	760	c.420G>A	c.(418-420)ccG>ccA	p.P140P	TTLL4_ENST00000442769.1_Silent_p.P140P|TTLL4_ENST00000457313.1_5'UTR|TTLL4_ENST00000258398.4_Silent_p.P140P	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	140					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)		GTTCGAGCCCGTCAGAAAAAA	0.542													A|||	2371	0.473442	0.8585	0.4366	5008	,	,		20218	0.1409		0.4662	False		,,,				2504	0.3292				p.P140P	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.G420A						PASS	.	A		3577,829	329.9+/-301.2	1455,667,81	95.0	98.0	97.0		420	-2.1	0.0	2	dbSNP_107	97	4094,4506	592.0+/-392.9	994,2106,1200	no	coding-synonymous	TTLL4	NM_014640.4		2449,2773,1281	AA,AG,GG		47.6047,18.8153,41.0195		140/1200	219602819	7671,5335	2203	4300	6503	SO:0001819	synonymous_variant	9654	exon3			GAGCCCGTCAGAA		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.420G>A	2.37:g.219602819G>A		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	49	36	0.734694	NM_014640	A8K6V5|Q8WW29	Silent	SNP	ENST00000392102.1	37	CCDS2422.1																																																																																			G|0.459;A|0.541	0.541	strong		0.542	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
OR12D3	81797	hgsc.bcm.edu	37	6	29342825	29342825	+	Silent	SNP	G	G	A	rs3749970	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29342825G>A	ENST00000396806.3	-	1	243	c.240C>T	c.(238-240)ctC>ctT	p.L80L	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						CGAGGTTTACGAGCAGCTTGG	0.448													G|||	1437	0.286941	0.0651	0.3646	5008	,	,		19264	0.255		0.494	False		,,,				2504	0.3517				p.L80L		Atlas-SNP	.											OR12D3,NS,carcinoma,0,1	OR12D3	55	1	0			c.C240T						PASS	.	G		394,2624		22,350,1137	58.0	60.0	59.0		240	-8.4	0.0	6	dbSNP_107	59	2592,2826		632,1328,749	no	coding-synonymous	OR12D3	NM_030959.2		654,1678,1886	AA,AG,GG		47.8405,13.055,35.3959		80/317	29342825	2986,5450	1509	2709	4218	SO:0001819	synonymous_variant	81797	exon1			GTTTACGAGCAGC		CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.240C>T	6.37:g.29342825G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Silent	SNP	ENST00000396806.3	37	CCDS4658.1																																																																																			G|0.667;A|0.333	0.333	strong		0.448	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
MSH6	2956	hgsc.bcm.edu	37	2	48025764	48025764	+	Silent	SNP	C	C	T	rs1800937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:48025764C>T	ENST00000234420.5	+	4	794	c.642C>T	c.(640-642)taC>taT	p.Y214Y	FBXO11_ENST00000405808.1_Intron|MSH6_ENST00000538136.1_5'UTR|MSH6_ENST00000540021.1_Silent_p.Y84Y	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	214					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GCACAACTTACGTAACAGATA	0.358			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	143	0.0285543	0.0038	0.0432	5008	,	,		21755	0.0		0.1034	False		,,,				2504	0.0041				p.Y214Y		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.C642T	GRCh37	CM085566|CM990714	MSH6	M	rs1800937	PASS	.	C		98,4308	77.8+/-116.1	1,96,2106	72.0	71.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	642	-6.3	0.0	2	dbSNP_89	71	801,7799	184.3+/-232.3	33,735,3532	no	coding-synonymous	MSH6	NM_000179.2		34,831,5638	TT,TC,CC		9.314,2.2242,6.9122		214/1361	48025764	899,12107	2203	4300	6503	SO:0001819	synonymous_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AACTTACGTAACA	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.642C>T	2.37:g.48025764C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	22	11	0.5	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			C|0.942;T|0.058	0.058	strong		0.358	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
SERPINF2	5345	hgsc.bcm.edu	37	17	1649022	1649022	+	Silent	SNP	C	C	T	rs35259159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1649022C>T	ENST00000324015.3	+	5	263	c.186C>T	c.(184-186)gcC>gcT	p.A62A	SERPINF2_ENST00000382061.4_Silent_p.A62A|SERPINF2_ENST00000450523.2_Intron	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	62					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	GCCAGACTGCCCTGAAGAGTC	0.642													C|||	92	0.0183706	0.0015	0.0389	5008	,	,		14485	0.0		0.0596	False		,,,				2504	0.0031				p.A62A		Atlas-SNP	.											.	SERPINF2	33	.	0			c.C186T						PASS	.	C	,,	70,4336	63.5+/-100.7	0,70,2133	41.0	43.0	43.0		186,186,	4.1	0.0	17	dbSNP_126	43	510,8090	143.4+/-199.5	20,470,3810	no	coding-synonymous,coding-synonymous,intron	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	,,	20,540,5943	TT,TC,CC		5.9302,1.5887,4.4595	,,	62/492,62/492,	1649022	580,12426	2203	4300	6503	SO:0001819	synonymous_variant	5345	exon5			GACTGCCCTGAAG	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.186C>T	17.37:g.1649022C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Silent	SNP	ENST00000324015.3	37	CCDS11011.1																																																																																			C|0.960;T|0.040	0.040	strong		0.642	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
A2ML1	144568	hgsc.bcm.edu	37	12	9013755	9013755	+	Missense_Mutation	SNP	C	C	T	rs1860967	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9013755C>T	ENST00000299698.7	+	28	3544	c.3364C>T	c.(3364-3366)Cgg>Tgg	p.R1122W	A2ML1_ENST00000539547.1_Missense_Mutation_p.R631W	NM_001282424.1|NM_144670.4	NP_001269353.1|NP_653271			alpha-2-macroglobulin-like 1											NS(2)|breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(2)|lung(36)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	80						TCAGGGTCTACGGTGTCTCAA	0.438													C|||	2165	0.432308	0.1067	0.5231	5008	,	,		-128	0.7857		0.3867	False		,,,				2504	0.4908				p.R1122W		Atlas-SNP	.											A2ML1,NS,lymphoid_neoplasm,-2,1	A2ML1	199	1	0			c.C3364T						PASS	.	C	TRP/ARG	598,3340		53,492,1424	136.0	137.0	137.0		3364	0.4	0.3	12	dbSNP_92	137	3096,5212		579,1938,1637	yes	missense	A2ML1	NM_144670.3	101	632,2430,3061	TT,TC,CC		37.2653,15.1854,30.165	possibly-damaging	1122/1455	9013755	3694,8552	1969	4154	6123	SO:0001583	missense	144568	exon28			GGTCTACGGTGTC	AK057908	CCDS8596.2, CCDS73439.1	12p13	2010-12-14	2005-09-01	2005-09-01	ENSG00000166535	ENSG00000166535			23336	protein-coding gene	gene with protein product		610627	"""C3 and PZP-like, alpha-2-macroglobulin domain containing 9"""	CPAMD9		16298998	Standard	NM_144670		Approved	FLJ25179	uc001quz.5	A8K2U0	OTTHUMG00000128499	ENST00000299698.7:c.3364C>T	12.37:g.9013755C>T	ENSP00000299698:p.Arg1122Trp	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	171	87	0.508772	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	1003	0.4592490842490842	62	0.12601626016260162	178	0.49171270718232046	465	0.8129370629370629	298	0.39313984168865435	C	7.164	0.586213	0.13749	0.151854	0.372653	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.37915	1.17;1.17;1.17	3.56	0.387	0.16259	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	1.110230	0.06791	N	0.787057	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	P	0.49090	0.919	P	0.49140	0.601	T	0.36187	-0.9758	9	0.37606	T	0.19	.	2.615	0.04901	0.4748:0.2729:0.1551:0.0972	rs1860967;rs17729723;rs56907838;rs1860967	1122	A8K2U0	A2ML1_HUMAN	W	1122;1122;672;631	ENSP00000299698:R1122W;ENSP00000443174:R672W;ENSP00000438292:R631W	ENSP00000299698:R1122W	R	+	1	2	A2ML1	8905022	0.000000	0.05858	0.310000	0.25168	0.419000	0.31324	-0.361000	0.07612	0.072000	0.16694	0.563000	0.77884	CGG	C|0.568;T|0.432	0.432	strong		0.438	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
LETM2	137994	hgsc.bcm.edu	37	8	38250202	38250202	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:38250202A>G	ENST00000379957.4	+	3	317	c.190A>G	c.(190-192)Aat>Gat	p.N64D	LETM2_ENST00000524874.1_Missense_Mutation_p.N64D|LETM2_ENST00000297720.5_Missense_Mutation_p.N17D|LETM2_ENST00000519476.2_Missense_Mutation_p.N64D|LETM2_ENST00000523983.2_Missense_Mutation_p.N17D	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	64						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			TCAGCCAGGCAATACAGTACT	0.453																																					p.N17D		Atlas-SNP	.											.	LETM2	57	.	0			c.A49G						PASS	.						86.0	89.0	88.0					8																	38250202		2203	4300	6503	SO:0001583	missense	137994	exon3			CCAGGCAATACAG	AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"""EF-hand domain containing"""	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.190A>G	8.37:g.38250202A>G	ENSP00000369291:p.Asn64Asp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001199659	A6NMG3|Q8NCR2|Q96LL1	Missense_Mutation	SNP	ENST00000379957.4	37		.	.	.	.	.	.	.	.	.	.	A	6.285	0.420678	0.11928	.	.	ENSG00000165046	ENST00000527334;ENST00000519476;ENST00000297720;ENST00000524874;ENST00000379957;ENST00000523983;ENST00000526356	.	.	.	5.75	1.81	0.25067	.	1.355500	0.04352	N	0.355909	T	0.30386	0.0763	L	0.56769	1.78	0.09310	N	0.999997	B;B;P	0.34462	0.201;0.094;0.454	B;B;B	0.30401	0.016;0.016;0.115	T	0.14504	-1.0470	9	0.18276	T	0.48	.	2.9332	0.05805	0.3552:0.4136:0.098:0.1332	.	64;64;64	Q2VYF4;E9PMA4;A8K1M9	LETM2_HUMAN;.;.	D	64;64;17;64;64;17;64	.	ENSP00000297720:N17D	N	+	1	0	LETM2	38369359	0.000000	0.05858	0.020000	0.16555	0.053000	0.15095	-0.173000	0.09854	0.059000	0.16252	0.533000	0.62120	AAT	.	.	none		0.453	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652	
NDUFS2	4720	hgsc.bcm.edu	37	1	161182208	161182208	+	Missense_Mutation	SNP	C	C	G	rs11576415	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161182208C>G	ENST00000367993.3	+	11	1502	c.1054C>G	c.(1054-1056)Cct>Gct	p.P352A	NDUFS2_ENST00000392179.4_Missense_Mutation_p.P352A|FCER1G_ENST00000289902.1_5'Flank|NDUFS2_ENST00000465923.1_3'UTR|FCER1G_ENST00000367992.3_5'Flank	NM_004550.4	NP_004541.1	O75306	NDUS2_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzyme Q reductase)	352			P -> A (in dbSNP:rs11576415).		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)	AAACAAGATGCCTCCTGGGGA	0.527													C|||	247	0.0493211	0.0068	0.0317	5008	,	,		17350	0.0099		0.1083	False		,,,				2504	0.0992				p.P352A		Atlas-SNP	.											NDUFS2,lymph_node,lymphoid_neoplasm,0,1	NDUFS2	33	1	0			c.C1054G						PASS	.	C	ALA/PRO,ALA/PRO	80,4326	70.9+/-108.8	2,76,2125	106.0	87.0	93.0		1054,1054	4.9	1.0	1	dbSNP_120	93	813,7787	190.0+/-236.6	40,733,3527	yes	missense,missense	NDUFS2	NM_001166159.1,NM_004550.4	27,27	42,809,5652	GG,GC,CC		9.4535,1.8157,6.8661	probably-damaging,probably-damaging	352/458,352/464	161182208	893,12113	2203	4300	6503	SO:0001583	missense	4720	exon10			AAGATGCCTCCTG	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.1054C>G	1.37:g.161182208C>G	ENSP00000356972:p.Pro352Ala	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	52	23	0.442308	NM_001166159	D3DVG7|J3KPM7|Q5VTW0|Q969P3|Q9UEV3	Missense_Mutation	SNP	ENST00000367993.3	37	CCDS1224.1	112	0.05128205128205128	6	0.012195121951219513	14	0.03867403314917127	6	0.01048951048951049	86	0.11345646437994723	C	25.4	4.634647	0.87660	0.018157	0.094535	ENSG00000158864	ENST00000367993;ENST00000392179	D;D	0.90261	-2.64;-2.64	4.86	4.86	0.63082	NADH-quinone oxidoreductase, subunit D (1);	0.000000	0.85682	D	0.000000	D	0.95843	0.8647	M	0.89785	3.06	0.54753	P	1.7000000000044757E-5	D;P;P	0.89917	1.0;0.83;0.83	D;P;P	0.97110	1.0;0.734;0.734	D	0.96599	0.9443	9	0.87932	D	0	.	17.14	0.86750	0.0:1.0:0.0:0.0	rs11576415;rs52789797;rs11576415	301;352;352	B7Z792;Q53HG2;O75306	.;.;NDUS2_HUMAN	A	352	ENSP00000356972:P352A;ENSP00000376018:P352A	ENSP00000356972:P352A	P	+	1	0	NDUFS2	159448832	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.129000	0.77225	2.412000	0.81896	0.650000	0.86243	CCT	C|0.937;G|0.063	0.063	strong		0.527	NDUFS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083015.1	NM_004550	
TBC1D8	11138	hgsc.bcm.edu	37	2	101627925	101627925	+	Missense_Mutation	SNP	C	C	T	rs1062062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:101627925C>T	ENST00000376840.4	-	18	2859	c.2860G>A	c.(2860-2862)Ggg>Agg	p.G954R	RPL31_ENST00000409650.1_Intron|RPL31_ENST00000409028.4_Intron|RPL31_ENST00000409038.1_Intron|TBC1D8_ENST00000409318.1_Missense_Mutation_p.G969R			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	954			G -> R (in dbSNP:rs1062062).		blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						TTGGGTTTCCCGAAAACCAGG	0.512													C|||	220	0.0439297	0.0015	0.0634	5008	,	,		19114	0.001		0.1262	False		,,,				2504	0.047				p.G954R		Atlas-SNP	.											TBC1D8,NS,carcinoma,+1,2	TBC1D8	169	2	0			c.G2860A						PASS	.	C	,ARG/GLY	101,3747		0,101,1823	100.0	106.0	104.0		,2860	5.7	0.1	2	dbSNP_86	104	1073,7173		85,903,3135	yes	intron,missense	RPL31,TBC1D8	NM_001098577.2,NM_001102426.1	,125	85,1004,4958	TT,TC,CC		13.0124,2.6247,9.7073	,benign	,954/1141	101627925	1174,10920	1924	4123	6047	SO:0001583	missense	11138	exon18			GTTTCCCGAAAAC	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.2860G>A	2.37:g.101627925C>T	ENSP00000366036:p.Gly954Arg	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	37	CCDS46375.1	119	0.05448717948717949	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	91	0.12005277044854881	C	14.07	2.427061	0.43122	0.026247	0.130124	ENSG00000204634	ENST00000376840;ENST00000409318	T;T	0.03212	4.01;4.01	5.67	5.67	0.87782	.	0.000000	0.64402	D	0.000006	T	0.00073	0.0002	L	0.42245	1.32	0.42692	P	0.0064109999999999445	B	0.15930	0.015	B	0.09377	0.004	T	0.46428	-0.9192	9	0.34782	T	0.22	-41.0133	14.9126	0.70770	0.1432:0.8568:0.0:0.0	rs1062062;rs3203171;rs17719773;rs52808790;rs1062062	954	O95759	TBCD8_HUMAN	R	954;969	ENSP00000366036:G954R;ENSP00000386856:G969R	ENSP00000366036:G954R	G	-	1	0	TBC1D8	100994357	0.083000	0.21467	0.082000	0.20525	0.967000	0.64934	2.987000	0.49378	2.828000	0.97474	0.655000	0.94253	GGG	C|0.941;T|0.059	0.059	strong		0.512	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487172	32487172	+	Silent	SNP	C	C	T	rs72508430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32487172C>T	ENST00000374975.3	-	3	689	c.627G>A	c.(625-627)gtG>gtA	p.V209V		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GAGGGCTCGTCACGCTTGGGT	0.488													C|||	1669	0.333267	0.4554	0.281	5008	,	,		12303	0.2966		0.2982	False		,,,				2504	0.2791				p.V209V		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,-2,1	HLA-DRB5	31	1	0			c.G627A						scavenged	.						73.0	83.0	80.0					6																	32487172		1892	3753	5645	SO:0001819	synonymous_variant	3127	exon3			GCTCGTCACGCTT		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.627G>A	6.37:g.32487172C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	52	0.509804	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			C|0.764;T|0.235	0.235	strong		0.488	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ZNF358	140467	hgsc.bcm.edu	37	19	7584223	7584223	+	Missense_Mutation	SNP	A	A	G	rs11555037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7584223A>G	ENST00000597229.1	+	2	265	c.95A>G	c.(94-96)aAt>aGt	p.N32S	CTD-2207O23.12_ENST00000599312.1_3'UTR|ZNF358_ENST00000394341.2_Missense_Mutation_p.N32S|CTD-2207O23.11_ENST00000602083.1_RNA	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	32			N -> S (in dbSNP:rs11555037).		embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						CTAGACCCCAATCCTGAAGAT	0.567													A|||	979	0.195487	0.1044	0.1772	5008	,	,		12926	0.1042		0.326	False		,,,				2504	0.2914				p.N32S		Atlas-SNP	.											.	ZNF358	41	.	0			c.A95G						PASS	.	A	SER/ASN	523,3855		36,451,1702	52.0	60.0	58.0		95	0.3	0.0	19	dbSNP_120	58	2575,6005		375,1825,2090	yes	missense	ZNF358	NM_018083.4	46	411,2276,3792	GG,GA,AA		30.0117,11.9461,23.908	benign	32/569	7584223	3098,9860	2189	4290	6479	SO:0001583	missense	140467	exon2			ACCCCAATCCTGA	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"""Zinc fingers, C2H2-type"""	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.95A>G	19.37:g.7584223A>G	ENSP00000472305:p.Asn32Ser	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	53	53	1	NM_018083	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	37	CCDS32890.2	434	0.1987179487179487	64	0.13008130081300814	72	0.19889502762430938	51	0.08916083916083917	247	0.3258575197889182	A	0.007	-1.982298	0.00448	0.119461	0.300117	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.05649	3.41	4.73	0.314	0.15847	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.46289	-0.9202	8	0.09590	T	0.72	-0.2651	7.971	0.30127	0.612:0.0:0.388:0.0	rs11555037	32	Q9NW07	ZN358_HUMAN	S	32	ENSP00000377873:N32S	ENSP00000354703:N32S	N	+	2	0	ZNF358	7490223	0.000000	0.05858	0.003000	0.11579	0.186000	0.23388	0.385000	0.20685	0.078000	0.16900	0.456000	0.33151	AAT	A|0.768;G|0.231;T|0.000	0.231	strong		0.567	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1		
C1RL	51279	hgsc.bcm.edu	37	12	7252597	7252597	+	Silent	SNP	G	G	A	rs61917913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7252597G>A	ENST00000266542.4	-	4	608	c.516C>T	c.(514-516)agC>agT	p.S172S	C1RL_ENST00000544702.1_Silent_p.S172S|C1RL_ENST00000545280.1_Silent_p.S56S|C1RL_ENST00000504702.2_5'Flank	NM_016546.2	NP_057630.2	Q9NZP8	C1RL_HUMAN	complement component 1, r subcomponent-like	172					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						TGCTGGCCTCGCTGATGGGCT	0.577													G|||	74	0.0147764	0.0008	0.0202	5008	,	,		-128	0.001		0.0268	False		,,,				2504	0.0317				p.S172S		Atlas-SNP	.											C1RL,colon,carcinoma,0,1	C1RL	39	1	0			c.C516T						PASS	.	G		35,4371	40.0+/-72.8	0,35,2168	36.0	34.0	35.0		516	2.4	0.0	12	dbSNP_129	35	363,8237	120.6+/-179.8	6,351,3943	no	coding-synonymous	C1RL	NM_016546.2		6,386,6111	AA,AG,GG		4.2209,0.7944,3.0601		172/488	7252597	398,12608	2203	4300	6503	SO:0001819	synonymous_variant	51279	exon4			GGCCTCGCTGATG	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.516C>T	12.37:g.7252597G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_016546	Q53GX9	Silent	SNP	ENST00000266542.4	37	CCDS8573.1																																																																																			G|0.976;A|0.024	0.024	strong		0.577	C1RL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398367.1	NM_016546	
PKD1L1	168507	hgsc.bcm.edu	37	7	47927744	47927744	+	Missense_Mutation	SNP	C	C	T	rs56100904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47927744C>T	ENST00000289672.2	-	17	2730	c.2680G>A	c.(2680-2682)Gtc>Atc	p.V894I		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	894	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		V -> I (in dbSNP:rs56100904).		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						GAGATGTGGACGAATCTGAAA	0.393													C|||	515	0.102835	0.3011	0.0519	5008	,	,		20812	0.0188		0.0139	False		,,,				2504	0.0491				p.V894I		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G2680A						PASS	.	C	ILE/VAL	1145,3261	407.8+/-334.4	146,853,1204	72.0	68.0	69.0		2680	-6.9	0.0	7	dbSNP_129	69	203,8397	88.9+/-151.2	1,201,4098	yes	missense	PKD1L1	NM_138295.3	29	147,1054,5302	TT,TC,CC		2.3605,25.9873,10.3644	benign	894/2850	47927744	1348,11658	2203	4300	6503	SO:0001583	missense	168507	exon17			TGTGGACGAATCT	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.2680G>A	7.37:g.47927744C>T	ENSP00000289672:p.Val894Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	202	0.0924908424908425	162	0.32926829268292684	19	0.052486187845303865	10	0.017482517482517484	11	0.014511873350923483	C	10.37	1.331202	0.24167	0.259873	0.023605	ENSG00000158683	ENST00000289672	T	0.71341	-0.56	5.55	-6.95	0.01628	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.664722	0.13853	N	0.358205	T	0.00012	0.0000	L	0.39397	1.21	0.80722	P	0.0	B	0.29862	0.259	B	0.24155	0.051	T	0.03278	-1.1053	9	0.44086	T	0.13	-12.9875	8.4418	0.32820	0.0:0.3909:0.2684:0.3407	rs56100904	894	Q8TDX9	PK1L1_HUMAN	I	894	ENSP00000289672:V894I	ENSP00000289672:V894I	V	-	1	0	PKD1L1	47894269	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-1.612000	0.02061	-1.526000	0.01760	-2.913000	0.00091	GTC	C|0.902;T|0.098	0.098	strong		0.393	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
LGALS14	56891	hgsc.bcm.edu	37	19	40195183	40195183	+	Splice_Site	SNP	C	C	T	rs117106744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40195183C>T	ENST00000392052.3	+	1	238	c.15C>T	c.(13-15)ccC>ccT	p.P5P	LGALS14_ENST00000360675.3_5'UTR	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14	5				SLPV -> ITPG (in Ref. 1; AAP97241). {ECO:0000305}.	apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			CATCACTACCCGTGAGTTGAA	0.423													C|||	7	0.00139776	0.0	0.0014	5008	,	,		22816	0.0		0.006	False		,,,				2504	0.0				p.P5P		Atlas-SNP	.											.	LGALS14	38	.	0			c.C15T						PASS	.	C	,	14,4336		0,14,2161	62.0	63.0	63.0		15,	-1.8	0.0	19	dbSNP_132	63	73,8495		0,73,4211	yes	coding-synonymous-near-splice,utr-5	LGALS14	NM_020129.2,NM_203471.1	,	0,87,6372	TT,TC,CC		0.852,0.3218,0.6735	,	5/140,	40195183	87,12831	2175	4284	6459	SO:0001630	splice_region_variant	56891	exon1			ACTACCCGTGAGT	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.15+1C>T	19.37:g.40195183C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	214	103	0.481308	NM_020129	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Silent	SNP	ENST00000392052.3	37	CCDS46073.1																																																																																			C|0.996;T|0.004	0.004	strong		0.423	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	Silent
OR1F1	4992	hgsc.bcm.edu	37	16	3254972	3254972	+	Silent	SNP	T	T	C	rs2075851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3254972T>C	ENST00000304646.2	+	1	726	c.726T>C	c.(724-726)ggT>ggC	p.G242G	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	242					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						CCACCTGTGGTTCTCACCTGG	0.502													C|||	1954	0.390176	0.1203	0.5101	5008	,	,		22057	0.5685		0.4294	False		,,,				2504	0.4458				p.G242G		Atlas-SNP	.											.	OR1F1	36	.	0			c.T726C						PASS	.	C		824,3570	747.3+/-411.8	72,680,1445	207.0	188.0	194.0		726	-0.9	0.9	16	dbSNP_96	194	3762,4838	615.5+/-396.4	828,2106,1366	no	coding-synonymous	OR1F1	NM_012360.1		900,2786,2811	CC,CT,TT		43.7442,18.7528,35.2932		242/313	3254972	4586,8408	2197	4300	6497	SO:0001819	synonymous_variant	4992	exon1			CTGTGGTTCTCAC	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"""GPCR / Class A : Olfactory receptors"""	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.726T>C	16.37:g.3254972T>C		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	64	0.410256	NM_012360	O15246|Q6IFL5	Silent	SNP	ENST00000304646.2	37	CCDS10496.1																																																																																			T|0.618;C|0.382	0.382	strong		0.502	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1		
KIF4B	285643	hgsc.bcm.edu	37	5	154396017	154396017	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:154396017C>T	ENST00000435029.4	+	1	2758	c.2598C>T	c.(2596-2598)gcC>gcT	p.A866A		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	866	Interaction with PRC1. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			CCAAGTGTGCCCTGAAATATT	0.473																																					p.A866A		Atlas-SNP	.											KIF4B_ENST00000435029,NS,carcinoma,0,2	KIF4B	307	2	0			c.C2598T						scavenged	.						79.0	78.0	78.0					5																	154396017		2203	4300	6503	SO:0001819	synonymous_variant	285643	exon1			GTGTGCCCTGAAA	AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.2598C>T	5.37:g.154396017C>T		Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	216	4	0.0185185	NM_001099293		Silent	SNP	ENST00000435029.4	37	CCDS47324.1																																																																																			.	.	none		0.473	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
MBTPS1	8720	hgsc.bcm.edu	37	16	84115483	84115483	+	Silent	SNP	G	G	A	rs3743631	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84115483G>A	ENST00000343411.3	-	11	1812	c.1317C>T	c.(1315-1317)ccC>ccT	p.P439P	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	439	Peptidase S8.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TCATACTGGCGGGATTCACCA	0.517													A|||	2650	0.529153	0.5696	0.5159	5008	,	,		5965	0.6974		0.4384	False		,,,				2504	0.4039				p.P439P		Atlas-SNP	.											MBTPS1,NS,carcinoma,0,1	MBTPS1	85	1	0			c.C1317T						PASS	.	A		2310,2090	572.1+/-383.2	604,1102,494	56.0	58.0	57.0		1317	-5.0	0.8	16	dbSNP_107	57	3609,4991	626.1+/-397.8	757,2095,1448	no	coding-synonymous	MBTPS1	NM_003791.2		1361,3197,1942	AA,AG,GG		41.9651,47.5,45.5308		439/1053	84115483	5919,7081	2200	4300	6500	SO:0001819	synonymous_variant	8720	exon11			ACTGGCGGGATTC	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.1317C>T	16.37:g.84115483G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																			G|0.504;A|0.496	0.496	strong		0.517	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
RTBDN	83546	hgsc.bcm.edu	37	19	12936693	12936693	+	Missense_Mutation	SNP	C	C	T	rs148952767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12936693C>T	ENST00000458671.2	-	6	669	c.517G>A	c.(517-519)Gtg>Atg	p.V173M	RTBDN_ENST00000322912.5_Missense_Mutation_p.V205M|RTBDN_ENST00000393233.2_3'UTR|RTBDN_ENST00000592204.1_Missense_Mutation_p.V183M|CTD-2265O21.3_ENST00000588469.1_RNA|RTBDN_ENST00000589272.1_3'UTR	NM_001080997.2	NP_001074466.1	Q9BSG5	RTBDN_HUMAN	retbindin	173						extracellular region (GO:0005576)				kidney(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12						GGAGCAGCCACCGGTAGGGCG	0.647											OREG0025275	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	19	0.00379393	0.0	0.0086	5008	,	,		13754	0.0		0.0109	False		,,,				2504	0.002				p.V205M		Atlas-SNP	.											.	RTBDN	26	.	0			c.G613A						PASS	.	C	MET/VAL,MET/VAL	4,4396		0,4,2196	29.0	26.0	27.0		517,613	1.9	0.0	19	dbSNP_134	27	77,8513		0,77,4218	yes	missense,missense	RTBDN	NM_001080997.1,NM_031429.1	21,21	0,81,6414	TT,TC,CC		0.8964,0.0909,0.6236	probably-damaging,probably-damaging	173/230,205/262	12936693	81,12909	2200	4295	6495	SO:0001583	missense	83546	exon7			CAGCCACCGGTAG	AY028917	CCDS12283.1, CCDS45994.1, CCDS59355.1, CCDS59356.1	19p13	2006-03-22				ENSG00000132026			30310	protein-coding gene	gene with protein product		609553				12107411	Standard	NM_001080997		Approved	FLJ36353	uc002mvj.4	Q9BSG5		ENST00000458671.2:c.517G>A	19.37:g.12936693C>T	ENSP00000416375:p.Val173Met	Somatic	84	0	0	683	WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_031429	F1T0I8|Q9BWT5	Missense_Mutation	SNP	ENST00000458671.2	37	CCDS45994.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	16.73	3.204950	0.58234	9.09E-4	0.008964	ENSG00000132026	ENST00000322912;ENST00000458671	T;T	0.79033	-1.23;-1.23	4.36	1.89	0.25635	Folate receptor-like (1);	0.581337	0.14332	N	0.326316	T	0.79673	0.4486	M	0.70595	2.14	0.19300	N	0.999978	D;D	0.89917	1.0;1.0	D;D	0.74674	0.973;0.984	T	0.68949	-0.5274	10	0.72032	D	0.01	-26.9761	5.851	0.18694	0.0:0.7037:0.0:0.2963	.	205;173	Q9BSG5-2;Q9BSG5	.;RTBDN_HUMAN	M	205;173	ENSP00000326253:V205M;ENSP00000416375:V173M	ENSP00000326253:V205M	V	-	1	0	RTBDN	12797693	0.043000	0.20138	0.045000	0.18777	0.048000	0.14542	0.110000	0.15437	0.404000	0.25506	0.591000	0.81541	GTG	C|0.993;T|0.007	0.007	strong		0.647	RTBDN-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451513.1	NM_031429	
RPL13	6137	hgsc.bcm.edu	37	16	89627460	89627460	+	Silent	SNP	T	T	G	rs2280370	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:89627460T>G	ENST00000393099.3	+	1	342	c.93T>G	c.(91-93)cgT>cgG	p.R31R	RPL13_ENST00000567815.1_Silent_p.R31R|RPL13_ENST00000311528.5_Silent_p.R31R|SNORD68_ENST00000363214.1_RNA|RPL13_ENST00000452368.3_Silent_p.R31R	NM_033251.2	NP_150254.1	P26373	RL13_HUMAN	ribosomal protein L13	31					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)|cytosolic ribosome (GO:0022626)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(3)|skin(1)|upper_aerodigestive_tract(2)	6		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		AGCCGGCCCGTAAGATCCGCA	0.721													G|||	956	0.190895	0.2988	0.1282	5008	,	,		12808	0.1458		0.17	False		,,,				2504	0.1575				p.R31R		Atlas-SNP	.											RPL13,colon,carcinoma,0,1	RPL13	11	1	0			c.T93G						PASS	.	G	,	1087,3151		143,801,1175	11.0	12.0	12.0		93,93	0.1	0.6	16	dbSNP_100	12	1498,6884		135,1228,2828	no	coding-synonymous,coding-synonymous	RPL13	NM_000977.3,NM_033251.2	,	278,2029,4003	GG,GT,TT		17.8716,25.6489,20.4834	,	31/212,31/212	89627460	2585,10035	2119	4191	6310	SO:0001819	synonymous_variant	6137	exon2			GGCCCGTAAGATC	AB007172	CCDS10979.1, CCDS58492.1	16q24.3	2011-04-06			ENSG00000167526	ENSG00000167526		"""L ribosomal proteins"""	10303	protein-coding gene	gene with protein product		113703				9582194	Standard	NM_000977		Approved	D16S444E, BBC1, L13	uc002fnm.2	P26373	OTTHUMG00000133770	ENST00000393099.3:c.93T>G	16.37:g.89627460T>G		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_001243131	B4DLX3|F5H1S2|Q3KQT8|Q567Q8|Q9BPX0	Silent	SNP	ENST00000393099.3	37	CCDS10979.1																																																																																			G|1.000;|0.000	1.000	weak		0.721	RPL13-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258294.2	NM_000977	
WDYHV1	55093	hgsc.bcm.edu	37	8	124440174	124440174	+	Missense_Mutation	SNP	A	A	G	rs6999234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124440174A>G	ENST00000287387.2	+	2	219	c.94A>G	c.(94-96)Att>Gtt	p.I32V	WDYHV1_ENST00000518125.1_5'Flank|WDYHV1_ENST00000523356.1_Missense_Mutation_p.I32V|WDYHV1_ENST00000517609.1_3'UTR|WDYHV1_ENST00000523984.1_5'UTR	NM_018024.1	NP_060494.1	Q96HA8	NTAQ1_HUMAN	WDYHV motif containing 1	32			I -> V (in dbSNP:rs6999234). {ECO:0000269|PubMed:15489334}.		cellular protein modification process (GO:0006464)	cytosol (GO:0005829)|nucleus (GO:0005634)	protein-N-terminal glutamine amidohydrolase activity (GO:0070773)	p.I32V(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(3)	17						TGAAGAAAATATTTGGAAGCT	0.299													A|||	2055	0.410343	0.3427	0.3919	5008	,	,		17407	0.5863		0.3121	False		,,,				2504	0.4346				p.I32V		Atlas-SNP	.											WDYHV1,NS,carcinoma,0,2	WDYHV1	30	2	1	Substitution - Missense(1)	prostate(1)	c.A94G						PASS	.	A	VAL/ILE	1598,2808	494.5+/-363.0	293,1012,898	111.0	127.0	121.0		94	4.1	1.0	8	dbSNP_116	121	3028,5572	465.2+/-366.4	540,1948,1812	yes	missense	WDYHV1	NM_018024.1	29	833,2960,2710	GG,GA,AA		35.2093,36.2687,35.5682	benign	32/206	124440174	4626,8380	2203	4300	6503	SO:0001583	missense	55093	exon2			GAAAATATTTGGA	AK001066	CCDS6344.1, CCDS64965.1	8q24.13	2008-10-01	2008-10-01	2008-10-01		ENSG00000156795			25490	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 32"""	C8orf32		12477932	Standard	NM_018024		Approved	FLJ10204	uc003yqn.1	Q96HA8		ENST00000287387.2:c.94A>G	8.37:g.124440174A>G	ENSP00000287387:p.Ile32Val	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_018024	B4DE68|Q9NW95	Missense_Mutation	SNP	ENST00000287387.2	37	CCDS6344.1	841	0.3850732600732601	140	0.2845528455284553	136	0.3756906077348066	327	0.5716783216783217	238	0.31398416886543534	A	1.977	-0.435011	0.04669	0.362687	0.352093	ENSG00000156795	ENST00000287387;ENST00000522194;ENST00000523356	T;T;T	0.12147	2.71;2.71;2.71	5.23	4.06	0.47325	Protein N-terminal glutamine amidohydrolase, alpha beta roll (1);Protein N-terminal glutamine amidohydrolase (1);	0.185347	0.47455	N	0.000236	T	0.00012	0.0000	N	0.03016	-0.435	0.09310	P	1.0	B	0.13145	0.007	B	0.15052	0.012	T	0.43861	-0.9365	9	0.02654	T	1	-14.2764	6.5742	0.22555	0.739:0.0:0.261:0.0	rs6999234;rs17856266;rs52803422;rs60874123;rs6999234	32	Q96HA8	NTAQ1_HUMAN	V	32	ENSP00000287387:I32V;ENSP00000434252:I32V;ENSP00000428615:I32V	ENSP00000287387:I32V	I	+	1	0	WDYHV1	124509355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.320000	0.51991	0.827000	0.34685	0.477000	0.44152	ATT	A|0.626;G|0.374	0.374	strong		0.299	WDYHV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381772.1	NM_018024	
GPR179	440435	hgsc.bcm.edu	37	17	36486004	36486004	+	Missense_Mutation	SNP	T	T	C	rs55727040	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36486004T>C	ENST00000342292.4	-	11	3468	c.3448A>G	c.(3448-3450)Aag>Gag	p.K1150E	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1150			K -> E (in dbSNP:rs55727040).		visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				AGGGACTCCTTGTCATCGGAG	0.622													C|||	805	0.160743	0.4887	0.0994	5008	,	,		18575	0.0		0.0746	False		,,,				2504	0.0153				p.K1150E		Atlas-SNP	.											.	GPR179	170	.	0			c.A3448G						PASS	.	C	GLU/LYS	1575,2633		286,1003,815	147.0	149.0	148.0		3448	5.1	0.8	17	dbSNP_129	148	437,8025		10,417,3804	yes	missense	GPR179	NM_001004334.2	56	296,1420,4619	CC,CT,TT		5.1643,37.4287,15.88	benign	1150/2368	36486004	2012,10658	2104	4231	6335	SO:0001583	missense	440435	exon11			ACTCCTTGTCATC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3448A>G	17.37:g.36486004T>C	ENSP00000345060:p.Lys1150Glu	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	72	30	0.416667	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	288	0.13186813186813187	206	0.4186991869918699	38	0.10497237569060773	0	0.0	44	0.05804749340369393	C	0.135	-1.109424	0.01813	0.374287	0.051643	ENSG00000188888	ENST00000342292	T	0.37058	1.22	5.09	5.09	0.68999	.	0.000000	0.51477	N	0.000097	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.39583	-0.9607	9	0.02654	T	1	-12.5624	11.095	0.48139	0.0:0.9133:0.0:0.0867	rs55727040	1150	Q6PRD1	GP179_HUMAN	E	1150	ENSP00000345060:K1150E	ENSP00000345060:K1150E	K	-	1	0	GPR179	33739530	0.000000	0.05858	0.837000	0.33122	0.087000	0.18053	0.195000	0.17155	1.380000	0.46344	-0.355000	0.07637	AAG	T|0.897;C|0.103	0.103	strong		0.622	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
MUC16	94025	hgsc.bcm.edu	37	19	9085004	9085004	+	Missense_Mutation	SNP	T	T	C	rs11085805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9085004T>C	ENST00000397910.4	-	1	7014	c.6811A>G	c.(6811-6813)Act>Gct	p.T2271A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2271	Ser-rich.|Thr-rich.		T -> A (in dbSNP:rs11085805).		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						AATGAATGAGTTGTCTTTTCT	0.448													T|||	952	0.190096	0.0711	0.2709	5008	,	,		21748	0.3036		0.172	False		,,,				2504	0.1953				p.T2271A		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,+1,2	MUC16	4315	2	0			c.A6811G						PASS	.	T	ALA/THR	277,3563		5,267,1648	66.0	63.0	64.0		6811	-0.4	0.0	19	dbSNP_120	64	1482,6780		126,1230,2775	yes	missense	MUC16	NM_024690.2	58	131,1497,4423	CC,CT,TT		17.9375,7.2135,14.5348	benign	2271/14508	9085004	1759,10343	1920	4131	6051	SO:0001583	missense	94025	exon1			AATGAGTTGTCTT	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.6811A>G	19.37:g.9085004T>C	ENSP00000381008:p.Thr2271Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	109	54	0.495413	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	t	0.055	-1.238975	0.01493	0.072135	0.179375	ENSG00000181143	ENST00000397910	T	0.02301	4.35	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.46247	-0.9205	7	0.87932	D	0	.	.	.	.	rs11085805;rs52821244;rs59875884;rs11085805	2271	B5ME49	.	A	2271	ENSP00000381008:T2271A	ENSP00000381008:T2271A	T	-	1	0	MUC16	8946004	0.003000	0.15002	0.016000	0.15963	0.016000	0.09150	-0.705000	0.05052	-0.874000	0.04027	-0.902000	0.02854	ACT	T|0.812;C|0.188	0.188	strong		0.448	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ARHGAP5	394	hgsc.bcm.edu	37	14	32562733	32562733	+	Missense_Mutation	SNP	A	A	G	rs151151743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:32562733A>G	ENST00000345122.3	+	2	3173	c.2858A>G	c.(2857-2859)aAt>aGt	p.N953S	ARHGAP5_ENST00000432921.1_Missense_Mutation_p.N953S|ARHGAP5_ENST00000539826.2_Missense_Mutation_p.N953S|ARHGAP5_ENST00000556611.1_Missense_Mutation_p.N953S|ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000433497.1_Intron	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	953					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|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)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TTGTCTGATAATACAAGGGAA	0.338													A|||	39	0.00778754	0.0234	0.0072	5008	,	,		18733	0.0		0.003	False		,,,				2504	0.0				p.N953S	NSCLC(9;77 350 3443 29227 41353)	Atlas-SNP	.											.	ARHGAP5	166	.	0			c.A2858G						PASS	.	A	SER/ASN,SER/ASN	98,4306	73.1+/-111.1	2,94,2106	44.0	44.0	44.0		2858,2858	2.0	1.0	14	dbSNP_134	44	6,8588	5.0+/-18.6	0,6,4291	no	missense,missense	ARHGAP5	NM_001030055.1,NM_001173.2	46,46	2,100,6397	GG,GA,AA		0.0698,2.2252,0.8001	benign,benign	953/1503,953/1502	32562733	104,12894	2202	4297	6499	SO:0001583	missense	394	exon2			CTGATAATACAAG	U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.2858A>G	14.37:g.32562733A>G	ENSP00000371897:p.Asn953Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001173	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Missense_Mutation	SNP	ENST00000345122.3	37	CCDS32062.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	A	4.097	0.015998	0.07959	0.022252	6.98E-4	ENSG00000100852	ENST00000556611;ENST00000539826;ENST00000345122;ENST00000432921	T;T;T;T	0.08458	3.09;3.09;3.09;3.09	5.66	2.0	0.26442	.	0.203147	0.64402	N	0.000013	T	0.01421	0.0046	N	0.04724	-0.175	0.38579	D	0.950144	B;B	0.06786	0.001;0.001	B;B	0.19666	0.026;0.011	T	0.45116	-0.9283	10	0.08837	T	0.75	.	5.5761	0.17225	0.5755:0.1364:0.2881:0.0	.	953;953	Q13017-2;Q13017	.;RHG05_HUMAN	S	953	ENSP00000452222:N953S;ENSP00000441692:N953S;ENSP00000371897:N953S;ENSP00000393307:N953S	ENSP00000371897:N953S	N	+	2	0	ARHGAP5	31632484	0.987000	0.35691	1.000000	0.80357	0.995000	0.86356	0.303000	0.19210	0.158000	0.19367	0.528000	0.53228	AAT	A|0.993;G|0.007	0.007	strong		0.338	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
MORC4	79710	hgsc.bcm.edu	37	X	106221323	106221323	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:106221323C>A	ENST00000355610.4	-	8	1317	c.1043G>T	c.(1042-1044)gGg>gTg	p.G348V	MORC4_ENST00000255495.7_Missense_Mutation_p.G348V|MORC4_ENST00000535534.1_Missense_Mutation_p.G96V	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	348						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						CACCTGGCACCCCACCTTCTC	0.383																																					p.G348V		Atlas-SNP	.											.	MORC4	155	.	0			c.G1043T						PASS	.						160.0	159.0	160.0					X																	106221323		2203	4300	6503	SO:0001583	missense	79710	exon8			TGGCACCCCACCT	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.1043G>T	X.37:g.106221323C>A	ENSP00000347821:p.Gly348Val	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	71	61	0.859155	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	C	19.17	3.775432	0.70107	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.37752	2.41;1.18;2.41	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	M	0.72118	2.19	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.63739	-0.6569	10	0.87932	D	0	-13.769	15.1835	0.72978	0.0:1.0:0.0:0.0	.	96;348;348	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	V	348;96;348	ENSP00000347821:G348V;ENSP00000440359:G96V;ENSP00000255495:G348V	ENSP00000255495:G348V	G	-	2	0	MORC4	106107979	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	5.777000	0.68931	2.393000	0.81446	0.538000	0.68166	GGG	.	.	none		0.383	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
FKBP1A	2280	hgsc.bcm.edu	37	20	1350709	1350709	+	3'UTR	SNP	T	T	C	rs8392	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1350709T>C	ENST00000400137.4	-	0	534				SDCBP2-AS1_ENST00000609285.1_RNA|FKBP1A_ENST00000460490.1_5'UTR|FKBP1A_ENST00000381724.3_3'UTR|SDCBP2-AS1_ENST00000446423.1_RNA|SDCBP2-AS1_ENST00000609470.1_RNA	NM_000801.4	NP_000792.1	P62942	FKB1A_HUMAN	FK506 binding protein 1A, 12kDa						'de novo' protein folding (GO:0006458)|amyloid fibril formation (GO:1990000)|calcium ion transmembrane transport (GO:0070588)|chaperone-mediated protein folding (GO:0061077)|extracellular fibril organization (GO:0043206)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein binding (GO:0032092)|positive regulation of protein ubiquitination (GO:0031398)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|protein peptidyl-prolyl isomerization (GO:0000413)|protein refolding (GO:0042026)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of amyloid precursor protein catabolic process (GO:1902991)|regulation of immune response (GO:0050776)|regulation of protein localization (GO:0032880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|SMAD protein complex assembly (GO:0007183)|T cell activation (GO:0042110)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|terminal cisterna (GO:0014802)|Z disc (GO:0030018)	activin binding (GO:0048185)|FK506 binding (GO:0005528)|ion channel binding (GO:0044325)|macrolide binding (GO:0005527)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|type I transforming growth factor beta receptor binding (GO:0034713)			central_nervous_system(1)|lung(1)|upper_aerodigestive_tract(1)	3					Pimecrolimus(DB00337)|Sirolimus(DB00877)|Tacrolimus(DB00864)	GATCCCTCCATGGCAGATCTG	0.502													T|||	1719	0.343251	0.5129	0.3458	5008	,	,		19072	0.0883		0.4155	False		,,,				2504	0.3006				p.P86P		Atlas-SNP	.											.	FKBP1A	6	.	0			c.A258G						PASS	.																																			SO:0001624	3_prime_UTR_variant	2280	exon4			CCTCCATGGCAGA	M92423	CCDS13014.1, CCDS74688.1	20p13	2013-03-20	2002-08-29		ENSG00000088832	ENSG00000088832			3711	protein-coding gene	gene with protein product	"""calstabin 1"""	186945	"""FK506-binding protein 1A (12kD)"""	FKBP1		1930186	Standard	NM_000801		Approved	FKBP-12, FKBP12, PKC12, PPIASE, FKBP12C	uc002wey.3	P62942	OTTHUMG00000031666	ENST00000400137.4:c.*44A>G	20.37:g.1350709T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	49	25	0.510204	NM_001199786	D3DVW6|P20071|Q4VC47|Q6FGD9|Q6LEU3|Q9H103|Q9H566	Silent	SNP	ENST00000400137.4	37	CCDS13014.1																																																																																			T|0.408;G|0.125;C|0.192;A|0.276	0.192	strong		0.502	FKBP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077534.2		
SDHA	6389	hgsc.bcm.edu	37	5	226160	226160	+	Silent	SNP	A	A	C	rs6555055	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:226160A>C	ENST00000264932.6	+	5	734	c.619A>C	c.(619-621)Agg>Cgg	p.R207R	SDHA_ENST00000510361.1_Silent_p.R159R|SDHA_ENST00000504309.1_Silent_p.R207R	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	207					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)	CTTATATGGAAGGGTAAGGCC	0.597									Familial Paragangliomas				A|||	1239	0.247404	0.6233	0.2406	5008	,	,		18908	0.0585		0.1113	False		,,,				2504	0.0787				p.R207R		Atlas-SNP	.											.	SDHA	80	.	0			c.A619C						PASS	.	A		2355,2051		636,1083,484	43.0	42.0	42.0		619	-0.4	1.0	5	dbSNP_116	42	1169,7431		74,1021,3205	no	coding-synonymous	SDHA	NM_004168.2		710,2104,3689	CC,CA,AA		13.593,46.5502,27.0952		207/665	226160	3524,9482	2203	4300	6503	SO:0001819	synonymous_variant	6389	exon5	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	TATGGAAGGGTAA	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.619A>C	5.37:g.226160A>C		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	128	55	0.429688	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			A|0.751;C|0.249	0.249	strong		0.597	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
PCNT	5116	hgsc.bcm.edu	37	21	47836395	47836395	+	Missense_Mutation	SNP	T	T	G	rs1044998	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47836395T>G	ENST00000359568.5	+	30	6670	c.6563T>G	c.(6562-6564)aTg>aGg	p.M2188R	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2188			M -> R (in dbSNP:rs1044998). {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)					TGTCAGGACATGTCTCTTTCT	0.532													G|||	893	0.178315	0.4856	0.0937	5008	,	,		18521	0.004		0.0934	False		,,,				2504	0.09				p.M2188R		Atlas-SNP	.											.	PCNT	283	.	0			c.T6563G						PASS	.	G	ARG/MET	1911,2495	622.5+/-394.0	414,1083,706	83.0	99.0	94.0		6563	-0.7	0.0	21	dbSNP_86	94	652,7948	788.5+/-407.6	15,622,3663	yes	missense	PCNT	NM_006031.5	91	429,1705,4369	GG,GT,TT		7.5814,43.3727,19.7063	benign	2188/3337	47836395	2563,10443	2203	4300	6503	SO:0001583	missense	5116	exon30			AGGACATGTCTCT	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.6563T>G	21.37:g.47836395T>G	ENSP00000352572:p.Met2188Arg	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	346	0.15842490842490842	233	0.4735772357723577	37	0.10220994475138122	2	0.0034965034965034965	74	0.09762532981530343	G	0.110	-1.140387	0.01728	0.433727	0.075814	ENSG00000160299	ENST00000359568	T	0.01438	4.89	4.96	-0.739	0.11120	.	0.483054	0.15544	N	0.256798	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	0.11155	-1.0599	9	0.12430	T	0.62	.	1.6985	0.02867	0.1695:0.3829:0.2133:0.2342	rs1044998;rs1044998	2070;2188	O95613-2;O95613	.;PCNT_HUMAN	R	2188	ENSP00000352572:M2188R	ENSP00000352572:M2188R	M	+	2	0	PCNT	46660823	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.113000	0.15499	-0.403000	0.07622	-0.729000	0.03580	ATG	T|0.820;G|0.180	0.180	strong		0.532	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
WDR92	116143	hgsc.bcm.edu	37	2	68364478	68364478	+	Missense_Mutation	SNP	T	T	C	rs13009282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:68364478T>C	ENST00000295121.6	-	6	837	c.721A>G	c.(721-723)Atg>Gtg	p.M241V	RP11-474G23.1_ENST00000406334.3_3'UTR|WDR92_ENST00000492039.2_5'UTR|WDR92_ENST00000409164.1_Missense_Mutation_p.M241V|WDR92_ENST00000406245.2_Missense_Mutation_p.M140V	NM_138458.3	NP_612467.1	Q96MX6	WDR92_HUMAN	WD repeat domain 92	241			M -> V (in dbSNP:rs13009282).		apoptotic process (GO:0006915)|histone lysine methylation (GO:0034968)		methylated histone binding (GO:0035064)	p.M241V(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(3)|stomach(1)	12						TGTGTTCTCATGTCAAAAACA	0.373													T|||	888	0.177316	0.1641	0.1988	5008	,	,		18917	0.1538		0.2177	False		,,,				2504	0.1626				p.M241V		Atlas-SNP	.											WDR92,NS,carcinoma,0,1	WDR92	21	1	1	Substitution - Missense(1)	stomach(1)	c.A721G						PASS	.	T	VAL/MET	703,3703	293.6+/-282.7	62,579,1562	148.0	141.0	143.0		721	4.8	1.0	2	dbSNP_121	143	2215,6385	376.4+/-338.1	274,1667,2359	yes	missense	WDR92	NM_138458.2	21	336,2246,3921	CC,CT,TT		25.7558,15.9555,22.4358	benign	241/358	68364478	2918,10088	2203	4300	6503	SO:0001583	missense	116143	exon6			TTCTCATGTCAAA	AK056303	CCDS1884.1, CCDS58712.1	2p14	2013-01-09			ENSG00000243667	ENSG00000243667		"""WD repeat domain containing"""	25176	protein-coding gene	gene with protein product		610729				16487927	Standard	NM_138458		Approved	FLJ31741, Monad	uc002see.2	Q96MX6	OTTHUMG00000152561	ENST00000295121.6:c.721A>G	2.37:g.68364478T>C	ENSP00000295121:p.Met241Val	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	116	66	0.568965	NM_001256476	Q96CR6	Missense_Mutation	SNP	ENST00000295121.6	37	CCDS1884.1	379	0.17353479853479853	64	0.13008130081300814	60	0.16574585635359115	89	0.1555944055944056	166	0.21899736147757257	T	12.86	2.063138	0.36373	0.159555	0.257558	ENSG00000243667	ENST00000295121;ENST00000406245;ENST00000409164	D;T;T	0.89552	-2.53;1.71;-0.02	6.03	4.81	0.61882	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.132323	0.47852	D	0.000212	T	0.00073	0.0002	L	0.45137	1.4	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.04961	-1.0915	9	0.33940	T	0.23	.	12.2344	0.54508	0.1273:0.0:0.0:0.8727	rs13009282;rs17589505;rs52821939;rs60739059;rs13009282	241	Q96MX6	WDR92_HUMAN	V	241;140;241	ENSP00000295121:M241V;ENSP00000384518:M140V;ENSP00000386746:M241V	ENSP00000295121:M241V	M	-	1	0	WDR92	68217982	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.431000	0.52814	2.308000	0.77769	0.533000	0.62120	ATG	T|0.804;C|0.196	0.196	strong		0.373	WDR92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251754.2	NM_138458	
MCC	4163	hgsc.bcm.edu	37	5	112399791	112399791	+	Silent	SNP	G	G	A	rs2227947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:112399791G>A	ENST00000302475.4	-	12	2096	c.1533C>T	c.(1531-1533)aaC>aaT	p.N511N	MCC_ENST00000515367.2_Silent_p.N448N|MCC_ENST00000408903.3_Silent_p.N701N|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	511					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)		CCTTGGCAGCGTTCTCAGCTG	0.597													G|||	2571	0.513379	0.1407	0.67	5008	,	,		21510	0.6349		0.6571	False		,,,				2504	0.6329				p.N701N		Atlas-SNP	.											.	MCC	234	.	0			c.C2103T						PASS	.	G	,	941,3463	355.6+/-313.1	112,717,1373	70.0	66.0	68.0		2103,1533	-3.2	1.0	5	dbSNP_98	68	5505,3095	658.1+/-401.5	1761,1983,556	no	coding-synonymous,coding-synonymous	MCC	NM_001085377.1,NM_002387.2	,	1873,2700,1929	AA,AG,GG		35.9884,21.3669,49.5694	,	701/1020,511/830	112399791	6446,6558	2202	4300	6502	SO:0001819	synonymous_variant	4163	exon14			GGCAGCGTTCTCA		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.1533C>T	5.37:g.112399791G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_001085377	D3DT05|Q6ZR04	Silent	SNP	ENST00000302475.4	37	CCDS4111.1																																																																																			G|0.494;A|0.506	0.506	strong		0.597	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
ABCD3	5825	hgsc.bcm.edu	37	1	94930345	94930345	+	Silent	SNP	G	G	A	rs16946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:94930345G>A	ENST00000370214.4	+	3	186	c.162G>A	c.(160-162)aaG>aaA	p.K54K	ABCD3_ENST00000315713.5_Silent_p.K54K|ABCD3_ENST00000394233.2_Silent_p.K54K|ABCD3_ENST00000536817.1_5'UTR|ABCD3_ENST00000454898.2_Silent_p.K78K	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	54	Interaction with PEX19.|Targeting to peroxisomes.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		AGGGGAAAAAGGAGCGAGCTG	0.343													G|||	1402	0.279952	0.0998	0.3919	5008	,	,		17199	0.1994		0.502	False		,,,				2504	0.2986				p.K54K		Atlas-SNP	.											.	ABCD3	62	.	0			c.G162A						PASS	.	G	,	696,3710	285.7+/-278.4	52,592,1559	126.0	126.0	126.0		162,162	1.0	1.0	1	dbSNP_60	126	4145,4455	561.4+/-387.8	1021,2103,1176	no	coding-synonymous,coding-synonymous	ABCD3	NM_001122674.1,NM_002858.3	,	1073,2695,2735	AA,AG,GG		48.1977,15.7966,37.2213	,	54/237,54/660	94930345	4841,8165	2203	4300	6503	SO:0001819	synonymous_variant	5825	exon3			GAAAAAGGAGCGA	M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"""ATP binding cassette transporters / subfamily D"""	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.162G>A	1.37:g.94930345G>A		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	157	154	0.980892	NM_002858	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Silent	SNP	ENST00000370214.4	37	CCDS749.1																																																																																			G|0.652;A|0.348	0.348	strong		0.343	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029597.1	NM_002858	
BTNL2	56244	hgsc.bcm.edu	37	6	32362745	32362745	+	Missense_Mutation	SNP	G	G	A	rs28362678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32362745G>A	ENST00000374993.1	-	6	1135	c.1136C>T	c.(1135-1137)cCg>cTg	p.P379L	BTNL2_ENST00000414363.1_Missense_Mutation_p.P169L|BTNL2_ENST00000544175.1_Missense_Mutation_p.P102L|BTNL2_ENST00000540315.1_Missense_Mutation_p.P169L|BTNL2_ENST00000429232.2_3'UTR|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Missense_Mutation_p.P285L|BTNL2_ENST00000454136.3_Missense_Mutation_p.P379L	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	379			P -> L (in dbSNP:rs28362678).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						AGAGCACATCGGCTGCATTTC	0.562													g|||	822	0.164137	0.1422	0.1599	5008	,	,		19220	0.1597		0.163	False		,,,				2504	0.2025				p.P379L		Atlas-SNP	.											.	BTNL2	50	.	0			c.C1136T						PASS	.		LEU/PRO	551,3855	248.1+/-256.1	28,495,1680	199.0	185.0	190.0		1136	2.6	0.1	6	dbSNP_125	190	1241,7359	248.3+/-276.0	92,1057,3151	yes	missense	BTNL2	NM_019602.1	98	120,1552,4831	AA,AG,GG		14.4302,12.5057,13.7783	benign	379/456	32362745	1792,11214	2203	4300	6503	SO:0001583	missense	56244	exon6			CACATCGGCTGCA	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1136C>T	6.37:g.32362745G>A	ENSP00000364132:p.Pro379Leu	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		347	0.15888278388278387	60	0.12195121951219512	64	0.17679558011049723	105	0.18356643356643357	118	0.15567282321899736	g	0.025	-1.381882	0.01204	0.125057	0.144302	ENSG00000204290	ENST00000468270;ENST00000374995;ENST00000414363;ENST00000374993;ENST00000540315;ENST00000544175	T;T;T;T;T	0.02103	4.45;4.45;4.45;4.45;4.45	5.08	2.61	0.31194	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	0.000000	0.35805	N	0.002980	T	0.00073	0.0002	N	0.00004	-3.375	0.58432	P	9.000000000036756E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18085	-1.0348	9	0.02654	T	1	.	4.4337	0.11540	0.7367:0.0:0.0919:0.1714	rs28362678	169;379	Q9UIR0-4;Q9UIR0	.;BTNL2_HUMAN	L	379;285;169;379;169;102	ENSP00000364134:P285L;ENSP00000390512:P169L;ENSP00000364132:P379L;ENSP00000444714:P169L;ENSP00000443364:P102L	ENSP00000364132:P379L	P	-	2	0	BTNL2	32470723	0.023000	0.18921	0.096000	0.21009	0.008000	0.06430	3.176000	0.50863	0.413000	0.25759	-1.757000	0.00672	CCG	G|0.859;A|0.141	0.141	strong		0.562	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
NBPF10	100132406	hgsc.bcm.edu	37	1	145293515	145293515	+	Missense_Mutation	SNP	A	A	G	rs12565078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145293515A>G	ENST00000369339.3	+	3	363	c.110A>G	c.(109-111)aAc>aGc	p.N37S	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.N37S|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	308						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CAGTTCAGAAACCTCAAAGAG	0.478																																					p.N37S		Atlas-SNP	.											.	NBPF10	221	.	0			c.A110G						PASS	.																																			SO:0001583	missense	100132406	exon1			TCAGAAACCTCAA	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	ENST00000369339.3:c.110A>G	1.37:g.145293515A>G	ENSP00000358345:p.Asn37Ser	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	94	28	0.297872	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	0.712	-0.786747	0.02907	.	.	ENSG00000163386	ENST00000369339;ENST00000342960	T	0.03094	4.05	1.06	-0.231	0.13086	.	.	.	.	.	T	0.00875	0.0029	L	0.46157	1.445	0.09310	N	1	B	0.06786	0.001	B	0.11329	0.006	T	0.48456	-0.9034	9	0.11794	T	0.64	.	3.1661	0.06536	0.7225:0.0:0.2775:0.0	rs12565078;rs57282873	37	A8MQ30	.	S	37	ENSP00000345684:N37S	ENSP00000345684:N37S	N	+	2	0	NBPF10	144004872	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	0.914000	0.28624	-0.082000	0.12640	-1.412000	0.01120	AAC	A|0.731;G|0.269	0.269	strong		0.478	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
C10orf120	399814	hgsc.bcm.edu	37	10	124457906	124457906	+	Silent	SNP	C	C	T	rs2901343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124457906C>T	ENST00000329446.4	-	3	382	c.351G>A	c.(349-351)ccG>ccA	p.P117P		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	117										endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				GTTTGTAGTCCGGAGACAGCA	0.448													C|||	2208	0.440895	0.4062	0.3343	5008	,	,		21925	0.5179		0.4046	False		,,,				2504	0.5215				p.P117P		Atlas-SNP	.											.	C10orf120	55	.	0			c.G351A						PASS	.	C		1826,2580	533.4+/-373.7	390,1046,767	199.0	207.0	204.0		351	-5.8	0.0	10	dbSNP_101	204	3552,5048	517.2+/-379.0	737,2078,1485	no	coding-synonymous	C10orf120	NM_001010912.1		1127,3124,2252	TT,TC,CC		41.3023,41.4435,41.3501		117/336	124457906	5378,7628	2203	4300	6503	SO:0001819	synonymous_variant	399814	exon3			GTAGTCCGGAGAC		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.351G>A	10.37:g.124457906C>T		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	195	82	0.420513	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1	942	0.43131868131868134	220	0.44715447154471544	144	0.39779005524861877	277	0.48426573426573427	301	0.3970976253298153	C	3.300	-0.143157	0.06669	0.414435	0.413023	ENSG00000183559	ENST00000432000	.	.	.	4.82	-5.83	0.02325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38329	-0.9666	3	.	.	.	-0.0498	8.0998	0.30850	0.0:0.4681:0.1245:0.4073	rs2901343;rs60009641;rs2901343	.	.	.	Q	110	.	.	R	-	2	0	C10orf120	124447896	0.076000	0.21285	0.000000	0.03702	0.001000	0.01503	-0.598000	0.05706	-1.334000	0.02244	-1.379000	0.01178	CGG	C|0.580;T|0.420	0.420	strong		0.448	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
MYO9A	4649	hgsc.bcm.edu	37	15	72180440	72180440	+	Silent	SNP	C	C	T	rs148060237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:72180440C>T	ENST00000356056.5	-	27	5632	c.5160G>A	c.(5158-5160)tcG>tcA	p.S1720S	MYO9A_ENST00000564571.1_Silent_p.S1720S|MYO9A_ENST00000424560.1_Silent_p.S1791S|MYO9A_ENST00000563542.1_5'Flank|MYO9A_ENST00000444904.1_Silent_p.S1701S	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1720	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CATCAACTGACGAAAATCGCT	0.333													C|||	38	0.00758786	0.0008	0.0072	5008	,	,		17410	0.0		0.0288	False		,,,				2504	0.0031				p.S1720S		Atlas-SNP	.											.	MYO9A	203	.	0			c.G5160A						PASS	.	C		17,4379	24.3+/-50.5	0,17,2181	119.0	110.0	113.0		5160	0.3	1.0	15	dbSNP_134	113	186,8408	84.0+/-146.5	1,184,4112	no	coding-synonymous	MYO9A	NM_006901.2		1,201,6293	TT,TC,CC		2.1643,0.3867,1.5627		1720/2549	72180440	203,12787	2198	4297	6495	SO:0001819	synonymous_variant	4649	exon27			AACTGACGAAAAT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5160G>A	15.37:g.72180440C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	92	45	0.48913	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Silent	SNP	ENST00000356056.5	37	CCDS10239.1																																																																																			C|0.983;T|0.017	0.017	strong		0.333	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
FLT4	2324	hgsc.bcm.edu	37	5	180043388	180043388	+	Silent	SNP	G	G	A	rs1130378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:180043388G>A	ENST00000261937.6	-	23	3276	c.3198C>T	c.(3196-3198)ccC>ccT	p.P1066P	FLT4_ENST00000502649.1_Silent_p.P1066P|FLT4_ENST00000393347.3_Silent_p.P1066P	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1066	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	GGACGTAGTCGGGGTCTTTGT	0.597													A|||	1204	0.240415	0.1566	0.1888	5008	,	,		20056	0.2619		0.2823	False		,,,				2504	0.3252				p.P1066P	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C3198T						PASS	.	A	,	749,3657	753.7+/-412.4	64,621,1518	114.0	104.0	108.0		3198,3198	0.6	1.0	5	dbSNP_86	108	2536,6064	691.9+/-404.5	393,1750,2157	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	457,2371,3675	AA,AG,GG		29.4884,16.9995,25.2576	,	1066/1299,1066/1364	180043388	3285,9721	2203	4300	6503	SO:0001819	synonymous_variant	2324	exon23			GTAGTCGGGGTCT	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.3198C>T	5.37:g.180043388G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.751;A|0.249	0.249	strong		0.597	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
KCNQ1	3784	hgsc.bcm.edu	37	11	2869086	2869086	+	Silent	SNP	C	C	T	rs144610043|rs397508102		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2869086C>T	ENST00000155840.5	+	16	1992	c.1884C>T	c.(1882-1884)ggC>ggT	p.G628G	KCNQ1_ENST00000335475.5_Silent_p.G501G|KCNQ1-AS1_ENST00000440887.2_RNA|KCNQ1_ENST00000526095.1_3'UTR	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	628				LHGGSTPGSGGPPREGGAHITQPCGS -> MQQGGPTCNSR SQVVASNE (in Ref. 4; AAM94040). {ECO:0000305}.	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)	CCGGCAGCGGCGGCCCCCCCA	0.701																																					p.G628G		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1884T						PASS	.						10.0	10.0	10.0					11																	2869086		2141	4219	6360	SO:0001819	synonymous_variant	3784	exon16			CAGCGGCGGCCCC	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.1884C>T	11.37:g.2869086C>T		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	66	36	0.545455	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			.	.	none		0.701	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634313	32634313	+	Missense_Mutation	SNP	C	C	G	rs1049059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32634313C>G	ENST00000399082.3	-	1	116	c.72G>C	c.(70-72)atG>atC	p.M24I	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.M24I|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.M24I|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.M24I|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.M24I			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	24			M -> I (in allele DQB1*05:01 and allele DQB1*05:02; dbSNP:rs1049059).		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)"""	GGGAGCTCAGCATCGCCAGCA	0.592									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1079	0.215455	0.2292	0.1556	5008	,	,		9016	0.246		0.1998	False		,,,				2504	0.2239				p.M24I	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G72C						PASS	.	C	ILE/MET	827,3095		135,557,1269	53.0	51.0	52.0		72	3.3	0.8	6	dbSNP_86	52	1504,6734		266,972,2881	yes	missense	HLA-DQB1	NM_002123.4	10	401,1529,4150	GG,GC,CC		18.2569,21.0862,19.1694	benign	24/262	32634313	2331,9829	1961	4119	6080	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GCTCAGCATCGCC		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.72G>C	6.37:g.32634313C>G	ENSP00000382032:p.Met24Ile	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	30	23	0.766667	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		452	0.20695970695970695	119	0.241869918699187	68	0.1878453038674033	95	0.1660839160839161	170	0.22427440633245382	.	11.84	1.758307	0.31137	0.210862	0.182569	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T;T	0.05319	3.84;3.46;3.46;3.46;3.46	4.16	3.26	0.37387	.	1626.350000	0.00559	U	0.000273	T	0.03095	0.0091	L	0.45581	1.43	0.58432	P	6.999999999979245E-6	B;B;B;B	0.11235	0.004;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.0;0.0;0.0	T	0.33879	-0.9851	9	0.72032	D	0.01	.	8.968	0.35887	0.2209:0.7791:0.0:0.0	rs1049059;rs3189135;rs12722100;rs17416190;rs35062088	34;24;24;24	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	I	24	ENSP00000382032:M24I;ENSP00000382029:M24I;ENSP00000364080:M24I;ENSP00000407332:M24I;ENSP00000382034:M24I	ENSP00000364080:M24I	M	-	3	0	HLA-DQB1	32742291	0.969000	0.33509	0.824000	0.32777	0.039000	0.13416	0.620000	0.24403	0.933000	0.37291	0.298000	0.19748	ATG	C|0.813;G|0.187	0.187	strong		0.592	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
IL17RC	84818	hgsc.bcm.edu	37	3	9965582	9965582	+	Missense_Mutation	SNP	G	G	A	rs75692599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9965582G>A	ENST00000295981.3	+	8	1071	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	IL17RC_ENST00000383812.4_Missense_Mutation_p.V199M|IL17RC_ENST00000455057.1_Missense_Mutation_p.V199M|IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000416074.2_Missense_Mutation_p.V70M|IL17RC_ENST00000413608.1_Missense_Mutation_p.V214M|IL17RC_ENST00000403601.3_Missense_Mutation_p.V214M	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	285					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						CTGGCTCAACGTGTCAGCAGA	0.567													G|||	24	0.00479233	0.003	0.0058	5008	,	,		19241	0.0		0.0159	False		,,,				2504	0.0				p.V285M		Atlas-SNP	.											.	IL17RC	55	.	0			c.G853A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	10,4396	16.8+/-37.8	0,10,2193	83.0	76.0	78.0		640,640,595,595,640,853	2.2	0.1	3	dbSNP_131	78	202,8398	87.9+/-150.2	5,192,4103	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	21,21,21,21,21,21	5,202,6296	AA,AG,GG		2.3488,0.227,1.63	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	214/708,214/691,199/689,199/706,214/721,285/792	9965582	212,12794	2203	4300	6503	SO:0001583	missense	84818	exon8			CTCAACGTGTCAG	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.853G>A	3.37:g.9965582G>A	ENSP00000295981:p.Val285Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	15	0.006868131868131868	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	11	0.014511873350923483	G	8.788	0.929765	0.18131	0.00227	0.023488	ENSG00000163702	ENST00000383812;ENST00000438091;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	5.47	2.2	0.27929	.	0.636179	0.13137	N	0.410970	T	0.17577	0.0422	M	0.64997	1.995	0.09310	N	1	D;D;P;P;D;D;D;D;D	0.76494	0.981;0.999;0.943;0.943;0.994;0.99;0.966;0.997;0.997	B;P;B;B;P;P;B;P;P	0.57283	0.428;0.817;0.246;0.246;0.557;0.557;0.428;0.654;0.704	T	0.06625	-1.0816	10	0.62326	D	0.03	-8.7325	4.2685	0.10775	0.0961:0.1562:0.5875:0.1602	.	199;70;199;214;214;214;199;285;214	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;I17RC_HUMAN;.	M	199;174;285;189;214;70;199;214	ENSP00000373323:V199M;ENSP00000414609:V174M;ENSP00000295981:V285M;ENSP00000401128:V189M;ENSP00000384969:V214M;ENSP00000395315:V70M;ENSP00000407894:V199M;ENSP00000396064:V214M	ENSP00000295981:V285M	V	+	1	0	IL17RC	9940582	0.951000	0.32395	0.104000	0.21259	0.258000	0.26162	1.493000	0.35605	0.687000	0.31509	0.638000	0.83543	GTG	G|0.988;A|0.012	0.012	strong		0.567	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
KCNMB1	3779	hgsc.bcm.edu	37	5	169805956	169805956	+	Missense_Mutation	SNP	C	C	G	rs2301149	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:169805956C>G	ENST00000274629.4	-	4	770	c.328G>C	c.(328-330)Gtg>Ctg	p.V110L	KCNIP1_ENST00000518527.1_Intron|KCNIP1_ENST00000377360.4_Intron	NM_004137.3	NP_004128.1	Q16558	KCMB1_HUMAN	potassium large conductance calcium-activated channel, subfamily M, beta member 1	110			V -> L (in dbSNP:rs2301149).		blood coagulation (GO:0007596)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|response to calcium ion (GO:0051592)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|potassium channel regulator activity (GO:0015459)			endometrium(1)|large_intestine(1)|lung(7)|ovary(2)	11	Renal(175;0.000159)|Lung NSC(126;0.0165)|all_lung(126;0.026)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.175)	Miconazole(DB01110)|Procaine(DB00721)	TAATTGTCCACGCTGCCTGGG	0.547													G|||	617	0.123203	0.1316	0.111	5008	,	,		16028	0.1339		0.1004	False		,,,				2504	0.1329				p.E110Q		Atlas-SNP	.											KCNMB1,NS,carcinoma,0,1	KCNMB1	38	1	0			c.G328C						PASS	.	G	,LEU/VAL	466,3940	782.7+/-414.6	24,418,1761	62.0	64.0	63.0		,328	3.0	1.0	5	dbSNP_100	63	725,7875	785.9+/-407.6	36,653,3611	yes	intron,missense	KCNMB1,KCNIP1	NM_001034838.1,NM_004137.2	,32	60,1071,5372	GG,GC,CC		8.4302,10.5765,9.1573	,benign	,110/192	169805956	1191,11815	2203	4300	6503	SO:0001583	missense	3779	exon4			TGTCCACGCTGCC	AF035046	CCDS4373.1	5q34	2012-02-23			ENSG00000145936	ENSG00000145936		"""Potassium channels"""	6285	protein-coding gene	gene with protein product	"""BK channel beta subunit"""	603951				8799178, 9888999	Standard	NM_004137		Approved	hslo-beta	uc003maq.2	Q16558	OTTHUMG00000130439	ENST00000274629.4:c.328G>C	5.37:g.169805956C>G	ENSP00000274629:p.Val110Leu	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	101	60	0.594059	NM_004137	O00707|O00708|P78475|Q53YR0|Q8TAX3|Q93005	Missense_Mutation	SNP	ENST00000274629.4	37	CCDS4373.1	235	0.10760073260073261	53	0.10772357723577236	47	0.1298342541436464	70	0.12237762237762238	65	0.08575197889182058	G	9.771	1.172679	0.21704	0.105765	0.084302	ENSG00000145936	ENST00000274629	T	0.08984	3.03	5.17	3.03	0.35002	.	0.407302	0.25175	N	0.032575	T	0.00039	0.0001	N	0.00347	-1.61	0.09310	P	0.99999999356255	B	0.02656	0.0	B	0.01281	0.0	T	0.38286	-0.9668	8	.	.	.	.	6.0615	0.19841	0.184:0.2949:0.5211:0.0	rs2301149;rs57496667;rs2301149	110	Q16558	KCMB1_HUMAN	L	110	ENSP00000274629:V110L	.	V	-	1	0	KCNMB1	169738534	1.000000	0.71417	0.996000	0.52242	0.461000	0.32589	1.632000	0.37102	0.580000	0.29522	-0.335000	0.08231	GTG	C|0.898;G|0.102	0.102	strong		0.547	KCNMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252830.3		
MUC4	4585	hgsc.bcm.edu	37	3	195506752	195506752	+	Missense_Mutation	SNP	C	C	T	rs554841787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506752C>T	ENST00000463781.3	-	2	12158	c.11699G>A	c.(11698-11700)cGt>cAt	p.R3900H	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.R3900H	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)		GGTGGCGTGACGTGTGGATGC	0.587													.|||	63	0.0125799	0.0	0.0086	5008	,	,		8251	0.003		0.0149	False		,,,				2504	0.0399				p.R3900H		Atlas-SNP	.											.	MUC4	1505	.	0			c.G11699A						PASS	.						10.0	9.0	9.0					3																	195506752		525	990	1515	SO:0001583	missense	4585	exon2			GCGTGACGTGTGG	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.11699G>A	3.37:g.195506752C>T	ENSP00000417498:p.Arg3900His	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	70	23	0.328571	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	6.268	0.417524	0.11870	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.52;1.57	.	.	.	.	.	.	.	.	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	1	P	0.35793	0.521	B	0.11329	0.006	T	0.18147	-1.0346	7	.	.	.	.	2.8356	0.05513	0.4983:0.5012:2.0E-4:3.0E-4	.	3772	E7ESK3	.	H	3900	ENSP00000417498:R3900H;ENSP00000420243:R3900H	.	R	-	2	0	MUC4	196991531	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.055000	0.11807	0.064000	0.16427	0.064000	0.15345	CGT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLFN11	91607	hgsc.bcm.edu	37	17	33690619	33690619	+	Missense_Mutation	SNP	G	G	T	rs72825958	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33690619G>T	ENST00000394566.1	-	4	480	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	SLFN11_ENST00000308377.4_Missense_Mutation_p.P70T	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	70					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)			autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		ATCTCCACGGGATGCTCAACC	0.458													G|||	435	0.086861	0.1104	0.0965	5008	,	,		18989	0.001		0.172	False		,,,				2504	0.0491				p.P70T		Atlas-SNP	.											.	SLFN11	112	.	0			c.C208A						PASS	.	G	THR/PRO,THR/PRO,THR/PRO,THR/PRO,THR/PRO	515,3891	237.1+/-249.0	28,459,1716	149.0	142.0	144.0		208,208,208,208,208	1.4	0.0	17	dbSNP_130	144	1474,7126	280.8+/-294.7	149,1176,2975	yes	missense,missense,missense,missense,missense	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	38,38,38,38,38	177,1635,4691	TT,TG,GG		17.1395,11.6886,15.2929	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	70/902,70/902,70/902,70/902,70/902	33690619	1989,11017	2203	4300	6503	SO:0001583	missense	91607	exon2			CCACGGGATGCTC	AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.208C>A	17.37:g.33690619G>T	ENSP00000378067:p.Pro70Thr	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	152	74	0.486842	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	208	0.09523809523809523	48	0.0975609756097561	42	0.11602209944751381	1	0.0017482517482517483	117	0.15435356200527706	G	7.878	0.729570	0.15507	0.116886	0.171395	ENSG00000172716	ENST00000308377;ENST00000394566;ENST00000430814;ENST00000441608;ENST00000427966	T;T;T;T;T	0.22134	4.58;4.58;1.97;2.31;1.97	3.67	1.41	0.22369	.	0.273855	0.20421	N	0.092676	T	0.00039	0.0001	M	0.65498	2.005	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.14811	-1.0459	9	0.20519	T	0.43	.	5.7866	0.18336	0.0:0.219:0.5556:0.2254	.	70	Q7Z7L1	SLN11_HUMAN	T	70	ENSP00000312402:P70T;ENSP00000378067:P70T;ENSP00000397454:P70T;ENSP00000393615:P70T;ENSP00000395140:P70T	ENSP00000312402:P70T	P	-	1	0	SLFN11	30714732	0.002000	0.14202	0.001000	0.08648	0.008000	0.06430	0.264000	0.18497	0.869000	0.35703	0.655000	0.94253	CCC	G|0.859;T|0.141	0.141	strong		0.458	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270	
PSD4	23550	hgsc.bcm.edu	37	2	113943470	113943470	+	Silent	SNP	A	A	G	rs2241976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113943470A>G	ENST00000245796.6	+	5	1461	c.1266A>G	c.(1264-1266)ggA>ggG	p.G422G	PSD4_ENST00000441564.3_Intron	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	422					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGGAGGGTGGACACCCCCAGG	0.642													G|||	2892	0.577476	0.7352	0.5187	5008	,	,		17134	0.6012		0.4523	False		,,,				2504	0.5102				p.G422G		Atlas-SNP	.											.	PSD4	74	.	0			c.A1266G						PASS	.	G		3040,1366		1062,916,225	24.0	26.0	26.0		1266	-0.1	0.0	2	dbSNP_98	26	3595,5005		763,2069,1468	no	coding-synonymous	PSD4	NM_012455.2		1825,2985,1693	GG,GA,AA		41.8023,31.0032,48.9851		422/1057	113943470	6635,6371	2203	4300	6503	SO:0001819	synonymous_variant	23550	exon5			GGGTGGACACCCC	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.1266A>G	2.37:g.113943470A>G		Somatic	177	1	0.00564972		WXS	Illumina HiSeq	Phase_I	164	159	0.969512	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	37	CCDS33276.1																																																																																			A|0.460;G|0.540	0.540	strong		0.642	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
R3HDM4	91300	hgsc.bcm.edu	37	19	899444	899444	+	Silent	SNP	C	C	T	rs2965284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:899444C>T	ENST00000361574.5	-	7	772	c.699G>A	c.(697-699)tcG>tcA	p.S233S	R3HDM4_ENST00000587975.1_Silent_p.S212S	NM_138774.3	NP_620129.2	Q96D70	R3HD4_HUMAN	R3H domain containing 4	233	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)										ACTTACTGGCCGAGATGAGGT	0.657													C|||	408	0.0814696	0.0159	0.1081	5008	,	,		12934	0.0109		0.1809	False		,,,				2504	0.1217				p.S233S		Atlas-SNP	.											C19orf22,NS,carcinoma,0,1	.	.	1	0			c.G699A						PASS	.	C		177,4229	114.6+/-152.6	5,167,2031	46.0	47.0	47.0		699	-7.7	1.0	19	dbSNP_101	47	1656,6944	300.6+/-305.0	170,1316,2814	no	coding-synonymous	C19orf22	NM_138774.3		175,1483,4845	TT,TC,CC		19.2558,4.0172,14.0935		233/269	899444	1833,11173	2203	4300	6503	SO:0001819	synonymous_variant	91300	exon7			ACTGGCCGAGATG	BC012775	CCDS12048.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000198858	ENSG00000198858			28270	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 22"""	C19orf22		12477932	Standard	NM_138774		Approved	MGC16353	uc002lqg.2	Q96D70		ENST00000361574.5:c.699G>A	19.37:g.899444C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	73	36	0.493151	NM_138774		Silent	SNP	ENST00000361574.5	37	CCDS12048.1																																																																																			C|0.877;T|0.123	0.123	strong		0.657	R3HDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458209.1	NM_138774	
IGSF3	3321	hgsc.bcm.edu	37	1	117122130	117122130	+	Missense_Mutation	SNP	T	T	C	rs6703791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:117122130T>C	ENST00000369486.3	-	10	3983	c.3218A>G	c.(3217-3219)cAa>cGa	p.Q1073R	IGSF3_ENST00000369483.1_Missense_Mutation_p.Q1093R|IGSF3_ENST00000318837.6_Missense_Mutation_p.Q1093R	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1073	Ig-like C2-type 8.		Q -> R (in dbSNP:rs6703791).		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)		GCCTGTATCTTGGGGGCTTGC	0.632													C|||	1724	0.344249	0.3472	0.304	5008	,	,		19301	0.5169		0.167	False		,,,				2504	0.3732				p.Q1093R		Atlas-SNP	.											.	IGSF3	294	.	0			c.A3278G						PASS	.	C	ARG/GLN,ARG/GLN	1555,2851	667.5+/-401.9	285,985,933	47.0	50.0	49.0		3218,3278	-4.5	0.0	1	dbSNP_116	49	1560,7040	743.0+/-407.2	137,1286,2877	yes	missense,missense	IGSF3	NM_001007237.1,NM_001542.2	43,43	422,2271,3810	CC,CT,TT		18.1395,35.2928,23.9505	benign,benign	1073/1195,1093/1215	117122130	3115,9891	2203	4300	6503	SO:0001583	missense	3321	exon11			GTATCTTGGGGGC	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.3218A>G	1.37:g.117122130T>C	ENSP00000358498:p.Gln1073Arg	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	720	0.32967032967032966	175	0.3556910569105691	106	0.292817679558011	316	0.5524475524475524	123	0.16226912928759896	C	0.016	-1.511898	0.00984	0.352928	0.181395	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.21191	2.02;2.02;2.02	4.67	-4.48	0.03515	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.403970	0.04240	N	0.336820	T	0.03827	0.0108	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	0.31364	-0.9946	9	0.16420	T	0.52	-7.9962	15.5741	0.76362	0.0:0.1649:0.0:0.8351	rs6703791;rs56967300;rs6703791	1073;1093	O75054;A6NJZ6	IGSF3_HUMAN;.	R	1073;1093;1093	ENSP00000358498:Q1073R;ENSP00000358495:Q1093R;ENSP00000321184:Q1093R	ENSP00000321184:Q1093R	Q	-	2	0	IGSF3	116923653	0.000000	0.05858	0.001000	0.08648	0.063000	0.16089	-0.212000	0.09319	-1.780000	0.01279	-1.403000	0.01137	CAA	T|0.725;C|0.275	0.275	strong		0.632	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
QRFPR	84109	hgsc.bcm.edu	37	4	122301622	122301622	+	Missense_Mutation	SNP	A	A	C	rs17438900	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:122301622A>C	ENST00000394427.2	-	1	592	c.181T>G	c.(181-183)Ttt>Gtt	p.F61V	QRFPR_ENST00000334383.5_Missense_Mutation_p.F61V	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	61			F -> V (in dbSNP:rs17438900).		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)	p.F61V(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GCATTGCCAAAGAGCGCCAGG	0.627													A|||	507	0.101238	0.0189	0.1484	5008	,	,		15024	0.0704		0.2266	False		,,,				2504	0.0818				p.F61V		Atlas-SNP	.											QRFPR,NS,carcinoma,0,1	QRFPR	65	1	1	Substitution - Missense(1)	prostate(1)	c.T181G						PASS	.	A	VAL/PHE	248,4158	142.3+/-177.5	9,230,1964	73.0	62.0	65.0		181	3.9	1.0	4	dbSNP_123	65	1997,6603	349.2+/-327.3	234,1529,2537	yes	missense	QRFPR	NM_198179.2	50	243,1759,4501	CC,CA,AA		23.2209,5.6287,17.2613	benign	61/432	122301622	2245,10761	2203	4300	6503	SO:0001583	missense	84109	exon1			TGCCAAAGAGCGC	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.181T>G	4.37:g.122301622A>C	ENSP00000377948:p.Phe61Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	166	165	0.993976	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	279	0.12774725274725274	10	0.02032520325203252	50	0.13812154696132597	46	0.08041958041958042	173	0.22823218997361477	A	5.780	0.328349	0.10956	0.056287	0.232209	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.35421	1.31;1.31	5.18	3.92	0.45320	.	0.213542	0.49305	D	0.000148	T	0.00012	0.0000	N	0.20986	0.625	0.22787	P	0.99873549	B;B;B	0.13145	0.001;0.003;0.007	B;B;B	0.12837	0.001;0.003;0.008	T	0.12142	-1.0559	9	0.02654	T	1	.	11.4128	0.49935	0.8489:0.1511:0.0:0.0	rs17438900;rs52798239;rs17438900	61;61;61	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	V	61	ENSP00000377948:F61V;ENSP00000335610:F61V	ENSP00000335610:F61V	F	-	1	0	QRFPR	122521072	0.982000	0.34865	0.999000	0.59377	0.993000	0.82548	2.020000	0.41010	1.930000	0.55929	0.383000	0.25322	TTT	A|0.852;C|0.147	0.147	strong		0.627	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
FAT4	79633	hgsc.bcm.edu	37	4	126237971	126237971	+	Silent	SNP	C	C	T	rs72928772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:126237971C>T	ENST00000394329.3	+	1	418	c.405C>T	c.(403-405)ttC>ttT	p.F135F		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	135	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCCCCGTTTTCCCGGACCCCT	0.607											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	653	0.130391	0.0696	0.1354	5008	,	,		17170	0.0982		0.2197	False		,,,				2504	0.1503				p.F135F		Atlas-SNP	.											.	FAT4	1752	.	0			c.C405T						PASS	.	C		353,3723		14,325,1699	33.0	38.0	36.0		405	5.4	1.0	4	dbSNP_130	36	1818,6592		193,1432,2580	no	coding-synonymous	FAT4	NM_024582.4		207,1757,4279	TT,TC,CC		21.6171,8.6605,17.3875		135/4982	126237971	2171,10315	2038	4205	6243	SO:0001819	synonymous_variant	79633	exon1			CGTTTTCCCGGAC	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.405C>T	4.37:g.126237971C>T		Somatic	76	0	0	1548	WXS	Illumina HiSeq	Phase_I	56	56	1	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			C|0.831;T|0.169	0.169	strong		0.607	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FSD1L	83856	hgsc.bcm.edu	37	9	108230553	108230553	+	Missense_Mutation	SNP	G	G	T	rs41316532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:108230553G>T	ENST00000481272.1	+	4	406	c.287G>T	c.(286-288)aGt>aTt	p.S96I	FSD1L_ENST00000495708.1_Missense_Mutation_p.S96I|FSD1L_ENST00000480279.1_3'UTR|FSD1L_ENST00000374710.3_Missense_Mutation_p.S64I|FSD1L_ENST00000394926.3_Missense_Mutation_p.S64I|FSD1L_ENST00000484973.1_Missense_Mutation_p.S64I|FSD1L_ENST00000539376.1_5'UTR|FSD1L_ENST00000374716.4_Missense_Mutation_p.S64I	NM_001145313.1	NP_001138785.1	Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing 1-like	96										NS(1)|endometrium(1)	2						GTAAAAGAAAGTATGATTAAC	0.303													G|||	21	0.00419329	0.0008	0.0029	5008	,	,		15362	0.0		0.0119	False		,,,				2504	0.0061				p.S96I		Atlas-SNP	.											.	FSD1L	31	.	0			c.G287T						PASS	.	G	ILE/SER,ILE/SER,ILE/SER	3,1381		0,3,689	105.0	97.0	99.0		287,191,191	6.0	1.0	9	dbSNP_127	99	29,3143		0,29,1557	yes	missense,missense,missense	FSD1L	NM_001145313.1,NM_031919.3,NM_207647.2	142,142,142	0,32,2246	TT,TG,GG		0.9142,0.2168,0.7024	benign,benign,benign	96/531,64/146,64/499	108230553	32,4524	692	1586	2278	SO:0001583	missense	83856	exon4			AAGAAAGTATGAT	AF316830	CCDS6765.2, CCDS47999.1, CCDS6765.3, CCDS75870.1	9q31	2013-02-11	2006-03-10	2006-03-10	ENSG00000106701	ENSG00000106701		"""Fibronectin type III domain containing"""	13753	protein-coding gene	gene with protein product		609829	"""cystatin and DUF19 domain containing 1"", ""coiled-coil domain containing 10"""	CSDUFD1, CCDC10, FSD1NL, FSD1CL		11267680	Standard	XM_005252254		Approved		uc004bcq.2	Q9BXM9	OTTHUMG00000020426	ENST00000481272.1:c.287G>T	9.37:g.108230553G>T	ENSP00000417492:p.Ser96Ile	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	156	77	0.49359	NM_001145313	A2A338|A6NKH7|B7Z5S6|B7Z5W3|Q5T879|Q5T880	Missense_Mutation	SNP	ENST00000481272.1	37	CCDS47999.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	21.6	4.170296	0.78452	0.002168	0.009142	ENSG00000106701	ENST00000495708;ENST00000374716;ENST00000374710;ENST00000481272;ENST00000484973;ENST00000394926	T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89	5.98	5.98	0.97165	.	0.000000	0.64402	U	0.000001	T	0.47691	0.1459	L	0.51422	1.61	0.80722	D	1	B;D;D;D	0.57257	0.222;0.964;0.979;0.958	B;P;P;P	0.57960	0.405;0.68;0.83;0.731	T	0.33548	-0.9864	10	0.33141	T	0.24	.	19.208	0.93742	0.0:0.0:1.0:0.0	rs41316532;rs62575097	64;96;64;64	F8W946;Q9BXM9;Q9BXM9-2;Q9BXM9-3	.;FSD1L_HUMAN;.;.	I	96;64;64;96;64;64	ENSP00000420624:S96I;ENSP00000363848:S64I;ENSP00000363842:S64I;ENSP00000417492:S96I;ENSP00000419691:S64I;ENSP00000378384:S64I	ENSP00000363842:S64I	S	+	2	0	FSD1L	107270374	1.000000	0.71417	0.988000	0.46212	0.996000	0.88848	5.539000	0.67199	2.843000	0.97960	0.585000	0.79938	AGT	G|0.992;T|0.008	0.008	strong		0.303	FSD1L-007	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349935.1	NM_207647	
HYDIN	54768	hgsc.bcm.edu	37	16	71025245	71025245	+	Silent	SNP	C	C	T	rs1774516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	140	6	0.0428571		WXS	Illumina HiSeq	Phase_I	184	19	0.103261	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		
BEND7	222389	hgsc.bcm.edu	37	10	13534851	13534851	+	Silent	SNP	A	A	G	rs2251555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13534851A>G	ENST00000396900.2	-	5	596	c.597T>C	c.(595-597)ccT>ccC	p.P199P	BEND7_ENST00000341083.3_Silent_p.P147P|BEND7_ENST00000378605.3_Silent_p.P160P|BEND7_ENST00000396898.2_Silent_p.P212P			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	199						extracellular vesicular exosome (GO:0070062)		p.P147P(1)|p.P160P(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						GGGAAATTGGAGGTTGTTGTC	0.413													G|||	2407	0.480631	0.4887	0.5533	5008	,	,		19988	0.3403		0.5378	False		,,,				2504	0.5041				p.P160P		Atlas-SNP	.											BEND7_ENST00000378605,colon,carcinoma,0,4	BEND7	85	4	2	Substitution - coding silent(2)	stomach(2)	c.T480C						PASS	.	G	,	2261,2143	543.9+/-376.4	580,1101,521	71.0	73.0	73.0		480,441	4.5	1.0	10	dbSNP_100	73	4934,3666	513.7+/-378.2	1412,2110,778	no	coding-synonymous,coding-synonymous	BEND7	NM_001100912.1,NM_152751.2	,	1992,3211,1299	GG,GA,AA		42.6279,48.6603,44.6709	,	160/375,147/469	13534851	7195,5809	2202	4300	6502	SO:0001819	synonymous_variant	222389	exon4			AATTGGAGGTTGT	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.597T>C	10.37:g.13534851A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	83	52	0.626506	NM_001100912	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				A|0.476;G|0.524	0.524	strong		0.413	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
FAM129A	116496	hgsc.bcm.edu	37	1	184801065	184801065	+	Silent	SNP	T	T	C	rs487675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:184801065T>C	ENST00000367511.3	-	6	826	c.633A>G	c.(631-633)caA>caG	p.Q211Q	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	211					negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						CTAAAAAGGCTTGGGCTTCAA	0.418													T|||	1421	0.283746	0.3812	0.2363	5008	,	,		19811	0.1558		0.3429	False		,,,				2504	0.2566				p.Q211Q		Atlas-SNP	.											FAM129A,colon,carcinoma,0,1	FAM129A	98	1	0			c.A633G						PASS	.	T		1616,2790	494.5+/-363.0	291,1034,878	88.0	88.0	88.0		633	5.5	1.0	1	dbSNP_83	88	2927,5673	452.1+/-362.9	488,1951,1861	no	coding-synonymous	FAM129A	NM_052966.2		779,2985,2739	CC,CT,TT		34.0349,36.6773,34.93		211/929	184801065	4543,8463	2203	4300	6503	SO:0001819	synonymous_variant	116496	exon6			AAAGGCTTGGGCT	AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.633A>G	1.37:g.184801065T>C		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	133	63	0.473684	NM_052966	Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Silent	SNP	ENST00000367511.3	37	CCDS1364.1																																																																																			T|0.682;C|0.318	0.318	strong		0.418	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1		
VEZF1	7716	hgsc.bcm.edu	37	17	56056550	56056550	+	Silent	SNP	C	C	G	rs1135655	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56056550C>G	ENST00000581208.1	-	5	1141	c.1101G>C	c.(1099-1101)ctG>ctC	p.L367L	VEZF1_ENST00000584396.1_Silent_p.L358L	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	367					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						CCCACAGTCTCAGTGTTTCTA	0.468													C|||	301	0.0601038	0.0817	0.0663	5008	,	,		18612	0.001		0.0974	False		,,,				2504	0.0491				p.L367L		Atlas-SNP	.											.	VEZF1	50	.	0			c.G1101C						PASS	.	C		381,4025	193.6+/-218.7	20,341,1842	324.0	284.0	298.0		1101	5.7	1.0	17	dbSNP_86	298	891,7709	200.0+/-243.9	42,807,3451	no	coding-synonymous	VEZF1	NM_007146.2		62,1148,5293	GG,GC,CC		10.3605,8.6473,9.7801		367/522	56056550	1272,11734	2203	4300	6503	SO:0001819	synonymous_variant	7716	exon5			CAGTCTCAGTGTT	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.1101G>C	17.37:g.56056550C>G		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	246	106	0.430894	NM_007146		Silent	SNP	ENST00000581208.1	37	CCDS32687.1																																																																																			C|0.907;G|0.093	0.093	strong		0.468	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
PCDHAC1	56135	hgsc.bcm.edu	37	5	140307746	140307746	+	Silent	SNP	C	C	G	rs155820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140307746C>G	ENST00000253807.2	+	1	1269	c.1269C>G	c.(1267-1269)ccC>ccG	p.P423P	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.P423P|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	423	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGCTCACCCCCACTTAGCA	0.507													c|||	1783	0.35603	0.23	0.3948	5008	,	,		19684	0.5476		0.333	False		,,,				2504	0.3252				p.P423P		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.C1269G						PASS	.	C	,,,,,,,,,,,,,,,,,	1120,3286	394.7+/-329.4	150,820,1233	73.0	73.0	73.0		1269,,,,,,,,,,,,,,,,,1269	1.8	0.4	5	dbSNP_79	73	2818,5782	437.7+/-358.7	448,1922,1930	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	598,2742,3163	GG,GC,CC		32.7674,25.4199,30.2783	,,,,,,,,,,,,,,,,,	423/964,,,,,,,,,,,,,,,,,423/819	140307746	3938,9068	2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			CTCACCCCCACTT	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1269C>G	5.37:g.140307746C>G		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	50	31	0.62	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			C|0.680;G|0.320	0.320	strong		0.507	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
USP14	9097	hgsc.bcm.edu	37	18	166819	166819	+	Splice_Site	SNP	T	T	C	rs563155	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:166819T>C	ENST00000261601.7	+	3	286	c.195T>C	c.(193-195)aaT>aaC	p.N65N	USP14_ENST00000582707.1_Splice_Site_p.N65N|USP14_ENST00000383589.2_Intron|USP14_ENST00000400266.3_Intron	NM_005151.3	NP_005142.1	P54578	UBP14_HUMAN	ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase)	65	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				negative regulation of endopeptidase activity (GO:0010951)|protein deubiquitination (GO:0016579)|regulation of chemotaxis (GO:0050920)|regulation of proteasomal protein catabolic process (GO:0061136)|synaptic transmission (GO:0007268)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|synapse (GO:0045202)	cysteine-type endopeptidase activity (GO:0004197)|endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)|tRNA guanylyltransferase activity (GO:0008193)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(2)	11		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				AAATAAAAAATGTAAGTATTA	0.294													T|||	774	0.154553	0.174	0.134	5008	,	,		14788	0.006		0.2117	False		,,,				2504	0.2372				p.N65N		Atlas-SNP	.											.	USP14	41	.	0			c.T195C						PASS	.	T	,	779,3627	313.3+/-293.0	67,645,1491	125.0	131.0	129.0		195,195	4.4	1.0	18	dbSNP_83	129	1914,6686	337.2+/-322.2	223,1468,2609	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	USP14	NM_001037334.1,NM_005151.3	,	290,2113,4100	CC,CT,TT		22.2558,17.6804,20.7058	,	65/460,65/495	166819	2693,10313	2203	4300	6503	SO:0001630	splice_region_variant	9097	exon3			AAAAAATGTAAGT	U30888	CCDS32780.1, CCDS32781.1	18p11.32	2006-10-06	2005-08-08			ENSG00000101557		"""Ubiquitin-specific peptidases"""	12612	protein-coding gene	gene with protein product		607274	"""ubiquitin specific protease 14 (tRNA-guanine transglycosylase)"""			12838346	Standard	NM_001037334		Approved	TGT	uc002kkf.1	P54578		ENST00000261601.7:c.195+1T>C	18.37:g.166819T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	32	32	1	NM_001037334	J3QRZ5|Q53XY5	Silent	SNP	ENST00000261601.7	37	CCDS32780.1																																																																																			T|0.812;C|0.188	0.188	strong		0.294	USP14-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440305.3	NM_005151	Silent
STAP2	55620	hgsc.bcm.edu	37	19	4324564	4324564	+	Intron	SNP	C	C	T	rs57455784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4324564C>T	ENST00000594605.1	-	12	1196				STAP2_ENST00000600324.1_Silent_p.V391V|STAP2_ENST00000597593.1_5'Flank	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2							cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)	23		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		tgtggtggctcacgccggtaa	0.567													t|||	513	0.102436	0.18	0.0735	5008	,	,		16606	0.0655		0.0686	False		,,,				2504	0.091				p.V391V		Atlas-SNP	.											STAP2,NS,carcinoma,-2,1	STAP2	38	1	0			c.G1173A						PASS	.		,	580,3726		36,508,1609	14.0	13.0	13.0		,1173	-0.8	0.0	19	dbSNP_129	13	586,7812		23,540,3636	no	intron,coding-synonymous	STAP2	NM_001013841.1,NM_017720.2	,	59,1048,5245	TT,TC,CC		6.9779,13.4696,9.1782	,	,391/450	4324564	1166,11538	2153	4199	6352	SO:0001627	intron_variant	55620	exon12			GTGGCTCACGCCG	AJ245719	CCDS12128.1, CCDS45926.1	19p13.3	2011-05-03	2007-08-09		ENSG00000178078	ENSG00000178078			30430	protein-coding gene	gene with protein product		607881				10980601, 11441184	Standard	XM_005259592		Approved	STAP-2, BKS	uc002mac.3	Q9UGK3		ENST00000594605.1:c.1073-38G>A	19.37:g.4324564C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	49	29	0.591837	NM_017720	A6NKK3|Q9NXI2	Silent	SNP	ENST00000594605.1	37	CCDS45926.1																																																																																			C|0.906;T|0.094	0.094	strong		0.567	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841	
ZNF543	125919	hgsc.bcm.edu	37	19	57838018	57838018	+	Missense_Mutation	SNP	C	C	G	rs6510057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57838018C>G	ENST00000321545.4	+	3	508	c.163C>G	c.(163-165)Cca>Gca	p.P55A		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	55	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		P -> A (in dbSNP:rs6510057). {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)		TTTGTTCAAACCAGAGCTGAT	0.493													c|||	2264	0.452077	0.5439	0.5043	5008	,	,		16382	0.2798		0.5308	False		,,,				2504	0.3875				p.P55A		Atlas-SNP	.											.	ZNF543	61	.	0			c.C163G						PASS	.	C	ALA/PRO	2399,2007	615.4+/-392.6	649,1101,453	82.0	76.0	78.0		163	0.2	0.1	19	dbSNP_116	78	4776,3824	610.7+/-395.7	1348,2080,872	yes	missense	ZNF543	NM_213598.3	27	1997,3181,1325	GG,GC,CC		44.4651,45.5515,44.8332	benign	55/601	57838018	7175,5831	2203	4300	6503	SO:0001583	missense	125919	exon3			TTCAAACCAGAGC	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.163C>G	19.37:g.57838018C>G	ENSP00000322545:p.Pro55Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	996	0.45604395604395603	246	0.5	177	0.4889502762430939	165	0.28846153846153844	408	0.5382585751978892	C	6.412	0.444210	0.12164	0.544485	0.555349	ENSG00000178229	ENST00000321545	T	0.00995	5.46	2.4	0.225	0.15325	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	B	0.17465	0.022	B	0.14578	0.011	T	0.16100	-1.0414	8	0.51188	T	0.08	.	4.3985	0.11374	0.0:0.6549:0.0:0.3451	rs6510057;rs17373672;rs6510057	55	Q08ER8	ZN543_HUMAN	A	55	ENSP00000322545:P55A	ENSP00000322545:P55A	P	+	1	0	ZNF543	62529830	0.001000	0.12720	0.134000	0.22075	0.064000	0.16182	0.584000	0.23864	0.120000	0.18254	0.467000	0.42956	CCA	C|0.496;G|0.504	0.504	strong		0.493	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
DCBLD2	131566	hgsc.bcm.edu	37	3	98619997	98619997	+	Silent	SNP	G	G	C	rs17852693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:98619997G>C	ENST00000326840.6	-	1	536	c.174C>G	c.(172-174)ctC>ctG	p.L58L	CTD-2021J15.1_ENST00000474798.1_RNA|DCBLD2_ENST00000326857.9_Silent_p.L58L|DCBLD2_ENST00000469648.1_5'Flank	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	58					cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						Cgagcagcaggagcaggacaa	0.682													G|||	751	0.14996	0.2171	0.0922	5008	,	,		13967	0.0446		0.165	False		,,,				2504	0.1933				p.L58L		Atlas-SNP	.											.	DCBLD2	62	.	0			c.C174G						PASS	.	G		662,2882		59,544,1169	15.0	18.0	17.0		174	1.2	0.9	3	dbSNP_123	17	930,6334		59,812,2761	no	coding-synonymous	DCBLD2	NM_080927.3		118,1356,3930	CC,CG,GG		12.8029,18.6795,14.7298		58/776	98619997	1592,9216	1772	3632	5404	SO:0001819	synonymous_variant	131566	exon1			CAGCAGGAGCAGG		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.174C>G	3.37:g.98619997G>C		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	26	14	0.538462	NM_080927	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Silent	SNP	ENST00000326840.6	37	CCDS46878.1																																																																																			G|0.859;C|0.141	0.141	strong		0.682	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927	
AGMAT	79814	hgsc.bcm.edu	37	1	15905501	15905501	+	Silent	SNP	G	G	A	rs41270261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15905501G>A	ENST00000375826.3	-	4	715	c.573C>T	c.(571-573)acC>acT	p.T191T	DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	191					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		GGGCCTTGTCGGTCGTGTCCG	0.642													G|||	462	0.0922524	0.087	0.1124	5008	,	,		16216	0.0308		0.1421	False		,,,				2504	0.0971				p.T191T	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											AGMAT,colon,carcinoma,0,1	AGMAT	25	1	0			c.C573T						PASS	.	G		401,4005	201.5+/-224.5	22,357,1824	63.0	60.0	61.0		573	-11.7	0.0	1	dbSNP_127	61	1212,7388	244.2+/-273.5	81,1050,3169	no	coding-synonymous	AGMAT	NM_024758.4		103,1407,4993	AA,AG,GG		14.093,9.1012,12.402		191/353	15905501	1613,11393	2203	4300	6503	SO:0001819	synonymous_variant	79814	exon4			CTTGTCGGTCGTG	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.573C>T	1.37:g.15905501G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	84	78	0.928571	NM_024758	Q5TDH1|Q9H5J3	Silent	SNP	ENST00000375826.3	37	CCDS160.1																																																																																			G|0.883;A|0.117	0.117	strong		0.642	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
VEPH1	79674	hgsc.bcm.edu	37	3	157131788	157131788	+	Missense_Mutation	SNP	A	A	C	rs1378796	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:157131788A>C	ENST00000362010.2	-	6	1095	c.788T>G	c.(787-789)gTc>gGc	p.V263G	VEPH1_ENST00000392832.2_Missense_Mutation_p.V263G|VEPH1_ENST00000392833.2_Missense_Mutation_p.V263G|VEPH1_ENST00000469007.1_5'UTR|VEPH1_ENST00000543418.1_Missense_Mutation_p.V263G	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	263			V -> G (in dbSNP:rs1378796). {ECO:0000269|PubMed:17974005}.			plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TGGCTCATAGACTGCTATCTC	0.413													C|||	965	0.192692	0.2171	0.0764	5008	,	,		18217	0.2292		0.1014	False		,,,				2504	0.2986				p.V263G		Atlas-SNP	.											.	VEPH1	129	.	0			c.T788G						PASS	.	C	GLY/VAL,GLY/VAL,GLY/VAL	875,3531	742.9+/-411.4	95,685,1423	130.0	128.0	128.0		788,788,788	4.1	0.0	3	dbSNP_88	128	803,7797	782.6+/-407.6	54,695,3551	yes	missense,missense,missense	VEPH1	NM_001167911.1,NM_001167912.1,NM_024621.2	109,109,109	149,1380,4974	CC,CA,AA		9.3372,19.8593,12.9017	benign,benign,benign	263/789,263/834,263/834	157131788	1678,11328	2203	4300	6503	SO:0001583	missense	79674	exon6			TCATAGACTGCTA	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.788T>G	3.37:g.157131788A>C	ENSP00000354919:p.Val263Gly	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001167911	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	37	CCDS3179.1	362	0.16575091575091574	105	0.21341463414634146	35	0.09668508287292818	143	0.25	79	0.10422163588390501	C	6.245	0.413268	0.11812	0.198593	0.093372	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	5.9	4.07	0.47477	.	0.352984	0.34460	N	0.003953	T	0.00012	0.0000	N	0.00926	-1.1	0.23524	P	0.9974934	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37220	-0.9715	9	0.19147	T	0.46	0.6544	5.4219	0.16405	0.2628:0.5436:0.1266:0.067	rs1378796;rs61645738;rs1378796	263;263	Q14D04-2;Q14D04	.;MELT_HUMAN	G	263	ENSP00000376578:V263G;ENSP00000354919:V263G;ENSP00000446258:V263G;ENSP00000376577:V263G	ENSP00000354919:V263G	V	-	2	0	VEPH1	158614482	0.143000	0.22626	0.014000	0.15608	0.659000	0.38960	0.209000	0.17435	0.382000	0.24878	-0.127000	0.14921	GTC	A|0.850;C|0.150	0.150	strong		0.413	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
KIAA0226	9711	hgsc.bcm.edu	37	3	197432029	197432029	+	Silent	SNP	C	C	A	rs60457064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:197432029C>A	ENST00000296343.5	-	3	236	c.237G>T	c.(235-237)acG>acT	p.T79T	KIAA0226_ENST00000467303.1_5'UTR|KIAA0226_ENST00000449205.1_Silent_p.T79T|KIAA0226_ENST00000389665.5_Silent_p.T79T|KIAA0226_ENST00000273582.5_Silent_p.T19T	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	79	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		GCCAGTAATCCGTCTGGCGGC	0.537													A|||	768	0.153355	0.3699	0.0692	5008	,	,		20417	0.0308		0.1034	False		,,,				2504	0.0982				p.T79T	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.G237T						PASS	.	A	,	1255,2771		172,911,930	54.0	54.0	54.0		57,237	-1.5	1.0	3	dbSNP_129	54	787,7569		38,711,3429	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	210,1622,4359	AA,AC,CC		9.4184,31.1724,16.4917	,	19/928,79/973	197432029	2042,10340	2013	4178	6191	SO:0001819	synonymous_variant	9711	exon3			GTAATCCGTCTGG	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.237G>T	3.37:g.197432029C>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	307	0.14056776556776557	179	0.3638211382113821	27	0.07458563535911603	24	0.04195804195804196	77	0.10158311345646438	A	10.54	1.379884	0.24944	0.311724	0.094184	ENSG00000145016	ENST00000413360	.	.	.	5.63	-1.45	0.08828	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999995791	.	.	.	.	.	.	.	.	.	.	.	.	.	.	0.7535	0.00994	0.2454:0.3228:0.2227:0.2091	rs60457064;rs61744833	.	.	.	X	58	.	.	G	-	1	0	KIAA0226	198916426	0.045000	0.20229	0.960000	0.40013	0.967000	0.64934	-0.645000	0.05409	-0.430000	0.07318	-0.269000	0.10298	GGA	C|0.877;A|0.123	0.123	strong		0.537	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
ZNF813	126017	hgsc.bcm.edu	37	19	53990002	53990002	+	Silent	SNP	G	G	A	rs12974996	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53990002G>A	ENST00000396403.4	+	3	260	c.132G>A	c.(130-132)ctG>ctA	p.L44L	ZNF813_ENST00000396421.4_Silent_p.L44L	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	44	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		ATAGGAACCTGGTCTCCCTGG	0.483																																					p.L44L		Atlas-SNP	.											.	ZNF813	81	.	0			c.G132A						PASS	.						60.0	66.0	64.0					19																	53990002		2193	4255	6448	SO:0001819	synonymous_variant	126017	exon3			GAACCTGGTCTCC	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.132G>A	19.37:g.53990002G>A		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	52	15	0.288462	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			G|0.500;A|0.500	0.500	strong		0.483	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
MAP10	54627	hgsc.bcm.edu	37	1	232941354	232941354	+	Silent	SNP	G	G	T	rs12567597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:232941354G>T	ENST00000418460.1	+	1	712	c.585G>T	c.(583-585)ctG>ctT	p.L195L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	53					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										CGCGCGGTCTGTGCCCCGCCG	0.716													G|||	613	0.122404	0.1263	0.1412	5008	,	,		13004	0.1726		0.0964	False		,,,				2504	0.0787				p.L195L		Atlas-SNP	.											.	.	.	.	0			c.G585T						PASS	.	G		372,3506		17,338,1584	4.0	6.0	6.0		585	2.2	0.1	1	dbSNP_120	6	833,7271		45,743,3264	no	coding-synonymous	KIAA1383	NM_019090.2		62,1081,4848	TT,TG,GG		10.2789,9.5926,10.0568		195/1048	232941354	1205,10777	1939	4052	5991	SO:0001819	synonymous_variant	54627	exon1			CGGTCTGTGCCCC	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.585G>T	1.37:g.232941354G>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	18	8	0.444444	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																			G|0.858;T|0.142	0.142	strong		0.716	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
XPC	7508	hgsc.bcm.edu	37	3	14187449	14187449	+	Missense_Mutation	SNP	G	G	T	rs2228001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14187449G>T	ENST00000285021.7	-	16	3029	c.2815C>A	c.(2815-2817)Cag>Aag	p.Q939K	XPC_ENST00000449060.2_Missense_Mutation_p.Q902K|RP11-434D12.1_ENST00000601399.1_Intron|RP11-434D12.1_ENST00000608606.1_Intron|AC093495.4_ENST00000420253.1_RNA|AC093495.4_ENST00000428681.3_RNA	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	939	Interaction with ERCC2 and GTF2H1.		Q -> K (in dbSNP:rs2228001). {ECO:0000269|PubMed:12177305, ECO:0000269|PubMed:8168482, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GCTCACAGCTGCTCAAATGGG	0.587			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				T|||	3429	0.684704	0.7511	0.7176	5008	,	,		18472	0.6667		0.5954	False		,,,				2504	0.682				p.Q939K		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	.	XPC	60	.	0			c.C2815A	GRCh37	CM070359	XPC	M	rs2228001	PASS	.	T	LYS/GLN,LYS/GLN	2775,1027		1008,759,134	68.0	75.0	73.0		2704,2815	4.2	1.0	3	dbSNP_98	73	4949,3279		1507,1935,672	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	53,53	2515,2694,806	TT,TG,GG		39.8517,27.0121,35.7938	benign,benign	902/904,939/941	14187449	7724,4306	1901	4114	6015	SO:0001583	missense	7508	exon16	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACAGCTGCTCAAA		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.2815C>A	3.37:g.14187449G>T	ENSP00000285021:p.Gln939Lys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	1433	0.6561355311355311	350	0.7113821138211383	264	0.7292817679558011	371	0.6486013986013986	448	0.5910290237467019	T	4.792	0.147259	0.09134	0.729879	0.601483	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.25085	1.93;1.82	5.39	4.24	0.50183	.	0.104089	0.64402	N	0.000004	T	0.00012	0.0000	N	0.00104	-2.125	0.58432	P	2.9999999999752447E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40608	-0.9554	9	0.02654	T	1	-18.7298	7.9245	0.29865	0.0:0.071:0.1388:0.7902	rs2228001;rs3729583;rs17620623;rs17856505;rs60736379;rs2228001	902;939	E9PH69;Q01831	.;XPC_HUMAN	K	939;902	ENSP00000285021:Q939K;ENSP00000404002:Q902K	ENSP00000285021:Q939K	Q	-	1	0	XPC	14162450	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	2.905000	0.48727	0.882000	0.36016	-0.539000	0.04255	CAG	G|0.341;T|0.659	0.659	strong		0.587	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
HLA-F	3134	hgsc.bcm.edu	37	6	29693019	29693019	+	Silent	SNP	G	G	A	rs201844059		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29693019G>A	ENST00000376861.1	+	5	1206	c.822G>A	c.(820-822)gaG>gaA	p.E274E	HLA-F_ENST00000334668.4_Silent_p.E274E|HLA-F_ENST00000259951.7_Silent_p.E274E|HLA-F_ENST00000440587.2_Silent_p.E156E|HLA-F_ENST00000434407.2_Intron			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	274	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|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)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						CTCCTGGAGAGGAACAGAGAT	0.612													.|||	1	0.000199681	0.0	0.0014	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0				p.E274E		Atlas-SNP	.											.	HLA-F	41	.	0			c.G822A						PASS	.	G	,,	2,4404		0,2,2201	53.0	47.0	49.0		,822,822	-0.1	0.9	6		49	8,8592		0,8,4292	no	intron,coding-synonymous,coding-synonymous	HLA-F	NM_001098478.1,NM_001098479.1,NM_018950.2	,,	0,10,6493	AA,AG,GG		0.093,0.0454,0.0769	,,	,274/443,274/347	29693019	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	3134	exon4			TGGAGAGGAACAG	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.822G>A	6.37:g.29693019G>A		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	156	60	0.384615	NM_001098479	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Silent	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	0.413	-0.912347	0.02415	4.54E-4	9.3E-4	ENSG00000204642	ENST00000429294	.	.	.	1.92	-0.104	0.13605	.	.	.	.	.	T	0.28466	0.0704	.	.	.	0.39086	D	0.961008	.	.	.	.	.	.	T	0.15464	-1.0436	4	.	.	.	.	4.3592	0.11194	0.3972:0.0:0.6028:0.0	.	.	.	.	K	153	.	.	R	+	2	0	HLA-F	29800998	0.000000	0.05858	0.855000	0.33649	0.268000	0.26511	-0.944000	0.03913	-0.248000	0.09583	-0.436000	0.05848	AGG	G|0.999;A|0.001	0.001	weak		0.612	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950	
FAM131C	348487	hgsc.bcm.edu	37	1	16385042	16385042	+	Missense_Mutation	SNP	G	G	A	rs77667563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16385042G>A	ENST00000375662.4	-	7	916	c.733C>T	c.(733-735)Cgg>Tgg	p.R245W	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	245	Pro-rich.									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)		GGCAGCCGCCGCCGATGCTGC	0.741																																					p.R245W		Atlas-SNP	.											FAM131C,NS,other,0,1	FAM131C	21	1	0			c.C733T						PASS	.						2.0	2.0	2.0					1																	16385042		1409	3130	4539	SO:0001583	missense	348487	exon7			GCCGCCGCCGATG		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.733C>T	1.37:g.16385042G>A	ENSP00000364814:p.Arg245Trp	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	60	36	0.6	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	773	0.35393772893772896	210	0.4268292682926829	106	0.292817679558011	224	0.3916083916083916	233	0.3073878627968338	G	11.88	1.771185	0.31320	.	.	ENSG00000185519	ENST00000375662	T	0.15487	2.42	4.8	-0.971	0.10303	.	2.839240	0.01092	N	0.005214	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.65815	0.995	P	0.46825	0.528	T	0.32428	-0.9907	9	0.54805	T	0.06	-7.4813	4.4045	0.11402	0.1749:0.0:0.3887:0.4365	.	245	Q96AQ9	F131C_HUMAN	W	245	ENSP00000364814:R245W	ENSP00000364814:R245W	R	-	1	2	FAM131C	16257629	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.080000	0.11339	-0.172000	0.10779	0.549000	0.68633	CGG	G|0.646;A|0.354	0.354	strong		0.741	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
EEF2K	29904	hgsc.bcm.edu	37	16	22237273	22237273	+	Missense_Mutation	SNP	C	C	G	rs17841292	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:22237273C>G	ENST00000263026.5	+	2	697	c.223C>G	c.(223-225)Ccg>Gcg	p.P75A		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	75			P -> A (in dbSNP:rs17841292). {ECO:0000269|PubMed:17344846}.		insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CAGCGGGTCCCCGGCAAACTC	0.522													C|||	638	0.127396	0.0098	0.183	5008	,	,		17833	0.2589		0.0686	False		,,,				2504	0.1718				p.P75A	NSCLC(195;1411 2157 20319 27471 51856)	Atlas-SNP	.											EEF2K_ENST00000263026,NS,carcinoma,0,2	EEF2K	142	2	0			c.C223G						PASS	.	C	ALA/PRO	111,4283	85.3+/-124.0	1,109,2087	67.0	63.0	64.0		223	5.8	1.0	16	dbSNP_123	64	661,7939	167.0+/-218.8	33,595,3672	yes	missense	EEF2K	NM_013302.3	27	34,704,5759	GG,GC,CC		7.686,2.5262,5.9412	probably-damaging	75/726	22237273	772,12222	2197	4300	6497	SO:0001583	missense	29904	exon2			GGGTCCCCGGCAA	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.223C>G	16.37:g.22237273C>G	ENSP00000263026:p.Pro75Ala	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_013302	Q8N588	Missense_Mutation	SNP	ENST00000263026.5	37	CCDS10604.1	275	0.1259157509157509	7	0.014227642276422764	69	0.19060773480662985	148	0.25874125874125875	51	0.06728232189973615	C	17.10	3.303620	0.60305	0.025262	0.07686	ENSG00000103319	ENST00000263026	T	0.08634	3.07	5.79	5.79	0.91817	Protein kinase-like domain (1);	0.116424	0.64402	D	0.000018	T	0.00012	0.0000	L	0.57536	1.79	0.09310	P	0.99999891149	D	0.76494	0.999	D	0.80764	0.994	T	0.10543	-1.0625	9	0.40728	T	0.16	-15.5253	20.0435	0.97601	0.0:1.0:0.0:0.0	rs17841292;rs52824624;rs17841292	75	O00418	EF2K_HUMAN	A	75	ENSP00000263026:P75A	ENSP00000263026:P75A	P	+	1	0	EEF2K	22144774	1.000000	0.71417	0.981000	0.43875	0.225000	0.24961	3.913000	0.56394	2.731000	0.93534	0.650000	0.86243	CCG	C|0.912;G|0.088	0.088	strong		0.522	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302	
FLNC	2318	hgsc.bcm.edu	37	7	128487893	128487893	+	Silent	SNP	G	G	A	rs2291568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128487893G>A	ENST00000325888.8	+	25	4692	c.4431G>A	c.(4429-4431)ctG>ctA	p.L1477L	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.L1477L	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1477					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						GGGCGCCCCTGCAGGTGGCTG	0.692													G|||	1291	0.257788	0.4228	0.1556	5008	,	,		15695	0.378		0.0358	False		,,,				2504	0.2117				p.L1477L		Atlas-SNP	.											.	FLNC	339	.	0			c.G4431A						PASS	.	G	,	1352,2470		260,832,819	41.0	49.0	47.0		4431,4431	3.2	1.0	7	dbSNP_100	47	356,7870		5,346,3762	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	265,1178,4581	AA,AG,GG		4.3277,35.3741,14.1766	,	1477/2693,1477/2726	128487893	1708,10340	1911	4113	6024	SO:0001819	synonymous_variant	2318	exon25			GCCCCTGCAGGTG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.4431G>A	7.37:g.128487893G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	67	38	0.567164	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			A|0.179;C|0.011	0.179	strong		0.692	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
FKBP15	23307	hgsc.bcm.edu	37	9	115968797	115968797	+	Missense_Mutation	SNP	C	C	T	rs1133618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115968797C>T	ENST00000238256.3	-	4	433	c.316G>A	c.(316-318)Gcc>Acc	p.A106T	FKBP15_ENST00000493847.1_5'UTR	NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	106	Important for function in growth cone organization. {ECO:0000250}.		A -> T (in dbSNP:rs1133618).		endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						ACCTCTCTGGCTGTGTGGTTC	0.423													C|||	952	0.190096	0.3298	0.2161	5008	,	,		17470	0.0228		0.2078	False		,,,				2504	0.137				p.A106T		Atlas-SNP	.											.	FKBP15	128	.	0			c.G316A						PASS	.	C	THR/ALA	1052,2738		152,748,995	116.0	112.0	113.0		316	2.8	1.0	9	dbSNP_86	113	1576,6668		170,1236,2716	yes	missense	FKBP15	NM_015258.1	58	322,1984,3711	TT,TC,CC		19.1169,27.7573,21.8381	benign	106/1220	115968797	2628,9406	1895	4122	6017	SO:0001583	missense	23307	exon4			CTCTGGCTGTGTG	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.316G>A	9.37:g.115968797C>T	ENSP00000238256:p.Ala106Thr	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	403	0.18452380952380953	150	0.3048780487804878	76	0.20994475138121546	13	0.022727272727272728	164	0.21635883905013192	C	5.870	0.344614	0.11126	0.277573	0.191169	ENSG00000119321	ENST00000446284;ENST00000238256;ENST00000414250	T;T;T	0.42513	0.97;0.97;0.97	5.71	2.84	0.33178	.	.	.	.	.	T	0.00012	0.0000	N	0.11789	0.175	0.41464	P	0.011938000000000004	B;B;B	0.12630	0.006;0.002;0.004	B;B;B	0.16289	0.015;0.003;0.007	T	0.40232	-0.9574	8	0.10377	T	0.69	-1.6684	6.3222	0.21225	0.1488:0.6889:0.0:0.1623	rs1133618;rs3195502;rs11558693;rs52819213;rs56950186;rs1133618	106;106;106	Q5T1M5-2;Q5T1M5-3;Q5T1M5	.;.;FKB15_HUMAN	T	131;106;131	ENSP00000416158:A131T;ENSP00000238256:A106T;ENSP00000415733:A131T	ENSP00000238256:A106T	A	-	1	0	FKBP15	115008618	0.899000	0.30636	0.999000	0.59377	0.993000	0.82548	1.143000	0.31553	0.329000	0.23460	0.563000	0.77884	GCC	C|0.805;T|0.195	0.195	strong		0.423	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
ARPP21	10777	hgsc.bcm.edu	37	3	35778773	35778773	+	Silent	SNP	A	A	G	rs2278757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:35778773A>G	ENST00000187397.4	+	16	2019	c.1563A>G	c.(1561-1563)ccA>ccG	p.P521P	ARPP21_ENST00000444190.1_Silent_p.P467P|ARPP21_ENST00000458225.1_Silent_p.P487P|ARPP21_ENST00000337271.5_Silent_p.P467P|ARPP21_ENST00000417925.1_Silent_p.P487P	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	521	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						AACAGCAGCCACCACAGCAGC	0.637													G|||	2044	0.408147	0.5825	0.4035	5008	,	,		13700	0.1468		0.4732	False		,,,				2504	0.3783				p.P521P		Atlas-SNP	.											.	ARPP21	153	.	0			c.A1563G						PASS	.	G		2479,1923		711,1057,433	36.0	42.0	40.0		1563	-2.0	0.0	3	dbSNP_100	40	4104,4488		995,2114,1187	no	coding-synonymous	ARPP21	NM_016300.4		1706,3171,1620	GG,GA,AA		47.7654,43.6847,49.3382		521/813	35778773	6583,6411	2201	4296	6497	SO:0001819	synonymous_variant	10777	exon16			GCAGCCACCACAG	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"""R3H domain containing 3"""	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1563A>G	3.37:g.35778773A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_016300	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Silent	SNP	ENST00000187397.4	37	CCDS2661.1																																																																																			A|0.525;G|0.475	0.475	strong		0.637	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399	
KIAA0753	9851	hgsc.bcm.edu	37	17	6538355	6538355	+	Silent	SNP	G	G	A	rs2301873	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6538355G>A	ENST00000361413.3	-	2	427	c.69C>T	c.(67-69)agC>agT	p.S23S	KIAA0753_ENST00000542606.1_5'UTR|KIAA0753_ENST00000572370.1_Intron	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	23						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		CTTTGGGGTCGCTCCTCCCAT	0.413													G|||	1684	0.336262	0.2655	0.3271	5008	,	,		16510	0.2897		0.4543	False		,,,				2504	0.365				p.S23S		Atlas-SNP	.											KIAA0753,NS,carcinoma,0,1	KIAA0753	63	1	0			c.C69T						PASS	.	G		1105,2703		158,789,957	108.0	98.0	101.0		69	0.3	0.0	17	dbSNP_100	101	3516,4718		754,2008,1355	no	coding-synonymous	KIAA0753	NM_014804.2		912,2797,2312	AA,AG,GG		42.701,29.0179,38.374		23/968	6538355	4621,7421	1904	4117	6021	SO:0001819	synonymous_variant	9851	exon2			GGGGTCGCTCCTC		CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.69C>T	17.37:g.6538355G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Silent	SNP	ENST00000361413.3	37	CCDS42247.1																																																																																			G|0.637;A|0.363	0.363	strong		0.413	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
CCDC65	85478	hgsc.bcm.edu	37	12	49314862	49314862	+	Silent	SNP	C	C	A	rs10875894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49314862C>A	ENST00000320516.4	+	7	1364	c.1176C>A	c.(1174-1176)acC>acA	p.T392T	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Silent_p.T392T	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	392										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						AGGAGCTCACCAAGGTAAAGC	0.498													C|||	1544	0.308307	0.1014	0.4942	5008	,	,		18415	0.4454		0.4095	False		,,,				2504	0.2106				p.T392T		Atlas-SNP	.											CCDC65,NS,carcinoma,+1,2	CCDC65	41	2	0			c.C1176A						scavenged	.	C		690,3716	279.6+/-274.9	70,550,1583	45.0	48.0	47.0		1176	-5.2	0.0	12	dbSNP_120	47	3281,5319	484.2+/-371.3	618,2045,1637	no	coding-synonymous	CCDC65	NM_033124.4		688,2595,3220	AA,AC,CC		38.1512,15.6605,30.5321		392/485	49314862	3971,9035	2203	4300	6503	SO:0001819	synonymous_variant	85478	exon7			GCTCACCAAGGTA		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.1176C>A	12.37:g.49314862C>A		Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Silent	SNP	ENST00000320516.4	37	CCDS8772.1																																																																																			C|0.681;A|0.319	0.319	strong		0.498	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
C19orf53	28974	hgsc.bcm.edu	37	19	13885484	13885484	+	Missense_Mutation	SNP	A	A	G	rs10104	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:13885484A>G	ENST00000588234.1	+	2	426	c.116A>G	c.(115-117)aAg>aGg	p.K39R	CTB-5E10.3_ENST00000586894.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA|CTB-5E10.3_ENST00000586297.1_RNA|C19orf53_ENST00000593274.1_5'Flank	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53	39			K -> R (in dbSNP:rs10104).							breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			ATCGCTCCCAAGAAGGCGCGC	0.677													A|||	1891	0.377596	0.4032	0.3184	5008	,	,		16120	0.4266		0.2555	False		,,,				2504	0.4601				p.K39R		Atlas-SNP	.											.	C19orf53	14	.	0			c.A116G						PASS	.	A	ARG/LYS	1770,2636	506.7+/-366.5	349,1072,782	72.0	83.0	79.0		116	5.2	1.0	19	dbSNP_52	79	2227,6371	364.9+/-333.7	305,1617,2377	yes	missense	C19orf53	NM_014047.2	26	654,2689,3159	GG,GA,AA		25.9014,40.1725,30.7367	probably-damaging	39/100	13885484	3997,9007	2203	4299	6502	SO:0001583	missense	28974	exon2			CTCCCAAGAAGGC	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"""leydig cell tumor 10 kDa protein homolog"""					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5		ENST00000588234.1:c.116A>G	19.37:g.13885484A>G	ENSP00000465432:p.Lys39Arg	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	246	111	0.451219	NM_014047	B2R4J9	Missense_Mutation	SNP	ENST00000588234.1	37	CCDS12298.1	738	0.33791208791208793	210	0.4268292682926829	103	0.2845303867403315	233	0.40734265734265734	192	0.2532981530343008	A	34	5.402346	0.96030	0.401725	0.259014	ENSG00000104979	ENST00000221576	.	.	.	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	D	0.69078	0.997	D	0.80764	0.994	T	0.27706	-1.0066	7	0.87932	D	0	.	13.346	0.60573	1.0:0.0:0.0:0.0	rs10104;rs1128778;rs1559148;rs11557473;rs17112907;rs17295622;rs59089349;rs10104	39	Q9UNZ5	L10K_HUMAN	R	39	.	ENSP00000221576:K39R	K	+	2	0	C19orf53	13746484	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.204000	0.65180	2.102000	0.63906	0.524000	0.50904	AAG	A|0.669;G|0.331	0.331	strong		0.677	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047	
DCHS1	8642	hgsc.bcm.edu	37	11	6644600	6644600	+	Silent	SNP	C	C	T	rs72911011	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6644600C>T	ENST00000299441.3	-	21	8718	c.8307G>A	c.(8305-8307)gcG>gcA	p.A2769A	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2769	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AGGGCACTCGCGCACGCAACT	0.597													T|||	624	0.124601	0.0908	0.1571	5008	,	,		19220	0.0754		0.2117	False		,,,				2504	0.1084				p.A2769A		Atlas-SNP	.											.	DCHS1	277	.	0			c.G8307A						PASS	.	T		481,3919		36,409,1755	52.0	47.0	48.0		8307	2.7	1.0	11	dbSNP_130	48	1715,6877		167,1381,2748	no	coding-synonymous	DCHS1	NM_003737.2		203,1790,4503	TT,TC,CC		19.9604,10.9318,16.9027		2769/3299	6644600	2196,10796	2200	4296	6496	SO:0001819	synonymous_variant	8642	exon21			CACTCGCGCACGC	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.8307G>A	11.37:g.6644600C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			C|0.839;T|0.161	0.161	strong		0.597	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
POLE	5426	hgsc.bcm.edu	37	12	133236000	133236000	+	Silent	SNP	C	C	T	rs5744857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133236000C>T	ENST00000320574.5	-	26	3199	c.3156G>A	c.(3154-3156)acG>acA	p.T1052T	POLE_ENST00000535270.1_Silent_p.T1025T	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1052					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TGCTGATGGACGTAGACTTCT	0.567								DNA polymerases (catalytic subunits)					T|||	3032	0.605431	0.7602	0.5317	5008	,	,		19097	0.6736		0.4314	False		,,,				2504	0.5573				p.T1052T		Atlas-SNP	.											POLE_ENST00000320574,caecum,carcinoma,-1,2	POLE	416	2	0			c.G3156A						scavenged	.	T		3091,1315	441.8+/-346.5	1076,939,188	90.0	81.0	84.0		3156	-11.7	0.0	12	dbSNP_114	84	3704,4896	619.9+/-397.0	798,2108,1394	no	coding-synonymous	POLE	NM_006231.2		1874,3047,1582	TT,TC,CC		43.0698,29.8457,47.7549		1052/2287	133236000	6795,6211	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon26			GATGGACGTAGAC		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.3156G>A	12.37:g.133236000C>T		Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	121	63	0.520661	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			C|0.443;T|0.557	0.557	strong		0.567	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
CEBPZ	10153	hgsc.bcm.edu	37	2	37441091	37441091	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37441091C>A	ENST00000234170.5	-	10	2606	c.2461G>T	c.(2461-2463)Gtt>Ttt	p.V821F	AC007390.5_ENST00000438935.2_Intron|RP11-423P10.2_ENST00000606229.1_RNA	NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	821					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				TTAACAGCAACTTTTTTATAA	0.299																																					p.V821F		Atlas-SNP	.											.	CEBPZ	68	.	0			c.G2461T						PASS	.						132.0	128.0	130.0					2																	37441091		2201	4299	6500	SO:0001583	missense	10153	exon10			CAGCAACTTTTTT	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.2461G>T	2.37:g.37441091C>A	ENSP00000234170:p.Val821Phe	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	76	32	0.421053	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	37	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	C	6.869	0.529703	0.13127	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.14640	2.49	5.41	3.53	0.40419	Armadillo-type fold (1);	0.871941	0.10183	N	0.705591	T	0.13713	0.0332	L	0.47716	1.5	0.29558	N	0.850814	B	0.09022	0.002	B	0.08055	0.003	T	0.15925	-1.0420	10	0.87932	D	0	.	7.0108	0.24861	0.5827:0.3154:0.0:0.1019	.	821	Q03701	CEBPZ_HUMAN	F	821	ENSP00000234170:V821F	ENSP00000234170:V821F	V	-	1	0	CEBPZ	37294595	0.982000	0.34865	1.000000	0.80357	0.994000	0.84299	1.441000	0.35035	0.577000	0.29470	-0.181000	0.13052	GTT	.	.	none		0.299	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
GSG2	83903	hgsc.bcm.edu	37	17	3628212	3628212	+	Missense_Mutation	SNP	T	T	C	rs220461	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3628212T>C	ENST00000325418.4	+	1	1002	c.983T>C	c.(982-984)aTa>aCa	p.I328T	CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_Intron|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	328			I -> T (in dbSNP:rs220461). {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)										CCAAGGGGAATAGACAGGCTG	0.552													T|||	1270	0.253594	0.0219	0.1556	5008	,	,		19545	0.3006		0.3072	False		,,,				2504	0.5327				p.I328T		Atlas-SNP	.											.	GSG2	48	.	0			c.T983C						PASS	.	T	,THR/ILE	309,4097	162.2+/-194.2	17,275,1911	55.0	51.0	52.0		,983	-8.7	0.0	17	dbSNP_79	52	2743,5857	426.7+/-355.4	435,1873,1992	yes	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,89	452,2148,3903	CC,CT,TT		31.8953,7.0132,23.4661	,benign	,328/799	3628212	3052,9954	2203	4300	6503	SO:0001583	missense	83903	exon1			GGGGAATAGACAG	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.983T>C	17.37:g.3628212T>C	ENSP00000325290:p.Ile328Thr	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	31	31	1	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	494	0.2261904761904762	15	0.03048780487804878	65	0.17955801104972377	177	0.3094405594405594	237	0.31266490765171506	T	1.096	-0.662582	0.03454	0.070132	0.318953	ENSG00000177602	ENST00000325418	T	0.06933	3.24	4.33	-8.67	0.00863	.	0.902637	0.09044	N	0.856810	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.49688	-0.8913	9	0.87932	D	0	-23.7501	9.806	0.40792	0.1041:0.6357:0.1141:0.1461	rs220461;rs3809807;rs17463403;rs58374758;rs220461	328	Q8TF76	HASP_HUMAN	T	328	ENSP00000325290:I328T	ENSP00000325290:I328T	I	+	2	0	GSG2	3574961	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.294000	0.01144	-2.050000	0.00905	-1.064000	0.02280	ATA	T|0.769;C|0.230	0.230	strong		0.552	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
DDX60	55601	hgsc.bcm.edu	37	4	169158471	169158471	+	Silent	SNP	T	T	G	rs6552559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169158471T>G	ENST00000393743.3	-	32	4668	c.4377A>C	c.(4375-4377)ggA>ggC	p.G1459G		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1459					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)		CATGGAAGAGTCCATTTACAA	0.353													G|||	987	0.197085	0.4372	0.2378	5008	,	,		11893	0.1329		0.0666	False		,,,				2504	0.044				p.G1459G		Atlas-SNP	.											.	DDX60	304	.	0			c.A4377C						PASS	.	G		1677,2729	645.6+/-398.2	297,1083,823	48.0	45.0	46.0		4377	-4.2	0.3	4	dbSNP_116	46	517,8081	787.2+/-407.6	17,483,3799	no	coding-synonymous	DDX60	NM_017631.5		314,1566,4622	GG,GT,TT		6.013,38.0617,16.8717		1459/1713	169158471	2194,10810	2203	4299	6502	SO:0001819	synonymous_variant	55601	exon32			GAAGAGTCCATTT	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.4377A>C	4.37:g.169158471T>G		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_017631	Q6PK35|Q9NVE3	Silent	SNP	ENST00000393743.3	37	CCDS34097.1																																																																																			T|0.825;G|0.175	0.175	strong		0.353	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
TEX33	339669	hgsc.bcm.edu	37	22	37398201	37398201	+	Missense_Mutation	SNP	C	C	A	rs743750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37398201C>A	ENST00000405091.2	-	4	417	c.166G>T	c.(166-168)Gcc>Tcc	p.A56S	TEX33_ENST00000402860.3_5'UTR|TEX33_ENST00000381821.1_Missense_Mutation_p.A56S			O43247	TEX33_HUMAN	testis expressed 33	56																	TGAGCGCTGGCTCCCAGGGGC	0.622													C|||	1388	0.277157	0.1475	0.2205	5008	,	,		15009	0.5347		0.2286	False		,,,				2504	0.2771				p.A56S		Atlas-SNP	.											.	TEX33	25	.	0			c.G166T						PASS	.	C	SER/ALA,	230,1154		22,186,484	13.0	16.0	15.0		166,	-6.0	0.0	22	dbSNP_86	15	601,2581		55,491,1045	yes	missense,utr-5	C22orf33	NM_001163857.1,NM_178552.3	99,	77,677,1529	AA,AC,CC		18.8875,16.6185,18.1997	possibly-damaging,	56/281,	37398201	831,3735	692	1591	2283	SO:0001583	missense	339669	exon3			CGCTGGCTCCCAG	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.166G>T	22.37:g.37398201C>A	ENSP00000386118:p.Ala56Ser	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Missense_Mutation	SNP	ENST00000405091.2	37	CCDS54524.1	637	0.2916666666666667	81	0.16463414634146342	68	0.1878453038674033	324	0.5664335664335665	164	0.21635883905013192	.	8.314	0.822738	0.16678	0.166185	0.188875	ENSG00000185264	ENST00000405091;ENST00000381821	.	.	.	3.63	-6.03	0.02185	.	1.396580	0.04721	N	0.419334	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.48681	-0.9014	8	0.15066	T	0.55	.	0.2721	0.00232	0.3851:0.1837:0.1498:0.2814	rs743750;rs56891577	56	O43247	EAN57_HUMAN	S	56	.	ENSP00000371243:A56S	A	-	1	0	C22orf33	35728147	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.341000	0.02647	-0.445000	0.07159	-0.145000	0.13849	GCC	C|0.716;A|0.284	0.284	strong		0.622	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552	
TNC	3371	hgsc.bcm.edu	37	9	117819436	117819436	+	Silent	SNP	C	C	T	rs17819466	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:117819436C>T	ENST00000350763.4	-	15	4986	c.4575G>A	c.(4573-4575)acG>acA	p.T1525T	TNC_ENST00000542877.1_Silent_p.T1161T|TNC_ENST00000345230.3_Intron|TNC_ENST00000423613.2_Intron|TNC_ENST00000537320.1_Intron|TNC_ENST00000340094.3_Silent_p.T1161T|TNC_ENST00000341037.4_Silent_p.T1434T|TNC_ENST00000346706.3_Intron|TNC_ENST00000535648.1_Silent_p.T1161T|TNC_ENST00000481475.1_5'Flank	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1525	Fibronectin type-III 10. {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						ATGTACCTGTCGTGGCTGTGG	0.512													C|||	309	0.0617013	0.0068	0.0807	5008	,	,		19306	0.0079		0.1272	False		,,,				2504	0.1104				p.T1525T		Atlas-SNP	.											.	TNC	282	.	0			c.G4575A						PASS	.	C		98,4308	78.3+/-116.7	2,94,2107	90.0	71.0	77.0		4575	0.3	1.0	9	dbSNP_123	77	1114,7486	225.5+/-261.6	78,958,3264	yes	coding-synonymous	TNC	NM_002160.3		80,1052,5371	TT,TC,CC		12.9535,2.2242,9.3188		1525/2202	117819436	1212,11794	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon15			ACCTGTCGTGGCT		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.4575G>A	9.37:g.117819436C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1	134	0.06135531135531135	6	0.012195121951219513	32	0.08839779005524862	2	0.0034965034965034965	94	0.12401055408970976	C	3.938	-0.014771	0.07681	0.022242	0.129535	ENSG00000041982	ENST00000544972	.	.	.	5.95	0.271	0.15640	.	.	.	.	.	T	0.00300	0.0009	.	.	.	0.09310	P	0.9999999999999798	.	.	.	.	.	.	T	0.14811	-1.0459	3	.	.	.	.	3.8234	0.08845	0.0981:0.1626:0.348:0.3913	rs17819466;rs17819466	.	.	.	N	179	.	.	D	-	1	0	TNC	116859257	0.759000	0.28416	0.998000	0.56505	0.580000	0.36256	-0.155000	0.10115	0.111000	0.17947	-2.538000	0.00180	GAC	C|0.913;T|0.087	0.087	strong		0.512	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
SLX4	84464	hgsc.bcm.edu	37	16	3640785	3640785	+	Missense_Mutation	SNP	C	C	T	rs59939128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3640785C>T	ENST00000294008.3	-	12	3494	c.2854G>A	c.(2854-2856)Gcg>Acg	p.A952T		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	952	Interaction with PLK1 and TERF2-TERF2IP.		A -> M (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TGGCCAAGCGCCTCCTCTGGC	0.647								Direct reversal of damage					C|||	336	0.0670927	0.0961	0.0764	5008	,	,		16756	0.0496		0.0646	False		,,,				2504	0.0419				p.A952T		Atlas-SNP	.											SLX4,NS,carcinoma,+2,1	SLX4	173	1	0			c.G2854A						PASS	.	C	THR/ALA	476,3918	215.1+/-234.2	27,422,1748	47.0	50.0	49.0		2854	-1.4	0.0	16	dbSNP_129	49	562,8038	137.9+/-194.8	14,534,3752	no	missense	SLX4	NM_032444.2	58	41,956,5500	TT,TC,CC		6.5349,10.833,7.9883	probably-damaging	952/1835	3640785	1038,11956	2197	4300	6497	SO:0001583	missense	84464	exon12			CAAGCGCCTCCTC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2854G>A	16.37:g.3640785C>T	ENSP00000294008:p.Ala952Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	148	0.06776556776556776	53	0.10772357723577236	24	0.06629834254143646	23	0.04020979020979021	48	0.0633245382585752	C	9.916	1.210756	0.22289	0.10833	0.065349	ENSG00000188827	ENST00000294008	T	0.01369	4.97	4.64	-1.42	0.08913	.	1.163550	0.06146	N	0.673336	T	0.00039	0.0001	L	0.42245	1.32	0.09310	N	1	B	0.21452	0.056	B	0.19666	0.026	T	0.47799	-0.9089	10	0.27082	T	0.32	.	1.7256	0.02921	0.1415:0.4632:0.1378:0.2575	rs59939128	952	Q8IY92	SLX4_HUMAN	T	952	ENSP00000294008:A952T	ENSP00000294008:A952T	A	-	1	0	SLX4	3580786	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.014000	0.12656	-0.235000	0.09767	0.549000	0.68633	GCG	C|0.927;T|0.073	0.073	strong		0.647	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
PRG4	10216	hgsc.bcm.edu	37	1	186275564	186275564	+	Missense_Mutation	SNP	C	C	T	rs12128607	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186275564C>T	ENST00000445192.2	+	7	758	c.713C>T	c.(712-714)aCg>aTg	p.T238M	PRG4_ENST00000367484.3_Missense_Mutation_p.T197M|PRG4_ENST00000367483.4_Missense_Mutation_p.T197M|PRG4_ENST00000367485.4_Missense_Mutation_p.T145M|PRG4_ENST00000367486.3_Missense_Mutation_p.T195M	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	238					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						ACTCCTGACACGTCTACCACC	0.438													C|||	109	0.0217652	0.0136	0.013	5008	,	,		16291	0.001		0.0388	False		,,,				2504	0.0429				p.T238M		Atlas-SNP	.											.	PRG4	259	.	0			c.C713T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR	93,4313	75.2+/-113.4	0,93,2110	250.0	233.0	239.0		713,311,434,590	-7.9	0.0	1	dbSNP_120	239	388,8212	125.3+/-183.9	12,364,3924	yes	missense,missense,missense,missense	PRG4	NM_005807.3,NM_001127710.1,NM_001127709.1,NM_001127708.1	81,81,81,81	12,457,6034	TT,TC,CC		4.5116,2.1108,3.6983	benign,benign,benign,benign	238/1405,104/1271,145/1312,197/1364	186275564	481,12525	2203	4300	6503	SO:0001583	missense	10216	exon7			CTGACACGTCTAC	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.713C>T	1.37:g.186275564C>T	ENSP00000399679:p.Thr238Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	68	37	0.544118	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	50	0.022893772893772892	13	0.026422764227642278	4	0.011049723756906077	0	0.0	33	0.04353562005277045	C	0.460	-0.889754	0.02511	0.021108	0.045116	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000533951;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T;T	0.45668	3.44;3.52;0.89;3.53;3.5;3.53	3.97	-7.94	0.01152	.	2.609310	0.01694	N	0.026792	T	0.03095	0.0091	N	0.08118	0	0.09310	N	1	B;B;B;B	0.25719	0.132;0.132;0.017;0.05	B;B;B;B	0.16722	0.016;0.016;0.007;0.016	T	0.10800	-1.0614	10	0.49607	T	0.09	1.0244	7.216	0.25959	0.0:0.4302:0.2348:0.3351	rs12128607;rs52825883;rs57508866;rs12128607	104;145;238;197	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	M	195;197;147;104;197;145;238	ENSP00000356456:T195M;ENSP00000356454:T197M;ENSP00000431330:T147M;ENSP00000356453:T197M;ENSP00000356455:T145M;ENSP00000399679:T238M	ENSP00000356452:T104M	T	+	2	0	PRG4	184542187	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.476000	0.00986	-1.461000	0.01909	-1.740000	0.00687	ACG	C|0.969;T|0.031	0.031	strong		0.438	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
SMG8	55181	hgsc.bcm.edu	37	17	57290383	57290383	+	Silent	SNP	G	G	A	rs3744383	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:57290383G>A	ENST00000543872.2	+	4	2463	c.2199G>A	c.(2197-2199)agG>agA	p.R733R	SMG8_ENST00000580498.1_3'UTR|SMG8_ENST00000300917.5_Silent_p.R733R|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	733					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						CTGAGAAGAGGCCAAACTTCG	0.468													A|||	2445	0.488219	0.7375	0.3646	5008	,	,		19687	0.4415		0.2942	False		,,,				2504	0.4867				p.R733R		Atlas-SNP	.											.	SMG8	79	.	0			c.G2199A						PASS	.	A		2915,1491	474.6+/-357.0	962,991,250	111.0	111.0	111.0		2199	1.0	1.0	17	dbSNP_107	111	2683,5917	684.6+/-404.0	413,1857,2030	no	coding-synonymous	SMG8	NM_018149.6		1375,2848,2280	AA,AG,GG		31.1977,33.8402,43.0417		733/992	57290383	5598,7408	2203	4300	6503	SO:0001819	synonymous_variant	55181	exon3			GAAGAGGCCAAAC	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.2199G>A	17.37:g.57290383G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	105	54	0.514286	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Silent	SNP	ENST00000543872.2	37	CCDS11615.1																																																																																			G|0.551;A|0.449	0.449	strong		0.468	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149	
NOTCH1	4851	hgsc.bcm.edu	37	9	139399213	139399213	+	Silent	SNP	G	G	A	rs568700183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139399213G>A	ENST00000277541.6	-	26	5005	c.4930C>T	c.(4930-4932)Ctg>Ttg	p.L1644L		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1644					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A1641fs*2(2)|p.E1637_Q1648del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGGCCCAGCAGGGCGTCAGGT	0.711			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2	0.000399361	0.0	0.0	5008	,	,		14356	0.0		0.002	False		,,,				2504	0.0				p.L1644L		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1,NS,lymphoid_neoplasm,+2,1	NOTCH1	1980	1	3	Deletion - Frameshift(2)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(3)	c.C4930T						PASS	.						6.0	7.0	7.0					9																	139399213		1882	3984	5866	SO:0001819	synonymous_variant	4851	exon26			CCAGCAGGGCGTC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.4930C>T	9.37:g.139399213G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	20	10	0.5	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			.	.	none		0.711	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
LAMA1	284217	hgsc.bcm.edu	37	18	6978233	6978233	+	Missense_Mutation	SNP	C	C	T	rs145781920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:6978233C>T	ENST00000389658.3	-	43	6245	c.6152G>A	c.(6151-6153)cGa>cAa	p.R2051Q		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2051	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTGTGTCTCTCGTAATGTGGT	0.602													C|||	2	0.000399361	0.0	0.0	5008	,	,		17990	0.0		0.002	False		,,,				2504	0.0				p.R2051Q		Atlas-SNP	.											.	LAMA1	458	.	0			c.G6152A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	231.0	199.0	210.0		6152	-10.1	0.0	18	dbSNP_134	210	10,8590	7.1+/-27.0	0,10,4290	yes	missense	LAMA1	NM_005559.3	43	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign	2051/3076	6978233	10,12996	2203	4300	6503	SO:0001583	missense	284217	exon43			GTCTCTCGTAATG	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.6152G>A	18.37:g.6978233C>T	ENSP00000374309:p.Arg2051Gln	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	174	85	0.488506	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	6.111	0.388642	0.11581	0.0	0.001163	ENSG00000101680	ENST00000389658	T	0.40756	1.02	5.64	-10.1	0.00402	Laminin II (1);	0.727738	0.12726	N	0.444249	T	0.14184	0.0343	N	0.03253	-0.375	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35649	-0.9780	10	0.10902	T	0.67	.	14.4677	0.67494	0.0841:0.5919:0.0:0.324	.	2051	P25391	LAMA1_HUMAN	Q	2051	ENSP00000374309:R2051Q	ENSP00000374309:R2051Q	R	-	2	0	LAMA1	6968233	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.580000	0.02121	-1.900000	0.01097	-1.874000	0.00550	CGA	C|0.999;T|0.001	0.001	strong		0.602	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
TONSL	4796	hgsc.bcm.edu	37	8	145665407	145665407	+	Missense_Mutation	SNP	C	C	T	rs2229315	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145665407C>T	ENST00000409379.3	-	11	1506	c.1477G>A	c.(1477-1479)Ggc>Agc	p.G493S	AC084125.4_ENST00000442850.1_RNA|AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	493	Glu-rich.		G -> S (in dbSNP:rs2229315). {ECO:0000269|PubMed:11246458, ECO:0000269|PubMed:7738005}.		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						CCCTCACCGCCCTCTGAGAGC	0.667													T|||	2418	0.482827	0.5938	0.4741	5008	,	,		17076	0.3849		0.5338	False		,,,				2504	0.3875				p.G493S		Atlas-SNP	.											.	TONSL	128	.	0			c.G1477A						PASS	.	T	SER/GLY	2541,1857		746,1049,404	22.0	24.0	24.0		1477	5.5	1.0	8	dbSNP_98	24	4593,3999		1242,2109,945	yes	missense	TONSL	NM_013432.4	56	1988,3158,1349	TT,TC,CC		46.5433,42.2237,45.0808	benign	493/1379	145665407	7134,5856	2199	4296	6495	SO:0001583	missense	4796	exon11			CACCGCCCTCTGA		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.1477G>A	8.37:g.145665407C>T	ENSP00000386239:p.Gly493Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	125	123	0.984	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	37	CCDS34968.2	1123	0.5141941391941391	286	0.5813008130081301	178	0.49171270718232046	240	0.4195804195804196	419	0.5527704485488126	T	3.873	-0.027475	0.07589	0.577763	0.534567	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.37235	1.21	5.51	5.51	0.81932	.	0.312887	0.37955	N	0.001864	T	0.00012	0.0000	N	0.02539	-0.55	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44190	-0.9344	9	0.02654	T	1	.	9.7751	0.40614	0.0:0.0819:0.0:0.9181	rs2229315;rs2306384;rs59210356;rs2306384	493	Q96HA7	TONSL_HUMAN	S	493	ENSP00000386239:G493S	ENSP00000386239:G493S	G	-	1	0	TONSL	145636215	0.958000	0.32768	0.996000	0.52242	0.437000	0.31866	1.065000	0.30592	0.934000	0.37316	-0.254000	0.11334	GGC	T|0.531;G|0.000;C|0.469	0.531	strong		0.667	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
MARCH10	162333	hgsc.bcm.edu	37	17	60814273	60814273	+	Missense_Mutation	SNP	A	A	G	rs9891498	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:60814273A>G	ENST00000311269.5	-	6	1230	c.956T>C	c.(955-957)tTt>tCt	p.F319S	RP11-156L14.1_ENST00000584597.1_RNA|MARCH10_ENST00000583600.1_Missense_Mutation_p.F357S|RP11-156L14.1_ENST00000577270.1_RNA|RP11-156L14.1_ENST00000579201.1_RNA|MARCH10_ENST00000456609.2_Missense_Mutation_p.F319S|RP11-156L14.1_ENST00000582564.1_RNA|MARCH10_ENST00000544856.2_Missense_Mutation_p.F318S	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	319			F -> S (in dbSNP:rs9891498). {ECO:0000269|PubMed:14702039}.		protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						TGTCCCCCCAAATCTACTTCT	0.458													A|||	1362	0.271965	0.1324	0.3876	5008	,	,		19391	0.2083		0.4215	False		,,,				2504	0.2904				p.F319S		Atlas-SNP	.											.	MARCH10	102	.	0			c.T956C						PASS	.	A	SER/PHE,SER/PHE	820,3586	318.8+/-295.8	86,648,1469	192.0	194.0	193.0		956,956	2.8	0.0	17	dbSNP_119	193	3386,5214	487.7+/-372.2	717,1952,1631	yes	missense,missense	MARCH10	NM_001100875.1,NM_152598.2	155,155	803,2600,3100	GG,GA,AA		39.3721,18.611,32.3389	probably-damaging,probably-damaging	319/809,319/809	60814273	4206,8800	2203	4300	6503	SO:0001583	missense	162333	exon6			CCCCCAAATCTAC	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.956T>C	17.37:g.60814273A>G	ENSP00000311496:p.Phe319Ser	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	163	71	0.435583	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	37	CCDS11635.1	651	0.2980769230769231	64	0.13008130081300814	149	0.4116022099447514	116	0.20279720279720279	322	0.42480211081794195	A	8.846	0.943485	0.18281	0.18611	0.393721	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.59083	0.29;0.29;0.29	5.17	2.75	0.32379	.	0.378995	0.22924	N	0.053999	T	0.00012	0.0000	M	0.72118	2.19	0.80722	P	0.0	D;D;D	0.63880	0.988;0.993;0.988	P;P;P	0.55391	0.601;0.775;0.601	T	0.33369	-0.9871	9	0.66056	D	0.02	-8.2489	8.95	0.35783	0.6338:0.3662:0.0:0.0	rs9891498;rs52833447;rs9891498	318;318;319	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	S	319;319;318	ENSP00000416177:F319S;ENSP00000311496:F319S;ENSP00000443746:F318S	ENSP00000311496:F319S	F	-	2	0	MARCH10	58168005	0.002000	0.14202	0.011000	0.14972	0.021000	0.10359	1.449000	0.35123	0.775000	0.33450	0.459000	0.35465	TTT	A|0.682;G|0.318	0.318	strong		0.458	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
DOCK7	85440	hgsc.bcm.edu	37	1	62923326	62923326	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:62923326T>C	ENST00000340370.5	-	48	6187	c.6170A>G	c.(6169-6171)aAg>aGg	p.K2057R	DOCK7_ENST00000251157.5_Missense_Mutation_p.K2077R	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	2088	DHR-2.				activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TTGATACTCCTTTTGATCCGG	0.408																																					p.K2077R		Atlas-SNP	.											DOCK7,rectum,carcinoma,+1,1	DOCK7	184	1	0			c.A6230G						scavenged	.						193.0	188.0	190.0					1																	62923326		2203	4300	6503	SO:0001583	missense	85440	exon48			TACTCCTTTTGAT		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.6170A>G	1.37:g.62923326T>C	ENSP00000340742:p.Lys2057Arg	Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	262	6	0.0229008	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	T	13.49	2.253307	0.39797	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441	T;T	0.18338	2.22;2.22	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.08537	0.0212	N	0.02368	-0.58	0.80722	D	1	B;B;B;B;B;B	0.21520	0.022;0.033;0.057;0.033;0.025;0.003	B;B;B;B;B;B	0.26864	0.074;0.036;0.05;0.034;0.044;0.026	T	0.37753	-0.9692	10	0.15066	T	0.55	.	16.4943	0.84223	0.0:0.0:0.0:1.0	.	2088;2077;2057;2046;2048;2079	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	DOCK7_HUMAN;.;.;.;.;.	R	2088;2077;2057;818	ENSP00000251157:K2077R;ENSP00000340742:K2057R	ENSP00000251157:K2077R	K	-	2	0	DOCK7	62695914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.219000	0.72231	2.291000	0.77112	0.533000	0.62120	AAG	.	.	none		0.408	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
DDX60	55601	hgsc.bcm.edu	37	4	169208334	169208334	+	Missense_Mutation	SNP	C	C	T	rs72693161	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169208334C>T	ENST00000393743.3	-	10	1495	c.1204G>A	c.(1204-1206)Gat>Aat	p.D402N		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	402					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)		ATAATGGTATCTCCCAAATTC	0.348													C|||	110	0.0219649	0.003	0.0317	5008	,	,		15574	0.001		0.0557	False		,,,				2504	0.0276				p.D402N		Atlas-SNP	.											.	DDX60	304	.	0			c.G1204A						PASS	.	C	ASN/ASP	46,4360	48.9+/-83.8	0,46,2157	71.0	69.0	70.0		1204	-4.8	0.0	4	dbSNP_130	70	402,8194	126.7+/-185.1	9,384,3905	yes	missense	DDX60	NM_017631.5	23	9,430,6062	TT,TC,CC		4.6766,1.044,3.4456	benign	402/1713	169208334	448,12554	2203	4298	6501	SO:0001583	missense	55601	exon10			TGGTATCTCCCAA	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.1204G>A	4.37:g.169208334C>T	ENSP00000377344:p.Asp402Asn	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	111	40	0.36036	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	61	0.027930402930402932	4	0.008130081300813009	15	0.04143646408839779	0	0.0	42	0.055408970976253295	C	8.804	0.933698	0.18206	0.01044	0.046766	ENSG00000137628	ENST00000393743	T	0.17691	2.26	4.72	-4.83	0.03161	.	0.929670	0.08987	N	0.865043	T	0.01061	0.0035	L	0.41824	1.3	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.34279	-0.9835	10	0.23891	T	0.37	.	7.3402	0.26633	0.0:0.3146:0.1136:0.5719	.	402	Q8IY21	DDX60_HUMAN	N	402	ENSP00000377344:D402N	ENSP00000377344:D402N	D	-	1	0	DDX60	169444909	0.000000	0.05858	0.004000	0.12327	0.504000	0.33889	-0.555000	0.05999	-1.071000	0.03145	-0.373000	0.07131	GAT	C|0.970;T|0.030	0.030	strong		0.348	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
CCT8L2	150160	hgsc.bcm.edu	37	22	17072411	17072411	+	Missense_Mutation	SNP	G	G	T	rs41277596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:17072411G>T	ENST00000359963.3	-	1	1289	c.1030C>A	c.(1030-1032)Cca>Aca	p.P344T		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	344					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CACTTGCCTGGCCTCTGGGGA	0.547													g|||	17	0.00339457	0.0	0.0072	5008	,	,		19488	0.0		0.0109	False		,,,				2504	0.001				p.P344T		Atlas-SNP	.											.	CCT8L2	150	.	0			c.C1030A						PASS	.	G	THR/PRO	3,4403	6.2+/-15.9	0,3,2200	101.0	100.0	100.0		1030	0.7	0.7	22	dbSNP_127	100	69,8531	41.2+/-98.3	0,69,4231	no	missense	CCT8L2	NM_014406.4	38	0,72,6431	TT,TG,GG		0.8023,0.0681,0.5536	probably-damaging	344/558	17072411	72,12934	2203	4300	6503	SO:0001583	missense	150160	exon1			TGCCTGGCCTCTG	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1030C>A	22.37:g.17072411G>T	ENSP00000353048:p.Pro344Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_014406	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	15	0.006868131868131868	0	0.0	5	0.013812154696132596	0	0.0	10	0.013192612137203167	g	1.736	-0.492944	0.04322	6.81E-4	0.008023	ENSG00000198445	ENST00000359963	T	0.77877	-1.13	1.98	0.711	0.18162	.	0.201946	0.24693	U	0.036363	T	0.61726	0.2370	L	0.41236	1.265	0.24066	N	0.99599	B	0.34255	0.445	B	0.41723	0.365	T	0.60367	-0.7277	10	0.72032	D	0.01	-14.4681	5.6792	0.17765	0.0:0.347:0.653:0.0	rs41277596	344	Q96SF2	TCPQM_HUMAN	T	344	ENSP00000353048:P344T	ENSP00000353048:P344T	P	-	1	0	CCT8L2	15452411	0.005000	0.15991	0.710000	0.30468	0.079000	0.17450	0.660000	0.25009	1.115000	0.41800	0.379000	0.24179	CCA	G|0.994;T|0.006	0.006	strong		0.547	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
SYT3	84258	hgsc.bcm.edu	37	19	51133356	51133356	+	Silent	SNP	C	C	G	rs10407511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51133356C>G	ENST00000338916.4	-	3	1380	c.747G>C	c.(745-747)cgG>cgC	p.R249R	SYT3_ENST00000600079.1_Silent_p.R249R|SYT3_ENST00000593901.1_Silent_p.R249R|SYT3_ENST00000544769.1_Silent_p.R249R	NM_032298.2	NP_115674.1	Q9BQG1	SYT3_HUMAN	synaptotagmin III	249					calcium ion-dependent exocytosis (GO:0017156)|positive regulation of vesicle fusion (GO:0031340)|response to calcium ion (GO:0051592)	cell junction (GO:0030054)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(2)|prostate(2)|skin(3)|urinary_tract(2)	35		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00462)|GBM - Glioblastoma multiforme(134;0.0188)		GGGCAGGTGGCCGCTCCTCAC	0.657													C|||	2980	0.595048	0.8585	0.7176	5008	,	,		11931	0.1696		0.6879	False		,,,				2504	0.4949				p.R249R		Atlas-SNP	.											.	SYT3	85	.	0			c.G747C						PASS	.	C	,,	3556,850	730.5+/-410.2	1444,668,91	32.0	32.0	32.0		747,747,747	1.3	1.0	19	dbSNP_119	32	5733,2867	658.0+/-401.5	1915,1903,482	no	coding-synonymous,coding-synonymous,coding-synonymous	SYT3	NM_001160328.1,NM_001160329.1,NM_032298.2	,,	3359,2571,573	GG,GC,CC		33.3372,19.2919,28.5791	,,	249/591,249/591,249/591	51133356	9289,3717	2203	4300	6503	SO:0001819	synonymous_variant	84258	exon3			AGGTGGCCGCTCC	AL136594	CCDS12798.1	19q13.33	2014-07-02			ENSG00000213023	ENSG00000213023		"""Synaptotagmins"""	11511	protein-coding gene	gene with protein product		600327				7749232	Standard	NM_032298		Approved		uc002psv.3	Q9BQG1	OTTHUMG00000183064	ENST00000338916.4:c.747G>C	19.37:g.51133356C>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_032298	Q8N5Z1|Q8N640	Silent	SNP	ENST00000338916.4	37	CCDS12798.1																																																																																			C|0.328;G|0.672	0.672	strong		0.657	SYT3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464910.1	NM_032298	
POR	5447	hgsc.bcm.edu	37	7	75615006	75615006	+	Missense_Mutation	SNP	C	C	T	rs1057868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:75615006C>T	ENST00000461988.1	+	13	1613	c.1508C>T	c.(1507-1509)gCc>gTc	p.A503V	POR_ENST00000545601.1_Missense_Mutation_p.A311V|POR_ENST00000394893.1_Missense_Mutation_p.A503V|POR_ENST00000439269.1_Missense_Mutation_p.A241V|POR_ENST00000419840.1_Missense_Mutation_p.A317V|POR_ENST00000450476.1_Missense_Mutation_p.A402V|TMEM120A_ENST00000493111.2_RNA|TMEM120A_ENST00000338761.4_RNA	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	500	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	AAGGAGCCTGCCGGGGAGAAC	0.657													C|||	1433	0.286142	0.1702	0.2795	5008	,	,		15499	0.374		0.2952	False		,,,				2504	0.3476				p.A503V		Atlas-SNP	.											.	POR	46	.	0			c.C1508T	GRCh37	CM057356	POR	M	rs1057868	PASS	.	C	VAL/ALA	698,3446		75,548,1449	12.0	16.0	14.0		1508	3.5	0.0	7	dbSNP_86	14	2247,6049		309,1629,2210	yes	missense	POR	NM_000941.2	64	384,2177,3659	TT,TC,CC		27.0853,16.8436,23.6736	benign	503/681	75615006	2945,9495	2072	4148	6220	SO:0001583	missense	5447	exon13			AGCCTGCCGGGGA	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1508C>T	7.37:g.75615006C>T	ENSP00000419970:p.Ala503Val	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	95	59	0.621053	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Missense_Mutation	SNP	ENST00000461988.1	37	CCDS5579.1	628	0.2875457875457875	68	0.13821138211382114	106	0.292817679558011	223	0.38986013986013984	231	0.30474934036939316	C	7.739	0.700936	0.15172	0.168436	0.270853	ENSG00000127948	ENST00000461988;ENST00000419840;ENST00000394893;ENST00000545601;ENST00000450476;ENST00000439269	D;D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64;-1.64	4.4	3.51	0.40186	Riboflavin synthase-like beta-barrel (1);Ferredoxin reductase-type FAD-binding domain (1);	0.267846	0.35903	N	0.002907	T	0.00012	0.0000	N	0.13235	0.315	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.17167	-1.0378	9	0.29301	T	0.29	-1.5153	8.3965	0.32559	0.0:0.8905:0.0:0.1095	rs1057868;rs3198400;rs17840495;rs17846082;rs17859083;rs57699079	500;402;311;509	P16435;E7EVY7;F5H468;Q59ED7	NCPR_HUMAN;.;.;.	V	503;317;503;311;402;241	ENSP00000419970:A503V;ENSP00000414244:A317V;ENSP00000378355:A503V;ENSP00000446149:A311V;ENSP00000416572:A402V;ENSP00000412490:A241V	ENSP00000378355:A503V	A	+	2	0	POR	75452942	0.033000	0.19621	0.003000	0.11579	0.158000	0.22134	0.907000	0.28531	1.188000	0.43014	0.561000	0.74099	GCC	C|0.723;T|0.277	0.277	strong		0.657	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
CPA6	57094	hgsc.bcm.edu	37	8	68421768	68421768	+	Missense_Mutation	SNP	G	G	C	rs17853192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:68421768G>C	ENST00000297770.4	-	5	733	c.518C>G	c.(517-519)tCt>tGt	p.S173C	CPA6_ENST00000518549.1_Missense_Mutation_p.S173C|CPA6_ENST00000297769.4_Missense_Mutation_p.S25C	NM_020361.4	NP_065094.3	Q8N4T0	CBPA6_HUMAN	carboxypeptidase A6	173			S -> C (in dbSNP:rs17853192). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.			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)			AATAAAAAGAGATCTTCCCTC	0.303													G|||	446	0.0890575	0.003	0.0951	5008	,	,		16285	0.1974		0.0905	False		,,,				2504	0.0879				p.S173C		Atlas-SNP	.											.	CPA6	69	.	0			c.C518G						PASS	.	G	CYS/SER	64,4342	61.1+/-98.1	1,62,2140	60.0	61.0	61.0		518	5.5	1.0	8	dbSNP_123	61	712,7878	174.2+/-224.5	18,676,3601	yes	missense	CPA6	NM_020361.4	112	19,738,5741	CC,CG,GG		8.2887,1.4526,5.9711	probably-damaging	173/438	68421768	776,12220	2203	4295	6498	SO:0001583	missense	57094	exon5			AAAAGAGATCTTC	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.518C>G	8.37:g.68421768G>C	ENSP00000297770:p.Ser173Cys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	101	60	0.594059	NM_020361	Q8NEX8|Q8TDE8|Q9NRI9	Missense_Mutation	SNP	ENST00000297770.4	37	CCDS6200.1	216	0.0989010989010989	2	0.0040650406504065045	38	0.10497237569060773	109	0.19055944055944055	67	0.08839050131926121	G	24.7	4.555195	0.86231	0.014526	0.082887	ENSG00000165078	ENST00000297769;ENST00000297770;ENST00000518549	T;T;T	0.11604	2.76;2.76;3.86	5.49	5.49	0.81192	Peptidase M14, carboxypeptidase A (3);	0.293173	0.39341	N	0.001395	T	0.00039	0.0001	M	0.78916	2.43	0.28202	P	0.9272937	D;D;P	0.76494	0.997;0.999;0.937	P;P;P	0.59288	0.847;0.855;0.755	T	0.00051	-1.2192	9	0.72032	D	0.01	.	18.9697	0.92709	0.0:0.0:1.0:0.0	rs17853192	173;25;173	Q8N4T0-2;Q8N4T0-3;Q8N4T0	.;.;CBPA6_HUMAN	C	25;173;173	ENSP00000297769:S25C;ENSP00000297770:S173C;ENSP00000431112:S173C	ENSP00000297769:S25C	S	-	2	0	CPA6	68584322	1.000000	0.71417	0.961000	0.40146	0.994000	0.84299	8.236000	0.89805	2.582000	0.87167	0.650000	0.86243	TCT	G|0.925;C|0.075	0.075	strong		0.303	CPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379296.2	NM_020361	
KIF21A	55605	hgsc.bcm.edu	37	12	39735348	39735348	+	Missense_Mutation	SNP	C	C	A	rs79089655	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:39735348C>A	ENST00000361418.5	-	14	1895	c.1880G>T	c.(1879-1881)gGt>gTt	p.G627V	KIF21A_ENST00000544797.2_Missense_Mutation_p.G614V|KIF21A_ENST00000541463.2_Missense_Mutation_p.G614V|KIF21A_ENST00000361961.3_Missense_Mutation_p.G614V|KIF21A_ENST00000395670.3_Missense_Mutation_p.G627V			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	627					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				AGAACTTTCACCCCCATCAAT	0.378													C|||	81	0.0161741	0.0	0.0187	5008	,	,		18852	0.0		0.0417	False		,,,				2504	0.0266				p.G627V		Atlas-SNP	.											.	KIF21A	238	.	0			c.G1880T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	38,4368	41.6+/-74.8	0,38,2165	117.0	114.0	115.0		1841,1880,1841,1841	3.7	1.0	12	dbSNP_131	115	390,8210	124.1+/-182.9	12,366,3922	yes	missense,missense,missense,missense	KIF21A	NM_001173463.1,NM_001173464.1,NM_001173465.1,NM_017641.3	109,109,109,109	12,404,6087	AA,AC,CC		4.5349,0.8625,3.2908	benign,benign,benign,benign	614/1638,627/1675,614/1622,614/1662	39735348	428,12578	2203	4300	6503	SO:0001583	missense	55605	exon14			CTTTCACCCCCAT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.1880G>T	12.37:g.39735348C>A	ENSP00000354878:p.Gly627Val	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	45	0.020604395604395604	0	0.0	7	0.019337016574585635	0	0.0	38	0.05013192612137203	C	10.10	1.258070	0.23051	0.008625	0.045349	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463	T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36	5.5	3.65	0.41850	.	0.289256	0.24534	N	0.037688	T	0.11580	0.0282	N	0.14661	0.345	0.43982	D	0.996675	B;B;B;B	0.29162	0.235;0.0;0.0;0.0	B;B;B;B	0.37304	0.246;0.001;0.001;0.002	T	0.07481	-1.0770	10	0.27082	T	0.32	.	2.1801	0.03872	0.1913:0.5129:0.1254:0.1704	.	614;614;627;614	F5H219;F5H0C3;Q7Z4S6;Q7Z4S6-2	.;.;KI21A_HUMAN;.	V	614;627;627;614;627;614	ENSP00000354851:G614V;ENSP00000379029:G627V;ENSP00000445606:G614V;ENSP00000354878:G627V;ENSP00000438075:G614V	ENSP00000344501:G627V	G	-	2	0	KIF21A	38021615	1.000000	0.71417	0.993000	0.49108	0.744000	0.42396	2.088000	0.41663	0.656000	0.30886	0.655000	0.94253	GGT	C|0.971;A|0.029	0.029	strong		0.378	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
XRN1	54464	hgsc.bcm.edu	37	3	142123841	142123841	+	Silent	SNP	C	C	T	rs2306700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142123841C>T	ENST00000264951.4	-	16	1908	c.1791G>A	c.(1789-1791)gaG>gaA	p.E597E	RNU6-1294P_ENST00000515995.1_RNA|XRN1_ENST00000392981.2_Silent_p.E597E	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	597					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						ACATTAGGCACTCACTATGTT	0.408													C|||	609	0.121605	0.1604	0.0965	5008	,	,		18450	0.1002		0.1481	False		,,,				2504	0.0818				p.E597E		Atlas-SNP	.											.	XRN1	138	.	0			c.G1791A						PASS	.	C	,	645,3761	277.8+/-273.9	46,553,1604	169.0	152.0	158.0		1791,1791	-0.4	1.0	3	dbSNP_100	158	1196,7404	242.6+/-272.5	79,1038,3183	no	coding-synonymous,coding-synonymous	XRN1	NM_001042604.1,NM_019001.3	,	125,1591,4787	TT,TC,CC		13.907,14.6391,14.155	,	597/1694,597/1707	142123841	1841,11165	2203	4300	6503	SO:0001819	synonymous_variant	54464	exon16			TAGGCACTCACTA	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.1791G>A	3.37:g.142123841C>T		Somatic	273	1	0.003663		WXS	Illumina HiSeq	Phase_I	247	245	0.991903	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																			C|0.867;T|0.133	0.133	strong		0.408	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	
TRRAP	8295	hgsc.bcm.edu	37	7	98580987	98580987	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:98580987C>T	ENST00000359863.4	+	59	9115	c.8906C>T	c.(8905-8907)aCg>aTg	p.T2969M	TRRAP_ENST00000446306.3_Missense_Mutation_p.T2951M|TRRAP_ENST00000355540.3_Missense_Mutation_p.T2951M	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2969	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				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)			GACATGAAGACGGTGGTGAAG	0.542																																					p.T2969M		Atlas-SNP	.											TRRAP_ENST00000359863,NS,carcinoma,+1,2	TRRAP	863	2	0			c.C8906T						scavenged	.						185.0	136.0	153.0					7																	98580987		2203	4300	6503	SO:0001583	missense	8295	exon59			TGAAGACGGTGGT	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.8906C>T	7.37:g.98580987C>T	ENSP00000352925:p.Thr2969Met	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	156	2	0.0128205	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Missense_Mutation	SNP	ENST00000359863.4	37	CCDS59066.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.6|28.6	4.937895|4.937895	0.92526|0.92526	.|.	.|.	ENSG00000196367|ENSG00000196367	ENST00000456197|ENST00000359863;ENST00000355540;ENST00000446306	.|T;T	.|0.69685	.|-0.42;-0.42	5.48|5.48	5.48|5.48	0.80851|0.80851	.|PIK-related kinase (1);PIK-related kinase, FAT (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.67887|0.67887	0.2941|0.2941	N|N	0.11560|0.11560	0.145|0.145	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.999;0.999	.|D;D;D	.|0.67725	.|0.953;0.95;0.946	T|T	0.71738|0.71738	-0.4502|-0.4502	5|10	.|0.40728	.|T	.|0.16	.|.	19.3398|19.3398	0.94336|0.94336	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|2951;2690;2969	.|Q9Y4A5-2;Q59FH1;Q9Y4A5	.|.;.;TRRAP_HUMAN	W|M	2691|2969;2951;2950	.|ENSP00000352925:T2969M;ENSP00000347733:T2951M	.|ENSP00000347733:T2951M	R|T	+|+	1|2	2|0	TRRAP|TRRAP	98418923|98418923	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.985000|0.985000	0.73830|0.73830	7.818000|7.818000	0.86416|0.86416	2.571000|2.571000	0.86741|0.86741	0.650000|0.650000	0.86243|0.86243	CGG|ACG	.	.	none		0.542	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
ABCD4	5826	hgsc.bcm.edu	37	14	74759477	74759477	+	Missense_Mutation	SNP	C	C	T	rs4148077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:74759477C>T	ENST00000356924.4	-	9	1053	c.910G>A	c.(910-912)Gca>Aca	p.A304T	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000557588.1_Intron|ABCD4_ENST00000298816.7_Missense_Mutation_p.A200T	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	304	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.		A -> T (in dbSNP:rs4148077). {ECO:0000269|PubMed:12111378, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.6}.		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)		CTAAGCTCTGCGGGACTCAGG	0.562													C|||	1354	0.270367	0.1475	0.2723	5008	,	,		22696	0.247		0.3857	False		,,,				2504	0.3405				p.A304T		Atlas-SNP	.											.	ABCD4	54	.	0			c.G910A						PASS	.	C	THR/ALA	870,3536	338.6+/-305.4	84,702,1417	87.0	75.0	79.0		910	2.1	1.0	14	dbSNP_110	79	3129,5471	476.6+/-369.4	553,2023,1724	yes	missense	ABCD4	NM_005050.3	58	637,2725,3141	TT,TC,CC		36.3837,19.7458,30.7473	benign	304/607	74759477	3999,9007	2203	4300	6503	SO:0001583	missense	5826	exon9			GCTCTGCGGGACT	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.910G>A	14.37:g.74759477C>T	ENSP00000349396:p.Ala304Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	106	48	0.45283	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	590	0.27014652014652013	65	0.13211382113821138	104	0.287292817679558	138	0.24125874125874125	283	0.3733509234828496	C	11.92	1.782746	0.31502	0.197458	0.363837	ENSG00000119688	ENST00000356924;ENST00000298816;ENST00000537629	D;D	0.94613	-3.47;-3.47	5.79	2.14	0.27477	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.269560	0.42548	N	0.000685	T	0.00012	0.0000	N	0.25201	0.72	0.30896	P	0.729751	B;B;B;B	0.10296	0.003;0.003;0.001;0.003	B;B;B;B	0.08055	0.003;0.003;0.003;0.003	T	0.11348	-1.0591	9	0.07990	T	0.79	.	4.3634	0.11213	0.0:0.3228:0.1675:0.5096	rs4148077;rs57678766;rs4148077	200;200;304;304	F8W7M4;B7Z4V6;A8K5L7;O14678	.;.;.;ABCD4_HUMAN	T	304;200;41	ENSP00000349396:A304T;ENSP00000298816:A200T	ENSP00000298816:A200T	A	-	1	0	ABCD4	73829230	0.355000	0.24921	0.998000	0.56505	0.889000	0.51656	0.645000	0.24782	0.453000	0.26858	-0.367000	0.07326	GCA	C|0.709;T|0.291	0.291	strong		0.562	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
DCK	1633	hgsc.bcm.edu	37	4	71888240	71888240	+	Missense_Mutation	SNP	C	C	T	rs67437265	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71888240C>T	ENST00000286648.5	+	3	761	c.364C>T	c.(364-366)Cct>Tct	p.P122S	DCK_ENST00000504952.1_Missense_Mutation_p.P122S|DCK_ENST00000504730.1_Missense_Mutation_p.P122S	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	122				P -> S (in Ref. 4; AAV38744/AAV38745). {ECO:0000305}.	deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxycytidine kinase activity (GO:0004137)|drug binding (GO:0008144)|nucleoside kinase activity (GO:0019206)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Cytarabine(DB00987)|Decitabine(DB01262)|Emtricitabine(DB00879)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Lamivudine(DB00709)|Nelarabine(DB01280)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	TGCAGAGAAACCTGTATTATT	0.388													C|||	165	0.0329473	0.0635	0.0216	5008	,	,		18820	0.0387		0.0099	False		,,,				2504	0.0174				p.P122S		Atlas-SNP	.											.	DCK	23	.	0			c.C364T	GRCh37	CM076146	DCK	M	rs67437265	PASS	.	C	SER/PRO	209,4197	128.6+/-165.4	7,195,2001	110.0	111.0	111.0		364	5.8	1.0	4	dbSNP_130	111	87,8513	48.9+/-108.6	0,87,4213	yes	missense	DCK	NM_000788.2	74	7,282,6214	TT,TC,CC		1.0116,4.7435,2.2759	benign	122/261	71888240	296,12710	2203	4300	6503	SO:0001583	missense	1633	exon3			GAGAAACCTGTAT	M60527	CCDS3548.1	4q13.3-q21.1	2008-02-05			ENSG00000156136	ENSG00000156136	2.7.1.74		2704	protein-coding gene	gene with protein product		125450				8406512	Standard	NM_000788		Approved		uc003hfx.3	P27707	OTTHUMG00000129908	ENST00000286648.5:c.364C>T	4.37:g.71888240C>T	ENSP00000286648:p.Pro122Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_000788	B2R8V6|Q5TZY7|Q6FI11	Missense_Mutation	SNP	ENST00000286648.5	37	CCDS3548.1	73	0.033424908424908424	29	0.05894308943089431	9	0.024861878453038673	25	0.043706293706293704	10	0.013192612137203167	C	31	5.089919	0.94149	0.047435	0.010116	ENSG00000156136	ENST00000286648;ENST00000504730;ENST00000504952	D;D;D	0.97811	-4.55;-4.55;-4.55	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.89989	0.6875	L	0.57536	1.79	0.09310	P	0.999999999887503	D	0.89917	1.0	D	0.81914	0.995	D	0.86615	0.1875	8	.	.	.	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	122	P27707	DCK_HUMAN	S	122	ENSP00000286648:P122S;ENSP00000425578:P122S;ENSP00000421508:P122S	.	P	+	1	0	DCK	72107104	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.625000	0.83145	2.757000	0.94681	0.563000	0.77884	CCT	C|0.975;T|0.025	0.025	strong		0.388	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2		
RSAD1	55316	hgsc.bcm.edu	37	17	48557326	48557326	+	Missense_Mutation	SNP	G	G	A	rs2290862	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48557326G>A	ENST00000258955.2	+	3	440	c.355G>A	c.(355-357)Gca>Aca	p.A119T		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	119			A -> T (in dbSNP:rs2290862). {ECO:0000269|PubMed:15489334}.		porphyrin-containing compound biosynthetic process (GO:0006779)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|coproporphyrinogen oxidase activity (GO:0004109)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TGTGGCACAGGCAGCCCACCT	0.607											OREG0024566	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	2927	0.584465	0.9115	0.5807	5008	,	,		14507	0.2222		0.6262	False		,,,				2504	0.4755				p.A119T		Atlas-SNP	.											.	RSAD1	36	.	0			c.G355A						PASS	.	A	THR/ALA	3825,581	256.1+/-261.0	1665,495,43	47.0	54.0	51.0		355	0.0	0.0	17	dbSNP_100	51	5389,3211	483.2+/-371.1	1698,1993,609	yes	missense	RSAD1	NM_018346.1	58	3363,2488,652	AA,AG,GG		37.3372,13.1866,29.1558	benign	119/443	48557326	9214,3792	2203	4300	6503	SO:0001583	missense	55316	exon3			GCACAGGCAGCCC	AK002026	CCDS11569.1	17q21.33	2004-11-08			ENSG00000136444	ENSG00000136444			25634	protein-coding gene	gene with protein product						12477932	Standard	NM_018346		Approved	FLJ11164	uc002iqw.1	Q9HA92	OTTHUMG00000162126	ENST00000258955.2:c.355G>A	17.37:g.48557326G>A	ENSP00000258955:p.Ala119Thr	Somatic	109	0	0	955	WXS	Illumina HiSeq	Phase_I	116	115	0.991379	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Missense_Mutation	SNP	ENST00000258955.2	37	CCDS11569.1	1274	0.5833333333333334	446	0.9065040650406504	234	0.6464088397790055	124	0.21678321678321677	470	0.6200527704485488	A	9.385	1.074063	0.20147	0.868134	0.626628	ENSG00000136444	ENST00000258955	T	0.22336	1.96	4.64	0.0196	0.14121	Elongator protein 3/MiaB/NifB (1);Radical SAM, alpha/beta horseshoe (1);Radical SAM (1);	1.279430	0.05015	N	0.471753	T	0.00012	0.0000	N	0.02721	-0.515	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.20107	-1.0285	9	0.19590	T	0.45	3.2733	6.9334	0.24453	0.3137:0.0:0.565:0.1213	rs2290862;rs17857387;rs2290862	119	Q9HA92	RSAD1_HUMAN	T	119	ENSP00000258955:A119T	ENSP00000258955:A119T	A	+	1	0	RSAD1	45912325	0.003000	0.15002	0.009000	0.14445	0.879000	0.50718	0.282000	0.18829	-0.048000	0.13401	-1.794000	0.00625	GCA	G|0.331;A|0.669	0.669	strong		0.607	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346	
VPS13A	23230	hgsc.bcm.edu	37	9	79985181	79985181	+	Silent	SNP	C	C	T	rs117485827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:79985181C>T	ENST00000360280.3	+	64	8936	c.8676C>T	c.(8674-8676)atC>atT	p.I2892I	VPS13A_ENST00000357409.5_Silent_p.I2892I|VPS13A_ENST00000376636.3_Silent_p.I2853I|VPS13A_ENST00000376634.4_Silent_p.I2892I	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2892					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AGGGAGCCATCCAGGGTCCTG	0.398													C|||	12	0.00239617	0.0015	0.0029	5008	,	,		19582	0.0		0.007	False		,,,				2504	0.001				p.I2892I		Atlas-SNP	.											.	VPS13A	735	.	0			c.C8676T						PASS	.	C	,,,	13,4393	19.1+/-41.9	0,13,2190	75.0	74.0	75.0		8559,8676,8676,8676	1.5	1.0	9	dbSNP_132	75	90,8510	51.5+/-111.7	1,88,4211	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	1,101,6401	TT,TC,CC		1.0465,0.2951,0.7919	,,,	2853/3136,2892/3070,2892/3096,2892/3175	79985181	103,12903	2203	4300	6503	SO:0001819	synonymous_variant	23230	exon64			AGCCATCCAGGGT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.8676C>T	9.37:g.79985181C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	51	0.536842	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			C|0.993;T|0.007	0.007	strong		0.398	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
MICA	100507436	hgsc.bcm.edu	37	6	31379109	31379109	+	Missense_Mutation	SNP	G	G	A	rs1051794	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31379109G>A	ENST00000449934.2	+	3	640	c.586G>A	c.(586-588)Gaa>Aaa	p.E196K	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				GCGATATCTAGAATCCGGCGT	0.532													g|||	1826	0.364617	0.4796	0.4049	5008	,	,		21041	0.2996		0.3141	False		,,,				2504	0.2996				p.E196K		Atlas-SNP	.											.	MICA	21	.	0			c.G586A						PASS	.	G	LYS/GLU	580,804		132,316,244	98.0	87.0	91.0		586	-0.8	0.0	6	dbSNP_86	91	919,2263		126,667,798	yes	missense	MICA	NM_001177519.1	56	258,983,1042	AA,AG,GG		28.8812,41.9075,32.8296	benign	196/333	31379109	1499,3067	692	1591	2283	SO:0001583	missense	100507436	exon3			TATCTAGAATCCG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.586G>A	6.37:g.31379109G>A	ENSP00000413079:p.Glu196Lys	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	799	0.3658424908424908	227	0.4613821138211382	169	0.46685082872928174	160	0.27972027972027974	243	0.32058047493403696	N	4.401	0.074063	0.08485	0.419075	0.288812	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934	T	0.00864	5.6	1.31	-0.805	0.10879	.	3.050000	0.01394	N	0.013352	T	0.00271	0.0008	.	.	.	0.80722	P	0.0	B;B	0.12013	0.004;0.005	B;B	0.20577	0.012;0.03	T	0.47071	-0.9145	8	0.32370	T	0.25	.	2.9805	0.05952	0.2051:0.2819:0.5129:0.0	rs1051794;rs3192171;rs3819267;rs9266809;rs17417510;rs17845519;rs17858409;rs17883860;rs59858174;rs1051794	58;196	Q5SS58;Q96QC4	.;.	K	58;196;153;196	ENSP00000413079:E196K	ENSP00000365394:E196K	E	+	1	0	MICA	31487088	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.226000	0.09139	-0.322000	0.08615	-1.206000	0.01644	GAA	G|0.642;A|0.358	0.358	strong		0.532	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
GTF2A1L	11036	hgsc.bcm.edu	37	2	48873662	48873662	+	Silent	SNP	T	T	C	rs13396590	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:48873662T>C	ENST00000403751.3	+	6	496	c.459T>C	c.(457-459)caT>caC	p.H153H	STON1-GTF2A1L_ENST00000402114.2_Silent_p.H857H|STON1-GTF2A1L_ENST00000309827.2_Silent_p.H857H|STON1-GTF2A1L_ENST00000394754.1_Silent_p.H857H|GTF2A1L_ENST00000430487.2_Silent_p.H119H|STON1-GTF2A1L_ENST00000405008.1_Silent_p.H857H|LHCGR_ENST00000420913.3_5'UTR|STON1-GTF2A1L_ENST00000394751.3_Silent_p.H810H|GTF2A1L_ENST00000468326.1_3'UTR	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	153					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)			TTCTTCAGCATCCAATTCAGC	0.373													T|||	399	0.0796725	0.2405	0.0375	5008	,	,		16983	0.0		0.0517	False		,,,				2504	0.0031				p.H857H		Atlas-SNP	.											.	STON1-GTF2A1L	180	.	0			c.T2571C						PASS	.	T	,,,,	937,3469	356.9+/-313.7	96,745,1362	98.0	98.0	98.0		357,2571,2430,459,2571	0.9	1.0	2	dbSNP_121	98	542,8058	148.9+/-204.1	22,498,3780	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTF2A1L,STON1-GTF2A1L	NM_001193487.1,NM_001198593.1,NM_001198594.1,NM_006872.3,NM_172311.2	,,,,	118,1243,5142	CC,CT,TT		6.3023,21.2665,11.3717	,,,,	119/445,857/1159,810/1136,153/479,857/1183	48873662	1479,11527	2203	4300	6503	SO:0001819	synonymous_variant	286749	exon8			TCAGCATCCAATT	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.459T>C	2.37:g.48873662T>C		Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	259	112	0.432432	NM_001198593	B4DY14|Q53FD9|Q5D050	Silent	SNP	ENST00000403751.3	37	CCDS46281.1																																																																																			T|0.899;C|0.101	0.101	strong		0.373	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872	
EEF2K	29904	hgsc.bcm.edu	37	16	22237118	22237118	+	Missense_Mutation	SNP	A	A	G	rs9935059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:22237118A>G	ENST00000263026.5	+	2	542	c.68A>G	c.(67-69)cAt>cGt	p.H23R		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	23			H -> R (in dbSNP:rs9935059). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CGAGCTGGCCATGATGGTGAT	0.552													a|||	1128	0.22524	0.323	0.2075	5008	,	,		18457	0.3085		0.0716	False		,,,				2504	0.1779				p.H23R	NSCLC(195;1411 2157 20319 27471 51856)	Atlas-SNP	.											.	EEF2K	142	.	0			c.A68G						PASS	.	G	ARG/HIS	1457,2937	471.7+/-356.1	269,919,1009	57.0	56.0	57.0		68	-5.9	0.0	16	dbSNP_119	57	680,7920	169.4+/-220.8	34,612,3654	yes	missense	EEF2K	NM_013302.3	29	303,1531,4663	GG,GA,AA		7.907,33.1589,16.4461	benign	23/726	22237118	2137,10857	2197	4300	6497	SO:0001583	missense	29904	exon2			CTGGCCATGATGG	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.68A>G	16.37:g.22237118A>G	ENSP00000263026:p.His23Arg	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_013302	Q8N588	Missense_Mutation	SNP	ENST00000263026.5	37	CCDS10604.1	435	0.19917582417582416	135	0.27439024390243905	79	0.21823204419889503	170	0.2972027972027972	51	0.06728232189973615	a	2.075	-0.412143	0.04799	0.331589	0.07907	ENSG00000103319	ENST00000263026	T	0.07444	3.19	5.6	-5.86	0.02304	.	0.750933	0.13237	N	0.403188	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	0.48502	-0.9030	9	0.23302	T	0.38	-9.8593	9.3942	0.38392	0.2814:0.4212:0.2974:0.0	rs9935059;rs17856954;rs52837232;rs56726855;rs9935059	23	O00418	EF2K_HUMAN	R	23	ENSP00000263026:H23R	ENSP00000263026:H23R	H	+	2	0	EEF2K	22144619	0.000000	0.05858	0.001000	0.08648	0.135000	0.20990	-0.057000	0.11768	-1.286000	0.02384	-0.253000	0.11424	CAT	A|0.816;G|0.184	0.184	strong		0.552	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302	
ZNF33A	7581	hgsc.bcm.edu	37	10	38345455	38345455	+	Silent	SNP	A	A	G	rs12242343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38345455A>G	ENST00000458705.2	+	5	2558	c.2400A>G	c.(2398-2400)ggA>ggG	p.G800G	ZNF33A_ENST00000307441.9_Silent_p.G800G|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Silent_p.G807G|ZNF33A_ENST00000374618.3_Silent_p.G801G			Q06730	ZN33A_HUMAN	zinc finger protein 33A	800					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CACACTGTGGAGAAAGCCCTG	0.388													A|||	140	0.0279553	0.0915	0.013	5008	,	,		18836	0.0		0.0099	False		,,,				2504	0.0				p.G801G		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2403G						PASS	.	A	,	359,4047	175.9+/-205.1	19,321,1863	61.0	59.0	60.0		2403,2400	1.9	0.1	10	dbSNP_120	60	53,8547	32.3+/-84.9	0,53,4247	no	coding-synonymous,coding-synonymous	ZNF33A	NM_006954.1,NM_006974.2	,	19,374,6110	GG,GA,AA		0.6163,8.148,3.1678	,	801/812,800/811	38345455	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			CTGTGGAGAAAGC	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2400A>G	10.37:g.38345455A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	71	40	0.56338	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	37	CCDS31182.1																																																																																			A|0.968;G|0.032	0.032	strong		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
SEMG1	6406	hgsc.bcm.edu	37	20	43837052	43837052	+	Missense_Mutation	SNP	C	C	A	rs199672858	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43837052C>A	ENST00000372781.3	+	2	1171	c.1114C>A	c.(1114-1116)Cgc>Agc	p.R372S	SEMG1_ENST00000244069.6_Missense_Mutation_p.R312S	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	372	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.		R -> L (in dbSNP:rs2233887). {ECO:0000269|PubMed:14629036}.		insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TGTATCCCAACGCAGTATTTA	0.418																																					p.R372S		Atlas-SNP	.											SEMG1,bladder,carcinoma,0,3	SEMG1	71	3	0			c.C1114A						scavenged	.						77.0	71.0	73.0					20																	43837052		2203	4300	6503	SO:0001583	missense	6406	exon2			TCCCAACGCAGTA		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.1114C>A	20.37:g.43837052C>A	ENSP00000361867:p.Arg372Ser	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	137	2	0.0145985	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.712711	0.00712	.	.	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.03951	3.75;3.75	0.951	-1.9	0.07665	.	.	.	.	.	T	0.00754	0.0025	N	0.00082	-2.215	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	9	0.09590	T	0.72	.	0.297	0.00267	0.2228:0.2395:0.2981:0.2396	.	312;372	P04279-2;P04279	.;SEMG1_HUMAN	S	312;372	ENSP00000244069:R312S;ENSP00000361867:R372S	ENSP00000244069:R312S	R	+	1	0	SEMG1	43270466	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.965000	0.03829	-2.064000	0.00888	-1.625000	0.00788	CGC	C|1.000;T|0.000	.	alt		0.418	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
ZMYND11	10771	hgsc.bcm.edu	37	10	267222	267222	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:267222T>C	ENST00000397962.3	+	4	792	c.364T>C	c.(364-366)Tat>Cat	p.Y122H	ZMYND11_ENST00000381591.1_Missense_Mutation_p.Y122H|ZMYND11_ENST00000381607.4_Intron|ZMYND11_ENST00000309776.4_Missense_Mutation_p.Y82H|ZMYND11_ENST00000509513.2_Missense_Mutation_p.Y122H|ZMYND11_ENST00000381584.1_Missense_Mutation_p.Y105H|ZMYND11_ENST00000602682.1_Intron|ZMYND11_ENST00000558098.2_Missense_Mutation_p.Y122H|ZMYND11_ENST00000403354.1_Intron|ZMYND11_ENST00000397959.3_Intron|ZMYND11_ENST00000381604.4_Missense_Mutation_p.Y82H|ZMYND11_ENST00000402736.1_Missense_Mutation_p.Y122H|ZMYND11_ENST00000545619.1_Intron|ZMYND11_ENST00000381602.4_Missense_Mutation_p.Y82H|ZMYND11_ENST00000535374.1_Intron			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	122					cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		TTTTCGTGTGTATCATTCCAA	0.448																																					p.Y122H		Atlas-SNP	.											ZMYND11_ENST00000397962,NS,carcinoma,-1,3	ZMYND11	72	3	0			c.T364C						scavenged	.						331.0	290.0	304.0					10																	267222		2203	4300	6503	SO:0001583	missense	10771	exon4			CGTGTGTATCATT	X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"""Zinc fingers, MYND-type"""	16966	protein-coding gene	gene with protein product		608668	"""zinc finger, MYND domain containing 11"""			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.364T>C	10.37:g.267222T>C	ENSP00000381053:p.Tyr122His	Somatic	400	0	0		WXS	Illumina HiSeq	Phase_I	353	4	0.0113314	NM_212479	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Missense_Mutation	SNP	ENST00000397962.3	37	CCDS7052.2	.	.	.	.	.	.	.	.	.	.	T	20.9	4.072533	0.76415	.	.	ENSG00000015171	ENST00000397962;ENST00000309776;ENST00000381602;ENST00000509513;ENST00000381591;ENST00000402736;ENST00000381604;ENST00000397955;ENST00000381584	D;D;D;D;D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54;-2.54;-2.54;-2.54;-2.54	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.95037	0.8393	M	0.86953	2.85	0.41827	D	0.990050	D;D;D;D	0.76494	0.999;0.995;0.998;0.998	D;P;D;D	0.76071	0.979;0.829;0.987;0.987	D	0.95694	0.8743	9	0.72032	D	0.01	-19.6067	15.8761	0.79162	0.0:0.0:0.0:1.0	.	122;122;82;122	Q2LD45;Q2LD48;B0QZE3;E7ENI9	.;.;.;.	H	122;82;82;122;122;122;82;137;105	ENSP00000381053:Y122H;ENSP00000309992:Y82H;ENSP00000371015:Y82H;ENSP00000424205:Y122H;ENSP00000371003:Y122H;ENSP00000386010:Y122H;ENSP00000371017:Y82H;ENSP00000381046:Y137H;ENSP00000370996:Y105H	ENSP00000309992:Y82H	Y	+	1	0	ZMYND11	257222	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.698000	0.84413	2.139000	0.66308	0.533000	0.62120	TAT	.	.	none		0.448	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329922	55329922	+	Missense_Mutation	SNP	A	A	T	rs1049150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55329922A>T	ENST00000391728.4	+	3	256	c.223A>T	c.(223-225)Ata>Tta	p.I75L	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.I75L|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.I75L|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.I75L|KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.I75L	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	75	Ig-like C2-type 1.		I -> L (in dbSNP:rs1049150).		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CCATGGCAGAATATTCCAGGA	0.502													a|||	2960	0.591054	0.7284	0.5548	5008	,	,		13827	0.7679		0.3708	False		,,,				2504	0.4755				p.I75L		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A223T						PASS	.	A	LEU/ILE	2877,1471		1110,657,407	92.0	103.0	99.0		223	-2.3	0.0	19	dbSNP_86	99	2857,5383		929,999,2192	yes	missense	KIR3DL1	NM_013289.2	5	2039,1656,2599	TT,TA,AA		34.6723,33.8316,45.5513		75/445	55329922	5734,6854	2174	4120	6294	SO:0001583	missense	3811	exon3			GGCAGAATATTCC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.223A>T	19.37:g.55329922A>T	ENSP00000375608:p.Ile75Leu	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	.	.	.	.	.	.	.	.	.	.	-	2.863	-0.235718	0.05944	0.661684	0.346723	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.11495	2.77;2.77;2.77;2.77;2.77	1.25	-2.26	0.06867	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.56199	1.76	0.80722	P	0.0	B;B	0.21520	0.057;0.0	P;B	0.54629	0.757;0.007	T	0.48896	-0.8994	8	0.48119	T	0.1	.	2.0951	0.03666	0.4108:0.2966:0.0:0.2927	rs1049150;rs3189240;rs11670412;rs16986032;rs57228949	75;75	F6QF33;P43629	.;KI3L1_HUMAN	L	75;75;75;53;75;75	ENSP00000384528:I75L;ENSP00000443350:I75L;ENSP00000442355:I75L;ENSP00000375608:I75L;ENSP00000326868:I75L	ENSP00000326868:I75L	I	+	1	0	KIR3DL1	60021734	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.200000	0.03029	-0.748000	0.04753	0.155000	0.16302	ATA	A|0.545;T|0.455	0.455	strong		0.502	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
CDC37L1	55664	hgsc.bcm.edu	37	9	4679847	4679847	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:4679847A>C	ENST00000381854.3	+	1	282	c.80A>C	c.(79-81)gAc>gCc	p.D27A	CDC37L1_ENST00000381858.1_Missense_Mutation_p.D27A|CDC37L1_ENST00000479095.1_3'UTR|RP11-6J24.6_ENST00000607997.1_lincRNA	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	27	Self-association.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		AGTGACTTCGACGTGTTCCCC	0.697											OREG0019085	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D27A		Atlas-SNP	.											.	CDC37L1	19	.	0			c.A80C						PASS	.						43.0	49.0	47.0					9																	4679847		2202	4299	6501	SO:0001583	missense	55664	exon1			ACTTCGACGTGTT	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"""CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1"", ""cell division cycle 37 homolog (S. cerevisiae)-like 1"""				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.80A>C	9.37:g.4679847A>C	ENSP00000371278:p.Asp27Ala	Somatic	78	0	0	620	WXS	Illumina HiSeq	Phase_I	105	38	0.361905	NM_017913	B1AL70|Q9NWS3|Q9NX16	Missense_Mutation	SNP	ENST00000381854.3	37	CCDS6454.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.894709	0.33442	.	.	ENSG00000106993	ENST00000381858;ENST00000381854	T;T	0.44083	0.93;0.93	5.09	5.09	0.68999	.	0.233816	0.37053	N	0.002269	T	0.46908	0.1417	N	0.19112	0.55	0.32054	N	0.596549	D	0.63880	0.993	D	0.70227	0.968	T	0.57300	-0.7835	10	0.72032	D	0.01	-13.2073	11.1808	0.48627	1.0:0.0:0.0:0.0	.	27	Q7L3B6	CD37L_HUMAN	A	27	ENSP00000371282:D27A;ENSP00000371278:D27A	ENSP00000371278:D27A	D	+	2	0	CDC37L1	4669847	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.755000	0.55197	2.139000	0.66308	0.455000	0.32223	GAC	.	.	none		0.697	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913	
UQCRC1	7384	hgsc.bcm.edu	37	3	48638801	48638801	+	Missense_Mutation	SNP	C	C	T	rs62618742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:48638801C>T	ENST00000203407.5	-	7	1222	c.806G>A	c.(805-807)cGc>cAc	p.R269H		NM_003365.2	NP_003356.2	P31930	QCR1_HUMAN	ubiquinol-cytochrome c reductase core protein I	269					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|response to activity (GO:0014823)|response to alkaloid (GO:0043279)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GCCAGTGAAGCGGCATGGAGT	0.592													C|||	55	0.0109824	0.0038	0.0216	5008	,	,		22859	0.0		0.0318	False		,,,				2504	0.0031				p.R269H	NSCLC(81;1112 1427 27031 32409 45529)	Atlas-SNP	.											UQCRC1,NS,carcinoma,-1,2	UQCRC1	42	2	0			c.G806A						PASS	.	C	HIS/ARG	35,4371	40.8+/-73.8	0,35,2168	118.0	99.0	106.0		806	5.4	1.0	3	dbSNP_129	106	255,8345	100.1+/-161.6	2,251,4047	yes	missense	UQCRC1	NM_003365.2	29	2,286,6215	TT,TC,CC		2.9651,0.7944,2.2297	probably-damaging	269/481	48638801	290,12716	2203	4300	6503	SO:0001583	missense	7384	exon7			GTGAAGCGGCATG	BC009586	CCDS2774.1	3p21	2011-07-04			ENSG00000010256	ENSG00000010256	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12585	protein-coding gene	gene with protein product		191328				8407948	Standard	NM_003365		Approved	D3S3191, QCR1, UQCR1	uc003cub.1	P31930	OTTHUMG00000133539	ENST00000203407.5:c.806G>A	3.37:g.48638801C>T	ENSP00000203407:p.Arg269His	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_003365	B2R7R8|Q96DD2	Missense_Mutation	SNP	ENST00000203407.5	37	CCDS2774.1	28	0.01282051282051282	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	21	0.027704485488126648	C	18.89	3.719279	0.68844	0.007944	0.029651	ENSG00000010256	ENST00000203407	T	0.29655	1.56	5.43	5.43	0.79202	Peptidase M16, C-terminal (1);Peptidase M16, core (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.000000	0.85682	D	0.000000	T	0.32436	0.0829	M	0.70787	2.145	0.80722	D	1	P;D	0.89917	0.459;1.0	B;D	0.91635	0.157;0.999	T	0.38714	-0.9648	10	0.40728	T	0.16	-24.5828	19.2398	0.93877	0.0:1.0:0.0:0.0	rs62618742	154;269	B4DUL5;P31930	.;QCR1_HUMAN	H	269	ENSP00000203407:R269H	ENSP00000203407:R269H	R	-	2	0	UQCRC1	48613805	1.000000	0.71417	1.000000	0.80357	0.571000	0.35966	7.722000	0.84778	2.549000	0.85964	0.561000	0.74099	CGC	C|0.979;T|0.021	0.021	strong		0.592	UQCRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257517.1	NM_003365	
GFM2	84340	hgsc.bcm.edu	37	5	74017499	74017499	+	Missense_Mutation	SNP	C	C	T	rs1048167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:74017499C>T	ENST00000296805.3	-	21	2778	c.2321G>A	c.(2320-2322)cGg>cAg	p.R774Q	GFM2_ENST00000345239.2_Missense_Mutation_p.R727Q|GFM2_ENST00000515125.1_5'UTR|GFM2_ENST00000509430.1_Missense_Mutation_p.R774Q	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		ACCACTTCTCCGGTTGAGCAG	0.368													C|||	619	0.123602	0.2284	0.1095	5008	,	,		17618	0.0218		0.1382	False		,,,				2504	0.0818				p.R774Q		Atlas-SNP	.											.	GFM2	38	.	0			c.G2321A						PASS	.	C	GLN/ARG,GLN/ARG	991,3415	371.5+/-320.0	112,767,1324	96.0	99.0	98.0		2321,2180	-3.3	0.4	5	dbSNP_86	98	1066,7534	225.4+/-261.5	64,938,3298	yes	missense,missense	GFM2	NM_032380.3,NM_170691.1	43,43	176,1705,4622	TT,TC,CC		12.3953,22.4921,15.8158	benign,benign	774/780,727/733	74017499	2057,10949	2203	4300	6503	SO:0001583	missense	84340	exon21			CTTCTCCGGTTGA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.2321G>A	5.37:g.74017499C>T	ENSP00000296805:p.Arg774Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_032380		Missense_Mutation	SNP	ENST00000296805.3	37	CCDS4023.1	271	0.12408424908424909	122	0.24796747967479674	47	0.1298342541436464	15	0.026223776223776224	87	0.11477572559366754	C	11.05	1.525283	0.27299	0.224921	0.123953	ENSG00000164347	ENST00000296805;ENST00000345239;ENST00000546082;ENST00000509430	T;T;T	0.54279	0.58;0.58;0.58	5.98	-3.33	0.04958	Elongation factor G/III/V (1);	0.433895	0.26836	N	0.022253	T	0.00012	0.0000	N	0.08118	0	0.50467	P	1.24000000000013E-4	B;B;B	0.18741	0.03;0.003;0.017	B;B;B	0.25987	0.065;0.01;0.048	T	0.22103	-1.0226	9	0.44086	T	0.13	0.0332	13.1975	0.59746	0.0:0.3691:0.0:0.6309	rs1048167;rs3188149;rs1048167	772;727;774	Q969S9-3;Q969S9-2;Q969S9	.;.;RRF2M_HUMAN	Q	774;727;596;774	ENSP00000296805:R774Q;ENSP00000296804:R727Q;ENSP00000427004:R774Q	ENSP00000296805:R774Q	R	-	2	0	GFM2	74053255	0.779000	0.28652	0.446000	0.26920	0.257000	0.26127	-0.165000	0.09968	-0.678000	0.05224	0.650000	0.86243	CGG	C|0.856;T|0.144	0.144	strong		0.368	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
MTA1	9112	hgsc.bcm.edu	37	14	105930406	105930406	+	Missense_Mutation	SNP	G	G	A	rs4983413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:105930406G>A	ENST00000331320.7	+	13	1328	c.1114G>A	c.(1114-1116)Gtc>Atc	p.V372I	MTA1_ENST00000406191.1_Missense_Mutation_p.V372I|MTA1_ENST00000435036.2_5'UTR|MTA1_ENST00000405646.1_Missense_Mutation_p.V355I	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	372			V -> I (in dbSNP:rs4983413).		circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.V372I(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		CGTCAACAACGTCAAGGCCGG	0.617													G|||	1427	0.284944	0.0121	0.3314	5008	,	,		12491	0.622		0.2366	False		,,,				2504	0.3231				p.V372I		Atlas-SNP	.											MTA1,NS,carcinoma,0,1	MTA1	61	1	1	Substitution - Missense(1)	stomach(1)	c.G1114A						scavenged	.	G	ILE/VAL,ILE/VAL	233,4173	138.0+/-173.8	9,215,1979	73.0	76.0	75.0		1114,1114	1.7	1.0	14	dbSNP_111	75	1995,6605	349.7+/-327.5	235,1525,2540	yes	missense,missense	MTA1	NM_001203258.1,NM_004689.3	29,29	244,1740,4519	AA,AG,GG		23.1977,5.2882,17.1306	benign,benign	372/431,372/716	105930406	2228,10778	2203	4300	6503	SO:0001583	missense	9112	exon13			AACAACGTCAAGG	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1114G>A	14.37:g.105930406G>A	ENSP00000333633:p.Val372Ile	Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	164	84	0.512195	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Missense_Mutation	SNP	ENST00000331320.7	37	CCDS32169.1	655	0.2999084249084249	11	0.022357723577235773	110	0.30386740331491713	360	0.6293706293706294	174	0.22955145118733508	G	12.92	2.082237	0.36758	0.052882	0.231977	ENSG00000182979	ENST00000414153;ENST00000331320;ENST00000406191;ENST00000405646;ENST00000434050	T;T;T;T	0.30981	1.52;1.52;1.51;1.53	4.61	1.66	0.24008	.	0.396957	0.27080	N	0.021022	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.99999999865637	B;B	0.31274	0.164;0.317	B;B	0.26202	0.036;0.067	T	0.36187	-0.9758	9	0.36615	T	0.2	-21.1079	7.0619	0.25131	0.1661:0.1403:0.6937:0.0	rs4983413;rs60510827;rs4983413	164;372	Q59FW1;Q13330	.;MTA1_HUMAN	I	281;372;372;355;164	ENSP00000333633:V372I;ENSP00000385702:V372I;ENSP00000384180:V355I;ENSP00000394106:V164I	ENSP00000333633:V372I	V	+	1	0	MTA1	105001451	0.813000	0.29090	0.972000	0.41901	0.734000	0.41952	1.456000	0.35201	0.366000	0.24427	0.563000	0.77884	GTC	G|0.782;A|0.218	0.218	strong		0.617	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
IRF2BP1	26145	hgsc.bcm.edu	37	19	46388379	46388379	+	Silent	SNP	C	C	G	rs3826892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46388379C>G	ENST00000302165.3	-	1	997	c.654G>C	c.(652-654)cgG>cgC	p.R218R		NM_015649.1	NP_056464.1	Q8IU81	I2BP1_HUMAN	interferon regulatory factor 2 binding protein 1	218					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)		ATTCCTCTGCCCGGCCTCGCA	0.627													C|||	797	0.159145	0.1067	0.2104	5008	,	,		16734	0.3938		0.0656	False		,,,				2504	0.0481				p.R218R		Atlas-SNP	.											IRF2BP1,NS,carcinoma,0,1	IRF2BP1	23	1	0			c.G654C						PASS	.	C		430,3976	204.8+/-226.9	24,382,1797	87.0	91.0	89.0		654	-0.6	1.0	19	dbSNP_107	89	494,8106	140.5+/-197.0	15,464,3821	no	coding-synonymous	IRF2BP1	NM_015649.1		39,846,5618	GG,GC,CC		5.7442,9.7594,7.1044		218/585	46388379	924,12082	2203	4300	6503	SO:0001819	synonymous_variant	26145	exon1			CTCTGCCCGGCCT	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.654G>C	19.37:g.46388379C>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	32	16	0.5	NM_015649	Q53EL7|Q6DC95|Q9BRZ9|Q9Y4P4	Silent	SNP	ENST00000302165.3	37	CCDS12678.1																																																																																			C|0.899;G|0.101	0.101	strong		0.627	IRF2BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461683.1	NM_015649	
SORCS3	22986	hgsc.bcm.edu	37	10	106974224	106974224	+	Missense_Mutation	SNP	C	C	A	rs200098588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:106974224C>A	ENST00000369701.3	+	18	2627	c.2400C>A	c.(2398-2400)aaC>aaA	p.N800K	SORCS3_ENST00000369699.4_Missense_Mutation_p.N86K	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	800					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGTCCAACAACTGCACAGATG	0.522													c|||	5	0.000998403	0.0038	0.0	5008	,	,		18731	0.0		0.0	False		,,,				2504	0.0				p.N800K	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C2400A						PASS	.		LYS/ASN	20,4386	26.2+/-53.5	0,20,2183	124.0	104.0	111.0		2400	5.0	1.0	10		111	0,8600		0,0,4300	yes	missense	SORCS3	NM_014978.1	94	0,20,6483	AA,AC,CC		0.0,0.4539,0.1538	possibly-damaging	800/1223	106974224	20,12986	2203	4300	6503	SO:0001583	missense	22986	exon18			CAACAACTGCACA	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2400C>A	10.37:g.106974224C>A	ENSP00000358715:p.Asn800Lys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	123	62	0.504065	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	13.79	2.343489	0.41498	0.004539	0.0	ENSG00000156395	ENST00000369701;ENST00000369699	T;T	0.68025	-0.3;-0.3	5.89	4.98	0.66077	VPS10 (1);PKD domain (1);	0.151901	0.56097	N	0.000021	T	0.74921	0.3780	L	0.41573	1.285	0.54753	D	0.999989	D	0.76494	0.999	D	0.70935	0.971	T	0.74000	-0.3805	9	.	.	.	.	17.0953	0.86633	0.0:0.8732:0.1268:0.0	.	800	Q9UPU3	SORC3_HUMAN	K	800;86	ENSP00000358715:N800K;ENSP00000358713:N86K	.	N	+	3	2	SORCS3	106964214	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.828000	0.55753	1.482000	0.48325	0.558000	0.71614	AAC	C|1.000;A|0.000	0.000	strong		0.522	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
PHF10	55274	hgsc.bcm.edu	37	6	170115902	170115902	+	Missense_Mutation	SNP	A	A	C	rs562092150		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:170115902A>C	ENST00000339209.4	-	6	718	c.595T>G	c.(595-597)Tat>Gat	p.Y199D	PHF10_ENST00000366780.4_Missense_Mutation_p.Y197D|PHF10_ENST00000464779.1_5'Flank	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	199	SAY.				nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)	p.Y111D(2)|p.Y199D(1)		endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		TTCTTAATATACTCAGGCACT	0.353																																					p.Y199D		Atlas-SNP	.											PHF10_ENST00000339209,NS,carcinoma,0,3	PHF10	76	3	3	Substitution - Missense(3)	lung(2)|prostate(1)	c.T595G						scavenged	.						81.0	83.0	82.0					6																	170115902		2202	4299	6501	SO:0001583	missense	55274	exon6			TAATATACTCAGG	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"""Zinc fingers, PHD-type"""	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.595T>G	6.37:g.170115902A>C	ENSP00000341805:p.Tyr199Asp	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	122	16	0.131148	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Missense_Mutation	SNP	ENST00000339209.4	37	CCDS5308.2	.	.	.	.	.	.	.	.	.	.	A	26.0	4.691335	0.88735	.	.	ENSG00000130024	ENST00000366780;ENST00000339209	T;T	0.29917	1.55;1.55	6.06	6.06	0.98353	.	0.107337	0.64402	D	0.000003	T	0.47266	0.1436	M	0.65975	2.015	0.80722	D	1	P;D;D	0.89917	0.955;1.0;0.995	P;D;P	0.85130	0.78;0.997;0.741	T	0.50759	-0.8790	10	0.87932	D	0	-18.8351	15.7905	0.78357	1.0:0.0:0.0:0.0	.	111;197;199	Q5T069;Q8WUB8-2;Q8WUB8	.;.;PHF10_HUMAN	D	197;199	ENSP00000355743:Y197D;ENSP00000341805:Y199D	ENSP00000341805:Y199D	Y	-	1	0	PHF10	169857827	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.676000	0.91199	2.324000	0.78689	0.533000	0.62120	TAT	.	.	none		0.353	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288	
DNMBP	23268	hgsc.bcm.edu	37	10	101716484	101716484	+	Silent	SNP	G	G	A	rs3750715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:101716484G>A	ENST00000324109.4	-	4	838	c.747C>T	c.(745-747)gtC>gtT	p.V249V	DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Silent_p.V249V	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	249	SH3 4. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)		TGTACAGGGCGACCCCATAGG	0.522													G|||	380	0.0758786	0.0144	0.0216	5008	,	,		17381	0.2937		0.008	False		,,,				2504	0.0429				p.V249V		Atlas-SNP	.											.	DNMBP	173	.	0			c.C747T						PASS	.			50,4356	53.6+/-89.4	1,48,2154	78.0	82.0	80.0		747	-4.8	0.3	10	dbSNP_107	80	49,8551	32.8+/-85.7	0,49,4251	no	coding-synonymous	DNMBP	NM_015221.2		1,97,6405	AA,AG,GG		0.5698,1.1348,0.7612		249/1578	101716484	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	23268	exon4			CAGGGCGACCCCA	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.747C>T	10.37:g.101716484G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	67	37	0.552239	NM_015221	Q8IVY3|Q9Y2L3	Silent	SNP	ENST00000324109.4	37	CCDS7485.1																																																																																			G|0.963;N|0.001	.	strong		0.522	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
FAT4	79633	hgsc.bcm.edu	37	4	126372742	126372742	+	Missense_Mutation	SNP	G	G	A	rs1567047	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:126372742G>A	ENST00000394329.3	+	9	10584	c.10571G>A	c.(10570-10572)gGc>gAc	p.G3524D	FAT4_ENST00000335110.5_Missense_Mutation_p.G1822D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3524	Cadherin 34. {ECO:0000255|PROSITE- ProRule:PRU00043}.		G -> D (in dbSNP:rs1567047).		branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AAACGGCCAGGCACTTTGGTG	0.478													G|||	1155	0.230631	0.0242	0.2522	5008	,	,		18233	0.3909		0.2952	False		,,,				2504	0.2628				p.G3524D		Atlas-SNP	.											.	FAT4	1752	.	0			c.G10571A						PASS	.	G	ASP/GLY	292,4114	157.8+/-190.6	10,272,1921	121.0	118.0	119.0		10571	5.8	0.9	4	dbSNP_88	119	2578,6022	417.3+/-352.4	400,1778,2122	yes	missense	FAT4	NM_024582.4	94	410,2050,4043	AA,AG,GG		29.9767,6.6273,22.0667	probably-damaging	3524/4982	126372742	2870,10136	2203	4300	6503	SO:0001583	missense	79633	exon9			GGCCAGGCACTTT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.10571G>A	4.37:g.126372742G>A	ENSP00000377862:p.Gly3524Asp	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	140	139	0.992857	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	565	0.2586996336996337	15	0.03048780487804878	107	0.2955801104972376	225	0.39335664335664333	218	0.287598944591029	G	23.6	4.435957	0.83885	0.066273	0.299767	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.54071	0.59;0.59	5.77	5.77	0.91146	Cadherin (3);Cadherin-like (1);	0.000000	0.33670	U	0.004671	T	0.00012	0.0000	M	0.77616	2.38	0.09310	P	0.9999999999954321	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.05801	-1.0863	9	0.66056	D	0.02	.	19.9983	0.97395	0.0:0.0:1.0:0.0	rs1567047;rs52797800;rs60153785;rs1567047	1822;3524;3524	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	D	3524;1822	ENSP00000377862:G3524D;ENSP00000335169:G1822D	ENSP00000335169:G1822D	G	+	2	0	FAT4	126592192	1.000000	0.71417	0.935000	0.37517	0.783000	0.44284	9.666000	0.98612	2.724000	0.93272	0.561000	0.74099	GGC	G|0.769;A|0.231	0.231	strong		0.478	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
CUL5	8065	hgsc.bcm.edu	37	11	107965639	107965639	+	Silent	SNP	G	G	A	rs146843253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:107965639G>A	ENST00000393094.2	+	15	2284	c.1668G>A	c.(1666-1668)ccG>ccA	p.P556P		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	556					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		ACTTGATACCGGAAGTAGAAG	0.353													G|||	5	0.000998403	0.0038	0.0	5008	,	,		16265	0.0		0.0	False		,,,				2504	0.0				p.P556P		Atlas-SNP	.											.	CUL5	71	.	0			c.G1668A						PASS	.	G		4,4398	8.1+/-20.4	0,4,2197	58.0	63.0	61.0		1668	0.6	1.0	11	dbSNP_134	61	0,8596		0,0,4298	no	coding-synonymous	CUL5	NM_003478.3		0,4,6495	AA,AG,GG		0.0,0.0909,0.0308		556/781	107965639	4,12994	2201	4298	6499	SO:0001819	synonymous_variant	8065	exon15			GATACCGGAAGTA	X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.1668G>A	11.37:g.107965639G>A		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	92	53	0.576087	NM_003478	A8K960|O14766|Q9BZC6	Silent	SNP	ENST00000393094.2	37	CCDS31668.1																																																																																			G|1.000;A|0.000	0.000	strong		0.353	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1		
OTOP3	347741	hgsc.bcm.edu	37	17	72943434	72943434	+	Missense_Mutation	SNP	G	G	A	rs35702634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72943434G>A	ENST00000328801.4	+	6	1484	c.1484G>A	c.(1483-1485)cGc>cAc	p.R495H		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	495						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)					GAGCCTCCCCGCAGAGGCTCC	0.652													G|||	30	0.00599042	0.0008	0.0101	5008	,	,		18312	0.0		0.0219	False		,,,				2504	0.0				p.R495H		Atlas-SNP	.											OTOP3,NS,carcinoma,+1,1	OTOP3	64	1	0			c.G1484A						PASS	.	G	HIS/ARG	16,4390		1,14,2188	24.0	25.0	25.0		1484	3.9	0.9	17	dbSNP_126	25	142,8458		1,140,4159	yes	missense	OTOP3	NM_178233.1	29	2,154,6347	AA,AG,GG		1.6512,0.3631,1.2148	probably-damaging	495/597	72943434	158,12848	2203	4300	6503	SO:0001583	missense	347741	exon6			CTCCCCGCAGAGG	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.1484G>A	17.37:g.72943434G>A	ENSP00000328090:p.Arg495His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	56	0.554455	NM_178233		Missense_Mutation	SNP	ENST00000328801.4	37	CCDS11709.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	13.60	2.285261	0.40394	0.003631	0.016512	ENSG00000182938	ENST00000328801	T	0.08896	3.04	3.86	3.86	0.44501	.	1.397770	0.04505	N	0.381917	T	0.06645	0.0170	L	0.44542	1.39	0.30176	N	0.800857	D	0.76494	0.999	P	0.60173	0.87	T	0.07328	-1.0778	10	0.15066	T	0.55	-12.6018	12.2683	0.54691	0.0:0.2304:0.7696:0.0	rs35702634	495	Q7RTS5	OTOP3_HUMAN	H	495	ENSP00000328090:R495H	ENSP00000328090:R495H	R	+	2	0	OTOP3	70455029	0.699000	0.27786	0.942000	0.38095	0.296000	0.27459	2.594000	0.46189	1.989000	0.58080	0.462000	0.41574	CGC	G|0.989;A|0.011	0.011	strong		0.652	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
PTPN5	84867	hgsc.bcm.edu	37	11	18751041	18751041	+	Silent	SNP	C	C	T	rs1550870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18751041C>T	ENST00000358540.2	-	14	1993	c.1563G>A	c.(1561-1563)gtG>gtA	p.V521V	PTPN5_ENST00000396171.4_Silent_p.V521V|PTPN5_ENST00000396166.3_Silent_p.V127V|PTPN5_ENST00000396168.1_Silent_p.V497V|PTPN5_ENST00000477854.1_Silent_p.V325V|PTPN5_ENST00000396167.2_Silent_p.V489V|PTPN5_ENST00000396170.1_Silent_p.V489V|RP11-1081L13.4_ENST00000527285.1_RNA	NM_006906.1	NP_008837.1	P54829	PTN5_HUMAN	protein tyrosine phosphatase, non-receptor type 5 (striatum-enriched)	521	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|prostate(1)|skin(4)	27						GGATGTCCACCACACCCTCCT	0.667													C|||	1590	0.317492	0.3185	0.3055	5008	,	,		15381	0.2619		0.4423	False		,,,				2504	0.2536				p.V521V		Atlas-SNP	.											.	PTPN5	163	.	0			c.G1563A						PASS	.	C	,,	1410,2988	454.2+/-350.6	239,932,1028	47.0	46.0	46.0		1467,1563,1563	3.3	1.0	11	dbSNP_88	46	3945,4641	539.1+/-383.5	925,2095,1273	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPN5	NM_001039970.1,NM_006906.1,NM_032781.3	,,	1164,3027,2301	TT,TC,CC		45.9469,32.06,41.2431	,,	489/534,521/566,521/566	18751041	5355,7629	2199	4293	6492	SO:0001819	synonymous_variant	84867	exon14			GTCCACCACACCC	BC064807	CCDS7845.1, CCDS41626.1, CCDS60746.1	11p15.1	2011-06-09			ENSG00000110786	ENSG00000110786		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9657	protein-coding gene	gene with protein product		176879				1714595	Standard	NM_001278236		Approved	STEP, PTPSTEP	uc001mpc.4	P54829	OTTHUMG00000134304	ENST00000358540.2:c.1563G>A	11.37:g.18751041C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	40	38	0.95	NM_032781	B3KXG7|B7Z386|B7ZAF5|D3DQY7|Q6P1Z2|Q8N2A1|Q8NDP8	Silent	SNP	ENST00000358540.2	37	CCDS7845.1																																																																																			C|0.633;T|0.367	0.367	strong		0.667	PTPN5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259196.2	NM_001039970	
LIPI	149998	hgsc.bcm.edu	37	21	15481365	15481365	+	Missense_Mutation	SNP	G	G	T	rs7278737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:15481365G>T	ENST00000536861.1	-	10	1331	c.1332C>A	c.(1330-1332)gaC>gaA	p.D444E	AP001347.6_ENST00000428809.1_RNA|AP001347.6_ENST00000432621.1_RNA|LIPI_ENST00000344577.2_Missense_Mutation_p.D465E			Q6XZB0	LIPI_HUMAN	lipase, member I	444			D -> E (in dbSNP:rs7278737). {ECO:0000269|PubMed:12719377}.		lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)			endometrium(1)|kidney(13)|large_intestine(9)|liver(3)|lung(24)|ovary(3)|urinary_tract(1)	54				Epithelial(23;0.000155)|COAD - Colon adenocarcinoma(22;0.0015)|Colorectal(24;0.00693)|Lung(58;0.166)		CTTCCTCTCTGTCTTTAAGTA	0.338													T|||	2599	0.51897	0.503	0.5403	5008	,	,		16535	0.5099		0.502	False		,,,				2504	0.5521				p.D465E		Atlas-SNP	.											LIPI,caecum,carcinoma,-2,1	LIPI	95	1	0			c.C1395A	GRCh37	CM035699	LIPI	M	rs7278737	PASS	.	T	GLU/ASP	2238,2168	584.2+/-386.0	562,1114,527	160.0	168.0	165.0		1395	0.1	0.1	21	dbSNP_116	165	4250,4348	578.6+/-390.7	1064,2122,1113	yes	missense	LIPI	NM_198996.2	45	1626,3236,1640	TT,TG,GG		49.4301,49.2056,49.8923	benign	465/482	15481365	6488,6516	2203	4299	6502	SO:0001583	missense	149998	exon10			CTCTCTGTCTTTA	BC028732	CCDS13564.1	21q11.2	2012-07-31			ENSG00000188992	ENSG00000188992			18821	protein-coding gene	gene with protein product	"""membrane-associated phospholipase A1 beta"", ""cancer/testis antigen 17"""	609252				12719377	Standard	XM_005260924		Approved	PRED5, LPDL, CT17, mPA-PLA1beta, PLA1C	uc002yjm.3	Q6XZB0	OTTHUMG00000074258	ENST00000536861.1:c.1332C>A	21.37:g.15481365G>T	ENSP00000440381:p.Asp444Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_198996	G1JSG3|G1JSG4|G1JSG5|G1JSG6|G1JSG7|G1JSG8|G1JSG9	Missense_Mutation	SNP	ENST00000536861.1	37		1085	0.4967948717948718	252	0.5121951219512195	199	0.5497237569060773	265	0.4632867132867133	369	0.4868073878627968	t	0	-2.714912	0.00093	0.507944	0.494301	ENSG00000188992	ENST00000344577;ENST00000536861	D;D	0.86097	-2.07;-2.02	3.7	0.125	0.14718	.	0.058071	0.64402	N	0.000003	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35599	-0.9782	9	0.02654	T	1	.	3.8141	0.08808	0.0:0.3319:0.2:0.4681	rs7278737;rs52812022;rs57390284;rs7278737	465	Q6XZB0-2	.	E	465;444	ENSP00000343331:D465E;ENSP00000440381:D444E	ENSP00000343331:D465E	D	-	3	2	LIPI	14403236	0.186000	0.23225	0.055000	0.19348	0.092000	0.18411	0.194000	0.17135	-0.228000	0.09869	-0.976000	0.02587	GAC	G|0.501;T|0.499	0.499	strong		0.338	LIPI-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_198996	
EPPK1	83481	hgsc.bcm.edu	37	8	144940267	144940267	+	Silent	SNP	G	G	A	rs28441354		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144940267G>A	ENST00000525985.1	-	2	7226	c.7155C>T	c.(7153-7155)ggC>ggT	p.G2385G				P58107	EPIPL_HUMAN	epiplakin 1	2385						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)			GGTCGAAGAAGCCCTTGGTGT	0.642																																					p.G2385G		Atlas-SNP	.											.	EPPK1	199	.	0			c.C7155T						PASS	.						274.0	257.0	263.0					8																	144940267		2190	4273	6463	SO:0001819	synonymous_variant	83481	exon1			GAAGAAGCCCTTG	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.7155C>T	8.37:g.144940267G>A		Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	227	13	0.0572687	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.995;A|0.005	0.005	weak		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
KRT8	3856	hgsc.bcm.edu	37	12	53294381	53294381	+	Silent	SNP	T	T	C	rs8608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:53294381T>C	ENST00000552551.1	-	5	1113	c.681A>G	c.(679-681)ctA>ctG	p.L227L	KRT8_ENST00000293308.6_Silent_p.L227L|KRT8_ENST00000546897.1_Silent_p.L227L|KRT8_ENST00000552150.1_Silent_p.L255L			P05787	K2C8_HUMAN	keratin 8	227	Coil 1B.|Rod.				cell differentiation involved in embryonic placenta development (GO:0060706)|extrinsic apoptotic signaling pathway (GO:0097191)|hepatocyte apoptotic process (GO:0097284)|response to hydrostatic pressure (GO:0051599)|response to other organism (GO:0051707)|sarcomere organization (GO:0045214)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	scaffold protein binding (GO:0097110)|structural molecule activity (GO:0005198)			endometrium(5)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(357;0.108)	Tenecteplase(DB00031)	CCTCTTCATATAGCTGCCTGA	0.582													C|||	2842	0.567492	0.3986	0.6182	5008	,	,		18626	0.6042		0.5318	False		,,,				2504	0.7587				p.L255L		Atlas-SNP	.											.	KRT8	41	.	0			c.A765G						PASS	.	C		1920,2486	626.3+/-394.7	423,1074,706	112.0	110.0	111.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	681	1.5	1.0	12	dbSNP_52	111	4399,4201	569.6+/-389.2	1144,2111,1045	no	coding-synonymous	KRT8	NM_002273.3		1567,3185,1751	CC,CT,TT		48.8488,43.5769,48.5853		227/484	53294381	6319,6687	2203	4300	6503	SO:0001819	synonymous_variant	3856	exon5			TTCATATAGCTGC	BC000654	CCDS8841.1, CCDS58234.1	12q13.13	2013-01-16			ENSG00000170421	ENSG00000170421		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6446	protein-coding gene	gene with protein product		148060				2434381, 1705144, 16831889	Standard	NM_002273		Approved	CARD2, K8, CK8, CYK8, K2C8, KO	uc009zmk.1	P05787	OTTHUMG00000169881	ENST00000552551.1:c.681A>G	12.37:g.53294381T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_001256282	A8K4H3|B0AZN5|F8VXB4|Q14099|Q14716|Q14717|Q53GJ0|Q6DHW5|Q6GMY0|Q6P4C7|Q96J60	Silent	SNP	ENST00000552551.1	37	CCDS8841.1																																																																																			T|0.483;C|0.517	0.517	strong		0.582	KRT8-001	KNOWN	alternative_5_UTR|overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406385.1	NM_002273	
LILRB3	11025	hgsc.bcm.edu	37	19	54724457	54724457	+	Missense_Mutation	SNP	T	T	C	rs1052995	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54724457T>C	ENST00000391750.1	-	7	1335	c.1199A>G	c.(1198-1200)tAc>tGc	p.Y400C	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Missense_Mutation_p.Y400C|LILRB3_ENST00000407860.2_Missense_Mutation_p.Y400C|LILRB3_ENST00000424807.1_Missense_Mutation_p.Y400C|LILRB3_ENST00000346401.6_Missense_Mutation_p.Y400C|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.Y400C|LILRA6_ENST00000270464.5_Missense_Mutation_p.Y400C			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	400	Ig-like C2-type 4.		Y -> F (in dbSNP:rs8105096).|Y -> H (in dbSNP:rs1052992).|Y -> R (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:9548455, ECO:0000269|Ref.3}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTTGGAGCTGTATGAGCCGTA	0.602													.|||	1376	0.27476	0.3306	0.2522	5008	,	,		9425	0.0476		0.2883	False		,,,				2504	0.4356				p.Y400C		Atlas-SNP	.											.	LILRB3	67	.	0			c.A1199G						PASS	.						19.0	12.0	14.0					19																	54724457		2178	3945	6123	SO:0001583	missense	11025	exon6			GAGCTGTATGAGC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1199A>G	19.37:g.54724457T>C	ENSP00000375630:p.Tyr400Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	87	39	0.448276	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	368	0.1684981684981685	146	0.2967479674796748	74	0.20441988950276244	20	0.03496503496503497	128	0.16886543535620052	C	8.457	0.854468	0.17106	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464	T;T;T;T;T;T;T	0.00753	5.74;5.74;5.74;5.74;5.74;5.74;5.74	2.88	-5.77	0.02369	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.834670	0.00465	N	0.000119	T	0.00012	0.0000	M	0.69823	2.125	0.80722	P	0.0	B;B;B;B;B;B	0.30870	0.298;0.001;0.001;0.108;0.053;0.004	P;B;B;B;B;B	0.56343	0.796;0.007;0.021;0.093;0.1;0.009	T	0.42682	-0.9437	9	0.39692	T	0.17	.	3.7917	0.08722	0.3774:0.2784:0.0:0.3442	rs1052995;rs2361812;rs3193479	400;400;400;400;400;400	B5MCX0;F8WCY4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;LIRB3_HUMAN;.	C	400	ENSP00000375630:Y400C;ENSP00000412771:Y400C;ENSP00000345184:Y400C;ENSP00000245620:Y400C;ENSP00000384274:Y400C;ENSP00000390120:Y400C;ENSP00000270464:Y400C	ENSP00000270464:Y400C	Y	-	2	0	LILRB3;LILRA6	59416269	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-8.592000	0.00019	-2.477000	0.00525	-4.852000	0.00002	TAC	T|1.000;|0.000	.	strong		0.602	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
TBC1D2	55357	hgsc.bcm.edu	37	9	100995721	100995721	+	Missense_Mutation	SNP	A	A	G	rs879369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100995721A>G	ENST00000375064.1	-	4	796	c.758T>C	c.(757-759)tTg>tCg	p.L253S	TBC1D2_ENST00000342112.5_Missense_Mutation_p.L35S|TBC1D2_ENST00000375066.5_Missense_Mutation_p.L253S	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	253			L -> S (in dbSNP:rs879369). {ECO:0000269|PubMed:11785977, ECO:0000269|PubMed:14702039}.		positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GTCAGAGGCCAAGGGCTGCTC	0.622													G|||	2065	0.41234	0.8011	0.3372	5008	,	,		19660	0.1756		0.339	False		,,,				2504	0.2597				p.L253S		Atlas-SNP	.											.	TBC1D2	70	.	0			c.T758C						PASS	.	G	SER/LEU	3240,1166	410.4+/-335.4	1196,848,159	104.0	93.0	97.0		758	-6.0	0.0	9	dbSNP_86	97	2730,5870	681.8+/-403.7	425,1880,1995	yes	missense	TBC1D2	NM_018421.3	145	1621,2728,2154	GG,GA,AA		31.7442,26.4639,45.9019	benign	253/918	100995721	5970,7036	2203	4300	6503	SO:0001583	missense	55357	exon4			GAGGCCAAGGGCT	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.758T>C	9.37:g.100995721A>G	ENSP00000364205:p.Leu253Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	59	36	0.610169	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		882	0.40384615384615385	382	0.7764227642276422	130	0.35911602209944754	99	0.17307692307692307	271	0.3575197889182058	G	0.006	-2.118793	0.00346	0.735361	0.317442	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112	T;T;T	0.13196	2.61;3.15;2.61	4.95	-5.96	0.02234	.	1.754710	0.02901	N	0.135376	T	0.00012	0.0000	L	0.35723	1.085	0.80722	P	0.0	B;B	0.11235	0.003;0.004	B;B	0.06405	0.001;0.002	T	0.34104	-0.9842	9	0.18710	T	0.47	.	15.9903	0.80199	0.7218:0.0:0.2782:0.0	rs879369;rs17761260;rs61283010;rs879369	253;253	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	S	253;253;35	ENSP00000364205:L253S;ENSP00000364207:L253S;ENSP00000341567:L35S	ENSP00000341567:L35S	L	-	2	0	TBC1D2	100035542	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.964000	0.01512	-2.065000	0.00887	-2.930000	0.00088	TTG	T|0.000;G|0.439;C|0.000;A|0.561	0.439	strong		0.622	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
PLG	5340	hgsc.bcm.edu	37	6	161139480	161139480	+	Silent	SNP	C	C	T	rs1130656	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:161139480C>T	ENST00000308192.9	+	8	1005	c.942C>T	c.(940-942)ttC>ttT	p.F314F		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	314	Kringle 3. {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)	p.F314F(1)		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)	CAGAAAACTTCCCCTGCAAGT	0.493													T|||	1752	0.34984	0.2368	0.2824	5008	,	,		17527	0.4554		0.3897	False		,,,				2504	0.4008				p.F314F		Atlas-SNP	.											PLG,NS,carcinoma,0,1	PLG	150	1	1	Substitution - coding silent(1)	prostate(1)	c.C942T						PASS	.	T		1176,3230	711.8+/-408.0	161,854,1188	115.0	121.0	119.0		942	-7.0	0.9	6	dbSNP_86	119	3466,5134	634.2+/-398.8	711,2044,1545	no	coding-synonymous	PLG	NM_000301.3		872,2898,2733	TT,TC,CC		40.3023,26.6909,35.6912		314/811	161139480	4642,8364	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon8			AAACTTCCCCTGC	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.942C>T	6.37:g.161139480C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	25	25	1	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			C|0.636;T|0.364	0.364	strong		0.493	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
GOLGA3	2802	hgsc.bcm.edu	37	12	133389998	133389998	+	Silent	SNP	T	T	C	rs7134809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133389998T>C	ENST00000450791.2	-	3	597	c.414A>G	c.(412-414)acA>acG	p.T138T	GOLGA3_ENST00000204726.3_Silent_p.T138T|GOLGA3_ENST00000456883.2_Silent_p.T138T|GOLGA3_ENST00000545875.1_Silent_p.T138T|GOLGA3_ENST00000537452.1_Silent_p.T138T			Q08378	GOGA3_HUMAN	golgin A3	138	Interaction with GOPC.				intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		GGGGAGAATCTGTAGAGCCTG	0.507													T|||	363	0.072484	0.0106	0.0735	5008	,	,		19223	0.0446		0.171	False		,,,				2504	0.0828				p.T138T		Atlas-SNP	.											.	GOLGA3	234	.	0			c.A414G						PASS	.	T	,	129,4277	95.7+/-134.4	3,123,2077	48.0	44.0	45.0		414,414	-2.5	0.0	12	dbSNP_116	45	1437,7163	275.0+/-291.5	134,1169,2997	no	coding-synonymous,coding-synonymous	GOLGA3	NM_001172557.1,NM_005895.3	,	137,1292,5074	CC,CT,TT		16.7093,2.9278,12.0406	,	138/1135,138/1499	133389998	1566,11440	2203	4300	6503	SO:0001819	synonymous_variant	2802	exon4			AGAATCTGTAGAG	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.414A>G	12.37:g.133389998T>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																			T|0.897;C|0.103	0.103	strong		0.507	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274415	39274415	+	Silent	SNP	C	C	T	rs425487		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	81	3	0.037037		WXS	Illumina HiSeq	Phase_I	108	5	0.0462963	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		
CTCFL	140690	hgsc.bcm.edu	37	20	56098733	56098733	+	Missense_Mutation	SNP	T	T	C	rs6025606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:56098733T>C	ENST00000608263.1	-	1	1190	c.529A>G	c.(529-531)Act>Gct	p.T177A	CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000371196.2_Missense_Mutation_p.T177A|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000429804.3_Missense_Mutation_p.T177A|CTCFL_ENST00000609232.1_Missense_Mutation_p.T177A|CTCFL_ENST00000608425.1_Missense_Mutation_p.T177A|CTCFL_ENST00000608440.1_Missense_Mutation_p.T177A|CTCFL_ENST00000481655.2_Missense_Mutation_p.T177A|CTCFL_ENST00000422869.2_Missense_Mutation_p.T177A|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000423479.3_Missense_Mutation_p.T177A|CTCFL_ENST00000432255.2_Missense_Mutation_p.T177A|CTCFL_ENST00000243914.3_Missense_Mutation_p.T177A|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000608158.1_Missense_Mutation_p.T177A	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	177			T -> A (in dbSNP:rs6025606). {ECO:0000269|PubMed:12011441, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17962299}.		cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			ATCAGTCCAGTAGTTTCAGCC	0.448													C|||	3751	0.749002	0.9312	0.6859	5008	,	,		19587	0.7361		0.661	False		,,,				2504	0.6513				p.T177A		Atlas-SNP	.											.	CTCFL	97	.	0			c.A529G						PASS	.	C	ALA/THR	3866,540	241.2+/-251.7	1693,480,30	102.0	110.0	108.0		529	-6.6	0.0	20	dbSNP_114	108	5431,3169	479.7+/-370.2	1728,1975,597	yes	missense	CTCFL	NM_080618.2	58	3421,2455,627	CC,CT,TT		36.8488,12.256,28.5176	benign	177/664	56098733	9297,3709	2203	4300	6503	SO:0001583	missense	140690	exon1			GTCCAGTAGTTTC		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.529A>G	20.37:g.56098733T>C	ENSP00000476783:p.Thr177Ala	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	115	114	0.991304	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	1627	0.74496336996337	452	0.9186991869918699	245	0.6767955801104972	437	0.763986013986014	493	0.6503957783641161	C	4.405	0.074755	0.08485	0.87744	0.631512	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000422869	T;T;T;T;T;T;T;T;T	0.10192	2.9;2.92;2.92;3.08;2.96;3.24;2.95;3.55;2.95	4.28	-6.63	0.01807	.	0.670897	0.12935	N	0.427068	T	0.00012	0.0000	N	0.25426	0.745	0.80722	P	0.0	B;B;B;B;B;B	0.12013	0.0;0.005;0.001;0.001;0.0;0.0	B;B;B;B;B;B	0.08055	0.001;0.003;0.001;0.001;0.0;0.0	T	0.42032	-0.9475	9	0.06099	T	0.92	3.0E-4	1.3564	0.02183	0.2061:0.305:0.1133:0.3756	rs6025606;rs52798292;rs58854357;rs6025606	177;177;177;177;177;177	A6XGM3;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;CTCFL_HUMAN	A	177	ENSP00000415579:T177A;ENSP00000243914:T177A;ENSP00000360239:T177A;ENSP00000415329:T177A;ENSP00000392034:T177A;ENSP00000413713:T177A;ENSP00000403369:T177A;ENSP00000409344:T177A;ENSP00000399061:T177A	ENSP00000243914:T177A	T	-	1	0	CTCFL	55532139	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.240000	0.00544	-2.144000	0.00802	-1.355000	0.01225	ACT	T|0.260;C|0.740	0.740	strong		0.448	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
TAS2R3	50831	hgsc.bcm.edu	37	7	141464765	141464765	+	Silent	SNP	C	C	T	rs2270009	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141464765C>T	ENST00000247879.2	+	1	869	c.807C>T	c.(805-807)ggC>ggT	p.G269G	SSBP1_ENST00000465582.1_Intron	NM_016943.2	NP_058639.1	Q9NYW6	TA2R3_HUMAN	taste receptor, type 2, member 3	269					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)	14	Melanoma(164;0.0171)					AGATGATTGGCGAAGTAATGA	0.388													C|||	2150	0.429313	0.1725	0.5202	5008	,	,		23769	0.6667		0.4632	False		,,,				2504	0.4325				p.G269G		Atlas-SNP	.											.	TAS2R3	40	.	0			c.C807T						PASS	.	C		987,3419	370.0+/-319.4	119,749,1335	151.0	136.0	141.0		807	-1.5	0.0	7	dbSNP_100	141	4205,4395	569.9+/-389.3	1019,2167,1114	no	coding-synonymous	TAS2R3	NM_016943.2		1138,2916,2449	TT,TC,CC		48.8953,22.4013,39.92		269/317	141464765	5192,7814	2203	4300	6503	SO:0001819	synonymous_variant	50831	exon1			GATTGGCGAAGTA	AF227130	CCDS5867.1	7q31.3-q32	2012-08-22			ENSG00000127362	ENSG00000127362		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14910	protein-coding gene	gene with protein product		604868					Standard	NM_016943		Approved	T2R3	uc003vwp.1	Q9NYW6	OTTHUMG00000157637	ENST00000247879.2:c.807C>T	7.37:g.141464765C>T		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_016943	A4D1U2|Q645W2|Q75MV6	Silent	SNP	ENST00000247879.2	37	CCDS5867.1																																																																																			C|0.568;N|0.000	.	strong		0.388	TAS2R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349288.1		
APLF	200558	hgsc.bcm.edu	37	2	68753240	68753240	+	Missense_Mutation	SNP	T	T	A	rs35002937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:68753240T>A	ENST00000303795.4	+	6	841	c.670T>A	c.(670-672)Tcc>Acc	p.S224T		NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	224			S -> T (in dbSNP:rs35002937).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						CAAAGATAAATCCCAGCTAAA	0.348													A|||	1150	0.229633	0.5991	0.1182	5008	,	,		16373	0.0367		0.1213	False		,,,				2504	0.1196				p.S224T		Atlas-SNP	.											APLF,colon,carcinoma,0,1	APLF	69	1	0			c.T670A						PASS	.	A	THR/SER	2385,2021	561.6+/-380.8	667,1051,485	85.0	88.0	87.0		670	3.6	0.1	2	dbSNP_126	87	1147,7453	766.1+/-407.6	81,985,3234	yes	missense	APLF	NM_173545.2	58	748,2036,3719	AA,AT,TT		13.3372,45.8693,27.1567	benign	224/512	68753240	3532,9474	2203	4300	6503	SO:0001583	missense	200558	exon6			GATAAATCCCAGC	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.670T>A	2.37:g.68753240T>A	ENSP00000307004:p.Ser224Thr	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	167	76	0.45509	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	447	0.20467032967032966	290	0.5894308943089431	43	0.11878453038674033	22	0.038461538461538464	92	0.12137203166226913	a	0.004	-2.284029	0.00251	0.541307	0.133372	ENSG00000169621	ENST00000303795	T	0.22336	1.96	4.75	3.6	0.41247	.	0.790106	0.11661	N	0.541829	T	0.00012	0.0000	N	0.00119	-2.075	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.45687	-0.9244	9	0.02654	T	1	.	4.1048	0.10032	0.7239:0.0:0.0962:0.1799	rs35002937	224;224	F8WET0;Q8IW19	.;APLF_HUMAN	T	224	ENSP00000307004:S224T	ENSP00000307004:S224T	S	+	1	0	APLF	68606744	0.270000	0.24152	0.145000	0.22337	0.037000	0.13140	0.150000	0.16263	0.421000	0.25980	-0.344000	0.07964	TCC	T|0.754;A|0.246	0.246	strong		0.348	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
KRT7	3855	hgsc.bcm.edu	37	12	52635360	52635360	+	Silent	SNP	G	G	A	rs999665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52635360G>A	ENST00000331817.5	+	5	981	c.798G>A	c.(796-798)gcG>gcA	p.A266A		NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	266	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.A266A(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	AGGTCAAGGCGCAGTATGAGG	0.602													G|||	2122	0.423722	0.3714	0.4366	5008	,	,		20705	0.3145		0.5378	False		,,,				2504	0.4806				p.A266A		Atlas-SNP	.											KRT7,NS,carcinoma,0,1	KRT7	48	1	1	Substitution - coding silent(1)	stomach(1)	c.G798A						PASS	.	G		1871,2535	540.8+/-375.6	387,1097,719	91.0	81.0	85.0		798	-0.1	0.7	12	dbSNP_86	85	4739,3861	608.7+/-395.4	1285,2169,846	no	coding-synonymous	KRT7	NM_005556.3		1672,3266,1565	AA,AG,GG		44.8953,42.4648,49.1773		266/470	52635360	6610,6396	2203	4300	6503	SO:0001819	synonymous_variant	3855	exon5			CAAGGCGCAGTAT		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.798G>A	12.37:g.52635360G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	94	91	0.968085	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Silent	SNP	ENST00000331817.5	37	CCDS8822.1																																																																																			G|0.514;A|0.486	0.486	strong		0.602	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
MMEL1	79258	hgsc.bcm.edu	37	1	2541269	2541269	+	Splice_Site	SNP	A	A	G	rs10797440	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2541269A>G	ENST00000378412.3	-	5	455	c.294T>C	c.(292-294)gcT>gcC	p.A98A	MMEL1_ENST00000502556.1_Splice_Site_p.A98A|MMEL1_ENST00000288709.6_Splice_Site_p.A89A			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	98						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)		GGATCCTGGCAGCTGCTCGTC	0.627													g|||	2662	0.53155	0.7027	0.4885	5008	,	,		18168	0.5357		0.33	False		,,,				2504	0.5337				p.A98A		Atlas-SNP	.											.	MMEL1	64	.	0			c.T294C						PASS	.	G		2887,1519		947,993,263	75.0	62.0	66.0		294	-3.0	0.8	1	dbSNP_120	66	2852,5748		475,1902,1923	yes	coding-synonymous-near-splice	MMEL1	NM_033467.3		1422,2895,2186	GG,GA,AA		33.1628,34.4757,44.1258		98/780	2541269	5739,7267	2203	4300	6503	SO:0001630	splice_region_variant	79258	exon5			CCTGGCAGCTGCT	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.293-1T>C	1.37:g.2541269A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	99	97	0.979798	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Silent	SNP	ENST00000378412.3	37	CCDS30569.2																																																																																			A|0.542;G|0.458	0.458	strong		0.627	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	Silent
TEX43	389320	hgsc.bcm.edu	37	5	125968301	125968301	+	Silent	SNP	C	C	T	rs6887295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:125968301C>T	ENST00000357147.3	+	2	163	c.150C>T	c.(148-150)gtC>gtT	p.V50V		NM_207408.1	NP_997291.1	Q6ZNM6	TEX43_HUMAN		50										large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	7						GACGTTATGTCATGCCTTGGA	0.368													T|||	676	0.134984	0.4818	0.0375	5008	,	,		21723	0.001		0.0	False		,,,				2504	0.0123				p.V50V		Atlas-SNP	.											.	C5orf48	21	.	0			c.C150T						PASS	.	T		1693,2713	652.3+/-399.4	334,1025,844	109.0	104.0	105.0		150	-6.3	0.1	5	dbSNP_116	105	12,8588	818.7+/-406.8	0,12,4288	no	coding-synonymous	C5orf48	NM_207408.1		334,1037,5132	TT,TC,CC		0.1395,38.4249,13.1093		50/135	125968301	1705,11301	2203	4300	6503	SO:0001819	synonymous_variant	389320	exon2			TTATGTCATGCCT																												ENST00000357147.3:c.150C>T	5.37:g.125968301C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_207408		Silent	SNP	ENST00000357147.3	37	CCDS4139.1																																																																																			C|0.870;T|0.130	0.130	strong		0.368	C5orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250923.1		
RNF123	63891	hgsc.bcm.edu	37	3	49740895	49740895	+	Missense_Mutation	SNP	A	A	G	rs35726701	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49740895A>G	ENST00000327697.6	+	21	1930	c.1786A>G	c.(1786-1788)Aag>Gag	p.K596E	RNF123_ENST00000432042.1_Missense_Mutation_p.K450E	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	596			K -> E (in dbSNP:rs35726701).		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)		CTATAATGGCAAGGTGGACTA	0.627											OREG0015571	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	44	0.00878594	0.0	0.0144	5008	,	,		18188	0.0		0.0308	False		,,,				2504	0.0031				p.K596E		Atlas-SNP	.											.	RNF123	100	.	0			c.A1786G						PASS	.	A	GLU/LYS	18,4388	25.3+/-52.1	0,18,2185	44.0	44.0	44.0		1786	4.9	1.0	3	dbSNP_126	44	184,8416	82.0+/-144.6	2,180,4118	yes	missense	RNF123	NM_022064.2	56	2,198,6303	GG,GA,AA		2.1395,0.4085,1.5531	probably-damaging	596/1315	49740895	202,12804	2203	4300	6503	SO:0001583	missense	63891	exon21			AATGGCAAGGTGG	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.1786A>G	3.37:g.49740895A>G	ENSP00000328287:p.Lys596Glu	Somatic	184	0	0	964	WXS	Illumina HiSeq	Phase_I	197	106	0.538071	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	31	0.014194139194139194	0	0.0	6	0.016574585635359115	0	0.0	25	0.032981530343007916	A	29.4	4.999794	0.93227	0.004085	0.021395	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.75704	-0.65;-0.96	4.92	4.92	0.64577	.	0.000000	0.64402	D	0.000011	T	0.55705	0.1937	N	0.24115	0.695	0.80722	D	1	D;D	0.63880	0.965;0.993	P;D	0.70935	0.637;0.971	T	0.71820	-0.4477	10	0.48119	T	0.1	-27.3396	13.7416	0.62852	1.0:0.0:0.0:0.0	rs35726701;rs61760877	450;596	C9J266;Q5XPI4	.;RN123_HUMAN	E	596;596;450	ENSP00000328287:K596E;ENSP00000392443:K450E	ENSP00000328287:K596E	K	+	1	0	RNF123	49715899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.722000	0.91452	1.857000	0.53885	0.482000	0.46254	AAG	A|0.986;G|0.014	0.014	strong		0.627	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064	
DIP2A	23181	hgsc.bcm.edu	37	21	47961711	47961711	+	Silent	SNP	G	G	A	rs2070435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47961711G>A	ENST00000417564.2	+	18	2100	c.2079G>A	c.(2077-2079)ctG>ctA	p.L693L	DIP2A_ENST00000318711.7_Silent_p.L694L|DIP2A_ENST00000435722.3_Silent_p.L693L|DIP2A_ENST00000457905.3_Silent_p.L693L|DIP2A_ENST00000466639.1_Silent_p.L650L|DIP2A_ENST00000400274.1_Silent_p.L689L|DIP2A_ENST00000427143.2_Silent_p.L629L			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	693					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)		AAGCAGTCCTGTCGATGAACG	0.478													A|||	1940	0.38738	0.5408	0.2147	5008	,	,		21409	0.4058		0.3439	False		,,,				2504	0.3282				p.L693L		Atlas-SNP	.											.	DIP2A	332	.	0			c.G2079A						PASS	.	A	,,,,,,	1869,2021		443,983,519	126.0	126.0	126.0		1887,1950,2067,2079,2079,2079,2079	-2.5	0.7	21	dbSNP_96	126	2643,5651		423,1797,1927	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146115.1,NM_001146116.1,NM_015151.3,NM_206889.2,NM_206890.2,NM_206891.2	,,,,,,	866,2780,2446	AA,AG,GG		31.8664,48.0463,37.0322	,,,,,,	629/1111,650/799,689/1568,693/1572,693/890,693/842,693/813	47961711	4512,7672	1945	4147	6092	SO:0001819	synonymous_variant	23181	exon18			AGTCCTGTCGATG	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.2079G>A	21.37:g.47961711G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			G|0.580;A|0.420	0.420	strong		0.478	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
C1QTNF8	390664	hgsc.bcm.edu	37	16	1143605	1143605	+	Missense_Mutation	SNP	C	C	A	rs116934818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1143605C>A	ENST00000328449.5	-	4	928	c.655G>T	c.(655-657)Gtg>Ttg	p.V219L		NM_207419.3	NP_997302.2	P60827	C1QT8_HUMAN	C1q and tumor necrosis factor related protein 8	219	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				lung(2)|prostate(1)|skin(1)	4		Hepatocellular(780;0.00369)				AACATGCGCACCCAGACGGCG	0.716													C|||	54	0.0107827	0.0008	0.0187	5008	,	,		8643	0.0		0.0298	False		,,,				2504	0.0102				p.V219L		Atlas-SNP	.											.	C1QTNF8	15	.	0			c.G655T						PASS	.	C	LEU/VAL	17,4307		1,15,2146	12.0	13.0	13.0		655	3.2	1.0	16	dbSNP_132	13	170,8368		1,168,4100	yes	missense	C1QTNF8	NM_207419.3	32	2,183,6246	AA,AC,CC		1.9911,0.3932,1.4539	possibly-damaging	219/253	1143605	187,12675	2162	4269	6431	SO:0001583	missense	390664	exon4			TGCGCACCCAGAC	AY358832	CCDS32358.1	16p13.3	2014-08-12			ENSG00000184471	ENSG00000184471			31374	protein-coding gene	gene with protein product		614147				12975309	Standard	NM_207419		Approved	UNQ5829, CTRP8	uc010uuw.1	P60827	OTTHUMG00000167756	ENST00000328449.5:c.655G>T	16.37:g.1143605C>A	ENSP00000330426:p.Val219Leu	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	36	15	0.416667	NM_207419	B7U178	Missense_Mutation	SNP	ENST00000328449.5	37	CCDS32358.1	32	0.014652014652014652	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	22	0.029023746701846966	C	12.81	2.050482	0.36181	0.003932	0.019911	ENSG00000184471	ENST00000328449	D	0.82711	-1.64	3.24	3.24	0.37175	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.46442	D	0.000298	T	0.53190	0.1781	L	0.52759	1.655	0.36281	D	0.855751	P	0.43231	0.801	P	0.45610	0.487	T	0.71265	-0.4644	10	0.02654	T	1	.	5.9986	0.19507	0.0:0.6915:0.1956:0.1129	.	219	P60827	C1QT8_HUMAN	L	219	ENSP00000330426:V219L	ENSP00000330426:V219L	V	-	1	0	C1QTNF8	1083606	1.000000	0.71417	0.979000	0.43373	0.865000	0.49528	1.250000	0.32850	1.654000	0.50703	0.557000	0.71058	GTG	C|0.987;A|0.013	0.013	strong		0.716	C1QTNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396120.1	XM_372606	
NUGGC	389643	hgsc.bcm.edu	37	8	27898580	27898580	+	Silent	SNP	T	T	C	rs17058502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27898580T>C	ENST00000413272.2	-	13	1741	c.1599A>G	c.(1597-1599)agA>agG	p.R533R	NUGGC_ENST00000341513.6_Silent_p.R533R	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	533					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										CCAAGCATGCTCTGAGGATGC	0.562													C|||	555	0.110823	0.174	0.1052	5008	,	,		18994	0.0516		0.1213	False		,,,				2504	0.0798				p.R533R		Atlas-SNP	.											.	.	.	.	0			c.A1599G						PASS	.	C		606,3486		42,522,1482	49.0	49.0	49.0		1599	0.3	0.0	8	dbSNP_123	49	934,7488		54,826,3331	no	coding-synonymous	C8orf80	NM_001010906.1		96,1348,4813	CC,CT,TT		11.09,14.8094,12.3062		533/797	27898580	1540,10974	2046	4211	6257	SO:0001819	synonymous_variant	389643	exon13			GCATGCTCTGAGG	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1599A>G	8.37:g.27898580T>C		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																			T|0.884;C|0.116	0.116	strong		0.562	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
UBXN2B	137886	hgsc.bcm.edu	37	8	59358556	59358556	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:59358556G>A	ENST00000399598.2	+	7	884	c.762G>A	c.(760-762)gtG>gtA	p.V254V		NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	254	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						ATGATTCAGTGCCAACAACAA	0.373																																					p.V254V		Atlas-SNP	.											.	UBXN2B	36	.	0			c.G762A						PASS	.						139.0	122.0	128.0					8																	59358556		1863	4092	5955	SO:0001819	synonymous_variant	137886	exon7			TTCAGTGCCAACA	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"""UBX domain containing"""	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.762G>A	8.37:g.59358556G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_001077619	B3KWZ3	Silent	SNP	ENST00000399598.2	37	CCDS43741.1																																																																																			.	.	none		0.373	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	
WLS	79971	hgsc.bcm.edu	37	1	68624878	68624878	+	Silent	SNP	C	C	T	rs3748705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:68624878C>T	ENST00000262348.4	-	3	685	c.432G>A	c.(430-432)gcG>gcA	p.A144A	WLS_ENST00000370976.3_Silent_p.A53A|WLS_ENST00000540432.1_Silent_p.A144A|GNG12-AS1_ENST00000420587.1_RNA|GNG12-AS1_ENST00000413628.1_RNA|WLS_ENST00000354777.2_Silent_p.A142A	NM_024911.6	NP_079187.3	Q5T9L3	WLS_HUMAN	wntless Wnt ligand secretion mediator	144	Interacts with Wnt proteins. {ECO:0000250}.				anterior/posterior axis specification (GO:0009948)|mesoderm formation (GO:0001707)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(4)|prostate(3)|urinary_tract(1)	20						ACTCAGCAAACGCGTCATCAC	0.468													C|||	1751	0.349641	0.2368	0.4524	5008	,	,		19034	0.4127		0.3648	False		,,,				2504	0.3487				p.A144A		Atlas-SNP	.											.	WLS	97	.	0			c.G432A						PASS	.	C	,,	1114,3292	401.3+/-331.9	170,774,1259	161.0	130.0	141.0		426,159,432	2.0	0.0	1	dbSNP_107	141	2961,5639	460.9+/-365.3	524,1913,1863	no	coding-synonymous,coding-synonymous,coding-synonymous	WLS	NM_001002292.3,NM_001193334.1,NM_024911.6	,,	694,2687,3122	TT,TC,CC		34.4302,25.2837,31.3317	,,	142/544,53/451,144/542	68624878	4075,8931	2203	4300	6503	SO:0001819	synonymous_variant	79971	exon3			AGCAAACGCGTCA	BX538320	CCDS642.1, CCDS30750.1, CCDS53331.1	1p31.2	2013-10-03	2013-10-03	2010-03-02	ENSG00000116729	ENSG00000116729			30238	protein-coding gene	gene with protein product	"""wntless homolog"""	611514	"""chromosome 1 open reading frame 139"", ""G protein-coupled receptor 177"", ""wntless homolog (Drosophila)"""	C1orf139, GPR177		12761501	Standard	NM_024911		Approved	FLJ23091, MRP, wls, EVI, mig-14	uc001dee.3	Q5T9L3	OTTHUMG00000009153	ENST00000262348.4:c.432G>A	1.37:g.68624878C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	89	40	0.449438	NM_024911	B2RNT2|Q5JRS7|Q7Z2Z9|Q8NC43	Silent	SNP	ENST00000262348.4	37	CCDS642.1	811	0.37133699633699635	131	0.266260162601626	172	0.47513812154696133	238	0.4160839160839161	270	0.3562005277044855	C	0.224	-1.026590	0.02045	0.252837	0.344302	ENSG00000116729	ENST00000534713	.	.	.	5.94	1.98	0.26296	.	.	.	.	.	T	0.30039	0.0752	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.09185	-1.0686	3	.	.	.	-3.2332	8.3848	0.32494	0.0:0.6047:0.2134:0.1818	rs3748705;rs17845107;rs17857898;rs52813654;rs59688613;rs3748705	.	.	.	H	47	.	.	R	-	2	0	WLS	68397466	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	0.049000	0.14099	-0.074000	0.12820	-0.810000	0.03169	CGT	C|0.664;T|0.336	0.336	strong		0.468	WLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025368.1	NM_024911	
DNAH17	8632	hgsc.bcm.edu	37	17	76567708	76567708	+	Silent	SNP	G	G	A	rs555197985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76567708G>A	ENST00000585328.1	-	4	820	c.696C>T	c.(694-696)gaC>gaT	p.D232D	DNAH17_ENST00000389840.5_Silent_p.D232D	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	232	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)			GCAGCCGAGTGTCCCAGAACT	0.642													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		17482	0.0		0.0	False		,,,				2504	0.0				p.D232D		Atlas-SNP	.											.	DNAH17	347	.	0			c.C696T						PASS	.						60.0	66.0	64.0					17																	76567708		2030	4179	6209	SO:0001819	synonymous_variant	8632	exon4			CCGAGTGTCCCAG	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.696C>T	17.37:g.76567708G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	143	73	0.51049	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				.	.	none		0.642	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
NEU2	4759	hgsc.bcm.edu	37	2	233899126	233899126	+	Missense_Mutation	SNP	C	C	A	rs2233391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233899126C>A	ENST00000233840.3	+	2	502	c.502C>A	c.(502-504)Cac>Aac	p.H168N		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	168			H -> N (in dbSNP:rs2233391). {ECO:0000269|PubMed:10191093, ECO:0000269|PubMed:15489334}.		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)	TTTGCAGCTTCACGACAGGGC	0.647													C|||	1162	0.232029	0.1626	0.3026	5008	,	,		16182	0.0298		0.502	False		,,,				2504	0.2065				p.H168N		Atlas-SNP	.											.	NEU2	42	.	0			c.C502A						PASS	.	C	ASN/HIS	941,3465	354.1+/-312.5	111,719,1373	53.0	57.0	56.0		502	0.7	0.0	2	dbSNP_98	56	4110,4490	560.1+/-387.5	960,2190,1150	yes	missense	NEU2	NM_005383.2	68	1071,2909,2523	AA,AC,CC		47.7907,21.3572,38.8359	benign	168/381	233899126	5051,7955	2203	4300	6503	SO:0001583	missense	4759	exon2			CAGCTTCACGACA	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.502C>A	2.37:g.233899126C>A	ENSP00000233840:p.His168Asn	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	107	58	0.542056	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	37	CCDS2501.1	605	0.27701465201465203	79	0.16056910569105692	128	0.35359116022099446	10	0.017482517482517484	388	0.5118733509234829	C	4.530	0.098352	0.08681	0.213572	0.477907	ENSG00000115488	ENST00000233840	D	0.87334	-2.24	4.88	0.688	0.18027	Neuraminidase (2);	1.629240	0.03019	N	0.150453	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.19583	0.037	B	0.29440	0.102	T	0.26018	-1.0115	9	0.42905	T	0.14	-4.7507	4.0599	0.09834	0.3565:0.3407:0.2323:0.0705	rs2233391;rs57824073;rs2233391	168	Q9Y3R4	NEUR2_HUMAN	N	168	ENSP00000233840:H168N	ENSP00000233840:H168N	H	+	1	0	NEU2	233607370	0.001000	0.12720	0.014000	0.15608	0.019000	0.09904	0.044000	0.13992	0.097000	0.17492	0.561000	0.74099	CAC	C|0.668;A|0.332	0.332	strong		0.647	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248924	48248924	+	Silent	SNP	G	G	A	rs3181870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48248924G>A	ENST00000246802.5	+	1	146	c.108G>A	c.(106-108)cgG>cgA	p.R36R	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	36						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CGCTGAGGCGGCGGCGGCGAG	0.667													G|||	61	0.0121805	0.0008	0.0216	5008	,	,		9559	0.0		0.0338	False		,,,				2504	0.0112				p.R36R	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.G108A						PASS	.	G		13,4393		0,13,2190	35.0	43.0	40.0		108	4.6	1.0	19	dbSNP_105	40	182,8414		5,172,4121	no	coding-synonymous	GLTSCR2	NM_015710.4		5,185,6311	AA,AG,GG		2.1173,0.2951,1.4998		36/479	48248924	195,12807	2203	4298	6501	SO:0001819	synonymous_variant	29997	exon1			GAGGCGGCGGCGG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.108G>A	19.37:g.48248924G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	156	71	0.455128	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			G|0.981;A|0.019	0.019	strong		0.667	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
KIAA1671	85379	hgsc.bcm.edu	37	22	25577667	25577667	+	Splice_Site	SNP	G	G	A	rs199924926		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:25577667G>A	ENST00000406486.4	+	11	5463	c.5076G>A	c.(5074-5076)gaG>gaA	p.E1692E	KIAA1671_ENST00000401395.1_Splice_Site_p.E199E|KIAA1671_ENST00000358431.3_Splice_Site_p.E1692E			Q9BY89	K1671_HUMAN	KIAA1671	1692										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						TTGCAACAGAGGAGAAATCAC	0.512													G|||	1	0.000199681	0.0	0.0	5008	,	,		19953	0.0		0.001	False		,,,				2504	0.0				p.E1692E		Atlas-SNP	.											.	KIAA1671	28	.	0			c.G5076A						PASS	.						55.0	57.0	56.0					22																	25577667		692	1591	2283	SO:0001630	splice_region_variant	85379	exon8			AACAGAGGAGAAA		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.5075-1G>A	22.37:g.25577667G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			.	.	weak		0.512	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	Silent
APOH	350	hgsc.bcm.edu	37	17	64216815	64216815	+	Missense_Mutation	SNP	C	C	T	rs8178847	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:64216815C>T	ENST00000205948.6	-	5	498	c.461G>A	c.(460-462)cGt>cAt	p.R154H		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	154	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.		R -> H (in dbSNP:rs8178847). {ECO:0000269|Ref.8}.		blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			CTTATAAACACGAAGTGTTGC	0.383													c|||	352	0.0702875	0.115	0.0418	5008	,	,		19173	0.0516		0.0696	False		,,,				2504	0.0501				p.R154H	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.G461A						PASS	.	T	HIS/ARG	397,4009	790.4+/-415.0	17,363,1823	116.0	113.0	114.0		461	1.6	0.0	17	dbSNP_117	114	560,8040	794.3+/-407.5	17,526,3757	yes	missense	APOH	NM_000042.2	29	34,889,5580	TT,TC,CC		6.5116,9.0104,7.3581	benign	154/346	64216815	957,12049	2203	4300	6503	SO:0001583	missense	350	exon5			TAAACACGAAGTG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.461G>A	17.37:g.64216815C>T	ENSP00000205948:p.Arg154His	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	148	79	0.533784	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	167	0.07646520146520147	62	0.12601626016260162	16	0.04419889502762431	35	0.06118881118881119	54	0.0712401055408971	t	3.786	-0.044700	0.07452	0.090104	0.065116	ENSG00000091583	ENST00000205948	T	0.63417	-0.04	5.42	1.59	0.23543	Complement control module (2);Sushi/SCR/CCP (3);	1.273270	0.04813	N	0.435553	T	0.00356	0.0011	N	0.08118	0	0.80722	P	0.0	P	0.40731	0.728	B	0.25884	0.064	T	0.03008	-1.1083	9	0.33141	T	0.24	.	4.8598	0.13577	0.0:0.3473:0.2571:0.3956	rs8178847;rs61420267;rs8178847	154	P02749	APOH_HUMAN	H	154	ENSP00000205948:R154H	ENSP00000205948:R154H	R	-	2	0	APOH	61647277	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	0.005000	0.13129	0.492000	0.27815	-0.213000	0.12676	CGT	C|0.927;T|0.073	0.073	strong		0.383	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
RALGAPA1	253959	hgsc.bcm.edu	37	14	36153177	36153177	+	Missense_Mutation	SNP	T	T	C	rs2274068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:36153177T>C	ENST00000389698.3	-	20	3181	c.2791A>G	c.(2791-2793)Acc>Gcc	p.T931A	RALGAPA1_ENST00000258840.6_Missense_Mutation_p.T978A|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.T944A|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.T931A	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	931			T -> A (in dbSNP:rs2274068). {ECO:0000269|PubMed:19520869}.		activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CCAGTGTCGGTTCCAAAGCCA	0.393													C|||	2373	0.473842	0.7557	0.2277	5008	,	,		16999	0.5804		0.1918	False		,,,				2504	0.4479				p.T931A		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.A2791G						PASS	.	C	ALA/THR,ALA/THR	2911,1495	472.0+/-356.2	977,957,269	44.0	54.0	51.0		2791,2791	1.6	1.0	14	dbSNP_100	51	1527,7073	744.4+/-407.2	155,1217,2928	yes	missense,missense	RALGAPA1	NM_014990.1,NM_194301.2	58,58	1132,2174,3197	CC,CT,TT		17.7558,33.931,34.1227	benign,benign	931/2037,931/2084	36153177	4438,8568	2203	4300	6503	SO:0001583	missense	253959	exon20			TGTCGGTTCCAAA	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2791A>G	14.37:g.36153177T>C	ENSP00000374348:p.Thr931Ala	Somatic	205	1	0.00487805		WXS	Illumina HiSeq	Phase_I	146	146	1	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	37	CCDS32065.1	953	0.43635531135531136	353	0.717479674796748	106	0.292817679558011	350	0.6118881118881119	144	0.18997361477572558	C	0.993	-0.693402	0.03303	0.66069	0.177558	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	D;D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.26;-3.27	5.46	1.57	0.23409	.	0.641598	0.15948	N	0.236867	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.0;0.001;0.0;0.0	T	0.45775	-0.9238	9	0.16420	T	0.52	-0.4299	6.214	0.20646	0.0:0.4158:0.1279:0.4563	rs2274068;rs52819701;rs57932556;rs2274068	978;944;978;931;931	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	A	931;931;931;978;944;978	ENSP00000374348:T931A;ENSP00000302647:T931A;ENSP00000258840:T978A;ENSP00000371803:T944A;ENSP00000451877:T978A	ENSP00000258840:T978A	T	-	1	0	RALGAPA1	35222928	0.959000	0.32827	0.984000	0.44739	0.864000	0.49448	0.203000	0.17315	0.025000	0.15241	-0.197000	0.12766	ACC	T|0.603;C|0.397	0.397	strong		0.393	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
RASGRP3	25780	hgsc.bcm.edu	37	2	33759395	33759395	+	Silent	SNP	C	C	T	rs35933402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:33759395C>T	ENST00000403687.3	+	11	1829	c.1089C>T	c.(1087-1089)tcC>tcT	p.S363S	RASGRP3_ENST00000402538.3_Silent_p.S363S|RASGRP3_ENST00000407811.1_Silent_p.S363S	NM_001139488.1	NP_001132960.1	Q8IV61	GRP3_HUMAN	RAS guanyl releasing protein 3 (calcium and DAG-regulated)	363	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				MAPK cascade (GO:0000165)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)	guanyl-nucleotide exchange factor complex (GO:0032045)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap GTPase activator activity (GO:0046582)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|signal transducer activity (GO:0004871)			large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|stomach(2)	11	all_hematologic(175;0.115)					TGTAGCTTTCCCTGGACCTCT	0.328													C|||	442	0.0882588	0.0484	0.1931	5008	,	,		17421	0.006		0.1501	False		,,,				2504	0.089				p.S363S		Atlas-SNP	.											.	RASGRP3	87	.	0			c.C1089T						PASS	.	C	,,	200,3414		7,186,1614	103.0	88.0	93.0		1089,1089,1089	1.7	1.0	2	dbSNP_126	93	1225,6923		81,1063,2930	no	coding-synonymous,coding-synonymous,coding-synonymous	RASGRP3	NM_001139488.1,NM_015376.2,NM_170672.2	,,	88,1249,4544	TT,TC,CC		15.0344,5.534,12.1153	,,	363/691,363/690,363/691	33759395	1425,10337	1807	4074	5881	SO:0001819	synonymous_variant	25780	exon12			GCTTTCCCTGGAC	AB020653	CCDS46256.1, CCDS54346.1	2p25.1-p24.1	2013-01-10			ENSG00000152689	ENSG00000152689		"""EF-hand domain containing"""	14545	protein-coding gene	gene with protein product		609531				10048485, 10934204	Standard	NM_170672		Approved	KIAA0846, GRP3	uc002roy.3	Q8IV61	OTTHUMG00000152124	ENST00000403687.3:c.1089C>T	2.37:g.33759395C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	113	42	0.371681	NM_170672	D6W583|O94931|Q53SD7	Silent	SNP	ENST00000403687.3	37	CCDS46256.1																																																																																			C|0.890;T|0.110	0.110	strong		0.328	RASGRP3-006	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325462.2	NM_015376	
DNER	92737	hgsc.bcm.edu	37	2	230456365	230456365	+	Silent	SNP	C	C	T	rs138325902	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:230456365C>T	ENST00000341772.4	-	2	650	c.516G>A	c.(514-516)acG>acA	p.T172T		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	172					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		GCAGTGTCACCGTTGCCTGAG	0.522													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18817	0.0		0.0	False		,,,				2504	0.0				p.T172T		Atlas-SNP	.											DNER,colon,carcinoma,-1,2	DNER	129	2	0			c.G516A						scavenged	.	C		3,4403	6.2+/-15.9	0,3,2200	86.0	79.0	81.0		516	-8.9	0.0	2	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DNER	NM_139072.3		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		172/738	230456365	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	92737	exon2			TGTCACCGTTGCC	AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.516G>A	2.37:g.230456365C>T		Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	161	2	0.0124224	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Silent	SNP	ENST00000341772.4	37	CCDS33390.1																																																																																			C|1.000;T|0.000	0.000	strong		0.522	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072	
KIAA1755	85449	hgsc.bcm.edu	37	20	36842086	36842086	+	Silent	SNP	G	G	A	rs112401596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36842086G>A	ENST00000279024.4	-	14	3232	c.2961C>T	c.(2959-2961)acC>acT	p.T987T		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	987										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)				TGACCCTTGAGGTCTTGTCCA	0.642													G|||	31	0.0061901	0.003	0.0058	5008	,	,		17289	0.0		0.0169	False		,,,				2504	0.0061				p.T987T		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C2961T						PASS	.	G		19,4387		0,19,2184	21.0	19.0	20.0		2961	-0.3	0.0	20	dbSNP_132	20	179,8421		2,175,4123	no	coding-synonymous	KIAA1755	NM_001029864.1		2,194,6307	AA,AG,GG		2.0814,0.4312,1.5224		987/1201	36842086	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon14			CCTTGAGGTCTTG	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.2961C>T	20.37:g.36842086G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.986;A|0.014	0.014	strong		0.642	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
ZNF790	388536	hgsc.bcm.edu	37	19	37310344	37310344	+	Missense_Mutation	SNP	T	T	C	rs3745775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37310344T>C	ENST00000356725.4	-	5	1022	c.902A>G	c.(901-903)cAg>cGg	p.Q301R	CTD-2162K18.5_ENST00000588906.1_RNA|CTD-2162K18.5_ENST00000587278.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	301			Q -> R (in dbSNP:rs3745775). {ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			ATGAATTCTCTGATGTCGAGT	0.383													T|||	1455	0.290535	0.2988	0.2161	5008	,	,		19923	0.2232		0.2922	False		,,,				2504	0.3998				p.Q301R		Atlas-SNP	.											.	ZNF790	89	.	0			c.A902G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	1261,3145	425.7+/-340.9	183,895,1125	55.0	57.0	56.0		902,902,902,902	2.1	0.2	19	dbSNP_107	56	2337,6263	385.3+/-341.4	335,1667,2298	no	missense,missense,missense,missense	ZNF790	NM_001242800.1,NM_001242801.1,NM_001242802.1,NM_206894.3	43,43,43,43	518,2562,3423	CC,CT,TT		27.1744,28.6201,27.6642	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	301/637,301/637,301/637,301/637	37310344	3598,9408	2203	4300	6503	SO:0001583	missense	388536	exon5			ATTCTCTGATGTC	BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"""Zinc fingers, C2H2-type"", ""-"""	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.902A>G	19.37:g.37310344T>C	ENSP00000349161:p.Gln301Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	569	0.26053113553113555	152	0.3089430894308943	89	0.24585635359116023	121	0.21153846153846154	207	0.27308707124010556	T	13.67	2.307549	0.40795	0.286201	0.271744	ENSG00000197863	ENST00000356725	T	0.17691	2.26	3.14	2.11	0.27256	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.12831	0.26	0.58432	P	1.0000000000287557E-6	B	0.23185	0.081	B	0.18263	0.021	T	0.44907	-0.9297	8	0.52906	T	0.07	.	7.2311	0.26043	0.0:0.1139:0.0:0.8861	rs3745775;rs17846550;rs17859625;rs52814390;rs3745775	301	Q6PG37	ZN790_HUMAN	R	301	ENSP00000349161:Q301R	ENSP00000349161:Q301R	Q	-	2	0	ZNF790	42002184	0.002000	0.14202	0.207000	0.23584	0.976000	0.68499	0.644000	0.24766	0.425000	0.26087	0.402000	0.26972	CAG	T|0.723;C|0.277	0.277	strong		0.383	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894	
C8B	732	hgsc.bcm.edu	37	1	57415310	57415310	+	Missense_Mutation	SNP	G	G	A	rs12085435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:57415310G>A	ENST00000371237.4	-	6	848	c.782C>T	c.(781-783)cCt>cTt	p.P261L	C8B_ENST00000543257.1_Missense_Mutation_p.P209L|C8B_ENST00000535057.1_Missense_Mutation_p.P199L	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	261	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.		P -> L (in dbSNP:rs12085435).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						AAATATTCCAGGTATTTTAAA	0.348													G|||	211	0.0421326	0.0575	0.0375	5008	,	,		18532	0.0		0.0547	False		,,,				2504	0.0552				p.P261L		Atlas-SNP	.											.	C8B	107	.	0			c.C782T						PASS	.	G	LEU/PRO	286,4120	158.1+/-190.9	8,270,1925	123.0	124.0	124.0		782	0.9	0.0	1	dbSNP_120	124	478,8122	140.1+/-196.7	14,450,3836	yes	missense	C8B	NM_000066.2	98	22,720,5761	AA,AG,GG		5.5581,6.4911,5.8742	benign	261/592	57415310	764,12242	2203	4300	6503	SO:0001583	missense	732	exon6			ATTCCAGGTATTT	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.782C>T	1.37:g.57415310G>A	ENSP00000360281:p.Pro261Leu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	92	0.04212454212454213	34	0.06910569105691057	18	0.049723756906077346	0	0.0	40	0.052770448548812667	G	10.43	1.347429	0.24426	0.064911	0.055581	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.27557	1.84;1.85;1.66	5.19	0.854	0.19007	Membrane attack complex component/perforin (MACPF) domain (1);	2.075460	0.02088	N	0.052888	T	0.03011	0.0089	M	0.63428	1.95	0.45594	P	0.001466999999999996	B;B;B	0.15141	0.007;0.012;0.002	B;B;B	0.16289	0.015;0.015;0.002	T	0.17107	-1.0380	9	0.35671	T	0.21	0.0672	9.3642	0.38215	0.0677:0.0:0.5616:0.3708	rs12085435;rs52790403;rs12085435	209;199;261	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	L	261;209;199	ENSP00000360281:P261L;ENSP00000442548:P209L;ENSP00000440113:P199L	ENSP00000360281:P261L	P	-	2	0	C8B	57187898	0.016000	0.18221	0.000000	0.03702	0.006000	0.05464	0.513000	0.22770	0.222000	0.20900	-0.293000	0.09583	CCT	G|0.944;A|0.056	0.056	strong		0.348	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
SELPLG	6404	hgsc.bcm.edu	37	12	109017673	109017673	+	Silent	SNP	C	C	T	rs63748999|rs558357966|rs372173288	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109017673C>T	ENST00000550948.1	-	2	635	c.411G>A	c.(409-411)gtG>gtA	p.V137V	SELPLG_ENST00000388962.3_Intron|SELPLG_ENST00000228463.6_Silent_p.V153V			Q14242	SELPL_HUMAN	selectin P ligand	137	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						CCTCCGTGGGCACTGGTTGAG	0.617													c|||	441	0.0880591	0.0272	0.0504	5008	,	,		19600	0.2034		0.0795	False		,,,				2504	0.0869				p.V153V		Atlas-SNP	.											SELPLG_ENST00000550948,NS,carcinoma,-1,7	SELPLG	138	7	0			c.G459A						scavenged	.						159.0	124.0	136.0					12																	109017673		2199	4274	6473	SO:0001819	synonymous_variant	6404	exon2			CGTGGGCACTGGT		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.411G>A	12.37:g.109017673C>T		Somatic	178	2	0.011236		WXS	Illumina HiSeq	Phase_I	149	34	0.228188	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Silent	SNP	ENST00000550948.1	37	CCDS31895.2																																																																																			.	.	none		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
KCTD15	79047	hgsc.bcm.edu	37	19	34302280	34302280	+	Silent	SNP	C	C	G	rs10426916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:34302280C>G	ENST00000430256.3	+	5	924	c.516C>G	c.(514-516)cgC>cgG	p.R172R	KCTD15_ENST00000588881.1_Silent_p.R172R|KCTD15_ENST00000284006.6_Silent_p.R172R|KCTD15_ENST00000589786.1_Silent_p.R172R			Q96SI1	KCD15_HUMAN	potassium channel tetramerization domain containing 15	172					multicellular organismal development (GO:0007275)|protein homooligomerization (GO:0051260)					endometrium(1)|lung(2)|pancreas(1)|urinary_tract(1)	5	Esophageal squamous(110;0.162)					TGGTGGTGCGCGTCACGCCCG	0.682													C|||	600	0.119808	0.1679	0.0764	5008	,	,		10922	0.0853		0.0875	False		,,,				2504	0.1544				p.R172R	Melanoma(36;646 1094 5145 14504 45302)|GBM(25;193 541 1518 14388 52178)	Atlas-SNP	.											KCTD15,NS,carcinoma,0,1	KCTD15	18	1	0			c.C516G						PASS	.	C	,,	722,3666		67,588,1539	19.0	15.0	17.0		516,516,516	-4.3	1.0	19	dbSNP_119	17	840,7734		39,762,3486	no	coding-synonymous,coding-synonymous,coding-synonymous	KCTD15	NM_001129994.1,NM_001129995.1,NM_024076.2	,,	106,1350,5025	GG,GC,CC		9.7971,16.454,12.0506	,,	172/284,172/284,172/235	34302280	1562,11400	2194	4287	6481	SO:0001819	synonymous_variant	79047	exon6			GGTGCGCGTCACG	AK025590	CCDS12434.1, CCDS46039.1	19q13.12	2013-06-20	2013-06-20			ENSG00000153885			23297	protein-coding gene	gene with protein product		615240	"""potassium channel tetramerisation domain containing 15"""			12477932	Standard	NM_024076		Approved	MGC25497	uc002nuw.4	Q96SI1		ENST00000430256.3:c.516C>G	19.37:g.34302280C>G		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	19	7	0.368421	NM_001129995	A8K600|Q9BVI6	Silent	SNP	ENST00000430256.3	37	CCDS46039.1	230	0.10531135531135531	80	0.16260162601626016	40	0.11049723756906077	42	0.07342657342657342	68	0.08970976253298153	C	10.84	1.464255	0.26335	0.16454	0.097971	ENSG00000153885	ENST00000413790	.	.	.	5.02	-4.3	0.03710	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999999996	.	.	.	.	.	.	T	0.30822	-0.9965	4	0.87932	D	0	.	0.4485	0.00497	0.3369:0.1579:0.2837:0.2214	rs10426916	.	.	.	G	47	.	ENSP00000406942:A47G	A	+	2	0	KCTD15	38994120	0.000000	0.05858	0.997000	0.53966	0.944000	0.59088	-1.766000	0.01797	-0.141000	0.11374	0.591000	0.81541	GCG	C|0.880;G|0.120	0.120	strong		0.682	KCTD15-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451462.2	NM_024076	
FRY	10129	hgsc.bcm.edu	37	13	32776616	32776616	+	Missense_Mutation	SNP	T	T	A	rs61750791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32776616T>A	ENST00000380250.3	+	31	4466	c.3970T>A	c.(3970-3972)Tgt>Agt	p.C1324S		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1324						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CCTCTTGTCATGTGAGCTGGC	0.493													T|||	495	0.0988419	0.003	0.0389	5008	,	,		15378	0.2649		0.0358	False		,,,				2504	0.1646				p.C1324S		Atlas-SNP	.											.	FRY	312	.	0			c.T3970A						PASS	.	T	SER/CYS	36,3976		0,36,1970	81.0	81.0	81.0		3970	2.8	0.0	13	dbSNP_129	81	360,7966		10,340,3813	yes	missense	FRY	NM_023037.2	112	10,376,5783	AA,AT,TT		4.3238,0.8973,3.2096	benign	1324/3014	32776616	396,11942	2006	4163	6169	SO:0001583	missense	10129	exon31			TTGTCATGTGAGC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3970T>A	13.37:g.32776616T>A	ENSP00000369600:p.Cys1324Ser	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	116	61	0.525862	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	213	0.09752747252747253	1	0.0020325203252032522	16	0.04419889502762431	172	0.3006993006993007	24	0.0316622691292876	T	0.309	-0.969295	0.02232	0.008973	0.043238	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.20200	2.09	5.39	2.81	0.32909	.	0.428442	0.28521	N	0.015051	T	0.00012	0.0000	N	0.11560	0.145	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.46789	-0.9166	9	0.10111	T	0.7	.	4.345	0.11129	0.2479:0.1404:0.0:0.6117	rs61750791	1324	Q5TBA9	FRY_HUMAN	S	1324;163	ENSP00000369600:C1324S	ENSP00000369600:C1324S	C	+	1	0	FRY	31674616	0.637000	0.27216	0.030000	0.17652	0.107000	0.19398	2.088000	0.41663	0.307000	0.22880	0.374000	0.22700	TGT	T|0.916;A|0.084	0.084	strong		0.493	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234883	26234883	+	Silent	SNP	A	A	G	rs2050950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26234883A>G	ENST00000244534.5	-	1	333	c.279T>C	c.(277-279)acT>acC	p.T93T		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	93	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.T93fs*35(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				TCTGCACCAGAGTACCTTTGC	0.542													G|||	842	0.168131	0.2262	0.111	5008	,	,		17770	0.1012		0.1571	False		,,,				2504	0.2106				p.T93T		Atlas-SNP	.											.	HIST1H1D	40	.	1	Deletion - Frameshift(1)	endometrium(1)	c.T279C						PASS	.	G		851,3555		77,697,1429	100.0	107.0	105.0		279	2.5	0.9	6	dbSNP_94	105	1155,7445		70,1015,3215	no	coding-synonymous	HIST1H1D	NM_005320.2		147,1712,4644	GG,GA,AA		13.4302,19.3146,15.4237		93/222	26234883	2006,11000	2203	4300	6503	SO:0001819	synonymous_variant	3007	exon1			CACCAGAGTACCT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.279T>C	6.37:g.26234883A>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	166	73	0.439759	NM_005320	B2R751|Q2M2I2	Silent	SNP	ENST00000244534.5	37	CCDS4597.1																																																																																			A|0.854;G|0.146	0.146	strong		0.542	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
ZNF813	126017	hgsc.bcm.edu	37	19	53995004	53995004	+	Silent	SNP	G	G	A	rs2708845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53995004G>A	ENST00000396403.4	+	4	1646	c.1518G>A	c.(1516-1518)cgG>cgA	p.R506R	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	506					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		GTTTTAATCGGAAAACACACC	0.403													.|||	3921	0.782947	0.9304	0.8084	5008	,	,		24042	0.6498		0.7485	False		,,,				2504	0.7382				p.R506R		Atlas-SNP	.											ZNF813_ENST00000396403,colon,carcinoma,+1,1	ZNF813	81	1	0			c.G1518A						scavenged	.	G		3949,449		1780,389,30	49.0	53.0	52.0		1518	-2.6	0.0	19	dbSNP_100	52	6290,2308		2323,1644,332	no	coding-synonymous	ZNF813	NM_001004301.3		4103,2033,362	AA,AG,GG		26.8435,10.2092,21.2142		506/618	53995004	10239,2757	2199	4299	6498	SO:0001819	synonymous_variant	126017	exon4			TAATCGGAAAACA	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.1518G>A	19.37:g.53995004G>A		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			G|0.248;A|0.752	0.752	strong		0.403	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
AQR	9716	hgsc.bcm.edu	37	15	35198879	35198879	+	Silent	SNP	G	G	A	rs80093103	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:35198879G>A	ENST00000156471.5	-	18	1923	c.1698C>T	c.(1696-1698)acC>acT	p.T566T		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	566					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		TGGGACGTACGGTAATTAAAA	0.383													G|||	235	0.0469249	0.0567	0.0346	5008	,	,		17934	0.0		0.0716	False		,,,				2504	0.0654				p.T566T		Atlas-SNP	.											.	AQR	139	.	0			c.C1698T						PASS	.	G		200,3580		4,192,1694	119.0	107.0	111.0		1698	-7.1	1.0	15	dbSNP_132	111	586,7660		15,556,3552	no	coding-synonymous	AQR	NM_014691.2		19,748,5246	AA,AG,GG		7.1065,5.291,6.5358		566/1486	35198879	786,11240	1890	4123	6013	SO:0001819	synonymous_variant	9716	exon18			ACGTACGGTAATT	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.1698C>T	15.37:g.35198879G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	75	42	0.56	NM_014691	A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Silent	SNP	ENST00000156471.5	37	CCDS42013.1																																																																																			G|0.946;A|0.054	0.054	strong		0.383	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
NLRC3	197358	hgsc.bcm.edu	37	16	3613928	3613928	+	RNA	SNP	A	A	G	rs45483498	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3613928A>G	ENST00000301749.7	-	0	1415				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000359128.5_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GCCTAGCGCCATCCCCGTGAG	0.652													G|||	419	0.0836661	0.146	0.0865	5008	,	,		17828	0.0546		0.0666	False		,,,				2504	0.045				p.M337T		Atlas-SNP	.											.	NLRC3	103	.	0			c.T1010C						PASS	.	G	THR/MET	431,3617		16,399,1609	31.0	35.0	34.0		1010	-8.2	0.0	16	dbSNP_127	34	572,7766		15,542,3612	yes	missense	NLRC3	NM_178844.2	81	31,941,5221	GG,GA,AA		6.8602,10.6472,8.0979	benign	337/1066	3613928	1003,11383	2024	4169	6193			197358	exon5			AGCGCCATCCCCG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613928A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	19	11	0.578947	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		183	0.08379120879120878	81	0.16463414634146342	25	0.06906077348066299	28	0.04895104895104895	49	0.06464379947229551	G	0.001	-3.320587	0.00018	0.106472	0.068602	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57	5.01	-8.16	0.01061	.	2.217780	0.01727	N	0.028623	T	0.00496	0.0016	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.55970	-0.8056	8	0.02654	T	1	.	18.5924	0.91218	0.7703:0.0:0.2297:0.0	rs45483498	384	C9JLH9	.	T	337;337;337;384;319	ENSP00000301749:M337T;ENSP00000352039:M337T;ENSP00000414415:M384T;ENSP00000323897:M319T	ENSP00000301749:M337T	M	-	2	0	NLRC3	3553929	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.679000	0.05203	-3.082000	0.00250	-3.171000	0.00057	ATG	A|0.926;G|0.074	0.074	strong		0.652	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
GPR156	165829	hgsc.bcm.edu	37	3	119886101	119886101	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:119886101G>A	ENST00000464295.1	-	10	2668	c.2223C>T	c.(2221-2223)caC>caT	p.H741H	GPR156_ENST00000315843.3_Silent_p.H741H|GPR156_ENST00000461057.1_Silent_p.H737H			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	741						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		CAAAATAGCTGTGTTGAGAAG	0.567																																					p.H741H		Atlas-SNP	.											.	GPR156	85	.	0			c.C2223T						PASS	.						58.0	65.0	63.0					3																	119886101		2203	4300	6503	SO:0001819	synonymous_variant	165829	exon9			ATAGCTGTGTTGA	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"""GPCR / Class C : Orphans"""	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.2223C>T	3.37:g.119886101G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Silent	SNP	ENST00000464295.1	37	CCDS2997.1																																																																																			.	.	none		0.567	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002	
ATP8B3	148229	hgsc.bcm.edu	37	19	1785185	1785185	+	Missense_Mutation	SNP	C	C	T	rs16994563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1785185C>T	ENST00000310127.6	-	27	3743	c.3505G>A	c.(3505-3507)Gta>Ata	p.V1169I	ATP8B3_ENST00000539485.1_Missense_Mutation_p.V1179I|ATP8B3_ENST00000525591.1_Missense_Mutation_p.V1132I	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1169					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)		GTGGGGGATACTCTGAAGAGC	0.612													.|||	214	0.0427316	0.0711	0.0288	5008	,	,		18455	0.0		0.0447	False		,,,				2504	0.0562				p.V1169I		Atlas-SNP	.											.	ATP8B3	108	.	0			c.G3505A						PASS	.	C	ILE/VAL,ILE/VAL	272,4030		8,256,1887	41.0	53.0	49.0		3394,3505	-8.9	0.0	19	dbSNP_123	49	395,8113		11,373,3870	yes	missense,missense	ATP8B3	NM_001178002.1,NM_138813.2	29,29	19,629,5757	TT,TC,CC		4.6427,6.3226,5.2069	benign,benign	1132/1264,1169/1301	1785185	667,12143	2151	4254	6405	SO:0001583	missense	148229	exon27			GGGATACTCTGAA	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.3505G>A	19.37:g.1785185C>T	ENSP00000311336:p.Val1169Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	71	24	0.338028	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	88	0.040293040293040296	39	0.07926829268292683	11	0.03038674033149171	0	0.0	38	0.05013192612137203	C	3.428	-0.116672	0.06838	0.063226	0.046427	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	D;D;D	0.88431	-2.38;-2.38;-2.38	4.46	-8.91	0.00778	.	1.173860	0.06045	N	0.655633	T	0.08758	0.0217	N	0.04203	-0.255	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.53322	-0.8455	10	0.02654	T	1	.	2.5714	0.04796	0.1029:0.2964:0.3139:0.2868	rs16994563;rs16994563	1169;1132	O60423;Q7Z485	AT8B3_HUMAN;.	I	1169;1179;1132	ENSP00000311336:V1169I;ENSP00000443574:V1179I;ENSP00000437115:V1132I	ENSP00000311336:V1169I	V	-	1	0	ATP8B3	1736185	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-2.684000	0.00835	-1.914000	0.01078	-0.459000	0.05422	GTA	C|0.954;T|0.046	0.046	strong		0.612	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
RRBP1	6238	hgsc.bcm.edu	37	20	17602571	17602571	+	Missense_Mutation	SNP	A	A	G	rs2229886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:17602571A>G	ENST00000377813.1	-	14	3472	c.3169T>C	c.(3169-3171)Tgt>Cgt	p.C1057R	RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000246043.4_Missense_Mutation_p.C1057R|RRBP1_ENST00000377807.2_Missense_Mutation_p.C624R|RRBP1_ENST00000360807.4_Missense_Mutation_p.C624R|RRBP1_ENST00000455029.2_Missense_Mutation_p.C398R			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1057					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TCAATCAGACAGAGCTGCTTC	0.617													A|||	99	0.0197684	0.0008	0.0303	5008	,	,		15560	0.001		0.0477	False		,,,				2504	0.0286				p.C624R		Atlas-SNP	.											.	RRBP1	157	.	0			c.T1870C						PASS	.	A	ARG/CYS,ARG/CYS	52,4354	50.2+/-85.5	2,48,2153	63.0	70.0	68.0		1870,1870	-0.2	0.0	20	dbSNP_98	68	479,8121	139.5+/-196.2	5,469,3826	yes	missense,missense	RRBP1	NM_001042576.1,NM_004587.2	180,180	7,517,5979	GG,GA,AA		5.5698,1.1802,4.0827	benign,benign	624/978,624/978	17602571	531,12475	2203	4300	6503	SO:0001583	missense	6238	exon14			TCAGACAGAGCTG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.3169T>C	20.37:g.17602571A>G	ENSP00000367044:p.Cys1057Arg	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	37		51	0.023351648351648352	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	38	0.05013192612137203	A	0.010	-1.795706	0.00617	0.011802	0.055698	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.98	-0.19	0.13256	.	2.041510	0.02459	N	0.086394	T	0.00998	0.0033	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14420	-1.0473	10	0.17832	T	0.49	2.3478	3.1217	0.06393	0.0856:0.1954:0.3645:0.3545	rs2229886;rs34246888	581;624	A1A5C4;Q9P2E9-3	.;.	R	624;1057;624;1057;398	ENSP00000354045:C624R;ENSP00000367044:C1057R;ENSP00000367038:C624R;ENSP00000246043:C1057R;ENSP00000401206:C398R	ENSP00000246043:C1057R	C	-	1	0	RRBP1	17550571	0.000000	0.05858	0.009000	0.14445	0.003000	0.03518	-0.055000	0.11807	0.106000	0.17784	-0.232000	0.12228	TGT	A|0.964;G|0.036	0.036	strong		0.617	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576	
AMBRA1	55626	hgsc.bcm.edu	37	11	46431914	46431914	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:46431914A>C	ENST00000458649.2	-	16	3539	c.3121T>G	c.(3121-3123)Tta>Gta	p.L1041V	AMBRA1_ENST00000426438.1_Missense_Mutation_p.L1012V|AMBRA1_ENST00000534300.1_Missense_Mutation_p.L981V|AMBRA1_ENST00000533727.1_Missense_Mutation_p.L922V|AMBRA1_ENST00000528950.1_Missense_Mutation_p.L1012V|AMBRA1_ENST00000298834.3_Missense_Mutation_p.L981V|AMBRA1_ENST00000314845.3_Missense_Mutation_p.L951V			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1041					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		CCAGAGTTTAAGGCCCTAAAA	0.507																																					p.L1044V		Atlas-SNP	.											.	AMBRA1	201	.	0			c.T3130G						PASS	.						91.0	81.0	84.0					11																	46431914		2201	4299	6500	SO:0001583	missense	55626	exon18			AGTTTAAGGCCCT	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.3121T>G	11.37:g.46431914A>C	ENSP00000415327:p.Leu1041Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	87	34	0.390805	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	A	18.00	3.526152	0.64860	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.71222	-0.37;-0.55;-0.14;-0.27;-0.14;-0.24;-0.27	5.86	5.86	0.93980	.	0.249598	0.35436	N	0.003219	T	0.54415	0.1857	N	0.12182	0.205	0.41696	D	0.989373	B;B;B;B;P;B	0.34639	0.012;0.116;0.106;0.25;0.461;0.116	B;B;B;B;B;B	0.32393	0.006;0.103;0.042;0.103;0.145;0.103	T	0.62300	-0.6883	10	0.87932	D	0	.	14.8261	0.70113	1.0:0.0:0.0:0.0	.	1041;1012;981;922;1044;951	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	V	951;922;981;1012;981;1041;1012	ENSP00000318313:L951V;ENSP00000433372:L922V;ENSP00000431926:L981V;ENSP00000410899:L1012V;ENSP00000298834:L981V;ENSP00000415327:L1041V;ENSP00000433945:L1012V	ENSP00000298834:L981V	L	-	1	2	AMBRA1	46388490	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.398000	0.59697	2.240000	0.73641	0.533000	0.62120	TTA	.	.	none		0.507	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
HLA-A	3105	hgsc.bcm.edu	37	6	29910752	29910752	+	Missense_Mutation	SNP	G	G	C	rs1136683	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910752G>C	ENST00000396634.1	+	4	633	c.292G>C	c.(292-294)Gac>Cac	p.D98H	HLA-A_ENST00000376809.5_Missense_Mutation_p.D98H|HLA-A_ENST00000376806.5_Missense_Mutation_p.D98H|HLA-A_ENST00000376802.2_Missense_Mutation_p.D98H			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	98	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GTCACAGACTGACCGAGTGGA	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	1142	0.228035	0.1778	0.3012	5008	,	,		10698	0.2966		0.3141	False		,,,				2504	0.0849				p.D98H		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.G292C						PASS	.	T	HIS/ASP	760,3636		79,602,1517	68.0	73.0	71.0		292	-7.2	0.0	6	dbSNP_131	71	2250,6334		356,1538,2398	no	missense	HLA-A	NM_002116.7	81	435,2140,3915	CC,CG,GG		26.2116,17.2884,23.1895	possibly-damaging	98/366	29910752	3010,9970	2198	4292	6490	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CAGACTGACCGAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.292G>C	6.37:g.29910752G>C	ENSP00000379873:p.Asp98His	Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	80	41	0.5125	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	607	0.27793040293040294	92	0.18699186991869918	90	0.24861878453038674	170	0.2972027972027972	255	0.33641160949868076	.	0.246	-1.009865	0.02095	0.172884	0.262116	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.46;9.46;9.46;9.46	3.57	-7.15	0.01521	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	8.950690	0.01007	U	0.003778	T	0.00039	0.0001	L	0.37507	1.11	0.80722	P	0.0	B;B;B;P;B	0.44241	0.003;0.004;0.009;0.829;0.009	B;B;B;D;B	0.69824	0.016;0.136;0.17;0.966;0.17	T	0.51204	-0.8735	9	0.22706	T	0.39	.	1.9089	0.03283	0.1091:0.1996:0.2109:0.4803	rs1136683;rs2231000;rs3173423;rs12721692;rs16867781;rs16896598;rs28749147;rs41554813	98;98;98;98;98	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	H	98	ENSP00000379873:D98H;ENSP00000366002:D98H;ENSP00000366005:D98H;ENSP00000365998:D98H	ENSP00000348012:D98H	D	+	1	0	HLA-A	30018731	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.437000	0.02419	-1.229000	0.02564	-0.349000	0.07799	GAC	C|0.195;G|0.805	0.195	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
RAB6B	51560	hgsc.bcm.edu	37	3	133547692	133547692	+	Silent	SNP	G	G	A	rs2293373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:133547692G>A	ENST00000285208.4	-	8	916	c.567C>T	c.(565-567)atC>atT	p.I189I	RAB6B_ENST00000543906.1_Silent_p.I189I|RAB6B_ENST00000469959.1_Intron|RAB6B_ENST00000486858.1_Silent_p.I176I	NM_016577.3	NP_057661.3	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family	189					GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	11						GCTTGATGTCGATCACTGCAG	0.597													G|||	1014	0.202476	0.0091	0.2666	5008	,	,		16826	0.3869		0.171	False		,,,				2504	0.2607				p.I189I		Atlas-SNP	.											.	RAB6B	36	.	0			c.C567T						PASS	.	G		154,4252	106.0+/-144.5	5,144,2054	111.0	122.0	118.0		567	-4.8	0.9	3	dbSNP_100	118	1274,7326	253.9+/-279.4	100,1074,3126	no	coding-synonymous	RAB6B	NM_016577.3		105,1218,5180	AA,AG,GG		14.814,3.4952,10.9795		189/209	133547692	1428,11578	2203	4300	6503	SO:0001819	synonymous_variant	51560	exon8			GATGTCGATCACT	AF166492	CCDS3082.1	3q22.1	2008-05-15			ENSG00000154917	ENSG00000154917		"""RAB, member RAS oncogene"""	14902	protein-coding gene	gene with protein product		615852					Standard	NM_016577		Approved		uc003epy.3	Q9NRW1	OTTHUMG00000159749	ENST00000285208.4:c.567C>T	3.37:g.133547692G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	16	0.340426	NM_016577	B2R5Z9|B7Z337|D3DND3|Q92929	Silent	SNP	ENST00000285208.4	37	CCDS3082.1																																																																																			G|0.856;A|0.144	0.144	strong		0.597	RAB6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357152.1		
SRRM2	23524	hgsc.bcm.edu	37	16	2812647	2812647	+	Silent	SNP	C	C	T	rs2240142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2812647C>T	ENST00000301740.8	+	11	2667	c.2118C>T	c.(2116-2118)agC>agT	p.S706S		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	706	Arg-rich.|Ser-rich.				mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						GCAGTAGAAGCTTAGTTAGAC	0.517													C|||	876	0.17492	0.2012	0.1311	5008	,	,		19523	0.2589		0.167	False		,,,				2504	0.092				p.S706S		Atlas-SNP	.											SRRM2,NS,lymphoid_neoplasm,0,1	SRRM2	263	1	0			c.C2118T						PASS	.	C		837,3559	327.2+/-299.9	72,693,1433	72.0	74.0	74.0		2118	2.0	1.0	16	dbSNP_98	74	1348,7252	261.4+/-283.8	106,1136,3058	no	coding-synonymous	SRRM2	NM_016333.3		178,1829,4491	TT,TC,CC		15.6744,19.04,16.8129		706/2753	2812647	2185,10811	2198	4300	6498	SO:0001819	synonymous_variant	23524	exon11			TAGAAGCTTAGTT	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2118C>T	16.37:g.2812647C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	64	25	0.390625	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																			C|0.826;T|0.174	0.174	strong		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
SFTPD	6441	hgsc.bcm.edu	37	10	81706324	81706324	+	Missense_Mutation	SNP	A	A	G	rs721917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:81706324A>G	ENST00000372292.3	-	2	132	c.92T>C	c.(91-93)aTg>aCg	p.M31T		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	31			M -> T (in dbSNP:rs721917). {ECO:0000269|PubMed:1339284, ECO:0000269|PubMed:19100526, ECO:0000269|Ref.3, 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)			AGCACTGGGCATTGTTCTGTG	0.617													g|||	2527	0.504593	0.4009	0.379	5008	,	,		20859	0.6151		0.4205	False		,,,				2504	0.7065				p.M31T		Atlas-SNP	.											SFTPD,NS,carcinoma,+1,1	SFTPD	43	1	0			c.T92C	GRCh37	CM021324	SFTPD	M	rs721917	PASS	.	G	THR/MET	1769,2637	643.9+/-397.9	376,1017,810	122.0	102.0	109.0		92	-1.4	0.0	10	dbSNP_86	109	3610,4990	626.4+/-397.8	761,2088,1451	yes	missense	SFTPD	NM_003019.4	81	1137,3105,2261	GG,GA,AA		41.9767,40.1498,41.3578	benign	31/376	81706324	5379,7627	2203	4300	6503	SO:0001583	missense	6441	exon2			CTGGGCATTGTTC	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.92T>C	10.37:g.81706324A>G	ENSP00000361366:p.Met31Thr	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Missense_Mutation	SNP	ENST00000372292.3	37	CCDS7362.1	1021	0.4674908424908425	202	0.4105691056910569	149	0.4116022099447514	357	0.6241258741258742	313	0.4129287598944591	G	7.685	0.689886	0.15039	0.401498	0.419767	ENSG00000133661	ENST00000372292;ENST00000444384	D;D	0.91068	-2.62;-2.78	5.59	-1.35	0.09114	.	1.689840	0.03546	N	0.224694	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	0.25779	-1.0122	9	0.10636	T	0.68	0.1384	6.1062	0.20075	0.576:0.0:0.3085:0.1155	rs721917;rs3750874;rs17887190;rs52794086;rs58664997;rs721917	31	P35247	SFTPD_HUMAN	T	31;44	ENSP00000361366:M31T;ENSP00000394325:M44T	ENSP00000361366:M31T	M	-	2	0	SFTPD	81696304	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.298000	0.08265	-0.475000	0.06852	-1.088000	0.02184	ATG	A|0.559;G|0.441	0.441	strong		0.617	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		
CIITA	4261	hgsc.bcm.edu	37	16	11001770	11001770	+	Silent	SNP	G	G	T	rs34654419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:11001770G>T	ENST00000324288.8	+	11	2554	c.2421G>T	c.(2419-2421)ctG>ctT	p.L807L	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	807					aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.L807L(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						GGCAGCTGCTGGAGCTGCTGC	0.687			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """								G|||	1081	0.215855	0.2057	0.3876	5008	,	,		12685	0.1329		0.1869	False		,,,				2504	0.2229				p.L807L		Atlas-SNP	.		Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	CIITA_ENST00000324288,NS,lymphoid_neoplasm,0,1	CIITA	92	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2421T						PASS	.	G		828,3494		88,652,1421	19.0	27.0	24.0		2421	2.8	1.0	16	dbSNP_126	24	1706,6752		189,1328,2712	no	coding-synonymous	CIITA	NM_000246.3		277,1980,4133	TT,TG,GG		20.1703,19.1578,19.8279		807/1131	11001770	2534,10246	2161	4229	6390	SO:0001819	synonymous_variant	4261	exon11			GCTGCTGGAGCTG	U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.2421G>T	16.37:g.11001770G>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																			T|0.193;G|0.806;C|0.000	0.193	strong		0.687	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
COL18A1	80781	hgsc.bcm.edu	37	21	46895427	46895427	+	Missense_Mutation	SNP	G	G	T	rs62000965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46895427G>T	ENST00000359759.4	+	4	2042	c.2021G>T	c.(2020-2022)cGg>cTg	p.R674L	COL18A1_ENST00000400337.2_Missense_Mutation_p.R259L|COL18A1_ENST00000355480.5_Missense_Mutation_p.R439L			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	674	Nonhelical region 1 (NC1).				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)		GGGGACGCCCGGGAGCTTCTC	0.692													G|||	96	0.0191693	0.0666	0.0115	5008	,	,		14324	0.0		0.0	False		,,,				2504	0.0				p.R439L		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1316T						PASS	.	G	LEU/ARG,LEU/ARG	231,3473		6,219,1627	13.0	16.0	15.0		776,1316	-4.6	0.0	21	dbSNP_129	15	1,8171		0,1,4085	no	missense,missense	COL18A1	NM_130445.2,NM_030582.3	102,102	6,220,5712	TT,TG,GG		0.0122,6.2365,1.9535	benign,benign	259/1340,439/1520	46895427	232,11644	1852	4086	5938	SO:0001583	missense	80781	exon4			ACGCCCGGGAGCT		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.2021G>T	21.37:g.46895427G>T	ENSP00000352798:p.Arg674Leu	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	148	65	0.439189	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	9.059	0.994091	0.19043	0.062365	1.22E-4	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90563	-2.66;-2.69;-2.57	2.98	-4.62	0.03370	.	1.760170	0.02944	N	0.140855	T	0.11452	0.0279	N	0.24115	0.695	0.09310	N	1	B;B;B	0.29716	0.166;0.255;0.255	B;B;B	0.25614	0.028;0.062;0.045	T	0.57528	-0.7796	10	0.25751	T	0.34	.	5.8286	0.18568	0.6231:0.1574:0.2195:0.0	rs62000965	674;439;259	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	L	259;259;439;674;674	ENSP00000383191:R259L;ENSP00000347665:R439L;ENSP00000352798:R674L	ENSP00000347665:R439L	R	+	2	0	COL18A1	45719855	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-2.199000	0.01238	-1.208000	0.02634	0.196000	0.17591	CGG	G|0.976;T|0.024	0.024	strong		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
HLA-B	3106	hgsc.bcm.edu	37	6	31324574	31324574	+	Silent	SNP	C	C	T	rs9266175	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31324574C>T	ENST00000412585.2	-	2	262	c.234G>A	c.(232-234)caG>caA	p.Q78Q		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	78	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CCGGCCCCTCCTGCTCTATCC	0.632									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	136	0.0271565	0.0325	0.0403	5008	,	,		7926	0.004		0.0398	False		,,,				2504	0.0215				p.Q78Q		Atlas-SNP	.											.	HLA-B	54	.	0			c.G234A						PASS	.	C		116,4178		10,96,2041	51.0	50.0	50.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	234	2.3	0.6	6	dbSNP_118	50	345,7995		48,249,3873	no	coding-synonymous	HLA-B	NM_005514.6		58,345,5914	TT,TC,CC		4.1367,2.7014,3.6489		78/363	31324574	461,12173	2147	4170	6317	SO:0001819	synonymous_variant	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CCCCTCCTGCTCT	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.234G>A	6.37:g.31324574C>T		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_005514	Q29764	Silent	SNP	ENST00000412585.2	37	CCDS34394.1																																																																																			C|0.970;T|0.030	0.030	strong		0.632	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SCN10A	6336	hgsc.bcm.edu	37	3	38798171	38798171	+	Silent	SNP	C	C	T	rs62244070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38798171C>T	ENST00000449082.2	-	9	1283	c.1284G>A	c.(1282-1284)gaG>gaA	p.E428E		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	428					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	AAACCTCCTGCTCCTTCCGGA	0.498													C|||	1039	0.207468	0.0794	0.1052	5008	,	,		19656	0.372		0.2485	False		,,,				2504	0.2413				p.E428E		Atlas-SNP	.											.	SCN10A	359	.	0			c.G1284A						PASS	.	C		474,3932	222.3+/-239.2	25,424,1754	126.0	124.0	124.0		1284	0.0	1.0	3	dbSNP_129	124	2158,6442	370.4+/-335.9	271,1616,2413	no	coding-synonymous	SCN10A	NM_006514.2		296,2040,4167	TT,TC,CC		25.093,10.7581,20.2368		428/1957	38798171	2632,10374	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon9			CTCCTGCTCCTTC	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1284G>A	3.37:g.38798171C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	40	40	1	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			C|0.785;T|0.215	0.215	strong		0.498	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
C11orf21	29125	hgsc.bcm.edu	37	11	2323089	2323089	+	5'UTR	SNP	C	C	T	rs188839109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2323089C>T	ENST00000381153.3	-	0	201				TSPAN32_ENST00000381121.3_5'Flank|C11orf21_ENST00000470369.1_5'UTR|TSPAN32_ENST00000182290.4_5'Flank|TSPAN32_ENST00000451520.2_5'Flank			Q9P2W6	CK021_HUMAN	chromosome 11 open reading frame 21							cytoplasm (GO:0005737)											AGAACGAGGCCATGTCTTCCT	0.652											OREG0003773	type=REGULATORY REGION|Gene=TSPAN32|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	28	0.00559105	0.0008	0.0101	5008	,	,		16840	0.0		0.0159	False		,,,				2504	0.0041				p.M1I		Atlas-SNP	.											.	C11orf21	11	.	0			c.G3A						PASS	.	C	ILE/MET	3,1381		0,3,689	62.0	64.0	64.0		3	1.4	0.0	11		64	43,3139		1,41,1549	yes	missense	C11orf21	NM_001142946.1	10	1,44,2238	TT,TC,CC		1.3514,0.2168,1.0074	benign	1/179	2323089	46,4520	692	1591	2283	SO:0001623	5_prime_UTR_variant	29125	exon1			CGAGGCCATGTCT	AB029488	CCDS44518.1	11p15.5	2012-08-09			ENSG00000110665	ENSG00000110665			13231	protein-coding gene	gene with protein product		611033				11054561	Standard	NM_001142946		Approved		uc009ydj.2	Q9P2W6	OTTHUMG00000009759	ENST00000381153.3:c.-51G>A	11.37:g.2323089C>T		Somatic	54	0	0	602	WXS	Illumina HiSeq	Phase_I	70	34	0.485714	NM_001142946		Missense_Mutation	SNP	ENST00000381153.3	37		15	0.006868131868131868	0	0.0	8	0.022099447513812154	0	0.0	7	0.009234828496042216	C	5.850	0.341111	0.11069	0.002168	0.013514	ENSG00000110665	ENST00000456145	.	.	.	1.41	1.41	0.22369	.	.	.	.	.	T	0.27798	0.0684	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43048	-0.9415	7	0.87932	D	0	.	6.4156	0.21715	0.0:1.0:0.0:0.0	.	1	E9PAM5	.	I	1	.	ENSP00000406541:M1I	M	-	3	0	C11orf21	2279665	0.000000	0.05858	0.008000	0.14137	0.013000	0.08279	-0.053000	0.11846	1.158000	0.42547	0.388000	0.25769	ATG	C|0.993;T|0.007	0.007	strong		0.652	C11orf21-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000026908.2	NM_001142946	
NUP98	4928	hgsc.bcm.edu	37	11	3723941	3723941	+	Silent	SNP	C	C	T	rs35488940	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:3723941C>T	ENST00000324932.7	-	23	3684	c.3264G>A	c.(3262-3264)ccG>ccA	p.P1088P	NUP98_ENST00000355260.3_Silent_p.P1088P|NUP98_ENST00000359171.4_Silent_p.P1088P	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	1105					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)		CTGTTTTCAACGGAACCTCAG	0.512			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML								C|||	116	0.0231629	0.0076	0.036	5008	,	,		18553	0.001		0.0726	False		,,,				2504	0.0072				p.P1088P		Atlas-SNP	.		Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	NUP98	149	.	0			c.G3264A						PASS	.	C	,	76,4326	65.8+/-103.3	1,74,2126	94.0	79.0	84.0		3264,3264	-3.0	0.3	11	dbSNP_126	84	671,7925	169.4+/-220.8	23,625,3650	no	coding-synonymous,coding-synonymous	NUP98	NM_016320.4,NM_139132.3	,	24,699,5776	TT,TC,CC		7.806,1.7265,5.747	,	1088/1801,1088/1727	3723941	747,12251	2201	4298	6499	SO:0001819	synonymous_variant	4928	exon23			TTTCAACGGAACC	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.3264G>A	11.37:g.3723941C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	176	72	0.409091	NM_016320	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	37	CCDS7746.1																																																																																			C|0.951;T|0.049	0.049	strong		0.512	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
TTC8	123016	hgsc.bcm.edu	37	14	89319359	89319359	+	Silent	SNP	G	G	A	rs141304350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:89319359G>A	ENST00000345383.5	+	7	723	c.639G>A	c.(637-639)aaG>aaA	p.K213K	TTC8_ENST00000536576.1_5'UTR|TTC8_ENST00000354441.6_Intron|TTC8_ENST00000358622.5_Silent_p.K25K|TTC8_ENST00000380656.2_Silent_p.K223K|TTC8_ENST00000338104.6_Silent_p.K239K|TTC8_ENST00000346301.4_Silent_p.K183K	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	249					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						CTCAGTACAAGGACTGGTGGT	0.378													G|||	5	0.000998403	0.0	0.0029	5008	,	,		16565	0.0		0.001	False		,,,				2504	0.002				p.K223K		Atlas-SNP	.											.	TTC8	42	.	0			c.G669A						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	91.0	80.0	84.0		669,639,549	5.3	1.0	14	dbSNP_134	84	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	TTC8	NM_144596.2,NM_198309.2,NM_198310.2	,,	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	,,	223/516,213/506,183/476	89319359	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	123016	exon8			GTACAAGGACTGG	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"""Tetratricopeptide (TTC) repeat domain containing"""	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.639G>A	14.37:g.89319359G>A		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	151	73	0.483444	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Silent	SNP	ENST00000345383.5	37	CCDS9885.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	9.139	1.013312	0.19277	2.27E-4	5.81E-4	ENSG00000165533	ENST00000554686	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	T	0.60907	0.2305	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58317	-0.7657	4	.	.	.	-26.5066	9.7161	0.40276	0.1556:0.0:0.8444:0.0	.	.	.	.	K	173	.	.	R	+	2	0	TTC8	88389112	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.332000	0.65911	2.660000	0.90430	0.655000	0.94253	AGG	G|1.000;A|0.000	0.000	strong		0.378	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596	
EMR1	2015	hgsc.bcm.edu	37	19	6913707	6913707	+	Missense_Mutation	SNP	C	C	T	rs466876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6913707C>T	ENST00000312053.4	+	11	1203	c.1166C>T	c.(1165-1167)aCg>aTg	p.T389M	EMR1_ENST00000450315.3_Missense_Mutation_p.T212M|EMR1_ENST00000381407.5_Missense_Mutation_p.T248M|EMR1_ENST00000250572.8_Missense_Mutation_p.T389M|EMR1_ENST00000381404.4_Missense_Mutation_p.T337M	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	389	Ser/Thr-rich.		T -> M (in dbSNP:rs466876). {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)					CAAATATCCACGTGGACTAAA	0.438													C|||	705	0.140775	0.177	0.196	5008	,	,		18718	0.004		0.1948	False		,,,				2504	0.138				p.T389M		Atlas-SNP	.											.	EMR1	153	.	0			c.C1166T						PASS	.	C	MET/THR	741,3665	306.0+/-289.3	68,605,1530	95.0	90.0	92.0		1166	-9.7	0.0	19	dbSNP_80	92	1911,6689	338.1+/-322.6	211,1489,2600	yes	missense	EMR1	NM_001974.3	81	279,2094,4130	TT,TC,CC		22.2209,16.818,20.3906	probably-damaging	389/887	6913707	2652,10354	2203	4300	6503	SO:0001583	missense	2015	exon11			TATCCACGTGGAC	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.1166C>T	19.37:g.6913707C>T	ENSP00000311545:p.Thr389Met	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	101	45	0.445545	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	284	0.13003663003663005	66	0.13414634146341464	70	0.19337016574585636	2	0.0034965034965034965	146	0.19261213720316622	C	10.83	1.459854	0.26248	0.16818	0.222209	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407;ENST00000450315	T;T;T;T;T	0.78364	-1.14;-1.17;-1.17;-0.01;0.35	4.83	-9.66	0.00534	.	.	.	.	.	T	0.00109	0.0003	M	0.69823	2.125	0.80722	P	0.0	P;P;D;P;D	0.63046	0.857;0.685;0.992;0.685;0.987	B;B;P;B;P	0.54706	0.26;0.036;0.759;0.036;0.579	T	0.48559	-0.9025	8	0.46703	T	0.11	.	4.571	0.12210	0.4322:0.1773:0.0:0.3905	rs466876;rs2228532;rs17704704;rs52812871;rs58365493;rs466876	212;248;389;337;389	E7EPX9;B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;.;EMR1_HUMAN	M	389;389;337;389;248;212	ENSP00000311545:T389M;ENSP00000370811:T337M;ENSP00000250572:T389M;ENSP00000370814:T248M;ENSP00000405974:T212M	ENSP00000250572:T389M	T	+	2	0	EMR1	6864707	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.390000	0.07332	-1.890000	0.01111	-0.142000	0.14014	ACG	C|0.824;T|0.176	0.176	strong		0.438	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
CAPN12	147968	hgsc.bcm.edu	37	19	39230748	39230748	+	Silent	SNP	C	C	G	rs34911882	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39230748C>G	ENST00000328867.4	-	5	980	c.672G>C	c.(670-672)ctG>ctC	p.L224L	CTD-2540F13.2_ENST00000602255.1_RNA|CAPN12_ENST00000601953.1_Silent_p.L75L	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	224	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)			GGGCAGAGAACAGCCCCATGC	0.622													G|||	348	0.0694888	0.056	0.0821	5008	,	,		15992	0.0476		0.0616	False		,,,				2504	0.1094				p.L224L		Atlas-SNP	.											.	CAPN12	43	.	0			c.G672C						PASS	.	G		213,4193	804.6+/-415.8	7,199,1997	44.0	39.0	40.0		672	4.8	1.0	19	dbSNP_126	40	545,8055	793.6+/-407.5	12,521,3767	no	coding-synonymous	CAPN12	NM_144691.3		19,720,5764	GG,GC,CC		6.3372,4.8343,5.8281		224/720	39230748	758,12248	2203	4300	6503	SO:0001819	synonymous_variant	147968	exon5			AGAGAACAGCCCC	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.672G>C	19.37:g.39230748C>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			C|0.943;G|0.057	0.057	strong		0.622	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
ZNF354A	6940	hgsc.bcm.edu	37	5	178139355	178139355	+	Silent	SNP	T	T	C	rs113805764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:178139355T>C	ENST00000335815.2	-	5	1721	c.1524A>G	c.(1522-1524)tcA>tcG	p.S508S		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	508					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		GATTACTAAGTGATGAGTTAC	0.403													C|||	49	0.00978435	0.0083	0.013	5008	,	,		19708	0.0		0.0249	False		,,,				2504	0.0041				p.S508S		Atlas-SNP	.											.	ZNF354A	74	.	0			c.A1524G						PASS	.	C		30,4376	823.4+/-416.5	0,30,2173	118.0	116.0	117.0		1524	-1.5	1.0	5	dbSNP_132	117	134,8466	810.1+/-407.1	0,134,4166	no	coding-synonymous	ZNF354A	NM_005649.2		0,164,6339	CC,CT,TT		1.5581,0.6809,1.261		508/606	178139355	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			ACTAAGTGATGAG	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1524A>G	5.37:g.178139355T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	77	16	0.207792	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			T|0.988;C|0.012	0.012	strong		0.403	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
SVEP1	79987	hgsc.bcm.edu	37	9	113234507	113234507	+	Missense_Mutation	SNP	T	T	C	rs10817025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113234507T>C	ENST00000401783.2	-	15	3032	c.2696A>G	c.(2695-2697)aAg>aGg	p.K899R	SVEP1_ENST00000374469.1_Missense_Mutation_p.K876R|SVEP1_ENST00000302728.8_Missense_Mutation_p.K899R|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	899			K -> R (in dbSNP:rs10817025).		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						CCGTGAGGACTTGGCATTGCC	0.423													C|||	997	0.199081	0.1354	0.2147	5008	,	,		18190	0.0754		0.2893	False		,,,				2504	0.3088				p.K899R		Atlas-SNP	.											.	SVEP1	326	.	0			c.A2696G						PASS	.	C	ARG/LYS	644,3256		58,528,1364	153.0	156.0	155.0		2696	4.2	1.0	9	dbSNP_120	155	2497,5801		391,1715,2043	yes	missense	SVEP1	NM_153366.3	26	449,2243,3407	CC,CT,TT		30.0916,16.5128,25.7501	benign	899/3572	113234507	3141,9057	1950	4149	6099	SO:0001583	missense	79987	exon15			GAGGACTTGGCAT	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.2696A>G	9.37:g.113234507T>C	ENSP00000384917:p.Lys899Arg	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	182	182	1	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	418	0.19139194139194138	76	0.15447154471544716	88	0.2430939226519337	36	0.06293706293706294	218	0.287598944591029	C	0.012	-1.676236	0.00751	0.165128	0.300916	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.77877	-1.01;-1.02;-1.13	5.25	4.15	0.48705	.	0.396625	0.29438	N	0.012160	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	0.10291	-1.0636	9	0.11794	T	0.64	.	7.1732	0.25730	0.0:0.5639:0.2523:0.1837	rs10817025;rs17806789;rs52830999;rs56677016;rs10817025	899;899	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	R	899;876;899	ENSP00000384917:K899R;ENSP00000363593:K876R;ENSP00000304118:K899R	ENSP00000304118:K899R	K	-	2	0	SVEP1	112274328	0.926000	0.31397	0.960000	0.40013	0.121000	0.20230	0.716000	0.25836	1.247000	0.43917	-0.128000	0.14901	AAG	T|0.798;C|0.202	0.202	strong		0.423	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
OR2G2	81470	hgsc.bcm.edu	37	1	247752019	247752019	+	Missense_Mutation	SNP	G	G	C	rs1151687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:247752019G>C	ENST00000320065.1	+	1	358	c.358G>C	c.(358-360)Gtg>Ctg	p.V120L	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	120			V -> L (in dbSNP:rs1151687).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			CCTCCCGGCTGTGATGTCCTG	0.527													G|||	2902	0.579473	0.1641	0.6686	5008	,	,		21117	0.7599		0.7147	False		,,,				2504	0.7526				p.V120L		Atlas-SNP	.											OR2G2,NS,adenoma,0,2	OR2G2	88	2	0			c.G358C						PASS	.	G	LEU/VAL	1107,3299	396.7+/-330.2	141,825,1237	271.0	216.0	235.0		358	3.4	0.4	1	dbSNP_87	235	6090,2510	694.3+/-404.7	2149,1792,359	yes	missense	OR2G2	NM_001001915.1	32	2290,2617,1596	CC,CG,GG		29.186,25.1248,44.664	benign	120/318	247752019	7197,5809	2203	4300	6503	SO:0001583	missense	81470	exon1			CCGGCTGTGATGT	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.358G>C	1.37:g.247752019G>C	ENSP00000326349:p.Val120Leu	Somatic	282	1	0.0035461		WXS	Illumina HiSeq	Phase_I	292	125	0.428082	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	1326	0.6071428571428571	85	0.17276422764227642	250	0.6906077348066298	440	0.7692307692307693	551	0.7269129287598944	G	13.50	2.254468	0.39896	0.251248	0.70814	ENSG00000177489	ENST00000320065	T	0.05139	3.49	4.29	3.37	0.38596	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31859	U	0.006958	T	0.00012	0.0000	M	0.64567	1.98	0.58432	P	1.999999999946489E-6	B	0.24823	0.112	B	0.27715	0.082	T	0.05146	-1.0903	9	0.72032	D	0.01	.	9.7522	0.40483	0.1027:0.0:0.8973:0.0	rs1151687;rs1630639;rs17252960;rs52794366;rs61426876;rs1151687	120	Q8NGZ5	OR2G2_HUMAN	L	120	ENSP00000326349:V120L	ENSP00000326349:V120L	V	+	1	0	OR2G2	245818642	0.005000	0.15991	0.378000	0.26068	0.993000	0.82548	0.628000	0.24522	1.008000	0.39264	0.591000	0.81541	GTG	G|0.435;C|0.565	0.565	strong		0.527	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31239449	31239449	+	Missense_Mutation	SNP	C	C	G	rs28626310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31239449C>G	ENST00000376228.5	-	2	284	c.270G>C	c.(268-270)aaG>aaC	p.K90N	HLA-C_ENST00000383329.3_Missense_Mutation_p.K90N	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	90	Alpha-1.		K -> N (in dbSNP:rs28626310).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGCGCTTGTACTTCTGTGTCT	0.701													c|||	710	0.141773	0.1452	0.1282	5008	,	,		12148	0.0516		0.168	False		,,,				2504	0.2127				p.K90N		Atlas-SNP	.											.	HLA-C	92	.	0			c.G270C						PASS	.	C	ASN/LYS	438,2584		26,386,1099	48.0	49.0	48.0		270	-5.5	0.0	6	dbSNP_125	48	999,4419		91,817,1801	no	missense	HLA-C	NM_002117.5	94	117,1203,2900	GG,GC,CC		18.4385,14.4937,17.0261	benign	90/367	31239449	1437,7003	1511	2709	4220	SO:0001583	missense	3107	exon2			CTTGTACTTCTGT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.270G>C	6.37:g.31239449C>G	ENSP00000365402:p.Lys90Asn	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	222	220	0.990991	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	260|260	0.11904761904761904|0.11904761904761904	60|60	0.12195121951219512|0.12195121951219512	47|47	0.1298342541436464|0.1298342541436464	26|26	0.045454545454545456|0.045454545454545456	127|127	0.16754617414248021|0.16754617414248021	-|-	0.008|0.008	-1.894729|-1.894729	0.00522|0.00522	0.144937|0.144937	0.184385|0.184385	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.48;9.48|.	2.75|2.75	-5.49|-5.49	0.02584|0.02584	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	2211.810000|.	0.00541|.	N|.	0.000226|.	T|T	0.01489|0.01489	0.0048|0.0048	N|N	0.01751|0.01751	-0.74|-0.74	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.10296|.	0.003;0.003;0.001;0.003|.	B;B;B;B|.	0.21151|.	0.033;0.033;0.033;0.022|.	T|T	0.22941|0.22941	-1.0202|-1.0202	9|4	0.36615|.	T|.	0.2|.	.|.	3.7958|3.7958	0.08738|0.08738	0.0845:0.197:0.1701:0.5485|0.0845:0.197:0.1701:0.5485	rs28626310;rs41555912|rs28626310;rs41555912	90;90;90;90|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	N|L	90;90;90;127|90	ENSP00000365402:K90N;ENSP00000372819:K90N|.	ENSP00000365402:K90N|.	K|V	-|-	3|1	2|0	HLA-C|HLA-C	31347428|31347428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-9.984000|-9.984000	0.00008|0.00008	-6.044000|-6.044000	0.00007|0.00007	-3.594000|-3.594000	0.00028|0.00028	AAG|GTA	C|0.840;G|0.160	0.160	strong		0.701	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
PCDHGB3	56102	hgsc.bcm.edu	37	5	140778256	140778256	+	Intron	SNP	G	G	A	rs6867460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140778256G>A	ENST00000576222.1	+	1	2546				PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAAACAGGATGGTAGTAAATA	0.433													.|||	1016	0.202875	0.32	0.1902	5008	,	,		18939	0.1548		0.1024	False		,,,				2504	0.2065				p.G188S		Atlas-SNP	.											.	.	.	.	0			c.G562A						PASS	.	G	,,,,,,,,,,,SER/GLY,,SER/GLY	1172,2540		197,778,881	69.0	72.0	71.0		,,,,,,,,,,,562,,562	4.8	0.8	5	dbSNP_116	71	1005,7179		65,875,3152	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032099.1	,,,,,,,,,,,56,,56	262,1653,4033	AA,AG,GG		12.2801,31.5733,18.3003	,,,,,,,,,,,,,	,,,,,,,,,,,188/924,,188/819	140778256	2177,9719	1856	4092	5948	SO:0001627	intron_variant	56101	exon1			CAGGATGGTAGTA	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+25880G>A	5.37:g.140778256G>A		Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	111	110	0.990991	NM_018925	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			G|0.804;A|0.196	0.196	strong		0.433	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
RNF20	56254	hgsc.bcm.edu	37	9	104324545	104324545	+	Silent	SNP	G	G	A	rs10521057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104324545G>A	ENST00000389120.3	+	20	2859	c.2769G>A	c.(2767-2769)ccG>ccA	p.P923P		NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	923					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		TGACCTGTCCGTGCTGTAACA	0.418													G|||	928	0.185304	0.0038	0.0865	5008	,	,		20396	0.3562		0.1938	False		,,,				2504	0.316				p.P923P		Atlas-SNP	.											RNF20,NS,carcinoma,0,1	RNF20	110	1	0			c.G2769A						PASS	.	G		179,4227	117.1+/-155.0	3,173,2027	157.0	143.0	148.0		2769	-11.7	0.5	9	dbSNP_119	148	1583,7017	296.3+/-302.9	145,1293,2862	no	coding-synonymous	RNF20	NM_019592.5		148,1466,4889	AA,AG,GG		18.407,4.0626,13.5476		923/976	104324545	1762,11244	2203	4300	6503	SO:0001819	synonymous_variant	56254	exon20			CTGTCCGTGCTGT	AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.2769G>A	9.37:g.104324545G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Silent	SNP	ENST00000389120.3	37	CCDS35084.1																																																																																			G|0.836;A|0.164	0.164	strong		0.418	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
OR10K2	391107	hgsc.bcm.edu	37	1	158390501	158390501	+	Silent	SNP	G	G	A	rs34616883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158390501G>A	ENST00000314902.2	-	1	155	c.156C>T	c.(154-156)gaC>gaT	p.D52D		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					GAAGGGCCCTGTCCAGGACAA	0.512													G|||	1405	0.280551	0.2186	0.2695	5008	,	,		22238	0.1687		0.4592	False		,,,				2504	0.3037				p.D52D		Atlas-SNP	.											OR10K2,NS,carcinoma,0,1	OR10K2	69	1	0			c.C156T						PASS	.	G		1068,3338	389.1+/-327.2	134,800,1269	170.0	141.0	151.0		156	1.1	1.0	1	dbSNP_126	151	3769,4831	534.6+/-382.6	807,2155,1338	no	coding-synonymous	OR10K2	NM_001004476.1		941,2955,2607	AA,AG,GG		43.8256,24.2397,37.1905		52/313	158390501	4837,8169	2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			GGCCCTGTCCAGG	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.156C>T	1.37:g.158390501G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	245	119	0.485714	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			G|0.643;A|0.357	0.357	strong		0.512	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
SLC4A1	6521	hgsc.bcm.edu	37	17	42335135	42335135	+	Silent	SNP	C	C	T	rs5017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42335135C>T	ENST00000262418.6	-	12	1478	c.1323G>A	c.(1321-1323)ctG>ctA	p.L441L	SLC4A1_ENST00000471005.1_5'Flank|AC003043.1_ENST00000597382.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	441	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		CAGTGGAGATCAGCAGCTCCG	0.587													C|||	115	0.0229633	0.003	0.0375	5008	,	,		19938	0.001		0.0676	False		,,,				2504	0.0164				p.L441L		Atlas-SNP	.											.	SLC4A1	104	.	0			c.G1323A						PASS	.	C		77,4329	68.7+/-106.4	2,73,2128	84.0	76.0	79.0		1323	3.6	1.0	17	dbSNP_52	79	714,7886	174.9+/-225.1	32,650,3618	no	coding-synonymous	SLC4A1	NM_000342.3		34,723,5746	TT,TC,CC		8.3023,1.7476,6.0818		441/912	42335135	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	6521	exon12			GGAGATCAGCAGC		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.1323G>A	17.37:g.42335135C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	116	52	0.448276	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Silent	SNP	ENST00000262418.6	37	CCDS11481.1																																																																																			C|0.948;T|0.052	0.052	strong		0.587	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
UTP15	84135	hgsc.bcm.edu	37	5	72874907	72874907	+	Silent	SNP	A	A	C	rs343122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:72874907A>C	ENST00000296792.4	+	11	1467	c.1212A>C	c.(1210-1212)ggA>ggC	p.G404G	UTP15_ENST00000543251.1_Silent_p.G214G|UTP15_ENST00000508491.1_Silent_p.G385G	NM_001284431.1|NM_032175.2	NP_001271360.1|NP_115551.2	Q8TED0	UTP15_HUMAN	UTP15, U3 small nucleolar ribonucleoprotein, homolog (S. cerevisiae)	404					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	15		Lung NSC(167;0.00405)|Ovarian(174;0.0129)		OV - Ovarian serous cystadenocarcinoma(47;7.76e-55)		ATCGAAGAGGAGTCCTTGCAA	0.373													A|||	647	0.129193	0.0976	0.1527	5008	,	,		18085	0.0585		0.2187	False		,,,				2504	0.136				p.G404G		Atlas-SNP	.											.	UTP15	30	.	0			c.A1212C						PASS	.	A		566,3840	252.7+/-259.0	41,484,1678	119.0	124.0	122.0		1212	3.3	1.0	5	dbSNP_79	122	1917,6683	339.9+/-323.4	230,1457,2613	no	coding-synonymous	UTP15	NM_032175.2		271,1941,4291	CC,CA,AA		22.2907,12.8461,19.0912		404/519	72874907	2483,10523	2203	4300	6503	SO:0001819	synonymous_variant	84135	exon11			AAGAGGAGTCCTT	AL831972	CCDS34186.1, CCDS68893.1, CCDS68894.1	5q13.2	2013-01-10	2006-04-20		ENSG00000164338	ENSG00000164338		"""WD repeat domain containing"""	25758	protein-coding gene	gene with protein product			"""UTP15, U3 small nucleolar ribonucleoprotein, homolog (yeast)"""			12477932	Standard	NM_032175		Approved	FLJ12787, NET21, FLJ23637	uc003kcw.1	Q8TED0	OTTHUMG00000162453	ENST00000296792.4:c.1212A>C	5.37:g.72874907A>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	114	54	0.473684	NM_032175	B4DU75|B4DXK8|Q6IA60|Q96E08|Q9H9F8	Silent	SNP	ENST00000296792.4	37	CCDS34186.1	296	0.13553113553113552	47	0.09552845528455285	64	0.17679558011049723	23	0.04020979020979021	162	0.21372031662269128	A	10.51	1.369190	0.24771	0.128461	0.222907	ENSG00000164338	ENST00000509005	.	.	.	5.68	3.27	0.37495	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.07790	-1.0754	3	.	.	.	.	8.4101	0.32638	0.7937:0.1372:0.0691:0.0	rs343122;rs1667442;rs17551643;rs17845364;rs17858217;rs343122	.	.	.	A	431	.	.	E	+	2	0	UTP15	72910663	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.317000	0.43770	0.503000	0.28060	0.533000	0.62120	GAG	A|0.839;C|0.161	0.161	strong		0.373	UTP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368965.1	NM_032175	
OR7D4	125958	hgsc.bcm.edu	37	19	9325116	9325116	+	Missense_Mutation	SNP	G	G	A	rs5020278	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9325116G>A	ENST00000308682.2	-	1	426	c.398C>T	c.(397-399)aCg>aTg	p.T133M		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	133			T -> M (impaired response to androstenone and androstadienone; when associated with W-88; dbSNP:rs5020278). {ECO:0000269|PubMed:17873857}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						CATGATGACCGTGTAGTGCAG	0.488													G|||	739	0.147564	0.0567	0.1066	5008	,	,		20522	0.2153		0.2018	False		,,,				2504	0.1738				p.T133M		Atlas-SNP	.											.	OR7D4	66	.	0			c.C398T						PASS	.	G	MET/THR	350,4056	181.9+/-209.8	7,336,1860	86.0	81.0	83.0		398	-4.5	0.0	19	dbSNP_113	83	1573,7027	292.3+/-300.8	138,1297,2865	yes	missense	OR7D4	NM_001005191.2	81	145,1633,4725	AA,AG,GG		18.2907,7.9437,14.7855	benign	133/313	9325116	1923,11083	2203	4300	6503	SO:0001583	missense	125958	exon1			ATGACCGTGTAGT		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.398C>T	19.37:g.9325116G>A	ENSP00000310488:p.Thr133Met	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	157	69	0.43949	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	ENST00000308682.2	37	CCDS32901.1	341	0.15613553113553114	22	0.044715447154471545	38	0.10497237569060773	129	0.22552447552447552	152	0.20052770448548812	G	1.270	-0.613412	0.03690	0.079437	0.182907	ENSG00000174667	ENST00000308682	T	0.20200	2.09	4.0	-4.5	0.03493	GPCR, rhodopsin-like superfamily (1);	0.998718	0.08103	N	0.997365	T	0.00012	0.0000	L	0.60067	1.865	0.80722	P	0.0	B	0.29909	0.261	B	0.17098	0.017	T	0.33574	-0.9863	9	0.21014	T	0.42	.	7.1843	0.25791	0.5595:0.1222:0.3183:0.0	rs5020278	133	Q8NG98	OR7D4_HUMAN	M	133	ENSP00000310488:T133M	ENSP00000310488:T133M	T	-	2	0	OR7D4	9186116	0.000000	0.05858	0.000000	0.03702	0.352000	0.29268	-4.418000	0.00237	-0.901000	0.03891	-0.436000	0.05848	ACG	G|0.845;A|0.155	0.155	strong		0.488	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537258	88537258	+	Silent	SNP	T	T	C	rs199966097		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537258T>C	ENST00000282478.7	+	4	3477	c.3444T>C	c.(3442-3444)agT>agC	p.S1148S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1148S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1148	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)	p.S1148S(1)		breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gtgacagcagtgaaagcagcg	0.562																																					p.S1148S		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	1	Substitution - coding silent(1)	kidney(1)	c.T3444C						scavenged	.						47.0	63.0	57.0					4																	88537258		1566	2841	4407	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGAAAGC	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3444T>C	4.37:g.88537258T>C		Somatic	142	4	0.028169		WXS	Illumina HiSeq	Phase_I	153	20	0.130719	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.562	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
APOH	350	hgsc.bcm.edu	37	17	64208285	64208285	+	Missense_Mutation	SNP	C	C	G	rs1801690	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:64208285C>G	ENST00000205948.6	-	8	1041	c.1004G>C	c.(1003-1005)tGg>tCg	p.W335S		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	335	Sushi-like.		W -> S (in allele APOH*3W; loss of phosphatidylserine-binding; dbSNP:rs1801690). {ECO:0000269|PubMed:9063752, ECO:0000269|Ref.8}.		blood coagulation, intrinsic pathway (GO:0007597)|negative regulation of angiogenesis (GO:0016525)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|plasminogen activation (GO:0031639)|positive regulation of blood coagulation (GO:0030194)|positive regulation of lipoprotein lipase activity (GO:0051006)|regulation of fibrinolysis (GO:0051917)|triglyceride metabolic process (GO:0006641)|triglyceride transport (GO:0034197)	cell surface (GO:0009986)|chylomicron (GO:0042627)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipid binding (GO:0005543)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(6;9.74e-08)			ATCAGTTTTCCAAAAAGCCAG	0.368													C|||	183	0.0365415	0.0023	0.0288	5008	,	,		17997	0.0546		0.0567	False		,,,				2504	0.0491				p.W335S	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											APOH,rectum,carcinoma,+1,1	APOH	45	1	0			c.G1004C	GRCh37	CM970095	APOH	M	rs1801690	PASS	.	C	SER/TRP	38,4368	42.3+/-75.8	2,34,2167	97.0	98.0	98.0		1004	5.7	1.0	17	dbSNP_89	98	441,8159	133.8+/-191.2	10,421,3869	yes	missense	APOH	NM_000042.2	177	12,455,6036	GG,GC,CC		5.1279,0.8625,3.6829	possibly-damaging	335/346	64208285	479,12527	2203	4300	6503	SO:0001583	missense	350	exon8			GTTTTCCAAAAAG		CCDS11663.1	17q24.2	2013-01-24				ENSG00000091583		"""Apolipoproteins"""	616	protein-coding gene	gene with protein product	"""beta-2-glycoprotein I"""	138700		B2G1		1582254	Standard	NM_000042		Approved	BG	uc002jfn.4	P02749		ENST00000205948.6:c.1004G>C	17.37:g.64208285C>G	ENSP00000205948:p.Trp335Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	103	53	0.514563	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	98	0.04487179487179487	1	0.0020325203252032522	13	0.03591160220994475	38	0.06643356643356643	46	0.06068601583113457	c	17.13	3.310302	0.60414	0.008625	0.051279	ENSG00000091583	ENST00000205948	T	0.22336	1.96	5.7	5.7	0.88788	Complement control module (2);Beta-2-glycoprotein-1 fifth domain (2);	0.362482	0.30151	N	0.010297	T	0.04679	0.0127	M	0.75447	2.3	0.09310	P	0.99999727626	D	0.76494	0.999	D	0.67900	0.954	T	0.02933	-1.1092	9	0.17832	T	0.49	.	15.3453	0.74330	0.0:1.0:0.0:0.0	rs1801690;rs8178862;rs17763527;rs1801690	335	P02749	APOH_HUMAN	S	335	ENSP00000205948:W335S	ENSP00000205948:W335S	W	-	2	0	APOH	61638747	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	3.506000	0.53364	2.679000	0.91253	0.555000	0.69702	TGG	C|0.960;G|0.040	0.040	strong		0.368	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
TOPBP1	11073	hgsc.bcm.edu	37	3	133327457	133327457	+	Silent	SNP	T	T	C	rs1051772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:133327457T>C	ENST00000260810.5	-	27	4478	c.4347A>G	c.(4345-4347)tcA>tcG	p.S1449S		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1449	BRCT 8. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TATTAACTCCTGAGTCATCTG	0.393								Other conserved DNA damage response genes					T|||	466	0.0930511	0.1694	0.0706	5008	,	,		18764	0.0506		0.1044	False		,,,				2504	0.0378				p.S1449S	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A4347G						PASS	.	T		557,3143		40,477,1333	122.0	111.0	114.0		4347	-10.9	0.4	3	dbSNP_86	114	786,7420		29,728,3346	no	coding-synonymous	TOPBP1	NM_007027.3		69,1205,4679	CC,CT,TT		9.5784,15.0541,11.28		1449/1523	133327457	1343,10563	1850	4103	5953	SO:0001819	synonymous_variant	11073	exon27			AACTCCTGAGTCA	AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.4347A>G	3.37:g.133327457T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	118	49	0.415254	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Silent	SNP	ENST00000260810.5	37	CCDS46919.1																																																																																			T|0.900;C|0.100	0.100	strong		0.393	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
B3GALNT1	8706	hgsc.bcm.edu	37	3	160804167	160804167	+	Missense_Mutation	SNP	C	C	T	rs2231257	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:160804167C>T	ENST00000392781.2	-	8	1123	c.376G>A	c.(376-378)Gac>Aac	p.D126N	B3GALNT1_ENST00000320474.4_Missense_Mutation_p.D126N|B3GALNT1_ENST00000392780.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000417187.1_Intron|B3GALNT1_ENST00000473285.1_Missense_Mutation_p.D126N|B3GALNT1_ENST00000392779.2_Missense_Mutation_p.D126N|B3GALNT1_ENST00000488170.1_Missense_Mutation_p.D126N	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	126			D -> N (in dbSNP:rs2231257). {ECO:0000269|Ref.8}.		oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			AACATTTTGTCTTCCTTTTCA	0.393													C|||	260	0.0519169	0.0038	0.0591	5008	,	,		20257	0.0417		0.0298	False		,,,				2504	0.1452				p.D126N		Atlas-SNP	.											.	B3GALNT1	34	.	0			c.G376A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	49,4357	48.9+/-83.8	1,47,2155	107.0	103.0	105.0		376,376,376,376,376	5.7	1.0	3	dbSNP_98	105	290,8310	107.8+/-168.5	3,284,4013	yes	missense,missense,missense,missense,missense	B3GALNT1	NM_001038628.1,NM_003781.3,NM_033167.2,NM_033168.2,NM_033169.2	23,23,23,23,23	4,331,6168	TT,TC,CC		3.3721,1.1121,2.6065	benign,benign,benign,benign,benign	126/332,126/332,126/332,126/332,126/332	160804167	339,12667	2203	4300	6503	SO:0001583	missense	8706	exon8			TTTTGTCTTCCTT	Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"""Blood group antigens"", ""Beta 3-glycosyltransferases"""	918	protein-coding gene	gene with protein product	"""globoside synthase"", ""P antigen synthase"""	603094	"""UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)"", ""UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"""	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.376G>A	3.37:g.160804167C>T	ENSP00000376532:p.Asp126Asn	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	29	0.42029	NM_001038628	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Missense_Mutation	SNP	ENST00000392781.2	37	CCDS3193.1	58	0.026556776556776556	4	0.008130081300813009	14	0.03867403314917127	22	0.038461538461538464	18	0.023746701846965697	C	9.800	1.180328	0.21787	0.011121	0.033721	ENSG00000169255	ENST00000320474;ENST00000392779;ENST00000392780;ENST00000392781;ENST00000473285;ENST00000488170	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.73	5.73	0.89815	.	1.905830	0.02222	N	0.064124	T	0.27169	0.0666	L	0.31476	0.935	0.40277	D	0.978357	D	0.71674	0.998	D	0.63113	0.911	T	0.35773	-0.9775	10	0.38643	T	0.18	.	18.8796	0.92351	0.0:1.0:0.0:0.0	rs2231257;rs52824161;rs2231257	126	O75752	B3GL1_HUMAN	N	126	ENSP00000323479:D126N;ENSP00000376530:D126N;ENSP00000376531:D126N;ENSP00000376532:D126N;ENSP00000418226:D126N;ENSP00000420163:D126N	ENSP00000323479:D126N	D	-	1	0	B3GALNT1	162286861	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	4.898000	0.63238	2.701000	0.92244	0.561000	0.74099	GAC	C|0.973;T|0.027	0.027	strong		0.393	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167	
CXXC1	30827	hgsc.bcm.edu	37	18	47813157	47813157	+	Silent	SNP	C	C	A	rs375253589		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:47813157C>A	ENST00000285106.6	-	2	789	c.75G>T	c.(73-75)gcG>gcT	p.A25A	CXXC1_ENST00000589940.1_Silent_p.A25A|CXXC1_ENST00000412036.2_Silent_p.A25A|CXXC1_ENST00000587396.1_5'UTR	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	25					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						AGTAGATGGGCGCATTCTCCC	0.612																																					p.A25A		Atlas-SNP	.											.	CXXC1	50	.	0			c.G75T						PASS	.	C	,	0,4406		0,0,2203	115.0	91.0	99.0		75,75	-4.2	1.0	18		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	,	25/661,25/657	47813157	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon2			GATGGGCGCATTC	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.75G>T	18.37:g.47813157C>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	138	62	0.449275	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			.	.	weak		0.612	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
SNED1	25992	hgsc.bcm.edu	37	2	241991198	241991198	+	Silent	SNP	C	C	T	rs138612536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:241991198C>T	ENST00000310397.8	+	13	1773	c.1773C>T	c.(1771-1773)aaC>aaT	p.N591N	SNED1_ENST00000469006.1_3'UTR|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000342631.6_Silent_p.N591N|SNED1_ENST00000401884.1_Silent_p.N591N|SNED1_ENST00000405547.3_Silent_p.N591N	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	591	EGF-like 8. {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)		CCTGCCGGAACGGGGGCACGT	0.692													C|||	10	0.00199681	0.0	0.0043	5008	,	,		16266	0.0		0.006	False		,,,				2504	0.001				p.N591N		Atlas-SNP	.											.	SNED1	76	.	0			c.C1773T						PASS	.	C		4,4012		0,4,2004	8.0	11.0	10.0		1773	0.3	1.0	2	dbSNP_134	10	44,8186		0,44,4071	no	coding-synonymous	SNED1	NM_001080437.1		0,48,6075	TT,TC,CC		0.5346,0.0996,0.392		591/1414	241991198	48,12198	2008	4115	6123	SO:0001819	synonymous_variant	25992	exon13			CCGGAACGGGGGC	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.1773C>T	2.37:g.241991198C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	119	64	0.537815	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Silent	SNP	ENST00000310397.8	37	CCDS46562.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	7.019	0.558409	0.13436	9.96E-4	0.005346	ENSG00000162804	ENST00000401644	.	.	.	3.9	0.258	0.15578	.	.	.	.	.	T	0.47116	0.1428	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41592	-0.9500	4	.	.	.	.	8.4102	0.32638	0.0:0.4713:0.0:0.5287	.	.	.	.	W	288	.	.	R	+	1	2	SNED1	241639871	0.002000	0.14202	0.998000	0.56505	0.767000	0.43475	-1.458000	0.02372	-0.014000	0.14175	-0.463000	0.05309	CGG	C|0.999;T|0.001	0.001	strong		0.692	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
DEFA5	1670	hgsc.bcm.edu	37	8	6913031	6913031	+	Silent	SNP	G	G	A	rs2272719	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:6913031G>A	ENST00000330590.2	-	2	243	c.207C>T	c.(205-207)acC>acT	p.T69T		NM_021010.1	NP_066290.1	Q01523	DEF5_HUMAN	defensin, alpha 5, Paneth cell-specific	69					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)		p.T69T(1)		NS(1)|lung(4)|skin(1)|stomach(1)	7				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		CACAACGGCCGGTTCGGCAAT	0.567													.|||	1468	0.293131	0.1475	0.428	5008	,	,		16586	0.2927		0.3598	False		,,,				2504	0.3262				p.T69T		Atlas-SNP	.											DEFA5,NS,carcinoma,0,1	DEFA5	17	1	1	Substitution - coding silent(1)	stomach(1)	c.C207T						PASS	.	G		836,3570		79,678,1446	42.0	41.0	42.0		207	-2.3	0.0	8	dbSNP_100	42	3311,5289		625,2061,1614	no	coding-synonymous	DEFA5	NM_021010.1		704,2739,3060	AA,AG,GG		38.5,18.9741,31.8853		69/95	6913031	4147,8859	2203	4300	6503	SO:0001819	synonymous_variant	1670	exon2			ACGGCCGGTTCGG	BC069690	CCDS5963.1	8p23.1	2007-02-20			ENSG00000164816	ENSG00000164816		"""Defensins, alpha"""	2764	protein-coding gene	gene with protein product		600472		DEF5		1429669	Standard	NM_021010		Approved	HD-5	uc003wra.1	Q01523	OTTHUMG00000090383	ENST00000330590.2:c.207C>T	8.37:g.6913031G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	57	27	0.473684	NM_021010	A0JDY6|Q3KNV2	Silent	SNP	ENST00000330590.2	37	CCDS5963.1																																																																																			G|0.682;A|0.318	0.318	strong		0.567	DEFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206755.1	NM_021010	
ZNF442	79973	hgsc.bcm.edu	37	19	12462839	12462839	+	Missense_Mutation	SNP	G	G	A	rs117612375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12462839G>A	ENST00000242804.4	-	5	833	c.251C>T	c.(250-252)cCc>cTc	p.P84L	ZNF442_ENST00000438182.1_Missense_Mutation_p.P15L	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	84	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						GCTCCTCCTGGGATTTCTGTG	0.353													G|||	32	0.00638978	0.0015	0.0115	5008	,	,		16082	0.0		0.0189	False		,,,				2504	0.0031				p.P84L		Atlas-SNP	.											.	ZNF442	102	.	0			c.C251T						PASS	.	G	LEU/PRO	18,4388	25.3+/-52.1	0,18,2185	135.0	123.0	127.0		251	0.2	0.1	19	dbSNP_132	127	217,8383	91.9+/-153.9	4,209,4087	yes	missense	ZNF442	NM_030824.2	98	4,227,6272	AA,AG,GG		2.5233,0.4085,1.8069	benign	84/628	12462839	235,12771	2203	4300	6503	SO:0001583	missense	79973	exon5			CTCCTGGGATTTC	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"""Zinc fingers, C2H2-type"", ""-"""	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.251C>T	19.37:g.12462839G>A	ENSP00000242804:p.Pro84Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	135	53	0.392593	NM_030824	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	19	0.0086996336996337	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	13	0.017150395778364115	G	2.001	-0.429453	0.04701	0.004085	0.025233	ENSG00000198342	ENST00000242804;ENST00000438182;ENST00000424168	T;T;T	0.05319	3.53;3.46;4.11	1.51	0.168	0.15012	Krueppel-associated box (3);	.	.	.	.	T	0.01156	0.0038	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.48007	-0.9072	9	0.16896	T	0.51	.	4.5249	0.11976	0.0:0.0:0.3704:0.6296	.	84	Q9H7R0	ZN442_HUMAN	L	84;15;15	ENSP00000242804:P84L;ENSP00000388634:P15L;ENSP00000404935:P15L	ENSP00000242804:P84L	P	-	2	0	ZNF442	12323839	0.000000	0.05858	0.126000	0.21872	0.664000	0.39144	0.012000	0.13287	-0.177000	0.10690	0.313000	0.20887	CCC	G|0.985;A|0.015	0.015	strong		0.353	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824	
TOMM40	10452	hgsc.bcm.edu	37	19	45397229	45397229	+	Silent	SNP	G	G	A	rs1160983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45397229G>A	ENST00000426677.2	+	5	729	c.549G>A	c.(547-549)tcG>tcA	p.S183S	TOMM40_ENST00000592434.1_Silent_p.S183S|TOMM40_ENST00000252487.5_Silent_p.S183S|TOMM40_ENST00000405636.2_Silent_p.S183S	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	183					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		CCCAGCAGTCGAAGTTTGTGA	0.652													G|||	269	0.0537141	0.0893	0.0216	5008	,	,		16952	0.0913		0.0298	False		,,,				2504	0.0143				p.S183S		Atlas-SNP	.											.	TOMM40	13	.	0			c.G549A						PASS	.	G	,,	393,4013	185.7+/-212.7	20,353,1830	50.0	49.0	50.0		549,549,549	-9.5	1.0	19	dbSNP_87	50	286,8314	103.8+/-164.8	5,276,4019	no	coding-synonymous,coding-synonymous,coding-synonymous	TOMM40	NM_001128916.1,NM_001128917.1,NM_006114.2	,,	25,629,5849	AA,AG,GG		3.3256,8.9197,5.2207	,,	183/362,183/362,183/362	45397229	679,12327	2203	4300	6503	SO:0001819	synonymous_variant	10452	exon5			GCAGTCGAAGTTT	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.549G>A	19.37:g.45397229G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Silent	SNP	ENST00000426677.2	37	CCDS12646.1																																																																																			G|0.950;A|0.050	0.050	strong		0.652	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1		
EFHB	151651	hgsc.bcm.edu	37	3	19975139	19975139	+	Silent	SNP	C	C	T	rs17180771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:19975139C>T	ENST00000295824.9	-	1	533	c.372G>A	c.(370-372)cgG>cgA	p.R124R	EFHB_ENST00000344838.4_Intron|EFHB_ENST00000498089.1_5'UTR	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	124							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						GCTGTATTATCCGTTCATGGG	0.507													C|||	528	0.105431	0.0076	0.1988	5008	,	,		20102	0.0149		0.2435	False		,,,				2504	0.1227				p.R124R		Atlas-SNP	.											.	EFHB	186	.	0			c.G372A						PASS	.	C		218,4102		4,210,1946	81.0	84.0	83.0		372	-0.8	0.0	3	dbSNP_123	83	1992,6532		239,1514,2509	no	coding-synonymous	EFHB	NM_144715.3		243,1724,4455	TT,TC,CC		23.3693,5.0463,17.2065		124/834	19975139	2210,10634	2160	4262	6422	SO:0001819	synonymous_variant	151651	exon1			TATTATCCGTTCA	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.372G>A	3.37:g.19975139C>T		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	214	96	0.448598	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Silent	SNP	ENST00000295824.9	37	CCDS33715.2																																																																																			C|0.881;T|0.119	0.119	strong		0.507	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
CCDC138	165055	hgsc.bcm.edu	37	2	109408208	109408208	+	Missense_Mutation	SNP	G	G	A	rs6740879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:109408208G>A	ENST00000295124.4	+	4	404	c.344G>A	c.(343-345)aGa>aAa	p.R115K	CCDC138_ENST00000412964.2_Missense_Mutation_p.R115K|CCDC138_ENST00000470608.1_3'UTR	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	115			R -> K (in dbSNP:rs6740879).					p.R115K(1)		endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						AATGATTATAGAGTTAGTACC	0.274													G|||	1302	0.259984	0.3623	0.1888	5008	,	,		15706	0.0913		0.2346	False		,,,				2504	0.3722				p.R115K		Atlas-SNP	.											CCDC138,NS,carcinoma,0,1	CCDC138	49	1	1	Substitution - Missense(1)	stomach(1)	c.G344A						PASS	.	G	LYS/ARG	1502,2894	447.9+/-348.5	259,984,955	71.0	83.0	79.0		344	3.0	0.1	2	dbSNP_116	79	1977,6613	338.9+/-322.9	232,1513,2550	yes	missense	CCDC138	NM_144978.1	26	491,2497,3505	AA,AG,GG		23.0151,34.1674,26.7904	possibly-damaging	115/666	109408208	3479,9507	2198	4295	6493	SO:0001583	missense	165055	exon4			ATTATAGAGTTAG	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.344G>A	2.37:g.109408208G>A	ENSP00000295124:p.Arg115Lys	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	486|486	0.22252747252747251|0.22252747252747251	182|182	0.3699186991869919|0.3699186991869919	74|74	0.20441988950276244|0.20441988950276244	53|53	0.09265734265734266|0.09265734265734266	177|177	0.23350923482849603|0.23350923482849603	G|G	11.12|11.12	1.545024|1.545024	0.27652|0.27652	0.341674|0.341674	0.230151|0.230151	ENSG00000163006|ENSG00000163006	ENST00000456512|ENST00000412964;ENST00000295124	.|D;D	.|0.90133	.|-2.62;-2.62	5.77|5.77	2.99|2.99	0.34606|0.34606	.|.	.|0.522350	.|0.19228	.|N	.|0.119493	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.10296	.|0.003;0.003	.|B;B	.|0.09377	.|0.004;0.004	T|T	0.15521|0.15521	-1.0434|-1.0434	4|9	.|0.05721	.|T	.|0.95	-0.7705|-0.7705	9.3348|9.3348	0.38043|0.38043	0.2322:0.0:0.7678:0.0|0.2322:0.0:0.7678:0.0	rs6740879;rs60240712;rs6740879|rs6740879;rs60240712;rs6740879	.|115;115	.|Q96M89-2;Q96M89	.|.;CC138_HUMAN	K|K	13|115	.|ENSP00000411800:R115K;ENSP00000295124:R115K	.|ENSP00000295124:R115K	E|R	+|+	1|2	0|0	CCDC138|CCDC138	108774640|108774640	0.000000|0.000000	0.05858|0.05858	0.114000|0.114000	0.21550|0.21550	0.749000|0.749000	0.42624|0.42624	0.164000|0.164000	0.16542|0.16542	0.791000|0.791000	0.33826|0.33826	0.655000|0.655000	0.94253|0.94253	GAG|AGA	G|0.747;A|0.253	0.253	strong		0.274	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	
CENPF	1063	hgsc.bcm.edu	37	1	214787130	214787130	+	Silent	SNP	G	G	A	rs2070064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:214787130G>A	ENST00000366955.3	+	2	201	c.33G>A	c.(31-33)ggG>ggA	p.G11G		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0	Interaction with SNAP25 and required for localization to the cytoplasm. {ECO:0000250}.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GGAAAGAAGGGCTGCCTACAA	0.413													C|||	1183	0.236222	0.0522	0.3156	5008	,	,		14102	0.121		0.499	False		,,,				2504	0.2771				p.G11G	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											CENPF,NS,carcinoma,0,1	CENPF	321	1	0			c.G33A						PASS	.	C		525,3881		42,441,1720	75.0	82.0	80.0		33	3.1	1.0	1	dbSNP_96	80	4450,4150		1142,2166,992	no	coding-synonymous	CENPF	NM_016343.3		1184,2607,2712	AA,AG,GG		48.2558,11.9156,38.2516		11/3115	214787130	4975,8031	2203	4300	6503	SO:0001819	synonymous_variant	1063	exon2			AGAAGGGCTGCCT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.33G>A	1.37:g.214787130G>A		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	205	94	0.458537	NM_016343	Q13171|Q13246|Q5VVM7	Silent	SNP	ENST00000366955.3	37	CCDS31023.1																																																																																			G|0.653;A|0.345	0.345	strong		0.413	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
MLPH	79083	hgsc.bcm.edu	37	2	238427194	238427194	+	Missense_Mutation	SNP	T	T	C	rs3751109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238427194T>C	ENST00000264605.3	+	5	752	c.458T>C	c.(457-459)cTg>cCg	p.L153P	MLPH_ENST00000409373.1_Missense_Mutation_p.L153P|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.L153P|MLPH_ENST00000410032.1_Missense_Mutation_p.L153P|MLPH_ENST00000338530.4_Missense_Mutation_p.L153P	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	153			L -> P (in dbSNP:rs3751109).		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)		GGGCCTGAACTGATATCTGAA	0.542													N|||	895	0.178714	0.3714	0.0994	5008	,	,		18796	0.0843		0.1412	False		,,,				2504	0.1104				p.L153P		Atlas-SNP	.											.	MLPH	41	.	0			c.T458C						PASS	.		PRO/LEU,PRO/LEU	1523,2881		256,1011,935	66.0	65.0	65.0		458,458	-2.8	0.0	2	dbSNP_107	65	1456,7144		126,1204,2970	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	98,98	382,2215,3905	CC,CT,TT		16.9302,34.5822,22.9083	benign,benign	153/573,153/601	238427194	2979,10025	2202	4300	6502	SO:0001583	missense	79083	exon5			CTGAACTGATATC	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.458T>C	2.37:g.238427194T>C	ENSP00000264605:p.Leu153Pro	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	212	107	0.504717	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	370	0.16941391941391942	174	0.35365853658536583	38	0.10497237569060773	47	0.08216783216783216	111	0.14643799472295516	N	2.707	-0.269709	0.05716	0.345822	0.169302	ENSG00000115648	ENST00000410032;ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T;T;T;T;T	0.27557	1.67;2.09;2.08;1.92;1.66	2.24	-2.76	0.05896	.	228.317000	0.01298	U	0.010207	T	0.00012	0.0000	N	0.03608	-0.345	0.58432	P	1.0000000000287557E-6	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.001;0.001;0.0;0.0;0.0;0.0;0.0	T	0.36286	-0.9754	9	0.30078	T	0.28	0.0312	0.1965	0.00140	0.3586:0.227:0.1603:0.2541	rs3751109;rs52817184;rs58583705;rs3751109	153;37;153;153;153;153;153	B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36;G5E9G5	.;.;.;.;.;MELPH_HUMAN;.	P	153	ENSP00000386338:L153P;ENSP00000264605:L153P;ENSP00000414849:L153P;ENSP00000341845:L153P;ENSP00000386780:L153P	ENSP00000264605:L153P	L	+	2	0	MLPH	238091933	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.672000	0.05244	-1.189000	0.02702	-1.342000	0.01247	CTG	T|0.795;C|0.205	0.205	strong		0.542	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
OR51B5	282763	hgsc.bcm.edu	37	11	5364450	5364450	+	Missense_Mutation	SNP	A	A	G	rs11036912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5364450A>G	ENST00000300773.2	-	1	359	c.305T>C	c.(304-306)aTa>aCa	p.I102T	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	102			I -> T (in dbSNP:rs11036912).		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)		AAGTGAGTGTATAAAGTAGGC	0.527													A|||	1631	0.325679	0.2595	0.4035	5008	,	,		19574	0.1796		0.4404	False		,,,				2504	0.3926				p.I102T		Atlas-SNP	.											.	OR51B5	60	.	0			c.T305C						PASS	.	A	THR/ILE	1229,3173	422.3+/-339.7	168,893,1140	44.0	43.0	43.0		305	4.8	0.8	11	dbSNP_120	43	3843,4751	536.5+/-383.0	857,2129,1311	yes	missense	OR51B5	NM_001005567.2	89	1025,3022,2451	GG,GA,AA		44.7172,27.9191,39.0274	probably-damaging	102/313	5364450	5072,7924	2201	4297	6498	SO:0001583	missense	282763	exon5			GAGTGTATAAAGT	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.305T>C	11.37:g.5364450A>G	ENSP00000300773:p.Ile102Thr	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	40	18	0.45	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	713	0.32646520146520147	133	0.2703252032520325	151	0.4171270718232044	92	0.16083916083916083	337	0.4445910290237467	A	17.95	3.513868	0.64522	0.279191	0.447172	ENSG00000242180	ENST00000300773	T	0.03272	3.99	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44902	D	0.000403	T	0.00012	0.0000	M	0.85859	2.78	0.38638	P	0.048454	D	0.62365	0.991	P	0.60949	0.881	T	0.47699	-0.9097	9	0.87932	D	0	.	13.295	0.60292	1.0:0.0:0.0:0.0	rs11036912;rs56641153;rs60921752;rs11036912	102	Q9H339	O51B5_HUMAN	T	102	ENSP00000300773:I102T	ENSP00000300773:I102T	I	-	2	0	OR51B5	5321026	0.006000	0.16342	0.849000	0.33467	0.945000	0.59286	2.296000	0.43584	2.017000	0.59298	0.529000	0.55759	ATA	A|0.645;G|0.355	0.355	strong		0.527	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
PARP4	143	hgsc.bcm.edu	37	13	25000617	25000617	+	Missense_Mutation	SNP	C	C	G	rs7571	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25000617C>G	ENST00000381989.3	-	33	5071	c.4966G>C	c.(4966-4968)Gct>Cct	p.A1656P		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1656	Interaction with the major vault protein.			A -> P (in Ref. 1; AAD47250, 2; AAC62491 and 3; BAA11494). {ECO:0000305}.	cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.A1656P(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GAAATAGAAGCGTCATCCATT	0.343													g|||	2103	0.419928	0.6233	0.3559	5008	,	,		18196	0.3671		0.4105	False		,,,				2504	0.2546				p.A1656P		Atlas-SNP	.											PARP4,NS,carcinoma,0,1	PARP4	142	1	1	Substitution - Missense(1)	stomach(1)	c.G4966C						PASS	.	G	PRO/ALA	2507,1899	541.0+/-375.7	709,1089,405	79.0	80.0	79.0		4966	-4.3	0.0	13	dbSNP_52	79	3207,5393	651.2+/-400.8	594,2019,1687	yes	missense	PARP4	NM_006437.3	27	1303,3108,2092	GG,GC,CC		37.2907,43.1003,43.9336	probably-damaging	1656/1725	25000617	5714,7292	2203	4300	6503	SO:0001583	missense	143	exon33			TAGAAGCGTCATC	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.4966G>C	13.37:g.25000617C>G	ENSP00000371419:p.Ala1656Pro	Somatic	309	0	0		WXS	Illumina HiSeq	Phase_I	267	264	0.988764	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	926	0.423992673992674	300	0.6097560975609756	126	0.34806629834254144	185	0.32342657342657344	315	0.4155672823218997	g	6.453	0.451821	0.12283	0.568997	0.372907	ENSG00000102699	ENST00000381989	D	0.88509	-2.39	4.09	-4.32	0.03688	.	0.441750	0.17430	N	0.174485	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	B	0.09022	0.002	B	0.06405	0.002	T	0.40572	-0.9556	9	0.27082	T	0.32	.	3.8199	0.08832	0.1321:0.2003:0.5103:0.1573	rs7571;rs1130967;rs3190437;rs4987096;rs52806064;rs7571	1656	Q9UKK3	PARP4_HUMAN	P	1656	ENSP00000371419:A1656P	ENSP00000371419:A1656P	A	-	1	0	PARP4	23898617	0.000000	0.05858	0.000000	0.03702	0.133000	0.20885	-2.291000	0.01147	-0.515000	0.06479	-0.371000	0.07208	GCT	C|0.568;G|0.432	0.432	strong		0.343	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
ZNF45	7596	hgsc.bcm.edu	37	19	44417575	44417575	+	Silent	SNP	A	A	G	rs417699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44417575A>G	ENST00000269973.5	-	10	3103	c.2013T>C	c.(2011-2013)ttT>ttC	p.F671F	ZNF45_ENST00000589703.1_Silent_p.F671F|RP11-15A1.2_ENST00000586247.1_RNA	NM_003425.3	NP_003416.1	Q02386	ZNF45_HUMAN	zinc finger protein 45	671					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						CTGATGAAGGAAAGTCCTTGT	0.398													A|||	2712	0.541534	0.388	0.6585	5008	,	,		21581	0.8046		0.5149	False		,,,				2504	0.4223				p.F671F		Atlas-SNP	.											ZNF45,NS,carcinoma,-2,2	ZNF45	51	2	0			c.T2013C						PASS	.	A		1758,2648		357,1044,802	75.0	69.0	71.0		2013	-3.6	0.0	19	dbSNP_80	71	4342,4258		1118,2106,1076	no	coding-synonymous	ZNF45	NM_003425.3		1475,3150,1878	GG,GA,AA		49.5116,39.9001,46.9014		671/683	44417575	6100,6906	2203	4300	6503	SO:0001819	synonymous_variant	7596	exon10			TGAAGGAAAGTCC	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.2013T>C	19.37:g.44417575A>G		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_003425	P17016|P78472|Q9P1U9	Silent	SNP	ENST00000269973.5	37	CCDS12632.1																																																																																			A|0.474;G|0.526	0.526	strong		0.398	ZNF45-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459919.1	NM_003425	
GYS2	2998	hgsc.bcm.edu	37	12	21690035	21690035	+	Missense_Mutation	SNP	C	C	G	rs117639846	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:21690035C>G	ENST00000261195.2	-	16	2219	c.1965G>C	c.(1963-1965)caG>caC	p.Q655H		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	655					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CATCACTGCTCTGAGGACTGG	0.463													C|||	70	0.0139776	0.0023	0.0317	5008	,	,		17274	0.0		0.0358	False		,,,				2504	0.0092				p.Q655H	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											.	GYS2	110	.	0			c.G1965C						PASS	.	C	HIS/GLN	30,4376	36.0+/-67.5	0,30,2173	145.0	107.0	120.0		1965	-0.3	1.0	12	dbSNP_132	120	259,8341	101.0+/-162.3	3,253,4044	yes	missense	GYS2	NM_021957.3	24	3,283,6217	GG,GC,CC		3.0116,0.6809,2.2221	benign	655/704	21690035	289,12717	2203	4300	6503	SO:0001583	missense	2998	exon16			ACTGCTCTGAGGA		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1965G>C	12.37:g.21690035C>G	ENSP00000261195:p.Gln655His	Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	328	158	0.481707	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	40	0.018315018315018316	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	24	0.0316622691292876	C	14.30	2.494609	0.44352	0.006809	0.030116	ENSG00000111713	ENST00000261195	T	0.63255	-0.03	4.93	-0.34	0.12643	.	0.119130	0.64402	N	0.000019	T	0.05044	0.0135	N	0.01297	-0.9	0.28694	N	0.904415	B	0.02656	0.0	B	0.04013	0.001	T	0.10660	-1.0620	10	0.09590	T	0.72	-9.3153	2.381	0.04354	0.1124:0.2438:0.3936:0.2502	.	655	P54840	GYS2_HUMAN	H	655	ENSP00000261195:Q655H	ENSP00000261195:Q655H	Q	-	3	2	GYS2	21581302	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	0.581000	0.23819	0.249000	0.21456	0.655000	0.94253	CAG	C|0.978;G|0.022	0.022	strong		0.463	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
MUC16	94025	hgsc.bcm.edu	37	19	9088017	9088017	+	Missense_Mutation	SNP	T	T	G	rs1596797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9088017T>G	ENST00000397910.4	-	1	4001	c.3798A>C	c.(3796-3798)aaA>aaC	p.K1266N		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1266	Thr-rich.		K -> N (in dbSNP:rs1596797).		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						CCATGGTAAGTTTGATGGTGC	0.493													G|||	3988	0.796326	0.9652	0.8084	5008	,	,		23591	0.7292		0.6958	False		,,,				2504	0.7321				p.K1266N		Atlas-SNP	.											.	MUC16	4315	.	0			c.A3798C						PASS	.	G	ASN/LYS	3844,376		1751,342,17	398.0	393.0	395.0		3798	-2.0	0.0	19	dbSNP_88	395	5914,2552		2065,1784,384	yes	missense	MUC16	NM_024690.2	94	3816,2126,401	GG,GT,TT		30.1441,8.91,23.0806	benign	1266/14508	9088017	9758,2928	2110	4233	6343	SO:0001583	missense	94025	exon1			GGTAAGTTTGATG	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.3798A>C	19.37:g.9088017T>G	ENSP00000381008:p.Lys1266Asn	Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	230	133	0.578261	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	1732	0.793040293040293	470	0.9552845528455285	287	0.7928176795580111	447	0.7814685314685315	528	0.6965699208443272	g	1.037	-0.680086	0.03353	0.9109	0.698559	ENSG00000181143	ENST00000397910	T	0.02737	4.18	1.01	-2.01	0.07410	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.30909	-0.9962	8	0.87932	D	0	.	0.4032	0.00429	0.1891:0.2004:0.2088:0.4016	rs1596797;rs17516813;rs52807986;rs60662216;rs1596797	1266	B5ME49	.	N	1266	ENSP00000381008:K1266N	ENSP00000381008:K1266N	K	-	3	2	MUC16	8949017	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.685000	0.01930	-2.513000	0.00502	-0.677000	0.03784	AAA	T|0.205;G|0.795	0.795	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LBP	3929	hgsc.bcm.edu	37	20	36979265	36979265	+	Silent	SNP	T	T	C	rs2232582	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36979265T>C	ENST00000217407.2	+	3	452	c.291T>C	c.(289-291)ccT>ccC	p.P97P		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	97					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)				GGCCTGTCCCTGGCCAGGGCC	0.617													C|||	1068	0.213259	0.4221	0.1023	5008	,	,		21538	0.0734		0.1322	False		,,,				2504	0.2372				p.P97P		Atlas-SNP	.											.	LBP	60	.	0			c.T291C						PASS	.	C		1635,2771	658.5+/-400.4	306,1023,874	88.0	80.0	83.0		291	-9.4	0.0	20	dbSNP_98	83	1364,7236	755.0+/-407.5	111,1142,3047	no	coding-synonymous	LBP	NM_004139.2		417,2165,3921	CC,CT,TT		15.8605,37.1085,23.0586		97/482	36979265	2999,10007	2203	4300	6503	SO:0001819	synonymous_variant	3929	exon3			TGTCCCTGGCCAG		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.291T>C	20.37:g.36979265T>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	58	33	0.568965	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																			T|0.792;C|0.208	0.208	strong		0.617	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
INPP4A	3631	hgsc.bcm.edu	37	2	99172244	99172244	+	Missense_Mutation	SNP	A	A	G	rs2278206	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:99172244A>G	ENST00000523221.1	+	15	1810	c.1810A>G	c.(1810-1812)Act>Gct	p.T604A	INPP4A_ENST00000074304.5_Missense_Mutation_p.T604A|INPP4A_ENST00000409463.1_Intron|INPP4A_ENST00000409540.3_Intron|INPP4A_ENST00000545415.1_Intron|INPP4A_ENST00000409851.3_Missense_Mutation_p.T599A|INPP4A_ENST00000409016.4_Intron			Q96PE3	INP4A_HUMAN	inositol polyphosphate-4-phosphatase, type I, 107kDa	604			T -> A (in dbSNP:rs2278206).		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						CATGCCCTCCACTGCATGCCA	0.552													G|||	1424	0.284345	0.2375	0.3069	5008	,	,		21373	0.3155		0.2654	False		,,,				2504	0.319				p.T604A		Atlas-SNP	.											.	INPP4A	205	.	0			c.A1810G	GRCh37	CM084964	INPP4A	M	rs2278206	PASS	.	G	ALA/THR,ALA/THR,,	351,1033		51,249,392	205.0	209.0	207.0		1810,1795,,	2.4	0.3	2	dbSNP_100	207	805,2377		104,597,890	yes	missense,missense,intron,intron	INPP4A	NM_001134224.1,NM_001134225.1,NM_001566.2,NM_004027.2	58,58,,	155,846,1282	GG,GA,AA		25.2986,25.3613,25.3176	benign,benign,,	604/978,599/973,,	99172244	1156,3410	692	1591	2283	SO:0001583	missense	3631	exon17			CCCTCCACTGCAT	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.1810A>G	2.37:g.99172244A>G	ENSP00000427722:p.Thr604Ala	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001134224	O15326|Q13187|Q53TD8|Q8TC02	Missense_Mutation	SNP	ENST00000523221.1	37	CCDS46369.1	601	0.2751831501831502	127	0.258130081300813	110	0.30386740331491713	171	0.29895104895104896	193	0.2546174142480211	G	1.804	-0.476376	0.04414	0.253613	0.252986	ENSG00000040933	ENST00000409851;ENST00000074304;ENST00000523221	T;T;T	0.15718	2.4;2.4;2.4	5.14	2.4	0.29515	.	0.498696	0.19604	N	0.110315	T	0.00012	0.0000	N	0.08118	0	0.24989	P	0.99154762	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47623	-0.9103	8	.	.	.	-1.1761	1.3523	0.02175	0.3134:0.1264:0.4149:0.1452	rs2278206;rs60846330;rs2278206	604;599	Q96PE3;Q96PE3-3	INP4A_HUMAN;.	A	599;604;604	ENSP00000386777:T599A;ENSP00000074304:T604A;ENSP00000427722:T604A	.	T	+	1	0	INPP4A	98538676	0.004000	0.15560	0.339000	0.25562	0.915000	0.54546	0.194000	0.17135	0.092000	0.17331	-1.653000	0.00756	ACT	A|0.729;G|0.271	0.271	strong		0.552	INPP4A-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376095.1	NM_001566	
COL27A1	85301	hgsc.bcm.edu	37	9	117033022	117033022	+	Silent	SNP	T	T	C	rs4143245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:117033022T>C	ENST00000356083.3	+	36	3961	c.3570T>C	c.(3568-3570)ctT>ctC	p.L1190L	COL27A1_ENST00000477421.2_3'UTR	NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1190	Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						AGCCAGGCCTTGAGGGTGACA	0.617													C|||	1957	0.390775	0.4213	0.4942	5008	,	,		20384	0.3175		0.4185	False		,,,				2504	0.3231				p.L1190L		Atlas-SNP	.											.	COL27A1	200	.	0			c.T3570C						PASS	.	C		1692,2714	653.6+/-399.6	304,1084,815	97.0	89.0	92.0		3570	-9.7	0.1	9	dbSNP_110	92	3498,5102	634.1+/-398.8	716,2066,1518	no	coding-synonymous	COL27A1	NM_032888.2		1020,3150,2333	CC,CT,TT		40.6744,38.4022,39.9047		1190/1861	117033022	5190,7816	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon36			AGGCCTTGAGGGT	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.3570T>C	9.37:g.117033022T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	137	135	0.985401	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			T|0.601;C|0.399	0.399	strong		0.617	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
CLTCL1	8218	hgsc.bcm.edu	37	22	19263266	19263266	+	Missense_Mutation	SNP	C	C	A	rs34869740	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19263266C>A	ENST00000263200.10	-	2	202	c.130G>T	c.(130-132)Gtt>Ttt	p.V44F	CLTCL1_ENST00000427926.1_Missense_Mutation_p.V44F|CLTCL1_ENST00000353891.5_Missense_Mutation_p.V44F	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	44	Globular terminal domain.|WD40-like repeat 1.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TGCTCACCAACTTTCTCTCGG	0.468			T	?	ALCL								C|||	45	0.00898562	0.0	0.0058	5008	,	,		17693	0.001		0.004	False		,,,				2504	0.0368				p.V44F		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.G130T						PASS	.	C	PHE/VAL,PHE/VAL	2,3930		0,2,1964	64.0	64.0	64.0		130,130	1.9	0.0	22	dbSNP_126	64	71,8235		0,71,4082	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	50,50	0,73,6046	AA,AC,CC		0.8548,0.0509,0.5965	possibly-damaging,possibly-damaging	44/1584,44/1641	19263266	73,12165	1966	4153	6119	SO:0001583	missense	8218	exon2			CACCAACTTTCTC		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.130G>T	22.37:g.19263266C>A	ENSP00000445677:p.Val44Phe	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	14.65	2.600102	0.46423	5.09E-4	0.008548	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926;ENST00000449918	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.07	1.93	0.25924	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.078972	0.50627	D	0.000108	T	0.53642	0.1809	M	0.87827	2.91	0.45914	D	0.998752	B;D	0.54047	0.177;0.964	B;D	0.64321	0.325;0.924	T	0.59053	-0.7526	10	0.56958	D	0.05	-6.7814	8.2311	0.31599	0.1561:0.7604:0.0:0.0836	rs34869740	44;44	P53675-2;P53675	.;CLH2_HUMAN	F	44	ENSP00000439662:V44F;ENSP00000445677:V44F;ENSP00000441158:V44F;ENSP00000443264:V44F	ENSP00000445677:V44F	V	-	1	0	CLTCL1	17643266	1.000000	0.71417	0.009000	0.14445	0.231000	0.25187	3.255000	0.51484	0.367000	0.24454	-0.142000	0.14014	GTT	C|0.994;A|0.006	0.006	strong		0.468	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
MLC1	23209	hgsc.bcm.edu	37	22	50512732	50512732	+	Silent	SNP	G	G	A	rs138153307		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50512732G>A	ENST00000311597.5	-	8	1233	c.627C>T	c.(625-627)gcC>gcT	p.A209A	MLC1_ENST00000535444.1_Silent_p.A130A|MLC1_ENST00000483836.1_5'Flank|MLC1_ENST00000450140.2_Silent_p.A157A|MLC1_ENST00000431262.2_Silent_p.A179A|MLC1_ENST00000395876.2_Silent_p.A209A|MLC1_ENST00000538737.1_Silent_p.A175A	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	209					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CCCCGAGGACGGCAGAGATGC	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		16208	0.0		0.001	False		,,,				2504	0.0				p.A209A		Atlas-SNP	.											.	MLC1	48	.	0			c.C627T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	108.0	76.0	87.0		627,627	-10.2	0.1	22	dbSNP_134	87	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	MLC1	NM_015166.3,NM_139202.2	,	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	,	209/378,209/378	50512732	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	23209	exon8			GAGGACGGCAGAG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.627C>T	22.37:g.50512732G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	66	32	0.484848	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			G|0.999;A|0.001	0.001	strong		0.572	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
C11orf45	219833	hgsc.bcm.edu	37	11	128772452	128772452	+	Silent	SNP	C	C	T	rs11221503	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:128772452C>T	ENST00000524878.1	-	4	608	c.438G>A	c.(436-438)taG>taA	p.*146*	KCNJ5_ENST00000529694.1_Intron|C11orf45_ENST00000310799.3_Silent_p.*146*|C11orf45_ENST00000530168.1_5'UTR|KCNJ5_ENST00000338350.4_Intron			Q8TAV5	CK045_HUMAN	chromosome 11 open reading frame 45	0						extracellular region (GO:0005576)				endometrium(1)|kidney(1)|lung(2)|pancreas(1)|prostate(2)	7	all_hematologic(175;0.0641)	Lung NSC(97;0.00521)|Breast(109;0.00715)|all_lung(97;0.0111)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.00531)|LUSC - Lung squamous cell carcinoma(976;0.0193)|Lung(977;0.0195)		GGAGACAGGGCTAGTTAGGAC	0.602													C|||	589	0.117612	0.0151	0.1585	5008	,	,		18070	0.0903		0.2316	False		,,,				2504	0.138				p.X146X		Atlas-SNP	.											.	C11orf45	14	.	0			c.G438A						PASS	.	C	,	239,4161		12,215,1973	71.0	54.0	59.0		,438	1.6	0.0	11	dbSNP_120	59	1799,6795		216,1367,2714	no	intron,coding-synonymous	KCNJ5,C11orf45	NM_000890.3,NM_145013.1	,	228,1582,4687	TT,TC,CC		20.9332,5.4318,15.6842	,	,146/146	128772452	2038,10956	2200	4297	6497	SO:0001819	synonymous_variant	219833	exon4			ACAGGGCTAGTTA	AK125634	CCDS8478.1	11q24.3	2012-05-30			ENSG00000174370	ENSG00000174370			28584	protein-coding gene	gene with protein product							Standard	NM_001256088		Approved	MGC35558, FLJ43646	uc001qeu.3	Q8TAV5	OTTHUMG00000165796	ENST00000524878.1:c.438G>A	11.37:g.128772452C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	72	29	0.402778	NM_145013	B2RAD0	Silent	SNP	ENST00000524878.1	37	CCDS8478.1																																																																																			C|0.869;T|0.131	0.131	strong		0.602	C11orf45-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386243.1	NM_145013	
STAB1	23166	hgsc.bcm.edu	37	3	52555957	52555957	+	Silent	SNP	T	T	C	rs386660931|rs9853056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52555957T>C	ENST00000321725.6	+	58	6337	c.6261T>C	c.(6259-6261)cgT>cgC	p.R2087R		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2087	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076, 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)		GGGATGGCCGTGTGTGTACAG	0.642													C|||	2823	0.563698	0.7534	0.6571	5008	,	,		20880	0.4613		0.5646	False		,,,				2504	0.3456				p.R2087R		Atlas-SNP	.											STAB1,NS,carcinoma,0,1	STAB1	178	1	0			c.T6261C						PASS	.	C		3082,1322	438.8+/-345.5	1070,942,190	124.0	118.0	120.0		6261	-3.5	0.0	3	dbSNP_119	120	4906,3694	528.8+/-381.4	1408,2090,802	no	coding-synonymous	STAB1	NM_015136.2		2478,3032,992	CC,CT,TT		42.9535,30.0182,38.5727		2087/2571	52555957	7988,5016	2202	4300	6502	SO:0001819	synonymous_variant	23166	exon58			TGGCCGTGTGTGT	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.6261T>C	3.37:g.52555957T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	98	45	0.459184	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			T|0.399;C|0.601	0.601	strong		0.642	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
TAB2	23118	hgsc.bcm.edu	37	6	149700491	149700491	+	Silent	SNP	G	G	A	rs3734296	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:149700491G>A	ENST00000367456.1	+	4	2017	c.1440G>A	c.(1438-1440)gtG>gtA	p.V480V	TAB2_ENST00000392282.1_Silent_p.V480V|TAB2_ENST00000286332.5_Silent_p.V480V|TAB2_ENST00000538427.1_Silent_p.V480V|TAB2_ENST00000536230.1_Silent_p.V448V			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	480					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						CACCAGGGGTGGTGTCCCCTA	0.453													G|||	1092	0.218051	0.0552	0.2507	5008	,	,		18785	0.5496		0.0944	False		,,,				2504	0.2004				p.V480V		Atlas-SNP	.											.	TAB2	55	.	0			c.G1440A						PASS	.	G		277,4129	156.3+/-189.4	8,261,1934	91.0	87.0	89.0		1440	-4.4	0.2	6	dbSNP_107	89	909,7691	202.7+/-245.9	53,803,3444	no	coding-synonymous	TAB2	NM_015093.4		61,1064,5378	AA,AG,GG		10.5698,6.2869,9.1189		480/694	149700491	1186,11820	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon5			AGGGGTGGTGTCC	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 2"""	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.1440G>A	6.37:g.149700491G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	48	44	0.916667	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			G|0.856;A|0.144	0.144	strong		0.453	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3		
TNRC6A	27327	hgsc.bcm.edu	37	16	24834233	24834233	+	Silent	SNP	C	C	T	rs2303085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:24834233C>T	ENST00000395799.3	+	24	5541	c.5412C>T	c.(5410-5412)caC>caT	p.H1804H	TNRC6A_ENST00000432286.2_Silent_p.H282H|TNRC6A_ENST00000315183.7_Silent_p.H1755H	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1804	RRM.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.H1804H(1)		breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GCATGCAGCACGGCCCGCTGA	0.557													c|||	1106	0.220847	0.1626	0.2637	5008	,	,		22656	0.4038		0.166	False		,,,				2504	0.137				p.H1804H		Atlas-SNP	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	1	Substitution - coding silent(1)	stomach(1)	c.C5412T						PASS	.	C		692,3702	289.5+/-280.5	45,602,1550	124.0	101.0	109.0		5412	1.9	1.0	16	dbSNP_100	109	1175,7425	239.4+/-270.5	78,1019,3203	no	coding-synonymous	TNRC6A	NM_014494.2		123,1621,4753	TT,TC,CC		13.6628,15.7487,14.3682		1804/1963	24834233	1867,11127	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon24			GCAGCACGGCCCG	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.5412C>T	16.37:g.24834233C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	108	53	0.490741	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2	506	0.2316849816849817	63	0.12804878048780488	80	0.22099447513812154	230	0.4020979020979021	133	0.17546174142480211	c	9.384	1.073739	0.20147	0.157487	0.136628	ENSG00000090905	ENST00000450465	.	.	.	5.27	1.87	0.25490	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44787	-0.9305	3	.	.	.	-6.083	7.3864	0.26884	0.0:0.4108:0.0:0.5892	rs2303085;rs57489138;rs2303085	.	.	.	W	695	.	.	R	+	1	2	TNRC6A	24741734	0.979000	0.34478	1.000000	0.80357	0.993000	0.82548	0.189000	0.17037	0.338000	0.23692	-0.310000	0.09108	CGG	C|0.816;T|0.184	0.184	strong		0.557	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
ZNF774	342132	hgsc.bcm.edu	37	15	90903502	90903502	+	Missense_Mutation	SNP	G	G	A	rs11854320	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:90903502G>A	ENST00000354377.3	+	4	625	c.439G>A	c.(439-441)Gta>Ata	p.V147I	ZNF774_ENST00000379090.5_Intron|ZNF774_ENST00000558115.1_3'UTR	NM_001004309.2	NP_001004309.2	Q6NX45	ZN774_HUMAN	zinc finger protein 774	147			V -> I (in dbSNP:rs11854320).		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.V147I(1)		breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|stomach(1)	14	Melanoma(11;0.00551)|Lung NSC(78;0.0158)|all_lung(78;0.0331)		BRCA - Breast invasive adenocarcinoma(143;0.0224)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			GGATGGATATGTAGGAGAGAA	0.493													G|||	482	0.096246	0.1694	0.1066	5008	,	,		19912	0.0427		0.1163	False		,,,				2504	0.0245				p.V147I		Atlas-SNP	.											ZNF774,NS,carcinoma,0,1	ZNF774	35	1	1	Substitution - Missense(1)	stomach(1)	c.G439A						PASS	.	G	ILE/VAL	772,3626	310.8+/-291.8	74,624,1501	74.0	76.0	75.0		439	1.5	0.0	15	dbSNP_120	75	953,7643	207.9+/-249.5	60,833,3405	yes	missense	ZNF774	NM_001004309.2	29	134,1457,4906	AA,AG,GG		11.0866,17.5534,13.2754	benign	147/484	90903502	1725,11269	2199	4298	6497	SO:0001583	missense	342132	exon4			GGATATGTAGGAG	BC067279	CCDS32330.1	15q26.1	2013-01-08				ENSG00000196391		"""Zinc fingers, C2H2-type"""	33108	protein-coding gene	gene with protein product							Standard	NM_001004309		Approved	MGC75360	uc002bpk.4	Q6NX45		ENST00000354377.3:c.439G>A	15.37:g.90903502G>A	ENSP00000346348:p.Val147Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_001004309	A8K020	Missense_Mutation	SNP	ENST00000354377.3	37	CCDS32330.1	245	0.11217948717948718	79	0.16056910569105692	38	0.10497237569060773	35	0.06118881118881119	93	0.12269129287598944	G	9.491	1.100722	0.20552	0.175534	0.110866	ENSG00000196391	ENST00000354377	T	0.05925	3.37	5.51	1.5	0.22942	.	0.528567	0.14024	N	0.346624	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.9999999999047681	B	0.06786	0.001	B	0.04013	0.001	T	0.38067	-0.9678	9	0.66056	D	0.02	.	6.8497	0.24008	0.4968:0.0:0.5032:0.0	rs11854320;rs52813081;rs11854320	147	Q6NX45	ZN774_HUMAN	I	147	ENSP00000346348:V147I	ENSP00000346348:V147I	V	+	1	0	ZNF774	88704506	0.000000	0.05858	0.014000	0.15608	0.205000	0.24178	-0.425000	0.07017	0.270000	0.21984	0.655000	0.94253	GTA	G|0.879;A|0.121	0.121	strong		0.493	ZNF774-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418048.1	NM_001004309	
COL22A1	169044	hgsc.bcm.edu	37	8	139703107	139703107	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:139703107C>T	ENST00000303045.6	-	36	3211	c.2765G>A	c.(2764-2766)gGa>gAa	p.G922E	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.G922E	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	922	Collagen-like 7.|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)			ACCGACATGTCCGGGAGCACC	0.532										HNSCC(7;0.00092)																											p.G922E		Atlas-SNP	.											COL22A1,caecum,carcinoma,-1,2	COL22A1	390	2	0			c.G2765A						scavenged	.						55.0	49.0	51.0					8																	139703107		2202	4300	6502	SO:0001583	missense	169044	exon36			ACATGTCCGGGAG	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.2765G>A	8.37:g.139703107C>T	ENSP00000303153:p.Gly922Glu	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	115	3	0.026087	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.128967	0.56721	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99429	-5.89;-5.89	5.46	5.46	0.80206	.	0.000000	0.48767	U	0.000177	D	0.99732	0.9895	H	0.97940	4.11	0.52501	D	0.999957	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.97306	0.9934	10	0.87932	D	0	.	15.1644	0.72811	0.0:1.0:0.0:0.0	.	922;922	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	922;922;635	ENSP00000303153:G922E;ENSP00000387655:G922E	ENSP00000303153:G922E	G	-	2	0	COL22A1	139772289	0.994000	0.37717	0.984000	0.44739	0.696000	0.40369	3.494000	0.53273	2.739000	0.93911	0.643000	0.83706	GGA	.	.	none		0.532	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
SPTBN4	57731	hgsc.bcm.edu	37	19	41008049	41008049	+	Silent	SNP	A	A	G	rs814526	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41008049A>G	ENST00000352632.3	+	9	998	c.912A>G	c.(910-912)gtA>gtG	p.V304V	SPTBN4_ENST00000595535.1_Silent_p.V304V|SPTBN4_ENST00000598249.1_Silent_p.V304V|SPTBN4_ENST00000344104.3_Silent_p.V304V|SPTBN4_ENST00000338932.3_Silent_p.V304V			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	304					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)			TGGACCAGGTATTGGAGGTGG	0.602													G|||	1891	0.377596	0.6596	0.2507	5008	,	,		17749	0.1766		0.3598	False		,,,				2504	0.3119				p.V304V		Atlas-SNP	.											.	SPTBN4	213	.	0			c.A912G						PASS	.	G		2696,1710	514.4+/-368.6	815,1066,322	67.0	64.0	65.0		912	0.9	0.9	19	dbSNP_86	65	3140,5460	655.9+/-401.3	554,2032,1714	no	coding-synonymous	SPTBN4	NM_020971.2		1369,3098,2036	GG,GA,AA		36.5116,38.8107,44.8716		304/2565	41008049	5836,7170	2203	4300	6503	SO:0001819	synonymous_variant	57731	exon9			CCAGGTATTGGAG	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.912A>G	19.37:g.41008049A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			A|0.581;G|0.419	0.419	strong		0.602	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
PLD2	5338	hgsc.bcm.edu	37	17	4721376	4721376	+	Missense_Mutation	SNP	A	A	G	rs17854914	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4721376A>G	ENST00000263088.6	+	18	2026	c.1895A>G	c.(1894-1896)gAg>gGg	p.E632G	PLD2_ENST00000572940.1_Missense_Mutation_p.E632G	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	632	Catalytic.		E -> G (in dbSNP:rs17854914). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)	p.E632G(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	ACCATCAGGGAGAGCCAGCAC	0.572													A|||	380	0.0758786	0.0234	0.0836	5008	,	,		19234	0.0675		0.163	False		,,,				2504	0.0603				p.E632G		Atlas-SNP	.											PLD2,NS,carcinoma,0,1	PLD2	138	1	1	Substitution - Missense(1)	stomach(1)	c.A1895G						PASS	.	A	GLY/GLU	162,4244	105.6+/-144.1	2,158,2043	84.0	65.0	72.0		1895	4.8	1.0	17	dbSNP_123	72	1242,7358	243.9+/-273.3	106,1030,3164	yes	missense	PLD2	NM_002663.4	98	108,1188,5207	GG,GA,AA		14.4419,3.6768,10.795	possibly-damaging	632/934	4721376	1404,11602	2203	4300	6503	SO:0001583	missense	5338	exon18			TCAGGGAGAGCCA	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1895A>G	17.37:g.4721376A>G	ENSP00000263088:p.Glu632Gly	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	200	0.09157509157509157	8	0.016260162601626018	36	0.09944751381215469	41	0.07167832167832168	115	0.1517150395778364	A	14.76	2.631171	0.46944	0.036768	0.144419	ENSG00000129219	ENST00000263088	T	0.30182	1.54	4.77	4.77	0.60923	.	0.170853	0.51477	D	0.000095	T	0.00144	0.0004	N	0.26042	0.785	0.27570	P	0.9499091	B;B;P	0.35139	0.033;0.057;0.486	B;B;B	0.40329	0.022;0.064;0.326	T	0.21484	-1.0244	9	0.31617	T	0.26	-15.9283	12.2194	0.54425	1.0:0.0:0.0:0.0	rs17854914	489;632;632	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	G	632	ENSP00000263088:E632G	ENSP00000263088:E632G	E	+	2	0	PLD2	4668342	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	3.862000	0.56009	1.787000	0.52448	0.454000	0.30748	GAG	A|0.896;G|0.104	0.104	strong		0.572	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
FBXO39	162517	hgsc.bcm.edu	37	17	6690161	6690161	+	Silent	SNP	C	C	T	rs17853331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6690161C>T	ENST00000321535.4	+	3	1216	c.1086C>T	c.(1084-1086)atC>atT	p.I362I		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	362										NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						ACCTCCTCATCATATCCTGCA	0.463													C|||	1544	0.308307	0.1944	0.3026	5008	,	,		18317	0.5823		0.2038	False		,,,				2504	0.2914				p.I362I		Atlas-SNP	.											.	FBXO39	50	.	0			c.C1086T						PASS	.	C		844,3562	333.1+/-302.8	95,654,1454	110.0	97.0	102.0		1086	3.5	1.0	17	dbSNP_123	102	1817,6783	326.6+/-317.4	195,1427,2678	no	coding-synonymous	FBXO39	NM_153230.2		290,2081,4132	TT,TC,CC		21.1279,19.1557,20.4598		362/443	6690161	2661,10345	2203	4300	6503	SO:0001819	synonymous_variant	162517	exon3			CCTCATCATATCC	BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.1086C>T	17.37:g.6690161C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	166	63	0.379518	NM_153230		Silent	SNP	ENST00000321535.4	37	CCDS11082.1																																																																																			C|0.771;T|0.229	0.229	strong		0.463	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
TET3	200424	hgsc.bcm.edu	37	2	74300717	74300717	+	Silent	SNP	T	T	C	rs7560668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:74300717T>C	ENST00000409262.3	+	2	2131	c.2131T>C	c.(2131-2133)Ttg>Ctg	p.L711L		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	711					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)	p.L711L(1)		NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TTATACTCACTTGGGATCTGG	0.413													C|||	1801	0.359625	0.7579	0.2968	5008	,	,		18502	0.1111		0.3201	False		,,,				2504	0.1626				p.L711L		Atlas-SNP	.											TET3,NS,carcinoma,0,1	TET3	101	1	1	Substitution - coding silent(1)	stomach(1)	c.T2131C						PASS	.	C		2453,1245		822,809,218	51.0	55.0	53.0		2131	4.5	1.0	2	dbSNP_116	53	2481,5709		368,1745,1982	no	coding-synonymous	TET3	NM_144993.1		1190,2554,2200	CC,CT,TT		30.293,33.6668,41.504		711/1661	74300717	4934,6954	1849	4095	5944	SO:0001819	synonymous_variant	200424	exon2			ACTCACTTGGGAT		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.2131T>C	2.37:g.74300717T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	59	34	0.576271	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																			T|0.639;C|0.361	0.361	strong		0.413	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4		
SCN9A	6335	hgsc.bcm.edu	37	2	167128972	167128972	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:167128972G>A	ENST00000409435.1	-	16	3287	c.3288C>T	c.(3286-3288)tcC>tcT	p.S1096S	SCN9A_ENST00000375387.4_Silent_p.S1097S|SCN9A_ENST00000409672.1_Silent_p.S1085S|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.S1097S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1096					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)	p.S1085S(1)		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)	TTTCCAAATCGGATTCCCCAG	0.413																																					p.S1085S		Atlas-SNP	.											SCN9A,colon,carcinoma,0,1	SCN9A	296	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C3255T						PASS	.						71.0	65.0	67.0					2																	167128972		1897	4121	6018	SO:0001819	synonymous_variant	6335	exon17			CAAATCGGATTCC	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.3288C>T	2.37:g.167128972G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	150	78	0.52	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.413	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
MYO15A	51168	hgsc.bcm.edu	37	17	18064730	18064730	+	Silent	SNP	C	C	T	rs8077577	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18064730C>T	ENST00000205890.5	+	57	9824	c.9486C>T	c.(9484-9486)gaC>gaT	p.D3162D	MYO15A_ENST00000418233.3_Silent_p.D426D|MYO15A_ENST00000451725.2_Silent_p.D54D	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	3162	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.|Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					TCCTCCAAGACGTGAGCCGGA	0.632													C|||	789	0.157548	0.2231	0.1758	5008	,	,		18343	0.0149		0.2038	False		,,,				2504	0.1554				p.D3162D		Atlas-SNP	.											.	MYO15A	268	.	0			c.C9486T						PASS	.	C		873,3373		104,665,1354	75.0	80.0	78.0		9486	-5.0	0.0	17	dbSNP_116	78	1733,6747		173,1387,2680	no	coding-synonymous	MYO15A	NM_016239.3		277,2052,4034	TT,TC,CC		20.4363,20.5605,20.4778		3162/3531	18064730	2606,10120	2123	4240	6363	SO:0001819	synonymous_variant	51168	exon56			CCAAGACGTGAGC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.9486C>T	17.37:g.18064730C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																			C|0.806;T|0.194	0.194	strong		0.632	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
MYBPC1	4604	hgsc.bcm.edu	37	12	102045163	102045163	+	Missense_Mutation	SNP	C	C	G	rs3817552	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:102045163C>G	ENST00000550270.1	+	14	1443	c.1443C>G	c.(1441-1443)caC>caG	p.H481Q	MYBPC1_ENST00000547405.1_Missense_Mutation_p.H455Q|MYBPC1_ENST00000549145.1_Missense_Mutation_p.H494Q|RP11-755O11.2_ENST00000547027.1_RNA|MYBPC1_ENST00000553190.1_Missense_Mutation_p.H481Q|MYBPC1_ENST00000361466.2_Missense_Mutation_p.H506Q|RP11-755O11.2_ENST00000552081.1_RNA|MYBPC1_ENST00000551300.1_Missense_Mutation_p.H382Q|MYBPC1_ENST00000547509.1_Missense_Mutation_p.H467Q|MYBPC1_ENST00000392934.3_Missense_Mutation_p.H468Q|MYBPC1_ENST00000536007.1_Missense_Mutation_p.H462Q|MYBPC1_ENST00000452455.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000545503.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000361685.2_Missense_Mutation_p.H506Q|MYBPC1_ENST00000360610.2_Missense_Mutation_p.H481Q|MYBPC1_ENST00000441232.1_Missense_Mutation_p.H481Q|MYBPC1_ENST00000541119.1_Missense_Mutation_p.H469Q|MYBPC1_ENST00000550501.1_Intron			Q00872	MYPC1_HUMAN	myosin binding protein C, slow type	481	Ig-like C2-type 4.		H -> Q (in dbSNP:rs3817552).		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						AGGTGGTTCACAAGGGAAGGT	0.428													C|||	857	0.171126	0.1278	0.0893	5008	,	,		20876	0.2986		0.1501	False		,,,				2504	0.1779				p.H506Q		Atlas-SNP	.											.	MYBPC1	235	.	0			c.C1518G	GRCh37	CM065330	MYBPC1	M	rs3817552	PASS	.	C	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	571,3835	253.7+/-259.5	31,509,1663	112.0	115.0	114.0		1518,1518,1443,1443	3.6	1.0	12	dbSNP_107	114	1273,7327	253.7+/-279.3	101,1071,3128	yes	missense,missense,missense,missense	MYBPC1	NM_002465.2,NM_206819.1,NM_206820.1,NM_206821.1	24,24,24,24	132,1580,4791	GG,GC,CC		14.8023,12.9596,14.1781	probably-damaging,probably-damaging,probably-damaging,probably-damaging	506/1172,506/1149,481/1142,481/1124	102045163	1844,11162	2203	4300	6503	SO:0001583	missense	4604	exon16			GGTTCACAAGGGA		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.1443C>G	12.37:g.102045163C>G	ENSP00000449702:p.His481Gln	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_206819	B4DKR5|B7Z8G8|B7ZL02|B7ZL09|B7ZL10|E7ESM5|E7EWS6|G3XAE8|Q15497|Q17RR7|Q569K7|Q86T48|Q86TC8|Q8N3L2	Missense_Mutation	SNP	ENST00000550270.1	37	CCDS9085.1	385	0.1762820512820513	63	0.12804878048780488	36	0.09944751381215469	167	0.291958041958042	119	0.15699208443271767	C	16.76	3.211904	0.58452	0.129596	0.148023	ENSG00000196091	ENST00000547405;ENST00000452455;ENST00000441232;ENST00000360610;ENST00000392934;ENST00000547509;ENST00000361685;ENST00000549145;ENST00000553190;ENST00000540770;ENST00000545503;ENST00000536007;ENST00000541119;ENST00000361466;ENST00000551300;ENST00000550270	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.48	3.63	0.41609	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000059	T	0.00012	0.0000	L	0.48986	1.54	0.19575	P	0.9999645718	P;D;D;D;D;D;D;D;D;D;D	0.89917	0.947;1.0;1.0;0.999;0.999;0.976;0.999;0.999;0.997;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.93;0.999;0.998;0.998;0.997;0.949;0.997;0.999;0.986;0.998;0.999	T	0.15206	-1.0445	9	0.87932	D	0	.	5.075	0.14626	0.158:0.6341:0.0:0.2079	rs3817552;rs52790499;rs3817552	462;469;481;481;468;455;481;481;506;506;494	B7ZL02;B7ZL10;E7EWS6;B7ZL09;E7ESM5;Q17RR7;Q00872-3;Q00872;G3XAE8;Q00872-2;F8VZY0	.;.;.;.;.;.;.;MYPC1_HUMAN;.;.;.	Q	455;481;481;481;468;467;506;494;481;506;481;462;469;506;382;481	ENSP00000448175:H455Q;ENSP00000400908:H481Q;ENSP00000388989:H481Q;ENSP00000353822:H481Q;ENSP00000376665:H468Q;ENSP00000447362:H467Q;ENSP00000354845:H506Q;ENSP00000447660:H494Q;ENSP00000447900:H481Q;ENSP00000440034:H481Q;ENSP00000446128:H462Q;ENSP00000442847:H469Q;ENSP00000354849:H506Q;ENSP00000447116:H382Q;ENSP00000449702:H481Q	ENSP00000353822:H481Q	H	+	3	2	MYBPC1	100569294	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	2.317000	0.43770	1.289000	0.44618	0.655000	0.94253	CAC	C|0.844;G|0.156	0.156	strong		0.428	MYBPC1-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000408806.1		
KRT33B	3884	hgsc.bcm.edu	37	17	39521058	39521058	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39521058C>G	ENST00000251646.3	-	6	1119	c.1070G>C	c.(1069-1071)cGg>cCg	p.R357P		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	357	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)				CAGCAGGCTCCGGTATGTGTT	0.597																																					p.R357P		Atlas-SNP	.											KRT33B,NS,carcinoma,-1,1	KRT33B	46	1	0			c.G1070C						PASS	.						74.0	83.0	80.0					17																	39521058		2191	4300	6491	SO:0001583	missense	3884	exon6			AGGCTCCGGTATG	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.1070G>C	17.37:g.39521058C>G	ENSP00000251646:p.Arg357Pro	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	115	57	0.495652	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	c	14.69	2.609786	0.46527	.	.	ENSG00000131738	ENST00000251646	D	0.94793	-3.52	4.72	2.74	0.32292	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.64402	D	0.000012	D	0.98197	0.9404	H	0.99454	4.575	0.31011	N	0.71926	D	0.64830	0.994	D	0.77557	0.99	D	0.94737	0.7915	10	0.87932	D	0	.	8.178	0.31294	0.0:0.7468:0.0:0.2532	.	357	Q14525	KT33B_HUMAN	P	357	ENSP00000251646:R357P	ENSP00000251646:R357P	R	-	2	0	KRT33B	36774584	0.992000	0.36948	1.000000	0.80357	0.118000	0.20060	2.344000	0.44010	1.341000	0.45600	0.555000	0.69702	CGG	.	.	none		0.597	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
TSHZ3	57616	hgsc.bcm.edu	37	19	31769763	31769763	+	Silent	SNP	G	G	A	rs12461253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:31769763G>A	ENST00000240587.4	-	2	1263	c.936C>T	c.(934-936)gtC>gtT	p.V312V		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	312					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)					TTTTGGCGGCGACAGGAGTGA	0.537													G|||	1753	0.35004	0.236	0.3098	5008	,	,		14828	0.5734		0.2962	False		,,,				2504	0.3579				p.V312V		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C936T						PASS	.	G		994,3412	369.3+/-319.0	118,758,1327	85.0	86.0	86.0		936	-10.2	0.0	19	dbSNP_120	86	2506,6094	410.2+/-350.1	367,1772,2161	no	coding-synonymous	TSHZ3	NM_020856.2		485,2530,3488	AA,AG,GG		29.1395,22.5601,26.9107		312/1082	31769763	3500,9506	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			GGCGGCGACAGGA	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.936C>T	19.37:g.31769763G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	107	52	0.485981	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.689;A|0.311	0.311	strong		0.537	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
KRT83	3889	hgsc.bcm.edu	37	12	52708420	52708420	+	Missense_Mutation	SNP	G	G	A	rs2857671	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52708420G>A	ENST00000293670.3	-	9	1539	c.1477C>T	c.(1477-1479)Cat>Tat	p.H493Y	AC121757.1_ENST00000594763.1_5'Flank	NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	493	Tail.		H -> Y (in dbSNP:rs2857671). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9084137}.		aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GCCACTTAATGCCTCCCCTGG	0.632													N|||	3687	0.736222	0.9652	0.5908	5008	,	,		15096	0.6776		0.6412	False		,,,				2504	0.6881				p.H493Y	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,0,1	KRT83	64	1	0			c.C1477T						PASS	.	A	TYR/HIS	4032,336		1875,282,27	18.0	17.0	17.0		1477	4.2	0.7	12	dbSNP_100	17	5655,2909		1881,1893,508	yes	missense	KRT83	NM_002282.3	83	3756,2175,535	AA,AG,GG		33.9678,7.6923,25.0928	benign	493/494	52708420	9687,3245	2184	4282	6466	SO:0001583	missense	3889	exon9			CTTAATGCCTCCC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.1477C>T	12.37:g.52708420G>A	ENSP00000293670:p.His493Tyr	Somatic	131	1	0.00763359		WXS	Illumina HiSeq	Phase_I	169	163	0.964497	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Missense_Mutation	SNP	ENST00000293670.3	37	CCDS8823.1	1571	0.7193223443223443	469	0.9532520325203252	233	0.643646408839779	385	0.6730769230769231	484	0.6385224274406333	A	7.216	0.596344	0.13875	0.923077	0.660322	ENSG00000170523	ENST00000293670	T	0.80566	-1.39	4.21	4.21	0.49690	.	0.544663	0.15264	N	0.271655	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	0.43130	-0.9410	9	0.02654	T	1	.	6.7862	0.23675	0.8884:0.0:0.1116:0.0	rs2857671;rs59455799;rs2857671	493	P78385	KRT83_HUMAN	Y	493	ENSP00000293670:H493Y	ENSP00000293670:H493Y	H	-	1	0	KRT83	50994687	0.000000	0.05858	0.712000	0.30502	0.011000	0.07611	0.466000	0.22019	0.590000	0.29694	-0.817000	0.03123	CAT	G|0.240;A|0.760	0.760	strong		0.632	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
FAM25A	643161	hgsc.bcm.edu	37	10	88782100	88782100	+	Missense_Mutation	SNP	G	G	C	rs7079587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:88782100G>C	ENST00000343959.4	+	2	122	c.103G>C	c.(103-105)Gtg>Ctg	p.V35L	RP11-96C23.14_ENST00000444180.3_RNA	NM_001146157.2	NP_001139629.1	B3EWG3	FM25A_HUMAN	family with sequence similarity 25, member A	35			V -> L (in dbSNP:rs7079587).							stomach(1)	1						GGTGAAGGAGGTGGTGGGACA	0.622													.|||	189	0.0377396	0.0855	0.036	5008	,	,		20449	0.0		0.0388	False		,,,				2504	0.0123				p.V35L		Atlas-SNP	.											.	FAM25A	4	.	0			c.G103C						PASS	.	G	LEU/VAL	100,1284		2,96,594	42.0	39.0	40.0		103	3.9	1.0	10	dbSNP_116	40	117,3065		3,111,1477	no	missense	FAM25A	NM_001146157.2	32	5,207,2071	CC,CG,GG		3.6769,7.2254,4.7525	probably-damaging	35/90	88782100	217,4349	692	1591	2283	SO:0001583	missense	643161	exon2			AAGGAGGTGGTGG		CCDS44451.1	10q23.2	2008-08-13			ENSG00000188100	ENSG00000188100			23436	protein-coding gene	gene with protein product							Standard	NM_001146157		Approved	bA96C23.5	uc010qmo.2	B3EWG3	OTTHUMG00000018664	ENST00000343959.4:c.103G>C	10.37:g.88782100G>C	ENSP00000342790:p.Val35Leu	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	21	13	0.619048	NM_001146157	B2RV02|Q5VTM1	Missense_Mutation	SNP	ENST00000343959.4	37	CCDS44451.1	91|91	0.041666666666666664|0.041666666666666664	48|48	0.0975609756097561|0.0975609756097561	15|15	0.04143646408839779|0.04143646408839779	2|2	0.0034965034965034965|0.0034965034965034965	26|26	0.03430079155672823|0.03430079155672823	G|G	12.56|12.56	1.974538|1.974538	0.34848|0.34848	0.072254|0.072254	0.036769|0.036769	ENSG00000188100|ENSG00000188100	ENST00000343959|ENST00000444180	.|.	.|.	.|.	3.93|3.93	3.93|3.93	0.45458|0.45458	.|.	.|0.000000	.|0.49305	.|D	.|0.000156	T|T	0.03390|0.03390	0.0098|0.0098	.|.	.|.	.|.	0.32906|0.32906	D|D	0.51392|0.51392	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.49021|0.49021	-0.8982|-0.8982	4|6	.|0.59425	.|D	.|0.04	-18.7332|-18.7332	13.1877|13.1877	0.59691|0.59691	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs7079587;rs52814476;rs7079587|rs7079587;rs52814476;rs7079587	.|.	.|.	.|.	A|L	41|35	.|.	.|ENSP00000417034:V35L	G|V	+|+	2|1	0|0	FAM25A|FAM25A	88772080|88772080	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.148000|0.148000	0.21650|0.21650	4.172000|4.172000	0.58243|0.58243	2.216000|2.216000	0.71823|0.71823	0.478000|0.478000	0.44815|0.44815	GGT|GTG	G|0.964;C|0.036	0.036	strong		0.622	FAM25A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049182.2		
PLEKHF1	79156	hgsc.bcm.edu	37	19	30165157	30165157	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:30165157G>T	ENST00000436066.3	+	2	877	c.411G>T	c.(409-411)acG>acT	p.T137T	PLEKHF1_ENST00000592810.1_Silent_p.T137T	NM_024310.4	NP_077286.3	Q96S99	PKHF1_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 1	137					apoptotic process (GO:0006915)|endosome organization (GO:0007032)|positive regulation of autophagy (GO:0010508)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|protein localization to plasma membrane (GO:0072659)|vesicle organization (GO:0016050)	endosome membrane (GO:0010008)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|lung(3)|ovary(1)|prostate(1)	6	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)			TGAGGGCCACGGGCCGCCCGC	0.682																																					p.T137T		Atlas-SNP	.											.	PLEKHF1	16	.	0			c.G411T						PASS	.						23.0	26.0	25.0					19																	30165157		2200	4296	6496	SO:0001819	synonymous_variant	79156	exon2			GGCCACGGGCCGC	AF434818	CCDS12417.1	19q11	2013-01-10				ENSG00000166289		"""Zinc fingers, FYVE domain containing"", ""Pleckstrin homology (PH) domain containing"""	20764	protein-coding gene	gene with protein product		615200					Standard	NM_024310		Approved	APPD, MGC4090, PHAFIN1, ZFYVE15	uc002nsh.4	Q96S99		ENST00000436066.3:c.411G>T	19.37:g.30165157G>T		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	15	7	0.466667	NM_024310	Q96K11|Q9BUB9	Silent	SNP	ENST00000436066.3	37	CCDS12417.1																																																																																			.	.	none		0.682	PLEKHF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459323.1	NM_024310	
BSN	8927	hgsc.bcm.edu	37	3	49690627	49690627	+	Missense_Mutation	SNP	G	G	A	rs35762866	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49690627G>A	ENST00000296452.4	+	5	3752	c.3638G>A	c.(3637-3639)gGc>gAc	p.G1213D		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1213			G -> D (in dbSNP:rs35762866).		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)		GGACCCCATGGCGGCCCCTCT	0.657													G|||	184	0.0367412	0.0015	0.0764	5008	,	,		14865	0.0		0.1064	False		,,,				2504	0.0225				p.G1213D		Atlas-SNP	.											.	BSN	272	.	0			c.G3638A						PASS	.	G	ASP/GLY	94,4272		2,90,2091	12.0	15.0	14.0		3638	1.0	0.0	3	dbSNP_126	14	957,7609		49,859,3375	no	missense	BSN	NM_003458.3	94	51,949,5466	AA,AG,GG		11.1721,2.153,8.1271	probably-damaging	1213/3927	49690627	1051,11881	2183	4283	6466	SO:0001583	missense	8927	exon5			CCCATGGCGGCCC	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.3638G>A	3.37:g.49690627G>A	ENSP00000296452:p.Gly1213Asp	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	69	39	0.565217	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	105	0.04807692307692308	3	0.006097560975609756	21	0.058011049723756904	0	0.0	81	0.10686015831134564	G	9.470	1.095325	0.20471	0.02153	0.111721	ENSG00000164061	ENST00000296452	T	0.20200	2.09	5.12	1.05	0.20165	.	0.430079	0.24516	N	0.037853	T	0.00300	0.0009	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31586	-0.9938	10	0.12766	T	0.61	.	10.6173	0.45458	0.0695:0.3747:0.5558:0.0	rs35762866	1213	Q9UPA5	BSN_HUMAN	D	1213	ENSP00000296452:G1213D	ENSP00000296452:G1213D	G	+	2	0	BSN	49665631	0.033000	0.19621	0.001000	0.08648	0.725000	0.41563	2.208000	0.42797	-0.090000	0.12462	0.462000	0.41574	GGC	G|0.940;A|0.060	0.060	strong		0.657	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
THNSL1	79896	hgsc.bcm.edu	37	10	25313818	25313818	+	Silent	SNP	C	C	T	rs7086282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:25313818C>T	ENST00000524413.1	+	3	2013	c.1666C>T	c.(1666-1668)Cta>Tta	p.L556L	THNSL1_ENST00000376356.4_Silent_p.L556L			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	556						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.L556L(1)		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)	GGAAAGAAAACTAGCACAAAC	0.353													T|||	2549	0.508986	0.6936	0.5389	5008	,	,		19211	0.4861		0.3459	False		,,,				2504	0.4294				p.L556L		Atlas-SNP	.											THNSL1,NS,carcinoma,0,1	THNSL1	70	1	1	Substitution - coding silent(1)	stomach(1)	c.C1666T						scavenged	.	T		2813,1593	481.0+/-359.0	899,1015,289	50.0	54.0	53.0		1666	-0.9	0.5	10	dbSNP_116	53	3044,5556	655.5+/-401.3	507,2030,1763	no	coding-synonymous	THNSL1	NM_024838.4		1406,3045,2052	TT,TC,CC		35.3953,36.1552,45.0331		556/744	25313818	5857,7149	2203	4300	6503	SO:0001819	synonymous_variant	79896	exon3			AGAAAACTAGCAC	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.1666C>T	10.37:g.25313818C>T		Somatic	68	1	0.0147059		WXS	Illumina HiSeq	Phase_I	45	43	0.955556	NM_024838	B3KWL1|D3DRV3|Q5VV21	Silent	SNP	ENST00000524413.1	37	CCDS7147.1																																																																																			C|0.530;T|0.470	0.470	strong		0.353	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838	
MAP3K5	4217	hgsc.bcm.edu	37	6	137026266	137026266	+	Silent	SNP	T	T	G	rs9321567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:137026266T>G	ENST00000359015.4	-	3	954	c.594A>C	c.(592-594)atA>atC	p.I198I		NM_005923.3	NP_005914.1	Q99683	M3K5_HUMAN	mitogen-activated protein kinase kinase kinase 5	198					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)		TCTGGCAAATTATTTCCTGAA	0.244													G|||	3212	0.641374	0.798	0.647	5008	,	,		14936	0.5823		0.4652	False		,,,				2504	0.6677				p.I198I		Atlas-SNP	.											.	MAP3K5	136	.	0			c.A594C						PASS	.	G		3181,1073		1218,745,164	21.0	24.0	23.0		594	1.5	1.0	6	dbSNP_119	23	4117,4319		1035,2047,1136	no	coding-synonymous	MAP3K5	NM_005923.3		2253,2792,1300	GG,GT,TT		48.8028,25.2233,42.4901		198/1375	137026266	7298,5392	2127	4218	6345	SO:0001819	synonymous_variant	4217	exon3			GCAAATTATTTCC	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.594A>C	6.37:g.137026266T>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	40	37	0.925	NM_005923	A6NIA0|B4DGB2|Q5THN3|Q99461	Silent	SNP	ENST00000359015.4	37	CCDS5179.1																																																																																			T|0.413;G|0.587	0.587	strong		0.244	MAP3K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042383.1		
PRMT9	90826	hgsc.bcm.edu	37	4	148560193	148560193	+	Missense_Mutation	SNP	C	C	T	rs11557361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:148560193C>T	ENST00000322396.6	-	11	2482	c.2240G>A	c.(2239-2241)tGt>tAt	p.C747Y	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Missense_Mutation_p.C634Y	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		747	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.		C -> Y (in dbSNP:rs11557361).			cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TAAAGGTATACAGGGCAATGA	0.368													C|||	41	0.0081869	0.0	0.0101	5008	,	,		16840	0.0		0.0338	False		,,,				2504	0.0				p.C747Y		Atlas-SNP	.											.	PRMT10	68	.	0			c.G2240A						PASS	.	C	TYR/CYS	21,4385	26.2+/-53.5	0,21,2182	98.0	99.0	98.0		2240	5.2	0.7	4	dbSNP_120	98	245,8355	97.7+/-159.3	1,243,4056	yes	missense	PRMT10	NM_138364.2	194	1,264,6238	TT,TC,CC		2.8488,0.4766,2.0452	probably-damaging	747/846	148560193	266,12740	2203	4300	6503	SO:0001583	missense	90826	exon11			GGTATACAGGGCA																												ENST00000322396.6:c.2240G>A	4.37:g.148560193C>T	ENSP00000314396:p.Cys747Tyr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	31	0.014194139194139194	0	0.0	2	0.0055248618784530384	0	0.0	29	0.03825857519788918	C	8.851	0.944484	0.18356	0.004766	0.028488	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.33438	1.41;1.41	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.06645	0.0170	L	0.54323	1.7	0.58432	D	0.999996	P	0.51653	0.947	B	0.42282	0.382	T	0.08330	-1.0727	10	0.02654	T	1	-33.0667	13.1858	0.59680	0.0:0.9234:0.0:0.0766	rs11557361;rs52794661;rs11557361	747	Q6P2P2	ANM10_HUMAN	Y	747;634	ENSP00000314396:C747Y;ENSP00000439508:C634Y	ENSP00000314396:C747Y	C	-	2	0	PRMT10	148779643	1.000000	0.71417	0.665000	0.29768	0.998000	0.95712	5.321000	0.65846	2.428000	0.82296	0.650000	0.86243	TGT	C|0.981;T|0.019	0.019	strong		0.368	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
SLC16A13	201232	hgsc.bcm.edu	37	17	6942111	6942111	+	Silent	SNP	G	G	T	rs33979567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6942111G>T	ENST00000308027.6	+	3	1292	c.984G>T	c.(982-984)gtG>gtT	p.V328V		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	328						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CCTTCTCCGTGCTGCCTGAAC	0.602													G|||	986	0.196885	0.3086	0.1643	5008	,	,		17805	0.0615		0.2068	False		,,,				2504	0.1984				p.V328V		Atlas-SNP	.											SLC16A13,colon,carcinoma,0,1	SLC16A13	28	1	0			c.G984T						PASS	.	G		1273,3133	421.3+/-339.3	177,919,1107	73.0	81.0	78.0		984	-2.0	0.9	17	dbSNP_126	78	1845,6755	320.3+/-314.5	206,1433,2661	no	coding-synonymous	SLC16A13	NM_201566.2		383,2352,3768	TT,TG,GG		21.4535,28.8924,23.9736		328/427	6942111	3118,9888	2203	4300	6503	SO:0001819	synonymous_variant	201232	exon3			CTCCGTGCTGCCT	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"""Solute carriers"""	31037	protein-coding gene	gene with protein product	"""monocarboxylic acid transporter 13"""		"""solute carrier family 16 (monocarboxylic acid transporters), member 13"""				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.984G>T	17.37:g.6942111G>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_201566	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																			G|0.773;T|0.227	0.227	strong		0.602	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2		
OR6C74	254783	hgsc.bcm.edu	37	12	55641295	55641295	+	Missense_Mutation	SNP	A	A	G	rs4388990	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55641295A>G	ENST00000343870.4	+	1	314	c.224A>G	c.(223-225)tAc>tGc	p.Y75C		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	75			Y -> C (in dbSNP:rs4388990).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						ACAACTGTCTACATTCCCAAA	0.403													G|||	1181	0.235823	0.149	0.2334	5008	,	,		19409	0.1171		0.333	False		,,,				2504	0.3773				p.Y75C		Atlas-SNP	.											.	OR6C74	52	.	0			c.A224G						PASS	.	G	CYS/TYR	818,3588	324.5+/-298.6	65,688,1450	173.0	174.0	174.0		224	2.9	0.0	12	dbSNP_111	174	2719,5881	434.2+/-357.7	426,1867,2007	yes	missense	OR6C74	NM_001005490.1	194	491,2555,3457	GG,GA,AA		31.6163,18.5656,27.1951	benign	75/313	55641295	3537,9469	2203	4300	6503	SO:0001583	missense	254783	exon1			CTGTCTACATTCC		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"""GPCR / Class A : Olfactory receptors"""	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.224A>G	12.37:g.55641295A>G	ENSP00000342836:p.Tyr75Cys	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	203	88	0.433498	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	495	0.22664835164835165	76	0.15447154471544716	98	0.27071823204419887	74	0.12937062937062938	247	0.3258575197889182	a	0.003	-2.548705	0.00140	0.185656	0.316163	ENSG00000197706	ENST00000343870	T	0.00882	5.58	4.83	2.93	0.34026	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	N	0.000024	T	0.00012	0.0000	N	0.00507	-1.42	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33343	-0.9872	9	0.02654	T	1	.	3.4523	0.07503	0.0764:0.2412:0.3214:0.361	rs4388990;rs17382973;rs52809662;rs60288258;rs4388990	75	A6NCV1	O6C74_HUMAN	C	75	ENSP00000342836:Y75C	ENSP00000342836:Y75C	Y	+	2	0	OR6C74	53927562	0.000000	0.05858	0.009000	0.14445	0.351000	0.29236	-0.367000	0.07553	0.300000	0.22699	-0.229000	0.12294	TAC	A|0.750;G|0.250	0.250	strong		0.403	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
PLA2G4E	123745	hgsc.bcm.edu	37	15	42281719	42281719	+	Silent	SNP	G	G	A	rs1668579	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:42281719G>A	ENST00000399518.3	-	15	2103	c.1617C>T	c.(1615-1617)ggC>ggT	p.G539G	PLA2G4E_ENST00000413860.2_Silent_p.G510G|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	527	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		ACTTCTGCAGGCCCACCTCGT	0.632											OREG0023079	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2122	0.423722	0.6861	0.2291	5008	,	,		17989	0.2927		0.2803	False		,,,				2504	0.4898				p.G539G		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C1617T						PASS	.	G		2548,1826		772,1004,411	32.0	38.0	36.0		1617	1.2	1.0	15	dbSNP_89	36	2258,6326		303,1652,2337	no	coding-synonymous	PLA2G4E	NM_001206670.1		1075,2656,2748	AA,AG,GG		26.3048,41.7467,37.0891		539/869	42281719	4806,8152	2187	4292	6479	SO:0001819	synonymous_variant	123745	exon15			CTGCAGGCCCACC		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.1617C>T	15.37:g.42281719G>A		Somatic	56	0	0	907	WXS	Illumina HiSeq	Phase_I	79	78	0.987342	NM_001206670	Q6ZSC0	Silent	SNP	ENST00000399518.3	37	CCDS55962.1																																																																																			G|0.630;A|0.370	0.370	strong		0.632	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	
SHROOM3	57619	hgsc.bcm.edu	37	4	77631425	77631425	+	Missense_Mutation	SNP	T	T	A	rs3821979	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77631425T>A	ENST00000296043.6	+	3	1393	c.440T>A	c.(439-441)cTt>cAt	p.L147H	SHROOM3_ENST00000473602.1_3'UTR	NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	147			L -> H (in dbSNP:rs3821979).		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)			GGGGTTAAACTTCGGCTGAAG	0.577													T|||	1097	0.21905	0.1611	0.2032	5008	,	,		18546	0.3363		0.1093	False		,,,				2504	0.3006				p.L147H		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T440A	GRCh37	CM063143	SHROOM3	M	rs3821979	PASS	.	T	HIS/LEU	760,3646	310.0+/-291.3	62,636,1505	85.0	73.0	77.0		440	3.8	1.0	4	dbSNP_107	77	1131,7469	233.3+/-266.6	83,965,3252	yes	missense	SHROOM3	NM_020859.3	99	145,1601,4757	AA,AT,TT		13.1512,17.2492,14.5394	probably-damaging	147/1997	77631425	1891,11115	2203	4300	6503	SO:0001583	missense	57619	exon3			TTAAACTTCGGCT	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.440T>A	4.37:g.77631425T>A	ENSP00000296043:p.Leu147His	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	111	42	0.378378	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	404	0.184981684981685	80	0.16260162601626016	70	0.19337016574585636	173	0.30244755244755245	81	0.10686015831134564	T	15.60	2.882384	0.51908	0.172492	0.131512	ENSG00000138771	ENST00000296043	T	0.34472	1.36	4.96	3.78	0.43462	.	0.000000	0.36101	N	0.002789	T	0.00012	0.0000	M	0.62723	1.935	0.31241	P	0.695171	D	0.71674	0.998	P	0.60789	0.879	T	0.15896	-1.0421	9	0.87932	D	0	-2.793	7.8964	0.29708	0.0:0.0961:0.0:0.9039	rs3821979;rs52831344;rs3821979	147	Q8TF72	SHRM3_HUMAN	H	147	ENSP00000296043:L147H	ENSP00000296043:L147H	L	+	2	0	SHROOM3	77850449	0.921000	0.31238	1.000000	0.80357	0.879000	0.50718	0.142000	0.16096	1.002000	0.39104	0.482000	0.46254	CTT	T|0.843;A|0.157	0.157	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
HAGHL	84264	hgsc.bcm.edu	37	16	778024	778024	+	Silent	SNP	T	T	C	rs1406814	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:778024T>C	ENST00000341413.4	+	3	446	c.165T>C	c.(163-165)caT>caC	p.H55H	HAGHL_ENST00000561546.1_Silent_p.H55H|HAGHL_ENST00000564545.1_Intron|HAGHL_ENST00000564537.1_Silent_p.H55H|HAGHL_ENST00000389703.3_Silent_p.H55H|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000549114.1_Silent_p.H55H|NARFL_ENST00000562862.1_5'Flank			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	55							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				CCACCCACCATCACTGGTGAG	0.721													t|||	2574	0.513978	0.5862	0.4928	5008	,	,		8072	0.7579		0.2425	False		,,,				2504	0.4591				p.H55H	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											HAGHL,NS,carcinoma,0,1	HAGHL	18	1	0			c.T165C						PASS	.			2208,2150		571,1066,542	22.0	29.0	27.0		165	-1.6	1.0	16	dbSNP_88	27	1792,6782		199,1394,2694	no	coding-synonymous	HAGHL	NM_032304.2		770,2460,3236	CC,CT,TT		20.9004,49.3346,30.931		55/283	778024	4000,8932	2179	4287	6466	SO:0001819	synonymous_variant	84264	exon2			CCACCATCACTGG	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.165T>C	16.37:g.778024T>C		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37																																																																																				T|0.616;C|0.384	0.384	strong		0.721	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
FRY	10129	hgsc.bcm.edu	37	13	32776153	32776153	+	Silent	SNP	T	T	C	rs9567420	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32776153T>C	ENST00000380250.3	+	30	4318	c.3822T>C	c.(3820-3822)taT>taC	p.Y1274Y		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1274						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		GAGAGATTTATGAAATCTCCA	0.368													T|||	495	0.0988419	0.003	0.0389	5008	,	,		18615	0.2649		0.0358	False		,,,				2504	0.1646				p.Y1274Y		Atlas-SNP	.											.	FRY	312	.	0			c.T3822C						PASS	.	T		36,3746		0,36,1855	139.0	124.0	129.0		3822	3.2	1.0	13	dbSNP_119	129	357,7873		10,337,3768	no	coding-synonymous	FRY	NM_023037.2		10,373,5623	CC,CT,TT		4.3378,0.9519,3.2717		1274/3014	32776153	393,11619	1891	4115	6006	SO:0001819	synonymous_variant	10129	exon30			GATTTATGAAATC	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3822T>C	13.37:g.32776153T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_023037	Q9Y3N6	Silent	SNP	ENST00000380250.3	37	CCDS41875.1																																																																																			T|0.918;C|0.082	0.082	strong		0.368	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
BRD8	10902	hgsc.bcm.edu	37	5	137475787	137475787	+	Silent	SNP	C	C	T	rs423258	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:137475787C>T	ENST00000254900.5	-	27	4055	c.3684G>A	c.(3682-3684)gtG>gtA	p.V1228V	NME5_ENST00000265191.2_5'Flank	NM_139199.1	NP_631938	Q9H0E9	BRD8_HUMAN	bromodomain containing 8	1228					cell surface receptor signaling pathway (GO:0007166)|chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|intracellular receptor signaling pathway (GO:0030522)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Swr1 complex (GO:0000812)	sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid hormone receptor activity (GO:0004887)	p.V1228V(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(3)|urinary_tract(1)	35			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TTCCATCATCCACTGGGTTAG	0.433													C|||	1486	0.296725	0.0862	0.4035	5008	,	,		17057	0.3839		0.3091	False		,,,				2504	0.4029				p.V1228V		Atlas-SNP	.											BRD8,NS,carcinoma,0,1	BRD8	192	1	1	Substitution - coding silent(1)	stomach(1)	c.G3684A						PASS	.	C		653,3753	281.1+/-275.7	51,551,1601	157.0	149.0	152.0		3684	4.2	0.8	5	dbSNP_80	152	3061,5539	471.7+/-368.2	535,1991,1774	no	coding-synonymous	BRD8	NM_139199.1		586,2542,3375	TT,TC,CC		35.593,14.8207,28.5561		1228/1236	137475787	3714,9292	2203	4300	6503	SO:0001819	synonymous_variant	10902	exon27			ATCATCCACTGGG	AF016270	CCDS4198.1, CCDS34241.1, CCDS54907.1	5q31	2008-02-05			ENSG00000112983	ENSG00000112983			19874	protein-coding gene	gene with protein product		602848				8611617, 9368056	Standard	NM_001164326		Approved	SMAP, p120	uc003lcf.1	Q9H0E9	OTTHUMG00000129204	ENST00000254900.5:c.3684G>A	5.37:g.137475787C>T		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	163	84	0.515337	NM_139199	O43178|Q15355|Q58AB0|Q59GN0|Q969M9	Silent	SNP	ENST00000254900.5	37	CCDS4198.1																																																																																			C|0.714;T|0.286	0.286	strong		0.433	BRD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251282.3	NM_006696	
EFHB	151651	hgsc.bcm.edu	37	3	19930003	19930003	+	Silent	SNP	G	G	A	rs4858714	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:19930003G>A	ENST00000295824.9	-	10	2027	c.1866C>T	c.(1864-1866)ttC>ttT	p.F622F	EFHB_ENST00000344838.4_Silent_p.F492F	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	622	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						GAAAATTTGCGAATTCCAGAT	0.348													G|||	1161	0.231829	0.4561	0.2406	5008	,	,		14673	0.0159		0.2495	False		,,,				2504	0.1268				p.F622F		Atlas-SNP	.											.	EFHB	186	.	0			c.C1866T						PASS	.	G		1866,2540		379,1108,716	52.0	52.0	52.0		1866	-1.3	1.0	3	dbSNP_111	52	2188,6402		289,1610,2396	no	coding-synonymous	EFHB	NM_144715.3		668,2718,3112	AA,AG,GG		25.4715,42.3513,31.1942		622/834	19930003	4054,8942	2203	4295	6498	SO:0001819	synonymous_variant	151651	exon10			ATTTGCGAATTCC	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.1866C>T	3.37:g.19930003G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Silent	SNP	ENST00000295824.9	37	CCDS33715.2																																																																																			G|0.728;A|0.272	0.272	strong		0.348	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715	
MED24	9862	hgsc.bcm.edu	37	17	38186106	38186106	+	Silent	SNP	C	C	T	rs11555255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38186106C>T	ENST00000394128.2	-	13	1242	c.1161G>A	c.(1159-1161)gcG>gcA	p.A387A	SNORD124_ENST00000459577.1_RNA|MED24_ENST00000394127.2_Silent_p.A374A|MED24_ENST00000394126.1_Silent_p.A412A|MED24_ENST00000501516.3_Silent_p.A406A|MED24_ENST00000356271.3_Silent_p.A374A	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	387					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					GCTCTCGGTCCGCTTTGCTGT	0.557													C|||	528	0.105431	0.1551	0.1182	5008	,	,		20173	0.006		0.164	False		,,,				2504	0.0716				p.A387A		Atlas-SNP	.											.	MED24	89	.	0			c.G1161A						PASS	.	C	,	737,3669	304.1+/-288.3	63,611,1529	221.0	165.0	184.0		1122,1161	-4.2	0.2	17	dbSNP_120	184	1401,7199	270.7+/-289.1	115,1171,3014	no	coding-synonymous,coding-synonymous	MED24	NM_001079518.1,NM_014815.3	,	178,1782,4543	TT,TC,CC		16.2907,16.7272,16.4386	,	374/977,387/990	38186106	2138,10868	2203	4300	6503	SO:0001819	synonymous_variant	9862	exon13			TCGGTCCGCTTTG	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.1161G>A	17.37:g.38186106C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	174	69	0.396552	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Silent	SNP	ENST00000394128.2	37	CCDS11359.1																																																																																			T|0.119;G|0.156;C|0.699;A|0.025	0.119	strong		0.557	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
CD6	923	hgsc.bcm.edu	37	11	60776186	60776186	+	Missense_Mutation	SNP	C	C	T	rs11230562	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60776186C>T	ENST00000313421.7	+	4	836	c.650C>T	c.(649-651)aCg>aTg	p.T217M	CD6_ENST00000346437.4_Missense_Mutation_p.T217M|CD6_ENST00000545105.1_Intron|CD6_ENST00000344028.5_Missense_Mutation_p.T217M|CD6_ENST00000352009.5_Missense_Mutation_p.T217M|CD6_ENST00000452451.2_Missense_Mutation_p.T217M	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	217	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		T -> M (in dbSNP:rs11230562). {ECO:0000269|PubMed:17371992}.		cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						TTGCACTTCACGCCCGGCCGC	0.692													C|||	442	0.0882588	0.0106	0.1239	5008	,	,		12755	0.0357		0.2386	False		,,,				2504	0.0675				p.T217M	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.C650T						PASS	.	C	MET/THR	238,4154		12,214,1970	26.0	22.0	24.0		650	0.7	0.2	11	dbSNP_120	24	2045,6541		256,1533,2504	yes	missense	CD6	NM_006725.3	81	268,1747,4474	TT,TC,CC		23.8178,5.4189,17.5913	probably-damaging	217/669	60776186	2283,10695	2196	4293	6489	SO:0001583	missense	923	exon4			ACTTCACGCCCGG		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.650C>T	11.37:g.60776186C>T	ENSP00000323280:p.Thr217Met	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Missense_Mutation	SNP	ENST00000313421.7	37	CCDS7999.1	252|252	0.11538461538461539|0.11538461538461539	8|8	0.016260162601626018|0.016260162601626018	52|52	0.143646408839779|0.143646408839779	12|12	0.02097902097902098|0.02097902097902098	180|180	0.23746701846965698|0.23746701846965698	C|C	12.39|12.39	1.924082|1.924082	0.34002|0.34002	0.054189|0.054189	0.238178|0.238178	ENSG00000013725|ENSG00000013725	ENST00000538611|ENST00000344028;ENST00000346437;ENST00000313421;ENST00000542157;ENST00000433107;ENST00000452451;ENST00000352009	.|T;T;T;T;T;T;T	.|0.29142	.|1.58;1.58;1.58;1.58;1.58;1.58;1.58	4.08|4.08	0.667|0.667	0.17907|0.17907	.|Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.|0.634924	.|0.12753	.|N	.|0.441986	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	P|P	0.0|0.0	.|P;D;D;D;D	.|0.71674	.|0.709;0.998;0.994;0.997;0.996	.|B;P;P;P;P	.|0.61533	.|0.157;0.813;0.729;0.823;0.89	T|T	0.16748|0.16748	-1.0392|-1.0392	4|9	.|0.87932	.|D	.|0	.|.	8.527|8.527	0.33311|0.33311	0.2324:0.2692:0.4984:0.0|0.2324:0.2692:0.4984:0.0	rs11230562|rs11230562	.|217;217;217;217;217	.|E7ER04;P30203-5;P30203-4;P30203;Q8N4Q7	.|.;.;.;CD6_HUMAN;.	C|M	61|217	.|ENSP00000344108:T217M;ENSP00000345566:T217M;ENSP00000323280:T217M;ENSP00000440055:T217M;ENSP00000410638:T217M;ENSP00000390676:T217M;ENSP00000340628:T217M	.|ENSP00000323280:T217M	R|T	+|+	1|2	0|0	CD6|CD6	60532762|60532762	0.000000|0.000000	0.05858|0.05858	0.175000|0.175000	0.22980|0.22980	0.321000|0.321000	0.28281|0.28281	-0.081000|-0.081000	0.11321|0.11321	0.343000|0.343000	0.23821|0.23821	0.561000|0.561000	0.74099|0.74099	CGC|ACG	C|0.852;T|0.148	0.148	strong		0.692	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
TBX1	6899	hgsc.bcm.edu	37	22	19766782	19766782	+	Missense_Mutation	SNP	C	C	T	rs4819522	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19766782C>T	ENST00000329705.7	+	9	1178	c.1049C>T	c.(1048-1050)aCg>aTg	p.T350M	TBX1_ENST00000359500.3_Intron	NM_080646.1	NP_542377.1	O43435	TBX1_HUMAN	T-box 1	350			T -> M (in dbSNP:rs4819522).		angiogenesis (GO:0001525)|anterior/posterior pattern specification (GO:0009952)|aorta morphogenesis (GO:0035909)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|blood vessel morphogenesis (GO:0048514)|blood vessel remodeling (GO:0001974)|cell fate specification (GO:0001708)|cell proliferation (GO:0008283)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|coronary artery morphogenesis (GO:0060982)|determination of left/right symmetry (GO:0007368)|ear morphogenesis (GO:0042471)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic viscerocranium morphogenesis (GO:0048703)|enamel mineralization (GO:0070166)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|lymph vessel development (GO:0001945)|mesenchymal cell apoptotic process (GO:0097152)|mesoderm development (GO:0007498)|middle ear morphogenesis (GO:0042474)|muscle cell fate commitment (GO:0042693)|muscle organ development (GO:0007517)|muscle organ morphogenesis (GO:0048644)|muscle tissue morphogenesis (GO:0060415)|negative regulation of cell differentiation (GO:0045596)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|otic vesicle morphogenesis (GO:0071600)|outer ear morphogenesis (GO:0042473)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|parathyroid gland development (GO:0060017)|pattern specification process (GO:0007389)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of tongue muscle cell differentiation (GO:2001037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of organ morphogenesis (GO:2000027)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retinoic acid receptor signaling pathway (GO:0048384)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|social behavior (GO:0035176)|soft palate development (GO:0060023)|thymus development (GO:0048538)|thyroid gland development (GO:0030878)|tongue morphogenesis (GO:0043587)|transcription, DNA-templated (GO:0006351)|vagus nerve morphogenesis (GO:0021644)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(1)|lung(3)|ovary(2)	8	Colorectal(54;0.0993)	all_lung(157;3.05e-06)				AAAGCTGAGACGTCTAGGAAC	0.547													C|||	1048	0.209265	0.1551	0.255	5008	,	,		19033	0.119		0.169	False		,,,				2504	0.3845				p.T350M		Atlas-SNP	.											TBX1_ENST00000329705,colon,carcinoma,0,1	TBX1	62	1	0			c.C1049T						PASS	.	C	,MET/THR	666,3740	284.0+/-277.4	61,544,1598	93.0	78.0	83.0		,1049	-3.4	0.0	22	dbSNP_111	83	1577,7023	295.1+/-302.2	155,1267,2878	yes	intron,missense	TBX1	NM_005992.1,NM_080646.1	,81	216,1811,4476	TT,TC,CC		18.3372,15.1158,17.2459	,	,350/399	19766782	2243,10763	2203	4300	6503	SO:0001583	missense	6899	exon9			CTGAGACGTCTAG	AF012131	CCDS13765.1, CCDS13766.1, CCDS13767.1	22q11.21	2014-09-17			ENSG00000184058	ENSG00000184058		"""T-boxes"""	11592	protein-coding gene	gene with protein product		602054	"""velocardiofacial syndrome"""	VCF		9268629, 23000736	Standard	NM_080646		Approved	CATCH22	uc002zqa.1	O43435	OTTHUMG00000150421	ENST00000329705.7:c.1049C>T	22.37:g.19766782C>T	ENSP00000331176:p.Thr350Met	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_080646	C6G493|C6G494|O43436|Q96RJ2	Missense_Mutation	SNP	ENST00000329705.7	37	CCDS13766.1	368	0.1684981684981685	90	0.18292682926829268	83	0.2292817679558011	68	0.11888111888111888	127	0.16754617414248021	C	12.48	1.950373	0.34377	0.151158	0.183372	ENSG00000184058	ENST00000329705	D	0.86956	-2.19	1.69	-3.37	0.04898	.	.	.	.	.	T	0.00109	0.0003	N	0.19112	0.55	0.80722	P	0.0	D	0.69078	0.997	P	0.53861	0.736	T	0.17410	-1.0370	8	0.44086	T	0.13	.	3.5111	0.07708	0.0:0.2533:0.4805:0.2661	rs4819522;rs59530459;rs4819522	350	O43435	TBX1_HUMAN	M	350	ENSP00000331176:T350M	ENSP00000331176:T350M	T	+	2	0	TBX1	18146782	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.716000	0.04991	-0.727000	0.04888	0.555000	0.69702	ACG	C|0.829;T|0.171	0.171	strong		0.547	TBX1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318033.1	NM_080647	
ETFDH	2110	hgsc.bcm.edu	37	4	159627845	159627845	+	Silent	SNP	T	T	C	rs77484245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:159627845T>C	ENST00000511912.1	+	12	1865	c.1533T>C	c.(1531-1533)gaT>gaC	p.D511D	ETFDH_ENST00000307738.5_Silent_p.D464D	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	511					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)		CAAAACCCGATGGACAGATCA	0.433													T|||	10	0.00199681	0.0	0.0	5008	,	,		16740	0.0		0.0099	False		,,,				2504	0.0				p.D511D		Atlas-SNP	.											.	ETFDH	57	.	0			c.T1533C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	203.0	192.0	196.0		1533	-1.0	0.9	4	dbSNP_132	196	54,8546	33.8+/-87.4	0,54,4246	no	coding-synonymous	ETFDH	NM_004453.2		0,57,6446	CC,CT,TT		0.6279,0.0681,0.4383		511/618	159627845	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	2110	exon12			ACCCGATGGACAG	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.1533T>C	4.37:g.159627845T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	91	38	0.417582	NM_004453	B4E3R9|J3KND9|Q7Z347	Silent	SNP	ENST00000511912.1	37	CCDS3800.1																																																																																			T|0.996;C|0.004	0.004	strong		0.433	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2		
PROP1	5626	hgsc.bcm.edu	37	5	177422908	177422908	+	Silent	SNP	A	A	G	rs1135320	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:177422908A>G	ENST00000308304.2	-	1	335	c.27T>C	c.(25-27)gcT>gcC	p.A9A		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	9					blood vessel development (GO:0001568)|canonical Wnt signaling pathway (GO:0060070)|cell migration (GO:0016477)|central nervous system development (GO:0007417)|dorsal/ventral pattern formation (GO:0009953)|hypophysis morphogenesis (GO:0048850)|hypothalamus cell differentiation (GO:0021979)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatotropin secreting cell differentiation (GO:0060126)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(9)|stomach(1)	13	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTGGCTTCTCAGCCTGGCGCC	0.622													G|||	2242	0.447684	0.2481	0.4942	5008	,	,		14630	0.5595		0.4712	False		,,,				2504	0.545				p.A9A		Atlas-SNP	.											.	PROP1	28	.	0			c.T27C						PASS	.	G		1262,3144		181,900,1122	75.0	67.0	70.0		27	-0.8	0.0	5	dbSNP_86	70	3850,4750		887,2076,1337	no	coding-synonymous	PROP1	NM_006261.4		1068,2976,2459	GG,GA,AA		44.7674,28.6428,39.3049		9/227	177422908	5112,7894	2203	4300	6503	SO:0001819	synonymous_variant	5626	exon1			CTTCTCAGCCTGG	AF076215	CCDS4430.1	5q35.3	2011-06-20	2007-07-12		ENSG00000175325	ENSG00000175325		"""Homeoboxes / PRD class"""	9455	protein-coding gene	gene with protein product		601538	"""prophet of Pit1, paired-like homeodomain transcription factor"""			9462743	Standard	NM_006261		Approved		uc003mif.1	O75360	OTTHUMG00000130887	ENST00000308304.2:c.27T>C	5.37:g.177422908A>G		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_006261		Silent	SNP	ENST00000308304.2	37	CCDS4430.1																																																																																			A|0.580;G|0.420	0.420	strong		0.622	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
SRSF6	6431	hgsc.bcm.edu	37	20	42087079	42087079	+	Silent	SNP	C	C	G	rs147967864	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:42087079C>G	ENST00000244020.3	+	2	292	c.186C>G	c.(184-186)ggC>ggG	p.G62G		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	62	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						AGCTCTGCGGCGAGCGCGTGA	0.721													C|||	96	0.0191693	0.0015	0.0303	5008	,	,		7632	0.0		0.0606	False		,,,				2504	0.0123				p.G62G		Atlas-SNP	.											.	SRSF6	37	.	0			c.C186G						PASS	.	C		40,4106		0,40,2033	6.0	6.0	6.0		186	-2.8	1.0	20	dbSNP_134	6	413,7863		7,399,3732	no	coding-synonymous	SRSF6	NM_006275.5		7,439,5765	GG,GC,CC		4.9903,0.9648,3.6468		62/345	42087079	453,11969	2073	4138	6211	SO:0001819	synonymous_variant	6431	exon2			CTGCGGCGAGCGC	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10788	protein-coding gene	gene with protein product	"""pre-mRNA splicing factor SRP55"", ""SR splicing factor 6"""	601944	"""splicing factor, arginine/serine-rich 6"""	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.186C>G	20.37:g.42087079C>G		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	23	15	0.652174	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Silent	SNP	ENST00000244020.3	37	CCDS13318.1																																																																																			C|0.972;G|0.028	0.028	strong		0.721	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275	
NCAPD2	9918	hgsc.bcm.edu	37	12	6638116	6638116	+	Silent	SNP	C	C	T	rs740850	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:6638116C>T	ENST00000315579.5	+	27	4282	c.3483C>T	c.(3481-3483)aaC>aaT	p.N1161N	NCAPD2_ENST00000545962.1_Silent_p.N1116N	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1161					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						TACAGGGCAACGCAATCTATA	0.542													C|||	1724	0.344249	0.5265	0.4207	5008	,	,		17817	0.2054		0.2823	False		,,,				2504	0.2505				p.N1161N		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3483T						PASS	.	C		2211,2195	590.0+/-387.3	554,1103,546	96.0	102.0	100.0		3483	-4.3	0.4	12	dbSNP_86	100	2320,6280	389.7+/-343.0	324,1672,2304	no	coding-synonymous	NCAPD2	NM_014865.3		878,2775,2850	TT,TC,CC		26.9767,49.8184,34.8378		1161/1402	6638116	4531,8475	2203	4300	6503	SO:0001819	synonymous_variant	9918	exon27			GGGCAACGCAATC	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.3483C>T	12.37:g.6638116C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	128	66	0.515625	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			C|0.653;T|0.347	0.347	strong		0.542	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
KLRG2	346689	hgsc.bcm.edu	37	7	139138950	139138950	+	Missense_Mutation	SNP	C	C	G	rs17160911	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:139138950C>G	ENST00000340940.4	-	4	1085	c.1016G>C	c.(1015-1017)gGc>gCc	p.G339A	KLRG2_ENST00000393039.2_Intron	NM_198508.2	NP_940910.1	A4D1S0	KLRG2_HUMAN	killer cell lectin-like receptor subfamily G, member 2	339	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.		G -> A (in dbSNP:rs17160911).			integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|large_intestine(2)|lung(3)	6	Melanoma(164;0.233)					TGGGTATCTGCCCAGGAAGTC	0.667													C|||	877	0.17512	0.2088	0.1311	5008	,	,		14984	0.2113		0.1252	False		,,,				2504	0.1748				p.G339A		Atlas-SNP	.											KLRG2,NS,carcinoma,0,3	KLRG2	22	3	0			c.G1016C						PASS	.						13.0	10.0	11.0					7																	139138950		1870	3571	5441	SO:0001583	missense	346689	exon4			TATCTGCCCAGGA	AK126174	CCDS5854.1	7q34	2011-08-30			ENSG00000188883	ENSG00000188883		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	24778	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member B"""						Standard	XM_005250311		Approved	FLJ44186, CLEC15B	uc003vvb.3	A4D1S0	OTTHUMG00000157705	ENST00000340940.4:c.1016G>C	7.37:g.139138950C>G	ENSP00000339356:p.Gly339Ala	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_198508	Q2NL79|Q6ZTV6	Missense_Mutation	SNP	ENST00000340940.4	37	CCDS5854.1	340	0.15567765567765568	93	0.18902439024390244	46	0.1270718232044199	110	0.19230769230769232	91	0.12005277044854881	C	6.481	0.456958	0.12283	.	.	ENSG00000188883	ENST00000340940	T	0.16897	2.31	4.78	2.9	0.33743	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.692200	0.12721	N	0.444710	T	0.00012	0.0000	N	0.08118	0	0.20764	P	0.999855632	B	0.18166	0.026	B	0.19391	0.025	T	0.40942	-0.9536	9	0.07325	T	0.83	-8.5467	7.5752	0.27931	0.1896:0.6275:0.1829:0.0	rs17160911;rs17160911	339	A4D1S0	KLRG2_HUMAN	A	339	ENSP00000339356:G339A	ENSP00000339356:G339A	G	-	2	0	KLRG2	138789490	0.488000	0.25996	0.542000	0.28115	0.903000	0.53119	0.271000	0.18626	0.578000	0.29487	0.655000	0.94253	GGC	C|0.832;G|0.166	0.166	strong		0.667	KLRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349433.1	NM_198508	
CPAMD8	27151	hgsc.bcm.edu	37	19	17062905	17062905	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17062905G>A	ENST00000443236.1	-	20	2554	c.2523C>T	c.(2521-2523)gcC>gcT	p.A841A		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	794						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						GGGAGGGCTCGGCGATGCCTA	0.617																																					p.A841A		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C2523T						PASS	.						27.0	30.0	29.0					19																	17062905		2015	4149	6164	SO:0001819	synonymous_variant	27151	exon20			GGGCTCGGCGATG	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.2523C>T	19.37:g.17062905G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	31	0.54386	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899355	0.33535	.	.	ENSG00000160111	ENST00000443236	.	.	.	3.14	-6.29	0.02013	.	.	.	.	.	T	0.35278	0.0926	.	.	.	0.50467	D	0.999877	.	.	.	.	.	.	T	0.37619	-0.9698	4	.	.	.	.	1.5938	0.02659	0.4277:0.1287:0.2994:0.1442	.	.	.	.	L	852	.	.	P	-	2	0	CPAMD8	16923905	0.005000	0.15991	0.000000	0.03702	0.825000	0.46686	-0.070000	0.11523	-1.304000	0.02329	0.491000	0.48974	CCG	.	.	none		0.617	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
PTPRB	5787	hgsc.bcm.edu	37	12	71002865	71002865	+	Silent	SNP	T	T	A	rs2717430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:71002865T>A	ENST00000261266.5	-	2	338	c.309A>T	c.(307-309)acA>acT	p.T103T	PTPRB_ENST00000551525.1_Silent_p.T320T|PTPRB_ENST00000334414.6_Silent_p.T321T|PTPRB_ENST00000451516.2_Silent_p.T103T|PTPRB_ENST00000550358.1_Silent_p.T321T|PTPRB_ENST00000538708.1_Silent_p.T103T|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550857.1_Silent_p.T103T	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	103	Fibronectin type-III 1. {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)			GCAAGACCACTGTTCTCTCTT	0.458													A|||	3002	0.599441	0.7965	0.5187	5008	,	,		18563	0.5982		0.4085	False		,,,				2504	0.5879				p.T321T		Atlas-SNP	.											.	PTPRB	676	.	0			c.A963T						PASS	.	A	,,,	2652,1146		935,782,182	144.0	151.0	148.0		963,309,309,309	-2.1	0.0	12	dbSNP_100	148	3247,5007		616,2015,1496	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	,,,	1551,2797,1678	AA,AT,TT		39.3385,30.1738,48.9462	,,,	321/2216,103/1908,103/1908,103/1998	71002865	5899,6153	1899	4127	6026	SO:0001819	synonymous_variant	5787	exon4			GACCACTGTTCTC	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.309A>T	12.37:g.71002865T>A		Somatic	289	0	0		WXS	Illumina HiSeq	Phase_I	238	96	0.403361	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	37	CCDS44944.1	1223	0.559981684981685	387	0.7865853658536586	168	0.46408839779005523	353	0.6171328671328671	315	0.4155672823218997	A	7.513	0.655153	0.14580	0.698262	0.393385	ENSG00000127329	ENST00000547715	.	.	.	4.75	-2.07	0.07276	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.27502	-1.0072	3	.	.	.	.	1.5427	0.02558	0.3042:0.2637:0.3038:0.1283	rs2717430;rs3825186;rs17846473;rs17859531;rs56467609;rs59996312;rs2717430	.	.	.	C	95	.	.	S	-	1	0	PTPRB	69289132	0.000000	0.05858	0.010000	0.14722	0.925000	0.55904	-0.240000	0.08952	-0.560000	0.06102	-0.336000	0.08194	AGT	T|0.423;A|0.577	0.577	strong		0.458	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
FAM198A	729085	hgsc.bcm.edu	37	3	43074430	43074430	+	Silent	SNP	A	A	G	rs2948619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:43074430A>G	ENST00000430121.2	+	2	770	c.675A>G	c.(673-675)ggA>ggG	p.G225G	KRBOX1_ENST00000443313.1_Intron	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	225						extracellular region (GO:0005576)				endometrium(1)	1						TGGCCTCAGGAGCTCATCAGT	0.597													G|||	3381	0.67512	0.6407	0.7118	5008	,	,		20629	0.8016		0.5606	False		,,,				2504	0.683				p.G225G		Atlas-SNP	.											.	FAM198A	23	.	0			c.A675G						PASS	.	G		870,514		277,316,99	20.0	24.0	23.0		675	0.6	0.0	3	dbSNP_101	23	1760,1422		491,778,322	no	coding-synonymous	FAM198A	NM_001129908.2		768,1094,421	GG,GA,AA		44.6889,37.1387,42.4004		225/576	43074430	2630,1936	692	1591	2283	SO:0001819	synonymous_variant	729085	exon2			CTCAGGAGCTCAT	AL117530	CCDS46808.1	3p22.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000144649	ENSG00000144649			24485	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 41"""	C3orf41			Standard	NM_001129908		Approved	DKFZP434B172	uc003cmp.4	Q9UFP1	OTTHUMG00000156449	ENST00000430121.2:c.675A>G	3.37:g.43074430A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	81	34	0.419753	NM_001129908	B3KR48	Silent	SNP	ENST00000430121.2	37	CCDS46808.1																																																																																			A|0.349;G|0.651	0.651	strong		0.597	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
OR8K1	390157	hgsc.bcm.edu	37	11	56113575	56113575	+	Missense_Mutation	SNP	A	A	G	rs10896271	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56113575A>G	ENST00000279783.2	+	1	155	c.61A>G	c.(61-63)Atg>Gtg	p.M21V		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	21			M -> V (in dbSNP:rs10896271).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					ATTTATTCTCATGGGGATTAC	0.413										HNSCC(65;0.19)			A|||	2308	0.460863	0.2292	0.6052	5008	,	,		18475	0.6438		0.3708	False		,,,				2504	0.5757				p.M21V		Atlas-SNP	.											.	OR8K1	93	.	0			c.A61G						PASS	.	A	VAL/MET	1111,3291	400.4+/-331.6	149,813,1239	99.0	94.0	95.0		61	-4.6	0.0	11	dbSNP_120	95	3193,5399	483.3+/-371.1	616,1961,1719	yes	missense	OR8K1	NM_001002907.1	21	765,2774,2958	GG,GA,AA		37.1625,25.2385,33.123	benign	21/320	56113575	4304,8690	2201	4296	6497	SO:0001583	missense	390157	exon1			ATTCTCATGGGGA	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.61A>G	11.37:g.56113575A>G	ENSP00000279783:p.Met21Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Missense_Mutation	SNP	ENST00000279783.2	37	CCDS31528.1	963	0.4409340659340659	108	0.21951219512195122	218	0.6022099447513812	368	0.6433566433566433	269	0.3548812664907652	A	8.032	0.761871	0.15914	0.252385	0.371625	ENSG00000150261	ENST00000279783	T	0.00420	7.47	5.18	-4.56	0.03431	.	0.771273	0.11542	N	0.553627	T	0.00012	0.0000	N	0.13327	0.33	0.80722	P	0.0	B	0.12630	0.006	B	0.11329	0.006	T	0.05582	-1.0876	9	0.11794	T	0.64	-2.9812	7.8372	0.29376	0.2343:0.5844:0.0689:0.1124	rs10896271;rs52795616;rs56517428;rs56995399;rs10896271	21	Q8NGG5	OR8K1_HUMAN	V	21	ENSP00000279783:M21V	ENSP00000279783:M21V	M	+	1	0	OR8K1	55870151	0.000000	0.05858	0.020000	0.16555	0.985000	0.73830	-3.088000	0.00610	-0.806000	0.04398	0.448000	0.29417	ATG	A|0.616;G|0.384	0.384	strong		0.413	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
MLLT6	4302	hgsc.bcm.edu	37	17	36873149	36873149	+	Silent	SNP	C	C	T	rs9892493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36873149C>T	ENST00000325718.7	+	10	1657	c.1566C>T	c.(1564-1566)tcC>tcT	p.S522S	MIR4726_ENST00000577947.1_RNA|CTB-58E17.9_ENST00000579499.1_RNA	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	522					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(3)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8	Breast(7;4.43e-21)					TGGTCAGCTCCGGCCTGGGAG	0.657			T	MLL	AL								C|||	707	0.141174	0.2821	0.0821	5008	,	,		17704	0.0308		0.0457	False		,,,				2504	0.2045				p.S522S		Atlas-SNP	.		Dom	yes		17	17q21	4302	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6 (AF17)"""		L	.	MLLT6	80	.	0			c.C1566T						PASS	.	C		987,3419	350.0+/-310.6	119,749,1335	24.0	25.0	24.0		1566	-10.3	0.4	17	dbSNP_119	24	511,8089	141.2+/-197.6	22,467,3811	no	coding-synonymous	MLLT6	NM_005937.3		141,1216,5146	TT,TC,CC		5.9419,22.4013,11.5178		522/1094	36873149	1498,11508	2203	4300	6503	SO:0001819	synonymous_variant	4302	exon10			CAGCTCCGGCCTG		CCDS11327.1	17q21	2014-04-10	2001-11-28		ENSG00000108292	ENSG00000275023		"""Zinc fingers, PHD-type"""	7138	protein-coding gene	gene with protein product	"""Myeloid/lymphoid or mixed-lineage leukemia, translocated to, 6"", ""trithorax homolog"""	600328	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 6"""			8058765	Standard	NM_005937		Approved	AF17, FLJ23480	uc002hqi.4	P55198	OTTHUMG00000188498	ENST00000325718.7:c.1566C>T	17.37:g.36873149C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	101	47	0.465347	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	37	CCDS11327.1																																																																																			C|0.869;T|0.131	0.131	strong		0.657	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937	
EVPL	2125	hgsc.bcm.edu	37	17	74003463	74003463	+	Silent	SNP	G	G	A	rs17886642	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74003463G>A	ENST00000301607.3	-	22	6076	c.5823C>T	c.(5821-5823)acC>acT	p.T1941T	EVPL_ENST00000586740.1_Silent_p.T1963T|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1941	Globular 2.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TGAGCCCCCCGGTCAGGTGCT	0.677													G|||	214	0.0427316	0.0749	0.0346	5008	,	,		15870	0.0089		0.0557	False		,,,				2504	0.0266				p.T1941T		Atlas-SNP	.											.	EVPL	155	.	0			c.C5823T						PASS	.	G		286,4120	153.7+/-187.2	5,276,1922	38.0	37.0	37.0		5823	-11.0	0.1	17	dbSNP_124	37	428,8170	129.8+/-187.9	17,394,3888	no	coding-synonymous	EVPL	NM_001988.2		22,670,5810	AA,AG,GG		4.9779,6.4911,5.4906		1941/2034	74003463	714,12290	2203	4299	6502	SO:0001819	synonymous_variant	2125	exon22			CCCCCCGGTCAGG	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.5823C>T	17.37:g.74003463G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	93	45	0.483871	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.945;A|0.055	0.055	strong		0.677	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103152919	103152919	+	Silent	SNP	G	G	A	rs12574626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:103152919G>A	ENST00000375735.2	+	72	10917	c.10773G>A	c.(10771-10773)acG>acA	p.T3591T	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.T3598T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3591					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		AATGGGATACGTTTACAGGTG	0.284													G|||	970	0.19369	0.4198	0.1282	5008	,	,		15088	0.0913		0.1272	False		,,,				2504	0.1084				p.T3598T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G10794A						PASS	.	G	,	1299,2303		234,831,736	87.0	88.0	88.0		10794,10773	-11.7	0.6	11	dbSNP_120	88	952,7168		62,828,3170	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	296,1659,3906	AA,AG,GG		11.7241,36.0633,19.2032	,	3598/4315,3591/4308	103152919	2251,9471	1801	4060	5861	SO:0001819	synonymous_variant	79659	exon73			GGATACGTTTACA	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10773G>A	11.37:g.103152919G>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	40	11	0.275	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			G|0.808;A|0.192	0.192	strong		0.284	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
FBXO32	114907	hgsc.bcm.edu	37	8	124553222	124553222	+	Silent	SNP	G	G	C	rs4871385	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124553222G>C	ENST00000517956.1	-	1	224	c.33C>G	c.(31-33)ccC>ccG	p.P11P	FBXO32_ENST00000443022.2_Silent_p.P11P	NM_058229.3|NM_148177.2	NP_478136.1|NP_680482.1	Q969P5	FBX32_HUMAN	F-box protein 32	11					cellular response to dexamethasone stimulus (GO:0071549)|protein ubiquitination (GO:0016567)|response to denervation involved in regulation of muscle adaptation (GO:0014894)	nucleolus (GO:0005730)|Z disc (GO:0030018)				autonomic_ganglia(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)|stomach(1)	21	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AGTTCTGCCCGGGGGACCGCC	0.692													G|||	607	0.121206	0.1301	0.196	5008	,	,		10969	0.0218		0.1968	False		,,,				2504	0.0808				p.P11P		Atlas-SNP	.											.	FBXO32	39	.	0			c.C33G						PASS	.	G	,	593,3811		43,507,1652	28.0	30.0	30.0		33,33	-2.8	1.0	8	dbSNP_111	30	1625,6975		161,1303,2836	yes	coding-synonymous,coding-synonymous	FBXO32	NM_001242463.1,NM_058229.3	,	204,1810,4488	CC,CG,GG		18.8953,13.465,17.0563	,	11/263,11/356	124553222	2218,10786	2202	4300	6502	SO:0001819	synonymous_variant	114907	exon1			CTGCCCGGGGGAC	AJ420108	CCDS6345.1, CCDS56553.1	8q24.13	2008-01-28	2004-06-15		ENSG00000156804	ENSG00000156804		"""F-boxes /  ""other"""""	16731	protein-coding gene	gene with protein product		606604	"""F-box only protein 32"""			11679633, 11717410	Standard	NM_058229		Approved	MAFbx, ATROGIN1, Fbx32	uc003yqr.3	Q969P5	OTTHUMG00000164981	ENST00000517956.1:c.33C>G	8.37:g.124553222G>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	123	90	0.731707	NM_001242463	A4KYM0	Silent	SNP	ENST00000517956.1	37	CCDS6345.1																																																																																			G|0.855;C|0.145	0.145	strong		0.692	FBXO32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381281.1		
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383041	39383041	+	Silent	SNP	C	C	T	rs71371479		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39383041C>T	ENST00000377721.3	+	1	142	c.135C>T	c.(133-135)tcC>tcT	p.S45S	KRTAP9-2_ENST00000455970.2_Silent_p.S45S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	45	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.S45S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GCTGTGTGTCCAGCTGCTGCC	0.647																																					p.S45S		Atlas-SNP	.											KRTAP9-2,NS,carcinoma,0,1	KRTAP9-2	24	1	1	Substitution - coding silent(1)	prostate(1)	c.C135T						scavenged	.						62.0	56.0	58.0					17																	39383041		2203	4299	6502	SO:0001819	synonymous_variant	83899	exon1			TGTGTCCAGCTGC	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.135C>T	17.37:g.39383041C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Silent	SNP	ENST00000377721.3	37	CCDS32651.1																																																																																			C|0.500;T|0.500	0.500	weak		0.647	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
SLX4	84464	hgsc.bcm.edu	37	16	3640274	3640274	+	Missense_Mutation	SNP	G	G	A	rs714181	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3640274G>A	ENST00000294008.3	-	12	4005	c.3365C>T	c.(3364-3366)cCg>cTg	p.P1122L		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1122	Interaction with PLK1 and TERF2-TERF2IP.		P -> L (in dbSNP:rs714181). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GTCAATAGACGGAGATTTTTC	0.493								Direct reversal of damage					A|||	1200	0.239617	0.5484	0.147	5008	,	,		18117	0.0843		0.0865	False		,,,				2504	0.2055				p.P1122L		Atlas-SNP	.											.	SLX4	173	.	0			c.C3365T						PASS	.	A	LEU/PRO	2027,2367	610.6+/-391.6	463,1101,633	104.0	99.0	101.0		3365	-0.7	0.0	16	dbSNP_86	101	723,7877	786.7+/-407.6	23,677,3600	yes	missense	SLX4	NM_032444.2	98	486,1778,4233	AA,AG,GG		8.407,46.1311,21.1636	benign	1122/1835	3640274	2750,10244	2197	4300	6497	SO:0001583	missense	84464	exon12			ATAGACGGAGATT	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.3365C>T	16.37:g.3640274G>A	ENSP00000294008:p.Pro1122Leu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	431	0.19734432234432234	272	0.5528455284552846	55	0.15193370165745856	48	0.08391608391608392	56	0.07387862796833773	A	2.635	-0.285532	0.05605	0.461311	0.08407	ENSG00000188827	ENST00000294008	T	0.16897	2.31	6.07	-0.664	0.11406	.	0.670897	0.14312	N	0.327602	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.10296	0.003	B	0.06405	0.002	T	0.41928	-0.9481	9	0.22706	T	0.39	.	6.0854	0.19964	0.3816:0.0:0.4976:0.1208	rs714181;rs17857104;rs52826780;rs60671054;rs714181	1122	Q8IY92	SLX4_HUMAN	L	1122	ENSP00000294008:P1122L	ENSP00000294008:P1122L	P	-	2	0	SLX4	3580275	0.001000	0.12720	0.000000	0.03702	0.605000	0.37080	0.088000	0.14979	-0.331000	0.08501	-0.254000	0.11334	CCG	G|0.785;N|0.000	.	strong		0.493	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
LRP2	4036	hgsc.bcm.edu	37	2	170150671	170150671	+	Silent	SNP	G	G	A	rs2229266	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:170150671G>A	ENST00000263816.3	-	6	924	c.639C>T	c.(637-639)gaC>gaT	p.D213D	LRP2_ENST00000443831.1_Silent_p.D213D	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	213	LDL-receptor class A 5. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AAGCATGTTCGTCACTGCCGT	0.458													A|||	1854	0.370208	0.3616	0.487	5008	,	,		21773	0.4643		0.2386	False		,,,				2504	0.3374				p.D213D		Atlas-SNP	.											.	LRP2	751	.	0			c.C639T						PASS	.	A		1436,2970	682.7+/-404.2	260,916,1027	156.0	127.0	137.0		639	4.4	1.0	2	dbSNP_98	137	2251,6349	708.8+/-405.7	310,1631,2359	no	coding-synonymous	LRP2	NM_004525.2		570,2547,3386	AA,AG,GG		26.1744,32.5919,28.3485		213/4656	170150671	3687,9319	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon6			ATGTTCGTCACTG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.639C>T	2.37:g.170150671G>A		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	315	145	0.460317	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.567;T|0.068	.	strong		0.458	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
FDX1L	112812	hgsc.bcm.edu	37	19	10426422	10426422	+	Silent	SNP	A	A	C	rs378395	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10426422A>C	ENST00000393708.3	-	2	177	c.159T>G	c.(157-159)gcT>gcG	p.A53A	CTD-2369P2.12_ENST00000586529.1_3'UTR|FDX1L_ENST00000492239.1_5'UTR|FDX1L_ENST00000541276.1_Silent_p.A56A|FDX1L_ENST00000494368.1_5'UTR|CTD-2369P2.10_ENST00000452032.2_Silent_p.A53A	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	53					oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			CCTCCTCTCCAGCCGGGCGCG	0.726													C|||	2468	0.492812	0.6097	0.5576	5008	,	,		9095	0.3403		0.4781	False		,,,				2504	0.4611				p.A53A		Atlas-SNP	.											FDX1L,NS,carcinoma,0,1	FDX1L	21	1	0			c.T159G						scavenged	.	C		2227,1909		667,893,508	4.0	6.0	6.0		159	-3.4	0.0	19	dbSNP_80	6	3532,4618		870,1792,1413	no	coding-synonymous	FDX1L	NM_001031734.2		1537,2685,1921	CC,CA,AA		43.3374,46.1557,46.8745		53/184	10426422	5759,6527	2068	4075	6143	SO:0001819	synonymous_variant	112812	exon2			CTCTCCAGCCGGG	AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.159T>G	19.37:g.10426422A>C		Somatic	15	4	0.266667		WXS	Illumina HiSeq	Phase_I	18	17	0.944444	NM_001031734	Q8N8B8	Silent	SNP	ENST00000393708.3	37	CCDS32905.1																																																																																			A|0.532;C|0.468	0.468	strong		0.726	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2		
CACNA1H	8912	hgsc.bcm.edu	37	16	1270111	1270111	+	Missense_Mutation	SNP	G	G	A	rs1054644	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1270111G>A	ENST00000348261.5	+	35	6427	c.6179G>A	c.(6178-6180)cGc>cAc	p.R2060H	CACNA1H_ENST00000358590.4_Missense_Mutation_p.R2054H|CACNA1H_ENST00000565831.1_Missense_Mutation_p.R2054H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2060			R -> H (in dbSNP:rs1054644). {ECO:0000269|PubMed:11157797, ECO:0000269|PubMed:12891677}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TCCCCACCACGCTCCCCACGG	0.701													G|||	453	0.0904553	0.0091	0.0605	5008	,	,		13953	0.0317		0.1133	False		,,,				2504	0.2587				p.R2060H		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G6179A						PASS	.	G	HIS/ARG,HIS/ARG	86,3852		0,86,1883	12.0	17.0	15.0		6161,6179	0.2	0.0	16	dbSNP_86	15	1025,7215		66,893,3161	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	29,29	66,979,5044	AA,AG,GG		12.4393,2.1838,9.123	benign,benign	2054/2348,2060/2354	1270111	1111,11067	1969	4120	6089	SO:0001583	missense	8912	exon35			CACCACGCTCCCC	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.6179G>A	16.37:g.1270111G>A	ENSP00000334198:p.Arg2060His	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	42	21	0.5	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	136	0.06227106227106227	2	0.0040650406504065045	30	0.08287292817679558	10	0.017482517482517484	94	0.12401055408970976	G	6.758	0.508691	0.12883	0.021838	0.124393	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96716	-4.1;-4.05	4.62	0.238	0.15480	.	5.379820	0.00447	N	0.000094	T	0.15435	0.0372	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B	0.15141	0.002;0.007;0.012;0.008;0.002	B;B;B;B;B	0.10450	0.001;0.004;0.004;0.005;0.001	T	0.71500	-0.4574	9	0.36615	T	0.2	.	7.3151	0.26495	0.1585:0.3894:0.452:0.0	rs1054644;rs1534983;rs3195162;rs58564346	806;784;790;2054;2060	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	H	2060;2054	ENSP00000334198:R2060H;ENSP00000351401:R2054H	ENSP00000334198:R2060H	R	+	2	0	CACNA1H	1210112	0.000000	0.05858	0.010000	0.14722	0.132000	0.20833	-0.014000	0.12656	-0.059000	0.13154	0.306000	0.20318	CGC	G|0.936;A|0.064	0.064	strong		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
BANP	54971	hgsc.bcm.edu	37	16	88071611	88071611	+	Silent	SNP	C	C	T	rs149196674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88071611C>T	ENST00000393207.1	+	11	1493	c.1272C>T	c.(1270-1272)gaC>gaT	p.D424D	BANP_ENST00000393208.2_Silent_p.D396D|BANP_ENST00000355163.5_Silent_p.D402D|BANP_ENST00000479780.2_Silent_p.D393D|BANP_ENST00000286122.7_Silent_p.D424D|BANP_ENST00000538234.1_Silent_p.D435D|BANP_ENST00000355022.4_Silent_p.D396D	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	424	Gln-rich.				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)		TGGGGCAGGACGGTCAGGTGA	0.612													c|||	2	0.000399361	0.0015	0.0	5008	,	,		11861	0.0		0.0	False		,,,				2504	0.0				p.D435D		Atlas-SNP	.											.	BANP	67	.	0			c.C1305T						PASS	.	C	,,,,,,	4,4392	8.1+/-20.4	0,4,2194	118.0	99.0	106.0		1296,1206,1179,1305,1272,1188,1188	-6.3	0.7	16	dbSNP_134	106	0,8600		0,0,4300	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	,,,,,,	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	,,,,,,	432/506,402/498,393/467,435/509,424/520,396/470,396/492	88071611	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	54971	exon11			GCAGGACGGTCAG	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.1272C>T	16.37:g.88071611C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	130	69	0.530769	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
F13A1	2162	hgsc.bcm.edu	37	6	6152137	6152137	+	Missense_Mutation	SNP	C	C	G	rs5988	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:6152137C>G	ENST00000264870.3	-	14	2219	c.1954G>C	c.(1954-1956)Gag>Cag	p.E652Q		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	652			Q -> E (in allele F13A*1A and allele F13A*1B; dbSNP:rs5988). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.5}.		blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TTGGTAAACTCAACTGTCACA	0.448													C|||	971	0.19389	0.2292	0.2046	5008	,	,		20265	0.0923		0.2406	False		,,,				2504	0.1953				p.E652Q		Atlas-SNP	.											.	F13A1	135	.	0			c.G1954C						PASS	.	C	GLN/GLU	881,3525	343.6+/-307.7	100,681,1422	89.0	80.0	83.0		1954	4.5	1.0	6	dbSNP_52	83	2003,6597	349.8+/-327.6	237,1529,2534	yes	missense	F13A1	NM_000129.3	29	337,2210,3956	GG,GC,CC		23.2907,19.9955,22.1744	benign	652/733	6152137	2884,10122	2203	4300	6503	SO:0001583	missense	2162	exon14			TAAACTCAACTGT	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1954G>C	6.37:g.6152137C>G	ENSP00000264870:p.Glu652Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	88	50	0.568182	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	CCDS4496.1	412	0.18864468864468864	93	0.18902439024390244	91	0.2513812154696133	60	0.1048951048951049	168	0.22163588390501318	C	15.85	2.954677	0.53293	0.199955	0.232907	ENSG00000124491	ENST00000264870	T	0.68765	-0.35	5.37	4.5	0.54988	.	0.000000	0.85682	D	0.000000	T	0.48995	0.1531	.	.	.	0.20873	P	0.999837872	.	.	.	.	.	.	T	0.49643	-0.8918	6	0.17832	T	0.49	.	13.3365	0.60520	0.1587:0.8413:0.0:0.0	rs5988;rs3191130;rs52826565;rs5988	.	.	.	Q	652	ENSP00000264870:E652Q	ENSP00000264870:E652Q	E	-	1	0	F13A1	6097136	0.999000	0.42202	0.994000	0.49952	0.406000	0.30931	4.372000	0.59530	1.484000	0.48361	0.650000	0.86243	GAG	C|0.786;G|0.214	0.214	strong		0.448	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
CASZ1	54897	hgsc.bcm.edu	37	1	10713997	10713997	+	Missense_Mutation	SNP	G	G	A	rs61736955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:10713997G>A	ENST00000377022.3	-	11	2434	c.2117C>T	c.(2116-2118)cCg>cTg	p.P706L	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Missense_Mutation_p.P706L	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	706					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)		CAGCGAGGGCGGCAGCCCCAG	0.667													G|||	6	0.00119808	0.0015	0.0014	5008	,	,		15352	0.0		0.003	False		,,,				2504	0.0				p.P706L		Atlas-SNP	.											CASZ1,caecum,carcinoma,+1,1	CASZ1	150	1	0			c.C2117T						scavenged	.	G	LEU/PRO,LEU/PRO	6,4398	11.4+/-27.6	0,6,2196	46.0	49.0	48.0		2117,2117	4.8	1.0	1	dbSNP_129	48	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	98,98	0,17,6485	AA,AG,GG		0.1279,0.1362,0.1307	benign,benign	706/1760,706/1167	10713997	17,12987	2202	4300	6502	SO:0001583	missense	54897	exon11			GAGGGCGGCAGCC	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.2117C>T	1.37:g.10713997G>A	ENSP00000366221:p.Pro706Leu	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	77	3	0.038961	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	25.7	4.664037	0.88251	0.001362	0.001279	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.84	4.84	0.62591	.	0.215662	0.49916	D	0.000140	T	0.64305	0.2586	L	0.43152	1.355	0.58432	D	0.999997	D;D;D	0.67145	0.996;0.991;0.981	P;P;B	0.54460	0.753;0.535;0.254	T	0.66548	-0.5896	9	0.54805	T	0.06	-26.0106	18.842	0.92188	0.0:0.0:1.0:0.0	.	730;706;706	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	L	706	.	ENSP00000339445:P706L	P	-	2	0	CASZ1	10636584	1.000000	0.71417	0.978000	0.43139	0.950000	0.60333	9.315000	0.96313	2.619000	0.88677	0.561000	0.74099	CCG	G|0.998;A|0.002	0.002	strong		0.667	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
ENTHD2	146705	hgsc.bcm.edu	37	17	79202956	79202956	+	Silent	SNP	T	T	C	rs2048057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79202956T>C	ENST00000300714.3	-	12	1407	c.1350A>G	c.(1348-1350)ccA>ccG	p.P450P	ENTHD2_ENST00000374769.2_Silent_p.P366P|AC027601.1_ENST00000569559.1_RNA|AC027601.1_ENST00000575922.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	450						cytoplasmic vesicle (GO:0031410)											CCGTGCCCCCTGGGATCCGTT	0.692													T|||	2308	0.460863	0.0703	0.6282	5008	,	,		11278	0.6756		0.4682	False		,,,				2504	0.6411				p.P450P		Atlas-SNP	.											C17orf56,colon,carcinoma,0,1	.	.	1	0			c.A1350G						PASS	.	T		605,3801	246.2+/-254.9	51,503,1649	31.0	30.0	30.0		1350	-6.9	0.0	17	dbSNP_94	30	4124,4476	528.6+/-381.4	1006,2112,1182	no	coding-synonymous	C17orf56	NM_144679.2		1057,2615,2831	CC,CT,TT		47.9535,13.7313,36.3601		450/526	79202956	4729,8277	2203	4300	6503	SO:0001819	synonymous_variant	146705	exon12			GCCCCCTGGGATC	AK056090	CCDS11779.1	17q25.3	2012-07-18	2012-07-18	2012-07-18	ENSG00000167302	ENSG00000167302			26458	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 56"""	C17orf56			Standard	NM_144679		Approved	FLJ31528	uc002jzu.2	Q96N21	OTTHUMG00000177866	ENST00000300714.3:c.1350A>G	17.37:g.79202956T>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_144679	Q6ZQU0|Q6ZSQ9	Silent	SNP	ENST00000300714.3	37	CCDS11779.1																																																																																			A|0.000;C|0.395;T|0.605	0.395	strong		0.692	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679	
DDX28	55794	hgsc.bcm.edu	37	16	68055495	68055495	+	Silent	SNP	G	G	C	rs13816|rs372701071	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68055495G>C	ENST00000332395.5	-	1	2275	c.1611C>G	c.(1609-1611)ccC>ccG	p.P537P	DUS2_ENST00000358896.6_5'Flank|DUS2_ENST00000432752.1_5'Flank|DUS2_ENST00000565263.1_5'Flank	NM_018380.3	NP_060850.2	Q9NUL7	DDX28_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 28	537						mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)	p.P537P(1)		central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0116)|Epithelial(162;0.0474)|all cancers(182;0.233)		AGGTTGCTTGGGGCAAAGGCT	0.512													C|||	959	0.191494	0.3124	0.183	5008	,	,		20171	0.1002		0.1461	False		,,,				2504	0.1748				p.P537P		Atlas-SNP	.											DDX28,NS,carcinoma,0,1	DDX28	29	1	1	Substitution - coding silent(1)	stomach(1)	c.C1611G						PASS	.	C		1257,3139	698.2+/-406.3	190,877,1131	45.0	45.0	45.0		1611	-0.0	0.2	16	dbSNP_52	45	1220,7380	762.2+/-407.6	105,1010,3185	no	coding-synonymous	DDX28	NM_018380.3		295,1887,4316	CC,CG,GG		14.186,28.5942,19.0597		537/541	68055495	2477,10519	2198	4300	6498	SO:0001819	synonymous_variant	55794	exon1			TGCTTGGGGCAAA	AF329821	CCDS10858.1	16q22.1-q22.3	2008-02-05	2003-06-13		ENSG00000182810	ENSG00000182810		"""DEAD-boxes"""	17330	protein-coding gene	gene with protein product		607618	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 28"""			10493829, 11350955	Standard	NM_018380		Approved	MDDX28, FLJ11282	uc002evh.2	Q9NUL7	OTTHUMG00000137549	ENST00000332395.5:c.1611C>G	16.37:g.68055495G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_018380		Silent	SNP	ENST00000332395.5	37	CCDS10858.1																																																																																			T|0.000;G|0.812;C|0.188	0.188	strong		0.512	DDX28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268883.1	NM_018380	
TRPM5	29850	hgsc.bcm.edu	37	11	2432666	2432666	+	Missense_Mutation	SNP	C	C	T	rs34364959	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2432666C>T	ENST00000155858.6	-	18	2706	c.2698G>A	c.(2698-2700)Ggc>Agc	p.G900S	TRPM5_ENST00000528453.1_Missense_Mutation_p.G900S|TRPM5_ENST00000452833.1_Missense_Mutation_p.G902S|TRPM5_ENST00000533060.1_Missense_Mutation_p.G900S	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)		TCCAGGCGGCCGTCATGGGGG	0.617													C|||	259	0.0517173	0.0356	0.062	5008	,	,		15018	0.0427		0.1133	False		,,,				2504	0.0123				p.G900S	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G2698A						PASS	.	C	SER/GLY	214,4188	124.9+/-162.1	5,204,1992	34.0	38.0	36.0		2698	-4.3	0.1	11	dbSNP_126	36	808,7780	181.9+/-230.5	43,722,3529	yes	missense	TRPM5	NM_014555.3	56	48,926,5521	TT,TC,CC		9.4085,4.8614,7.8676	benign	900/1166	2432666	1022,11968	2201	4294	6495	SO:0001583	missense	29850	exon18			GGCGGCCGTCATG	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.2698G>A	11.37:g.2432666C>T	ENSP00000155858:p.Gly900Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	73	37	0.506849	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	158	0.07234432234432235	29	0.05894308943089431	26	0.0718232044198895	23	0.04020979020979021	80	0.10554089709762533	C	4.086	0.013949	0.07959	0.048614	0.094085	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453	T;T;T;T;T	0.62232	0.04;0.04;0.04;0.04;0.04	3.89	-4.32	0.03688	Ion transport (1);	0.360410	0.28927	N	0.013686	T	0.00328	0.0010	N	0.00289	-1.7	0.38436	P	0.05342800000000003	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.24476	-1.0159	9	0.07482	T	0.82	-11.0608	11.7545	0.51868	0.0:0.1898:0.0:0.8102	rs34364959	900;902;900	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	S	894;900;902;900;900	ENSP00000434383:G894S;ENSP00000155858:G900S;ENSP00000387965:G902S;ENSP00000434121:G900S;ENSP00000436809:G900S	ENSP00000155858:G900S	G	-	1	0	TRPM5	2389242	0.018000	0.18449	0.072000	0.20136	0.715000	0.41141	-0.133000	0.10451	-0.724000	0.04908	-1.165000	0.01757	GGC	C|0.930;T|0.070	0.070	strong		0.617	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
CHGB	1114	hgsc.bcm.edu	37	20	5904040	5904040	+	Missense_Mutation	SNP	G	G	A	rs742711	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5904040G>A	ENST00000378961.4	+	4	1454	c.1250G>A	c.(1249-1251)cGc>cAc	p.R417H		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	417			R -> H (in dbSNP:rs742711). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.R417H(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						GGAAAGGGACGCCATCACAGA	0.527													G|||	1158	0.23123	0.0734	0.2334	5008	,	,		20807	0.379		0.2584	False		,,,				2504	0.2628				p.R417H		Atlas-SNP	.											CHGB,NS,carcinoma,0,1	CHGB	112	1	1	Substitution - Missense(1)	stomach(1)	c.G1250A	GRCh37	CM043991	CHGB	M	rs742711	PASS	.	G	HIS/ARG	521,3885	238.4+/-249.8	37,447,1719	80.0	80.0	80.0		1250	-10.8	0.0	20	dbSNP_86	80	2277,6323	378.7+/-339.0	302,1673,2325	yes	missense	CHGB	NM_001819.2	29	339,2120,4044	AA,AG,GG		26.4767,11.8248,21.5131	benign	417/678	5904040	2798,10208	2203	4300	6503	SO:0001583	missense	1114	exon4			AGGGACGCCATCA		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.1250G>A	20.37:g.5904040G>A	ENSP00000368244:p.Arg417His	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	529	0.24221611721611722	49	0.09959349593495935	77	0.212707182320442	206	0.36013986013986016	197	0.2598944591029024	G	1.700	-0.501792	0.04261	0.118248	0.264767	ENSG00000089199	ENST00000378961	T	0.01963	4.53	5.4	-10.8	0.00216	.	2.054640	0.02189	N	0.061130	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.15473	0.013	B	0.06405	0.002	T	0.48536	-0.9027	9	0.10902	T	0.67	1.7578	6.6545	0.22981	0.2912:0.3742:0.2747:0.0599	rs742711;rs52814619;rs61667157;rs742711	417	P05060	SCG1_HUMAN	H	417	ENSP00000368244:R417H	ENSP00000368244:R417H	R	+	2	0	CHGB	5852040	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-2.806000	0.00758	-2.864000	0.00326	-1.788000	0.00630	CGC	G|0.775;A|0.225	0.225	strong		0.527	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
MRPL39	54148	hgsc.bcm.edu	37	21	26965205	26965205	+	Silent	SNP	T	T	C	rs1057885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:26965205T>C	ENST00000352957.4	-	8	881	c.840A>G	c.(838-840)gtA>gtG	p.V280V	MRPL39_ENST00000307301.7_Silent_p.V280V	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	280						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						GAACTGCTGATACTTCATACT	0.373													C|||	3668	0.732428	0.7284	0.8199	5008	,	,		16504	0.7153		0.8121	False		,,,				2504	0.6115				p.V280V		Atlas-SNP	.											.	MRPL39	61	.	0			c.A840G						PASS	.	C	,	3308,1098	396.7+/-330.2	1229,850,124	94.0	88.0	90.0		840,840	0.1	1.0	21	dbSNP_86	90	7111,1489	283.7+/-296.3	2954,1203,143	no	coding-synonymous,coding-synonymous	MRPL39	NM_017446.3,NM_080794.3	,	4183,2053,267	CC,CT,TT		17.314,24.9206,19.8908	,	280/339,280/354	26965205	10419,2587	2203	4300	6503	SO:0001819	synonymous_variant	54148	exon8			TGCTGATACTTCA	AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"""Mitochondrial ribosomal proteins / large subunits"""	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.840A>G	21.37:g.26965205T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	78	26	0.333333	NM_017446	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Silent	SNP	ENST00000352957.4	37	CCDS13573.1																																																																																			T|0.211;C|0.789	0.789	strong		0.373	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446	
WDR81	124997	hgsc.bcm.edu	37	17	1640709	1640709	+	Silent	SNP	C	C	T	rs1045794|rs587780509	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1640709C>T	ENST00000409644.1	+	10	5556	c.5556C>T	c.(5554-5556)acC>acT	p.T1852T	WDR81_ENST00000437219.2_Silent_p.T649T|WDR81_ENST00000419248.1_Silent_p.T625T|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000545662.1_Silent_p.T483T|WDR81_ENST00000446363.1_Silent_p.T491T|WDR81_ENST00000309182.5_Silent_p.T801T	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1852					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)		ATTCCTTGACCGTCTGGAAGG	0.617													C|||	739	0.147564	0.0545	0.2277	5008	,	,		20197	0.1726		0.2227	False		,,,				2504	0.1135				p.T1852T		Atlas-SNP	.											WDR81_ENST00000437219,NS,carcinoma,+1,3	WDR81	180	3	0			c.C5556T						PASS	.	C	,,,	368,4034	185.0+/-212.2	22,324,1855	165.0	105.0	125.0		1947,5556,1875,2403	-7.2	0.7	17	dbSNP_86	125	1903,6695	335.1+/-321.3	224,1455,2620	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	,,,	246,1779,4475	TT,TC,CC		22.1331,8.3598,17.4692	,,,	649/739,1852/1942,625/715,801/891	1640709	2271,10729	2201	4299	6500	SO:0001819	synonymous_variant	124997	exon10			CTTGACCGTCTGG	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.5556C>T	17.37:g.1640709C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Silent	SNP	ENST00000409644.1	37	CCDS54062.1																																																																																			C|0.826;N|0.001	.	strong		0.617	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
ALK	238	hgsc.bcm.edu	37	2	29416615	29416615	+	Silent	SNP	G	G	A	rs56132472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29416615G>A	ENST00000389048.3	-	29	5244	c.4338C>T	c.(4336-4338)acC>acT	p.T1446T	ALK_ENST00000431873.1_Silent_p.T276T	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1446					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)	CAGAGGAGGTGGTAGGCAGAG	0.617			"""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|||	296	0.0591054	0.0779	0.0648	5008	,	,		15538	0.001		0.1233	False		,,,				2504	0.0235				p.T1446T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C4338T						PASS	.			375,4031	187.8+/-214.3	15,345,1843	76.0	80.0	78.0		4338	1.4	0.0	2	dbSNP_129	78	968,7632	210.7+/-251.5	48,872,3380	no	coding-synonymous	ALK	NM_004304.4		63,1217,5223	AA,AG,GG		11.2558,8.5111,10.326		1446/1621	29416615	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGAGGTGGTAGGC	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.4338C>T	2.37:g.29416615G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	86	40	0.465116	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.903;A|0.097	0.097	strong		0.617	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
DNAH5	1767	hgsc.bcm.edu	37	5	13762972	13762972	+	Silent	SNP	T	T	C	rs6554812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13762972T>C	ENST00000265104.4	-	60	10244	c.10140A>G	c.(10138-10140)gaA>gaG	p.E3380E	DNAH5_ENST00000504001.3_5'UTR	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3380	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GACTCAAAAATTCTATCACCT	0.373									Kartagener syndrome				C|||	1554	0.310304	0.3722	0.2709	5008	,	,		21726	0.1052		0.3012	False		,,,				2504	0.4755				p.E3380E		Atlas-SNP	.											DNAH5,NS,carcinoma,-2,1	DNAH5	868	1	0			c.A10140G						PASS	.	C		1601,2805	665.6+/-401.6	294,1013,896	77.0	74.0	75.0		10140	-5.2	0.7	5	dbSNP_116	75	2272,6328	707.4+/-405.6	306,1660,2334	no	coding-synonymous	DNAH5	NM_001369.2		600,2673,3230	CC,CT,TT		26.4186,36.3368,29.7786		3380/4625	13762972	3873,9133	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon60	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAAAAATTCTATC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.10140A>G	5.37:g.13762972T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.714;C|0.286	0.286	strong		0.373	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
ZNF518B	85460	hgsc.bcm.edu	37	4	10447168	10447168	+	Missense_Mutation	SNP	C	C	G	rs66538112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:10447168C>G	ENST00000326756.3	-	3	1223	c.785G>C	c.(784-786)gGt>gCt	p.G262A		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	262					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						GAGAGAGAAACCTGACAGTTG	0.368													C|||	957	0.191094	0.0764	0.2767	5008	,	,		21647	0.2063		0.2435	False		,,,				2504	0.2157				p.G262A		Atlas-SNP	.											.	ZNF518B	116	.	0			c.G785C						PASS	.	C	ALA/GLY	486,3920	228.5+/-243.3	21,444,1738	218.0	213.0	215.0		785	1.2	0.0	4	dbSNP_130	215	2225,6375	379.5+/-339.3	307,1611,2382	yes	missense	ZNF518B	NM_053042.2	60	328,2055,4120	GG,GC,CC		25.8721,11.0304,20.8442	benign	262/1075	10447168	2711,10295	2203	4300	6503	SO:0001583	missense	85460	exon3			GAGAAACCTGACA	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.785G>C	4.37:g.10447168C>G	ENSP00000317614:p.Gly262Ala	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	434	0.1987179487179487	46	0.09349593495934959	83	0.2292817679558011	119	0.20804195804195805	186	0.24538258575197888	C	14.38	2.518259	0.44763	0.110304	0.258721	ENSG00000178163	ENST00000326756	T	0.01414	4.92	6.17	1.25	0.21368	.	0.855383	0.09877	N	0.744208	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	0.34279	-0.9835	9	0.11182	T	0.66	-6.6905	6.0007	0.19519	0.0:0.4868:0.2423:0.2709	.	262	Q9C0D4	Z518B_HUMAN	A	262	ENSP00000317614:G262A	ENSP00000317614:G262A	G	-	2	0	ZNF518B	10056266	0.000000	0.05858	0.027000	0.17364	0.751000	0.42716	0.168000	0.16622	0.486000	0.27676	0.655000	0.94253	GGT	C|0.795;G|0.205	0.205	strong		0.368	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
ZNF175	7728	hgsc.bcm.edu	37	19	52085095	52085095	+	Silent	SNP	G	G	A	rs35431178	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52085095G>A	ENST00000262259.2	+	4	613	c.255G>A	c.(253-255)ccG>ccA	p.P85P	ZNF175_ENST00000436511.2_Silent_p.P85P	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	85	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		AAAAGGAGCCGCGTGTGGAGG	0.458													g|||	231	0.0461262	0.0303	0.072	5008	,	,		18263	0.002		0.1083	False		,,,				2504	0.0307				p.P85P		Atlas-SNP	.											.	ZNF175	65	.	0			c.G255A						PASS	.	A		172,4234	113.8+/-151.8	3,166,2034	85.0	78.0	80.0		255	-1.2	0.0	19	dbSNP_126	80	992,7608	213.6+/-253.5	62,868,3370	yes	coding-synonymous	ZNF175	NM_007147.2		65,1034,5404	AA,AG,GG		11.5349,3.9038,8.9497		85/712	52085095	1164,11842	2203	4300	6503	SO:0001819	synonymous_variant	7728	exon4			GGAGCCGCGTGTG	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.255G>A	19.37:g.52085095G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	76	37	0.486842	NM_007147	A8K9H2	Silent	SNP	ENST00000262259.2	37	CCDS12837.1																																																																																			G|0.916;A|0.084	0.084	strong		0.458	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
TNRC18	84629	hgsc.bcm.edu	37	7	5427652	5427652	+	Silent	SNP	G	G	A	rs4720623	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5427652G>A	ENST00000430969.1	-	5	2151	c.1803C>T	c.(1801-1803)gcC>gcT	p.A601A	TNRC18_ENST00000399537.4_Silent_p.A601A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	601							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CAGGGCGCACGGCCACGGCGT	0.667													G|||	2102	0.419728	0.7693	0.3703	5008	,	,		12690	0.1756		0.2535	False		,,,				2504	0.4049				p.A601A		Atlas-SNP	.											.	TNRC18	311	.	0			c.C1803T						PASS	.	G		2598,1330		889,820,255	6.0	8.0	7.0		1803	-5.4	0.7	7	dbSNP_111	7	2219,5961		360,1499,2231	no	coding-synonymous	TNRC18	NM_001080495.2		1249,2319,2486	AA,AG,GG		27.1271,33.8595,39.7836		601/2969	5427652	4817,7291	1964	4090	6054	SO:0001819	synonymous_variant	84629	exon5			GCGCACGGCCACG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.1803C>T	7.37:g.5427652G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.633;A|0.367	0.367	strong		0.667	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
RIC1	57589	hgsc.bcm.edu	37	9	5774225	5774225	+	Silent	SNP	T	T	G	rs3739648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5774225T>G	ENST00000414202.2	+	26	4442	c.4251T>G	c.(4249-4251)acT>acG	p.T1417T	KIAA1432_ENST00000418622.3_Silent_p.T1338T|KIAA1432_ENST00000449720.2_Silent_p.T1301T	NM_001206557.1|NM_020829.3	NP_001193486.1|NP_065880.2														breast(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(23)|prostate(1)|upper_aerodigestive_tract(1)	45		Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000525)|Lung(218;0.122)		AGGATGGGACTTACGACTGTT	0.498													T|||	1662	0.331869	0.1233	0.2968	5008	,	,		19529	0.5853		0.2853	False		,,,				2504	0.4254				p.T1417T		Atlas-SNP	.											KIAA1432,NS,carcinoma,+2,1	KIAA1432	97	1	0			c.T4251G						PASS	.	T	,	610,3796	266.5+/-267.3	47,516,1640	79.0	66.0	71.0		4140,4251	0.3	1.0	9	dbSNP_107	71	2639,5961	424.5+/-354.7	408,1823,2069	no	coding-synonymous,coding-synonymous	KIAA1432	NM_001206557.1,NM_020829.3	,	455,2339,3709	GG,GT,TT		30.686,13.8448,24.9808	,	1380/1387,1417/1424	5774225	3249,9757	2203	4300	6503	SO:0001819	synonymous_variant	57589	exon26			TGGGACTTACGAC																												ENST00000414202.2:c.4251T>G	9.37:g.5774225T>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_020829		Silent	SNP	ENST00000414202.2	37	CCDS34982.2	741	0.3392857142857143	48	0.0975609756097561	114	0.3149171270718232	350	0.6118881118881119	229	0.3021108179419525	T	6.032	0.374309	0.11409	0.138448	0.30686	ENSG00000107036	ENST00000545641	.	.	.	5.7	0.353	0.16058	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999835	.	.	.	.	.	.	T	0.47812	-0.9088	3	.	.	.	-11.366	10.5079	0.44845	0.0:0.439:0.0:0.561	rs3739648;rs58954556;rs3739648	.	.	.	V	1309	.	.	L	+	1	2	KIAA1432	5764225	0.988000	0.35896	0.997000	0.53966	0.989000	0.77384	0.146000	0.16180	0.127000	0.18452	0.379000	0.24179	TTA	T|0.717;G|0.283	0.283	strong		0.498	KIAA1432-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051636.3		
CLEC4D	338339	hgsc.bcm.edu	37	12	8667897	8667897	+	Missense_Mutation	SNP	A	A	G	rs4304840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:8667897A>G	ENST00000299665.2	+	2	287	c.94A>G	c.(94-96)Agt>Ggt	p.S32G		NM_080387.4	NP_525126.2	Q8WXI8	CLC4D_HUMAN	C-type lectin domain family 4, member D	32			S -> G (in dbSNP:rs4304840). {ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			large_intestine(4)|lung(6)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Lung SC(5;0.184)					CTTACTTCTCAGTGTCTGTTT	0.378													A|||	1504	0.300319	0.5923	0.1844	5008	,	,		-128	0.122		0.2475	False		,,,				2504	0.226				p.S32G		Atlas-SNP	.											.	CLEC4D	46	.	0			c.A94G						PASS	.	A	GLY/SER	2420,1986	618.2+/-393.1	668,1084,451	232.0	197.0	209.0		94	-0.3	0.3	12	dbSNP_111	209	1987,6613	348.8+/-327.2	249,1489,2562	yes	missense	CLEC4D	NM_080387.4	56	917,2573,3013	GG,GA,AA		23.1047,45.0749,33.8844	benign	32/216	8667897	4407,8599	2203	4300	6503	SO:0001583	missense	338339	exon2			CTTCTCAGTGTCT	AF411850	CCDS8593.1	12p13.31	2005-09-21	2005-02-09	2005-02-11		ENSG00000166527		"""C-type lectin domain containing"""	14554	protein-coding gene	gene with protein product		609964	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 8"""	CLECSF8			Standard	NM_080387		Approved	Mpcl	uc001qun.3	Q8WXI8		ENST00000299665.2:c.94A>G	12.37:g.8667897A>G	ENSP00000299665:p.Ser32Gly	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	244	106	0.434426	NM_080387	Q8N5J5	Missense_Mutation	SNP	ENST00000299665.2	37	CCDS8593.1	621	0.28434065934065933	279	0.5670731707317073	66	0.18232044198895028	88	0.15384615384615385	188	0.24802110817941952	a	0.126	-1.119811	0.01785	0.549251	0.231047	ENSG00000166527	ENST00000382064;ENST00000299665	T;T	0.05513	3.43;3.7	3.36	-0.299	0.12808	.	.	.	.	.	T	0.00012	0.0000	L	0.43152	1.355	0.52501	P	4.199999999998649E-5	B	0.10296	0.003	B	0.04013	0.001	T	0.29518	-1.0009	8	0.36615	T	0.2	.	7.1227	0.25454	0.7959:0.0:0.2041:0.0	rs4304840;rs60537162;rs4304840	32	Q8WXI8	CLC4D_HUMAN	G	32	ENSP00000371496:S32G;ENSP00000299665:S32G	ENSP00000299665:S32G	S	+	1	0	CLEC4D	8559164	0.031000	0.19500	0.321000	0.25320	0.003000	0.03518	-0.178000	0.09782	-0.089000	0.12484	-1.335000	0.01260	AGT	A|0.678;G|0.322	0.322	strong		0.378	CLEC4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400565.1	NM_080387	
DNAH10	196385	hgsc.bcm.edu	37	12	124366300	124366300	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124366300G>T	ENST00000409039.3	+	50	8434	c.8409G>T	c.(8407-8409)ggG>ggT	p.G2803G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2803	AAA 4. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGCTGGTCGGGGTAGGGGGCT	0.582																																					p.G2803G		Atlas-SNP	.											.	DNAH10	888	.	0			c.G8409T						PASS	.						17.0	20.0	19.0					12																	124366300		1775	3736	5511	SO:0001819	synonymous_variant	196385	exon50			GGTCGGGGTAGGG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.8409G>T	12.37:g.124366300G>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			.	.	none		0.582	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
INO80C	125476	hgsc.bcm.edu	37	18	33048617	33048617	+	Silent	SNP	G	G	A	rs34130630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:33048617G>A	ENST00000334598.7	-	5	653	c.537C>T	c.(535-537)acC>acT	p.T179T	INO80C_ENST00000586489.1_Silent_p.T124T|INO80C_ENST00000590757.1_Silent_p.T82T|RP11-322E11.5_ENST00000591141.1_lincRNA|INO80C_ENST00000592173.1_Intron|INO80C_ENST00000441607.2_Silent_p.T215T|RP11-322E11.6_ENST00000589258.1_Intron	NM_194281.3	NP_919257.2	Q6PI98	IN80C_HUMAN	INO80 complex subunit C	179					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)				central_nervous_system(1)|endometrium(1)|lung(3)|prostate(2)|skin(1)	8						CCAGGTAGCCGGTGACGACGT	0.542													G|||	64	0.0127796	0.0461	0.0043	5008	,	,		15661	0.0		0.0	False		,,,				2504	0.0				p.T215T		Atlas-SNP	.											.	INO80C	18	.	0			c.C645T						PASS	.	G	,	174,4232	115.0+/-153.0	6,162,2035	136.0	138.0	137.0		645,537	-10.5	1.0	18	dbSNP_126	137	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	INO80C	NM_001098817.1,NM_194281.3	,	6,167,6330	AA,AG,GG		0.0581,3.9492,1.3763	,	215/229,179/193	33048617	179,12827	2203	4300	6503	SO:0001819	synonymous_variant	125476	exon7			GTAGCCGGTGACG		CCDS11914.1, CCDS45853.1	18q12.2	2011-07-06	2008-08-07	2008-08-07	ENSG00000153391	ENSG00000153391		"""INO80 complex subunits"""	26994	protein-coding gene	gene with protein product	"""IES6 homolog (S. cerevisiae)"""		"""chromosome 18 open reading frame 37"""	C18orf37		16230350	Standard	NM_001098817		Approved	FLJ38183, hIes6, IES6	uc010dmt.3	Q6PI98	OTTHUMG00000132564	ENST00000334598.7:c.537C>T	18.37:g.33048617G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	65	38	0.584615	NM_001098817	B4DUI4|E9PCS7|Q86WR1|Q8N994	Silent	SNP	ENST00000334598.7	37	CCDS11914.1																																																																																			G|0.986;A|0.014	0.014	strong		0.542	INO80C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255768.1	NM_194281	
TYK2	7297	hgsc.bcm.edu	37	19	10475649	10475649	+	Missense_Mutation	SNP	C	C	T	rs2304255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10475649C>T	ENST00000525621.1	-	8	1568	c.1087G>A	c.(1087-1089)Ggc>Agc	p.G363S	TYK2_ENST00000524462.1_Missense_Mutation_p.G178S|TYK2_ENST00000529370.1_Missense_Mutation_p.G363S|TYK2_ENST00000264818.6_Missense_Mutation_p.G363S	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	363	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		G -> S (in dbSNP:rs2304255). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.2}.		cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			GCCGGCTGGCCGACTGCCTTG	0.617													C|||	219	0.04373	0.0053	0.0403	5008	,	,		15700	0.0298		0.0746	False		,,,				2504	0.0808				p.G363S		Atlas-SNP	.											.	TYK2	126	.	0			c.G1087A	GRCh37	CM083204	TYK2	M	rs2304255	PASS	.	C	SER/GLY	77,4329	67.6+/-105.2	2,73,2128	43.0	44.0	43.0		1087	-6.4	0.0	19	dbSNP_100	43	674,7926	168.0+/-219.6	32,610,3658	yes	missense	TYK2	NM_003331.4	56	34,683,5786	TT,TC,CC		7.8372,1.7476,5.7743	benign	363/1188	10475649	751,12255	2203	4300	6503	SO:0001583	missense	7297	exon8			GCTGGCCGACTGC		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.1087G>A	19.37:g.10475649C>T	ENSP00000431885:p.Gly363Ser	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_003331	Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	37	CCDS12236.1	92	0.04212454212454213	5	0.01016260162601626	21	0.058011049723756904	15	0.026223776223776224	51	0.06728232189973615	C	10.27	1.303916	0.23736	0.017476	0.078372	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792;ENST00000529370	T;T;T;T	0.08634	3.07;3.07;3.07;3.07	3.61	-6.36	0.01969	FERM domain (1);	2.738210	0.01190	N	0.007314	T	0.00271	0.0008	N	0.14661	0.345	0.09310	N	1	B;B	0.22346	0.068;0.002	B;B	0.06405	0.002;0.001	T	0.35301	-0.9794	10	0.14656	T	0.56	0.0237	6.797	0.23731	0.0:0.3393:0.133:0.5277	rs2304255	363;363	E9PPF2;P29597	.;TYK2_HUMAN	S	178;363;363;110;363	ENSP00000433203:G178S;ENSP00000431885:G363S;ENSP00000264818:G363S;ENSP00000432728:G363S	ENSP00000264818:G363S	G	-	1	0	TYK2	10336649	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.683000	0.00835	-1.143000	0.02866	0.471000	0.43371	GGC	C|0.948;T|0.052	0.052	strong		0.617	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
NQO2	4835	hgsc.bcm.edu	37	6	3012778	3012778	+	Splice_Site	SNP	G	G	A	rs17300141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:3012778G>A	ENST00000338130.2	+	7	885	c.173G>A	c.(172-174)gGt>gAt	p.G58D	NQO2_ENST00000380430.1_Splice_Site_p.G58D|NQO2_ENST00000380455.4_Splice_Site_p.G58D|NQO2_ENST00000380454.4_Splice_Site_p.G58D|NQO2_ENST00000380441.1_Splice_Site_p.G58D			P16083	NQO2_HUMAN	NAD(P)H dehydrogenase, quinone 2	58			G -> D (in dbSNP:rs17300141). {ECO:0000269|Ref.4}.		memory (GO:0007613)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	dihydronicotinamide riboside quinone reductase activity (GO:0001512)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADPH dehydrogenase (quinone) activity (GO:0008753)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(93;0.0412)	all_hematologic(90;0.0895)			Dabigatran etexilate(DB06695)|Flavin adenine dinucleotide(DB03147)|Melatonin(DB01065)|Menadione(DB00170)|Primaquine(DB01087)	TCCCCGACAGGTACTCTTTCT	0.502													G|||	89	0.0177716	0.0015	0.0101	5008	,	,		19975	0.0		0.0268	False		,,,				2504	0.0542				p.G58D		Atlas-SNP	.											.	NQO2	21	.	0			c.G173A						PASS	.	G	ASP/GLY	19,4387	26.2+/-53.5	0,19,2184	120.0	111.0	114.0		173	4.5	0.3	6	dbSNP_123	114	256,8344	101.0+/-162.3	3,250,4047	yes	missense-near-splice	NQO2	NM_000904.3	94	3,269,6231	AA,AG,GG		2.9767,0.4312,2.1144	probably-damaging	58/232	3012778	275,12731	2203	4300	6503	SO:0001630	splice_region_variant	4835	exon4			CGACAGGTACTCT	U07736	CCDS4481.1, CCDS75388.1	6p25.2	2012-09-20	2001-11-30	2001-12-07	ENSG00000124588	ENSG00000124588	1.6.5.2		7856	protein-coding gene	gene with protein product		160998	"""NAD(P)H menadione oxidoreductase 2, dioxin-inducible"""	NMOR2		1691923	Standard	XM_005249152		Approved	QR2, DHQV, DIA6	uc003mus.2	P16083	OTTHUMG00000014130	ENST00000338130.2:c.173-1G>A	6.37:g.3012778G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_000904	B2R492|Q5TD04	Missense_Mutation	SNP	ENST00000338130.2	37	CCDS4481.1	33	0.01510989010989011	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	26	0.03430079155672823	G	14.39	2.521675	0.44866	0.004312	0.029767	ENSG00000124588	ENST00000426637;ENST00000380472;ENST00000538898;ENST00000397717;ENST00000338130;ENST00000380441;ENST00000380455;ENST00000380454;ENST00000380430	T;T;T;T;T;T;T;T	0.09817	2.94;2.94;2.94;2.94;2.94;2.94;2.94;2.94	5.35	4.48	0.54585	Flavodoxin-like fold (1);	0.050045	0.85682	D	0.000000	T	0.31167	0.0788	M	0.89715	3.055	0.43959	D	0.996633	B;D	0.89917	0.0;1.0	B;D	0.73380	0.006;0.98	T	0.45011	-0.9290	9	.	.	.	.	17.6518	0.88167	0.0:0.1249:0.8751:0.0	rs17300141;rs17300141	58;105	P16083;Q59EN2	NQO2_HUMAN;.	D	58;58;105;58;58;58;58;58;58	ENSP00000406951:G58D;ENSP00000369839:G58D;ENSP00000380829:G58D;ENSP00000337773:G58D;ENSP00000369806:G58D;ENSP00000369822:G58D;ENSP00000369821:G58D;ENSP00000369795:G58D	.	G	+	2	0	NQO2	2957777	1.000000	0.71417	0.311000	0.25182	0.004000	0.04260	5.151000	0.64875	0.752000	0.32923	-0.795000	0.03280	GGT	G|0.978;A|0.022	0.022	strong		0.502	NQO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039651.1		Missense_Mutation
ZNF443	10224	hgsc.bcm.edu	37	19	12541214	12541214	+	Missense_Mutation	SNP	G	G	T	rs7256321	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12541214G>T	ENST00000301547.5	-	4	1969	c.1772C>A	c.(1771-1773)cCa>cAa	p.P591Q	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	591			P -> Q (in dbSNP:rs7256321).		apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						ACCACATTGTGGACATTCATA	0.408													.|||	1959	0.391174	0.4781	0.3098	5008	,	,		20631	0.3462		0.2793	False		,,,				2504	0.4928				p.P591Q		Atlas-SNP	.											.	ZNF443	63	.	0			c.C1772A						PASS	.	T	GLN/PRO	1955,2451	609.7+/-391.4	414,1127,662	122.0	123.0	123.0		1772	0.1	0.0	19	dbSNP_116	123	2457,6143	692.6+/-404.6	372,1713,2215	yes	missense	ZNF443	NM_005815.4	76	786,2840,2877	TT,TG,GG		28.5698,44.3713,33.9228	benign	591/672	12541214	4412,8594	2203	4300	6503	SO:0001583	missense	10224	exon4			CATTGTGGACATT	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1772C>A	19.37:g.12541214G>T	ENSP00000301547:p.Pro591Gln	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	165	79	0.478788	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	754	0.34523809523809523	230	0.46747967479674796	108	0.2983425414364641	200	0.34965034965034963	216	0.2849604221635884	T	3.000	-0.206168	0.06180	0.443713	0.285698	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.07114	3.22	1.26	0.0802	0.14419	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (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	0.41305	-0.9516	8	0.35671	T	0.21	.	3.8843	0.09091	0.202:0.0:0.41:0.388	rs7256321;rs52809206;rs57419563;rs7256321	591	Q9Y2A4	ZN443_HUMAN	Q	591;563	ENSP00000301547:P591Q	ENSP00000301547:P591Q	P	-	2	0	ZNF443	12402214	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-1.848000	0.01673	-0.519000	0.06444	-0.533000	0.04299	CCA	G|0.659;T|0.341	0.341	strong		0.408	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
EMC10	284361	hgsc.bcm.edu	37	19	50983930	50983930	+	Silent	SNP	C	C	T	rs10409679	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50983930C>T	ENST00000334976.6	+	5	541	c.495C>T	c.(493-495)ccC>ccT	p.P165P	EMC10_ENST00000376918.3_Silent_p.P165P|EMC10_ENST00000598585.1_Silent_p.P165P|CTD-2545M3.2_ENST00000598194.1_RNA	NM_206538.2	NP_996261.1	Q5UCC4	EMC10_HUMAN	ER membrane protein complex subunit 10	165						ER membrane protein complex (GO:0072546)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)											TGACGCACCCCGGGGGCTGCC	0.697													C|||	2712	0.541534	0.3389	0.6297	5008	,	,		13105	0.5556		0.5875	False		,,,				2504	0.6912				p.P165P		Atlas-SNP	.											C19orf63_ENST00000376918,rectum,carcinoma,0,2	.	.	2	0			c.C495T						scavenged	.	C	,	1652,2732		318,1016,858	24.0	25.0	25.0		495,495	-8.5	0.1	19	dbSNP_119	25	5033,3555		1498,2037,759	no	coding-synonymous,coding-synonymous	C19orf63	NM_175063.4,NM_206538.2	,	1816,3053,1617	TT,TC,CC		41.395,37.6825,48.4659	,	165/255,165/263	50983930	6685,6287	2192	4294	6486	SO:0001819	synonymous_variant	284361	exon5			GCACCCCGGGGGC	BC062607	CCDS12796.1, CCDS42594.1	19q13.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000161671	ENSG00000161671			27609	protein-coding gene	gene with protein product	"""hematopoietic signal peptide-containing secreted 1"", ""hematopoietic signal peptide-containing membrane domain-containing 1"""	614545	"""chromosome 19 open reading frame 63"""	C19orf63		12975309, 22119785	Standard	NM_175063		Approved	INM02, HSS1, HSM1	uc002psl.3	Q5UCC4		ENST00000334976.6:c.495C>T	19.37:g.50983930C>T		Somatic	29	1	0.0344828		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	NM_175063	Q5UCC6|Q69YT5|Q6UWP3|Q86YL4|Q8N541	Silent	SNP	ENST00000334976.6	37	CCDS12796.1																																																																																			C|0.493;T|0.507	0.507	strong		0.697	EMC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464760.2	NM_175063	
AGRN	375790	hgsc.bcm.edu	37	1	978800	978800	+	Silent	SNP	C	C	T	rs375687903		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:978800C>T	ENST00000379370.2	+	8	1616	c.1566C>T	c.(1564-1566)ctC>ctT	p.L522L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	522	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		CCTGTACCCTCGGGCGGGAGA	0.682																																					p.L522L		Atlas-SNP	.											.	AGRN	110	.	0			c.C1566T						PASS	.	C		0,4374		0,0,2187	35.0	35.0	35.0		1566	-7.6	0.1	1		35	2,8588		0,2,4293	no	coding-synonymous	AGRN	NM_198576.3		0,2,6480	TT,TC,CC		0.0233,0.0,0.0154		522/2046	978800	2,12962	2187	4295	6482	SO:0001819	synonymous_variant	375790	exon8			TACCCTCGGGCGG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.1566C>T	1.37:g.978800C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	80	4	0.05	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			.	.	none		0.682	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
CLCNKA	1187	hgsc.bcm.edu	37	1	16349137	16349137	+	Missense_Mutation	SNP	G	G	A	rs9442189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16349137G>A	ENST00000331433.4	+	2	42	c.23G>A	c.(22-24)cGt>cAt	p.R8H	CLCNKA_ENST00000420078.1_Missense_Mutation_p.R8H|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.R8H|CLCNKA_ENST00000439316.2_Missense_Mutation_p.R8H			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	8			R -> H (in dbSNP:rs9442189).		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	GTGGGGCTGCGTGAGGGCTTC	0.667													G|||	61	0.0121805	0.0	0.0058	5008	,	,		17257	0.001		0.0278	False		,,,				2504	0.0286				p.R8H		Atlas-SNP	.											.	CLCNKA	56	.	0			c.G23A						PASS	.	G	HIS/ARG,HIS/ARG	12,4378		1,10,2184	48.0	42.0	44.0		23,23	2.2	0.6	1	dbSNP_119	44	182,8400		2,178,4111	yes	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	29,29	3,188,6295	AA,AG,GG		2.1207,0.2733,1.4955	benign,benign	8/687,8/688	16349137	194,12778	2195	4291	6486	SO:0001583	missense	1187	exon2			GGCTGCGTGAGGG		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.23G>A	1.37:g.16349137G>A	ENSP00000332771:p.Arg8His	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	128	7	0.0546875	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	G	10.27	1.304871	0.23736	0.002733	0.021207	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.86562	-1.93;-1.93;-2.14;-1.93	4.12	2.15	0.27550	.	0.835714	0.10474	U	0.670447	T	0.68595	0.3018	M	0.75447	2.3	0.23138	N	0.998237	B;B;B	0.29671	0.254;0.254;0.254	B;B;B	0.25614	0.062;0.062;0.062	T	0.69221	-0.5202	10	0.62326	D	0.03	.	6.152	0.20316	0.2539:0.0:0.7461:0.0	rs9442189;rs9442189	8;8;8	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	H	8	ENSP00000364844:R8H;ENSP00000410353:R8H;ENSP00000414445:R8H;ENSP00000332771:R8H	ENSP00000332771:R8H	R	+	2	0	CLCNKA	16221724	0.001000	0.12720	0.588000	0.28705	0.445000	0.32107	-0.259000	0.08721	0.337000	0.23665	-0.657000	0.03884	CGT	G|0.989;A|0.011	0.011	strong		0.667	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1264941	1264941	+	Silent	SNP	G	G	A	rs200834421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1264941G>A	ENST00000529681.1	+	31	6889	c.6831G>A	c.(6829-6831)acG>acA	p.T2277T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.T2280T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2277	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)		GCCACACCACGGCCACCTCCA	0.682													g|||	24	0.00479233	0.0008	0.0058	5008	,	,		15879	0.0		0.0129	False		,,,				2504	0.0061				p.T2277T		Atlas-SNP	.											MUC5B,NS,carcinoma,+1,2	MUC5B	473	2	0			c.G6831A						PASS	.	G		9,4263		0,9,2127	98.0	136.0	123.0		6831	-6.0	0.0	11		123	100,8354		0,100,4127	no	coding-synonymous	MUC5B	NM_002458.2		0,109,6254	AA,AG,GG		1.1829,0.2107,0.8565		2277/5763	1264941	109,12617	2136	4227	6363	SO:0001819	synonymous_variant	727897	exon31			CACCACGGCCACC	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.6831G>A	11.37:g.1264941G>A		Somatic	537	0	0		WXS	Illumina HiSeq	Phase_I	607	179	0.294893	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.988;A|0.012	0.012	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95091201	95091201	+	Missense_Mutation	SNP	A	A	G	rs34899	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:95091201A>G	ENST00000379982.3	+	6	1292	c.784A>G	c.(784-786)Aat>Gat	p.N262D	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	262	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.		N -> D (in dbSNP:rs34899). {ECO:0000269|PubMed:10048485, ECO:0000269|PubMed:12426103}.		ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		TTACAACCCCAATTTAAAGAA	0.423													G|||	2379	0.47504	0.357	0.3415	5008	,	,		16213	0.6895		0.4324	False		,,,				2504	0.5521				p.N262D		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.A784G						PASS	.	G	ASP/ASN	1711,2695	651.9+/-399.3	318,1075,810	170.0	163.0	165.0		784	5.2	0.0	5	dbSNP_76	165	3579,5021	628.2+/-398.1	732,2115,1453	yes	missense	RHOBTB3	NM_014899.3	23	1050,3190,2263	GG,GA,AA		41.6163,38.8334,40.6735	benign	262/612	95091201	5290,7716	2203	4300	6503	SO:0001583	missense	22836	exon6			AACCCCAATTTAA	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.784A>G	5.37:g.95091201A>G	ENSP00000369318:p.Asn262Asp	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	220	218	0.990909	NM_014899	A0PJA4|A8K1W9|Q8IW06	Missense_Mutation	SNP	ENST00000379982.3	37	CCDS4077.1	1046	0.47893772893772896	176	0.35772357723577236	136	0.3756906077348066	414	0.7237762237762237	320	0.42216358839050133	G	0.007	-1.962568	0.00461	0.388334	0.416163	ENSG00000164292	ENST00000379982	T	0.69175	-0.38	6.08	5.21	0.72293	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (1);	0.356359	0.35646	N	0.003075	T	0.00012	0.0000	N	0.01874	-0.695	0.44018	P	0.003263000000000016	B	0.02656	0.0	B	0.01281	0.0	T	0.45920	-0.9228	9	0.02654	T	1	-9.0521	12.9585	0.58444	0.1877:0.0:0.8123:0.0	rs34899;rs1221525;rs3201267;rs17857251;rs52811008;rs57550478;rs34899	262	O94955	RHBT3_HUMAN	D	262	ENSP00000369318:N262D	ENSP00000369318:N262D	N	+	1	0	RHOBTB3	95116957	1.000000	0.71417	0.013000	0.15412	0.000000	0.00434	2.538000	0.45710	0.484000	0.27630	-2.314000	0.00255	AAT	A|0.561;G|0.439	0.439	strong		0.423	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
ACTR3C	653857	hgsc.bcm.edu	37	7	149990455	149990455	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149990455T>C	ENST00000539352.1	-	3	350	c.99A>G	c.(97-99)acA>acG	p.T33T	ACTR3C_ENST00000252071.4_Silent_p.T33T	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	33						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.T33T(1)									TCCCCGTTAATGTACGTTCAC	0.468																																					p.T33T		Atlas-SNP	.											Q9C0K3_HUMAN,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	kidney(1)	c.A99G						scavenged	.						165.0	135.0	144.0					7																	149990455		692	1591	2283	SO:0001819	synonymous_variant	653857	exon3			CGTTAATGTACGT		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.99A>G	7.37:g.149990455T>C		Somatic	545	3	0.00550459		WXS	Illumina HiSeq	Phase_I	558	13	0.0232975	NM_001164459	Q5CZI4	Silent	SNP	ENST00000539352.1	37	CCDS47744.1																																																																																			.	.	weak		0.468	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2		
CD2AP	23607	hgsc.bcm.edu	37	6	47563608	47563608	+	Missense_Mutation	SNP	A	A	G	rs138727736	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:47563608A>G	ENST00000359314.5	+	12	1576	c.1120A>G	c.(1120-1122)Aca>Gca	p.T374A		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	374	Pro-rich.				mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			TGAAAAATCAACACTGGAACA	0.353													A|||	23	0.00459265	0.0	0.0115	5008	,	,		14171	0.001		0.003	False		,,,				2504	0.0112				p.T374A		Atlas-SNP	.											.	CD2AP	43	.	0			c.A1120G	GRCh37	CM090139	CD2AP	M	rs138727736	PASS	.	A	ALA/THR	2,4404	4.2+/-10.8	0,2,2201	149.0	169.0	162.0		1120	-5.2	0.0	6	dbSNP_134	162	46,8554	28.5+/-78.6	0,46,4254	yes	missense	CD2AP	NM_012120.2	58	0,48,6455	GG,GA,AA		0.5349,0.0454,0.3691	benign	374/640	47563608	48,12958	2203	4300	6503	SO:0001583	missense	23607	exon12			AAATCAACACTGG	AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.1120A>G	6.37:g.47563608A>G	ENSP00000352264:p.Thr374Ala	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	8	0.003663003663003663	0	0.0	6	0.016574585635359115	0	0.0	2	0.002638522427440633	A	3.633	-0.075108	0.07184	4.54E-4	0.005349	ENSG00000198087	ENST00000359314	T	0.22945	1.93	5.57	-5.18	0.02840	.	5.281300	0.00481	N	0.000133	T	0.01627	0.0052	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21690	-1.0238	10	0.07644	T	0.81	4.6781	2.2995	0.04159	0.4573:0.1057:0.271:0.166	.	374	Q9Y5K6	CD2AP_HUMAN	A	374	ENSP00000352264:T374A	ENSP00000352264:T374A	T	+	1	0	CD2AP	47671567	0.000000	0.05858	0.011000	0.14972	0.933000	0.57130	-1.282000	0.02799	-0.673000	0.05259	-0.467000	0.05162	ACA	A|0.995;G|0.005	0.005	strong		0.353	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2		
VPS13D	55187	hgsc.bcm.edu	37	1	12443033	12443033	+	Splice_Site	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12443033A>G	ENST00000358136.3	+	58	11320		c.e58-1		VPS13D_ENST00000356315.4_Splice_Site|VPS13D_ENST00000496628.1_Splice_Site	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)		AATGTCTTTTAGGCCAAAGGA	0.423																																					.		Atlas-SNP	.											VPS13D,NS,carcinoma,0,1	VPS13D	316	1	0			c.11191-2A>G						scavenged	.						190.0	176.0	181.0					1																	12443033		2203	4300	6503	SO:0001630	splice_region_variant	55187	exon58			TCTTTTAGGCCAA	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.11191-1A>G	1.37:g.12443033A>G		Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	209	3	0.0143541	NM_015378		Splice_Site	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	A	20.5	4.000790	0.74818	.	.	ENSG00000048707	ENST00000356315;ENST00000358136;ENST00000011700	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4447	0.83919	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VPS13D	12365620	1.000000	0.71417	0.954000	0.39281	0.755000	0.42902	8.603000	0.90871	2.284000	0.76573	0.528000	0.53228	.	.	.	none		0.423	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	Intron
PCDHGB3	56102	hgsc.bcm.edu	37	5	140751128	140751128	+	Missense_Mutation	SNP	C	C	G	rs2240697	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140751128C>G	ENST00000576222.1	+	1	1298	c.1167C>G	c.(1165-1167)aaC>aaG	p.N389K	PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	389	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		N -> K (in dbSNP:rs2240697).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAAAAGGAAACTTCCCCTTTA	0.443													.|||	2801	0.559305	0.8994	0.6326	5008	,	,		21441	0.3274		0.4264	False		,,,				2504	0.4233				p.N389K		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.C1167G						PASS	.	G	,,,,,,,LYS/ASN,LYS/ASN	3221,629		1358,505,62	53.0	54.0	54.0		,,,,,,,1167,1167	-9.9	0.0	5	dbSNP_98	54	3580,4674		759,2062,1306	yes	intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032097.1	,,,,,,,94,94	2117,2567,1368	GG,GC,CC		43.3729,16.3377,43.812	,,,,,,,,	,,,,,,,389/930,389/815	140751128	6801,5303	1925	4127	6052	SO:0001583	missense	56102	exon1			AGGAAACTTCCCC	AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.1167C>G	5.37:g.140751128C>G	ENSP00000461862:p.Asn389Lys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			C|0.477;G|0.523	0.523	strong		0.443	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
AKAP6	9472	hgsc.bcm.edu	37	14	33004975	33004975	+	Silent	SNP	G	G	A	rs35436895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:33004975G>A	ENST00000280979.4	+	3	710	c.540G>A	c.(538-540)acG>acA	p.T180T	AKAP6_ENST00000557272.1_Silent_p.T180T|AKAP6_ENST00000557354.1_Silent_p.T180T	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	180					action potential (GO:0001508)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cAMP biosynthetic process (GO:0030818)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell growth (GO:0030307)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of delayed rectifier potassium channel activity (GO:1902261)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of potassium ion transmembrane transport (GO:1901381)|positive regulation of protein phosphatase type 2B activity (GO:0032514)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|protein targeting (GO:0006605)|regulation of membrane repolarization (GO:0060306)|regulation of protein kinase A signaling (GO:0010738)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)	calcium channel complex (GO:0034704)|caveola (GO:0005901)|cytoplasm (GO:0005737)|intercalated disc (GO:0014704)|junctional sarcoplasmic reticulum membrane (GO:0014701)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	adenylate cyclase binding (GO:0008179)|ion channel binding (GO:0044325)|protein anchor (GO:0043495)|protein complex scaffold (GO:0032947)|protein kinase A binding (GO:0051018)|protein kinase A regulatory subunit binding (GO:0034237)			NS(2)|breast(10)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(25)|lung(42)|ovary(5)|pancreas(2)|prostate(3)|skin(9)|urinary_tract(2)	122	Breast(36;0.0388)|Prostate(35;0.15)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00677)|STAD - Stomach adenocarcinoma(7;0.116)	GBM - Glioblastoma multiforme(265;0.019)		CTAGGCAGACGGACATTCTGC	0.493													G|||	328	0.0654952	0.1483	0.0533	5008	,	,		21839	0.001		0.0606	False		,,,				2504	0.0337				p.T180T	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.G540A						PASS	.	G		629,3777	272.5+/-270.8	37,555,1611	87.0	86.0	87.0		540	-8.7	0.8	14	dbSNP_126	87	499,8101	143.1+/-199.2	13,473,3814	no	coding-synonymous	AKAP6	NM_004274.4		50,1028,5425	AA,AG,GG		5.8023,14.276,8.6729		180/2320	33004975	1128,11878	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon3			GCAGACGGACATT	AB002309	CCDS9644.1	14q12	2008-08-11			ENSG00000151320	ENSG00000151320		"""A-kinase anchor proteins"""	376	protein-coding gene	gene with protein product	"""protein kinase A anchoring protein 6"""	604691				7721854, 9205841	Standard	NM_004274		Approved	KIAA0311, mAKAP, AKAP100, PRKA6, ADAP6	uc001wrq.3	Q13023	OTTHUMG00000140207	ENST00000280979.4:c.540G>A	14.37:g.33004975G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	183	85	0.464481	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			G|0.924;A|0.076	0.076	strong		0.493	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274	
SP1	6667	hgsc.bcm.edu	37	12	53777171	53777171	+	Silent	SNP	A	A	G	rs3741651	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:53777171A>G	ENST00000327443.4	+	3	1538	c.1440A>G	c.(1438-1440)caA>caG	p.Q480Q	SP1_ENST00000426431.2_Silent_p.Q473Q	NM_001251825.1|NM_138473.2	NP_001238754.1|NP_612482.2	P08047	SP1_HUMAN	Sp1 transcription factor	480	Transactivation domain B (Gln-rich).				cellular lipid metabolic process (GO:0044255)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic placenta development (GO:0001892)|embryonic process involved in female pregnancy (GO:0060136)|embryonic skeletal system development (GO:0048706)|enucleate erythrocyte differentiation (GO:0043353)|gene expression (GO:0010467)|liver development (GO:0001889)|lung development (GO:0030324)|megakaryocyte differentiation (GO:0030219)|ossification (GO:0001503)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|trophectodermal cell differentiation (GO:0001829)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	bHLH transcription factor binding (GO:0043425)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|histone deacetylase binding (GO:0042826)|HMG box domain binding (GO:0071837)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.00527)		CACAAGCCCAAACAATCACCT	0.557													G|||	941	0.187899	0.2216	0.2147	5008	,	,		21711	0.1796		0.162	False		,,,				2504	0.1585				p.Q480Q		Atlas-SNP	.											.	SP1	57	.	0			c.A1440G						PASS	.	G	,	884,3522	742.6+/-411.4	95,694,1414	169.0	162.0	164.0		1419,1440	4.7	1.0	12	dbSNP_107	164	1506,7094	748.0+/-407.3	126,1254,2920	no	coding-synonymous,coding-synonymous	SP1	NM_003109.1,NM_138473.2	,	221,1948,4334	GG,GA,AA		17.5116,20.0635,18.3761	,	473/779,480/786	53777171	2390,10616	2203	4300	6503	SO:0001819	synonymous_variant	6667	exon3			AGCCCAAACAATC	J03133	CCDS8857.1, CCDS44898.1	12q13.1	2013-01-08						"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11205	protein-coding gene	gene with protein product	"""specificity protein 1"""	189906				1662663	Standard	NM_003109		Approved		uc001scw.3	P08047	OTTHUMG00000170047	ENST00000327443.4:c.1440A>G	12.37:g.53777171A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	160	86	0.5375	NM_138473	E4Z9M7|G5E9M8|Q86TN8|Q9H3Q5|Q9NR51|Q9NY21|Q9NYE7	Silent	SNP	ENST00000327443.4	37	CCDS8857.1																																																																																			A|0.814;G|0.186	0.186	strong		0.557	SP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407044.1		
CYP26C1	340665	hgsc.bcm.edu	37	10	94824166	94824166	+	Missense_Mutation	SNP	G	G	A	rs11187265	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:94824166G>A	ENST00000285949.5	+	4	734	c.734G>A	c.(733-735)cGg>cAg	p.R245Q		NM_183374.2	NP_899230.2	Q6V0L0	CP26C_HUMAN	cytochrome P450, family 26, subfamily C, polypeptide 1	245			R -> Q (in dbSNP:rs11187265).		anterior/posterior pattern specification (GO:0009952)|central nervous system development (GO:0007417)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|organelle fusion (GO:0048284)|oxidation-reduction process (GO:0055114)|retinoic acid catabolic process (GO:0034653)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|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)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			central_nervous_system(1)|lung(3)|ovary(1)	5		Colorectal(252;0.122)				CAGCTGCATCGGCACCTGGAG	0.602													g|||	370	0.0738818	0.0696	0.1643	5008	,	,		20138	0.001		0.0924	False		,,,				2504	0.0716				p.R245Q		Atlas-SNP	.											.	CYP26C1	25	.	0			c.G734A						PASS	.	A	GLN/ARG	310,4096	165.4+/-196.9	14,282,1907	54.0	52.0	52.0		734	-5.5	0.9	10	dbSNP_120	52	796,7804	186.7+/-234.1	36,724,3540	yes	missense	CYP26C1	NM_183374.2	43	50,1006,5447	AA,AG,GG		9.2558,7.0359,8.5038	benign	245/523	94824166	1106,11900	2203	4300	6503	SO:0001583	missense	340665	exon4			TGCATCGGCACCT		CCDS7425.1	10q23.33	2003-11-20			ENSG00000187553	ENSG00000187553		"""Cytochrome P450s"""	20577	protein-coding gene	gene with protein product		608428					Standard	XR_246086		Approved		uc010qns.2	Q6V0L0	OTTHUMG00000018766	ENST00000285949.5:c.734G>A	10.37:g.94824166G>A	ENSP00000285949:p.Arg245Gln	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_183374	Q5VXH6	Missense_Mutation	SNP	ENST00000285949.5	37	CCDS7425.1	169	0.07738095238095238	42	0.08536585365853659	59	0.16298342541436464	1	0.0017482517482517483	67	0.08839050131926121	g	12.30	1.897735	0.33535	0.070359	0.092558	ENSG00000187553	ENST00000285949	T	0.65916	-0.18	5.33	-5.47	0.02600	.	1.122760	0.06534	N	0.742051	T	0.00210	0.0006	N	0.13043	0.29	0.80722	P	0.0	B	0.06786	0.001	B	0.13407	0.009	T	0.04103	-1.0977	9	0.31617	T	0.26	-4.0957	16.8136	0.85727	0.8792:0.0:0.1208:0.0	rs11187265;rs58644142	245	Q6V0L0	CP26C_HUMAN	Q	245	ENSP00000285949:R245Q	ENSP00000285949:R245Q	R	+	2	0	CYP26C1	94814156	0.004000	0.15560	0.879000	0.34478	0.768000	0.43524	0.072000	0.14617	-0.815000	0.04346	-2.396000	0.00226	CGG	G|0.914;A|0.086	0.086	strong		0.602	CYP26C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049409.2	NM_183374	
CPNE3	8895	hgsc.bcm.edu	37	8	87567193	87567193	+	Missense_Mutation	SNP	C	C	T	rs2304789	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:87567193C>T	ENST00000521271.1	+	15	1397	c.1235C>T	c.(1234-1236)aCg>aTg	p.T412M	CPNE3_ENST00000198765.4_Missense_Mutation_p.T412M	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	412	VWFA.		T -> M (in dbSNP:rs2304789). {ECO:0000269|PubMed:14702039}.		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						GCTGCAGCCACGCAACAGCAG	0.463													C|||	1066	0.212859	0.2829	0.17	5008	,	,		17111	0.0139		0.332	False		,,,				2504	0.2311				p.T412M		Atlas-SNP	.											.	CPNE3	65	.	0			c.C1235T						PASS	.	C	MET/THR	1380,3026	454.0+/-350.5	217,946,1040	110.0	102.0	105.0		1235	5.7	1.0	8	dbSNP_100	105	2740,5860	437.5+/-358.6	427,1886,1987	yes	missense	CPNE3	NM_003909.3	81	644,2832,3027	TT,TC,CC		31.8605,31.3209,31.6777	benign	412/538	87567193	4120,8886	2203	4300	6503	SO:0001583	missense	8895	exon15			CAGCCACGCAACA	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.1235C>T	8.37:g.87567193C>T	ENSP00000430934:p.Thr412Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_003909	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	479	0.21932234432234432	155	0.3150406504065041	69	0.19060773480662985	10	0.017482517482517484	245	0.3232189973614776	C	14.49	2.550189	0.45383	0.313209	0.318605	ENSG00000085719	ENST00000198765;ENST00000521271	T;T	0.23348	1.91;1.91	5.66	5.66	0.87406	von Willebrand factor, type A (1);Copine (1);	0.224009	0.46758	D	0.000267	T	0.00012	0.0000	L	0.38649	1.16	0.09310	P	1.0	P	0.34826	0.471	B	0.32624	0.149	T	0.44832	-0.9302	9	0.42905	T	0.14	-22.0502	20.1115	0.97913	0.0:1.0:0.0:0.0	rs2304789;rs59566172;rs2304789	412	O75131	CPNE3_HUMAN	M	412	ENSP00000198765:T412M;ENSP00000430934:T412M	ENSP00000198765:T412M	T	+	2	0	CPNE3	87636309	0.936000	0.31750	0.998000	0.56505	0.958000	0.62258	3.088000	0.50175	2.814000	0.96858	0.655000	0.94253	ACG	C|0.730;T|0.270	0.270	strong		0.463	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1		
C5orf45	51149	hgsc.bcm.edu	37	5	179280379	179280379	+	Splice_Site	SNP	T	T	C	rs1650893	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:179280379T>C	ENST00000292586.6	-	2	215	c.125A>G	c.(124-126)cAg>cGg	p.Q42R	C5orf45_ENST00000518235.1_Splice_Site_p.Q42R|C5orf45_ENST00000523084.1_5'UTR|C5orf45_ENST00000518219.1_Splice_Site_p.Q42R|C5orf45_ENST00000403396.2_Splice_Site_p.A57A|C5orf45_ENST00000520698.1_Splice_Site_p.Q42R|C5orf45_ENST00000521333.1_Splice_Site_p.Q42R|C5orf45_ENST00000376931.2_Splice_Site_p.Q42R	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	42			Q -> R (in dbSNP:rs1650893).							breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						AGGACTCACCTGCAAAAAGGA	0.468																																					p.Q42R		Atlas-SNP	.											.	C5orf45	23	.	0			c.A125G						PASS	.	C	ARG/GLN,ARG/GLN	3826,580	257.7+/-262.0	1667,492,44	87.0	86.0	86.0		125,125	2.2	1.0	5	dbSNP_89	86	4692,3908	546.4+/-385.0	1302,2088,910	yes	missense-near-splice,missense-near-splice	C5orf45	NM_001017987.2,NM_016175.3	43,43	2969,2580,954	CC,CT,TT		45.4419,13.1639,34.5072	benign,benign	42/289,42/344	179280379	8518,4488	2203	4300	6503	SO:0001630	splice_region_variant	51149	exon2			CTCACCTGCAAAA		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.126+1A>G	5.37:g.179280379T>C		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	37	CCDS34319.1	1527	0.6991758241758241	450	0.9146341463414634	242	0.6685082872928176	454	0.7937062937062938	381	0.5026385224274407	C	4.225	0.040529	0.08196	0.868361	0.545581	ENSG00000161010	ENST00000518235;ENST00000520698;ENST00000376931;ENST00000518219;ENST00000292586;ENST00000521333	T;T;T;T;T;T	0.22539	3.15;1.95;2.03;3.15;3.15;3.15	4.03	2.25	0.28309	.	0.407546	0.18935	N	0.127081	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.9999999999957803	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	0.36407	-0.9749	9	0.02654	T	1	-19.3807	6.5112	0.22222	0.0:0.6013:0.0:0.3987	rs1650893;rs17680752;rs57810424;rs1650893	42;42;42;42	E7EMV9;B7Z1T6;E9PAK6;Q6NTE8	.;.;.;CE045_HUMAN	R	42	ENSP00000430298:Q42R;ENSP00000427849:Q42R;ENSP00000366130:Q42R;ENSP00000428460:Q42R;ENSP00000292586:Q42R;ENSP00000429651:Q42R	ENSP00000292586:Q42R	Q	-	2	0	C5orf45	179212985	0.211000	0.23529	0.982000	0.44146	0.812000	0.45895	0.012000	0.13287	0.281000	0.22233	-0.119000	0.15052	CAG	T|0.318;C|0.682	0.682	strong		0.468	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	Missense_Mutation
KCNH8	131096	hgsc.bcm.edu	37	3	19498417	19498417	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:19498417C>T	ENST00000328405.2	+	11	2249	c.1983C>T	c.(1981-1983)ttC>ttT	p.F661F		NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8	661					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)	p.F661F(1)		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						CTCACAAATTCGTGGAAGACA	0.413																																					p.F661F	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											KCNH8,rectum,carcinoma,0,2	KCNH8	189	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C1983T						scavenged	.						133.0	112.0	119.0					3																	19498417		2203	4298	6501	SO:0001819	synonymous_variant	131096	exon11			CAAATTCGTGGAA	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.1983C>T	3.37:g.19498417C>T		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	187	3	0.0160428	NM_144633	B7Z2I7|Q59GQ6	Silent	SNP	ENST00000328405.2	37	CCDS2632.1																																																																																			.	.	none		0.413	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	
FAM187B	148109	hgsc.bcm.edu	37	19	35718938	35718938	+	Missense_Mutation	SNP	C	C	T	rs564117	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35718938C>T	ENST00000324675.3	-	1	694	c.646G>A	c.(646-648)Gtc>Atc	p.V216I		NM_152481.1	NP_689694.1	Q17R55	F187B_HUMAN	family with sequence similarity 187, member B	216			V -> I (in dbSNP:rs564117).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	9						TCAAAAATGACGTAATCCACC	0.542													C|||	863	0.172324	0.2716	0.1354	5008	,	,		20025	0.0188		0.2008	False		,,,				2504	0.1933				p.V216I		Atlas-SNP	.											FAM187B,caecum,carcinoma,0,1	FAM187B	28	1	0			c.G646A						PASS	.	C	ILE/VAL	1161,3245	409.3+/-334.9	164,833,1206	99.0	82.0	88.0		646	-10.0	0.0	19	dbSNP_83	88	1679,6921	306.9+/-308.1	165,1349,2786	yes	missense	FAM187B	NM_152481.1	29	329,2182,3992	TT,TC,CC		19.5233,26.3504,21.8361	benign	216/370	35718938	2840,10166	2203	4300	6503	SO:0001583	missense	148109	exon1			AAATGACGTAATC	AK098526	CCDS12448.1	19q13.12	2008-10-16	2008-10-16	2008-10-16	ENSG00000177558	ENSG00000177558			26366	protein-coding gene	gene with protein product			"""transmembrane protein 162"""	TMEM162			Standard	NM_152481		Approved	FLJ25660	uc002nyk.1	Q17R55	OTTHUMG00000164450	ENST00000324675.3:c.646G>A	19.37:g.35718938C>T	ENSP00000323355:p.Val216Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	199	95	0.477387	NM_152481	Q8N7G6	Missense_Mutation	SNP	ENST00000324675.3	37	CCDS12448.1	332	0.152014652014652	123	0.25	62	0.1712707182320442	3	0.005244755244755245	144	0.18997361477572558	C	6.670	0.492149	0.12702	0.263504	0.195233	ENSG00000177558	ENST00000324675	T	0.22945	1.93	5.01	-10.0	0.00425	.	1.372100	0.05061	N	0.479938	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B	0.24368	0.102	B	0.17979	0.02	T	0.22208	-1.0223	9	0.06099	T	0.92	-9.6868	4.7828	0.13210	0.1076:0.2031:0.106:0.5833	rs564117;rs52835776;rs56745910;rs564117	216	Q17R55	F187B_HUMAN	I	216	ENSP00000323355:V216I	ENSP00000323355:V216I	V	-	1	0	FAM187B	40410778	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.444000	0.01012	-1.365000	0.02158	-0.150000	0.13652	GTC	C|0.811;T|0.189	0.189	strong		0.542	FAM187B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378854.1	NM_152481	
TEKT1	83659	hgsc.bcm.edu	37	17	6716242	6716242	+	Missense_Mutation	SNP	G	G	A	rs3744395	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6716242G>A	ENST00000338694.2	-	6	889	c.760C>T	c.(760-762)Cgc>Tgc	p.R254C	TEKT1_ENST00000535086.1_Missense_Mutation_p.R108C	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	254			R -> C (in dbSNP:rs3744395).			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)				CACTGCTTGCGCAGATCATTG	0.547													G|||	1234	0.246406	0.1006	0.2853	5008	,	,		19693	0.4365		0.2087	False		,,,				2504	0.2587				p.R254C		Atlas-SNP	.											.	TEKT1	49	.	0			c.C760T						PASS	.	G	CYS/ARG	541,3865	246.2+/-254.9	40,461,1702	205.0	170.0	182.0		760	0.2	0.5	17	dbSNP_107	182	1780,6820	321.3+/-315.0	178,1424,2698	yes	missense	TEKT1	NM_053285.1	180	218,1885,4400	AA,AG,GG		20.6977,12.2787,17.8456	benign	254/419	6716242	2321,10685	2203	4300	6503	SO:0001583	missense	83659	exon6			GCTTGCGCAGATC		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.760C>T	17.37:g.6716242G>A	ENSP00000341346:p.Arg254Cys	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	163	89	0.546012	NM_053285	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	37	CCDS11083.1	543	0.24862637362637363	38	0.07723577235772358	85	0.23480662983425415	267	0.46678321678321677	153	0.20184696569920843	G	10.51	1.371713	0.24857	0.122787	0.206977	ENSG00000167858	ENST00000338694;ENST00000535086	T;T	0.03004	4.08;4.08	4.79	0.207	0.15214	.	0.388910	0.29152	N	0.012988	T	0.00012	0.0000	L	0.42632	1.34	0.23043	P	0.99838246	B	0.19583	0.037	B	0.21546	0.035	T	0.43523	-0.9386	9	0.45353	T	0.12	.	4.4768	0.11748	0.1689:0.0:0.3788:0.4522	rs3744395;rs52821534;rs57626019;rs3744395	254	Q969V4	TEKT1_HUMAN	C	254;108	ENSP00000341346:R254C;ENSP00000444142:R108C	ENSP00000341346:R254C	R	-	1	0	TEKT1	6656966	0.970000	0.33590	0.489000	0.27452	0.533000	0.34776	1.082000	0.30803	-0.088000	0.12506	0.591000	0.81541	CGC	G|0.790;A|0.210	0.210	strong		0.547	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285	
C14orf182	283551	hgsc.bcm.edu	37	14	50472405	50472405	+	Missense_Mutation	SNP	G	G	A	rs6572635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:50472405G>A	ENST00000399206.1	-	1	1833	c.113C>T	c.(112-114)cCg>cTg	p.P38L	C14orf182_ENST00000529902.1_5'UTR	NM_001012706.1	NP_001012724.1	A1A4T8	CN182_HUMAN	chromosome 14 open reading frame 182	38			P -> L (in dbSNP:rs6572635).							large_intestine(2)|urinary_tract(1)	3						AAGACCTCTCGGTTCGTGAAT	0.537													G|||	1481	0.295727	0.3873	0.317	5008	,	,		18805	0.124		0.2773	False		,,,				2504	0.3528				p.P38L		Atlas-SNP	.											C14orf182,bladder,carcinoma,+1,1	C14orf182	8	1	0			c.C113T						PASS	.	G	LEU/PRO	1523,2561		289,945,808	269.0	286.0	281.0		113	1.7	0.0	14	dbSNP_116	281	2240,6136		301,1638,2249	yes	missense	C14orf182	NM_001012706.1	98	590,2583,3057	AA,AG,GG		26.7431,37.2919,30.2006	probably-damaging	38/108	50472405	3763,8697	2042	4188	6230	SO:0001583	missense	283551	exon1			CCTCTCGGTTCGT	AK090420	CCDS41949.1	14q22.1	2009-02-24			ENSG00000214900	ENSG00000214900			27503	protein-coding gene	gene with protein product							Standard	NM_001012706		Approved		uc001wxi.1	A1A4T8		ENST00000399206.1:c.113C>T	14.37:g.50472405G>A	ENSP00000382157:p.Pro38Leu	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	223	100	0.44843	NM_001012706	A8MYX4	Missense_Mutation	SNP	ENST00000399206.1	37	CCDS41949.1	555	0.2541208791208791	165	0.3353658536585366	106	0.292817679558011	79	0.1381118881118881	205	0.2704485488126649	G	10.57	1.385916	0.25031	0.372919	0.267431	ENSG00000214900	ENST00000399206	T	0.62639	0.01	3.63	1.72	0.24424	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.36412	0.552	B	0.28916	0.096	T	0.29427	-1.0012	7	0.87932	D	0	.	4.3609	0.11201	0.1184:0.0:0.6603:0.2213	rs6572635;rs56709337;rs6572635	38	A1A4T8-2	.	L	38	ENSP00000382157:P38L	ENSP00000382157:P38L	P	-	2	0	C14orf182	49542155	0.050000	0.20438	0.004000	0.12327	0.014000	0.08584	0.925000	0.28791	0.492000	0.27815	-0.263000	0.10527	CCG	G|0.739;A|0.261	0.261	strong		0.537	C14orf182-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395717.1	NM_001012706	
ACADL	33	hgsc.bcm.edu	37	2	211068100	211068100	+	Silent	SNP	A	A	G	rs148069105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211068100A>G	ENST00000233710.3	-	8	1166	c.939T>C	c.(937-939)taT>taC	p.Y313Y	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	313					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		TTTGTTTAACATAGTTCCTGG	0.343																																					p.Y313Y		Atlas-SNP	.											.	ACADL	38	.	0			c.T939C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	113.0	98.0	103.0		939	-5.7	0.9	2	dbSNP_134	103	12,8586	9.1+/-34.3	0,12,4287	no	coding-synonymous	ACADL	NM_001608.3		0,13,6489	GG,GA,AA		0.1396,0.0227,0.1		313/431	211068100	13,12991	2203	4299	6502	SO:0001819	synonymous_variant	33	exon8			TTTAACATAGTTC	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"""acyl-Coenzyme A dehydrogenase, long chain"""			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.939T>C	2.37:g.211068100A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_001608	B2R8T3|Q8IUN8	Silent	SNP	ENST00000233710.3	37	CCDS2389.1																																																																																			A|0.999;G|0.001	0.001	strong		0.343	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	
POMGNT2	84892	hgsc.bcm.edu	37	3	43121743	43121743	+	Missense_Mutation	SNP	C	C	T	rs199612856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:43121743C>T	ENST00000344697.2	-	2	1526	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R394Q	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	394					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										CATCATGTTCCGCCAGGCTAC	0.587													C|||	5	0.000998403	0.0	0.0	5008	,	,		22992	0.002		0.0	False		,,,				2504	0.0031				p.R394Q		Atlas-SNP	.											.	.	.	.	0			c.G1181A						PASS	.						80.0	71.0	74.0					3																	43121743		2203	4300	6503	SO:0001583	missense	84892	exon2			ATGTTCCGCCAGG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1181G>A	3.37:g.43121743C>T	ENSP00000344125:p.Arg394Gln	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	185	92	0.497297	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	11.87	1.767376	0.31320	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.77229	-1.08;-1.08	5.53	1.22	0.21188	.	0.363726	0.31233	N	0.008011	T	0.57946	0.2088	N	0.17278	0.47	0.37391	D	0.912468	B	0.09022	0.002	B	0.10450	0.005	T	0.48127	-0.9062	10	0.30078	T	0.28	-25.7255	7.9623	0.30079	0.0:0.4895:0.0:0.5105	.	394	Q8NAT1	AGO61_HUMAN	Q	394	ENSP00000408992:R394Q;ENSP00000344125:R394Q	ENSP00000344125:R394Q	R	-	2	0	C3orf39	43096747	0.970000	0.33590	0.988000	0.46212	0.986000	0.74619	0.528000	0.23002	0.318000	0.23185	0.650000	0.86243	CGG	C|1.000;T|0.000	0.000	strong		0.587	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
MYBPC2	4606	hgsc.bcm.edu	37	19	50967640	50967640	+	Missense_Mutation	SNP	G	G	A	rs25667	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50967640G>A	ENST00000357701.5	+	27	3317	c.3266G>A	c.(3265-3267)cGt>cAt	p.R1089H		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	1089	Ig-like C2-type 7.		R -> H (in dbSNP:rs25667).		cell adhesion (GO:0007155)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			breast(1)	1		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.0079)|GBM - Glioblastoma multiforme(134;0.0144)		ATGGAAATCCGTGAAGATCCC	0.537													G|||	705	0.140775	0.0136	0.2522	5008	,	,		20485	0.126		0.2207	False		,,,				2504	0.1667				p.R1089H		Atlas-SNP	.											.	MYBPC2	103	.	0			c.G3266A						PASS	.	G	HIS/ARG	171,4039		2,167,1936	55.0	59.0	58.0		3266	-0.5	0.0	19	dbSNP_72	58	1622,6868		164,1294,2787	yes	missense	MYBPC2	NM_004533.3	29	166,1461,4723	AA,AG,GG		19.1048,4.0618,14.1181	benign	1089/1142	50967640	1793,10907	2105	4245	6350	SO:0001583	missense	4606	exon27			AAATCCGTGAAGA		CCDS46152.1	19q13.33	2013-02-11	2001-11-28		ENSG00000086967	ENSG00000086967		"""Myosin binding proteins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7550	protein-coding gene	gene with protein product	"""fast-type muscle myosin-binding-protein C"""	160793	"""myosin-binding protein C, fast-type"""			8375400	Standard	NM_004533		Approved	MYBPCF, MYBPC, MGC163408	uc002psf.2	Q14324		ENST00000357701.5:c.3266G>A	19.37:g.50967640G>A	ENSP00000350332:p.Arg1089His	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	57	23	0.403509	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	339	0.15521978021978022	9	0.018292682926829267	88	0.2430939226519337	80	0.13986013986013987	162	0.21372031662269128	g	2.377	-0.342929	0.05243	0.040618	0.191048	ENSG00000086967	ENST00000357701	T	0.68331	-0.32	3.99	-0.521	0.11931	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.234288	0.17079	N	0.187854	T	0.00012	0.0000	N	0.16862	0.45	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.06679	-1.0813	9	0.45353	T	0.12	.	5.3863	0.16220	0.2583:0.1555:0.5862:0.0	rs25667;rs2230840;rs17403009;rs17718746;rs52798518;rs56519860;rs61720718;rs17403009	1089	Q14324	MYPC2_HUMAN	H	1089	ENSP00000350332:R1089H	ENSP00000350332:R1089H	R	+	2	0	MYBPC2	55659452	0.000000	0.05858	0.001000	0.08648	0.385000	0.30292	0.074000	0.14662	0.199000	0.20427	0.457000	0.33378	CGT	A|0.143;C|0.000;G|0.857	0.143	strong		0.537	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533	
CLRN2	645104	hgsc.bcm.edu	37	4	17524570	17524570	+	Missense_Mutation	SNP	C	C	G	rs13147559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:17524570C>G	ENST00000511148.2	+	2	439	c.337C>G	c.(337-339)Ctg>Gtg	p.L113V		NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	113			L -> V (in dbSNP:rs13147559).			integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						GGCCCTGGCTCTGGTCAGCAT	0.577													C|||	479	0.095647	0.0053	0.1513	5008	,	,		18490	0.0893		0.1342	False		,,,				2504	0.1452				p.L113V		Atlas-SNP	.											.	CLRN2	40	.	0			c.C337G						PASS	.	C	VAL/LEU	127,4155		0,127,2014	103.0	109.0	107.0		337	4.2	1.0	4	dbSNP_121	107	1141,7363		91,959,3202	yes	missense	CLRN2	NM_001079827.2	32	91,1086,5216	GG,GC,CC		13.4172,2.9659,9.9171	benign	113/233	17524570	1268,11518	2141	4252	6393	SO:0001583	missense	645104	exon2			CTGGCTCTGGTCA		CCDS47032.1	4p15.32	2008-01-17			ENSG00000249581	ENSG00000249581			33939	protein-coding gene	gene with protein product						12080385	Standard	NM_001079827		Approved		uc003gpg.1	A0PK11	OTTHUMG00000160273	ENST00000511148.2:c.337C>G	4.37:g.17524570C>G	ENSP00000424711:p.Leu113Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_001079827		Missense_Mutation	SNP	ENST00000511148.2	37	CCDS47032.1	204	0.09340659340659341	6	0.012195121951219513	38	0.10497237569060773	51	0.08916083916083917	109	0.1437994722955145	C	16.71	3.197607	0.58126	0.029659	0.134172	ENSG00000249581	ENST00000511148	D	0.83419	-1.72	5.06	4.22	0.49857	.	0.088467	0.47455	D	0.000233	T	0.02083	0.0065	L	0.38175	1.15	0.22771	P	0.99875403	P	0.47484	0.896	P	0.46758	0.526	T	0.47611	-0.9104	9	0.42905	T	0.14	-13.4468	13.1191	0.59316	0.0:0.9213:0.0:0.0787	rs13147559;rs17518172;rs13147559	113	A0PK11	CLRN2_HUMAN	V	113	ENSP00000424711:L113V	ENSP00000424711:L113V	L	+	1	2	CLRN2	17133668	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.944000	0.56629	1.148000	0.42385	-0.253000	0.11424	CTG	C|0.904;G|0.095	0.095	strong		0.577	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827	
ESPN	83715	hgsc.bcm.edu	37	1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	rs200602012		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:6500762G>A	ENST00000377828.1	+	4	920	c.752G>A	c.(751-753)gGc>gAc	p.G251D	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	251					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GCGAGCCGCGGCCACACCAAG	0.726																																					p.G251D		Atlas-SNP	.											.	ESPN	32	.	0			c.G752A						PASS	.						5.0	6.0	5.0					1																	6500762		1942	3927	5869	SO:0001583	missense	83715	exon4			GCCGCGGCCACAC	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.752G>A	1.37:g.6500762G>A	ENSP00000367059:p.Gly251Asp	Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	16	11	0.6875	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650081	0.87958	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.72394	-0.65;0.89	3.84	3.84	0.44239	Ankyrin repeat-containing domain (5);	0.233607	0.34959	N	0.003544	T	0.81772	0.4893	M	0.80982	2.52	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	D	0.83857	0.0266	10	0.54805	T	0.06	-5.9744	12.6418	0.56714	0.0:0.0:1.0:0.0	.	251	B1AK53	ESPN_HUMAN	D	251;36	ENSP00000367059:G251D;ENSP00000401793:G36D	ENSP00000367059:G251D	G	+	2	0	ESPN	6423349	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.972000	0.93424	1.989000	0.58080	0.430000	0.28490	GGC	G|0.991;A|0.010	0.010	weak		0.726	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
TRPC1	7220	hgsc.bcm.edu	37	3	142524858	142524858	+	Silent	SNP	G	G	A	rs1132030	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142524858G>A	ENST00000476941.1	+	13	2649	c.2163G>A	c.(2161-2163)agG>agA	p.R721R	TRPC1_ENST00000273482.6_Silent_p.R687R	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	721					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						AGGAATGGAGGAATTTGAAAC	0.348													A|||	1832	0.365815	0.736	0.1772	5008	,	,		17698	0.3552		0.2058	False		,,,				2504	0.1748				p.R721R		Atlas-SNP	.											.	TRPC1	82	.	0			c.G2163A						PASS	.	A		2808,1598	492.0+/-362.3	898,1012,293	91.0	102.0	98.0		2061	3.0	1.0	3	dbSNP_86	98	1606,6994	741.3+/-407.1	168,1270,2862	no	coding-synonymous	TRPC1	NM_003304.4		1066,2282,3155	AA,AG,GG		18.6744,36.2687,33.9382		687/760	142524858	4414,8592	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon13			ATGGAGGAATTTG	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.2163G>A	3.37:g.142524858G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	143	69	0.482517	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			A|0.353;G|0.647;T|0.000	0.353	strong		0.348	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
OR9K2	441639	hgsc.bcm.edu	37	12	55523860	55523860	+	Missense_Mutation	SNP	A	A	C	rs7305779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55523860A>C	ENST00000305377.5	+	1	396	c.308A>C	c.(307-309)gAa>gCa	p.E103A		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	103			E -> A (in dbSNP:rs7305779).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						TCTGTTATTGAACCCAAGGCT	0.423													C|||	1523	0.304113	0.4085	0.2421	5008	,	,		21118	0.1141		0.334	False		,,,				2504	0.3722				p.E103A		Atlas-SNP	.											.	OR9K2	63	.	0			c.A308C						PASS	.	C	ALA/GLU	1703,2703	652.6+/-399.4	308,1087,808	150.0	150.0	150.0		308	5.0	1.0	12	dbSNP_116	150	2777,5823	678.6+/-403.5	456,1865,1979	yes	missense	OR9K2	NM_001005243.1	107	764,2952,2787	CC,CA,AA		32.2907,38.6518,34.4456	benign	103/336	55523860	4480,8526	2203	4300	6503	SO:0001583	missense	441639	exon1			TTATTGAACCCAA	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.308A>C	12.37:g.55523860A>C	ENSP00000307598:p.Glu103Ala	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	624	0.2857142857142857	200	0.4065040650406504	102	0.281767955801105	73	0.12762237762237763	249	0.32849604221635886	C	0.294	-0.977862	0.02197	0.386518	0.322907	ENSG00000170605	ENST00000305377	T	0.00892	5.57	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	N	0.000123	T	0.00012	0.0000	N	0.00135	-2.02	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15350	-1.0440	9	0.17832	T	0.49	-6.9223	6.3141	0.21180	0.1599:0.695:0.0:0.1451	rs7305779;rs52807355;rs60412666;rs7305779	103	Q8NGE7	OR9K2_HUMAN	A	103	ENSP00000307598:E103A	ENSP00000307598:E103A	E	+	2	0	OR9K2	53810127	0.000000	0.05858	0.995000	0.50966	0.896000	0.52359	0.353000	0.20130	1.482000	0.48325	-0.127000	0.14921	GAA	A|0.677;C|0.323	0.323	strong		0.423	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
LGALS3BP	3959	hgsc.bcm.edu	37	17	76970803	76970803	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76970803G>A	ENST00000262776.3	-	4	651	c.343C>T	c.(343-345)Cac>Tac	p.H115Y	LGALS3BP_ENST00000585407.1_Missense_Mutation_p.H115Y|LGALS3BP_ENST00000591778.1_Missense_Mutation_p.H115Y	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	115	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			TCTCTCTCGTGCCTGCAGTTG	0.677																																					p.H115Y	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.C343T						PASS	.						76.0	56.0	63.0					17																	76970803		2203	4300	6503	SO:0001583	missense	3959	exon4			TCTCGTGCCTGCA	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"""BTB/POZ domain containing"", ""Endogenous ligands"""	6564	protein-coding gene	gene with protein product	"""L3 antigen"", ""Mac-2-binding protein"", ""serum protein 90K"", ""transport and golgi organization 10 homolog B (Drosophila)"""	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.343C>T	17.37:g.76970803G>A	ENSP00000262776:p.His115Tyr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	117	46	0.393162	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	37	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.748237	0.49257	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.34072	1.38	3.22	3.22	0.36961	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.000000	0.35615	N	0.003090	T	0.67420	0.2891	H	0.95114	3.625	0.41107	D	0.985716	D	0.89917	1.0	D	0.91635	0.999	T	0.75961	-0.3133	10	0.87932	D	0	-44.0802	10.1799	0.42961	0.0:0.0:1.0:0.0	.	115	Q08380	LG3BP_HUMAN	Y	115;103	ENSP00000262776:H115Y	ENSP00000262776:H115Y	H	-	1	0	LGALS3BP	74482398	1.000000	0.71417	0.034000	0.17996	0.284000	0.27059	8.854000	0.92228	2.091000	0.63221	0.313000	0.20887	CAC	.	.	none		0.677	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567	
FCGBP	8857	hgsc.bcm.edu	37	19	40392802	40392802	+	Missense_Mutation	SNP	C	C	T	rs149844303		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40392802C>T	ENST00000221347.6	-	16	7709	c.7702G>A	c.(7702-7704)Gcc>Acc	p.A2568T		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2568	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AGGTCGTAGGCCACACGCAGG	0.582																																					p.A2568T		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G7702A						scavenged	.						4.0	4.0	4.0					19																	40392802		1744	3652	5396	SO:0001583	missense	8857	exon16			CGTAGGCCACACG	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.7702G>A	19.37:g.40392802C>T	ENSP00000221347:p.Ala2568Thr	Somatic	378	0	0		WXS	Illumina HiSeq	Phase_I	404	107	0.264851	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	4.458	0.084878	0.08583	.	.	ENSG00000090920	ENST00000221347	T	0.59224	0.28	2.66	1.61	0.23674	von Willebrand factor, type D domain (3);	.	.	.	.	T	0.32255	0.0823	N	0.01197	-0.965	0.21762	N	0.999551	B	0.28880	0.226	P	0.44447	0.45	T	0.50268	-0.8848	9	0.09843	T	0.71	.	5.9813	0.19409	0.0:0.7321:0.0:0.2679	.	2568	Q9Y6R7	FCGBP_HUMAN	T	2568	ENSP00000221347:A2568T	ENSP00000221347:A2568T	A	-	1	0	FCGBP	45084642	0.000000	0.05858	0.998000	0.56505	0.350000	0.29205	-2.239000	0.01198	1.495000	0.48549	0.298000	0.19748	GCC	.	.	weak		0.582	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZFP28	140612	hgsc.bcm.edu	37	19	57065189	57065189	+	Silent	SNP	T	T	C	rs145011	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57065189T>C	ENST00000301318.3	+	8	1106	c.1035T>C	c.(1033-1035)ttT>ttC	p.F345F	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	345					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F345F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		ACTATGTGTTTGGAAGGAAGC	0.388													T|||	1160	0.231629	0.0545	0.304	5008	,	,		18113	0.3294		0.2396	False		,,,				2504	0.3108				p.F345F	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											ZFP28,NS,carcinoma,0,1	ZFP28	99	1	1	Substitution - coding silent(1)	stomach(1)	c.T1035C						PASS	.	T		322,4084	170.5+/-200.9	9,304,1890	84.0	77.0	80.0		1035	3.7	1.0	19	dbSNP_80	80	2173,6427	372.1+/-336.5	298,1577,2425	no	coding-synonymous	ZFP28	NM_020828.1		307,1881,4315	CC,CT,TT		25.2674,7.3082,19.1835		345/869	57065189	2495,10511	2203	4300	6503	SO:0001819	synonymous_variant	140612	exon8			TGTGTTTGGAAGG		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"""Zinc fingers, C2H2-type"", ""-"""	17801	protein-coding gene	gene with protein product			"""zinc finger protein 28 homolog (mouse)"""				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.1035T>C	19.37:g.57065189T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	130	72	0.553846	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Silent	SNP	ENST00000301318.3	37	CCDS12946.1																																																																																			T|0.798;C|0.202	0.202	strong		0.388	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
DDX60L	91351	hgsc.bcm.edu	37	4	169282355	169282355	+	Missense_Mutation	SNP	T	T	C	rs2684348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169282355T>C	ENST00000511577.1	-	37	5183	c.4936A>G	c.(4936-4938)Atg>Gtg	p.M1646V	DDX60L_ENST00000260184.7_Missense_Mutation_p.M1646V			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1646				M -> V (in Ref. 1; AL832950). {ECO:0000305}.			ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AGCTGTCCCATACGCATCCTA	0.299													T|||	2897	0.578474	0.3707	0.6167	5008	,	,		18188	0.75		0.6441	False		,,,				2504	0.5879				p.M1646V		Atlas-SNP	.											.	DDX60L	116	.	0			c.A4936G						PASS	.	T	VAL/MET	1486,2140		290,906,617	73.0	66.0	68.0		4936	-2.1	0.0	4	dbSNP_100	68	5368,2794		1757,1854,470	yes	missense	DDX60L	NM_001012967.1	21	2047,2760,1087	CC,CT,TT		34.2318,40.9818,41.8561	benign	1646/1707	169282355	6854,4934	1813	4081	5894	SO:0001583	missense	91351	exon37			GTCCCATACGCAT	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.4936A>G	4.37:g.169282355T>C	ENSP00000422423:p.Met1646Val	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		1320	0.6043956043956044	185	0.37601626016260165	222	0.6132596685082873	431	0.7534965034965035	482	0.6358839050131926	T	3.030	-0.199862	0.06219	0.409818	0.657682	ENSG00000181381	ENST00000260184;ENST00000511577	T;T	0.16324	2.35;2.35	2.06	-2.12	0.07165	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.14438	0.01	B	0.11329	0.006	T	0.17531	-1.0366	8	0.36615	T	0.2	.	3.1607	0.06520	0.0:0.3961:0.2817:0.3222	rs2684348;rs3749496;rs56535970;rs59537052;rs2684348	1646	Q5H9U9	DDX6L_HUMAN	V	1646	ENSP00000260184:M1646V;ENSP00000422423:M1646V	ENSP00000260184:M1646V	M	-	1	0	DDX60L	169518930	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-0.934000	0.03955	-0.359000	0.08150	0.254000	0.18369	ATG	T|0.390;C|0.610	0.610	strong		0.299	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
LRRN2	10446	hgsc.bcm.edu	37	1	204589066	204589066	+	Missense_Mutation	SNP	C	C	T	rs36012907	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204589066C>T	ENST00000367175.1	-	1	2267	c.55G>A	c.(55-57)Gct>Act	p.A19T	LRRN2_ENST00000367177.3_Missense_Mutation_p.A19T|LRRN2_ENST00000367176.3_Missense_Mutation_p.A19T|LRRN2_ENST00000496057.1_5'UTR			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	19			A -> T (in dbSNP:rs36012907). {ECO:0000269|PubMed:12975309}.		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)			ACGGGCACAGCGGCAGTGGCA	0.647													C|||	122	0.024361	0.0015	0.0576	5008	,	,		17470	0.0		0.0726	False		,,,				2504	0.0072				p.A19T		Atlas-SNP	.											.	LRRN2	81	.	0			c.G55A						PASS	.	C	THR/ALA,THR/ALA	87,4313		1,85,2114	19.0	22.0	21.0		55,55	1.6	0.2	1	dbSNP_126	21	824,7774		39,746,3514	yes	missense,missense	LRRN2	NM_201630.1,NM_006338.2	58,58	40,831,5628	TT,TC,CC		9.5836,1.9773,7.0088	benign,benign	19/714,19/714	204589066	911,12087	2200	4299	6499	SO:0001583	missense	10446	exon3			GCACAGCGGCAGT	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.55G>A	1.37:g.204589066C>T	ENSP00000356143:p.Ala19Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	66	34	0.515152	NM_006338	B2R624|Q5T0Y0|Q6UXM0|Q8N182	Missense_Mutation	SNP	ENST00000367175.1	37	CCDS1448.1	78	0.03571428571428571	1	0.0020325203252032522	28	0.07734806629834254	0	0.0	49	0.06464379947229551	C	9.501	1.103266	0.20632	0.019773	0.095836	ENSG00000170382	ENST00000367176;ENST00000367177;ENST00000367175	T;T;T	0.60424	0.19;0.19;0.19	5.79	1.63	0.23807	.	0.748708	0.11411	N	0.566775	T	0.01092	0.0036	N	0.22421	0.69	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.03287	-1.1052	10	0.21540	T	0.41	.	5.964	0.19315	0.0:0.6342:0.1354:0.2304	rs36012907	19	O75325	LRRN2_HUMAN	T	19	ENSP00000356144:A19T;ENSP00000356145:A19T;ENSP00000356143:A19T	ENSP00000356143:A19T	A	-	1	0	LRRN2	202855689	0.198000	0.23374	0.196000	0.23383	0.976000	0.68499	0.673000	0.25203	0.352000	0.24053	0.650000	0.86243	GCT	C|0.942;T|0.058	0.058	strong		0.647	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338	
ATG4D	84971	hgsc.bcm.edu	37	19	10659659	10659659	+	Silent	SNP	C	C	T	rs2304165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10659659C>T	ENST00000309469.4	+	6	1088	c.915C>T	c.(913-915)ccC>ccT	p.P305P	ATG4D_ENST00000540862.1_Intron|RNU7-140P_ENST00000459546.1_RNA	NM_032885.4	NP_116274.3	Q86TL0	ATG4D_HUMAN	autophagy related 4D, cysteine peptidase	305					apoptotic process (GO:0006915)|autophagy (GO:0006914)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	19			Epithelial(33;9.2e-06)|all cancers(31;3.9e-05)			TCCTGGTGCCCGTGCGACTGG	0.632													C|||	654	0.130591	0.1097	0.0994	5008	,	,		17103	0.1081		0.1541	False		,,,				2504	0.18				p.P305P		Atlas-SNP	.											.	ATG4D	47	.	0			c.C915T						PASS	.	C		497,3909	231.0+/-245.0	26,445,1732	119.0	89.0	100.0		915	-11.1	0.7	19	dbSNP_100	100	1159,7441	237.6+/-269.4	80,999,3221	no	coding-synonymous	ATG4D	NM_032885.4		106,1444,4953	TT,TC,CC		13.4767,11.2801,12.7326		305/475	10659659	1656,11350	2203	4300	6503	SO:0001819	synonymous_variant	84971	exon6			GGTGCCCGTGCGA	AJ312332	CCDS12241.1	19p13.2	2014-02-12	2012-06-06	2005-09-11	ENSG00000130734	ENSG00000130734			20789	protein-coding gene	gene with protein product		611340	"""AUT-like 4, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog D (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog D (S. cerevisiae)"""	AUTL4, APG4D		12446702	Standard	NM_032885		Approved	APG4-D	uc002mov.3	Q86TL0	OTTHUMG00000180582	ENST00000309469.4:c.915C>T	19.37:g.10659659C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_032885	Q969K0	Silent	SNP	ENST00000309469.4	37	CCDS12241.1																																																																																			C|0.875;T|0.125	0.125	strong		0.632	ATG4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452022.1	NM_032885	
NAGPA	51172	hgsc.bcm.edu	37	16	5075633	5075633	+	Missense_Mutation	SNP	G	G	A	rs7188856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:5075633G>A	ENST00000312251.3	-	10	1413	c.1394C>T	c.(1393-1395)aCt>aTt	p.T465I	RP11-165E7.1_ENST00000588778.1_RNA|NAGPA_ENST00000381955.3_Missense_Mutation_p.T431I	NM_016256.3	NP_057340.2	Q9UK23	NAGPA_HUMAN	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase	465			T -> I (in dbSNP:rs7188856). {ECO:0000269|PubMed:10551838}.		carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|lysosome organization (GO:0007040)|protein glycosylation (GO:0006486)|protein targeting to lysosome (GO:0006622)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity (GO:0003944)			endometrium(4)|large_intestine(4)|lung(3)|urinary_tract(1)	12					N-Acetyl-D-glucosamine(DB00141)	GTTTGCTGCAGTGCTGATCAG	0.642													G|||	1006	0.200879	0.0893	0.2997	5008	,	,		17690	0.1736		0.3419	False		,,,				2504	0.1646				p.T465I		Atlas-SNP	.											.	NAGPA	30	.	0			c.C1394T						PASS	.	G	ILE/THR	586,3806	257.4+/-261.8	30,526,1640	34.0	36.0	36.0		1394	-3.2	0.0	16	dbSNP_116	36	3005,5595	460.3+/-365.1	531,1943,1826	yes	missense	NAGPA	NM_016256.3	89	561,2469,3466	AA,AG,GG		34.9419,13.3424,27.6401	possibly-damaging	465/516	5075633	3591,9401	2196	4300	6496	SO:0001583	missense	51172	exon10			GCTGCAGTGCTGA	AF187072	CCDS10527.1	16p13.3	2008-02-05			ENSG00000103174	ENSG00000103174	3.1.4.45		17378	protein-coding gene	gene with protein product		607985				10551838, 12058031	Standard	NM_016256		Approved	APAA, UCE	uc002cyg.3	Q9UK23	OTTHUMG00000090515	ENST00000312251.3:c.1394C>T	16.37:g.5075633G>A	ENSP00000310998:p.Thr465Ile	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	201	110	0.547264	NM_016256	B2RAS1|Q96EJ8	Missense_Mutation	SNP	ENST00000312251.3	37	CCDS10527.1	498	0.22802197802197802	49	0.09959349593495935	99	0.27348066298342544	94	0.16433566433566432	256	0.33773087071240104	G	0.034	-1.317453	0.01331	0.133424	0.349419	ENSG00000103174	ENST00000312251;ENST00000381955	T;T	0.24151	2.28;1.87	5.18	-3.19	0.05171	.	1.101780	0.06824	N	0.792789	T	0.00012	0.0000	L	0.56769	1.78	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.37430	-0.9706	9	0.52906	T	0.07	0.3722	11.7169	0.51659	0.5135:0.0:0.4865:0.0	rs7188856;rs17634473;rs7188856	465;431	Q9UK23;Q9UK23-2	NAGPA_HUMAN;.	I	465;431	ENSP00000310998:T465I;ENSP00000371381:T431I	ENSP00000310998:T465I	T	-	2	0	NAGPA	5015634	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.505000	0.02273	-1.423000	0.02002	-1.134000	0.01955	ACT	G|0.758;A|0.242	0.242	strong		0.642	NAGPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207003.1	NM_016256	
MYOM2	9172	hgsc.bcm.edu	37	8	2048831	2048831	+	Missense_Mutation	SNP	A	A	G	rs968381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:2048831A>G	ENST00000262113.4	+	20	2747	c.2606A>G	c.(2605-2607)aAc>aGc	p.N869S	MYOM2_ENST00000523438.1_Missense_Mutation_p.N294S	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	869	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		N -> S (in dbSNP:rs968381). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505783}.		muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		ACAACAGCCAACCGTTATTTA	0.527													A|||	2306	0.460463	0.6831	0.3573	5008	,	,		18243	0.4048		0.335	False		,,,				2504	0.4192				p.N869S		Atlas-SNP	.											MYOM2,NS,carcinoma,0,1	MYOM2	251	1	0			c.A2606G						PASS	.	A	SER/ASN	2828,1578	659.7+/-400.6	920,988,295	65.0	70.0	68.0		2606	4.4	0.0	8	dbSNP_86	68	2853,5747	443.3+/-360.3	494,1865,1941	yes	missense	MYOM2	NM_003970.2	46	1414,2853,2236	GG,GA,AA		33.1744,35.8148,43.6798	benign	869/1466	2048831	5681,7325	2203	4300	6503	SO:0001583	missense	9172	exon20			CAGCCAACCGTTA		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2606A>G	8.37:g.2048831A>G	ENSP00000262113:p.Asn869Ser	Somatic	112	1	0.00892857		WXS	Illumina HiSeq	Phase_I	96	96	1	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	928	0.4249084249084249	318	0.6463414634146342	133	0.3674033149171271	227	0.3968531468531469	250	0.32981530343007914	A	5.934	0.356400	0.11239	0.641852	0.331744	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.56941	0.43;0.43	5.55	4.38	0.52667	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.278757	0.39210	N	0.001422	T	0.00012	0.0000	L	0.33137	0.985	0.53688	P	2.199999999996649E-5	B	0.15473	0.013	B	0.17979	0.02	T	0.41502	-0.9505	9	0.34782	T	0.22	.	11.4648	0.50232	0.9293:0.0:0.0707:0.0	rs968381;rs3758066;rs17857421;rs52824117;rs57664364;rs968381	869	P54296	MYOM2_HUMAN	S	869;294	ENSP00000262113:N869S;ENSP00000428396:N294S	ENSP00000262113:N869S	N	+	2	0	MYOM2	2036238	0.543000	0.26434	0.016000	0.15963	0.004000	0.04260	3.935000	0.56560	0.937000	0.37394	0.523000	0.50628	AAC	A|0.561;G|0.439	0.439	strong		0.527	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
BCHE	590	hgsc.bcm.edu	37	3	165491280	165491280	+	Missense_Mutation	SNP	C	C	T	rs1803274	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:165491280C>T	ENST00000264381.3	-	4	1865	c.1699G>A	c.(1699-1701)Gca>Aca	p.A567T	BCHE_ENST00000540653.1_Missense_Mutation_p.A29T	NM_000055.2	NP_000046.1	P06276	CHLE_HUMAN	butyrylcholinesterase	567			A -> T (in BChE deficiency; allele K variant; with reduced enzyme activity; dbSNP:rs1803274). {ECO:0000269|PubMed:11928765, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7634491, ECO:0000269|PubMed:9191541}.		cellular protein metabolic process (GO:0044267)|choline metabolic process (GO:0019695)|cocaine metabolic process (GO:0050783)|learning (GO:0007612)|negative regulation of cell proliferation (GO:0008285)|negative regulation of synaptic transmission (GO:0050805)|neuroblast differentiation (GO:0014016)|response to alkaloid (GO:0043279)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to glucocorticoid (GO:0051384)|synaptic transmission, cholinergic (GO:0007271)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)	acetylcholinesterase activity (GO:0003990)|beta-amyloid binding (GO:0001540)|catalytic activity (GO:0003824)|choline binding (GO:0033265)|cholinesterase activity (GO:0004104)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(34)|ovary(4)|pancreas(2)|stomach(1)	55					Aclidinium(DB08897)|Ambenonium(DB01122)|Bambuterol(DB01408)|Chloroprocaine(DB01161)|Chlorphenesin(DB00856)|Chlorpromazine(DB00477)|Choline(DB00122)|Cinchocaine(DB00527)|Cisplatin(DB00515)|Clevidipine(DB04920)|Cyclopentolate(DB00979)|Decamethonium(DB01245)|Demecarium(DB00944)|Diethylcarbamazine(DB00711)|Dipivefrin(DB00449)|Doxacurium chloride(DB01135)|Drospirenone(DB01395)|Echothiophate(DB01057)|Edrophonium(DB01010)|Ephedrine(DB01364)|Ethopropazine(DB00392)|Galantamine(DB00674)|Hexafluronium(DB00941)|Irinotecan(DB00762)|Isoflurophate(DB00677)|Malathion(DB00772)|Mefloquine(DB00358)|Mirabegron(DB08893)|Mivacurium(DB01226)|Neostigmine(DB01400)|Nizatidine(DB00585)|Oxybuprocaine(DB00892)|Pancuronium(DB01337)|Pegvisomant(DB00082)|Pentagastrin(DB00183)|Perindopril(DB00790)|Pipecuronium(DB01338)|Pralidoxime(DB00733)|Procainamide(DB01035)|Procaine(DB00721)|Pyridostigmine(DB00545)|Ramipril(DB00178)|Rivastigmine(DB00989)|Succinylcholine(DB00202)|Sulpiride(DB00391)|Terbutaline(DB00871)|Triamcinolone(DB00620)|Triflupromazine(DB00508)|Trimethaphan(DB01116)	TCCCATTCTGCTTCATCAATA	0.303													C|||	794	0.158546	0.1725	0.1225	5008	,	,		13648	0.1339		0.1859	False		,,,				2504	0.1626				p.A567T		Atlas-SNP	.											.	BCHE	136	.	0			c.G1699A	GRCh37	CM920127	BCHE	M	rs1803274	PASS	.	C	THR/ALA	835,3569	327.2+/-299.9	84,667,1451	91.0	85.0	87.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1699	4.1	1.0	3	dbSNP_89	87	1735,6863	309.8+/-309.6	171,1393,2735	yes	missense	BCHE	NM_000055.2	58	255,2060,4186	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	20.1791,18.96,19.7662	benign	567/603	165491280	2570,10432	2202	4299	6501	SO:0001583	missense	590	exon4			ATTCTGCTTCATC	M16541	CCDS3198.1	3q26.1-q26.2	2013-07-10			ENSG00000114200	ENSG00000114200	3.1.1.8		983	protein-coding gene	gene with protein product		177400	"""cholinesterase 1"", ""cholinesterase (serum) 2"""	CHE1, CHE2		1769657, 2318303	Standard	NM_000055		Approved	E1	uc003fem.4	P06276	OTTHUMG00000158131	ENST00000264381.3:c.1699G>A	3.37:g.165491280C>T	ENSP00000264381:p.Ala567Thr	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	96	53	0.552083	NM_000055	A8K7P8	Missense_Mutation	SNP	ENST00000264381.3	37	CCDS3198.1	351	0.16071428571428573	69	0.1402439024390244	47	0.1298342541436464	93	0.16258741258741258	142	0.18733509234828497	C	15.90	2.969877	0.53614	0.1896	0.201791	ENSG00000114200	ENST00000264381;ENST00000479451;ENST00000540653	T;T;T	0.77620	-0.18;-1.1;-1.11	5.03	4.14	0.48551	Acetylcholinesterase, tetramerisation (2);	0.339910	0.27433	N	0.019382	T	0.00210	0.0006	L	0.61218	1.895	0.37967	P	0.06682699999999997	B	0.06786	0.001	B	0.15052	0.012	T	0.24083	-1.0170	9	0.52906	T	0.07	.	11.9722	0.53069	0.0:0.9138:0.0:0.0862	rs1803274;rs3773869;rs17713328;rs17846898;rs52816414;rs60242395;rs1803274	567	P06276	CHLE_HUMAN	T	567;97;29	ENSP00000264381:A567T;ENSP00000418325:A97T;ENSP00000443583:A29T	ENSP00000264381:A567T	A	-	1	0	BCHE	166973974	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.872000	0.63050	1.206000	0.43276	0.650000	0.86243	GCA	C|0.822;T|0.178	0.178	strong		0.303	BCHE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350254.1		
LRRC45	201255	hgsc.bcm.edu	37	17	79983367	79983367	+	Silent	SNP	C	C	T	rs117200853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79983367C>T	ENST00000306688.3	+	5	987	c.645C>T	c.(643-645)gaC>gaT	p.D215D	STRA13_ENST00000584347.1_5'Flank|STRA13_ENST00000392359.3_5'Flank|STRA13_ENST00000580435.1_5'Flank|STRA13_ENST00000306704.6_5'Flank|STRA13_ENST00000583767.1_5'Flank	NM_144999.2	NP_659436.1	Q96CN5	LRC45_HUMAN	leucine rich repeat containing 45	215						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)			TCCCTGGAGACGTCCTCAGAG	0.652													c|||	27	0.00539137	0.0	0.0	5008	,	,		19065	0.0268		0.0	False		,,,				2504	0.0				p.D215D		Atlas-SNP	.											.	LRRC45	22	.	0			c.C645T						PASS	.	T		2,4400	4.2+/-10.8	0,2,2199	74.0	71.0	72.0		645	-1.4	0.0	17	dbSNP_132	72	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	LRRC45	NM_144999.2		0,3,6497	TT,TC,CC		0.0116,0.0454,0.0231		215/671	79983367	3,12997	2201	4299	6500	SO:0001819	synonymous_variant	201255	exon5			TGGAGACGTCCTC	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.645C>T	17.37:g.79983367C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_144999		Silent	SNP	ENST00000306688.3	37	CCDS11797.1																																																																																			C|0.997;T|0.003	0.003	strong		0.652	LRRC45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442058.1	NM_144999	
AMY2A	279	hgsc.bcm.edu	37	1	104166590	104166590	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:104166590C>G	ENST00000414303.2	+	8	1268	c.1204C>G	c.(1204-1206)Cga>Gga	p.R402G	AMY2A_ENST00000497748.1_3'UTR	NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	402					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)	p.R402*(1)		endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	CTGTGAACATCGATGGCGCCA	0.343																																					p.R402G		Atlas-SNP	.											AMY2A,colon,carcinoma,0,1	AMY2A	36	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1204G						scavenged	.						9.0	9.0	9.0					1																	104166590		1665	3373	5038	SO:0001583	missense	279	exon8			GAACATCGATGGC	BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"""amylase, alpha 2A; pancreatic"""	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.1204C>G	1.37:g.104166590C>G	ENSP00000397582:p.Arg402Gly	Somatic	468	0	0		WXS	Illumina HiSeq	Phase_I	492	93	0.189024	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	37	CCDS783.1	.	.	.	.	.	.	.	.	.	.	-	13.88	2.369406	0.42003	.	.	ENSG00000243480	ENST00000414303;ENST00000393932	.	.	.	2.94	1.99	0.26369	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81384	0.4811	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.83784	0.0227	9	0.87932	D	0	.	9.5171	0.39113	0.3781:0.6219:0.0:0.0	.	402	P04746	AMYP_HUMAN	G	402	.	ENSP00000377509:R402G	R	+	1	2	AMY2A	103968113	0.999000	0.42202	0.992000	0.48379	0.892000	0.51952	1.860000	0.39428	0.540000	0.28808	0.305000	0.20034	CGA	.	.	weak		0.343	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699	
F5	2153	hgsc.bcm.edu	37	1	169511403	169511403	+	Silent	SNP	G	G	A	rs41272457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:169511403G>A	ENST00000367797.3	-	13	3126	c.2925C>T	c.(2923-2925)ccC>ccT	p.P975P	F5_ENST00000367796.3_Silent_p.P980P	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	975	B.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	AGGCATTCTGGGGGCTGATCA	0.468													G|||	26	0.00519169	0.0008	0.0115	5008	,	,		19616	0.0		0.0169	False		,,,				2504	0.0				p.P975P		Atlas-SNP	.											F5,NS,carcinoma,-2,1	F5	301	1	0			c.C2925T						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	106.0	110.0	109.0		2925	0.7	0.1	1	dbSNP_127	109	195,8405	86.3+/-148.7	2,191,4107	no	coding-synonymous	F5	NM_000130.4		2,206,6295	AA,AG,GG		2.2674,0.3404,1.6146		975/2225	169511403	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	2153	exon13			ATTCTGGGGGCTG	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.2925C>T	1.37:g.169511403G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																			G|0.986;A|0.014	0.014	strong		0.468	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
GABRG3	2567	hgsc.bcm.edu	37	15	27772676	27772676	+	Silent	SNP	C	C	T	rs140679	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:27772676C>T	ENST00000333743.6	+	8	1217	c.963C>T	c.(961-963)acC>acT	p.T321T	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	321					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)	TTTTTGTGACCGTGTGCTTCC	0.557													C|||	2586	0.516374	0.3026	0.6844	5008	,	,		20370	0.6577		0.5467	False		,,,				2504	0.5092				p.T321T	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.C963T						PASS	.	C		1351,2995		231,889,1053	139.0	127.0	131.0		963	-8.3	0.5	15	dbSNP_78	131	4580,3972		1233,2114,929	no	coding-synonymous	GABRG3	NM_033223.4		1464,3003,1982	TT,TC,CC		46.4453,31.0861,45.9839		321/468	27772676	5931,6967	2173	4276	6449	SO:0001819	synonymous_variant	2567	exon8			TGTGACCGTGTGC		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.963C>T	15.37:g.27772676C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1	1190	0.5448717948717948	150	0.3048780487804878	238	0.6574585635359116	394	0.6888111888111889	408	0.5382585751978892	C	9.780	1.175068	0.21704	0.310861	0.535547	ENSG00000182256	ENST00000451330	.	.	.	5.48	-8.26	0.01021	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.00995	-1.1487	3	.	.	.	.	18.8379	0.92169	0.0:0.1181:0.0:0.8819	rs140679;rs17649404;rs140679	.	.	.	L	84	.	.	P	+	2	0	GABRG3	25446271	0.001000	0.12720	0.503000	0.27626	0.903000	0.53119	-1.707000	0.01893	-2.099000	0.00849	-0.251000	0.11542	CCG	C|0.472;T|0.528	0.528	strong		0.557	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
POLK	51426	hgsc.bcm.edu	37	5	74877266	74877266	+	Silent	SNP	C	C	T	rs3213801	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:74877266C>T	ENST00000241436.4	+	7	1099	c.927C>T	c.(925-927)gcC>gcT	p.A309A	POLK_ENST00000352007.5_Silent_p.A309A|POLK_ENST00000515295.1_Silent_p.A309A|POLK_ENST00000504026.1_Silent_p.A309A|POLK_ENST00000506928.1_3'UTR|POLK_ENST00000508526.1_Silent_p.A309A|POLK_ENST00000380481.3_Silent_p.A219A	NM_016218.2	NP_057302.1	Q9UBT6	POLK_HUMAN	polymerase (DNA directed) kappa	309	UmuC.				DNA repair (GO:0006281)|nucleotide-excision repair, DNA gap filling (GO:0006297)	nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			endometrium(1)|kidney(4)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	27		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)|Prostate(461;0.184)		OV - Ovarian serous cystadenocarcinoma(47;2.9e-54)|all cancers(79;1.27e-42)		CACTGACAGCCAGTGCAGGTA	0.343								DNA polymerases (catalytic subunits)					C|||	1357	0.270966	0.2148	0.1801	5008	,	,		16892	0.3333		0.2197	False		,,,				2504	0.3998				p.A309A		Atlas-SNP	.											.	POLK	123	.	0			c.C927T						PASS	.	C		969,3435	333.9+/-303.2	109,751,1342	47.0	50.0	49.0		927	2.9	1.0	5	dbSNP_106	49	1792,6808	315.9+/-312.5	185,1422,2693	no	coding-synonymous	POLK	NM_016218.2		294,2173,4035	TT,TC,CC		20.8372,22.0027,21.2319		309/871	74877266	2761,10243	2202	4300	6502	SO:0001819	synonymous_variant	51426	exon7			GACAGCCAGTGCA	AB027564	CCDS4030.1	5q13	2012-05-18			ENSG00000122008	ENSG00000122008		"""DNA polymerases"""	9183	protein-coding gene	gene with protein product	"""polymerase (DNA-directed) kappa"", ""DINB protein"", ""DNA polymerase kappa"""	605650		DINB1		10887153, 10518552	Standard	NM_016218		Approved	POLQ, DINP	uc003kdw.3	Q9UBT6	OTTHUMG00000102107	ENST00000241436.4:c.927C>T	5.37:g.74877266C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	97	1	NM_016218	B2RBD2|Q5Q9G5|Q5Q9G6|Q5Q9G7|Q5Q9G8|Q86VJ8|Q8IZY0|Q8IZY1|Q8NB30|Q96L01|Q96Q86|Q96Q87|Q9UHC5	Silent	SNP	ENST00000241436.4	37	CCDS4030.1																																																																																			C|0.762;T|0.238	0.238	strong		0.343	POLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219945.3	NM_016218	
SNTB2	6645	hgsc.bcm.edu	37	16	69221510	69221510	+	Silent	SNP	C	C	G	rs10650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:69221510C>G	ENST00000336278.4	+	1	479	c.441C>G	c.(439-441)ccC>ccG	p.P147P		NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)	147	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|microtubule (GO:0005874)|protein complex (GO:0043234)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	13		Ovarian(137;0.101)		OV - Ovarian serous cystadenocarcinoma(108;0.208)		AGATCTTCCCCGGGCTGGCTG	0.716													G|||	905	0.180711	0.3003	0.1671	5008	,	,		5567	0.0417		0.2296	False		,,,				2504	0.1217				p.P147P	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.C441G						PASS	.	G		1114,3104		166,782,1161	7.0	9.0	8.0		441	2.9	1.0	16	dbSNP_52	8	1807,6475		241,1325,2575	no	coding-synonymous	SNTB2	NM_006750.3		407,2107,3736	GG,GC,CC		21.8184,26.4106,23.368		147/541	69221510	2921,9579	2109	4141	6250	SO:0001819	synonymous_variant	6645	exon1			CTTCCCCGGGCTG	U40572	CCDS10873.1	16q22.1	2008-05-14	2002-08-29		ENSG00000168807	ENSG00000168807			11169	protein-coding gene	gene with protein product		600027	"""syntrophin, beta 2 (dystrophin-associated protein A1, 59kD, basic component 2)"""	SNT2B2, SNTL, D16S2531E		8576247, 8183929	Standard	NM_006750		Approved	EST25263, SNT3	uc002ewu.3	Q13425	OTTHUMG00000137567	ENST00000336278.4:c.441C>G	16.37:g.69221510C>G		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	28	15	0.535714	NM_006750	Q9BY09	Silent	SNP	ENST00000336278.4	37	CCDS10873.1	400	0.18315018315018314	144	0.2926829268292683	62	0.1712707182320442	30	0.05244755244755245	164	0.21635883905013192	G	13.11	2.137905	0.37728	0.264106	0.218184	ENSG00000168807	ENST00000525632;ENST00000360496	T	0.31510	1.49	4.91	2.86	0.33363	.	0.067858	0.64402	N	0.000013	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17992	-1.0351	6	0.87932	D	0	3.495	8.6306	0.33917	0.1548:0.1286:0.7166:0.0	rs10650;rs1136061;rs1136064;rs3169308;rs17354236	.	.	.	R	16;8	ENSP00000432201:P16R	ENSP00000353686:P8R	P	+	2	0	SNTB2	67779011	0.942000	0.31987	1.000000	0.80357	0.953000	0.61014	0.499000	0.22546	0.564000	0.29238	-0.215000	0.12644	CCG	C|0.815;G|0.185	0.185	strong		0.716	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1		
GAS2L3	283431	hgsc.bcm.edu	37	12	101017839	101017839	+	Missense_Mutation	SNP	C	C	T	rs148236676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101017839C>T	ENST00000539410.1	+	9	1642	c.1256C>T	c.(1255-1257)cCa>cTa	p.P419L	GAS2L3_ENST00000266754.5_Missense_Mutation_p.P419L|GAS2L3_ENST00000547754.1_Missense_Mutation_p.P419L|GAS2L3_ENST00000537247.1_Missense_Mutation_p.P315L			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	419					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						ACTTCTTCACCAGCTTTACCA	0.423													C|||	17	0.00339457	0.0008	0.0115	5008	,	,		19471	0.0		0.006	False		,,,				2504	0.002				p.P419L		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1256T						PASS	.	C	LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	91.0	93.0	92.0		1256	4.1	0.0	12	dbSNP_134	92	61,8539	37.8+/-93.5	0,61,4239	yes	missense	GAS2L3	NM_174942.1	98	0,68,6435	TT,TC,CC		0.7093,0.1589,0.5228	benign	419/695	101017839	68,12938	2203	4300	6503	SO:0001583	missense	283431	exon10			CTTCACCAGCTTT	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1256C>T	12.37:g.101017839C>T	ENSP00000439672:p.Pro419Leu	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	4.648	0.120536	0.08881	0.001589	0.007093	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	T;T;T;T	0.25085	1.86;1.86;1.82;1.86	4.95	4.06	0.47325	.	0.368200	0.25089	N	0.033227	T	0.16041	0.0386	L	0.43152	1.355	0.28581	N	0.910137	B	0.09022	0.002	B	0.08055	0.003	T	0.11966	-1.0566	10	0.62326	D	0.03	-3.2328	10.2064	0.43116	0.0:0.7873:0.1365:0.0761	.	419	Q86XJ1	GA2L3_HUMAN	L	419;419;315;419	ENSP00000266754:P419L;ENSP00000448955:P419L;ENSP00000442406:P315L;ENSP00000439672:P419L	ENSP00000266754:P419L	P	+	2	0	GAS2L3	99541970	0.005000	0.15991	0.008000	0.14137	0.047000	0.14425	2.030000	0.41108	1.080000	0.41073	0.603000	0.83216	CCA	C|0.995;T|0.005	0.005	strong		0.423	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
ABCD4	5826	hgsc.bcm.edu	37	14	74759301	74759301	+	Silent	SNP	G	G	T	rs4148078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:74759301G>T	ENST00000356924.4	-	10	1124	c.981C>A	c.(979-981)ctC>ctA	p.L327L	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000298816.7_Silent_p.L223L	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	327	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)		ACAGGTCGATGAGCTGGGTGA	0.592													G|||	1317	0.262979	0.121	0.2695	5008	,	,		22556	0.247		0.3857	False		,,,				2504	0.3405				p.L327L		Atlas-SNP	.											.	ABCD4	54	.	0			c.C981A						PASS	.	G		765,3641	310.2+/-291.5	64,637,1502	83.0	68.0	73.0		981	4.7	1.0	14	dbSNP_110	73	3127,5473	474.3+/-368.8	552,2023,1725	no	coding-synonymous	ABCD4	NM_005050.3		616,2660,3227	TT,TG,GG		36.3605,17.3627,29.9247		327/607	74759301	3892,9114	2203	4300	6503	SO:0001819	synonymous_variant	5826	exon10			GTCGATGAGCTGG	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.981C>A	14.37:g.74759301G>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	30	0.365854	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Silent	SNP	ENST00000356924.4	37	CCDS9828.1																																																																																			G|0.719;T|0.281	0.281	strong		0.592	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050	
HOXB1	3211	hgsc.bcm.edu	37	17	46607958	46607958	+	Missense_Mutation	SNP	T	T	A	rs12939811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:46607958T>A	ENST00000239174.6	-	1	401	c.309A>T	c.(307-309)caA>caT	p.Q103H	HOXB1_ENST00000577092.1_Missense_Mutation_p.Q103H	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	103			Q -> H (in dbSNP:rs12939811).		anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CTCCTTCTGATTGACCCAGAG	0.667													T|||	573	0.114417	0.0651	0.1023	5008	,	,		14669	0.0982		0.1928	False		,,,				2504	0.1258				p.Q103H		Atlas-SNP	.											.	HOXB1	67	.	0			c.A309T						PASS	.	T	HIS/GLN	343,4063	170.1+/-200.6	14,315,1874	63.0	66.0	65.0		309	-5.7	0.0	17	dbSNP_121	65	1621,6979	282.0+/-295.3	153,1315,2832	yes	missense	HOXB1	NM_002144.3	24	167,1630,4706	AA,AT,TT		18.8488,7.7848,15.1007	possibly-damaging	103/302	46607958	1964,11042	2203	4300	6503	SO:0001583	missense	3211	exon1			TTCTGATTGACCC		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.309A>T	17.37:g.46607958T>A	ENSP00000355140:p.Gln103His	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	38	13	0.342105	NM_002144	Q4VB03	Missense_Mutation	SNP	ENST00000239174.6	37	CCDS32675.1	248	0.11355311355311355	27	0.054878048780487805	34	0.09392265193370165	38	0.06643356643356643	149	0.19656992084432717	T	8.428	0.847945	0.17034	0.077848	0.188488	ENSG00000120094	ENST00000239174	D	0.89875	-2.58	4.37	-5.68	0.02436	.	0.000000	0.41712	D	0.000838	T	0.00328	0.0010	L	0.52011	1.625	0.80722	P	0.0	P	0.38642	0.641	B	0.34824	0.19	T	0.48525	-0.9028	9	0.62326	D	0.03	.	11.7967	0.52104	0.0:0.5455:0.3026:0.1518	rs12939811;rs52833084;rs12939811	103	P14653	HXB1_HUMAN	H	103	ENSP00000355140:Q103H	ENSP00000355140:Q103H	Q	-	3	2	HOXB1	43962957	0.003000	0.15002	0.000000	0.03702	0.737000	0.42083	-1.050000	0.03510	-1.633000	0.01539	-0.925000	0.02716	CAA	T|0.866;A|0.134	0.134	strong		0.667	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
NDUFS1	4719	hgsc.bcm.edu	37	2	207006676	207006676	+	Silent	SNP	T	T	C	rs1801318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:207006676T>C	ENST00000233190.6	-	12	1517	c.1251A>G	c.(1249-1251)agA>agG	p.R417R	NDUFS1_ENST00000455934.2_Silent_p.R431R|NDUFS1_ENST00000440274.1_Silent_p.R381R|NDUFS1_ENST00000423725.1_Silent_p.R360R|NDUFS1_ENST00000432169.1_Silent_p.R306R|NDUFS1_ENST00000449699.1_Silent_p.R417R|NDUFS1_ENST00000457011.1_Silent_p.R301R	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	417				R -> W (in Ref. 1; CAA43412). {ECO:0000305}.	apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TCTTTCGAATTCTAGCATTAA	0.318													T|||	1552	0.309904	0.4508	0.2882	5008	,	,		14407	0.2133		0.341	False		,,,				2504	0.2025				p.R431R		Atlas-SNP	.											.	NDUFS1	82	.	0			c.A1293G						PASS	.	T	,,,,	1934,2472	544.5+/-376.5	429,1076,698	78.0	74.0	76.0		1143,918,1080,1293,1251	3.5	1.0	2	dbSNP_89	76	2755,5845	432.9+/-357.3	454,1847,1999	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDUFS1	NM_001199981.1,NM_001199982.1,NM_001199983.1,NM_001199984.1,NM_005006.6	,,,,	883,2923,2697	CC,CT,TT		32.0349,43.8947,36.0526	,,,,	381/692,306/617,360/671,431/742,417/728	207006676	4689,8317	2203	4300	6503	SO:0001819	synonymous_variant	4719	exon12			TCGAATTCTAGCA		CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1251A>G	2.37:g.207006676T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	114	43	0.377193	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Silent	SNP	ENST00000233190.6	37	CCDS2366.1																																																																																			T|0.644;C|0.356;A|0.000	0.356	strong		0.318	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006	
RIN3	79890	hgsc.bcm.edu	37	14	93118668	93118668	+	Missense_Mutation	SNP	C	C	T	rs3742717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93118668C>T	ENST00000216487.7	+	6	1433	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	425	Pro-rich.		T -> I (in dbSNP:rs3742717).|T -> M (in dbSNP:rs3742717). {ECO:0000269|PubMed:14702039}.		endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CCTGAGGACACGCCCCGGGAG	0.647													C|||	1465	0.292532	0.1755	0.2767	5008	,	,		13345	0.4415		0.1948	False		,,,				2504	0.409				p.T425M		Atlas-SNP	.											RIN3,rectum,carcinoma,-1,1	RIN3	81	1	0			c.C1274T						PASS	.	C	MET/THR	758,3648	305.8+/-289.2	72,614,1517	56.0	64.0	61.0		1274	-0.5	0.0	14	dbSNP_107	61	1458,7142	277.9+/-293.1	112,1234,2954	yes	missense	RIN3	NM_024832.3	81	184,1848,4471	TT,TC,CC		16.9535,17.2038,17.0383	possibly-damaging	425/986	93118668	2216,10790	2203	4300	6503	SO:0001583	missense	79890	exon6			AGGACACGCCCCG	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.1274C>T	14.37:g.93118668C>T	ENSP00000216487:p.Thr425Met	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	601	0.2751831501831502	88	0.17886178861788618	98	0.27071823204419887	250	0.4370629370629371	165	0.21767810026385223	C	2.949	-0.217068	0.06101	0.172038	0.169535	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.06142	3.34	3.82	-0.538	0.11868	.	1.010830	0.07976	N	0.984748	T	0.00012	0.0000	N	0.02011	-0.69	0.58432	P	1.999999999946489E-6	B;B;B;B	0.30741	0.293;0.002;0.002;0.106	B;B;B;B	0.20767	0.031;0.001;0.001;0.004	T	0.39663	-0.9603	9	0.48119	T	0.1	-7.5748	2.5115	0.04658	0.101:0.3798:0.2266:0.2926	rs3742717;rs3742717	425;471;350;425	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	M	425;349	ENSP00000216487:T425M	ENSP00000216487:T425M	T	+	2	0	RIN3	92188421	.	.	0.037000	0.18230	0.023000	0.10783	.	.	0.239000	0.21243	-0.657000	0.03884	ACG	C|0.777;T|0.223	0.223	strong		0.647	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
BTN1A1	696	hgsc.bcm.edu	37	6	26505362	26505362	+	Missense_Mutation	SNP	G	G	A	rs3736781	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26505362G>A	ENST00000244513.6	+	3	703	c.637G>A	c.(637-639)Gcg>Acg	p.A213T		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	213	Ig-like V-type 2.		A -> T (in dbSNP:rs3736781). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8611614, ECO:0000269|Ref.3}.			extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						AGACACTTCTGCGAAAAATGT	0.453													G|||	2846	0.568291	0.5129	0.5879	5008	,	,		19887	0.746		0.4423	False		,,,				2504	0.5757				p.A213T		Atlas-SNP	.											.	BTN1A1	68	.	0			c.G637A						PASS	.	G	THR/ALA	2288,2118	600.7+/-389.6	588,1112,503	106.0	108.0	108.0		637	-10.5	0.0	6	dbSNP_107	108	4044,4556	557.3+/-387.0	984,2076,1240	yes	missense	BTN1A1	NM_001732.2	58	1572,3188,1743	AA,AG,GG		47.0233,48.0708,48.6852	benign	213/527	26505362	6332,6674	2203	4300	6503	SO:0001583	missense	696	exon3			ACTTCTGCGAAAA	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.637G>A	6.37:g.26505362G>A	ENSP00000244513:p.Ala213Thr	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	37	CCDS4614.1	1195	0.5471611721611722	229	0.4654471544715447	206	0.569060773480663	413	0.722027972027972	347	0.4577836411609499	G	10.72	1.428849	0.25726	0.519292	0.470233	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.75938	-0.98	5.63	-10.5	0.00291	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.626750	0.03193	N	0.173551	T	0.26231	0.0640	N	0.05351	-0.065	0.80722	P	0.0	B	0.12013	0.005	B	0.20577	0.03	T	0.08207	-1.0733	9	0.19147	T	0.46	.	9.9966	0.41902	0.1031:0.5725:0.3244:0.0	rs3736781;rs52816922;rs57753800;rs3736781	213	Q13410	BT1A1_HUMAN	T	213	ENSP00000244513:A213T	ENSP00000244513:A213T	A	+	1	0	BTN1A1	26613341	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.603000	0.02077	-1.142000	0.02869	-0.345000	0.07892	GCG	G|0.485;A|0.515	0.515	strong		0.453	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
BTBD6	90135	hgsc.bcm.edu	37	14	105716377	105716377	+	Silent	SNP	C	C	T	rs45452103	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:105716377C>T	ENST00000392554.3	+	4	1123	c.826C>T	c.(826-828)Ctg>Ttg	p.L276L	BRF1_ENST00000551787.1_5'Flank|BRF1_ENST00000440513.3_Intron|BRF1_ENST00000379937.2_Intron|BTBD6_ENST00000327471.3_Silent_p.L201L|BRF1_ENST00000546474.1_Intron|BRF1_ENST00000327359.3_Intron|BTBD6_ENST00000463376.2_Silent_p.L201L|BRF1_ENST00000379932.4_5'Flank|BRF1_ENST00000446501.2_5'Flank|BTBD6_ENST00000536364.1_Silent_p.L276L|BRF1_ENST00000392557.4_5'Flank			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	276						cytoplasm (GO:0005737)				endometrium(1)|lung(3)	4		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.0163)|Epithelial(46;0.0391)	Epithelial(152;0.18)		GAGGCATGTTCTGGGGCGAGC	0.607													C|||	43	0.00858626	0.0008	0.0159	5008	,	,		18651	0.0		0.0229	False		,,,				2504	0.0082				p.L276L		Atlas-SNP	.											.	BTBD6	24	.	0			c.C826T						PASS	.	C	,,,,	16,4386		0,16,2185	49.0	48.0	48.0		,,,,826	-6.2	0.0	14	dbSNP_127	48	217,8371		3,211,4080	no	intron,intron,intron,intron,coding-synonymous	BRF1,BTBD6	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001519.3,NM_033271.2	,,,,	3,227,6265	TT,TC,CC		2.5268,0.3635,1.7937	,,,,	,,,,276/486	105716377	233,12757	2201	4294	6495	SO:0001819	synonymous_variant	90135	exon5			CATGTTCTGGGGC	AF353674	CCDS10002.1, CCDS10002.2	14q32.33	2013-01-08			ENSG00000184887	ENSG00000184887		"""BTB/POZ domain containing"""	19897	protein-coding gene	gene with protein product							Standard	NM_033271		Approved	BDPL	uc010tyq.2	Q96KE9	OTTHUMG00000029887	ENST00000392554.3:c.826C>T	14.37:g.105716377C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_033271	Q8IVQ7|Q9BR94	Silent	SNP	ENST00000392554.3	37	CCDS10002.2																																																																																			C|0.983;T|0.017	0.017	strong		0.607	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4		
MMP10	4319	hgsc.bcm.edu	37	11	102650246	102650246	+	Silent	SNP	G	G	A	rs17860949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:102650246G>A	ENST00000279441.4	-	2	372	c.336C>T	c.(334-336)caC>caT	p.H112H		NM_002425.2	NP_002416.1	P09238	MMP10_HUMAN	matrix metallopeptidase 10 (stromelysin 2)	112					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)	TGTATGTAAGGTGGGTTTTCC	0.418													G|||	598	0.119409	0.1475	0.0836	5008	,	,		19880	0.0952		0.1312	False		,,,				2504	0.1196				p.H112H		Atlas-SNP	.											.	MMP10	44	.	0			c.C336T						PASS	.	G		634,3772	272.8+/-271.0	46,542,1615	82.0	72.0	75.0		336	1.1	0.5	11	dbSNP_123	75	1075,7523	226.8+/-262.4	65,945,3289	no	coding-synonymous	MMP10	NM_002425.2		111,1487,4904	AA,AG,GG		12.5029,14.3895,13.1421		112/477	102650246	1709,11295	2203	4299	6502	SO:0001819	synonymous_variant	4319	exon2			TGTAAGGTGGGTT	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.336C>T	11.37:g.102650246G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	120	53	0.441667	NM_002425	B2R9X9|Q53HH9	Silent	SNP	ENST00000279441.4	37	CCDS8321.1																																																																																			G|0.872;A|0.128	0.128	strong		0.418	MMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398014.1		
SEC14L4	284904	hgsc.bcm.edu	37	22	30887919	30887919	+	Silent	SNP	G	G	A	rs61741444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30887919G>A	ENST00000255858.7	-	10	896	c.813C>T	c.(811-813)tgC>tgT	p.C271C	RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000540456.1_Silent_p.C256C|SEC14L4_ENST00000392772.2_Silent_p.C217C|SEC14L4_ENST00000381982.3_Silent_p.C271C|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	271	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	TCACCTGCTCGCACAGGTAGT	0.617													G|||	275	0.0549121	0.0681	0.0187	5008	,	,		18577	0.0		0.0328	False		,,,				2504	0.1421				p.C271C		Atlas-SNP	.											.	SEC14L4	43	.	0			c.C813T						PASS	.	G	,	278,4128	155.9+/-189.0	17,244,1942	61.0	52.0	55.0		813,813	1.8	0.0	22	dbSNP_129	55	272,8328	103.6+/-164.7	5,262,4033	no	coding-synonymous,coding-synonymous	SEC14L4	NM_001161368.1,NM_174977.3	,	22,506,5975	AA,AG,GG		3.1628,6.3096,4.2288	,	271/361,271/407	30887919	550,12456	2203	4300	6503	SO:0001819	synonymous_variant	284904	exon10			CTGCTCGCACAGG	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.813C>T	22.37:g.30887919G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	102	38	0.372549	NM_001161368	A5D6W7|A6NCV4	Silent	SNP	ENST00000255858.7	37	CCDS13878.1																																																																																			G|0.962;A|0.038	0.038	strong		0.617	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
TIMELESS	8914	hgsc.bcm.edu	37	12	56814653	56814653	+	Missense_Mutation	SNP	G	G	A	rs2291739	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56814653G>A	ENST00000553532.1	-	25	3203	c.3053C>T	c.(3052-3054)cCg>cTg	p.P1018L	TIMELESS_ENST00000229201.4_Missense_Mutation_p.P1017L|TIMELESS_ENST00000554616.1_Missense_Mutation_p.P515L					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						CCATAGGAGCGGGATAGAAAA	0.532													G|||	1961	0.391573	0.3124	0.3703	5008	,	,		19667	0.2768		0.5636	False		,,,				2504	0.455				p.P1018L		Atlas-SNP	.											.	TIMELESS	107	.	0			c.C3053T						PASS	.	G	LEU/PRO	1561,2845	490.8+/-361.9	285,991,927	85.0	86.0	85.0		3053	5.4	0.9	12	dbSNP_100	85	4786,3814	612.1+/-395.9	1319,2148,833	yes	missense	TIMELESS	NM_003920.3	98	1604,3139,1760	AA,AG,GG		44.3488,35.429,48.8006	possibly-damaging	1018/1209	56814653	6347,6659	2203	4300	6503	SO:0001583	missense	8914	exon25			AGGAGCGGGATAG	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.3053C>T	12.37:g.56814653G>A	ENSP00000450607:p.Pro1018Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	912	0.4175824175824176	157	0.31910569105691056	144	0.39779005524861877	185	0.32342657342657344	426	0.5620052770448549	G	18.07	3.541190	0.65085	0.35429	0.556512	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.59364	2.69;2.69;0.27	5.4	5.4	0.78164	Timeless C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.63843	1.955	0.09310	P	0.99999396782	D	0.89917	1.0	D	0.72338	0.977	T	0.51379	-0.8713	9	0.54805	T	0.06	-20.2551	18.3181	0.90227	0.0:0.0:1.0:0.0	rs2291739;rs11551824;rs17118587;rs58784244;rs2291739	1018	Q9UNS1	TIM_HUMAN	L	1017;1018;515	ENSP00000229201:P1017L;ENSP00000450607:P1018L;ENSP00000450848:P515L	ENSP00000229201:P1018L	P	-	2	0	TIMELESS	55100920	1.000000	0.71417	0.907000	0.35723	0.019000	0.09904	9.170000	0.94795	2.708000	0.92522	0.561000	0.74099	CCG	G|0.548;A|0.452	0.452	strong		0.532	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
MYO9B	4650	hgsc.bcm.edu	37	19	17305440	17305440	+	Silent	SNP	T	T	C	rs1064305	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17305440T>C	ENST00000594824.1	+	22	3351	c.3204T>C	c.(3202-3204)ggT>ggC	p.G1068G	MYO9B_ENST00000397274.2_Silent_p.G1068G|MYO9B_ENST00000595618.1_Silent_p.G1068G			Q13459	MYO9B_HUMAN	myosin IXB	1068	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						CAAGAGCAGGTGCTGAGGAGG	0.642													C|||	3226	0.644169	0.7905	0.7046	5008	,	,		16150	0.7401		0.3877	False		,,,				2504	0.5685				p.G1068G		Atlas-SNP	.											.	MYO9B	264	.	0			c.T3204C						PASS	.	C	,	3162,1184		1162,838,173	18.0	23.0	21.0		3204,3204	-8.2	0.0	19	dbSNP_86	21	3437,5121		723,1991,1565	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1885,2829,1738	CC,CT,TT		40.1613,27.2434,48.8608	,	1068/2023,1068/2158	17305440	6599,6305	2173	4279	6452	SO:0001819	synonymous_variant	4650	exon22			AGCAGGTGCTGAG		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.3204T>C	19.37:g.17305440T>C		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				T|0.392;C|0.608	0.608	strong		0.642	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
MYO9B	4650	hgsc.bcm.edu	37	19	17312992	17312992	+	Silent	SNP	C	C	T	rs2305765	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17312992C>T	ENST00000594824.1	+	28	4863	c.4716C>T	c.(4714-4716)gtC>gtT	p.V1572V	MYO9B_ENST00000397274.2_Silent_p.V1572V|MYO9B_ENST00000595618.1_Silent_p.V1572V			Q13459	MYO9B_HUMAN	myosin IXB	1572	Tail.				actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						ACCAGATCGTCGTCAGCAACC	0.577													C|||	3007	0.600439	0.5991	0.6729	5008	,	,		21436	0.746		0.3897	False		,,,				2504	0.6176				p.V1572V		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,+2,2	MYO9B	264	2	0			c.C4716T						PASS	.	C	,	2172,1850		592,988,431	50.0	53.0	52.0		4716,4716	-9.0	0.7	19	dbSNP_100	52	3313,5069		672,1969,1550	no	coding-synonymous,coding-synonymous	MYO9B	NM_001130065.1,NM_004145.3	,	1264,2957,1981	TT,TC,CC		39.5252,45.997,44.2196	,	1572/2023,1572/2158	17312992	5485,6919	2011	4191	6202	SO:0001819	synonymous_variant	4650	exon28			GATCGTCGTCAGC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.4716C>T	19.37:g.17312992C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Silent	SNP	ENST00000594824.1	37																																																																																				C|0.436;T|0.564	0.564	strong		0.577	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
SOGA1	140710	hgsc.bcm.edu	37	20	35414905	35414905	+	Missense_Mutation	SNP	G	G	T	rs73109216	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:35414905G>T	ENST00000357779.3	-	15	4581	c.4255C>A	c.(4255-4257)Ctc>Atc	p.L1419I	SOGA1_ENST00000237536.4_Missense_Mutation_p.L1657I|SOGA1_ENST00000456801.2_Missense_Mutation_p.L1260I|SOGA1_ENST00000279034.6_Intron			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	1419					insulin receptor signaling pathway (GO:0008286)|negative regulation of gluconeogenesis (GO:0045721)|regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(5)|kidney(1)|lung(21)|urinary_tract(1)	28						CTGGGGGGGAGTGCCCTCTCC	0.662													G|||	261	0.0521166	0.003	0.1412	5008	,	,		17075	0.0		0.0825	False		,,,				2504	0.0777				p.L1657I		Atlas-SNP	.											.	SOGA1	136	.	0			c.C4969A						PASS	.						38.0	44.0	42.0					20																	35414905		692	1591	2283	SO:0001583	missense	140710	exon15			GGGGGAGTGCCCT	AK126630	CCDS46598.1, CCDS54459.1	20q11.23	2012-03-01	2012-02-27	2012-02-27	ENSG00000149639	ENSG00000149639			16111	protein-coding gene	gene with protein product	"""suppressor of glucose by autophagy"", ""suppressor of glucose from autophagy"""		"""chromosome 20 open reading frame 117"", ""KIAA0889"""	C20orf117, KIAA0889		20813965	Standard	NM_080627		Approved	dJ132F21.1, FLJ44670, SOGA	uc021wcx.1	O94964	OTTHUMG00000032395	ENST00000357779.3:c.4255C>A	20.37:g.35414905G>T	ENSP00000350424:p.Leu1419Ile	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	9	0.391304	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		109	0.04990842490842491	3	0.006097560975609756	44	0.12154696132596685	0	0.0	62	0.08179419525065963	G	10.85	1.467932	0.26335	.	.	ENSG00000149639	ENST00000237536;ENST00000456801;ENST00000357779	T;T;T	0.17213	2.29;2.3;2.3	4.72	2.72	0.32119	.	1.008940	0.07937	N	0.978596	T	0.00178	0.0005	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.43360	-0.9396	8	0.62326	D	0.03	-0.4527	11.4719	0.50275	0.0:0.6416:0.3584:0.0	.	.	.	.	I	1657;1260;1419	ENSP00000237536:L1657I;ENSP00000413886:L1260I;ENSP00000350424:L1419I	ENSP00000237536:L1657I	L	-	1	0	KIAA0889	34848319	0.100000	0.21855	0.005000	0.12908	0.474000	0.32979	3.383000	0.52471	0.704000	0.31869	-0.539000	0.04255	CTC	G|0.950;T|0.050	0.050	strong		0.662	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77327042	77327042	+	Silent	SNP	C	C	T	rs61754842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:77327042C>T	ENST00000282849.5	-	20	3538	c.3120G>A	c.(3118-3120)caG>caA	p.Q1040Q	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1040	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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						CACAGCCCTCCTGCAGCTCAG	0.607													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		15978	0.0		0.005	False		,,,				2504	0.0031				p.Q1040Q		Atlas-SNP	.											ADAMTS18,breast,lymphoid_neoplasm,-2,1	ADAMTS18	270	1	0			c.G3120A						PASS	.	C		8,4388	14.3+/-33.2	0,8,2190	86.0	81.0	82.0		3120	3.0	1.0	16	dbSNP_129	82	65,8535	40.8+/-97.7	1,63,4236	no	coding-synonymous	ADAMTS18	NM_199355.2		1,71,6426	TT,TC,CC		0.7558,0.182,0.5617		1040/1222	77327042	73,12923	2198	4300	6498	SO:0001819	synonymous_variant	170692	exon20			GCCCTCCTGCAGC	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.3120G>A	16.37:g.77327042C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	61	39	0.639344	NM_199355	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																			C|0.995;T|0.005	0.005	strong		0.607	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
IP6K3	117283	hgsc.bcm.edu	37	6	33703230	33703230	+	Silent	SNP	G	G	A	rs545787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33703230G>A	ENST00000293756.4	-	2	350	c.24C>T	c.(22-24)gaC>gaT	p.D8D	IP6K3_ENST00000451316.1_Silent_p.D8D	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	8					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						TGTCCCCGGCGTCTGCGCTGT	0.607													G|||	1672	0.333866	0.7171	0.2378	5008	,	,		19059	0.0675		0.331	False		,,,				2504	0.1616				p.D8D		Atlas-SNP	.											IP6K3_ENST00000451316,NS,carcinoma,0,2	IP6K3	52	2	0			c.C24T						PASS	.	G	,	2841,1565	654.5+/-399.8	909,1023,271	48.0	37.0	41.0		24,24	-10.5	0.0	6	dbSNP_83	41	3127,5473	468.6+/-367.3	593,1941,1766	no	coding-synonymous,coding-synonymous	IP6K3	NM_001142883.1,NM_054111.4	,	1502,2964,2037	AA,AG,GG		36.3605,35.5197,45.8865	,	8/411,8/411	33703230	5968,7038	2203	4300	6503	SO:0001819	synonymous_variant	117283	exon3			CCCGGCGTCTGCG	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.24C>T	6.37:g.33703230G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	48	24	0.5	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	37	CCDS34435.1																																																																																			G|0.598;A|0.402	0.402	strong		0.607	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
RAI1	10743	hgsc.bcm.edu	37	17	17700573	17700573	+	Silent	SNP	T	T	C	rs4925112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:17700573T>C	ENST00000353383.1	+	3	4780	c.4311T>C	c.(4309-4311)ccT>ccC	p.P1437P	RAI1_ENST00000261641.6_Silent_p.P1437P	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1437					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CCCTGCAGCCTGGGGGGACTG	0.587													C|||	474	0.0946486	0.2655	0.0447	5008	,	,		16820	0.0069		0.0577	False		,,,				2504	0.0276				p.P1437P		Atlas-SNP	.											.	RAI1	121	.	0			c.T4311C						PASS	.	C		1089,3317	685.0+/-404.5	142,805,1256	30.0	35.0	33.0		4311	-1.9	0.0	17	dbSNP_111	33	518,8082	771.5+/-407.7	19,480,3801	no	coding-synonymous	RAI1	NM_030665.3		161,1285,5057	CC,CT,TT		6.0233,24.7163,12.3558		1437/1907	17700573	1607,11399	2203	4300	6503	SO:0001819	synonymous_variant	10743	exon3			GCAGCCTGGGGGG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.4311T>C	17.37:g.17700573T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			T|0.888;C|0.112	0.112	strong		0.587	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
OR2T5	401993	hgsc.bcm.edu	37	1	248651959	248651959	+	Nonsense_Mutation	SNP	C	C	T	rs76332972	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248651959C>T	ENST00000366473.2	+	1	75	c.70C>T	c.(70-72)Cga>Tga	p.R24*		NM_001004697.1	NP_001004697.1	Q6IEZ7	OR2T5_HUMAN	olfactory receptor, family 2, subfamily T, member 5	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R24*(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(2)|pancreas(1)|skin(2)	9	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACTCTTCAGACGATCCAAACA	0.488																																					p.R24X		Atlas-SNP	.											OR2T5,lymph_node,lymphoid_neoplasm,0,1	OR2T5	17	1	1	Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C70T						scavenged	.						142.0	158.0	153.0					1																	248651959		2199	4298	6497	SO:0001587	stop_gained	401993	exon1			TTCAGACGATCCA	BK004465	CCDS31118.1	1q44	2012-08-09			ENSG00000203661	ENSG00000203661		"""GPCR / Class A : Olfactory receptors"""	15017	protein-coding gene	gene with protein product							Standard	NM_001004697		Approved		uc001iem.1	Q6IEZ7	OTTHUMG00000040481	ENST00000366473.2:c.70C>T	1.37:g.248651959C>T	ENSP00000355429:p.Arg24*	Somatic	727	0	0		WXS	Illumina HiSeq	Phase_I	800	132	0.165	NM_001004697		Nonsense_Mutation	SNP	ENST00000366473.2	37	CCDS31118.1	.	.	.	.	.	.	.	.	.	.	c	15.09	2.729737	0.48833	.	.	ENSG00000203661	ENST00000366473	.	.	.	2.64	1.54	0.23209	.	0.522929	0.16025	N	0.233106	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	.	5.1952	0.15233	0.2:0.4456:0.3544:0.0	.	.	.	.	X	24	.	ENSP00000355429:R24X	R	+	1	2	OR2T5	246718582	0.000000	0.05858	0.615000	0.29064	0.085000	0.17905	-1.396000	0.02513	1.222000	0.43521	0.413000	0.27773	CGA	C|0.983;T|0.016	0.016	strong		0.488	OR2T5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097422.1	NM_001004697	
SCARA3	51435	hgsc.bcm.edu	37	8	27528446	27528446	+	Missense_Mutation	SNP	T	T	C	rs17057523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27528446T>C	ENST00000301904.3	+	6	1419	c.1399T>C	c.(1399-1401)Ttc>Ctc	p.F467L	SCARA3_ENST00000337221.4_Intron	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	467	Collagen-like 1.		F -> L (in dbSNP:rs17057523). {ECO:0000269|Ref.2}.		receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		ACCAAGAGGATTCAAAGGAGA	0.662													C|||	610	0.121805	0.0635	0.1066	5008	,	,		16266	0.2302		0.0755	False		,,,				2504	0.1472				p.F467L		Atlas-SNP	.											.	SCARA3	93	.	0			c.T1399C						PASS	.	C	LEU/PHE,	350,4056		15,320,1868	63.0	73.0	69.0		1399,	2.8	1.0	8	dbSNP_123	69	542,8052		12,518,3767	yes	missense,intron	SCARA3	NM_016240.2,NM_182826.1	22,	27,838,5635	CC,CT,TT		6.3067,7.9437,6.8615	benign,	467/607,	27528446	892,12108	2203	4297	6500	SO:0001583	missense	51435	exon6			AGAGGATTCAAAG	AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"""macrophage scavenger receptor-like 1"""	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.1399T>C	8.37:g.27528446T>C	ENSP00000301904:p.Phe467Leu	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	67	28	0.41791	NM_016240	Q9UM15|Q9UM16	Missense_Mutation	SNP	ENST00000301904.3	37	CCDS34871.1	261	0.11950549450549451	24	0.04878048780487805	35	0.09668508287292818	148	0.25874125874125875	54	0.0712401055408971	C	10.10	1.258527	0.23051	0.079437	0.063067	ENSG00000168077	ENST00000301904	D	0.93076	-3.16	5.61	2.79	0.32731	.	0.731067	0.13533	N	0.380768	T	0.00039	0.0001	N	0.02103	-0.685	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.08229	-1.0732	9	0.11182	T	0.66	-4.7032	6.3532	0.21387	0.0:0.6357:0.1344:0.2299	rs17057523;rs17057523	467	Q6AZY7	SCAR3_HUMAN	L	467	ENSP00000301904:F467L	ENSP00000301904:F467L	F	+	1	0	SCARA3	27584365	0.031000	0.19500	1.000000	0.80357	0.091000	0.18340	-0.047000	0.11963	0.309000	0.22966	-1.147000	0.01851	TTC	T|0.908;C|0.092	0.092	strong		0.662	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240	
PARP4	143	hgsc.bcm.edu	37	13	25009297	25009297	+	Missense_Mutation	SNP	G	G	T	rs1050112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25009297G>T	ENST00000381989.3	-	31	4087	c.3982C>A	c.(3982-3984)Ccc>Acc	p.P1328T		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1328				P -> T (in Ref. 1; AAD47250, 2; AAC62491 and 3; BAA11494). {ECO:0000305}.	cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GCAGTCGGGGGAAGATAGGAA	0.493													g|||	1928	0.384984	0.4849	0.3473	5008	,	,		19272	0.3601		0.4115	False		,,,				2504	0.2751				p.P1328T		Atlas-SNP	.											.	PARP4	142	.	0			c.C3982A						PASS	.	G	THR/PRO	2075,2331	570.1+/-382.8	471,1133,599	84.0	91.0	89.0		3982	-4.7	0.0	13	dbSNP_86	89	3204,5396	483.3+/-371.1	594,2016,1690	yes	missense	PARP4	NM_006437.3	38	1065,3149,2289	TT,TG,GG		37.2558,47.0949,40.589	benign	1328/1725	25009297	5279,7727	2203	4300	6503	SO:0001583	missense	143	exon31			TCGGGGGAAGATA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3982C>A	13.37:g.25009297G>T	ENSP00000371419:p.Pro1328Thr	Somatic	167	1	0.00598802		WXS	Illumina HiSeq	Phase_I	130	125	0.961538	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	842	0.38553113553113555	226	0.45934959349593496	121	0.3342541436464088	181	0.31643356643356646	314	0.41424802110817943	g	0.123	-1.122756	0.01785	0.470949	0.372558	ENSG00000102699	ENST00000381989	T	0.01705	4.68	2.34	-4.69	0.03299	.	18.580100	0.00559	U	0.000278	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.13145	0.007	B	0.12156	0.007	T	0.43572	-0.9383	9	0.15499	T	0.54	.	8.7913	0.34852	0.4246:0.0:0.5754:0.0	rs1050112;rs3190396;rs3742175;rs58385276;rs1050112	1328	Q9UKK3	PARP4_HUMAN	T	1328	ENSP00000371419:P1328T	ENSP00000371419:P1328T	P	-	1	0	PARP4	23907297	0.003000	0.15002	0.000000	0.03702	0.000000	0.00434	0.632000	0.24583	-1.483000	0.01858	-1.800000	0.00619	CCC	G|0.603;T|0.397	0.397	strong		0.493	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
TTC5	91875	hgsc.bcm.edu	37	14	20770036	20770036	+	Missense_Mutation	SNP	T	T	C	rs3742945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20770036T>C	ENST00000258821.3	-	2	196	c.140A>G	c.(139-141)cAg>cGg	p.Q47R		NM_138376.2	NP_612385.2	Q8N0Z6	TTC5_HUMAN	tetratricopeptide repeat domain 5	47			Q -> R (in dbSNP:rs3742945). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		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)		CATCTCCTTCTGCACATCCTG	0.458													C|||	3734	0.745607	0.7579	0.8559	5008	,	,		22041	0.7956		0.7406	False		,,,				2504	0.6043				p.Q47R		Atlas-SNP	.											TTC5,NS,adenoma,0,1	TTC5	34	1	0			c.A140G						scavenged	.	C	ARG/GLN	3294,1112	398.1+/-330.7	1231,832,140	237.0	181.0	200.0		140	0.4	0.9	14	dbSNP_107	200	6294,2306	387.1+/-342.1	2309,1676,315	yes	missense	TTC5	NM_138376.2	43	3540,2508,455	CC,CT,TT		26.814,25.2383,26.2802	benign	47/441	20770036	9588,3418	2203	4300	6503	SO:0001583	missense	91875	exon2			TCCTTCTGCACAT	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.140A>G	14.37:g.20770036T>C	ENSP00000258821:p.Gln47Arg	Somatic	215	2	0.00930233		WXS	Illumina HiSeq	Phase_I	217	98	0.451613	NM_138376	A8MQ18|Q96HF9	Missense_Mutation	SNP	ENST00000258821.3	37	CCDS9546.1	1696	0.7765567765567766	370	0.7520325203252033	302	0.8342541436464088	459	0.8024475524475524	565	0.7453825857519789	C	0.248	-1.008434	0.02112	0.747617	0.73186	ENSG00000136319	ENST00000258821	T	0.28666	1.6	4.31	0.384	0.16244	Tetratricopeptide-like helical (1);	0.511690	0.21623	N	0.071602	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	0.27262	-1.0079	9	0.08179	T	0.78	.	8.8128	0.34978	0.0:0.4622:0.0:0.5378	rs3742945;rs17845175;rs17856898;rs17857985;rs17859578;rs52798233;rs60485527;rs3742945	47	Q8N0Z6	TTC5_HUMAN	R	47	ENSP00000258821:Q47R	ENSP00000258821:Q47R	Q	-	2	0	TTC5	19839876	0.000000	0.05858	0.892000	0.35008	0.788000	0.44548	-0.336000	0.07863	-0.367000	0.08052	-0.996000	0.02517	CAG	T|0.243;C|0.757	0.757	strong		0.458	TTC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073529.4	NM_138376	
KCTD19	146212	hgsc.bcm.edu	37	16	67327642	67327642	+	Missense_Mutation	SNP	C	C	T	rs145649592	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67327642C>T	ENST00000304372.5	-	12	2078	c.2023G>A	c.(2023-2025)Gag>Aag	p.E675K		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	675					protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		GAAGCAGCCTCGCTTCCCAAG	0.617													C|||	14	0.00279553	0.0	0.0029	5008	,	,		17949	0.0		0.006	False		,,,				2504	0.0061				p.E675K		Atlas-SNP	.											.	KCTD19	82	.	0			c.G2023A						PASS	.	C	LYS/GLU	2,4160		0,2,2079	76.0	86.0	83.0		2023	4.9	0.9	16	dbSNP_134	83	43,8353		0,43,4155	yes	missense	KCTD19	NM_001100915.1	56	0,45,6234	TT,TC,CC		0.5121,0.0481,0.3583	probably-damaging	675/927	67327642	45,12513	2081	4198	6279	SO:0001583	missense	146212	exon12			CAGCCTCGCTTCC	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 19"""				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.2023G>A	16.37:g.67327642C>T	ENSP00000305702:p.Glu675Lys	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	37	CCDS42179.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	13.27	2.187741	0.38609	4.81E-4	0.005121	ENSG00000168676	ENST00000304372	T	0.58940	0.3	5.86	4.92	0.64577	.	0.101032	0.43747	D	0.000539	T	0.37945	0.1022	N	0.24115	0.695	0.27940	N	0.937539	D	0.67145	0.996	P	0.48063	0.565	T	0.31052	-0.9957	10	0.32370	T	0.25	-21.685	9.3289	0.38010	0.0:0.8369:0.0:0.1631	.	675	Q17RG1	KCD19_HUMAN	K	675	ENSP00000305702:E675K	ENSP00000305702:E675K	E	-	1	0	KCTD19	65885143	0.747000	0.28283	0.940000	0.37924	0.914000	0.54420	1.272000	0.33109	1.493000	0.48517	-0.244000	0.11960	GAG	C|0.997;T|0.003	0.003	strong		0.617	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367	
C9orf135	138255	hgsc.bcm.edu	37	9	72472831	72472831	+	Silent	SNP	C	C	T	rs10780682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:72472831C>T	ENST00000377197.3	+	4	474	c.387C>T	c.(385-387)acC>acT	p.T129T	C9orf135_ENST00000466872.2_3'UTR|C9orf135_ENST00000527647.1_Silent_p.T129T	NM_001010940.1	NP_001010940.1	Q5VTT2	CI135_HUMAN	chromosome 9 open reading frame 135	129						integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						TTAGGGTCACCGGATTGCCTG	0.403													c|||	1355	0.270567	0.0938	0.2925	5008	,	,		19323	0.4067		0.331	False		,,,				2504	0.2914				p.T129T		Atlas-SNP	.											.	C9orf135	25	.	0			c.C387T						PASS	.	T		620,3786	268.3+/-268.4	52,516,1635	108.0	99.0	102.0		387	-0.0	1.0	9	dbSNP_120	102	2875,5725	450.6+/-362.4	469,1937,1894	no	coding-synonymous	C9orf135	NM_001010940.1		521,2453,3529	TT,TC,CC		33.4302,14.0717,26.8722		129/230	72472831	3495,9511	2203	4300	6503	SO:0001819	synonymous_variant	138255	exon4			GGTCACCGGATTG		CCDS35041.1	9q21.11	2013-06-07	2013-06-07	2013-06-07	ENSG00000204711	ENSG00000204711			31422	protein-coding gene	gene with protein product							Standard	XM_005251705		Approved		uc004ahl.3	Q5VTT2	OTTHUMG00000019985	ENST00000377197.3:c.387C>T	9.37:g.72472831C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001010940	A7E2U4|B2RN61	Silent	SNP	ENST00000377197.3	37	CCDS35041.1	631	0.2889194139194139	42	0.08536585365853659	112	0.30939226519337015	209	0.36538461538461536	268	0.35356200527704484	c	0.127	-1.118773	0.01785	0.140717	0.334302	ENSG00000204711	ENST00000480564	.	.	.	5.2	-0.0103	0.13997	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999979904	.	.	.	.	.	.	T	0.44452	-0.9327	3	.	.	.	-10.0596	4.5019	0.11869	0.1462:0.1956:0.0:0.6582	rs10780682;rs17518953;rs56592328;rs10780682	.	.	.	W	103	.	.	R	+	1	2	C9orf135	71662651	0.991000	0.36638	0.986000	0.45419	0.004000	0.04260	0.095000	0.15127	-0.170000	0.10816	-1.120000	0.02017	CGG	C|0.722;T|0.278	0.278	strong		0.403	C9orf135-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052591.1	NM_001010940	
TTC27	55622	hgsc.bcm.edu	37	2	32983526	32983526	+	Silent	SNP	C	C	T	rs2273665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:32983526C>T	ENST00000317907.4	+	13	1851	c.1620C>T	c.(1618-1620)aaC>aaT	p.N540N		NM_001193509.1|NM_017735.4	NP_001180438.1|NP_060205.3	Q6P3X3	TTC27_HUMAN	tetratricopeptide repeat domain 27	540								p.N540N(1)		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						ATCTTCGGAACAAGGAGTTTC	0.527													C|||	1467	0.292931	0.1536	0.3718	5008	,	,		17491	0.3671		0.4125	False		,,,				2504	0.226				p.N540N		Atlas-SNP	.											TTC27,NS,carcinoma,0,1	TTC27	71	1	1	Substitution - coding silent(1)	stomach(1)	c.C1620T						PASS	.	C	,	923,3483	351.3+/-311.2	88,747,1368	100.0	92.0	94.0		1470,1620	5.9	0.7	2	dbSNP_100	94	3528,5072	514.7+/-378.4	732,2064,1504	no	coding-synonymous,coding-synonymous	TTC27	NM_001193509.1,NM_017735.4	,	820,2811,2872	TT,TC,CC		41.0233,20.9487,34.2227	,	490/794,540/844	32983526	4451,8555	2203	4300	6503	SO:0001819	synonymous_variant	55622	exon13			TCGGAACAAGGAG	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.1620C>T	2.37:g.32983526C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_017735	A6NKJ0|Q96SS5|Q9BVF1|Q9NWR4|Q9NXG4	Silent	SNP	ENST00000317907.4	37	CCDS33176.1																																																																																			C|0.676;N|0.000	.	strong		0.527	TTC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325395.1	NM_017735	
MDN1	23195	hgsc.bcm.edu	37	6	90497589	90497589	+	Missense_Mutation	SNP	A	A	C	rs4707569	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90497589A>C	ENST00000369393.3	-	8	1433	c.1318T>G	c.(1318-1320)Ttt>Gtt	p.F440V	MDN1_ENST00000428876.1_Missense_Mutation_p.F440V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	440			F -> V (in dbSNP:rs4707569).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GTTGCAAAAAACTGAAATCCA	0.463													A|||	771	0.153954	0.1399	0.1398	5008	,	,		17057	0.2163		0.1819	False		,,,				2504	0.09				p.F440V		Atlas-SNP	.											.	MDN1	478	.	0			c.T1318G						PASS	.	A	VAL/PHE	719,3687	292.1+/-281.9	63,593,1547	102.0	97.0	99.0		1318	4.4	1.0	6	dbSNP_111	99	1536,7064	284.2+/-296.5	142,1252,2906	yes	missense	MDN1	NM_014611.1	50	205,1845,4453	CC,CA,AA		17.8605,16.3187,17.3382	benign	440/5597	90497589	2255,10751	2203	4300	6503	SO:0001583	missense	23195	exon8			CAAAAAACTGAAA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.1318T>G	6.37:g.90497589A>C	ENSP00000358400:p.Phe440Val	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	14	12	0.857143	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	370	0.16941391941391942	54	0.10975609756097561	45	0.12430939226519337	127	0.22202797202797203	144	0.18997361477572558	A	11.90	1.777902	0.31502	0.163187	0.178605	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.46819	0.86;0.86	5.65	4.45	0.53987	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.051750	0.85682	D	0.000000	T	0.16428	0.0395	N	0.13235	0.315	0.27005	P	0.9648156999999999	P;B	0.40000	0.698;0.036	B;B	0.40702	0.338;0.065	T	0.07009	-1.0795	9	0.51188	T	0.08	.	8.4306	0.32755	0.7872:0.0:0.2128:0.0	rs4707569;rs61658597;rs4707569	440;440	Q6ZVV6;Q9NU22	.;MDN1_HUMAN	V	440	ENSP00000358400:F440V;ENSP00000413970:F440V	ENSP00000358400:F440V	F	-	1	0	MDN1	90554310	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.988000	0.56951	1.031000	0.39867	0.460000	0.39030	TTT	A|0.832;C|0.168	0.168	strong		0.463	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
URB1	9875	hgsc.bcm.edu	37	21	33757947	33757947	+	Missense_Mutation	SNP	A	A	T	rs58978310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33757947A>T	ENST00000382751.3	-	2	304	c.189T>A	c.(187-189)gaT>gaA	p.D63E		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	63						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						CATCATACACATCTTCTCGTG	0.388													A|||	603	0.120407	0.2443	0.0821	5008	,	,		18902	0.0417		0.1133	False		,,,				2504	0.0685				p.D63E		Atlas-SNP	.											.	URB1	176	.	0			c.T189A						PASS	.	A	GLU/ASP	317,1067		32,253,407	184.0	140.0	154.0		189	-7.4	0.0	21	dbSNP_129	154	369,2813		27,315,1249	yes	missense	URB1	NM_014825.2	45	59,568,1656	TT,TA,AA		11.5965,22.9046,15.0241	benign	63/2272	33757947	686,3880	692	1591	2283	SO:0001583	missense	9875	exon2			ATACACATCTTCT	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.189T>A	21.37:g.33757947A>T	ENSP00000372199:p.Asp63Glu	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	132	67	0.507576	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	250	0.11446886446886446	114	0.23170731707317074	31	0.0856353591160221	22	0.038461538461538464	83	0.10949868073878628	A	8.880	0.951322	0.18431	0.229046	0.115965	ENSG00000142207	ENST00000382751	T	0.31510	1.49	5.29	-7.38	0.01407	.	0.198259	0.41823	D	0.000815	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	5.000000000032756E-6	B	0.21071	0.051	B	0.12156	0.007	T	0.25012	-1.0144	9	0.19590	T	0.45	-17.1729	3.9847	0.09511	0.4121:0.2161:0.2974:0.0745	rs58978310	63	O60287	NPA1P_HUMAN	E	63	ENSP00000372199:D63E	ENSP00000372199:D63E	D	-	3	2	URB1	32679818	0.000000	0.05858	0.001000	0.08648	0.523000	0.34469	-1.471000	0.02344	-1.062000	0.03181	-0.464000	0.05259	GAT	A|0.887;T|0.113	0.113	strong		0.388	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
LRRC15	131578	hgsc.bcm.edu	37	3	194080916	194080916	+	Missense_Mutation	SNP	G	G	A	rs13070515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194080916G>A	ENST00000347624.3	-	2	942	c.857C>T	c.(856-858)cCg>cTg	p.P286L	LRRC15_ENST00000428839.1_Missense_Mutation_p.P292L|LRRC15_ENST00000439944.2_Missense_Mutation_p.P292L	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	286			P -> L (in dbSNP:rs13070515). {ECO:0000269|PubMed:11785964, ECO:0000269|PubMed:12923058}.		negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		GAAGATCCCCGGAGAGAGCTC	0.567													G|||	585	0.116813	0.093	0.1052	5008	,	,		18233	0.0685		0.2107	False		,,,				2504	0.1104				p.P292L		Atlas-SNP	.											.	LRRC15	137	.	0			c.C875T						PASS	.	G	LEU/PRO,LEU/PRO	432,3974	204.8+/-226.9	17,398,1788	80.0	88.0	86.0		875,857	5.2	0.5	3	dbSNP_121	86	2014,6586	352.1+/-328.5	240,1534,2526	no	missense,missense	LRRC15	NM_001135057.2,NM_130830.4	98,98	257,1932,4314	AA,AG,GG		23.4186,9.8048,18.8067	probably-damaging,probably-damaging	292/588,286/582	194080916	2446,10560	2203	4300	6503	SO:0001583	missense	131578	exon3			ATCCCCGGAGAGA	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.857C>T	3.37:g.194080916G>A	ENSP00000306276:p.Pro286Leu	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	190	106	0.557895	NM_001135057	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	303	0.13873626373626374	42	0.08536585365853659	42	0.11602209944751381	48	0.08391608391608392	171	0.22559366754617413	G	19.66	3.868769	0.72065	0.098048	0.234186	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.10860	2.83;2.83;2.83	5.15	5.15	0.70609	.	.	.	.	.	T	0.00012	0.0000	M	0.76938	2.355	0.09310	P	0.99999898181	D;D	0.89917	0.999;1.0	D;D	0.72338	0.948;0.977	T	0.03587	-1.1022	8	0.38643	T	0.18	.	15.3756	0.74602	0.0:0.1397:0.8603:0.0	rs13070515;rs52793039;rs61442620;rs13070515	286;292	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	L	286;292;292	ENSP00000306276:P286L;ENSP00000389128:P292L;ENSP00000413707:P292L	ENSP00000306276:P286L	P	-	2	0	LRRC15	195562211	1.000000	0.71417	0.500000	0.27589	0.931000	0.56810	6.486000	0.73629	2.566000	0.86566	0.655000	0.94253	CCG	G|0.843;A|0.157	0.157	strong		0.567	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
ZNF646	9726	hgsc.bcm.edu	37	16	31092075	31092075	+	Missense_Mutation	SNP	G	G	A	rs7196726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31092075G>A	ENST00000394979.2	+	1	4853	c.4430G>A	c.(4429-4431)gGc>gAc	p.G1477D	ZNF646_ENST00000300850.5_Missense_Mutation_p.G1477D			O15015	ZN646_HUMAN	zinc finger protein 646	1477			G -> D (in dbSNP:rs7196726).		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						CATAGTGGAGGCTGGGTTCCT	0.607													G|||	2395	0.478235	0.652	0.4294	5008	,	,		18558	0.1121		0.3748	False		,,,				2504	0.7618				p.G1477D		Atlas-SNP	.											.	ZNF646	133	.	0			c.G4430A						PASS	.	G	ASP/GLY	2709,1685	641.1+/-397.4	848,1013,336	55.0	69.0	64.0		4430	-4.8	0.0	16	dbSNP_116	64	3122,5478	471.1+/-368.0	567,1988,1745	yes	missense	ZNF646	NM_014699.3	94	1415,3001,2081	AA,AG,GG		36.3023,38.3477,44.8746	benign	1477/1833	31092075	5831,7163	2197	4300	6497	SO:0001583	missense	9726	exon2			GTGGAGGCTGGGT	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.4430G>A	16.37:g.31092075G>A	ENSP00000378429:p.Gly1477Asp	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	44	25	0.568182	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		767	0.35119047619047616	305	0.6199186991869918	139	0.3839779005524862	47	0.08216783216783216	276	0.3641160949868074	G	0.007	-1.953373	0.00470	0.616523	0.363023	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.07327	3.2;3.23	4.92	-4.78	0.03209	.	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.36648	-0.9739	8	0.17369	T	0.5	0.0157	4.0415	0.09753	0.1982:0.2104:0.4904:0.1011	rs7196726;rs52802967;rs59245988;rs7196726	1477	O15015-2	.	D	1477	ENSP00000300850:G1477D;ENSP00000378429:G1477D	ENSP00000300850:G1477D	G	+	2	0	ZNF646	30999576	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	-0.620000	0.05565	-0.989000	0.03485	-0.145000	0.13849	GGC	G|0.587;A|0.413	0.413	strong		0.607	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57076080	57076080	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57076080C>T	ENST00000532437.1	-	5	4416	c.4105G>A	c.(4105-4107)Ggg>Agg	p.G1369R	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.G1369R			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1369	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)				TGGCTCACCCCGCCCACCCCA	0.667																																					p.G1369R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4105A						PASS	.						59.0	69.0	65.0					11																	57076080		2201	4296	6497	SO:0001583	missense	85456	exon6			TCACCCCGCCCAC	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.4105G>A	11.37:g.57076080C>T	ENSP00000437271:p.Gly1369Arg	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	C	8.708	0.911309	0.17833	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.28666	1.6;1.6	4.78	1.35	0.21983	.	1.049680	0.07553	N	0.915820	T	0.12944	0.0314	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31916	-0.9926	10	0.20046	T	0.44	-1.079	6.365	0.21449	0.0:0.4339:0.4537:0.1124	.	1369	Q9C0C2	TB182_HUMAN	R	1369	ENSP00000350990:G1369R;ENSP00000437271:G1369R	ENSP00000350990:G1369R	G	-	1	0	TNKS1BP1	56832656	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.405000	0.21015	0.512000	0.28257	0.462000	0.41574	GGG	.	.	none		0.667	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
DOC2A	8448	hgsc.bcm.edu	37	16	30017536	30017536	+	Missense_Mutation	SNP	G	G	C	rs202062683	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30017536G>C	ENST00000350119.4	-	11	1364	c.1174C>G	c.(1174-1176)Cct>Gct	p.P392A	DOC2A_ENST00000564979.1_Missense_Mutation_p.P392A|DOC2A_ENST00000564944.1_Missense_Mutation_p.P392A	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	392	Interaction with UNC13D.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						CCGGCCGCAGGGGGCAGCTCA	0.692													G|||	12	0.00239617	0.0023	0.0029	5008	,	,		15719	0.0		0.006	False		,,,				2504	0.001				p.P392A		Atlas-SNP	.											.	DOC2A	40	.	0			c.C1174G						PASS	.	G	ALA/PRO	3,4359		0,3,2178	9.0	9.0	9.0		1174	1.9	0.3	16		9	73,8487		0,73,4207	no	missense	DOC2A	NM_003586.2	27	0,76,6385	CC,CG,GG		0.8528,0.0688,0.5881	possibly-damaging	392/401	30017536	76,12846	2181	4280	6461	SO:0001583	missense	8448	exon11			CCGCAGGGGGCAG	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.1174C>G	16.37:g.30017536G>C	ENSP00000340017:p.Pro392Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	37	CCDS10666.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.413386	0.00191	6.88E-4	0.008528	ENSG00000149927	ENST00000350119	T	0.61040	0.14	5.09	1.85	0.25348	.	0.263699	0.27048	N	0.021185	T	0.31765	0.0807	L	0.44542	1.39	0.25635	N	0.986269	P	0.35745	0.518	B	0.30316	0.114	T	0.34153	-0.9840	10	0.02654	T	1	.	12.9913	0.58620	0.0:0.4802:0.5198:0.0	.	392	Q14183	DOC2A_HUMAN	A	392	ENSP00000340017:P392A	ENSP00000340017:P392A	P	-	1	0	DOC2A	29925037	0.913000	0.31002	0.274000	0.24659	0.075000	0.17131	-0.678000	0.05209	0.214000	0.20742	0.491000	0.48974	CCT	.	.	weak		0.692	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14850375	14850375	+	Silent	SNP	G	G	A	rs3126404	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:14850375G>A	ENST00000358984.4	+	35	3381	c.3201G>A	c.(3199-3201)ttG>ttA	p.L1067L		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	1067										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						CAAGTAATTTGAATCAGGTAA	0.303													G|||	2366	0.472444	0.5408	0.4251	5008	,	,		14547	0.4157		0.5149	False		,,,				2504	0.4284				p.L1067L		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.G3201A						PASS	.						34.0	34.0	34.0					18																	14850375		692	1568	2260	SO:0001819	synonymous_variant	374860	exon35			TAATTTGAATCAG	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.3201G>A	18.37:g.14850375G>A		Somatic	168	1	0.00595238		WXS	Illumina HiSeq	Phase_I	117	115	0.982906	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																			G|0.167;A|0.833	0.833	weak		0.303	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
CSMD3	114788	hgsc.bcm.edu	37	8	113364696	113364696	+	Silent	SNP	A	A	G	rs11778209	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:113364696A>G	ENST00000297405.5	-	39	6448	c.6204T>C	c.(6202-6204)taT>taC	p.Y2068Y	CSMD3_ENST00000343508.3_Silent_p.Y2028Y|CSMD3_ENST00000352409.3_Silent_p.Y1998Y|CSMD3_ENST00000455883.2_Silent_p.Y1964Y	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)				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						CTCCAACCATATATCTGTCTC	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	1253	0.2502	0.0673	0.3156	5008	,	,		16747	0.3938		0.2435	False		,,,				2504	0.3098				p.Y2068Y		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,-1,2	CSMD3	2325	2	0			c.T6204C						PASS	.	A	,,	373,4033	191.6+/-217.2	21,331,1851	111.0	103.0	106.0		5892,6204,6084	-7.8	0.8	8	dbSNP_120	106	1916,6682	339.2+/-323.1	218,1480,2601	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	239,1811,4452	GG,GA,AA		22.2843,8.4657,17.6023	,,	1964/3539,2068/3708,2028/3668	113364696	2289,10715	2203	4299	6502	SO:0001819	synonymous_variant	114788	exon39			AACCATATATCTG	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.6204T>C	8.37:g.113364696A>G		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	129	77	0.596899	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.790;G|0.210	0.210	strong		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
NPVF	64111	hgsc.bcm.edu	37	7	25267934	25267934	+	Missense_Mutation	SNP	T	T	C	rs877834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:25267934T>C	ENST00000222674.2	-	1	171	c.125A>G	c.(124-126)gAc>gGc	p.D42G		NM_022150.3	NP_071433	Q9HCQ7	NPVF_HUMAN	neuropeptide VF precursor	42			D -> G (in dbSNP:rs877834). {ECO:0000269|PubMed:11951088}.		negative regulation of gonadotropin secretion (GO:0032277)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|urinary_tract(1)	15						AGAATATTTGTCATAATTTTC	0.279													T|||	1238	0.247204	0.0908	0.2594	5008	,	,		18226	0.5129		0.1849	False		,,,				2504	0.2403				p.D42G		Atlas-SNP	.											.	NPVF	36	.	0			c.A125G						PASS	.	T	GLY/ASP	482,3916	217.8+/-236.0	32,418,1749	54.0	60.0	58.0		125	0.3	0.0	7	dbSNP_86	58	1574,7004	291.3+/-300.3	141,1292,2856	yes	missense	NPVF	NM_022150.3	94	173,1710,4605	CC,CT,TT		18.3493,10.9595,15.8446	benign	42/197	25267934	2056,10920	2199	4289	6488	SO:0001583	missense	64111	exon1			TATTTGTCATAAT	AB040290	CCDS5395.1	7p21-p15	2013-02-28	2006-10-06	2006-10-06	ENSG00000105954	ENSG00000105954		"""Endogenous ligands"""	13782	protein-coding gene	gene with protein product	"""RFamide-related peptide precursor"", ""FMRFamide-related peptide precursor"""		"""chromosome 7 open reading frame 9"""	C7orf9		11951088, 11173868	Standard	NM_022150		Approved	RFRP	uc003sxo.3	Q9HCQ7	OTTHUMG00000128509	ENST00000222674.2:c.125A>G	7.37:g.25267934T>C	ENSP00000222674:p.Asp42Gly	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_022150	A4D164|Q7LE27|Q96PI9	Missense_Mutation	SNP	ENST00000222674.2	37	CCDS5395.1	572	0.2619047619047619	44	0.08943089430894309	92	0.2541436464088398	293	0.5122377622377622	143	0.18865435356200527	T	8.124	0.781553	0.16120	0.109595	0.183493	ENSG00000105954	ENST00000222674	T	0.30981	1.51	5.57	0.266	0.15617	.	0.473353	0.19711	N	0.107806	T	0.00012	0.0000	L	0.54908	1.71	0.58432	P	1.0000000000287557E-6	B	0.11235	0.004	B	0.11329	0.006	T	0.43310	-0.9399	9	0.35671	T	0.21	-12.9291	4.4368	0.11554	0.0:0.281:0.1623:0.5567	rs877834;rs1130038;rs3177707;rs3188502;rs16873801;rs17412537;rs57473358;rs877834	42	Q9HCQ7	RFRP_HUMAN	G	42	ENSP00000222674:D42G	ENSP00000222674:D42G	D	-	2	0	NPVF	25234459	0.091000	0.21658	0.004000	0.12327	0.871000	0.50021	0.069000	0.14552	0.085000	0.17107	0.528000	0.53228	GAC	C|0.206;N|0.000	0.206	strong		0.279	NPVF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250315.1	NM_022150	
RWDD3	25950	hgsc.bcm.edu	37	1	95699829	95699829	+	Missense_Mutation	SNP	A	A	G	rs142820652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:95699829A>G	ENST00000370202.4	+	1	119	c.43A>G	c.(43-45)Att>Gtt	p.I15V	RP11-57H12.3_ENST00000421762.1_RNA|RP11-57H12.6_ENST00000604534.1_Intron|RP11-57H12.3_ENST00000419846.1_RNA|RWDD3_ENST00000429514.2_5'UTR|RWDD3_ENST00000263893.6_Missense_Mutation_p.I15V|RWDD3_ENST00000495272.1_3'UTR	NM_001199682.1|NM_015485.4	NP_001186611.1|NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3	15	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)|positive regulation of protein sumoylation (GO:0033235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				kidney(1)|large_intestine(2)|lung(6)|ovary(1)	10		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		CCTGGCCGCGATTTTCTGCAG	0.721													A|||	22	0.00439297	0.0008	0.013	5008	,	,		9310	0.0		0.0099	False		,,,				2504	0.002				p.I15V		Atlas-SNP	.											.	RWDD3	24	.	0			c.A43G						PASS	.	A	VAL/ILE,VAL/ILE,,VAL/ILE	9,3957		0,9,1974	23.0	36.0	32.0		43,43,,43	4.7	1.0	1	dbSNP_134	32	109,8191		2,105,4043	yes	missense,missense,intron,missense	RWDD3,TMEM56-RWDD3	NM_001128142.1,NM_001199682.1,NM_001199691.1,NM_015485.4	29,29,,29	2,114,6017	GG,GA,AA		1.3133,0.2269,0.962	possibly-damaging,possibly-damaging,,possibly-damaging	15/196,15/201,,15/268	95699829	118,12148	1983	4150	6133	SO:0001583	missense	25950	exon1			GCCGCGATTTTCT	BC010936	CCDS41357.1, CCDS44177.1	1p22.1	2012-12-07			ENSG00000122481	ENSG00000122481			21393	protein-coding gene	gene with protein product		615875				11230166	Standard	NM_015485		Approved	DKFZP566K023	uc009wdu.3	Q9Y3V2	OTTHUMG00000010910	ENST00000370202.4:c.43A>G	1.37:g.95699829A>G	ENSP00000359221:p.Ile15Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	148	77	0.52027	NM_015485	A6NP44|A8K9F0|C9J9L7|C9JI45|Q08AJ7|Q6FID3|Q9BX35	Missense_Mutation	SNP	ENST00000370202.4	37	CCDS41357.1	15	0.006868131868131868	0	0.0	5	0.013812154696132596	0	0.0	10	0.013192612137203167	A	18.34	3.602895	0.66445	0.002269	0.013133	ENSG00000122481	ENST00000370202;ENST00000263893	T;T	0.52983	0.64;0.64	4.68	4.68	0.58851	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.057455	0.64402	D	0.000004	T	0.29976	0.0750	.	.	.	0.80722	D	1	B;B;B	0.19200	0.034;0.014;0.004	B;B;B	0.29862	0.076;0.108;0.045	T	0.20371	-1.0277	9	0.44086	T	0.13	-3.7415	14.2871	0.66254	1.0:0.0:0.0:0.0	.	15;15;15	Q9Y3V2;D3DT49;Q9Y3V2-2	RWDD3_HUMAN;.;.	V	15	ENSP00000359221:I15V;ENSP00000263893:I15V	ENSP00000263893:I15V	I	+	1	0	RWDD3	95472417	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.106000	0.64597	1.960000	0.56953	0.459000	0.35465	ATT	A|0.993;G|0.007	0.007	strong		0.721	RWDD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030078.1	NM_015485	
C2CD2	25966	hgsc.bcm.edu	37	21	43329572	43329572	+	Silent	SNP	T	T	C	rs61735800	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43329572T>C	ENST00000380486.3	-	8	1255	c.1014A>G	c.(1012-1014)tcA>tcG	p.S338S	C2CD2_ENST00000329623.7_Silent_p.S183S	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	338	C2.					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						ACCCACCTTCTGAGGATCGCC	0.537													T|||	196	0.0391374	0.0023	0.036	5008	,	,		17187	0.0		0.0378	False		,,,				2504	0.1329				p.S338S		Atlas-SNP	.											.	C2CD2	47	.	0			c.A1014G						PASS	.	T	,	35,4371	40.0+/-72.8	0,35,2168	85.0	72.0	76.0		1014,549	-5.3	0.4	21	dbSNP_129	76	399,8201	127.7+/-186.0	14,371,3915	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	14,406,6083	CC,CT,TT		4.6395,0.7944,3.3369	,	338/697,183/542	43329572	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon8			ACCTTCTGAGGAT	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.1014A>G	21.37:g.43329572T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1																																																																																			T|0.968;C|0.032	0.032	strong		0.537	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
HERPUD1	9709	hgsc.bcm.edu	37	16	56969148	56969148	+	Splice_Site	SNP	G	G	A	rs2217332	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:56969148G>A	ENST00000439977.2	+	2	346	c.149G>A	c.(148-150)cGt>cAt	p.R50H	HERPUD1_ENST00000570273.1_3'UTR|HERPUD1_ENST00000344114.4_Splice_Site_p.R50H|HERPUD1_ENST00000379792.2_Splice_Site_p.R50H|HERPUD1_ENST00000300302.5_Splice_Site_p.R50H	NM_001010989.1|NM_014685.2	NP_001010989.1|NP_055500.1	Q15011	HERP1_HUMAN	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	50	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.		R -> H (in dbSNP:rs2217332).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of protein binding (GO:0032092)|regulation of protein ubiquitination (GO:0031396)|response to unfolded protein (GO:0006986)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.R50H(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|stomach(1)	11						CATGATCAGCGTCCAGAGGAC	0.393			T	ERG	prostate								G|||	745	0.148762	0.1172	0.1729	5008	,	,		20673	0.0823		0.1471	False		,,,				2504	0.2444				p.R50H		Atlas-SNP	.		Dom	yes		16	16q12.2-q13	9709	"""homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1"""		E	HERPUD1,NS,carcinoma,0,1	HERPUD1	28	1	1	Substitution - Missense(1)	stomach(1)	c.G149A						scavenged	.	G	HIS/ARG,HIS/ARG,HIS/ARG	564,3832	253.0+/-259.1	42,480,1676	138.0	120.0	126.0	http://www.ncbi.nlm.nih.gov/pubmed?term	149,149,149	3.1	1.0	16	dbSNP_96	126	1340,7260	262.4+/-284.4	110,1120,3070	yes	missense-near-splice,missense-near-splice,missense-near-splice	HERPUD1	NM_001010989.1,NM_001010990.1,NM_014685.2	29,29,29	152,1600,4746	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	15.5814,12.8298,14.6507	benign,benign,benign	50/391,50/367,50/392	56969148	1904,11092	2198	4300	6498	SO:0001630	splice_region_variant	9709	exon2			ATCAGCGTCCAGA	AB034989	CCDS10771.1, CCDS45492.1	16q13	2008-05-14			ENSG00000051108	ENSG00000051108			13744	protein-coding gene	gene with protein product		608070				10922362, 10708769	Standard	NM_001010989		Approved	KIAA0025, Mif1, HERP, SUP	uc002eke.2	Q15011	OTTHUMG00000133276	ENST00000439977.2:c.148-1G>A	16.37:g.56969148G>A		Somatic	149	2	0.0134228		WXS	Illumina HiSeq	Phase_I	167	84	0.502994	NM_014685	E9PGD1|O60644|Q6IAN8|Q96D92	Missense_Mutation	SNP	ENST00000439977.2	37	CCDS10771.1	256	0.11721611721611722	50	0.1016260162601626	60	0.16574585635359115	34	0.05944055944055944	112	0.14775725593667546	G	9.103	1.004518	0.19199	0.128298	0.155814	ENSG00000051108	ENST00000439977;ENST00000379792;ENST00000300302;ENST00000344114	T;T;T;T	0.73258	-0.73;-0.73;-0.73;-0.73	6.04	3.06	0.35304	Ubiquitin supergroup (1);Ubiquitin (2);	0.645525	0.16761	N	0.200620	T	0.00210	0.0006	N	0.24115	0.695	0.51482	P	7.599999999996498E-5	B;B;B;B;B;B	0.14012	0.009;0.002;0.003;0.0;0.001;0.001	B;B;B;B;B;B	0.15484	0.013;0.004;0.002;0.002;0.0;0.003	T	0.04053	-1.0981	9	0.45353	T	0.12	-23.2151	4.5891	0.12297	0.2351:0.0:0.6121:0.1528	rs2217332;rs11553779;rs52796206;rs60487936;rs2217332	50;50;50;50;50;50	B4E3N8;Q15011-3;A4UAE9;E9PGD1;Q15011-2;Q15011	.;.;.;.;.;HERP1_HUMAN	H	50	ENSP00000409555:R50H;ENSP00000369118:R50H;ENSP00000300302:R50H;ENSP00000340931:R50H	ENSP00000300302:R50H	R	+	2	0	HERPUD1	55526649	0.001000	0.12720	0.990000	0.47175	0.784000	0.44337	-0.041000	0.12084	0.901000	0.36495	-0.254000	0.11334	CGT	G|0.870;A|0.130	0.130	strong		0.393	HERPUD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257056.5		Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195515568	195515568	+	Silent	SNP	C	C	T	rs62282504	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195515568C>T	ENST00000463781.3	-	2	3342	c.2883G>A	c.(2881-2883)ggG>ggA	p.G961G	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.G961G	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	966	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TTTTACCAGACCCTGAAGGTG	0.567													.|||	996	0.198882	0.3283	0.1484	5008	,	,		24380	0.0516		0.2584	False		,,,				2504	0.1503				p.G961G		Atlas-SNP	.											.	MUC4	1505	.	0			c.G2883A						PASS	.		,,	1218,3152		163,892,1130	137.0	141.0	140.0		,2883,	-2.9	0.0	3	dbSNP_129	140	1999,6521		238,1523,2499	no	intron,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	401,2415,3629	TT,TC,CC		23.4624,27.8719,24.9573	,,	,961/5413,	195515568	3217,9673	2185	4260	6445	SO:0001819	synonymous_variant	4585	exon2			ACCAGACCCTGAA	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.2883G>A	3.37:g.195515568C>T		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	267	127	0.475655	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			C|0.783;T|0.217	0.217	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EXT1	2131	hgsc.bcm.edu	37	8	118832020	118832020	+	Silent	SNP	G	G	A	rs17439693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:118832020G>A	ENST00000378204.2	-	6	2237	c.1431C>T	c.(1429-1431)ccC>ccT	p.P477P		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	477					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)			TGAATTTGGAGGGGGGCTTTA	0.517			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses				G|||	602	0.120208	0.0787	0.1772	5008	,	,		18267	0.0308		0.2445	False		,,,				2504	0.1002				p.P477P		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.C1431T						PASS	.	G		467,3939	217.4+/-235.8	21,425,1757	69.0	78.0	75.0		1431	-3.1	1.0	8	dbSNP_123	75	1670,6930	302.0+/-305.7	181,1308,2811	no	coding-synonymous	EXT1	NM_000127.2		202,1733,4568	AA,AG,GG		19.4186,10.5992,16.4309		477/747	118832020	2137,10869	2203	4300	6503	SO:0001819	synonymous_variant	2131	exon6	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	TTTGGAGGGGGGC	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.1431C>T	8.37:g.118832020G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	164	95	0.579268	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1																																																																																			G|0.849;A|0.151	0.151	strong		0.517	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
KRT75	9119	hgsc.bcm.edu	37	12	52822258	52822258	+	Silent	SNP	A	A	G	rs401926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52822258A>G	ENST00000252245.5	-	7	1384	c.1164T>C	c.(1162-1164)tgT>tgC	p.C388C	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	388	Coil 2.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		GCAAGCTGGAACACTGTAAGG	0.572													G|||	3068	0.61262	0.6437	0.6888	5008	,	,		21530	0.6796		0.6143	False		,,,				2504	0.4458				p.C388C		Atlas-SNP	.											.	KRT75	75	.	0			c.T1164C						PASS	.	G		2732,1674	500.0+/-364.6	845,1042,316	38.0	33.0	35.0		1164	-2.0	0.1	12	dbSNP_80	35	5143,3457	500.4+/-375.2	1528,2087,685	no	coding-synonymous	KRT75	NM_004693.2		2373,3129,1001	GG,GA,AA		40.1977,37.9936,39.451		388/552	52822258	7875,5131	2203	4300	6503	SO:0001819	synonymous_variant	9119	exon7			GCTGGAACACTGT	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.1164T>C	12.37:g.52822258A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	90	43	0.477778	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																			A|0.368;G|0.632	0.632	strong		0.572	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
GPR116	221395	hgsc.bcm.edu	37	6	46827239	46827239	+	Missense_Mutation	SNP	C	C	T	rs9395218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46827239C>T	ENST00000283296.7	-	17	2689	c.2401G>A	c.(2401-2403)Gtc>Atc	p.V801I	GPR116_ENST00000545669.1_Missense_Mutation_p.V230I|GPR116_ENST00000456426.2_Missense_Mutation_p.V659I|GPR116_ENST00000362015.4_Missense_Mutation_p.V801I|GPR116_ENST00000265417.7_Missense_Mutation_p.V801I	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	801			V -> I (in dbSNP:rs9395218). {ECO:0000269|PubMed:17974005}.		energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CCAAGGATGACATTAACCGTA	0.398													C|||	1437	0.286941	0.2738	0.2738	5008	,	,		19972	0.3571		0.1968	False		,,,				2504	0.3344				p.V801I	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G2401A						PASS	.	C	ILE/VAL,ILE/VAL	1111,3295	357.4+/-313.9	129,853,1221	37.0	37.0	37.0		2401,2401	-3.8	0.0	6	dbSNP_119	37	1721,6879	289.0+/-299.1	170,1381,2749	no	missense,missense	GPR116	NM_001098518.1,NM_015234.4	29,29	299,2234,3970	TT,TC,CC		20.0116,25.2156,21.7746	benign,benign	801/1347,801/1347	46827239	2832,10174	2203	4300	6503	SO:0001583	missense	221395	exon17			GGATGACATTAAC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2401G>A	6.37:g.46827239C>T	ENSP00000283296:p.Val801Ile	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	137	60	0.437956	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	637	0.2916666666666667	156	0.3170731707317073	99	0.27348066298342544	223	0.38986013986013984	159	0.20976253298153033	C	0.095	-1.161749	0.01673	0.252156	0.200116	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000456426;ENST00000545557;ENST00000265417;ENST00000545669	T;T;T;T;T	0.26810	1.72;2.1;1.74;1.72;1.71	5.58	-3.83	0.04269	.	0.768838	0.11639	N	0.543978	T	0.04861	0.0131	N	0.21097	0.63	0.58432	P	1.0000000000287557E-6	B;B;B;B;B	0.19935	0.014;0.002;0.016;0.04;0.016	B;B;B;B;B	0.24155	0.023;0.005;0.005;0.051;0.005	T	0.44726	-0.9309	9	0.15952	T	0.53	-6.8349	11.0734	0.48016	0.0976:0.2321:0.0:0.6703	rs9395218;rs57548061;rs9395218	230;356;801;659;801	F5GWK9;B4DTV3;E9PBS6;Q8IZF2-3;Q8IZF2	.;.;.;.;GP116_HUMAN	I	801;801;801;659;172;801;230	ENSP00000283296:V801I;ENSP00000354563:V801I;ENSP00000412866:V659I;ENSP00000265417:V801I;ENSP00000441581:V230I	ENSP00000265417:V801I	V	-	1	0	GPR116	46935198	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-0.596000	0.05720	-0.881000	0.03992	-0.378000	0.06908	GTC	C|0.761;T|0.239	0.239	strong		0.398	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
FCGBP	8857	hgsc.bcm.edu	37	19	40360928	40360928	+	Silent	SNP	G	G	A	rs1053686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40360928G>A	ENST00000221347.6	-	33	15487	c.15480C>T	c.(15478-15480)cgC>cgT	p.R5160R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	5160	Cys-rich.|TIL 12.					extracellular vesicular exosome (GO:0070062)		p.R5160R(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			AAAGCAGGAAGCGGTCGTCGC	0.622													G|||	590	0.117812	0.1271	0.1988	5008	,	,		16856	0.0387		0.1431	False		,,,				2504	0.1033				p.R5160R		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	1	Substitution - coding silent(1)	stomach(1)	c.C15480T						PASS	.	G		689,3717	290.1+/-280.8	58,573,1572	68.0	65.0	66.0		15480	1.4	1.0	19	dbSNP_86	66	1357,7243	265.3+/-286.1	110,1137,3053	no	coding-synonymous	FCGBP	NM_003890.2		168,1710,4625	AA,AG,GG		15.7791,15.6378,15.7312		5160/5406	40360928	2046,10960	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon33			CAGGAAGCGGTCG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.15480C>T	19.37:g.40360928G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.865;N|0.000	.	strong		0.622	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
HTT	3064	hgsc.bcm.edu	37	4	3215835	3215835	+	Missense_Mutation	SNP	T	T	C	rs362331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3215835T>C	ENST00000355072.5	+	50	7070	c.6925T>C	c.(6925-6927)Tac>Cac	p.Y2309H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2309			Y -> H (in dbSNP:rs362331).		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)		CTCCCTCATCTACTGTGTGCA	0.582													C|||	2210	0.441294	0.5862	0.4294	5008	,	,		19331	0.3859		0.4334	False		,,,				2504	0.319				p.Y2309H		Atlas-SNP	.											HTT,NS,carcinoma,0,1	HTT	221	1	0			c.T6925C						PASS	.	C	HIS/TYR	2355,1813		681,993,410	34.0	38.0	36.0		6925	5.7	1.0	4	dbSNP_79	36	3533,4873		764,2005,1434	yes	missense	HTT	NM_002111.6	83	1445,2998,1844	CC,CT,TT		42.0295,43.4981,46.8268	benign	2309/3143	3215835	5888,6686	2084	4203	6287	SO:0001583	missense	3064	exon50			CTCATCTACTGTG	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.6925T>C	4.37:g.3215835T>C	ENSP00000347184:p.Tyr2309His	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	120	61	0.508333	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	995	0.4555860805860806	281	0.5711382113821138	161	0.4447513812154696	220	0.38461538461538464	333	0.4393139841688654	C	9.562	1.118641	0.20877	0.565019	0.420295	ENSG00000197386	ENST00000355072	T	0.04603	3.59	5.7	5.7	0.88788	.	0.117131	0.64402	N	0.000015	T	0.00012	0.0000	N	0.00583	-1.355	0.47065	P	6.969999999999477E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.21518	-1.0243	9	0.13853	T	0.58	.	8.2136	0.31499	0.2523:0.6699:0.0:0.0778	rs362331;rs878244;rs2229983;rs3821970;rs17793687;rs52791365;rs58994081;rs362331	2309	P42858	HD_HUMAN	H	2309	ENSP00000347184:Y2309H	ENSP00000347184:Y2309H	Y	+	1	0	HTT	3185633	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.175000	0.50855	1.427000	0.47276	-0.119000	0.15052	TAC	C|0.453;N|0.000	0.453	strong		0.582	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
SALL1	6299	hgsc.bcm.edu	37	16	51173710	51173710	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:51173710G>A	ENST00000251020.4	-	2	2456	c.2423C>T	c.(2422-2424)tCt>tTt	p.S808F	SALL1_ENST00000440970.1_Missense_Mutation_p.S711F|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	808					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S808Y(2)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ACCTGTGTCAGACTCCATGGA	0.507																																					p.S808F	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											SALL1,NS,carcinoma,0,1	SALL1	301	1	2	Substitution - Missense(2)	lung(2)	c.C2423T						scavenged	.						117.0	124.0	121.0					16																	51173710		2198	4300	6498	SO:0001583	missense	6299	exon2			GTGTCAGACTCCA	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2423C>T	16.37:g.51173710G>A	ENSP00000251020:p.Ser808Phe	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	185	2	0.0108108	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022360	0.35701	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.08102	3.13;3.14	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.20251	0.0487	M	0.63843	1.955	0.80722	D	1	D	0.69078	0.997	P	0.56278	0.795	T	0.06570	-1.0819	10	0.11794	T	0.64	.	19.0945	0.93244	0.0:0.0:1.0:0.0	.	808	Q9NSC2	SALL1_HUMAN	F	808;711;772	ENSP00000251020:S808F;ENSP00000407914:S711F	ENSP00000251020:S808F	S	-	2	0	SALL1	49731211	1.000000	0.71417	0.923000	0.36655	0.001000	0.01503	9.869000	0.99810	2.511000	0.84671	0.454000	0.30748	TCT	.	.	none		0.507	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
ZNF544	27300	hgsc.bcm.edu	37	19	58774071	58774071	+	Missense_Mutation	SNP	A	A	G	rs260462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58774071A>G	ENST00000596652.1	+	6	2333	c.2099A>G	c.(2098-2100)cAa>cGa	p.Q700R	ZNF544_ENST00000415203.2_Missense_Mutation_p.Q672R|CTD-3138B18.4_ENST00000600029.1_Intron|ZNF544_ENST00000596929.1_Intron|ZNF544_ENST00000595981.1_Intron|ZNF544_ENST00000269829.4_Missense_Mutation_p.Q700R|ZNF544_ENST00000600044.1_Missense_Mutation_p.Q672R|ZNF544_ENST00000596825.1_3'UTR|ZNF544_ENST00000599227.1_3'UTR|ZNF544_ENST00000600220.1_Missense_Mutation_p.Q672R|ZNF544_ENST00000599953.1_Missense_Mutation_p.Q558R|CTD-3138B18.5_ENST00000597230.1_RNA			Q6NX49	ZN544_HUMAN	zinc finger protein 544	700			Q -> R (in dbSNP:rs260462). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1, ECO:0000269|Ref.3}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		TTCCGGCAGCAATCTCAACTT	0.473													G|||	2641	0.527356	0.4297	0.5403	5008	,	,		21994	0.5873		0.5915	False		,,,				2504	0.5225				p.Q700R		Atlas-SNP	.											.	ZNF544	57	.	0			c.A2099G						PASS	.	G	ARG/GLN	2054,2352	608.0+/-391.1	478,1098,627	149.0	152.0	151.0		2099	-5.1	0.0	19	dbSNP_79	151	4894,3706	529.1+/-381.5	1402,2090,808	yes	missense	ZNF544	NM_014480.2	43	1880,3188,1435	GG,GA,AA		43.093,46.6182,46.5785	benign	700/716	58774071	6948,6058	2203	4300	6503	SO:0001583	missense	27300	exon7			GGCAGCAATCTCA	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.2099A>G	19.37:g.58774071A>G	ENSP00000469635:p.Gln700Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_014480	A8K6J1|Q9UEX4	Missense_Mutation	SNP	ENST00000596652.1	37	CCDS12973.1	1203	0.5508241758241759	215	0.4369918699186992	208	0.574585635359116	333	0.5821678321678322	447	0.5897097625329816	G	0.018	-1.486893	0.01018	0.466182	0.56907	ENSG00000198131	ENST00000269829;ENST00000415203;ENST00000441758	T;T	0.35605	1.3;1.3	3.46	-5.14	0.02875	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.04162	-0.26	0.58432	P	1.999999999946489E-6	B;B	0.18741	0.0;0.03	B;B	0.01281	0.0;0.0	T	0.37430	-0.9706	8	0.02654	T	1	.	10.0317	0.42105	0.742:0.1228:0.1353:0.0	rs260462;rs3826676;rs17310168;rs61664023;rs260462	672;700	B7ZAY1;Q6NX49	.;ZN544_HUMAN	R	700;672;252	ENSP00000269829:Q700R;ENSP00000394341:Q672R	ENSP00000269829:Q700R	Q	+	2	0	ZNF544	63465883	0.000000	0.05858	0.000000	0.03702	0.227000	0.25037	-3.353000	0.00501	-1.370000	0.02144	-0.213000	0.12676	CAA	A|0.455;G|0.545	0.545	strong		0.473	ZNF544-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466754.1	NM_014480	
SLC39A4	55630	hgsc.bcm.edu	37	8	145639726	145639726	+	Missense_Mutation	SNP	T	T	C	rs2272662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145639726T>C	ENST00000301305.3	-	6	1174	c.1069A>G	c.(1069-1071)Acc>Gcc	p.T357A	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.T332A	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	357			T -> A (in dbSNP:rs2272662). {ECO:0000269|PubMed:12032886, ECO:0000269|PubMed:14702039}.		cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)	p.T357A(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			ATGTAGTGGGTGACCCCCCTG	0.657													T|||	1971	0.39357	0.0711	0.4669	5008	,	,		16204	0.4861		0.5686	False		,,,				2504	0.502				p.T357A		Atlas-SNP	.											SLC39A4,NS,carcinoma,0,1	SLC39A4	54	1	1	Substitution - Missense(1)	prostate(1)	c.A1069G						PASS	.	T	ALA/THR,ALA/THR	644,3742		61,522,1610	47.0	40.0	42.0		994,1069	-1.0	0.2	8	dbSNP_100	42	4952,3634		1443,2066,784	yes	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	58,58	1504,2588,2394	CC,CT,TT		42.3247,14.6831,43.1391	benign,benign	332/623,357/648	145639726	5596,7376	2193	4293	6486	SO:0001583	missense	55630	exon6			AGTGGGTGACCCC	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.1069A>G	8.37:g.145639726T>C	ENSP00000301305:p.Thr357Ala	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	358	357	0.997207	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	926	0.423992673992674	39	0.07926829268292683	162	0.44751381215469616	285	0.4982517482517482	440	0.5804749340369393	T	8.761	0.923532	0.18056	0.146831	0.576753	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.46063	0.88;0.88	5.03	-0.978	0.10279	.	0.621523	0.17481	N	0.172725	T	0.00012	0.0000	L	0.28504	0.86	0.46113	P	0.0011229999999999851	B;B	0.26002	0.012;0.139	B;B	0.28305	0.011;0.088	T	0.42832	-0.9428	9	0.41790	T	0.15	-18.2025	3.8096	0.08791	0.4831:0.1973:0.0:0.3196	rs2272662;rs17232582;rs2272662	357;332	Q6P5W5;A6NDY5	S39A4_HUMAN;.	A	332;357	ENSP00000276833:T332A;ENSP00000301305:T357A	ENSP00000276833:T332A	T	-	1	0	SLC39A4	145610534	0.768000	0.28519	0.183000	0.23137	0.175000	0.22909	1.314000	0.33597	-0.019000	0.14055	0.467000	0.42956	ACC	T|0.606;C|0.394	0.394	strong		0.657	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
LRRN1	57633	hgsc.bcm.edu	37	3	3886847	3886847	+	Silent	SNP	G	G	C	rs3749349	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:3886847G>C	ENST00000319331.3	+	2	1283	c.522G>C	c.(520-522)ctG>ctC	p.L174L	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	174						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		GGCTCCACCTGAACTCCAACA	0.403													G|||	1070	0.213658	0.295	0.147	5008	,	,		18549	0.2679		0.1044	False		,,,				2504	0.2076				p.L174L		Atlas-SNP	.											.	LRRN1	82	.	0			c.G522C						PASS	.	G		1040,3366	371.0+/-319.8	118,804,1281	98.0	105.0	102.0		522	-4.1	1.0	3	dbSNP_107	102	1063,7537	223.1+/-260.0	63,937,3300	no	coding-synonymous	LRRN1	NM_020873.5		181,1741,4581	CC,CG,GG		12.3605,23.6042,16.1695		174/717	3886847	2103,10903	2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			CCACCTGAACTCC	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.522G>C	3.37:g.3886847G>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			G|0.820;C|0.180	0.180	strong		0.403	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
KCNQ3	3786	hgsc.bcm.edu	37	8	133153451	133153451	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:133153451C>T	ENST00000388996.4	-	10	1810	c.1390G>A	c.(1390-1392)Gtt>Att	p.V464I	KCNQ3_ENST00000519445.1_Missense_Mutation_p.V464I|KCNQ3_ENST00000521134.1_Missense_Mutation_p.V344I	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	464					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)	TTTAAGCCAACAGGCTTTGGT	0.448																																					p.V464I		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G1390A						PASS	.						135.0	140.0	138.0					8																	133153451		2203	4300	6503	SO:0001583	missense	3786	exon10			AGCCAACAGGCTT	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.1390G>A	8.37:g.133153451C>T	ENSP00000373648:p.Val464Ile	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	124	41	0.330645	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573918	0.65765	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99594	-6.25;-6.25;-6.25	5.63	5.63	0.86233	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.189166	0.45606	D	0.000344	D	0.97102	0.9053	N	0.03608	-0.345	0.32328	N	0.561483	P;P	0.42123	0.771;0.771	B;B	0.39971	0.315;0.315	D	0.98773	1.0729	10	0.41790	T	0.15	-9.8868	13.6375	0.62230	0.1545:0.8455:0.0:0.0	.	464;464	E7ET42;O43525	.;KCNQ3_HUMAN	I	464;344;464;453;343	ENSP00000373648:V464I;ENSP00000429799:V344I;ENSP00000428790:V464I	ENSP00000373648:V464I	V	-	1	0	KCNQ3	133222633	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.046000	0.49846	2.652000	0.90054	0.655000	0.94253	GTT	.	.	none		0.448	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
RNF43	54894	hgsc.bcm.edu	37	17	56492800	56492800	+	Missense_Mutation	SNP	T	T	C	rs3744093	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56492800T>C	ENST00000584437.1	-	1	2094	c.139A>G	c.(139-141)Att>Gtt	p.I47V	RNF43_ENST00000577716.1_Missense_Mutation_p.I47V|RNF43_ENST00000407977.2_Missense_Mutation_p.I47V|RNF43_ENST00000580014.1_5'Flank|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Intron|RNF43_ENST00000500597.2_Missense_Mutation_p.I47V|RNF43_ENST00000583753.1_Missense_Mutation_p.I47V			Q68DV7	RNF43_HUMAN	ring finger protein 43	47			I -> V (in dbSNP:rs3744093). {ECO:0000269|PubMed:14702039}.		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTCTGATAATAGCTTTCTGT	0.517													T|||	1872	0.373802	0.1694	0.5317	5008	,	,		17973	0.5258		0.3718	False		,,,				2504	0.3834				p.I47V		Atlas-SNP	.											.	RNF43	157	.	0			c.A139G						PASS	.	T	VAL/ILE	958,3448	362.1+/-316.0	116,726,1361	100.0	92.0	95.0		139	3.2	1.0	17	dbSNP_107	95	3312,5288	494.7+/-373.9	638,2036,1626	yes	missense	RNF43	NM_017763.4	29	754,2762,2987	CC,CT,TT		38.5116,21.7431,32.831	benign	47/784	56492800	4270,8736	2203	4300	6503	SO:0001583	missense	54894	exon2			TGATAATAGCTTT		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.139A>G	17.37:g.56492800T>C	ENSP00000463069:p.Ile47Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	91	46	0.505495	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	855	0.3914835164835165	94	0.1910569105691057	184	0.5082872928176796	298	0.5209790209790209	279	0.36807387862796836	T	9.051	0.992132	0.18966	0.217431	0.385116	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09350	3.24;2.99	5.49	3.19	0.36642	.	0.436978	0.21813	N	0.068731	T	0.00012	0.0000	N	0.14661	0.345	0.42420	P	0.007365999999999984	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.40924	-0.9537	9	0.17832	T	0.49	-11.177	6.2359	0.20762	0.0:0.1484:0.1361:0.7155	rs3744093;rs52822933;rs58301389;rs3744093	47;47	Q68DV7-2;Q68DV7	.;RNF43_HUMAN	V	47	ENSP00000385328:I47V;ENSP00000441969:I47V	ENSP00000385328:I47V	I	-	1	0	RNF43	53847799	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.086000	0.30853	0.973000	0.38340	0.533000	0.62120	ATT	T|0.651;C|0.349	0.349	strong		0.517	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
LRIT3	345193	hgsc.bcm.edu	37	4	110790911	110790911	+	Missense_Mutation	SNP	A	A	T	rs764205	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:110790911A>T	ENST00000594814.1	+	4	1006	c.1006A>T	c.(1006-1008)Atg>Ttg	p.M336L	LRIT3_ENST00000327908.3_Missense_Mutation_p.M153L|LRIT3_ENST00000379920.3_Missense_Mutation_p.M291L|LRIT3_ENST00000409621.2_Missense_Mutation_p.M153L	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	336	Ig-like.		M -> L (in dbSNP:rs764205). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.M153L(1)|p.M291L(1)		cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		TCTGGCTGGGATGTCAGAAGC	0.468													A|||	2352	0.469649	0.3911	0.3963	5008	,	,		19885	0.4901		0.6392	False		,,,				2504	0.4325				p.M336L		Atlas-SNP	.											LRIT3_ENST00000379920,NS,carcinoma,0,2	LRIT3	107	2	2	Substitution - Missense(2)	prostate(2)	c.A1006T						PASS	.	A	LEU/MET	1908,2498	546.6+/-377.1	406,1096,701	138.0	139.0	139.0		871	3.1	0.3	4	dbSNP_86	139	5561,3039	662.5+/-402.0	1832,1897,571	yes	missense	LRIT3	NM_198506.2	15	2238,2993,1272	TT,TA,AA		35.3372,43.3046,42.5727	benign	291/635	110790911	7469,5537	2203	4300	6503	SO:0001583	missense	345193	exon4			GCTGGGATGTCAG	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.1006A>T	4.37:g.110790911A>T	ENSP00000469759:p.Met336Leu	Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	192	188	0.979167	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	1113	0.5096153846153846	189	0.38414634146341464	164	0.4530386740331492	279	0.48776223776223776	481	0.6345646437994723	A	13.13	2.144734	0.37825	0.433046	0.646628	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.66280	-0.2;-0.2;-0.2	5.53	3.12	0.35913	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.818267	0.11931	N	0.515666	T	0.00012	0.0000	L	0.31578	0.945	0.80722	P	0.0	B;B	0.32543	0.375;0.016	B;B	0.28991	0.097;0.02	T	0.46541	-0.9184	9	0.28530	T	0.3	.	8.1285	0.31014	0.7812:0.0:0.2188:0.0	rs764205;rs52790369;rs764205	291;153	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	L	153;291;153	ENSP00000328222:M153L;ENSP00000369252:M291L;ENSP00000386734:M153L	ENSP00000328222:M153L	M	+	1	0	LRIT3	111010360	0.257000	0.24022	0.330000	0.25442	0.992000	0.81027	2.364000	0.44187	0.404000	0.25506	0.533000	0.62120	ATG	T|0.561;N|0.000	0.561	strong		0.468	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
SEMA6D	80031	hgsc.bcm.edu	37	15	48056050	48056050	+	Missense_Mutation	SNP	G	G	A	rs151039709	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:48056050G>A	ENST00000316364.5	+	10	1190	c.751G>A	c.(751-753)Gtg>Atg	p.V251M	SEMA6D_ENST00000558014.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000389428.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000558816.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000389433.2_Missense_Mutation_p.V251M|SEMA6D_ENST00000358066.4_Missense_Mutation_p.V251M|SEMA6D_ENST00000355997.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000536845.2_Missense_Mutation_p.V251M|SEMA6D_ENST00000537942.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000389425.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000354744.4_Missense_Mutation_p.V251M|SEMA6D_ENST00000389432.2_Missense_Mutation_p.V251M	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	251	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		TGGGCAGGCTGTGTATTCCCG	0.473																																					p.V251M		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G751A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	2,4394	4.2+/-10.8	0,2,2196	132.0	131.0	131.0		751,751,751,751,751,751,751	4.9	0.9	15	dbSNP_134	131	1,8593	1.2+/-3.3	0,1,4296	yes	missense,missense,missense,missense,missense,missense,missense	SEMA6D	NM_001198999.1,NM_020858.1,NM_024966.2,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	21,21,21,21,21,21,21	0,3,6492	AA,AG,GG		0.0116,0.0455,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	251/1012,251/1012,251/477,251/999,251/1018,251/1074,251/598	48056050	3,12987	2198	4297	6495	SO:0001583	missense	80031	exon10			CAGGCTGTGTATT	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.751G>A	15.37:g.48056050G>A	ENSP00000324857:p.Val251Met	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	131	62	0.473282	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513526	0.85389	4.55E-4	1.16E-4	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66	5.87	4.93	0.64822	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.105633	0.64402	D	0.000005	T	0.37489	0.1005	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.98;1.0	D;D;D;P;D	0.71870	0.975;0.952;0.975;0.821;0.975	T	0.25641	-1.0126	10	0.66056	D	0.02	.	16.8154	0.85733	0.0:0.1288:0.8712:0.0	.	251;251;251;251;251	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	M	251	ENSP00000442040:V251M;ENSP00000446152:V251M;ENSP00000324857:V251M;ENSP00000374084:V251M;ENSP00000374083:V251M;ENSP00000346786:V251M;ENSP00000350770:V251M;ENSP00000374079:V251M;ENSP00000348276:V251M;ENSP00000374076:V251M	ENSP00000324857:V251M	V	+	1	0	SEMA6D	45843342	1.000000	0.71417	0.918000	0.36340	0.881000	0.50899	6.757000	0.74924	1.452000	0.47756	0.655000	0.94253	GTG	G|1.000;A|0.000	0.000	strong		0.473	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
OR2J2	26707	hgsc.bcm.edu	37	6	29141632	29141632	+	Missense_Mutation	SNP	T	T	C	rs3116855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29141632T>C	ENST00000377167.2	+	1	322	c.220T>C	c.(220-222)Tac>Cac	p.Y74H		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	74			H -> Y (in allele 6M1-6*02 and allele 6M1-6*03; dbSNP:rs3116855). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						GGATCTCTGCTACACCACCAG	0.483													T|||	1585	0.316494	0.0408	0.4035	5008	,	,		18639	0.3512		0.5149	False		,,,				2504	0.3875				p.Y74H		Atlas-SNP	.											.	OR2J2	51	.	0			c.T220C						PASS	.	T	HIS/TYR	462,3530		39,384,1573	148.0	136.0	140.0		220	2.3	1.0	6	dbSNP_103	140	4139,4289		1028,2083,1103	no	missense	OR2J2	NM_030905.2	83	1067,2467,2676	CC,CT,TT		49.1101,11.5731,37.0451	benign	74/313	29141632	4601,7819	1996	4214	6210	SO:0001583	missense	26707	exon1			CTCTGCTACACCA		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.220T>C	6.37:g.29141632T>C	ENSP00000366372:p.Tyr74His	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	246	117	0.47561	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	37	CCDS43434.1	778	0.35622710622710624	22	0.044715447154471545	150	0.4143646408839779	198	0.34615384615384615	408	0.5382585751978892	T	11.43	1.636528	0.29068	0.115731	0.491101	ENSG00000204700	ENST00000377167	T	0.01388	4.95	2.3	2.3	0.28687	.	.	.	.	.	T	0.02848	0.0085	M	0.87038	2.855	0.38904	P	0.04260799999999998	.	.	.	.	.	.	T	0.08700	-1.0709	6	0.72032	D	0.01	.	9.0762	0.36522	0.0:0.0:0.0:1.0	rs3116855;rs57471851	.	.	.	H	74	ENSP00000366372:Y74H	ENSP00000366372:Y74H	Y	+	1	0	OR2J2	29249611	0.028000	0.19301	1.000000	0.80357	0.423000	0.31445	2.328000	0.43867	1.039000	0.40074	0.172000	0.16884	TAC	T|0.593;C|0.407	0.407	strong		0.483	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2		
PKD1L1	168507	hgsc.bcm.edu	37	7	47869038	47869038	+	Silent	SNP	T	T	C	rs7788583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47869038T>C	ENST00000289672.2	-	44	6770	c.6720A>G	c.(6718-6720)gcA>gcG	p.A2240A		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2240					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)	p.A2240A(1)	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						CAACCTCGCCTGCACAGTCAG	0.408													T|||	981	0.195887	0.3359	0.1297	5008	,	,		18191	0.0704		0.174	False		,,,				2504	0.2055				p.A2240A		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,1	PKD1L1	328	1	1	Substitution - coding silent(1)	stomach(1)	c.A6720G						PASS	.	T		1357,3049	447.9+/-348.5	206,945,1052	91.0	98.0	96.0		6720	-7.0	0.0	7	dbSNP_116	96	1519,7081	285.8+/-297.4	121,1277,2902	no	coding-synonymous	PKD1L1	NM_138295.3		327,2222,3954	CC,CT,TT		17.6628,30.7989,22.1129		2240/2850	47869038	2876,10130	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon44			CTCGCCTGCACAG	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.6720A>G	7.37:g.47869038T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	63	40	0.634921	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			T|0.785;C|0.215	0.215	strong		0.408	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
RILPL1	353116	hgsc.bcm.edu	37	12	124017850	124017850	+	Silent	SNP	G	G	C	rs28492040	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124017850G>C	ENST00000376874.4	-	1	415	c.180C>G	c.(178-180)gtC>gtG	p.V60V		NM_178314.3	NP_847884.2	Q5EBL4	RIPL1_HUMAN	Rab interacting lysosomal protein-like 1	60					epithelial cell morphogenesis (GO:0003382)|intracellular protein transport (GO:0006886)|regulation of neuron death (GO:1901214)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.00067)|all cancers(50;0.00836)|BRCA - Breast invasive adenocarcinoma(302;0.197)		GGATCTCCAGGACGCGCACGA	0.687													G|||	590	0.117812	0.1225	0.121	5008	,	,		11260	0.0109		0.1909	False		,,,				2504	0.1442				p.V60V		Atlas-SNP	.											RILPL1,NS,carcinoma,0,1	RILPL1	23	1	0			c.C180G						PASS	.	G		592,3648		49,494,1577	10.0	15.0	13.0		180	0.9	1.0	12	dbSNP_125	13	1561,6859		151,1259,2800	no	coding-synonymous	RILPL1	NM_178314.3		200,1753,4377	CC,CG,GG		18.5392,13.9623,17.0063		60/404	124017850	2153,10507	2120	4210	6330	SO:0001819	synonymous_variant	353116	exon1			CTCCAGGACGCGC	AK097550	CCDS45006.1	12q24.31	2007-11-27			ENSG00000188026	ENSG00000188026			26814	protein-coding gene	gene with protein product		614092				14668488	Standard	NM_178314		Approved	FLJ39378	uc001ufe.2	Q5EBL4	OTTHUMG00000168686	ENST00000376874.4:c.180C>G	12.37:g.124017850G>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_178314	Q66K36|Q8N1M0	Silent	SNP	ENST00000376874.4	37	CCDS45006.1																																																																																			G|0.882;C|0.118	0.118	strong		0.687	RILPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400595.1	NM_178314	
HEATR5B	54497	hgsc.bcm.edu	37	2	37289177	37289177	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37289177G>T	ENST00000233099.5	-	11	1696	c.1601C>A	c.(1600-1602)gCt>gAt	p.A534D	HEATR5B_ENST00000354531.2_Missense_Mutation_p.A534D	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	534						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AAGATCTTCAGCAATACTAAC	0.348																																					p.A534D		Atlas-SNP	.											.	HEATR5B	185	.	0			c.C1601A						PASS	.						96.0	99.0	98.0					2																	37289177		2203	4300	6503	SO:0001583	missense	54497	exon11			TCTTCAGCAATAC	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.1601C>A	2.37:g.37289177G>T	ENSP00000233099:p.Ala534Asp	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	40	11	0.275	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127527	0.94473	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.08458	3.09;3.09	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.40767	0.1130	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.49082	-0.8976	10	0.87932	D	0	-21.1412	19.8411	0.96685	0.0:0.0:1.0:0.0	.	534	Q9P2D3	HTR5B_HUMAN	D	534	ENSP00000233099:A534D;ENSP00000346531:A534D	ENSP00000233099:A534D	A	-	2	0	HEATR5B	37142681	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.624000	0.98398	2.683000	0.91414	0.655000	0.94253	GCT	.	.	none		0.348	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
LGR6	59352	hgsc.bcm.edu	37	1	202288293	202288293	+	Silent	SNP	C	C	T	rs56234832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:202288293C>T	ENST00000367278.3	+	18	2951	c.2862C>T	c.(2860-2862)ggC>ggT	p.G954G	LGR6_ENST00000439764.2_Silent_p.G815G|LGR6_ENST00000255432.7_Silent_p.G902G	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	954	Poly-Gly.				G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						CAGGGGGTGGCGGCTTTCAGC	0.587													C|||	328	0.0654952	0.0136	0.1009	5008	,	,		18241	0.0466		0.1113	False		,,,				2504	0.0828				p.G954G		Atlas-SNP	.											.	LGR6	102	.	0			c.C2862T						PASS	.	C	,,	96,4310	77.8+/-116.1	3,90,2110	46.0	50.0	48.0		2862,2445,2706	-0.6	0.0	1	dbSNP_129	48	1126,7474	232.9+/-266.4	79,968,3253	no	coding-synonymous,coding-synonymous,coding-synonymous	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	,,	82,1058,5363	TT,TC,CC		13.093,2.1788,9.3957	,,	954/968,815/829,902/916	202288293	1222,11784	2203	4300	6503	SO:0001819	synonymous_variant	59352	exon18			GGGTGGCGGCTTT	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2862C>T	1.37:g.202288293C>T		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	123	64	0.520325	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Silent	SNP	ENST00000367278.3	37	CCDS30971.1																																																																																			C|0.914;T|0.086	0.086	strong		0.587	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
COL5A2	1290	hgsc.bcm.edu	37	2	189904233	189904233	+	Silent	SNP	T	T	G	rs10197596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:189904233T>G	ENST00000374866.3	-	51	3964	c.3690A>C	c.(3688-3690)acA>acC	p.T1230T		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1230			T -> S. {ECO:0000269|PubMed:11940702}.		axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			CAAGAGCAGCTGTAAGGTGGC	0.498													T|||	557	0.111222	0.0673	0.1095	5008	,	,		18440	0.121		0.1143	False		,,,				2504	0.1585				p.T1230T		Atlas-SNP	.											.	COL5A2	230	.	0			c.A3690C						PASS	.	T		322,4084	161.8+/-193.9	13,296,1894	30.0	30.0	30.0		3690	-5.4	1.0	2	dbSNP_119	30	882,7718	190.4+/-236.9	44,794,3462	no	coding-synonymous	COL5A2	NM_000393.3		57,1090,5356	GG,GT,TT		10.2558,7.3082,9.2573		1230/1500	189904233	1204,11802	2203	4300	6503	SO:0001819	synonymous_variant	1290	exon51			AGCAGCTGTAAGG	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.3690A>C	2.37:g.189904233T>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	77	41	0.532468	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	37	CCDS33350.1																																																																																			T|0.896;G|0.104	0.104	strong		0.498	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
WT1	7490	hgsc.bcm.edu	37	11	32417945	32417945	+	Silent	SNP	T	T	C	rs16754	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:32417945T>C	ENST00000379079.2	-	7	744	c.471A>G	c.(469-471)cgA>cgG	p.R157R	WT1_ENST00000530998.1_Silent_p.R140R|WT1_ENST00000448076.3_Silent_p.R369R|WT1_ENST00000332351.3_Silent_p.R369R	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	301					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.?(2)|p.R301fs*16(2)|p.R302fs*15(2)|p.R301fs*3(1)|p.R301fs*11(1)|p.R302fs*11(1)|p.R301fs*17(1)|p.R301fs*6(1)|p.V300fs*6(1)|p.R301fs*19(1)|p.D299fs*15(1)|p.R301fs*73(1)|p.R302fs*12(1)|p.R302fs*5(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			CAGGCACACGTCGCACATCCT	0.522			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome				C|||	1660	0.33147	0.121	0.3156	5008	,	,		20951	0.6984		0.172	False		,,,				2504	0.4131				p.R369R		Atlas-SNP	.	yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	WT1_ENST00000379079,colon,carcinoma,0,7	WT1	744	7	17	Complex - frameshift(9)|Deletion - Frameshift(3)|Insertion - Frameshift(3)|Unknown(2)	haematopoietic_and_lymphoid_tissue(15)|kidney(2)	c.A1107G						PASS	.	C	,,,,	497,3907	780.4+/-414.4	29,439,1734	87.0	77.0	80.0		1056,471,420,1107,1107	-2.8	0.9	11	dbSNP_60	80	1197,7401	763.6+/-407.6	84,1029,3186	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WT1	NM_000378.4,NM_001198551.1,NM_001198552.1,NM_024424.3,NM_024426.4	,,,,	113,1468,4920	CC,CT,TT		13.9218,11.2852,13.0288	,,,,	352/498,157/303,140/289,369/515,369/518	32417945	1694,11308	2202	4299	6501	SO:0001819	synonymous_variant	7490	exon7	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	CACACGTCGCACA		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.471A>G	11.37:g.32417945T>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	24	9	0.375	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Silent	SNP	ENST00000379079.2	37	CCDS55751.1	703	0.3218864468864469	57	0.11585365853658537	104	0.287292817679558	407	0.7115384615384616	135	0.17810026385224276	C	9.160	1.018548	0.19355	0.112852	0.139218	ENSG00000184937	ENST00000527882	.	.	.	6.17	-2.75	0.05914	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.35500	-0.9786	3	.	.	.	.	7.3485	0.26676	0.0:0.3562:0.2657:0.3781	rs16754;rs5030275;rs17846027;rs17859011;rs59880152;rs16754	.	.	.	A	60	.	.	T	-	1	0	WT1	32374521	0.001000	0.12720	0.854000	0.33618	0.876000	0.50452	-1.287000	0.02785	-0.854000	0.04131	-0.119000	0.15052	ACG	T|0.782;C|0.218	0.218	strong		0.522	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378	
RANBP6	26953	hgsc.bcm.edu	37	9	6012734	6012734	+	Silent	SNP	A	A	C	rs106033	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:6012734A>C	ENST00000259569.5	-	1	2884	c.2874T>G	c.(2872-2874)ctT>ctG	p.L958L	RANBP6_ENST00000485372.1_5'Flank	NM_001243202.1|NM_001243203.1|NM_012416.3	NP_001230131.1|NP_001230132.1|NP_036548.1	O60518	RNBP6_HUMAN	RAN binding protein 6	958					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(5)|large_intestine(8)|lung(9)|ovary(7)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	51		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00522)|Lung(218;0.101)		CTTTTACCAGAAGTGGAACAG	0.403													C|||	2134	0.426118	0.5734	0.3112	5008	,	,		20773	0.4266		0.2435	False		,,,				2504	0.4959				p.L958L		Atlas-SNP	.											.	RANBP6	127	.	0			c.T2874G						PASS	.	C		2286,2120	576.0+/-384.1	575,1136,492	85.0	80.0	82.0		2874	2.6	1.0	9	dbSNP_79	82	1997,6603	721.1+/-406.3	220,1557,2523	no	coding-synonymous	RANBP6	NM_012416.3		795,2693,3015	CC,CA,AA		23.2209,48.1162,32.931		958/1106	6012734	4283,8723	2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			TACCAGAAGTGGA	AF039023	CCDS6467.1	9p24.1	2008-03-26			ENSG00000137040	ENSG00000137040			9851	protein-coding gene	gene with protein product							Standard	NM_001243202		Approved		uc003zjr.3	O60518	OTTHUMG00000019512	ENST00000259569.5:c.2874T>G	9.37:g.6012734A>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	37	CCDS6467.1																																																																																			A|0.647;C|0.353	0.353	strong		0.403	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416	
HLA-A	3105	hgsc.bcm.edu	37	6	29912147	29912147	+	Silent	SNP	C	C	T	rs1059686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29912147C>T	ENST00000396634.1	+	6	1209	c.868C>T	c.(868-870)Ctg>Ttg	p.L290L	HLA-A_ENST00000376809.5_Silent_p.L290L|HLA-A_ENST00000376806.5_Silent_p.L290L|HLA-A_ENST00000376802.2_Silent_p.L290L			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	290	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCATGAGGGTCTGCCCAAGCC	0.597									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.L290L		Atlas-SNP	.											.	HLA-A	89	.	0			c.C868T						PASS	.	C		786,2236		78,630,803	67.0	59.0	62.0		868	3.7	1.0	6	dbSNP_86	62	1703,3715		244,1215,1250	no	coding-synonymous	HLA-A	NM_002116.7		322,1845,2053	TT,TC,CC		31.4323,26.0093,29.4905		290/366	29912147	2489,5951	1511	2709	4220	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGGGTCTGCCCA	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.868C>T	6.37:g.29912147C>T		Somatic	304	0	0		WXS	Illumina HiSeq	Phase_I	181	57	0.314917	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.711;T|0.289	0.289	strong		0.597	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
STEAP2	261729	hgsc.bcm.edu	37	7	89854446	89854446	+	Missense_Mutation	SNP	T	T	G	rs194520	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:89854446T>G	ENST00000287908.3	+	2	443	c.50T>G	c.(49-51)tTt>tGt	p.F17C	STEAP2_ENST00000394621.2_Missense_Mutation_p.F17C|STEAP2_ENST00000394626.1_Missense_Mutation_p.F17C|STEAP2_ENST00000394622.2_Missense_Mutation_p.F17C|STEAP2_ENST00000394632.1_Missense_Mutation_p.F17C|STEAP2_ENST00000394629.2_Missense_Mutation_p.F17C|STEAP2_ENST00000402625.2_Missense_Mutation_p.F17C	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	17			F -> C (in dbSNP:rs194520). {ECO:0000269|PubMed:12095985, ECO:0000269|PubMed:12429817, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:18669648, ECO:0000269|Ref.3}.	F -> V (in Ref. 2; AAN04080). {ECO:0000305}.	copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					AGTGAAACTTTTTTACCTAAT	0.398													T|||	1689	0.33726	0.2859	0.3862	5008	,	,		19519	0.1825		0.5119	False		,,,				2504	0.3517				p.F17C		Atlas-SNP	.											.	STEAP2	78	.	0			c.T50G						PASS	.	T	CYS/PHE,CYS/PHE,CYS/PHE	1497,2909	477.9+/-358.1	263,971,969	129.0	120.0	123.0		50,50,50	5.8	1.0	7	dbSNP_79	123	4544,4056	593.5+/-393.2	1218,2108,974	yes	missense,missense,missense	STEAP2	NM_001040665.1,NM_001040666.1,NM_152999.3	205,205,205	1481,3079,1943	GG,GT,TT		47.1628,33.9764,46.4478	possibly-damaging,possibly-damaging,possibly-damaging	17/491,17/455,17/491	89854446	6041,6965	2203	4300	6503	SO:0001583	missense	261729	exon3			AAACTTTTTTACC	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"""prostate cancer associated protein 1"", ""six transmembrane epithelial antigen of the prostate 2"""	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.50T>G	7.37:g.89854446T>G	ENSP00000287908:p.Phe17Cys	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	129	129	1	NM_001244946	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Missense_Mutation	SNP	ENST00000287908.3	37	CCDS5615.1	798	0.36538461538461536	150	0.3048780487804878	146	0.40331491712707185	108	0.1888111888111888	394	0.5197889182058048	T	16.93	3.259318	0.59321	0.339764	0.528372	ENSG00000157214	ENST00000428074;ENST00000287908;ENST00000394626;ENST00000394622;ENST00000394632;ENST00000394624;ENST00000426158;ENST00000394621;ENST00000402625;ENST00000394629	T;T;T;T;T;T;T;T;T	0.36157	2.1;3.4;3.14;3.4;3.12;1.27;3.4;3.14;3.14	5.83	5.83	0.93111	.	0.115725	0.64402	D	0.000011	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999950613	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.81914	0.995;0.984;0.984;0.993	T	0.48547	-0.9026	9	0.45353	T	0.12	-24.3129	16.2127	0.82178	0.0:0.0:0.0:1.0	rs194520;rs17621279;rs57850425;rs194520	17;17;17;17	G5E9C6;Q6YPB2;Q8NFT2;B5MC02	.;.;STEA2_HUMAN;.	C	17	ENSP00000401783:F17C;ENSP00000287908:F17C;ENSP00000378123:F17C;ENSP00000378120:F17C;ENSP00000378128:F17C;ENSP00000415931:F17C;ENSP00000378119:F17C;ENSP00000384191:F17C;ENSP00000378125:F17C	ENSP00000287908:F17C	F	+	2	0	STEAP2	89692382	1.000000	0.71417	0.995000	0.50966	0.982000	0.71751	5.041000	0.64196	2.236000	0.73375	0.533000	0.62120	TTT	T|0.602;G|0.398	0.398	strong		0.398	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999	
NLRP5	126206	hgsc.bcm.edu	37	19	56549532	56549532	+	Silent	SNP	A	A	G	rs306447	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56549532A>G	ENST00000390649.3	+	10	2757	c.2757A>G	c.(2755-2757)agA>agG	p.R919R		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	919					cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)	p.R919R(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		ATGCCTTGAGAGTCTCCCAGT	0.522													G|||	1518	0.303115	0.4834	0.1758	5008	,	,		21896	0.3016		0.2406	False		,,,				2504	0.2157				p.R919R		Atlas-SNP	.											NLRP5,NS,carcinoma,0,1	NLRP5	217	1	1	Substitution - coding silent(1)	stomach(1)	c.A2757G						PASS	.	G		1782,2452		384,1014,719	133.0	134.0	134.0		2757	-2.2	0.0	19	dbSNP_79	134	1872,6602		218,1436,2583	no	coding-synonymous	NLRP5	NM_153447.4		602,2450,3302	GG,GA,AA		22.0911,42.0879,28.7535		919/1201	56549532	3654,9054	2117	4237	6354	SO:0001819	synonymous_variant	126206	exon10			CTTGAGAGTCTCC	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.2757A>G	19.37:g.56549532A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	161	66	0.409938	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			A|0.693;G|0.307	0.307	strong		0.522	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
FBXO42	54455	hgsc.bcm.edu	37	1	16641899	16641899	+	Silent	SNP	C	C	T	rs2273311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16641899C>T	ENST00000375592.3	-	2	231	c.15G>A	c.(13-15)tcG>tcA	p.S5S	FBXO42_ENST00000478089.1_5'Flank	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	5										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)		CTTCACTGTCCGAGGAGCTGG	0.463													C|||	1790	0.357428	0.0469	0.3372	5008	,	,		20434	0.6786		0.4235	False		,,,				2504	0.3926				p.S5S		Atlas-SNP	.											.	FBXO42	53	.	0			c.G15A						PASS	.	C		529,3877	241.5+/-251.9	35,459,1709	83.0	70.0	75.0		15	-4.1	0.9	1	dbSNP_100	75	3417,5183	503.5+/-375.9	688,2041,1571	no	coding-synonymous	FBXO42	NM_018994.1		723,2500,3280	TT,TC,CC		39.7326,12.0064,30.3398		5/718	16641899	3946,9060	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon2			ACTGTCCGAGGAG	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.15G>A	1.37:g.16641899C>T		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	155	8	0.0516129	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			C|0.658;T|0.342	0.342	strong		0.463	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
FLNC	2318	hgsc.bcm.edu	37	7	128491603	128491603	+	Silent	SNP	T	T	C	rs3816884	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128491603T>C	ENST00000325888.8	+	35	6024	c.5763T>C	c.(5761-5763)acT>acC	p.T1921T	RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Silent_p.T1888T	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1921					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						ATCTGCCGACTGCGCCTGGAG	0.597													C|||	1447	0.288938	0.534	0.1671	5008	,	,		20776	0.378		0.0368	False		,,,				2504	0.2117				p.T1921T		Atlas-SNP	.											FLNC,NS,lymphoid_neoplasm,+1,1	FLNC	339	1	0			c.T5763C						scavenged	.	C	,	2036,2370	593.1+/-387.9	497,1042,664	95.0	111.0	105.0		5664,5763	-11.4	0.0	7	dbSNP_107	105	385,8215	798.7+/-407.4	7,371,3922	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	504,1413,4586	CC,CT,TT		4.4767,46.2097,18.6145	,	1888/2693,1921/2726	128491603	2421,10585	2203	4300	6503	SO:0001819	synonymous_variant	2318	exon35			GCCGACTGCGCCT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.5763T>C	7.37:g.128491603T>C		Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	186	97	0.521505	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			T|0.793;C|0.207	0.207	strong		0.597	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
C1QTNF1	114897	hgsc.bcm.edu	37	17	77040185	77040185	+	Silent	SNP	G	G	C	rs4789853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:77040185G>C	ENST00000339142.2	+	3	690	c.135G>C	c.(133-135)tcG>tcC	p.S45S	C1QTNF1_ENST00000580474.1_Silent_p.S45S|C1QTNF1_ENST00000578229.1_5'UTR|C1QTNF1_ENST00000392445.2_Silent_p.S45S|C1QTNF1_ENST00000579760.1_Silent_p.S45S|C1QTNF1_ENST00000581774.1_Silent_p.S45S|C1QTNF1_ENST00000580454.1_Silent_p.S45S|C1QTNF1_ENST00000583904.1_Silent_p.S45S|C1QTNF1_ENST00000354124.3_Silent_p.S55S|C1QTNF1_ENST00000311661.4_Intron	NM_198593.3	NP_940995.1	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	45					negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase B signaling (GO:0051897)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|regulation of glucose metabolic process (GO:0010906)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(2)	14			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)			AGCTGCCGTCGCCTCCGGACC	0.677													C|||	2303	0.459864	0.5499	0.4928	5008	,	,		19352	0.5387		0.2883	False		,,,				2504	0.41				p.S45S		Atlas-SNP	.											.	C1QTNF1	62	.	0			c.G135C						PASS	.	C	,,	2253,2153	573.6+/-383.6	593,1067,543	40.0	34.0	36.0		135,135,	-1.8	0.0	17	dbSNP_111	36	2554,6046	682.2+/-403.8	392,1770,2138	no	coding-synonymous,coding-synonymous,intron	C1QTNF1	NM_030968.2,NM_198593.2,NM_198594.1	,,	985,2837,2681	CC,CG,GG		29.6977,48.8652,36.9599	,,	45/282,45/282,	77040185	4807,8199	2203	4300	6503	SO:0001819	synonymous_variant	114897	exon2			GCCGTCGCCTCCG	AF329840	CCDS11761.1, CCDS11762.1	17q25	2012-07-02			ENSG00000173918	ENSG00000173918			14324	protein-coding gene	gene with protein product	"""G protein coupled receptor interacting protein"""	610365				12409230	Standard	NM_198593		Approved	CTRP1, ZSIG37, GIP, FLJ90694	uc002jwp.4	Q9BXJ1	OTTHUMG00000177533	ENST00000339142.2:c.135G>C	17.37:g.77040185G>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	42	20	0.47619	NM_030968	Q6ZMH6|Q96NF2|Q9GZR4	Silent	SNP	ENST00000339142.2	37	CCDS11761.1																																																																																			G|0.616;C|0.384	0.384	strong		0.677	C1QTNF1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437388.2	NM_030968	
SDC2	6383	hgsc.bcm.edu	37	8	97605800	97605800	+	Silent	SNP	C	C	T	rs1126681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:97605800C>T	ENST00000302190.4	+	2	1074	c.153C>T	c.(151-153)taC>taT	p.Y51Y	SDC2_ENST00000518385.1_Intron|SDC2_ENST00000522911.1_Silent_p.Y22Y|SDC2_ENST00000519914.1_Silent_p.Y22Y	NM_002998.3	NP_002989.2	P34741	SDC2_HUMAN	syndecan 2	51					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dendrite morphogenesis (GO:0048813)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|regulation of dendrite morphogenesis (GO:0048814)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)	p.Y51Y(2)		breast(1)|cervix(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(1)|stomach(2)	16	Breast(36;3.41e-05)				Sargramostim(DB00020)	ACGATGACTACGCTTCTGCGT	0.473													C|||	1132	0.226038	0.0484	0.1628	5008	,	,		21516	0.3591		0.2217	False		,,,				2504	0.3783				p.Y51Y		Atlas-SNP	.											SDC2,NS,carcinoma,0,2	SDC2	33	2	2	Substitution - coding silent(2)	prostate(1)|stomach(1)	c.C153T						scavenged	.	C		362,4044	186.0+/-213.0	14,334,1855	142.0	108.0	119.0		153	-6.0	0.9	8	dbSNP_86	119	1894,6706	335.6+/-321.5	207,1480,2613	no	coding-synonymous	SDC2	NM_002998.3		221,1814,4468	TT,TC,CC		22.0233,8.2161,17.3458		51/202	97605800	2256,10750	2203	4300	6503	SO:0001819	synonymous_variant	6383	exon2			TGACTACGCTTCT	BC030133	CCDS6272.1	8q22-q23	2011-08-11	2007-02-15		ENSG00000169439	ENSG00000169439		"""Proteoglycans / Cell Surface : Syndecans"", ""CD molecules"""	10659	protein-coding gene	gene with protein product	"""syndecan proteoglycan 2"""	142460	"""heparan sulfate proteoglycan 1, cell surface-associated"""	HSPG, HSPG1		8187643	Standard	NM_002998		Approved	fibroglycan, SYND2, CD362	uc003yhv.1	P34741	OTTHUMG00000164689	ENST00000302190.4:c.153C>T	8.37:g.97605800C>T		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_002998	B3KQA3|Q6PIS6|Q9H6V1	Silent	SNP	ENST00000302190.4	37	CCDS6272.1																																																																																			C|0.804;T|0.196	0.196	strong		0.473	SDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379750.1	NM_002998	
PPP6R2	9701	hgsc.bcm.edu	37	22	50873497	50873497	+	Silent	SNP	C	C	T	rs1134848	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50873497C>T	ENST00000216061.5	+	14	1873	c.1503C>T	c.(1501-1503)agC>agT	p.S501S	PPP6R2_ENST00000395741.3_Silent_p.S502S|PPP6R2_ENST00000395744.3_Silent_p.S501S|PPP6R2_ENST00000359139.3_Silent_p.S501S			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	501						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						CGCACATCAGCGAGGTCATCC	0.677													C|||	265	0.0529153	0.0106	0.0879	5008	,	,		16008	0.001		0.1431	False		,,,				2504	0.046				p.S502S		Atlas-SNP	.											PPP6R2,NS,carcinoma,0,1	PPP6R2	71	1	0			c.C1506T						PASS	.	C	,,,	105,4295	79.3+/-117.8	2,101,2097	58.0	42.0	48.0		1503,1506,1503,1503	-0.5	0.8	22	dbSNP_86	48	1228,7370	239.3+/-270.5	84,1060,3155	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	,,,	86,1161,5252	TT,TC,CC		14.2824,2.3864,10.2554	,,,	501/960,502/934,501/928,501/933	50873497	1333,11665	2200	4299	6499	SO:0001819	synonymous_variant	9701	exon13			CATCAGCGAGGTC	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.1503C>T	22.37:g.50873497C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	50	14	0.28	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Silent	SNP	ENST00000216061.5	37																																																																																				C|0.920;T|0.080	0.080	strong		0.677	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
SCUBE2	57758	hgsc.bcm.edu	37	11	9051475	9051475	+	Missense_Mutation	SNP	G	G	C	rs3751057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:9051475G>C	ENST00000309263.3	-	18	2444	c.2372C>G	c.(2371-2373)aCt>aGt	p.T791S	SCUBE2_ENST00000520467.1_Missense_Mutation_p.T763S|SCUBE2_ENST00000457346.2_Missense_Mutation_p.T820S|SCUBE2_ENST00000450649.2_Missense_Mutation_p.T665S|RP11-467K18.2_ENST00000531592.1_RNA			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	791			T -> S (in dbSNP:rs3751057).			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GTCAGTCGTAGTATTTCCTGG	0.433													G|||	475	0.0948482	0.1097	0.0519	5008	,	,		20560	0.121		0.0676	False		,,,				2504	0.1063				p.T763S		Atlas-SNP	.											.	SCUBE2	102	.	0			c.C2288G						PASS	.	G	SER/THR,SER/THR	476,3926	226.2+/-241.8	20,436,1745	208.0	202.0	204.0		1994,2288	5.2	1.0	11	dbSNP_107	204	703,7889	173.2+/-223.7	27,649,3620	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	58,58	47,1085,5365	CC,CG,GG		8.182,10.8133,9.0734	probably-damaging,probably-damaging	665/808,763/972	9051475	1179,11815	2201	4296	6497	SO:0001583	missense	57758	exon18			GTCGTAGTATTTC	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.2372C>G	11.37:g.9051475G>C	ENSP00000310658:p.Thr791Ser	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	239	116	0.485356	NM_020974	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		176	0.08058608058608059	57	0.11585365853658537	17	0.04696132596685083	53	0.09265734265734266	49	0.06464379947229551	G	26.1	4.705731	0.89018	0.108133	0.08182	ENSG00000175356	ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02	5.19	5.19	0.71726	Tyrosine-protein kinase ephrin type A/B receptor-like (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.06050	0.0157	M	0.84585	2.705	0.09310	P	0.9999999293489	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.999	T	0.55127	-0.8189	9	0.62326	D	0.03	.	18.7036	0.91630	0.0:0.0:1.0:0.0	rs3751057;rs52803158;rs56444362;rs3751057	665;763;791	Q9NQ36-3;Q9NQ36-2;Q9NQ36	.;.;SCUB2_HUMAN	S	820;791;665;763	ENSP00000390481:T820S;ENSP00000310658:T791S;ENSP00000415187:T665S;ENSP00000429969:T763S	ENSP00000310658:T791S	T	-	2	0	SCUBE2	9008051	1.000000	0.71417	0.964000	0.40570	0.981000	0.71138	7.879000	0.87236	2.415000	0.81967	0.491000	0.48974	ACT	G|0.908;C|0.092	0.092	strong		0.433	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057711	46057711	+	Missense_Mutation	SNP	G	G	C	rs4818948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057711G>C	ENST00000380095.1	+	1	439	c.377G>C	c.(376-378)tGc>tCc	p.C126S	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	126	15 X 5 AA repeats of C-C-X(3).		C -> S (in dbSNP:rs4818948).			keratin filament (GO:0045095)		p.C126S(1)		NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TCCCCTTCATGCTGCCAGCAG	0.612													G|||	1378	0.27516	0.4781	0.2233	5008	,	,		22902	0.0526		0.2406	False		,,,				2504	0.3027				p.C126S		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,0,1	KRTAP10-10	37	1	1	Substitution - Missense(1)	prostate(1)	c.G377C						PASS	.	G	,SER/CYS	1974,2432	555.8+/-379.4	449,1076,678	260.0	233.0	242.0		,377	2.2	0.7	21	dbSNP_111	242	2165,6435	369.3+/-335.4	281,1603,2416	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,112	730,2679,3094	CC,CG,GG		25.1744,44.8025,31.8238	,possibly-damaging	,126/252	46057711	4139,8867	2203	4300	6503	SO:0001583	missense	353333	exon1			CTTCATGCTGCCA	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.377G>C	21.37:g.46057711G>C	ENSP00000369438:p.Cys126Ser	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	155	73	0.470968	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	539	0.2467948717948718	232	0.4715447154471545	88	0.2430939226519337	31	0.05419580419580419	188	0.24802110817941952	g	9.775	1.173863	0.21704	0.448025	0.251744	ENSG00000221859	ENST00000380095	T	0.01446	4.88	3.08	2.19	0.27852	.	.	.	.	.	T	0.00012	0.0000	M	0.92317	3.295	0.35991	P	0.163292	B	0.26708	0.157	B	0.30316	0.114	T	0.23904	-1.0175	8	0.40728	T	0.16	.	4.9606	0.14065	0.1295:0.2156:0.6549:0.0	rs4818948;rs52837069;rs58818342	126	P60014	KR10A_HUMAN	S	126	ENSP00000369438:C126S	ENSP00000369438:C126S	C	+	2	0	KRTAP10-10	44882139	0.467000	0.25831	0.745000	0.31077	0.268000	0.26511	2.512000	0.45485	0.411000	0.25702	-0.374000	0.07098	TGC	G|0.711;C|0.289	0.289	strong		0.612	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
MAP3K2	10746	hgsc.bcm.edu	37	2	128079806	128079806	+	Silent	SNP	A	A	G	rs3732209	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:128079806A>G	ENST00000409947.1	-	12	1143	c.861T>C	c.(859-861)gcT>gcC	p.A287A	MAP3K2_ENST00000344908.5_Silent_p.A287A			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	287					activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	GGGTCCTTCTAGCTCTTGGAA	0.358													A|||	1034	0.20647	0.2663	0.1729	5008	,	,		16203	0.0179		0.2803	False		,,,				2504	0.2679				p.A287A		Atlas-SNP	.											.	MAP3K2	78	.	0			c.T861C						PASS	.	A		933,2701		124,685,1008	55.0	53.0	53.0		861	-0.6	1.0	2	dbSNP_107	53	2553,5581		408,1737,1922	no	coding-synonymous	MAP3K2	NM_006609.4		532,2422,2930	GG,GA,AA		31.3868,25.6742,29.6227		287/620	128079806	3486,8282	1817	4067	5884	SO:0001819	synonymous_variant	10746	exon11			CCTTCTAGCTCTT	AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6854	protein-coding gene	gene with protein product	"""MAP/ERK kinase kinase 2"""	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.861T>C	2.37:g.128079806A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	47	20	0.425532	NM_006609	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Silent	SNP	ENST00000409947.1	37	CCDS46404.1																																																																																			A|0.788;G|0.212	0.212	strong		0.358	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1	NM_006609	
UBASH3A	53347	hgsc.bcm.edu	37	21	43863521	43863521	+	Silent	SNP	A	A	G	rs386818914|rs868092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43863521A>G	ENST00000319294.6	+	13	1762	c.1731A>G	c.(1729-1731)ccA>ccG	p.P577P	UBASH3A_ENST00000398367.1_Intron|UBASH3A_ENST00000291535.6_Silent_p.P539P	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	577	Phosphatase-like.				negative regulation of T cell receptor signaling pathway (GO:0050860)|regulation of cytokine production (GO:0001817)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						ACACCTGTCCACAGGACAGTA	0.552													G|||	3089	0.616813	0.59	0.6556	5008	,	,		19473	0.5169		0.6879	False		,,,				2504	0.6554				p.P577P		Atlas-SNP	.											.	UBASH3A	72	.	0			c.A1731G						PASS	.	G	,	2768,1638	484.6+/-360.1	858,1052,293	65.0	47.0	53.0		1617,1731	-3.9	0.0	21	dbSNP_86	53	6298,2302	371.3+/-336.2	2315,1668,317	no	coding-synonymous,coding-synonymous	UBASH3A	NM_001001895.2,NM_018961.3	,	3173,2720,610	GG,GA,AA		26.7674,37.1766,30.2937	,	539/624,577/662	43863521	9066,3940	2203	4300	6503	SO:0001819	synonymous_variant	53347	exon13			CTGTCCACAGGAC	AJ277750	CCDS13687.1, CCDS33566.1, CCDS58791.1	21q22.3	2010-04-28	2010-04-28		ENSG00000160185	ENSG00000160185			12462	protein-coding gene	gene with protein product		605736				11281453	Standard	NM_018961		Approved	STS-2, TULA, CLIP4	uc002zbf.3	P57075	OTTHUMG00000086805	ENST00000319294.6:c.1731A>G	21.37:g.43863521A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	Silent	SNP	ENST00000319294.6	37	CCDS13687.1																																																																																			A|0.359;G|0.641	0.641	strong		0.552	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895	
OR7A17	26333	hgsc.bcm.edu	37	19	14991459	14991459	+	Missense_Mutation	SNP	C	C	T	rs13345394	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14991459C>T	ENST00000327462.2	-	1	805	c.709G>A	c.(709-711)Gca>Aca	p.A237T		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	237			A -> T (in dbSNP:rs13345394).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					GTGGAAAATGCCTTGTACTTC	0.498													.|||	230	0.0459265	0.1036	0.0476	5008	,	,		20481	0.0159		0.0149	False		,,,				2504	0.0297				p.A237T		Atlas-SNP	.											.	OR7A17	37	.	0			c.G709A						PASS	.	C	THR/ALA	400,4006	199.4+/-223.0	16,368,1819	110.0	97.0	102.0		709	2.3	0.3	19	dbSNP_121	102	250,8350	99.5+/-161.0	3,244,4053	no	missense	OR7A17	NM_030901.1	58	19,612,5872	TT,TC,CC		2.907,9.0785,4.9977	benign	237/310	14991459	650,12356	2203	4300	6503	SO:0001583	missense	26333	exon1			AAAATGCCTTGTA	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"""GPCR / Class A : Olfactory receptors"""	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.709G>A	19.37:g.14991459C>T	ENSP00000328144:p.Ala237Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_030901	Q6IFQ6|Q96R98	Missense_Mutation	SNP	ENST00000327462.2	37	CCDS12319.1	68	0.031135531135531136	33	0.06707317073170732	16	0.04419889502762431	8	0.013986013986013986	11	0.014511873350923483	c	12.62	1.991591	0.35131	0.090785	0.02907	ENSG00000185385	ENST00000327462	T	0.00357	7.89	3.37	2.29	0.28610	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38548	U	0.001647	T	0.00039	0.0001	L	0.61218	1.895	0.26061	N	0.981357	D	0.64830	0.994	D	0.66602	0.945	T	0.48445	-0.9035	10	0.87932	D	0	.	9.8486	0.41043	0.207:0.793:0.0:0.0	rs13345394	237	O14581	OR7AH_HUMAN	T	237	ENSP00000328144:A237T	ENSP00000328144:A237T	A	-	1	0	OR7A17	14852459	1.000000	0.71417	0.335000	0.25508	0.029000	0.11900	3.726000	0.54977	0.756000	0.33013	-0.578000	0.04140	GCA	C|0.959;T|0.041	0.041	strong		0.498	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
ADCK4	79934	hgsc.bcm.edu	37	19	41209477	41209477	+	Silent	SNP	C	C	T	rs11538385	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41209477C>T	ENST00000324464.3	-	9	1069	c.768G>A	c.(766-768)gcG>gcA	p.A256A	ADCK4_ENST00000450541.1_Silent_p.A215A|ADCK4_ENST00000243583.6_Silent_p.A215A	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	256	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			TCTTGAGTACCGCCAGCAGGT	0.622													C|||	1149	0.229433	0.084	0.196	5008	,	,		17506	0.2361		0.3032	False		,,,				2504	0.3671				p.A256A		Atlas-SNP	.											ADCK4_ENST00000324464,colon,carcinoma,-1,6	ADCK4	92	6	0			c.G768A						PASS	.	C	,	543,3863	240.9+/-251.5	35,473,1695	55.0	57.0	56.0		645,768	-10.1	0.5	19	dbSNP_120	56	2474,6126	404.1+/-348.0	353,1768,2179	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	388,2241,3874	TT,TC,CC		28.7674,12.3241,23.197	,	215/504,256/545	41209477	3017,9989	2203	4300	6503	SO:0001819	synonymous_variant	79934	exon9			GAGTACCGCCAGC	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.768G>A	19.37:g.41209477C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	99	54	0.545455	NM_024876	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			C|0.773;T|0.227	0.227	strong		0.622	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
ERCC4	2072	hgsc.bcm.edu	37	16	14041958	14041958	+	Silent	SNP	T	T	C	rs1799801	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:14041958T>C	ENST00000311895.7	+	11	2514	c.2505T>C	c.(2503-2505)tcT>tcC	p.S835S		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	835					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						CAGCAGATTCTGAAACCCTTC	0.527			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	1208	0.241214	0.1694	0.2104	5008	,	,		18126	0.2589		0.2942	False		,,,				2504	0.2873				p.S835S		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""		E	.	ERCC4	100	.	0			c.T2505C						PASS	.	C		762,3632	753.2+/-412.4	55,652,1490	47.0	46.0	47.0		2505	-12.3	0.0	16	dbSNP_89	47	2528,6072	692.1+/-404.6	369,1790,2141	no	coding-synonymous	ERCC4	NM_005236.2		424,2442,3631	CC,CT,TT		29.3953,17.3418,25.3194		835/917	14041958	3290,9704	2197	4300	6497	SO:0001819	synonymous_variant	2072	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGATTCTGAAACC	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"""xeroderma pigmentosum, complementation group F"""	133520	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.2505T>C	16.37:g.14041958T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	88	37	0.420455	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Silent	SNP	ENST00000311895.7	37	CCDS32390.1																																																																																			T|0.754;C|0.246	0.246	strong		0.527	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	
PCDHB7	56129	hgsc.bcm.edu	37	5	140553581	140553581	+	Missense_Mutation	SNP	G	G	C	rs2910313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140553581G>C	ENST00000231137.3	+	1	1339	c.1165G>C	c.(1165-1167)Gtc>Ctc	p.V389L		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	389	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> L (in dbSNP:rs2910313).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCAGGACGATGTCCCCTTCAT	0.463													C|||	3142	0.627396	0.6891	0.6369	5008	,	,		18866	0.6607		0.5477	False		,,,				2504	0.5849				p.V389L		Atlas-SNP	.											PCDHB7,colon,carcinoma,0,1	PCDHB7	231	1	0			c.G1165C						scavenged	.	C	LEU/VAL	2933,1473	473.1+/-356.6	969,995,239	75.0	76.0	76.0		1165	2.7	0.4	5	dbSNP_101	76	4900,3700	530.1+/-381.7	1417,2066,817	yes	missense	PCDHB7	NM_018940.2	32	2386,3061,1056	CC,CG,GG		43.0233,33.4317,39.774	benign	389/794	140553581	7833,5173	2203	4300	6503	SO:0001583	missense	56129	exon1			GACGATGTCCCCT	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1165G>C	5.37:g.140553581G>C	ENSP00000231137:p.Val389Leu	Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	89	88	0.988764	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	1340	0.6135531135531136	336	0.6829268292682927	210	0.580110497237569	378	0.6608391608391608	416	0.5488126649076517	C	0.176	-1.066570	0.01934	0.665683	0.569767	ENSG00000113212	ENST00000231137;ENST00000543636	T	0.51071	0.72	4.61	2.73	0.32206	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.01086	-1.025	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.46898	-0.9158	8	0.02654	T	1	.	10.0458	0.42186	0.2543:0.4998:0.2459:0.0	rs2910313;rs3733696;rs17286898;rs17844450;rs60742292;rs2910313	389	Q9Y5E2	PCDB7_HUMAN	L	389;172	ENSP00000231137:V389L	ENSP00000231137:V389L	V	+	1	0	PCDHB7	140533765	0.000000	0.05858	0.355000	0.25773	0.824000	0.46624	-0.008000	0.12788	0.096000	0.17463	-0.127000	0.14921	GTC	G|0.392;C|0.608	0.608	strong		0.463	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
TYRO3	7301	hgsc.bcm.edu	37	15	41870083	41870083	+	Splice_Site	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:41870083G>T	ENST00000263798.3	+	19	2506		c.e19-1		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CTCCACCCCAGGTATGATCTC	0.517																																					.		Atlas-SNP	.											TYRO3_ENST00000263798,colon,carcinoma,0,4	TYRO3	169	4	0			c.2283-1G>T						scavenged	.						40.0	43.0	42.0					15																	41870083		2198	4286	6484	SO:0001630	splice_region_variant	7301	exon19			ACCCCAGGTATGA	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.2283-1G>T	15.37:g.41870083G>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	44	3	0.0681818	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	G	19.30	3.801139	0.70567	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3931	0.98965	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39657375	1.000000	0.71417	1.000000	0.80357	0.753000	0.42808	9.682000	0.98655	2.824000	0.97209	0.655000	0.94253	.	.	.	none		0.517	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron
MSH5	4439	hgsc.bcm.edu	37	6	31708328	31708328	+	Missense_Mutation	SNP	C	C	T	rs2075789	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31708328C>T	ENST00000375755.3	+	2	371	c.85C>T	c.(85-87)Cca>Tca	p.P29S	MSH5_ENST00000534153.4_Missense_Mutation_p.P29S|MSH5-SAPCD1_ENST00000493662.2_Missense_Mutation_p.P29S|MSH5_ENST00000375740.3_Missense_Mutation_p.P29S|MSH5_ENST00000375703.3_Missense_Mutation_p.P29S|MSH5_ENST00000375750.3_Missense_Mutation_p.P29S|MSH5_ENST00000482280.1_3'UTR|CLIC1_ENST00000395892.1_5'Flank|MSH5_ENST00000375742.3_Missense_Mutation_p.P29S	NM_002441.4	NP_002432.1	O43196	MSH5_HUMAN	mutS homolog 5	29			P -> S (in dbSNP:rs2075789). {ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|chiasma assembly (GO:0051026)|homologous chromosome segregation (GO:0045143)|mismatch repair (GO:0006298)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|mismatched DNA binding (GO:0030983)			breast(1)|ovary(2)|skin(2)	5						CAGCCCGGCCCCAGTGCCGGG	0.662								Direct reversal of damage;Mismatch excision repair (MMR)					C|||	510	0.101837	0.0189	0.1599	5008	,	,		10387	0.1339		0.1004	False		,,,				2504	0.1411				p.P29S		Atlas-SNP	.											.	MSH5	108	.	0			c.C85T	GRCh37	CM056007	MSH5	M	rs2075789	PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	129,3883		3,123,1880	4.0	5.0	5.0		85,85,85,85	-2.4	0.0	6	dbSNP_96	5	669,7393		29,611,3391	no	missense,missense,missense,missense	MSH5	NM_002441.4,NM_025259.5,NM_172165.3,NM_172166.3	74,74,74,74	32,734,5271	TT,TC,CC		8.2982,3.2154,6.6092	benign,benign,benign,benign	29/835,29/823,29/836,29/835	31708328	798,11276	2006	4031	6037	SO:0001583	missense	4439	exon2			CCGGCCCCAGTGC	AF070071	CCDS4720.1, CCDS34409.1, CCDS34410.1, CCDS34409.2	6p21.3	2013-09-12	2013-09-12		ENSG00000204410	ENSG00000204410			7328	protein-coding gene	gene with protein product		603382	"""mutS (E. coli) homolog 5"", ""mutS homolog 5 (E. coli)"""			9740671, 9787078, 17977839	Standard	NM_002441		Approved		uc011hbg.2	O43196	OTTHUMG00000167551	ENST00000375755.3:c.85C>T	6.37:g.31708328C>T	ENSP00000364908:p.Pro29Ser	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_172165	B0V033|B0V034|O60586|Q5BLU9|Q5SSR1|Q8IW44|Q9BQC7	Missense_Mutation	SNP	ENST00000375755.3	37	CCDS4720.1	264	0.12087912087912088	22	0.044715447154471545	53	0.1464088397790055	105	0.18356643356643357	84	0.11081794195250659	C	13.55	2.269554	0.40095	0.032154	0.082982	ENSG00000204410	ENST00000375755;ENST00000375742;ENST00000375750;ENST00000425703;ENST00000534153;ENST00000375703;ENST00000375740	T;T;T;T;T;T;T	0.33865	1.39;1.39;1.39;1.39;1.39;1.39;1.39	4.77	-2.41	0.06562	.	0.568137	0.16081	N	0.230492	T	0.12603	0.0306	L	0.47716	1.5	0.24266	P	0.995262	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.0;0.001;0.002	T	0.19679	-1.0298	9	0.59425	D	0.04	-16.3891	9.1915	0.37202	0.0:0.2641:0.5718:0.1641	rs2075789;rs2075789	29;29;29;29	O43196-4;O43196;O43196-2;O43196-3	.;MSH5_HUMAN;.;.	S	29	ENSP00000364908:P29S;ENSP00000364894:P29S;ENSP00000364903:P29S;ENSP00000402842:P29S;ENSP00000431693:P29S;ENSP00000364855:P29S;ENSP00000364892:P29S	ENSP00000364855:P29S	P	+	1	0	MSH5	31816307	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.008000	0.12788	-0.336000	0.08438	-0.150000	0.13652	CCA	C|0.881;T|0.119	0.119	strong		0.662	MSH5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076243.4		
CRB2	286204	hgsc.bcm.edu	37	9	126132919	126132919	+	Silent	SNP	G	G	A	rs33984675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:126132919G>A	ENST00000373631.3	+	7	1588	c.1587G>A	c.(1585-1587)gcG>gcA	p.A529A	CRB2_ENST00000359999.3_Silent_p.A529A|CRB2_ENST00000373629.2_Silent_p.A197A	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	529	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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						TCCATCTAGCGACCCTGGAGC	0.642													G|||	990	0.197684	0.059	0.1758	5008	,	,		19807	0.252		0.2753	False		,,,				2504	0.2648				p.A529A		Atlas-SNP	.											.	CRB2	86	.	0			c.G1587A						PASS	.	G		383,4023	192.3+/-217.7	17,349,1837	72.0	66.0	68.0		1587	3.0	0.5	9	dbSNP_126	68	2696,5904	430.3+/-356.5	430,1836,2034	no	coding-synonymous	CRB2	NM_173689.5		447,2185,3871	AA,AG,GG		31.3488,8.6927,23.6737		529/1286	126132919	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon7			TCTAGCGACCCTG	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.1587G>A	9.37:g.126132919G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	44	14	0.318182	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			G|0.766;A|0.234	0.234	strong		0.642	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
RBMX	27316	hgsc.bcm.edu	37	X	135958730	135958730	+	Missense_Mutation	SNP	C	C	A	rs78702689		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135958730C>A	ENST00000320676.7	-	5	627	c.473G>T	c.(472-474)gGg>gTg	p.G158V	RBMX_ENST00000562646.1_Missense_Mutation_p.G158V|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Missense_Mutation_p.G30V|RBMX_ENST00000570135.1_Missense_Mutation_p.G23V|SNORD61_ENST00000384252.1_RNA|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	158					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					AGGAGGACCCCCACTTCTTGG	0.458																																					p.G158V		Atlas-SNP	.											.	RBMX	149	.	0			c.G473T						PASS	.						119.0	109.0	112.0					X																	135958730		2203	4300	6503	SO:0001583	missense	27316	exon5			GGACCCCCACTTC		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.473G>T	X.37:g.135958730C>A	ENSP00000359645:p.Gly158Val	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	342	73	0.21345	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	15.16	2.752212	0.49362	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.79141	-1.24	5.39	4.53	0.55603	.	0.000000	0.64402	U	0.000001	T	0.77618	0.4157	M	0.65975	2.015	0.09310	P	0.9999999999628356	B;P	0.43287	0.047;0.802	B;B	0.41466	0.011;0.358	T	0.82932	-0.0212	9	0.49607	T	0.09	.	15.5319	0.75970	0.0:0.8651:0.1349:0.0	.	158;145	P38159;Q8N8Y7	HNRPG_HUMAN;.	V	158;145	ENSP00000359645:G158V	ENSP00000359645:G158V	G	-	2	0	RBMX	135786396	1.000000	0.71417	0.978000	0.43139	0.845000	0.48019	5.153000	0.64888	1.075000	0.40932	-0.288000	0.09946	GGG	.	.	weak		0.458	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
YDJC	150223	hgsc.bcm.edu	37	22	21982892	21982892	+	Missense_Mutation	SNP	C	C	T	rs2298428	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:21982892C>T	ENST00000292778.6	-	5	836	c.787G>A	c.(787-789)Gct>Act	p.A263T	YDJC_ENST00000398873.3_3'UTR	NM_001017964.1	NP_001017964.1	A8MPS7	YDJC_HUMAN	YdjC homolog (bacterial)	263			A -> T (in dbSNP:rs2298428).		carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)					Colorectal(54;0.105)					CAAGAGAAAGCGTCGGGGCCT	0.701													C|||	1126	0.22484	0.0227	0.3631	5008	,	,		11576	0.4117		0.1769	False		,,,				2504	0.2566				p.A263T		Atlas-SNP	.											.	YDJC	8	.	0			c.G787A						PASS	.	C	THR/ALA	218,4160		4,210,1975	13.0	14.0	13.0	http://www.ncbi.nlm.nih.gov/pubmed?term	787	4.3	0.7	22	dbSNP_100	13	1582,6978		142,1298,2840	yes	missense	YDJC	NM_001017964.1	58	146,1508,4815	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	18.4813,4.9794,13.9125	benign	263/324	21982892	1800,11138	2189	4280	6469	SO:0001583	missense	150223	exon5			AGAAAGCGTCGGG		CCDS33613.1	22q11.21	2008-02-26			ENSG00000161179	ENSG00000161179			27158	protein-coding gene	gene with protein product						18177738	Standard	XM_005261347		Approved		uc002zvb.2	A8MPS7	OTTHUMG00000150822	ENST00000292778.6:c.787G>A	22.37:g.21982892C>T	ENSP00000292778:p.Ala263Thr	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	31	20	0.645161	NM_001017964	Q2YDT4|Q4V9R7	Missense_Mutation	SNP	ENST00000292778.6	37	CCDS33613.1	495	0.22664835164835165	20	0.04065040650406504	115	0.31767955801104975	223	0.38986013986013984	137	0.18073878627968337	C	24.5	4.541910	0.85917	0.049794	0.184813	ENSG00000161179	ENST00000292778	T	0.42131	0.98	4.32	4.32	0.51571	Polysaccharide deacetylase (1);	0.104489	0.64402	D	0.000007	T	0.00012	0.0000	L	0.54323	1.7	0.09310	P	1.0	P	0.46784	0.884	B	0.39068	0.289	T	0.47368	-0.9123	9	0.13470	T	0.59	-16.7508	14.3921	0.66986	0.0:1.0:0.0:0.0	rs2298428;rs52827392;rs56745961;rs2298428	263	A8MPS7	YDJC_HUMAN	T	263	ENSP00000292778:A263T	ENSP00000292778:A263T	A	-	1	0	YDJC	20312892	1.000000	0.71417	0.677000	0.29947	0.942000	0.58702	7.032000	0.76498	2.245000	0.73994	0.650000	0.86243	GCT	C|0.795;T|0.205	0.205	strong		0.701	YDJC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320213.1		
NMNAT2	23057	hgsc.bcm.edu	37	1	183255908	183255908	+	Missense_Mutation	SNP	T	T	C	rs41314643	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:183255908T>C	ENST00000287713.6	-	5	671	c.337A>G	c.(337-339)Atc>Gtc	p.I113V	NMNAT2_ENST00000473046.1_5'UTR|NMNAT2_ENST00000294868.4_Missense_Mutation_p.I108V	NM_015039.3	NP_055854.1	Q9BZQ4	NMNA2_HUMAN	nicotinamide nucleotide adenylyltransferase 2	113					NAD biosynthetic process (GO:0009435)|NAD metabolic process (GO:0019674)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|late endosome (GO:0005770)|synapse (GO:0045202)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(7)|skin(2)	18						TTGGAGAGGATGCAGCCAGTC	0.493													.|||	25	0.00499201	0.0008	0.0058	5008	,	,		20337	0.0		0.0179	False		,,,				2504	0.002				p.I113V		Atlas-SNP	.											.	NMNAT2	48	.	0			c.A337G						PASS	.	T	VAL/ILE,VAL/ILE	12,4394		0,12,2191	160.0	138.0	145.0		337,322	5.7	1.0	1	dbSNP_127	145	148,8452		0,148,4152	yes	missense,missense	NMNAT2	NM_015039.3,NM_170706.3	29,29	0,160,6343	CC,CT,TT		1.7209,0.2724,1.2302	possibly-damaging,possibly-damaging	113/308,108/303	183255908	160,12846	2203	4300	6503	SO:0001583	missense	23057	exon5			AGAGGATGCAGCC	AF288395	CCDS1353.1, CCDS1354.1	1q25	2008-02-05	2003-04-30	2003-05-02	ENSG00000157064	ENSG00000157064			16789	protein-coding gene	gene with protein product		608701	"""chromosome 1 open reading frame 15"""	C1orf15		11318611, 12359228	Standard	NM_015039		Approved	KIAA0479, PNAT2	uc001gqc.2	Q9BZQ4	OTTHUMG00000035519	ENST00000287713.6:c.337A>G	1.37:g.183255908T>C	ENSP00000287713:p.Ile113Val	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	216	99	0.458333	NM_015039	O75067|Q5T1Q3|Q8WU99|Q96QW1	Missense_Mutation	SNP	ENST00000287713.6	37	CCDS1353.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	.	16.97	3.269873	0.59540	0.002724	0.017209	ENSG00000157064	ENST00000287713;ENST00000294868	D;D	0.97529	-4.42;-4.29	5.69	5.69	0.88448	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.372428	0.30347	N	0.009835	D	0.94049	0.8093	L	0.28115	0.83	0.58432	D	0.999998	D;B;P	0.69078	0.997;0.421;0.876	D;B;D	0.80764	0.994;0.232;0.927	D	0.92941	0.6372	10	0.28530	T	0.3	-13.9444	15.6035	0.76642	0.0:0.0:0.0:1.0	rs41314643	113;113;108	A8K5S5;Q9BZQ4;Q9BZQ4-2	.;NMNA2_HUMAN;.	V	113;108	ENSP00000287713:I113V;ENSP00000294868:I108V	ENSP00000287713:I113V	I	-	1	0	NMNAT2	181522531	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.533000	0.81994	2.162000	0.67917	0.533000	0.62120	ATC	T|0.989;C|0.011	0.011	strong		0.493	NMNAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086255.1		
MAGEB10	139422	hgsc.bcm.edu	37	X	27839572	27839572	+	Missense_Mutation	SNP	T	T	C	rs1368769	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:27839572T>C	ENST00000356790.2	+	3	394	c.149T>C	c.(148-150)tTc>tCc	p.F50S		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	50			F -> S (in dbSNP:rs1368769). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						AAGGATGTTTTCCAGAGTTCA	0.517													C|||	1304	0.34543	0.3775	0.2248	3775	,	,		13537	0.0645		0.3827	False		,,,				2504	0.2035				p.F50S		Atlas-SNP	.											.	MAGEB10	107	.	0			c.T149C						PASS	.	C	SER/PHE	1913,1920		398,834,283,399,288	57.0	49.0	52.0		149	1.5	0.0	X	dbSNP_88	52	3580,3148		693,1196,998,539,874	yes	missense	MAGEB10	NM_182506.3	155	1091,2030,1281,938,1162	CC,CT,C,TT,T		46.7895,49.9087,47.9879	benign	50/348	27839572	5493,5068	2202	4300	6502	SO:0001583	missense	139422	exon3			ATGTTTTCCAGAG		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.149T>C	X.37:g.27839572T>C	ENSP00000368304:p.Phe50Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	37	CCDS35221.1	604	0.3640747438215793	137	0.3549222797927461	64	0.2119205298013245	25	0.04562043795620438	199	0.33728813559322035	C	0.077	-1.191488	0.01607	0.499087	0.532105	ENSG00000177689	ENST00000356790	T	0.04156	3.69	2.37	1.45	0.22620	Melanoma associated antigen, MAGE, N-terminal (1);	.	.	.	.	T	0.00012	0.0000	N	0.00483	-1.445	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38585	-0.9654	8	0.02654	T	1	.	3.2031	0.06656	0.0:0.524:0.2915:0.1845	rs1368769;rs59237909;rs1368769	50	Q96LZ2	MAGBA_HUMAN	S	50	ENSP00000368304:F50S	ENSP00000368304:F50S	F	+	2	0	MAGEB10	27749493	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.595000	0.05727	0.002000	0.14630	-0.416000	0.06073	TTC	0|0.029;C|0.421	0.421	strong		0.517	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67236097	67236097	+	Missense_Mutation	SNP	A	A	T	rs1060575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:67236097A>T	ENST00000282670.2	+	3	275	c.147A>T	c.(145-147)gaA>gaT	p.E49D	TCTEX1D1_ENST00000491611.1_3'UTR	NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	49			E -> D (in dbSNP:rs1060575).							large_intestine(2)|lung(10)|skin(1)	13						CTTATATGGAAGAACCCAGTC	0.328													T|||	664	0.132588	0.0862	0.1023	5008	,	,		19085	0.1488		0.1511	False		,,,				2504	0.181				p.E49D		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.A147T						PASS	.	T	ASP/GLU	378,4028	792.1+/-415.1	18,342,1843	180.0	175.0	177.0		147	2.5	1.0	1	dbSNP_86	177	1188,7412	763.8+/-407.6	85,1018,3197	yes	missense	TCTEX1D1	NM_152665.2	45	103,1360,5040	TT,TA,AA		13.814,8.5792,12.0406	benign	49/180	67236097	1566,11440	2203	4300	6503	SO:0001583	missense	200132	exon3			TATGGAAGAACCC	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.147A>T	1.37:g.67236097A>T	ENSP00000282670:p.Glu49Asp	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	76	27	0.355263	NM_152665	Q06YR9|Q5VYE1	Missense_Mutation	SNP	ENST00000282670.2	37	CCDS633.1	266	0.12179487179487179	37	0.07520325203252033	42	0.11602209944751381	82	0.14335664335664336	105	0.13852242744063326	T	0.109	-1.141193	0.01728	0.085792	0.13814	ENSG00000152760	ENST00000282670	T	0.13901	2.55	6.06	2.55	0.30701	.	0.147752	0.64402	N	0.000016	T	0.00524	0.0017	N	0.00151	-1.98	0.46609	P	8.709999999999551E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42378	-0.9455	9	0.02654	T	1	-10.0546	4.7902	0.13245	0.1273:0.2766:0.0:0.596	rs1060575;rs1498353;rs3201482;rs17441805;rs52832612;rs1060575	49	Q8N7M0	TC1D1_HUMAN	D	49	ENSP00000282670:E49D	ENSP00000282670:E49D	E	+	3	2	TCTEX1D1	67008685	1.000000	0.71417	0.990000	0.47175	0.008000	0.06430	1.263000	0.33004	-0.032000	0.13758	-1.091000	0.02175	GAA	A|0.878;N|0.000	.	strong		0.328	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665	
FMN1	342184	hgsc.bcm.edu	37	15	33091079	33091079	+	Silent	SNP	A	A	G	rs7162695	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:33091079A>G	ENST00000559047.1	-	16	4055	c.4056T>C	c.(4054-4056)ttT>ttC	p.F1352F	FMN1_ENST00000334528.9_Silent_p.F1129F|FMN1_ENST00000561249.1_Silent_p.F1254F			Q68DA7	FMN1_HUMAN	formin 1	1352	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				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)		ACCACACCATAAACACGTAGC	0.398													A|||	820	0.163738	0.2035	0.1297	5008	,	,		19514	0.1032		0.168	False		,,,				2504	0.1922				p.F1129F		Atlas-SNP	.											.	FMN1	174	.	0			c.T3387C						PASS	.	A		713,3037		73,567,1235	111.0	100.0	103.0		3387	4.7	1.0	15	dbSNP_116	103	1165,7077		73,1019,3029	no	coding-synonymous	FMN1	NM_001103184.2		146,1586,4264	GG,GA,AA		14.1349,19.0133,15.6604		1129/1197	33091079	1878,10114	1875	4121	5996	SO:0001819	synonymous_variant	342184	exon15			CACCATAAACACG	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.4056T>C	15.37:g.33091079A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Silent	SNP	ENST00000559047.1	37																																																																																				A|0.853;G|0.147	0.147	strong		0.398	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
EXOSC3	51010	hgsc.bcm.edu	37	9	37782111	37782111	+	Silent	SNP	C	C	T	rs7158	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37782111C>T	ENST00000327304.5	-	3	510	c.498G>A	c.(496-498)caG>caA	p.Q166Q	RP11-613M10.9_ENST00000540557.1_Intron|EXOSC3_ENST00000396521.3_Intron|EXOSC3_ENST00000490516.1_Intron	NM_016042.3	NP_057126.2	Q9NQT5	EXOS3_HUMAN	exosome component 3	166					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)		CAACCACAAACTGGCCATAGA	0.433													T|||	2825	0.564097	0.612	0.5908	5008	,	,		18244	0.5337		0.4841	False		,,,				2504	0.5941				p.Q166Q		Atlas-SNP	.											.	EXOSC3	8	.	0			c.G498A						PASS	.	T	,	2606,1800	529.2+/-372.6	793,1020,390	78.0	74.0	75.0		,498	-7.3	0.2	9	dbSNP_52	75	4276,4324	578.7+/-390.8	1073,2130,1097	no	intron,coding-synonymous	EXOSC3	NM_001002269.1,NM_016042.2	,	1866,3150,1487	TT,TC,CC		49.7209,40.8534,47.086	,	,166/276	37782111	6882,6124	2203	4300	6503	SO:0001819	synonymous_variant	51010	exon3			CACAAACTGGCCA	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.498G>A	9.37:g.37782111C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_016042	A8K0K6|Q5QP85|Q9Y3A8	Silent	SNP	ENST00000327304.5	37	CCDS35016.1																																																																																			C|0.471;T|0.529	0.529	strong		0.433	EXOSC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052478.3	NM_016042	
DIP2A	23181	hgsc.bcm.edu	37	21	47910523	47910523	+	Silent	SNP	A	A	G	rs7279002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47910523A>G	ENST00000417564.2	+	3	195	c.174A>G	c.(172-174)ccA>ccG	p.P58P	DIP2A_ENST00000318711.7_Silent_p.P58P|DIP2A_ENST00000435722.3_Silent_p.P58P|DIP2A_ENST00000457905.3_Silent_p.P58P|DIP2A_ENST00000466639.1_Silent_p.P58P|DIP2A_ENST00000400274.1_Silent_p.P58P|DIP2A_ENST00000427143.2_Intron			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	58	DMAP-interaction.				multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		GAATAGACCCATCTCTGCAAG	0.463													A|||	1797	0.358826	0.5053	0.1988	5008	,	,		19194	0.4067		0.2545	False		,,,				2504	0.3323				p.P58P		Atlas-SNP	.											.	DIP2A	332	.	0			c.A174G						PASS	.	A	,,,,,,	1640,2134		358,924,605	37.0	39.0	38.0		,174,174,174,174,174,174	-10.3	0.0	21	dbSNP_116	38	1911,6281		243,1425,2428	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIP2A	NM_001146114.1,NM_001146115.1,NM_001146116.1,NM_015151.3,NM_206889.2,NM_206890.2,NM_206891.2	,,,,,,	601,2349,3033	GG,GA,AA		23.3276,43.4552,29.6757	,,,,,,	,58/799,58/1568,58/1572,58/890,58/842,58/813	47910523	3551,8415	1887	4096	5983	SO:0001819	synonymous_variant	23181	exon3			AGACCCATCTCTG	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.174A>G	21.37:g.47910523A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	140	68	0.485714	NM_206891	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Silent	SNP	ENST00000417564.2	37	CCDS46655.1																																																																																			A|0.634;G|0.366	0.366	strong		0.463	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
ZNF677	342926	hgsc.bcm.edu	37	19	53740822	53740822	+	Silent	SNP	T	T	C	rs8113436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53740822T>C	ENST00000598513.1	-	5	1308	c.1158A>G	c.(1156-1158)gaA>gaG	p.E386E	ZNF677_ENST00000333952.4_Silent_p.E386E	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	386					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.E386E(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		GGCTTGAACGTTCAGCAAAGG	0.408													C|||	2328	0.464856	0.2148	0.4294	5008	,	,		20847	0.752		0.4324	False		,,,				2504	0.5654				p.E386E		Atlas-SNP	.											ZNF677,NS,carcinoma,0,1	ZNF677	94	1	1	Substitution - coding silent(1)	stomach(1)	c.A1158G						PASS	.	C		1072,3334	722.6+/-409.3	106,860,1237	104.0	91.0	95.0		1158	-1.5	0.0	19	dbSNP_116	95	3605,4995	624.8+/-397.6	746,2113,1441	no	coding-synonymous	ZNF677	NM_182609.2		852,2973,2678	CC,CT,TT		41.9186,24.3305,35.9603		386/585	53740822	4677,8329	2203	4300	6503	SO:0001819	synonymous_variant	342926	exon5			TGAACGTTCAGCA	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1158A>G	19.37:g.53740822T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	113	53	0.469027	NM_182609		Silent	SNP	ENST00000598513.1	37	CCDS12861.1																																																																																			T|0.600;C|0.400	0.400	strong		0.408	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
NIN	51199	hgsc.bcm.edu	37	14	51224658	51224658	+	Silent	SNP	T	T	A	rs2073348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:51224658T>A	ENST00000382041.3	-	18	3280	c.3090A>T	c.(3088-3090)tcA>tcT	p.S1030S	NIN_ENST00000389868.3_Intron|NIN_ENST00000324330.9_Silent_p.S1030S|NIN_ENST00000245441.5_Silent_p.S1030S|NIN_ENST00000530997.2_Silent_p.S1030S|NIN_ENST00000382043.4_Intron|NIN_ENST00000453196.1_Silent_p.S1030S	NM_016350.4|NM_182946.1	NP_057434.4|NP_891991	Q8N4C6	NIN_HUMAN	ninein (GSK3B interacting protein)	1030					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)					TCTGAAGCATTGAGAGAGGAG	0.507			T	PDGFRB	MPD								T|||	1607	0.320887	0.1732	0.4308	5008	,	,		20879	0.503		0.3131	False		,,,				2504	0.2628				p.S1030S		Atlas-SNP	.		Dom	yes		14	14q24	51199	ninein (GSK3B interacting protein)		L	.	NIN	475	.	0			c.A3090T						PASS	.	T	,,,	852,3554	332.8+/-302.6	80,692,1431	115.0	115.0	115.0		,3090,3090,3090	0.2	0.0	14	dbSNP_96	115	2726,5874	432.1+/-357.0	446,1834,2020	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	NIN	NM_016350.4,NM_020921.3,NM_182944.2,NM_182946.1	,,,	526,2526,3451	AA,AT,TT		31.6977,19.3373,27.5104	,,,	,1030/2134,1030/2047,1030/2091	51224658	3578,9428	2203	4300	6503	SO:0001819	synonymous_variant	51199	exon18			AAGCATTGAGAGA	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.3090A>T	14.37:g.51224658T>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	193	81	0.419689	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	785	0.35943223443223443	84	0.17073170731707318	162	0.44751381215469616	295	0.5157342657342657	244	0.32189973614775724	T	0.013	-1.619033	0.00828	0.193373	0.316977	ENSG00000100503	ENST00000530997;ENST00000389869;ENST00000530853	.	.	.	5.3	0.168	0.15012	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.45352	-0.9267	3	.	.	.	2.8874	0.9128	0.01298	0.3731:0.159:0.3153:0.1526	rs2073348;rs2073348	.	.	.	Y	521	.	.	N	-	1	0	NIN	50294408	0.000000	0.05858	0.002000	0.10522	0.065000	0.16274	-0.765000	0.04730	0.042000	0.15717	-0.232000	0.12228	AAT	A|0.311;N|0.000	0.311	strong		0.507	NIN-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395207.2	NM_182946	
CELSR1	9620	hgsc.bcm.edu	37	22	46805772	46805772	+	Missense_Mutation	SNP	C	C	T	rs11704506	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:46805772C>T	ENST00000262738.3	-	8	4938	c.4939G>A	c.(4939-4941)Gct>Act	p.A1647T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1647					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)		CTCCGAGCAGCGCAGCCTGGC	0.627													C|||	48	0.00958466	0.0015	0.013	5008	,	,		17743	0.0		0.0348	False		,,,				2504	0.002				p.A1647T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G4939A						PASS	.	C	THR/ALA	39,4367	43.8+/-77.6	1,37,2165	126.0	107.0	114.0		4939	0.8	0.0	22	dbSNP_120	114	295,8305	109.0+/-169.6	6,283,4011	yes	missense	CELSR1	NM_014246.1	58	7,320,6176	TT,TC,CC		3.4302,0.8852,2.568	benign	1647/3015	46805772	334,12672	2203	4300	6503	SO:0001583	missense	9620	exon8			GAGCAGCGCAGCC	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.4939G>A	22.37:g.46805772C>T	ENSP00000262738:p.Ala1647Thr	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	70	43	0.614286	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	35	0.016025641025641024	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	26	0.03430079155672823	C	8.987	0.976677	0.18812	0.008852	0.034302	ENSG00000075275	ENST00000262738	T	0.78246	-1.16	4.41	0.781	0.18561	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.295815	0.25964	U	0.027179	T	0.30324	0.0761	N	0.13003	0.285	0.18873	N	0.999988	B	0.24675	0.109	B	0.14578	0.011	T	0.29792	-1.0000	10	0.44086	T	0.13	.	5.6632	0.17680	0.2461:0.5904:0.0:0.1635	rs11704506	1647	Q9NYQ6	CELR1_HUMAN	T	1647	ENSP00000262738:A1647T	ENSP00000262738:A1647T	A	-	1	0	CELSR1	45184436	0.000000	0.05858	0.033000	0.17914	0.653000	0.38743	-0.276000	0.08514	0.415000	0.25817	0.655000	0.94253	GCT	C|0.979;T|0.021	0.021	strong		0.627	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
C16orf89	146556	hgsc.bcm.edu	37	16	5106184	5106184	+	Silent	SNP	C	C	T	rs741164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:5106184C>T	ENST00000315997.5	-	5	834	c.633G>A	c.(631-633)ggG>ggA	p.G211G	C16orf89_ENST00000472572.3_Silent_p.G211G|C16orf89_ENST00000422873.1_Silent_p.G249G|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000350219.4_Silent_p.G249G|C16orf89_ENST00000474471.3_Silent_p.G211G	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	211						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						CCTGTGTGCACCCCCTCTGGG	0.547													T|||	2619	0.522963	0.3971	0.6398	5008	,	,		15812	0.5665		0.6292	False		,,,				2504	0.456				p.G211G		Atlas-SNP	.											.	C16orf89	64	.	0			c.G633A						PASS	.	T	,	1976,2308		475,1026,641	99.0	103.0	102.0		633,633	-11.4	0.0	16	dbSNP_86	102	5301,3219		1655,1991,614	no	coding-synonymous,coding-synonymous	C16orf89	NM_001098514.2,NM_152459.4	,	2130,3017,1255	TT,TC,CC		37.7817,46.1251,43.1662	,	211/362,211/403	5106184	7277,5527	2142	4260	6402	SO:0001819	synonymous_variant	146556	exon5			TGTGCACCCCCTC		CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.633G>A	16.37:g.5106184C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	118	58	0.491525	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Silent	SNP	ENST00000315997.5	37	CCDS42116.2																																																																																			C|0.432;T|0.568	0.568	strong		0.547	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37505179	37505179	+	Silent	SNP	T	T	C	rs57914746	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:37505179T>C	ENST00000602533.1	+	32	2871	c.2772T>C	c.(2770-2772)gaT>gaC	p.D924D	ANKRD30A_ENST00000374660.1_Silent_p.D1043D|ANKRD30A_ENST00000361713.1_Silent_p.D924D			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	980					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						TTCAAAAAGATCACTGTGAAC	0.328													T|||	795	0.158746	0.2837	0.1095	5008	,	,		15900	0.1161		0.171	False		,,,				2504	0.0562				p.D924D		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.T2772C						PASS	.	T		1060,2562		174,712,925	71.0	67.0	68.0		2772	-5.3	0.0	10	dbSNP_129	68	1418,6720		131,1156,2782	no	coding-synonymous	ANKRD30A	NM_052997.2		305,1868,3707	CC,CT,TT		17.4244,29.2656,21.0714		924/1342	37505179	2478,9282	1811	4069	5880	SO:0001819	synonymous_variant	91074	exon32			AAAAGATCACTGT	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.2772T>C	10.37:g.37505179T>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	169	65	0.384615	NM_052997	Q5W025	Silent	SNP	ENST00000602533.1	37																																																																																				T|0.822;C|0.178	0.178	strong		0.328	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
DHCR24	1718	hgsc.bcm.edu	37	1	55319902	55319902	+	Silent	SNP	A	A	G	rs718265	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:55319902A>G	ENST00000371269.3	-	7	1124	c.1026T>C	c.(1024-1026)atT>atC	p.I342I	DHCR24_ENST00000537443.1_Silent_p.I126I|DHCR24_ENST00000535035.1_Silent_p.I301I	NM_014762.3	NP_055577.1	Q15392	DHC24_HUMAN	24-dehydrocholesterol reductase	342					amyloid precursor protein catabolic process (GO:0042987)|apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cholesterol biosynthetic process (GO:0006695)|male genitalia development (GO:0030539)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|oxidation-reduction process (GO:0055114)|plasminogen activation (GO:0031639)|protein localization (GO:0008104)|Ras protein signal transduction (GO:0007265)|regulation of neuron death (GO:1901214)|response to hormone (GO:0009725)|response to oxidative stress (GO:0006979)|skin development (GO:0043588)|small molecule metabolic process (GO:0044281)|tissue development (GO:0009888)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	delta24(24-1) sterol reductase activity (GO:0000246)|delta24-sterol reductase activity (GO:0050614)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|peptide antigen binding (GO:0042605)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			large_intestine(2)|liver(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7						CAAAGGGGATAATGTCCTGGA	0.537													G|||	3143	0.627596	0.6256	0.585	5008	,	,		21670	0.4167		0.6809	False		,,,				2504	0.8231				p.I342I	Pancreas(39;516 1021 24601 30715 32780)	Atlas-SNP	.											.	DHCR24	31	.	0			c.T1026C						PASS	.	G		2702,1704	513.6+/-368.4	830,1042,331	71.0	82.0	78.0		1026	4.8	1.0	1	dbSNP_86	78	5962,2638	424.5+/-354.7	2088,1786,426	yes	coding-synonymous	DHCR24	NM_014762.3		2918,2828,757	GG,GA,AA		30.6744,38.6745,33.3846		342/517	55319902	8664,4342	2203	4300	6503	SO:0001819	synonymous_variant	1718	exon7			GGGGATAATGTCC	AF261758	CCDS600.1	1p32.3	2008-02-05			ENSG00000116133	ENSG00000116133			2859	protein-coding gene	gene with protein product		606418				11519011	Standard	NM_014762		Approved	KIAA0018, seladin-1	uc001cyc.1	Q15392	OTTHUMG00000009989	ENST00000371269.3:c.1026T>C	1.37:g.55319902A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	79	1	NM_014762	B7Z817|D3DQ51|Q9HBA8	Silent	SNP	ENST00000371269.3	37	CCDS600.1																																																																																			A|0.363;G|0.637	0.637	strong		0.537	DHCR24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027680.1	NM_014762	
SPG7	6687	hgsc.bcm.edu	37	16	89613123	89613123	+	Missense_Mutation	SNP	A	A	G	rs2292954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:89613123A>G	ENST00000268704.2	+	11	1522	c.1507A>G	c.(1507-1509)Acc>Gcc	p.T503A		NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	503			T -> A (neutral polymorphism; dbSNP:rs2292954). {ECO:0000269|PubMed:16534102, ECO:0000269|PubMed:20186691}.		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CCAGTCCAGCACCTTTTACTC	0.597													A|||	533	0.10643	0.0106	0.1124	5008	,	,		15594	0.131		0.168	False		,,,				2504	0.1431				p.T503A		Atlas-SNP	.											.	SPG7	75	.	0			c.A1507G						PASS	.	A	ALA/THR	168,4228	111.2+/-149.4	3,162,2033	103.0	101.0	102.0		1507	4.3	1.0	16	dbSNP_100	102	1666,6934	305.7+/-307.6	152,1362,2786	yes	missense	SPG7	NM_003119.2	58	155,1524,4819	GG,GA,AA		19.3721,3.8217,14.112	benign	503/796	89613123	1834,11162	2198	4300	6498	SO:0001583	missense	6687	exon11			TCCAGCACCTTTT	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.1507A>G	16.37:g.89613123A>G	ENSP00000268704:p.Thr503Ala	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	259	0.11858974358974358	9	0.018292682926829267	43	0.11878453038674033	77	0.1346153846153846	130	0.17150395778364116	A	13.33	2.204196	0.38905	0.038217	0.193721	ENSG00000197912	ENST00000268704	D	0.94650	-3.48	5.42	4.33	0.51752	Peptidase M41, FtsH (2);	0.298369	0.46145	D	0.000305	T	0.00695	0.0023	N	0.11927	0.2	0.09310	P	0.9999999999866063	B	0.02656	0.0	B	0.06405	0.002	T	0.45131	-0.9282	9	0.30854	T	0.27	-1.1817	10.9407	0.47273	0.9266:0.0:0.0734:0.0	rs2292954;rs3205047;rs17404897;rs17775132;rs52815392;rs59421193;rs2292954	503	Q9UQ90	SPG7_HUMAN	A	503	ENSP00000268704:T503A	ENSP00000268704:T503A	T	+	1	0	SPG7	88140624	0.998000	0.40836	1.000000	0.80357	0.908000	0.53690	2.181000	0.42547	0.915000	0.36847	0.459000	0.35465	ACC	G|0.121;N|0.000	0.121	strong		0.597	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
CCDC180	100499483	hgsc.bcm.edu	37	9	100071728	100071728	+	Silent	SNP	G	G	A	rs3747507	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100071728G>A	ENST00000357054.1	+	17	1586	c.651G>A	c.(649-651)agG>agA	p.R217R	CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000529487.1_Silent_p.R78R|CCDC180_ENST00000411667.2_Silent_p.R78R|CCDC180_ENST00000375202.2_Silent_p.R78R|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_Silent_p.R217R			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	217						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CGGCCACCAGGAAGCGGGCTG	0.607													G|||	1365	0.272564	0.2958	0.3501	5008	,	,		18304	0.2887		0.1839	False		,,,				2504	0.2607				p.R78R		Atlas-SNP	.											.	.	.	.	0			c.G234A						PASS	.	G		1183,3223	413.7+/-336.6	156,871,1176	56.0	55.0	56.0		234	2.4	1.0	9	dbSNP_107	56	1567,7033	295.0+/-302.2	137,1293,2870	no	coding-synonymous	C9orf174	NM_020893.2		293,2164,4046	AA,AG,GG		18.2209,26.8498,21.1441		78/1702	100071728	2750,10256	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			CACCAGGAAGCGG	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.651G>A	9.37:g.100071728G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	35	0.416667	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37																																																																																				G|0.774;A|0.226	0.226	strong		0.607	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
TRIM51	84767	hgsc.bcm.edu	37	11	55652963	55652963	+	Missense_Mutation	SNP	A	A	G	rs2063276	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55652963A>G	ENST00000449290.2	+	2	151	c.59A>G	c.(58-60)aAc>aGc	p.N20S	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	20						intracellular (GO:0005622)	zinc ion binding (GO:0008270)										ATCTGCATGAACTACTTCCTA	0.502													N|||	3414	0.681709	0.6452	0.683	5008	,	,		18043	0.7649		0.6153	False		,,,				2504	0.7127				p.N20S		Atlas-SNP	.											.	.	.	.	0			c.A59G						PASS	.	A	SER/ASN	897,487		308,281,103	21.0	18.0	19.0		59	0.8	0.0	11	dbSNP_94	19	1962,1198		615,732,233	no	missense	SPRYD5	NM_032681.3	46	923,1013,336	GG,GA,AA		37.9114,35.1879,37.0819	possibly-damaging	20/453	55652963	2859,1685	692	1580	2272	SO:0001583	missense	84767	exon2			GCATGAACTACTT	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.59A>G	11.37:g.55652963A>G	ENSP00000395086:p.Asn20Ser	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	198	196	0.989899	NM_032681	A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37		1411	0.6460622710622711	304	0.6178861788617886	235	0.649171270718232	421	0.736013986013986	451	0.5949868073878628	.	6.155	0.396776	0.11638	0.648121	0.620886	ENSG00000124900	ENST00000449290	D	0.83914	-1.78	0.803	0.803	0.18691	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.	.	.	.	T	0.00012	0.0000	N	0.16266	0.395	0.36627	P	0.12391600000000003	P	0.44429	0.835	P	0.49477	0.612	T	0.42155	-0.9468	8	0.59425	D	0.04	.	5.8508	0.18691	0.9999:0.0:1.0E-4:0.0	rs2063276	20	Q9BSJ1	SPRY5_HUMAN	S	20	ENSP00000395086:N20S	ENSP00000395086:N20S	N	+	2	0	SPRYD5	55409539	0.831000	0.29352	0.005000	0.12908	0.120000	0.20174	1.010000	0.29898	0.624000	0.30286	0.128000	0.15822	AAC	A|0.360;G|0.640	0.640	strong		0.502	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
SLC17A1	6568	hgsc.bcm.edu	37	6	25820126	25820126	+	Missense_Mutation	SNP	C	C	A	rs149708935		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:25820126C>A	ENST00000244527.4	-	4	340	c.225G>T	c.(223-225)tgG>tgT	p.W75C	SLC17A1_ENST00000468082.1_Missense_Mutation_p.W75C|SLC17A1_ENST00000427328.1_Missense_Mutation_p.W75C|SLC17A1_ENST00000476801.1_Missense_Mutation_p.W75C	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	75					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						TATCTGGGCTCCAATTATACA	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		19051	0.0		0.001	False		,,,				2504	0.0				p.W75C		Atlas-SNP	.											.	SLC17A1	71	.	0			c.G225T						PASS	.	C	CYS/TRP	1,4403	2.1+/-5.4	0,1,2201	63.0	68.0	66.0		225	4.3	1.0	6	dbSNP_134	66	9,8591	7.1+/-27.0	0,9,4291	yes	missense	SLC17A1	NM_005074.3	215	0,10,6492	AA,AC,CC		0.1047,0.0227,0.0769	probably-damaging	75/468	25820126	10,12994	2202	4300	6502	SO:0001583	missense	6568	exon4			TGGGCTCCAATTA		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"""Solute carriers"""	10929	protein-coding gene	gene with protein product		182308	"""solute carrier family 17 (sodium phosphate), member 1"""	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.225G>T	6.37:g.25820126C>A	ENSP00000244527:p.Trp75Cys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	68	27	0.397059	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	37	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.994860	0.35226	2.27E-4	0.001047	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	4.33	4.33	0.51752	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.43110	D	0.000602	T	0.77350	0.4117	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82697	-0.0329	10	0.87932	D	0	.	12.53	0.56109	0.0:1.0:0.0:0.0	.	75;75	Q14916-2;Q14916	.;NPT1_HUMAN	C	75	ENSP00000244527:W75C;ENSP00000410549:W75C;ENSP00000420614:W75C;ENSP00000420546:W75C	ENSP00000244527:W75C	W	-	3	0	SLC17A1	25928105	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	4.467000	0.60155	2.423000	0.82170	0.650000	0.86243	TGG	C|1.000;A|0.000	0.000	weak		0.408	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2		
SERPINA11	256394	hgsc.bcm.edu	37	14	94912896	94912896	+	Missense_Mutation	SNP	T	T	G	rs1885137	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:94912896T>G	ENST00000334708.3	-	3	753	c.689A>C	c.(688-690)gAa>gCa	p.E230A	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	230			E -> A (in dbSNP:rs1885137).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		AAAGAAACTTTCCTGCTTCTG	0.488													T|||	1304	0.260383	0.0613	0.2695	5008	,	,		21655	0.1835		0.4503	False		,,,				2504	0.407				p.E230A		Atlas-SNP	.											.	SERPINA11	53	.	0			c.A689C						PASS	.	T	ALA/GLU	587,3819	258.6+/-262.5	46,495,1662	154.0	145.0	148.0		689	-6.3	0.1	14	dbSNP_92	148	3525,5075	515.2+/-378.5	700,2125,1475	yes	missense	SERPINA11	NM_001080451.1	107	746,2620,3137	GG,GT,TT		40.9884,13.3227,31.6162	benign	230/423	94912896	4112,8894	2203	4300	6503	SO:0001583	missense	256394	exon3			AAACTTTCCTGCT	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"""Serine (or cysteine) peptidase inhibitors"""	19193	protein-coding gene	gene with protein product			"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"""			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.689A>C	14.37:g.94912896T>G	ENSP00000335024:p.Glu230Ala	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	142	140	0.985915	NM_001080451	B2RV07	Missense_Mutation	SNP	ENST00000334708.3	37	CCDS32149.1	613	0.2806776556776557	45	0.09146341463414634	108	0.2983425414364641	105	0.18356643356643357	355	0.4683377308707124	T	1.786	-0.480780	0.04383	0.133227	0.409884	ENSG00000186910	ENST00000334708	D	0.87887	-2.31	5.01	-6.34	0.01982	Serpin domain (3);	1.038600	0.07607	N	0.924607	T	0.00012	0.0000	L	0.58669	1.825	0.80722	P	0.0	B	0.24721	0.11	B	0.29077	0.098	T	0.35325	-0.9793	9	0.39692	T	0.17	.	3.0149	0.06057	0.1042:0.3435:0.2876:0.2647	rs57740714	230	Q86U17	SPA11_HUMAN	A	230	ENSP00000335024:E230A	ENSP00000335024:E230A	E	-	2	0	SERPINA11	93982649	0.000000	0.05858	0.091000	0.20842	0.252000	0.25951	-1.228000	0.02948	-0.657000	0.05373	0.454000	0.30748	GAA	G|0.312;N|0.000	0.312	strong		0.488	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451	
KRT32	3882	hgsc.bcm.edu	37	17	39619115	39619115	+	Missense_Mutation	SNP	G	G	A	rs2071563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39619115G>A	ENST00000225899.3	-	6	1287	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M		NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	395	Coil 2.|Rod.		T -> M (in dbSNP:rs2071563).		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)				GCTCCGGTACGTGTTGATCTC	0.632													G|||	1847	0.36881	0.4259	0.402	5008	,	,		16423	0.3363		0.4245	False		,,,				2504	0.2444				p.T395M		Atlas-SNP	.											.	KRT32	57	.	0			c.C1184T						PASS	.	G	MET/THR	1809,2597	530.3+/-372.9	371,1067,765	72.0	73.0	72.0		1184	5.1	1.0	17	dbSNP_96	72	3226,5374	483.7+/-371.2	622,1982,1696	no	missense	KRT32	NM_002278.3	81	993,3049,2461	AA,AG,GG		37.5116,41.0576,38.7129	probably-damaging	395/449	39619115	5035,7971	2203	4300	6503	SO:0001583	missense	3882	exon6			CGGTACGTGTTGA	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.1184C>T	17.37:g.39619115G>A	ENSP00000225899:p.Thr395Met	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	92	55	0.597826	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	869	0.39789377289377287	213	0.4329268292682927	125	0.3453038674033149	208	0.36363636363636365	323	0.4261213720316623	G	17.48	3.400513	0.62177	0.410576	0.375116	ENSG00000108759	ENST00000225899	D	0.91996	-2.95	5.07	5.07	0.68467	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.40554	N	0.001074	T	0.00012	0.0000	H	0.95114	3.625	0.31049	P	0.715462	D	0.89917	1.0	D	0.97110	1.0	T	0.00000	-1.5298	9	0.72032	D	0.01	.	17.8011	0.88587	0.0:0.0:1.0:0.0	rs2071563;rs52800623;rs58844466;rs2071563	395	Q14532	K1H2_HUMAN	M	395	ENSP00000225899:T395M	ENSP00000225899:T395M	T	-	2	0	KRT32	36872641	0.563000	0.26594	0.969000	0.41365	0.720000	0.41350	2.380000	0.44327	2.493000	0.84123	0.561000	0.74099	ACG	G|0.611;A|0.389	0.389	strong		0.632	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
BST1	683	hgsc.bcm.edu	37	4	15709252	15709252	+	Missense_Mutation	SNP	G	G	A	rs2302464	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:15709252G>A	ENST00000265016.4	+	3	629	c.434G>A	c.(433-435)cGa>cAa	p.R145Q	BST1_ENST00000382346.3_Missense_Mutation_p.R160Q	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	145			R -> Q (in dbSNP:rs2302464).		humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|transferase activity (GO:0016740)	p.R145Q(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|stomach(3)|urinary_tract(1)	8						AGCTGGTGTCGACAGAAAAAT	0.443													G|||	396	0.0790735	0.0287	0.0259	5008	,	,		14972	0.2232		0.0199	False		,,,				2504	0.0971				p.R145Q		Atlas-SNP	.											BST1,NS,carcinoma,0,1	BST1	30	1	1	Substitution - Missense(1)	stomach(1)	c.G434A						PASS	.	G	GLN/ARG	201,4205	125.3+/-162.5	4,193,2006	114.0	109.0	110.0		434	3.8	1.0	4	dbSNP_100	110	228,8372	94.2+/-156.2	1,226,4073	yes	missense	BST1	NM_004334.2	43	5,419,6079	AA,AG,GG		2.6512,4.562,3.2985	probably-damaging	145/319	15709252	429,12577	2203	4300	6503	SO:0001583	missense	683	exon3			GGTGTCGACAGAA	D21878	CCDS3416.1	4p15	2010-05-04			ENSG00000109743	ENSG00000109743	3.2.2.5	"""CD molecules"""	1118	protein-coding gene	gene with protein product	"""NAD(+) nucleosidase"", ""ADP-ribosyl cyclase 2"""	600387				8202488	Standard	NM_004334		Approved	CD157	uc003goh.4	Q10588	OTTHUMG00000097739	ENST00000265016.4:c.434G>A	4.37:g.15709252G>A	ENSP00000265016:p.Arg145Gln	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	180	99	0.55	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	172|172	0.07875457875457875|0.07875457875457875	10|10	0.02032520325203252|0.02032520325203252	11|11	0.03038674033149171|0.03038674033149171	136|136	0.23776223776223776|0.23776223776223776	15|15	0.01978891820580475|0.01978891820580475	G|G	17.72|17.72	3.459767|3.459767	0.63401|0.63401	0.04562|0.04562	0.026512|0.026512	ENSG00000109743|ENSG00000109743	ENST00000505785|ENST00000265016;ENST00000382346	.|T;T	.|0.17854	.|2.25;2.25	5.62|5.62	3.84|3.84	0.44239|0.44239	.|.	.|0.124747	.|0.53938	.|D	.|0.000054	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.68952|0.68952	2.095|2.095	0.28171|0.28171	P|P	0.9285529|0.9285529	.|D	.|0.89917	.|1.0	.|P	.|0.52909	.|0.713	T|T	0.21484|0.21484	-1.0244|-1.0244	4|9	.|0.45353	.|T	.|0.12	-4.1085|-4.1085	8.1902|8.1902	0.31363|0.31363	0.0858:0.1559:0.7582:0.0|0.0858:0.1559:0.7582:0.0	rs2302464;rs11548109;rs52836531;rs58881266;rs2302464|rs2302464;rs11548109;rs52836531;rs58881266;rs2302464	.|145	.|Q10588	.|BST1_HUMAN	N|Q	41|145;160	.|ENSP00000265016:R145Q;ENSP00000371783:R160Q	.|ENSP00000265016:R145Q	D|R	+|+	1|2	0|0	BST1|BST1	15318350|15318350	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.737000|0.737000	0.42083|0.42083	3.645000|3.645000	0.54389|0.54389	1.373000|1.373000	0.46208|0.46208	0.591000|0.591000	0.81541|0.81541	GAC|CGA	G|0.944;A|0.056	0.056	strong		0.443	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334	
PARM1	25849	hgsc.bcm.edu	37	4	75937971	75937971	+	Missense_Mutation	SNP	C	C	T	rs3822109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:75937971C>T	ENST00000307428.7	+	2	592	c.380C>T	c.(379-381)tCg>tTg	p.S127L	RP11-44F21.2_ENST00000513770.1_RNA|PARM1_ENST00000513238.1_Intron	NM_015393.3	NP_056208.2	Q6UWI2	PARM1_HUMAN	prostate androgen-regulated mucin-like protein 1	127			S -> L (in dbSNP:rs3822109). {ECO:0000269|PubMed:11230166}.		positive regulation of telomerase activity (GO:0051973)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|plasma membrane (GO:0005886)		p.S127L(1)		cervix(1)|endometrium(2)|lung(4)|ovary(1)	8						GAACACAGCTCGGGCACTCCT	0.582													C|||	1666	0.332668	0.2905	0.2767	5008	,	,		20761	0.1617		0.4612	False		,,,				2504	0.4734				p.S127L		Atlas-SNP	.											PARM1_ENST00000307428,NS,carcinoma,0,1	PARM1	52	1	1	Substitution - Missense(1)	stomach(1)	c.C380T						PASS	.	C	LEU/SER	1319,2921		213,893,1014	140.0	146.0	144.0		380	-3.3	0.0	4	dbSNP_107	144	3658,4810		809,2040,1385	yes	missense	PARM1	NM_015393.3	145	1022,2933,2399	TT,TC,CC		43.1979,31.1085,39.1643	benign	127/311	75937971	4977,7731	2120	4234	6354	SO:0001583	missense	25849	exon2			ACAGCTCGGGCAC	AK022311	CCDS47077.1	4q13.3-q21.3	2010-02-17	2009-09-28		ENSG00000169116	ENSG00000169116			24536	protein-coding gene	gene with protein product	"""Prostatic androgen-repressed message 1"", ""Castration-induced prostatic apoptosis-related protein 1"", ""WSC4, cell wall integrity and stress response component 4 homolog (S. cerevisiae)"""					10499539, 12772192, 18027867	Standard	NM_015393		Approved	DKFZP564O0823, Cipar1, WSC4	uc003hih.2	Q6UWI2	OTTHUMG00000160827	ENST00000307428.7:c.380C>T	4.37:g.75937971C>T	ENSP00000370224:p.Ser127Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_015393	B3KMQ9|Q96DV8|Q9Y4S1	Missense_Mutation	SNP	ENST00000307428.7	37	CCDS47077.1	698	0.31959706959706957	142	0.2886178861788618	99	0.27348066298342544	88	0.15384615384615385	369	0.4868073878627968	C	8.244	0.807576	0.16467	0.311085	0.431979	ENSG00000169116	ENST00000307428	T	0.47869	0.83	5.34	-3.27	0.05048	.	1.740060	0.02914	N	0.137058	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39542	-0.9609	9	0.20519	T	0.43	7.3413	2.3283	0.04228	0.1265:0.2844:0.1241:0.465	rs3822109;rs17196707;rs52813318;rs59916458;rs3822109	127	Q6UWI2	PARM1_HUMAN	L	127	ENSP00000370224:S127L	ENSP00000370224:S127L	S	+	2	0	PARM1	76156995	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.478000	0.06575	-1.309000	0.02315	-0.993000	0.02533	TCG	C|0.691;T|0.309	0.309	strong		0.582	PARM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362494.1	NM_015393	
DNAH9	1770	hgsc.bcm.edu	37	17	11835331	11835331	+	Splice_Site	SNP	G	G	A	rs17612861	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:11835331G>A	ENST00000262442.4	+	64	12174	c.12106G>A	c.(12106-12108)Gac>Aac	p.D4036N	DNAH9_ENST00000608377.1_Splice_Site_p.D348N|DNAH9_ENST00000454412.2_Splice_Site_p.D3960N|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4036	AAA 6. {ECO:0000250}.		D -> N (in dbSNP:rs17612861).		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)		CTCATTTCAGGACACTCTGGA	0.478													G|||	1052	0.210064	0.0363	0.2594	5008	,	,		20759	0.1806		0.341	False		,,,				2504	0.3057				p.D4036N		Atlas-SNP	.											.	DNAH9	695	.	0			c.G12106A						PASS	.	G	ASN/ASP,ASN/ASP	370,4036	187.1+/-213.8	22,326,1855	331.0	310.0	317.0		12106,1042	3.8	1.0	17	dbSNP_123	317	2876,5724	450.8+/-362.5	485,1906,1909	yes	missense-near-splice,missense-near-splice	DNAH9	NM_001372.3,NM_004662.2	23,23	507,2232,3764	AA,AG,GG		33.4419,8.3976,24.9577	benign,benign	4036/4487,348/799	11835331	3246,9760	2203	4300	6503	SO:0001630	splice_region_variant	1770	exon64			TTTCAGGACACTC	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.12106-1G>A	17.37:g.11835331G>A		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	208	91	0.4375	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	495	0.22664835164835165	28	0.056910569105691054	103	0.2845303867403315	104	0.18181818181818182	260	0.34300791556728233	G	3.711	-0.059467	0.07317	0.083976	0.334419	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001	T;T;T	0.10382	2.88;4.57;2.88	4.82	3.83	0.44106	Dynein heavy chain (1);	0.174933	0.48286	D	0.000200	T	0.00012	0.0000	M	0.71036	2.16	0.09310	P	1.0	B	0.27823	0.19	B	0.37387	0.248	T	0.48502	-0.9030	8	.	.	.	.	13.4777	0.61318	0.0769:0.0:0.9231:0.0	rs17612861;rs17612861	4036	Q9NYC9	DYH9_HUMAN	N	4036;3960;2542;348	ENSP00000262442:D4036N;ENSP00000414874:D3960N;ENSP00000379323:D348N	.	D	+	1	0	DNAH9	11776056	1.000000	0.71417	1.000000	0.80357	0.509000	0.34042	5.387000	0.66243	2.477000	0.83638	0.563000	0.77884	GAC	G|0.766;A|0.233	0.233	strong		0.478	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	Missense_Mutation
GATA5	140628	hgsc.bcm.edu	37	20	61040453	61040453	+	Silent	SNP	C	C	G	rs6061243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:61040453C>G	ENST00000252997.2	-	6	1042	c.981G>C	c.(979-981)tcG>tcC	p.S327S		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	327					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GCTTGGCTTTCGAAGTGGCTG	0.672													C|||	2677	0.534545	0.7171	0.4755	5008	,	,		12861	0.4613		0.4642	False		,,,				2504	0.4775				p.S327S		Atlas-SNP	.											GATA5,NS,carcinoma,-1,1	GATA5	22	1	0			c.G981C						PASS	.	C		2852,1552		949,954,299	29.0	30.0	30.0		981	2.8	0.0	20	dbSNP_114	30	4161,4435		1004,2153,1141	no	coding-synonymous	GATA5	NM_080473.4		1953,3107,1440	GG,GC,CC		48.4062,35.2407,46.0538		327/398	61040453	7013,5987	2202	4298	6500	SO:0001819	synonymous_variant	140628	exon6			GGCTTTCGAAGTG	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.981G>C	20.37:g.61040453C>G		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			C|0.467;G|0.533	0.533	strong		0.672	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
SLC39A4	55630	hgsc.bcm.edu	37	8	145641564	145641564	+	Missense_Mutation	SNP	T	T	G	rs2280839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145641564T>G	ENST00000276833.5	-	1	332	c.29A>C	c.(28-30)gAa>gCa	p.E10A	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000301305.3_Intron	NM_001280557.1|NM_017767.2	NP_001267486.1|NP_060237	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	0					cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			AGGGCCTGTTTCCCTTTCAAG	0.662													T|||	2174	0.434105	0.4561	0.4135	5008	,	,		15139	0.38		0.5268	False		,,,				2504	0.3793				p.E10A		Atlas-SNP	.											.	SLC39A4	54	.	0			c.A29C						PASS	.	T	ALA/GLU,	1914,2120		462,990,565	27.0	34.0	32.0		29,	-3.1	0.0	8	dbSNP_100	32	4429,3911		1205,2019,946	yes	missense,intron	SLC39A4	NM_017767.2,NM_130849.2	107,	1667,3009,1511	GG,GT,TT		46.8945,47.4467,48.7393	,	10/623,	145641564	6343,6031	2017	4170	6187	SO:0001583	missense	55630	exon1			CCTGTTTCCCTTT	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000276833.5:c.29A>C	8.37:g.145641564T>G	ENSP00000276833:p.Glu10Ala	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_017767	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000276833.5	37	CCDS43782.1	1061	0.4858058608058608	242	0.491869918699187	166	0.4585635359116022	238	0.4160839160839161	415	0.5474934036939314	T	13.03	2.114534	0.37339	0.474467	0.531055	ENSG00000147804	ENST00000276833	T	0.61627	0.09	3.0	-3.1	0.05315	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.45396	-0.9264	8	0.87932	D	0	.	5.3	0.15773	0.0:0.5884:0.1949:0.2167	rs2280839;rs61327800;rs2280839	10	A6NDY5	.	A	10	ENSP00000276833:E10A	ENSP00000276833:E10A	E	-	2	0	SLC39A4	145612372	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.695000	0.05109	-0.557000	0.06126	0.254000	0.18369	GAA	T|0.522;G|0.478	0.478	strong		0.662	SLC39A4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382687.2		
ZDHHC8	29801	hgsc.bcm.edu	37	22	20134739	20134739	+	3'UTR	SNP	C	C	T	rs9605070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20134739C>T	ENST00000334554.7	+	0	4255				ZDHHC8_ENST00000405930.3_Silent_p.S774S	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8						locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					TTTTCCCCAGCCTCTCGGGGC	0.721													C|||	674	0.134585	0.0129	0.1138	5008	,	,		13169	0.0873		0.2207	False		,,,				2504	0.274				p.S774S		Atlas-SNP	.											ZDHHC8_ENST00000405930,rectum,carcinoma,0,1	ZDHHC8	77	1	0			c.C2322T						PASS	.																																			SO:0001624	3_prime_UTR_variant	29801	exon11			CCCCAGCCTCTCG	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.*1816C>T	22.37:g.20134739C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																			C|0.880;T|0.120	0.120	strong		0.721	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
TUBB8	347688	hgsc.bcm.edu	37	10	93714	93714	+	Silent	SNP	A	A	C	rs41288743		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:93714A>C	ENST00000309812.4	-	4	680	c.618T>G	c.(616-618)gcT>gcG	p.A206A	TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000332708.5_3'UTR|TUBB8_ENST00000447903.2_Silent_p.A134A	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	206					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		TGTCATACAGAGCTTCGTTAT	0.537																																					p.A206A	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											TUBB8,NS,carcinoma,0,1	TUBB8	62	1	0			c.T618G						scavenged	.						94.0	87.0	90.0					10																	93714		2203	4299	6502	SO:0001819	synonymous_variant	347688	exon4			ATACAGAGCTTCG	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.618T>G	10.37:g.93714A>C		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	58	9	0.155172	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1																																																																																			.	.	weak		0.537	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
KIFC3	3801	hgsc.bcm.edu	37	16	57794643	57794643	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:57794643C>T	ENST00000379655.4	-	16	2484	c.2227G>A	c.(2227-2229)Gta>Ata	p.V743I	KIFC3_ENST00000445690.2_Missense_Mutation_p.V743I|KIFC3_ENST00000562903.1_Missense_Mutation_p.V604I|KIFC3_ENST00000465878.2_Missense_Mutation_p.V604I|KIFC3_ENST00000541240.1_Missense_Mutation_p.V765I|KIFC3_ENST00000421376.2_Missense_Mutation_p.V604I|KIFC3_ENST00000539578.1_Missense_Mutation_p.V685I|KIFC3_ENST00000540079.2_Missense_Mutation_p.V641I|KIFC3_ENST00000543930.1_Missense_Mutation_p.V601I	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	743	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				CTCACCTGTACCACCATGAGG	0.622																																					p.V743I		Atlas-SNP	.											.	KIFC3	55	.	0			c.G2227A						PASS	.						49.0	52.0	51.0					16																	57794643		2198	4299	6497	SO:0001583	missense	3801	exon16			CCTGTACCACCAT	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"""Kinesins"""	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.2227G>A	16.37:g.57794643C>T	ENSP00000368976:p.Val743Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	87	4	0.045977	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	37	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	C	17.13	3.311199	0.60414	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	4.99	4.99	0.66335	Kinesin, motor domain (3);	0.061337	0.64402	D	0.000004	D	0.83321	0.5229	M	0.69823	2.125	0.54753	D	0.999987	P;P;P;P;P;P	0.42692	0.571;0.747;0.787;0.554;0.571;0.52	B;B;P;B;B;B	0.52386	0.428;0.411;0.697;0.377;0.312;0.346	D	0.85208	0.1019	10	0.72032	D	0.01	.	13.0651	0.59028	0.0:0.8385:0.1614:0.0	.	765;685;601;641;743;604	B7Z484;F5H4I9;B7Z896;F5H3M2;Q9BVG8;A8K6S2	.;.;.;.;KIFC3_HUMAN;.	I	743;743;604;765;641;601;685	ENSP00000368976:V743I;ENSP00000401696:V743I;ENSP00000396399:V604I;ENSP00000442008:V765I;ENSP00000438805:V641I;ENSP00000444012:V601I;ENSP00000444884:V685I	ENSP00000368976:V743I	V	-	1	0	KIFC3	56352144	1.000000	0.71417	1.000000	0.80357	0.463000	0.32649	4.881000	0.63114	2.341000	0.79615	0.205000	0.17691	GTA	.	.	none		0.622	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550	
HOXC6	3223	hgsc.bcm.edu	37	12	54422479	54422479	+	Silent	SNP	G	G	A	rs145731630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:54422479G>A	ENST00000243108.4	+	1	338	c.174G>A	c.(172-174)caG>caA	p.Q58Q	HOXC4_ENST00000303406.4_Intron|HOXC6_ENST00000394331.3_5'UTR|RP11-834C11.14_ENST00000512206.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	58					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ATTCGCCACAGGAGAATGTCG	0.512													G|||	6	0.00119808	0.0	0.0	5008	,	,		17413	0.0		0.002	False		,,,				2504	0.0041				p.Q58Q		Atlas-SNP	.											.	HOXC6	30	.	0			c.G174A						PASS	.	G	,,	7,4399	12.9+/-30.5	0,7,2196	87.0	81.0	83.0		174,,	2.5	1.0	12	dbSNP_134	83	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous,intron,utr-5	HOXC4,HOXC6	NM_004503.3,NM_014620.4,NM_153693.3	,,	0,53,6450	AA,AG,GG		0.5349,0.1589,0.4075	,,	58/236,,	54422479	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	3223	exon1			GCCACAGGAGAAT		CCDS8871.1, CCDS41792.1	12q13.13	2011-06-20	2005-12-22		ENSG00000197757	ENSG00000197757		"""Homeoboxes / ANTP class : HOXL subclass"""	5128	protein-coding gene	gene with protein product		142972	"""homeo box C6"""	HOX3C, HOX3		1973146, 1358459	Standard	NM_153693		Approved		uc001sev.3	P09630	OTTHUMG00000160027	ENST00000243108.4:c.174G>A	12.37:g.54422479G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_004503	B2RBV2|Q6DK09	Silent	SNP	ENST00000243108.4	37	CCDS8871.1																																																																																			G|0.997;A|0.003	0.003	strong		0.512	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2		
NLRX1	79671	hgsc.bcm.edu	37	11	119043656	119043656	+	Missense_Mutation	SNP	C	C	T	rs643423	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:119043656C>T	ENST00000409109.1	+	4	774	c.187C>T	c.(187-189)Ccc>Tcc	p.P63S	NLRX1_ENST00000474751.2_3'UTR|NLRX1_ENST00000409991.1_Missense_Mutation_p.P63S|NLRX1_ENST00000525863.1_Missense_Mutation_p.P63S|NLRX1_ENST00000409265.4_Missense_Mutation_p.P63S|NLRX1_ENST00000292199.2_Missense_Mutation_p.P63S	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	63			P -> S (in dbSNP:rs643423). {ECO:0000269|PubMed:12766759, ECO:0000269|PubMed:14702039}.		innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CGCTCCCCCACCCGGGAGGCA	0.632													T|||	3417	0.682308	0.6936	0.402	5008	,	,		16229	0.8829		0.5497	False		,,,				2504	0.7955				p.P63S		Atlas-SNP	.											.	NLRX1	128	.	0			c.C187T						PASS	.	T	SER/PRO,SER/PRO	2863,1537	486.0+/-360.5	927,1009,264	72.0	71.0	72.0		187,187	-4.8	0.0	11	dbSNP_83	72	4487,4103	563.2+/-388.1	1169,2149,977	yes	missense,missense	NLRX1	NM_024618.2,NM_170722.1	74,74	2096,3158,1241	TT,TC,CC		47.7648,34.9318,43.418	benign,benign	63/976,63/922	119043656	7350,5640	2200	4295	6495	SO:0001583	missense	79671	exon4			CCCCCACCCGGGA	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.187C>T	11.37:g.119043656C>T	ENSP00000387334:p.Pro63Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	1387	0.63507326007326	319	0.6483739837398373	162	0.44751381215469616	496	0.8671328671328671	410	0.5408970976253298	T	0.040	-1.287510	0.01387	0.650682	0.522352	ENSG00000160703	ENST00000454811;ENST00000449394;ENST00000422249;ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T;T;T;T	0.69806	1.67;1.67;1.67;-0.3;-0.3;-0.43;-0.3;-0.43	5.4	-4.75	0.03239	.	1.123620	0.06731	N	0.776696	T	0.00012	0.0000	N	0.04880	-0.145	0.80722	P	0.0	B;B	0.12013	0.005;0.0	B;B	0.06405	0.002;0.0	T	0.32161	-0.9917	9	0.06099	T	0.92	.	11.9448	0.52922	0.0:0.6535:0.1091:0.2373	rs643423;rs59337253;rs643423	63;63	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	S	63	ENSP00000400268:P63S;ENSP00000402801:P63S;ENSP00000402381:P63S;ENSP00000386851:P63S;ENSP00000292199:P63S;ENSP00000386858:P63S;ENSP00000387334:P63S;ENSP00000433442:P63S	ENSP00000292199:P63S	P	+	1	0	NLRX1	118548866	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.208000	0.01229	-1.172000	0.02762	-1.177000	0.01723	CCC	C|0.405;T|0.595	0.595	strong		0.632	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
ACAN	176	hgsc.bcm.edu	37	15	89417238	89417238	+	Missense_Mutation	SNP	A	A	G	rs1126823	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89417238A>G	ENST00000561243.1	+	16	7499	c.7499A>G	c.(7498-7500)cAg>cGg	p.Q2500R	ACAN_ENST00000439576.2_Missense_Mutation_p.Q2500R|ACAN_ENST00000352105.7_Intron|ACAN_ENST00000559004.1_Missense_Mutation_p.Q2462R			P16112	PGCA_HUMAN	aggrecan	2385					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GAGGAGCCTCAGATCACCTGC	0.642													G|||	2037	0.406749	0.7557	0.2939	5008	,	,		17716	0.2639		0.2366	False		,,,				2504	0.3374				p.Q2500R		Atlas-SNP	.											.	ACAN	220	.	0			c.A7499G						PASS	.	G	,ARG/GLN	2941,1391		1018,905,243	37.0	46.0	43.0		,7499	2.9	1.0	15	dbSNP_86	43	2138,6378		265,1608,2385	yes	intron,missense	ACAN	NM_001135.3,NM_013227.3	,43	1283,2513,2628	GG,GA,AA		25.1057,32.1099,39.5314	,benign	,2500/2531	89417238	5079,7769	2166	4258	6424	SO:0001583	missense	176	exon17			AGCCTCAGATCAC	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.7499A>G	15.37:g.89417238A>G	ENSP00000453342:p.Gln2500Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_013227	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	778	0.35622710622710624	355	0.7215447154471545	116	0.32044198895027626	142	0.24825174825174826	165	0.21767810026385223	G	3.690	-0.063804	0.07273	0.678901	0.251057	ENSG00000157766	ENST00000439576;ENST00000268134	T	0.65178	-0.14	5.17	2.92	0.33932	.	0.000000	0.29752	N	0.011285	T	0.00012	0.0000	.	.	.	0.49582	P	1.9299999999999873E-4	B	0.06786	0.001	B	0.04013	0.001	T	0.43621	-0.9380	8	0.02654	T	1	-7.0478	11.1267	0.48322	0.2384:0.0:0.7616:0.0	rs1126823;rs2280467;rs3182090;rs17415701;rs52823483;rs56687304;rs1126823	2500	E7EX88	.	R	2500;2386	ENSP00000387356:Q2500R	ENSP00000268134:Q2386R	Q	+	2	0	ACAN	87218242	1.000000	0.71417	0.993000	0.49108	0.969000	0.65631	1.990000	0.40717	0.591000	0.29711	-0.119000	0.15052	CAG	A|0.613;G|0.387	0.387	strong		0.642	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
CNDP2	55748	hgsc.bcm.edu	37	18	72178161	72178161	+	Silent	SNP	T	T	C	rs2278159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:72178161T>C	ENST00000324262.4	+	6	886	c.570T>C	c.(568-570)taT>taC	p.Y190Y	CNDP2_ENST00000324301.8_Silent_p.Y106Y|CNDP2_ENST00000579847.1_Silent_p.Y190Y	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	190					cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.Y190Y(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		ATGTGGACTATGTCTGCATTT	0.507													T|||	1013	0.202276	0.0779	0.3026	5008	,	,		23053	0.2986		0.162	False		,,,				2504	0.2413				p.Y190Y		Atlas-SNP	.											CNDP2,NS,carcinoma,0,1	CNDP2	55	1	1	Substitution - coding silent(1)	stomach(1)	c.T570C						PASS	.	T	,	493,3913	230.4+/-244.6	34,425,1744	146.0	127.0	134.0		318,570	1.8	0.9	18	dbSNP_100	134	1634,6966	303.4+/-306.4	133,1368,2799	no	coding-synonymous,coding-synonymous	CNDP2	NM_001168499.1,NM_018235.2	,	167,1793,4543	CC,CT,TT		19.0,11.1893,16.354	,	106/392,190/476	72178161	2127,10879	2203	4300	6503	SO:0001819	synonymous_variant	55748	exon6			GGACTATGTCTGC	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.570T>C	18.37:g.72178161T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Silent	SNP	ENST00000324262.4	37	CCDS12006.1																																																																																			T|0.825;C|0.175	0.175	strong		0.507	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
FAS	355	hgsc.bcm.edu	37	10	90771829	90771829	+	Silent	SNP	T	T	C	rs3218617|rs2234978	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90771829T>C	ENST00000355279.2	+	7	642	c.642T>C	c.(640-642)acT>acC	p.T214T	FAS_ENST00000352159.4_Silent_p.T214T|FAS_ENST00000355740.2_Silent_p.T214T|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000357339.2_Silent_p.T193T			P49327	FAS_HUMAN	Fas cell surface death receptor	976	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	AATCTCCAACTTTAAATCCTG	0.318													C|||	3883	0.775359	0.6475	0.7911	5008	,	,		20218	0.9573		0.7028	False		,,,				2504	0.8241				p.T214T		Atlas-SNP	.											.	FAS	47	.	0			c.T642C	GRCh37	CM045201	FAS	M	rs2234978	PASS	.	C	,,	3020,1386	455.7+/-351.1	1031,958,214	103.0	105.0	104.0	http://www.ncbi.nlm.nih.gov/pubmed?term	642,579,642	-0.6	0.0	10	dbSNP_98	104	6022,2578	418.0+/-352.6	2115,1792,393	yes	coding-synonymous,coding-synonymous,coding-synonymous	FAS	NM_000043.4,NM_152871.2,NM_152872.2	,,	3146,2750,607	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	29.9767,31.4571,30.4782	,,	214/336,193/315,214/221	90771829	9042,3964	2203	4300	6503	SO:0001819	synonymous_variant	355	exon7			TCCAACTTTAAAT	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11920	protein-coding gene	gene with protein product	"""TNF receptor superfamily member 6"""	134637	"""tumor necrosis factor receptor superfamily, member 6"", ""Fas (TNF receptor superfamily, member 6)"""	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.642T>C	10.37:g.90771829T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	83	81	0.975904	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000355279.2	37	CCDS7395.1																																																																																			T|0.261;C|0.739	0.739	strong		0.318	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2		
PXDN	7837	hgsc.bcm.edu	37	2	1642697	1642697	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:1642697C>T	ENST00000252804.4	-	21	4177	c.4127G>A	c.(4126-4128)cGc>cAc	p.R1376H		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1376					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)		TGCATCTGAGCGTGTGCTGAA	0.532																																					p.R1376H		Atlas-SNP	.											PXDN,NS,carcinoma,0,1	PXDN	255	1	0			c.G4127A						PASS	.						129.0	135.0	133.0					2																	1642697		2138	4242	6380	SO:0001583	missense	7837	exon21			TCTGAGCGTGTGC	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.4127G>A	2.37:g.1642697C>T	ENSP00000252804:p.Arg1376His	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	135	65	0.481481	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.529441	0.27387	.	.	ENSG00000130508	ENST00000252804	T	0.61158	0.13	5.43	-3.33	0.04958	.	0.635120	0.17081	N	0.187772	T	0.21347	0.0514	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30621	-0.9972	10	0.10636	T	0.68	-21.916	7.9384	0.29944	0.0:0.428:0.121:0.451	.	1376	Q92626	PXDN_HUMAN	H	1376	ENSP00000252804:R1376H	ENSP00000252804:R1376H	R	-	2	0	PXDN	1621704	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.482000	0.06544	-0.753000	0.04721	-0.471000	0.05019	CGC	.	.	none		0.532	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
C5orf52	100190949	hgsc.bcm.edu	37	5	157102185	157102185	+	Missense_Mutation	SNP	A	A	G	rs6884959	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:157102185A>G	ENST00000409999.3	+	2	360	c.298A>G	c.(298-300)Aca>Gca	p.T100A		NM_001145132.1	NP_001138604.1	A6NGY3	CE052_HUMAN	chromosome 5 open reading frame 52	100										endometrium(2)|lung(1)	3						TAACCGCATCACACAACGAAT	0.428													.|||	2594	0.517971	0.9085	0.3775	5008	,	,		19463	0.2887		0.3907	False		,,,				2504	0.4571				p.T100A		Atlas-SNP	.											.	C5orf52	17	.	0			c.A298G						PASS	.	G	ALA/THR	1167,217		490,187,15	104.0	98.0	99.0		298	2.2	1.0	5	dbSNP_116	99	1236,1946		246,744,601	yes	missense	C5orf52	NM_001145132.1	58	736,931,616	GG,GA,AA		38.8435,15.6792,47.3719	benign	100/160	157102185	2403,2163	692	1591	2283	SO:0001583	missense	100190949	exon2			CGCATCACACAAC	BG721329	CCDS47329.1	5q33.3	2012-02-24			ENSG00000187658	ENSG00000187658			35121	protein-coding gene	gene with protein product							Standard	NM_001145132		Approved		uc011ddt.2	A6NGY3	OTTHUMG00000154518	ENST00000409999.3:c.298A>G	5.37:g.157102185A>G	ENSP00000387027:p.Thr100Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	88	87	0.988636	NM_001145132		Missense_Mutation	SNP	ENST00000409999.3	37	CCDS47329.1	1047	0.4793956043956044	442	0.8983739837398373	131	0.36187845303867405	177	0.3094405594405594	297	0.391820580474934	G	0.058	-1.231532	0.01505	0.843208	0.388435	ENSG00000187658	ENST00000409999	T	0.26373	1.74	2.22	2.22	0.28083	.	.	.	.	.	T	0.00012	0.0000	N	0.01168	-0.975	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.31475	-0.9942	8	0.02654	T	1	-15.7143	5.0875	0.14691	0.188:0.0:0.812:0.0	rs6884959;rs17451564;rs52828955;rs58650472;rs6884959	100	A6NGY3	CE052_HUMAN	A	100	ENSP00000387027:T100A	ENSP00000387027:T100A	T	+	1	0	C5orf52	157034763	0.854000	0.29725	0.974000	0.42286	0.771000	0.43674	0.383000	0.20651	0.269000	0.21961	-0.642000	0.03964	ACA	A|0.478;G|0.522	0.522	strong		0.428	C5orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335664.1	NM_001145132	
PNMA3	29944	hgsc.bcm.edu	37	X	152226542	152226542	+	Missense_Mutation	SNP	T	T	C	rs6526155	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:152226542T>C	ENST00000370264.4	+	1	1156	c.1130T>C	c.(1129-1131)gTg>gCg	p.V377A	PNMA3_ENST00000370265.4_Missense_Mutation_p.V377A|PNMA3_ENST00000447306.1_Missense_Mutation_p.V377A			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	377				V -> A (in Ref. 1; AAF05627, 2; CAB66812 and 5; AAI05097/AAI05099). {ECO:0000305}.	positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					AGTTTTGATGTGAGGCCTTCC	0.637													t|||	3412	0.903841	0.7103	0.7032	3775	,	,		13250	0.7063		0.668	False		,,,				2504	0.6145				p.V377A		Atlas-SNP	.											.	PNMA3	81	.	0			c.T1130C						PASS	.	C	ALA/VAL	3616,217		1459,164,534,8,37	29.0	32.0	31.0		1130	-0.9	0.0	X	dbSNP_116	31	5770,957		1781,594,1614,53,257	yes	missense	PNMA3	NM_013364.4	64	3240,758,2148,61,294	CC,CT,C,TT,T		14.2263,5.6614,11.1174	benign	377/464	152226542	9386,1174	2202	4299	6501	SO:0001583	missense	29944	exon2			TTGATGTGAGGCC	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"""Paraneoplastic Ma antigens"""	18742	protein-coding gene	gene with protein product	"""paraneoplastic cancer-testis-brain antigen"""	300675	"""paraneoplastic antigen MA3"""			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.1130T>C	X.37:g.152226542T>C	ENSP00000359286:p.Val377Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	36	35	0.972222	NM_013364	D3DWT7|Q9H0A4	Missense_Mutation	SNP	ENST00000370264.4	37	CCDS35435.2	1517	0.9144062688366486	238	0.8623188405797102	171	0.8724489795918368	270	0.8940397350993378	358	0.7955555555555556	N	0.007	-1.948235	0.00475	0.943386	0.857737	ENSG00000183837	ENST00000370265;ENST00000447306;ENST00000370264	T;T;T	0.14640	2.49;2.49;2.49	2.15	-0.952	0.10366	.	.	.	.	.	T	0.00012	0.0000	N	0.00413	-1.525	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	8	0.02654	T	1	.	4.8244	0.13408	0.1791:0.6286:0.0:0.1923	rs6526155;rs57735631;rs6526155	377	Q9UL41	PNMA3_HUMAN	A	377	ENSP00000359288:V377A;ENSP00000407642:V377A;ENSP00000359286:V377A	ENSP00000359286:V377A	V	+	2	0	PNMA3	151977198	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.803000	0.01740	-0.844000	0.04184	-2.608000	0.00160	GTG	0|0.013;C|0.892	0.892	strong		0.637	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364	
GSDMA	284110	hgsc.bcm.edu	37	17	38131187	38131187	+	Missense_Mutation	SNP	C	C	A	rs56030650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38131187C>A	ENST00000301659.4	+	10	1059	c.941C>A	c.(940-942)aCc>aAc	p.T314N		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	314			T -> N (in dbSNP:rs56030650). {ECO:0000269|PubMed:15489334}.		apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CATGAAGTGACCCTGGAGGCA	0.547													C|||	1917	0.382788	0.3132	0.3847	5008	,	,		15256	0.4742		0.4573	False		,,,				2504	0.3047				p.T314N		Atlas-SNP	.											.	GSDMA	26	.	0			c.C941A						PASS	.	C	ASN/THR	1260,2530		201,858,836	41.0	41.0	41.0		941	4.0	1.0	17	dbSNP_129	41	3880,4342		922,2036,1153	yes	missense	GSDMA	NM_178171.4	65	1123,2894,1989	AA,AC,CC		47.1905,33.2454,42.7905	probably-damaging	314/446	38131187	5140,6872	1895	4111	6006	SO:0001583	missense	284110	exon10			AAGTGACCCTGGA	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.941C>A	17.37:g.38131187C>A	ENSP00000301659:p.Thr314Asn	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	93	92	0.989247	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	914	0.4184981684981685	143	0.29065040650406504	149	0.4116022099447514	275	0.4807692307692308	347	0.4577836411609499	C	12.65	2.002462	0.35320	0.332454	0.471905	ENSG00000167914	ENST00000301659	T	0.23348	1.91	6.03	3.96	0.45880	.	0.424311	0.22282	N	0.062101	T	0.00012	0.0000	L	0.57536	1.79	0.33723	P	0.38275899999999996	D	0.54772	0.968	P	0.50314	0.637	T	0.49570	-0.8926	9	0.25751	T	0.34	-10.8739	13.3157	0.60405	0.0:0.6007:0.3993:0.0	rs56030650;rs56793200;rs61759528	314	Q96QA5	GSDMA_HUMAN	N	314	ENSP00000301659:T314N	ENSP00000301659:T314N	T	+	2	0	GSDMA	35384713	0.996000	0.38824	0.987000	0.45799	0.177000	0.22998	1.437000	0.34991	0.779000	0.33543	0.655000	0.94253	ACC	C|0.572;A|0.428	0.428	strong		0.547	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
TAF1C	9013	hgsc.bcm.edu	37	16	84212571	84212571	+	Silent	SNP	C	C	A	rs1804500	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84212571C>A	ENST00000567759.1	-	14	2768	c.2586G>T	c.(2584-2586)cgG>cgT	p.R862R	TAF1C_ENST00000341690.6_Silent_p.R768R|TAF1C_ENST00000566732.1_Silent_p.R836R|TAF1C_ENST00000378541.4_Silent_p.R862R|TAF1C_ENST00000541676.1_Silent_p.R769R|TAF1C_ENST00000570117.1_Silent_p.R530R	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	862					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)	p.R862R(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						GAGGCTTCTTCCGGAGGGGCT	0.647													C|||	1372	0.273962	0.0923	0.4092	5008	,	,		14562	0.372		0.341	False		,,,				2504	0.2536				p.R862R		Atlas-SNP	.											TAF1C,NS,carcinoma,0,1	TAF1C	60	1	1	Substitution - coding silent(1)	stomach(1)	c.G2586T						PASS	.	C	,	589,3811	258.0+/-262.2	43,503,1654	48.0	53.0	51.0		2586,2304	0.9	0.2	16	dbSNP_89	51	3045,5555	465.6+/-366.6	554,1937,1809	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	597,2440,3463	AA,AC,CC		35.407,13.3864,27.9538	,	862/870,768/776	84212571	3634,9366	2200	4300	6500	SO:0001819	synonymous_variant	9013	exon14			CTTCTTCCGGAGG	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.2586G>T	16.37:g.84212571C>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	24	23	0.958333	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			C|0.709;A|0.291	0.291	strong		0.647	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
NACA2	342538	hgsc.bcm.edu	37	17	59668021	59668021	+	Missense_Mutation	SNP	G	G	C	rs61739273	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:59668021G>C	ENST00000521764.1	-	1	542	c.521C>G	c.(520-522)aCa>aGa	p.T174R		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	174					myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					TTCTACACCTGTTTCATCGAC	0.423													G|||	747	0.149161	0.0575	0.1037	5008	,	,		21948	0.1667		0.1471	False		,,,				2504	0.2894				p.T174R		Atlas-SNP	.											NACA2,NS,carcinoma,0,2	NACA2	33	2	0			c.C521G						PASS	.	G	ARG/THR	329,4077	171.9+/-202.1	15,299,1889	304.0	274.0	284.0		521	0.8	0.8	17	dbSNP_129	284	1249,7351	248.6+/-276.2	97,1055,3148	yes	missense	NACA2	NM_199290.3	71	112,1354,5037	CC,CG,GG		14.5233,7.4671,12.1329	possibly-damaging	174/216	59668021	1578,11428	2203	4300	6503	SO:0001583	missense	342538	exon1			ACACCTGTTTCAT	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.521C>G	17.37:g.59668021G>C	ENSP00000427802:p.Thr174Arg	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	197	99	0.502538	NM_199290	Q2VIR9	Missense_Mutation	SNP	ENST00000521764.1	37	CCDS11630.1	254	0.1163003663003663	26	0.052845528455284556	40	0.11049723756906077	73	0.12762237762237763	115	0.1517150395778364	G	12.97	2.098780	0.37048	0.074671	0.145233	ENSG00000253506	ENST00000521764	T	0.48836	0.8	0.753	0.753	0.18404	.	0.154695	0.40728	U	0.001024	T	0.00384	0.0012	M	0.92367	3.3	0.20403	P	0.9999081527	B	0.29909	0.261	B	0.29440	0.102	T	0.10847	-1.0612	8	.	.	.	.	7.3227	0.26536	0.0:0.0:1.0:0.0	rs61739273	174	Q9H009	NACA2_HUMAN	R	174	ENSP00000427802:T174R	.	T	-	2	0	NACA2	57022803	1.000000	0.71417	0.822000	0.32727	0.313000	0.28021	3.630000	0.54273	0.702000	0.31825	0.411000	0.27672	ACA	G|0.868;C|0.132	0.132	strong		0.423	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786832	75786832	+	Missense_Mutation	SNP	C	C	T	rs11122676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:75786832C>T	ENST00000478296.1	-	4	2068	c.1792G>A	c.(1792-1794)Gta>Ata	p.V598I	ZNF717_ENST00000400845.3_Missense_Mutation_p.V641I|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.V648I|MIR4273_ENST00000582824.1_RNA			Q9BY31	ZN717_HUMAN	zinc finger protein 717	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)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TCATTACATACGTAAGGTTTC	0.428													c|||	3378	0.674521	0.5204	0.7277	5008	,	,		9783	0.8254		0.7326	False		,,,				2504	0.6299				p.V648I		Atlas-SNP	.											.	ZNF717	160	.	0			c.G1942A						PASS	.						41.0	45.0	44.0					3																	75786832		633	1557	2190	SO:0001583	missense	100131827	exon5			TACATACGTAAGG	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1792G>A	3.37:g.75786832C>T	ENSP00000419377:p.Val598Ile	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		875	0.40064102564102566	211	0.42886178861788615	156	0.430939226519337	210	0.36713286713286714	298	0.39313984168865435	.	6.675	0.493088	0.12702	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.18810	2.19;2.19;2.19	1.71	-1.23	0.09465	.	.	.	.	.	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.46498	-0.9187	8	0.49607	T	0.09	.	3.1934	0.06625	0.2062:0.5238:0.0:0.27	rs11122676;rs13061393;rs59040583	648	C9JSV9	.	I	598;648;641	ENSP00000419377:V598I;ENSP00000409514:V648I;ENSP00000383643:V641I	ENSP00000383643:V641I	V	-	1	0	ZNF717	75869522	0.000000	0.05858	0.004000	0.12327	0.005000	0.04900	-6.469000	0.00065	-0.338000	0.08413	-1.572000	0.00871	GTA	C|0.574;T|0.426	0.426	strong		0.428	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
LTBP1	4052	hgsc.bcm.edu	37	2	33540248	33540248	+	Silent	SNP	G	G	A	rs1058840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:33540248G>A	ENST00000404816.2	+	24	3995	c.3642G>A	c.(3640-3642)ccG>ccA	p.P1214P	LTBP1_ENST00000404525.1_Silent_p.P835P|LTBP1_ENST00000407925.1_Silent_p.P888P|LTBP1_ENST00000390003.4_Silent_p.P889P|LTBP1_ENST00000402934.1_Silent_p.P835P|LTBP1_ENST00000418533.2_Silent_p.P888P|LTBP1_ENST00000272273.5_Silent_p.P154P|LTBP1_ENST00000354476.3_Silent_p.P1215P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1214	EGF-like 12; 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)				TCTGTGGTCCGCAAGGGGAGT	0.413													a|||	2305	0.460264	0.3169	0.6282	5008	,	,		19677	0.3095		0.6481	False		,,,				2504	0.4969				p.P1214P		Atlas-SNP	.											.	LTBP1	317	.	0			c.G3642A						PASS	.	A	,,,,	1629,2777	661.1+/-400.8	306,1017,880	104.0	97.0	100.0		2664,2664,2505,2505,3642	1.3	1.0	2	dbSNP_86	100	5630,2970	461.2+/-365.4	1867,1896,537	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	2173,2913,1417	AA,AG,GG		34.5349,36.9723,44.1873	,,,,	888/1396,888/1354,835/1343,835/1301,1214/1722	33540248	7259,5747	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon24			TGGTCCGCAAGGG		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.3642G>A	2.37:g.33540248G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	107	46	0.429907	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2	1060	0.48534798534798534	152	0.3089430894308943	224	0.6187845303867403	175	0.30594405594405594	509	0.6715039577836411	a	8.289	0.817316	0.16607	0.369723	0.654651	ENSG00000049323	ENST00000415140	.	.	.	4.98	1.28	0.21552	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999966383	.	.	.	.	.	.	T	0.36286	-0.9754	3	.	.	.	.	0.9771	0.01428	0.244:0.1469:0.1269:0.4822	rs1058840;rs1453844;rs3199480;rs1058840	.	.	.	H	176	.	.	R	+	2	0	LTBP1	33393752	0.221000	0.23642	0.987000	0.45799	0.844000	0.47949	-0.419000	0.07071	-0.276000	0.09206	-1.002000	0.02502	CGC	G|0.480;A|0.519	0.519	strong		0.413	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46102015	46102015	+	Silent	SNP	C	C	T	rs7283084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46102015C>T	ENST00000391617.1	-	1	63	c.24G>A	c.(22-24)tcG>tcA	p.S8S	TSPEAR_ENST00000323084.4_Intron	NM_181686.1	NP_859014.1	P59990	KR121_HUMAN	keratin associated protein 12-1	8						keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|skin(2)	5						GCTGGCAGCCCGAGGAGCAGC	0.657													T|||	735	0.146765	0.1838	0.121	5008	,	,		15749	0.0813		0.1461	False		,,,				2504	0.183				p.S8S		Atlas-SNP	.											.	KRTAP12-1	9	.	0			c.G24A						PASS	.	T	,	692,3628		50,592,1518	29.0	36.0	34.0		,24	-6.5	0.0	21	dbSNP_116	34	1344,7178		109,1126,3026	no	intron,coding-synonymous	TSPEAR,KRTAP12-1	NM_144991.2,NM_181686.1	,	159,1718,4544	TT,TC,CC		15.7709,16.0185,15.8542	,	,8/97	46102015	2036,10806	2160	4261	6421	SO:0001819	synonymous_variant	353332	exon1			GCAGCCCGAGGAG	AJ566388	CCDS42966.1	21q22.3	2006-03-13			ENSG00000187175	ENSG00000187175		"""Keratin associated proteins"""	20529	protein-coding gene	gene with protein product							Standard	NM_181686		Approved	KRTAP12.1, KAP12.1	uc002zfv.3	P59990	OTTHUMG00000057639	ENST00000391617.1:c.24G>A	21.37:g.46102015C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	161	79	0.490683	NM_181686	Q0VAS3	Silent	SNP	ENST00000391617.1	37	CCDS42966.1																																																																																			C|0.871;T|0.129	0.129	strong		0.657	KRTAP12-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128043.1	NM_181686	
AEN	64782	hgsc.bcm.edu	37	15	89169484	89169484	+	Missense_Mutation	SNP	C	C	T	rs3743477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89169484C>T	ENST00000332810.3	+	2	195	c.44C>T	c.(43-45)cCt>cTt	p.P15L	AEN_ENST00000379231.3_Missense_Mutation_p.P15L	NM_022767.3	NP_073604.3	Q8WTP8	AEN_HUMAN	apoptosis enhancing nuclease	15			P -> L (in dbSNP:rs3743477).		intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			NS(1)|kidney(1)|large_intestine(1)|lung(4)	7						TGCCTGTGCCCTTCCCTCACC	0.607													C|||	370	0.0738818	0.1407	0.0403	5008	,	,		14946	0.002		0.0507	False		,,,				2504	0.1053				p.P15L		Atlas-SNP	.											.	AEN	29	.	0			c.C44T						PASS	.	C	LEU/PRO	509,3891	220.7+/-238.1	37,435,1728	30.0	29.0	30.0		44	2.3	0.0	15	dbSNP_107	30	440,8158	130.3+/-188.3	8,424,3867	yes	missense	AEN	NM_022767.3	98	45,859,5595	TT,TC,CC		5.1175,11.5682,7.3011	possibly-damaging	15/326	89169484	949,12049	2200	4299	6499	SO:0001583	missense	64782	exon2			TGTGCCCTTCCCT	BC020988	CCDS10344.1	15q26.1	2008-07-15	2008-07-15	2008-07-15	ENSG00000181026	ENSG00000181026			25722	protein-coding gene	gene with protein product		610177	"""interferon stimulated exonuclease gene 20kDa-like 1"""	ISG20L1		18264133, 16171785	Standard	NM_022767		Approved	FLJ12484, FLJ12562	uc002bmt.2	Q8WTP8	OTTHUMG00000148681	ENST00000332810.3:c.44C>T	15.37:g.89169484C>T	ENSP00000331944:p.Pro15Leu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	37	14	0.378378	NM_022767	C9J571|Q9BSA5|Q9H9X7	Missense_Mutation	SNP	ENST00000332810.3	37	CCDS10344.1	109	0.04990842490842491	53	0.10772357723577236	15	0.04143646408839779	1	0.0017482517482517483	40	0.052770448548812667	C	16.59	3.165784	0.57476	0.115682	0.051175	ENSG00000181026	ENST00000332810;ENST00000379231	T;T	0.19532	2.18;2.14	4.18	2.28	0.28536	.	2.187660	0.02165	N	0.059148	T	0.00241	0.0007	L	0.29908	0.895	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.002	T	0.21690	-1.0238	9	0.72032	D	0.01	-13.6823	4.3383	0.11097	0.0:0.595:0.1892:0.2158	rs3743477;rs60876175;rs3743477	15;15	Q8WTP8-2;Q8WTP8	.;AEN_HUMAN	L	15	ENSP00000331944:P15L;ENSP00000368533:P15L	ENSP00000331944:P15L	P	+	2	0	AEN	86970488	0.003000	0.15002	0.003000	0.11579	0.795000	0.44927	1.554000	0.36266	0.246000	0.21394	0.563000	0.77884	CCT	C|0.930;T|0.070	0.070	strong		0.607	AEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309071.1	NM_022767	
BCKDHA	593	hgsc.bcm.edu	37	19	41920030	41920030	+	Missense_Mutation	SNP	C	C	T	rs34442879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41920030C>T	ENST00000269980.2	+	4	820	c.452C>T	c.(451-453)aCg>aTg	p.T151M	CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.T185M|BCKDHA_ENST00000595085.1_Missense_Mutation_p.T185M|BCKDHA_ENST00000457836.2_Missense_Mutation_p.T129M	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	151			T -> M (in dbSNP:rs34442879).		branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						CTGGACAACACGGACCTGGTG	0.602													C|||	21	0.00419329	0.0	0.0058	5008	,	,		18861	0.001		0.0139	False		,,,				2504	0.002				p.T151M		Atlas-SNP	.											.	BCKDHA	36	.	0			c.C452T	GRCh37	CM021497	BCKDHA	M	rs34442879	PASS	.	C	MET/THR,MET/THR	7,4399	14.3+/-33.2	0,7,2196	73.0	57.0	63.0		452,452	4.7	0.9	19	dbSNP_126	63	91,8509	50.6+/-110.7	2,87,4211	yes	missense,missense	BCKDHA	NM_000709.3,NM_001164783.1	81,81	2,94,6407	TT,TC,CC		1.0581,0.1589,0.7535	possibly-damaging,possibly-damaging	151/446,151/445	41920030	98,12908	2203	4300	6503	SO:0001583	missense	593	exon4			ACAACACGGACCT	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.452C>T	19.37:g.41920030C>T	ENSP00000269980:p.Thr151Met	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	107	60	0.560748	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	12|12	0.005494505494505495|0.005494505494505495	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	20.7|20.7	4.042043|4.042043	0.75732|0.75732	0.001589|0.001589	0.010581|0.010581	ENSG00000248098|ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000541315|ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000378196	.|D;D;D;D	.|0.96011	.|-3.88;-3.88;-3.88;-3.88	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Dehydrogenase, E1 component (1);	.|0.167160	.|0.51477	.|D	.|0.000089	D|D	0.94961|0.94961	0.8370|0.8370	L|L	0.57536|0.57536	1.79|1.79	0.40759|0.40759	D|D	0.98298|0.98298	.|D;D;D;P	.|0.54964	.|0.969;0.962;0.963;0.953	.|P;P;P;P	.|0.56788	.|0.806;0.622;0.622;0.488	D|D	0.94832|0.94832	0.7997|0.7997	5|10	.|0.62326	.|D	.|0.03	-23.707|-23.707	16.8305|16.8305	0.85943|0.85943	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34442879|rs34442879	.|129;151;151;185	.|B4DP47;Q59EI3;P12694;F5H5P2	.|.;.;ODBA_HUMAN;.	W|M	87|185;151;122;129;151	.|ENSP00000443246:T185M;ENSP00000269980:T151M;ENSP00000440345:T122M;ENSP00000416000:T129M	.|ENSP00000269980:T151M	R|T	+|+	1|2	2|0	BCKDHA|BCKDHA;CTC-435M10.3	46611870|46611870	0.488000|0.488000	0.25996|0.25996	0.874000|0.874000	0.34290|0.34290	0.931000|0.931000	0.56810|0.56810	1.755000|1.755000	0.38379|0.38379	2.578000|2.578000	0.87016|0.87016	0.563000|0.563000	0.77884|0.77884	CGG|ACG	C|0.993;T|0.007	0.007	strong		0.602	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
DROSHA	29102	hgsc.bcm.edu	37	5	31409252	31409252	+	Silent	SNP	A	A	G	rs2241337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:31409252A>G	ENST00000511367.2	-	32	4009	c.3765T>C	c.(3763-3765)aaT>aaC	p.N1255N	DROSHA_ENST00000344624.3_Silent_p.N1255N|DROSHA_ENST00000442743.1_Silent_p.N1218N|DROSHA_ENST00000513349.1_Silent_p.N1218N	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	1255	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TCCAATCCTGATTCAAAATGA	0.413													A|||	1537	0.306909	0.2519	0.2839	5008	,	,		17757	0.4772		0.2137	False		,,,				2504	0.318				p.N1255N		Atlas-SNP	.											.	DROSHA	130	.	0			c.T3765C						PASS	.	A	,	890,2784		115,660,1062	62.0	58.0	59.0		3654,3765	4.1	1.0	5	dbSNP_98	59	1561,6621		151,1259,2681	no	coding-synonymous,coding-synonymous	DROSHA	NM_001100412.1,NM_013235.4	,	266,1919,3743	GG,GA,AA		19.0785,24.2243,20.6731	,	1218/1338,1255/1375	31409252	2451,9405	1837	4091	5928	SO:0001819	synonymous_variant	29102	exon32			ATCCTGATTCAAA	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.3765T>C	5.37:g.31409252A>G		Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	181	83	0.458564	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Silent	SNP	ENST00000511367.2	37	CCDS47195.1																																																																																			A|0.696;G|0.304	0.304	strong		0.413	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68704028	68704028	+	Missense_Mutation	SNP	C	C	T	rs2236654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68704028C>T	ENST00000255078.3	+	13	2191	c.2080C>T	c.(2080-2082)Cgg>Tgg	p.R694W		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	694	SS DNA-binding. {ECO:0000250}.		R -> W (in dbSNP:rs2236654).		ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CAGACAGGGCCGGAAGAAGCC	0.672													C|||	666	0.132987	0.149	0.1902	5008	,	,		14528	0.0208		0.2644	False		,,,				2504	0.0511				p.R694W		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.C2080T						PASS	.	C	TRP/ARG	766,3634	285.7+/-278.4	70,626,1504	22.0	27.0	25.0		2080	3.5	0.0	11	dbSNP_98	25	2129,6453	341.7+/-324.1	265,1599,2427	yes	missense	IGHMBP2	NM_002180.2	101	335,2225,3931	TT,TC,CC		24.8077,17.4091,22.3001	probably-damaging	694/994	68704028	2895,10087	2200	4291	6491	SO:0001583	missense	3508	exon13			CAGGGCCGGAAGA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.2080C>T	11.37:g.68704028C>T	ENSP00000255078:p.Arg694Trp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	365	0.1671245421245421	80	0.16260162601626016	75	0.20718232044198895	12	0.02097902097902098	198	0.2612137203166227	C	15.48	2.845377	0.51164	0.174091	0.248077	ENSG00000132740	ENST00000255078	D	0.90732	-2.72	3.53	3.53	0.40419	.	6.158650	0.00520	N	0.000184	T	0.00109	0.0003	L	0.50333	1.59	0.31973	P	0.606961	B	0.15473	0.013	B	0.08055	0.003	T	0.38993	-0.9635	9	0.66056	D	0.02	-34.8022	11.0997	0.48166	0.0:0.8104:0.1896:0.0	rs2236654;rs2236654	694	P38935	SMBP2_HUMAN	W	694	ENSP00000255078:R694W	ENSP00000255078:R694W	R	+	1	2	IGHMBP2	68460604	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	0.198000	0.17217	1.982000	0.57802	0.561000	0.74099	CGG	C|0.807;T|0.193	0.193	strong		0.672	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
SWSAP1	126074	hgsc.bcm.edu	37	19	11486514	11486514	+	Missense_Mutation	SNP	A	A	G	rs317926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11486514A>G	ENST00000312423.2	+	2	571	c.512A>G	c.(511-513)gAt>gGt	p.D171G	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	171			D -> G (in dbSNP:rs317926).		ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)										CTGCAGCCAGATGCACCAGGT	0.642													A|||	69	0.013778	0.0507	0.0029	5008	,	,		16689	0.0		0.0	False		,,,				2504	0.0				p.D171G		Atlas-SNP	.											C19orf39,NS,carcinoma,0,1	.	.	1	0			c.A512G						PASS	.	A	GLY/ASP	196,4210	117.5+/-155.4	3,190,2010	42.0	40.0	41.0		512	0.5	0.0	19	dbSNP_79	41	3,8597	3.0+/-9.4	0,3,4297	no	missense	C19orf39	NM_175871.3	94	3,193,6307	GG,GA,AA		0.0349,4.4485,1.5301	possibly-damaging	171/230	11486514	199,12807	2203	4300	6503	SO:0001583	missense	126074	exon2			AGCCAGATGCACC	AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"""zinc finger, SWIM-type containing 7 associated protein 1"", ""SWS1-associated protein 1"""	614536	"""chromosome 19 open reading frame 39"""	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.512A>G	19.37:g.11486514A>G	ENSP00000310008:p.Asp171Gly	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_175871	Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	CCDS12259.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	A	9.198	1.027667	0.19512	0.044485	3.49E-4	ENSG00000173928	ENST00000312423	T	0.48522	0.81	5.15	0.528	0.17089	.	1.321610	0.04957	N	0.461333	T	0.13072	0.0317	L	0.60455	1.87	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16778	-1.0391	10	0.48119	T	0.1	1.0742	1.487	0.02449	0.5539:0.1458:0.16:0.1402	rs317926;rs318715;rs317926	171	Q6NVH7	CS039_HUMAN	G	171	ENSP00000310008:D171G	ENSP00000310008:D171G	D	+	2	0	C19orf39	11347514	0.000000	0.05858	0.000000	0.03702	0.315000	0.28087	0.288000	0.18939	-0.287000	0.09064	0.533000	0.62120	GAT	A|0.984;G|0.016	0.016	strong		0.642	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57070170	57070170	+	Silent	SNP	C	C	T	rs34905018	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57070170C>T	ENST00000532437.1	-	6	4757	c.4446G>A	c.(4444-4446)ttG>ttA	p.L1482L	TNKS1BP1_ENST00000358252.3_Silent_p.L1482L			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1482	Acidic.|Tankyrase-binding.				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)				CTTCCTCCTCCAACAGGCCCC	0.706													c|||	47	0.00938498	0.0015	0.0288	5008	,	,		13982	0.0		0.0229	False		,,,				2504	0.002				p.L1482L		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4446A						PASS	.			23,4377		0,23,2177	14.0	15.0	14.0		4446	-2.7	0.0	11	dbSNP_126	14	196,8390		2,192,4099	no	coding-synonymous	TNKS1BP1	NM_033396.2		2,215,6276	TT,TC,CC		2.2828,0.5227,1.6864		1482/1730	57070170	219,12767	2200	4293	6493	SO:0001819	synonymous_variant	85456	exon7			CTCCTCCAACAGG	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.4446G>A	11.37:g.57070170C>T		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.987;T|0.013	0.013	strong		0.706	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
GPR144	347088	hgsc.bcm.edu	37	9	127215772	127215772	+	Missense_Mutation	SNP	C	C	G	rs72616654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:127215772C>G	ENST00000334810.1	+	4	796	c.796C>G	c.(796-798)Cac>Gac	p.H266D				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	266	Pentaxin.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						CTCGGTGCGTCACGCCCTCAG	0.761													G|||	2623	0.523762	0.4834	0.6009	5008	,	,		6568	0.4494		0.5726	False		,,,				2504	0.5501				p.H266D		Atlas-SNP	.											.	GPR144	33	.	0			c.C796G						PASS	.						4.0	5.0	4.0					9																	127215772		654	1515	2169	SO:0001583	missense	347088	exon4			GTGCGTCACGCCC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.796C>G	9.37:g.127215772C>G	ENSP00000335156:p.His266Asp	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	16	16	1	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1149	0.5260989010989011	257	0.5223577235772358	216	0.5966850828729282	250	0.4370629370629371	426	0.5620052770448549	G	1.281	-0.610443	0.03690	.	.	ENSG00000180264	ENST00000334810	T	0.05996	3.36	3.81	2.9	0.33743	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.00012	0.0000	N	0.00707	-1.245	0.53688	P	2.2999999999995246E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.21861	-1.0233	8	0.08837	T	0.75	.	7.5506	0.27796	0.0951:0.1682:0.7367:0.0	.	266	Q7Z7M1	GP144_HUMAN	D	266	ENSP00000335156:H266D	ENSP00000335156:H266D	H	+	1	0	GPR144	126255593	0.998000	0.40836	0.052000	0.19188	0.277000	0.26821	3.079000	0.50104	0.133000	0.18654	-0.647000	0.03941	CAC	C|0.491;G|0.509	0.509	strong		0.761	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
XPC	7508	hgsc.bcm.edu	37	3	14214524	14214524	+	Missense_Mutation	SNP	G	G	A	rs2229089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14214524G>A	ENST00000285021.7	-	2	356	c.142C>T	c.(142-144)Ctc>Ttc	p.L48F	XPC_ENST00000449060.2_Missense_Mutation_p.L48F	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	48	Glu-rich (acidic).		L -> F (in dbSNP:rs3731062). {ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						ACTTTGGAGAGAAGGCTCTTC	0.483			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	50	0.00998403	0.0008	0.0216	5008	,	,		19224	0.0		0.0219	False		,,,				2504	0.0123				p.L48F		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	.	XPC	60	.	0			c.C142T						PASS	.	G	PHE/LEU,PHE/LEU	19,3737		0,19,1859	72.0	67.0	68.0		142,142	1.0	0.0	3	dbSNP_107	68	236,7980		3,230,3875	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	22,22	3,249,5734	AA,AG,GG		2.8724,0.5059,2.13	benign,benign	48/904,48/941	14214524	255,11717	1878	4108	5986	SO:0001583	missense	7508	exon2	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGGAGAGAAGGCT		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.142C>T	3.37:g.14214524G>A	ENSP00000285021:p.Leu48Phe	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	172	84	0.488372	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	28	0.01282051282051282	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	18	0.023746701846965697	G	1.971	-0.436605	0.04636	0.005059	0.028724	ENSG00000154767	ENST00000285021;ENST00000449060;ENST00000511155	T;T;T	0.67698	-0.28;-0.28;-0.28	5.13	1.03	0.20045	.	1.648110	0.03098	N	0.160669	T	0.35219	0.0924	L	0.50333	1.59	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.10450	0.005;0.005	T	0.15578	-1.0432	10	0.11794	T	0.64	0.0038	8.6953	0.34291	0.1441:0.3458:0.5101:0.0	rs3731062;rs52808398;rs3731062	48;48	E9PH69;Q01831	.;XPC_HUMAN	F	48;48;42	ENSP00000285021:L48F;ENSP00000404002:L48F;ENSP00000423867:L42F	ENSP00000285021:L48F	L	-	1	0	XPC	14189528	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	0.221000	0.17680	-0.061000	0.13110	-0.795000	0.03280	CTC	G|0.985;A|0.015	0.015	strong		0.483	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
ZNF415	55786	hgsc.bcm.edu	37	19	53612757	53612757	+	Missense_Mutation	SNP	T	T	G	rs1054485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53612757T>G	ENST00000500065.4	-	4	874	c.541A>C	c.(541-543)Att>Ctt	p.I181L	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.I181L|ZNF415_ENST00000440291.1_Missense_Mutation_p.I168L|ZNF415_ENST00000455735.2_Missense_Mutation_p.I229L|ZNF415_ENST00000421033.1_Missense_Mutation_p.I193L|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.I229L	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	229					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		GTAGAAGAAATTATTTGGGGT	0.373													T|||	2729	0.544928	0.4856	0.647	5008	,	,		20846	0.6131		0.497	False		,,,				2504	0.5317				p.I181L		Atlas-SNP	.											.	ZNF415	68	.	0			c.A541C						PASS	.	T	LEU/ILE,LEU/ILE,LEU/ILE	2216,2190	589.9+/-387.2	560,1096,547	102.0	99.0	100.0		541,541,541	-0.9	0.0	19	dbSNP_86	100	4206,4394	569.2+/-389.2	1035,2136,1129	yes	missense,missense,missense	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	5,5,5	1595,3232,1676	GG,GT,TT		48.907,49.7049,49.3772	benign,benign,benign	181/556,181/556,181/556	53612757	6422,6584	2203	4300	6503	SO:0001583	missense	55786	exon4			AAGAAATTATTTG	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.541A>C	19.37:g.53612757T>G	ENSP00000439435:p.Ile181Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	1211	0.5544871794871795	253	0.5142276422764228	234	0.6464088397790055	345	0.6031468531468531	379	0.5	T	11.38	1.621813	0.28889	0.502951	0.48907	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.06142	3.34;3.34;3.34;3.34;3.34;3.34	2.74	-0.885	0.10593	.	.	.	.	.	T	0.00012	0.0000	M	0.73430	2.235	0.80722	P	0.0	P;P;P;P;P	0.49862	0.6;0.465;0.65;0.6;0.929	B;B;P;B;P	0.53549	0.235;0.118;0.658;0.235;0.729	T	0.37009	-0.9724	8	0.52906	T	0.07	.	2.6202	0.04914	0.1996:0.2513:0.0:0.5492	rs1054485;rs3170113;rs52810498;rs56879151;rs1054485	181;229;181;168;193	F5H287;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;ZN415_HUMAN;.;.;.	L	181;181;229;193;229;168	ENSP00000243643:I181L;ENSP00000439435:I181L;ENSP00000396492:I229L;ENSP00000395055:I193L;ENSP00000388787:I229L;ENSP00000414601:I168L	ENSP00000243643:I181L	I	-	1	0	ZNF415	58304569	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	0.170000	0.16663	-0.431000	0.07307	0.260000	0.18958	ATT	T|0.487;G|0.508	0.508	strong		0.373	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
MAGEA6	4105	hgsc.bcm.edu	37	X	151870117	151870117	+	Silent	SNP	T	T	C	rs369345489		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:151870117T>C	ENST00000329342.5	+	3	1032	c.807T>C	c.(805-807)taT>taC	p.Y269Y		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	269	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					CTGCATGCTATGAGTTCCTGT	0.527																																					p.Y269Y		Atlas-SNP	.											.	MAGEA6	53	.	0			c.T807C						PASS	.	T	,	0,3834		0,0,0,1632,570	139.0	136.0	137.0		807,807	-1.8	0.0	X		137	2,6726		0,1,1,2427,1871	no	coding-synonymous,coding-synonymous	MAGEA6	NM_005363.2,NM_175868.1	,	0,1,1,4059,2441	CC,CT,C,TT,T		0.0297,0.0,0.0189	,	269/315,269/315	151870117	2,10560	2202	4300	6502	SO:0001819	synonymous_variant	4105	exon3			ATGCTATGAGTTC		CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"""MAGE-6 antigen"", ""melanoma-associated antigen 6"", ""melanoma antigen family A 6"", ""cancer/testis antigen family 1, member 6"""	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.807T>C	X.37:g.151870117T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_005363	A8IF93|Q6NW44	Silent	SNP	ENST00000329342.5	37	CCDS14708.1																																																																																			.	.	weak		0.527	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363	
DUSP4	1846	hgsc.bcm.edu	37	8	29197685	29197685	+	Missense_Mutation	SNP	G	G	A	rs371579846		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:29197685G>A	ENST00000240100.2	-	2	898	c.509C>T	c.(508-510)cCg>cTg	p.P170L	DUSP4_ENST00000240101.2_Missense_Mutation_p.P79L	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	170					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)		GGGGGGAACCGGGGGTGGGAT	0.602											OREG0018686	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P170L		Atlas-SNP	.											.	DUSP4	58	.	0			c.C509T						PASS	.	G	LEU/PRO,LEU/PRO	2,4404		0,2,2201	17.0	22.0	21.0		509,236	4.1	0.0	8		21	0,8600		0,0,4300	no	missense,missense	DUSP4	NM_001394.6,NM_057158.3	98,98	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging	170/395,79/304	29197685	2,13004	2203	4300	6503	SO:0001583	missense	1846	exon2			GGAACCGGGGGTG	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.509C>T	8.37:g.29197685G>A	ENSP00000240100:p.Pro170Leu	Somatic	47	0	0	807	WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	37	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.237221	0.39498	4.54E-4	0.0	ENSG00000120875	ENST00000240100;ENST00000240101	T;T	0.03413	4.17;3.94	5.01	4.13	0.48395	Rhodanese-like (1);	0.585786	0.16408	N	0.215753	T	0.03739	0.0106	L	0.42245	1.32	0.58432	D	0.999995	P;P	0.35774	0.458;0.519	B;B	0.24974	0.017;0.057	T	0.48433	-0.9036	10	0.59425	D	0.04	.	9.9081	0.41388	0.0962:0.0:0.9038:0.0	.	170;79	Q13115;G5E930	DUS4_HUMAN;.	L	170;79	ENSP00000240100:P170L;ENSP00000240101:P79L	ENSP00000240100:P170L	P	-	2	0	DUSP4	29253604	1.000000	0.71417	0.019000	0.16419	0.332000	0.28634	5.751000	0.68720	1.427000	0.47276	0.650000	0.86243	CCG	.	.	weak		0.602	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394	
CHD3	1107	hgsc.bcm.edu	37	17	7807904	7807904	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:7807904G>A	ENST00000330494.7	+	25	4189	c.4039G>A	c.(4039-4041)Gtt>Att	p.V1347I	SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000380358.4_Missense_Mutation_p.V1406I|CHD3_ENST00000358181.4_Missense_Mutation_p.V1347I	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1347					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TCGCAAGCAAGTTAACTACAA	0.547																																					p.V1406I		Atlas-SNP	.											.	CHD3	169	.	0			c.G4216A						PASS	.						98.0	82.0	87.0					17																	7807904		2203	4300	6503	SO:0001583	missense	1107	exon25			AAGCAAGTTAACT	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.4039G>A	17.37:g.7807904G>A	ENSP00000332628:p.Val1347Ile	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.177879	0.78564	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.91631	-2.88;-2.81;-2.82	4.9	4.9	0.64082	Domain of unknown function DUF1087 (1);	0.000000	0.41712	D	0.000823	D	0.95284	0.8470	M	0.64404	1.975	0.80722	D	1	D;D;D	0.69078	0.99;0.992;0.997	D;D;D	0.79108	0.98;0.989;0.992	D	0.95219	0.8332	10	0.54805	T	0.06	-19.8382	18.2591	0.90028	0.0:0.0:1.0:0.0	.	1347;1347;1406	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	I	1406;1347;1347	ENSP00000369716:V1406I;ENSP00000350907:V1347I;ENSP00000332628:V1347I	ENSP00000332628:V1347I	V	+	1	0	CHD3	7748629	1.000000	0.71417	0.869000	0.34112	0.998000	0.95712	9.263000	0.95617	2.539000	0.85634	0.561000	0.74099	GTT	.	.	none		0.547	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
POFUT2	23275	hgsc.bcm.edu	37	21	46707778	46707778	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46707778T>C	ENST00000349485.5	-	1	35	c.9A>G	c.(7-9)acA>acG	p.T3T	POFUT2_ENST00000331343.7_Silent_p.T3T|BX322557.10_ENST00000454115.2_RNA	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	3					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		CGAAGCTGAGTGTCGCCATGG	0.706																																					p.T3T		Atlas-SNP	.											.	POFUT2	77	.	0			c.A9G						PASS	.						5.0	6.0	6.0					21																	46707778		2017	3977	5994	SO:0001819	synonymous_variant	23275	exon1			GCTGAGTGTCGCC	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.9A>G	21.37:g.46707778T>C		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	20	12	0.6	NM_015227	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			.	.	none		0.706	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	
FAM198A	729085	hgsc.bcm.edu	37	3	43073761	43073761	+	Silent	SNP	G	G	A	rs658958	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:43073761G>A	ENST00000430121.2	+	2	101	c.6G>A	c.(4-6)gcG>gcA	p.A2A	KRBOX1_ENST00000443313.1_Intron|KRBOX1_ENST00000418093.2_3'UTR	NM_001129908.2	NP_001123380.2	Q9UFP1	F198A_HUMAN	family with sequence similarity 198, member A	2						extracellular region (GO:0005576)				endometrium(1)	1						TCTCTCAGGCGTCTTGGCTCC	0.527													G|||	2195	0.438299	0.3404	0.5331	5008	,	,		20480	0.6518		0.4066	False		,,,				2504	0.316				p.A2A		Atlas-SNP	.											FAM198A_ENST00000430121,caecum,carcinoma,0,1	FAM198A	23	1	0			c.G6A						PASS	.	G		454,930		72,310,310	27.0	26.0	27.0		6	-5.3	0.8	3	dbSNP_83	27	1298,1884		269,760,562	no	coding-synonymous	FAM198A	NM_001129908.2		341,1070,872	AA,AG,GG		40.792,32.8035,38.3706		2/576	43073761	1752,2814	692	1591	2283	SO:0001819	synonymous_variant	729085	exon2			TCAGGCGTCTTGG	AL117530	CCDS46808.1	3p22.1	2012-11-29	2009-10-19	2009-10-19	ENSG00000144649	ENSG00000144649			24485	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 41"""	C3orf41			Standard	NM_001129908		Approved	DKFZP434B172	uc003cmp.4	Q9UFP1	OTTHUMG00000156449	ENST00000430121.2:c.6G>A	3.37:g.43073761G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_001129908	B3KR48	Silent	SNP	ENST00000430121.2	37	CCDS46808.1																																																																																			G|0.533;A|0.467	0.467	strong		0.527	FAM198A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344240.3	NM_001129908	
HRNR	388697	hgsc.bcm.edu	37	1	152192395	152192395	+	Silent	SNP	G	G	A	rs61814946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152192395G>A	ENST00000368801.2	-	3	1785	c.1710C>T	c.(1708-1710)agC>agT	p.S570S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	570					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.S570S(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)			ATGGGCCACGGCTTGAAGACC	0.587													g|||	474	0.0946486	0.0045	0.0879	5008	,	,		20660	0.0942		0.1322	False		,,,				2504	0.183				p.S570S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	1	Substitution - coding silent(1)	stomach(1)	c.C1710T						PASS	.	G		125,4281		0,125,2078	175.0	184.0	181.0		1710	-7.4	0.0	1	dbSNP_129	181	1267,7333		107,1053,3140	no	coding-synonymous	HRNR	NM_001009931.1		107,1178,5218	AA,AG,GG		14.7326,2.837,10.7028		570/2851	152192395	1392,11614	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			GCCACGGCTTGAA	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.1710C>T	1.37:g.152192395G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	179	91	0.50838	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			G|0.895;A|0.105	0.105	strong		0.587	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
CCNG1	900	hgsc.bcm.edu	37	5	162868910	162868910	+	Missense_Mutation	SNP	T	T	G	rs11541970	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:162868910T>G	ENST00000340828.2	+	4	761	c.537T>G	c.(535-537)ttT>ttG	p.F179L	CCNG1_ENST00000510664.1_Missense_Mutation_p.F51L|CCNG1_ENST00000393929.1_Missense_Mutation_p.F179L|CCNG1_ENST00000511683.2_Missense_Mutation_p.F45L|CCNG1_ENST00000512163.1_Missense_Mutation_p.F45L|AC112205.1_ENST00000599797.1_Intron|CCNG1_ENST00000504553.1_Missense_Mutation_p.F45L	NM_004060.3	NP_004051.1	P51959	CCNG1_HUMAN	cyclin G1	179			F -> L (in dbSNP:rs11541970). {ECO:0000269|Ref.7}.		brain development (GO:0007420)|cell growth (GO:0016049)|mitotic G2 DNA damage checkpoint (GO:0007095)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|response to organonitrogen compound (GO:0010243)|syncytium formation (GO:0006949)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(2)	12	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0597)|OV - Ovarian serous cystadenocarcinoma(192;0.107)|Epithelial(171;0.164)		GCATTAATTTTGAAAGACTAG	0.274													T|||	89	0.0177716	0.0015	0.0245	5008	,	,		17785	0.0		0.0338	False		,,,				2504	0.0368				p.F179L		Atlas-SNP	.											.	CCNG1	28	.	0			c.T537G						PASS	.	T	LEU/PHE,LEU/PHE	31,4361	27.2+/-55.0	0,31,2165	41.0	44.0	43.0		537,537	5.9	1.0	5	dbSNP_120	43	304,8280	100.6+/-161.9	4,296,3992	yes	missense,missense	CCNG1	NM_004060.3,NM_199246.1	22,22	4,327,6157	GG,GT,TT		3.5415,0.7058,2.5817	benign,benign	179/296,179/296	162868910	335,12641	2196	4292	6488	SO:0001583	missense	900	exon5			TAATTTTGAAAGA	D78341	CCDS4360.1	5q32-q34	2010-11-15			ENSG00000113328	ENSG00000113328			1592	protein-coding gene	gene with protein product		601578		CCNG		8954786, 8806701	Standard	NM_004060		Approved		uc003lzb.3	P51959	OTTHUMG00000130380	ENST00000340828.2:c.537T>G	5.37:g.162868910T>G	ENSP00000344635:p.Phe179Leu	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	173	80	0.462428	NM_199246	B2R7B2|B4DLW7|D3DQK7|Q15757|Q96L32	Missense_Mutation	SNP	ENST00000340828.2	37	CCDS4360.1	35	0.016025641025641024	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	25	0.032981530343007916	T	1.855	-0.463985	0.04476	0.007058	0.035415	ENSG00000113328	ENST00000512163;ENST00000393929;ENST00000340828;ENST00000511683;ENST00000510664;ENST00000504553	T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98	5.94	5.94	0.96194	.	0.229984	0.48767	D	0.000180	T	0.01558	0.0050	N	0.04508	-0.205	0.43292	D	0.995278	B	0.02656	0.0	B	0.04013	0.001	T	0.20306	-1.0279	10	0.02654	T	1	1.7064	8.1647	0.31220	0.1328:0.0:0.1388:0.7284	rs11541970;rs12523365;rs17887122;rs52814352;rs11541970	179	P51959	CCNG1_HUMAN	L	45;179;179;45;51;45	ENSP00000424315:F45L;ENSP00000377506:F179L;ENSP00000344635:F179L;ENSP00000424141:F45L;ENSP00000422379:F51L;ENSP00000427086:F45L	ENSP00000344635:F179L	F	+	3	2	CCNG1	162801488	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.656000	0.37355	2.275000	0.75901	0.528000	0.53228	TTT	T|0.977;G|0.023	0.023	strong		0.274	CCNG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252750.3	NM_004060	
NPLOC4	55666	hgsc.bcm.edu	37	17	79526402	79526402	+	Silent	SNP	G	G	C	rs4073997	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79526402G>C	ENST00000331134.6	-	17	1925	c.1710C>G	c.(1708-1710)ggC>ggG	p.G570G	NPLOC4_ENST00000572760.1_Missense_Mutation_p.A35G|NPLOC4_ENST00000573876.1_Missense_Mutation_p.A35G	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	570					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CCCCGACGGCGCCGTACTCAT	0.617													G|||	834	0.166534	0.0257	0.3271	5008	,	,		16445	0.1052		0.2545	False		,,,				2504	0.2157				p.G570G		Atlas-SNP	.											NPLOC4,NS,carcinoma,0,1	NPLOC4	27	1	0			c.C1710G						scavenged	.	G		279,3853		7,265,1794	21.0	27.0	25.0		1710	-10.0	0.0	17	dbSNP_108	25	2421,5949		335,1751,2099	no	coding-synonymous	NPLOC4	NM_017921.2		342,2016,3893	CC,CG,GG		28.9247,6.7522,21.5965		570/609	79526402	2700,9802	2066	4185	6251	SO:0001819	synonymous_variant	55666	exon17			GACGGCGCCGTAC	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.1710C>G	17.37:g.79526402G>C		Somatic	239	2	0.0083682		WXS	Illumina HiSeq	Phase_I	254	128	0.503937	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Silent	SNP	ENST00000331134.6	37	CCDS45812.1																																																																																			G|0.821;C|0.179	0.179	strong		0.617	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1		
DPP4	1803	hgsc.bcm.edu	37	2	162929979	162929979	+	Silent	SNP	A	A	G	rs17574	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:162929979A>G	ENST00000360534.3	-	2	584	c.24T>C	c.(22-24)ctT>ctC	p.L8L	AC008063.2_ENST00000418335.1_RNA	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	8					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	GCAGTCCCAGAAGAACCTTCC	0.547													G|||	1065	0.21266	0.211	0.1744	5008	,	,		16929	0.0466		0.3459	False		,,,				2504	0.2761				p.L8L		Atlas-SNP	.											.	DPP4	90	.	0			c.T24C						PASS	.	G		1037,3369	726.6+/-409.7	121,795,1287	73.0	71.0	71.0		24	2.9	1.0	2	dbSNP_63	71	2979,5621	666.2+/-402.3	527,1925,1848	no	coding-synonymous	DPP4	NM_001935.3		648,2720,3135	GG,GA,AA		34.6395,23.5361,30.8781		8/767	162929979	4016,8990	2203	4300	6503	SO:0001819	synonymous_variant	1803	exon2			TCCCAGAAGAACC	M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.24T>C	2.37:g.162929979A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_001935	Q53TN1	Silent	SNP	ENST00000360534.3	37	CCDS2216.1																																																																																			A|0.720;G|0.280	0.280	strong		0.547	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2		
NUMA1	4926	hgsc.bcm.edu	37	11	71725281	71725281	+	Silent	SNP	G	G	A	rs200298289		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71725281G>A	ENST00000393695.3	-	15	3599	c.3268C>T	c.(3268-3270)Ctg>Ttg	p.L1090L	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Silent_p.L1090L|NUMA1_ENST00000351960.6_Intron	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TGTTCCTTCAGTTGCTTCACG	0.562			T	RARA	APL																																p.L1090L		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.C3268T						PASS	.						127.0	139.0	135.0					11																	71725281		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			CCTTCAGTTGCTT	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.3268C>T	11.37:g.71725281G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	209	104	0.497608	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			A|0.001;G|0.999	0.001	weak		0.562	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
SLC25A13	10165	hgsc.bcm.edu	37	7	95800820	95800820	+	Silent	SNP	T	T	C	rs2301629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:95800820T>C	ENST00000265631.5	-	12	1330	c.1194A>G	c.(1192-1194)ttA>ttG	p.L398L	SLC25A13_ENST00000542654.1_Silent_p.L290L|SLC25A13_ENST00000416240.2_Silent_p.L399L			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	398					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	CAACTCCCAATAACTGTGGCA	0.353													T|||	2049	0.409145	0.2481	0.3357	5008	,	,		19178	0.6071		0.3469	False		,,,				2504	0.5389				p.L399L		Atlas-SNP	.											SLC25A13,caecum,carcinoma,0,1	SLC25A13	131	1	0			c.A1197G						PASS	.	T	,	1175,3231	412.4+/-336.1	170,835,1198	82.0	79.0	80.0		1197,1194	-0.1	1.0	7	dbSNP_100	80	2989,5611	463.7+/-366.0	520,1949,1831	no	coding-synonymous,coding-synonymous	SLC25A13	NM_001160210.1,NM_014251.2	,	690,2784,3029	CC,CT,TT		34.7558,26.6682,32.016	,	399/677,398/676	95800820	4164,8842	2203	4300	6503	SO:0001819	synonymous_variant	10165	exon12			TCCCAATAACTGT	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.1194A>G	7.37:g.95800820T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	185	93	0.502703	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Silent	SNP	ENST00000265631.5	37	CCDS5645.1																																																																																			T|0.645;C|0.355	0.355	strong		0.353	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
P2RX3	5024	hgsc.bcm.edu	37	11	57114109	57114109	+	Missense_Mutation	SNP	G	G	A	rs34572680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57114109G>A	ENST00000263314.2	+	2	245	c.211G>A	c.(211-213)Gcc>Acc	p.A71T		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	71					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						CGGACTCTACGCCAACAGAGT	0.567													G|||	96	0.0191693	0.003	0.0375	5008	,	,		21427	0.004		0.0368	False		,,,				2504	0.0256				p.A71T		Atlas-SNP	.											.	P2RX3	55	.	0			c.G211A						PASS	.	G	THR/ALA	50,4352	50.2+/-85.5	0,50,2151	136.0	95.0	109.0		211	4.7	1.0	11	dbSNP_126	109	371,8221	123.1+/-182.0	8,355,3933	yes	missense	P2RX3	NM_002559.3	58	8,405,6084	AA,AG,GG		4.318,1.1358,3.24	possibly-damaging	71/398	57114109	421,12573	2201	4296	6497	SO:0001583	missense	5024	exon2			CTCTACGCCAACA	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.211G>A	11.37:g.57114109G>A	ENSP00000263314:p.Ala71Thr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	37	CCDS7953.1	48	0.02197802197802198	2	0.0040650406504065045	12	0.03314917127071823	4	0.006993006993006993	30	0.0395778364116095	G	13.93	2.384147	0.42308	0.011358	0.04318	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.04156	3.69	4.66	4.66	0.58398	.	0.243784	0.41605	D	0.000844	T	0.00580	0.0019	N	0.04508	-0.205	0.29540	N	0.852188	P	0.45212	0.853	B	0.38106	0.265	T	0.34054	-0.9844	10	0.56958	D	0.05	-25.3858	8.6535	0.34049	0.1014:0.0:0.8986:0.0	rs34572680;rs58315342	71	P56373	P2RX3_HUMAN	T	71	ENSP00000263314:A71T	ENSP00000263314:A71T	A	+	1	0	P2RX3	56870685	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	3.662000	0.54510	2.408000	0.81797	0.561000	0.74099	GCC	G|0.971;A|0.029	0.029	strong		0.567	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
TRDMT1	1787	hgsc.bcm.edu	37	10	17199778	17199778	+	Silent	SNP	C	C	A	rs11254408	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:17199778C>A	ENST00000377799.3	-	8	596	c.549G>T	c.(547-549)ctG>ctT	p.L183L	TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000488990.1_Silent_p.L60L|TRDMT1_ENST00000412821.3_Silent_p.L159L|TRDMT1_ENST00000351358.4_Silent_p.L137L|TRDMT1_ENST00000377766.5_Missense_Mutation_p.D112Y|TRDMT1_ENST00000457442.2_Silent_p.L102L|TRDMT1_ENST00000358282.7_3'UTR	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	183	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	GGAACTCCATCAGTACCTGGC	0.303													C|||	579	0.115615	0.1006	0.2176	5008	,	,		19108	0.0387		0.1511	False		,,,				2504	0.1063				p.L183L		Atlas-SNP	.											.	TRDMT1	46	.	0			c.G549T						PASS	.	C		490,3916	212.8+/-232.6	30,430,1743	58.0	54.0	55.0		549	2.7	1.0	10	dbSNP_120	55	1191,7405	237.4+/-269.2	84,1023,3191	no	coding-synonymous	TRDMT1	NM_004412.5		114,1453,4934	AA,AC,CC		13.8553,11.1212,12.9288		183/392	17199778	1681,11321	2203	4298	6501	SO:0001819	synonymous_variant	1787	exon8			CTCCATCAGTACC	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.549G>T	10.37:g.17199778C>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	32	20	0.625	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1	249	0.11401098901098901	47	0.09552845528455285	79	0.21823204419889503	22	0.038461538461538464	101	0.13324538258575197	C	4.516	0.095704	0.08681	0.111212	0.138553	ENSG00000107614	ENST00000377766;ENST00000313936	.	.	.	5.62	2.73	0.32206	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999746285	.	.	.	.	.	.	T	0.20672	-1.0268	3	.	.	.	-10.0428	2.5502	0.04747	0.1307:0.5243:0.1415:0.2035	rs11254408;rs17846414;rs17859458;rs52813160;rs57865105;rs11254408	.	.	.	Y	112;117	.	.	D	-	1	0	TRDMT1	17239784	0.979000	0.34478	1.000000	0.80357	0.260000	0.26232	0.517000	0.22832	0.841000	0.35020	-0.219000	0.12488	GAT	C|0.884;A|0.116	0.116	strong		0.303	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
PRMT6	55170	hgsc.bcm.edu	37	1	107599918	107599918	+	Missense_Mutation	SNP	C	C	T	rs2232016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:107599918C>T	ENST00000370078.1	+	1	618	c.581C>T	c.(580-582)gCc>gTc	p.A194V	PRMT6_ENST00000361318.5_Missense_Mutation_p.A135V			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	194	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.		A -> V (in dbSNP:rs2232016). {ECO:0000269|PubMed:15489334}.		base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)			biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		CTCTTCATAGCCCCCATCAGC	0.642													C|||	627	0.1252	0.0098	0.0865	5008	,	,		17486	0.1448		0.1918	False		,,,				2504	0.2198				p.A194V		Atlas-SNP	.											.	PRMT6	55	.	0			c.C581T						PASS	.	C	VAL/ALA	175,3777		2,171,1803	35.0	37.0	37.0		581	5.5	1.0	1	dbSNP_98	37	1727,6597		160,1407,2595	yes	missense	PRMT6	NM_018137.2	64	162,1578,4398	TT,TC,CC		20.7472,4.4281,15.4936	probably-damaging	194/376	107599918	1902,10374	1976	4162	6138	SO:0001583	missense	55170	exon1			TCATAGCCCCCAT	AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"""Protein arginine methyltransferases"""	18241	protein-coding gene	gene with protein product		608274	"""HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"""	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.581C>T	1.37:g.107599918C>T	ENSP00000359095:p.Ala194Val	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	102	55	0.539216	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Missense_Mutation	SNP	ENST00000370078.1	37	CCDS41360.2	280	0.1282051282051282	8	0.016260162601626018	30	0.08287292817679558	89	0.1555944055944056	153	0.20184696569920843	C	31	5.100072	0.94197	0.044281	0.207472	ENSG00000198890	ENST00000361318;ENST00000370078	T;T	0.22336	1.96;1.96	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.16471	0.0396	M	0.62723	1.935	0.09310	P	0.99999585951	P	0.37997	0.614	B	0.39379	0.298	T	0.03148	-1.1067	9	0.33940	T	0.23	-17.7437	16.9117	0.86142	0.0:1.0:0.0:0.0	rs2232016;rs3748839;rs52822166;rs59101028;rs2232016	194	Q96LA8	ANM6_HUMAN	V	135;194	ENSP00000355145:A135V;ENSP00000359095:A194V	ENSP00000355145:A135V	A	+	2	0	PRMT6	107401441	0.952000	0.32445	0.991000	0.47740	0.981000	0.71138	3.666000	0.54540	2.584000	0.87258	0.442000	0.29010	GCC	C|0.849;T|0.151	0.151	strong		0.642	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137	
ELF3	1999	hgsc.bcm.edu	37	1	201981774	201981774	+	Missense_Mutation	SNP	G	G	A	rs55729978	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201981774G>A	ENST00000359651.3	+	4	3677	c.485G>A	c.(484-486)gGc>gAc	p.G162D	RP11-465N4.4_ENST00000419190.1_RNA|RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.G162D|ELF3_ENST00000367284.5_Missense_Mutation_p.G162D					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						CCAGACCAGGGCAGCCCCTTT	0.642													G|||	364	0.0726837	0.2421	0.0159	5008	,	,		14680	0.0		0.0229	False		,,,				2504	0.0102				p.G162D		Atlas-SNP	.											ELF3_ENST00000359651,NS,carcinoma,0,2	ELF3	92	2	0			c.G485A						PASS	.	G	ASP/GLY,ASP/GLY	690,3716		51,588,1564	28.0	34.0	32.0		485,485	3.3	1.0	1	dbSNP_129	32	147,8451		1,145,4153	yes	missense,missense	ELF3	NM_001114309.1,NM_004433.4	94,94	52,733,5717	AA,AG,GG		1.7097,15.6605,6.4365	benign,benign	162/372,162/372	201981774	837,12167	2203	4299	6502	SO:0001583	missense	1999	exon5			ACCAGGGCAGCCC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.485G>A	1.37:g.201981774G>A	ENSP00000352673:p.Gly162Asp	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	96	40	0.416667	NM_001114309		Missense_Mutation	SNP	ENST00000359651.3	37	CCDS1419.1	157	0.07188644688644688	129	0.2621951219512195	9	0.024861878453038673	0	0.0	19	0.025065963060686015	G	10.76	1.441663	0.25900	0.156605	0.017097	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044;ENST00000446188	T;T;T;T	0.56103	2.47;2.47;2.47;0.48	5.2	3.29	0.37713	.	0.821186	0.11026	N	0.607832	T	0.00012	0.0000	L	0.37561	1.115	0.27380	P	0.9554544	B	0.10296	0.003	B	0.09377	0.004	T	0.09796	-1.0658	9	0.37606	T	0.19	.	7.8653	0.29533	0.0862:0.164:0.7499:0.0	rs55729978	162	P78545	ELF3_HUMAN	D	162;162;162;162;160	ENSP00000352673:G162D;ENSP00000356253:G162D;ENSP00000356252:G162D;ENSP00000405162:G160D	ENSP00000311348:G162D	G	+	2	0	ELF3	200248397	0.174000	0.23070	0.988000	0.46212	0.681000	0.39784	0.316000	0.19469	1.168000	0.42723	0.655000	0.94253	GGC	G|0.938;A|0.062	0.062	strong		0.642	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37455581	37455581	+	Missense_Mutation	SNP	G	G	A	rs372025602		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:37455581G>A	ENST00000374660.1	+	19	2044	c.1945G>A	c.(1945-1947)Gcg>Acg	p.A649T	ANKRD30A_ENST00000602533.1_Intron|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.A649T			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	586					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						ACCCAAGGCTGCGCATCAAAA	0.299																																					p.A649T		Atlas-SNP	.											ANKRD30A,NS,haematopoietic_neoplasm,-1,1	ANKRD30A	448	1	0			c.G1945A						scavenged	.						3.0	3.0	3.0					10																	37455581		1392	3131	4523	SO:0001583	missense	91074	exon19			AAGGCTGCGCATC	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	ENST00000374660.1:c.1945G>A	10.37:g.37455581G>A	ENSP00000363792:p.Ala649Thr	Somatic	732	0	0		WXS	Illumina HiSeq	Phase_I	633	12	0.0189573	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000374660.1	37		.	.	.	.	.	.	.	.	.	.	.	0.005	-2.154522	0.00325	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.04706	3.57;3.57	0.8	-1.46	0.08800	.	.	.	.	.	T	0.01765	0.0056	N	0.03948	-0.315	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.46091	-0.9216	9	0.07813	T	0.8	.	5.9694	0.19342	0.3251:0.0:0.6749:0.0	.	705	Q9BXX3	AN30A_HUMAN	T	649	ENSP00000354432:A649T;ENSP00000363792:A649T	ENSP00000354432:A649T	A	+	1	0	ANKRD30A	37495587	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.427000	0.06999	-1.633000	0.01539	-1.346000	0.01242	GCG	GCG|0.500;ACA|0.500	.	alt		0.299	ANKRD30A-002	PUTATIVE	NMD_exception|basic	protein_coding	protein_coding	OTTHUMT00000047589.2	NM_052997	
TAF5L	27097	hgsc.bcm.edu	37	1	229730452	229730452	+	Silent	SNP	G	G	A	rs2295625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:229730452G>A	ENST00000366676.1	-	4	1361	c.1362C>T	c.(1360-1362)agC>agT	p.S454S	TAF5L_ENST00000258281.2_Silent_p.S454S			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	454					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CCTGCTGAGCGCTCCACAGCC	0.572													G|||	1520	0.303514	0.0938	0.2666	5008	,	,		20263	0.3254		0.4612	False		,,,				2504	0.4284				p.S454S		Atlas-SNP	.											.	TAF5L	76	.	0			c.C1362T						PASS	.	G		649,3757	274.6+/-272.0	44,561,1598	82.0	86.0	85.0		1362	-5.3	0.0	1	dbSNP_100	85	3987,4613	548.2+/-385.3	931,2125,1244	no	coding-synonymous	TAF5L	NM_014409.3		975,2686,2842	AA,AG,GG		46.3605,14.7299,35.6451		454/590	229730452	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	27097	exon5			CTGAGCGCTCCAC	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"""WD repeat domain containing"""	17304	protein-coding gene	gene with protein product	"""PCAF associated factor 65 beta"""		"""TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.1362C>T	1.37:g.229730452G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	124	68	0.548387	NM_014409	Q5TDI5|Q5TDI6|Q8IW31	Silent	SNP	ENST00000366676.1	37	CCDS1581.1																																																																																			G|0.674;A|0.326	0.326	strong		0.572	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409	
ITGAE	3682	hgsc.bcm.edu	37	17	3632836	3632836	+	Missense_Mutation	SNP	G	G	A	rs1716	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3632836G>A	ENST00000263087.4	-	24	2946	c.2848C>T	c.(2848-2850)Cgg>Tgg	p.R950W	ITGAE_ENST00000571185.1_Intron|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)	950			R -> W (in dbSNP:rs1716). {ECO:0000269|PubMed:10673275}.		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)		GCCAAAGACCGTCTTTCATTG	0.498													G|||	1329	0.265375	0.0537	0.1599	5008	,	,		21959	0.2956		0.3221	False		,,,				2504	0.5368				p.R950W	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.C2848T	GRCh37	CM065287	ITGAE	M	rs1716	PASS	.	G	TRP/ARG	417,3989	204.5+/-226.7	25,367,1811	217.0	173.0	188.0		2848	-0.3	0.0	17	dbSNP_36	188	2871,5729	451.3+/-362.6	473,1925,1902	yes	missense	ITGAE	NM_002208.4	101	498,2292,3713	AA,AG,GG		33.3837,9.4644,25.2806	probably-damaging	950/1180	3632836	3288,9718	2203	4300	6503	SO:0001583	missense	3682	exon24			AAGACCGTCTTTC	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.2848C>T	17.37:g.3632836G>A	ENSP00000263087:p.Arg950Trp	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	133	129	0.969925	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	511	0.23397435897435898	25	0.0508130081300813	65	0.17955801104972377	174	0.3041958041958042	247	0.3258575197889182	G	15.97	2.990592	0.54041	0.094644	0.333837	ENSG00000083457	ENST00000263087	T	0.47177	0.85	4.6	-0.312	0.12758	Integrin alpha-2 (1);	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	D	0.76494	0.999	P	0.57679	0.825	T	0.15263	-1.0443	8	0.66056	D	0.02	.	1.8277	0.03124	0.1589:0.0972:0.3601:0.3838	rs1716;rs52790797;rs56955069;rs1716	950	P38570	ITAE_HUMAN	W	950	ENSP00000263087:R950W	ENSP00000263087:R950W	R	-	1	2	ITGAE	3579585	0.000000	0.05858	0.000000	0.03702	0.246000	0.25737	-0.208000	0.09371	0.007000	0.14760	-0.262000	0.10625	CGG	G|0.755;A|0.245	0.245	strong		0.498	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
PKHD1	5314	hgsc.bcm.edu	37	6	51491884	51491884	+	Missense_Mutation	SNP	T	T	C	rs4715227	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:51491884T>C	ENST00000371117.3	-	66	11971	c.11696A>G	c.(11695-11697)cAg>cGg	p.Q3899R		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3899			Q -> R (in dbSNP:rs4715227). {ECO:0000269|PubMed:12846734, ECO:0000269|PubMed:12874454}.		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)					ATTATTAGTCTGGGATTCAGG	0.388													T|||	2771	0.553315	0.4569	0.5937	5008	,	,		18238	0.5813		0.5358	False		,,,				2504	0.6442				p.Q3899R		Atlas-SNP	.											.	PKHD1	927	.	0			c.A11696G						PASS	.	T	ARG/GLN	2120,2286	577.4+/-384.4	528,1064,611	241.0	243.0	243.0		11696	4.0	1.0	6	dbSNP_111	243	4690,3910	605.3+/-394.9	1270,2150,880	yes	missense	PKHD1	NM_138694.3	43	1798,3214,1491	CC,CT,TT		45.4651,48.1162,47.6396	benign	3899/4075	51491884	6810,6196	2203	4300	6503	SO:0001583	missense	5314	exon66			TTAGTCTGGGATT	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.11696A>G	6.37:g.51491884T>C	ENSP00000360158:p.Gln3899Arg	Somatic	188	1	0.00531915		WXS	Illumina HiSeq	Phase_I	168	167	0.994048	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	1181	0.5407509157509157	222	0.45121951219512196	213	0.5883977900552486	332	0.5804195804195804	414	0.5461741424802111	T	10.02	1.237296	0.22711	0.481162	0.545349	ENSG00000170927	ENST00000371117	D	0.87809	-2.3	5.19	3.99	0.46301	.	0.707453	0.12437	N	0.469060	T	0.75925	0.3916	L	0.59436	1.845	0.09310	P	0.99999999935508	B	0.30793	0.295	B	0.31686	0.134	T	0.72151	-0.4377	9	0.66056	D	0.02	.	8.2376	0.31636	0.1768:0.0:0.0:0.8232	rs4715227;rs52814903;rs56452478;rs58387623;rs4715227	3899	P08F94	PKHD1_HUMAN	R	3899	ENSP00000360158:Q3899R	ENSP00000360158:Q3899R	Q	-	2	0	PKHD1	51599843	0.981000	0.34729	0.954000	0.39281	0.169000	0.22640	1.965000	0.40471	1.048000	0.40298	0.533000	0.62120	CAG	T|0.467;C|0.533	0.533	strong		0.388	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
TAMM41	132001	hgsc.bcm.edu	37	3	11880760	11880760	+	Missense_Mutation	SNP	T	T	C	rs7641243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:11880760T>C	ENST00000444133.2	-	3	489	c.347A>G	c.(346-348)aAc>aGc	p.N116S	TAMM41_ENST00000273037.5_Missense_Mutation_p.N116S|TAMM41_ENST00000455809.1_Missense_Mutation_p.N116S			Q96BW9	TAM41_HUMAN	TAM41, mitochondrial translocator assembly and maintenance protein, homolog (S. cerevisiae)	116			N -> S (in dbSNP:rs7641243).		cardiolipin biosynthetic process (GO:0032049)|CDP-diacylglycerol biosynthetic process (GO:0016024)	extrinsic component of mitochondrial inner membrane (GO:0031314)	phosphatidate cytidylyltransferase activity (GO:0004605)										AATCAGAACGTTAGTGCTAAT	0.353													T|||	933	0.186302	0.1853	0.1095	5008	,	,		19113	0.2381		0.1153	False		,,,				2504	0.2618				p.N116S		Atlas-SNP	.											.	.	.	.	0			c.A347G						PASS	.	T	SER/ASN	750,3656	308.8+/-290.8	64,622,1517	94.0	92.0	93.0		347	0.7	0.0	3	dbSNP_116	93	963,7637	208.9+/-250.2	55,853,3392	yes	missense	TAMM41	NM_138807.2	46	119,1475,4909	CC,CT,TT		11.1977,17.0222,13.1708	benign	116/317	11880760	1713,11293	2203	4300	6503	SO:0001583	missense	132001	exon3			AGAACGTTAGTGC		CCDS2607.1, CCDS68345.1	3p25.2	2013-10-18	2011-08-09	2011-08-09	ENSG00000144559	ENSG00000144559			25187	protein-coding gene	gene with protein product		614948	"""chromosome 3 open reading frame 31"""	C3orf31		19237595	Standard	XM_005264873		Approved	MGC16471, DKFZp434E0519	uc003bwh.3	Q96BW9	OTTHUMG00000129741	ENST00000444133.2:c.347A>G	3.37:g.11880760T>C	ENSP00000388598:p.Asn116Ser	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_138807	B4DIY7|C9J2U4	Missense_Mutation	SNP	ENST00000444133.2	37		335	0.1533882783882784	75	0.1524390243902439	37	0.10220994475138122	135	0.23601398601398602	88	0.11609498680738786	T	3.784	-0.045076	0.07452	0.170222	0.111977	ENSG00000144559	ENST00000455809;ENST00000273037;ENST00000444133	T;T;T	0.28454	1.61;1.61;1.61	5.3	0.686	0.18015	.	0.588590	0.19358	N	0.116225	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.14012	0.009;0.0;0.0	B;B;B	0.18871	0.023;0.001;0.001	T	0.42189	-0.9466	9	0.22109	T	0.4	-23.6775	6.8204	0.23855	0.0:0.3744:0.0:0.6256	rs7641243;rs57899216;rs7641243	116;116;116	B4DIY7;C9J2U4;Q96BW9	.;.;TAM41_HUMAN	S	116	ENSP00000398596:N116S;ENSP00000273037:N116S;ENSP00000388598:N116S	ENSP00000273037:N116S	N	-	2	0	TAMM41	11855760	0.089000	0.21612	0.000000	0.03702	0.408000	0.30992	2.998000	0.49465	0.240000	0.21263	-1.064000	0.02280	AAC	T|0.854;C|0.146	0.146	strong		0.353	TAMM41-008	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000339258.2	NM_138807	
DENND5A	23258	hgsc.bcm.edu	37	11	9225486	9225486	+	Missense_Mutation	SNP	C	C	G	rs952374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:9225486C>G	ENST00000328194.3	-	4	990	c.670G>C	c.(670-672)Gag>Cag	p.E224Q	DENND5A_ENST00000530044.1_Missense_Mutation_p.E224Q	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	224	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.		E -> Q (in dbSNP:rs952374). {ECO:0000269|PubMed:10470851, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						TGGAGTTGCTCCAGCACGCTC	0.552													C|||	1879	0.3752	0.2103	0.464	5008	,	,		20880	0.4573		0.2773	False		,,,				2504	0.5511				p.E224Q		Atlas-SNP	.											.	DENND5A	84	.	0			c.G670C						PASS	.	C	GLN/GLU	973,3429	366.6+/-317.9	119,735,1347	95.0	80.0	85.0		670	4.5	1.0	11	dbSNP_86	85	2407,6185	400.1+/-346.7	368,1671,2257	yes	missense	DENND5A	NM_015213.3	29	487,2406,3604	GG,GC,CC		28.0144,22.1036,26.012	benign	224/1288	9225486	3380,9614	2201	4296	6497	SO:0001583	missense	23258	exon4			GTTGCTCCAGCAC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.670G>C	11.37:g.9225486C>G	ENSP00000328524:p.Glu224Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	118	48	0.40678	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	37	CCDS31423.1	744	0.34065934065934067	111	0.22560975609756098	160	0.4419889502762431	268	0.46853146853146854	205	0.2704485488126649	C	8.966	0.971813	0.18736	0.221036	0.280144	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.11712	2.75;2.75	5.42	4.49	0.54785	DENN (3);	0.159837	0.56097	N	0.000030	T	0.00012	0.0000	N	0.10874	0.06	0.09310	P	1.0	B;B	0.20550	0.046;0.002	B;B	0.19148	0.024;0.014	T	0.45585	-0.9251	9	0.15066	T	0.55	.	15.7483	0.77965	0.0:0.8585:0.1415:0.0	rs952374;rs3813397;rs52811808;rs952374	224;224	E9PS91;Q6IQ26	.;DEN5A_HUMAN	Q	224	ENSP00000328524:E224Q;ENSP00000435866:E224Q	ENSP00000328524:E224Q	E	-	1	0	DENND5A	9182062	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.220000	0.42908	1.233000	0.43693	0.650000	0.86243	GAG	C|0.715;G|0.285	0.285	strong		0.552	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
TBC1D10A	83874	hgsc.bcm.edu	37	22	30700607	30700607	+	Silent	SNP	T	T	G	rs4823089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30700607T>G	ENST00000215790.7	-	2	386	c.222A>C	c.(220-222)gtA>gtC	p.V74V	TBC1D10A_ENST00000403477.3_Silent_p.V81V|TBC1D10A_ENST00000403362.1_5'UTR|TBC1D10A_ENST00000490449.1_5'UTR	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	74					activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)			cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						CCTCCAGGGGTACTTCCTCCA	0.607													G|||	792	0.158147	0.1384	0.1571	5008	,	,		21842	0.1448		0.2535	False		,,,				2504	0.1012				p.V81V		Atlas-SNP	.											.	TBC1D10A	49	.	0			c.A243C						PASS	.	G	,	682,3724	762.1+/-413.1	57,568,1578	78.0	60.0	66.0		243,222	-1.9	1.0	22	dbSNP_111	66	2208,6392	709.0+/-405.7	288,1632,2380	no	coding-synonymous,coding-synonymous	TBC1D10A	NM_001204240.1,NM_031937.2	,	345,2200,3958	GG,GT,TT		25.6744,15.4789,22.2205	,	81/516,74/509	30700607	2890,10116	2203	4300	6503	SO:0001819	synonymous_variant	83874	exon2			CAGGGGTACTTCC	AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"""EBP50-PDZ interactor of 64 kD"""	610020	"""TBC1 domain family, member 10"""	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.222A>C	22.37:g.30700607T>G		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	90	90	1	NM_001204240	B3KXT8|O76053|Q20WK7|Q543A2	Silent	SNP	ENST00000215790.7	37	CCDS13874.1																																																																																			T|0.801;G|0.199	0.199	strong		0.607	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937	
CPED1	79974	hgsc.bcm.edu	37	7	120764477	120764477	+	Silent	SNP	G	G	C	rs1524498	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:120764477G>C	ENST00000310396.5	+	8	1478	c.1011G>C	c.(1009-1011)gcG>gcC	p.A337A	CPED1_ENST00000450913.2_Silent_p.A337A|CPED1_ENST00000423795.1_Silent_p.A117A	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	337						endoplasmic reticulum (GO:0005783)											TACTGCTAGCGGCTGAAGTAT	0.373																																					p.A337A		Atlas-SNP	.											.	.	.	.	0			c.G1011C						PASS	.	G	,	1139,3267	405.1+/-333.4	148,843,1212	78.0	77.0	77.0		1011,1011	-0.9	1.0	7	dbSNP_88	77	3818,4782	538.0+/-383.3	859,2100,1341	no	coding-synonymous,coding-synonymous	C7orf58	NM_001105533.1,NM_024913.4	,	1007,2943,2553	CC,CG,GG		44.3953,25.8511,38.1132	,	337/784,337/1027	120764477	4957,8049	2203	4300	6503	SO:0001819	synonymous_variant	79974	exon7			GCTAGCGGCTGAA		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.1011G>C	7.37:g.120764477G>C		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	108	52	0.481481	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Silent	SNP	ENST00000310396.5	37	CCDS34739.1																																																																																			G|0.561;C|0.439	0.439	strong		0.373	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
MAT2A	4144	hgsc.bcm.edu	37	2	85769711	85769711	+	Silent	SNP	C	C	G	rs1078004	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:85769711C>G	ENST00000306434.3	+	7	915	c.792C>G	c.(790-792)cgC>cgG	p.R264R	MAT2A_ENST00000409017.1_Silent_p.R201R	NM_005911.5	NP_005902.1	P31153	METK2_HUMAN	methionine adenosyltransferase II, alpha	264					cellular nitrogen compound metabolic process (GO:0034641)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|S-adenosylmethionine biosynthetic process (GO:0006556)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|methionine adenosyltransferase complex (GO:0048269)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|methionine adenosyltransferase activity (GO:0004478)	p.R264R(1)		breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	9					L-Methionine(DB00134)|S-Adenosylmethionine(DB00118)	TGACTGGACGCAAAATCATTG	0.453													G|||	2468	0.492812	0.7194	0.3934	5008	,	,		20209	0.3859		0.494	False		,,,				2504	0.3661				p.R264R		Atlas-SNP	.											MAT2A,NS,carcinoma,0,1	MAT2A	23	1	1	Substitution - coding silent(1)	stomach(1)	c.C792G						scavenged	.	G		2978,1428	464.2+/-353.8	1016,946,241	132.0	141.0	138.0		792	2.8	1.0	2	dbSNP_86	138	3955,4645	602.6+/-394.5	911,2133,1256	yes	coding-synonymous	MAT2A	NM_005911.5		1927,3079,1497	GG,GC,CC		45.9884,32.4103,46.6938		264/396	85769711	6933,6073	2203	4300	6503	SO:0001819	synonymous_variant	4144	exon7			TGGACGCAAAATC		CCDS1977.1	2p11.2	2008-06-03			ENSG00000168906	ENSG00000168906			6904	protein-coding gene	gene with protein product		601468				1426236, 9703951	Standard	NM_005911		Approved	SAMS2, MATA2, MATII	uc002spr.3	P31153	OTTHUMG00000130174	ENST00000306434.3:c.792C>G	2.37:g.85769711C>G		Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	191	88	0.460733	NM_005911	A8K511|B4DN45|D6W5L1|Q53SP5	Silent	SNP	ENST00000306434.3	37	CCDS1977.1																																																																																			C|0.483;G|0.517	0.517	strong		0.453	MAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252491.2	NM_005911	
XIRP2	129446	hgsc.bcm.edu	37	2	168104370	168104370	+	Silent	SNP	A	A	C	rs61748715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168104370A>C	ENST00000409195.1	+	9	6557	c.6468A>C	c.(6466-6468)acA>acC	p.T2156T	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.T1934T|XIRP2_ENST00000295237.9_Silent_p.T2156T|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1981	Pro-rich.				actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TAACTGATACACAAAGCTCCA	0.408													A|||	865	0.172724	0.2882	0.1196	5008	,	,		16320	0.12		0.1123	False		,,,				2504	0.1708				p.T2156T		Atlas-SNP	.											.	XIRP2	914	.	0			c.A6468C						PASS	.	A	,,,,	949,2749		133,683,1033	39.0	38.0	38.0		,,5802,,6468	-3.4	0.0	2	dbSNP_129	38	792,7392		43,706,3343	no	intron,intron,coding-synonymous,intron,coding-synonymous	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,,,	176,1389,4376	CC,CA,AA		9.6774,25.6625,14.6524	,,,,	,,1934/3328,,2156/3550	168104370	1741,10141	1849	4092	5941	SO:0001819	synonymous_variant	129446	exon9			TGATACACAAAGC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6468A>C	2.37:g.168104370A>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	84	34	0.404762	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			A|0.860;C|0.140	0.140	strong		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
DOC2A	8448	hgsc.bcm.edu	37	16	30017985	30017985	+	Missense_Mutation	SNP	C	C	T	rs201869632		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30017985C>T	ENST00000350119.4	-	9	1082	c.892G>A	c.(892-894)Gat>Aat	p.D298N	DOC2A_ENST00000564979.1_Missense_Mutation_p.D298N|DOC2A_ENST00000564944.1_Missense_Mutation_p.D298N	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	298	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Interaction with UNC13D.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						TTGTCCACATCGGGCCTCAGG	0.602													c|||	1	0.000199681	0.0	0.0	5008	,	,		17833	0.001		0.0	False		,,,				2504	0.0				p.D298N		Atlas-SNP	.											DOC2A,caecum,carcinoma,+2,1	DOC2A	40	1	0			c.G892A						scavenged	.						152.0	135.0	141.0					16																	30017985		2197	4300	6497	SO:0001583	missense	8448	exon9			CCACATCGGGCCT	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.892G>A	16.37:g.30017985C>T	ENSP00000340017:p.Asp298Asn	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	126	2	0.015873	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	37	CCDS10666.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	14.62	2.589120	0.46110	.	.	ENSG00000149927	ENST00000350119	T	0.72942	-0.7	5.64	5.64	0.86602	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.56097	D	0.000031	T	0.78541	0.4299	L	0.48260	1.515	0.47905	D	0.999547	D	0.89917	1.0	D	0.78314	0.991	T	0.71066	-0.4700	10	0.13853	T	0.58	.	17.5629	0.87912	0.0:1.0:0.0:0.0	.	298	Q14183	DOC2A_HUMAN	N	298	ENSP00000340017:D298N	ENSP00000340017:D298N	D	-	1	0	DOC2A	29925486	1.000000	0.71417	0.805000	0.32314	0.278000	0.26855	7.443000	0.80521	2.821000	0.97095	0.651000	0.88453	GAT	C|1.000;T|0.000	0.000	strong		0.602	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
FAM65B	9750	hgsc.bcm.edu	37	6	24828490	24828490	+	Missense_Mutation	SNP	C	C	T	rs9461073	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:24828490C>T	ENST00000259698.4	-	19	2778	c.2603G>A	c.(2602-2604)cGg>cAg	p.R868Q	FAM65B_ENST00000538035.1_Missense_Mutation_p.R847Q	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	868			R -> Q (in dbSNP:rs9461073). {ECO:0000269|PubMed:9205841}.		cell differentiation (GO:0030154)|muscle organ development (GO:0007517)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	25						AGGCTCAGCCCGGTCCAGAAT	0.483													C|||	1136	0.226837	0.3812	0.2161	5008	,	,		18254	0.1786		0.172	False		,,,				2504	0.1319				p.R868Q		Atlas-SNP	.											.	FAM65B	134	.	0			c.G2603A						PASS	.	C	GLN/ARG	479,905		99,281,312	48.0	47.0	47.0		2603	1.1	0.1	6	dbSNP_119	47	621,2561		61,499,1031	yes	missense	FAM65B	NM_014722.2	43	160,780,1343	TT,TC,CC		19.516,34.6098,24.0911	probably-damaging	868/1069	24828490	1100,3466	692	1591	2283	SO:0001583	missense	9750	exon19			TCAGCCCGGTCCA	U49187	CCDS47383.1, CCDS47384.1, CCDS69057.1, CCDS69058.1, CCDS75410.1	6p22.3-p21.32	2012-11-30	2008-06-13	2008-06-13	ENSG00000111913	ENSG00000111913			13872	protein-coding gene	gene with protein product	"""myogenesis-related and NCAM-associated protein homolog (chicken)"""	611410	"""chromosome 6 open reading frame 32"""	C6orf32		9205841, 17150207, 17825087	Standard	NM_001286447		Approved	KIAA0386, DIFF48, MYONAP	uc003neo.1	Q9Y4F9	OTTHUMG00000014375	ENST00000259698.4:c.2603G>A	6.37:g.24828490C>T	ENSP00000259698:p.Arg868Gln	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	501	0.22939560439560439	172	0.34959349593495936	82	0.2265193370165746	117	0.20454545454545456	130	0.17150395778364116	C	8.286	0.816702	0.16607	0.346098	0.19516	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.77489	-1.1;-1.1	5.92	1.15	0.20763	.	0.325476	0.35466	N	0.003186	T	0.54303	0.1850	M	0.63843	1.955	0.23882	P	0.9965719	B;B	0.25390	0.068;0.125	B;B	0.16722	0.007;0.016	T	0.38329	-0.9666	9	0.23302	T	0.38	-8.9543	11.5826	0.50900	0.0:0.6318:0.0:0.3682	rs9461073;rs12183109;rs52829952;rs56611383;rs61535973;rs12183109	847;868	F5GX51;Q9Y4F9	.;FA65B_HUMAN	Q	868;847	ENSP00000259698:R868Q;ENSP00000441138:R847Q	ENSP00000259698:R868Q	R	-	2	0	FAM65B	24936469	0.986000	0.35501	0.050000	0.19076	0.446000	0.32137	2.234000	0.43035	-0.061000	0.13110	-1.945000	0.00491	CGG	C|0.769;G|0.000;T|0.230	0.230	strong		0.483	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2		
ALMS1	7840	hgsc.bcm.edu	37	2	73679990	73679990	+	Missense_Mutation	SNP	T	T	A	rs6724782	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73679990T>A	ENST00000264448.6	+	8	6444	c.6333T>A	c.(6331-6333)agT>agA	p.S2111R	ALMS1_ENST00000409009.1_Missense_Mutation_p.S2069R|ALMS1_ENST00000377715.1_Missense_Mutation_p.S2111R	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2111	34 X 47 AA approximate tandem repeat.		S -> R (in dbSNP:rs6724782). {ECO:0000269|PubMed:11941370}.		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						TGCCAGGTAGTCATGTAACTG	0.403													A|||	1822	0.363818	0.8775	0.3919	5008	,	,		20591	0.0089		0.2276	False		,,,				2504	0.1554				p.S2111R		Atlas-SNP	.											.	ALMS1	384	.	0			c.T6333A						PASS	.	A	ARG/SER	2748,966		1032,684,141	37.0	36.0	36.0		6333	-5.1	0.0	2	dbSNP_116	36	1956,6228		226,1504,2362	yes	missense	ALMS1	NM_015120.4	110	1258,2188,2503	AA,AT,TT		23.9003,26.0097,39.5361	benign	2111/4168	73679990	4704,7194	1857	4092	5949	SO:0001583	missense	7840	exon8			AGGTAGTCATGTA	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.6333T>A	2.37:g.73679990T>A	ENSP00000264448:p.Ser2111Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	72	28	0.388889	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	737	0.3374542124542125	425	0.8638211382113821	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	A	0.003	-2.434460	0.00182	0.739903	0.239003	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.12774	3.53;3.53;2.65	3.99	-5.06	0.02946	.	1.049810	0.07584	N	0.920720	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.39292	-0.9621	9	0.02654	T	1	.	0.5589	0.00676	0.257:0.124:0.2356:0.3834	rs6724782;rs17349573;rs17848883;rs52820401;rs56921282;rs6724782	2111;2069;2111	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	R	2069;2111;2111	ENSP00000386627:S2069R;ENSP00000264448:S2111R;ENSP00000366944:S2111R	ENSP00000264448:S2111R	S	+	3	2	ALMS1	73533498	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-0.204000	0.09425	-1.484000	0.01856	-0.375000	0.07067	AGT	T|0.691;A|0.309	0.309	strong		0.403	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135721036	135721036	+	Silent	SNP	C	C	T	rs34629706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:135721036C>T	ENST00000264977.3	+	2	1313	c.696C>T	c.(694-696)tgC>tgT	p.C232C	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	232					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						TAAAGATGTGCTTGGACATCT	0.328													C|||	177	0.0353435	0.0023	0.0216	5008	,	,		19948	0.001		0.0954	False		,,,				2504	0.0634				p.C232C		Atlas-SNP	.											PPP2R3A,colon,carcinoma,+1,1	PPP2R3A	114	1	0			c.C696T						PASS	.	C	,	62,4318		0,62,2128	42.0	46.0	45.0		,696	3.4	1.0	3	dbSNP_126	45	643,7951		18,607,3672	no	intron,coding-synonymous	PPP2R3A	NM_001190447.1,NM_002718.4	,	18,669,5800	TT,TC,CC		7.482,1.4155,5.4339	,	,232/1151	135721036	705,12269	2190	4297	6487	SO:0001819	synonymous_variant	5523	exon2			GATGTGCTTGGAC	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.696C>T	3.37:g.135721036C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	44	20	0.454545	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																			C|0.945;T|0.055	0.055	strong		0.328	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
KRTAP12-1	353332	hgsc.bcm.edu	37	21	46101939	46101939	+	Missense_Mutation	SNP	C	C	T	rs9984476	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46101939C>T	ENST00000391617.1	-	1	139	c.100G>A	c.(100-102)Gtg>Atg	p.V34M	TSPEAR_ENST00000323084.4_Intron	NM_181686.1	NP_859014.1	P59990	KR121_HUMAN	keratin associated protein 12-1	34	14 X 5 AA approximate repeats.					keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(1)|skin(2)	5						GGCACGCACACGGAGGACTGG	0.682													C|||	617	0.123203	0.0946	0.121	5008	,	,		17173	0.0813		0.1461	False		,,,				2504	0.183				p.V34M		Atlas-SNP	.											.	KRTAP12-1	9	.	0			c.G100A						PASS	.	C	,MET/VAL	384,3986		22,340,1823	56.0	66.0	63.0		,100	-1.7	0.0	21	dbSNP_119	63	1371,7175		115,1141,3017	yes	intron,missense	TSPEAR,KRTAP12-1	NM_144991.2,NM_181686.1	,21	137,1481,4840	TT,TC,CC		16.0426,8.7872,13.5878	,possibly-damaging	,34/97	46101939	1755,11161	2185	4273	6458	SO:0001583	missense	353332	exon1			CGCACACGGAGGA	AJ566388	CCDS42966.1	21q22.3	2006-03-13			ENSG00000187175	ENSG00000187175		"""Keratin associated proteins"""	20529	protein-coding gene	gene with protein product							Standard	NM_181686		Approved	KRTAP12.1, KAP12.1	uc002zfv.3	P59990	OTTHUMG00000057639	ENST00000391617.1:c.100G>A	21.37:g.46101939C>T	ENSP00000375475:p.Val34Met	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	167	80	0.479042	NM_181686	Q0VAS3	Missense_Mutation	SNP	ENST00000391617.1	37	CCDS42966.1	243	0.11126373626373626	41	0.08333333333333333	43	0.11878453038674033	47	0.08216783216783216	112	0.14775725593667546	c	10.82	1.458239	0.26161	0.087872	0.160426	ENSG00000187175	ENST00000391617	T	0.01388	4.95	3.12	-1.71	0.08133	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	P	0.50156	0.932	B	0.41571	0.36	T	0.50882	-0.8775	7	0.87932	D	0	.	6.3655	0.21453	0.484:0.3748:0.1412:0.0	rs9984476	34	P59990	KR121_HUMAN	M	34	ENSP00000375475:V34M	ENSP00000375475:V34M	V	-	1	0	KRTAP12-1	44926367	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.796000	0.01750	-0.476000	0.06842	0.407000	0.27541	GTG	C|0.877;T|0.123	0.123	strong		0.682	KRTAP12-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128043.1	NM_181686	
PCMTD1	115294	hgsc.bcm.edu	37	8	52733102	52733102	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:52733102G>A	ENST00000360540.5	-	7	1289	c.883C>T	c.(883-885)Ctt>Ttt	p.L295F	PCMTD1_ENST00000522514.1_Missense_Mutation_p.L295F|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000544451.1_Missense_Mutation_p.L219F	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	295						cytoplasm (GO:0005737)	protein-L-isoaspartate (D-aspartate) O-methyltransferase activity (GO:0004719)	p.L295F(2)		NS(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(17)|prostate(2)|skin(8)|soft_tissue(1)	37		Lung NSC(129;0.0795)|all_lung(136;0.144)				TGAGGAATAAGCTGATTACCC	0.418																																					p.L295F		Atlas-SNP	.											PCMTD1,extremity,malignant_melanoma,0,3	PCMTD1	73	3	2	Substitution - Missense(2)	NS(1)|skin(1)	c.C883T						scavenged	.						178.0	172.0	174.0					8																	52733102		2203	4300	6503	SO:0001583	missense	115294	exon6			GAATAAGCTGATT		CCDS6148.1, CCDS69480.1	8q11.23	2010-08-05			ENSG00000168300	ENSG00000168300			30483	protein-coding gene	gene with protein product							Standard	XM_005251146		Approved	FLJ10883	uc003xqx.4	Q96MG8	OTTHUMG00000164246	ENST00000360540.5:c.883C>T	8.37:g.52733102G>A	ENSP00000353739:p.Leu295Phe	Somatic	266	0	0		WXS	Illumina HiSeq	Phase_I	328	6	0.0182927	NM_052937	Q96FK9	Missense_Mutation	SNP	ENST00000360540.5	37	CCDS6148.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.025780	0.75390	.	.	ENSG00000168300	ENST00000360540;ENST00000544451;ENST00000522514	T;T;T	0.49720	0.77;0.77;0.77	5.97	5.1	0.69264	.	0.063724	0.64402	N	0.000004	T	0.64800	0.2631	L	0.57536	1.79	0.80722	D	1	D;B;P	0.76494	0.999;0.412;0.954	D;B;P	0.85130	0.997;0.148;0.649	T	0.65459	-0.6163	10	0.46703	T	0.11	-65.0248	14.9395	0.70983	0.0681:0.0:0.9319:0.0	.	165;219;295	B4E2B4;F5H1M8;Q96MG8	.;.;PCMD1_HUMAN	F	295;219;295	ENSP00000353739:L295F;ENSP00000444026:L219F;ENSP00000428099:L295F	ENSP00000353739:L295F	L	-	1	0	PCMTD1	52895655	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	7.107000	0.77047	1.532000	0.49169	0.655000	0.94253	CTT	.	.	none		0.418	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937	
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75785100	75785100	+	Silent	SNP	C	C	T	rs11180483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:75785100C>T	ENST00000550916.1	+	1	251	c.204C>T	c.(202-204)gtC>gtT	p.V68V	GLIPR1L2_ENST00000441218.1_5'Flank|GLIPR1L2_ENST00000547164.1_Silent_p.V68V|GLIPR1L2_ENST00000320460.4_Silent_p.V68V|GLIPR1L2_ENST00000378689.2_Silent_p.V68V|CAPS2_ENST00000442339.2_5'Flank|GLIPR1L2_ENST00000435775.1_Silent_p.V68V|GLIPR1L2_ENST00000378692.3_5'UTR	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	68	SCP.					integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						GGGGCGACGTCATTCCCCGAG	0.562											OREG0021999	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1614	0.322284	0.2254	0.2608	5008	,	,		16266	0.4673		0.3767	False		,,,				2504	0.2914				p.V68V		Atlas-SNP	.											.	GLIPR1L2	54	.	0			c.C204T						PASS	.	C		1207,3199	421.3+/-339.3	159,889,1155	108.0	82.0	91.0		204	0.8	0.0	12	dbSNP_120	91	3405,5195	503.3+/-375.9	686,2033,1581	no	coding-synonymous	GLIPR1L2	NM_152436.1		845,2922,2736	TT,TC,CC		39.593,27.3945,35.4606		68/254	75785100	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	144321	exon1			CGACGTCATTCCC	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.204C>T	12.37:g.75785100C>T		Somatic	136	0	0	1163	WXS	Illumina HiSeq	Phase_I	149	66	0.442953	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Silent	SNP	ENST00000550916.1	37	CCDS58258.1																																																																																			C|0.653;T|0.347	0.347	strong		0.562	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
SPP1	6696	hgsc.bcm.edu	37	4	88902692	88902692	+	Silent	SNP	T	T	C	rs4754	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88902692T>C	ENST00000395080.3	+	6	409	c.282T>C	c.(280-282)gaT>gaC	p.D94D	SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000237623.7_Silent_p.D80D|SPP1_ENST00000360804.4_Silent_p.D67D	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	94					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)	p.D94D(1)		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)		AAGATGATGATGACCATGTGG	0.433													T|||	1808	0.361022	0.1543	0.3775	5008	,	,		19176	0.7054		0.2813	False		,,,				2504	0.3558				p.D107D		Atlas-SNP	.											SPP1,NS,carcinoma,0,1	SPP1	35	1	1	Substitution - coding silent(1)	prostate(1)	c.T321C	GRCh37	CM033816	SPP1	M	rs4754	PASS	.	T	,,	784,3622	315.5+/-294.2	59,666,1478	269.0	248.0	255.0		240,282,201	-9.9	0.0	4	dbSNP_52	255	2339,6261	391.6+/-343.7	348,1643,2309	no	coding-synonymous,coding-synonymous,coding-synonymous	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	,,	407,2309,3787	CC,CT,TT		27.1977,17.7939,24.012	,,	80/301,94/315,67/288	88902692	3123,9883	2203	4300	6503	SO:0001819	synonymous_variant	6696	exon7			TGATGATGACCAT		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.282T>C	4.37:g.88902692T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	192	77	0.401042	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	37	CCDS43250.1																																																																																			T|0.713;C|0.287	0.287	strong		0.433	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
PCDHGA7	56108	hgsc.bcm.edu	37	5	140763029	140763029	+	Missense_Mutation	SNP	A	A	G	rs2072315	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140763029A>G	ENST00000518325.1	+	1	563	c.563A>G	c.(562-564)gAa>gGa	p.E188G	PCDHGB1_ENST00000523390.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	188	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> G (in dbSNP:rs2072315).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(1)|endometrium(8)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|skin(1)|stomach(3)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAGACGATGAAACTAAGTAC	0.627													.|||	2720	0.543131	0.8495	0.6254	5008	,	,		17317	0.3264		0.4225	False		,,,				2504	0.4182				p.E188G		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.A563G						PASS	.	G	,,,,,,GLY/GLU,,,,GLY/GLU	3433,813		1403,627,93	23.0	28.0	26.0		,,,,,,563,,,,563	4.2	0.9	5	dbSNP_96	26	3661,4845		784,2093,1376	yes	intron,intron,intron,intron,intron,intron,missense,intron,intron,intron,missense	PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032087.1	,,,,,,98,,,,98	2187,2720,1469	GG,GA,AA		43.0402,19.1474,44.3695	,,,,,,,,,,	,,,,,,188/933,,,,188/818	140763029	7094,5658	2123	4253	6376	SO:0001583	missense	56108	exon1			ACGATGAAACTAA	AF152514	CCDS54927.1, CCDS75336.1	5q31	2010-01-26				ENSG00000253537		"""Cadherins / Protocadherins : Clustered"""	8705	other	protocadherin		606294				10380929	Standard	NM_018920		Approved	PCDH-GAMMA-A7		Q9Y5G6		ENST00000518325.1:c.563A>G	5.37:g.140763029A>G	ENSP00000430024:p.Glu188Gly	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	188	187	0.994681	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	1144	0.5238095238095238	399	0.8109756097560976	218	0.6022099447513812	189	0.3304195804195804	338	0.44591029023746703	.	0.867	-0.733271	0.03135	0.808526	0.430402	ENSG00000253537	ENST00000518325	T	0.19532	2.14	5.11	4.23	0.50019	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00005	-3.27	0.37323	P	0.09037799999999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39375	-0.9617	8	0.02654	T	1	.	12.4703	0.55783	0.1437:0.0:0.8563:0.0	rs2072315;rs17603026;rs52792598;rs57573292;rs2072315	188;188	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	G	188	ENSP00000430024:E188G	ENSP00000430024:E188G	E	+	2	0	PCDHGA7	140743213	0.916000	0.31088	0.908000	0.35775	0.368000	0.29767	1.416000	0.34759	1.290000	0.44636	-0.119000	0.15052	GAA	A|0.473;G|0.527	0.527	strong		0.627	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920	
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:16285491C>T	ENST00000395837.1	+	2	451	c.270C>T	c.(268-270)acC>acT	p.T90T	UBB_ENST00000302182.3_Silent_p.T90T|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000578649.1_Intron|UBB_ENST00000535788.1_Intron|UBB_ENST00000395839.1_Silent_p.T90T	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	90	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCATCACCCTGGAAGTGG	0.552																																					p.T90T	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,bladder,carcinoma,0,2	UBB	30	2	0			c.C270T						scavenged	.						75.0	76.0	75.0					17																	16285491		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			CATCACCCTGGAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.270C>T	17.37:g.16285491C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	126	3	0.0238095	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39412119	39412119	+	Missense_Mutation	SNP	C	C	A	rs77134625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39412119C>A	ENST00000394008.1	+	1	484	c.482C>A	c.(481-483)tCc>tAc	p.S161Y		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	146						keratin filament (GO:0045095)		p.S161Y(2)		endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACCTGTGTGTCCAGCTGCTGC	0.562																																					p.S161Y		Atlas-SNP	.											KRTAP9-9,extremity,malignant_melanoma,0,2	KRTAP9-9	24	2	2	Substitution - Missense(2)	skin(2)	c.C482A						scavenged	.						164.0	171.0	168.0					17																	39412119		2203	4300	6503	SO:0001583	missense	81870	exon1			GTGTGTCCAGCTG	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.482C>A	17.37:g.39412119C>A	ENSP00000377576:p.Ser161Tyr	Somatic	171	1	0.00584795		WXS	Illumina HiSeq	Phase_I	224	10	0.0446429	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	.	.	.	.	.	.	.	.	.	.	.	3.519	-0.098224	0.07010	.	.	ENSG00000198083	ENST00000431129;ENST00000394008	T	0.01685	4.69	2.73	-0.887	0.10587	.	.	.	.	.	T	0.05731	0.0150	M	0.86420	2.815	0.09310	N	0.999997	D	0.59357	0.985	P	0.55011	0.766	T	0.25467	-1.0131	9	0.28530	T	0.3	.	3.6845	0.08323	0.4207:0.4476:0.0:0.1317	.	146	Q9BYP9	KRA99_HUMAN	Y	167;161	ENSP00000377576:S161Y	ENSP00000377576:S161Y	S	+	2	0	KRTAP9-9	36665645	0.059000	0.20769	0.062000	0.19696	0.810000	0.45777	0.135000	0.15952	-0.133000	0.11537	-0.360000	0.07572	TCC	C|0.946;A|0.054	0.054	strong		0.562	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
NAT8	9027	hgsc.bcm.edu	37	2	73868328	73868328	+	Missense_Mutation	SNP	A	A	G	rs13538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73868328A>G	ENST00000272425.3	-	2	577	c.428T>C	c.(427-429)tTt>tCt	p.F143S		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						ACTGTCCACAAAGAGATGAAA	0.562													.|||	1350	0.269569	0.6172	0.2622	5008	,	,		19442	0.005		0.2097	False		,,,				2504	0.1391				p.F143S		Atlas-SNP	.											.	NAT8	26	.	0			c.T428C						PASS	.	A	SER/PHE	2321,2085	605.2+/-390.5	620,1081,502	73.0	76.0	75.0	http://www.ncbi.nlm.nih.gov/pubmed?term	428	-7.7	0.0	2	dbSNP_52	75	1917,6683	339.4+/-323.1	206,1505,2589	no	missense	NAT8	NM_003960.3	155	826,2586,3091	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	22.2907,47.3218,32.585	benign	143/228	73868328	4238,8768	2203	4300	6503	SO:0001583	missense	9027	exon2			TCCACAAAGAGAT	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"""N-acetyltransferase 8"""			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.428T>C	2.37:g.73868328A>G	ENSP00000272425:p.Phe143Ser	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	113	60	0.530973	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	37	CCDS1926.1	548	0.2509157509157509	302	0.6138211382113821	81	0.22375690607734808	4	0.006993006993006993	161	0.21240105540897097	a	0.010	-1.771572	0.00645	0.526782	0.222907	ENSG00000144035	ENST00000272425	T	0.22539	1.95	3.86	-7.73	0.01245	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.610629	0.17818	N	0.160960	T	0.00012	0.0000	N	0.02960	-0.455	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26018	-1.0115	9	0.09084	T	0.74	-0.7893	3.5914	0.07990	0.4:0.2826:0.2389:0.0785	rs13538;rs3174952;rs17009281;rs13538	143	Q9UHE5	NAT8_HUMAN	S	143	ENSP00000272425:F143S	ENSP00000272425:F143S	F	-	2	0	NAT8	73721836	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.187000	0.16998	-2.616000	0.00442	-3.803000	0.00020	TTT	A|0.708;G|0.292	0.292	strong		0.562	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960	
SHD	56961	hgsc.bcm.edu	37	19	4288332	4288332	+	Missense_Mutation	SNP	A	A	G	rs888930	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4288332A>G	ENST00000543264.2	+	5	2272	c.809A>G	c.(808-810)aAc>aGc	p.N270S	SHD_ENST00000599689.1_Intron	NM_020209.3	NP_064594.3	Q96IW2	SHD_HUMAN	Src homology 2 domain containing transforming protein D	270	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		N -> S (in dbSNP:rs888930). {ECO:0000269|PubMed:14702039}.					p.N270S(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|stomach(1)	14				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0337)|STAD - Stomach adenocarcinoma(1328;0.18)		AGTGAGACCAACCCCCAGGAC	0.582													G|||	2424	0.484026	0.6203	0.5591	5008	,	,		18076	0.3393		0.3787	False		,,,				2504	0.5041				p.N270S		Atlas-SNP	.											SHD,NS,carcinoma,0,3	SHD	33	3	1	Substitution - Missense(1)	stomach(1)	c.A809G						PASS	.	G	SER/ASN	2534,1872	537.6+/-374.8	745,1044,414	78.0	66.0	70.0		809	4.0	1.0	19	dbSNP_86	70	3154,5446	653.7+/-401.1	567,2020,1713	yes	missense	SHD	NM_020209.3	46	1312,3064,2127	GG,GA,AA		36.6744,42.4875,43.7337	benign	270/341	4288332	5688,7318	2203	4300	6503	SO:0001583	missense	56961	exon5			AGACCAACCCCCA	BC007206	CCDS12125.1	19p13.3	2013-02-14				ENSG00000105251		"""SH2 domain containing"""	30633	protein-coding gene	gene with protein product		610481				9315092	Standard	NM_020209		Approved		uc002lzw.2	Q96IW2		ENST00000543264.2:c.809A>G	19.37:g.4288332A>G	ENSP00000446058:p.Asn270Ser	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_020209	Q96NC2	Missense_Mutation	SNP	ENST00000543264.2	37	CCDS12125.1	1011	0.46291208791208793	331	0.6727642276422764	197	0.5441988950276243	198	0.34615384615384615	285	0.3759894459102902	G	7.008	0.556285	0.13436	0.575125	0.366744	ENSG00000105251	ENST00000543264;ENST00000221852	D	0.88046	-2.33	5.02	3.99	0.46301	SH2 motif (4);	0.262943	0.40554	N	0.001075	T	0.00012	0.0000	N	0.02181	-0.65	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.41752	-0.9491	9	0.02654	T	1	-4.3447	9.4055	0.38460	0.1725:0.0:0.8275:0.0	rs888930;rs1043817;rs3170373;rs52826654;rs59490546;rs888930	270	Q96IW2	SHD_HUMAN	S	270;185	ENSP00000446058:N270S	ENSP00000221852:N185S	N	+	2	0	SHD	4239332	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	5.276000	0.65580	0.738000	0.32606	-0.222000	0.12452	AAC	A|0.552;G|0.446	0.446	strong		0.582	SHD-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458082.1	NM_020209	
HGD	3081	hgsc.bcm.edu	37	3	120389316	120389316	+	Missense_Mutation	SNP	T	T	A	rs2255543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:120389316T>A	ENST00000283871.5	-	4	699	c.240A>T	c.(238-240)caA>caT	p.Q80H	HGD_ENST00000488183.1_5'UTR	NM_000187.3	NP_000178.2	Q93099	HGD_HUMAN	homogentisate 1,2-dioxygenase	80			Q -> H (in dbSNP:rs2255543). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8782815, ECO:0000269|PubMed:9244427, ECO:0000269|Ref.2, ECO:0000269|Ref.6}.		cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	homogentisate 1,2-dioxygenase activity (GO:0004411)|metal ion binding (GO:0046872)			cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)	25				GBM - Glioblastoma multiforme(114;0.158)		TGTGAGTGACTTGGCCTTCGT	0.423													A|||	3664	0.731629	0.7821	0.8112	5008	,	,		18477	0.6429		0.7654	False		,,,				2504	0.6636				p.Q80H		Atlas-SNP	.											.	HGD	65	.	0			c.A240T						PASS	.	A	HIS/GLN	3335,1071	391.9+/-328.3	1253,829,121	156.0	154.0	155.0		240	-2.2	0.1	3	dbSNP_100	155	6328,2264	381.8+/-340.2	2308,1712,276	yes	missense	HGD	NM_000187.3	24	3561,2541,397	AA,AT,TT		26.3501,24.3078,25.6578	benign	80/446	120389316	9663,3335	2203	4296	6499	SO:0001583	missense	3081	exon4			AGTGACTTGGCCT		CCDS3000.1	3q	2010-04-27	2010-04-27		ENSG00000113924	ENSG00000113924	1.13.11.5		4892	protein-coding gene	gene with protein product	"""homogentisate oxidase"""	607474	"""homogentisate 1,2-dioxygenase (homogentisate oxidase)"""	AKU		8188241	Standard	NM_000187		Approved	HGO	uc003edw.3	Q93099	OTTHUMG00000159441	ENST00000283871.5:c.240A>T	3.37:g.120389316T>A	ENSP00000283871:p.Gln80His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_000187	A8K417|B2R8Z0	Missense_Mutation	SNP	ENST00000283871.5	37	CCDS3000.1	1610	0.7371794871794872	395	0.8028455284552846	294	0.8121546961325967	354	0.6188811188811189	567	0.7480211081794196	A	8.908	0.957997	0.18507	0.756922	0.736499	ENSG00000113924	ENST00000283871;ENST00000476082	D;D	0.98849	-5.18;-5.18	6.06	-2.23	0.06930	Cupin, RmlC-type (1);	0.267414	0.42172	N	0.000750	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	0.43829	-0.9367	9	0.10902	T	0.67	-5.7751	3.4407	0.07462	0.3518:0.1236:0.4048:0.1198	rs2255543;rs17140273;rs17856617;rs61795578	80	Q93099	HGD_HUMAN	H	80;39	ENSP00000283871:Q80H;ENSP00000419560:Q39H	ENSP00000283871:Q80H	Q	-	3	2	HGD	121872006	0.001000	0.12720	0.075000	0.20258	0.950000	0.60333	-0.244000	0.08903	-0.300000	0.08895	-0.257000	0.10917	CAA	T|0.269;A|0.731	0.731	strong		0.423	HGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355410.1		
KIAA0391	9692	hgsc.bcm.edu	37	14	35735967	35735967	+	Missense_Mutation	SNP	A	A	G	rs11156878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:35735967A>G	ENST00000557565.1	+	6	1691	c.1310A>G	c.(1309-1311)aAt>aGt	p.N437S	KIAA0391_ENST00000604948.1_Missense_Mutation_p.N342S|KIAA0391_ENST00000250377.7_Missense_Mutation_p.N342S|KIAA0391_ENST00000605870.1_Missense_Mutation_p.N65S|KIAA0391_ENST00000321130.10_Missense_Mutation_p.N421S|KIAA0391_ENST00000534898.4_Missense_Mutation_p.N437S|KIAA0391_ENST00000603544.1_Missense_Mutation_p.N421S	NM_001282234.1	NP_001269163.1	O15091	MRRP3_HUMAN	KIAA0391	437			N -> S (in dbSNP:rs11156878). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		tRNA processing (GO:0008033)	mitochondrion (GO:0005739)				central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	14	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;2.93e-05)|LUAD - Lung adenocarcinoma(48;3.86e-05)|Epithelial(34;0.0114)|all cancers(34;0.0277)	GBM - Glioblastoma multiforme(112;0.0593)		GCCAAACGGAATCTGCGACTG	0.473													A|||	488	0.0974441	0.0318	0.1268	5008	,	,		19353	0.0595		0.1879	False		,,,				2504	0.1115				p.N437S		Atlas-SNP	.											.	KIAA0391	35	.	0			c.A1310G						PASS	.	A	SER/ASN	268,4138	151.4+/-185.3	9,250,1944	210.0	201.0	204.0		1310	5.6	1.0	14	dbSNP_120	204	1446,7154	277.5+/-292.9	124,1198,2978	yes	missense	KIAA0391	NM_014672.2	46	133,1448,4922	GG,GA,AA		16.814,6.0826,13.1785	benign	437/584	35735967	1714,11292	2203	4300	6503	SO:0001583	missense	9692	exon6			AACGGAATCTGCG	AB002389	CCDS32063.1, CCDS58312.1, CCDS58313.1, CCDS58314.1	14q13.2	2013-06-18			ENSG00000100890	ENSG00000100890			19958	protein-coding gene	gene with protein product	"""mitochondrial RNase P subunit 3"", ""proteinaceous RNase P"""	609947				9205841, 18984158	Standard	NM_001256678		Approved	MRPP3, PRORP	uc001wsy.2	O15091		ENST00000557565.1:c.1310A>G	14.37:g.35735967A>G	ENSP00000454657:p.Asn437Ser	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	203	95	0.46798	NM_014672	B4DXD9|B4E0S8|B4E211|C4AM93|D3DS99|D3DSA1|Q86SZ4|Q86YB5|Q8N5L5	Missense_Mutation	SNP	ENST00000557565.1	37	CCDS32063.1	227	0.10393772893772894	18	0.036585365853658534	52	0.143646408839779	26	0.045454545454545456	131	0.17282321899736147	A	14.91	2.675032	0.47781	0.060826	0.16814	ENSG00000100890	ENST00000554896;ENST00000250377;ENST00000321130;ENST00000534898;ENST00000556121;ENST00000556912;ENST00000557404	T;T;T;T	0.46451	0.9;0.9;0.87;1.0	5.62	5.62	0.85841	.	0.166808	0.53938	D	0.000048	T	0.00144	0.0004	L	0.46885	1.475	0.32908	P	0.485866	B;B	0.25772	0.134;0.134	B;B	0.29862	0.108;0.108	T	0.08617	-1.0713	9	0.24483	T	0.36	-13.9399	14.8151	0.70028	1.0:0.0:0.0:0.0	rs11156878;rs60527017;rs11156878	421;437	O15091-2;O15091	.;MRRP3_HUMAN	S	342;342;421;437;421;65;65	ENSP00000250377:N342S;ENSP00000324697:N421S;ENSP00000440915:N437S;ENSP00000450898:N65S	ENSP00000250377:N342S	N	+	2	0	KIAA0391	34805718	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.276000	0.65580	2.142000	0.66516	0.528000	0.53228	AAT	A|0.882;G|0.118	0.118	strong		0.473	KIAA0391-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000411280.1	NM_014672	
EVC	2121	hgsc.bcm.edu	37	4	5733236	5733236	+	Missense_Mutation	SNP	C	C	G	rs146729456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5733236C>G	ENST00000264956.6	+	4	653	c.469C>G	c.(469-471)Cct>Gct	p.P157A	EVC_ENST00000509451.1_Missense_Mutation_p.P157A|EVC_ENST00000382674.2_Missense_Mutation_p.P157A	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	157					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)				AGAGGCCTCTCCTTCCAGCAG	0.612													C|||	15	0.00299521	0.0008	0.0014	5008	,	,		17399	0.0		0.0119	False		,,,				2504	0.001				p.P157A		Atlas-SNP	.											.	EVC	90	.	0			c.C469G						PASS	.	C	ALA/PRO	8,4398	14.3+/-33.2	0,8,2195	71.0	74.0	73.0		469	4.0	0.0	4	dbSNP_134	73	64,8536	39.3+/-95.6	1,62,4237	yes	missense	EVC	NM_153717.2	27	1,70,6432	GG,GC,CC		0.7442,0.1816,0.5536	probably-damaging	157/993	5733236	72,12934	2203	4300	6503	SO:0001583	missense	2121	exon4			GCCTCTCCTTCCA	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.469C>G	4.37:g.5733236C>G	ENSP00000264956:p.Pro157Ala	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	166	76	0.457831	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	8	0.003663003663003663	1	0.0020325203252032522	0	0.0	0	0.0	7	0.009234828496042216	C	5.980	0.364833	0.11296	0.001816	0.007442	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.52295	0.67;0.67;0.75	3.95	3.95	0.45737	.	0.216956	0.40385	N	0.001110	T	0.29093	0.0723	L	0.50333	1.59	0.09310	N	1	B	0.25312	0.123	B	0.21360	0.034	T	0.12344	-1.0551	10	0.35671	T	0.21	.	7.1792	0.25763	0.2043:0.625:0.1707:0.0	.	157	P57679	EVC_HUMAN	A	157	ENSP00000264956:P157A;ENSP00000372120:P157A;ENSP00000426774:P157A	ENSP00000264956:P157A	P	+	1	0	EVC	5784137	0.115000	0.22152	0.019000	0.16419	0.172000	0.22775	1.547000	0.36190	2.206000	0.71126	0.561000	0.74099	CCT	C|0.995;G|0.005	0.005	strong		0.612	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
ADAM21	8747	hgsc.bcm.edu	37	14	70924507	70924507	+	Silent	SNP	A	A	C	rs3751524	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:70924507A>C	ENST00000603540.1	+	2	549	c.291A>C	c.(289-291)gcA>gcC	p.A97A	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.A97A	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	97					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.A97A(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)		ATGACCGTGCACTCCTGGAGG	0.512																																					p.A97A		Atlas-SNP	.											ADAM21,NS,carcinoma,0,1	ADAM21	181	1	1	Substitution - coding silent(1)	stomach(1)	c.A291C						scavenged	.						95.0	103.0	101.0					14																	70924507		2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			CCGTGCACTCCTG	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.291A>C	14.37:g.70924507A>C		Somatic	124	1	0.00806452		WXS	Illumina HiSeq	Phase_I	156	115	0.737179	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			A|0.780;C|0.220	0.220	strong		0.512	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
ZNF417	147687	hgsc.bcm.edu	37	19	58420152	58420152	+	Silent	SNP	C	C	A	rs17845779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58420152C>A	ENST00000312026.5	-	3	1658	c.1494G>T	c.(1492-1494)ggG>ggT	p.G498G	ZNF417_ENST00000536263.1_Silent_p.G299G|ZNF417_ENST00000595559.1_Silent_p.G497G|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	498					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G498G(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		GAAATGATTTCCCACATTCAT	0.398													A|||	1399	0.279353	0.2761	0.2248	5008	,	,		21369	0.2847		0.2992	False		,,,				2504	0.2965				p.G498G		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - coding silent(1)	stomach(1)	c.G1494T						PASS	.						104.0	85.0	91.0					19																	58420152		2203	4296	6499	SO:0001819	synonymous_variant	147687	exon3			TGATTTCCCACAT	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1494G>T	19.37:g.58420152C>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	143	139	0.972028	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			C|0.765;A|0.235	0.235	strong		0.398	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14851756	14851756	+	Silent	SNP	G	G	A	rs9676225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:14851756G>A	ENST00000358984.4	+	36	3636	c.3456G>A	c.(3454-3456)acG>acA	p.T1152T		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	1152										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						AAGTTCTGACGGCAGAGAACA	0.383													A|||	2647	0.528554	0.7421	0.4438	5008	,	,		15669	0.4157		0.5159	False		,,,				2504	0.4294				p.T1152T		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,+2,1	ANKRD30B	237	1	0			c.G3456A						scavenged	.						23.0	22.0	22.0					18																	14851756		462	1334	1796	SO:0001819	synonymous_variant	374860	exon36			TCTGACGGCAGAG	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.3456G>A	18.37:g.14851756G>A		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	149	147	0.986577	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																			G|0.500;A|0.500	0.500	strong		0.383	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
ZNF700	90592	hgsc.bcm.edu	37	19	12060627	12060627	+	Silent	SNP	A	A	G	rs78201704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12060627A>G	ENST00000254321.5	+	4	1931	c.1788A>G	c.(1786-1788)caA>caG	p.Q596Q	ZNF763_ENST00000538752.1_Intron|CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000591944.1_Intron|ZNF700_ENST00000482090.1_Silent_p.Q578Q|ZNF763_ENST00000590798.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	596					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.Q596Q(1)	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						AGTGTAAGCAATGTGGGAAAG	0.473													a|||	75	0.014976	0.0492	0.0058	5008	,	,		23157	0.0		0.006	False		,,,				2504	0.0				p.Q599Q		Atlas-SNP	.											ZNF700,NS,carcinoma,0,1	ZNF700	81	1	1	Substitution - coding silent(1)	pancreas(1)	c.A1797G						PASS	.	A		254,4152	145.4+/-180.2	8,238,1957	105.0	103.0	104.0		1788	-1.0	0.0	19	dbSNP_131	104	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous	ZNF700	NM_144566.1		8,268,6227	GG,GA,AA		0.3488,5.7649,2.1836		596/743	12060627	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	90592	exon4			TAAGCAATGTGGG	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.1788A>G	19.37:g.12060627A>G		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_001271848	B9EGU4	Silent	SNP	ENST00000254321.5	37	CCDS32915.1																																																																																			A|0.979;G|0.021	0.021	strong		0.473	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566	
PCDHB16	57717	hgsc.bcm.edu	37	5	140563579	140563579	+	Missense_Mutation	SNP	C	C	T	rs17844646	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140563579C>T	ENST00000361016.2	+	1	2600	c.1445C>T	c.(1444-1446)aCc>aTc	p.T482I		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	482	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.			T -> I (in Ref. 3; BAB13447). {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)			GACTCAGGCACCAACGCCCAG	0.657													C|||	1318	0.263179	0.0129	0.3069	5008	,	,		11803	0.5308		0.2376	False		,,,				2504	0.3211				p.T482I		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C1445T						PASS	.						56.0	52.0	54.0					5																	140563579		2203	4279	6482	SO:0001583	missense	57717	exon1			CAGGCACCAACGC	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.1445C>T	5.37:g.140563579C>T	ENSP00000354293:p.Thr482Ile	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	116	44	0.37931	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	569	0.26053113553113555	7	0.014227642276422764	87	0.24033149171270718	303	0.5297202797202797	172	0.22691292875989447	c	13.55	2.269951	0.40095	.	.	ENSG00000196963	ENST00000361016	T	0.52983	0.64	4.26	2.24	0.28232	Cadherin (4);Cadherin-like (1);	1.787010	0.03514	N	0.220040	T	0.00012	0.0000	N	0.20328	0.56	0.54753	P	1.4999999999987246E-5	P	0.45986	0.87	P	0.48524	0.58	T	0.39820	-0.9595	9	0.42905	T	0.14	.	7.8603	0.29506	0.3851:0.4774:0.1376:0.0	rs17844646	482	Q9NRJ7	PCDBG_HUMAN	I	482	ENSP00000354293:T482I	ENSP00000354293:T482I	T	+	2	0	PCDHB16	140543763	0.000000	0.05858	0.841000	0.33234	0.574000	0.36063	-0.036000	0.12185	0.747000	0.32809	0.580000	0.79431	ACC	C|0.878;T|0.122	0.122	strong		0.657	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
PRR4	11272	hgsc.bcm.edu	37	12	10999780	10999780	+	Missense_Mutation	SNP	C	C	T	rs1063193	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:10999780C>T	ENST00000228811.4	-	3	324	c.287G>A	c.(286-288)cGa>cAa	p.R96Q	PRR4_ENST00000540107.1_Silent_p.P38P|PRR4_ENST00000536668.1_5'UTR|PRR4_ENST00000544994.1_Intron	NM_007244.2	NP_009175.2	Q16378	PROL4_HUMAN	proline rich 4 (lacrimal)	96			R -> Q (in dbSNP:rs1063193). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7544782}.		retina homeostasis (GO:0001895)|visual perception (GO:0007601)	extracellular space (GO:0005615)				endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	9						GTGTCCTCGTCGGGGTGGTCG	0.552													C|||	2613	0.521765	0.1354	0.621	5008	,	,		17977	0.7093		0.6252	False		,,,				2504	0.6738				p.R96Q		Atlas-SNP	.											.	PRR4	17	.	0			c.G287A						PASS	.	C	,GLN/ARG	850,3204		104,642,1281	237.0	243.0	241.0		,287	-3.5	0.0	12	dbSNP_86	241	4834,3512		1420,1994,759	yes	intron,missense	PRR4	NM_001098538.2,NM_007244.2	,43	1524,2636,2040	TT,TC,CC		42.08,20.9669,45.8387	,possibly-damaging	,96/135	10999780	5684,6716	2027	4173	6200	SO:0001583	missense	11272	exon3			CCTCGTCGGGGTG		CCDS41756.1, CCDS55804.1	12p13	2008-02-05		2004-05-28		ENSG00000111215			18020	protein-coding gene	gene with protein product		605359		PROL4		7544782	Standard	NM_007244		Approved	LPRP	uc001qyz.4	Q16378		ENST00000228811.4:c.287G>A	12.37:g.10999780C>T	ENSP00000228811:p.Arg96Gln	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	180	178	0.988889	NM_007244	A8KA69|F5H0D7|Q8NFB3	Missense_Mutation	SNP	ENST00000228811.4	37	CCDS41756.1	1179|1179	0.5398351648351648|0.5398351648351648	82|82	0.16666666666666666|0.16666666666666666	226|226	0.6243093922651933|0.6243093922651933	405|405	0.708041958041958|0.708041958041958	466|466	0.6147757255936676|0.6147757255936676	C|C	4.225|4.225	0.040567|0.040567	0.08196|0.08196	0.209669|0.209669	0.5792|0.5792	ENSG00000111215|ENSG00000111215	ENST00000431566|ENST00000228811	.|T	.|0.04502	.|3.61	1.75|1.75	-3.51|-3.51	0.04696|0.04696	.|.	.|0.773335	.|0.09533	.|N	.|0.789250	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	.|0.12630	.|0.006	.|B	.|0.04013	.|0.001	T|T	0.33803|0.33803	-0.9854|-0.9854	5|9	0.87932|0.06494	D|T	0|0.89	.|.	5.6305|5.6305	0.17508|0.17508	0.0:0.3969:0.3388:0.2644|0.0:0.3969:0.3388:0.2644	rs1063193;rs3204222;rs17742967;rs17857476;rs52805968;rs1063193|rs1063193;rs3204222;rs17742967;rs17857476;rs52805968;rs1063193	.|96	.|Q16378	.|PROL4_HUMAN	N|Q	80|96	.|ENSP00000228811:R96Q	ENSP00000405056:D80N|ENSP00000228811:R96Q	D|R	-|-	1|2	0|0	PRR4|PRR4	10891047|10891047	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-2.213000|-2.213000	0.01224|0.01224	-3.059000|-3.059000	0.00257|0.00257	-1.465000|-1.465000	0.01017|0.01017	GAC|CGA	C|0.469;T|0.531	0.531	strong		0.552	PRR4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400049.1	NM_007244	
WDR5	11091	hgsc.bcm.edu	37	9	137017126	137017126	+	Silent	SNP	A	A	G	rs34523253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:137017126A>G	ENST00000358625.3	+	9	777	c.606A>G	c.(604-606)tcA>tcG	p.S202S	WDR5_ENST00000425041.1_Silent_p.S202S	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	202					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		ACACCGCCTCAGGCCAGTGCC	0.562													G|||	394	0.0786741	0.2489	0.0375	5008	,	,		18445	0.0		0.0328	False		,,,				2504	0.0061				p.S202S		Atlas-SNP	.											WDR5,NS,carcinoma,+1,1	WDR5	29	1	0			c.A606G						PASS	.	G	,	925,3481	737.9+/-410.9	90,745,1368	158.0	157.0	157.0		606,606	-7.5	0.0	9	dbSNP_126	157	247,8353	808.4+/-407.2	4,239,4057	no	coding-synonymous,coding-synonymous	WDR5	NM_017588.2,NM_052821.3	,	94,984,5425	GG,GA,AA		2.8721,20.9941,9.0112	,	202/335,202/335	137017126	1172,11834	2203	4300	6503	SO:0001819	synonymous_variant	11091	exon8			CGCCTCAGGCCAG	AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"""WD repeat domain containing"""	12757	protein-coding gene	gene with protein product	"""SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)"", ""cilia and flagella associated protein 89"""	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.606A>G	9.37:g.137017126A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	149	74	0.496644	NM_052821	Q91VA5|Q9NWX7|Q9UGP9	Silent	SNP	ENST00000358625.3	37	CCDS6981.1																																																																																			A|0.920;G|0.080	0.080	strong		0.562	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1	NM_052821	
CATSPERD	257062	hgsc.bcm.edu	37	19	5772950	5772950	+	Missense_Mutation	SNP	G	G	A	rs61180947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5772950G>A	ENST00000381624.3	+	20	1976	c.1915G>A	c.(1915-1917)Ggg>Agg	p.G639R	CATSPERD_ENST00000309164.7_3'UTR	NM_152784.3	NP_689997.3	Q86XM0	CTSRD_HUMAN	catsper channel auxiliary subunit delta	639					multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)											AAAGGAATTCGGGGGGCCCTT	0.582													G|||	1150	0.229633	0.0098	0.3905	5008	,	,		16949	0.3839		0.2356	False		,,,				2504	0.2474				p.G639R		Atlas-SNP	.											.	.	.	.	0			c.G1915A						PASS	.	G	ARG/GLY	193,3609		5,183,1713	47.0	51.0	50.0		1915	1.6	0.0	19	dbSNP_129	50	1791,6429		202,1387,2521	yes	missense	TMEM146	NM_152784.3	125	207,1570,4234	AA,AG,GG		21.7883,5.0763,16.5031	probably-damaging	639/799	5772950	1984,10038	1901	4110	6011	SO:0001583	missense	257062	exon20			GAATTCGGGGGGC	BC043005	CCDS12149.2	19p13.3	2013-10-11	2012-02-22	2012-02-22	ENSG00000174898	ENSG00000174898			28598	protein-coding gene	gene with protein product			"""transmembrane protein 146"""	TMEM146		21224844	Standard	NM_152784		Approved	MGC39581	uc002mda.3	Q86XM0	OTTHUMG00000143036	ENST00000381624.3:c.1915G>A	19.37:g.5772950G>A	ENSP00000371037:p.Gly639Arg	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	67	43	0.641791	NM_152784	Q6ZRP1	Missense_Mutation	SNP	ENST00000381624.3	37	CCDS12149.2	579	0.2651098901098901	7	0.014227642276422764	135	0.3729281767955801	244	0.42657342657342656	193	0.2546174142480211	G	9.822	1.186111	0.21870	0.050763	0.217883	ENSG00000174898	ENST00000381624;ENST00000381613	T	0.25085	1.82	2.73	1.63	0.23807	.	1.526280	0.04359	N	0.357052	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	D	0.76494	0.999	P	0.54924	0.764	T	0.36768	-0.9734	9	0.42905	T	0.14	-3.1778	7.393	0.26921	0.0:0.2719:0.7281:0.0	rs61180947	639	Q86XM0	TM146_HUMAN	R	639;308	ENSP00000371037:G639R	ENSP00000371026:G308R	G	+	1	0	TMEM146	5723950	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.637000	0.24659	0.676000	0.31285	0.561000	0.74099	GGG	G|0.749;A|0.251	0.251	strong		0.582	CATSPERD-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286953.2	NM_152784	
SEC16A	9919	hgsc.bcm.edu	37	9	139371700	139371700	+	Missense_Mutation	SNP	G	G	A	rs371074782		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139371700G>A	ENST00000313050.7	-	1	441	c.368C>T	c.(367-369)cCg>cTg	p.P123L	SEC16A_ENST00000431893.2_5'Flank|SEC16A_ENST00000371706.3_5'Flank|SEC16A_ENST00000290037.6_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)		ACCAGAAAACGGACTGGCATG	0.577																																					p.P123L		Atlas-SNP	.											.	SEC16A	249	.	0			c.C368T						PASS	.	G	LEU/PRO	0,4068		0,0,2034	82.0	86.0	85.0		368	-7.8	0.0	9		85	1,8361		0,1,4180	no	missense	SEC16A	NM_014866.1	98	0,1,6214	AA,AG,GG		0.012,0.0,0.0080	benign	123/2358	139371700	1,12429	2034	4181	6215	SO:0001583	missense	9919	exon3			GAAAACGGACTGG	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.368C>T	9.37:g.139371700G>A	ENSP00000325827:p.Pro123Leu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	118	10	0.0847458	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000313050.7	37	CCDS55351.1	.	.	.	.	.	.	.	.	.	.	G	8.006	0.756537	0.15846	0.0	1.2E-4	ENSG00000148396	ENST00000313050	T	0.21031	2.03	5.02	-7.76	0.01232	.	.	.	.	.	T	0.06645	0.0170	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38090	-0.9677	8	.	.	.	.	6.51	0.22216	0.607:0.0887:0.2148:0.0895	.	123	F1T0I1	.	L	123	ENSP00000325827:P123L	.	P	-	2	0	SEC16A	138491521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.064000	0.14437	-1.641000	0.01523	-0.794000	0.03295	CCG	.	.	weak		0.577	SEC16A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088459	
AK9	221264	hgsc.bcm.edu	37	6	109837147	109837147	+	Silent	SNP	A	A	G	rs150078049	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:109837147A>G	ENST00000424296.2	-	31	4054	c.3978T>C	c.(3976-3978)tgT>tgC	p.C1326C		NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	1326					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)										GTATTGGATGACATTTCTCAA	0.393													A|||	31	0.0061901	0.0008	0.0159	5008	,	,		16735	0.0		0.0149	False		,,,				2504	0.0041				p.C1326C		Atlas-SNP	.											.	AKD1	223	.	0			c.T3978C						PASS	.	A		3,1381		0,3,689	285.0	246.0	258.0		3978	3.3	1.0	6	dbSNP_134	258	41,3141		0,41,1550	no	coding-synonymous	AKD1	NM_001145128.2		0,44,2239	GG,GA,AA		1.2885,0.2168,0.9636		1326/1912	109837147	44,4522	692	1591	2283	SO:0001819	synonymous_variant	221264	exon31			TGGATGACATTTC	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.3978T>C	6.37:g.109837147A>G		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	116	11	0.0948276	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	37	CCDS55048.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	A	7.041	0.562595	0.13498	0.002168	0.012885	ENSG00000155085	ENST00000470564	.	.	.	5.7	3.34	0.38264	.	.	.	.	.	T	0.42539	0.1207	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36529	-0.9744	4	.	.	.	.	7.4003	0.26960	0.6753:0.0:0.3247:0.0	.	.	.	.	A	164	.	.	V	-	2	0	AKD1	109943840	1.000000	0.71417	1.000000	0.80357	0.703000	0.40648	2.053000	0.41326	0.993000	0.38866	0.528000	0.53228	GTC	A|0.990;G|0.010	0.010	strong		0.393	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
RIMS2	9699	hgsc.bcm.edu	37	8	105261725	105261725	+	Silent	SNP	G	G	A	rs59975412|rs2028945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:105261725G>A	ENST00000436393.2	+	26	3895	c.3654G>A	c.(3652-3654)caG>caA	p.Q1218Q	RIMS2_ENST00000339750.2_Silent_p.Q136Q|RIMS2_ENST00000406091.3_Silent_p.Q1200Q|RIMS2_ENST00000507740.1_Silent_p.Q1014Q|RIMS2_ENST00000262231.10_Silent_p.Q1039Q			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1262					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			GTGACATTCAGGTAGGAATGA	0.418										HNSCC(12;0.0054)			G|||	1182	0.236022	0.1316	0.2579	5008	,	,		15861	0.5357		0.0765	False		,,,				2504	0.2168				p.Q1200Q		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G3600A						PASS	.	G	,	425,3307		20,385,1461	69.0	69.0	69.0		3600,3042	3.7	1.0	8	dbSNP_94	69	544,7624		21,502,3561	no	coding-synonymous,coding-synonymous	RIMS2	NM_001100117.2,NM_014677.4	,	41,887,5022	AA,AG,GG		6.6601,11.388,8.1429	,	1200/1350,1014/1164	105261725	969,10931	1866	4084	5950	SO:0001819	synonymous_variant	9699	exon22			CATTCAGGTAGGA	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000436393.2:c.3654G>A	8.37:g.105261725G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000436393.2	37																																																																																				.	.	weak		0.418	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
TUBA8	51807	hgsc.bcm.edu	37	22	18613739	18613739	+	Missense_Mutation	SNP	G	G	T	rs146821364		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18613739G>T	ENST00000330423.3	+	5	1259	c.1186G>T	c.(1186-1188)Gac>Tac	p.D396Y	TUBA8_ENST00000316027.6_Missense_Mutation_p.D330Y	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	396					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						CCACAAGTTCGACCTCATGTA	0.622																																					p.D396Y		Atlas-SNP	.											TUBA8,NS,carcinoma,0,1	TUBA8	36	1	0			c.G1186T						PASS	.	G	TYR/ASP,TYR/ASP	1,4405		0,1,2202	63.0	58.0	60.0		988,1186	5.2	1.0	22	dbSNP_134	60	0,8600		0,0,4300	no	missense,missense	TUBA8	NM_001193414.1,NM_018943.2	160,160	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	330/384,396/450	18613739	1,13005	2203	4300	6503	SO:0001583	missense	51807	exon5			AAGTTCGACCTCA	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"""Tubulins"""	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.1186G>T	22.37:g.18613739G>T	ENSP00000333326:p.Asp396Tyr	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	143	61	0.426573	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	.	.	.	.	.	.	.	.	.	.	.	18.66	3.671959	0.67928	2.27E-4	0.0	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	D;D;D	0.86097	-2.07;-2.07;-2.07	5.19	5.19	0.71726	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.097032	0.64402	D	0.000002	D	0.95089	0.8409	H	0.96489	3.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.991;0.989;1.0	D	0.96490	0.9363	10	0.87932	D	0	.	18.0766	0.89428	0.0:0.0:1.0:0.0	.	330;420;396	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	Y	330;396;420	ENSP00000318575:D330Y;ENSP00000333326:D396Y;ENSP00000412646:D420Y	ENSP00000318575:D330Y	D	+	1	0	TUBA8	16993739	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.835000	0.99442	2.569000	0.86673	0.655000	0.94253	GAC	G|1.000;T|0.000	0.000	weak		0.622	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943	
MYO18A	399687	hgsc.bcm.edu	37	17	27424316	27424316	+	Silent	SNP	G	G	A	rs8067806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:27424316G>A	ENST00000527372.1	-	27	4335	c.4155C>T	c.(4153-4155)acC>acT	p.T1385T	MYO18A_ENST00000533112.1_Silent_p.T1385T|MYO18A_ENST00000354329.4_Silent_p.T1385T|MYO18A_ENST00000531253.1_Silent_p.T1385T	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	1385					actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GCCGTTTCTTGGTGAAGTCCA	0.632													G|||	1320	0.263578	0.1755	0.1571	5008	,	,		15890	0.5833		0.167	False		,,,				2504	0.228				p.T1385T	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.C4155T						PASS	.	G	,	724,3438		69,586,1426	53.0	57.0	56.0		4155,4155	4.8	1.0	17	dbSNP_116	56	1292,7086		85,1122,2982	no	coding-synonymous,coding-synonymous	MYO18A	NM_078471.3,NM_203318.1	,	154,1708,4408	AA,AG,GG		15.4213,17.3955,16.0766	,	1385/2055,1385/2040	27424316	2016,10524	2081	4189	6270	SO:0001819	synonymous_variant	399687	exon27			TTTCTTGGTGAAG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.4155C>T	17.37:g.27424316G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	75	33	0.44	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Silent	SNP	ENST00000527372.1	37	CCDS45642.1																																																																																			G|0.745;A|0.255	0.255	strong		0.632	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
LEPRE1	64175	hgsc.bcm.edu	37	1	43228049	43228049	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43228049G>A	ENST00000296388.5	-	2	614	c.563C>T	c.(562-564)aCc>aTc	p.T188I	LEPRE1_ENST00000236040.4_Missense_Mutation_p.T188I|LEPRE1_ENST00000397054.3_Missense_Mutation_p.T188I			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	188					bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TCCAGACATGGTTTGGTAATA	0.428																																					p.T188I		Atlas-SNP	.											.	LEPRE1	130	.	0			c.C563T						PASS	.						168.0	159.0	162.0					1																	43228049		2203	4300	6503	SO:0001583	missense	64175	exon2			GACATGGTTTGGT	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.563C>T	1.37:g.43228049G>A	ENSP00000296388:p.Thr188Ile	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	117	51	0.435897	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489214	0.44249	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.32988	1.43;1.43;1.43	5.82	4.88	0.63580	Tetratricopeptide-like helical (1);	0.083955	0.85682	D	0.000000	T	0.21962	0.0529	L	0.40543	1.245	0.29400	N	0.862025	P;P;B;P	0.45283	0.855;0.708;0.391;0.544	B;B;B;B	0.37480	0.251;0.251;0.116;0.162	T	0.17077	-1.0381	10	0.45353	T	0.12	-25.5115	7.968	0.30111	0.0835:0.1631:0.7534:0.0	.	188;188;53;188	Q32P28-2;Q32P28-3;B4DNM8;Q32P28	.;.;.;P3H1_HUMAN	I	188;188;188;53	ENSP00000380245:T188I;ENSP00000236040:T188I;ENSP00000296388:T188I	ENSP00000236040:T188I	T	-	2	0	LEPRE1	43000636	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.101000	0.41787	1.400000	0.46741	0.563000	0.77884	ACC	.	.	none		0.428	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
PKD1	5310	hgsc.bcm.edu	37	16	2152387	2152387	+	Missense_Mutation	SNP	A	A	G	rs77028972|rs372874584	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2152387A>G	ENST00000262304.4	-	25	9404	c.9196T>C	c.(9196-9198)Ttt>Ctt	p.F3066L	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Missense_Mutation_p.F3066L	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3066			F -> L (in PKD1; dbSNP:rs77028972). {ECO:0000269|PubMed:10854095, ECO:0000269|PubMed:10923040, ECO:0000269|PubMed:11115377, ECO:0000269|PubMed:11571556, ECO:0000269|PubMed:11857740, ECO:0000269|PubMed:15772804, ECO:0000269|PubMed:18837007, ECO:0000269|PubMed:9285784}.		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						CTCACAGGAAACACAAAGCGG	0.667													a|||	1086	0.216853	0.5552	0.1758	5008	,	,		17100	0.0		0.164	False		,,,				2504	0.0665				p.F3066L		Atlas-SNP	.											.	PKD1	184	.	0			c.T9196C						PASS	.	A	LEU/PHE,LEU/PHE	1321,2867		371,579,1144	9.0	11.0	10.0		9196,9196	-2.7	0.0	16	dbSNP_131	10	698,7632		87,524,3554	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	22,22	458,1103,4698	GG,GA,AA		8.3794,31.5425,16.1288	benign,benign	3066/4303,3066/4304	2152387	2019,10499	2094	4165	6259	SO:0001583	missense	5310	exon25			CAGGAAACACAAA	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.9196T>C	16.37:g.2152387A>G	ENSP00000262304:p.Phe3066Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	97	37	0.381443	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	408	0.18681318681318682	224	0.45528455284552843	65	0.17955801104972377	0	0.0	119	0.15699208443271767	A	13.02	2.111127	0.37242	0.315425	0.083794	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.36878	1.23;1.23	4.38	-2.71	0.05986	.	0.509864	0.21167	N	0.079044	T	0.00012	0.0000	L	0.60455	1.87	0.80722	P	0.0	P;B	0.51791	0.948;0.212	P;B	0.44990	0.466;0.079	T	0.43718	-0.9374	9	0.12430	T	0.62	.	4.6591	0.12634	0.3675:0.0:0.3781:0.2544	rs9935834	3066;3066	P98161-3;P98161	.;PKD1_HUMAN	L	3066;3066;2401	ENSP00000262304:F3066L;ENSP00000399501:F3066L	ENSP00000262304:F3066L	F	-	1	0	PKD1	2092388	0.924000	0.31332	0.001000	0.08648	0.000000	0.00434	0.754000	0.26390	-0.349000	0.08274	-0.624000	0.04008	TTT	A|0.500;G|0.500	0.500	weak		0.667	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
PLD2	5338	hgsc.bcm.edu	37	17	4720522	4720522	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4720522A>T	ENST00000263088.6	+	17	1914	c.1783A>T	c.(1783-1785)Aca>Tca	p.T595S	PLD2_ENST00000572940.1_Missense_Mutation_p.T595S	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	595	Catalytic.				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)	GCTCCCCTTCACACTTCCAGG	0.602																																					p.T595S		Atlas-SNP	.											.	PLD2	138	.	0			c.A1783T						PASS	.						225.0	193.0	204.0					17																	4720522		2203	4300	6503	SO:0001583	missense	5338	exon17			CCCTTCACACTTC	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.1783A>T	17.37:g.4720522A>T	ENSP00000263088:p.Thr595Ser	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	187	79	0.42246	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	A	2.773	-0.255213	0.05829	.	.	ENSG00000129219	ENST00000263088	T	0.05447	3.44	4.48	2.18	0.27775	.	0.430330	0.25572	N	0.029760	T	0.03053	0.0090	N	0.13327	0.33	0.27520	N	0.951422	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.001;0.006;0.002	T	0.40232	-0.9574	10	0.21540	T	0.41	0.6258	3.2221	0.06719	0.6276:0.0:0.1983:0.1741	.	452;595;595	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	S	595	ENSP00000263088:T595S	ENSP00000263088:T595S	T	+	1	0	PLD2	4667488	0.016000	0.18221	0.659000	0.29680	0.288000	0.27193	0.396000	0.20867	0.747000	0.32809	0.454000	0.30748	ACA	.	.	none		0.602	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
ABAT	18	hgsc.bcm.edu	37	16	8868776	8868776	+	Silent	SNP	C	C	A	rs1641022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:8868776C>A	ENST00000396600.2	+	13	1922	c.984C>A	c.(982-984)gtC>gtA	p.V328V	ABAT_ENST00000268251.8_Silent_p.V328V|ABAT_ENST00000569156.1_Silent_p.V328V|ABAT_ENST00000425191.2_Silent_p.V328V|ABAT_ENST00000567812.1_Silent_p.V343V	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	328					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)			breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	TGGACGAGGTCCAGACCGGAG	0.592													C|||	1590	0.317492	0.0552	0.3429	5008	,	,		18174	0.4167		0.4374	False		,,,				2504	0.4284				p.V328V		Atlas-SNP	.											.	ABAT	46	.	0			c.C984A						PASS	.	C	,,	531,3863	240.3+/-251.1	27,477,1693	59.0	56.0	57.0		984,984,984	-1.1	1.0	16	dbSNP_89	57	3661,4939	524.1+/-380.5	782,2097,1421	no	coding-synonymous,coding-synonymous,coding-synonymous	ABAT	NM_000663.4,NM_001127448.1,NM_020686.5	,,	809,2574,3114	AA,AC,CC		42.5698,12.0847,32.261	,,	328/501,328/501,328/501	8868776	4192,8802	2197	4300	6497	SO:0001819	synonymous_variant	18	exon13			CGAGGTCCAGACC	L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"""4-aminobutyrate transaminase"""	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.984C>A	16.37:g.8868776C>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	87	86	0.988506	NM_001127448	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Silent	SNP	ENST00000396600.2	37	CCDS10534.1																																																																																			C|0.674;A|0.326	0.326	strong		0.592	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2	NM_020686	
FDFT1	2222	hgsc.bcm.edu	37	8	11667179	11667179	+	Silent	SNP	C	C	T	rs8417	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:11667179C>T	ENST00000220584.4	+	3	423	c.201C>T	c.(199-201)aaC>aaT	p.N67N	FDFT1_ENST00000538689.1_5'UTR|FDFT1_ENST00000525777.1_5'UTR|FDFT1_ENST00000525900.1_Silent_p.N60N|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000530664.1_Silent_p.N3N|FDFT1_ENST00000528643.1_5'UTR|FDFT1_ENST00000528812.1_Silent_p.N3N|FDFT1_ENST00000443614.2_Silent_p.N67N	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	67					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)		TTTACAGCAACGCAGTGTGCA	0.393													C|||	1191	0.237819	0.0923	0.2406	5008	,	,		20475	0.4474		0.1918	False		,,,				2504	0.2638				p.N67N		Atlas-SNP	.											.	FDFT1	25	.	0			c.C201T						PASS	.	C		514,3892	235.8+/-248.2	25,464,1714	74.0	70.0	72.0		201	-2.9	0.5	8	dbSNP_52	72	1652,6948	305.2+/-307.3	168,1316,2816	no	coding-synonymous	FDFT1	NM_004462.3		193,1780,4530	TT,TC,CC		19.2093,11.6659,16.6539		67/418	11667179	2166,10840	2203	4300	6503	SO:0001819	synonymous_variant	2222	exon3			CAGCAACGCAGTG	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.201C>T	8.37:g.11667179C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	110	51	0.463636	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Silent	SNP	ENST00000220584.4	37	CCDS5985.1																																																																																			C|0.809;T|0.191	0.191	strong		0.393	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
HSPA6	3310	hgsc.bcm.edu	37	1	161496134	161496134	+	Missense_Mutation	SNP	C	C	G	rs753856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161496134C>G	ENST00000309758.4	+	1	2099	c.1686C>G	c.(1684-1686)gaC>gaG	p.D562E	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	562			D -> E (in dbSNP:rs753856). {ECO:0000269|Ref.2}.		ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCCTTAGGGACAAGATTCCCG	0.547													C|||	617	0.123203	0.0265	0.1268	5008	,	,		20455	0.2837		0.1143	False		,,,				2504	0.0951				p.D562E		Atlas-SNP	.											.	HSPA6	53	.	0			c.C1686G						PASS	.	C	GLU/ASP	168,4238		2,164,2037	26.0	26.0	26.0		1686	1.6	0.8	1	dbSNP_86	26	889,7709		46,797,3456	no	missense	HSPA6	NM_002155.3	45	48,961,5493	GG,GC,CC		10.3396,3.813,8.1283	benign	562/644	161496134	1057,11947	2203	4299	6502	SO:0001583	missense	3310	exon1			TAGGGACAAGATT		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.1686C>G	1.37:g.161496134C>G	ENSP00000310219:p.Asp562Glu	Somatic	291	0	0		WXS	Illumina HiSeq	Phase_I	232	225	0.969828	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	302	0.1382783882783883	19	0.03861788617886179	39	0.10773480662983426	153	0.2674825174825175	91	0.12005277044854881	.	13.45	2.240135	0.39598	0.03813	0.103396	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.15139	2.45	3.6	1.6	0.23607	.	0.237482	0.21074	U	0.080613	T	0.08088	0.0202	L	0.35542	1.07	0.44539	P	0.0025079999999999547	B	0.29115	0.233	P	0.45099	0.469	T	0.25745	-1.0123	9	0.51188	T	0.08	.	5.4576	0.16600	0.1978:0.6893:0.0:0.113	rs753856;rs52815568;rs753856	562	P17066	HSP76_HUMAN	E	562;538	ENSP00000310219:D562E	ENSP00000310219:D562E	D	+	3	2	HSPA6	159762758	0.158000	0.22850	0.770000	0.31555	0.633000	0.38033	0.049000	0.14099	0.167000	0.19631	0.591000	0.81541	GAC	C|0.914;G|0.086	0.086	strong		0.547	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
TMEM2	23670	hgsc.bcm.edu	37	9	74360096	74360096	+	Missense_Mutation	SNP	C	C	T	rs25689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:74360096C>T	ENST00000377044.4	-	4	1411	c.872G>A	c.(871-873)cGc>cAc	p.R291H	TMEM2_ENST00000377066.5_Missense_Mutation_p.R291H	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	291			R -> H (in dbSNP:rs25689).|R -> L (in dbSNP:rs25689).|R -> P (in dbSNP:rs25689).		multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GCTCTCATTGCGGTATTCATG	0.483													T|||	1423	0.284145	0.3608	0.2752	5008	,	,		19539	0.1766		0.2187	False		,,,				2504	0.365				p.R291H		Atlas-SNP	.											.	TMEM2	112	.	0			c.G872A						PASS	.	T	HIS/ARG,HIS/ARG	1447,2959	681.5+/-404.0	239,969,995	100.0	98.0	99.0		872,872	6.0	1.0	9	dbSNP_72	99	1817,6783	732.2+/-406.8	187,1443,2670	yes	missense,missense	TMEM2	NM_001135820.1,NM_013390.2	29,29	426,2412,3665	TT,TC,CC		21.1279,32.8416,25.0961	benign,benign	291/1321,291/1384	74360096	3264,9742	2203	4300	6503	SO:0001583	missense	23670	exon4			TCATTGCGGTATT		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.872G>A	9.37:g.74360096C>T	ENSP00000366243:p.Arg291His	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	513	0.2348901098901099	169	0.3434959349593496	81	0.22375690607734808	102	0.17832167832167833	161	0.21240105540897097	T	10.08	1.251990	0.22880	0.328416	0.211279	ENSG00000135048	ENST00000377044;ENST00000377066	T;T	0.73152	-0.72;-0.66	6.03	6.03	0.97812	.	0.486723	0.25836	N	0.027997	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	P	0.999999999999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18147	-1.0346	9	0.33940	T	0.23	.	9.0014	0.36083	0.0:0.0672:0.134:0.7989	rs25689;rs3739782;rs59504885;rs25689	291;291	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	H	291	ENSP00000366243:R291H;ENSP00000366266:R291H	ENSP00000366243:R291H	R	-	2	0	TMEM2	73549916	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	1.925000	0.40074	1.106000	0.41623	-0.254000	0.11334	CGC	T|0.248;C|0.752	0.248	strong		0.483	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390	
RHOD	29984	hgsc.bcm.edu	37	11	66834252	66834252	+	Silent	SNP	C	C	T	rs2282502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:66834252C>T	ENST00000308831.2	+	3	349	c.264C>T	c.(262-264)gaC>gaT	p.D88D	RHOD_ENST00000532559.1_Intron|RHOD_ENST00000533360.1_Silent_p.D88D	NM_014578.3	NP_055393	O00212	RHOD_HUMAN	ras homolog family member D	88					actin filament bundle assembly (GO:0051017)|focal adhesion assembly (GO:0048041)|GTP catabolic process (GO:0006184)|lamellipodium assembly (GO:0030032)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			lung(3)	3						TCTACCCTGACGCCAGCGTCC	0.617													c|||	1912	0.381789	0.1566	0.5115	5008	,	,		19622	0.4524		0.3628	False		,,,				2504	0.5409				p.D88D		Atlas-SNP	.											.	RHOD	8	.	0			c.C264T						PASS	.	T		832,3568	327.7+/-300.2	82,668,1450	160.0	144.0	149.0		264	-9.8	0.1	11	dbSNP_100	149	3126,5464	476.4+/-369.4	574,1978,1743	no	coding-synonymous	RHOD	NM_014578.3		656,2646,3193	TT,TC,CC		36.3912,18.9091,30.4696		88/211	66834252	3958,9032	2200	4295	6495	SO:0001819	synonymous_variant	29984	exon3			CCCTGACGCCAGC	D85815	CCDS8155.1, CCDS73330.1	11q14.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000173156	ENSG00000173156			670	protein-coding gene	gene with protein product	"""Rho-related protein HP1"", ""Rho-related GTP-binding protein RhoD"""	605781	"""ras homolog gene family, member D"""	ARHD		9116026	Standard	NM_014578		Approved	RhoHP1, RhoD, Rho	uc001ojv.3	O00212	OTTHUMG00000167102	ENST00000308831.2:c.264C>T	11.37:g.66834252C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_014578		Silent	SNP	ENST00000308831.2	37	CCDS8155.1																																																																																			C|0.683;G|0.000;T|0.317	0.317	strong		0.617	RHOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393136.1	NM_014578	
SDK1	221935	hgsc.bcm.edu	37	7	4153824	4153824	+	Silent	SNP	A	A	G	rs2141076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4153824A>G	ENST00000404826.2	+	25	3880	c.3741A>G	c.(3739-3741)gaA>gaG	p.E1247E	SDK1_ENST00000389531.3_Silent_p.E1247E	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1247	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AGTGGATGGAATACGAGCTGC	0.642													A|||	655	0.130791	0.2504	0.0836	5008	,	,		15561	0.001		0.1223	False		,,,				2504	0.1452				p.E1247E		Atlas-SNP	.											.	SDK1	361	.	0			c.A3741G						PASS	.	A		995,3411	369.1+/-318.9	121,753,1329	49.0	47.0	48.0		3741	-2.6	0.9	7	dbSNP_96	48	1163,7437	237.4+/-269.2	72,1019,3209	no	coding-synonymous	SDK1	NM_152744.3		193,1772,4538	GG,GA,AA		13.5233,22.5828,16.5923		1247/2214	4153824	2158,10848	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon25			GATGGAATACGAG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3741A>G	7.37:g.4153824A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			A|0.851;G|0.149	0.149	strong		0.642	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
FAM188B	84182	hgsc.bcm.edu	37	7	30880413	30880413	+	Missense_Mutation	SNP	G	G	A	rs34970833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:30880413G>A	ENST00000265299.6	+	9	1471	c.1394G>A	c.(1393-1395)tGt>tAt	p.C465Y	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	465			C -> Y (in dbSNP:rs34970833).							endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GTCCAAGGCTGTGTCCTACAG	0.507													G|||	81	0.0161741	0.0008	0.0187	5008	,	,		19811	0.0		0.0427	False		,,,				2504	0.0245				p.C465Y		Atlas-SNP	.											.	FAM188B	62	.	0			c.G1394A						PASS	.	G	TYR/CYS	42,3928		0,42,1943	87.0	88.0	87.0		1394	4.9	1.0	7	dbSNP_126	87	439,7905		9,421,3742	yes	missense	FAM188B	NM_032222.2	194	9,463,5685	AA,AG,GG		5.2613,1.0579,3.9061	benign	465/758	30880413	481,11833	1985	4172	6157	SO:0001583	missense	84182	exon9			AAGGCTGTGTCCT	AK026027	CCDS43565.1	7p14.3	2010-08-17	2009-07-14	2009-07-14	ENSG00000106125	ENSG00000106125			21916	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 67"""	C7orf67			Standard	NM_032222		Approved	FLJ22374	uc003tbt.3	Q4G0A6	OTTHUMG00000152800	ENST00000265299.6:c.1394G>A	7.37:g.30880413G>A	ENSP00000265299:p.Cys465Tyr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	43	0.019688644688644688	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	34	0.044854881266490766	G	15.49	2.848205	0.51164	0.010579	0.052613	ENSG00000106125	ENST00000265299	T	0.27256	1.68	4.93	4.93	0.64822	.	0.108661	0.64402	D	0.000004	T	0.02610	0.0079	N	0.11201	0.11	0.58432	D	0.999998	B	0.26635	0.155	B	0.30105	0.111	T	0.08391	-1.0724	10	0.87932	D	0	-9.9148	15.6843	0.77396	0.0:0.0:1.0:0.0	rs34970833	465	Q4G0A6	F188B_HUMAN	Y	465	ENSP00000265299:C465Y	ENSP00000265299:C465Y	C	+	2	0	FAM188B	30846938	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.468000	0.53086	2.571000	0.86741	0.561000	0.74099	TGT	G|0.973;A|0.027	0.027	strong		0.507	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	
DHX38	9785	hgsc.bcm.edu	37	16	72130815	72130815	+	Silent	SNP	C	C	A	rs1050362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:72130815C>A	ENST00000268482.3	+	3	927	c.418C>A	c.(418-420)Cgg>Agg	p.R140R	DHX38_ENST00000536867.1_Intron|TXNL4B_ENST00000426362.2_5'Flank	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	140					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				GCGGGAGCGGCGGGAACATGG	0.537													C|||	2395	0.478235	0.7874	0.3156	5008	,	,		19363	0.3105		0.3549	False		,,,				2504	0.4755				p.R140R	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,right_upper_lobe,carcinoma,-2,2	DHX38	91	2	0			c.C418A						PASS	.	C		3048,1348	692.2+/-405.5	1072,904,222	151.0	146.0	148.0		418	4.1	1.0	16	dbSNP_86	148	3214,5386	484.9+/-371.5	591,2032,1677	no	coding-synonymous	DHX38	NM_014003.3		1663,2936,1899	AA,AC,CC		37.3721,30.6642,48.1841		140/1228	72130815	6262,6734	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon3			GAGCGGCGGGAAC	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.418C>A	16.37:g.72130815C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	114	61	0.535088	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			C|0.529;A|0.471	0.471	strong		0.537	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
SORD	6652	hgsc.bcm.edu	37	15	45361180	45361180	+	Missense_Mutation	SNP	A	A	T	rs55739437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:45361180A>T	ENST00000267814.9	+	7	896	c.716A>T	c.(715-717)cAg>cTg	p.Q239L	SORD_ENST00000558580.1_Missense_Mutation_p.Q218L	NM_003104.5	NP_003095.2	Q00796	DHSO_HUMAN	sorbitol dehydrogenase	239			Q -> L (in dbSNP:rs55739437). {ECO:0000269|PubMed:7782086}.		fructose biosynthetic process (GO:0046370)|glucose metabolic process (GO:0006006)|L-xylitol catabolic process (GO:0051160)|L-xylitol metabolic process (GO:0051164)|sorbitol catabolic process (GO:0006062)|sperm motility (GO:0030317)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)	carbohydrate binding (GO:0030246)|L-iditol 2-dehydrogenase activity (GO:0003939)|NAD binding (GO:0051287)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(3)|lung(4)	9		all_cancers(109;3.43e-12)|all_epithelial(112;2.33e-10)|Lung NSC(122;6.01e-07)|all_lung(180;4.38e-06)|Melanoma(134;0.0122)		all cancers(107;1.6e-18)|GBM - Glioblastoma multiforme(94;4.95e-07)|COAD - Colon adenocarcinoma(120;0.0704)|Colorectal(133;0.0706)		GTAGAAGGTCAGCTGGGGTGC	0.582													.|||	1678	0.335064	0.6664	0.2867	5008	,	,		12388	0.2202		0.1799	False		,,,				2504	0.1994				p.Q239L		Atlas-SNP	.											.	SORD	24	.	0			c.A716T						PASS	.	T	LEU/GLN	2459,1937		652,1155,391	33.0	38.0	36.0		716	4.7	0.1	15	dbSNP_129	36	1338,7258		46,1246,3006	yes	missense	SORD	NM_003104.5	113	698,2401,3397	TT,TA,AA		15.5654,44.0628,29.2257	benign	239/358	45361180	3797,9195	2198	4298	6496	SO:0001583	missense	6652	exon7			AAGGTCAGCTGGG		CCDS10116.1	15q15-q21.1	2012-10-02			ENSG00000140263	ENSG00000140263	1.1.1.14		11184	protein-coding gene	gene with protein product		182500				7782086	Standard	NM_003104		Approved		uc001zul.4	Q00796	OTTHUMG00000131265	ENST00000267814.9:c.716A>T	15.37:g.45361180A>T	ENSP00000267814:p.Gln239Leu	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	226	90	0.39823	NM_003104	B2R655|B7Z3A6|J3JZZ5|Q16682|Q9UMD6	Missense_Mutation	SNP	ENST00000267814.9	37	CCDS10116.1	503	0.2303113553113553	287	0.5833333333333334	70	0.19337016574585636	64	0.11188811188811189	82	0.10817941952506596	T	7.574	0.667425	0.14710	0.559372	0.155654	ENSG00000140263	ENST00000267814	T	0.04234	3.67	4.74	4.74	0.60224	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.335846	0.28459	N	0.015261	T	0.00012	0.0000	N	0.00670	-1.27	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15464	-1.0436	9	0.21014	T	0.42	-13.1845	10.1157	0.42589	0.1501:0.0:0.0:0.8499	rs55739437;rs62621228	160;239	B4DKI2;Q00796	.;DHSO_HUMAN	L	239	ENSP00000267814:Q239L	ENSP00000267814:Q239L	Q	+	2	0	SORD	43148472	0.996000	0.38824	0.078000	0.20375	0.622000	0.37654	2.525000	0.45598	0.669000	0.31146	-0.527000	0.04329	CAG	A|0.734;T|0.266	0.266	strong		0.582	SORD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254033.3		
MICAL3	57553	hgsc.bcm.edu	37	22	18304821	18304821	+	Silent	SNP	G	G	A	rs45514595	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18304821G>A	ENST00000441493.2	-	24	3775	c.3423C>T	c.(3421-3423)ccC>ccT	p.P1141P		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1141	Pro-rich.				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)		TCGGTGAGGCGGGCAGCTTCT	0.577													G|||	431	0.0860623	0.1422	0.0389	5008	,	,		18938	0.0823		0.0586	False		,,,				2504	0.0757				p.P1141P		Atlas-SNP	.											.	MICAL3	53	.	0			c.C3423T						PASS	.	G		586,3606		39,508,1549	106.0	118.0	114.0		3423	-7.5	0.0	22	dbSNP_127	114	457,7967		9,439,3764	no	coding-synonymous	MICAL3	NM_015241.2		48,947,5313	AA,AG,GG		5.425,13.979,8.2673		1141/2003	18304821	1043,11573	2096	4212	6308	SO:0001819	synonymous_variant	57553	exon24			TGAGGCGGGCAGC	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.3423C>T	22.37:g.18304821G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	38	11	0.289474	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1	189	0.08653846153846154	67	0.13617886178861788	17	0.04696132596685083	54	0.0944055944055944	51	0.06728232189973615	G	4.226	0.040865	0.08196	0.13979	0.05425	ENSG00000093100	ENST00000252134	.	.	.	3.74	-7.49	0.01355	.	.	.	.	.	T	0.00271	0.0008	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.33650	-0.9860	4	0.87932	D	0	.	6.8292	0.23900	0.3494:0.1729:0.4777:0.0	rs45514595;rs60227255;rs61741792	.	.	.	L	123	.	ENSP00000252134:P123L	P	-	2	0	XXbac-B461K10.4	16684821	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.878000	0.04192	-1.682000	0.01446	-0.378000	0.06908	CCG	G|0.921;A|0.079	0.079	strong		0.577	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
IL20RA	53832	hgsc.bcm.edu	37	6	137323213	137323213	+	Missense_Mutation	SNP	G	G	A	rs1342642	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:137323213G>A	ENST00000316649.5	-	7	1379	c.1144C>T	c.(1144-1146)Ctc>Ttc	p.L382F	IL20RA_ENST00000468393.1_5'Flank|RP11-204P2.3_ENST00000458017.1_RNA|IL20RA_ENST00000541547.1_Missense_Mutation_p.L333F|IL20RA_ENST00000367748.1_Missense_Mutation_p.L271F	NM_001278722.1|NM_014432.2	NP_001265651.1|NP_055247	Q9UHF4	I20RA_HUMAN	interleukin 20 receptor, alpha	382			L -> F (in dbSNP:rs1342642). {ECO:0000269|Ref.1}.		cytokine-mediated signaling pathway (GO:0019221)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of bone resorption (GO:0045124)	integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	27	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000351)|OV - Ovarian serous cystadenocarcinoma(155;0.00459)		TGCTGGGTGAGAGAAGTACCT	0.463													G|||	1000	0.199681	0.2383	0.183	5008	,	,		19502	0.0714		0.2594	False		,,,				2504	0.2301				p.L382F		Atlas-SNP	.											.	IL20RA	54	.	0			c.C1144T						PASS	.	G	PHE/LEU	977,3429	366.4+/-317.8	118,741,1344	79.0	74.0	76.0		1144	0.2	0.0	6	dbSNP_88	76	2322,6278	387.8+/-342.3	319,1684,2297	yes	missense	IL20RA	NM_014432.2	22	437,2425,3641	AA,AG,GG		27.0,22.1743,25.3652	possibly-damaging	382/554	137323213	3299,9707	2203	4300	6503	SO:0001583	missense	53832	exon7			GGGTGAGAGAAGT	AF184971	CCDS5181.1, CCDS64535.1, CCDS64536.1	6q23.3	2008-02-05			ENSG00000016402	ENSG00000016402		"""Interleukins and interleukin receptors"""	6003	protein-coding gene	gene with protein product		605620				10875937, 11163236	Standard	NM_001278724		Approved	ZCYTOR7, IL-20R1	uc003qhj.3	Q9UHF4	OTTHUMG00000015654	ENST00000316649.5:c.1144C>T	6.37:g.137323213G>A	ENSP00000314976:p.Leu382Phe	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	79	64	0.810127	NM_014432	B4DLR5|F5H675|Q14CW2|Q6UWA9|Q96SH8	Missense_Mutation	SNP	ENST00000316649.5	37	CCDS5181.1	450	0.20604395604395603	137	0.2784552845528455	69	0.19060773480662985	47	0.08216783216783216	197	0.2598944591029024	G	15.12	2.740564	0.49045	0.221743	0.27	ENSG00000016402	ENST00000316649;ENST00000367748;ENST00000541547	T;T;T	0.62232	0.3;1.76;0.04	5.76	0.246	0.15516	.	6.474150	0.00914	N	0.002515	T	0.48150	0.1484	L	0.56769	1.78	0.80722	P	0.0	P;P	0.49961	0.899;0.93	P;B	0.48840	0.592;0.38	T	0.18745	-1.0327	9	0.46703	T	0.11	-0.0228	6.7229	0.23340	0.0755:0.4712:0.3326:0.1207	rs1342642;rs17310128;rs52809262;rs61018497;rs1342642	271;382	Q9UHF4-2;Q9UHF4	.;I20RA_HUMAN	F	382;271;333	ENSP00000314976:L382F;ENSP00000356722:L271F;ENSP00000437843:L333F	ENSP00000314976:L382F	L	-	1	0	IL20RA	137364906	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.732000	0.26072	0.013000	0.14918	0.655000	0.94253	CTC	G|0.794;N|0.001	.	strong		0.463	IL20RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042393.1	NM_014432	
APCDD1L	164284	hgsc.bcm.edu	37	20	57045667	57045667	+	Silent	SNP	T	T	C	rs1980576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:57045667T>C	ENST00000371149.3	-	2	416	c.186A>G	c.(184-186)acA>acG	p.T62T	APCDD1L_ENST00000439429.1_Silent_p.T73T	NM_153360.1	NP_699191.1	Q8NCL9	APCDL_HUMAN	adenomatosis polyposis coli down-regulated 1-like	62						integral component of membrane (GO:0016021)				large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(1)	18	Lung NSC(12;0.000856)|all_lung(29;0.0025)		BRCA - Breast invasive adenocarcinoma(13;5.6e-11)|Epithelial(14;1.67e-07)|all cancers(14;1.48e-06)			AGTCTTACCCTGTGGAGATCC	0.567													C|||	2303	0.459864	0.6157	0.4265	5008	,	,		17671	0.3978		0.3688	False		,,,				2504	0.4305				p.T62T		Atlas-SNP	.											.	APCDD1L	48	.	0			c.A186G						PASS	.	C		2475,1931		711,1053,439	57.0	45.0	49.0		186	-4.1	1.0	20	dbSNP_92	49	3123,5475		553,2017,1729	no	coding-synonymous	APCDD1L	NM_153360.1		1264,3070,2168	CC,CT,TT		36.3224,43.8266,43.0483		62/502	57045667	5598,7406	2203	4299	6502	SO:0001819	synonymous_variant	164284	exon2			TTACCCTGTGGAG	AK074647	CCDS13467.1	20q13.32	2006-07-07			ENSG00000198768	ENSG00000198768			26892	protein-coding gene	gene with protein product							Standard	NM_153360		Approved	FLJ90166	uc002xze.1	Q8NCL9	OTTHUMG00000032845	ENST00000371149.3:c.186A>G	20.37:g.57045667T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_153360		Silent	SNP	ENST00000371149.3	37	CCDS13467.1																																																																																			T|0.564;C|0.436	0.436	strong		0.567	APCDD1L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000079881.2	NM_153360	
STAB1	23166	hgsc.bcm.edu	37	3	52558133	52558133	+	Silent	SNP	T	T	C	rs13621	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52558133T>C	ENST00000321725.6	+	68	7636	c.7560T>C	c.(7558-7560)gaT>gaC	p.D2520D		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2520					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)		ATGATGCTGATGACGACTTCT	0.607													C|||	1958	0.390974	0.3343	0.5115	5008	,	,		18731	0.4296		0.4652	False		,,,				2504	0.2658				p.D2520D		Atlas-SNP	.											.	STAB1	178	.	0			c.T7560C						PASS	.	C		1356,3050	689.8+/-405.2	215,926,1062	168.0	154.0	159.0		7560	-11.6	0.0	3	dbSNP_52	159	4027,4573	598.1+/-393.9	980,2067,1253	no	coding-synonymous	STAB1	NM_015136.2		1195,2993,2315	CC,CT,TT		46.8256,30.7762,41.3886		2520/2571	52558133	5383,7623	2203	4300	6503	SO:0001819	synonymous_variant	23166	exon68			TGCTGATGACGAC	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.7560T>C	3.37:g.52558133T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	138	68	0.492754	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1	990	0.4532967032967033	163	0.3313008130081301	189	0.5220994475138122	282	0.493006993006993	356	0.46965699208443273	C	0.092	-1.165587	0.01673	0.307762	0.468256	ENSG00000010327	ENST00000469989	.	.	.	5.78	-11.6	0.00059	.	.	.	.	.	.	.	.	.	.	.	0.39327	P	0.03464400000000001	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.3452	0.11129	0.128:0.3704:0.2691:0.2325	rs13621;rs1131676;rs3191792;rs4687623;rs11547690;rs58635685	.	.	.	R	127	.	.	X	+	1	0	STAB1	52533173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.305000	0.00256	-3.572000	0.00139	-4.178000	0.00010	TGA	A|0.000;C|0.428;G|0.000;T|0.572	0.428	strong		0.607	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
C1orf123	54987	hgsc.bcm.edu	37	1	53681699	53681699	+	Silent	SNP	T	T	G	rs1134688	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:53681699T>G	ENST00000294360.4	-	7	410	c.369A>C	c.(367-369)tcA>tcC	p.S123S	RP5-1024G6.2_ENST00000452466.1_RNA|C1orf123_ENST00000470385.1_5'UTR	NM_017887.1	NP_060357.1	Q9NWV4	CA123_HUMAN	chromosome 1 open reading frame 123	123						extracellular vesicular exosome (GO:0070062)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|pancreas(2)|skin(1)	6						AGGCTGTCCCTGACTCCACAC	0.517													T|||	500	0.0998403	0.0227	0.1542	5008	,	,		19147	0.0813		0.2078	False		,,,				2504	0.0736				p.S123S		Atlas-SNP	.											.	C1orf123	9	.	0			c.A369C						PASS	.	T		240,4166	140.8+/-176.2	7,226,1970	142.0	131.0	135.0		369	-11.4	0.4	1	dbSNP_86	135	1933,6667	341.2+/-323.9	208,1517,2575	no	coding-synonymous	C1orf123	NM_017887.1		215,1743,4545	GG,GT,TT		22.4767,5.4471,16.7077		123/161	53681699	2173,10833	2203	4300	6503	SO:0001819	synonymous_variant	54987	exon7			TGTCCCTGACTCC	BC010908	CCDS576.1	1p32.3	2011-02-18			ENSG00000162384	ENSG00000162384			26059	protein-coding gene	gene with protein product						12477932	Standard	NM_017887		Approved	FLJ20580	uc001cvd.3	Q9NWV4	OTTHUMG00000008940	ENST00000294360.4:c.369A>C	1.37:g.53681699T>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_017887		Silent	SNP	ENST00000294360.4	37	CCDS576.1	280	0.1282051282051282	14	0.028455284552845527	68	0.1878453038674033	53	0.09265734265734266	145	0.19129287598944592	T	7.846	0.722953	0.15439	0.054471	0.224767	ENSG00000162384	ENST00000371480	.	.	.	5.7	-11.4	0.00090	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.28522	-1.0041	4	0.59425	D	0.04	-2.5814	7.3621	0.26752	0.0716:0.093:0.2523:0.5831	rs1134688;rs2297665;rs3196986;rs17369346	.	.	.	P	103	.	ENSP00000360535:Q103P	Q	-	2	0	C1orf123	53454287	0.000000	0.05858	0.433000	0.26760	0.044000	0.14063	-2.547000	0.00931	-2.135000	0.00811	-0.993000	0.02533	CAG	T|0.843;G|0.157	0.157	strong		0.517	C1orf123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024751.1	NM_017887	
ZNF341	84905	hgsc.bcm.edu	37	20	32376745	32376745	+	Silent	SNP	C	C	T	rs140105337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:32376745C>T	ENST00000375200.1	+	13	2294	c.1929C>T	c.(1927-1929)atC>atT	p.I643I	RP4-553F4.6_ENST00000443171.1_RNA|ZNF341_ENST00000342427.2_Silent_p.I636I|RP4-553F4.6_ENST00000439444.1_RNA|RP4-553F4.6_ENST00000423074.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	643					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						ACATGTTGATCCACGAGCCCT	0.547													C|||	47	0.00938498	0.0015	0.013	5008	,	,		17818	0.0		0.0288	False		,,,				2504	0.0072				p.I636I		Atlas-SNP	.											.	ZNF341	73	.	0			c.C1908T						PASS	.	C		29,4377	35.2+/-66.4	0,29,2174	124.0	102.0	109.0		1908	2.8	1.0	20	dbSNP_134	109	214,8386	90.4+/-152.6	3,208,4089	no	coding-synonymous	ZNF341	NM_032819.3		3,237,6263	TT,TC,CC		2.4884,0.6582,1.8684		636/848	32376745	243,12763	2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GTTGATCCACGAG	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.1929C>T	20.37:g.32376745C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	165	78	0.472727	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				C|0.983;T|0.017	0.017	strong		0.547	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
HR	55806	hgsc.bcm.edu	37	8	21984945	21984945	+	Missense_Mutation	SNP	C	C	T	rs12675375	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:21984945C>T	ENST00000381418.4	-	3	2490	c.1010G>A	c.(1009-1011)gGt>gAt	p.G337D	HR_ENST00000312841.8_Missense_Mutation_p.G337D	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	337			G -> D (in dbSNP:rs12675375). {ECO:0000269|PubMed:10051399, ECO:0000269|PubMed:9445480, ECO:0000269|PubMed:9736769}.		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		AGGGCCAAGACCCCCACCTTT	0.667													C|||	1484	0.296326	0.1884	0.2118	5008	,	,		16981	0.372		0.2952	False		,,,				2504	0.4254				p.G337D		Atlas-SNP	.											HR,NS,carcinoma,0,1	HR	71	1	0			c.G1010A						PASS	.	C	ASP/GLY,ASP/GLY	860,3544	323.7+/-298.2	79,702,1421	33.0	39.0	37.0		1010,1010	1.6	0.0	8	dbSNP_120	37	2790,5810	430.1+/-356.4	478,1834,1988	yes	missense,missense	HR	NM_005144.4,NM_018411.4	94,94	557,2536,3409	TT,TC,CC		32.4419,19.5277,28.0683	benign,benign	337/1190,337/1135	21984945	3650,9354	2202	4300	6502	SO:0001583	missense	55806	exon3			CCAAGACCCCCAC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.1010G>A	8.37:g.21984945C>T	ENSP00000370826:p.Gly337Asp	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	108	55	0.509259	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	585	0.26785714285714285	66	0.13414634146341464	85	0.23480662983425415	218	0.3811188811188811	216	0.2849604221635884	C	7.416	0.635780	0.14386	0.195277	0.324419	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.70045	-0.45;-0.45	5.79	1.65	0.23941	.	0.645821	0.14411	N	0.321271	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.14805	0.011;0.007	B;B	0.14578	0.011;0.005	T	0.27739	-1.0065	9	0.05436	T	0.98	-0.0625	4.6009	0.12352	0.0:0.4401:0.3431:0.2168	rs12675375;rs57637529	337;337	O43593-2;O43593	.;HAIR_HUMAN	D	337	ENSP00000370826:G337D;ENSP00000326765:G337D	ENSP00000326765:G337D	G	-	2	0	HR	22040890	0.000000	0.05858	0.000000	0.03702	0.638000	0.38207	0.573000	0.23699	0.009000	0.14813	-0.502000	0.04539	GGT	C|0.723;T|0.277	0.277	strong		0.667	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
KRT6B	3854	hgsc.bcm.edu	37	12	52844243	52844243	+	Silent	SNP	A	A	G	rs28414881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52844243A>G	ENST00000252252.3	-	2	749	c.702T>C	c.(700-702)cgT>cgC	p.R234R		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	234	Coil 1B.|Rod.				ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CCGAGTCCAGACGACCCCGTT	0.552													A|||	394	0.0786741	0.0061	0.0821	5008	,	,		24489	0.1875		0.0875	False		,,,				2504	0.0532				p.R234R		Atlas-SNP	.											KRT6B,NS,carcinoma,-1,1	KRT6B	90	1	0			c.T702C						scavenged	.						211.0	184.0	193.0					12																	52844243		2203	4300	6503	SO:0001819	synonymous_variant	3854	exon2			GTCCAGACGACCC	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.702T>C	12.37:g.52844243A>G		Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	388	62	0.159794	NM_005555	P48669	Silent	SNP	ENST00000252252.3	37	CCDS8828.1																																																																																			A|0.959;G|0.041	0.041	strong		0.552	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
MNX1	3110	hgsc.bcm.edu	37	7	156802363	156802363	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:156802363C>T	ENST00000252971.6	-	1	982	c.682G>A	c.(682-684)Gac>Aac	p.D228N	MNX1_ENST00000543409.1_5'Flank|MNX1_ENST00000469500.1_5'Flank|MNX1-AS2_ENST00000429228.1_RNA|MNX1-AS1_ENST00000480284.1_RNA	NM_005515.3	NP_005506.3	P50219	MNX1_HUMAN	motor neuron and pancreas homeobox 1	228					anatomical structure morphogenesis (GO:0009653)|diaphragm development (GO:0060539)|dorsal/ventral neural tube patterning (GO:0021904)|endocrine pancreas development (GO:0031018)|humoral immune response (GO:0006959)|motor neuron axon guidance (GO:0008045)|nerve development (GO:0021675)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGTTGAAGTCGGGCATCTTA	0.716																																					p.D228N		Atlas-SNP	.											.	MNX1	17	.	0			c.G682A						PASS	.						11.0	12.0	12.0					7																	156802363		2137	4195	6332	SO:0001583	missense	3110	exon1			TGAAGTCGGGCAT	AF107457	CCDS34788.1, CCDS55187.1	7q36	2012-03-09	2007-08-09	2007-08-09	ENSG00000130675	ENSG00000130675		"""Homeoboxes / ANTP class : HOXL subclass"""	4979	protein-coding gene	gene with protein product		142994	"""homeo box HB9"", ""homeobox HB9"""	HLXB9		9843207	Standard	NM_001165255		Approved	HB9, HOXHB9, SCRA1	uc003wmz.4	P50219	OTTHUMG00000157181	ENST00000252971.6:c.682G>A	7.37:g.156802363C>T	ENSP00000252971:p.Asp228Asn	Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_005515	F5H401|Q9Y648	Missense_Mutation	SNP	ENST00000252971.6	37	CCDS34788.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.603729	0.87157	.	.	ENSG00000130675	ENST00000252971;ENST00000542972	D	0.95656	-3.77	3.12	2.21	0.28008	Homeodomain-like (1);	0.000000	0.40222	U	0.001156	D	0.96034	0.8708	M	0.65498	2.005	0.80722	D	1	D	0.71674	0.998	P	0.59115	0.852	D	0.95038	0.8175	10	0.66056	D	0.02	-25.9529	11.1823	0.48636	0.0:0.8115:0.1885:0.0	.	228	P50219	MNX1_HUMAN	N	228;58	ENSP00000252971:D228N	ENSP00000252971:D228N	D	-	1	0	MNX1	156495124	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	4.845000	0.62853	0.536000	0.28733	0.549000	0.68633	GAC	.	.	none		0.716	MNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347796.3		
OR2T5	401993	hgsc.bcm.edu	37	1	248652011	248652011	+	Missense_Mutation	SNP	A	A	T	rs150528589	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248652011A>T	ENST00000366473.2	+	1	127	c.122A>T	c.(121-123)aAg>aTg	p.K41M		NM_001004697.1	NP_001004697.1	Q6IEZ7	OR2T5_HUMAN	olfactory receptor, family 2, subfamily T, member 5	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K41M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(2)|pancreas(1)|skin(2)	9	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTTTTCCTGAAGGCGTTGTCT	0.478													.|||	1961	0.391573	0.7307	0.2147	5008	,	,		28057	0.3542		0.1889	False		,,,				2504	0.3057				p.K41M		Atlas-SNP	.											OR2T5,NS,other,0,1	OR2T5	17	1	1	Substitution - Missense(1)	pancreas(1)	c.A122T						scavenged	.	T	MET/LYS	2044,2150		554,936,607	81.0	103.0	96.0		122	1.3	0.2	1	dbSNP_134	96	674,7914		4,666,3624	no	missense	OR2T5	NM_001004697.1	95	558,1602,4231	TT,TA,AA		7.8482,48.7363,21.2643	benign	41/316	248652011	2718,10064	2097	4294	6391	SO:0001583	missense	401993	exon1			TCCTGAAGGCGTT	BK004465	CCDS31118.1	1q44	2012-08-09			ENSG00000203661	ENSG00000203661		"""GPCR / Class A : Olfactory receptors"""	15017	protein-coding gene	gene with protein product							Standard	NM_001004697		Approved		uc001iem.1	Q6IEZ7	OTTHUMG00000040481	ENST00000366473.2:c.122A>T	1.37:g.248652011A>T	ENSP00000355429:p.Lys41Met	Somatic	747	2	0.00267738		WXS	Illumina HiSeq	Phase_I	734	109	0.148501	NM_001004697		Missense_Mutation	SNP	ENST00000366473.2	37	CCDS31118.1	.	.	.	.	.	.	.	.	.	.	t	0.019	-1.457006	0.01071	0.487363	0.078482	ENSG00000203661	ENST00000366473	T	0.00424	7.45	2.64	1.27	0.21489	.	0.130450	0.36409	N	0.002609	T	0.00012	0.0000	N	0.00023	-2.71	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18398	-1.0338	9	0.02654	T	1	.	7.1342	0.25519	0.3491:0.0:0.0:0.6509	.	41	Q6IEZ7	OR2T5_HUMAN	M	41	ENSP00000355429:K41M	ENSP00000355429:K41M	K	+	2	0	OR2T5	246718634	0.007000	0.16637	0.198000	0.23420	0.062000	0.15995	1.733000	0.38156	0.108000	0.17862	-1.793000	0.00626	AAG	A|0.250;T|0.750	0.750	weak		0.478	OR2T5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097422.1	NM_001004697	
COL14A1	7373	hgsc.bcm.edu	37	8	121222046	121222046	+	Missense_Mutation	SNP	G	G	A	rs61753752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:121222046G>A	ENST00000297848.3	+	12	1643	c.1373G>A	c.(1372-1374)aGc>aAc	p.S458N	COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000247781.3_Missense_Mutation_p.S363N|COL14A1_ENST00000537875.1_Missense_Mutation_p.S458N|COL14A1_ENST00000309791.4_Missense_Mutation_p.S458N	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)			ACTGAGAACAGCATGCGAGTC	0.468													G|||	5	0.000998403	0.0	0.0029	5008	,	,		14372	0.0		0.003	False		,,,				2504	0.0				p.S458N		Atlas-SNP	.											COL14A1,NS,carcinoma,-1,1	COL14A1	292	1	0			c.G1373A						PASS	.	G	ASN/SER	2,4404	2.1+/-5.4	0,2,2201	119.0	111.0	114.0		1373	5.3	1.0	8	dbSNP_129	114	26,8574	18.5+/-59.3	0,26,4274	yes	missense	COL14A1	NM_021110.1	46	0,28,6475	AA,AG,GG		0.3023,0.0454,0.2153	probably-damaging	458/1797	121222046	28,12978	2203	4300	6503	SO:0001583	missense	7373	exon12			AGAACAGCATGCG		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.1373G>A	8.37:g.121222046G>A	ENSP00000297848:p.Ser458Asn	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	114	56	0.491228	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	17.53	3.412148	0.62511	4.54E-4	0.003023	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620	T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01	5.31	5.31	0.75309	Fibronectin, type III (4);	0.148564	0.64402	D	0.000013	T	0.79616	0.4476	M	0.84156	2.68	0.48135	D	0.999599	D;D	0.67145	0.996;0.99	P;P	0.60173	0.857;0.87	T	0.82534	-0.0409	10	0.87932	D	0	.	19.1802	0.93620	0.0:0.0:1.0:0.0	rs61753752	458;458	Q05707-2;Q05707	.;COEA1_HUMAN	N	458;458;458;363;271	ENSP00000443974:S458N;ENSP00000311809:S458N;ENSP00000297848:S458N;ENSP00000247781:S363N;ENSP00000409461:S271N	ENSP00000247781:S363N	S	+	2	0	COL14A1	121291227	1.000000	0.71417	0.960000	0.40013	0.256000	0.26092	4.592000	0.61027	2.748000	0.94277	0.650000	0.86243	AGC	G|0.998;A|0.002	0.002	strong		0.468	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
MEF2D	4209	hgsc.bcm.edu	37	1	156450719	156450719	+	Silent	SNP	G	G	A	rs1185700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156450719G>A	ENST00000348159.4	-	4	783	c.303C>T	c.(301-303)ccC>ccT	p.P101P	MEF2D_ENST00000464356.2_Intron|MEF2D_ENST00000353795.3_Intron|MEF2D_ENST00000360595.3_Silent_p.P101P|MEF2D_ENST00000340875.5_Intron|MEF2D_ENST00000368240.2_Silent_p.P101P	NM_005920.2	NP_005911.1	Q14814	MEF2D_HUMAN	myocyte enhancer factor 2D	101					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|chondrocyte differentiation (GO:0002062)|endochondral ossification (GO:0001958)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|histone deacetylase binding (GO:0042826)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|urinary_tract(1)	15	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCTCCCCGTCGGGCTCGGGGC	0.677											OREG0013874	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1165	0.232628	0.1808	0.2983	5008	,	,		14474	0.245		0.2386	False		,,,				2504	0.2372				p.P101P		Atlas-SNP	.											.	MEF2D	43	.	0			c.C303T						PASS	.	G		932,3472	332.3+/-302.4	90,752,1360	74.0	84.0	81.0		303	-7.7	0.8	1	dbSNP_87	81	1987,6611	330.6+/-319.3	245,1497,2557	no	coding-synonymous	MEF2D	NM_005920.2		335,2249,3917	AA,AG,GG		23.11,21.1626,22.4504		101/522	156450719	2919,10083	2202	4299	6501	SO:0001819	synonymous_variant	4209	exon4			CCCGTCGGGCTCG	BC054520	CCDS1143.1, CCDS60304.1	1q12-q23	2008-02-05	2007-04-24		ENSG00000116604	ENSG00000116604		"""Myocyte enhancer factors"""	6997	protein-coding gene	gene with protein product		600663				8269842	Standard	NM_005920		Approved		uc001fpb.4	Q14814	OTTHUMG00000033095	ENST00000348159.4:c.303C>T	1.37:g.156450719G>A		Somatic	105	1	0.00952381	1778	WXS	Illumina HiSeq	Phase_I	124	121	0.975806	NM_005920	D3DVC0|Q14815|Q5T9U5|Q5T9U6	Silent	SNP	ENST00000348159.4	37	CCDS1143.1																																																																																			G|0.766;A|0.234	0.234	strong		0.677	MEF2D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080562.2	NM_005920	
CEP164	22897	hgsc.bcm.edu	37	11	117209340	117209340	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:117209340T>C	ENST00000278935.3	+	3	185	c.38T>C	c.(37-39)gTt>gCt	p.V13A		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	13	Interaction with ATRIP.				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)		p.V13G(1)		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)		GATCAGCTGGTTCTGGAAGAA	0.488																																					p.V13A		Atlas-SNP	.											CEP164,colon,carcinoma,0,1	CEP164	121	1	1	Substitution - Missense(1)	large_intestine(1)	c.T38C						scavenged	.						153.0	148.0	150.0					11																	117209340		2201	4296	6497	SO:0001583	missense	22897	exon2			AGCTGGTTCTGGA	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.38T>C	11.37:g.117209340T>C	ENSP00000278935:p.Val13Ala	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	152	5	0.0328947	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.704397	0.88924	.	.	ENSG00000110274	ENST00000525734;ENST00000278935;ENST00000527609;ENST00000533570;ENST00000529538	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	4.94	4.94	0.65067	.	0.178467	0.26948	N	0.021683	T	0.69333	0.3099	M	0.77486	2.375	0.43007	D	0.994536	P;P;P	0.49961	0.884;0.68;0.93	B;B;P	0.47915	0.358;0.356;0.561	T	0.75863	-0.3167	10	0.72032	D	0.01	-5.9579	13.7153	0.62693	0.0:0.0:0.0:1.0	.	13;13;13	E9PI34;Q9UPV0;Q9UPV0-2	.;CE164_HUMAN;.	A	13	ENSP00000436609:V13A;ENSP00000278935:V13A;ENSP00000436351:V13A;ENSP00000431302:V13A	ENSP00000278935:V13A	V	+	2	0	CEP164	116714550	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.146000	0.77373	2.070000	0.61991	0.533000	0.62120	GTT	.	.	none		0.488	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	
UBXN6	80700	hgsc.bcm.edu	37	19	4457650	4457650	+	Silent	SNP	C	C	T	rs1044510	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4457650C>T	ENST00000301281.6	-	1	169	c.45G>A	c.(43-45)aaG>aaA	p.K15K	CTB-50L17.16_ENST00000591414.1_lincRNA|CTB-50L17.9_ENST00000592034.1_RNA|UBXN6_ENST00000394765.3_5'Flank	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	15						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						GTCCCGCGCTCTTGAACTTGA	0.697													C|||	2034	0.40615	0.3374	0.4294	5008	,	,		3297	0.6171		0.2763	False		,,,				2504	0.3988				p.K15K		Atlas-SNP	.											.	UBXN6	27	.	0			c.G45A						PASS	.	C		1456,2946	448.5+/-348.7	253,950,998	34.0	31.0	32.0		45	3.1	1.0	19	dbSNP_86	32	2433,6161	385.4+/-341.5	334,1765,2198	no	coding-synonymous	UBXN6	NM_025241.2		587,2715,3196	TT,TC,CC		28.3104,33.0759,29.9246		15/442	4457650	3889,9107	2201	4297	6498	SO:0001819	synonymous_variant	80700	exon1			CGCGCTCTTGAAC	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.45G>A	19.37:g.4457650C>T		Somatic	15	0	0		WXS	Illumina HiSeq	Phase_I	27	13	0.481481	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Silent	SNP	ENST00000301281.6	37	CCDS12129.1																																																																																			C|0.660;T|0.340	0.340	strong		0.697	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
NXPE4	54827	hgsc.bcm.edu	37	11	114442103	114442103	+	Missense_Mutation	SNP	A	A	G	rs550897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:114442103A>G	ENST00000375478.3	-	6	1372	c.1192T>C	c.(1192-1194)Tat>Cat	p.Y398H	NXPE4_ENST00000424261.2_Missense_Mutation_p.Y114H	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	398			Y -> H (in dbSNP:rs550897). {ECO:0000269|PubMed:15375555}.			extracellular vesicular exosome (GO:0070062)											GGATAACAATATTTTTGCCAC	0.423													G|||	3275	0.653954	0.9054	0.5605	5008	,	,		19012	0.6746		0.4682	False		,,,				2504	0.5501				p.Y398H		Atlas-SNP	.											.	.	.	.	0			c.T1192C						PASS	.	G	HIS/TYR,HIS/TYR	3195,621		1345,505,58	212.0	190.0	197.0		1192,340	4.5	0.2	11	dbSNP_83	197	4029,4229		963,2103,1063	yes	missense,missense	FAM55D	NM_001077639.1,NM_017678.2	83,83	2308,2608,1121	GG,GA,AA		48.7891,16.2736,40.169	benign,benign	398/545,114/261	114442103	7224,4850	1908	4129	6037	SO:0001583	missense	54827	exon6			AACAATATTTTTG	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1192T>C	11.37:g.114442103A>G	ENSP00000364627:p.Tyr398His	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	95	0.989583	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	1352	0.6190476190476191	436	0.8861788617886179	191	0.5276243093922652	381	0.666083916083916	344	0.45382585751978893	G	1.074	-0.668989	0.03403	0.837264	0.487891	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.10960	2.82;2.82	5.44	4.54	0.55810	.	0.000000	0.64402	N	0.000005	T	0.00012	0.0000	N	0.00003	-3.415	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35798	-0.9774	9	0.02654	T	1	.	11.2986	0.49292	0.1497:0.0:0.8503:0.0	rs550897;rs52827494;rs58118885;rs550897	398	Q6UWF7	FA55D_HUMAN	H	114;398	ENSP00000401503:Y114H;ENSP00000364627:Y398H	ENSP00000364627:Y398H	Y	-	1	0	FAM55D	113947313	0.999000	0.42202	0.201000	0.23476	0.807000	0.45602	4.178000	0.58284	0.804000	0.34136	-0.166000	0.13349	TAT	T|0.007;G|0.608	0.608	strong		0.423	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20854303	20854303	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:20854303G>T	ENST00000266509.2	+	3	549	c.181G>T	c.(181-183)Ggc>Tgc	p.G61C	SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.G61C|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.G61C|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.G61C	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	61					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	ATTGGCAGAAGGCTATCTGAA	0.418																																					p.G61C		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.G181T						PASS	.						272.0	207.0	229.0					12																	20854303		2203	4300	6503	SO:0001583	missense	53919	exon3			GCAGAAGGCTATC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.181G>T	12.37:g.20854303G>T	ENSP00000266509:p.Gly61Cys	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	179	74	0.413408	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981799	0.74474	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.09	5.09	0.68999	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.046510	0.85682	D	0.000000	T	0.70996	0.3288	M	0.80183	2.485	0.41867	D	0.990257	D;D;D	0.62365	0.973;0.98;0.991	P;P;D	0.64506	0.852;0.852;0.926	T	0.74435	-0.3666	10	0.66056	D	0.02	.	6.0855	0.19964	0.2193:0.0:0.7807:0.0	.	61;61;61	B7Z3Q3;Q5JPA4;Q9NYB5	.;.;SO1C1_HUMAN	C	61	ENSP00000444149:G61C;ENSP00000438665:G61C;ENSP00000266509:G61C;ENSP00000370964:G61C	ENSP00000266509:G61C	G	+	1	0	SLCO1C1	20745570	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.764000	0.62264	2.652000	0.90054	0.655000	0.94253	GGC	.	.	none		0.418	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
TRAF5	7188	hgsc.bcm.edu	37	1	211533352	211533352	+	Silent	SNP	A	A	G	rs2230779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:211533352A>G	ENST00000261464.5	+	5	531	c.477A>G	c.(475-477)gcA>gcG	p.A159A	TRAF5_ENST00000462410.1_3'UTR|TRAF5_ENST00000336184.2_Silent_p.A159A|TRAF5_ENST00000367004.3_Silent_p.A159A|TRAF5_ENST00000427925.2_Intron	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	159					apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|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)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		ATTTGAGTGCATCCTGTCAGT	0.423													A|||	241	0.048123	0.0189	0.036	5008	,	,		23107	0.0327		0.0577	False		,,,				2504	0.1022				p.A159A		Atlas-SNP	.											.	TRAF5	64	.	0			c.A477G						PASS	.	A	,,	126,4280	93.4+/-132.2	1,124,2078	142.0	132.0	135.0		477,477,477	-1.0	0.7	1	dbSNP_98	135	506,8094	144.0+/-200.0	18,470,3812	no	coding-synonymous,coding-synonymous,coding-synonymous	TRAF5	NM_001033910.2,NM_004619.3,NM_145759.2	,,	19,594,5890	GG,GA,AA		5.8837,2.8597,4.8593	,,	159/558,159/558,159/558	211533352	632,12374	2203	4300	6503	SO:0001819	synonymous_variant	7188	exon5			GAGTGCATCCTGT	AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"""RING-type (C3HC4) zinc fingers"""	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.477A>G	1.37:g.211533352A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	117	63	0.538462	NM_004619	B4DIS9|B4E0A2|Q6FHY1	Silent	SNP	ENST00000261464.5	37	CCDS1497.1																																																																																			A|0.954;G|0.046	0.046	strong		0.423	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619	
CNTN5	53942	hgsc.bcm.edu	37	11	99690461	99690461	+	Missense_Mutation	SNP	A	A	G	rs10893933		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:99690461A>G	ENST00000524871.1	+	4	532	c.242A>G	c.(241-243)aAt>aGt	p.N81S	CNTN5_ENST00000279463.3_Missense_Mutation_p.N81S|CNTN5_ENST00000418526.2_Intron|CNTN5_ENST00000527185.1_Missense_Mutation_p.N81S|CNTN5_ENST00000528682.1_Missense_Mutation_p.N81S	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	81			N -> S (in dbSNP:rs10893933).		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)		TCCCCCATCAATCTTTATCAT	0.428																																					p.N81S		Atlas-SNP	.											.	CNTN5	324	.	0			c.A242G						PASS	.						53.0	52.0	52.0					11																	99690461		1877	4084	5961	SO:0001583	missense	53942	exon3			CCATCAATCTTTA	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.242A>G	11.37:g.99690461A>G	ENSP00000435637:p.Asn81Ser	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	113	16	0.141593	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Missense_Mutation	SNP	ENST00000524871.1	37	CCDS53696.1	.	.	.	.	.	.	.	.	.	.	A	5.900	0.350168	0.11182	.	.	ENSG00000149972	ENST00000527185;ENST00000528682;ENST00000524871;ENST00000279463	T;T;T;T	0.53857	0.6;0.67;0.67;0.67	5.06	1.42	0.22433	.	0.775582	0.11744	N	0.533735	T	0.31513	0.0799	N	0.19112	0.55	0.31324	P	0.685664	B;B	0.19445	0.036;0.036	B;B	0.15052	0.012;0.012	T	0.37619	-0.9698	9	0.08179	T	0.78	.	8.939	0.35718	0.7862:0.0:0.2138:0.0	rs10893933;rs10893933	81;81	E9PKE8;O94779	.;CNTN5_HUMAN	S	81	ENSP00000433575:N81S;ENSP00000436185:N81S;ENSP00000435637:N81S;ENSP00000279463:N81S	ENSP00000279463:N81S	N	+	2	0	CNTN5	99195671	0.984000	0.35163	0.688000	0.30117	0.746000	0.42486	2.566000	0.45948	0.128000	0.18479	0.528000	0.53228	AAT	A|1.000;|0.000	.	strong		0.428	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138761034	138761034	+	Missense_Mutation	SNP	G	G	C	rs2297241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:138761034G>C	ENST00000242351.5	-	6	2011	c.1695C>G	c.(1693-1695)caC>caG	p.H565Q	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.H687Q|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.H565Q	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	565			H -> Q (in dbSNP:rs2297241). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.		defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CAACTTACAGGTGGATTCCGG	0.468													G|||	1207	0.241014	0.2398	0.3444	5008	,	,		20631	0.3929		0.1233	False		,,,				2504	0.1339				p.H565Q		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.C1695G						PASS	.	G	GLN/HIS,GLN/HIS	988,3418	370.3+/-319.5	120,748,1335	151.0	142.0	145.0		1695,1695	-2.9	0.0	7	dbSNP_100	145	1137,7463	235.1+/-267.8	69,999,3232	yes	missense,missense	ZC3HAV1	NM_020119.3,NM_024625.3	24,24	189,1747,4567	CC,CG,GG		13.2209,22.424,16.3386	benign,benign	565/903,565/700	138761034	2125,10881	2203	4300	6503	SO:0001583	missense	56829	exon6			TTACAGGTGGATT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.1695C>G	7.37:g.138761034G>C	ENSP00000242351:p.His565Gln	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	200	96	0.48	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	573|573	0.2623626373626374|0.2623626373626374	124|124	0.25203252032520324|0.25203252032520324	112|112	0.30939226519337015|0.30939226519337015	241|241	0.42132867132867136|0.42132867132867136	96|96	0.1266490765171504|0.1266490765171504	G|G	7.208|7.208	0.594847|0.594847	0.13875|0.13875	0.22424|0.22424	0.132209|0.132209	ENSG00000105939|ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247|ENST00000460845	T;T;T|.	0.16897|.	3.33;3.32;2.31|.	5.14|5.14	-2.93|-2.93	0.05598|0.05598	.|.	3.503140|.	0.00575|.	N|.	0.000302|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.51422|0.51422	1.61|1.61	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.06405|.	0.002;0.0|.	T|T	0.41945|0.41945	-0.9480|-0.9480	9|4	0.15499|.	T|.	0.54|.	.|.	1.9853|1.9853	0.03435|0.03435	0.2468:0.2353:0.4042:0.1138|0.2468:0.2353:0.4042:0.1138	rs2297241;rs10353718;rs52819929;rs59789226;rs2297241|rs2297241;rs10353718;rs52819929;rs59789226;rs2297241	565;565|.	Q7Z2W4-2;Q7Z2W4|.	.;ZCCHV_HUMAN|.	Q|A	565;687;565;325|130	ENSP00000242351:H565Q;ENSP00000418385:H687Q;ENSP00000419855:H565Q|.	ENSP00000242351:H565Q|.	H|P	-|-	3|1	2|0	ZC3HAV1|ZC3HAV1	138411574|138411574	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.235000|-0.235000	0.09016|0.09016	-0.476000|-0.476000	0.06842|0.06842	-0.302000|-0.302000	0.09304|0.09304	CAC|CCT	G|0.797;C|0.203	0.203	strong		0.468	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
ANKRD27	84079	hgsc.bcm.edu	37	19	33106621	33106621	+	Silent	SNP	C	C	T	rs405858|rs200055396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33106621C>T	ENST00000306065.4	-	22	2276	c.2118G>A	c.(2116-2118)gcG>gcA	p.A706A		NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	706					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					ATTCGGGGTCCGCTGCACTGA	0.557													c|||	2408	0.480831	0.4365	0.4755	5008	,	,		18541	0.3175		0.662	False		,,,				2504	0.5266				p.A706A		Atlas-SNP	.											ANKRD27,NS,carcinoma,-1,1	ANKRD27	86	1	0			c.G2118A						PASS	.	T		2072,2334	569.1+/-382.5	494,1084,625	142.0	103.0	116.0		2118	-10.4	0.0	19	dbSNP_80	116	5865,2735	681.9+/-403.8	1974,1917,409	no	coding-synonymous	ANKRD27	NM_032139.2		2468,3001,1034	TT,TC,CC		31.8023,47.0268,38.9743		706/1051	33106621	7937,5069	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon22			GGGGTCCGCTGCA	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.2118G>A	19.37:g.33106621C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	136	136	1	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			C|0.445;T|0.555	0.555	strong		0.557	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
SLFN13	146857	hgsc.bcm.edu	37	17	33768334	33768334	+	Missense_Mutation	SNP	T	T	G	rs75812929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33768334T>G	ENST00000285013.6	-	6	2249	c.1974A>C	c.(1972-1974)aaA>aaC	p.K658N	SLFN13_ENST00000360502.2_Missense_Mutation_p.K340N|SLFN13_ENST00000526861.1_Missense_Mutation_p.K658N|SLFN13_ENST00000542635.1_Missense_Mutation_p.K658N|SLFN13_ENST00000533791.1_Missense_Mutation_p.K658N|SLFN13_ENST00000534689.1_Missense_Mutation_p.K340N	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	658						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)		TGTGTTCAAATTTTTCTCTTA	0.393													G|||	830	0.165735	0.2163	0.1715	5008	,	,		16584	0.3284		0.0457	False		,,,				2504	0.0491				p.K658N		Atlas-SNP	.											.	SLFN13	79	.	0			c.A1974C						PASS	.						78.0	92.0	87.0					17																	33768334		2201	4300	6501	SO:0001583	missense	146857	exon6			TTCAAATTTTTCT	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.1974A>C	17.37:g.33768334T>G	ENSP00000285013:p.Lys658Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	49	17	0.346939	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	327	0.14972527472527472	75	0.1524390243902439	48	0.13259668508287292	180	0.3146853146853147	24	0.0316622691292876	g	1.109	-0.658679	0.03454	.	.	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82	3.29	-0.451	0.12214	Domain of unknown function DUF2075 (1);	1.965960	0.02356	N	0.076421	T	0.00012	0.0000	N	0.00419	-1.52	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.12066	-1.0562	9	0.13108	T	0.6	.	1.3366	0.02146	0.1235:0.1878:0.3065:0.3823	.	340;658	Q68D06-2;Q68D06	.;SLN13_HUMAN	N	658;340;658;658;340	ENSP00000285013:K658N;ENSP00000353692:K340N;ENSP00000434439:K658N;ENSP00000444016:K658N;ENSP00000435442:K340N	ENSP00000285013:K658N	K	-	3	2	SLFN13	30792447	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.743000	0.04845	-0.082000	0.12640	-0.982000	0.02568	AAA	T|0.900;G|0.100	0.100	strong		0.393	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
ZNF212	7988	hgsc.bcm.edu	37	7	148950895	148950895	+	Missense_Mutation	SNP	C	C	T	rs34185245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:148950895C>T	ENST00000335870.2	+	5	1005	c.877C>T	c.(877-879)Cat>Tat	p.H293Y		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	293			H -> Y (in dbSNP:rs34185245).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|ovary(1)|prostate(1)	9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			GCAGAAATCTCATAGGCAGGT	0.547													C|||	52	0.0103834	0.0008	0.0144	5008	,	,		19032	0.0		0.0398	False		,,,				2504	0.001				p.H293Y		Atlas-SNP	.											.	ZNF212	28	.	0			c.C877T						PASS	.	C	TYR/HIS	22,4384	29.9+/-59.1	0,22,2181	67.0	69.0	68.0		877	-1.7	0.0	7	dbSNP_126	68	285,8315	107.0+/-167.8	4,277,4019	yes	missense	ZNF212	NM_012256.3	83	4,299,6200	TT,TC,CC		3.314,0.4993,2.3604	benign	293/496	148950895	307,12699	2203	4300	6503	SO:0001583	missense	7988	exon5			AAATCTCATAGGC	U38864	CCDS5896.1	7q36.1	2013-01-08			ENSG00000170260	ENSG00000170260		"""Zinc fingers, C2H2-type"", ""-"""	13004	protein-coding gene	gene with protein product		602386				9169157	Standard	NM_012256		Approved	C2H2-150	uc003wfp.3	Q9UDV6	OTTHUMG00000158968	ENST00000335870.2:c.877C>T	7.37:g.148950895C>T	ENSP00000338572:p.His293Tyr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	87	43	0.494253	NM_012256	B2RCF4|Q13396|Q8N664	Missense_Mutation	SNP	ENST00000335870.2	37	CCDS5896.1	31	0.014194139194139194	0	0.0	3	0.008287292817679558	0	0.0	28	0.036939313984168866	C	4.600	0.111436	0.08831	0.004993	0.03314	ENSG00000170260	ENST00000335870	T	0.07444	3.19	5.37	-1.73	0.08081	.	0.903033	0.09466	N	0.798366	T	0.01029	0.0034	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42865	-0.9426	10	0.54805	T	0.06	-0.0535	1.0724	0.01624	0.1635:0.3734:0.1646:0.2985	rs34185245	293	Q9UDV6	ZN212_HUMAN	Y	293	ENSP00000338572:H293Y	ENSP00000338572:H293Y	H	+	1	0	ZNF212	148581828	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.975000	0.03790	-0.330000	0.08514	-0.140000	0.14226	CAT	C|0.982;T|0.018	0.018	strong		0.547	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256	
CROCC	9696	hgsc.bcm.edu	37	1	17273443	17273443	+	Missense_Mutation	SNP	C	C	T	rs74657070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17273443C>T	ENST00000375541.5	+	17	2540	c.2471C>T	c.(2470-2472)aCg>aTg	p.T824M	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CAGCTCCCCACGCTGCGCCAT	0.701													c|||	151	0.0301518	0.0469	0.0375	5008	,	,		20767	0.0		0.0537	False		,,,				2504	0.0092				p.T824M		Atlas-SNP	.											CROCC,NS,carcinoma,-1,1	CROCC	185	1	0			c.C2471T						PASS	.	C	MET/THR	171,4089		0,171,1959	9.0	9.0	9.0		2471	1.2	0.0	1	dbSNP_131	9	329,7969		0,329,3820	no	missense	CROCC	NM_014675.3	81	0,500,5779	TT,TC,CC		3.9648,4.0141,3.9815	possibly-damaging	824/2018	17273443	500,12058	2130	4149	6279	SO:0001583	missense	9696	exon17			TCCCCACGCTGCG	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.2471C>T	1.37:g.17273443C>T	ENSP00000364691:p.Thr824Met	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	121	7	0.0578512	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	56	0.02564102564102564	10	0.02032520325203252	9	0.024861878453038673	0	0.0	37	0.048812664907651716	C	1.643	-0.515945	0.04200	0.040141	0.039648	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09911	2.93	3.18	1.2	0.21068	.	.	.	.	.	T	0.00815	0.0027	N	0.14661	0.345	0.09310	N	1	B;P;P	0.46020	0.053;0.769;0.871	B;B;B	0.39876	0.01;0.216;0.312	T	0.36648	-0.9739	9	0.46703	T	0.11	.	4.9245	0.13887	0.2224:0.6507:0.0:0.1269	.	687;127;824	A1L0S8;Q5TZA2-2;Q5TZA2	.;.;CROCC_HUMAN	M	824;705	ENSP00000364691:T824M	ENSP00000364691:T824M	T	+	2	0	CROCC	17146030	0.000000	0.05858	0.006000	0.13384	0.035000	0.12851	-0.679000	0.05203	0.322000	0.23283	0.462000	0.41574	ACG	C|0.974;T|0.026	0.026	strong		0.701	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
FIP1L1	81608	hgsc.bcm.edu	37	4	54324914	54324914	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:54324914C>T	ENST00000337488.6	+	17	1788	c.1594C>T	c.(1594-1596)Cga>Tga	p.R532*	FIP1L1_ENST00000507166.1_Intron|FIP1L1_ENST00000306932.6_Nonsense_Mutation_p.R458*|FIP1L1_ENST00000358575.5_Nonsense_Mutation_p.R526*	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	532	Arg-rich.|Glu-rich.|Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TAGAGAAAGACGACACAGGGA	0.393			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.R532X		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.C1594T						PASS	.						98.0	110.0	106.0					4																	54324914		2203	4300	6503	SO:0001587	stop_gained	81608	exon17			GAAAGACGACACA	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"""FIP1 like 1 (S. cerevisiae)"", ""FIP1L1 cleavage and polyadenylation specific factor subunit"""			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1594C>T	4.37:g.54324914C>T	ENSP00000336752:p.Arg532*	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	213	92	0.431925	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Nonsense_Mutation	SNP	ENST00000337488.6	37	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044750	0.93685	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	.	.	.	4.93	4.02	0.46733	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7173	10.9749	0.47461	0.3547:0.6453:0.0:0.0	.	.	.	.	X	532;526;458;192	.	ENSP00000302993:R458X	R	+	1	2	FIP1L1	54019671	1.000000	0.71417	0.953000	0.39169	0.010000	0.07245	1.951000	0.40333	2.706000	0.92434	0.591000	0.81541	CGA	.	.	none		0.393	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	
SYN1	6853	hgsc.bcm.edu	37	X	47466361	47466361	+	Silent	SNP	A	A	G	rs1142636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:47466361A>G	ENST00000295987.7	-	3	634	c.510T>C	c.(508-510)aaT>aaC	p.N170N	SYN1_ENST00000340666.4_Silent_p.N170N	NM_006950.3	NP_008881.2	P17600	SYN1_HUMAN	synapsin I	170	C; actin-binding and synaptic-vesicle binding.				neurotransmitter secretion (GO:0007269)|regulation of neurotransmitter secretion (GO:0046928)|regulation of synaptic vesicle exocytosis (GO:2000300)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(6)|lung(6)|ovary(1)	21						CCTTCACCCCATTCCGAAGAA	0.498													G|||	1392	0.368742	0.3616	0.2911	3775	,	,		10146	0.1954		0.2684	False		,,,				2504	0.2505				p.N170N		Atlas-SNP	.											.	SYN1	84	.	0			c.T510C						PASS	.	G	,	1660,2175		312,793,243,527,328	128.0	104.0	112.0		510,510	2.2	1.0	X	dbSNP_86	112	2547,4181		350,1166,681,912,1191	no	coding-synonymous,coding-synonymous	SYN1	NM_006950.3,NM_133499.2	,	662,1959,924,1439,1519	GG,GA,G,AA,A		37.8567,43.2855,39.8277	,	170/706,170/670	47466361	4207,6356	2203	4300	6503	SO:0001819	synonymous_variant	6853	exon3			CACCCCATTCCGA		CCDS14280.1, CCDS35233.1	Xp11.2	2012-10-02			ENSG00000008056	ENSG00000008056			11494	protein-coding gene	gene with protein product		313440					Standard	NM_133499		Approved		uc004die.3	P17600	OTTHUMG00000021454	ENST00000295987.7:c.510T>C	X.37:g.47466361A>G		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_006950	B1AJQ1|O75825|Q5H9A9	Silent	SNP	ENST00000295987.7	37	CCDS14280.1																																																																																			T|0.141;G|0.294;C|0.097;A|0.468	0.294	strong		0.498	SYN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056445.1	NM_006950	
LILRB5	10990	hgsc.bcm.edu	37	19	54754778	54754778	+	Missense_Mutation	SNP	G	G	A	rs150660840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54754778G>A	ENST00000316219.5	-	13	1752	c.1645C>T	c.(1645-1647)Ccc>Tcc	p.P549S	CTD-2337J16.1_ENST00000595133.1_lincRNA|LILRB5_ENST00000449561.2_Missense_Mutation_p.P550S|LILRB5_ENST00000345866.6_Missense_Mutation_p.P450S|LILRB5_ENST00000450632.1_Silent_p.P619P	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	549					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACATCCTGGGGGGCTTCAGAT	0.632																																					p.P550S		Atlas-SNP	.											LILRB5,NS,carcinoid-endocrine_tumour,+1,1	LILRB5	176	1	0			c.C1648T						scavenged	.	G	SER/PRO,SER/PRO,SER/PRO	50,4356	36.8+/-68.6	2,46,2155	38.0	43.0	42.0		1648,1348,1645	0.3	0.0	19	dbSNP_134	42	5,8587	3.7+/-12.6	0,5,4291	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	74,74,74	2,51,6446	AA,AG,GG		0.0582,1.1348,0.4231	benign,benign,benign	550/592,450/492,549/591	54754778	55,12943	2203	4296	6499	SO:0001583	missense	10990	exon13			CCTGGGGGGCTTC	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1645C>T	19.37:g.54754778G>A	ENSP00000320390:p.Pro549Ser	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	193	8	0.0414508	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559321	0.27827	0.011348	5.82E-4	ENSG00000105609	ENST00000316219;ENST00000449561;ENST00000345866	T;T;T	0.00543	6.77;6.74;6.68	2.75	0.32	0.15878	.	.	.	.	.	T	0.00496	0.0016	M	0.72894	2.215	0.09310	N	0.999999	B;B;P	0.43169	0.235;0.041;0.8	B;B;B	0.41036	0.202;0.054;0.346	T	0.46596	-0.9180	9	0.59425	D	0.04	.	3.188	0.06607	0.1533:0.0:0.5888:0.2579	.	450;550;549	O75023-2;O75023-3;O75023	.;.;LIRB5_HUMAN	S	549;550;450	ENSP00000320390:P549S;ENSP00000406478:P550S;ENSP00000263430:P450S	ENSP00000320390:P549S	P	-	1	0	LILRB5	59446590	0.000000	0.05858	0.034000	0.17996	0.619000	0.37552	-0.640000	0.05440	0.033000	0.15463	0.585000	0.79938	CCC	G|0.994;A|0.006	0.006	strong		0.632	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
NTF3	4908	hgsc.bcm.edu	37	12	5603935	5603935	+	Silent	SNP	C	C	T	rs10849277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:5603935C>T	ENST00000331010.6	+	1	638	c.555C>T	c.(553-555)ccC>ccT	p.P185P	NTF3_ENST00000423158.3_Silent_p.P198P|NTF3_ENST00000535299.1_Intron	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	185					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						GCAACTCTCCCGTCAAACAAT	0.507													C|||	534	0.106629	0.0257	0.0937	5008	,	,		16020	0.0228		0.2048	False		,,,				2504	0.2106				p.P198P	GBM(194;1104 2182 8339 9578 18493)	Atlas-SNP	.											.	NTF3	50	.	0			c.C594T						PASS	.	C	,	259,4147	146.5+/-181.1	12,235,1956	61.0	61.0	61.0		594,555	-1.0	1.0	12	dbSNP_120	61	1625,6975	300.9+/-305.2	148,1329,2823	no	coding-synonymous,coding-synonymous	NTF3	NM_001102654.1,NM_002527.4	,	160,1564,4779	TT,TC,CC		18.8953,5.8783,14.4856	,	198/271,185/258	5603935	1884,11122	2203	4300	6503	SO:0001819	synonymous_variant	4908	exon2			CTCTCCCGTCAAA		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.555C>T	12.37:g.5603935C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	48	20	0.416667	NM_001102654	B7Z1T5|Q6FH50	Silent	SNP	ENST00000331010.6	37	CCDS8538.1																																																																																			C|0.874;T|0.126	0.126	strong		0.507	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1		
DEFB108B	245911	hgsc.bcm.edu	37	11	71548520	71548520	+	Missense_Mutation	SNP	A	A	T	rs12285495	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71548520A>T	ENST00000328698.1	+	2	134	c.134A>T	c.(133-135)cAt>cTt	p.H45L	DEFB108B_ENST00000529157.1_3'UTR	NM_001002035.1	NP_001002035.1	Q8NET1	D108B_HUMAN	defensin, beta 108B	45			H -> L (in dbSNP:rs12285495).		defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|kidney(1)|lung(2)|skin(1)	5						ACAGAAATCCATGTTGGGAGA	0.468													.|||	2256	0.450479	0.3427	0.3732	5008	,	,		15708	0.3631		0.5984	False		,,,				2504	0.589				p.H45L		Atlas-SNP	.											.	DEFB108B	6	.	0			c.A134T						PASS	.	A	LEU/HIS	1682,2718		316,1050,834	105.0	112.0	110.0		134	0.2	0.1	11	dbSNP_120	110	5213,3373		1581,2051,661	no	missense	DEFB108B	NM_001002035.1	99	1897,3101,1495	TT,TA,AA		39.2849,38.2273,46.9044	possibly-damaging	45/74	71548520	6895,6091	2200	4293	6493	SO:0001583	missense	245911	exon2			AAATCCATGTTGG	AF529416	CCDS31631.1	11q13.4	2011-03-29			ENSG00000184276	ENSG00000184276		"""Defensins, beta"""	29966	protein-coding gene	gene with protein product							Standard	NM_001002035		Approved		uc010rqr.2	Q8NET1	OTTHUMG00000167533	ENST00000328698.1:c.134A>T	11.37:g.71548520A>T	ENSP00000333234:p.His45Leu	Somatic	284	1	0.00352113		WXS	Illumina HiSeq	Phase_I	238	108	0.453782	NM_001002035		Missense_Mutation	SNP	ENST00000328698.1	37	CCDS31631.1	1030	0.4716117216117216	192	0.3902439024390244	158	0.43646408839779005	214	0.3741258741258741	466	0.6147757255936676	.	10.86	1.470492	0.26423	0.382273	0.607151	ENSG00000184276	ENST00000328698	T	0.10668	2.85	1.51	0.238	0.15480	.	0.755014	0.10839	N	0.628422	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.33394	-0.9870	8	0.72032	D	0.01	.	3.4459	0.07481	0.6409:0.0:0.0:0.3591	rs12285495;rs59318528	45	Q8NET1	D108B_HUMAN	L	45	ENSP00000333234:H45L	ENSP00000333234:H45L	H	+	2	0	DEFB108B	71226168	0.003000	0.15002	0.126000	0.21872	0.339000	0.28857	0.195000	0.17155	0.055000	0.16094	0.329000	0.21502	CAT	A|0.486;T|0.514	0.514	strong		0.468	DEFB108B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394945.1	NM_001002035	
SH3BP5	9467	hgsc.bcm.edu	37	3	15373858	15373858	+	Missense_Mutation	SNP	C	C	T	rs115738660	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:15373858C>T	ENST00000383791.3	-	1	278	c.58G>A	c.(58-60)Gcc>Acc	p.A20T	SH3BP5_ENST00000253688.5_5'UTR|SH3BP5_ENST00000465894.2_Intron|SH3BP5_ENST00000426925.1_Intron|SH3BP5_ENST00000408919.3_Intron	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	20	Glu-rich.				intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						tcgtccCGGGCAGGCGGCAGG	0.726													C|||	165	0.0329473	0.0091	0.0403	5008	,	,		11973	0.0		0.0368	False		,,,				2504	0.09				p.A20T		Atlas-SNP	.											SH3BP5,NS,carcinoma,0,1	SH3BP5	32	1	0			c.G58A						PASS	.	C	,THR/ALA	37,4229		0,37,2096	17.0	16.0	16.0		,58	-1.0	0.1	3	dbSNP_132	16	267,8125		5,257,3934	yes	intron,missense	SH3BP5	NM_001018009.2,NM_004844.3	,58	5,294,6030	TT,TC,CC		3.1816,0.8673,2.4016	,probably-damaging	,20/456	15373858	304,12354	2133	4196	6329	SO:0001583	missense	9467	exon1			CCCGGGCAGGCGG	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"""SH3 binding protein"""	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.58G>A	3.37:g.15373858C>T	ENSP00000373301:p.Ala20Thr	Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_004844	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	37	CCDS2625.2	55	0.025183150183150184	2	0.0040650406504065045	23	0.06353591160220995	0	0.0	30	0.0395778364116095	C	11.22	1.575856	0.28092	0.008673	0.031816	ENSG00000131370	ENST00000383791	.	.	.	3.53	-1.01	0.10169	.	0.938283	0.08691	N	0.907977	T	0.02571	0.0078	N	0.24115	0.695	0.28931	N	0.891572	B	0.02656	0.0	B	0.01281	0.0	T	0.22277	-1.0221	9	0.87932	D	0	-4.6136	1.5963	0.02665	0.3703:0.3329:0.1816:0.1151	.	20	O60239	3BP5_HUMAN	T	20	.	ENSP00000373301:A20T	A	-	1	0	SH3BP5	15348862	0.013000	0.17824	0.074000	0.20217	0.077000	0.17291	0.884000	0.28214	-0.018000	0.14079	0.455000	0.32223	GCC	C|0.973;T|0.027	0.027	strong		0.726	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844	
ADAD2	161931	hgsc.bcm.edu	37	16	84224967	84224967	+	Missense_Mutation	SNP	G	G	A	rs8044695|rs554488585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84224967G>A	ENST00000315906.5	+	1	183	c.131G>A	c.(130-132)gGg>gAg	p.G44E	ADAD2_ENST00000268624.3_Missense_Mutation_p.G44E|ADAD2_ENST00000567413.1_3'UTR|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	44			G -> E (in dbSNP:rs8044695). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						AGTGCCTgggggcccgcgccc	0.751														3435	0.685903	0.8616	0.6686	5008	,	,		11640	0.6677		0.6471	False		,,,				2504	0.5194				p.G44E		Atlas-SNP	.											.	ADAD2	46	.	0			c.G131A						PASS	.	A	GLU/GLY,GLU/GLY	3145,519		1356,433,43	5.0	7.0	7.0		131,131	-1.1	0.0	16	dbSNP_116	7	5102,2224		1808,1486,369	no	missense,missense	ADAD2	NM_001145400.1,NM_139174.3	98,98	3164,1919,412	AA,AG,GG		30.3576,14.1648,24.9591	benign,benign	44/584,44/666	84224967	8247,2743	1832	3663	5495	SO:0001583	missense	161931	exon1			CCTGGGGGCCCGC	AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.131G>A	16.37:g.84224967G>A	ENSP00000325153:p.Gly44Glu	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001145400	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	37	CCDS45536.1	1545	0.7074175824175825	420	0.8536585365853658	227	0.6270718232044199	403	0.7045454545454546	495	0.6530343007915568	A	0.689	-0.795256	0.02862	0.858352	0.696424	ENSG00000140955	ENST00000315906;ENST00000268624	T;T	0.16196	2.36;2.47	3.61	-1.07	0.09968	.	1.276770	0.06034	N	0.653713	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.30297	-0.9983	9	0.02654	T	1	-5.6132	8.9029	0.35505	0.4397:0.0:0.5603:0.0	rs8044695;rs57310648	44;44	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	E	44	ENSP00000325153:G44E;ENSP00000268624:G44E	ENSP00000268624:G44E	G	+	2	0	ADAD2	82782468	0.057000	0.20700	0.000000	0.03702	0.002000	0.02628	-0.069000	0.11542	-0.575000	0.05982	-1.305000	0.01319	GGG	G|0.291;A|0.709	0.709	strong		0.751	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
TMC1	117531	hgsc.bcm.edu	37	9	75303653	75303653	+	Silent	SNP	C	C	T	rs2589615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:75303653C>T	ENST00000297784.5	+	6	585	c.45C>T	c.(43-45)gaC>gaT	p.D15D	TMC1_ENST00000396237.3_Silent_p.D15D|TMC1_ENST00000340019.3_Silent_p.D15D	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	15	Arg/Asp/Glu/Lys-rich (highly charged).				auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						AAAAAGAAGACGAGACTGAGG	0.368													C|||	2558	0.510783	0.77	0.4496	5008	,	,		19992	0.4187		0.4085	False		,,,				2504	0.4039				p.D15D	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.C45T						PASS	.	C		3161,1245	694.7+/-405.8	1149,863,191	90.0	90.0	90.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	45	-5.3	0.2	9	dbSNP_100	90	3698,4902	521.2+/-379.8	775,2148,1377	no	coding-synonymous	TMC1	NM_138691.2		1924,3011,1568	TT,TC,CC		43.0,28.2569,47.2628		15/761	75303653	6859,6147	2203	4300	6503	SO:0001819	synonymous_variant	117531	exon6			AGAAGACGAGACT	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.45C>T	9.37:g.75303653C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_138691	A8MVZ2|B1AM91	Silent	SNP	ENST00000297784.5	37	CCDS6643.1																																																																																			C|0.478;T|0.522	0.522	strong		0.368	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		
DTX2	113878	hgsc.bcm.edu	37	7	76111994	76111994	+	Silent	SNP	C	C	G	rs1638075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:76111994C>G	ENST00000324432.5	+	5	948	c.438C>G	c.(436-438)gcC>gcG	p.A146A	DTX2_ENST00000430490.2_Silent_p.A146A|DTX2_ENST00000446600.1_Silent_p.A55A|DTX2_ENST00000413936.2_Silent_p.A146A|DTX2_ENST00000307569.8_Silent_p.A146A|DTX2_ENST00000446820.2_Silent_p.A146A	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	146	WWE 2. {ECO:0000255|PROSITE- ProRule:PRU00248}.				Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.A146A(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						TGGACTTGGCCCCCCTGGGGT	0.622													.|||	629	0.125599	0.0537	0.1369	5008	,	,		16537	0.0516		0.2276	False		,,,				2504	0.1861				p.A146A		Atlas-SNP	.											DTX2,NS,carcinoma,0,1	DTX2	64	1	1	Substitution - coding silent(1)	stomach(1)	c.C438G						PASS	.	C	,,,	400,4006		21,358,1824	50.0	42.0	44.0		438,438,438,438	-10.8	0.0	7	dbSNP_89	44	2054,6542		249,1556,2493	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	270,1914,4317	GG,GC,CC		23.8948,9.0785,18.874	,,,	146/623,146/623,146/576,146/623	76111994	2454,10548	2203	4298	6501	SO:0001819	synonymous_variant	113878	exon2			CTTGGCCCCCCTG		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.438C>G	7.37:g.76111994C>G		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	236	118	0.5	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			.	.	weak		0.622	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
ORC1	4998	hgsc.bcm.edu	37	1	52854961	52854961	+	Missense_Mutation	SNP	G	G	A	rs3087476	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:52854961G>A	ENST00000371568.3	-	7	1333	c.1115C>T	c.(1114-1116)gCg>gTg	p.A372V	ORC1_ENST00000371566.1_Missense_Mutation_p.A372V	NM_001190818.1|NM_001190819.1|NM_004153.3	NP_001177747.1|NP_001177748.1|NP_004144.2	Q13415	ORC1_HUMAN	origin recognition complex, subunit 1	372			A -> V (in dbSNP:rs3087476).		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear origin of replication recognition complex (GO:0005664)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGTAGAGGTCGCTTCATTCTG	0.488													G|||	40	0.00798722	0.0008	0.0274	5008	,	,		17953	0.0		0.0169	False		,,,				2504	0.0031				p.A372V		Atlas-SNP	.											.	ORC1	79	.	0			c.C1115T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	21,4385	28.1+/-56.4	0,21,2182	183.0	152.0	162.0		1115,1115,1115	3.2	0.0	1	dbSNP_102	162	187,8413	84.8+/-147.2	1,185,4114	yes	missense,missense,missense	ORC1	NM_001190818.1,NM_001190819.1,NM_004153.3	64,64,64	1,206,6296	AA,AG,GG		2.1744,0.4766,1.5993	benign,benign,benign	372/862,372/857,372/862	52854961	208,12798	2203	4300	6503	SO:0001583	missense	4998	exon7			GAGGTCGCTTCAT		CCDS566.1	1p32	2010-10-12	2010-10-12	2010-10-12	ENSG00000085840	ENSG00000085840		"""ATPases / AAA-type"""	8487	protein-coding gene	gene with protein product	"""origin recognition complex, subunit 1, S. cerevisiae, homolog-like"", ""origin recognition complex 1"", ""replication control protein 1"""	601902	"""origin recognition complex, subunit 1 (yeast homolog)-like"", ""origin recognition complex, subunit 1-like (yeast)"", ""origin recognition complex, subunit 1 homolog (S. cerevisiae)"""	ORC1L		8884289	Standard	NM_004153		Approved	HSORC1, PARC1	uc001ctu.3	Q13415	OTTHUMG00000008104	ENST00000371568.3:c.1115C>T	1.37:g.52854961G>A	ENSP00000360623:p.Ala372Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_004153	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	37	CCDS566.1	22	0.010073260073260074	0	0.0	9	0.024861878453038673	0	0.0	13	0.017150395778364115	G	4.830	0.154299	0.09236	0.004766	0.021744	ENSG00000085840	ENST00000371568;ENST00000371566	T;T	0.41758	0.99;0.99	4.09	3.18	0.36537	.	0.915504	0.09579	N	0.783048	T	0.18215	0.0437	L	0.54323	1.7	0.09310	N	0.999995	B;B	0.29936	0.262;0.214	B;B	0.16289	0.015;0.015	T	0.13150	-1.0520	10	0.15066	T	0.55	-1.7724	7.8715	0.29569	0.1099:0.0:0.8901:0.0	rs3087476;rs52790522;rs56469779;rs3087476	372;372	B7Z8H0;Q13415	.;ORC1_HUMAN	V	372	ENSP00000360623:A372V;ENSP00000360621:A372V	ENSP00000360621:A372V	A	-	2	0	ORC1	52627549	0.027000	0.19231	0.015000	0.15790	0.002000	0.02628	2.075000	0.41538	1.325000	0.45301	-0.136000	0.14681	GCG	G|0.984;A|0.016	0.016	strong		0.488	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153	
FLNC	2318	hgsc.bcm.edu	37	7	128486446	128486446	+	Silent	SNP	C	C	T	rs75770585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128486446C>T	ENST00000325888.8	+	23	4317	c.4056C>T	c.(4054-4056)cgC>cgT	p.R1352R	FLNC_ENST00000346177.6_Silent_p.R1352R	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1352					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						ATCCCACCCGCGTCCGAGCCT	0.622													C|||	804	0.160543	0.2012	0.1354	5008	,	,		17535	0.3234		0.0328	False		,,,				2504	0.0869				p.R1352R		Atlas-SNP	.											FLNC,NS,carcinoma,+1,1	FLNC	339	1	0			c.C4056T						PASS	.	C	,	661,3489		60,541,1474	47.0	55.0	53.0		4056,4056	-10.1	0.0	7	dbSNP_131	53	337,8063		4,329,3867	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	64,870,5341	TT,TC,CC		4.0119,15.9277,7.9522	,	1352/2693,1352/2726	128486446	998,11552	2075	4200	6275	SO:0001819	synonymous_variant	2318	exon23			CACCCGCGTCCGA	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.4056C>T	7.37:g.128486446C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			C|0.890;T|0.110	0.110	strong		0.622	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
POM121L2	94026	hgsc.bcm.edu	37	6	27279852	27279852	+	Missense_Mutation	SNP	T	T	C	rs2235233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:27279852T>C	ENST00000444565.1	-	1	97	c.98A>G	c.(97-99)cAg>cGg	p.Q33R	POM121L2_ENST00000377451.2_Missense_Mutation_p.Q33R	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	33										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						GTGAAGGGGCTGAGGTGGCCG	0.632													T|||	1084	0.216454	0.0144	0.2622	5008	,	,		14287	0.379		0.2008	False		,,,				2504	0.3057				p.Q33R		Atlas-SNP	.											.	POM121L2	61	.	0			c.A98G						PASS	.	T	ARG/GLN	76,1308		1,74,617	21.0	27.0	25.0		98	-0.4	0.0	6	dbSNP_98	25	752,2430		92,568,931	yes	missense	POM121L2	NM_033482.3	43	93,642,1548	CC,CT,TT		23.6329,5.4913,18.134	benign	33/1036	27279852	828,3738	692	1591	2283	SO:0001583	missense	94026	exon1			AGGGGCTGAGGTG	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.98A>G	6.37:g.27279852T>C	ENSP00000392726:p.Gln33Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	490	0.22435897435897437	10	0.02032520325203252	97	0.26795580110497236	227	0.3968531468531469	156	0.20580474934036938	T	0.003	-2.507600	0.00155	0.054913	0.236329	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.13307	2.6;2.62	3.19	-0.415	0.12355	.	.	.	.	.	T	0.01870	0.0059	L	0.29908	0.895	0.80722	P	0.0	B	0.16603	0.018	B	0.18871	0.023	T	0.47018	-0.9149	8	0.08837	T	0.75	.	3.1692	0.06546	0.0:0.2608:0.2664:0.4728	rs2235233;rs52826507;rs59279970;rs2235233	33	C9J1I7	.	R	33	ENSP00000366671:Q33R;ENSP00000392726:Q33R	ENSP00000366671:Q33R	Q	-	2	0	POM121L2	27387831	0.415000	0.25416	0.004000	0.12327	0.012000	0.07955	0.398000	0.20899	-0.078000	0.12730	0.459000	0.35465	CAG	T|0.762;C|0.238	0.238	strong		0.632	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
KIF26A	26153	hgsc.bcm.edu	37	14	104641612	104641612	+	Silent	SNP	T	T	C	rs4906422	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:104641612T>C	ENST00000423312.2	+	12	2487	c.2487T>C	c.(2485-2487)ggT>ggC	p.G829G	KIF26A_ENST00000315264.7_Silent_p.G690G	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	829					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		CCTCCAAGGGTCCCCGAGACG	0.682													C|||	1475	0.294529	0.1127	0.3545	5008	,	,		14159	0.3998		0.3022	False		,,,				2504	0.3814				p.G829G		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	0			c.T2487C						PASS	.	C		495,3585		34,427,1579	15.0	18.0	17.0		2487	-2.1	0.0	14	dbSNP_111	17	2411,5939		389,1633,2153	no	coding-synonymous	KIF26A	NM_015656.1		423,2060,3732	CC,CT,TT		28.8743,12.1324,23.3789		829/1883	104641612	2906,9524	2040	4175	6215	SO:0001819	synonymous_variant	26153	exon12			CAAGGGTCCCCGA	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.2487T>C	14.37:g.104641612T>C		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			T|0.708;C|0.292	0.292	strong		0.682	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
CR1	1378	hgsc.bcm.edu	37	1	207787831	207787831	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:207787831G>T	ENST00000367049.4	+	40	6658	c.6658G>T	c.(6658-6660)Gaa>Taa	p.E2220*	CR1_ENST00000367052.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000367053.1_Nonsense_Mutation_p.E1770*|CR1_ENST00000400960.2_Nonsense_Mutation_p.E1770*|CR1_ENST00000367051.1_Nonsense_Mutation_p.E1770*	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1770					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.E2220*(6)|p.E1775*(6)		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						TCCAGTGTGTGAACGTGAGTA	0.408																																					p.E2220X		Atlas-SNP	.											CR1_ENST00000367049,NS,carcinoma,0,12	CR1	354	12	12	Substitution - Nonsense(12)	kidney(8)|endometrium(4)	c.G6658T						scavenged	.						131.0	122.0	125.0					1																	207787831		1887	4127	6014	SO:0001587	stop_gained	1378	exon40			GTGTGTGAACGTG	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.6658G>T	1.37:g.207787831G>T	ENSP00000356016:p.Glu2220*	Somatic	235	2	0.00851064		WXS	Illumina HiSeq	Phase_I	262	9	0.0343511	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Nonsense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	G	45	12.061806	0.99632	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	.	.	.	4.29	4.29	0.51040	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	.	12.9543	0.58418	0.0:0.0:1.0:0.0	.	.	.	.	X	1770;1770;1770;1770;2220	.	ENSP00000356016:E2220X	E	+	1	0	CR1	205854454	1.000000	0.71417	0.999000	0.59377	0.893000	0.52053	2.536000	0.45693	2.316000	0.78162	0.436000	0.28706	GAA	.	.	none		0.408	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
CDK2	1017	hgsc.bcm.edu	37	12	56360876	56360876	+	Silent	SNP	G	G	A	rs2069398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56360876G>A	ENST00000266970.4	+	1	324	c.84G>A	c.(82-84)gaG>gaA	p.E28E	CDK2_ENST00000354056.4_Silent_p.E28E|PMEL_ENST00000536427.1_5'Flank|CDK2_ENST00000440311.2_Silent_p.E28E|PMEL_ENST00000539511.1_5'Flank|PMEL_ENST00000360714.4_5'Flank|PMEL_ENST00000550447.1_5'Flank|PMEL_ENST00000552882.1_5'Flank|PMEL_ENST00000550464.1_5'Flank|PMEL_ENST00000548493.1_5'Flank|PMEL_ENST00000548747.1_5'Flank|PMEL_ENST00000548689.1_5'Flank|CDK2_ENST00000553376.1_Silent_p.E28E|PMEL_ENST00000449260.2_5'Flank|RP11-973D8.4_ENST00000554022.1_RNA	NM_001798.3	NP_001789.2	P24941	CDK2_HUMAN	cyclin-dependent kinase 2	28	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			LTGEV -> STGQM (in Ref. 5; BAA32794). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|blood coagulation (GO:0007596)|cellular response to nitric oxide (GO:0071732)|centrosome duplication (GO:0051298)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone phosphorylation (GO:0016572)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|mitotic nuclear division (GO:0007067)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transport (GO:0006813)|Ras protein signal transduction (GO:0007265)|regulation of gene silencing (GO:0060968)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	Cajal body (GO:0015030)|centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|condensed chromosome (GO:0000793)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|X chromosome (GO:0000805)|Y chromosome (GO:0000806)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	18			UCEC - Uterine corpus endometrioid carcinoma (6;0.123)|OV - Ovarian serous cystadenocarcinoma(18;0.235)		Bosutinib(DB06616)	TGACGGGAGAGGTGGTGGCGC	0.572													A|||	592	0.118211	0.3207	0.0764	5008	,	,		15851	0.001		0.0656	False		,,,				2504	0.0491				p.E28E		Atlas-SNP	.											.	CDK2	27	.	0			c.G84A						PASS	.	A	,	1226,3180	699.7+/-406.5	171,884,1148	133.0	125.0	128.0		84,84	2.3	1.0	12	dbSNP_96	128	665,7935	785.3+/-407.6	23,619,3658	no	coding-synonymous,coding-synonymous	CDK2	NM_001798.3,NM_052827.2	,	194,1503,4806	AA,AG,GG		7.7326,27.8257,14.5394	,	28/299,28/265	56360876	1891,11115	2203	4300	6503	SO:0001819	synonymous_variant	1017	exon1			GGGAGAGGTGGTG	M68520	CCDS8898.1, CCDS8899.1	12q13	2011-11-08				ENSG00000123374		"""Cyclin-dependent kinases"""	1771	protein-coding gene	gene with protein product		116953				1717994, 8275715	Standard	NM_001798		Approved		uc001sit.4	P24941		ENST00000266970.4:c.84G>A	12.37:g.56360876G>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	21	0.477273	NM_052827	A8K7C6|O75100	Silent	SNP	ENST00000266970.4	37	CCDS8898.1																																																																																			G|0.871;A|0.129	0.129	strong		0.572	CDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409650.1		
MRPS30	10884	hgsc.bcm.edu	37	5	44815069	44815069	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:44815069C>A	ENST00000507110.1	+	5	1123	c.1085C>A	c.(1084-1086)aCa>aAa	p.T362K		NM_016640.3	NP_057724.2	Q9NP92	RT30_HUMAN	mitochondrial ribosomal protein S30	362					apoptotic process (GO:0006915)|translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(11)|prostate(1)	20	Lung NSC(6;8.08e-07)					GCTGTGATCACAGATGGAAAA	0.373																																					p.T362K		Atlas-SNP	.											MRPS30_ENST00000507110,NS,carcinoma,+1,2	MRPS30	90	2	0			c.C1085A						scavenged	.						161.0	164.0	163.0					5																	44815069		2203	4300	6503	SO:0001583	missense	10884	exon5			TGATCACAGATGG	AF146192	CCDS3951.1	5q11	2012-09-13		2001-11-09	ENSG00000112996	ENSG00000112996		"""Mitochondrial ribosomal proteins / small subunits"""	8769	protein-coding gene	gene with protein product		611991		PDCD9		10640817, 11279123	Standard	NM_016640		Approved	PAP	uc003joh.3	Q9NP92	OTTHUMG00000096967	ENST00000507110.1:c.1085C>A	5.37:g.44815069C>A	ENSP00000424328:p.Thr362Lys	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	120	3	0.025	NM_016640	Q96I91|Q96Q19|Q9H0P8|Q9NSF9|Q9NZ76	Missense_Mutation	SNP	ENST00000507110.1	37	CCDS3951.1	.	.	.	.	.	.	.	.	.	.	C	33	5.196050	0.94960	.	.	ENSG00000112996	ENST00000507110	T	0.32515	1.45	5.86	5.86	0.93980	.	0.047675	0.85682	D	0.000000	T	0.61375	0.2342	M	0.81341	2.54	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.63812	-0.6552	10	0.87932	D	0	-23.2635	20.1823	0.98208	0.0:1.0:0.0:0.0	.	362	Q9NP92	RT30_HUMAN	K	362	ENSP00000424328:T362K	ENSP00000424328:T362K	T	+	2	0	MRPS30	44850826	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.648000	0.83479	2.771000	0.95319	0.650000	0.86243	ACA	.	.	none		0.373	MRPS30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214033.2	NM_016640	
CFAP46	54777	hgsc.bcm.edu	37	10	134671150	134671150	+	Missense_Mutation	SNP	T	T	C	rs148181302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134671150T>C	ENST00000368586.5	-	39	5618	c.5518A>G	c.(5518-5520)Atg>Gtg	p.M1840V	TTC40_ENST00000263170.5_Start_Codon_SNP_p.M1V	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCCTCAGCCATGGCGCCCTGG	0.587													T|||	46	0.0091853	0.0	0.0072	5008	,	,		16300	0.002		0.0129	False		,,,				2504	0.0266				p.M1840V		Atlas-SNP	.											.	TTC40	100	.	0			c.A5518G						PASS	.	T	VAL/MET	5,4401	8.1+/-20.4	0,5,2198	138.0	91.0	107.0		454	-1.8	0.0	10	dbSNP_134	107	54,8546	22.8+/-68.1	0,54,4246	no	missense	C10orf92	NM_001200049.1	21	0,59,6444	CC,CT,TT		0.6279,0.1135,0.4536	benign	152/1028	134671150	59,12947	2203	4300	6503	SO:0001583	missense	54777	exon39			CAGCCATGGCGCC																												ENST00000368586.5:c.5518A>G	10.37:g.134671150T>C	ENSP00000357575:p.Met1840Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.868758	0.00063	0.001135	0.006279	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.12465	3.08;2.68	0.924	-1.8	0.07907	.	.	.	.	.	T	0.01870	0.0059	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39482	-0.9612	9	0.02654	T	1	.	4.0252	0.09683	0.0:0.4768:0.0:0.5232	.	1	Q8IYW2	CJ092_HUMAN	V	1840;1	ENSP00000357575:M1840V;ENSP00000263170:M1V	ENSP00000263170:M1V	M	-	1	0	C10orf93	134521140	0.379000	0.25123	0.002000	0.10522	0.048000	0.14542	-0.121000	0.10643	-0.572000	0.06006	0.055000	0.15244	ATG	T|0.991;C|0.009	0.009	strong		0.587	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
CENPF	1063	hgsc.bcm.edu	37	1	214814059	214814059	+	Missense_Mutation	SNP	T	T	G	rs61732042	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:214814059T>G	ENST00000366955.3	+	12	2546	c.2378T>G	c.(2377-2379)aTg>aGg	p.M793R		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)		CAGCCTGCCATGCATCATTCC	0.428													T|||	175	0.0349441	0.0038	0.0634	5008	,	,		20500	0.0337		0.0437	False		,,,				2504	0.0491				p.M793R	Colon(80;575 1284 11000 14801 43496)	Atlas-SNP	.											.	CENPF	321	.	0			c.T2378G						PASS	.	T	ARG/MET	32,4364	32.6+/-62.9	1,30,2167	47.0	48.0	48.0		2378	3.2	0.0	1	dbSNP_129	48	307,8289	106.0+/-166.9	4,299,3995	yes	missense	CENPF	NM_016343.3	91	5,329,6162	GG,GT,TT		3.5714,0.7279,2.6093	possibly-damaging	793/3115	214814059	339,12653	2198	4298	6496	SO:0001583	missense	1063	exon12			CTGCCATGCATCA	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.2378T>G	1.37:g.214814059T>G	ENSP00000355922:p.Met793Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_016343	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	78	0.03571428571428571	3	0.006097560975609756	31	0.0856353591160221	15	0.026223776223776224	29	0.03825857519788918	T	4.409	0.075666	0.08485	0.007279	0.035714	ENSG00000117724	ENST00000366955	T	0.03152	4.03	5.59	3.25	0.37280	.	0.896444	0.09308	N	0.819942	T	0.00144	0.0004	.	.	.	0.09310	N	1	P	0.51537	0.946	B	0.40329	0.326	T	0.48559	-0.9025	9	0.51188	T	0.08	.	1.7398	0.02950	0.2843:0.0795:0.1477:0.4885	rs61732042	793	P49454	CENPF_HUMAN	R	793	ENSP00000355922:M793R	ENSP00000355922:M793R	M	+	2	0	CENPF	212880682	0.014000	0.17966	0.002000	0.10522	0.384000	0.30261	0.225000	0.17757	0.400000	0.25396	0.496000	0.49642	ATG	T|0.968;G|0.032	0.032	strong		0.428	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
CCDC6	8030	hgsc.bcm.edu	37	10	61665886	61665886	+	Silent	SNP	C	C	A	rs1171830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:61665886C>A	ENST00000263102.6	-	1	528	c.297G>T	c.(295-297)gtG>gtT	p.V99V		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	99						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)		CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		TCACGATGGTCACGCTGGCTT	0.657			T	RET	NSCLC								C|||	1880	0.375399	0.0393	0.4726	5008	,	,		12230	0.627		0.4523	False		,,,				2504	0.4223				p.V99V		Atlas-SNP	.		Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	CCDC6	44	.	0			c.G297T						PASS	.	C		501,3905	230.4+/-244.6	46,409,1748	58.0	55.0	56.0		297	2.5	1.0	10	dbSNP_87	56	4054,4546	556.5+/-386.9	955,2144,1201	no	coding-synonymous	CCDC6	NM_005436.4		1001,2553,2949	AA,AC,CC		47.1395,11.3709,35.0223		99/475	61665886	4555,8451	2203	4300	6503	SO:0001819	synonymous_variant	8030	exon1			GATGGTCACGCTG	S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.297G>T	10.37:g.61665886C>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	43	24	0.55814	NM_005436	Q15250|Q6GSG7	Silent	SNP	ENST00000263102.6	37	CCDS7257.1																																																																																			C|0.638;A|0.362	0.362	strong		0.657	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
HIST4H4	121504	hgsc.bcm.edu	37	12	14923988	14923988	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:14923988G>T	ENST00000539745.1	-	1	77	c.31C>A	c.(31-33)Ctg>Atg	p.L11M	HIST4H4_ENST00000541592.1_5'Flank	NM_175054.2	NP_778224.1	P62805	H4_HUMAN	histone cluster 4, H4	11					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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)	6						CCCTTACCCAGCCCCTTGCCA	0.617																																					p.L11M		Atlas-SNP	.											.	HIST4H4	13	.	0			c.C31A						PASS	.						46.0	52.0	50.0					12																	14923988		2203	4300	6503	SO:0001583	missense	121504	exon1			TACCCAGCCCCTT	AY128653	CCDS8665.1	12p12.3	2011-01-27	2006-10-11			ENSG00000197837		"""Histones / Replication-dependent"""	20510	protein-coding gene	gene with protein product		615069	"""histone 4, H4"""			12408966	Standard	NM_175054		Approved	MGC24116	uc001rcf.4	P62805		ENST00000539745.1:c.31C>A	12.37:g.14923988G>T	ENSP00000443017:p.Leu11Met	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_175054	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000539745.1	37	CCDS8665.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.660167	0.29515	.	.	ENSG00000197837	ENST00000539745	.	.	.	4.07	4.07	0.47477	.	0.000000	0.43260	U	0.000587	T	0.64080	0.2566	.	.	.	0.51482	D	0.999927	.	.	.	.	.	.	T	0.67409	-0.5678	6	0.87932	D	0	.	7.8764	0.29597	0.1106:0.0:0.8894:0.0	.	.	.	.	M	11	.	ENSP00000350767:L11M	L	-	1	2	HIST4H4	14815255	1.000000	0.71417	0.737000	0.30932	0.392000	0.30506	3.606000	0.54095	2.275000	0.75901	0.650000	0.86243	CTG	.	.	none		0.617	HIST4H4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400844.1	NM_175054	
C21orf58	54058	hgsc.bcm.edu	37	21	47734777	47734777	+	Silent	SNP	G	G	A	rs56036022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47734777G>A	ENST00000291691.7	-	5	1598	c.462C>T	c.(460-462)gaC>gaT	p.D154D	C21orf58_ENST00000397682.3_Silent_p.D48D|C21orf58_ENST00000397679.1_Silent_p.D48D|C21orf58_ENST00000397683.1_Silent_p.D48D|C21orf58_ENST00000397680.1_Silent_p.D48D	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	154										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GAGAGAGCTCGTCCAGGAGGT	0.701													G|||	174	0.0347444	0.1248	0.0101	5008	,	,		14424	0.0		0.002	False		,,,				2504	0.0				p.D154D		Atlas-SNP	.											.	C21orf58	25	.	0			c.C462T						PASS	.	G		383,3735		17,349,1693	9.0	11.0	10.0		462	-9.5	0.2	21	dbSNP_129	10	8,8092		0,8,4042	no	coding-synonymous	C21orf58	NM_058180.3		17,357,5735	AA,AG,GG		0.0988,9.3006,3.2002		154/323	47734777	391,11827	2059	4050	6109	SO:0001819	synonymous_variant	54058	exon5			GAGCTCGTCCAGG		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.462C>T	21.37:g.47734777G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	91	40	0.43956	NM_058180	B3KPI1	Silent	SNP	ENST00000291691.7	37	CCDS13735.1																																																																																			G|0.975;A|0.025	0.025	strong		0.701	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180	
L3HYPDH	112849	hgsc.bcm.edu	37	14	59950690	59950690	+	Silent	SNP	A	A	C	rs2296842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:59950690A>C	ENST00000247194.4	-	1	458	c.345T>G	c.(343-345)gcT>gcG	p.A115A	JKAMP_ENST00000356057.5_5'Flank|JKAMP_ENST00000554271.1_5'Flank|JKAMP_ENST00000425728.2_5'Flank|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000556985.1_5'Flank|L3HYPDH_ENST00000487285.1_5'Flank|JKAMP_ENST00000261247.9_5'Flank	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	115					metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	CGAAGTCCAAAGCGAAGCGGC	0.706											OREG0022712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1328	0.265176	0.1861	0.3833	5008	,	,		16051	0.1825		0.2376	False		,,,				2504	0.4018				p.A115A		Atlas-SNP	.											C14orf149,NS,carcinoma,0,1	.	.	1	0			c.T345G						PASS	.	A		853,3413		111,631,1391	10.0	10.0	10.0		345	-9.7	0.0	14	dbSNP_100	10	1857,6475		235,1387,2544	no	coding-synonymous	C14orf149	NM_144581.1		346,2018,3935	CC,CA,AA		22.2876,19.9953,21.5114		115/355	59950690	2710,9888	2133	4166	6299	SO:0001819	synonymous_variant	112849	exon1			GTCCAAAGCGAAG	AI762327	CCDS9739.1	14q23.1	2012-08-15	2012-08-15	2012-08-15	ENSG00000126790	ENSG00000126790	4.2.1.77		20488	protein-coding gene	gene with protein product	"""trans-L-3-hydroxyproline dehydratase"""	614811	"""chromosome 14 open reading frame 149"""	C14orf149		22528483	Standard	NM_144581		Approved	FLJ25436	uc001xee.1	Q96EM0	OTTHUMG00000028941	ENST00000247194.4:c.345T>G	14.37:g.59950690A>C		Somatic	6	0	0	1042	WXS	Illumina HiSeq	Phase_I	9	5	0.555556	NM_144581	Q96LJ5	Silent	SNP	ENST00000247194.4	37	CCDS9739.1																																																																																			A|0.786;C|0.214	0.214	strong		0.706	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581	
NPHP3	27031	hgsc.bcm.edu	37	3	132409455	132409455	+	Silent	SNP	C	C	T	rs16839515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132409455C>T	ENST00000337331.5	-	19	2696	c.2610G>A	c.(2608-2610)ccG>ccA	p.P870P	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	870					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GAAAAAGCCACGGGAGTTCAT	0.393													C|||	316	0.063099	0.1286	0.0086	5008	,	,		14771	0.0694		0.0169	False		,,,				2504	0.0542				p.P870P		Atlas-SNP	.											.	NPHP3	110	.	0			c.G2610A						PASS	.	C		469,3937	222.3+/-239.2	29,411,1763	96.0	100.0	99.0		2610	-11.2	0.0	3	dbSNP_123	99	143,8457	71.3+/-133.9	1,141,4158	yes	coding-synonymous	NPHP3	NM_153240.4		30,552,5921	TT,TC,CC		1.6628,10.6446,4.7055		870/1331	132409455	612,12394	2203	4300	6503	SO:0001819	synonymous_variant	27031	exon19			AAGCCACGGGAGT	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	7907	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.2610G>A	3.37:g.132409455C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	153	72	0.470588	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Silent	SNP	ENST00000337331.5	37	CCDS3078.1																																																																																			C|0.950;T|0.050	0.050	strong		0.393	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240	
VRK3	51231	hgsc.bcm.edu	37	19	50484234	50484234	+	Silent	SNP	G	G	A	rs16981617	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:50484234G>A	ENST00000599538.1	-	13	1918	c.1254C>T	c.(1252-1254)tgC>tgT	p.C418C	VRK3_ENST00000316763.3_Silent_p.C418C|VRK3_ENST00000443401.2_Silent_p.C187C|VRK3_ENST00000594948.1_Silent_p.C418C|VRK3_ENST00000601341.1_Silent_p.C368C|VRK3_ENST00000377011.2_Silent_p.C368C			Q8IV63	VRK3_HUMAN	vaccinia related kinase 3	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)	p.C418C(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|skin(2)|stomach(2)|urinary_tract(1)	23		all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00166)|OV - Ovarian serous cystadenocarcinoma(262;0.00652)		TCCAGTGACCGCAGGGTCCCA	0.567													G|||	852	0.170128	0.1278	0.2421	5008	,	,		15492	0.2867		0.0646	False		,,,				2504	0.1646				p.C418C	Pancreas(6;90 181 4352 12603 17050 34726 35237 44094)	Atlas-SNP	.											VRK3,NS,carcinoma,0,1	VRK3	49	1	1	Substitution - coding silent(1)	stomach(1)	c.C1254T						PASS	.	G	,	554,3852	241.2+/-251.7	36,482,1685	33.0	29.0	30.0		1104,1254	-1.2	0.0	19	dbSNP_123	30	603,7997	152.8+/-207.3	21,561,3718	no	coding-synonymous,coding-synonymous	VRK3	NM_001025778.1,NM_016440.3	,	57,1043,5403	AA,AG,GG		7.0116,12.5738,8.8959	,	368/425,418/475	50484234	1157,11849	2203	4300	6503	SO:0001819	synonymous_variant	51231	exon13			GTGACCGCAGGGT	AB031052	CCDS12791.1, CCDS33076.1	19q13.33	2011-01-14			ENSG00000105053	ENSG00000105053			18996	protein-coding gene	gene with protein product							Standard	XM_005258971		Approved		uc002prh.1	Q8IV63		ENST00000599538.1:c.1254C>T	19.37:g.50484234G>A		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	33	18	0.545455	NM_016440	A6NEG5|A8KA53|Q502Y2|Q9P2V8	Silent	SNP	ENST00000599538.1	37	CCDS12791.1																																																																																			G|0.883;A|0.117	0.117	strong		0.567	VRK3-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464815.1	NM_016440	
RPL9	6133	hgsc.bcm.edu	37	4	39458051	39458051	+	Silent	SNP	A	A	G	rs2125313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:39458051A>G	ENST00000449470.2	-	4	814	c.366T>C	c.(364-366)taT>taC	p.Y122Y	LIAS_ENST00000340169.2_5'Flank|LIAS_ENST00000261434.3_5'Flank|RPL9_ENST00000295955.9_Silent_p.Y122Y|LIAS_ENST00000513731.1_5'Flank|LIAS_ENST00000381846.1_5'Flank	NM_001024921.2	NP_001020092.1	P32969	RL9_HUMAN	ribosomal protein L9	122					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)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribosome (GO:0005840)	RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(1)|skin(1)	8						CCCTGCGGATATATTTTTCAC	0.413													G|||	3470	0.692891	0.5272	0.8069	5008	,	,		16663	0.7212		0.6799	False		,,,				2504	0.82				p.Y122Y		Atlas-SNP	.											.	RPL9	16	.	0			c.T366C						PASS	.	G	,	2426,1980	541.7+/-375.8	691,1044,468	46.0	48.0	47.0		366,366	1.5	1.0	4	dbSNP_96	47	6023,2577	416.3+/-352.1	2093,1837,370	no	coding-synonymous,coding-synonymous	RPL9	NM_000661.4,NM_001024921.2	,	2784,2881,838	GG,GA,AA		29.9651,44.9387,35.0377	,	122/193,122/193	39458051	8449,4557	2203	4300	6503	SO:0001819	synonymous_variant	6133	exon5			GCGGATATATTTT	D14531	CCDS3452.1	4p13	2011-04-06			ENSG00000163682	ENSG00000163682		"""L ribosomal proteins"""	10369	protein-coding gene	gene with protein product		603686				8597601, 8415001	Standard	XM_005262661		Approved	L9	uc021sso.1	P32969	OTTHUMG00000099367	ENST00000449470.2:c.366T>C	4.37:g.39458051A>G		Somatic	344	0	0		WXS	Illumina HiSeq	Phase_I	332	330	0.993976	NM_000661		Silent	SNP	ENST00000449470.2	37	CCDS3452.1	1487	0.6808608058608059	261	0.5304878048780488	285	0.787292817679558	428	0.7482517482517482	513	0.6767810026385225	G	1.549	-0.539856	0.04053	0.550613	0.700349	ENSG00000163682	ENST00000508595	.	.	.	5.66	1.53	0.23141	.	0.000000	0.64402	U	0.000001	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.25187	-1.0139	5	0.30078	T	0.28	.	10.5401	0.45029	0.4386:0.0:0.5614:0.0	rs2125313;rs61653338	.	.	.	H	119	.	ENSP00000425250:Y119H	Y	-	1	0	RPL9	39134446	1.000000	0.71417	0.996000	0.52242	0.185000	0.23345	1.174000	0.31932	0.088000	0.17205	-0.974000	0.02594	TAT	A|0.341;G|0.659	0.659	strong		0.413	RPL9-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361018.1		
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383073	39383073	+	Missense_Mutation	SNP	G	G	C	rs9902235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39383073G>C	ENST00000377721.3	+	1	174	c.167G>C	c.(166-168)tGc>tCc	p.C56S	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.C56S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	56	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].		C -> S (in dbSNP:rs9902235). {ECO:0000269|PubMed:11279113, ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CGCCCAACTTGCTGTCAAAAC	0.652													.|||	3551	0.709065	0.6044	0.8329	5008	,	,		21802	0.6319		0.7455	False		,,,				2504	0.8047				p.C56S		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.G167C						PASS	.						71.0	63.0	66.0					17																	39383073		2203	4300	6503	SO:0001583	missense	83899	exon1			CAACTTGCTGTCA	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.167G>C	17.37:g.39383073G>C	ENSP00000366950:p.Cys56Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	82	39	0.47561	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	1526	0.6987179487179487	300	0.6097560975609756	297	0.8204419889502762	366	0.6398601398601399	563	0.7427440633245382	.	10.45	1.352814	0.24512	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.02323	4.46;4.34	2.89	1.92	0.25849	.	.	.	.	.	T	0.00012	0.0000	M	0.78637	2.42	0.33658	P	0.39071599999999995	B	0.25351	0.124	B	0.25614	0.062	T	0.08371	-1.0725	8	0.45353	T	0.12	.	4.9649	0.14085	0.2821:0.0:0.7179:0.0	rs9902235;rs60513024	56	Q9BYQ4	KRA92_HUMAN	S	56	ENSP00000366950:C56S;ENSP00000398325:C56S	ENSP00000366950:C56S	C	+	2	0	KRTAP9-2	36636599	0.077000	0.21312	0.247000	0.24249	0.193000	0.23685	0.915000	0.28638	0.793000	0.33875	0.552000	0.68991	TGC	G|0.287;C|0.713	0.713	strong		0.652	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
GRID1	2894	hgsc.bcm.edu	37	10	88126071	88126071	+	Splice_Site	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:88126071C>T	ENST00000327946.7	-	1	164	c.79G>A	c.(79-81)Ggt>Agt	p.G27S		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	27					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						CCGCGCTTACCGATGTGGATG	0.716										Multiple Myeloma(13;0.14)																											p.G27S		Atlas-SNP	.											.	GRID1	204	.	0			c.G79A						PASS	.						9.0	9.0	9.0					10																	88126071		2110	4138	6248	SO:0001630	splice_region_variant	2894	exon1			GCTTACCGATGTG	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.79+1G>A	10.37:g.88126071C>T		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	20	13	0.65	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.491269	0.64074	.	.	ENSG00000182771	ENST00000327946	D	0.95588	-3.75	2.24	2.24	0.28232	.	0.288147	0.21374	U	0.075581	D	0.94198	0.8138	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.65684	0.937	D	0.91741	0.5404	9	.	.	.	.	9.8853	0.41257	0.0:1.0:0.0:0.0	.	27	Q9ULK0	GRID1_HUMAN	S	27	ENSP00000330148:G27S	.	G	-	1	0	GRID1	88116051	1.000000	0.71417	0.972000	0.41901	0.495000	0.33615	6.014000	0.70784	1.228000	0.43614	0.305000	0.20034	GGT	.	.	none		0.716	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	Missense_Mutation
SLC12A8	84561	hgsc.bcm.edu	37	3	124802881	124802881	+	Silent	SNP	A	A	G	rs2981483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124802881A>G	ENST00000393469.4	-	13	2047	c.1998T>C	c.(1996-1998)ccT>ccC	p.P666P	SLC12A8_ENST00000423114.2_Silent_p.P695P|SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000469902.1_Silent_p.P666P|SLC12A8_ENST00000430155.2_Silent_p.P467P|SLC12A8_ENST00000314584.7_Silent_p.P327P	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	666					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						TCTGCTCCTGAGGGGACCGCA	0.542													A|||	3126	0.624201	0.8026	0.5994	5008	,	,		20216	0.5813		0.5388	False		,,,				2504	0.5327				p.P666P		Atlas-SNP	.											.	SLC12A8	81	.	0			c.T1998C						PASS	.	A	,	3160,928		1254,652,138	31.0	35.0	34.0		1998,1998	3.3	0.9	3	dbSNP_101	34	4356,4046		1153,2050,998	no	coding-synonymous,coding-synonymous	SLC12A8	NM_001195483.1,NM_024628.5	,	2407,2702,1136	GG,GA,AA		48.1552,22.7006,39.8239	,	666/715,666/715	124802881	7516,4974	2044	4201	6245	SO:0001819	synonymous_variant	84561	exon14			CTCCTGAGGGGAC		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1998T>C	3.37:g.124802881A>G		Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	133	133	1	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Silent	SNP	ENST00000393469.4	37	CCDS43143.1																																																																																			A|0.406;G|0.594	0.594	strong		0.542	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
POLG	5428	hgsc.bcm.edu	37	15	89859994	89859994	+	Missense_Mutation	SNP	C	C	A	rs3087374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89859994C>A	ENST00000268124.5	-	23	4041	c.3708G>T	c.(3706-3708)caG>caT	p.Q1236H	POLG_ENST00000442287.2_Missense_Mutation_p.Q1236H|FANCI_ENST00000300027.8_3'UTR|FANCI_ENST00000310775.7_3'UTR	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	1236			Q -> H (in dbSNP:rs3087374). {ECO:0000269|PubMed:12975295, ECO:0000269|PubMed:14635118, ECO:0000269|PubMed:15917273, ECO:0000269|PubMed:16639411, ECO:0000269|PubMed:18828154, ECO:0000269|Ref.4}.		aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			ATGGTCCAGGCTGGCTTCGTT	0.507								DNA polymerases (catalytic subunits)					C|||	135	0.0269569	0.0053	0.0403	5008	,	,		18701	0.0		0.0855	False		,,,				2504	0.0143				p.Q1236H	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.G3708T						PASS	.	C	,HIS/GLN,HIS/GLN,	77,4323	67.0+/-104.6	1,75,2124	100.0	93.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,3708,3708,	5.0	1.0	15	dbSNP_102	96	697,7901	172.6+/-223.3	37,623,3639	yes	utr-3,missense,missense,utr-3	POLG,FANCI	NM_001113378.1,NM_001126131.1,NM_002693.2,NM_018193.2	,24,24,	38,698,5763	AA,AC,CC		8.1065,1.75,5.9548	,probably-damaging,probably-damaging,	,1236/1240,1236/1240,	89859994	774,12224	2200	4299	6499	SO:0001583	missense	5428	exon23			TCCAGGCTGGCTT	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.3708G>T	15.37:g.89859994C>A	ENSP00000268124:p.Gln1236His	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	122	58	0.47541	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	37	CCDS10350.1	83	0.038003663003663	3	0.006097560975609756	20	0.055248618784530384	0	0.0	60	0.079155672823219	C	13.83	2.353593	0.41700	0.0175	0.081065	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.96396	-4.0;-4.0	5.95	5.03	0.67393	.	1.522350	0.03753	N	0.256947	T	0.52996	0.1769	N	0.14661	0.345	0.37226	P	0.09453999999999996	P	0.43169	0.8	B	0.41723	0.365	T	0.77879	-0.2423	9	0.45353	T	0.12	0.0151	9.8053	0.40789	0.0:0.8577:0.0:0.1423	rs3087374;rs3176244;rs17804776;rs61472028;rs3087374	1236	P54098	DPOG1_HUMAN	H	1236	ENSP00000268124:Q1236H;ENSP00000399851:Q1236H	ENSP00000268124:Q1236H	Q	-	3	2	POLG	87660998	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	1.426000	0.34870	2.824000	0.97209	0.655000	0.94253	CAG	C|0.950;A|0.050	0.050	strong		0.507	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
IFRD1	3475	hgsc.bcm.edu	37	7	112112279	112112279	+	Silent	SNP	G	G	A	rs2074796	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:112112279G>A	ENST00000403825.3	+	10	1308	c.1047G>A	c.(1045-1047)cgG>cgA	p.R349R	IFRD1_ENST00000535603.1_Silent_p.R299R|IFRD1_ENST00000005558.4_Silent_p.R349R	NM_001550.3	NP_001541.2	O00458	IFRD1_HUMAN	interferon-related developmental regulator 1	349					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						GTTAGGAACGGGATTTTCCAA	0.378													G|||	1233	0.246206	0.3623	0.1614	5008	,	,		20407	0.1915		0.2525	False		,,,				2504	0.1994				p.R349R		Atlas-SNP	.											IFRD1,NS,carcinoma,+1,2	IFRD1	46	2	0			c.G1047A						PASS	.	G	,,,	1516,2890	482.1+/-359.3	257,1002,944	118.0	117.0	117.0		1047,897,897,1047	1.7	1.0	7	dbSNP_96	117	2108,6492	362.6+/-332.8	265,1578,2457	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFRD1	NM_001007245.2,NM_001197079.1,NM_001197080.1,NM_001550.3	,,,	522,2580,3401	AA,AG,GG		24.5116,34.4076,27.8641	,,,	349/452,299/402,299/402,349/452	112112279	3624,9382	2203	4300	6503	SO:0001819	synonymous_variant	3475	exon11			GGAACGGGATTTT	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.1047G>A	7.37:g.112112279G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_001007245	B7Z5G1|O75234|Q5U013|Q9BVE4	Silent	SNP	ENST00000403825.3	37	CCDS34736.1																																																																																			G|0.736;A|0.264	0.264	strong		0.378	IFRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338700.1	NM_001550	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296616	39296616	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39296616C>T	ENST00000345847.4	-	1	123	c.124G>A	c.(124-126)Gtg>Atg	p.V42M		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	42	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						CAGCTGGACACACAGCAGCTG	0.677																																					p.V42M		Atlas-SNP	.											KRTAP4-6,bladder,carcinoma,+2,3	KRTAP4-6	46	3	0			c.G124A						scavenged	.																																			SO:0001583	missense	81871	exon1			TGGACACACAGCA	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.124G>A	17.37:g.39296616C>T	ENSP00000328270:p.Val42Met	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	82	4	0.0487805	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	.	.	.	.	.	.	.	.	.	.	.	4.888	0.165129	0.09339	.	.	ENSG00000198090	ENST00000345847	T	0.00623	6.15	4.5	-2.62	0.06152	.	1.424950	0.05585	U	0.573641	T	0.02342	0.0072	M	0.86651	2.83	0.09310	N	1	.	.	.	.	.	.	T	0.23511	-1.0186	8	0.51188	T	0.08	.	9.9921	0.41877	0.0:0.3944:0.0:0.6056	.	.	.	.	M	42	ENSP00000328270:V42M	ENSP00000328270:V42M	V	-	1	0	KRTAP4-6	36550142	.	.	0.000000	0.03702	0.016000	0.09150	.	.	-0.888000	0.03956	-0.806000	0.03193	GTG	.	.	none		0.677	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
ALS2CL	259173	hgsc.bcm.edu	37	3	46729757	46729757	+	Missense_Mutation	SNP	C	C	G	rs7642448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46729757C>G	ENST00000318962.4	-	3	216	c.133G>C	c.(133-135)Gag>Cag	p.E45Q	ALS2CL_ENST00000415953.1_Missense_Mutation_p.E45Q	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	45			E -> Q (in dbSNP:rs7642448). {ECO:0000269|PubMed:17974005}.		endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CGCAGGCACTCTCTGCCCCAG	0.617													C|||	2246	0.448482	0.736	0.3991	5008	,	,		20682	0.3046		0.3161	False		,,,				2504	0.3793				p.E45Q		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G133C						PASS	.	C	GLN/GLU,GLN/GLU	2839,1567	657.0+/-400.2	921,997,285	36.0	37.0	37.0		133,133	4.4	0.6	3	dbSNP_116	37	2641,5959	418.8+/-352.9	400,1841,2059	yes	missense,missense	ALS2CL	NM_001190707.1,NM_147129.3	29,29	1321,2838,2344	GG,GC,CC		30.7093,35.5651,42.1344	possibly-damaging,possibly-damaging	45/954,45/954	46729757	5480,7526	2203	4300	6503	SO:0001583	missense	259173	exon3			GGCACTCTCTGCC	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.133G>C	3.37:g.46729757C>G	ENSP00000313670:p.Glu45Gln	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	103	102	0.990291	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	875	0.40064102564102566	337	0.6849593495934959	146	0.40331491712707185	159	0.27797202797202797	233	0.3073878627968338	C	11.66	1.703594	0.30232	0.644349	0.307093	ENSG00000178038	ENST00000318962;ENST00000415953	T;T	0.56275	0.47;0.47	4.36	4.36	0.52297	.	0.111814	0.39407	N	0.001379	T	0.00012	0.0000	L	0.34521	1.04	0.09310	P	0.9999999999980187	D	0.60575	0.988	P	0.52109	0.69	T	0.40739	-0.9547	9	0.39692	T	0.17	.	12.5671	0.56316	0.0:1.0:0.0:0.0	rs7642448;rs59127538;rs7642448	45	Q60I27	AL2CL_HUMAN	Q	45	ENSP00000313670:E45Q;ENSP00000413223:E45Q	ENSP00000313670:E45Q	E	-	1	0	ALS2CL	46704761	0.845000	0.29573	0.643000	0.29450	0.182000	0.23217	3.504000	0.53347	2.413000	0.81919	0.591000	0.81541	GAG	C|0.587;G|0.413	0.413	strong		0.617	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	
JRK	8629	hgsc.bcm.edu	37	8	143746050	143746050	+	RNA	SNP	C	C	T	rs2976399	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143746050C>T	ENST00000507178.2	-	0	1760							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ggatctcctccgccgtcctgg	0.657													C|||	2208	0.440895	0.466	0.2925	5008	,	,		17155	0.4841		0.3469	False		,,,				2504	0.5644				p.G476R		Atlas-SNP	.											.	.	.	.	0			c.G1426A						PASS	.	C	ARG/GLY,ARG/GLY	1797,2389		398,1001,694	19.0	23.0	22.0		1428,1428	2.0	0.0	8	dbSNP_101	22	2759,5647		478,1803,1922	no	missense,missense	JRK	NM_001077527.1,NM_003724.2	125,125	876,2804,2616	TT,TC,CC		32.8218,42.9288,36.1817	benign,benign	476/557,476/569	143746050	4556,8036	2093	4203	6296			8629	exon3			CTCCTCCGCCGTC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746050C>T		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	35	14	0.4	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				C|0.577;T|0.423	0.423	strong		0.657	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
USP10	9100	hgsc.bcm.edu	37	16	84778766	84778766	+	Missense_Mutation	SNP	C	C	T	rs139338093	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84778766C>T	ENST00000219473.7	+	4	792	c.679C>T	c.(679-681)Cct>Tct	p.P227S	USP10_ENST00000570191.1_Missense_Mutation_p.P231S|USP10_ENST00000562743.1_3'UTR	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	227					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						GCCTGACAGTCCTTTCCCCGG	0.602													C|||	93	0.0185703	0.0008	0.0144	5008	,	,		17012	0.002		0.0209	False		,,,				2504	0.0603				p.P231S		Atlas-SNP	.											USP10,NS,carcinoma,0,1	USP10	51	1	0			c.C691T						PASS	.	C	SER/PRO	16,3848		0,16,1916	19.0	20.0	20.0		679	-0.2	0.0	16	dbSNP_134	20	178,8038		4,170,3934	no	missense	USP10	NM_005153.2	74	4,186,5850	TT,TC,CC		2.1665,0.4141,1.606	benign	227/799	84778766	194,11886	1932	4108	6040	SO:0001583	missense	9100	exon5			GACAGTCCTTTCC	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.679C>T	16.37:g.84778766C>T	ENSP00000219473:p.Pro227Ser	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	107	42	0.392523	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	29	0.013278388278388278	0	0.0	7	0.019337016574585635	0	0.0	22	0.029023746701846966	C	0.004	-2.380381	0.00205	0.004141	0.021665	ENSG00000103194	ENST00000219473	T	0.05258	3.47	4.96	-0.145	0.13436	.	1.212090	0.05596	N	0.575524	T	0.00784	0.0026	N	0.02802	-0.49	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.39583	-0.9607	10	0.02654	T	1	-0.9725	6.0667	0.19868	0.0:0.4472:0.1427:0.4101	.	231;227	Q14694-3;Q14694	.;UBP10_HUMAN	S	227	ENSP00000219473:P227S	ENSP00000219473:P227S	P	+	1	0	USP10	83336267	0.670000	0.27512	0.007000	0.13788	0.050000	0.14768	0.319000	0.19522	-0.198000	0.10333	0.491000	0.48974	CCT	C|0.985;T|0.015	0.015	strong		0.602	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
SMCO2	341346	hgsc.bcm.edu	37	12	27654898	27654898	+	Silent	SNP	C	C	T	rs61731840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:27654898C>T	ENST00000535986.1	+	8	876	c.876C>T	c.(874-876)acC>acT	p.T292T	SMCO2_ENST00000298876.4_Silent_p.T242T|SMCO2_ENST00000416383.1_Silent_p.T292T			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	292						integral component of membrane (GO:0016021)											ATGTCCTCACCGTCACTGGAC	0.403													C|||	587	0.117212	0.0318	0.1282	5008	,	,		20543	0.0327		0.2336	False		,,,				2504	0.1922				p.T292T		Atlas-SNP	.											.	.	.	.	0			c.C876T						PASS	.	C		79,1287		10,59,614	259.0	219.0	231.0		876	1.6	0.0	12	dbSNP_129	231	806,2374		121,564,905	no	coding-synonymous	C12orf70	NM_001145010.1		131,623,1519	TT,TC,CC		25.3459,5.7833,19.4677		292/344	27654898	885,3661	683	1590	2273	SO:0001819	synonymous_variant	0	exon9			CCTCACCGTCACT		CCDS44852.1	12p11.23	2013-03-11	2013-03-11	2013-03-11	ENSG00000165935	ENSG00000165935			34448	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 70"""	C12orf70			Standard	NM_001145010		Approved	LOC341346	uc010sjq.2	A6NFE2	OTTHUMG00000169205	ENST00000535986.1:c.876C>T	12.37:g.27654898C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	125	56	0.448	NM_001145010		Silent	SNP	ENST00000535986.1	37	CCDS44852.1																																																																																			C|0.842;T|0.158	0.158	strong		0.403	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
ELMO2	63916	hgsc.bcm.edu	37	20	45003211	45003211	+	Silent	SNP	C	C	T	rs8124302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:45003211C>T	ENST00000290246.6	-	14	1328	c.1134G>A	c.(1132-1134)ctG>ctA	p.L378L	ELMO2_ENST00000372176.1_Silent_p.L290L|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000454865.2_Silent_p.L110L|ELMO2_ENST00000439931.2_Silent_p.L390L|ELMO2_ENST00000396391.1_Silent_p.L378L|ELMO2_ENST00000352077.2_Silent_p.L376L|ELMO2_ENST00000445496.2_Silent_p.L195L	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	378	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				TAGCCAAGTACAGCATGTTGT	0.517													C|||	5	0.000998403	0.0	0.0	5008	,	,		21226	0.0		0.004	False		,,,				2504	0.001				p.L378L		Atlas-SNP	.											.	ELMO2	51	.	0			c.G1134A						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	120.0	99.0	106.0		1134,1134	0.4	1.0	20	dbSNP_116	106	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous,coding-synonymous	ELMO2	NM_133171.3,NM_182764.1	,	0,32,6471	TT,TC,CC		0.314,0.1135,0.246	,	378/721,378/721	45003211	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	63916	exon13			CAAGTACAGCATG	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.1134G>A	20.37:g.45003211C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																			C|0.997;T|0.003	0.003	strong		0.517	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33549387	33549387	+	Silent	SNP	G	G	A	rs61748195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:33549387G>A	ENST00000504830.1	-	21	4562	c.4227C>T	c.(4225-4227)gcC>gcT	p.A1409A	ADAMTS12_ENST00000352040.3_Silent_p.A1324A	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1409	TSP type-1 6. {ECO:0000255|PROSITE- ProRule:PRU00210}.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A1409A(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GAGGAATGCCGGCCAGGAACT	0.612										HNSCC(64;0.19)			G|||	219	0.04373	0.0189	0.0519	5008	,	,		18823	0.0		0.1093	False		,,,				2504	0.0491				p.A1409A		Atlas-SNP	.											ADAMTS12,colon,carcinoma,0,1	ADAMTS12	464	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C4227T						scavenged	.	G		143,4263	102.1+/-140.7	0,143,2060	72.0	76.0	75.0		4227	-10.7	0.0	5	dbSNP_129	75	1015,7585	217.4+/-256.1	52,911,3337	no	coding-synonymous	ADAMTS12	NM_030955.2		52,1054,5397	AA,AG,GG		11.8023,3.2456,8.9036		1409/1595	33549387	1158,11848	2203	4300	6503	SO:0001819	synonymous_variant	81792	exon21			AATGCCGGCCAGG	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.4227C>T	5.37:g.33549387G>A		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Silent	SNP	ENST00000504830.1	37	CCDS34140.1																																																																																			G|0.923;A|0.077	0.077	strong		0.612	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
MKI67	4288	hgsc.bcm.edu	37	10	129901066	129901066	+	Missense_Mutation	SNP	C	C	A	rs114687140	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:129901066C>A	ENST00000368654.3	-	13	9413	c.9038G>T	c.(9037-9039)cGc>cTc	p.R3013L	MKI67_ENST00000368653.3_Missense_Mutation_p.R2653L	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	3013					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)				TGGCATGCAGCGCAGCCTCTT	0.572													C|||	159	0.0317492	0.031	0.036	5008	,	,		16508	0.0188		0.0586	False		,,,				2504	0.0153				p.R3013L		Atlas-SNP	.											.	MKI67	363	.	0			c.G9038T						PASS	.	C	LEU/ARG,LEU/ARG	134,4272	94.8+/-133.5	0,134,2069	72.0	69.0	70.0		7958,9038	1.8	0.0	10	dbSNP_132	70	476,8124	139.0+/-195.8	14,448,3838	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	102,102	14,582,5907	AA,AC,CC		5.5349,3.0413,4.6901	benign,benign	2653/2897,3013/3257	129901066	610,12396	2203	4300	6503	SO:0001583	missense	4288	exon13			ATGCAGCGCAGCC	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.9038G>T	10.37:g.129901066C>A	ENSP00000357643:p.Arg3013Leu	Somatic	181	1	0.00552486		WXS	Illumina HiSeq	Phase_I	138	136	0.985507	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	88	0.040293040293040296	14	0.028455284552845527	17	0.04696132596685083	9	0.015734265734265736	48	0.0633245382585752	C	8.522	0.869052	0.17322	0.030413	0.055349	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01821	4.65;4.62	3.93	1.84	0.25277	.	1.494710	0.04225	N	0.334167	T	0.00210	0.0006	N	0.24115	0.695	0.09310	N	1	P;B;B	0.34662	0.462;0.276;0.17	B;B;B	0.29716	0.106;0.049;0.033	T	0.44667	-0.9313	10	0.27785	T	0.31	.	4.1152	0.10077	0.229:0.6479:0.0:0.1231	.	3012;2653;3013	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	L	3013;2653;3012	ENSP00000357643:R3013L;ENSP00000357642:R2653L	ENSP00000357642:R2653L	R	-	2	0	MKI67	129791056	.	.	0.001000	0.08648	0.033000	0.12548	.	.	0.972000	0.38314	-0.258000	0.10820	CGC	C|0.955;A|0.045	0.045	strong		0.572	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
DDX5	1655	hgsc.bcm.edu	37	17	62496670	62496670	+	Missense_Mutation	SNP	A	A	C	rs1140409	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:62496670A>C	ENST00000225792.5	-	12	1839	c.1438T>G	c.(1438-1440)Tca>Gca	p.S480A	MIR3064_ENST00000581130.1_RNA|DDX5_ENST00000580026.1_5'UTR|DDX5_ENST00000578804.1_Missense_Mutation_p.S480A|DDX5_ENST00000450599.2_Missense_Mutation_p.S401A|MIR5047_ENST00000579212.1_RNA	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	480	Transactivation domain.		S -> A (in dbSNP:rs1140409).		cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			TCCTTACCTGAACCTCTGTCT	0.403			T	ETV4	prostate								A|||	146	0.0291534	0.003	0.0461	5008	,	,		21998	0.0		0.0835	False		,,,				2504	0.0266				p.S480A	NSCLC(22;406 813 4871 19580 40307)	Atlas-SNP	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5	101	.	0			c.T1438G	GRCh37	CM066777	DDX5	M	rs1140409	PASS	.	A	ALA/SER	51,4355	50.9+/-86.3	1,49,2153	88.0	78.0	81.0		1438	4.6	1.0	17	dbSNP_86	81	615,7985	158.6+/-212.1	27,561,3712	yes	missense	DDX5	NM_004396.3	99	28,610,5865	CC,CA,AA		7.1512,1.1575,5.1207	benign	480/615	62496670	666,12340	2203	4300	6503	SO:0001583	missense	1655	exon12			TACCTGAACCTCT	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"""DEAD-boxes"""	2746	protein-coding gene	gene with protein product		180630	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"""	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.1438T>G	17.37:g.62496670A>C	ENSP00000225792:p.Ser480Ala	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Missense_Mutation	SNP	ENST00000225792.5	37	CCDS11659.1	88	0.040293040293040296	3	0.006097560975609756	19	0.052486187845303865	0	0.0	66	0.0870712401055409	A	4.506	0.093795	0.08632	0.011575	0.071512	ENSG00000108654	ENST00000540698;ENST00000450599;ENST00000225792	.	.	.	5.73	4.64	0.57946	.	0.338429	0.30311	N	0.009909	T	0.01800	0.0057	L	0.29908	0.895	0.38284	D	0.942529	B;B;B	0.17852	0.013;0.024;0.024	B;B;B	0.14023	0.004;0.01;0.01	T	0.04229	-1.0967	9	0.18710	T	0.47	.	7.5474	0.27775	0.7721:0.1564:0.0715:0.0	rs1140409;rs2229795;rs3179861;rs3204465;rs52828247;rs57832194;rs1140409	401;480;480	B4DLW8;B5BUE6;P17844	.;.;DDX5_HUMAN	A	480;410;469	.	ENSP00000225792:S469A	S	-	1	0	DDX5	59927132	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	4.358000	0.59442	1.096000	0.41439	0.533000	0.62120	TCA	A|0.953;C|0.047	0.047	strong		0.403	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396	
OR2H2	7932	hgsc.bcm.edu	37	6	29555778	29555778	+	Silent	SNP	A	A	G	rs2235698	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29555778A>G	ENST00000383640.2	+	1	96	c.57A>G	c.(55-57)ccA>ccG	p.P19P	GABBR1_ENST00000355973.3_Intron	NM_007160.3	NP_009091.3	O95918	OR2H2_HUMAN	olfactory receptor, family 2, subfamily H, member 2	19					defense response (GO:0006952)|detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|mating (GO:0007618)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|urinary_tract(1)	14						CTGAACACCCAGGGCTGGAAA	0.557													A|||	1347	0.26897	0.1573	0.2997	5008	,	,		19973	0.3393		0.2555	False		,,,				2504	0.3395				p.P19P		Atlas-SNP	.											OR2H2,NS,carcinoma,+1,1	OR2H2	29	1	0			c.A57G						PASS	.	A		622,2400		74,474,963	173.0	178.0	176.0		57	-1.5	0.1	6	dbSNP_98	176	1286,4132		168,950,1591	no	coding-synonymous	OR2H2	NM_007160.3		242,1424,2554	GG,GA,AA		23.7357,20.5824,22.6066		19/313	29555778	1908,6532	1511	2709	4220	SO:0001819	synonymous_variant	7932	exon1			ACACCCAGGGCTG		CCDS34365.1	6p22.2-p21.31	2012-08-09				ENSG00000204657		"""GPCR / Class A : Olfactory receptors"""	8253	protein-coding gene	gene with protein product		600578					Standard	XM_005249407		Approved	hs6M1-12	uc003nmr.1	O95918		ENST00000383640.2:c.57A>G	6.37:g.29555778A>G		Somatic	218	1	0.00458716		WXS	Illumina HiSeq	Phase_I	211	97	0.459716	NM_007160	Q15062|Q2M1Y3|Q5STL8|Q5SUK1|Q6IFN7|Q6NTB7|Q96R14	Silent	SNP	ENST00000383640.2	37	CCDS34365.1																																																																																			A|0.764;G|0.236	0.236	strong		0.557	OR2H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076057.2		
HLA-A	3105	hgsc.bcm.edu	37	6	29912086	29912086	+	Silent	SNP	G	G	A	rs199474634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29912086G>A	ENST00000396634.1	+	6	1148	c.807G>A	c.(805-807)gcG>gcA	p.A269A	HLA-A_ENST00000376809.5_Silent_p.A269A|HLA-A_ENST00000376806.5_Silent_p.A269A|HLA-A_ENST00000376802.2_Silent_p.A269A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	269	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGAAGTGGGCGGCTGTGGTGG	0.627									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	759	0.151558	0.1241	0.1744	5008	,	,		17320	0.2034		0.1113	False		,,,				2504	0.1605				p.A269A		Atlas-SNP	.											.	HLA-A	89	.	0			c.G807A						PASS	.						31.0	30.0	31.0					6																	29912086		1510	2704	4214	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GTGGGCGGCTGTG	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.807G>A	6.37:g.29912086G>A		Somatic	301	0	0		WXS	Illumina HiSeq	Phase_I	170	92	0.541176	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.580;A|0.420	0.420	strong		0.627	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
RYR3	6263	hgsc.bcm.edu	37	15	33905410	33905410	+	Missense_Mutation	SNP	A	A	G	rs2229116	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:33905410A>G	ENST00000389232.4	+	19	2261	c.2191A>G	c.(2191-2193)Atc>Gtc	p.I731V	RYR3_ENST00000415757.3_Missense_Mutation_p.I731V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	731	B30.2/SPRY 1. {ECO:0000255|PROSITE- ProRule:PRU00548}.		I -> V (in dbSNP:rs2229116). {ECO:0000269|PubMed:9515741}.		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)		TGTGGCTTCCATCAACCAGCA	0.602													A|||	1012	0.202077	0.1271	0.3314	5008	,	,		18103	0.1587		0.2247	False		,,,				2504	0.2331				p.I731V		Atlas-SNP	.											RYR3,colon,carcinoma,0,1	RYR3	760	1	0			c.A2191G						scavenged	.	A	VAL/ILE	576,3604		30,516,1544	38.0	41.0	40.0	http://www.ncbi.nlm.nih.gov/pubmed?term	2191	3.1	1.0	15	dbSNP_98	40	1824,6658		203,1418,2620	yes	missense	RYR3	NM_001036.3	29	233,1934,4164	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	21.5044,13.7799,18.9544	benign	731/4871	33905410	2400,10262	2090	4241	6331	SO:0001583	missense	6263	exon19			GCTTCCATCAACC		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.2191A>G	15.37:g.33905410A>G	ENSP00000373884:p.Ile731Val	Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	122	65	0.532787	NM_001243996	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	477	0.2184065934065934	89	0.18089430894308944	114	0.3149171270718232	98	0.17132867132867133	176	0.23218997361477572	A	8.841	0.942258	0.18281	0.137799	0.215044	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	T;T	0.68331	-0.32;-0.32	5.4	3.06	0.35304	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.296753	0.33457	N	0.004896	T	0.00012	0.0000	N	0.19112	0.55	0.39187	P	0.037104000000000026	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.18147	-1.0346	9	0.15952	T	0.53	.	2.9905	0.05981	0.4962:0.232:0.2718:0.0	rs2229116;rs2277889;rs8042362;rs17817397;rs52825179;rs58186010;rs2229116	731;731	Q15413-2;Q15413	.;RYR3_HUMAN	V	731	ENSP00000373884:I731V;ENSP00000399610:I731V	ENSP00000354735:I731V	I	+	1	0	RYR3	31692702	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	0.792000	0.26929	1.079000	0.41038	0.529000	0.55759	ATC	A|0.790;G|0.210	0.210	strong		0.602	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
OR8H2	390151	hgsc.bcm.edu	37	11	55873149	55873149	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55873149C>T	ENST00000313503.1	+	1	631	c.631C>T	c.(631-633)Ctt>Ttt	p.L211F		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	211						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					GATGGTGTCCCTTTTCACAAT	0.403										HNSCC(53;0.14)																											p.L211F		Atlas-SNP	.											OR8H2,colon,carcinoma,0,1	OR8H2	117	1	0			c.C631T						scavenged	.						188.0	173.0	178.0					11																	55873149		2201	4296	6497	SO:0001583	missense	390151	exon1			GTGTCCCTTTTCA	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.631C>T	11.37:g.55873149C>T	ENSP00000323982:p.Leu211Phe	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	176	3	0.0170455	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	.	.	.	.	.	.	.	.	.	.	c	9.959	1.222167	0.22457	.	.	ENSG00000181767	ENST00000313503	T	0.40476	1.03	3.58	0.476	0.16779	GPCR, rhodopsin-like superfamily (1);	0.460978	0.18656	N	0.134859	T	0.22322	0.0538	N	0.11364	0.135	0.09310	N	1	P	0.35944	0.529	B	0.41202	0.35	T	0.09930	-1.0652	10	0.40728	T	0.16	.	3.8608	0.08994	0.0:0.4593:0.2007:0.3399	.	211	Q8N162	OR8H2_HUMAN	F	211	ENSP00000323982:L211F	ENSP00000323982:L211F	L	+	1	0	OR8H2	55629725	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-1.049000	0.03514	0.259000	0.21709	0.440000	0.28878	CTT	.	.	none		0.403	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
TMEM187	8269	hgsc.bcm.edu	37	X	153247954	153247954	+	Silent	SNP	C	C	T	rs6571303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153247954C>T	ENST00000369982.4	+	2	1188	c.441C>T	c.(439-441)tgC>tgT	p.C147C	MIR3202-1_ENST00000580198.1_RNA	NM_003492.2	NP_003483.1	Q14656	TM187_HUMAN	transmembrane protein 187	147						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|large_intestine(1)|lung(1)|prostate(2)	5	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CTCTTGAGTGCGTCTCCCTGG	0.667													C|||	1480	0.392053	0.0711	0.3588	3775	,	,		12334	0.5546		0.1421	False		,,,				2504	0.4448				p.C147C		Atlas-SNP	.											.	TMEM187	21	.	0			c.C441T						PASS	.	C		420,3415		18,322,62,1292,509	37.0	28.0	31.0		441	-4.6	0.0	X	dbSNP_116	31	1200,5527		72,709,347,1647,1524	no	coding-synonymous	TMEM187	NM_003492.2		90,1031,409,2939,2033	TT,TC,T,CC,C		17.8386,10.9518,15.338		147/262	153247954	1620,8942	2203	4299	6502	SO:0001819	synonymous_variant	8269	exon2			TGAGTGCGTCTCC	X92475	CCDS14739.1	Xq28	2007-03-14	2007-03-14	2007-03-14	ENSG00000177854	ENSG00000177854			13705	protein-coding gene	gene with protein product		300059	"""chromosome X open reading frame 12"""	CXorf12		8661027	Standard	NM_003492		Approved	ITBA1, DXS9878E	uc004fjq.2	Q14656	OTTHUMG00000024220	ENST00000369982.4:c.441C>T	X.37:g.153247954C>T		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	28	28	1	NM_003492	B2RC47|Q6IAV7	Silent	SNP	ENST00000369982.4	37	CCDS14739.1																																																																																			C|0.755;0|0.003	.	strong		0.667	TMEM187-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061093.1	NM_003492	
VKORC1	79001	hgsc.bcm.edu	37	16	31106015	31106015	+	Silent	SNP	C	C	T	rs55894764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31106015C>T	ENST00000394975.2	-	1	263	c.36G>A	c.(34-36)cgG>cgA	p.R12R	RP11-196G11.1_ENST00000529564.1_Silent_p.R12R|VKORC1_ENST00000394971.3_5'Flank|VKORC1_ENST00000300851.6_Silent_p.R12R|VKORC1_ENST00000354895.4_Silent_p.R12R|VKORC1_ENST00000498155.1_Intron|VKORC1_ENST00000319788.7_Silent_p.R12R	NM_024006.4	NP_076869.1	Q9BQB6	VKOR1_HUMAN	vitamin K epoxide reductase complex, subunit 1	12					blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular protein metabolic process (GO:0044267)|drug metabolic process (GO:0017144)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|vitamin K metabolic process (GO:0042373)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	quinone binding (GO:0048038)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			lung(3)|urinary_tract(1)	4					Acenocoumarol(DB01418)|Dicoumarol(DB00266)|Menadione(DB00170)|Phenindione(DB00498)|Phenprocoumon(DB00946)|Warfarin(DB00682)	AAAGAGCGAGCCGCACCCAGC	0.721													C|||	43	0.00858626	0.0008	0.0187	5008	,	,		13567	0.0		0.0268	False		,,,				2504	0.002				p.R12R		Atlas-SNP	.											.	VKORC1	9	.	0			c.G36A						PASS	.	C	,	12,4280		0,12,2134	13.0	13.0	13.0		36,36	2.5	1.0	16	dbSNP_129	13	92,8316		0,92,4112	no	coding-synonymous,coding-synonymous	VKORC1	NM_024006.4,NM_206824.1	,	0,104,6246	TT,TC,CC		1.0942,0.2796,0.8189	,	12/164,12/93	31106015	104,12596	2146	4204	6350	SO:0001819	synonymous_variant	79001	exon1			AGCGAGCCGCACC		CCDS10703.1, CCDS10704.1	16p11.2	2008-02-05	2004-07-23		ENSG00000167397	ENSG00000167397			23663	protein-coding gene	gene with protein product		608547	"""vitamin K dependent clotting factors deficiency 2"""	VKCFD2			Standard	NM_024006		Approved		uc002eas.3	Q9BQB6	OTTHUMG00000047408	ENST00000394975.2:c.36G>A	16.37:g.31106015C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	47	27	0.574468	NM_024006	A6NIQ6|B2R4Z6|Q6UX90|Q7Z2R4	Silent	SNP	ENST00000394975.2	37	CCDS10703.1																																																																																			C|0.990;T|0.010	0.010	strong		0.721	VKORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108582.1	NM_024006	
ELSPBP1	64100	hgsc.bcm.edu	37	19	48519244	48519244	+	Silent	SNP	A	A	G	rs35792818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48519244A>G	ENST00000339841.2	+	4	481	c.303A>G	c.(301-303)tcA>tcG	p.S101S	ELSPBP1_ENST00000597519.1_Intron	NM_022142.4	NP_071425.3	Q96BH3	ESPB1_HUMAN	epididymal sperm binding protein 1	101	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				single fertilization (GO:0007338)	extracellular region (GO:0005576)				NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(6)	10		all_cancers(25;8.7e-09)|all_lung(116;1.15e-06)|all_epithelial(76;1.17e-06)|Lung NSC(112;2.56e-06)|all_neural(266;0.0138)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;0.000253)|all cancers(93;0.00129)|Epithelial(262;0.0314)|GBM - Glioblastoma multiforme(486;0.0606)		TGTGGTGCTCAGTCACCTCTG	0.507													g|||	810	0.161741	0.2103	0.1254	5008	,	,		21204	0.0724		0.1531	False		,,,				2504	0.2229				p.S101S		Atlas-SNP	.											ELSPBP1,NS,NS,+1,1	ELSPBP1	29	1	0			c.A303G						PASS	.	G		885,3521	742.5+/-411.4	86,713,1404	136.0	115.0	122.0		303	-7.1	0.3	19	dbSNP_126	122	1294,7306	759.1+/-407.5	91,1112,3097	no	coding-synonymous	ELSPBP1	NM_022142.4		177,1825,4501	GG,GA,AA		15.0465,20.0862,16.7538		101/224	48519244	2179,10827	2203	4300	6503	SO:0001819	synonymous_variant	64100	exon4			GTGCTCAGTCACC	AJ278478	CCDS12708.1	19q13.33	2009-09-17							14417	protein-coding gene	gene with protein product	"""epididymal protein 12"""	607443					Standard	NM_022142		Approved	HE12, E12, EDDM12	uc002pht.3	Q96BH3		ENST00000339841.2:c.303A>G	19.37:g.48519244A>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	127	53	0.417323	NM_022142	Q96RT0|Q9H4C8	Silent	SNP	ENST00000339841.2	37	CCDS12708.1																																																																																			A|0.837;G|0.163	0.163	strong		0.507	ELSPBP1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465207.1		
TTN	7273	hgsc.bcm.edu	37	2	179580418	179580418	+	Missense_Mutation	SNP	C	C	T	rs397517517		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179580418C>T	ENST00000591111.1	-	87	24996	c.24772G>A	c.(24772-24774)Ggg>Agg	p.G8258R	TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G8575R|TTN_ENST00000342992.6_Missense_Mutation_p.G7331R|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000359218.5_Intron			Q8WZ42	TITIN_HUMAN	titin	12436	Ig-like 65.				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)			TCTGGAGACCCACCGATTTTG	0.413																																					p.G8575R		Atlas-SNP	.											.	TTN	18412	.	0			c.G25723A						PASS	.						59.0	57.0	57.0					2																	179580418		1876	4113	5989	SO:0001583	missense	7273	exon89			GAGACCCACCGAT	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.24772G>A	2.37:g.179580418C>T	ENSP00000465570:p.Gly8258Arg	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	45	0.387931	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	17.59	3.426474	0.62733	.	.	ENSG00000155657	ENST00000342992	T	0.79940	-1.32	5.33	5.33	0.75918	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.94896	0.8350	H	0.99475	4.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97121	0.9811	9	0.87932	D	0	.	19.3896	0.94574	0.0:1.0:0.0:0.0	.	8258	Q8WZ42	TITIN_HUMAN	R	7331	ENSP00000343764:G7331R	ENSP00000343764:G7331R	G	-	1	0	TTN	179288663	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.040000	0.70980	2.637000	0.89404	0.655000	0.94253	GGG	.	.	none		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
D2HGDH	728294	hgsc.bcm.edu	37	2	242690675	242690675	+	Missense_Mutation	SNP	G	G	A	rs1106639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:242690675G>A	ENST00000321264.4	+	8	1221	c.1012G>A	c.(1012-1014)Gtc>Atc	p.V338I	D2HGDH_ENST00000403782.1_Missense_Mutation_p.V204I|D2HGDH_ENST00000486953.1_Intron	NM_152783.3	NP_689996.4	Q8N465	D2HDH_HUMAN	D-2-hydroxyglutarate dehydrogenase	338			V -> I (in dbSNP:rs1106639).		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)		TCCGTTTTACGTCCTCATCGA	0.607													G|||	1120	0.223642	0.3003	0.183	5008	,	,		19404	0.122		0.2604	False		,,,				2504	0.2157				p.V338I		Atlas-SNP	.											D2HGDH,caecum,carcinoma,0,1	D2HGDH	39	1	0			c.G1012A						scavenged	.	G	ILE/VAL	1238,3168	426.6+/-341.2	171,896,1136	74.0	69.0	71.0		1012	3.2	0.1	2	dbSNP_86	71	2282,6310	385.3+/-341.4	321,1640,2335	yes	missense	D2HGDH	NM_152783.3	29	492,2536,3471	AA,AG,GG		26.5596,28.098,27.0811	benign	338/522	242690675	3520,9478	2203	4296	6499	SO:0001583	missense	728294	exon8			TTTTACGTCCTCA	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.1012G>A	2.37:g.242690675G>A	ENSP00000315351:p.Val338Ile	Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	183	96	0.52459	NM_152783	B4E3L6|E7ENP2|Q6IQ24|Q8N5Q8	Missense_Mutation	SNP	ENST00000321264.4	37	CCDS33426.1	462|462	0.21153846153846154|0.21153846153846154	123|123	0.25|0.25	69|69	0.19060773480662985|0.19060773480662985	73|73	0.12762237762237763|0.12762237762237763	197|197	0.2598944591029024|0.2598944591029024	G|G	10.56|10.56	1.384144|1.384144	0.25031|0.25031	0.28098|0.28098	0.265596|0.265596	ENSG00000180902|ENSG00000180902	ENST00000432449|ENST00000321264;ENST00000403782;ENST00000454048	.|D;D;T	.|0.83837	.|-1.77;-1.77;-1.44	5.06|5.06	3.24|3.24	0.37175|0.37175	.|FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	.|0.134831	.|0.50627	.|D	.|0.000114	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.33137|0.33137	0.985|0.985	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.24483	.|0.104	.|B	.|0.27380	.|0.079	T|T	0.04467|0.04467	-1.0949|-1.0949	4|9	.|0.23302	.|T	.|0.38	.|.	6.8186|6.8186	0.23845|0.23845	0.1531:0.1456:0.7014:0.0|0.1531:0.1456:0.7014:0.0	rs1106639|rs1106639	.|338	.|Q8N465	.|D2HDH_HUMAN	H|I	91|338;204;39	.|ENSP00000315351:V338I;ENSP00000384723:V204I;ENSP00000404596:V39I	.|ENSP00000315351:V338I	R|V	+|+	2|1	0|0	D2HGDH|D2HGDH	242339348|242339348	0.941000|0.941000	0.31946|0.31946	0.070000|0.070000	0.20053|0.20053	0.539000|0.539000	0.34962|0.34962	1.731000|1.731000	0.38135|0.38135	0.524000|0.524000	0.28502|0.28502	0.561000|0.561000	0.74099|0.74099	CGT|GTC	G|0.742;A|0.258	0.258	strong		0.607	D2HGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322794.2	NM_152783	
OBSCN	84033	hgsc.bcm.edu	37	1	228525008	228525008	+	Missense_Mutation	SNP	G	G	A	rs3795809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228525008G>A	ENST00000422127.1	+	66	16768	c.16724G>A	c.(16723-16725)cGc>cAc	p.R5575H	OBSCN_ENST00000366707.4_Missense_Mutation_p.R3209H|OBSCN_ENST00000366709.4_Missense_Mutation_p.R2694H|OBSCN_ENST00000284548.11_Missense_Mutation_p.R5575H|OBSCN_ENST00000570156.2_Missense_Mutation_p.R6532H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5575			R -> H (in dbSNP:rs3795809).		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)				GCATCCCCCCGCCATGGCCGA	0.647													G|||	384	0.0766773	0.0189	0.1744	5008	,	,		18983	0.0556		0.1252	False		,,,				2504	0.0573				p.R6532H		Atlas-SNP	.											OBSCN_ENST00000570156,caecum,carcinoma,0,3	OBSCN	2142	3	0			c.G19595A						PASS	.	G	HIS/ARG,HIS/ARG	146,3960		1,144,1908	24.0	32.0	29.0		16724,16724	4.4	0.9	1	dbSNP_107	29	1133,7223		70,993,3115	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	71,1137,5023	AA,AG,GG		13.5591,3.5558,10.2632	possibly-damaging,possibly-damaging	5575/7969,5575/6621	228525008	1279,11183	2053	4178	6231	SO:0001583	missense	84033	exon77			CCCCCCGCCATGG	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.16724G>A	1.37:g.228525008G>A	ENSP00000409493:p.Arg5575His	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	234	115	0.491453	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	204	0.09340659340659341	8	0.016260162601626018	65	0.17955801104972377	32	0.055944055944055944	99	0.13060686015831136	G	17.96	3.516358	0.64634	0.035558	0.135591	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.35421	1.31;1.31;1.31;1.31	4.37	4.37	0.52481	.	0.164006	0.40554	N	0.001072	T	0.00073	0.0002	L	0.44542	1.39	0.26854	P	0.9681028	B;P	0.36249	0.123;0.545	B;B	0.23852	0.032;0.049	T	0.12372	-1.0550	9	0.41790	T	0.15	.	17.4671	0.87635	0.0:0.0:1.0:0.0	rs3795809;rs59686075;rs3795809	5575;5575	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	5575;5575;3209;2694	ENSP00000284548:R5575H;ENSP00000409493:R5575H;ENSP00000355668:R3209H;ENSP00000355670:R2694H	ENSP00000284548:R5575H	R	+	2	0	OBSCN	226591631	1.000000	0.71417	0.858000	0.33744	0.006000	0.05464	6.878000	0.75567	2.437000	0.82529	0.655000	0.94253	CGC	G|0.913;A|0.087	0.087	strong		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
GRM7	2917	hgsc.bcm.edu	37	3	6903297	6903297	+	Silent	SNP	C	C	T	rs3749380	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:6903297C>T	ENST00000357716.4	+	1	496	c.222C>T	c.(220-222)aaC>aaT	p.N74N	GRM7_ENST00000486284.1_Silent_p.N74N|GRM7_ENST00000403881.1_Silent_p.N74N|GRM7_ENST00000402647.2_Silent_p.N74N|GRM7_ENST00000389336.4_Silent_p.N74N	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	74					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						AGAGGGAAAACGGGATCCACA	0.642													C|||	2088	0.416933	0.3593	0.4496	5008	,	,		14695	0.3214		0.4066	False		,,,				2504	0.5808				p.N74N		Atlas-SNP	.											GRM7,caecum,carcinoma,0,1	GRM7	223	1	0			c.C222T	GRCh37	CM085114	GRM7	M	rs3749380	PASS	.	C	,	1431,2975	431.2+/-342.8	223,985,995	30.0	28.0	29.0	http://www.ncbi.nlm.nih.gov/pubmed?term	222,222	3.6	1.0	3	dbSNP_107	29	3236,5364	451.8+/-362.8	641,1954,1705	yes	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	864,2939,2700	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	37.6279,32.4784,35.8834	,	74/916,74/923	6903297	4667,8339	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon1			GGAAAACGGGATC	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.222C>T	3.37:g.6903297C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	76	0.974359	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			C|0.630;T|0.370	0.370	strong		0.642	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
EPHB3	2049	hgsc.bcm.edu	37	3	184289152	184289152	+	Silent	SNP	A	A	G	rs13069661	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:184289152A>G	ENST00000330394.2	+	2	617	c.165A>G	c.(163-165)acA>acG	p.T55T	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	55	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell migration (GO:0016477)|central nervous system projection neuron axonogenesis (GO:0021952)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|digestive tract morphogenesis (GO:0048546)|ephrin receptor signaling pathway (GO:0048013)|palate development (GO:0060021)|positive regulation of synapse assembly (GO:0051965)|protein autophosphorylation (GO:0046777)|regulation of axonogenesis (GO:0050770)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell-cell adhesion (GO:0022407)|regulation of Rac GTPase activity (GO:0032314)|retinal ganglion cell axon guidance (GO:0031290)|substrate adhesion-dependent cell spreading (GO:0034446)|thymus development (GO:0048538)|urogenital system development (GO:0001655)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|ephrin receptor activity (GO:0005003)			breast(5)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(22)|ovary(5)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	51	all_cancers(143;1.89e-10)|Ovarian(172;0.0339)		Epithelial(37;1.27e-34)|OV - Ovarian serous cystadenocarcinoma(80;3.8e-22)			TGGCGTGGACATCTCATCCAG	0.527													A|||	1059	0.211462	0.1415	0.111	5008	,	,		19852	0.3264		0.2217	False		,,,				2504	0.2485				p.T55T		Atlas-SNP	.											EPHB3,NS,adenoma,0,1	EPHB3	114	1	0			c.A165G						PASS	.	A		690,3716	289.2+/-280.3	57,576,1570	181.0	169.0	173.0		165	-0.7	1.0	3	dbSNP_121	173	1752,6848	318.0+/-313.5	152,1448,2700	no	coding-synonymous	EPHB3	NM_004443.3		209,2024,4270	GG,GA,AA		20.3721,15.6605,18.7759		55/999	184289152	2442,10564	2203	4300	6503	SO:0001819	synonymous_variant	2049	exon2			GTGGACATCTCAT	X75208	CCDS3268.1	3q27.1	2013-09-19	2004-10-28		ENSG00000182580	ENSG00000182580		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3394	protein-coding gene	gene with protein product		601839	"""EphB3"""	ETK2		8397371	Standard	NM_004443		Approved	Hek2, Tyro6	uc003foz.3	P54753	OTTHUMG00000156710	ENST00000330394.2:c.165A>G	3.37:g.184289152A>G		Somatic	281	0	0		WXS	Illumina HiSeq	Phase_I	336	165	0.491071	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			A|0.802;G|0.198	0.198	strong		0.527	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144931461	144931461	+	Intron	SNP	A	A	T	rs41315685	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144931461A>T	ENST00000369354.3	-	6	826				PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.L83Q|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.L83Q|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000479408.2_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						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)		CTTCTCCAGTAGCAGCTTTTG	0.498			T	PDGFRB	MPD																																p.L83Q		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.T248A						PASS	.	A	GLN/LEU,,,,	549,3857		0,549,1654	183.0	190.0	188.0		248,,,,	5.3	1.0	1	dbSNP_127	188	2105,6495		0,2105,2195	yes	missense,intron,intron,intron,intron	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	113,,,,	0,2654,3849	TT,TA,AA		24.4767,12.4603,20.406	,,,,	83/1133,,,,	144931461	2654,10352	2203	4300	6503	SO:0001627	intron_variant	9659	exon1			TCCAGTAGCAGCT	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.637-7640T>A	1.37:g.144931461A>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	209	39	0.186603	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	439	0.20100732600732601	50	0.1016260162601626	86	0.23756906077348067	109	0.19055944055944055	194	0.2559366754617414	A	22.1	4.250987	0.80135	0.124603	0.244767	ENSG00000178104	ENST00000369353;ENST00000313431;ENST00000529945	T;T	0.19250	2.16;2.17	5.29	5.29	0.74685	.	.	.	.	.	T	0.32194	0.0821	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.10753	-1.0616	9	0.87932	D	0	.	13.1705	0.59595	1.0:0.0:0.0:0.0	rs41315685	83	Q5VU43-2	.	Q	83	ENSP00000316434:L83Q;ENSP00000433392:L83Q	ENSP00000316434:L83Q	L	-	2	0	PDE4DIP	143642818	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.339000	0.96797	1.993000	0.58246	0.374000	0.22700	CTA	A|0.382;T|0.618	0.618	strong		0.498	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
ZNF713	349075	hgsc.bcm.edu	37	7	56007498	56007498	+	Silent	SNP	A	A	G	rs112798657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:56007498A>G	ENST00000429591.2	+	4	1130	c.1092A>G	c.(1090-1092)aaA>aaG	p.K364K	MRPS17_ENST00000426595.1_Intron	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	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(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TCTGTGGCAAAGCCTTCAGTC	0.423													A|||	6	0.00119808	0.0	0.0029	5008	,	,		18360	0.0		0.002	False		,,,				2504	0.002				p.K364K		Atlas-SNP	.											.	ZNF713	47	.	0			c.A1092G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	65.0	66.0	66.0		1092	0.8	1.0	7	dbSNP_132	66	20,8580	14.0+/-48.4	0,20,4280	no	coding-synonymous	ZNF713	NM_182633.1		0,22,6481	GG,GA,AA		0.2326,0.0454,0.1692		364/431	56007498	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	349075	exon4			TGGCAAAGCCTTC	AK097282	CCDS34639.1	7p11.2	2013-01-08			ENSG00000178665	ENSG00000178665		"""Zinc fingers, C2H2-type"", ""-"""	22043	protein-coding gene	gene with protein product							Standard	NM_182633		Approved	FLJ39963	uc003trc.1	Q8N859	OTTHUMG00000156175	ENST00000429591.2:c.1092A>G	7.37:g.56007498A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	72	41	0.569444	NM_182633		Silent	SNP	ENST00000429591.2	37	CCDS34639.1																																																																																			A|0.998;G|0.002	0.002	strong		0.423	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633	
CEP170	9859	hgsc.bcm.edu	37	1	243329211	243329211	+	Missense_Mutation	SNP	G	G	T	rs2728430		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:243329211G>T	ENST00000366542.1	-	13	2102	c.2051C>A	c.(2050-2052)aCa>aAa	p.T684K	CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366544.1_Missense_Mutation_p.T586K|RP11-261C10.4_ENST00000422938.1_RNA|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.T586K	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	684						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GTATACCTGTGTAGGTGTTTC	0.408																																					p.T684K		Atlas-SNP	.											CEP170,NS,carcinoma,-1,1	CEP170	153	1	0			c.C2051A						scavenged	.						160.0	135.0	143.0					1																	243329211		1845	4100	5945	SO:0001583	missense	9859	exon13			ACCTGTGTAGGTG	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2051C>A	1.37:g.243329211G>T	ENSP00000355500:p.Thr684Lys	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	247	34	0.137652	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.048|4.048	0.006608|0.006608	0.07866|0.07866	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543	.|T;T;T	.|0.43294	.|1.0;0.95;0.96	5.25|5.25	5.25|5.25	0.73442|0.73442	.|.	.|0.490310	.|0.21930	.|N	.|0.067032	T|T	0.34077|0.34077	0.0885|0.0885	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|B;B;B;B	.|0.30361	.|0.089;0.039;0.277;0.03	.|B;B;B;B	.|0.26969	.|0.075;0.05;0.049;0.045	T|T	0.12553|0.12553	-1.0543|-1.0543	5|10	.|0.11182	.|T	.|0.66	-0.0033|-0.0033	17.8235|17.8235	0.88657|0.88657	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs2728430|rs2728430	.|647;586;586;684	.|B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.|.;.;.;CE170_HUMAN	N|K	648|684;586;586	.|ENSP00000355500:T684K;ENSP00000355502:T586K;ENSP00000355501:T586K	.|ENSP00000355500:T684K	H|T	-|-	1|2	0|0	CEP170|CEP170	241395834|241395834	0.984000|0.984000	0.35163|0.35163	0.007000|0.007000	0.13788|0.13788	0.882000|0.882000	0.50991|0.50991	3.771000|3.771000	0.55318|0.55318	2.445000|2.445000	0.82738|0.82738	0.484000|0.484000	0.47621|0.47621	CAC|ACA	.	.	weak		0.408	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
BCAM	4059	hgsc.bcm.edu	37	19	45316588	45316588	+	Missense_Mutation	SNP	G	G	A	rs28399654	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45316588G>A	ENST00000270233.6	+	5	608	c.586G>A	c.(586-588)Gta>Ata	p.V196I	BCAM_ENST00000589651.1_Missense_Mutation_p.V196I	NM_001013257.2|NM_005581.4	NP_001013275.1|NP_005572.2	P50895	BCAM_HUMAN	basal cell adhesion molecule (Lutheran blood group)	196	Ig-like V-type 2.		V -> I (in dbSNP:rs28399654). {ECO:0000269|Ref.2}.		cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	laminin binding (GO:0043236)|laminin receptor activity (GO:0005055)|transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22	Lung NSC(12;0.000789)|all_lung(12;0.00218)	Ovarian(192;0.0728)|all_neural(266;0.112)				GGAGGTGCCCGTAGAGATGAA	0.687													G|||	44	0.00878594	0.0015	0.0173	5008	,	,		15655	0.0		0.0288	False		,,,				2504	0.001				p.V196I		Atlas-SNP	.											.	BCAM	53	.	0			c.G586A						PASS	.	G	ILE/VAL,ILE/VAL	21,4385		0,21,2182	35.0	37.0	36.0		586,586	-4.5	0.7	19	dbSNP_125	36	290,8300		7,276,4012	yes	missense,missense	BCAM	NM_001013257.1,NM_005581.3	29,29	7,297,6194	AA,AG,GG		3.376,0.4766,2.393	benign,benign	196/589,196/629	45316588	311,12685	2203	4295	6498	SO:0001583	missense	4059	exon5			GTGCCCGTAGAGA	X83425	CCDS12644.1, CCDS42575.1	19q12-q13	2014-07-18	2006-02-23	2006-01-12		ENSG00000187244		"""CD molecules"", ""Blood group antigens"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6722	protein-coding gene	gene with protein product		612773	"""Lutheran blood group (Auberger b antigen included)"", ""basal cell adhesion molecule (Lu and Au blood groups)"""	LU			Standard	NM_005581		Approved	CD239	uc002ozu.4	P50895		ENST00000270233.6:c.586G>A	19.37:g.45316588G>A	ENSP00000270233:p.Val196Ile	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	67	42	0.626866	NM_001013257	A8MYF9|A9YWT5|A9YWT6|Q86VC7	Missense_Mutation	SNP	ENST00000270233.6	37	CCDS12644.1	31	0.014194139194139194	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	22	0.029023746701846966	.	1.290	-0.607948	0.03717	0.004766	0.03376	ENSG00000187244	ENST00000270233;ENST00000391955	T;T	0.58940	0.3;0.33	4.48	-4.49	0.03504	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.08980	0.0222	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.09530	-1.0670	9	0.23302	T	0.38	-7.0325	0.2649	0.00223	0.2385:0.2871:0.1925:0.2819	rs28399654	196	P50895	BCAM_HUMAN	I	196	ENSP00000270233:V196I;ENSP00000375817:V196I	ENSP00000270233:V196I	V	+	1	0	BCAM	50008428	0.001000	0.12720	0.739000	0.30968	0.211000	0.24417	-0.426000	0.07008	-0.826000	0.04284	-0.379000	0.06801	GTA	G|0.983;A|0.017	0.017	strong		0.687	BCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453220.1	NM_005581	
ALMS1	7840	hgsc.bcm.edu	37	2	73746923	73746923	+	Silent	SNP	C	C	T	rs11884776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73746923C>T	ENST00000264448.6	+	11	9669	c.9558C>T	c.(9556-9558)acC>acT	p.T3186T	ALMS1_ENST00000409009.1_Silent_p.T3144T	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3186					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						AGATGAAGACCCCACTTTCTG	0.363													T|||	1286	0.256789	0.5741	0.2349	5008	,	,		17135	0.005		0.2137	False		,,,				2504	0.1472				p.T3186T		Atlas-SNP	.											.	ALMS1	384	.	0			c.C9558T						PASS	.			1737,1889		416,905,492	79.0	77.0	77.0		9558	-2.7	0.0	2	dbSNP_120	77	1840,6310		197,1446,2432	no	coding-synonymous	ALMS1	NM_015120.4		613,2351,2924	TT,TC,CC		22.5767,47.904,30.3753		3186/4168	73746923	3577,8199	1813	4075	5888	SO:0001819	synonymous_variant	7840	exon11			GAAGACCCCACTT	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.9558C>T	2.37:g.73746923C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	147	58	0.394558	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.742;T|0.258	0.258	strong		0.363	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
OR10G3	26533	hgsc.bcm.edu	37	14	22038525	22038525	+	Silent	SNP	G	G	T	rs11626693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:22038525G>T	ENST00000303532.1	-	1	350	c.351C>A	c.(349-351)acC>acA	p.T117T		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		AGGCCATTAGGGTGTAGAGGA	0.527													G|||	1822	0.363818	0.5371	0.2277	5008	,	,		21719	0.2966		0.3072	False		,,,				2504	0.3538				p.T117T		Atlas-SNP	.											.	OR10G3	40	.	0			c.C351A						PASS	.	G		2158,2248	583.6+/-385.9	549,1060,594	58.0	56.0	56.0		351	-3.3	0.1	14	dbSNP_120	56	2429,6171	401.1+/-347.0	347,1735,2218	no	coding-synonymous	OR10G3	NM_001005465.1		896,2795,2812	TT,TG,GG		28.2442,48.9787,35.2683		117/314	22038525	4587,8419	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			CATTAGGGTGTAG		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"""GPCR / Class A : Olfactory receptors"""	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.351C>A	14.37:g.22038525G>T		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			G|0.656;T|0.344	0.344	strong		0.527	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
CCDC85C	317762	hgsc.bcm.edu	37	14	99988570	99988570	+	Missense_Mutation	SNP	C	C	G	rs75827961	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:99988570C>G	ENST00000380243.4	-	3	941	c.875G>C	c.(874-876)gGc>gCc	p.G292A	CCDC85C_ENST00000555822.1_5'UTR|CCDC85C_ENST00000557769.1_5'UTR|CCNK_ENST00000555049.1_Intron	NM_001144995.1	NP_001138467.1	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C	292					cerebral cortex development (GO:0021987)	apical junction complex (GO:0043296)|tight junction (GO:0005923)				endometrium(1)|skin(1)	2						CTCTCCGGAGCCTGCCTGCTG	0.672													C|||	434	0.0866613	0.2723	0.036	5008	,	,		17507	0.004		0.0149	False		,,,				2504	0.0307				p.G292A		Atlas-SNP	.											.	CCDC85C	3	.	0			c.G875C						PASS	.	C	ALA/GLY	297,1087		38,221,433	52.0	54.0	53.0		875	3.9	0.6	14	dbSNP_131	53	62,3120		1,60,1530	yes	missense	CCDC85C	NM_001144995.1	60	39,281,1963	GG,GC,CC		1.9485,21.4595,7.8625	benign	292/420	99988570	359,4207	692	1591	2283	SO:0001583	missense	317762	exon3			CCGGAGCCTGCCT		CCDS45161.1	14q32.31	2009-02-18				ENSG00000205476			35459	protein-coding gene	gene with protein product							Standard	NM_001144995		Approved		uc010avr.3	A6NKD9		ENST00000380243.4:c.875G>C	14.37:g.99988570C>G	ENSP00000369592:p.Gly292Ala	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	27	14	0.518519	NM_001144995		Missense_Mutation	SNP	ENST00000380243.4	37	CCDS45161.1	150|150	0.06868131868131869|0.06868131868131869	120|120	0.24390243902439024|0.24390243902439024	16|16	0.04419889502762431|0.04419889502762431	3|3	0.005244755244755245|0.005244755244755245	11|11	0.014511873350923483|0.014511873350923483	C|C	14.01|14.01	2.408809|2.408809	0.42715|0.42715	0.214595|0.214595	0.019485|0.019485	ENSG00000205476|ENSG00000205476	ENST00000557576|ENST00000380243;ENST00000554996;ENST00000556348	.|.	.|.	.|.	4.83|4.83	3.87|3.87	0.44632|0.44632	.|.	.|0.218004	.|0.34435	.|U	.|0.003978	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.45005|0.45005	P|P	0.0019780000000000353|0.0019780000000000353	.|B	.|0.30406	.|0.278	.|B	.|0.30179	.|0.112	T|T	0.26643|0.26643	-1.0097|-1.0097	4|8	.|0.19147	.|T	.|0.46	-19.1362|-19.1362	7.8087|7.8087	0.29217|0.29217	0.162:0.5454:0.2926:0.0|0.162:0.5454:0.2926:0.0	.|.	.|292	.|A6NKD9	.|CC85C_HUMAN	P|A	28|292;63;44	.|.	.|ENSP00000369592:G292A	A|G	-|-	1|2	0|0	CCDC85C|CCDC85C	99058323|99058323	0.441000|0.441000	0.25626|0.25626	0.560000|0.560000	0.28344|0.28344	0.439000|0.439000	0.31926|0.31926	1.727000|1.727000	0.38095|0.38095	2.212000|2.212000	0.71576|0.71576	0.655000|0.655000	0.94253|0.94253	GCT|GGC	C|0.930;G|0.070	0.070	strong		0.672	CCDC85C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413802.1	NM_001144995	
PCNT	5116	hgsc.bcm.edu	37	21	47783655	47783655	+	Silent	SNP	C	C	G	rs61407822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47783655C>G	ENST00000359568.5	+	14	2522	c.2415C>G	c.(2413-2415)gcC>gcG	p.A805A	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	805					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)					AACAGGCAGCCCAGATCCTGG	0.542													C|||	775	0.154752	0.4682	0.062	5008	,	,		18913	0.004		0.0249	False		,,,				2504	0.0859				p.A805A		Atlas-SNP	.											.	PCNT	283	.	0			c.C2415G						PASS	.	C		1762,2644	520.9+/-370.4	356,1050,797	65.0	67.0	66.0		2415	-3.4	0.1	21	dbSNP_129	66	117,8483	59.8+/-121.6	0,117,4183	no	coding-synonymous	PCNT	NM_006031.5		356,1167,4980	GG,GC,CC		1.3605,39.9909,14.4472		805/3337	47783655	1879,11127	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon14			GGCAGCCCAGATC	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.2415C>G	21.37:g.47783655C>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	111	55	0.495495	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.868;G|0.132	0.132	strong		0.542	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
ZNF443	10224	hgsc.bcm.edu	37	19	12541544	12541544	+	Missense_Mutation	SNP	A	A	C	rs74181783|rs35055629|rs386806904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12541544A>C	ENST00000301547.5	-	4	1639	c.1442T>G	c.(1441-1443)cTt>cGt	p.L481R	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	481					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|pancreas(1)|prostate(1)	28						GGCTTTCCCAAGTTTGCATTT	0.403													.|||	1959	0.391174	0.4788	0.3084	5008	,	,		20939	0.3462		0.2793	False		,,,				2504	0.4928				p.L481R		Atlas-SNP	.											.	ZNF443	63	.	0			c.T1442G						PASS	.	C	ARG/LEU	1682,2720		405,872,924	64.0	69.0	68.0		1442	1.3	0.0	19	dbSNP_126	68	1891,6709		354,1183,2763	no	missense	ZNF443	NM_005815.4	102	759,2055,3687	CC,CA,AA		21.9884,38.2099,27.4804	benign	481/672	12541544	3573,9429	2201	4300	6501	SO:0001583	missense	10224	exon4			TTCCCAAGTTTGC	AB011414	CCDS32918.1	19p13.13	2013-01-08			ENSG00000180855	ENSG00000180855		"""Zinc fingers, C2H2-type"", ""-"""	20878	protein-coding gene	gene with protein product		606697				9731181	Standard	NM_005815		Approved	ZK1	uc002mtu.3	Q9Y2A4	OTTHUMG00000156404	ENST00000301547.5:c.1442T>G	19.37:g.12541544A>C	ENSP00000301547:p.Leu481Arg	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	651	0.2980769230769231	197	0.40040650406504064	97	0.26795580110497236	182	0.3181818181818182	175	0.23087071240105542	a	7.438	0.640038	0.14386	0.382099	0.219884	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.20881	2.04	1.26	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.25789	0.76	0.58432	P	6.999999999979245E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.44528	-0.9322	8	0.66056	D	0.02	.	7.9492	0.30003	0.2481:0.7519:0.0:0.0	rs35055629;rs59512099;rs62114863	481	Q9Y2A4	ZN443_HUMAN	R	481	ENSP00000301547:L481R	ENSP00000301547:L481R	L	-	2	0	ZNF443	12402544	0.947000	0.32204	0.019000	0.16419	0.009000	0.06853	1.653000	0.37323	0.121000	0.18284	-0.363000	0.07495	CTT	A|0.687;C|0.313	0.313	strong		0.403	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815	
PKD1L2	114780	hgsc.bcm.edu	37	16	81211496	81211496	+	RNA	SNP	C	C	A	rs9935113	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81211496C>A	ENST00000527937.1	-	0	319				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000337114.4_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGAACGGTGCCCTCCTCTGGG	0.597													C|||	1042	0.208067	0.2791	0.1744	5008	,	,		17905	0.1052		0.171	False		,,,				2504	0.2802				p.G785C		Atlas-SNP	.											.	PKD1L2	361	.	0			c.G2353T						PASS	.	C	CYS/GLY,CYS/GLY	1011,3087		126,759,1164	79.0	81.0	80.0		2353,2353	4.9	0.6	16	dbSNP_119	80	1412,6976		122,1168,2904	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	159,159	248,1927,4068	AA,AC,CC		16.8336,24.6706,19.4057	probably-damaging,probably-damaging	785/992,785/2460	81211496	2423,10063	2049	4194	6243			114780	exon14			CGGTGCCCTCCTC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81211496C>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	54	22	0.407407	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		368|368	0.1684981684981685|0.1684981684981685	132|132	0.2682926829268293|0.2682926829268293	59|59	0.16298342541436464|0.16298342541436464	53|53	0.09265734265734266|0.09265734265734266	124|124	0.16358839050131926|0.16358839050131926	C|C	14.11|14.11	2.437976|2.437976	0.43326|0.43326	0.246706|0.246706	0.168336|0.168336	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114|ENST00000526632	D;D|.	0.85629|.	-2.01;-2.01|.	4.89|4.89	4.89|4.89	0.63831|0.63831	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);|.	0.067594|0.067594	0.64402|0.64402	D|D	0.000012|0.000012	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.33815|0.33815	P|P	0.37165400000000004|0.37165400000000004	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.997;0.998|.	T|T	0.01290|0.01290	-1.1394|-1.1394	8|4	0.87932|.	D|.	0|.	-13.2573|-13.2573	15.0685|15.0685	0.72014|0.72014	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs9935113;rs52837465;rs57029035;rs9935113|rs9935113;rs52837465;rs57029035;rs9935113	785;785|.	Q7Z442-3;Q7Z442|.	.;PK1L2_HUMAN|.	C|V	100;785|312	ENSP00000436309:G100C;ENSP00000337397:G785C|.	ENSP00000337397:G785C|.	G|G	-|-	1|2	0|0	PKD1L2|PKD1L2	79768997|79768997	1.000000|1.000000	0.71417|0.71417	0.603000|0.603000	0.28903|0.28903	0.040000|0.040000	0.13550|0.13550	3.894000|3.894000	0.56250|0.56250	2.289000|2.289000	0.77006|0.77006	0.549000|0.549000	0.68633|0.68633	GGC|GGG	C|0.823;A|0.177	0.177	strong		0.597	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
ADAMTS5	11096	hgsc.bcm.edu	37	21	28315841	28315841	+	Silent	SNP	G	G	A	rs61088614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:28315841G>A	ENST00000284987.5	-	3	1384	c.1263C>T	c.(1261-1263)gaC>gaT	p.D421D		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	421	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						ATTTGGAATCGTCATGGGAGA	0.418													G|||	251	0.0501198	0.1755	0.0144	5008	,	,		20735	0.0		0.006	False		,,,				2504	0.0031				p.D421D	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.C1263T						PASS	.	G		601,3805	262.8+/-265.1	44,513,1646	75.0	70.0	72.0		1263	-10.1	0.1	21	dbSNP_129	72	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	ADAMTS5	NM_007038.3		44,541,5918	AA,AG,GG		0.3256,13.6405,4.8362		421/931	28315841	629,12377	2203	4300	6503	SO:0001819	synonymous_variant	11096	exon3			GGAATCGTCATGG	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1263C>T	21.37:g.28315841G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	114	55	0.482456	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																			G|0.957;A|0.043	0.043	strong		0.418	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
OR4K15	81127	hgsc.bcm.edu	37	14	20444193	20444193	+	Silent	SNP	A	A	C	rs2318556	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20444193A>C	ENST00000305051.5	+	1	591	c.516A>C	c.(514-516)tcA>tcC	p.S172S		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	172						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TCCTCATTTCATGGTTTGTGG	0.443													C|||	1885	0.376398	0.7481	0.2017	5008	,	,		22524	0.1498		0.2435	False		,,,				2504	0.3681				p.S172S		Atlas-SNP	.											.	OR4K15	82	.	0			c.A516C						PASS	.	C		3043,1363		1041,961,201	148.0	147.0	147.0		516	-3.8	0.0	14	dbSNP_100	147	2447,6151		337,1773,2189	no	coding-synonymous	OR4K15	NM_001005486.1		1378,2734,2390	CC,CA,AA		28.4601,30.9351,42.2178		172/349	20444193	5490,7514	2203	4299	6502	SO:0001819	synonymous_variant	81127	exon1			CATTTCATGGTTT		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.516A>C	14.37:g.20444193A>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	211	103	0.488152	NM_001005486	B9EIL3|Q6IEZ4	Silent	SNP	ENST00000305051.5	37	CCDS32026.1																																																																																			A|0.619;C|0.380;G|0.001	0.380	strong		0.443	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
RBMX	27316	hgsc.bcm.edu	37	X	135956411	135956411	+	Missense_Mutation	SNP	C	C	A	rs35085326		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135956411C>A	ENST00000320676.7	-	9	1220	c.1066G>T	c.(1066-1068)Ggg>Tgg	p.G356W	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Missense_Mutation_p.G228W|RBMX_ENST00000570135.1_Missense_Mutation_p.G221W|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	356	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GGAGGGTACCCCCTTTCCATA	0.562																																					p.G356W		Atlas-SNP	.											.	RBMX	149	.	0			c.G1066T						PASS	.						81.0	78.0	79.0					X																	135956411		2203	4299	6502	SO:0001583	missense	27316	exon9			GGTACCCCCTTTC		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1066G>T	X.37:g.135956411C>A	ENSP00000359645:p.Gly356Trp	Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	398	168	0.422111	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	18	0.0108499095840868	0	0.0	5	0.013812154696132596	0	0.0	14	0.018469656992084433	.	13.49	2.252860	0.39797	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.78364	-1.17	5.66	5.66	0.87406	.	0.000000	0.85682	U	0.000000	T	0.79335	0.4428	M	0.63843	1.955	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.84437	0.0580	10	0.66056	D	0.02	.	18.7648	0.91868	0.0:1.0:0.0:0.0	rs35085326	356	P38159	HNRPG_HUMAN	W	356;343	ENSP00000359645:G356W	ENSP00000359645:G356W	G	-	1	0	RBMX	135784077	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.845000	0.62853	2.377000	0.81083	0.596000	0.82720	GGG	C|0.989;A|0.011	0.011	strong		0.562	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
POLR2J3	548644	hgsc.bcm.edu	37	7	102212939	102212939	+	Missense_Mutation	SNP	G	G	C	rs139049967	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:102212939G>C	ENST00000511313.1	-	1	91	c.30C>G	c.(28-30)ttC>ttG	p.F10L	POLR2J3_ENST00000504157.1_5'UTR|POLR2J3_ENST00000513438.1_Missense_Mutation_p.F10L|RP11-514P8.7_ENST00000514917.2_Intron			Q9H1A7	RPB1C_HUMAN	polymerase (RNA) II (DNA directed) polypeptide J3	10					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)										CGAAGAGCAAGAACGACTCGA	0.662																																					p.F10L		Atlas-SNP	.											.	POLR2J3	2	.	0			c.C30G						PASS	.	G	LEU/PHE	124,4270		0,124,2073	52.0	53.0	53.0		30	1.0	0.7	7	dbSNP_134	53	451,8069		0,451,3809	no	missense	POLR2J3	NM_001097615.2	22	0,575,5882	CC,CG,GG		5.2934,2.822,4.4525	possibly-damaging	10/116	102212939	575,12339	2197	4260	6457	SO:0001583	missense	548644	exon1			GAGCAAGAACGAC		CCDS47673.1	7q22.1	2013-01-21			ENSG00000168255	ENSG00000168255		"""RNA polymerase subunits"""	33853	protein-coding gene	gene with protein product						15586814	Standard	NM_001097615		Approved		uc010lid.1	Q9H1A7	OTTHUMG00000150384	ENST00000511313.1:c.30C>G	7.37:g.102212939G>C	ENSP00000422109:p.Phe10Leu	Somatic	679	0	0		WXS	Illumina HiSeq	Phase_I	1015	180	0.17734	NM_001097615	A6NKA1	Missense_Mutation	SNP	ENST00000511313.1	37		.	.	.	.	.	.	.	.	.	.	g	16.96	3.264917	0.59431	0.02822	0.052934	ENSG00000168255	ENST00000513506;ENST00000511313;ENST00000513438	D;D;D	0.91945	-2.94;-2.94;-2.94	0.976	0.976	0.19727	DNA-directed RNA polymerase, RBP11-like (1);	0.000000	0.85682	D	0.000000	T	0.69984	0.3172	M	0.79343	2.45	0.80722	D	1	D	0.71674	0.998	P	0.50659	0.647	T	0.78563	-0.2156	10	0.48119	T	0.1	.	3.3598	0.07182	0.3078:0.0:0.6922:0.0	.	10	Q9GZM3	RPB1B_HUMAN	L	10	ENSP00000421085:F10L;ENSP00000422109:F10L;ENSP00000421950:F10L	ENSP00000368645:F10L	F	-	3	2	POLR2J3	102000044	1.000000	0.71417	0.708000	0.30435	0.103000	0.19146	0.264000	0.18497	0.453000	0.26858	0.184000	0.17185	TTC	G|0.980;C|0.020	0.020	strong		0.662	POLR2J3-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000358591.1	NM_001097615	
TARBP1	6894	hgsc.bcm.edu	37	1	234569192	234569192	+	Silent	SNP	T	T	C	rs3754311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:234569192T>C	ENST00000040877.1	-	14	2357	c.2358A>G	c.(2356-2358)gcA>gcG	p.A786A		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	786					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)			GCTGAATGGATGCATTTTTCA	0.383													T|||	894	0.178514	0.1959	0.2003	5008	,	,		21597	0.2163		0.1064	False		,,,				2504	0.1748				p.A786A		Atlas-SNP	.											.	TARBP1	111	.	0			c.A2358G						PASS	.	T		757,3649	310.0+/-291.3	71,615,1517	132.0	126.0	128.0		2358	-5.2	0.6	1	dbSNP_107	128	917,7683	204.2+/-247.0	40,837,3423	no	coding-synonymous	TARBP1	NM_005646.3		111,1452,4940	CC,CT,TT		10.6628,17.1811,12.871		786/1622	234569192	1674,11332	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon14			AATGGATGCATTT		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.2358A>G	1.37:g.234569192T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			T|0.848;C|0.152	0.152	strong		0.383	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289714	98289714	+	Missense_Mutation	SNP	G	G	C	rs2635164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:98289714G>C	ENST00000322128.3	-	1	462	c.359C>G	c.(358-360)aCt>aGt	p.T120S		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	120			T -> S (in dbSNP:rs2635164).		cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					CACGAAGACAGTGTCTGCGGC	0.721													G|||	1178	0.235224	0.5129	0.1787	5008	,	,		12121	0.0933		0.1372	False		,,,				2504	0.1472				p.T120S		Atlas-SNP	.											.	TSPYL5	48	.	0			c.C359G						PASS	.	G	SER/THR	1792,2522		386,1020,751	10.0	12.0	11.0		359	3.3	0.6	8	dbSNP_100	11	1062,7310		85,892,3209	yes	missense	TSPYL5	NM_033512.2	58	471,1912,3960	CC,CG,GG		12.6851,41.5392,22.4972	possibly-damaging	120/418	98289714	2854,9832	2157	4186	6343	SO:0001583	missense	85453	exon1			AAGACAGTGTCTG	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.359C>G	8.37:g.98289714G>C	ENSP00000322802:p.Thr120Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	445	0.20375457875457875	228	0.4634146341463415	66	0.18232044198895028	45	0.07867132867132867	106	0.13984168865435356	G	5.440	0.266334	0.10294	0.415392	0.126851	ENSG00000180543	ENST00000322128	T	0.12774	2.65	4.16	3.27	0.37495	.	0.252185	0.20796	N	0.085534	T	0.00012	0.0000	N	0.00926	-1.1	0.45194	P	0.001794999999999991	P	0.37061	0.58	B	0.35114	0.196	T	0.30650	-0.9971	9	0.02654	T	1	-2.746	8.3789	0.32459	0.1076:0.0:0.8924:0.0	rs2635164	120	Q86VY4	TSYL5_HUMAN	S	120	ENSP00000322802:T120S	ENSP00000322802:T120S	T	-	2	0	TSPYL5	98358890	0.973000	0.33851	0.646000	0.29493	0.871000	0.50021	1.939000	0.40213	1.298000	0.44778	0.650000	0.86243	ACT	G|0.810;C|0.190	0.190	strong		0.721	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
RBMXL2	27288	hgsc.bcm.edu	37	11	7110548	7110548	+	Missense_Mutation	SNP	C	C	T	rs11041170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7110548C>T	ENST00000306904.5	+	1	384	c.197C>T	c.(196-198)gCc>gTc	p.A66V		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	66	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.		A -> V (in dbSNP:rs11041170). {ECO:0000269|PubMed:10958650}.			nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAGGCCGCCGCCAGAGACATG	0.647													C|||	759	0.151558	0.2337	0.1628	5008	,	,		9247	0.0139		0.2316	False		,,,				2504	0.092				p.A66V		Atlas-SNP	.											.	RBMXL2	47	.	0			c.C197T						PASS	.	C	VAL/ALA	998,3396		105,788,1304	22.0	21.0	21.0		197	-0.5	1.0	11	dbSNP_120	21	1993,6599		240,1513,2543	no	missense	RBMXL2	NM_014469.4	64	345,2301,3847	TT,TC,CC		23.196,22.7128,23.0325	benign	66/393	7110548	2991,9995	2197	4296	6493	SO:0001583	missense	27288	exon1			CCGCCGCCAGAGA	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"""RNA binding motif (RRM) containing"""	17886	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G T"""	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.197C>T	11.37:g.7110548C>T	ENSP00000304139:p.Ala66Val	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	25	0.378788	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	37	CCDS7777.1	364	0.16666666666666666	119	0.241869918699187	62	0.1712707182320442	11	0.019230769230769232	172	0.22691292875989447	C	10.62	1.401357	0.25291	0.227128	0.23196	ENSG00000170748	ENST00000306904	T	0.13778	2.56	2.51	-0.49	0.12049	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.068562	0.64402	N	0.000014	T	0.00012	0.0000	N	0.00707	-1.245	0.29091	P	0.882081	B	0.06786	0.001	B	0.13407	0.009	T	0.46076	-0.9217	9	0.36615	T	0.2	.	6.1131	0.20112	0.0:0.4557:0.0:0.5443	rs11041170	66	O75526	HNRGT_HUMAN	V	66	ENSP00000304139:A66V	ENSP00000304139:A66V	A	+	2	0	RBMXL2	7067124	0.996000	0.38824	0.978000	0.43139	0.984000	0.73092	1.429000	0.34903	-0.131000	0.11578	-0.463000	0.05309	GCC	C|0.795;T|0.205	0.205	strong		0.647	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469	
IRAK4	51135	hgsc.bcm.edu	37	12	44177511	44177511	+	Missense_Mutation	SNP	G	G	A	rs55944915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:44177511G>A	ENST00000448290.2	+	10	1243	c.1172G>A	c.(1171-1173)cGt>cAt	p.R391H	IRAK4_ENST00000431837.1_Missense_Mutation_p.R267H|IRAK4_ENST00000440781.2_Missense_Mutation_p.R267H|IRAK4_ENST00000551736.1_Missense_Mutation_p.R391H	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	391	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs55944915). {ECO:0000269|PubMed:17344846}.		cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		GATGAACACCGTGAACCTCAG	0.308													G|||	35	0.00698882	0.0008	0.0072	5008	,	,		17222	0.0		0.0159	False		,,,				2504	0.0133				p.R391H		Atlas-SNP	.											.	IRAK4	77	.	0			c.G1172A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	16,4390	23.3+/-48.9	0,16,2187	98.0	99.0	99.0		1172,800,800,800,1172	5.7	1.0	12	dbSNP_129	99	130,8470	65.6+/-127.9	2,126,4172	yes	missense,missense,missense,missense,missense	IRAK4	NM_001114182.2,NM_001145256.1,NM_001145257.1,NM_001145258.1,NM_016123.3	29,29,29,29,29	2,142,6359	AA,AG,GG		1.5116,0.3631,1.1226	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	391/461,267/337,267/337,267/337,391/461	44177511	146,12860	2203	4300	6503	SO:0001583	missense	51135	exon10			AACACCGTGAACC	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		ENST00000448290.2:c.1172G>A	12.37:g.44177511G>A	ENSP00000390651:p.Arg391His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	58	35	0.603448	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	37	CCDS8744.1	14	0.00641025641025641	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	23.9	4.466425	0.84425	0.003631	0.015116	ENSG00000198001	ENST00000440781;ENST00000431837;ENST00000448290;ENST00000551736	D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22	5.68	5.68	0.88126	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.113219	0.64402	D	0.000012	D	0.93344	0.7878	M	0.71296	2.17	0.58432	D	0.999993	D	0.76494	0.999	D	0.65684	0.937	D	0.92969	0.6396	10	0.87932	D	0	-14.5611	19.8002	0.96504	0.0:0.0:1.0:0.0	rs55944915	391	Q9NWZ3	IRAK4_HUMAN	H	267;267;391;391	ENSP00000408734:R267H;ENSP00000390327:R267H;ENSP00000390651:R391H;ENSP00000446490:R391H	ENSP00000390327:R267H	R	+	2	0	IRAK4	42463778	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.622000	0.67750	2.674000	0.91012	0.655000	0.94253	CGT	G|0.989;A|0.011	0.011	strong		0.308	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
CREB3L2	64764	hgsc.bcm.edu	37	7	137600690	137600690	+	Missense_Mutation	SNP	C	C	T	rs273957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:137600690C>T	ENST00000330387.6	-	3	739	c.388G>A	c.(388-390)Gtt>Att	p.V130I	CREB3L2_ENST00000456390.1_Missense_Mutation_p.V130I|CREB3L2_ENST00000452463.1_Missense_Mutation_p.V130I|CREB3L2_ENST00000458726.1_Missense_Mutation_p.V67I	NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	130			V -> I (in dbSNP:rs273957). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:12915480, ECO:0000269|PubMed:15489334}.		cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)		FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						TCGTCTGTAACTGGCTCTGTC	0.498			T	FUS	fibromyxoid sarcoma								T|||	4028	0.804313	0.9743	0.6888	5008	,	,		18642	0.9435		0.6262	False		,,,				2504	0.6963				p.V130I		Atlas-SNP	.		Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	CREB3L2	62	.	0			c.G388A						PASS	.	T	ILE/VAL	4026,380	192.6+/-218.0	1838,350,15	230.0	195.0	207.0		388	5.0	0.0	7	dbSNP_79	207	5274,3326	496.3+/-374.3	1619,2036,645	yes	missense	CREB3L2	NM_194071.2	29	3457,2386,660	TT,TC,CC		38.6744,8.6246,28.4945	benign	130/521	137600690	9300,3706	2203	4300	6503	SO:0001583	missense	64764	exon3			CTGTAACTGGCTC	AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"""basic leucine zipper proteins"""	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.388G>A	7.37:g.137600690C>T	ENSP00000329140:p.Val130Ile	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	210	107	0.509524	NM_001253775	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	37	CCDS34760.1	1715	0.7852564102564102	474	0.9634146341463414	231	0.638121546961326	530	0.9265734265734266	480	0.633245382585752	T	0.084	-1.178926	0.01633	0.913754	0.613256	ENSG00000182158	ENST00000330387;ENST00000417785;ENST00000456390;ENST00000452463;ENST00000458726;ENST00000420629	T;T;T;T;T	0.62941	0.42;-0.01;0.97;0.95;0.92	6.17	5.01	0.66863	.	0.560307	0.19154	N	0.121368	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.36212	-0.9757	9	0.28530	T	0.3	-12.9472	1.8782	0.03222	0.1233:0.1347:0.2569:0.4852	rs273957;rs1646552;rs17855863;rs56868645;rs273957	130;130;130	Q70SY1-3;Q70SY1-2;Q70SY1	.;.;CR3L2_HUMAN	I	130;130;130;130;67;123	ENSP00000329140:V130I;ENSP00000403550:V130I;ENSP00000410314:V130I;ENSP00000388917:V67I;ENSP00000402889:V123I	ENSP00000329140:V130I	V	-	1	0	CREB3L2	137251230	0.000000	0.05858	0.013000	0.15412	0.058000	0.15608	0.420000	0.21263	0.554000	0.29061	-0.254000	0.11334	GTT	C|0.243;T|0.757	0.757	strong		0.498	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071	
GOT2	2806	hgsc.bcm.edu	37	16	58743454	58743454	+	Missense_Mutation	SNP	A	A	C	rs30842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58743454A>C	ENST00000245206.5	-	9	1165	c.1037T>G	c.(1036-1038)gTc>gGc	p.V346G	GOT2_ENST00000434819.2_Missense_Mutation_p.V303G	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	346			V -> G (in dbSNP:rs30842). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:3207426, ECO:0000269|PubMed:4052435}.		2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	GTCAGCCATGACTTTCACTTC	0.502													C|||	3782	0.755192	0.8994	0.7824	5008	,	,		19314	0.6607		0.7097	False		,,,				2504	0.6851				p.V346G		Atlas-SNP	.											.	GOT2	42	.	0			c.T1037G						PASS	.	C	GLY/VAL	3785,611	265.6+/-266.7	1627,531,40	253.0	247.0	249.0		1037	5.3	1.0	16	dbSNP_76	249	5901,2699	433.0+/-357.3	2034,1833,433	yes	missense	GOT2	NM_002080.2	109	3661,2364,473	CC,CA,AA		31.3837,13.899,25.4694	benign	346/431	58743454	9686,3310	2198	4300	6498	SO:0001583	missense	2806	exon9			GCCATGACTTTCA		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.1037T>G	16.37:g.58743454A>C	ENSP00000245206:p.Val346Gly	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Missense_Mutation	SNP	ENST00000245206.5	37	CCDS10801.1	1611	0.7376373626373627	438	0.8902439024390244	277	0.7651933701657458	376	0.6573426573426573	520	0.6860158311345647	C	3.270	-0.149293	0.06585	0.86101	0.686163	ENSG00000125166	ENST00000245206;ENST00000434819	D;D	0.90261	-2.64;-2.64	5.31	5.31	0.75309	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.162273	0.53938	N	0.000059	T	0.00012	0.0000	N	0.00327	-1.64	0.33927	P	0.35837300000000005	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42649	-0.9439	8	.	.	.	5.2238	14.6551	0.68828	0.1464:0.8536:0.0:0.0	rs30842;rs17821579;rs56935811;rs30842	303;346	E7ERW2;P00505	.;AATM_HUMAN	G	346;303	ENSP00000245206:V346G;ENSP00000394100:V303G	.	V	-	2	0	GOT2	57300955	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.160000	0.50739	1.252000	0.44001	-0.127000	0.14921	GTC	A|0.252;C|0.748	0.748	strong		0.502	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
DAGLB	221955	hgsc.bcm.edu	37	7	6452461	6452461	+	Missense_Mutation	SNP	G	G	A	rs1133850	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6452461G>A	ENST00000297056.6	-	13	1719	c.1550C>T	c.(1549-1551)gCg>gTg	p.A517V	DAGLB_ENST00000436575.1_Missense_Mutation_p.A476V|DAGLB_ENST00000425398.2_Missense_Mutation_p.A388V|DAGLB_ENST00000428902.2_Silent_p.R376R	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	517					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		ATTGCAGTGCGCGACCACTCG	0.567													G|||	258	0.0515176	0.0318	0.0173	5008	,	,		19812	0.0863		0.0119	False		,,,				2504	0.1074				p.A517V		Atlas-SNP	.											.	DAGLB	74	.	0			c.C1550T						PASS	.	G	VAL/ALA,VAL/ALA	104,4294		1,102,2096	67.0	55.0	59.0		1163,1550	5.5	0.2	7	dbSNP_86	59	175,8415		0,175,4120	yes	missense,missense	DAGLB	NM_001142936.1,NM_139179.3	64,64	1,277,6216	AA,AG,GG		2.0373,2.3647,2.1481	benign,benign	388/544,517/673	6452461	279,12709	2199	4295	6494	SO:0001583	missense	221955	exon13			CAGTGCGCGACCA	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1550C>T	7.37:g.6452461G>A	ENSP00000297056:p.Ala517Val	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	93	49	0.526882	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Missense_Mutation	SNP	ENST00000297056.6	37	CCDS5350.1	86	0.039377289377289376	13	0.026422764227642278	9	0.024861878453038673	57	0.09965034965034965	7	0.009234828496042216	G	11.41	1.629348	0.28978	0.023647	0.020373	ENSG00000164535	ENST00000297056;ENST00000425398;ENST00000436575	T;T;T	0.47528	0.86;0.84;0.86	5.52	5.52	0.82312	.	0.060022	0.64402	D	0.000002	T	0.01387	0.0045	L	0.57536	1.79	0.80722	D	1	P;P;P;D	0.58620	0.875;0.847;0.722;0.983	B;B;B;B	0.40285	0.14;0.111;0.067;0.325	T	0.00443	-1.1736	10	0.36615	T	0.2	-16.632	13.0681	0.59045	0.0736:0.0:0.9264:0.0	rs1133850;rs3178524;rs3195931;rs17419026	388;331;517;214	B4DQU0;B4DQQ6;Q8NCG7;B3KRA0	.;.;DGLB_HUMAN;.	V	517;388;476	ENSP00000297056:A517V;ENSP00000391171:A388V;ENSP00000404785:A476V	ENSP00000297056:A517V	A	-	2	0	DAGLB	6418986	1.000000	0.71417	0.171000	0.22900	0.005000	0.04900	7.081000	0.76844	2.752000	0.94435	0.655000	0.94253	GCG	G|0.971;A|0.029	0.029	strong		0.567	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
PDE1C	5137	hgsc.bcm.edu	37	7	31920395	31920395	+	Silent	SNP	G	G	A	rs61729940	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:31920395G>A	ENST00000396191.1	-	3	662	c.207C>T	c.(205-207)gcC>gcT	p.A69A	PDE1C_ENST00000321453.7_Silent_p.A69A|PDE1C_ENST00000396193.1_Silent_p.A129A|PDE1C_ENST00000396182.2_Silent_p.A69A|PDE1C_ENST00000396184.3_Silent_p.A69A	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	69					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CAAGCACTGTGGCTGCATATT	0.318													G|||	613	0.122404	0.028	0.0893	5008	,	,		17872	0.2103		0.1153	False		,,,				2504	0.1902				p.A129A		Atlas-SNP	.											.	PDE1C	465	.	0			c.C387T						PASS	.	G	,,,,	162,4244	109.9+/-148.2	3,156,2044	151.0	144.0	147.0		207,207,387,207,207	3.6	1.0	7	dbSNP_129	147	936,7664	206.9+/-248.8	55,826,3419	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE1C	NM_001191056.1,NM_001191057.1,NM_001191058.1,NM_001191059.1,NM_005020.2	,,,,	58,982,5463	AA,AG,GG		10.8837,3.6768,8.4423	,,,,	69/635,69/710,129/770,69/710,69/635	31920395	1098,11908	2203	4300	6503	SO:0001819	synonymous_variant	5137	exon4			CACTGTGGCTGCA	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.207C>T	7.37:g.31920395G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Silent	SNP	ENST00000396191.1	37	CCDS55099.1																																																																																			A|0.094;G|0.906;T|0.000	0.094	strong		0.318	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
RAD23B	5887	hgsc.bcm.edu	37	9	110084328	110084328	+	Missense_Mutation	SNP	C	C	T	rs1805329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:110084328C>T	ENST00000358015.3	+	7	1097	c.746C>T	c.(745-747)gCt>gTt	p.A249V	RAD23B_ENST00000416373.2_Missense_Mutation_p.A177V	NM_001244713.1|NM_002874.4	NP_001231642.1|NP_002865.1	P54727	RD23B_HUMAN	RAD23 homolog B (S. cerevisiae)	249			A -> V (in dbSNP:rs1805329). {ECO:0000269|PubMed:15064313, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		DNA repair (GO:0006281)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|XPC complex (GO:0071942)	damaged DNA binding (GO:0003684)|polyubiquitin binding (GO:0031593)|single-stranded DNA binding (GO:0003697)			breast(3)|cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						AGTACTGGGGCTCCTCAGTCT	0.502								Direct reversal of damage;Nucleotide excision repair (NER)					C|||	765	0.152756	0.0076	0.3055	5008	,	,		14900	0.2014		0.1789	False		,,,				2504	0.1636				p.A249V		Atlas-SNP	.											.	RAD23B	31	.	0			c.C746T	GRCh37	CM057926	RAD23B	M	rs1805329	PASS	.	C	VAL/ALA	216,4190	130.6+/-167.2	7,202,1994	53.0	54.0	54.0		746	5.3	0.9	9	dbSNP_98	54	1577,7023	295.9+/-302.6	159,1259,2882	yes	missense	RAD23B	NM_002874.4	64	166,1461,4876	TT,TC,CC		18.3372,4.9024,13.7859	benign	249/410	110084328	1793,11213	2203	4300	6503	SO:0001583	missense	5887	exon7			CTGGGGCTCCTCA		CCDS6769.1, CCDS59138.1	9q31.2	2008-07-21	2001-11-28		ENSG00000119318	ENSG00000119318			9813	protein-coding gene	gene with protein product	"""XP-C repair complementing protein"", ""XP-C repair complementing complex 58 kDa"""	600062	"""RAD23 (S. cerevisiae) homolog B"""			7851894, 8168482	Standard	NM_002874		Approved	HHR23B, P58, HR23B	uc004bde.3	P54727	OTTHUMG00000020446	ENST00000358015.3:c.746C>T	9.37:g.110084328C>T	ENSP00000350708:p.Ala249Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	140	71	0.507143	NM_002874	B3KWK8|G5E9P0|Q7Z5K8|Q8WUB0	Missense_Mutation	SNP	ENST00000358015.3	37	CCDS6769.1	365	0.1671245421245421	8	0.016260162601626018	88	0.2430939226519337	109	0.19055944055944055	160	0.21108179419525067	C	17.70	3.455281	0.63401	0.049024	0.183372	ENSG00000119318	ENST00000358015;ENST00000416373	T;T	0.20598	2.08;2.06	5.28	5.28	0.74379	.	0.710413	0.14969	N	0.287917	T	0.00012	0.0000	N	0.24115	0.695	0.38373	P	0.05508299999999999	B;B;B	0.30889	0.005;0.073;0.299	B;B;B	0.28553	0.015;0.011;0.091	T	0.47249	-0.9132	9	0.30078	T	0.28	-9.4451	19.2797	0.94048	0.0:1.0:0.0:0.0	rs1805329;rs2227991;rs2266668;rs4134750;rs4987013;rs17845630;rs17858561;rs52825339;rs1805329	228;249;249	B7Z4W4;B4DEA3;P54727	.;.;RD23B_HUMAN	V	249;177	ENSP00000350708:A249V;ENSP00000405623:A177V	ENSP00000350708:A249V	A	+	2	0	RAD23B	109124149	0.872000	0.30054	0.858000	0.33744	0.972000	0.66771	3.697000	0.54764	2.626000	0.88956	0.555000	0.69702	GCT	C|0.850;T|0.150	0.150	strong		0.502	RAD23B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053548.1	NM_002874	
DLST	1743	hgsc.bcm.edu	37	14	75359670	75359670	+	Silent	SNP	G	G	A	rs2230237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:75359670G>A	ENST00000334220.4	+	8	637	c.576G>A	c.(574-576)caG>caA	p.Q192Q	DLST_ENST00000555190.1_3'UTR|DLST_ENST00000334212.6_Silent_p.Q106Q	NM_001933.4	NP_001924.2	P36957	ODO2_HUMAN	dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex)	192					cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|generation of precursor metabolites and energy (GO:0006091)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|oxoglutarate dehydrogenase complex (GO:0045252)	dihydrolipoyllysine-residue succinyltransferase activity (GO:0004149)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(234;0.00698)		CGCCCTCACAGCCTCCTTCTG	0.557													g|||	3335	0.665935	0.9781	0.5749	5008	,	,		19404	0.4196		0.5308	False		,,,				2504	0.7014				p.Q192Q		Atlas-SNP	.											DLST,colon,carcinoma,0,1	DLST	42	1	0			c.G576A						PASS	.	G		3954,452	783.2+/-414.6	1781,392,30	62.0	53.0	56.0		576	-6.1	0.5	14	dbSNP_98	56	4563,4037	595.0+/-393.4	1224,2115,961	no	coding-synonymous	DLST	NM_001933.4		3005,2507,991	AA,AG,GG		46.9419,10.2587,34.5148		192/454	75359670	8517,4489	2203	4300	6503	SO:0001819	synonymous_variant	1743	exon8			CTCACAGCCTCCT		CCDS9833.1	14q23.1	2008-08-11			ENSG00000119689	ENSG00000119689	2.3.1.61		2911	protein-coding gene	gene with protein product		126063		DLTS		8009371	Standard	NM_001933		Approved		uc001xqv.2	P36957		ENST00000334220.4:c.576G>A	14.37:g.75359670G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	132	55	0.416667	NM_001933	B7Z5W8|E7ESY5|Q7LDY7|Q9BQ32	Silent	SNP	ENST00000334220.4	37	CCDS9833.1																																																																																			G|0.365;A|0.635	0.635	strong		0.557	DLST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413637.1		
C14orf178	283579	hgsc.bcm.edu	37	14	78234796	78234796	+	Splice_Site	SNP	C	C	T	rs8015313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:78234796C>T	ENST00000355883.3	+	2	285	c.76C>T	c.(76-78)Cat>Tat	p.H26Y	C14orf178_ENST00000439131.2_Intron|C14orf178_ENST00000556047.1_Splice_Site_p.H26Y|C14orf178_ENST00000557011.1_Intron	NM_174943.3	NP_777603.1	Q8N769	CN178_HUMAN	chromosome 14 open reading frame 178	26			H -> Y (in dbSNP:rs8015313). {ECO:0000269|PubMed:15489334}.							large_intestine(1)|lung(2)|ovary(1)|prostate(1)	5			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0273)		tttttaCAGGCATGATCAACC	0.308													C|||	601	0.120008	0.0643	0.1167	5008	,	,		16259	0.0456		0.2435	False		,,,				2504	0.1472				p.H26Y		Atlas-SNP	.											.	C14orf178	11	.	0			c.C76T						PASS	.	C	,TYR/HIS	404,4002	182.2+/-210.1	15,374,1814	94.0	99.0	97.0		,76	0.2	0.0	14	dbSNP_116	97	1863,6735	325.1+/-316.8	221,1421,2657	no	intron,missense-near-splice	C14orf178	NM_001173978.1,NM_174943.3	,83	236,1795,4471	TT,TC,CC		21.6678,9.1693,17.4331	,possibly-damaging	,26/123	78234796	2267,10737	2203	4299	6502	SO:0001630	splice_region_variant	283579	exon2			TACAGGCATGATC	AK098842	CCDS9868.1, CCDS53906.1	14q24.3	2012-03-13			ENSG00000197734	ENSG00000197734			26385	protein-coding gene	gene with protein product						12477932	Standard	NM_001173978		Approved	FLJ25976	uc021rwv.1	Q8N769	OTTHUMG00000171528	ENST00000355883.3:c.75-1C>T	14.37:g.78234796C>T		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_174943	Q2HIX2|Q3KNR7	Missense_Mutation	SNP	ENST00000355883.3	37	CCDS9868.1	312	0.14285714285714285	40	0.08130081300813008	47	0.1298342541436464	34	0.05944055944055944	191	0.2519788918205805	C	1.844	-0.466764	0.04476	0.091693	0.216678	ENSG00000197734	ENST00000355883;ENST00000556047	T;T	0.64438	2.33;-0.1	1.23	0.211	0.15236	.	.	.	.	.	T	0.00012	0.0000	N	0.01168	-0.975	0.80722	P	0.0	P	0.41041	0.736	B	0.37508	0.252	T	0.07083	-1.0791	8	0.42905	T	0.14	.	2.9245	0.05780	0.0:0.6476:0.0:0.3524	rs8015313;rs52814974;rs8015313	26	Q8N769	CN178_HUMAN	Y	26	ENSP00000348145:H26Y;ENSP00000451531:H26Y	ENSP00000348145:H26Y	H	+	1	0	C14orf178	77304549	0.000000	0.05858	0.014000	0.15608	0.136000	0.21042	-0.754000	0.04787	0.585000	0.29608	0.591000	0.81541	CAT	C|0.835;T|0.165	0.165	strong		0.308	C14orf178-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413920.1	NM_174943	Missense_Mutation
IL17RC	84818	hgsc.bcm.edu	37	3	9962634	9962634	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9962634C>T	ENST00000295981.3	+	7	1034	c.816C>T	c.(814-816)aaC>aaT	p.N272N	IL17RC_ENST00000383812.4_Intron|IL17RC_ENST00000455057.1_Intron|IL17RC_ENST00000498214.1_Intron|IL17RC_ENST00000416074.2_Intron|IL17RC_ENST00000413608.1_Silent_p.N201N|RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000403601.3_Silent_p.N201N	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	272					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						AAGTCTGGAACAGCATCCCGA	0.612																																					p.N272N		Atlas-SNP	.											.	IL17RC	55	.	0			c.C816T						PASS	.						27.0	30.0	29.0					3																	9962634		2203	4300	6503	SO:0001819	synonymous_variant	84818	exon7			CTGGAACAGCATC	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.816C>T	3.37:g.9962634C>T		Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	332	176	0.53012	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			.	.	none		0.612	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57070089	57070089	+	Silent	SNP	C	C	T	rs34498883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57070089C>T	ENST00000532437.1	-	6	4838	c.4527G>A	c.(4525-4527)ccG>ccA	p.P1509P	TNKS1BP1_ENST00000358252.3_Silent_p.P1509P			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1509	Acidic.|Tankyrase-binding.				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)				CATCAGGCTGCGGCCTCCAGG	0.677													G|||	102	0.0203674	0.0023	0.0389	5008	,	,		15780	0.002		0.0457	False		,,,				2504	0.0245				p.P1509P		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4527A						PASS	.	G		46,4356		0,46,2155	26.0	26.0	26.0		4527	-4.9	0.9	11	dbSNP_126	26	401,8191		8,385,3903	no	coding-synonymous	TNKS1BP1	NM_033396.2		8,431,6058	TT,TC,CC		4.6671,1.045,3.44		1509/1730	57070089	447,12547	2201	4296	6497	SO:0001819	synonymous_variant	85456	exon7			AGGCTGCGGCCTC	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.4527G>A	11.37:g.57070089C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	24	0.40678	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.969;T|0.031	0.031	strong		0.677	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
PYGB	5834	hgsc.bcm.edu	37	20	25264814	25264814	+	Silent	SNP	T	T	C	rs2227892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25264814T>C	ENST00000216962.4	+	14	1805	c.1695T>C	c.(1693-1695)gaT>gaC	p.D565D		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	565					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						CCATGTTCGATGTGCATGTGA	0.552													C|||	2689	0.536941	0.4516	0.3473	5008	,	,		20398	0.9107		0.4334	False		,,,				2504	0.5082				p.D565D		Atlas-SNP	.											.	PYGB	84	.	0			c.T1695C						PASS	.	C		1903,2503	629.0+/-395.2	401,1101,701	228.0	159.0	183.0		1695	-4.5	0.9	20	dbSNP_98	183	3754,4846	616.5+/-396.5	813,2128,1359	no	coding-synonymous	PYGB	NM_002862.3		1214,3229,2060	CC,CT,TT		43.6512,43.1911,43.4953		565/844	25264814	5657,7349	2203	4300	6503	SO:0001819	synonymous_variant	5834	exon14			GTTCGATGTGCAT		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1695T>C	20.37:g.25264814T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	95	41	0.431579	NM_002862	Q96AK1|Q9NPX8	Silent	SNP	ENST00000216962.4	37	CCDS13171.1																																																																																			T|0.523;C|0.477	0.477	strong		0.552	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
DLK2	65989	hgsc.bcm.edu	37	6	43418691	43418691	+	Silent	SNP	G	G	A	rs1214748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43418691G>A	ENST00000357338.3	-	6	1438	c.738C>T	c.(736-738)acC>acT	p.T246T	DLK2_ENST00000372488.3_Silent_p.T246T|DLK2_ENST00000414245.1_Silent_p.T240T|DLK2_ENST00000372485.1_Silent_p.T240T	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	246	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			CAAGCTCACAGGTCTTGCCAC	0.657													A|||	1397	0.278954	0.5424	0.2147	5008	,	,		17896	0.0804		0.2863	False		,,,				2504	0.1656				p.T246T		Atlas-SNP	.											.	DLK2	22	.	0			c.C738T						PASS	.	A	,	2210,2196	571.7+/-383.1	559,1092,552	57.0	62.0	60.0		738,738	-2.5	1.0	6	dbSNP_87	60	2673,5927	671.5+/-402.8	426,1821,2053	no	coding-synonymous,coding-synonymous	DLK2	NM_023932.2,NM_206539.1	,	985,2913,2605	AA,AG,GG		31.0814,49.8411,37.5442	,	246/384,246/384	43418691	4883,8123	2203	4300	6503	SO:0001819	synonymous_variant	65989	exon6			CTCACAGGTCTTG	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.738C>T	6.37:g.43418691G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	121	51	0.421488	NM_023932	B3KNZ7|Q5T3T8|Q9BQ54	Silent	SNP	ENST00000357338.3	37	CCDS4897.1	577	0.2641941391941392	247	0.5020325203252033	81	0.22375690607734808	41	0.07167832167832168	208	0.27440633245382584	A	7.951	0.744851	0.15710	0.501589	0.310814	ENSG00000171462	ENST00000430324	.	.	.	4.94	-2.45	0.06481	.	.	.	.	.	T	0.11793	0.0287	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.27434	-1.0074	3	.	.	.	.	4.7667	0.13135	0.2858:0.1157:0.4846:0.1138	rs1214748;rs1674840;rs58292939;rs1214748	.	.	.	L	152	.	.	P	-	2	0	DLK2	43526669	0.115000	0.22152	0.995000	0.50966	0.918000	0.54935	-0.388000	0.07352	-0.280000	0.09154	-0.521000	0.04368	CCT	A|0.330;C|0.006	0.330	strong		0.657	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
OR1B1	347169	hgsc.bcm.edu	37	9	125391127	125391127	+	Missense_Mutation	SNP	C	C	T	rs1476859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:125391127C>T	ENST00000304833.3	-	1	725	c.688G>A	c.(688-690)Gct>Act	p.A230T	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	230			A -> T (in dbSNP:rs1476859).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						CGTAGAATAGCGGCCCCAATT	0.532													T|||	1948	0.388978	0.0567	0.4885	5008	,	,		19766	0.7917		0.2763	False		,,,				2504	0.4683				p.A230T		Atlas-SNP	.											.	OR1B1	48	.	0			c.G688A						PASS	.		THR/ALA	409,3997	788.8+/-414.9	15,379,1809	70.0	69.0	69.0		688	3.6	0.3	9	dbSNP_88	69	2570,6030	690.3+/-404.4	355,1860,2085	yes	missense	OR1B1	NM_001004450.1	58	370,2239,3894	TT,TC,CC		29.8837,9.2828,22.9048	benign	230/319	125391127	2979,10027	2203	4300	6503	SO:0001583	missense	347169	exon1			GAATAGCGGCCCC	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.688G>A	9.37:g.125391127C>T	ENSP00000303151:p.Ala230Thr	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_001004450	Q6IFN3	Missense_Mutation	SNP	ENST00000304833.3	37	CCDS35126.1	872	0.3992673992673993	45	0.09146341463414634	157	0.43370165745856354	458	0.8006993006993007	212	0.2796833773087071	t	0.066	-1.211780	0.01555	0.092828	0.298837	ENSG00000171484	ENST00000304833	T	0.00188	8.59	4.72	3.58	0.41010	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45606	N	0.000348	T	0.00012	0.0000	N	0.05592	-0.015	0.80722	P	0.0	B	0.18863	0.031	B	0.27262	0.078	T	0.21861	-1.0233	9	0.20046	T	0.44	-8.3372	7.3753	0.26825	0.0:0.2542:0.0:0.7458	rs1476859;rs52796272;rs60552170;rs1476859	230	Q8NGR6	OR1B1_HUMAN	T	230	ENSP00000303151:A230T	ENSP00000303151:A230T	A	-	1	0	OR1B1	124430948	0.000000	0.05858	0.289000	0.24876	0.188000	0.23474	-1.675000	0.01947	0.398000	0.25338	-0.288000	0.09946	GCT	C|0.691;T|0.309	0.309	strong		0.532	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
CPAMD8	27151	hgsc.bcm.edu	37	19	17017878	17017878	+	Missense_Mutation	SNP	G	G	A	rs56408444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17017878G>A	ENST00000443236.1	-	30	4083	c.4052C>T	c.(4051-4053)gCg>gTg	p.A1351V	RN7SL835P_ENST00000579920.1_RNA	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1304						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						GGCCAGGGGCGCAGCAGACTC	0.657													G|||	952	0.190096	0.025	0.3401	5008	,	,		12421	0.2431		0.2217	False		,,,				2504	0.2198				p.A1351V		Atlas-SNP	.											CPAMD8,NS,carcinoma,0,1	CPAMD8	192	1	0			c.C4052T						PASS	.	G	VAL/ALA	210,4100		8,194,1953	33.0	42.0	39.0		4052	-4.2	0.0	19	dbSNP_129	39	1662,6842		171,1320,2761	yes	missense	CPAMD8	NM_015692.2	64	179,1514,4714	AA,AG,GG		19.5437,4.8724,14.609	benign	1351/1933	17017878	1872,10942	2155	4252	6407	SO:0001583	missense	27151	exon30			AGGGGCGCAGCAG	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.4052C>T	19.37:g.17017878G>A	ENSP00000402505:p.Ala1351Val	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	436|436	0.19963369963369965|0.19963369963369965	15|15	0.03048780487804878|0.03048780487804878	121|121	0.3342541436464088|0.3342541436464088	134|134	0.23426573426573427|0.23426573426573427	166|166	0.21899736147757257|0.21899736147757257	G|G	0.607|0.607	-0.826442|-0.826442	0.02734|0.02734	0.048724|0.048724	0.195437|0.195437	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.07|3.07	-4.18|-4.18	0.03846|0.03846	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);|.	1.891200|.	0.04120|.	N|.	0.316189|.	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|.	0.22346|.	0.068|.	B|.	0.10450|.	0.005|.	T|T	0.44817|0.44817	-0.9303|-0.9303	8|4	0.02654|.	T|.	1|.	.|.	6.1572|6.1572	0.20344|0.20344	0.702:0.1636:0.1344:0.0|0.702:0.1636:0.1344:0.0	rs56408444;rs62128040|rs56408444;rs62128040	1304|.	Q8IZJ3|.	CPMD8_HUMAN|.	V|C	1351|1362	.|.	ENSP00000291440:A1351V|.	A|R	-|-	2|1	0|0	CPAMD8|CPAMD8	16878878|16878878	0.055000|0.055000	0.20627|0.20627	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	1.347000|1.347000	0.33975|0.33975	-0.651000|-0.651000	0.05415|0.05415	0.536000|0.536000	0.68110|0.68110	GCG|CGC	G|0.803;A|0.197	0.197	strong		0.657	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
GAREML	150946	hgsc.bcm.edu	37	2	26407120	26407120	+	Missense_Mutation	SNP	A	A	T	rs116239749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26407120A>T	ENST00000401533.2	+	4	533	c.403A>T	c.(403-405)Agc>Tgc	p.S135C	GAREML_ENST00000407684.1_Missense_Mutation_p.S58C	NM_001168241.1	NP_001161713.1	Q75VX8	GAREL_HUMAN	GRB2 associated, regulator of MAPK1-like	135	CABIT.					extracellular vesicular exosome (GO:0070062)											GGGCGAGTTCAGCGAGGACAG	0.637													A|||	10	0.00199681	0.0	0.0	5008	,	,		14452	0.0		0.0089	False		,,,				2504	0.001				p.S135C		Atlas-SNP	.											.	.	.	.	0			c.A403T						PASS	.	A	CYS/SER,CYS/SER	2,1382		0,2,690	35.0	32.0	33.0		403,172	4.6	1.0	2	dbSNP_132	33	35,3147		0,35,1556	yes	missense,missense	FAM59B	NM_001168241.1,NM_001191033.1	112,112	0,37,2246	TT,TA,AA		1.0999,0.1445,0.8103	probably-damaging,probably-damaging	135/875,58/665	26407120	37,4529	692	1591	2283	SO:0001583	missense	150946	exon4			GAGTTCAGCGAGG	AK090454, AB015349, AB124552	CCDS54336.1, CCDS54337.1	2p23.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000157833	ENSG00000157833			27172	protein-coding gene	gene with protein product			"""family with sequence similarity 59, member B"""	FAM59B			Standard	NM_001168241		Approved	KIAA2038, FLJ00375	uc002rgw.2	Q75VX8	OTTHUMG00000151935	ENST00000401533.2:c.403A>T	2.37:g.26407120A>T	ENSP00000384593:p.Ser135Cys	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	142	77	0.542253	NM_001168241	B5MC97|B7WNK9|Q8NF27|Q9UIK8	Missense_Mutation	SNP	ENST00000401533.2	37	CCDS54336.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	22.5	4.302172	0.81136	0.001445	0.010999	ENSG00000157833	ENST00000401533;ENST00000407684	T;T	0.16743	2.32;2.32	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.29355	0.0731	M	0.61703	1.905	0.46798	D	0.999206	D;D	0.76494	0.999;0.999	D;D	0.77004	0.975;0.989	T	0.08953	-1.0697	10	0.87932	D	0	-15.1645	12.1651	0.54125	1.0:0.0:0.0:0.0	.	58;135	B7WNK9;Q75VX8	.;FA59B_HUMAN	C	135;58	ENSP00000384593:S135C;ENSP00000384581:S58C	ENSP00000384593:S135C	S	+	1	0	FAM59B	26260624	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.718000	0.91430	1.813000	0.52934	0.528000	0.53228	AGC	A|0.997;T|0.003	0.003	strong		0.637	GAREML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324498.2	NM_001168241	
DOCK6	57572	hgsc.bcm.edu	37	19	11332570	11332570	+	Silent	SNP	T	T	A	rs3810307	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11332570T>A	ENST00000294618.7	-	28	3518	c.3507A>T	c.(3505-3507)ctA>ctT	p.L1169L	DOCK6_ENST00000319867.7_Silent_p.L508L	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1169					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GTGCAATCGATAGCAGTGGCA	0.602													t|||	1570	0.313498	0.5582	0.2579	5008	,	,		22542	0.2986		0.1431	False		,,,				2504	0.2127				p.L1169L		Atlas-SNP	.											.	DOCK6	104	.	0			c.A3507T						PASS	.	A		2025,2151		492,1041,555	95.0	105.0	102.0		3507	-0.2	0.4	19	dbSNP_107	102	1579,6867		156,1267,2800	no	coding-synonymous	DOCK6	NM_020812.2		648,2308,3355	AA,AT,TT		18.6952,48.4914,28.5533		1169/2048	11332570	3604,9018	2088	4223	6311	SO:0001819	synonymous_variant	57572	exon28			AATCGATAGCAGT		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.3507A>T	19.37:g.11332570T>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			T|0.723;A|0.277	0.277	strong		0.602	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
EXTL1	2134	hgsc.bcm.edu	37	1	26349245	26349245	+	Silent	SNP	C	C	T	rs35744844	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26349245C>T	ENST00000374280.3	+	1	975	c.108C>T	c.(106-108)ccC>ccT	p.P36P		NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	36					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		CATTGCCTCCCAGACCTCGGC	0.647													C|||	162	0.0323482	0.003	0.0331	5008	,	,		18651	0.002		0.1093	False		,,,				2504	0.0235				p.P36P		Atlas-SNP	.											.	EXTL1	61	.	0			c.C108T						PASS	.	C		80,4326	69.8+/-107.6	2,76,2125	46.0	49.0	48.0		108	1.3	0.0	1	dbSNP_126	48	755,7845	179.5+/-228.6	40,675,3585	no	coding-synonymous	EXTL1	NM_004455.2		42,751,5710	TT,TC,CC		8.7791,1.8157,6.4201		36/677	26349245	835,12171	2203	4300	6503	SO:0001819	synonymous_variant	2134	exon1			GCCTCCCAGACCT	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.108C>T	1.37:g.26349245C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	99	6	0.0606061	NM_004455	Q6GSC1	Silent	SNP	ENST00000374280.3	37	CCDS271.1																																																																																			C|0.943;T|0.057	0.057	strong		0.647	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
GPR174	84636	hgsc.bcm.edu	37	X	78426988	78426988	+	Missense_Mutation	SNP	T	T	C	rs3827440	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:78426988T>C	ENST00000276077.1	+	1	520	c.484T>C	c.(484-486)Tct>Cct	p.S162P		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	162			S -> P (in dbSNP:rs3827440).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						TGATGATACCTCTGGCAATAG	0.478										HNSCC(63;0.18)			C|||	1762	0.466755	0.295	0.2795	3775	,	,		16019	0.3214		0.4722	False		,,,				2504	0.3875				p.S162P		Atlas-SNP	.											.	GPR174	79	.	0			c.T484C						PASS	.	C	PRO/SER	1610,2225		295,775,245,562,326	146.0	122.0	130.0		484	-0.7	0.0	X	dbSNP_107	130	4000,2728		853,1140,1154,435,718	yes	missense	GPR174	NM_032553.1	74	1148,1915,1399,997,1044	CC,CT,C,TT,T		40.547,41.9817,46.8901	benign	162/334	78426988	5610,4953	2203	4300	6503	SO:0001583	missense	84636	exon1			GATACCTCTGGCA	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"""GPCR / Class A : Orphans"""	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.484T>C	X.37:g.78426988T>C	ENSP00000276077:p.Ser162Pro	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	135	135	1	NM_032553	Q2M3F7	Missense_Mutation	SNP	ENST00000276077.1	37	CCDS14443.1	811	0.48884870403857744	89	0.22938144329896906	84	0.27631578947368424	126	0.2903225806451613	247	0.4678030303030303	c	0.334	-0.954319	0.02285	0.419817	0.59453	ENSG00000147138	ENST00000276077	T	0.72394	-0.65	4.9	-0.728	0.11162	GPCR, rhodopsin-like superfamily (1);	0.576894	0.16771	N	0.200215	T	0.00012	0.0000	N	0.03154	-0.405	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44483	-0.9325	9	0.31617	T	0.26	.	1.2954	0.02068	0.1958:0.364:0.2129:0.2273	rs3827440;rs17317566;rs52829871;rs57422205;rs3827440	162	Q9BXC1	GP174_HUMAN	P	162	ENSP00000276077:S162P	ENSP00000276077:S162P	S	+	1	0	GPR174	78313644	.	.	0.002000	0.10522	0.086000	0.17979	.	.	-0.544000	0.06232	-1.470000	0.01010	TCT	T|0.495;0|0.014	.	strong		0.478	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144922252	144922252	+	Missense_Mutation	SNP	C	C	G	rs147451175	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144922252C>G	ENST00000369354.3	-	8	1105	c.916G>C	c.(916-918)Ggt>Cgt	p.G306R	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.G443R|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.G443R|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.G469R|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.G306R|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.G469R|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.G306R|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.G93R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.G306R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.G372R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	306					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)		TCATTTTGACCTTCAATTACC	0.398			T	PDGFRB	MPD								C|||	19	0.00379393	0.0	0.0072	5008	,	,		45130	0.0		0.0089	False		,,,				2504	0.0051				p.G469R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G1405C						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	163.0	141.0	148.0		1405,916,1114,916,916	3.1	1.0	1	dbSNP_134	148	52,8548	29.6+/-80.5	0,52,4248	yes	missense,missense,missense,missense,missense	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	125,125,125,125,125	0,55,6448	GG,GC,CC		0.6047,0.0681,0.4229	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	469/1133,306/970,372/2241,306/2363,306/2347	144922252	55,12951	2203	4300	6503	SO:0001583	missense	9659	exon4			TTTGACCTTCAAT	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.916G>C	1.37:g.144922252C>G	ENSP00000358360:p.Gly306Arg	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	144	26	0.180556	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	19.82	3.898738	0.72639	6.81E-4	0.006047	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.12774	4.6;4.69;4.69;4.7;4.69;3.72;3.72;2.67;2.67;2.65	5.92	3.07	0.35406	.	.	.	.	.	T	0.18964	0.0455	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.985;0.997;0.998;0.994	D;P;D;D;D	0.71870	0.931;0.859;0.954;0.975;0.929	T	0.00931	-1.1510	9	0.48119	T	0.1	.	9.4783	0.38884	0.0:0.7702:0.0:0.2298	.	469;306;469;372;306	E9PL24;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;MYOME_HUMAN	R	372;306;306;469;443;443;306;306;469;469;93	ENSP00000327209:G372R;ENSP00000358360:G306R;ENSP00000358363:G306R;ENSP00000435654:G443R;ENSP00000358366:G443R;ENSP00000358357:G306R;ENSP00000358355:G306R;ENSP00000316434:G469R;ENSP00000433392:G469R;ENSP00000436791:G93R	ENSP00000327209:G372R	G	-	1	0	PDE4DIP	143633609	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.718000	0.38001	0.411000	0.25702	0.650000	0.86243	GGT	C|0.996;G|0.004	0.004	strong		0.398	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
GZMB	3002	hgsc.bcm.edu	37	14	25101548	25101548	+	Silent	SNP	G	G	A	rs1126639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:25101548G>A	ENST00000216341.4	-	3	427	c.321C>T	c.(319-321)aaC>aaT	p.N107N	GZMB_ENST00000526004.1_Intron|RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Intron|GZMB_ENST00000415355.3_Silent_p.N95N|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Silent_p.N141N			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	107	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.N107N(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		GCATGATGTCGTTGGAGAAGT	0.542													G|||	1514	0.302316	0.3775	0.2118	5008	,	,		17994	0.2867		0.2475	False		,,,				2504	0.3374				p.N107N		Atlas-SNP	.											GZMB_ENST00000382542,brain,glioma,0,3	GZMB	73	3	1	Substitution - coding silent(1)	stomach(1)	c.C321T						scavenged	.						130.0	147.0	142.0					14																	25101548		2203	4297	6500	SO:0001819	synonymous_variant	3002	exon3			GATGTCGTTGGAG	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.321C>T	14.37:g.25101548G>A		Somatic	337	1	0.00296736		WXS	Illumina HiSeq	Phase_I	248	54	0.217742	NM_004131	Q8N1D2|Q9UCC1	Silent	SNP	ENST00000216341.4	37	CCDS9633.1																																																																																			G|0.721;A|0.279	0.279	strong		0.542	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
FAM208B	54906	hgsc.bcm.edu	37	10	5790738	5790738	+	Missense_Mutation	SNP	G	G	A	rs183849963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5790738G>A	ENST00000328090.5	+	15	5979	c.5354G>A	c.(5353-5355)tGt>tAt	p.C1785Y		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1785																	ACTTCTGTTTGTGGAATAGCC	0.498													G|||	5	0.000998403	0.0	0.0029	5008	,	,		20410	0.0		0.003	False		,,,				2504	0.0				p.C1785Y		Atlas-SNP	.											.	.	.	.	0			c.G5354A						PASS	.	G	TYR/CYS	2,3712		0,2,1855	82.0	79.0	80.0		5354	3.0	0.1	10		80	26,8222		1,24,4099	yes	missense	FAM208B	NM_017782.4	194	1,26,5954	AA,AG,GG		0.3152,0.0539,0.2341	probably-damaging	1785/2431	5790738	28,11934	1857	4124	5981	SO:0001583	missense	54906	exon15			CTGTTTGTGGAAT	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.5354G>A	10.37:g.5790738G>A	ENSP00000328426:p.Cys1785Tyr	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	106	41	0.386792	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.608	-0.080146	0.07141	5.39E-4	0.003152	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.05258	3.47	5.82	2.98	0.34508	.	0.369488	0.27000	N	0.021434	T	0.04272	0.0118	L	0.29908	0.895	0.09310	N	1	B	0.19583	0.037	B	0.20184	0.028	T	0.45920	-0.9228	10	0.14252	T	0.57	.	5.9626	0.19308	0.1676:0.1569:0.6754:0.0	.	1785	Q5VWN6	F208B_HUMAN	Y	1785;980	ENSP00000328426:C1785Y	ENSP00000328426:C1785Y	C	+	2	0	C10orf18	5830744	0.330000	0.24705	0.086000	0.20670	0.005000	0.04900	0.357000	0.20199	0.383000	0.24910	-0.302000	0.09304	TGT	G|0.999;A|0.001	0.001	strong		0.498	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
MYOM2	9172	hgsc.bcm.edu	37	8	2071174	2071174	+	Missense_Mutation	SNP	T	T	C	rs17854780	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:2071174T>C	ENST00000262113.4	+	29	3644	c.3503T>C	c.(3502-3504)gTt>gCt	p.V1168A	MYOM2_ENST00000523438.1_Missense_Mutation_p.V593A	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1168	Ig-like C2-type 4.		V -> A (in dbSNP:rs17854780). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505783}.		muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		AAGGATGATGTTCTGTATGAA	0.423													T|||	485	0.096845	0.0219	0.0836	5008	,	,		17722	0.1865		0.1382	False		,,,				2504	0.0726				p.V1168A		Atlas-SNP	.											.	MYOM2	251	.	0			c.T3503C						PASS	.	T	ALA/VAL	166,4240	108.2+/-146.6	2,162,2039	116.0	102.0	107.0		3503	-0.7	0.0	8	dbSNP_123	107	1001,7599	215.6+/-254.9	50,901,3349	yes	missense	MYOM2	NM_003970.2	64	52,1063,5388	CC,CT,TT		11.6395,3.7676,8.9728	benign	1168/1466	2071174	1167,11839	2203	4300	6503	SO:0001583	missense	9172	exon29			ATGATGTTCTGTA		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.3503T>C	8.37:g.2071174T>C	ENSP00000262113:p.Val1168Ala	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	112	50	0.446429	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	280	0.1282051282051282	11	0.022357723577235773	45	0.12430939226519337	120	0.2097902097902098	104	0.13720316622691292	T	0.016	-1.520068	0.00967	0.037676	0.116395	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.11930	2.73;2.73	5.11	-0.659	0.11424	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.625487	0.16634	N	0.205926	T	0.00012	0.0000	L	0.38838	1.175	0.80722	P	0.0	B	0.09022	0.002	B	0.13407	0.009	T	0.44314	-0.9336	9	0.07990	T	0.79	.	10.6101	0.45417	0.0:0.4134:0.0:0.5866	rs17854780	1168	P54296	MYOM2_HUMAN	A	1168;593	ENSP00000262113:V1168A;ENSP00000428396:V593A	ENSP00000262113:V1168A	V	+	2	0	MYOM2	2058581	0.069000	0.21087	0.020000	0.16555	0.053000	0.15095	0.323000	0.19593	-0.203000	0.10251	0.460000	0.39030	GTT	T|0.900;C|0.100	0.100	strong		0.423	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
DENND6B	414918	hgsc.bcm.edu	37	22	50755782	50755782	+	Silent	SNP	G	G	A	rs145811594	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50755782G>A	ENST00000413817.3	-	5	464	c.393C>T	c.(391-393)ttC>ttT	p.F131F	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	131					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										ACACGTAGCCGAAGTAGTGTG	0.637													G|||	28	0.00559105	0.0	0.0043	5008	,	,		12216	0.0		0.0129	False		,,,				2504	0.0123				p.F131F		Atlas-SNP	.											FAM116B,colon,carcinoma,0,1	.	.	1	0			c.C393T						scavenged	.	G		4,4192		0,4,2094	54.0	62.0	60.0		393	-9.6	0.6	22	dbSNP_134	60	63,8363		1,61,4151	no	coding-synonymous	FAM116B	NM_001001794.3		1,65,6245	AA,AG,GG		0.7477,0.0953,0.5308		131/586	50755782	67,12555	2098	4213	6311	SO:0001819	synonymous_variant	414918	exon5			GTAGCCGAAGTAG	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.393C>T	22.37:g.50755782G>A		Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	1.803	-0.476686	0.04414	9.53E-4	0.007477	ENSG00000205593	ENST00000433760	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.41696	0.1170	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60712	-0.7209	4	.	.	.	-6.8758	10.8518	0.46775	0.3823:0.1029:0.5148:0.0	.	.	.	.	L	103	.	.	S	-	2	0	FAM116B	49098354	0.005000	0.15991	0.579000	0.28588	0.026000	0.11368	-0.863000	0.04259	-2.344000	0.00622	-1.855000	0.00564	TCG	G|0.992;A|0.008	0.008	strong		0.637	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
FMN2	56776	hgsc.bcm.edu	37	1	240492734	240492734	+	Missense_Mutation	SNP	G	G	A	rs3795677	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:240492734G>A	ENST00000319653.9	+	10	4633	c.4403G>A	c.(4402-4404)cGt>cAt	p.R1468H	FMN2_ENST00000545751.1_Missense_Mutation_p.R64H	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1468	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.		R -> H (in dbSNP:rs3795677). {ECO:0000269|Ref.3}.		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)			TGCTCAATTCGTCGCAAACTG	0.408													G|||	1607	0.320887	0.3381	0.3588	5008	,	,		18670	0.3185		0.2883	False		,,,				2504	0.3067				p.R1468H		Atlas-SNP	.											FMN2,NS,carcinoma,+1,1	FMN2	451	1	0			c.G4403A						PASS	.	G	HIS/ARG	1380,3026	456.3+/-351.3	201,978,1024	144.0	136.0	138.0		4403	1.7	1.0	1	dbSNP_107	138	2363,6237	394.1+/-344.6	308,1747,2245	yes	missense	FMN2	NM_020066.4	29	509,2725,3269	AA,AG,GG		27.4767,31.3209,28.779	possibly-damaging	1468/1723	240492734	3743,9263	2203	4300	6503	SO:0001583	missense	56776	exon10			CAATTCGTCGCAA	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.4403G>A	1.37:g.240492734G>A	ENSP00000318884:p.Arg1468His	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	249	115	0.461847	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	705	0.3228021978021978	158	0.32113821138211385	127	0.35082872928176795	196	0.34265734265734266	224	0.2955145118733509	G	7.918	0.737991	0.15574	0.313209	0.274767	ENSG00000155816	ENST00000319653;ENST00000545751;ENST00000537355	T;T	0.18502	2.21;2.21	5.65	1.72	0.24424	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.324081	0.26065	N	0.026552	T	0.00012	0.0000	N	0.25890	0.77	0.09310	P	0.9999999999949641	B;B;B;P	0.34837	0.002;0.005;0.008;0.472	B;B;B;B	0.37780	0.002;0.005;0.008;0.258	T	0.31586	-0.9938	9	0.06365	T	0.9	.	11.8887	0.52616	0.2878:0.0:0.7122:0.0	rs3795677;rs17679152;rs56984583;rs3795677	64;114;97;1468	B4DP05;F5H2C1;B4DN09;Q9NZ56	.;.;.;FMN2_HUMAN	H	1468;64;95	ENSP00000318884:R1468H;ENSP00000437918:R64H	ENSP00000318884:R1468H	R	+	2	0	FMN2	238559357	0.000000	0.05858	0.998000	0.56505	0.979000	0.70002	-0.225000	0.09151	0.059000	0.16252	-0.940000	0.02684	CGT	G|0.684;A|0.316	0.316	strong		0.408	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
MYO15A	51168	hgsc.bcm.edu	37	17	18055229	18055229	+	Silent	SNP	G	G	A	rs854772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18055229G>A	ENST00000205890.5	+	41	8195	c.7857G>A	c.(7855-7857)ggG>ggA	p.G2619G	MYO15A_ENST00000585180.1_5'Flank|MYO15A_ENST00000418233.3_5'Flank	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2619	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.G2619G(1)		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)					TCCTGAAAGGGCAGATGACCC	0.607													G|||	1957	0.390775	0.4713	0.4798	5008	,	,		11995	0.0804		0.6004	False		,,,				2504	0.3231				p.G2619G		Atlas-SNP	.											MYO15A,NS,carcinoma,0,1	MYO15A	268	1	1	Substitution - coding silent(1)	stomach(1)	c.G7857A						PASS	.	G		2077,1845		570,937,454	35.0	38.0	37.0		7857	-2.4	0.6	17	dbSNP_86	37	5243,3055		1681,1881,587	no	coding-synonymous	MYO15A	NM_016239.3		2251,2818,1041	AA,AG,GG		36.8161,47.0423,40.0982		2619/3531	18055229	7320,4900	1961	4149	6110	SO:0001819	synonymous_variant	51168	exon40			GAAAGGGCAGATG	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.7857G>A	17.37:g.18055229G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_016239	B4DFC7	Silent	SNP	ENST00000205890.5	37	CCDS42271.1																																																																																			G|0.577;A|0.423	0.423	strong		0.607	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
SPAG17	200162	hgsc.bcm.edu	37	1	118530796	118530796	+	Silent	SNP	C	C	T	rs12040811	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:118530796C>T	ENST00000336338.5	-	39	5618	c.5553G>A	c.(5551-5553)caG>caA	p.Q1851Q		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1851						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TAGCCAAAGACTGCTTGAATA	0.363													c|||	693	0.138379	0.0522	0.0461	5008	,	,		19230	0.3403		0.0626	False		,,,				2504	0.1902				p.Q1851Q		Atlas-SNP	.											.	SPAG17	263	.	0			c.G5553A						PASS	.	T		216,4190	131.0+/-167.6	3,210,1990	65.0	62.0	63.0		5553	-3.5	0.1	1	dbSNP_120	63	496,8104	142.3+/-198.5	16,464,3820	no	coding-synonymous	SPAG17	NM_206996.2		19,674,5810	TT,TC,CC		5.7674,4.9024,5.4744		1851/2224	118530796	712,12294	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon39			CAAAGACTGCTTG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5553G>A	1.37:g.118530796C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			C|0.915;T|0.085	0.085	strong		0.363	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
SSR1	6745	hgsc.bcm.edu	37	6	7310259	7310259	+	Missense_Mutation	SNP	A	A	G	rs10004	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:7310259A>G	ENST00000244763.4	-	2	169	c.83T>C	c.(82-84)tTg>tCg	p.L28S	SSR1_ENST00000397511.2_Missense_Mutation_p.L28S|SSR1_ENST00000479365.1_Missense_Mutation_p.L28S|SSR1_ENST00000489567.1_Missense_Mutation_p.L28S|SSR1_ENST00000474597.1_Missense_Mutation_p.L28S|SSR1_ENST00000488834.1_5'UTR|SSR1_ENST00000462112.1_Missense_Mutation_p.L28S|SSR1_ENST00000534851.1_Missense_Mutation_p.L28S	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	28			L -> S (in dbSNP:rs10004). {ECO:0000269|PubMed:8050590, ECO:0000269|Ref.6}.		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|positive regulation of cell proliferation (GO:0008284)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.L28S(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|prostate(1)	9	Ovarian(93;0.0398)					CACTGCTAACAAGCCTAATGA	0.363													G|||	1474	0.294329	0.5144	0.1542	5008	,	,		17650	0.2609		0.2455	False		,,,				2504	0.181				p.L28S		Atlas-SNP	.											SSR1,NS,carcinoma,0,1	SSR1	21	1	1	Substitution - Missense(1)	lung(1)	c.T83C						PASS	.	G	SER/LEU	2004,2402	613.7+/-392.2	439,1126,638	124.0	121.0	122.0		83	3.0	0.0	6	dbSNP_52	122	2258,6342	707.5+/-405.6	305,1648,2347	yes	missense	SSR1	NM_003144.3	145	744,2774,2985	GG,GA,AA		26.2558,45.4834,32.7695	benign	28/287	7310259	4262,8744	2203	4300	6503	SO:0001583	missense	6745	exon2			GCTAACAAGCCTA		CCDS4499.1	6p24.3	2010-11-24	2008-08-26		ENSG00000124783	ENSG00000124783			11323	protein-coding gene	gene with protein product	"""translocon-associated protein alpha"""	600868					Standard	NM_001292008		Approved	TRAPA	uc003mxf.4	P43307	OTTHUMG00000014202	ENST00000244763.4:c.83T>C	6.37:g.7310259A>G	ENSP00000244763:p.Leu28Ser	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	91	42	0.461538	NM_003144	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	Missense_Mutation	SNP	ENST00000244763.4	37	CCDS4499.1	642	0.29395604395604397	241	0.4898373983739837	65	0.17955801104972377	144	0.2517482517482518	192	0.2532981530343008	G	8.517	0.867893	0.17250	0.454834	0.262558	ENSG00000124783	ENST00000474597;ENST00000244763;ENST00000397511;ENST00000534851;ENST00000489567;ENST00000479365;ENST00000462112	T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93	3.91	3.04	0.35103	.	0.456420	0.21293	N	0.076926	T	0.10252	0.0251	N	0.20986	0.625	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.17379	-1.0371	9	0.20519	T	0.43	.	7.6038	0.28091	0.3016:0.0:0.6984:0.0	rs10004;rs1139088;rs3203131;rs7746261;rs11552673;rs17295574;rs52829480;rs58553065;rs7746261	28;28;28	C9J5W0;C9JBX5;P43307	.;.;SSRA_HUMAN	S	28	ENSP00000418617:L28S;ENSP00000244763:L28S;ENSP00000380647:L28S;ENSP00000443020:L28S;ENSP00000420730:L28S;ENSP00000417911:L28S;ENSP00000417290:L28S	ENSP00000244763:L28S	L	-	2	0	SSR1	7255258	0.995000	0.38212	0.028000	0.17463	0.602000	0.36980	3.670000	0.54569	0.625000	0.30304	-0.748000	0.03510	TTG	T|0.123;G|0.260	0.260	strong		0.363	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039775.2		
LRIG3	121227	hgsc.bcm.edu	37	12	59282702	59282702	+	Silent	SNP	T	T	C	rs17533647	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:59282702T>C	ENST00000320743.3	-	6	988	c.702A>G	c.(700-702)acA>acG	p.T234T	LRIG3_ENST00000379141.4_Silent_p.T174T	NM_153377.4	NP_700356.2	Q6UXM1	LRIG3_HUMAN	leucine-rich repeats and immunoglobulin-like domains 3	234					otolith morphogenesis (GO:0032474)	cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)			LRIG3/ROS1(2)	breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(12)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48			GBM - Glioblastoma multiforme(1;1.17e-18)			GGCCTTGGAATGTCAGTCCAT	0.378			T	ROS1	NSCLC								T|||	306	0.0611022	0.0129	0.0461	5008	,	,		19089	0.0397		0.1163	False		,,,				2504	0.1022				p.T234T		Atlas-SNP	.		Dom	yes		12	12q14.1	121227	leucine-rich repeats and immunoglobulin-like domains 3		E	LRIG3,NS,carcinoma,-2,1	LRIG3	120	1	0			c.A702G						PASS	.	T	,	148,4258	101.2+/-139.8	4,140,2059	198.0	185.0	189.0		522,702	-11.0	0.8	12	dbSNP_123	189	995,7605	214.6+/-254.2	51,893,3356	no	coding-synonymous,coding-synonymous	LRIG3	NM_001136051.1,NM_153377.3	,	55,1033,5415	CC,CT,TT		11.5698,3.3591,8.7883	,	174/1060,234/1120	59282702	1143,11863	2203	4300	6503	SO:0001819	synonymous_variant	121227	exon6			TTGGAATGTCAGT	AY505340	CCDS8960.1, CCDS44933.1	12q13.2	2013-01-11				ENSG00000139263		"""Immunoglobulin superfamily / I-set domain containing"""	30991	protein-coding gene	gene with protein product		608870					Standard	NM_153377		Approved	FLJ90440, KIAA3016	uc001sqr.4	Q6UXM1	OTTHUMG00000169940	ENST00000320743.3:c.702A>G	12.37:g.59282702T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	132	50	0.378788	NM_153377	Q6UXL7|Q8NC72	Silent	SNP	ENST00000320743.3	37	CCDS8960.1																																																																																			T|0.928;C|0.072	0.072	strong		0.378	LRIG3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406623.1	NM_153377	
C6orf15	29113	hgsc.bcm.edu	37	6	31079236	31079236	+	Silent	SNP	G	G	A	rs1265055	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31079236G>A	ENST00000259870.3	-	2	903	c.900C>T	c.(898-900)gtC>gtT	p.V300V		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	300	Pro-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GAGGGCGGAGGACTCCAGGAG	0.537													A|||	2663	0.531749	0.5461	0.5663	5008	,	,		16514	0.4871		0.5139	False		,,,				2504	0.5521				p.V300V		Atlas-SNP	.											.	C6orf15	29	.	0			c.C900T						PASS	.	A		2008,1490		576,856,317	40.0	39.0	39.0		900	-0.3	0.0	6	dbSNP_87	39	3825,3141		1074,1677,732	no	coding-synonymous	C6orf15	NM_014070.2		1650,2533,1049	AA,AG,GG		45.0904,42.5958,44.2565		300/326	31079236	5833,4631	1749	3483	5232	SO:0001819	synonymous_variant	29113	exon2			GCGGAGGACTCCA	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.900C>T	6.37:g.31079236G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			G|0.484;A|0.516	0.516	strong		0.537	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
CCDC28B	79140	hgsc.bcm.edu	37	1	32669645	32669645	+	Splice_Site	SNP	C	C	T	rs41263993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:32669645C>T	ENST00000373602.5	+	3	677	c.330C>T	c.(328-330)ttC>ttT	p.F110F	RP4-622L5.7_ENST00000373604.4_RNA|RP4-622L5.7_ENST00000421616.1_RNA|IQCC_ENST00000537469.1_5'Flank|CCDC28B_ENST00000421922.2_Splice_Site_p.F110F|IQCC_ENST00000291358.6_5'Flank|CCDC28B_ENST00000483009.1_3'UTR	NM_024296.3	NP_077272.2	Q9BUN5	CC28B_HUMAN	coiled-coil domain containing 28B	110					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TGCAGGCCTTCGGTGAGTCCT	0.607													C|||	28	0.00559105	0.0015	0.0115	5008	,	,		18193	0.0		0.0139	False		,,,				2504	0.0041				p.F110F		Atlas-SNP	.											.	CCDC28B	21	.	0			c.C330T	GRCh37	CS066273	CCDC28B	S	rs41263993	PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	45.0	46.0	46.0		330	-9.5	0.7	1	dbSNP_127	46	169,8431	78.1+/-140.7	4,161,4135	yes	coding-synonymous-near-splice	CCDC28B	NM_024296.3		4,168,6331	TT,TC,CC		1.9651,0.1589,1.3532		110/201	32669645	176,12830	2203	4300	6503	SO:0001630	splice_region_variant	79140	exon3			GGCCTTCGGTGAG	BC022848	CCDS354.2, CCDS72749.1	1p36.11-p34.2	2008-02-05			ENSG00000160050	ENSG00000160050			28163	protein-coding gene	gene with protein product		610162				16327777	Standard	XM_006710892		Approved	MGC1203, RP4-622L5.5	uc001bul.1	Q9BUN5	OTTHUMG00000005738	ENST00000373602.5:c.331+1C>T	1.37:g.32669645C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	49	5	0.102041	NM_024296	A8K789|Q8TBV8	Silent	SNP	ENST00000373602.5	37	CCDS354.2																																																																																			C|0.987;T|0.013	0.013	strong		0.607	CCDC28B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015723.4	NM_024296	Silent
EPN3	55040	hgsc.bcm.edu	37	17	48618360	48618360	+	Missense_Mutation	SNP	C	C	T	rs78111408	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48618360C>T	ENST00000268933.3	+	7	1765	c.1186C>T	c.(1186-1188)Cac>Tac	p.H396Y	EPN3_ENST00000541226.1_3'UTR|RP11-94C24.8_ENST00000513017.1_RNA|EPN3_ENST00000537145.1_Missense_Mutation_p.H424Y	NM_017957.2	NP_060427.2	Q9H201	EPN3_HUMAN	epsin 3	396	5 X 3 AA repeats of [DE]-P-W.			H -> Y (in Ref. 2; BAA91378). {ECO:0000305}.		clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	14	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;2.88e-09)			CTCTCCCCACCACAAACTCCC	0.657													C|||	273	0.0545128	0.0711	0.1196	5008	,	,		14888	0.0417		0.0189	False		,,,				2504	0.0358				p.H396Y		Atlas-SNP	.											.	EPN3	32	.	0			c.C1186T						PASS	.	C	TYR/HIS	227,4165		6,215,1975	22.0	27.0	26.0		1186	3.2	0.9	17	dbSNP_131	26	114,8476		0,114,4181	yes	missense	EPN3	NM_017957.2	83	6,329,6156	TT,TC,CC		1.3271,5.1685,2.6267	benign	396/633	48618360	341,12641	2196	4295	6491	SO:0001583	missense	55040	exon7			CCCCACCACAAAC	AF324241	CCDS11570.1	17q21.33	2008-07-18				ENSG00000049283			18235	protein-coding gene	gene with protein product		607264				10951261, 11359770	Standard	NM_017957		Approved	FLJ20778, MGC129899	uc002ira.4	Q9H201		ENST00000268933.3:c.1186C>T	17.37:g.48618360C>T	ENSP00000268933:p.His396Tyr	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_017957	A8K6J3|A8KAB2|Q9BVN6|Q9NWK2	Missense_Mutation	SNP	ENST00000268933.3	37	CCDS11570.1	105	0.04807692307692308	31	0.06300813008130081	37	0.10220994475138122	22	0.038461538461538464	15	0.01978891820580475	C	12.42	1.932055	0.34096	0.051685	0.013271	ENSG00000049283	ENST00000268933;ENST00000442715;ENST00000537145	T;T	0.25912	1.77;1.77	5.17	3.15	0.36227	.	1.939920	0.03239	U	0.180031	T	0.00754	0.0025	L	0.59436	1.845	0.09310	P	0.9999999845108	P;P;B	0.47302	0.893;0.868;0.245	B;B;B	0.40825	0.242;0.341;0.222	T	0.08722	-1.0708	9	0.33940	T	0.23	-7.1704	8.1335	0.31041	0.1567:0.7622:0.0:0.0811	.	424;424;396	B4DK18;F6QWW5;Q9H201	.;.;EPN3_HUMAN	Y	396;424;424	ENSP00000268933:H396Y;ENSP00000439512:H424Y	ENSP00000268933:H396Y	H	+	1	0	EPN3	45973359	0.001000	0.12720	0.923000	0.36655	0.496000	0.33645	0.822000	0.27352	0.555000	0.29079	0.561000	0.74099	CAC	C|0.964;T|0.036	0.036	strong		0.657	EPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367573.1	NM_017957	
AKAP2	11217	hgsc.bcm.edu	37	9	112900466	112900466	+	Missense_Mutation	SNP	C	C	T	rs61735424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:112900466C>T	ENST00000259318.7	+	2	2156	c.1949C>T	c.(1948-1950)gCg>gTg	p.A650V	PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.A881V|AKAP2_ENST00000555236.1_Missense_Mutation_p.A881V|AKAP2_ENST00000510514.5_Missense_Mutation_p.A881V|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.A881V|AKAP2_ENST00000374525.1_Missense_Mutation_p.A739V|AKAP2_ENST00000482335.1_3'UTR|AKAP2_ENST00000434623.2_Missense_Mutation_p.A739V	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	650										breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						GAAGACAGGGCGCTCAGGGAA	0.552													C|||	80	0.0159744	0.0023	0.0202	5008	,	,		16777	0.0		0.0358	False		,,,				2504	0.0276				p.A881V		Atlas-SNP	.											.	PALM2-AKAP2	117	.	0			c.C2642T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	46,4360	43.1+/-76.7	1,44,2158	24.0	29.0	27.0		2216,1949,2216,2642,2642	-4.0	0.0	9	dbSNP_129	27	412,8188	127.5+/-185.8	15,382,3903	yes	missense,missense,missense,missense,missense	AKAP2,PALM2-AKAP2	NM_001004065.4,NM_001136562.2,NM_001198656.1,NM_007203.4,NM_147150.2	64,64,64,64,64	16,426,6061	TT,TC,CC		4.7907,1.044,3.5215	benign,benign,benign,benign,benign	739/949,650/860,739/962,881/1104,881/1091	112900466	458,12548	2203	4300	6503	SO:0001583	missense	445815	exon8			ACAGGGCGCTCAG	AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.1949C>T	9.37:g.112900466C>T	ENSP00000259318:p.Ala650Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_007203	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Missense_Mutation	SNP	ENST00000259318.7	37	CCDS48003.1	46	0.021062271062271064	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	34	0.044854881266490766	C	7.473	0.647030	0.14516	0.01044	0.047907	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000480388;ENST00000259318	T;T;T;T;T;T;T;T	0.46819	1.59;1.59;1.59;1.59;1.59;1.59;0.86;1.59	5.88	-3.95	0.04118	.	0.846275	0.10511	N	0.666141	T	0.03959	0.0111	N	0.20685	0.6	0.09310	N	0.999991	B;B;B;B;B;B;B;B	0.19583	0.002;0.002;0.017;0.037;0.022;0.007;0.007;0.004	B;B;B;B;B;B;B;B	0.11329	0.002;0.002;0.002;0.006;0.003;0.006;0.006;0.002	T	0.09037	-1.0693	10	0.39692	T	0.17	-2.4798	3.2787	0.06907	0.1348:0.2282:0.1082:0.5288	rs61735424	650;739;733;739;740;881;881;699	Q9Y2D5;Q9Y2D5-7;B4E2K2;Q9Y2D5-5;B1ALY1;Q9Y2D5-6;Q9Y2D5-4;C9JVY5	AKAP2_HUMAN;.;.;.;.;.;.;.	V	881;881;881;881;739;739;699;650	ENSP00000363654:A881V;ENSP00000305861:A881V;ENSP00000451476:A881V;ENSP00000421522:A881V;ENSP00000404782:A739V;ENSP00000363649:A739V;ENSP00000419268:A699V;ENSP00000259318:A650V	ENSP00000259318:A650V	A	+	2	0	PALM2-AKAP2;AKAP2	111940287	0.006000	0.16342	0.007000	0.13788	0.919000	0.55068	-0.009000	0.12765	-0.573000	0.05998	-0.880000	0.02959	GCG	C|0.969;T|0.031	0.031	strong		0.552	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3	NM_001004065	
FBXO6	26270	hgsc.bcm.edu	37	1	11728894	11728894	+	Missense_Mutation	SNP	G	G	A	rs3125818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:11728894G>A	ENST00000376753.4	+	2	314	c.179G>A	c.(178-180)cGa>cAa	p.R60Q		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	60			R -> Q (in dbSNP:rs3125818).		DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		AAGTGCCTGCGAGAGGGCTTC	0.627													.|||	683	0.136382	0.0726	0.1758	5008	,	,		19109	0.1498		0.1173	False		,,,				2504	0.2004				p.R60Q	NSCLC(54;506 1562 46490 51389)	Atlas-SNP	.											FBXO6,NS,carcinoma,0,1	FBXO6	17	1	0			c.G179A						PASS	.	G	GLN/ARG	361,4045	187.1+/-213.8	10,341,1852	60.0	64.0	63.0		179	-3.5	0.0	1	dbSNP_103	63	975,7625	212.5+/-252.8	53,869,3378	no	missense	FBXO6	NM_018438.5	43	63,1210,5230	AA,AG,GG		11.3372,8.1934,10.2722	benign	60/294	11728894	1336,11670	2203	4300	6503	SO:0001583	missense	26270	exon2			GCCTGCGAGAGGG	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"""F-boxes /  ""other"""""	13585	protein-coding gene	gene with protein product		605647	"""F-box only protein 6"""			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.179G>A	1.37:g.11728894G>A	ENSP00000365944:p.Arg60Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	164	10	0.0609756	NM_018438	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	251|251	0.11492673992673992|0.11492673992673992	30|30	0.06097560975609756|0.06097560975609756	62|62	0.1712707182320442|0.1712707182320442	73|73	0.12762237762237763|0.12762237762237763	86|86	0.11345646437994723|0.11345646437994723	G|G	7.166|7.166	0.586706|0.586706	0.13749|0.13749	0.081934|0.081934	0.113372|0.113372	ENSG00000116663|ENSG00000116663	ENST00000449067|ENST00000376753	.|T	.|0.49139	.|0.79	5.15|5.15	-3.48|-3.48	0.04739|0.04739	.|F-box domain, Skp2-like (1);	.|0.120339	.|0.56097	.|N	.|0.000038	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45470|0.45470	1.425|1.425	0.47511|0.47511	P|P	5.579999999999474E-4|5.579999999999474E-4	.|B	.|0.32128	.|0.357	.|B	.|0.29716	.|0.106	T|T	0.14008|0.14008	-1.0488|-1.0488	4|9	.|0.18276	.|T	.|0.48	-12.4923|-12.4923	5.8202|5.8202	0.18524|0.18524	0.1932:0.0:0.3929:0.4138|0.1932:0.0:0.3929:0.4138	rs3125818;rs9430593;rs52826022;rs3125818|rs3125818;rs9430593;rs52826022;rs3125818	.|60	.|Q9NRD1	.|FBX6_HUMAN	K|Q	48|60	.|ENSP00000365944:R60Q	.|ENSP00000365944:R60Q	E|R	+|+	1|2	0|0	FBXO6|FBXO6	11651481|11651481	0.007000|0.007000	0.16637|0.16637	0.002000|0.002000	0.10522|0.10522	0.042000|0.042000	0.13812|0.13812	-0.088000|-0.088000	0.11198|0.11198	-0.548000|-0.548000	0.06199|0.06199	-0.175000|-0.175000	0.13238|0.13238	GAG|CGA	.	.	weak		0.627	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438	
TOPORS	10210	hgsc.bcm.edu	37	9	32541532	32541532	+	Silent	SNP	A	A	G	rs12348918	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:32541532A>G	ENST00000360538.2	-	3	3107	c.2991T>C	c.(2989-2991)gaT>gaC	p.D997D	TOPORS_ENST00000379858.1_Silent_p.D932D	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	997					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D997D(1)		large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		CTTCTCTTACATCGAGAGTTT	0.423													A|||	572	0.114217	0.093	0.1412	5008	,	,		20493	0.0079		0.2545	False		,,,				2504	0.089				p.D997D		Atlas-SNP	.											TOPORS_ENST00000360538,NS,carcinoma,0,2	TOPORS	127	2	1	Substitution - coding silent(1)	prostate(1)	c.T2991C						scavenged	.	A	,	551,3855	248.4+/-256.2	34,483,1686	164.0	158.0	160.0		2796,2991	3.1	1.0	9	dbSNP_120	160	2111,6489	363.7+/-333.3	260,1591,2449	no	coding-synonymous,coding-synonymous	TOPORS	NM_001195622.1,NM_005802.4	,	294,2074,4135	GG,GA,AA		24.5465,12.5057,20.4675	,	932/981,997/1046	32541532	2662,10344	2203	4300	6503	SO:0001819	synonymous_variant	10210	exon3			TCTTACATCGAGA	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.2991T>C	9.37:g.32541532A>G		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	111	51	0.459459	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Silent	SNP	ENST00000360538.2	37	CCDS6527.1																																																																																			A|0.832;G|0.168	0.168	strong		0.423	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
NOD2	64127	hgsc.bcm.edu	37	16	50733859	50733859	+	Silent	SNP	C	C	G	rs2067085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:50733859C>G	ENST00000300589.2	+	2	639	c.534C>G	c.(532-534)tcC>tcG	p.S178S	NOD2_ENST00000526417.2_3'UTR	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	178	CARD 2. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				TCACACCGTCCCAGAGGGTGA	0.537													C|||	1235	0.246605	0.2784	0.2954	5008	,	,		20716	0.0496		0.4264	False		,,,				2504	0.1871				p.S178S		Atlas-SNP	.											NOD2,NS,carcinoma,0,1	NOD2	118	1	0			c.C534G						PASS	.	C		1300,3096	440.8+/-346.1	196,908,1094	64.0	53.0	57.0		534	0.6	1.0	16	dbSNP_96	57	3520,5080	512.4+/-377.9	740,2040,1520	no	coding-synonymous	NOD2	NM_022162.1		936,2948,2614	GG,GC,CC		40.9302,29.5723,37.0883		178/1041	50733859	4820,8176	2198	4300	6498	SO:0001819	synonymous_variant	64127	exon2			ACCGTCCCAGAGG	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.534C>G	16.37:g.50733859C>G		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	16	9	0.5625	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1																																																																																			C|0.673;G|0.327	0.327	strong		0.537	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159254	18159254	+	Missense_Mutation	SNP	A	A	G	rs4274188	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18159254A>G	ENST00000396275.2	+	3	866	c.505A>G	c.(505-507)Aat>Gat	p.N169D		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	169			N -> D (in dbSNP:rs4274188). {ECO:0000269|PubMed:11551509, ECO:0000269|PubMed:11850634, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3, ECO:0000269|Ref.5}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TAGTGGTGCTAATTCTGTTTG	0.502													N|||	3721	0.743011	0.5371	0.8357	5008	,	,		21763	0.874		0.7773	False		,,,				2504	0.7853				p.N169D		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.A505G						PASS	.	G	ASP/ASN	2550,1850	538.2+/-374.9	740,1070,390	191.0	169.0	176.0		505	-1.8	0.0	11	dbSNP_111	176	6595,1991	349.1+/-327.3	2520,1555,218	yes	missense	MRGPRX3	NM_054031.3	23	3260,2625,608	GG,GA,AA		23.1889,42.0455,29.578	benign	169/323	18159254	9145,3841	2200	4293	6493	SO:0001583	missense	117195	exon3			GGTGCTAATTCTG		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.505A>G	11.37:g.18159254A>G	ENSP00000379571:p.Asn169Asp	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	174	174	1	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Missense_Mutation	SNP	ENST00000396275.2	37	CCDS7830.1	1689	0.7733516483516484	266	0.540650406504065	298	0.8232044198895028	527	0.9213286713286714	598	0.7889182058047494	G	0.008	-1.880533	0.00537	0.579545	0.768111	ENSG00000179826	ENST00000396275;ENST00000531264	T;T	0.33654	1.4;1.4	1.46	-1.77	0.07982	GPCR, rhodopsin-like superfamily (1);	2.754660	0.01288	N	0.009926	T	0.00012	0.0000	N	0.01289	-0.905	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.36480	-0.9746	9	0.02654	T	1	.	7.8269	0.29320	0.7645:0.0:0.2355:0.0	rs4274188;rs52829739;rs57864166;rs4274188	169	Q96LB0	MRGX3_HUMAN	D	169	ENSP00000379571:N169D;ENSP00000436242:N169D	ENSP00000379571:N169D	N	+	1	0	MRGPRX3	18115830	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.235000	0.01202	-1.182000	0.02727	-0.471000	0.05019	AAT	A|0.278;G|0.722	0.722	strong		0.502	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
CFAP46	54777	hgsc.bcm.edu	37	10	134698626	134698626	+	Missense_Mutation	SNP	T	T	C	rs73393250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134698626T>C	ENST00000368586.5	-	27	3708	c.3608A>G	c.(3607-3609)aAc>aGc	p.N1203S	TTC40_ENST00000368582.2_Missense_Mutation_p.N1203S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTGGATGGCGTTGTTGTAGCA	0.572													C|||	672	0.134185	0.3608	0.0418	5008	,	,		15794	0.0198		0.0249	False		,,,				2504	0.1237				p.N1203S		Atlas-SNP	.											.	TTC40	100	.	0			c.A3608G						PASS	.																																			SO:0001583	missense	54777	exon27			ATGGCGTTGTTGT																												ENST00000368586.5:c.3608A>G	10.37:g.134698626T>C	ENSP00000357575:p.Asn1203Ser	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	89	36	0.404494	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	220	0.10073260073260074	179	0.3638211382113821	13	0.03591160220994475	12	0.02097902097902098	16	0.021108179419525065	C	0.901	-0.722113	0.03182	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.45668	2.87;0.89	4.16	1.74	0.24563	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.38693	-0.9649	5	0.38643	T	0.18	.	9.5036	0.39033	0.0:0.1788:0.0:0.8212	.	.	.	.	S	1203	ENSP00000357575:N1203S;ENSP00000357571:N1203S	ENSP00000357571:N1203S	N	-	2	0	C10orf93	134548616	0.400000	0.25295	0.007000	0.13788	0.003000	0.03518	1.216000	0.32443	-0.245000	0.09625	-1.247000	0.01520	AAC	T|0.913;C|0.087	0.087	strong		0.572	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
COL4A4	1286	hgsc.bcm.edu	37	2	227920747	227920747	+	Missense_Mutation	SNP	C	C	T	rs150979437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227920747C>T	ENST00000396625.3	-	30	2837	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	COL4A4_ENST00000329662.7_Missense_Mutation_p.R877Q	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	877	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TGCCCCAGGCCGTCCTGGGAG	0.627													C|||	26	0.00519169	0.0	0.0	5008	,	,		15399	0.0258		0.0	False		,,,				2504	0.0				p.R877Q		Atlas-SNP	.											.	COL4A4	215	.	0			c.G2630A						PASS	.	C	GLN/ARG	4,3654		0,4,1825	36.0	39.0	39.0		2630	-1.9	0.0	2	dbSNP_134	39	27,8121		0,27,4047	no	missense	COL4A4	NM_000092.4	43	0,31,5872	TT,TC,CC		0.3314,0.1093,0.2626	benign	877/1691	227920747	31,11775	1829	4074	5903	SO:0001583	missense	1286	exon30			CCAGGCCGTCCTG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2630G>A	2.37:g.227920747C>T	ENSP00000379866:p.Arg877Gln	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	224	0.10256410256410256	71	0.1443089430894309	23	0.06353591160220995	44	0.07692307692307693	86	0.11345646437994723	C	3.151	-0.174203	0.06421	0.001093	0.003314	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93307	-3.2;-3.2	5.63	-1.9	0.07665	.	.	.	.	.	T	0.02533	0.0077	N	0.16743	0.435	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.40701	-0.9549	9	0.13470	T	0.59	.	2.2257	0.03983	0.2432:0.4338:0.1032:0.2199	.	877	P53420	CO4A4_HUMAN	Q	877	ENSP00000379866:R877Q;ENSP00000328553:R877Q	ENSP00000328553:R877Q	R	-	2	0	COL4A4	227628991	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.006000	0.13152	-0.756000	0.04703	-0.271000	0.10264	CGG	C|0.930;T|0.070	0.070	strong		0.627	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
MORN4	118812	hgsc.bcm.edu	37	10	99376152	99376152	+	Silent	SNP	A	A	G	rs3814556	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99376152A>G	ENST00000307450.6	-	5	472	c.309T>C	c.(307-309)ccT>ccC	p.P103P	PI4K2A_ENST00000555577.1_Intron|MORN4_ENST00000335628.3_Silent_p.P161P|MORN4_ENST00000478953.1_Nonstop_Mutation_p.*67R|PI4K2A_ENST00000370649.3_Intron	NM_001098831.1|NM_178832.3	NP_001092301.1|NP_849154.1	Q8NDC4	MORN4_HUMAN	MORN repeat containing 4	103								p.P103P(2)		large_intestine(1)|lung(1)|stomach(2)	4						GAGAACCATCAGGGAAAGTCA	0.493													G|||	1675	0.334465	0.6142	0.2608	5008	,	,		21271	0.2837		0.1978	False		,,,				2504	0.2014				p.P103P		Atlas-SNP	.											MORN4_ENST00000307450,NS,carcinoma,0,2	MORN4	24	2	2	Substitution - coding silent(2)	stomach(2)	c.T309C						PASS	.	G	,	2385,2021	560.3+/-380.4	650,1085,468	45.0	44.0	44.0		309,309	-10.1	0.1	10	dbSNP_107	44	1889,6711	724.4+/-406.5	195,1499,2606	no	coding-synonymous,coding-synonymous	MORN4	NM_001098831.1,NM_178832.3	,	845,2584,3074	GG,GA,AA		21.9651,45.8693,32.8618	,	103/147,103/147	99376152	4274,8732	2203	4300	6503	SO:0001819	synonymous_variant	118812	exon5			ACCATCAGGGAAA	AJ431726	CCDS7468.1	10q24.2	2008-06-23	2008-06-23	2008-06-23	ENSG00000171160	ENSG00000171160			24001	protein-coding gene	gene with protein product	"""44050 protein"""		"""chromosome 10 open reading frame 83"""	C10orf83		12477932	Standard	NM_178832		Approved	bA548K23.4, FLJ25925	uc001koe.3	Q8NDC4	OTTHUMG00000018861	ENST00000307450.6:c.309T>C	10.37:g.99376152A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	50	22	0.44	NM_001098831	Q86Y54	Silent	SNP	ENST00000307450.6	37	CCDS7468.1	697	0.3191391941391941	298	0.6056910569105691	95	0.26243093922651933	161	0.28146853146853146	143	0.18865435356200527	G	1.553	-0.538700	0.04053	0.541307	0.219651	ENSG00000171160	ENST00000478953	.	.	.	5.03	-10.1	0.00402	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999911	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.3015	3.4743	0.07578	0.3815:0.164:0.3555:0.0991	rs3814556;rs17850630;rs60361165;rs3814556	.	.	.	R	67	.	.	X	-	1	0	MORN4	99366142	0.000000	0.05858	0.146000	0.22360	0.884000	0.51177	-2.921000	0.00693	-3.319000	0.00188	-1.163000	0.01768	TGA	A|0.673;G|0.327	0.327	strong		0.493	MORN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049730.1	NM_178832	
C21orf91	54149	hgsc.bcm.edu	37	21	19169155	19169155	+	Missense_Mutation	SNP	G	G	C	rs1047978	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:19169155G>C	ENST00000400558.3	-	3	498	c.408C>G	c.(406-408)gaC>gaG	p.D136E	C21orf91_ENST00000284881.4_Missense_Mutation_p.D136E|C21orf91_ENST00000400559.3_Missense_Mutation_p.D136E|AL109761.5_ENST00000428689.1_RNA|C21orf91_ENST00000493464.1_5'UTR	NM_001100421.1	NP_001093891.1			chromosome 21 open reading frame 91											endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9				Epithelial(23;8.76e-05)|all cancers(11;0.000422)|OV - Ovarian serous cystadenocarcinoma(11;0.0107)|Lung(58;0.0129)|COAD - Colon adenocarcinoma(22;0.0303)|LUSC - Lung squamous cell carcinoma(23;0.0381)|Colorectal(24;0.0929)		GTACTTGGGAGTCAAACTGTG	0.388													G|||	1305	0.260583	0.0431	0.3112	5008	,	,		17958	0.3383		0.3996	False		,,,				2504	0.2955				p.D136E		Atlas-SNP	.											.	C21orf91	21	.	0			c.C408G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP	258,3392		9,240,1576	135.0	122.0	126.0		408,408,408	3.4	1.0	21	dbSNP_86	126	2813,5373		495,1823,1775	yes	missense,missense,missense	C21orf91	NM_001100420.1,NM_001100421.1,NM_017447.3	45,45,45	504,2063,3351	CC,CG,GG		34.3635,7.0685,25.9463	probably-damaging,probably-damaging,probably-damaging	136/298,136/222,136/297	19169155	3071,8765	1825	4093	5918	SO:0001583	missense	54149	exon3			TTGGGAGTCAAAC	AF239726	CCDS42907.1, CCDS42908.1, CCDS42909.1	21q21.1	2011-12-12	2003-07-22		ENSG00000154642	ENSG00000154642			16459	protein-coding gene	gene with protein product	"""cold sore susceptibility gene 1"", ""early undifferentiated retina and lens"""		"""chromosome 21 open reading frame 38"""	C21orf38, C21orf14		22039568	Standard	NM_001100421		Approved	YG81, EURL, CSSG1	uc002yko.4	Q9NYK6	OTTHUMG00000074509	ENST00000400558.3:c.408C>G	21.37:g.19169155G>C	ENSP00000383403:p.Asp136Glu	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	81	43	0.530864	NM_017447		Missense_Mutation	SNP	ENST00000400558.3	37	CCDS42909.1	655	0.2999084249084249	25	0.0508130081300813	118	0.3259668508287293	211	0.3688811188811189	301	0.3970976253298153	G	18.17	3.565398	0.65651	0.070685	0.343635	ENSG00000154642	ENST00000284881;ENST00000400559;ENST00000400558;ENST00000405964	T;T;T;T	0.24908	1.83;1.83;1.83;1.83	6.16	3.36	0.38483	.	0.083092	0.85682	D	0.000000	T	0.00012	0.0000	M	0.70275	2.135	0.09310	P	0.9999999999974772	P;D	0.52996	0.946;0.957	B;P	0.47376	0.41;0.545	T	0.46414	-0.9193	8	.	.	.	-20.4981	9.6083	0.39648	0.2714:0.0:0.7286:0.0	rs1047978;rs3174905;rs17695314;rs17845464;rs17858342;rs52816870;rs1047978	136;136	Q9NYK6-3;Q9NYK6	.;EURL_HUMAN	E	136	ENSP00000284881:D136E;ENSP00000383404:D136E;ENSP00000383403:D136E;ENSP00000385566:D136E	.	D	-	3	2	C21orf91	18091026	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	0.841000	0.27613	0.924000	0.37069	0.650000	0.86243	GAC	G|0.690;C|0.310	0.310	strong		0.388	C21orf91-002	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000158214.1	NM_017447	
KRT75	9119	hgsc.bcm.edu	37	12	52824352	52824352	+	Silent	SNP	G	G	A	rs395623	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52824352G>A	ENST00000252245.5	-	5	1228	c.1008C>T	c.(1006-1008)gcC>gcT	p.A336A	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	336	Coil 2.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		ACTCAGCCTCGGCCCGGCTGC	0.552													G|||	1214	0.242412	0.0272	0.232	5008	,	,		19985	0.4494		0.3708	False		,,,				2504	0.1953				p.A336A		Atlas-SNP	.											.	KRT75	75	.	0			c.C1008T						PASS	.	G		317,4089	170.9+/-201.2	15,287,1901	178.0	160.0	166.0		1008	-11.5	0.1	12	dbSNP_80	166	3227,5373	487.3+/-372.1	610,2007,1683	no	coding-synonymous	KRT75	NM_004693.2		625,2294,3584	AA,AG,GG		37.5233,7.1947,27.249		336/552	52824352	3544,9462	2203	4300	6503	SO:0001819	synonymous_variant	9119	exon5			AGCCTCGGCCCGG	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.1008C>T	12.37:g.52824352G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	50	0.442478	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																			G|0.709;A|0.291	0.291	strong		0.552	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
SLC39A4	55630	hgsc.bcm.edu	37	8	145641417	145641417	+	Missense_Mutation	SNP	G	G	A	rs117535951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145641417G>A	ENST00000301305.3	-	2	356	c.251C>T	c.(250-252)cCg>cTg	p.P84L	SLC39A4_ENST00000531013.1_5'Flank|SLC39A4_ENST00000276833.5_Missense_Mutation_p.P59L	NM_130849.2	NP_570901	Q6P5W5	S39A4_HUMAN	solute carrier family 39 (zinc transporter), member 4	84			P -> L (in AEZ; unknown pathological significance). {ECO:0000269|PubMed:12032886}.		cellular response to zinc ion starvation (GO:0034224)|cellular zinc ion homeostasis (GO:0006882)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	14	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;1.12e-40)|all cancers(56;8.17e-36)|BRCA - Breast invasive adenocarcinoma(115;0.0407)|Colorectal(110;0.055)			GACCGGGCCCGGGGGCAGCCC	0.731													G|||	65	0.0129792	0.003	0.013	5008	,	,		13157	0.0		0.0477	False		,,,				2504	0.0041				p.P84L		Atlas-SNP	.											.	SLC39A4	54	.	0			c.C251T	GRCh37	CM021683	SLC39A4	M	rs117535951	PASS	.	G	LEU/PRO,LEU/PRO	26,4332		1,24,2154	8.0	12.0	11.0		176,251	-1.0	0.0	8	dbSNP_132	11	301,8215		4,293,3961	no	missense,missense	SLC39A4	NM_017767.2,NM_130849.2	98,98	5,317,6115	AA,AG,GG		3.5345,0.5966,2.54	benign,benign	59/623,84/648	145641417	327,12547	2179	4258	6437	SO:0001583	missense	55630	exon2			GGGCCCGGGGGCA	AK025537	CCDS6424.1, CCDS43782.1	8q24.3	2013-05-22			ENSG00000147804	ENSG00000147804		"""Solute carriers"""	17129	protein-coding gene	gene with protein product		607059	"""acrodermatitis enteropathica, zinc-deficiency type"""	AEZ		12801924, 12659941, 14709598	Standard	NM_017767		Approved	ZIP4, AWMS2	uc003zcq.3	Q6P5W5		ENST00000301305.3:c.251C>T	8.37:g.145641417G>A	ENSP00000301305:p.Pro84Leu	Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	25	18	0.72	NM_130849	Q7L5S5|Q9H6T8|Q9NXC4	Missense_Mutation	SNP	ENST00000301305.3	37	CCDS6424.1	44	0.020146520146520148	3	0.006097560975609756	7	0.019337016574585635	0	0.0	34	0.044854881266490766	G	13.11	2.140083	0.37728	0.005966	0.035345	ENSG00000147804	ENST00000276833;ENST00000301305	T;T	0.54866	0.55;0.55	4.17	-1.05	0.10036	.	1.964980	0.02332	N	0.073983	T	0.07188	0.0182	N	0.14661	0.345	0.09310	N	1	P;P	0.38745	0.645;0.645	B;B	0.30251	0.058;0.113	T	0.05037	-1.0910	10	0.18276	T	0.48	3.0E-4	3.5004	0.07670	0.0903:0.1321:0.4503:0.3273	.	84;59	Q6P5W5;A6NDY5	S39A4_HUMAN;.	L	59;84	ENSP00000276833:P59L;ENSP00000301305:P84L	ENSP00000276833:P59L	P	-	2	0	SLC39A4	145612225	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-0.417000	0.07088	-0.101000	0.12219	0.306000	0.20318	CCG	G|0.980;A|0.020	0.020	strong		0.731	SLC39A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382688.1		
JAKMIP1	152789	hgsc.bcm.edu	37	4	6114561	6114561	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:6114561C>T	ENST00000282924.5	-	2	502	c.17G>A	c.(16-18)cGg>cAg	p.R6Q	JAKMIP1_ENST00000457227.2_Intron|JAKMIP1_ENST00000410077.2_Missense_Mutation_p.R6Q|JAKMIP1_ENST00000409371.3_Missense_Mutation_p.R6Q|JAKMIP1_ENST00000409021.3_Missense_Mutation_p.R6Q|JAKMIP1_ENST00000409831.1_Missense_Mutation_p.R6Q	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	6	Mediates association with microtubules.				cognition (GO:0050890)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|microtubule (GO:0005874)|ribonucleoprotein complex (GO:0030529)	GABA receptor binding (GO:0050811)|RNA binding (GO:0003723)			NS(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						GCCCTTGCTCCGGCCTTTCTT	0.627																																					p.R6Q		Atlas-SNP	.											JAKMIP1_ENST00000409021,caecum,carcinoma,0,6	JAKMIP1	250	6	0			c.G17A						scavenged	.						103.0	80.0	88.0					4																	6114561		2203	4300	6503	SO:0001583	missense	152789	exon2			TTGCTCCGGCCTT	AK056126	CCDS3385.1, CCDS47005.1	4p16.1	2013-10-11	2009-08-13		ENSG00000152969	ENSG00000152969			26460	protein-coding gene	gene with protein product		611195				18941173	Standard	NM_144720		Approved	MARLIN1, JAMIP1, Gababrbp, FLJ31564	uc010idb.1	Q96N16	OTTHUMG00000125491	ENST00000282924.5:c.17G>A	4.37:g.6114561C>T	ENSP00000282924:p.Arg6Gln	Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	74	2	0.027027	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Missense_Mutation	SNP	ENST00000282924.5	37	CCDS3385.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740462	0.89573	.	.	ENSG00000152969	ENST00000409021;ENST00000409371;ENST00000418227;ENST00000425341;ENST00000429819;ENST00000282924;ENST00000409831;ENST00000410077	T;T;T;T;T	0.40756	1.39;1.07;1.38;1.38;1.02	3.94	3.94	0.45596	.	0.000000	0.64402	D	0.000015	T	0.55893	0.1949	M	0.74881	2.28	0.30624	N	0.758174	D;D;D;D;D	0.64830	0.989;0.977;0.994;0.989;0.977	P;P;P;P;P	0.53224	0.581;0.525;0.721;0.581;0.601	T	0.65117	-0.6246	10	0.87932	D	0	.	15.1499	0.72689	0.0:1.0:0.0:0.0	.	6;6;6;6;6	B4DHZ8;F2Z2K5;Q96N16-5;Q96N16-2;Q96N16	.;.;.;.;JKIP1_HUMAN	Q	6	ENSP00000386711:R6Q;ENSP00000387042:R6Q;ENSP00000282924:R6Q;ENSP00000386925:R6Q;ENSP00000386745:R6Q	ENSP00000282924:R6Q	R	-	2	0	JAKMIP1	6165462	0.999000	0.42202	1.000000	0.80357	0.647000	0.38526	5.164000	0.64954	2.041000	0.60428	0.591000	0.81541	CGG	.	.	none		0.627	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720	
C12orf71	728858	hgsc.bcm.edu	37	12	27234200	27234200	+	Silent	SNP	T	T	C	rs708165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:27234200T>C	ENST00000429849.2	-	2	747	c.717A>G	c.(715-717)aaA>aaG	p.K239K		NM_001080406.1	NP_001073875.1	A8MTZ7	CL071_HUMAN	chromosome 12 open reading frame 71	239										endometrium(2)|large_intestine(1)|lung(4)|skin(1)	8						GATGGGGACTTTTGGTGGCAT	0.522													C|||	1003	0.20028	0.1316	0.2176	5008	,	,		19100	0.0357		0.4433	False		,,,				2504	0.2004				p.K239K		Atlas-SNP	.											.	C12orf71	20	.	0			c.A717G						PASS	.	C		744,3398		66,612,1393	89.0	87.0	88.0		717	0.2	0.0	12	dbSNP_86	88	3764,4680		843,2078,1301	no	coding-synonymous	C12orf71	NM_001080406.1		909,2690,2694	CC,CT,TT		44.576,17.9623,35.8176		239/270	27234200	4508,8078	2071	4222	6293	SO:0001819	synonymous_variant	728858	exon2			GGGACTTTTGGTG		CCDS44851.1	12p11.23	2008-07-25			ENSG00000214700	ENSG00000214700			34452	protein-coding gene	gene with protein product							Standard	NM_001080406		Approved	LOC728858	uc001rhq.3	A8MTZ7	OTTHUMG00000169274	ENST00000429849.2:c.717A>G	12.37:g.27234200T>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	55	25	0.454545	NM_001080406		Silent	SNP	ENST00000429849.2	37	CCDS44851.1																																																																																			T|0.739;C|0.261	0.261	strong		0.522	C12orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403258.1	NM_001080406	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417718	138417718	+	Silent	SNP	A	A	G	rs3807154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:138417718A>G	ENST00000310018.2	-	17	2094	c.1812T>C	c.(1810-1812)caT>caC	p.H604H	ATP6V0A4_ENST00000393054.1_Silent_p.H604H|ATP6V0A4_ENST00000353492.4_Silent_p.H604H	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	604			H -> Q (in dbSNP:rs3807154).		ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						GCTGAGATACATGGACGTCAA	0.423													A|||	3393	0.677516	0.4236	0.7824	5008	,	,		16443	0.8472		0.7237	False		,,,				2504	0.7239				p.H604H		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.T1812C						PASS	.	A	,,	2049,2357	567.3+/-382.1	480,1089,634	141.0	129.0	133.0		1812,1812,1812	0.5	0.0	7	dbSNP_107	133	6185,2415	699.3+/-405.1	2233,1719,348	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	,,	2713,2808,982	GG,GA,AA		28.0814,46.5048,36.6908	,,	604/841,604/841,604/841	138417718	8234,4772	2203	4300	6503	SO:0001819	synonymous_variant	50617	exon16			AGATACATGGACG	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1812T>C	7.37:g.138417718A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_130841	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																			A|0.340;G|0.660	0.660	strong		0.423	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632782	32632782	+	Missense_Mutation	SNP	G	G	A	rs12722115	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32632782G>A	ENST00000399084.1	-	3	350	c.172C>T	c.(172-174)Ctt>Ttt	p.L58F	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.L58F|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.L58F|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.L58F|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	58	Beta-1.		Y -> G (in allele DQB1*03:05, allele DQB1*03:17, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:23; requires 2 nucleotide substitutions).|Y -> L (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:15, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	CTGGTCACAAGACGCACGCGC	0.632									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.L58F	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C172T						PASS	.						28.0	30.0	29.0					6																	32632782		2115	4196	6311	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCACAAGACGCAC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.172C>T	6.37:g.32632782G>A	ENSP00000382034:p.Leu58Phe	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	33	22	0.666667	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399084.1	37	CCDS43451.1	691	0.3163919413919414	162	0.32926829268292684	112	0.30939226519337015	223	0.38986013986013984	194	0.2559366754617414	.	0.009	-1.808428	0.00606	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.00291	8.27;8.27;8.27;8.27	3.91	-7.81	0.01210	.	1.484940	0.04916	U	0.454080	T	0.00039	0.0001	L	0.28608	0.87	0.80722	P	0.0	P;B;B;B;B	0.49783	0.928;0.204;0.002;0.001;0.0	B;B;B;B;B	0.39738	0.308;0.127;0.009;0.013;0.005	T	0.54906	-0.8223	9	0.02654	T	1	.	3.2276	0.06737	0.4621:0.2728:0.1732:0.0919	rs12722115	68;58;23;58;58	Q59F80;A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.;.	F	58	ENSP00000382029:L58F;ENSP00000364080:L58F;ENSP00000407332:L58F;ENSP00000382034:L58F	ENSP00000364080:L58F	L	-	1	0	HLA-DQB1	32740760	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.064000	0.00025	-3.742000	0.00113	-2.356000	0.00241	CTT	G|0.644;C|0.073;A|0.283	0.283	strong		0.632	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
FAM129C	199786	hgsc.bcm.edu	37	19	17650053	17650053	+	Silent	SNP	G	G	A	rs74546231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17650053G>A	ENST00000335393.4	+	7	921	c.783G>A	c.(781-783)gtG>gtA	p.V261V	FAM129C_ENST00000300971.2_Silent_p.V261V|FAM129C_ENST00000332386.5_Silent_p.V261V|FAM129C_ENST00000599164.1_Silent_p.V230V|FAM129C_ENST00000352727.3_Silent_p.V261V|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000600871.1_Silent_p.V207V|FAM129C_ENST00000595684.1_Silent_p.V261V|FAM129C_ENST00000599124.1_Silent_p.V230V|FAM129C_ENST00000601861.1_Silent_p.V230V	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	261										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						ACGACGACGTGACCCTAGGCT	0.726													g|||	95	0.0189696	0.0023	0.0274	5008	,	,		12413	0.0		0.0636	False		,,,				2504	0.0092				p.V261V		Atlas-SNP	.											FAM129C_ENST00000332386,NS,carcinoma,0,2	FAM129C	110	2	0			c.G783A						PASS	.	G	,	67,4321		1,65,2128	19.0	19.0	19.0		783,783	0.5	1.0	19	dbSNP_132	19	594,7986		21,552,3717	no	coding-synonymous,coding-synonymous	FAM129C	NM_001098524.1,NM_173544.4	,	22,617,5845	AA,AG,GG		6.9231,1.5269,5.0972	,	261/652,261/698	17650053	661,12307	2194	4290	6484	SO:0001819	synonymous_variant	199786	exon7			CGACGTGACCCTA	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.783G>A	19.37:g.17650053G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																			G|0.962;A|0.038	0.038	strong		0.726	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
AEN	64782	hgsc.bcm.edu	37	15	89169653	89169653	+	Silent	SNP	G	G	A	rs34649587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89169653G>A	ENST00000332810.3	+	2	364	c.213G>A	c.(211-213)gcG>gcA	p.A71A	AEN_ENST00000379231.3_Silent_p.A71A	NM_022767.3	NP_073604.3	Q8WTP8	AEN_HUMAN	apoptosis enhancing nuclease	71					intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)			NS(1)|kidney(1)|large_intestine(1)|lung(4)	7						TCGGGGCAGCGACAGCAACTG	0.657													G|||	202	0.0403355	0.0461	0.0245	5008	,	,		15562	0.002		0.0457	False		,,,				2504	0.0777				p.A71A		Atlas-SNP	.											.	AEN	29	.	0			c.G213A						PASS	.	G		179,4217	107.8+/-146.2	4,171,2023	27.0	27.0	27.0		213	-8.9	0.0	15	dbSNP_126	27	353,8241	114.2+/-174.2	3,347,3947	no	coding-synonymous	AEN	NM_022767.3		7,518,5970	AA,AG,GG		4.1075,4.0719,4.0955		71/326	89169653	532,12458	2198	4297	6495	SO:0001819	synonymous_variant	64782	exon2			GGCAGCGACAGCA	BC020988	CCDS10344.1	15q26.1	2008-07-15	2008-07-15	2008-07-15	ENSG00000181026	ENSG00000181026			25722	protein-coding gene	gene with protein product		610177	"""interferon stimulated exonuclease gene 20kDa-like 1"""	ISG20L1		18264133, 16171785	Standard	NM_022767		Approved	FLJ12484, FLJ12562	uc002bmt.2	Q8WTP8	OTTHUMG00000148681	ENST00000332810.3:c.213G>A	15.37:g.89169653G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_022767	C9J571|Q9BSA5|Q9H9X7	Silent	SNP	ENST00000332810.3	37	CCDS10344.1																																																																																			G|0.963;A|0.037	0.037	strong		0.657	AEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309071.1	NM_022767	
CCDC68	80323	hgsc.bcm.edu	37	18	52605188	52605188	+	Splice_Site	SNP	C	C	T	rs1344011|rs17852674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:52605188C>T	ENST00000591504.1	-	5	619	c.345G>A	c.(343-345)aaG>aaA	p.K115K	CCDC68_ENST00000337363.4_Splice_Site_p.K115K|CCDC68_ENST00000432185.1_Splice_Site_p.K115K	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	115										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|stomach(1)	14				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		AAAGTCATACCTTGATTTTCA	0.353													C|||	891	0.177915	0.0106	0.1542	5008	,	,		17983	0.3036		0.2455	False		,,,				2504	0.2219				p.K115K		Atlas-SNP	.											.	CCDC68	38	.	0			c.G345A						PASS	.	C	,	206,4200	123.7+/-161.0	8,190,2005	106.0	98.0	101.0		345,345	5.7	1.0	18	dbSNP_88	101	1979,6621	338.9+/-322.9	233,1513,2554	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	CCDC68	NM_001143829.1,NM_025214.2	,	241,1703,4559	TT,TC,CC		23.0116,4.6754,16.7999	,	115/336,115/336	52605188	2185,10821	2203	4300	6503	SO:0001630	splice_region_variant	80323	exon5			TCATACCTTGATT		CCDS11959.1	18q21	2006-02-07			ENSG00000166510	ENSG00000166510			24350	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma associated antigen"""					11149944, 15142679	Standard	NM_025214		Approved	SE57-1	uc002lft.3	Q9H2F9	OTTHUMG00000132708	ENST00000591504.1:c.345+1G>A	18.37:g.52605188C>T		Somatic	245	0	0		WXS	Illumina HiSeq	Phase_I	207	99	0.478261	NM_025214	B2R9I3	Silent	SNP	ENST00000591504.1	37	CCDS11959.1																																																																																			C|0.784;T|0.216	0.216	strong		0.353	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256006.1	NM_025214	Silent
ANKHD1	54882	hgsc.bcm.edu	37	5	139838786	139838786	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:139838786A>C	ENST00000360839.2	+	9	1672	c.1518A>C	c.(1516-1518)gaA>gaC	p.E506D	ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.E506D|ANKHD1_ENST00000297183.6_Missense_Mutation_p.E506D|ANKHD1_ENST00000394723.3_Missense_Mutation_p.E506D|ANKHD1_ENST00000394722.3_Missense_Mutation_p.E495D	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	506						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAACTCAAGAAACTGCTCTTA	0.363																																					p.E506D		Atlas-SNP	.											ANKHD1-EIF4EBP3,rectum,carcinoma,+2,2	ANKHD1	233	2	0			c.A1518C						PASS	.						75.0	77.0	76.0					5																	139838786		2203	4300	6503	SO:0001583	missense	54882	exon9			TCAAGAAACTGCT	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1518A>C	5.37:g.139838786A>C	ENSP00000354085:p.Glu506Asp	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	150	70	0.466667	NM_024668	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.912101	0.72983	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	T;T;T;T;T;T	0.64618	-0.11;-0.11;2.39;2.39;2.39;-0.11	5.51	5.51	0.81932	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.61565	0.2357	N	0.11927	0.2	0.58432	D	0.999997	D;D;D;D;D	0.89917	0.999;0.997;0.992;0.971;1.0	D;D;D;P;D	0.80764	0.98;0.992;0.989;0.77;0.994	T	0.66826	-0.5825	10	0.62326	D	0.03	.	9.8994	0.41338	0.879:0.0:0.121:0.0	.	506;506;506;495;506	Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.;.;ANKH1_HUMAN;.;.	D	506;520;506;506;21;506;506;495;506	ENSP00000354085:E506D;ENSP00000297183:E506D;ENSP00000394489:E506D;ENSP00000378212:E506D;ENSP00000378211:E495D;ENSP00000432016:E506D	ENSP00000432016:E506D	E	+	3	2	ANKHD1-EIF4EBP3;ANKHD1	139818970	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.935000	0.56560	2.105000	0.64084	0.454000	0.30748	GAA	.	.	none		0.363	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	
MUC4	4585	hgsc.bcm.edu	37	3	195510133	195510133	+	Missense_Mutation	SNP	T	T	C	rs371587475		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195510133T>C	ENST00000463781.3	-	2	8777	c.8318A>G	c.(8317-8319)aAc>aGc	p.N2773S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.N2773S	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.N2773S(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)		TGAGGAAGTGTTGGTGACAGG	0.582																																					p.N2773S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	1	Substitution - Missense(1)	kidney(1)	c.A8318G						scavenged	.						42.0	25.0	30.0					3																	195510133		688	1543	2231	SO:0001583	missense	4585	exon2			GAAGTGTTGGTGA	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.8318A>G	3.37:g.195510133T>C	ENSP00000417498:p.Asn2773Ser	Somatic	229	5	0.0218341		WXS	Illumina HiSeq	Phase_I	123	7	0.0569106	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	0.344	-0.948616	0.02304	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.5;1.44	1.02	-1.52	0.08637	.	.	.	.	.	T	0.10465	0.0256	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.32929	-0.9888	8	.	.	.	.	4.3758	0.11270	0.0:0.4779:0.0:0.5221	.	2645	E7ESK3	.	S	2773	ENSP00000417498:N2773S;ENSP00000420243:N2773S	.	N	-	2	0	MUC4	196994912	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-4.761000	0.00189	-0.419000	0.07439	0.063000	0.15292	AAC	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC16	94025	hgsc.bcm.edu	37	19	9072875	9072875	+	Silent	SNP	G	G	A	rs73009098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9072875G>A	ENST00000397910.4	-	3	14774	c.14571C>T	c.(14569-14571)gtC>gtT	p.V4857V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4859	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						TTGGAGATGTGACTTTAGATG	0.438													G|||	935	0.186701	0.0923	0.2536	5008	,	,		24451	0.3254		0.1322	False		,,,				2504	0.18				p.V4857V		Atlas-SNP	.											.	MUC16	4315	.	0			c.C14571T						PASS	.			389,3697		16,357,1670	186.0	175.0	179.0		14571	-1.3	0.0	19	dbSNP_130	179	1160,7216		73,1014,3101	no	coding-synonymous	MUC16	NM_024690.2		89,1371,4771	AA,AG,GG		13.8491,9.5203,12.4298		4857/14508	9072875	1549,10913	2043	4188	6231	SO:0001819	synonymous_variant	94025	exon3			AGATGTGACTTTA	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.14571C>T	19.37:g.9072875G>A		Somatic	442	0	0		WXS	Illumina HiSeq	Phase_I	441	204	0.462585	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.809;A|0.191	0.191	strong		0.438	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
RNF43	54894	hgsc.bcm.edu	37	17	56435885	56435885	+	Missense_Mutation	SNP	G	G	T	rs2526374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56435885G>T	ENST00000584437.1	-	8	3207	c.1252C>A	c.(1252-1254)Ctg>Atg	p.L418M	RNF43_ENST00000577716.1_Missense_Mutation_p.L418M|RNF43_ENST00000407977.2_Missense_Mutation_p.L418M|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Missense_Mutation_p.L291M|RNF43_ENST00000500597.2_Missense_Mutation_p.L377M|RNF43_ENST00000577625.1_Missense_Mutation_p.L291M|RNF43_ENST00000583753.1_Missense_Mutation_p.L377M			Q68DV7	RNF43_HUMAN	ring finger protein 43	418			L -> M (in dbSNP:rs2526374). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15492824}.		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGTGGCTCAGTCCCCAGCCT	0.662													G|||	2001	0.399561	0.4009	0.4669	5008	,	,		16939	0.4494		0.329	False		,,,				2504	0.3712				p.L418M		Atlas-SNP	.											.	RNF43	157	.	0			c.C1252A						PASS	.	G	MET/LEU	1773,2633	519.1+/-369.9	380,1013,810	32.0	35.0	34.0		1252	4.2	0.0	17	dbSNP_100	34	3088,5512	466.1+/-366.7	565,1958,1777	yes	missense	RNF43	NM_017763.4	15	945,2971,2587	TT,TG,GG		35.907,40.2406,37.3751	possibly-damaging	418/784	56435885	4861,8145	2203	4300	6503	SO:0001583	missense	54894	exon9			GGCTCAGTCCCCA		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1252C>A	17.37:g.56435885G>T	ENSP00000463069:p.Leu418Met	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	868	0.3974358974358974	199	0.40447154471544716	163	0.45027624309392267	257	0.4493006993006993	249	0.32849604221635886	G	12.56	1.974857	0.34848	0.402406	0.35907	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09255	3.15;3.0	4.2	4.2	0.49525	.	0.272333	0.30492	N	0.009510	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D;D;P	0.61697	0.969;0.99;0.948	P;P;P	0.58266	0.677;0.836;0.478	T	0.46693	-0.9173	9	0.51188	T	0.08	-12.9741	9.6456	0.39865	0.1015:0.0:0.8985:0.0	rs2526374;rs3744094;rs17222355;rs56712610;rs2526374	377;418;418	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	M	418;377	ENSP00000385328:L418M;ENSP00000441969:L377M	ENSP00000385328:L418M	L	-	1	2	RNF43	53790884	0.025000	0.19082	0.040000	0.18447	0.574000	0.36063	2.082000	0.41605	2.179000	0.69175	0.195000	0.17529	CTG	G|0.612;T|0.388	0.388	strong		0.662	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
DSPP	1834	hgsc.bcm.edu	37	4	88536919	88536919	+	Silent	SNP	T	T	C	rs369387818		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88536919T>C	ENST00000282478.7	+	4	3138	c.3105T>C	c.(3103-3105)gaT>gaC	p.D1035D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1035D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1035	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.D1035D(2)		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)		acagcagcgatagcagtgaca	0.517																																					p.D1035D		Atlas-SNP	.											DSPP,NS,carcinoma,0,3	DSPP	174	3	2	Substitution - coding silent(2)	kidney(2)	c.T3105C						PASS	.						63.0	70.0	67.0					4																	88536919		1560	2747	4307	SO:0001819	synonymous_variant	1834	exon5			CAGCGATAGCAGT	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.3105T>C	4.37:g.88536919T>C		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	134	26	0.19403	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	
CAPN15	6650	hgsc.bcm.edu	37	16	602313	602313	+	Silent	SNP	C	C	A	rs9930550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:602313C>A	ENST00000219611.2	+	11	2883	c.2520C>A	c.(2518-2520)gcC>gcA	p.A840A	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	840					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCTCGGACGCCGTGGACAGCC	0.736													a|||	3181	0.635184	0.6248	0.5951	5008	,	,		13115	0.8393		0.3569	False		,,,				2504	0.7536				p.A840A		Atlas-SNP	.											SOLH,NS,carcinoma,0,2	SOLH	47	2	0			c.C2520A						scavenged	.	A		2415,1821		744,927,447	7.0	9.0	9.0		2520	-10.8	0.0	16	dbSNP_119	9	3038,5314		594,1850,1732	no	coding-synonymous	SOLH	NM_005632.2		1338,2777,2179	AA,AC,CC		36.3745,42.9887,43.319		840/1087	602313	5453,7135	2118	4176	6294	SO:0001819	synonymous_variant	6650	exon11			GGACGCCGTGGAC	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2520C>A	16.37:g.602313C>A		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																			C|0.433;A|0.567	0.567	strong		0.736	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
CHST12	55501	hgsc.bcm.edu	37	7	2472429	2472429	+	Missense_Mutation	SNP	C	C	A	rs3735099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:2472429C>A	ENST00000258711.6	+	2	290	c.155C>A	c.(154-156)cCc>cAc	p.P52H		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	52			P -> H (in dbSNP:rs3735099).		carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CTGCCCACGCCCGGGCCGGAC	0.642													C|||	378	0.0754792	0.0144	0.0562	5008	,	,		15137	0.1538		0.0398	False		,,,				2504	0.1278				p.P52H		Atlas-SNP	.											.	CHST12	39	.	0			c.C155A						PASS	.	C	HIS/PRO	76,4326	65.8+/-103.3	1,74,2126	44.0	52.0	49.0		155	4.0	0.0	7	dbSNP_107	49	388,8210	122.4+/-181.4	12,364,3923	yes	missense	CHST12	NM_018641.4	77	13,438,6049	AA,AC,CC		4.5127,1.7265,3.5692	benign	52/415	2472429	464,12536	2201	4299	6500	SO:0001583	missense	55501	exon2			CCACGCCCGGGCC	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.155C>A	7.37:g.2472429C>A	ENSP00000258711:p.Pro52His	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	65	39	0.6	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	128	0.05860805860805861	4	0.008130081300813009	21	0.058011049723756904	76	0.13286713286713286	27	0.03562005277044855	C	6.667	0.491694	0.12702	0.017265	0.045127	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.61274	0.12;0.95	4.94	4.03	0.46877	.	0.345170	0.30752	N	0.008949	T	0.00468	0.0015	L	0.29908	0.895	0.80722	P	0.0	P	0.46020	0.871	B	0.41466	0.358	T	0.12016	-1.0564	9	0.49607	T	0.09	-18.3823	4.5533	0.12124	0.2222:0.6374:0.0:0.1405	rs3735099	52	Q9NRB3	CHSTC_HUMAN	H	52	ENSP00000258711:P52H;ENSP00000411207:P52H	ENSP00000258711:P52H	P	+	2	0	CHST12	2438955	0.004000	0.15560	0.047000	0.18901	0.116000	0.19942	1.979000	0.40608	1.017000	0.39495	0.555000	0.69702	CCC	C|0.957;A|0.043	0.043	strong		0.642	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
FBF1	85302	hgsc.bcm.edu	37	17	73910027	73910027	+	Silent	SNP	C	C	T	rs61736662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73910027C>T	ENST00000586717.1	-	26	3324	c.3051G>A	c.(3049-3051)gaG>gaA	p.E1017E	FBF1_ENST00000319129.5_Silent_p.E1017E|FBF1_ENST00000389570.4_Silent_p.E1018E|RP11-552F3.12_ENST00000587556.1_5'Flank			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	1017	Gln-rich.				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						tccgcagccgctcctgctgtt	0.692													C|||	179	0.0357428	0.0477	0.0288	5008	,	,		15400	0.0		0.0517	False		,,,				2504	0.045				p.E1017E		Atlas-SNP	.											.	FBF1	48	.	0			c.G3051A						PASS	.	C		143,4049		2,139,1955	8.0	11.0	10.0		3051	1.4	0.8	17	dbSNP_129	10	335,8069		3,329,3870	no	coding-synonymous	FBF1	NM_001080542.1		5,468,5825	TT,TC,CC		3.9862,3.4113,3.7949		1017/1134	73910027	478,12118	2096	4202	6298	SO:0001819	synonymous_variant	85302	exon26			CAGCCGCTCCTGC	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.3051G>A	17.37:g.73910027C>T		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	66	45	0.681818	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				C|0.964;T|0.036	0.036	strong		0.692	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
IL16	3603	hgsc.bcm.edu	37	15	81598269	81598269	+	Missense_Mutation	SNP	T	T	G	rs11556218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:81598269T>G	ENST00000302987.4	+	16	3441	c.3441T>G	c.(3439-3441)aaT>aaG	p.N1147K	IL16_ENST00000394652.2_Missense_Mutation_p.N446K|IL16_ENST00000394660.2_Missense_Mutation_p.N1147K|RP11-761I4.4_ENST00000607019.1_RNA			Q14005	IL16_HUMAN	interleukin 16	1147	Interaction with PPP1R12A, PPP1R12B and PPP1R12C.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.		N -> K (in dbSNP:rs11556218). {ECO:0000269|Ref.8}.		immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						TGTTTCCAAATGGGCTGGCCT	0.517													T|||	733	0.146366	0.2398	0.1614	5008	,	,		21813	0.1647		0.0746	False		,,,				2504	0.0644				p.N1147K		Atlas-SNP	.											.	IL16	254	.	0			c.T3441G						PASS	.	T	LYS/ASN,LYS/ASN,LYS/ASN	882,3524	339.4+/-305.8	102,678,1423	123.0	136.0	132.0		3441,1338,3441	-6.3	0.0	15	dbSNP_120	132	719,7881	174.0+/-224.4	26,667,3607	yes	missense,missense,missense	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	94,94,94	128,1345,5030	GG,GT,TT		8.3605,20.0182,12.3097	probably-damaging,probably-damaging,probably-damaging	1147/1332,446/632,1147/1333	81598269	1601,11405	2203	4300	6503	SO:0001583	missense	3603	exon17			TCCAAATGGGCTG	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3441T>G	15.37:g.81598269T>G	ENSP00000302935:p.Asn1147Lys	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	331	0.15155677655677655	119	0.241869918699187	51	0.1408839779005525	110	0.19230769230769232	51	0.06728232189973615	T	8.917	0.960140	0.18507	0.200182	0.083605	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.27720	1.65;1.65;1.65	4.64	-6.3	0.02007	PDZ/DHR/GLGF (4);	0.128958	0.35320	N	0.003299	T	0.00012	0.0000	N	0.17345	0.48	0.32261	P	0.5701890000000001	P;D;P;D;D;B	0.89917	0.95;0.989;0.669;1.0;0.977;0.357	D;D;B;D;P;B	0.85130	0.933;0.964;0.265;0.997;0.896;0.344	T	0.07597	-1.0764	9	0.52906	T	0.07	.	11.1807	0.48627	0.0:0.1663:0.0945:0.7392	rs11556218;rs17875535	979;640;684;537;1147;1147	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	K	1147;979;1147;684;537;446;446	ENSP00000378155:N1147K;ENSP00000302935:N1147K;ENSP00000378147:N446K	ENSP00000302935:N1147K	N	+	3	2	IL16	79385324	0.000000	0.05858	0.007000	0.13788	0.001000	0.01503	-1.379000	0.02554	-1.160000	0.02804	-1.815000	0.00603	AAT	T|0.860;G|0.140	0.140	strong		0.517	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
OR5AK2	390181	hgsc.bcm.edu	37	11	56756516	56756516	+	Missense_Mutation	SNP	G	G	C	rs12420424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56756516G>C	ENST00000326855.2	+	1	170	c.128G>C	c.(127-129)aGt>aCt	p.S43T		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	43			S -> T (in dbSNP:rs12420424).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						ATGGGTAATAGTGGAATAATC	0.373													C|||	298	0.0595048	0.0227	0.121	5008	,	,		20007	0.002		0.0825	False		,,,				2504	0.1012				p.S43T		Atlas-SNP	.											.	OR5AK2	45	.	0			c.G128C						PASS	.	C	THR/SER	162,4240	810.9+/-416.0	5,152,2044	126.0	115.0	119.0		128	1.3	0.1	11	dbSNP_120	119	679,7913	786.9+/-407.6	31,617,3648	no	missense	OR5AK2	NM_001005323.1	58	36,769,5692	CC,CG,GG		7.9027,3.6801,6.4722	benign	43/310	56756516	841,12153	2201	4296	6497	SO:0001583	missense	390181	exon1			GTAATAGTGGAAT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.128G>C	11.37:g.56756516G>C	ENSP00000322784:p.Ser43Thr	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	254	136	0.535433	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	117	0.05357142857142857	9	0.018292682926829267	41	0.1132596685082873	2	0.0034965034965034965	65	0.08575197889182058	C	1.888	-0.456271	0.04540	0.036801	0.079027	ENSG00000181273	ENST00000326855	T	0.00438	7.42	3.66	1.29	0.21616	GPCR, rhodopsin-like superfamily (1);	0.682371	0.12010	N	0.507981	T	0.00012	0.0000	N	0.03891	-0.335	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.29336	-1.0015	9	0.62326	D	0.03	-9.7249	4.4129	0.11441	0.0:0.325:0.1707:0.5043	rs12420424	43	Q8NH90	O5AK2_HUMAN	T	43	ENSP00000322784:S43T	ENSP00000322784:S43T	S	+	2	0	OR5AK2	56513092	0.000000	0.05858	0.085000	0.20634	0.153000	0.21895	0.588000	0.23924	-0.114000	0.11936	-1.041000	0.02371	AGT	G|0.938;C|0.062	0.062	strong		0.373	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
FDXACB1	91893	hgsc.bcm.edu	37	11	111747297	111747297	+	Silent	SNP	A	A	G	rs7124696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:111747297A>G	ENST00000260257.4	-	4	647	c.600T>C	c.(598-600)ttT>ttC	p.F200F	C11orf1_ENST00000528125.1_5'Flank|ALG9_ENST00000527377.1_5'UTR|FDXACB1_ENST00000542429.1_Silent_p.F51F|C11orf1_ENST00000530214.1_5'Flank|ALG9_ENST00000524880.1_Silent_p.F200F|C11orf1_ENST00000260276.3_5'Flank	NM_138378.2	NP_612387.1	Q9BRP7	FDXA1_HUMAN	ferredoxin-fold anticodon binding domain containing 1	200					phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA processing (GO:0008033)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(3)	19						GAGAACCTTCAAAAGGTAAGC	0.423													G|||	1228	0.245208	0.1982	0.3228	5008	,	,		20985	0.1944		0.33	False		,,,				2504	0.2188				p.F200F		Atlas-SNP	.											.	FDXACB1	74	.	0			c.T600C						PASS	.	G		805,2911		85,635,1138	127.0	123.0	124.0		600	0.9	0.0	11	dbSNP_116	124	2534,5660		397,1740,1960	no	coding-synonymous	FDXACB1	NM_138378.2		482,2375,3098	GG,GA,AA		30.9251,21.6631,28.0353		200/625	111747297	3339,8571	1858	4097	5955	SO:0001819	synonymous_variant	91893	exon4			ACCTTCAAAAGGT		CCDS44729.1	11q23.1	2011-04-15			ENSG00000255561	ENSG00000255561			25110	protein-coding gene	gene with protein product	"""hypothetical protein BC006136"""						Standard	NR_038364		Approved	LOC91893, hCG_2033039	uc001pmc.4	Q9BRP7	OTTHUMG00000166795	ENST00000260257.4:c.600T>C	11.37:g.111747297A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	94	44	0.468085	NM_138378	A0PJW7|B4DUU2	Silent	SNP	ENST00000260257.4	37	CCDS44729.1																																																																																			A|0.738;G|0.262	0.262	strong		0.423	FDXACB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391497.1	NM_138378	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37488689	37488689	+	Missense_Mutation	SNP	G	G	C	rs1209750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:37488689G>C	ENST00000602533.1	+	30	2682	c.2583G>C	c.(2581-2583)aaG>aaC	p.K861N	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.K980N|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.K861N			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	917					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						AACAAAAGAAGGTTGAAGAAA	0.274													.|||	2415	0.482228	0.671	0.5029	5008	,	,		15886	0.3244		0.5875	False		,,,				2504	0.2669				p.K861N		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.G2583C						PASS	.	C	ASN/LYS	2319,1241		752,815,213	88.0	79.0	81.0		2583	-1.7	0.0	10	dbSNP_87	81	4648,3468		1323,2002,733	yes	missense	ANKRD30A	NM_052997.2	94	2075,2817,946	CC,CG,GG		42.7304,34.8596,40.3306	benign	861/1342	37488689	6967,4709	1780	4058	5838	SO:0001583	missense	91074	exon30			AAAGAAGGTTGAA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.2583G>C	10.37:g.37488689G>C	ENSP00000473551:p.Lys861Asn	Somatic	356	0	0		WXS	Illumina HiSeq	Phase_I	265	264	0.996226	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		1139	0.5215201465201466	324	0.6585365853658537	196	0.5414364640883977	167	0.291958041958042	452	0.5963060686015831	N	0.022	-1.408058	0.01155	0.651404	0.572696	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.05580	3.42;3.42	0.868	-1.74	0.08056	.	.	.	.	.	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.28324	0.207	B	0.18561	0.022	T	0.42275	-0.9461	8	0.27082	T	0.32	.	4.0495	0.09788	0.2908:0.3384:0.3708:0.0	rs1209750;rs1782096;rs16906089;rs17606786;rs52817964;rs1209750	917	Q9BXX3	AN30A_HUMAN	N	861;980	ENSP00000354432:K861N;ENSP00000363792:K980N	ENSP00000354432:K861N	K	+	3	2	ANKRD30A	37528695	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.926000	0.03988	-3.843000	0.00100	-2.001000	0.00444	AAG	A|0.002;C|0.510;G|0.489	0.510	strong		0.274	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
HABP2	3026	hgsc.bcm.edu	37	10	115352005	115352005	+	IGR	SNP	A	A	G	rs11196389	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:115352005A>G	ENST00000351270.3	+	0	3009				NRAP_ENST00000369358.4_Missense_Mutation_p.L1539P|NRAP_ENST00000369360.3_Missense_Mutation_p.L1504P|NRAP_ENST00000359988.3_Missense_Mutation_p.L1531P|NRAP_ENST00000360478.3_Missense_Mutation_p.L1496P	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2						cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	GATGGCATCCAGCCTGAAGTC	0.522													A|||	439	0.0876597	0.0439	0.0735	5008	,	,		14827	0.1062		0.1193	False		,,,				2504	0.1053				p.L1531P		Atlas-SNP	.											.	NRAP	208	.	0			c.T4592C						PASS	.	A	PRO/LEU,PRO/LEU	233,4173	138.8+/-174.5	4,225,1974	76.0	74.0	74.0		4487,4592	5.7	1.0	10	dbSNP_120	74	1052,7548	223.0+/-259.9	69,914,3317	yes	missense,missense	NRAP	NM_006175.3,NM_198060.2	98,98	73,1139,5291	GG,GA,AA		12.2326,5.2882,9.8801	benign,benign	1496/1696,1531/1731	115352005	1285,11721	2203	4300	6503	SO:0001628	intergenic_variant	4892	exon39			GCATCCAGCCTGA		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073		10.37:g.115352005A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	105	63	0.6	NM_001261463	A8K467|B7Z8U5|F5H5M6|O00663	Missense_Mutation	SNP	ENST00000351270.3	37	CCDS7577.1	193	0.08836996336996338	20	0.04065040650406504	27	0.07458563535911603	62	0.10839160839160839	84	0.11081794195250659	A	17.47	3.396449	0.62177	0.052882	0.122326	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.21031	2.29;2.25;2.1;2.03	5.67	5.67	0.87782	.	0.081237	0.51477	D	0.000086	T	0.00608	0.0020	L	0.49513	1.565	0.09310	P	0.999999578023	D;D;D	0.71674	0.997;0.998;0.997	D;D;D	0.74023	0.968;0.982;0.959	T	0.00704	-1.1602	9	0.23891	T	0.37	.	16.2045	0.82114	1.0:0.0:0.0:0.0	rs11196389;rs17699051;rs52828911;rs59253488;rs11196389	1531;1496;1531	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	P	1539;1504;1531;1496	ENSP00000358365:L1539P;ENSP00000358367:L1504P;ENSP00000353078:L1531P;ENSP00000353666:L1496P	ENSP00000353078:L1531P	L	-	2	0	NRAP	115341995	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.076000	0.76806	2.288000	0.76882	0.533000	0.62120	CTG	A|0.904;G|0.095	0.095	strong		0.522	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713821	32713821	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32713821C>A	ENST00000374940.3	+	3	687	c.585C>A	c.(583-585)ggC>ggA	p.G195G		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	195	Alpha-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	AGCACTGGGGCCTGGACGAGC	0.493																																					p.G195G		Atlas-SNP	.											HLA-DQA2,NS,carcinoma,+2,1	HLA-DQA2	27	1	0			c.C585A						scavenged	.						170.0	197.0	188.0					6																	32713821		1511	2709	4220	SO:0001819	synonymous_variant	3118	exon3			CTGGGGCCTGGAC		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.585C>A	6.37:g.32713821C>A		Somatic	513	1	0.00194932		WXS	Illumina HiSeq	Phase_I	475	35	0.0736842	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			C|0.778;A|0.222	0.222	strong		0.493	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
PHIP	55023	hgsc.bcm.edu	37	6	79692751	79692751	+	Missense_Mutation	SNP	G	G	A	rs11547228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:79692751G>A	ENST00000275034.4	-	23	2788	c.2621C>T	c.(2620-2622)aCc>aTc	p.T874I	PHIP_ENST00000479165.1_5'Flank	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	874	Lys-rich.		T -> I (in dbSNP:rs11547228). {ECO:0000269|PubMed:15489334}.		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)		TGCTTTCTTGGTTTTATTCTT	0.363													G|||	378	0.0754792	0.0091	0.0793	5008	,	,		15136	0.1121		0.1034	False		,,,				2504	0.0961				p.T874I		Atlas-SNP	.											.	PHIP	177	.	0			c.C2621T						PASS	.	G	ILE/THR	114,4292	86.3+/-125.0	2,110,2091	115.0	113.0	114.0		2621	4.0	1.0	6	dbSNP_120	114	893,7707	199.4+/-243.5	39,815,3446	yes	missense	PHIP	NM_017934.5	89	41,925,5537	AA,AG,GG		10.3837,2.5874,7.7426	possibly-damaging	874/1822	79692751	1007,11999	2203	4300	6503	SO:0001583	missense	55023	exon23			TTCTTGGTTTTAT	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.2621C>T	6.37:g.79692751G>A	ENSP00000275034:p.Thr874Ile	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	53	42	0.792453	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000275034.4	37	CCDS4987.1	161	0.07371794871794872	6	0.012195121951219513	31	0.0856353591160221	46	0.08041958041958042	78	0.10290237467018469	G	10.22	1.290529	0.23564	0.025874	0.103837	ENSG00000146247	ENST00000275034	T	0.31510	1.49	4.96	3.96	0.45880	.	0.222208	0.38897	N	0.001540	T	0.09423	0.0232	L	0.31752	0.955	0.31581	P	0.655165	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10823	-1.0613	8	.	.	.	-6.2807	10.7795	0.46369	0.1315:0.0:0.8685:0.0	rs11547228;rs52809064;rs11547228	874;874	A7J992;Q8WWQ0	.;PHIP_HUMAN	I	874	ENSP00000275034:T874I	.	T	-	2	0	PHIP	79749470	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.612000	0.46343	2.295000	0.77249	0.467000	0.42956	ACC	G|0.923;A|0.077	0.077	strong		0.363	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
ESYT3	83850	hgsc.bcm.edu	37	3	138191448	138191448	+	Missense_Mutation	SNP	A	A	T	rs35537868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:138191448A>T	ENST00000389567.4	+	18	2170	c.1984A>T	c.(1984-1986)Aca>Tca	p.T662S		NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	662			T -> S (in dbSNP:rs35537868).		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						ATCCCAAGAGACAGGCCCAGA	0.567													A|||	711	0.141973	0.1203	0.0317	5008	,	,		20274	0.3938		0.0268	False		,,,				2504	0.1084				p.T662S		Atlas-SNP	.											.	ESYT3	64	.	0			c.A1984T						PASS	.	A	SER/THR	415,3821		17,381,1720	127.0	146.0	140.0		1984	2.1	1.0	3	dbSNP_126	140	188,8254		1,186,4034	yes	missense	ESYT3	NM_031913.3	58	18,567,5754	TT,TA,AA		2.227,9.797,4.7563	benign	662/887	138191448	603,12075	2118	4221	6339	SO:0001583	missense	83850	exon18			CAAGAGACAGGCC	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.1984A>T	3.37:g.138191448A>T	ENSP00000374218:p.Thr662Ser	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	97	56	0.57732	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	289	0.13232600732600733	47	0.09552845528455285	12	0.03314917127071823	207	0.3618881118881119	23	0.030343007915567283	A	7.640	0.680602	0.14907	0.09797	0.02227	ENSG00000158220	ENST00000389567	T	0.36340	1.26	4.55	2.07	0.26955	.	0.937577	0.08830	N	0.887450	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	0.9999999745606	B	0.09022	0.002	B	0.04013	0.001	T	0.42582	-0.9443	9	0.07482	T	0.82	-26.6927	4.7614	0.13110	0.7091:0.1898:0.1011:0.0	rs35537868;rs57355924	662	A0FGR9	ESYT3_HUMAN	S	662	ENSP00000374218:T662S	ENSP00000374218:T662S	T	+	1	0	ESYT3	139674138	0.982000	0.34865	0.978000	0.43139	0.968000	0.65278	0.718000	0.25866	0.242000	0.21303	0.379000	0.24179	ACA	A|0.902;T|0.098	0.098	strong		0.567	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913	
BPIFB6	128859	hgsc.bcm.edu	37	20	31619515	31619515	+	Missense_Mutation	SNP	G	G	A	rs41293138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:31619515G>A	ENST00000349552.1	+	1	62	c.62G>A	c.(61-63)gGg>gAg	p.G21E		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	21						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GCTGACCCTGGGGCACTGCTG	0.662													G|||	10	0.00199681	0.0008	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0				p.G21E		Atlas-SNP	.											.	.	.	.	0			c.G62A						PASS	.	G	GLU/GLY	9,4397	15.5+/-35.6	0,9,2194	43.0	33.0	37.0		62	4.8	1.0	20	dbSNP_127	37	62,8538	36.4+/-91.3	1,60,4239	yes	missense	BPIFB6	NM_174897.2	98	1,69,6433	AA,AG,GG		0.7209,0.2043,0.5459	possibly-damaging	21/454	31619515	71,12935	2203	4300	6503	SO:0001583	missense	128859	exon1			ACCCTGGGGCACT	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.62G>A	20.37:g.31619515G>A	ENSP00000344929:p.Gly21Glu	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	165	50	0.30303	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	17.66	3.445168	0.63178	0.002043	0.007209	ENSG00000167104	ENST00000349552	T	0.02498	4.27	4.85	4.85	0.62838	.	0.117103	0.38111	N	0.001818	T	0.06325	0.0163	L	0.57536	1.79	0.38042	D	0.935492	D	0.62365	0.991	P	0.56823	0.807	T	0.03587	-1.1022	10	0.59425	D	0.04	.	13.4708	0.61281	0.0:0.0:1.0:0.0	rs41293138	21	Q8NFQ5	BPIB6_HUMAN	E	21	ENSP00000344929:G21E	ENSP00000344929:G21E	G	+	2	0	BPIFB6	31083176	1.000000	0.71417	0.981000	0.43875	0.451000	0.32288	4.825000	0.62708	2.240000	0.73641	0.561000	0.74099	GGG	G|0.995;A|0.005	0.005	strong		0.662	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28338298	28338298	+	Missense_Mutation	SNP	C	C	G	rs457947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:28338298C>G	ENST00000284987.5	-	1	534	c.413G>C	c.(412-414)gGt>gCt	p.G138A		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	138			G -> A (in dbSNP:rs457947). {ECO:0000269|PubMed:10438522, ECO:0000269|PubMed:15489334}.		defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						GCGGGGACTACCGTCCACTGT	0.662													C|||	701	0.139976	0.2489	0.17	5008	,	,		14671	0.004		0.1332	False		,,,				2504	0.1186				p.G138A	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G413C						PASS	.	C	ALA/GLY	1025,3381		112,801,1290	28.0	26.0	27.0		413	4.6	1.0	21	dbSNP_80	27	1407,7191		127,1153,3019	yes	missense	ADAMTS5	NM_007038.3	60	239,1954,4309	GG,GC,CC		16.3643,23.2637,18.7019	possibly-damaging	138/931	28338298	2432,10572	2203	4299	6502	SO:0001583	missense	11096	exon1			GGACTACCGTCCA	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.413G>C	21.37:g.28338298C>G	ENSP00000284987:p.Gly138Ala	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	294	0.1346153846153846	119	0.241869918699187	62	0.1712707182320442	1	0.0017482517482517483	112	0.14775725593667546	C	10.96	1.499434	0.26861	0.232637	0.163643	ENSG00000154736	ENST00000284987	T	0.09723	2.95	4.57	4.57	0.56435	Peptidase M12B, propeptide (1);	0.163396	0.44097	D	0.000487	T	0.00012	0.0000	L	0.45228	1.405	0.31486	P	0.666612	P	0.47604	0.898	P	0.49192	0.602	T	0.51748	-0.8666	9	0.26408	T	0.33	.	12.9996	0.58667	0.0:0.8377:0.1623:0.0	rs457947	138	Q9UNA0	ATS5_HUMAN	A	138	ENSP00000284987:G138A	ENSP00000284987:G138A	G	-	2	0	ADAMTS5	27260169	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	3.780000	0.55386	2.344000	0.79699	0.563000	0.77884	GGT	C|0.834;G|0.166	0.166	strong		0.662	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
HHLA1	10086	hgsc.bcm.edu	37	8	133092138	133092138	+	Missense_Mutation	SNP	G	G	A	rs2403730	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:133092138G>A	ENST00000414222.1	-	10	751	c.752C>T	c.(751-753)cCc>cTc	p.P251L	HHLA1_ENST00000434736.2_Missense_Mutation_p.P287L|OC90_ENST00000262283.5_Intron	NM_001145095.1	NP_001138567.1	C9JL84	HHLA1_HUMAN	HERV-H LTR-associating 1	251						extracellular region (GO:0005576)		p.P251L(1)		endometrium(6)|kidney(1)|lung(2)|skin(1)|stomach(2)	12						CCAGTGTCCGGGGCTTGTACT	0.552													G|||	1284	0.25639	0.1672	0.389	5008	,	,		18254	0.1984		0.3032	False		,,,				2504	0.2945				p.P251L		Atlas-SNP	.											HHLA1,NS,carcinoma,0,1	HHLA1	35	1	1	Substitution - Missense(1)	stomach(1)	c.C752T						PASS	.	G	LEU/PRO	285,1099		31,223,438	108.0	83.0	90.0		752	-0.7	0.0	8	dbSNP_100	90	1033,2149		152,729,710	yes	missense	HHLA1	NM_001145095.1	98	183,952,1148	AA,AG,GG		32.4639,20.5925,28.8655	benign	251/532	133092138	1318,3248	692	1591	2283	SO:0001583	missense	10086	exon10			TGTCCGGGGCTTG	AF110315		8q24	2011-03-01			ENSG00000132297	ENSG00000132297			4904	protein-coding gene	gene with protein product		604109		PLA2L		10329003	Standard	NM_001145095		Approved		uc011liy.1	C9JL84	OTTHUMG00000140390	ENST00000414222.1:c.752C>T	8.37:g.133092138G>A	ENSP00000388322:p.Pro251Leu	Somatic	342	1	0.00292398		WXS	Illumina HiSeq	Phase_I	400	163	0.4075	NM_001145095		Missense_Mutation	SNP	ENST00000414222.1	37		551	0.2522893772893773	69	0.1402439024390244	135	0.3729281767955801	125	0.21853146853146854	222	0.2928759894459103	G	10.85	1.468091	0.26335	0.205925	0.324639	ENSG00000132297	ENST00000414222;ENST00000434736	.	.	.	4.82	-0.714	0.11219	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.10450	0.001;0.005	T	0.45026	-0.9289	7	0.26408	T	0.33	.	0.6554	0.00834	0.3373:0.1655:0.3274:0.1697	rs2403730;rs3739279;rs17571473;rs52807392;rs56513099;rs59545753;rs2403730	251;108	C9JL84;C9JL84-2	HHLA1_HUMAN;.	L	251;287	.	ENSP00000388322:P251L	P	-	2	0	HHLA1	133161320	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.195000	0.09546	-0.034000	0.13713	-0.142000	0.14014	CCC	G|0.754;A|0.246	0.246	strong		0.552	HHLA1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XR_017860	
TNXB	7148	hgsc.bcm.edu	37	6	32017173	32017173	+	Missense_Mutation	SNP	G	G	C	rs41270450	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32017173G>C	ENST00000375244.3	-	28	9832	c.9631C>G	c.(9631-9633)Cgt>Ggt	p.R3211G	TNXB_ENST00000375247.2_Missense_Mutation_p.R3209G			P22105	TENX_HUMAN	tenascin XB	3256					actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCCCTGACACGCACCACCTGG	0.687													G|||	112	0.0223642	0.0008	0.0303	5008	,	,		15893	0.003		0.0726	False		,,,				2504	0.0143				p.R3209G		Atlas-SNP	.											.	TNXB	553	.	0			c.C9625G						PASS	.	G	GLY/ARG	30,2550		0,30,1260	58.0	62.0	61.0		9625	4.4	1.0	6	dbSNP_127	61	238,4860		2,234,2313	no	missense	TNXB	NM_019105.6	125	2,264,3573	CC,CG,GG		4.6685,1.1628,3.4905	benign	3209/4243	32017173	268,7410	1290	2549	3839	SO:0001583	missense	7148	exon28			TGACACGCACCAC	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9631C>G	6.37:g.32017173G>C	ENSP00000364393:p.Arg3211Gly	Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	221	106	0.479638	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		79	0.036172161172161175	1	0.0020325203252032522	14	0.03867403314917127	2	0.0034965034965034965	62	0.08179419525065963	G	6.181	0.401533	0.11696	0.011628	0.046685	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.58060	0.36;0.36	4.43	4.43	0.53597	.	0.000000	0.48286	D	0.000181	T	0.38878	0.1057	M	0.83852	2.665	0.80722	P	0.0	B	0.22146	0.065	B	0.19148	0.024	T	0.44034	-0.9354	9	0.19147	T	0.46	.	13.9686	0.64225	0.0:0.0:1.0:0.0	rs41270450;rs61740266	3209	P22105-3	.	G	3211;3209	ENSP00000364393:R3211G;ENSP00000364396:R3209G	ENSP00000364393:R3211G	R	-	1	0	TNXB	32125151	0.954000	0.32549	0.993000	0.49108	0.003000	0.03518	3.096000	0.50243	2.011000	0.59026	0.313000	0.20887	CGT	G|0.940;C|0.060	0.060	strong		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
OR2L3	391192	hgsc.bcm.edu	37	1	248224746	248224746	+	Missense_Mutation	SNP	G	G	T	rs6697812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248224746G>T	ENST00000359959.3	+	1	763	c.763G>T	c.(763-765)Gtc>Ttc	p.V255F	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(7)|lung(28)|prostate(1)|skin(1)|urinary_tract(1)	41	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0278)			TGCACCTTTTGTCTACACTTA	0.493													g|||	137	0.0273562	0.0068	0.0432	5008	,	,		20709	0.0		0.0905	False		,,,				2504	0.0072				p.V255F		Atlas-SNP	.											.	OR2L3	97	.	0			c.G763T						PASS	.	G	PHE/VAL,	60,4346	58.1+/-94.6	0,60,2143	125.0	118.0	120.0		763,	-4.0	0.0	1	dbSNP_116	120	756,7838	177.5+/-227.1	32,692,3573	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	50,	32,752,5716	TT,TG,GG		8.7968,1.3618,6.2769	benign,	255/313,	248224746	816,12184	2203	4297	6500	SO:0001583	missense	391192	exon1			CCTTTTGTCTACA	AB065950	CCDS31104.1	1q44	2012-08-09			ENSG00000198128	ENSG00000198128		"""GPCR / Class A : Olfactory receptors"""	15009	protein-coding gene	gene with protein product							Standard	NM_001004687		Approved		uc001idx.1	Q8NG85	OTTHUMG00000040195	ENST00000359959.3:c.763G>T	1.37:g.248224746G>T	ENSP00000353044:p.Val255Phe	Somatic	226	1	0.00442478		WXS	Illumina HiSeq	Phase_I	249	116	0.465863	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	73	0.033424908424908424	5	0.01016260162601626	16	0.04419889502762431	0	0.0	52	0.06860158311345646	G	0.008	-1.882849	0.00532	0.013618	0.087968	ENSG00000198128	ENST00000359959	T	0.36878	1.23	2.01	-4.03	0.04021	GPCR, rhodopsin-like superfamily (1);	1.925040	0.04254	N	0.339066	T	0.00384	0.0012	N	0.01267	-0.92	0.09310	N	1	B	0.02656	0.0	B	0.12156	0.007	T	0.06588	-1.0818	10	0.24483	T	0.36	.	1.0083	0.01492	0.2749:0.1294:0.3575:0.2383	rs6697812	255	Q8NG85	OR2L3_HUMAN	F	255	ENSP00000353044:V255F	ENSP00000353044:V255F	V	+	1	0	OR2L3	246291369	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.951000	0.00048	-2.222000	0.00727	-3.156000	0.00058	GTC	.	.	weak		0.493	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687	
RPGRIP1	57096	hgsc.bcm.edu	37	14	21790040	21790040	+	Missense_Mutation	SNP	G	G	T	rs10151259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21790040G>T	ENST00000400017.2	+	13	1639	c.1639G>T	c.(1639-1641)Gct>Tct	p.A547S	RPGRIP1_ENST00000556336.1_Missense_Mutation_p.A520S|RPGRIP1_ENST00000206660.6_Missense_Mutation_p.A547S|RPGRIP1_ENST00000553500.1_3'UTR|RPGRIP1_ENST00000382933.4_Missense_Mutation_p.A189S|RPGRIP1_ENST00000557771.1_Missense_Mutation_p.A520S|RPGRIP1_ENST00000307974.4_5'Flank	NM_020366.3	NP_065099.3	Q96KN7	RPGR1_HUMAN	retinitis pigmentosa GTPase regulator interacting protein 1	547			A -> S (in CORD13; dbSNP:rs10151259). {ECO:0000269|PubMed:10958648, ECO:0000269|PubMed:12920076}.		eye photoreceptor cell development (GO:0042462)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	axoneme (GO:0005930)|nonmotile primary cilium (GO:0031513)				breast(3)|endometrium(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(4)|pancreas(1)|prostate(3)|stomach(1)	39	all_cancers(95;0.0017)	all_cancers(140;0.0973)	Epithelial(56;6.24e-07)|all cancers(55;6.56e-06)	GBM - Glioblastoma multiforme(265;0.00888)		GATGACAAAAGCTGACAATGA	0.393													G|||	838	0.167332	0.2315	0.1412	5008	,	,		20902	0.004		0.2366	False		,,,				2504	0.1963				p.A547S		Atlas-SNP	.											.	RPGRIP1	213	.	0			c.G1639T	GRCh37	CM032029	RPGRIP1	M	rs10151259	PASS	.	G	SER/ALA	775,3007		86,603,1202	80.0	76.0	77.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1639	3.0	1.0	14	dbSNP_119	77	2017,6207		230,1557,2325	yes	missense	RPGRIP1	NM_020366.3	99	316,2160,3527	TT,TG,GG		24.5258,20.4918,23.255	probably-damaging	547/1287	21790040	2792,9214	1891	4112	6003	SO:0001583	missense	57096	exon13			ACAAAAGCTGACA	AF227257	CCDS45080.1	14q11.2	2013-06-06			ENSG00000092200	ENSG00000092200			13436	protein-coding gene	gene with protein product		605446		RPGRIP		10958647, 10958648	Standard	NM_020366		Approved	RGI1, LCA6, CORD13	uc001wag.3	Q96KN7	OTTHUMG00000170758	ENST00000400017.2:c.1639G>T	14.37:g.21790040G>T	ENSP00000382895:p.Ala547Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	86	85	0.988372	NM_020366	Q7Z2W6|Q8IXV5|Q96QA8|Q9HB94|Q9HB95|Q9HBK6|Q9NR40	Missense_Mutation	SNP	ENST00000400017.2	37	CCDS45080.1	352	0.16117216117216118	115	0.23373983739837398	55	0.15193370165745856	0	0.0	182	0.24010554089709762	G	13.80	2.344142	0.41498	0.204918	0.245258	ENSG00000092200	ENST00000556336;ENST00000557771;ENST00000400017;ENST00000206660;ENST00000382933;ENST00000555587;ENST00000554303	T;T;T;T;T;T;T	0.79554	-0.1;-0.86;-0.9;-0.9;-0.47;-1.22;-1.28	4.86	3.04	0.35103	.	0.320649	0.34223	N	0.004147	T	0.00073	0.0002	L	0.52266	1.64	0.09310	P	0.99999999479642	D;D;D;D	0.89917	1.0;0.97;1.0;1.0	D;P;D;D	0.91635	0.999;0.747;0.999;0.998	T	0.14117	-1.0484	9	0.29301	T	0.29	-9.0074	5.6994	0.17873	0.1672:0.0:0.6767:0.1561	rs61722408	22;189;163;547	G3V3I7;Q96KN7-4;Q96KN7-5;Q96KN7	.;.;.;RPGR1_HUMAN	S	520;520;547;547;189;22;20	ENSP00000450445:A520S;ENSP00000451219:A520S;ENSP00000382895:A547S;ENSP00000206660:A547S;ENSP00000372391:A189S;ENSP00000451262:A22S;ENSP00000450426:A20S	ENSP00000206660:A547S	A	+	1	0	RPGRIP1	20859880	0.990000	0.36364	0.991000	0.47740	0.402000	0.30811	0.774000	0.26675	0.777000	0.33496	-0.384000	0.06662	GCT	A|0.059;C|0.298	.	strong		0.393	RPGRIP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410258.1	NM_020366	
PSD4	23550	hgsc.bcm.edu	37	2	113940681	113940681	+	Silent	SNP	T	T	C	rs3748914	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113940681T>C	ENST00000245796.6	+	2	843	c.648T>C	c.(646-648)agT>agC	p.S216S	PSD4_ENST00000441564.3_Silent_p.S216S	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	216					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AAGACAGCAGTGAGCCTGAGG	0.637													C|||	2881	0.57528	0.7375	0.5173	5008	,	,		17550	0.6042		0.4423	False		,,,				2504	0.5041				p.S216S		Atlas-SNP	.											PSD4,NS,carcinoma,0,1	PSD4	74	1	0			c.T648C						PASS	.	C		3023,1383	456.3+/-351.3	1046,931,226	61.0	65.0	63.0		648	-9.4	0.0	2	dbSNP_107	63	3513,5087	632.4+/-398.6	732,2049,1519	no	coding-synonymous	PSD4	NM_012455.2		1778,2980,1745	CC,CT,TT		40.8488,31.389,49.7463		216/1057	113940681	6536,6470	2203	4300	6503	SO:0001819	synonymous_variant	23550	exon2			CAGCAGTGAGCCT	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.648T>C	2.37:g.113940681T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Silent	SNP	ENST00000245796.6	37	CCDS33276.1																																																																																			C|0.529;N|0.000	0.529	strong		0.637	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
GBGT1	26301	hgsc.bcm.edu	37	9	136029138	136029138	+	Silent	SNP	G	G	A	rs35902535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136029138G>A	ENST00000372040.3	-	7	1181	c.870C>T	c.(868-870)ggC>ggT	p.G290G	GBGT1_ENST00000372043.3_Missense_Mutation_p.A284V|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000540636.1_Silent_p.G273G|RALGDS_ENST00000542690.1_Intron	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	290					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		CAGCCATGATGCCATTGGCCT	0.587													G|||	210	0.0419329	0.0333	0.0403	5008	,	,		17659	0.002		0.0795	False		,,,				2504	0.0573				p.G290G		Atlas-SNP	.											.	GBGT1	25	.	0			c.C870T						PASS	.	G		200,4206	124.9+/-162.1	8,184,2011	121.0	113.0	116.0		870	2.3	1.0	9	dbSNP_126	116	618,7982	160.3+/-213.4	16,586,3698	no	coding-synonymous	GBGT1	NM_021996.4		24,770,5709	AA,AG,GG		7.186,4.5393,6.2894		290/348	136029138	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CATGATGCCATTG	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.870C>T	9.37:g.136029138G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	52	0.52	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	105	0.04807692307692308	21	0.042682926829268296	15	0.04143646408839779	2	0.0034965034965034965	67	0.08839050131926121	G	12.72	2.022220	0.35701	0.045393	0.07186	ENSG00000148288	ENST00000372043	T	0.23348	1.91	5.38	2.31	0.28768	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00460	-1.1726	6	0.87932	D	0	-15.1162	5.0909	0.14708	0.2677:0.3054:0.4269:0.0	rs35902535;rs62638711	.	.	.	V	284	ENSP00000361113:A284V	ENSP00000361113:A284V	A	-	2	0	GBGT1	135018959	0.629000	0.27146	0.992000	0.48379	0.929000	0.56500	0.761000	0.26489	0.542000	0.28846	0.561000	0.74099	GCA	G|0.944;A|0.056	0.056	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
SS18L1	26039	hgsc.bcm.edu	37	20	60738566	60738566	+	Silent	SNP	C	C	T	rs73309164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60738566C>T	ENST00000331758.3	+	6	635	c.609C>T	c.(607-609)ggC>ggT	p.G203G	SS18L1_ENST00000421564.1_Silent_p.G203G|SS18L1_ENST00000370848.4_Silent_p.G206G|SS18L1_ENST00000491916.1_3'UTR	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	203	Gln-rich.|Methionine-rich intra-molecular domain. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)			SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			CGGCGCAGGGCGGCAGCCAGC	0.697			T	SSX1	synovial sarcoma								C|||	342	0.0682907	0.1543	0.0432	5008	,	,		12141	0.001		0.0507	False		,,,				2504	0.0573				p.G203G		Atlas-SNP	.		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	SS18L1_ENST00000331758,NS,carcinoma,0,1	SS18L1	37	1	0			c.C609T						scavenged	.	C		659,3743		48,563,1590	32.0	35.0	34.0		609	-1.8	1.0	20	dbSNP_131	34	443,8147		16,411,3868	no	coding-synonymous	SS18L1	NM_198935.1		64,974,5458	TT,TC,CC		5.1572,14.9705,8.4821		203/397	60738566	1102,11890	2201	4295	6496	SO:0001819	synonymous_variant	26039	exon6			GCAGGGCGGCAGC	AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.609C>T	20.37:g.60738566C>T		Somatic	116	1	0.00862069		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_198935	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Silent	SNP	ENST00000331758.3	37	CCDS13491.1																																																																																			C|0.928;T|0.072	0.072	strong		0.697	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2		
CCM2	83605	hgsc.bcm.edu	37	7	45104131	45104131	+	Missense_Mutation	SNP	G	G	A	rs11552377	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45104131G>A	ENST00000258781.6	+	4	507	c.358G>A	c.(358-360)Gtc>Atc	p.V120I	CCM2_ENST00000461377.1_3'UTR|CCM2_ENST00000541586.1_Missense_Mutation_p.V62I|CCM2_ENST00000475551.1_Missense_Mutation_p.V114I|CCM2_ENST00000474617.1_Missense_Mutation_p.V114I|CCM2_ENST00000544363.1_Missense_Mutation_p.V120I|CCM2_ENST00000381112.3_Missense_Mutation_p.V141I	NM_031443.3	NP_113631.1	Q9BSQ5	CCM2_HUMAN	cerebral cavernous malformation 2	120	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.		V -> I (in dbSNP:rs11552377). {ECO:0000269|PubMed:14740320}.		blood vessel endothelial cell differentiation (GO:0060837)|cell-cell junction organization (GO:0045216)|endothelial cell development (GO:0001885)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|inner ear development (GO:0048839)|integrin-mediated signaling pathway (GO:0007229)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|stress-activated MAPK cascade (GO:0051403)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)	cytoplasm (GO:0005737)|protein complex (GO:0043234)				NS(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						TGCGTACAACGTCAAGCTGGC	0.587													G|||	541	0.108027	0.0166	0.1671	5008	,	,		19600	0.1091		0.174	False		,,,				2504	0.1207				p.V141I		Atlas-SNP	.											.	CCM2	42	.	0			c.G421A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	176,4230	114.6+/-152.6	1,174,2028	79.0	53.0	62.0		421,184,358,358	3.2	1.0	7	dbSNP_120	62	1582,7018	295.9+/-302.6	140,1302,2858	yes	missense,missense,missense,missense	CCM2	NM_001029835.2,NM_001167934.1,NM_001167935.1,NM_031443.3	29,29,29,29	141,1476,4886	AA,AG,GG		18.3953,3.9946,13.5168	benign,benign,benign,benign	141/466,62/387,120/354,120/445	45104131	1758,11248	2203	4300	6503	SO:0001583	missense	83605	exon4			TACAACGTCAAGC	BC004903	CCDS5500.1, CCDS34630.1, CCDS55108.1, CCDS55109.1	7p13	2014-09-17	2004-02-13	2004-02-18	ENSG00000136280	ENSG00000136280			21708	protein-coding gene	gene with protein product	"""malcavernin"""	607929	"""chromosome 7 open reading frame 22"""	C7orf22		9811928	Standard	NM_001029835		Approved	MGC4607	uc003tms.3	Q9BSQ5	OTTHUMG00000129246	ENST00000258781.6:c.358G>A	7.37:g.45104131G>A	ENSP00000258781:p.Val120Ile	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	51	33	0.647059	NM_001029835	A4D2L4|B3KUV0|D3DVL4|E9PDJ3|F5H0E1|F5H551|Q71RE5|Q8TAT4	Missense_Mutation	SNP	ENST00000258781.6	37	CCDS5500.1	254	0.1163003663003663	8	0.016260162601626018	65	0.17955801104972377	50	0.08741258741258741	131	0.17282321899736147	G	10.82	1.458249	0.26161	0.039946	0.183953	ENSG00000136280	ENST00000258781;ENST00000541586;ENST00000544363;ENST00000475551;ENST00000381112;ENST00000474617	T;T;T;T;T;T	0.54071	0.59;0.59;0.93;0.59;0.59;0.93	5.32	3.15	0.36227	Phosphotyrosine interaction domain (1);	0.255439	0.39544	N	0.001340	T	0.00073	0.0002	L	0.28115	0.83	0.29732	P	0.8377749999999999	P;P;B;B;B;B	0.40032	0.586;0.699;0.027;0.015;0.027;0.015	B;B;B;B;B;B	0.29176	0.099;0.083;0.009;0.006;0.017;0.006	T	0.12319	-1.0552	9	0.18710	T	0.47	-40.2272	9.6734	0.40026	0.2402:0.0:0.7598:0.0	rs11552377;rs17451775;rs11552377	113;83;141;120;62;120	B7Z5A6;B7Z8D5;E9PDJ3;F5H0E1;F5H551;Q9BSQ5	.;.;.;.;.;CCM2_HUMAN	I	120;62;120;114;141;114	ENSP00000258781:V120I;ENSP00000444725:V62I;ENSP00000438035:V120I;ENSP00000417180:V114I;ENSP00000370503:V141I;ENSP00000419474:V114I	ENSP00000258781:V120I	V	+	1	0	CCM2	45070656	0.995000	0.38212	0.998000	0.56505	0.962000	0.63368	2.274000	0.43390	1.244000	0.43870	0.655000	0.94253	GTC	G|0.879;A|0.121	0.121	strong		0.587	CCM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251348.1	NM_031443	
ZNF232	7775	hgsc.bcm.edu	37	17	5012935	5012935	+	Missense_Mutation	SNP	A	A	C	rs200108859		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5012935A>C	ENST00000250076.3	-	3	906	c.252T>G	c.(250-252)caT>caG	p.H84Q	ZNF232_ENST00000575538.1_Intron|ZNF232_ENST00000416429.2_Missense_Mutation_p.H57Q|ZNF232_ENST00000575898.1_Missense_Mutation_p.H84Q|AC012146.7_ENST00000571138.1_RNA|AC012146.7_ENST00000413077.1_RNA	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	57	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)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						GGTAGCGGAGATGCCTGAAGC	0.557																																					p.H84Q		Atlas-SNP	.											.	ZNF232	42	.	0			c.T252G						PASS	.	A	GLN/HIS	0,4406		0,0,2203	154.0	125.0	135.0		252	-6.3	0.8	17		135	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF232	NM_014519.2	24	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	benign	84/445	5012935	1,13005	2203	4300	6503	SO:0001583	missense	7775	exon3			GCGGAGATGCCTG	AF080169	CCDS11068.1	17p13.2	2013-01-09			ENSG00000167840	ENSG00000167840		"""-"", ""Zinc fingers, C2H2-type"""	13026	protein-coding gene	gene with protein product						11311944	Standard	NM_014519		Approved	ZSCAN11	uc002gat.3	Q9UNY5	OTTHUMG00000099450	ENST00000250076.3:c.252T>G	17.37:g.5012935A>C	ENSP00000250076:p.His84Gln	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	184	86	0.467391	NM_014519		Missense_Mutation	SNP	ENST00000250076.3	37	CCDS11068.1	.	.	.	.	.	.	.	.	.	.	A	0.344	-0.948705	0.02304	0.0	1.16E-4	ENSG00000167840	ENST00000250076;ENST00000416429	T;T	0.03772	3.81;3.81	3.15	-6.3	0.02007	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.277051	0.19503	N	0.112683	T	0.00998	0.0033	N	0.01096	-1.015	0.23581	N	0.997361	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.11329	0.006;0.001;0.0;0.0	T	0.25433	-1.0132	10	0.02654	T	1	.	5.1735	0.15122	0.419:0.432:0.0:0.1491	.	84;57;57;57	B4DNA7;B4DP49;Q9UNY5;Q9UNY5-2	.;.;ZN232_HUMAN;.	Q	84;57	ENSP00000250076:H84Q;ENSP00000416430:H57Q	ENSP00000250076:H84Q	H	-	3	2	ZNF232	4953659	0.000000	0.05858	0.841000	0.33234	0.923000	0.55619	-1.797000	0.01749	-1.716000	0.01387	-0.472000	0.04984	CAT	.	.	weak		0.557	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14803745	14803745	+	Missense_Mutation	SNP	A	A	G	rs45533337		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:14803745A>G	ENST00000358984.4	+	24	2386	c.2206A>G	c.(2206-2208)Act>Gct	p.T736A	ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	736										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						TTTCCTTGAGACTCTCTTACA	0.289																																					p.T736A		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,0,2	ANKRD30B	237	2	0			c.A2206G						scavenged	.						25.0	22.0	23.0					18																	14803745		688	1579	2267	SO:0001583	missense	374860	exon24			CTTGAGACTCTCT	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.2206A>G	18.37:g.14803745A>G	ENSP00000351875:p.Thr736Ala	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	372	103	0.276882	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	37	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	N	5.153	0.213833	0.09810	.	.	ENSG00000180777	ENST00000358984;ENST00000320584;ENST00000277669	T	0.06371	3.31	1.16	1.16	0.20824	.	.	.	.	.	T	0.04861	0.0131	L	0.29908	0.895	0.09310	N	1	B	0.16396	0.017	B	0.08055	0.003	T	0.36817	-0.9732	9	0.87932	D	0	.	4.5782	0.12245	1.0:0.0:0.0:0.0	.	736	F8WAG3	.	A	736;11;4	ENSP00000351875:T736A	ENSP00000277669:T4A	T	+	1	0	ANKRD30B	14793745	0.037000	0.19845	0.001000	0.08648	0.001000	0.01503	1.570000	0.36439	0.807000	0.34208	0.440000	0.28878	ACT	A|1.000;|0.000	.	weak		0.289	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
ECD	11319	hgsc.bcm.edu	37	10	74916173	74916173	+	Silent	SNP	T	T	A	rs12241093	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:74916173T>A	ENST00000372979.4	-	5	656	c.450A>T	c.(448-450)gcA>gcT	p.A150A	ECD_ENST00000610256.1_5'Flank|ECD_ENST00000430082.2_Silent_p.A150A|ECD_ENST00000454759.2_Silent_p.A150A	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	150					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)					ATTTTCTTGGTGCAGGGATAA	0.413													T|||	889	0.177516	0.1657	0.0994	5008	,	,		17841	0.3145		0.0537	False		,,,				2504	0.2352				p.A150A		Atlas-SNP	.											.	ECD	50	.	0			c.A450T						PASS	.	T	,,	665,3741	282.5+/-276.6	57,551,1595	116.0	115.0	115.0		450,450,450	3.6	1.0	10	dbSNP_120	115	571,8029	153.9+/-208.2	26,519,3755	no	coding-synonymous,coding-synonymous,coding-synonymous	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	,,	83,1070,5350	AA,AT,TT		6.6395,15.0931,9.5033	,,	150/678,150/602,150/645	74916173	1236,11770	2203	4300	6503	SO:0001819	synonymous_variant	11319	exon5			TCTTGGTGCAGGG	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		ENST00000372979.4:c.450A>T	10.37:g.74916173T>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	115	49	0.426087	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	37	CCDS7321.1																																																																																			T|0.885;A|0.115	0.115	strong		0.413	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
CCDC69	26112	hgsc.bcm.edu	37	5	150578574	150578574	+	Silent	SNP	A	A	G	rs3734038	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:150578574A>G	ENST00000355417.2	-	4	477	c.303T>C	c.(301-303)aaT>aaC	p.N101N	CCDC69_ENST00000521308.1_5'UTR	NM_015621.2	NP_056436.2	A6NI79	CCD69_HUMAN	coiled-coil domain containing 69	101										haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|stomach(1)	9		Medulloblastoma(196;0.091)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGCCTCTTCATTCTTTCCTT	0.602													A|||	1077	0.215056	0.0189	0.3718	5008	,	,		19358	0.1954		0.2535	False		,,,				2504	0.3497				p.N101N		Atlas-SNP	.											.	CCDC69	30	.	0			c.T303C						PASS	.	A		286,4120	157.4+/-190.3	8,270,1925	296.0	249.0	265.0		303	-1.8	0.0	5	dbSNP_107	265	2042,6558	355.5+/-329.9	236,1570,2494	no	coding-synonymous	CCDC69	NM_015621.2		244,1840,4419	GG,GA,AA		23.7442,6.4911,17.8994		101/297	150578574	2328,10678	2203	4300	6503	SO:0001819	synonymous_variant	26112	exon4			CTCTTCATTCTTT		CCDS4312.1	5q33.1	2008-02-05			ENSG00000198624	ENSG00000198624			24487	protein-coding gene	gene with protein product						12477932	Standard	NM_015621		Approved	FLJ13705, DKFZP434C171	uc011dcq.3	A6NI79	OTTHUMG00000130127	ENST00000355417.2:c.303T>C	5.37:g.150578574A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	99	0.99	NM_015621	A8K9X6	Silent	SNP	ENST00000355417.2	37	CCDS4312.1																																																																																			A|0.820;G|0.180	0.180	strong		0.602	CCDC69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252435.1	NM_015621	
MUC5B	727897	hgsc.bcm.edu	37	11	1250488	1250488	+	Silent	SNP	C	C	T	rs2075859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1250488C>T	ENST00000529681.1	+	9	1123	c.1065C>T	c.(1063-1065)tgC>tgT	p.C355C	MUC5B_ENST00000531082.1_3'UTR|MUC5B_ENST00000447027.1_Silent_p.C355C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	355	TIL 1.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGCAGCTCTGCGAGGACCACT	0.682													c|||	1967	0.392772	0.2814	0.4366	5008	,	,		14317	0.6052		0.34	False		,,,				2504	0.3476				p.C355C		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C1065T						PASS	.	C		1063,3051		143,777,1137	22.0	28.0	26.0		1065	-0.9	0.8	11	dbSNP_96	26	2915,5479		531,1853,1813	no	coding-synonymous	MUC5B	NM_002458.2		674,2630,2950	TT,TC,CC		34.7272,25.8386,31.8036		355/5763	1250488	3978,8530	2057	4197	6254	SO:0001819	synonymous_variant	727897	exon9			GCTCTGCGAGGAC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.1065C>T	11.37:g.1250488C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.604;T|0.396	0.396	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PCNXL3	399909	hgsc.bcm.edu	37	11	65392695	65392695	+	Silent	SNP	C	C	T	rs1205259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:65392695C>T	ENST00000355703.3	+	17	3512	c.2973C>T	c.(2971-2973)ctC>ctT	p.L991L		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	991						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						TCTGTGGCCTCCTGGTGGCAC	0.632													C|||	1178	0.235224	0.3245	0.2421	5008	,	,		13681	0.1349		0.337	False		,,,				2504	0.1084				p.L991L		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C2973T						PASS	.	C		1463,2935		241,981,977	45.0	48.0	47.0		2973	2.6	1.0	11	dbSNP_87	47	2975,5607		519,1937,1835	no	coding-synonymous	PCNXL3	NM_032223.2		760,2918,2812	TT,TC,CC		34.6656,33.2651,34.1911		991/2035	65392695	4438,8542	2199	4291	6490	SO:0001819	synonymous_variant	399909	exon17			TGGCCTCCTGGTG	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.2973C>T	11.37:g.65392695C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.733;T|0.267	0.267	strong		0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
ABCA7	10347	hgsc.bcm.edu	37	19	1051214	1051214	+	Silent	SNP	A	A	G	rs3752240	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1051214A>G	ENST00000263094.6	+	20	2976	c.2745A>G	c.(2743-2745)gtA>gtG	p.V915V	ABCA7_ENST00000433129.1_Silent_p.V915V|ABCA7_ENST00000435683.2_Silent_p.V777V	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	915	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGCCGCTGTAGTGGGCCCCG	0.647													G|||	1448	0.289137	0.3676	0.4107	5008	,	,		16484	0.1101		0.3509	False		,,,				2504	0.2178				p.V915V		Atlas-SNP	.											.	ABCA7	174	.	0			c.A2745G						PASS	.	G		1639,2733	648.0+/-398.6	306,1027,853	57.0	55.0	55.0		2745	-9.0	0.0	19	dbSNP_107	55	3093,5483	656.0+/-401.3	577,1939,1772	no	coding-synonymous	ABCA7	NM_019112.3		883,2966,2625	GG,GA,AA		36.0658,37.4886,36.5462		915/2147	1051214	4732,8216	2186	4288	6474	SO:0001819	synonymous_variant	10347	exon20			CGCTGTAGTGGGC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2745A>G	19.37:g.1051214A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			A|0.653;G|0.347	0.347	strong		0.647	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
SLIRP	81892	hgsc.bcm.edu	37	14	78182188	78182188	+	Missense_Mutation	SNP	T	T	A	rs199752740		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:78182188T>A	ENST00000557342.1	+	3	271	c.230T>A	c.(229-231)cTa>cAa	p.L77Q	SLIRP_ENST00000557623.1_Missense_Mutation_p.L77Q|SLIRP_ENST00000238688.5_Missense_Mutation_p.L77Q|SLIRP_ENST00000557431.1_Missense_Mutation_p.L77Q	NM_001267864.1|NM_031210.5	NP_001254793.1|NP_112487.1	Q9GZT3	SLIRP_HUMAN	SRA stem-loop interacting RNA binding protein	77	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mitochondrion morphogenesis (GO:0070584)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	acrosomal vesicle (GO:0001669)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|sperm flagellum (GO:0036126)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			kidney(1)|prostate(1)	2						CGGAATGCACTACAACAGGAA	0.328																																					p.L77Q		Atlas-SNP	.											.	SLIRP	6	.	0			c.T230A						PASS	.	T	GLN/LEU	0,4398		0,0,2199	75.0	89.0	84.0		230	5.8	1.0	14		84	2,8594	1.2+/-3.3	0,2,4296	no	missense	SLIRP	NM_031210.4	113	0,2,6495	AA,AT,TT		0.0233,0.0,0.0154	probably-damaging	77/110	78182188	2,12992	2199	4298	6497	SO:0001583	missense	81892	exon3			ATGCACTACAACA	AF253980	CCDS9866.1, CCDS58331.1, CCDS73668.1	14q24.3	2013-02-12	2011-06-17	2011-06-17	ENSG00000119705	ENSG00000119705		"""RNA binding motif (RRM) containing"""	20495	protein-coding gene	gene with protein product		610211	"""chromosome 14 open reading frame 156"""	C14orf156		16762838	Standard	NM_031210		Approved	DC50	uc001xue.5	Q9GZT3		ENST00000557342.1:c.230T>A	14.37:g.78182188T>A	ENSP00000450909:p.Leu77Gln	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	222	102	0.459459	NM_001267864	J3KMY7	Missense_Mutation	SNP	ENST00000557342.1	37	CCDS9866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.956115|3.956115	0.73902|0.73902	0.0|0.0	2.33E-4|2.33E-4	ENSG00000119705|ENSG00000119705	ENST00000557342;ENST00000238688;ENST00000557623;ENST00000557431|ENST00000556831;ENST00000553981	T;T;T;T|.	0.21734|.	1.99;1.99;1.99;1.99|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.162010|.	0.41396|.	D|.	0.000897|.	T|T	0.77631|0.77631	0.4159|0.4159	M|M	0.79693|0.79693	2.465|2.465	0.44247|0.44247	D|D	0.997098|0.997098	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.78669|0.78669	-0.2114|-0.2114	10|5	0.87932|.	D|.	0|.	-5.4684|-5.4684	16.3818|16.3818	0.83467|0.83467	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	77|.	Q9GZT3|.	SLIRP_HUMAN|.	Q|N	77|75;50	ENSP00000450909:L77Q;ENSP00000238688:L77Q;ENSP00000452057:L77Q;ENSP00000450849:L77Q|.	ENSP00000238688:L77Q|.	L|Y	+|+	2|1	0|0	SLIRP|SLIRP	77251941|77251941	0.839000|0.839000	0.29477|0.29477	0.998000|0.998000	0.56505|0.56505	0.946000|0.946000	0.59487|0.59487	6.378000|6.378000	0.73150|0.73150	2.330000|2.330000	0.79161|0.79161	0.528000|0.528000	0.53228|0.53228	CTA|TAC	T|0.999;A|0.001	0.001	weak		0.328	SLIRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413901.1	NM_031210	
SDHA	6389	hgsc.bcm.edu	37	5	254599	254599	+	Missense_Mutation	SNP	A	A	T	rs6960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:254599A>T	ENST00000264932.6	+	14	2001	c.1886A>T	c.(1885-1887)tAt>tTt	p.Y629F	SDHA_ENST00000510361.1_Missense_Mutation_p.Y581F|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Missense_Mutation_p.Y548F	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	629			Y -> F (in dbSNP:rs6960). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8142412, ECO:0000269|Ref.5}.		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)	ACCCTGTCCTATGTGGACGTT	0.612									Familial Paragangliomas																												p.Y629F		Atlas-SNP	.											SDHA,adrenal_gland,pheochromocytoma,0,1	SDHA	80	1	0			c.A1886T						scavenged	.	A	PHE/TYR	788,3328		66,656,1336	10.0	15.0	14.0		1886	2.8	0.0	5	dbSNP_52	14	381,8115		9,363,3876	no	missense	SDHA	NM_004168.2	22	75,1019,5212	TT,TA,AA		4.4845,19.1448,9.269	benign	629/665	254599	1169,11443	2058	4248	6306	SO:0001583	missense	6389	exon14	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	TGTCCTATGTGGA	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.1886A>T	5.37:g.254599A>T	ENSP00000264932:p.Tyr629Phe	Somatic	635	3	0.00472441		WXS	Illumina HiSeq	Phase_I	565	173	0.306195	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	9.930|9.930	1.214643|1.214643	0.22289|0.22289	0.191448|0.191448	0.044845|0.044845	ENSG00000073578|ENSG00000073578	ENST00000509564|ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	D|T;T;T	0.81996|0.80304	-1.56|-1.36;-1.36;-1.36	4.05|4.05	2.85|2.85	0.33270|0.33270	.|Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (1);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);	.|0.000000	.|0.64402	.|U	.|0.000001	T|T	0.00241|0.00241	0.0007|0.0007	L|L	0.45352|0.45352	1.415|1.415	0.20074|0.20074	P|P	0.9999330642|0.9999330642	.|B;B;B;B	.|0.12013	.|0.005;0.0;0.0;0.002	.|B;B;B;B	.|0.14023	.|0.008;0.01;0.001;0.01	T|T	0.09292|0.09292	-1.0681|-1.0681	6|9	0.66056|0.33141	D|T	0.02|0.24	.|.	8.2512|8.2512	0.31724|0.31724	0.822:0.0:0.0:0.178|0.822:0.0:0.0:0.178	rs6960;rs3211476;rs6888348|rs6960;rs3211476;rs6888348	.|581;223;548;629	.|E9PBJ5;B3KYA5;D6RFM5;P31040	.|.;.;.;DHSA_HUMAN	L|F	87|629;484;548;581	ENSP00000421911:M87L|ENSP00000264932:Y629F;ENSP00000426514:Y548F;ENSP00000427703:Y581F	ENSP00000421911:M87L|ENSP00000264932:Y629F	M|Y	+|+	1|2	0|0	SDHA|SDHA	307599|307599	0.998000|0.998000	0.40836|0.40836	0.007000|0.007000	0.13788|0.13788	0.089000|0.089000	0.18198|0.18198	4.002000|4.002000	0.57053|0.57053	0.553000|0.553000	0.29044|0.29044	0.386000|0.386000	0.25728|0.25728	ATG|TAT	A|0.865;T|0.135	0.135	strong		0.612	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
NPBWR2	2832	hgsc.bcm.edu	37	20	62737568	62737568	+	Missense_Mutation	SNP	T	T	C	rs4809401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62737568T>C	ENST00000369768.1	-	1	956	c.617A>G	c.(616-618)cAg>cGg	p.Q206R		NM_005286.2	NP_005277.2	P48146	NPBW2_HUMAN	neuropeptides B/W receptor 2	206			Q -> R (in dbSNP:rs4809401). {ECO:0000269|PubMed:7590751, ECO:0000269|Ref.7}.		G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(38;2.58e-11)|all_epithelial(29;6.4e-13)|Lung NSC(23;1.25e-09)|all_lung(23;4.21e-09)					GAACCAGACCTGCTCGGGCCA	0.627													C|||	444	0.0886581	0.0227	0.0937	5008	,	,		20409	0.0863		0.1431	False		,,,				2504	0.1207				p.Q206R		Atlas-SNP	.											NPBWR2,NS,carcinoma,0,1	NPBWR2	36	1	0			c.A617G						PASS	.	C	ARG/GLN	169,4231	791.1+/-415.1	3,163,2034	50.0	44.0	46.0		617	0.7	0.0	20	dbSNP_111	46	1047,7537	759.0+/-407.5	60,927,3305	yes	missense	NPBWR2	NM_005286.2	43	63,1090,5339	CC,CT,TT		12.1971,3.8409,9.3654	benign	206/334	62737568	1216,11768	2200	4292	6492	SO:0001583	missense	2832	exon1			CAGACCTGCTCGG	U22492	CCDS13557.1	20q13.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000125522	ENSG00000125522		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4530	protein-coding gene	gene with protein product		600731	"""G protein-coupled receptor 8"""	GPR8		12401809	Standard	NM_005286		Approved		uc011abt.2	P48146	OTTHUMG00000033032	ENST00000369768.1:c.617A>G	20.37:g.62737568T>C	ENSP00000358783:p.Gln206Arg	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_005286	Q6NWQ6|Q9H4K3	Missense_Mutation	SNP	ENST00000369768.1	37	CCDS13557.1	203	0.09294871794871795	17	0.034552845528455285	36	0.09944751381215469	45	0.07867132867132867	105	0.13852242744063326	C	0.815	-0.750803	0.03041	0.038409	0.121971	ENSG00000125522	ENST00000369768	T	0.36520	1.25	3.9	0.669	0.17918	GPCR, rhodopsin-like superfamily (1);	0.299706	0.29417	N	0.012216	T	0.00109	0.0003	N	0.02802	-0.49	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.33007	-0.9885	9	0.09843	T	0.71	.	8.2073	0.31463	0.0:0.5476:0.0:0.4524	rs4809401;rs59506105;rs4809401	206	P48146	NPBW2_HUMAN	R	206	ENSP00000358783:Q206R	ENSP00000358783:Q206R	Q	-	2	0	NPBWR2	62208012	0.000000	0.05858	0.024000	0.17045	0.026000	0.11368	-0.290000	0.08354	-0.505000	0.06568	-1.668000	0.00747	CAG	T|0.908;C|0.092	0.092	strong		0.627	NPBWR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080300.1	NM_005286	
FLII	2314	hgsc.bcm.edu	37	17	18148485	18148485	+	Silent	SNP	G	G	A	rs7498	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18148485G>A	ENST00000327031.4	-	30	4002	c.3777C>T	c.(3775-3777)caC>caT	p.H1259H	FLII_ENST00000379450.4_Silent_p.H1173H|FLII_ENST00000579294.1_Silent_p.H1248H|FLII_ENST00000545457.2_Silent_p.H1204H|FLII_ENST00000578558.1_Missense_Mutation_p.T669M	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1259					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					CGCTCCAGGCGTGGAAGCAGC	0.627													A|||	1280	0.255591	0.2882	0.2622	5008	,	,		18123	0.3204		0.2435	False		,,,				2504	0.1524				p.H1259H		Atlas-SNP	.											.	FLII	79	.	0			c.C3777T						PASS	.	A		1213,3193	699.9+/-406.5	168,877,1158	85.0	93.0	90.0		3777	-7.1	0.6	17	dbSNP_52	90	2167,6433	706.2+/-405.5	271,1625,2404	no	coding-synonymous	FLII	NM_002018.2		439,2502,3562	AA,AG,GG		25.1977,27.5306,25.988		1259/1270	18148485	3380,9626	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon30			CCAGGCGTGGAAG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3777C>T	17.37:g.18148485G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	123	123	1	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			G|0.728;A|0.272	0.272	strong		0.627	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
PER3	8863	hgsc.bcm.edu	37	1	7880683	7880683	+	Missense_Mutation	SNP	T	T	G	rs10462020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:7880683T>G	ENST00000361923.2	+	15	2091	c.1916T>G	c.(1915-1917)gTc>gGc	p.V639G	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.V647G	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	639	CSNK1E binding domain. {ECO:0000250}.		V -> G (associated with delayed sleep phase syndrome (DSPS); dbSNP:rs10462020). {ECO:0000269|PubMed:11306557, ECO:0000269|PubMed:12655319}.		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)		ATTGTCCATGTCCCACCCCCA	0.483													T|||	604	0.120607	0.0696	0.2133	5008	,	,		18504	0.0079		0.1968	False		,,,				2504	0.1616				p.V639G		Atlas-SNP	.											.	PER3	95	.	0			c.T1916G	GRCh37	CM035907	PER3	M	rs10462020	PASS	.	T	GLY/VAL	424,3982	206.5+/-228.1	19,386,1798	80.0	66.0	71.0		1916	-6.9	0.0	1	dbSNP_119	71	1643,6957	302.9+/-306.2	162,1319,2819	yes	missense	PER3	NM_016831.1	109	181,1705,4617	GG,GT,TT		19.1047,9.6232,15.8927	possibly-damaging	639/1202	7880683	2067,10939	2203	4300	6503	SO:0001583	missense	8863	exon15			TCCATGTCCCACC	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.1916T>G	1.37:g.7880683T>G	ENSP00000355031:p.Val639Gly	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	138	123	0.891304	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	258	0.11813186813186813	48	0.0975609756097561	62	0.1712707182320442	8	0.013986013986013986	140	0.18469656992084432	T	15.17	2.752957	0.49362	0.096232	0.191047	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.28069	1.7;1.63	4.43	-6.91	0.01649	.	0.368047	0.27056	N	0.021160	T	0.00073	0.0002	M	0.72118	2.19	0.52099	P	5.3999999999998494E-5	B;P;P;B	0.51791	0.22;0.913;0.948;0.22	B;P;P;B	0.53861	0.115;0.548;0.736;0.115	T	0.04178	-1.0971	9	0.87932	D	0	.	8.5405	0.33390	0.0:0.4789:0.1186:0.4024	rs10462020;rs60667815;rs10462020	639;647;647;639	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	G	647;639	ENSP00000366755:V647G;ENSP00000355031:V639G	ENSP00000355031:V639G	V	+	2	0	PER3	7803270	0.260000	0.24053	0.000000	0.03702	0.010000	0.07245	0.680000	0.25306	-1.725000	0.01371	0.459000	0.35465	GTC	T|0.862;G|0.138	0.138	strong		0.483	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
ATP1A4	480	hgsc.bcm.edu	37	1	160136350	160136350	+	Silent	SNP	G	G	A	rs7529215	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:160136350G>A	ENST00000368081.4	+	8	1551	c.1080G>A	c.(1078-1080)gcG>gcA	p.A360A		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	360					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGCGCATGGCGCGGAAGAACT	0.567													g|||	2345	0.468251	0.2806	0.5375	5008	,	,		19774	0.4851		0.5457	False		,,,				2504	0.5757				p.A360A		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G1080A						PASS	.	A		1475,2931	473.1+/-356.6	267,941,995	88.0	79.0	82.0		1080	-8.6	0.0	1	dbSNP_116	82	4867,3733	618.0+/-396.7	1413,2041,846	no	coding-synonymous	ATP1A4	NM_144699.3		1680,2982,1841	AA,AG,GG		43.407,33.4771,48.7621		360/1030	160136350	6342,6664	2203	4300	6503	SO:0001819	synonymous_variant	480	exon8			CATGGCGCGGAAG	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.1080G>A	1.37:g.160136350G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	170	167	0.982353	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																			G|0.522;A|0.478	0.478	strong		0.567	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
MICA	100507436	hgsc.bcm.edu	37	6	31378388	31378388	+	Missense_Mutation	SNP	G	G	A	rs1051785|rs386699190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31378388G>A	ENST00000449934.2	+	2	193	c.139G>A	c.(139-141)Gct>Act	p.A47T	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				AGGGTTTCTTGCTGAGGTACA	0.532													g|||	324	0.0646965	0.0832	0.0533	5008	,	,		19486	0.0665		0.0736	False		,,,				2504	0.0368				p.A47T		Atlas-SNP	.											MICA,bladder,carcinoma,+1,1	MICA	21	1	0			c.G139A						PASS	.						21.0	23.0	22.0					6																	31378388		692	1591	2283	SO:0001583	missense	100507436	exon2			TTTCTTGCTGAGG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.139G>A	6.37:g.31378388G>A	ENSP00000413079:p.Ala47Thr	Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	237	232	0.978903	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	142	0.06501831501831502	33	0.06707317073170732	23	0.06353591160220995	39	0.06818181818181818	47	0.06200527704485488	N	11.46	1.646749	0.29246	.	.	ENSG00000204520	ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.01981	4.52;4.52	2.89	-2.53	0.06326	.	0.450854	0.16219	N	0.224130	T	0.00524	0.0017	.	.	.	0.80722	P	0.0	B	0.25007	0.116	B	0.29942	0.109	T	0.47005	-0.9150	8	0.36615	T	0.2	.	1.2016	0.01886	0.1299:0.1868:0.3044:0.3789	rs1051785;rs3192166;rs16899588;rs17200151;rs17883926	47	Q96QC4	.	T	47;47;47;34	ENSP00000413079:A47T;ENSP00000402410:A34T	ENSP00000365394:A47T	A	+	1	0	MICA	31486367	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.423000	0.07034	-0.415000	0.07484	0.306000	0.20318	GCT	G|0.934;A|0.066	0.066	strong		0.532	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
NCKAP5	344148	hgsc.bcm.edu	37	2	133540708	133540708	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:133540708C>T	ENST00000409261.1	-	14	4049	c.3676G>A	c.(3676-3678)Gaa>Aaa	p.E1226K	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000473859.1_5'Flank|NCKAP5_ENST00000317721.6_Missense_Mutation_p.E1226K|NCKAP5_ENST00000405974.3_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1226										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						AGTGCTGTTTCCAGGGGAAGC	0.502																																					p.E1226K		Atlas-SNP	.											NCKAP5,NS,carcinoma,0,1	NCKAP5	322	1	0			c.G3676A						scavenged	.						116.0	111.0	113.0					2																	133540708		1940	4162	6102	SO:0001583	missense	344148	exon14			CTGTTTCCAGGGG	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.3676G>A	2.37:g.133540708C>T	ENSP00000387128:p.Glu1226Lys	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	195	5	0.025641	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740635	0.89573	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10960	2.82;2.82	5.28	5.28	0.74379	.	0.423150	0.16895	U	0.195177	T	0.13072	0.0317	L	0.29908	0.895	0.80722	D	1	P	0.52316	0.952	P	0.49085	0.6	T	0.14783	-1.0460	10	0.11182	T	0.66	.	17.2841	0.87136	0.0:1.0:0.0:0.0	.	1226	O14513	NCKP5_HUMAN	K	1226	ENSP00000387128:E1226K;ENSP00000380603:E1226K	ENSP00000380603:E1226K	E	-	1	0	NCKAP5	133257178	0.283000	0.24277	0.054000	0.19295	0.307000	0.27823	1.924000	0.40065	2.738000	0.93877	0.655000	0.94253	GAA	.	.	none		0.502	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
TTLL10	254173	hgsc.bcm.edu	37	1	1115503	1115503	+	Missense_Mutation	SNP	T	T	C	rs111751804	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1115503T>C	ENST00000379290.1	+	6	462	c.289T>C	c.(289-291)Tgt>Cgt	p.C97R	TTLL10-AS1_ENST00000379317.1_RNA|TTLL10_ENST00000379288.3_Missense_Mutation_p.C24R|TTLL10_ENST00000379289.1_Missense_Mutation_p.C97R			Q6ZVT0	TTL10_HUMAN	tubulin tyrosine ligase-like family, member 10	97					cellular protein modification process (GO:0006464)					haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;4.75e-36)|OV - Ovarian serous cystadenocarcinoma(86;5.82e-22)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGATGGACACTGTGGGCCGGA	0.677													T|||	53	0.0105831	0.0038	0.0072	5008	,	,		11056	0.0		0.0308	False		,,,				2504	0.0123				p.C97R		Atlas-SNP	.											.	TTLL10	66	.	0			c.T289C						PASS	.	T	ARG/CYS,ARG/CYS	18,4382		0,18,2182	25.0	31.0	29.0		289,70	-3.2	0.0	1	dbSNP_132	29	217,8375		6,205,4085	yes	missense,missense	TTLL10	NM_001130045.1,NM_153254.2	180,180	6,223,6267	CC,CT,TT		2.5256,0.4091,1.8088	benign,benign	97/674,24/405	1115503	235,12757	2200	4296	6496	SO:0001583	missense	254173	exon6			GGACACTGTGGGC	AK093438	CCDS8.1, CCDS44036.1	1p36.33	2014-01-28	2005-07-29	2005-07-29	ENSG00000162571	ENSG00000162571		"""Tubulin tyrosine ligase-like family"""	26693	protein-coding gene	gene with protein product			"""tubulin tyrosine ligase-like family, member 5"""	TTLL5		15890843	Standard	NM_153254		Approved	FLJ36119	uc001acy.2	Q6ZVT0	OTTHUMG00000000851	ENST00000379290.1:c.289T>C	1.37:g.1115503T>C	ENSP00000368592:p.Cys97Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	72	66	0.916667	NM_001130045	B1AMF6|Q5T2W4|Q5T2W5|Q8N9X2	Missense_Mutation	SNP	ENST00000379290.1	37	CCDS44036.1	28	0.01282051282051282	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	23	0.030343007915567283	T	2.361	-0.346594	0.05208	0.004091	0.025256	ENSG00000162571	ENST00000379290;ENST00000379289;ENST00000379288	T;T;T	0.16743	3.39;3.39;2.32	3.4	-3.17	0.05202	.	.	.	.	.	T	0.02888	0.0086	N	0.22421	0.69	0.09310	N	1	B;B	0.22683	0.073;0.044	B;B	0.22753	0.041;0.025	T	0.32188	-0.9916	9	0.52906	T	0.07	.	5.0326	0.14417	0.0:0.4086:0.1734:0.418	.	24;97	Q6ZVT0-3;Q6ZVT0	.;TTL10_HUMAN	R	97;97;24	ENSP00000368592:C97R;ENSP00000368591:C97R;ENSP00000368590:C24R	ENSP00000368590:C24R	C	+	1	0	TTLL10	1105366	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.367000	0.07553	-0.708000	0.05015	-1.055000	0.02315	TGT	T|0.985;C|0.015	0.015	strong		0.677	TTLL10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002421.3	NM_153254	
AKAP9	10142	hgsc.bcm.edu	37	7	91708898	91708898	+	Missense_Mutation	SNP	A	A	G	rs35759833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:91708898A>G	ENST00000359028.2	+	32	7712	c.7487A>G	c.(7486-7488)aAa>aGa	p.K2496R	AKAP9_ENST00000356239.3_Missense_Mutation_p.K2484R|AKAP9_ENST00000358100.2_Missense_Mutation_p.K2496R			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2496	Glu-rich.		K -> R (in dbSNP:rs35759833).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACATACTTCAAATCTTTTGAA	0.378			T	BRAF	papillary thyroid								A|||	328	0.0654952	0.0136	0.0605	5008	,	,		19752	0.0327		0.1252	False		,,,				2504	0.1115				p.K2484R		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,colon,carcinoma,0,2	AKAP9	788	2	0			c.A7451G						PASS	.	A	ARG/LYS,ARG/LYS	134,4272	93.4+/-132.2	2,130,2071	54.0	56.0	55.0		7451,7427	-8.7	0.0	7	dbSNP_126	55	1095,7505	225.7+/-261.6	72,951,3277	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	26,26	74,1081,5348	GG,GA,AA		12.7326,3.0413,9.4495	benign,benign	2484/3908,2476/3900	91708898	1229,11777	2203	4300	6503	SO:0001583	missense	10142	exon31			ACTTCAAATCTTT	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.7487A>G	7.37:g.91708898A>G	ENSP00000351922:p.Lys2496Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	48	27	0.5625	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		146	0.06684981684981685	10	0.02032520325203252	24	0.06629834254143646	9	0.015734265734265736	103	0.1358839050131926	A	2.366	-0.345577	0.05208	0.030413	0.127326	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.03386	4.04;4.04;4.05;3.95	4.37	-8.74	0.00838	.	1.680560	0.03658	N	0.242093	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.45293	-0.9271	9	0.11794	T	0.64	.	5.2652	0.15595	0.1954:0.2911:0.423:0.0905	rs35759833;rs61749903	2488;2496;2484;2476	Q99996-6;Q99996;Q99996-2;Q99996-3	.;AKAP9_HUMAN;.;.	R	2484;2496;2496;2488;330	ENSP00000348573:K2484R;ENSP00000351922:K2496R;ENSP00000350813:K2496R;ENSP00000378042:K330R	ENSP00000348573:K2484R	K	+	2	0	AKAP9	91546834	0.000000	0.05858	0.000000	0.03702	0.172000	0.22775	-0.864000	0.04254	-1.991000	0.00976	-0.334000	0.08254	AAA	A|0.911;G|0.089	0.089	strong		0.378	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768416	31768416	+	Silent	SNP	A	A	G	rs3745784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:31768416A>G	ENST00000240587.4	-	2	2610	c.2283T>C	c.(2281-2283)gcT>gcC	p.A761A		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	761					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)					TGGCCACAGCAGCCTTCTCCG	0.592													G|||	1558	0.311102	0.5923	0.2637	5008	,	,		15913	0.249		0.1133	False		,,,				2504	0.2321				p.A761A		Atlas-SNP	.											.	TSHZ3	549	.	0			c.T2283C						PASS	.	G		2295,2111	570.4+/-382.8	610,1075,518	63.0	64.0	64.0		2283	-8.5	0.7	19	dbSNP_107	64	1147,7453	759.6+/-407.6	79,989,3232	no	coding-synonymous	TSHZ3	NM_020856.2		689,2064,3750	GG,GA,AA		13.3372,47.9119,26.4647		761/1082	31768416	3442,9564	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CACAGCAGCCTTC	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.2283T>C	19.37:g.31768416A>G		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	115	56	0.486957	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			A|0.717;G|0.283	0.283	strong		0.592	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
DNAAF1	123872	hgsc.bcm.edu	37	16	84203939	84203939	+	Missense_Mutation	SNP	C	C	T	rs11644164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84203939C>T	ENST00000378553.5	+	8	1629	c.1505C>T	c.(1504-1506)cCg>cTg	p.P502L	DNAAF1_ENST00000563818.1_3'UTR	NM_178452.4	NP_848547.4	Q8NEP3	DAAF1_HUMAN	dynein, axonemal, assembly factor 1	502	Pro-rich.		P -> L (in dbSNP:rs11644164). {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)			NS(1)|endometrium(7)|kidney(1)|large_intestine(6)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(4)|urinary_tract(1)	41						CCACCACCACCGCCCCTGGGA	0.617													C|||	1405	0.280551	0.1188	0.3732	5008	,	,		17054	0.3393		0.3668	False		,,,				2504	0.2843				p.P502L		Atlas-SNP	.											.	DNAAF1	81	.	0			c.C1505T						PASS	.	C	LEU/PRO	700,3684		61,578,1553	27.0	29.0	29.0		1505	-0.2	0.0	16	dbSNP_120	29	3176,5402		595,1986,1708	yes	missense	DNAAF1	NM_178452.4	98	656,2564,3261	TT,TC,CC		37.0249,15.9672,29.9028	benign	502/726	84203939	3876,9086	2192	4289	6481	SO:0001583	missense	123872	exon8			CACCACCGCCCCT	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.1505C>T	16.37:g.84203939C>T	ENSP00000367815:p.Pro502Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	35	35	1	NM_178452	B4DJA3|Q69YI8|Q69YJ0|Q69YW5|Q96LP3|Q96MB6	Missense_Mutation	SNP	ENST00000378553.5	37	CCDS10943.2	675	0.3090659340659341	64	0.13008130081300814	126	0.34806629834254144	209	0.36538461538461536	276	0.3641160949868074	C	0.594	-0.831873	0.02713	0.159672	0.370249	ENSG00000154099	ENST00000378553	T	0.24538	1.85	1.8	-0.199	0.13220	.	3.054110	0.02863	N	0.130553	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.12013	0.005;0.003	B;B	0.08055	0.003;0.003	T	0.42749	-0.9433	9	0.35671	T	0.21	.	4.3436	0.11122	0.0:0.6311:0.0:0.3689	rs11644164;rs17845734;rs17858684;rs52814244;rs11644164	266;502	Q8NEP3-2;Q8NEP3	.;DAAF1_HUMAN	L	502	ENSP00000367815:P502L	ENSP00000367815:P502L	P	+	2	0	DNAAF1	82761440	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.991000	0.03728	-0.028000	0.13850	-0.751000	0.03497	CCG	C|0.703;T|0.297	0.297	strong		0.617	DNAAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250328.3	NM_178452	
OR7D4	125958	hgsc.bcm.edu	37	19	9325252	9325252	+	Missense_Mutation	SNP	G	G	A	rs61729907	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9325252G>A	ENST00000308682.2	-	1	290	c.262C>T	c.(262-264)Cgg>Tgg	p.R88W		NM_001005191.2	NP_001005191.1	Q8NG98	OR7D4_HUMAN	olfactory receptor, family 7, subfamily D, member 4	88			R -> W (impaired response to androstenone and androstadienone; when associated with M-133; dbSNP:rs61729907). {ECO:0000269|PubMed:17873857}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|skin(3)|stomach(1)	26						TCTTTGCTCCGTGCCTGGATG	0.493													G|||	739	0.147564	0.0567	0.1066	5008	,	,		23181	0.2163		0.2008	False		,,,				2504	0.1738				p.R88W		Atlas-SNP	.											.	OR7D4	66	.	0			c.C262T						PASS	.	G	TRP/ARG	350,4056	181.2+/-209.3	7,336,1860	80.0	72.0	74.0		262	0.4	0.0	19	dbSNP_129	74	1572,7028	291.5+/-300.3	137,1298,2865	no	missense	OR7D4	NM_001005191.2	101	144,1634,4725	AA,AG,GG		18.2791,7.9437,14.7778	probably-damaging	88/313	9325252	1922,11084	2203	4300	6503	SO:0001583	missense	125958	exon1			TGCTCCGTGCCTG		CCDS32901.1	19p13.2	2013-12-17		2004-03-10	ENSG00000174667	ENSG00000174667		"""GPCR / Class A : Olfactory receptors"""	8380	protein-coding gene	gene with protein product		611538		OR7D4P			Standard	NM_001005191		Approved	hg105, OR19-B	uc002mla.2	Q8NG98	OTTHUMG00000179936	ENST00000308682.2:c.262C>T	19.37:g.9325252G>A	ENSP00000310488:p.Arg88Trp	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	155	76	0.490323	NM_001005191	A8CAH8|A8CAH9|A8CAI0|A8CAI1|B9EH79	Missense_Mutation	SNP	ENST00000308682.2	37	CCDS32901.1	341	0.15613553113553114	22	0.044715447154471545	38	0.10497237569060773	130	0.22727272727272727	151	0.19920844327176782	G	7.331	0.619028	0.14129	0.079437	0.182791	ENSG00000174667	ENST00000308682	T	0.05447	3.44	4.0	0.407	0.16371	GPCR, rhodopsin-like superfamily (1);	1.279690	0.05122	N	0.490958	T	0.00012	0.0000	L	0.39633	1.23	0.80722	P	0.0	P	0.44659	0.84	B	0.38562	0.276	T	0.47749	-0.9093	9	0.72032	D	0.01	.	8.2617	0.31788	0.0867:0.2955:0.6177:0.0	.	88	Q8NG98	OR7D4_HUMAN	W	88	ENSP00000310488:R88W	ENSP00000310488:R88W	R	-	1	2	OR7D4	9186252	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.901000	0.01597	0.095000	0.17434	0.436000	0.28706	CGG	G|0.845;A|0.155	0.155	strong		0.493	OR7D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449004.1		
RBMX	27316	hgsc.bcm.edu	37	X	135958704	135958704	+	Missense_Mutation	SNP	G	G	C	rs112089728		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135958704G>C	ENST00000320676.7	-	5	653	c.499C>G	c.(499-501)Cct>Gct	p.P167A	RBMX_ENST00000562646.1_Missense_Mutation_p.P167A|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Missense_Mutation_p.P39A|RBMX_ENST00000570135.1_Missense_Mutation_p.P32A|SNORD61_ENST00000384252.1_RNA|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	167					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.P167A(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					GGTCCTGAAGGTGCAGATCTC	0.453																																					p.P167A		Atlas-SNP	.											.	RBMX	149	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C499G						PASS	.						122.0	109.0	113.0					X																	135958704		2203	4300	6503	SO:0001583	missense	27316	exon5			CTGAAGGTGCAGA		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.499C>G	X.37:g.135958704G>C	ENSP00000359645:p.Pro167Ala	Somatic	251	0	0		WXS	Illumina HiSeq	Phase_I	340	54	0.158824	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	19.40	3.820034	0.71028	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.79247	-1.25	5.52	5.52	0.82312	.	0.000000	0.85682	U	0.000000	T	0.74306	0.3699	L	0.53561	1.675	0.09310	P	0.999999244383	P;B	0.38335	0.627;0.162	B;B	0.32980	0.156;0.037	T	0.80574	-0.1322	9	0.62326	D	0.03	.	18.5809	0.91171	0.0:0.0:1.0:0.0	.	167;154	P38159;Q8N8Y7	HNRPG_HUMAN;.	A	167;154	ENSP00000359645:P167A	ENSP00000359645:P167A	P	-	1	0	RBMX	135786370	1.000000	0.71417	0.984000	0.44739	0.984000	0.73092	8.740000	0.91579	2.331000	0.79229	0.592000	0.82586	CCT	.	.	weak		0.453	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
FGD4	121512	hgsc.bcm.edu	37	12	32735236	32735236	+	Silent	SNP	C	C	T	rs904582	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:32735236C>T	ENST00000427716.2	+	4	859	c.435C>T	c.(433-435)gaC>gaT	p.D145D	FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000546442.1_Silent_p.D52D|FGD4_ENST00000534526.2_Silent_p.D282D|FGD4_ENST00000472289.1_Silent_p.D145D|FGD4_ENST00000525053.1_Silent_p.D257D|FGD4_ENST00000531134.1_Silent_p.D230D	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	145	Actin filament-binding. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|microspike assembly (GO:0030035)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	27	Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)					CCACAACAGACAGCTGTGATG	0.488													T|||	2339	0.467053	0.7247	0.4928	5008	,	,		1102	0.2401		0.4036	False		,,,				2504	0.3998				p.D145D		Atlas-SNP	.											.	FGD4	86	.	0			c.C435T						PASS	.	T		3031,1375	434.7+/-344.0	1023,985,195	93.0	90.0	91.0		435	-0.2	0.0	12	dbSNP_86	91	3458,5142	637.0+/-399.2	710,2038,1552	no	coding-synonymous	FGD4	NM_139241.2		1733,3023,1747	TT,TC,CC		40.2093,31.2074,49.8924		145/767	32735236	6489,6517	2203	4300	6503	SO:0001819	synonymous_variant	121512	exon4			AACAGACAGCTGT	AK057294	CCDS8727.1	12p11.1	2014-09-17	2004-08-24		ENSG00000139132	ENSG00000139132		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19125	protein-coding gene	gene with protein product		611104	"""FGD1 family, member 4"""			11527409	Standard	NM_139241		Approved	FRABP, frabin, ZFYVE6, CMT4H	uc001rkz.3	Q96M96	OTTHUMG00000137374	ENST00000427716.2:c.435C>T	12.37:g.32735236C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	93	47	0.505376	NM_139241	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																			C|0.515;T|0.485	0.485	strong		0.488	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241	
HUNK	30811	hgsc.bcm.edu	37	21	33371123	33371123	+	Missense_Mutation	SNP	C	C	T	rs10775648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33371123C>T	ENST00000270112.2	+	11	2131	c.1771C>T	c.(1771-1773)Cgc>Tgc	p.R591C		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	591			R -> C (in dbSNP:rs10775648). {ECO:0000269|PubMed:17344846}.		multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						CAGCTTGGCTCGCAGAAATTC	0.567													C|||	1051	0.209864	0.0431	0.2378	5008	,	,		17721	0.2897		0.2256	False		,,,				2504	0.317				p.R591C		Atlas-SNP	.											.	HUNK	74	.	0			c.C1771T						PASS	.	C	CYS/ARG	351,4055	182.9+/-210.6	12,327,1864	56.0	48.0	51.0		1771	3.5	0.0	21	dbSNP_120	51	1960,6640	345.9+/-325.9	234,1492,2574	yes	missense	HUNK	NM_014586.1	180	246,1819,4438	TT,TC,CC		22.7907,7.9664,17.7687	probably-damaging	591/715	33371123	2311,10695	2203	4300	6503	SO:0001583	missense	30811	exon11			TTGGCTCGCAGAA	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"""hormonally upregulated Neu-associated kinase"""			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.1771C>T	21.37:g.33371123C>T	ENSP00000270112:p.Arg591Cys	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	43	0.511905	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	458	0.2097069597069597	21	0.042682926829268296	81	0.22375690607734808	195	0.3409090909090909	161	0.21240105540897097	C	15.63	2.890611	0.52014	0.079664	0.227907	ENSG00000142149	ENST00000270112	T	0.70869	-0.52	4.39	3.5	0.40072	.	0.236050	0.33772	N	0.004580	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	D	0.62365	0.991	P	0.47528	0.549	T	0.15723	-1.0427	9	0.62326	D	0.03	-14.5311	8.5968	0.33721	0.0:0.7514:0.157:0.0916	rs10775648;rs58214837;rs10775648	591	P57058	HUNK_HUMAN	C	591	ENSP00000270112:R591C	ENSP00000270112:R591C	R	+	1	0	HUNK	32292994	0.165000	0.22948	0.001000	0.08648	0.901000	0.52897	3.127000	0.50484	1.050000	0.40346	0.491000	0.48974	CGC	C|0.807;T|0.193	0.193	strong		0.567	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626627	140626627	+	Missense_Mutation	SNP	G	G	A	rs618096	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140626627G>A	ENST00000231173.3	+	1	1481	c.1481G>A	c.(1480-1482)cGg>cAg	p.R494Q		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	494	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> Q (in dbSNP:rs618096). {ECO:0000269|PubMed:15489334}.		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGCCGCCCCGGGACCCGCAC	0.662													A|||	3253	0.649561	0.7935	0.6326	5008	,	,		13818	0.6597		0.5497	False		,,,				2504	0.5593				p.R494Q		Atlas-SNP	.											.	PCDHB15	138	.	0			c.G1481A						PASS	.	A	GLN/ARG	3324,1082	380.9+/-323.9	1256,812,135	71.0	85.0	81.0		1481	-7.2	0.0	5	dbSNP_83	81	4890,3710	520.5+/-379.7	1426,2038,836	no	missense	PCDHB15	NM_018935.2	43	2682,2850,971	AA,AG,GG		43.1395,24.5574,36.8445	benign	494/788	140626627	8214,4792	2203	4300	6503	SO:0001583	missense	56121	exon1			CGCCCCGGGACCC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1481G>A	5.37:g.140626627G>A	ENSP00000231173:p.Arg494Gln	Somatic	216	2	0.00925926		WXS	Illumina HiSeq	Phase_I	233	229	0.982833	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	1380	0.6318681318681318	386	0.7845528455284553	209	0.5773480662983426	374	0.6538461538461539	411	0.5422163588390502	A	0.007	-2.005608	0.00426	0.754426	0.568605	ENSG00000113248	ENST00000231173	T	0.60424	0.19	4.62	-7.24	0.01475	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.01529	-0.815	0.80722	P	0.0	B	0.10296	0.003	B	0.12156	0.007	T	0.43426	-0.9392	8	0.02654	T	1	.	0.8001	0.01074	0.204:0.2148:0.2998:0.2814	rs618096;rs3776092;rs17844624;rs17857171;rs59503282	494	Q9Y5E8	PCDBF_HUMAN	Q	494	ENSP00000231173:R494Q	ENSP00000231173:R494Q	R	+	2	0	PCDHB15	140606811	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.069000	0.01381	-1.231000	0.02557	-2.572000	0.00171	CGG	G|0.364;A|0.636	0.636	strong		0.662	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
JPH2	57158	hgsc.bcm.edu	37	20	42743454	42743454	+	Silent	SNP	A	A	G	rs6093935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:42743454A>G	ENST00000372980.3	-	5	2945	c.2073T>C	c.(2071-2073)ttT>ttC	p.F691F		NM_020433.4	NP_065166.2	Q9BR39	JPH2_HUMAN	junctophilin 2	691					calcium ion homeostasis (GO:0055074)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport into cytosol (GO:0060402)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle tissue development (GO:0055024)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium-release channel activity (GO:0015278)|phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			GGAGGTGAACAAAGAGGATGG	0.622													G|||	1289	0.257388	0.469	0.219	5008	,	,		18425	0.1101		0.3101	False		,,,				2504	0.0961				p.F691F		Atlas-SNP	.											.	JPH2	86	.	0			c.T2073C						PASS	.	G		1973,2431	592.6+/-387.8	437,1099,666	117.0	75.0	89.0		2073	-0.3	1.0	20	dbSNP_114	89	2636,5964	668.3+/-402.5	404,1828,2068	no	coding-synonymous	JPH2	NM_020433.4		841,2927,2734	GG,GA,AA		30.6512,44.8002,35.4429		691/697	42743454	4609,8395	2202	4300	6502	SO:0001819	synonymous_variant	57158	exon5			GTGAACAAAGAGG	AL034419	CCDS13325.1, CCDS13326.1	20q12-q13.11	2014-09-17			ENSG00000149596	ENSG00000149596			14202	protein-coding gene	gene with protein product		605267				10891348, 10949023	Standard	XM_006723832		Approved	JP-2	uc002xli.1	Q9BR39	OTTHUMG00000033037	ENST00000372980.3:c.2073T>C	20.37:g.42743454A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	113	65	0.575221	NM_020433	E1P5X1|O95913|Q5JY74|Q9UJN4	Silent	SNP	ENST00000372980.3	37	CCDS13325.1																																																																																			A|0.685;G|0.315	0.315	strong		0.622	JPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080307.1		
GSTM5	2949	hgsc.bcm.edu	37	1	110257831	110257831	+	Missense_Mutation	SNP	T	T	C	rs2227963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110257831T>C	ENST00000256593.3	+	7	594	c.536T>C	c.(535-537)cTa>cCa	p.L179P	GSTM5_ENST00000369813.1_Missense_Mutation_p.L138P|GSTM5_ENST00000369812.5_Missense_Mutation_p.L198P|GSTM5_ENST00000492718.1_3'UTR	NM_000851.3	NP_000842.2	P46439	GSTM5_HUMAN	glutathione S-transferase mu 5	179	GST C-terminal.		L -> P (in dbSNP:rs2227963).		glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)	p.L179P(4)		NS(1)|central_nervous_system(6)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	21		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Colorectal(144;0.0131)|all cancers(265;0.0252)|Epithelial(280;0.0265)|Lung(183;0.0425)|COAD - Colon adenocarcinoma(174;0.0474)|LUSC - Lung squamous cell carcinoma(189;0.228)	Glutathione(DB00143)	GACGCCTTCCTAAACTTGAAG	0.478													T|||	703	0.140375	0.3941	0.0663	5008	,	,		19912	0.001		0.0845	False		,,,				2504	0.0511				p.L179P		Atlas-SNP	.											GSTM5,scalp,carcinoma,0,13	GSTM5	89	13	4	Substitution - Missense(4)	central_nervous_system(3)|skin(1)	c.T536C						PASS	.	T	PRO/LEU	1097,3309		276,545,1382	189.0	205.0	199.0		536	3.1	0.7	1	dbSNP_98	199	399,8201		16,367,3917	yes	missense	GSTM5	NM_000851.3	98	292,912,5299	CC,CT,TT		4.6395,24.8979,11.5024	benign	179/219	110257831	1496,11510	2203	4300	6503	SO:0001583	missense	2949	exon7			CCTTCCTAAACTT	L02321	CCDS811.1	1p13.3	2012-06-21	2008-11-26		ENSG00000134201	ENSG00000134201	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4637	protein-coding gene	gene with protein product		138385	"""glutathione S-transferase M5"""			8473333	Standard	NM_000851		Approved		uc001dyn.3	P46439	OTTHUMG00000011644	ENST00000256593.3:c.536T>C	1.37:g.110257831T>C	ENSP00000256593:p.Leu179Pro	Somatic	447	2	0.00447427		WXS	Illumina HiSeq	Phase_I	472	234	0.495763	NM_000851	A8K0V8|Q6PD78	Missense_Mutation	SNP	ENST00000256593.3	37	CCDS811.1	295	0.13507326007326007	204	0.4146341463414634	26	0.0718232044198895	0	0.0	65	0.08575197889182058	t	0.004	-2.358658	0.00214	0.248979	0.046395	ENSG00000134201	ENST00000256593;ENST00000369813;ENST00000369812	T;T;T	0.00691	5.84;5.84;5.84	5.02	3.11	0.35812	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.335277	0.25598	N	0.029571	T	0.00039	0.0001	N	0.00005	-3.3	0.27811	P	0.9421374	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.07673	-1.0760	9	0.02654	T	1	.	6.4549	0.21924	0.317:0.597:0.0:0.0859	rs2227963;rs61309452	138;179	Q5T8Q9;P46439	.;GSTM5_HUMAN	P	179;138;198	ENSP00000256593:L179P;ENSP00000358828:L138P;ENSP00000358827:L198P	ENSP00000256593:L179P	L	+	2	0	GSTM5	110059354	0.997000	0.39634	0.702000	0.30337	0.065000	0.16274	3.314000	0.51943	0.584000	0.29591	-0.206000	0.12725	CTA	T|0.847;C|0.153	0.153	strong		0.478	GSTM5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032200.1	NM_000851	
COL4A2	1284	hgsc.bcm.edu	37	13	111119396	111119396	+	Missense_Mutation	SNP	G	G	C	rs3803230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:111119396G>C	ENST00000360467.5	+	27	2354	c.2048G>C	c.(2047-2049)gGa>gCa	p.G683A		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	683	Triple-helical region.		G -> A (in dbSNP:rs3803230). {ECO:0000269|PubMed:21527998, ECO:0000269|PubMed:22209247, ECO:0000269|PubMed:3345760}.		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)			GGTTGCATAGGAGGGCCCAAG	0.597													G|||	520	0.103834	0.0923	0.1052	5008	,	,		16600	0.1081		0.1233	False		,,,				2504	0.0941				p.G683A		Atlas-SNP	.											.	COL4A2	178	.	0			c.G2048C						PASS	.	G	ALA/GLY	372,3502		17,338,1582	103.0	110.0	108.0		2048	1.4	0.5	13	dbSNP_107	108	883,7369		37,809,3280	yes	missense	COL4A2	NM_001846.2	60	54,1147,4862	CC,CG,GG		10.7004,9.6025,10.3497	benign	683/1713	111119396	1255,10871	1937	4126	6063	SO:0001583	missense	1284	exon27			GCATAGGAGGGCC	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.2048G>C	13.37:g.111119396G>C	ENSP00000353654:p.Gly683Ala	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	98	55	0.561224	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Missense_Mutation	SNP	ENST00000360467.5	37	CCDS41907.1	216	0.0989010989010989	39	0.07926829268292683	46	0.1270718232044199	50	0.08741258741258741	81	0.10686015831134564	G	0.482	-0.879608	0.02530	0.096025	0.107004	ENSG00000134871	ENST00000360467;ENST00000257309	D	0.97850	-4.57	4.22	1.39	0.22231	.	0.886687	0.09520	N	0.791026	T	0.07999	0.0200	N	0.01277	-0.915	0.58432	P	9.99999999995449E-6	B	0.10296	0.003	B	0.14023	0.01	T	0.67284	-0.5709	9	0.11485	T	0.65	.	4.9098	0.13816	0.2096:0.1933:0.5971:0.0	rs3803230;rs52833101;rs3803230	683	P08572	CO4A2_HUMAN	A	683	ENSP00000353654:G683A	ENSP00000257309:G683A	G	+	2	0	COL4A2	109917397	0.686000	0.27661	0.524000	0.27887	0.611000	0.37282	0.487000	0.22356	0.136000	0.18733	0.609000	0.83330	GGA	G|0.898;C|0.102	0.102	strong		0.597	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846	
TRIM31	11074	hgsc.bcm.edu	37	6	30075864	30075864	+	Silent	SNP	A	A	G	rs2023472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30075864A>G	ENST00000376734.3	-	6	974	c.849T>C	c.(847-849)caT>caC	p.H283H	TRIM31-AS1_ENST00000440874.1_RNA|TRIM31_ENST00000540829.1_Silent_p.H283H|TRIM31_ENST00000485864.1_5'UTR	NM_007028.3	NP_008959.3	Q9BZY9	TRI31_HUMAN	tripartite motif containing 31	283					innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral release from host cell (GO:1902186)	mitochondrion (GO:0005739)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.H283H(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(2)	15						TGATGGAGTCATGTCTTGATT	0.438													A|||	3694	0.73762	0.6346	0.7104	5008	,	,		20070	0.869		0.6362	False		,,,				2504	0.865				p.H283H		Atlas-SNP	.											TRIM31,NS,carcinoma,0,1	TRIM31	40	1	1	Substitution - coding silent(1)	prostate(1)	c.T849C						PASS	.	A		1983,1039		647,689,175	75.0	74.0	74.0		849	0.7	0.4	6	dbSNP_94	74	3328,2090		1018,1292,399	yes	coding-synonymous	TRIM31	NM_007028.3		1665,1981,574	GG,GA,AA		38.5751,34.3812,37.0735		283/426	30075864	5311,3129	1511	2709	4220	SO:0001819	synonymous_variant	11074	exon6			GGAGTCATGTCTT	AF230386	CCDS34374.1	6p21.3	2013-01-09	2011-01-25		ENSG00000204616	ENSG00000204616		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16289	protein-coding gene	gene with protein product		609316	"""tripartite motif-containing 31"""			11331580	Standard	XM_006714977		Approved	RNF, HCGI, C6orf13, HCG1	uc003npg.1	Q9BZY9	OTTHUMG00000031064	ENST00000376734.3:c.849T>C	6.37:g.30075864A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_007028	A6NLX6|A9R9Q4|Q53H52|Q5RI37|Q5SRJ7|Q5SRJ8|Q5SS28|Q96AK4|Q96AP8|Q99579|Q9BZY8	Silent	SNP	ENST00000376734.3	37	CCDS34374.1																																																																																			A|0.348;G|0.652	0.652	strong		0.438	TRIM31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076081.2		
DIS3L	115752	hgsc.bcm.edu	37	15	66625161	66625161	+	Silent	SNP	A	A	G	rs11071885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:66625161A>G	ENST00000319212.4	+	16	2819	c.2769A>G	c.(2767-2769)ccA>ccG	p.P923P	RP11-352G18.2_ENST00000565993.1_RNA|DIS3L_ENST00000319194.5_Silent_p.P840P	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	923					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						AATGGAAACCAGGATCCCTTC	0.383													A|||	404	0.0806709	0.0923	0.0648	5008	,	,		16248	0.0427		0.1044	False		,,,				2504	0.091				p.P923P		Atlas-SNP	.											.	DIS3L	175	.	0			c.A2769G						PASS	.	A	,	337,4065	176.2+/-205.4	16,305,1880	82.0	80.0	80.0		2769,2520	3.2	1.0	15	dbSNP_120	80	734,7864	179.0+/-228.3	25,684,3590	no	coding-synonymous,coding-synonymous	DIS3L	NM_001143688.1,NM_133375.3	,	41,989,5470	GG,GA,AA		8.5369,7.6556,8.2385	,	923/1055,840/972	66625161	1071,11929	2201	4299	6500	SO:0001819	synonymous_variant	115752	exon16			GAAACCAGGATCC		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.2769A>G	15.37:g.66625161A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	128	58	0.453125	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	37	CCDS45286.1																																																																																			A|0.924;G|0.076	0.076	strong		0.383	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375	
TREM1	54210	hgsc.bcm.edu	37	6	41250179	41250179	+	Silent	SNP	C	C	T	rs2234239	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41250179C>T	ENST00000244709.4	-	2	423	c.360G>A	c.(358-360)aaG>aaA	p.K120K	TREM1_ENST00000591620.1_Silent_p.K120K|TREM1_ENST00000334475.6_Silent_p.K120K|TREM1_ENST00000589614.1_Silent_p.K120K	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	120	Ig-like V-type.				blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					TGTGAGGCTCCTTGGGAGGCT	0.542													C|||	110	0.0219649	0.0053	0.0403	5008	,	,		20298	0.0		0.0616	False		,,,				2504	0.0133				p.K120K		Atlas-SNP	.											.	TREM1	38	.	0			c.G360A						PASS	.	C	,,	43,4363	45.3+/-79.5	0,43,2160	75.0	58.0	64.0		360,360,360	-8.5	0.0	6	dbSNP_98	64	458,8142	135.7+/-192.9	8,442,3850	no	coding-synonymous,coding-synonymous,coding-synonymous	TREM1	NM_001242589.1,NM_001242590.1,NM_018643.3	,,	8,485,6010	TT,TC,CC		5.3256,0.9759,3.8521	,,	120/226,120/151,120/235	41250179	501,12505	2203	4300	6503	SO:0001819	synonymous_variant	54210	exon2			AGGCTCCTTGGGA	AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.360G>A	6.37:g.41250179C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	142	65	0.457746	NM_001242590	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Silent	SNP	ENST00000244709.4	37	CCDS4854.1																																																																																			C|0.964;T|0.036	0.036	strong		0.542	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643	
KHK	3795	hgsc.bcm.edu	37	2	27315252	27315252	+	Missense_Mutation	SNP	G	G	A	rs2304681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27315252G>A	ENST00000260599.6	+	2	658	c.145G>A	c.(145-147)Gtt>Att	p.V49I	KHK_ENST00000490823.1_3'UTR|KHK_ENST00000260598.5_Missense_Mutation_p.V49I	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	49			V -> I (in dbSNP:rs2304681). {ECO:0000269|PubMed:7833921}.		carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCTGCACCGTTCTCTCCCT	0.632													G|||	1660	0.33147	0.3033	0.5043	5008	,	,		19742	0.2312		0.3767	False		,,,				2504	0.3037				p.V49I		Atlas-SNP	.											KHK_ENST00000260598,colon,carcinoma,0,2	KHK	60	2	0			c.G145A						PASS	.	G	ILE/VAL,ILE/VAL	1399,3007	459.0+/-352.1	230,939,1034	76.0	63.0	67.0		145,145	2.7	0.0	2	dbSNP_100	67	3231,5369	486.6+/-371.9	622,1987,1691	yes	missense,missense	KHK	NM_000221.2,NM_006488.2	29,29	852,2926,2725	AA,AG,GG		37.5698,31.7522,35.599	benign,benign	49/299,49/299	27315252	4630,8376	2203	4300	6503	SO:0001583	missense	3795	exon2			TGCACCGTTCTCT		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.145G>A	2.37:g.27315252G>A	ENSP00000260599:p.Val49Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_006488	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Missense_Mutation	SNP	ENST00000260599.6	37	CCDS1734.1	745	0.3411172161172161	156	0.3170731707317073	172	0.47513812154696133	150	0.26223776223776224	267	0.35224274406332456	G	19.83	3.900193	0.72754	0.317522	0.375698	ENSG00000138030	ENST00000260599;ENST00000260598;ENST00000429697	T;T;T	0.77877	-1.13;-1.13;-1.13	5.5	2.71	0.32032	Carbohydrate/purine kinase (1);	0.183501	0.47852	N	0.000205	T	0.00012	0.0000	M	0.69185	2.1	0.24585	P	0.99385471	B;P;B	0.35821	0.045;0.523;0.045	B;B;B	0.32393	0.012;0.145;0.012	T	0.43734	-0.9373	9	0.18710	T	0.47	-18.5598	7.773	0.29019	0.336:0.0:0.664:0.0	rs2304681;rs13006404;rs17845083;rs17847238;rs17857867;rs57123139;rs2304681	49;49;49	Q6IBK2;P50053-2;P50053	.;.;KHK_HUMAN	I	49	ENSP00000260599:V49I;ENSP00000260598:V49I;ENSP00000404741:V49I	ENSP00000260598:V49I	V	+	1	0	KHK	27168756	1.000000	0.71417	0.013000	0.15412	0.966000	0.64601	4.090000	0.57693	0.701000	0.31803	0.462000	0.41574	GTT	G|0.649;A|0.351	0.351	strong		0.632	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1		
PTPRB	5787	hgsc.bcm.edu	37	12	70983895	70983895	+	Missense_Mutation	SNP	A	A	C	rs2165627	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:70983895A>C	ENST00000261266.5	-	6	1274	c.1245T>G	c.(1243-1245)gaT>gaG	p.D415E	PTPRB_ENST00000551525.1_Missense_Mutation_p.D632E|PTPRB_ENST00000334414.6_Missense_Mutation_p.D633E|PTPRB_ENST00000451516.2_Intron|PTPRB_ENST00000550358.1_Missense_Mutation_p.D633E|PTPRB_ENST00000538708.1_Missense_Mutation_p.D415E|PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550857.1_Intron	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	415	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.		D -> E (in dbSNP:rs2165627).		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)			GCACCACAGAATCATTGAAGA	0.517											OREG0021990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	405	0.0808706	0.1006	0.0994	5008	,	,		19579	0.001		0.1382	False		,,,				2504	0.0644				p.D633E		Atlas-SNP	.											.	PTPRB	676	.	0			c.T1899G						PASS	.	A	GLU/ASP,,GLU/ASP,GLU/ASP	452,3570		27,398,1586	136.0	137.0	137.0		1899,,1245,1245	-7.8	0.0	12	dbSNP_96	137	1210,7174		98,1014,3080	yes	missense,intron,missense,missense	PTPRB	NM_001109754.2,NM_001206971.1,NM_001206972.1,NM_002837.4	45,,45,45	125,1412,4666	CC,CA,AA		14.4323,11.2382,13.3967	benign,,benign,benign	633/2216,,415/1908,415/1998	70983895	1662,10744	2011	4192	6203	SO:0001583	missense	5787	exon8			CACAGAATCATTG	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.1245T>G	12.37:g.70983895A>C	ENSP00000261266:p.Asp415Glu	Somatic	201	0	0	1126	WXS	Illumina HiSeq	Phase_I	202	95	0.470297	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Missense_Mutation	SNP	ENST00000261266.5	37	CCDS44944.1	179	0.08195970695970696	46	0.09349593495934959	36	0.09944751381215469	1	0.0017482517482517483	96	0.1266490765171504	A	0.080	-1.185358	0.01620	0.112382	0.144323	ENSG00000127329	ENST00000334414;ENST00000550358;ENST00000544694;ENST00000538708;ENST00000261266;ENST00000551525;ENST00000548122	T;T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49;0.49	5.63	-7.79	0.01218	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.798952	0.12212	N	0.489224	T	0.00178	0.0005	N	0.25890	0.77	0.50313	P	1.3099999999999223E-4	B;B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0;0.001	B;B;B;B;B;B	0.15484	0.005;0.013;0.002;0.001;0.002;0.003	T	0.27468	-1.0073	9	0.02654	T	1	.	1.1433	0.01770	0.3065:0.1864:0.3229:0.1842	rs2165627;rs52835640;rs57683885;rs2165627	415;512;632;633;415;633	F5H3G6;Q6ZR19;F8VSD5;P23467-3;P23467;F8VU56	.;.;.;.;PTPRB_HUMAN;.	E	633;633;633;415;415;632;512	ENSP00000334928:D633E;ENSP00000448058:D633E;ENSP00000438927:D415E;ENSP00000261266:D415E;ENSP00000448349:D632E;ENSP00000446982:D512E	ENSP00000261266:D415E	D	-	3	2	PTPRB	69270162	0.000000	0.05858	0.003000	0.11579	0.240000	0.25518	-0.482000	0.06544	-1.511000	0.01794	-0.316000	0.08728	GAT	A|0.905;C|0.095	0.095	strong		0.517	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
HAS1	3036	hgsc.bcm.edu	37	19	52222552	52222552	+	Silent	SNP	G	G	A	rs11084112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52222552G>A	ENST00000222115.1	-	2	643	c.609C>T	c.(607-609)cgC>cgT	p.R203R	HAS1_ENST00000594621.1_Silent_p.R57R|HAS1_ENST00000601714.1_Silent_p.R210R|HAS1_ENST00000540069.2_Silent_p.R202R	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	203					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)	p.R203R(1)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		ACACGCACCTGCGAGTCCTCA	0.706													g|||	1797	0.358826	0.4206	0.4251	5008	,	,		14038	0.2113		0.334	False		,,,				2504	0.4059				p.R203R	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											HAS1,NS,lymphoid_neoplasm,0,1	HAS1	61	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C609T						PASS	.	G		1890,2514		429,1032,741	29.0	27.0	28.0		609	1.3	0.9	19	dbSNP_120	28	2798,5784		448,1902,1941	no	coding-synonymous	HAS1	NM_001523.2		877,2934,2682	AA,AG,GG		32.6031,42.9155,36.1004		203/579	52222552	4688,8298	2202	4291	6493	SO:0001819	synonymous_variant	3036	exon2			GCACCTGCGAGTC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.609C>T	19.37:g.52222552G>A		Somatic	17	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																			G|0.658;A|0.342	0.342	strong		0.706	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
CSPG4	1464	hgsc.bcm.edu	37	15	75982058	75982058	+	Missense_Mutation	SNP	T	T	A	rs147116973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75982058T>A	ENST00000308508.5	-	3	1440	c.1348A>T	c.(1348-1350)Agg>Tgg	p.R450W		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	450	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						TGCACATGCCTCCACTCAAGC	0.647																																					p.R450W		Atlas-SNP	.											CSPG4,NS,haematopoietic_neoplasm,0,1	CSPG4	175	1	0			c.A1348T						scavenged	.						53.0	52.0	53.0					15																	75982058		2197	4293	6490	SO:0001583	missense	1464	exon3			CATGCCTCCACTC	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.1348A>T	15.37:g.75982058T>A	ENSP00000312506:p.Arg450Trp	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	199	21	0.105528	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	10.03	1.238374	0.22711	.	.	ENSG00000173546	ENST00000308508	T	0.20332	2.08	5.26	3.18	0.36537	.	0.318723	0.26328	N	0.025018	T	0.24044	0.0582	M	0.65498	2.005	0.22330	N	0.999195	D	0.55800	0.973	B	0.43754	0.43	T	0.16541	-1.0399	10	0.87932	D	0	.	9.1439	0.36921	0.0:0.1134:0.5474:0.3393	.	450	Q6UVK1	CSPG4_HUMAN	W	450	ENSP00000312506:R450W	ENSP00000312506:R450W	R	-	1	2	CSPG4	73769113	0.968000	0.33430	0.998000	0.56505	0.385000	0.30292	1.547000	0.36190	1.229000	0.43630	-0.238000	0.12139	AGG	T|0.988;A|0.013	0.013	strong		0.647	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
COX18	285521	hgsc.bcm.edu	37	4	73930552	73930552	+	Silent	SNP	G	G	A	rs3762883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:73930552G>A	ENST00000295890.4	-	4	754	c.663C>T	c.(661-663)ccC>ccT	p.P221P	COX18_ENST00000507544.2_Silent_p.P222P	NM_173827.2	NP_776188.1	Q8N8Q8	COX18_HUMAN	COX18 cytochrome C oxidase assembly factor	221					protein insertion into mitochondrial membrane (GO:0051204)|protein transport (GO:0015031)|respiratory chain complex IV assembly (GO:0008535)	integral component of mitochondrial inner membrane (GO:0031305)	protein transporter activity (GO:0008565)			large_intestine(4)|lung(2)	6	Breast(15;0.00096)		Epithelial(6;1.26e-06)|OV - Ovarian serous cystadenocarcinoma(6;9.45e-06)|all cancers(17;2.05e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			AAGTGGAGTCGGGTGCAGTGA	0.383													c|||	1710	0.341454	0.1891	0.2983	5008	,	,		17295	0.3879		0.4563	False		,,,				2504	0.4121				p.P221P		Atlas-SNP	.											.	COX18	20	.	0			c.C663T						PASS	.	T		1055,3351		146,763,1294	77.0	76.0	77.0		663	0.5	0.3	4	dbSNP_107	77	3677,4923		774,2129,1397	no	coding-synonymous	COX18	NM_173827.2		920,2892,2691	AA,AG,GG		42.7558,23.9446,36.3832		221/334	73930552	4732,8274	2203	4300	6503	SO:0001819	synonymous_variant	285521	exon4			GGAGTCGGGTGCA	AY957564	CCDS3554.1, CCDS75139.1	4q13.3	2013-06-12	2013-06-12		ENSG00000163626	ENSG00000163626		"""Mitochondrial respiratory chain complex assembly factors"""	26801	protein-coding gene	gene with protein product		610428	"""COX18 cytochrome c oxidase assembly homolog (S. cerevisiae)"", ""cytochrome c oxidase assembly homolog 18 (yeast)"""			16212937, 16911509	Standard	XM_005265679		Approved	FLJ38991	uc003hgm.1	Q8N8Q8	OTTHUMG00000129917	ENST00000295890.4:c.663C>T	4.37:g.73930552G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	201	106	0.527363	NM_173827	Q2PB66|Q2PB67|Q2PB68|Q49B97|Q6IPP9	Silent	SNP	ENST00000295890.4	37	CCDS3554.1																																																																																			G|0.650;C|0.000;A|0.350	0.350	strong		0.383	COX18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252169.2	NM_173827	
LRCH3	84859	hgsc.bcm.edu	37	3	197566254	197566254	+	Silent	SNP	T	T	C	rs17850206	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:197566254T>C	ENST00000425562.2	+	10	1314	c.1314T>C	c.(1312-1314)taT>taC	p.Y438Y	LRCH3_ENST00000334859.4_Silent_p.Y438Y|LRCH3_ENST00000441090.2_Silent_p.Y284Y|LRCH3_ENST00000438796.2_Silent_p.Y438Y|LRCH3_ENST00000536618.1_Silent_p.Y33Y|LRCH3_ENST00000414675.2_Silent_p.Y410Y			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	438						cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		TGAGAAGATATTTACATCAAA	0.318													T|||	1594	0.318291	0.2368	0.4265	5008	,	,		16403	0.371		0.331	False		,,,				2504	0.2843				p.Y438Y		Atlas-SNP	.											.	LRCH3	96	.	0			c.T1314C						PASS	.	T		1090,3316	393.3+/-328.8	134,822,1247	51.0	51.0	51.0		1314	-4.3	0.0	3	dbSNP_123	51	3062,5534	467.2+/-367.0	536,1990,1772	no	coding-synonymous	LRCH3	NM_032773.2		670,2812,3019	CC,CT,TT		35.6212,24.739,31.9335		438/713	197566254	4152,8850	2203	4298	6501	SO:0001819	synonymous_variant	84859	exon10			AAGATATTTACAT	AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.1314T>C	3.37:g.197566254T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_032773	B4E0T7|Q96FP9|Q9NT52	Silent	SNP	ENST00000425562.2	37																																																																																				T|0.669;C|0.331	0.331	strong		0.318	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1	NM_032773	
MYL10	93408	hgsc.bcm.edu	37	7	101256833	101256833	+	Silent	SNP	T	T	C	rs2240389	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:101256833T>C	ENST00000223167.4	-	8	780	c.603A>G	c.(601-603)gcA>gcG	p.A201A		NM_138403.4	NP_612412.2	Q9BUA6	MYL10_HUMAN	myosin, light chain 10, regulatory	201	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.					mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	12						CTGGGGGAAATGCTGCAAACA	0.562													C|||	1143	0.228235	0.3056	0.2695	5008	,	,		18535	0.1448		0.2565	False		,,,				2504	0.1513				p.A201A	Esophageal Squamous(24;575 709 17516 40384 51639)	Atlas-SNP	.											.	MYL10	32	.	0			c.A603G						PASS	.	C		1283,3123	700.3+/-406.6	176,931,1096	143.0	122.0	129.0		603	-9.6	0.1	7	dbSNP_98	129	2333,6267	704.1+/-405.4	317,1699,2284	no	coding-synonymous	MYL10	NM_138403.4		493,2630,3380	CC,CT,TT		27.1279,29.1194,27.8026		201/227	101256833	3616,9390	2203	4300	6503	SO:0001819	synonymous_variant	93408	exon8			GGGAAATGCTGCA	BC002778	CCDS34713.1	7q22.1	2013-01-10			ENSG00000106436	ENSG00000106436		"""Myosins / Light chain"", ""EF-hand domain containing"""	29825	protein-coding gene	gene with protein product						1628631	Standard	NM_138403		Approved	MGC3479, MYLC2PL, PLRLC	uc003uyr.3	Q9BUA6	OTTHUMG00000157137	ENST00000223167.4:c.603A>G	7.37:g.101256833T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_138403		Silent	SNP	ENST00000223167.4	37	CCDS34713.1																																																																																			T|0.742;C|0.258	0.258	strong		0.562	MYL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347575.1	NM_138403	
GZMB	3002	hgsc.bcm.edu	37	14	25101629	25101629	+	Silent	SNP	T	T	C	rs10909625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:25101629T>C	ENST00000216341.4	-	3	346	c.240A>G	c.(238-240)aaA>aaG	p.K80K	GZMB_ENST00000526004.1_Intron|RP11-104E19.1_ENST00000557736.1_RNA|GZMB_ENST00000382540.1_Intron|GZMB_ENST00000415355.3_Silent_p.K68K|RP11-104E19.1_ENST00000555300.1_RNA|GZMB_ENST00000382542.1_Silent_p.K114K			P10144	GRAB_HUMAN	granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)	80	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|intrinsic apoptotic signaling pathway (GO:0097193)|Notch signaling pathway (GO:0007219)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.K80K(1)		endometrium(2)|large_intestine(1)|lung(4)|stomach(4)|urinary_tract(2)	13				GBM - Glioblastoma multiforme(265;0.028)		GCTCCTGTTCTTTGATATTGT	0.517													C|||	1515	0.302516	0.379	0.2118	5008	,	,		16974	0.2867		0.2475	False		,,,				2504	0.3364				p.K80K		Atlas-SNP	.											GZMB,NS,carcinoma,0,1	GZMB	73	1	1	Substitution - coding silent(1)	stomach(1)	c.A240G						PASS	.						93.0	106.0	102.0					14																	25101629		2203	4300	6503	SO:0001819	synonymous_variant	3002	exon3			CTGTTCTTTGATA	BC030195	CCDS9633.1	14q11.2	2008-08-13			ENSG00000100453	ENSG00000100453			4709	protein-coding gene	gene with protein product	"""fragmentin 2"", ""cytotoxic serine protease B"", ""cathepsin G-like 1"", ""T-cell serine protease 1-3E"""	123910		CTLA1, CSPB		2323780	Standard	NM_004131		Approved	CCPI, CGL-1, CSP-B, CGL1, CTSGL1, HLP, SECT	uc001wps.2	P10144	OTTHUMG00000029369	ENST00000216341.4:c.240A>G	14.37:g.25101629T>C		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	286	89	0.311189	NM_004131	Q8N1D2|Q9UCC1	Silent	SNP	ENST00000216341.4	37	CCDS9633.1																																																																																			T|0.742;C|0.258	0.258	strong		0.517	GZMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276540.3	NM_004131	
HRH2	3274	hgsc.bcm.edu	37	5	175110379	175110379	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:175110379G>A	ENST00000231683.2	+	1	1916	c.143G>A	c.(142-144)cGg>cAg	p.R48Q	HRH2_ENST00000377291.2_Missense_Mutation_p.R48Q	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2	48					digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	TTGAACCGCCGGCTCCGCAAC	0.592																																					p.R48Q		Atlas-SNP	.											HRH2_ENST00000377291,colon,carcinoma,+1,2	HRH2	108	2	0			c.G143A						scavenged	.						184.0	155.0	165.0					5																	175110379		2203	4300	6503	SO:0001583	missense	3274	exon2			ACCGCCGGCTCCG		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"""GPCR / Class A : Histamine receptors"""	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660	ENST00000231683.2:c.143G>A	5.37:g.175110379G>A	ENSP00000231683:p.Arg48Gln	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	260	6	0.0230769	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Missense_Mutation	SNP	ENST00000231683.2	37	CCDS4395.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.689201	0.68271	.	.	ENSG00000113749	ENST00000377291;ENST00000231683	T;T	0.72615	-0.67;-0.67	5.34	4.48	0.54585	GPCR, rhodopsin-like superfamily (1);	0.060573	0.64402	N	0.000003	T	0.57504	0.2058	L	0.41027	1.25	0.49051	D	0.999743	B;B	0.31989	0.05;0.35	B;B	0.31101	0.025;0.124	T	0.51919	-0.8644	10	0.20519	T	0.43	.	9.4518	0.38731	0.1607:0.0:0.8393:0.0	.	48;48	P25021;Q7Z5R9	HRH2_HUMAN;.	Q	48	ENSP00000366506:R48Q;ENSP00000231683:R48Q	ENSP00000231683:R48Q	R	+	2	0	HRH2	175042985	1.000000	0.71417	0.998000	0.56505	0.866000	0.49608	2.816000	0.48026	1.268000	0.44264	0.462000	0.41574	CGG	.	.	none		0.592	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1		
SLC25A47	283600	hgsc.bcm.edu	37	14	100795139	100795139	+	Missense_Mutation	SNP	G	G	T	rs35007880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:100795139G>T	ENST00000361529.3	+	5	482	c.404G>T	c.(403-405)cGg>cTg	p.R135L	SLC25A47_ENST00000557052.1_5'UTR	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	135					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						CAGCAGCGGCGGCTTTCGGCC	0.682													G|||	1639	0.327276	0.0424	0.3127	5008	,	,		17253	0.2262		0.492	False		,,,				2504	0.6575				p.R135L	GBM(11;1289 1351)	Atlas-SNP	.											SLC25A47,NS,carcinoma,0,1	SLC25A47	36	1	0			c.G404T						scavenged	.	G	LEU/ARG	440,3886		47,346,1770	21.0	23.0	22.0		404	3.9	0.9	14	dbSNP_126	22	4022,4358		1006,2010,1174	yes	missense	SLC25A47	NM_207117.2	102	1053,2356,2944	TT,TG,GG		47.9952,10.1711,35.1173	probably-damaging	135/309	100795139	4462,8244	2163	4190	6353	SO:0001583	missense	283600	exon5			AGCGGCGGCTTTC		CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"""Solute carriers"""	20115	protein-coding gene	gene with protein product		609911	"""chromosome 14 open reading frame 68"""	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.404G>T	14.37:g.100795139G>T	ENSP00000354886:p.Arg135Leu	Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_207117	B2RP39|Q68CL2|Q6PZD8|Q86U14	Missense_Mutation	SNP	ENST00000361529.3	37	CCDS9959.1	604	0.2765567765567766	24	0.04878048780487805	118	0.3259668508287293	101	0.17657342657342656	361	0.4762532981530343	G	8.690	0.907281	0.17833	0.101711	0.479952	ENSG00000140107	ENST00000361529	D	0.81659	-1.52	4.89	3.93	0.45458	Mitochondrial carrier domain (2);	2.605420	0.01942	N	0.042002	T	0.00012	0.0000	L	0.33485	1.01	0.18873	P	0.9999839802	P	0.50528	0.936	P	0.47206	0.541	T	0.42649	-0.9439	9	0.10636	T	0.68	-0.5229	3.1999	0.06646	0.0966:0.3091:0.4294:0.1649	rs35007880	135	Q6Q0C1	S2547_HUMAN	L	135	ENSP00000354886:R135L	ENSP00000354886:R135L	R	+	2	0	SLC25A47	99864892	0.942000	0.31987	0.930000	0.37139	0.463000	0.32649	1.603000	0.36794	2.262000	0.75019	0.491000	0.48974	CGG	G|0.667;T|0.333	0.333	strong		0.682	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1		
SERPINF1	5176	hgsc.bcm.edu	37	17	1680002	1680002	+	Silent	SNP	T	T	C	rs6828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1680002T>C	ENST00000254722.4	+	7	1126	c.963T>C	c.(961-963)taT>taC	p.Y321Y		NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	321					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						AGCTGAGTTATGAAGGCGAAG	0.552													C|||	3890	0.776757	0.9198	0.7565	5008	,	,		20324	0.7758		0.7386	False		,,,				2504	0.638				p.Y321Y		Atlas-SNP	.											.	SERPINF1	31	.	0			c.T963C						PASS	.	C		3928,478	225.2+/-241.2	1746,436,21	111.0	101.0	104.0		963	-8.6	0.1	17	dbSNP_52	104	6088,2512	411.9+/-350.6	2162,1764,374	no	coding-synonymous	SERPINF1	NM_002615.5		3908,2200,395	CC,CT,TT		29.2093,10.8488,22.9894		321/419	1680002	10016,2990	2203	4300	6503	SO:0001819	synonymous_variant	5176	exon7			GAGTTATGAAGGC	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"""Serine (or cysteine) peptidase inhibitors"""	8824	protein-coding gene	gene with protein product	"""pigment epithelium-derived factor"", ""proliferation-inducing protein 35"""	172860	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"""	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.963T>C	17.37:g.1680002T>C		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Silent	SNP	ENST00000254722.4	37	CCDS11012.1																																																																																			C|0.782;G|0.000;N|0.000;T|0.218	0.782	strong		0.552	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615	
ADAMTS19	171019	hgsc.bcm.edu	37	5	128863518	128863518	+	Silent	SNP	A	A	G	rs61749629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:128863518A>G	ENST00000274487.4	+	5	1291	c.1146A>G	c.(1144-1146)gaA>gaG	p.E382E	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	382	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		TGCTCCATGAAACTCCAGTAA	0.308													A|||	164	0.0327476	0.0219	0.0231	5008	,	,		12185	0.0069		0.0477	False		,,,				2504	0.0654				p.E382E		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.A1146G						PASS	.	A		98,4308	78.3+/-116.7	0,98,2105	88.0	94.0	92.0		1146	4.4	1.0	5	dbSNP_129	92	324,8276	111.8+/-172.0	5,314,3981	no	coding-synonymous	ADAMTS19	NM_133638.3		5,412,6086	GG,GA,AA		3.7674,2.2242,3.2447		382/1208	128863518	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	171019	exon5			CCATGAAACTCCA	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.1146A>G	5.37:g.128863518A>G		Somatic	210	0	0		WXS	Illumina HiSeq	Phase_I	208	89	0.427885	NM_133638		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			A|0.968;G|0.032	0.032	strong		0.308	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
ABCC6	368	hgsc.bcm.edu	37	16	16251599	16251599	+	Missense_Mutation	SNP	C	C	T	rs2238472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:16251599C>T	ENST00000205557.7	-	27	3832	c.3803G>A	c.(3802-3804)cGg>cAg	p.R1268Q		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1268	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.		R -> Q (associated with lower plasma triglycerides and higher plasma HDL cholesterol; dbSNP:rs2238472). {ECO:0000269|PubMed:10811882, ECO:0000269|PubMed:10913334, ECO:0000269|PubMed:11536079, ECO:0000269|PubMed:11776382, ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:18987736}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCCAAAGTCCCGGAACTCGAT	0.622													C|||	908	0.18131	0.0673	0.2983	5008	,	,		18599	0.125		0.3012	False		,,,				2504	0.1871				p.R1268Q		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3803A	GRCh37	CM001044	ABCC6	M	rs2238472	PASS	.	C	GLN/ARG	473,3921	222.6+/-239.4	29,415,1753	52.0	45.0	48.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3803	2.0	0.6	16	dbSNP_98	48	2437,6163	401.1+/-347.0	345,1747,2208	yes	missense	ABCC6	NM_001171.5	43	374,2162,3961	TT,TC,CC		28.3372,10.7647,22.395	benign	1268/1504	16251599	2910,10084	2197	4300	6497	SO:0001583	missense	368	exon27			AAGTCCCGGAACT	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3803G>A	16.37:g.16251599C>T	ENSP00000205557:p.Arg1268Gln	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	423	0.1936813186813187	41	0.08333333333333333	90	0.24861878453038674	68	0.11888111888111888	224	0.2955145118733509	c	11.76	1.734060	0.30684	0.107647	0.283372	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.90563	-2.69	5.09	2.01	0.26516	ABC transporter-like (1);	0.165125	0.27654	N	0.018411	T	0.00012	0.0000	N	0.17901	0.54	0.09310	P	0.9999999999913843	B	0.24576	0.106	B	0.12156	0.007	T	0.02639	-1.1130	9	0.25106	T	0.35	.	10.2379	0.43294	0.0:0.7787:0.0:0.2213	rs2238472;rs17289934;rs52824827;rs60072648;rs2238472	1268	O95255	MRP6_HUMAN	Q	1268;206	ENSP00000205557:R1268Q	ENSP00000205557:R1268Q	R	-	2	0	ABCC6	16159100	0.000000	0.05858	0.612000	0.29024	0.951000	0.60555	-0.326000	0.07965	0.191000	0.20236	0.530000	0.56133	CGG	C|0.810;T|0.190	0.190	strong		0.622	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
GRIN3B	116444	hgsc.bcm.edu	37	19	1004808	1004808	+	Silent	SNP	C	C	T	rs61736783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1004808C>T	ENST00000234389.3	+	3	1327	c.1308C>T	c.(1306-1308)gaC>gaT	p.D436D	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	436					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)	CAGACGAAGACGGGCAGTGCC	0.687													c|||	486	0.0970447	0.0424	0.0389	5008	,	,		15462	0.1706		0.0646	False		,,,				2504	0.1697				p.D436D		Atlas-SNP	.											.	GRIN3B	46	.	0			c.C1308T						PASS	.	C		200,4206	122.9+/-160.3	4,192,2007	51.0	50.0	51.0		1308	-5.2	0.9	19	dbSNP_129	51	531,8063	143.7+/-199.7	19,493,3785	no	coding-synonymous	GRIN3B	NM_138690.1		23,685,5792	TT,TC,CC		6.1787,4.5393,5.6231		436/1044	1004808	731,12269	2203	4297	6500	SO:0001819	synonymous_variant	116444	exon3			CGAAGACGGGCAG		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.1308C>T	19.37:g.1004808C>T		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	55	34	0.618182	NM_138690	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																			C|0.936;T|0.064	0.064	strong		0.687	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
SELP	6403	hgsc.bcm.edu	37	1	169563951	169563951	+	Missense_Mutation	SNP	T	T	G	rs6136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:169563951T>G	ENST00000263686.6	-	13	2303	c.2266A>C	c.(2266-2268)Act>Cct	p.T756P	SELP_ENST00000367791.2_Missense_Mutation_p.T570P|SELP_ENST00000367794.2_Missense_Mutation_p.T694P|SELP_ENST00000367793.2_Missense_Mutation_p.T694P|SELP_ENST00000458599.2_Missense_Mutation_p.T572P|SELP_ENST00000367792.2_Missense_Mutation_p.T572P|SELP_ENST00000367786.2_Missense_Mutation_p.T694P|SELP_ENST00000367788.2_Missense_Mutation_p.T694P	NM_003005.3	NP_002996.2	P16109	LYAM3_HUMAN	selectin P (granule membrane protein 140kDa, antigen CD62)	756	Sushi 9. {ECO:0000255|PROSITE- ProRule:PRU00302}.		T -> P (reduced frequency in patients with myocardial infarction; dbSNP:rs6136). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:9668170, ECO:0000269|Ref.2}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|defense response to Gram-negative bacterium (GO:0050829)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of platelet activation (GO:0010572)|regulation of integrin activation (GO:0033623)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|platelet dense granule membrane (GO:0031088)	fucose binding (GO:0042806)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|lipopolysaccharide binding (GO:0001530)|oligosaccharide binding (GO:0070492)|sialic acid binding (GO:0033691)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(32)|ovary(4)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_hematologic(923;0.208)				Dalteparin(DB06779)|Heparin(DB01109)|Nadroparin(DB08813)	GGCACGGTAGTTGACCAGTGG	0.428													T|||	180	0.0359425	0.0045	0.0821	5008	,	,		20781	0.002		0.0885	False		,,,				2504	0.0266				p.T756P		Atlas-SNP	.											.	SELP	132	.	0			c.A2266C	GRCh37	CM981792	SELP	M	rs6136	PASS	.	T	PRO/THR	99,4307	80.4+/-118.8	0,99,2104	169.0	150.0	156.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2266	-3.9	0.0	1	dbSNP_52	156	914,7686	203.7+/-246.6	51,812,3437	yes	missense	SELP	NM_003005.3	38	51,911,5541	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	10.6279,2.2469,7.7887	benign	756/831	169563951	1013,11993	2203	4300	6503	SO:0001583	missense	6403	exon13			CGGTAGTTGACCA	BC068533	CCDS1282.1	1q22-q25	2008-02-05	2002-08-29		ENSG00000174175	ENSG00000174175		"""CD molecules"""	10721	protein-coding gene	gene with protein product		173610	"""selectin P (granule membrane protein 140kD, antigen CD62)"""	GRMP		1375831	Standard	NM_003005		Approved	CD62, PSEL, PADGEM, GMP140, CD62P	uc001ggi.4	P16109	OTTHUMG00000034685	ENST00000263686.6:c.2266A>C	1.37:g.169563951T>G	ENSP00000263686:p.Thr756Pro	Somatic	213	0	0		WXS	Illumina HiSeq	Phase_I	221	103	0.466063	NM_003005	Q5R344|Q8IVD1	Missense_Mutation	SNP	ENST00000263686.6	37	CCDS1282.1	96|96	0.04395604395604396|0.04395604395604396	4|4	0.008130081300813009|0.008130081300813009	23|23	0.06353591160220995|0.06353591160220995	2|2	0.0034965034965034965|0.0034965034965034965	67|67	0.08839050131926121|0.08839050131926121	T|T	6.484|6.484	0.457412|0.457412	0.12342|0.12342	0.022469|0.022469	0.106279|0.106279	ENSG00000174175|ENSG00000174175	ENST00000446728|ENST00000367795;ENST00000367790;ENST00000426706;ENST00000367789;ENST00000263686;ENST00000544572;ENST00000367793;ENST00000367794;ENST00000367792;ENST00000367791;ENST00000367788;ENST00000367786;ENST00000458599	.|T;T;T;T;T;T;T	.|0.72615	.|-0.67;-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	5.42|5.42	-3.92|-3.92	0.04155|0.04155	.|Complement control module (2);Sushi/SCR/CCP (3);	.|1.036980	.|0.07619	.|N	.|0.926748	T|T	0.45677|0.45677	0.1354|0.1354	N|N	0.05383|0.05383	-0.06|-0.06	0.09310|0.09310	N|N	1|1	.|P;P;P	.|0.42785	.|0.79;0.758;0.75	.|P;P;P	.|0.50896	.|0.653;0.555;0.521	T|T	0.52689|0.52689	-0.8542|-0.8542	5|10	.|0.59425	.|D	.|0.04	-0.4071|-0.4071	15.7515|15.7515	0.77989|0.77989	0.0:0.7904:0.0:0.2096|0.0:0.7904:0.0:0.2096	rs6136;rs1801717;rs17588388;rs52807558;rs58472342;rs6136|rs6136;rs1801717;rs17588388;rs52807558;rs58472342;rs6136	.|756;756;756	.|Q6NUL9;P16109;G3V1U2	.|.;LYAM3_HUMAN;.	T|P	571|570;756;755;572;756;756;694;694;572;570;694;694;679	.|ENSP00000263686:T756P;ENSP00000356767:T694P;ENSP00000356768:T694P;ENSP00000356766:T572P;ENSP00000356765:T570P;ENSP00000356762:T694P;ENSP00000356760:T694P	.|ENSP00000263686:T756P	N|T	-|-	2|1	0|0	SELP|SELP	167830575|167830575	0.004000|0.004000	0.15560|0.15560	0.001000|0.001000	0.08648|0.08648	0.056000|0.056000	0.15407|0.15407	-0.777000|-0.777000	0.04669|0.04669	-0.636000|-0.636000	0.05524|0.05524	-0.250000|-0.250000	0.11733|0.11733	AAC|ACT	T|0.930;G|0.070	0.070	strong		0.428	SELP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083916.4	NM_003005	
ZNF25	219749	hgsc.bcm.edu	37	10	38241220	38241220	+	Silent	SNP	T	T	C	rs146555827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38241220T>C	ENST00000302609.7	-	6	1418	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	AL117337.1_ENST00000582458.1_RNA|ZNF25_ENST00000374633.1_5'UTR	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	402					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ACTTCCCACATTCCTTGCATG	0.433																																					p.E402E		Atlas-SNP	.											.	ZNF25	66	.	0			c.A1206G						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	92.0	90.0	90.0		1206	-4.1	0.7	10	dbSNP_134	90	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ZNF25	NM_145011.2		0,10,6493	CC,CT,TT		0.1047,0.0227,0.0769		402/457	38241220	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	219749	exon6			CCCACATTCCTTG	AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"""Zinc fingers, C2H2-type"", ""-"""	13043	protein-coding gene	gene with protein product		194528	"""zinc finger protein 25 (KOX 19)"""			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.1206A>G	10.37:g.38241220T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	92	51	0.554348	NM_145011	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Silent	SNP	ENST00000302609.7	37	CCDS7195.1																																																																																			T|0.999;C|0.001	0.001	strong		0.433	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966	
CHGA	1113	hgsc.bcm.edu	37	14	93399101	93399101	+	Missense_Mutation	SNP	C	C	T	rs729940	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93399101C>T	ENST00000216492.5	+	7	1475	c.1195C>T	c.(1195-1197)Cgg>Tgg	p.R399W	CHGA_ENST00000334654.4_Missense_Mutation_p.R248W	NM_001275.3	NP_001266.1	P10645	CMGA_HUMAN	chromogranin A (parathyroid secretory protein 1)	399			R -> W (in dbSNP:rs729940). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:2445752, ECO:0000269|PubMed:8120054}.		regulation of blood pressure (GO:0008217)	extracellular region (GO:0005576)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|secretory granule (GO:0030141)				cervix(1)|large_intestine(1)|lung(3)|skin(3)	8		all_cancers(154;0.0843)		Epithelial(152;0.102)|COAD - Colon adenocarcinoma(157;0.208)|all cancers(159;0.224)		GCCATCCTCCCGGGAGGACAG	0.687													C|||	623	0.124401	0.0121	0.2061	5008	,	,		14971	0.2004		0.164	False		,,,				2504	0.0992				p.R399W	Colon(31;154 822 45066 49155)|NSCLC(28;804 1157 13734 25204)	Atlas-SNP	.											.	CHGA	32	.	0			c.C1195T						PASS	.	C	TRP/ARG	148,4206		7,134,2036	11.0	13.0	12.0		1195	1.2	0.1	14	dbSNP_86	12	1200,7320		80,1040,3140	no	missense	CHGA	NM_001275.3	101	87,1174,5176	TT,TC,CC		14.0845,3.3992,10.4707	possibly-damaging	399/458	93399101	1348,11526	2177	4260	6437	SO:0001583	missense	1113	exon7			TCCTCCCGGGAGG		CCDS9906.1	14q32	2012-10-02			ENSG00000100604	ENSG00000100604			1929	protein-coding gene	gene with protein product	"""vasostatin"", ""pancreastatin"", ""parastatin"""	118910				3403545	Standard	NM_001275		Approved		uc001ybc.4	P10645		ENST00000216492.5:c.1195C>T	14.37:g.93399101C>T	ENSP00000216492:p.Arg399Trp	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	61	33	0.540984	NM_001275	B2R9E9|Q53FA8|Q6NR84|Q96E84|Q96GL7|Q9BQB5	Missense_Mutation	SNP	ENST00000216492.5	37	CCDS9906.1	332	0.152014652014652	9	0.018292682926829267	84	0.23204419889502761	114	0.1993006993006993	125	0.16490765171503957	C	13.08	2.129737	0.37630	0.033992	0.140845	ENSG00000100604	ENST00000216492;ENST00000334654	T;T	0.01821	4.62;4.62	4.71	1.2	0.21068	.	0.839077	0.10441	N	0.674355	T	0.00012	0.0000	M	0.71581	2.175	0.80722	P	0.0	D;D	0.89917	1.0;0.997	D;D	0.70935	0.971;0.913	T	0.45440	-0.9261	9	0.59425	D	0.04	-3.6408	6.2358	0.20762	0.4752:0.2822:0.2426:0.0	rs729940;rs1058460;rs17847003;rs729940	248;399	G5E968;P10645	.;CMGA_HUMAN	W	399;248	ENSP00000216492:R399W;ENSP00000334023:R248W	ENSP00000216492:R399W	R	+	1	2	CHGA	92468854	0.000000	0.05858	0.140000	0.22221	0.387000	0.30353	0.516000	0.22817	0.327000	0.23409	0.555000	0.69702	CGG	C|0.876;T|0.124	0.124	strong		0.687	CHGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412411.1	NM_001275	
FAM209A	200232	hgsc.bcm.edu	37	20	55099978	55099978	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:55099978C>T	ENST00000371328.3	+	1	437	c.114C>T	c.(112-114)taC>taT	p.Y38Y	GCNT7_ENST00000243913.4_Intron|FAM209A_ENST00000481560.1_3'UTR	NM_001012971.3	NP_001012989.2	Q5JX71	F209A_HUMAN	family with sequence similarity 209, member A	38						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)											AGGTGCAATACGGAGAGCACT	0.517																																					p.Y38Y		Atlas-SNP	.											.	.	.	.	0			c.C114T						PASS	.						158.0	142.0	148.0					20																	55099978		2203	4300	6503	SO:0001819	synonymous_variant	200232	exon1			GCAATACGGAGAG	AL109806	CCDS33493.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000124103	ENSG00000124103			16100	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 106"""	C20orf106			Standard	NM_001012971		Approved	dJ1153D9.3		Q5JX71	OTTHUMG00000032799	ENST00000371328.3:c.114C>T	20.37:g.55099978C>T		Somatic	241	0	0		WXS	Illumina HiSeq	Phase_I	183	22	0.120219	NM_001012971	Q05C43	Silent	SNP	ENST00000371328.3	37	CCDS33493.1																																																																																			.	.	none		0.517	FAM209A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079815.2		
PODXL2	50512	hgsc.bcm.edu	37	3	127379635	127379635	+	Missense_Mutation	SNP	C	C	T	rs34691761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:127379635C>T	ENST00000342480.6	+	3	803	c.764C>T	c.(763-765)cCg>cTg	p.P255L		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	255					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						ACAGTGACTCCGGGGGACCAG	0.627													C|||	13	0.00259585	0.0	0.0058	5008	,	,		18265	0.0		0.0089	False		,,,				2504	0.0				p.P255L		Atlas-SNP	.											.	PODXL2	53	.	0			c.C764T						PASS	.	C	LEU/PRO	3,4403	6.2+/-15.9	0,3,2200	35.0	39.0	37.0		764	-0.9	0.0	3	dbSNP_126	37	47,8553	30.1+/-81.4	1,45,4254	yes	missense	PODXL2	NM_015720.2	98	1,48,6454	TT,TC,CC		0.5465,0.0681,0.3844	benign	255/606	127379635	50,12956	2203	4300	6503	SO:0001583	missense	50512	exon3			TGACTCCGGGGGA	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.764C>T	3.37:g.127379635C>T	ENSP00000345359:p.Pro255Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	123	49	0.398374	NM_015720	Q6UVY4|Q8WUV6	Missense_Mutation	SNP	ENST00000342480.6	37	CCDS3044.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	0	-2.607312	0.00121	6.81E-4	0.005465	ENSG00000114631	ENST00000342480;ENST00000302192	T	0.20738	2.05	4.67	-0.937	0.10415	.	1.475550	0.04280	N	0.343618	T	0.07863	0.0197	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31806	-0.9930	10	0.20519	T	0.43	0.0338	9.3502	0.38133	0.0:0.4699:0.0:0.5301	rs34691761	255	Q9NZ53	PDXL2_HUMAN	L	255	ENSP00000345359:P255L	ENSP00000304498:P255L	P	+	2	0	PODXL2	128862325	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.299000	0.08254	-0.341000	0.08376	-0.573000	0.04149	CCG	C|0.995;T|0.005	0.005	strong		0.627	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
C2orf71	388939	hgsc.bcm.edu	37	2	29295476	29295476	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29295476C>T	ENST00000331664.5	-	1	1651	c.1652G>A	c.(1651-1653)aGg>aAg	p.R551K		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	551					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						AAACTTGATCCTTTCGCTGAT	0.592																																					p.R551K		Atlas-SNP	.											.	C2orf71	146	.	0			c.G1652A						PASS	.						48.0	51.0	50.0					2																	29295476		2016	4170	6186	SO:0001583	missense	388939	exon1			TTGATCCTTTCGC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1652G>A	2.37:g.29295476C>T	ENSP00000332809:p.Arg551Lys	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	103	52	0.504854	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386668	0.25031	.	.	ENSG00000179270	ENST00000331664	T	0.20738	2.05	5.17	2.4	0.29515	.	0.258207	0.38111	N	0.001807	T	0.10035	0.0246	N	0.25647	0.755	0.27894	N	0.939233	B	0.32040	0.353	B	0.25884	0.064	T	0.25606	-1.0127	10	0.12766	T	0.61	-19.7104	5.7968	0.18392	0.0:0.4904:0.0:0.5096	.	551	A6NGG8	CB071_HUMAN	K	551	ENSP00000332809:R551K	ENSP00000332809:R551K	R	-	2	0	C2orf71	29148980	1.000000	0.71417	0.999000	0.59377	0.868000	0.49771	2.616000	0.46376	0.593000	0.29745	0.561000	0.74099	AGG	.	.	none		0.592	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
PCDHB11	56125	hgsc.bcm.edu	37	5	140579367	140579367	+	Missense_Mutation	SNP	G	G	A	rs917535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140579367G>A	ENST00000354757.3	+	1	20	c.20G>A	c.(19-21)cGc>cAc	p.R7H	PCDHB11_ENST00000536699.1_5'UTR	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	7			R -> H (in dbSNP:rs917535).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAAGGGACACGCACTCAGCAG	0.502													G|||	319	0.0636981	0.2012	0.0461	5008	,	,		20878	0.0		0.0169	False		,,,				2504	0.0041				p.R7H		Atlas-SNP	.											PCDHB11,NS,carcinoma,+1,1	PCDHB11	162	1	0			c.G20A						PASS	.	G	HIS/ARG	786,3620	317.7+/-295.3	79,628,1496	87.0	82.0	84.0		20	-1.6	0.0	5	dbSNP_86	84	151,8449	73.5+/-136.2	0,151,4149	yes	missense	PCDHB11	NM_018931.2	29	79,779,5645	AA,AG,GG		1.7558,17.8393,7.2044	benign	7/798	140579367	937,12069	2203	4300	6503	SO:0001583	missense	56125	exon1			GGACACGCACTCA	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.20G>A	5.37:g.140579367G>A	ENSP00000346802:p.Arg7His	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	132	0.06043956043956044	101	0.20528455284552846	18	0.049723756906077346	0	0.0	13	0.017150395778364115	G	9.526	1.109447	0.20714	0.178393	0.017558	ENSG00000197479	ENST00000354757	T	0.52057	0.68	2.69	-1.64	0.08318	.	.	.	.	.	T	0.00039	0.0001	L	0.56124	1.755	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.20773	-1.0265	8	0.21540	T	0.41	.	8.2191	0.31530	0.7595:0.0:0.2405:0.0	rs917535;rs52792734;rs917535	7	Q9Y5F2	PCDBB_HUMAN	H	7	ENSP00000346802:R7H	ENSP00000346802:R7H	R	+	2	0	PCDHB11	140559551	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.282000	0.08445	-0.293000	0.08986	0.460000	0.39030	CGC	G|0.931;A|0.069	0.069	strong		0.502	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
DHX33	56919	hgsc.bcm.edu	37	17	5366947	5366947	+	Missense_Mutation	SNP	G	G	A	rs8069315	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5366947G>A	ENST00000225296.3	-	2	552	c.352C>T	c.(352-354)Cgc>Tgc	p.R118C	DHX33_ENST00000433302.3_Intron	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	118	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		R -> C (in dbSNP:rs8069315).		positive regulation of transcription from RNA polymerase I promoter (GO:0045943)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|rDNA binding (GO:0000182)			breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						ATGCCCTGGCGGCTGATCCCT	0.512													G|||	542	0.108227	0.233	0.0677	5008	,	,		18270	0.0228		0.1233	False		,,,				2504	0.0409				p.R118C		Atlas-SNP	.											.	DHX33	41	.	0			c.C352T						PASS	.	G	,CYS/ARG	904,3502	348.7+/-310.1	100,704,1399	79.0	72.0	74.0		,352	5.0	1.0	17	dbSNP_116	74	982,7618	212.2+/-252.6	57,868,3375	yes	intron,missense	DHX33	NM_001199699.1,NM_020162.3	,180	157,1572,4774	AA,AG,GG		11.4186,20.5175,14.501	,probably-damaging	,118/708	5366947	1886,11120	2203	4300	6503	SO:0001583	missense	56919	exon2			CCTGGCGGCTGAT	AL359945	CCDS11072.1	17p13	2003-06-13	2003-06-13	2003-06-13	ENSG00000005100	ENSG00000005100		"""DEAH-boxes"""	16718	protein-coding gene	gene with protein product		614405	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 33"""	DDX33			Standard	NM_020162		Approved	FLJ21972, DKFZp762F2011	uc002gca.3	Q9H6R0	OTTHUMG00000102041	ENST00000225296.3:c.352C>T	17.37:g.5366947G>A	ENSP00000225296:p.Arg118Cys	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	248	0.11355311355311355	109	0.22154471544715448	31	0.0856353591160221	12	0.02097902097902098	96	0.1266490765171504	G	27.4	4.825669	0.90955	0.205175	0.114186	ENSG00000005100	ENST00000225296	T	0.07800	3.16	5.04	5.04	0.67666	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.81614	2.55	0.09310	P	1.0	B	0.25850	0.136	B	0.20955	0.032	T	0.15292	-1.0442	9	0.72032	D	0.01	.	17.3684	0.87369	0.0:0.0:1.0:0.0	rs8069315;rs52830117;rs57788243;rs8069315	118	Q9H6R0	DHX33_HUMAN	C	118	ENSP00000225296:R118C	ENSP00000225296:R118C	R	-	1	0	DHX33	5307671	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	4.532000	0.60608	2.340000	0.79590	0.563000	0.77884	CGC	G|0.856;A|0.144	0.144	strong		0.512	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162	
ANKRD66	100287718	hgsc.bcm.edu	37	6	46726500	46726500	+	Missense_Mutation	SNP	C	C	A	rs9472839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46726500C>A	ENST00000565422.1	+	5	603	c.598C>A	c.(598-600)Cag>Aag	p.Q200K	RP11-268F1.3_ENST00000438738.1_lincRNA|ANKRD66_ENST00000536046.1_Missense_Mutation_p.Q171K	NM_001162435.2	NP_001155907.2	B4E2M5	ANR66_HUMAN	ankyrin repeat domain 66	200																	CGCTGCCCAGCAGAAGGGGCT	0.537													C|||	506	0.101038	0.2148	0.0865	5008	,	,		17497	0.0		0.1074	False		,,,				2504	0.0552				p.Q200K		Atlas-SNP	.											.	.	.	.	0			c.C598A						PASS	.	C	LYS/GLN	214,1170		15,184,493	38.0	37.0	38.0		598	4.7	0.0	6	dbSNP_119	38	385,2797		31,323,1237	yes	missense	LOC100287718	NM_001162435.2	53	46,507,1730	AA,AC,CC		12.0993,15.4624,13.1187	benign	200/252	46726500	599,3967	692	1591	2283	SO:0001583	missense	100287718	exon5			GCCCAGCAGAAGG	AK304342	CCDS59024.1	6p12.3	2013-01-11			ENSG00000230062	ENSG00000230062		"""Ankyrin repeat domain containing"""	44669	protein-coding gene	gene with protein product							Standard	NM_001162435		Approved		uc011dwf.2	B4E2M5	OTTHUMG00000014791	ENST00000565422.1:c.598C>A	6.37:g.46726500C>A	ENSP00000454770:p.Gln200Lys	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_001162435		Missense_Mutation	SNP	ENST00000565422.1	37	CCDS59024.1																																																																																			C|0.903;A|0.097	0.097	strong		0.537	ANKRD66-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432045.1	NM_001162435	
OR51B6	390058	hgsc.bcm.edu	37	11	5373311	5373311	+	Missense_Mutation	SNP	T	T	C	rs201581003|rs386750142|rs5006883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373311T>C	ENST00000380219.1	+	1	574	c.574T>C	c.(574-576)Ttc>Ctc	p.F192L	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	192			F -> L (in dbSNP:rs5006883). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGACATCACCTTCAACCGTCT	0.438													T|||	1172	0.234026	0.3275	0.2349	5008	,	,		23945	0.0863		0.2644	False		,,,				2504	0.228				p.F192L		Atlas-SNP	.											OR51B6,NS,carcinoma,-1,1	OR51B6	53	1	0			c.T574C						PASS	.	T	LEU/PHE	973,3429		172,629,1400	218.0	193.0	202.0		574	5.2	1.0	11	dbSNP_113	202	1931,6663		302,1327,2668	yes	missense	OR51B6	NM_001004750.1	22	474,1956,4068	CC,CT,TT		22.4692,22.1036,22.3453	possibly-damaging	192/313	5373311	2904,10092	2201	4297	6498	SO:0001583	missense	390058	exon1			ATCACCTTCAACC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.574T>C	11.37:g.5373311T>C	ENSP00000369568:p.Phe192Leu	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	173	70	0.404624	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	473	0.21657509157509158	160	0.3252032520325203	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	T	14.91	2.677503	0.47886	0.221036	0.224692	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00021	9.02	5.15	5.15	0.70609	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000030	T	0.00012	0.0000	L	0.45422	1.42	0.33219	P	0.44557800000000003	D	0.89917	1.0	D	0.91635	0.999	T	0.48570	-0.9024	9	0.40728	T	0.16	.	5.3614	0.16089	0.0:0.0883:0.1795:0.7322	rs5006883;rs52793310;rs59096293;rs5006883	192	Q9H340	O51B6_HUMAN	L	191;192	ENSP00000369568:F192L	ENSP00000369568:F192L	F	+	1	0	OR51B6	5329887	0.000000	0.05858	0.998000	0.56505	0.555000	0.35460	-1.108000	0.03313	2.157000	0.67596	0.455000	0.32223	TTC	T|0.772;C|0.228	0.228	strong		0.438	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
CILP2	148113	hgsc.bcm.edu	37	19	19653231	19653231	+	Missense_Mutation	SNP	T	T	A	rs186322474		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19653231T>A	ENST00000291495.5	+	5	725	c.640T>A	c.(640-642)Tcg>Acg	p.S214T	CILP2_ENST00000586018.1_Missense_Mutation_p.S220T|CILP2_ENST00000588333.2_3'UTR	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	214						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						CCTCCTGGGCTCGGTGGTCAC	0.627																																					p.S214T		Atlas-SNP	.											.	CILP2	84	.	0			c.T640A						PASS	.	T	THR/SER	0,4406		0,0,2203	34.0	31.0	32.0		640	1.5	0.1	19		32	2,8598	2.2+/-6.3	0,2,4298	no	missense	CILP2	NM_153221.2	58	0,2,6501	AA,AT,TT		0.0233,0.0,0.0154	benign	214/1157	19653231	2,13004	2203	4300	6503	SO:0001583	missense	148113	exon5			CTGGGCTCGGTGG	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.640T>A	19.37:g.19653231T>A	ENSP00000291495:p.Ser214Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	T	1.434	-0.569499	0.03910	0.0	2.33E-4	ENSG00000160161	ENST00000291495	T	0.39229	1.09	5.23	1.46	0.22682	Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.617705	0.16243	N	0.223061	T	0.17577	0.0422	N	0.13235	0.315	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.18871	0.023;0.014	T	0.18871	-1.0323	10	0.10902	T	0.67	-14.2755	0.421	0.00456	0.4059:0.1494:0.1428:0.3019	.	214;214	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	T	214	ENSP00000291495:S214T	ENSP00000291495:S214T	S	+	1	0	CILP2	19514231	0.001000	0.12720	0.086000	0.20670	0.209000	0.24338	0.967000	0.29344	-0.119000	0.11830	0.454000	0.30748	TCG	T|0.999;A|0.001	0.001	weak		0.627	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
WDR87	83889	hgsc.bcm.edu	37	19	38375666	38375666	+	Missense_Mutation	SNP	C	C	T	rs73027451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38375666C>T	ENST00000303868.5	-	6	8752	c.8528G>A	c.(8527-8529)cGg>cAg	p.R2843Q	WDR87_ENST00000447313.2_Missense_Mutation_p.R2882Q	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2843										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						GATCCCATACCGGGCAATGCC	0.557													C|||	830	0.165735	0.1573	0.1455	5008	,	,		19065	0.12		0.1938	False		,,,				2504	0.2096				p.R2843Q		Atlas-SNP	.											.	WDR87	191	.	0			c.G8528A						PASS	.	C	GLN/ARG	252,1132		27,198,467	34.0	34.0	34.0		8528	2.5	0.9	19	dbSNP_130	34	550,2632		43,464,1084	yes	missense	WDR87	NM_031951.3	43	70,662,1551	TT,TC,CC		17.2847,18.2081,17.5646	benign	2843/2874	38375666	802,3764	692	1591	2283	SO:0001583	missense	83889	exon6			CCATACCGGGCAA	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.8528G>A	19.37:g.38375666C>T	ENSP00000368025:p.Arg2843Gln	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	99	97	0.979798	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	340	0.15567765567765568	65	0.13211382113821138	51	0.1408839779005525	73	0.12762237762237763	151	0.19920844327176782	C	10.23	1.292736	0.23564	0.182081	0.172847	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.09538	2.97;2.97	4.67	2.45	0.29901	.	.	.	.	.	T	0.00012	0.0000	N	0.01352	-0.895	0.51012	P	9.40000000000385E-5	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.44772	-0.9306	8	0.02654	T	1	.	5.7628	0.18209	0.0:0.2157:0.0:0.7843	.	2843;2882	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	Q	2882;2843	ENSP00000405012:R2882Q;ENSP00000368025:R2843Q	ENSP00000368025:R2843Q	R	-	2	0	WDR87	43067506	0.783000	0.28701	0.943000	0.38184	0.496000	0.33645	0.953000	0.29162	0.905000	0.36596	-0.693000	0.03709	CGG	C|0.835;T|0.166	0.166	strong		0.557	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
PSG2	5670	hgsc.bcm.edu	37	19	43585253	43585253	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:43585253C>T	ENST00000406487.1	-	2	308	c.210G>A	c.(208-210)ggG>ggA	p.G70G	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	70	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.G70G(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				CCCTGATTTGCCCTTTGTACC	0.433																																					p.G70G		Atlas-SNP	.											PSG2,NS,carcinoma,0,2	PSG2	84	2	2	Substitution - coding silent(2)	prostate(2)	c.G210A						scavenged	.						92.0	96.0	94.0					19																	43585253		2201	4285	6486	SO:0001819	synonymous_variant	5670	exon2			GATTTGCCCTTTG		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.210G>A	19.37:g.43585253C>T		Somatic	190	4	0.0210526		WXS	Illumina HiSeq	Phase_I	208	4	0.0192308	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			.	.	none		0.433	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
CRX	1406	hgsc.bcm.edu	37	19	48342985	48342985	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48342985T>A	ENST00000221996.7	+	4	867	c.661T>A	c.(661-663)Tac>Aac	p.Y221N	CRX_ENST00000539067.1_Missense_Mutation_p.Y221N|TPRX2P_ENST00000535362.1_Intron	NM_000554.4	NP_000545.1	O43186	CRX_HUMAN	cone-rod homeobox	221					circadian rhythm (GO:0007623)|organ morphogenesis (GO:0009887)|positive regulation of photoreceptor cell differentiation (GO:0046534)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|leucine zipper domain binding (GO:0043522)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|prostate(2)|urinary_tract(1)	23		all_cancers(25;2.76e-09)|all_epithelial(76;7.01e-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;0.000266)|all cancers(93;0.000788)|Epithelial(262;0.0226)|GBM - Glioblastoma multiforme(486;0.0521)		CCTAGACCCCTACCTTTCTCC	0.672																																					p.Y221N	Pancreas(57;461 1196 22201 40716 47188)	Atlas-SNP	.											CRX,NS,carcinoma,-2,1	CRX	52	1	0			c.T661A						scavenged	.						109.0	123.0	118.0					19																	48342985		2203	4300	6503	SO:0001583	missense	1406	exon4			GACCCCTACCTTT	AF024711	CCDS12706.1	19q13.3	2013-01-08				ENSG00000105392		"""Homeoboxes / PRD class"""	2383	protein-coding gene	gene with protein product	"""orthodenticle homeobox 3"""	602225		CORD2		9390563, 9537410	Standard	NM_000554		Approved	CRD, LCA7, OTX3	uc002phq.4	O43186		ENST00000221996.7:c.661T>A	19.37:g.48342985T>A	ENSP00000221996:p.Tyr221Asn	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	63	2	0.031746	NM_000554	Q0QD45	Missense_Mutation	SNP	ENST00000221996.7	37	CCDS12706.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.974563	0.74246	.	.	ENSG00000105392	ENST00000221996;ENST00000539067	D;D	0.93426	-3.22;-3.22	4.21	4.21	0.49690	Transcription factor Otx, C-terminal (1);	0.070281	0.64402	D	0.000015	D	0.95990	0.8694	M	0.76938	2.355	0.49389	D	0.999787	D	0.76494	0.999	D	0.87578	0.998	D	0.95916	0.8927	10	0.62326	D	0.03	-5.2933	11.2877	0.49230	0.0:0.0:0.0:1.0	.	221	O43186	CRX_HUMAN	N	221	ENSP00000221996:Y221N;ENSP00000445565:Y221N	ENSP00000221996:Y221N	Y	+	1	0	CRX	53034797	1.000000	0.71417	0.997000	0.53966	0.856000	0.48823	4.480000	0.60243	1.760000	0.52011	0.383000	0.25322	TAC	.	.	none		0.672	CRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409812.4	NM_000554	
KDM1B	221656	hgsc.bcm.edu	37	6	18213988	18213988	+	Silent	SNP	C	C	T	rs6903583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:18213988C>T	ENST00000297792.5	+	15	1566	c.1389C>T	c.(1387-1389)gcC>gcT	p.A463A	KDM1B_ENST00000397244.1_Silent_p.A464A|KDM1B_ENST00000546309.2_Intron|KDM1B_ENST00000388870.2_Silent_p.A696A			Q8NB78	KDM1B_HUMAN	lysine (K)-specific demethylase 1B	695					DNA methylation involved in gamete generation (GO:0043046)|histone H3-K4 demethylation (GO:0034720)|multicellular organismal development (GO:0007275)|regulation of DNA methylation (GO:0044030)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-monomethyl-K4 specific) (GO:0034649)|oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|large_intestine(6)|lung(8)|skin(3)|upper_aerodigestive_tract(1)	25						GGCTTTTTGCCGTGTTCTATG	0.423													C|||	701	0.139976	0.2118	0.1715	5008	,	,		19432	0.005		0.2107	False		,,,				2504	0.0869				p.A463A		Atlas-SNP	.											.	KDM1B	58	.	0			c.C1389T						PASS	.	C		912,3494	352.1+/-311.5	106,700,1397	170.0	164.0	166.0		1389	-1.9	0.9	6	dbSNP_116	166	1918,6682	340.5+/-323.6	226,1466,2608	no	coding-synonymous	KDM1B	NM_153042.3		332,2166,4005	TT,TC,CC		22.3023,20.699,21.7592		463/591	18213988	2830,10176	2203	4300	6503	SO:0001819	synonymous_variant	221656	exon15			TTTTGCCGTGTTC	AK125318	CCDS34343.1	6p22.3	2011-07-01	2009-09-29	2009-09-29	ENSG00000165097	ENSG00000165097		"""Chromatin-modifying enzymes / K-demethylases"""	21577	protein-coding gene	gene with protein product		613081	"""amine oxidase, flavin containing 1"", ""chromosome 6 open reading frame 193"", ""amine oxidase (flavin containing) domain 1"""	C6orf193, AOF1		19407342, 19727073	Standard	NM_153042		Approved	FLJ34109, FLJ33898, dJ298J15.2, bA204B7.3, FLJ43328, LSD2	uc003ncn.1	Q8NB78	OTTHUMG00000014316	ENST00000297792.5:c.1389C>T	6.37:g.18213988C>T		Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	239	102	0.426778	NM_153042	A2A2C5|A2A2C6|Q5TGV3|Q6AI15|Q6ZUU4|Q8N258|Q96EL7	Silent	SNP	ENST00000297792.5	37	CCDS34343.1	348	0.15934065934065933	101	0.20528455284552846	72	0.19889502762430938	2	0.0034965034965034965	173	0.22823218997361477	C	11.72	1.721985	0.30503	0.20699	0.223023	ENSG00000165097	ENST00000449850	.	.	.	5.88	-1.92	0.07618	.	.	.	.	.	T	0.19327	0.0464	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.19063	-1.0317	3	.	.	.	-23.6373	7.6149	0.28152	0.0:0.4205:0.126:0.4534	rs6903583;rs6903583	.	.	.	L	513	.	.	P	+	2	0	KDM1B	18321967	0.306000	0.24490	0.946000	0.38457	0.991000	0.79684	-0.426000	0.07008	-0.302000	0.08869	-0.238000	0.12139	CCG	C|0.808;T|0.192	0.192	strong		0.423	KDM1B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277080.1	NM_153042	
COX11	1353	hgsc.bcm.edu	37	17	53038654	53038654	+	3'UTR	SNP	A	A	C	rs1802212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:53038654A>C	ENST00000299335.3	-	0	2409				COX11_ENST00000573912.1_5'Flank|TOM1L1_ENST00000445275.2_3'UTR|TOM1L1_ENST00000348161.4_3'UTR|TOM1L1_ENST00000540336.1_3'UTR|TOM1L1_ENST00000572158.1_3'UTR|TOM1L1_ENST00000575882.1_3'UTR|TOM1L1_ENST00000536554.1_3'UTR	NM_004375.3	NP_004366.1	Q9Y6N1	COX11_HUMAN	cytochrome c oxidase assembly homolog 11 (yeast)						hydrogen ion transmembrane transport (GO:1902600)|negative regulation of glucokinase activity (GO:0033132)|respiratory chain complex IV assembly (GO:0008535)|respiratory gaseous exchange (GO:0007585)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)|electron carrier activity (GO:0009055)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|ovary(1)|prostate(1)	9						TAAAACGTAGACTCTGTGCAG	0.398													A|||	759	0.151558	0.0605	0.1585	5008	,	,		20632	0.129		0.2714	False		,,,				2504	0.1697				p.S228A		Atlas-SNP	.											.	COX11	16	.	0			c.T682G						PASS	.						93.0	76.0	81.0					17																	53038654		692	1591	2283	SO:0001624	3_prime_UTR_variant	1353	exon4			ACGTAGACTCTGT	AF044321	CCDS11583.1, CCDS58579.1	17q22	2012-10-15	2012-10-15			ENSG00000166260		"""Mitochondrial respiratory chain complex assembly factors"""	2261	protein-coding gene	gene with protein product	"""cytochrome c oxidase subunit 11"", ""cytochrome c oxidase assembly protein COX11"""	603648	"""COX11 (yeast) homolog, cytochrome c oxidase assembly protein"", ""COX11 cytochrome c oxidase assembly homolog (yeast)"""			9878253	Standard	NM_004375		Approved	COX11P	uc010wng.1	Q9Y6N1		ENST00000299335.3:c.*1440T>G	17.37:g.53038654A>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_001162861	D3DTY5|I3L220|Q6FHB7|Q9BRX0|Q9UME8	Missense_Mutation	SNP	ENST00000299335.3	37	CCDS11583.1																																																																																			A|0.835;C|0.165	0.165	strong		0.398	COX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439182.1	NM_004375	
FCGBP	8857	hgsc.bcm.edu	37	19	40406019	40406019	+	Silent	SNP	G	G	A	rs2355719	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40406019G>A	ENST00000221347.6	-	10	4834	c.4827C>T	c.(4825-4827)tgC>tgT	p.C1609C		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1609	Cys-rich.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CATGGCACGTGCACTGCTGCC	0.632													A|||	1308	0.261182	0.1566	0.402	5008	,	,		20345	0.2163		0.3419	False		,,,				2504	0.2658				p.C1609C		Atlas-SNP	.											.	FCGBP	416	.	0			c.C4827T						PASS	.						77.0	55.0	62.0					19																	40406019		2203	4298	6501	SO:0001819	synonymous_variant	8857	exon10			GCACGTGCACTGC	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.4827C>T	19.37:g.40406019G>A		Somatic	691	1	0.00144718		WXS	Illumina HiSeq	Phase_I	560	366	0.653571	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.717;A|0.283	0.283	strong		0.632	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CD93	22918	hgsc.bcm.edu	37	20	23065209	23065209	+	Missense_Mutation	SNP	G	G	A	rs3746731	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:23065209G>A	ENST00000246006.4	-	1	1768	c.1621C>T	c.(1621-1623)Cca>Tca	p.P541S		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	541			P -> S (in dbSNP:rs3746731). {ECO:0000269|PubMed:9047234}.		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)					CAGACGCCTGGGGACCCACTG	0.647													G|||	2710	0.541134	0.3427	0.6254	5008	,	,		14072	0.6468		0.5378	False		,,,				2504	0.6442				p.P541S		Atlas-SNP	.											.	CD93	84	.	0			c.C1621T						PASS	.	G	SER/PRO	1618,2788	478.1+/-358.1	315,988,900	41.0	48.0	46.0		1621	3.8	0.0	20	dbSNP_107	46	4873,3727	601.1+/-394.3	1401,2071,828	yes	missense	CD93	NM_012072.3	74	1716,3059,1728	AA,AG,GG		43.3372,36.7227,49.9077	benign	541/653	23065209	6491,6515	2203	4300	6503	SO:0001583	missense	22918	exon1			CGCCTGGGGACCC	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.1621C>T	20.37:g.23065209G>A	ENSP00000246006:p.Pro541Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	54	31	0.574074	NM_012072	O00274	Missense_Mutation	SNP	ENST00000246006.4	37	CCDS13149.1	1158	0.5302197802197802	172	0.34959349593495936	212	0.585635359116022	381	0.666083916083916	393	0.5184696569920845	G	12.35	1.910938	0.33721	0.367227	0.566628	ENSG00000125810	ENST00000246006	T	0.80909	-1.43	5.79	3.84	0.44239	.	0.103824	0.42964	N	0.000623	T	0.00012	0.0000	L	0.42245	1.32	0.80722	P	0.0	B	0.27882	0.192	B	0.28139	0.086	T	0.48536	-0.9027	9	0.21014	T	0.42	-3.5181	9.3645	0.38217	0.1654:0.0:0.8346:0.0	rs3746731;rs17682552;rs61032248;rs3746731	541	Q9NPY3	C1QR1_HUMAN	S	541	ENSP00000246006:P541S	ENSP00000246006:P541S	P	-	1	0	CD93	23013209	0.037000	0.19845	0.006000	0.13384	0.044000	0.14063	2.358000	0.44134	0.778000	0.33520	0.655000	0.94253	CCA	G|0.481;A|0.519	0.519	strong		0.647	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072	
OTOGL	283310	hgsc.bcm.edu	37	12	80764360	80764360	+	Missense_Mutation	SNP	C	C	T	rs146572555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:80764360C>T	ENST00000547103.1	+	55	6569	c.6563C>T	c.(6562-6564)aCc>aTc	p.T2188I	OTOGL_ENST00000458043.2_Missense_Mutation_p.T2200I|OTOGL_ENST00000546620.1_Missense_Mutation_p.T219I			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2188					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						GTAGGGAGTACCTGGCACTAC	0.308													C|||	14	0.00279553	0.0068	0.0029	5008	,	,		13968	0.0		0.003	False		,,,				2504	0.0				p.T2200I		Atlas-SNP	.											.	OTOGL	235	.	0			c.C6599T						PASS	.	C	ILE/THR	12,4394	17.9+/-39.9	0,12,2191	132.0	129.0	130.0		6599	0.1	0.0	12	dbSNP_134	130	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OTOGL	NM_173591.3	89	0,16,6487	TT,TC,CC		0.0465,0.2724,0.123	benign	2200/2345	80764360	16,12990	2203	4300	6503	SO:0001583	missense	283310	exon55			GGAGTACCTGGCA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6563C>T	12.37:g.80764360C>T	ENSP00000447211:p.Thr2188Ile	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	47	29	0.617021	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		15|15	0.006868131868131868|0.006868131868131868	9|9	0.018292682926829267|0.018292682926829267	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	6.727|6.727	0.502843|0.502843	0.12822|0.12822	0.002724|0.002724	4.65E-4|4.65E-4	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182	.|T;T;T;T	.|0.46063	.|2.23;2.23;2.13;0.88	5.44|5.44	0.118|0.118	0.14667|0.14667	.|.	.|0.315004	.|0.30869	.|N	.|0.008710	T|T	0.21801|0.21801	0.0525|0.0525	M|M	0.62723|0.62723	1.935|1.935	0.09310|0.09310	N|N	1|1	.|B	.|0.14012	.|0.009	.|B	.|0.16289	.|0.015	T|T	0.30357|0.30357	-0.9981|-0.9981	5|10	.|0.72032	.|D	.|0.01	.|.	9.8313|9.8313	0.40944|0.40944	0.0:0.6306:0.0:0.3694|0.0:0.6306:0.0:0.3694	.|.	.|565	.|Q3ZCN5	.|OTOGL_HUMAN	S|I	608|2188;2200;219;217	.|ENSP00000447211:T2188I;ENSP00000400895:T2200I;ENSP00000449094:T219I;ENSP00000449641:T217I	.|ENSP00000400895:T2200I	P|T	+|+	1|2	0|0	OTOGL|OTOGL	79288491|79288491	0.990000|0.990000	0.36364|0.36364	0.019000|0.019000	0.16419|0.16419	0.184000|0.184000	0.23303|0.23303	2.773000|2.773000	0.47686|0.47686	-0.268000|-0.268000	0.09312|0.09312	-0.229000|-0.229000	0.12294|0.12294	CCT|ACC	C|0.997;T|0.003	0.003	strong		0.308	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
MYPN	84665	hgsc.bcm.edu	37	10	69926319	69926319	+	Silent	SNP	C	C	A	rs61854624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:69926319C>A	ENST00000358913.5	+	10	2357	c.1869C>A	c.(1867-1869)acC>acA	p.T623T	MYPN_ENST00000540630.1_Silent_p.T623T|MYPN_ENST00000354393.2_Silent_p.T348T	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	623					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						CCAGACAGACCAGGCCCGATT	0.567													C|||	584	0.116613	0.0091	0.2622	5008	,	,		16743	0.0962		0.164	False		,,,				2504	0.1309				p.T623T		Atlas-SNP	.											MYPN,NS,carcinoma,+1,1	MYPN	189	1	0			c.C1869A						PASS	.	C		148,4258	103.0+/-141.5	2,144,2057	77.0	69.0	72.0		1869	1.0	0.4	10	dbSNP_129	72	1492,7108	283.6+/-296.2	149,1194,2957	no	coding-synonymous	MYPN	NM_032578.2		151,1338,5014	AA,AC,CC		17.3488,3.3591,12.6096		623/1321	69926319	1640,11366	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon10			ACAGACCAGGCCC	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.1869C>A	10.37:g.69926319C>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	96	44	0.458333	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			A|0.133;C|0.867;G|0.000	0.133	strong		0.567	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
MRPS5	64969	hgsc.bcm.edu	37	2	95775761	95775761	+	Silent	SNP	G	G	A	rs113259652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:95775761G>A	ENST00000272418.2	-	4	511	c.303C>T	c.(301-303)ggC>ggT	p.G101G		NM_031902.3	NP_114108.1	P82675	RT05_HUMAN	mitochondrial ribosomal protein S5	101					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						CTGCTAAAGCGCCTTTCCACA	0.398													G|||	66	0.0131789	0.0061	0.0072	5008	,	,		19690	0.001		0.0348	False		,,,				2504	0.0174				p.G101G		Atlas-SNP	.											.	MRPS5	52	.	0			c.C303T						PASS	.	G		41,4365	44.6+/-78.6	1,39,2163	123.0	126.0	125.0		303	-11.5	0.5	2	dbSNP_132	125	462,8138	137.8+/-194.7	25,412,3863	no	coding-synonymous	MRPS5	NM_031902.3		26,451,6026	AA,AG,GG		5.3721,0.9305,3.8674		101/431	95775761	503,12503	2203	4300	6503	SO:0001819	synonymous_variant	64969	exon4			TAAAGCGCCTTTC	AB049940	CCDS2010.1	2p11.2-q11.2	2012-09-13			ENSG00000144029	ENSG00000144029		"""Mitochondrial ribosomal proteins / small subunits"""	14498	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S5"""	611972					Standard	NM_031902		Approved	MRP-S5, S5mt	uc002sub.3	P82675	OTTHUMG00000130394	ENST00000272418.2:c.303C>T	2.37:g.95775761G>A		Somatic	398	0	0		WXS	Illumina HiSeq	Phase_I	357	348	0.97479	NM_031902	Q4ZFY5|Q96LJ6|Q9BWI4|Q9BYC4	Silent	SNP	ENST00000272418.2	37	CCDS2010.1																																																																																			G|0.968;A|0.032	0.032	strong		0.398	MRPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252772.1	NM_031902	
MXRA5	25878	hgsc.bcm.edu	37	X	3241317	3241317	+	Silent	SNP	T	T	C	rs1635249	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3241317T>C	ENST00000217939.6	-	5	2563	c.2409A>G	c.(2407-2409)ccA>ccG	p.P803P		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	803						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TTTTAATCAATGGGGGTACTT	0.473													C|||	2833	0.750464	0.6868	0.5216	3775	,	,		13934	0.5595		0.5278	False		,,,				2504	0.4785				p.P803P		Atlas-SNP	.											.	MXRA5	815	.	0			c.A2409G						PASS	.	C		3376,459		1280,321,495,31,76	141.0	140.0	140.0		2409	-1.1	0.0	X	dbSNP_89	140	4342,2386		1019,1110,1194,299,678	no	coding-synonymous	MXRA5	NM_015419.3		2299,1431,1689,330,754	CC,CT,C,TT,T		35.4637,11.9687,26.9336		803/2829	3241317	7718,2845	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon5			AATCAATGGGGGT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2409A>G	X.37:g.3241317T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	78	78	1	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			0|0.003;C|0.737	0.737	strong		0.473	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
SIGLEC7	27036	hgsc.bcm.edu	37	19	51650520	51650520	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51650520C>T	ENST00000317643.6	+	6	1236	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D	SIGLEC7_ENST00000305628.7_Silent_p.D296D|SIGLEC7_ENST00000600577.1_Intron	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	389					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		CAGCAGCGGACGTGGGAGACA	0.577																																					p.D389D		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.C1167T						PASS	.						124.0	99.0	107.0					19																	51650520		2203	4300	6503	SO:0001819	synonymous_variant	27036	exon6			AGCGGACGTGGGA	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10876	protein-coding gene	gene with protein product		604410	"""sialic acid binding Ig-like lectin 19, pseudogene"", ""sialic acid binding Ig-like lectin, pseudogene 2"""	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.1167C>T	19.37:g.51650520C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	154	79	0.512987	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	37	CCDS12826.1																																																																																			.	.	none		0.577	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543	
FBLN2	2199	hgsc.bcm.edu	37	3	13612936	13612936	+	Missense_Mutation	SNP	A	A	G	rs3732666	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:13612936A>G	ENST00000295760.7	+	2	1150	c.1081A>G	c.(1081-1083)Agc>Ggc	p.S361G	FBLN2_ENST00000404922.3_Missense_Mutation_p.S361G|FBLN2_ENST00000492059.1_Missense_Mutation_p.S361G|FBLN2_ENST00000535798.1_Missense_Mutation_p.S387G	NM_001998.2	NP_001989.2	P98095	FBLN2_HUMAN	fibulin 2	361	N.|Subdomain NB (Cys-free).		S -> G (in dbSNP:rs3732666).		extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(3)|prostate(3)|urinary_tract(1)	24			UCEC - Uterine corpus endometrioid carcinoma (1;0.00416)			GCATGCACCGAGCCTGGGCAA	0.662													G|||	2341	0.467452	0.7587	0.2824	5008	,	,		16187	0.5496		0.1869	False		,,,				2504	0.409				p.S361G		Atlas-SNP	.											.	FBLN2	137	.	0			c.A1081G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER	2822,1480		954,914,283	35.0	47.0	43.0		1081,1081,1081	1.9	0.0	3	dbSNP_107	43	1671,6801		179,1313,2744	no	missense,missense,missense	FBLN2	NM_001004019.1,NM_001165035.1,NM_001998.2	56,56,56	1133,2227,3027	GG,GA,AA		19.7238,34.4026,35.173	benign,benign,benign	361/1232,361/1232,361/1185	13612936	4493,8281	2151	4236	6387	SO:0001583	missense	2199	exon2			GCACCGAGCCTGG	X82494	CCDS46761.1, CCDS46762.1	3p25-p24	2010-06-15			ENSG00000163520	ENSG00000163520		"""Fibulins"""	3601	protein-coding gene	gene with protein product		135821				7806230	Standard	NM_001165035		Approved		uc011ava.2	P98095	OTTHUMG00000155437	ENST00000295760.7:c.1081A>G	3.37:g.13612936A>G	ENSP00000295760:p.Ser361Gly	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	38	0.447059	NM_001998	B7Z9C5|Q8IUI0|Q8IUI1	Missense_Mutation	SNP	ENST00000295760.7	37	CCDS46762.1	913	0.41804029304029305	342	0.6951219512195121	98	0.27071823204419887	340	0.5944055944055944	133	0.17546174142480211	G	5.775	0.327445	0.10956	0.655974	0.197238	ENSG00000163520	ENST00000535798;ENST00000404922;ENST00000295760;ENST00000492059	T;T;T;T	0.79554	-1.28;-1.23;-1.19;-1.23	4.82	1.9	0.25705	.	2.938210	0.00827	N	0.001632	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.42949	-0.9421	9	0.20519	T	0.43	.	4.8974	0.13757	0.2617:0.1534:0.5849:0.0	rs3732666;rs3732666	361;361;387	P98095;P98095-2;F5H1F3	FBLN2_HUMAN;.;.	G	387;361;361;361	ENSP00000445705:S387G;ENSP00000384169:S361G;ENSP00000295760:S361G;ENSP00000420042:S361G	ENSP00000295760:S361G	S	+	1	0	FBLN2	13587937	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.151000	0.10175	-0.056000	0.13221	-0.124000	0.14976	AGC	A|0.603;G|0.397	0.397	strong		0.662	FBLN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000340083.3	NM_001004019	
KLC3	147700	hgsc.bcm.edu	37	19	45849909	45849909	+	Silent	SNP	A	A	G	rs9749618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45849909A>G	ENST00000391946.2	+	3	468	c.366A>G	c.(364-366)gaA>gaG	p.E122E	KLC3_ENST00000470402.1_Silent_p.E136E|KLC3_ENST00000585434.1_Silent_p.E122E	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	122					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TGCGGGAGGAACTGGAGGAGA	0.701													A|||	983	0.196286	0.0809	0.1873	5008	,	,		11388	0.0873		0.334	False		,,,				2504	0.3292				p.E122E		Atlas-SNP	.											KLC3,colon,carcinoma,0,1	KLC3	37	1	0			c.A366G						PASS	.	A		444,3498		44,356,1571	5.0	7.0	6.0		366	1.9	1.0	19	dbSNP_119	6	2326,5724		403,1520,2102	no	coding-synonymous	KLC3	NM_177417.2		447,1876,3673	GG,GA,AA		28.8944,11.2633,23.0987		122/505	45849909	2770,9222	1971	4025	5996	SO:0001819	synonymous_variant	147700	exon3			GGAGGAACTGGAG	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.366A>G	19.37:g.45849909A>G		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	30	19	0.633333	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	37	CCDS12660.2																																																																																			A|0.790;G|0.210	0.210	strong		0.701	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
KIF26B	55083	hgsc.bcm.edu	37	1	245850095	245850095	+	Silent	SNP	C	C	T	rs871840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:245850095C>T	ENST00000407071.2	+	12	4250	c.3810C>T	c.(3808-3810)gaC>gaT	p.D1270D	KIF26B_ENST00000366518.4_Silent_p.D889D	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	1270					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			AGGCCCAGGACGCAGGGAGCA	0.617													C|||	729	0.145567	0.2307	0.1571	5008	,	,		18948	0.0179		0.2425	False		,,,				2504	0.0542				p.D1270D		Atlas-SNP	.											.	KIF26B	343	.	0			c.C3810T						PASS	.	C		960,3346		116,728,1309	34.0	40.0	38.0		3810	-4.6	0.1	1	dbSNP_86	38	2168,6316		283,1602,2357	no	coding-synonymous	KIF26B	NM_018012.3		399,2330,3666	TT,TC,CC		25.554,22.2945,24.4566		1270/2109	245850095	3128,9662	2153	4242	6395	SO:0001819	synonymous_variant	55083	exon12			CCAGGACGCAGGG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.3810C>T	1.37:g.245850095C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			C|0.808;T|0.192	0.192	strong		0.617	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
TAB2	23118	hgsc.bcm.edu	37	6	149730846	149730846	+	Silent	SNP	G	G	A	rs652921	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:149730846G>A	ENST00000367456.1	+	8	2650	c.2073G>A	c.(2071-2073)agG>agA	p.R691R	TAB2_ENST00000286332.5_Silent_p.R691R|TAB2_ENST00000538427.1_Silent_p.R691R|TAB2_ENST00000536230.1_Silent_p.R659R			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	691					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						AGATGCCAAGGCATTTCTGAG	0.428													G|||	1089	0.217452	0.0552	0.2507	5008	,	,		19114	0.5496		0.0944	False		,,,				2504	0.1973				p.R691R		Atlas-SNP	.											.	TAB2	55	.	0			c.G2073A						PASS	.	G		276,4130	155.9+/-189.0	7,262,1934	153.0	143.0	146.0		2073	5.9	1.0	6	dbSNP_83	146	909,7691	203.0+/-246.1	53,803,3444	no	coding-synonymous	TAB2	NM_015093.4		60,1065,5378	AA,AG,GG		10.5698,6.2642,9.1112		691/694	149730846	1185,11821	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon9			GCCAAGGCATTTC	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 2"""	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.2073G>A	6.37:g.149730846G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	80	66	0.825	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			G|0.850;A|0.150	0.150	strong		0.428	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3		
NUTM2A	728118	hgsc.bcm.edu	37	10	88988115	88988115	+	Missense_Mutation	SNP	G	G	A	rs200168540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:88988115G>A	ENST00000381707.2	+	2	861	c.478G>A	c.(478-480)Gca>Aca	p.A160T	NUTM2A_ENST00000381689.4_Missense_Mutation_p.A160T|NUTM2A-AS1_ENST00000451940.2_RNA	NM_001099338.1	NP_001092808.1	Q8IVF1	NTM2A_HUMAN	NUT family member 2A	160				A -> T (in Ref. 1; BAC23116). {ECO:0000305}.													TCCCGGCCCAGCACACGGGCC	0.677																																					p.A160T		Atlas-SNP	.											FAM22D,NS,haematopoietic_neoplasm,0,2	FAM22A	20	2	0			c.G478A						scavenged	.						9.0	11.0	10.0					10																	88988115		1199	3080	4279	SO:0001583	missense	728118	exon2			GGCCCAGCACACG		CCDS44452.1	10q23.2	2013-03-15	2013-03-14	2013-03-14	ENSG00000184923	ENSG00000184923			23438	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member A"""	FAM22A			Standard	NM_001099338		Approved		uc001kek.3	Q8IVF1	OTTHUMG00000018670	ENST00000381707.2:c.478G>A	10.37:g.88988115G>A	ENSP00000371126:p.Ala160Thr	Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	327	79	0.24159	NM_001099338	A6NMX5|C9JDI1|Q5VZW1	Missense_Mutation	SNP	ENST00000381707.2	37	CCDS44452.1	.	.	.	.	.	.	.	.	.	.	g	5.987	0.366044	0.11352	.	.	ENSG00000184923	ENST00000381689;ENST00000381707;ENST00000416901	T;T	0.24151	1.87;1.87	1.29	0.214	0.15249	Nuclear Testis  protein, N-terminal (1);	.	.	.	.	T	0.16811	0.0404	L	0.38531	1.155	0.80722	P	0.0	B	0.14012	0.009	B	0.17098	0.017	T	0.24621	-1.0155	8	0.27082	T	0.32	.	5.55	0.17086	0.0:0.4213:0.5787:0.0	.	160	Q8IVF1	FA22A_HUMAN	T	160;160;87	ENSP00000371107:A160T;ENSP00000371126:A160T	ENSP00000371107:A160T	A	+	1	0	FAM22A	88978095	0.000000	0.05858	0.003000	0.11579	0.034000	0.12701	-0.329000	0.07935	0.096000	0.17463	0.374000	0.22700	GCA	G|0.375;A|0.625	0.625	strong		0.677	NUTM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049198.2	NM_001099338	
TNFRSF14	8764	hgsc.bcm.edu	37	1	2493168	2493168	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2493168G>A	ENST00000355716.4	+	6	907	c.608G>A	c.(607-609)tGg>tAg	p.W203*		NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	203					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell migration (GO:2000406)|T cell costimulation (GO:0031295)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			kidney(1)	1	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;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;1.11e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000326)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.199)		CACTGGGTATGGTGGTTTCTC	0.607			"""Mis, N, F"""		follicular lymphoma																																p.W203X		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""		L	.	TNFRSF14	89	.	0			c.G608A						PASS	.						91.0	83.0	86.0					1																	2493168		2203	4300	6503	SO:0001587	stop_gained	8764	exon6			GGGTATGGTGGTT	U70321	CCDS44046.1	1p36.32	2012-02-27	2011-08-11		ENSG00000157873	ENSG00000157873		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11912	protein-coding gene	gene with protein product	"""herpesvirus entry mediator"""	602746	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""			8898196, 9162061	Standard	XM_006711018		Approved	HVEM, ATAR, TR2, LIGHTR, HVEA, CD270	uc001ajt.1	Q92956	OTTHUMG00000000792	ENST00000355716.4:c.608G>A	1.37:g.2493168G>A	ENSP00000347948:p.Trp203*	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	47	0.652778	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Nonsense_Mutation	SNP	ENST00000355716.4	37	CCDS44046.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243726	0.58995	.	.	ENSG00000157873	ENST00000434817;ENST00000435221;ENST00000451778;ENST00000355716	.	.	.	1.34	1.34	0.21922	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-4.8029	6.0814	0.19942	0.0:0.0:1.0:0.0	.	.	.	.	X	203	.	ENSP00000347948:W203X	W	+	2	0	TNFRSF14	2481250	0.000000	0.05858	0.005000	0.12908	0.025000	0.11179	-0.033000	0.12246	1.091000	0.41335	0.205000	0.17691	TGG	.	.	none		0.607	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1		
HDHD3	81932	hgsc.bcm.edu	37	9	116136198	116136198	+	Missense_Mutation	SNP	C	C	T	rs1043836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:116136198C>T	ENST00000238379.5	-	2	1334	c.437G>A	c.(436-438)gGg>gAg	p.G146E	HDHD3_ENST00000374180.3_Missense_Mutation_p.G146E|HDHD3_ENST00000485934.1_5'UTR	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	146			G -> E (in dbSNP:rs1043836).			mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						GCCAAGGCCCCCCAGGATGCC	0.637													C|||	2939	0.586861	0.4909	0.7017	5008	,	,		19117	0.4663		0.6233	False		,,,				2504	0.7219				p.G146E		Atlas-SNP	.											.	HDHD3	10	.	0			c.G437A						PASS	.	C	GLU/GLY	2429,1977	619.5+/-393.4	691,1047,465	131.0	135.0	134.0		437	-11.7	0.0	9	dbSNP_86	134	5411,3189	654.2+/-401.1	1688,2035,577	yes	missense	HDHD3	NM_031219.2	98	2379,3082,1042	TT,TC,CC		37.0814,44.8706,39.7201	benign	146/252	116136198	7840,5166	2203	4300	6503	SO:0001583	missense	81932	exon2			AGGCCCCCCAGGA	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.437G>A	9.37:g.116136198C>T	ENSP00000238379:p.Gly146Glu	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	108	63	0.583333	NM_031219	B2RD47	Missense_Mutation	SNP	ENST00000238379.5	37	CCDS6793.1	1232	0.5641025641025641	261	0.5304878048780488	242	0.6685082872928176	249	0.4353146853146853	480	0.633245382585752	C	0.003	-2.446595	0.00178	0.551294	0.629186	ENSG00000119431	ENST00000238379;ENST00000374180	T;T	0.37411	1.2;1.2	5.86	-11.7	0.00046	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	2.149360	0.01594	N	0.021720	T	0.00012	0.0000	N	0.00738	-1.235	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.32241	-0.9914	9	0.05436	T	0.98	3.8269	5.1556	0.15032	0.1484:0.1388:0.4437:0.2691	rs1043836;rs1618890;rs3177108;rs59015924;rs1043836	146	Q9BSH5	HDHD3_HUMAN	E	146	ENSP00000238379:G146E;ENSP00000363295:G146E	ENSP00000238379:G146E	G	-	2	0	HDHD3	115176019	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-1.497000	0.02289	-3.303000	0.00192	-2.128000	0.00344	GGG	C|0.419;T|0.581	0.581	strong		0.637	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219	
PCDHGA9	56107	hgsc.bcm.edu	37	5	140783596	140783596	+	Silent	SNP	C	C	T	rs1363448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140783596C>T	ENST00000573521.1	+	1	1077	c.1077C>T	c.(1075-1077)gaC>gaT	p.D359D	PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	359	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAGAGAAGACGCACCTCAGG	0.428													.|||	2713	0.541733	0.8427	0.6182	5008	,	,		18694	0.3274		0.4235	False		,,,				2504	0.4233				p.D359D		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.C1077T						PASS	.	T	,,,,,,,,,,,,,,	3199,771		1305,589,91	76.0	78.0	77.0		,,,,,,,,1077,,,,,,1077	-1.5	0.5	5	dbSNP_88	77	3605,4723		774,2057,1333	no	intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,,,,,,,	2079,2646,1424	TT,TC,CC		43.2877,19.4207,44.6739	,,,,,,,,,,,,,,	,,,,,,,,359/933,,,,,,359/829	140783596	6804,5494	1985	4164	6149	SO:0001819	synonymous_variant	56107	exon1			AGAAGACGCACCT	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.1077C>T	5.37:g.140783596C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	195	195	1	NM_032089	A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			C|0.540;T|0.460	0.460	strong		0.428	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
RADIL	55698	hgsc.bcm.edu	37	7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	rs117943885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4841614C>T	ENST00000399583.3	-	12	2699	c.2512G>A	c.(2512-2514)Gtg>Atg	p.V838M	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.V598M	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	838					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)		TCAAGGACCACGTGGTGCATA	0.677													C|||	64	0.0127796	0.0015	0.0187	5008	,	,		13575	0.0		0.0249	False		,,,				2504	0.0245				p.V838M		Atlas-SNP	.											.	RADIL	110	.	0			c.G2512A						PASS	.	C	MET/VAL	10,3304		0,10,1647	5.0	6.0	6.0		2512	-3.5	0.0	7	dbSNP_132	6	139,6811		3,133,3339	yes	missense	RADIL	NM_018059.4	21	3,143,4986	TT,TC,CC		2.0,0.3018,1.4517	benign	838/1076	4841614	149,10115	1657	3475	5132	SO:0001583	missense	55698	exon12			GGACCACGTGGTG	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.2512G>A	7.37:g.4841614C>T	ENSP00000382492:p.Val838Met	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	78	33	0.423077	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	C	8.995	0.978733	0.18812	0.003018	0.02	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.07114	3.29;3.22	4.15	-3.5	0.04710	.	0.941613	0.08946	N	0.870830	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.06405	0.002;0.0	T	0.41645	-0.9497	10	0.51188	T	0.08	-1.412	5.9949	0.19489	0.0:0.1746:0.2538:0.5716	.	838;146	Q96JH8;Q75LH2	RADIL_HUMAN;.	M	838;809;572;598	ENSP00000382492:V838M;ENSP00000442966:V598M	ENSP00000320946:V809M	V	-	1	0	RADIL	4808140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.693000	0.05121	-1.147000	0.02851	-1.340000	0.01251	GTG	C|0.984;T|0.016	0.016	strong		0.677	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
EPPK1	83481	hgsc.bcm.edu	37	8	144944225	144944225	+	Missense_Mutation	SNP	C	C	T	rs118079568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144944225C>T	ENST00000525985.1	-	2	3268	c.3197G>A	c.(3196-3198)cGt>cAt	p.R1066H				P58107	EPIPL_HUMAN	epiplakin 1	1066						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)			AACATAGCCACGCTGAATGGC	0.642													C|||	26	0.00519169	0.0008	0.0144	5008	,	,		18612	0.001		0.0139	False		,,,				2504	0.0				p.R1066H		Atlas-SNP	.											.	EPPK1	199	.	0			c.G3197A						PASS	.	C	HIS/ARG	10,4230		1,8,2111	36.0	40.0	39.0		3197	3.6	0.9	8	dbSNP_132	39	145,8341		1,143,4099	yes	missense	EPPK1	NM_031308.1	29	2,151,6210	TT,TC,CC		1.7087,0.2358,1.218	probably-damaging	1066/2420	144944225	155,12571	2120	4243	6363	SO:0001583	missense	83481	exon1			TAGCCACGCTGAA	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.3197G>A	8.37:g.144944225C>T	ENSP00000436337:p.Arg1066His	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	167	90	0.538922	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		22	0.010073260073260074	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	17.80	3.478453	0.63849	0.002358	0.017087	ENSG00000227184	ENST00000525985	T	0.79247	-1.25	4.54	3.64	0.41730	.	.	.	.	.	T	0.79227	0.4410	M	0.79693	2.465	0.28124	N	0.930474	D	0.89917	1.0	D	0.72338	0.977	T	0.75428	-0.3321	9	0.66056	D	0.02	.	11.5171	0.50529	0.1804:0.8195:0.0:0.0	.	1066	E9PPU0	.	H	1066	ENSP00000436337:R1066H	ENSP00000436337:R1066H	R	-	2	0	EPPK1	145016213	0.117000	0.22190	0.871000	0.34182	0.301000	0.27625	0.709000	0.25734	1.067000	0.40740	0.563000	0.77884	CGT	C|0.990;T|0.010	0.010	strong		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
SH3PXD2A	9644	hgsc.bcm.edu	37	10	105362179	105362179	+	Silent	SNP	G	G	A	rs3740473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105362179G>A	ENST00000369774.4	-	15	3072	c.2796C>T	c.(2794-2796)cgC>cgT	p.R932R	SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000355946.2_Silent_p.R904R|SH3PXD2A_ENST00000540321.1_Silent_p.R799R|SH3PXD2A_ENST00000538130.1_Silent_p.R767R|SH3PXD2A_ENST00000427662.2_Intron			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	932					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)		GTGCTTGGACGCGCCTCTCGA	0.627													G|||	504	0.100639	0.0794	0.0937	5008	,	,		19159	0.1964		0.1014	False		,,,				2504	0.0348				p.R904R		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.C2712T						PASS	.	G		438,3968	211.2+/-231.4	19,400,1784	132.0	122.0	125.0		2712	-3.7	0.9	10	dbSNP_107	125	777,7823	184.3+/-232.3	31,715,3554	no	coding-synonymous	SH3PXD2A	NM_014631.2		50,1115,5338	AA,AG,GG		9.0349,9.941,9.3418		904/1106	105362179	1215,11791	2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			TTGGACGCGCCTC	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.2796C>T	10.37:g.105362179G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		278	0.12728937728937728	48	0.0975609756097561	36	0.09944751381215469	112	0.1958041958041958	82	0.10817941952506596	G	0.016	-1.518392	0.00967	0.09941	0.090349	ENSG00000107957	ENST00000420222	T	0.32023	1.47	4.77	-3.7	0.04437	.	0.422513	0.27294	N	0.020036	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999999	.	.	.	.	.	.	T	0.13926	-1.0491	6	0.56958	D	0.05	-4.2558	1.1603	0.01804	0.2235:0.2681:0.3065:0.2019	rs3740473;rs3740473	.	.	.	C	859	ENSP00000395781:R859C	ENSP00000395781:R859C	R	-	1	0	SH3PXD2A	105352169	0.003000	0.15002	0.891000	0.34965	0.119000	0.20118	-1.259000	0.02861	-0.878000	0.04007	-1.172000	0.01736	CGT	G|0.894;A|0.106	0.106	strong		0.627	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631	
LAMB3	3914	hgsc.bcm.edu	37	1	209796329	209796329	+	Missense_Mutation	SNP	T	T	A	rs12748250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:209796329T>A	ENST00000356082.4	-	17	2688	c.2554A>T	c.(2554-2556)Atg>Ttg	p.M852L	LAMB3_ENST00000367030.3_Missense_Mutation_p.M852L|MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000391911.1_Missense_Mutation_p.M852L	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	852	Domain I.		M -> L (in dbSNP:rs12748250). {ECO:0000269|Ref.6}.		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)		GCACTTACCATCTGCCTGGTC	0.632													T|||	513	0.102436	0.0439	0.0865	5008	,	,		15100	0.001		0.159	False		,,,				2504	0.2393				p.M852L		Atlas-SNP	.											.	LAMB3	136	.	0			c.A2554T						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	236,4168		4,228,1970	78.0	91.0	86.0		2554,2554,2554	5.2	1.0	1	dbSNP_121	86	1313,7283		104,1105,3089	yes	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	15,15,15	108,1333,5059	AA,AT,TT		15.2745,5.3588,11.9154	benign,benign,benign	852/1173,852/1173,852/1173	209796329	1549,11451	2202	4298	6500	SO:0001583	missense	3914	exon17			TTACCATCTGCCT	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.2554A>T	1.37:g.209796329T>A	ENSP00000348384:p.Met852Leu	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	174	0.07967032967032966	20	0.04065040650406504	31	0.0856353591160221	1	0.0017482517482517483	122	0.16094986807387862	T	11.55	1.673222	0.29693	0.053588	0.152745	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.19394	2.15;2.15;2.15	5.21	5.21	0.72293	.	0.142994	0.64402	D	0.000011	T	0.00073	0.0002	M	0.61703	1.905	0.32625	P	0.522823	B	0.18610	0.029	B	0.17433	0.018	T	0.10064	-1.0646	9	0.28530	T	0.3	.	11.6693	0.51391	0.0:0.0:0.1479:0.8521	rs12748250;rs17388506	852	Q13751	LAMB3_HUMAN	L	852	ENSP00000375778:M852L;ENSP00000348384:M852L;ENSP00000355997:M852L	ENSP00000348384:M852L	M	-	1	0	LAMB3	207862952	1.000000	0.71417	1.000000	0.80357	0.600000	0.36913	1.767000	0.38501	1.992000	0.58205	0.374000	0.22700	ATG	T|0.890;A|0.110	0.110	strong		0.632	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
PSG1	5669	hgsc.bcm.edu	37	19	43383680	43383680	+	Silent	SNP	G	G	T	rs1141653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:43383680G>T	ENST00000436291.2	-	1	170	c.54C>A	c.(52-54)ctC>ctA	p.L18L	PSG1_ENST00000244296.2_Silent_p.L18L|PSG1_ENST00000403380.3_Silent_p.L18L|PSG1_ENST00000595124.1_Silent_p.L18L|PSG1_ENST00000601073.1_5'UTR|PSG1_ENST00000312439.6_Silent_p.L18L|PSG1_ENST00000595356.1_Silent_p.L18L	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	18					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)				CTGTGAGCAGGAGCCCCTTCC	0.552													.|||	1633	0.326078	0.4614	0.2046	5008	,	,		18648	0.4167		0.1014	False		,,,				2504	0.3671				p.L18L		Atlas-SNP	.											.	PSG1	196	.	0			c.C54A						PASS	.	G	,,	1275,1745		292,691,527	157.0	140.0	146.0		54,54,54	0.4	0.1	19	dbSNP_86	146	576,4838		45,486,2176	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	,,	337,1177,2703	TT,TG,GG		10.6391,42.2185,21.9469	,,	18/420,18/418,18/427	43383680	1851,6583	1510	2707	4217	SO:0001819	synonymous_variant	5669	exon1			GAGCAGGAGCCCC		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.54C>A	19.37:g.43383680G>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	15	5	0.333333	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Silent	SNP	ENST00000436291.2	37	CCDS54275.1																																																																																			G|0.775;T|0.225	0.225	strong		0.552	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
UBD	10537	hgsc.bcm.edu	37	6	29523952	29523952	+	Missense_Mutation	SNP	A	A	G	rs2076485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29523952A>G	ENST00000377050.4	-	2	426	c.203T>C	c.(202-204)aTt>aCt	p.I68T	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	68	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.		I -> T (in dbSNP:rs2076485).		aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						CTCTTTGTCAATGCCATAAGA	0.507													A|||	909	0.18151	0.0295	0.2089	5008	,	,		21002	0.1756		0.2495	False		,,,				2504	0.3037				p.I68T		Atlas-SNP	.											UBD,caecum,carcinoma,0,1	UBD	13	1	0			c.T203C						PASS	.	A	THR/ILE	205,2817		5,195,1311	63.0	63.0	63.0		203	3.0	1.0	6	dbSNP_96	63	1423,3995		187,1049,1473	yes	missense	UBD	NM_006398.3	89	192,1244,2784	GG,GA,AA		26.2643,6.7836,19.2891	probably-damaging	68/166	29523952	1628,6812	1511	2709	4220	SO:0001583	missense	10537	exon2			TTGTCAATGCCAT	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.203T>C	6.37:g.29523952A>G	ENSP00000366249:p.Ile68Thr	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	173	173	1	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Missense_Mutation	SNP	ENST00000377050.4	37	CCDS4662.1	381	0.17445054945054944	16	0.032520325203252036	69	0.19060773480662985	99	0.17307692307692307	197	0.2598944591029024	A	16.06	3.016838	0.54576	0.067836	0.262643	ENSG00000213886	ENST00000377050	T	0.80566	-1.39	5.38	3.0	0.34707	Ubiquitin supergroup (1);Ubiquitin (2);	0.797152	0.10010	N	0.727390	D	0.86590	0.5969	M	0.90705	3.14	0.23795	P	0.99682049	D	0.89917	1.0	D	0.77557	0.99	T	0.79225	-0.1891	9	0.87932	D	0	-28.5473	7.0335	0.24980	0.8189:0.0:0.1811:0.0	rs2076485;rs17177888;rs17431005;rs2076485	68	O15205	UBD_HUMAN	T	68	ENSP00000366249:I68T	ENSP00000366249:I68T	I	-	2	0	UBD	29631931	0.627000	0.27129	0.991000	0.47740	0.853000	0.48598	1.033000	0.30191	0.352000	0.24053	-0.321000	0.08615	ATT	G|0.183;N|0.000	0.183	strong		0.507	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3		
MYRIP	25924	hgsc.bcm.edu	37	3	40231810	40231810	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:40231810C>T	ENST00000302541.6	+	10	1863	c.1521C>T	c.(1519-1521)acC>acT	p.T507T	MYRIP_ENST00000396217.3_Silent_p.T418T|MYRIP_ENST00000425621.1_Silent_p.T507T|MYRIP_ENST00000444716.1_Silent_p.T507T|MYRIP_ENST00000539167.1_Silent_p.T320T|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	507	Actin-binding.|Myosin-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)		GCAGGGAGACCTCGGACAGCA	0.642																																					p.T507T		Atlas-SNP	.											.	MYRIP	98	.	0			c.C1521T						PASS	.						60.0	67.0	65.0					3																	40231810		2203	4300	6503	SO:0001819	synonymous_variant	25924	exon10			GGAGACCTCGGAC	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.1521C>T	3.37:g.40231810C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	186	86	0.462366	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Silent	SNP	ENST00000302541.6	37	CCDS2689.1																																																																																			.	.	none		0.642	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
PRPF4B	8899	hgsc.bcm.edu	37	6	4031998	4031998	+	Missense_Mutation	SNP	A	A	G	rs9503893	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:4031998A>G	ENST00000337659.6	+	2	347	c.247A>G	c.(247-249)Att>Gtt	p.I83V	PRPF4B_ENST00000538861.1_Missense_Mutation_p.I69V	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	83	Arg/Lys-rich (basic).		I -> V (in dbSNP:rs9503893). {ECO:0000269|PubMed:11418604, ECO:0000269|PubMed:12077342, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17081983, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:19413330, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:21406692, ECO:0000269|PubMed:9628581}.		mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				aagaaaagaGATTATTGATGC	0.318													G|||	3583	0.715455	0.7368	0.7277	5008	,	,		19812	0.7877		0.6352	False		,,,				2504	0.6861				p.I83V		Atlas-SNP	.											.	PRPF4B	140	.	0			c.A247G						PASS	.	G	VAL/ILE	3286,1120	397.2+/-330.3	1238,810,155	82.0	75.0	77.0		247	2.6	0.3	6	dbSNP_119	77	5747,2853	444.0+/-360.5	1902,1943,455	yes	missense	PRPF4B	NM_003913.4	29	3140,2753,610	GG,GA,AA		33.1744,25.4199,30.5474	benign	83/1008	4031998	9033,3973	2203	4300	6503	SO:0001583	missense	8899	exon2			AAAGAGATTATTG	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"""PRP4 pre-mRNA processing factor 4 homolog B (yeast)"""			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.247A>G	6.37:g.4031998A>G	ENSP00000337194:p.Ile83Val	Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	187	187	1	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Missense_Mutation	SNP	ENST00000337659.6	37	CCDS4488.1	1554	0.7115384615384616	357	0.725609756097561	262	0.7237569060773481	445	0.777972027972028	490	0.6464379947229552	G	0.007	-1.937150	0.00484	0.745801	0.668256	ENSG00000112739	ENST00000337659;ENST00000538861	T;T	0.65916	-0.18;-0.18	5.4	2.64	0.31445	.	0.667598	0.14335	N	0.326098	T	0.13329	0.0323	N	0.04508	-0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15178	-1.0446	9	0.10377	T	0.69	.	7.1493	0.25601	0.2049:0.1237:0.6714:0.0	rs9503893;rs17292762;rs17857033;rs52826967;rs60980650;rs9503893	83	Q13523	PRP4B_HUMAN	V	83;69	ENSP00000337194:I83V;ENSP00000439331:I69V	ENSP00000337194:I83V	I	+	1	0	PRPF4B	3976997	0.518000	0.26234	0.262000	0.24481	0.567000	0.35839	1.462000	0.35266	0.014000	0.14944	-0.355000	0.07637	ATT	A|0.296;G|0.704	0.704	strong		0.318	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2		
OR10Z1	128368	hgsc.bcm.edu	37	1	158577167	158577167	+	Silent	SNP	A	A	T	rs2427808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158577167A>T	ENST00000361284.1	+	1	939	c.939A>T	c.(937-939)ggA>ggT	p.G313G		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	313						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TGGGTAAAGGATGAAGGTTAC	0.488													A|||	548	0.109425	0.0461	0.098	5008	,	,		19696	0.0794		0.1332	False		,,,				2504	0.2096				p.G313G		Atlas-SNP	.											.	OR10Z1	99	.	0			c.A939T						PASS	.	A		306,4100	165.1+/-196.6	12,282,1909	89.0	91.0	90.0		939	1.9	0.7	1	dbSNP_100	90	1113,7487	229.7+/-264.3	88,937,3275	no	coding-synonymous	OR10Z1	NM_001004478.1		100,1219,5184	TT,TA,AA		12.9419,6.9451,10.9103		313/314	158577167	1419,11587	2203	4300	6503	SO:0001819	synonymous_variant	128368	exon1			TAAAGGATGAAGG	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"""GPCR / Class A : Olfactory receptors"""	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.939A>T	1.37:g.158577167A>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_001004478	Q5VYL0|Q6IFR7	Silent	SNP	ENST00000361284.1	37	CCDS30901.1																																																																																			A|0.898;T|0.102	0.102	strong		0.488	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204237416	204237416	+	Missense_Mutation	SNP	C	C	T	rs10900571	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204237416C>T	ENST00000272203.3	-	4	443	c.127G>A	c.(127-129)Gtc>Atc	p.V43I	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.V43I	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	43			V -> I (in dbSNP:rs10900571). {ECO:0000269|PubMed:10231032, ECO:0000269|PubMed:15489334}.							breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			CCAAAGGCGACGGCTTTGCGG	0.612													C|||	3168	0.632588	0.475	0.7637	5008	,	,		15353	0.8046		0.661	False		,,,				2504	0.546				p.V43I		Atlas-SNP	.											PLEKHA6,NS,adenoma,0,1	PLEKHA6	115	1	0			c.G127A						PASS	.	C	ILE/VAL	2220,2186	590.6+/-387.4	573,1074,556	94.0	79.0	84.0		127	0.3	1.0	1	dbSNP_120	84	5795,2805	677.5+/-403.4	1967,1861,472	yes	missense	PLEKHA6	NM_014935.2	29	2540,2935,1028	TT,TC,CC		32.6163,49.6142,38.3746	benign	43/1049	204237416	8015,4991	2203	4300	6503	SO:0001583	missense	22874	exon4			AGGCGACGGCTTT	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.127G>A	1.37:g.204237416C>T	ENSP00000272203:p.Val43Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	56	1	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	1475	0.6753663003663004	250	0.508130081300813	270	0.7458563535911602	451	0.7884615384615384	504	0.6649076517150396	C	9.890	1.203838	0.22121	0.503858	0.673837	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.11495	2.77;2.77	5.28	0.27	0.15635	.	0.456688	0.24490	N	0.038076	T	0.00012	0.0000	N	0.00690	-1.25	0.45690	P	0.0013999999999999568	B	0.02656	0.0	B	0.01281	0.0	T	0.08597	-1.0714	9	0.17369	T	0.5	-16.3408	10.037	0.42135	0.0:0.2364:0.0:0.7636	rs10900571;rs59453359;rs10900571	43	Q9Y2H5	PKHA6_HUMAN	I	43	ENSP00000272203:V43I;ENSP00000402046:V43I	ENSP00000272203:V43I	V	-	1	0	PLEKHA6	202504039	1.000000	0.71417	0.976000	0.42696	0.696000	0.40369	1.067000	0.30616	-0.138000	0.11434	-0.194000	0.12790	GTC	C|0.359;T|0.641	0.641	strong		0.612	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
FAM205A	259308	hgsc.bcm.edu	37	9	34725047	34725047	+	Silent	SNP	C	C	T	rs78716275		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34725047C>T	ENST00000378788.3	-	4	2229	c.2190G>A	c.(2188-2190)ccG>ccA	p.P730P		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	730						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						GATGCAGGTCCGGGTCACTTG	0.552																																					p.P730P		Atlas-SNP	.											.	FAM205A	45	.	0			c.G2190A						PASS	.						95.0	56.0	68.0					9																	34725047		692	1591	2283	SO:0001819	synonymous_variant	259308	exon4			CAGGTCCGGGTCA		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.2190G>A	9.37:g.34725047C>T		Somatic	369	0	0		WXS	Illumina HiSeq	Phase_I	360	126	0.35	NM_001141917	A8MVW7	Silent	SNP	ENST00000378788.3	37	CCDS55305.1																																																																																			T|1.000;|0.000	1.000	weak		0.552	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
ZNF416	55659	hgsc.bcm.edu	37	19	58084930	58084930	+	Silent	SNP	G	G	A	rs3746222	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58084930G>A	ENST00000196489.3	-	4	564	c.342C>T	c.(340-342)acC>acT	p.T114T		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	114					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(5)|lung(12)|prostate(1)	22		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		GCAAAATGTCGGTCAGGAATG	0.507													G|||	839	0.167532	0.202	0.1369	5008	,	,		20042	0.0942		0.2078	False		,,,				2504	0.1769				p.T114T		Atlas-SNP	.											.	ZNF416	50	.	0			c.C342T						PASS	.	G		852,3554	334.4+/-303.4	76,700,1427	121.0	104.0	110.0		342	-2.1	0.0	19	dbSNP_107	110	1661,6939	307.2+/-308.3	153,1355,2792	no	coding-synonymous	ZNF416	NM_017879.1		229,2055,4219	AA,AG,GG		19.314,19.3373,19.3219		114/595	58084930	2513,10493	2203	4300	6503	SO:0001819	synonymous_variant	55659	exon4			AATGTCGGTCAGG	BC000130	CCDS12954.1	19q13.4	2013-01-08				ENSG00000083817		"""Zinc fingers, C2H2-type"", ""-"""	20645	protein-coding gene	gene with protein product							Standard	NM_017879		Approved	FLJ20557	uc002qpf.3	Q9BWM5		ENST00000196489.3:c.342C>T	19.37:g.58084930G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	158	91	0.575949	NM_017879	Q9NWW8	Silent	SNP	ENST00000196489.3	37	CCDS12954.1																																																																																			G|0.828;A|0.172	0.172	strong		0.507	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879	
TM4SF20	79853	hgsc.bcm.edu	37	2	228243905	228243905	+	Missense_Mutation	SNP	G	G	A	rs7574414	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:228243905G>A	ENST00000304568.3	-	1	117	c.80C>T	c.(79-81)gCg>gTg	p.A27V		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	27			A -> V (in dbSNP:rs7574414). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A27V(1)		breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		TAGAGGTATCGCATTGAGAAC	0.483													G|||	530	0.105831	0.0068	0.0807	5008	,	,		19698	0.1935		0.1511	False		,,,				2504	0.1207				p.A27V		Atlas-SNP	.											TM4SF20,NS,carcinoma,0,1	TM4SF20	24	1	1	Substitution - Missense(1)	stomach(1)	c.C80T						scavenged	.	G	VAL/ALA	115,4291	87.8+/-126.4	0,115,2088	127.0	125.0	126.0		80	1.8	0.0	2	dbSNP_116	126	1209,7391	244.2+/-273.5	81,1047,3172	yes	missense	TM4SF20	NM_024795.3	64	81,1162,5260	AA,AG,GG		14.0581,2.6101,10.1799	benign	27/230	228243905	1324,11682	2203	4300	6503	SO:0001583	missense	79853	exon1			GGTATCGCATTGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.80C>T	2.37:g.228243905G>A	ENSP00000303028:p.Ala27Val	Somatic	91	1	0.010989		WXS	Illumina HiSeq	Phase_I	99	52	0.525253	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	275	0.1259157509157509	4	0.008130081300813009	32	0.08839779005524862	114	0.1993006993006993	125	0.16490765171503957	G	3.354	-0.131890	0.06753	0.026101	0.140581	ENSG00000168955	ENST00000304568	T	0.26518	1.73	5.77	1.78	0.24846	.	0.883848	0.09827	N	0.750664	T	0.00012	0.0000	L	0.41356	1.27	0.80722	P	0.0	D	0.53462	0.96	B	0.37047	0.24	T	0.10917	-1.0609	9	0.06891	T	0.86	-3.7897	5.2601	0.15567	0.1976:0.3385:0.4638:0.0	rs7574414;rs7574414	27	Q53R12	T4S20_HUMAN	V	27	ENSP00000303028:A27V	ENSP00000303028:A27V	A	-	2	0	TM4SF20	227952149	0.000000	0.05858	0.034000	0.17996	0.029000	0.11900	0.089000	0.15002	0.711000	0.32018	0.591000	0.81541	GCG	G|0.889;A|0.111	0.111	strong		0.483	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
VEPH1	79674	hgsc.bcm.edu	37	3	157034921	157034921	+	Missense_Mutation	SNP	C	C	T	rs145883418	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:157034921C>T	ENST00000362010.2	-	10	2112	c.1805G>A	c.(1804-1806)aGt>aAt	p.S602N	VEPH1_ENST00000392832.2_Missense_Mutation_p.S602N|RP11-550I24.2_ENST00000487238.1_RNA|RP11-550I24.2_ENST00000494885.1_RNA|VEPH1_ENST00000392833.2_Missense_Mutation_p.S602N|RP11-550I24.2_ENST00000475102.1_RNA|VEPH1_ENST00000543418.1_Missense_Mutation_p.S602N	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	602						plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ACTGGACTTACTGTATAGGCA	0.398													C|||	5	0.000998403	0.0	0.0043	5008	,	,		15410	0.0		0.002	False		,,,				2504	0.0				p.S602N		Atlas-SNP	.											.	VEPH1	129	.	0			c.G1805A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	1,4405	2.1+/-5.4	0,1,2202	144.0	136.0	138.0		1805,1805,1805	5.6	1.0	3	dbSNP_134	138	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	VEPH1	NM_001167911.1,NM_001167912.1,NM_024621.2	46,46,46	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	benign,benign,benign	602/789,602/834,602/834	157034921	5,13001	2203	4300	6503	SO:0001583	missense	79674	exon10			GACTTACTGTATA	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.1805G>A	3.37:g.157034921C>T	ENSP00000354919:p.Ser602Asn	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	140	62	0.442857	NM_001167911	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Missense_Mutation	SNP	ENST00000362010.2	37	CCDS3179.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	18.15	3.559511	0.65538	2.27E-4	4.65E-4	ENSG00000197415	ENST00000392833;ENST00000362010;ENST00000543418;ENST00000392832	T;T;T;T	0.10382	2.88;2.91;2.88;2.91	5.6	5.6	0.85130	.	0.094038	0.64402	D	0.000001	T	0.16171	0.0389	L	0.61218	1.895	0.80722	D	1	P;P	0.39181	0.663;0.5	B;B	0.37833	0.259;0.062	T	0.01245	-1.1407	10	0.37606	T	0.19	-2.1824	18.3899	0.90479	0.0:1.0:0.0:0.0	.	602;602	Q14D04-2;Q14D04	.;MELT_HUMAN	N	602	ENSP00000376578:S602N;ENSP00000354919:S602N;ENSP00000446258:S602N;ENSP00000376577:S602N	ENSP00000354919:S602N	S	-	2	0	VEPH1	158517615	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	5.393000	0.66279	2.645000	0.89757	0.655000	0.94253	AGT	C|0.999;T|0.001	0.001	strong		0.398	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
VCX2	51480	hgsc.bcm.edu	37	X	8138165	8138165	+	Missense_Mutation	SNP	C	C	G	rs1058237		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:8138165C>G	ENST00000317103.4	-	3	634	c.328G>C	c.(328-330)Gtg>Ctg	p.V110L		NM_016378.2	NP_057462.2	Q9H322	VCX2_HUMAN	variable charge, X-linked 2	110	2 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.		V -> L (in dbSNP:rs1058237). {ECO:0000269|PubMed:10607842, ECO:0000269|PubMed:10903929, ECO:0000269|PubMed:15489334}.							endometrium(1)	1		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GGTTCTTCCACCTCGCTCTCC	0.637													G|||	3167	0.83894	0.6505	0.6484	3775	,	,		3693	0.7242		0.5795	False		,,,				2504	0.5562				p.V110L		Atlas-SNP	.											.	VCX2	16	.	0			c.G328C						PASS	.						38.0	47.0	44.0					X																	8138165		2171	4239	6410	SO:0001583	missense	51480	exon3			CTTCCACCTCGCT	AF159127	CCDS35200.1	Xp22.32	2008-02-05			ENSG00000177504	ENSG00000177504			18158	protein-coding gene	gene with protein product		300532				10607842	Standard	NM_016378		Approved	VCX-2r, VCX-2R	uc004csb.3	Q9H322	OTTHUMG00000021105	ENST00000317103.4:c.328G>C	X.37:g.8138165C>G	ENSP00000321309:p.Val110Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	90	82	0.911111	NM_016378	A3KPB6|Q4V9T2|Q9P0H5	Missense_Mutation	SNP	ENST00000317103.4	37	CCDS35200.1	1080	0.650994575045208	166	0.45108695652173914	133	0.5732758620689655	217	0.638235294117647	228	0.41155234657039713	G	0.004	-2.260355	0.00262	.	.	ENSG00000177504	ENST00000317103	T	0.12465	2.68	0.0465	0.0465	0.14256	.	.	.	.	.	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	0.39781	-0.9597	7	0.06099	T	0.92	.	.	.	.	rs1058237;rs3198852;rs16998641	110	Q9H322	VCX2_HUMAN	L	110	ENSP00000321309:V110L	ENSP00000321309:V110L	V	-	1	0	VCX2	8098165	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.675000	0.05227	-1.450000	0.01936	-1.461000	0.01025	GTG	C|0.349;G|0.651	0.651	strong		0.637	VCX2-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055690.1	NM_016378	
CLEC11A	6320	hgsc.bcm.edu	37	19	51228634	51228634	+	Silent	SNP	G	G	A	rs11084024	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51228634G>A	ENST00000250340.4	+	4	1079	c.882G>A	c.(880-882)gaG>gaA	p.E294E	CLEC11A_ENST00000599973.1_Missense_Mutation_p.E311K	NM_002975.2	NP_002966.1	Q9Y240	CLC11_HUMAN	C-type lectin domain family 11, member A	294	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|growth factor activity (GO:0008083)			kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	7		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00641)|GBM - Glioblastoma multiforme(134;0.028)		GCACGCTCGAGAACTGCGTGG	0.711													G|||	759	0.151558	0.1853	0.1182	5008	,	,		13732	0.0506		0.2505	False		,,,				2504	0.1319				p.E294E		Atlas-SNP	.											.	CLEC11A	23	.	0			c.G882A						PASS	.	G		796,3586		69,658,1464	17.0	16.0	17.0		882	3.5	1.0	19	dbSNP_120	17	1859,6691		212,1435,2628	no	coding-synonymous	CLEC11A	NM_002975.2		281,2093,4092	AA,AG,GG		21.7427,18.1652,20.5305		294/324	51228634	2655,10277	2191	4275	6466	SO:0001819	synonymous_variant	6320	exon4			GCTCGAGAACTGC	AF087658	CCDS12800.1	19q13.3	2010-04-27	2005-02-09	2005-02-11		ENSG00000105472		"""C-type lectin domain containing"""	10576	protein-coding gene	gene with protein product		604713	"""stem cell growth factor; lymphocyte secreted C-type lectin"""	SCGF		9207134, 9442024	Standard	NM_002975		Approved	P47, LSLCL, CLECSF3	uc002psy.3	Q9Y240		ENST00000250340.4:c.882G>A	19.37:g.51228634G>A		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_002975	B2RAD4	Silent	SNP	ENST00000250340.4	37	CCDS12800.1																																																																																			G|0.808;A|0.192	0.192	strong		0.711	CLEC11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464062.1	NM_002975	
ASTE1	28990	hgsc.bcm.edu	37	3	130743812	130743812	+	Silent	SNP	G	G	A	rs35558913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130743812G>A	ENST00000264992.3	-	3	780	c.339C>T	c.(337-339)taC>taT	p.Y113Y	NEK11_ENST00000412440.2_5'Flank|NEK11_ENST00000510688.1_5'Flank|NEK11_ENST00000511262.1_5'Flank|NEK11_ENST00000510769.1_5'Flank|NEK11_ENST00000356918.4_5'Flank|NEK11_ENST00000429253.2_5'Flank|NEK11_ENST00000383366.4_5'Flank|ASTE1_ENST00000514044.1_Silent_p.Y113Y|NEK11_ENST00000507910.1_5'Flank	NM_014065.2	NP_054784.2	Q2TB18	ASTE1_HUMAN	asteroid homolog 1 (Drosophila)	113					DNA repair (GO:0006281)		nuclease activity (GO:0004518)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	22						AGGGACATACGTACCCACTCC	0.443													A|||	834	0.166534	0.1157	0.1369	5008	,	,		19760	0.131		0.2197	False		,,,				2504	0.2382				p.Y113Y		Atlas-SNP	.											.	ASTE1	67	.	0			c.C339T						PASS	.	A		627,3779	767.6+/-413.5	40,547,1616	113.0	106.0	108.0		339	2.9	0.5	3	dbSNP_126	108	1854,6746	730.0+/-406.7	195,1464,2641	no	coding-synonymous	ASTE1	NM_014065.2		235,2011,4257	AA,AG,GG		21.5581,14.2306,19.0758		113/680	130743812	2481,10525	2203	4300	6503	SO:0001819	synonymous_variant	28990	exon3			ACATACGTACCCA	AF113539	CCDS3068.1, CCDS75007.1	3q21.3	2005-11-17			ENSG00000034533	ENSG00000034533			25021	protein-coding gene	gene with protein product							Standard	NM_014065		Approved	HT001	uc003env.1	Q2TB18	OTTHUMG00000159644	ENST00000264992.3:c.339C>T	3.37:g.130743812G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_014065	B4DFL9|Q3MIB6|Q8N6G4|Q96JY1|Q9UHX6	Silent	SNP	ENST00000264992.3	37	CCDS3068.1																																																																																			G|0.817;A|0.183	0.183	strong		0.443	ASTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356659.1	NM_014065	
KRT25	147183	hgsc.bcm.edu	37	17	38911327	38911327	+	Missense_Mutation	SNP	C	C	G	rs35076248	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38911327C>G	ENST00000312150.4	-	1	257	c.197G>C	c.(196-198)gGc>gCc	p.G66A		NM_181534.3	NP_853512.1			keratin 25											endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				CACAGTGAAGCCAGCACAGGG	0.547													C|||	828	0.165335	0.202	0.2839	5008	,	,		16929	0.1657		0.1163	False		,,,				2504	0.0818				p.G66A		Atlas-SNP	.											.	KRT25	63	.	0			c.G197C						PASS	.	C	ALA/GLY	810,3596	323.2+/-298.0	87,636,1480	111.0	104.0	106.0		197	4.7	1.0	17	dbSNP_126	106	1026,7574	219.1+/-257.3	57,912,3331	yes	missense	KRT25	NM_181534.3	60	144,1548,4811	GG,GC,CC		11.9302,18.384,14.1166	benign	66/451	38911327	1836,11170	2203	4300	6503	SO:0001583	missense	147183	exon1			GTGAAGCCAGCAC	AK129503	CCDS11373.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000204897	ENSG00000204897		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30839	protein-coding gene	gene with protein product			"""keratin 25A"""	KRT25A		16831889	Standard	NM_181534		Approved		uc002hve.3	Q7Z3Z0	OTTHUMG00000133373	ENST00000312150.4:c.197G>C	17.37:g.38911327C>G	ENSP00000310573:p.Gly66Ala	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_181534		Missense_Mutation	SNP	ENST00000312150.4	37	CCDS11373.1	352	0.16117216117216118	86	0.17479674796747968	85	0.23480662983425415	102	0.17832167832167833	79	0.10422163588390501	C	10.31	1.315443	0.23908	0.18384	0.119302	ENSG00000204897	ENST00000394042;ENST00000312150	D	0.83163	-1.69	5.76	4.74	0.60224	.	0.476832	0.21849	N	0.068208	T	0.00073	0.0002	N	0.11560	0.145	0.33559	P	0.40291200000000005	B	0.10296	0.003	B	0.08055	0.003	T	0.01940	-1.1243	9	0.26408	T	0.33	.	16.2755	0.82642	0.0:0.8675:0.1325:0.0	rs35076248;rs58179350	66	Q7Z3Z0	K1C25_HUMAN	A	66	ENSP00000310573:G66A	ENSP00000310573:G66A	G	-	2	0	KRT25	36164853	0.002000	0.14202	0.995000	0.50966	0.398000	0.30690	0.975000	0.29449	2.727000	0.93392	0.655000	0.94253	GGC	C|0.849;G|0.151	0.151	strong		0.547	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534	
CLDN8	9073	hgsc.bcm.edu	37	21	31587793	31587793	+	Missense_Mutation	SNP	A	A	G	rs686364	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:31587793A>G	ENST00000399899.1	-	1	598	c.451T>C	c.(451-453)Tca>Cca	p.S151P	CLDN8_ENST00000286809.1_Missense_Mutation_p.S151P	NM_199328.2	NP_955360.1	P56748	CLD8_HUMAN	claudin 8	151			S -> P (in dbSNP:rs686364). {ECO:0000269|Ref.3}.		calcium-independent cell-cell adhesion (GO:0016338)	basolateral plasma membrane (GO:0016323)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|large_intestine(6)|lung(6)	15						TTCACTATTGAGTTATAGAAA	0.498													G|||	2097	0.41873	0.7216	0.2651	5008	,	,		19712	0.4484		0.2773	False		,,,				2504	0.2331				p.S151P		Atlas-SNP	.											.	CLDN8	40	.	0			c.T451C						PASS	.	G	PRO/SER	2900,1506	480.4+/-358.8	947,1006,250	72.0	72.0	72.0		451	4.0	1.0	21	dbSNP_83	72	2098,6502	717.1+/-406.1	271,1556,2473	yes	missense	CLDN8	NM_199328.2	74	1218,2562,2723	GG,GA,AA		24.3953,34.1807,38.4284	benign	151/226	31587793	4998,8008	2203	4300	6503	SO:0001583	missense	9073	exon1			CTATTGAGTTATA	AJ250711	CCDS13587.1	21q22.1	2008-07-31			ENSG00000156284	ENSG00000156284		"""Claudins"""	2050	protein-coding gene	gene with protein product		611231				9892664	Standard	NM_199328		Approved		uc002ynu.2	P56748	OTTHUMG00000081872	ENST00000399899.1:c.451T>C	21.37:g.31587793A>G	ENSP00000382783:p.Ser151Pro	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	135	70	0.518519	NM_199328	D3DSE3|Q53EX7	Missense_Mutation	SNP	ENST00000399899.1	37	CCDS13587.1	883	0.4043040293040293	340	0.6910569105691057	102	0.281767955801105	242	0.4230769230769231	199	0.262532981530343	G	0.021	-1.429690	0.01117	0.658193	0.243953	ENSG00000156284	ENST00000399899;ENST00000286809;ENST00000536721	D;D	0.88741	-2.42;-2.42	4.84	3.96	0.45880	.	0.056944	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00014	-2.91	0.46113	P	0.0011250000000000426	B	0.02656	0.0	B	0.01281	0.0	T	0.48445	-0.9035	9	0.02654	T	1	.	11.4472	0.50131	0.1492:0.0:0.8508:0.0	rs686364;rs3746849;rs52794641;rs56681626;rs686364	151	P56748	CLD8_HUMAN	P	151	ENSP00000382783:S151P;ENSP00000286809:S151P	ENSP00000286809:S151P	S	-	1	0	CLDN8	30509664	1.000000	0.71417	0.983000	0.44433	0.029000	0.11900	7.728000	0.84847	0.776000	0.33473	-0.790000	0.03334	TCA	T|0.003;G|0.402	0.402	strong		0.498	CLDN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000182260.1	NM_199328	
ADCY1	107	hgsc.bcm.edu	37	7	45753324	45753324	+	Silent	SNP	G	G	A	rs2293106	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45753324G>A	ENST00000297323.7	+	20	3112	c.3090G>A	c.(3088-3090)agG>agA	p.R1030R		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	1030	Interaction with calmodulin. {ECO:0000250}.				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)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|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)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGCTGAGAAGGTGCCCCTACC	0.532													G|||	837	0.167133	0.32	0.1167	5008	,	,		20093	0.121		0.173	False		,,,				2504	0.0378				p.R1030R		Atlas-SNP	.											.	ADCY1	187	.	0			c.G3090A						PASS	.	G		1341,3065	447.5+/-348.4	212,917,1074	84.0	79.0	81.0		3090	2.8	0.0	7	dbSNP_100	81	1443,7157	277.1+/-292.7	125,1193,2982	no	coding-synonymous	ADCY1	NM_021116.2		337,2110,4056	AA,AG,GG		16.7791,30.4358,21.4055		1030/1120	45753324	2784,10222	2203	4300	6503	SO:0001819	synonymous_variant	107	exon20			GAGAAGGTGCCCC	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"""Adenylate cyclases"""	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.3090G>A	7.37:g.45753324G>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	45	0.529412	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																			G|0.797;A|0.203	0.203	strong		0.532	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116	
FAIM	55179	hgsc.bcm.edu	37	3	138329862	138329862	+	Intron	SNP	G	G	A	rs811322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:138329862G>A	ENST00000393035.2	+	1	87				FAIM_ENST00000360570.3_Intron|FAIM_ENST00000393034.2_Intron|FAIM_ENST00000338446.4_Silent_p.P21P	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule						apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						TGGTATCTCCGGACTCTGCCA	0.463													A|||	3538	0.70647	0.5492	0.7262	5008	,	,		17908	0.9802		0.5567	False		,,,				2504	0.7771				p.P21P		Atlas-SNP	.											.	FAIM	27	.	0			c.G63A						PASS	.	A	,,,	2501,1905	545.4+/-376.8	704,1093,406	199.0	191.0	194.0		63,,,	2.1	0.0	3	dbSNP_86	194	4922,3678	526.6+/-381.0	1438,2046,816	no	coding-synonymous,intron,intron,intron	FAIM	NM_001033030.1,NM_001033031.1,NM_001033032.1,NM_018147.3	,,,	2142,3139,1222	AA,AG,GG		42.7674,43.2365,42.9263	,,,	21/214,,,	138329862	7423,5583	2203	4300	6503	SO:0001627	intron_variant	55179	exon2			ATCTCCGGACTCT	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.-23+2083G>A	3.37:g.138329862G>A		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	222	96	0.432432	NM_001033030	Q6IAN2	Silent	SNP	ENST00000393035.2	37	CCDS3103.1																																																																																			A|0.616;C|0.002	0.616	strong		0.463	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032	
POLR1D	51082	hgsc.bcm.edu	37	13	28239838	28239838	+	Silent	SNP	T	T	C	rs41291678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:28239838T>C	ENST00000399697.3	+	3	235	c.117T>C	c.(115-117)ctT>ctC	p.L39L	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)			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)		AGTGTCCTCTTGCTAGCACCA	0.403													T|||	78	0.0155751	0.0015	0.013	5008	,	,		18485	0.0		0.0577	False		,,,				2504	0.0092				p.L39L		Atlas-SNP	.											.	POLR1D	31	.	0			c.T117C						PASS	.	T	,	53,4353	52.3+/-87.9	2,49,2152	87.0	79.0	81.0		33,117	-2.0	1.0	13	dbSNP_127	81	487,8113	141.6+/-197.9	11,465,3824	no	coding-synonymous,coding-synonymous	POLR1D	NM_001206559.1,NM_152705.2	,	13,514,5976	CC,CT,TT		5.6628,1.2029,4.1519	,	11/95,39/123	28239838	540,12466	2203	4300	6503	SO:0001819	synonymous_variant	51082	exon3			TCCTCTTGCTAGC	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.117T>C	13.37:g.28239838T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	160	80	0.5	NM_152705	Q5TBX2|Q96BR3	Silent	SNP	ENST00000399697.3	37	CCDS9324.1																																																																																			T|0.965;C|0.035	0.035	strong		0.403	POLR1D-004	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044306.1	NM_015972, NM_152705	
DPYD	1806	hgsc.bcm.edu	37	1	97981395	97981395	+	Missense_Mutation	SNP	T	T	C	rs1801159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:97981395T>C	ENST00000370192.3	-	13	1727	c.1627A>G	c.(1627-1629)Ata>Gta	p.I543V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	543			I -> V (in allele DPYD*5; dbSNP:rs1801159). {ECO:0000269|PubMed:15489334}.		beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AAAGGATTTATAAACTTCAAT	0.448													T|||	926	0.184904	0.1536	0.2666	5008	,	,		14548	0.2659		0.1879	False		,,,				2504	0.0828				p.I543V		Atlas-SNP	.											.	DPYD	219	.	0			c.A1627G	GRCh37	CM033371	DPYD	M	rs1801159	PASS	.	T	VAL/ILE	684,3722	287.8+/-279.5	56,572,1575	80.0	75.0	77.0		1627	-3.1	0.0	1	dbSNP_89	77	1704,6896	311.6+/-310.4	192,1320,2788	yes	missense	DPYD	NM_000110.3	29	248,1892,4363	CC,CT,TT		19.814,15.5243,18.3608	benign	543/1026	97981395	2388,10618	2203	4300	6503	SO:0001583	missense	1806	exon13			GATTTATAAACTT	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1627A>G	1.37:g.97981395T>C	ENSP00000359211:p.Ile543Val	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	447	0.20467032967032966	100	0.2032520325203252	69	0.19060773480662985	148	0.25874125874125875	130	0.17150395778364116	T	12.85	2.060151	0.36373	0.155243	0.19814	ENSG00000188641	ENST00000370192	T	0.74002	-0.8	5.05	-3.13	0.05266	Aldolase-type TIM barrel (1);	0.378314	0.31612	N	0.007342	T	0.22044	0.0531	N	0.11427	0.14	0.09310	P	0.99999788442	B	0.02656	0.0	B	0.01281	0.0	T	0.26224	-1.0109	9	0.02654	T	1	0.1698	9.7016	0.40189	0.0:0.1666:0.6128:0.2206	rs1801159;rs17116825;rs58945530;rs1801159	543	Q12882	DPYD_HUMAN	V	543	ENSP00000359211:I543V	ENSP00000359211:I543V	I	-	1	0	DPYD	97753983	0.993000	0.37304	0.026000	0.17262	0.842000	0.47809	1.371000	0.34250	-0.215000	0.10063	0.477000	0.44152	ATA	T|0.802;C|0.198	0.198	strong		0.448	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
ABCC12	94160	hgsc.bcm.edu	37	16	48139232	48139232	+	Nonsense_Mutation	SNP	G	G	A	rs151150316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:48139232G>A	ENST00000311303.3	-	19	2836	c.2491C>T	c.(2491-2493)Cag>Tag	p.Q831*	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_Nonsense_Mutation_p.Q828*	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	831	ABC transmembrane type-1 2. {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)				CTGTTGCCCTGGGGCCCACAG	0.517													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20402	0.0		0.002	False		,,,				2504	0.0				p.Q831X		Atlas-SNP	.											.	ABCC12	190	.	0			c.C2491T						PASS	.	G	stop/GLN	5,4397	8.1+/-20.4	0,5,2196	61.0	49.0	53.0		2491	3.2	0.0	16	dbSNP_134	53	37,8563	22.8+/-68.1	0,37,4263	yes	stop-gained	ABCC12	NM_033226.2		0,42,6459	AA,AG,GG		0.4302,0.1136,0.323		831/1360	48139232	42,12960	2201	4300	6501	SO:0001587	stop_gained	94160	exon19			TGCCCTGGGGCCC	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.2491C>T	16.37:g.48139232G>A	ENSP00000311030:p.Gln831*	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	39	25	0.641026	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Nonsense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	35	5.497679	0.96355	0.001136	0.004302	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	.	.	.	5.21	3.23	0.37069	.	1.089020	0.06851	N	0.797314	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	9.3552	0.38161	0.1553:0.0:0.8447:0.0	.	.	.	.	X	831;828;749	.	ENSP00000311030:Q831X	Q	-	1	0	ABCC12	46696733	0.001000	0.12720	0.009000	0.14445	0.127000	0.20565	0.706000	0.25690	2.405000	0.81733	0.655000	0.94253	CAG	G|0.998;A|0.002	0.002	strong		0.517	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
DGCR2	9993	hgsc.bcm.edu	37	22	19026613	19026613	+	Missense_Mutation	SNP	A	A	G	rs2072123	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19026613A>G	ENST00000263196.7	-	10	1665	c.1418T>C	c.(1417-1419)gTg>gCg	p.V473A	DGCR2_ENST00000545799.1_3'UTR|DGCR2_ENST00000537045.1_Missense_Mutation_p.V432A	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	473			V -> A (in dbSNP:rs2072123). {ECO:0000269|PubMed:7655455}.		cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					GCTGACCTCCACAGGCTCAAA	0.642													G|||	2161	0.43151	0.5696	0.4078	5008	,	,		16113	0.3442		0.3559	False		,,,				2504	0.4294				p.V473A		Atlas-SNP	.											.	DGCR2	45	.	0			c.T1418C						PASS	.	G	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	2235,2169		580,1075,547	36.0	37.0	37.0		1295,1286,1409,1418	-4.4	0.0	22	dbSNP_96	37	3254,5346		636,1982,1682	yes	missense,missense,missense,missense	DGCR2	NM_001173533.1,NM_001173534.1,NM_001184781.1,NM_005137.2	64,64,64,64	1216,3057,2229	GG,GA,AA		37.8372,49.2507,42.2101	benign,benign,benign,benign	432/510,429/507,470/548,473/551	19026613	5489,7515	2202	4300	6502	SO:0001583	missense	9993	exon10			ACCTCCACAGGCT	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"""integral membrane protein DGCR2"""	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1418T>C	22.37:g.19026613A>G	ENSP00000263196:p.Val473Ala	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	109	52	0.477064	NM_005137	A6NIB5|A8K6K5|B5TY34|B7Z935	Missense_Mutation	SNP	ENST00000263196.7	37	CCDS33598.1	862	0.3946886446886447	254	0.516260162601626	145	0.4005524861878453	193	0.3374125874125874	270	0.3562005277044855	G	0.469	-0.885473	0.02511	0.507493	0.378372	ENSG00000070413	ENST00000537045;ENST00000263196	T;T	0.41400	1.0;1.0	5.61	-4.41	0.03590	.	0.768784	0.12964	N	0.424762	T	0.00012	0.0000	N	0.04043	-0.29	0.51012	P	9.300000000000974E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.35895	-0.9770	9	0.07175	T	0.84	.	2.7147	0.05184	0.4604:0.0899:0.2668:0.1829	rs2072123;rs17743390;rs56724907;rs2072123	429;473	B7Z3T5;P98153	.;IDD_HUMAN	A	432;473	ENSP00000440062:V432A;ENSP00000263196:V473A	ENSP00000263196:V473A	V	-	2	0	DGCR2	17406613	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.707000	0.05041	-1.523000	0.01767	-1.714000	0.00712	GTG	T|0.004;G|0.408	0.408	strong		0.642	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137	
FASN	2194	hgsc.bcm.edu	37	17	80044211	80044211	+	Silent	SNP	G	G	A	rs41283365	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80044211G>A	ENST00000306749.2	-	22	3869	c.3651C>T	c.(3649-3651)ggC>ggT	p.G1217G		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1217					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)	AGTCCAGGAGGCCGCTGAGCA	0.667													.|||	326	0.0650958	0.0098	0.0965	5008	,	,		17221	0.004		0.172	False		,,,				2504	0.0706				p.G1217G	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C3651T						PASS	.	G		165,4197		5,155,2021	27.0	23.0	25.0		3651	-1.8	0.6	17	dbSNP_127	25	1636,6952		145,1346,2803	no	coding-synonymous	FASN	NM_004104.4		150,1501,4824	AA,AG,GG		19.0498,3.7827,13.9073		1217/2512	80044211	1801,11149	2181	4294	6475	SO:0001819	synonymous_variant	2194	exon22			CAGGAGGCCGCTG	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.3651C>T	17.37:g.80044211G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			G|0.885;A|0.115	0.115	strong		0.667	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
STK31	56164	hgsc.bcm.edu	37	7	23811800	23811800	+	Missense_Mutation	SNP	G	G	T	rs10247878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:23811800G>T	ENST00000355870.3	+	15	1987	c.1868G>T	c.(1867-1869)aGt>aTt	p.S623I	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.S600I|STK31_ENST00000428484.1_Missense_Mutation_p.S600I|STK31_ENST00000433467.2_Missense_Mutation_p.S623I	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	623			S -> I (in dbSNP:rs10247878). {ECO:0000269|PubMed:17344846}.	NKS -> KKI (in Ref. 1; AAK31978). {ECO:0000305}.		acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTAAATAAGAGTCCCAGTGTG	0.299													G|||	373	0.0744808	0.0431	0.0908	5008	,	,		16735	0.0476		0.16	False		,,,				2504	0.045				p.S623I		Atlas-SNP	.											.	STK31	175	.	0			c.G1868T						PASS	.	G	ILE/SER,ILE/SER,ILE/SER	263,4139	141.9+/-177.2	8,247,1946	46.0	48.0	47.0		1799,1868,1799	2.3	1.0	7	dbSNP_119	47	1404,7184	265.6+/-286.2	107,1190,2997	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	142,142,142	115,1437,4943	TT,TG,GG		16.3484,5.9746,12.8329	benign,benign,benign	600/997,623/1020,600/997	23811800	1667,11323	2201	4294	6495	SO:0001583	missense	56164	exon15			ATAAGAGTCCCAG	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1868G>T	7.37:g.23811800G>T	ENSP00000348132:p.Ser623Ile	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	222	0.10164835164835165	26	0.052845528455284556	47	0.1298342541436464	24	0.04195804195804196	125	0.16490765171503957	G	11.86	1.763990	0.31228	0.059746	0.163484	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.70869	-0.52;1.21;-0.52;-0.52	5.19	2.34	0.29019	.	0.238536	0.42821	D	0.000653	T	0.00384	0.0012	M	0.62723	1.935	0.42167	P	0.008380000000000054	P;B	0.39216	0.664;0.0	B;B	0.31191	0.125;0.002	T	0.04664	-1.0935	9	0.37606	T	0.19	-0.6498	8.4601	0.32923	0.1231:0.2418:0.6351:0.0	rs10247878;rs10247878	623;623	B4DZ06;Q9BXU1	.;STK31_HUMAN	I	623;623;600;600	ENSP00000348132:S623I;ENSP00000411852:S623I;ENSP00000346660:S600I;ENSP00000406146:S600I	ENSP00000346660:S600I	S	+	2	0	STK31	23778325	0.983000	0.35010	0.987000	0.45799	0.867000	0.49689	1.051000	0.30417	0.188000	0.20168	-0.266000	0.10368	AGT	G|0.876;T|0.124	0.124	strong		0.299	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
TMEM244	253582	hgsc.bcm.edu	37	6	130152520	130152520	+	Missense_Mutation	SNP	A	A	C	rs7776426	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:130152520A>C	ENST00000368143.1	-	5	413	c.331T>G	c.(331-333)Ttc>Gtc	p.F111V	TMEM244_ENST00000438392.1_Missense_Mutation_p.F111V	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	111			F -> V (in dbSNP:rs7776426).			integral component of membrane (GO:0016021)											GTCAAGGGGAATTCCAACATA	0.308													A|||	1215	0.242612	0.1823	0.245	5008	,	,		17149	0.1359		0.4583	False		,,,				2504	0.2106				p.F111V		Atlas-SNP	.											.	.	.	.	0			c.T331G						PASS	.	A	VAL/PHE	1105,3299	393.1+/-328.7	146,813,1243	65.0	63.0	64.0		331	3.3	0.9	6	dbSNP_116	64	4096,4504	559.5+/-387.4	1003,2090,1207	yes	missense	C6orf191	NM_001010876.1	50	1149,2903,2450	CC,CA,AA		47.6279,25.0908,39.9954	benign	111/129	130152520	5201,7803	2202	4300	6502	SO:0001583	missense	253582	exon5			AGGGGAATTCCAA		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.331T>G	6.37:g.130152520A>C	ENSP00000357125:p.Phe111Val	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	148	13	0.0878378	NM_001010876		Missense_Mutation	SNP	ENST00000368143.1	37	CCDS34536.1	605	0.27701465201465203	92	0.18699186991869918	98	0.27071823204419887	73	0.12762237762237763	342	0.45118733509234826	A	16.85	3.235466	0.58886	0.250908	0.476279	ENSG00000203756	ENST00000368143;ENST00000438392	T;T	0.34667	1.35;1.35	4.5	3.31	0.37934	.	0.067056	0.64402	U	0.000012	T	0.24275	0.0588	L	0.55481	1.735	0.32129	P	0.587021	P	0.46912	0.886	P	0.47573	0.55	T	0.07083	-1.0791	9	0.54805	T	0.06	-16.8847	9.7114	0.40247	0.8444:0.0:0.0:0.1556	rs7776426;rs17395737;rs52808693;rs58635664;rs7776426	111	Q5VVB8	CF191_HUMAN	V	111	ENSP00000357125:F111V;ENSP00000403755:F111V	ENSP00000357125:F111V	F	-	1	0	C6orf191	130194213	1.000000	0.71417	0.935000	0.37517	0.865000	0.49528	2.021000	0.41020	0.664000	0.31047	0.455000	0.32223	TTC	A|0.663;C|0.337	0.337	strong		0.308	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
ZNF70	7621	hgsc.bcm.edu	37	22	24086107	24086107	+	Silent	SNP	A	A	G	rs5759985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:24086107A>G	ENST00000341976.3	-	2	1681	c.1221T>C	c.(1219-1221)atT>atC	p.I407I		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	407					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						TATAGTGCTCAATGAGGGCTG	0.582													g|||	2787	0.55651	0.7927	0.4006	5008	,	,		18529	0.6865		0.3579	False		,,,				2504	0.4182				p.I407I		Atlas-SNP	.											ZNF70,NS,carcinoma,-1,1	ZNF70	49	1	0			c.T1221C						PASS	.	G		3262,1144	405.8+/-333.6	1225,812,166	124.0	119.0	121.0		1221	-5.1	0.4	22	dbSNP_114	121	3116,5484	658.5+/-401.6	596,1924,1780	no	coding-synonymous	ZNF70	NM_021916.2		1821,2736,1946	GG,GA,AA		36.2326,25.9646,49.0389		407/447	24086107	6378,6628	2203	4300	6503	SO:0001819	synonymous_variant	7621	exon2			GTGCTCAATGAGG	X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"""Zinc fingers, C2H2-type"""	13140	protein-coding gene	gene with protein product		194544	"""zinc finger protein 70 (Cos17)"""			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.1221T>C	22.37:g.24086107A>G		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	192	98	0.510417	NM_021916		Silent	SNP	ENST00000341976.3	37	CCDS13812.1																																																																																			A|0.481;G|0.519	0.519	strong		0.582	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916	
PGS1	9489	hgsc.bcm.edu	37	17	76421443	76421443	+	IGR	SNP	G	G	A	rs1134541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76421443G>A	ENST00000262764.6	+	0	2201				DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.Y4398Y|DNAH17_ENST00000585328.1_Silent_p.Y4370Y|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)			TGAAGAGTCCGTACACGTAGG	0.532													G|||	536	0.107029	0.1997	0.072	5008	,	,		20979	0.0288		0.0905	False		,,,				2504	0.1043				p.Y4375Y	Esophageal Squamous(45;182 1126 10685 43198)	Atlas-SNP	.											.	DNAH17	347	.	0			c.C13125T						PASS	.	G		726,3680	301.3+/-286.8	57,612,1534	101.0	101.0	101.0		13125	0.4	1.0	17	dbSNP_86	101	800,7800	187.3+/-234.6	47,706,3547	no	coding-synonymous	DNAH17	NM_173628.3		104,1318,5081	AA,AG,GG		9.3023,16.4775,11.733		4375/4463	76421443	1526,11480	2203	4300	6503	SO:0001628	intergenic_variant	8632	exon80			GAGTCCGTACACG		CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76421443G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_173628	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Silent	SNP	ENST00000262764.6	37	CCDS42391.1																																																																																			G|0.885;A|0.115	0.115	strong		0.532	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1	NM_024419	
SLC5A12	159963	hgsc.bcm.edu	37	11	26705310	26705310	+	Silent	SNP	A	A	G	rs3924551	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:26705310A>G	ENST00000396005.3	-	11	1611	c.1302T>C	c.(1300-1302)aaT>aaC	p.N434N		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	434					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						TTACCTTCCAATTCACAAAAG	0.512													G|||	2179	0.435104	0.3185	0.3689	5008	,	,		17943	0.3472		0.6342	False		,,,				2504	0.5256				p.N434N		Atlas-SNP	.											SLC5A12,NS,carcinoma,0,1	SLC5A12	134	1	0			c.T1302C						PASS	.	G		1423,2351		277,869,741	61.0	58.0	59.0		1302	5.6	1.0	11	dbSNP_108	59	5099,3155		1582,1935,610	no	coding-synonymous	SLC5A12	NM_178498.3		1859,2804,1351	GG,GA,AA		38.2239,37.7054,45.7765		434/619	26705310	6522,5506	1887	4127	6014	SO:0001819	synonymous_variant	159963	exon11			CTTCCAATTCACA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1302T>C	11.37:g.26705310A>G		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			A|0.542;G|0.458	0.458	strong		0.512	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
PARP4	143	hgsc.bcm.edu	37	13	25052393	25052393	+	Missense_Mutation	SNP	G	G	T	rs79107024	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25052393G>T	ENST00000381989.3	-	13	1575	c.1470C>A	c.(1468-1470)caC>caA	p.H490Q		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	490	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.H490Q(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTCTCCCGGGTGTGAGTACT	0.418																																					p.H490Q		Atlas-SNP	.											.	PARP4	142	.	1	Substitution - Missense(1)	lung(1)	c.C1470A						PASS	.						106.0	86.0	92.0					13																	25052393		2203	4300	6503	SO:0001583	missense	143	exon13			TCCCGGGTGTGAG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1470C>A	13.37:g.25052393G>T	ENSP00000371419:p.His490Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	174	44	0.252874	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	285	0.1304945054945055	99	0.20121951219512196	44	0.12154696132596685	36	0.06293706293706294	106	0.13984168865435356	G	3.333	-0.136204	0.06711	.	.	ENSG00000102699	ENST00000381989	T	0.13420	2.59	3.91	-0.744	0.11101	Poly(ADP-ribose) polymerase, catalytic domain (2);	0.898333	0.09533	N	0.789209	T	0.00012	0.0000	L	0.60067	1.865	0.24090	N	0.995918	B	0.14805	0.011	B	0.13407	0.009	T	0.44314	-0.9336	10	0.16896	T	0.51	-1.9083	3.6715	0.08276	0.2177:0.0:0.3285:0.4537	.	490	Q9UKK3	PARP4_HUMAN	Q	490	ENSP00000371419:H490Q	ENSP00000371419:H490Q	H	-	3	2	PARP4	23950393	0.588000	0.26799	0.018000	0.16275	0.865000	0.49528	-0.111000	0.10807	-0.008000	0.14320	0.644000	0.83932	CAC	G|0.874;T|0.126	0.126	strong		0.418	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
MYO16	23026	hgsc.bcm.edu	37	13	109707827	109707827	+	Silent	SNP	T	T	C	rs9521141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:109707827T>C	ENST00000357550.2	+	26	3194	c.3153T>C	c.(3151-3153)gaT>gaC	p.D1051D	MYO16_ENST00000457511.2_Silent_p.D563D|MYO16_ENST00000356711.2_Silent_p.D1051D	NM_001198950.1	NP_001185879.1			myosin XVI									p.D1051D(1)		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)			AGCTGCCAGATACTTTTGATA	0.408													T|||	460	0.091853	0.0023	0.1124	5008	,	,		17509	0.0992		0.1402	False		,,,				2504	0.1411				p.D1073D		Atlas-SNP	.											MYO16,NS,carcinoma,0,1	MYO16	285	1	1	Substitution - coding silent(1)	stomach(1)	c.T3219C						PASS	.	T	,	126,4280	93.0+/-131.7	2,122,2079	135.0	132.0	133.0		3219,3153	-4.4	0.0	13	dbSNP_119	133	1123,7475	233.6+/-266.8	84,955,3260	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	86,1077,5339	CC,CT,TT		13.0612,2.8597,9.6047	,	1073/1881,1051/1859	109707827	1249,11755	2203	4299	6502	SO:0001819	synonymous_variant	23026	exon27			GCCAGATACTTTT		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.3153T>C	13.37:g.109707827T>C		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	128	64	0.5	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			T|0.910;C|0.090	0.090	strong		0.408	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
PSME2	5721	hgsc.bcm.edu	37	14	24615435	24615435	+	Silent	SNP	T	T	C	rs4575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24615435T>C	ENST00000216802.5	-	2	702	c.63A>G	c.(61-63)agA>agG	p.R21R	RNF31_ENST00000559275.1_5'Flank|RNF31_ENST00000382687.3_5'Flank|PSME2_ENST00000471700.2_5'UTR|PSME2_ENST00000560410.1_Intron|RNF31_ENST00000324103.6_5'Flank	NM_002818.2	NP_002809.2	Q9UL46	PSME2_HUMAN	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)	21					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)				endometrium(1)|lung(3)|prostate(2)	6				GBM - Glioblastoma multiforme(265;0.00839)		AAAGATTCTGTCTGAAGACCT	0.507													C|||	2844	0.567891	0.7905	0.5447	5008	,	,		17071	0.6369		0.3231	False		,,,				2504	0.4642				p.R21R		Atlas-SNP	.											.	PSME2	21	.	0			c.A63G						PASS	.	C		3076,1330	445.5+/-347.7	1085,906,212	96.0	97.0	97.0		63	4.0	1.0	14	dbSNP_52	97	2376,6224	701.4+/-405.2	338,1700,2262	no	coding-synonymous	PSME2	NM_002818.2		1423,2606,2474	CC,CT,TT		27.6279,30.1861,41.9191		21/240	24615435	5452,7554	2203	4300	6503	SO:0001819	synonymous_variant	5721	exon2			ATTCTGTCTGAAG		CCDS9614.1	14q11.2	2010-03-10			ENSG00000100911	ENSG00000100911		"""Proteasome (prosome, macropain) subunits"""	9569	protein-coding gene	gene with protein product		602161				7789512	Standard	NM_002818		Approved	PA28beta	uc001wmj.3	Q9UL46	OTTHUMG00000028797	ENST00000216802.5:c.63A>G	14.37:g.24615435T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	56	29	0.517857	NM_002818	Q15129	Silent	SNP	ENST00000216802.5	37	CCDS9614.1																																																																																			T|0.531;C|0.469	0.469	strong		0.507	PSME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071918.3	NM_002818	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632714	32632714	+	Silent	SNP	G	G	C	rs3210148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32632714G>C	ENST00000399084.1	-	3	418	c.240C>G	c.(238-240)cgC>cgG	p.R80R	HLA-DQB1_ENST00000399079.3_Silent_p.R80R|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Silent_p.R80R|HLA-DQB1_ENST00000374943.4_Silent_p.R80R|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	80	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GCGTCACCGCGCGGTACACCC	0.637									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	4215	0.841653	0.7496	0.8674	5008	,	,		5285	0.9395		0.7942	False		,,,				2504	0.8957				p.R80R	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C240G						PASS	.	C		2911,1327		1276,359,484	38.0	38.0	38.0		240	3.1	0.0	6	dbSNP_105	38	5890,2528		2647,596,966	no	coding-synonymous	HLA-DQB1	NM_002123.4		3923,955,1450	CC,CG,GG		30.0309,31.3119,30.4599		80/262	32632714	8801,3855	2119	4209	6328	SO:0001819	synonymous_variant	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CACCGCGCGGTAC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.240C>G	6.37:g.32632714G>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	33	33	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			G|0.427;C|0.573	0.573	strong		0.637	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
OR1N1	138883	hgsc.bcm.edu	37	9	125289521	125289521	+	Missense_Mutation	SNP	G	G	A	rs374849660|rs10818708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:125289521G>A	ENST00000304880.2	-	1	51	c.52C>T	c.(52-54)Cct>Tct	p.P18S		NM_012363.1	NP_036495.1	Q8NGS0	OR1N1_HUMAN	olfactory receptor, family 1, subfamily N, member 1	18			P -> S (in dbSNP:rs10818708).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|large_intestine(2)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15						TGCTCTGGAGGCGCTGATATT	0.478													A|||	3548	0.708466	0.8222	0.5908	5008	,	,		20268	0.87		0.4781	False		,,,				2504	0.7086				p.P18S		Atlas-SNP	.											.	OR1N1	38	.	0			c.C52T						PASS	.	A	SER/PRO	3438,968	362.9+/-316.3	1339,760,104	48.0	51.0	50.0		52	-1.9	0.0	9	dbSNP_120	50	3949,4651	599.6+/-394.1	913,2123,1264	yes	missense	OR1N1	NM_012363.1	74	2252,2883,1368	AA,AG,GG		45.9186,21.97,43.2031	benign	18/312	125289521	7387,5619	2203	4300	6503	SO:0001583	missense	138883	exon1			CTGGAGGCGCTGA	U86216	CCDS6844.1	9q34.11	2012-08-09			ENSG00000171505	ENSG00000171505		"""GPCR / Class A : Olfactory receptors"""	8221	protein-coding gene	gene with protein product				OR1N3		9500546	Standard	NM_012363		Approved	OR1-26	uc004bmn.1	Q8NGS0	OTTHUMG00000020608	ENST00000304880.2:c.52C>T	9.37:g.125289521G>A	ENSP00000306974:p.Pro18Ser	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_012363	A3KFM1|O43870|Q6IF16|Q96R93	Missense_Mutation	SNP	ENST00000304880.2	37	CCDS6844.1	1457	0.6671245421245421	390	0.7926829268292683	204	0.56353591160221	514	0.8986013986013986	349	0.4604221635883905	A	7.273	0.607534	0.14002	0.7803	0.459186	ENSG00000171505	ENST00000304880	T	0.03951	3.75	3.89	-1.86	0.07760	.	1.794630	0.03879	N	0.276772	T	0.00012	0.0000	N	0.02391	-0.57	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.18555	-1.0333	9	0.39692	T	0.17	.	0.5119	0.00597	0.3794:0.1262:0.2473:0.2471	rs10818708;rs17278112;rs60628604;rs10818708	18	Q8NGS0	OR1N1_HUMAN	S	18	ENSP00000306974:P18S	ENSP00000306974:P18S	P	-	1	0	OR1N1	124329342	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-4.505000	0.00223	-0.454000	0.07066	-0.407000	0.06327	CCT	.	.	alt		0.478	OR1N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053938.1		
GUCY1B3	2983	hgsc.bcm.edu	37	4	156721198	156721198	+	Silent	SNP	C	C	T	rs2229202	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:156721198C>T	ENST00000264424.8	+	9	1229	c.1147C>T	c.(1147-1149)Ctg>Ttg	p.L383L	GUCY1B3_ENST00000502959.1_Silent_p.L405L|GUCY1B3_ENST00000503520.1_Silent_p.L383L|GUCY1B3_ENST00000507146.1_Silent_p.L315L|GUCY1B3_ENST00000513437.1_Silent_p.L315L|GUCY1B3_ENST00000505154.1_Silent_p.L315L|GUCY1B3_ENST00000505764.1_Silent_p.L363L	NM_000857.2	NP_000848.1	Q02153	GCYB1_HUMAN	guanylate cyclase 1, soluble, beta 3	383					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)	cytoplasm (GO:0005737)|guanylate cyclase complex, soluble (GO:0008074)|intracellular membrane-bounded organelle (GO:0043231)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.L383L(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.148)		GTTAAGAGCCCTGGAAGATGA	0.398													C|||	801	0.159944	0.2156	0.111	5008	,	,		19760	0.123		0.1531	False		,,,				2504	0.1646				p.L383L		Atlas-SNP	.											GUCY1B3,NS,carcinoma,0,1	GUCY1B3	65	1	1	Substitution - coding silent(1)	prostate(1)	c.C1147T						PASS	.	C		722,3066		78,566,1250	90.0	89.0	90.0		1147	1.0	0.9	4	dbSNP_98	90	1241,6983		96,1049,2967	no	coding-synonymous	GUCY1B3	NM_000857.2		174,1615,4217	TT,TC,CC		15.09,19.0602,16.342		383/620	156721198	1963,10049	1894	4112	6006	SO:0001819	synonymous_variant	2983	exon9			AGAGCCCTGGAAG	AF020340	CCDS47154.1, CCDS75203.1	4q31.3-q33	2008-03-18			ENSG00000061918	ENSG00000061918	4.6.1.2		4687	protein-coding gene	gene with protein product		139397		GUC1B3		1352257	Standard	XM_005262959		Approved	GC-SB3, GC-S-beta-1	uc003ipc.3	Q02153	OTTHUMG00000161698	ENST00000264424.8:c.1147C>T	4.37:g.156721198C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	66	66	1	NM_000857	B7Z426|Q86WY5	Silent	SNP	ENST00000264424.8	37	CCDS47154.1																																																																																			C|0.851;T|0.149	0.149	strong		0.398	GUCY1B3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365770.2		
FREM2	341640	hgsc.bcm.edu	37	13	39261784	39261784	+	Silent	SNP	C	C	A	rs8002488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39261784C>A	ENST00000280481.7	+	1	519	c.303C>A	c.(301-303)ccC>ccA	p.P101P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	101					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)		AGGTGCAGCCCGGGGACCGCT	0.677													C|||	289	0.0577077	0.2073	0.0216	5008	,	,		14748	0.0		0.0	False		,,,				2504	0.0				p.P101P		Atlas-SNP	.											.	FREM2	385	.	0			c.C303A						PASS	.	C		759,3645		77,605,1520	16.0	17.0	17.0		303	-5.8	0.9	13	dbSNP_116	17	11,8585		0,11,4287	no	coding-synonymous	FREM2	NM_207361.4		77,616,5807	AA,AC,CC		0.128,17.2343,5.9231		101/3170	39261784	770,12230	2202	4298	6500	SO:0001819	synonymous_variant	341640	exon1			GCAGCCCGGGGAC	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.303C>A	13.37:g.39261784C>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	66	38	0.575758	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.944;A|0.056	0.056	strong		0.677	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
SYTL1	84958	hgsc.bcm.edu	37	1	27680292	27680292	+	Silent	SNP	A	A	G	rs8533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:27680292A>G	ENST00000543823.1	+	14	2100	c.1638A>G	c.(1636-1638)gaA>gaG	p.E546E	SYTL1_ENST00000490170.1_3'UTR|SYTL1_ENST00000318074.5_Silent_p.E534E			Q8IYJ3	SYTL1_HUMAN	synaptotagmin-like 1	546					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|melanosome (GO:0042470)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)			NS(1)|large_intestine(4)|lung(5)|ovary(1)|urinary_tract(1)	12		Colorectal(325;0.000147)|all_lung(284;0.000366)|Lung NSC(340;0.000548)|Renal(390;0.00211)|Breast(348;0.0115)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0908)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.5e-28)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.0013)|KIRC - Kidney renal clear cell carcinoma(1967;0.00158)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AGCCGTGCGAATGGGTGGATG	0.637													G|||	2736	0.546326	0.6891	0.4813	5008	,	,		16013	0.2431		0.7247	False		,,,				2504	0.5286				p.E546E		Atlas-SNP	.											.	SYTL1	57	.	0			c.A1638G						PASS	.	G	,	3038,1368	453.6+/-350.4	1032,974,197	63.0	56.0	59.0		1638,1602	1.8	1.0	1	dbSNP_52	59	6294,2306	387.2+/-342.1	2311,1672,317	no	coding-synonymous,coding-synonymous	SYTL1	NM_001193308.1,NM_032872.2	,	3343,2646,514	GG,GA,AA		26.814,31.0486,28.2485	,	546/563,534/551	27680292	9332,3674	2203	4300	6503	SO:0001819	synonymous_variant	84958	exon15			GTGCGAATGGGTG	AK027902	CCDS298.1, CCDS53286.1	1p35.3	2008-02-05			ENSG00000142765	ENSG00000142765			15584	protein-coding gene	gene with protein product		608042				12137562	Standard	NM_032872		Approved	SLP1, JFC1, FLJ14996, exophilin-7	uc001bnw.2	Q8IYJ3	OTTHUMG00000005770	ENST00000543823.1:c.1638A>G	1.37:g.27680292A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	223	223	1	NM_001193308	Q5SSC9|Q96BB6|Q96GU6|Q96S89|Q96SI0	Silent	SNP	ENST00000543823.1	37	CCDS53286.1																																																																																			A|0.367;G|0.633	0.633	strong		0.637	SYTL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032872	
TMEM132E	124842	hgsc.bcm.edu	37	17	32953258	32953258	+	Silent	SNP	G	G	A	rs4795954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:32953258G>A	ENST00000321639.5	+	2	508	c.180G>A	c.(178-180)gaG>gaA	p.E60E		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	60						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TCCTGCGGGAGGCGCGGCCCC	0.731													G|||	893	0.178315	0.0318	0.1657	5008	,	,		13279	0.3403		0.1382	False		,,,				2504	0.2597				p.E60E		Atlas-SNP	.											.	TMEM132E	122	.	0			c.G180A						PASS	.	G		187,4153		6,175,1989	10.0	10.0	10.0		180	1.7	0.8	17	dbSNP_111	10	1127,7357		85,957,3200	no	coding-synonymous	TMEM132E	NM_207313.1		91,1132,5189	AA,AG,GG		13.2838,4.3088,10.2464		60/985	32953258	1314,11510	2170	4242	6412	SO:0001819	synonymous_variant	124842	exon2			GCGGGAGGCGCGG	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.180G>A	17.37:g.32953258G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	71	35	0.492958	NM_207313	Q8WUF4|Q8WVA5	Silent	SNP	ENST00000321639.5	37	CCDS11283.1																																																																																			G|0.870;A|0.130	0.130	strong		0.731	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
CLCN3	1182	hgsc.bcm.edu	37	4	170634390	170634390	+	Silent	SNP	C	C	T	rs1058868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:170634390C>T	ENST00000513761.1	+	12	2869	c.2310C>T	c.(2308-2310)atC>atT	p.I770I	CLCN3_ENST00000504131.2_Silent_p.I753I|CLCN3_ENST00000347613.4_Silent_p.I770I|CLCN3_ENST00000360642.3_Silent_p.I743I	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	770	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)	p.I770I(1)		breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		CAATGGAGATCGTGGTGGATA	0.483													T|||	589	0.117612	0.1021	0.098	5008	,	,		19300	0.1766		0.1213	False		,,,				2504	0.0879				p.I770I		Atlas-SNP	.											CLCN3,NS,carcinoma,+1,2	CLCN3	85	2	1	Substitution - coding silent(1)	stomach(1)	c.C2310T						scavenged	.	T	,	391,4015	790.6+/-415.0	12,367,1824	111.0	99.0	103.0		2310,2310	-6.9	0.8	4	dbSNP_123	103	1095,7505	769.0+/-407.6	78,939,3283	no	coding-synonymous,coding-synonymous	CLCN3	NM_001829.3,NM_173872.3	,	90,1306,5107	TT,TC,CC		12.7326,8.8743,11.4255	,	770/819,770/867	170634390	1486,11520	2203	4300	6503	SO:0001819	synonymous_variant	1182	exon12			GGAGATCGTGGTG	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"""Ion channels / Chloride channels : Voltage-sensitive"""	2021	protein-coding gene	gene with protein product		600580	"""chloride channel 3"""				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.2310C>T	4.37:g.170634390C>T		Somatic	153	1	0.00653595		WXS	Illumina HiSeq	Phase_I	154	82	0.532468	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Silent	SNP	ENST00000513761.1	37	CCDS34101.1																																																																																			C|0.879;T|0.121	0.121	strong		0.483	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2		
PDZRN3	23024	hgsc.bcm.edu	37	3	73433369	73433369	+	Missense_Mutation	SNP	G	G	A	rs3205537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:73433369G>A	ENST00000263666.4	-	10	2462	c.2348C>T	c.(2347-2349)gCg>gTg	p.A783V	PDZRN3_ENST00000466780.1_Missense_Mutation_p.A440V|PDZRN3_ENST00000479530.1_Missense_Mutation_p.A500V|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Missense_Mutation_p.A440V|PDZRN3_ENST00000535920.1_Missense_Mutation_p.A505V	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	783			A -> V (in dbSNP:rs3205537). {ECO:0000269|PubMed:17974005}.		neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		GATGCCCTCCGCCGCTCTCCT	0.647													G|||	1364	0.272364	0.0635	0.3415	5008	,	,		16006	0.4435		0.3549	False		,,,				2504	0.2444				p.A783V		Atlas-SNP	.											.	PDZRN3	196	.	0			c.C2348T						PASS	.	G	VAL/ALA	468,3938	217.8+/-236.0	30,408,1765	35.0	38.0	37.0		2348	4.1	0.2	3	dbSNP_105	37	2851,5749	440.9+/-359.6	471,1909,1920	yes	missense	PDZRN3	NM_015009.1	64	501,2317,3685	AA,AG,GG		33.1512,10.6219,25.519	possibly-damaging	783/1067	73433369	3319,9687	2203	4300	6503	SO:0001583	missense	23024	exon10			CCCTCCGCCGCTC	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2348C>T	3.37:g.73433369G>A	ENSP00000263666:p.Ala783Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	709	0.32463369963369965	41	0.08333333333333333	119	0.3287292817679558	267	0.46678321678321677	282	0.3720316622691293	G	1.520	-0.547126	0.04024	0.106219	0.331512	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530;ENST00000492909	T;T;T;T;T;T	0.10099	2.91;3.61;3.5;3.5;3.62;3.58	4.93	4.05	0.47172	.	1.618580	0.02891	N	0.134123	T	0.00012	0.0000	L	0.57536	1.79	0.58432	P	5.000000000032756E-6	B;B;B;B	0.27286	0.005;0.011;0.003;0.174	B;B;B;B	0.14578	0.005;0.004;0.003;0.011	T	0.48536	-0.9027	9	0.23891	T	0.37	.	13.1789	0.59642	0.0793:0.0:0.9207:0.0	rs3205537;rs3732435;rs52810062;rs57871998;rs3205537	505;500;500;783	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	V	783;505;440;440;500;481	ENSP00000263666:A783V;ENSP00000442026:A505V;ENSP00000418168:A440V;ENSP00000418484:A440V;ENSP00000418624:A500V;ENSP00000419250:A481V	ENSP00000263666:A783V	A	-	2	0	PDZRN3	73516059	0.713000	0.27926	0.216000	0.23742	0.081000	0.17604	2.975000	0.49281	1.030000	0.39839	0.655000	0.94253	GCG	G|0.729;A|0.271	0.271	strong		0.647	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139397707G>A	ENST00000277541.6	-	27	5169	c.5094C>T	c.(5092-5094)gaC>gaT	p.D1698D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1698					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1699D(11)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATGCGGCCACGTCGGTGGCAC	0.632			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2772	0.553514	0.5552	0.5115	5008	,	,		17626	0.9018		0.4046	False		,,,				2504	0.3753				p.D1698D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	11	Substitution - coding silent(11)	haematopoietic_and_lymphoid_tissue(11)	c.C5094T						PASS	.	G		2208,2062		587,1034,514	57.0	67.0	64.0		5094	-4.9	0.8	9	dbSNP_52	64	3010,5508		545,1920,1794	no	coding-synonymous	NOTCH1	NM_017617.3		1132,2954,2308	AA,AG,GG		35.3369,48.2904,40.8039		1698/2556	139397707	5218,7570	2135	4259	6394	SO:0001819	synonymous_variant	4851	exon27			GGCCACGTCGGTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5094C>T	9.37:g.139397707G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	84	30	0.357143	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.466;A|0.534	0.534	strong		0.632	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
SLC39A12	221074	hgsc.bcm.edu	37	10	18254606	18254606	+	Silent	SNP	C	C	A	rs691513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:18254606C>A	ENST00000377369.2	+	4	1011	c.738C>A	c.(736-738)acC>acA	p.T246T	SLC39A12_ENST00000377371.3_Silent_p.T246T|SLC39A12_ENST00000377374.4_Silent_p.T246T|SLC39A12_ENST00000539911.1_Silent_p.T112T	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	246					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						GTACGAATACCCTCCGCCTAT	0.418													C|||	1660	0.33147	0.2443	0.4006	5008	,	,		18941	0.3889		0.3608	False		,,,				2504	0.3108				p.T246T		Atlas-SNP	.											.	SLC39A12	181	.	0			c.C738A						PASS	.	C	,	1136,3270	404.2+/-333.0	147,842,1214	48.0	46.0	47.0		738,738	0.9	0.5	10	dbSNP_83	47	2935,5665	453.3+/-363.2	502,1931,1867	no	coding-synonymous,coding-synonymous	SLC39A12	NM_001145195.1,NM_152725.3	,	649,2773,3081	AA,AC,CC		34.1279,25.783,31.3009	,	246/692,246/655	18254606	4071,8935	2203	4300	6503	SO:0001819	synonymous_variant	221074	exon4			GAATACCCTCCGC		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.738C>A	10.37:g.18254606C>A		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	69	67	0.971014	NM_152725	B7ZL35|C9JJL4|Q49AN8|Q4G0L3|Q5VWV8|Q5VWV9|Q6NZY5|Q96NN4	Silent	SNP	ENST00000377369.2	37	CCDS44362.1																																																																																			C|0.672;A|0.328	0.328	strong		0.418	SLC39A12-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_152725	
ZDHHC11	79844	hgsc.bcm.edu	37	5	843723	843723	+	Missense_Mutation	SNP	C	C	A	rs3863148		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:843723C>A	ENST00000283441.8	-	4	1003	c.620G>T	c.(619-621)aGg>aTg	p.R207M	ZDHHC11_ENST00000511539.1_5'UTR|ZDHHC11_ENST00000503758.2_5'Flank|ZDHHC11_ENST00000424784.2_Missense_Mutation_p.R207M	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	207						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)			ACCTTCATACCTGGGGTCCGT	0.657																																					p.R207M		Atlas-SNP	.											ZDHHC11_ENST00000424784,rectum,carcinoma,0,2	ZDHHC11	97	2	0			c.G620T						PASS	.						56.0	47.0	50.0					5																	843723		2201	4290	6491	SO:0001583	missense	79844	exon4			TCATACCTGGGGT	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.620G>T	5.37:g.843723C>A	ENSP00000283441:p.Arg207Met	Somatic	372	0	0		WXS	Illumina HiSeq	Phase_I	502	132	0.262948	NM_024786	Q6UWR9	Missense_Mutation	SNP	ENST00000283441.8	37	CCDS3857.1	601	0.2751831501831502	211	0.42886178861788615	83	0.2292817679558011	121	0.21153846153846154	186	0.24538258575197888	t	11.12	1.543781	0.27563	.	.	ENSG00000188818	ENST00000424784;ENST00000283441	T;T	0.25085	1.82;1.82	3.98	-2.98	0.05513	.	16.107500	0.01230	U	0.008323	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B	0.06786	0.001	B	0.14023	0.01	T	0.44143	-0.9347	9	0.36615	T	0.2	0.0249	3.3426	0.07124	0.353:0.2826:0.0:0.3644	rs3863148;rs4993147	207	Q9H8X9	ZDH11_HUMAN	M	207	ENSP00000397719:R207M;ENSP00000283441:R207M	ENSP00000283441:R207M	R	-	2	0	ZDHHC11	896723	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.765000	0.04730	-1.644000	0.01517	-0.858000	0.03015	AGG	C|0.500;A|0.500	0.500	weak		0.657	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
OR51F1	256892	hgsc.bcm.edu	37	11	4790575	4790575	+	Silent	SNP	A	A	G	rs12788102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4790575A>G	ENST00000380383.1	-	1	593	c.594T>C	c.(592-594)tgT>tgC	p.C198C	OR51F1_ENST00000343430.3_Silent_p.C191C|MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	198						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)		GAATGTCTGAACATGCTAATT	0.383													A|||	243	0.0485224	0.0151	0.0965	5008	,	,		24195	0.0		0.1412	False		,,,				2504	0.0143				p.C191C		Atlas-SNP	.											.	OR51F1	60	.	0			c.T573C						PASS	.	A		214,4188	129.8+/-166.5	2,210,1989	146.0	141.0	143.0		573	2.8	1.0	11	dbSNP_121	143	1159,7437	238.5+/-269.9	94,971,3233	no	coding-synonymous	OR51F1	NM_001004752.1		96,1181,5222	GG,GA,AA		13.483,4.8614,10.5632		191/313	4790575	1373,11625	2201	4298	6499	SO:0001819	synonymous_variant	256892	exon1			GTCTGAACATGCT	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.594T>C	11.37:g.4790575A>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	204	118	0.578431	NM_001004752		Silent	SNP	ENST00000380383.1	37																																																																																				A|0.911;G|0.089	0.089	strong		0.383	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
COL6A5	256076	hgsc.bcm.edu	37	3	130124989	130124989	+	Silent	SNP	C	C	T	rs4688761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130124989C>T	ENST00000432398.2	+	16	4889	c.4395C>T	c.(4393-4395)gaC>gaT	p.D1465D	COL6A5_ENST00000265379.6_Silent_p.D1465D	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1465	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						GTCATGGAGACGATGGGATTG	0.403													C|||	2048	0.408946	0.2867	0.4625	5008	,	,		18935	0.1796		0.7256	False		,,,				2504	0.4468				p.D1465D		Atlas-SNP	.											.	COL6A5	205	.	0			c.C4395T						PASS	.	C		506,878		95,316,281	156.0	125.0	134.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4395	-11.7	0.0	3	dbSNP_111	134	2259,923		807,645,139	no	coding-synonymous	COL6A5	NM_153264.5		902,961,420	TT,TC,CC		29.0069,36.5607,39.4437		1465/2527	130124989	2765,1801	692	1591	2283	SO:0001819	synonymous_variant	256076	exon16			TGGAGACGATGGG	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.4395C>T	3.37:g.130124989C>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	161	158	0.981366	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				C|0.577;T|0.423	0.423	strong		0.403	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
CPB1	1360	hgsc.bcm.edu	37	3	148575250	148575250	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148575250C>T	ENST00000491148.1	+	11	1322	c.988C>T	c.(988-990)Ctg>Ttg	p.L330L	CPB1_ENST00000282957.4_Silent_p.L330L|CPB1_ENST00000498639.1_3'UTR|RP11-680B3.2_ENST00000488190.1_RNA			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	330						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)			GCAGAATGCCCTGGCTAAAGC	0.423																																					p.L330L		Atlas-SNP	.											.	CPB1	74	.	0			c.C988T						PASS	.						111.0	102.0	105.0					3																	148575250		2203	4300	6503	SO:0001819	synonymous_variant	1360	exon10			AATGCCCTGGCTA	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.988C>T	3.37:g.148575250C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	126	56	0.444444	NM_001871	O60834|Q53XJ0|Q96BQ8	Silent	SNP	ENST00000491148.1	37	CCDS33874.1																																																																																			.	.	none		0.423	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871	
FAAH2	158584	hgsc.bcm.edu	37	X	57313357	57313357	+	Silent	SNP	T	T	C	rs2516023|rs111920515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:57313357T>C	ENST00000374900.4	+	1	219	c.99T>C	c.(97-99)ggT>ggC	p.G33G		NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	33						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						TCTTAGGGGGTCCAAAGTTTG	0.547										HNSCC(52;0.14)			.|||	2000	0.529801	0.73	0.3516	3775	,	,		12395	0.2927		0.2157	False		,,,				2504	0.2853				p.G33G		Atlas-SNP	.											.	FAAH2	66	.	0			c.T99C						PASS	.	C		3381,454		1271,331,508,30,63	38.0	35.0	36.0		99	-1.8	0.0	X	dbSNP_100	36	1792,4936		157,959,519,1312,1353	no	coding-synonymous	FAAH2	NM_174912.3		1428,1290,1027,1342,1416	CC,CT,C,TT,T		26.635,11.8383,48.9728		33/533	57313357	5173,5390	2203	4300	6503	SO:0001819	synonymous_variant	158584	exon1			AGGGGGTCCAAAG	AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"""amidase domain containing"""	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.99T>C	X.37:g.57313357T>C		Somatic	113	1	0.00884956		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_174912	Q86VT2|Q96N98	Silent	SNP	ENST00000374900.4	37	CCDS14375.1																																																																																			0|0.003;C|0.507	0.507	strong		0.547	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912	
RBL2	5934	hgsc.bcm.edu	37	16	53503934	53503934	+	Silent	SNP	G	G	A	rs1131220	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:53503934G>A	ENST00000262133.6	+	15	2219	c.2082G>A	c.(2080-2082)acG>acA	p.T694T	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Intron	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	694	Pocket; binds E1A.|Spacer.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						ATGGAGGGACGCCTGGGCGCA	0.547													g|||	2531	0.505391	0.8517	0.4049	5008	,	,		17469	0.1786		0.4662	False		,,,				2504	0.4857				p.T694T		Atlas-SNP	.											.	RBL2	115	.	0			c.G2082A						PASS	.	A		3382,1014	728.0+/-409.9	1314,754,130	76.0	75.0	75.0		2082	1.0	0.4	16	dbSNP_86	75	4177,4423	565.4+/-388.5	1028,2121,1151	no	coding-synonymous	RBL2	NM_005611.3		2342,2875,1281	AA,AG,GG		48.5698,23.0664,41.8359		694/1140	53503934	7559,5437	2198	4300	6498	SO:0001819	synonymous_variant	5934	exon15			AGGGACGCCTGGG	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2082G>A	16.37:g.53503934G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	152	149	0.980263	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	37	CCDS10748.1																																																																																			G|0.461;A|0.539	0.539	strong		0.547	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
YAE1D1	57002	hgsc.bcm.edu	37	7	39606107	39606107	+	Silent	SNP	G	G	A	rs1051162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:39606107G>A	ENST00000223273.2	+	1	133	c.90G>A	c.(88-90)gcG>gcA	p.A30A	YAE1D1_ENST00000432096.2_Silent_p.A30A|AC011290.4_ENST00000439751.2_RNA|YAE1D1_ENST00000448268.1_Silent_p.A30A	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	30								p.A30A(1)									CGCTCCTGGCGCAGCGGGAAT	0.587													G|||	778	0.155351	0.298	0.072	5008	,	,		17313	0.1131		0.0984	False		,,,				2504	0.1237				p.A30A		Atlas-SNP	.											C7orf36,NS,carcinoma,0,1	YAE1D1	2	1	1	Substitution - coding silent(1)	stomach(1)	c.G90A						scavenged	.	G		1033,3373	380.6+/-323.8	125,783,1295	87.0	78.0	81.0		90	-0.0	0.7	7	dbSNP_86	81	806,7794	188.4+/-235.4	30,746,3524	no	coding-synonymous	C7orf36	NM_020192.3		155,1529,4819	AA,AG,GG		9.3721,23.4453,14.1396		30/227	39606107	1839,11167	2203	4300	6503	SO:0001819	synonymous_variant	57002	exon1			CCTGGCGCAGCGG	AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 36"""	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.90G>A	7.37:g.39606107G>A		Somatic	50	1	0.02		WXS	Illumina HiSeq	Phase_I	66	28	0.424242	NM_020192	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Silent	SNP	ENST00000223273.2	37	CCDS5459.1																																																																																			G|0.842;A|0.158	0.158	strong		0.587	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250586.1	NM_020192	
PLA2G5	5322	hgsc.bcm.edu	37	1	20417066	20417066	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:20417066G>A	ENST00000375108.3	+	5	566	c.298G>A	c.(298-300)Ggg>Agg	p.G100R	PLA2G5_ENST00000486277.1_3'UTR	NM_000929.2	NP_000920.1	P39877	PA2G5_HUMAN	phospholipase A2, group V	100					arachidonic acid secretion (GO:0050482)|glycerophospholipid biosynthetic process (GO:0046474)|leukotriene biosynthetic process (GO:0019370)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|heparin binding (GO:0008201)			NS(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		TGCAGAGCCCGGGCCCTTCTG	0.557																																					p.G100R		Atlas-SNP	.											.	PLA2G5	21	.	0			c.G298A						PASS	.						145.0	127.0	133.0					1																	20417066		2203	4300	6503	SO:0001583	missense	5322	exon5			GAGCCCGGGCCCT	U03090	CCDS202.1	1p36-p34	2008-09-19			ENSG00000127472	ENSG00000127472	3.1.1.4		9038	protein-coding gene	gene with protein product		601192				8838795, 8300559	Standard	NM_000929		Approved		uc001bcy.3	P39877	OTTHUMG00000002698	ENST00000375108.3:c.298G>A	1.37:g.20417066G>A	ENSP00000364249:p.Gly100Arg	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	174	65	0.373563	NM_000929	Q8N435	Missense_Mutation	SNP	ENST00000375108.3	37	CCDS202.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.498320	0.64186	.	.	ENSG00000127472	ENST00000375108	T	0.26223	1.75	5.77	5.77	0.91146	Phospholipase A2 (3);	0.847373	0.10252	N	0.697050	T	0.46639	0.1403	L	0.48642	1.525	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.71656	0.974;0.939	T	0.39251	-0.9623	10	0.51188	T	0.08	-16.3128	15.4945	0.75637	0.0:0.0:1.0:0.0	.	100;73	P39877;B3KUQ4	PA2G5_HUMAN;.	R	100	ENSP00000364249:G100R	ENSP00000364249:G100R	G	+	1	0	PLA2G5	20289653	0.484000	0.25964	0.010000	0.14722	0.004000	0.04260	3.297000	0.51810	2.720000	0.93068	0.557000	0.71058	GGG	.	.	none		0.557	PLA2G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007668.1	NM_000929	
NAT6	24142	hgsc.bcm.edu	37	3	50334568	50334568	+	Silent	SNP	G	G	A	rs199554290		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50334568G>A	ENST00000443842.1	-	2	1134	c.327C>T	c.(325-327)agC>agT	p.S109S	NAT6_ENST00000354862.4_Silent_p.S131S|HYAL3_ENST00000415204.1_Intron|NAT6_ENST00000443094.2_Silent_p.S109S|NAT6_ENST00000417393.1_Silent_p.S109S|HYAL3_ENST00000336307.1_Intron|HYAL3_ENST00000359051.3_Intron|HYAL3_ENST00000450982.1_Intron|HYAL3_ENST00000513170.1_Intron			Q93015	NAT6_HUMAN	N-acetyltransferase 6 (GCN5-related)	109	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					cytoplasm (GO:0005737)	N-acetyltransferase activity (GO:0008080)			endometrium(3)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TGGGGTGGGGGCTTAGCAGCA	0.647																																					p.S131S		Atlas-SNP	.											.	NAT6	14	.	0			c.C393T						PASS	.	G	,,,,,,,	3,4157		0,3,2077	20.0	25.0	23.0		327,327,,,,,,393	1.6	0.9	3		23	20,8362		0,20,4171	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	HYAL3,NAT6	NM_001200016.1,NM_001200018.1,NM_001200029.1,NM_001200030.1,NM_001200031.1,NM_001200032.1,NM_003549.3,NM_012191.3	,,,,,,,	0,23,6248	AA,AG,GG		0.2386,0.0721,0.1834	,,,,,,,	109/287,109/287,,,,,,131/309	50334568	23,12519	2080	4191	6271	SO:0001819	synonymous_variant	24142	exon2			GTGGGGGCTTAGC	AF040705	CCDS43095.1, CCDS56258.1	3p21.3	2011-11-16	2008-09-24		ENSG00000243477	ENSG00000243477	2.3.1.-		30252	protein-coding gene	gene with protein product		607073	"""N-acetyltransferase 6"""			11929860, 11085536	Standard	NM_012191		Approved	FUS2		Q93015	OTTHUMG00000156939	ENST00000443842.1:c.327C>T	3.37:g.50334568G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	113	66	0.584071	NM_012191	Q93014	Silent	SNP	ENST00000443842.1	37	CCDS56258.1																																																																																			G|0.997;A|0.003	0.003	weak		0.647	NAT6-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346681.1	NM_012191	
APBA3	9546	hgsc.bcm.edu	37	19	3753874	3753874	+	Silent	SNP	G	G	A	rs34868972	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:3753874G>A	ENST00000316757.3	-	6	1100	c.900C>T	c.(898-900)atC>atT	p.I300I	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	300	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)		GCACGCAGCCGATGTCGGCTG	0.697													G|||	460	0.091853	0.0098	0.1369	5008	,	,		12674	0.0089		0.1839	False		,,,				2504	0.1616				p.I300I		Atlas-SNP	.											.	APBA3	28	.	0			c.C900T						PASS	.	G		135,4159		4,127,2016	10.0	12.0	11.0		900	1.9	1.0	19	dbSNP_126	11	1381,7037		89,1203,2917	no	coding-synonymous	APBA3	NM_004886.3		93,1330,4933	AA,AG,GG		16.4053,3.1439,11.9257		300/576	3753874	1516,11196	2147	4209	6356	SO:0001819	synonymous_variant	9546	exon6			GCAGCCGATGTCG	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.900C>T	19.37:g.3753874G>A		Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	39	18	0.461538	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.908;A|0.092	0.092	strong		0.697	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
TEK	7010	hgsc.bcm.edu	37	9	27197368	27197368	+	Silent	SNP	T	T	C	rs35357088	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:27197368T>C	ENST00000380036.4	+	12	2122	c.1680T>C	c.(1678-1680)aaT>aaC	p.N560N	TEK_ENST00000406359.4_Silent_p.N517N|TEK_ENST00000519097.1_Silent_p.N413N|RNA5SP280_ENST00000411230.1_RNA	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	560	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)	CCACTCTAAATTTGACCTGGC	0.383													T|||	250	0.0499201	0.0008	0.1945	5008	,	,		20057	0.001		0.0895	False		,,,				2504	0.0235				p.N560N		Atlas-SNP	.											.	TEK	250	.	0			c.T1680C						PASS	.	T		62,4344	58.1+/-94.6	0,62,2141	76.0	78.0	78.0		1680	3.2	1.0	9	dbSNP_126	78	518,8082	145.4+/-201.1	21,476,3803	no	coding-synonymous	TEK	NM_000459.3		21,538,5944	CC,CT,TT		6.0233,1.4072,4.4595		560/1125	27197368	580,12426	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon12			TCTAAATTTGACC	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.1680T>C	9.37:g.27197368T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			T|0.951;C|0.049	0.049	strong		0.383	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
TFAP2D	83741	hgsc.bcm.edu	37	6	50682935	50682935	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:50682935C>G	ENST00000008391.3	+	2	374	c.146C>G	c.(145-147)tCc>tGc	p.S49C		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					TTAACTTACTCCACCACCGGC	0.547																																					p.S49C		Atlas-SNP	.											.	TFAP2D	144	.	0			c.C146G						PASS	.						245.0	195.0	212.0					6																	50682935		2203	4300	6503	SO:0001583	missense	83741	exon2			CTTACTCCACCAC	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"""	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.146C>G	6.37:g.50682935C>G	ENSP00000008391:p.Ser49Cys	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	206	10	0.0485437	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.404207	0.42613	.	.	ENSG00000008197	ENST00000008391	D	0.97505	-4.41	5.07	5.07	0.68467	.	0.127543	0.53938	D	0.000045	D	0.91112	0.7202	N	0.08118	0	0.54753	D	0.999988	B	0.28713	0.22	B	0.33846	0.171	D	0.90227	0.4276	10	0.87932	D	0	0.3288	18.8076	0.92045	0.0:1.0:0.0:0.0	.	49	Q7Z6R9	AP2D_HUMAN	C	49	ENSP00000008391:S49C	ENSP00000008391:S49C	S	+	2	0	TFAP2D	50790894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.763000	0.68818	2.498000	0.84270	0.655000	0.94253	TCC	.	.	none		0.547	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238	
RNH1	6050	hgsc.bcm.edu	37	11	494942	494942	+	Silent	SNP	G	G	C	rs7983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:494942G>C	ENST00000534797.1	-	8	2646	c.1239C>G	c.(1237-1239)gcC>gcG	p.A413A	RNH1_ENST00000354420.2_Silent_p.A413A|RNH1_ENST00000438658.2_Silent_p.A413A|RNH1_ENST00000397615.2_Silent_p.A413A|RNH1_ENST00000533410.1_Silent_p.A413A|RNH1_ENST00000397614.1_Silent_p.A413A|RNH1_ENST00000397604.3_Silent_p.A413A|RNH1_ENST00000356187.5_Silent_p.A413A			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0					mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCAGGATGCCGGCGTCCCCCA	0.692													C|||	1667	0.332867	0.5272	0.366	5008	,	,		15352	0.1865		0.3101	False		,,,				2504	0.2209				p.A413A		Atlas-SNP	.											.	RNH1	24	.	0			c.C1239G						PASS	.	C	,,,,,,,	2181,2223		564,1053,585	26.0	28.0	27.0		1239,1239,1239,1239,1239,1239,1239,1239	-6.5	0.0	11	dbSNP_52	27	2704,5896		430,1844,2026	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNH1	NM_002939.3,NM_203383.1,NM_203384.1,NM_203385.1,NM_203386.1,NM_203387.1,NM_203388.1,NM_203389.1	,,,,,,,	994,2897,2611	CC,CG,GG		31.4419,49.5232,37.5654	,,,,,,,	413/462,413/462,413/462,413/462,413/462,413/462,413/462,413/462	494942	4885,8119	2202	4300	6502	SO:0001819	synonymous_variant	6050	exon9			GATGCCGGCGTCC		CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.1239C>G	11.37:g.494942G>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	192	77	0.401042	NM_203384	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Silent	SNP	ENST00000534797.1	37	CCDS7697.1																																																																																			G|0.627;C|0.373	0.373	strong		0.692	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389	
GABBR1	2550	hgsc.bcm.edu	37	6	29581041	29581041	+	Silent	SNP	A	A	G	rs29225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29581041A>G	ENST00000377034.4	-	12	1880	c.1545T>C	c.(1543-1545)tcT>tcC	p.S515S	GABBR1_ENST00000355973.3_Silent_p.S398S|GABBR1_ENST00000377012.4_Silent_p.S398S|GABBR1_ENST00000377016.4_Silent_p.S453S|GABBR1_ENST00000376977.3_Silent_p.S515S	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	515					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	G-protein coupled GABA receptor activity (GO:0004965)			endometrium(3)|kidney(1)|large_intestine(13)|liver(1)|lung(16)|ovary(5)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47					Baclofen(DB00181)|Progabide(DB00837)|Vigabatrin(DB01080)	CAAAGGACGAAGAGTTCATTG	0.502													G|||	529	0.105631	0.0946	0.0807	5008	,	,		18230	0.12		0.0974	False		,,,				2504	0.1319				p.S515S		Atlas-SNP	.											.	GABBR1	95	.	0			c.T1545C						PASS	.	G	,,	273,2747		10,253,1247	120.0	134.0	129.0		1545,1194,1359	3.9	1.0	6	dbSNP_76	129	561,4857		35,491,2183	no	coding-synonymous,coding-synonymous,coding-synonymous	GABBR1	NM_001470.2,NM_021903.2,NM_021904.2	,,	45,744,3430	GG,GA,AA		10.3544,9.0397,9.8839	,,	515/962,398/845,453/900	29581041	834,7604	1510	2709	4219	SO:0001819	synonymous_variant	2550	exon12			GGACGAAGAGTTC	Y11044	CCDS4663.1, CCDS4664.1, CCDS4665.1	6p21.3	2012-08-29			ENSG00000204681	ENSG00000204681		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4070	protein-coding gene	gene with protein product	"""GABA-B receptor"""	603540				9753614, 9798068	Standard	NM_001470		Approved	hGB1a, GPRC3A	uc003nmt.4	Q9UBS5	OTTHUMG00000031095	ENST00000377034.4:c.1545T>C	6.37:g.29581041A>G		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	109	35	0.321101	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1																																																																																			A|0.902;G|0.098	0.098	strong		0.502	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3		
PCDHB6	56130	hgsc.bcm.edu	37	5	140531746	140531746	+	Missense_Mutation	SNP	C	C	G	rs246703	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140531746C>G	ENST00000231136.1	+	1	1908	c.1908C>G	c.(1906-1908)caC>caG	p.H636Q	PCDHB6_ENST00000543635.1_Missense_Mutation_p.H500Q	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	636	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.		H -> Q (in dbSNP:rs246703). {ECO:0000269|PubMed:14702039}.		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGCCAAGCACAGGCTGGTGG	0.682													C|||	3155	0.629992	0.6717	0.6499	5008	,	,		15508	0.6627		0.5567	False		,,,				2504	0.6012				p.H636Q		Atlas-SNP	.											.	PCDHB6	161	.	0			c.C1908G						PASS	.	C	GLN/HIS	2644,1496		894,856,320	31.0	34.0	33.0		1908	-0.5	1.0	5	dbSNP_79	33	4689,3573		1417,1855,859	no	missense	PCDHB6	NM_018939.2	24	2311,2711,1179	GG,GC,CC		43.2462,36.1353,40.8724	benign	636/795	140531746	7333,5069	2070	4131	6201	SO:0001583	missense	56130	exon1			CAAGCACAGGCTG	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.1908C>G	5.37:g.140531746C>G	ENSP00000231136:p.His636Gln	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	1342	0.6144688644688645	326	0.6626016260162602	216	0.5966850828729282	378	0.6608391608391608	422	0.5567282321899736	C	0.008	-1.933915	0.00488	0.638647	0.567538	ENSG00000113211	ENST00000543635;ENST00000231136	T;T	0.52526	0.66;0.66	4.51	-0.534	0.11883	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.02247	-0.625	0.34547	P	0.289049	B	0.23735	0.09	B	0.26517	0.07	T	0.41431	-0.9509	8	0.40728	T	0.16	.	17.2158	0.86943	0.0:0.3713:0.6287:0.0	rs246703;rs17844441;rs59402700;rs246703	636	Q9Y5E3	PCDB6_HUMAN	Q	500;636	ENSP00000438466:H500Q;ENSP00000231136:H636Q	ENSP00000231136:H636Q	H	+	3	2	PCDHB6	140511930	0.000000	0.05858	0.989000	0.46669	0.222000	0.24845	-2.253000	0.01184	0.064000	0.16427	0.556000	0.70494	CAC	C|0.397;G|0.603	0.603	strong		0.682	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
DEK	7913	hgsc.bcm.edu	37	6	18264210	18264210	+	Silent	SNP	G	G	A	rs11544757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:18264210G>A	ENST00000397239.3	-	2	456	c.9C>T	c.(7-9)gcC>gcT	p.A3A	DEK_ENST00000244776.7_Silent_p.A3A	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	3					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			CAGGGGCCGAGGCGGACATGC	0.672			T	NUP214	AML								G|||	824	0.164537	0.031	0.1124	5008	,	,		12151	0.246		0.2087	False		,,,				2504	0.2526				p.A3A		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.C9T						PASS	.	G	,	297,4109	154.0+/-187.5	10,277,1916	25.0	27.0	26.0		9,9	-1.1	0.0	6	dbSNP_120	26	1789,6811	306.2+/-307.8	198,1393,2709	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	208,1670,4625	AA,AG,GG		20.8023,6.7408,16.0388	,	3/342,3/376	18264210	2086,10920	2203	4300	6503	SO:0001819	synonymous_variant	7913	exon2			GGCCGAGGCGGAC	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.9C>T	6.37:g.18264210G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	41	21	0.512195	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			G|0.838;C|0.000;A|0.162	0.162	strong		0.672	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
TBC1D2	55357	hgsc.bcm.edu	37	9	100991430	100991430	+	Splice_Site	SNP	C	C	A	rs1573025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100991430C>A	ENST00000375064.1	-	5	820	c.782G>T	c.(781-783)gGg>gTg	p.G261V	TBC1D2_ENST00000493589.2_5'Flank|TBC1D2_ENST00000342112.5_Splice_Site_p.G43V|TBC1D2_ENST00000375066.5_Splice_Site_p.G261V	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	261			G -> V (in dbSNP:rs1573025). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15164053, ECO:0000269|Ref.9}.		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)		TGGCTCTCTCCCTGCTCAAGA	0.498													C|||	821	0.163938	0.1384	0.2017	5008	,	,		20558	0.1597		0.1779	False		,,,				2504	0.1616				p.G261V		Atlas-SNP	.											TBC1D2,mouth,carcinoma,+1,1	TBC1D2	70	1	0			c.G782T						PASS	.	C	VAL/GLY	595,3811	261.3+/-264.2	41,513,1649	87.0	75.0	79.0		782	1.6	0.3	9	dbSNP_88	79	1459,7141	278.7+/-293.6	118,1223,2959	yes	missense-near-splice	TBC1D2	NM_018421.3	109	159,1736,4608	AA,AC,CC		16.9651,13.5043,15.7927	possibly-damaging	261/918	100991430	2054,10952	2203	4300	6503	SO:0001630	splice_region_variant	55357	exon5			TCTCTCCCTGCTC	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.782-1G>T	9.37:g.100991430C>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	113	51	0.451327	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		376	0.17216117216117216	65	0.13211382113821138	80	0.22099447513812154	91	0.1590909090909091	140	0.18469656992084432	C	8.935	0.964516	0.18583	0.135043	0.169651	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112	T;T;T	0.13420	2.59;3.14;2.59	4.52	1.59	0.23543	.	0.547535	0.18242	N	0.147207	T	0.00012	0.0000	L	0.52364	1.645	0.30637	P	0.756913	P;D	0.53312	0.501;0.959	B;P	0.48030	0.116;0.564	T	0.33394	-0.9870	9	0.25751	T	0.34	.	3.32	0.07047	0.2047:0.5714:0.0:0.2239	rs1573025;rs61050974;rs1573025	261;261	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	V	261;261;43	ENSP00000364205:G261V;ENSP00000364207:G261V;ENSP00000341567:G43V	ENSP00000341567:G43V	G	-	2	0	TBC1D2	100031251	0.279000	0.24239	0.259000	0.24435	0.799000	0.45148	0.447000	0.21710	0.142000	0.18901	-0.330000	0.08379	GGG	C|0.837;A|0.163	0.163	strong		0.498	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	Missense_Mutation
OBSCN	84033	hgsc.bcm.edu	37	1	228437757	228437757	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228437757C>A	ENST00000422127.1	+	14	4169	c.4125C>A	c.(4123-4125)gcC>gcA	p.A1375A	OBSCN_ENST00000570156.2_Silent_p.A1467A|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.A1375A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1375	Ig-like 14.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCGAGGTGGCCCAGGCCCAGA	0.642																																					p.A1467A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C4401A						PASS	.						69.0	72.0	71.0					1																	228437757		2065	4189	6254	SO:0001819	synonymous_variant	84033	exon15			GGTGGCCCAGGCC	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.4125C>A	1.37:g.228437757C>A		Somatic	290	1	0.00344828		WXS	Illumina HiSeq	Phase_I	258	95	0.368217	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
CCDC154	645811	hgsc.bcm.edu	37	16	1484791	1484791	+	Silent	SNP	C	C	T	rs7192233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1484791C>T	ENST00000389176.3	-	16	1942	c.1776G>A	c.(1774-1776)ccG>ccA	p.P592P	CCDC154_ENST00000409671.1_Silent_p.P440P	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	592						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						GCGGCGTCCGCGGGCCCTCCT	0.677													C|||	474	0.0946486	0.2012	0.0476	5008	,	,		11664	0.0516		0.0567	False		,,,				2504	0.0675				p.P585P		Atlas-SNP	.											.	CCDC154	27	.	0			c.G1755A						PASS	.						17.0	23.0	21.0					16																	1484791		691	1586	2277	SO:0001819	synonymous_variant	645811	exon16			CGTCCGCGGGCCC			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.1776G>A	16.37:g.1484791C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	95	49	0.515789	NM_001143980	G9JV18	Silent	SNP	ENST00000389176.3	37																																																																																				C|0.911;T|0.089	0.089	strong		0.677	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
BTN3A1	11119	hgsc.bcm.edu	37	6	26405835	26405835	+	Missense_Mutation	SNP	G	G	A	rs56161420	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26405835G>A	ENST00000289361.6	+	2	412	c.44G>A	c.(43-45)cGt>cAt	p.R15H	BTN3A1_ENST00000414912.2_Missense_Mutation_p.R15H|BTN3A1_ENST00000476549.2_Missense_Mutation_p.R15H|BTN3A1_ENST00000425234.2_Missense_Mutation_p.R15H	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	15			R -> H (in dbSNP:rs56161420). {ECO:0000269|PubMed:14702039}.		activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						CTCAACTTTCGTGTCTGCCTC	0.473													G|||	720	0.14377	0.1619	0.1643	5008	,	,		20713	0.0308		0.165	False		,,,				2504	0.1994				p.R15H		Atlas-SNP	.											BTN3A1_ENST00000476549,NS,carcinoma,0,4	BTN3A1	80	4	0			c.G44A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	787,3619		66,655,1482	241.0	185.0	204.0		44,44,44,44	-3.2	0.0	6	dbSNP_129	204	1477,7123		126,1225,2949	yes	missense,missense,missense,missense	BTN3A1	NM_001145008.1,NM_001145009.1,NM_007048.5,NM_194441.2	29,29,29,29	192,1880,4431	AA,AG,GG		17.1744,17.862,17.4074	benign,benign,benign,benign	15/462,15/379,15/514,15/353	26405835	2264,10742	2203	4300	6503	SO:0001583	missense	11119	exon2			ACTTTCGTGTCTG	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.44G>A	6.37:g.26405835G>A	ENSP00000289361:p.Arg15His	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	225	116	0.515556	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	37	CCDS4608.1	291	0.13324175824175824	94	0.1910569105691057	60	0.16574585635359115	12	0.02097902097902098	125	0.16490765171503957	.	4.425	0.078648	0.08533	0.17862	0.171744	ENSG00000026950	ENST00000476549;ENST00000289361;ENST00000450085;ENST00000425234;ENST00000427334;ENST00000506698;ENST00000414912	T;T;T;T;T;T;T	0.46451	3.98;1.21;3.42;3.96;0.95;2.55;0.87	1.58	-3.16	0.05217	.	.	.	.	.	T	0.03011	0.0089	N	0.00621	-1.32	0.80722	P	0.0	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.36841	-0.9731	8	0.39692	T	0.17	.	2.4136	0.04430	0.2889:0.0:0.2541:0.457	rs56161420	15;15;15;15	E9PGB4;O00481-3;O00481-2;O00481	.;.;.;BT3A1_HUMAN	H	15	ENSP00000420010:R15H;ENSP00000289361:R15H;ENSP00000394937:R15H;ENSP00000396684:R15H;ENSP00000399393:R15H;ENSP00000427013:R15H;ENSP00000406667:R15H	ENSP00000289361:R15H	R	+	2	0	BTN3A1	26513814	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.000000	0.12993	-0.905000	0.03871	-1.935000	0.00506	CGT	G|0.835;A|0.165	0.165	strong		0.473	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
CNDP2	55748	hgsc.bcm.edu	37	18	72176083	72176083	+	Missense_Mutation	SNP	T	T	C	rs2278161	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:72176083T>C	ENST00000324262.4	+	5	692	c.376T>C	c.(376-378)Tat>Cat	p.Y126H	CNDP2_ENST00000324301.8_Intron|CNDP2_ENST00000579847.1_Missense_Mutation_p.Y126H	NM_018235.2	NP_060705.2	Q96KP4	CNDP2_HUMAN	CNDP dipeptidase 2 (metallopeptidase M20 family)	126			Y -> H (in dbSNP:rs2278161). {ECO:0000269|Ref.2}.		cellular nitrogen compound metabolic process (GO:0034641)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)	p.Y126H(1)		breast(1)|cervix(1)|endometrium(3)|large_intestine(7)|lung(5)|ovary(2)|skin(2)|stomach(3)	24		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.22)		AGGCAAGCTGTATGGGAGAGG	0.522													T|||	1081	0.215855	0.0802	0.3156	5008	,	,		18577	0.3006		0.1899	False		,,,				2504	0.2679				p.Y126H		Atlas-SNP	.											CNDP2,NS,carcinoma,0,1	CNDP2	55	1	1	Substitution - Missense(1)	stomach(1)	c.T376C						PASS	.	T	,HIS/TYR	521,3885	239.0+/-250.2	41,439,1723	83.0	76.0	78.0		,376	5.6	0.9	18	dbSNP_100	78	1919,6681	340.5+/-323.6	190,1539,2571	yes	intron,missense	CNDP2	NM_001168499.1,NM_018235.2	,83	231,1978,4294	CC,CT,TT		22.314,11.8248,18.7606	,probably-damaging	,126/476	72176083	2440,10566	2203	4300	6503	SO:0001583	missense	55748	exon5			AAGCTGTATGGGA	AK001692	CCDS12006.1, CCDS54190.1	18q22.3	2014-07-14	2004-07-12		ENSG00000133313	ENSG00000133313	3.4.13.18		24437	protein-coding gene	gene with protein product	"""cytosolic nonspecific dipeptidase"""	169800	"""peptidase A"""	PEPA		12473676	Standard	NM_018235		Approved	FLJ10830, CN2, HsT2298, CPGL	uc002llm.2	Q96KP4	OTTHUMG00000132853	ENST00000324262.4:c.376T>C	18.37:g.72176083T>C	ENSP00000325548:p.Tyr126His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	98	42	0.428571	NM_018235	B3KUG4|Q8WY59|Q9BQ94|Q9NVB4	Missense_Mutation	SNP	ENST00000324262.4	37	CCDS12006.1	435	0.19917582417582416	37	0.07520325203252033	95	0.26243093922651933	170	0.2972027972027972	133	0.17546174142480211	T	13.04	2.119143	0.37436	0.118248	0.22314	ENSG00000133313	ENST00000324262	T	0.53640	0.61	5.57	5.57	0.84162	.	0.055379	0.85682	D	0.000000	T	0.00012	0.0000	H	0.97516	4.02	0.09310	P	1.0	P;P	0.36065	0.535;0.535	P;P	0.55545	0.778;0.778	T	0.01420	-1.1359	9	0.72032	D	0.01	-29.6742	15.7428	0.77914	0.0:0.0:0.0:1.0	rs2278161;rs11539408;rs17816172;rs52835248;rs60808093;rs2278161	114;126	B4DV28;Q96KP4	.;CNDP2_HUMAN	H	126	ENSP00000325548:Y126H	ENSP00000325548:Y126H	Y	+	1	0	CNDP2	70327063	1.000000	0.71417	0.950000	0.38849	0.459000	0.32528	7.629000	0.83207	2.114000	0.64651	0.533000	0.62120	TAT	T|0.801;C|0.198	0.198	strong		0.522	CNDP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256327.1	NM_018235	
AZGP1	563	hgsc.bcm.edu	37	7	99569394	99569394	+	Silent	SNP	G	G	A	rs17295356	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99569394G>A	ENST00000292401.4	-	2	448	c.312C>T	c.(310-312)atC>atT	p.I104I	AZGP1_ENST00000411734.1_Silent_p.I101I	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	104					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					AATACTCCACGATGTCTTTCA	0.532													G|||	1875	0.374401	0.0734	0.4885	5008	,	,		18963	0.6409		0.4105	False		,,,				2504	0.3885				p.I104I		Atlas-SNP	.											.	AZGP1	41	.	0			c.C312T						PASS	.	G		587,3819	258.9+/-262.7	40,507,1656	164.0	134.0	144.0		312	1.5	0.6	7	dbSNP_123	144	3376,5224	500.0+/-375.1	682,2012,1606	no	coding-synonymous	AZGP1	NM_001185.3		722,2519,3262	AA,AG,GG		39.2558,13.3227,30.4706		104/299	99569394	3963,9043	2203	4300	6503	SO:0001819	synonymous_variant	563	exon2			CTCCACGATGTCT	BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"""Immunoglobulin superfamily / C1-set domain containing"""	910	protein-coding gene	gene with protein product		194460	"""alpha-2-glycoprotein 1, zinc"""			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.312C>T	7.37:g.99569394G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_001185	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Silent	SNP	ENST00000292401.4	37	CCDS5680.1																																																																																			G|0.657;A|0.343	0.343	strong		0.532	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185	
ZNF180	7733	hgsc.bcm.edu	37	19	44983567	44983567	+	Missense_Mutation	SNP	C	C	G	rs2253563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44983567C>G	ENST00000221327.4	-	4	548	c.267G>C	c.(265-267)tgG>tgC	p.W89C	ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.W64C|ZNF180_ENST00000592529.1_Missense_Mutation_p.W62C|ZNF180_ENST00000586637.1_Missense_Mutation_p.E99Q|ZNF180_ENST00000587047.1_Intron	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	89	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		W -> C (in dbSNP:rs2253563). {ECO:0000269|PubMed:12743021}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GAGCAGGGTTCCAAGTACCCT	0.478													C|||	2273	0.453874	0.6498	0.3242	5008	,	,		18619	0.4395		0.4672	False		,,,				2504	0.2822				p.W89C	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.G267C						PASS	.	C	CYS/TRP	2730,1676	655.1+/-399.9	849,1032,322	122.0	114.0	117.0		267	5.0	0.1	19	dbSNP_100	117	3818,4782	540.4+/-383.8	857,2104,1339	yes	missense	ZNF180	NM_013256.3	215	1706,3136,1661	GG,GC,CC		44.3953,38.039,49.654	benign	89/693	44983567	6548,6458	2203	4300	6503	SO:0001583	missense	7733	exon4			AGGGTTCCAAGTA	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.267G>C	19.37:g.44983567C>G	ENSP00000221327:p.Trp89Cys	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	50	0.49505	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	1041	0.4766483516483517	292	0.5934959349593496	125	0.3453038674033149	275	0.4807692307692308	349	0.4604221635883905	C	15.74	2.921938	0.52653	0.61961	0.443953	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.01745	4.66;4.66	4.99	4.99	0.66335	Krueppel-associated box (4);	0.490245	0.15313	N	0.268959	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	1.0	P;P;P	0.51449	0.932;0.945;0.945	P;P;P	0.51415	0.54;0.669;0.669	T	0.04165	-1.0972	9	0.72032	D	0.01	-1.7767	16.1451	0.81562	0.0:1.0:0.0:0.0	rs2253563;rs52801407;rs2253563	64;88;89	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	C	89;64	ENSP00000221327:W89C;ENSP00000375818:W64C	ENSP00000221327:W89C	W	-	3	0	ZNF180	49675407	0.008000	0.16893	0.055000	0.19348	0.774000	0.43823	0.896000	0.28377	2.458000	0.83093	0.650000	0.86243	TGG	C|0.508;G|0.492	0.492	strong		0.478	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
LARS2	23395	hgsc.bcm.edu	37	3	45557707	45557707	+	Silent	SNP	G	G	A	rs11549809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:45557707G>A	ENST00000415258.1	+	16	2124	c.1983G>A	c.(1981-1983)acG>acA	p.T661T	LARS2_ENST00000265537.3_Silent_p.T661T|LARS2_ENST00000414984.1_Silent_p.T618T|LARS2_ENST00000467936.1_3'UTR			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	661					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	GGATCGACACGATTCGGCTCT	0.483													G|||	1233	0.246206	0.1982	0.2536	5008	,	,		20280	0.1935		0.332	False		,,,				2504	0.272				p.T661T		Atlas-SNP	.											.	LARS2	48	.	0			c.G1983A						PASS	.	G		957,3449	363.1+/-316.4	100,757,1346	253.0	202.0	219.0		1983	-6.6	0.0	3	dbSNP_120	219	2733,5867	437.2+/-358.5	431,1871,1998	no	coding-synonymous	LARS2	NM_015340.3		531,2628,3344	AA,AG,GG		31.7791,21.7204,28.3715		661/904	45557707	3690,9316	2203	4300	6503	SO:0001819	synonymous_variant	23395	exon17			CGACACGATTCGG	AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	17095	protein-coding gene	gene with protein product	"""leucine tRNA ligase 2, mitochondrial"""	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.1983G>A	3.37:g.45557707G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	100	49	0.49	NM_015340		Silent	SNP	ENST00000415258.1	37	CCDS2728.1																																																																																			G|0.727;A|0.273	0.273	strong		0.483	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340	
KCNJ16	3773	hgsc.bcm.edu	37	17	68128417	68128417	+	Silent	SNP	C	C	T	rs34408089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:68128417C>T	ENST00000589377.1	+	2	352	c.189C>T	c.(187-189)acC>acT	p.T63T	KCNJ16_ENST00000586462.1_Silent_p.T102T|KCNJ16_ENST00000392670.1_Silent_p.T63T|KCNJ16_ENST00000585558.1_Silent_p.T98T|KCNJ16_ENST00000392671.1_Silent_p.T63T|KCNJ16_ENST00000283936.1_Silent_p.T63T	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	63					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					ACATCTTCACCACTCTTGTGG	0.413													C|||	84	0.0167732	0.0159	0.0115	5008	,	,		21473	0.0		0.0288	False		,,,				2504	0.0266				p.T63T		Atlas-SNP	.											.	KCNJ16	72	.	0			c.C189T						PASS	.	C	,,	73,4333	65.3+/-102.7	1,71,2131	283.0	249.0	261.0		189,189,189	3.1	1.0	17	dbSNP_126	261	220,8380	92.6+/-154.6	2,216,4082	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNJ16	NM_018658.1,NM_170741.1,NM_170742.1	,,	3,287,6213	TT,TC,CC		2.5581,1.6568,2.2528	,,	63/419,63/419,63/419	68128417	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	3773	exon6			CTTCACCACTCTT	AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.189C>T	17.37:g.68128417C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	137	69	0.50365	NM_001270422		Silent	SNP	ENST00000589377.1	37	CCDS11687.1																																																																																			C|0.976;T|0.024	0.024	strong		0.413	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658	
DDX60L	91351	hgsc.bcm.edu	37	4	169299528	169299528	+	Missense_Mutation	SNP	T	T	C	rs13110927	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169299528T>C	ENST00000511577.1	-	33	4709	c.4462A>G	c.(4462-4464)Aat>Gat	p.N1488D	DDX60L_ENST00000260184.7_Missense_Mutation_p.N1488D			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1488				N -> D (in Ref. 1; AL832950). {ECO:0000305}.			ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		AAACTTAAATTAGCATTTTGG	0.303													T|||	2255	0.45028	0.202	0.5288	5008	,	,		14971	0.6339		0.498	False		,,,				2504	0.4918				p.N1488D		Atlas-SNP	.											.	DDX60L	116	.	0			c.A4462G						PASS	.	T	ASP/ASN	896,2662		126,644,1009	39.0	34.0	35.0		4462	-2.2	0.0	4	dbSNP_121	35	4073,3987		1074,1925,1031	yes	missense	DDX60L	NM_001012967.1	23	1200,2569,2040	CC,CT,TT		49.4665,25.1827,42.7698	benign	1488/1707	169299528	4969,6649	1779	4030	5809	SO:0001583	missense	91351	exon33			TTAAATTAGCATT	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.4462A>G	4.37:g.169299528T>C	ENSP00000422423:p.Asn1488Asp	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	185	88	0.475676	NM_001012967	Q96ND6	Missense_Mutation	SNP	ENST00000511577.1	37		1036	0.47435897435897434	87	0.17682926829268292	193	0.5331491712707183	371	0.6486013986013986	385	0.5079155672823219	T	0.058	-1.232019	0.01505	0.251827	0.505335	ENSG00000181381	ENST00000260184;ENST00000511577	T;T	0.17213	2.29;2.29	3.14	-2.16	0.07080	.	.	.	.	.	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39683	-0.9602	8	0.13853	T	0.58	.	8.1605	0.31196	0.0:0.0922:0.4846:0.4232	rs13110927;rs17612081;rs52827582;rs60464051;rs13110927	1488	Q5H9U9	DDX6L_HUMAN	D	1488	ENSP00000260184:N1488D;ENSP00000422423:N1488D	ENSP00000260184:N1488D	N	-	1	0	DDX60L	169536103	0.000000	0.05858	0.000000	0.03702	0.062000	0.15995	-0.476000	0.06591	-1.279000	0.02405	-2.160000	0.00327	AAT	T|0.533;C|0.467	0.467	strong		0.303	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
PLCB1	23236	hgsc.bcm.edu	37	20	8737734	8737734	+	Silent	SNP	G	G	A	rs2076413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:8737734G>A	ENST00000338037.6	+	24	2592	c.2565G>A	c.(2563-2565)gcG>gcA	p.A855A	PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Silent_p.A855A|PLCB1_ENST00000378641.3_Silent_p.A855A	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	855					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						CAAGTGAAGCGAGAACGACTC	0.473													G|||	1063	0.21226	0.1104	0.2219	5008	,	,		17943	0.13		0.3022	False		,,,				2504	0.3354				p.P855P		Atlas-SNP	.											.	PLCB1	394	.	0			c.T2565A						PASS	.	G	,	588,3818	257.0+/-261.6	43,502,1658	71.0	74.0	73.0		2565,2565	-1.6	0.8	20	dbSNP_96	73	2688,5912	430.6+/-356.6	451,1786,2063	no	coding-synonymous,coding-synonymous	PLCB1	NM_015192.2,NM_182734.1	,	494,2288,3721	AA,AG,GG		31.2558,13.3454,25.1884	,	855/1217,855/1174	8737734	3276,9730	2203	4300	6503	SO:0001819	synonymous_variant	23236	exon24			TGAAGCGAGAACG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.2565G>A	20.37:g.8737734G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	100	42	0.42	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1																																																																																			G|0.773;A|0.227	0.227	strong		0.473	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
BTNL2	56244	hgsc.bcm.edu	37	6	32362703	32362703	+	Missense_Mutation	SNP	G	G	T	rs41521946|rs28362676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32362703G>T	ENST00000374993.1	-	6	1177	c.1178C>A	c.(1177-1179)cCa>cAa	p.P393Q	BTNL2_ENST00000414363.1_Missense_Mutation_p.P183Q|BTNL2_ENST00000544175.1_Missense_Mutation_p.P116Q|BTNL2_ENST00000540315.1_Missense_Mutation_p.P183Q|BTNL2_ENST00000429232.2_3'UTR|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Missense_Mutation_p.P299Q|BTNL2_ENST00000454136.3_Missense_Mutation_p.P393Q	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	393			P -> Q (in dbSNP:rs41521946).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						GTCCCTCCATGGCACGTGGGG	0.567													g|||	821	0.163938	0.1422	0.1599	5008	,	,		19943	0.1587		0.163	False		,,,				2504	0.2025				p.P393Q		Atlas-SNP	.											.	BTNL2	50	.	0			c.C1178A						PASS	.		GLN/PRO	11,4395		3,5,2195	232.0	217.0	222.0		1178	2.7	0.9	6	dbSNP_127	222	16,8584		2,12,4286	yes	missense	BTNL2	NM_019602.1	76	5,17,6481	TT,TG,GG		0.186,0.2497,0.2076	benign	393/456	32362703	27,12979	2203	4300	6503	SO:0001583	missense	56244	exon6			CTCCATGGCACGT	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1178C>A	6.37:g.32362703G>T	ENSP00000364132:p.Pro393Gln	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	106	37	0.349057	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		264	0.12087912087912088	46	0.09349593495934959	53	0.1464088397790055	84	0.14685314685314685	81	0.10686015831134564	g	0.004	-2.270351	0.00257	0.002497	0.00186	ENSG00000204290	ENST00000468270;ENST00000374995;ENST00000414363;ENST00000374993;ENST00000540315;ENST00000544175	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79	5.08	2.67	0.31697	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	0.332477	0.22018	N	0.065766	T	0.06142	0.0159	N	0.00013	-2.925	0.50467	P	1.2199999999995548E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.36311	-0.9753	9	0.02654	T	1	.	4.2208	0.10556	0.0:0.1079:0.2104:0.6817	rs41521946;rs61730582	183;393	Q9UIR0-4;Q9UIR0	.;BTNL2_HUMAN	Q	393;299;183;393;183;116	ENSP00000364134:P299Q;ENSP00000390512:P183Q;ENSP00000364132:P393Q;ENSP00000444714:P183Q;ENSP00000443364:P116Q	ENSP00000364132:P393Q	P	-	2	0	BTNL2	32470681	0.480000	0.25933	0.898000	0.35279	0.024000	0.10985	0.414000	0.21164	0.971000	0.38288	-0.504000	0.04507	CCA	G|0.871;T|0.129	0.129	strong		0.567	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
URB1	9875	hgsc.bcm.edu	37	21	33717877	33717877	+	Silent	SNP	G	G	A	rs2833779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33717877G>A	ENST00000382751.3	-	23	3991	c.3876C>T	c.(3874-3876)tcC>tcT	p.S1292S	RN7SL109P_ENST00000493105.2_RNA	NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1292						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						GAATGACAGCGGAAGACACTA	0.537													G|||	866	0.172923	0.2958	0.0908	5008	,	,		20039	0.1379		0.1213	False		,,,				2504	0.1544				p.S1292S		Atlas-SNP	.											.	URB1	176	.	0			c.C3876T						PASS	.	G		386,998		59,268,365	26.0	26.0	26.0		3876	-6.5	0.6	21	dbSNP_100	26	404,2778		29,346,1216	no	coding-synonymous	URB1	NM_014825.2		88,614,1581	AA,AG,GG		12.6964,27.8902,17.3018		1292/2272	33717877	790,3776	692	1591	2283	SO:0001819	synonymous_variant	9875	exon23			GACAGCGGAAGAC	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.3876C>T	21.37:g.33717877G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			G|0.822;A|0.178	0.178	strong		0.537	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
ZNF683	257101	hgsc.bcm.edu	37	1	26691174	26691174	+	Missense_Mutation	SNP	C	C	A	rs11247933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26691174C>A	ENST00000436292.1	-	4	983	c.863G>T	c.(862-864)cGt>cTt	p.R288L	ZNF683_ENST00000349618.3_Missense_Mutation_p.R288L|ZNF683_ENST00000403843.1_Missense_Mutation_p.R288L|ZNF683_ENST00000374204.1_Missense_Mutation_p.R288L			Q8IZ20	ZN683_HUMAN	zinc finger protein 683	288			R -> L (in dbSNP:rs11247933).		natural killer cell differentiation (GO:0001779)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)	15		all_cancers(24;2.39e-25)|Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;7.26e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00637)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;1.76e-26)|Colorectal(126;1.38e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|BRCA - Breast invasive adenocarcinoma(304;0.00099)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00793)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.159)|LUSC - Lung squamous cell carcinoma(448;0.233)		CATGCCACCACGCTCCAGGCC	0.617													C|||	1319	0.263379	0.1233	0.4193	5008	,	,		16688	0.2778		0.341	False		,,,				2504	0.2474				p.R288L		Atlas-SNP	.											.	ZNF683	51	.	0			c.G863T						PASS	.	C	LEU/ARG,LEU/ARG	720,3686	295.9+/-283.9	58,604,1541	75.0	77.0	76.0		863,863	-7.0	0.0	1	dbSNP_120	76	3089,5511	470.5+/-367.8	547,1995,1758	yes	missense,missense	ZNF683	NM_001114759.1,NM_173574.2	102,102	605,2599,3299	AA,AC,CC		35.9186,16.3414,29.2865	benign,benign	288/505,288/505	26691174	3809,9197	2203	4300	6503	SO:0001583	missense	257101	exon4			CCACCACGCTCCA	BC029505	CCDS279.2	1p36.11	2013-01-08			ENSG00000176083	ENSG00000176083		"""Zinc fingers, C2H2-type"""	28495	protein-coding gene	gene with protein product	"""hypothetical protein MGC33414"""					12477932	Standard	NM_173574		Approved	MGC33414	uc009vsj.1	Q8IZ20	OTTHUMG00000003521	ENST00000436292.1:c.863G>T	1.37:g.26691174C>A	ENSP00000388792:p.Arg288Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	93	85	0.913979	NM_173574	Q5T141|Q5T146|Q5T147|Q5T149|Q8NEN4	Missense_Mutation	SNP	ENST00000436292.1	37		620	0.2838827838827839	64	0.13008130081300814	144	0.39779005524861877	147	0.256993006993007	265	0.3496042216358839	C	7.602	0.672902	0.14776	0.163414	0.359186	ENSG00000176083	ENST00000403843;ENST00000436292;ENST00000374204;ENST00000349618	T;T;T;T	0.09630	3.01;3.01;2.96;2.96	3.52	-7.04	0.01578	.	2.010380	0.02183	N	0.060622	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.12630	0.006;0.003	B;B	0.17098	0.017;0.008	T	0.44467	-0.9326	9	0.10377	T	0.69	3.2031	3.8651	0.09013	0.1064:0.2623:0.1055:0.5259	rs11247933;rs52829071;rs59372706;rs11247933	288;288	Q8IZ20-2;Q8IZ20	.;ZN683_HUMAN	L	288	ENSP00000384782:R288L;ENSP00000388792:R288L;ENSP00000363320:R288L;ENSP00000344095:R288L	ENSP00000344095:R288L	R	-	2	0	ZNF683	26563761	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.192000	0.01245	-2.439000	0.00551	-1.134000	0.01955	CGT	C|0.728;A|0.272	0.272	strong		0.617	ZNF683-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000009794.2	NM_173574	
TLR6	10333	hgsc.bcm.edu	37	4	38830012	38830012	+	Silent	SNP	G	G	C	rs3821985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:38830012G>C	ENST00000381950.1	-	1	1148	c.1083C>G	c.(1081-1083)acC>acG	p.T361T	TLR6_ENST00000436693.2_Silent_p.T361T			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	361					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AAACGTTCTGGGTAAAGTTCA	0.328													G|||	2228	0.444888	0.6944	0.3112	5008	,	,		21947	0.3958		0.3141	False		,,,				2504	0.3875				p.T361T		Atlas-SNP	.											.	TLR6	67	.	0			c.C1083G						PASS	.	G		2785,1619	659.7+/-400.6	875,1035,292	54.0	54.0	54.0		1083	3.0	1.0	4	dbSNP_107	54	2939,5661	458.0+/-364.5	519,1901,1880	no	coding-synonymous	TLR6	NM_006068.4		1394,2936,2172	CC,CG,GG		34.1744,36.762,44.0172		361/797	38830012	5724,7280	2202	4300	6502	SO:0001819	synonymous_variant	10333	exon2			GTTCTGGGTAAAG		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1083C>G	4.37:g.38830012G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Silent	SNP	ENST00000381950.1	37	CCDS3446.1																																																																																			G|0.583;C|0.417	0.417	strong		0.328	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
KRT6B	3854	hgsc.bcm.edu	37	12	52844265	52844265	+	Missense_Mutation	SNP	T	T	C	rs652423	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52844265T>C	ENST00000252252.3	-	2	727	c.680A>G	c.(679-681)aAc>aGc	p.N227S		NM_005555.3	NP_005546.2	P04259	K2C6B_HUMAN	keratin 6B	227	Coil 1B.|Rod.		N -> S (in dbSNP:rs652423). {ECO:0000269|PubMed:2410904, ECO:0000269|PubMed:7543104}.		ectoderm development (GO:0007398)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(19)|ovary(4)|prostate(2)	40				BRCA - Breast invasive adenocarcinoma(357;0.083)		CCCCACGATGTTGTCCAGCTG	0.577																																					p.N227S		Atlas-SNP	.											.	KRT6B	90	.	0			c.A680G						PASS	.	T	SER/ASN	1455,2951		207,1041,955	196.0	184.0	188.0		680	-1.9	0.0	12	dbSNP_83	188	2618,5982		109,2400,1791	no	missense	KRT6B	NM_005555.3	46	316,3441,2746	CC,CT,TT		30.4419,33.0232,31.3163	benign	227/565	52844265	4073,8933	2203	4300	6503	SO:0001583	missense	3854	exon2			ACGATGTTGTCCA	BC034535	CCDS8828.1	12q13.13	2013-01-16	2004-08-11		ENSG00000185479	ENSG00000185479		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6444	protein-coding gene	gene with protein product		148042	"""keratin-like 1 (a type II keratin sequence)"""	KRTL1		1713141, 16831889	Standard	NM_005555		Approved		uc001sak.3	P04259	OTTHUMG00000169593	ENST00000252252.3:c.680A>G	12.37:g.52844265T>C	ENSP00000252252:p.Asn227Ser	Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	360	129	0.358333	NM_005555	P48669	Missense_Mutation	SNP	ENST00000252252.3	37	CCDS8828.1	772	0.3534798534798535	193	0.39227642276422764	108	0.2983425414364641	241	0.42132867132867136	230	0.3034300791556728	T	0.014	-1.578709	0.00879	0.330232	0.304419	ENSG00000185479	ENST00000252252;ENST00000544607	D	0.90620	-2.7	2.77	-1.87	0.07737	Filament (1);	0.650670	0.15055	N	0.283073	T	0.00012	0.0000	N	0.00996	-1.065	0.80722	P	0.0	B	0.18013	0.025	B	0.20577	0.03	T	0.09378	-1.0677	9	0.02654	T	1	.	5.5903	0.17297	0.121:0.4745:0.3226:0.0818	rs652423;rs1707773;rs2942779;rs7311892;rs11531212;rs58544103;rs652423	227	P04259	K2C6B_HUMAN	S	227	ENSP00000252252:N227S	ENSP00000252252:N227S	N	-	2	0	KRT6B	51130532	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.048000	0.03517	-0.421000	0.07416	-0.817000	0.03123	AAC	T|0.604;C|0.396	0.396	strong		0.577	KRT6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404969.1	NM_005555	
POU5F1B	5462	hgsc.bcm.edu	37	8	128428751	128428751	+	Missense_Mutation	SNP	A	A	G	rs13274084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:128428751A>G	ENST00000465342.2	+	2	1797	c.640A>G	c.(640-642)Aat>Gat	p.N214D	POU5F1B_ENST00000391675.1_Missense_Mutation_p.N214D|CASC8_ENST00000523825.1_RNA|CASC8_ENST00000501396.1_RNA|CASC8_ENST00000502082.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	214			N -> D (in dbSNP:rs13274084). {ECO:0000269|PubMed:21341266, ECO:0000269|Ref.3}.		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						AGCTGACAACAATGAAAATCT	0.507													a|||	330	0.0658946	0.0091	0.0793	5008	,	,		20047	0.0575		0.1382	False		,,,				2504	0.0675				p.N214D		Atlas-SNP	.											.	POU5F1B	32	.	0			c.A640G	GRCh37	CM073273	POU5F1B	M	rs13274084	PASS	.						17.0	19.0	18.0					8																	128428751		692	1591	2283	SO:0001583	missense	5462	exon1			GACAACAATGAAA	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.640A>G	8.37:g.128428751A>G	ENSP00000419298:p.Asn214Asp	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	182	100	0.549451	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	179	0.08195970695970696	7	0.014227642276422764	35	0.09668508287292818	33	0.057692307692307696	104	0.13720316622691292	A	8.566	0.878897	0.17395	.	.	ENSG00000212993	ENST00000465342;ENST00000391675	T;T	0.79141	-1.24;-1.24	1.14	-2.28	0.06826	Homeodomain-related (1);	0.000000	0.56097	D	0.000033	T	0.01092	0.0036	M	0.75615	2.305	0.41841	P	0.009875999999999996	B	0.09022	0.002	B	0.13407	0.009	T	0.25572	-1.0128	9	0.66056	D	0.02	.	3.5631	0.07889	0.331:0.4766:0.1924:0.0	rs13274084	214	Q06416	P5F1B_HUMAN	D	214	ENSP00000419298:N214D;ENSP00000375557:N214D	ENSP00000375557:N214D	N	+	1	0	POU5F1B	128497933	0.015000	0.18098	0.008000	0.14137	0.200000	0.23975	0.874000	0.28065	-0.663000	0.05331	0.113000	0.15668	AAT	A|0.856;G|0.144	0.144	strong		0.507	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
OGG1	4968	hgsc.bcm.edu	37	3	9798773	9798773	+	Missense_Mutation	SNP	C	C	G	rs1052133|rs1052134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9798773C>G	ENST00000344629.7	+	7	1320	c.977C>G	c.(976-978)tCc>tGc	p.S326C	OGG1_ENST00000302008.8_Intron|OGG1_ENST00000302003.7_Missense_Mutation_p.P332A|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000339511.5_3'UTR|OGG1_ENST00000349503.5_Intron			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	326			S -> C (common polymorphism in the Japanese population; dbSNP:rs1052133). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.13}.		acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					CTGCGCCAATCCCGCCATGCT	0.597								Base excision repair (BER), DNA glycosylases					C|||	1513	0.302117	0.1551	0.2939	5008	,	,		18217	0.5476		0.2028	False		,,,				2504	0.3558				p.P332A		Atlas-SNP	.											.	OGG1	57	.	0			c.C994G	GRCh37	CM993185	OGG1	M	rs1052133	PASS	.	C	CYS/SER,,ALA/PRO,,,,,	767,3639	311.1+/-291.9	74,619,1510	106.0	115.0	112.0		977,,994,,,,,	-1.3	0.0	3	dbSNP_86	112	1979,6621	346.1+/-326.1	235,1509,2556	yes	missense,utr-3,missense,intron,intron,intron,intron,intron	OGG1	NM_002542.5,NM_016819.3,NM_016820.3,NM_016821.2,NM_016826.2,NM_016827.2,NM_016828.2,NM_016829.2	112,,27,,,,,	309,2128,4066	GG,GC,CC		23.0116,17.4081,21.1133	benign,,benign,,,,,	326/346,,332/411,,,,,	9798773	2746,10260	2203	4300	6503	SO:0001583	missense	4968	exon7			GCCAATCCCGCCA	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"""8-hydroxyguanine DNA glycosylase"", ""OGG1 type 1e"", ""OGG1 type 1d"", ""OGG1 type 1g"", ""OGG1 type 1h"""	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.977C>G	3.37:g.9798773C>G	ENSP00000342851:p.Ser326Cys	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	93	46	0.494624	NM_016820	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	652|652|652	0.29853479853479853|0.29853479853479853|0.29853479853479853	79|79|79	0.16056910569105692|0.16056910569105692|0.16056910569105692	108|108|108	0.2983425414364641|0.2983425414364641|0.2983425414364641	311|311|311	0.5437062937062938|0.5437062937062938|0.5437062937062938	154|154|154	0.20316622691292877|0.20316622691292877|0.20316622691292877	C|C|C	4.259|4.259|4.259	0.047094|0.047094|0.047094	0.08243|0.08243|0.08243	0.174081|0.174081|0.174081	0.230116|0.230116|0.230116	ENSG00000114026|ENSG00000114026|ENSG00000114026	ENST00000416333|ENST00000302003;ENST00000339542|ENST00000344629	.|T|T	.|0.59502|0.50813	.|0.26|0.73	5.05|5.05|5.05	-1.32|-1.32|-1.32	0.09201|0.09201|0.09201	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	0.00012|0.00012|0.00012	0.0000|0.0000|0.0000	L|L|L	0.39898|0.39898|0.39898	1.24|1.24|1.24	0.80722|0.80722|0.80722	P|P|P	0.0|0.0|0.0	.|B;B;B;B|B;B	.|0.29481|0.25235	.|0.228;0.245;0.103;0.035|0.121;0.121	.|B;B;B;B|B;B	.|0.31946|0.39660	.|0.121;0.138;0.085;0.027|0.306;0.306	T|T|T	0.48536|0.48536|0.48536	-0.9027|-0.9027|-0.9027	4|8|8	.|0.07990|0.56958	.|T|D	.|0.79|0.05	.|.|.	3.5612|3.5612|3.5612	0.07882|0.07882|0.07882	0.4329:0.3147:0.0:0.2523|0.4329:0.3147:0.0:0.2523|0.4329:0.3147:0.0:0.2523	rs1052133;rs1805372;rs3192526;rs4134729;rs17844853;rs17857568;rs59989261;rs1052133|rs1052133;rs1805372;rs3192526;rs4134729;rs17844853;rs17857568;rs59989261;rs1052133|rs1052133;rs1805372;rs3192526;rs4134729;rs17844853;rs17857568;rs59989261;rs1052133	.|119;103;332;332|326;326	.|F8WA07;Q9HCR8;O15527-3;E5KPN0|E5KPN1;O15527	.|.;.;.;.|.;OGG1_HUMAN	M|A|C	98|332;119|326	.|ENSP00000305584:P332A|ENSP00000342851:S326C	.|ENSP00000305584:P332A|ENSP00000342851:S326C	I|P|S	+|+|+	3|1|2	3|0|0	OGG1|OGG1|OGG1	9773773|9773773|9773773	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.006000|0.006000|0.006000	0.05464|0.05464|0.05464	0.037000|0.037000|0.037000	0.13840|0.13840|0.13840	-0.141000|-0.141000|-0.141000	0.11374|0.11374|0.11374	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	ATC|CCC|TCC	C|1.000;|0.000	.	weak		0.597	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821	
SIRPA	140885	hgsc.bcm.edu	37	20	1896059	1896059	+	Missense_Mutation	SNP	G	G	A	rs386811663|rs115287948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1896059G>A	ENST00000358771.4	+	2	546	c.394G>A	c.(394-396)Gtg>Atg	p.V132M	SIRPA_ENST00000356025.3_Missense_Mutation_p.V132M|SIRPA_ENST00000400068.3_Missense_Mutation_p.V132M	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	132	Ig-like V-type.		V -> T (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CCCCGATGACGTGGAGTTTAA	0.527													G|||	2050	0.409345	0.2761	0.4222	5008	,	,		15841	0.625		0.3171	False		,,,				2504	0.453				p.V132M	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											SIRPA,caecum,carcinoma,0,2	SIRPA	83	2	0			c.G394A						PASS	.						108.0	93.0	98.0					20																	1896059		2198	4290	6488	SO:0001583	missense	140885	exon3			GATGACGTGGAGT	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.394G>A	20.37:g.1896059G>A	ENSP00000351621:p.Val132Met	Somatic	362	0	0		WXS	Illumina HiSeq	Phase_I	211	32	0.151659	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	G	9.326	1.059262	0.19987	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.64991	-0.13;-0.13;-0.13	5.11	-2.28	0.06826	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	2.497550	0.01234	N	0.008420	T	0.49558	0.1564	L	0.28192	0.835	0.80722	P	0.0	B;B;B	0.27765	0.084;0.005;0.188	B;B;B	0.27887	0.057;0.01;0.084	T	0.39702	-0.9601	9	0.33141	T	0.24	.	9.8059	0.40792	0.7439:0.0:0.2561:0.0	.	112;132;132	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	M	132	ENSP00000382941:V132M;ENSP00000348307:V132M;ENSP00000351621:V132M	ENSP00000348307:V132M	V	+	1	0	SIRPA	1844059	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.421000	0.07053	-0.198000	0.10333	-1.101000	0.02118	GTG	G|0.679;A|0.321	0.321	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
RHCE	6006	hgsc.bcm.edu	37	1	25717365	25717365	+	Missense_Mutation	SNP	C	C	G	rs609320	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:25717365C>G	ENST00000294413.7	-	5	734	c.676G>C	c.(676-678)Gct>Cct	p.A226P	RHCE_ENST00000455194.1_Intron|RHCE_ENST00000349320.3_Missense_Mutation_p.A210P|RHCE_ENST00000349438.4_Missense_Mutation_p.A226P|RHCE_ENST00000346452.4_Intron|RHCE_ENST00000340849.4_Intron|RHCE_ENST00000413854.1_Missense_Mutation_p.A226P|RHCE_ENST00000243186.6_Missense_Mutation_p.A226P|RHCE_ENST00000425135.1_Missense_Mutation_p.A226P|RHCE_ENST00000374352.2_Missense_Mutation_p.A210P	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	226			P -> A (in E/Rh5 antigen; dbSNP:rs609320). {ECO:0000269|PubMed:11380456, ECO:0000269|PubMed:11902138, ECO:0000269|PubMed:12393640, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16710414, ECO:0000269|Ref.11, 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)		CTCAGCAGAGCAGAGTTGACA	0.542													C|||	720	0.14377	0.0802	0.232	5008	,	,		19967	0.2024		0.16	False		,,,				2504	0.09				p.A226P		Atlas-SNP	.											.	RHCE	36	.	0			c.G676C	GRCh37	CM930646	RHCE	M	rs609320	PASS	.	C	PRO/ALA,,,PRO/ALA	508,3898	233.3+/-246.5	30,448,1725	176.0	157.0	163.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	676,,,676	3.2	0.9	1	dbSNP_83	163	1324,7276	259.4+/-282.6	99,1126,3075	yes	missense,intron,intron,missense	RHCE	NM_020485.4,NM_138616.3,NM_138617.3,NM_138618.3	27,,,27	129,1574,4800	GG,GC,CC		15.3953,11.5297,14.0858	benign,,,benign	226/418,,,226/355	25717365	1832,11174	2203	4300	6503	SO:0001583	missense	6006	exon5			GCAGAGCAGAGTT	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.676G>C	1.37:g.25717365C>G	ENSP00000294413:p.Ala226Pro	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	196	179	0.913265	NM_138618	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	354	0.1620879120879121	38	0.07723577235772358	65	0.17955801104972377	126	0.2202797202797203	125	0.16490765171503957	c	12.85	2.061295	0.36373	0.115297	0.153953	ENSG00000188672	ENST00000413854;ENST00000539650;ENST00000374352;ENST00000243186;ENST00000425135;ENST00000349320;ENST00000294413;ENST00000447203;ENST00000349438	T;T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62;1.62	4.08	3.15	0.36227	.	0.434706	0.24222	N	0.040430	T	0.00012	0.0000	.	.	.	0.30859	P	0.733735	B;B	0.18968	0.032;0.026	B;B	0.32724	0.151;0.01	T	0.14868	-1.0457	8	0.59425	D	0.04	-2.9938	8.181	0.31311	0.0:0.887:0.0:0.113	rs609320;rs1053357;rs3765375;rs7543659;rs9660380;rs52813416;rs609320	210;226	Q5VSJ9;Q5VSJ8	.;.	P	226;168;210;226;226;210;226;226;226	ENSP00000415417:A226P;ENSP00000363472:A210P;ENSP00000243186:A226P;ENSP00000392809:A226P;ENSP00000311185:A210P;ENSP00000294413:A226P;ENSP00000334570:A226P	ENSP00000243186:A226P	A	-	1	0	RHCE	25589952	0.070000	0.21116	0.948000	0.38648	0.569000	0.35902	1.282000	0.33226	1.027000	0.39758	0.591000	0.81541	GCT	C|0.855;G|0.145	0.145	strong		0.542	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485	
GPR116	221395	hgsc.bcm.edu	37	6	46826979	46826979	+	Silent	SNP	A	A	G	rs9381487	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46826979A>G	ENST00000283296.7	-	17	2949	c.2661T>C	c.(2659-2661)taT>taC	p.Y887Y	GPR116_ENST00000545669.1_Silent_p.Y316Y|GPR116_ENST00000456426.2_Silent_p.Y745Y|GPR116_ENST00000362015.4_Silent_p.Y887Y|GPR116_ENST00000265417.7_Silent_p.Y887Y	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	887					energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			AGTTTTCTAGATAGCTCTTGT	0.463													A|||	1609	0.321286	0.3714	0.2839	5008	,	,		20789	0.3621		0.1998	False		,,,				2504	0.363				p.Y887Y	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.T2661C						PASS	.	A	,	1464,2942	472.6+/-356.4	224,1016,963	79.0	79.0	79.0		2661,2661	1.3	0.0	6	dbSNP_119	79	1784,6816	320.1+/-314.5	186,1412,2702	no	coding-synonymous,coding-synonymous	GPR116	NM_001098518.1,NM_015234.4	,	410,2428,3665	GG,GA,AA		20.7442,33.2274,24.9731	,	887/1347,887/1347	46826979	3248,9758	2203	4300	6503	SO:0001819	synonymous_variant	221395	exon17			TTCTAGATAGCTC	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.2661T>C	6.37:g.46826979A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	141	67	0.475177	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			A|0.733;G|0.267	0.267	strong		0.463	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
ARMC5	79798	hgsc.bcm.edu	37	16	31476458	31476458	+	Intron	SNP	C	C	T	rs11150624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31476458C>T	ENST00000563544.1	+	5	2410				ARMC5_ENST00000538189.1_Intron|ARMC5_ENST00000268314.4_Intron|ARMC5_ENST00000457010.2_Missense_Mutation_p.A705V|ARMC5_ENST00000408912.3_Intron|ARMC5_ENST00000412665.2_Intron			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5											central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TGCAGCCCCGCGCCCAGGATC	0.622													C|||	1523	0.304113	0.0507	0.5735	5008	,	,		20389	0.4494		0.4463	False		,,,				2504	0.1595				p.A705V		Atlas-SNP	.											ARMC5_ENST00000457010,brain,glioma,0,1	ARMC5	94	1	0			c.C2114T						scavenged	.	C	,VAL/ALA	443,3739		26,391,1674	49.0	55.0	53.0		,2114	-7.3	0.0	16	dbSNP_120	53	3593,4857		780,2033,1412	yes	intron,missense	ARMC5	NM_001105247.1,NM_024742.2	,64	806,2424,3086	TT,TC,CC		42.5207,10.593,31.9506	,	,705/726	31476458	4036,8596	2091	4225	6316	SO:0001627	intron_variant	79798	exon4			GCCCCGCGCCCAG	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.1864+250C>T	16.37:g.31476458C>T		Somatic	84	1	0.0119048		WXS	Illumina HiSeq	Phase_I	72	33	0.458333	NM_024742	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	858	0.39285714285714285	28	0.056910569105691054	209	0.5773480662983426	277	0.48426573426573427	344	0.45382585751978893	C	8.087	0.773579	0.16051	0.10593	0.425207	ENSG00000140691	ENST00000457010	T	0.21543	2.0	3.63	-7.27	0.01461	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.20261	0.043	B	0.14578	0.011	T	0.45101	-0.9284	6	.	.	.	.	4.3423	0.11115	0.1614:0.4832:0.2508:0.1046	rs11150624;rs56855049;rs11150624	704	Q96C12-4	.	V	705	ENSP00000399561:A705V	.	A	+	2	0	ARMC5	31383959	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.168000	0.03123	-1.705000	0.01406	-1.359000	0.01217	GCG	C|0.636;T|0.364	0.364	strong		0.622	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
SYNE1	23345	hgsc.bcm.edu	37	6	152443744	152443744	+	Missense_Mutation	SNP	G	G	T	rs2295190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:152443744G>T	ENST00000367255.5	-	146	26822	c.26221C>A	c.(26221-26223)Ctg>Atg	p.L8741M	SYNE1_ENST00000448038.1_Missense_Mutation_p.L8693M|SYNE1_ENST00000423061.1_Missense_Mutation_p.L8693M|ESR1_ENST00000427531.2_Intron|SYNE1_ENST00000265368.4_Missense_Mutation_p.L8741M|SYNE1_ENST00000356820.4_Missense_Mutation_p.L3265M|SYNE1_ENST00000354674.4_Missense_Mutation_p.L919M|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000341594.5_Missense_Mutation_p.L8353M|SYNE1_ENST00000539504.1_Missense_Mutation_p.L896M	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8741	KASH. {ECO:0000255|PROSITE- ProRule:PRU00385}.		L -> M (in dbSNP:rs2295190).		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)		ACTCTGAACAGGAAGCCGCGG	0.557										HNSCC(10;0.0054)			G|||	385	0.076877	0.0204	0.0533	5008	,	,		19383	0.0675		0.1491	False		,,,				2504	0.1053				p.L8741M		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C26221A						PASS	.	G	MET/LEU,MET/LEU	152,4254	105.6+/-144.1	2,148,2053	94.0	97.0	96.0		26077,26221	0.6	0.8	6	dbSNP_100	96	1202,7398	243.8+/-273.2	74,1054,3172	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	15,15	76,1202,5225	TT,TG,GG		13.9767,3.4498,10.4106	possibly-damaging,possibly-damaging	8693/8750,8741/8798	152443744	1354,11652	2203	4300	6503	SO:0001583	missense	23345	exon146			TGAACAGGAAGCC	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.26221C>A	6.37:g.152443744G>T	ENSP00000356224:p.Leu8741Met	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	53	7	0.132075	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	202	0.0924908424908425	18	0.036585365853658534	21	0.058011049723756904	42	0.07342657342657342	121	0.15963060686015831	G	17.90	3.503200	0.64298	0.034498	0.139767	ENSG00000131018	ENST00000367255;ENST00000539504;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000313630;ENST00000367247;ENST00000354674	T;T;T;T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75;1.75;1.75;1.75	5.56	0.627	0.17675	Klarsicht/ANC-1/syne-1 homology (2);	0.330699	0.21571	N	0.072401	T	0.36166	0.0957	M	0.84433	2.695	0.31636	P	0.648409	D;D;D	0.64830	0.994;0.994;0.993	D;D;D	0.69824	0.966;0.966;0.943	T	0.34378	-0.9831	9	0.72032	D	0.01	.	8.7024	0.34334	0.5975:0.0:0.4025:0.0	rs2295190;rs2295190	8741;8741;8693	Q8NF91;E7EQI5;Q8NF91-4	SYNE1_HUMAN;.;.	M	8741;896;8693;8741;8693;8353;3265;926;921;919	ENSP00000356224:L8741M;ENSP00000441052:L896M;ENSP00000396024:L8693M;ENSP00000265368:L8741M;ENSP00000390975:L8693M;ENSP00000341887:L8353M;ENSP00000349276:L3265M;ENSP00000346701:L919M	ENSP00000265368:L8741M	L	-	1	2	SYNE1	152485437	1.000000	0.71417	0.840000	0.33206	0.821000	0.46438	1.590000	0.36654	0.025000	0.15241	0.655000	0.94253	CTG	G|0.898;T|0.102	0.102	strong		0.557	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
TOMM40	10452	hgsc.bcm.edu	37	19	45395714	45395714	+	Silent	SNP	T	T	C	rs157581	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45395714T>C	ENST00000426677.2	+	2	519	c.339T>C	c.(337-339)ttT>ttC	p.F113F	TOMM40_ENST00000592434.1_Silent_p.F113F|TOMM40_ENST00000252487.5_Silent_p.F113F|TOMM40_ENST00000405636.2_Silent_p.F113F|CTB-129P6.4_ENST00000585408.1_RNA	NM_001128917.1	NP_001122389.1	O96008	TOM40_HUMAN	translocase of outer mitochondrial membrane 40 homolog (yeast)	113					cellular protein metabolic process (GO:0044267)|ion transport (GO:0006811)|protein targeting to mitochondrion (GO:0006626)|protein transmembrane transport (GO:0071806)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of mitochondrial outer membrane (GO:0031307)|mitochondrial outer membrane translocase complex (GO:0005742)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein transmembrane transporter activity (GO:0008320)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(1)	5	Lung NSC(12;0.0018)|all_lung(12;0.00481)			OV - Ovarian serous cystadenocarcinoma(262;0.0033)|Epithelial(262;0.176)		GTAACCATTTTCAGGTGAGCC	0.547													.|||	1534	0.30631	0.5023	0.2507	5008	,	,		21063	0.246		0.2078	False		,,,				2504	0.2444				p.F113F		Atlas-SNP	.											.	TOMM40	13	.	0			c.T339C	GRCh37	CM073386	TOMM40	M	rs157581	PASS	.	C	,,	2058,2348	604.8+/-390.4	482,1094,627	174.0	146.0	155.0		339,339,339	3.3	1.0	19	dbSNP_79	155	1803,6797	729.3+/-406.7	180,1443,2677	no	coding-synonymous,coding-synonymous,coding-synonymous	TOMM40	NM_001128916.1,NM_001128917.1,NM_006114.2	,,	662,2537,3304	CC,CT,TT		20.9651,46.709,29.6863	,,	113/362,113/362,113/362	45395714	3861,9145	2203	4300	6503	SO:0001819	synonymous_variant	10452	exon2			CCATTTTCAGGTG	AF043250	CCDS12646.1	19q13	2008-07-04				ENSG00000130204			18001	protein-coding gene	gene with protein product		608061				10980201, 15644312	Standard	NM_006114		Approved	PEREC1, D19S1177E, C19orf1, TOM40, PER-EC1	uc002paa.4	O96008		ENST00000426677.2:c.339T>C	19.37:g.45395714T>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_001128917	Q86VW4|Q8WY09|Q8WY10|Q8WY11|Q9BR95	Silent	SNP	ENST00000426677.2	37	CCDS12646.1																																																																																			T|0.698;C|0.302	0.302	strong		0.547	TOMM40-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453241.1		
MYO7A	4647	hgsc.bcm.edu	37	11	76924066	76924066	+	Missense_Mutation	SNP	G	G	A	rs1132036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76924066G>A	ENST00000409709.3	+	47	6696	c.6424G>A	c.(6424-6426)Gat>Aat	p.D2142N	MYO7A_ENST00000458637.2_Missense_Mutation_p.D2102N|MYO7A_ENST00000409619.2_Missense_Mutation_p.D2093N|MYO7A_ENST00000605744.1_3'UTR	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2142	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.		D -> N (in dbSNP:rs1132036).		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						CAGCCTCATCGATCCCAAAAC	0.532													G|||	151	0.0301518	0.1089	0.0086	5008	,	,		20348	0.0		0.001	False		,,,				2504	0.0				p.D2142N		Atlas-SNP	.											MYO7A,rectum,carcinoma,0,1	MYO7A	164	1	0			c.G6424A						scavenged	.	G	ASN/ASP,ASN/ASP	312,3634		18,276,1679	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6424,6304	3.8	0.9	11	dbSNP_86	57	2,8300		0,2,4149	yes	missense,missense	MYO7A	NM_000260.3,NM_001127180.1	23,23	18,278,5828	AA,AG,GG		0.0241,7.9067,2.5637	benign,benign	2142/2216,2102/2176	76924066	314,11934	1973	4151	6124	SO:0001583	missense	4647	exon47			CTCATCGATCCCA	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.6424G>A	11.37:g.76924066G>A	ENSP00000386331:p.Asp2142Asn	Somatic	86	1	0.0116279		WXS	Illumina HiSeq	Phase_I	67	23	0.343284	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	57	0.0260989010989011	52	0.10569105691056911	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.65	2.300715	0.40694	0.079067	2.41E-4	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	4.74	3.83	0.44106	FERM domain (1);Pleckstrin homology-type (1);	0.201491	0.49916	D	0.000122	T	0.02649	0.0080	N	0.20328	0.56	0.58432	D	0.999998	B;B	0.31485	0.068;0.325	B;B	0.20384	0.014;0.029	T	0.05146	-1.0903	10	0.24483	T	0.36	.	13.242	0.60002	0.0776:0.0:0.9224:0.0	rs1132036;rs3192425;rs7117511;rs11546951;rs17417614;rs52822228;rs1132036	2102;2142	F8VUN5;Q13402	.;MYO7A_HUMAN	N	2142;2102;2093;1315;2141;2111;2018;1284	ENSP00000386331:D2142N;ENSP00000392185:D2102N;ENSP00000386635:D2093N;ENSP00000417017:D1284N	ENSP00000345075:D2018N	D	+	1	0	MYO7A	76601714	1.000000	0.71417	0.932000	0.37286	0.858000	0.48976	5.057000	0.64294	1.117000	0.41842	0.585000	0.79938	GAT	G|0.966;A|0.034	0.034	strong		0.532	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
EYS	346007	hgsc.bcm.edu	37	6	65301787	65301787	+	Missense_Mutation	SNP	G	G	C	rs12663622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301787G>C	ENST00000370621.3	-	26	4499	c.3973C>G	c.(3973-3975)Caa>Gaa	p.Q1325E	EYS_ENST00000370616.2_Missense_Mutation_p.Q1325E|EYS_ENST00000503581.1_Missense_Mutation_p.Q1325E			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1325			Q -> E. {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.Q1325E(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						ATCAGTTCTTGGAGTAAGTAG	0.438													C|||	470	0.0938498	0.0151	0.1182	5008	,	,		18617	0.1567		0.0984	False		,,,				2504	0.1135				p.Q1325E		Atlas-SNP	.											EYS_ENST00000370621,NS,carcinoma,0,1	EYS	527	1	1	Substitution - Missense(1)	stomach(1)	c.C3973G						PASS	.	C	GLU/GLN	49,1335		1,47,644	106.0	95.0	98.0		3973	-2.6	0.0	6	dbSNP_120	98	446,2734		41,364,1185	yes	missense	EYS	NM_001142800.1	29	42,411,1829	CC,CG,GG		14.0252,3.5405,10.8457	benign	1325/3145	65301787	495,4069	692	1590	2282	SO:0001583	missense	346007	exon26			GTTCTTGGAGTAA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.3973C>G	6.37:g.65301787G>C	ENSP00000359655:p.Gln1325Glu	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	49	49	1	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		213	0.09752747252747253	5	0.01016260162601626	44	0.12154696132596685	85	0.1486013986013986	79	0.10422163588390501	C	0.023	-1.398118	0.01175	0.035405	0.140252	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.82255	-1.59;-1.58;-1.58	5.62	-2.6	0.06190	.	.	.	.	.	T	0.36248	0.0960	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	0.02190	-1.1198	8	0.10636	T	0.68	.	8.1349	0.31048	0.0:0.3662:0.1081:0.5256	rs12663622;rs17217973;rs56471280;rs12663622	1325;1325	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	E	1325	ENSP00000424243:Q1325E;ENSP00000359655:Q1325E;ENSP00000359650:Q1325E	ENSP00000359650:Q1325E	Q	-	1	0	EYS	65358508	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.151000	0.03175	-1.430000	0.01985	-1.622000	0.00790	CAA	G|0.905;C|0.095	0.095	strong		0.438	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
RYR1	6261	hgsc.bcm.edu	37	19	38991516	38991516	+	Silent	SNP	G	G	A	rs2228072	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38991516G>A	ENST00000359596.3	+	47	7500	c.7500G>A	c.(7498-7500)gcG>gcA	p.A2500A	RYR1_ENST00000355481.4_Silent_p.A2500A|RYR1_ENST00000360985.3_Silent_p.A2500A			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	2500	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	ACCACAAGGCGTCCATGGTGC	0.637													g|||	755	0.150759	0.1339	0.1124	5008	,	,		18488	0.1776		0.0845	False		,,,				2504	0.2413				p.A2500A		Atlas-SNP	.											.	RYR1	708	.	0			c.G7500A						PASS	.	A	,	527,3879	241.5+/-251.9	27,473,1703	103.0	70.0	81.0		7500,7500	-8.4	0.7	19	dbSNP_98	81	742,7858	179.0+/-228.3	33,676,3591	no	coding-synonymous,coding-synonymous	RYR1	NM_000540.2,NM_001042723.1	,	60,1149,5294	AA,AG,GG		8.6279,11.961,9.757	,	2500/5039,2500/5034	38991516	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	6261	exon47			CAAGGCGTCCATG	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.7500G>A	19.37:g.38991516G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	145	58	0.4	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Silent	SNP	ENST00000359596.3	37	CCDS33011.1																																																																																			A|0.101;G|0.899	0.101	strong		0.637	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
LIPN	643418	hgsc.bcm.edu	37	10	90524237	90524237	+	Silent	SNP	T	T	C	rs430517	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90524237T>C	ENST00000404459.1	+	3	297	c.297T>C	c.(295-297)gcT>gcC	p.A99A		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	99					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		AGAATTATGCTAATGGAAGCC	0.488													C|||	1356	0.270767	0.2428	0.2954	5008	,	,		17144	0.3502		0.2207	False		,,,				2504	0.2607				p.A99A		Atlas-SNP	.											.	LIPN	28	.	0			c.T297C						PASS	.	C		1014,2780		141,732,1024	87.0	87.0	87.0		297	3.6	1.0	10	dbSNP_80	87	1859,6413		241,1377,2518	no	coding-synonymous	LIPN	NM_001102469.1		382,2109,3542	CC,CT,TT		22.4734,26.7264,23.8107		99/399	90524237	2873,9193	1897	4136	6033	SO:0001819	synonymous_variant	643418	exon3			TTATGCTAATGGA		CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"""lipase-like, ab-hydrolase domain containing 4"""	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.297T>C	10.37:g.90524237T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	31	0.418919	NM_001102469	A7KIH9	Silent	SNP	ENST00000404459.1	37	CCDS44456.1																																																																																			T|0.738;C|0.262	0.262	strong		0.488	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751	
F11	2160	hgsc.bcm.edu	37	4	187195373	187195373	+	Silent	SNP	C	C	T	rs5973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187195373C>T	ENST00000403665.2	+	5	781	c.429C>T	c.(427-429)gaC>gaT	p.D143D	F11_ENST00000492972.2_Silent_p.D143D|F11_ENST00000264692.4_Intron	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	143	Apple 2. {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)	GCACGGATGACGTCCACTGCC	0.483													C|||	315	0.0628994	0.1853	0.0418	5008	,	,		18531	0.0		0.0358	False		,,,				2504	0.0051				p.D143D		Atlas-SNP	.											.	F11	65	.	0			c.C429T						PASS	.	C		647,3759	277.2+/-273.6	51,545,1607	171.0	139.0	150.0		429	-1.3	0.0	4	dbSNP_52	150	249,8351	98.4+/-159.9	5,239,4056	no	coding-synonymous	F11	NM_000128.3		56,784,5663	TT,TC,CC		2.8953,14.6845,6.8891		143/626	187195373	896,12110	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon5			GGATGACGTCCAC	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.429C>T	4.37:g.187195373C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	198	94	0.474747	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1																																																																																			C|0.938;T|0.062	0.062	strong		0.483	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4		
KANSL1	284058	hgsc.bcm.edu	37	17	44109474	44109474	+	Missense_Mutation	SNP	G	G	A	rs7220988	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:44109474G>A	ENST00000262419.6	-	14	3499	c.3029C>T	c.(3028-3030)cCg>cTg	p.P1010L	KANSL1_ENST00000574590.1_Missense_Mutation_p.P1010L|KANSL1_ENST00000432791.1_Missense_Mutation_p.P1010L|KANSL1_ENST00000572904.1_Missense_Mutation_p.P1010L|KANSL1_ENST00000393476.3_Missense_Mutation_p.P304L|KANSL1_ENST00000575318.1_Missense_Mutation_p.P946L	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	1010	Sufficient for interaction with KAT8.		P -> L (in dbSNP:rs7220988). {ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		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)											TAAGTGTCGCGGAGTGTCCCG	0.597													G|||	1567	0.312899	0.2186	0.2651	5008	,	,		13953	0.1062		0.3579	False		,,,				2504	0.6411				p.P1010L		Atlas-SNP	.											.	.	.	.	0			c.C3029T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	1093,3313	393.5+/-328.9	121,851,1231	62.0	60.0	60.0		3026,3029,3029	4.6	1.0	17	dbSNP_116	60	3412,5188	502.6+/-375.7	702,2008,1590	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	98,98,98	823,2859,2821	AA,AG,GG		39.6744,24.8071,34.6379	benign,benign,benign	1009/1105,1010/1106,1010/1106	44109474	4505,8501	2203	4300	6503	SO:0001583	missense	284058	exon14			TGTCGCGGAGTGT	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.3029C>T	17.37:g.44109474G>A	ENSP00000262419:p.Pro1010Leu	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	537	0.24587912087912087	110	0.22357723577235772	105	0.2900552486187845	54	0.0944055944055944	268	0.35356200527704484	G	14.23	2.474360	0.43942	0.248071	0.396744	ENSG00000120071	ENST00000262419;ENST00000432791;ENST00000393476	T;T;T	0.39997	1.05;1.05;1.05	5.72	4.63	0.57726	.	0.394200	0.25402	N	0.030934	T	0.00012	0.0000	N	0.02539	-0.55	0.33231	P	0.444067	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	0.42849	-0.9427	9	0.07990	T	0.79	-1.2731	6.9006	0.24281	0.807:0.0:0.193:0.0	rs7220988;rs17298984;rs52815397;rs60940197;rs7220988	278;341;1010;1010	B3KT49;Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;.;K1267_HUMAN	L	1010;1010;304	ENSP00000262419:P1010L;ENSP00000387393:P1010L;ENSP00000377117:P304L	ENSP00000262419:P1010L	P	-	2	0	KIAA1267	41465321	0.949000	0.32298	0.984000	0.44739	0.979000	0.70002	3.997000	0.57016	0.995000	0.38917	0.561000	0.74099	CCG	G|0.694;A|0.306	0.306	strong		0.597	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443	
MICAL2	9645	hgsc.bcm.edu	37	11	12248590	12248590	+	Missense_Mutation	SNP	A	A	G	rs35228638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12248590A>G	ENST00000256194.4	+	15	2195	c.1907A>G	c.(1906-1908)tAt>tGt	p.Y636C	MICAL2_ENST00000379612.3_Missense_Mutation_p.Y636C|MICAL2_ENST00000342902.5_Missense_Mutation_p.Y636C|MICAL2_ENST00000537344.1_Missense_Mutation_p.Y636C|MICAL2_ENST00000527546.1_Missense_Mutation_p.Y636C	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	636					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)		CGCAAAAACTATGGAGAAAAT	0.453													A|||	12	0.00239617	0.0	0.0014	5008	,	,		21389	0.0		0.0109	False		,,,				2504	0.0				p.Y636C		Atlas-SNP	.											.	MICAL2	114	.	0			c.A1907G						PASS	.	A	CYS/TYR	13,4389	19.1+/-41.9	0,13,2188	111.0	101.0	104.0		1907	3.8	1.0	11	dbSNP_126	104	97,8491	54.0+/-114.7	2,93,4199	yes	missense	MICAL2	NM_014632.2	194	2,106,6387	GG,GA,AA		1.1295,0.2953,0.8468	benign	636/1125	12248590	110,12880	2201	4294	6495	SO:0001583	missense	9645	exon15			AAAACTATGGAGA	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.1907A>G	11.37:g.12248590A>G	ENSP00000256194:p.Tyr636Cys	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	124	51	0.41129	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	7.192	0.591637	0.13812	0.002953	0.011295	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.24	4.88	3.75	0.43078	.	0.567421	0.17466	N	0.173256	T	0.40222	0.1108	L	0.44542	1.39	0.31618	N	0.650676	B;B;B;B;B;B	0.10296	0.003;0.001;0.001;0.0;0.001;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.001;0.001	T	0.50457	-0.8826	10	0.46703	T	0.11	.	10.4565	0.44553	0.9224:0.0:0.0776:0.0	rs35228638	169;636;636;636;636;636	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	C	636;169;636;636;636;636	ENSP00000441689:Y636C;ENSP00000256194:Y636C;ENSP00000433965:Y636C;ENSP00000344894:Y636C;ENSP00000368932:Y636C	ENSP00000256194:Y636C	Y	+	2	0	MICAL2	12205166	1.000000	0.71417	0.977000	0.42913	0.336000	0.28762	4.903000	0.63272	0.881000	0.35993	0.533000	0.62120	TAT	A|0.992;G|0.008	0.008	strong		0.453	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
NDST1	3340	hgsc.bcm.edu	37	5	149919739	149919739	+	Silent	SNP	G	G	C	rs1290147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149919739G>C	ENST00000261797.6	+	8	2164	c.1662G>C	c.(1660-1662)acG>acC	p.T554T	NDST1_ENST00000523767.1_Silent_p.T554T	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	554	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)			ACTCCTGGACGAACCTCCGGC	0.607													C|||	4041	0.806909	0.969	0.7233	5008	,	,		21713	0.7808		0.673	False		,,,				2504	0.8119				p.T554T		Atlas-SNP	.											NDST1,NS,carcinoma,+1,1	NDST1	79	1	0			c.G1662C						PASS	.	C		4066,340	177.3+/-206.3	1877,312,14	76.0	68.0	71.0		1662	3.5	1.0	5	dbSNP_87	71	5630,2970	461.9+/-365.5	1830,1970,500	no	coding-synonymous	NDST1	NM_001543.4		3707,2282,514	CC,CG,GG		34.5349,7.7167,25.4498		554/883	149919739	9696,3310	2203	4300	6503	SO:0001819	synonymous_variant	3340	exon8			CTGGACGAACCTC	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.1662G>C	5.37:g.149919739G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	126	125	0.992063	NM_001543	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																			G|0.238;C|0.762	0.762	strong		0.607	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12921110	12921110	+	Missense_Mutation	SNP	A	A	G	rs12139546	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12921110A>G	ENST00000240189.2	+	4	988	c.901A>G	c.(901-903)Act>Gct	p.T301A		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	301			T -> A (in dbSNP:rs12139546).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTTGGAATTAACTTGTGGCAA	0.483													.|||	544	0.108626	0.1271	0.098	5008	,	,		22266	0.128		0.1074	False		,,,				2504	0.0726				p.T301A		Atlas-SNP	.											PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	0			c.A901G						PASS	.	A	ALA/THR	621,3781	261.3+/-264.2	70,481,1650	106.0	109.0	108.0		901	0.8	0.0	1	dbSNP_120	108	968,7624	204.4+/-247.1	75,818,3403	yes	missense	PRAMEF2	NM_023014.1	58	145,1299,5053	GG,GA,AA		11.2663,14.1072,12.2287	possibly-damaging	301/475	12921110	1589,11405	2201	4296	6497	SO:0001583	missense	65122	exon4			GAATTAACTTGTG		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.901A>G	1.37:g.12921110A>G	ENSP00000240189:p.Thr301Ala	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	133	6	0.0451128	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	232	0.10622710622710622	45	0.09146341463414634	36	0.09944751381215469	62	0.10839160839160839	89	0.11741424802110818	A	10.84	1.463907	0.26335	0.141072	0.112663	ENSG00000120952	ENST00000240189	T	0.51817	0.69	0.824	0.824	0.18818	.	0.135173	0.49916	D	0.000126	T	0.00440	0.0014	M	0.76727	2.345	0.80722	P	0.0	P	0.42337	0.776	P	0.46659	0.523	T	0.03576	-1.1023	9	0.46703	T	0.11	.	3.9396	0.09321	1.0:0.0:0.0:0.0	rs12139546	301	O60811	PRAM2_HUMAN	A	301	ENSP00000240189:T301A	ENSP00000240189:T301A	T	+	1	0	PRAMEF2	12843697	0.001000	0.12720	0.002000	0.10522	0.052000	0.14988	0.189000	0.17037	0.624000	0.30286	0.145000	0.16022	ACT	A|0.887;G|0.113	0.113	strong		0.483	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
AKAP12	9590	hgsc.bcm.edu	37	6	151674270	151674270	+	Missense_Mutation	SNP	G	G	A	rs34713284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151674270G>A	ENST00000253332.1	+	3	4933	c.4744G>A	c.(4744-4746)Gtg>Atg	p.V1582M	AKAP12_ENST00000402676.2_Missense_Mutation_p.V1582M|AKAP12_ENST00000354675.6_Missense_Mutation_p.V1484M|AKAP12_ENST00000359755.5_Missense_Mutation_p.V1477M			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1582				V -> M (in Ref. 4; CAH18338 and 7; AAA35931). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		ACAAGCTCACGTGATAAAAGC	0.483													G|||	395	0.0788738	0.0537	0.0764	5008	,	,		22475	0.0099		0.0895	False		,,,				2504	0.1748				p.V1582M	Melanoma(141;1616 1805 10049 24534 51979)	Atlas-SNP	.											.	AKAP12	170	.	0			c.G4744A						PASS	.	G	MET/VAL,MET/VAL	225,4181	136.5+/-172.5	1,223,1979	86.0	86.0	86.0		4744,4450	-5.1	0.0	6	dbSNP_126	86	773,7827	183.7+/-231.9	31,711,3558	yes	missense,missense	AKAP12	NM_005100.3,NM_144497.2	21,21	32,934,5537	AA,AG,GG		8.9884,5.1067,7.6734	benign,benign	1582/1783,1484/1685	151674270	998,12008	2203	4300	6503	SO:0001583	missense	9590	exon4			GCTCACGTGATAA	U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.4744G>A	6.37:g.151674270G>A	ENSP00000253332:p.Val1582Met	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	55	8	0.145455	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	133	0.060897435897435896	30	0.06097560975609756	28	0.07734806629834254	8	0.013986013986013986	67	0.08839050131926121	G	8.712	0.912287	0.17907	0.051067	0.089884	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.08634	3.07;3.07;3.09;3.09	5.01	-5.13	0.02884	.	3.546040	0.01076	N	0.004913	T	0.01287	0.0042	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.17465	0.021;0.021;0.022	B;B;B	0.12156	0.007;0.007;0.003	T	0.44620	-0.9316	9	0.46703	T	0.11	.	2.9664	0.05909	0.1834:0.217:0.4193:0.1803	rs34713284;rs61748677	1477;1484;1582	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	M	1582;1582;1484;1477	ENSP00000384537:V1582M;ENSP00000253332:V1582M;ENSP00000346702:V1484M;ENSP00000352794:V1477M	ENSP00000253332:V1582M	V	+	1	0	AKAP12	151715963	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.048000	0.03517	-0.603000	0.05767	-2.616000	0.00158	GTG	G|0.924;A|0.076	0.076	strong		0.483	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
COL3A1	1281	hgsc.bcm.edu	37	2	189864582	189864582	+	Silent	SNP	T	T	C	rs1801184	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:189864582T>C	ENST00000304636.3	+	32	2414	c.2244T>C	c.(2242-2244)ggT>ggC	p.G748G	COL3A1_ENST00000317840.5_Silent_p.G748G	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	748	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)	AACCAGGCGGTCCAGGTGCTG	0.473													T|||	1062	0.212061	0.2814	0.2334	5008	,	,		17179	0.0685		0.2922	False		,,,				2504	0.1687				p.G748G		Atlas-SNP	.											.	COL3A1	292	.	0			c.T2244C						PASS	.	T		1217,3189		164,889,1150	78.0	70.0	73.0		2244	-4.5	0.0	2	dbSNP_89	73	2489,6107		383,1723,2192	no	coding-synonymous	COL3A1	NM_000090.3		547,2612,3342	CC,CT,TT		28.9553,27.6214,28.5033		748/1467	189864582	3706,9296	2203	4298	6501	SO:0001819	synonymous_variant	1281	exon32			AGGCGGTCCAGGT	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.2244T>C	2.37:g.189864582T>C		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	170	169	0.994118	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|0.738;C|0.262	0.262	strong		0.473	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
NPBWR1	2831	hgsc.bcm.edu	37	8	53852871	53852871	+	Missense_Mutation	SNP	A	A	T	rs33977775	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:53852871A>T	ENST00000331251.3	+	1	1881	c.404A>T	c.(403-405)tAc>tTc	p.Y135F		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	135			Y -> F (in dbSNP:rs33977775).		G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCCGACCGCTACCTGGTGGTG	0.667													A|||	436	0.0870607	0.0038	0.085	5008	,	,		16505	0.12		0.1302	False		,,,				2504	0.1227				p.Y135F		Atlas-SNP	.											.	NPBWR1	38	.	0			c.A404T						PASS	.	A	PHE/TYR	131,4271		3,125,2073	28.0	29.0	29.0		404	5.1	1.0	8	dbSNP_126	29	1016,7574		60,896,3339	yes	missense	NPBWR1	NM_005285.3	22	63,1021,5412	TT,TA,AA		11.8277,2.9759,8.8285	probably-damaging	135/329	53852871	1147,11845	2201	4295	6496	SO:0001583	missense	2831	exon1			ACCGCTACCTGGT	BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.404A>T	8.37:g.53852871A>T	ENSP00000330284:p.Tyr135Phe	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	57	24	0.421053	NM_005285	Q6NTC7	Missense_Mutation	SNP	ENST00000331251.3	37	CCDS6151.1	205	0.09386446886446886	5	0.01016260162601626	34	0.09392265193370165	70	0.12237762237762238	96	0.1266490765171504	A	27.3	4.816662	0.90790	0.029759	0.118277	ENSG00000183729	ENST00000331251	D	0.87029	-2.2	5.06	5.06	0.68205	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49305	D	0.000144	T	0.16385	0.0394	M	0.78801	2.425	0.21416	P	0.999690328	D	0.89917	1.0	D	0.91635	0.999	T	0.61232	-0.7104	9	0.87932	D	0	.	14.9709	0.71232	1.0:0.0:0.0:0.0	rs33977775	135	P48145	NPBW1_HUMAN	F	135	ENSP00000330284:Y135F	ENSP00000330284:Y135F	Y	+	2	0	NPBWR1	54015424	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.875000	0.75551	2.120000	0.65058	0.533000	0.62120	TAC	A|0.907;T|0.093	0.093	strong		0.667	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
CFAP44	55779	hgsc.bcm.edu	37	3	113145006	113145006	+	Silent	SNP	C	C	T	rs73239107	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113145006C>T	ENST00000295868.2	-	4	534	c.372G>A	c.(370-372)ctG>ctA	p.L124L	WDR52-AS1_ENST00000473329.1_RNA|WDR52-AS1_ENST00000498480.1_RNA|WDR52_ENST00000393845.2_Silent_p.L124L	NM_018338.3	NP_060808.2														breast(2)|central_nervous_system(3)|endometrium(3)|kidney(5)|large_intestine(7)|lung(26)|prostate(1)|urinary_tract(2)	49						TGTTTGAATCCAGAGTCACAA	0.403													C|||	1050	0.209665	0.0159	0.2421	5008	,	,		19072	0.4067		0.2107	False		,,,				2504	0.2444				p.L124L		Atlas-SNP	.											.	WDR52	151	.	0			c.G372A						PASS	.	C	,	233,4173	138.8+/-174.5	5,223,1975	235.0	238.0	237.0		372,372	-11.7	0.0	3	dbSNP_130	237	1633,6967	301.3+/-305.4	155,1323,2822	no	coding-synonymous,coding-synonymous	WDR52	NM_001164496.1,NM_018338.3	,	160,1546,4797	TT,TC,CC		18.9884,5.2882,14.3472	,	124/1855,124/983	113145006	1866,11140	2203	4300	6503	SO:0001819	synonymous_variant	55779	exon4			TGAATCCAGAGTC																												ENST00000295868.2:c.372G>A	3.37:g.113145006C>T		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	192	93	0.484375	NM_001164496		Silent	SNP	ENST00000295868.2	37	CCDS2972.1																																																																																			C|0.832;T|0.168	0.168	strong		0.403	WDR52-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354128.3		
VWA3A	146177	hgsc.bcm.edu	37	16	22137603	22137603	+	Missense_Mutation	SNP	G	G	A	rs55732851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:22137603G>A	ENST00000389398.5	+	17	1733	c.1637G>A	c.(1636-1638)tGt>tAt	p.C546Y	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	546	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		AACAAGGACTGTTTCAACCTC	0.537													g|||	466	0.0930511	0.1914	0.0793	5008	,	,		17791	0.0506		0.0626	False		,,,				2504	0.045				p.C546Y		Atlas-SNP	.											.	VWA3A	115	.	0			c.G1637A						PASS	.	G	TYR/CYS	671,3365		57,557,1404	111.0	112.0	112.0		1637	-9.9	0.0	16	dbSNP_129	112	640,7712		27,586,3563	yes	missense	VWA3A	NM_173615.3	194	84,1143,4967	AA,AG,GG		7.6628,16.6254,10.5828	benign	546/1185	22137603	1311,11077	2018	4176	6194	SO:0001583	missense	146177	exon17			AGGACTGTTTCAA	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.1637G>A	16.37:g.22137603G>A	ENSP00000374049:p.Cys546Tyr	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	144	71	0.493056	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	210	0.09615384615384616	112	0.22764227642276422	32	0.08839779005524862	20	0.03496503496503497	46	0.06068601583113457	g	0.004	-2.287083	0.00248	0.166254	0.076628	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.20881	2.04	4.97	-9.94	0.00449	.	1.202480	0.05532	N	0.564148	T	0.00012	0.0000	N	0.13043	0.29	0.31162	P	0.704214	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.30621	-0.9972	9	0.02654	T	1	.	0.4202	0.00455	0.2611:0.259:0.242:0.2379	rs55732851	546;170	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	Y	546;169	ENSP00000374049:C546Y	ENSP00000299840:C169Y	C	+	2	0	VWA3A	22045104	0.002000	0.14202	0.033000	0.17914	0.491000	0.33493	-1.206000	0.03011	-2.453000	0.00541	-2.230000	0.00291	TGT	G|0.908;A|0.092	0.092	strong		0.537	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
SCN1B	6324	hgsc.bcm.edu	37	19	35524944	35524944	+	Intron	SNP	G	G	C	rs67486287	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35524944G>C	ENST00000262631.5	+	3	585				SCN1B_ENST00000415950.3_Missense_Mutation_p.R250T|CTD-2527I21.9_ENST00000601692.1_RNA|SCN1B_ENST00000595652.1_Intron|SCN1B_ENST00000596348.1_Intron	NM_001037.4	NP_001028.1	Q07699	SCN1B_HUMAN	sodium channel, voltage-gated, type I, beta subunit						axon guidance (GO:0007411)|cardiac conduction (GO:0061337)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cell adhesion (GO:0007155)|corticospinal neuron axon guidance (GO:0021966)|locomotion (GO:0040011)|membrane depolarization (GO:0051899)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during Purkinje myocyte cell action potential (GO:0086047)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to pyrethroid (GO:0046684)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	extracellular region (GO:0005576)|intercalated disc (GO:0014704)|node of Ranvier (GO:0033268)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	sodium channel inhibitor activity (GO:0019871)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)|voltage-gated sodium channel activity involved in Purkinje myocyte action potential (GO:0086062)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(3)	11	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)		Valproic Acid(DB00313)|Zonisamide(DB00909)	ctgagccaaagggttgtcctg	0.557													G|||	597	0.119209	0.0582	0.1297	5008	,	,		21167	0.1825		0.1461	False		,,,				2504	0.1012				p.R250T		Atlas-SNP	.											.	SCN1B	32	.	0			c.G749C						PASS	.	G	,THR/ARG	136,2124		5,126,999	91.0	102.0	99.0		,749	1.8	0.0	19	dbSNP_130	99	639,3757		42,555,1601	yes	intron,missense	SCN1B	NM_001037.4,NM_199037.3	,71	47,681,2600	CC,CG,GG		14.5359,6.0177,11.6436	,benign	,250/269	35524944	775,5881	1130	2198	3328	SO:0001627	intron_variant	6324	exon3			GCCAAAGGGTTGT		CCDS12441.1, CCDS46047.1	19q13.12	2014-09-17	2012-02-28		ENSG00000105711	ENSG00000105711		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10586	protein-coding gene	gene with protein product		600235	"""sodium channel, voltage-gated, type I, beta polypeptide"", ""sodium channel, voltage-gated, type I, beta"""			8394762	Standard	NM_001037		Approved		uc002nxo.2	Q07699	OTTHUMG00000182472	ENST00000262631.5:c.448+301G>C	19.37:g.35524944G>C		Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	238	115	0.483193	NM_199037	Q5TZZ4|Q6TN97	Missense_Mutation	SNP	ENST00000262631.5	37	CCDS12441.1	282	0.12912087912087913	24	0.04878048780487805	49	0.13535911602209943	93	0.16258741258741258	116	0.15303430079155672	G	11.85	1.761724	0.31228	0.060177	0.145359	ENSG00000105711	ENST00000415950	D	0.90004	-2.6	2.9	1.84	0.25277	.	.	.	.	.	T	0.00936	0.0031	.	.	.	0.80722	P	0.0	B	0.28636	0.218	B	0.25140	0.058	T	0.24870	-1.0148	6	.	.	.	.	5.1292	0.14901	0.1738:0.0:0.8262:0.0	.	250	Q07699-2	.	T	250	ENSP00000396915:R250T	.	R	+	2	0	SCN1B	40216784	0.034000	0.19679	0.007000	0.13788	0.021000	0.10359	0.862000	0.27899	0.750000	0.32877	0.549000	0.68633	AGG	G|0.870;C|0.130	0.130	strong		0.557	SCN1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461567.1		
ALDH1A1	216	hgsc.bcm.edu	37	9	75545882	75545882	+	Silent	SNP	G	G	A	rs13959	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:75545882G>A	ENST00000297785.3	-	3	279	c.225C>T	c.(223-225)tcC>tcT	p.S75S	ALDH1A1_ENST00000482210.1_5'UTR|ALDH1A1_ENST00000376939.1_Silent_p.S75S	NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	75					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	TACGCCACGGGGATCCAATCT	0.468													A|||	2050	0.409345	0.1664	0.4885	5008	,	,		18441	0.4554		0.503	False		,,,				2504	0.5378				p.S75S		Atlas-SNP	.											.	ALDH1A1	98	.	0			c.C225T						PASS	.	A		1101,3305	720.0+/-409.0	128,845,1230	84.0	87.0	86.0		225	-1.8	1.0	9	dbSNP_52	86	4295,4305	578.0+/-390.7	1051,2193,1056	no	coding-synonymous	ALDH1A1	NM_000689.4		1179,3038,2286	AA,AG,GG		49.9419,24.9887,41.4885		75/502	75545882	5396,7610	2203	4300	6503	SO:0001819	synonymous_variant	216	exon3			CCACGGGGATCCA	K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"""Aldehyde dehydrogenases"""	402	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 1"""	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.225C>T	9.37:g.75545882G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_000689	O00768|Q5SYR1	Silent	SNP	ENST00000297785.3	37	CCDS6644.1																																																																																			G|0.598;A|0.402	0.402	strong		0.468	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1		
PCDHB14	56122	hgsc.bcm.edu	37	5	140605078	140605078	+	Silent	SNP	C	C	T	rs2907322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140605078C>T	ENST00000239449.4	+	1	2001	c.2001C>T	c.(1999-2001)tcC>tcT	p.S667S	PCDHB14_ENST00000515856.2_Silent_p.S514S	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	667	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACGGCTTCTCCCAGCCCTACC	0.701													c|||	900	0.179712	0.292	0.1412	5008	,	,		12341	0.0933		0.161	False		,,,				2504	0.1636				p.S667S	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C2001T						PASS	.						35.0	41.0	39.0					5																	140605078		2117	4180	6297	SO:0001819	synonymous_variant	56122	exon1			CTTCTCCCAGCCC	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2001C>T	5.37:g.140605078C>T		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	15	12	0.8	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.835;T|0.165	0.165	strong		0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
ADAMTS17	170691	hgsc.bcm.edu	37	15	100821467	100821467	+	Silent	SNP	G	G	A	rs7496640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:100821467G>A	ENST00000268070.4	-	4	861	c.756C>T	c.(754-756)gcC>gcT	p.A252A		NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	252	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		ACCTCTGGGCGGCCTCGGCCC	0.642													G|||	2504	0.5	0.5	0.5605	5008	,	,		14806	0.505		0.3499	False		,,,				2504	0.6063				p.A252A		Atlas-SNP	.											ADAMTS17,NS,carcinoma,0,1	ADAMTS17	127	1	0			c.C756T						PASS	.	G		2145,2261	572.9+/-383.4	517,1111,575	64.0	70.0	68.0		756	-9.6	0.9	15	dbSNP_116	68	2862,5738	445.9+/-361.1	447,1968,1885	no	coding-synonymous	ADAMTS17	NM_139057.2		964,3079,2460	AA,AG,GG		33.2791,48.6836,38.4976		252/1096	100821467	5007,7999	2203	4300	6503	SO:0001819	synonymous_variant	170691	exon4			CTGGGCGGCCTCG	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.756C>T	15.37:g.100821467G>A		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_139057	Q2I7G4|Q6ZN75	Silent	SNP	ENST00000268070.4	37	CCDS10383.1																																																																																			G|0.576;A|0.424	0.424	strong		0.642	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
LRRC16A	55604	hgsc.bcm.edu	37	6	25426768	25426768	+	Missense_Mutation	SNP	G	G	A	rs9358856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:25426768G>A	ENST00000329474.6	+	4	597	c.229G>A	c.(229-231)Gtt>Att	p.V77I	LRRC16A_ENST00000377969.3_5'UTR	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	77			V -> I (in dbSNP:rs9358856).		actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						TCATGGCGTCGTTTGCAGCAA	0.408													A|||	815	0.16274	0.09	0.1484	5008	,	,		19093	0.2331		0.1511	False		,,,				2504	0.2106				p.V77I		Atlas-SNP	.											.	LRRC16A	168	.	0			c.G229A						PASS	.	A	ILE/VAL,ILE/VAL	299,3583		16,267,1658	94.0	88.0	90.0		229,229	-1.4	0.0	6	dbSNP_119	90	1196,7108		87,1022,3043	yes	missense,missense	LRRC16A	NM_001173977.1,NM_017640.5	29,29	103,1289,4701	AA,AG,GG		14.4027,7.7022,12.2682	benign,benign	77/1366,77/1372	25426768	1495,10691	1941	4152	6093	SO:0001583	missense	55604	exon4			GGCGTCGTTTGCA	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.229G>A	6.37:g.25426768G>A	ENSP00000331983:p.Val77Ile	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	241	117	0.485477	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	350	0.16025641025641027	49	0.09959349593495935	56	0.15469613259668508	132	0.23076923076923078	113	0.14907651715039577	A	5.636	0.301961	0.10678	0.077022	0.144027	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.14516	2.5	5.54	-1.37	0.09056	.	1.154350	0.06291	N	0.699218	T	0.01287	0.0042	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	0.45600	-0.9250	9	0.36615	T	0.2	.	1.8191	0.03106	0.4794:0.2254:0.1867:0.1084	rs9358856;rs58242797;rs9358856	77;77;77	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	I	77	ENSP00000331983:V77I	ENSP00000331983:V77I	V	+	1	0	LRRC16A	25534747	0.000000	0.05858	0.001000	0.08648	0.263000	0.26337	0.227000	0.17795	-0.844000	0.04184	-1.530000	0.00923	GTT	G|0.846;A|0.154	0.154	strong		0.408	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
PLA2G7	7941	hgsc.bcm.edu	37	6	46679303	46679303	+	Missense_Mutation	SNP	A	A	G	rs1805018	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:46679303A>G	ENST00000274793.7	-	7	789	c.593T>C	c.(592-594)aTa>aCa	p.I198T	PLA2G7_ENST00000541026.1_Missense_Mutation_p.I71T|PLA2G7_ENST00000537365.1_Missense_Mutation_p.I198T|PLA2G7_ENST00000538237.1_Missense_Mutation_p.I153T	NM_005084.3	NP_005075.3	Q13093	PAFA_HUMAN	phospholipase A2, group VII (platelet-activating factor acetylhydrolase, plasma)	198			I -> T (common polymorphism; associated with asthma and atopy; dbSNP:rs1805018). {ECO:0000269|PubMed:10733466, ECO:0000269|Ref.3}.		cellular protein metabolic process (GO:0044267)|lipid catabolic process (GO:0016042)|lipid oxidation (GO:0034440)|low-density lipoprotein particle remodeling (GO:0034374)|plasma lipoprotein particle oxidation (GO:0034441)|positive regulation of inflammatory response (GO:0050729)|positive regulation of monocyte chemotaxis (GO:0090026)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|low-density lipoprotein particle (GO:0034362)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|skin(1)|soft_tissue(1)	14			Lung(136;0.192)			CTTGTCCCCTATTTCTGCAGC	0.418													A|||	667	0.133187	0.2557	0.0317	5008	,	,		18840	0.129		0.0547	False		,,,				2504	0.1247				p.I198T		Atlas-SNP	.											.	PLA2G7	49	.	0			c.T593C	GRCh37	CM001308	PLA2G7	M	rs1805018	PASS	.	A	THR/ILE,THR/ILE	940,3466	358.1+/-314.2	101,738,1364	241.0	217.0	225.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	593,593	-7.6	0.0	6	dbSNP_89	225	438,8162	133.1+/-190.7	18,402,3880	yes	missense,missense	PLA2G7	NM_001168357.1,NM_005084.3	89,89	119,1140,5244	GG,GA,AA		5.093,21.3345,10.5951	benign,benign	198/442,198/442	46679303	1378,11628	2203	4300	6503	SO:0001583	missense	7941	exon7			TCCCCTATTTCTG	U20157	CCDS4917.1	6p21.2-p12	2008-09-19			ENSG00000146070	ENSG00000146070	3.1.1.4		9040	protein-coding gene	gene with protein product		601690				7700381, 8624782	Standard	NM_005084		Approved	PAFAH, LDL-PLA2	uc021zae.1	Q13093	OTTHUMG00000014789	ENST00000274793.7:c.593T>C	6.37:g.46679303A>G	ENSP00000274793:p.Ile198Thr	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	148	60	0.405405	NM_005084	A5HTT5|Q15692|Q5VTT1|Q8IVA2	Missense_Mutation	SNP	ENST00000274793.7	37	CCDS4917.1	279	0.12774725274725274	131	0.266260162601626	13	0.03591160220994475	87	0.1520979020979021	48	0.0633245382585752	A	4.680	0.126470	0.08931	0.213345	0.05093	ENSG00000146070	ENST00000274793;ENST00000537365;ENST00000538237;ENST00000541026	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.05	-7.6	0.01303	.	1.215970	0.05387	N	0.538317	T	0.12390	0.0301	L	0.38531	1.155	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.12915	-1.0529	9	0.19147	T	0.46	.	8.1166	0.30946	0.1521:0.1102:0.611:0.1266	rs1805018;rs52817955;rs60619452;rs1805018	71;153;198;198	B4DLM5;F5GYY6;A8K2W6;Q13093	.;.;.;PAFA_HUMAN	T	198;198;153;71	ENSP00000274793:I198T;ENSP00000445666:I198T;ENSP00000441416:I153T;ENSP00000444164:I71T	ENSP00000274793:I198T	I	-	2	0	PLA2G7	46787262	0.000000	0.05858	0.000000	0.03702	0.158000	0.22134	-1.095000	0.03356	-0.911000	0.03843	-0.379000	0.06801	ATA	A|0.878;G|0.122	0.122	strong		0.418	PLA2G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040802.1		
FAM221B	392307	hgsc.bcm.edu	37	9	35826058	35826058	+	Missense_Mutation	SNP	T	T	C	rs13294256	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35826058T>C	ENST00000423537.2	-	2	370	c.101A>G	c.(100-102)cAt>cGt	p.H34R	TMEM8B_ENST00000377996.1_Intron	NM_001012446.3	NP_001012448.2	A6H8Z2	F221B_HUMAN	family with sequence similarity 221, member B	34			H -> R (in dbSNP:rs13294256). {ECO:0000269|PubMed:15489334}.							endometrium(2)|kidney(1)|lung(4)	7						TTCAGAGATATGGTTCTCCTG	0.517											OREG0019180	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	1148	0.229233	0.208	0.1988	5008	,	,		20257	0.375		0.1998	False		,,,				2504	0.1595				p.H34R		Atlas-SNP	.											.	FAM221B	38	.	0			c.A101G						PASS	.		ARG/HIS	731,3079		78,575,1252	75.0	76.0	76.0		101	-4.1	0.0	9	dbSNP_121	76	1570,6650		146,1278,2686	yes	missense	C9orf128	NM_001012446.2	29	224,1853,3938	CC,CT,TT		19.0998,19.1864,19.1272	benign	34/403	35826058	2301,9729	1905	4110	6015	SO:0001583	missense	392307	exon2			GAGATATGGTTCT	BX648702	CCDS43799.1, CCDS43799.2	9p13.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000204930	ENSG00000204930			30762	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 128"""	C9orf128			Standard	NM_001012446		Approved		uc010mlc.2	A6H8Z2	OTTHUMG00000019880	ENST00000423537.2:c.101A>G	9.37:g.35826058T>C	ENSP00000415299:p.His34Arg	Somatic	80	0	0	858	WXS	Illumina HiSeq	Phase_I	73	29	0.39726	NM_001012446	Q5TCW2	Missense_Mutation	SNP	ENST00000423537.2	37	CCDS43799.2	551	0.2522893772893773	105	0.21341463414634146	82	0.2265193370165746	220	0.38461538461538464	144	0.18997361477572558	t	5.958	0.360791	0.11296	0.191864	0.190998	ENSG00000204930	ENST00000423537;ENST00000377984;ENST00000472182	T;T;T	0.29397	2.6;2.33;1.57	3.8	-4.13	0.03904	.	1.108070	0.06941	N	0.812752	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	9	0.08381	T	0.77	-20.1312	1.2171	0.01916	0.2466:0.1181:0.1707:0.4646	rs13294256;rs59381554	34	A6H8Z2	CI128_HUMAN	R	34	ENSP00000415299:H34R;ENSP00000367222:H34R;ENSP00000420279:H34R	ENSP00000367222:H34R	H	-	2	0	C9orf128	35816058	0.000000	0.05858	0.000000	0.03702	0.318000	0.28184	-3.012000	0.00647	-1.431000	0.01982	-2.108000	0.00357	CAT	T|0.764;C|0.236	0.236	strong		0.517	FAM221B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355861.1	NM_001012446	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121616250	121616250	+	Silent	SNP	G	G	A	rs4629793	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:121616250G>A	ENST00000393386.2	+	5	891	c.480G>A	c.(478-480)gcG>gcA	p.A160A	PTPRZ1_ENST00000449182.1_Silent_p.A160A	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	160	Alpha-carbonic anhydrase.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						GCTTTGATGCGGACCGATTTT	0.313													g|||	1388	0.277157	0.0514	0.353	5008	,	,		15770	0.3323		0.4722	False		,,,				2504	0.271				p.A160A		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G480A						PASS	.	A	,,	488,3918	225.9+/-241.6	36,416,1751	110.0	104.0	106.0		480,480,480	-10.9	0.0	7	dbSNP_111	106	3599,4993	518.5+/-379.3	766,2067,1463	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	802,2483,3214	AA,AG,GG		41.8878,11.0758,31.4433	,,	160/1456,160/1449,160/2316	121616250	4087,8911	2203	4296	6499	SO:0001819	synonymous_variant	5803	exon5			TGATGCGGACCGA	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.480G>A	7.37:g.121616250G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	49	45	0.918367	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			G|0.681;A|0.319	0.319	strong		0.313	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
ACOX2	8309	hgsc.bcm.edu	37	3	58517520	58517520	+	Silent	SNP	A	A	G	rs57216393	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:58517520A>G	ENST00000302819.5	-	6	894	c.603T>C	c.(601-603)caT>caC	p.H201H	ACOX2_ENST00000459701.2_Silent_p.H201H	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	201					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)		GGACCAGGGCATGGGTGGCTG	0.627													G|||	355	0.0708866	0.2262	0.0375	5008	,	,		18088	0.0		0.0189	False		,,,				2504	0.0112				p.H201H		Atlas-SNP	.											.	ACOX2	53	.	0			c.T603C						PASS	.	G		884,3522	741.6+/-411.3	92,700,1411	59.0	53.0	55.0		603	-9.4	0.1	3	dbSNP_129	55	184,8416	810.9+/-407.1	3,178,4119	no	coding-synonymous	ACOX2	NM_003500.3		95,878,5530	GG,GA,AA		2.1395,20.0635,8.2116		201/682	58517520	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			CAGGGCATGGGTG	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.603T>C	3.37:g.58517520A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	53	28	0.528302	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.923;G|0.077	0.077	strong		0.627	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
PLEKHG4B	153478	hgsc.bcm.edu	37	5	143534	143534	+	Missense_Mutation	SNP	G	G	A	rs13436090	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:143534G>A	ENST00000283426.6	+	3	709	c.659G>A	c.(658-660)cGc>cAc	p.R220H	Y_RNA_ENST00000362670.1_RNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	220			R -> H (in dbSNP:rs13436090).				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)		GTGCAGGTCCGCACCAGGAGC	0.642													G|||	755	0.150759	0.3896	0.0951	5008	,	,		19059	0.0139		0.1233	False		,,,				2504	0.0368				p.R220H		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,0,1	PLEKHG4B	167	1	0			c.G659A						scavenged	.	G	HIS/ARG	1618,2786		300,1018,884	57.0	60.0	59.0		659	2.8	0.0	5	dbSNP_121	59	1064,7526		59,946,3290	yes	missense	PLEKHG4B	NM_052909.3	29	359,1964,4174	AA,AG,GG		12.3865,36.7393,20.6403	probably-damaging	220/1272	143534	2682,10312	2202	4295	6497	SO:0001583	missense	153478	exon3			AGGTCCGCACCAG	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.659G>A	5.37:g.143534G>A	ENSP00000283426:p.Arg220His	Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	87	33	0.37931	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	331	0.15155677655677655	189	0.38414634146341464	35	0.09668508287292818	11	0.019230769230769232	96	0.1266490765171504	.	0.533	-0.857029	0.02630	0.367393	0.123865	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.21932	1.98;1.98	2.83	2.83	0.33086	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.42372	P	0.007546000000000053	D	0.54207	0.965	B	0.38156	0.266	T	0.39623	-0.9605	8	0.15066	T	0.55	.	6.0072	0.19553	0.1539:0.0:0.8461:0.0	rs13436090;rs60136113;rs13436090	220	Q96PX9	PKH4B_HUMAN	H	220;134	ENSP00000283426:R220H;ENSP00000422493:R134H	ENSP00000283426:R220H	R	+	2	0	PLEKHG4B	196534	0.997000	0.39634	0.038000	0.18304	0.017000	0.09413	2.258000	0.43249	1.273000	0.44346	0.467000	0.42956	CGC	G|0.819;A|0.181	0.181	strong		0.642	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
INADL	10207	hgsc.bcm.edu	37	1	62232130	62232130	+	Silent	SNP	T	T	C	rs11207827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:62232130T>C	ENST00000371158.2	+	4	483	c.369T>C	c.(367-369)atT>atC	p.I123I	INADL_ENST00000316485.6_Silent_p.I123I	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	123					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						ACTCAGTCATTCAACAGATGG	0.388													T|||	1284	0.25639	0.3094	0.1744	5008	,	,		15265	0.369		0.2346	False		,,,				2504	0.1493				p.I123I		Atlas-SNP	.											.	INADL	179	.	0			c.T369C						PASS	.	T		1415,2991	455.3+/-351.0	237,941,1025	86.0	84.0	85.0		369	-1.1	1.0	1	dbSNP_120	85	2102,6498	359.3+/-331.5	269,1564,2467	no	coding-synonymous	INADL	NM_176877.2		506,2505,3492	CC,CT,TT		24.4419,32.1153,27.0414		123/1802	62232130	3517,9489	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon4			AGTCATTCAACAG	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.369T>C	1.37:g.62232130T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	75	27	0.36	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			T|0.727;C|0.273	0.273	strong		0.388	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
CLCA2	9635	hgsc.bcm.edu	37	1	86909493	86909493	+	Silent	SNP	C	C	T	rs2390059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:86909493C>T	ENST00000370565.4	+	10	1674	c.1512C>T	c.(1510-1512)gtC>gtT	p.V504V		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	504					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		GTGAAAATGTCAAACCTCACC	0.383													T|||	561	0.112021	0.171	0.1081	5008	,	,		17482	0.0585		0.0934	False		,,,				2504	0.1094				p.V504V	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.C1512T						PASS	.	T		765,3641	754.9+/-412.5	69,627,1507	110.0	99.0	102.0		1512	-7.1	0.0	1	dbSNP_100	102	709,7891	787.1+/-407.6	30,649,3621	no	coding-synonymous	CLCA2	NM_006536.5		99,1276,5128	TT,TC,CC		8.2442,17.3627,11.3332		504/944	86909493	1474,11532	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon10			AAATGTCAAACCT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1512C>T	1.37:g.86909493C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			T|0.113;G|0.000;C|0.887	0.113	strong		0.383	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
COL4A4	1286	hgsc.bcm.edu	37	2	227872182	227872182	+	Silent	SNP	G	G	A	rs2228557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227872182G>A	ENST00000396625.3	-	48	5139	c.4932C>T	c.(4930-4932)ttC>ttT	p.F1644F	COL4A4_ENST00000329662.7_Silent_p.F1641F	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1644	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		ACTTATTTGCGAAAAAGTGGC	0.537													A|||	2576	0.514377	0.6369	0.4741	5008	,	,		19939	0.4048		0.4205	False		,,,				2504	0.5869				p.F1644F		Atlas-SNP	.											.	COL4A4	215	.	0			c.C4932T						PASS	.	A		2238,1660		642,954,353	187.0	197.0	193.0		4932	1.8	1.0	2	dbSNP_98	193	3379,4923		687,2005,1459	no	coding-synonymous	COL4A4	NM_000092.4		1329,2959,1812	AA,AG,GG		40.701,42.5859,46.041		1644/1691	227872182	5617,6583	1949	4151	6100	SO:0001819	synonymous_variant	1286	exon48			ATTTGCGAAAAAG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4932C>T	2.37:g.227872182G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	125	52	0.416	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			G|0.540;A|0.460	0.460	strong		0.537	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
SCN5A	6331	hgsc.bcm.edu	37	3	38674712	38674712	+	Silent	SNP	T	T	C	rs6599230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38674712T>C	ENST00000333535.4	-	2	236	c.87A>G	c.(85-87)gcA>gcG	p.A29A	SCN5A_ENST00000443581.1_Silent_p.A29A|SCN5A_ENST00000455624.2_Silent_p.A29A|SCN5A_ENST00000425664.1_Silent_p.A29A|SCN5A_ENST00000449557.2_Silent_p.A29A|SCN5A_ENST00000450102.2_Silent_p.A29A|SCN5A_ENST00000413689.1_Silent_p.A29A|SCN5A_ENST00000451551.2_Silent_p.A29A|SCN5A_ENST00000423572.2_Silent_p.A29A|SCN5A_ENST00000414099.2_Silent_p.A29A			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	29					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CTTGCTTCTCTGCCATGCGCT	0.637													t|||	3915	0.781749	0.9228	0.719	5008	,	,		17646	0.6677		0.7883	False		,,,				2504	0.7464				p.A29A		Atlas-SNP	.											.	SCN5A	634	.	0			c.A87G						PASS	.	C	,,,,,	3601,421		1604,393,14	33.0	36.0	35.0		87,87,87,87,87,87	-9.1	0.1	3	dbSNP_116	35	6703,1601		2703,1297,152	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	,,,,,	4307,1690,166	CC,CT,TT		19.2799,10.4674,16.4043	,,,,,	29/2016,29/2017,29/1999,29/1984,29/1963,29/2017	38674712	10304,2022	2011	4152	6163	SO:0001819	synonymous_variant	6331	exon2			CTTCTCTGCCATG	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.87A>G	3.37:g.38674712T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	80	80	1	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	37	CCDS46796.1																																																																																			T|0.233;C|0.767	0.767	strong		0.637	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
NOM1	64434	hgsc.bcm.edu	37	7	156762248	156762248	+	Missense_Mutation	SNP	G	G	A	rs12919	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:156762248G>A	ENST00000275820.3	+	11	2449	c.2434G>A	c.(2434-2436)Gtg>Atg	p.V812M		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	812			V -> M (in dbSNP:rs12919).			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)		AAAGCTGGGGGTGTTACGTGA	0.512													A|||	2411	0.48143	0.556	0.536	5008	,	,		16487	0.2778		0.5706	False		,,,				2504	0.4601				p.V812M		Atlas-SNP	.											NOM1,rectum,carcinoma,0,1	NOM1	73	1	0			c.G2434A						PASS	.	A	MET/VAL	2437,1969	555.5+/-379.3	672,1093,438	107.0	109.0	108.0		2434	-3.1	0.0	7	dbSNP_52	108	4907,3693	529.1+/-381.5	1388,2131,781	yes	missense	NOM1	NM_138400.1	21	2060,3224,1219	AA,AG,GG		42.9419,44.6891,43.5338	benign	812/861	156762248	7344,5662	2203	4300	6503	SO:0001583	missense	64434	exon11			CTGGGGGTGTTAC	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.2434G>A	7.37:g.156762248G>A	ENSP00000275820:p.Val812Met	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	8	8	1	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	1047	0.4793956043956044	274	0.556910569105691	199	0.5497237569060773	154	0.2692307692307692	420	0.554089709762533	A	0.021	-1.421065	0.01126	0.553109	0.570581	ENSG00000146909	ENST00000275820	T	0.11169	2.8	5.41	-3.13	0.05266	.	0.201867	0.64402	N	0.000012	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B	0.09022	0.002	B	0.08055	0.003	T	0.20009	-1.0288	9	0.15066	T	0.55	-9.8241	3.0886	0.06286	0.4413:0.1173:0.3376:0.1038	rs12919;rs17354962;rs56648938;rs61096186;rs12919	812	Q5C9Z4	NOM1_HUMAN	M	812	ENSP00000275820:V812M	ENSP00000275820:V812M	V	+	1	0	NOM1	156455009	0.011000	0.17503	0.001000	0.08648	0.280000	0.26924	-0.199000	0.09491	-1.325000	0.02269	-0.516000	0.04426	GTG	G|0.474;A|0.526	0.526	strong		0.512	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
PHLDA2	7262	hgsc.bcm.edu	37	11	2950558	2950558	+	Silent	SNP	A	A	G	rs13390	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2950558A>G	ENST00000314222.4	-	1	127	c.37T>C	c.(37-39)Ttg>Ctg	p.L13L		NM_003311.3	NP_003302.1	Q53GA4	PHLA2_HUMAN	pleckstrin homology-like domain, family A, member 2	13	PH.				apoptotic process (GO:0006915)|organ morphogenesis (GO:0009887)|placenta development (GO:0001890)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|regulation of gene expression (GO:0010468)|regulation of glycogen metabolic process (GO:0070873)	cytoplasm (GO:0005737)|membrane (GO:0016020)				central_nervous_system(1)	1		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		CGCTTCTCCAACTCGCCCTCG	0.701													A|||	355	0.0708866	0.0552	0.0879	5008	,	,		8654	0.002		0.173	False		,,,				2504	0.046				p.L13L		Atlas-SNP	.											PHLDA2,NS,carcinoma,0,1	PHLDA2	10	1	0			c.T37C						PASS	.	A		297,4093		10,277,1908	14.0	16.0	15.0		37	2.6	1.0	11	dbSNP_52	15	1543,7035		141,1261,2887	no	coding-synonymous	PHLDA2	NM_003311.3		151,1538,4795	GG,GA,AA		17.9879,6.7654,14.1888		13/153	2950558	1840,11128	2195	4289	6484	SO:0001819	synonymous_variant	7262	exon1			TCTCCAACTCGCC	AF035444	CCDS7741.1	11p15.4	2013-01-10	2003-09-26	2003-10-01	ENSG00000181649	ENSG00000181649		"""Pleckstrin homology (PH) domain containing"""	12385	protein-coding gene	gene with protein product		602131	"""tumor suppressing subtransferable candidate 3"""	TSSC3		9328465, 9403053	Standard	NM_003311		Approved	IPL, BWR1C, HLDA2	uc001lxa.1	Q53GA4	OTTHUMG00000010926	ENST00000314222.4:c.37T>C	11.37:g.2950558A>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	40	19	0.475	NM_003311	O00496	Silent	SNP	ENST00000314222.4	37	CCDS7741.1																																																																																			A|0.893;G|0.107	0.107	strong		0.701	PHLDA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030116.1	NM_003311	
NRXN1	9378	hgsc.bcm.edu	37	2	51254901	51254901	+	Silent	SNP	G	G	A	rs1045874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:51254901G>A	ENST00000406316.2	-	2	1987	c.511C>T	c.(511-513)Ctg>Ttg	p.L171L	NRXN1_ENST00000405581.1_Silent_p.L171L|NRXN1_ENST00000406859.3_Silent_p.L171L|NRXN1_ENST00000401669.2_Silent_p.L171L|NRXN1_ENST00000402717.3_Silent_p.L171L|NRXN1_ENST00000405472.3_Silent_p.L171L|NRXN1_ENST00000404971.1_Silent_p.L171L	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	171	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			ACCGAGGCCAGGGTGAGCTTG	0.677													G|||	1067	0.213059	0.4841	0.0663	5008	,	,		13008	0.1151		0.0736	False		,,,				2504	0.1953				p.L171L		Atlas-SNP	.											NRXN1_ENST00000536085,NS,carcinoma,0,3	NRXN1	1118	3	0			c.C511T						PASS	.	G	,	1545,2567		281,983,792	25.0	30.0	28.0		511,511	2.8	1.0	2	dbSNP_86	28	625,7733		33,559,3587	no	coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4	,	314,1542,4379	AA,AG,GG		7.4779,37.573,17.4018	,	171/1548,171/1478	51254901	2170,10300	2056	4179	6235	SO:0001819	synonymous_variant	9378	exon2			AGGCCAGGGTGAG	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.511C>T	2.37:g.51254901G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	163	76	0.466258	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			G|0.853;A|0.147	0.147	strong		0.677	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
SIRPB1	10326	hgsc.bcm.edu	37	20	1592265	1592265	+	Intron	SNP	A	A	G	rs45471597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1592265A>G	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Silent_p.T57T|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Silent_p.T57T|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GGATCAGGGAAGTCACAGTGC	0.557													N|||	3350	0.66893	0.739	0.5331	5008	,	,		8651	0.7669		0.5318	False		,,,				2504	0.7106				p.T57T		Atlas-SNP	.											.	SIRPB1	83	.	0			c.T171C						PASS	.						64.0	72.0	70.0					20																	1592265		447	1337	1784	SO:0001627	intron_variant	10326	exon2			CAGGGAAGTCACA	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8249T>C	20.37:g.1592265A>G		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	41	39	0.951219	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			A|0.417;G|0.583	0.583	strong		0.557	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
USP6	9098	hgsc.bcm.edu	37	17	5042715	5042715	+	Missense_Mutation	SNP	G	G	A	rs61740308	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5042715G>A	ENST00000574788.1	+	22	3474	c.1244G>A	c.(1243-1245)tGt>tAt	p.C415Y	USP6_ENST00000332776.4_Missense_Mutation_p.C415Y|USP6_ENST00000304328.5_Missense_Mutation_p.C98Y|USP6_ENST00000250066.6_Missense_Mutation_p.C415Y			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	415					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						TCCACGCCCTGTCCTGGTGGG	0.652			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								G|||	509	0.101637	0.1982	0.0375	5008	,	,		17890	0.0784		0.1153	False		,,,				2504	0.0266				p.C415Y		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.G1244A						PASS	.	G	TYR/CYS	709,3697	291.3+/-281.4	61,587,1555	45.0	49.0	48.0		1244	0.1	0.1	17	dbSNP_129	48	951,7649	207.3+/-249.1	52,847,3401	yes	missense	USP6	NM_004505.2	194	113,1434,4956	AA,AG,GG		11.0581,16.0917,12.7633	possibly-damaging	415/1407	5042715	1660,11346	2203	4300	6503	SO:0001583	missense	9098	exon14			CGCCCTGTCCTGG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1244G>A	17.37:g.5042715G>A	ENSP00000460380:p.Cys415Tyr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	80	34	0.425	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	250	0.11446886446886446	97	0.19715447154471544	16	0.04419889502762431	52	0.09090909090909091	85	0.11213720316622691	G	9.321	1.058159	0.19987	0.160917	0.110581	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.27402	2.42;2.91;1.67	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	P;P	0.42518	0.782;0.676	P;B	0.48738	0.588;0.384	T	0.24368	-1.0162	7	0.72032	D	0.01	.	.	.	.	rs61740308	98;415	P35125-2;P35125	.;UBP6_HUMAN	Y	415;415;98	ENSP00000328010:C415Y;ENSP00000250066:C415Y;ENSP00000305473:C98Y	ENSP00000250066:C415Y	C	+	2	0	USP6	4983439	0.003000	0.15002	0.063000	0.19743	0.063000	0.16089	-0.046000	0.11983	0.132000	0.18615	0.134000	0.15878	TGT	G|0.881;A|0.119	0.119	strong		0.652	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
DGKQ	1609	hgsc.bcm.edu	37	4	961397	961397	+	Silent	SNP	C	C	T	rs2305487	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:961397C>T	ENST00000273814.3	-	8	1000	c.927G>A	c.(925-927)gtG>gtA	p.V309V	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	309					blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCTTCTTCTCACCGCGTCGT	0.687													c|||	161	0.0321486	0.0015	0.0403	5008	,	,		10295	0.0605		0.0467	False		,,,				2504	0.0235				p.V309V	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.G927A						PASS	.			35,4367	40.0+/-72.8	0,35,2166	61.0	59.0	60.0		927	2.2	0.2	4	dbSNP_100	60	372,8228	121.5+/-180.6	7,358,3935	no	coding-synonymous	DGKQ	NM_001347.2		7,393,6101	TT,TC,CC		4.3256,0.7951,3.1303		309/943	961397	407,12595	2201	4300	6501	SO:0001819	synonymous_variant	1609	exon8			TCTTCTCACCGCG	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"""diacylglycerol kinase, theta (110kD)"""	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.927G>A	4.37:g.961397C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	154	66	0.428571	NM_001347	Q6P3W4	Silent	SNP	ENST00000273814.3	37	CCDS3342.1																																																																																			T|0.037;G|0.000;C|0.963	0.037	strong		0.687	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		
RELN	5649	hgsc.bcm.edu	37	7	103155864	103155864	+	Silent	SNP	A	A	G	rs56345626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:103155864A>G	ENST00000428762.1	-	50	8046	c.7887T>C	c.(7885-7887)ccT>ccC	p.P2629P	CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Silent_p.P2629P|RELN_ENST00000343529.5_Silent_p.P2629P	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	2629					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CTTTAGCATCAGGAGGGAGAA	0.478													A|||	876	0.17492	0.1339	0.1513	5008	,	,		18623	0.254		0.1849	False		,,,				2504	0.1554				p.P2629P	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T7887C						PASS	.	A	,	560,3846	245.3+/-254.3	43,474,1686	48.0	49.0	49.0		7887,7887	1.5	1.0	7	dbSNP_129	49	1643,6957	299.9+/-304.7	156,1331,2813	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	199,1805,4499	GG,GA,AA		19.1047,12.7099,16.9383	,	2629/3461,2629/3459	103155864	2203,10803	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon50			AGCATCAGGAGGG		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.7887T>C	7.37:g.103155864A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			A|0.829;G|0.171	0.171	strong		0.478	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
SVOPL	136306	hgsc.bcm.edu	37	7	138312122	138312122	+	Missense_Mutation	SNP	A	A	C	rs2305816	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:138312122A>C	ENST00000419765.3	-	11	1187	c.1154T>G	c.(1153-1155)tTc>tGc	p.F385C	SNORA40_ENST00000516379.1_RNA|SVOPL_ENST00000421622.1_Missense_Mutation_p.F265C|SVOPL_ENST00000288513.5_Missense_Mutation_p.F233C|SVOPL_ENST00000436657.1_Missense_Mutation_p.F233C|SVOPL_ENST00000463557.1_5'UTR	NM_001139456.1	NP_001132928.1	Q8N434	SVOPL_HUMAN	SVOP-like	385			F -> C (in dbSNP:rs2305816).			integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	19						GAGGAGAAGGAAGAATAAAGC	0.413													A|||	2386	0.476438	0.3533	0.5187	5008	,	,		21102	0.3452		0.7416	False		,,,				2504	0.4755				p.F385C		Atlas-SNP	.											.	SVOPL	111	.	0			c.T1154G						PASS	.	A	CYS/PHE,CYS/PHE	1775,2631	526.0+/-371.8	363,1049,791	112.0	101.0	105.0		1154,698	5.6	1.0	7	dbSNP_100	105	6365,2235	708.0+/-405.6	2356,1653,291	yes	missense,missense	SVOPL	NM_001139456.1,NM_174959.2	205,205	2719,2702,1082	CC,CA,AA		25.9884,40.286,37.4135	probably-damaging,probably-damaging	385/493,233/341	138312122	8140,4866	2203	4300	6503	SO:0001583	missense	136306	exon11			AGAAGGAAGAATA	BC036796	CCDS5848.1, CCDS47721.1	7q34	2011-07-12	2007-04-04		ENSG00000157703	ENSG00000157703			27034	protein-coding gene	gene with protein product		611700	"""SV2 related protein homolog (rat)-like"""				Standard	NM_001139456		Approved	MGC46715	uc011kqh.2	Q8N434	OTTHUMG00000155870	ENST00000419765.3:c.1154T>G	7.37:g.138312122A>C	ENSP00000405482:p.Phe385Cys	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_001139456		Missense_Mutation	SNP	ENST00000419765.3	37	CCDS47721.1	1126	0.5155677655677655	193	0.39227642276422764	195	0.5386740331491713	176	0.3076923076923077	562	0.741424802110818	A	18.49	3.635035	0.67130	0.40286	0.740116	ENSG00000157703	ENST00000288513;ENST00000421622;ENST00000436657;ENST00000419765	T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.089556	0.85682	D	0.000000	T	0.00012	0.0000	L	0.58583	1.82	0.20821	P	0.999842922	D;D	0.89917	1.0;0.999	D;D	0.74348	0.983;0.912	T	0.50874	-0.8776	9	0.32370	T	0.25	-35.6448	15.8094	0.78547	1.0:0.0:0.0:0.0	rs2305816;rs10353447;rs52807130;rs61581409;rs2305816	385;233	Q8N434;Q8N434-2	SVOPL_HUMAN;.	C	233;265;233;385	ENSP00000288513:F233C;ENSP00000412830:F265C;ENSP00000417018:F233C;ENSP00000405482:F385C	ENSP00000288513:F233C	F	-	2	0	SVOPL	137962662	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	4.588000	0.60999	2.141000	0.66446	0.533000	0.62120	TTC	A|0.433;C|0.567	0.567	strong		0.413	SVOPL-005	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342092.4	NM_174959	
IQGAP3	128239	hgsc.bcm.edu	37	1	156526387	156526387	+	Missense_Mutation	SNP	C	C	G	rs11264498	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156526387C>G	ENST00000361170.2	-	12	1238	c.1228G>C	c.(1228-1230)Gtg>Ctg	p.V410L		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	410			V -> L (in dbSNP:rs11264498).		activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACAGGGTACACTGGAGGCAGC	0.602													C|||	1894	0.378195	0.1407	0.5519	5008	,	,		17223	0.4286		0.6272	False		,,,				2504	0.2679				p.V410L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.G1228C						PASS	.	C	LEU/VAL	1045,3361	383.5+/-324.9	126,793,1284	55.0	46.0	49.0		1228	5.5	1.0	1	dbSNP_120	49	5490,3110	655.3+/-401.2	1773,1944,583	yes	missense	IQGAP3	NM_178229.4	32	1899,2737,1867	GG,GC,CC		36.1628,23.7177,49.754	probably-damaging	410/1632	156526387	6535,6471	2203	4300	6503	SO:0001583	missense	128239	exon12			GGTACACTGGAGG	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.1228G>C	1.37:g.156526387C>G	ENSP00000354451:p.Val410Leu	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	136	133	0.977941	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	1032	0.4725274725274725	82	0.16666666666666666	207	0.5718232044198895	262	0.458041958041958	481	0.6345646437994723	C	23.0	4.361937	0.82353	0.237177	0.638372	ENSG00000183856	ENST00000361170	T	0.13089	2.62	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	T	0.26991	0.0661	L	0.58354	1.805	0.09310	P	0.9999999329442	D	0.64830	0.994	D	0.70716	0.97	T	0.01004	-1.1484	9	0.72032	D	0.01	-21.1507	18.0563	0.89365	0.0:1.0:0.0:0.0	rs11264498;rs17391967;rs52823677;rs57058839;rs11264498	410	Q86VI3	IQGA3_HUMAN	L	410	ENSP00000354451:V410L	ENSP00000354451:V410L	V	-	1	0	IQGAP3	154793011	1.000000	0.71417	0.988000	0.46212	0.445000	0.32107	5.769000	0.68865	2.589000	0.87451	0.491000	0.48974	GTG	C|0.513;G|0.487	0.487	strong		0.602	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
OR5AK2	390181	hgsc.bcm.edu	37	11	56757056	56757056	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56757056C>T	ENST00000326855.2	+	1	710	c.668C>T	c.(667-669)gCc>gTc	p.A223V		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						TACATCATGGCCACCATCCTG	0.433																																					p.A223V		Atlas-SNP	.											.	OR5AK2	45	.	0			c.C668T						PASS	.						175.0	160.0	165.0					11																	56757056		2201	4296	6497	SO:0001583	missense	390181	exon1			TCATGGCCACCAT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.668C>T	11.37:g.56757056C>T	ENSP00000322784:p.Ala223Val	Somatic	290	0	0		WXS	Illumina HiSeq	Phase_I	313	118	0.376997	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.735318	0.00681	.	.	ENSG00000181273	ENST00000326855	T	0.36157	1.27	3.97	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	0.590959	0.13870	N	0.357078	T	0.16811	0.0404	N	0.12853	0.265	0.09310	N	1	B	0.15719	0.014	B	0.24006	0.05	T	0.25779	-1.0122	10	0.19147	T	0.46	-0.0979	2.6585	0.05019	0.1802:0.5133:0.1997:0.1068	.	223	Q8NH90	O5AK2_HUMAN	V	223	ENSP00000322784:A223V	ENSP00000322784:A223V	A	+	2	0	OR5AK2	56513632	0.000000	0.05858	0.001000	0.08648	0.044000	0.14063	-0.408000	0.07169	0.435000	0.26365	0.400000	0.26472	GCC	.	.	none		0.433	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
RNF43	54894	hgsc.bcm.edu	37	17	56435080	56435080	+	Missense_Mutation	SNP	G	G	C	rs9652855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56435080G>C	ENST00000584437.1	-	8	4012	c.2057C>G	c.(2056-2058)cCc>cGc	p.P686R	RNF43_ENST00000577716.1_Missense_Mutation_p.P686R|RNF43_ENST00000407977.2_Missense_Mutation_p.P686R|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Missense_Mutation_p.P559R|RNF43_ENST00000500597.2_Missense_Mutation_p.P645R|RNF43_ENST00000577625.1_Missense_Mutation_p.P559R|RNF43_ENST00000583753.1_Missense_Mutation_p.P645R			Q68DV7	RNF43_HUMAN	ring finger protein 43	686	Pro-rich.		P -> R (in dbSNP:rs9652855). {ECO:0000269|PubMed:17974005}.		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCCACACTGGGGGTGTAATG	0.622													G|||	392	0.0782748	0.1377	0.0548	5008	,	,		17838	0.0		0.1223	False		,,,				2504	0.0501				p.P686R		Atlas-SNP	.											RNF43,lower_third,carcinoma,+1,1	RNF43	157	1	0			c.C2057G						PASS	.	G	ARG/PRO	521,3885	229.4+/-244.0	28,465,1710	90.0	103.0	98.0		2057	3.1	0.0	17	dbSNP_119	98	1082,7518	221.9+/-259.1	77,928,3295	yes	missense	RNF43	NM_017763.4	103	105,1393,5005	CC,CG,GG		12.5814,11.8248,12.3251	possibly-damaging	686/784	56435080	1603,11403	2203	4300	6503	SO:0001583	missense	54894	exon9			ACACTGGGGGTGT		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.2057C>G	17.37:g.56435080G>C	ENSP00000463069:p.Pro686Arg	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	111	64	0.576577	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	174	0.07967032967032966	61	0.12398373983739837	25	0.06906077348066299	0	0.0	88	0.11609498680738786	G	9.516	1.107052	0.20714	0.118248	0.125814	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.08807	3.19;3.05	5.18	3.1	0.35709	.	0.559581	0.16403	N	0.215931	T	0.00073	0.0002	L	0.32530	0.975	0.80722	P	0.0	B;B;B	0.12630	0.001;0.006;0.001	B;B;B	0.12156	0.002;0.007;0.001	T	0.15665	-1.0429	9	0.87932	D	0	-10.8686	8.1407	0.31082	0.0:0.1739:0.6457:0.1804	rs9652855;rs52806304;rs9652855	645;686;686	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	R	686;645	ENSP00000385328:P686R;ENSP00000441969:P645R	ENSP00000385328:P686R	P	-	2	0	RNF43	53790079	0.034000	0.19679	0.016000	0.15963	0.738000	0.42128	2.033000	0.41136	0.699000	0.31761	0.511000	0.50034	CCC	G|0.886;C|0.114	0.114	strong		0.622	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
CROCC	9696	hgsc.bcm.edu	37	1	17250836	17250836	+	Silent	SNP	A	A	G	rs57174186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17250836A>G	ENST00000375541.5	+	3	282	c.213A>G	c.(211-213)acA>acG	p.T71T	CROCC_ENST00000467938.1_Intron	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TGCCGGCCACAGAGATGGCAT	0.657																																					p.T71T		Atlas-SNP	.											CROCC,NS,carcinoma,0,3	CROCC	185	3	0			c.A213G						PASS	.	G		1667,2739		0,1667,536	38.0	33.0	35.0		213	-7.0	0.0	1	dbSNP_129	35	2771,5827		0,2771,1528	no	coding-synonymous	CROCC	NM_014675.3		0,4438,2064	GG,GA,AA		32.2284,37.8348,34.128		71/2018	17250836	4438,8566	2203	4299	6502	SO:0001819	synonymous_variant	9696	exon3			GGCCACAGAGATG	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.213A>G	1.37:g.17250836A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	125	52	0.416	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			A|0.638;G|0.362	0.362	strong		0.657	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
SPOCD1	90853	hgsc.bcm.edu	37	1	32280610	32280610	+	Missense_Mutation	SNP	T	T	C	rs6664445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:32280610T>C	ENST00000360482.2	-	2	454	c.325A>G	c.(325-327)Act>Gct	p.T109A	SPOCD1_ENST00000533231.1_Missense_Mutation_p.T109A|SPOCD1_ENST00000257100.3_Intron|SPOCD1_ENST00000373648.2_Missense_Mutation_p.T109A	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	109			T -> A (in dbSNP:rs6664445). {ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		CTCCCCTGAGTAGGCACCGAG	0.602													C|||	3443	0.6875	0.6399	0.6671	5008	,	,		16234	0.7212		0.673	False		,,,				2504	0.7464				p.T109A		Atlas-SNP	.											.	SPOCD1	109	.	0			c.A325G						PASS	.	C	ALA/THR	2807,1599	479.4+/-358.5	902,1003,298	43.0	50.0	48.0		325	2.3	0.0	1	dbSNP_116	48	5930,2670	414.9+/-351.6	2029,1872,399	yes	missense	SPOCD1	NM_144569.4	58	2931,2875,697	CC,CT,TT		31.0465,36.2914,32.8233	benign	109/1217	32280610	8737,4269	2203	4300	6503	SO:0001583	missense	90853	exon2			CCTGAGTAGGCAC	AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.325A>G	1.37:g.32280610T>C	ENSP00000353670:p.Thr109Ala	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	80	79	0.9875	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	1476	0.6758241758241759	335	0.6808943089430894	228	0.6298342541436464	402	0.7027972027972028	511	0.6741424802110818	C	0.018	-1.480039	0.01035	0.637086	0.689535	ENSG00000134668	ENST00000360482;ENST00000373648;ENST00000533231	T;T;T	0.28069	2.2;1.63;2.19	3.27	2.32	0.28847	.	.	.	.	.	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	0.43589	-0.9382	8	0.02654	T	1	-1.7406	4.6382	0.12536	0.0:0.6486:0.2255:0.1258	rs6664445;rs17505841;rs52812184;rs59257153;rs6664445	109;109	Q6ZMY3-2;Q6ZMY3	.;SPOC1_HUMAN	A	109	ENSP00000353670:T109A;ENSP00000362752:T109A;ENSP00000435851:T109A	ENSP00000353670:T109A	T	-	1	0	SPOCD1	32053197	0.008000	0.16893	0.008000	0.14137	0.004000	0.04260	0.365000	0.20348	0.388000	0.25054	-0.119000	0.15052	ACT	C|0.680;N|0.001	0.680	strong		0.602	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569	
ARMS2	387715	hgsc.bcm.edu	37	10	124214448	124214448	+	Missense_Mutation	SNP	G	G	T	rs10490924	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124214448G>T	ENST00000528446.1	+	1	280	c.205G>T	c.(205-207)Gct>Tct	p.A69S		NM_001099667.1	NP_001093137.1	P0C7Q2	ARMS2_HUMAN	age-related maculopathy susceptibility 2	69			A -> S (in dbSNP:rs10490924). {ECO:0000269|PubMed:16174643, ECO:0000269|PubMed:16642439, ECO:0000269|PubMed:16936732, ECO:0000269|PubMed:17000705, ECO:0000269|PubMed:17053108, ECO:0000269|PubMed:17210852, ECO:0000269|PubMed:17675241, ECO:0000269|PubMed:17884985, ECO:0000269|PubMed:18423869, ECO:0000269|PubMed:18436811, ECO:0000269|PubMed:18452766}.		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)				GATCCCAGCTGCTAAAATCCA	0.537													G|||	1435	0.286542	0.2458	0.2478	5008	,	,		19203	0.4038		0.1948	False		,,,				2504	0.3425				p.A69S		Atlas-SNP	.											.	ARMS2	7	.	0			c.G205T	GRCh37	CM066533	ARMS2	M	rs10490924	PASS	.	G	SER/ALA	824,3200		89,646,1277	95.0	94.0	94.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	205	1.0	0.0	10	dbSNP_119	94	1724,6652		182,1360,2646	yes	missense	ARMS2	NM_001099667.1	99	271,2006,3923	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	20.5826,20.4771,20.5484	benign	69/108	124214448	2548,9852	2012	4188	6200	SO:0001583	missense	387715	exon1			CCAGCTGCTAAAA	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.205G>T	10.37:g.124214448G>T	ENSP00000436682:p.Ala69Ser	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	165	74	0.448485	NM_001099667	B2Y7I5	Missense_Mutation	SNP	ENST00000528446.1	37	CCDS53585.1	597	0.2733516483516483	126	0.25609756097560976	90	0.24861878453038674	230	0.4020979020979021	151	0.19920844327176782	G	8.897	0.955517	0.18507	0.204771	0.205826	ENSG00000254636	ENST00000528446	T	0.38401	1.14	1.97	0.998	0.19857	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.64830	0.994	D	0.68353	0.957	T	0.41822	-0.9487	8	0.87932	D	0	.	6.1676	0.20398	0.0:0.3219:0.6781:0.0	rs10490924;rs10490924	69	P0C7Q2	ARMS2_HUMAN	S	69	ENSP00000436682:A69S	ENSP00000436682:A69S	A	+	1	0	ARMS2	124204438	0.006000	0.16342	0.005000	0.12908	0.078000	0.17371	0.208000	0.17415	0.370000	0.24538	0.491000	0.48974	GCT	G|0.712;T|0.288	0.288	strong		0.537	ARMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109727.2		
OR10S1	219873	hgsc.bcm.edu	37	11	123848212	123848212	+	Missense_Mutation	SNP	C	C	T	rs17759513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:123848212C>T	ENST00000531945.1	-	1	276	c.187G>A	c.(187-189)Ggc>Agc	p.G63S		NM_001004474.1	NP_001004474.1	Q8NGN2	O10S1_HUMAN	olfactory receptor, family 10, subfamily S, member 1	63			G -> S (in dbSNP:rs17759513).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	36		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GAGTCAGAGCCCACAGTTAGG	0.527													C|||	867	0.173123	0.1301	0.2147	5008	,	,		22925	0.1171		0.2903	False		,,,				2504	0.1391				p.G63S		Atlas-SNP	.											.	OR10S1	78	.	0			c.G187A						PASS	.	C	SER/GLY	660,3744	281.1+/-275.7	45,570,1587	71.0	63.0	66.0		187	1.9	1.0	11	dbSNP_123	66	2219,6379	374.8+/-337.5	296,1627,2376	yes	missense	OR10S1	NM_001004474.1	56	341,2197,3963	TT,TC,CC		25.8083,14.9864,22.1427	benign	63/332	123848212	2879,10123	2202	4299	6501	SO:0001583	missense	219873	exon1			CAGAGCCCACAGT	BK004509	CCDS31701.1	11q24.1	2012-08-09			ENSG00000196248	ENSG00000196248		"""GPCR / Class A : Olfactory receptors"""	14807	protein-coding gene	gene with protein product							Standard	NM_001004474		Approved		uc001pzm.1	Q8NGN2	OTTHUMG00000165963	ENST00000531945.1:c.187G>A	11.37:g.123848212C>T	ENSP00000431914:p.Gly63Ser	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_001004474	B9EH43|Q6IEV3|Q96R78	Missense_Mutation	SNP	ENST00000531945.1	37	CCDS31701.1	433	0.19826007326007325	65	0.13211382113821138	87	0.24033149171270718	73	0.12762237762237763	208	0.27440633245382584	C	9.701	1.154552	0.21371	0.149864	0.258083	ENSG00000196248	ENST00000531945	T	0.01076	5.37	4.84	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	1.379400	0.05329	U	0.527956	T	0.00012	0.0000	N	0.03930	-0.32	0.52099	P	5.900000000003125E-5	B	0.14438	0.01	B	0.08055	0.003	T	0.41680	-0.9495	9	0.22109	T	0.4	-6.4442	4.5215	0.11960	0.1454:0.5349:0.0:0.3197	rs17759513;rs52797693;rs60266391;rs17759513	63	Q8NGN2	O10S1_HUMAN	S	63	ENSP00000431914:G63S	ENSP00000431914:G63S	G	-	1	0	OR10S1	123353422	0.000000	0.05858	0.998000	0.56505	0.996000	0.88848	-0.391000	0.07323	0.668000	0.31126	0.638000	0.83543	GGC	C|0.792;N|0.000	.	strong		0.527	OR10S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387265.2	NM_001004474	
MAOA	4128	hgsc.bcm.edu	37	X	43603391	43603391	+	Silent	SNP	T	T	C	rs1137070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:43603391T>C	ENST00000338702.3	+	14	1533	c.1410T>C	c.(1408-1410)gaT>gaC	p.D470D	MAOA_ENST00000542639.1_Silent_p.D337D	NM_000240.3	NP_000231.1	P21397	AOFA_HUMAN	monoamine oxidase A	470					cellular biogenic amine metabolic process (GO:0006576)|dopamine catabolic process (GO:0042420)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	primary amine oxidase activity (GO:0008131)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	18					Almotriptan(DB00918)|Dopamine(DB00988)|Ephedra(DB01363)|Flavin adenine dinucleotide(DB03147)|Furazolidone(DB00614)|Isocarboxazid(DB01247)|Linezolid(DB00601)|Methamphetamine(DB01577)|Minaprine(DB00805)|Moclobemide(DB01171)|Nandrolone decanoate(DB08804)|Naratriptan(DB00952)|Nicotine(DB00184)|Pargyline(DB01626)|Phenelzine(DB00780)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Riboflavin(DB00140)|Rizatriptan(DB00953)|Selegiline(DB01037)|Sertraline(DB01104)|Sumatriptan(DB00669)|Testosterone(DB00624)|Tranylcypromine(DB00752)|Zolmitriptan(DB00315)|Zonisamide(DB00909)	CCGAGAAAGATATCTGGGTAC	0.423													C|||	2083	0.551788	0.4879	0.4597	3775	,	,		15525	0.3214		0.5388	False		,,,				2504	0.2587				p.D470D		Atlas-SNP	.											.	MAOA	48	.	0			c.T1410C						PASS	.	C		2378,1457		621,781,355,230,216	132.0	119.0	123.0		1410	-0.1	0.0	X	dbSNP_86	123	4733,1995		1214,976,1329,238,543	no	coding-synonymous	MAOA	NM_000240.2		1835,1757,1684,468,759	CC,CT,C,TT,T		29.6522,37.9922,32.6801		470/528	43603391	7111,3452	2203	4300	6503	SO:0001819	synonymous_variant	4128	exon14			GAAAGATATCTGG		CCDS14260.1, CCDS59163.1	Xp11.4-p11.3	2008-02-05			ENSG00000189221	ENSG00000189221	1.4.3.4		6833	protein-coding gene	gene with protein product		309850					Standard	NM_000240		Approved		uc004dfy.4	P21397	OTTHUMG00000021387	ENST00000338702.3:c.1410T>C	X.37:g.43603391T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	96	0.989691	NM_000240	B4DF46|Q16426	Silent	SNP	ENST00000338702.3	37	CCDS14260.1																																																																																			0|0.014;C|0.615	0.615	strong		0.423	MAOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056300.1	NM_000240	
AGMAT	79814	hgsc.bcm.edu	37	1	15904318	15904318	+	Silent	SNP	C	C	T	rs11544523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15904318C>T	ENST00000375826.3	-	5	904	c.762G>A	c.(760-762)tcG>tcA	p.S254S	DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	254					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		GAGGAACCAGCGACTTCATCC	0.537													C|||	1189	0.23742	0.4493	0.1873	5008	,	,		21655	0.0565		0.2177	False		,,,				2504	0.1933				p.S254S	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.G762A						PASS	.	C		1892,2514	543.7+/-376.3	400,1092,711	83.0	75.0	77.0		762	-10.8	0.4	1	dbSNP_120	77	1922,6678	339.6+/-323.3	198,1526,2576	yes	coding-synonymous	AGMAT	NM_024758.4		598,2618,3287	TT,TC,CC		22.3488,42.9414,29.3249		254/353	15904318	3814,9192	2203	4300	6503	SO:0001819	synonymous_variant	79814	exon5			AACCAGCGACTTC	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.762G>A	1.37:g.15904318C>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	95	87	0.915789	NM_024758	Q5TDH1|Q9H5J3	Silent	SNP	ENST00000375826.3	37	CCDS160.1																																																																																			C|0.729;T|0.271	0.271	strong		0.537	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
NASP	4678	hgsc.bcm.edu	37	1	46073361	46073361	+	Nonsense_Mutation	SNP	C	C	T	rs78094239	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:46073361C>T	ENST00000350030.3	+	6	865	c.778C>T	c.(778-780)Cag>Tag	p.Q260*	NASP_ENST00000402363.3_Nonsense_Mutation_p.Q262*|NASP_ENST00000372052.4_Intron|NASP_ENST00000351223.3_Intron|NASP_ENST00000537798.1_Nonsense_Mutation_p.Q196*	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	260	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)					AAAAGGAGGTCAGGAGAAGCA	0.478																																					p.Q260X		Atlas-SNP	.											NASP,colon,carcinoma,-1,1	NASP	77	1	0			c.C778T						scavenged	.						45.0	48.0	47.0					1																	46073361		2203	4300	6503	SO:0001587	stop_gained	4678	exon6			GGAGGTCAGGAGA	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.778C>T	1.37:g.46073361C>T	ENSP00000255120:p.Gln260*	Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	142	4	0.028169	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Nonsense_Mutation	SNP	ENST00000350030.3	37	CCDS524.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366295	0.41902	.	.	ENSG00000132780	ENST00000537798;ENST00000402363;ENST00000341288;ENST00000350030;ENST00000470768	.	.	.	4.34	3.41	0.39046	.	0.414434	0.26446	N	0.024338	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.1249	12.7247	0.57164	0.0:0.8332:0.1668:0.0	.	.	.	.	X	196;262;160;260;223	.	.	Q	+	1	0	NASP	45845948	0.181000	0.23161	0.905000	0.35620	0.753000	0.42808	0.549000	0.23329	1.391000	0.46566	0.650000	0.86243	CAG	C|0.980;T|0.020	0.020	strong		0.478	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
TGM7	116179	hgsc.bcm.edu	37	15	43571390	43571390	+	Silent	SNP	C	C	G	rs567357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43571390C>G	ENST00000452443.2	-	11	1768	c.1764G>C	c.(1762-1764)gcG>gcC	p.A588A		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	588					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	CTTCAACCTCCGCGATGCCAG	0.532													G|||	2672	0.533546	0.9682	0.3415	5008	,	,		19932	0.4058		0.337	False		,,,				2504	0.4162				p.A588A		Atlas-SNP	.											.	TGM7	86	.	0			c.G1764C						PASS	.	G		3742,662	282.2+/-276.4	1593,556,53	98.0	82.0	88.0		1764	-8.4	0.0	15	dbSNP_83	88	2812,5786	676.2+/-403.3	474,1864,1961	no	coding-synonymous	TGM7	NM_052955.2		2067,2420,2014	GG,GC,CC		32.7053,15.0318,49.5924		588/711	43571390	6554,6448	2202	4299	6501	SO:0001819	synonymous_variant	116179	exon11			AACCTCCGCGATG	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1764G>C	15.37:g.43571390C>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_052955		Silent	SNP	ENST00000452443.2	37	CCDS32213.1																																																																																			C|0.491;G|0.509	0.509	strong		0.532	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
CHIA	27159	hgsc.bcm.edu	37	1	111857208	111857208	+	Missense_Mutation	SNP	G	G	A	rs3818822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:111857208G>A	ENST00000369740.1	+	5	407	c.304G>A	c.(304-306)Ggg>Agg	p.G102R	CHIA_ENST00000430615.1_5'UTR|CHIA_ENST00000353665.6_5'UTR|CHIA_ENST00000483391.1_5'UTR|CHIA_ENST00000343320.6_Missense_Mutation_p.G102R|CHIA_ENST00000451398.2_5'UTR	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	102			G -> R (in dbSNP:rs3818822). {ECO:0000269|PubMed:19435888}.		apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		CTGGAACTTCGGGACTGCCCC	0.453													G|||	649	0.129593	0.1936	0.0807	5008	,	,		16492	0.0933		0.0984	False		,,,				2504	0.1472				p.G102R		Atlas-SNP	.											.	CHIA	115	.	0			c.G304A						PASS	.	G	,ARG/GLY	610,3136		42,526,1305	110.0	107.0	108.0		,304	4.6	1.0	1	dbSNP_107	108	880,7322		46,788,3267	yes	utr-5,missense	CHIA	NM_021797.2,NM_201653.2	,125	88,1314,4572	AA,AG,GG		10.7291,16.284,12.4707	,probably-damaging	,102/477	111857208	1490,10458	1873	4101	5974	SO:0001583	missense	27159	exon5			AACTTCGGGACTG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.304G>A	1.37:g.111857208G>A	ENSP00000358755:p.Gly102Arg	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	67	36	0.537313	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	230	0.10531135531135531	83	0.16869918699186992	34	0.09392265193370165	51	0.08916083916083917	62	0.08179419525065963	G	19.93	3.918008	0.73098	0.16284	0.107291	ENSG00000134216	ENST00000422815;ENST00000369740;ENST00000343320	T;T;T	0.05855	3.38;3.38;3.38	4.56	4.56	0.56223	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.080948	0.47455	N	0.000223	T	0.28499	0.0705	H	0.95816	3.725	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.49293	-0.8955	9	0.87932	D	0	1.0E-4	15.1925	0.73057	0.0:0.0:1.0:0.0	rs3818822;rs52810904;rs60274821;rs3818822	102	Q9BZP6	CHIA_HUMAN	R	46;102;102	ENSP00000387671:G46R;ENSP00000358755:G102R;ENSP00000341828:G102R	ENSP00000341828:G102R	G	+	1	0	CHIA	111658731	1.000000	0.71417	1.000000	0.80357	0.563000	0.35712	8.823000	0.92018	2.233000	0.73108	0.462000	0.41574	GGG	G|0.888;A|0.112	0.112	strong		0.453	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
ZNF862	643641	hgsc.bcm.edu	37	7	149556518	149556518	+	Silent	SNP	C	C	T	rs4725833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149556518C>T	ENST00000223210.4	+	6	1370	c.1125C>T	c.(1123-1125)gcC>gcT	p.A375A	RP4-751H13.7_ENST00000608963.1_RNA|ZNF862_ENST00000478024.1_3'UTR	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	375	KRAB 2. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CAGGACCTGCCGCTGCCAAGC	0.562													T|||	2641	0.527356	0.7973	0.4452	5008	,	,		19304	0.3323		0.5795	False		,,,				2504	0.3681				p.A375A		Atlas-SNP	.											.	ZNF862	97	.	0			c.C1125T						PASS	.	T		3121,887		1233,655,116	21.0	24.0	23.0		1125	-5.9	0.9	7	dbSNP_111	23	5047,3295		1582,1883,706	no	coding-synonymous	ZNF862	NM_001099220.1		2815,2538,822	TT,TC,CC		39.4989,22.1307,33.8623		375/1170	149556518	8168,4182	2004	4171	6175	SO:0001819	synonymous_variant	643641	exon6			ACCTGCCGCTGCC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.1125C>T	7.37:g.149556518C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	34	34	1	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			C|0.427;T|0.573	0.573	strong		0.562	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
SZT2	23334	hgsc.bcm.edu	37	1	43906896	43906896	+	Silent	SNP	A	A	G	rs2027130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43906896A>G	ENST00000562955.1	+	52	7185	c.7185A>G	c.(7183-7185)gaA>gaG	p.E2395E	SZT2_ENST00000372442.1_Silent_p.E1553E	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2452					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						GTAAAACAGAATGTGGGGATT	0.547													A|||	983	0.196286	0.0885	0.3847	5008	,	,		19153	0.0823		0.4205	False		,,,				2504	0.0951				p.E2395E		Atlas-SNP	.											.	SZT2	383	.	0			c.A7185G						PASS	.	A		586,3820	254.6+/-260.1	40,506,1657	140.0	150.0	147.0		7185	3.1	1.0	1	dbSNP_94	147	3555,5045	515.1+/-378.5	756,2043,1501	no	coding-synonymous	SZT2	NM_015284.3		796,2549,3158	GG,GA,AA		41.3372,13.3,31.8392		2395/3376	43906896	4141,8865	2203	4300	6503	SO:0001819	synonymous_variant	23334	exon52			AACAGAATGTGGG	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.7185A>G	1.37:g.43906896A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	83	83	1	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																			A|0.698;G|0.302	0.302	strong		0.547	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
ACOX2	8309	hgsc.bcm.edu	37	3	58512237	58512237	+	Silent	SNP	A	A	G	rs1127745	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:58512237A>G	ENST00000302819.5	-	10	1593	c.1302T>C	c.(1300-1302)tgT>tgC	p.C434C	ACOX2_ENST00000459701.2_Silent_p.C420C	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	434					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		CCTCGTAGGTACAGGAGGCCG	0.612													G|||	1418	0.283147	0.6982	0.1599	5008	,	,		18520	0.2262		0.0775	False		,,,				2504	0.0798				p.C434C		Atlas-SNP	.											.	ACOX2	53	.	0			c.T1302C						PASS	.	G		2761,1645	504.9+/-366.0	877,1007,319	82.0	66.0	71.0		1302	0.2	0.8	3	dbSNP_86	71	847,7753	780.1+/-407.7	37,773,3490	no	coding-synonymous	ACOX2	NM_003500.3		914,1780,3809	GG,GA,AA		9.8488,37.3355,27.741		434/682	58512237	3608,9398	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon10			GTAGGTACAGGAG	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.1302T>C	3.37:g.58512237A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	142	55	0.387324	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.718;G|0.282	0.282	strong		0.612	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
SBNO1	55206	hgsc.bcm.edu	37	12	123806219	123806219	+	Missense_Mutation	SNP	C	C	T	rs1060105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:123806219C>T	ENST00000602398.1	-	17	2313	c.2186G>A	c.(2185-2187)aGt>aAt	p.S729N	SBNO1_ENST00000602750.1_Missense_Mutation_p.S728N|SBNO1_ENST00000420886.2_Missense_Mutation_p.S729N|SBNO1_ENST00000267176.4_Missense_Mutation_p.S728N			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	729			S -> N (in dbSNP:rs1060105).		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)		GTCGTCAGAACTGCTACCAGT	0.433													C|||	624	0.124601	0.0514	0.1888	5008	,	,		19285	0.002		0.2227	False		,,,				2504	0.2035				p.S729N		Atlas-SNP	.											.	SBNO1	138	.	0			c.G2186A						PASS	.	C	ASN/SER,ASN/SER	363,4043	186.7+/-213.5	13,337,1853	225.0	202.0	209.0		2186,2183	5.5	1.0	12	dbSNP_86	209	1698,6902	311.3+/-310.3	154,1390,2756	yes	missense,missense	SBNO1	NM_001167856.1,NM_018183.3	46,46	167,1727,4609	TT,TC,CC		19.7442,8.2388,15.8465	probably-damaging,probably-damaging	729/1394,728/1393	123806219	2061,10945	2203	4300	6503	SO:0001583	missense	55206	exon16			TCAGAACTGCTAC	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.2186G>A	12.37:g.123806219C>T	ENSP00000473665:p.Ser729Asn	Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	290	152	0.524138	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Missense_Mutation	SNP	ENST00000602398.1	37	CCDS53844.1	278	0.12728937728937728	31	0.06300813008130081	70	0.19337016574585636	0	0.0	177	0.23350923482849603	C	20.9	4.064827	0.76187	0.082388	0.197442	ENSG00000139697	ENST00000420886;ENST00000267176	T;T	0.32515	1.45;1.45	5.48	5.48	0.80851	.	0.043447	0.85682	D	0.000000	T	0.00039	0.0001	L	0.44542	1.39	0.09310	P	0.99999865456	B;B;D	0.57899	0.085;0.138;0.981	B;B;D	0.66351	0.017;0.037;0.943	T	0.02202	-1.1196	9	0.18276	T	0.48	-13.2537	19.3611	0.94438	0.0:1.0:0.0:0.0	rs1060105;rs3200951;rs17568382;rs17880539;rs52804765;rs56434819;rs60926174;rs1060105	729;728;727	A3KN83;A3KN83-2;A3KN83-3	SBNO1_HUMAN;.;.	N	729;728	ENSP00000387361:S729N;ENSP00000267176:S728N	ENSP00000267176:S728N	S	-	2	0	SBNO1	122372172	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.921000	0.75805	2.551000	0.86045	0.563000	0.77884	AGT	C|0.855;T|0.145	0.145	strong		0.433	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
MUC16	94025	hgsc.bcm.edu	37	19	9088772	9088772	+	Missense_Mutation	SNP	T	T	C	rs17000950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9088772T>C	ENST00000397910.4	-	1	3246	c.3043A>G	c.(3043-3045)Agg>Ggg	p.R1015G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1015	Thr-rich.		R -> G (in dbSNP:rs17000950).		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						GATGGTTCCCTGATAGAAGTT	0.468													T|||	952	0.190096	0.0711	0.2709	5008	,	,		23512	0.3046		0.172	False		,,,				2504	0.1943				p.R1015G		Atlas-SNP	.											.	MUC16	4315	.	0			c.A3043G						PASS	.	T	GLY/ARG	293,3673		7,279,1697	221.0	208.0	212.0		3043	1.4	0.0	19	dbSNP_123	212	1484,6842		126,1232,2805	yes	missense	MUC16	NM_024690.2	125	133,1511,4502	CC,CT,TT		17.8237,7.3878,14.4566	probably-damaging	1015/14508	9088772	1777,10515	1983	4163	6146	SO:0001583	missense	94025	exon1			GTTCCCTGATAGA	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.3043A>G	19.37:g.9088772T>C	ENSP00000381008:p.Arg1015Gly	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	159	84	0.528302	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	451	0.2065018315018315	37	0.07520325203252033	89	0.24585635359116023	194	0.33916083916083917	131	0.17282321899736147	t	3.114	-0.181980	0.06340	0.073878	0.178237	ENSG00000181143	ENST00000397910	T	0.02890	4.12	1.36	1.36	0.22044	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.54772	0.968	P	0.61874	0.895	T	0.54417	-0.8297	8	0.87932	D	0	.	4.8612	0.13585	0.0:0.0:0.0:1.0	rs17000950;rs52824067;rs17000950	1015	B5ME49	.	G	1015	ENSP00000381008:R1015G	ENSP00000381008:R1015G	R	-	1	2	MUC16	8949772	0.000000	0.05858	0.021000	0.16686	0.046000	0.14306	-0.105000	0.10907	0.872000	0.35775	0.260000	0.18958	AGG	T|0.797;C|0.203	0.203	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ARHGAP9	64333	hgsc.bcm.edu	37	12	57873042	57873042	+	Missense_Mutation	SNP	T	T	C	rs33927108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57873042T>C	ENST00000356411.2	-	2	286	c.148A>G	c.(148-150)Agg>Ggg	p.R50G	ARHGAP9_ENST00000393797.2_Missense_Mutation_p.R121G|ARHGAP9_ENST00000430041.2_5'Flank|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000550288.1_Missense_Mutation_p.R129G|ARHGAP9_ENST00000393791.3_Missense_Mutation_p.R50G|ARHGAP9_ENST00000424809.2_Missense_Mutation_p.R50G			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	50	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.		R -> G (in dbSNP:rs33927108).		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)			AGTAGGAACCTATCCCCTTCA	0.587													T|||	314	0.0626997	0.0061	0.072	5008	,	,		19106	0.1171		0.0765	False		,,,				2504	0.0624				p.R50G		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.A148G						PASS	.	T	GLY/ARG,GLY/ARG	47,4359	49.6+/-84.7	0,47,2156	112.0	98.0	103.0		148,148	3.6	1.0	12	dbSNP_126	103	558,8042	152.8+/-207.3	13,532,3755	yes	missense,missense	ARHGAP9	NM_001080157.1,NM_032496.2	125,125	13,579,5911	CC,CT,TT		6.4884,1.0667,4.6517	possibly-damaging,possibly-damaging	50/641,50/732	57873042	605,12401	2203	4300	6503	SO:0001583	missense	64333	exon1			GGAACCTATCCCC	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.148A>G	12.37:g.57873042T>C	ENSP00000348782:p.Arg50Gly	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	92	43	0.467391	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Missense_Mutation	SNP	ENST00000356411.2	37		163	0.07463369963369963	3	0.006097560975609756	29	0.08011049723756906	76	0.13286713286713286	55	0.07255936675461741	T	16.03	3.005793	0.54254	0.010667	0.064884	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000424809;ENST00000393797;ENST00000340423	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	4.79	3.59	0.41128	Src homology-3 domain (4);	0.077166	0.49916	D	0.000140	T	0.01254	0.0041	M	0.89353	3.025	0.38969	P	0.041291999999999995	P;B;P;B;B	0.51449	0.945;0.44;0.643;0.16;0.192	P;B;B;B;B	0.57468	0.821;0.272;0.331;0.128;0.202	T	0.49925	-0.8887	9	0.87932	D	0	.	7.8853	0.29646	0.0:0.0:0.2744:0.7256	rs33927108	50;129;50;50;50	B4E248;Q6ZN13;Q9BRR9;Q9BRR9-2;E9PDX9	.;.;RHG09_HUMAN;.;.	G	50;50;50;121;99	ENSP00000377380:R50G;ENSP00000348782:R50G;ENSP00000394307:R50G;ENSP00000377386:R121G	ENSP00000344852:R99G	R	-	1	2	ARHGAP9	56159309	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	2.562000	0.45914	1.908000	0.55244	0.533000	0.62120	AGG	T|0.941;C|0.059	0.059	strong		0.587	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
SELPLG	6404	hgsc.bcm.edu	37	12	109017680	109017680	+	Missense_Mutation	SNP	T	T	G	rs63748999|rs200527674|rs372173288	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109017680T>G	ENST00000550948.1	-	2	628	c.404A>C	c.(403-405)cAa>cCa	p.Q135P	SELPLG_ENST00000388962.3_Intron|SELPLG_ENST00000228463.6_Missense_Mutation_p.Q151P			Q14242	SELPL_HUMAN	selectin P ligand	135	12 X 10 AA tandem repeats.		Missing (in short form; not an alternative splicing; dbSNP:rs63748999). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7505206}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interleukin-6 (GO:0071354)|leukocyte adhesive activation (GO:0050902)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.Q135P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|prostate(3)|skin(1)	12						GGGCACTGGTTGAGTGGTCTG	0.617																																					p.Q151P		Atlas-SNP	.											SELPLG_ENST00000550948,NS,haematopoietic_neoplasm,0,1	SELPLG	138	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A452C						scavenged	.						165.0	129.0	141.0					12																	109017680		2201	4282	6483	SO:0001583	missense	6404	exon2			ACTGGTTGAGTGG		CCDS31895.1, CCDS31895.2, CCDS55881.1	12q24	2014-01-30						"""CD molecules"", ""Endogenous ligands"""	10722	protein-coding gene	gene with protein product		600738				7505206	Standard	NM_003006		Approved	PSGL-1, CD162	uc010sxe.2	Q14242		ENST00000550948.1:c.404A>C	12.37:g.109017680T>G	ENSP00000447752:p.Gln135Pro	Somatic	175	1	0.00571429		WXS	Illumina HiSeq	Phase_I	161	22	0.136646	NM_001206609	A8K2Y0|B4DQC3|B7Z5C7|J3KMX6|Q12775|Q6GTW7|Q8N7J7	Missense_Mutation	SNP	ENST00000550948.1	37	CCDS31895.2	.	.	.	.	.	.	.	.	.	.	N	7.318	0.616396	0.14129	.	.	ENSG00000110876	ENST00000550948;ENST00000228463	T;T	0.28666	1.6;1.6	3.51	-7.02	0.01589	.	3.684700	0.01036	N	0.004222	T	0.23727	0.0574	L	0.54323	1.7	0.09310	N	1	P;P	0.47604	0.898;0.898	B;B	0.40165	0.321;0.321	T	0.41088	-0.9528	10	0.29301	T	0.29	1.368	4.4646	0.11682	0.2642:0.4833:0.0955:0.157	.	151;135	B7Z5C7;Q14242	.;SELPL_HUMAN	P	135;151	ENSP00000447752:Q135P;ENSP00000228463:Q151P	ENSP00000228463:Q151P	Q	-	2	0	SELPLG	107541809	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.658000	0.05329	-1.703000	0.01409	-0.441000	0.05720	CAA	T|0.986;G|0.014	0.014	strong		0.617	SELPLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403904.1		
KIAA1755	85449	hgsc.bcm.edu	37	20	36845738	36845738	+	Missense_Mutation	SNP	C	C	T	rs760998	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36845738C>T	ENST00000279024.4	-	13	3089	c.2818G>A	c.(2818-2820)Gag>Aag	p.E940K		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	940			E -> K (in dbSNP:rs760998). {ECO:0000269|PubMed:11214970}.							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)				TGGGTCAGCTCAGCCTGGAAG	0.667													T|||	1685	0.336462	0.2504	0.3429	5008	,	,		14156	0.5188		0.2982	False		,,,				2504	0.2996				p.E940K		Atlas-SNP	.											KIAA1755,NS,carcinoma,0,1	KIAA1755	145	1	0			c.G2818A						scavenged	.	T	LYS/GLU	1119,3285	703.8+/-407.0	143,833,1226	41.0	36.0	37.0		2818	3.5	0.2	20	dbSNP_86	37	2711,5889	666.8+/-402.4	415,1881,2004	yes	missense	KIAA1755	NM_001029864.1	56	558,2714,3230	TT,TC,CC		31.5233,25.4087,29.4525	benign	940/1201	36845738	3830,9174	2202	4300	6502	SO:0001583	missense	85449	exon13			TCAGCTCAGCCTG	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.2818G>A	20.37:g.36845738C>T	ENSP00000279024:p.Glu940Lys	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	129	73	0.565891	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	765	0.35027472527472525	125	0.2540650406504065	121	0.3342541436464088	283	0.49475524475524474	236	0.3113456464379947	T	1.353	-0.590772	0.03799	0.254087	0.315233	ENSG00000149633	ENST00000279024;ENST00000373398;ENST00000435901	T;T	0.21031	3.53;2.03	4.59	3.46	0.39613	.	0.419614	0.20255	N	0.095994	T	0.00012	0.0000	N	0.00138	-2.015	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46569	-0.9182	9	0.02654	T	1	.	5.9032	0.18978	0.0:0.0899:0.1666:0.7435	rs760998;rs57283281;rs760998	940;448	Q5JYT7;E9PFS1	K1755_HUMAN;.	K	940;448;239	ENSP00000279024:E940K;ENSP00000393503:E239K	ENSP00000279024:E940K	E	-	1	0	KIAA1755	36279152	0.981000	0.34729	0.171000	0.22900	0.605000	0.37080	2.366000	0.44204	0.271000	0.22005	-0.361000	0.07541	GAG	C|0.680;T|0.320	0.320	strong		0.667	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204198209	204198209	+	Silent	SNP	A	A	G	rs3795571	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204198209A>G	ENST00000272203.3	-	19	2923	c.2607T>C	c.(2605-2607)caT>caC	p.H869H	PLEKHA6_ENST00000414478.1_Silent_p.H889H	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	869										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			TGTCTACCTCATGGATGCTGC	0.632													G|||	2566	0.51238	0.6967	0.5389	5008	,	,		19143	0.4802		0.4344	False		,,,				2504	0.3579				p.H869H		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.T2607C						PASS	.	G		2912,1494	475.3+/-357.3	971,970,262	41.0	43.0	42.0		2607	-2.6	1.0	1	dbSNP_107	42	3938,4662	598.8+/-394.0	891,2156,1253	no	coding-synonymous	PLEKHA6	NM_014935.2		1862,3126,1515	GG,GA,AA		45.7907,33.9083,47.332		869/1049	204198209	6850,6156	2203	4300	6503	SO:0001819	synonymous_variant	22874	exon19			TACCTCATGGATG	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2607T>C	1.37:g.204198209A>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_014935	A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	37	CCDS1444.1																																																																																			A|0.469;G|0.531	0.531	strong		0.632	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
AMACR	23600	hgsc.bcm.edu	37	5	34004707	34004707	+	Missense_Mutation	SNP	C	C	T	rs10941112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:34004707C>T	ENST00000335606.6	-	3	612	c.524G>A	c.(523-525)gGc>gAc	p.G175D	AMACR_ENST00000382085.3_Missense_Mutation_p.G175D|AMACR_ENST00000382068.3_Intron|AMACR_ENST00000382072.2_Intron|AMACR_ENST00000441713.2_Intron|RP11-1084J3.4_ENST00000382079.3_Intron|AMACR_ENST00000512079.1_Missense_Mutation_p.G175D|AMACR_ENST00000514195.1_Intron|AMACR_ENST00000426255.2_Missense_Mutation_p.G175D|AMACR_ENST00000502637.1_Missense_Mutation_p.G175D	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	175			G -> D (in dbSNP:rs10941112). {ECO:0000269|PubMed:11060344, ECO:0000269|Ref.4}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						CTGACCCTTGCCAGTGCGTGT	0.458													C|||	1265	0.252596	0.0242	0.4006	5008	,	,		16552	0.3472		0.504	False		,,,				2504	0.1002				p.G175D		Atlas-SNP	.											.	AMACR	38	.	0			c.G524A						PASS	.	C	ASP/GLY,ASP/GLY,	483,3923	227.2+/-242.5	32,419,1752	151.0	133.0	139.0		524,524,	5.9	1.0	5	dbSNP_120	139	4514,4086	593.3+/-393.1	1170,2174,956	yes	missense,missense,intron	AMACR	NM_001167595.1,NM_014324.5,NM_203382.2	94,94,	1202,2593,2708	TT,TC,CC		47.5116,10.9623,38.4207	probably-damaging,probably-damaging,	175/395,175/383,	34004707	4997,8009	2203	4300	6503	SO:0001583	missense	23600	exon3			CCCTTGCCAGTGC	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.524G>A	5.37:g.34004707C>T	ENSP00000334424:p.Gly175Asp	Somatic	284	0	0		WXS	Illumina HiSeq	Phase_I	314	130	0.414013	NM_014324	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	768	0.3516483516483517	16	0.032520325203252036	160	0.4419889502762431	202	0.3531468531468531	390	0.5145118733509235	C	35	5.477865	0.96291	0.109623	0.524884	ENSG00000242110	ENST00000335606;ENST00000382085;ENST00000502637	T;T;T	0.72505	-0.66;-0.66;-0.66	5.92	5.92	0.95590	CoA-transferase family III domain (2);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.98786	4.33	0.09310	P	1.0	P;P;P	0.50066	0.915;0.931;0.931	P;P;P	0.56434	0.622;0.798;0.798	T	0.25950	-1.0117	9	0.56958	D	0.05	-21.7172	20.3206	0.98668	0.0:1.0:0.0:0.0	rs10941112;rs52822382;rs59795499;rs10941112	175;175;175	F8W9N1;D6RB81;Q9UHK6	.;.;AMACR_HUMAN	D	175	ENSP00000334424:G175D;ENSP00000371517:G175D;ENSP00000424351:G175D	ENSP00000334424:G175D	G	-	2	0	AMACR	34040464	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.414000	0.59802	2.809000	0.96659	0.655000	0.94253	GGC	C|0.655;T|0.345	0.345	strong		0.458	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
CHPF	79586	hgsc.bcm.edu	37	2	220404726	220404726	+	Silent	SNP	G	G	A	rs1043832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220404726G>A	ENST00000243776.6	-	4	1955	c.1707C>T	c.(1705-1707)caC>caT	p.H569H	CHPF_ENST00000535926.1_Silent_p.H407H	NM_024536.5	NP_078812	Q8IZ52	CHSS2_HUMAN	chondroitin polymerizing factor	569	Ala-rich.				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)	21		Renal(207;0.0183)		Epithelial(149;3.02e-08)|all cancers(144;3.41e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		GCTCTGCCACGTGGGCCTTGA	0.662													G|||	1534	0.30631	0.1891	0.4841	5008	,	,		17582	0.2738		0.4523	False		,,,				2504	0.2219				p.H569H		Atlas-SNP	.											.	CHPF	56	.	0			c.C1707T						PASS	.	G	,	1094,3308		126,842,1233	27.0	32.0	30.0		1221,1707	-4.6	0.9	2	dbSNP_86	30	3973,4621		940,2093,1264	yes	coding-synonymous,coding-synonymous	CHPF	NM_001195731.1,NM_024536.5	,	1066,2935,2497	AA,AG,GG		46.2299,24.8523,38.9889	,	407/614,569/776	220404726	5067,7929	2201	4297	6498	SO:0001819	synonymous_variant	79586	exon4			TGCCACGTGGGCC	BC008878	CCDS2443.1, CCDS56169.1	2q35	2014-02-12			ENSG00000123989	ENSG00000123989	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24291	protein-coding gene	gene with protein product	"""chondroitin sulfate synthase 2"""	610405				11230166, 12716890	Standard	NM_024536		Approved	CSS2, CHSY2	uc002vmc.4	Q8IZ52	OTTHUMG00000058929	ENST00000243776.6:c.1707C>T	2.37:g.220404726G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	171	82	0.479532	NM_024536	B4DXU0|Q6UXD6|Q7L4G1|Q9H0F8|Q9H618	Silent	SNP	ENST00000243776.6	37	CCDS2443.1																																																																																			G|0.620;C|0.000;A|0.380	0.380	strong		0.662	CHPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130268.1	NM_024536	
IFI30	10437	hgsc.bcm.edu	37	19	18288069	18288069	+	Silent	SNP	A	A	G	rs7125	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18288069A>G	ENST00000407280.3	+	5	778	c.603A>G	c.(601-603)ccA>ccG	p.P201P	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	201					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)	p.P201P(1)		endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						TCCAGCCACCACACGAGTATG	0.572													G|||	2130	0.425319	0.5825	0.4769	5008	,	,		17497	0.2103		0.5308	False		,,,				2504	0.2894				p.P201P		Atlas-SNP	.											IFI30,NS,carcinoma,0,1	IFI30	12	1	1	Substitution - coding silent(1)	stomach(1)	c.A603G						PASS	.	G		2433,1853		713,1007,423	35.0	38.0	37.0		603	-10.2	0.0	19	dbSNP_52	37	4504,4014		1247,2010,1002	no	coding-synonymous	IFI30	NM_006332.3		1960,3017,1425	GG,GA,AA		47.1237,43.2338,45.8216		201/251	18288069	6937,5867	2143	4259	6402	SO:0001819	synonymous_variant	10437	exon5			GCCACCACACGAG	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"""gamma-interferon-inducible lysosomal thiol reductase"", ""interferon gamma-inducible protein 30 preproprotein"""	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.603A>G	19.37:g.18288069A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	164	163	0.993902	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	37	CCDS46015.1																																																																																			A|0.525;C|0.003	.	strong		0.572	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332	
BAG4	9530	hgsc.bcm.edu	37	8	38034402	38034402	+	Silent	SNP	G	G	A	rs61731143	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:38034402G>A	ENST00000287322.4	+	1	286	c.15G>A	c.(13-15)agG>agA	p.R5R	LSM1_ENST00000311351.4_5'Flank|LSM1_ENST00000520755.1_5'Flank|BAG4_ENST00000521282.1_Intron|BAG4_ENST00000432471.2_Silent_p.R5R|LSM1_ENST00000522515.1_5'Flank	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	5					cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				CGGCCCTGAGGCGCTCGGGCT	0.701													G|||	16	0.00319489	0.0	0.0144	5008	,	,		12933	0.0		0.006	False		,,,				2504	0.0				p.R5R		Atlas-SNP	.											.	BAG4	32	.	0			c.G15A						PASS	.	G	,	3,4047		0,3,2022	12.0	10.0	11.0		15,15	3.6	1.0	8	dbSNP_129	11	56,7836		0,56,3890	no	coding-synonymous,coding-synonymous	BAG4	NM_001204878.1,NM_004874.3	,	0,59,5912	AA,AG,GG		0.7096,0.0741,0.4941	,	5/422,5/458	38034402	59,11883	2025	3946	5971	SO:0001819	synonymous_variant	9530	exon1			CCTGAGGCGCTCG	AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"""silencer of death domains"""	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.15G>A	8.37:g.38034402G>A		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_001204878	B4E217|O95818	Silent	SNP	ENST00000287322.4	37	CCDS6104.1																																																																																			G|0.995;A|0.005	0.005	strong		0.701	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874	
FAM53B	9679	hgsc.bcm.edu	37	10	126370638	126370638	+	Silent	SNP	G	G	A	rs148943049		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:126370638G>A	ENST00000337318.3	-	4	655	c.444C>T	c.(442-444)agC>agT	p.S148S	RP11-12J10.3_ENST00000494792.1_3'UTR|FAM53B_ENST00000280780.6_Silent_p.S148S|FAM53B_ENST00000392754.3_Silent_p.S148S	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	148										cervix(1)|lung(5)|ovary(2)|pancreas(1)	9		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		CGCTGCCCCCGCTGTAGCAGC	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.001				p.S148S		Atlas-SNP	.											.	FAM53B	22	.	0			c.C444T						PASS	.	G		0,4406		0,0,2203	28.0	29.0	28.0		444	-8.4	0.2	10	dbSNP_134	28	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	FAM53B	NM_014661.3		0,9,6494	AA,AG,GG		0.1047,0.0,0.0692		148/423	126370638	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	9679	exon4			GCCCCCGCTGTAG	D50930	CCDS7641.1	10q26.13	2004-11-24	2004-11-24	2004-11-24	ENSG00000189319	ENSG00000189319			28968	protein-coding gene	gene with protein product			"""KIAA0140"""	KIAA0140		8590280	Standard	NM_014661		Approved	bA12J10.2	uc001lhv.1	Q14153	OTTHUMG00000019215	ENST00000337318.3:c.444C>T	10.37:g.126370638G>A		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_014661	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Silent	SNP	ENST00000337318.3	37	CCDS7641.1																																																																																			G|0.999;A|0.001	0.001	strong		0.612	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661	
FAM205A	259308	hgsc.bcm.edu	37	9	34723744	34723744	+	Missense_Mutation	SNP	C	C	A	rs4878588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34723744C>A	ENST00000378788.3	-	4	3532	c.3493G>T	c.(3493-3495)Gct>Tct	p.A1165S		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	1165				A -> S (in Ref. 1; BAC86357). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CCCTGTGAAGCCTGGGGCAAC	0.522													C|||	2010	0.401358	0.0613	0.4035	5008	,	,		19037	0.6181		0.4881	False		,,,				2504	0.547				p.A1165S		Atlas-SNP	.											.	FAM205A	45	.	0			c.G3493T						PASS	.	C	SER/ALA	160,1224		8,144,540	87.0	65.0	72.0		3493	-2.8	0.0	9	dbSNP_111	72	1546,1636		367,812,412	no	missense	FAM205A	NM_001141917.1	99	375,956,952	AA,AC,CC		48.5858,11.5607,37.3631	possibly-damaging	1165/1336	34723744	1706,2860	692	1591	2283	SO:0001583	missense	259308	exon4			GTGAAGCCTGGGG		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.3493G>T	9.37:g.34723744C>A	ENSP00000417711:p.Ala1165Ser	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	80	31	0.3875	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	903	0.41346153846153844	42	0.08536585365853659	149	0.4116022099447514	333	0.5821678321678322	379	0.5	C	14.84	2.654219	0.47467	0.115607	0.485858	ENSG00000205108	ENST00000378788	T	0.27720	1.65	4.04	-2.84	0.05751	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	B	0.24258	0.1	B	0.24848	0.056	T	0.45659	-0.9246	8	0.41790	T	0.15	.	0.9704	0.01414	0.1608:0.2732:0.1579:0.4081	rs4878588	1165	Q6ZU69	F205A_HUMAN	S	1165	ENSP00000417711:A1165S	ENSP00000417711:A1165S	A	-	1	0	RP11-195F19.10	34713744	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.721000	0.04963	-0.454000	0.07066	-0.907000	0.02831	GCT	C|0.575;A|0.425	0.425	strong		0.522	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
COG5	10466	hgsc.bcm.edu	37	7	106897237	106897237	+	Intron	SNP	A	A	C	rs17349904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:106897237A>C	ENST00000347053.3	-	15	1830				COG5_ENST00000393603.2_Silent_p.V594V|COG5_ENST00000297135.3_Silent_p.V594V	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5						intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						GACTGGAAACAACCTAGAACA	0.338													A|||	650	0.129792	0.0136	0.121	5008	,	,		16049	0.1587		0.2028	False		,,,				2504	0.1881				p.V594V		Atlas-SNP	.											.	COG5	78	.	0			c.T1782G						PASS	.	A	,,	220,4186	131.0+/-167.6	6,208,1989	78.0	78.0	78.0		1782,1782,	-3.4	1.0	7	dbSNP_123	78	1847,6753	326.9+/-317.6	207,1433,2660	no	coding-synonymous,coding-synonymous,intron	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	,,	213,1641,4649	CC,CA,AA		21.4767,4.9932,15.8927	,,	594/824,594/861,	106897237	2067,10939	2203	4300	6503	SO:0001627	intron_variant	10466	exon16			GGAAACAACCTAG	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1779+1480T>G	7.37:g.106897237A>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	33	0.532258	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Silent	SNP	ENST00000347053.3	37	CCDS5743.1																																																																																			A|0.851;C|0.149	0.149	strong		0.338	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
ASB8	140461	hgsc.bcm.edu	37	12	48543584	48543584	+	Silent	SNP	G	G	C	rs3936179	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48543584G>C	ENST00000317697.3	-	4	601	c.432C>G	c.(430-432)gtC>gtG	p.V144V	ASB8_ENST00000539528.1_3'UTR|ASB8_ENST00000536953.1_3'UTR|ASB8_ENST00000535055.1_3'UTR|ASB8_ENST00000537754.1_5'UTR|ASB8_ENST00000536549.1_Silent_p.V144V	NM_024095.3	NP_077000.1	Q9H765	ASB8_HUMAN	ankyrin repeat and SOCS box containing 8	144					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|large_intestine(2)|lung(5)|soft_tissue(1)	11						CCAGGGCATTGACAGAGGCCC	0.527													G|||	135	0.0269569	0.0136	0.0346	5008	,	,		19708	0.0		0.0835	False		,,,				2504	0.0092				p.V144V		Atlas-SNP	.											.	ASB8	25	.	0			c.C432G						PASS	.	G		116,4290	88.2+/-126.9	0,116,2087	78.0	73.0	74.0		432	4.2	1.0	12	dbSNP_108	74	726,7874	176.6+/-226.4	31,664,3605	no	coding-synonymous	ASB8	NM_024095.3		31,780,5692	CC,CG,GG		8.4419,2.6328,6.4739		144/289	48543584	842,12164	2203	4300	6503	SO:0001819	synonymous_variant	140461	exon4			GGCATTGACAGAG	AK024908	CCDS8761.1	12q13.12	2013-01-10	2011-01-25			ENSG00000177981		"""Ankyrin repeat domain containing"""	17183	protein-coding gene	gene with protein product		615053	"""ankyrin repeat and SOCS box-containing 8"""			12076535	Standard	NM_024095		Approved	MGC5540, FLJ21255	uc001rrh.3	Q9H765		ENST00000317697.3:c.432C>G	12.37:g.48543584G>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	154	84	0.545455	NM_024095	A8K1P2|Q547Q2	Silent	SNP	ENST00000317697.3	37	CCDS8761.1																																																																																			G|0.946;C|0.054	0.054	strong		0.527	ASB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396497.1		
DNAH6	1768	hgsc.bcm.edu	37	2	84880695	84880695	+	Silent	SNP	G	G	A	rs12992282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:84880695G>A	ENST00000237449.6	+	33	5339	c.5331G>A	c.(5329-5331)ggG>ggA	p.G1777G	DNAH6_ENST00000389394.3_Silent_p.G1777G|DNAH6_ENST00000398278.2_Silent_p.G1777G			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	1777	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						AAAAACTTGGGATAGAAAATT	0.383													G|||	201	0.0401358	0.0106	0.0533	5008	,	,		20330	0.0		0.1421	False		,,,				2504	0.0072				p.G1777G		Atlas-SNP	.											.	DNAH6	194	.	0			c.G5331A						PASS	.	G		37,1347		0,37,655	71.0	64.0	66.0		5331	-7.3	0.0	2	dbSNP_121	66	489,2693		40,409,1142	no	coding-synonymous	DNAH6	NM_001370.1		40,446,1797	AA,AG,GG		15.3677,2.6734,11.5199		1777/4159	84880695	526,4040	692	1591	2283	SO:0001819	synonymous_variant	1768	exon34			ACTTGGGATAGAA	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.5331G>A	2.37:g.84880695G>A		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	94	46	0.489362	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.925;A|0.075	0.075	strong		0.383	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
PARP9	83666	hgsc.bcm.edu	37	3	122274757	122274757	+	Silent	SNP	G	G	C	rs73192127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:122274757G>C	ENST00000360356.2	-	4	593	c.366C>G	c.(364-366)gtC>gtG	p.V122V	PARP9_ENST00000492382.1_Intron|PARP9_ENST00000471785.1_Silent_p.V87V|PARP9_ENST00000477522.2_Silent_p.V87V|PARP9_ENST00000462315.1_Silent_p.V87V	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	122	Macro 1. {ECO:0000255|PROSITE- ProRule:PRU00490}.				cell migration (GO:0016477)|double-strand break repair (GO:0006302)|regulation of response to interferon-gamma (GO:0060330)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	34				GBM - Glioblastoma multiforme(114;0.0519)		CATCTTTCCAGACTGATAACT	0.498													G|||	938	0.1873	0.0651	0.2046	5008	,	,		17635	0.2312		0.2594	False		,,,				2504	0.2209				p.V122V		Atlas-SNP	.											PARP9,caecum,carcinoma,+2,1	PARP9	72	1	0			c.C366G						PASS	.	G	,,,,,	428,3978	208.2+/-229.3	18,392,1793	106.0	92.0	97.0		366,261,261,261,261,366	2.5	1.0	3	dbSNP_130	97	2252,6348	381.6+/-340.1	297,1658,2345	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARP9	NM_001146102.1,NM_001146103.1,NM_001146104.1,NM_001146105.1,NM_001146106.1,NM_031458.2	,,,,,	315,2050,4138	CC,CG,GG		26.186,9.714,20.6059	,,,,,	122/855,87/820,87/820,87/820,87/711,122/855	122274757	2680,10326	2203	4300	6503	SO:0001819	synonymous_variant	83666	exon4			TTTCCAGACTGAT	AF307339	CCDS3014.1, CCDS54633.1, CCDS54634.1	3q13-q21	2010-02-16			ENSG00000138496	ENSG00000138496		"""Poly (ADP-ribose) polymerases"""	24118	protein-coding gene	gene with protein product		612065				11110709	Standard	NM_031458		Approved	BAL, BAL1	uc003efi.3	Q8IXQ6	OTTHUMG00000159522	ENST00000360356.2:c.366C>G	3.37:g.122274757G>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_031458	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Silent	SNP	ENST00000360356.2	37	CCDS3014.1																																																																																			G|0.793;C|0.207	0.207	strong		0.498	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458	
LILRB3	11025	hgsc.bcm.edu	37	19	54724458	54724458	+	Missense_Mutation	SNP	A	A	G	rs1052993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54724458A>G	ENST00000391750.1	-	7	1334	c.1198T>C	c.(1198-1200)Tac>Cac	p.Y400H	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Missense_Mutation_p.Y400H|LILRB3_ENST00000407860.2_Missense_Mutation_p.Y400H|LILRB3_ENST00000424807.1_Missense_Mutation_p.Y400H|LILRB3_ENST00000346401.6_Missense_Mutation_p.Y400H|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.Y400H|LILRA6_ENST00000270464.5_Missense_Mutation_p.Y400H			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	400	Ig-like C2-type 4.		Y -> F (in dbSNP:rs8105096).|Y -> H (in dbSNP:rs1052992).|Y -> R (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:9548455, ECO:0000269|Ref.3}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TTGGAGCTGTATGAGCCGTAG	0.607													.|||	1462	0.291933	0.4334	0.2651	5008	,	,		9334	0.0456		0.2853	False		,,,				2504	0.3804				p.Y400H		Atlas-SNP	.											.	LILRB3	67	.	0			c.T1198C						PASS	.						19.0	12.0	15.0					19																	54724458		2189	4016	6205	SO:0001583	missense	11025	exon6			AGCTGTATGAGCC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1198T>C	19.37:g.54724458A>G	ENSP00000375630:p.Tyr400His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	369	0.16895604395604397	146	0.2967479674796748	75	0.20718232044198895	22	0.038461538461538464	126	0.1662269129287599	G	0.777	-0.763618	0.02996	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464	T;T;T;T;T;T;T	0.00730	5.77;5.77;5.77;5.77;5.77;5.77;5.77	2.88	0.113	0.14631	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.834670	0.00465	N	0.000119	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B;B;B;B;B;B	0.09022	0.0;0.0;0.001;0.002;0.001;0.0	B;B;B;B;B;B	0.12837	0.004;0.003;0.008;0.006;0.005;0.001	T	0.41770	-0.9490	9	0.12766	T	0.61	.	2.4703	0.04562	0.3331:0.0:0.444:0.2229	rs1052993;rs2917664;rs3193477;rs3951832	400;400;400;400;400;400	B5MCX0;F8WCY4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;LIRB3_HUMAN;.	H	400	ENSP00000375630:Y400H;ENSP00000412771:Y400H;ENSP00000345184:Y400H;ENSP00000245620:Y400H;ENSP00000384274:Y400H;ENSP00000390120:Y400H;ENSP00000270464:Y400H	ENSP00000270464:Y400H	Y	-	1	0	LILRB3;LILRA6	59416270	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.453000	0.02383	-0.165000	0.10908	-0.330000	0.08379	TAC	A|1.000;|0.000	.	strong		0.607	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
DCTD	1635	hgsc.bcm.edu	37	4	183815688	183815688	+	Silent	SNP	A	A	G	rs4742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:183815688A>G	ENST00000438320.2	-	4	605	c.315T>C	c.(313-315)gtT>gtC	p.V105V	DCTD_ENST00000510370.1_Silent_p.V105V|DCTD_ENST00000357067.3_Silent_p.V116V	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	105					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	dCMP deaminase activity (GO:0004132)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|urinary_tract(1)	18		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)	Cytarabine(DB00987)	GGAACAAGGCAACATACATAC	0.463													A|||	1556	0.310703	0.5182	0.1974	5008	,	,		20632	0.2202		0.2913	False		,,,				2504	0.2239				p.V116V		Atlas-SNP	.											.	DCTD	30	.	0			c.T348C						PASS	.	A	,	2254,2152	595.3+/-388.4	592,1070,541	199.0	159.0	172.0		348,315	-5.9	0.3	4	dbSNP_52	172	2636,5964	426.0+/-355.2	399,1838,2063	no	coding-synonymous,coding-synonymous	DCTD	NM_001012732.1,NM_001921.2	,	991,2908,2604	GG,GA,AA		30.6512,48.8425,37.598	,	116/190,105/179	183815688	4890,8116	2203	4300	6503	SO:0001819	synonymous_variant	1635	exon4			CAAGGCAACATAC	L12136	CCDS3831.1, CCDS34108.1	4q35.1	2008-08-01			ENSG00000129187	ENSG00000129187	3.5.4.12		2710	protein-coding gene	gene with protein product		607638					Standard	XM_005262778		Approved		uc003ivg.3	P32321	OTTHUMG00000160685	ENST00000438320.2:c.315T>C	4.37:g.183815688A>G		Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	155	73	0.470968	NM_001012732	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Silent	SNP	ENST00000438320.2	37	CCDS3831.1																																																																																			T|0.125;G|0.280;C|0.062;A|0.534	0.280	strong		0.463	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2		
INPP5J	27124	hgsc.bcm.edu	37	22	31529463	31529463	+	Silent	SNP	C	C	A	rs35342535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:31529463C>A	ENST00000331075.5	+	11	2452	c.2403C>A	c.(2401-2403)acC>acA	p.T801T	INPP5J_ENST00000412277.2_Silent_p.T734T|INPP5J_ENST00000404390.3_Silent_p.T433T|INPP5J_ENST00000402238.1_Intron|INPP5J_ENST00000404453.1_Silent_p.T166T|INPP5J_ENST00000401755.1_Silent_p.T166T|INPP5J_ENST00000400294.2_Silent_p.T434T|INPP5J_ENST00000405300.1_Silent_p.T434T	NM_001284285.1	NP_001271214.1	Q15735	PI5PA_HUMAN	inositol polyphosphate-5-phosphatase J	801	Required for ruffle localization. {ECO:0000250}.				inositol phosphate metabolic process (GO:0043647)|negative regulation of microtubule polymerization (GO:0031115)|negative regulation of neuron projection development (GO:0010977)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(1)	12						ATGGGAATACCTACCAGGTAC	0.537													C|||	1301	0.259784	0.1906	0.281	5008	,	,		19967	0.0208		0.3877	False		,,,				2504	0.453				p.T433T		Atlas-SNP	.											.	INPP5J	94	.	0			c.C1299A						PASS	.	C		834,3112		86,662,1225	97.0	95.0	95.0		1299	2.3	1.0	22	dbSNP_126	95	3215,5099		632,1951,1574	no	coding-synonymous	INPP5J	NM_001002837.1		718,2613,2799	AA,AC,CC		38.6697,21.1353,33.0261		433/639	31529463	4049,8211	1973	4157	6130	SO:0001819	synonymous_variant	27124	exon11			GAATACCTACCAG	U45975	CCDS46687.1, CCDS63453.1, CCDS63454.1, CCDS63455.1, CCDS74847.1	22q12.2	2008-09-09	2008-09-09	2008-09-09	ENSG00000185133	ENSG00000185133			8956	protein-coding gene	gene with protein product		606481	"""phosphatidylinositol (4,5) bisphosphate 5-phosphatase, A"""	PIB5PA		10591208	Standard	NM_001284287		Approved	INPP5	uc003aju.4	Q15735	OTTHUMG00000151206	ENST00000331075.5:c.2403C>A	22.37:g.31529463C>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_001002837	B3KS54|Q32M61|Q6ZTH6|Q8N902|Q9UDT9	Silent	SNP	ENST00000331075.5	37																																																																																				C|0.726;A|0.274	0.274	strong		0.537	INPP5J-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000321784.1	NM_001002837	
FRRS1	391059	hgsc.bcm.edu	37	1	100174670	100174670	+	Missense_Mutation	SNP	C	C	T	rs12145706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:100174670C>T	ENST00000414213.1	-	17	2294	c.1693G>A	c.(1693-1695)Gct>Act	p.A565T	FRRS1_ENST00000287474.5_Missense_Mutation_p.M555I|FRRS1_ENST00000492943.1_5'Flank			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	565						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)		TTTTTAAAAGCATGACCCTGA	0.343													C|||	809	0.161542	0.4508	0.0605	5008	,	,		18784	0.0853		0.0388	False		,,,				2504	0.047				p.M555I		Atlas-SNP	.											.	FRRS1	50	.	0			c.G1665A						PASS	.	C	ILE/MET	1569,2837	481.4+/-359.1	280,1009,914	57.0	60.0	59.0		1665	1.4	1.0	1	dbSNP_120	59	313,8287	111.6+/-171.8	6,301,3993	yes	missense	FRRS1	NM_001013660.2	10	286,1310,4907	TT,TC,CC		3.6395,35.6105,14.4702	benign	555/627	100174670	1882,11124	2203	4300	6503	SO:0001583	missense	391059	exon17			TAAAAGCATGACC	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.1693G>A	1.37:g.100174670C>T	ENSP00000393884:p.Ala565Thr	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	73	34	0.465753	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		305|305	0.13965201465201466|0.13965201465201466	210|210	0.4268292682926829|0.4268292682926829	20|20	0.055248618784530384|0.055248618784530384	45|45	0.07867132867132867|0.07867132867132867	30|30	0.0395778364116095|0.0395778364116095	C|C	8.188|8.188	0.795358|0.795358	0.16327|0.16327	0.356105|0.356105	0.036395|0.036395	ENSG00000156869|ENSG00000156869	ENST00000414213|ENST00000287474	.|.	.|.	.|.	5.43|5.43	1.41|1.41	0.22369|0.22369	.|.	.|7.020340	.|0.00397	.|N	.|0.000056	T|T	0.09335|0.09335	0.0230|0.0230	.|.	.|.	.|.	0.54753|0.54753	P|P	1.0999999999983245E-5|1.0999999999983245E-5	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.23154|0.23154	-1.0196|-1.0196	4|7	0.23891|0.56958	T|D	0.37|0.05	9.3087|9.3087	0.9891|0.9891	0.01453|0.01453	0.1516:0.3357:0.1477:0.365|0.1516:0.3357:0.1477:0.365	rs12145706;rs52814946;rs60060637;rs12145706|rs12145706;rs52814946;rs60060637;rs12145706	.|555	.|Q6ZNA5-2	.|.	T|I	565|555	.|.	ENSP00000393884:A565T|ENSP00000287474:M555I	A|M	-|-	1|3	0|0	FRRS1|FRRS1	99947258|99947258	0.039000|0.039000	0.19947|0.19947	0.990000|0.990000	0.47175|0.47175	0.958000|0.958000	0.62258|0.62258	0.021000|0.021000	0.13489|0.13489	0.254000|0.254000	0.21573|0.21573	-0.321000|-0.321000	0.08615|0.08615	GCT|ATG	C|0.857;T|0.143	0.143	strong		0.343	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
ALDH9A1	223	hgsc.bcm.edu	37	1	165667781	165667781	+	Silent	SNP	T	T	G	rs12408101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:165667781T>G	ENST00000354775.4	-	1	319	c.15A>C	c.(13-15)gcA>gcC	p.A5A	ALDH9A1_ENST00000538148.1_5'Flank|RP11-466F5.6_ENST00000400982.2_RNA|ALDH9A1_ENST00000461664.1_5'Flank	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	0					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					CGGCCAGGCCTGCTCGGAGAA	0.721													T|||	594	0.11861	0.0779	0.2176	5008	,	,		11031	0.004		0.2584	False		,,,				2504	0.0777				p.A5A	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											ALDH9A1_ENST00000354775,NS,carcinoma,0,1	ALDH9A1	75	1	0			c.A15C						PASS	.	T		400,3912		27,346,1783	9.0	13.0	12.0		15	-6.6	0.0	1	dbSNP_120	12	2056,6430		227,1602,2414	yes	coding-synonymous	ALDH9A1	NM_000696.3		254,1948,4197	GG,GT,TT		24.2281,9.2764,19.1905		5/519	165667781	2456,10342	2156	4243	6399	SO:0001819	synonymous_variant	223	exon1			CAGGCCTGCTCGG	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"""Aldehyde dehydrogenases"""	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.15A>C	1.37:g.165667781T>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	44	22	0.5	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	ENST00000354775.4	37	CCDS1250.2																																																																																			T|0.850;G|0.150	0.150	strong		0.721	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1		
FMN1	342184	hgsc.bcm.edu	37	15	33261232	33261232	+	Silent	SNP	G	G	A	rs2930131	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:33261232G>A	ENST00000559047.1	-	5	2669	c.2670C>T	c.(2668-2670)ccC>ccT	p.P890P	SNORD77_ENST00000391113.1_RNA|FMN1_ENST00000334528.9_Silent_p.P667P|FMN1_ENST00000561249.1_Silent_p.P792P			Q68DA7	FMN1_HUMAN	formin 1	890	FH1.|Pro-rich.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TTGGAGGTGCGGGAGACAAAG	0.637													G|||	2664	0.531949	0.1165	0.6873	5008	,	,		7252	0.7976		0.5865	False		,,,				2504	0.6534				p.P667P		Atlas-SNP	.											.	FMN1	174	.	0			c.C2001T						PASS	.	G		791,3219		97,597,1311	23.0	21.0	22.0		2001	-1.5	0.4	15	dbSNP_101	22	4781,3539		1426,1929,805	no	coding-synonymous	FMN1	NM_001103184.2		1523,2526,2116	AA,AG,GG		42.5361,19.7257,45.1906		667/1197	33261232	5572,6758	2005	4160	6165	SO:0001819	synonymous_variant	342184	exon4			AGGTGCGGGAGAC	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.2670C>T	15.37:g.33261232G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	75	74	0.986667	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Silent	SNP	ENST00000559047.1	37																																																																																				G|0.489;A|0.511	0.511	strong		0.637	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
KIAA0226	9711	hgsc.bcm.edu	37	3	197432036	197432036	+	Missense_Mutation	SNP	C	C	T	rs61743568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:197432036C>T	ENST00000296343.5	-	3	229	c.230G>A	c.(229-231)cGc>cAc	p.R77H	KIAA0226_ENST00000467303.1_5'UTR|KIAA0226_ENST00000449205.1_Missense_Mutation_p.R77H|KIAA0226_ENST00000389665.5_Missense_Mutation_p.R77H|KIAA0226_ENST00000273582.5_Missense_Mutation_p.R17H	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	77	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		ATCCGTCTGGCGGCGGCACGC	0.537													C|||	329	0.0656949	0.1188	0.0403	5008	,	,		20385	0.0		0.0984	False		,,,				2504	0.046				p.R77H	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.G230A						PASS	.	C	HIS/ARG,HIS/ARG	437,3599		26,385,1607	54.0	53.0	53.0		50,230	-1.5	1.0	3	dbSNP_129	53	724,7632		32,660,3486	yes	missense,missense	KIAA0226	NM_001145642.2,NM_014687.1	29,29	58,1045,5093	TT,TC,CC		8.6644,10.8276,9.3689	benign,benign	17/928,77/973	197432036	1161,11231	2018	4178	6196	SO:0001583	missense	9711	exon3			GTCTGGCGGCGGC	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.230G>A	3.37:g.197432036C>T	ENSP00000296343:p.Arg77His	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	147	0.0673076923076923	57	0.11585365853658537	15	0.04143646408839779	0	0.0	75	0.09894459102902374	C	14.78	2.637975	0.47153	0.108276	0.086644	ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665;ENST00000449205	T;T;T;T	0.12569	2.67;2.67;2.67;2.67	5.63	-1.51	0.08664	RUN (2);	0.482830	0.20874	N	0.084104	T	0.00109	0.0003	N	0.22421	0.69	0.35867	P	0.17206900000000003	B;B;B	0.27140	0.169;0.012;0.015	B;B;B	0.17433	0.018;0.002;0.007	T	0.27673	-1.0067	9	0.41790	T	0.15	.	11.5696	0.50826	0.0:0.3548:0.0:0.6452	.	77;17;77	E9PEM3;Q92622-2;Q92622	.;.;RUBIC_HUMAN	H	17;77;77;77	ENSP00000273582:R17H;ENSP00000296343:R77H;ENSP00000374316:R77H;ENSP00000390962:R77H	ENSP00000273582:R17H	R	-	2	0	KIAA0226	198916433	0.935000	0.31712	0.991000	0.47740	0.824000	0.46624	0.195000	0.17155	-0.170000	0.10816	-0.134000	0.14843	CGC	C|0.929;T|0.071	0.071	strong		0.537	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
KANK2	25959	hgsc.bcm.edu	37	19	11303943	11303943	+	Silent	SNP	A	A	G	rs3745681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11303943A>G	ENST00000586659.1	-	4	1127	c.813T>C	c.(811-813)gtT>gtC	p.V271V	KANK2_ENST00000589359.1_Silent_p.V271V|KANK2_ENST00000589894.1_Silent_p.V271V|KANK2_ENST00000432929.2_Silent_p.V271V|KANK2_ENST00000355150.5_Silent_p.V271V			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	271					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCCGTTCTCGAACCCAGGTGC	0.692													G|||	2531	0.505391	0.6483	0.4265	5008	,	,		15958	0.4514		0.3787	False		,,,				2504	0.5542				p.V271V		Atlas-SNP	.											KANK2,NS,carcinoma,0,1	KANK2	47	1	0			c.T813C						PASS	.	G	,	2625,1773		791,1043,365	26.0	28.0	27.0		813,813	-2.5	0.9	19	dbSNP_107	27	3333,5259		652,2029,1615	no	coding-synonymous,coding-synonymous	KANK2	NM_001136191.2,NM_015493.6	,	1443,3072,1980	GG,GA,AA		38.7919,40.3138,45.8661	,	271/852,271/860	11303943	5958,7032	2199	4296	6495	SO:0001819	synonymous_variant	25959	exon2			TTCTCGAACCCAG	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.813T>C	19.37:g.11303943A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	27	12	0.444444	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Silent	SNP	ENST00000586659.1	37	CCDS12255.1																																																																																			A|0.544;G|0.456	0.456	strong		0.692	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
REPIN1	29803	hgsc.bcm.edu	37	7	150068605	150068605	+	Missense_Mutation	SNP	G	G	A	rs17173702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150068605G>A	ENST00000425389.2	+	1	353	c.275G>A	c.(274-276)cGt>cAt	p.R92H	RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000397281.2_Missense_Mutation_p.R92H|REPIN1_ENST00000482680.1_3'UTR|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000518462.1_3'UTR|REPIN1_ENST00000444957.1_Missense_Mutation_p.R92H|REPIN1_ENST00000540729.1_Missense_Mutation_p.R92H|REPIN1_ENST00000518514.1_3'UTR|REPIN1_ENST00000489432.2_Missense_Mutation_p.R149H|REPIN1_ENST00000466559.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	92			R -> H (in dbSNP:rs17173702).		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			GAGTGTGGCCGTCGCTTTCGC	0.672													G|||	1164	0.232428	0.0227	0.1527	5008	,	,		14905	0.3988		0.2793	False		,,,				2504	0.3528				p.R149H		Atlas-SNP	.											.	REPIN1	74	.	0			c.G446A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	217,4035		8,201,1917	20.0	23.0	22.0		446,275,275,275	3.6	0.0	7	dbSNP_123	22	2270,6180		287,1696,2242	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	29,29,29,29	295,1897,4159	AA,AG,GG		26.8639,5.1035,19.5796	probably-damaging,probably-damaging,probably-damaging,probably-damaging	149/625,92/568,92/568,92/568	150068605	2487,10215	2126	4225	6351	SO:0001583	missense	29803	exon3			GTGGCCGTCGCTT	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.275G>A	7.37:g.150068605G>A	ENSP00000388287:p.Arg92His	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	546	0.25	15	0.03048780487804878	63	0.17403314917127072	243	0.42482517482517484	225	0.29683377308707126	G	10.69	1.420773	0.25639	0.051035	0.268639	ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389	T;T;T;T;T;T;T;T	0.55588	0.51;2.37;2.37;2.37;2.37;2.37;2.37;2.37	5.54	3.6	0.41247	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	.	.	.	.	T	0.00012	0.0000	L	0.49778	1.585	0.47511	P	5.600000000000049E-4	B;B	0.17268	0.021;0.021	B;B	0.15052	0.012;0.012	T	0.34725	-0.9817	8	0.87932	D	0	-6.7004	4.7515	0.13063	0.1912:0.1804:0.6283:0.0	rs17173702	149;92	C9J3L7;Q9BWE0	.;REPI1_HUMAN	H	92;92;92;92;149;151;152;149;92	ENSP00000428562:R92H;ENSP00000445016:R92H;ENSP00000380451:R92H;ENSP00000407714:R92H;ENSP00000417291:R149H;ENSP00000419789:R151H;ENSP00000419872:R152H;ENSP00000388287:R92H	ENSP00000380451:R92H	R	+	2	0	REPIN1	149699538	0.000000	0.05858	0.014000	0.15608	0.772000	0.43724	0.281000	0.18810	1.305000	0.44909	0.462000	0.41574	CGT	G|0.761;C|0.000;A|0.238	0.238	strong		0.672	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
OR51B5	282763	hgsc.bcm.edu	37	11	5364276	5364276	+	Missense_Mutation	SNP	G	G	A	rs4910551	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5364276G>A	ENST00000300773.2	-	1	533	c.479C>T	c.(478-480)cCc>cTc	p.P160L	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	160			P -> L (in dbSNP:rs4910551).		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)		AAAATAGAGGGGCCTGATTGG	0.448													G|||	1627	0.32488	0.2595	0.402	5008	,	,		18577	0.1786		0.4404	False		,,,				2504	0.3906				p.P160L		Atlas-SNP	.											.	OR51B5	60	.	0			c.C479T						PASS	.	G	LEU/PRO	1224,3178	418.5+/-338.3	168,888,1145	54.0	62.0	59.0		479	1.7	0.0	11	dbSNP_111	59	3838,4756	534.9+/-382.7	857,2124,1316	yes	missense	OR51B5	NM_001005567.2	98	1025,3012,2461	AA,AG,GG		44.6591,27.8055,38.9504	benign	160/313	5364276	5062,7934	2201	4297	6498	SO:0001583	missense	282763	exon5			TAGAGGGGCCTGA	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.479C>T	11.37:g.5364276G>A	ENSP00000300773:p.Pro160Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	712	0.326007326007326	133	0.2703252032520325	151	0.4171270718232044	91	0.1590909090909091	337	0.4445910290237467	G	1.914	-0.450089	0.04572	0.278055	0.446591	ENSG00000242180	ENST00000300773	T	0.00745	5.75	4.76	1.66	0.24008	GPCR, rhodopsin-like superfamily (1);	0.194812	0.25445	N	0.030627	T	0.00012	0.0000	N	0.00197	-1.87	0.80722	P	0.0	P	0.37276	0.589	P	0.46208	0.507	T	0.18461	-1.0336	9	0.02654	T	1	.	1.2242	0.01930	0.2411:0.1579:0.4388:0.1622	rs4910551;rs52808914;rs57207460;rs4910551	160	Q9H339	O51B5_HUMAN	L	160	ENSP00000300773:P160L	ENSP00000300773:P160L	P	-	2	0	OR51B5	5320852	0.000000	0.05858	0.003000	0.11579	0.101000	0.19017	-0.781000	0.04648	0.609000	0.30018	0.650000	0.86243	CCC	G|0.650;A|0.350	0.350	strong		0.448	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
IL7R	3575	hgsc.bcm.edu	37	5	35876274	35876274	+	Missense_Mutation	SNP	A	A	G	rs3194051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:35876274A>G	ENST00000303115.3	+	8	1195	c.1066A>G	c.(1066-1068)Atc>Gtc	p.I356V	IL7R_ENST00000343305.4_3'UTR	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	356			I -> V (in dbSNP:rs3194051). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2038316, ECO:0000269|PubMed:2317865}.		B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			GGATGTAGTCATCACTCCAGA	0.507			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						A|||	1106	0.220847	0.348	0.1816	5008	,	,		18793	0.0625		0.2823	False		,,,				2504	0.1769				p.I356V		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	.	IL7R	200	.	0			c.A1066G						PASS	.	A	VAL/ILE	1542,2864	485.7+/-360.4	269,1004,930	89.0	85.0	86.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1066	3.2	0.0	5	dbSNP_105	86	2271,6329	383.8+/-340.9	301,1669,2330	yes	missense	IL7R	NM_002185.2	29	570,2673,3260	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	26.407,34.9977,29.3172	benign	356/460	35876274	3813,9193	2203	4300	6503	SO:0001583	missense	3575	exon8			GTAGTCATCACTC	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.1066A>G	5.37:g.35876274A>G	ENSP00000306157:p.Ile356Val	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	99	98	0.989899	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	493	0.22573260073260074	164	0.3333333333333333	81	0.22375690607734808	28	0.04895104895104895	220	0.29023746701846964	A	4.605	0.112367	0.08831	0.349977	0.26407	ENSG00000168685	ENST00000303115;ENST00000505875	T;T	0.33438	1.88;1.41	5.6	3.23	0.37069	.	0.345580	0.27437	N	0.019361	T	0.00012	0.0000	L	0.56769	1.78	0.58432	P	4.000000000004E-6	B	0.20368	0.044	B	0.19148	0.024	T	0.43734	-0.9373	9	0.13108	T	0.6	-24.3005	6.0166	0.19607	0.6534:0.1963:0.0:0.1503	rs3194051;rs16902513;rs52816604;rs58270601;rs3194051	356	P16871	IL7RA_HUMAN	V	356;122	ENSP00000306157:I356V;ENSP00000420923:I122V	ENSP00000306157:I356V	I	+	1	0	IL7R	35912031	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	0.576000	0.23744	0.408000	0.25621	0.533000	0.62120	ATC	A|0.740;G|0.260	0.260	strong		0.507	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
ARHGAP31	57514	hgsc.bcm.edu	37	3	119133554	119133554	+	Silent	SNP	G	G	A	rs61740281	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:119133554G>A	ENST00000264245.4	+	12	3310	c.2778G>A	c.(2776-2778)gcG>gcA	p.A926A		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	926					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						TGAAAGACGCGCACAAGGCCC	0.602													G|||	650	0.129792	0.1263	0.1282	5008	,	,		19317	0.0863		0.1471	False		,,,				2504	0.1626				p.A926A	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											ARHGAP31,NS,carcinoma,+1,2	ARHGAP31	175	2	0			c.G2778A						PASS	.	G		445,3459		26,393,1533	102.0	103.0	103.0		2778	0.4	0.1	3	dbSNP_129	103	1106,7192		80,946,3123	no	coding-synonymous	ARHGAP31	NM_020754.2		106,1339,4656	AA,AG,GG		13.3285,11.3986,12.711		926/1445	119133554	1551,10651	1952	4149	6101	SO:0001819	synonymous_variant	57514	exon12			AGACGCGCACAAG		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"""Rho GTPase activating proteins"""	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.2778G>A	3.37:g.119133554G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_020754	Q9ULL6	Silent	SNP	ENST00000264245.4	37	CCDS43135.1																																																																																			G|0.878;A|0.122	0.122	strong		0.602	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2		
GOLGB1	2804	hgsc.bcm.edu	37	3	121414061	121414061	+	Missense_Mutation	SNP	C	C	T	rs1127412	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:121414061C>T	ENST00000340645.5	-	13	5419	c.5294G>A	c.(5293-5295)gGt>gAt	p.G1765D	GOLGB1_ENST00000393667.3_Missense_Mutation_p.G1770D	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1765			G -> D (in dbSNP:rs1127412). {ECO:0000269|PubMed:18487259, ECO:0000269|PubMed:7511208, ECO:0000269|PubMed:8198703}.		Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AGATACATTACCTTCTATCTG	0.383													C|||	1253	0.2502	0.1649	0.1614	5008	,	,		23338	0.4841		0.2515	False		,,,				2504	0.1861				p.G1770D		Atlas-SNP	.											.	GOLGB1	319	.	0			c.G5309A						PASS	.	C	ASP/GLY	708,3698	292.7+/-282.2	54,600,1549	259.0	242.0	248.0		5294	-9.9	0.0	3	dbSNP_86	248	2114,6486	365.4+/-333.9	278,1558,2464	yes	missense	GOLGB1	NM_004487.3	94	332,2158,4013	TT,TC,CC		24.5814,16.069,21.6977	benign	1765/3260	121414061	2822,10184	2203	4300	6503	SO:0001583	missense	2804	exon13			ACATTACCTTCTA	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.5294G>A	3.37:g.121414061C>T	ENSP00000341848:p.Gly1765Asp	Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	252	121	0.480159	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	610	0.2793040293040293	79	0.16056910569105692	71	0.19613259668508287	267	0.46678321678321677	193	0.2546174142480211	C	1.818	-0.473049	0.04445	0.16069	0.245814	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.13089	2.62;2.62	5.8	-9.92	0.00455	.	2.277780	0.01577	N	0.020871	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.44267	-0.9339	9	0.15066	T	0.55	.	1.5861	0.02644	0.1697:0.1956:0.1763:0.4583	rs1127412;rs52834346;rs56608721;rs1127412	1690;1770;1765	F1T0J2;E7EP74;Q14789	.;.;GOGB1_HUMAN	D	1765;1770	ENSP00000341848:G1765D;ENSP00000377275:G1770D	ENSP00000341848:G1765D	G	-	2	0	GOLGB1	122896751	0.000000	0.05858	0.000000	0.03702	0.385000	0.30292	-0.790000	0.04604	-1.808000	0.01234	-0.311000	0.09066	GGT	C|0.760;T|0.240	0.240	strong		0.383	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
PLEC	5339	hgsc.bcm.edu	37	8	144992900	144992900	+	Silent	SNP	G	G	A	rs17062686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144992900G>A	ENST00000322810.4	-	32	11669	c.11500C>T	c.(11500-11502)Ctg>Ttg	p.L3834L	PLEC_ENST00000354589.3_Silent_p.L3697L|PLEC_ENST00000357649.2_Silent_p.L3701L|PLEC_ENST00000527096.1_Silent_p.L3720L|PLEC_ENST00000398774.2_Silent_p.L3665L|PLEC_ENST00000354958.2_Silent_p.L3675L|PLEC_ENST00000436759.2_Silent_p.L3724L|PLEC_ENST00000356346.3_Silent_p.L3683L|PLEC_ENST00000345136.3_Silent_p.L3697L	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3834	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						GAACCGGGCAGGTAGACACCA	0.667													G|||	85	0.0169728	0.0023	0.0115	5008	,	,		16451	0.0		0.0517	False		,,,				2504	0.0225				p.L3834L		Atlas-SNP	.											.	PLEC	1144	.	0			c.C11500T						PASS	.	G	,,,,,,,	32,3900		1,30,1935	20.0	26.0	24.0		11170,11047,11023,11500,10993,11089,11101,11089	-0.8	0.0	8	dbSNP_123	24	408,7866		8,392,3737	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	9,422,5672	AA,AG,GG		4.9311,0.8138,3.6048	,,,,,,,	3724/4575,3683/4534,3675/4526,3834/4685,3665/4516,3697/4548,3701/4552,3697/4548	144992900	440,11766	1966	4137	6103	SO:0001819	synonymous_variant	5339	exon32			CGGGCAGGTAGAC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11500C>T	8.37:g.144992900G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	103	47	0.456311	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.970;A|0.030	0.030	strong		0.667	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
BTN3A3	10384	hgsc.bcm.edu	37	6	26443853	26443853	+	Silent	SNP	C	C	A	rs17611438	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26443853C>A	ENST00000244519.2	+	3	294	c.51C>A	c.(49-51)tcC>tcA	p.S17S	BTN3A3_ENST00000339789.4_Intron|BTN3A3_ENST00000361232.3_Intron	NM_006994.4	NP_008925.1	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3	17					T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30						TTCATGTCTCCCTCTTCTTGG	0.438													C|||	725	0.144768	0.1634	0.1772	5008	,	,		17327	0.0308		0.165	False		,,,				2504	0.1933				p.S17S		Atlas-SNP	.											.	BTN3A3	56	.	0			c.C51A						PASS	.	C	,,	788,3618	318.8+/-295.8	65,658,1480	295.0	238.0	257.0		,51,	0.1	0.0	6	dbSNP_129	257	1450,7150	279.1+/-293.8	125,1200,2975	no	intron,coding-synonymous,intron	BTN3A3	NM_001242803.1,NM_006994.4,NM_197974.2	,,	190,1858,4455	AA,AC,CC		16.8605,17.8847,17.2074	,,	,17/585,	26443853	2238,10768	2203	4300	6503	SO:0001819	synonymous_variant	10384	exon3			TGTCTCCCTCTTC	U90548	CCDS4611.1, CCDS4612.1, CCDS4612.2	6p22.1	2014-01-14			ENSG00000111801	ENSG00000111801		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1140	protein-coding gene	gene with protein product		613595				10354554, 9149941	Standard	NM_006994		Approved	BTF3, BTN3.3	uc003nhz.3	O00478	OTTHUMG00000014451	ENST00000244519.2:c.51C>A	6.37:g.26443853C>A		Somatic	358	0	0		WXS	Illumina HiSeq	Phase_I	342	160	0.467836	NM_006994	B4DWI7|E9PCP5	Silent	SNP	ENST00000244519.2	37	CCDS4611.1																																																																																			C|0.836;A|0.164	0.164	strong		0.438	BTN3A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040116.2	NM_006994	
GAL3ST2	64090	hgsc.bcm.edu	37	2	242716380	242716380	+	Missense_Mutation	SNP	A	A	T	rs12469459	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:242716380A>T	ENST00000192314.6	+	1	141	c.10A>T	c.(10-12)Atg>Ttg	p.M4L		NM_022134.2	NP_071417.2	Q9H3Q3	G3ST2_HUMAN	galactose-3-O-sulfotransferase 2	4			M -> L (in dbSNP:rs12469459). {ECO:0000269|PubMed:11029462, ECO:0000269|PubMed:15489334}.		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)		GATGATGTCCATGCTGGGCGG	0.647													A|||	1855	0.370407	0.5416	0.2392	5008	,	,		16908	0.3978		0.3052	False		,,,				2504	0.271				p.M4L		Atlas-SNP	.											.	GAL3ST2	34	.	0			c.A10T						PASS	.	A	LEU/MET	2113,2293		498,1117,588	32.0	29.0	30.0		10	-3.9	0.0	2	dbSNP_120	30	2588,6010		399,1790,2110	yes	missense	GAL3ST2	NM_022134.2	15	897,2907,2698	TT,TA,AA		30.1,47.9573,36.1504	benign	4/399	242716380	4701,8303	2203	4299	6502	SO:0001583	missense	64090	exon1			ATGTCCATGCTGG	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.10A>T	2.37:g.242716380A>T	ENSP00000192314:p.Met4Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_022134	Q17RK0|Q57Z52	Missense_Mutation	SNP	ENST00000192314.6	37	CCDS33427.1	827	0.37866300366300365	274	0.556910569105691	97	0.26795580110497236	228	0.3986013986013986	228	0.3007915567282322	A	0.005	-2.212774	0.00289	0.479573	0.301	ENSG00000154252	ENST00000192314	T	0.12039	2.72	1.94	-3.88	0.04205	.	783.549000	0.00166	U	0.000000	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	0.45041	-0.9288	9	0.02654	T	1	.	0.4254	0.00463	0.317:0.1971:0.2914:0.1945	rs12469459	4	Q9H3Q3	G3ST2_HUMAN	L	4	ENSP00000192314:M4L	ENSP00000192314:M4L	M	+	1	0	GAL3ST2	242365053	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.059000	0.01393	-1.477000	0.01872	-0.441000	0.05720	ATG	A|0.631;T|0.369	0.369	strong		0.647	GAL3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322792.1	NM_022134	
CFAP74	85452	hgsc.bcm.edu	37	1	1916890	1916890	+	IGR	SNP	C	C	T	rs3795280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1916890C>T	ENST00000434971.2	-	0	339							Q69YW0	CA222_HUMAN												breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|stomach(1)	11	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.82e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.75e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GCTCTGCAAACAGGCGTCTGG	0.662													c|||	2196	0.438498	0.6573	0.2795	5008	,	,		18797	0.4335		0.3082	False		,,,				2504	0.3947				p.L145L		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G435A						PASS	.	T		2382,1730		693,996,367	67.0	73.0	71.0		435	2.8	0.6	1	dbSNP_107	71	2744,5634		450,1844,1895	no	coding-synonymous	KIAA1751	NM_001080484.1		1143,2840,2262	TT,TC,CC		32.7524,42.072,41.0408		145/763	1916890	5126,7364	2056	4189	6245	SO:0001628	intergenic_variant	85452	exon6			TGCAAACAGGCGT																													1.37:g.1916890C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	136	123	0.904412	NM_001080484		Silent	SNP	ENST00000434971.2	37																																																																																				C|0.606;T|0.394	0.394	strong		0.662	C1orf222-201	KNOWN	basic	protein_coding	protein_coding			
KLHL30	377007	hgsc.bcm.edu	37	2	239059484	239059484	+	Silent	SNP	T	T	C	rs7605194	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:239059484T>C	ENST00000409223.1	+	8	1622	c.1515T>C	c.(1513-1515)aaT>aaC	p.N505N	KLHL30_ENST00000305959.4_Silent_p.N487N			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	505										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)		TGCATGAGAATGGCGCGCTGG	0.667													C|||	4299	0.858427	0.9728	0.7824	5008	,	,		16744	0.9256		0.7038	False		,,,				2504	0.8476				p.N505N		Atlas-SNP	.											.	KLHL30	79	.	0			c.T1515C						PASS	.	C		4102,260		1930,242,9	18.0	24.0	22.0		1515	-0.2	0.9	2	dbSNP_116	22	6212,2312		2258,1696,308	no	coding-synonymous	KLHL30	NM_198582.3		4188,1938,317	CC,CT,TT		27.1234,5.9606,19.9596		505/579	239059484	10314,2572	2181	4262	6443	SO:0001819	synonymous_variant	377007	exon8			TGAGAATGGCGCG		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.1515T>C	2.37:g.239059484T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	152	149	0.980263	NM_198582	Q6ZUS1	Silent	SNP	ENST00000409223.1	37	CCDS46555.2																																																																																			T|0.149;C|0.851	0.851	strong		0.667	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
UBXN11	91544	hgsc.bcm.edu	37	1	26608879	26608879	+	Missense_Mutation	SNP	C	C	T	rs1134581|rs140364749		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608879C>T	ENST00000374222.1	-	16	1938	c.1474G>A	c.(1474-1476)Ggc>Agc	p.G492S	UBXN11_ENST00000314675.7_Missense_Mutation_p.G372S|UBXN11_ENST00000374217.2_Missense_Mutation_p.G459S|UBXN11_ENST00000357089.4_Missense_Mutation_p.G459S|UBXN11_ENST00000374223.1_Missense_Mutation_p.G249S|UBXN11_ENST00000374221.3_Missense_Mutation_p.G492S			Q5T124	UBX11_HUMAN	UBX domain protein 11	492	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggactggggccgggaccggga	0.716																																					p.G492S		Atlas-SNP	.											UBXN11,NS,carcinoma,+2,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1474A						scavenged	.						29.0	36.0	34.0					1																	26608879		1760	4012	5772	SO:0001583	missense	91544	exon16			TGGGGCCGGGACC	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.1474G>A	1.37:g.26608879C>T	ENSP00000363339:p.Gly492Ser	Somatic	34	7	0.205882		WXS	Illumina HiSeq	Phase_I	42	32	0.761905	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	.	.	.	.	.	.	.	.	.	.	C	0.123	-1.123266	0.01770	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19669	2.2;2.13;2.57;2.55;2.55;2.57	1.27	-2.55	0.06288	.	.	.	.	.	T	0.05686	0.0149	N	0.02011	-0.69	0.19575	N	0.999966	B;B;B;B	0.18461	0.028;0.015;0.028;0.016	B;B;B;B	0.06405	0.001;0.001;0.002;0.001	T	0.32188	-0.9916	9	0.16896	T	0.51	.	3.7345	0.08506	0.0:0.3022:0.1997:0.4981	rs1134581;rs3196813	459;454;372;492	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	372;249;459;492;492;459	ENSP00000324721:G372S;ENSP00000363340:G249S;ENSP00000349601:G459S;ENSP00000363338:G492S;ENSP00000363339:G492S;ENSP00000363334:G459S	ENSP00000324721:G372S	G	-	1	0	UBXN11	26481466	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.484000	0.02316	-1.758000	0.01315	-0.582000	0.04134	GGC	C|1.000;|0.000	.	weak		0.716	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57069568	57069568	+	Missense_Mutation	SNP	T	T	C	rs35272228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57069568T>C	ENST00000532437.1	-	7	5125	c.4814A>G	c.(4813-4815)cAc>cGc	p.H1605R	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.H1605R			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1605	Arg/Glu/Lys-rich (charged).				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)				CTGGAACAGGTGTGCATCCGA	0.597													C|||	101	0.0201677	0.0023	0.0389	5008	,	,		18503	0.002		0.0447	False		,,,				2504	0.0245				p.H1605R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A4814G						PASS	.	C	ARG/HIS	46,4356	822.0+/-416.4	0,46,2155	118.0	117.0	117.0		4814	4.3	0.7	11	dbSNP_126	117	402,8190	800.9+/-407.4	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	29	8,432,6057	CC,CT,TT		4.6788,1.045,3.4477	benign	1605/1730	57069568	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon8			AACAGGTGTGCAT	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.4814A>G	11.37:g.57069568T>C	ENSP00000437271:p.His1605Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	23	0.396552	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	C	2.177	-0.388487	0.04932	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.27402	1.67;1.67	5.22	4.31	0.51392	.	0.082812	0.51477	N	0.000091	T	0.00936	0.0031	N	0.00289	-1.7	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33701	-0.9858	10	0.05959	T	0.93	-9.0253	9.3555	0.38164	0.0:0.8307:0.0:0.1693	rs35272228	1605;187	Q9C0C2;Q86TK2	TB182_HUMAN;.	R	1605	ENSP00000350990:H1605R;ENSP00000437271:H1605R	ENSP00000350990:H1605R	H	-	2	0	TNKS1BP1	56826144	0.228000	0.23718	0.705000	0.30386	0.649000	0.38597	0.896000	0.28377	0.608000	0.30000	-0.974000	0.02594	CAC	T|0.969;C|0.031	0.031	strong		0.597	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
HCLS1	3059	hgsc.bcm.edu	37	3	121354583	121354583	+	Splice_Site	SNP	G	G	A	rs3772126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:121354583G>A	ENST00000314583.3	-	9	781	c.690C>T	c.(688-690)gcC>gcT	p.A230A	HCLS1_ENST00000473883.1_5'UTR|HCLS1_ENST00000428394.2_Splice_Site_p.A193A	NM_005335.4	NP_005326	P14317	HCLS1_HUMAN	hematopoietic cell-specific Lyn substrate 1	230					actin filament polymerization (GO:0030041)|cellular response to cytokine stimulus (GO:0071345)|erythrocyte differentiation (GO:0030218)|intracellular signal transduction (GO:0035556)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell proliferation (GO:0008284)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|regulation of actin filament polymerization (GO:0030833)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	protein kinase binding (GO:0019901)|RNA polymerase II transcription factor binding (GO:0001085)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				GBM - Glioblastoma multiforme(114;0.0912)		AAGCCTCACCGGCTTCTATGG	0.507													G|||	1093	0.218251	0.0507	0.1571	5008	,	,		19404	0.4802		0.2505	False		,,,				2504	0.1851				p.A230A		Atlas-SNP	.											.	HCLS1	78	.	0			c.C690T						PASS	.	G		329,4077	172.7+/-202.6	12,305,1886	127.0	130.0	129.0		690	2.2	1.0	3	dbSNP_107	129	2112,6488	365.1+/-333.8	278,1556,2466	yes	coding-synonymous-near-splice	HCLS1	NM_005335.4		290,1861,4352	AA,AG,GG		24.5581,7.4671,18.7683		230/487	121354583	2441,10565	2203	4300	6503	SO:0001630	splice_region_variant	3059	exon9			CTCACCGGCTTCT		CCDS3003.1	3q13	2007-08-03			ENSG00000180353	ENSG00000180353			4844	protein-coding gene	gene with protein product	"""cortactin-like"""	601306				8978766, 15710041	Standard	NM_001292041		Approved	HS1, CTTNL	uc003eeh.4	P14317	OTTHUMG00000159409	ENST00000314583.3:c.691+1C>T	3.37:g.121354583G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_005335	B4DQ69|Q53Y93|Q6IBK9|Q9UDK0	Silent	SNP	ENST00000314583.3	37	CCDS3003.1																																																																																			G|0.788;A|0.212	0.212	strong		0.507	HCLS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355144.1	NM_005335	Silent
MRGPRX4	117196	hgsc.bcm.edu	37	11	18194944	18194944	+	Silent	SNP	T	T	A	rs11024531	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18194944T>A	ENST00000314254.3	+	1	561	c.141T>A	c.(139-141)gtT>gtA	p.V47V	RP11-113D6.6_ENST00000527671.1_Intron	NM_054032.3	NP_473373.2	Q96LA9	MRGX4_HUMAN	MAS-related GPR, member X4	47						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						GAAACGCGGTTGTGCTCTGGC	0.557													T|||	1374	0.274361	0.0862	0.3617	5008	,	,		21062	0.504		0.2734	False		,,,				2504	0.2311				p.V47V		Atlas-SNP	.											.	MRGPRX4	68	.	0			c.T141A						PASS	.	T		534,3864	243.4+/-253.1	29,476,1694	145.0	129.0	134.0		141	-1.1	0.0	11	dbSNP_120	134	2251,6335	380.7+/-339.8	310,1631,2352	no	coding-synonymous	MRGPRX4	NM_054032.3		339,2107,4046	AA,AT,TT		26.2171,12.1419,21.4495		47/323	18194944	2785,10199	2199	4293	6492	SO:0001819	synonymous_variant	117196	exon1			CGCGGTTGTGCTC	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.141T>A	11.37:g.18194944T>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	182	181	0.994505	NM_054032	Q3KNU3|Q3KNU4|Q502W0|Q8TDD6|Q8TDD7	Silent	SNP	ENST00000314254.3	37	CCDS7831.1																																																																																			T|0.760;A|0.240	0.240	strong		0.557	MRGPRX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389788.1	NM_054032	
SLC35G5	83650	hgsc.bcm.edu	37	8	11188752	11188752	+	Missense_Mutation	SNP	G	G	A	rs6990563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:11188752G>A	ENST00000382435.4	+	1	356	c.137G>A	c.(136-138)gGt>gAt	p.G46D		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	46			G -> D (in dbSNP:rs6990563).			integral component of membrane (GO:0016021)											GCCCTGCTGGGTGGGGGCCTG	0.677													G|||	2136	0.426518	0.1467	0.3718	5008	,	,		16974	0.7351		0.4553	False		,,,				2504	0.4959				p.G46D		Atlas-SNP	.											.	.	.	.	0			c.G137A						PASS	.	G	ASP/GLY	896,3510	343.6+/-307.7	91,714,1398	48.0	55.0	52.0		137	0.3	1.0	8	dbSNP_116	52	4014,4586	552.0+/-386.0	952,2110,1238	no	missense	SLC35G5	NM_054028.1	94	1043,2824,2636	AA,AG,GG		46.6744,20.3359,37.7518	probably-damaging	46/339	11188752	4910,8096	2203	4300	6503	SO:0001583	missense	83650	exon1			TGCTGGGTGGGGG	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.137G>A	8.37:g.11188752G>A	ENSP00000371872:p.Gly46Asp	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	904	0.4139194139194139	73	0.1483739837398374	134	0.3701657458563536	378	0.6608391608391608	319	0.420844327176781	G	15.55	2.867345	0.51588	0.203359	0.466744	ENSG00000177710	ENST00000382435	T	0.42900	0.96	0.34	0.34	0.15985	.	0.000000	0.45867	D	0.000330	T	0.00012	0.0000	L	0.27053	0.805	0.23391	P	0.99777562	D	0.71674	0.998	D	0.63597	0.916	T	0.42068	-0.9473	9	0.66056	D	0.02	-4.0269	6.5344	0.22344	2.0E-4:0.0:0.9998:0.0	rs6990563;rs58184334	46	Q96KT7	S35G5_HUMAN	D	46	ENSP00000371872:G46D	ENSP00000371872:G46D	G	+	2	0	SLC35G5	11226162	1.000000	0.71417	0.966000	0.40874	0.252000	0.25951	3.390000	0.52523	0.426000	0.26116	0.089000	0.15464	GGT	.	.	weak		0.677	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
FRA10AC1	118924	hgsc.bcm.edu	37	10	95441272	95441272	+	Missense_Mutation	SNP	G	G	A	rs11187583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:95441272G>A	ENST00000359204.4	-	11	949	c.752C>T	c.(751-753)tCt>tTt	p.S251F	FRA10AC1_ENST00000371430.2_Missense_Mutation_p.S251F|FRA10AC1_ENST00000394100.2_Missense_Mutation_p.S251F|FRA10AC1_ENST00000536233.1_Missense_Mutation_p.S251F	NM_145246.4	NP_660289.2	Q70Z53	F10C1_HUMAN	fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) candidate 1	251	Lys-rich.		S -> F (in dbSNP:rs11187583).			nucleus (GO:0005634)				NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(1)	14						TTCTGCAGAAGATAATCTGGA	0.303													G|||	409	0.0816693	0.093	0.0965	5008	,	,		15209	0.0337		0.1193	False		,,,				2504	0.0665				p.S251F		Atlas-SNP	.											FRA10AC1_ENST00000371426,colon,carcinoma,-1,2	FRA10AC1	68	2	0			c.C752T						PASS	.	G	PHE/SER	385,4019	194.0+/-219.0	18,349,1835	177.0	156.0	163.0		752	5.2	0.9	10	dbSNP_120	163	974,7624	211.0+/-251.7	65,844,3390	yes	missense	FRA10AC1	NM_145246.4	155	83,1193,5225	AA,AG,GG		11.3282,8.7421,10.4522	possibly-damaging	251/316	95441272	1359,11643	2202	4299	6501	SO:0001583	missense	118924	exon11			GCAGAAGATAATC	AK090955	CCDS7430.1	10q23.33	2014-01-28	2010-05-25	2010-05-25	ENSG00000148690	ENSG00000148690			1162	protein-coding gene	gene with protein product		608866	"""chromosome 10 open reading frame 4"""	C10orf4		15203205	Standard	NM_145246		Approved		uc001kiz.2	Q70Z53	OTTHUMG00000018776	ENST00000359204.4:c.752C>T	10.37:g.95441272G>A	ENSP00000360488:p.Ser251Phe	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	133	76	0.571429	NM_145246	C9JCR4|C9JCR5|C9JMY4|Q70Z49|Q70Z50|Q70Z51|Q70Z52|Q8N293|Q8WVH5|Q96JQ8	Missense_Mutation	SNP	ENST00000359204.4	37	CCDS7430.1	188	0.08608058608058608	42	0.08536585365853659	46	0.1270718232044199	14	0.024475524475524476	86	0.11345646437994723	G	15.10	2.734050	0.48939	0.087421	0.113282	ENSG00000148690	ENST00000359204;ENST00000536233;ENST00000371426;ENST00000371430;ENST00000394100	T;T;T;T	0.25579	1.81;1.8;1.79;1.8	5.17	5.17	0.71159	.	0.293421	0.37857	N	0.001919	T	0.00328	0.0010	L	0.59436	1.845	0.38708	P	0.04685600000000001	P	0.48407	0.91	B	0.43575	0.424	T	0.03139	-1.1068	9	0.66056	D	0.02	-3.4566	15.7456	0.77939	0.0:0.0:1.0:0.0	rs11187583;rs52826468;rs11187583	251	Q70Z53	F10C1_HUMAN	F	251	ENSP00000360488:S251F;ENSP00000438405:S251F;ENSP00000360484:S251F;ENSP00000377660:S251F	ENSP00000360488:S251F	S	-	2	0	FRA10AC1	95431262	1.000000	0.71417	0.890000	0.34922	0.831000	0.47069	4.748000	0.62148	2.572000	0.86782	0.655000	0.94253	TCT	G|0.902;A|0.098	0.098	strong		0.303	FRA10AC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049439.1	NM_145246	
OR51B4	79339	hgsc.bcm.edu	37	11	5322737	5322737	+	Missense_Mutation	SNP	A	A	G	rs10837771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5322737A>G	ENST00000380224.1	-	1	489	c.440T>C	c.(439-441)aTg>aCg	p.M147T	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	147			M -> T (in dbSNP:rs10837771). {ECO:0000269|PubMed:15489334}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAACCTCTCATCAGTACCCC	0.458													A|||	2215	0.442292	0.1195	0.4582	5008	,	,		21763	0.747		0.4473	False		,,,				2504	0.5481				p.M147T		Atlas-SNP	.											.	OR51B4	64	.	0			c.T440C						PASS	.	A	THR/MET	730,3672	300.1+/-286.2	63,604,1534	147.0	139.0	142.0		440	2.6	0.0	11	dbSNP_120	142	3745,4849	534.2+/-382.6	801,2143,1353	yes	missense	OR51B4	NM_033179.2	81	864,2747,2887	GG,GA,AA		43.5769,16.5834,34.4337	benign	147/311	5322737	4475,8521	2201	4297	6498	SO:0001583	missense	79339	exon1			CCTCTCATCAGTA	BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"""GPCR / Class A : Olfactory receptors"""	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.440T>C	11.37:g.5322737A>G	ENSP00000369573:p.Met147Thr	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	179	176	0.98324	NM_033179	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	37	CCDS7757.1	1016	0.4652014652014652	76	0.15447154471544716	173	0.47790055248618785	435	0.7604895104895105	332	0.43799472295514513	A	0.539	-0.854514	0.02630	0.165834	0.435769	ENSG00000183251	ENST00000380224	T	0.35973	1.28	4.93	2.63	0.31362	GPCR, rhodopsin-like superfamily (1);	1.310660	0.05269	N	0.517263	T	0.00012	0.0000	L	0.28192	0.835	0.80722	P	0.0	B	0.16166	0.016	B	0.16289	0.015	T	0.40905	-0.9538	9	0.22109	T	0.4	.	8.3225	0.32136	0.8362:0.0:0.1638:0.0	rs10837771;rs52828011;rs60441744;rs10837771	147	Q9Y5P0	O51B4_HUMAN	T	147	ENSP00000369573:M147T	ENSP00000369573:M147T	M	-	2	0	OR51B4	5279313	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	0.397000	0.20883	0.386000	0.24997	0.533000	0.62120	ATG	A|0.589;G|0.411	0.411	strong		0.458	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179	
MS4A4A	51338	hgsc.bcm.edu	37	11	60059810	60059810	+	Missense_Mutation	SNP	A	A	G	rs10750931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60059810A>G	ENST00000337908.4	+	2	244	c.154A>G	c.(154-156)Aaa>Gaa	p.K52E	MS4A4A_ENST00000355131.3_Missense_Mutation_p.K33E|MS4A4A_ENST00000395016.3_Missense_Mutation_p.K33E|MS4A4A_ENST00000532114.1_Missense_Mutation_p.K52E	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	52			K -> E (in dbSNP:rs10750931).			integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						ACATCTGTGGAAAGGATTGCA	0.493													A|||	774	0.154553	0.1785	0.0865	5008	,	,		18493	0.1349		0.17	False		,,,				2504	0.1748				p.K52E		Atlas-SNP	.											.	MS4A4A	76	.	0			c.A154G						PASS	.	A	GLU/LYS,GLU/LYS	789,3617	315.8+/-294.3	63,663,1477	72.0	68.0	69.0		97,154	2.7	0.0	11	dbSNP_120	69	1375,7225	265.3+/-286.1	121,1133,3046	yes	missense,missense	MS4A4A	NM_024021.3,NM_148975.2	56,56	184,1796,4523	GG,GA,AA		15.9884,17.9074,16.6385	probably-damaging,probably-damaging	33/221,52/240	60059810	2164,10842	2203	4300	6503	SO:0001583	missense	51338	exon2			CTGTGGAAAGGAT	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"""membrane-spanning 4-domains, subfamily A, member 4"""	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.154A>G	11.37:g.60059810A>G	ENSP00000338648:p.Lys52Glu	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Missense_Mutation	SNP	ENST00000337908.4	37	CCDS7982.1	303	0.13873626373626374	71	0.1443089430894309	36	0.09944751381215469	84	0.14685314685314685	112	0.14775725593667546	a	4.213	0.038245	0.08148	0.179074	0.159884	ENSG00000110079	ENST00000532114;ENST00000337908;ENST00000355131;ENST00000395016	T;T;T;T	0.18960	2.18;3.06;3.06;3.06	2.72	2.72	0.32119	.	4.907770	0.01044	U	0.004353	T	0.00039	0.0001	L	0.52573	1.65	0.80722	P	0.0	P;P	0.37122	0.521;0.583	B;B	0.33121	0.158;0.144	T	0.20940	-1.0260	9	0.07990	T	0.79	-4.393	7.272	0.26262	1.0:0.0:0.0:0.0	rs10750931;rs59456462;rs10750931	52;52	Q96JQ5-2;Q96JQ5	.;M4A4A_HUMAN	E	52;52;33;33	ENSP00000434506:K52E;ENSP00000338648:K52E;ENSP00000347252:K33E;ENSP00000378462:K33E	ENSP00000338648:K52E	K	+	1	0	MS4A4A	59816386	0.957000	0.32711	0.046000	0.18839	0.051000	0.14879	1.126000	0.31344	1.490000	0.48466	0.377000	0.23210	AAA	A|0.845;G|0.155	0.155	strong		0.493	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2		
RBM6	10180	hgsc.bcm.edu	37	3	50114515	50114515	+	Silent	SNP	C	C	T	rs7061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50114515C>T	ENST00000266022.4	+	21	3580	c.3321C>T	c.(3319-3321)taC>taT	p.Y1107Y	RBM6_ENST00000422955.1_Silent_p.Y585Y|RBM6_ENST00000539992.1_Silent_p.Y449Y|RBM6_ENST00000421682.1_Silent_p.Y103Y|RBM6_ENST00000442092.1_Silent_p.Y585Y|RBM6_ENST00000443081.1_Silent_p.Y975Y	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	1107					RNA processing (GO:0006396)	nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|skin(4)|urinary_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;6.81e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0084)|Kidney(197;0.00977)		ACGAGACTTACCGAGATGCTG	0.458													c|||	3741	0.747005	0.7458	0.6945	5008	,	,		15235	0.879		0.5686	False		,,,				2504	0.8333				p.Y1107Y		Atlas-SNP	.											.	RBM6	85	.	0			c.C3321T						PASS	.	T	,	3176,1230	424.2+/-340.4	1145,886,172	93.0	88.0	89.0		1755,3321	3.0	1.0	3	dbSNP_52	89	4903,3697	529.7+/-381.6	1369,2165,766	no	coding-synonymous,coding-synonymous	RBM6	NM_001167582.1,NM_005777.2	,	2514,3051,938	TT,TC,CC		42.9884,27.9165,37.8825	,	585/602,1107/1124	50114515	8079,4927	2203	4300	6503	SO:0001819	synonymous_variant	10180	exon21			GACTTACCGAGAT	AF069517	CCDS2809.1, CCDS54586.1	3p21.3	2013-01-28			ENSG00000004534	ENSG00000004534		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	9903	protein-coding gene	gene with protein product		606886				10352938	Standard	NM_001167582		Approved	DEF-3, 3G2, NY-LU-12, g16, DEF3	uc003cyc.3	P78332	OTTHUMG00000156736	ENST00000266022.4:c.3321C>T	3.37:g.50114515C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	112	45	0.401786	NM_005777	O60549|O75524|Q86SS3	Silent	SNP	ENST00000266022.4	37	CCDS2809.1																																																																																			C|0.329;T|0.671	0.671	strong		0.458	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777	
PCDHB5	26167	hgsc.bcm.edu	37	5	140517069	140517069	+	Missense_Mutation	SNP	C	C	T	rs139772435	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140517069C>T	ENST00000231134.5	+	1	2270	c.2053C>T	c.(2053-2055)Ctc>Ttc	p.L685F		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	685					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCCGACTCGCTCACTGTCTA	0.697													C|||	2	0.000399361	0.0	0.0014	5008	,	,		14469	0.0		0.001	False		,,,				2504	0.0				p.L685F		Atlas-SNP	.											.	PCDHB5	184	.	0			c.C2053T						PASS	.	C	PHE/LEU	2,4396		0,2,2197	69.0	72.0	71.0		2053	4.7	0.9	5	dbSNP_134	71	23,8567		0,23,4272	no	missense	PCDHB5	NM_015669.2	22	0,25,6469	TT,TC,CC		0.2678,0.0455,0.1925	probably-damaging	685/796	140517069	25,12963	2199	4295	6494	SO:0001583	missense	26167	exon1			GACTCGCTCACTG	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2053C>T	5.37:g.140517069C>T	ENSP00000231134:p.Leu685Phe	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_015669	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.312064	0.60414	4.55E-4	0.002678	ENSG00000113209	ENST00000231134	T	0.56103	0.48	4.71	4.71	0.59529	.	.	.	.	.	T	0.75191	0.3816	H	0.94964	3.605	0.26118	N	0.980598	D	0.62365	0.991	D	0.63793	0.918	T	0.70182	-0.4942	9	0.72032	D	0.01	.	6.5527	0.22444	0.0:0.6862:0.1544:0.1595	.	685	Q9Y5E4	PCDB5_HUMAN	F	685	ENSP00000231134:L685F	ENSP00000231134:L685F	L	+	1	0	PCDHB5	140497253	0.039000	0.19947	0.895000	0.35142	0.093000	0.18481	0.276000	0.18716	2.337000	0.79520	0.430000	0.28490	CTC	C|0.997;T|0.003	0.003	strong		0.697	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
TMEM244	253582	hgsc.bcm.edu	37	6	130154667	130154667	+	Missense_Mutation	SNP	T	T	C	rs9492393	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:130154667T>C	ENST00000368143.1	-	4	339	c.257A>G	c.(256-258)gAa>gGa	p.E86G	TMEM244_ENST00000438392.1_Missense_Mutation_p.E86G	NM_001010876.1	NP_001010876.1	Q5VVB8	TM244_HUMAN	transmembrane protein 244	86			E -> G (in dbSNP:rs9492393).			integral component of membrane (GO:0016021)											AACCCATTCTTCCACAACTGG	0.338													T|||	1874	0.374201	0.4924	0.2666	5008	,	,		18277	0.2252		0.3161	False		,,,				2504	0.5041				p.E86G		Atlas-SNP	.											.	.	.	.	0			c.A257G						PASS	.	T	GLY/GLU	1983,2423	556.5+/-379.5	441,1101,661	138.0	133.0	135.0		257	3.3	0.9	6	dbSNP_119	135	2949,5651	458.6+/-364.7	529,1891,1880	yes	missense	C6orf191	NM_001010876.1	98	970,2992,2541	CC,CT,TT		34.2907,45.0068,37.921	possibly-damaging	86/129	130154667	4932,8074	2203	4300	6503	SO:0001583	missense	253582	exon4			CATTCTTCCACAA		CCDS34536.1	6q22.33	2012-02-21	2012-02-21	2012-02-21	ENSG00000203756	ENSG00000203756			21571	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 191"""	C6orf191			Standard	NM_001010876		Approved	bA174C7.4	uc003qbs.3	Q5VVB8	OTTHUMG00000015553	ENST00000368143.1:c.257A>G	6.37:g.130154667T>C	ENSP00000357125:p.Glu86Gly	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	57	53	0.929825	NM_001010876		Missense_Mutation	SNP	ENST00000368143.1	37	CCDS34536.1	718	0.32875457875457875	243	0.49390243902439024	110	0.30386740331491713	126	0.2202797202797203	239	0.3153034300791557	T	18.85	3.711909	0.68730	0.450068	0.342907	ENSG00000203756	ENST00000368143;ENST00000438392	T;T	0.43294	0.95;0.95	4.56	3.34	0.38264	.	0.127582	0.51477	D	0.000091	T	0.36771	0.0979	L	0.55481	1.735	0.29184	P	0.8763110000000001	D	0.67145	0.996	P	0.58130	0.833	T	0.26780	-1.0093	9	0.39692	T	0.17	-31.9529	10.3674	0.44033	0.0:0.0:0.1653:0.8347	rs9492393;rs17474335;rs52836697;rs58382452;rs9492393	86	Q5VVB8	CF191_HUMAN	G	86	ENSP00000357125:E86G;ENSP00000403755:E86G	ENSP00000357125:E86G	E	-	2	0	C6orf191	130196360	1.000000	0.71417	0.853000	0.33588	0.997000	0.91878	4.306000	0.59117	0.661000	0.30985	0.528000	0.53228	GAA	T|0.633;C|0.367	0.367	strong		0.338	TMEM244-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042194.1	NM_001010876	
PLIN4	729359	hgsc.bcm.edu	37	19	4512613	4512613	+	Silent	SNP	T	T	G	rs74327986	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4512613T>G	ENST00000301286.3	-	3	1316	c.1317A>C	c.(1315-1317)acA>acC	p.T439T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	439	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TGTCCACGCCTGTCTGGATGG	0.572													t|||	544	0.108626	0.261	0.0865	5008	,	,		21727	0.001		0.1004	False		,,,				2504	0.0378				p.T439T		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1317C						PASS	.	T		689,3363		76,537,1413	143.0	154.0	150.0		1317	-9.5	0.0	19	dbSNP_132	150	638,7726		41,556,3585	no	coding-synonymous	PLIN4	NM_001080400.1		117,1093,4998	GG,GT,TT		7.6279,17.0039,10.6878		439/1358	4512613	1327,11089	2026	4182	6208	SO:0001819	synonymous_variant	729359	exon3			CACGCCTGTCTGG	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.1317A>C	19.37:g.4512613T>G		Somatic	180	1	0.00555556		WXS	Illumina HiSeq	Phase_I	81	79	0.975309	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			T|0.916;G|0.084	0.084	strong		0.572	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
PRRC2A	7916	hgsc.bcm.edu	37	6	31604010	31604010	+	Silent	SNP	C	C	G	rs13716	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31604010C>G	ENST00000376033.2	+	26	5883	c.5649C>G	c.(5647-5649)ccC>ccG	p.P1883P	PRRC2A_ENST00000376007.4_Silent_p.P1883P	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1883						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						ACCTACCCCCCGGCCCAGCCC	0.532													C|||	1228	0.245208	0.0174	0.3401	5008	,	,		14355	0.3472		0.3221	False		,,,				2504	0.3016				p.P1883P		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C5649G						PASS	.	C	,	200,2802		16,168,1317	107.0	144.0	131.0		5649,5649	-10.5	0.0	6	dbSNP_52	131	1667,3751		271,1125,1313	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	287,1293,2630	GG,GC,CC		30.7678,6.6622,22.1734	,	1883/2158,1883/2158	31604010	1867,6553	1501	2709	4210	SO:0001819	synonymous_variant	7916	exon26			ACCCCCCGGCCCA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.5649C>G	6.37:g.31604010C>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	119	54	0.453782	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			C|0.731;G|0.269	0.269	strong		0.532	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55330019	55330019	+	Missense_Mutation	SNP	C	C	T	rs143159382|rs368503966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55330019C>T	ENST00000391728.4	+	3	353	c.320C>T	c.(319-321)tCg>tTg	p.S107L	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.S107L|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.S107L|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.S107L|KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.S107L	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	107					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		ACTGGGTGGTCGGCACCCAGC	0.582													c|||	507	0.101238	0.087	0.1398	5008	,	,		12571	0.001		0.2416	False		,,,				2504	0.0521				p.S107L		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.C320T	GRCh37	CM035771	KIR3DL1	M	rs143159382	PASS	.	C	LEU/SER	471,3883		73,325,1779	69.0	67.0	67.0		320	0.1	0.0	19	dbSNP_134	67	1730,6508		431,868,2820	no	missense	KIR3DL1	NM_013289.2	145	504,1193,4599	TT,TC,CC		21.0002,10.8176,17.4794		107/445	55330019	2201,10391	2177	4119	6296	SO:0001583	missense	3811	exon3			GGTGGTCGGCACC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.320C>T	19.37:g.55330019C>T	ENSP00000375608:p.Ser107Leu	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	246	0.11263736263736264	32	0.06504065040650407	43	0.11878453038674033	0	0.0	171	0.22559366754617413	-	12.28	1.891501	0.33442	0.108176	0.210002	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.01145	5.27;5.27;5.27;5.27;5.27	1.25	0.0636	0.14349	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	H	0.99011	4.4	0.80722	P	0.0	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.996;0.995	T	0.04840	-1.0923	8	0.66056	D	0.02	.	5.1966	0.15241	0.0:0.6264:0.3736:0.0	.	107;107;107	Q15702;F6QF33;P43629	.;.;KI3L1_HUMAN	L	107;107;107;85;107;107	ENSP00000384528:S107L;ENSP00000443350:S107L;ENSP00000442355:S107L;ENSP00000375608:S107L;ENSP00000326868:S107L	ENSP00000326868:S107L	S	+	2	0	KIR3DL1	60021831	0.004000	0.15560	0.001000	0.08648	0.056000	0.15407	0.687000	0.25407	0.096000	0.17463	0.184000	0.17185	TCG	C|0.884;T|0.116	0.116	strong		0.582	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
ZNF326	284695	hgsc.bcm.edu	37	1	90484253	90484253	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:90484253G>A	ENST00000340281.4	+	9	1227	c.1084G>A	c.(1084-1086)Gtg>Atg	p.V362M	ZNF326_ENST00000455342.2_Missense_Mutation_p.V156M|ZNF326_ENST00000370447.3_Missense_Mutation_p.V273M	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	362					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)		GGAGTGTATGGTGAATAAATT	0.289																																					p.V362M		Atlas-SNP	.											.	ZNF326	60	.	0			c.G1084A						PASS	.						52.0	57.0	55.0					1																	90484253		2198	4280	6478	SO:0001583	missense	284695	exon9			TGTATGGTGAATA	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.1084G>A	1.37:g.90484253G>A	ENSP00000340796:p.Val362Met	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	148	66	0.445946	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.094288	0.76870	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.17528	2.27;2.27;2.27	5.56	5.56	0.83823	.	0.066635	0.64402	D	0.000018	T	0.32496	0.0831	M	0.62723	1.935	0.50313	D	0.999865	D;D	0.63046	0.992;0.992	D;P	0.66847	0.947;0.9	T	0.02457	-1.1156	10	0.62326	D	0.03	-10.1859	19.1298	0.93400	0.0:0.0:1.0:0.0	.	362;362	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	M	362;362;273;156	ENSP00000340796:V362M;ENSP00000359476:V273M;ENSP00000403470:V156M	ENSP00000340796:V362M	V	+	1	0	ZNF326	90256841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.778000	0.75043	2.620000	0.88729	0.650000	0.86243	GTG	.	.	none		0.289	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
FER1L6	654463	hgsc.bcm.edu	37	8	125107201	125107201	+	Silent	SNP	G	G	A	rs6470219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:125107201G>A	ENST00000522917.1	+	35	4823	c.4617G>A	c.(4615-4617)ccG>ccA	p.P1539P	FER1L6-AS2_ENST00000520031.1_RNA|FER1L6_ENST00000399018.1_Silent_p.P1539P	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	1539						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)			AGGATATCCCGGAAGTCGGGT	0.493													G|||	3596	0.718051	0.6059	0.683	5008	,	,		18760	0.6419		0.8678	False		,,,				2504	0.819				p.P1539P		Atlas-SNP	.											.	FER1L6	268	.	0			c.G4617A						PASS	.	G		2465,1349		784,897,226	90.0	84.0	86.0		4617	-11.0	0.0	8	dbSNP_116	86	7106,1152		3055,996,78	no	coding-synonymous	FER1L6	NM_001039112.2		3839,1893,304	AA,AG,GG		13.9501,35.3697,20.7174		1539/1858	125107201	9571,2501	1907	4129	6036	SO:0001819	synonymous_variant	654463	exon35			TATCCCGGAAGTC	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.4617G>A	8.37:g.125107201G>A		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_001039112		Silent	SNP	ENST00000522917.1	37	CCDS43767.1																																																																																			G|0.248;A|0.752	0.752	strong		0.493	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
ZNF862	643641	hgsc.bcm.edu	37	7	149558409	149558409	+	Silent	SNP	G	G	C	rs2240361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149558409G>C	ENST00000223210.4	+	7	2405	c.2160G>C	c.(2158-2160)ctG>ctC	p.L720L	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	720					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CGCAGCTGCTGCCTGTCCACT	0.647													G|||	1906	0.380591	0.2405	0.4741	5008	,	,		18325	0.3284		0.5865	False		,,,				2504	0.3456				p.L720L		Atlas-SNP	.											.	ZNF862	97	.	0			c.G2160C						PASS	.	G		1404,2736		251,902,917	26.0	28.0	27.0		2160	4.4	1.0	7	dbSNP_98	27	5043,3367		1539,1965,701	no	coding-synonymous	ZNF862	NM_001099220.1		1790,2867,1618	CC,CG,GG		40.0357,33.913,48.6295		720/1170	149558409	6447,6103	2070	4205	6275	SO:0001819	synonymous_variant	643641	exon7			GCTGCTGCCTGTC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.2160G>C	7.37:g.149558409G>C		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			G|0.536;C|0.464	0.464	strong		0.647	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
DYX1C1	161582	hgsc.bcm.edu	37	15	55722882	55722882	+	Nonsense_Mutation	SNP	C	C	A	rs57809907	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:55722882C>A	ENST00000321149.3	-	10	1616	c.1249G>T	c.(1249-1251)Gaa>Taa	p.E417*	DYX1C1_ENST00000448430.2_Intron|DYX1C1_ENST00000380679.1_Intron|DYX1C1_ENST00000348518.3_3'UTR|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000457155.2_3'UTR	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	417					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		GATTTTAGTTCTGTTCCTTGA	0.338													C|||	879	0.175519	0.4818	0.0706	5008	,	,		13441	0.0089		0.0865	False		,,,				2504	0.0992				p.E417X		Atlas-SNP	.											DYX1C1,NS,carcinoma,+2,1	DYX1C1	54	1	0			c.G1249T	GRCh37	CM035520	DYX1C1	M	rs57809907	PASS	.	C	,,stop/GLU	1825,2559	532.5+/-373.5	383,1059,750	107.0	107.0	107.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,1249	4.7	1.0	15	dbSNP_129	107	765,7809	181.3+/-230.0	28,709,3550	yes	utr-3,intron,stop-gained	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	,,	411,1768,4300	AA,AC,CC		8.9223,41.6286,19.9877	,,	,,417/421	55722882	2590,10368	2192	4287	6479	SO:0001587	stop_gained	161582	exon10			TTAGTTCTGTTCC		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.1249G>T	15.37:g.55722882C>A	ENSP00000323275:p.Glu417*	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_130810	Q6P5Y9|Q8N1S6	Nonsense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	344	0.1575091575091575	243	0.49390243902439024	26	0.0718232044198895	6	0.01048951048951049	69	0.09102902374670185	C	38	7.101446	0.98063	0.416286	0.089223	ENSG00000256061	ENST00000321149	.	.	.	5.6	4.68	0.58851	.	0.670270	0.13414	U	0.389654	.	.	.	.	.	.	0.09310	P	0.9999999862604	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	7.7377	0.28823	0.0:0.717:0.1348:0.1483	rs57809907	.	.	.	X	417	.	ENSP00000323275:E417X	E	-	1	0	DYX1C1	53510174	0.000000	0.05858	1.000000	0.80357	0.996000	0.88848	-0.079000	0.11357	1.350000	0.45770	0.558000	0.71614	GAA	C|0.819;A|0.181	0.181	strong		0.338	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
ABHD12	26090	hgsc.bcm.edu	37	20	25282967	25282967	+	Missense_Mutation	SNP	C	C	T	rs746748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25282967C>T	ENST00000339157.5	-	12	1317	c.1045G>A	c.(1045-1047)Gca>Aca	p.A349T	ABHD12_ENST00000376542.3_Missense_Mutation_p.A349T	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	349			A -> T (in dbSNP:rs746748).		adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						CGAGCTGGTGCGGCGATGCTA	0.567													C|||	92	0.0183706	0.0023	0.0216	5008	,	,		19152	0.0		0.0666	False		,,,				2504	0.0072				p.A349T		Atlas-SNP	.											.	ABHD12	46	.	0			c.G1045A						PASS	.	C	THR/ALA,THR/ALA	53,4353	52.9+/-88.7	0,53,2150	90.0	81.0	84.0		1045,1045	5.0	1.0	20	dbSNP_86	84	502,8098	143.4+/-199.5	13,476,3811	yes	missense,missense	ABHD12	NM_001042472.2,NM_015600.4	58,58	13,529,5961	TT,TC,CC		5.8372,1.2029,4.2673	benign,benign	349/399,349/405	25282967	555,12451	2203	4300	6503	SO:0001583	missense	26090	exon12			CTGGTGCGGCGAT	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"""Abhydrolase domain containing"""	15868	protein-coding gene	gene with protein product		613599	"""chromosome 20 open reading frame 22"""	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.1045G>A	20.37:g.25282967C>T	ENSP00000341408:p.Ala349Thr	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	43	28	0.651163	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	37	CCDS42857.1	54	0.024725274725274724	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	43	0.05672823218997362	C	14.05	2.420951	0.42918	0.012029	0.058372	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543	T;T	0.22336	1.96;1.97	4.97	4.97	0.65823	.	0.108901	0.64402	D	0.000008	T	0.03348	0.0097	N	0.25286	0.73	0.80722	D	1	P;D;P	0.71674	0.608;0.998;0.645	B;P;B	0.61201	0.142;0.885;0.044	T	0.01630	-1.1308	10	0.18710	T	0.47	-12.0589	18.0286	0.89276	0.0:1.0:0.0:0.0	rs746748;rs57380705;rs746748	311;349;349	Q8N2K0-3;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	T	349;349;311	ENSP00000365725:A349T;ENSP00000341408:A349T	ENSP00000341408:A349T	A	-	1	0	ABHD12	25230967	0.994000	0.37717	0.998000	0.56505	0.766000	0.43426	3.171000	0.50824	2.582000	0.87167	0.561000	0.74099	GCA	C|0.958;A|0.000	.	strong		0.567	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600	
KLK3	354	hgsc.bcm.edu	37	19	51361472	51361472	+	Missense_Mutation	SNP	C	C	A	rs2003783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51361472C>A	ENST00000326003.2	+	3	435	c.394C>A	c.(394-396)Ctc>Atc	p.L132I	KLK3_ENST00000593997.1_Missense_Mutation_p.L132I|KLK3_ENST00000360617.3_Missense_Mutation_p.L132I|KLK3_ENST00000597483.1_Missense_Mutation_p.L89I|KLK3_ENST00000595952.1_Missense_Mutation_p.L89I	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3	132	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		L -> I (in dbSNP:rs2003783). {ECO:0000269|PubMed:23842001}.		cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		GCCTGCCGAGCTCACGGATGC	0.617													A|||	446	0.0890575	0.1483	0.0879	5008	,	,		19555	0.0694		0.0954	False		,,,				2504	0.0235				p.L132I	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.C394A						PASS	.	A	ILE/LEU,ILE/LEU,ILE/LEU	634,3772	766.9+/-413.5	51,532,1620	74.0	63.0	67.0		394,265,394	-3.7	0.0	19	dbSNP_92	67	743,7857	785.8+/-407.6	28,687,3585	yes	missense,missense,missense	KLK3	NM_001030047.1,NM_001030048.1,NM_001648.2	5,5,5	79,1219,5205	AA,AC,CC		8.6395,14.3895,10.5874	,,	132/239,89/219,132/262	51361472	1377,11629	2203	4300	6503	SO:0001583	missense	354	exon3			GCCGAGCTCACGG	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.394C>A	19.37:g.51361472C>A	ENSP00000314151:p.Leu132Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	112	54	0.482143	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Missense_Mutation	SNP	ENST00000326003.2	37	CCDS12807.1	214	0.09798534798534798	67	0.13617886178861788	39	0.10773480662983426	48	0.08391608391608392	60	0.079155672823219	A	0.007	-2.005041	0.00426	0.143895	0.086395	ENSG00000142515	ENST00000326003;ENST00000422986;ENST00000360617	T;T	0.08008	3.14;3.14	2.31	-3.68	0.04463	.	0.404855	0.18025	N	0.154101	T	0.00039	0.0001	L	0.31157	0.91	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.002;0.003	T	0.46693	-0.9173	9	0.02654	T	1	.	9.9961	0.41900	0.1921:0.7008:0.1071:0.0	rs2003783;rs2271091;rs16987763;rs52794924;rs2003783	132;89	G3XAE3;G3V0H4	.;.	I	132;89;132	ENSP00000314151:L132I;ENSP00000353829:L132I	ENSP00000314151:L132I	L	+	1	0	KLK3	56053284	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.882000	0.04174	-1.811000	0.01229	-1.453000	0.01033	CTC	C|0.896;A|0.104	0.104	strong		0.617	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
ARHGAP4	393	hgsc.bcm.edu	37	X	153176254	153176254	+	Silent	SNP	A	A	G	rs2070097	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153176254A>G	ENST00000350060.5	-	15	1757	c.1716T>C	c.(1714-1716)caT>caC	p.H572H	ARHGAP4_ENST00000537206.1_Silent_p.H549H|ARHGAP4_ENST00000370028.3_Silent_p.H612H|ARHGAP4_ENST00000467421.1_5'UTR|ARHGAP4_ENST00000370016.1_Silent_p.H551H|ARHGAP4_ENST00000393721.1_Silent_p.H394H	NM_001666.4	NP_001657.3	P98171	RHG04_HUMAN	Rho GTPase activating protein 4	572	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|negative regulation of axon extension (GO:0030517)|negative regulation of fibroblast migration (GO:0010764)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)	Rho GTPase activator activity (GO:0005100)|SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGTCCAGGTCATGGGCAGTGC	0.682											OREG0003617	type=REGULATORY REGION|Gene=ARHGAP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	2661	0.704901	0.6914	0.4928	3775	,	,		6158	0.5437		0.3062	False		,,,				2504	0.5613				p.H612H		Atlas-SNP	.											.	ARHGAP4	103	.	0			c.T1836C						PASS	.	G	,	3240,563		1191,370,488,60,73	13.0	15.0	15.0		1836,1716	-6.9	0.0	X	dbSNP_96	15	2616,4076		384,1102,746,931,1112	no	coding-synonymous,coding-synonymous	ARHGAP4	NM_001164741.1,NM_001666.4	,	1575,1472,1234,991,1185	GG,GA,G,AA,A		39.0915,14.8041,44.202	,	612/987,572/947	153176254	5856,4639	2182	4275	6457	SO:0001819	synonymous_variant	393	exon16			CAGGTCATGGGCA	X78817	CCDS14736.1, CCDS55540.1	Xq28	2010-02-09			ENSG00000089820	ENSG00000089820		"""Rho GTPase activating proteins"""	674	protein-coding gene	gene with protein product	"""Rho-GAP hematopoietic protein C1"""	300023				8570618	Standard	NM_001666		Approved	KIAA0131, C1, p115, RhoGAP4, SrGAP4	uc004fjk.2	P98171	OTTHUMG00000024226	ENST00000350060.5:c.1716T>C	X.37:g.153176254A>G		Somatic	53	0	0	1753	WXS	Illumina HiSeq	Phase_I	22	22	1	NM_001164741	Q14144|Q86UY3	Silent	SNP	ENST00000350060.5	37	CCDS14736.1	1043	0.6286919831223629	234	0.7959183673469388	118	0.44696969696969696	218	0.5828877005347594	163	0.26547231270358307	a	0.105	-1.146679	0.01714	0.851959	0.390915	ENSG00000089820	ENST00000454164;ENST00000442172	.	.	.	4.61	-6.94	0.01633	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.24137	P	0.99574145	.	.	.	.	.	.	T	0.07009	-1.0795	3	.	.	.	.	7.0917	0.25287	0.6809:0.0919:0.1343:0.0929	rs2070097;rs17846493;rs17859557;rs61248836;rs2070097	.	.	.	T	72;61	.	.	M	-	2	0	ARHGAP4	152829448	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.160000	0.03147	-2.323000	0.00639	-2.187000	0.00313	ATG	A|0.354;G|0.646	0.646	strong		0.682	ARHGAP4-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061119.1	NM_001666	
HSPA9	3313	hgsc.bcm.edu	37	5	137902339	137902339	+	Silent	SNP	T	T	C	rs1042665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:137902339T>C	ENST00000297185.3	-	9	1073	c.948A>G	c.(946-948)aaA>aaG	p.K316K	HSPA9_ENST00000501917.2_5'UTR	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	316					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			AGAGTTCACATTTAGCCTTTT	0.408													T|||	2103	0.419928	0.3464	0.2464	5008	,	,		18698	0.7629		0.2485	False		,,,				2504	0.4652				p.K316K		Atlas-SNP	.											.	HSPA9	49	.	0			c.A948G						PASS	.	T		1401,3005	460.3+/-352.6	225,951,1027	156.0	143.0	147.0		948	-1.3	0.8	5	dbSNP_86	147	1896,6704	337.2+/-322.2	191,1514,2595	no	coding-synonymous	HSPA9	NM_004134.6		416,2465,3622	CC,CT,TT		22.0465,31.7975,25.3498		316/680	137902339	3297,9709	2203	4300	6503	SO:0001819	synonymous_variant	3313	exon9			TTCACATTTAGCC	L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.948A>G	5.37:g.137902339T>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Silent	SNP	ENST00000297185.3	37	CCDS4208.1																																																																																			T|0.686;C|0.314	0.314	strong		0.408	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497917	32497917	+	Missense_Mutation	SNP	C	C	A	rs71549220	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32497917C>A	ENST00000374975.3	-	1	147	c.85G>T	c.(85-87)Gct>Tct	p.A29S		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5									p.A29S(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GTGTCCCCAGCCAAAGCCAGT	0.547													C|||	443	0.0884585	0.0847	0.111	5008	,	,		20515	0.0417		0.1372	False		,,,				2504	0.0757				p.A29S		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	1	Substitution - Missense(1)	stomach(1)	c.G85T						PASS	.	C	SER/ALA	315,4091		5,305,1893	102.0	105.0	104.0		85	3.6	0.0	6	dbSNP_130	104	739,7861		26,687,3587	no	missense	HLA-DRB5	NM_002125.3	99	31,992,5480	AA,AC,CC		8.593,7.1493,8.104	benign	29/267	32497917	1054,11952	2203	4300	6503	SO:0001583	missense	3127	exon1			CCCCAGCCAAAGC		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.85G>T	6.37:g.32497917C>A	ENSP00000364114:p.Ala29Ser	Somatic	265	1	0.00377358		WXS	Illumina HiSeq	Phase_I	174	88	0.505747	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	12.42	1.933464	0.34096	0.071493	0.08593	ENSG00000198502	ENST00000374975	T	0.00256	8.42	4.54	3.61	0.41365	MHC classes I/II-like antigen recognition protein (1);	0.581841	0.16240	N	0.223213	T	0.00073	0.0002	L	0.54965	1.715	0.09310	N	1	B	0.12630	0.006	B	0.19666	0.026	T	0.40850	-0.9541	10	0.62326	D	0.03	.	9.2292	0.37425	0.2691:0.7309:0.0:0.0	.	29	Q30154	DRB5_HUMAN	S	29	ENSP00000364114:A29S	ENSP00000364114:A29S	A	-	1	0	HLA-DRB5	32605895	0.017000	0.18338	0.005000	0.12908	0.148000	0.21650	0.184000	0.16939	1.002000	0.39104	0.485000	0.47835	GCT	C|0.956;A|0.044	0.044	strong		0.547	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
HFM1	164045	hgsc.bcm.edu	37	1	91781413	91781413	+	Silent	SNP	T	T	G	rs281992	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91781413T>G	ENST00000370425.3	-	28	3197	c.3099A>C	c.(3097-3099)atA>atC	p.I1033I	HFM1_ENST00000294696.5_Silent_p.I265I|HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000370424.3_Silent_p.I712I	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	1033	SEC63.				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)		CTGCGTCACCTATGATTAAGG	0.313													T|||	3821	0.762979	0.7489	0.7233	5008	,	,		16634	0.8244		0.6928	False		,,,				2504	0.819				p.I1033I		Atlas-SNP	.											.	HFM1	188	.	0			c.A3099C						PASS	.	T		3214,1190	705.5+/-407.3	1169,876,157	81.0	79.0	80.0		3099	4.1	1.0	1	dbSNP_79	80	5730,2864	669.3+/-402.6	1911,1908,478	no	coding-synonymous	HFM1	NM_001017975.3		3080,2784,635	GG,GT,TT		33.3256,27.0209,31.1894		1033/1436	91781413	8944,4054	2202	4297	6499	SO:0001819	synonymous_variant	164045	exon28			GTCACCTATGATT	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.3099A>C	1.37:g.91781413T>G		Somatic	222	0	0		WXS	Illumina HiSeq	Phase_I	270	123	0.455556	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	1632	0.7472527472527473	377	0.766260162601626	245	0.6767955801104972	492	0.8601398601398601	518	0.683377308707124	T	7.896	0.733391	0.15574	0.729791	0.666744	ENSG00000162669	ENST00000430465	.	.	.	5.25	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4943	0.38978	0.2822:0.0:0.0:0.7178	rs281992;rs4098249;rs17131379;rs59890582;rs281992	.	.	.	S	245	.	.	X	-	2	0	HFM1	91554001	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	1.237000	0.32695	0.800000	0.34041	0.377000	0.23210	TAG	T|0.278;G|0.722	0.722	strong		0.313	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
SH3RF2	153769	hgsc.bcm.edu	37	5	145393364	145393364	+	Missense_Mutation	SNP	C	C	T	rs758037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145393364C>T	ENST00000511217.1	+	4	851	c.799C>T	c.(799-801)Cgc>Tgc	p.R267C	SH3RF2_ENST00000359120.4_Missense_Mutation_p.R267C			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	267			R -> C (in dbSNP:rs758037). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		negative regulation of phosphatase activity (GO:0010923)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|phosphatase binding (GO:0019902)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)|zinc ion binding (GO:0008270)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCAGTCATCCCGCACAAAAAA	0.527													C|||	3050	0.609026	0.3986	0.5692	5008	,	,		21429	0.7212		0.6312	False		,,,				2504	0.7832				p.R267C		Atlas-SNP	.											.	SH3RF2	58	.	0			c.C799T						PASS	.	C	CYS/ARG	1926,2480	548.2+/-377.5	403,1120,680	81.0	72.0	75.0		799	1.2	0.0	5	dbSNP_86	75	5245,3355	642.9+/-399.9	1604,2037,659	yes	missense	SH3RF2	NM_152550.3	180	2007,3157,1339	TT,TC,CC		39.0116,43.7131,44.8639	probably-damaging	267/730	145393364	7171,5835	2203	4300	6503	SO:0001583	missense	153769	exon5			TCATCCCGCACAA	AL833297	CCDS4280.1	5q32	2013-01-09	2011-11-04	2011-11-04	ENSG00000156463	ENSG00000156463		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26299	protein-coding gene	gene with protein product	"""heart protein phosphatase 1-binding protein"", ""POSH-eliminating RING protein"""	613377	"""protein phosphatase 1, regulatory subunit 39"""	PPP1R39		22128169	Standard	NM_152550		Approved	FLJ23654, RNF158, Hepp1, POSHER	uc003lnt.3	Q8TEC5	OTTHUMG00000129685	ENST00000511217.1:c.799C>T	5.37:g.145393364C>T	ENSP00000424497:p.Arg267Cys	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	125	62	0.496	NM_152550	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Missense_Mutation	SNP	ENST00000511217.1	37	CCDS4280.1	1340	0.6135531135531136	218	0.44308943089430897	221	0.6104972375690608	406	0.7097902097902098	495	0.6530343007915568	C	10.01	1.233918	0.22626	0.437131	0.609884	ENSG00000156463	ENST00000359120;ENST00000511217	T;T	0.04654	3.58;3.58	5.32	1.22	0.21188	Src homology-3 domain (1);	0.630714	0.16224	N	0.223914	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.01281	0.0	T	0.06391	-1.0829	9	0.54805	T	0.06	-1.4343	5.6818	0.17780	0.3218:0.5332:0.0:0.1451	rs758037;rs3733938;rs52807951;rs57396297;rs758037	267	Q8TEC5	SH3R2_HUMAN	C	267	ENSP00000352028:R267C;ENSP00000424497:R267C	ENSP00000352028:R267C	R	+	1	0	SH3RF2	145373557	0.001000	0.12720	0.001000	0.08648	0.671000	0.39405	0.651000	0.24873	-0.025000	0.13918	-0.230000	0.12252	CGC	C|0.411;T|0.589	0.589	strong		0.527	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550	
AGPAT3	56894	hgsc.bcm.edu	37	21	45389034	45389034	+	Silent	SNP	C	C	T	rs61737069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45389034C>T	ENST00000398063.2	+	4	876	c.384C>T	c.(382-384)taC>taT	p.Y128Y	AGPAT3_ENST00000398058.1_Silent_p.Y128Y|AGPAT3_ENST00000479117.1_3'UTR|AGPAT3_ENST00000327505.2_Silent_p.Y128Y|AGPAT3_ENST00000398061.1_Silent_p.Y128Y|AGPAT3_ENST00000546158.1_Silent_p.Y128Y|AGPAT3_ENST00000291572.8_Silent_p.Y128Y	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	128					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		AGCTGCTCTACGTGCCCCTCA	0.632													C|||	42	0.00838658	0.0023	0.0072	5008	,	,		19868	0.0		0.0179	False		,,,				2504	0.0164				p.Y128Y	Pancreas(60;623 1650 5574 52796)	Atlas-SNP	.											.	AGPAT3	37	.	0			c.C384T						PASS	.	C	,	18,4388	25.3+/-52.1	0,18,2185	130.0	105.0	113.0		384,384	0.4	1.0	21	dbSNP_129	113	171,8429	78.9+/-141.6	1,169,4130	no	coding-synonymous,coding-synonymous	AGPAT3	NM_001037553.1,NM_020132.4	,	1,187,6315	TT,TC,CC		1.9884,0.4085,1.4532	,	128/377,128/377	45389034	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	56894	exon4			GCTCTACGTGCCC	AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	326	protein-coding gene	gene with protein product		614794					Standard	XM_005261159		Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.384C>T	21.37:g.45389034C>T		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	167	93	0.556886	NM_001037553	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	Silent	SNP	ENST00000398063.2	37	CCDS13703.1																																																																																			C|0.986;T|0.014	0.014	strong		0.632	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195722.1	NM_020132	
KAT2B	8850	hgsc.bcm.edu	37	3	20141356	20141356	+	Silent	SNP	C	C	T	rs35424474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:20141356C>T	ENST00000263754.4	+	4	1034	c.579C>T	c.(577-579)ctC>ctT	p.L193L	KAT2B_ENST00000426228.1_3'UTR	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	193					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						CTTTGCAGCTCTTGAGAAAGT	0.353													C|||	376	0.0750799	0.0136	0.17	5008	,	,		16730	0.0079		0.1471	False		,,,				2504	0.0859				p.L193L		Atlas-SNP	.											.	KAT2B	73	.	0			c.C579T						PASS	.	C		151,4249		5,141,2054	34.0	35.0	35.0		579	5.5	1.0	3	dbSNP_126	35	1341,7247		99,1143,3052	no	coding-synonymous	KAT2B	NM_003884.4		104,1284,5106	TT,TC,CC		15.6148,3.4318,11.4875		193/833	20141356	1492,11496	2200	4294	6494	SO:0001819	synonymous_variant	8850	exon4			GCAGCTCTTGAGA	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.579C>T	3.37:g.20141356C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	91	37	0.406593	NM_003884	Q6NSK1	Silent	SNP	ENST00000263754.4	37	CCDS2634.1																																																																																			C|0.893;T|0.107	0.107	strong		0.353	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884	
PKD1	5310	hgsc.bcm.edu	37	16	2152388	2152388	+	Silent	SNP	C	C	G	rs372874584|rs9935834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2152388C>G	ENST00000262304.4	-	25	9403	c.9195G>C	c.(9193-9195)gtG>gtC	p.V3065V	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Silent_p.V3065V	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3065					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						TCACAGGAAACACAAAGCGGA	0.667													g|||	1086	0.216853	0.5552	0.1758	5008	,	,		17139	0.0		0.164	False		,,,				2504	0.0665				p.V3065V		Atlas-SNP	.											.	PKD1	184	.	0			c.G9195C						PASS	.	G	,	1341,2849		374,593,1128	9.0	11.0	10.0		9195,9195	2.4	0.0	16	dbSNP_131	10	718,7618		88,542,3538	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	462,1135,4666	GG,GC,CC		8.6132,32.0048,16.4378	,	3065/4303,3065/4304	2152388	2059,10467	2095	4168	6263	SO:0001819	synonymous_variant	5310	exon25			AGGAAACACAAAG	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.9195G>C	16.37:g.2152388C>G		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	95	36	0.378947	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			C|0.824;G|0.177	0.177	strong		0.667	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
XYLT1	64131	hgsc.bcm.edu	37	16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	rs113276942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:17353090G>C	ENST00000261381.6	-	3	752	c.668C>G	c.(667-669)gCc>gGc	p.A223G		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	223					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GTTGGCTGCGGCTCTGTCCCC	0.592													G|||	265	0.0529153	0.1914	0.0173	5008	,	,		17039	0.0		0.0	False		,,,				2504	0.0				p.A223G		Atlas-SNP	.											XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	0			c.C668G						PASS	.	G	GLY/ALA	697,3697	288.1+/-279.7	67,563,1567	106.0	117.0	113.0		668	4.5	0.0	16	dbSNP_132	113	19,8581	11.2+/-40.8	0,19,4281	yes	missense	XYLT1	NM_022166.3	60	67,582,5848	CC,CG,GG		0.2209,15.8625,5.5102	benign	223/960	17353090	716,12278	2197	4300	6497	SO:0001583	missense	64131	exon3			GCTGCGGCTCTGT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.668C>G	16.37:g.17353090G>C	ENSP00000261381:p.Ala223Gly	Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	144	78	0.541667	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	89	0.04075091575091575	81	0.16463414634146342	8	0.022099447513812154	0	0.0	0	0.0	G	9.870	1.198774	0.22121	0.158625	0.002209	ENSG00000103489	ENST00000261381	T	0.04809	3.55	5.43	4.47	0.54385	.	0.429861	0.27500	N	0.019098	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B	0.32245	0.361	B	0.19148	0.024	T	0.49021	-0.8982	10	0.31617	T	0.26	-19.7884	11.4244	0.50001	0.1501:0.0:0.8499:0.0	.	223	Q86Y38	XYLT1_HUMAN	G	223	ENSP00000261381:A223G	ENSP00000261381:A223G	A	-	2	0	XYLT1	17260591	0.015000	0.18098	0.011000	0.14972	0.446000	0.32137	1.886000	0.39688	1.296000	0.44742	0.655000	0.94253	GCC	G|0.950;C|0.050	0.050	strong		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
UGT2B15	7366	hgsc.bcm.edu	37	4	69512847	69512847	+	Missense_Mutation	SNP	T	T	G	rs4148269	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:69512847T>G	ENST00000338206.5	-	6	1577	c.1568A>C	c.(1567-1569)aAa>aCa	p.K523T		NM_001076.3	NP_001067.2	P54855	UDB15_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B15	523			K -> T (in dbSNP:rs4148269). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15618667, ECO:0000269|PubMed:7835232, ECO:0000269|PubMed:8399210, ECO:0000269|PubMed:9295060}.		cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)									Acetaminophen(DB00316)|Dabigatran etexilate(DB06695)|Ezetimibe(DB00973)|Lorazepam(DB00186)|Morphine(DB00295)|Oxazepam(DB00842)|Valproic Acid(DB00313)	CTTCTTTCCTTTTTTGGCAAG	0.393													g|||	1841	0.367612	0.1263	0.5029	5008	,	,		18726	0.1895		0.6362	False		,,,				2504	0.5051				p.K523T		Atlas-SNP	.											.	UGT2B15	48	.	0			c.A1568C						PASS	.	G	THR/LYS	989,3417		127,735,1341	130.0	134.0	133.0		1568	-0.3	0.0	4	dbSNP_110	133	5436,3154		1764,1908,623	no	missense	UGT2B15	NM_001076.2	78	1891,2643,1964	GG,GT,TT		36.7171,22.4467,49.4383	benign	523/531	69512847	6425,6571	2203	4295	6498	SO:0001583	missense	7366	exon6			TTTCCTTTTTTGG	AF180322	CCDS3524.1	4q13	2008-02-05	2005-07-20		ENSG00000196620	ENSG00000196620		"""UDP glucuronosyltransferases"""	12546	protein-coding gene	gene with protein product		600069	"""UDP glycosyltransferase 2 family, polypeptide B15"""			7835904	Standard	NM_001076		Approved	UGT2B8	uc021xow.1	P54855	OTTHUMG00000161507	ENST00000338206.5:c.1568A>C	4.37:g.69512847T>G	ENSP00000341045:p.Lys523Thr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	264	263	0.996212	NM_001076	A6NDX0|A6NNJ4|A8K054|P23765|Q9UK63	Missense_Mutation	SNP	ENST00000338206.5	37	CCDS3524.1	713	0.32646520146520147	50	0.1016260162601626	165	0.4558011049723757	83	0.1451048951048951	415	0.5474934036939314	N	0.429	-0.904425	0.02453	0.224467	0.632829	ENSG00000196620	ENST00000338206	T	0.60797	0.16	2.96	-0.317	0.12736	.	0.654479	0.13025	N	0.419785	T	0.00012	0.0000	N	0.11698	0.16	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45352	-0.9267	9	0.18710	T	0.47	.	5.4944	0.16795	0.1049:0.0:0.4116:0.4835	.	523	P54855	UDB15_HUMAN	T	523	ENSP00000341045:K523T	ENSP00000341045:K523T	K	-	2	0	UGT2B15	69195442	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.153000	0.01287	-0.289000	0.09038	-0.231000	0.12243	AAA	T|0.588;G|0.412	0.412	strong		0.393	UGT2B15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365172.1	NM_001076	
DHX35	60625	hgsc.bcm.edu	37	20	37667182	37667182	+	Missense_Mutation	SNP	C	C	T	rs3752302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37667182C>T	ENST00000252011.3	+	22	2141	c.2108C>T	c.(2107-2109)cCg>cTg	p.P703L	DHX35_ENST00000373325.2_Missense_Mutation_p.P679L|DHX35_ENST00000373323.4_Missense_Mutation_p.P672L	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	703			P -> L (in dbSNP:rs3752302).		mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				GTCCAGGACCCGTGAGAGGAG	0.582													A|||	890	0.177716	0.1543	0.2061	5008	,	,		19716	0.2937		0.1252	False		,,,				2504	0.1237				p.P703L		Atlas-SNP	.											.	DHX35	82	.	0			c.C2108T						PASS	.	A	LEU/PRO,LEU/PRO	688,3718		64,560,1579	72.0	65.0	68.0		2108,2015	4.3	1.0	20	dbSNP_107	68	1045,7555		58,929,3313	yes	missense,missense	DHX35	NM_021931.3,NM_001190809.1	98,98	122,1489,4892	TT,TC,CC		12.1512,15.6151,13.3246	benign,benign	703/704,672/673	37667182	1733,11273	2203	4300	6503	SO:0001583	missense	60625	exon22			AGGACCCGTGAGA	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"""DEAH-boxes"""	15861	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"""	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.2108C>T	20.37:g.37667182C>T	ENSP00000252011:p.Pro703Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	36	0.486486	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Missense_Mutation	SNP	ENST00000252011.3	37	CCDS13310.1	372	0.17032967032967034	70	0.14227642276422764	62	0.1712707182320442	139	0.243006993006993	101	0.13324538258575197	A	24.7	4.557654	0.86231	0.156151	0.121512	ENSG00000101452	ENST00000373325;ENST00000252011;ENST00000373323;ENST00000373321;ENST00000449559	T;T;T;T	0.28255	4.21;4.32;4.24;1.62	5.46	4.35	0.52113	.	0.206520	0.34046	N	0.004310	T	0.00012	0.0000	N	0.08118	0	0.41066	P	0.014588999999999963	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24764	-1.0151	9	0.87932	D	0	.	6.6546	0.22981	0.6873:0.1442:0.0:0.1685	rs3752302;rs56814879;rs3752302	672;703	F5GXM6;Q9H5Z1	.;DHX35_HUMAN	L	679;703;672;183;167	ENSP00000362422:P679L;ENSP00000252011:P703L;ENSP00000362420:P672L;ENSP00000397997:P167L	ENSP00000252011:P703L	P	+	2	0	DHX35	37100596	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	0.715000	0.25822	0.433000	0.26313	-0.256000	0.11100	CCG	C|0.855;T|0.145	0.145	strong		0.582	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931	
SULT1C3	442038	hgsc.bcm.edu	37	2	108863767	108863767	+	Silent	SNP	A	A	C	rs9308806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:108863767A>C	ENST00000329106.2	+	1	117	c.117A>C	c.(115-117)gtA>gtC	p.V39V	SULT1C3_ENST00000376700.1_Silent_p.V39V	NM_001008743.1	NP_001008743.1	Q6IMI6	ST1C3_HUMAN	sulfotransferase family, cytosolic, 1C, member 3	39					sulfur compound metabolic process (GO:0006790)	cytoplasm (GO:0005737)	alcohol sulfotransferase activity (GO:0004027)|aryl sulfotransferase activity (GO:0004062)			breast(1)|kidney(1)|large_intestine(1)|lung(8)|prostate(1)|skin(4)	16						GGGAAAAAGTATGTAATTTCC	0.368													.|||	4240	0.846645	0.9909	0.7882	5008	,	,		17764	0.8998		0.7137	False		,,,				2504	0.7751				p.V39V		Atlas-SNP	.											.	SULT1C3	53	.	0			c.A117C						PASS	.	C		4159,247	143.5+/-178.5	1966,227,10	92.0	101.0	98.0		117	-2.5	0.0	2	dbSNP_119	98	6015,2585	418.8+/-352.9	2130,1755,415	no	coding-synonymous	SULT1C3	NM_001008743.1		4096,1982,425	CC,CA,AA		30.0581,5.606,21.7746		39/305	108863767	10174,2832	2203	4300	6503	SO:0001819	synonymous_variant	442038	exon1			AAAAGTATGTAAT	BC146362	CCDS33267.1	2q12.3	2007-07-26			ENSG00000196228	ENSG00000196228		"""Sulfotransferases, cytosolic"""	33543	protein-coding gene	gene with protein product						14676822, 17425406	Standard	NM_001008743		Approved		uc010ywo.2	Q6IMI6	OTTHUMG00000153227	ENST00000329106.2:c.117A>C	2.37:g.108863767A>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	175	174	0.994286	NM_001008743	Q6IMI5	Silent	SNP	ENST00000329106.2	37	CCDS33267.1																																																																																			A|0.190;C|0.810	0.810	strong		0.368	SULT1C3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330255.1	NM_001008743	
GRIN3A	116443	hgsc.bcm.edu	37	9	104385711	104385711	+	Missense_Mutation	SNP	C	C	T	rs10989563|rs35768024	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104385711C>T	ENST00000361820.3	-	5	3103	c.2503G>A	c.(2503-2505)Gat>Aat	p.D835N		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	835			D -> N (in dbSNP:rs10989563). {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)	TTCTCTGGATCATTCCTATAT	0.438													C|||	659	0.131589	0.0703	0.1671	5008	,	,		19009	0.0466		0.2386	False		,,,				2504	0.1667				p.D835N		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G2503A						PASS	.	C	ASN/ASP	396,4010		22,352,1829	116.0	105.0	109.0		2503	5.7	1.0	9	dbSNP_120	109	1649,6951		257,1135,2908	yes	missense	GRIN3A	NM_133445.2	23	279,1487,4737	TT,TC,CC		19.1744,8.9877,15.7235	probably-damaging	835/1116	104385711	2045,10961	2203	4300	6503	SO:0001583	missense	116443	exon5			CTGGATCATTCCT		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.2503G>A	9.37:g.104385711C>T	ENSP00000355155:p.Asp835Asn	Somatic	154	1	0.00649351		WXS	Illumina HiSeq	Phase_I	128	125	0.976562	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	251	0.11492673992673992	24	0.04878048780487805	63	0.17403314917127072	22	0.038461538461538464	142	0.18733509234828497	C	28.4	4.921160	0.92249	0.089877	0.191744	ENSG00000198785	ENST00000361820	T	0.27104	1.69	5.72	5.72	0.89469	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.113021	0.64402	D	0.000020	T	0.00109	0.0003	L	0.57536	1.79	0.09310	P	0.9999999709858	D	0.76494	0.999	D	0.72338	0.977	T	0.00081	-1.2106	9	0.25751	T	0.34	.	19.8937	0.96942	0.0:1.0:0.0:0.0	rs10989563;rs10989563	835	Q8TCU5	NMD3A_HUMAN	N	835	ENSP00000355155:D835N	ENSP00000355155:D835N	D	-	1	0	GRIN3A	103425532	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.716000	0.92895	0.650000	0.86243	GAT	CA|0.500;TG|0.500	.	alt		0.438	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974405	22974405	+	Missense_Mutation	SNP	C	C	T	rs61736406	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22974405C>T	ENST00000356864.3	+	5	1173	c.641C>T	c.(640-642)aCc>aTc	p.T214I	TNFRSF10C_ENST00000540813.1_Missense_Mutation_p.T112I	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	214					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.T214N(7)		endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAGACAATGACCACCAGCCCG	0.612																																					p.T214I		Atlas-SNP	.											TNFRSF10C,NS,carcinoma,0,5	TNFRSF10C	30	5	7	Substitution - Missense(7)	prostate(4)|large_intestine(3)	c.C641T						PASS	.						63.0	71.0	68.0					8																	22974405		2203	4298	6501	SO:0001583	missense	8794	exon5			CAATGACCACCAG	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.641C>T	8.37:g.22974405C>T	ENSP00000349324:p.Thr214Ile	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	152	35	0.230263	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	32	0.014652014652014652	27	0.054878048780487805	3	0.008287292817679558	0	0.0	2	0.002638522427440633	c	0.284	-0.984715	0.02180	.	.	ENSG00000173535	ENST00000356864;ENST00000540813;ENST00000544885	T;T	0.62498	0.02;0.38	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.06872	0.0175	N	0.03608	-0.345	0.09310	N	1	B	0.22909	0.077	B	0.06405	0.002	T	0.19031	-1.0318	9	0.62326	D	0.03	.	5.2848	0.15696	0.3272:0.6728:0.0:0.0	.	214	O14798	TR10C_HUMAN	I	214;112;214	ENSP00000349324:T214I;ENSP00000437612:T112I	ENSP00000349324:T214I	T	+	2	0	TNFRSF10C	23030350	0.033000	0.19621	0.001000	0.08648	0.141000	0.21300	0.550000	0.23345	-2.089000	0.00860	-2.399000	0.00225	ACC	A|0.000;C|0.990;T|0.009	0.009	strong		0.612	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
SLC22A1	6580	hgsc.bcm.edu	37	6	160543123	160543123	+	Silent	SNP	T	T	C	rs1867351	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:160543123T>C	ENST00000366963.4	+	1	303	c.156T>C	c.(154-156)agT>agC	p.S52S	SLC22A1_ENST00000324965.4_Silent_p.S52S|SLC22A1_ENST00000457470.2_Silent_p.S52S	NM_003057.2|NM_153187.1	NP_003048.1|NP_694857.1	O15245	S22A1_HUMAN	solute carrier family 22 (organic cation transporter), member 1	52					dopamine transport (GO:0015872)|drug transmembrane transport (GO:0006855)|epinephrine transport (GO:0048241)|establishment or maintenance of transmembrane electrochemical gradient (GO:0010248)|norepinephrine transport (GO:0015874)|organic cation transport (GO:0015695)|protein homooligomerization (GO:0051260)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	acetylcholine transmembrane transporter activity (GO:0005277)|dopamine transmembrane transporter activity (GO:0005329)|norepinephrine transmembrane transporter activity (GO:0005333)|organic cation transmembrane transporter activity (GO:0015101)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)		SLC22A1/CUTA(2)	breast(1)|endometrium(3)|large_intestine(3)|lung(13)|upper_aerodigestive_tract(1)	21		Breast(66;0.000776)|Ovarian(120;0.00556)		OV - Ovarian serous cystadenocarcinoma(65;2.73e-17)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)	Acebutolol(DB01193)|Acepromazine(DB01614)|Aciclovir(DB00787)|Amantadine(DB00915)|Amiloride(DB00594)|Aminohippurate(DB00345)|Caspofungin(DB00520)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Choline(DB00122)|Cimetidine(DB00501)|Cladribine(DB00242)|Clonidine(DB00575)|Codeine(DB00318)|Cytarabine(DB00987)|Desipramine(DB01151)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Disopyramide(DB00280)|Dopamine(DB00988)|Epinephrine(DB00668)|Estradiol(DB00783)|Estropipate(DB04574)|Ganciclovir(DB01004)|Gentian Violet(DB00406)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Lamivudine(DB00709)|Latanoprost(DB00654)|Metformin(DB00331)|Midazolam(DB00683)|Nelfinavir(DB00220)|Nicotine(DB00184)|Norepinephrine(DB00368)|Oxaliplatin(DB00526)|Pancuronium(DB01337)|Phenformin(DB00914)|Phenoxybenzamine(DB00925)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Prazosin(DB00457)|Probenecid(DB01032)|Procainamide(DB01035)|Progesterone(DB00396)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rocuronium(DB00728)|Saquinavir(DB01232)|Spermine(DB00127)|Testosterone(DB00624)|Thiamine(DB00152)|Thioproperazine(DB01622)|Thiothixene(DB01623)|Tubocurarine(DB01199)|Vecuronium(DB01339)|Verapamil(DB00661)	ACTGCCAGAGTCCTGGGGTGG	0.637													C|||	1408	0.28115	0.326	0.2882	5008	,	,		18882	0.3909		0.1849	False		,,,				2504	0.2014				p.S52S		Atlas-SNP	.											.	SLC22A1	69	.	0			c.T156C						PASS	.	C	,	1305,3101	697.3+/-406.2	202,901,1100	80.0	88.0	86.0		156,156	2.6	0.9	6	dbSNP_92	86	1742,6858	734.5+/-406.9	173,1396,2731	no	coding-synonymous,coding-synonymous	SLC22A1	NM_003057.2,NM_153187.1	,	375,2297,3831	CC,CT,TT		20.2558,29.6187,23.4276	,	52/555,52/507	160543123	3047,9959	2203	4300	6503	SO:0001819	synonymous_variant	6580	exon1			CCAGAGTCCTGGG	U77086	CCDS5274.1, CCDS5275.1	6q25.3	2013-05-22			ENSG00000175003	ENSG00000175003		"""Solute carriers"""	10963	protein-coding gene	gene with protein product		602607				9605850	Standard	NM_003057		Approved	OCT1	uc003qtc.3	O15245	OTTHUMG00000015947	ENST00000366963.4:c.156T>C	6.37:g.160543123T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	55	48	0.872727	NM_153187	A6NFF3|A8K1H2|C9JSU6|O15395|Q9NQD4	Silent	SNP	ENST00000366963.4	37	CCDS5274.1																																																																																			T|0.754;C|0.246	0.246	strong		0.637	SLC22A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042938.2		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79067055	79067055	+	Missense_Mutation	SNP	C	C	T	rs2277549	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79067055C>T	ENST00000388820.4	-	12	1997	c.1787G>A	c.(1786-1788)cGc>cAc	p.R596H	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	596	Cys-rich.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						GAAGGAGGGGCGGCCAGCAGG	0.632													C|||	1262	0.251997	0.2005	0.2205	5008	,	,		21700	0.1825		0.3459	False		,,,				2504	0.319				p.R596H		Atlas-SNP	.											ADAMTS7,NS,carcinoma,-1,1	ADAMTS7	142	1	0			c.G1787A						PASS	.						47.0	53.0	51.0					15																	79067055		2196	4291	6487	SO:0001583	missense	11173	exon12			GAGGGGCGGCCAG	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.1787G>A	15.37:g.79067055C>T	ENSP00000373472:p.Arg596His	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	57	51	0.894737	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	596	0.27289377289377287	116	0.23577235772357724	97	0.26795580110497236	115	0.20104895104895104	268	0.35356200527704484	C	1.326	-0.598073	0.03744	.	.	ENSG00000136378	ENST00000388820	T	0.00438	7.42	3.3	-6.6	0.01824	.	1.548120	0.03595	N	0.232532	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.18461	0.003;0.028	B;B	0.09377	0.002;0.004	T	0.14090	-1.0485	9	0.36615	T	0.2	.	10.1071	0.42539	0.0:0.1661:0.1123:0.7216	rs2277549	596;596	A8MQ00;Q9UKP4	.;ATS7_HUMAN	H	596	ENSP00000373472:R596H	ENSP00000373472:R596H	R	-	2	0	ADAMTS7	76854110	0.000000	0.05858	0.007000	0.13788	0.727000	0.41649	-2.867000	0.00722	-1.837000	0.01189	-1.036000	0.02392	CGC	C|0.727;T|0.273	0.273	strong		0.632	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
SPATA31A3	727830	hgsc.bcm.edu	37	9	40702846	40702846	+	Missense_Mutation	SNP	C	C	T	rs200010477	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:40702846C>T	ENST00000356699.5	+	4	532	c.503C>T	c.(502-504)aCc>aTc	p.T168I	RP11-395E19.5_ENST00000432614.1_lincRNA|SPATA31A3_ENST00000463536.1_3'UTR	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	168	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGGCCTCCACCCCATCACCA	0.592																																					p.T168I		Atlas-SNP	.											FAM75A3_ENST00000356699,NS,carcinoma,-1,6	.	.	6	0			c.C503T						scavenged	.						29.0	32.0	32.0					9																	40702846		1192	2948	4140	SO:0001583	missense	727830	exon4			CCTCCACCCCATC			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A3"""	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.503C>T	9.37:g.40702846C>T	ENSP00000349132:p.Thr168Ile	Somatic	263	0	0		WXS	Illumina HiSeq	Phase_I	330	184	0.557576	NM_001083124		Missense_Mutation	SNP	ENST00000356699.5	37	CCDS47969.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.507524	0.27036	.	.	ENSG00000147926	ENST00000356699	T	0.05580	3.42	2.04	-3.77	0.04346	.	2.363890	0.02457	N	0.086169	T	0.05044	0.0135	L	0.41415	1.275	0.80722	P	0.0	P	0.37101	0.582	B	0.33339	0.162	T	0.22695	-1.0209	9	0.51188	T	0.08	1.2989	0.8573	0.01185	0.376:0.2856:0.1919:0.1465	.	168	Q5VYP0	F75A3_HUMAN	I	168	ENSP00000349132:T168I	ENSP00000349132:T168I	T	+	2	0	FAM75A3	40692846	0.000000	0.05858	0.000000	0.03702	0.053000	0.15095	-0.670000	0.05256	-0.955000	0.03636	-0.714000	0.03626	ACC	.	.	weak		0.592	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124	
OBSL1	23363	hgsc.bcm.edu	37	2	220420785	220420785	+	Silent	SNP	G	G	A	rs3087971	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220420785G>A	ENST00000404537.1	-	14	4622	c.4566C>T	c.(4564-4566)tgC>tgT	p.C1522C	OBSL1_ENST00000603926.1_Silent_p.C1522C|OBSL1_ENST00000373876.1_Silent_p.C1430C|OBSL1_ENST00000265318.4_Missense_Mutation_p.A1389V|OBSL1_ENST00000265317.5_Silent_p.C421C	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1522	Ig-like 12.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GGTGGCTCTCGCAGCCGTAGG	0.632													G|||	1148	0.229233	0.2224	0.2983	5008	,	,		15387	0.2837		0.2734	False		,,,				2504	0.0879				p.C1522C		Atlas-SNP	.											.	OBSL1	120	.	0			c.C4566T						PASS	.	G	,	944,3286		124,696,1295	41.0	45.0	43.0		4566,4566	-6.8	0.7	2	dbSNP_102	43	2355,6105		334,1687,2209	no	coding-synonymous,coding-synonymous	OBSL1	NM_001173431.1,NM_015311.2	,	458,2383,3504	AA,AG,GG		27.8369,22.3168,25.9968	,	1522/1544,1522/1897	220420785	3299,9391	2115	4230	6345	SO:0001819	synonymous_variant	23363	exon14			GCTCTCGCAGCCG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4566C>T	2.37:g.220420785G>A		Somatic	281	1	0.00355872		WXS	Illumina HiSeq	Phase_I	319	164	0.514107	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1	576	0.26373626373626374	93	0.18902439024390244	104	0.287292817679558	171	0.29895104895104896	208	0.27440633245382584	G	1.900	-0.453356	0.04540	0.223168	0.278369	ENSG00000124006	ENST00000265318;ENST00000456147	T	0.56941	0.43	4.39	-6.84	0.01687	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.42041	P	0.008920999999999957	.	.	.	.	.	.	T	0.39860	-0.9593	5	0.87932	D	0	.	14.8475	0.70270	0.569:0.0:0.431:0.0	rs3087971	.	.	.	V	1389;424	ENSP00000265318:A1389V	ENSP00000265318:A1389V	A	-	2	0	OBSL1	220129029	0.000000	0.05858	0.679000	0.29978	0.262000	0.26303	-2.148000	0.01292	-1.935000	0.01049	-0.458000	0.05436	GCG	G|0.730;A|0.270	0.270	strong		0.632	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
SLC9C1	285335	hgsc.bcm.edu	37	3	111887792	111887792	+	Missense_Mutation	SNP	C	C	A	rs76007436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:111887792C>A	ENST00000305815.5	-	25	3421	c.3169G>T	c.(3169-3171)Gct>Tct	p.A1057S	SLC9C1_ENST00000487372.1_Missense_Mutation_p.A1009S	NM_183061.1	NP_898884.1	Q4G0N8	SL9C1_HUMAN	solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1	1057					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.A1057S(1)									TCTTCTACAGCTCCATGTATG	0.318													C|||	155	0.0309505	0.0038	0.0375	5008	,	,		20825	0.0		0.0924	False		,,,				2504	0.0317				p.A1057S		Atlas-SNP	.											SLC9A10,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	pancreas(1)	c.G3169T						PASS	.	C	SER/ALA	78,4326	67.6+/-105.2	2,74,2126	123.0	130.0	127.0		3169	-1.2	1.0	3	dbSNP_132	127	798,7800	186.4+/-233.9	37,724,3538	yes	missense	SLC9A10	NM_183061.1	99	39,798,5664	AA,AC,CC		9.2812,1.7711,6.7374	benign	1057/1178	111887792	876,12126	2202	4299	6501	SO:0001583	missense	285335	exon25			CTACAGCTCCATG	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.3169G>T	3.37:g.111887792C>A	ENSP00000306627:p.Ala1057Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	125	65	0.52	NM_183061	Q6ZRP4|Q7RTP2	Missense_Mutation	SNP	ENST00000305815.5	37	CCDS33817.1	89	0.04075091575091575	3	0.006097560975609756	14	0.03867403314917127	0	0.0	72	0.09498680738786279	C	3.770	-0.047885	0.07407	0.017711	0.092812	ENSG00000172139	ENST00000305815;ENST00000487372	T;T	0.75367	-0.93;-0.92	6.06	-1.16	0.09678	.	0.667620	0.14233	N	0.332601	T	0.02119	0.0066	N	0.10916	0.065	0.22240	N	0.99927	B;B	0.13145	0.007;0.003	B;B	0.16722	0.016;0.006	T	0.05370	-1.0889	10	0.02654	T	1	-0.233	4.8076	0.13328	0.5825:0.2235:0.0:0.194	.	1009;1057	Q4G0N8-2;Q4G0N8	.;S9A10_HUMAN	S	1057;1009	ENSP00000306627:A1057S;ENSP00000420688:A1009S	ENSP00000306627:A1057S	A	-	1	0	SLC9A10	113370482	0.940000	0.31905	0.983000	0.44433	0.905000	0.53344	-0.132000	0.10467	-0.086000	0.12550	0.650000	0.86243	GCT	C|0.941;A|0.059	0.059	strong		0.318	SLC9C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354066.1	NM_183061	
NLRP4	147945	hgsc.bcm.edu	37	19	56373462	56373462	+	Missense_Mutation	SNP	G	G	A	rs12462372	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56373462G>A	ENST00000301295.6	+	5	2545	c.2123G>A	c.(2122-2124)cGt>cAt	p.R708H	NLRP4_ENST00000346986.5_Missense_Mutation_p.R708H|NLRP4_ENST00000587891.1_Missense_Mutation_p.R633H	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	708			R -> H (in dbSNP:rs12462372).		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)		AAACTCTCTCGTGATGACATC	0.473													G|||	528	0.105431	0.0038	0.1599	5008	,	,		22235	0.2391		0.0586	False		,,,				2504	0.1145				p.R708H		Atlas-SNP	.											NLRP4_ENST00000301295,colon,carcinoma,+1,7	NLRP4	331	7	0			c.G2123A						PASS	.	G	HIS/ARG	59,4347	56.2+/-92.4	0,59,2144	143.0	128.0	133.0		2123	-6.5	0.0	19	dbSNP_120	133	407,8193	128.3+/-186.6	11,385,3904	yes	missense	NLRP4	NM_134444.4	29	11,444,6048	AA,AG,GG		4.7326,1.3391,3.583	benign	708/995	56373462	466,12540	2203	4300	6503	SO:0001583	missense	147945	exon5			TCTCTCGTGATGA	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.2123G>A	19.37:g.56373462G>A	ENSP00000301295:p.Arg708His	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	137	73	0.532847	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	225	0.10302197802197802	3	0.006097560975609756	32	0.08839779005524862	142	0.24825174825174826	48	0.0633245382585752	G	0.018	-1.476288	0.01035	0.013391	0.047326	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.53206	0.63;0.63	3.26	-6.52	0.01872	.	.	.	.	.	T	0.00012	0.0000	N	0.05487	-0.04	0.80722	P	0.0	B;B;B	0.27882	0.037;0.183;0.192	B;B;B	0.21546	0.019;0.035;0.015	T	0.21518	-1.0243	8	0.23891	T	0.37	.	8.1119	0.30920	0.689:0.1268:0.1842:0.0	rs12462372;rs52792345;rs60975652;rs12462372	708;633;708	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	H	708	ENSP00000301295:R708H;ENSP00000344787:R708H	ENSP00000301295:R708H	R	+	2	0	NLRP4	61065274	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.408000	0.01042	-1.815000	0.01222	-0.251000	0.11542	CGT	G|0.927;A|0.073	0.073	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
OR13C5	138799	hgsc.bcm.edu	37	9	107361439	107361439	+	Missense_Mutation	SNP	G	G	C	rs4629933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107361439G>C	ENST00000374779.2	-	1	349	c.256C>G	c.(256-258)Ctt>Gtt	p.L86V		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	86			L -> V (in dbSNP:rs4629933).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTTTCTGAAAGGAAGCTCACT	0.527													G|||	3389	0.676717	0.7504	0.5937	5008	,	,		20678	0.9573		0.4225	False		,,,				2504	0.6084				p.L86V		Atlas-SNP	.											.	OR13C5	60	.	0			c.C256G						PASS	.						27.0	42.0	37.0					9																	107361439		2189	4294	6483	SO:0001583	missense	138799	exon1			CTGAAAGGAAGCT		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.256C>G	9.37:g.107361439G>C	ENSP00000363911:p.Leu86Val	Somatic	579	0	0		WXS	Illumina HiSeq	Phase_I	429	74	0.172494	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	1384	0.6336996336996337	336	0.6829268292682927	201	0.5552486187845304	521	0.9108391608391608	326	0.43007915567282323	G	14.72	2.618900	0.46736	.	.	ENSG00000255800	ENST00000374779	T	0.01369	4.97	4.03	-8.0	0.01126	GPCR, rhodopsin-like superfamily (1);	0.289560	0.17451	U	0.173772	T	0.00012	0.0000	L	0.48877	1.53	0.80722	P	0.0	P	0.51791	0.948	B	0.42555	0.391	T	0.48570	-0.9024	9	0.32370	T	0.25	.	1.5125	0.02499	0.1543:0.3065:0.2305:0.3087	rs4629933;rs7025562	86	Q8NGS8	O13C5_HUMAN	V	86	ENSP00000363911:L86V	ENSP00000363911:L86V	L	-	1	0	OR13C5	106401260	0.000000	0.05858	0.000000	0.03702	0.515000	0.34225	-1.382000	0.02546	-1.158000	0.02811	0.531000	0.56144	CTT	G|0.308;C|0.692	0.692	strong		0.527	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
TMEM9B	56674	hgsc.bcm.edu	37	11	8977830	8977830	+	Silent	SNP	A	A	G	rs2568068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:8977830A>G	ENST00000534025.1	-	3	672	c.213T>C	c.(211-213)gtT>gtC	p.V71V	TMEM9B_ENST00000525069.1_5'UTR|TMEM9B_ENST00000528117.1_5'UTR|TMEM9B_ENST00000309134.5_5'UTR	NM_020644.1	NP_065695.1	Q9NQ34	TMM9B_HUMAN	TMEM9 domain family, member B	71					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)			breast(1)|lung(1)|prostate(1)	3				Epithelial(150;4.39e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0237)		TGGGCTCCACAACATGAAGGC	0.423													A|||	1677	0.334864	0.4395	0.2363	5008	,	,		19737	0.4494		0.2097	False		,,,				2504	0.274				p.V71V		Atlas-SNP	.											.	TMEM9B	6	.	0			c.T213C						PASS	.	A		1667,2735	509.1+/-367.1	301,1065,835	84.0	78.0	80.0		213	-2.3	1.0	11	dbSNP_100	80	1789,6803	320.4+/-314.6	181,1427,2688	no	coding-synonymous	TMEM9B	NM_020644.1		482,2492,3523	GG,GA,AA		20.8217,37.8692,26.5969		71/199	8977830	3456,9538	2201	4296	6497	SO:0001819	synonymous_variant	56674	exon3			CTCCACAACATGA	AJ400877	CCDS7796.1, CCDS66021.1	11p15.3	2008-02-05	2005-10-06	2005-10-06	ENSG00000175348	ENSG00000175348			1168	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 15"""	C11orf15		11528127	Standard	NM_001286095		Approved		uc001mhe.1	Q9NQ34	OTTHUMG00000165676	ENST00000534025.1:c.213T>C	11.37:g.8977830A>G		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	46	19	0.413043	NM_020644	Q7Z649	Silent	SNP	ENST00000534025.1	37	CCDS7796.1																																																																																			T|0.006;G|0.283	0.283	strong		0.423	TMEM9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385722.1		
PTGIS	5740	hgsc.bcm.edu	37	20	48156236	48156236	+	Missense_Mutation	SNP	C	C	T	rs148768155	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:48156236C>T	ENST00000244043.4	-	5	573	c.544G>A	c.(544-546)Gga>Aga	p.G182R	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	182					apoptotic signaling pathway (GO:0097190)|arachidonic acid metabolic process (GO:0019369)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|positive regulation of angiogenesis (GO:0045766)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|prostaglandin-I synthase activity (GO:0008116)	p.G182R(1)		endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|ovary(3)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(12;2.37e-05)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)		Epoprostenol(DB01240)|Phenylbutazone(DB00812)	GCCTCAATTCCGTAAAGAGTC	0.617																																					p.G182R		Atlas-SNP	.											PTGIS,scalp,carcinoma,0,1	PTGIS	60	1	1	Substitution - Missense(1)	skin(1)	c.G544A						PASS	.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	40.0	38.0	39.0		544	5.2	1.0	20	dbSNP_134	39	16,8584	11.9+/-42.8	0,16,4284	yes	missense	PTGIS	NM_000961.3	125	0,17,6486	TT,TC,CC		0.186,0.0227,0.1307	probably-damaging	182/501	48156236	17,12989	2203	4300	6503	SO:0001583	missense	5740	exon5			CAATTCCGTAAAG		CCDS13419.1	20q13	2013-11-18			ENSG00000124212	ENSG00000124212	5.3.99.4	"""Cytochrome P450s"""	9603	protein-coding gene	gene with protein product	"""cytochrome P450, family 8, subfamily A, polypeptide 1"""	601699				8812456	Standard	NM_000961		Approved	PGIS, CYP8A1	uc002xut.3	Q16647	OTTHUMG00000033077	ENST00000244043.4:c.544G>A	20.37:g.48156236C>T	ENSP00000244043:p.Gly182Arg	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Missense_Mutation	SNP	ENST00000244043.4	37	CCDS13419.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352346	0.82132	2.27E-4	0.00186	ENSG00000124212	ENST00000244043	T	0.03330	3.97	5.15	5.15	0.70609	.	0.124305	0.53938	D	0.000060	T	0.18841	0.0452	M	0.85041	2.73	0.53688	D	0.999976	D	0.76494	0.999	P	0.59424	0.857	T	0.00802	-1.1560	10	0.87932	D	0	-19.949	17.39	0.87427	0.0:1.0:0.0:0.0	.	182	Q16647	PTGIS_HUMAN	R	182	ENSP00000244043:G182R	ENSP00000244043:G182R	G	-	1	0	PTGIS	47589643	0.995000	0.38212	0.997000	0.53966	0.738000	0.42128	4.987000	0.63857	2.416000	0.81992	0.561000	0.74099	GGA	C|0.999;T|0.001	0.001	strong		0.617	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2		
PTPRD	5789	hgsc.bcm.edu	37	9	8389364	8389364	+	Silent	SNP	C	C	G	rs2279776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:8389364C>G	ENST00000381196.4	-	34	4797	c.4254G>C	c.(4252-4254)ggG>ggC	p.G1418G	PTPRD_ENST00000356435.5_Silent_p.G1418G|PTPRD_ENST00000397611.3_Silent_p.G1008G|PTPRD_ENST00000537002.1_Silent_p.G1008G|PTPRD_ENST00000397606.3_Silent_p.G1011G|PTPRD_ENST00000360074.4_Silent_p.G1405G|PTPRD_ENST00000358503.5_Silent_p.G1396G|PTPRD_ENST00000355233.5_Silent_p.G1012G|PTPRD_ENST00000486161.1_Silent_p.G1011G|PTPRD_ENST00000397617.3_Silent_p.G1011G|PTPRD_ENST00000540109.1_Silent_p.G1418G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1418	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		GCTTCCTATACCCATCTATGT	0.458										TSP Lung(15;0.13)			G|||	2786	0.55631	0.6195	0.451	5008	,	,		18503	0.6329		0.4354	False		,,,				2504	0.591				p.G1418G		Atlas-SNP	.											.	PTPRD	1348	.	0			c.G4254C						PASS	.	G	,,,,,	2547,1859	540.5+/-375.5	733,1081,389	184.0	172.0	176.0		3024,3033,4254,3033,3036,3006	-0.9	0.9	9	dbSNP_100	176	3757,4843	616.4+/-396.5	832,2093,1375	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPRD	NM_001040712.2,NM_001171025.1,NM_002839.3,NM_130391.3,NM_130392.3,NM_130393.3	,,,,,	1565,3174,1764	GG,GC,CC		43.686,42.1925,48.4699	,,,,,	1008/1503,1011/1506,1418/1913,1011/1506,1012/1507,1002/1497	8389364	6304,6702	2203	4300	6503	SO:0001819	synonymous_variant	5789	exon37			CCTATACCCATCT	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4254G>C	9.37:g.8389364C>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	141	0.979167	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	37	CCDS43786.1																																																																																			C|0.506;G|0.494	0.494	strong		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
TPST2	8459	hgsc.bcm.edu	37	22	26937087	26937087	+	Silent	SNP	C	C	A	rs5761587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26937087C>A	ENST00000338754.4	-	3	780	c.510G>T	c.(508-510)tcG>tcT	p.S170S	TPST2_ENST00000398110.2_Silent_p.S170S|TPST2_ENST00000403880.1_Silent_p.S170S	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	170					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						GGAACAGGCGCGACAGGTAGA	0.617													C|||	198	0.0395367	0.0121	0.0403	5008	,	,		19873	0.0169		0.0885	False		,,,				2504	0.0491				p.S170S		Atlas-SNP	.											.	TPST2	23	.	0			c.G510T						PASS	.	C	,	124,4282	92.5+/-131.2	0,124,2079	96.0	74.0	81.0		510,510	-2.7	1.0	22	dbSNP_114	81	828,7772	191.7+/-237.8	41,746,3513	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	41,870,5592	AA,AC,CC		9.6279,2.8143,7.3197	,	170/378,170/378	26937087	952,12054	2203	4300	6503	SO:0001819	synonymous_variant	8459	exon3			CAGGCGCGACAGG	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.510G>T	22.37:g.26937087C>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	54	24	0.444444	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			C|0.935;A|0.065	0.065	strong		0.617	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
KALRN	8997	hgsc.bcm.edu	37	3	124369744	124369744	+	Silent	SNP	C	C	T	rs12106716	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124369744C>T	ENST00000291478.5	+	5	823	c.660C>T	c.(658-660)aaC>aaT	p.N220N	KALRN_ENST00000393496.1_Silent_p.N258N|KALRN_ENST00000459915.1_Silent_p.N9N|KALRN_ENST00000360013.3_Silent_p.N1917N|KALRN_ENST00000428018.2_Silent_p.N188N	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1916					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CTCCTAAAAACCCAGAAGAAG	0.552													C|||	446	0.0890575	0.1339	0.111	5008	,	,		19385	0.001		0.1014	False		,,,				2504	0.091				p.N1917N		Atlas-SNP	.											.	KALRN	556	.	0			c.C5751T						PASS	.	C	,	643,3763	275.7+/-272.7	49,545,1609	93.0	84.0	87.0		5751,660	4.0	1.0	3	dbSNP_120	87	1048,7552	221.5+/-258.9	63,922,3315	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	112,1467,4924	TT,TC,CC		12.186,14.5937,13.0017	,	1917/2987,220/1290	124369744	1691,11315	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon38			TAAAAACCCAGAA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.660C>T	3.37:g.124369744C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	187	0.08562271062271062	73	0.1483739837398374	43	0.11878453038674033	0	0.0	71	0.09366754617414248	C	1.724	-0.495982	0.04291	0.145937	0.12186	ENSG00000160145	ENST00000354186	.	.	.	4.83	3.96	0.45880	.	.	.	.	.	T	0.00552	0.0018	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.13899	-1.0492	3	.	.	.	.	12.8883	0.58057	0.0:0.9206:0.0:0.0794	rs12106716	.	.	.	I	1886	.	.	T	+	2	0	KALRN	125852434	1.000000	0.71417	1.000000	0.80357	0.210000	0.24377	2.823000	0.48081	1.250000	0.43966	0.655000	0.94253	ACC	C|0.888;T|0.112	0.112	strong		0.552	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
PDLIM2	64236	hgsc.bcm.edu	37	8	22442908	22442908	+	Missense_Mutation	SNP	G	G	A	rs11989168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22442908G>A	ENST00000397760.4	+	6	936	c.536G>A	c.(535-537)cGa>cAa	p.R179Q	PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000409141.1_Missense_Mutation_p.R179Q|PDLIM2_ENST00000397761.2_Missense_Mutation_p.R179Q|PDLIM2_ENST00000339162.7_Missense_Mutation_p.R179Q|PDLIM2_ENST00000409417.1_Missense_Mutation_p.R179Q|PDLIM2_ENST00000265810.4_Missense_Mutation_p.R179Q|PDLIM2_ENST00000308354.7_Missense_Mutation_p.R429Q			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	179						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		CCTGGAAGCCGACAGGTGAGG	0.667													G|||	25	0.00499201	0.0144	0.0072	5008	,	,		11606	0.0		0.001	False		,,,				2504	0.0				p.R429Q		Atlas-SNP	.											PDLIM2_ENST00000308354,colon,carcinoma,+1,2	PDLIM2	42	2	0			c.G1286A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	57,4345		0,57,2144	26.0	20.0	22.0		1286,536,536	-2.1	0.1	8	dbSNP_120	22	4,8590		0,4,4293	yes	missense,missense,missense	PDLIM2	NM_021630.5,NM_176871.3,NM_198042.3	43,43,43	0,61,6437	AA,AG,GG		0.0465,1.2949,0.4694	benign,benign,benign	429/603,179/367,179/279	22442908	61,12935	2201	4297	6498	SO:0001583	missense	64236	exon6			GAAGCCGACAGGT	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.536G>A	8.37:g.22442908G>A	ENSP00000380867:p.Arg179Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	37		15	0.006868131868131868	10	0.02032520325203252	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	8.308	0.821380	0.16678	0.012949	4.65E-4	ENSG00000120913	ENST00000456545;ENST00000308354;ENST00000452226;ENST00000397760;ENST00000339162;ENST00000397761;ENST00000429812;ENST00000409141;ENST00000265810;ENST00000409417	T;T;T;T;T;T;T;T;T;T	0.25749	2.06;3.57;2.65;2.65;2.64;2.65;1.78;2.64;2.74;2.65	4.75	-2.07	0.07276	.	0.808770	0.10844	N	0.627938	T	0.01730	0.0055	N	0.00162	-1.95	0.09310	N	1	B;B;B;B	0.23490	0.005;0.086;0.007;0.052	B;B;B;B	0.15052	0.003;0.012;0.002;0.007	T	0.39623	-0.9605	10	0.11485	T	0.65	-0.0402	4.6558	0.12617	0.477:0.0:0.3754:0.1476	rs11989168	179;179;179;179	Q96JY6-3;Q96JY6-4;Q96JY6;C9JS55	.;.;PDLI2_HUMAN;.	Q	179;429;179;179;179;179;179;179;179;179	ENSP00000401992:R179Q;ENSP00000312634:R429Q;ENSP00000394376:R179Q;ENSP00000380867:R179Q;ENSP00000342035:R179Q;ENSP00000380868:R179Q;ENSP00000407643:R179Q;ENSP00000386868:R179Q;ENSP00000265810:R179Q;ENSP00000387084:R179Q	ENSP00000265810:R179Q	R	+	2	0	PDLIM2	22498853	0.000000	0.05858	0.068000	0.19968	0.166000	0.22503	-0.518000	0.06267	-0.292000	0.08999	-0.448000	0.05591	CGA	G|0.993;A|0.007	0.007	strong		0.667	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1		
CADPS2	93664	hgsc.bcm.edu	37	7	122303321	122303321	+	Silent	SNP	C	C	T	rs2251761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:122303321C>T	ENST00000449022.2	-	3	775	c.756G>A	c.(754-756)ctG>ctA	p.L252L	CADPS2_ENST00000313070.7_Silent_p.L252L|CADPS2_ENST00000412584.2_Silent_p.L252L|CADPS2_ENST00000334010.7_Silent_p.L252L	NM_017954.10	NP_060424.9	Q86UW7	CAPS2_HUMAN	Ca++-dependent secretion activator 2	252					cellular response to starvation (GO:0009267)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasmic membrane-bounded vesicle (GO:0016023)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(2)	43						GCTGGTGTTCCAGTTTTTTAA	0.408													T|||	3596	0.718051	0.6536	0.6585	5008	,	,		18704	0.7579		0.7306	False		,,,				2504	0.7935				p.L252L		Atlas-SNP	.											.	CADPS2	116	.	0			c.G756A						PASS	.	T	,,	2509,1195		873,763,216	87.0	82.0	83.0		756,756,756	-3.8	1.0	7	dbSNP_100	83	6216,1978		2357,1502,238	no	coding-synonymous,coding-synonymous,coding-synonymous	CADPS2	NM_001009571.3,NM_001167940.1,NM_017954.10	,,	3230,2265,454	TT,TC,CC		24.1396,32.2624,26.6683	,,	252/1256,252/1301,252/1297	122303321	8725,3173	1852	4097	5949	SO:0001819	synonymous_variant	93664	exon3			GTGTTCCAGTTTT		CCDS47691.1, CCDS55158.1	7q31.32	2013-01-10	2008-08-28		ENSG00000081803	ENSG00000081803		"""Pleckstrin homology (PH) domain containing"""	16018	protein-coding gene	gene with protein product		609978	"""Ca++-dependent activator protein for secretion 2"""				Standard	NM_017954		Approved		uc010lkq.3	Q86UW7	OTTHUMG00000157093	ENST00000449022.2:c.756G>A	7.37:g.122303321C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_001167940	A4D0X3|B7ZM56|Q658Q2|Q7Z5T7|Q8IZW9|Q8N7M4|Q9H6P4|Q9HCI1|Q9NWK8	Silent	SNP	ENST00000449022.2	37	CCDS55158.1																																																																																			C|0.261;T|0.739	0.739	strong		0.408	CADPS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347414.2	NM_017954	
PSG1	5669	hgsc.bcm.edu	37	19	43372941	43372941	+	Missense_Mutation	SNP	T	T	C	rs28374299	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:43372941T>C	ENST00000436291.2	-	4	1071	c.955A>G	c.(955-957)Atc>Gtc	p.I319V	PSG1_ENST00000244296.2_Missense_Mutation_p.I319V|PSG1_ENST00000403380.3_Missense_Mutation_p.I226V|PSG1_ENST00000595124.1_Missense_Mutation_p.I226V|PSG1_ENST00000312439.6_Missense_Mutation_p.I319V|PSG1_ENST00000595356.1_Missense_Mutation_p.I319V	NM_001184825.1|NM_001184826.1	NP_001171754.1|NP_001171755.1	P11464	PSG1_HUMAN	pregnancy specific beta-1-glycoprotein 1	319	Ig-like C2-type 2.			I -> V (in Ref. 5 and 6). {ECO:0000305}.	female pregnancy (GO:0007565)	extracellular region (GO:0005576)				breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	30		Prostate(69;0.00682)				TCACTGCGGATGCCACCATAT	0.502													.|||	1426	0.284744	0.3094	0.1945	5008	,	,		20508	0.4167		0.1014	False		,,,				2504	0.3681				p.I319V		Atlas-SNP	.											.	PSG1	196	.	0			c.A955G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	847,2169		130,587,791	49.0	56.0	53.0		955,955,955	-1.5	0.0	19	dbSNP_125	53	568,4832		42,484,2174	no	missense,missense,missense	PSG1	NM_001184825.1,NM_001184826.1,NM_006905.2	29,29,29	172,1071,2965	CC,CT,TT		10.5185,28.0836,16.8132	,,	319/420,319/418,319/427	43372941	1415,7001	1508	2700	4208	SO:0001583	missense	5669	exon4			TGCGGATGCCACC		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.955A>G	19.37:g.43372941T>C	ENSP00000413041:p.Ile319Val	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_001184826	O75236|P11462|P11463|Q15231|Q15241|Q15243|Q16660|Q6ICR4|Q9P1W5|Q9UQ79	Missense_Mutation	SNP	ENST00000436291.2	37	CCDS54275.1	495	0.22664835164835165	140	0.2845528455284553	52	0.143646408839779	226	0.3951048951048951	77	0.10158311345646438	N	1.087	-0.665276	0.03428	0.280836	0.105185	ENSG00000231924	ENST00000436291;ENST00000403380;ENST00000312439;ENST00000244296	T;T;T;T	0.12039	2.72;2.72;2.72;2.72	1.79	-1.49	0.08718	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.49571	1.57	0.80722	P	0.0	B;B;B;B;B	0.14012	0.0;0.009;0.001;0.0;0.002	B;B;B;B;B	0.15484	0.005;0.013;0.008;0.005;0.008	T	0.47302	-0.9128	8	0.25106	T	0.35	.	2.4632	0.04547	0.2681:0.0:0.2731:0.4588	rs28374299;rs60861449	319;226;319;319;319	P11464-4;G5E9F7;P11464;P11464-3;P11464-2	.;.;PSG1_HUMAN;.;.	V	319;226;319;319	ENSP00000413041:I319V;ENSP00000385386:I226V;ENSP00000308970:I319V;ENSP00000244296:I319V	ENSP00000244296:I319V	I	-	1	0	PSG1	48064781	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.114000	0.01329	-0.750000	0.04740	0.352000	0.21897	ATC	T|0.830;C|0.170	0.170	strong		0.502	PSG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321426.1		
SDHA	6389	hgsc.bcm.edu	37	5	251541	251541	+	Silent	SNP	A	A	G	rs77210621	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:251541A>G	ENST00000264932.6	+	13	1867	c.1752A>G	c.(1750-1752)gcA>gcG	p.A584A	SDHA_ENST00000510361.1_Silent_p.A536A|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Intron	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	584					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)	GAGCAGAGGCACGGAAGGAGT	0.622									Familial Paragangliomas				G|||	1244	0.248403	0.6271	0.2406	5008	,	,		18487	0.0585		0.1113	False		,,,				2504	0.0787				p.A584A		Atlas-SNP	.											SDHA,NS,carcinoma,+2,1	SDHA	80	1	0			c.A1752G						PASS	.	G		2339,2067		634,1071,498	44.0	54.0	51.0		1752	-6.9	0.9	5	dbSNP_131	51	1167,7433		76,1015,3209	no	coding-synonymous	SDHA	NM_004168.2		710,2086,3707	GG,GA,AA		13.5698,46.9133,26.9568		584/665	251541	3506,9500	2203	4300	6503	SO:0001819	synonymous_variant	6389	exon13	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	AGAGGCACGGAAG	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.1752A>G	5.37:g.251541A>G		Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	234	88	0.376068	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			A|0.757;G|0.243	0.243	strong		0.622	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
MUC16	94025	hgsc.bcm.edu	37	19	9070873	9070873	+	Missense_Mutation	SNP	A	A	G	rs79202331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9070873A>G	ENST00000397910.4	-	3	16776	c.16573T>C	c.(16573-16575)Tcc>Ccc	p.S5525P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5527	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						CTGCTAGAGGAGATTTCTGTT	0.507													A|||	24	0.00479233	0.0015	0.0043	5008	,	,		20120	0.0		0.0149	False		,,,				2504	0.0041				p.S5525P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T16573C						PASS	.		PRO/SER	3,3913		0,3,1955	157.0	142.0	147.0		16573	0.9	0.0	19	dbSNP_131	147	59,8275		0,59,4108	yes	missense	MUC16	NM_024690.2	74	0,62,6063	GG,GA,AA		0.7079,0.0766,0.5061	benign	5525/14508	9070873	62,12188	1958	4167	6125	SO:0001583	missense	94025	exon3			TAGAGGAGATTTC	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.16573T>C	19.37:g.9070873A>G	ENSP00000381008:p.Ser5525Pro	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	248	115	0.46371	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	14	0.00641025641025641	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	9	0.011873350923482849	a	3.455	-0.111140	0.06881	7.66E-4	0.007079	ENSG00000181143	ENST00000397910	T	0.02709	4.19	1.89	0.851	0.18989	.	.	.	.	.	T	0.01730	0.0055	L	0.32530	0.975	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.33471	-0.9867	8	0.87932	D	0	.	3.8711	0.09036	0.8048:0.0:0.1952:0.0	.	5525	B5ME49	.	P	5525	ENSP00000381008:S5525P	ENSP00000381008:S5525P	S	-	1	0	MUC16	8931873	0.005000	0.15991	0.001000	0.08648	0.086000	0.17979	0.206000	0.17375	0.192000	0.20272	-0.933000	0.02702	TCC	A|0.993;G|0.007	0.007	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SP110	3431	hgsc.bcm.edu	37	2	231036866	231036866	+	Silent	SNP	G	G	A	rs13018234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231036866G>A	ENST00000358662.4	-	16	1809	c.1731C>T	c.(1729-1731)tgC>tgT	p.C577C	AC009950.2_ENST00000594622.1_RNA|AC009950.2_ENST00000609120.1_RNA|AC009950.2_ENST00000600787.1_RNA|AC009950.2_ENST00000595586.2_RNA|SP110_ENST00000258381.6_Silent_p.C577C|AC009950.2_ENST00000454058.1_RNA	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	577					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)		TCTTCATCCTGCAGAAGGTGC	0.547													G|||	341	0.0680911	0.0832	0.1095	5008	,	,		23598	0.003		0.1074	False		,,,				2504	0.045				p.C577C		Atlas-SNP	.											.	SP110	105	.	0			c.C1731T						PASS	.	G	,	392,4014	195.0+/-219.7	22,348,1833	135.0	125.0	128.0		1731,1731	1.7	0.9	2	dbSNP_121	128	1019,7581	218.0+/-256.5	48,923,3329	no	coding-synonymous,coding-synonymous	SP110	NM_004509.3,NM_080424.2	,	70,1271,5162	AA,AG,GG		11.8488,8.897,10.8488	,	577/690,577/714	231036866	1411,11595	2203	4300	6503	SO:0001819	synonymous_variant	3431	exon16			CATCCTGCAGAAG	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.1731C>T	2.37:g.231036866G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	119	59	0.495798	NM_080424	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Silent	SNP	ENST00000358662.4	37	CCDS2474.1																																																																																			G|0.906;A|0.094	0.094	strong		0.547	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
FANCM	57697	hgsc.bcm.edu	37	14	45665468	45665468	+	Missense_Mutation	SNP	C	C	G	rs3736772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:45665468C>G	ENST00000267430.5	+	21	5519	c.5434C>G	c.(5434-5436)Ccg>Gcg	p.P1812A	FANCM_ENST00000542564.2_Missense_Mutation_p.P1786A	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1812	Interaction with FAAP24 and EME1.		P -> A (in dbSNP:rs3736772). {ECO:0000269|PubMed:10997877}.		DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TCTTAGACTTCCGCAGGAAGG	0.433								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	532	0.10623	0.0068	0.1081	5008	,	,		19672	0.119		0.1143	False		,,,				2504	0.2178				p.P1812A		Atlas-SNP	.											.	FANCM	225	.	0			c.C5434G						PASS	.	C	ALA/PRO	103,4303	80.4+/-118.8	2,99,2102	128.0	125.0	126.0		5434	3.3	0.0	14	dbSNP_107	126	910,7690	202.7+/-245.9	49,812,3439	yes	missense	FANCM	NM_020937.2	27	51,911,5541	GG,GC,CC		10.5814,2.3377,7.7887	benign	1812/2049	45665468	1013,11993	2203	4300	6503	SO:0001583	missense	57697	exon21	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGACTTCCGCAGG	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.5434C>G	14.37:g.45665468C>G	ENSP00000267430:p.Pro1812Ala	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	131	70	0.534351	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	200|200	0.09157509157509157|0.09157509157509157	5|5	0.01016260162601626|0.01016260162601626	31|31	0.0856353591160221|0.0856353591160221	67|67	0.11713286713286714|0.11713286713286714	97|97	0.1279683377308707|0.1279683377308707	C|C	9.077|9.077	0.998283|0.998283	0.19043|0.19043	0.023377|0.023377	0.105814|0.105814	ENSG00000187790|ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250|ENST00000554809	T;T;T|.	0.22134|.	2.56;2.56;1.97|.	5.27|5.27	3.29|3.29	0.37713|0.37713	.|.	0.497750|.	0.19898|.	N|.	0.103568|.	T|T	0.00608|0.00608	0.0020|0.0020	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	P|P	0.0|0.0	B;B|.	0.10296|.	0.003;0.001|.	B;B|.	0.10450|.	0.005;0.002|.	T|T	0.13442|0.13442	-1.0509|-1.0509	9|4	0.45353|.	T|.	0.12|.	.|.	14.4521|14.4521	0.67392|0.67392	0.0:0.5818:0.4182:0.0|0.0:0.5818:0.4182:0.0	rs3736772;rs3736772|rs3736772;rs3736772	1786;1812|.	B2RTQ9;Q8IYD8|.	.;FANCM_HUMAN|.	A|C	1812;1786;1328|779	ENSP00000267430:P1812A;ENSP00000442493:P1786A;ENSP00000452033:P1328A|.	ENSP00000267430:P1812A|.	P|S	+|+	1|2	0|0	FANCM|FANCM	44735218|44735218	0.032000|0.032000	0.19561|0.19561	0.009000|0.009000	0.14445|0.14445	0.415000|0.415000	0.31203|0.31203	1.240000|1.240000	0.32731|0.32731	1.186000|1.186000	0.42985|0.42985	0.563000|0.563000	0.77884|0.77884	CCG|TCC	C|0.917;G|0.083	0.083	strong		0.433	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
CP	1356	hgsc.bcm.edu	37	3	148917570	148917570	+	Missense_Mutation	SNP	G	G	A	rs35331711	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148917570G>A	ENST00000264613.6	-	8	1692	c.1430C>T	c.(1429-1431)cCg>cTg	p.P477L	CP_ENST00000462336.1_5'Flank	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	477	F5/8 type A 2.|Plastocyanin-like 3.		P -> L (in dbSNP:rs35331711). {ECO:0000269|PubMed:15557511}.		cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CACCCCAATCGGCTCAATACT	0.458													G|||	5	0.000998403	0.0	0.0	5008	,	,		19072	0.0		0.005	False		,,,				2504	0.0				p.P477L		Atlas-SNP	.											CP,NS,carcinoma,-1,1	CP	112	1	0			c.C1430T						PASS	.	G	LEU/PRO	4,4402	6.2+/-15.9	0,4,2199	207.0	179.0	188.0		1430	5.8	0.9	3	dbSNP_126	188	38,8562	25.1+/-72.6	0,38,4262	yes	missense	CP	NM_000096.3	98	0,42,6461	AA,AG,GG		0.4419,0.0908,0.3229	probably-damaging	477/1066	148917570	42,12964	2203	4300	6503	SO:0001583	missense	1356	exon8			CCAATCGGCTCAA	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.1430C>T	3.37:g.148917570G>A	ENSP00000264613:p.Pro477Leu	Somatic	252	0	0		WXS	Illumina HiSeq	Phase_I	270	133	0.492593	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	17.65	3.442409	0.63067	9.08E-4	0.004419	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98717	-5.09;-5.09	5.79	5.79	0.91817	Cupredoxin (2);	0.160858	0.56097	D	0.000026	D	0.98639	0.9544	M	0.82056	2.57	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;0.951;0.995;0.995	D	0.96481	0.9356	10	0.29301	T	0.29	-13.5846	17.8293	0.88676	0.0:0.0:1.0:0.0	rs35331711	477;477;477;477	A5PL27;A8K5A4;P00450;Q1L857	.;.;CERU_HUMAN;.	L	477;260	ENSP00000264613:P477L;ENSP00000420545:P260L	ENSP00000264613:P477L	P	-	2	0	CP	150400260	1.000000	0.71417	0.929000	0.37066	0.021000	0.10359	7.903000	0.87398	2.739000	0.93911	0.655000	0.94253	CCG	G|0.998;A|0.002	0.002	strong		0.458	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	
SAMD10	140700	hgsc.bcm.edu	37	20	62607160	62607160	+	Silent	SNP	C	C	T	rs817343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62607160C>T	ENST00000369886.3	-	4	645	c.471G>A	c.(469-471)gcG>gcA	p.A157A	ZNF512B_ENST00000217130.3_Intron|ZNF512B_ENST00000450537.1_Intron|SAMD10_ENST00000498830.1_5'UTR	NM_080621.4	NP_542188.1	Q9BYL1	SAM10_HUMAN	sterile alpha motif domain containing 10	157	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.									kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|prostate(1)	7	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					GCAGCTTCTCCGCATTCAGCC	0.682													C|||	1301	0.259784	0.469	0.17	5008	,	,		18212	0.0456		0.1769	False		,,,				2504	0.3466				p.A157A		Atlas-SNP	.											SAMD10,rectum,carcinoma,0,2	SAMD10	16	2	0			c.G471A						PASS	.	C		1825,2553		410,1005,774	15.0	18.0	17.0		471	-6.0	0.8	20	dbSNP_86	17	1455,7105		123,1209,2948	no	coding-synonymous	SAMD10	NM_080621.4		533,2214,3722	TT,TC,CC		16.9977,41.6857,25.3517		157/203	62607160	3280,9658	2189	4280	6469	SO:0001819	synonymous_variant	140700	exon4			CTTCTCCGCATTC		CCDS13549.1	20q13.33	2013-01-10	2004-07-15	2004-07-16	ENSG00000130590	ENSG00000130590		"""Sterile alpha motif (SAM) domain containing"""	16129	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 136"""	C20orf136			Standard	NM_080621		Approved		uc002yhm.2	Q9BYL1	OTTHUMG00000033011	ENST00000369886.3:c.471G>A	20.37:g.62607160C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_080621		Silent	SNP	ENST00000369886.3	37	CCDS13549.1																																																																																			C|0.770;T|0.230	0.230	strong		0.682	SAMD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080255.1	NM_080621	
NR4A3	8013	hgsc.bcm.edu	37	9	102595685	102595685	+	Silent	SNP	C	C	T	rs10988904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:102595685C>T	ENST00000395097.2	+	5	1932	c.1203C>T	c.(1201-1203)gcC>gcT	p.A401A	NR4A3_ENST00000338488.4_Silent_p.A401A|NR4A3_ENST00000330847.1_Silent_p.A412A	NM_006981.3|NM_173200.2	NP_008912.2|NP_775292.1	Q92570	NR4A3_HUMAN	nuclear receptor subfamily 4, group A, member 3	401					gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)		TCF12/NR4A3(2)|TAF15/NR4A3(33)|EWSR1/NR4A3(146)|TFG/NR4A3(2)				Acute lymphoblastic leukemia(62;0.0559)|all_hematologic(171;0.189)				TGATGAATGCCCTTGTCCGAG	0.453			T	EWSR1	extraskeletal myxoid chondrosarcoma								C|||	1455	0.290535	0.4191	0.2695	5008	,	,		19484	0.1687		0.3857	False		,,,				2504	0.1595				p.A412A		Atlas-SNP	.		Dom	yes		9	9q22	8013	"""nuclear receptor subfamily 4, group A, member 3 (NOR1)"""		M	.	NR4A3	80	.	0			c.C1236T						PASS	.	C	,,	1679,2727	508.9+/-367.1	319,1041,843	201.0	182.0	189.0		1203,1203,1236	4.8	1.0	9	dbSNP_120	189	3124,5476	475.6+/-369.2	575,1974,1751	no	coding-synonymous,coding-synonymous,coding-synonymous	NR4A3	NM_006981.3,NM_173199.2,NM_173200.2	,,	894,3015,2594	TT,TC,CC		36.3256,38.1071,36.9291	,,	401/627,401/444,412/638	102595685	4803,8203	2203	4300	6503	SO:0001819	synonymous_variant	8013	exon6			GAATGCCCTTGTC	U12767	CCDS6742.1, CCDS6743.1, CCDS6744.1	9q22	2013-01-16			ENSG00000119508	ENSG00000119508		"""Nuclear hormone receptors"""	7982	protein-coding gene	gene with protein product		600542				8614405	Standard	NM_006981		Approved	CSMF, CHN, NOR1, MINOR	uc004baf.1	Q92570	OTTHUMG00000021030	ENST00000395097.2:c.1203C>T	9.37:g.102595685C>T		Somatic	237	0	0		WXS	Illumina HiSeq	Phase_I	197	195	0.989848	NM_173200	A2A3I7|Q12935|Q14979|Q16420|Q4VXA8|Q4VXA9|Q9UEK2|Q9UEK3	Silent	SNP	ENST00000395097.2	37	CCDS6743.1																																																																																			C|0.649;T|0.351	0.351	strong		0.453	NR4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055482.1		
CABLES2	81928	hgsc.bcm.edu	37	20	60968596	60968596	+	Silent	SNP	A	A	G	rs1570027	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60968596A>G	ENST00000279101.5	-	6	788	c.780T>C	c.(778-780)caT>caC	p.H260H		NM_031215.2	NP_112492.2	Q9BTV7	CABL2_HUMAN	Cdk5 and Abl enzyme substrate 2	260					cell cycle (GO:0007049)|cell division (GO:0051301)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)			endometrium(2)|kidney(1)|lung(6)|pancreas(1)|skin(1)	11	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCAGCAGGCCATGGCTGTCAC	0.592													A|||	1014	0.202476	0.2035	0.2666	5008	,	,		19142	0.1498		0.2336	False		,,,				2504	0.1779				p.H260H		Atlas-SNP	.											.	CABLES2	30	.	0			c.T780C						PASS	.	A		1036,3370	381.6+/-324.1	114,808,1281	119.0	117.0	117.0		780	-6.5	0.1	20	dbSNP_88	117	1917,6683	338.5+/-322.8	228,1461,2611	no	coding-synonymous	CABLES2	NM_031215.2		342,2269,3892	GG,GA,AA		22.2907,23.5134,22.7049		260/479	60968596	2953,10053	2203	4300	6503	SO:0001819	synonymous_variant	81928	exon6			CAGGCCATGGCTG	BC003122	CCDS33503.1	20q13.33	2004-01-09	2004-01-09	2004-01-09	ENSG00000149679	ENSG00000149679			16143	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 150"""	C20orf150		12477932	Standard	NM_031215		Approved	dJ908M14.2, ik3-2	uc002ycv.2	Q9BTV7	OTTHUMG00000032912	ENST00000279101.5:c.780T>C	20.37:g.60968596A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	121	121	1	NM_031215	Q5JWL0|Q9BYK0	Silent	SNP	ENST00000279101.5	37	CCDS33503.1	436	0.19963369963369965	104	0.21138211382113822	102	0.281767955801105	64	0.11188811188811189	166	0.21899736147757257	A	0.144	-1.099321	0.01843	0.235134	0.222907	ENSG00000149679	ENST00000453274	.	.	.	5.15	-6.47	0.01902	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.999999999946489E-6	.	.	.	.	.	.	T	0.12192	-1.0557	3	.	.	.	-24.4711	14.808	0.69971	0.4038:0.0:0.5962:0.0	rs1570027;rs1570027	.	.	.	T	54	.	.	M	-	2	0	CABLES2	60401991	0.000000	0.05858	0.058000	0.19502	0.035000	0.12851	-1.013000	0.03645	-1.179000	0.02737	-0.468000	0.05107	ATG	A|0.785;G|0.215	0.215	strong		0.592	CABLES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080027.2	XM_037265	
CHST12	55501	hgsc.bcm.edu	37	7	2472455	2472455	+	Missense_Mutation	SNP	A	A	T	rs3735100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:2472455A>T	ENST00000258711.6	+	2	316	c.181A>T	c.(181-183)Acg>Tcg	p.T61S		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	61			T -> S (in dbSNP:rs3735100).		carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CAGGGAGCTCACGGCCGACTC	0.672													A|||	380	0.0758786	0.0159	0.0562	5008	,	,		15044	0.1538		0.0398	False		,,,				2504	0.1278				p.T61S		Atlas-SNP	.											.	CHST12	39	.	0			c.A181T						PASS	.	A	SER/THR	76,4330	65.3+/-102.7	1,74,2128	43.0	51.0	48.0		181	-9.4	0.0	7	dbSNP_107	48	389,8211	124.4+/-183.2	12,365,3923	no	missense	CHST12	NM_018641.4	58	13,439,6051	TT,TA,AA		4.5233,1.7249,3.5753	benign	61/415	2472455	465,12541	2203	4300	6503	SO:0001583	missense	55501	exon2			GAGCTCACGGCCG	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.181A>T	7.37:g.2472455A>T	ENSP00000258711:p.Thr61Ser	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	57	36	0.631579	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	130	0.05952380952380952	6	0.012195121951219513	21	0.058011049723756904	76	0.13286713286713286	27	0.03562005277044855	A	0.007	-1.960094	0.00465	0.017249	0.045233	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.60548	0.18;1.03	4.71	-9.42	0.00610	.	2.237280	0.02005	N	0.046589	T	0.00271	0.0008	N	0.08118	0	0.80722	P	0.0	B	0.14438	0.01	B	0.06405	0.002	T	0.04065	-1.0980	9	0.07813	T	0.8	-22.5122	4.0833	0.09935	0.1289:0.403:0.307:0.1611	rs3735100;rs11537795;rs3735100	61	Q9NRB3	CHSTC_HUMAN	S	61	ENSP00000258711:T61S;ENSP00000411207:T61S	ENSP00000258711:T61S	T	+	1	0	CHST12	2438981	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-4.483000	0.00227	-2.176000	0.00770	-0.425000	0.05940	ACG	A|0.956;T|0.044	0.044	strong		0.672	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
PRKD3	23683	hgsc.bcm.edu	37	2	37494591	37494591	+	Silent	SNP	A	A	G	rs2302650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37494591A>G	ENST00000379066.1	-	14	2628	c.1866T>C	c.(1864-1866)aaT>aaC	p.N622N	PRKD3_ENST00000234179.2_Silent_p.N622N			O94806	KPCD3_HUMAN	protein kinase D3	622	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)				TAGCCACTTCATTACGGAGTT	0.299													A|||	958	0.191294	0.1074	0.1902	5008	,	,		15632	0.2292		0.1362	False		,,,				2504	0.3231				p.N622N	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.T1866C						PASS	.	A		498,3906	229.1+/-243.8	20,458,1724	126.0	130.0	129.0		1866	3.5	1.0	2	dbSNP_100	129	1071,7529	225.4+/-261.5	71,929,3300	no	coding-synonymous	PRKD3	NM_005813.3		91,1387,5024	GG,GA,AA		12.4535,11.3079,12.0655		622/891	37494591	1569,11435	2202	4300	6502	SO:0001819	synonymous_variant	23683	exon13			CACTTCATTACGG	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.1866T>C	2.37:g.37494591A>G		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	75	44	0.586667	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1	321	0.14697802197802198	38	0.07723577235772358	58	0.16022099447513813	131	0.229020979020979	94	0.12401055408970976	A	8.165	0.790357	0.16258	0.113079	0.124535	ENSG00000115825	ENST00000452104	.	.	.	4.7	3.5	0.40072	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06197	-1.0840	3	.	.	.	-19.4624	10.7028	0.45937	0.9228:0.0:0.0772:0.0	rs2302650;rs17481627;rs2302650	.	.	.	T	69	.	.	M	-	2	0	PRKD3	37348095	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.234000	0.43035	0.707000	0.31934	0.455000	0.32223	ATG	A|0.838;G|0.162	0.162	strong		0.299	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
SPTB	6710	hgsc.bcm.edu	37	14	65263300	65263300	+	Missense_Mutation	SNP	C	C	T	rs229587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:65263300C>T	ENST00000389721.5	-	10	1348	c.1316G>A	c.(1315-1317)aGt>aAt	p.S439N	SPTB_ENST00000556626.1_Missense_Mutation_p.S439N|SPTB_ENST00000389720.3_Missense_Mutation_p.S439N|SPTB_ENST00000542895.1_Missense_Mutation_p.S439N|SPTB_ENST00000389722.3_Missense_Mutation_p.S439N	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	439			S -> N (in dbSNP:rs229587). {ECO:0000269|PubMed:2195026}.		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)		CTGGTTTTCACTGAGCCAGGT	0.602													T|||	2338	0.466853	0.6921	0.3429	5008	,	,		18547	0.3532		0.3439	False		,,,				2504	0.4939				p.S439N		Atlas-SNP	.											.	SPTB	378	.	0			c.G1316A						PASS	.	T	ASN/SER,ASN/SER	2796,1610	497.6+/-363.9	883,1030,290	74.0	74.0	74.0		1316,1316	0.8	1.0	14	dbSNP_79	74	2879,5721	672.1+/-402.9	476,1927,1897	yes	missense,missense	SPTB	NM_000347.5,NM_001024858.2	46,46	1359,2957,2187	TT,TC,CC		33.4767,36.5411,43.6337	benign,benign	439/2138,439/2329	65263300	5675,7331	2203	4300	6503	SO:0001583	missense	6710	exon10			TTTTCACTGAGCC		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.1316G>A	14.37:g.65263300C>T	ENSP00000374371:p.Ser439Asn	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	904	0.4139194139194139	324	0.6585365853658537	123	0.3397790055248619	197	0.34440559440559443	260	0.34300791556728233	T	10.09	1.256188	0.22965	0.634589	0.334767	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76	5.81	0.765	0.18470	.	0.289195	0.38326	N	0.001739	T	0.00012	0.0000	L	0.46819	1.47	0.53005	P	3.500000000000725E-5	B;B	0.10296	0.003;0.002	B;B	0.17722	0.019;0.007	T	0.43278	-0.9401	9	0.17369	T	0.5	.	10.3943	0.44192	0.0:0.6243:0.0:0.3757	rs229587;rs17180455;rs60734774;rs229587	439;443	P11277;Q59FP5	SPTB1_HUMAN;.	N	443;439;439;439;439;439	ENSP00000374372:S439N;ENSP00000451752:S439N;ENSP00000374371:S439N;ENSP00000443882:S439N;ENSP00000374370:S439N	ENSP00000374370:S439N	S	-	2	0	SPTB	64333053	0.003000	0.15002	0.989000	0.46669	0.933000	0.57130	0.269000	0.18589	-0.081000	0.12662	-0.982000	0.02568	AGT	C|0.569;N|0.000	.	strong		0.602	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
ATXN3	4287	hgsc.bcm.edu	37	14	92549586	92549586	+	Silent	SNP	G	G	A	rs16999141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92549586G>A	ENST00000532032.1	-	7	501	c.492C>T	c.(490-492)gtC>gtT	p.V164V	ATXN3_ENST00000340660.6_Silent_p.V109V|ATXN3_ENST00000503767.1_Silent_p.V149V|ATXN3_ENST00000502250.1_5'UTR|ATXN3_ENST00000393287.5_Silent_p.V164V|ATXN3_ENST00000429774.2_Silent_p.V149V|ATXN3_ENST00000554491.1_5'UTR|ATXN3_ENST00000545170.1_Silent_p.V164V			P54252	ATX3_HUMAN	ataxin 3	164	Josephin. {ECO:0000255|PROSITE- ProRule:PRU00331}.				actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|cellular response to misfolded protein (GO:0071218)|intermediate filament cytoskeleton organization (GO:0045104)|microtubule cytoskeleton organization (GO:0000226)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|monoubiquitinated protein deubiquitination (GO:0035520)|nervous system development (GO:0007399)|nucleotide-excision repair (GO:0006289)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of cell-substrate adhesion (GO:0010810)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|Lys48-specific deubiquitinase activity (GO:1990380)|Lys63-specific deubiquitinase activity (GO:0061578)|omega peptidase activity (GO:0008242)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.V164V(1)		endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)	12		all_cancers(154;0.0768)		COAD - Colon adenocarcinoma(157;0.224)		CACCCTTAACGACAAATATAG	0.368													A|||	2838	0.566693	0.736	0.3905	5008	,	,		16657	0.5565		0.4513	False		,,,				2504	0.592				p.V164V	Esophageal Squamous(190;752 2094 29897 44875 49530)	Atlas-SNP	.											ATXN3,NS,carcinoma,0,1	ATXN3	46	1	1	Substitution - coding silent(1)	stomach(1)	c.C492T						scavenged	.	A	,,,,,,,,,,,	2945,1461	470.4+/-355.7	991,963,249	79.0	76.0	77.0		447,339,,,,,129,,282,,492,327	3.1	1.0	14	dbSNP_123	77	4099,4501	590.9+/-392.8	998,2103,1199	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,coding-synonymous,utr-5,coding-synonymous,intron,coding-synonymous,coding-synonymous	ATXN3	NM_001127696.1,NM_001127697.2,NM_001164774.1,NM_001164776.1,NM_001164777.1,NM_001164778.1,NM_001164779.1,NM_001164780.1,NM_001164781.1,NM_001164782.1,NM_004993.5,NM_030660.4	,,,,,,,,,,,	1989,3066,1448	AA,AG,GG		47.6628,33.1593,45.8404	,,,,,,,,,,,	149/347,113/311,,,,,43/241,,94/292,,164/362,109/307	92549586	7044,5962	2203	4300	6503	SO:0001819	synonymous_variant	4287	exon7			CTTAACGACAAAT	U64820	CCDS9900.1, CCDS32143.1, CCDS45154.1, CCDS53908.1, CCDS73680.1	14q21	2014-09-17	2004-08-12	2004-08-13	ENSG00000066427	ENSG00000066427		"""Ataxins"""	7106	protein-coding gene	gene with protein product		607047	"""Machado-Joseph disease (spinocerebellar ataxia 3, olivopontocerebellar ataxia 3, autosomal dominant, ataxin 3)"""	SCA3, MJD		8358439	Standard	NM_004993		Approved	ATX3, JOS	uc001yac.4	P54252	OTTHUMG00000162212	ENST00000532032.1:c.492C>T	14.37:g.92549586G>A		Somatic	45	2	0.0444444		WXS	Illumina HiSeq	Phase_I	57	57	1	NM_004993	A7LFZ5|D6RDL9|E9PB63|O15284|O15285|O15286|Q8N189|Q96TC3|Q96TC4|Q9H3N0	Silent	SNP	ENST00000532032.1	37																																																																																				G|0.463;A|0.537	0.537	strong		0.368	ATXN3-015	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388065.1	NM_004993	
NPC1	4864	hgsc.bcm.edu	37	18	21112206	21112206	+	Missense_Mutation	SNP	C	C	T	rs1805084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:21112206C>T	ENST00000269228.5	-	25	4351	c.3797G>A	c.(3796-3798)cGa>cAa	p.R1266Q	NPC1_ENST00000412552.2_Missense_Mutation_p.R948Q	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	1266			R -> Q (common polymorphism in Japanese; dbSNP:rs1805084). {ECO:0000269|PubMed:10480349, ECO:0000269|PubMed:12955717, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TCCTTTGTATCGCTCTTCAGT	0.488													C|||	752	0.15016	0.2973	0.1052	5008	,	,		22594	0.1895		0.0288	False		,,,				2504	0.0675				p.R1266Q		Atlas-SNP	.											NPC1,NS,carcinoma,0,1	NPC1	114	1	0			c.G3797A						PASS	.	C	GLN/ARG	1017,3389	376.3+/-322.0	119,779,1305	199.0	180.0	187.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3797	3.0	0.0	18	dbSNP_89	187	258,8342	101.4+/-162.7	4,250,4046	yes	missense	NPC1	NM_000271.4	43	123,1029,5351	TT,TC,CC		3.0,23.0822,9.8032	benign	1266/1279	21112206	1275,11731	2203	4300	6503	SO:0001583	missense	4864	exon25			TTGTATCGCTCTT	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.3797G>A	18.37:g.21112206C>T	ENSP00000269228:p.Arg1266Gln	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	273	144	0.527473	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	307	0.14056776556776557	134	0.27235772357723576	36	0.09944751381215469	116	0.20279720279720279	21	0.027704485488126648	C	12.35	1.910924	0.33721	0.230822	0.03	ENSG00000141458	ENST00000269228;ENST00000412552	T;T	0.71461	-0.57;-0.57	6.07	3.05	0.35203	.	0.057794	0.64402	N	0.000002	T	0.00012	0.0000	L	0.48362	1.52	0.22762	P	0.99876013	B;B	0.10296	0.001;0.003	B;B	0.09377	0.003;0.004	T	0.07578	-1.0765	9	0.26408	T	0.33	-4.4228	9.3982	0.38415	0.0:0.7459:0.1169:0.1372	rs1805084;rs16940114;rs52813482;rs59968378;rs1805084	1277;1266	Q59GR1;O15118	.;NPC1_HUMAN	Q	1266;948	ENSP00000269228:R1266Q;ENSP00000408606:R948Q	ENSP00000269228:R1266Q	R	-	2	0	NPC1	19366204	0.952000	0.32445	0.012000	0.15200	0.155000	0.21991	2.179000	0.42528	0.334000	0.23590	0.655000	0.94253	CGA	C|0.886;T|0.114	0.114	strong		0.488	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
XPC	7508	hgsc.bcm.edu	37	3	14199887	14199887	+	Missense_Mutation	SNP	G	G	A	rs2228000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14199887G>A	ENST00000285021.7	-	9	1710	c.1496C>T	c.(1495-1497)gCg>gTg	p.A499V	XPC_ENST00000449060.2_Missense_Mutation_p.A462V	NM_001145769.1|NM_004628.4	NP_001139241.1|NP_004619.3	Q01831	XPC_HUMAN	xeroderma pigmentosum, complementation group C	499	Interaction with RAD23B.		A -> V (in dbSNP:rs2228000). {ECO:0000269|PubMed:12177305, ECO:0000269|PubMed:8168482, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|intra-S DNA damage checkpoint (GO:0031573)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage recognition (GO:0000715)|nucleotide-excision repair, DNA damage removal (GO:0000718)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to drug (GO:0042493)|response to UV-B (GO:0010224)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|XPC complex (GO:0071942)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|heteroduplex DNA loop binding (GO:0000404)|single-stranded DNA binding (GO:0003697)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGAGGATGCCGCTGGCAAGCT	0.537			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	1167	0.233027	0.093	0.245	5008	,	,		20742	0.4127		0.2584	False		,,,				2504	0.2025				p.A499V		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (C)	3	3p25	7508	"""xeroderma pigmentosum, complementation group C"""		E	XPC,caecum,carcinoma,+1,1	XPC	60	1	0			c.C1496T	GRCh37	CM057944	XPC	M	rs2228000	PASS	.	G	VAL/ALA,VAL/ALA	288,2848		18,252,1298	71.0	64.0	66.0		1385,1496	-1.0	0.0	3	dbSNP_98	66	1778,5386		219,1340,2023	yes	missense,missense	XPC	NM_001145769.1,NM_004628.4	64,64	237,1592,3321	AA,AG,GG		24.8185,9.1837,20.0583	benign,benign	462/904,499/941	14199887	2066,8234	1568	3582	5150	SO:0001583	missense	7508	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GATGCCGCTGGCA		CCDS46763.1	3p25.1	2014-09-17			ENSG00000154767	ENSG00000154767			12816	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group C protein"""	613208				1522891	Standard	NM_004628		Approved	XPCC, RAD4	uc011ave.2	Q01831	OTTHUMG00000155526	ENST00000285021.7:c.1496C>T	3.37:g.14199887G>A	ENSP00000285021:p.Ala499Val	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	82	33	0.402439	NM_004628	B4DIP3|E9PB96|E9PH69|Q53GT7|Q96AX0	Missense_Mutation	SNP	ENST00000285021.7	37	CCDS46763.1	541	0.24771062271062272	39	0.07926829268292683	93	0.2569060773480663	210	0.36713286713286714	199	0.262532981530343	G	9.045	0.990686	0.18966	0.091837	0.248185	ENSG00000154767	ENST00000285021;ENST00000449060	T;T	0.36699	1.24;1.26	5.34	-1.03	0.10102	.	0.809781	0.11805	N	0.527757	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B;B	0.23185	0.081;0.004	B;B	0.19946	0.027;0.004	T	0.45745	-0.9240	9	0.30854	T	0.27	0.064	4.6128	0.12411	0.1193:0.0886:0.4136:0.3785	rs2228000;rs3729586;rs52792520;rs2228000	462;499	E9PH69;Q01831	.;XPC_HUMAN	V	499;462	ENSP00000285021:A499V;ENSP00000404002:A462V	ENSP00000285021:A499V	A	-	2	0	XPC	14174889	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-0.927000	0.03766	-0.797000	0.03246	GCG	G|0.772;A|0.228	0.228	strong		0.537	XPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340517.3	NM_004628	
PIGT	51604	hgsc.bcm.edu	37	20	44052992	44052992	+	Silent	SNP	G	G	A	rs13217	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:44052992G>A	ENST00000279036.6	+	10	1451	c.1371G>A	c.(1369-1371)acG>acA	p.T457T	PIGT_ENST00000543458.2_Silent_p.T401T|PIGT_ENST00000372689.5_Silent_p.T390T|PIGT_ENST00000279035.9_Silent_p.T355T|PIGT_ENST00000341555.5_Silent_p.T263T|PIGT_ENST00000535404.1_Silent_p.T302T|PIGT_ENST00000545755.1_Silent_p.T195T	NM_015937.5	NP_057021.2	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class T	457					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|post-translational protein modification (GO:0043687)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)	p.T457T(1)		breast(1)|endometrium(2)|kidney(5)|large_intestine(4)|lung(7)|pancreas(1)|skin(1)|stomach(1)	22		Myeloproliferative disorder(115;0.0122)				CCGAGTACACGCCAGATCCTA	0.582													G|||	1375	0.274561	0.0628	0.3199	5008	,	,		19965	0.2411		0.5129	False		,,,				2504	0.318				p.T457T		Atlas-SNP	.											PIGT_ENST00000279036,caecum,carcinoma,0,3	PIGT	85	3	1	Substitution - coding silent(1)	stomach(1)	c.G1371A						scavenged	.	G	,,,	640,3766	272.8+/-271.0	50,540,1613	82.0	76.0	78.0		1203,1170,1065,1371	-7.4	0.8	20	dbSNP_52	78	4441,4159	587.6+/-392.2	1138,2165,997	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PIGT	NM_001184728.1,NM_001184729.1,NM_001184730.1,NM_015937.4	,,,	1188,2705,2610	AA,AG,GG		48.3605,14.5256,39.0666	,,,	401/523,390/512,355/477,457/579	44052992	5081,7925	2203	4300	6503	SO:0001819	synonymous_variant	51604	exon10			GTACACGCCAGAT		CCDS13353.1, CCDS54464.1, CCDS54465.1, CCDS54466.1	20q12-q13.12	2013-02-26	2006-06-28		ENSG00000124155	ENSG00000124155		"""Phosphatidylinositol glycan anchor biosynthesis"""	14938	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610272	"""phosphatidylinositol glycan, class T"""			15713669	Standard	NM_015937		Approved		uc002xoh.3	Q969N2	OTTHUMG00000032574	ENST00000279036.6:c.1371G>A	20.37:g.44052992G>A		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	96	48	0.5	NM_015937	B2RND5|B7Z3N1|B7Z7I8|E1P622|G8JLF5|Q2NL69|Q7Z3N7|Q9BQY7|Q9BQY8|Q9UJG6|Q9Y2Z5	Silent	SNP	ENST00000279036.6	37	CCDS13353.1																																																																																			G|0.654;A|0.346	0.346	strong		0.582	PIGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079434.2	NM_015937	
TAF1C	9013	hgsc.bcm.edu	37	16	84213434	84213434	+	Missense_Mutation	SNP	A	A	T	rs2230129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84213434A>T	ENST00000567759.1	-	14	1905	c.1723T>A	c.(1723-1725)Ttg>Atg	p.L575M	TAF1C_ENST00000341690.6_Missense_Mutation_p.L481M|TAF1C_ENST00000566732.1_Missense_Mutation_p.L549M|TAF1C_ENST00000378541.4_Missense_Mutation_p.L575M|TAF1C_ENST00000541676.1_Missense_Mutation_p.L482M|TAF1C_ENST00000570117.1_Missense_Mutation_p.L243M	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	575			L -> M (in dbSNP:rs2230129). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						GCTGAGGGCAAGGGCGGGACG	0.677													A|||	1604	0.320288	0.1626	0.4481	5008	,	,		16102	0.375		0.3936	False		,,,				2504	0.3108				p.L575M		Atlas-SNP	.											.	TAF1C	60	.	0			c.T1723A						PASS	.	A	MET/LEU,MET/LEU	693,3309		90,513,1398	9.0	11.0	10.0		1723,1441	1.2	0.0	16	dbSNP_98	10	2966,4846		667,1632,1607	yes	missense,missense	TAF1C	NM_005679.3,NM_139353.2	15,15	757,2145,3005	TT,TA,AA		37.9672,17.3163,30.9717	possibly-damaging,possibly-damaging	575/870,481/776	84213434	3659,8155	2001	3906	5907	SO:0001583	missense	9013	exon14			AGGGCAAGGGCGG	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.1723T>A	16.37:g.84213434A>T	ENSP00000455265:p.Leu575Met	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	118	117	0.991525	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	769	0.35210622710622713	94	0.1910569105691057	144	0.39779005524861877	237	0.4143356643356643	294	0.38786279683377306	A	13.25	2.181226	0.38511	0.173163	0.379672	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000544090	T;T;T	0.04275	3.75;3.66;3.66	4.48	1.24	0.21308	.	0.935040	0.08398	U	0.951847	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	P;D;P;P	0.55605	0.899;0.972;0.899;0.899	P;P;P;P	0.52217	0.466;0.693;0.466;0.466	T	0.48559	-0.9025	9	0.29301	T	0.29	.	4.1716	0.10332	0.2289:0.1919:0.5792:0.0	rs2230129;rs2278041;rs4150171;rs17856788;rs2230129	549;98;575;481	Q15572-6;F5H0H4;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	M	575;482;481;98	ENSP00000367802:L575M;ENSP00000437900:L482M;ENSP00000345305:L481M	ENSP00000345305:L481M	L	-	1	2	TAF1C	82770935	0.000000	0.05858	0.001000	0.08648	0.214000	0.24535	-1.933000	0.01553	-0.011000	0.14247	0.260000	0.18958	TTG	A|0.640;T|0.360	0.360	strong		0.677	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
SCN10A	6336	hgsc.bcm.edu	37	3	38763863	38763863	+	Silent	SNP	G	G	C	rs6771157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38763863G>C	ENST00000449082.2	-	19	3392	c.3393C>G	c.(3391-3393)acC>acG	p.T1131T		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1131					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	ATGGACTCTTGGTGGTATCCA	0.547													G|||	1100	0.219649	0.121	0.121	5008	,	,		20313	0.376		0.2465	False		,,,				2504	0.2342				p.T1131T		Atlas-SNP	.											.	SCN10A	359	.	0			c.C3393G						PASS	.	G		626,3780	269.5+/-269.1	47,532,1624	166.0	143.0	151.0		3393	-1.6	0.0	3	dbSNP_116	151	2238,6362	379.8+/-339.4	288,1662,2350	no	coding-synonymous	SCN10A	NM_006514.2		335,2194,3974	CC,CG,GG		26.0233,14.2079,22.0206		1131/1957	38763863	2864,10142	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon19			ACTCTTGGTGGTA	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.3393C>G	3.37:g.38763863G>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	110	52	0.472727	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			G|0.767;C|0.233	0.233	strong		0.547	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
DNHD1	144132	hgsc.bcm.edu	37	11	6592951	6592951	+	Missense_Mutation	SNP	T	T	C	rs11604362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6592951T>C	ENST00000527990.2	+	41	13997	c.13997T>C	c.(13996-13998)aTa>aCa	p.I4666T	DNHD1_ENST00000254579.6_Missense_Mutation_p.I4666T			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4666			I -> T (in dbSNP:rs11604362).		microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TGGGACCCAATAGCTGGAGCC	0.632													T|||	10	0.00199681	0.0	0.0058	5008	,	,		17689	0.0		0.006	False		,,,				2504	0.0				p.I4666T		Atlas-SNP	.											.	DNHD1	198	.	0			c.T13997C						PASS	.	T	THR/ILE	10,4218		0,10,2104	38.0	49.0	45.0		13997	-0.8	0.0	11	dbSNP_120	45	65,8389		0,65,4162	yes	missense	DNHD1	NM_144666.2	89	0,75,6266	CC,CT,TT		0.7689,0.2365,0.5914	benign	4666/4754	6592951	75,12607	2114	4227	6341	SO:0001583	missense	144132	exon43			ACCCAATAGCTGG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.13997T>C	11.37:g.6592951T>C	ENSP00000436180:p.Ile4666Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	127	75	0.590551	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	T	0.823	-0.748044	0.03065	0.002365	0.007689	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.07444	3.19;3.19	4.75	-0.827	0.10802	Dynein heavy chain (1);	1.500610	0.03937	N	0.286257	T	0.01489	0.0048	N	0.00538	-1.39	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	0.40001	-0.9586	10	0.14252	T	0.57	0.038	3.778	0.08668	0.3386:0.1861:0.0:0.4753	rs11604362;rs11604362	3754;719;4666	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	T	4666;4666;934	ENSP00000254579:I4666T;ENSP00000436180:I4666T	ENSP00000254579:I4666T	I	+	2	0	DNHD1	6549527	0.000000	0.05858	0.003000	0.11579	0.389000	0.30415	-0.299000	0.08254	0.009000	0.14813	-0.274000	0.10170	ATA	T|0.994;C|0.006	0.006	strong		0.632	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
PEX6	5190	hgsc.bcm.edu	37	6	42932200	42932200	+	Missense_Mutation	SNP	G	G	T	rs386700658|rs1129187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42932200G>T	ENST00000304611.8	-	17	2885	c.2816C>A	c.(2815-2817)cCa>cAa	p.P939Q	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	939			P -> Q (in dbSNP:rs1129187). {ECO:0000269|PubMed:11355018, ECO:0000269|PubMed:19105186}.		ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			TGAGCTACCTGGCTCCAGCCC	0.632													G|||	1660	0.33147	0.3699	0.3516	5008	,	,		18582	0.1012		0.4622	False		,,,				2504	0.3681				p.P939Q		Atlas-SNP	.											PEX6,colon,carcinoma,0,1	PEX6	44	1	0			c.C2816A						PASS	.	G	GLN/PRO	1720,2686	496.0+/-363.4	332,1056,815	48.0	45.0	46.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2816	0.6	0.0	6	dbSNP_86	46	3832,4768	515.8+/-378.7	834,2164,1302	yes	missense	PEX6	NM_000287.3	76	1166,3220,2117	TT,TG,GG		44.5581,39.0377,42.688	benign	939/981	42932200	5552,7454	2203	4300	6503	SO:0001583	missense	5190	exon17			CTACCTGGCTCCA	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.2816C>A	6.37:g.42932200G>T	ENSP00000303511:p.Pro939Gln	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	54	0.442623	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	719	0.3292124542124542	169	0.3434959349593496	130	0.35911602209944754	71	0.12412587412587413	349	0.4604221635883905	G	12.52	1.963729	0.34659	0.390377	0.445581	ENSG00000124587	ENST00000304611	D	0.94758	-3.51	5.96	0.549	0.17213	.	0.978492	0.08443	N	0.945108	T	0.82116	0.4967	L	0.48362	1.52	0.09310	P	1.0	B	0.11235	0.004	B	0.11329	0.006	T	0.63989	-0.6512	9	0.37606	T	0.19	-1.1722	2.5906	0.04841	0.2743:0.1118:0.4992:0.1148	rs1129187;rs3186790;rs9471979;rs17415506;rs59470433;rs1129187	939	Q13608	PEX6_HUMAN	Q	939	ENSP00000303511:P939Q	ENSP00000303511:P939Q	P	-	2	0	PEX6	43040178	0.000000	0.05858	0.008000	0.14137	0.910000	0.53928	0.232000	0.17891	-0.182000	0.10602	0.650000	0.86243	CCA	G|0.617;T|0.383	0.383	strong		0.632	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
PLEKHG1	57480	hgsc.bcm.edu	37	6	151152390	151152390	+	Missense_Mutation	SNP	G	G	A	rs79596384	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:151152390G>A	ENST00000358517.2	+	15	2354	c.2143G>A	c.(2143-2145)Gca>Aca	p.A715T	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.A715T			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	715							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(19)|ovary(5)|prostate(4)|stomach(1)|urinary_tract(3)	53			BRCA - Breast invasive adenocarcinoma(37;0.0923)	OV - Ovarian serous cystadenocarcinoma(155;6.69e-13)		CTCTCTTTACGCACAAACAGA	0.557													G|||	144	0.028754	0.0008	0.0014	5008	,	,		20437	0.121		0.005	False		,,,				2504	0.0153				p.A715T		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.G2143A						PASS	.	G	THR/ALA	6,4400	11.4+/-27.6	0,6,2197	53.0	51.0	51.0		2143	-3.3	0.0	6	dbSNP_132	51	38,8562	26.3+/-74.7	0,38,4262	yes	missense	PLEKHG1	NM_001029884.1	58	0,44,6459	AA,AG,GG		0.4419,0.1362,0.3383	benign	715/1386	151152390	44,12962	2203	4300	6503	SO:0001583	missense	57480	exon16			CTTTACGCACAAA	AB033035	CCDS34552.1	6q25.1	2013-01-11			ENSG00000120278	ENSG00000120278		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	20884	protein-coding gene	gene with protein product						10574462	Standard	XM_005267064		Approved	KIAA1209, ARHGEF41	uc003qny.1	Q9ULL1	OTTHUMG00000015824	ENST00000358517.2:c.2143G>A	6.37:g.151152390G>A	ENSP00000351318:p.Ala715Thr	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	55	51	0.927273	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	37	CCDS34552.1	78	0.03571428571428571	0	0.0	0	0.0	76	0.13286713286713286	2	0.002638522427440633	G	1.015	-0.686697	0.03328	0.001362	0.004419	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	T;T	0.58506	0.33;0.33	5.61	-3.34	0.04943	.	0.885659	0.10271	N	0.694776	T	0.07999	0.0200	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.01281	0.0;0.0;0.0	T	0.26608	-1.0098	10	0.11485	T	0.65	.	2.436	0.04483	0.3227:0.3114:0.2663:0.0996	.	522;715;715	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	T	715	ENSP00000356297:A715T;ENSP00000351318:A715T	ENSP00000351318:A715T	A	+	1	0	PLEKHG1	151194083	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.694000	0.01915	-0.450000	0.07107	-0.367000	0.07326	GCA	G|0.989;A|0.011	0.011	strong		0.557	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1		
PXDNL	137902	hgsc.bcm.edu	37	8	52323908	52323908	+	Missense_Mutation	SNP	A	A	G	rs117864200	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:52323908A>G	ENST00000356297.4	-	16	2064	c.1964T>C	c.(1963-1965)aTt>aCt	p.I655T	PXDNL_ENST00000543296.1_Missense_Mutation_p.I655T	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	655					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)				CATTTCCACAATCAGTGGGTC	0.493													A|||	48	0.00958466	0.0008	0.013	5008	,	,		17432	0.0		0.0278	False		,,,				2504	0.0102				p.I655T		Atlas-SNP	.											.	PXDNL	414	.	0			c.T1964C						PASS	.	A	THR/ILE	19,3901		0,19,1941	57.0	58.0	58.0		1964	2.4	0.0	8	dbSNP_132	58	209,8091		3,203,3944	yes	missense	PXDNL	NM_144651.4	89	3,222,5885	GG,GA,AA		2.5181,0.4847,1.8658	benign	655/1464	52323908	228,11992	1960	4150	6110	SO:0001583	missense	137902	exon16			TCCACAATCAGTG		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.1964T>C	8.37:g.52323908A>G	ENSP00000348645:p.Ile655Thr	Somatic	221	0	0		WXS	Illumina HiSeq	Phase_I	229	108	0.471616	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	26	0.011904761904761904	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	19	0.025065963060686015	A	0.022	-1.416402	0.01136	0.004847	0.025181	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.62941	0.04;-0.01	4.46	2.41	0.29592	.	.	.	.	.	T	0.09291	0.0229	N	0.00926	-1.1	0.25894	N	0.983434	B	0.02656	0.0	B	0.04013	0.001	T	0.18713	-1.0328	9	0.02654	T	1	.	7.7251	0.28755	0.2431:0.0:0.7569:0.0	.	655	A1KZ92	PXDNL_HUMAN	T	655	ENSP00000348645:I655T;ENSP00000444865:I655T	ENSP00000348645:I655T	I	-	2	0	PXDNL	52486461	1.000000	0.71417	0.001000	0.08648	0.004000	0.04260	5.607000	0.67648	0.196000	0.20367	-0.408000	0.06270	ATT	A|0.986;G|0.014	0.014	strong		0.493	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
SYCE1L	100130958	hgsc.bcm.edu	37	16	77243330	77243330	+	Silent	SNP	C	C	T	rs61740088	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:77243330C>T	ENST00000378644.4	+	6	376	c.321C>T	c.(319-321)ctC>ctT	p.L107L	RP11-538I12.2_ENST00000569032.1_RNA	NM_001129979.1	NP_001123451.1	A8MT33	SYC1L_HUMAN	synaptonemal complex central element protein 1-like	107					synaptonemal complex assembly (GO:0007130)	synaptonemal complex (GO:0000795)				breast(1)|prostate(1)	2						tgAGGATCCTCCAGATGCACT	0.567													C|||	121	0.0241613	0.0348	0.0187	5008	,	,		16912	0.0		0.0249	False		,,,				2504	0.0378				p.L107L		Atlas-SNP	.											.	SYCE1L	10	.	0			c.C321T						PASS	.	C		38,1346		1,36,655	73.0	82.0	80.0		321	-0.8	1.0	16	dbSNP_129	80	81,3101		0,81,1510	no	coding-synonymous	SYCE1L	NM_001129979.1		1,117,2165	TT,TC,CC		2.5456,2.7457,2.6062		107/243	77243330	119,4447	692	1591	2283	SO:0001819	synonymous_variant	100130958	exon6			GATCCTCCAGATG		CCDS45533.1	16q23.1	2009-10-06			ENSG00000205078	ENSG00000205078			37236	protein-coding gene	gene with protein product	"""meiosis-related protein"""					16328886	Standard	NM_001129979		Approved	MRP2	uc010vnh.1	A8MT33		ENST00000378644.4:c.321C>T	16.37:g.77243330C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_001129979	A6NF23	Silent	SNP	ENST00000378644.4	37	CCDS45533.1																																																																																			C|0.979;T|0.021	0.021	strong		0.567	SYCE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433889.1	NM_001129979	
NINL	22981	hgsc.bcm.edu	37	20	25456888	25456888	+	Silent	SNP	A	A	G	rs437635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25456888A>G	ENST00000278886.6	-	17	3112	c.3039T>C	c.(3037-3039)agT>agC	p.S1013S	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	1013					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CAACCTCCACACTGTGCTTGT	0.682													G|||	2795	0.558107	0.5356	0.3559	5008	,	,		14219	0.9067		0.4304	False		,,,				2504	0.5041				p.S1013S		Atlas-SNP	.											.	NINL	148	.	0			c.T3039C						PASS	.	G		2241,2165	583.5+/-385.8	552,1137,514	58.0	62.0	60.0		3039	0.2	0.0	20	dbSNP_80	60	3727,4873	615.9+/-396.4	794,2139,1367	no	coding-synonymous	NINL	NM_025176.4		1346,3276,1881	GG,GA,AA		43.3372,49.1375,45.8865		1013/1383	25456888	5968,7038	2203	4300	6503	SO:0001819	synonymous_variant	22981	exon17			CTCCACACTGTGC		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.3039T>C	20.37:g.25456888A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	90	42	0.466667	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Silent	SNP	ENST00000278886.6	37	CCDS33452.1																																																																																			A|0.506;G|0.494	0.494	strong		0.682	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176	
MT-ND2	4536	hgsc.bcm.edu	37	M	4917	4917	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:4917A>G	ENST00000361453.3	+	1	448	c.448A>G	c.(448-450)Aac>Gac	p.N150D	MT-RNR2_ENST00000387347.2_RNA|MT-TA_ENST00000387392.1_RNA|MT-CO2_ENST00000361739.1_5'Flank|MT-CO1_ENST00000361624.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TC_ENST00000387405.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TW_ENST00000387382.1_RNA			P03891	NU2M_HUMAN	mitochondrially encoded NADH dehydrogenase 2	150			N -> D (in LHON; secondary mutation; does not seem to directly cause the disease). {ECO:0000269|PubMed:1900003, ECO:0000269|PubMed:9475751}.|N -> S. {ECO:0000269|PubMed:1757091}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|lung(1)	3						CTCCCTCACTAAACGTAAGCC	0.468																																					p.N150D		Atlas-SNP	.											.	.	.	.	0			c.A448G						PASS	.																																			SO:0001583	missense	0	exon1			TCACTAAACGTAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198763	ENSG00000198763	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7456	protein-coding gene	gene with protein product	"""complex I ND2 subunit"", ""NADH-ubiquinone oxidoreductase chain 2"""	516001	"""NADH dehydrogenase 2"""	MTND2			Standard			Approved	ND2, NAD2		P03891		ENST00000361453.3:c.448A>G	M.37:g.4917A>G	ENSP00000355046:p.Asn150Asp	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361453	Q34769|Q9TGI0|Q9TGI1|Q9TGI2|Q9TGI3|Q9TGI4	Missense_Mutation	SNP	ENST00000361453.3	37																																																																																				.	.	none		0.468	MT-ND2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024027	
MYO1D	4642	hgsc.bcm.edu	37	17	30980871	30980871	+	Missense_Mutation	SNP	T	T	A	rs138039699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:30980871T>A	ENST00000318217.5	-	19	2889	c.2585A>T	c.(2584-2586)cAc>cTc	p.H862L	MYO1D_ENST00000579584.1_Missense_Mutation_p.H862L|MYO1D_ENST00000394649.4_Missense_Mutation_p.H774L|RP11-220C2.1_ENST00000582272.1_RNA	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	862	Myosin tail. {ECO:0000255}.				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)			CTTACGGACGTGACAGGAAAA	0.408													T|||	5	0.000998403	0.0	0.0	5008	,	,		22025	0.0		0.003	False		,,,				2504	0.002				p.H862L		Atlas-SNP	.											.	MYO1D	93	.	0			c.A2585T						PASS	.	T	LEU/HIS	2,4404	4.2+/-10.8	0,2,2201	135.0	109.0	118.0		2585	5.9	1.0	17	dbSNP_134	118	28,8572	20.4+/-63.3	0,28,4272	yes	missense	MYO1D	NM_015194.1	99	0,30,6473	AA,AT,TT		0.3256,0.0454,0.2307	benign	862/1007	30980871	30,12976	2203	4300	6503	SO:0001583	missense	4642	exon19			CGGACGTGACAGG	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.2585A>T	17.37:g.30980871T>A	ENSP00000324527:p.His862Leu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	16.55	3.153297	0.57259	4.54E-4	0.003256	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.35421	1.31	5.89	5.89	0.94794	Myosin tail 2 (1);	0.000000	0.40554	U	0.001063	T	0.41026	0.1141	M	0.65498	2.005	0.80722	D	1	P;B	0.35033	0.481;0.292	B;B	0.40982	0.345;0.186	T	0.21415	-1.0246	10	0.12103	T	0.63	.	14.2432	0.65971	0.0:0.0:0.0:1.0	.	773;862	Q7Z3N6;O94832	.;MYO1D_HUMAN	L	862;54	ENSP00000324527:H862L	ENSP00000324527:H862L	H	-	2	0	MYO1D	28004984	1.000000	0.71417	0.994000	0.49952	0.931000	0.56810	7.278000	0.78587	2.251000	0.74343	0.482000	0.46254	CAC	T|0.998;A|0.002	0.002	strong		0.408	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
HLTF	6596	hgsc.bcm.edu	37	3	148786085	148786085	+	Missense_Mutation	SNP	T	T	C	rs2305868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148786085T>C	ENST00000310053.5	-	8	1125	c.932A>G	c.(931-933)aAc>aGc	p.N311S	HLTF_ENST00000392912.2_Missense_Mutation_p.N311S|HLTF_ENST00000494055.1_Missense_Mutation_p.N311S|HLTF_ENST00000465259.1_Missense_Mutation_p.N311S	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	311			N -> S (in dbSNP:rs2305868).		chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			ATCATGGAAGTTGGTAAGGAT	0.363													T|||	102	0.0203674	0.0038	0.0317	5008	,	,		17102	0.0278		0.0288	False		,,,				2504	0.0184				p.N311S		Atlas-SNP	.											.	HLTF	87	.	0			c.A932G						PASS	.	T	SER/ASN,SER/ASN	23,4383	30.8+/-60.4	0,23,2180	153.0	161.0	159.0		932,932	6.0	1.0	3	dbSNP_100	159	238,8362	97.0+/-158.7	4,230,4066	yes	missense,missense	HLTF	NM_003071.3,NM_139048.2	46,46	4,253,6246	CC,CT,TT		2.7674,0.522,2.0068	probably-damaging,probably-damaging	311/1010,311/1010	148786085	261,12745	2203	4300	6503	SO:0001583	missense	6596	exon8			TGGAAGTTGGTAA	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.932A>G	3.37:g.148786085T>C	ENSP00000308944:p.Asn311Ser	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	69	37	0.536232	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	56	0.02564102564102564	0	0.0	15	0.04143646408839779	19	0.033216783216783216	22	0.029023746701846966	T	19.09	3.759929	0.69763	0.00522	0.027674	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000416117;ENST00000392913	D;D;D;D	0.93307	-3.2;-3.2;-3.2;-3.2	6.01	6.01	0.97437	DEAD-like helicase (1);SNF2-related (1);	.	.	.	.	T	0.74809	0.3765	L	0.37630	1.12	0.50632	D	0.999883	B;P;P	0.42827	0.394;0.791;0.679	P;P;P	0.46917	0.531;0.462;0.461	T	0.81174	-0.1053	9	0.33141	T	0.24	-8.68	8.9767	0.35939	0.0:0.0817:0.0:0.9183	rs2305868;rs17729483;rs52828545;rs2305868	311;311;311	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	S	311;311;311;311;308;308	ENSP00000420745:N311S;ENSP00000308944:N311S;ENSP00000376644:N311S;ENSP00000420429:N311S	ENSP00000308944:N311S	N	-	2	0	HLTF	150268775	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.197000	0.65141	2.307000	0.77673	0.528000	0.53228	AAC	T|0.977;C|0.023	0.023	strong		0.363	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296466	39296466	+	Missense_Mutation	SNP	G	G	A	rs35985080	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39296466G>A	ENST00000345847.4	-	1	273	c.274C>T	c.(274-276)Ccc>Tcc	p.P92S		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	92	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						CAGCACTGGGGTCTGCAGCAG	0.657													G|||	225	0.0449281	0.0023	0.0591	5008	,	,		18117	0.0		0.1034	False		,,,				2504	0.0787				p.P92S		Atlas-SNP	.											.	KRTAP4-6	46	.	0			c.C274T						PASS	.																																			SO:0001583	missense	81871	exon1			ACTGGGGTCTGCA	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.274C>T	17.37:g.39296466G>A	ENSP00000328270:p.Pro92Ser	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	71	36	0.507042	NM_030976	Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	CCDS54125.1	100	0.045787545787545784	1	0.0020325203252032522	25	0.06906077348066299	0	0.0	74	0.09762532981530343	.	16.42	3.119382	0.56505	.	.	ENSG00000198090	ENST00000345847	T	0.01887	4.58	4.48	0.151	0.14888	.	.	.	.	.	T	0.00144	0.0004	M	0.70275	2.135	0.09310	N	1	.	.	.	.	.	.	T	0.40459	-0.9562	7	0.42905	T	0.14	.	4.591	0.12306	0.2604:0.0:0.5861:0.1534	rs35985080	.	.	.	S	92	ENSP00000328270:P92S	ENSP00000328270:P92S	P	-	1	0	KRTAP4-6	36549992	0.018000	0.18449	0.000000	0.03702	0.894000	0.52154	0.189000	0.17037	-0.192000	0.10432	0.603000	0.83216	CCC	G|0.952;A|0.048	0.048	strong		0.657	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964299	37964299	+	Silent	SNP	C	C	G	rs2281098	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37964299C>G	ENST00000249014.4	+	3	1068	c.648C>G	c.(646-648)ctC>ctG	p.L216L		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	216					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)					TCATGAGCCTCCCAGAAGCCC	0.662													C|||	2300	0.459265	0.3154	0.6297	5008	,	,		11542	0.3204		0.5626	False		,,,				2504	0.5695				p.L216L		Atlas-SNP	.											.	CDC42EP1	53	.	0			c.C648G						PASS	.	C		1510,2894		282,946,974	33.0	36.0	35.0		648	-0.5	1.0	22	dbSNP_100	35	4908,3690		1434,2040,825	no	coding-synonymous	CDC42EP1	NM_152243.2		1716,2986,1799	GG,GC,CC		42.917,34.287,49.3616		216/392	37964299	6418,6584	2202	4299	6501	SO:0001819	synonymous_variant	11135	exon3			GAGCCTCCCAGAA	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.648C>G	22.37:g.37964299C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	18	0.243243	NM_152243	A8K825|Q96GN1	Silent	SNP	ENST00000249014.4	37	CCDS13949.1																																																																																			C|0.541;G|0.459	0.459	strong		0.662	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
SOX30	11063	hgsc.bcm.edu	37	5	157078402	157078402	+	Missense_Mutation	SNP	C	C	T	rs41275269	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:157078402C>T	ENST00000265007.6	-	1	1026	c.685G>A	c.(685-687)Gag>Aag	p.E229K	SOX30_ENST00000311371.5_Missense_Mutation_p.E229K|SOX30_ENST00000519442.1_Intron	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	229					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GACGCGGGCTCCGCGCCGAGC	0.637													.|||	35	0.00698882	0.0	0.0216	5008	,	,		15776	0.0		0.0179	False		,,,				2504	0.002				p.E229K	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.G685A						PASS	.	C	LYS/GLU,LYS/GLU	15,4391	22.3+/-47.3	0,15,2188	46.0	51.0	49.0		685,685	5.1	0.3	5	dbSNP_127	49	174,8426	74.5+/-137.1	3,168,4129	no	missense,missense	SOX30	NM_007017.2,NM_178424.1	56,56	3,183,6317	TT,TC,CC		2.0233,0.3404,1.4532	possibly-damaging,possibly-damaging	229/502,229/754	157078402	189,12817	2203	4300	6503	SO:0001583	missense	11063	exon1			CGGGCTCCGCGCC	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.685G>A	5.37:g.157078402C>T	ENSP00000265007:p.Glu229Lys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	13.03	2.114800	0.37339	0.003404	0.020233	ENSG00000039600	ENST00000311371;ENST00000265007	D;D	0.98120	-4.73;-4.34	5.05	5.05	0.67936	.	0.136638	0.33496	N	0.004848	D	0.90776	0.7104	L	0.27053	0.805	0.23708	N	0.997056	P;P	0.42584	0.784;0.678	B;B	0.43274	0.414;0.117	D	0.87575	0.2480	10	0.66056	D	0.02	.	10.0974	0.42484	0.1509:0.703:0.1461:0.0	rs41275269	229;229	O94993-2;O94993	.;SOX30_HUMAN	K	229	ENSP00000309343:E229K;ENSP00000265007:E229K	ENSP00000265007:E229K	E	-	1	0	SOX30	157010980	0.744000	0.28250	0.350000	0.25708	0.024000	0.10985	2.984000	0.49353	2.350000	0.79820	0.305000	0.20034	GAG	C|0.988;T|0.012	0.012	strong		0.637	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
CDH24	64403	hgsc.bcm.edu	37	14	23518918	23518918	+	Silent	SNP	T	T	C	rs11623976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23518918T>C	ENST00000267383.5	-	10	1721	c.1629A>G	c.(1627-1629)agA>agG	p.R543R	CDH24_ENST00000485922.1_5'UTR|CDH24_ENST00000554034.1_Silent_p.R505R|CDH24_ENST00000397359.3_Silent_p.R543R|CDH24_ENST00000487137.2_Silent_p.R505R			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	543	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)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|delta-catenin binding (GO:0070097)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(95;3.3e-05)			GBM - Glioblastoma multiforme(265;0.00654)		CAACTTCATCTCTGTCCAGGG	0.582													T|||	584	0.116613	0.0204	0.1398	5008	,	,		19997	0.004		0.2604	False		,,,				2504	0.1984				p.R543R		Atlas-SNP	.											.	CDH24	129	.	0			c.A1629G						PASS	.	T	,	249,4157	143.5+/-178.5	6,237,1960	60.0	53.0	56.0		1629,1515	2.3	1.0	14	dbSNP_120	56	2068,6532	357.3+/-330.7	248,1572,2480	no	coding-synonymous,coding-synonymous	CDH24	NM_022478.3,NM_144985.3	,	254,1809,4440	CC,CT,TT		24.0465,5.6514,17.8149	,	543/820,505/782	23518918	2317,10689	2203	4300	6503	SO:0001819	synonymous_variant	64403	exon11			TTCATCTCTGTCC	AL137477	CCDS9585.1, CCDS9586.1	14q11.2	2010-08-20	2009-11-20		ENSG00000139880	ENSG00000139880		"""Cadherins / Major cadherins"""	14265	protein-coding gene	gene with protein product			"""cadherin-like 24"""			12734196	Standard	NM_022478		Approved	CDH11L	uc001wil.3	Q86UP0	OTTHUMG00000028715	ENST00000267383.5:c.1629A>G	14.37:g.23518918T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_022478	D3DS44|Q86UP1|Q9NT84	Silent	SNP	ENST00000267383.5	37	CCDS9585.1																																																																																			T|0.841;C|0.159	0.159	strong		0.582	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478	
SYMPK	8189	hgsc.bcm.edu	37	19	46319415	46319415	+	Silent	SNP	G	G	C	rs1132645	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46319415G>C	ENST00000245934.7	-	26	3625	c.3381C>G	c.(3379-3381)gcC>gcG	p.A1127A	RSPH6A_ENST00000597055.1_5'Flank|RSPH6A_ENST00000221538.3_5'Flank|SYMPK_ENST00000598155.1_5'UTR	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1127					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		CTGGGGCCGGGGCCAAGGTCA	0.652													G|||	1793	0.358027	0.2905	0.232	5008	,	,		11505	0.6409		0.3181	False		,,,				2504	0.2883				p.A1127A		Atlas-SNP	.											.	SYMPK	104	.	0			c.C3381G						PASS	.						3.0	3.0	3.0					19																	46319415		1528	3134	4662	SO:0001819	synonymous_variant	8189	exon26			GGCCGGGGCCAAG	U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3381C>G	19.37:g.46319415G>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	48	26	0.541667	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			G|0.613;C|0.387	0.387	strong		0.652	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
NR5A2	2494	hgsc.bcm.edu	37	1	200143281	200143281	+	Silent	SNP	C	C	T	rs1060060	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:200143281C>T	ENST00000367362.3	+	8	1815	c.1569C>T	c.(1567-1569)aaC>aaT	p.N523N	NR5A2_ENST00000236914.3_Silent_p.N477N|NR5A2_ENST00000544748.1_Silent_p.N451N	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	523					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					AGCACCTGAACGGGGATGTGC	0.448													C|||	1775	0.354433	0.3669	0.3213	5008	,	,		17133	0.5179		0.2913	False		,,,				2504	0.2577				p.C523C	Melanoma(179;1138 2773 15678 26136)	Atlas-SNP	.											NR5A2,NS,carcinoma,+1,1	NR5A2	83	1	0			c.C1569T						PASS	.	C	,	1499,2907	478.1+/-358.1	267,965,971	60.0	55.0	56.0		1431,1569	-0.3	1.0	1	dbSNP_86	56	2522,6078	413.5+/-351.2	386,1750,2164	no	coding-synonymous,coding-synonymous	NR5A2	NM_003822.3,NM_205860.1	,	653,2715,3135	TT,TC,CC		29.3256,34.0218,30.9165	,	477/496,523/542	200143281	4021,8985	2203	4300	6503	SO:0001819	synonymous_variant	2494	exon8			CCTGAACGGGGAT	U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.1569C>T	1.37:g.200143281C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_205860	B4E2P3|O95642|Q147U3	Silent	SNP	ENST00000367362.3	37	CCDS1401.1																																																																																			T|0.348;G|0.007	0.348	strong		0.448	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2		
C10orf90	118611	hgsc.bcm.edu	37	10	128193368	128193368	+	Missense_Mutation	SNP	C	C	T	rs11245008	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:128193368C>T	ENST00000284694.7	-	3	521	c.401G>A	c.(400-402)cGc>cAc	p.R134H	C10orf90_ENST00000544758.1_Missense_Mutation_p.R231H|C10orf90_ENST00000454341.1_Missense_Mutation_p.R134H|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000356858.3_Missense_Mutation_p.R87H|C10orf90_ENST00000392694.1_Missense_Mutation_p.R87H	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	134	Required for interaction with HDAC1. {ECO:0000250}.		R -> H (in dbSNP:rs11245008).		mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		AAACCCTCTGCGGGGGCCCCC	0.672											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1077	0.215056	0.4592	0.1599	5008	,	,		14007	0.129		0.1153	False		,,,				2504	0.1155				p.R134H		Atlas-SNP	.											.	C10orf90	121	.	0			c.G401A						PASS	.	C	HIS/ARG	1634,2730		321,992,869	28.0	33.0	32.0		401	-9.9	0.0	10	dbSNP_120	32	1103,7457		75,953,3252	yes	missense	C10orf90	NM_001004298.2	29	396,1945,4121	TT,TC,CC		12.8855,37.4427,21.1777	benign	134/700	128193368	2737,10187	2182	4280	6462	SO:0001583	missense	118611	exon3			CCTCTGCGGGGGC	BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.401G>A	10.37:g.128193368C>T	ENSP00000284694:p.Arg134His	Somatic	86	0	0	1563	WXS	Illumina HiSeq	Phase_I	70	24	0.342857	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	449	0.20558608058608058	217	0.4410569105691057	59	0.16298342541436464	85	0.1486013986013986	88	0.11609498680738786	C	9.636	1.137739	0.21123	0.374427	0.128855	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.26810	2.01;2.01;2.03;2.02;1.71	4.97	-9.93	0.00452	.	1.535690	0.03830	N	0.268998	T	0.00012	0.0000	N	0.04636	-0.2	0.80722	P	0.0	B;B;B;B;B	0.18741	0.003;0.008;0.03;0.008;0.008	B;B;B;B;B	0.14578	0.003;0.002;0.011;0.003;0.003	T	0.31052	-0.9957	9	0.30078	T	0.28	-0.0577	11.4554	0.50179	0.0:0.2321:0.1567:0.6112	rs11245008;rs60449744;rs11245008	231;231;87;134;134	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	H	87;134;134;231;134;87;87	ENSP00000284694:R134H;ENSP00000398786:R134H;ENSP00000444369:R231H;ENSP00000405995:R134H;ENSP00000376459:R87H	ENSP00000284694:R134H	R	-	2	0	C10orf90	128183358	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-2.225000	0.01212	-3.872000	0.00096	-1.421000	0.01109	CGC	C|0.781;T|0.219	0.219	strong		0.672	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
SP140L	93349	hgsc.bcm.edu	37	2	231222675	231222675	+	Missense_Mutation	SNP	T	T	C	rs4973318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231222675T>C	ENST00000415673.2	+	3	349	c.263T>C	c.(262-264)aTg>aCg	p.M88T	SP140L_ENST00000243810.6_Missense_Mutation_p.M88T|SP140L_ENST00000458341.1_Start_Codon_SNP_p.M1T|SP140_ENST00000486687.2_3'UTR|SP140L_ENST00000396563.4_Missense_Mutation_p.M88T|SP140L_ENST00000444636.1_Missense_Mutation_p.M88T	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	88	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.		M -> T (in dbSNP:rs4973318).			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						ACAAATAAAATGTTTGAAGTA	0.363													T|||	414	0.0826677	0.0098	0.121	5008	,	,		20932	0.1042		0.1252	False		,,,				2504	0.0879				p.M88T		Atlas-SNP	.											.	SP140L	68	.	0			c.T263C						PASS	.	T	THR/MET	96,4192		0,96,2048	117.0	126.0	123.0		263	2.2	0.4	2	dbSNP_111	123	1016,7550		64,888,3331	yes	missense	SP140L	NM_138402.4	81	64,984,5379	CC,CT,TT		11.8608,2.2388,8.651	possibly-damaging	88/581	231222675	1112,11742	2144	4283	6427	SO:0001583	missense	93349	exon3			ATAAAATGTTTGA	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.263T>C	2.37:g.231222675T>C	ENSP00000397911:p.Met88Thr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	199	0.09111721611721611	6	0.012195121951219513	45	0.12430939226519337	61	0.10664335664335664	87	0.11477572559366754	T	8.718	0.913676	0.17907	0.022388	0.118608	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563;ENST00000458341	D;D;D;D;D	0.94793	-3.52;-3.52;-3.52;-3.52;-3.52	3.36	2.19	0.27852	.	.	.	.	.	T	0.29321	0.0730	M	0.79926	2.475	0.58432	P	1.0000000000287557E-6	P;B	0.45011	0.848;0.123	P;B	0.50231	0.635;0.026	T	0.70124	-0.4958	8	0.62326	D	0.03	.	5.4578	0.16600	0.0:0.1412:0.0:0.8588	rs4973318;rs52807436;rs59203650;rs4973318	1;88	Q9H930-3;Q9H930-4	.;.	T	88;88;88;88;1	ENSP00000395195:M88T;ENSP00000397911:M88T;ENSP00000243810:M88T;ENSP00000379811:M88T;ENSP00000395223:M1T	ENSP00000243810:M88T	M	+	2	0	SP140L	230930919	0.339000	0.24784	0.403000	0.26384	0.260000	0.26232	1.100000	0.31025	0.460000	0.27045	0.397000	0.26171	ATG	T|0.905;C|0.095	0.095	strong		0.363	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402	
MLPH	79083	hgsc.bcm.edu	37	2	238427251	238427251	+	Missense_Mutation	SNP	G	G	A	rs3751107	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238427251G>A	ENST00000264605.3	+	5	809	c.515G>A	c.(514-516)gGc>gAc	p.G172D	MLPH_ENST00000409373.1_Missense_Mutation_p.G172D|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Missense_Mutation_p.G172D|MLPH_ENST00000410032.1_Missense_Mutation_p.G172D|MLPH_ENST00000338530.4_Missense_Mutation_p.G172D	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	172			G -> D (in dbSNP:rs3751107).		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)		GGAGAACCTGGCTCAGAGGCC	0.582													N|||	895	0.178714	0.3714	0.0994	5008	,	,		18072	0.0843		0.1412	False		,,,				2504	0.1104				p.G172D		Atlas-SNP	.											.	MLPH	41	.	0			c.G515A						PASS	.		ASP/GLY,ASP/GLY	1527,2879		255,1017,931	66.0	72.0	70.0		515,515	1.5	0.0	2	dbSNP_107	70	1458,7142		126,1206,2968	yes	missense,missense	MLPH	NM_001042467.1,NM_024101.5	94,94	381,2223,3899	AA,AG,GG		16.9535,34.6573,22.9509	benign,benign	172/573,172/601	238427251	2985,10021	2203	4300	6503	SO:0001583	missense	79083	exon5			AACCTGGCTCAGA	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.515G>A	2.37:g.238427251G>A	ENSP00000264605:p.Gly172Asp	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	169	87	0.514793	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	370	0.16941391941391942	174	0.35365853658536583	38	0.10497237569060773	47	0.08216783216783216	111	0.14643799472295516	N	0	-2.589005	0.00128	0.346573	0.169535	ENSG00000115648	ENST00000410032;ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T;T;T;T;T	0.26067	1.76;2.14;2.12;1.96;1.77	2.65	1.49	0.22878	.	3.191120	0.02093	U	0.053301	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	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	0.06405	0.001;0.0;0.001;0.001;0.002;0.001;0.0	T	0.40289	-0.9571	9	0.11485	T	0.65	-12.4387	4.6532	0.12605	0.702:0.0:0.298:0.0	rs3751107;rs52809179;rs60441489;rs3751107	172;56;172;172;172;172;172	B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36;G5E9G5	.;.;.;.;.;MELPH_HUMAN;.	D	172	ENSP00000386338:G172D;ENSP00000264605:G172D;ENSP00000414849:G172D;ENSP00000341845:G172D;ENSP00000386780:G172D	ENSP00000264605:G172D	G	+	2	0	MLPH	238091990	0.001000	0.12720	0.002000	0.10522	0.016000	0.09150	-0.123000	0.10611	0.059000	0.16252	-1.342000	0.01247	GGC	G|0.795;A|0.205	0.205	strong		0.582	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	
COL2A1	1280	hgsc.bcm.edu	37	12	48375568	48375568	+	Silent	SNP	A	A	G	rs1635553	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48375568A>G	ENST00000380518.3	-	36	2564	c.2400T>C	c.(2398-2400)aaT>aaC	p.N800N	COL2A1_ENST00000337299.6_Silent_p.N731N|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	800	Triple-helical region.				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)	CCTTCTCGCCATTAGCACCAG	0.637													G|||	2418	0.482827	0.4879	0.3703	5008	,	,		17163	0.5476		0.4632	False		,,,				2504	0.5092				p.N800N		Atlas-SNP	.											COL2A1_ENST00000380518,NS,carcinoma,0,2	COL2A1	368	2	0			c.T2400C						PASS	.	G	,	1927,2385		453,1021,682	51.0	38.0	43.0		2400,2193	-8.6	0.4	12	dbSNP_89	43	3856,4604		908,2040,1282	yes	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	1361,3061,1964	GG,GA,AA		45.5792,44.6892,45.2787	,	800/1488,731/1419	48375568	5783,6989	2156	4230	6386	SO:0001819	synonymous_variant	1280	exon36			CTCGCCATTAGCA	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.2400T>C	12.37:g.48375568A>G		Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	128	127	0.992188	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	37	CCDS41778.1																																																																																			A|0.519;G|0.481	0.481	strong		0.637	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
CR1L	1379	hgsc.bcm.edu	37	1	207850879	207850879	+	Silent	SNP	C	C	T	rs34509370	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:207850879C>T	ENST00000508064.2	+	2	303	c.243C>T	c.(241-243)aaC>aaT	p.N81N	CR1L_ENST00000530905.1_3'UTR	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	81	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GCCTAAAAAACTCAGTCTGGA	0.423													N|||	535	0.106829	0.034	0.1441	5008	,	,		18366	0.0327		0.2525	False		,,,				2504	0.1053				p.N81N		Atlas-SNP	.											.	CR1L	97	.	0			c.C243T						PASS	.	C		256,3420		14,228,1596	186.0	167.0	173.0		243	-0.5	0.0	1	dbSNP_126	173	2160,6006		280,1600,2203	no	coding-synonymous	CR1L	NM_175710.1		294,1828,3799	TT,TC,CC		26.4511,6.9641,20.402		81/570	207850879	2416,9426	1838	4083	5921	SO:0001819	synonymous_variant	1379	exon2			AAAAAACTCAGTC	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.243C>T	1.37:g.207850879C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	182	88	0.483516	NM_175710	Q32MC9|Q8NEU7	Silent	SNP	ENST00000508064.2	37	CCDS44310.1																																																																																			C|0.836;T|0.164	0.164	strong		0.423	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
ATF3	467	hgsc.bcm.edu	37	1	212788567	212788567	+	Silent	SNP	C	C	T	rs2229346	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:212788567C>T	ENST00000341491.4	+	2	469	c.204C>T	c.(202-204)agC>agT	p.S68S	ATF3_ENST00000366987.2_Silent_p.S68S|ATF3_ENST00000492118.1_Intron|ATF3_ENST00000336937.4_Silent_p.S39S|ATF3_ENST00000366985.1_Silent_p.S11S|ATF3_ENST00000366983.1_Silent_p.S68S|RN7SL512P_ENST00000578962.1_RNA	NM_001040619.2|NM_001206488.2|NM_001674.3	NP_001035709.1|NP_001193417.2|NP_001665.1	P18847	ATF3_HUMAN	activating transcription factor 3	68					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)|gluconeogenesis (GO:0006094)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|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 regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)	Pseudoephedrine(DB00852)	TCACTGTCAGCGACAGACCCC	0.547													C|||	360	0.071885	0.0015	0.2507	5008	,	,		19204	0.1488		0.0239	False		,,,				2504	0.0102				p.S68S		Atlas-SNP	.											.	ATF3	22	.	0			c.C204T						PASS	.	C	,,,,,,	40,4366	43.8+/-77.6	0,40,2163	59.0	58.0	58.0		204,204,,204,117,,204	3.0	0.8	1	dbSNP_98	58	225,8375	91.4+/-153.5	1,223,4076	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous,coding-synonymous,intron,coding-synonymous	ATF3	NM_001030287.3,NM_001040619.2,NM_001206484.2,NM_001206485.1,NM_001206486.2,NM_001206488.2,NM_001674.3	,,,,,,	1,263,6239	TT,TC,CC		2.6163,0.9079,2.0375	,,,,,,	68/182,68/136,,68/121,39/107,,68/182	212788567	265,12741	2203	4300	6503	SO:0001819	synonymous_variant	467	exon2			TGTCAGCGACAGA	L19871	CCDS1506.1, CCDS41464.1, CCDS55688.1, CCDS58059.1	1q32.3	2013-01-10			ENSG00000162772	ENSG00000162772		"""basic leucine zipper proteins"""	785	protein-coding gene	gene with protein product		603148				7515060	Standard	NM_001674		Approved		uc021pit.1	P18847	OTTHUMG00000036747	ENST00000341491.4:c.204C>T	1.37:g.212788567C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	38	0.44186	NM_001674	Q5VTZ2|Q6ICQ9|Q7Z566|Q8WYM6	Silent	SNP	ENST00000341491.4	37	CCDS1506.1																																																																																			C|0.951;G|0.000;T|0.049	0.049	strong		0.547	ATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089296.1	NM_001674	
AFF4	27125	hgsc.bcm.edu	37	5	132232315	132232315	+	Silent	SNP	G	G	A	rs739863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:132232315G>A	ENST00000265343.5	-	11	2386	c.2007C>T	c.(2005-2007)ccC>ccT	p.P669P	AFF4_ENST00000378595.3_Silent_p.P669P	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	669					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATTGCTCTCGGGGTACTTAG	0.443													G|||	527	0.105232	0.0144	0.0937	5008	,	,		19428	0.1141		0.1451	False		,,,				2504	0.1861				p.P669P	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.C2007T						PASS	.	G		161,4245	108.6+/-147.0	3,155,2045	79.0	81.0	80.0		2007	1.6	1.0	5	dbSNP_86	80	1370,7230	263.0+/-284.7	114,1142,3044	no	coding-synonymous	AFF4	NM_014423.3		117,1297,5089	AA,AG,GG		15.9302,3.6541,11.7715		669/1164	132232315	1531,11475	2203	4300	6503	SO:0001819	synonymous_variant	27125	exon11			GCTCTCGGGGTAC	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2007C>T	5.37:g.132232315G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	119	49	0.411765	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Silent	SNP	ENST00000265343.5	37	CCDS4164.1																																																																																			G|0.892;A|0.108	0.108	strong		0.443	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
FCGBP	8857	hgsc.bcm.edu	37	19	40366374	40366374	+	Silent	SNP	G	G	C	rs2053089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40366374G>C	ENST00000221347.6	-	30	13867	c.13860C>G	c.(13858-13860)ccC>ccG	p.P4620P		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4620	VWFD 11. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGTCGTCTGCGGGGTCCTGGT	0.687													G|||	632	0.126198	0.0363	0.2277	5008	,	,		12502	0.0466		0.2197	False		,,,				2504	0.1616				p.P4620P		Atlas-SNP	.											FCGBP,NS,carcinoma,-1,1	FCGBP	416	1	0			c.C13860G						PASS	.	G		355,4049		19,317,1866	40.0	47.0	45.0		13860	-8.6	0.0	19	dbSNP_94	45	2068,6530		258,1552,2489	no	coding-synonymous	FCGBP	NM_003890.2		277,1869,4355	CC,CG,GG		24.0521,8.0609,18.6356		4620/5406	40366374	2423,10579	2202	4299	6501	SO:0001819	synonymous_variant	8857	exon30			GTCTGCGGGGTCC	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.13860C>G	19.37:g.40366374G>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	139	62	0.446043	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.828;C|0.172	0.172	strong		0.687	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF227	7770	hgsc.bcm.edu	37	19	44739399	44739399	+	Silent	SNP	T	T	C	rs2279072	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44739399T>C	ENST00000313040.7	+	6	1021	c.816T>C	c.(814-816)caT>caC	p.H272H	ZNF227_ENST00000589005.1_Silent_p.H221H|ZNF227_ENST00000391961.2_Silent_p.H221H	NM_182490.1	NP_872296.1	Q86WZ6	ZN227_HUMAN	zinc finger protein 227	272					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(2)|stomach(1)|urinary_tract(1)	24		Prostate(69;0.0435)				CGAATGTTCATACAGGAGAAA	0.453													C|||	3183	0.635583	0.705	0.7104	5008	,	,		17959	0.5327		0.5706	False		,,,				2504	0.6616				p.H272H		Atlas-SNP	.											.	ZNF227	62	.	0			c.T816C						PASS	.	C		3121,1285	433.1+/-343.5	1116,889,198	47.0	47.0	47.0		816	1.7	0.0	19	dbSNP_100	47	4846,3754	528.6+/-381.4	1383,2080,837	no	coding-synonymous	ZNF227	NM_182490.1		2499,2969,1035	CC,CT,TT		43.6512,29.1648,38.7437		272/800	44739399	7967,5039	2203	4300	6503	SO:0001819	synonymous_variant	7770	exon6			TGTTCATACAGGA	AK092253	CCDS12636.1, CCDS74388.1	19q13.32	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	13020	protein-coding gene	gene with protein product							Standard	XM_005259232		Approved		uc002oyu.3	Q86WZ6		ENST00000313040.7:c.816T>C	19.37:g.44739399T>C		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	112	112	1	NM_182490	B3KRU7|B7Z5P9	Silent	SNP	ENST00000313040.7	37	CCDS12636.1																																																																																			T|0.393;C|0.607	0.607	strong		0.453	ZNF227-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460720.1	NM_182490	
CDH18	1016	hgsc.bcm.edu	37	5	19591174	19591174	+	Silent	SNP	A	A	G	rs17285716	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:19591174A>G	ENST00000507958.1	-	9	1981	c.991T>C	c.(991-993)Tta>Cta	p.L331L	CDH18_ENST00000274170.4_Silent_p.L331L|CDH18_ENST00000502796.1_Silent_p.L331L|CDH18_ENST00000382275.1_Silent_p.L331L|CDH18_ENST00000506372.1_Silent_p.L331L|CDH18_ENST00000511273.1_Silent_p.L331L			Q13634	CAD18_HUMAN	cadherin 18, type 2	331	Cadherin 3. {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)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					ACCTTCTTTAAAGAAAGGATT	0.403													A|||	480	0.0958466	0.0151	0.1945	5008	,	,		16900	0.004		0.1799	False		,,,				2504	0.1431				p.L331L		Atlas-SNP	.											CDH18_ENST00000507958,NS,adenoma,0,4	CDH18	561	4	0			c.T991C						PASS	.	A	,	208,4198	127.8+/-164.7	7,194,2002	88.0	77.0	81.0		991,991	4.1	1.0	5	dbSNP_123	81	1595,7005	295.4+/-302.4	131,1333,2836	no	coding-synonymous,coding-synonymous	CDH18	NM_001167667.1,NM_004934.3	,	138,1527,4838	GG,GA,AA		18.5465,4.7208,13.8628	,	331/575,331/791	19591174	1803,11203	2203	4300	6503	SO:0001819	synonymous_variant	1016	exon7			TCTTTAAAGAAAG	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.991T>C	5.37:g.19591174A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	92	41	0.445652	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Silent	SNP	ENST00000507958.1	37	CCDS3889.1																																																																																			A|0.879;G|0.121	0.121	strong		0.403	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
ISYNA1	51477	hgsc.bcm.edu	37	19	18545786	18545786	+	Silent	SNP	G	G	T	rs1045631	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18545786G>T	ENST00000338128.8	-	11	1831	c.1614C>A	c.(1612-1614)acC>acA	p.T538T	ISYNA1_ENST00000578963.1_Silent_p.T410T|ISYNA1_ENST00000317018.6_Silent_p.T336T|ISYNA1_ENST00000545187.1_Silent_p.T388T|ISYNA1_ENST00000457269.4_Silent_p.T484T	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	538					inositol biosynthetic process (GO:0006021)|inositol phosphate metabolic process (GO:0043647)|phospholipid biosynthetic process (GO:0008654)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-3-phosphate synthase activity (GO:0004512)			breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	12						TGCAGCCATTGGTGGCAGCGG	0.617																																					p.T538T		Atlas-SNP	.											.	ISYNA1	31	.	0			c.C1614A						PASS	.	G	,,	1037,3369	371.0+/-319.8	126,785,1292	56.0	60.0	59.0		1452,1164,1614	0.9	0.0	19	dbSNP_86	59	1746,6852	310.2+/-309.8	179,1388,2732	no	coding-synonymous,coding-synonymous,coding-synonymous	ISYNA1	NM_001170938.1,NM_001170939.1,NM_016368.4	,,	305,2173,4024	TT,TG,GG		20.307,23.5361,21.4011	,,	484/505,388/409,538/559	18545786	2783,10221	2203	4299	6502	SO:0001819	synonymous_variant	51477	exon11			GCCATTGGTGGCA		CCDS12379.1, CCDS54234.1, CCDS62603.1	19p13.11	2014-09-04			ENSG00000105655	ENSG00000105655	5.5.1.4		29821	protein-coding gene	gene with protein product	"""myo-inositol 1-phosphate synthase"""	611670				15024000, 12941308	Standard	NM_016368		Approved	Ino1, INOS, IPS	uc002njd.2	Q9NPH2	OTTHUMG00000179027	ENST00000338128.8:c.1614C>A	19.37:g.18545786G>T		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	159	83	0.522013	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			G|0.788;T|0.212	0.212	strong		0.617	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368	
AKR1C3	8644	hgsc.bcm.edu	37	10	5138607	5138607	+	Silent	SNP	G	G	A	rs7741	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5138607G>A	ENST00000380554.3	+	2	742	c.90G>A	c.(88-90)ccG>ccA	p.P30P	U8_ENST00000459536.1_RNA|AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000605149.1_Silent_p.P7P|AKR1C3_ENST00000470862.2_3'UTR	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	30					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	TCCAGGTTCCGAGAAGTAAAG	0.438													G|||	1083	0.216254	0.3381	0.196	5008	,	,		20326	0.0		0.3648	False		,,,				2504	0.136				p.P30P		Atlas-SNP	.											.	AKR1C3	21	.	0			c.G90A						PASS	.	G		1485,2921	475.7+/-357.4	246,993,964	72.0	68.0	69.0		90	-3.2	0.0	10	dbSNP_52	69	3041,5557	468.9+/-367.4	544,1953,1802	no	coding-synonymous	AKR1C3	NM_003739.4		790,2946,2766	AA,AG,GG		35.3687,33.704,34.8047		30/324	5138607	4526,8478	2203	4299	6502	SO:0001819	synonymous_variant	8644	exon2			GGTTCCGAGAAGT	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.90G>A	10.37:g.5138607G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	141	49	0.347518	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Silent	SNP	ENST00000380554.3	37	CCDS7063.1																																																																																			G|0.710;A|0.290	0.290	strong		0.438	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
PLAC8L1	153770	hgsc.bcm.edu	37	5	145464130	145464130	+	Silent	SNP	T	T	C	rs1859897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145464130T>C	ENST00000311450.4	-	4	456	c.399A>G	c.(397-399)acA>acG	p.T133T		NM_001029869.1	NP_001025040.1	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	133										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|stomach(2)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTTCACACAGTGTGCCCTAGG	0.527													T|||	178	0.0355431	0.1218	0.0216	5008	,	,		17606	0.0		0.002	False		,,,				2504	0.0				p.T133T		Atlas-SNP	.											.	PLAC8L1	17	.	0			c.A399G						PASS	.	T		480,3926	226.5+/-242.0	28,424,1751	95.0	93.0	93.0		399	-10.1	0.0	5	dbSNP_92	93	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	PLAC8L1	NM_001029869.1		28,440,6035	CC,CT,TT		0.186,10.8942,3.8136		133/178	145464130	496,12510	2203	4300	6503	SO:0001819	synonymous_variant	153770	exon4			ACACAGTGTGCCC		CCDS34264.1	5q32	2008-02-05			ENSG00000173261	ENSG00000173261			31746	protein-coding gene	gene with protein product							Standard	XM_005268381		Approved		uc003lnv.3	A1L4L8	OTTHUMG00000163418	ENST00000311450.4:c.399A>G	5.37:g.145464130T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	70	42	0.6	NM_001029869		Silent	SNP	ENST00000311450.4	37	CCDS34264.1																																																																																			T|0.967;C|0.033	0.033	strong		0.527	PLAC8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373290.1	XM_087761	
TAAR1	134864	hgsc.bcm.edu	37	6	132966348	132966348	+	Silent	SNP	G	G	A	rs8192619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:132966348G>A	ENST00000275216.1	-	1	794	c.795C>T	c.(793-795)tgC>tgT	p.C265C		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	265					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	TAAAGAAAGGGCACCAGCATA	0.368													G|||	397	0.0792732	0.0545	0.0749	5008	,	,		18338	0.1359		0.0497	False		,,,				2504	0.0879				p.C265C		Atlas-SNP	.											.	TAAR1	41	.	0			c.C795T						PASS	.	G		282,4122	156.6+/-189.7	13,256,1933	86.0	77.0	80.0		795	0.5	1.0	6	dbSNP_117	80	467,8131	137.3+/-194.3	12,443,3844	no	coding-synonymous	TAAR1	NM_138327.1		25,699,5777	AA,AG,GG		5.4315,6.4033,5.7607		265/340	132966348	749,12253	2202	4299	6501	SO:0001819	synonymous_variant	134864	exon1			GAAAGGGCACCAG	AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"""GPCR / Class A : Trace amine associated receptors"""	17734	protein-coding gene	gene with protein product		609333	"""trace amine receptor 1"""	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.795C>T	6.37:g.132966348G>A		Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	91	89	0.978022	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Silent	SNP	ENST00000275216.1	37	CCDS5158.1																																																																																			G|0.935;A|0.065	0.065	strong		0.368	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327	
UTP20	27340	hgsc.bcm.edu	37	12	101761753	101761753	+	Splice_Site	SNP	A	A	G	rs117476305	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101761753A>G	ENST00000261637.4	+	48	6557	c.6383A>G	c.(6382-6384)aAg>aGg	p.K2128R		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2128					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						ATGGATGTGAAGGTAAGCATC	0.433													A|||	15	0.00299521	0.0	0.0043	5008	,	,		19984	0.0		0.0099	False		,,,				2504	0.002				p.K2128R		Atlas-SNP	.											.	UTP20	222	.	0			c.A6383G						PASS	.	A	ARG/LYS	3,4403	6.2+/-15.9	0,3,2200	240.0	211.0	221.0		6383	4.4	1.0	12	dbSNP_132	221	99,8501	54.4+/-115.2	0,99,4201	yes	missense-near-splice	UTP20	NM_014503.2	26	0,102,6401	GG,GA,AA		1.1512,0.0681,0.7843	possibly-damaging	2128/2786	101761753	102,12904	2203	4300	6503	SO:0001630	splice_region_variant	27340	exon48			ATGTGAAGGTAAG	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.6384+1A>G	12.37:g.101761753A>G		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	125	58	0.464	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	A	14.07	2.424265	0.43020	6.81E-4	0.011512	ENSG00000120800	ENST00000261637	T	0.65364	-0.15	5.59	4.44	0.53790	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	L	0.52126	1.63	0.58432	D	0.999997	P	0.40431	0.717	B	0.35039	0.194	T	0.38866	-0.9641	10	0.25751	T	0.34	-13.9985	11.5039	0.50454	0.9298:0.0:0.0702:0.0	.	2128	O75691	UTP20_HUMAN	R	2128	ENSP00000261637:K2128R	ENSP00000261637:K2128R	K	+	2	0	UTP20	100285884	1.000000	0.71417	1.000000	0.80357	0.225000	0.24961	5.758000	0.68776	0.942000	0.37525	0.528000	0.53228	AAG	A|0.991;G|0.009	0.009	strong		0.433	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	Missense_Mutation
MICAL3	57553	hgsc.bcm.edu	37	22	18300775	18300775	+	Missense_Mutation	SNP	G	G	A	rs61744842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18300775G>A	ENST00000441493.2	-	26	5004	c.4652C>T	c.(4651-4653)cCg>cTg	p.P1551L	MICAL3_ENST00000580469.1_5'Flank	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	1551					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)		CTCGGGGCGCGGCCAGCAGGA	0.637													G|||	293	0.0585064	0.0522	0.0245	5008	,	,		10866	0.0813		0.0517	False		,,,				2504	0.0746				p.P1551L		Atlas-SNP	.											.	MICAL3	53	.	0			c.C4652T						PASS	.	G	LEU/PRO	234,3752		6,222,1765	29.0	31.0	30.0		4652	0.1	0.0	22	dbSNP_129	30	333,7957		6,321,3818	yes	missense	MICAL3	NM_015241.2	98	12,543,5583	AA,AG,GG		4.0169,5.8705,4.6188	benign	1551/2003	18300775	567,11709	1993	4145	6138	SO:0001583	missense	57553	exon26			GGGCGCGGCCAGC	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.4652C>T	22.37:g.18300775G>A	ENSP00000416015:p.Pro1551Leu	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	134|134	0.06135531135531135|0.06135531135531135	26|26	0.052845528455284556|0.052845528455284556	9|9	0.024861878453038673|0.024861878453038673	54|54	0.0944055944055944|0.0944055944055944	45|45	0.059366754617414245|0.059366754617414245	G|G	5.405|5.405	0.259839|0.259839	0.10239|0.10239	0.058705|0.058705	0.040169|0.040169	ENSG00000093100|ENSG00000093100	ENST00000441493|ENST00000252134	T|.	0.63417|.	-0.04|.	4.81|4.81	0.0718|0.0718	0.14384|0.14384	.|.	.|.	.|.	.|.	.|.	T|T	0.01156|0.01156	0.0038|0.0038	L|L	0.34521|0.34521	1.04|1.04	0.58432|0.58432	P|P	1.0000000000287557E-6|1.0000000000287557E-6	B|.	0.09022|.	0.002|.	B|.	0.04013|.	0.001|.	T|T	0.17349|0.17349	-1.0372|-1.0372	8|4	0.30078|.	T|.	0.28|.	.|.	5.1696|5.1696	0.15103|0.15103	0.3073:0.1387:0.554:0.0|0.3073:0.1387:0.554:0.0	.|.	1551|.	Q7RTP6|.	MICA3_HUMAN|.	L|C	1551|533	ENSP00000416015:P1551L|.	ENSP00000416015:P1551L|.	P|R	-|-	2|1	0|0	XXbac-B461K10.4|XXbac-B461K10.4	16680775|16680775	0.233000|0.233000	0.23772|0.23772	0.000000|0.000000	0.03702|0.03702	0.039000|0.039000	0.13416|0.13416	1.915000|1.915000	0.39976|0.39976	0.126000|0.126000	0.18424|0.18424	-1.141000|-1.141000	0.01876|0.01876	CCG|CGC	G|0.944;A|0.056	0.056	strong		0.637	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1		
RAET1G	353091	hgsc.bcm.edu	37	6	150240829	150240829	+	Missense_Mutation	SNP	G	G	C	rs9397449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:150240829G>C	ENST00000367360.2	-	2	276	c.209C>G	c.(208-210)aCa>aGa	p.T70R	RAET1E-AS1_ENST00000605899.1_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1E-AS1_ENST00000446954.2_RNA|RAET1G_ENST00000479265.1_Missense_Mutation_p.T70R	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		GGGTGTGACTGTCTTGCTGCC	0.517													g|||	1132	0.226038	0.1021	0.111	5008	,	,		20972	0.5317		0.1501	False		,,,				2504	0.2382				p.T70R		Atlas-SNP	.											.	RAET1G	31	.	0			c.C209G						PASS	.	C	ARG/THR	492,3914	780.8+/-414.5	27,438,1738	278.0	261.0	267.0		209	-2.0	0.0	6	dbSNP_119	267	1130,7470	767.0+/-407.6	83,964,3253	no	missense	RAET1G	NM_001001788.2	71	110,1402,4991	CC,CG,GG		13.1395,11.1666,12.4712	benign	70/335	150240829	1622,11384	2203	4300	6503	SO:0001583	missense	353091	exon2			GTGACTGTCTTGC	AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"""retinoic acid early transcript 1G pseudogene"""			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.209C>G	6.37:g.150240829G>C	ENSP00000356329:p.Thr70Arg	Somatic	677	0	0		WXS	Illumina HiSeq	Phase_I	352	262	0.744318	NM_001001788		Missense_Mutation	SNP	ENST00000367360.2	37	CCDS43514.1	503	0.2303113553113553	47	0.09552845528455285	46	0.1270718232044199	308	0.5384615384615384	102	0.1345646437994723	C	2.358	-0.347240	0.05208	0.111666	0.131395	ENSG00000203722	ENST00000367360;ENST00000479265	T;T	0.00626	6.13;6.13	2.4	-2.05	0.07321	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	.	.	.	.	T	0.00144	0.0004	L	0.29908	0.895	0.80722	P	0.0	B	0.21688	0.059	B	0.26094	0.066	T	0.43540	-0.9385	8	0.02654	T	1	.	0.992	0.01459	0.1668:0.1581:0.398:0.2771	rs9397449;rs60358512;rs9397449	70	Q6H3X3	RET1G_HUMAN	R	70	ENSP00000356329:T70R;ENSP00000417503:T70R	ENSP00000356329:T70R	T	-	2	0	RAET1G	150282522	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.137000	0.01304	-0.955000	0.03636	-3.292000	0.00046	ACA	G|0.807;C|0.193	0.193	strong		0.517	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2		
SEMA3F	6405	hgsc.bcm.edu	37	3	50197097	50197097	+	Silent	SNP	C	C	T	rs1046953	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50197097C>T	ENST00000002829.3	+	2	526	c.42C>T	c.(40-42)acC>acT	p.T14T	SEMA3F_ENST00000434342.1_Silent_p.T14T|SEMA3F_ENST00000413852.1_Intron	NM_004186.3	NP_004177.3	Q13275	SEM3F_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F	14					axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|negative regulation of axon extension involved in axon guidance (GO:0048843)|nerve development (GO:0021675)|neural crest cell migration (GO:0001755)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	extracellular space (GO:0005615)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|receptor activity (GO:0004872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	17				BRCA - Breast invasive adenocarcinoma(193;0.00013)|KIRC - Kidney renal clear cell carcinoma(197;0.00599)|Kidney(197;0.00688)		CCCTACTGACCGGGGCCTGGC	0.617													T|||	1879	0.3752	0.3177	0.2983	5008	,	,		16725	0.1915		0.4026	False		,,,				2504	0.6687				p.T14T		Atlas-SNP	.											.	SEMA3F	62	.	0			c.C42T						PASS	.	T		1471,2935	677.1+/-403.3	252,967,984	60.0	57.0	58.0		42	-2.4	0.9	3	dbSNP_86	58	3510,5090	632.3+/-398.6	708,2094,1498	no	coding-synonymous	SEMA3F	NM_004186.3		960,3061,2482	TT,TC,CC		40.814,33.3863,38.2977		14/786	50197097	4981,8025	2203	4300	6503	SO:0001819	synonymous_variant	6405	exon2			ACTGACCGGGGCC	U33920	CCDS2811.1	3p21.3	2013-01-11			ENSG00000001617	ENSG00000001617		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10728	protein-coding gene	gene with protein product	"""sema IV"""	601124				8786119, 8649831	Standard	NM_004186		Approved	SEMAK, Sema4	uc003cyj.3	Q13275	OTTHUMG00000156806	ENST00000002829.3:c.42C>T	3.37:g.50197097C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	58	32	0.551724	NM_004186	C9JQ85|Q13274|Q13372|Q15704|Q6GTR4	Silent	SNP	ENST00000002829.3	37	CCDS2811.1																																																																																			C|0.626;T|0.374	0.374	strong		0.617	SEMA3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345929.1	NM_004186	
TMEM14E	645843	hgsc.bcm.edu	37	3	152058449	152058449	+	Missense_Mutation	SNP	A	A	G	rs13077912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:152058449A>G	ENST00000408960.3	-	1	330	c.245T>C	c.(244-246)cTa>cCa	p.L82P	MBNL1_ENST00000492948.1_Intron|MBNL1_ENST00000355460.2_Intron|MBNL1_ENST00000282486.6_Intron|MBNL1_ENST00000463374.1_Intron|MBNL1_ENST00000545754.1_Intron|MBNL1_ENST00000485509.1_Intron|MBNL1_ENST00000498502.1_Intron|MBNL1_ENST00000493459.1_Intron|MBNL1_ENST00000324196.5_Intron|MBNL1_ENST00000282488.7_Intron|MBNL1_ENST00000324210.5_Intron|MBNL1_ENST00000357472.3_Intron|MBNL1_ENST00000485910.1_Intron	NM_001123228.1	NP_001116700.1	Q6UXP3	TM14E_HUMAN	transmembrane protein 14E	82			L -> P (in dbSNP:rs13077912).			integral component of membrane (GO:0016021)				lung(1)	1						CCAGAGTGTTAGAATCTTATT	0.443													A|||	346	0.0690895	0.0484	0.085	5008	,	,		19975	0.0099		0.161	False		,,,				2504	0.0521				p.L82P		Atlas-SNP	.											.	TMEM14E	6	.	0			c.T245C						PASS	.	A	PRO/LEU,,,,,,,	189,2947		8,173,1387	111.0	98.0	102.0		245,,,,,,,	0.9	0.0	3	dbSNP_121	102	1123,6041		95,933,2554	yes	missense,intron,intron,intron,intron,intron,intron,intron	MBNL1,TMEM14E	NM_001123228.1,NM_021038.3,NM_207292.1,NM_207293.1,NM_207294.1,NM_207295.1,NM_207296.1,NM_207297.1	98,,,,,,,	103,1106,3941	GG,GA,AA		15.6756,6.0268,12.7379	probably-damaging,,,,,,,	82/126,,,,,,,	152058449	1312,8988	1568	3582	5150	SO:0001583	missense	645843	exon1			AGTGTTAGAATCT		CCDS43161.1	3q25.1	2011-09-15			ENSG00000221962	ENSG00000221962			34386	protein-coding gene	gene with protein product							Standard	NM_001123228		Approved		uc010hvo.3	Q6UXP3	OTTHUMG00000159652	ENST00000408960.3:c.245T>C	3.37:g.152058449A>G	ENSP00000386163:p.Leu82Pro	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	186	96	0.516129	NM_001123228		Missense_Mutation	SNP	ENST00000408960.3	37	CCDS43161.1	188	0.08608058608058608	27	0.054878048780487805	38	0.10497237569060773	5	0.008741258741258742	118	0.15567282321899736	A	11.16	1.557587	0.27827	0.060268	0.156756	ENSG00000221962	ENST00000408960	T	0.35421	1.31	2.12	0.919	0.19392	.	.	.	.	.	T	0.00144	0.0004	N	0.19112	0.55	0.80722	P	0.0	D	0.76494	0.999	D	0.66497	0.944	T	0.06935	-1.0799	8	0.45353	T	0.12	.	3.901	0.09161	0.8047:0.0:0.1953:0.0	rs13077912;rs52798054;rs13077912	82	Q6UXP3	TM14E_HUMAN	P	82	ENSP00000386163:L82P	ENSP00000386163:L82P	L	-	2	0	TMEM14E	153541139	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.111000	0.15458	0.249000	0.21456	-0.361000	0.07541	CTA	A|0.902;G|0.098	0.098	strong		0.443	TMEM14E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356703.1	NM_001123228	
TTI1	9675	hgsc.bcm.edu	37	20	36642101	36642101	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36642101C>T	ENST00000373448.2	-	3	356	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	TTI1_ENST00000487362.1_Splice_Site|TTI1_ENST00000373447.3_Missense_Mutation_p.V40M|TTI1_ENST00000449821.1_Missense_Mutation_p.V40M	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	40					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						CTGTCACTCACAGCTTGTAGT	0.517																																					p.V40M		Atlas-SNP	.											.	TTI1	104	.	0			c.G118A						PASS	.						143.0	117.0	126.0					20																	36642101		2203	4300	6503	SO:0001583	missense	9675	exon3			CACTCACAGCTTG	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.118G>A	20.37:g.36642101C>T	ENSP00000362547:p.Val40Met	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710534	0.48517	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.68181	-0.31;-0.31;-0.31	5.33	3.35	0.38373	Armadillo-type fold (1);	0.247212	0.40908	D	0.000983	T	0.69522	0.3120	M	0.62723	1.935	0.40385	D	0.979489	P	0.46512	0.879	P	0.51385	0.668	T	0.69624	-0.5095	10	0.36615	T	0.2	-9.5996	10.6162	0.45451	0.0:0.8401:0.0:0.1599	.	40	O43156	TTI1_HUMAN	M	40	ENSP00000362547:V40M;ENSP00000362546:V40M;ENSP00000407270:V40M	ENSP00000362546:V40M	V	-	1	0	TTI1	36075515	0.976000	0.34144	0.815000	0.32552	0.871000	0.50021	2.440000	0.44855	1.457000	0.47850	0.655000	0.94253	GTG	.	.	none		0.517	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657	
ALAS2	212	hgsc.bcm.edu	37	X	55039959	55039959	+	Silent	SNP	G	G	T	rs150055592	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:55039959G>T	ENST00000330807.5	-	10	1697	c.1560C>A	c.(1558-1560)ccC>ccA	p.P520P	ALAS2_ENST00000396198.3_Silent_p.P507P|ALAS2_ENST00000335854.4_Silent_p.P483P|ALAS2_ENST00000498636.1_Intron	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	520			P -> L (in dbSNP:rs201062903). {ECO:0000269|PubMed:21309041}.		cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	GGTGGGGGGAGGGTGCCAAGC	0.577													G|||	10	0.00264901	0.0	0.0029	3775	,	,		12458	0.0		0.008	False		,,,				2504	0.0				p.P520P		Atlas-SNP	.											.	ALAS2	163	.	0			c.C1560A						PASS	.	G	,,	1,3834		0,1,0,1631,571	62.0	51.0	55.0		1560,1449,1521	1.4	1.0	X	dbSNP_134	55	42,6686		0,25,17,2403,1855	no	coding-synonymous,coding-synonymous,coding-synonymous	ALAS2	NM_000032.4,NM_001037967.3,NM_001037968.3	,,	0,26,17,4034,2426	TT,TG,T,GG,G		0.6243,0.0261,0.4071	,,	520/588,483/551,507/575	55039959	43,10520	2203	4300	6503	SO:0001819	synonymous_variant	212	exon10			GGGGGAGGGTGCC		CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"""sideroblastic/hypochromic anemia"""	301300	"""aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"""	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.1560C>A	X.37:g.55039959G>T		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	66	64	0.969697	NM_000032	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Silent	SNP	ENST00000330807.5	37	CCDS14366.1																																																																																			G|0.997;T|0.003	0.003	strong		0.577	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032	
NUP133	55746	hgsc.bcm.edu	37	1	229622162	229622162	+	Silent	SNP	A	A	G	rs1065675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:229622162A>G	ENST00000261396.3	-	11	1547	c.1456T>C	c.(1456-1458)Ttg>Ctg	p.L486L	NUP133_ENST00000537506.1_Silent_p.L470L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	486					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.L486L(1)		NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GACCCTTCCAAGTCTTCTGCC	0.378													G|||	1521	0.303714	0.5809	0.3285	5008	,	,		19446	0.1607		0.2097	False		,,,				2504	0.1554				p.L486L		Atlas-SNP	.											NUP133,NS,carcinoma,0,1	NUP133	111	1	1	Substitution - coding silent(1)	stomach(1)	c.T1456C						PASS	.	G		2316,2090	569.8+/-382.7	600,1116,487	105.0	110.0	108.0		1456	-1.6	0.1	1	dbSNP_86	108	1864,6736	729.8+/-406.7	201,1462,2637	no	coding-synonymous	NUP133	NM_018230.2		801,2578,3124	GG,GA,AA		21.6744,47.4353,32.139		486/1157	229622162	4180,8826	2203	4300	6503	SO:0001819	synonymous_variant	55746	exon11			CTTCCAAGTCTTC		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1456T>C	1.37:g.229622162A>G		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	109	109	1	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	37	CCDS1579.1																																																																																			A|0.690;G|0.310	0.310	strong		0.378	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
TEX26	122046	hgsc.bcm.edu	37	13	31531009	31531009	+	Splice_Site	SNP	G	G	A	rs12857479	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:31531009G>A	ENST00000380473.3	+	4	325		c.e4-1			NM_152325.1	NP_689538.1	Q8N6G2	TEX26_HUMAN	testis expressed 26																		TGCTTTGATAGGACATTTTCC	0.403													G|||	1276	0.254792	0.0469	0.3141	5008	,	,		19264	0.2946		0.3628	False		,,,				2504	0.3415				.		Atlas-SNP	.											.	.	.	.	0			c.313-1G>A						PASS	.	G		438,3968	209.5+/-230.2	35,368,1800	90.0	82.0	85.0			4.7	0.1	13	dbSNP_121	85	3185,5415	480.1+/-370.3	608,1969,1723	yes	splice-3	C13orf26	NM_152325.1		643,2337,3523	AA,AG,GG		37.0349,9.941,27.8564			31531009	3623,9383	2203	4300	6503	SO:0001630	splice_region_variant	122046	exon4			TTGATAGGACATT	BC030277	CCDS9339.1	13q12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000175664	ENSG00000175664			28622	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 26"""	C13orf26		12477932	Standard	NM_152325		Approved	MGC40178	uc001uti.3	Q8N6G2	OTTHUMG00000016682	ENST00000380473.3:c.313-1G>A	13.37:g.31531009G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	65	27	0.415385	NM_152325		Splice_Site	SNP	ENST00000380473.3	37	CCDS9339.1	571	0.26144688644688646	20	0.04065040650406504	116	0.32044198895027626	156	0.2727272727272727	279	0.36807387862796836	G	9.869	1.198433	0.22037	0.09941	0.370349	ENSG00000175664	ENST00000380473	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999998197	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1627	0.59552	0.0:0.0:1.0:0.0	rs12857479;rs17535176;rs12857479	.	.	.	.	-1	.	.	.	+	.	.	C13orf26	30429009	0.910000	0.30920	0.073000	0.20177	0.014000	0.08584	2.665000	0.46791	2.145000	0.66743	0.591000	0.81541	.	G|0.732;A|0.268	0.268	strong		0.403	TEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044380.2	NM_152325	Intron
OR51G1	79324	hgsc.bcm.edu	37	11	4945196	4945196	+	Missense_Mutation	SNP	T	T	G	rs1378739	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4945196T>G	ENST00000321961.2	-	1	441	c.374A>C	c.(373-375)tAc>tCc	p.Y125S	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005237.1	NP_001005237.1	Q8NGK1	O51G1_HUMAN	olfactory receptor, family 51, subfamily G, member 1	125			Y -> S (in dbSNP:rs1378739). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(3)|skin(4)|soft_tissue(1)	25		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.58e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		GACGGCCACGTAGCGGTCAAT	0.507													T|||	3292	0.657348	0.7231	0.6484	5008	,	,		22751	0.7222		0.5686	False		,,,				2504	0.5992				p.Y125S		Atlas-SNP	.											.	OR51G1	74	.	0			c.A374C						PASS	.	T	SER/TYR	3078,1324	695.5+/-405.9	1059,960,182	110.0	98.0	102.0		374	3.0	1.0	11	dbSNP_88	102	4985,3611	625.5+/-397.7	1451,2083,764	yes	missense	OR51G1	NM_001005237.1	144	2510,3043,946	GG,GT,TT		42.0079,30.0772,37.9674	probably-damaging	125/322	4945196	8063,4935	2201	4298	6499	SO:0001583	missense	79324	exon1			GCCACGTAGCGGT	AB065793	CCDS31366.1	11p15.4	2012-08-09			ENSG00000176879	ENSG00000176879		"""GPCR / Class A : Olfactory receptors"""	14738	protein-coding gene	gene with protein product				OR51G3P			Standard	NM_001005237		Approved		uc010qyr.2	Q8NGK1	OTTHUMG00000066532	ENST00000321961.2:c.374A>C	11.37:g.4945196T>G	ENSP00000322546:p.Tyr125Ser	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_001005237	B9EGW8|Q6IFH6	Missense_Mutation	SNP	ENST00000321961.2	37	CCDS31366.1	1442	0.6602564102564102	372	0.7560975609756098	244	0.6740331491712708	410	0.7167832167832168	416	0.5488126649076517	T	9.340	1.062863	0.19987	0.699228	0.579921	ENSG00000176879	ENST00000321961	T	0.57436	0.4	4.2	2.99	0.34606	GPCR, rhodopsin-like superfamily (1);	0.227317	0.22524	U	0.058922	T	0.00012	0.0000	M	0.86953	2.85	0.30227	P	0.796256	P	0.41748	0.761	B	0.37346	0.247	T	0.38542	-0.9656	9	0.87932	D	0	.	9.0162	0.36170	0.1644:0.0:0.0:0.8356	rs1378739;rs17337943	125	Q8NGK1	O51G1_HUMAN	S	125	ENSP00000322546:Y125S	ENSP00000322546:Y125S	Y	-	2	0	OR51G1	4901772	0.085000	0.21516	0.996000	0.52242	0.061000	0.15899	0.375000	0.20518	1.760000	0.52011	0.455000	0.32223	TAC	T|0.355;G|0.645	0.645	strong		0.507	OR51G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142345.1	NM_001005237	
OR51B4	79339	hgsc.bcm.edu	37	11	5323071	5323071	+	Missense_Mutation	SNP	C	C	T	rs7118113	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5323071C>T	ENST00000380224.1	-	1	155	c.106G>A	c.(106-108)Gtc>Atc	p.V36I	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_033179.2	NP_149419.2	Q9Y5P0	O51B4_HUMAN	olfactory receptor, family 51, subfamily B, member 4	36			V -> I (in dbSNP:rs7118113). {ECO:0000269|PubMed:10220430, ECO:0000269|PubMed:15489334}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAAAAAGGACGGAGAAGTAG	0.498													T|||	3408	0.680511	0.4191	0.7392	5008	,	,		20064	0.878		0.6918	False		,,,				2504	0.7771				p.V36I		Atlas-SNP	.											.	OR51B4	64	.	0			c.G106A						PASS	.	T	ILE/VAL	2010,2392	614.9+/-392.5	469,1072,660	93.0	93.0	93.0		106	0.6	0.0	11	dbSNP_116	93	6072,2522	411.2+/-350.4	2152,1768,377	yes	missense	OR51B4	NM_033179.2	29	2621,2840,1037	TT,TC,CC		29.3461,45.6611,37.8116	benign	36/311	5323071	8082,4914	2201	4297	6498	SO:0001583	missense	79339	exon1			AAAGGACGGAGAA	BC069094	CCDS7757.1	11p15.4	2012-08-09			ENSG00000183251	ENSG00000183251		"""GPCR / Class A : Olfactory receptors"""	14708	protein-coding gene	gene with protein product							Standard	NM_033179		Approved		uc010qza.2	Q9Y5P0	OTTHUMG00000066665	ENST00000380224.1:c.106G>A	11.37:g.5323071C>T	ENSP00000369573:p.Val36Ile	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	163	162	0.993865	NM_033179	A7MAV5|Q6NTD7	Missense_Mutation	SNP	ENST00000380224.1	37	CCDS7757.1	1503	0.6881868131868132	209	0.4247967479674797	285	0.787292817679558	490	0.8566433566433567	519	0.6846965699208444	T	4.857	0.159254	0.09236	0.456611	0.706539	ENSG00000183251	ENST00000380224	T	0.00174	8.62	4.39	0.647	0.17796	.	0.437830	0.19154	N	0.121369	T	0.00012	0.0000	N	0.02391	-0.57	0.80722	P	0.0	B	0.11235	0.004	B	0.09377	0.004	T	0.49031	-0.8981	9	0.33940	T	0.23	.	4.0178	0.09652	0.1585:0.3359:0.0:0.5056	rs7118113;rs52804227;rs57571260;rs7118113	36	Q9Y5P0	O51B4_HUMAN	I	36	ENSP00000369573:V36I	ENSP00000369573:V36I	V	-	1	0	OR51B4	5279647	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.096000	0.03353	-0.040000	0.13580	-1.062000	0.02293	GTC	C|0.342;T|0.658	0.658	strong		0.498	OR51B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142956.2	NM_033179	
CLCNKA	1187	hgsc.bcm.edu	37	1	16356501	16356501	+	Missense_Mutation	SNP	G	G	A	rs1805152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16356501G>A	ENST00000331433.4	+	14	1358	c.1339G>A	c.(1339-1341)Gcc>Acc	p.A447T	CLCNKA_ENST00000420078.1_Missense_Mutation_p.A447T|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000375692.1_Missense_Mutation_p.A447T|CLCNKA_ENST00000439316.2_Missense_Mutation_p.A404T			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	447			A -> T (in dbSNP:rs1805152). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.3}.		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	TCTTGCCGTCGCCTTCCCTGA	0.667													G|||	3248	0.648562	0.7496	0.4467	5008	,	,		17134	0.7669		0.5577	False		,,,				2504	0.6268				p.A447T		Atlas-SNP	.											.	CLCNKA	56	.	0			c.G1339A	GRCh37	CM072953	CLCNKA	M	rs1805152	PASS	.	G	THR/ALA,THR/ALA	3140,1266	696.7+/-406.1	1113,914,176	57.0	52.0	54.0		1339,1339	0.3	0.4	1	dbSNP_89	54	4681,3919	600.4+/-394.2	1301,2079,920	yes	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	58,58	2414,2993,1096	AA,AG,GG		45.5698,28.7335,39.8662	benign,benign	447/687,447/688	16356501	7821,5185	2203	4300	6503	SO:0001583	missense	1187	exon14			GCCGTCGCCTTCC		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.1339G>A	1.37:g.16356501G>A	ENSP00000332771:p.Ala447Thr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	104	103	0.990385	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	1382	0.6327838827838828	366	0.7439024390243902	172	0.47513812154696133	429	0.75	415	0.5474934036939314	g	5.346	0.249091	0.10130	0.712665	0.544302	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.92805	-3.11;-3.11;-3.11;-3.11	3.3	0.33	0.15929	Chloride channel, core (2);	0.385560	0.27429	N	0.019415	T	0.00012	0.0000	L	0.35593	1.075	0.40900	P	0.015854000000000035	B;B;B	0.12630	0.006;0.002;0.002	B;B;B	0.12837	0.005;0.008;0.008	T	0.43589	-0.9382	9	0.39692	T	0.17	.	5.6763	0.17751	0.4911:0.0:0.5089:0.0	rs1805152;rs16852321;rs61522399;rs1805152	404;447;447	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	T	447;447;404;447	ENSP00000364844:A447T;ENSP00000410353:A447T;ENSP00000414445:A404T;ENSP00000332771:A447T	ENSP00000332771:A447T	A	+	1	0	CLCNKA	16229088	0.005000	0.15991	0.447000	0.26932	0.113000	0.19764	0.055000	0.14229	0.223000	0.20920	-1.745000	0.00682	GCC	G|0.379;A|0.621	0.621	strong		0.667	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155219662	155219662	+	Missense_Mutation	SNP	G	G	C	rs17031394	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155219662G>C	ENST00000357232.4	-	18	4438	c.4439C>G	c.(4438-4440)aCa>aGa	p.T1480R		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1480	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> R (in dbSNP:rs17031394).		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)		GTAATAAAGTGTGGGAAAAGA	0.478													G|||	861	0.171925	0.1679	0.1138	5008	,	,		19525	0.1528		0.173	False		,,,				2504	0.2372				p.T1480R		Atlas-SNP	.											DCHS2,NS,carcinoma,0,1	DCHS2	594	1	0			c.C4439G						PASS	.	G	ARG/THR	804,3602	321.3+/-297.0	71,662,1470	148.0	153.0	151.0		4439	-10.2	0.0	4	dbSNP_123	151	1519,7081	287.7+/-298.4	146,1227,2927	yes	missense	DCHS2	NM_017639.3	71	217,1889,4397	CC,CG,GG		17.6628,18.2478,17.861	benign	1480/2917	155219662	2323,10683	2203	4300	6503	SO:0001583	missense	54798	exon18			TAAAGTGTGGGAA	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.4439C>G	4.37:g.155219662G>C	ENSP00000349768:p.Thr1480Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	328	0.15018315018315018	74	0.15040650406504066	55	0.15193370165745856	76	0.13286713286713286	123	0.16226912928759896	G	2.409	-0.335762	0.05278	0.182478	0.176628	ENSG00000197410	ENST00000357232	T	0.19532	2.14	5.76	-10.2	0.00374	Cadherin (2);Cadherin-like (1);	1.791620	0.02455	N	0.086019	T	0.00012	0.0000	N	0.04275	-0.24	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.17228	-1.0376	9	0.09084	T	0.74	.	3.735	0.08507	0.1925:0.0767:0.412:0.3188	rs17031394;rs52814635;rs17031394	1480	Q6V1P9	PCD23_HUMAN	R	1480	ENSP00000349768:T1480R	ENSP00000349768:T1480R	T	-	2	0	DCHS2	155439112	0.000000	0.05858	0.000000	0.03702	0.481000	0.33189	-1.181000	0.03085	-1.726000	0.01370	0.650000	0.86243	ACA	G|0.830;C|0.170	0.170	strong		0.478	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
PCDHB10	56126	hgsc.bcm.edu	37	5	140572475	140572475	+	Missense_Mutation	SNP	A	A	C	rs143882112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140572475A>C	ENST00000239446.4	+	1	534	c.350A>C	c.(349-351)tAc>tCc	p.Y117S		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	117	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)			TTTCAGATTTACCGGGCTGAG	0.423													A|||	10	0.00199681	0.0	0.0014	5008	,	,		18659	0.0		0.005	False		,,,				2504	0.0041				p.Y117S		Atlas-SNP	.											.	PCDHB10	177	.	0			c.A350C						PASS	.	A	SER/TYR	3,4397	6.2+/-15.9	0,3,2197	58.0	62.0	60.0		350	0.7	1.0	5	dbSNP_134	60	35,8561	22.8+/-68.1	0,35,4263	no	missense	PCDHB10	NM_018930.3	144	0,38,6460	CC,CA,AA		0.4072,0.0682,0.2924	benign	117/801	140572475	38,12958	2200	4298	6498	SO:0001583	missense	56126	exon1			AGATTTACCGGGC	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.350A>C	5.37:g.140572475A>C	ENSP00000239446:p.Tyr117Ser	Somatic	384	0	0		WXS	Illumina HiSeq	Phase_I	383	192	0.501305	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	A	9.700	1.154338	0.21371	6.82E-4	0.004072	ENSG00000120324	ENST00000239446	T	0.48836	0.8	3.46	0.694	0.18062	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.38957	0.1060	M	0.77313	2.365	0.09310	N	1	B	0.16396	0.017	B	0.16722	0.016	T	0.48990	-0.8985	9	0.87932	D	0	.	8.2003	0.31421	0.5632:0.0:0.0:0.4368	.	117	Q9UN67	PCDBA_HUMAN	S	117	ENSP00000239446:Y117S	ENSP00000239446:Y117S	Y	+	2	0	PCDHB10	140552659	0.000000	0.05858	0.960000	0.40013	0.946000	0.59487	-1.086000	0.03386	0.522000	0.28464	0.449000	0.29647	TAC	A|0.996;C|0.004	0.004	strong		0.423	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
SUCNR1	56670	hgsc.bcm.edu	37	3	151599267	151599267	+	Silent	SNP	C	C	T	rs139804843		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:151599267C>T	ENST00000362032.5	+	3	1041	c.936C>T	c.(934-936)caC>caT	p.H312H	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	312						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	AACTGAGACACAACTTCAAAT	0.433																																					p.H312H		Atlas-SNP	.											.	SUCNR1	31	.	0			c.C936T						PASS	.	C		0,4406		0,0,2203	93.0	94.0	93.0		936	-7.4	0.0	3	dbSNP_134	93	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SUCNR1	NM_033050.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		312/335	151599267	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	56670	exon3			GAGACACAACTTC	AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"""GPCR / Class A : Orphans"""	4542	protein-coding gene	gene with protein product		606381	"""G protein-coupled receptor 91"""	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.936C>T	3.37:g.151599267C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_033050	A8K305|Q8TDQ8	Silent	SNP	ENST00000362032.5	37	CCDS3162.1																																																																																			C|1.000;T|0.000	0.000	weak		0.433	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050	
IGF2R	3482	hgsc.bcm.edu	37	6	160517481	160517481	+	Silent	SNP	C	C	T	rs1803989	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:160517481C>T	ENST00000356956.1	+	45	6814	c.6666C>T	c.(6664-6666)ctC>ctT	p.L2222L	IGF2R_ENST00000475584.1_3'UTR|RP11-288H12.3_ENST00000569097.1_RNA	NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	2222					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ACGGCGATCTCGATGTCGTGT	0.498													C|||	1149	0.229433	0.2564	0.2017	5008	,	,		22131	0.4216		0.0547	False		,,,				2504	0.1943				p.L2222L		Atlas-SNP	.											.	IGF2R	251	.	0			c.C6666T						PASS	.	C		1012,3394	376.3+/-322.0	133,746,1324	287.0	203.0	232.0		6666	-7.7	0.3	6	dbSNP_89	232	493,8107	143.3+/-199.3	15,463,3822	no	coding-synonymous	IGF2R	NM_000876.2		148,1209,5146	TT,TC,CC		5.7326,22.9687,11.5716		2222/2492	160517481	1505,11501	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon45			CGATCTCGATGTC	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.6666C>T	6.37:g.160517481C>T		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	74	59	0.797297	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			C|0.839;T|0.161	0.161	strong		0.498	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
DNAJB8	165721	hgsc.bcm.edu	37	3	128181964	128181964	+	Missense_Mutation	SNP	G	G	A	rs142768827		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:128181964G>A	ENST00000469083.1	-	2	2682	c.125C>T	c.(124-126)gCg>gTg	p.A42V	DNAJB8-AS1_ENST00000471626.1_RNA|DNAJB8_ENST00000319153.3_Missense_Mutation_p.A42V			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	42	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)		CTTCTTCTCCGCCTCCTCCTT	0.592																																					p.A42V		Atlas-SNP	.											.	DNAJB8	34	.	0			c.C125T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	162.0	160.0	161.0		125	4.4	0.8	3	dbSNP_134	161	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAJB8	NM_153330.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	42/233	128181964	1,13005	2203	4300	6503	SO:0001583	missense	165721	exon3			TTCTCCGCCTCCT		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.125C>T	3.37:g.128181964G>A	ENSP00000417418:p.Ala42Val	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	203	75	0.369458	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	37	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.949383	0.53186	0.0	1.16E-4	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.39056	1.1;1.1	4.42	4.42	0.53409	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.76391	-0.2976	10	0.87932	D	0	.	17.0136	0.86413	0.0:0.0:1.0:0.0	.	42	Q8NHS0	DNJB8_HUMAN	V	42	ENSP00000417418:A42V;ENSP00000316053:A42V	ENSP00000316053:A42V	A	-	2	0	DNAJB8	129664654	1.000000	0.71417	0.844000	0.33320	0.003000	0.03518	7.784000	0.85713	2.003000	0.58678	0.561000	0.74099	GCG	G|1.000;A|0.000	0.000	weak		0.592	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
SGK223	157285	hgsc.bcm.edu	37	8	8234714	8234714	+	Missense_Mutation	SNP	C	C	T	rs3896980	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:8234714C>T	ENST00000520004.1	-	3	1469	c.1205G>A	c.(1204-1206)cGg>cAg	p.R402Q	SGK223_ENST00000330777.4_Missense_Mutation_p.R402Q			Q86YV5	SG223_HUMAN		404							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGTAGCCTCCCGGGGGTGGGC	0.642													C|||	2283	0.455871	0.3903	0.4366	5008	,	,		16058	0.6409		0.3052	False		,,,				2504	0.5225				p.R402Q	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G1205A						PASS	.	C	GLN/ARG	1363,2447		257,849,799	28.0	32.0	31.0		1205	1.0	0.0	8	dbSNP_108	31	2494,5700		391,1712,1994	yes	missense	SGK223	NM_001080826.1	43	648,2561,2793	TT,TC,CC		30.4369,35.7743,32.131	probably-damaging	402/1403	8234714	3857,8147	1905	4097	6002	SO:0001583	missense	0	exon2			GCCTCCCGGGGGT																												ENST00000520004.1:c.1205G>A	8.37:g.8234714C>T	ENSP00000428054:p.Arg402Gln	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	78	43	0.551282	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	961	0.440018315018315	202	0.4105691056910569	144	0.39779005524861877	392	0.6853146853146853	223	0.2941952506596306	C	8.815	0.936192	0.18206	0.357743	0.304369	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.57595	0.39;0.39	5.02	1.03	0.20045	.	0.467819	0.18850	N	0.129440	T	0.00012	0.0000	L	0.57536	1.79	0.80722	P	0.0	P	0.40398	0.716	B	0.22880	0.042	T	0.45862	-0.9232	9	0.35671	T	0.21	.	0.8844	0.01241	0.1558:0.3864:0.1731:0.2847	rs3896980;rs60739349	402	Q86YV5	SG223_HUMAN	Q	402	ENSP00000330930:R402Q;ENSP00000428054:R402Q	ENSP00000330930:R402Q	R	-	2	0	AC068353.1	8272124	0.000000	0.05858	0.016000	0.15963	0.307000	0.27823	0.001000	0.13038	0.644000	0.30656	-0.136000	0.14681	CGG	C|0.612;T|0.388	0.388	strong		0.642	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
C18orf8	29919	hgsc.bcm.edu	37	18	21100240	21100240	+	Silent	SNP	C	C	T	rs1367083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:21100240C>T	ENST00000269221.3	+	10	1034	c.924C>T	c.(922-924)ccC>ccT	p.P308P	C18orf8_ENST00000590868.1_Silent_p.P260P	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	308						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					CCGTGCTTCCCGCTCGATCGA	0.532													C|||	3102	0.619409	0.5522	0.6513	5008	,	,		18050	0.8849		0.4742	False		,,,				2504	0.5634				p.P308P		Atlas-SNP	.											.	C18orf8	58	.	0			c.C924T						PASS	.	C		2372,2034	610.4+/-391.6	636,1100,467	139.0	112.0	121.0		924	-11.0	0.0	18	dbSNP_88	121	4103,4497	562.1+/-387.9	968,2167,1165	no	coding-synonymous	C18orf8	NM_013326.3		1604,3267,1632	TT,TC,CC		47.7093,46.1643,49.7847		308/658	21100240	6475,6531	2203	4300	6503	SO:0001819	synonymous_variant	29919	exon10			GCTTCCCGCTCGA	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.924C>T	18.37:g.21100240C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	126	57	0.452381	NM_013326	Q9BU17|Q9Y5M0	Silent	SNP	ENST00000269221.3	37	CCDS32803.1																																																																																			T|0.538;G|0.000;C|0.462;A|0.000	0.538	strong		0.532	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
REPIN1	29803	hgsc.bcm.edu	37	7	150068620	150068620	+	Missense_Mutation	SNP	C	C	T	rs17173703	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:150068620C>T	ENST00000425389.2	+	1	368	c.290C>T	c.(289-291)gCc>gTc	p.A97V	RP4-584D14.5_ENST00000488310.1_RNA|REPIN1_ENST00000397281.2_Missense_Mutation_p.A97V|REPIN1_ENST00000482680.1_3'UTR|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000518462.1_3'UTR|REPIN1_ENST00000444957.1_Missense_Mutation_p.A97V|REPIN1_ENST00000540729.1_Missense_Mutation_p.A97V|REPIN1_ENST00000518514.1_3'UTR|REPIN1_ENST00000489432.2_Missense_Mutation_p.A154V|REPIN1_ENST00000466559.1_3'UTR	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	97			A -> V (in dbSNP:rs17173703).		DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			TTTCGCCATGCCCCCTTCTTA	0.687													C|||	1164	0.232428	0.0227	0.1527	5008	,	,		14808	0.3988		0.2793	False		,,,				2504	0.3528				p.A154V		Atlas-SNP	.											.	REPIN1	74	.	0			c.C461T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	212,4040		8,196,1922	20.0	23.0	22.0		461,290,290,290	3.6	1.0	7	dbSNP_123	22	2231,6223		284,1663,2280	yes	missense,missense,missense,missense	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	64,64,64,64	292,1859,4202	TT,TC,CC		26.3899,4.9859,19.2271	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	154/625,97/568,97/568,97/568	150068620	2443,10263	2126	4227	6353	SO:0001583	missense	29803	exon3			GCCATGCCCCCTT	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.290C>T	7.37:g.150068620C>T	ENSP00000388287:p.Ala97Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Missense_Mutation	SNP	ENST00000425389.2	37	CCDS43677.1	546	0.25	15	0.03048780487804878	63	0.17403314917127072	243	0.42482517482517484	225	0.29683377308707126	C	16.32	3.091429	0.55968	0.049859	0.263899	ENSG00000214022	ENST00000519397;ENST00000540729;ENST00000397281;ENST00000444957;ENST00000489432;ENST00000475514;ENST00000488943;ENST00000461637;ENST00000425389	T;T;T;T;T;T;T;T	0.52754	0.65;2.45;2.45;2.45;2.45;2.45;2.45;2.45	5.54	3.63	0.41609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	.	.	.	.	T	0.00012	0.0000	L	0.39566	1.225	0.33306	P	0.43454800000000005	P;P	0.38745	0.645;0.645	P;B	0.46975	0.533;0.405	T	0.46693	-0.9173	8	0.48119	T	0.1	-8.9286	7.3226	0.26536	0.0:0.6246:0.2862:0.0892	rs17173703	154;97	C9J3L7;Q9BWE0	.;REPI1_HUMAN	V	97;97;97;97;154;156;157;154;97	ENSP00000428562:A97V;ENSP00000445016:A97V;ENSP00000380451:A97V;ENSP00000407714:A97V;ENSP00000417291:A154V;ENSP00000419789:A156V;ENSP00000419872:A157V;ENSP00000388287:A97V	ENSP00000380451:A97V	A	+	2	0	REPIN1	149699553	0.814000	0.29104	0.999000	0.59377	0.982000	0.71751	0.878000	0.28126	1.340000	0.45581	0.462000	0.41574	GCC	C|0.765;T|0.235	0.235	strong		0.687	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
IGSF8	93185	hgsc.bcm.edu	37	1	160062472	160062472	+	Silent	SNP	C	C	T	rs2295622	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:160062472C>T	ENST00000368086.1	-	5	1542	c.1326G>A	c.(1324-1326)gaG>gaA	p.E442E	IGSF8_ENST00000314485.7_Silent_p.E442E|IGSF8_ENST00000460351.1_5'Flank			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	442	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|nervous system development (GO:0007399)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(19)|pancreas(1)|prostate(1)|skin(1)	33	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)			ATGCCACAGCCTCCAGCACCA	0.662													C|||	774	0.154553	0.0189	0.2507	5008	,	,		19452	0.2252		0.1869	False		,,,				2504	0.1636				p.E442E		Atlas-SNP	.											.	IGSF8	59	.	0			c.G1326A						PASS	.	C	,	175,4113		5,165,1974	29.0	27.0	28.0		1326,1326	1.9	1.0	1	dbSNP_100	28	1656,6740		154,1348,2696	no	coding-synonymous,coding-synonymous	IGSF8	NM_001206665.2,NM_052868.4	,	159,1513,4670	TT,TC,CC		19.7237,4.0812,14.4355	,	442/614,442/614	160062472	1831,10853	2144	4198	6342	SO:0001819	synonymous_variant	93185	exon5			CACAGCCTCCAGC	AF407274	CCDS1195.1	1q23.1	2013-01-11			ENSG00000162729	ENSG00000162729		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17813	protein-coding gene	gene with protein product		606644				11504738, 11673522	Standard	NM_001206665		Approved	CD81P3, EWI2, PGRL, CD316	uc009wtf.3	Q969P0	OTTHUMG00000024075	ENST00000368086.1:c.1326G>A	1.37:g.160062472C>T		Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	26	26	1	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Silent	SNP	ENST00000368086.1	37	CCDS1195.1																																																																																			T|0.156;G|0.000;C|0.844	0.156	strong		0.662	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868	
NOL10	79954	hgsc.bcm.edu	37	2	10717806	10717806	+	Missense_Mutation	SNP	C	C	T	rs2287059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:10717806C>T	ENST00000381685.5	-	20	2008	c.1903G>A	c.(1903-1905)Gac>Aac	p.D635N	NOL10_ENST00000538384.1_Missense_Mutation_p.D609N|NOL10_ENST00000345985.3_Missense_Mutation_p.D585N|NOL10_ENST00000542668.1_Missense_Mutation_p.D585N	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	635			D -> N (in dbSNP:rs2287059).			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		ACGGTGGTGTCGGATACACTC	0.333													C|||	668	0.133387	0.0113	0.1844	5008	,	,		20026	0.128		0.2744	False		,,,				2504	0.1227				p.D635N		Atlas-SNP	.											.	NOL10	22	.	0			c.G1903A						PASS	.	C	ASN/ASP	261,4145	148.4+/-182.8	13,235,1955	155.0	131.0	139.0		1903	6.0	1.0	2	dbSNP_100	139	2613,5987	418.0+/-352.6	397,1819,2084	yes	missense	NOL10	NM_024894.2	23	410,2054,4039	TT,TC,CC		30.3837,5.9237,22.0975	benign	635/689	10717806	2874,10132	2203	4300	6503	SO:0001583	missense	79954	exon20			TGGTGTCGGATAC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1903G>A	2.37:g.10717806C>T	ENSP00000371101:p.Asp635Asn	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	212	102	0.481132	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	362	0.16575091575091574	10	0.02032520325203252	75	0.20718232044198895	73	0.12762237762237763	204	0.2691292875989446	C	15.24	2.773842	0.49786	0.059237	0.303837	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.43294	0.95;2.28;1.56;2.28	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.67953	2.075	0.09310	P	0.999999821855	B;B;P	0.35411	0.003;0.003;0.5	B;B;B	0.34038	0.004;0.004;0.174	T	0.26538	-1.0100	9	0.16896	T	0.51	-1.9775	20.4777	0.99188	0.0:1.0:0.0:0.0	rs2287059;rs52834264;rs56708754;rs2287059	609;635;585	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	N	585;635;585;609	ENSP00000263837:D585N;ENSP00000371101:D635N;ENSP00000437625:D585N;ENSP00000439663:D609N	ENSP00000263837:D585N	D	-	1	0	NOL10	10635257	0.997000	0.39634	0.961000	0.40146	0.711000	0.40976	4.025000	0.57225	2.840000	0.97914	0.655000	0.94253	GAC	C|0.810;T|0.190	0.190	strong		0.333	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
HELZ2	85441	hgsc.bcm.edu	37	20	62195087	62195087	+	Silent	SNP	A	A	G	rs310630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62195087A>G	ENST00000467148.1	-	8	5157	c.5088T>C	c.(5086-5088)tcT>tcC	p.S1696S	HELZ2_ENST00000427522.2_Silent_p.S1127S	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1696					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)										CAGAGTAGGCAGAGCCCCCAT	0.677													G|||	2264	0.452077	0.7141	0.4409	5008	,	,		15038	0.1567		0.4732	False		,,,				2504	0.3885				p.S1696S		Atlas-SNP	.											PRIC285,NS,carcinoma,0,3	.	.	3	0			c.T5088C						PASS	.	G	,	2906,1454		977,952,251	13.0	14.0	14.0		5088,3381	-2.3	0.0	20	dbSNP_79	14	3958,4606		948,2062,1272	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	1925,3014,1523	GG,GA,AA		46.2167,33.3486,46.8895	,	1696/2650,1127/2081	62195087	6864,6060	2180	4282	6462	SO:0001819	synonymous_variant	85441	exon9			GTAGGCAGAGCCC	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.5088T>C	20.37:g.62195087A>G		Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	20	11	0.55	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			A|0.512;G|0.488	0.488	strong		0.677	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
ONECUT1	3175	hgsc.bcm.edu	37	15	53081800	53081800	+	Silent	SNP	G	G	C	rs61735385	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:53081800G>C	ENST00000305901.5	-	1	409	c.282C>G	c.(280-282)ccC>ccG	p.P94P	ONECUT1_ENST00000561401.2_Intron	NM_004498.2	NP_004489.1	Q9UBC0	HNF6_HUMAN	one cut homeobox 1	94					B cell differentiation (GO:0030183)|cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|endoderm development (GO:0007492)|epithelial cell development (GO:0002064)|glucose metabolic process (GO:0006006)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|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)|regulation of transcription, DNA-templated (GO:0006355)|spleen development (GO:0048536)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	17				all cancers(107;0.0708)		TCATACCTGGGGGAGTCTCGC	0.672													G|||	220	0.0439297	0.0144	0.0274	5008	,	,		14480	0.005		0.0875	False		,,,				2504	0.091				p.P94P		Atlas-SNP	.											.	ONECUT1	48	.	0			c.C282G						PASS	.	G		112,4276	85.3+/-124.0	1,110,2083	63.0	55.0	58.0		282	3.1	1.0	15	dbSNP_129	58	879,7707	194.8+/-240.1	37,805,3451	no	coding-synonymous	ONECUT1	NM_004498.1		38,915,5534	CC,CG,GG		10.2376,2.5524,7.6384		94/466	53081800	991,11983	2194	4293	6487	SO:0001819	synonymous_variant	3175	exon1			ACCTGGGGGAGTC	U77975	CCDS10150.1	15q21.3	2012-03-09	2007-07-16		ENSG00000169856	ENSG00000169856		"""Homeoboxes / CUT class"""	8138	protein-coding gene	gene with protein product		604164	"""one cut domain, family member 1"""	HNF6, HNF6A		8887657, 8790352	Standard	NM_004498		Approved	HNF-6	uc002aci.2	Q9UBC0	OTTHUMG00000131899	ENST00000305901.5:c.282C>G	15.37:g.53081800G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	96	38	0.395833	NM_004498	B2RTV4|Q99744|Q9UMR6	Silent	SNP	ENST00000305901.5	37	CCDS10150.1																																																																																			G|0.928;C|0.072	0.072	strong		0.672	ONECUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254849.2		
ZNF835	90485	hgsc.bcm.edu	37	19	57175484	57175484	+	Silent	SNP	A	A	G	rs7250003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57175484A>G	ENST00000537055.2	-	2	1314	c.1083T>C	c.(1081-1083)ccT>ccC	p.P361P		NM_001005850.2	NP_001005850.2	Q9Y2P0	ZN835_HUMAN	zinc finger protein 835	361					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P383P(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(22)|pancreas(3)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	47						GGCAGGGGTAAGGCCGCTCTC	0.682													.|||	2374	0.474042	0.6679	0.4078	5008	,	,		16463	0.4732		0.3151	False		,,,				2504	0.4233				p.P361P		Atlas-SNP	.											ZNF835,NS,carcinoma,0,2	ZNF835	106	2	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.T1083C						scavenged	.	G		2885,1519		962,961,279	21.0	21.0	21.0		1083	-2.0	0.0	19	dbSNP_116	21	2566,6026		394,1778,2124	no	coding-synonymous	ZNF835	NM_001005850.2		1356,2739,2403	GG,GA,AA		29.865,34.4914,41.9437		361/538	57175484	5451,7545	2202	4296	6498	SO:0001819	synonymous_variant	90485	exon2			GGGGTAAGGCCGC	AK023017	CCDS56105.1	19q13.43	2013-01-08			ENSG00000127903	ENSG00000127903		"""Zinc fingers, C2H2-type"""	34332	protein-coding gene	gene with protein product							Standard	NM_001005850		Approved	BC37295_3	uc010ygn.2	Q9Y2P0		ENST00000537055.2:c.1083T>C	19.37:g.57175484A>G		Somatic	37	1	0.027027		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_001005850	B7Z5Y0|G3V1S0	Silent	SNP	ENST00000537055.2	37	CCDS56105.1																																																																																			A|0.575;G|0.425	0.425	strong		0.682	ZNF835-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459800.1	NM_001005850	
OR8D2	283160	hgsc.bcm.edu	37	11	124189306	124189306	+	Missense_Mutation	SNP	G	G	A	rs2466620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124189306G>A	ENST00000357438.2	-	1	878	c.788C>T	c.(787-789)cCt>cTt	p.P263L		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	263			P -> L (in dbSNP:rs2466620).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		AGTGCTGGAAGGGGGCTTGAA	0.448													G|||	1390	0.277556	0.4531	0.2003	5008	,	,		18104	0.1895		0.1292	False		,,,				2504	0.3384				p.P263L		Atlas-SNP	.											.	OR8D2	65	.	0			c.C788T						PASS	.	G	LEU/PRO	1863,2539	538.7+/-375.1	384,1095,722	135.0	142.0	140.0		788	1.4	0.0	11	dbSNP_100	140	1278,7320	250.7+/-277.5	112,1054,3133	yes	missense	OR8D2	NM_001002918.1	98	496,2149,3855	AA,AG,GG		14.8639,42.3217,24.1615	benign	263/312	124189306	3141,9859	2201	4299	6500	SO:0001583	missense	283160	exon1			CTGGAAGGGGGCT	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"""GPCR / Class A : Olfactory receptors"""	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.788C>T	11.37:g.124189306G>A	ENSP00000350022:p.Pro263Leu	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	83	40	0.481928	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	520	0.23809523809523808	224	0.45528455284552843	71	0.19613259668508287	124	0.21678321678321677	101	0.13324538258575197	g	14.01	2.407143	0.42715	0.423217	0.148639	ENSG00000197263	ENST00000357438	T	0.00164	8.64	3.34	1.41	0.22369	GPCR, rhodopsin-like superfamily (1);	0.294224	0.24506	N	0.037940	T	0.00012	0.0000	N	0.26162	0.8	0.80722	P	0.0	P	0.40000	0.698	B	0.43413	0.419	T	0.00001	-1.2671	9	0.66056	D	0.02	.	8.25	0.31712	0.0937:0.4291:0.4772:0.0	rs2466620;rs52820798;rs59068946;rs2466620	263	Q9GZM6	OR8D2_HUMAN	L	263	ENSP00000350022:P263L	ENSP00000350022:P263L	P	-	2	0	OR8D2	123694516	0.008000	0.16893	0.003000	0.11579	0.975000	0.68041	1.552000	0.36244	0.435000	0.26365	0.530000	0.56133	CCT	G|0.761;A|0.239	0.239	strong		0.448	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918	
TYK2	7297	hgsc.bcm.edu	37	19	10472452	10472452	+	Silent	SNP	G	G	A	rs12720355	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10472452G>A	ENST00000525621.1	-	13	2434	c.1953C>T	c.(1951-1953)atC>atT	p.I651I	TYK2_ENST00000524462.1_Silent_p.I466I|TYK2_ENST00000529370.1_Silent_p.I651I|TYK2_ENST00000264818.6_Silent_p.I651I	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	651	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			TCACCAGGGCGATGTCATGGT	0.652													g|||	25	0.00499201	0.0008	0.0058	5008	,	,		15733	0.0		0.0139	False		,,,				2504	0.0061				p.I651I		Atlas-SNP	.											.	TYK2	126	.	0			c.C1953T						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	83.0	81.0	82.0		1953	-3.9	0.4	19	dbSNP_121	82	132,8468	66.7+/-129.0	1,130,4169	no	coding-synonymous	TYK2	NM_003331.4		1,143,6359	AA,AG,GG		1.5349,0.2951,1.1149		651/1188	10472452	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	7297	exon13			CAGGGCGATGTCA		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.1953C>T	19.37:g.10472452G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_003331	Q6QB10|Q96CH0	Silent	SNP	ENST00000525621.1	37	CCDS12236.1																																																																																			G|0.992;A|0.008	0.008	strong		0.652	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	rs6004901	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26423124G>C	ENST00000407587.2	+	43	7356	c.7187G>C	c.(7186-7188)gGc>gCc	p.G2396A	MYO18B_ENST00000335473.7_Missense_Mutation_p.G2395A|MYO18B_ENST00000536101.1_Missense_Mutation_p.G2395A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2395						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GACGATGCGGGCTGTCCAGAC	0.592													G|||	488	0.0974441	0.2663	0.0476	5008	,	,		15885	0.004		0.0348	False		,,,				2504	0.0654				p.G2395A		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7184C						PASS	.	G	ALA/GLY	855,3101		95,665,1218	66.0	72.0	70.0		7184	-1.6	0.0	22	dbSNP_114	70	253,8029		6,241,3894	yes	missense	MYO18B	NM_032608.5	60	101,906,5112	CC,CG,GG		3.0548,21.6127,9.0538	benign	2395/2568	26423124	1108,11130	1978	4141	6119	SO:0001583	missense	84700	exon43			ATGCGGGCTGTCC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7187G>C	22.37:g.26423124G>C	ENSP00000386096:p.Gly2396Ala	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		166|166	0.076007326007326|0.076007326007326	119|119	0.241869918699187|0.241869918699187	22|22	0.06077348066298342|0.06077348066298342	4|4	0.006993006993006993|0.006993006993006993	21|21	0.027704485488126648|0.027704485488126648	G|G	0.007|0.007	-1.985354|-1.985354	0.00443|0.00443	0.216127|0.216127	0.030548|0.030548	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.86956	.|-2.17;-2.17;-2.19	5.12|5.12	-1.6|-1.6	0.08426|0.08426	.|.	.|0.491877	.|0.18417	.|N	.|0.141867	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.06786	.|0.001;0.001;0.001;0.001;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.001;0.003;0.003	T|T	0.02877|0.02877	-1.1099|-1.1099	4|9	.|0.19147	.|T	.|0.46	.|.	1.509|1.509	0.02492|0.02492	0.1649:0.2383:0.3545:0.2424|0.1649:0.2383:0.3545:0.2424	rs6004901;rs52824215;rs6004901|rs6004901;rs52824215;rs6004901	.|1908;2397;2395;2396;2395	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	P|A	345|2395;2395;2396	.|ENSP00000441229:G2395A;ENSP00000334563:G2395A;ENSP00000386096:G2396A	.|ENSP00000334563:G2395A	A|G	+|+	1|2	0|0	MYO18B|MYO18B	24753124|24753124	0.003000|0.003000	0.15002|0.15002	0.011000|0.011000	0.14972|0.14972	0.130000|0.130000	0.20726|0.20726	0.135000|0.135000	0.15952|0.15952	0.154000|0.154000	0.19237|0.19237	-0.264000|-0.264000	0.10439|0.10439	GCT|GGC	G|0.912;C|0.088	0.088	strong		0.592	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
QSOX1	5768	hgsc.bcm.edu	37	1	180165582	180165582	+	Missense_Mutation	SNP	C	C	T	rs140386908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:180165582C>T	ENST00000367602.3	+	12	1728	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W	QSOX1_ENST00000367600.5_Missense_Mutation_p.R552W			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	552					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						GTCAGCTGCCCGGAGGGATGT	0.617													C|||	5	0.000998403	0.0	0.0	5008	,	,		17428	0.0		0.005	False		,,,				2504	0.0				p.R552W		Atlas-SNP	.											QSOX1,NS,carcinoma,-2,1	QSOX1	79	1	0			c.C1654T						PASS	.	C	TRP/ARG,TRP/ARG	6,4400	11.4+/-27.6	0,6,2197	94.0	102.0	99.0		1654,1654	0.0	0.0	1	dbSNP_134	99	44,8556	29.0+/-79.6	0,44,4256	yes	missense,missense	QSOX1	NM_001004128.2,NM_002826.4	101,101	0,50,6453	TT,TC,CC		0.5116,0.1362,0.3844	benign,benign	552/605,552/748	180165582	50,12956	2203	4300	6503	SO:0001583	missense	5768	exon12			GCTGCCCGGAGGG	U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1654C>T	1.37:g.180165582C>T	ENSP00000356574:p.Arg552Trp	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	176	81	0.460227	NM_002826	Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	37	CCDS1337.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	11.89	1.774377	0.31411	0.001362	0.005116	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.05855	3.49;3.38	5.31	0.0275	0.14155	.	0.938345	0.09080	N	0.851519	T	0.03095	0.0091	L	0.31926	0.97	0.09310	N	1	B;B;B;B	0.19073	0.019;0.019;0.013;0.033	B;B;B;B	0.10450	0.002;0.002;0.003;0.005	T	0.43393	-0.9394	10	0.48119	T	0.1	-5.4642	2.0394	0.03547	0.1298:0.4214:0.2287:0.2201	.	552;552;552;552	A8K4C2;A8K477;O00391;O00391-2	.;.;QSOX1_HUMAN;.	W	552	ENSP00000356574:R552W;ENSP00000356572:R552W	ENSP00000356572:R552W	R	+	1	2	QSOX1	178432205	0.002000	0.14202	0.014000	0.15608	0.022000	0.10575	0.308000	0.19314	0.591000	0.29711	0.511000	0.50034	CGG	C|0.997;T|0.003	0.003	strong		0.617	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1	NM_002826	
GNAT3	346562	hgsc.bcm.edu	37	7	80088041	80088041	+	Silent	SNP	G	G	A	rs2074674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:80088041G>A	ENST00000398291.3	-	8	1104	c.1011C>T	c.(1009-1011)gaC>gaT	p.D337D	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	337					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						CTGTAACTGCGTCAAACACAA	0.338													A|||	2341	0.467452	0.4168	0.4481	5008	,	,		16205	0.7421		0.3201	False		,,,				2504	0.4182				p.D337D		Atlas-SNP	.											GNAT3_ENST00000398291,NS,carcinoma,0,2	GNAT3	65	2	0			c.C1011T						PASS	.	A		1537,2159		327,883,638	80.0	80.0	80.0		1011	3.2	1.0	7	dbSNP_96	80	2628,5574		444,1740,1917	no	coding-synonymous	GNAT3	NM_001102386.1		771,2623,2555	AA,AG,GG		32.041,41.5855,35.0059		337/355	80088041	4165,7733	1848	4101	5949	SO:0001819	synonymous_variant	346562	exon8			AACTGCGTCAAAC		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.1011C>T	7.37:g.80088041G>A		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Silent	SNP	ENST00000398291.3	37	CCDS47625.1																																																																																			G|0.553;A|0.447	0.447	strong		0.338	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	
UFSP1	402682	hgsc.bcm.edu	37	7	100486754	100486754	+	Missense_Mutation	SNP	G	G	C	rs12666989	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100486754G>C	ENST00000388761.2	-	1	585	c.139C>G	c.(139-141)Ctg>Gtg	p.L47V		NM_001015072.3	NP_001015072.2	Q6NVU6	UFSP1_HUMAN	UFM1-specific peptidase 1 (non-functional)	47			L -> V (in dbSNP:rs12666989). {ECO:0000269|PubMed:12690205, ECO:0000269|PubMed:14702039}.			extracellular vesicular exosome (GO:0070062)	thiolester hydrolase activity (GO:0016790)|UFM1 hydrolase activity (GO:0071567)			lung(1)|stomach(1)	2	Lung NSC(181;0.041)|all_lung(186;0.0581)					AGCCTCTCCAGCTCCCCGTGC	0.692													G|||	443	0.0884585	0.0416	0.1023	5008	,	,		14356	0.0308		0.1829	False		,,,				2504	0.1043				p.L47V		Atlas-SNP	.											.	UFSP1	8	.	0			c.C139G						PASS	.	G	VAL/LEU	248,4154		6,236,1959	28.0	29.0	28.0	http://www.ncbi.nlm.nih.gov/pubmed?term	139	2.5	0.1	7	dbSNP_120	28	1532,7068		151,1230,2919	yes	missense	UFSP1	NM_001015072.3	32	157,1466,4878	CC,CG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	17.814,5.6338,13.6902	benign	47/143	100486754	1780,11222	2201	4300	6501	SO:0001583	missense	402682	exon1			TCTCCAGCTCCCC	AF312032	CCDS34710.1	7q22.1	2008-03-25			ENSG00000176125	ENSG00000176125			33821	protein-coding gene	gene with protein product		611481				17182609, 18321862	Standard	NM_001015072		Approved	UFSP	uc003uxc.4	Q6NVU6	OTTHUMG00000159662	ENST00000388761.2:c.139C>G	7.37:g.100486754G>C	ENSP00000373413:p.Leu47Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	63	32	0.507937	NM_001015072	A4D2E4|A8K8V2|B6ZDG6|Q9BXP6	Missense_Mutation	SNP	ENST00000388761.2	37	CCDS34710.1	231	0.10576923076923077	21	0.042682926829268296	43	0.11878453038674033	19	0.033216783216783216	148	0.19525065963060687	G	0.030	-1.339530	0.01277	0.056338	0.17814	ENSG00000176125	ENST00000388761	T	0.29655	1.56	4.43	2.54	0.30619	.	0.545587	0.15337	N	0.267700	T	0.00012	0.0000	N	0.17872	0.535	0.48901	P	2.769999999999717E-4	P	0.42078	0.77	B	0.41299	0.353	T	0.20940	-1.0260	9	0.12430	T	0.62	-22.0861	7.534	0.27700	0.0963:0.1689:0.7348:0.0	rs12666989;rs17880260;rs12666989	47	Q6NVU6	UFSP1_HUMAN	V	47	ENSP00000373413:L47V	ENSP00000373413:L47V	L	-	1	2	UFSP1	100324690	0.022000	0.18835	0.111000	0.21465	0.010000	0.07245	0.527000	0.22987	0.567000	0.29293	0.484000	0.47621	CTG	G|0.879;C|0.121	0.121	strong		0.692	UFSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356751.1	NM_001015072	
C17orf97	400566	hgsc.bcm.edu	37	17	263592	263592	+	Missense_Mutation	SNP	G	G	A	rs71369083|rs71145728|rs532458474|rs71369084		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:263592G>A	ENST00000360127.6	+	2	974	c.958G>A	c.(958-960)Gag>Aag	p.E320K	AC108004.3_ENST00000466740.2_RNA|C17orf97_ENST00000571106.1_Intron	NM_001013672.4	NP_001013694.4	Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	350	20 X 10 AA approximative tandem repeat of A-L-K-G-F-H-P-D-P-E.									breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						CACTGACCCCGAGGCCCTCAA	0.692																																					p.E320K		Atlas-SNP	.											C17orf97_ENST00000360127,NS,haematopoietic_neoplasm,0,1	C17orf97	76	1	0			c.G958A						scavenged	.						20.0	24.0	23.0					17																	263592		2197	4297	6494	SO:0001583	missense	400566	exon2			GACCCCGAGGCCC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000360127.6:c.958G>A	17.37:g.263592G>A	ENSP00000353245:p.Glu320Lys	Somatic	287	0	0		WXS	Illumina HiSeq	Phase_I	172	5	0.0290698	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000360127.6	37	CCDS32519.2	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.608547	0.00842	.	.	ENSG00000187624	ENST00000360127	T	0.31247	1.5	2.05	-4.1	0.03940	.	.	.	.	.	T	0.09862	0.0242	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22661	-1.0210	9	0.09843	T	0.71	.	1.1097	0.01701	0.4009:0.1978:0.2653:0.136	.	320	Q6ZQX7-4	.	K	320	ENSP00000353245:E320K	ENSP00000353245:E320K	E	+	1	0	C17orf97	263938	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.949000	0.03893	-2.563000	0.00472	-0.974000	0.02594	GAG	G|0.020;A|0.980	0.980	strong		0.692	C17orf97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255648.4	NM_001013672	
PLIN4	729359	hgsc.bcm.edu	37	19	4512890	4512890	+	Missense_Mutation	SNP	G	G	A	rs199944112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4512890G>A	ENST00000301286.3	-	3	1039	c.1040C>T	c.(1039-1041)aCt>aTt	p.T347I		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	347	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						AGTTAGGACAGTCTTGGTGGT	0.577													G|||	613	0.122404	0.3404	0.0735	5008	,	,		19607	0.001		0.0765	False		,,,				2504	0.0348				p.T347I		Atlas-SNP	.											.	PLIN4	191	.	0			c.C1040T						PASS	.						45.0	88.0	76.0					19																	4512890		1706	4160	5866	SO:0001583	missense	729359	exon3			AGGACAGTCTTGG	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.1040C>T	19.37:g.4512890G>A	ENSP00000301286:p.Thr347Ile	Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	67	65	0.970149	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756798	0.49362	.	.	ENSG00000167676	ENST00000301286	T	0.05319	3.46	4.58	-2.82	0.05787	.	0.834705	0.10002	U	0.728326	T	0.06735	0.0172	M	0.63428	1.95	0.09310	N	1	P	0.49185	0.92	B	0.42386	0.386	T	0.29852	-0.9998	10	0.39692	T	0.17	-0.7204	3.5654	0.07897	0.0837:0.1338:0.3723:0.4103	.	347	Q96Q06	PLIN4_HUMAN	I	347	ENSP00000301286:T347I	ENSP00000301286:T347I	T	-	2	0	PLIN4	4463890	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.482000	0.22276	0.054000	0.16065	-0.373000	0.07131	ACT	G|0.996;A|0.004	0.004	weak		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
CLCNKA	1187	hgsc.bcm.edu	37	1	16351275	16351275	+	Missense_Mutation	SNP	A	A	G	rs10927887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16351275A>G	ENST00000331433.4	+	4	266	c.247A>G	c.(247-249)Agg>Ggg	p.R83G	CLCNKA_ENST00000420078.1_Missense_Mutation_p.R83G|CLCNKA_ENST00000464764.1_Intron|CLCNKA_ENST00000375692.1_Missense_Mutation_p.R83G|CLCNKA_ENST00000439316.2_Intron			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	83			R -> G (in dbSNP:rs10927887). {ECO:0000269|Ref.3}.		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	GTGGCTGTACAGGGAGATTGG	0.617													G|||	3220	0.642971	0.7201	0.4467	5008	,	,		9165	0.7688		0.5636	False		,,,				2504	0.6299				p.R83G		Atlas-SNP	.											.	CLCNKA	56	.	0			c.A247G						PASS	.	G	GLY/ARG,GLY/ARG	3067,1339	445.9+/-347.8	1060,947,196	101.0	77.0	85.0		247,247	0.9	1.0	1	dbSNP_120	85	4748,3852	542.8+/-384.3	1336,2076,888	no	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	125,125	2396,3023,1084	GG,GA,AA		44.7907,30.3904,39.9123	benign,benign	83/687,83/688	16351275	7815,5191	2203	4300	6503	SO:0001583	missense	1187	exon4			CTGTACAGGGAGA		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.247A>G	1.37:g.16351275A>G	ENSP00000332771:p.Arg83Gly	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	133	132	0.992481	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	1365	0.625	348	0.7073170731707317	172	0.47513812154696133	428	0.7482517482517482	417	0.5501319261213721	G	4.371	0.068461	0.08436	0.696096	0.552093	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000331433	D;D;D	0.92495	-3.05;-3.05;-3.05	4.0	0.872	0.19113	Chloride channel, core (2);	0.865352	0.10003	N	0.728172	T	0.00012	0.0000	L	0.45352	1.415	0.41837	P	0.009898999999999991	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46414	-0.9193	9	0.28530	T	0.3	.	7.3212	0.26528	0.3182:0.3866:0.2951:0.0	rs10927887	83;83	Q5T5Q4;P51800	.;CLCKA_HUMAN	G	83	ENSP00000364844:R83G;ENSP00000410353:R83G;ENSP00000332771:R83G	ENSP00000332771:R83G	R	+	1	2	CLCNKA	16223862	0.847000	0.29606	0.991000	0.47740	0.505000	0.33919	0.593000	0.23999	-0.153000	0.11137	-1.325000	0.01285	AGG	A|0.397;G|0.603	0.603	strong		0.617	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
EPHB4	2050	hgsc.bcm.edu	37	7	100410597	100410597	+	Silent	SNP	G	G	A	rs2230585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100410597G>A	ENST00000358173.3	-	12	2358	c.1890C>T	c.(1888-1890)tgC>tgT	p.C630C	EPHB4_ENST00000477446.1_5'Flank|EPHB4_ENST00000360620.3_Silent_p.C630C	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	630	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					GCCGCCCCCGGCACACCTCGC	0.647													G|||	1380	0.275559	0.1641	0.2867	5008	,	,		16499	0.3115		0.3668	False		,,,				2504	0.2873				p.C630C	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.C1890T						PASS	.	G		924,3482	354.9+/-312.8	91,742,1370	101.0	106.0	105.0		1890	2.9	1.0	7	dbSNP_98	105	3324,5276	494.2+/-373.8	632,2060,1608	no	coding-synonymous	EPHB4	NM_004444.4		723,2802,2978	AA,AG,GG		38.6512,20.9714,32.6618		630/988	100410597	4248,8758	2203	4300	6503	SO:0001819	synonymous_variant	2050	exon12			CCCCCGGCACACC	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.1890C>T	7.37:g.100410597G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	99	46	0.464646	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	37	CCDS5706.1																																																																																			G|0.683;A|0.317	0.317	strong		0.647	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
FLNC	2318	hgsc.bcm.edu	37	7	128477472	128477472	+	Silent	SNP	T	T	C	rs2291560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:128477472T>C	ENST00000325888.8	+	4	981	c.720T>C	c.(718-720)atT>atC	p.I240I	FLNC_ENST00000346177.6_Silent_p.I240I	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	240	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						CTGAGGAGATTGTGGACCCCA	0.577													C|||	610	0.121805	0.1248	0.062	5008	,	,		15037	0.121		0.1093	False		,,,				2504	0.1738				p.I240I		Atlas-SNP	.											.	FLNC	339	.	0			c.T720C						PASS	.	C	,	553,3797	223.3+/-239.8	39,475,1661	149.0	157.0	155.0		720,720	-9.7	0.6	7	dbSNP_100	155	952,7628	202.8+/-246.0	49,854,3387	no	coding-synonymous,coding-synonymous	FLNC	NM_001127487.1,NM_001458.4	,	88,1329,5048	CC,CT,TT		11.0956,12.7126,11.6396	,	240/2693,240/2726	128477472	1505,11425	2175	4290	6465	SO:0001819	synonymous_variant	2318	exon4			GGAGATTGTGGAC	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.720T>C	7.37:g.128477472T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	37	CCDS43644.1																																																																																			T|0.879;C|0.121	0.121	strong		0.577	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
TIMM50	92609	hgsc.bcm.edu	37	19	39980412	39980412	+	Silent	SNP	C	C	T	rs114194716	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39980412C>T	ENST00000607714.1	+	11	1036	c.1014C>T	c.(1012-1014)ttC>ttT	p.F338F	TIMM50_ENST00000599794.1_Silent_p.F142F|TIMM50_ENST00000314349.4_Silent_p.F441F|TIMM50_ENST00000544017.1_Silent_p.F225F			Q3ZCQ8	TIM50_HUMAN	translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)	338					cellular protein metabolic process (GO:0044267)|mitochondrial membrane organization (GO:0007006)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein targeting to mitochondrion (GO:0006626)|release of cytochrome c from mitochondria (GO:0001836)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial inner membrane presequence translocase complex (GO:0005744)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)	interleukin-2 receptor binding (GO:0005134)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)			NS(1)|endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)	14	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGAACCTCTTCCTTGGCTCCC	0.632													C|||	21	0.00419329	0.0008	0.0014	5008	,	,		16246	0.0		0.0089	False		,,,				2504	0.0102				p.F441F		Atlas-SNP	.											.	TIMM50	37	.	0			c.C1323T						PASS	.	C		17,4389	20.2+/-43.8	0,17,2186	65.0	58.0	61.0		1323	5.6	1.0	19	dbSNP_132	61	101,8499	54.4+/-115.2	0,101,4199	no	coding-synonymous	TIMM50	NM_001001563.1		0,118,6385	TT,TC,CC		1.1744,0.3858,0.9073		441/457	39980412	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	92609	exon11			CCTCTTCCTTGGC	BC009072	CCDS33023.1	19q13.2	2010-06-21	2006-04-04		ENSG00000105197	ENSG00000105197		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	23656	protein-coding gene	gene with protein product		607381	"""translocase of inner mitochondrial membrane 50 homolog (yeast)"""			12437925	Standard	NM_001001563		Approved	TIM50L	uc002olu.1	Q3ZCQ8		ENST00000607714.1:c.1014C>T	19.37:g.39980412C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	93	38	0.408602	NM_001001563	Q330K1|Q6QA00|Q96FJ5|Q96GY2|Q9H370	Silent	SNP	ENST00000607714.1	37																																																																																				C|0.991;T|0.009	0.009	strong		0.632	TIMM50-021	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470728.1	NM_001001563	
MMP24	10893	hgsc.bcm.edu	37	20	33834708	33834708	+	Silent	SNP	G	G	A	rs3764733	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:33834708G>A	ENST00000246186.6	+	2	397	c.312G>A	c.(310-312)gcG>gcA	p.A104A	EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000433764.1_RNA|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000566203.2_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	104					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	TGCACTCAGCGAAGGCCTTGC	0.507													G|||	737	0.147165	0.1165	0.1844	5008	,	,		21404	0.0615		0.1859	False		,,,				2504	0.2106				p.A104A		Atlas-SNP	.											.	MMP24	35	.	0			c.G312A						PASS	.	G		558,3502		41,476,1513	139.0	132.0	135.0		312	2.4	1.0	20	dbSNP_107	135	1593,6809		167,1259,2775	no	coding-synonymous	MMP24	NM_006690.3		208,1735,4288	AA,AG,GG		18.9598,13.7438,17.2605		104/646	33834708	2151,10311	2030	4201	6231	SO:0001819	synonymous_variant	10893	exon2			CTCAGCGAAGGCC	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"""membrane-type 5 matrix metalloproteinase"""	604871	"""matrix metalloproteinase 24 (membrane-inserted)"""			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.312G>A	20.37:g.33834708G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	197	100	0.507614	NM_006690	B7ZBG8|Q9H440	Silent	SNP	ENST00000246186.6	37	CCDS46593.1																																																																																			G|0.841;A|0.159	0.159	strong		0.507	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690	
ALPPL2	251	hgsc.bcm.edu	37	2	233271669	233271669	+	Missense_Mutation	SNP	C	C	T	rs16836187|rs139018608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233271669C>T	ENST00000295453.3	+	1	117	c.65C>T	c.(64-66)cCa>cTa	p.P22L		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	22					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	GGCATCATCCCAGGTAATGAG	0.647																																					p.P22L		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C65T						PASS	.						72.0	75.0	74.0					2																	233271669		2203	4300	6503	SO:0001583	missense	251	exon1			TCATCCCAGGTAA	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.65C>T	2.37:g.233271669C>T	ENSP00000295453:p.Pro22Leu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	203	19	0.0935961	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679525	0.47886	.	.	ENSG00000163286	ENST00000295453	D	0.83673	-1.75	2.19	2.19	0.27852	Alkaline-phosphatase-like, core domain (1);	0.185016	0.47093	D	0.000260	T	0.81187	0.4770	M	0.87097	2.86	0.58432	D	0.999995	P	0.44139	0.827	B	0.37304	0.246	T	0.82715	-0.0320	10	0.66056	D	0.02	.	7.8156	0.29258	0.2487:0.7513:0.0:0.0	rs16836187	22	P10696	PPBN_HUMAN	L	22	ENSP00000295453:P22L	ENSP00000295453:P22L	P	+	2	0	ALPPL2	232979913	0.080000	0.21391	0.999000	0.59377	0.074000	0.17049	0.145000	0.16157	1.528000	0.49103	0.205000	0.17691	CCA	C|1.000;|0.000	.	weak		0.647	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
HAP1	9001	hgsc.bcm.edu	37	17	39883350	39883350	+	Missense_Mutation	SNP	G	G	A	rs4523977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39883350G>A	ENST00000310778.5	-	10	1487	c.1478C>T	c.(1477-1479)aCg>aTg	p.T493M	HAP1_ENST00000341193.5_Missense_Mutation_p.T424M|HAP1_ENST00000347901.4_Missense_Mutation_p.T441M|HAP1_ENST00000393939.2_Missense_Mutation_p.T416M|JUP_ENST00000540235.1_Intron			P54257	HAP1_HUMAN	huntingtin-associated protein 1	493	Glu-rich.		T -> M (may influence the age-at-onset of Huntington disease; increases binding to mutated HTT; influences HTT degradation; dbSNP:rs4523977). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18192679}.		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)			CCTTAGAGACGTTCTGAGCTC	0.572													G|||	996	0.198882	0.0121	0.2017	5008	,	,		17882	0.249		0.2346	False		,,,				2504	0.3609				p.T441M		Atlas-SNP	.											.	HAP1	48	.	0			c.C1322T						PASS	.	G	MET/THR,MET/THR,MET/THR	194,4212	116.3+/-154.2	7,180,2016	37.0	38.0	38.0	http://www.ncbi.nlm.nih.gov/omim/143100,600947|http://omim.org/entry/600947|http://omim.org/entry/143100	1271,1247,1322	-4.3	0.0	17	dbSNP_111	38	1896,6704	301.4+/-305.4	213,1470,2617	yes	missense,missense,missense	HAP1	NM_001079870.1,NM_001079871.1,NM_177977.2	81,81,81	220,1650,4633	AA,AG,GG		22.0465,4.4031,16.0695	benign,benign,benign	424/603,416/595,441/620	39883350	2090,10916	2203	4300	6503	SO:0001583	missense	9001	exon9			AGAGACGTTCTGA	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.1478C>T	17.37:g.39883350G>A	ENSP00000309392:p.Thr493Met	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	40	21	0.525	NM_177977	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		439	0.20100732600732601	14	0.028455284552845527	78	0.2154696132596685	164	0.2867132867132867	183	0.24142480211081793	G	2.601	-0.293044	0.05568	0.044031	0.220465	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.07114	3.22;3.58;3.34;3.23	3.61	-4.26	0.03755	.	1.151170	0.06867	N	0.800198	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B;B;B;B	0.34181	0.44;0.44;0.44;0.066	B;B;B;B	0.21917	0.037;0.037;0.037;0.006	T	0.48559	-0.9025	9	0.28530	T	0.3	-0.8888	5.3193	0.15872	0.5082:0.1489:0.3429:0.0	rs4523977;rs52821238;rs56495117;rs57455245;rs4523977	416;424;441;493	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	M	416;493;441;424	ENSP00000377513:T416M;ENSP00000309392:T493M;ENSP00000334002:T441M;ENSP00000343170:T424M	ENSP00000309392:T493M	T	-	2	0	HAP1	37136876	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.167000	0.03126	-1.024000	0.03338	-0.224000	0.12420	ACG	G|0.825;A|0.175	0.175	strong		0.572	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949	
KIF26A	26153	hgsc.bcm.edu	37	14	104642422	104642422	+	Silent	SNP	A	A	G	rs3742947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:104642422A>G	ENST00000423312.2	+	12	3297	c.3297A>G	c.(3295-3297)gcA>gcG	p.A1099A	KIF26A_ENST00000315264.7_Silent_p.A960A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1099					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)		TGGAGGGGGCAGCCTGGGCCG	0.687													G|||	1559	0.311302	0.1437	0.3617	5008	,	,		14259	0.4067		0.3062	False		,,,				2504	0.409				p.A1099A		Atlas-SNP	.											.	KIF26A	84	.	0			c.A3297G						PASS	.	G		464,2976		33,398,1289	4.0	6.0	6.0		3297	-8.6	0.0	14	dbSNP_107	6	2073,5659		312,1449,2105	no	coding-synonymous	KIF26A	NM_015656.1		345,1847,3394	GG,GA,AA		26.8107,13.4884,22.7086		1099/1883	104642422	2537,8635	1720	3866	5586	SO:0001819	synonymous_variant	26153	exon12			GGGGGCAGCCTGG	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.3297A>G	14.37:g.104642422A>G		Somatic	19	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			A|0.697;G|0.303	0.303	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
KIAA1614	57710	hgsc.bcm.edu	37	1	180905263	180905263	+	Missense_Mutation	SNP	C	C	T	rs17302207	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:180905263C>T	ENST00000367588.4	+	5	2273	c.2218C>T	c.(2218-2220)Cgg>Tgg	p.R740W	KIAA1614_ENST00000367587.1_Missense_Mutation_p.R361W	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	740			R -> W (in dbSNP:rs17302207).							NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						TTTGGATTCCCGGACTCCATG	0.642													C|||	117	0.0233626	0.003	0.0692	5008	,	,		17612	0.0		0.0358	False		,,,				2504	0.0297				p.R740W		Atlas-SNP	.											.	KIAA1614	75	.	0			c.C2218T						PASS	.	C	TRP/ARG	45,3985		0,45,1970	57.0	62.0	60.0		2218	-8.6	0.0	1	dbSNP_123	60	349,8013		6,337,3838	yes	missense	KIAA1614	NM_020950.1	101	6,382,5808	TT,TC,CC		4.1736,1.1166,3.1795	benign	740/1191	180905263	394,11998	2015	4181	6196	SO:0001583	missense	57710	exon5			GATTCCCGGACTC	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.2218C>T	1.37:g.180905263C>T	ENSP00000356560:p.Arg740Trp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	61	36	0.590164	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	46	0.021062271062271064	4	0.008130081300813009	14	0.03867403314917127	0	0.0	28	0.036939313984168866	C	10.90	1.480064	0.26598	0.011166	0.041736	ENSG00000135835	ENST00000367588;ENST00000367587	T;T	0.23754	2.48;1.89	4.32	-8.65	0.00870	.	2.031530	0.02031	N	0.048510	T	0.02929	0.0087	N	0.17082	0.46	0.37269	D	0.907335	B	0.02656	0.0	B	0.01281	0.0	T	0.18493	-1.0335	9	0.72032	D	0.01	2.9363	5.955	0.19269	0.3127:0.1783:0.0:0.5089	rs17302207;rs52825007;rs17302207	740	Q5VZ46	K1614_HUMAN	W	740;361	ENSP00000356560:R740W;ENSP00000356559:R361W	ENSP00000356559:R361W	R	+	1	2	KIAA1614	179171886	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.418000	0.00478	-2.123000	0.00823	-0.291000	0.09656	CGG	C|0.975;T|0.025	0.025	strong		0.642	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
OR9K2	441639	hgsc.bcm.edu	37	12	55524172	55524172	+	Missense_Mutation	SNP	G	G	A	rs7306491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55524172G>A	ENST00000305377.5	+	1	708	c.620G>A	c.(619-621)cGc>cAc	p.R207H		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	207			R -> H (in dbSNP:rs7306491).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						TGTGATTCTCGCCCACTTCAG	0.358													G|||	1521	0.303714	0.4062	0.2435	5008	,	,		21809	0.1141		0.334	False		,,,				2504	0.3722				p.R207H		Atlas-SNP	.											.	OR9K2	63	.	0			c.G620A						PASS	.	G	HIS/ARG	1696,2710	512.4+/-368.1	304,1088,811	133.0	124.0	127.0		620	4.1	0.1	12	dbSNP_116	127	2777,5823	440.7+/-359.6	456,1865,1979	yes	missense	OR9K2	NM_001005243.1	29	760,2953,2790	AA,AG,GG		32.2907,38.493,34.3918	benign	207/336	55524172	4473,8533	2203	4300	6503	SO:0001583	missense	441639	exon1			ATTCTCGCCCACT	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.620G>A	12.37:g.55524172G>A	ENSP00000307598:p.Arg207His	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	157	72	0.458599	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	622	0.2847985347985348	198	0.4024390243902439	102	0.281767955801105	73	0.12762237762237763	249	0.32849604221635886	G	7.087	0.571398	0.13623	0.38493	0.322907	ENSG00000170605	ENST00000305377	T	0.00123	8.7	4.98	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.140643	0.34133	N	0.004231	T	0.00012	0.0000	N	0.02345	-0.59	0.58432	P	4.000000000004E-6	B	0.14805	0.011	B	0.18263	0.021	T	0.03566	-1.1024	9	0.66056	D	0.02	-9.1617	8.3649	0.32380	0.0866:0.2652:0.6482:0.0	rs7306491;rs52802498;rs59789791;rs7306491	207	Q8NGE7	OR9K2_HUMAN	H	207	ENSP00000307598:R207H	ENSP00000307598:R207H	R	+	2	0	OR9K2	53810439	0.000000	0.05858	0.085000	0.20634	0.302000	0.27658	-0.020000	0.12525	1.466000	0.48025	0.650000	0.86243	CGC	G|0.681;A|0.319	0.319	strong		0.358	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
TRPC1	7220	hgsc.bcm.edu	37	3	142503605	142503605	+	Silent	SNP	G	G	A	rs7621642	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142503605G>A	ENST00000476941.1	+	7	1506	c.1020G>A	c.(1018-1020)tcG>tcA	p.S340S	TRPC1_ENST00000273482.6_Silent_p.S306S	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	340					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)	p.S306S(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						GACAGATGTCGGGTTACCGAC	0.408													A|||	1989	0.397165	0.7602	0.1873	5008	,	,		18120	0.4077		0.2256	False		,,,				2504	0.2209				p.S340S		Atlas-SNP	.											TRPC1,NS,carcinoma,0,1	TRPC1	82	1	1	Substitution - coding silent(1)	stomach(1)	c.G1020A						scavenged	.	A		2947,1459	470.4+/-355.7	989,969,245	121.0	111.0	115.0		918	2.0	1.0	3	dbSNP_116	115	1792,6808	733.4+/-406.9	206,1380,2714	no	coding-synonymous	TRPC1	NM_003304.4		1195,2349,2959	AA,AG,GG		20.8372,33.1139,36.437		306/760	142503605	4739,8267	2203	4300	6503	SO:0001819	synonymous_variant	7220	exon7			GATGTCGGGTTAC	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.1020G>A	3.37:g.142503605G>A		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	118	63	0.533898	NM_001251845	Q14CE4	Silent	SNP	ENST00000476941.1	37	CCDS58856.1																																																																																			G|0.616;A|0.384	0.384	strong		0.408	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
EYS	346007	hgsc.bcm.edu	37	6	65303100	65303100	+	Missense_Mutation	SNP	T	T	C	rs17404123	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65303100T>C	ENST00000370621.3	-	25	4313	c.3787A>G	c.(3787-3789)Att>Gtt	p.I1263V	EYS_ENST00000370616.2_Missense_Mutation_p.I1263V|EYS_ENST00000503581.1_Missense_Mutation_p.I1263V			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1263			I -> V. {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.I51V(1)|p.I1263V(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GAAGGGGGAATTGTATATGTC	0.413													C|||	470	0.0938498	0.0151	0.1182	5008	,	,		14712	0.1567		0.0984	False		,,,				2504	0.1135				p.I1263V		Atlas-SNP	.											Q5T669_HUMAN,NS,carcinoma,0,2	EYS	527	2	2	Substitution - Missense(2)	stomach(2)	c.A3787G						PASS	.	C	VAL/ILE	49,1335		1,47,644	143.0	127.0	132.0		3787	0.8	0.0	6	dbSNP_123	132	446,2736		41,364,1186	yes	missense	EYS	NM_001142800.1	29	42,411,1830	CC,CT,TT		14.0163,3.5405,10.841	benign	1263/3145	65303100	495,4071	692	1591	2283	SO:0001583	missense	346007	exon25			GGGGAATTGTATA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.3787A>G	6.37:g.65303100T>C	ENSP00000359655:p.Ile1263Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	44	42	0.954545	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		214	0.09798534798534798	5	0.01016260162601626	44	0.12154696132596685	86	0.15034965034965034	79	0.10422163588390501	C	0.017	-1.504790	0.00992	0.035405	0.140163	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	T;T;T	0.81330	-1.48;-1.47;-1.47	4.73	0.768	0.18487	.	.	.	.	.	T	0.24160	0.0585	N	0.02539	-0.55	0.51233	P	8.900000000000574E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.02484	-1.1152	8	0.10902	T	0.67	.	1.9789	0.03422	0.2477:0.3697:0.2409:0.1417	rs17404123;rs52825351;rs17404123	1263;1263	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	V	1263	ENSP00000424243:I1263V;ENSP00000359655:I1263V;ENSP00000359650:I1263V	ENSP00000359650:I1263V	I	-	1	0	EYS	65359821	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.096000	0.11059	-0.446000	0.07149	-0.808000	0.03180	ATT	C|0.104;N|0.001	0.104	strong		0.413	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
FYTTD1	84248	hgsc.bcm.edu	37	3	197495334	197495334	+	Missense_Mutation	SNP	G	G	A	rs3205525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:197495334G>A	ENST00000241502.4	+	3	482	c.260G>A	c.(259-261)cGt>cAt	p.R87H	FYTTD1_ENST00000424384.2_Missense_Mutation_p.R20H|FYTTD1_ENST00000428395.2_5'UTR|FYTTD1_ENST00000415708.2_Missense_Mutation_p.R61H	NM_032288.6	NP_115664.2	Q96QD9	UIF_HUMAN	forty-two-three domain containing 1	87			R -> H (in dbSNP:rs3205525). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		mRNA export from nucleus (GO:0006406)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)	Lung NSC(153;0.132)	Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.175)		AGTCTGAATCGTAGAGGAAGA	0.408													G|||	3766	0.751997	0.4387	0.8156	5008	,	,		15901	0.9415		0.8469	False		,,,				2504	0.8374				p.R87H		Atlas-SNP	.											.	FYTTD1	34	.	0			c.G260A						PASS	.	G	HIS/ARG,HIS/ARG	2047,2359	566.7+/-382.0	487,1073,643	114.0	103.0	107.0		182,260	2.9	1.0	3	dbSNP_105	107	7253,1347	756.2+/-407.5	3044,1165,91	yes	missense,missense	FYTTD1	NM_001011537.2,NM_032288.6	29,29	3531,2238,734	AA,AG,GG		15.6628,46.4594,28.4945	benign,benign	61/293,87/319	197495334	9300,3706	2203	4300	6503	SO:0001583	missense	84248	exon3			TGAATCGTAGAGG	AJ344094	CCDS3329.1, CCDS43196.1, CCDS43196.2	3q29	2011-03-03			ENSG00000122068	ENSG00000122068			25407	protein-coding gene	gene with protein product	"""UAP56-interacting factor"""					19836239	Standard	NM_001011537		Approved	DKFZp761B1514, UIF	uc003fyi.2	Q96QD9	OTTHUMG00000155453	ENST00000241502.4:c.260G>A	3.37:g.197495334G>A	ENSP00000241502:p.Arg87His	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	56	30	0.535714	NM_032288	A8MY74|B2RCB2|B7Z3R4|B7Z7V1|B7Z8I0|B7ZAJ3|C9J7P6|C9JNG6|C9JTH3|C9JY50|Q96SL9|Q9BQI8	Missense_Mutation	SNP	ENST00000241502.4	37	CCDS3329.1	1695	0.7760989010989011	208	0.42276422764227645	295	0.8149171270718232	532	0.9300699300699301	660	0.8707124010554089	G	12.65	2.002436	0.35320	0.464594	0.843372	ENSG00000122068	ENST00000428738;ENST00000415708;ENST00000241502;ENST00000426031;ENST00000424384	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	4.68	2.88	0.33553	.	0.269768	0.35870	N	0.002925	T	0.00012	0.0000	N	0.22421	0.69	0.09310	P	0.9999999999999908	B;B	0.22683	0.059;0.073	B;B	0.18561	0.013;0.022	T	0.15009	-1.0452	9	0.45353	T	0.12	-3.0342	8.4033	0.32599	0.1852:0.0:0.8148:0.0	rs3205525;rs17853361;rs60200792;rs3205525	61;87	Q96QD9-2;Q96QD9	.;UIF_HUMAN	H	20;61;87;20;20	ENSP00000399896:R20H;ENSP00000393746:R61H;ENSP00000241502:R87H;ENSP00000389557:R20H;ENSP00000394631:R20H	ENSP00000241502:R87H	R	+	2	0	FYTTD1	198979731	1.000000	0.71417	0.959000	0.39883	0.906000	0.53458	2.145000	0.42207	0.714000	0.32081	0.644000	0.83932	CGT	G|0.268;A|0.732	0.732	strong		0.408	FYTTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340185.3	NM_032288	
RP1	6101	hgsc.bcm.edu	37	8	55542540	55542540	+	Missense_Mutation	SNP	G	G	A	rs61739567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:55542540G>A	ENST00000220676.1	+	4	6246	c.6098G>A	c.(6097-6099)tGt>tAt	p.C2033Y		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	2033			C -> Y (in dbSNP:rs61739567). {ECO:0000269|PubMed:10391212, 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)			GAAAGGTTTTGTATGAATTTC	0.338													G|||	1080	0.215655	0.0696	0.245	5008	,	,		18653	0.0675		0.4264	False		,,,				2504	0.3282				p.C2033Y	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G6098A						PASS	.	G	TYR/CYS	516,3888	233.6+/-246.7	35,446,1721	83.0	87.0	86.0		6098	0.4	0.0	8	dbSNP_129	86	3577,5023	515.5+/-378.6	716,2145,1439	yes	missense	RP1	NM_006269.1	194	751,2591,3160	AA,AG,GG		41.593,11.7166,31.4749	benign	2033/2157	55542540	4093,8911	2202	4300	6502	SO:0001583	missense	6101	exon4			GGTTTTGTATGAA	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.6098G>A	8.37:g.55542540G>A	ENSP00000220676:p.Cys2033Tyr	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	516	0.23626373626373626	41	0.08333333333333333	105	0.2900552486187845	43	0.07517482517482517	327	0.4313984168865435	G	0.001	-3.520656	0.00010	0.117166	0.41593	ENSG00000104237	ENST00000220676	T	0.18960	2.18	5.25	0.404	0.16355	.	0.555464	0.16627	N	0.206202	T	0.00012	0.0000	L	0.28274	0.84	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.46289	-0.9202	9	0.02654	T	1	.	0.7012	0.00908	0.2659:0.3374:0.2093:0.1874	rs61739567	2033	P56715	RP1_HUMAN	Y	2033	ENSP00000220676:C2033Y	ENSP00000220676:C2033Y	C	+	2	0	RP1	55705093	0.493000	0.26035	0.014000	0.15608	0.012000	0.07955	-0.012000	0.12699	0.153000	0.19213	0.591000	0.81541	TGT	A|0.295;G|0.705	0.295	strong		0.338	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
NES	10763	hgsc.bcm.edu	37	1	156641537	156641537	+	Missense_Mutation	SNP	C	C	T	rs951781	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156641537C>T	ENST00000368223.3	-	4	2575	c.2443G>A	c.(2443-2445)Gta>Ata	p.V815I		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	815	Tail.		V -> I (in dbSNP:rs951781). {ECO:0000269|PubMed:12880961}.		brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)	p.V815I(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACTGCCTCTACGCTCTCTTCT	0.418													C|||	1023	0.204273	0.0363	0.2738	5008	,	,		19193	0.12		0.3439	False		,,,				2504	0.3252				p.V815I		Atlas-SNP	.											NES,NS,carcinoma,0,1	NES	196	1	1	Substitution - Missense(1)	stomach(1)	c.G2443A						PASS	.	C	ILE/VAL	401,4005	199.1+/-222.7	19,363,1821	105.0	96.0	99.0		2443	-4.9	0.0	1	dbSNP_92	99	3050,5550	468.2+/-367.2	579,1892,1829	yes	missense	NES	NM_006617.1	29	598,2255,3650	TT,TC,CC		35.4651,9.1012,26.5339	benign	815/1622	156641537	3451,9555	2203	4300	6503	SO:0001583	missense	10763	exon4			CCTCTACGCTCTC	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.2443G>A	1.37:g.156641537C>T	ENSP00000357206:p.Val815Ile	Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	460	0.21062271062271062	18	0.036585365853658534	105	0.2900552486187845	73	0.12762237762237763	264	0.3482849604221636	C	11.39	1.624057	0.28889	0.091012	0.354651	ENSG00000132688	ENST00000368223	D	0.85258	-1.96	5.4	-4.93	0.03066	.	1.551100	0.04567	N	0.392662	T	0.58991	0.2161	L	0.38838	1.175	0.80722	P	0.0	B	0.18166	0.026	B	0.04013	0.001	T	0.52238	-0.8602	9	0.38643	T	0.18	.	7.4335	0.27141	0.0:0.2352:0.1919:0.5728	rs951781;rs17393839;rs57478265;rs951781	815	P48681	NEST_HUMAN	I	815	ENSP00000357206:V815I	ENSP00000357206:V815I	V	-	1	0	NES	154908161	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-1.666000	0.01963	-0.441000	0.07201	-0.251000	0.11542	GTA	C|0.783;T|0.217	0.217	strong		0.418	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
SSPO	23145	hgsc.bcm.edu	37	7	149479935	149479935	+	RNA	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149479935G>A	ENST00000378016.2	+	0	1901							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCTGTTCCAGGAGCTGTGCTG	0.612																																					p.G634E		Atlas-SNP	.											.	.	.	.	0			c.G1901A						PASS	.						36.0	40.0	39.0					7																	149479935		2080	4195	6275			23145	exon15			TTCCAGGAGCTGT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149479935G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	108	38	0.351852	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.	.	none		0.612	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CLCN6	1185	hgsc.bcm.edu	37	1	11906068	11906068	+	IGR	SNP	A	A	G	rs5065	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:11906068A>G	ENST00000346436.6	+	0	5583				NPPA-AS1_ENST00000446542.1_RNA|NPPA_ENST00000376476.1_Nonstop_Mutation_p.*102R|NPPA_ENST00000376480.3_Nonstop_Mutation_p.*152R|NPPA-AS1_ENST00000400892.2_RNA	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6						cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGTTATCTTCAGTACTGCAAA	0.517													G|||	897	0.179113	0.4183	0.1138	5008	,	,		18871	0.0129		0.1233	False		,,,				2504	0.1309				p.X152R		Atlas-SNP	.											.	NPPA	14	.	0			c.T454C	GRCh37	CM040788	NPPA	M	rs5065	PASS	.	G	ARG/stop	1800,2606	641.4+/-397.5	380,1040,783	151.0	136.0	141.0		454	0.9	1.0	1	dbSNP_52	141	1335,7265	756.5+/-407.5	97,1141,3062	yes	stop-lost	NPPA	NM_006172.3		477,2181,3845	GG,GA,AA		15.5233,40.8534,24.1043		152/152	11906068	3135,9871	2203	4300	6503	SO:0001628	intergenic_variant	4878	exon3			ATCTTCAGTACTG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299		1.37:g.11906068A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	121	10	0.0826446	NM_006172	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Missense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	304	0.1391941391941392	174	0.35365853658536583	41	0.1132596685082873	4	0.006993006993006993	85	0.11213720316622691	G	5.706	0.314728	0.10789	0.408534	0.155233	ENSG00000175206	ENST00000376480;ENST00000376476	.	.	.	5.47	0.954	0.19595	.	.	.	.	.	.	.	.	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.1248	0.03735	0.2569:0.1343:0.4715:0.1373	rs5065;rs198363;rs1130764;rs3189984;rs17413194;rs17856153;rs57081035;rs5065	.	.	.	R	152;102	.	.	X	-	1	0	NPPA	11828655	0.997000	0.39634	0.976000	0.42696	0.154000	0.21943	0.306000	0.19279	0.041000	0.15688	-0.128000	0.14901	TGA	A|0.796;G|0.204	0.204	strong		0.517	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
GRWD1	83743	hgsc.bcm.edu	37	19	48954421	48954421	+	Missense_Mutation	SNP	G	G	A	rs2302951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48954421G>A	ENST00000253237.5	+	6	1189	c.956G>A	c.(955-957)cGg>cAg	p.R319Q		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	319			R -> Q (in dbSNP:rs2302951). {ECO:0000269|PubMed:11853319}.			cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		TGGAGCCGCCGGGAGCCCTTC	0.637													G|||	966	0.192891	0.2224	0.3674	5008	,	,		15500	0.1468		0.1511	False		,,,				2504	0.1196				p.R319Q		Atlas-SNP	.											.	GRWD1	41	.	0			c.G956A						PASS	.	G	GLN/ARG	824,3582	303.8+/-288.1	91,642,1470	36.0	41.0	40.0		956	4.0	1.0	19	dbSNP_100	40	1178,7422	230.4+/-264.8	81,1016,3203	yes	missense	GRWD1	NM_031485.3	43	172,1658,4673	AA,AG,GG		13.6977,18.7018,15.3929	benign	319/447	48954421	2002,11004	2203	4300	6503	SO:0001583	missense	83743	exon6			GCCGCCGGGAGCC	AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"""WD repeat domain containing"""	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.956G>A	19.37:g.48954421G>A	ENSP00000253237:p.Arg319Gln	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	89	37	0.41573	NM_031485	Q8TF59	Missense_Mutation	SNP	ENST00000253237.5	37	CCDS12720.1	412	0.18864468864468864	109	0.22154471544715448	107	0.2955801104972376	85	0.1486013986013986	111	0.14643799472295516	G	9.540	1.113077	0.20795	0.187018	0.136977	ENSG00000105447	ENST00000253237	T	0.01279	5.06	4.04	4.04	0.47022	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.496699	0.19722	N	0.107562	T	0.00012	0.0000	N	0.02865	-0.47	0.36616	P	0.124533	B	0.02656	0.0	B	0.08055	0.003	T	0.41052	-0.9530	9	0.10377	T	0.69	.	6.2909	0.21059	0.2069:0.0:0.7931:0.0	rs2302951;rs58433112;rs2302951	319	Q9BQ67	GRWD1_HUMAN	Q	319	ENSP00000253237:R319Q	ENSP00000253237:R319Q	R	+	2	0	GRWD1	53646233	0.559000	0.26562	1.000000	0.80357	0.996000	0.88848	0.690000	0.25451	2.276000	0.75962	0.561000	0.74099	CGG	G|0.830;A|0.170	0.170	strong		0.637	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1	NM_031485	
DNAH5	1767	hgsc.bcm.edu	37	5	13864728	13864728	+	Silent	SNP	C	C	A	rs6554827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13864728C>A	ENST00000265104.4	-	28	4478	c.4374G>T	c.(4372-4374)cgG>cgT	p.R1458R	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1458	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)	p.R1458R(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCTTCAAGGCCCGGGGAAGCT	0.478									Kartagener syndrome																												p.R1458R		Atlas-SNP	.											DNAH5,NS,carcinoma,0,1	DNAH5	868	1	1	Substitution - coding silent(1)	stomach(1)	c.G4374T						scavenged	.	C		1386,3020	457.5+/-351.6	229,928,1046	59.0	60.0	60.0		4374	0.9	1.0	5	dbSNP_116	60	3807,4793	537.7+/-383.3	893,2021,1386	no	coding-synonymous	DNAH5	NM_001369.2		1122,2949,2432	AA,AC,CC		44.2674,31.4571,39.9277		1458/4625	13864728	5193,7813	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon28	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CAAGGCCCGGGGA	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.4374G>T	5.37:g.13864728C>A		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			C|0.626;A|0.374	0.374	strong		0.478	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
RIN3	79890	hgsc.bcm.edu	37	14	93118198	93118198	+	Silent	SNP	C	C	T	rs3814830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93118198C>T	ENST00000216487.7	+	6	963	c.804C>T	c.(802-804)gcC>gcT	p.A268A	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	268	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CCTCTGATGCCACCTCACCCA	0.682													T|||	1422	0.283946	0.3389	0.2911	5008	,	,		7197	0.2758		0.169	False		,,,				2504	0.3313				p.A268A		Atlas-SNP	.											.	RIN3	81	.	0			c.C804T						PASS	.	T		1418,2988	685.2+/-404.5	229,960,1014	72.0	71.0	71.0		804	3.4	0.5	14	dbSNP_107	71	1253,7347	760.6+/-407.6	84,1085,3131	no	coding-synonymous	RIN3	NM_024832.3		313,2045,4145	TT,TC,CC		14.5698,32.1834,20.5367		268/986	93118198	2671,10335	2203	4300	6503	SO:0001819	synonymous_variant	79890	exon6			TGATGCCACCTCA	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.804C>T	14.37:g.93118198C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Silent	SNP	ENST00000216487.7	37	CCDS32144.1																																																																																			C|0.764;T|0.236	0.236	strong		0.682	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
SYP	6855	hgsc.bcm.edu	37	X	49047924	49047924	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:49047924A>G	ENST00000263233.4	-	6	984	c.912T>C	c.(910-912)ggT>ggC	p.G304G	SYP_ENST00000538567.1_Silent_p.G186G|SYP_ENST00000479808.1_Silent_p.G304G	NM_003179.2	NP_003170.1	P08247	SYPH_HUMAN	synaptophysin	304	Repeats, Gly-rich.				cellular response to organic substance (GO:0071310)|endocytosis (GO:0006897)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle membrane organization (GO:0048499)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	cholesterol binding (GO:0015485)|protein self-association (GO:0043621)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)	15		all_lung(315;0.00016)				AGGTGGGTGCACCCTGCGGGC	0.647																																					p.G304G		Atlas-SNP	.											.	SYP	71	.	0			c.T912C						PASS	.						20.0	19.0	19.0					X																	49047924		2203	4296	6499	SO:0001819	synonymous_variant	6855	exon6			GGGTGCACCCTGC	X06389	CCDS14321.1	Xp11.23-p11.22	2014-02-19			ENSG00000102003	ENSG00000102003			11506	protein-coding gene	gene with protein product		313475				3120152, 19377476	Standard	NM_003179		Approved	MRX96	uc004dmz.1	P08247	OTTHUMG00000034557	ENST00000263233.4:c.912T>C	X.37:g.49047924A>G		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	31	30	0.967742	NM_003179	B2R7L6|B7Z359|Q6P2F7	Silent	SNP	ENST00000263233.4	37	CCDS14321.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.694606	0.30052	.	.	ENSG00000102003	ENST00000472598	.	.	.	5.5	0.389	0.16269	.	.	.	.	.	T	0.40040	0.1101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32929	-0.9888	4	.	.	.	-9.7988	0.3716	0.00380	0.2718:0.3005:0.1615:0.2662	.	.	.	.	A	194	.	.	V	-	2	0	SYP	48934868	0.083000	0.21467	1.000000	0.80357	0.997000	0.91878	-0.907000	0.04067	0.693000	0.31634	0.486000	0.48141	GTG	.	.	none		0.647	SYP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083625.2	NM_003179	
CHD7	55636	hgsc.bcm.edu	37	8	61765419	61765419	+	Silent	SNP	G	G	A	rs6999971	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:61765419G>A	ENST00000423902.2	+	31	6614	c.6135G>A	c.(6133-6135)ccG>ccA	p.P2045P	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2045					adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			TAATTGAGCCGATCACAGAGG	0.517													G|||	79	0.0157748	0.0061	0.0187	5008	,	,		17725	0.0		0.0487	False		,,,				2504	0.0092				p.P2045P		Atlas-SNP	.											.	CHD7	534	.	0			c.G6135A						PASS	.	G		26,3774		0,26,1874	104.0	107.0	106.0		6135	-7.4	0.6	8	dbSNP_116	106	315,7921		10,295,3813	no	coding-synonymous	CHD7	NM_017780.3		10,321,5687	AA,AG,GG		3.8247,0.6842,2.8332		2045/2998	61765419	341,11695	1900	4118	6018	SO:0001819	synonymous_variant	55636	exon31			TGAGCCGATCACA	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.6135G>A	8.37:g.61765419G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	36	0.5625	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																			G|0.976;A|0.024	0.024	strong		0.517	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
MAP4K5	11183	hgsc.bcm.edu	37	14	50910675	50910675	+	Missense_Mutation	SNP	C	C	G	rs35768475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:50910675C>G	ENST00000013125.4	-	19	1737	c.1419G>C	c.(1417-1419)aaG>aaC	p.K473N		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	473			N -> K (in dbSNP:rs35768475). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					CTCGTTTGTCCTTTTTTCGTG	0.348													C|||	27	0.00539137	0.0008	0.0058	5008	,	,		20678	0.0		0.0139	False		,,,				2504	0.0082				p.K473N		Atlas-SNP	.											.	MAP4K5	48	.	0			c.G1419C						PASS	.	C	ASN/LYS,ASN/LYS	3,3813		0,3,1905	206.0	188.0	194.0		1419,1419	2.7	1.0	14	dbSNP_126	194	77,8153		1,75,4039	yes	missense,missense	MAP4K5	NM_006575.4,NM_198794.2	94,94	1,78,5944	GG,GC,CC		0.9356,0.0786,0.6641	benign,benign	473/847,473/847	50910675	80,11966	1908	4115	6023	SO:0001583	missense	11183	exon19			TTTGTCCTTTTTT	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.1419G>C	14.37:g.50910675C>G	ENSP00000013125:p.Lys473Asn	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	165	78	0.472727	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	37		10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	C	15.99	2.996145	0.54147	7.86E-4	0.009356	ENSG00000012983	ENST00000013125	T	0.74209	-0.82	5.44	2.67	0.31697	.	0.000000	0.85682	D	0.000000	T	0.78027	0.4219	.	.	.	0.53005	D	0.999965	D;P	0.76494	0.999;0.804	D;B	0.78314	0.991;0.412	T	0.77373	-0.2612	9	0.45353	T	0.12	.	8.6476	0.34016	0.0:0.6265:0.0:0.3735	rs35768475	147;473	B3KWC4;B2R928	.;.	N	473	ENSP00000013125:K473N	ENSP00000013125:K473N	K	-	3	2	MAP4K5	49980425	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.487000	0.22356	0.295000	0.22570	-0.127000	0.14921	AAG	C|0.994;G|0.006	0.006	strong		0.348	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575	
THSD7A	221981	hgsc.bcm.edu	37	7	11521542	11521542	+	Silent	SNP	T	T	C	rs3735502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:11521542T>C	ENST00000423059.4	-	7	2141	c.1890A>G	c.(1888-1890)ccA>ccG	p.P630P	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	630					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		CTTTCGGGCATGGGGCATCAC	0.527										HNSCC(18;0.044)			C|||	926	0.184904	0.1188	0.183	5008	,	,		18109	0.1786		0.2505	False		,,,				2504	0.2147				p.P630P		Atlas-SNP	.											.	THSD7A	219	.	0			c.A1890G						PASS	.	C		481,3721		30,421,1650	99.0	99.0	99.0		1890	-12.3	0.0	7	dbSNP_107	99	2218,6240		319,1580,2330	no	coding-synonymous	THSD7A	NM_015204.2		349,2001,3980	CC,CT,TT		26.2237,11.4469,21.3191		630/1658	11521542	2699,9961	2101	4229	6330	SO:0001819	synonymous_variant	221981	exon7			CGGGCATGGGGCA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.1890A>G	7.37:g.11521542T>C		Somatic	229	1	0.00436681		WXS	Illumina HiSeq	Phase_I	204	102	0.5	NM_015204		Silent	SNP	ENST00000423059.4	37	CCDS47543.1																																																																																			T|0.800;C|0.200	0.200	strong		0.527	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
SLC2A1	6513	hgsc.bcm.edu	37	1	43395635	43395635	+	Silent	SNP	C	C	T	rs2229682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43395635C>T	ENST00000426263.3	-	5	766	c.588G>A	c.(586-588)ccG>ccA	p.P196P	SLC2A1_ENST00000475162.1_Intron|SLC2A1_ENST00000415851.2_Intron	NM_006516.2	NP_006507.2	P11166	GTR1_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 1	196					carbohydrate metabolic process (GO:0005975)|cellular response to glucose starvation (GO:0042149)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|L-ascorbic acid metabolic process (GO:0019852)|protein complex assembly (GO:0006461)|regulation of insulin secretion (GO:0050796)|response to osmotic stress (GO:0006970)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|female pronucleus (GO:0001939)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|midbody (GO:0030496)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|identical protein binding (GO:0042802)|protein self-association (GO:0043621)|xenobiotic transporter activity (GO:0042910)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|pancreas(2)	13	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0122)			Etomidate(DB00292)	GCAGCAGGGCCGGGATGAAGA	0.647													C|||	599	0.119609	0.0242	0.2075	5008	,	,		18800	0.0804		0.1928	False		,,,				2504	0.1513				p.P196P		Atlas-SNP	.											SLC2A1,NS,meningioma,-2,1	SLC2A1	36	1	0			c.G588A						PASS	.	C		217,4189	130.2+/-166.9	6,205,1992	82.0	79.0	80.0		588	-7.7	0.6	1	dbSNP_98	80	1749,6851	316.8+/-312.9	171,1407,2722	no	coding-synonymous	SLC2A1	NM_006516.2		177,1612,4714	TT,TC,CC		20.3372,4.9251,15.1161		196/493	43395635	1966,11040	2203	4300	6503	SO:0001819	synonymous_variant	6513	exon5			CAGGGCCGGGATG	K03195	CCDS477.1	1p34.2	2013-05-22			ENSG00000117394	ENSG00000117394		"""Solute carriers"""	11005	protein-coding gene	gene with protein product		138140	"""human T-cell leukemia virus (I and II) receptor"""	GLUT1, GLUT, HTLVR		8839927, 14622599, 18451999	Standard	NM_006516		Approved	DYT18	uc001cik.2	P11166	OTTHUMG00000007657	ENST00000426263.3:c.588G>A	1.37:g.43395635C>T		Somatic	289	1	0.00346021		WXS	Illumina HiSeq	Phase_I	266	137	0.515038	NM_006516	A8K9S6|B2R620|D3DPX0|O75535|Q147X2	Silent	SNP	ENST00000426263.3	37	CCDS477.1																																																																																			T|0.144;G|0.000;C|0.856	0.144	strong		0.647	SLC2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020358.2	NM_006516	
MADCAM1	8174	hgsc.bcm.edu	37	19	501900	501900	+	Missense_Mutation	SNP	C	C	A	rs3745925	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:501900C>A	ENST00000215637.3	+	4	945	c.899C>A	c.(898-900)cCc>cAc	p.P300H	MADCAM1_ENST00000382683.4_Intron|AC005775.2_ENST00000592413.1_RNA|MADCAM1_ENST00000587541.1_Missense_Mutation_p.P81H|MADCAM1_ENST00000346144.4_Intron	NM_130760.2	NP_570116.2	Q13477	MADCA_HUMAN	mucosal vascular addressin cell adhesion molecule 1	300	Mucin-like.		P -> H (in dbSNP:rs3745925).		aging (GO:0007568)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|embryo development (GO:0009790)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding involved in cell-matrix adhesion (GO:0098640)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(4)|prostate(1)|skin(2)	10		all_cancers(10;4.25e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGGCTGGGCCCACGCAGGGA	0.667													C|||	1088	0.217252	0.2103	0.2017	5008	,	,		11442	0.3224		0.2386	False		,,,				2504	0.1074				p.P300H		Atlas-SNP	.											.	MADCAM1	29	.	0			c.C899A						PASS	.	C	HIS/PRO,	870,3470		95,680,1395	8.0	9.0	8.0		899,	-0.8	0.0	19	dbSNP_107	8	1715,6805		191,1333,2736	yes	missense,intron	MADCAM1	NM_130760.2,NM_130762.2	77,	286,2013,4131	AA,AC,CC		20.1291,20.0461,20.1011	probably-damaging,	300/383,	501900	2585,10275	2170	4260	6430	SO:0001583	missense	8174	exon4			CTGGGCCCACGCA	U43628	CCDS12028.1, CCDS12029.1	19p13.3	2013-01-11			ENSG00000099866	ENSG00000099866		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6765	protein-coding gene	gene with protein product	"""mucosal addressin cell adhesion molecule-1"""	102670				9162097, 8609404	Standard	NM_130762		Approved	MACAM1	uc002los.3	Q13477	OTTHUMG00000180548	ENST00000215637.3:c.899C>A	19.37:g.501900C>A	ENSP00000215637:p.Pro300His	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	59	37	0.627119	NM_130760	A5PKV4|B2RPL9|O60222|O75867|Q5UGI7	Missense_Mutation	SNP	ENST00000215637.3	37	CCDS12028.1	566	0.2591575091575092	102	0.2073170731707317	82	0.2265193370165746	192	0.3356643356643357	190	0.25065963060686014	c	0.244	-1.011721	0.02095	0.200461	0.201291	ENSG00000099866	ENST00000537731;ENST00000542525;ENST00000543297;ENST00000215637	T	0.10382	2.88	1.75	-0.825	0.10809	.	1.969940	0.03219	U	0.177235	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.67145	0.996	P	0.46172	0.506	T	0.28964	-1.0027	9	0.46703	T	0.11	.	0.5786	0.00708	0.2459:0.3319:0.2439:0.1782	rs3745925;rs58652856;rs3745925	300	Q13477	MADCA_HUMAN	H	324;316;308;300	ENSP00000215637:P300H	ENSP00000215637:P300H	P	+	2	0	MADCAM1	452900	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.049000	0.14099	-0.143000	0.11334	0.650000	0.86243	CCC	C|0.760;A|0.240	0.240	strong		0.667	MADCAM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451884.1	NM_130760	
HIF3A	64344	hgsc.bcm.edu	37	19	46812451	46812451	+	Missense_Mutation	SNP	C	C	T	rs61750957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46812451C>T	ENST00000377670.4	+	6	636	c.605C>T	c.(604-606)gCg>gTg	p.A202V	HIF3A_ENST00000600383.1_Missense_Mutation_p.A133V|HIF3A_ENST00000300862.3_Missense_Mutation_p.A200V|RNU6-924P_ENST00000362926.1_RNA|HIF3A_ENST00000472815.1_Missense_Mutation_p.A133V|HIF3A_ENST00000339613.2_Missense_Mutation_p.A146V|HIF3A_ENST00000420102.2_Missense_Mutation_p.A151V|HIF3A_ENST00000525854.1_3'UTR|HIF3A_ENST00000244303.6_Missense_Mutation_p.A133V	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	202				A -> V (in Ref. 5; BAB55324). {ECO:0000305}.	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)		AAGCCACCTGCGCAGACTTCT	0.652													C|||	365	0.0728834	0.1346	0.0375	5008	,	,		15870	0.0427		0.0676	False		,,,				2504	0.0511				p.A202V		Atlas-SNP	.											.	HIF3A	154	.	0			c.C605T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	579,3827	252.1+/-258.6	38,503,1662	42.0	46.0	44.0		398,599,605,398	1.0	0.0	19	dbSNP_129	44	618,7982	160.4+/-213.5	28,562,3710	yes	missense,missense,missense,missense	HIF3A	NM_022462.4,NM_152794.3,NM_152795.3,NM_152796.2	64,64,64,64	66,1065,5372	TT,TC,CC		7.186,13.1412,9.2034	benign,benign,benign,benign	133/601,200/668,202/670,133/451	46812451	1197,11809	2203	4300	6503	SO:0001583	missense	64344	exon6			CACCTGCGCAGAC	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.605C>T	19.37:g.46812451C>T	ENSP00000366898:p.Ala202Val	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	144	74	0.513889	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	37	CCDS12681.2	148	0.06776556776556776	62	0.12601626016260162	15	0.04143646408839779	24	0.04195804195804196	47	0.06200527704485488	C	10.37	1.331867	0.24167	0.131412	0.07186	ENSG00000124440	ENST00000475432;ENST00000244302;ENST00000377670;ENST00000457865;ENST00000414707;ENST00000244303;ENST00000339613;ENST00000457771;ENST00000291300;ENST00000300862;ENST00000420102	T;T;T;T;T	0.64803	0.57;-0.11;0.44;0.57;-0.12	4.4	0.966	0.19667	.	0.584295	0.14420	N	0.320722	T	0.00412	0.0013	L	0.38175	1.15	0.80722	P	0.0	B;P;B;B;P;B;P;B	0.45078	0.056;0.85;0.045;0.336;0.643;0.027;0.585;0.334	B;B;B;B;B;B;B;B	0.28011	0.04;0.085;0.015;0.022;0.054;0.006;0.054;0.032	T	0.04307	-1.0961	9	0.38643	T	0.18	.	4.0977	0.09998	0.0:0.5364:0.174:0.2896	rs61750957	151;133;200;151;146;202;202;202	F5H884;B4DNA2;Q9Y2N7-2;B4DSD9;A8MPQ1;Q9Y2N7;B0M185;E7EWV6	.;.;.;.;.;HIF3A_HUMAN;.;.	V	202;202;202;116;202;133;146;133;146;200;151	ENSP00000366898:A202V;ENSP00000244303:A133V;ENSP00000341877:A146V;ENSP00000300862:A200V;ENSP00000407771:A151V	ENSP00000244302:A202V	A	+	2	0	HIF3A	51504291	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	0.343000	0.19944	0.209000	0.20645	-0.258000	0.10820	GCG	C|0.920;T|0.080	0.080	strong		0.652	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3		
TSSC4	10078	hgsc.bcm.edu	37	11	2424541	2424541	+	Missense_Mutation	SNP	C	C	G	rs2234279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2424541C>G	ENST00000333256.6	+	3	1121	c.678C>G	c.(676-678)caC>caG	p.H226Q	TSSC4_ENST00000380992.1_Intron|TSSC4_ENST00000451491.2_Missense_Mutation_p.H226Q|TSSC4_ENST00000380996.5_Missense_Mutation_p.H162Q|TSSC4_ENST00000467308.1_Intron|AC124057.5_ENST00000433035.1_RNA			Q9Y5U2	TSSC4_HUMAN	tumor suppressing subtransferable candidate 4	226										endometrium(3)|large_intestine(1)|lung(4)	8		all_epithelial(84;0.000161)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.0137)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.00145)|LUSC - Lung squamous cell carcinoma(625;0.19)		AAGCCAGACACGAGAGGAAGA	0.657													c|||	670	0.133786	0.3411	0.0735	5008	,	,		16131	0.1151		0.0258	False		,,,				2504	0.0266				p.H226Q		Atlas-SNP	.											.	TSSC4	19	.	0			c.C678G						PASS	.	T	GLN/HIS	1263,3139	418.3+/-338.2	200,863,1138	41.0	49.0	47.0		678	-7.3	0.0	11	dbSNP_98	47	259,8339	97.7+/-159.3	5,249,4045	yes	missense	TSSC4	NM_005706.2	24	205,1112,5183	GG,GC,CC		3.0123,28.6915,11.7077	benign	226/330	2424541	1522,11478	2201	4299	6500	SO:0001583	missense	10078	exon2			CAGACACGAGAGG	AF125568	CCDS7735.1, CCDS73241.1	11p15.5	2008-02-05			ENSG00000184281	ENSG00000184281			12386	protein-coding gene	gene with protein product		603852				10072438	Standard	XM_005252722		Approved		uc001lwl.3	Q9Y5U2	OTTHUMG00000009895	ENST00000333256.6:c.678C>G	11.37:g.2424541C>G	ENSP00000331087:p.His226Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	138	64	0.463768	NM_005706	C9JS66|Q86VL2|Q9BRS6	Missense_Mutation	SNP	ENST00000333256.6	37	CCDS7735.1	279	0.12774725274725274	165	0.3353658536585366	30	0.08287292817679558	68	0.11888111888111888	16	0.021108179419525065	c	0.016	-1.531603	0.00951	0.286915	0.030123	ENSG00000184281	ENST00000380996;ENST00000333256;ENST00000440813;ENST00000451491	T;T;T;T	0.21191	2.3;2.56;2.02;2.56	3.67	-7.33	0.01431	.	1.177240	0.06289	U	0.698832	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	1.0000000000287557E-6	B;B	0.33379	0.41;0.41	B;B	0.30179	0.112;0.112	T	0.25293	-1.0136	9	0.32370	T	0.25	-0.1137	4.7935	0.13261	0.0803:0.2104:0.1601:0.5493	rs2234279	226;162	Q9Y5U2;Q9Y5U2-2	TSSC4_HUMAN;.	Q	162;226;162;226	ENSP00000370384:H162Q;ENSP00000331087:H226Q;ENSP00000416937:H162Q;ENSP00000411224:H226Q	ENSP00000331087:H226Q	H	+	3	2	TSSC4	2381117	0.000000	0.05858	0.001000	0.08648	0.124000	0.20399	-1.962000	0.01514	-2.708000	0.00395	-1.297000	0.01338	CAC	C|0.883;G|0.117	0.117	strong		0.657	TSSC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027369.3	NM_005706	
SLC12A7	10723	hgsc.bcm.edu	37	5	1081702	1081702	+	Silent	SNP	A	A	G	rs6865765	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:1081702A>G	ENST00000264930.5	-	9	1330	c.1287T>C	c.(1285-1287)ccT>ccC	p.P429P		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	429					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CGGTCACGGAAGGGAAGTAGA	0.622													G|||	2115	0.422324	0.4834	0.3184	5008	,	,		17294	0.3601		0.4791	False		,,,				2504	0.4192				p.P429P		Atlas-SNP	.											.	SLC12A7	97	.	0			c.T1287C						PASS	.	G		2186,2218	586.5+/-386.5	557,1072,573	96.0	84.0	88.0		1287	-6.6	0.6	5	dbSNP_116	88	4176,4424	582.9+/-391.5	999,2178,1123	no	coding-synonymous	SLC12A7	NM_006598.2		1556,3250,1696	GG,GA,AA		48.5581,49.6367,48.9234		429/1084	1081702	6362,6642	2202	4300	6502	SO:0001819	synonymous_variant	10723	exon9			CACGGAAGGGAAG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.1287T>C	5.37:g.1081702A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	89	45	0.505618	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	37	CCDS34129.1																																																																																			A|0.538;G|0.462	0.462	strong		0.622	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
MUC6	4588	hgsc.bcm.edu	37	11	1017575	1017575	+	Silent	SNP	C	C	T	rs76222533		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1017575C>T	ENST00000421673.2	-	31	5276	c.5226G>A	c.(5224-5226)acG>acA	p.T1742T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1742	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGGTTTTGGCCGTGCTAAATG	0.537													-|||	1	0.000199681	0.0	0.0014	5008	,	,		39036	0.0		0.0	False		,,,				2504	0.0				p.T1742T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	2	0			c.G5226A						scavenged	.						697.0	677.0	684.0					11																	1017575		2190	4282	6472	SO:0001819	synonymous_variant	4588	exon31			TTTGGCCGTGCTA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5226G>A	11.37:g.1017575C>T		Somatic	465	31	0.0666667		WXS	Illumina HiSeq	Phase_I	592	55	0.0929054	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			C|0.500;T|0.500	0.500	strong		0.537	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
PRMT7	54496	hgsc.bcm.edu	37	16	68390697	68390697	+	Silent	SNP	C	C	T	rs61733486	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68390697C>T	ENST00000339507.5	+	18	2735	c.1905C>T	c.(1903-1905)ccC>ccT	p.P635P	PRMT7_ENST00000348497.4_Silent_p.P487P|PRMT7_ENST00000449359.3_Silent_p.P585P|PRMT7_ENST00000441236.1_Silent_p.P585P			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	635	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CTGCAGACCCCGAGGTAGTGC	0.687													c|||	226	0.0451278	0.0688	0.0533	5008	,	,		16243	0.0		0.0477	False		,,,				2504	0.0511				p.P635P		Atlas-SNP	.											.	PRMT7	51	.	0			c.C1905T						PASS	.		,	302,4088		13,276,1906	20.0	20.0	20.0		1755,1905	3.8	0.2	16	dbSNP_129	20	492,8106		12,468,3819	no	coding-synonymous,coding-synonymous	PRMT7	NM_001184824.1,NM_019023.2	,	25,744,5725	TT,TC,CC		5.7223,6.8793,6.1133	,	585/643,635/693	68390697	794,12194	2195	4299	6494	SO:0001819	synonymous_variant	54496	exon18			AGACCCCGAGGTA	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.1905C>T	16.37:g.68390697C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	128	52	0.40625	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Silent	SNP	ENST00000339507.5	37	CCDS10866.1																																																																																			C|0.941;T|0.059	0.059	strong		0.687	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
ACSS3	79611	hgsc.bcm.edu	37	12	81627215	81627215	+	Missense_Mutation	SNP	G	G	T	rs145641313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:81627215G>T	ENST00000548058.1	+	13	2594	c.1684G>T	c.(1684-1686)Gca>Tca	p.A562S	ACSS3_ENST00000548324.1_Missense_Mutation_p.A244S|ACSS3_ENST00000261206.3_Missense_Mutation_p.A561S			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	562						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						AATAAATGTTGCAGGTCACAG	0.393													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18493	0.0		0.0	False		,,,				2504	0.0				p.A562S		Atlas-SNP	.											.	ACSS3	118	.	0			c.G1684T						PASS	.	G	SER/ALA	3,4403	6.2+/-15.9	0,3,2200	227.0	221.0	223.0		1684	5.8	1.0	12	dbSNP_134	223	0,8600		0,0,4300	yes	missense	ACSS3	NM_024560.2	99	0,3,6500	TT,TG,GG		0.0,0.0681,0.0231	possibly-damaging	562/687	81627215	3,13003	2203	4300	6503	SO:0001583	missense	79611	exon13			AATGTTGCAGGTC		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1684G>T	12.37:g.81627215G>T	ENSP00000449535:p.Ala562Ser	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	154	63	0.409091	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	37	CCDS9022.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	32	5.163767	0.94727	6.81E-4	0.0	ENSG00000111058	ENST00000548058;ENST00000261206;ENST00000548324	T;T;T	0.46451	2.94;2.94;0.87	5.84	5.84	0.93424	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	N	0.26130	0.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.44667	-0.9313	10	0.30854	T	0.27	-15.5203	19.7715	0.96367	0.0:0.0:1.0:0.0	.	244;562	Q9H6R3-2;Q9H6R3	.;ACSS3_HUMAN	S	562;561;244	ENSP00000449535:A562S;ENSP00000261206:A561S;ENSP00000448965:A244S	ENSP00000261206:A561S	A	+	1	0	ACSS3	80151346	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.315000	0.78998	2.777000	0.95525	0.650000	0.86243	GCA	G|0.999;T|0.001	0.001	strong		0.393	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	
DENND3	22898	hgsc.bcm.edu	37	8	142170884	142170884	+	Silent	SNP	C	C	T	rs2289001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:142170884C>T	ENST00000262585.2	+	9	1388	c.1110C>T	c.(1108-1110)ttC>ttT	p.F370F	DENND3_ENST00000424248.1_Intron|DENND3_ENST00000519811.1_Silent_p.F450F	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	370	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				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)			TGAGCATCTTCAGGTACGTGA	0.602											OREG0019024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1468	0.293131	0.1339	0.3386	5008	,	,		18390	0.3393		0.2724	False		,,,				2504	0.4499				p.F370F		Atlas-SNP	.											DENND3,NS,carcinoma,0,1	DENND3	127	1	0			c.C1110T						PASS	.	C		731,3661		64,603,1529	40.0	34.0	36.0		1110	5.1	1.0	8	dbSNP_100	36	2515,6069		397,1721,2174	no	coding-synonymous	DENND3	NM_014957.2		461,2324,3703	TT,TC,CC		29.2987,16.6439,25.0154		370/1199	142170884	3246,9730	2196	4292	6488	SO:0001819	synonymous_variant	22898	exon9			CATCTTCAGGTAC	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.1110C>T	8.37:g.142170884C>T		Somatic	216	0	0	1669	WXS	Illumina HiSeq	Phase_I	201	199	0.99005	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	37	CCDS34947.1																																																																																			C|0.724;T|0.276	0.276	strong		0.602	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957	
OR11H6	122748	hgsc.bcm.edu	37	14	20692574	20692574	+	Missense_Mutation	SNP	T	T	C	rs17277221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20692574T>C	ENST00000315519.2	+	1	784	c.706T>C	c.(706-708)Tac>Cac	p.Y236H		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	236			Y -> H (in dbSNP:rs17277221).			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)		CTTGGGATCTTACACTCTGGT	0.488													t|||	1958	0.390974	0.4735	0.3516	5008	,	,		21936	0.2371		0.4781	False		,,,				2504	0.3763				p.Y236H		Atlas-SNP	.											OR11H6,NS,carcinoma,-2,1	OR11H6	60	1	0			c.T706C						PASS	.	T	HIS/TYR	2257,2149	595.4+/-388.4	611,1035,557	119.0	105.0	110.0		706	4.8	0.9	14	dbSNP_123	110	4157,4443	566.4+/-388.7	997,2163,1140	yes	missense	OR11H6	NM_001004480.1	83	1608,3198,1697	CC,CT,TT		48.3372,48.7744,49.3157	probably-damaging	236/331	20692574	6414,6592	2203	4300	6503	SO:0001583	missense	122748	exon1			GGATCTTACACTC		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.706T>C	14.37:g.20692574T>C	ENSP00000319071:p.Tyr236His	Somatic	300	0	0		WXS	Illumina HiSeq	Phase_I	293	116	0.395904	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	870	0.3983516483516483	237	0.4817073170731707	135	0.3729281767955801	123	0.21503496503496503	375	0.4947229551451187	T	14.82	2.649305	0.47362	0.512256	0.483372	ENSG00000176219	ENST00000315519	T	0.00515	6.87	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45361	D	0.000378	T	0.00012	0.0000	H	0.98005	4.125	0.28486	P	0.9147168	D	0.89917	1.0	D	0.97110	1.0	T	0.19976	-1.0289	9	0.87932	D	0	.	12.2972	0.54854	0.0:0.0:0.0:1.0	rs17277221;rs52833578;rs56750236;rs17277221	236	Q8NGC7	O11H6_HUMAN	H	236	ENSP00000319071:Y236H	ENSP00000319071:Y236H	Y	+	1	0	OR11H6	19762414	1.000000	0.71417	0.906000	0.35671	0.290000	0.27261	4.432000	0.59922	2.000000	0.58554	0.386000	0.25728	TAC	C|0.445;N|0.000	0.445	strong		0.488	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
POC5	134359	hgsc.bcm.edu	37	5	74998598	74998598	+	Silent	SNP	G	G	A	rs35130836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:74998598G>A	ENST00000428202.2	-	5	534	c.345C>T	c.(343-345)caC>caT	p.H115H	POC5_ENST00000510798.1_5'UTR|POC5_ENST00000446329.2_Silent_p.H90H|POC5_ENST00000504862.1_5'UTR|POC5_ENST00000514838.2_Silent_p.H87H|POC5_ENST00000380475.2_5'UTR	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	115					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CCATGACTGGGTGAGAAGGCT	0.398													G|||	410	0.081869	0.0719	0.0807	5008	,	,		21011	0.0288		0.0755	False		,,,				2504	0.1575				p.H115H		Atlas-SNP	.											.	POC5	82	.	0			c.C345T						PASS	.	G	,	310,3732		13,284,1724	94.0	96.0	95.0		345,270	1.6	1.0	5	dbSNP_126	95	654,7738		30,594,3572	no	coding-synonymous,coding-synonymous	POC5	NM_001099271.1,NM_152408.2	,	43,878,5296	AA,AG,GG		7.7931,7.6695,7.7529	,	115/576,90/551	74998598	964,11470	2021	4196	6217	SO:0001819	synonymous_variant	134359	exon5			GACTGGGTGAGAA	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.345C>T	5.37:g.74998598G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	157	59	0.375796	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Silent	SNP	ENST00000428202.2	37	CCDS47236.1																																																																																			G|0.931;A|0.069	0.069	strong		0.398	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
HLA-A	3105	hgsc.bcm.edu	37	6	29911957	29911957	+	Silent	SNP	G	G	A	rs12721755	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911957G>A	ENST00000396634.1	+	6	1019	c.678G>A	c.(676-678)agG>agA	p.R226R	HLA-A_ENST00000376809.5_Silent_p.R226R|HLA-A_ENST00000376806.5_Silent_p.R226R|HLA-A_ENST00000376802.2_Silent_p.R226R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	226	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCACCCTGAGGTGCTGGGCCC	0.607									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	779	0.155551	0.1286	0.1787	5008	,	,		19595	0.2093		0.1113	False		,,,				2504	0.1656				p.R226R		Atlas-SNP	.											.	HLA-A	89	.	0			c.G678A						PASS	.	G		433,2583		61,311,1136	73.0	95.0	87.0		678	1.8	1.0	6	dbSNP_126	87	602,4810		55,492,2159	no	coding-synonymous	HLA-A	NM_002116.7		116,803,3295	AA,AG,GG		11.1234,14.3568,12.2805		226/366	29911957	1035,7393	1508	2706	4214	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCTGAGGTGCTGG	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.678G>A	6.37:g.29911957G>A		Somatic	386	1	0.00259067		WXS	Illumina HiSeq	Phase_I	192	113	0.588542	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	weak		0.607	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
RP1	6101	hgsc.bcm.edu	37	8	55539395	55539395	+	Missense_Mutation	SNP	A	A	T	rs2293869	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:55539395A>T	ENST00000220676.1	+	4	3101	c.2953A>T	c.(2953-2955)Aat>Tat	p.N985Y		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	985			N -> Y (associated with susceptibility to hypertriglyceridemia; dbSNP:rs2293869). {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)			GACAGGAGATAATCTATGTAA	0.353													A|||	1252	0.25	0.1952	0.2522	5008	,	,		19567	0.0675		0.4264	False		,,,				2504	0.3292				p.N985Y	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A2953T	GRCh37	CM035763	RP1	M	rs2293869	PASS	.	A	TYR/ASN	944,3462	356.1+/-313.4	107,730,1366	128.0	137.0	134.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2953	1.9	0.0	8	dbSNP_100	134	3584,5016	516.2+/-378.8	719,2146,1435	yes	missense	RP1	NM_006269.1	143	826,2876,2801	TT,TA,AA		41.6744,21.4253,34.8147	possibly-damaging	985/2157	55539395	4528,8478	2203	4300	6503	SO:0001583	missense	6101	exon4			GGAGATAATCTAT	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.2953A>T	8.37:g.55539395A>T	ENSP00000220676:p.Asn985Tyr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	569	0.26053113553113555	91	0.18495934959349594	108	0.2983425414364641	43	0.07517482517482517	327	0.4313984168865435	A	10.45	1.354246	0.24512	0.214253	0.416744	ENSG00000104237	ENST00000220676	T	0.56444	0.46	5.62	1.94	0.25998	.	0.392400	0.24447	N	0.038456	T	0.00012	0.0000	M	0.64997	1.995	0.80722	P	0.0	D	0.57899	0.981	P	0.57371	0.819	T	0.39210	-0.9625	9	0.87932	D	0	.	5.9509	0.19246	0.6673:0.1275:0.2052:0.0	rs2293869;rs52800054;rs2293869	985	P56715	RP1_HUMAN	Y	985	ENSP00000220676:N985Y	ENSP00000220676:N985Y	N	+	1	0	RP1	55701948	0.054000	0.20591	0.004000	0.12327	0.148000	0.21650	1.592000	0.36676	0.093000	0.17368	0.533000	0.62120	AAT	A|0.687;T|0.313	0.313	strong		0.353	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
NFKB2	4791	hgsc.bcm.edu	37	10	104160959	104160959	+	Silent	SNP	C	C	T	rs11574851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:104160959C>T	ENST00000369966.3	+	19	2344	c.2094C>T	c.(2092-2094)aaC>aaT	p.N698N	NFKB2_ENST00000428099.1_Silent_p.N698N|NFKB2_ENST00000189444.6_Silent_p.N698N	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	698			Missing (in truncated form EB308).|Missing (in truncated form p80HT).		extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	ATGCTGAAAACGAGGAGCCCC	0.622			T	IGH@	B-NHL								c|||	159	0.0317492	0.0053	0.0245	5008	,	,		15702	0.0556		0.0467	False		,,,				2504	0.0327				p.N698N		Atlas-SNP	.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2	48	.	0			c.C2094T						PASS	.	T	,,	43,4127		0,43,2042	72.0	81.0	78.0		2094,2094,2094	-7.8	0.9	10	dbSNP_120	78	422,7992		7,408,3792	no	coding-synonymous,coding-synonymous,coding-synonymous	NFKB2	NM_001077493.1,NM_001077494.1,NM_002502.3	,,	7,451,5834	TT,TC,CC		5.0155,1.0312,3.6952	,,	698/900,698/901,698/900	104160959	465,12119	2085	4207	6292	SO:0001819	synonymous_variant	4791	exon19			TGAAAACGAGGAG	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"""Ankyrin repeat domain containing"""	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.2094C>T	10.37:g.104160959C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Silent	SNP	ENST00000369966.3	37	CCDS41564.1																																																																																			C|0.963;T|0.037	0.037	strong		0.622	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2		
TACC2	10579	hgsc.bcm.edu	37	10	123970530	123970530	+	Missense_Mutation	SNP	T	T	C	rs2295873	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123970530T>C	ENST00000369005.1	+	9	6930	c.6590T>C	c.(6589-6591)gTg>gCg	p.V2197A	TACC2_ENST00000513429.1_Missense_Mutation_p.V343A|TACC2_ENST00000368999.1_Missense_Mutation_p.V275A|TACC2_ENST00000360561.3_Missense_Mutation_p.V275A|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000369004.3_Missense_Mutation_p.V275A|TACC2_ENST00000453444.2_Missense_Mutation_p.V2201A|TACC2_ENST00000358010.1_Missense_Mutation_p.V343A|TACC2_ENST00000334433.3_Missense_Mutation_p.V2197A|TACC2_ENST00000260733.3_Missense_Mutation_p.V275A|TACC2_ENST00000515273.1_Missense_Mutation_p.V2201A|TACC2_ENST00000515603.1_Missense_Mutation_p.V2152A	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2197			V -> A (in dbSNP:rs2295873).		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)				GAGCCCGCTGTGGGGCCCAAA	0.617													C|||	1754	0.35024	0.7065	0.281	5008	,	,		15542	0.3532		0.0875	False		,,,				2504	0.1851				p.V2197A		Atlas-SNP	.											.	TACC2	271	.	0			c.T6590C						PASS	.	C	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	2737,1665	449.8+/-349.2	862,1013,326	41.0	53.0	49.0		824,824,1028,6590	2.5	0.0	10	dbSNP_100	49	1056,7542	754.0+/-407.5	64,928,3307	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	64,64,64,64	926,1941,3633	CC,CT,TT		12.2819,37.8237,29.1769	benign,benign,benign,benign	275/1027,275/997,343/1095,2197/2949	123970530	3793,9207	2201	4299	6500	SO:0001583	missense	10579	exon9			CCGCTGTGGGGCC	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.6590T>C	10.37:g.123970530T>C	ENSP00000358001:p.Val2197Ala	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	698	0.31959706959706957	331	0.6727642276422764	88	0.2430939226519337	211	0.3688811188811189	68	0.08970976253298153	C	0.049	-1.256442	0.01457	0.621763	0.122819	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539;ENST00000505639	T;T;T;T;T;T;T;T;T;T;T;T;T	0.16897	4.17;3.69;4.12;4.17;4.17;3.69;4.12;3.57;3.57;3.58;3.57;3.15;2.31	5.43	2.55	0.30701	.	0.226096	0.22853	N	0.054834	T	0.00012	0.0000	N	0.01277	-0.915	0.80722	P	0.0	B;B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0;0.001;0.0;0.001;0.0	T	0.33085	-0.9882	9	0.07325	T	0.83	-0.3972	10.3307	0.43820	0.0:0.7334:0.0:0.2666	rs2295873;rs52808225;rs57698446;rs2295873	292;2201;275;2152;2201;275;275;343;2197	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	A	2197;343;2201;2152;2197;343;2201;2187;275;275;275;275;292;38	ENSP00000358001:V2197A;ENSP00000425062:V343A;ENSP00000424467:V2201A;ENSP00000427618:V2152A;ENSP00000334280:V2197A;ENSP00000350701:V343A;ENSP00000395048:V2201A;ENSP00000353763:V275A;ENSP00000357995:V275A;ENSP00000422815:V275A;ENSP00000260733:V275A;ENSP00000420967:V292A;ENSP00000426303:V38A	ENSP00000260733:V275A	V	+	2	0	TACC2	123960520	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.572000	0.23684	0.684000	0.31448	-0.726000	0.03593	GTG	T|0.693;C|0.307	0.307	strong		0.617	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
SYT1	6857	hgsc.bcm.edu	37	12	79611374	79611374	+	Silent	SNP	C	C	T	rs2037743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:79611374C>T	ENST00000261205.4	+	4	732	c.75C>T	c.(73-75)aaC>aaT	p.N25N	SYT1_ENST00000457153.2_Silent_p.N25N|SYT1_ENST00000552744.1_Silent_p.N25N|SYT1_ENST00000393240.3_Silent_p.N25N	NM_005639.2	NP_005630.1	P21579	SYT1_HUMAN	synaptotagmin I	25					calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|detection of calcium ion (GO:0005513)|glutamate secretion (GO:0014047)|neurotransmitter secretion (GO:0007269)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of vesicle fusion (GO:0031340)|protein homooligomerization (GO:0051260)|regulation of exocytosis (GO:0017157)|regulation of regulated secretory pathway (GO:1903305)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking (GO:0048278)	cell junction (GO:0030054)|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)|dense core granule (GO:0031045)|endocytic vesicle membrane (GO:0030666)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	1-phosphatidylinositol binding (GO:0005545)|calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|transporter activity (GO:0005215)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|pancreas(2)|skin(6)	25						TGCCAAGCAACGCCACAGAGC	0.507													T|||	3134	0.625799	0.7814	0.7233	5008	,	,		16372	0.4603		0.6869	False		,,,				2504	0.454				p.N25N		Atlas-SNP	.											.	SYT1	70	.	0			c.C75T						PASS	.	T	,,	3430,976	368.3+/-318.6	1339,752,112	64.0	64.0	64.0		75,75,75	-0.1	0.6	12	dbSNP_94	64	5892,2708	433.4+/-357.4	2017,1858,425	no	coding-synonymous,coding-synonymous,coding-synonymous	SYT1	NM_001135805.1,NM_001135806.1,NM_005639.2	,,	3356,2610,537	TT,TC,CC		31.4884,22.1516,28.3254	,,	25/423,25/423,25/423	79611374	9322,3684	2203	4300	6503	SO:0001819	synonymous_variant	6857	exon5			AAGCAACGCCACA		CCDS9017.1	12q21.2	2013-09-20			ENSG00000067715	ENSG00000067715		"""Synaptotagmins"""	11509	protein-coding gene	gene with protein product		185605		SYT, SVP65		1840599	Standard	NM_001135805		Approved	P65	uc001syv.3	P21579	OTTHUMG00000134326	ENST00000261205.4:c.75C>T	12.37:g.79611374C>T		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	38	11	0.289474	NM_001135805	Q6AI31	Silent	SNP	ENST00000261205.4	37	CCDS9017.1																																																																																			C|0.312;T|0.688	0.688	strong		0.507	SYT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259415.1	NM_005639	
TMEM214	54867	hgsc.bcm.edu	37	2	27260469	27260469	+	Missense_Mutation	SNP	G	G	A	rs1124649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27260469G>A	ENST00000238788.9	+	9	1113	c.1051G>A	c.(1051-1053)Gtg>Atg	p.V351M	TMEM214_ENST00000404032.3_Missense_Mutation_p.V306M	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214	351			V -> M (in dbSNP:rs1124649).		apoptotic process (GO:0006915)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						CCGACTGAAAGTGCTGGCATT	0.542													G|||	1518	0.303115	0.4478	0.4006	5008	,	,		18858	0.0655		0.3091	False		,,,				2504	0.2771				p.V351M		Atlas-SNP	.											.	TMEM214	41	.	0			c.G1051A						PASS	.	G	MET/VAL,MET/VAL	1640,2310		333,974,668	111.0	116.0	115.0		916,1051	5.7	1.0	2	dbSNP_86	115	2550,5770		395,1760,2005	yes	missense,missense	TMEM214	NM_001083590.1,NM_017727.4	21,21	728,2734,2673	AA,AG,GG		30.649,41.519,34.1483	probably-damaging,probably-damaging	306/645,351/690	27260469	4190,8080	1975	4160	6135	SO:0001583	missense	54867	exon9			CTGAAAGTGCTGG		CCDS42664.1, CCDS46242.1	2p23.3	2013-06-19			ENSG00000119777	ENSG00000119777			25983	protein-coding gene	gene with protein product						23661706	Standard	NM_001083590		Approved	FLJ20254	uc002ria.4	Q6NUQ4	OTTHUMG00000151999	ENST00000238788.9:c.1051G>A	2.37:g.27260469G>A	ENSP00000238788:p.Val351Met	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	180	93	0.516667	NM_017727	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Missense_Mutation	SNP	ENST00000238788.9	37	CCDS42664.1	605	0.27701465201465203	208	0.42276422764227645	141	0.38950276243093923	33	0.057692307692307696	223	0.2941952506596306	G	19.92	3.915582	0.73098	0.41519	0.30649	ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397	T;T	0.55588	0.51;0.51	5.69	5.69	0.88448	.	0.057286	0.64402	D	0.000001	T	0.00012	0.0000	M	0.74258	2.255	0.09310	P	0.999999747868	D;D	0.89917	1.0;0.998	D;D	0.81914	0.995;0.991	T	0.20874	-1.0262	9	0.52906	T	0.07	-21.5626	17.5913	0.87997	0.0:0.0:1.0:0.0	rs1124649;rs17529988;rs60677582;rs1124649	306;351	Q6NUQ4-2;Q6NUQ4	.;TM214_HUMAN	M	351;306;91	ENSP00000238788:V351M;ENSP00000384417:V306M	ENSP00000238788:V351M	V	+	1	0	TMEM214	27113973	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.222000	0.95196	2.700000	0.92200	0.561000	0.74099	GTG	G|0.713;A|0.287	0.287	strong		0.542	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727	
IGSF9B	22997	hgsc.bcm.edu	37	11	133807819	133807819	+	Silent	SNP	G	G	A	rs329635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:133807819G>A	ENST00000321016.8	-	4	677	c.447C>T	c.(445-447)atC>atT	p.I149I	IGSF9B_ENST00000533871.2_Silent_p.I149I			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	149	Ig-like 2.				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)		CCTTGGCCTCGATGTACTGGG	0.572													G|||	391	0.0780751	0.0719	0.0836	5008	,	,		18828	0.001		0.1332	False		,,,				2504	0.1053				p.I149I		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C447T						PASS	.	G		369,3869		13,343,1763	62.0	67.0	65.0		447	-2.8	1.0	11	dbSNP_79	65	992,7466		58,876,3295	no	coding-synonymous	IGSF9B	NM_014987.1		71,1219,5058	AA,AG,GG		11.7285,8.7069,10.7199		149/1350	133807819	1361,11335	2119	4229	6348	SO:0001819	synonymous_variant	22997	exon4			GGCCTCGATGTAC	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.447C>T	11.37:g.133807819G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	188	89	0.473404	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				G|0.918;A|0.082	0.082	strong		0.572	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
DST	667	hgsc.bcm.edu	37	6	56420538	56420538	+	Missense_Mutation	SNP	C	C	T	rs11756977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56420538C>T	ENST00000361203.3	-	56	14115	c.14108G>A	c.(14107-14109)cGt>cAt	p.R4703H	DST_ENST00000446842.2_Missense_Mutation_p.R4379H|DST_ENST00000421834.2_Missense_Mutation_p.R2617H|DST_ENST00000370769.4_Missense_Mutation_p.R4705H|DST_ENST00000370754.5_Missense_Mutation_p.R4883H|DST_ENST00000312431.6_3'UTR|DST_ENST00000244364.6_Missense_Mutation_p.R2291H|DST_ENST00000370788.2_Missense_Mutation_p.R2617H			Q03001	DYST_HUMAN	dystonin	4703				R -> H (in Ref. 4; BAC04449). {ECO:0000305}.	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)			CACAATCCCACGTAAAGAAGG	0.488													T|||	1680	0.335463	0.388	0.2767	5008	,	,		18739	0.3482		0.2744	False		,,,				2504	0.3558				p.R2291H		Atlas-SNP	.											.	DST	1427	.	0			c.G6872A						PASS	.	T	HIS/ARG	1356,2558		223,910,824	48.0	48.0	48.0		6872	5.7	1.0	6	dbSNP_120	48	2460,5870		352,1756,2057	yes	missense	DST	NM_015548.4	29	575,2666,2881	TT,TC,CC		29.5318,34.6449,31.1663	benign	2291/5172	56420538	3816,8428	1957	4165	6122	SO:0001583	missense	667	exon41			ATCCCACGTAAAG	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.14108G>A	6.37:g.56420538C>T	ENSP00000354508:p.Arg4703His	Somatic	215	1	0.00465116		WXS	Illumina HiSeq	Phase_I	179	89	0.497207	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		679	0.3108974358974359	197	0.40040650406504064	109	0.3011049723756906	183	0.31993006993006995	190	0.25065963060686014	T	13.13	2.144711	0.37825	0.346449	0.295318	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.35789	1.32;1.29;1.29;1.29;1.32;1.29;1.29	5.67	5.67	0.87782	.	0.000000	0.56097	N	0.000027	T	0.03348	0.0097	N	0.00347	-1.61	0.18873	P	0.99999	B;B;B;B;B	0.09022	0.002;0.001;0.001;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.001;0.0;0.0	T	0.25813	-1.0121	9	0.28530	T	0.3	.	9.192	0.37204	0.0:0.1399:0.0:0.8601	rs11756977;rs52809460;rs58737419;rs11756977	2617;4705;4883;4703;2291	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	H	2291;4883;4705;2617;4379;2617;4703	ENSP00000244364:R2291H;ENSP00000359790:R4883H;ENSP00000359805:R4705H;ENSP00000400883:R2617H;ENSP00000393645:R4379H;ENSP00000359824:R2617H;ENSP00000354508:R4703H	ENSP00000244364:R2291H	R	-	2	0	DST	56528497	0.966000	0.33281	0.957000	0.39632	0.986000	0.74619	1.649000	0.37281	1.083000	0.41159	-0.254000	0.11334	CGT	C|0.677;N|0.002	.	strong		0.488	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
AIM1	202	hgsc.bcm.edu	37	6	106960447	106960447	+	Silent	SNP	G	G	A	rs11152999	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:106960447G>A	ENST00000369066.3	+	1	718	c.231G>A	c.(229-231)gaG>gaA	p.E77E		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		CGAGCCCAGAGTCCAAGCCCA	0.677													G|||	1274	0.254393	0.1135	0.3026	5008	,	,		14075	0.4395		0.166	False		,,,				2504	0.3108				p.E77E		Atlas-SNP	.											.	AIM1	161	.	0			c.G231A						PASS	.	G		504,3782		37,430,1676	10.0	11.0	11.0		231	2.7	0.0	6	dbSNP_120	11	1197,7241		91,1015,3113	no	coding-synonymous	AIM1	NM_001624.2		128,1445,4789	AA,AG,GG		14.1858,11.7592,13.3684		77/1724	106960447	1701,11023	2143	4219	6362	SO:0001819	synonymous_variant	202	exon1			CCCAGAGTCCAAG	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.231G>A	6.37:g.106960447G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	45	7	0.155556	NM_001624	Q6P2P0|Q9BTM3	Silent	SNP	ENST00000369066.3	37	CCDS34506.1																																																																																			G|0.804;A|0.196	0.196	strong		0.677	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1		
SCN5A	6331	hgsc.bcm.edu	37	3	38592406	38592406	+	Silent	SNP	A	A	G	rs1805126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38592406A>G	ENST00000333535.4	-	28	5606	c.5457T>C	c.(5455-5457)gaT>gaC	p.D1819D	SCN5A_ENST00000414099.2_Silent_p.D1801D|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000449557.2_Silent_p.D1765D|SCN5A_ENST00000451551.2_Silent_p.D1765D|SCN5A_ENST00000413689.1_Silent_p.D1819D|SCN5A_ENST00000455624.2_Silent_p.D1786D|SCN5A_ENST00000443581.1_Silent_p.D1818D|SCN5A_ENST00000425664.1_Silent_p.D1801D|SCN5A_ENST00000450102.2_Silent_p.D1765D|SCN5A_ENST00000423572.2_Silent_p.D1818D			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1819			D -> N (in LQT3; digenic; associated with Gly-100 mutation on the KCNH2 gene). {ECO:0000269|PubMed:16922724}.		AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CAGACAGGGCATCGGCAAAGT	0.517													A|||	2466	0.492412	0.7042	0.4265	5008	,	,		20365	0.5784		0.3648	False		,,,				2504	0.2955				p.D1819D		Atlas-SNP	.											.	SCN5A	634	.	0			c.T5457C	GRCh37	CM057565	SCN5A	M	rs1805126	PASS	.	A	,,,,,	2694,1612		858,978,317	58.0	65.0	63.0		5454,5457,5403,5358,5295,5457	-8.1	0.4	3	dbSNP_89	63	2850,5694		489,1872,1911	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	,,,,,	1347,2850,2228	GG,GA,AA		33.3567,37.4361,43.144	,,,,,	1818/2016,1819/2017,1801/1999,1786/1984,1765/1963,1819/2017	38592406	5544,7306	2153	4272	6425	SO:0001819	synonymous_variant	6331	exon28			CAGGGCATCGGCA	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.5457T>C	3.37:g.38592406A>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	68	34	0.5	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	37	CCDS46796.1																																																																																			A|0.498;G|0.502	0.502	strong		0.517	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919064	12919064	+	Missense_Mutation	SNP	T	T	G	rs3204790	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12919064T>G	ENST00000240189.2	+	2	287	c.200T>G	c.(199-201)gTa>gGa	p.V67G		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	67			V -> G (in dbSNP:rs3204790).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.V67G(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCCTCTGGTATCGCTGATG	0.557													.|||	934	0.186502	0.1437	0.1297	5008	,	,		22643	0.3333		0.1531	False		,,,				2504	0.1677				p.V67G		Atlas-SNP	.											PRAMEF2,NS,carcinoma,0,1	PRAMEF2	85	1	1	Substitution - Missense(1)	prostate(1)	c.T200G						scavenged	.	G	GLY/VAL	705,3697	757.4+/-412.7	76,553,1572	144.0	150.0	148.0		200	0.8	0.1	1	dbSNP_105	148	1295,7297	751.5+/-407.4	117,1061,3118	no	missense	PRAMEF2	NM_023014.1	109	193,1614,4690	GG,GT,TT		15.0722,16.0154,15.3917	benign	67/475	12919064	2000,10994	2201	4296	6497	SO:0001583	missense	65122	exon2			CTCTGGTATCGCT		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.200T>G	1.37:g.12919064T>G	ENSP00000240189:p.Val67Gly	Somatic	269	4	0.0148699		WXS	Illumina HiSeq	Phase_I	228	19	0.0833333	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	480	0.21978021978021978	76	0.15447154471544716	59	0.16298342541436464	188	0.32867132867132864	157	0.20712401055408972	G	0.004	-2.285905	0.00251	0.160154	0.150722	ENSG00000120952	ENST00000240189	T	0.04049	3.72	0.842	0.842	0.18927	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00004	-3.36	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.37220	-0.9715	9	0.02654	T	1	.	4.0419	0.09755	0.0:0.0:0.5905:0.4095	rs3204790;rs17038653	67	O60811	PRAM2_HUMAN	G	67	ENSP00000240189:V67G	ENSP00000240189:V67G	V	+	2	0	PRAMEF2	12841651	0.017000	0.18338	0.148000	0.22405	0.037000	0.13140	-0.608000	0.05641	-0.047000	0.13423	-1.044000	0.02363	GTA	T|0.824;G|0.176	0.176	strong		0.557	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
SLC22A24	283238	hgsc.bcm.edu	37	11	62863518	62863518	+	Missense_Mutation	SNP	A	A	G	rs7113279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62863518A>G	ENST00000417740.1	-	6	1456	c.1015T>C	c.(1015-1017)Tcc>Ccc	p.S339P		NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	0					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						CGGAACAGGGAAAAAATGGAT	0.413													A|||	2438	0.486821	0.4319	0.5014	5008	,	,		20606	0.504		0.5109	False		,,,				2504	0.5082				p.S339P		Atlas-SNP	.											.	SLC22A24	31	.	0			c.T1015C						PASS	.	A	PRO/SER	580,804		121,338,233	129.0	111.0	117.0		1015	-1.4	0.0	11	dbSNP_116	117	1683,1499		443,797,351	yes	missense	SLC22A24	NM_001136506.2	74	564,1135,584	GG,GA,AA		47.1087,41.9075,49.562	benign	339/553	62863518	2263,2303	692	1591	2283	SO:0001583	missense	283238	exon6			ACAGGGAAAAAAT		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.1015T>C	11.37:g.62863518A>G	ENSP00000396586:p.Ser339Pro	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	50	0.46729	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		1102	0.5045787545787546	232	0.4715447154471545	166	0.4585635359116022	326	0.5699300699300699	378	0.49868073878627966	A	10.33	1.321238	0.23994	0.419075	0.528913	ENSG00000197658	ENST00000417740	T	0.74421	-0.84	3.68	-1.36	0.09085	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.24721	0.11	B	0.20184	0.028	T	0.44329	-0.9335	8	0.72032	D	0.01	.	7.2206	0.25985	0.1761:0.4681:0.3559:0.0	rs7113279;rs52811481;rs7113279	339	C9JC66	.	P	339	ENSP00000396586:S339P	ENSP00000396586:S339P	S	-	1	0	SLC22A24	62620094	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.498000	0.02287	-0.351000	0.08249	0.481000	0.45027	TCC	A|0.492;G|0.508	0.508	strong		0.413	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
FCGR3A	2214	hgsc.bcm.edu	37	1	161514542	161514542	+	Missense_Mutation	SNP	A	A	C	rs396991	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161514542A>C	ENST00000436743.1	-	5	680	c.526T>G	c.(526-528)Ttt>Gtt	p.F176V	FCGR3A_ENST00000443193.1_Missense_Mutation_p.F211V|FCGR3A_ENST00000367969.3_Missense_Mutation_p.F212V|FCGR3A_ENST00000540048.1_Missense_Mutation_p.F176V|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'Flank	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)	176	Ig-like C2-type 2.		F -> V (shows a higher binding capacity of IgG1, IgG3 and IgG4; dbSNP:rs396991). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7700021, ECO:0000269|PubMed:9242542, ECO:0000269|PubMed:9276722, ECO:0000269|Ref.3}.		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)	TTACTCCCAAAAAGCCCCCTG	0.478																																					p.F212V		Atlas-SNP	.											.	FCGR3A	38	.	0			c.T634G	GRCh37	CM992625	FCGR3A	M	rs396991	PASS	.	C	VAL/PHE,VAL/PHE,VAL/PHE,VAL/PHE,VAL/PHE	1150,3256		243,664,1296	74.0	75.0	75.0		523,526,526,631,634	-0.1	0.0	1	dbSNP_80	75	2412,6188		505,1402,2393	no	missense,missense,missense,missense,missense	FCGR3A	NM_001127596.1,NM_001127595.1,NM_001127593.1,NM_001127592.1,NM_000569.6	50,50,50,50,50	748,2066,3689	CC,CA,AA		28.0465,26.1008,27.3874	benign,benign,benign,benign,benign	175/254,176/255,176/255,211/290,212/291	161514542	3562,9444	2203	4300	6503	SO:0001583	missense	2214	exon4			TCCCAAAAAGCCC	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.526T>G	1.37:g.161514542A>C	ENSP00000416607:p.Phe176Val	Somatic	268	1	0.00373134		WXS	Illumina HiSeq	Phase_I	241	238	0.987552	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	535|535	0.24496336996336995|0.24496336996336995	106|106	0.21544715447154472|0.21544715447154472	71|71	0.19613259668508287|0.19613259668508287	154|154	0.2692307692307692|0.2692307692307692	204|204	0.2691292875989446|0.2691292875989446	N|N	8.451|8.451	0.853189|0.853189	0.17106|0.17106	0.261008|0.261008	0.280465|0.280465	ENSG00000203747|ENSG00000203747	ENST00000426740|ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048	.|T;T;T;T;T	.|0.11604	.|2.76;2.76;2.76;2.76;2.76	5.03|5.03	-0.103|-0.103	0.13609|0.13609	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.285436|0.285436	0.25027|0.25027	N|N	0.033707|0.033707	T|T	0.00998|0.00998	0.0033|0.0033	N|N	0.04355|0.04355	-0.22|-0.22	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	0.46925|0.46925	-0.9156|-0.9156	5|9	.|0.44086	.|T	.|0.13	.|.	0.3561|0.3561	0.00357|0.00357	0.2836:0.1629:0.1472:0.4063|0.2836:0.1629:0.1472:0.4063	rs396991;rs2229097;rs3171040;rs4151086;rs17857127;rs61228128|rs396991;rs2229097;rs3171040;rs4151086;rs17857127;rs61228128	.|176;211	.|P08637;E9PG94	.|FCG3A_HUMAN;.	L|V	192|212;211;176;176;176	.|ENSP00000356946:F212V;ENSP00000392047:F211V;ENSP00000416607:F176V;ENSP00000356944:F176V;ENSP00000444971:F176V	.|ENSP00000356944:F176V	F|F	-|-	3|1	2|0	FCGR3A|FCGR3A	159781166|159781166	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.208000|-0.208000	0.09371|0.09371	-0.464000|-0.464000	0.06963|0.06963	-5.115000|-5.115000	0.00001|0.00001	TTT|TTT	A|0.681;C|0.319	0.319	strong		0.478	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42824907	42824907	+	Silent	SNP	G	G	A	rs9471932	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42824907G>A	ENST00000314073.5	+	10	2363	c.2187G>A	c.(2185-2187)gcG>gcA	p.A729A	GLTSCR1L_ENST00000394168.1_Silent_p.A729A			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	729																	TAAGTGATGCGGTACAGAGAC	0.522													G|||	303	0.0605032	0.0968	0.0634	5008	,	,		17543	0.0069		0.0716	False		,,,				2504	0.0532				p.A729A		Atlas-SNP	.											KIAA0240,NS,carcinoma,0,1	.	.	1	0			c.G2187A						PASS	.	G		406,4000	201.5+/-224.5	16,374,1813	171.0	146.0	154.0		2187	-4.8	0.4	6	dbSNP_119	154	487,8113	140.6+/-197.1	13,461,3826	no	coding-synonymous	KIAA0240	NM_015349.1		29,835,5639	AA,AG,GG		5.6628,9.2147,6.8661		729/1080	42824907	893,12113	2203	4300	6503	SO:0001819	synonymous_variant	23506	exon9			TGATGCGGTACAG	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"""KIAA0240"""	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.2187G>A	6.37:g.42824907G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	91	43	0.472527	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	37	CCDS34451.1																																																																																			G|0.933;A|0.067	0.067	strong		0.522	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	
ATP13A5	344905	hgsc.bcm.edu	37	3	193031926	193031926	+	Missense_Mutation	SNP	C	C	T	rs2280268	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:193031926C>T	ENST00000342358.4	-	19	2332	c.2215G>A	c.(2215-2217)Ggc>Agc	p.G739S	ATP13A5_ENST00000495496.1_5'Flank|ATP13A5-AS1_ENST00000414634.1_RNA	NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	739			G -> S (in dbSNP:rs2280268).			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)		ACTTGGCTGCCTGGAGGGATC	0.473													C|||	2658	0.530751	0.323	0.5375	5008	,	,		20027	0.6508		0.6382	False		,,,				2504	0.5726				p.G739S		Atlas-SNP	.											ATP13A5,NS,adenoma,0,1	ATP13A5	171	1	0			c.G2215A						PASS	.	C	SER/GLY	1626,2780	501.3+/-365.0	303,1020,880	135.0	130.0	132.0		2215	3.1	0.3	3	dbSNP_100	132	5385,3215	651.1+/-400.8	1678,2029,593	yes	missense	ATP13A5	NM_198505.2	56	1981,3049,1473	TT,TC,CC		37.3837,36.9042,46.0941	benign	739/1219	193031926	7011,5995	2203	4300	6503	SO:0001583	missense	344905	exon19			GGCTGCCTGGAGG	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.2215G>A	3.37:g.193031926C>T	ENSP00000341942:p.Gly739Ser	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	110	110	1	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	1196	0.5476190476190477	159	0.3231707317073171	191	0.5276243093922652	366	0.6398601398601399	480	0.633245382585752	C	13.70	2.316653	0.40996	0.369042	0.626163	ENSG00000187527	ENST00000342358	T	0.56776	0.44	5.82	3.11	0.35812	HAD-like domain (2);	0.354783	0.27768	N	0.017935	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B	0.21225	0.053	B	0.26517	0.07	T	0.46652	-0.9176	9	0.02654	T	1	-3.7118	5.3979	0.16278	0.0:0.6241:0.1456:0.2303	rs2280268;rs60693121;rs2280268	739	Q4VNC0	AT135_HUMAN	S	739	ENSP00000341942:G739S	ENSP00000341942:G739S	G	-	1	0	ATP13A5	194514620	0.000000	0.05858	0.284000	0.24805	0.991000	0.79684	0.468000	0.22051	0.397000	0.25310	0.655000	0.94253	GGC	C|0.467;T|0.533	0.533	strong		0.473	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
NFIL3	4783	hgsc.bcm.edu	37	9	94172975	94172975	+	Silent	SNP	C	C	T	rs33973463	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:94172975C>T	ENST00000297689.3	-	2	436	c.42G>A	c.(40-42)gcG>gcA	p.A14A		NM_005384.2	NP_005375.2	Q16649	NFIL3_HUMAN	nuclear factor, interleukin 3 regulated	14					cellular response to interleukin-4 (GO:0071353)|circadian rhythm (GO:0007623)|immune response (GO:0006955)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|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 sequence-specific DNA binding (GO:0000979)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	16						CATCAAGAGACGCCTGCTCCT	0.443													C|||	230	0.0459265	0.0174	0.0331	5008	,	,		18459	0.0655		0.0676	False		,,,				2504	0.0511				p.A14A	Esophageal Squamous(152;732 1832 10053 26981 51762)	Atlas-SNP	.											.	NFIL3	43	.	0			c.G42A						PASS	.	C		126,4280	93.0+/-131.7	3,120,2080	91.0	90.0	90.0		42	-9.1	0.0	9	dbSNP_126	90	616,7984	158.6+/-212.1	23,570,3707	no	coding-synonymous	NFIL3	NM_005384.2		26,690,5787	TT,TC,CC		7.1628,2.8597,5.7051		14/463	94172975	742,12264	2203	4300	6503	SO:0001819	synonymous_variant	4783	exon2			AAGAGACGCCTGC	X64318	CCDS6690.1	9q22	2013-01-10			ENSG00000165030	ENSG00000165030		"""basic leucine zipper proteins"""	7787	protein-coding gene	gene with protein product		605327		IL3BP1		7565758, 1620116	Standard	NM_005384		Approved	E4BP4, NFIL3A, NF-IL3A	uc004arh.3	Q16649	OTTHUMG00000020209	ENST00000297689.3:c.42G>A	9.37:g.94172975C>T		Somatic	214	1	0.0046729		WXS	Illumina HiSeq	Phase_I	192	191	0.994792	NM_005384	B2R9Y8|Q14211|Q6FGQ8|Q96HS0	Silent	SNP	ENST00000297689.3	37	CCDS6690.1																																																																																			C|0.941;T|0.059	0.059	strong		0.443	NFIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053038.2	NM_005384	
FGFRL1	53834	hgsc.bcm.edu	37	4	1019011	1019011	+	Missense_Mutation	SNP	C	C	T	rs4647932	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1019011C>T	ENST00000398484.2	+	8	1971	c.1391C>T	c.(1390-1392)cCa>cTa	p.P464L	FGFRL1_ENST00000264748.6_Missense_Mutation_p.P464L|FGFRL1_ENST00000504138.1_Missense_Mutation_p.P464L|RP11-460I19.2_ENST00000503095.1_lincRNA|FGFRL1_ENST00000510644.1_Missense_Mutation_p.P464L			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	464			P -> L (in dbSNP:rs4647932).		diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGCCCAGGCCCAGTTGCTGGC	0.622													C|||	146	0.0291534	0.0068	0.0504	5008	,	,		14211	0.0218		0.0567	False		,,,				2504	0.0235				p.P464L		Atlas-SNP	.											FGFRL1,NS,carcinoma,0,1	FGFRL1	77	1	0			c.C1391T	GRCh37	CM067667	FGFRL1	M	rs4647932	PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	76,4306		1,74,2116	15.0	17.0	16.0		1391,1391,1391	1.5	0.0	4	dbSNP_111	16	578,8016		25,528,3744	yes	missense,missense,missense	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	98,98,98	26,602,5860	TT,TC,CC		6.7256,1.7344,5.0401	benign,benign,benign	464/505,464/505,464/505	1019011	654,12322	2191	4297	6488	SO:0001583	missense	53834	exon7			CAGGCCCAGTTGC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"""Immunoglobulin superfamily / I-set domain containing"""	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.1391C>T	4.37:g.1019011C>T	ENSP00000381498:p.Pro464Leu	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	108	57	0.527778	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Missense_Mutation	SNP	ENST00000398484.2	37	CCDS3344.1	72	0.03296703296703297	6	0.012195121951219513	21	0.058011049723756904	11	0.019230769230769232	34	0.044854881266490766	C	8.467	0.856661	0.17106	0.017344	0.067256	ENSG00000127418	ENST00000398484;ENST00000510644;ENST00000504138;ENST00000264748	T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78	4.38	1.5	0.22942	.	0.581982	0.16507	N	0.211416	T	0.09291	0.0229	L	0.27053	0.805	0.46185	D	0.99891	B	0.02656	0.0	B	0.06405	0.002	T	0.24048	-1.0171	10	0.87932	D	0	-0.8596	5.6428	0.17572	0.156:0.6709:0.0:0.1731	rs4647932;rs61088669;rs4647932	464	Q8N441	FGRL1_HUMAN	L	464	ENSP00000381498:P464L;ENSP00000425025:P464L;ENSP00000423091:P464L;ENSP00000264748:P464L	ENSP00000264748:P464L	P	+	2	0	FGFRL1	1009011	0.001000	0.12720	0.001000	0.08648	0.085000	0.17905	0.468000	0.22051	0.327000	0.23409	-0.137000	0.14449	CCA	C|0.955;T|0.045	0.045	strong		0.622	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	
LSM6	11157	hgsc.bcm.edu	37	4	147110790	147110790	+	Silent	SNP	A	A	T	rs41280529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:147110790A>T	ENST00000502781.1	+	4	944	c.225A>T	c.(223-225)acA>acT	p.T75T	LSM6_ENST00000296581.5_Silent_p.T75T			P62312	LSM6_HUMAN	LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)	75					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)|tRNA processing (GO:0008033)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)					all_hematologic(180;0.151)					ACATCAGTACACAGAAGAGAC	0.299													A|||	23	0.00459265	0.0015	0.0043	5008	,	,		18321	0.0		0.0179	False		,,,				2504	0.0				p.T75T	Ovarian(181;1591 2748 12147 31551)	Atlas-SNP	.											.	LSM6	5	.	0			c.A225T						PASS	.	A		9,4397	12.9+/-30.5	0,9,2194	68.0	75.0	72.0		225	-1.0	1.0	4	dbSNP_127	72	115,8483	61.7+/-123.6	0,115,4184	no	coding-synonymous	LSM6	NM_007080.2		0,124,6378	TT,TA,AA		1.3375,0.2043,0.9536		75/81	147110790	124,12880	2203	4299	6502	SO:0001819	synonymous_variant	11157	exon4			CAGTACACAGAAG	AF182292	CCDS3767.1	4q31.21	2008-02-05				ENSG00000164167			17017	protein-coding gene	gene with protein product		607286				10369684, 10523320	Standard	NM_007080		Approved	YDR378C	uc003ikq.4	P62312		ENST00000502781.1:c.225A>T	4.37:g.147110790A>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	49	0.411765	NM_007080	Q4W5J5|Q9Y4Y8	Silent	SNP	ENST00000502781.1	37	CCDS3767.1																																																																																			A|0.991;T|0.009	0.009	strong		0.299	LSM6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364929.1		
CLUAP1	23059	hgsc.bcm.edu	37	16	3586230	3586230	+	Missense_Mutation	SNP	C	C	T	rs9790	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3586230C>T	ENST00000576634.1	+	12	1345	c.1201C>T	c.(1201-1203)Cgg>Tgg	p.R401W	CLUAP1_ENST00000417763.2_Missense_Mutation_p.R235W|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000301749.7_RNA|NLRC3_ENST00000359128.5_RNA|CLUAP1_ENST00000445795.2_Missense_Mutation_p.R179W|CLUAP1_ENST00000341633.5_Missense_Mutation_p.R420W|CLUAP1_ENST00000571025.1_3'UTR|CLUAP1_ENST00000572600.1_Missense_Mutation_p.R235W	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	401			R -> W (in dbSNP:rs9790). {ECO:0000269|PubMed:15489334}.		cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						TCGAAGGGTCCGGAAATCTGA	0.483													C|||	894	0.178514	0.0189	0.2421	5008	,	,		18730	0.2044		0.1968	False		,,,				2504	0.3037				p.R401W		Atlas-SNP	.											.	CLUAP1	32	.	0			c.C1201T						PASS	.	C	TRP/ARG,TRP/ARG	230,4164	134.1+/-170.4	9,212,1976	98.0	88.0	92.0		1201,703	2.6	1.0	16	dbSNP_52	92	1674,6926	307.4+/-308.4	157,1360,2783	yes	missense,missense	CLUAP1	NM_015041.1,NM_024793.1	101,101	166,1572,4759	TT,TC,CC		19.4651,5.2344,14.6529	possibly-damaging,possibly-damaging	401/414,235/248	3586230	1904,11090	2197	4300	6497	SO:0001583	missense	23059	exon12			AGGGTCCGGAAAT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.1201C>T	16.37:g.3586230C>T	ENSP00000460850:p.Arg401Trp	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	39	0.364486	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	345	0.15796703296703296	12	0.024390243902439025	83	0.2292817679558011	93	0.16258741258741258	157	0.20712401055408972	C	12.62	1.992071	0.35131	0.052344	0.194651	ENSG00000103351	ENST00000341633;ENST00000417763;ENST00000445795	T;T	0.53857	0.86;0.6	5.82	2.59	0.31030	.	0.551296	0.20910	N	0.083496	T	0.00039	0.0001	L	0.44542	1.39	0.34424	P	0.302169	D;D	0.61697	0.987;0.99	P;B	0.46825	0.528;0.306	T	0.07195	-1.0785	9	0.72032	D	0.01	-9.3522	5.2258	0.15393	0.1638:0.6633:0.0:0.1729	rs9790;rs1135187;rs3197712;rs17794029;rs17851473;rs52802681;rs56635709;rs58045472;rs9790	235;401	Q96AJ1-2;Q96AJ1	.;CLUA1_HUMAN	W	401;235;179	ENSP00000388642:R235W;ENSP00000397710:R179W	ENSP00000344392:R401W	R	+	1	2	CLUAP1	3526231	0.501000	0.26099	0.996000	0.52242	0.381000	0.30169	0.678000	0.25277	1.473000	0.48159	0.484000	0.47621	CGG	C|0.851;N|0.000	.	strong		0.483	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
PNPLA1	285848	hgsc.bcm.edu	37	6	36260858	36260858	+	Silent	SNP	C	C	T	rs2239795	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36260858C>T	ENST00000394571.2	+	3	459	c.459C>T	c.(457-459)ttC>ttT	p.F153F	PNPLA1_ENST00000388715.3_Silent_p.F58F|PNPLA1_ENST00000312917.5_Silent_p.F58F	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	153	Patatin.				lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						GCAGCTGCTTCGTCCCGGTGT	0.662													C|||	2095	0.418331	0.5703	0.3213	5008	,	,		17655	0.3472		0.4155	False		,,,				2504	0.3579				p.F153F		Atlas-SNP	.											PNPLA1_ENST00000394571,NS,carcinoma,+2,2	PNPLA1	92	2	0			c.C459T						PASS	.	C	,,	2278,2128	598.9+/-389.2	596,1086,521	116.0	96.0	103.0		174,459,174	-5.1	0.9	6	dbSNP_98	103	3346,5254	497.8+/-374.6	654,2038,1608	no	coding-synonymous,coding-synonymous,coding-synonymous	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	,,	1250,3124,2129	TT,TC,CC		38.907,48.2978,43.2416	,,	58/447,153/533,58/438	36260858	5624,7382	2203	4300	6503	SO:0001819	synonymous_variant	285848	exon3			CTGCTTCGTCCCG		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.459C>T	6.37:g.36260858C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	67	32	0.477612	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Silent	SNP	ENST00000394571.2	37	CCDS54997.1																																																																																			C|0.568;T|0.432	0.432	strong		0.662	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
CEP170	9859	hgsc.bcm.edu	37	1	243319611	243319611	+	Missense_Mutation	SNP	T	T	C	rs148125417	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:243319611T>C	ENST00000366542.1	-	14	3874	c.3823A>G	c.(3823-3825)Atg>Gtg	p.M1275V	CEP170_ENST00000490813.1_Start_Codon_SNP_p.M1V|CEP170_ENST00000366544.1_Missense_Mutation_p.M1177V|CEP170_ENST00000481987.1_Start_Codon_SNP_p.M1V|CEP170_ENST00000366543.1_Missense_Mutation_p.M1141V	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1275	Targeting to centrosomes.|Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CTAGTAGGCATTGCTGATCCA	0.463													T|||	66	0.0131789	0.0015	0.0288	5008	,	,		14196	0.001		0.0338	False		,,,				2504	0.0092				p.M1275V		Atlas-SNP	.											.	CEP170	153	.	0			c.A3823G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	24,3654		0,24,1815	34.0	35.0	35.0		3529,3421,3823	4.9	1.0	1	dbSNP_134	35	298,7850		8,282,3784	no	missense,missense,missense	CEP170	NM_001042404.1,NM_001042405.1,NM_014812.2	21,21,21	8,306,5599	CC,CT,TT		3.6573,0.6525,2.7228	benign,benign,benign	1177/1487,1141/1461,1275/1585	243319611	322,11504	1839	4074	5913	SO:0001583	missense	9859	exon14			TAGGCATTGCTGA	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.3823A>G	1.37:g.243319611T>C	ENSP00000355500:p.Met1275Val	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	150	72	0.48	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	39	0.017857142857142856	1	0.0020325203252032522	11	0.03038674033149171	1	0.0017482517482517483	26	0.03430079155672823	T	11.58	1.681282	0.29872	0.006525	0.036573	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000481987;ENST00000532008;ENST00000490813;ENST00000413359;ENST00000464936;ENST00000492145	T;T;T;T	0.42513	1.0;0.99;0.97;2.17	4.87	4.87	0.63330	.	0.423844	0.29145	N	0.013015	T	0.03651	0.0104	N	0.02011	-0.69	0.80722	D	1	B;B;B;B	0.24132	0.098;0.053;0.053;0.012	B;B;B;B	0.21708	0.033;0.036;0.036;0.01	T	0.07366	-1.0776	10	0.30078	T	0.28	-6.2952	7.4618	0.27300	0.0:0.1703:0.0:0.8297	.	1238;1177;1141;1275	B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.;.;.;CE170_HUMAN	V	1275;1177;1141;1;200;1;84;1;1	ENSP00000355500:M1275V;ENSP00000355502:M1177V;ENSP00000355501:M1141V;ENSP00000394002:M84V	ENSP00000355500:M1275V	M	-	1	0	CEP170	241386234	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.327000	0.43858	1.820000	0.53075	0.454000	0.30748	ATG	T|0.982;C|0.018	0.018	strong		0.463	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
FCGBP	8857	hgsc.bcm.edu	37	19	40374034	40374034	+	Missense_Mutation	SNP	A	A	G	rs138587194		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40374034A>G	ENST00000221347.6	-	26	12051	c.12044T>C	c.(12043-12045)gTg>gCg	p.V4015A	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4015	Cys-rich.		V -> A (in dbSNP:rs3746009).			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)			GACTTTACCCACATGGCACGT	0.642																																					p.V4015A		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.T12044C						PASS	.						9.0	11.0	10.0					19																	40374034		2090	4127	6217	SO:0001583	missense	8857	exon26			TTACCCACATGGC	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.12044T>C	19.37:g.40374034A>G	ENSP00000221347:p.Val4015Ala	Somatic	372	1	0.00268817		WXS	Illumina HiSeq	Phase_I	1233	756	0.613139	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.085982	0.00371	.	.	ENSG00000090920	ENST00000221347	T	0.04603	3.59	2.99	1.93	0.25924	von Willebrand factor, type C (1);	.	.	.	.	T	0.01092	0.0036	N	0.00237	-1.79	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.41945	-0.9480	8	0.07482	T	0.82	.	6.8179	0.23841	0.2344:0.0:0.7656:0.0	.	4015	Q9Y6R7	FCGBP_HUMAN	A	4015	ENSP00000221347:V4015A	ENSP00000221347:V4015A	V	-	2	0	FCGBP	45065874	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.813000	0.27225	0.147000	0.19030	-2.348000	0.00243	GTG	A|0.200;G|0.800	0.800	strong		0.642	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PKD1	5310	hgsc.bcm.edu	37	16	2162887	2162887	+	Silent	SNP	A	A	G	rs2369068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2162887A>G	ENST00000262304.4	-	13	3271	c.3063T>C	c.(3061-3063)ggT>ggC	p.G1021G	PKD1_ENST00000423118.1_Silent_p.G1021G|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1021					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGACCTGCAGACCCTGCATCC	0.642													g|||	916	0.182907	0.5356	0.1427	5008	,	,		11079	0.0		0.0944	False		,,,				2504	0.0143				p.G1021G		Atlas-SNP	.											.	PKD1	184	.	0			c.T3063C						PASS	.	G	,	2023,2373	604.7+/-390.4	468,1087,643	128.0	123.0	125.0		3063,3063	1.6	0.4	16	dbSNP_100	125	911,7689	775.7+/-407.7	55,801,3444	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	523,1888,4087	GG,GA,AA		10.593,46.0191,22.5762	,	1021/4303,1021/4304	2162887	2934,10062	2198	4300	6498	SO:0001819	synonymous_variant	5310	exon13			CTGCAGACCCTGC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.3063T>C	16.37:g.2162887A>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	43	22	0.511628	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.796;G|0.204	0.204	strong		0.642	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
KCNH6	81033	hgsc.bcm.edu	37	17	61623052	61623052	+	Missense_Mutation	SNP	C	C	T	rs35819807	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61623052C>T	ENST00000583023.1	+	14	2785	c.2774C>T	c.(2773-2775)aCg>aTg	p.T925M	KCNH6_ENST00000581784.1_Missense_Mutation_p.T836M|KCNH6_ENST00000456941.2_Missense_Mutation_p.T836M|KCNH6_ENST00000314672.5_Missense_Mutation_p.T889M	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	925			T -> M (in dbSNP:rs35819807). {ECO:0000269|PubMed:14702039}.		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)	GCTGTGGCAACGGACAAAACT	0.567													C|||	701	0.139976	0.1626	0.1052	5008	,	,		18935	0.0367		0.2485	False		,,,				2504	0.1288				p.T925M		Atlas-SNP	.											.	KCNH6	122	.	0			c.C2774T						PASS	.	C	MET/THR,MET/THR	723,3683	298.4+/-285.3	64,595,1544	102.0	91.0	95.0		2774,2507	-7.6	0.0	17	dbSNP_126	95	2122,6478	366.0+/-334.1	277,1568,2455	yes	missense,missense	KCNH6	NM_030779.2,NM_173092.1	81,81	341,2163,3999	TT,TC,CC		24.6744,16.4094,21.8745	benign,benign	925/995,836/906	61623052	2845,10161	2203	4300	6503	SO:0001583	missense	81033	exon14			TGGCAACGGACAA	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.2774C>T	17.37:g.61623052C>T	ENSP00000463533:p.Thr925Met	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	343	0.15705128205128205	86	0.17479674796747968	45	0.12430939226519337	22	0.038461538461538464	190	0.25065963060686014	C	9.316	1.056938	0.19907	0.164094	0.246744	ENSG00000173826	ENST00000314672;ENST00000456941	D	0.99220	-5.58	5.02	-7.62	0.01294	.	1.666530	0.04760	N	0.426110	T	0.00356	0.0011	N	0.16478	0.41	0.80722	P	0.0	B;B;B	0.14012	0.007;0.003;0.009	B;B;B	0.09377	0.003;0.004;0.002	T	0.73575	-0.3939	9	0.30078	T	0.28	.	6.9583	0.24583	0.0995:0.493:0.2976:0.1098	rs35819807	889;836;925	B4DKC0;Q9H252-2;Q9H252	.;.;KCNH6_HUMAN	M	925;836	ENSP00000396900:T836M	ENSP00000318212:T925M	T	+	2	0	KCNH6	58976784	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.188000	0.17018	-1.025000	0.03334	-1.092000	0.02172	ACG	C|0.804;T|0.196	0.196	strong		0.567	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779	
BYSL	705	hgsc.bcm.edu	37	6	41895153	41895153	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41895153G>A	ENST00000230340.4	+	2	685	c.310G>A	c.(310-312)Gag>Aag	p.E104K		NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	104					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGAGGACGAGGAGTGGCCCAC	0.542																																					p.E104K		Atlas-SNP	.											.	BYSL	17	.	0			c.G310A						PASS	.						127.0	115.0	119.0					6																	41895153		2203	4300	6503	SO:0001583	missense	705	exon2			GACGAGGAGTGGC	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.310G>A	6.37:g.41895153G>A	ENSP00000230340:p.Glu104Lys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	135	52	0.385185	NM_004053	Q6P5W4|Q86W44|Q96IP8	Missense_Mutation	SNP	ENST00000230340.4	37	CCDS34450.1	.	.	.	.	.	.	.	.	.	.	G	34	5.317664	0.95682	.	.	ENSG00000112578	ENST00000230340	T	0.21734	1.99	5.37	4.5	0.54988	.	0.049967	0.85682	D	0.000000	T	0.12732	0.0309	M	0.74647	2.275	0.80722	D	1	B	0.12013	0.005	B	0.09377	0.004	T	0.04522	-1.0945	10	0.24483	T	0.36	-14.342	13.8124	0.63270	0.0747:0.0:0.9253:0.0	.	104	Q13895	BYST_HUMAN	K	104	ENSP00000230340:E104K	ENSP00000230340:E104K	E	+	1	0	BYSL	42003131	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	9.177000	0.94849	1.267000	0.44247	0.643000	0.83706	GAG	.	.	none		0.542	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2		
NPR2	4882	hgsc.bcm.edu	37	9	35802583	35802583	+	Silent	SNP	C	C	T	rs5812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35802583C>T	ENST00000342694.2	+	11	2049	c.1794C>T	c.(1792-1794)taC>taT	p.Y598Y		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	598	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	TCACTGAATACTGTCCTCGTG	0.468													T|||	1565	0.3125	0.4962	0.2334	5008	,	,		20745	0.3819		0.2008	False		,,,				2504	0.1636				p.Y598Y		Atlas-SNP	.											.	NPR2	162	.	0			c.C1794T						PASS	.	T		2011,2395	615.3+/-392.5	468,1075,660	111.0	100.0	104.0		1794	3.1	1.0	9	dbSNP_52	104	1736,6864	736.2+/-407.0	167,1402,2731	no	coding-synonymous	NPR2	NM_003995.3		635,2477,3391	TT,TC,CC		20.186,45.6423,28.8098		598/1048	35802583	3747,9259	2203	4300	6503	SO:0001819	synonymous_variant	4882	exon11			TGAATACTGTCCT	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.1794C>T	9.37:g.35802583C>T		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	216	107	0.49537	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1																																																																																			C|0.695;T|0.305	0.305	strong		0.468	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
ALDH1A3	220	hgsc.bcm.edu	37	15	101432798	101432798	+	Nonsense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:101432798C>G	ENST00000329841.5	+	4	961	c.429C>G	c.(427-429)taC>taG	p.Y143*	ALDH1A3_ENST00000346623.6_Intron|RP11-66B24.4_ENST00000560351.1_RNA	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	143					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	CCCTCAGATACTTTGCAGGGT	0.478																																					p.Y143X		Atlas-SNP	.											.	ALDH1A3	61	.	0			c.C429G						PASS	.						131.0	131.0	131.0					15																	101432798		2203	4300	6503	SO:0001587	stop_gained	220	exon4			CAGATACTTTGCA	U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"""Aldehyde dehydrogenases"""	409	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 3"""	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.429C>G	15.37:g.101432798C>G	ENSP00000332256:p.Tyr143*	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	127	70	0.551181	NM_000693	Q6NT64	Nonsense_Mutation	SNP	ENST00000329841.5	37	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.702411	0.88924	.	.	ENSG00000184254	ENST00000329841	.	.	.	5.52	2.11	0.27256	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.2979	0.43635	0.0:0.7892:0.0:0.2108	.	.	.	.	X	143	.	ENSP00000332256:Y143X	Y	+	3	2	ALDH1A3	99250321	0.827000	0.29292	0.998000	0.56505	0.980000	0.70556	-0.072000	0.11486	0.120000	0.18254	0.555000	0.69702	TAC	.	.	none		0.478	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2		
CLN5	1203	hgsc.bcm.edu	37	13	77566090	77566090	+	Missense_Mutation	SNP	C	C	T	rs77416795	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:77566090C>T	ENST00000377453.3	+	1	1296	c.4C>T	c.(4-6)Cgc>Tgc	p.R2C		NM_006493.2	NP_006484.1	O75503	CLN5_HUMAN	ceroid-lipofuscinosis, neuronal 5	0					brain development (GO:0007420)|cell death (GO:0008219)|glycosylation (GO:0070085)|lysosomal lumen acidification (GO:0007042)|neurogenesis (GO:0022008)|neuron maturation (GO:0042551)|protein catabolic process (GO:0030163)|signal peptide processing (GO:0006465)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|vacuolar lumen (GO:0005775)	mannose binding (GO:0005537)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0503)		AGGTGTCATGCGCCGGAACCT	0.706													C|||	698	0.139377	0.1293	0.2608	5008	,	,		12735	0.1071		0.0994	False		,,,				2504	0.1411				p.R2C		Atlas-SNP	.											CLN5,NS,carcinoma,-1,1	CLN5	32	1	0			c.C4T						PASS	.	C	CYS/ARG	400,3146		17,366,1390	3.0	4.0	3.0		4	2.1	0.0	13	dbSNP_131	3	731,6513		40,651,2931	yes	missense	CLN5	NM_006493.2	180	57,1017,4321	TT,TC,CC		10.0911,11.2803,10.4819		2/408	77566090	1131,9659	1773	3622	5395	SO:0001583	missense	1203	exon1			GTCATGCGCCGGA		CCDS9456.1	13q21.2-q32	2014-09-17			ENSG00000102805	ENSG00000102805			2076	protein-coding gene	gene with protein product		608102				7942847, 8661106	Standard	NM_006493		Approved		uc001vkc.3	O75503	OTTHUMG00000017100	ENST00000377453.3:c.4C>T	13.37:g.77566090C>T	ENSP00000366673:p.Arg2Cys	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_006493	B3KQK7	Missense_Mutation	SNP	ENST00000377453.3	37	CCDS9456.1	275	0.1259157509157509	67	0.13617886178861788	74	0.20441988950276244	58	0.10139860139860139	76	0.10026385224274406	C	14.02	2.409456	0.42715	0.112803	0.100911	ENSG00000102805	ENST00000377453	T	0.35605	1.3	3.0	2.13	0.27403	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.13845	-1.0494	5	0.87932	D	0	.	3.9634	0.09421	0.2315:0.6377:0.0:0.1308	.	.	.	.	C	2	ENSP00000366673:R2C	ENSP00000366673:R2C	R	+	1	0	CLN5	76464091	0.002000	0.14202	0.006000	0.13384	0.017000	0.09413	0.035000	0.13797	0.794000	0.33899	0.462000	0.41574	CGC	C|0.873;T|0.127	0.127	strong		0.706	CLN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045318.1	NM_006493	
ADAM2	2515	hgsc.bcm.edu	37	8	39695677	39695677	+	Missense_Mutation	SNP	C	C	A	rs34800519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39695677C>A	ENST00000265708.4	-	1	131	c.28G>T	c.(28-30)Ggg>Tgg	p.G10W	ADAM2_ENST00000347580.4_Missense_Mutation_p.G10W|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000521880.1_Missense_Mutation_p.G10W|ADAM2_ENST00000379853.2_Missense_Mutation_p.G10W	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	10			G -> W (in dbSNP:rs34800519).		adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		CCGCCGAGCCCGCTGAGCAGA	0.572													C|||	132	0.0263578	0.0923	0.0101	5008	,	,		16527	0.0		0.003	False		,,,				2504	0.0				p.G10W		Atlas-SNP	.											ADAM2,NS,carcinoma,+1,1	ADAM2	124	1	0			c.G28T						PASS	.	C	TRP/GLY	299,4107	164.4+/-196.0	19,261,1923	80.0	80.0	80.0		28	3.3	0.3	8	dbSNP_126	80	16,8584	11.9+/-42.8	0,16,4284	yes	missense	ADAM2	NM_001464.3	184	19,277,6207	AA,AC,CC		0.186,6.7862,2.422	probably-damaging	10/736	39695677	315,12691	2203	4300	6503	SO:0001583	missense	2515	exon1			CGAGCCCGCTGAG	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"""ADAM metallopeptidase domain containing"""	198	protein-coding gene	gene with protein product	"""cancer/testis antigen 15"""	601533	"""fertilin beta"""	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.28G>T	8.37:g.39695677C>A	ENSP00000265708:p.Gly10Trp	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	124	49	0.395161	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	37	CCDS34884.1	54	0.024725274725274724	47	0.09552845528455285	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	15.16	2.751827	0.49362	0.067862	0.00186	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.02258	5.01;4.37;5.24;5.21	3.26	3.26	0.37387	.	.	.	.	.	T	0.00300	0.0009	M	0.80982	2.52	0.19300	N	0.999973	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.98;0.999;0.991;0.971	T	0.04053	-1.0981	8	.	.	.	.	10.2854	0.43564	0.0:1.0:0.0:0.0	rs34800519	10;10;10;10	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	W	10	ENSP00000343854:G10W;ENSP00000369182:G10W;ENSP00000265708:G10W;ENSP00000429352:G10W	.	G	-	1	0	ADAM2	39814834	0.048000	0.20356	0.275000	0.24674	0.128000	0.20619	1.104000	0.31074	2.114000	0.64651	0.460000	0.39030	GGG	C|0.977;A|0.023	0.023	strong		0.572	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464	
MRPL39	54148	hgsc.bcm.edu	37	21	26969703	26969703	+	Silent	SNP	T	T	C	rs1135618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:26969703T>C	ENST00000352957.4	-	6	653	c.612A>G	c.(610-612)aaA>aaG	p.K204K	MRPL39_ENST00000307301.7_Silent_p.K204K	NM_017446.3	NP_059142	Q9NYK5	RM39_HUMAN	mitochondrial ribosomal protein L39	204						mitochondrial ribosome (GO:0005761)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	10						CATGAGCATCTTTTGTGAAGG	0.333													C|||	3670	0.732827	0.7284	0.8199	5008	,	,		16021	0.7153		0.8141	False		,,,				2504	0.6115				p.K204K		Atlas-SNP	.											.	MRPL39	61	.	0			c.A612G						PASS	.	C	,	3308,1092		1232,844,124	51.0	48.0	49.0		612,612	-1.6	1.0	21	dbSNP_86	49	7124,1476		2975,1174,151	no	coding-synonymous,coding-synonymous	MRPL39	NM_017446.3,NM_080794.3	,	4207,2018,275	CC,CT,TT		17.1628,24.8182,19.7538	,	204/339,204/354	26969703	10432,2568	2200	4300	6500	SO:0001819	synonymous_variant	54148	exon6			AGCATCTTTTGTG	AB051346	CCDS13573.1, CCDS33522.1	21q11.2-q21	2012-09-13			ENSG00000154719	ENSG00000154719		"""Mitochondrial ribosomal proteins / large subunits"""	14027	protein-coding gene	gene with protein product		611845				11543634	Standard	NM_080794		Approved	RPML5, MRP-L5, MGC104174, PRED66, PRED22, C21orf92, L39mt, MSTP003, MGC3400, FLJ20451	uc002yln.3	Q9NYK5	OTTHUMG00000078371	ENST00000352957.4:c.612A>G	21.37:g.26969703T>C		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	148	73	0.493243	NM_017446	C9JYA5|Q32Q74|Q5QTR3|Q96Q65|Q9BSQ7|Q9BZV6|Q9NX44	Silent	SNP	ENST00000352957.4	37	CCDS13573.1																																																																																			T|0.220;C|0.780	0.780	strong		0.333	MRPL39-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000171194.1	NM_017446	
SALL4	57167	hgsc.bcm.edu	37	20	50406871	50406871	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:50406871C>T	ENST00000217086.4	-	2	2262	c.2151G>A	c.(2149-2151)tcG>tcA	p.S717S	SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	717					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						TGGGTGATGCCGAGTGGATGC	0.577																																					p.S717S		Atlas-SNP	.											SALL4,NS,carcinoma,-1,1	SALL4	168	1	0			c.G2151A						scavenged	.						40.0	38.0	39.0					20																	50406871		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			TGATGCCGAGTGG	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.2151G>A	20.37:g.50406871C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	131	2	0.0152672	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			.	.	none		0.577	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
ADAM30	11085	hgsc.bcm.edu	37	1	120437718	120437718	+	Silent	SNP	G	G	A	rs2793823	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:120437718G>A	ENST00000369400.1	-	1	1400	c.1242C>T	c.(1240-1242)gaC>gaT	p.D414D		NM_021794.3	NP_068566.2	Q9UKF2	ADA30_HUMAN	ADAM metallopeptidase domain 30	414	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(11)|lung(16)|ovary(2)|skin(2)	38	all_cancers(5;7.07e-10)|all_epithelial(5;1.62e-10)|all_neural(166;0.153)|Breast(55;0.234)	all_lung(203;1.55e-06)|Lung NSC(69;1.04e-05)|all_epithelial(167;0.00138)		Lung(183;0.0204)|LUSC - Lung squamous cell carcinoma(189;0.117)		TGGAACCACAGTCACATTCCT	0.423													A|||	1656	0.330671	0.7171	0.2133	5008	,	,		22465	0.1052		0.1322	False		,,,				2504	0.3282				p.D414D		Atlas-SNP	.											.	ADAM30	88	.	0			c.C1242T						PASS	.	A		2579,1827	534.8+/-374.1	743,1093,367	174.0	167.0	170.0		1242	-5.5	0.7	1	dbSNP_100	170	1092,7508	769.0+/-407.6	74,944,3282	no	coding-synonymous	ADAM30	NM_021794.3		817,2037,3649	AA,AG,GG		12.6977,41.4662,28.2254		414/791	120437718	3671,9335	2203	4300	6503	SO:0001819	synonymous_variant	11085	exon1			ACCACAGTCACAT	AF171932	CCDS907.1	1p12	2012-05-16	2005-08-18		ENSG00000134249	ENSG00000134249		"""ADAM metallopeptidase domain containing"""	208	protein-coding gene	gene with protein product		604779	"""a disintegrin and metalloproteinase domain 30"""				Standard	NM_021794		Approved	svph4	uc001eij.3	Q9UKF2	OTTHUMG00000012176	ENST00000369400.1:c.1242C>T	1.37:g.120437718G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_021794	A8K8W8|Q5T3X6|Q9UKF1	Silent	SNP	ENST00000369400.1	37	CCDS907.1																																																																																			G|0.719;A|0.280	0.280	strong		0.423	ADAM30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033678.1	NM_021794	
FYCO1	79443	hgsc.bcm.edu	37	3	45996761	45996761	+	Silent	SNP	G	G	A	rs1463680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:45996761G>A	ENST00000296137.2	-	14	4129	c.3924C>T	c.(3922-3924)ctC>ctT	p.L1308L	FYCO1_ENST00000535325.1_Silent_p.L1308L|FYCO1_ENST00000438446.1_5'UTR	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	1308					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		CATTTGGGTCGAGAGAATCAG	0.507													A|||	4343	0.867212	0.9009	0.8401	5008	,	,		21329	0.9544		0.7435	False		,,,				2504	0.8783				p.L1308L		Atlas-SNP	.											.	FYCO1	115	.	0			c.C3924T						PASS	.	A		3841,565	250.9+/-257.8	1676,489,38	177.0	182.0	181.0		3924	-6.0	0.1	3	dbSNP_88	181	6186,2414	400.8+/-346.9	2202,1782,316	no	coding-synonymous	FYCO1	NM_024513.2		3878,2271,354	AA,AG,GG		28.0698,12.8234,22.9048		1308/1479	45996761	10027,2979	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon14			TGGGTCGAGAGAA	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.3924C>T	3.37:g.45996761G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	139	66	0.47482	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1	1877	0.8594322344322345	446	0.9065040650406504	303	0.8370165745856354	545	0.9527972027972028	583	0.7691292875989446	A	8.103	0.776982	0.16120	0.871766	0.719302	ENSG00000163820	ENST00000433878	.	.	.	5.82	-5.97	0.02227	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999821	.	.	.	.	.	.	T	0.19484	-1.0304	3	.	.	.	-0.2817	9.4543	0.38745	0.2298:0.4435:0.3267:0.0	rs1463680;rs17280512;rs57026309;rs1463680	.	.	.	L	97	.	.	S	-	2	0	FYCO1	45971765	0.097000	0.21791	0.137000	0.22149	0.764000	0.43329	-0.921000	0.04008	-0.777000	0.04572	-0.254000	0.11334	TCG	G|0.186;A|0.814	0.814	strong		0.507	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
PHACTR4	65979	hgsc.bcm.edu	37	1	28793149	28793149	+	Silent	SNP	C	C	G	rs61748637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:28793149C>G	ENST00000373839.3	+	6	954	c.693C>G	c.(691-693)ccC>ccG	p.P231P	PHACTR4_ENST00000373836.3_Silent_p.P241P|PHACTR4_ENST00000493669.1_3'UTR	NM_001048183.1	NP_001041648.1	Q8IZ21	PHAR4_HUMAN	phosphatase and actin regulator 4	231	Pro-rich.				actin cytoskeleton organization (GO:0030036)|closure of optic fissure (GO:0061386)|enteric nervous system development (GO:0048484)|negative regulation of integrin-mediated signaling pathway (GO:2001045)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of catalytic activity (GO:0043085)|regulation of cell cycle (GO:0051726)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)	actin binding (GO:0003779)|protein phosphatase 1 binding (GO:0008157)|protein phosphatase type 1 activator activity (GO:0071862)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	32		Colorectal(325;3.46e-05)|Lung NSC(340;4.37e-05)|all_lung(284;7.01e-05)|Renal(390;0.00121)|Breast(348;0.00345)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0261)		OV - Ovarian serous cystadenocarcinoma(117;1.35e-21)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0144)|READ - Rectum adenocarcinoma(331;0.0649)		CCCCAGCACCCAGGACTCTGC	0.582													C|||	258	0.0515176	0.0053	0.0375	5008	,	,		16180	0.0704		0.0835	False		,,,				2504	0.0716				p.P241P		Atlas-SNP	.											.	PHACTR4	64	.	0			c.C723G						PASS	.	C	,	62,4164		0,62,2051	57.0	65.0	62.0		693,723	4.6	1.0	1	dbSNP_129	62	603,7855		23,557,3649	no	coding-synonymous,coding-synonymous	PHACTR4	NM_001048183.1,NM_023923.3	,	23,619,5700	GG,GC,CC		7.1293,1.4671,5.2428	,	231/703,241/713	28793149	665,12019	2113	4229	6342	SO:0001819	synonymous_variant	65979	exon5			AGCACCCAGGACT	AF130081	CCDS41293.1, CCDS41294.1	1p35.2	2014-06-13			ENSG00000204138	ENSG00000204138		"""Phosphatase and actin regulators"""	25793	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 124"""	608726				11483580, 15107502	Standard	NM_023923		Approved	FLJ13171, PPP1R124	uc001bpy.3	Q8IZ21	OTTHUMG00000003541	ENST00000373839.3:c.693C>G	1.37:g.28793149C>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	121	114	0.942149	NM_023923	A2APK6|B9ZVW0|D3DPM3|Q68DD4|Q6NUN6|Q8N384|Q9H395|Q9H6X0|Q9H8W6	Silent	SNP	ENST00000373839.3	37	CCDS41293.1																																																																																			C|0.945;G|0.055	0.055	strong		0.582	PHACTR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009868.4	NM_023923	
CDH3	1001	hgsc.bcm.edu	37	16	68721533	68721533	+	Missense_Mutation	SNP	G	G	C	rs1126933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68721533G>C	ENST00000264012.4	+	12	2233	c.1689G>C	c.(1687-1689)caG>caC	p.Q563H	CDH3_ENST00000429102.2_Missense_Mutation_p.Q563H|CDH3_ENST00000581171.1_Missense_Mutation_p.Q508H	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	563	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> H (in dbSNP:rs1126933). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15805154, ECO:0000269|PubMed:2793940, ECO:0000269|Ref.3}.		adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		CTGTGCGCCAGGTGCTGAACA	0.577													G|||	1552	0.309904	0.0242	0.3991	5008	,	,		20646	0.5139		0.4046	False		,,,				2504	0.3252				p.Q563H		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G1689C						PASS	.	G	HIS/GLN	396,4000	197.7+/-221.8	17,362,1819	163.0	130.0	141.0		1689	-3.3	0.5	16	dbSNP_86	141	3590,5010	519.8+/-379.5	747,2096,1457	yes	missense	CDH3	NM_001793.4	24	764,2458,3276	CC,CG,GG		41.7442,9.0082,30.671	benign	563/830	68721533	3986,9010	2198	4300	6498	SO:0001583	missense	1001	exon12			GCGCCAGGTGCTG	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1689G>C	16.37:g.68721533G>C	ENSP00000264012:p.Gln563His	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	107	57	0.53271	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	37	CCDS10868.1	777	0.3557692307692308	14	0.028455284552845527	142	0.39226519337016574	306	0.534965034965035	315	0.4155672823218997	G	6.651	0.488628	0.12641	0.090082	0.417442	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.61158	0.13;0.13	5.05	-3.29	0.05017	Cadherin (1);Cadherin-like (1);	0.000000	0.39475	N	0.001353	T	0.00012	0.0000	L	0.33339	1.005	0.27598	P	0.9490638	B	0.18610	0.029	B	0.12837	0.008	T	0.46400	-0.9194	9	0.20519	T	0.43	.	7.6829	0.28524	0.358:0.1375:0.5045:0.0	rs1126933;rs17689848;rs52790482;rs1126933	563	P22223	CADH3_HUMAN	H	563;563;508	ENSP00000398485:Q563H;ENSP00000264012:Q563H	ENSP00000264012:Q563H	Q	+	3	2	CDH3	67279034	0.001000	0.12720	0.518000	0.27811	0.491000	0.33493	-0.055000	0.11807	-0.578000	0.05959	-0.471000	0.05019	CAG	G|0.672;C|0.328	0.328	strong		0.577	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
TJP2	9414	hgsc.bcm.edu	37	9	71863235	71863235	+	Intron	SNP	A	A	G	rs77236826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:71863235A>G	ENST00000377245.4	+	19	3088				TJP2_ENST00000535702.1_Intron|TJP2_ENST00000348208.4_Intron|TJP2_ENST00000539225.1_Intron|TJP2_ENST00000453658.2_Intron|TJP2_ENST00000265384.7_Missense_Mutation_p.H992R	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2						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						TGTGGAAGGCATTCCTAAGGG	0.592													A|||	266	0.053115	0.0469	0.0519	5008	,	,		20316	0.0069		0.0815	False		,,,				2504	0.0808				p.H992R		Atlas-SNP	.											TJP2_ENST00000265384,NS,haematopoietic_neoplasm,0,1	TJP2	120	1	0			c.A2975G						PASS	.	A	,,,ARG/HIS,,	77,1307		2,73,617	71.0	95.0	87.0		,,,2975,,	-9.9	0.0	9	dbSNP_132	87	239,2943		6,227,1358	yes	intron,intron,intron,missense,intron,intron	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,29,,	8,300,1975	GG,GA,AA		7.511,5.5636,6.9207	,,,,,	,,,992/994,,	71863235	316,4250	692	1591	2283	SO:0001627	intron_variant	9414	exon19			GAAGGCATTCCTA	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.2880+95A>G	9.37:g.71863235A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	147	64	0.435374	NM_001170630	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	121	0.0554029304029304	26	0.052845528455284556	23	0.06353591160220995	3	0.005244755244755245	69	0.09102902374670185	A	11.92	1.782859	0.31502	0.055636	0.07511	ENSG00000119139	ENST00000265384	T	0.08458	3.09	4.93	-9.87	0.00470	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42515	-0.9447	7	.	.	.	.	8.1873	0.31346	0.1595:0.0:0.5122:0.3283	.	992	Q9UDY2-5	.	R	992	ENSP00000265384:H992R	.	H	+	2	0	TJP2	71053055	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.094000	0.11094	-1.910000	0.01083	-1.167000	0.01749	CAT	A|0.944;G|0.056	0.056	strong		0.592	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
KIAA1109	84162	hgsc.bcm.edu	37	4	123280860	123280860	+	Silent	SNP	T	T	C	rs1127348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:123280860T>C	ENST00000264501.4	+	85	15157	c.14784T>C	c.(14782-14784)caT>caC	p.H4928H	KIAA1109_ENST00000388738.3_Silent_p.H4928H			Q2LD37	K1109_HUMAN	KIAA1109	4928					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						ATACATGGCATCTAGAACCTA	0.323													T|||	610	0.121805	0.0068	0.1311	5008	,	,		19004	0.123		0.2416	False		,,,				2504	0.1462				p.H4928H		Atlas-SNP	.											KIAA1109,colon,carcinoma,0,1	KIAA1109	424	1	0			c.T14784C						PASS	.	T		142,3558		5,132,1713	119.0	106.0	110.0		14784	5.9	1.0	4	dbSNP_86	110	1764,6428		193,1378,2525	no	coding-synonymous	KIAA1109	NM_015312.3		198,1510,4238	CC,CT,TT		21.5332,3.8378,16.0276		4928/5006	123280860	1906,9986	1850	4096	5946	SO:0001819	synonymous_variant	84162	exon83			ATGGCATCTAGAA	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.14784T>C	4.37:g.123280860T>C		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Silent	SNP	ENST00000264501.4	37	CCDS43267.1	310	0.14194139194139194	3	0.006097560975609756	51	0.1408839779005525	75	0.13111888111888112	181	0.23878627968337732	T	7.423	0.637044	0.14386	0.038378	0.215332	ENSG00000138688	ENST00000306802	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.06661	-1.0814	3	.	.	.	.	12.2461	0.54571	0.0:0.0678:0.0:0.9322	rs1127348;rs2306366;rs17388140;rs60969099;rs1127348	.	.	.	T	1304	.	.	I	+	2	0	KIAA1109	123500310	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.379000	0.44318	2.282000	0.76494	0.528000	0.53228	ATC	T|0.843;C|0.157	0.157	strong		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
KRTAP12-2	353323	hgsc.bcm.edu	37	21	46086407	46086407	+	Missense_Mutation	SNP	C	C	T	rs12481809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46086407C>T	ENST00000360770.3	-	1	437	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	TSPEAR_ENST00000323084.4_Intron	NM_181684.2	NP_859012.1	P59991	KR122_HUMAN	keratin associated protein 12-2	133	23 X 5 AA approximate repeats.					keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(1)|lung(3)	5						CTGCAGAGGACGCTGGTGCAG	0.622													C|||	731	0.145966	0.0946	0.1657	5008	,	,		19372	0.0923		0.2068	False		,,,				2504	0.1943				p.V133I		Atlas-SNP	.											.	KRTAP12-2	10	.	0			c.G397A						PASS	.	C	,ILE/VAL	403,3907		22,359,1774	54.0	60.0	58.0		,397	1.5	0.1	21	dbSNP_120	58	1732,6738		170,1392,2673	yes	intron,missense	TSPEAR,KRTAP12-2	NM_144991.2,NM_181684.2	,29	192,1751,4447	TT,TC,CC		20.4486,9.3503,16.7058	,benign	,133/147	46086407	2135,10645	2155	4235	6390	SO:0001583	missense	353323	exon1			AGAGGACGCTGGT	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.397G>A	21.37:g.46086407C>T	ENSP00000354001:p.Val133Ile	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	253	127	0.501976	NM_181684	A6NIS1|A6NMS9|Q0VAS4	Missense_Mutation	SNP	ENST00000360770.3	37	CCDS42965.1	321	0.14697802197802198	45	0.09146341463414634	61	0.1685082872928177	56	0.0979020979020979	159	0.20976253298153033	c	2.766	-0.256710	0.05829	0.093503	0.204486	ENSG00000221864	ENST00000360770;ENST00000539483	T	0.02656	4.21	3.62	1.54	0.23209	.	.	.	.	.	T	0.00012	0.0000	L	0.39898	1.24	0.80722	P	0.0	B	0.29936	0.262	B	0.23150	0.044	T	0.46762	-0.9168	8	0.24483	T	0.36	.	5.7725	0.18261	0.1361:0.2197:0.6442:0.0	rs12481809	133	P59991	KR122_HUMAN	I	133;83	ENSP00000354001:V133I	ENSP00000354001:V133I	V	-	1	0	KRTAP12-2	44910835	0.005000	0.15991	0.063000	0.19743	0.005000	0.04900	0.296000	0.19083	0.697000	0.31718	-0.502000	0.04539	GTC	C|0.844;T|0.156	0.156	strong		0.622	KRTAP12-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128039.1	NM_181684	
PRKCZ	5590	hgsc.bcm.edu	37	1	1987993	1987993	+	IGR	SNP	T	T	C	rs12184	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1987993T>C								RP11-547D24.3 (6484 upstream) : PRKCZ (16907 downstream)																							AGTGCAGGGATGAAGGCCTCA	0.627													C|||	3355	0.669928	0.8873	0.402	5008	,	,		14345	0.9454		0.3429	False		,,,				2504	0.6186				p.D88D		Atlas-SNP	.											.	PRKCZ	84	.	0			c.T264C						PASS	.	C		3609,797	317.4+/-295.1	1478,653,72	74.0	65.0	68.0		264	-3.4	0.6	1	dbSNP_52	68	2955,5645	667.1+/-402.4	516,1923,1861	no	coding-synonymous	PRKCZ	NM_002744.4		1994,2576,1933	CC,CT,TT		34.3605,18.089,49.531		88/593	1987993	6564,6442	2203	4300	6503	SO:0001628	intergenic_variant	5590	exon3			CAGGGATGAAGGC																													1.37:g.1987993T>C		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	188	172	0.914894	NM_002744		Silent	SNP		37																																																																																				T|0.462;C|0.538	0.538	strong	0	0.627								
CSF2RA	1438	hgsc.bcm.edu	37	X	1401646	1401646	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:1401646C>G	ENST00000381524.3	+	3	236	c.50C>G	c.(49-51)gCa>gGa	p.A17G	CSF2RA_ENST00000381529.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000355432.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000355805.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000432318.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000381500.1_Missense_Mutation_p.A17G|CSF2RA_ENST00000417535.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000361536.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000381509.3_Missense_Mutation_p.A17G|CSF2RA_ENST00000494969.2_Missense_Mutation_p.A17G|CSF2RA_ENST00000501036.2_5'UTR			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	17					response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	CCACACCCAGCATTCCTCCTG	0.527													c|||	1070	0.213658	0.6914	0.0749	5008	,	,		20490	0.0308		0.0477	False		,,,				2504	0.0256				p.A17G	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.C50G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA,,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	2532,1874		717,1098,388	260.0	267.0	264.0		50,50,50,,50,50,50,50,50	0.2	0.0	X	dbSNP_134	264	358,8234		12,334,3950	yes	missense,missense,missense,utr-5,missense,missense,missense,missense,missense	CSF2RA	NM_001161529.1,NM_001161530.1,NM_001161531.1,NM_001161532.1,NM_006140.4,NM_172245.2,NM_172246.2,NM_172247.2,NM_172249.2	60,60,60,,60,60,60,60,60	729,1432,4338	GG,GC,CC		4.1667,42.5329,22.2342	possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	17/401,17/435,17/411,,17/401,17/401,17/378,17/334,17/234	1401646	2890,10108	2203	4296	6499	SO:0001583	missense	1438	exon1			ACCCAGCATTCCT	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.50C>G	X.37:g.1401646C>G	ENSP00000370935:p.Ala17Gly	Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	454	185	0.407489	NM_172247	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Missense_Mutation	SNP	ENST00000381524.3	37	CCDS35191.1	395	0.18086080586080586	317	0.6443089430894309	25	0.06906077348066299	16	0.027972027972027972	37	0.048812664907651716	.	8.761	0.923502	0.18056	0.574671	0.041667	ENSG00000198223	ENST00000381529;ENST00000432318;ENST00000361536;ENST00000381507;ENST00000381524;ENST00000412290;ENST00000419094;ENST00000381509;ENST00000355805;ENST00000355432;ENST00000417535;ENST00000381500	D;D;D;D;T;T;D;T;T;D;D	0.95238	-3.32;-3.32;-3.65;-3.32;0.61;1.55;-3.45;0.54;0.77;-3.17;-3.65	1.21	0.191	0.15130	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.20563	N	0.999885	D;P;D;D;D;P	0.61697	0.972;0.953;0.978;0.99;0.99;0.953	P;P;P;P;P;P	0.59948	0.866;0.739;0.649;0.763;0.719;0.739	T	0.24154	-1.0168	8	0.25751	T	0.34	.	3.6875	0.08334	0.0:0.7058:0.0:0.2942	.	17;17;17;17;17;17	P15509-2;A7J003;P15509-3;P15509-6;P15509-5;P15509	.;.;.;.;.;CSF2R_HUMAN	G	17	ENSP00000370940:A17G;ENSP00000416437:A17G;ENSP00000354836:A17G;ENSP00000370935:A17G;ENSP00000410667:A17G;ENSP00000397452:A17G;ENSP00000370920:A17G;ENSP00000348058:A17G;ENSP00000347606:A17G;ENSP00000394227:A17G;ENSP00000370911:A17G	ENSP00000347606:A17G	A	+	2	0	CSF2RA	1361646	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.182000	0.16900	-0.211000	0.10124	0.350000	0.21858	GCA	C|0.794;G|0.206	0.206	strong		0.527	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
ITPR2	3709	hgsc.bcm.edu	37	12	26774149	26774149	+	Silent	SNP	T	T	C	rs61754418	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:26774149T>C	ENST00000381340.3	-	26	3785	c.3369A>G	c.(3367-3369)gtA>gtG	p.V1123V	RP11-666F17.1_ENST00000414098.2_RNA|ITPR2_ENST00000545902.1_5'UTR	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1123					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)	CAGACTTTTCTACTGTCAGTC	0.418													T|||	67	0.0133786	0.0	0.0072	5008	,	,		18134	0.0		0.0229	False		,,,				2504	0.0399				p.V1123V		Atlas-SNP	.											.	ITPR2	270	.	0			c.A3369G						PASS	.	T		5,3773		0,5,1884	328.0	302.0	310.0		3369	-5.8	0.7	12	dbSNP_129	310	126,8128		1,124,4002	no	coding-synonymous	ITPR2	NM_002223.2		1,129,5886	CC,CT,TT		1.5265,0.1323,1.0888		1123/2702	26774149	131,11901	1889	4127	6016	SO:0001819	synonymous_variant	3709	exon26			CTTTTCTACTGTC	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.3369A>G	12.37:g.26774149T>C		Somatic	274	1	0.00364964		WXS	Illumina HiSeq	Phase_I	351	179	0.509971	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			T|0.987;C|0.013	0.013	strong		0.418	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
GPR179	440435	hgsc.bcm.edu	37	17	36485753	36485753	+	Silent	SNP	G	G	C	rs35803744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36485753G>C	ENST00000342292.4	-	11	3719	c.3699C>G	c.(3697-3699)ctC>ctG	p.L1233L	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1233					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CAGCGCTGCCGAGGGACTGGA	0.572													C|||	1523	0.304113	0.8026	0.1628	5008	,	,		17462	0.125		0.1561	False		,,,				2504	0.0675				p.L1233L		Atlas-SNP	.											.	GPR179	170	.	0			c.C3699G						PASS	.	C		2595,1261		896,803,229	82.0	91.0	88.0		3699	-0.3	0.1	17	dbSNP_126	88	1026,7264		67,892,3186	no	coding-synonymous	GPR179	NM_001004334.2		963,1695,3415	CC,CG,GG		12.3764,32.7023,29.8123		1233/2368	36485753	3621,8525	1928	4145	6073	SO:0001819	synonymous_variant	440435	exon11			GCTGCCGAGGGAC		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3699C>G	17.37:g.36485753G>C		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	119	119	1	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			G|0.772;C|0.228	0.228	strong		0.572	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
MRPL40	64976	hgsc.bcm.edu	37	22	19423250	19423250	+	Missense_Mutation	SNP	G	G	A	rs7575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19423250G>A	ENST00000333130.3	+	4	1039	c.386G>A	c.(385-387)cGt>cAt	p.R129H	MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000541063.1_Intron|HIRA_ENST00000546308.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	129			R -> H (in dbSNP:rs7575). {ECO:0000269|PubMed:9790763}.		anatomical structure morphogenesis (GO:0009653)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					CAGCAAGAGCGTAAGATGGAG	0.552													A|||	1204	0.240415	0.4629	0.1599	5008	,	,		20621	0.1369		0.1302	False		,,,				2504	0.2168				p.R129H		Atlas-SNP	.											.	MRPL40	13	.	0			c.G386A						PASS	.	A	HIS/ARG	1771,2635	645.0+/-398.1	343,1085,775	151.0	153.0	152.0		386	4.1	0.4	22	dbSNP_52	152	1071,7529	769.9+/-407.6	59,953,3288	yes	missense	MRPL40	NM_003776.2	29	402,2038,4063	AA,AG,GG		12.4535,40.1952,21.8515	benign	129/207	19423250	2842,10164	2203	4300	6503	SO:0001583	missense	64976	exon4			AAGAGCGTAAGAT	AB051624	CCDS13760.1	22q11.2	2012-09-13	2002-11-13		ENSG00000185608	ENSG00000185608		"""Mitochondrial ribosomal proteins / large subunits"""	14491	protein-coding gene	gene with protein product		605089	"""nuclear localization signal deleted in velocardiofacial syndrome"""	NLVCF		9790763, 11543634	Standard	NM_003776		Approved	MRP-L22	uc002zpg.3	Q9NQ50	OTTHUMG00000150136	ENST00000333130.3:c.386G>A	22.37:g.19423250G>A	ENSP00000333401:p.Arg129His	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	112	49	0.4375	NM_003776	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	37	CCDS13760.1	451	0.2065018315018315	228	0.4634146341463415	63	0.17403314917127072	67	0.11713286713286714	93	0.12269129287598944	A	1.612	-0.523852	0.04141	0.401952	0.124535	ENSG00000185608	ENST00000333130	T	0.46451	0.87	5.22	4.14	0.48551	.	0.279462	0.38381	N	0.001715	T	0.00012	0.0000	N	0.00128	-2.045	0.52099	P	5.299999999996974E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45659	-0.9246	9	0.02654	T	1	-2.778	8.2618	0.31790	0.7973:0.133:0.0697:0.0	rs7575;rs3177312;rs56481519;rs57534682;rs7575	129	Q9NQ50	RM40_HUMAN	H	129	ENSP00000333401:R129H	ENSP00000333401:R129H	R	+	2	0	MRPL40	17803250	0.994000	0.37717	0.381000	0.26106	0.244000	0.25665	3.268000	0.51585	1.001000	0.39076	-0.360000	0.07572	CGT	G|0.776;A|0.224	0.224	strong		0.552	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776	
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56704399	56704399	+	Missense_Mutation	SNP	G	G	A	rs61745809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56704399G>A	ENST00000586855.2	-	2	336	c.23C>T	c.(22-24)tCa>tTa	p.S8L	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.S8L			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	8					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S8L(1)		breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CTGACCCCATGAGAGTGTCCA	0.502													G|||	417	0.0832668	0.0068	0.1599	5008	,	,		17266	0.249		0.0358	False		,,,				2504	0.0102				p.S8L		Atlas-SNP	.											ZSCAN5B_ENST00000358992,NS,carcinoma,0,1	ZSCAN5B	160	1	1	Substitution - Missense(1)	stomach(1)	c.C23T						PASS	.	G	LEU/SER	14,1370		0,14,678	31.0	27.0	28.0		23	-1.5	0.0	19	dbSNP_129	28	83,3099		1,81,1509	yes	missense	ZSCAN5B	NM_001080456.2	145	1,95,2187	AA,AG,GG		2.6084,1.0116,2.1244	possibly-damaging	8/496	56704399	97,4469	692	1591	2283	SO:0001583	missense	342933	exon1			CCCCATGAGAGTG		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"""-"", ""Zinc fingers, C2H2-type"""	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.23C>T	19.37:g.56704399G>A	ENSP00000466072:p.Ser8Leu	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_001080456		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	221	0.10119047619047619	5	0.01016260162601626	41	0.1132596685082873	146	0.25524475524475526	29	0.03825857519788918	G	11.49	1.652951	0.29336	0.010116	0.026084	ENSG00000197213	ENST00000358992	T	0.06528	3.29	1.15	-1.46	0.08800	.	.	.	.	.	T	0.00012	0.0000	M	0.67953	2.075	0.80722	P	0.0	P	0.43094	0.799	B	0.40901	0.343	T	0.35822	-0.9773	8	0.35671	T	0.21	.	1.7451	0.02961	0.2442:0.0:0.4275:0.3283	rs61745809	8	A6NJL1	ZSA5B_HUMAN	L	8	ENSP00000351883:S8L	ENSP00000351883:S8L	S	-	2	0	ZSCAN5B	61396211	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.116000	0.15561	-0.404000	0.07610	0.467000	0.42956	TCA	G|0.915;A|0.085	0.085	strong		0.502	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558317	140558317	+	Silent	SNP	C	C	G	rs17844489	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140558317C>G	ENST00000239444.2	+	1	947	c.702C>G	c.(700-702)gtC>gtG	p.V234V	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	234	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.			V -> L (in Ref. 4; AAG10031). {ECO:0000305}.	homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TTGAAGTTGTCGATGTCAATG	0.507													C|||	673	0.134385	0.0136	0.1441	5008	,	,		24808	0.3333		0.0805	False		,,,				2504	0.1411				p.V234V		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C702G						PASS	.						180.0	225.0	210.0					5																	140558317		2202	4276	6478	SO:0001819	synonymous_variant	56128	exon1			AGTTGTCGATGTC	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.702C>G	5.37:g.140558317C>G		Somatic	970	0	0		WXS	Illumina HiSeq	Phase_I	211	51	0.241706	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			C|0.981;G|0.019	0.019	strong		0.507	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
PCDHGC3	5098	hgsc.bcm.edu	37	5	140857798	140857798	+	Silent	SNP	T	T	C	rs1423148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140857798T>C	ENST00000308177.3	+	1	2219	c.2115T>C	c.(2113-2115)ttT>ttC	p.F705F	PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA11_ENST00000518882.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	705					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGTGGGGTTTGTGGTCACAG	0.498											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2776	0.554313	0.8903	0.6182	5008	,	,		19318	0.3264		0.4225	False		,,,				2504	0.4254				p.F705F		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.T2115C						PASS	.	C	,,,,,,,,,,,,,,,,,,,,,,	3637,769	308.8+/-290.8	1499,639,65	205.0	250.0	235.0		2115,,,,,,,,,,,,,,,,,,,,,2115,	-1.6	0.6	5	dbSNP_88	235	3681,4919	618.6+/-396.8	779,2123,1398	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032092.1,NM_032402.1,NM_032403.1	,,,,,,,,,,,,,,,,,,,,,,	2278,2762,1463	CC,CT,TT		42.8023,17.4535,43.7337	,,,,,,,,,,,,,,,,,,,,,,	705/935,,,,,,,,,,,,,,,,,,,,,705/864,	140857798	7318,5688	2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GGGGTTTGTGGTC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.2115T>C	5.37:g.140857798T>C		Somatic	94	0	0	1659	WXS	Illumina HiSeq	Phase_I	104	57	0.548077	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			A|0.002;C|0.545	0.545	strong		0.498	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
MUC4	4585	hgsc.bcm.edu	37	3	195515100	195515100	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195515100G>A	ENST00000463781.3	-	2	3810	c.3351C>T	c.(3349-3351)caC>caT	p.H1117H	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.H1117H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	556					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGTGTGACCTGTGG	0.567																																					p.H1117H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	0			c.C3351T						scavenged	.						14.0	8.0	9.0					3																	195515100		671	1543	2214	SO:0001819	synonymous_variant	4585	exon2			GGTGGTGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3351C>T	3.37:g.195515100G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	98	5	0.0510204	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SDHA	6389	hgsc.bcm.edu	37	5	256509	256509	+	Missense_Mutation	SNP	G	G	A	rs6962	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:256509G>A	ENST00000264932.6	+	15	2084	c.1969G>A	c.(1969-1971)Gtc>Atc	p.V657I	SDHA_ENST00000510361.1_Missense_Mutation_p.V609I|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Missense_Mutation_p.V576I	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	657			V -> I (in dbSNP:rs6962). {ECO:0000269|PubMed:8142412}.		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)	CTGTGCCACCGTCCCGCCAGC	0.438									Familial Paragangliomas				G|||	878	0.175319	0.3744	0.2046	5008	,	,		20065	0.0585		0.1064	False		,,,				2504	0.0767				p.V657I		Atlas-SNP	.											SDHA,adrenal_gland,pheochromocytoma,0,1	SDHA	80	1	0			c.G1969A						PASS	.	G	ILE/VAL	1438,2968		218,1002,983	69.0	75.0	73.0		1969	4.1	0.1	5	dbSNP_52	73	1117,7483		56,1005,3239	no	missense	SDHA	NM_004168.2	29	274,2007,4222	AA,AG,GG		12.9884,32.6373,19.6448	benign	657/665	256509	2555,10451	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	GCCACCGTCCCGC	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.1969G>A	5.37:g.256509G>A	ENSP00000264932:p.Val657Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	122	59	0.483607	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	37	CCDS3853.1	352	0.16117216117216118	170	0.34552845528455284	73	0.20165745856353592	24	0.04195804195804196	85	0.11213720316622691	N	4.173	0.030679	0.08101	0.326373	0.129884	ENSG00000073578	ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	T;T;T	0.79940	-1.32;-1.32;-1.32	4.12	4.12	0.48240	Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (1);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);	0.079953	0.50627	U	0.000106	T	0.00012	0.0000	L	0.35542	1.07	0.18873	P	0.9999825533	B;B;B;B	0.32939	0.391;0.126;0.013;0.021	B;B;B;B	0.31016	0.123;0.07;0.009;0.022	T	0.09885	-1.0654	9	0.12430	T	0.62	.	13.8591	0.63548	0.0:0.0:1.0:0.0	rs6962;rs3211500;rs6962	609;251;576;657	E9PBJ5;B3KYA5;D6RFM5;P31040	.;.;.;DHSA_HUMAN	I	657;512;576;609	ENSP00000264932:V657I;ENSP00000426514:V576I;ENSP00000427703:V609I	ENSP00000264932:V657I	V	+	1	0	SDHA	309509	1.000000	0.71417	0.066000	0.19879	0.104000	0.19210	4.233000	0.58651	1.861000	0.53984	0.305000	0.20034	GTC	G|0.823;A|0.177	0.177	strong		0.438	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
KIF11	3832	hgsc.bcm.edu	37	10	94369247	94369247	+	Silent	SNP	C	C	T	rs145656661		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:94369247C>T	ENST00000260731.3	+	6	769	c.679C>T	c.(679-681)Ctg>Ttg	p.L227L		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	227	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)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGCAGCTACTCTGATGAATGC	0.378																																					p.L227L	Colon(47;212 1003 2764 4062 8431)	Atlas-SNP	.											.	KIF11	58	.	0			c.C679T						PASS	.	C		0,4406		0,0,2203	201.0	222.0	215.0		679	-4.9	0.0	10	dbSNP_134	215	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KIF11	NM_004523.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		227/1057	94369247	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3832	exon6			GCTACTCTGATGA	X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"""Kinesins"""	6388	protein-coding gene	gene with protein product		148760	"""kinesin-like 1"""	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.679C>T	10.37:g.94369247C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	54	20	0.37037	NM_004523	A0AV49|B2RMV3|Q15716|Q5VWX0	Silent	SNP	ENST00000260731.3	37	CCDS7422.1																																																																																			C|1.000;T|0.000	0.000	weak		0.378	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523	
ZWILCH	55055	hgsc.bcm.edu	37	15	66832466	66832466	+	Missense_Mutation	SNP	A	A	G	rs75532475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:66832466A>G	ENST00000307897.5	+	17	1985	c.1605A>G	c.(1603-1605)atA>atG	p.I535M	ZWILCH_ENST00000535141.2_Missense_Mutation_p.I421M|ZWILCH_ENST00000446801.2_Missense_Mutation_p.I421M|ZWILCH_ENST00000565627.1_Missense_Mutation_p.I421M	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	535					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						GAGTGGAAATATATAGTGGTC	0.368													A|||	394	0.0786741	0.0802	0.0692	5008	,	,		18473	0.0437		0.1064	False		,,,				2504	0.091				p.I535M		Atlas-SNP	.											.	ZWILCH	46	.	0			c.A1605G						PASS	.	A	MET/ILE	324,4078	171.6+/-201.8	14,296,1891	91.0	92.0	92.0		1605	-0.2	0.0	15	dbSNP_131	92	736,7862	179.3+/-228.5	25,686,3588	yes	missense	ZWILCH	NM_017975.3	10	39,982,5479	GG,GA,AA		8.5601,7.3603,8.1538	benign	535/592	66832466	1060,11940	2201	4299	6500	SO:0001583	missense	55055	exon17			GGAAATATATAGT	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.1605A>G	15.37:g.66832466A>G	ENSP00000311429:p.Ile535Met	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	162	81	0.5	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	37	CCDS10219.1	158	0.07234432234432235	37	0.07520325203252033	23	0.06353591160220995	20	0.03496503496503497	78	0.10290237467018469	A	12.43	1.934311	0.34096	0.073603	0.085601	ENSG00000174442	ENST00000307897;ENST00000446801;ENST00000535141	T;T;T	0.39406	1.08;1.08;1.08	5.4	-0.236	0.13067	.	0.198949	0.52532	D	0.000071	T	0.02727	0.0082	M	0.64997	1.995	0.20638	N	0.999874	B	0.34313	0.448	P	0.53360	0.724	T	0.48525	-0.9028	10	0.72032	D	0.01	-15.8954	16.2849	0.82714	0.2605:0.7394:0.0:0.0	.	535	Q9H900	ZWILC_HUMAN	M	535;421;421	ENSP00000311429:I535M;ENSP00000402217:I421M;ENSP00000437749:I421M	ENSP00000311429:I535M	I	+	3	3	ZWILCH	64619520	0.621000	0.27077	0.016000	0.15963	0.334000	0.28698	0.241000	0.18065	-0.191000	0.10448	0.528000	0.53228	ATA	A|0.924;G|0.076	0.076	strong		0.368	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975	
GPATCH8	23131	hgsc.bcm.edu	37	17	42475670	42475670	+	Missense_Mutation	SNP	T	T	C	rs760339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42475670T>C	ENST00000591680.1	-	8	3805	c.3775A>G	c.(3775-3777)Agc>Ggc	p.S1259G	GPATCH8_ENST00000434000.1_Missense_Mutation_p.S1181G	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1259			S -> G (in dbSNP:rs760339). {ECO:0000269|PubMed:10477733}.				metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GGCTGACTGCTGCTATCCAGG	0.582													T|||	21	0.00419329	0.0	0.0043	5008	,	,		18567	0.0		0.003	False		,,,				2504	0.0153				p.S1259G		Atlas-SNP	.											.	GPATCH8	114	.	0			c.A3775G						PASS	.	T	GLY/SER	0,4406		0,0,2203	126.0	124.0	125.0		3775	-1.1	0.8	17	dbSNP_86	125	32,8568	22.2+/-67.0	0,32,4268	yes	missense	GPATCH8	NM_001002909.2	56	0,32,6471	CC,CT,TT		0.3721,0.0,0.246	benign	1259/1503	42475670	32,12974	2203	4300	6503	SO:0001583	missense	23131	exon8			GACTGCTGCTATC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.3775A>G	17.37:g.42475670T>C	ENSP00000467556:p.Ser1259Gly	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	0.003	-2.450966	0.00175	0.0	0.003721	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.11169	2.8	4.76	-1.12	0.09808	.	0.595775	0.18361	N	0.143579	T	0.02012	0.0063	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	10	0.06365	T	0.9	-4.6956	9.4564	0.38758	0.0:0.6109:0.0:0.3891	rs760339;rs760339	1259	Q9UKJ3	GPTC8_HUMAN	G	1259;1181	ENSP00000395016:S1181G	ENSP00000335486:S1259G	S	-	1	0	GPATCH8	39831196	0.060000	0.20803	0.835000	0.33067	0.534000	0.34807	0.338000	0.19858	-0.063000	0.13065	-0.479000	0.04858	AGC	T|0.997;C|0.003	0.003	strong		0.582	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
POLE	5426	hgsc.bcm.edu	37	12	133219831	133219831	+	Silent	SNP	T	T	C	rs5744944	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133219831T>C	ENST00000320574.5	-	35	4573	c.4530A>G	c.(4528-4530)gcA>gcG	p.A1510A	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Silent_p.A1483A	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1510					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CAAAGACGGATGCCCTGCGCT	0.602								DNA polymerases (catalytic subunits)					C|||	3031	0.605232	0.761	0.5317	5008	,	,		20994	0.6736		0.4304	False		,,,				2504	0.5562				p.A1510A		Atlas-SNP	.											.	POLE	416	.	0			c.A4530G						PASS	.	C		3091,1315	441.2+/-346.3	1076,939,188	101.0	91.0	94.0		4530	-11.9	0.1	12	dbSNP_114	94	3703,4897	619.4+/-396.9	797,2109,1394	no	coding-synonymous	POLE	NM_006231.2		1873,3048,1582	CC,CT,TT		43.0581,29.8457,47.7626		1510/2287	133219831	6794,6212	2203	4300	6503	SO:0001819	synonymous_variant	5426	exon35			GACGGATGCCCTG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.4530A>G	12.37:g.133219831T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	60	24	0.4	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			T|0.448;C|0.552	0.552	strong		0.602	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
ARID4A	5926	hgsc.bcm.edu	37	14	58831142	58831142	+	Missense_Mutation	SNP	A	A	G	rs1051858|rs386777941	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:58831142A>G	ENST00000355431.3	+	20	2708	c.2335A>G	c.(2335-2337)Aca>Gca	p.T779A	ARID4A_ENST00000395168.3_Missense_Mutation_p.T779A|ARID4A_ENST00000431317.2_Missense_Mutation_p.T779A|ARID4A_ENST00000348476.3_Missense_Mutation_p.T779A	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	779			T -> A (in dbSNP:rs1051858). {ECO:0000269|PubMed:8414517}.		erythrocyte development (GO:0048821)|histone H3-K4 trimethylation (GO:0080182)|histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|central_nervous_system(1)|cervix(4)|endometrium(8)|kidney(2)|large_intestine(14)|lung(19)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						AATGGAAAAAACAGAAGAAGT	0.328													G|||	1750	0.349441	0.3434	0.2291	5008	,	,		15678	0.5169		0.34	False		,,,				2504	0.2802				p.T779A		Atlas-SNP	.											.	ARID4A	222	.	0			c.A2335G						PASS	.	G	ALA/THR,ALA/THR,ALA/THR	1506,2898		247,1012,943	38.0	43.0	41.0		2335,2335,2335	1.5	0.0	14	dbSNP_86	41	2835,5745		450,1935,1905	yes	missense,missense,missense	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	58,58,58	697,2947,2848	GG,GA,AA		33.042,34.1962,33.4335	benign,benign,benign	779/1258,779/1204,779/1189	58831142	4341,8643	2202	4290	6492	SO:0001583	missense	5926	exon20			GAAAAAACAGAAG	S57153	CCDS9732.1, CCDS9733.1, CCDS45114.1	14q22.3	2013-02-07	2004-01-28	2004-01-28	ENSG00000032219	ENSG00000032219		"""-"""	9885	protein-coding gene	gene with protein product		180201	"""retinoblastoma-binding protein 1"""	RBBP1		1857421, 8455946	Standard	NM_023000		Approved	RBP1, RBP-1	uc001xdp.3	P29374	OTTHUMG00000140320	ENST00000355431.3:c.2335A>G	14.37:g.58831142A>G	ENSP00000347602:p.Thr779Ala	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	121	60	0.495868	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	839	0.3841575091575092	157	0.31910569105691056	99	0.27348066298342544	306	0.534965034965035	277	0.3654353562005277	G	0.733	-0.779318	0.02929	0.341962	0.33042	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.13778	2.59;2.58;2.58;2.58;2.56	5.46	1.52	0.23074	.	1.543180	0.03203	N	0.174991	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.45293	-0.9271	9	0.09338	T	0.73	-0.0033	2.1538	0.03807	0.3574:0.1167:0.4062:0.1196	rs1051858;rs17214268;rs52814271;rs57783039;rs1051858	779;779;779	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	A	779;779;779;779;457	ENSP00000347602:T779A;ENSP00000344556:T779A;ENSP00000378597:T779A;ENSP00000397368:T779A;ENSP00000416053:T457A	ENSP00000344556:T779A	T	+	1	0	ARID4A	57900895	0.001000	0.12720	0.007000	0.13788	0.872000	0.50106	-0.111000	0.10807	-0.195000	0.10382	-0.128000	0.14901	ACA	A|0.645;G|0.354	0.354	strong		0.328	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001	
ZNF415	55786	hgsc.bcm.edu	37	19	53612745	53612745	+	Missense_Mutation	SNP	T	T	C	rs1133327	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53612745T>C	ENST00000500065.4	-	4	886	c.553A>G	c.(553-555)Atc>Gtc	p.I185V	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000601493.1_5'UTR|ZNF415_ENST00000243643.4_Missense_Mutation_p.I185V|ZNF415_ENST00000440291.1_Missense_Mutation_p.I172V|ZNF415_ENST00000455735.2_Missense_Mutation_p.I233V|ZNF415_ENST00000421033.1_Missense_Mutation_p.I197V|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000448501.1_Missense_Mutation_p.I233V	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	233					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		TGGGTTTTGATGGTAGAAGAA	0.363													C|||	2729	0.544928	0.4856	0.647	5008	,	,		21213	0.6131		0.497	False		,,,				2504	0.5317				p.I185V		Atlas-SNP	.											.	ZNF415	68	.	0			c.A553G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE	2216,2190	586.9+/-386.6	560,1096,547	100.0	96.0	97.0		553,553,553	1.7	0.0	19	dbSNP_86	97	4206,4394	585.0+/-391.8	1035,2136,1129	yes	missense,missense,missense	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	29,29,29	1595,3232,1676	CC,CT,TT		48.907,49.7049,49.3772	benign,benign,benign	185/556,185/556,185/556	53612745	6422,6584	2203	4300	6503	SO:0001583	missense	55786	exon4			TTTTGATGGTAGA	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.553A>G	19.37:g.53612745T>C	ENSP00000439435:p.Ile185Val	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	132	131	0.992424	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Missense_Mutation	SNP	ENST00000500065.4	37	CCDS54313.1	1211	0.5544871794871795	253	0.5142276422764228	234	0.6464088397790055	345	0.6031468531468531	379	0.5	C	0.331	-0.956230	0.02267	0.502951	0.48907	ENSG00000170954	ENST00000243643;ENST00000500065;ENST00000448501;ENST00000421033;ENST00000455735;ENST00000440291	T;T;T;T;T;T	0.06768	3.26;3.26;3.26;3.26;3.26;3.26	2.74	1.68	0.24146	.	.	.	.	.	T	0.00012	0.0000	N	0.01188	-0.97	0.80722	P	0.0	B;B;B;B;B	0.13145	0.0;0.0;0.007;0.0;0.0	B;B;B;B;B	0.09377	0.0;0.0;0.004;0.0;0.0	T	0.10660	-1.0620	8	0.30854	T	0.27	.	5.2931	0.15737	0.0:0.7068:0.0:0.2932	rs1133327;rs1560098;rs3170112;rs16984463;rs60143060;rs1133327	185;233;185;172;197	F5H287;Q09FC8;Q09FC8-5;Q09FC8-4;Q09FC8-2	.;ZN415_HUMAN;.;.;.	V	185;185;233;197;233;172	ENSP00000243643:I185V;ENSP00000439435:I185V;ENSP00000396492:I233V;ENSP00000395055:I197V;ENSP00000388787:I233V;ENSP00000414601:I172V	ENSP00000243643:I185V	I	-	1	0	ZNF415	58304557	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.787000	0.01764	0.075000	0.16796	-1.741000	0.00685	ATC	T|0.490;C|0.510	0.510	strong		0.363	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
CDON	50937	hgsc.bcm.edu	37	11	125848261	125848261	+	Silent	SNP	C	C	T	rs3740904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:125848261C>T	ENST00000392693.3	-	18	3421	c.3294G>A	c.(3292-3294)acG>acA	p.T1098T	CDON_ENST00000263577.7_Silent_p.T1098T|CDON_ENST00000531738.1_Silent_p.T475T	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1098					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.T1098T(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)		GAGGCACGGCCGTGTACATTC	0.438													C|||	2001	0.399561	0.382	0.4337	5008	,	,		19124	0.4127		0.3797	False		,,,				2504	0.4059				p.T1098T		Atlas-SNP	.											CDON,NS,carcinoma,0,1	CDON	137	1	1	Substitution - coding silent(1)	stomach(1)	c.G3294A						PASS	.	C		1534,2868	476.6+/-357.7	256,1022,923	82.0	63.0	70.0		3294	-3.9	0.7	11	dbSNP_107	70	3100,5498	465.6+/-366.6	571,1958,1770	yes	coding-synonymous	CDON	NM_016952.4		827,2980,2693	TT,TC,CC		36.0549,34.8478,35.6462		1098/1265	125848261	4634,8366	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon18			CACGGCCGTGTAC	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.3294G>A	11.37:g.125848261C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	63	1	NM_016952	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			C|0.626;T|0.374	0.374	strong		0.438	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
PTK7	5754	hgsc.bcm.edu	37	6	43109751	43109751	+	Silent	SNP	G	G	A	rs6905948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43109751G>A	ENST00000230419.4	+	12	2072	c.1851G>A	c.(1849-1851)ggG>ggA	p.G617G	PTK7_ENST00000352931.2_Silent_p.G617G|PTK7_ENST00000349241.2_Silent_p.G487G|PTK7_ENST00000481273.1_Silent_p.G625G|PTK7_ENST00000345201.2_Silent_p.G577G	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	617	Ig-like C2-type 7.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			AGGCCCAGGGGGACCCCAAGC	0.597													G|||	1693	0.338059	0.4781	0.4179	5008	,	,		17142	0.0972		0.3887	False		,,,				2504	0.2883				p.G625G		Atlas-SNP	.											PTK7,NS,carcinoma,+2,1	PTK7	101	1	0			c.G1875A						PASS	.	G	,,,	1975,2431	547.8+/-377.4	451,1073,679	54.0	58.0	57.0		1851,1731,1461,1851	-8.6	1.0	6	dbSNP_116	57	3262,5338	481.8+/-370.7	596,2070,1634	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTK7	NM_002821.3,NM_152880.2,NM_152881.2,NM_152882.2	,,,	1047,3143,2313	AA,AG,GG		37.9302,44.8252,40.266	,,,	617/1071,577/1031,487/941,617/1015	43109751	5237,7769	2203	4300	6503	SO:0001819	synonymous_variant	5754	exon12			CCAGGGGGACCCC	AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9618	protein-coding gene	gene with protein product		601890	"""PTK7 protein tyrosine kinase 7"""			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.1851G>A	6.37:g.43109751G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	49	48	0.979592	NM_001270398	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Silent	SNP	ENST00000230419.4	37	CCDS4884.1																																																																																			G|0.619;A|0.381	0.381	strong		0.597	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2		
ZNF283	284349	hgsc.bcm.edu	37	19	44352639	44352639	+	Missense_Mutation	SNP	G	G	A	rs1061768	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44352639G>A	ENST00000324461.7	+	7	2183	c.1886G>A	c.(1885-1887)cGt>cAt	p.R629H	ZNF283_ENST00000588797.1_Missense_Mutation_p.R490H	NM_181845.1	NP_862828.1	Q8N7M2	ZN283_HUMAN	zinc finger protein 283	629			R -> H (in dbSNP:rs1061768).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(4)	8		Prostate(69;0.0352)				CTTTATCAACGTAAGGAATTC	0.398													G|||	750	0.14976	0.1316	0.1787	5008	,	,		20278	0.0744		0.2227	False		,,,				2504	0.1564				p.R629H		Atlas-SNP	.											.	ZNF283	83	.	0			c.G1886A						PASS	.	G	HIS/ARG	565,3571		23,519,1526	102.0	110.0	107.0		1886	2.6	0.2	19	dbSNP_86	107	1754,6704		175,1404,2650	yes	missense	ZNF283	NM_181845.1	29	198,1923,4176	AA,AG,GG		20.7378,13.6605,18.4135	benign	629/680	44352639	2319,10275	2068	4229	6297	SO:0001583	missense	284349	exon7			ATCAACGTAAGGA	AK098175	CCDS46097.1, CCDS74387.1	19q13.31	2013-01-08			ENSG00000167637	ENSG00000167637		"""Zinc fingers, C2H2-type"", ""-"""	13077	protein-coding gene	gene with protein product						12743021	Standard	NM_181845		Approved		uc002oxr.4	Q8N7M2		ENST00000324461.7:c.1886G>A	19.37:g.44352639G>A	ENSP00000327314:p.Arg629His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	85	51	0.6	NM_181845	B4DGZ5|B7WP04|Q6RFR9|Q86WM6	Missense_Mutation	SNP	ENST00000324461.7	37	CCDS46097.1	357	0.16346153846153846	83	0.16869918699186992	53	0.1464088397790055	45	0.07867132867132867	176	0.23218997361477572	G	12.00	1.805208	0.31961	0.136605	0.207378	ENSG00000167637	ENST00000324461	T	0.14766	2.48	2.61	2.61	0.31194	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.11201	0.11	0.09310	P	1.0	P	0.36660	0.564	B	0.31337	0.128	T	0.42716	-0.9435	8	0.87932	D	0	.	12.3634	0.55215	0.0:0.0:1.0:0.0	rs1061768;rs3170394;rs56865400;rs1061768	629	Q8N7M2	ZN283_HUMAN	H	629	ENSP00000327314:R629H	ENSP00000327314:R629H	R	+	2	0	ZNF283	49044479	0.986000	0.35501	0.234000	0.24042	0.459000	0.32528	3.677000	0.54619	1.440000	0.47531	0.563000	0.77884	CGT	G|0.832;A|0.168	0.168	strong		0.398	ZNF283-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459909.1	NM_181845	
PCDHB15	56121	hgsc.bcm.edu	37	5	140625429	140625429	+	Missense_Mutation	SNP	C	C	A	rs142267472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140625429C>A	ENST00000231173.3	+	1	283	c.283C>A	c.(283-285)Ctg>Atg	p.L95M		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	95	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCGGGAGAAGCTGTGTGGCCC	0.478													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17237	0.0		0.005	False		,,,				2504	0.0041				p.L95M		Atlas-SNP	.											.	PCDHB15	138	.	0			c.C283A						PASS	.	C	MET/LEU	3,4403	6.2+/-15.9	0,3,2200	58.0	64.0	62.0		283	3.0	1.0	5	dbSNP_134	62	35,8565	24.6+/-71.5	0,35,4265	yes	missense	PCDHB15	NM_018935.2	15	0,38,6465	AA,AC,CC		0.407,0.0681,0.2922	benign	95/788	140625429	38,12968	2203	4300	6503	SO:0001583	missense	56121	exon1			GAGAAGCTGTGTG	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.283C>A	5.37:g.140625429C>A	ENSP00000231173:p.Leu95Met	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	83	51	0.614458	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	12.76	2.034503	0.35893	6.81E-4	0.00407	ENSG00000113248	ENST00000231173	T	0.42900	0.96	4.92	2.98	0.34508	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.52175	0.1718	M	0.82132	2.575	0.32911	D	0.514457	B	0.30021	0.265	P	0.51324	0.666	T	0.66532	-0.5900	9	0.62326	D	0.03	.	7.4699	0.27342	0.4586:0.4516:0.0:0.0898	.	95	Q9Y5E8	PCDBF_HUMAN	M	95	ENSP00000231173:L95M	ENSP00000231173:L95M	L	+	1	2	PCDHB15	140605613	0.000000	0.05858	1.000000	0.80357	0.587000	0.36485	-0.295000	0.08298	0.472000	0.27344	0.491000	0.48974	CTG	C|0.997;A|0.003	0.003	strong		0.478	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
NT5DC3	51559	hgsc.bcm.edu	37	12	104186946	104186946	+	Silent	SNP	G	G	T	rs1866295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:104186946G>T	ENST00000392876.3	-	9	1055	c.1015C>A	c.(1015-1017)Cgg>Agg	p.R339R		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	339						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						ACTCACCTCCGCTTATCATTA	0.403													G|||	2051	0.409545	0.2829	0.3199	5008	,	,		20518	0.6319		0.2406	False		,,,				2504	0.589				p.R339R		Atlas-SNP	.											.	NT5DC3	113	.	0			c.C1015A						PASS	.	G		1180,3226	414.4+/-336.8	152,876,1175	142.0	150.0	147.0		1015	5.0	1.0	12	dbSNP_92	147	2078,6522	361.9+/-332.5	254,1570,2476	no	coding-synonymous	NT5DC3	NM_001031701.2		406,2446,3651	TT,TG,GG		24.1628,26.7817,25.05		339/549	104186946	3258,9748	2203	4300	6503	SO:0001819	synonymous_variant	51559	exon9			ACCTCCGCTTATC	AB032786	CCDS41824.1	12q22-q23.1	2006-02-03			ENSG00000111696	ENSG00000111696			30826	protein-coding gene	gene with protein product		611076					Standard	NM_001031701		Approved	TU12B1-TY, FLJ11266	uc010swe.1	Q86UY8	OTTHUMG00000157017	ENST00000392876.3:c.1015C>A	12.37:g.104186946G>T		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	168	91	0.541667	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Silent	SNP	ENST00000392876.3	37	CCDS41824.1																																																																																			G|0.708;T|0.292	0.292	strong		0.403	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575	
ZFAT	57623	hgsc.bcm.edu	37	8	135669810	135669810	+	Missense_Mutation	SNP	C	C	T	rs17778003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:135669810C>T	ENST00000377838.3	-	2	364	c.190G>A	c.(190-192)Gga>Aga	p.G64R	ZFAT_ENST00000523399.1_Missense_Mutation_p.G64R|ZFAT_ENST00000429442.2_Missense_Mutation_p.G52R|ZFAT_ENST00000520727.1_Missense_Mutation_p.G52R|ZFAT_ENST00000520356.1_Missense_Mutation_p.G52R|ZFAT_ENST00000520214.1_Missense_Mutation_p.G52R	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	64			G -> R (in dbSNP:rs17778003). {ECO:0000269|PubMed:15294872, ECO:0000269|PubMed:15489334}.		hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			TTACCATCTCCGGTTTTGCTT	0.502													C|||	390	0.0778754	0.1543	0.0576	5008	,	,		17712	0.0		0.0915	False		,,,				2504	0.0552				p.G64R		Atlas-SNP	.											.	ZFAT	265	.	0			c.G190A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	526,3206		34,458,1374	64.0	65.0	65.0		154,154,190,154,190	4.8	0.9	8	dbSNP_123	65	713,7463		36,641,3411	yes	missense,missense,missense,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	125,125,125,125,125	70,1099,4785	TT,TC,CC		8.7206,14.0943,10.4048	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	52/1232,52/1232,64/1182,52/1146,64/1244	135669810	1239,10669	1866	4088	5954	SO:0001583	missense	57623	exon2			CATCTCCGGTTTT	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.190G>A	8.37:g.135669810C>T	ENSP00000367069:p.Gly64Arg	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	131	79	0.603053	NM_001174157	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	167	0.07646520146520147	69	0.1402439024390244	22	0.06077348066298342	0	0.0	76	0.10026385224274406	C	16.70	3.197184	0.58126	0.140943	0.087206	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946;ENST00000518191	T;T;T;T;T;T;T	0.35236	2.83;2.76;2.76;2.76;2.76;2.73;1.32	5.72	4.85	0.62838	.	0.388252	0.27105	N	0.020917	T	0.00440	0.0014	L	0.32530	0.975	0.24250	P	0.99532701	P;D;P;P	0.89917	0.647;1.0;0.552;0.647	B;D;B;B	0.77004	0.07;0.989;0.098;0.048	T	0.07102	-1.0790	9	0.46703	T	0.11	-8.6547	12.1796	0.54204	0.0:0.9183:0.0:0.0817	rs17778003;rs52819913;rs60328983;rs17778003	64;52;52;64	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	R	52;52;52;64;52;52;64;52;52	ENSP00000427879:G52R;ENSP00000427831:G52R;ENSP00000394501:G52R;ENSP00000367069:G64R;ENSP00000428483:G52R;ENSP00000429091:G64R;ENSP00000428192:G52R	ENSP00000326997:G52R	G	-	1	0	ZFAT	135738992	0.984000	0.35163	0.872000	0.34217	0.662000	0.39071	2.688000	0.46984	1.416000	0.47057	0.655000	0.94253	GGA	C|0.919;T|0.081	0.081	strong		0.502	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
SUPT3H	8464	hgsc.bcm.edu	37	6	45290634	45290634	+	Missense_Mutation	SNP	G	G	A	rs9472463	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:45290634G>A	ENST00000371460.1	-	3	337	c.20C>T	c.(19-21)aCg>aTg	p.T7M	SUPT3H_ENST00000371461.2_Missense_Mutation_p.T7M|SUPT3H_ENST00000306867.5_Intron|SUPT3H_ENST00000459689.1_Intron|SUPT3H_ENST00000371459.1_Intron	NM_181356.2	NP_852001.1	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog (S. cerevisiae)	0					chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|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)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	transcription coactivator activity (GO:0003713)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	12						GTTGAAGAACGTTGTTCCAAA	0.413													G|||	23	0.00459265	0.0008	0.0029	5008	,	,		16239	0.0		0.0179	False		,,,				2504	0.002				p.T7M		Atlas-SNP	.											.	SUPT3H	75	.	0			c.C20T						PASS	.	G	,MET/THR	16,4390	24.3+/-50.5	0,16,2187	108.0	95.0	99.0		,20	4.3	1.0	6	dbSNP_119	99	133,8467	67.0+/-129.4	1,131,4168	yes	intron,missense	SUPT3H	NM_003599.2,NM_181356.1	,81	1,147,6355	AA,AG,GG		1.5465,0.3631,1.1456	,	,7/329	45290634	149,12857	2203	4300	6503	SO:0001583	missense	8464	exon3			AAGAACGTTGTTC	AF069734	CCDS34465.1, CCDS34466.1, CCDS75464.1	6p21.1-p12.3	2008-05-15	2001-11-28		ENSG00000196284	ENSG00000196284			11466	protein-coding gene	gene with protein product		602947	"""suppressor of Ty (S.cerevisiae) 3 homolog"""			9674425, 9726987	Standard	NM_003599		Approved	SPT3, SPT3L	uc003oxp.4	O75486	OTTHUMG00000014773	ENST00000371460.1:c.20C>T	6.37:g.45290634G>A	ENSP00000360515:p.Thr7Met	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	175	79	0.451429	NM_181356	A6NKG9|B2R9Q5|O76066|Q5TAV9|Q86VN7	Missense_Mutation	SNP	ENST00000371460.1	37	CCDS34466.1	17	0.007783882783882784	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	G	14.57	2.574496	0.45902	0.003631	0.015465	ENSG00000196284	ENST00000371460;ENST00000371461	T;T	0.48836	0.8;0.8	5.23	4.34	0.51931	.	1.633690	0.03317	N	0.191370	T	0.22044	0.0531	.	.	.	0.27760	N	0.94385	B	0.12013	0.005	B	0.14023	0.01	T	0.18398	-1.0338	9	0.87932	D	0	.	8.3299	0.32180	0.08:0.0:0.7657:0.1543	rs9472463;rs52806481;rs56415076;rs9472463	7	O75486-3	.	M	7	ENSP00000360515:T7M;ENSP00000360516:T7M	ENSP00000360515:T7M	T	-	2	0	SUPT3H	45398612	1.000000	0.71417	0.972000	0.41901	0.993000	0.82548	2.849000	0.48286	1.293000	0.44690	0.557000	0.71058	ACG	G|0.989;A|0.011	0.011	strong		0.413	SUPT3H-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106910.3	NM_181356	
CNRIP1	25927	hgsc.bcm.edu	37	2	68511584	68511584	+	Silent	SNP	A	A	G	rs735815	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:68511584A>G	ENST00000409559.3	-	3	362	c.363T>C	c.(361-363)tcT>tcC	p.S121S		NM_001111101.1	NP_001104571.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	0								p.S121S(1)		kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						CATATGTAAGAGAGATCTCTT	0.378													A|||	1974	0.394169	0.121	0.4481	5008	,	,		21161	0.5516		0.4404	False		,,,				2504	0.5153				p.S121S		Atlas-SNP	.											CNRIP1_ENST00000409559,NS,carcinoma,0,1	CNRIP1	45	1	1	Substitution - coding silent(1)	stomach(1)	c.T363C						PASS	.	A		267,1117		24,219,449	124.0	109.0	114.0		363	0.5	0.0	2	dbSNP_86	114	1368,1814		309,750,532	no	coding-synonymous	CNRIP1	NM_001111101.1		333,969,981	GG,GA,AA		42.9918,19.2919,35.8081		121/129	68511584	1635,2931	692	1591	2283	SO:0001819	synonymous_variant	25927	exon3			TGTAAGAGAGATC	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	ENST00000409559.3:c.363T>C	2.37:g.68511584A>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	65	36	0.553846	NM_001111101	B2R4D0|Q49AN4|Q9UFZ0	Silent	SNP	ENST00000409559.3	37	CCDS46311.1																																																																																			A|0.599;G|0.401	0.401	strong		0.378	CNRIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000326817.2	NM_015463	
EDC4	23644	hgsc.bcm.edu	37	16	67911517	67911517	+	Silent	SNP	T	T	C	rs8060686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67911517T>C	ENST00000358933.5	+	6	986	c.747T>C	c.(745-747)tgT>tgC	p.C249C	AC040162.1_ENST00000408599.1_RNA|EDC4_ENST00000574770.1_3'UTR	NM_014329.4	NP_055144.3	Q6P2E9	EDC4_HUMAN	enhancer of mRNA decapping 4	249					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(4)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	41		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0042)|Epithelial(162;0.0185)|all cancers(182;0.121)		AAGACTGCTGTGAGGAGAGCA	0.602													C|||	1637	0.326877	0.73	0.2867	5008	,	,		21883	0.0685		0.1799	False		,,,				2504	0.228				p.C249C		Atlas-SNP	.											.	EDC4	101	.	0			c.T747C						PASS	.	C		2778,1618	500.5+/-364.7	876,1026,296	75.0	79.0	78.0	http://www.ncbi.nlm.nih.gov/pubmed?term	747	1.6	1.0	16	dbSNP_116	78	1513,7087	747.6+/-407.3	164,1185,2951	yes	coding-synonymous	EDC4	NM_014329.3		1040,2211,3247	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	17.593,36.8062,33.0179		249/1402	67911517	4291,8705	2198	4300	6498	SO:0001819	synonymous_variant	23644	exon6			CTGCTGTGAGGAG	U17474	CCDS10849.1	16q22.1	2008-02-05			ENSG00000038358	ENSG00000038358			17157	protein-coding gene	gene with protein product		606030				9067524	Standard	NM_014329		Approved	RCD-8, Ge-1, HEDLS	uc002eur.3	Q6P2E9	OTTHUMG00000137543	ENST00000358933.5:c.747T>C	16.37:g.67911517T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	95	57	0.6	NM_014329	A6NGM1|A8K4T4|Q13025|Q13826|Q6ZR12|Q7Z6H7	Silent	SNP	ENST00000358933.5	37	CCDS10849.1																																																																																			T|0.669;C|0.331	0.331	strong		0.602	EDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268874.2	NM_014329	
XRN2	22803	hgsc.bcm.edu	37	20	21349188	21349188	+	Silent	SNP	G	G	A	rs149896399		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:21349188G>A	ENST00000377191.3	+	27	2639	c.2544G>A	c.(2542-2544)ccG>ccA	p.P848P	XRN2_ENST00000539513.1_Silent_p.P794P|XRN2_ENST00000430571.2_Silent_p.P772P	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	848					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						TATACAGGCCGCTTTTGAGAG	0.408													G|||	1	0.000199681	0.0	0.0	5008	,	,		17892	0.0		0.0	False		,,,				2504	0.001				p.P848P		Atlas-SNP	.											.	XRN2	90	.	0			c.G2544A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	120.0	117.0	118.0		2544	-5.0	0.2	20	dbSNP_134	118	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	XRN2	NM_012255.3		0,16,6487	AA,AG,GG		0.1744,0.0227,0.123		848/951	21349188	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	22803	exon27			CAGGCCGCTTTTG	AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.2544G>A	20.37:g.21349188G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	79	26	0.329114	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Silent	SNP	ENST00000377191.3	37	CCDS13144.1																																																																																			G|0.999;A|0.001	0.001	strong		0.408	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255	
HYDIN	54768	hgsc.bcm.edu	37	16	71163693	71163693	+	Silent	SNP	A	A	G	rs4788770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:71163693A>G	ENST00000393567.2	-	9	1227	c.1077T>C	c.(1075-1077)gaT>gaC	p.D359D	HYDIN_ENST00000538248.1_Silent_p.D386D|HYDIN_ENST00000393550.2_Silent_p.D359D|HYDIN_ENST00000288168.10_Silent_p.D376D|HYDIN_ENST00000448691.1_Silent_p.D359D|HYDIN_ENST00000448089.2_Silent_p.D359D|HYDIN_ENST00000541601.1_Silent_p.D376D|HYDIN_ENST00000321489.5_Silent_p.D359D	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	359					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CATCAGTCTCATCCTTCTCCT	0.453																																					p.D386D		Atlas-SNP	.											.	HYDIN	788	.	0			c.T1158C						PASS	.						21.0	21.0	21.0					16																	71163693		2197	4279	6476	SO:0001819	synonymous_variant	54768	exon9			AGTCTCATCCTTC	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.1077T>C	16.37:g.71163693A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	156	46	0.294872	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			A|0.625;G|0.375	0.375	strong		0.453	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
CLCNKB	1188	hgsc.bcm.edu	37	1	16380252	16380252	+	Silent	SNP	C	C	T	rs2275167|rs111663047	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16380252C>T	ENST00000375679.4	+	16	1852	c.1741C>T	c.(1741-1743)Ctg>Ttg	p.L581L	CLCNKB_ENST00000375667.3_Silent_p.L412L	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	581	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CAAGTATCCCCTGGTGGAGAG	0.602													C|||	3073	0.613618	0.5734	0.5	5008	,	,		18903	0.8016		0.6123	False		,,,				2504	0.5562				p.L581L		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1741T						PASS	.	C	,	2552,1854		757,1038,408	87.0	69.0	75.0		1741,1234	1.6	0.5	1	dbSNP_100	75	5399,3201		1760,1879,661	no	coding-synonymous,coding-synonymous	CLCNKB	NM_000085.3,NM_001165945.1	,	2517,2917,1069	TT,TC,CC		37.2209,42.079,38.8667	,	581/688,412/519	16380252	7951,5055	2203	4300	6503	SO:0001819	synonymous_variant	1188	exon16			TATCCCCTGGTGG	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1741C>T	1.37:g.16380252C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	173	153	0.884393	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Silent	SNP	ENST00000375679.4	37	CCDS168.1																																																																																			C|0.383;T|0.617	0.617	strong		0.602	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626571	140626571	+	Silent	SNP	C	C	A	rs652104	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140626571C>A	ENST00000231173.3	+	1	1425	c.1425C>A	c.(1423-1425)gcC>gcA	p.A475A		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	475	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A475A(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GTGTCAGCGCCACAGACAGAG	0.657													C|||	1264	0.252396	0.0113	0.2911	5008	,	,		14631	0.5258		0.2316	False		,,,				2504	0.2904				p.A475A		Atlas-SNP	.											PCDHB15,NS,carcinoma,0,1	PCDHB15	138	1	1	Substitution - coding silent(1)	stomach(1)	c.C1425A						scavenged	.						68.0	76.0	73.0					5																	140626571		2203	4289	6492	SO:0001819	synonymous_variant	56121	exon1			CAGCGCCACAGAC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1425C>A	5.37:g.140626571C>A		Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			C|0.766;A|0.234	0.234	strong		0.657	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
CEACAM16	388551	hgsc.bcm.edu	37	19	45211407	45211407	+	Silent	SNP	C	C	T	rs61744497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45211407C>T	ENST00000405314.2	+	5	1312	c.1215C>T	c.(1213-1215)acC>acT	p.T405T	CEACAM16_ENST00000587331.1_Silent_p.T405T|CTB-171A8.1_ENST00000590796.1_RNA			Q2WEN9	CEA16_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 16	405					sensory perception of sound (GO:0007605)	extracellular region (GO:0005576)|stereocilium bundle tip (GO:0032426)				endometrium(3)|large_intestine(2)|lung(3)|ovary(1)	9	Lung NSC(12;0.000698)|all_lung(12;0.002)	Prostate(69;0.0376)|Ovarian(192;0.231)				CACTCAAGACCGTCACAGTGC	0.622													C|||	543	0.108427	0.0106	0.0447	5008	,	,		19901	0.2282		0.1551	False		,,,				2504	0.1145				p.T405T		Atlas-SNP	.											.	CEACAM16	56	.	0			c.C1215T						PASS	.	C		135,4095		2,131,1982	30.0	31.0	31.0		1215	-1.8	1.0	19	dbSNP_129	31	1185,7257		87,1011,3123	no	coding-synonymous	CEACAM16	NM_001039213.2		89,1142,5105	TT,TC,CC		14.037,3.1915,10.4167		405/426	45211407	1320,11352	2115	4221	6336	SO:0001819	synonymous_variant	388551	exon6			CAAGACCGTCACA		CCDS54278.1	19q13.31	2014-01-27			ENSG00000213892	ENSG00000213892		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31948	protein-coding gene	gene with protein product		614591				21368133	Standard	NM_001039213		Approved	DFNA4B	uc010xxd.2	Q2WEN9	OTTHUMG00000151519	ENST00000405314.2:c.1215C>T	19.37:g.45211407C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	161	99	0.614907	NM_001039213	A7LI12	Silent	SNP	ENST00000405314.2	37	CCDS54278.1																																																																																			C|0.867;T|0.133	0.133	strong		0.622	CEACAM16-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding		XM_371177	
SLC12A8	84561	hgsc.bcm.edu	37	3	124826408	124826408	+	Missense_Mutation	SNP	T	T	C	rs6773138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124826408T>C	ENST00000393469.4	-	9	1671	c.1622A>G	c.(1621-1623)aAg>aGg	p.K541R	SLC12A8_ENST00000423114.2_Missense_Mutation_p.K570R|SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000469902.1_Missense_Mutation_p.K541R|SLC12A8_ENST00000430155.2_Missense_Mutation_p.K342R|SLC12A8_ENST00000314584.7_Missense_Mutation_p.K294R	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	541			K -> R (in dbSNP:rs6773138).		potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						CCCTTCGCTCTTGGAAGTCTG	0.557													C|||	649	0.129593	0.2912	0.0548	5008	,	,		19346	0.0635		0.0278	False		,,,				2504	0.137				p.K541R		Atlas-SNP	.											.	SLC12A8	81	.	0			c.A1622G						PASS	.	C	ARG/LYS,ARG/LYS	1016,3172		125,766,1203	97.0	105.0	102.0		1622,1622	0.3	0.0	3	dbSNP_116	102	278,8192		3,272,3960	yes	missense,missense	SLC12A8	NM_001195483.1,NM_024628.5	26,26	128,1038,5163	CC,CT,TT		3.2822,24.2598,10.2228	benign,benign	541/715,541/715	124826408	1294,11364	2094	4235	6329	SO:0001583	missense	84561	exon10			TCGCTCTTGGAAG		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1622A>G	3.37:g.124826408T>C	ENSP00000377112:p.Lys541Arg	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	180	100	0.555556	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	CCDS43143.1	207	0.09478021978021978	139	0.28252032520325204	16	0.04419889502762431	35	0.06118881118881119	17	0.022427440633245383	C	3.631	-0.075615	0.07184	0.242598	0.032822	ENSG00000221955	ENST00000430155;ENST00000393469;ENST00000423114;ENST00000469902;ENST00000314584	D;D;D;D;T	0.88201	-1.84;-2.34;-2.35;-2.34;-1.44	5.27	0.269	0.15631	.	.	.	.	.	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.0;0.002	T	0.08827	-1.0703	8	0.10902	T	0.67	.	5.3238	0.15895	0.0948:0.5567:0.0932:0.2553	rs6773138;rs52837397;rs56737175;rs6773138	294;570;541;342	A0AV02-4;A0AV02-2;A0AV02;A0AV02-3	.;.;S12A8_HUMAN;.	R	342;541;570;541;294	ENSP00000415713:K342R;ENSP00000377112:K541R;ENSP00000404243:K570R;ENSP00000418783:K541R;ENSP00000323632:K294R	ENSP00000323632:K294R	K	-	2	0	SLC12A8	126309098	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.682000	0.05185	-0.078000	0.12730	-1.736000	0.00690	AAG	T|0.903;C|0.097	0.097	strong		0.557	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
NME8	51314	hgsc.bcm.edu	37	7	37934147	37934147	+	Silent	SNP	A	A	T	rs41276027|rs386712272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:37934147A>T	ENST00000199447.4	+	16	1851	c.1479A>T	c.(1477-1479)atA>atT	p.I493I	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Silent_p.I493I	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	493	NDK 3.		I -> T (in dbSNP:rs56128139). {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)										CTGAGCAAATAGAGAAAATTT	0.303													A|||	790	0.157748	0.0151	0.2291	5008	,	,		17450	0.1359		0.3419	False		,,,				2504	0.1329				p.I493I		Atlas-SNP	.											.	.	.	.	0			c.A1479T						PASS	.	A		2,4404		0,2,2201	59.0	61.0	61.0		1479	-3.0	0.0	7	dbSNP_127	61	47,8551		6,35,4258	no	coding-synonymous	TXNDC3	NM_016616.4		6,37,6459	TT,TA,AA		0.5466,0.0454,0.3768		493/589	37934147	49,12955	2203	4299	6502	SO:0001819	synonymous_variant	51314	exon16			GCAAATAGAGAAA	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.1479A>T	7.37:g.37934147A>T		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	225	225	1	NM_016616	Q9NZH1	Silent	SNP	ENST00000199447.4	37	CCDS5452.1																																																																																			A|0.761;T|0.239	0.239	strong		0.303	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
TPTE2	93492	hgsc.bcm.edu	37	13	20006620	20006620	+	Silent	SNP	C	C	T	rs147012324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:20006620C>T	ENST00000400230.2	-	16	1259	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	TPTE2_ENST00000400103.2_Silent_p.S294S|TPTE2_ENST00000457266.2_Silent_p.S294S|TPTE2_ENST00000382977.4_Silent_p.S405S|TPTE2_ENST00000390680.2_Silent_p.S328S|TPTE2_ENST00000382975.4_Silent_p.S365S|TPTE2_ENST00000382978.1_Silent_p.S365S|TPTE2_ENST00000255310.6_Silent_p.S328S			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	405	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S405S(2)|p.S328S(2)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TACCACGAATCGAATAAATAA	0.388																																					p.S405S		Atlas-SNP	.											TPTE2_ENST00000400230,NS,carcinoma,0,6	TPTE2	225	6	4	Substitution - coding silent(4)	prostate(2)|lung(2)	c.G1215A						scavenged	.						32.0	29.0	30.0					13																	20006620		2203	4297	6500	SO:0001819	synonymous_variant	93492	exon17			ACGAATCGAATAA	AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1215G>A	13.37:g.20006620C>T		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	229	57	0.248908	NM_199254	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Silent	SNP	ENST00000400230.2	37	CCDS45014.1																																																																																			.	.	weak		0.388	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
TGM6	343641	hgsc.bcm.edu	37	20	2377204	2377204	+	Silent	SNP	C	C	T	rs16984872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:2377204C>T	ENST00000202625.2	+	4	538	c.477C>T	c.(475-477)agC>agT	p.S159S	TGM6_ENST00000381423.1_Silent_p.S159S|TGM6_ENST00000477505.1_Intron	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	159					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	ACGTGCTCAGCGACAGCGGCA	0.612													C|||	193	0.0385383	0.1225	0.0259	5008	,	,		19129	0.0		0.0099	False		,,,				2504	0.0031				p.S159S		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.C477T						PASS	.	C		447,3959	215.8+/-234.7	28,391,1784	96.0	85.0	89.0		477	-5.3	0.9	20	dbSNP_123	89	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	TGM6	NM_198994.2		28,478,5997	TT,TC,CC		1.0116,10.1453,4.1058		159/707	2377204	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon4			GCTCAGCGACAGC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.477C>T	20.37:g.2377204C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	250	115	0.46	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			C|0.960;T|0.040	0.040	strong		0.612	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
MECOM	2122	hgsc.bcm.edu	37	3	169098992	169098992	+	Missense_Mutation	SNP	G	G	A	rs7622799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:169098992G>A	ENST00000494292.1	-	2	455	c.358C>T	c.(358-360)Ccc>Tcc	p.P120S	MECOM_ENST00000485957.1_5'UTR	NM_004991.3	NP_004982.2	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	120			P -> S (in dbSNP:rs7622799).		regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P114S(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CCATAACTGGGGTCTTTCAGG	0.408													G|||	766	0.152955	0.1362	0.3329	5008	,	,		20490	0.1558		0.1233	False		,,,				2504	0.0757				p.P120S		Atlas-SNP	.											MDS1,NS,carcinoma,0,1	MECOM	216	1	1	Substitution - Missense(1)	stomach(1)	c.C358T						PASS	.	G	,SER/PRO	483,3245		32,419,1413	90.0	87.0	88.0		,358	4.5	1.0	3	dbSNP_116	88	932,7278		53,826,3226	yes	intron,missense	MECOM	NM_001205194.1,NM_004991.3	,74	85,1245,4639	AA,AG,GG		11.352,12.956,11.8529	,possibly-damaging	,120/1240	169098992	1415,10523	1864	4105	5969	SO:0001583	missense	2122	exon2			AACTGGGGTCTTT	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000494292.1:c.358C>T	3.37:g.169098992G>A	ENSP00000417899:p.Pro120Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	133	58	0.43609	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000494292.1	37		344	0.1575091575091575	59	0.11991869918699187	89	0.24585635359116023	94	0.16433566433566432	102	0.1345646437994723	G	1.493	-0.554124	0.03996	0.12956	0.11352	ENSG00000085276	ENST00000494292	T	0.71698	-0.59	5.4	4.52	0.55395	.	0.105398	0.42964	N	0.000640	T	0.00012	0.0000	N	0.12746	0.255	0.09310	P	1.0	B;B	0.30281	0.275;0.0	B;B	0.28916	0.096;0.002	T	0.06734	-1.0810	9	0.46703	T	0.11	.	13.2366	0.59972	0.0775:0.0:0.9225:0.0	rs7622799;rs52817261;rs59561788;rs7622799	120;120	Q13465;Q03112-3	MDS1_HUMAN;.	S	120	ENSP00000417899:P120S	ENSP00000417899:P120S	P	-	1	0	MECOM	170581686	1.000000	0.71417	0.974000	0.42286	0.381000	0.30169	2.496000	0.45346	1.252000	0.44001	0.650000	0.86243	CCC	G|0.861;A|0.139	0.139	strong		0.408	MECOM-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000351517.3	NM_005241, NM_004991	
RADIL	55698	hgsc.bcm.edu	37	7	4876064	4876064	+	Silent	SNP	G	G	A	rs150209652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4876064G>A	ENST00000399583.3	-	3	895	c.708C>T	c.(706-708)ccC>ccT	p.P236P	RADIL_ENST00000536091.1_Silent_p.P236P|RADIL_ENST00000538469.1_5'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	236					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)		CGTCGGGGCCGGGCTCCTCGG	0.706													G|||	60	0.0119808	0.0015	0.0173	5008	,	,		12929	0.0		0.0249	False		,,,				2504	0.0215				p.P236P		Atlas-SNP	.											.	RADIL	110	.	0			c.C708T						PASS	.	G		15,4077		0,15,2031	12.0	19.0	17.0		708	-9.7	0.0	7	dbSNP_134	17	196,8144		5,186,3979	no	coding-synonymous	RADIL	NM_018059.4		5,201,6010	AA,AG,GG		2.3501,0.3666,1.6972		236/1076	4876064	211,12221	2046	4170	6216	SO:0001819	synonymous_variant	55698	exon3			GGGGCCGGGCTCC	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.708C>T	7.37:g.4876064G>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	55	34	0.618182	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.987;A|0.013	0.013	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
ADAM32	203102	hgsc.bcm.edu	37	8	39091526	39091526	+	Silent	SNP	T	T	C	rs4515515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39091526T>C	ENST00000379907.4	+	16	1870	c.1743T>C	c.(1741-1743)acT>acC	p.T581T	ADAM32_ENST00000437682.2_Silent_p.T482T|ADAM32_ENST00000519315.1_Silent_p.T475T	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	581						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			TATGCATAACTGTAGACTACA	0.373													T|||	1081	0.215855	0.1233	0.2133	5008	,	,		13078	0.2937		0.2396	False		,,,				2504	0.2382				p.T581T		Atlas-SNP	.											ADAM32,NS,carcinoma,0,1	ADAM32	70	1	0			c.T1743C						PASS	.	T		552,3160		55,442,1359	71.0	62.0	65.0		1743	1.0	0.0	8	dbSNP_111	65	1959,6219		244,1471,2374	no	coding-synonymous	ADAM32	NM_145004.5		299,1913,3733	CC,CT,TT		23.9545,14.8707,21.1186		581/788	39091526	2511,9379	1856	4089	5945	SO:0001819	synonymous_variant	203102	exon16			CATAACTGTAGAC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1743T>C	8.37:g.39091526T>C		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_145004	Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																			T|0.781;C|0.219	0.219	strong		0.373	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
ZDHHC14	79683	hgsc.bcm.edu	37	6	157963743	157963743	+	Silent	SNP	G	G	A	rs2365611	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:157963743G>A	ENST00000359775.5	+	2	1261	c.372G>A	c.(370-372)acG>acA	p.T124T	ZDHHC14_ENST00000414563.2_Silent_p.T124T			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	124					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	17		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		CACGAGCCACGCCTGATGAAG	0.622													G|||	1988	0.396965	0.3457	0.4856	5008	,	,		15358	0.3839		0.4016	False		,,,				2504	0.4121				p.T124T		Atlas-SNP	.											.	ZDHHC14	39	.	0			c.G372A						PASS	.	G	,	1570,2836		298,974,931	26.0	28.0	27.0		372,372	-7.8	0.3	6	dbSNP_100	27	3367,5221		684,1999,1611	no	coding-synonymous,coding-synonymous	ZDHHC14	NM_024630.2,NM_153746.1	,	982,2973,2542	AA,AG,GG		39.2059,35.6332,37.9945	,	124/489,124/474	157963743	4937,8057	2203	4294	6497	SO:0001819	synonymous_variant	79683	exon2			AGCCACGCCTGAT	AF542388	CCDS5252.1, CCDS47510.1	6q25.3	2008-05-02			ENSG00000175048	ENSG00000175048		"""Zinc fingers, DHHC-type"""	20341	protein-coding gene	gene with protein product							Standard	NM_024630		Approved	FLJ20984, NEW1CP	uc003qqt.3	Q8IZN3	OTTHUMG00000015896	ENST00000359775.5:c.372G>A	6.37:g.157963743G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	41	10	0.243902	NM_024630	A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	Silent	SNP	ENST00000359775.5	37	CCDS5252.1																																																																																			G|0.627;A|0.373	0.373	strong		0.622	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746	
GOLGA4	2803	hgsc.bcm.edu	37	3	37368600	37368600	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:37368600A>T	ENST00000361924.2	+	14	5597	c.5223A>T	c.(5221-5223)ttA>ttT	p.L1741F	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.L1763F	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1741	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCAGTGTTTTACAAAGAAACT	0.388																																					p.L1763F		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A5289T						PASS	.						103.0	109.0	107.0					3																	37368600		2203	4299	6502	SO:0001583	missense	2803	exon15			TGTTTTACAAAGA	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5223A>T	3.37:g.37368600A>T	ENSP00000354486:p.Leu1741Phe	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	126	50	0.396825	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729120	0.48833	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.34472	1.36;1.36;1.37	4.39	-3.04	0.05412	.	0.000000	0.27636	N	0.018486	T	0.48642	0.1511	M	0.76002	2.32	0.18873	N	0.999985	D;D;D;D	0.89917	0.96;0.96;0.96;1.0	P;P;P;D	0.85130	0.731;0.684;0.684;0.997	T	0.35919	-0.9769	10	0.48119	T	0.1	.	5.1769	0.15139	0.4641:0.0:0.3958:0.1401	.	1741;1741;1763;1741	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	F	1741;1763;1612	ENSP00000354486:L1741F;ENSP00000349305:L1763F;ENSP00000405842:L1612F	ENSP00000349305:L1763F	L	+	3	2	GOLGA4	37343604	0.979000	0.34478	0.002000	0.10522	0.888000	0.51559	0.310000	0.19356	-0.410000	0.07542	-0.379000	0.06801	TTA	.	.	none		0.388	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
GPR50	9248	hgsc.bcm.edu	37	X	150349533	150349533	+	Missense_Mutation	SNP	G	G	A	rs62620754		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:150349533G>A	ENST00000218316.3	+	2	1547	c.1478G>A	c.(1477-1479)aGt>aAt	p.S493N	AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	493	Pro-rich.				cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					TCTGCCTTCAGTGCTGCCACC	0.582													G|||	351	0.0929801	0.1142	0.0476	3775	,	,		13457	0.0556		0.0666	False		,,,				2504	0.045				p.S493N		Atlas-SNP	.											.	GPR50	195	.	0			c.G1478A						PASS	.	G	ASN/SER	490,3157		20,361,89,1157,482	111.0	124.0	120.0		1478	3.5	0.0	X	dbSNP_129	120	558,6036		16,366,160,2006,1658	yes	missense	GPR50	NM_004224.3	46	36,727,249,3163,2140	AA,AG,A,GG,G		8.4622,13.4357,10.2334	possibly-damaging	493/618	150349533	1048,9193	2109	4206	6315	SO:0001583	missense	9248	exon2			CCTTCAGTGCTGC	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"""GPCR / Class A : Orphans"""	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.1478G>A	X.37:g.150349533G>A	ENSP00000218316:p.Ser493Asn	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	160	0.09644364074743822	35	0.078125	14	0.03932584269662921	24	0.043795620437956206	32	0.044444444444444446	G	14.27	2.485956	0.44147	0.134357	0.084622	ENSG00000102195	ENST00000218316	T	0.72942	-0.7	3.47	3.47	0.39725	.	0.000000	0.40469	N	0.001084	T	0.00815	0.0027	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	B	0.21905	0.062	B	0.19391	0.025	T	0.39187	-0.9626	9	0.87932	D	0	-8.5366	12.092	0.53733	0.0:0.0:1.0:0.0	rs62620754	493	Q13585	MTR1L_HUMAN	N	493	ENSP00000218316:S493N	ENSP00000218316:S493N	S	+	2	0	GPR50	150100191	0.004000	0.15560	0.038000	0.18304	0.546000	0.35178	1.144000	0.31565	1.996000	0.58369	0.529000	0.55759	AGT	G|0.903;A|0.097	0.097	strong		0.582	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224	
PTPRJ	5795	hgsc.bcm.edu	37	11	48157625	48157625	+	Silent	SNP	C	C	T	rs148782546	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:48157625C>T	ENST00000418331.2	+	9	2002	c.1650C>T	c.(1648-1650)taC>taT	p.Y550Y		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	550	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ACGTGGTCTACGTCACCACCA	0.512													C|||	12	0.00239617	0.0	0.0	5008	,	,		21414	0.0		0.0119	False		,,,				2504	0.0				p.Y550Y		Atlas-SNP	.											PTPRJ_ENST00000418331,caecum,carcinoma,0,2	PTPRJ	225	2	0			c.C1650T						PASS	.	C		3,4399	6.2+/-15.9	0,3,2198	184.0	160.0	168.0		1650	-11.2	0.0	11	dbSNP_134	168	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous	PTPRJ	NM_002843.3		0,6,6493	TT,TC,CC		0.0349,0.0682,0.0462		550/1338	48157625	6,12992	2201	4298	6499	SO:0001819	synonymous_variant	5795	exon9			GGTCTACGTCACC	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1650C>T	11.37:g.48157625C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	246	127	0.51626	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																			C|0.998;T|0.002	0.002	strong		0.512	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
ZNF221	7638	hgsc.bcm.edu	37	19	44471252	44471252	+	Missense_Mutation	SNP	T	T	C	rs61734609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44471252T>C	ENST00000251269.5	+	6	1926	c.1598T>C	c.(1597-1599)cTa>cCa	p.L533P	ZNF221_ENST00000592350.1_Missense_Mutation_p.L533P|ZNF221_ENST00000587682.1_Missense_Mutation_p.L533P	NM_013359.2	NP_037491	Q9UK13	ZN221_HUMAN	zinc finger protein 221	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)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(11)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	30		Prostate(69;0.0352)				GGAGAAAAGCTATACAAATGT	0.433													T|||	479	0.095647	0.0151	0.0893	5008	,	,		22087	0.1389		0.1163	False		,,,				2504	0.1431				p.L533P		Atlas-SNP	.											.	ZNF221	59	.	0			c.T1598C						PASS	.	T	PRO/LEU	128,4278	93.0+/-131.7	1,126,2076	94.0	87.0	90.0		1598	1.7	0.0	19	dbSNP_129	90	942,7658	207.2+/-249.0	44,854,3402	yes	missense	ZNF221	NM_013359.2	98	45,980,5478	CC,CT,TT		10.9535,2.9051,8.227	benign	533/618	44471252	1070,11936	2203	4300	6503	SO:0001583	missense	7638	exon6			AAAAGCTATACAA	AF187987	CCDS12633.1	19q13.31	2013-01-08				ENSG00000159905		"""Zinc fingers, C2H2-type"", ""-"""	13014	protein-coding gene	gene with protein product							Standard	NM_013359		Approved		uc002oxx.2	Q9UK13		ENST00000251269.5:c.1598T>C	19.37:g.44471252T>C	ENSP00000251269:p.Leu533Pro	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_013359	B2RAI6|Q2M2H2|Q9P1U8	Missense_Mutation	SNP	ENST00000251269.5	37	CCDS12633.1	223	0.1021062271062271	12	0.024390243902439025	36	0.09944751381215469	83	0.1451048951048951	92	0.12137203166226913	t	0.015	-1.548005	0.00926	0.029051	0.109535	ENSG00000159905	ENST00000251269	T	0.09911	2.93	2.9	1.74	0.24563	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.01405	-0.89	0.29025	P	0.886041	B	0.02656	0.0	B	0.04013	0.001	T	0.44590	-0.9318	8	0.02654	T	1	.	7.5568	0.27829	0.0:0.8416:0.0:0.1584	rs61734609	533	Q9UK13	ZN221_HUMAN	P	533	ENSP00000251269:L533P	ENSP00000251269:L533P	L	+	2	0	ZNF221	49163092	0.085000	0.21516	0.001000	0.08648	0.183000	0.23260	0.945000	0.29056	0.403000	0.25479	0.379000	0.24179	CTA	T|0.910;C|0.090	0.090	strong		0.433	ZNF221-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460068.1		
MEGF6	1953	hgsc.bcm.edu	37	1	3416449	3416449	+	Missense_Mutation	SNP	C	C	A	rs7553399	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:3416449C>A	ENST00000356575.4	-	22	2973	c.2747G>T	c.(2746-2748)cGg>cTg	p.R916L	MEGF6_ENST00000294599.4_Missense_Mutation_p.R811L	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	916	EGF-like 16. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> L (in dbSNP:rs7553399). {ECO:0000269|PubMed:9693030}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		ACACTGGCACCGCTGCTCACA	0.692													C|||	2846	0.568291	0.3177	0.6556	5008	,	,		14872	0.4355		0.7515	False		,,,				2504	0.7935				p.R916L	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.G2747T						PASS	.	C	LEU/ARG	1637,2359		387,863,748	6.0	9.0	8.0		2747	-4.2	0.0	1	dbSNP_116	8	6151,2071		2383,1385,343	yes	missense	MEGF6	NM_001409.3	102	2770,2248,1091	AA,AC,CC		25.1885,40.966,36.258	benign	916/1542	3416449	7788,4430	1998	4111	6109	SO:0001583	missense	1953	exon22			TGGCACCGCTGCT	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.2747G>T	1.37:g.3416449C>A	ENSP00000348982:p.Arg916Leu	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	1255	0.5746336996336996	180	0.36585365853658536	226	0.6243093922651933	261	0.4562937062937063	588	0.7757255936675461	C	10.13	1.265674	0.23136	0.40966	0.748115	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.67698	-0.28;-0.28	5.22	-4.22	0.03800	EGF-like, laminin (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.854162	0.10368	N	0.683155	T	0.00012	0.0000	L	0.46741	1.465	0.80722	P	0.0	B;B	0.20459	0.045;0.036	B;B	0.29077	0.098;0.041	T	0.36040	-0.9764	9	0.12766	T	0.61	-9.9931	10.1619	0.42858	0.0:0.2761:0.1018:0.6222	rs7553399;rs61163190;rs7553399	916;811	O75095;O75095-2	MEGF6_HUMAN;.	L	811;916	ENSP00000294599:R811L;ENSP00000348982:R916L	ENSP00000294599:R811L	R	-	2	0	MEGF6	3406309	0.000000	0.05858	0.000000	0.03702	0.688000	0.40055	-1.621000	0.02044	-1.012000	0.03387	0.561000	0.74099	CGG	C|0.437;A|0.563	0.563	strong		0.692	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
KIR3DL2	3812	hgsc.bcm.edu	37	19	55367311	55367311	+	Missense_Mutation	SNP	G	G	A	rs113800142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55367311G>A	ENST00000326321.3	+	5	926	c.893G>A	c.(892-894)cGt>cAt	p.R298H	KIR3DL2_ENST00000270442.5_Missense_Mutation_p.R298H|KIR3DL1_ENST00000402254.2_Intron	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	298	Ig-like C2-type 3.				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)		GGCTCTTTCCGTGCCCTGCCC	0.567													.|||	348	0.0694888	0.0794	0.0591	5008	,	,		10257	0.0397		0.0636	False		,,,				2504	0.1002				p.R298H		Atlas-SNP	.											KIR3DL2,NS,carcinoma,0,1	KIR3DL2	55	1	0			c.G893A						scavenged	.	G	HIS/ARG	173,3101		9,155,1473	5.0	6.0	6.0		893	-2.0	0.0	19	dbSNP_132	6	521,6479		39,443,3018	no	missense	KIR3DL2	NM_006737.3	29	48,598,4491	AA,AG,GG		7.4429,5.2841,6.7549	benign	298/456	55367311	694,9580	1637	3500	5137	SO:0001583	missense	3812	exon5			CTTTCCGTGCCCT	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.893G>A	19.37:g.55367311G>A	ENSP00000325525:p.Arg298His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_001242867	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	.	.	.	.	.	.	.	.	.	.	g	0.311	-0.967828	0.02232	0.052841	0.074429	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.00768	5.72;5.72	0.993	-1.99	0.07457	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	L	0.43701	1.375	0.09310	N	1	B;B;B	0.15930	0.015;0.011;0.013	B;B;B	0.06405	0.002;0.001;0.0	T	0.44544	-0.9321	9	0.52906	T	0.07	.	2.9371	0.05818	0.3559:0.2417:0.4024:0.0	.	298;298;103	Q95366;P43630;B5MCJ6	.;KI3L2_HUMAN;.	H	298	ENSP00000325525:R298H;ENSP00000270442:R298H	ENSP00000270442:R298H	R	+	2	0	KIR3DL2	60059123	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.304000	0.00256	-1.364000	0.02161	-1.254000	0.01491	CGT	G|0.910;A|0.091	0.091	strong		0.567	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1		
RIMBP3	85376	hgsc.bcm.edu	37	22	20457107	20457107	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20457107T>C	ENST00000426804.1	-	1	4679	c.4195A>G	c.(4195-4197)Agg>Ggg	p.R1399G	SCARNA17_ENST00000516762.1_RNA|SCARNA18_ENST00000516215.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1399										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)			GGCTCCCTCCTCTCCTCTCGC	0.607																																					p.R1399G		Atlas-SNP	.											RIMBP3,NS,carcinoma,+1,1	RIMBP3	42	1	0			c.A4195G						scavenged	.						62.0	73.0	69.0					22																	20457107		1974	4182	6156	SO:0001583	missense	85376	exon1			CCCTCCTCTCCTC	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.4195A>G	22.37:g.20457107T>C	ENSP00000391564:p.Arg1399Gly	Somatic	706	3	0.00424929		WXS	Illumina HiSeq	Phase_I	640	9	0.0140625	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	37	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	T	12.82	2.051390	0.36181	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.19394	2.15	3.58	2.49	0.30216	.	1.879570	0.02516	N	0.092068	T	0.19406	0.0466	L	0.29908	0.895	0.09310	N	1	P	0.41313	0.745	B	0.41236	0.351	T	0.16867	-1.0388	10	0.42905	T	0.14	-4.0304	5.9922	0.19472	0.2307:0.0:0.0:0.7693	.	1305	Q9UFD9	RIM3A_HUMAN	G	1305;1399	ENSP00000391564:R1399G	ENSP00000347318:R1305G	R	-	1	2	RIMBP3	18837107	0.001000	0.12720	0.009000	0.14445	0.042000	0.13812	0.646000	0.24797	0.521000	0.28445	0.347000	0.21830	AGG	.	.	none		0.607	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
KRT75	9119	hgsc.bcm.edu	37	12	52825363	52825363	+	Silent	SNP	G	G	A	rs1798640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52825363G>A	ENST00000252245.5	-	4	1054	c.834C>T	c.(832-834)ccC>ccT	p.P278P		NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	278	Coil 1B.|Rod.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		TGATCTCCTCGGGCAGAGATT	0.498													G|||	3070	0.613019	0.6422	0.6888	5008	,	,		19946	0.6825		0.6143	False		,,,				2504	0.4468				p.P278P		Atlas-SNP	.											.	KRT75	75	.	0			c.C834T						PASS	.	G		2729,1677	656.1+/-400.0	843,1043,317	178.0	153.0	162.0		834	-12.1	0.0	12	dbSNP_89	162	5143,3457	636.0+/-399.0	1531,2081,688	no	coding-synonymous	KRT75	NM_004693.2		2374,3124,1005	AA,AG,GG		40.1977,38.0617,39.4741		278/552	52825363	7872,5134	2203	4300	6503	SO:0001819	synonymous_variant	9119	exon4			CTCCTCGGGCAGA	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.834C>T	12.37:g.52825363G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	123	49	0.398374	NM_004693	B4DQU4|Q9NSA9	Silent	SNP	ENST00000252245.5	37	CCDS8827.1																																																																																			G|0.370;A|0.630	0.630	strong		0.498	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
LPPR2	64748	hgsc.bcm.edu	37	19	11473358	11473358	+	Missense_Mutation	SNP	C	C	G	rs11540666	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11473358C>G	ENST00000251473.5	+	7	1209	c.833C>G	c.(832-834)aCc>aGc	p.T278S	DKFZP761J1410_ENST00000591608.1_Missense_Mutation_p.T253S	NM_001170635.1|NM_022737.2	NP_001164106.1|NP_073574.2																					GCCATCGCCACCTTTTTGGTG	0.627													C|||	284	0.0567093	0.0061	0.0403	5008	,	,		14734	0.0397		0.0696	False		,,,				2504	0.1411				p.T278S		Atlas-SNP	.											LPPR2,lymph_node,lymphoid_neoplasm,0,1	LPPR2	21	1	0			c.C833G						PASS	.	C	SER/THR,SER/THR	66,4340	60.5+/-97.4	1,64,2138	48.0	41.0	43.0		758,833	4.4	1.0	19	dbSNP_120	43	645,7955	163.2+/-215.8	21,603,3676	yes	missense,missense	LPPR2	NM_001170635.1,NM_022737.2	58,58	22,667,5814	GG,GC,CC		7.5,1.498,5.4667	possibly-damaging,possibly-damaging	253/428,278/344	11473358	711,12295	2203	4300	6503	SO:0001583	missense	0	exon7			TCGCCACCTTTTT																												ENST00000251473.5:c.833C>G	19.37:g.11473358C>G	ENSP00000251473:p.Thr278Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	61	26	0.42623	NM_022737		Missense_Mutation	SNP	ENST00000251473.5	37	CCDS12258.1	90	0.04120879120879121	3	0.006097560975609756	19	0.052486187845303865	17	0.02972027972027972	51	0.06728232189973615	C	17.46	3.396146	0.62177	0.01498	0.075	ENSG00000105520	ENST00000251473	T	0.74632	-0.86	5.45	4.42	0.53409	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.216830	0.49305	D	0.000154	T	0.09113	0.0225	N	0.05441	-0.05	0.31713	N	0.639302	P;P	0.44877	0.845;0.687	P;B	0.44696	0.458;0.403	T	0.45396	-0.9264	10	0.37606	T	0.19	-32.5719	9.6179	0.39704	0.0:0.8373:0.0:0.1627	rs11540666;rs11667275;rs17775744;rs11667275	253;278	Q96GM1-2;Q96GM1	.;LPPR2_HUMAN	S	278	ENSP00000251473:T278S	ENSP00000251473:T278S	T	+	2	0	AC024575.1	11334358	0.316000	0.24580	1.000000	0.80357	0.976000	0.68499	1.088000	0.30877	1.308000	0.44962	0.561000	0.74099	ACC	C|0.954;G|0.046	0.046	strong		0.627	DKFZP761J1410-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458779.1		
ZNF69	7620	hgsc.bcm.edu	37	19	11998777	11998777	+	Silent	SNP	C	C	T	rs3810314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11998777C>T	ENST00000429654.2	+	1	179	c.39C>T	c.(37-39)ccC>ccT	p.P13P	ZNF69_ENST00000340180.5_Silent_p.P13P			Q9UC07	ZNF69_HUMAN	zinc finger protein 69	13					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|skin(2)	4				Lung(535;0.011)		GAGAGGACCCCGGGACATCTG	0.637													c|||	579	0.115615	0.3389	0.0432	5008	,	,		16314	0.0228		0.0239	False		,,,				2504	0.0552				p.P13P		Atlas-SNP	.											.	ZNF69	27	.	0			c.C39T						PASS	.	C		1247,3159	428.7+/-342.0	173,901,1129	77.0	66.0	70.0		39	-1.1	0.0	19	dbSNP_107	70	164,8436	76.9+/-139.5	1,162,4137	no	coding-synonymous	ZNF69	NM_021915.2		174,1063,5266	TT,TC,CC		1.907,28.3023,10.8488		13/150	11998777	1411,11595	2203	4300	6503	SO:0001819	synonymous_variant	7620	exon1			GGACCCCGGGACA	X60076	CCDS32914.1	19p13.2	2013-01-08	2006-05-12		ENSG00000198429	ENSG00000198429		"""Zinc fingers, C2H2-type"", ""-"""	13138	protein-coding gene	gene with protein product		194543	"""zinc finger protein 69 (Cos5)"""			1639391	Standard	NM_021915		Approved	Cos5	uc002mst.4	Q9UC07	OTTHUMG00000156526	ENST00000429654.2:c.39C>T	19.37:g.11998777C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	82	40	0.487805	NM_021915	Q86VA7	Silent	SNP	ENST00000429654.2	37																																																																																				C|0.897;T|0.103	0.103	strong		0.637	ZNF69-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000344082.1	NM_021915	
PAX7	5081	hgsc.bcm.edu	37	1	19018432	19018432	+	Silent	SNP	A	A	C	rs2076019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:19018432A>C	ENST00000375375.3	+	5	1369	c.771A>C	c.(769-771)acA>acC	p.T257T	PAX7_ENST00000400661.3_Silent_p.T255T|PAX7_ENST00000420770.2_Silent_p.T257T	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	257					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)		CCAAGCTGACAGAGGCGCGTG	0.587			T	FOXO1A	alveolar rhabdomyosarcoma								C|||	625	0.1248	0.0499	0.0908	5008	,	,		19367	0.2569		0.0557	False		,,,				2504	0.1851				p.T257T		Atlas-SNP	.		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	.	PAX7	127	.	0			c.A771C						PASS	.	C	,,	252,4150	789.8+/-415.0	6,240,1955	39.0	35.0	36.0		771,771,765	-9.7	0.4	1	dbSNP_96	36	460,8136	790.3+/-407.6	13,434,3851	no	coding-synonymous,coding-synonymous,coding-synonymous	PAX7	NM_001135254.1,NM_002584.2,NM_013945.2	,,	19,674,5806	CC,CA,AA		5.3513,5.7247,5.4778	,,	257/506,257/521,255/519	19018432	712,12286	2201	4298	6499	SO:0001819	synonymous_variant	5081	exon5			GCTGACAGAGGCG	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.771A>C	1.37:g.19018432A>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	62	57	0.919355	NM_002584	E9PFV9|Q0VA99|Q2PJS5	Silent	SNP	ENST00000375375.3	37	CCDS186.1																																																																																			A|0.915;C|0.085	0.085	strong		0.587	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584	
MUC1	4582	hgsc.bcm.edu	37	1	155161833	155161833	+	Silent	SNP	C	C	G	rs147687610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155161833C>G	ENST00000368395.1	-	2	371	c.300G>C	c.(298-300)tcG>tcC	p.S100S	MUC1_ENST00000368398.3_Intron|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000337604.5_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000343256.5_Intron|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000342482.4_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	880					cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGACTGGGACCGAGGTGACAT	0.687			T	IGH@	B-NHL								C|||	30	0.00599042	0.0008	0.0072	5008	,	,		9990	0.0		0.0109	False		,,,				2504	0.0133				p.S109S		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	.	MUC1	94	.	0			c.G327C						PASS	.																																			SO:0001819	synonymous_variant	4582	exon2			TGGGACCGAGGTG	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.300G>C	1.37:g.155161833C>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Silent	SNP	ENST00000368395.1	37	CCDS55640.1																																																																																			C|0.995;G|0.005	0.005	strong		0.687	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
SH2D4B	387694	hgsc.bcm.edu	37	10	82369219	82369219	+	Missense_Mutation	SNP	T	T	A	rs17107368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:82369219T>A	ENST00000470604.2	+	6	894	c.894T>A	c.(892-894)gaT>gaA	p.D298E	SH2D4B_ENST00000313455.4_Missense_Mutation_p.D251E|SH2D4B_ENST00000339284.2_Missense_Mutation_p.D299E|SH2D4B_ENST00000372150.3_3'UTR			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	298										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			TCTCCAGAGATGTCATCGTCC	0.597													T|||	751	0.14996	0.0242	0.1239	5008	,	,		14881	0.3442		0.171	False		,,,				2504	0.1166				p.D299E		Atlas-SNP	.											SH2D4B,colon,carcinoma,+2,1	SH2D4B	44	1	0			c.T897A						scavenged	.	T	GLU/ASP,GLU/ASP	235,4171	137.7+/-173.5	7,221,1975	76.0	73.0	74.0		753,897	-6.9	0.9	10	dbSNP_123	74	1463,7137	278.7+/-293.6	142,1179,2979	yes	missense,missense	SH2D4B	NM_001145719.1,NM_207372.2	45,45	149,1400,4954	AA,AT,TT		17.0116,5.3336,13.0555	benign,benign	251/310,299/358	82369219	1698,11308	2203	4300	6503	SO:0001583	missense	387694	exon6			CAGAGATGTCATC		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.894T>A	10.37:g.82369219T>A	ENSP00000417953:p.Asp298Glu	Somatic	92	1	0.0108696		WXS	Illumina HiSeq	Phase_I	89	42	0.47191	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		413	0.1891025641025641	18	0.036585365853658534	43	0.11878453038674033	219	0.38286713286713286	133	0.17546174142480211	T	4.624	0.116020	0.08831	0.053336	0.170116	ENSG00000178217	ENST00000339284;ENST00000470604;ENST00000313455	T;T;T	0.08193	3.12;3.12;3.12	5.32	-6.92	0.01644	.	0.496191	0.21175	N	0.078911	T	0.00012	0.0000	N	0.00666	-1.275	0.80722	P	0.0	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.002;0.001	T	0.28996	-1.0026	9	0.02654	T	1	-5.2867	1.4482	0.02369	0.1492:0.1968:0.3315:0.3224	rs17107368;rs52818132;rs17107368	298;251;299	Q5SQS7;Q5SQS7-3;Q5SQS7-2	SH24B_HUMAN;.;.	E	299;298;251	ENSP00000345295:D299E;ENSP00000417953:D298E;ENSP00000314242:D251E	ENSP00000314242:D251E	D	+	3	2	SH2D4B	82359199	0.007000	0.16637	0.901000	0.35422	0.780000	0.44128	-0.914000	0.04038	-0.527000	0.06374	-0.400000	0.06385	GAT	T|0.847;A|0.153	0.153	strong		0.597	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
MTMR9	66036	hgsc.bcm.edu	37	8	11162496	11162496	+	Silent	SNP	A	A	C	rs2164272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:11162496A>C	ENST00000221086.3	+	4	1037	c.564A>C	c.(562-564)ctA>ctC	p.L188L	MTMR9_ENST00000526292.1_Silent_p.L103L	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	188	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		TCCCAGTACTAAGCTATTACC	0.463													A|||	2004	0.40016	0.1536	0.353	5008	,	,		21032	0.7063		0.3917	False		,,,				2504	0.4601				p.L188L		Atlas-SNP	.											.	MTMR9	58	.	0			c.A564C						PASS	.	A		881,3525	342.8+/-307.3	94,693,1416	123.0	104.0	110.0		564	-5.6	0.9	8	dbSNP_96	110	3482,5118	510.7+/-377.6	707,2068,1525	no	coding-synonymous	MTMR9	NM_015458.3		801,2761,2941	CC,CA,AA		40.4884,19.9955,33.5461		188/550	11162496	4363,8643	2203	4300	6503	SO:0001819	synonymous_variant	66036	exon4			AGTACTAAGCTAT	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	14596	protein-coding gene	gene with protein product		606260	"""myotubularin related protein 8"""	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.564A>C	8.37:g.11162496A>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	101	101	1	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Silent	SNP	ENST00000221086.3	37	CCDS5979.1																																																																																			A|0.640;C|0.360	0.360	strong		0.463	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458	
PPA2	27068	hgsc.bcm.edu	37	4	106345379	106345379	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:106345379T>C	ENST00000341695.5	-	7	659	c.629A>G	c.(628-630)aAt>aGt	p.N210S	PPA2_ENST00000354147.3_Intron|PPA2_ENST00000348706.5_Missense_Mutation_p.N181S|PPA2_ENST00000310267.7_Missense_Mutation_p.N131S|PPA2_ENST00000380004.2_Missense_Mutation_p.N192S|PPA2_ENST00000432483.2_Missense_Mutation_p.N108S|PPA2_ENST00000357415.4_Missense_Mutation_p.N225S|PPA2_ENST00000509426.1_5'UTR	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	210					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		TTCAGGATCATTCGCATTGAT	0.348																																					p.N210S		Atlas-SNP	.											.	PPA2	23	.	0			c.A629G						PASS	.						136.0	134.0	134.0					4																	106345379		2203	4300	6503	SO:0001583	missense	27068	exon7			GGATCATTCGCAT		CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.629A>G	4.37:g.106345379T>C	ENSP00000343885:p.Asn210Ser	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	75	31	0.413333	NM_176869	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.95|14.95	2.687529|2.687529	0.48097|0.48097	.|.	.|.	ENSG00000138777|ENSG00000138777	ENST00000508518|ENST00000341695;ENST00000348706;ENST00000432483;ENST00000357415;ENST00000380004;ENST00000510015;ENST00000310267	.|T;T;T;T;T;T;T	.|0.43688	.|0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.4|5.4	4.14|4.14	0.48551|0.48551	.|.	.|0.202955	.|0.50627	.|D	.|0.000102	T|T	0.39708|0.39708	0.1088|0.1088	L|L	0.53671|0.53671	1.685|1.685	0.38017|0.38017	D|D	0.934732|0.934732	.|B;B;B;B;B	.|0.31680	.|0.009;0.335;0.182;0.181;0.023	.|B;B;B;B;B	.|0.34991	.|0.01;0.109;0.193;0.079;0.073	T|T	0.49214|0.49214	-0.8963|-0.8963	5|10	.|0.52906	.|T	.|0.07	-2.6133|-2.6133	11.196|11.196	0.48713|0.48713	0.0:0.0:0.1536:0.8464|0.0:0.0:0.1536:0.8464	.|.	.|131;108;181;192;210	.|B4DFH3;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.|.;.;.;.;IPYR2_HUMAN	V|S	189|210;181;108;225;192;137;131	.|ENSP00000343885:N210S;ENSP00000313061:N181S;ENSP00000389957:N108S;ENSP00000349996:N225S;ENSP00000369340:N192S;ENSP00000423363:N137S;ENSP00000311150:N131S	.|ENSP00000311150:N131S	M|N	-|-	1|2	0|0	PPA2|PPA2	106564828|106564828	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.794000|0.794000	0.44872|0.44872	5.215000|5.215000	0.65241|0.65241	2.045000|2.045000	0.60652|0.60652	0.459000|0.459000	0.35465|0.35465	ATG|AAT	.	.	none		0.348	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869	
LMNA	4000	hgsc.bcm.edu	37	1	156107534	156107534	+	Splice_Site	SNP	C	C	T	rs4641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156107534C>T	ENST00000368300.4	+	10	1910	c.1698C>T	c.(1696-1698)caC>caT	p.H566H	LMNA_ENST00000347559.2_Intron|LMNA_ENST00000392353.3_Silent_p.H485H|LMNA_ENST00000473598.2_Splice_Site_p.H467H|LMNA_ENST00000368301.2_Silent_p.H566H|LMNA_ENST00000496738.1_3'UTR|LMNA_ENST00000368297.1_Silent_p.H485H|LMNA_ENST00000448611.2_Splice_Site_p.H454H|LMNA_ENST00000368299.3_Splice_Site_p.H566H|LMNA_ENST00000361308.4_Silent_p.H566H	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C	566	Tail.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					ATCACCACCACGTGAGTGGTA	0.642									Werner syndrome;Hutchinson-Gilford Progeria Syndrome				C|||	1103	0.220248	0.0658	0.3012	5008	,	,		13360	0.2738		0.2247	False		,,,				2504	0.3119				p.H566H		Atlas-SNP	.											.	LMNA	31	.	0			c.C1698T	GRCh37	CM003892	LMNA	M	rs4641	PASS	.	C	,,	367,3797		20,327,1735	30.0	24.0	26.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1698,1698,	-3.2	0.9	1	dbSNP_52	26	2046,6038		296,1454,2292	yes	coding-synonymous,coding-synonymous-near-splice,intron	LMNA	NM_005572.3,NM_170707.2,NM_170708.2	,,	316,1781,4027	TT,TC,CC		25.3093,8.8136,19.7012	,,	566/573,566/665,	156107534	2413,9835	2082	4042	6124	SO:0001630	splice_region_variant	4000	exon10	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	CCACCACGTGAGT	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.1698+1C>T	1.37:g.156107534C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	37	16	0.432432	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Silent	SNP	ENST00000368300.4	37	CCDS1129.1																																																																																			C|0.808;T|0.192	0.192	strong		0.642	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	Silent
ADAMTS20	80070	hgsc.bcm.edu	37	12	43822171	43822171	+	Missense_Mutation	SNP	G	G	A	rs7310011	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:43822171G>A	ENST00000389420.3	-	26	3817	c.3818C>T	c.(3817-3819)tCc>tTc	p.S1273F	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.S391F|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.S1273F	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1273			S -> F (in dbSNP:rs7310011).		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)		CTGCACAGGGGAACTAGGAAA	0.458													G|||	183	0.0365415	0.0015	0.0086	5008	,	,		13663	0.0694		0.0348	False		,,,				2504	0.0716				p.S1273F		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.C3818T						PASS	.	G	PHE/SER	26,4380	31.7+/-61.6	0,26,2177	86.0	83.0	84.0		3818	4.9	0.8	12	dbSNP_116	84	242,8358	97.2+/-158.9	6,230,4064	yes	missense	ADAMTS20	NM_025003.3	155	6,256,6241	AA,AG,GG		2.814,0.5901,2.0606	benign	1273/1911	43822171	268,12738	2203	4300	6503	SO:0001583	missense	80070	exon26			ACAGGGGAACTAG	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.3818C>T	12.37:g.43822171G>A	ENSP00000374071:p.Ser1273Phe	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	156	80	0.512821	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	78	0.03571428571428571	0	0.0	5	0.013812154696132596	44	0.07692307692307693	29	0.03825857519788918	G	0.596	-0.830847	0.02713	0.005901	0.02814	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.61859	0.24;0.09;0.09;0.07	4.94	4.94	0.65067	.	0.000000	0.44285	D	0.000470	T	0.04497	0.0123	N	0.24115	0.695	0.09310	N	1	B;D	0.62365	0.105;0.991	B;P	0.52424	0.016;0.698	T	0.03344	-1.1046	10	0.48119	T	0.1	.	8.9011	0.35495	0.081:0.0:0.7667:0.1522	rs7310011	1273;391	P59510;E9PBD5	ATS20_HUMAN;.	F	1273;403;391;1273;1273	ENSP00000374071:S1273F;ENSP00000447427:S403F;ENSP00000378911:S391F;ENSP00000448341:S1273F	ENSP00000374068:S1273F	S	-	2	0	ADAMTS20	42108438	0.994000	0.37717	0.778000	0.31720	0.002000	0.02628	1.179000	0.31993	2.675000	0.91044	0.585000	0.79938	TCC	G|0.974;A|0.026	0.026	strong		0.458	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
RP1L1	94137	hgsc.bcm.edu	37	8	10465942	10465942	+	Missense_Mutation	SNP	T	T	A	rs28446662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10465942T>A	ENST00000382483.3	-	4	5889	c.5666A>T	c.(5665-5667)gAt>gTt	p.D1889V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1969					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GGTCTCTACATCTTCTGACTC	0.602													t|||	1189	0.23742	0.1679	0.3386	5008	,	,		16217	0.3929		0.2147	False		,,,				2504	0.1227				p.D1889V		Atlas-SNP	.											.	RP1L1	453	.	0			c.A5666T						PASS	.	T	VAL/ASP	726,3178		68,590,1294	158.0	174.0	169.0		5666	-2.8	0.0	8	dbSNP_125	169	1669,6635		168,1333,2651	no	missense	RP1L1	NM_178857.5	152	236,1923,3945	AA,AT,TT		20.0987,18.5963,19.6183	benign	1889/2401	10465942	2395,9813	1952	4152	6104	SO:0001583	missense	94137	exon4			TCTACATCTTCTG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.5666A>T	8.37:g.10465942T>A	ENSP00000371923:p.Asp1889Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	111	48	0.432432	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	566	0.2591575091575092	62	0.12601626016260162	102	0.281767955801105	238	0.4160839160839161	164	0.21635883905013192	t	3.686	-0.064495	0.07273	0.185963	0.200987	ENSG00000183638	ENST00000382483	T	0.07688	3.17	1.4	-2.8	0.05823	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.46105	-0.9215	8	0.30078	T	0.28	.	4.5421	0.12064	0.0:0.1945:0.191:0.6145	rs28446662	1889	A6NKC6	.	V	1889	ENSP00000371923:D1889V	ENSP00000371923:D1889V	D	-	2	0	RP1L1	10503352	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.203000	0.03019	-0.837000	0.04223	-0.375000	0.07067	GAT	T|0.764;A|0.236	0.236	strong		0.602	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
C1orf64	149563	hgsc.bcm.edu	37	1	16330816	16330816	+	Silent	SNP	C	C	T	rs1763617	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16330816C>T	ENST00000329454.2	+	1	86	c.18C>T	c.(16-18)gaC>gaT	p.D6D	RP11-5P18.5_ENST00000437156.1_RNA	NM_178840.2	NP_849162.1	Q8NEQ6	CA064_HUMAN	chromosome 1 open reading frame 64	6										breast(2)|endometrium(1)|lung(3)	6		Colorectal(325;0.000435)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;2.08e-05)|BRCA - Breast invasive adenocarcinoma(304;9.19e-05)|Kidney(64;0.000165)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0114)|READ - Rectum adenocarcinoma(331;0.0649)		CGTCAGAAGACCCCAGGGACT	0.642													C|||	977	0.195088	0.1369	0.2089	5008	,	,		15718	0.2917		0.1581	False		,,,				2504	0.2025				p.D6D		Atlas-SNP	.											.	C1orf64	16	.	0			c.C18T						PASS	.	C		662,3732		51,560,1586	39.0	37.0	37.0		18	2.0	0.0	1	dbSNP_89	37	1253,7331		89,1075,3128	no	coding-synonymous	C1orf64	NM_178840.2		140,1635,4714	TT,TC,CC		14.5969,15.066,14.7557		6/170	16330816	1915,11063	2197	4292	6489	SO:0001819	synonymous_variant	149563	exon1			AGAAGACCCCAGG	AK127425	CCDS166.1	1p36.13	2013-10-11			ENSG00000183888	ENSG00000183888			28339	protein-coding gene	gene with protein product	"""ER-related factor"""					22341523	Standard	NM_178840		Approved	MGC24047, ERRF	uc001axn.3	Q8NEQ6	OTTHUMG00000009523	ENST00000329454.2:c.18C>T	1.37:g.16330816C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	178	10	0.0561798	NM_178840	B3KXI9	Silent	SNP	ENST00000329454.2	37	CCDS166.1																																																																																			C|0.835;T|0.165	0.165	strong		0.642	C1orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026317.1	NM_178840	
GJA9	81025	hgsc.bcm.edu	37	1	39340607	39340607	+	Silent	SNP	A	A	G	rs16825625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:39340607A>G	ENST00000360786.3	-	1	1416	c.1164T>C	c.(1162-1164)cgT>cgC	p.R388R	RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000357771.3_Silent_p.R388R|GJA9_ENST00000454994.2_Silent_p.R388R|MYCBP_ENST00000397572.2_5'Flank|MYCBP_ENST00000489803.1_5'UTR			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	388					cell communication (GO:0007154)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			CTGGAATAGAACGGTGACCTC	0.423													A|||	270	0.0539137	0.0182	0.0504	5008	,	,		21207	0.0823		0.0706	False		,,,				2504	0.0583				p.R388R		Atlas-SNP	.											GJA9,NS,carcinoma,-1,1	GJA9	55	1	0			c.T1164C						PASS	.	A		173,4233	115.0+/-153.0	5,163,2035	184.0	172.0	176.0		1164	-1.2	0.0	1	dbSNP_123	176	870,7730	197.9+/-242.4	60,750,3490	no	coding-synonymous	GJA9	NM_030772.4		65,913,5525	GG,GA,AA		10.1163,3.9265,8.0194		388/516	39340607	1043,11963	2203	4300	6503	SO:0001819	synonymous_variant	81025	exon2			AATAGAACGGTGA	AF179597	CCDS432.1	1p34	2008-02-05	2007-11-06	2007-11-06	ENSG00000131233	ENSG00000131233		"""Ion channels / Gap junction proteins (connexins)"""	19155	protein-coding gene	gene with protein product	"""connexin 59"""	611923	"""gap junction protein, alpha 10, 59kDa"""	GJA10			Standard	NM_030772		Approved	CX59, CX58	uc021olr.1	P57773	OTTHUMG00000000482	ENST00000360786.3:c.1164T>C	1.37:g.39340607A>G		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	203	186	0.916256	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Silent	SNP	ENST00000360786.3	37	CCDS432.1																																																																																			A|0.929;G|0.071	0.071	strong		0.423	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772	
BTNL2	56244	hgsc.bcm.edu	37	6	32362702	32362702	+	Silent	SNP	T	T	C	rs28362676|rs41342846	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32362702T>C	ENST00000374993.1	-	6	1178	c.1179A>G	c.(1177-1179)ccA>ccG	p.P393P	BTNL2_ENST00000414363.1_Silent_p.P183P|BTNL2_ENST00000544175.1_Silent_p.P116P|BTNL2_ENST00000540315.1_Silent_p.P183P|BTNL2_ENST00000429232.2_3'UTR|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Silent_p.P299P|BTNL2_ENST00000454136.3_Silent_p.P393P	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	393			P -> Q (in dbSNP:rs41521946).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						TGTCCCTCCATGGCACGTGGG	0.562													t|||	821	0.163938	0.1422	0.1599	5008	,	,		19983	0.1587		0.163	False		,,,				2504	0.2025				p.P393P		Atlas-SNP	.											.	BTNL2	50	.	0			c.A1179G						PASS	.			15,4391	4.2+/-10.8	4,7,2192	233.0	218.0	223.0		1179	-0.1	0.9	6	dbSNP_127	223	23,8577		4,15,4281	no	coding-synonymous	BTNL2	NM_019602.1		8,22,6473	CC,CT,TT		0.2674,0.3404,0.2922		393/456	32362702	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	56244	exon6			CCTCCATGGCACG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1179A>G	6.37:g.32362702T>C		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	107	38	0.35514	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																				T|0.871;C|0.129	0.129	strong		0.562	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
BAI3	577	hgsc.bcm.edu	37	6	70064187	70064187	+	Silent	SNP	G	G	A	rs2296974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:70064187G>A	ENST00000370598.1	+	27	4343	c.3522G>A	c.(3520-3522)tcG>tcA	p.S1174S	BAI3_ENST00000546190.1_Silent_p.S138S|BAI3_ENST00000238918.8_Silent_p.S380S	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1174	Poly-Ser.				G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S1174S(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				CAGATTCTTCGAGTTCGTTTC	0.393													G|||	904	0.180511	0.2511	0.2421	5008	,	,		16467	0.121		0.1909	False		,,,				2504	0.092				p.S1174S		Atlas-SNP	.											BAI3,NS,carcinoma,0,1	BAI3	451	1	1	Substitution - coding silent(1)	stomach(1)	c.G3522A						PASS	.	G		1145,3261	407.5+/-334.3	138,869,1196	181.0	166.0	171.0		3522	-0.6	1.0	6	dbSNP_100	171	1691,6909	309.6+/-309.4	158,1375,2767	no	coding-synonymous	BAI3	NM_001704.2		296,2244,3963	AA,AG,GG		19.6628,25.9873,21.8053		1174/1523	70064187	2836,10170	2203	4300	6503	SO:0001819	synonymous_variant	577	exon27			TTCTTCGAGTTCG	AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.3522G>A	6.37:g.70064187G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	63	62	0.984127	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																			G|0.792;A|0.208	0.208	strong		0.393	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
ARSG	22901	hgsc.bcm.edu	37	17	66391276	66391276	+	Missense_Mutation	SNP	G	G	A	rs9972951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:66391276G>A	ENST00000448504.2	+	10	1950	c.1154G>A	c.(1153-1155)cGc>cAc	p.R385H	ARSG_ENST00000452479.2_Missense_Mutation_p.R221H|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	385			R -> H (in dbSNP:rs9972951).		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)			CAAGGACGGCGCTTTGATGGT	0.567													G|||	560	0.111821	0.0431	0.0173	5008	,	,		20707	0.2153		0.0328	False		,,,				2504	0.2464				p.R385H		Atlas-SNP	.											.	ARSG	55	.	0			c.G1154A						PASS	.	G	HIS/ARG	169,4237	112.5+/-150.6	3,163,2037	163.0	125.0	138.0		1154	-1.2	0.0	17	dbSNP_119	138	292,8308	108.2+/-168.9	3,286,4011	yes	missense	ARSG	NM_014960.3	29	6,449,6048	AA,AG,GG		3.3953,3.8357,3.5445	benign	385/526	66391276	461,12545	2203	4300	6503	SO:0001583	missense	22901	exon10			GACGGCGCTTTGA	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.1154G>A	17.37:g.66391276G>A	ENSP00000407193:p.Arg385His	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	160	79	0.49375	NM_001267727	Q6UXF2|Q9Y2K4	Missense_Mutation	SNP	ENST00000448504.2	37	CCDS11676.1	182	0.08333333333333333	27	0.054878048780487805	5	0.013812154696132596	131	0.229020979020979	19	0.025065963060686015	G	6.150	0.395892	0.11638	0.038357	0.033953	ENSG00000141337	ENST00000452479;ENST00000448504	.	.	.	5.25	-1.21	0.09524	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.556482	0.21166	N	0.079080	T	0.00012	0.0000	N	0.04994	-0.135	0.46222	P	0.0010679999999999579	B	0.12630	0.006	B	0.09377	0.004	T	0.32348	-0.9910	8	0.12430	T	0.62	.	9.6703	0.40008	0.456:0.0:0.544:0.0	rs9972951;rs61049422;rs9972951	385	Q96EG1	ARSG_HUMAN	H	385;284	.	ENSP00000407193:R284H	R	+	2	0	ARSG	63902871	0.909000	0.30893	0.016000	0.15963	0.599000	0.36880	0.221000	0.17680	-0.429000	0.07329	-0.378000	0.06908	CGC	G|0.931;A|0.069	0.069	strong		0.567	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
ACPP	55	hgsc.bcm.edu	37	3	132075707	132075707	+	Silent	SNP	A	A	G	rs2071505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132075707A>G	ENST00000336375.5	+	10	1236	c.1146A>G	c.(1144-1146)gaA>gaG	p.E382E	ACPP_ENST00000475741.1_Silent_p.E349E|ACPP_ENST00000351273.7_Intron	NM_001099.4	NP_001090.2	P15309	PPAP_HUMAN	acid phosphatase, prostate	382					adenosine metabolic process (GO:0046085)|dephosphorylation (GO:0016311)|nucleotide metabolic process (GO:0009117)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|purine nucleobase metabolic process (GO:0006144)|regulation of sensory perception of pain (GO:0051930)|thiamine metabolic process (GO:0006772)	apical part of cell (GO:0045177)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi cisterna (GO:0031985)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|vesicle membrane (GO:0012506)	5'-nucleotidase activity (GO:0008253)|acid phosphatase activity (GO:0003993)|choline binding (GO:0033265)|identical protein binding (GO:0042802)|lysophosphatidic acid phosphatase activity (GO:0052642)|phosphatase activity (GO:0016791)|thiamine phosphate phosphatase activity (GO:0042131)			NS(1)|breast(1)|endometrium(2)|large_intestine(5)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	27						AAGGTACTGAAGACAGTACAG	0.512													G|||	1984	0.396166	0.3608	0.4827	5008	,	,		18799	0.119		0.5378	False		,,,				2504	0.5225				p.E382E		Atlas-SNP	.											.	ACPP	118	.	0			c.A1146G						PASS	.	G	,	1709,2697	651.7+/-399.3	341,1027,835	112.0	100.0	104.0		1146,	3.8	0.0	3	dbSNP_96	104	4801,3799	537.7+/-383.3	1332,2137,831	no	coding-synonymous,intron	ACPP	NM_001099.4,NM_001134194.1	,	1673,3164,1666	GG,GA,AA		44.1744,38.788,49.9462	,	382/387,	132075707	6510,6496	2203	4300	6503	SO:0001819	synonymous_variant	55	exon10			TACTGAAGACAGT		CCDS3073.1, CCDS46916.1	3q22.1	2012-05-16			ENSG00000014257	ENSG00000014257	3.1.3.2		125	protein-coding gene	gene with protein product		171790					Standard	NM_001099		Approved	ACP3, ACP-3	uc003eop.4	P15309	OTTHUMG00000159650	ENST00000336375.5:c.1146A>G	3.37:g.132075707A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_001099	D3DNC6|Q5FBY0|Q96KY0|Q96QK9|Q96QM0	Silent	SNP	ENST00000336375.5	37	CCDS3073.1																																																																																			A|0.554;G|0.446	0.446	strong		0.512	ACPP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356699.2	NM_001099	
KMT2C	58508	hgsc.bcm.edu	37	7	151962289	151962289	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151962289C>T	ENST00000262189.6	-	8	1236	c.1018G>A	c.(1018-1020)Gaa>Aaa	p.E340K	KMT2C_ENST00000355193.2_Missense_Mutation_p.E340K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	340					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)										TTTGCATCTTCCTTCGCTATA	0.363																																					p.E340K		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,+2,2	MLL3	1564	2	0			c.G1018A						scavenged	.						80.0	74.0	76.0					7																	151962289		2203	4299	6502	SO:0001583	missense	58508	exon8			CATCTTCCTTCGC	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.1018G>A	7.37:g.151962289C>T	ENSP00000262189:p.Glu340Lys	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	172	11	0.0639535	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.437062	0.43224	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98947	-5.26;-5.26	4.65	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.42821	U	0.000650	D	0.97688	0.9242	N	0.25890	0.77	0.80722	D	1	D	0.60575	0.988	P	0.54759	0.76	D	0.98897	1.0775	10	0.62326	D	0.03	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	340	Q8NEZ4	MLL3_HUMAN	K	340	ENSP00000262189:E340K;ENSP00000347325:E340K	ENSP00000262189:E340K	E	-	1	0	MLL3	151593222	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GAA	.	.	none		0.363	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
EIF2AK3	9451	hgsc.bcm.edu	37	2	88913273	88913273	+	Missense_Mutation	SNP	G	G	C	rs867529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:88913273G>C	ENST00000303236.3	-	2	708	c.407C>G	c.(406-408)tCc>tGc	p.S136C	EIF2AK3_ENST00000419748.1_5'UTR	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	136			S -> C (in dbSNP:rs867529). {ECO:0000269|PubMed:10932183, ECO:0000269|PubMed:17344846}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|bone mineralization (GO:0030282)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|chondrocyte development (GO:0002063)|endocrine pancreas development (GO:0031018)|endoplasmic reticulum organization (GO:0007029)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER overload response (GO:0006983)|fat cell differentiation (GO:0045444)|insulin secretion (GO:0030073)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|lactation (GO:0007595)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of myelination (GO:0031642)|negative regulation of translation (GO:0017148)|negative regulation of translational initiation in response to stress (GO:0032057)|ossification (GO:0001503)|positive regulation of protein binding (GO:0032092)|positive regulation of signal transduction (GO:0009967)|protein autophosphorylation (GO:0046777)|protein homooligomerization (GO:0051260)|protein phosphorylation (GO:0006468)|regulation of fatty acid metabolic process (GO:0019217)|response to endoplasmic reticulum stress (GO:0034976)|skeletal system development (GO:0001501)|SREBP signaling pathway (GO:0032933)|translation (GO:0006412)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activity (GO:0004674)			ovary(3)	3						TGACACCAAGGAACCGGATCC	0.383													G|||	1405	0.280551	0.0166	0.3343	5008	,	,		16061	0.4851		0.2982	False		,,,				2504	0.3701				p.S136C	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.C407G						PASS	.	G	CYS/SER	256,4150	145.4+/-180.2	8,240,1955	123.0	109.0	114.0		407	5.4	1.0	2	dbSNP_86	114	2324,6276	389.8+/-343.1	313,1698,2289	yes	missense	EIF2AK3	NM_004836.5	112	321,1938,4244	CC,CG,GG		27.0233,5.8103,19.837	benign	136/1117	88913273	2580,10426	2203	4300	6503	SO:0001583	missense	9451	exon2			ACCAAGGAACCGG	AF110146	CCDS33241.1	2p12	2008-05-21			ENSG00000172071	ENSG00000172071			3255	protein-coding gene	gene with protein product		604032				10026192, 10575235	Standard	NM_004836		Approved	PEK, PERK	uc002stc.4	Q9NZJ5	OTTHUMG00000155046	ENST00000303236.3:c.407C>G	2.37:g.88913273G>C	ENSP00000307235:p.Ser136Cys	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	60	27	0.45	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	629	0.288003663003663	10	0.02032520325203252	123	0.3397790055248619	274	0.479020979020979	222	0.2928759894459103	G	14.41	2.527371	0.44969	0.058103	0.270233	ENSG00000172071	ENST00000303236	T	0.30981	1.51	5.38	5.38	0.77491	Quinonprotein alcohol dehydrogenase-like (2);	0.227346	0.46758	D	0.000261	T	0.00012	0.0000	L	0.33245	0.995	0.29294	P	0.8691530000000001	B	0.09022	0.002	B	0.08055	0.003	T	0.49011	-0.8983	9	0.39692	T	0.17	-10.5973	19.1382	0.93436	0.0:0.0:1.0:0.0	rs867529;rs1805163;rs52809782;rs867529	136	Q9NZJ5	E2AK3_HUMAN	C	136	ENSP00000307235:S136C	ENSP00000307235:S136C	S	-	2	0	EIF2AK3	88694388	1.000000	0.71417	1.000000	0.80357	0.812000	0.45895	5.704000	0.68347	2.507000	0.84556	0.655000	0.94253	TCC	G|0.764;C|0.236	0.236	strong		0.383	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836	
RBM47	54502	hgsc.bcm.edu	37	4	40427990	40427990	+	Silent	SNP	G	G	C	rs2292039	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:40427990G>C	ENST00000381793.2	-	6	2109	c.1713C>G	c.(1711-1713)ggC>ggG	p.G571G	RBM47_ENST00000514014.1_Silent_p.G533G|RP11-588L15.2_ENST00000514187.1_RNA|RBM47_ENST00000319592.4_Silent_p.G502G|RBM47_ENST00000295971.7_Silent_p.G571G|RBM47_ENST00000381795.6_Silent_p.G502G			A0AV96	RBM47_HUMAN	RNA binding motif protein 47	571	Ala-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(5)|endometrium(1)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	29						GAGGTATGTAGCCTGCGTATC	0.602													G|||	137	0.0273562	0.0023	0.0403	5008	,	,		15487	0.0109		0.0487	False		,,,				2504	0.047				p.G571G		Atlas-SNP	.											.	RBM47	146	.	0			c.C1713G						PASS	.	G	,	42,4364	46.0+/-80.4	0,42,2161	109.0	91.0	97.0		1713,1506	5.2	1.0	4	dbSNP_100	97	515,8085	145.3+/-201.0	18,479,3803	no	coding-synonymous,coding-synonymous	RBM47	NM_001098634.1,NM_019027.3	,	18,521,5964	CC,CG,GG		5.9884,0.9532,4.2826	,	571/594,502/525	40427990	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	54502	exon7			TATGTAGCCTGCG	AK000280	CCDS3460.1, CCDS43223.1	4p14	2013-02-12			ENSG00000163694	ENSG00000163694		"""RNA binding motif (RRM) containing"""	30358	protein-coding gene	gene with protein product							Standard	NM_019027		Approved	FLJ20273, NET18	uc003gvc.2	A0AV96	OTTHUMG00000128598	ENST00000381793.2:c.1713C>G	4.37:g.40427990G>C		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	90	47	0.522222	NM_001098634	A0PJK2|B5MED4|Q8NI52|Q8NI53|Q9NXG3	Silent	SNP	ENST00000381793.2	37	CCDS43223.1																																																																																			G|0.959;C|0.041	0.041	strong		0.602	RBM47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250456.2	NM_019027	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144854564	144854564	+	Silent	SNP	G	G	A	rs147331822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144854564G>A	ENST00000369354.3	-	42	7095	c.6906C>T	c.(6904-6906)aaC>aaT	p.N2302N	PDE4DIP_ENST00000369359.4_Silent_p.N2438N|PDE4DIP_ENST00000530740.1_Silent_p.N2387N|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Silent_p.N2302N|PDE4DIP_ENST00000313382.9_Silent_p.N2196N			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2302					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)		GCTGGTTGGCGTTCTTCAGAT	0.512			T	PDGFRB	MPD																																p.N2302N		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,colon,carcinoma,0,2	PDE4DIP	817	2	0			c.C6906T						scavenged	.	G	,,	199,4207		0,199,2004	306.0	260.0	276.0		6588,6906,6906	-5.9	0.2	1	dbSNP_134	276	626,7974		0,626,3674	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,825,5678	AA,AG,GG		7.2791,4.5166,6.3432	,,	2196/2241,2302/2363,2302/2347	144854564	825,12181	2203	4300	6503	SO:0001819	synonymous_variant	9659	exon42			GTTGGCGTTCTTC	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.6906C>T	1.37:g.144854564G>A		Somatic	285	2	0.00701754		WXS	Illumina HiSeq	Phase_I	230	28	0.121739	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|0.935;A|0.065	0.065	strong		0.512	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SLC35G2	80723	hgsc.bcm.edu	37	3	136574521	136574521	+	Silent	SNP	C	C	T	rs1052620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:136574521C>T	ENST00000446465.2	+	2	1847	c.1219C>T	c.(1219-1221)Cta>Tta	p.L407L	RP11-85F14.5_ENST00000474250.1_RNA|SLC35G2_ENST00000393079.3_Silent_p.L407L|RP11-85F14.5_ENST00000470236.1_RNA|RP11-85F14.5_ENST00000461864.1_RNA	NM_025246.2	NP_079522.2			solute carrier family 35, member G2																		CCAGGAAATACTAGACTCTCC	0.323													C|||	439	0.0876597	0.0098	0.0908	5008	,	,		16135	0.001		0.1889	False		,,,				2504	0.1759				p.L407L		Atlas-SNP	.											.	.	.	.	0			c.C1219T						PASS	.	C	,,	184,4222	116.7+/-154.6	6,172,2025	66.0	63.0	64.0		1219,1219,1219	3.0	1.0	3	dbSNP_86	64	2014,6586	339.1+/-323.0	232,1550,2518	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM22	NM_001097599.1,NM_001097600.1,NM_025246.2	,,	238,1722,4543	TT,TC,CC		23.4186,4.1761,16.8999	,,	407/413,407/413,407/413	136574521	2198,10808	2203	4300	6503	SO:0001819	synonymous_variant	80723	exon2			GAAATACTAGACT	BC022557	CCDS3091.1	3q22.3	2013-05-22	2012-03-09	2012-03-09	ENSG00000168917	ENSG00000168917		"""Solute carriers"""	28480	protein-coding gene	gene with protein product			"""transmembrane protein 22"""	TMEM22		11230166	Standard	NM_001097600		Approved	MGC3295, DKFZp564K2464	uc003erf.4	Q8TBE7	OTTHUMG00000159787	ENST00000446465.2:c.1219C>T	3.37:g.136574521C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	141	56	0.397163	NM_025246		Silent	SNP	ENST00000446465.2	37	CCDS3091.1																																																																																			C|0.857;T|0.143	0.143	strong		0.323	SLC35G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357317.1	NM_025246	
MYH7	4625	hgsc.bcm.edu	37	14	23902753	23902753	+	Silent	SNP	G	G	A	rs2069540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23902753G>A	ENST00000355349.3	-	3	351	c.189C>T	c.(187-189)acC>acT	p.T63T		NM_000257.2	NP_000248.2	P12883	MYH7_HUMAN	myosin, heavy chain 7, cardiac muscle, beta	63					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)			NS(3)|breast(4)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(19)|lung(57)|ovary(5)|prostate(9)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	137	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00725)		TGCCATACTCGGTCTCGGCAG	0.562													G|||	2606	0.520367	0.6392	0.4063	5008	,	,		22211	0.4137		0.4851	False		,,,				2504	0.5869				p.T63T		Atlas-SNP	.											.	MYH7	349	.	0			c.C189T						PASS	.	G		2698,1708	651.7+/-399.3	821,1056,326	124.0	96.0	106.0		189	-8.4	0.2	14	dbSNP_96	106	4163,4437	567.2+/-388.8	984,2195,1121	no	coding-synonymous	MYH7	NM_000257.2		1805,3251,1447	AA,AG,GG		48.407,38.7653,47.2474		63/1936	23902753	6861,6145	2203	4300	6503	SO:0001819	synonymous_variant	4625	exon3			ATACTCGGTCTCG	M58018	CCDS9601.1	14q11.2-q13	2014-09-17	2006-09-29		ENSG00000092054	ENSG00000092054		"""Myosins / Myosin superfamily : Class II"""	7577	protein-coding gene	gene with protein product		160760	"""myopathy, distal 1"", ""myosin, heavy polypeptide 7, cardiac muscle, beta"""	CMH1, MPD1		2494889, 8483915, 15322983	Standard	XM_005267696		Approved	CMD1S	uc001wjx.3	P12883	OTTHUMG00000028755	ENST00000355349.3:c.189C>T	14.37:g.23902753G>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	52	51	0.980769	NM_000257	A2TDB6|B6D424|Q14836|Q14837|Q14904|Q16579|Q2M1Y6|Q92679|Q9H1D5|Q9UDA2|Q9UMM8	Silent	SNP	ENST00000355349.3	37	CCDS9601.1																																																																																			G|0.488;A|0.512	0.512	strong		0.562	MYH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071798.3	NM_000257	
CGB7	94027	hgsc.bcm.edu	37	19	49557572	49557572	+	Silent	SNP	T	T	C	rs62127880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49557572T>C	ENST00000597853.1	-	5	3345	c.474A>G	c.(472-474)tcA>tcG	p.S158S	CGB7_ENST00000356213.4_Silent_p.S156S|CGB7_ENST00000596965.1_Silent_p.S158S|CGB7_ENST00000593309.1_5'Flank|CGB7_ENST00000377280.3_Silent_p.S158S			P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 7	158					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|peptide hormone processing (GO:0016486)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			lung(3)|urinary_tract(2)	5		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		TCGGGGTGTCTGAGGGCCCCG	0.627																																					p.S158S		Atlas-SNP	.											CGB7,NS,carcinoma,-1,1	CGB7	10	1	0			c.A474G						scavenged	.						31.0	31.0	31.0					19																	49557572		1499	2656	4155	SO:0001819	synonymous_variant	94027	exon3			GGTGTCTGAGGGC	K00092	CCDS33071.1	19q13.32	2008-02-05				ENSG00000196337			16451	protein-coding gene	gene with protein product		608826				6194155	Standard	NM_033142		Approved	CG-beta-a		P01233		ENST00000597853.1:c.474A>G	19.37:g.49557572T>C		Somatic	205	4	0.0195122		WXS	Illumina HiSeq	Phase_I	164	44	0.268293	NM_033142	A1A5E0|B9ZVP5|Q13991|Q14000|Q3KPI3|Q3SY41|Q8WTT5|Q8WXL1|Q8WXL2|Q8WXL3|Q8WXL4	Silent	SNP	ENST00000597853.1	37	CCDS33071.1																																																																																			T|0.962;C|0.038	0.038	strong		0.627	CGB7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466254.1	NM_033142	
OR8H3	390152	hgsc.bcm.edu	37	11	55889895	55889895	+	Missense_Mutation	SNP	C	C	T	rs61751933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55889895C>T	ENST00000313472.3	+	1	47	c.47C>T	c.(46-48)aCg>aTg	p.T16M		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	16						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T16M(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					TTCATCCTTACGGGACTGTCA	0.453													C|||	520	0.103834	0.0522	0.098	5008	,	,		19669	0.1429		0.1213	False		,,,				2504	0.1196				p.T16M		Atlas-SNP	.											OR8H3,NS,carcinoma,0,1	OR8H3	92	1	1	Substitution - Missense(1)	stomach(1)	c.C47T						PASS	.	C	MET/THR	246,4156	143.1+/-178.2	7,232,1962	183.0	175.0	178.0		47	0.8	0.1	11	dbSNP_131	178	1007,7585	216.6+/-255.6	54,899,3343	yes	missense	OR8H3	NM_001005201.1	81	61,1131,5305	TT,TC,CC		11.7202,5.5884,9.6429	benign	16/313	55889895	1253,11741	2201	4296	6497	SO:0001583	missense	390152	exon1			TCCTTACGGGACT	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.47C>T	11.37:g.55889895C>T	ENSP00000323928:p.Thr16Met	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	180	90	0.5	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	255	0.11675824175824176	34	0.06910569105691057	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	C	0.003	-2.579330	0.00129	0.055884	0.117202	ENSG00000181761	ENST00000313472	T	0.00421	7.46	3.43	0.837	0.18896	.	0.928117	0.09163	N	0.839876	T	0.00012	0.0000	N	0.01297	-0.9	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10382	-1.0632	9	0.36615	T	0.2	.	4.4628	0.11675	0.1467:0.1847:0.0:0.6686	rs61751933	16	Q8N146	OR8H3_HUMAN	M	16	ENSP00000323928:T16M	ENSP00000323928:T16M	T	+	2	0	OR8H3	55646471	0.000000	0.05858	0.086000	0.20670	0.074000	0.17049	-0.728000	0.04925	0.329000	0.23460	-1.252000	0.01501	ACG	C|0.900;T|0.100	0.100	strong		0.453	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55340841	55340841	+	Silent	SNP	G	G	C	rs150471749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55340841G>C	ENST00000391728.4	+	7	1059	c.1026G>C	c.(1024-1026)ctG>ctC	p.L342L	KIR3DL1_ENST00000541392.1_Silent_p.L325L|KIR3DL1_ENST00000326542.7_Silent_p.L325L|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000358178.4_Silent_p.L247L|KIR3DL1_ENST00000538269.1_Silent_p.L342L	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	342					immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		TGCACATTCTGATTGGGACCT	0.453													g|||	526	0.105032	0.0938	0.1427	5008	,	,		16179	0.001		0.2475	False		,,,				2504	0.0542				p.L342L		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.G1026C						PASS	.	G		318,4030		79,160,1935	273.0	206.0	229.0		1026	0.7	0.1	19	dbSNP_134	229	1261,7047		387,487,3280	no	coding-synonymous	KIR3DL1	NM_013289.2		466,647,5215	CC,CG,GG		15.1781,7.3137,12.4763		342/445	55340841	1579,11077	2174	4154	6328	SO:0001819	synonymous_variant	3811	exon7			CATTCTGATTGGG	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.1026G>C	19.37:g.55340841G>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	33	10	0.30303	NM_013289	O43473|Q14946|Q16541	Silent	SNP	ENST00000391728.4	37	CCDS42621.1																																																																																			G|0.905;C|0.096	0.096	strong		0.453	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
CHRM1	1128	hgsc.bcm.edu	37	11	62677529	62677529	+	Silent	SNP	C	C	T	rs2067478	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62677529C>T	ENST00000306960.3	-	2	1585	c.1044G>A	c.(1042-1044)caG>caA	p.Q348Q	AP000438.2_ENST00000543624.1_RNA	NM_000738.2	NP_000729.2	P11229	ACM1_HUMAN	cholinergic receptor, muscarinic 1	348					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cognition (GO:0050890)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of ion transport (GO:0043270)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of locomotion (GO:0040012)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)			large_intestine(5)|lung(3)|stomach(1)	9					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Benzatropine(DB00245)|Biperiden(DB00810)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbachol(DB00411)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clidinium(DB00771)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyclopentolate(DB00979)|Cycrimine(DB00942)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Doxylamine(DB00366)|Escitalopram(DB01175)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Flupentixol(DB00875)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methantheline(DB00940)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metoclopramide(DB01233)|Minaprine(DB00805)|Molindone(DB01618)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Oxyphenonium(DB00219)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pirenzepine(DB00670)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propantheline(DB00782)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Trospium(DB00209)|Ziprasidone(DB00246)	GCTTGGCCAGCTGCTCCTTTC	0.612													C|||	293	0.0585064	0.1286	0.0231	5008	,	,		19135	0.0169		0.0258	False		,,,				2504	0.0654				p.Q348Q		Atlas-SNP	.											.	CHRM1	29	.	0			c.G1044A						PASS	.	C		496,3906	230.7+/-244.8	25,446,1730	50.0	49.0	49.0		1044	1.5	1.0	11	dbSNP_96	49	307,8289	110.8+/-171.2	7,293,3998	no	coding-synonymous	CHRM1	NM_000738.2		32,739,5728	TT,TC,CC		3.5714,11.2676,6.1779		348/461	62677529	803,12195	2201	4298	6499	SO:0001819	synonymous_variant	1128	exon2			GGCCAGCTGCTCC	Y00508	CCDS8040.1	11q12-q13	2012-08-08				ENSG00000168539		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1950	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 1"""	118510					Standard	NM_000738		Approved		uc001nwi.3	P11229		ENST00000306960.3:c.1044G>A	11.37:g.62677529C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	56	25	0.446429	NM_000738	Q96RH1	Silent	SNP	ENST00000306960.3	37	CCDS8040.1																																																																																			C|0.938;T|0.062	0.062	strong		0.612	CHRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396178.1	NM_000738	
ABCG4	64137	hgsc.bcm.edu	37	11	119025270	119025270	+	Silent	SNP	G	G	A	rs200058802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:119025270G>A	ENST00000449422.2	+	5	713	c.525G>A	c.(523-525)gaG>gaA	p.E175E	ABCG4_ENST00000307417.3_Silent_p.E175E|ABCG4_ENST00000531739.1_Silent_p.E175E	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	175	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		AGAAGCAGGAGGTGAAGAAGG	0.592													G|||	4	0.000798722	0.0	0.0	5008	,	,		18764	0.0		0.0	False		,,,				2504	0.0041				p.E175E		Atlas-SNP	.											.	ABCG4	77	.	0			c.G525A						PASS	.	G	,	0,4400		0,0,2200	62.0	60.0	61.0		525,525	1.2	1.0	11		61	2,8588	2.2+/-6.3	0,2,4293	no	coding-synonymous,coding-synonymous	ABCG4	NM_001142505.1,NM_022169.4	,	0,2,6493	AA,AG,GG		0.0233,0.0,0.0154	,	175/647,175/647	119025270	2,12988	2200	4295	6495	SO:0001819	synonymous_variant	64137	exon5			GCAGGAGGTGAAG	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.525G>A	11.37:g.119025270G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Silent	SNP	ENST00000449422.2	37	CCDS8415.1																																																																																			G|0.999;A|0.001	0.001	weak		0.592	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
XRCC6BP1	91419	hgsc.bcm.edu	37	12	58350631	58350631	+	Silent	SNP	C	C	T	rs10122	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:58350631C>T	ENST00000300145.3	+	6	824	c.699C>T	c.(697-699)caC>caT	p.H233H	XRCC6BP1_ENST00000546709.1_3'UTR	NM_033276.2	NP_150592.1	Q9Y6H3	ATP23_HUMAN	XRCC6 binding protein 1	233					double-strand break repair via nonhomologous end joining (GO:0006303)|protein phosphorylation (GO:0006468)	DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)	DNA-dependent protein kinase activity (GO:0004677)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	11						GATATGCTCACAGAGACTTTG	0.333													T|||	2763	0.551717	0.556	0.5447	5008	,	,		16308	0.7262		0.3668	False		,,,				2504	0.5613				p.H233H		Atlas-SNP	.											.	XRCC6BP1	22	.	0			c.C699T						PASS	.	T		1976,1670		558,860,405	107.0	99.0	101.0		699	-0.2	1.0	12	dbSNP_52	101	3063,5089		568,1927,1581	no	coding-synonymous	XRCC6BP1	NM_033276.2		1126,2787,1986	TT,TC,CC		37.5736,45.8036,42.7106		233/247	58350631	5039,6759	1823	4076	5899	SO:0001819	synonymous_variant	91419	exon6			TGCTCACAGAGAC	AF078164	CCDS41802.1	12q14.1	2006-01-09				ENSG00000166896			29452	protein-coding gene	gene with protein product	"""Ku70 binding protein 3"""					10219089	Standard	XM_005269223		Approved	KUB3	uc001sqp.3	Q9Y6H3	OTTHUMG00000170493	ENST00000300145.3:c.699C>T	12.37:g.58350631C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	34	0.382022	NM_033276	Q1RLM4|Q96E81	Silent	SNP	ENST00000300145.3	37	CCDS41802.1																																																																																			C|0.485;T|0.515	0.515	strong		0.333	XRCC6BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409390.1	NM_033276	
DNAJC13	23317	hgsc.bcm.edu	37	3	132166302	132166302	+	Silent	SNP	T	T	G	rs116489157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132166302T>G	ENST00000260818.6	+	4	530	c.282T>G	c.(280-282)ctT>ctG	p.L94L	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	94					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CAGAACTTCTTACAGAAGCAT	0.318													T|||	22	0.00439297	0.0008	0.0058	5008	,	,		14614	0.0		0.0129	False		,,,				2504	0.0041				p.L94L		Atlas-SNP	.											.	DNAJC13	253	.	0			c.T282G						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	34.0	37.0	36.0		282	2.1	1.0	3	dbSNP_132	36	158,8432	71.6+/-134.2	2,154,4139	no	coding-synonymous	DNAJC13	NM_015268.3		2,164,6332	GG,GT,TT		1.8393,0.227,1.2927		94/2244	132166302	168,12828	2203	4295	6498	SO:0001819	synonymous_variant	23317	exon4			ACTTCTTACAGAA	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.282T>G	3.37:g.132166302T>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	137	76	0.554745	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	37	CCDS33857.1																																																																																			T|0.990;G|0.010	0.010	strong		0.318	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
MYOM1	8736	hgsc.bcm.edu	37	18	3173964	3173964	+	Silent	SNP	G	G	A	rs2230163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:3173964G>A	ENST00000356443.4	-	8	1479	c.1146C>T	c.(1144-1146)caC>caT	p.H382H	MYOM1_ENST00000400569.3_Silent_p.H382H|MYOM1_ENST00000261606.7_Silent_p.H382H	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	382					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AAGCCCCAGCGTGGAAGCGAG	0.408													A|||	1583	0.316094	0.4002	0.2262	5008	,	,		16674	0.2669		0.3062	False		,,,				2504	0.3272				p.H382H		Atlas-SNP	.											.	MYOM1	192	.	0			c.C1146T						PASS	.	A	,	1462,2268		303,856,706	82.0	78.0	79.0		1146,1146	-0.4	0.0	18	dbSNP_98	79	2593,5621		417,1759,1931	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	720,2615,2637	AA,AG,GG		31.5681,39.1957,33.9501	,	382/1686,382/1590	3173964	4055,7889	1865	4107	5972	SO:0001819	synonymous_variant	8736	exon8			CCCAGCGTGGAAG	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1146C>T	18.37:g.3173964G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			T|0.130;G|0.427;C|0.268;A|0.175	0.175	strong		0.408	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
VARS2	57176	hgsc.bcm.edu	37	6	30888169	30888169	+	Silent	SNP	G	G	A	rs2517468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30888169G>A	ENST00000321897.5	+	13	1985	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L	VARS2_ENST00000541562.1_Silent_p.L481L|VARS2_ENST00000542001.1_Silent_p.L311L|VARS2_ENST00000416670.2_Silent_p.L451L|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	451					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						AATGGGGCCTGTTCCGGGGCC	0.522													G|||	1113	0.222244	0.0983	0.2075	5008	,	,		16403	0.247		0.3559	False		,,,				2504	0.2372				p.L481L		Atlas-SNP	.											VARS2,NS,carcinoma,0,1	VARS2	60	1	0			c.G1443A						PASS	.	G	,,	615,3791	266.5+/-267.3	40,535,1628	47.0	50.0	49.0		933,1443,1353	2.3	1.0	6	dbSNP_100	49	3196,5404	483.9+/-371.3	581,2034,1685	no	coding-synonymous,coding-synonymous,coding-synonymous	VARS2	NM_001167733.1,NM_001167734.1,NM_020442.4	,,	621,2569,3313	AA,AG,GG		37.1628,13.9582,29.3019	,,	311/924,481/1094,451/1064	30888169	3811,9195	2203	4300	6503	SO:0001819	synonymous_variant	57176	exon14			GGGCCTGTTCCGG	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.1353G>A	6.37:g.30888169G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	35	0.376344	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																			G|0.731;A|0.269	0.269	strong		0.522	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
TLR6	10333	hgsc.bcm.edu	37	4	38829832	38829832	+	Silent	SNP	T	T	C	rs3775073	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:38829832T>C	ENST00000381950.1	-	1	1328	c.1263A>G	c.(1261-1263)aaA>aaG	p.K421K	TLR6_ENST00000436693.2_Silent_p.K421K			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	421					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGCAGTTTTCTTTATGTCTAC	0.378													C|||	2291	0.457468	0.7398	0.3156	5008	,	,		20740	0.3958		0.3141	False		,,,				2504	0.3875				p.K421K		Atlas-SNP	.											.	TLR6	67	.	0			c.A1263G						PASS	.	C		2910,1496	467.6+/-354.9	953,1004,246	100.0	107.0	105.0		1263	-2.5	0.0	4	dbSNP_107	105	2942,5658	665.9+/-402.3	519,1904,1877	no	coding-synonymous	TLR6	NM_006068.4		1472,2908,2123	CC,CT,TT		34.2093,33.9537,44.9946		421/797	38829832	5852,7154	2203	4300	6503	SO:0001819	synonymous_variant	10333	exon2			GTTTTCTTTATGT		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1263A>G	4.37:g.38829832T>C		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	140	78	0.557143	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Silent	SNP	ENST00000381950.1	37	CCDS3446.1																																																																																			T|0.564;C|0.436	0.436	strong		0.378	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
TMCO3	55002	hgsc.bcm.edu	37	13	114164578	114164578	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:114164578C>T	ENST00000434316.2	+	7	1423	c.1064C>T	c.(1063-1065)cCg>cTg	p.P355L	TMCO3_ENST00000474393.1_3'UTR|TMCO3_ENST00000375391.1_Missense_Mutation_p.P355L	NM_017905.4	NP_060375.4	Q6UWJ1	TMCO3_HUMAN	transmembrane and coiled-coil domains 3	355						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)			TTACAAGGGCCGTGTTACATG	0.478																																					p.P355L		Atlas-SNP	.											TMCO3,NS,carcinoma,-1,1	TMCO3	77	1	0			c.C1064T						scavenged	.						219.0	191.0	201.0					13																	114164578		2203	4300	6503	SO:0001583	missense	55002	exon7			AAGGGCCGTGTTA	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.1064C>T	13.37:g.114164578C>T	ENSP00000389399:p.Pro355Leu	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	201	4	0.0199005	NM_017905	Q5JSB1|Q6NUN1|Q8NG29|Q8TCI6|Q96EA6|Q9NWT2	Missense_Mutation	SNP	ENST00000434316.2	37	CCDS9537.1	.	.	.	.	.	.	.	.	.	.	C	8.948	0.967377	0.18659	.	.	ENSG00000150403	ENST00000434316;ENST00000375391	T;T	0.13901	2.55;2.55	4.99	4.14	0.48551	Cation/H+ exchanger (1);	0.114107	0.64402	D	0.000009	T	0.14184	0.0343	L	0.55481	1.735	0.47862	D	0.999539	P;P	0.44139	0.827;0.611	B;B	0.37091	0.241;0.167	T	0.02736	-1.1117	10	0.48119	T	0.1	-15.4103	13.4835	0.61351	0.0:0.9242:0.0:0.0758	.	355;355	Q6UWJ1;Q6UWJ1-2	TMCO3_HUMAN;.	L	355	ENSP00000389399:P355L;ENSP00000364540:P355L	ENSP00000364540:P355L	P	+	2	0	TMCO3	113212579	1.000000	0.71417	0.023000	0.16930	0.023000	0.10783	7.132000	0.77251	1.112000	0.41740	0.536000	0.68110	CCG	.	.	none		0.478	TMCO3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045931.3	NM_017905	
PALLD	23022	hgsc.bcm.edu	37	4	169433326	169433326	+	Missense_Mutation	SNP	T	T	C	rs397718410|rs7655494|rs373066707	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169433326T>C	ENST00000505667.1	+	2	844	c.671T>C	c.(670-672)aTg>aCg	p.M224T	PALLD_ENST00000261509.6_Missense_Mutation_p.M224T|PALLD_ENST00000333488.4_Missense_Mutation_p.M101T|PALLD_ENST00000335742.7_5'UTR			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	224			M -> I (in dbSNP:rs7671781).|M -> T (in dbSNP:rs7655494). {ECO:0000269|PubMed:14702039}.		cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		CAGAGCCCTATGGAAGACCAA	0.577									Pancreatic Cancer, Familial Clustering of				C|||	1200	0.239617	0.2368	0.1844	5008	,	,		17132	0.1935		0.33	False		,,,				2504	0.2372				p.M224T	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.T671C						PASS	.	C	THR/MET,THR/MET	1068,3338		151,766,1286	101.0	106.0	104.0		671,671	3.7	0.1	4	dbSNP_116	104	2621,5979		461,1699,2140	yes	missense,missense	PALLD	NM_001166108.1,NM_016081.3	81,81	612,2465,3426	CC,CT,TT		30.4767,24.2397,28.3638	benign,benign	224/1124,224/1107	169433326	3689,9317	2203	4300	6503	SO:0001583	missense	23022	exon2	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GCCCTATGGAAGA	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.671T>C	4.37:g.169433326T>C	ENSP00000425556:p.Met224Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	37	CCDS54818.1	447	0.20467032967032966	90	0.18292682926829268	68	0.1878453038674033	84	0.14685314685314685	205	0.2704485488126649	C	0.001	-2.912011	0.00056	0.242397	0.304767	ENSG00000129116	ENST00000261509;ENST00000505667;ENST00000508898;ENST00000333488	T;T;T;T	0.62364	0.14;0.41;0.03;0.11	5.41	3.67	0.42095	.	0.307711	0.17926	N	0.157333	T	0.00012	0.0000	N	0.01048	-1.04	0.52099	P	5.8000000000002494E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.24905	-1.0147	9	0.06365	T	0.9	.	1.7516	0.02973	0.1746:0.4889:0.1151:0.2214	rs7655494;rs7655494	224;224	B7ZMM5;B2RTX2	.;.	T	224;224;203;101	ENSP00000261509:M224T;ENSP00000425556:M224T;ENSP00000423063:M203T;ENSP00000328945:M101T	ENSP00000261509:M224T	M	+	2	0	PALLD	169669901	0.008000	0.16893	0.120000	0.21714	0.007000	0.05969	0.369000	0.20416	0.273000	0.22049	-0.880000	0.02959	ATG	T|0.732;C|0.268	0.268	strong		0.577	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
ITSN1	6453	hgsc.bcm.edu	37	21	35201947	35201947	+	Silent	SNP	C	C	T	rs1108000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:35201947C>T	ENST00000381318.3	+	27	3537	c.3249C>T	c.(3247-3249)gcC>gcT	p.A1083A	ITSN1_ENST00000399326.3_3'UTR|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399349.1_Silent_p.A1007A|ITSN1_ENST00000399355.2_Silent_p.A1012A|ITSN1_ENST00000381285.4_Silent_p.A1083A|ITSN1_ENST00000399367.3_Silent_p.A1078A|ITSN1_ENST00000381291.4_Silent_p.A1083A|ITSN1_ENST00000399352.1_Silent_p.A1078A|ITSN1_ENST00000399353.1_Silent_p.A1041A|ITSN1_ENST00000437442.2_Silent_p.A1078A|ITSN1_ENST00000379960.5_3'UTR	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1083	SH3 4. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						AGGTTATTGCCTCATACACCG	0.542													C|||	539	0.107628	0.0802	0.1052	5008	,	,		17744	0.1002		0.17	False		,,,				2504	0.09				p.A1083A		Atlas-SNP	.											.	ITSN1	166	.	0			c.C3249T						PASS	.	C	,	415,3991	203.5+/-225.9	21,373,1809	132.0	141.0	138.0		3249,3249	-2.8	0.7	21	dbSNP_86	138	1442,7158	276.7+/-292.4	104,1234,2962	no	coding-synonymous,coding-synonymous	ITSN1	NM_001001132.1,NM_003024.2	,	125,1607,4771	TT,TC,CC		16.7674,9.419,14.278	,	1083/1221,1083/1722	35201947	1857,11149	2203	4300	6503	SO:0001819	synonymous_variant	6453	exon27			TATTGCCTCATAC	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.3249C>T	21.37:g.35201947C>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_001001132	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Silent	SNP	ENST00000381318.3	37	CCDS33545.1																																																																																			C|0.872;T|0.128	0.128	strong		0.542	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248834	48248834	+	Silent	SNP	T	T	C	rs10404034	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48248834T>C	ENST00000246802.5	+	1	56	c.18T>C	c.(16-18)agT>agC	p.S6S	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	6						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CAGGAGGCAGTGGCGTTGGTG	0.642													T|||	301	0.0601038	0.0091	0.062	5008	,	,		11421	0.0089		0.1382	False		,,,				2504	0.1002				p.S6S	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.T18C						PASS	.	T		171,4235	114.2+/-152.2	5,161,2037	91.0	103.0	99.0		18	-4.3	0.0	19	dbSNP_119	99	1230,7370	247.2+/-275.4	89,1052,3159	no	coding-synonymous	GLTSCR2	NM_015710.4		94,1213,5196	CC,CT,TT		14.3023,3.8811,10.772		6/479	48248834	1401,11605	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon1			AGGCAGTGGCGTT	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.18T>C	19.37:g.48248834T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	119	70	0.588235	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			A|0.000;C|0.097;T|0.903	0.097	strong		0.642	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
CDH8	1006	hgsc.bcm.edu	37	16	61935330	61935330	+	Silent	SNP	T	T	C	rs368241476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:61935330T>C	ENST00000577390.1	-	3	1254	c.300A>G	c.(298-300)ctA>ctG	p.L100L	CDH8_ENST00000577730.1_Silent_p.L100L|CDH8_ENST00000584337.1_Silent_p.L100L|CDH8_ENST00000299345.6_Silent_p.L100L	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	100	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CATCACCTGATAGGATATACT	0.388																																					p.L100L		Atlas-SNP	.											.	CDH8	273	.	0			c.A300G						PASS	.	T		0,4406		0,0,2203	93.0	89.0	90.0		300	-3.0	1.0	16		90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CDH8	NM_001796.4		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		100/800	61935330	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1006	exon3			ACCTGATAGGATA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.300A>G	16.37:g.61935330T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	109	44	0.40367	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																			.	.	weak		0.388	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
TNS1	7145	hgsc.bcm.edu	37	2	218695102	218695102	+	Missense_Mutation	SNP	G	G	A	rs3796028	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:218695102G>A	ENST00000171887.4	-	21	3462	c.3010C>T	c.(3010-3012)Cgg>Tgg	p.R1004W	TNS1_ENST00000430930.1_Intron|TNS1_ENST00000419504.1_Missense_Mutation_p.R1004W	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1004			R -> W (in dbSNP:rs3796028).		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)		GGCTGGATCCGTCTTCTGGTA	0.567													G|||	1880	0.375399	0.32	0.4308	5008	,	,		19019	0.4276		0.3648	False		,,,				2504	0.3681				p.R1004W		Atlas-SNP	.											.	TNS1	251	.	0			c.C3010T						PASS	.	G	TRP/ARG	1375,3031	455.5+/-351.0	201,973,1029	84.0	73.0	77.0		3010	-1.2	1.0	2	dbSNP_107	77	2946,5654	457.3+/-364.3	501,1944,1855	yes	missense	TNS1	NM_022648.4	101	702,2917,2884	AA,AG,GG		34.2558,31.2074,33.2231	possibly-damaging	1004/1736	218695102	4321,8685	2203	4300	6503	SO:0001583	missense	7145	exon21			GGATCCGTCTTCT	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.3010C>T	2.37:g.218695102G>A	ENSP00000171887:p.Arg1004Trp	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	63	0.984375	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	842	0.38553113553113555	175	0.3556910569105691	144	0.39779005524861877	256	0.44755244755244755	267	0.35224274406332456	G	3.509	-0.100132	0.07010	0.312074	0.342558	ENSG00000079308	ENST00000171887;ENST00000419504	D;D	0.91407	-2.84;-2.83	4.4	-1.23	0.09465	.	7739.210000	0.00166	N	0.000000	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.999999888189	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34725	-0.9817	9	0.59425	D	0.04	.	4.2296	0.10597	0.0938:0.2993:0.47:0.1369	rs3796028;rs17789579;rs3796028	1004;1004	Q9HBL0;E9PF55	TENS1_HUMAN;.	W	1004	ENSP00000171887:R1004W;ENSP00000408724:R1004W	ENSP00000171887:R1004W	R	-	1	2	TNS1	218403347	0.797000	0.28877	0.993000	0.49108	0.017000	0.09413	-0.422000	0.07043	-0.055000	0.13244	-2.034000	0.00421	CGG	G|0.646;A|0.354	0.354	strong		0.567	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
CMYA5	202333	hgsc.bcm.edu	37	5	79032562	79032562	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:79032562A>G	ENST00000446378.2	+	2	8005	c.7974A>G	c.(7972-7974)gtA>gtG	p.V2658V		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2658					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		GAAATCTAGTATTAGAAAAGT	0.408																																					p.V2658V		Atlas-SNP	.											CMYA5_ENST00000446378,lower_third,carcinoma,0,2	CMYA5	643	2	0			c.A7974G						scavenged	.						48.0	48.0	48.0					5																	79032562		1831	4091	5922	SO:0001819	synonymous_variant	202333	exon2			TCTAGTATTAGAA	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.7974A>G	5.37:g.79032562A>G		Somatic	149	1	0.00671141		WXS	Illumina HiSeq	Phase_I	154	3	0.0194805	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.	.	none		0.408	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
HBS1L	10767	hgsc.bcm.edu	37	6	135287533	135287533	+	Silent	SNP	A	A	G	rs13064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:135287533A>G	ENST00000367837.5	-	17	2183	c.1977T>C	c.(1975-1977)ttT>ttC	p.F659F	HBS1L_ENST00000415177.2_Silent_p.F594F|HBS1L_ENST00000445176.2_Silent_p.F383F|HBS1L_ENST00000367824.4_Silent_p.F495F|HBS1L_ENST00000527578.1_Silent_p.F495F|HBS1L_ENST00000367826.2_Silent_p.F617F	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	659					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		CCAGCTCTTTAAAGTCTTTAT	0.368													A|||	1299	0.259385	0.1906	0.2378	5008	,	,		16977	0.245		0.3549	False		,,,				2504	0.2843				p.F659F		Atlas-SNP	.											.	HBS1L	75	.	0			c.T1977C						PASS	.	A	,	1011,3395	376.8+/-322.2	113,785,1305	143.0	136.0	138.0		1851,1977	-9.0	0.4	6	dbSNP_52	138	3205,5395	484.5+/-371.4	595,2015,1690	no	coding-synonymous,coding-synonymous	HBS1L	NM_001145158.1,NM_006620.3	,	708,2800,2995	GG,GA,AA		37.2674,22.946,32.4158	,	617/643,659/685	135287533	4216,8790	2203	4300	6503	SO:0001819	synonymous_variant	10767	exon17			CTCTTTAAAGTCT	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.1977T>C	6.37:g.135287533A>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	66	63	0.954545	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			A|0.692;G|0.308	0.308	strong		0.368	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
KRIT1	889	hgsc.bcm.edu	37	7	91842554	91842554	+	Silent	SNP	T	T	C	rs11542682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:91842554T>C	ENST00000340022.2	-	17	2998	c.1980A>G	c.(1978-1980)gtA>gtG	p.V660V	KRIT1_ENST00000394507.1_Silent_p.V660V|KRIT1_ENST00000412043.2_Silent_p.V660V|KRIT1_ENST00000394503.2_Silent_p.V612V|KRIT1_ENST00000394505.2_Silent_p.V660V	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	660	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|cell redox homeostasis (GO:0045454)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|positive regulation of protein binding (GO:0032092)|regulation of catalytic activity (GO:0050790)|regulation of establishment of cell polarity (GO:2000114)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|microtubule (GO:0005874)|plasma membrane (GO:0005886)	microtubule binding (GO:0008017)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)|small GTPase regulator activity (GO:0005083)	p.V660V(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(2)|stomach(1)	22	all_cancers(62;1.04e-09)|all_epithelial(64;5.75e-09)|Breast(17;0.00206)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TATTCACTCCTACATACACAG	0.363													t|||	904	0.180511	0.1589	0.1239	5008	,	,		18715	0.3403		0.0825	False		,,,				2504	0.1861				p.V660V		Atlas-SNP	.											KRIT1,NS,carcinoma,0,1	KRIT1	66	1	1	Substitution - coding silent(1)	stomach(1)	c.A1980G						PASS	.	G	,,,,	536,3870	243.4+/-253.1	40,456,1707	159.0	149.0	152.0		1836,1980,1980,1980,1980	-0.2	1.0	7	dbSNP_120	152	795,7805	186.0+/-233.6	39,717,3544	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KRIT1	NM_001013406.1,NM_004912.3,NM_194454.1,NM_194455.1,NM_194456.1	,,,,	79,1173,5251	CC,CT,TT		9.2442,12.1652,10.2337	,,,,	612/689,660/737,660/737,660/737,660/737	91842554	1331,11675	2203	4300	6503	SO:0001819	synonymous_variant	889	exon18			CACTCCTACATAC	AJ294850	CCDS5624.1, CCDS34679.1	7q21.2	2014-09-17	2005-03-15	2005-03-17	ENSG00000001631	ENSG00000001631		"""Ankyrin repeat domain containing"""	1573	protein-coding gene	gene with protein product		604214	"""cerebral cavernous malformations 1"""	CCM1		7604043, 11342228	Standard	NM_194455		Approved	CAM	uc003ulu.1	O00522	OTTHUMG00000131187	ENST00000340022.2:c.1980A>G	7.37:g.91842554T>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	101	51	0.504951	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Silent	SNP	ENST00000340022.2	37	CCDS5624.1																																																																																			T|0.867;C|0.133	0.133	strong		0.363	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1		
CFAP46	54777	hgsc.bcm.edu	37	10	134691424	134691424	+	Missense_Mutation	SNP	C	C	A	rs541673671	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691424C>A	ENST00000368586.5	-	30	4273	c.4173G>T	c.(4171-4173)aaG>aaT	p.K1391N	TTC40_ENST00000368582.2_Missense_Mutation_p.K1391N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						ttcccttctccttgtccttct	0.512													C|||	21	0.00419329	0.0008	0.0029	5008	,	,		17453	0.001		0.007	False		,,,				2504	0.0102				p.K1391N		Atlas-SNP	.											.	TTC40	100	.	0			c.G4173T						PASS	.																																			SO:0001583	missense	54777	exon30			CTTCTCCTTGTCC																												ENST00000368586.5:c.4173G>T	10.37:g.134691424C>A	ENSP00000357575:p.Lys1391Asn	Somatic	315	0	0		WXS	Illumina HiSeq	Phase_I	301	16	0.0531561	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	C	1.664	-0.510681	0.04231	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.05996	3.36;3.36	2.37	-3.18	0.05186	.	.	.	.	.	T	0.07593	0.0191	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.31530	-0.9940	6	0.46703	T	0.11	.	9.5036	0.39033	0.0:0.7879:0.0:0.2121	.	.	.	.	N	1391	ENSP00000357575:K1391N;ENSP00000357571:K1391N	ENSP00000357571:K1391N	K	-	3	2	C10orf93	134541414	0.078000	0.21339	0.000000	0.03702	0.019000	0.09904	-0.209000	0.09358	-0.946000	0.03677	-0.229000	0.12294	AAG	.	.	none		0.512	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
GLUL	2752	hgsc.bcm.edu	37	1	182356399	182356399	+	Silent	SNP	A	A	G	rs199769578|rs1058111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:182356399A>G	ENST00000331872.6	-	3	735	c.195T>C	c.(193-195)tcT>tcC	p.S65S	GLUL_ENST00000491322.1_5'UTR|GLUL_ENST00000417584.2_Silent_p.S65S|GLUL_ENST00000311223.5_Silent_p.S65S|GLUL_ENST00000339526.4_Silent_p.S65S	NM_001033044.2	NP_001028216.1	P15104	GLNA_HUMAN	glutamate-ammonia ligase	65					cell proliferation (GO:0008283)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to starvation (GO:0009267)|glutamate catabolic process (GO:0006538)|glutamine biosynthetic process (GO:0006542)|neurotransmitter uptake (GO:0001504)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of insulin secretion (GO:0032024)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein homooligomerization (GO:0051260)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glial cell projection (GO:0097386)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|protein complex (GO:0043234)|rough endoplasmic reticulum (GO:0005791)	ATP binding (GO:0005524)|glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|glutamate-ammonia ligase activity (GO:0004356)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)			endometrium(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	16					Ceftriaxone(DB01212)|Diazoxide(DB01119)|L-Glutamine(DB00130)|L-Methionine(DB00134)|Pegvisomant(DB00082)	GTAAAGTACTAGAGCCATCGA	0.468													A|||	3384	0.675719	0.7496	0.6167	5008	,	,		20033	0.8323		0.5408	False		,,,				2504	0.5951				p.S65S		Atlas-SNP	.											.	GLUL	38	.	0			c.T195C						PASS	.	A	,,	3239,1167	712.6+/-408.1	1199,841,163	93.0	95.0	94.0		195,195,195	-2.2	1.0	1	dbSNP_86	94	4441,4159	587.4+/-392.2	1156,2129,1015	no	coding-synonymous,coding-synonymous,coding-synonymous	GLUL	NM_001033044.2,NM_001033056.2,NM_002065.5	,,	2355,2970,1178	GG,GA,AA		48.3605,26.4866,40.9503	,,	65/374,65/374,65/374	182356399	7680,5326	2203	4300	6503	SO:0001819	synonymous_variant	2752	exon3			AGTACTAGAGCCA	AL161952	CCDS1344.1	1q31	2010-05-04	2010-05-04		ENSG00000135821	ENSG00000135821	6.3.1.2		4341	protein-coding gene	gene with protein product	"""glutamine synthetase"""	138290	"""glutamate-ammonia ligase (glutamine synthase)"""	GLNS		1681907, 2888076	Standard	NM_002065		Approved		uc001gpa.2	P15104	OTTHUMG00000037407	ENST00000331872.6:c.195T>C	1.37:g.182356399A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	132	66	0.5	NM_001033056	Q499Y9|Q5T9Z1|Q7Z3W4|Q8IZ17	Silent	SNP	ENST00000331872.6	37	CCDS1344.1																																																																																			T|0.000;G|0.662;C|0.000;A|0.338	0.662	strong		0.468	GLUL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091043.1	NM_002065	
SULT2B1	6820	hgsc.bcm.edu	37	19	49096065	49096065	+	Silent	SNP	C	C	T	rs2302948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49096065C>T	ENST00000201586.2	+	5	815	c.637C>T	c.(637-639)Ctg>Ttg	p.L213L	SULT2B1_ENST00000594274.1_3'UTR|SULT2B1_ENST00000323090.4_Silent_p.L198L	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	213					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		CTACGAGGAGCTGCAGCAGGT	0.602													C|||	838	0.167332	0.1914	0.1671	5008	,	,		17330	0.0883		0.2406	False		,,,				2504	0.1411				p.L213L		Atlas-SNP	.											.	SULT2B1	72	.	0			c.C637T						PASS	.	C	,	837,3569		81,675,1447	88.0	60.0	69.0		592,637	2.3	0.9	19	dbSNP_100	69	1952,6638		205,1542,2548	no	coding-synonymous,coding-synonymous	SULT2B1	NM_004605.2,NM_177973.1	,	286,2217,3995	TT,TC,CC		22.7241,18.9968,21.4604	,	198/351,213/366	49096065	2789,10207	2203	4295	6498	SO:0001819	synonymous_variant	6820	exon5			GAGGAGCTGCAGC	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.637C>T	19.37:g.49096065C>T		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	44	24	0.545455	NM_177973	O00205|O75814	Silent	SNP	ENST00000201586.2	37	CCDS12723.1																																																																																			C|0.814;T|0.186	0.186	strong		0.602	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605	
DCAF12L2	340578	hgsc.bcm.edu	37	X	125298690	125298690	+	Silent	SNP	G	G	A	rs3761552	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:125298690G>A	ENST00000360028.2	-	1	1244	c.1218C>T	c.(1216-1218)tgC>tgT	p.C406C	DCAF12L2_ENST00000538699.1_Silent_p.C406C			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	406										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						AGCCTCTGCCGCAGGCAAGCT	0.607													A|||	2113	0.559735	0.6293	0.4294	3775	,	,		13019	0.3859		0.2525	False		,,,				2504	0.3476				p.C406C		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.C1218T						PASS	.	A		2961,874		976,573,436,83,135	86.0	91.0	89.0		1218	1.8	0.9	X	dbSNP_107	89	2000,4728		221,987,571,1220,1301	no	coding-synonymous	DCAF12L2	NM_001013628.2		1197,1560,1007,1303,1436	AA,AG,A,GG,G		29.7265,22.7901,46.9658		406/464	125298690	4961,5602	2203	4300	6503	SO:0001819	synonymous_variant	340578	exon1			TCTGCCGCAGGCA	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.1218C>T	X.37:g.125298690G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_001013628	B2RN42	Silent	SNP	ENST00000360028.2	37	CCDS43991.1																																																																																			G|0.437;A|0.563	0.563	strong		0.607	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628	
CDRT15	146822	hgsc.bcm.edu	37	17	14140081	14140081	+	Nonsense_Mutation	SNP	G	G	A	rs11651890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:14140081G>A	ENST00000420162.2	-	1	85	c.70C>T	c.(70-72)Cga>Tga	p.R24*	CDRT15_ENST00000431716.2_5'UTR	NM_001007530.1	NP_001007531.1	Q96T59	CDRTF_HUMAN	CMT1A duplicated region transcript 15	24			R -> Q (in dbSNP:rs17679866).							endometrium(2)|large_intestine(1)|lung(2)|prostate(1)	6				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CGGCATCGTCGGAAAAGGCTC	0.582																																					p.R24X		Atlas-SNP	.											.	CDRT15	20	.	0			c.C70T						PASS	.						52.0	49.0	50.0					17																	14140081		2203	4298	6501	SO:0001587	stop_gained	146822	exon1			ATCGTCGGAAAAG	AF355097	CCDS32569.1	17p12	2012-11-19			ENSG00000223510	ENSG00000223510			14395	protein-coding gene	gene with protein product						11381029	Standard	NM_001007530		Approved		uc010vvu.2	Q96T59	OTTHUMG00000179686	ENST00000420162.2:c.70C>T	17.37:g.14140081G>A	ENSP00000402355:p.Arg24*	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	242	35	0.144628	NM_001007530	B2RUU5	Nonsense_Mutation	SNP	ENST00000420162.2	37	CCDS32569.1	214	0.09798534798534798	26	0.052845528455284556	34	0.09392265193370165	76	0.13286713286713286	78	0.10290237467018469	G	10.90	1.482013	0.26598	.	.	ENSG00000223510	ENST00000420162	.	.	.	0.675	-1.35	0.09114	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	.	.	.	rs11651890	.	.	.	X	24	.	ENSP00000402355:R24X	R	-	1	2	CDRT15	14080806	0.951000	0.32395	0.000000	0.03702	0.003000	0.03518	0.838000	0.27572	-1.643000	0.01519	-1.082000	0.02213	CGA	G|0.908;A|0.092	0.092	strong		0.582	CDRT15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252853.1	NM_001007530	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248907	48248907	+	Missense_Mutation	SNP	G	G	C	rs78530808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48248907G>C	ENST00000246802.5	+	1	129	c.91G>C	c.(91-93)Gac>Cac	p.D31H	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	31						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CACTTCGGTGGACCCAGCGCT	0.657													G|||	79	0.0157748	0.0053	0.0029	5008	,	,		9702	0.0069		0.0149	False		,,,				2504	0.0491				p.D31H	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.G91C						PASS	.	G	HIS/ASP	45,4361	48.2+/-83.0	0,45,2158	49.0	58.0	55.0		91	4.6	1.0	19	dbSNP_131	55	151,8449	70.7+/-133.2	0,151,4149	yes	missense	GLTSCR2	NM_015710.4	81	0,196,6307	CC,CG,GG		1.7558,1.0213,1.507	probably-damaging	31/479	48248907	196,12810	2203	4300	6503	SO:0001583	missense	29997	exon1			TCGGTGGACCCAG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.91G>C	19.37:g.48248907G>C	ENSP00000246802:p.Asp31His	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	147	81	0.55102	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Missense_Mutation	SNP	ENST00000246802.5	37	CCDS12705.1	20	0.009157509157509158	6	0.012195121951219513	1	0.0027624309392265192	2	0.0034965034965034965	11	0.014511873350923483	G	23.9	4.465428	0.84425	0.010213	0.017558	ENSG00000105373	ENST00000246802;ENST00000325566;ENST00000446535	T	0.34472	1.36	4.55	4.55	0.56014	.	0.276137	0.34133	N	0.004227	T	0.29945	0.0749	L	0.34521	1.04	0.52501	D	0.999954	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.65573	0.936;0.936;0.936	T	0.34625	-0.9821	10	0.87932	D	0	-24.6863	13.1558	0.59516	0.0:0.0:1.0:0.0	.	31;31;29	Q53YP0;Q9NZM5;Q96CS0	.;GSCR2_HUMAN;.	H	31	ENSP00000246802:D31H	ENSP00000246802:D31H	D	+	1	0	GLTSCR2	52940719	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	4.935000	0.63498	2.227000	0.72691	0.655000	0.94253	GAC	G|0.987;C|0.013	0.013	strong		0.657	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
MBL2	4153	hgsc.bcm.edu	37	10	54531242	54531242	+	Missense_Mutation	SNP	G	G	A	rs5030737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:54531242G>A	ENST00000373968.3	-	1	218	c.154C>T	c.(154-156)Cgt>Tgt	p.R52C		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	52	Collagen-like.		R -> C (in 0.05% of European and African populations; dbSNP:rs5030737). {ECO:0000269|PubMed:10447262, ECO:0000269|PubMed:15994813, ECO:0000269|PubMed:9743385}.		acute-phase response (GO:0006953)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of viral process (GO:0048525)|opsonization (GO:0008228)|positive regulation of phagocytosis (GO:0050766)|response to oxidative stress (GO:0006979)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium-dependent protein binding (GO:0048306)|mannose binding (GO:0005537)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21						GTGCCATCACGCCCATCTTTG	0.532													G|||	136	0.0271565	0.0015	0.0331	5008	,	,		19493	0.001		0.0596	False		,,,				2504	0.0511				p.R52C		Atlas-SNP	.											.	MBL2	55	.	0			c.C154T	GRCh37	CM960957	MBL2	M	rs5030737	PASS	.	G	CYS/ARG	52,4354	52.3+/-87.9	0,52,2151	132.0	119.0	123.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	154	3.1	0.9	10	dbSNP_113	123	596,8004	158.0+/-211.6	22,552,3726	yes	missense	MBL2	NM_000242.2	180	22,604,5877	AA,AG,GG		6.9302,1.1802,4.9823	probably-damaging	52/249	54531242	648,12358	2203	4300	6503	SO:0001583	missense	4153	exon1			CATCACGCCCATC	AF360991	CCDS7247.1	10q11.2	2014-09-17	2011-02-02		ENSG00000165471	ENSG00000165471		"""Collectins"""	6922	protein-coding gene	gene with protein product		154545	"""mannose-binding lectin (protein C) 2, soluble (opsonic defect)"""	MBL		1675710, 1672848	Standard	NM_000242		Approved	COLEC1	uc001jjt.3	P11226	OTTHUMG00000150270	ENST00000373968.3:c.154C>T	10.37:g.54531242G>A	ENSP00000363079:p.Arg52Cys	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	66	63	0.954545	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	37	CCDS7247.1	62	0.028388278388278388	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	50	0.06596306068601583	G	17.29	3.352757	0.61293	0.011802	0.069302	ENSG00000165471	ENST00000373968	D	0.93307	-3.2	3.99	3.07	0.35406	.	0.247365	0.25161	N	0.032677	T	0.78704	0.4325	M	0.92691	3.335	0.42641	A	0.993411	D	0.89917	1.0	D	0.72338	0.977	D	0.84502	0.0617	9	0.72032	D	0.01	-3.3749	9.1124	0.36737	0.0:0.0:0.7818:0.2182	rs5030737;rs5030737	52	P11226	MBL2_HUMAN	C	52	ENSP00000363079:R52C	ENSP00000363079:R52C	R	-	1	0	MBL2	54201248	0.017000	0.18338	0.910000	0.35882	0.950000	0.60333	1.121000	0.31283	1.263000	0.44181	0.655000	0.94253	CGT	G|0.957;A|0.043	0.043	strong		0.532	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242	
OR1F1	4992	hgsc.bcm.edu	37	16	3254470	3254470	+	Missense_Mutation	SNP	T	T	C	rs371443638|rs372744779|rs1834026	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3254470T>C	ENST00000304646.2	+	1	224	c.224T>C	c.(223-225)tTc>tCc	p.F75S	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	75			F -> S (in dbSNP:rs1834026).		signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						TGCTTCTCCTTCACCACCGTC	0.502													C|||	2163	0.431909	0.2738	0.5202	5008	,	,		23279	0.5655		0.4314	False		,,,				2504	0.4458				p.F75S		Atlas-SNP	.											.	OR1F1	36	.	0			c.T224C						PASS	.	C	SER/PHE	1368,3026	689.6+/-405.1	196,976,1025	250.0	211.0	224.0		224	4.3	1.0	16	dbSNP_92	224	3775,4825	614.7+/-396.3	837,2101,1362	no	missense	OR1F1	NM_012360.1	155	1033,3077,2387	CC,CT,TT		43.8953,31.1334,39.5798	benign	75/313	3254470	5143,7851	2197	4300	6497	SO:0001583	missense	4992	exon1			TCTCCTTCACCAC	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"""GPCR / Class A : Olfactory receptors"""	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.224T>C	16.37:g.3254470T>C	ENSP00000305424:p.Phe75Ser	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	271	136	0.501845	NM_012360	O15246|Q6IFL5	Missense_Mutation	SNP	ENST00000304646.2	37	CCDS10496.1	974	0.445970695970696	146	0.2967479674796748	177	0.4889502762430939	314	0.548951048951049	337	0.4445910290237467	C	0.414	-0.911763	0.02434	0.311334	0.438953	ENSG00000168124	ENST00000304646	T	0.00382	7.62	5.26	4.3	0.51218	GPCR, rhodopsin-like superfamily (1);	0.114286	0.39985	N	0.001220	T	0.00012	0.0000	N	0.00013	-2.935	0.47374	P	5.990000000000162E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.15235	-1.0444	9	0.02654	T	1	.	9.205	0.37285	0.0:0.7718:0.1461:0.0821	rs1834026;rs52825102;rs57080263;rs1834026	75	O43749	OR1F1_HUMAN	S	75	ENSP00000305424:F75S	ENSP00000305424:F75S	F	+	2	0	OR1F1	3194471	0.000000	0.05858	1.000000	0.80357	0.820000	0.46376	0.779000	0.26746	0.582000	0.29556	-0.665000	0.03846	TTC	T|0.581;G|0.003	.	strong		0.502	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1		
KRT80	144501	hgsc.bcm.edu	37	12	52579315	52579315	+	Silent	SNP	C	C	T	rs151324530	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52579315C>T	ENST00000394815.2	-	2	454	c.357G>A	c.(355-357)caG>caA	p.Q119Q	KRT80_ENST00000313234.5_Silent_p.Q119Q	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	119	Linker 1.|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)		AGTCCTGGCCCTGCAGGAAGC	0.632													C|||	3	0.000599042	0.0	0.0	5008	,	,		17710	0.0		0.003	False		,,,				2504	0.0				p.Q119Q	GBM(178;2309 2916 15678 35873)	Atlas-SNP	.											.	KRT80	68	.	0			c.G357A						PASS	.	C	,	3,4403	8.1+/-20.4	0,3,2200	46.0	45.0	45.0		357,357	4.2	1.0	12	dbSNP_134	45	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous	KRT80	NM_001081492.1,NM_182507.2	,	0,12,6491	TT,TC,CC		0.1047,0.0681,0.0923	,	119/423,119/453	52579315	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	144501	exon2			CTGGCCCTGCAGG	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.357G>A	12.37:g.52579315C>T		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	33	19	0.575758	NM_182507	Q6P1A5|Q7Z3Q0	Silent	SNP	ENST00000394815.2	37	CCDS8821.2																																																																																			C|0.999;T|0.001	0.001	strong		0.632	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507	
TGM5	9333	hgsc.bcm.edu	37	15	43545728	43545728	+	Silent	SNP	G	G	A	rs555001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43545728G>A	ENST00000220420.5	-	5	667	c.660C>T	c.(658-660)taC>taT	p.Y220Y	TGM5_ENST00000349114.4_Silent_p.Y138Y	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	220					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CTCTGCTGACGTAGACGGGGC	0.612													G|||	2388	0.476837	0.7579	0.3228	5008	,	,		18010	0.4127		0.336	False		,,,				2504	0.4172				p.Y220Y		Atlas-SNP	.											.	TGM5	88	.	0			c.C660T						PASS	.	G	,	2884,1520	673.0+/-402.7	961,962,279	70.0	63.0	65.0		414,660	-2.3	0.8	15	dbSNP_83	65	2798,5800	443.5+/-360.4	466,1866,1967	no	coding-synonymous,coding-synonymous	TGM5	NM_004245.3,NM_201631.3	,	1427,2828,2246	AA,AG,GG		32.5425,34.5141,43.701	,	138/639,220/721	43545728	5682,7320	2202	4299	6501	SO:0001819	synonymous_variant	9333	exon5			GCTGACGTAGACG	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.660C>T	15.37:g.43545728G>A		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_201631	O43549|Q0VF40|Q9UEZ4	Silent	SNP	ENST00000220420.5	37	CCDS32212.1																																																																																			G|0.539;A|0.461	0.461	strong		0.612	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
UBXN11	91544	hgsc.bcm.edu	37	1	26608855	26608855	+	Missense_Mutation	SNP	C	C	T	rs201756933		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608855C>T	ENST00000374222.1	-	16	1962	c.1498G>A	c.(1498-1500)Ggc>Agc	p.G500S	UBXN11_ENST00000314675.7_Missense_Mutation_p.G380S|UBXN11_ENST00000374217.2_Missense_Mutation_p.G467S|UBXN11_ENST00000357089.4_Missense_Mutation_p.G467S|UBXN11_ENST00000374223.1_Missense_Mutation_p.G257S|UBXN11_ENST00000374221.3_Missense_Mutation_p.G500S			Q5T124	UBX11_HUMAN	UBX domain protein 11	500	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						ggactggggccgggaccggga	0.731																																					p.G500S		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.G1498A						PASS	.						20.0	24.0	23.0					1																	26608855		1677	3891	5568	SO:0001583	missense	91544	exon16			TGGGGCCGGGACC	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.1498G>A	1.37:g.26608855C>T	ENSP00000363339:p.Gly500Ser	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	40	15	0.375	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	.	.	.	.	.	.	.	.	.	.	-	0.087	-1.172989	0.01646	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.18174	2.23;2.24;2.54;2.51;2.51;2.54	.	.	.	.	.	.	.	.	T	0.07143	0.0181	N	0.08118	0	0.18873	N	0.999989	.	.	.	.	.	.	T	0.37979	-0.9682	6	0.28530	T	0.3	.	4.1991	0.10457	0.0:0.6625:0.0:0.3375	.	467;462;380;500	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	380;257;467;500;500;467	ENSP00000324721:G380S;ENSP00000363340:G257S;ENSP00000349601:G467S;ENSP00000363338:G500S;ENSP00000363339:G500S;ENSP00000363334:G467S	ENSP00000324721:G380S	G	-	1	0	UBXN11	26481442	0.000000	0.05858	0.163000	0.22734	0.170000	0.22686	-0.959000	0.03853	-0.000000	0.14550	0.000000	0.15137	GGC	.	.	weak		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100847050	100847050	+	Silent	SNP	A	A	G	rs569270	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:100847050A>G	ENST00000298815.8	+	20	2121	c.2118A>G	c.(2116-2118)tcA>tcG	p.S706S	ARHGAP42_ENST00000524892.2_Silent_p.S672S	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	706	Ser-rich.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						GTGTTGCTTCAGTCACTAGCC	0.478													G|||	2805	0.560104	0.2027	0.6009	5008	,	,		21556	0.997		0.4344	False		,,,				2504	0.6933				p.S706S		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.A2118G						PASS	.	G		423,961		64,295,333	73.0	55.0	61.0		2118	-11.4	0.0	11	dbSNP_83	61	1402,1780		313,776,502	no	coding-synonymous	ARHGAP42	NM_152432.2		377,1071,835	GG,GA,AA		44.0603,30.5636,39.9693		706/875	100847050	1825,2741	692	1591	2283	SO:0001819	synonymous_variant	143872	exon20			TGCTTCAGTCACT			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.2118A>G	11.37:g.100847050A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				A|0.479;G|0.521	0.521	strong		0.478	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
NACAD	23148	hgsc.bcm.edu	37	7	45123937	45123937	+	Silent	SNP	T	T	C	rs112035890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45123937T>C	ENST00000490531.2	-	2	1861	c.1842A>G	c.(1840-1842)tcA>tcG	p.S614S		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	614					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						TTGGGGCTGATGAGAGATCTG	0.607																																					p.S614S		Atlas-SNP	.											.	NACAD	44	.	0			c.A1842G						PASS	.						9.0	9.0	9.0					7																	45123937		681	1559	2240	SO:0001819	synonymous_variant	23148	exon2			GGCTGATGAGAGA	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1842A>G	7.37:g.45123937T>C		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	50	10	0.2	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			T|0.946;C|0.054	0.054	strong		0.607	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
ODF2	4957	hgsc.bcm.edu	37	9	131262512	131262512	+	Missense_Mutation	SNP	G	G	A	rs142129915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131262512G>A	ENST00000434106.3	+	21	2831	c.2468G>A	c.(2467-2469)cGc>cAc	p.R823H	ODF2_ENST00000372807.5_Missense_Mutation_p.R818H|ODF2_ENST00000393527.3_Missense_Mutation_p.R799H|ODF2_ENST00000444119.2_Missense_Mutation_p.R799H|ODF2_ENST00000604420.1_Missense_Mutation_p.R823H|ODF2_ENST00000351030.3_Missense_Mutation_p.R818H	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	823					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						TCTCCCATCCGCTCCCGATCT	0.557													G|||	13	0.00259585	0.0	0.0014	5008	,	,		17126	0.001		0.005	False		,,,				2504	0.0061				p.R887H		Atlas-SNP	.											ODF2,NS,carcinoma,+1,1	ODF2	227	1	0			c.G2660A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	181.0	152.0	162.0		2453,2468,2396,2468,2660	5.5	1.0	9	dbSNP_134	162	66,8534	40.3+/-97.0	1,64,4235	yes	missense,missense,missense,missense,missense	ODF2	NM_001242352.1,NM_001242353.1,NM_002540.4,NM_153433.1,NM_153435.1	29,29,29,29,29	1,76,6426	AA,AG,GG		0.7674,0.2724,0.5997	benign,benign,benign,benign,benign	818/825,823/830,799/806,823/830,887/894	131262512	78,12928	2203	4300	6503	SO:0001583	missense	4957	exon21			CCATCCGCTCCCG	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2468G>A	9.37:g.131262512G>A	ENSP00000403453:p.Arg823His	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	111	58	0.522523	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	5	0.0022893772893772895	0	0.0	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	G	18.25	3.581992	0.65992	0.002724	0.007674	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.28666	1.64;1.6;1.65	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.15609	0.0376	L	0.32530	0.975	0.80722	D	1	P;B;B;B	0.44690	0.841;0.231;0.054;0.016	B;B;B;B	0.34536	0.185;0.04;0.018;0.002	T	0.02138	-1.1207	10	0.45353	T	0.12	-4.1319	13.6785	0.62469	0.0762:0.0:0.9238:0.0	.	818;168;823;799	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	H	818;823;799	ENSP00000342581:R818H;ENSP00000361882:R823H;ENSP00000307781:R799H	ENSP00000307781:R799H	R	+	2	0	ODF2	130302333	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.562000	0.53777	2.581000	0.87130	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.557	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
ITGA6	3655	hgsc.bcm.edu	37	2	173339808	173339808	+	Missense_Mutation	SNP	G	G	A	rs11895564	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:173339808G>A	ENST00000264106.6	+	8	1458	c.1255G>A	c.(1255-1257)Gca>Aca	p.A419T	ITGA6_ENST00000409080.1_Missense_Mutation_p.A380T|ITGA6_ENST00000375221.2_Missense_Mutation_p.A419T|ITGA6_ENST00000343713.4_Missense_Mutation_p.A375T|ITGA6_ENST00000409532.1_Missense_Mutation_p.A261T|ITGA6_ENST00000264107.7_Missense_Mutation_p.A380T			P23229	ITA6_HUMAN	integrin, alpha 6	419				A -> T (in Ref. 4; BAG59130 and 7; AAI36456/AAI36457). {ECO:0000305}.	amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			GTTTGGCATTGCAGTAAAAAA	0.333													G|||	1260	0.251597	0.3253	0.2248	5008	,	,		18864	0.0933		0.2793	False		,,,				2504	0.3057				p.A380T		Atlas-SNP	.											ITGA6,NS,NS,-1,1	ITGA6	171	1	0			c.G1138A						PASS	.	G	THR/ALA,THR/ALA	1505,2901	477.4+/-357.9	250,1005,948	78.0	79.0	78.0		1138,1138	4.5	1.0	2	dbSNP_120	78	2560,6040	415.9+/-351.9	370,1820,2110	yes	missense,missense	ITGA6	NM_000210.2,NM_001079818.1	58,58	620,2825,3058	AA,AG,GG		29.7674,34.158,31.2548	benign,benign	380/1074,380/1092	173339808	4065,8941	2203	4300	6503	SO:0001583	missense	3655	exon7			GGCATTGCAGTAA		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.1255G>A	2.37:g.173339808G>A	ENSP00000264106:p.Ala419Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		524	0.23992673992673993	164	0.3333333333333333	97	0.26795580110497236	53	0.09265734265734266	210	0.2770448548812665	G	20.9	4.068903	0.76301	0.34158	0.297674	ENSG00000091409	ENST00000409532;ENST00000264107;ENST00000264106;ENST00000375221;ENST00000343713;ENST00000409080;ENST00000442250;ENST00000458358	T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	5.35	4.46	0.54185	.	0.160749	0.56097	D	0.000036	T	0.00012	0.0000	L	0.56396	1.775	0.19775	P	0.9999532777	P;B;P;P	0.45428	0.571;0.042;0.858;0.858	B;B;P;P	0.58172	0.389;0.133;0.834;0.746	T	0.01413	-1.1361	8	.	.	.	.	13.3506	0.60599	0.0:0.0:0.7145:0.2855	rs11895564;rs52804239;rs61334157;rs11895564	375;419;380;380	P23229-4;P23229-9;G5E9H1;P23229-2	.;.;.;.	T	261;380;419;419;375;380;419;375	ENSP00000386614:A261T;ENSP00000264107:A380T;ENSP00000264106:A419T;ENSP00000364369:A419T;ENSP00000341078:A375T;ENSP00000386896:A380T;ENSP00000406694:A419T;ENSP00000394169:A375T	.	A	+	1	0	ITGA6	173048054	1.000000	0.71417	0.967000	0.41034	0.946000	0.59487	3.120000	0.50430	1.225000	0.43566	0.650000	0.86243	GCA	G|0.714;A|0.286	0.286	strong		0.333	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
SLFN14	342618	hgsc.bcm.edu	37	17	33875284	33875284	+	Missense_Mutation	SNP	G	G	A	rs9907259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33875284G>A	ENST00000415846.3	-	4	2748	c.2713C>T	c.(2713-2715)Ctt>Ttt	p.L905F		NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	905			L -> F (in dbSNP:rs9907259).				ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						TTTTCATAAAGCAGGTAGAGG	0.438													G|||	308	0.0615016	0.1558	0.0447	5008	,	,		20538	0.0		0.0457	False		,,,				2504	0.0256				p.L905F		Atlas-SNP	.											.	SLFN14	43	.	0			c.C2713T						PASS	.	G	PHE/LEU	181,1203		14,153,525	90.0	83.0	85.0		2713	3.3	1.0	17	dbSNP_119	85	165,3017		4,157,1430	yes	missense	SLFN14	NM_001129820.1	22	18,310,1955	AA,AG,GG		5.1854,13.078,7.5777	benign	905/913	33875284	346,4220	692	1591	2283	SO:0001583	missense	342618	exon4			CATAAAGCAGGTA		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.2713C>T	17.37:g.33875284G>A	ENSP00000391101:p.Leu905Phe	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	84	48	0.571429	NM_001129820	B2RTW9	Missense_Mutation	SNP	ENST00000415846.3	37	CCDS45650.1	104	0.047619047619047616	59	0.11991869918699187	17	0.04696132596685083	0	0.0	28	0.036939313984168866	G	11.78	1.741138	0.30865	0.13078	0.051854	ENSG00000236320	ENST00000415846	T	0.03441	3.93	5.38	3.35	0.38373	.	.	.	.	.	T	0.00039	0.0001	L	0.49640	1.575	0.23886	N	0.996568	B	0.21225	0.053	B	0.15484	0.013	T	0.47071	-0.9145	9	0.36615	T	0.2	.	6.7569	0.23518	0.2229:0.0:0.7771:0.0	rs9907259;rs52818084;rs9907259	905	P0C7P3	SLN14_HUMAN	F	905	ENSP00000391101:L905F	ENSP00000391101:L905F	L	-	1	0	SLFN14	30899397	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.390000	0.34464	0.764000	0.33197	0.655000	0.94253	CTT	G|0.939;A|0.061	0.061	strong		0.438	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
TTLL2	83887	hgsc.bcm.edu	37	6	167754360	167754360	+	Silent	SNP	C	C	T	rs77767783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167754360C>T	ENST00000239587.5	+	3	1060	c.972C>T	c.(970-972)ctC>ctT	p.L324L		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	324	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		AATGGACGCTCAGCAGATTTT	0.438													C|||	9	0.00179712	0.0	0.0043	5008	,	,		20069	0.0		0.006	False		,,,				2504	0.0				p.L324L		Atlas-SNP	.											.	TTLL2	82	.	0			c.C972T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	159.0	168.0	165.0		972	0.3	0.5	6	dbSNP_132	165	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	TTLL2	NM_031949.4		0,29,6474	TT,TC,CC		0.3256,0.0227,0.223		324/593	167754360	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			GACGCTCAGCAGA	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.972C>T	6.37:g.167754360C>T		Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	90	80	0.888889	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.998;T|0.002	0.002	strong		0.438	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
PLCE1	51196	hgsc.bcm.edu	37	10	96039597	96039597	+	Missense_Mutation	SNP	G	G	C	rs2274224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:96039597G>C	ENST00000371380.3	+	19	4959	c.4724G>C	c.(4723-4725)cGa>cCa	p.R1575P	PLCE1_ENST00000371385.3_Missense_Mutation_p.R1267P|PLCE1-AS1_ENST00000425267.3_RNA|PLCE1_ENST00000260766.3_Missense_Mutation_p.R1575P|PLCE1-AS1_ENST00000596633.1_RNA|PLCE1_ENST00000371375.1_Missense_Mutation_p.R1267P			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1575			R -> P (in dbSNP:rs2274224).	R -> Q (in Ref. 2; AAG28341). {ECO:0000305}.	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)				GCCAACCCCCGACCTGCCAAT	0.423											OREG0020383	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2435	0.486222	0.5893	0.3487	5008	,	,		17974	0.5377		0.4563	False		,,,				2504	0.4223				p.R1575P		Atlas-SNP	.											.	PLCE1	543	.	0			c.G4724C						PASS	.	C	PRO/ARG,PRO/ARG	2066,1722		575,916,403	82.0	86.0	85.0		3800,4724	4.6	1.0	10	dbSNP_100	85	3651,4573		789,2073,1250	yes	missense,missense	PLCE1	NM_001165979.1,NM_016341.3	103,103	1364,2989,1653	CC,CG,GG		44.3945,45.4593,47.5941	benign,benign	1267/1995,1575/2303	96039597	5717,6295	1894	4112	6006	SO:0001583	missense	51196	exon20			ACCCCCGACCTGC		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.4724G>C	10.37:g.96039597G>C	ENSP00000360431:p.Arg1575Pro	Somatic	109	1	0.00917431	1317	WXS	Illumina HiSeq	Phase_I	94	94	1	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	1024	0.46886446886446886	281	0.5711382113821138	135	0.3729281767955801	281	0.49125874125874125	327	0.4313984168865435	C	2.913	-0.224866	0.06022	0.545407	0.443945	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.23552	1.92;1.92;1.9;1.9	5.53	4.64	0.57946	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.611593	0.17706	N	0.164757	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	0.41556	-0.9502	9	0.23302	T	0.38	.	6.471	0.22007	0.1357:0.664:0.1307:0.0695	rs2274224;rs52813360;rs58077856;rs2274224	1559;1267;1575	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	P	1575;1575;1267;1267	ENSP00000260766:R1575P;ENSP00000360431:R1575P;ENSP00000360438:R1267P;ENSP00000360426:R1267P	ENSP00000260766:R1575P	R	+	2	0	PLCE1	96029587	0.000000	0.05858	0.998000	0.56505	0.819000	0.46315	0.795000	0.26972	0.920000	0.36970	-0.738000	0.03535	CGA	G|0.526;C|0.474	0.474	strong		0.423	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
LAMA2	3908	hgsc.bcm.edu	37	6	129722389	129722389	+	Silent	SNP	A	A	G	rs3749877	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:129722389A>G	ENST00000421865.2	+	38	5515	c.5466A>G	c.(5464-5466)gaA>gaG	p.E1822E		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1822	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		AGGCTGTTGAAAGCGGCAAAC	0.403													A|||	2727	0.544529	0.6581	0.4683	5008	,	,		20266	0.5516		0.4632	False		,,,				2504	0.5215				p.E1822E		Atlas-SNP	.											.	LAMA2	481	.	0			c.A5466G						PASS	.	A	,	2710,1696	653.6+/-399.6	833,1044,326	139.0	139.0	139.0		5466,5466	2.4	0.9	6	dbSNP_107	139	4002,4598	554.3+/-386.5	935,2132,1233	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	1768,3176,1559	GG,GA,AA		46.5349,38.493,48.393	,	1822/3123,1822/3119	129722389	6712,6294	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon38			TGTTGAAAGCGGC	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.5466A>G	6.37:g.129722389A>G		Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	16	13	0.8125	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			A|0.460;G|0.540	0.540	strong		0.403	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
ABCA7	10347	hgsc.bcm.edu	37	19	1061804	1061804	+	Silent	SNP	T	T	C	rs78320196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1061804T>C	ENST00000263094.6	+	41	5718	c.5487T>C	c.(5485-5487)aaT>aaC	p.N1829N	ABCA7_ENST00000433129.1_Silent_p.N1829N|ABCA7_ENST00000435683.2_Silent_p.N1691N	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1829	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGTGTGAATGGAGCAGGGA	0.587													C|||	299	0.0597045	0.025	0.0418	5008	,	,		18793	0.0337		0.0567	False		,,,				2504	0.1493				p.N1829N		Atlas-SNP	.											.	ABCA7	174	.	0			c.T5487C						PASS	.	C		117,4287	813.3+/-416.1	1,115,2086	114.0	94.0	101.0		5487	-3.2	1.0	19	dbSNP_132	101	392,8208	800.3+/-407.4	10,372,3918	no	coding-synonymous	ABCA7	NM_019112.3		11,487,6004	CC,CT,TT		4.5581,2.6567,3.9142		1829/2147	1061804	509,12495	2202	4300	6502	SO:0001819	synonymous_variant	10347	exon41			TGTGAATGGAGCA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5487T>C	19.37:g.1061804T>C		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	183	87	0.47541	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			T|0.960;C|0.040	0.040	strong		0.587	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
GPR179	440435	hgsc.bcm.edu	37	17	36491083	36491083	+	Missense_Mutation	SNP	C	C	T	rs4550493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36491083C>T	ENST00000342292.4	-	7	1498	c.1478G>A	c.(1477-1479)cGc>cAc	p.R493H		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	493					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CAGCCCCAGGCGCCGCAGCAG	0.662													C|||	153	0.0305511	0.0393	0.0231	5008	,	,		15406	0.0		0.0557	False		,,,				2504	0.0297				p.R493H		Atlas-SNP	.											GPR179,NS,carcinoma,0,1	GPR179	170	1	0			c.G1478A						PASS	.	C	HIS/ARG	128,3952		1,126,1913	6.0	9.0	8.0		1478	2.4	1.0	17	dbSNP_111	8	376,7876		10,356,3760	yes	missense	GPR179	NM_001004334.2	29	11,482,5673	TT,TC,CC		4.5565,3.1373,4.0869	benign	493/2368	36491083	504,11828	2040	4126	6166	SO:0001583	missense	440435	exon7			CCCAGGCGCCGCA		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.1478G>A	17.37:g.36491083C>T	ENSP00000345060:p.Arg493His	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	88	48	0.545455	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	79	0.036172161172161175	25	0.0508130081300813	10	0.027624309392265192	0	0.0	44	0.05804749340369393	C	10.81	1.455033	0.26161	0.031373	0.045565	ENSG00000188888	ENST00000342292	D	0.88046	-2.33	4.36	2.36	0.29203	GPCR, family 3, C-terminal (2);	0.469632	0.19365	N	0.116041	T	0.34513	0.0900	L	0.55481	1.735	0.28545	N	0.911901	B	0.06786	0.001	B	0.08055	0.003	T	0.48387	-0.9040	10	0.14656	T	0.56	-3.6302	3.9611	0.09410	0.1862:0.6134:0.0:0.2004	rs4550493	493	Q6PRD1	GP179_HUMAN	H	493	ENSP00000345060:R493H	ENSP00000345060:R493H	R	-	2	0	GPR179	33744609	1.000000	0.71417	0.977000	0.42913	0.747000	0.42532	2.343000	0.44001	0.484000	0.27630	-0.356000	0.07607	CGC	C|0.962;T|0.038	0.038	strong		0.662	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
SS18L1	26039	hgsc.bcm.edu	37	20	60737908	60737908	+	Silent	SNP	G	G	A	rs61744430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60737908G>A	ENST00000331758.3	+	5	503	c.477G>A	c.(475-477)tcG>tcA	p.S159S	SS18L1_ENST00000421564.1_Silent_p.S159S|SS18L1_ENST00000370848.4_Silent_p.S162S|SS18L1_ENST00000491916.1_3'UTR	NM_198935.1	NP_945173.1	O75177	CREST_HUMAN	synovial sarcoma translocation gene on chromosome 18-like 1	159	Methionine-rich intra-molecular domain. {ECO:0000250}.				chromatin modification (GO:0016568)|dendrite development (GO:0016358)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of dendrite development (GO:0050773)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|kinetochore (GO:0000776)|nuclear body (GO:0016604)|nucleus (GO:0005634)			SS18L1/SSX1(2)	ovary(2)|skin(1)	3	Breast(26;3.97e-09)		BRCA - Breast invasive adenocarcinoma(19;1.92e-08)			GACCCGCCTCGCAGGGCGTCC	0.647			T	SSX1	synovial sarcoma								G|||	374	0.0746805	0.1672	0.049	5008	,	,		16265	0.003		0.0537	False		,,,				2504	0.0634				p.S159S		Atlas-SNP	.		Dom	yes		20	20q13.3	26039	synovial sarcoma translocation gene on chromosome 18-like 1		M	.	SS18L1	37	.	0			c.G477A						PASS	.	G		692,3714	271.3+/-270.1	50,592,1561	44.0	37.0	40.0		477	-1.5	1.0	20	dbSNP_129	40	454,8146	131.0+/-188.9	17,420,3863	no	coding-synonymous	SS18L1	NM_198935.1		67,1012,5424	AA,AG,GG		5.2791,15.7059,8.8113		159/397	60737908	1146,11860	2203	4300	6503	SO:0001819	synonymous_variant	26039	exon5			CGCCTCGCAGGGC	AB014593	CCDS13491.1	20q13.3	2008-07-28			ENSG00000184402	ENSG00000184402			15592	protein-coding gene	gene with protein product		606472					Standard	XM_005260389		Approved	KIAA0693	uc002ycb.3	O75177	OTTHUMG00000032902	ENST00000331758.3:c.477G>A	20.37:g.60737908G>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	55	0.458333	NM_198935	A6NNE3|A8K620|B3KWR8|E1P5H7|Q5JXJ3|Q6MZV9|Q6NTH3|Q6XYD9|Q8NE69|Q9BR55|Q9H4K6	Silent	SNP	ENST00000331758.3	37	CCDS13491.1																																																																																			G|0.922;A|0.078	0.078	strong		0.647	SS18L1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080004.2		
TPRX1	284355	hgsc.bcm.edu	37	19	48305586	48305586	+	Missense_Mutation	SNP	G	G	A	rs145255760		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48305586G>A	ENST00000322175.3	-	2	837	c.682C>T	c.(682-684)Cca>Tca	p.P228S	TPRX1_ENST00000543508.1_Missense_Mutation_p.P218S|TPRX1_ENST00000535759.1_Missense_Mutation_p.P325S	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	228	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		attgggcctgggattgggcct	0.662																																					p.P228S	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.C682T						PASS	.						11.0	9.0	9.0					19																	48305586		1986	3954	5940	SO:0001583	missense	284355	exon2			GGCCTGGGATTGG		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.682C>T	19.37:g.48305586G>A	ENSP00000323455:p.Pro228Ser	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	44	13	0.295455	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	93	0.042582417582417584	4	0.008130081300813009	13	0.03591160220994475	1	0.0017482517482517483	75	0.09894459102902374	g	5.125	0.208615	0.09757	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D;T	0.93763	-2.04;-3.28;-0.16	0.401	-0.802	0.10889	.	.	.	.	.	T	0.11067	0.0270	N	0.03608	-0.345	0.09310	N	1	B	0.17268	0.021	B	0.11329	0.006	T	0.51748	-0.8666	8	0.40728	T	0.16	.	.	.	.	.	228	Q8N7U7	TPRX1_HUMAN	S	228;325;218	ENSP00000323455:P228S;ENSP00000438832:P325S;ENSP00000438712:P218S	ENSP00000323455:P228S	P	-	1	0	TPRX1	52997398	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.328000	0.19681	-0.453000	0.07076	-0.462000	0.05337	CCA	G|0.957;A|0.043	0.043	strong		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
DENND6B	414918	hgsc.bcm.edu	37	22	50753334	50753334	+	Silent	SNP	G	G	A	rs73439311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50753334G>A	ENST00000413817.3	-	10	846	c.775C>T	c.(775-777)Ctg>Ttg	p.L259L	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	259					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										ATATGAGTCAGCACAGGCCGG	0.677													G|||	1879	0.3752	0.2837	0.3746	5008	,	,		17225	0.2956		0.3767	False		,,,				2504	0.5798				p.L259L		Atlas-SNP	.											.	.	.	.	0			c.C775T						PASS	.	G		1169,3013		167,835,1089	26.0	33.0	31.0		775	5.0	1.0	22	dbSNP_130	31	3173,5217		624,1925,1646	no	coding-synonymous	FAM116B	NM_001001794.3		791,2760,2735	AA,AG,GG		37.8188,27.9531,34.5371		259/586	50753334	4342,8230	2091	4195	6286	SO:0001819	synonymous_variant	414918	exon10			GAGTCAGCACAGG	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.775C>T	22.37:g.50753334G>A		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	234	118	0.504274	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1																																																																																			G|0.651;A|0.349	0.349	strong		0.677	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
CTCFL	140690	hgsc.bcm.edu	37	20	56099114	56099114	+	Missense_Mutation	SNP	C	C	G	rs6070128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:56099114C>G	ENST00000608263.1	-	1	809	c.148G>C	c.(148-150)Gag>Cag	p.E50Q	CTCFL_ENST00000608903.1_Intron|CTCFL_ENST00000371196.2_Missense_Mutation_p.E50Q|CTCFL_ENST00000502686.2_Intron|CTCFL_ENST00000433949.3_Intron|CTCFL_ENST00000429804.3_Missense_Mutation_p.E50Q|CTCFL_ENST00000609232.1_Missense_Mutation_p.E50Q|CTCFL_ENST00000608425.1_Missense_Mutation_p.E50Q|CTCFL_ENST00000608440.1_Missense_Mutation_p.E50Q|CTCFL_ENST00000481655.2_Missense_Mutation_p.E50Q|CTCFL_ENST00000422869.2_Missense_Mutation_p.E50Q|CTCFL_ENST00000608858.1_Intron|CTCFL_ENST00000423479.3_Missense_Mutation_p.E50Q|CTCFL_ENST00000432255.2_Missense_Mutation_p.E50Q|CTCFL_ENST00000243914.3_Missense_Mutation_p.E50Q|CTCFL_ENST00000539382.1_Intron|CTCFL_ENST00000608158.1_Missense_Mutation_p.E50Q	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	50			E -> Q (in dbSNP:rs6070128).		cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			GAGGTACGCTCGGCCTCCAAC	0.582													C|||	1428	0.285144	0.0862	0.2882	5008	,	,		19373	0.3651		0.4165	False		,,,				2504	0.3344				p.E50Q		Atlas-SNP	.											CTCFL,caecum,carcinoma,0,1	CTCFL	97	1	0			c.G148C						PASS	.	C	GLN/GLU	565,3841	254.0+/-259.7	33,499,1671	154.0	169.0	164.0		148	-4.7	0.0	20	dbSNP_114	164	3513,5087	512.5+/-378.0	711,2091,1498	yes	missense	CTCFL	NM_080618.2	29	744,2590,3169	GG,GC,CC		40.8488,12.8234,31.3548	benign	50/664	56099114	4078,8928	2203	4300	6503	SO:0001583	missense	140690	exon1			TACGCTCGGCCTC		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.148G>C	20.37:g.56099114C>G	ENSP00000476783:p.Glu50Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	149	149	1	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	37	CCDS13459.1	688	0.315018315018315	45	0.09146341463414634	116	0.32044198895027626	219	0.38286713286713286	308	0.40633245382585753	C	6.687	0.495343	0.12762	0.128234	0.408488	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000422109;ENST00000426658;ENST00000432255;ENST00000422869	T;T;T;T;T;T;T;T;T	0.12147	2.71;2.75;2.75;2.93;2.81;3.1;2.79;3.39;2.79	4.0	-4.73	0.03259	.	1.342910	0.05297	N	0.522327	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.15141	0.0;0.0;0.005;0.012;0.005;0.011;0.0;0.0	B;B;B;B;B;B;B;B	0.12156	0.003;0.003;0.007;0.006;0.005;0.007;0.002;0.001	T	0.48514	-0.9029	9	0.22706	T	0.39	-1.0843	9.003	0.36094	0.0:0.2572:0.5775:0.1653	rs6070128;rs6070128	50;50;50;50;50;50;50;50	A6XGM3;A6XGM0;A6XGM9;A6XGM8;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;.;.;.;CTCFL_HUMAN	Q	50	ENSP00000415579:E50Q;ENSP00000243914:E50Q;ENSP00000360239:E50Q;ENSP00000415329:E50Q;ENSP00000392034:E50Q;ENSP00000413713:E50Q;ENSP00000403369:E50Q;ENSP00000409344:E50Q;ENSP00000399061:E50Q	ENSP00000243914:E50Q	E	-	1	0	CTCFL	55532520	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.230000	0.09083	-1.292000	0.02366	-0.150000	0.13652	GAG	C|0.675;G|0.325	0.325	strong		0.582	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
DTX3L	151636	hgsc.bcm.edu	37	3	122290579	122290579	+	Silent	SNP	C	C	T	rs2036342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:122290579C>T	ENST00000296161.4	+	5	2397	c.2208C>T	c.(2206-2208)gcC>gcT	p.A736A	DTX3L_ENST00000383661.3_Silent_p.A224A	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	736					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		AGCTGAAAGCCAAAGGAATTG	0.368													C|||	1720	0.34345	0.2731	0.2622	5008	,	,		19773	0.4355		0.3211	False		,,,				2504	0.4243				p.A736A		Atlas-SNP	.											.	DTX3L	59	.	0			c.C2208T						PASS	.	C		1296,3110	437.6+/-345.0	181,934,1088	103.0	97.0	99.0		2208	-10.5	0.0	3	dbSNP_94	99	2699,5901	430.0+/-356.4	439,1821,2040	no	coding-synonymous	DTX3L	NM_138287.3		620,2755,3128	TT,TC,CC		31.3837,29.4144,30.7166		736/741	122290579	3995,9011	2203	4300	6503	SO:0001819	synonymous_variant	151636	exon5			GAAAGCCAAAGGA		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"""RING-type (C3HC4) zinc fingers"""	30323	protein-coding gene	gene with protein product	"""rhysin 2"""	613143	"""deltex 3-like (Drosophila)"""			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.2208C>T	3.37:g.122290579C>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	95	94	0.989474	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Silent	SNP	ENST00000296161.4	37	CCDS3015.1																																																																																			C|0.681;T|0.319	0.319	strong		0.368	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287	
FAM19A3	284467	hgsc.bcm.edu	37	1	113264930	113264930	+	Silent	SNP	C	C	G	rs35995150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:113264930C>G	ENST00000361886.3	+	2	134	c.75C>G	c.(73-75)acC>acG	p.T25T	FAM19A3_ENST00000369630.3_Silent_p.T25T	NM_001004440.1|NM_182759.2	NP_001004440.1|NP_877436.1	Q7Z5A8	F19A3_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A3	25						extracellular region (GO:0005576)				lung(4)|ovary(1)	5	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GGCTGTGGACCCACCTGACCT	0.662													C|||	276	0.0551118	0.0045	0.049	5008	,	,		16390	0.001		0.1302	False		,,,				2504	0.1063				p.T25T		Atlas-SNP	.											.	FAM19A3	10	.	0			c.C75G						PASS	.	C	,	121,4285	88.2+/-126.9	2,117,2084	67.0	65.0	66.0		75,75	-3.3	0.0	1	dbSNP_126	66	1179,7421	239.6+/-270.6	77,1025,3198	no	coding-synonymous,coding-synonymous	FAM19A3	NM_001004440.1,NM_182759.2	,	79,1142,5282	GG,GC,CC		13.7093,2.7463,9.9954	,	25/170,25/134	113264930	1300,11706	2203	4300	6503	SO:0001819	synonymous_variant	284467	exon2			GTGGACCCACCTG	AY325119	CCDS856.1, CCDS30806.1	1p13.2	2008-02-05			ENSG00000184599	ENSG00000184599			21590	protein-coding gene	gene with protein product						15028294	Standard	NM_182759		Approved	TAFA-3	uc001ecu.3	Q7Z5A8	OTTHUMG00000012020	ENST00000361886.3:c.75C>G	1.37:g.113264930C>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	49	0.475728	NM_001004440	B7ZLU0|Q2M1P9|Q7Z5A6	Silent	SNP	ENST00000361886.3	37	CCDS856.1																																																																																			C|0.909;G|0.091	0.091	strong		0.662	FAM19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033255.1	NM_182759	
OTOGL	283310	hgsc.bcm.edu	37	12	80665473	80665473	+	Missense_Mutation	SNP	C	C	T	rs183159689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:80665473C>T	ENST00000547103.1	+	23	2543	c.2537C>T	c.(2536-2538)cCt>cTt	p.P846L	OTOGL_ENST00000458043.2_Missense_Mutation_p.P846L			Q3ZCN5	OTOGL_HUMAN	otogelin-like	846					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGCAGGTTTCCTGACCCTGAA	0.458													C|||	3	0.000599042	0.0	0.0	5008	,	,		17643	0.0		0.003	False		,,,				2504	0.0				p.P846L		Atlas-SNP	.											.	OTOGL	235	.	0			c.C2537T						PASS	.	C	LEU/PRO	4,3910		0,4,1953	97.0	100.0	99.0		2537	5.1	1.0	12		99	3,8259		0,3,4128	yes	missense	OTOGL	NM_173591.3	98	0,7,6081	TT,TC,CC		0.0363,0.1022,0.0575		846/2345	80665473	7,12169	1957	4131	6088	SO:0001583	missense	283310	exon23			GGTTTCCTGACCC	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.2537C>T	12.37:g.80665473C>T	ENSP00000447211:p.Pro846Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	156	74	0.474359	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	15.16	2.751832	0.49362	0.001022	3.63E-4	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.16324	2.35;2.35	5.14	5.14	0.70334	.	.	.	.	.	T	0.22475	0.0542	L	0.59912	1.85	0.58432	D	0.999999	.	.	.	.	.	.	T	0.00420	-1.1750	7	0.29301	T	0.29	.	14.6719	0.68951	0.1459:0.8541:0.0:0.0	.	.	.	.	L	846	ENSP00000447211:P846L;ENSP00000400895:P846L	ENSP00000400895:P846L	P	+	2	0	OTOGL	79189604	0.962000	0.33011	1.000000	0.80357	0.977000	0.68977	1.923000	0.40055	2.551000	0.86045	0.655000	0.94253	CCT	C|0.998;T|0.002	0.002	strong		0.458	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
IGSF10	285313	hgsc.bcm.edu	37	3	151155620	151155620	+	Silent	SNP	G	G	A	rs6781302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:151155620G>A	ENST00000282466.3	-	6	6728	c.6729C>T	c.(6727-6729)aaC>aaT	p.N2243N	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2243	Ig-like C2-type 9.			N -> S (in Ref. 3; AAH31063). {ECO:0000305}.	cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TAACAGTTCTGTTTGTATACA	0.438													G|||	2964	0.591853	0.5015	0.5937	5008	,	,		22139	0.5169		0.7565	False		,,,				2504	0.6207				p.N2243N		Atlas-SNP	.											.	IGSF10	279	.	0			c.C6729T						PASS	.	G	,,	2340,2066	605.2+/-390.5	628,1084,491	110.0	98.0	102.0		810,666,6729	3.7	0.1	3	dbSNP_116	102	6549,2051	720.2+/-406.3	2496,1557,247	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	3124,2641,738	AA,AG,GG		23.8488,46.8906,31.6546	,,	270/651,222/603,2243/2624	151155620	8889,4117	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			AGTTCTGTTTGTA	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6729C>T	3.37:g.151155620G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	64	1	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			G|0.352;A|0.648	0.648	strong		0.438	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
PROL1	58503	hgsc.bcm.edu	37	4	71275387	71275387	+	Silent	SNP	A	A	G	rs61336549	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71275387A>G	ENST00000399575.2	+	3	516	c.342A>G	c.(340-342)gtA>gtG	p.V114V	PROL1_ENST00000514338.1_3'UTR	NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	114	Pro-rich.				negative regulation of endopeptidase activity (GO:0010951)|regulation of sensory perception of pain (GO:0051930)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)|peptidase inhibitor activity (GO:0030414)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				CTTACTATGTAGGACCTATTA	0.393													A|||	563	0.11242	0.003	0.0634	5008	,	,		21102	0.2153		0.1014	False		,,,				2504	0.2004				p.V114V		Atlas-SNP	.											.	PROL1	46	.	0			c.A342G						PASS	.	A		65,3661		0,65,1798	204.0	198.0	200.0		342	2.0	0.0	4	dbSNP_129	200	691,7517		25,641,3438	no	coding-synonymous	PROL1	NM_021225.4		25,706,5236	GG,GA,AA		8.4186,1.7445,6.3348		114/249	71275387	756,11178	1863	4104	5967	SO:0001819	synonymous_variant	58503	exon3			CTATGTAGGACCT	S83198	CCDS43235.1	4q13.3	2011-10-28	2005-02-07		ENSG00000171199	ENSG00000171199			17279	protein-coding gene	gene with protein product		608936	"""proline rich 1"""			8670737	Standard	NM_021225		Approved	BPLP, PRL1, opiorphin	uc003hfi.3	Q99935	OTTHUMG00000160845	ENST00000399575.2:c.342A>G	4.37:g.71275387A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	157	72	0.458599	NM_021225	A8MZ07|P85047	Silent	SNP	ENST00000399575.2	37	CCDS43235.1																																																																																			A|0.903;G|0.097	0.097	strong		0.393	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225	
ZNF285	26974	hgsc.bcm.edu	37	19	44891010	44891010	+	Missense_Mutation	SNP	G	G	C	rs150792548	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44891010G>C	ENST00000330997.4	-	4	1461	c.1397C>G	c.(1396-1398)gCg>gGg	p.A466G	ZNF285_ENST00000591679.1_Missense_Mutation_p.A473G|CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000544719.2_Missense_Mutation_p.A466G	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	466					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A466G(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						AGAGCTATACGCAAAATCCTT	0.418																																					p.A466G		Atlas-SNP	.											ZNF285,NS,carcinoma,+1,2	ZNF285	86	2	1	Substitution - Missense(1)	skin(1)	c.C1397G						scavenged	.						83.0	84.0	83.0					19																	44891010		2203	4300	6503	SO:0001583	missense	26974	exon4			CTATACGCAAAAT	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.1397C>G	19.37:g.44891010G>C	ENSP00000333595:p.Ala466Gly	Somatic	127	2	0.015748		WXS	Illumina HiSeq	Phase_I	138	11	0.0797101	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	9.126	1.010205	0.19277	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.08008	3.14	3.46	0.829	0.18847	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08714	0.0216	L	0.45744	1.44	0.09310	N	1	B;B	0.34399	0.452;0.0	B;B	0.36666	0.23;0.001	T	0.29488	-1.0010	9	0.56958	D	0.05	.	6.4144	0.21708	0.1094:0.3586:0.532:0.0	.	490;466	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	G	489;466	ENSP00000333595:A466G	ENSP00000333595:A466G	A	-	2	0	ZNF285	49582850	0.000000	0.05858	0.002000	0.10522	0.860000	0.49131	-6.159000	0.00078	0.511000	0.28236	0.298000	0.19748	GCG	A|0.002;C|0.002;G|0.995	0.002	strong		0.418	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
RBMX	27316	hgsc.bcm.edu	37	X	135956391	135956391	+	Silent	SNP	A	A	G	rs34606958		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135956391A>G	ENST00000320676.7	-	9	1240	c.1086T>C	c.(1084-1086)gaT>gaC	p.D362D	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Silent_p.D234D|RBMX_ENST00000570135.1_Silent_p.D227D|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	362	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TGCTGTAGGAATCACGTGGAG	0.552																																					p.D362D		Atlas-SNP	.											.	RBMX	149	.	0			c.T1086C						PASS	.						66.0	63.0	64.0					X																	135956391		2203	4300	6503	SO:0001819	synonymous_variant	27316	exon9			GTAGGAATCACGT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1086T>C	X.37:g.135956391A>G		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	358	150	0.418994	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Silent	SNP	ENST00000320676.7	37	CCDS14661.1																																																																																			A|0.500;G|0.500	0.500	weak		0.552	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
TOP1MT	116447	hgsc.bcm.edu	37	8	144399993	144399993	+	Silent	SNP	G	G	A	rs146827342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144399993G>A	ENST00000329245.4	-	10	1264	c.1230C>T	c.(1228-1230)aaC>aaT	p.N410N	TOP1MT_ENST00000523676.1_Silent_p.N312N|TOP1MT_ENST00000519148.1_Silent_p.N312N|AC087793.1_ENST00000585120.1_RNA|TOP1MT_ENST00000521193.1_Silent_p.N312N	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	410		Interaction with DNA. {ECO:0000250}.			DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	GGAGGTGCTTGTTCAGGCTGG	0.617													G|||	5	0.000998403	0.0	0.0014	5008	,	,		16371	0.0		0.004	False		,,,				2504	0.0				p.N410N		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1230T						PASS	.	G		6,4400	12.9+/-30.5	0,6,2197	65.0	60.0	62.0		1230	1.9	0.4	8	dbSNP_134	62	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	TOP1MT	NM_052963.1		0,33,6470	AA,AG,GG		0.314,0.1362,0.2537		410/602	144399993	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	116447	exon10			GTGCTTGTTCAGG	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1230C>T	8.37:g.144399993G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	37	CCDS6400.1																																																																																			G|0.997;A|0.003	0.003	strong		0.617	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
FBN3	84467	hgsc.bcm.edu	37	19	8176945	8176945	+	Missense_Mutation	SNP	T	T	C	rs4804063	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8176945T>C	ENST00000600128.1	-	31	4291	c.3877A>G	c.(3877-3879)Agt>Ggt	p.S1293G	FBN3_ENST00000601739.1_Missense_Mutation_p.S1293G|FBN3_ENST00000270509.2_Missense_Mutation_p.S1293G			Q75N90	FBN3_HUMAN	fibrillin 3	1293	EGF-like 19; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		S -> G (in dbSNP:rs4804063).|S -> N (in dbSNP:rs4804063).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GAGGCGTGACTGTCACAGTTG	0.572													T|||	1541	0.307708	0.2814	0.2522	5008	,	,		12565	0.369		0.175	False		,,,				2504	0.456				p.S1293G		Atlas-SNP	.											.	FBN3	300	.	0			c.A3877G						PASS	.	T	GLY/SER	1200,3206	418.3+/-338.2	165,870,1168	162.0	133.0	142.0		3877	-5.6	0.0	19	dbSNP_111	142	1480,7120	280.9+/-294.7	137,1206,2957	yes	missense	FBN3	NM_032447.3	56	302,2076,4125	CC,CT,TT		17.2093,27.2356,20.6059	benign	1293/2810	8176945	2680,10326	2203	4300	6503	SO:0001583	missense	84467	exon30			CGTGACTGTCACA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.3877A>G	19.37:g.8176945T>C	ENSP00000470498:p.Ser1293Gly	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	142	71	0.5	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	563	0.25778388278388276	125	0.2540650406504065	90	0.24861878453038674	209	0.36538461538461536	139	0.18337730870712401	T	8.850	0.944307	0.18356	0.272356	0.172093	ENSG00000142449	ENST00000270509	D	0.88201	-2.35	4.34	-5.58	0.02512	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.518583	0.20895	U	0.083753	T	0.00012	0.0000	N	0.21324	0.655	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.09840	-1.0656	9	0.23302	T	0.38	.	7.9098	0.29785	0.0:0.3184:0.4344:0.2472	rs4804063;rs52819503;rs60677672;rs4804063	1293	Q75N90	FBN3_HUMAN	G	1293	ENSP00000270509:S1293G	ENSP00000270509:S1293G	S	-	1	0	FBN3	8082945	0.002000	0.14202	0.001000	0.08648	0.261000	0.26267	-0.077000	0.11394	-1.174000	0.02754	0.402000	0.26972	AGT	C|0.236;N|0.000	0.236	strong		0.572	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
STOX1	219736	hgsc.bcm.edu	37	10	70645376	70645376	+	Missense_Mutation	SNP	A	A	C	rs10509305	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:70645376A>C	ENST00000298596.6	+	3	1907	c.1824A>C	c.(1822-1824)gaA>gaC	p.E608D	STOX1_ENST00000421961.2_Missense_Mutation_p.E498D|STOX1_ENST00000399162.2_Intron|STOX1_ENST00000399165.4_Intron|STOX1_ENST00000399169.4_Missense_Mutation_p.E608D	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	608			E -> D (in dbSNP:rs10509305). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15806103}.			cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						TGAGATATGAAGTGTATGGTG	0.428													A|||	722	0.144169	0.0318	0.2161	5008	,	,		23136	0.0804		0.2187	False		,,,				2504	0.2342				p.E608D		Atlas-SNP	.											.	STOX1	75	.	0			c.A1824C	GRCh37	CM057372	STOX1	M	rs10509305	PASS	.	A	,,ASP/GLU,ASP/GLU,ASP/GLU	225,3635		5,215,1710	159.0	143.0	148.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,1824,1494,1824	1.1	0.0	10	dbSNP_119	148	1779,6497		196,1387,2555	yes	intron,intron,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	,,45,45,45	201,1602,4265	CC,CA,AA		21.4959,5.829,16.5129	,,benign,benign,benign	,,608/990,498/880,608/990	70645376	2004,10132	1930	4138	6068	SO:0001583	missense	219736	exon3			ATATGAAGTGTAT	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.1824A>C	10.37:g.70645376A>C	ENSP00000298596:p.Glu608Asp	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	49	0.510417	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	315	0.14423076923076922	14	0.028455284552845527	86	0.23756906077348067	55	0.09615384615384616	160	0.21108179419525067	A	0	-2.847190	0.00067	0.05829	0.214959	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.74106	-0.81;-0.81;-0.49	6.07	1.14	0.20703	.	1.071960	0.07228	N	0.861947	T	0.00012	0.0000	N	0.00162	-1.95	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06075	-1.0847	9	0.09338	T	0.73	.	0.0409	0.00008	0.2825:0.1869:0.213:0.3176	rs10509305;rs17470548;rs52799917;rs61365255;rs10509305	608	Q6ZVD7	STOX1_HUMAN	D	608;608;498	ENSP00000382121:E608D;ENSP00000298596:E608D;ENSP00000394509:E498D	ENSP00000298596:E608D	E	+	3	2	STOX1	70315382	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-0.860000	0.04272	-0.040000	0.13580	-2.501000	0.00191	GAA	A|0.858;C|0.142	0.142	strong		0.428	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
ANKRD35	148741	hgsc.bcm.edu	37	1	145562881	145562881	+	Silent	SNP	T	T	C	rs10910824	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145562881T>C	ENST00000355594.4	+	10	2656	c.2569T>C	c.(2569-2571)Ttg>Ctg	p.L857L		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	857										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)					AAAGGCTCTGTTGGAAAAGTA	0.682													C|||	2949	0.588858	0.6059	0.5389	5008	,	,		14224	0.7252		0.4384	False		,,,				2504	0.6155				p.L857L	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.T2569C						PASS	.	C		2392,2006		658,1076,465	17.0	21.0	20.0		2569	5.5	1.0	1	dbSNP_120	20	3528,5064		747,2034,1515	no	coding-synonymous	ANKRD35	NM_144698.3		1405,3110,1980	CC,CT,TT		41.0615,45.6116,45.5735		857/1002	145562881	5920,7070	2199	4296	6495	SO:0001819	synonymous_variant	148741	exon10			GCTCTGTTGGAAA	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.2569T>C	1.37:g.145562881T>C		Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	23	10	0.434783	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Silent	SNP	ENST00000355594.4	37	CCDS919.1																																																																																			A|0.133;C|0.355	0.355	strong		0.682	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
PPP5C	5536	hgsc.bcm.edu	37	19	46878989	46878989	+	Silent	SNP	G	G	A	rs4239538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46878989G>A	ENST00000012443.4	+	3	595	c.492G>A	c.(490-492)tcG>tcA	p.S164S	PPP5C_ENST00000391919.1_Silent_p.S58S	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	164					cell death (GO:0008219)|DNA repair (GO:0006281)|mitotic nuclear division (GO:0007067)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein dephosphorylation (GO:0006470)|protein heterooligomerization (GO:0051291)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|RNA binding (GO:0003723)|signal transducer activity (GO:0004871)			endometrium(4)|kidney(1)|large_intestine(5)|liver(2)|lung(4)|ovary(1)|pancreas(1)	18		Ovarian(192;0.0731)|all_neural(266;0.196)		OV - Ovarian serous cystadenocarcinoma(262;0.000196)|all cancers(93;0.00192)|GBM - Glioblastoma multiforme(486;0.0499)|Epithelial(262;0.0504)		TGGTGGACTCGCTGGACATCG	0.597													G|||	699	0.139577	0.0794	0.1931	5008	,	,		19732	0.0357		0.3022	False		,,,				2504	0.1227				p.S164S		Atlas-SNP	.											.	PPP5C	44	.	0			c.G492A						PASS	.	G	,	545,3857		36,473,1692	38.0	32.0	34.0		492,492	-6.1	0.1	19	dbSNP_111	34	2474,6124		316,1842,2141	no	coding-synonymous,coding-synonymous	PPP5C	NM_001204284.1,NM_006247.3	,	352,2315,3833	AA,AG,GG		28.7741,12.3807,23.2231	,	164/478,164/500	46878989	3019,9981	2201	4299	6500	SO:0001819	synonymous_variant	5536	exon3			GGACTCGCTGGAC		CCDS12684.1	19q13.3	2013-01-10			ENSG00000011485	ENSG00000011485	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	9322	protein-coding gene	gene with protein product		600658		PPP5		8666404	Standard	NM_006247		Approved	PP5	uc002pem.3	P53041	OTTHUMG00000134287	ENST00000012443.4:c.492G>A	19.37:g.46878989G>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	184	67	0.36413	NM_006247	Q16722|Q53XV2	Silent	SNP	ENST00000012443.4	37	CCDS12684.1																																																																																			G|0.628;A|0.372	0.372	strong		0.597	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247	
SLC6A5	9152	hgsc.bcm.edu	37	11	20673867	20673867	+	Silent	SNP	G	G	A	rs2276433	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:20673867G>A	ENST00000525748.1	+	15	2376	c.2103G>A	c.(2101-2103)gaG>gaA	p.E701E	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	701					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)	ACCAGTGGGAGCCCATGACCT	0.468													G|||	2395	0.478235	0.1543	0.5562	5008	,	,		16796	0.8234		0.4414	False		,,,				2504	0.5429				p.E701E		Atlas-SNP	.											.	SLC6A5	151	.	0			c.G2103A						PASS	.	G		816,3590	325.3+/-299.0	71,674,1458	224.0	197.0	206.0		2103	-2.2	1.0	11	dbSNP_100	206	3395,5205	502.8+/-375.8	681,2033,1586	no	coding-synonymous	SLC6A5	NM_004211.3		752,2707,3044	AA,AG,GG		39.4767,18.5202,32.3774		701/798	20673867	4211,8795	2203	4300	6503	SO:0001819	synonymous_variant	9152	exon15			GTGGGAGCCCATG	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.2103G>A	11.37:g.20673867G>A		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			G|0.601;T|0.003	.	strong		0.468	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
FCN2	2220	hgsc.bcm.edu	37	9	137779026	137779026	+	Missense_Mutation	SNP	C	C	T	rs17549193	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:137779026C>T	ENST00000291744.6	+	8	717	c.707C>T	c.(706-708)aCg>aTg	p.T236M	FCN2_ENST00000350339.2_Missense_Mutation_p.T198M	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	236	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		T -> M (in dbSNP:rs17549193).		complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		GATTCCCTGACGTTCCACAAC	0.468													C|||	1246	0.248802	0.3646	0.2493	5008	,	,		24104	0.0665		0.2753	False		,,,				2504	0.2526				p.T236M		Atlas-SNP	.											.	FCN2	55	.	0			c.C707T	GRCh37	CM051922	FCN2	M	rs17549193	PASS	.	C	MET/THR,MET/THR	1500,2906	479.0+/-358.4	252,996,955	161.0	141.0	148.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	707,593	2.1	0.0	9	dbSNP_123	148	2495,6105	409.4+/-349.8	363,1769,2168	yes	missense,missense	FCN2	NM_004108.2,NM_015837.2	81,81	615,2765,3123	TT,TC,CC		29.0116,34.0445,30.7166	benign,benign	236/314,198/276	137779026	3995,9011	2203	4300	6503	SO:0001583	missense	2220	exon8			CCCTGACGTTCCA	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.707C>T	9.37:g.137779026C>T	ENSP00000291744:p.Thr236Met	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	128	54	0.421875	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	528	0.24175824175824176	194	0.3943089430894309	93	0.2569060773480663	29	0.050699300699300696	212	0.2796833773087071	C	9.210	1.030738	0.19512	0.340445	0.290116	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.79247	-1.25;-1.25	4.05	2.06	0.26882	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.557101	0.14767	N	0.299635	T	0.00012	0.0000	M	0.75884	2.315	0.44395	P	0.0026960000000000317	P;P	0.44578	0.838;0.57	B;B	0.30855	0.121;0.1	T	0.11084	-1.0602	9	0.46703	T	0.11	.	6.6263	0.22830	0.1744:0.7225:0.0:0.1031	rs57863140	198;236	Q15485-2;Q15485	.;FCN2_HUMAN	M	198;236	ENSP00000291741:T198M;ENSP00000291744:T236M	ENSP00000291744:T236M	T	+	2	0	FCN2	136918847	0.011000	0.17503	0.023000	0.16930	0.042000	0.13812	0.771000	0.26633	0.628000	0.30357	0.563000	0.77884	ACG	C|0.716;T|0.284	0.284	strong		0.468	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
SMTN	6525	hgsc.bcm.edu	37	22	31491332	31491332	+	Missense_Mutation	SNP	C	C	T	rs5997872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:31491332C>T	ENST00000347557.2	+	12	1894	c.1676C>T	c.(1675-1677)gCg>gTg	p.A559V	SMTN_ENST00000333137.7_Missense_Mutation_p.A559V|SMTN_ENST00000404574.1_Missense_Mutation_p.A158V|SMTN_ENST00000358743.1_Missense_Mutation_p.A559V	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin	559			A -> V (in dbSNP:rs5997872).		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						GCAGTGGAAGCGGCCAATGGG	0.577													C|||	682	0.136182	0.18	0.085	5008	,	,		19766	0.0923		0.167	False		,,,				2504	0.1268				p.A644V		Atlas-SNP	.											.	SMTN	219	.	0			c.C1931T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	773,3633	313.8+/-293.3	67,639,1497	46.0	46.0	46.0		1931,1844,1676,1676,1676	0.3	0.0	22	dbSNP_114	46	1446,7154	276.3+/-292.2	116,1214,2970	yes	missense,missense,missense,missense,missense	SMTN	NM_001207017.1,NM_001207018.1,NM_006932.4,NM_134269.2,NM_134270.2	64,64,64,64,64	183,1853,4467	TT,TC,CC		16.814,17.5443,17.0614	benign,benign,benign,benign,benign	644/1003,615/972,559/918,559/916,559/941	31491332	2219,10787	2203	4300	6503	SO:0001583	missense	6525	exon13			TGGAAGCGGCCAA	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.1676C>T	22.37:g.31491332C>T	ENSP00000328635:p.Ala559Val	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_001207017	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Missense_Mutation	SNP	ENST00000347557.2	37	CCDS13886.1	309	0.14148351648351648	88	0.17886178861788618	42	0.11602209944751381	43	0.07517482517482517	136	0.17941952506596306	C	10.23	1.293795	0.23564	0.175443	0.16814	ENSG00000183963	ENST00000358743;ENST00000347557;ENST00000333137;ENST00000329852;ENST00000404496;ENST00000455608;ENST00000404574;ENST00000403419	T;T;T;T;D	0.92965	0.09;-0.35;-0.35;1.89;-3.14	4.98	0.294	0.15747	.	0.443704	0.16793	N	0.199311	T	0.00412	0.0013	N	0.04880	-0.145	0.80722	P	0.0	B;B;B;B;B;B;B;B	0.14805	0.011;0.002;0.0;0.001;0.004;0.005;0.002;0.008	B;B;B;B;B;B;B;B	0.11329	0.003;0.001;0.001;0.0;0.001;0.003;0.001;0.006	T	0.16837	-1.0389	9	0.09338	T	0.73	0.0324	4.2355	0.10623	0.0:0.4185:0.1659:0.4156	rs5997872;rs56513395;rs59306552;rs5997872	615;644;15;158;582;559;559;559	E7ETT8;B4E229;B5MBZ4;B5MCI0;B5MC56;E7EWD0;P53814;P53814-5	.;.;.;.;.;.;SMTN_HUMAN;.	V	559;559;559;557;582;36;158;15	ENSP00000351593:A559V;ENSP00000328635:A559V;ENSP00000329532:A559V;ENSP00000392329:A36V;ENSP00000383919:A158V	ENSP00000329393:A557V	A	+	2	0	SMTN	29821332	0.019000	0.18553	0.029000	0.17559	0.066000	0.16364	-0.029000	0.12329	0.010000	0.14839	0.561000	0.74099	GCG	C|0.847;T|0.153	0.153	strong		0.577	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
PCK1	5105	hgsc.bcm.edu	37	20	56137834	56137834	+	Silent	SNP	A	A	G	rs1062601	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:56137834A>G	ENST00000319441.4	+	4	653	c.489A>G	c.(487-489)tcA>tcG	p.S163S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.S31S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	163					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)			TGACGGATTCACCCTACGTGG	0.607													A|||	1573	0.314097	0.323	0.3372	5008	,	,		16924	0.0308		0.5229	False		,,,				2504	0.363				p.S163S		Atlas-SNP	.											.	PCK1	95	.	0			c.A489G						PASS	.	A		1505,2901	481.2+/-359.0	228,1049,926	73.0	61.0	65.0		489	-8.8	0.4	20	dbSNP_86	65	4342,4258	580.1+/-391.0	1083,2176,1041	no	coding-synonymous	PCK1	NM_002591.3		1311,3225,1967	GG,GA,AA		49.5116,34.158,44.9562		163/623	56137834	5847,7159	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon4			GGATTCACCCTAC		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.489A>G	20.37:g.56137834A>G		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	103	103	1	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			A|0.609;G|0.391	0.391	strong		0.607	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
JRK	8629	hgsc.bcm.edu	37	8	143746701	143746701	+	RNA	SNP	A	A	G	rs3802232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143746701A>G	ENST00000507178.2	-	0	1109							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ccacccaggcattcccctggg	0.567													G|||	2639	0.526957	0.7179	0.3213	5008	,	,		18708	0.5188		0.3907	False		,,,				2504	0.5634				p.N259N		Atlas-SNP	.											.	.	.	.	0			c.T777C						PASS	.	G	,	1645,1183		507,631,276	14.0	17.0	16.0		777,777	-1.2	0.0	8	dbSNP_107	16	2041,3571		395,1251,1160	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	902,1882,1436	GG,GA,AA		36.3685,41.8317,43.673	,	259/557,259/569	143746701	3686,4754	1414	2806	4220			8629	exon2			CCAGGCATTCCCC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746701A>G		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	23	0.298701	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				A|0.479;G|0.521	0.521	strong		0.567	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956210	18956210	+	Missense_Mutation	SNP	C	C	G	rs139433266		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18956210C>G	ENST00000302797.3	-	1	346	c.122G>C	c.(121-123)gGg>gCg	p.G41A	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	41					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						TCCTGTCAGCCCGACAAGGGA	0.562																																					p.G41A		Atlas-SNP	.											MRGPRX1,NS,carcinoma,-1,1	MRGPRX1	84	1	0			c.G122C						PASS	.	C	ALA/GLY	1,4387		0,1,2193	187.0	176.0	180.0		122	0.3	0.0	11	dbSNP_134	180	1,8571		0,1,4285	no	missense	MRGPRX1	NM_147199.3	60	0,2,6478	GG,GC,CC		0.0117,0.0228,0.0154	possibly-damaging	41/323	18956210	2,12958	2194	4286	6480	SO:0001583	missense	259249	exon1			GTCAGCCCGACAA		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.122G>C	11.37:g.18956210C>G	ENSP00000305766:p.Gly41Ala	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	127	73	0.574803	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	11.92	1.781660	0.31502	2.28E-4	1.17E-4	ENSG00000170255	ENST00000302797	T	0.18016	2.24	2.43	0.304	0.15796	.	0.000000	0.64402	D	0.000005	T	0.19765	0.0475	L	0.52905	1.665	0.09310	N	1	P	0.39003	0.654	P	0.47162	0.54	T	0.09100	-1.0690	10	0.66056	D	0.02	.	4.8899	0.13722	0.2076:0.6607:0.0:0.1317	.	41	Q96LB2	MRGX1_HUMAN	A	41	ENSP00000305766:G41A	ENSP00000305766:G41A	G	-	2	0	MRGPRX1	18912786	0.950000	0.32346	0.000000	0.03702	0.004000	0.04260	2.750000	0.47500	0.075000	0.16796	0.491000	0.48974	GGG	C|1.000;G|0.000	0.000	weak		0.562	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
SAPCD1	401251	hgsc.bcm.edu	37	6	31731881	31731881	+	Missense_Mutation	SNP	C	C	T	rs6905572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31731881C>T	ENST00000425424.1	+	3	355	c.296C>T	c.(295-297)cCg>cTg	p.P99L	SAPCD1_ENST00000415669.2_Missense_Mutation_p.P99L|VWA7_ENST00000467576.1_5'Flank|MSH5_ENST00000534153.4_3'UTR|MSH5-SAPCD1_ENST00000493662.2_3'UTR|SAPCD1-AS1_ENST00000419679.1_RNA			Q5SSQ6	SAPC1_HUMAN	suppressor APC domain containing 1	99			P -> L (in dbSNP:rs6905572).														GGTCGCCCCCCGTTAGCCCAG	0.443													C|||	669	0.133586	0.0772	0.1902	5008	,	,		20266	0.1359		0.1531	False		,,,				2504	0.1472				p.P99L		Atlas-SNP	.											.	.	.	.	0			c.C296T						PASS	.	C	LEU/PRO	359,4047	185.0+/-212.2	14,331,1858	85.0	88.0	87.0		296	-7.6	0.0	6	dbSNP_116	87	1048,7552	220.8+/-258.4	73,902,3325	yes	missense	C6orf26	NM_001039651.1	98	87,1233,5183	TT,TC,CC		12.186,8.148,10.8181	benign	99/179	31731881	1407,11599	2203	4300	6503	SO:0001583	missense	401251	exon3			GCCCCCCGTTAGC		CCDS34411.1	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000228727	ENSG00000228727			13938	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 26"""	C6orf26			Standard	NM_001039651		Approved	NG23		Q5SSQ6	OTTHUMG00000031131	ENST00000425424.1:c.296C>T	6.37:g.31731881C>T	ENSP00000413372:p.Pro99Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	54	0.504673	NM_001039651	A2ABF2|A2ABS9|Q9Y335	Missense_Mutation	SNP	ENST00000425424.1	37		332	0.152014652014652	31	0.06300813008130081	65	0.17955801104972377	107	0.18706293706293706	129	0.17018469656992086	C	6.891	0.533925	0.13188	0.08148	0.12186	ENSG00000228727	ENST00000433778;ENST00000415669;ENST00000425424	T;T	0.78481	-1.18;-1.18	4.98	-7.56	0.01322	.	.	.	.	.	T	0.32102	0.0818	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.15206	-1.0445	7	0.36615	T	0.2	2.3273	1.1891	0.01861	0.2468:0.3675:0.1529:0.2328	rs6905572;rs60684196;rs6905572	99	Q5SSQ6-2	.	L	99	ENSP00000411948:P99L;ENSP00000413372:P99L	ENSP00000411948:P99L	P	+	2	0	C6orf26	31839860	0.002000	0.14202	0.014000	0.15608	0.798000	0.45092	-0.609000	0.05635	-0.842000	0.04195	-1.106000	0.02097	CCG	C|0.879;T|0.121	0.121	strong		0.443	SAPCD1-203	KNOWN	basic	protein_coding	protein_coding		NM_001039651	
COL6A3	1293	hgsc.bcm.edu	37	2	238244923	238244923	+	Silent	SNP	C	C	T	rs11683438	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238244923C>T	ENST00000295550.4	-	40	9272	c.8820G>A	c.(8818-8820)acG>acA	p.T2940T	COL6A3_ENST00000353578.4_Silent_p.T2734T|COL6A3_ENST00000346358.4_Silent_p.T2740T|COL6A3_ENST00000347401.3_Silent_p.T2739T|COL6A3_ENST00000409809.1_Silent_p.T2734T|COL6A3_ENST00000472056.1_Silent_p.T2333T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2940	Ala-rich.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GCTTCGCTGCCGTTGCTGGCT	0.637													C|||	216	0.043131	0.003	0.0432	5008	,	,		17309	0.0089		0.1113	False		,,,				2504	0.0624				p.T2940T		Atlas-SNP	.											.	COL6A3	608	.	0			c.G8820A						PASS	.	C	,,	80,4320		1,78,2121	42.0	51.0	48.0		8820,6999,8202	-4.5	0.0	2	dbSNP_120	48	843,7757		43,757,3500	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	44,835,5621	TT,TC,CC		9.8023,1.8182,7.1	,,	2940/3178,2333/2571,2734/2972	238244923	923,12077	2200	4300	6500	SO:0001819	synonymous_variant	1293	exon40			CGCTGCCGTTGCT	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.8820G>A	2.37:g.238244923C>T		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			C|0.933;G|0.000;T|0.067	0.067	strong		0.637	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
NLRP8	126205	hgsc.bcm.edu	37	19	56467281	56467281	+	Silent	SNP	A	A	G	rs61750024	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56467281A>G	ENST00000291971.3	+	3	1928	c.1857A>G	c.(1855-1857)gaA>gaG	p.E619E	NLRP8_ENST00000590542.1_Silent_p.E619E	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	619					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)		TCCGGGAGGAAGCCTTTGTAA	0.458													A|||	273	0.0545128	0.062	0.0533	5008	,	,		19188	0.005		0.0736	False		,,,				2504	0.0767				p.E619E		Atlas-SNP	.											.	NLRP8	225	.	0			c.A1857G						PASS	.	A		302,4104	164.4+/-196.0	11,280,1912	94.0	88.0	90.0		1857	-2.7	0.1	19	dbSNP_129	90	532,8068	148.2+/-203.4	18,496,3786	no	coding-synonymous	NLRP8	NM_176811.2		29,776,5698	GG,GA,AA		6.186,6.8543,6.4124		619/1049	56467281	834,12172	2203	4300	6503	SO:0001819	synonymous_variant	126205	exon3			GGAGGAAGCCTTT	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.1857A>G	19.37:g.56467281A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			A|0.939;G|0.061	0.061	strong		0.458	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
BDH2	56898	hgsc.bcm.edu	37	4	104013796	104013796	+	Missense_Mutation	SNP	T	T	C	rs1054707	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:104013796T>C	ENST00000296424.4	-	4	329	c.209A>G	c.(208-210)aAt>aGt	p.N70S		NM_020139.3	NP_064524.3	Q9BUT1	BDH2_HUMAN	3-hydroxybutyrate dehydrogenase, type 2	70			N -> S (in dbSNP:rs1054707). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|heme metabolic process (GO:0042168)|iron ion homeostasis (GO:0055072)|siderophore biosynthetic process (GO:0019290)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	3-hydroxybutyrate dehydrogenase activity (GO:0003858)|NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|urinary_tract(1)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.02e-08)		CTCAACTTCATTGGCAAACTG	0.323													T|||	793	0.158347	0.0492	0.1772	5008	,	,		22524	0.1548		0.1501	False		,,,				2504	0.3047				p.N70S		Atlas-SNP	.											.	BDH2	18	.	0			c.A209G						PASS	.	T	SER/ASN	292,4114	156.3+/-189.4	9,274,1920	88.0	89.0	89.0		209	-2.6	0.3	4	dbSNP_86	89	1360,7240	264.3+/-285.5	117,1126,3057	no	missense	BDH2	NM_020139.3	46	126,1400,4977	CC,CT,TT		15.814,6.6273,12.7018	benign	70/246	104013796	1652,11354	2203	4300	6503	SO:0001583	missense	56898	exon4			ACTTCATTGGCAA	AF164790	CCDS3663.1	4q24	2011-09-14			ENSG00000164039	ENSG00000164039	1.1.1.30	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	32389	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 15C, member 1"""		"""dehydrogenase/reductase (SDR family) member 6"""	DHRS6		16380372, 19027726	Standard	XM_005263140		Approved	UCPA-OR, FLJ13261, UNQ6308, PRO20933, SDR15C1	uc003hwz.3	Q9BUT1	OTTHUMG00000074039	ENST00000296424.4:c.209A>G	4.37:g.104013796T>C	ENSP00000296424:p.Asn70Ser	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	238	110	0.462185	NM_020139	A8K295|B4DUF6|Q503A0|Q6IA46|Q6UWD3|Q9H8S8|Q9NRX8	Missense_Mutation	SNP	ENST00000296424.4	37	CCDS3663.1	278	0.12728937728937728	26	0.052845528455284556	61	0.1685082872928177	78	0.13636363636363635	113	0.14907651715039577	T	4.761	0.141483	0.09083	0.066273	0.15814	ENSG00000164039	ENST00000296424;ENST00000504285;ENST00000509245	T;T;D	0.87256	2.0;0.76;-2.23	4.83	-2.62	0.06152	NAD(P)-binding domain (1);	0.583303	0.19930	N	0.102891	T	0.00271	0.0008	N	0.01789	-0.72	0.45995	P	0.0011999999999999789	B	0.02656	0.0	B	0.01281	0.0	T	0.10730	-1.0617	9	0.13470	T	0.59	.	6.0507	0.19785	0.0:0.3221:0.1346:0.5433	rs1054707;rs3195228;rs11734617;rs17215638;rs17844934;rs17857667;rs1054707	70	Q9BUT1	BDH2_HUMAN	S	70	ENSP00000296424:N70S;ENSP00000427442:N70S;ENSP00000422891:N70S	ENSP00000296424:N70S	N	-	2	0	BDH2	104233245	0.972000	0.33761	0.280000	0.24747	0.327000	0.28475	0.038000	0.13862	-0.662000	0.05338	0.459000	0.35465	AAT	T|0.878;C|0.122	0.122	strong		0.323	BDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157159.2	NM_020139	
EHMT1	79813	hgsc.bcm.edu	37	9	140638461	140638461	+	Silent	SNP	T	T	C	rs1129768	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140638461T>C	ENST00000460843.1	+	6	1116	c.1089T>C	c.(1087-1089)ggT>ggC	p.G363G	EHMT1_ENST00000334856.6_Silent_p.G332G|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Silent_p.G363G	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	363					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ACGGCCATGGTGCAGAGCAGG	0.632													C|||	2348	0.46885	0.8744	0.5634	5008	,	,		17397	0.1171		0.3439	False		,,,				2504	0.3446				p.G363G		Atlas-SNP	.											.	EHMT1	196	.	0			c.T1089C						PASS	.	C	,	3443,963	361.1+/-315.5	1344,755,104	70.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1089,1089	-9.9	0.0	9	dbSNP_86	69	3110,5490	658.2+/-401.5	579,1952,1769	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	1923,2707,1873	CC,CT,TT		36.1628,21.8566,49.6156	,	363/809,363/1299	140638461	6553,6453	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon6			CCATGGTGCAGAG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1089T>C	9.37:g.140638461T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	19	0.431818	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			A|0.000;C|0.484;G|0.000;T|0.516	0.484	strong		0.632	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
IGSF22	283284	hgsc.bcm.edu	37	11	18743180	18743180	+	Missense_Mutation	SNP	C	C	G	rs10832975	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18743180C>G	ENST00000513874.1	-	4	419	c.280G>C	c.(280-282)Gcc>Ccc	p.A94P	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	94	Ig-like 1.		A -> P (in dbSNP:rs10832975).							NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						TGGGGTTTGGCGTTCCCCTGC	0.587											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1803	0.360024	0.171	0.5187	5008	,	,		17972	0.3224		0.3897	False		,,,				2504	0.5112				p.A94P		Atlas-SNP	.											IGSF22_ENST00000513874,NS,carcinoma,0,2	IGSF22	211	2	0			c.G280C						PASS	.	G	PRO/ALA	865,3119		102,661,1229	103.0	104.0	104.0		280	4.4	1.0	11	dbSNP_120	104	3270,5036		665,1940,1548	yes	missense	IGSF22	NM_173588.3	27	767,2601,2777	GG,GC,CC		39.3691,21.7118,33.6452	benign	94/1327	18743180	4135,8155	1992	4153	6145	SO:0001583	missense	283284	exon4			GTTTGGCGTTCCC	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.280G>C	11.37:g.18743180C>G	ENSP00000421191:p.Ala94Pro	Somatic	124	0	0	90	WXS	Illumina HiSeq	Phase_I	108	46	0.425926	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	767	0.35119047619047616	92	0.18699186991869918	186	0.5138121546961326	179	0.3129370629370629	310	0.40897097625329815	G	7.324	0.617487	0.14129	0.217118	0.393691	ENSG00000179057	ENST00000513874	T	0.57907	0.37	5.33	4.39	0.52855	.	0.256726	0.20434	N	0.092411	T	0.00012	0.0000	N	0.00025	-2.68	0.52501	P	4.700000000001925E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.49303	-0.8954	9	0.02654	T	1	.	13.1751	0.59621	0.0:0.3071:0.6929:0.0	rs10832975;rs52802422;rs56874939;rs10832975	94	D6RGV7	.	P	94	ENSP00000421191:A94P	ENSP00000322422:A94P	A	-	1	0	IGSF22	18699756	1.000000	0.71417	0.995000	0.50966	0.868000	0.49771	5.417000	0.66423	0.606000	0.29965	-0.120000	0.15030	GCC	C|0.636;G|0.364	0.364	strong		0.587	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
MYH4	4622	hgsc.bcm.edu	37	17	10360854	10360854	+	Missense_Mutation	SNP	C	C	T	rs12949680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:10360854C>T	ENST00000255381.2	-	16	1890	c.1780G>A	c.(1780-1782)Gcc>Acc	p.A594T	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	594	Myosin motor.		A -> T (in dbSNP:rs12949680).		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						AGCCAGCCGGCGATGTTGTAG	0.552													C|||	288	0.057508	0.0401	0.0346	5008	,	,		19095	0.0308		0.0517	False		,,,				2504	0.1309				p.A594T		Atlas-SNP	.											.	MYH4	349	.	0			c.G1780A						PASS	.	C	THR/ALA	195,4211	122.1+/-159.5	4,187,2012	107.0	106.0	107.0		1780	-1.3	0.0	17	dbSNP_121	107	526,8074	146.9+/-202.4	16,494,3790	no	missense	MYH4	NM_017533.2	58	20,681,5802	TT,TC,CC		6.1163,4.4258,5.5436	benign	594/1940	10360854	721,12285	2203	4300	6503	SO:0001583	missense	4622	exon16			AGCCGGCGATGTT		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.1780G>A	17.37:g.10360854C>T	ENSP00000255381:p.Ala594Thr	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	157	72	0.458599	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	103	0.04716117216117216	21	0.042682926829268296	16	0.04419889502762431	20	0.03496503496503497	46	0.06068601583113457	C	0.007	-1.979767	0.00448	0.044258	0.061163	ENSG00000141048	ENST00000255381	D	0.86432	-2.12	5.01	-1.26	0.09376	Myosin head, motor domain (2);	1.090020	0.07356	U	0.883241	T	0.10895	0.0266	N	0.00282	-1.705	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48536	-0.9027	10	0.02654	T	1	.	5.3299	0.15926	0.2266:0.211:0.0:0.5624	rs12949680	594	Q9Y623	MYH4_HUMAN	T	594	ENSP00000255381:A594T	ENSP00000255381:A594T	A	-	1	0	MYH4	10301579	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-0.206000	0.09398	-0.060000	0.13132	-0.291000	0.09656	GCC	C|0.945;T|0.055	0.055	strong		0.552	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
SEC16A	9919	hgsc.bcm.edu	37	9	139371405	139371405	+	Silent	SNP	G	G	C	rs11999532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139371405G>C	ENST00000371706.3	-	1	162	c.129C>G	c.(127-129)ggC>ggG	p.G43G	SEC16A_ENST00000431893.2_Silent_p.G43G|SEC16A_ENST00000313050.7_Silent_p.G221G|SEC16A_ENST00000290037.6_Silent_p.G43G			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	43					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)		AGGGCTGTGGGCCTCCCTGCA	0.657													G|||	680	0.135783	0.0454	0.2565	5008	,	,		18378	0.0536		0.2535	False		,,,				2504	0.136				p.G221G		Atlas-SNP	.											.	SEC16A	249	.	0			c.C663G						PASS	.	G		329,3933		13,303,1815	26.0	30.0	29.0		663	1.9	0.0	9	dbSNP_120	29	2197,6261		283,1631,2315	no	coding-synonymous	SEC16A	NM_014866.1		296,1934,4130	CC,CG,GG		25.9754,7.7194,19.8585		221/2358	139371405	2526,10194	2131	4229	6360	SO:0001819	synonymous_variant	9919	exon3			CTGTGGGCCTCCC	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.129C>G	9.37:g.139371405G>C		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.846;C|0.154	0.154	strong		0.657	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
ZNF385B	151126	hgsc.bcm.edu	37	2	180309622	180309622	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:180309622C>T	ENST00000410066.1	-	9	1781	c.1178G>A	c.(1177-1179)cGg>cAg	p.R393Q	ZNF385B_ENST00000409692.1_Missense_Mutation_p.R291Q|ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Missense_Mutation_p.R317Q|ZNF385B_ENST00000336917.5_Missense_Mutation_p.R291Q	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	393	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			ACTCGGGCTCCGCTGGAGTTT	0.502																																					p.R393Q	Colon(155;204 2491 32774 51842)	Atlas-SNP	.											ZNF385B,NS,carcinoma,-1,2	ZNF385B	68	2	0			c.G1178A						scavenged	.						235.0	229.0	231.0					2																	180309622		2203	4300	6503	SO:0001583	missense	151126	exon9			GGGCTCCGCTGGA	AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"""zinc finger protein 533"""	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.1178G>A	2.37:g.180309622C>T	ENSP00000386845:p.Arg393Gln	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	147	3	0.0204082	NM_152520	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	37	CCDS33339.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690674	0.88735	.	.	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692	T;T;T;T	0.33438	1.41;1.44;1.42;1.44	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.50222	0.1603	L	0.42245	1.32	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.81914	0.988;0.995	T	0.42015	-0.9476	10	0.49607	T	0.09	-13.0643	19.4571	0.94897	0.0:1.0:0.0:0.0	.	393;317	Q569K4;Q569K4-2	Z385B_HUMAN;.	Q	393;291;317;291	ENSP00000386845:R393Q;ENSP00000338225:R291Q;ENSP00000386379:R317Q;ENSP00000386507:R291Q	ENSP00000338225:R291Q	R	-	2	0	ZNF385B	180017867	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	4.829000	0.62737	2.597000	0.87782	0.557000	0.71058	CGG	.	.	none		0.502	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520	
SEC61A2	55176	hgsc.bcm.edu	37	10	12191933	12191933	+	Silent	SNP	C	C	T	rs10466280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:12191933C>T	ENST00000298428.9	+	6	524	c.435C>T	c.(433-435)gcC>gcT	p.A145A	SEC61A2_ENST00000379017.3_Silent_p.A145A|SEC61A2_ENST00000379020.4_Silent_p.A145A|SEC61A2_ENST00000379051.1_Silent_p.A145A|SEC61A2_ENST00000304267.8_Silent_p.A145A|SEC61A2_ENST00000379033.3_Silent_p.A123A|SEC61A2_ENST00000495368.1_3'UTR	NM_018144.3	NP_060614.2	Q9H9S3	S61A2_HUMAN	Sec61 alpha 2 subunit (S. cerevisiae)	145					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ribosome binding (GO:0043022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Renal(717;0.228)				AAATGGGTGCCGGAATCTGTC	0.418													C|||	2125	0.424321	0.41	0.4986	5008	,	,		19774	0.5258		0.4056	False		,,,				2504	0.3057				p.A145A		Atlas-SNP	.											.	SEC61A2	48	.	0			c.C435T						PASS	.	C	,,	1844,2562	538.7+/-375.1	401,1042,760	142.0	137.0	139.0		435,369,435	-3.7	0.9	10	dbSNP_119	139	3583,5017	519.1+/-379.4	736,2111,1453	no	coding-synonymous,coding-synonymous,coding-synonymous	SEC61A2	NM_001142627.1,NM_001142628.1,NM_018144.3	,,	1137,3153,2213	TT,TC,CC		41.6628,41.852,41.7269	,,	145/438,123/455,145/477	12191933	5427,7579	2203	4300	6503	SO:0001819	synonymous_variant	55176	exon6			GGGTGCCGGAATC	AF346603	CCDS7088.1, CCDS44358.1, CCDS44359.1	10p14	2004-01-06			ENSG00000065665	ENSG00000065665			17702	protein-coding gene	gene with protein product							Standard	NM_018144		Approved	FLJ10578	uc001ile.2	Q9H9S3	OTTHUMG00000017679	ENST00000298428.9:c.435C>T	10.37:g.12191933C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_001142627	A8K8D0|B4DX72|F8W773	Silent	SNP	ENST00000298428.9	37	CCDS7088.1	963	0.4409340659340659	184	0.37398373983739835	165	0.4558011049723757	295	0.5157342657342657	319	0.420844327176781	C	5.271	0.235421	0.10023	0.41852	0.416628	ENSG00000065665	ENST00000418772;ENST00000419021	.	.	.	5.07	-3.7	0.04437	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44636	-0.9315	3	.	.	.	-10.1484	6.6785	0.23108	0.1062:0.2462:0.0:0.6476	rs10466280;rs17558441;rs17845804;rs17858766;rs61561401;rs10466280	.	.	.	W	91;27	.	.	R	+	1	2	SEC61A2	12231939	0.942000	0.31987	0.874000	0.34290	0.562000	0.35680	-0.009000	0.12765	-1.051000	0.03226	-1.402000	0.01139	CGG	C|0.580;T|0.420	0.420	strong		0.418	SEC61A2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046795.1	NM_018144	
ADAM32	203102	hgsc.bcm.edu	37	8	39141120	39141120	+	Missense_Mutation	SNP	C	C	A	rs28705715	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39141120C>A	ENST00000379907.4	+	24	2461	c.2334C>A	c.(2332-2334)gaC>gaA	p.D778E	ADAM32_ENST00000524303.1_3'UTR|ADAM32_ENST00000437682.2_Missense_Mutation_p.D679E|ADAM32_ENST00000519315.1_Missense_Mutation_p.D620E	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	778			D -> E (in dbSNP:rs28705715).			integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			AATCACAGGACAGTACCCAAA	0.269													A|||	648	0.129393	0.4357	0.0375	5008	,	,		14029	0.0377		0.006	False		,,,				2504	0.002				p.D778E		Atlas-SNP	.											.	ADAM32	70	.	0			c.C2334A						PASS	.	A	GLU/ASP	1238,2366		234,770,798	67.0	69.0	69.0		2334	2.8	0.2	8	dbSNP_125	69	32,8104		1,30,4037	yes	missense	ADAM32	NM_145004.5	45	235,800,4835	AA,AC,CC		0.3933,34.3507,10.8177	benign	778/788	39141120	1270,10470	1802	4068	5870	SO:0001583	missense	203102	exon24			ACAGGACAGTACC	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.2334C>A	8.37:g.39141120C>A	ENSP00000369238:p.Asp778Glu	Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	195	116	0.594872	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	37	CCDS47846.1	236	0.10805860805860806	201	0.40853658536585363	14	0.03867403314917127	18	0.03146853146853147	3	0.00395778364116095	A	1.791	-0.479607	0.04383	0.343507	0.003933	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	D;D;D	0.87256	-2.18;-2.23;-2.18	3.99	2.85	0.33270	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.16541	-1.0399	8	0.02654	T	1	.	4.1598	0.10278	0.6831:0.2098:0.1071:0.0	rs28705715	679;150;620;778	E7EPX8;Q6ZP86;E7ER82;Q8TC27	.;.;.;ADA32_HUMAN	E	679;620;778	ENSP00000405978:D679E;ENSP00000429422:D620E;ENSP00000369238:D778E	ENSP00000369238:D778E	D	+	3	2	ADAM32	39260277	0.000000	0.05858	0.152000	0.22495	0.456000	0.32438	-0.152000	0.10159	0.373000	0.24621	-0.256000	0.11100	GAC	C|0.914;A|0.086	0.086	strong		0.269	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
ZNF585B	92285	hgsc.bcm.edu	37	19	37677748	37677748	+	Missense_Mutation	SNP	T	T	A	rs45626541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37677748T>A	ENST00000532828.2	-	5	942	c.691A>T	c.(691-693)Ata>Tta	p.I231L	ZNF585B_ENST00000531805.1_Missense_Mutation_p.I176L|CTC-454I21.3_ENST00000585860.2_Intron|ZNF585B_ENST00000527838.1_3'UTR|ZNF585B_ENST00000312908.5_5'UTR	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	231					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTCTCATGTATACTGAGATCT	0.393													T|||	1388	0.277157	0.3268	0.3876	5008	,	,		19250	0.0883		0.3579	False		,,,				2504	0.2434				p.I231L	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A691T						PASS	.	T	LEU/ILE	1570,2836	484.8+/-360.1	265,1040,898	122.0	119.0	120.0		691	0.2	0.0	19	dbSNP_127	120	3054,5546	463.1+/-365.9	519,2016,1765	yes	missense	ZNF585B	NM_152279.3	5	784,3056,2663	AA,AT,TT		35.5116,35.6332,35.5528	benign	231/770	37677748	4624,8382	2203	4300	6503	SO:0001583	missense	92285	exon5			CATGTATACTGAG	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.691A>T	19.37:g.37677748T>A	ENSP00000433773:p.Ile231Leu	Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	201	91	0.452736	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	609	0.27884615384615385	149	0.30284552845528456	128	0.35359116022099446	46	0.08041958041958042	286	0.37730870712401055	T	6.677	0.493463	0.12702	0.356332	0.355116	ENSG00000245680	ENST00000531805;ENST00000532828	T;T	0.17854	2.25;2.25	2.78	0.175	0.15045	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.194135	0.25058	N	0.033472	T	0.00012	0.0000	N	0.08118	0	0.58432	P	2.9999999999752447E-6	B;B	0.21688	0.033;0.059	B;B	0.22753	0.018;0.041	T	0.49818	-0.8899	9	0.27082	T	0.32	.	8.6099	0.33795	0.0:0.0:0.3604:0.6396	rs45626541	176;231	E9PQH3;Q52M93	.;Z585B_HUMAN	L	176;231	ENSP00000436774:I176L;ENSP00000433773:I231L	ENSP00000436774:I176L	I	-	1	0	ZNF585B	42369588	0.000000	0.05858	0.037000	0.18230	0.926000	0.56050	-2.382000	0.01064	0.265000	0.21872	0.374000	0.22700	ATA	T|0.676;A|0.324	0.324	strong		0.393	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
PDGFRL	5157	hgsc.bcm.edu	37	8	17447018	17447018	+	Missense_Mutation	SNP	C	C	A	rs374832042		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17447018C>A	ENST00000541323.1	+	3	542	c.97C>A	c.(97-99)Cca>Aca	p.P33T	PDGFRL_ENST00000398074.3_Missense_Mutation_p.P33T|PDGFRL_ENST00000251630.6_Missense_Mutation_p.P33T	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	33					G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		TCCAAAAGAACCAGGAGAGAA	0.433																																					p.P33T		Atlas-SNP	.											.	PDGFRL	27	.	0			c.C97A						PASS	.	C	THR/PRO	0,4406		0,0,2203	146.0	148.0	147.0		97	4.5	0.9	8		147	1,8599	1.2+/-3.3	0,1,4299	no	missense	PDGFRL	NM_006207.2	38	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	33/376	17447018	1,13005	2203	4300	6503	SO:0001583	missense	5157	exon3			AAAGAACCAGGAG	D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8805	protein-coding gene	gene with protein product		604584					Standard	NM_006207		Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.97C>A	8.37:g.17447018C>A	ENSP00000444211:p.Pro33Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	31	21	0.677419	NM_006207	A8K085|Q6FH04	Missense_Mutation	SNP	ENST00000541323.1	37	CCDS6003.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.737518	0.30774	0.0	1.16E-4	ENSG00000104213	ENST00000251630;ENST00000541323;ENST00000398074	T;T;T	0.32272	1.46;1.46;1.46	4.52	4.52	0.55395	.	0.256475	0.39146	N	0.001451	T	0.32102	0.0818	L	0.56769	1.78	0.32797	N	0.500418	B	0.27559	0.181	B	0.26969	0.075	T	0.37174	-0.9717	10	0.22706	T	0.39	-18.4186	17.8077	0.88606	0.0:1.0:0.0:0.0	.	33	Q15198	PGFRL_HUMAN	T	33	ENSP00000251630:P33T;ENSP00000444211:P33T;ENSP00000381149:P33T	ENSP00000251630:P33T	P	+	1	0	PDGFRL	17491278	0.996000	0.38824	0.943000	0.38184	0.677000	0.39632	2.992000	0.49417	2.503000	0.84419	0.591000	0.81541	CCA	.	.	weak		0.433	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207	
MYH10	4628	hgsc.bcm.edu	37	17	8455419	8455419	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8455419T>C	ENST00000269243.4	-	8	972	c.834A>G	c.(832-834)gaA>gaG	p.E278E	MYH10_ENST00000379980.4_Silent_p.E294E|MYH10_ENST00000360416.3_Silent_p.E288E|MYH10_ENST00000396239.1_Silent_p.E278E	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	278	Myosin motor.				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						GAAAAGTACGTTCATCTTTTG	0.308																																					p.E288E		Atlas-SNP	.											.	MYH10	148	.	0			c.A864G						PASS	.						48.0	49.0	49.0					17																	8455419		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			AGTACGTTCATCT	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.834A>G	17.37:g.8455419T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	131	6	0.0458015	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.	.	none		0.308	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
IFT81	28981	hgsc.bcm.edu	37	12	110600841	110600841	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:110600841G>C	ENST00000242591.5	+	11	1665	c.1159G>C	c.(1159-1161)Gat>Cat	p.D387H	IFT81_ENST00000552912.1_Missense_Mutation_p.D387H|IFT81_ENST00000361948.4_Missense_Mutation_p.D387H|IFT81_ENST00000549009.1_3'UTR	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	387					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						CCGTGAATTTGATGGTACTGA	0.413																																					p.D387H		Atlas-SNP	.											.	IFT81	86	.	0			c.G1159C						PASS	.						131.0	124.0	126.0					12																	110600841		2203	4300	6503	SO:0001583	missense	28981	exon11			GAATTTGATGGTA	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.1159G>C	12.37:g.110600841G>C	ENSP00000242591:p.Asp387His	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	37	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756569	0.49362	.	.	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	T	0.30714	1.52	5.42	5.42	0.78866	.	0.356693	0.31601	N	0.007377	T	0.32010	0.0815	L	0.50333	1.59	0.80722	D	1	B;P	0.46220	0.343;0.874	B;B	0.44224	0.398;0.444	T	0.03773	-1.1005	10	0.45353	T	0.12	-5.4288	11.8083	0.52169	0.0804:0.0:0.9196:0.0	.	387;387	Q8WYA0;Q8WYA0-3	IFT81_HUMAN;.	H	387;387;387;357	ENSP00000355372:D387H	ENSP00000242591:D387H	D	+	1	0	IFT81	109085224	1.000000	0.71417	0.621000	0.29145	0.917000	0.54804	6.328000	0.72915	2.553000	0.86117	0.655000	0.94253	GAT	.	.	none		0.413	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055	
OR8B4	283162	hgsc.bcm.edu	37	11	124294236	124294236	+	Missense_Mutation	SNP	A	A	G	rs4057749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124294236A>G	ENST00000356130.3	-	1	553	c.532T>C	c.(532-534)Tgt>Cgt	p.C178R		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	178			C -> R (in dbSNP:rs4057749). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		AGAACGTCACACAGATAATGG	0.507													A|||	1410	0.28155	0.4637	0.196	5008	,	,		21494	0.2163		0.1988	False		,,,				2504	0.2485				p.C178R		Atlas-SNP	.											.	OR8B4	60	.	0			c.T532C						PASS	.	A	ARG/CYS	1714,2688	514.1+/-368.5	337,1040,824	92.0	63.0	73.0		532	4.0	1.0	11	dbSNP_108	73	1966,6632	344.6+/-325.4	219,1528,2552	yes	missense	OR8B4	NM_001005196.1	180	556,2568,3376	GG,GA,AA		22.8658,38.9368,28.3077	probably-damaging	178/310	124294236	3680,9320	2201	4299	6500	SO:0001583	missense	283162	exon1			CGTCACACAGATA	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.532T>C	11.37:g.124294236A>G	ENSP00000348449:p.Cys178Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	111	111	1	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	580	0.26556776556776557	249	0.5060975609756098	71	0.19613259668508287	107	0.18706293706293706	153	0.20184696569920843	a	16.05	3.011484	0.54468	0.389368	0.228658	ENSG00000198657	ENST00000356130	T	0.62498	0.02	4.02	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000019	T	0.00012	0.0000	H	0.96048	3.76	0.09310	P	0.9999999884866	D	0.89917	1.0	D	0.81914	0.995	T	0.38499	-0.9658	9	0.72032	D	0.01	.	13.7135	0.62682	1.0:0.0:0.0:0.0	rs4057749;rs4057749	178	Q96RC9	OR8B4_HUMAN	R	178	ENSP00000348449:C178R	ENSP00000348449:C178R	C	-	1	0	OR8B4	123799446	1.000000	0.71417	1.000000	0.80357	0.486000	0.33341	7.016000	0.76393	2.070000	0.61991	0.529000	0.55759	TGT	A|0.720;G|0.280	0.280	strong		0.507	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
TRPM2	7226	hgsc.bcm.edu	37	21	45826486	45826486	+	Missense_Mutation	SNP	G	G	A	rs56379273	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45826486G>A	ENST00000397928.1	+	19	3245	c.2800G>A	c.(2800-2802)Gtc>Atc	p.V934I	TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300482.5_Missense_Mutation_p.V934I|TRPM2_ENST00000397932.2_Missense_Mutation_p.V934I|TRPM2_ENST00000300481.9_Missense_Mutation_p.V914I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	934					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GATGAAGGACGTCTTCTTCTT	0.627													g|||	30	0.00599042	0.0015	0.0086	5008	,	,		16988	0.0		0.0199	False		,,,				2504	0.002				p.V934I		Atlas-SNP	.											.	TRPM2	196	.	0			c.G2800A						PASS	.	G	ILE/VAL	12,4372	21.2+/-45.6	0,12,2180	41.0	39.0	40.0		2800	3.2	1.0	21	dbSNP_129	40	133,8439	66.7+/-129.0	0,133,4153	yes	missense	TRPM2	NM_003307.3	29	0,145,6333	AA,AG,GG		1.5516,0.2737,1.1192	possibly-damaging	934/1504	45826486	145,12811	2192	4286	6478	SO:0001583	missense	7226	exon19			AAGGACGTCTTCT	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2800G>A	21.37:g.45826486G>A	ENSP00000381023:p.Val934Ile	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	g	12.27	1.888364	0.33348	0.002737	0.015516	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	4.12	3.23	0.37069	Ion transport (1);	0.453240	0.21370	N	0.075647	T	0.49558	0.1564	L	0.41632	1.29	0.37070	D	0.898505	B;B;B	0.24043	0.096;0.056;0.056	B;B;B	0.19391	0.025;0.025;0.025	T	0.63382	-0.6650	10	0.62326	D	0.03	-29.5505	12.4046	0.55432	0.0842:0.0:0.9158:0.0	rs56379273	934;720;934	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	I	934;934;914;934	ENSP00000300482:V934I;ENSP00000381023:V934I;ENSP00000300481:V914I;ENSP00000381026:V934I	ENSP00000300481:V914I	V	+	1	0	TRPM2	44650914	0.998000	0.40836	1.000000	0.80357	0.981000	0.71138	2.350000	0.44063	0.861000	0.35504	0.536000	0.68110	GTC	G|0.988;A|0.012	0.012	strong		0.627	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
MYOM1	8736	hgsc.bcm.edu	37	18	3164385	3164385	+	Silent	SNP	C	C	T	rs11659820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:3164385C>T	ENST00000356443.4	-	10	1725	c.1392G>A	c.(1390-1392)cgG>cgA	p.R464R	MYOM1_ENST00000400569.3_Silent_p.R464R|MYOM1_ENST00000261606.7_Silent_p.R464R	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	464	Ig-like C2-type 2.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TCAGCGTTGCCCGCTCTCCAC	0.363													C|||	845	0.16873	0.2549	0.1744	5008	,	,		17303	0.0079		0.2366	False		,,,				2504	0.1442				p.R464R		Atlas-SNP	.											.	MYOM1	192	.	0			c.G1392A						PASS	.	C	,	1026,3042		131,764,1139	63.0	62.0	62.0		1392,1392	1.6	1.0	18	dbSNP_120	62	1743,6671		177,1389,2641	no	coding-synonymous,coding-synonymous	MYOM1	NM_003803.3,NM_019856.1	,	308,2153,3780	TT,TC,CC		20.7155,25.2212,22.1839	,	464/1686,464/1590	3164385	2769,9713	2034	4207	6241	SO:0001819	synonymous_variant	8736	exon10			CGTTGCCCGCTCT	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.1392G>A	18.37:g.3164385C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	106	51	0.481132	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			C|0.820;T|0.180	0.180	strong		0.363	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
GSPT1	2935	hgsc.bcm.edu	37	16	11981487	11981487	+	Silent	SNP	G	G	A	rs3752426	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:11981487G>A	ENST00000563468.1	-	5	509	c.483C>T	c.(481-483)ggC>ggT	p.G161G	GSPT1_ENST00000420576.2_Silent_p.G161G|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000439887.2_Silent_p.G298G|GSPT1_ENST00000434724.2_Silent_p.G299G|GSPT1_ENST00000564790.1_5'Flank			P15170	ERF3A_HUMAN	G1 to S phase transition 1	161	G3. {ECO:0000255|PROSITE- ProRule:PRU01059}.|tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				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						AACTCTTGTGGCCAGGGGCAT	0.423													G|||	601	0.120008	0.0257	0.2075	5008	,	,		16284	0.0109		0.3211	False		,,,				2504	0.091				p.G299G		Atlas-SNP	.											.	GSPT1	71	.	0			c.C897T						PASS	.	G	,,	335,4057	157.0+/-190.0	14,307,1875	148.0	152.0	151.0		894,483,897	2.3	1.0	16	dbSNP_107	151	2912,5684	447.6+/-361.6	475,1962,1861	no	coding-synonymous,coding-synonymous,coding-synonymous	GSPT1	NM_001130006.1,NM_001130007.1,NM_002094.3	,,	489,2269,3736	AA,AG,GG		33.8762,7.6275,25.0	,,	298/637,161/500,299/638	11981487	3247,9741	2196	4298	6494	SO:0001819	synonymous_variant	2935	exon7			CTTGTGGCCAGGG	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		ENST00000563468.1:c.483C>T	16.37:g.11981487G>A		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	188	188	1	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	37	CCDS45414.1																																																																																			G|0.830;A|0.170	0.170	strong		0.423	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094	
TRIM16	10626	hgsc.bcm.edu	37	17	15532147	15532147	+	Missense_Mutation	SNP	G	G	A	rs3174720	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:15532147G>A	ENST00000578237.1	-	11	2332	c.1477C>T	c.(1477-1479)Cgg>Tgg	p.R493W	TRIM16_ENST00000577886.1_Missense_Mutation_p.R277W|TRIM16_ENST00000336708.7_Missense_Mutation_p.R493W|TRIM16_ENST00000416464.2_Missense_Mutation_p.R363W|RP11-385D13.1_ENST00000455584.2_Intron|TRIM16_ENST00000579219.1_3'UTR			O95361	TRI16_HUMAN	tripartite motif containing 16	493	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> W (in dbSNP:rs3174720).		histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		CCGAGCCTCCGGAAAGGGCCA	0.527													G|||	98	0.0195687	0.0045	0.0086	5008	,	,		18681	0.006		0.0497	False		,,,				2504	0.0307				p.R493W		Atlas-SNP	.											.	TRIM16	45	.	0			c.C1477T						PASS	.	G	TRP/ARG	31,4375		0,31,2172	70.0	72.0	71.0		1477	2.7	0.2	17	dbSNP_105	71	419,8181		9,401,3890	no	missense	TRIM16	NM_006470.3	101	9,432,6062	AA,AG,GG		4.8721,0.7036,3.4599		493/565	15532147	450,12556	2203	4300	6503	SO:0001583	missense	10626	exon9			GCCTCCGGAAAGG	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.1477C>T	17.37:g.15532147G>A	ENSP00000463188:p.Arg493Trp	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	176	76	0.431818	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Missense_Mutation	SNP	ENST00000578237.1	37	CCDS11171.1	57	0.0260989010989011	5	0.01016260162601626	5	0.013812154696132596	6	0.01048951048951049	41	0.05408970976253298	.	14.47	2.544951	0.45280	0.007036	0.048721	ENSG00000221926	ENST00000336708;ENST00000416464	T;T	0.71341	-0.56;-0.56	4.72	2.66	0.31614	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.30947	0.0781	L	0.46567	1.45	0.29882	N	0.825973	D;D	0.71674	0.998;0.998	P;P	0.54174	0.744;0.744	T	0.52275	-0.8597	9	0.52906	T	0.07	.	7.3077	0.26457	0.0919:0.0:0.7349:0.1732	rs3174720;rs16941148	363;493	B3KP96;O95361	.;TRI16_HUMAN	W	493;363	ENSP00000338989:R493W;ENSP00000399918:R363W	ENSP00000338989:R493W	R	-	1	2	TRIM16	15472872	0.878000	0.30173	0.167000	0.22817	0.266000	0.26442	1.250000	0.32850	0.485000	0.27652	0.650000	0.86243	CGG	G|0.971;A|0.029	0.029	strong		0.527	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
SCAMP3	10067	hgsc.bcm.edu	37	1	155230131	155230131	+	Silent	SNP	C	C	T	rs1142287	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155230131C>T	ENST00000302631.3	-	4	485	c.378G>A	c.(376-378)ggG>ggA	p.G126G	SCAMP3_ENST00000355379.3_Silent_p.G100G|CLK2_ENST00000497188.1_5'Flank|SCAMP3_ENST00000472397.1_5'UTR	NM_005698.3	NP_005689.2	O14828	SCAM3_HUMAN	secretory carrier membrane protein 3	126					post-Golgi vesicle-mediated transport (GO:0006892)|protein transport (GO:0015031)|response to retinoic acid (GO:0032526)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|large_intestine(3)|lung(7)|ovary(4)|urinary_tract(1)	19	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TAGCTGTGCCCCCCAGGGCAG	0.592													C|||	2263	0.451877	0.5416	0.3199	5008	,	,		20022	0.6944		0.2753	False		,,,				2504	0.3558				p.G126G		Atlas-SNP	.											.	SCAMP3	33	.	0			c.G378A						PASS	.	C	,	2359,2047		635,1089,479	86.0	84.0	85.0	http://www.ncbi.nlm.nih.gov/pubmed?term	378,300	-1.6	0.4	1	dbSNP_86	85	2253,6347		306,1641,2353	yes	coding-synonymous,coding-synonymous	SCAMP3	NM_005698.3,NM_052837.2	,	941,2730,2832	TT,TC,CC	http://www.ncbi.nlm.nih.gov/pubmed?term	26.1977,46.4594,35.4606	,	126/348,100/322	155230131	4612,8394	2203	4300	6503	SO:0001819	synonymous_variant	10067	exon4			TGTGCCCCCCAGG	AF005039	CCDS1105.1, CCDS1106.1	1q21	2013-02-21			ENSG00000116521	ENSG00000116521		"""Secretory carrier membrane proteins"""	10565	protein-coding gene	gene with protein product	"""Propin 1"""	606913		C1orf3		9331372, 9658162	Standard	NM_005698		Approved		uc001fjs.3	O14828	OTTHUMG00000035874	ENST00000302631.3:c.378G>A	1.37:g.155230131C>T		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	36	0.62069	NM_005698	A9Z1W6|B1AVS6|O15128|Q96FR8|Q9BPY0	Silent	SNP	ENST00000302631.3	37	CCDS1105.1																																																																																			C|0.584;T|0.416	0.416	strong		0.592	SCAMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087399.1	NM_005698	
CCDC108	255101	hgsc.bcm.edu	37	2	219900300	219900300	+	Silent	SNP	A	A	C	rs77746575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219900300A>C	ENST00000341552.5	-	5	527	c.444T>G	c.(442-444)gcT>gcG	p.A148A	CCDC108_ENST00000324264.6_Silent_p.A83A|CCDC108_ENST00000441968.1_Silent_p.A148A|CCDC108_ENST00000409865.3_Silent_p.A137A|CCDC108_ENST00000453220.1_Silent_p.A148A|CCDC108_ENST00000295729.2_Silent_p.A83A|CCDC108_ENST00000410037.1_Silent_p.A83A	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	148						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCAGCTCCTCAGCCACCTCAA	0.517													A|||	2	0.000399361	0.0	0.0	5008	,	,		18210	0.0		0.002	False		,,,				2504	0.0				p.A148A		Atlas-SNP	.											CCDC108_ENST00000295729,colon,carcinoma,-2,2	CCDC108	208	2	0			c.T444G						PASS	.	A	,	0,4406		0,0,2203	167.0	151.0	156.0		249,444	-10.8	0.0	2	dbSNP_132	156	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	CCDC108	NM_152389.2,NM_194302.2	,	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	,	83/165,148/1926	219900300	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	255101	exon5			CTCCTCAGCCACC	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.444T>G	2.37:g.219900300A>C		Somatic	277	1	0.00361011		WXS	Illumina HiSeq	Phase_I	310	150	0.483871	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	37	CCDS2430.2																																																																																			A|0.999;C|0.001	0.001	strong		0.517	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
TARSL2	123283	hgsc.bcm.edu	37	15	102264476	102264476	+	Missense_Mutation	SNP	C	C	A	rs1143136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:102264476C>A	ENST00000335968.3	-	1	331	c.115G>T	c.(115-117)Gcg>Tcg	p.A39S		NM_152334.2	NP_689547.2	A2RTX5	SYTC2_HUMAN	threonyl-tRNA synthetase-like 2	39					threonyl-tRNA aminoacylation (GO:0006435)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(14)|ovary(2)|skin(1)|urinary_tract(1)	29	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000268)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CTGTAGGGCGCGTTCAGCTGC	0.746													C|||	963	0.192292	0.2897	0.2853	5008	,	,		9080	0.0099		0.2237	False		,,,				2504	0.1503				p.A39S		Atlas-SNP	.											.	TARSL2	63	.	0			c.G115T						PASS	.	C	SER/ALA	763,2699		89,585,1057	6.0	6.0	6.0		115	2.3	0.2	15	dbSNP_86	6	1417,5697		175,1067,2315	yes	missense	TARSL2	NM_152334.2	99	264,1652,3372	AA,AC,CC		19.9185,22.0393,20.6127	benign	39/803	102264476	2180,8396	1731	3557	5288	SO:0001583	missense	123283	exon1			AGGGCGCGTTCAG	AL833188	CCDS10394.1	15q26.3	2008-02-05			ENSG00000185418	ENSG00000185418			24728	protein-coding gene	gene with protein product							Standard	NM_152334		Approved	FLJ25005	uc002bxm.3	A2RTX5	OTTHUMG00000149869	ENST00000335968.3:c.115G>T	15.37:g.102264476C>A	ENSP00000338093:p.Ala39Ser	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_152334	B2RMP7|Q6B0A1|Q6IS76|Q96LW3|Q96MP4	Missense_Mutation	SNP	ENST00000335968.3	37	CCDS10394.1	442	0.20238095238095238	155	0.3150406504065041	103	0.2845303867403315	6	0.01048951048951049	178	0.23482849604221637	.	10.09	1.254065	0.22965	0.220393	0.199185	ENSG00000185418	ENST00000335968;ENST00000333018;ENST00000539112	.	.	.	3.28	2.33	0.28932	.	1.372480	0.04874	N	0.446500	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.27732	0.187	B	0.21151	0.033	T	0.18745	-1.0327	8	0.45353	T	0.12	-0.7096	7.7599	0.28946	0.2501:0.7499:0.0:0.0	rs1143136;rs58456433	39	A2RTX5	SYTC2_HUMAN	S	39	.	ENSP00000329291:A39S	A	-	1	0	TARSL2	100081999	0.256000	0.24012	0.208000	0.23602	0.288000	0.27193	0.678000	0.25277	0.708000	0.31955	0.298000	0.19748	GCG	C|0.794;A|0.206	0.206	strong		0.746	TARSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313619.3	NM_152334	
SETD6	79918	hgsc.bcm.edu	37	16	58550386	58550386	+	Missense_Mutation	SNP	G	G	A	rs147467868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58550386G>A	ENST00000219315.4	+	4	531	c.481G>A	c.(481-483)Gag>Aag	p.E161K	SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000310682.2_Missense_Mutation_p.E137K|SETD6_ENST00000394266.4_Intron			Q8TBK2	SETD6_HUMAN	SET domain containing 6	161	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						CTGCAGGCCAGAGGAGGAGCG	0.617													G|||	3	0.000599042	0.0	0.0014	5008	,	,		14632	0.0		0.002	False		,,,				2504	0.0				p.E161K		Atlas-SNP	.											.	SETD6	27	.	0			c.G481A						PASS	.	G	LYS/GLU,LYS/GLU	0,4396		0,0,2198	78.0	92.0	87.0		481,409	3.4	1.0	16	dbSNP_134	87	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	SETD6	NM_001160305.1,NM_024860.2	56,56	0,5,6493	AA,AG,GG		0.0581,0.0,0.0385	benign,benign	161/474,137/450	58550386	5,12991	2198	4300	6498	SO:0001583	missense	79918	exon4			AGGCCAGAGGAGG	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.481G>A	16.37:g.58550386G>A	ENSP00000219315:p.Glu161Lys	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_001160305	A8K380|B5ME38|Q9H787	Missense_Mutation	SNP	ENST00000219315.4	37	CCDS54013.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.38	2.815025	0.50527	0.0	5.81E-4	ENSG00000103037	ENST00000310682;ENST00000219315	T;T	0.15603	2.41;2.41	5.37	3.37	0.38596	SET domain (2);	0.113840	0.64402	D	0.000016	T	0.13628	0.0330	L	0.49455	1.56	0.49483	D	0.999793	B;B;B	0.30914	0.14;0.3;0.004	B;B;B	0.22152	0.018;0.038;0.006	T	0.06698	-1.0812	10	0.33940	T	0.23	-20.8516	8.6244	0.33881	0.0812:0.2933:0.6254:0.0	.	137;161;137	E9PC53;Q8TBK2;Q8TBK2-2	.;SETD6_HUMAN;.	K	137;161	ENSP00000310082:E137K;ENSP00000219315:E161K	ENSP00000219315:E161K	E	+	1	0	SETD6	57107887	0.999000	0.42202	0.956000	0.39512	0.884000	0.51177	2.924000	0.48876	1.215000	0.43411	0.313000	0.20887	GAG	G|0.999;A|0.001	0.001	strong		0.617	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
DSE	29940	hgsc.bcm.edu	37	6	116720514	116720514	+	Missense_Mutation	SNP	C	C	T	rs35548455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:116720514C>T	ENST00000331677.3	+	3	545	c.101C>T	c.(100-102)cCc>cTc	p.P34L	DSE_ENST00000359564.2_Missense_Mutation_p.P34L|DSE_ENST00000537543.1_Missense_Mutation_p.P53L|DSE_ENST00000452085.3_Missense_Mutation_p.P34L|DSE_ENST00000540275.1_3'UTR			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	34			P -> L (in dbSNP:rs35548455).		carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		GTTATGATTCCCTTCACCAAT	0.532													C|||	110	0.0219649	0.0023	0.049	5008	,	,		18805	0.0		0.0477	False		,,,				2504	0.0256				p.P34L		Atlas-SNP	.											.	DSE	98	.	0			c.C101T						PASS	.	C	LEU/PRO,LEU/PRO	70,4336	63.5+/-100.7	0,70,2133	90.0	77.0	81.0		101,101	5.7	1.0	6	dbSNP_126	81	583,8017	156.4+/-210.3	20,543,3737	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	98,98	20,613,5870	TT,TC,CC		6.7791,1.5887,5.0208	possibly-damaging,possibly-damaging	34/959,34/959	116720514	653,12353	2203	4300	6503	SO:0001583	missense	29940	exon2			TGATTCCCTTCAC	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.101C>T	6.37:g.116720514C>T	ENSP00000332151:p.Pro34Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	51	40	0.784314	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	61	0.027930402930402932	1	0.0020325203252032522	20	0.055248618784530384	0	0.0	40	0.052770448548812667	C	22.8	4.341742	0.81911	0.015887	0.067791	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.65	5.65	0.86999	.	0.112000	0.64402	D	0.000007	T	0.16938	0.0407	L	0.44542	1.39	0.80722	D	1	P;P	0.36535	0.557;0.557	B;B	0.34242	0.178;0.178	T	0.02417	-1.1162	10	0.59425	D	0.04	-19.329	19.9142	0.97043	0.0:1.0:0.0:0.0	rs35548455	53;34	B7Z765;Q9UL01	.;DSE_HUMAN	L	34;34;53;34;34	ENSP00000397597:P34L;ENSP00000404049:P34L;ENSP00000441152:P53L;ENSP00000332151:P34L;ENSP00000352567:P34L	ENSP00000332151:P34L	P	+	2	0	DSE	116827207	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.454000	0.66651	2.941000	0.99782	0.655000	0.94253	CCC	C|0.955;T|0.045	0.045	strong		0.532	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
ZNF880	400713	hgsc.bcm.edu	37	19	52887146	52887146	+	Nonsense_Mutation	SNP	A	A	T	rs398101268|rs34470614		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52887146A>T	ENST00000422689.2	+	4	328	c.313A>T	c.(313-315)Aaa>Taa	p.K105*	ZNF880_ENST00000424032.2_3'UTR	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	105					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						CAAGTCTCTTAAAAATCAACT	0.368																																					p.K105X		Atlas-SNP	.											ZNF880,colon,carcinoma,-1,1	ZNF880	45	1	0			c.A313T						scavenged	.						61.0	45.0	50.0					19																	52887146		690	1569	2259	SO:0001587	stop_gained	400713	exon4			TCTCTTAAAAATC	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.313A>T	19.37:g.52887146A>T	ENSP00000406318:p.Lys105*	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	89	3	0.0337079	NM_001145434	B4DNA6	Nonsense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	A	8.517	0.867766	0.17250	.	.	ENSG00000221923	ENST00000422689	.	.	.	1.6	-2.54	0.06307	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	1.7816	0.03033	0.4842:0.0:0.2398:0.276	.	.	.	.	X	105	.	ENSP00000406318:K105X	K	+	1	0	ZNF880	57578958	0.000000	0.05858	0.006000	0.13384	0.124000	0.20399	-1.231000	0.02939	-0.761000	0.04670	0.368000	0.22195	AAA	.	.	none		0.368	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57069375	57069375	+	Missense_Mutation	SNP	A	A	G	rs34069781	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57069375A>G	ENST00000532437.1	-	8	5188	c.4877T>C	c.(4876-4878)gTg>gCg	p.V1626A	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.V1626A			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1626	Arg/Glu/Lys-rich (charged).				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)				AGGTTCCTCCACTACCTCTTC	0.612													A|||	101	0.0201677	0.0023	0.0389	5008	,	,		17084	0.002		0.0447	False		,,,				2504	0.0245				p.V1626A		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.T4877C						PASS	.	A	ALA/VAL	46,4356	46.7+/-81.2	0,46,2155	78.0	72.0	74.0		4877	1.2	0.1	11	dbSNP_126	74	402,8190	128.3+/-186.6	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	64	8,432,6057	GG,GA,AA		4.6788,1.045,3.4477	benign	1626/1730	57069375	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon9			TCCTCCACTACCT	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.4877T>C	11.37:g.57069375A>G	ENSP00000437271:p.Val1626Ala	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	60	18	0.3	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	A	1.725	-0.495729	0.04291	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.29917	1.55;1.55	4.94	1.18	0.20946	.	0.844445	0.10282	N	0.693393	T	0.03053	0.0090	L	0.35723	1.085	0.09310	N	1	B;B	0.15930	0.015;0.0	B;B	0.16722	0.016;0.002	T	0.26744	-1.0094	10	0.20519	T	0.43	-7.5445	4.0079	0.09610	0.595:0.0:0.2591:0.1459	rs34069781	1626;208	Q9C0C2;Q86TK2	TB182_HUMAN;.	A	1626	ENSP00000350990:V1626A;ENSP00000437271:V1626A	ENSP00000350990:V1626A	V	-	2	0	TNKS1BP1	56825951	0.003000	0.15002	0.065000	0.19835	0.987000	0.75469	0.402000	0.20965	0.226000	0.20979	0.459000	0.35465	GTG	A|0.968;G|0.032;T|0.000	0.032	strong		0.612	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449399	89449399	+	Silent	SNP	T	T	C	rs77567101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449399T>C	ENST00000321792.5	-	2	538	c.111A>G	c.(109-111)gtA>gtG	p.V37V	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Silent_p.V37V	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	37	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										TTATCAAGAGTACTTCCACTA	0.428											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V37V		Atlas-SNP	.											.	.	.	.	0			c.A111G						PASS	.	T	,,,	1667,2739		0,1667,536	209.0	198.0	202.0		,,111,111	0.4	1.0	1	dbSNP_131	202	2526,6074		0,2526,1774	no	intron,intron,coding-synonymous,coding-synonymous	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,,	0,4193,2310	CC,CT,TT		29.3721,37.8348,32.239	,,,	,,37/391,37/391	89449399	4193,8813	2203	4300	6503	SO:0001819	synonymous_variant	494115	exon3			CAAGAGTACTTCC	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.111A>G	1.37:g.89449399T>C		Somatic	275	0	0	1267	WXS	Illumina HiSeq	Phase_I	424	79	0.186321	NM_001162536		Silent	SNP	ENST00000321792.5	37	CCDS716.1																																																																																			T|0.500;C|0.500	0.500	strong		0.428	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
AP2B1	163	hgsc.bcm.edu	37	17	33998904	33998904	+	Silent	SNP	T	T	C	rs17670584	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33998904T>C	ENST00000262325.7	+	15	2674	c.2121T>C	c.(2119-2121)taT>taC	p.Y707Y	AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000592545.1_Silent_p.Y683Y|AP2B1_ENST00000312678.8_Silent_p.Y721Y|AP2B1_ENST00000538556.1_Silent_p.Y650Y|AP2B1_ENST00000537622.2_Silent_p.Y721Y|AP2B1_ENST00000589344.1_Silent_p.Y721Y	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	707	Pro-rich (stalk region).				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)			NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		CTGGTGGATATGTGGCTCCTA	0.453													T|||	218	0.0435304	0.0446	0.0476	5008	,	,		18568	0.001		0.0924	False		,,,				2504	0.0327				p.Y721Y		Atlas-SNP	.											AP2B1,NS,chondrosarcoma,+1,1	AP2B1	70	1	0			c.T2163C						PASS	.	T	,	242,4164	142.3+/-177.5	6,230,1967	109.0	103.0	105.0		2163,2121	3.1	1.0	17	dbSNP_123	105	773,7827	184.3+/-232.3	41,691,3568	no	coding-synonymous,coding-synonymous	AP2B1	NM_001030006.1,NM_001282.2	,	47,921,5535	CC,CT,TT		8.9884,5.4925,7.8041	,	721/952,707/938	33998904	1015,11991	2203	4300	6503	SO:0001819	synonymous_variant	163	exon16			TGGATATGTGGCT	M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.2121T>C	17.37:g.33998904T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_001030006	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	37	CCDS32622.1																																																																																			T|0.929;C|0.071	0.071	strong		0.453	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		
LRRC15	131578	hgsc.bcm.edu	37	3	194080696	194080696	+	Silent	SNP	G	G	A	rs9682541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194080696G>A	ENST00000347624.3	-	2	1162	c.1077C>T	c.(1075-1077)aaC>aaT	p.N359N	LRRC15_ENST00000428839.1_Silent_p.N365N|LRRC15_ENST00000439944.2_Silent_p.N365N	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	359					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TGCGGAAGACGTTCCCGTCCA	0.587													A|||	582	0.116214	0.093	0.1052	5008	,	,		19476	0.0685		0.2107	False		,,,				2504	0.1074				p.N365N		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1095T						PASS	.	A	,	432,3974	786.5+/-414.8	16,400,1787	67.0	64.0	65.0		1095,1077	-9.8	0.0	3	dbSNP_119	65	2013,6587	721.4+/-406.4	240,1533,2527	no	coding-synonymous,coding-synonymous	LRRC15	NM_001135057.2,NM_130830.4	,	256,1933,4314	AA,AG,GG		23.407,9.8048,18.799	,	365/588,359/582	194080696	2445,10561	2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			GAAGACGTTCCCG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1077C>T	3.37:g.194080696G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	149	80	0.536913	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			G|0.844;A|0.156	0.156	strong		0.587	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
ZRANB3	84083	hgsc.bcm.edu	37	2	135988186	135988186	+	Silent	SNP	G	G	A	rs58917764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:135988186G>A	ENST00000264159.6	-	13	1967	c.1851C>T	c.(1849-1851)acC>acT	p.T617T	ZRANB3_ENST00000401392.1_Silent_p.T617T|ZRANB3_ENST00000536680.1_Silent_p.T617T|ZRANB3_ENST00000412849.1_5'UTR	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	617					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		GAAAGGCTGGGGTGGTTAACT	0.502													G|||	928	0.185304	0.1014	0.2277	5008	,	,		20255	0.1716		0.1103	False		,,,				2504	0.3599				p.T617T		Atlas-SNP	.											.	ZRANB3	109	.	0			c.C1851T						PASS	.	G		390,3480		20,350,1565	130.0	125.0	127.0		1851	-4.7	0.0	2	dbSNP_129	127	659,7611		24,611,3500	no	coding-synonymous	ZRANB3	NM_032143.2		44,961,5065	AA,AG,GG		7.9686,10.0775,8.6409		617/1080	135988186	1049,11091	1935	4135	6070	SO:0001819	synonymous_variant	84083	exon13			GGCTGGGGTGGTT	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1851C>T	2.37:g.135988186G>A		Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	299	154	0.51505	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Silent	SNP	ENST00000264159.6	37	CCDS46419.1																																																																																			G|0.871;A|0.129	0.129	strong		0.502	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
WRN	7486	hgsc.bcm.edu	37	8	31024654	31024654	+	Missense_Mutation	SNP	T	T	C	rs1346044	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:31024654T>C	ENST00000298139.5	+	34	4348	c.4099T>C	c.(4099-4101)Tgt>Cgt	p.C1367R	RP11-363L24.3_ENST00000521252.1_RNA	NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1367			C -> R (polymorphism associated with a higher risk of myocardial infarction; dbSNP:rs1346044). {ECO:0000269|PubMed:10069711, ECO:0000269|PubMed:11161804, ECO:0000269|PubMed:9021029, ECO:0000269|Ref.4}.		aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		TCAACCTTCATGTGATGTCAA	0.403			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				T|||	965	0.192692	0.1475	0.1729	5008	,	,		17332	0.1042		0.2664	False		,,,				2504	0.2832				p.C1367R	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.T4099C	GRCh37	CM971591	WRN	M	rs1346044	PASS	.	T	ARG/CYS	757,3649	308.8+/-290.8	69,619,1515	120.0	105.0	110.0		4099	2.5	0.1	8	dbSNP_88	110	2200,6400	374.4+/-337.4	301,1598,2401	yes	missense	WRN	NM_000553.4	180	370,2217,3916	CC,CT,TT		25.5814,17.1811,22.7357	possibly-damaging	1367/1433	31024654	2957,10049	2203	4300	6503	SO:0001583	missense	7486	exon34	Familial Cancer Database	WS, Adult Progeria	CCTTCATGTGATG		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.4099T>C	8.37:g.31024654T>C	ENSP00000298139:p.Cys1367Arg	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	157	156	0.993631	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	400	0.18315018315018314	81	0.16463414634146342	64	0.17679558011049723	56	0.0979020979020979	199	0.262532981530343	T	8.055	0.766747	0.15983	0.171811	0.255814	ENSG00000165392	ENST00000298139	T	0.44083	0.93	4.86	2.45	0.29901	.	0.692798	0.13759	N	0.364736	T	0.00012	0.0000	M	0.70595	2.14	0.27730	P	0.9448488	P	0.41265	0.744	B	0.39068	0.289	T	0.09487	-1.0672	9	0.48119	T	0.1	-0.0497	5.6058	0.17379	0.0:0.1646:0.1451:0.6903	rs1346044;rs2230015;rs17652782;rs17847579;rs52814593;rs58743977;rs1346044	1367	Q14191	WRN_HUMAN	R	1367	ENSP00000298139:C1367R	ENSP00000298139:C1367R	C	+	1	0	WRN	31144196	0.589000	0.26807	0.090000	0.20809	0.295000	0.27426	0.579000	0.23788	0.406000	0.25560	0.533000	0.62120	TGT	T|0.798;C|0.202	0.202	strong		0.403	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
VPS41	27072	hgsc.bcm.edu	37	7	38829465	38829465	+	Silent	SNP	C	C	T	rs1001476	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:38829465C>T	ENST00000310301.4	-	10	774	c.720G>A	c.(718-720)gtG>gtA	p.V240V	VPS41_ENST00000395969.2_Silent_p.V215V|VPS41_ENST00000466017.1_5'UTR	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	240					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						TCACTGAGCACACCTGGAAAA	0.363													T|||	592	0.118211	0.3533	0.0576	5008	,	,		20768	0.0		0.0676	False		,,,				2504	0.0174				p.V240V		Atlas-SNP	.											.	VPS41	102	.	0			c.G720A						PASS	.	T	,	1273,3133	702.5+/-406.9	194,885,1124	127.0	117.0	120.0		720,645	-6.5	0.9	7	dbSNP_86	120	607,7993	792.1+/-407.5	21,565,3714	no	coding-synonymous,coding-synonymous	VPS41	NM_014396.3,NM_080631.3	,	215,1450,4838	TT,TC,CC		7.0581,28.8924,14.4549	,	240/855,215/830	38829465	1880,11126	2203	4300	6503	SO:0001819	synonymous_variant	27072	exon10			TGAGCACACCTGG	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.720G>A	7.37:g.38829465C>T		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	125	55	0.44	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Silent	SNP	ENST00000310301.4	37	CCDS5457.1																																																																																			T|0.138;G|0.005	0.138	strong		0.363	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3		
PCDHB13	56123	hgsc.bcm.edu	37	5	140595375	140595375	+	Silent	SNP	C	C	T	rs2910331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140595375C>T	ENST00000341948.4	+	1	1867	c.1680C>T	c.(1678-1680)ttC>ttT	p.F560F		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	560	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACTCGCCCTTCGTGCTGTACC	0.721													C|||	879	0.175519	0.2716	0.1398	5008	,	,		16235	0.0933		0.161	False		,,,				2504	0.1708				p.F560F		Atlas-SNP	.											PCDHB13,NS,carcinoma,0,1	PCDHB13	142	1	0			c.C1680T						PASS	.						20.0	23.0	22.0					5																	140595375		2200	4291	6491	SO:0001819	synonymous_variant	56123	exon1			GCCCTTCGTGCTG	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.1680C>T	5.37:g.140595375C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	34	16	0.470588	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			.	.	weak		0.721	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026129	176026129	+	Missense_Mutation	SNP	C	C	A	rs142779818|rs550332435|rs199714570|rs371149640|rs386695335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176026129C>A	ENST00000303991.4	-	2	884	c.707G>T	c.(706-708)gGg>gTg	p.G236V		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	236				Missing (in Ref. 4; CAD38868). {ECO:0000305}.	neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCTCAAAGACCCAGGATCCTC	0.498																																					p.G236V		Atlas-SNP	.											.	GPRIN1	77	.	0			c.G707T						PASS	.						89.0	92.0	91.0					5																	176026129		2140	4202	6342	SO:0001583	missense	114787	exon2			AAAGACCCAGGAT	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.707G>T	5.37:g.176026129C>A	ENSP00000305839:p.Gly236Val	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	99	20	0.20202	NM_052899	C9JM70|Q8ND74|Q96PZ4	Missense_Mutation	SNP	ENST00000303991.4	37	CCDS4405.1	.	.	.	.	.	.	.	.	.	.	C	10.93	1.489235	0.26686	.	.	ENSG00000169258	ENST00000303991;ENST00000335532	T	0.08193	3.12	4.31	-5.97	0.02227	.	0.829122	0.09843	N	0.748618	T	0.07143	0.0181	M	0.74881	2.28	0.21256	N	0.999744	B	0.18013	0.025	B	0.18871	0.023	T	0.45600	-0.9250	10	0.24483	T	0.36	3.7158	0.2113	0.00156	0.3574:0.1616:0.2179:0.2631	.	236	Q7Z2K8	GRIN1_HUMAN	V	236	ENSP00000305839:G236V	ENSP00000305839:G236V	G	-	2	0	GPRIN1	175958735	0.000000	0.05858	0.001000	0.08648	0.496000	0.33645	-2.182000	0.01256	-0.780000	0.04553	0.313000	0.20887	GGG	C|0.851;A|0.149	0.149	strong		0.498	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
DDX42	11325	hgsc.bcm.edu	37	17	61888461	61888461	+	Silent	SNP	G	G	A	rs56197520	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61888461G>A	ENST00000578681.1	+	14	1927	c.1326G>A	c.(1324-1326)cgG>cgA	p.R442R	DDX42_ENST00000583590.1_Silent_p.R442R|DDX42_ENST00000359353.5_Silent_p.R323R|DDX42_ENST00000389924.2_Silent_p.R442R|DDX42_ENST00000457800.2_Silent_p.R442R	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	442	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						CAACTTTTCGGAAGAAGATTG	0.413													G|||	139	0.0277556	0.0023	0.0389	5008	,	,		18095	0.002		0.0825	False		,,,				2504	0.0245				p.R442R		Atlas-SNP	.											.	DDX42	86	.	0			c.G1326A						PASS	.	G	,	80,4326	69.8+/-107.6	1,78,2124	76.0	70.0	72.0		1326,1326	4.2	1.0	17	dbSNP_129	72	755,7845	178.9+/-228.2	35,685,3580	no	coding-synonymous,coding-synonymous	DDX42	NM_007372.2,NM_203499.1	,	36,763,5704	AA,AG,GG		8.7791,1.8157,6.4201	,	442/939,442/939	61888461	835,12171	2203	4300	6503	SO:0001819	synonymous_variant	11325	exon13			TTTTCGGAAGAAG	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.1326G>A	17.37:g.61888461G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	108	107	0.990741	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Silent	SNP	ENST00000578681.1	37	CCDS32704.1																																																																																			G|0.940;A|0.060	0.060	strong		0.413	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
WDR35	57539	hgsc.bcm.edu	37	2	20131079	20131079	+	Missense_Mutation	SNP	T	T	C	rs1191778	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:20131079T>C	ENST00000345530.3	-	25	3063	c.2948A>G	c.(2947-2949)gAa>gGa	p.E983G	WDR35_ENST00000281405.4_Missense_Mutation_p.E972G|WDR35_ENST00000416055.2_Missense_Mutation_p.E456G	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	983			E -> G (in dbSNP:rs1191778). {ECO:0000269|PubMed:14702039}.		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)					CTTCATCTGTTCATGGTATTG	0.358													T|||	1164	0.232428	0.1097	0.3588	5008	,	,		16337	0.1171		0.4443	False		,,,				2504	0.2096				p.E983G		Atlas-SNP	.											WDR35,NS,carcinoma,-1,1	WDR35	92	1	0			c.A2948G						scavenged	.	T	GLY/GLU,GLY/GLU	709,3697	293.8+/-282.8	52,605,1546	166.0	159.0	161.0		2948,2915	4.8	0.0	2	dbSNP_87	161	3463,5137	508.0+/-377.0	689,2085,1526	yes	missense,missense	WDR35	NM_001006657.1,NM_020779.3	98,98	741,2690,3072	CC,CT,TT		40.2674,16.0917,32.0775	benign,benign	983/1182,972/1171	20131079	4172,8834	2203	4300	6503	SO:0001583	missense	57539	exon25			ATCTGTTCATGGT	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.2948A>G	2.37:g.20131079T>C	ENSP00000314444:p.Glu983Gly	Somatic	135	1	0.00740741		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_001006657	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	611	0.27976190476190477	53	0.10772357723577236	139	0.3839779005524862	87	0.1520979020979021	332	0.43799472295514513	T	12.10	1.837657	0.32513	0.160917	0.402674	ENSG00000118965	ENST00000345530;ENST00000281405;ENST00000416055	T;T;T	0.74526	-0.23;-0.23;-0.85	4.82	4.82	0.62117	.	0.210756	0.48767	D	0.000173	T	0.00012	0.0000	M	0.76002	2.32	0.40456	P	0.01980599999999999	B;B;P	0.42692	0.348;0.073;0.787	B;B;P	0.46758	0.156;0.066;0.526	T	0.17806	-1.0357	9	0.54805	T	0.06	-18.7985	13.8697	0.63610	0.0:0.0:0.0:1.0	rs1191778;rs1658525;rs52827575;rs61210615;rs1191778	972;983;456	Q9P2L0-2;Q9P2L0;B3KR94	.;WDR35_HUMAN;.	G	983;972;456	ENSP00000314444:E983G;ENSP00000281405:E972G;ENSP00000399159:E456G	ENSP00000281405:E972G	E	-	2	0	WDR35	19994560	0.992000	0.36948	0.019000	0.16419	0.680000	0.39746	3.878000	0.56130	1.933000	0.56026	0.482000	0.46254	GAA	T|0.710;C|0.290	0.290	strong		0.358	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2	NM_020779	
CLDN1	9076	hgsc.bcm.edu	37	3	190039888	190039888	+	Silent	SNP	G	G	A	rs72466472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:190039888G>A	ENST00000295522.3	-	1	376	c.108C>T	c.(106-108)gcC>gcT	p.A36A		NM_021101.4	NP_066924.1	O95832	CLD1_HUMAN	claudin 1	36					calcium-independent cell-cell adhesion (GO:0016338)|cell adhesion (GO:0007155)|cell-cell junction organization (GO:0045216)|establishment of skin barrier (GO:0061436)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			lung(9)	9	all_cancers(143;2.95e-10)|Ovarian(172;0.0512)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.015)		TGTTGTCGCCGGCATAGGAGT	0.617													G|||	229	0.0457268	0.0	0.0648	5008	,	,		15776	0.0694		0.0398	False		,,,				2504	0.0757				p.A36A		Atlas-SNP	.											.	CLDN1	23	.	0			c.C108T						PASS	.	G		34,4372	39.2+/-71.8	0,34,2169	88.0	87.0	87.0		108	-6.2	0.6	3	dbSNP_130	87	257,8343	100.3+/-161.8	4,249,4047	no	coding-synonymous	CLDN1	NM_021101.4		4,283,6216	AA,AG,GG		2.9884,0.7717,2.2374		36/212	190039888	291,12715	2203	4300	6503	SO:0001819	synonymous_variant	9076	exon1			GTCGCCGGCATAG	AF101051	CCDS3295.1	3q28-q29	2008-07-18			ENSG00000163347	ENSG00000163347		"""Claudins"""	2032	protein-coding gene	gene with protein product	"""senescence-associated epithelial membrane protein 1"""	603718				10828592, 9892664	Standard	NM_021101		Approved	SEMP1, ILVASC	uc003fsh.3	O95832	OTTHUMG00000156214	ENST00000295522.3:c.108C>T	3.37:g.190039888G>A		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	181	90	0.497238	NM_021101		Silent	SNP	ENST00000295522.3	37	CCDS3295.1																																																																																			G|0.971;A|0.029	0.029	strong		0.617	CLDN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343516.2	NM_021101	
SETD9	133383	hgsc.bcm.edu	37	5	56209735	56209735	+	Missense_Mutation	SNP	A	A	G	rs40497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:56209735A>G	ENST00000285947.2	+	4	1011	c.625A>G	c.(625-627)Aaa>Gaa	p.K209E	SETD9_ENST00000475908.1_3'UTR|SETD9_ENST00000541720.1_Missense_Mutation_p.K209E	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	209	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		K -> E (in dbSNP:rs40497).				methyltransferase activity (GO:0008168)										CGGCCCTTTAAAAATGAGTGA	0.403													A|||	715	0.142772	0.0794	0.1772	5008	,	,		16227	0.0308		0.335	False		,,,				2504	0.1217				p.K209E		Atlas-SNP	.											.	.	.	.	0			c.A625G						PASS	.	A	GLU/LYS,GLU/LYS	529,3877	240.9+/-251.5	39,451,1713	101.0	97.0	98.0		625,625	3.3	1.0	5	dbSNP_76	98	2909,5691	455.3+/-363.7	481,1947,1872	yes	missense,missense	C5orf35	NM_001171990.1,NM_153706.3	56,56	520,2398,3585	GG,GA,AA		33.8256,12.0064,26.434	benign,benign	209/272,209/300	56209735	3438,9568	2203	4300	6503	SO:0001583	missense	133383	exon4			CCTTTAAAAATGA	BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 35"""	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.625A>G	5.37:g.56209735A>G	ENSP00000285947:p.Lys209Glu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	62	32	0.516129	NM_153706	F5H713	Missense_Mutation	SNP	ENST00000285947.2	37	CCDS3972.1	369	0.16895604395604397	40	0.08130081300813008	73	0.20165745856353592	15	0.026223776223776224	241	0.3179419525065963	A	13.40	2.227366	0.39399	0.120064	0.338256	ENSG00000155542	ENST00000285947;ENST00000541720	T;T	0.31769	1.49;1.48	5.73	3.33	0.38152	.	0.322809	0.35870	N	0.002937	T	0.00012	0.0000	L	0.60455	1.87	0.58432	P	2.9999999999752447E-6	B	0.24533	0.105	B	0.13407	0.009	T	0.38243	-0.9670	9	0.07990	T	0.79	-8.8601	7.1006	0.25336	0.7288:0.1317:0.1395:0.0	rs40497;rs17662843;rs60847384;rs40497	209	Q8NE22	CE035_HUMAN	E	209	ENSP00000285947:K209E;ENSP00000442886:K209E	ENSP00000285947:K209E	K	+	1	0	C5orf35	56245492	0.084000	0.21492	0.980000	0.43619	0.975000	0.68041	0.552000	0.23376	1.008000	0.39264	0.528000	0.53228	AAA	A|0.788;G|0.212	0.212	strong		0.403	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706	
PRDM11	56981	hgsc.bcm.edu	37	11	45245778	45245778	+	Missense_Mutation	SNP	G	G	T	rs35090414	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:45245778G>T	ENST00000530656.1	+	7	855	c.855G>T	c.(853-855)agG>agT	p.R285S	PRDM11_ENST00000263765.4_Missense_Mutation_p.R285S|CTD-2560E9.3_ENST00000527450.1_RNA|PRDM11_ENST00000528980.1_Intron|PRDM11_ENST00000424263.2_Missense_Mutation_p.R251S			Q9NQV5	PRD11_HUMAN	PR domain containing 11	285							methyltransferase activity (GO:0008168)			endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	26						GAGAGAAGAGGTTGCAGAGGG	0.502													G|||	228	0.0455272	0.0015	0.1441	5008	,	,		18715	0.0		0.0835	False		,,,				2504	0.0429				p.R251S	NSCLC(118;1511 1736 6472 36603 43224)	Atlas-SNP	.											PRDM11,caecum,carcinoma,0,2	PRDM11	53	2	0			c.G753T						PASS	.	G	SER/ARG	93,4307		1,91,2108	101.0	111.0	107.0		855	1.9	1.0	11	dbSNP_126	107	732,7866		36,660,3603	yes	missense	PRDM11	NM_020229.2	110	37,751,5711	TT,TG,GG		8.5136,2.1136,6.3471	benign	285/512	45245778	825,12173	2200	4299	6499	SO:0001583	missense	56981	exon7			GAAGAGGTTGCAG	AF275818	CCDS58130.1, CCDS73277.1	11p11	2008-07-21			ENSG00000019485	ENSG00000019485			13996	protein-coding gene	gene with protein product	"""PR-domain containing protein 11"""						Standard	NM_001256695		Approved	PFM8	uc031qab.1	Q9NQV5	OTTHUMG00000166478	ENST00000530656.1:c.855G>T	11.37:g.45245778G>T	ENSP00000435976:p.Arg285Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_001256695	Q8N9F1	Missense_Mutation	SNP	ENST00000530656.1	37		108	0.04945054945054945	3	0.006097560975609756	47	0.1298342541436464	0	0.0	58	0.07651715039577836	G	13.22	2.170746	0.38315	0.021136	0.085136	ENSG00000019485	ENST00000263765;ENST00000530656;ENST00000424263	T;T;T	0.47177	0.85;0.85;0.85	5.82	1.88	0.25563	.	0.391190	0.24818	N	0.035341	T	0.00241	0.0007	N	0.08118	0	0.39765	P	0.02791699999999997	B	0.17667	0.023	B	0.18561	0.022	T	0.13415	-1.0510	9	0.11485	T	0.65	-23.2779	10.403	0.44241	0.3803:0.0:0.6197:0.0	rs35090414;rs61880321	285	Q9NQV5	PRD11_HUMAN	S	285;285;251	ENSP00000263765:R285S;ENSP00000435976:R285S;ENSP00000394314:R251S	ENSP00000263765:R285S	R	+	3	2	PRDM11	45202354	0.999000	0.42202	0.999000	0.59377	0.998000	0.95712	0.657000	0.24963	0.373000	0.24621	0.655000	0.94253	AGG	G|0.940;T|0.060	0.060	strong		0.502	PRDM11-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000389928.1	NM_020229	
RFPL4B	442247	hgsc.bcm.edu	37	6	112671611	112671611	+	Missense_Mutation	SNP	G	G	A	rs11153361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:112671611G>A	ENST00000441065.2	+	3	1013	c.701G>A	c.(700-702)gGt>gAt	p.G234D	RP11-506B6.6_ENST00000585611.1_RNA|RP11-506B6.6_ENST00000587816.1_RNA|RP11-506B6.6_ENST00000590673.1_RNA	NM_001013734.2	NP_001013756.2	Q6ZWI9	RFPLB_HUMAN	ret finger protein-like 4B	234	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		G -> D (in dbSNP:rs11153361).				zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|skin(1)	14		all_cancers(87;9.44e-05)|all_hematologic(75;0.000114)|all_epithelial(87;0.00265)|Colorectal(196;0.0209)		all cancers(137;0.0202)|OV - Ovarian serous cystadenocarcinoma(136;0.0477)|Epithelial(106;0.0646)|GBM - Glioblastoma multiforme(226;0.0866)|BRCA - Breast invasive adenocarcinoma(108;0.244)		ACACATGATGGTTTCTTCTCT	0.463													A|||	818	0.163339	0.2141	0.134	5008	,	,		20250	0.0367		0.2286	False		,,,				2504	0.1789				p.G234D		Atlas-SNP	.											.	RFPL4B	36	.	0			c.G701A						PASS	.	A	ASP/GLY	976,3430		97,782,1324	65.0	61.0	62.0		701	-7.8	0.0	6	dbSNP_120	62	1868,6732		187,1494,2619	yes	missense	RFPL4B	NM_001013734.2	94	284,2276,3943	AA,AG,GG		21.7209,22.1516,21.8668	benign	234/264	112671611	2844,10162	2203	4300	6503	SO:0001583	missense	442247	exon3			ATGATGGTTTCTT	AK122906	CCDS34515.1	6q21	2007-04-24			ENSG00000251258	ENSG00000251258		"""RING-type (C3HC4) zinc fingers"""	33264	protein-coding gene	gene with protein product							Standard	NM_001013734		Approved	RNF211	uc003pvx.1	Q6ZWI9	OTTHUMG00000015390	ENST00000441065.2:c.701G>A	6.37:g.112671611G>A	ENSP00000423391:p.Gly234Asp	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	94	74	0.787234	NM_001013734	A2RU91	Missense_Mutation	SNP	ENST00000441065.2	37	CCDS34515.1	338	0.15476190476190477	92	0.18699186991869918	58	0.16022099447513813	24	0.04195804195804196	164	0.21635883905013192	A	0.329	-0.957504	0.02267	0.221516	0.217209	ENSG00000251258	ENST00000441065	T	0.66280	-0.2	3.92	-7.84	0.01196	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	21.575300	0.00166	N	0.000000	T	0.12178	0.0296	N	0.17312	0.475	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.14952	-1.0454	9	0.12430	T	0.62	.	2.0535	0.03576	0.3049:0.2993:0.2591:0.1367	rs11153361;rs52806668;rs59484835;rs11153361	234	Q6ZWI9	RFPLB_HUMAN	D	234	ENSP00000423391:G234D	ENSP00000423391:G234D	G	+	2	0	RFPL4B	112778304	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.890000	0.01613	-3.102000	0.00244	-1.523000	0.00931	GGT	G|0.808;A|0.192	0.192	strong		0.463	RFPL4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041885.2	NM_001013734	
FCGBP	8857	hgsc.bcm.edu	37	19	40392360	40392360	+	Missense_Mutation	SNP	G	G	A	rs200977347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40392360G>A	ENST00000221347.6	-	16	8151	c.8144C>T	c.(8143-8145)gCa>gTa	p.A2715V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2715						extracellular vesicular exosome (GO:0070062)		p.A2715V(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCTCCAGCTGCCTGGCAAGC	0.587													G|||	1248	0.249201	0.1619	0.3876	5008	,	,		13881	0.1935		0.33	False		,,,				2504	0.2434				p.A2715V		Atlas-SNP	.											FCGBP,rectum,carcinoma,0,1	FCGBP	416	1	1	Substitution - Missense(1)	large_intestine(1)	c.C8144T						scavenged	.						5.0	6.0	6.0					19																	40392360		1980	3956	5936	SO:0001583	missense	8857	exon16			CCAGCTGCCTGGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8144C>T	19.37:g.40392360G>A	ENSP00000221347:p.Ala2715Val	Somatic	536	1	0.00186567		WXS	Illumina HiSeq	Phase_I	169	30	0.177515	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.082846	0.36758	.	.	ENSG00000090920	ENST00000221347	T	0.77620	-1.11	2.58	-0.163	0.13363	Uncharacterised domain, cysteine-rich (2);	0.292022	0.32244	N	0.006362	D	0.82323	0.5012	M	0.76574	2.34	0.23331	N	0.997894	D	0.76494	0.999	D	0.79108	0.992	T	0.69347	-0.5169	10	0.33940	T	0.23	.	5.3676	0.16123	0.0:0.1728:0.3161:0.5111	.	2715	Q9Y6R7	FCGBP_HUMAN	V	2715	ENSP00000221347:A2715V	ENSP00000221347:A2715V	A	-	2	0	FCGBP	45084200	0.000000	0.05858	0.984000	0.44739	0.668000	0.39293	-0.272000	0.08560	0.383000	0.24910	0.298000	0.19748	GCA	.	.	weak		0.587	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ALOX15	246	hgsc.bcm.edu	37	17	4536241	4536241	+	Silent	SNP	T	T	C	rs743646	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4536241T>C	ENST00000570836.1	-	12	1551	c.1455A>G	c.(1453-1455)acA>acG	p.T485T	ALOX15_ENST00000545513.1_Silent_p.T507T|ALOX15_ENST00000574640.1_Silent_p.T446T|ALOX15_ENST00000293761.3_Silent_p.T485T			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	485	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		CAGCCACGTCTGTCTTATAGT	0.592													T|||	232	0.0463259	0.0045	0.0648	5008	,	,		18952	0.001		0.1342	False		,,,				2504	0.046				p.T485T		Atlas-SNP	.											.	ALOX15	70	.	0			c.A1455G						PASS	.	T		89,4317	73.6+/-111.7	1,87,2115	93.0	85.0	88.0		1455	-3.2	0.0	17	dbSNP_86	88	1057,7543	222.7+/-259.7	66,925,3309	no	coding-synonymous	ALOX15	NM_001140.3		67,1012,5424	CC,CT,TT		12.2907,2.02,8.8113		485/663	4536241	1146,11860	2203	4300	6503	SO:0001819	synonymous_variant	246	exon11			CACGTCTGTCTTA	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1455A>G	17.37:g.4536241T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	97	52	0.536082	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Silent	SNP	ENST00000570836.1	37	CCDS11049.1																																																																																			T|0.920;C|0.080	0.080	strong		0.592	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
PLCE1	51196	hgsc.bcm.edu	37	10	95931111	95931111	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:95931111T>C	ENST00000371380.3	+	3	1902	c.1667T>C	c.(1666-1668)cTt>cCt	p.L556P	PLCE1_ENST00000371385.3_Missense_Mutation_p.L248P|PLCE1_ENST00000260766.3_Missense_Mutation_p.L556P|PLCE1_ENST00000371375.1_Missense_Mutation_p.L248P			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	556	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				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)				GTCGACTACCTTTGCTTCTTA	0.532																																					p.L556P		Atlas-SNP	.											PLCE1_ENST00000371375,caecum,carcinoma,+1,3	PLCE1	543	3	0			c.T1667C						scavenged	.						151.0	151.0	151.0					10																	95931111		2040	4194	6234	SO:0001583	missense	51196	exon4			ACTACCTTTGCTT		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.1667T>C	10.37:g.95931111T>C	ENSP00000360431:p.Leu556Pro	Somatic	216	0	0		WXS	Illumina HiSeq	Phase_I	193	4	0.0207254	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.234216	0.79688	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	5.84	5.84	0.93424	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.64402	D	0.000003	T	0.62122	0.2402	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.63769	-0.6562	10	0.62326	D	0.03	.	16.2282	0.82315	0.0:0.0:0.0:1.0	.	556;248;556	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	P	556;556;248;248	ENSP00000260766:L556P;ENSP00000360431:L556P;ENSP00000360438:L248P;ENSP00000360426:L248P	ENSP00000260766:L556P	L	+	2	0	PLCE1	95921101	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	7.030000	0.76484	2.227000	0.72691	0.533000	0.62120	CTT	.	.	none		0.532	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
OR5D14	219436	hgsc.bcm.edu	37	11	55563900	55563900	+	Missense_Mutation	SNP	T	T	C	rs297055	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55563900T>C	ENST00000335605.1	+	1	869	c.869T>C	c.(868-870)cTg>cCg	p.L290P		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	290			L -> P (in dbSNP:rs297055).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L290P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				CTGAACCCTCTGATCTACAGC	0.408													t|||	1086	0.216853	0.326	0.1844	5008	,	,		17041	0.1458		0.2525	False		,,,				2504	0.1288				p.L290P		Atlas-SNP	.											OR5D14,NS,carcinoma,-1,3	OR5D14	116	3	1	Substitution - Missense(1)	stomach(1)	c.T869C						PASS	.	T	PRO/LEU	1414,2986	451.6+/-349.7	252,910,1038	55.0	54.0	55.0		869	5.1	1.0	11	dbSNP_79	55	2204,6388	368.9+/-335.3	305,1594,2397	yes	missense	OR5D14	NM_001004735.1	98	557,2504,3435	CC,CT,TT		25.6518,32.1364,27.8479	probably-damaging	290/315	55563900	3618,9374	2200	4296	6496	SO:0001583	missense	219436	exon1			ACCCTCTGATCTA	AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.869T>C	11.37:g.55563900T>C	ENSP00000334456:p.Leu290Pro	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	81	31	0.382716	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	524	0.23992673992673993	171	0.3475609756097561	66	0.18232044198895028	87	0.1520979020979021	200	0.2638522427440633	t	14.05	2.420915	0.42918	0.321364	0.256518	ENSG00000186113	ENST00000335605	T	0.46451	0.87	5.08	5.08	0.68730	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35179	N	0.003382	T	0.00012	0.0000	M	0.90369	3.11	0.44966	P	0.0020139999999999603	P	0.49559	0.925	P	0.45712	0.491	T	0.22208	-1.0223	9	0.87932	D	0	-13.9526	13.7086	0.62654	0.0:0.0:0.0:1.0	rs297055;rs52801945;rs60885889;rs297055	290	Q8NGL3	OR5DE_HUMAN	P	290	ENSP00000334456:L290P	ENSP00000334456:L290P	L	+	2	0	OR5D14	55320476	0.122000	0.22280	1.000000	0.80357	0.991000	0.79684	3.008000	0.49544	1.916000	0.55485	0.523000	0.50628	CTG	T|0.746;C|0.254	0.254	strong		0.408	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
OCA2	4948	hgsc.bcm.edu	37	15	28260053	28260053	+	Missense_Mutation	SNP	G	G	A	rs1800401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28260053G>A	ENST00000354638.3	-	9	1068	c.913C>T	c.(913-915)Cgg>Tgg	p.R305W	OCA2_ENST00000353809.5_Missense_Mutation_p.R305W|OCA2_ENST00000382996.2_Missense_Mutation_p.R305W	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	305			R -> W (polymorphism associated with nonblue eye color; could be a biomarker of cutaneous cancer risk; dbSNP:rs1800401). {ECO:0000269|PubMed:10987646, ECO:0000269|PubMed:12163334, ECO:0000269|PubMed:15889046, ECO:0000269|PubMed:7601462}.		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)		AGGGAGGCCCGGATGCTGATG	0.557									Oculocutaneous Albinism				G|||	413	0.0824681	0.1256	0.0605	5008	,	,		19962	0.005		0.0656	False		,,,				2504	0.137				p.R305W		Atlas-SNP	.											.	OCA2	173	.	0			c.C913T	GRCh37	CM025431	OCA2	M	rs1800401	PASS	.	G	TRP/ARG	590,3816	259.2+/-262.9	30,530,1643	108.0	79.0	89.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	913	3.7	0.2	15	dbSNP_89	89	426,8174	132.0+/-189.7	9,408,3883	yes	missense	OCA2	NM_000275.2	101	39,938,5526	AA,AG,GG		4.9535,13.3908,7.8118	probably-damaging	305/839	28260053	1016,11990	2203	4300	6503	SO:0001583	missense	4948	exon9	Familial Cancer Database		AGGCCCGGATGCT		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.913C>T	15.37:g.28260053G>A	ENSP00000346659:p.Arg305Trp	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	35	0.555556	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	138	0.06318681318681318	66	0.13414634146341464	26	0.0718232044198895	0	0.0	46	0.06068601583113457	G	11.65	1.700573	0.30142	0.133908	0.049535	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.91237	-2.72;-2.81;-2.69	5.55	3.69	0.42338	.	0.258640	0.38436	N	0.001682	T	0.09335	0.0230	L	0.51422	1.61	0.40502	P	0.019345999999999974	P;P	0.52170	0.949;0.951	P;B	0.48982	0.597;0.245	T	0.61739	-0.7001	9	0.72032	D	0.01	-11.0407	10.224	0.43214	0.1588:0.0:0.8412:0.0	rs1800401;rs17359372	305;305	Q04671-2;Q04671	.;P_HUMAN	W	305	ENSP00000346659:R305W;ENSP00000261276:R305W;ENSP00000372457:R305W	ENSP00000261276:R305W	R	-	1	2	OCA2	25933648	1.000000	0.71417	0.181000	0.23098	0.073000	0.16967	4.968000	0.63728	0.728000	0.32382	-0.768000	0.03414	CGG	G|0.922;A|0.078	0.078	strong		0.557	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
ZAR1L	646799	hgsc.bcm.edu	37	13	32885654	32885654	+	Missense_Mutation	SNP	T	T	C	rs445909	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32885654T>C	ENST00000533490.2	-	3	827	c.409A>G	c.(409-411)Acc>Gcc	p.T137A	ZAR1L_ENST00000345108.6_Missense_Mutation_p.T137A			A6NP61	ZAR1L_HUMAN	zygote arrest 1-like	137						cytoplasm (GO:0005737)				NS(1)|kidney(1)	2						CTGCGGCCGGTGGCGGGCGAA	0.731													t|||	1963	0.391973	0.3313	0.4135	5008	,	,		13345	0.4851		0.3976	False		,,,				2504	0.3569				p.T137A		Atlas-SNP	.											ZAR1L,NS,meningioma,0,1	ZAR1L	17	1	0			c.A409G						PASS	.						2.0	3.0	3.0					13																	32885654		518	1327	1845	SO:0001583	missense	646799	exon1			GGCCGGTGGCGGG		CCDS45023.1	13q13.1	2014-02-20			ENSG00000189167	ENSG00000189167			37116	protein-coding gene	gene with protein product	"""zinc finger, 3CxxC-type 7"""					18442940	Standard	NM_001136571		Approved	Z3CXXC7	uc010abc.1	A6NP61	OTTHUMG00000016694	ENST00000533490.2:c.409A>G	13.37:g.32885654T>C	ENSP00000437289:p.Thr137Ala	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	18	9	0.5	NM_001136571	B2RV03|B7ZBU2	Missense_Mutation	SNP	ENST00000533490.2	37	CCDS45023.1	879	0.4024725274725275	163	0.3313008130081301	139	0.3839779005524862	287	0.5017482517482518	290	0.38258575197889183	t	0.751	-0.772802	0.02951	.	.	ENSG00000189167	ENST00000345108	.	.	.	4.0	-6.3	0.02007	.	2.229460	0.02811	N	0.124375	T	0.00012	0.0000	N	0.03194	-0.395	0.80722	P	0.0	B	0.12013	0.005	B	0.10450	0.005	T	0.39014	-0.9634	8	0.05721	T	0.95	1.7448	7.7924	0.29127	0.0:0.3217:0.3846:0.2936	rs445909	137	A6NP61	ZAR1L_HUMAN	A	137	.	ENSP00000344616:T137A	T	-	1	0	ZAR1L	31783654	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.670000	0.05256	-0.840000	0.04206	-0.513000	0.04457	ACC	T|0.596;C|0.404	0.404	strong		0.731	ZAR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044403.5		
FOXK1	221937	hgsc.bcm.edu	37	7	4780514	4780514	+	Silent	SNP	G	G	T	rs3087749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4780514G>T	ENST00000328914.4	+	2	606	c.606G>T	c.(604-606)acG>acT	p.T202T	FOXK1_ENST00000446823.1_Silent_p.T39T	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		TCCAGTTCACGTCGCTCTATC	0.617													G|||	2844	0.567891	0.3222	0.5634	5008	,	,		14981	0.8502		0.4811	False		,,,				2504	0.7014				p.T202T		Atlas-SNP	.											.	FOXK1	64	.	0			c.G606T						PASS	.	G		1499,2907	479.2+/-358.4	267,965,971	187.0	188.0	188.0		606	-7.1	0.2	7	dbSNP_102	188	4078,4522	560.0+/-387.5	979,2120,1201	no	coding-synonymous	FOXK1	NM_001037165.1		1246,3085,2172	TT,TG,GG		47.4186,34.0218,42.8802		202/734	4780514	5577,7429	2203	4300	6503	SO:0001819	synonymous_variant	221937	exon2			GTTCACGTCGCTC	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.606G>T	7.37:g.4780514G>T		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	105	57	0.542857	NM_001037165		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																			G|0.511;T|0.489	0.489	strong		0.617	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
SEPT4	5414	hgsc.bcm.edu	37	17	56598655	56598655	+	Silent	SNP	C	C	T	rs1057065	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56598655C>T	ENST00000317268.3	-	9	1250	c.1074G>A	c.(1072-1074)cgG>cgA	p.R358R	SEPT4_ENST00000583114.1_Silent_p.R211R|SEPT4_ENST00000317256.6_Silent_p.R339R|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_Silent_p.R373R|SEPT4_ENST00000426861.1_3'UTR|SEPT4_ENST00000579371.1_Silent_p.R259R|SEPT4_ENST00000412945.3_Silent_p.R350R|SEPT4_ENST00000580844.1_Silent_p.R259R|SEPT4_ENST00000393086.1_Silent_p.R339R	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	358	Septin-type G.				apoptotic process (GO:0006915)|brain development (GO:0007420)|cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|positive regulation of apoptotic process (GO:0043065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of protein ubiquitination (GO:0031398)|regulation of apoptotic process (GO:0042981)|sperm capacitation (GO:0048240)|sperm mitochondrion organization (GO:0030382)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm annulus (GO:0097227)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural molecule activity (GO:0005198)			NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	18	Medulloblastoma(34;0.127)|all_neural(34;0.237)					CCCGAACTCGCCGCCCTCTGG	0.577											OREG0024614	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	118	0.0235623	0.0023	0.0115	5008	,	,		18520	0.001		0.0417	False		,,,				2504	0.0654				p.R373R		Atlas-SNP	.											SEPT4,colon,carcinoma,-2,1	SEPT4	48	1	0			c.G1119A						PASS	.	C	,,,	62,4344	59.3+/-96.0	1,60,2142	72.0	65.0	68.0		1050,1074,,1017	1.4	1.0	17	dbSNP_86	68	555,8045	151.5+/-206.2	20,515,3765	no	coding-synonymous,coding-synonymous,utr-3,coding-synonymous	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	,,,	21,575,5907	TT,TC,CC		6.4535,1.4072,4.744	,,,	350/471,358/479,,339/460	56598655	617,12389	2203	4300	6503	SO:0001819	synonymous_variant	5414	exon10			AACTCGCCGCCCT	AF073312	CCDS11609.1, CCDS11610.1, CCDS45743.1, CCDS56041.1, CCDS58581.1, CCDS58582.1	17q22	2013-01-21	2005-01-11	2005-01-12	ENSG00000108387	ENSG00000108387		"""Septins"""	9165	protein-coding gene	gene with protein product	"""bradeoin"", ""septin-M"""	603696	"""peanut-like 2 (Drosophila)"""	PNUTL2		9889007	Standard	NM_001198713		Approved	H5, CE5B3, hucep-7, ARTS, hCDCREL-2, MART	uc002iwm.2	O43236		ENST00000317268.3:c.1074G>A	17.37:g.56598655C>T		Somatic	78	0	0	1016	WXS	Illumina HiSeq	Phase_I	65	35	0.538462	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Silent	SNP	ENST00000317268.3	37	CCDS11610.1																																																																																			C|0.961;T|0.039	0.039	strong		0.577	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417	
ZNF543	125919	hgsc.bcm.edu	37	19	57840547	57840547	+	Missense_Mutation	SNP	A	A	G	rs10410649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57840547A>G	ENST00000321545.4	+	4	2062	c.1717A>G	c.(1717-1719)Atg>Gtg	p.M573V		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	573			M -> V (in dbSNP:rs10410649).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(2)|large_intestine(8)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	28		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		AAGACCTTTTATGACTGCACA	0.413													A|||	989	0.197484	0.3169	0.1816	5008	,	,		20065	0.0317		0.2843	False		,,,				2504	0.1288				p.M573V		Atlas-SNP	.											.	ZNF543	61	.	0			c.A1717G						PASS	.	A	VAL/MET	1351,3055	450.6+/-349.4	200,951,1052	87.0	81.0	84.0		1717	-2.8	0.0	19	dbSNP_119	84	2352,6248	393.0+/-344.2	323,1706,2271	yes	missense	ZNF543	NM_213598.3	21	523,2657,3323	GG,GA,AA		27.3488,30.6627,28.4715	benign	573/601	57840547	3703,9303	2203	4300	6503	SO:0001583	missense	125919	exon4			CCTTTTATGACTG	AL834534	CCDS33130.1	19q13.43	2013-01-08				ENSG00000178229		"""Zinc fingers, C2H2-type"", ""-"""	25281	protein-coding gene	gene with protein product							Standard	NM_213598		Approved	DKFZp434H055	uc002qoi.2	Q08ER8		ENST00000321545.4:c.1717A>G	19.37:g.57840547A>G	ENSP00000322545:p.Met573Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	110	58	0.527273	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	Missense_Mutation	SNP	ENST00000321545.4	37	CCDS33130.1	466	0.21336996336996336	152	0.3089430894308943	79	0.21823204419889503	18	0.03146853146853147	217	0.2862796833773087	A	4.434	0.080299	0.08533	0.306627	0.273488	ENSG00000178229	ENST00000321545	T	0.05513	3.43	2.45	-2.81	0.05805	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47573	-0.9107	8	0.52906	T	0.07	.	5.4467	0.16539	0.323:0.4652:0.2119:0.0	rs10410649;rs52820047;rs10410649	573	Q08ER8	ZN543_HUMAN	V	573	ENSP00000322545:M573V	ENSP00000322545:M573V	M	+	1	0	ZNF543	62532359	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.653000	0.05360	-0.852000	0.04141	0.379000	0.24179	ATG	A|0.737;G|0.263	0.263	strong		0.413	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865	
CLRN3	119467	hgsc.bcm.edu	37	10	129690990	129690990	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:129690990G>T	ENST00000368671.3	-	1	221	c.59C>A	c.(58-60)tCc>tAc	p.S20Y		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	20						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				TACAATGAAGGACCCAAGGCT	0.383																																					p.S20Y		Atlas-SNP	.											.	CLRN3	27	.	0			c.C59A						PASS	.						114.0	102.0	106.0					10																	129690990		2203	4300	6503	SO:0001583	missense	119467	exon1			ATGAAGGACCCAA	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"""transmembrane protein 12"""	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.59C>A	10.37:g.129690990G>T	ENSP00000357660:p.Ser20Tyr	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291288	0.59976	.	.	ENSG00000180745	ENST00000368671	T	0.71103	-0.54	5.52	5.52	0.82312	.	0.222808	0.38837	N	0.001554	T	0.81631	0.4863	M	0.62723	1.935	0.19945	N	0.999946	D	0.65815	0.995	D	0.66716	0.946	T	0.74615	-0.3606	10	0.66056	D	0.02	-14.6668	16.4802	0.84156	0.0:0.0:1.0:0.0	.	20	Q8NCR9	CLRN3_HUMAN	Y	20	ENSP00000357660:S20Y	ENSP00000357660:S20Y	S	-	2	0	CLRN3	129580980	0.324000	0.24652	0.009000	0.14445	0.104000	0.19210	4.040000	0.57333	2.880000	0.98712	0.655000	0.94253	TCC	.	.	none		0.383	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311	
LRRC28	123355	hgsc.bcm.edu	37	15	99892589	99892589	+	Missense_Mutation	SNP	G	G	A	rs139516247		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:99892589G>A	ENST00000301981.3	+	7	848	c.608G>A	c.(607-609)cGa>cAa	p.R203Q	LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000447360.2_Missense_Mutation_p.R203Q|LRRC28_ENST00000442993.2_3'UTR|LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000422500.2_Missense_Mutation_p.R134Q	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	203										endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			GGTCGATCTCGAGAACTACAG	0.353																																					p.R203Q		Atlas-SNP	.											LRRC28,NS,malignant_melanoma,+1,1	LRRC28	38	1	0			c.G608A						PASS	.	G	GLN/ARG	0,4394		0,0,2197	166.0	157.0	160.0		608	5.5	1.0	15	dbSNP_134	160	1,8593	1.2+/-3.3	0,1,4296	no	missense	LRRC28	NM_144598.2	43	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	benign	203/368	99892589	1,12987	2197	4297	6494	SO:0001583	missense	123355	exon7			GATCTCGAGAACT	AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.608G>A	15.37:g.99892589G>A	ENSP00000304923:p.Arg203Gln	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	33	16	0.484848	NM_144598	A8KA22|Q6UY49|Q6ZSS6	Missense_Mutation	SNP	ENST00000301981.3	37	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336020	0.60853	0.0	1.16E-4	ENSG00000168904	ENST00000301981;ENST00000447360;ENST00000422500	T;T;T	0.31247	2.23;2.23;1.5	5.52	5.52	0.82312	.	0.131334	0.49916	D	0.000129	T	0.51856	0.1699	M	0.62723	1.935	0.80722	D	1	D;D;B	0.76494	0.999;0.999;0.046	D;D;B	0.77557	0.984;0.99;0.003	T	0.35500	-0.9786	10	0.15499	T	0.54	.	18.4386	0.90656	0.0:0.0:1.0:0.0	.	134;203;203	B4DHL3;Q86X40-2;Q86X40	.;.;LRC28_HUMAN	Q	203;203;134	ENSP00000304923:R203Q;ENSP00000404520:R203Q;ENSP00000398606:R134Q	ENSP00000304923:R203Q	R	+	2	0	LRRC28	97710112	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.864000	0.62990	2.597000	0.87782	0.655000	0.94253	CGA	G|1.000;A|0.000	0.000	weak		0.353	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598	
WDR62	284403	hgsc.bcm.edu	37	19	36549690	36549690	+	Silent	SNP	C	C	T	rs11538454	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36549690C>T	ENST00000270301.7	+	2	186	c.186C>T	c.(184-186)ctC>ctT	p.L62L	WDR62_ENST00000401500.2_Silent_p.L62L|WDR62_ENST00000388999.3_Silent_p.L62L|WDR62_ENST00000378860.4_3'UTR			O43379	WDR62_HUMAN	WD repeat domain 62	62					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.L62L(1)		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)			AGGTGTCACTCGAGAAGGTGC	0.592													C|||	629	0.125599	0.0121	0.1326	5008	,	,		19827	0.1716		0.1958	False		,,,				2504	0.1544				p.L62L		Atlas-SNP	.											WDR62,NS,carcinoma,0,1	WDR62	102	1	1	Substitution - coding silent(1)	stomach(1)	c.C186T						PASS	.	C	,	184,4222	115.9+/-153.8	2,180,2021	84.0	72.0	76.0		186,186	-5.9	0.9	19	dbSNP_120	76	1813,6787	324.2+/-316.4	199,1415,2686	no	coding-synonymous,coding-synonymous	WDR62	NM_001083961.1,NM_173636.4	,	201,1595,4707	TT,TC,CC		21.0814,4.1761,15.3545	,	62/1524,62/1519	36549690	1997,11009	2203	4300	6503	SO:0001819	synonymous_variant	284403	exon2			GTCACTCGAGAAG	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.186C>T	19.37:g.36549690C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	70	38	0.542857	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			C|0.854;G|0.000;T|0.146	0.146	strong		0.592	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
ADAMTS20	80070	hgsc.bcm.edu	37	12	43828141	43828141	+	Missense_Mutation	SNP	T	T	A	rs7302446	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:43828141T>A	ENST00000389420.3	-	19	2626	c.2627A>T	c.(2626-2628)aAg>aTg	p.K876M	ADAMTS20_ENST00000395541.2_Missense_Mutation_p.K30M|ADAMTS20_ENST00000553158.1_Missense_Mutation_p.K876M	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	876	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.		K -> M (in dbSNP:rs7302446).		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)		ATGATCACTCTTATGTATGCA	0.338													T|||	183	0.0365415	0.0015	0.0086	5008	,	,		19783	0.0694		0.0348	False		,,,				2504	0.0716				p.K876M		Atlas-SNP	.											.	ADAMTS20	635	.	0			c.A2627T						PASS	.	T	MET/LYS	26,4380	29.9+/-59.1	0,26,2177	81.0	67.0	72.0		2627	3.7	1.0	12	dbSNP_116	72	239,8355	90.4+/-152.6	5,229,4063	yes	missense	ADAMTS20	NM_025003.3	95	5,255,6240	AA,AT,TT		2.781,0.5901,2.0385	probably-damaging	876/1911	43828141	265,12735	2203	4297	6500	SO:0001583	missense	80070	exon19			TCACTCTTATGTA	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.2627A>T	12.37:g.43828141T>A	ENSP00000374071:p.Lys876Met	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	133	69	0.518797	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	78	0.03571428571428571	0	0.0	5	0.013812154696132596	44	0.07692307692307693	29	0.03825857519788918	T	14.92	2.679115	0.47886	0.005901	0.02781	ENSG00000173157	ENST00000389420;ENST00000549670;ENST00000395541;ENST00000553158;ENST00000389417	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	4.91	3.72	0.42706	.	0.121955	0.35708	N	0.003035	T	0.10208	0.0250	M	0.77616	2.38	0.36197	D	0.850469	D;D	0.65815	0.988;0.995	P;P	0.58928	0.848;0.844	T	0.55749	-0.8092	10	0.66056	D	0.02	.	4.4211	0.11481	0.1495:0.1519:0.0:0.6986	rs7302446;rs52813354;rs7302446	876;30	P59510;E9PBD5	ATS20_HUMAN;.	M	876;42;30;876;876	ENSP00000374071:K876M;ENSP00000447427:K42M;ENSP00000378911:K30M;ENSP00000448341:K876M	ENSP00000374068:K876M	K	-	2	0	ADAMTS20	42114408	0.997000	0.39634	0.994000	0.49952	0.925000	0.55904	0.528000	0.23002	0.913000	0.36797	0.533000	0.62120	AAG	T|0.974;A|0.026	0.026	strong		0.338	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
CEP78	84131	hgsc.bcm.edu	37	9	80879149	80879149	+	Silent	SNP	C	C	T	rs1057650	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:80879149C>T	ENST00000424347.2	+	13	1831	c.1542C>T	c.(1540-1542)atC>atT	p.I514I	CEP78_ENST00000415759.2_Silent_p.I515I|CEP78_ENST00000277082.5_Silent_p.I514I|CEP78_ENST00000376598.2_Silent_p.I514I|CEP78_ENST00000376597.4_Silent_p.I515I			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa	514					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)		p.I514I(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						CAAATATGATCCTGGATGATG	0.373													C|||	424	0.0846645	0.1399	0.0778	5008	,	,		15567	0.0109		0.0835	False		,,,				2504	0.092				p.I515I		Atlas-SNP	.											CEP78,NS,carcinoma,0,1	CEP78	79	1	1	Substitution - coding silent(1)	stomach(1)	c.C1545T						PASS	.	C	,	482,3220		27,428,1396	107.0	100.0	102.0		1545,1545	2.3	1.0	9	dbSNP_86	102	693,7485		26,641,3422	no	coding-synonymous,coding-synonymous	CEP78	NM_001098802.1,NM_032171.1	,	53,1069,4818	TT,TC,CC		8.474,13.02,9.8906	,	515/723,515/707	80879149	1175,10705	1851	4089	5940	SO:0001819	synonymous_variant	84131	exon13			TATGATCCTGGAT	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 81"""	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.1542C>T	9.37:g.80879149C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	140	50	0.357143	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Silent	SNP	ENST00000424347.2	37																																																																																				C|0.921;T|0.079	0.079	strong		0.373	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991	
WDR62	284403	hgsc.bcm.edu	37	19	36575645	36575645	+	Splice_Site	SNP	G	G	A	rs2301734	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36575645G>A	ENST00000270301.7	+	12	1641	c.1641G>A	c.(1639-1641)acG>acA	p.T547T	WDR62_ENST00000401500.2_Splice_Site_p.T547T			O43379	WDR62_HUMAN	WD repeat domain 62	547					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.T547T(1)		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)			AGCCAGAGACGGGTGAGCCCG	0.632													G|||	626	0.125	0.0121	0.1311	5008	,	,		15366	0.1726		0.1948	False		,,,				2504	0.1524				p.T547T		Atlas-SNP	.											WDR62,NS,carcinoma,0,1	WDR62	102	1	1	Substitution - coding silent(1)	stomach(1)	c.G1641A						PASS	.	G	,	183,4223	116.7+/-154.6	2,179,2022	78.0	63.0	68.0		1641,1641	-9.0	0.9	19	dbSNP_100	68	1814,6786	326.4+/-317.4	199,1416,2685	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	WDR62	NM_001083961.1,NM_173636.4	,	201,1595,4707	AA,AG,GG		21.093,4.1534,15.3545	,	547/1524,547/1519	36575645	1997,11009	2203	4300	6503	SO:0001630	splice_region_variant	284403	exon12			AGAGACGGGTGAG	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.1642+1G>A	19.37:g.36575645G>A		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	48	21	0.4375	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Silent	SNP	ENST00000270301.7	37	CCDS33001.1																																																																																			G|0.854;A|0.146	0.146	strong		0.632	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	Silent
KDM3A	55818	hgsc.bcm.edu	37	2	86718360	86718360	+	Silent	SNP	C	C	T	rs61750310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:86718360C>T	ENST00000409556.1	+	26	4212	c.3847C>T	c.(3847-3849)Ctg>Ttg	p.L1283L	KDM3A_ENST00000542128.1_Silent_p.L1231L|KDM3A_ENST00000409064.1_Silent_p.L1283L|KDM3A_ENST00000312912.5_Silent_p.L1283L			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	1283					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						ATTCCGATATCTGTCACAGAC	0.398													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20979	0.0		0.002	False		,,,				2504	0.0				p.L1283L	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.C3847T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	114.0	111.0	112.0		3847,3847	2.6	1.0	2	dbSNP_129	112	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous,coding-synonymous	KDM3A	NM_001146688.1,NM_018433.5	,	0,29,6474	TT,TC,CC		0.3256,0.0227,0.223	,	1283/1322,1283/1322	86718360	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	55818	exon25			CGATATCTGTCAC	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.3847C>T	2.37:g.86718360C>T		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	171	87	0.508772	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	37	CCDS1990.1																																																																																			C|0.998;T|0.002	0.002	strong		0.398	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
FRG2B	441581	hgsc.bcm.edu	37	10	135438933	135438933	+	Silent	SNP	C	C	T	rs200793608		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:135438933C>T	ENST00000425520.1	-	4	559	c.507G>A	c.(505-507)ccG>ccA	p.P169P	FRG2B_ENST00000443774.1_Silent_p.P170P	NM_001080998.1	NP_001074467.1	Q96QU4	FRG2B_HUMAN	FSHD region gene 2 family, member B	169						nucleus (GO:0005634)				endometrium(2)|kidney(2)|lung(14)|ovary(1)|prostate(1)	20		all_cancers(35;7.01e-07)|all_epithelial(44;1.45e-05)|Lung NSC(174;0.027)|all_lung(145;0.0384)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)		OV - Ovarian serous cystadenocarcinoma(35;1.12e-06)|all cancers(32;1.43e-06)|Epithelial(32;1.71e-06)		TTCGAATTGACGGTGTTTGGA	0.552																																					p.P169P		Atlas-SNP	.											FRG2B,colon,carcinoma,-1,1	FRG2B	47	1	0			c.G507A						scavenged	.						126.0	151.0	143.0					10																	135438933		2193	4291	6484	SO:0001819	synonymous_variant	441581	exon4			AATTGACGGTGTT	AY744466	CCDS44502.1	10q26.3	2012-10-02			ENSG00000225899	ENSG00000225899			33518	protein-coding gene	gene with protein product						15520407	Standard	NM_001080998		Approved		uc010qvg.2	Q96QU4	OTTHUMG00000019328	ENST00000425520.1:c.507G>A	10.37:g.135438933C>T		Somatic	435	4	0.0091954		WXS	Illumina HiSeq	Phase_I	469	5	0.010661	NM_001080998	Q5VSQ1	Silent	SNP	ENST00000425520.1	37	CCDS44502.1																																																																																			C|0.996;T|0.004	0.004	weak		0.552	FRG2B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467780.1	NM_001080998	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651352	1651352	+	Silent	SNP	C	C	T	rs75391124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1651352C>T	ENST00000399676.2	+	1	320	c.282C>T	c.(280-282)ggC>ggT	p.G94G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	94	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G94G(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CTTGCGGGGGCTCCAAGAGAG	0.667													-|||	308	0.0615016	0.0257	0.0634	5008	,	,		6470	0.0119		0.0994	False		,,,				2504	0.1207				p.G94G		Atlas-SNP	.											KRTAP5-5,NS,haematopoietic_neoplasm,0,1	KRTAP5-5	86	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C282T						PASS	.	C		109,4295		1,107,2094	76.0	95.0	88.0		282	0.4	1.0	11	dbSNP_131	88	684,7910		29,626,3642	no	coding-synonymous	KRTAP5-5	NM_001001480.2		30,733,5736	TT,TC,CC		7.959,2.475,6.1009		94/238	1651352	793,12205	2202	4297	6499	SO:0001819	synonymous_variant	439915	exon1			CGGGGGCTCCAAG	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.282C>T	11.37:g.1651352C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	158	73	0.462025	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			C|0.929;T|0.071	0.071	strong		0.667	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
ZNF76	7629	hgsc.bcm.edu	37	6	35253974	35253974	+	Missense_Mutation	SNP	C	C	T	rs2228265	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35253974C>T	ENST00000373953.3	+	3	409	c.143C>T	c.(142-144)aCg>aTg	p.T48M	ZNF76_ENST00000339411.5_Missense_Mutation_p.T48M|ZNF76_ENST00000440666.2_Missense_Mutation_p.T48M	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	48	3 X 12 AA approximate repeats.		T -> M (in dbSNP:rs2228265).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						CACCAGGTGACGGTACAGAAA	0.567													C|||	452	0.0902556	0.295	0.049	5008	,	,		19862	0.002		0.0229	False		,,,				2504	0.0031				p.T48M	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.C143T						PASS	.	C	MET/THR	1059,3347	387.7+/-326.6	124,811,1268	117.0	100.0	106.0		143	3.8	1.0	6	dbSNP_98	106	208,8392	88.9+/-151.2	4,200,4096	yes	missense	ZNF76	NM_003427.3	81	128,1011,5364	TT,TC,CC		2.4186,24.0354,9.7417	benign	48/571	35253974	1267,11739	2203	4300	6503	SO:0001583	missense	7629	exon3			AGGTGACGGTACA	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"""Zinc fingers, C2H2-type"""	13149	protein-coding gene	gene with protein product		194549	"""zinc finger protein 76 (expressed in testis)"""	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.143C>T	6.37:g.35253974C>T	ENSP00000363064:p.Thr48Met	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	110	47	0.427273	NM_003427	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	187	0.08562271062271062	155	0.3150406504065041	16	0.04419889502762431	1	0.0017482517482517483	15	0.01978891820580475	C	15.78	2.934721	0.52866	0.240354	0.024186	ENSG00000065029	ENST00000469195;ENST00000448999;ENST00000373953;ENST00000417184;ENST00000440666;ENST00000339411	T;T;T;T	0.09723	2.97;2.99;2.95;3.0	4.72	3.85	0.44370	.	0.316668	0.22710	N	0.056590	T	0.03305	0.0096	L	0.29908	0.895	0.31358	P	0.681731	B;P;B;B	0.42757	0.002;0.789;0.423;0.011	B;B;B;B	0.37692	0.001;0.116;0.256;0.006	T	0.39396	-0.9616	9	0.45353	T	0.12	.	10.8061	0.46518	0.0:0.8397:0.0:0.1603	rs2228265;rs28360552;rs35686692;rs58806548	48;48;48;48	B7Z851;B7Z991;P36508-2;P36508	.;.;.;ZNF76_HUMAN	M	48	ENSP00000419106:T48M;ENSP00000363064:T48M;ENSP00000392243:T48M;ENSP00000344097:T48M	ENSP00000229405:T48M	T	+	2	0	ZNF76	35361952	0.934000	0.31675	0.983000	0.44433	0.958000	0.62258	2.231000	0.43009	1.338000	0.45544	0.655000	0.94253	ACG	C|0.910;T|0.090	0.090	strong		0.567	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	
CYSLTR2	57105	hgsc.bcm.edu	37	13	49281414	49281414	+	Missense_Mutation	SNP	G	G	A	rs143735193	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:49281414G>A	ENST00000282018.3	+	1	464	c.461G>A	c.(460-462)aGt>aAt	p.S154N		NM_020377.2	NP_065110.1	Q9NS75	CLTR2_HUMAN	cysteinyl leukotriene receptor 2	154					immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell death (GO:0010942)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cysteinyl leukotriene receptor activity (GO:0001631)|leukotriene receptor activity (GO:0004974)			endometrium(2)|large_intestine(4)|lung(12)|skin(2)	20		all_cancers(8;1.66e-53)|all_epithelial(8;1.96e-19)|all_lung(13;9.94e-09)|all_hematologic(8;7.13e-07)|Lung NSC(96;1.72e-06)|Breast(56;1.53e-05)|Acute lymphoblastic leukemia(8;6.86e-05)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0416)|Lung SC(185;0.0787)		GBM - Glioblastoma multiforme(99;1.19e-09)	Nedocromil(DB00716)	AGCATCAGGAGTGCCTGGATC	0.502													G|||	7	0.00139776	0.0	0.0029	5008	,	,		20192	0.0		0.004	False		,,,				2504	0.001				p.S154N		Atlas-SNP	.											.	CYSLTR2	55	.	0			c.G461A						PASS	.	G	ASN/SER	3,4403	6.2+/-15.9	0,3,2200	169.0	162.0	164.0		461	0.4	0.9	13	dbSNP_134	164	18,8582	14.0+/-48.4	0,18,4282	yes	missense	CYSLTR2	NM_020377.2	46	0,21,6482	AA,AG,GG		0.2093,0.0681,0.1615	benign	154/347	49281414	21,12985	2203	4300	6503	SO:0001583	missense	57105	exon1			TCAGGAGTGCCTG	AB038269	CCDS9412.1	13q14.2	2012-08-10			ENSG00000152207	ENSG00000152207		"""GPCR / Class A : Leukotriene receptors"""	18274	protein-coding gene	gene with protein product		605666				10913337, 1085123	Standard	NM_020377		Approved	CysLT(2), CYSLT2R	uc001vck.2	Q9NS75	OTTHUMG00000016906	ENST00000282018.3:c.461G>A	13.37:g.49281414G>A	ENSP00000282018:p.Ser154Asn	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_020377	Q9HCQ2	Missense_Mutation	SNP	ENST00000282018.3	37	CCDS9412.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	7.598	0.672190	0.14776	6.81E-4	0.002093	ENSG00000152207	ENST00000282018	T	0.36878	1.23	5.89	0.406	0.16366	GPCR, rhodopsin-like superfamily (1);	0.929547	0.09099	N	0.848725	T	0.22085	0.0532	N	0.17248	0.465	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.25950	-1.0117	10	0.26408	T	0.33	.	10.2957	0.43623	0.144:0.4292:0.4268:0.0	.	154	Q9NS75	CLTR2_HUMAN	N	154	ENSP00000282018:S154N	ENSP00000282018:S154N	S	+	2	0	CYSLTR2	48179415	0.000000	0.05858	0.899000	0.35326	0.782000	0.44232	0.468000	0.22051	0.058000	0.16222	-0.127000	0.14921	AGT	G|0.998;A|0.002	0.002	strong		0.502	CYSLTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044894.1		
MUC4	4585	hgsc.bcm.edu	37	3	195511116	195511116	+	Silent	SNP	A	A	G	rs200940092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195511116A>G	ENST00000463781.3	-	2	7794	c.7335T>C	c.(7333-7335)caT>caC	p.H2445H	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.H2445H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGCATGACCTGTGG	0.587																																					p.H2445H		Atlas-SNP	.											MUC4_ENST00000463781,caecum,carcinoma,-2,1	MUC4	1505	1	0			c.T7335C						scavenged	.						46.0	45.0	45.0					3																	195511116		675	1590	2265	SO:0001819	synonymous_variant	4585	exon2			GGTGGCATGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7335T>C	3.37:g.195511116A>G		Somatic	452	12	0.0265487		WXS	Illumina HiSeq	Phase_I	442	60	0.135747	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			A|0.965;G|0.034	0.034	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR8B4	283162	hgsc.bcm.edu	37	11	124294349	124294349	+	Missense_Mutation	SNP	C	C	A	rs7116575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124294349C>A	ENST00000356130.3	-	1	440	c.419G>T	c.(418-420)tGc>tTc	p.C140F		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	140			C -> F (in dbSNP:rs7116575). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CAGCAGAAAGCAGACCCTTGG	0.517													C|||	805	0.160743	0.2648	0.111	5008	,	,		21230	0.1984		0.0875	False		,,,				2504	0.092				p.C140F		Atlas-SNP	.											OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	0			c.G419T						scavenged	.	C	PHE/CYS	986,3416	368.6+/-318.7	111,764,1326	79.0	70.0	73.0		419	4.6	0.1	11	dbSNP_116	73	920,7678	203.1+/-246.2	38,844,3417	yes	missense	OR8B4	NM_001005196.1	205	149,1608,4743	AA,AC,CC		10.7002,22.3989,14.6615	probably-damaging	140/310	124294349	1906,11094	2201	4299	6500	SO:0001583	missense	283162	exon1			AGAAAGCAGACCC	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.419G>T	11.37:g.124294349C>A	ENSP00000348449:p.Cys140Phe	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	122	62	0.508197	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	336	0.15384615384615385	139	0.28252032520325204	29	0.08011049723756906	101	0.17657342657342656	67	0.08839050131926121	c	11.45	1.641959	0.29157	0.223989	0.107002	ENSG00000198657	ENST00000356130	T	0.00220	8.52	4.62	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000020	T	0.00012	0.0000	M	0.94142	3.5	0.20638	P	0.999879906	P	0.35944	0.529	B	0.44163	0.443	T	0.48536	-0.9027	9	0.72032	D	0.01	.	17.6029	0.88030	0.0:1.0:0.0:0.0	rs7116575;rs52820733;rs7116575	140	Q96RC9	OR8B4_HUMAN	F	140	ENSP00000348449:C140F	ENSP00000348449:C140F	C	-	2	0	OR8B4	123799559	0.919000	0.31177	0.107000	0.21349	0.018000	0.09664	2.958000	0.49145	2.564000	0.86499	0.655000	0.94253	TGC	C|0.845;A|0.155	0.155	strong		0.517	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
KIAA1324L	222223	hgsc.bcm.edu	37	7	86542455	86542455	+	Silent	SNP	C	C	T	rs35895874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:86542455C>T	ENST00000450689.2	-	14	1982	c.1797G>A	c.(1795-1797)ggG>ggA	p.G599G	KIAA1324L_ENST00000416314.1_Silent_p.G432G|KIAA1324L_ENST00000297222.6_Silent_p.G359G|KIAA1324L_ENST00000490995.1_5'UTR|KIAA1324L_ENST00000444627.1_Intron	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	599						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					AGGACGCCACCCCATCAACTG	0.478													C|||	387	0.0772764	0.1354	0.0605	5008	,	,		19116	0.003		0.0765	False		,,,				2504	0.0879				p.G599G		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.G1797A						PASS	.	C	,	566,3840	252.4+/-258.8	41,484,1678	116.0	100.0	105.0		1797,1296	4.8	1.0	7	dbSNP_126	105	834,7766	193.0+/-238.8	33,768,3499	no	coding-synonymous,coding-synonymous	KIAA1324L	NM_001142749.2,NM_152748.3	,	74,1252,5177	TT,TC,CC		9.6977,12.8461,10.7643	,	599/1030,432/863	86542455	1400,11606	2203	4300	6503	SO:0001819	synonymous_variant	222223	exon14			CGCCACCCCATCA	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"""EIG121-like"""	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.1797G>A	7.37:g.86542455C>T		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	84	84	1	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Silent	SNP	ENST00000450689.2	37	CCDS47632.1	144	0.06593406593406594	69	0.1402439024390244	17	0.04696132596685083	2	0.0034965034965034965	56	0.07387862796833773	C	10.26	1.301133	0.23650	0.128461	0.096977	ENSG00000164659	ENST00000423294	T	0.19105	2.17	5.82	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.00144	0.0004	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11131	-1.0600	6	0.45353	T	0.12	.	4.3467	0.11136	0.0:0.7213:0.0:0.2787	rs35895874;rs61294000	.	.	.	S	560	ENSP00000406961:G560S	ENSP00000406961:G560S	G	-	1	0	KIAA1324L	86380391	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	0.324000	0.19610	2.752000	0.94435	0.655000	0.94253	GGT	C|0.907;T|0.093	0.093	strong		0.478	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748	
ZNF587B	100293516	hgsc.bcm.edu	37	19	58352806	58352806	+	Missense_Mutation	SNP	T	T	C	rs35313547	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58352806T>C	ENST00000442832.4	+	3	998	c.764T>C	c.(763-765)gTt>gCt	p.V255A	CTD-2583A14.10_ENST00000598031.1_Intron|ZNF587B_ENST00000316462.4_Intron|ZNF587B_ENST00000594901.1_Missense_Mutation_p.V255A	NM_001204818.1	NP_001191747.1	E7ETH6	Z587B_HUMAN	zinc finger protein 587B	255					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AGCAAATATGTTAGCTTCAGT	0.388													.|||	662	0.132188	0.0151	0.1398	5008	,	,		22065	0.1925		0.173	False		,,,				2504	0.181				p.V255A		Atlas-SNP	.											.	.	.	.	0			c.T764C						PASS	.																																			SO:0001583	missense	100293516	exon3			AATATGTTAGCTT	AK299091	CCDS56109.1	19q13.43	2013-01-08				ENSG00000269343		"""Zinc fingers, C2H2-type"", ""-"""	37142	protein-coding gene	gene with protein product							Standard	NM_001204818		Approved		uc021vcp.1	E7ETH6		ENST00000442832.4:c.764T>C	19.37:g.58352806T>C	ENSP00000392410:p.Val255Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_001204818	B4DR41	Missense_Mutation	SNP	ENST00000442832.4	37	CCDS56109.1	285	0.1304945054945055	8	0.016260162601626018	46	0.1270718232044199	98	0.17132867132867133	133	0.17546174142480211	.	0.015	-1.569397	0.00895	.	.	ENSG00000198466	ENST00000442832	T	0.14391	2.51	2.01	-4.03	0.04021	.	.	.	.	.	T	0.00012	0.0000	N	0.03294	-0.36	.	.	.	B;B	0.18461	0.0;0.028	B;B	0.09377	0.001;0.004	T	0.37337	-0.9710	7	.	.	.	.	0.2177	0.00164	0.2831:0.1557:0.2683:0.2929	rs35313547;rs61733716	255;204	E7ETH6;Q92967	.;.	A	255	ENSP00000392410:V255A	.	V	+	2	0	ZNF587	63044618	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.768000	0.01794	-2.618000	0.00441	-1.004000	0.02495	GTT	T|0.866;C|0.134	0.134	strong		0.388	ZNF587B-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466834.2	NM_001204818	
OR51G2	81282	hgsc.bcm.edu	37	11	4936608	4936608	+	Missense_Mutation	SNP	C	C	G	rs12419598	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4936608C>G	ENST00000322013.3	-	1	314	c.286G>C	c.(286-288)Gaa>Caa	p.E96Q	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005238.1	NP_001005238.1	Q8NGK0	O51G2_HUMAN	olfactory receptor, family 51, subfamily G, member 2	96			E -> Q (in dbSNP:rs12419598).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|endometrium(1)|large_intestine(9)|lung(12)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		TGGCTAATTTCTCGTGCTCCA	0.502													C|||	261	0.0521166	0.0053	0.072	5008	,	,		21521	0.002		0.1223	False		,,,				2504	0.0808				p.E96Q		Atlas-SNP	.											.	OR51G2	70	.	0			c.G286C						PASS	.	C	GLN/GLU	124,4278	90.2+/-128.9	1,122,2078	91.0	82.0	85.0		286	5.5	0.1	11	dbSNP_120	85	1034,7562	220.5+/-258.2	62,910,3326	yes	missense	OR51G2	NM_001005238.1	29	63,1032,5404	GG,GC,CC		12.0289,2.8169,8.9091	benign	96/315	4936608	1158,11840	2201	4298	6499	SO:0001583	missense	81282	exon1			TAATTTCTCGTGC	AB065794	CCDS31365.1	11p15.4	2012-08-09			ENSG00000176893	ENSG00000176893		"""GPCR / Class A : Olfactory receptors"""	15198	protein-coding gene	gene with protein product							Standard	NM_001005238		Approved		uc001lzr.1	Q8NGK0	OTTHUMG00000066501	ENST00000322013.3:c.286G>C	11.37:g.4936608C>G	ENSP00000322593:p.Glu96Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_001005238	Q6IFH7	Missense_Mutation	SNP	ENST00000322013.3	37	CCDS31365.1	123	0.05631868131868132	5	0.01016260162601626	29	0.08011049723756906	1	0.0017482517482517483	88	0.11609498680738786	C	6.592	0.477565	0.12521	0.028169	0.120289	ENSG00000176893	ENST00000322013	T	0.00554	6.64	5.47	5.47	0.80525	GPCR, rhodopsin-like superfamily (1);	0.529639	0.17116	N	0.186427	T	0.00039	0.0001	M	0.67569	2.06	0.09310	N	1	B	0.32717	0.381	B	0.34301	0.179	T	0.48375	-0.9041	10	0.59425	D	0.04	.	18.052	0.89353	0.0:1.0:0.0:0.0	rs12419598;rs17252531	96	Q8NGK0	O51G2_HUMAN	Q	96	ENSP00000322593:E96Q	ENSP00000322593:E96Q	E	-	1	0	OR51G2	4893184	0.000000	0.05858	0.077000	0.20336	0.018000	0.09664	-0.312000	0.08113	2.847000	0.97988	0.655000	0.94253	GAA	C|0.921;G|0.079	0.079	strong		0.502	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238	
DNMT1	1786	hgsc.bcm.edu	37	19	10265593	10265593	+	Silent	SNP	G	G	T	rs2228613	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10265593G>T	ENST00000340748.4	-	19	1819	c.1584C>A	c.(1582-1584)atC>atA	p.I528I	DNMT1_ENST00000540357.1_Silent_p.I528I|DNMT1_ENST00000359526.4_Silent_p.I544I			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	528	DNA replication foci-targeting sequence. {ECO:0000250}.|Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CGATCTTGTTGATCAGGTCCT	0.498													G|||	199	0.0397364	0.0212	0.0403	5008	,	,		21065	0.001		0.0865	False		,,,				2504	0.0562				p.I544I		Atlas-SNP	.											.	DNMT1	148	.	0			c.C1632A						PASS	.	G	,	168,4238	112.1+/-150.2	2,164,2037	133.0	112.0	119.0		1632,1584	3.4	1.0	19	dbSNP_98	119	802,7798	187.9+/-235.0	37,728,3535	no	coding-synonymous,coding-synonymous	DNMT1	NM_001130823.1,NM_001379.2	,	39,892,5572	TT,TG,GG		9.3256,3.813,7.4581	,	544/1633,528/1617	10265593	970,12036	2203	4300	6503	SO:0001819	synonymous_variant	1786	exon20			CTTGTTGATCAGG	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.1584C>A	19.37:g.10265593G>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Silent	SNP	ENST00000340748.4	37	CCDS12228.1																																																																																			T|0.063;G|0.937;C|0.000	0.063	strong		0.498	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
CSPG4	1464	hgsc.bcm.edu	37	15	75981300	75981300	+	Silent	SNP	G	G	A	rs144158910	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75981300G>A	ENST00000308508.5	-	3	2198	c.2106C>T	c.(2104-2106)cgC>cgT	p.R702R		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	702	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.|Interaction with COL6A2. {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						CCCCAGTGACGCGGAACAGCA	0.667													G|||	27	0.00539137	0.0008	0.0101	5008	,	,		17603	0.0		0.0129	False		,,,				2504	0.0061				p.R702R		Atlas-SNP	.											.	CSPG4	175	.	0			c.C2106T						PASS	.	G		6,4388		0,6,2191	64.0	64.0	64.0		2106	-11.0	0.0	15	dbSNP_134	64	87,8499		0,87,4206	no	coding-synonymous	CSPG4	NM_001897.4		0,93,6397	AA,AG,GG		1.0133,0.1365,0.7165		702/2323	75981300	93,12887	2197	4293	6490	SO:0001819	synonymous_variant	1464	exon3			AGTGACGCGGAAC	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.2106C>T	15.37:g.75981300G>A		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.992;A|0.008	0.008	strong		0.667	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
VPS4A	27183	hgsc.bcm.edu	37	16	69354963	69354963	+	Silent	SNP	A	A	G	rs1127231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:69354963A>G	ENST00000254950.11	+	9	1017	c.861A>G	c.(859-861)aaA>aaG	p.K287K	COG8_ENST00000564419.1_Intron	NM_013245.2	NP_037377.1			vacuolar protein sorting 4 homolog A (S. cerevisiae)											NS(1)|central_nervous_system(1)|large_intestine(2)|lung(3)	7		Ovarian(137;0.101)				GGTTTGAAAAACGAATTTATA	0.552													G|||	1357	0.270966	0.3714	0.2147	5008	,	,		18592	0.0833		0.2863	False		,,,				2504	0.3528				p.K287K		Atlas-SNP	.											.	VPS4A	18	.	0			c.A861G						PASS	.	G		1673,2713		327,1019,847	38.0	42.0	41.0		861	4.5	1.0	16	dbSNP_86	41	2682,5914		427,1828,2043	no	coding-synonymous	VPS4A	NM_013245.2		754,2847,2890	GG,GA,AA		31.2006,38.1441,33.5464		287/438	69354963	4355,8627	2193	4298	6491	SO:0001819	synonymous_variant	27183	exon9			TGAAAAACGAATT	AF112215	CCDS45517.1	16q23.1	2010-04-21	2006-04-04		ENSG00000132612	ENSG00000132612		"""ATPases / AAA-type"""	13488	protein-coding gene	gene with protein product		609982	"""vacuolar protein sorting 4A (yeast homolog)"", ""vacuolar protein sorting 4A (yeast)"""			10637304, 11563910	Standard	NM_013245		Approved	VPS4, VPS4-1, FLJ22197, SKD2, SKD1, SKD1A	uc002eww.3	Q9UN37		ENST00000254950.11:c.861A>G	16.37:g.69354963A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_013245		Silent	SNP	ENST00000254950.11	37	CCDS45517.1																																																																																			A|0.722;G|0.278	0.278	strong		0.552	VPS4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430563.3	NM_013245	
KRT27	342574	hgsc.bcm.edu	37	17	38938557	38938557	+	Silent	SNP	G	G	A	rs67771170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38938557G>A	ENST00000301656.3	-	1	229	c.189C>T	c.(187-189)ggC>ggT	p.G63G		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				CACTTCCCCCGCCCAGACCTC	0.592													G|||	439	0.0876597	0.0023	0.0605	5008	,	,		16656	0.0704		0.1441	False		,,,				2504	0.182				p.G63G		Atlas-SNP	.											.	KRT27	41	.	0			c.C189T						PASS	.	G		128,4278	93.0+/-131.7	4,120,2079	89.0	78.0	82.0		189	-9.8	0.0	17	dbSNP_130	82	1124,7476	232.6+/-266.2	84,956,3260	no	coding-synonymous	KRT27	NM_181537.3		88,1076,5339	AA,AG,GG		13.0698,2.9051,9.6263		63/460	38938557	1252,11754	2203	4300	6503	SO:0001819	synonymous_variant	342574	exon1			TCCCCCGCCCAGA	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.189C>T	17.37:g.38938557G>A		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_181537		Silent	SNP	ENST00000301656.3	37	CCDS11375.1																																																																																			G|0.899;A|0.101	0.101	strong		0.592	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
TOP1MT	116447	hgsc.bcm.edu	37	8	144403485	144403485	+	Silent	SNP	G	G	C	rs11544482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144403485G>C	ENST00000329245.4	-	8	1066	c.1032C>G	c.(1030-1032)cgC>cgG	p.R344R	TOP1MT_ENST00000523676.1_Silent_p.R246R|TOP1MT_ENST00000519148.1_Silent_p.R246R|TOP1MT_ENST00000521193.1_Silent_p.R246R	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	344					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	CGTGCTCCACGCGGAGGGAAC	0.607													G|||	1374	0.274361	0.4962	0.1873	5008	,	,		14886	0.0774		0.3101	False		,,,				2504	0.2025				p.R344R		Atlas-SNP	.											TOP1MT,NS,carcinoma,0,1	TOP1MT	63	1	0			c.C1032G						PASS	.	G		2093,2311	562.2+/-380.9	510,1073,619	107.0	93.0	98.0		1032	-7.9	0.5	8	dbSNP_120	98	2403,6197	393.7+/-344.5	369,1665,2266	no	coding-synonymous	TOP1MT	NM_052963.1		879,2738,2885	CC,CG,GG		27.9419,47.525,34.574		344/602	144403485	4496,8508	2202	4300	6502	SO:0001819	synonymous_variant	116447	exon8			CTCCACGCGGAGG	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1032C>G	8.37:g.144403485G>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	71	1	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	37	CCDS6400.1																																																																																			G|0.684;C|0.316	0.316	strong		0.607	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
KRT28	162605	hgsc.bcm.edu	37	17	38955991	38955991	+	Missense_Mutation	SNP	C	C	T	rs7209228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38955991C>T	ENST00000306658.7	-	1	220	c.155G>A	c.(154-156)gGc>gAc	p.G52D		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)				ACTGCCCAAGCCCCCTCCCAA	0.567													C|||	521	0.104034	0.1256	0.1124	5008	,	,		17892	0.004		0.1829	False		,,,				2504	0.091				p.G52D	Melanoma(19;789 869 15380 26882 39836)	Atlas-SNP	.											.	KRT28	65	.	0			c.G155A						PASS	.	C	ASP/GLY	496,3910	230.7+/-244.8	31,434,1738	71.0	75.0	74.0		155	3.5	0.8	17	dbSNP_116	74	1518,7082	286.9+/-297.9	131,1256,2913	yes	missense	KRT28	NM_181535.3	94	162,1690,4651	TT,TC,CC		17.6512,11.2574,15.4852	benign	52/465	38955991	2014,10992	2203	4300	6503	SO:0001583	missense	162605	exon1			CCCAAGCCCCCTC	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.155G>A	17.37:g.38955991C>T	ENSP00000305263:p.Gly52Asp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_181535		Missense_Mutation	SNP	ENST00000306658.7	37	CCDS11376.1	239	0.10943223443223443	65	0.13211382113821138	47	0.1298342541436464	0	0.0	127	0.16754617414248021	C	14.98	2.696528	0.48202	0.112574	0.176512	ENSG00000173908	ENST00000306658	D	0.88354	-2.37	5.52	3.47	0.39725	.	0.453405	0.18702	N	0.133542	T	0.00580	0.0019	L	0.29908	0.895	0.41216	P	0.01352500000000001	P	0.43477	0.808	B	0.34590	0.186	T	0.24154	-1.0168	9	0.45353	T	0.12	.	14.9934	0.71412	0.0:0.7198:0.2802:0.0	rs7209228;rs52810060;rs59201813;rs7209228	52	Q7Z3Y7	K1C28_HUMAN	D	52	ENSP00000305263:G52D	ENSP00000305263:G52D	G	-	2	0	KRT28	36209517	0.015000	0.18098	0.846000	0.33378	0.886000	0.51366	2.612000	0.46343	0.765000	0.33221	0.650000	0.86243	GGC	C|0.859;T|0.141	0.141	strong		0.567	KRT28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257201.2	NM_181535	
DES	1674	hgsc.bcm.edu	37	2	220286142	220286142	+	Silent	SNP	G	G	A	rs1058284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220286142G>A	ENST00000373960.3	+	6	1190	c.1104G>A	c.(1102-1104)gcG>gcA	p.A368A		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	368	Coil 2B.|Rod.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		ACAACATTGCGCGCCTGGAGG	0.597													G|||	1671	0.333666	0.4607	0.3429	5008	,	,		17124	0.1835		0.3648	False		,,,				2504	0.2781				p.A368A		Atlas-SNP	.											DES,right_upper_lobe,carcinoma,+1,1	DES	53	1	0			c.G1104A						PASS	.	G		1945,2461	551.7+/-378.3	442,1061,700	60.0	59.0	60.0		1104	-10.2	0.0	2	dbSNP_86	60	3055,5545	469.1+/-367.5	567,1921,1812	no	coding-synonymous	DES	NM_001927.3		1009,2982,2512	AA,AG,GG		35.5233,44.1443,38.4438		368/471	220286142	5000,8006	2203	4300	6503	SO:0001819	synonymous_variant	1674	exon6			CATTGCGCGCCTG	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1104G>A	2.37:g.220286142G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	103	40	0.38835	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Silent	SNP	ENST00000373960.3	37	CCDS33383.1																																																																																			G|0.640;A|0.360	0.360	strong		0.597	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
ABCA13	154664	hgsc.bcm.edu	37	7	48349647	48349647	+	Missense_Mutation	SNP	C	C	T	rs3931814	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48349647C>T	ENST00000435803.1	+	24	9449	c.9425C>T	c.(9424-9426)gCg>gTg	p.A3142V		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	3142			A -> V (in dbSNP:rs3931814).		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						TGGATCGCAGCGGAGGAACTC	0.478													C|||	549	0.109625	0.0408	0.1513	5008	,	,		18983	0.1022		0.1163	False		,,,				2504	0.1738				p.A3142V		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C9425T						PASS	.	C	VAL/ALA	200,3686		5,190,1748	191.0	189.0	190.0		9425	-5.7	0.0	7	dbSNP_108	190	1182,7148		76,1030,3059	yes	missense	ABCA13	NM_152701.3	64	81,1220,4807	TT,TC,CC		14.1897,5.1467,11.313	benign	3142/5059	48349647	1382,10834	1943	4165	6108	SO:0001583	missense	154664	exon24			TCGCAGCGGAGGA	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.9425C>T	7.37:g.48349647C>T	ENSP00000411096:p.Ala3142Val	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	212	102	0.481132	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	230	0.10531135531135531	28	0.056910569105691054	56	0.15469613259668508	63	0.11013986013986014	83	0.10949868073878628	C	11.33	1.607817	0.28623	0.051467	0.141897	ENSG00000179869	ENST00000435803	D	0.85339	-1.97	5.71	-5.73	0.02398	.	1.533070	0.03922	N	0.283799	T	0.00815	0.0027	N	0.04508	-0.205	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.16335	-1.0406	9	0.24483	T	0.36	.	16.2603	0.82536	0.0:0.1942:0.0:0.8058	rs3931814;rs17630233;rs52795567;rs59578642;rs3931814	844;3142	Q86UQ4-3;Q86UQ4	.;ABCAD_HUMAN	V	3142	ENSP00000411096:A3142V	ENSP00000411096:A3142V	A	+	2	0	ABCA13	48320193	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.021000	0.03615	-1.034000	0.03295	-0.140000	0.14226	GCG	C|0.896;T|0.104	0.104	strong		0.478	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
NKX2-6	137814	hgsc.bcm.edu	37	8	23563908	23563908	+	Silent	SNP	A	A	G	rs61732911	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:23563908A>G	ENST00000325017.3	-	1	203	c.204T>C	c.(202-204)gaT>gaC	p.D68D	NKX2-6_ENST00000418222.1_5'UTR|RP11-175E9.1_ENST00000523874.1_RNA	NM_001136271.2	NP_001129743.2	A6NCS4	NKX26_HUMAN	NK2 homeobox 6	68					atrial cardiac muscle cell development (GO:0055014)|cell differentiation (GO:0030154)|digestive tract development (GO:0048565)|embryonic heart tube development (GO:0035050)|hypothalamus development (GO:0021854)|negative regulation of apoptotic process (GO:0043066)|pericardium development (GO:0060039)|pharyngeal system development (GO:0060037)|positive regulation of cell proliferation (GO:0008284)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GCTCCGAACCATCCAGCTTTC	0.617													G|||	835	0.166733	0.0666	0.2003	5008	,	,		13859	0.2044		0.2048	False		,,,				2504	0.2004				p.D68D		Atlas-SNP	.											.	NKX2-6	6	.	0			c.T204C						PASS	.	G		124,1260		6,112,574	29.0	33.0	32.0			-10.3	0.0	8	dbSNP_129	32	652,2530		60,532,999	no	utr-5	NKX2-6	NM_001136271.2		66,644,1573	GG,GA,AA		20.4903,8.9595,16.9952			23563908	776,3790	692	1591	2283	SO:0001819	synonymous_variant	137814	exon1			CGAACCATCCAGC	CN272646		8p21.2	2012-03-09	2011-06-01			ENSG00000180053		"""Homeoboxes / ANTP class : NKL subclass"""	32940	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	611770	"""NK2 transcription factor related, locus 6 (Drosophila)"""			15649947	Standard	NM_001136271		Approved	CSX2, NKX4-2	uc011kzy.3	A6NCS4		ENST00000325017.3:c.204T>C	8.37:g.23563908A>G		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	57	32	0.561404	NM_001136271		Silent	SNP	ENST00000325017.3	37																																																																																				A|0.816;G|0.184	0.184	strong		0.617	NKX2-6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376057.4	NM_001136271	
AZIN1	51582	hgsc.bcm.edu	37	8	103851052	103851052	+	Silent	SNP	T	T	C	rs1062048	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:103851052T>C	ENST00000337198.5	-	5	1532	c.369A>G	c.(367-369)gcA>gcG	p.A123A	AZIN1_ENST00000522311.1_5'UTR|AZIN1_ENST00000347770.4_Silent_p.A123A	NM_148174.2	NP_680479.1	O14977	AZIN1_HUMAN	antizyme inhibitor 1	123					cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|negative regulation of protein catabolic process (GO:0042177)|polyamine biosynthetic process (GO:0006596)|positive regulation of polyamine transmembrane transport (GO:1902269)|regulation of cellular amino acid metabolic process (GO:0006521)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|enzyme inhibitor activity (GO:0004857)|ornithine decarboxylase activator activity (GO:0042978)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	9	Lung NSC(17;0.000143)|all_lung(17;0.000294)		OV - Ovarian serous cystadenocarcinoma(57;0.000196)|STAD - Stomach adenocarcinoma(118;0.0414)			CAACTTTTGCTGCATACTTTA	0.353													T|||	1001	0.19988	0.0628	0.1599	5008	,	,		21040	0.1488		0.2634	False		,,,				2504	0.4008				p.A123A		Atlas-SNP	.											.	AZIN1	26	.	0			c.A369G						PASS	.	T	,	406,4000	199.8+/-223.2	17,372,1814	148.0	132.0	137.0		369,369	5.4	1.0	8	dbSNP_86	137	2250,6350	381.2+/-339.9	289,1672,2339	no	coding-synonymous,coding-synonymous	AZIN1	NM_015878.4,NM_148174.2	,	306,2044,4153	CC,CT,TT		26.1628,9.2147,20.4213	,	123/449,123/449	103851052	2656,10350	2203	4300	6503	SO:0001819	synonymous_variant	51582	exon6			TTTTGCTGCATAC	AAC25391	CCDS6295.1	8p22-q21.3	2005-03-21	2005-03-21	2005-03-21		ENSG00000155096			16432	protein-coding gene	gene with protein product	"""ornithine decarboxylase 1-like"""	607909	"""ornithine decarboxylase antizyme inhibitor"""	OAZIN		9349715, 9110174	Standard	XM_005250969		Approved	OAZI, ODC1L	uc003yky.3	O14977		ENST00000337198.5:c.369A>G	8.37:g.103851052T>C		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	217	98	0.451613	NM_015878	A6NCD5|Q6IBQ7|Q96D20	Silent	SNP	ENST00000337198.5	37	CCDS6295.1																																																																																			T|0.804;C|0.196	0.196	strong		0.353	AZIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380133.1		
ABCA7	10347	hgsc.bcm.edu	37	19	1047161	1047161	+	Silent	SNP	A	A	G	rs3752237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1047161A>G	ENST00000263094.6	+	15	2082	c.1851A>G	c.(1849-1851)ggA>ggG	p.G617G	ABCA7_ENST00000433129.1_Silent_p.G617G|ABCA7_ENST00000533574.1_3'UTR|ABCA7_ENST00000435683.2_Silent_p.G479G	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	617					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CACAGCTGGGAGACATCCTCC	0.672													G|||	3482	0.695288	0.6089	0.7695	5008	,	,		13710	0.8056		0.6004	False		,,,				2504	0.7434				p.G617G		Atlas-SNP	.											.	ABCA7	174	.	0			c.A1851G						PASS	.			2848,1554		936,976,289	39.0	36.0	37.0		1851	-2.8	1.0	19	dbSNP_107	37	5259,3329		1651,1957,686	no	coding-synonymous	ABCA7	NM_019112.3		2587,2933,975	GG,GA,AA		38.7634,35.3021,37.5905		617/2147	1047161	8107,4883	2201	4294	6495	SO:0001819	synonymous_variant	10347	exon15			GCTGGGAGACATC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.1851A>G	19.37:g.1047161A>G		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			A|0.347;G|0.653	0.653	strong		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720540	135720540	+	Missense_Mutation	SNP	A	A	G	rs9814557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:135720540A>G	ENST00000264977.3	+	2	817	c.200A>G	c.(199-201)gAt>gGt	p.D67G	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	67			D -> G (in dbSNP:rs9814557).|D -> N (in dbSNP:rs57374999).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AAAGATGCAGATCTGAACTCT	0.488													A|||	713	0.142372	0.0567	0.1369	5008	,	,		20072	0.0268		0.2773	False		,,,				2504	0.2423				p.D67G		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A200G						PASS	.	A	,GLY/ASP	448,3958	214.5+/-233.7	22,404,1777	111.0	91.0	98.0		,200	3.3	0.5	3	dbSNP_119	98	2694,5906	431.6+/-356.9	412,1870,2018	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,94	434,2274,3795	GG,GA,AA		31.3256,10.168,24.1581	,benign	,67/1151	135720540	3142,9864	2203	4300	6503	SO:0001583	missense	5523	exon2			ATGCAGATCTGAA	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.200A>G	3.37:g.135720540A>G	ENSP00000264977:p.Asp67Gly	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	299	0.13690476190476192	29	0.05894308943089431	56	0.15469613259668508	11	0.019230769230769232	203	0.2678100263852243	A	9.131	1.011458	0.19277	0.10168	0.313256	ENSG00000073711	ENST00000264977	T	0.14391	2.51	5.79	3.3	0.37823	.	0.350012	0.31461	N	0.007608	T	0.00012	0.0000	L	0.40543	1.245	0.58432	P	1.999999999946489E-6	B	0.23442	0.085	B	0.19666	0.026	T	0.41875	-0.9484	9	0.56958	D	0.05	.	8.4145	0.32664	0.7085:0.2165:0.0751:0.0	rs9814557;rs52807842;rs57498404;rs9814557	67	Q06190	P2R3A_HUMAN	G	67	ENSP00000264977:D67G	ENSP00000264977:D67G	D	+	2	0	PPP2R3A	137203230	1.000000	0.71417	0.534000	0.28014	0.980000	0.70556	3.716000	0.54904	1.032000	0.39892	0.523000	0.50628	GAT	A|0.801;G|0.199	0.199	strong		0.488	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
ZNF417	147687	hgsc.bcm.edu	37	19	58421128	58421128	+	Missense_Mutation	SNP	C	C	T	rs201944488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58421128C>T	ENST00000312026.5	-	3	682	c.518G>A	c.(517-519)cGc>cAc	p.R173H	ZNF417_ENST00000536263.1_5'UTR|ZNF417_ENST00000595559.1_Missense_Mutation_p.R172H|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	173				R -> H (in Ref. 3; AAH25783). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		CCCAAACTCGCGGAAGACAAA	0.478													c|||	1646	0.328674	0.2496	0.3069	5008	,	,		19752	0.3631		0.3708	False		,,,				2504	0.3722				p.R173H		Atlas-SNP	.											ZNF417,NS,carcinoma,+1,1	ZNF417	44	1	0			c.G518A						PASS	.	C	HIS/ARG	938,2814		296,346,1234	50.0	52.0	51.0		518	-3.3	0.0	19	dbSNP_134	51	3014,4976		1034,946,2015	no	missense	ZNF417	NM_152475.2	29	1330,1292,3249	TT,TC,CC		37.7222,25.0,33.657	benign	173/576	58421128	3952,7790	1876	3995	5871	SO:0001583	missense	147687	exon3			AACTCGCGGAAGA	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.518G>A	19.37:g.58421128C>T	ENSP00000311319:p.Arg173His	Somatic	407	0	0		WXS	Illumina HiSeq	Phase_I	678	558	0.823009	NM_152475	B4DEU1	Missense_Mutation	SNP	ENST00000312026.5	37	CCDS12965.1	554	0.25366300366300365	111	0.22560975609756098	90	0.24861878453038674	138	0.24125874125874125	215	0.2836411609498681	.	0.284	-0.984691	0.02180	0.25	0.377222	ENSG00000173480	ENST00000312026	T	0.06294	3.32	1.86	-3.31	0.04988	.	.	.	.	.	T	0.00012	0.0000	N	0.16201	0.385	0.53688	P	2.999999999997449E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47086	-0.9144	8	0.41790	T	0.15	.	7.2829	0.26322	0.0:0.4727:0.0:0.5273	.	173;173	F5H0M9;Q8TAU3	.;ZN417_HUMAN	H	173	ENSP00000311319:R173H	ENSP00000311319:R173H	R	-	2	0	ZNF417	63112940	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.558000	0.05978	-0.695000	0.05105	-2.164000	0.00325	CGC	C|0.500;T|0.500	0.500	weak		0.478	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106799997	106799997	+	Silent	SNP	G	G	A	rs257376	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:106799997G>A	ENST00000265717.4	+	11	1486	c.1227G>A	c.(1225-1227)acG>acA	p.T409T		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	409					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TGTTTGGAACGAACATGGATA	0.418													A|||	2352	0.469649	0.5083	0.4597	5008	,	,		16877	0.4514		0.5408	False		,,,				2504	0.3701				p.T409T		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G1227A						PASS	.	A		2197,2209	590.7+/-387.4	544,1109,550	146.0	127.0	133.0		1227	-0.9	1.0	7	dbSNP_79	133	4627,3973	553.1+/-386.2	1253,2121,926	yes	coding-synonymous	PRKAR2B	NM_002736.2		1797,3230,1476	AA,AG,GG		46.1977,49.8638,47.5319		409/419	106799997	6824,6182	2203	4300	6503	SO:0001819	synonymous_variant	5577	exon11			TGGAACGAACATG		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.1227G>A	7.37:g.106799997G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.497;A|0.503	0.503	strong		0.418	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
CIDEA	1149	hgsc.bcm.edu	37	18	12274104	12274104	+	Missense_Mutation	SNP	G	G	T	rs11545881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:12274104G>T	ENST00000320477.9	+	4	408	c.343G>T	c.(343-345)Gtc>Ttc	p.V115F	CIDEA_ENST00000521296.1_3'UTR	NM_001279.3	NP_001270.1	O60543	CIDEA_HUMAN	cell death-inducing DFFA-like effector a	115			V -> F (in dbSNP:rs45619832). {ECO:0000269|Ref.2}.		apoptotic process (GO:0006915)|cell death (GO:0008219)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of execution phase of apoptosis (GO:1900118)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of sequestering of triglyceride (GO:0010890)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|response to stilbenoid (GO:0035634)|temperature homeostasis (GO:0001659)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|mitochondrial envelope (GO:0005740)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(6)|ovary(1)|pancreas(1)|prostate(2)	13						CAGCCAGCACGTCCCCACTTG	0.582													G|||	1824	0.364217	0.1732	0.402	5008	,	,		19407	0.5278		0.3678	False		,,,				2504	0.4233				p.V115F		Atlas-SNP	.											.	CIDEA	32	.	0			c.G343T	GRCh37	CM053175	CIDEA	M	rs45619832	PASS	.	G	PHE/VAL	863,3543	339.9+/-306.0	96,671,1436	75.0	61.0	66.0		343	-7.5	0.0	18	dbSNP_127	66	3116,5484	475.3+/-369.1	571,1974,1755	yes	missense	CIDEA	NM_001279.3	50	667,2645,3191	TT,TG,GG		36.2326,19.5869,30.5936	benign	115/220	12274104	3979,9027	2203	4300	6503	SO:0001583	missense	1149	exon4			CAGCACGTCCCCA	AF041378	CCDS11856.1	18p11.21	2008-08-01			ENSG00000176194	ENSG00000176194			1976	protein-coding gene	gene with protein product		604440				9564035, 18509062	Standard	NM_001279		Approved	CIDE-A	uc002kqt.4	O60543	OTTHUMG00000131691	ENST00000320477.9:c.343G>T	18.37:g.12274104G>T	ENSP00000320209:p.Val115Phe	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	37	36	0.972973	NM_001279	B0YIY7|Q6UPR7	Missense_Mutation	SNP	ENST00000320477.9	37	CCDS11856.1	815	0.3731684981684982	86	0.17479674796747968	138	0.3812154696132597	312	0.5454545454545454	279	0.36807387862796836	G	10.66	1.411750	0.25465	0.195869	0.362326	ENSG00000176194	ENST00000320477	T	0.44083	0.93	5.03	-7.46	0.01369	.	4.069490	0.00732	N	0.000951	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	P;B	0.35923	0.528;0.236	B;B	0.28305	0.088;0.081	T	0.27773	-1.0064	9	0.10111	T	0.7	-6.1579	9.7264	0.40335	0.6478:0.1149:0.2373:0.0	rs45619832;rs57700938;rs61758075	149;115	Q8N5P9;O60543	.;CIDEA_HUMAN	F	115	ENSP00000320209:V115F	ENSP00000320209:V115F	V	+	1	0	CIDEA	12264104	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.415000	0.07106	-1.696000	0.01421	-1.731000	0.00696	GTC	C|0.000;G|0.668;T|0.332	0.332	strong		0.582	CIDEA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254599.2	NM_001279	
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73944185	73944185	+	Silent	SNP	T	T	C	rs2240357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:73944185T>C	ENST00000265755.3	+	9	1605	c.1212T>C	c.(1210-1212)taT>taC	p.Y404Y	GTF2IRD1_ENST00000455841.2_Silent_p.Y436Y|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000476977.1_Silent_p.Y404Y|GTF2IRD1_ENST00000424337.2_Silent_p.Y404Y	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	404					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CCTGCACTTATGGAGTCCCCA	0.602													C|||	1419	0.283347	0.2466	0.2968	5008	,	,		17167	0.4663		0.2107	False		,,,				2504	0.2096				p.Y436Y		Atlas-SNP	.											GTF2IRD1,caecum,carcinoma,+1,1	GTF2IRD1	91	1	0			c.T1308C						scavenged	.	C	,,	1050,3356	724.9+/-409.6	120,810,1273	55.0	54.0	54.0		1308,1212,1212	-6.7	0.8	7	dbSNP_98	54	1993,6607	722.5+/-406.4	224,1545,2531	no	coding-synonymous,coding-synonymous,coding-synonymous	GTF2IRD1	NM_001199207.1,NM_005685.3,NM_016328.2	,,	344,2355,3804	CC,CT,TT		23.1744,23.8311,23.3969	,,	436/977,404/945,404/960	73944185	3043,9963	2203	4300	6503	SO:0001819	synonymous_variant	9569	exon9			CACTTATGGAGTC	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1212T>C	7.37:g.73944185T>C		Somatic	67	1	0.0149254		WXS	Illumina HiSeq	Phase_I	68	29	0.426471	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Silent	SNP	ENST00000265755.3	37	CCDS5571.1																																																																																			T|0.735;C|0.265	0.265	strong		0.602	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
OR8J3	81168	hgsc.bcm.edu	37	11	55905078	55905078	+	Missense_Mutation	SNP	C	C	T	rs61742348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55905078C>T	ENST00000301529.1	-	1	116	c.117G>A	c.(115-117)atG>atA	p.M39I		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M39I(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					GGTTCCCTGCCATGGTCAGCA	0.498													C|||	517	0.103235	0.0499	0.098	5008	,	,		18332	0.1429		0.1213	False		,,,				2504	0.1196				p.M39I		Atlas-SNP	.											OR8J3,NS,carcinoma,0,2	OR8J3	112	2	2	Substitution - Missense(2)	stomach(1)|pancreas(1)	c.G117A						PASS	.	C	ILE/MET	239,4163	140.4+/-175.9	7,225,1969	136.0	132.0	134.0		117	1.3	0.0	11	dbSNP_129	134	1007,7585	216.6+/-255.6	54,899,3343	no	missense	OR8J3	NM_001004064.1	10	61,1124,5312	TT,TC,CC		11.7202,5.4294,9.589	benign	39/316	55905078	1246,11748	2201	4296	6497	SO:0001583	missense	81168	exon1			CCCTGCCATGGTC		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.117G>A	11.37:g.55905078C>T	ENSP00000301529:p.Met39Ile	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	163	78	0.478528	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	253	0.11584249084249085	32	0.06504065040650407	33	0.09116022099447514	88	0.15384615384615385	100	0.13192612137203166	C	10.71	1.426952	0.25726	0.054294	0.117202	ENSG00000167822	ENST00000301529	T	0.00524	6.82	3.26	1.31	0.21738	.	1.026030	0.07741	N	0.946937	T	0.00012	0.0000	N	0.05467	-0.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39231	-0.9624	9	0.59425	D	0.04	.	4.5064	0.11891	0.0:0.5487:0.162:0.2893	.	39	Q8NGG0	OR8J3_HUMAN	I	39	ENSP00000301529:M39I	ENSP00000301529:M39I	M	-	3	0	OR8J3	55661654	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-0.509000	0.06336	0.065000	0.16485	0.289000	0.19496	ATG	C|0.901;T|0.099	0.099	strong		0.498	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
NARFL	64428	hgsc.bcm.edu	37	16	784765	784765	+	Silent	SNP	C	C	T	rs9928077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:784765C>T	ENST00000251588.2	-	5	562	c.546G>A	c.(544-546)gcG>gcA	p.A182A	NARFL_ENST00000301694.5_Missense_Mutation_p.R138H|HAGHL_ENST00000569604.1_3'UTR|NARFL_ENST00000568545.1_Silent_p.A80A|NARFL_ENST00000540986.1_Silent_p.A80A|NARFL_ENST00000562862.1_5'Flank	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	182					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				GCAGGGGCAGCGCCTGTCTGC	0.597													C|||	1886	0.376597	0.149	0.464	5008	,	,		17362	0.6736		0.2406	False		,,,				2504	0.456				p.A182A		Atlas-SNP	.											NARFL,NS,carcinoma,0,1	NARFL	31	1	0			c.G546A						PASS	.	C		560,3840	246.8+/-255.3	31,498,1671	73.0	82.0	79.0		546	3.8	1.0	16	dbSNP_119	79	1831,6769	329.0+/-318.6	201,1429,2670	no	coding-synonymous	NARFL	NM_022493.1		232,1927,4341	TT,TC,CC		21.2907,12.7273,18.3923		182/477	784765	2391,10609	2200	4300	6500	SO:0001819	synonymous_variant	64428	exon5			GGGCAGCGCCTGT	AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"""iron-only hydrogenase-like protein 1"""	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.546G>A	16.37:g.784765C>T		Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	145	61	0.42069	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Silent	SNP	ENST00000251588.2	37	CCDS10425.1	820	0.37545787545787546	71	0.1443089430894309	149	0.4116022099447514	398	0.6958041958041958	202	0.26649076517150394	C	10.53	1.375962	0.24857	0.127273	0.212907	ENSG00000103245	ENST00000301694	T	0.30448	1.53	4.79	3.84	0.44239	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46927	P	7.420000000000204E-4	P	0.42078	0.77	B	0.33750	0.169	T	0.14420	-1.0473	7	0.46703	T	0.11	-20.9669	9.771	0.40589	0.0801:0.1424:0.7775:0.0	rs9928077;rs9928077	138	B4DEE7	.	H	138	ENSP00000301694:R138H	ENSP00000301694:R138H	R	-	2	0	NARFL	724766	0.999000	0.42202	0.983000	0.44433	0.135000	0.20990	1.588000	0.36633	1.020000	0.39573	-0.299000	0.09455	CGC	C|0.740;T|0.260	0.260	strong		0.597	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493	
NLRP2	55655	hgsc.bcm.edu	37	19	55494188	55494188	+	Silent	SNP	C	C	T	rs3826883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55494188C>T	ENST00000543010.1	+	6	1265	c.1122C>T	c.(1120-1122)gaC>gaT	p.D374D	NLRP2_ENST00000537859.1_Silent_p.D352D|NLRP2_ENST00000427260.2_Silent_p.D351D|NLRP2_ENST00000339757.7_Silent_p.D352D|NLRP2_ENST00000391721.4_Silent_p.D350D|NLRP2_ENST00000538819.1_Silent_p.D350D|NLRP2_ENST00000263437.6_Silent_p.D371D|NLRP2_ENST00000448584.2_Silent_p.D374D	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	374	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)			large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		ACTTTGGAGACGAGGACCAAG	0.622													C|||	546	0.109026	0.0794	0.1412	5008	,	,		18151	0.0516		0.2386	False		,,,				2504	0.0521				p.D374D		Atlas-SNP	.											.	NLRP2	161	.	0			c.C1122T						PASS	.	C	,,,	459,3947	208.8+/-229.8	28,403,1772	25.0	25.0	25.0		1122,1056,1053,1122	-3.3	0.0	19	dbSNP_107	25	1926,6662	317.0+/-313.0	221,1484,2589	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP2	NM_001174081.1,NM_001174082.1,NM_001174083.1,NM_017852.3	,,,	249,1887,4361	TT,TC,CC		22.4266,10.4176,18.3546	,,,	374/1063,352/1041,351/1040,374/1063	55494188	2385,10609	2203	4294	6497	SO:0001819	synonymous_variant	55655	exon6			TGGAGACGAGGAC	AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.1122C>T	19.37:g.55494188C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	138	75	0.543478	NM_017852	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Silent	SNP	ENST00000543010.1	37	CCDS12913.1																																																																																			C|0.833;T|0.167	0.167	strong		0.622	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
TRERF1	55809	hgsc.bcm.edu	37	6	42224546	42224546	+	Missense_Mutation	SNP	A	A	T	rs2295275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42224546A>T	ENST00000372922.4	-	12	3062	c.2500T>A	c.(2500-2502)Tgt>Agt	p.C834S	TRERF1_ENST00000541110.1_Missense_Mutation_p.C854S|TRERF1_ENST00000372917.4_Missense_Mutation_p.C751S|TRERF1_ENST00000340840.2_Missense_Mutation_p.C751S|TRERF1_ENST00000354325.2_Missense_Mutation_p.C751S	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	834	ELM2. {ECO:0000255|PROSITE- ProRule:PRU00512}.|Interacts with CREBBP.		C -> S (in dbSNP:rs2295275).		cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCACTGGAACAGCACAAATTC	0.458													A|||	253	0.0505192	0.003	0.0548	5008	,	,		20871	0.1042		0.0815	False		,,,				2504	0.0245				p.C834S		Atlas-SNP	.											.	TRERF1	124	.	0			c.T2500A	GRCh37	CM065497	TRERF1	M	rs2295275	PASS	.	A	SER/CYS	52,4354	52.3+/-87.9	0,52,2151	115.0	113.0	114.0		2500	5.6	1.0	6	dbSNP_100	114	682,7918	170.9+/-221.9	33,616,3651	yes	missense	TRERF1	NM_033502.2	112	33,668,5802	TT,TA,AA		7.9302,1.1802,5.6435	probably-damaging	834/1201	42224546	734,12272	2203	4300	6503	SO:0001583	missense	55809	exon12			TGGAACAGCACAA	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.2500T>A	6.37:g.42224546A>T	ENSP00000362013:p.Cys834Ser	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	169	78	0.461538	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	134	0.06135531135531135	0	0.0	26	0.0718232044198895	50	0.08741258741258741	58	0.07651715039577836	A	23.7	4.445165	0.83993	0.011802	0.079302	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62	5.63	5.63	0.86233	ELM2 domain (2);	0.000000	0.64402	D	0.000004	T	0.49098	0.1537	M	0.75615	2.305	0.09310	P	0.99999999753524	D;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;0.5	D;D;D;D;P	0.87578	0.997;0.998;0.998;0.997;0.619	T	0.55062	-0.8199	9	0.66056	D	0.02	-7.7396	16.1297	0.81418	1.0:0.0:0.0:0.0	rs2295275;rs17703993;rs52832820;rs2295275	751;854;834;590;590	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	S	854;751;834;751;751	ENSP00000439689:C854S;ENSP00000362008:C751S;ENSP00000362013:C834S;ENSP00000339438:C751S;ENSP00000346285:C751S	ENSP00000339438:C751S	C	-	1	0	TRERF1	42332524	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.173000	0.94815	2.270000	0.75569	0.460000	0.39030	TGT	A|0.937;T|0.063	0.063	strong		0.458	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
ZNF48	197407	hgsc.bcm.edu	37	16	30409699	30409699	+	Silent	SNP	C	C	T	rs9936065	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30409699C>T	ENST00000320159.2	+	2	1504	c.1128C>T	c.(1126-1128)cgC>cgT	p.R376R	SEPT1_ENST00000570039.1_5'Flank	NM_001214906.1|NM_001214907.1|NM_001214909.1|NM_152652.2	NP_001201835.1|NP_001201836.1|NP_001201838.1|NP_689865.2	Q96MX3	ZNF48_HUMAN	zinc finger protein 48	376					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)|pancreas(1)|skin(1)	21						CCCTTCTTCGCCACCGCCTCA	0.667													C|||	491	0.0980431	0.3147	0.049	5008	,	,		15084	0.0		0.0308	False		,,,				2504	0.0102				p.R376R		Atlas-SNP	.											ZNF48,NS,carcinoma,+2,1	ZNF48	34	1	0			c.C1128T						PASS	.	C	,,,	1110,3284	396.7+/-330.2	142,826,1229	91.0	58.0	69.0		1128,759,1128,1128	-1.2	1.0	16	dbSNP_119	69	347,8253	117.7+/-177.3	6,335,3959	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF48	NM_001214906.1,NM_001214907.1,NM_001214909.1,NM_152652.2	,,,	148,1161,5188	TT,TC,CC		4.0349,25.2617,11.2129	,,,	376/619,253/496,376/619,376/619	30409699	1457,11537	2197	4300	6497	SO:0001819	synonymous_variant	197407	exon3			TCTTCGCCACCGC	M88358, AK056313	CCDS10679.1, CCDS73868.1	16p11.2	2013-01-08			ENSG00000180035	ENSG00000180035		"""Zinc fingers, C2H2-type"""	13114	protein-coding gene	gene with protein product			"""zinc finger protein 553"""	ZNF553		1505991	Standard	NM_152652		Approved	DKFZp762K013, FLJ31751, MGC43952	uc021tgi.1	Q96MX3	OTTHUMG00000048195	ENST00000320159.2:c.1128C>T	16.37:g.30409699C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	110	56	0.509091	NM_001214906	Q15920|Q4G0R3|Q69YP3|Q96IL9	Silent	SNP	ENST00000320159.2	37	CCDS10679.1																																																																																			C|0.886;T|0.114	0.114	strong		0.667	ZNF48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255549.2	NM_152652	
EVC2	132884	hgsc.bcm.edu	37	4	5642274	5642274	+	Silent	SNP	T	T	C	rs13131655	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5642274T>C	ENST00000344408.5	-	10	1490	c.1437A>G	c.(1435-1437)gaA>gaG	p.E479E	EVC2_ENST00000344938.1_Silent_p.E479E|EVC2_ENST00000310917.2_Silent_p.E399E	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	479					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						ACTCTTCTGCTTCCTCCATTG	0.463													T|||	1152	0.230032	0.5318	0.1542	5008	,	,		22239	0.001		0.2237	False		,,,				2504	0.1186				p.E479E		Atlas-SNP	.											.	EVC2	202	.	0			c.A1437G						PASS	.	T	,	2027,2379	564.7+/-381.5	477,1073,653	411.0	346.0	368.0		1197,1437	0.0	0.9	4	dbSNP_121	368	1809,6791	325.9+/-317.1	185,1439,2676	no	coding-synonymous,coding-synonymous	EVC2	NM_001166136.1,NM_147127.4	,	662,2512,3329	CC,CT,TT		21.0349,46.0054,29.4941	,	399/1229,479/1309	5642274	3836,9170	2203	4300	6503	SO:0001819	synonymous_variant	132884	exon10			TTCTGCTTCCTCC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1437A>G	4.37:g.5642274T>C		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	195	87	0.446154	NM_147127	Q86YT3|Q86YT4|Q8NG49	Silent	SNP	ENST00000344408.5	37	CCDS3382.2																																																																																			T|0.716;C|0.284	0.284	strong		0.463	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
GAB4	128954	hgsc.bcm.edu	37	22	17469026	17469026	+	Silent	SNP	G	G	A	rs5992604	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:17469026G>A	ENST00000400588.1	-	3	617	c.510C>T	c.(508-510)caC>caT	p.H170H	GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	170										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)				AGCAGAGGCCGTGACTGGCTG	0.562													g|||	2125	0.424321	0.382	0.4611	5008	,	,		18368	0.4008		0.3966	False		,,,				2504	0.5082				p.H170H		Atlas-SNP	.											.	GAB4	95	.	0			c.C510T						PASS	.	-		1707,2563		370,967,798	45.0	57.0	53.0		510	-1.9	0.0	22	dbSNP_114	53	3592,4942		786,2020,1461	no	coding-synonymous	GAB4	NM_001037814.1		1156,2987,2259	AA,AG,GG		42.0905,39.9766,41.3855		170/575	17469026	5299,7505	2135	4267	6402	SO:0001819	synonymous_variant	128954	exon3			GAGGCCGTGACTG	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.510C>T	22.37:g.17469026G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			G|0.617;A|0.383	0.383	strong		0.562	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
KIAA1429	25962	hgsc.bcm.edu	37	8	95541302	95541302	+	Silent	SNP	A	A	G	rs957448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95541302A>G	ENST00000297591.5	-	7	951	c.876T>C	c.(874-876)ggT>ggC	p.G292G	KIAA1429_ENST00000421249.2_Silent_p.G292G|KIAA1429_ENST00000437199.1_Silent_p.G292G	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	292	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			ACCCACCTTCACcttcttcat	0.403													A|||	1768	0.353035	0.2723	0.438	5008	,	,		22682	0.4861		0.3101	False		,,,				2504	0.3088				p.G292G		Atlas-SNP	.											.	KIAA1429	176	.	0			c.T876C						PASS	.	A	,	1242,3164	427.0+/-341.4	189,864,1150	412.0	345.0	368.0		876,876	4.0	1.0	8	dbSNP_86	368	2131,6469	366.1+/-334.2	271,1589,2440	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	460,2453,3590	GG,GA,AA		24.7791,28.1888,25.9342	,	292/1813,292/1148	95541302	3373,9633	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon7			ACCTTCACCTTCT	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.876T>C	8.37:g.95541302A>G		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	167	82	0.491018	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			A|0.691;G|0.309	0.309	strong		0.403	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
LCT	3938	hgsc.bcm.edu	37	2	136594158	136594158	+	Silent	SNP	G	G	A	rs2236783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:136594158G>A	ENST00000264162.2	-	1	592	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	194	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CATCACTGAGGGTCTGGAGTT	0.517													g|||	1745	0.348442	0.1233	0.402	5008	,	,		19559	0.372		0.5964	False		,,,				2504	0.3354				p.T194T		Atlas-SNP	.											.	LCT	309	.	0			c.C582T						PASS	.			1049,3357		122,805,1276	147.0	110.0	123.0		582	-0.4	0.0	2	dbSNP_98	123	6004,2596		2182,1640,478	no	coding-synonymous	LCT	NM_002299.2		2304,2445,1754	AA,AG,GG		30.186,23.8084,45.7712		194/1928	136594158	7053,5953	2203	4300	6503	SO:0001819	synonymous_variant	3938	exon1			ACTGAGGGTCTGG	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.582C>T	2.37:g.136594158G>A		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	205	103	0.502439	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																			G|0.584;A|0.416	0.416	strong		0.517	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
LMF1	64788	hgsc.bcm.edu	37	16	961051	961051	+	Silent	SNP	C	C	T	rs2277893	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:961051C>T	ENST00000262301.11	-	4	561	c.543G>A	c.(541-543)ggG>ggA	p.G181G	LMF1_ENST00000399843.2_Silent_p.G181G|LMF1_ENST00000543238.1_Intron|LMF1_ENST00000539379.1_3'UTR|LMF1_ENST00000568897.1_5'UTR	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	181					chylomicron remnant clearance (GO:0034382)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of lipoprotein lipase activity (GO:0051006)|protein glycosylation in Golgi (GO:0033578)|protein maturation (GO:0051604)|protein secretion (GO:0009306)|regulation of cholesterol metabolic process (GO:0090181)|regulation of triglyceride metabolic process (GO:0090207)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)		p.G181G(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(1)	18		Hepatocellular(780;0.00308)				TCCCCAGGAACCCCGTCTCCA	0.532													C|||	1913	0.381989	0.5613	0.3631	5008	,	,		16735	0.3056		0.1769	False		,,,				2504	0.4427				p.G181G		Atlas-SNP	.											LMF1,NS,carcinoma,0,1	LMF1	42	1	1	Substitution - coding silent(1)	stomach(1)	c.G543A						PASS	.	C		1896,2084		473,950,567	46.0	52.0	50.0		543	-9.1	0.5	16	dbSNP_100	50	1512,6772		140,1232,2770	no	coding-synonymous	LMF1	NM_022773.2		613,2182,3337	TT,TC,CC		18.2521,47.6382,27.7886		181/568	961051	3408,8856	1990	4142	6132	SO:0001819	synonymous_variant	64788	exon4			CAGGAACCCCGTC	AK022743	CCDS45373.1	16p13.3	2008-02-05	2007-11-29	2007-11-29	ENSG00000103227	ENSG00000103227			14154	protein-coding gene	gene with protein product		611761	"""chromosome 16 open reading frame 26"", ""transmembrane protein 112"""	C16orf26, TMEM112		11157797, 17994020	Standard	NM_022773		Approved	FLJ12681, JFP11, FLJ22302, TMEM112A	uc021tae.1	Q96S06	OTTHUMG00000047848	ENST00000262301.11:c.543G>A	16.37:g.961051C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	67	35	0.522388	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Silent	SNP	ENST00000262301.11	37	CCDS45373.1																																																																																			C|0.748;T|0.252	0.252	strong		0.532	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773	
PPA1	5464	hgsc.bcm.edu	37	10	71969338	71969338	+	Silent	SNP	C	C	A	rs79719906	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:71969338C>A	ENST00000373232.3	-	7	714	c.615G>T	c.(613-615)gcG>gcT	p.A205A		NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	205					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						CTGCATTAAACGCAAACTCAT	0.358																																					p.A205A		Atlas-SNP	.											PPA1,NS,carcinoma,-1,2	PPA1	24	2	0			c.G615T						scavenged	.						113.0	110.0	111.0					10																	71969338		2203	4300	6503	SO:0001819	synonymous_variant	5464	exon7			ATTAAACGCAAAC	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"""cytosolic inorganic pyrophosphatase"", ""inorganic pyrophosphatase 1"", ""pyrophosphate phospho-hydrolase"""	179030	"""pyrophosphatase (inorganic)"""	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.615G>T	10.37:g.71969338C>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	167	5	0.0299401	NM_021129	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Silent	SNP	ENST00000373232.3	37	CCDS7299.1																																																																																			C|0.987;A|0.013	0.013	strong		0.358	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048490.2	NM_021129	
CYP2A7	1549	hgsc.bcm.edu	37	19	41383134	41383134	+	Silent	SNP	A	A	G	rs147847954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41383134A>G	ENST00000301146.4	-	7	1663	c.1122T>C	c.(1120-1122)gtT>gtC	p.V374V	CYP2A7_ENST00000291764.3_Silent_p.V323V|CTC-490E21.12_ENST00000601627.1_Intron	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	374						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGTCCTTTTTAACCCTGCGGG	0.537													.|||	60	0.0119808	0.0	0.0144	5008	,	,		18790	0.002		0.0457	False		,,,				2504	0.002				p.V374V		Atlas-SNP	.											.	CYP2A7	71	.	0			c.T1122C						PASS	.	A	,	24,4382	27.2+/-55.0	0,24,2179	102.0	90.0	94.0		1122,969	-2.4	0.0	19	dbSNP_134	94	294,8304	99.5+/-161.0	15,264,4020	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	15,288,6199	GG,GA,AA		3.4194,0.5447,2.4454	,	374/495,323/444	41383134	318,12686	2203	4299	6502	SO:0001819	synonymous_variant	1549	exon7			CTTTTTAACCCTG	NM_000764	CCDS12569.1, CCDS42570.1	19q13.2	2013-07-25	2003-01-14		ENSG00000198077	ENSG00000198077		"""Cytochrome P450s"""	2611	protein-coding gene	gene with protein product		608054	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 7"""			7668294, 15128046	Standard	NM_030589		Approved	CYP2A	uc002opm.3	P20853	OTTHUMG00000182715	ENST00000301146.4:c.1122T>C	19.37:g.41383134A>G		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	206	91	0.441748	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			A|0.978;G|0.022	0.022	strong		0.537	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589	
KRT36	8689	hgsc.bcm.edu	37	17	39643646	39643646	+	Missense_Mutation	SNP	G	G	A	rs2301354	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39643646G>A	ENST00000328119.6	-	5	943	c.944C>T	c.(943-945)aCg>aTg	p.T315M	KRT36_ENST00000393986.2_Missense_Mutation_p.T265M	NM_003771.4	NP_003762.1	O76013	KRT36_HUMAN	keratin 36	315	Coil 2.|Rod.		T -> M (in dbSNP:rs2301354).		regulation of keratinocyte differentiation (GO:0045616)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of epidermis (GO:0030280)			breast(2)|cervix(1)|kidney(2)|large_intestine(3)|lung(8)|skin(1)	17		Breast(137;0.000286)				CGCGTTGACCGTACGTCTCAG	0.637													G|||	2426	0.484425	0.4024	0.5447	5008	,	,		19858	0.3323		0.5398	False		,,,				2504	0.6524				p.T315M		Atlas-SNP	.											.	KRT36	52	.	0			c.C944T						PASS	.	G	MET/THR	1824,2582	531.5+/-373.2	374,1076,753	76.0	55.0	62.0		944	1.1	0.9	17	dbSNP_100	62	4702,3898	605.3+/-394.9	1277,2148,875	yes	missense	KRT36	NM_003771.4	81	1651,3224,1628	AA,AG,GG		45.3256,41.3981,49.8232	benign	315/468	39643646	6526,6480	2203	4300	6503	SO:0001583	missense	8689	exon5			TTGACCGTACGTC	Y16792	CCDS11395.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000126337	ENSG00000126337		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6454	protein-coding gene	gene with protein product		604540	"""keratin, hair, acidic, 6"""	KRTHA6		9756910, 16831889	Standard	XM_005257762		Approved		uc002hwt.3	O76013	OTTHUMG00000133431	ENST00000328119.6:c.944C>T	17.37:g.39643646G>A	ENSP00000329165:p.Thr315Met	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_003771	Q86XG4	Missense_Mutation	SNP	ENST00000328119.6	37	CCDS11395.1	992	0.4542124542124542	192	0.3902439024390244	222	0.6132596685082873	169	0.29545454545454547	409	0.5395778364116095	G	14.11	2.436719	0.43224	0.413981	0.546744	ENSG00000126337	ENST00000393986;ENST00000328119	D;D	0.89343	-2.5;-2.5	5.95	1.13	0.20643	Filament (1);	0.292907	0.24162	N	0.040964	T	0.00012	0.0000	M	0.82132	2.575	0.48288	P	3.790000000000182E-4	P	0.43826	0.818	B	0.41571	0.36	T	0.44997	-0.9291	9	0.72032	D	0.01	.	17.8773	0.88829	0.0:0.0:0.5399:0.4601	rs2301354;rs17581044;rs59835513;rs2301354	315	O76013	KRT36_HUMAN	M	265;315	ENSP00000377555:T265M;ENSP00000329165:T315M	ENSP00000329165:T315M	T	-	2	0	KRT36	36897172	0.000000	0.05858	0.929000	0.37066	0.676000	0.39594	-0.279000	0.08479	0.389000	0.25086	0.655000	0.94253	ACG	G|0.523;A|0.477	0.477	strong		0.637	KRT36-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259508.1	NM_003771	
GALNT13	114805	hgsc.bcm.edu	37	2	155102403	155102403	+	Silent	SNP	T	T	C	rs375635744		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:155102403T>C	ENST00000392825.3	+	7	1332	c.765T>C	c.(763-765)taT>taC	p.Y255Y	GALNT13_ENST00000409237.1_Silent_p.Y255Y	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	255					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)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						ACATGACTTATGGGGGTTTTA	0.413																																					p.Y255Y		Atlas-SNP	.											.	GALNT13	170	.	0			c.T765C						PASS	.	T		0,4406		0,0,2203	109.0	108.0	108.0		765	0.3	1.0	2		108	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GALNT13	NM_052917.2		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		255/557	155102403	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	114805	exon7			GACTTATGGGGGT	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23242	protein-coding gene	gene with protein product	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13"", ""polypeptide GalNAc transferase 13"""	608369	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"""			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.765T>C	2.37:g.155102403T>C		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	48	23	0.479167	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Silent	SNP	ENST00000392825.3	37	CCDS2199.1																																																																																			.	.	weak		0.413	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917	
OR2T8	343172	hgsc.bcm.edu	37	1	248085124	248085124	+	Missense_Mutation	SNP	G	G	A	rs4590708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248085124G>A	ENST00000319968.4	+	1	805	c.805G>A	c.(805-807)Gac>Aac	p.D269N		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			CACTAACCACGACAAGGTTGT	0.488													G|||	1755	0.350439	0.2769	0.2709	5008	,	,		12953	0.5387		0.1998	False		,,,				2504	0.4673				p.D269N		Atlas-SNP	.											.	OR2T8	67	.	0			c.G805A						PASS	.	G	ASN/ASP	1112,3294	383.0+/-324.7	143,826,1234	111.0	102.0	105.0		805	3.6	0.0	1	dbSNP_111	105	1898,6698	333.8+/-320.7	204,1490,2604	no	missense	OR2T8	NM_001005522.1	23	347,2316,3838	AA,AG,GG		22.08,25.2383,23.1503	benign	269/313	248085124	3010,9992	2203	4298	6501	SO:0001583	missense	343172	exon1			AACCACGACAAGG		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.805G>A	1.37:g.248085124G>A	ENSP00000326225:p.Asp269Asn	Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	304	191	0.628289	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	37	CCDS31100.1	684	0.3131868131868132	130	0.26422764227642276	95	0.26243093922651933	308	0.5384615384615384	151	0.19920844327176782	G	12.38	1.919763	0.33908	0.252383	0.2208	ENSG00000177462	ENST00000319968	T	0.00216	8.53	3.56	3.56	0.40772	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34133	U	0.004239	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	P	0.40970	0.734	B	0.43301	0.415	T	0.00000	-1.3415	9	0.66056	D	0.02	.	8.9138	0.35570	0.1066:0.0:0.8934:0.0	rs4590708	269	A6NH00	OR2T8_HUMAN	N	269	ENSP00000326225:D269N	ENSP00000326225:D269N	D	+	1	0	OR2T8	246151747	0.000000	0.05858	0.005000	0.12908	0.012000	0.07955	0.194000	0.17135	1.816000	0.52996	0.404000	0.27445	GAC	G|0.755;A|0.245	0.245	strong		0.488	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
NLRP5	126206	hgsc.bcm.edu	37	19	56515334	56515334	+	Silent	SNP	C	C	T	rs1560691	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56515334C>T	ENST00000390649.3	+	2	315	c.315C>T	c.(313-315)aaC>aaT	p.N105N		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	105	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				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)		AGAATGCCAACGTGGAATGTC	0.433													C|||	1007	0.201078	0.205	0.1744	5008	,	,		23874	0.3264		0.1332	False		,,,				2504	0.1554				p.N105N		Atlas-SNP	.											.	NLRP5	217	.	0			c.C315T						PASS	.	C		727,3297		62,603,1347	87.0	85.0	85.0		315	-5.8	0.0	19	dbSNP_88	85	912,7452		56,800,3326	no	coding-synonymous	NLRP5	NM_153447.4		118,1403,4673	TT,TC,CC		10.9039,18.0666,13.2305		105/1201	56515334	1639,10749	2012	4182	6194	SO:0001819	synonymous_variant	126206	exon2			TGCCAACGTGGAA	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.315C>T	19.37:g.56515334C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	115	60	0.521739	NM_153447	A8MTY4|Q86W29	Silent	SNP	ENST00000390649.3	37	CCDS12938.1																																																																																			C|0.797;T|0.203	0.203	strong		0.433	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
C9orf40	55071	hgsc.bcm.edu	37	9	77563087	77563087	+	Silent	SNP	C	C	T	rs2769058	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:77563087C>T	ENST00000376854.5	-	2	736	c.462G>A	c.(460-462)caG>caA	p.Q154Q		NM_017998.2	NP_060468.2	Q8IXQ3	CI040_HUMAN	chromosome 9 open reading frame 40	154								p.Q154Q(1)		lung(2)|stomach(1)	3						TCCTCCAGTACTGGAAGGTAT	0.383													C|||	1619	0.323283	0.2398	0.3458	5008	,	,		16486	0.3988		0.3429	False		,,,				2504	0.3221				p.Q154Q		Atlas-SNP	.											C9orf40,NS,carcinoma,0,1	C9orf40	5	1	1	Substitution - coding silent(1)	stomach(1)	c.G462A						PASS	.	C		1158,3248	410.4+/-335.4	156,846,1201	106.0	99.0	102.0		462	6.0	1.0	9	dbSNP_100	102	2773,5827	439.5+/-359.2	444,1885,1971	no	coding-synonymous	C9orf40	NM_017998.2		600,2731,3172	TT,TC,CC		32.2442,26.2823,30.2245		154/195	77563087	3931,9075	2203	4300	6503	SO:0001819	synonymous_variant	55071	exon2			CCAGTACTGGAAG	AK000972	CCDS6648.1	9q21.31	2012-03-15			ENSG00000135045	ENSG00000135045			23433	protein-coding gene	gene with protein product							Standard	NM_017998		Approved	FLJ10110	uc004ajo.4	Q8IXQ3	OTTHUMG00000020031	ENST00000376854.5:c.462G>A	9.37:g.77563087C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_017998	Q9NWD3	Silent	SNP	ENST00000376854.5	37	CCDS6648.1																																																																																			C|0.688;T|0.312	0.312	strong		0.383	C9orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052702.1	NM_017998	
CSPG4	1464	hgsc.bcm.edu	37	15	75980159	75980159	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75980159G>T	ENST00000308508.5	-	3	3339	c.3247C>A	c.(3247-3249)Cag>Aag	p.Q1083K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1083	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						AGGTCCTCCTGGGTGAAGCGG	0.637																																					p.Q1083K		Atlas-SNP	.											.	CSPG4	175	.	0			c.C3247A						PASS	.						67.0	64.0	65.0					15																	75980159		2197	4292	6489	SO:0001583	missense	1464	exon3			CCTCCTGGGTGAA	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.3247C>A	15.37:g.75980159G>T	ENSP00000312506:p.Gln1083Lys	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	184	92	0.5	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	25.0	4.590308	0.86851	.	.	ENSG00000173546	ENST00000308508	T	0.52754	0.65	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000006	T	0.69815	0.3153	M	0.78456	2.415	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.72246	-0.4349	10	0.49607	T	0.09	.	17.4549	0.87604	0.0:0.0:1.0:0.0	.	1083	Q6UVK1	CSPG4_HUMAN	K	1083	ENSP00000312506:Q1083K	ENSP00000312506:Q1083K	Q	-	1	0	CSPG4	73767214	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.869000	0.99810	2.356000	0.79943	0.555000	0.69702	CAG	.	.	none		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
DIRC1	116093	hgsc.bcm.edu	37	2	189599497	189599497	+	Missense_Mutation	SNP	A	A	C	rs72902678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:189599497A>C	ENST00000308100.4	-	2	421	c.151T>G	c.(151-153)Tct>Gct	p.S51A	AC079613.1_ENST00000431708.1_RNA	NM_052952.2	NP_443184.1	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	51			S -> A (in dbSNP:rs72902678). {ECO:0000269|PubMed:11587072}.							large_intestine(1)|lung(6)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			GCAGCAGCAGAAGAACAATTT	0.438													C|||	46	0.0091853	0.0015	0.0043	5008	,	,		19145	0.0		0.0258	False		,,,				2504	0.0153				p.S51A		Atlas-SNP	.											.	DIRC1	13	.	0			c.T151G						PASS	.	C	ALA/SER	20,4386	824.4+/-416.5	0,20,2183	163.0	153.0	156.0		151	-1.0	0.0	2	dbSNP_130	156	197,8403	810.5+/-407.1	4,189,4107	yes	missense	DIRC1	NM_052952.2	99	4,209,6290	CC,CA,AA		2.2907,0.4539,1.6685	benign	51/105	189599497	217,12789	2203	4300	6503	SO:0001583	missense	116093	exon2			CAGCAGAAGAACA	AY039011	CCDS2296.1	2q33	2008-05-22			ENSG00000174325	ENSG00000174325			15760	protein-coding gene	gene with protein product		606423				11587072	Standard	NM_052952		Approved		uc002uqi.1	Q969H9	OTTHUMG00000132646	ENST00000308100.4:c.151T>G	2.37:g.189599497A>C	ENSP00000307860:p.Ser51Ala	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	166	87	0.524096	NM_052952	Q08AK1	Missense_Mutation	SNP	ENST00000308100.4	37	CCDS2296.1	26	0.011904761904761904	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	24	0.0316622691292876	C	3.267	-0.149923	0.06585	0.004539	0.022907	ENSG00000174325	ENST00000308100	T	0.34667	1.35	3.32	-0.974	0.10293	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16808	-1.0390	9	0.87932	D	0	.	2.3607	0.04307	0.1301:0.428:0.2831:0.1587	.	51	Q969H9	DIRC1_HUMAN	A	51	ENSP00000307860:S51A	ENSP00000307860:S51A	S	-	1	0	DIRC1	189307742	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.093000	0.03362	-0.472000	0.06881	-2.196000	0.00310	TCT	A|0.985;C|0.015	0.015	strong		0.438	DIRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255897.2	NM_052952	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629868	32629868	+	Silent	SNP	A	A	G	rs1049088	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629868A>G	ENST00000399082.3	-	2	311	c.267T>C	c.(265-267)ctT>ctC	p.L89L	HLA-DQB1_ENST00000399079.3_Silent_p.L179L|HLA-DQB1_ENST00000434651.2_Silent_p.L179L|HLA-DQB1_ENST00000399084.1_Silent_p.L179L|HLA-DQB1_ENST00000374943.4_Silent_p.L179L|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	179	Beta-1.		D -> A (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:04, allele DQB1*03:05, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:14, allele DQB1*03:18 and allele DQB1*06:29; dbSNP:rs1071637).|D -> S (in allele DQB1*05:02, allele DQB1*05:04, allele DQB1*05:05, allele DQB1*06:10 and allele DQB1*06:25; requires 2 nucleotide substitutions).|D -> V (in allele DQB1*05:01, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:27, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:38 and allele DQB1*06:39).		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)"""	CATTCCTAATAAGGGGGGTGG	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1027	0.205072	0.2201	0.1484	5008	,	,		17034	0.2331		0.1909	False		,,,				2504	0.2106				p.L179L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.T537C						PASS	.	A		849,3543		81,687,1428	52.0	56.0	55.0		537	-4.1	0.2	6	dbSNP_86	55	1396,7202		112,1172,3015	no	coding-synonymous	HLA-DQB1	NM_002123.4		193,1859,4443	GG,GA,AA		16.2363,19.3306,17.2825		179/262	32629868	2245,10745	2196	4299	6495	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	CCTAATAAGGGGG		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.267T>C	6.37:g.32629868A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	109	59	0.541284	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|0.171;A|0.829	0.171	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751694	19751694	+	Silent	SNP	A	A	G	rs9507567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19751694A>G	ENST00000400113.3	-	4	533	c.429T>C	c.(427-429)ggT>ggC	p.G143G		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	143					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.G144fs*24(1)		NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		AGCCAGTGCCACCCCCAAAAC	0.567													G|||	153	0.0305511	0.0038	0.0461	5008	,	,		17041	0.0129		0.0596	False		,,,				2504	0.044				p.G143G		Atlas-SNP	.											.	TUBA3C	166	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.T429C						PASS	.	G		71,4335	819.3+/-416.3	1,69,2133	65.0	65.0	65.0		429	-1.1	1.0	13	dbSNP_119	65	500,8100	796.0+/-407.5	20,460,3820	no	coding-synonymous	TUBA3C	NM_006001.2		21,529,5953	GG,GA,AA		5.814,1.6114,4.3903		143/451	19751694	571,12435	2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			AGTGCCACCCCCA	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.429T>C	13.37:g.19751694A>G		Somatic	302	1	0.00331126		WXS	Illumina HiSeq	Phase_I	308	149	0.483766	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			A|0.959;G|0.041	0.041	strong		0.567	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
FAIM	55179	hgsc.bcm.edu	37	3	138347988	138347988	+	Missense_Mutation	SNP	T	T	C	rs13043	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:138347988T>C	ENST00000393035.2	+	4	489	c.380T>C	c.(379-381)tTg>tCg	p.L127S	FAIM_ENST00000360570.3_Missense_Mutation_p.L149S|FAIM_ENST00000393034.2_Missense_Mutation_p.L127S|FAIM_ENST00000464668.1_Missense_Mutation_p.L127S|FAIM_ENST00000338446.4_Missense_Mutation_p.L161S	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule	127			L -> S (in dbSNP:rs13043). {ECO:0000269|PubMed:12107411}.		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						GGTAAAAAATTGGAGACAGCG	0.313													T|||	893	0.178315	0.6256	0.0735	5008	,	,		17281	0.0		0.0139	False		,,,				2504	0.001				p.L161S		Atlas-SNP	.											.	FAIM	27	.	0			c.T482C						PASS	.	T	SER/LEU,SER/LEU,SER/LEU,SER/LEU	2378,2028	610.6+/-391.6	646,1086,471	134.0	150.0	144.0		482,446,380,380	4.9	0.9	3	dbSNP_52	144	131,8469	65.3+/-127.6	1,129,4170	yes	missense,missense,missense,missense	FAIM	NM_001033030.1,NM_001033031.1,NM_001033032.1,NM_018147.3	145,145,145,145	647,1215,4641	CC,CT,TT		1.5233,46.0281,19.2911	benign,benign,benign,benign	161/214,149/202,127/180,127/180	138347988	2509,10497	2203	4300	6503	SO:0001583	missense	55179	exon5			AAAAATTGGAGAC	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.380T>C	3.37:g.138347988T>C	ENSP00000376755:p.Leu127Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	149	77	0.516779	NM_001033030	Q6IAN2	Missense_Mutation	SNP	ENST00000393035.2	37	CCDS3103.1	338	0.15476190476190477	301	0.6117886178861789	26	0.0718232044198895	0	0.0	11	0.014511873350923483	T	15.38	2.816084	0.50527	0.539719	0.015233	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59	4.94	4.94	0.65067	.	0.123452	0.64402	D	0.000001	T	0.00012	0.0000	L	0.29908	0.895	0.32280	P	0.567723	B;B;B;P	0.36647	0.008;0.007;0.023;0.563	B;B;B;P	0.45610	0.043;0.019;0.069;0.487	T	0.42565	-0.9444	9	0.52906	T	0.07	-9.8443	12.8554	0.57882	0.0:0.0:0.0:1.0	rs13043;rs640979;rs1136174;rs1672960;rs3199418;rs11556767;rs16848257;rs52837206;rs56519713;rs57680134;rs13043	127;149;161;127	Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2;C9JDZ2	FAIM1_HUMAN;.;.;.	S	161;149;127;127;127;127	ENSP00000342805:L161S;ENSP00000353775:L149S;ENSP00000376755:L127S;ENSP00000376754:L127S;ENSP00000417642:L127S;ENSP00000420543:L127S	ENSP00000342805:L161S	L	+	2	0	FAIM	139830678	1.000000	0.71417	0.921000	0.36526	0.937000	0.57800	7.513000	0.81739	2.195000	0.70347	0.533000	0.62120	TTG	T|0.810;C|0.190	0.190	strong		0.313	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032	
TMEM132D	121256	hgsc.bcm.edu	37	12	130184947	130184947	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:130184947T>A	ENST00000422113.2	-	2	702	c.376A>T	c.(376-378)Aac>Tac	p.N126Y	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	126					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)		AGTTTCCAGTTAAGAGAAAAT	0.517																																					p.N126Y		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A376T						PASS	.						56.0	56.0	56.0					12																	130184947		2203	4300	6503	SO:0001583	missense	121256	exon2			TCCAGTTAAGAGA	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.376A>T	12.37:g.130184947T>A	ENSP00000408581:p.Asn126Tyr	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.462540	0.63513	.	.	ENSG00000151952	ENST00000422113	T	0.13307	2.6	5.33	5.33	0.75918	.	0.082670	0.48767	D	0.000166	T	0.38878	0.1057	M	0.79123	2.44	0.44754	D	0.997754	D	0.89917	1.0	D	0.78314	0.991	T	0.21075	-1.0256	9	.	.	.	-44.5477	15.3082	0.74011	0.0:0.0:0.0:1.0	.	126	Q14C87	T132D_HUMAN	Y	126	ENSP00000408581:N126Y	.	N	-	1	0	TMEM132D	128750900	1.000000	0.71417	0.881000	0.34555	0.437000	0.31866	4.073000	0.57570	2.001000	0.58596	0.454000	0.30748	AAC	.	.	none		0.517	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
FAM160B2	64760	hgsc.bcm.edu	37	8	21956108	21956108	+	Missense_Mutation	SNP	A	A	G	rs35497596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:21956108A>G	ENST00000289921.7	+	7	989	c.943A>G	c.(943-945)Acc>Gcc	p.T315A		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	315			T -> A (in dbSNP:rs35497596). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15498874}.							endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						AGACATTGCCACCTTAGAGGG	0.647													.|||	1895	0.378395	0.3729	0.2723	5008	,	,		16177	0.377		0.4026	False		,,,				2504	0.4376				p.T315A		Atlas-SNP	.											RAI16,NS,carcinoma,0,2	FAM160B2	35	2	0			c.A943G						PASS	.	G	ALA/THR	1386,2650		253,880,885	14.0	15.0	15.0		943	-6.1	0.0	8	dbSNP_126	15	3488,4854		735,2018,1418	yes	missense	FAM160B2	NM_022749.5	58	988,2898,2303	GG,GA,AA		41.8125,34.3409,39.3763	benign	315/744	21956108	4874,7504	2018	4171	6189	SO:0001583	missense	64760	exon7			ATTGCCACCTTAG	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"""retinoic acid induced 16"""	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.943A>G	8.37:g.21956108A>G	ENSP00000289921:p.Thr315Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	66	39	0.590909	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Missense_Mutation	SNP	ENST00000289921.7	37	CCDS6021.2	800	0.3663003663003663	174	0.35365853658536583	106	0.292817679558011	221	0.38636363636363635	299	0.3944591029023747	.	10.81	1.455570	0.26161	0.343409	0.418125	ENSG00000158863	ENST00000289921	T	0.62639	0.01	5.37	-6.05	0.02172	.	0.788308	0.12147	N	0.495270	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.15484	0.013	T	0.31503	-0.9941	9	0.25751	T	0.34	0.0394	10.6218	0.45484	0.6713:0.0:0.2318:0.0969	rs35497596	315	Q86V87	F16B2_HUMAN	A	315	ENSP00000289921:T315A	ENSP00000289921:T315A	T	+	1	0	FAM160B2	22012053	0.000000	0.05858	0.000000	0.03702	0.768000	0.43524	-0.607000	0.05648	-1.577000	0.01650	-1.016000	0.02456	ACC	A|0.627;G|0.373	0.373	strong		0.647	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		
HYKK	123688	hgsc.bcm.edu	37	15	78825562	78825562	+	Silent	SNP	C	C	T	rs12906951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78825562C>T	ENST00000569878.1	+	4	672	c.672C>T	c.(670-672)caC>caT	p.H224H	HYKK_ENST00000563233.1_Intron|HYKK_ENST00000388988.4_Silent_p.H224H|HYKK_ENST00000408962.2_Intron			A2RU49	HYKK_HUMAN	hydroxylysine kinase	224						cytoplasm (GO:0005737)	hydroxylysine kinase activity (GO:0047992)	p.H224H(2)									GTATCAATCACGGAGATCTTA	0.353													T|||	1183	0.236222	0.0998	0.2176	5008	,	,		19099	0.1528		0.3708	False		,,,				2504	0.3814				p.H224H		Atlas-SNP	.											AGPHD1,NS,carcinoma,0,1	AGPHD1	22	1	2	Substitution - coding silent(2)	prostate(2)	c.C672T						PASS	.	T	,	620,3032		59,502,1265	55.0	48.0	50.0		672,	-3.9	0.8	15	dbSNP_121	50	3377,4779		717,1943,1418	no	coding-synonymous,intron	AGPHD1	NM_001013619.2,NM_001083612.1	,	776,2445,2683	TT,TC,CC		41.4051,16.977,33.8499	,	224/374,	78825562	3997,7811	1826	4078	5904	SO:0001819	synonymous_variant	123688	exon5			CAATCACGGAGAT	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.672C>T	15.37:g.78825562C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	97	34	0.350515	NM_001013619	B7ZMA5|F8W6X5|Q6ZTN0	Silent	SNP	ENST00000569878.1	37	CCDS42063.1																																																																																			C|0.733;T|0.267	0.267	strong		0.353	HYKK-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435834.1	NM_001013619	
LRRC18	474354	hgsc.bcm.edu	37	10	50122109	50122109	+	Missense_Mutation	SNP	C	C	T	rs17772611	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50122109C>T	ENST00000374160.3	-	1	168	c.92G>A	c.(91-93)cGc>cAc	p.R31H	LRRC18_ENST00000298124.3_Missense_Mutation_p.R31H|RP11-523O18.7_ENST00000430438.1_RNA|WDFY4_ENST00000325239.5_Intron|WDFY4_ENST00000413659.2_Intron	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	31			R -> H (in dbSNP:rs17772611).			cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						CAAGTCAAGGCGCTTTTTCCC	0.478													C|||	565	0.112819	0.1437	0.0951	5008	,	,		21790	0.002		0.1441	False		,,,				2504	0.1656				p.R31H		Atlas-SNP	.											LRRC18,caecum,carcinoma,0,2	LRRC18	52	2	0			c.G92A						PASS	.	C	HIS/ARG,	624,3782	267.7+/-268.0	42,540,1621	87.0	76.0	80.0		92,	6.1	1.0	10	dbSNP_123	80	1201,7399	242.6+/-272.5	104,993,3203	yes	missense,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	29,	146,1533,4824	TT,TC,CC		13.9651,14.1625,14.032	probably-damaging,	31/262,	50122109	1825,11181	2203	4300	6503	SO:0001583	missense	474354	exon1			TCAAGGCGCTTTT	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.92G>A	10.37:g.50122109C>T	ENSP00000363275:p.Arg31His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	95	47	0.494737	NM_001006939	Q6UY02	Missense_Mutation	SNP	ENST00000374160.3	37	CCDS31197.1	231	0.10576923076923077	73	0.1483739837398374	43	0.11878453038674033	1	0.0017482517482517483	114	0.1503957783641161	C	33	5.264929	0.95399	0.141625	0.139651	ENSG00000165383	ENST00000374160;ENST00000298124	T;T	0.52057	0.68;0.68	6.06	6.06	0.98353	.	0.109676	0.56097	D	0.000023	T	0.00412	0.0013	N	0.16201	0.385	0.09310	P	0.999999840629	D	0.89917	1.0	D	0.97110	1.0	T	0.03130	-1.1069	8	.	.	.	.	20.6397	0.99537	0.0:1.0:0.0:0.0	rs17772611;rs58126032;rs17772611	31	Q8N456	LRC18_HUMAN	H	31	ENSP00000363275:R31H;ENSP00000298124:R31H	.	R	-	2	0	LRRC18	49792115	1.000000	0.71417	0.971000	0.41717	0.921000	0.55340	7.677000	0.84024	2.880000	0.98712	0.650000	0.86243	CGC	C|0.869;T|0.131	0.131	strong		0.478	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
SLC7A4	6545	hgsc.bcm.edu	37	22	21385985	21385985	+	Silent	SNP	C	C	T	rs402931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:21385985C>T	ENST00000382932.2	-	2	184	c.117G>A	c.(115-117)acG>acA	p.T39T	MIR649_ENST00000384843.1_RNA|AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Silent_p.T39T	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	39					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)	TCAGGTCCAGCGTGGACAGGC	0.647													C|||	566	0.113019	0.0182	0.1628	5008	,	,		17068	0.0357		0.2932	False		,,,				2504	0.1002				p.T39T		Atlas-SNP	.											.	SLC7A4	50	.	0			c.G117A						PASS	.	C		286,4120	157.0+/-190.0	15,256,1932	60.0	52.0	55.0		117	-10.7	0.0	22	dbSNP_80	55	2624,5976	417.4+/-352.4	414,1796,2090	no	coding-synonymous	SLC7A4	NM_004173.2		429,2052,4022	TT,TC,CC		30.5116,6.4911,22.3743		39/636	21385985	2910,10096	2203	4300	6503	SO:0001819	synonymous_variant	6545	exon2			GTCCAGCGTGGAC	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.117G>A	22.37:g.21385985C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	104	50	0.480769	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Silent	SNP	ENST00000382932.2	37	CCDS33608.1																																																																																			C|0.795;T|0.205	0.205	strong		0.647	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
STRADB	55437	hgsc.bcm.edu	37	2	202342402	202342402	+	Silent	SNP	G	G	T	rs12990557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:202342402G>T	ENST00000194530.3	+	8	974	c.609G>T	c.(607-609)ctG>ctT	p.L203L	STRADB_ENST00000392249.2_Silent_p.L203L	NM_001206864.1|NM_018571.5	NP_001193793.1|NP_061041.2	Q9C0K7	STRAB_HUMAN	STE20-related kinase adaptor beta	203	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|cell morphogenesis (GO:0000902)|insulin receptor signaling pathway (GO:0008286)|JNK cascade (GO:0007254)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			breast(1)|large_intestine(2)|lung(5)|prostate(1)|skin(3)|stomach(1)	13						TCTCTGGCCTGTCCCATCTGC	0.478													G|||	2363	0.471845	0.2239	0.4986	5008	,	,		589	0.494		0.5865	False		,,,				2504	0.6472				p.L203L		Atlas-SNP	.											.	STRADB	33	.	0			c.G609T						PASS	.	G	,	1179,3227	415.4+/-337.2	149,881,1173	128.0	126.0	127.0		609,609	3.3	1.0	2	dbSNP_121	127	5115,3477	633.7+/-398.8	1518,2079,699	no	coding-synonymous,coding-synonymous	STRADB	NM_001206864.1,NM_018571.5	,	1667,2960,1872	TT,TG,GG		40.4679,26.759,48.4228	,	203/378,203/419	202342402	6294,6704	2203	4296	6499	SO:0001819	synonymous_variant	55437	exon8			TGGCCTGTCCCAT	AB038950	CCDS2348.1, CCDS56161.1	2q33.1	2010-09-30	2008-09-15	2008-09-15	ENSG00000082146	ENSG00000082146			13205	protein-coding gene	gene with protein product		607333	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 2"""	ALS2CR2		11161814, 14511394	Standard	NM_018571		Approved	CALS-21, PAPK, ILPIPA, ILPIP	uc002uyd.4	Q9C0K7	OTTHUMG00000132831	ENST00000194530.3:c.609G>T	2.37:g.202342402G>T		Somatic	227	1	0.00440529		WXS	Illumina HiSeq	Phase_I	231	105	0.454545	NM_001206864	Q5BKY7|Q9P1L0	Silent	SNP	ENST00000194530.3	37	CCDS2348.1																																																																																			G|0.513;T|0.487	0.487	strong		0.478	STRADB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256297.1	NM_018571	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149216095	149216095	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149216095G>A	ENST00000309241.5	+	8	2109	c.2077G>A	c.(2077-2079)Gac>Aac	p.D693N	PPARGC1B_ENST00000360453.4_Missense_Mutation_p.D654N|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.D629N|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.D693N	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	693					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)			TGGAGACCATGACTACTGCCA	0.632																																					p.D693N		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G2077A						PASS	.						53.0	56.0	55.0					5																	149216095		2203	4300	6503	SO:0001583	missense	133522	exon8			GACCATGACTACT	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.2077G>A	5.37:g.149216095G>A	ENSP00000312649:p.Asp693Asn	Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.737115	0.89482	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.50813	0.77;0.73;0.81;0.75	4.47	4.47	0.54385	.	0.282850	0.37623	N	0.002014	T	0.66436	0.2789	M	0.81341	2.54	0.50632	D	0.99988	D;P;D;P;D	0.60575	0.976;0.948;0.976;0.93;0.988	P;P;P;P;P	0.57101	0.799;0.558;0.799;0.634;0.813	T	0.74300	-0.3710	10	0.87932	D	0	-13.9513	17.5766	0.87952	0.0:0.0:1.0:0.0	.	672;672;654;693;693	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	N	654;693;693;629	ENSP00000353638:D654N;ENSP00000377855:D693N;ENSP00000312649:D693N;ENSP00000384403:D629N	ENSP00000312649:D693N	D	+	1	0	PPARGC1B	149196288	1.000000	0.71417	0.986000	0.45419	0.993000	0.82548	8.449000	0.90337	2.212000	0.71576	0.456000	0.33151	GAC	.	.	none		0.632	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
ZNF91	7644	hgsc.bcm.edu	37	19	23545004	23545004	+	Silent	SNP	G	G	A	rs296092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:23545004G>A	ENST00000300619.7	-	4	982	c.777C>T	c.(775-777)atC>atT	p.I259I	ZNF91_ENST00000397082.2_Silent_p.I227I|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	259					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CTTTAGCACAGATTATTTTAT	0.368													A|||	1561	0.311701	0.4062	0.1571	5008	,	,		18337	0.369		0.2495	False		,,,				2504	0.2986				p.I259I		Atlas-SNP	.											.	ZNF91	349	.	0			c.C777T						PASS	.	A		1627,2737		317,993,872	109.0	121.0	117.0		777	-3.9	0.0	19	dbSNP_79	117	2290,6302		285,1720,2291	no	coding-synonymous	ZNF91	NM_003430.2		602,2713,3163	AA,AG,GG		26.6527,37.2823,30.2331		259/1192	23545004	3917,9039	2182	4296	6478	SO:0001819	synonymous_variant	7644	exon4			AGCACAGATTATT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.777C>T	19.37:g.23545004G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			G|0.682;A|0.318	0.318	strong		0.368	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
EGFR	1956	hgsc.bcm.edu	37	7	55238874	55238874	+	Silent	SNP	T	T	A	rs2227984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55238874T>A	ENST00000275493.2	+	16	2064	c.1887T>A	c.(1885-1887)acT>acA	p.T629T	EGFR_ENST00000455089.1_Silent_p.T584T|EGFR_ENST00000442591.1_Silent_p.T629T|EGFR_ENST00000454757.2_Silent_p.T576T	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	629					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)	ACAGATGCACTGGGCCAGGTC	0.398		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			T|||	1955	0.390375	0.2678	0.3977	5008	,	,		21298	0.5347		0.3559	False		,,,				2504	0.4376				p.T629T		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.T1887A						PASS	.	T		1213,3193	422.3+/-339.7	168,877,1158	135.0	120.0	125.0		1887	-5.9	0.0	7	dbSNP_123	125	2981,5619	461.9+/-365.5	537,1907,1856	no	coding-synonymous	EGFR	NM_005228.3		705,2784,3014	AA,AT,TT		34.6628,27.5306,32.2467		629/1211	55238874	4194,8812	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	ATGCACTGGGCCA		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.1887T>A	7.37:g.55238874T>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			T|0.645;A|0.355	0.355	strong		0.398	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
WNK2	65268	hgsc.bcm.edu	37	9	96021312	96021312	+	Missense_Mutation	SNP	G	G	A	rs10761203	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:96021312G>A	ENST00000297954.4	+	11	2482	c.2482G>A	c.(2482-2484)Gtg>Atg	p.V828M	WNK2_ENST00000395477.2_Missense_Mutation_p.V828M|WNK2_ENST00000395475.2_Missense_Mutation_p.V762M|WNK2_ENST00000427277.2_Missense_Mutation_p.V440M|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Missense_Mutation_p.V440M	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	828			V -> M (in dbSNP:rs10761203).		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						TGTGCCTCCCGTGCCACCACC	0.682													G|||	1570	0.313498	0.0681	0.5058	5008	,	,		11697	0.4345		0.4573	False		,,,				2504	0.2362				p.V828M		Atlas-SNP	.											WNK2_ENST00000297954,NS,carcinoma,0,2	WNK2	277	2	0			c.G2482A						PASS	.	G	MET/VAL	642,3764	263.4+/-265.5	47,548,1608	36.0	42.0	40.0		2482	2.9	0.7	9	dbSNP_120	40	4143,4455	555.8+/-386.7	991,2161,1147	yes	missense	WNK2	NM_006648.3	21	1038,2709,2755	AA,AG,GG		48.1856,14.571,36.7964	possibly-damaging	828/2218	96021312	4785,8219	2203	4299	6502	SO:0001583	missense	65268	exon11			CCTCCCGTGCCAC	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.2482G>A	9.37:g.96021312G>A	ENSP00000297954:p.Val828Met	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	256	117	0.457031	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		829|829	0.37957875457875456|0.37957875457875456	42|42	0.08536585365853659|0.08536585365853659	182|182	0.5027624309392266|0.5027624309392266	253|253	0.4423076923076923|0.4423076923076923	352|352	0.46437994722955145|0.46437994722955145	G|G	10.12|10.12	1.262253|1.262253	0.23051|0.23051	0.14571|0.14571	0.481856|0.481856	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000448039;ENST00000297954;ENST00000395477;ENST00000395475;ENST00000349097;ENST00000427277	.|T;T;T;T;T;T	.|0.73152	.|-0.72;-0.47;-0.47;-0.72;0.16;0.12	5.11|5.11	2.9|2.9	0.33743|0.33743	.|.	.|0.659654	.|0.14927	.|N	.|0.290292	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.29908|0.29908	0.895|0.895	0.45284|0.45284	P|P	0.0017179999999999973|0.0017179999999999973	.|P;B;P;P;P	.|0.40970	.|0.675;0.421;0.491;0.675;0.734	.|B;B;B;B;B	.|0.29353	.|0.056;0.056;0.036;0.056;0.101	T|T	0.46952|0.46952	-0.9154|-0.9154	4|9	.|0.44086	.|T	.|0.13	.|.	3.5811|3.5811	0.07954|0.07954	0.2889:0.0:0.5135:0.1976|0.2889:0.0:0.5135:0.1976	rs10761203;rs59411385;rs10761203|rs10761203;rs59411385;rs10761203	.|828;828;431;828;828	.|Q9Y3S1-2;Q9Y3S1-4;A6PVR4;F8W9F9;Q9Y3S1	.|.;.;.;.;WNK2_HUMAN	H|M	431|776;828;828;762;440;440	.|ENSP00000412465:V776M;ENSP00000297954:V828M;ENSP00000378860:V828M;ENSP00000378858:V762M;ENSP00000297876:V440M;ENSP00000411181:V440M	.|ENSP00000297954:V828M	R|V	+|+	2|1	0|0	WNK2|WNK2	95061133|95061133	0.530000|0.530000	0.26330|0.26330	0.668000|0.668000	0.29813|0.29813	0.126000|0.126000	0.20510|0.20510	1.047000|1.047000	0.30367|0.30367	1.143000|1.143000	0.42306|0.42306	0.462000|0.462000	0.41574|0.41574	CGT|GTG	G|0.644;A|0.356	0.356	strong		0.682	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
MUC16	94025	hgsc.bcm.edu	37	19	9085643	9085643	+	Missense_Mutation	SNP	A	A	G	rs1574479	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9085643A>G	ENST00000397910.4	-	1	6375	c.6172T>C	c.(6172-6174)Tct>Cct	p.S2058P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2058	Ser-rich.|Thr-rich.		S -> P (in dbSNP:rs1574479).		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						GTGGGGAGAGATGTAGTGAGG	0.478													A|||	952	0.190096	0.0711	0.2709	5008	,	,		21856	0.3036		0.172	False		,,,				2504	0.1953				p.S2058P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T6172C						PASS	.	A	PRO/SER	290,3690		5,280,1705	167.0	160.0	162.0		6172	0.7	0.0	19	dbSNP_88	162	1488,6820		127,1234,2793	yes	missense	MUC16	NM_024690.2	74	132,1514,4498	GG,GA,AA		17.9104,7.2864,14.4694	possibly-damaging	2058/14508	9085643	1778,10510	1990	4154	6144	SO:0001583	missense	94025	exon1			GGAGAGATGTAGT	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.6172T>C	19.37:g.9085643A>G	ENSP00000381008:p.Ser2058Pro	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	51	15	0.294118	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	a	2.263	-0.368789	0.05069	0.072864	0.179104	ENSG00000181143	ENST00000397910	T	0.02709	4.19	0.731	0.731	0.18277	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	P	0.42518	0.782	P	0.46110	0.504	T	0.51236	-0.8731	8	0.87932	D	0	.	3.8785	0.09068	1.0:0.0:0.0:0.0	rs1574479;rs52797107;rs1574479	2058	B5ME49	.	P	2058	ENSP00000381008:S2058P	ENSP00000381008:S2058P	S	-	1	0	MUC16	8946643	0.002000	0.14202	0.010000	0.14722	0.067000	0.16453	0.031000	0.13710	0.598000	0.29829	0.246000	0.17985	TCT	A|0.810;G|0.190	0.190	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PRR21	643905	hgsc.bcm.edu	37	2	240982116	240982116	+	Missense_Mutation	SNP	C	C	A	rs72993513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:240982116C>A	ENST00000408934.1	-	1	283	c.284G>T	c.(283-285)cGg>cTg	p.R95L		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	95	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						GACGAAGGGCCGTGGGTGAAG	0.617													-|||	1424	0.284345	0.357	0.196	5008	,	,		15582	0.2401		0.2823	False		,,,				2504	0.2965				p.R95L		Atlas-SNP	.											.	PRR21	53	.	0			c.G284T						PASS	.						105.0	100.0	102.0					2																	240982116		2135	4263	6398	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.284G>T	2.37:g.240982116C>A	ENSP00000386166:p.Arg95Leu	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	128	109	0.851562	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	530	0.24267399267399267	149	0.30284552845528456	71	0.19613259668508287	115	0.20104895104895104	195	0.25725593667546176	-	8.811	0.935251	0.18206	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.28454	1.61;1.61	1.79	-2.88	0.05682	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.41041	0.736	B	0.40256	0.324	T	0.33059	-0.9883	8	0.49607	T	0.09	.	3.7903	0.08718	0.0:0.4733:0.1957:0.331	.	95	Q8WXC7	PRR21_HUMAN	L	95	ENSP00000386166:R95L;ENSP00000418240:R95L	ENSP00000386166:R95L	R	-	2	0	PRR21	240630789	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.289000	0.02780	-0.793000	0.04475	-0.438000	0.05819	CGG	C|0.741;A|0.259	0.259	strong		0.617	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
CHD9	80205	hgsc.bcm.edu	37	16	53358439	53358439	+	Missense_Mutation	SNP	A	A	G	rs3743771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:53358439A>G	ENST00000398510.3	+	38	8413	c.8326A>G	c.(8326-8328)Aca>Gca	p.T2776A	CHD9_ENST00000564845.1_Missense_Mutation_p.T2760A|CHD9_ENST00000566029.1_Missense_Mutation_p.T2760A|CHD9_ENST00000447540.1_Missense_Mutation_p.T2761A			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	2776				T -> A (in Ref. 1; AAQ24287 and 6; BAA20767). {ECO:0000305}.	cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(32)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	78		all_cancers(37;0.0212)				TTCTCCTTCCACATCCTCTAC	0.428													A|||	1055	0.210663	0.1309	0.1571	5008	,	,		19386	0.2341		0.2704	False		,,,				2504	0.271				p.T2760A		Atlas-SNP	.											CHD9,NS,carcinoma,0,1	CHD9	203	1	0			c.A8278G						PASS	.	A	ALA/THR	581,3251		39,503,1374	50.0	49.0	49.0		8278	3.2	0.8	16	dbSNP_107	49	2358,5918		327,1704,2107	yes	missense	CHD9	NM_025134.4	58	366,2207,3481	GG,GA,AA		28.492,15.1618,24.2732	benign	2760/2882	53358439	2939,9169	1916	4138	6054	SO:0001583	missense	80205	exon39			CCTTCCACATCCT	AK022240	CCDS45485.1	16q12.2	2006-04-12				ENSG00000177200			25701	protein-coding gene	gene with protein product						9205841	Standard	XM_005256168		Approved	FLJ12178, KIAA0308, BC022889	uc002egy.3	Q3L8U1		ENST00000398510.3:c.8326A>G	16.37:g.53358439A>G	ENSP00000381522:p.Thr2776Ala	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	23	0.534884	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Missense_Mutation	SNP	ENST00000398510.3	37		494	0.2261904761904762	79	0.16056910569105692	70	0.19337016574585636	136	0.23776223776223776	209	0.2757255936675462	A	1.152	-0.646382	0.03531	0.151618	0.28492	ENSG00000177200	ENST00000447540;ENST00000398510;ENST00000450543	D	0.85484	-1.99	5.47	3.22	0.36961	.	0.110120	0.40064	N	0.001198	T	0.00012	0.0000	L	0.34521	1.04	0.24658	P	0.99348232	B;B;B;B	0.11235	0.001;0.004;0.002;0.004	B;B;B;B	0.13407	0.003;0.009;0.004;0.009	T	0.04178	-1.0971	9	0.05436	T	0.98	-7.4837	9.8557	0.41084	0.8604:0.0:0.1396:0.0	rs3743771;rs17395331;rs52814680;rs56719806;rs3743771	842;2761;2776;2760	C9JR69;Q3L8U1-3;Q3L8U1;Q3L8U1-2	.;.;CHD9_HUMAN;.	A	2761;2760;842	ENSP00000396345:T2761A	ENSP00000381522:T2760A	T	+	1	0	CHD9	51915940	0.970000	0.33590	0.847000	0.33407	0.734000	0.41952	2.344000	0.44010	0.457000	0.26962	0.533000	0.62120	ACA	A|0.774;G|0.225	0.225	strong		0.428	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134	
ADGB	79747	hgsc.bcm.edu	37	6	147045358	147045358	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:147045358T>G	ENST00000397944.3	+	18	2208	c.2132T>G	c.(2131-2133)cTt>cGt	p.L711R	ADGB_ENST00000367493.3_Missense_Mutation_p.L130R	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	711					oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						GAGCCTGGACTTCTCACAGCT	0.413																																					p.L711R		Atlas-SNP	.											.	ADGB	93	.	0			c.T2132G						PASS	.						156.0	128.0	136.0					6																	147045358		692	1591	2283	SO:0001583	missense	79747	exon18			CTGGACTTCTCAC	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.2132T>G	6.37:g.147045358T>G	ENSP00000381036:p.Leu711Arg	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	73	55	0.753425	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		.	.	.	.	.	.	.	.	.	.	T	15.88	2.962879	0.53507	.	.	ENSG00000118492	ENST00000397944;ENST00000367493	T	0.36520	1.25	5.58	5.58	0.84498	.	0.433362	0.21605	N	0.071881	T	0.46249	0.1383	M	0.70275	2.135	0.09310	N	1	D	0.71674	0.998	D	0.67103	0.949	T	0.47381	-0.9122	10	0.72032	D	0.01	-5.0251	13.2886	0.60258	0.0:0.0:0.0:1.0	.	711	Q8N7X0	CAN7L_HUMAN	R	711;130	ENSP00000381036:L711R	ENSP00000356463:L130R	L	+	2	0	C6orf103	147087051	0.116000	0.22171	0.349000	0.25694	0.380000	0.30137	2.892000	0.48625	2.127000	0.65507	0.533000	0.62120	CTT	.	.	none		0.413	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
DIAPH3	81624	hgsc.bcm.edu	37	13	60240961	60240961	+	Silent	SNP	C	C	T	rs9538494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:60240961C>T	ENST00000400324.4	-	28	3559	c.3339G>A	c.(3337-3339)ttG>ttA	p.L1113L	DIAPH3_ENST00000400320.1_Silent_p.L1067L|DIAPH3_ENST00000377908.2_Silent_p.L1102L|DIAPH3_ENST00000400319.1_Silent_p.L1043L|DIAPH3_ENST00000400330.1_Silent_p.L1113L	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	1113					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		ACCCTTCTGTCAACTGCACTT	0.368													C|||	736	0.146965	0.0242	0.2147	5008	,	,		17183	0.1071		0.2594	False		,,,				2504	0.1902				p.L1113L		Atlas-SNP	.											.	DIAPH3	139	.	0			c.G3339A						PASS	.	C		241,3523		9,223,1650	110.0	101.0	104.0		3339	4.1	1.0	13	dbSNP_119	104	2196,6046		292,1612,2217	no	coding-synonymous	DIAPH3	NM_001042517.1		301,1835,3867	TT,TC,CC		26.644,6.4028,20.2982		1113/1194	60240961	2437,9569	1882	4121	6003	SO:0001819	synonymous_variant	81624	exon28			TTCTGTCAACTGC	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.3339G>A	13.37:g.60240961C>T		Somatic	225	0	0		WXS	Illumina HiSeq	Phase_I	267	127	0.475655	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Silent	SNP	ENST00000400324.4	37	CCDS41898.1																																																																																			C|0.820;T|0.180	0.180	strong		0.368	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
MUC16	94025	hgsc.bcm.edu	37	19	9061559	9061559	+	Silent	SNP	C	C	G	rs1423052	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9061559C>G	ENST00000397910.4	-	3	26090	c.25887G>C	c.(25885-25887)acG>acC	p.T8629T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8631	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGACTTCAGACGTGGCTAATA	0.453													N|||	1919	0.383187	0.3472	0.4006	5008	,	,		22669	0.5933		0.2525	False		,,,				2504	0.3374				p.T8629T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G25887C						PASS	.			1265,2617		198,869,874	146.0	138.0	140.0		25887	-4.2	0.0	19	dbSNP_88	140	2154,6140		270,1614,2263	no	coding-synonymous	MUC16	NM_024690.2		468,2483,3137	GG,GC,CC		25.9706,32.5863,28.0798		8629/14508	9061559	3419,8757	1941	4147	6088	SO:0001819	synonymous_variant	94025	exon3			TTCAGACGTGGCT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.25887G>C	19.37:g.9061559C>G		Somatic	319	0	0		WXS	Illumina HiSeq	Phase_I	392	159	0.405612	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|0.616;G|0.384	0.384	strong		0.453	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PI3	5266	hgsc.bcm.edu	37	20	43803606	43803606	+	Missense_Mutation	SNP	G	G	A	rs41282752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43803606G>A	ENST00000243924.3	+	1	90	c.43G>A	c.(43-45)Gct>Act	p.A15T		NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived	15					copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				GTTCCTCATCGCTGGGACGCT	0.572													G|||	56	0.0111821	0.0015	0.0144	5008	,	,		18483	0.0		0.0348	False		,,,				2504	0.0092				p.A15T		Atlas-SNP	.											.	PI3	21	.	0			c.G43A						PASS	.	G	THR/ALA	30,4376	36.0+/-67.5	0,30,2173	181.0	137.0	152.0		43	1.9	0.0	20	dbSNP_127	152	348,8252	117.4+/-177.0	7,334,3959	yes	missense	PI3	NM_002638.3	58	7,364,6132	AA,AG,GG		4.0465,0.6809,2.9064	benign	15/118	43803606	378,12628	2203	4300	6503	SO:0001583	missense	5266	exon1			CTCATCGCTGGGA	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"""WAP four-disulfide core domain containing"""	8947	protein-coding gene	gene with protein product	"""skin-derived antileukoproteinase"", ""trappin-2"""	182257	"""protease inhibitor 3, skin-derived (SKALP)"""			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.43G>A	20.37:g.43803606G>A	ENSP00000243924:p.Ala15Thr	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	138	83	0.601449	NM_002638	E1P618|Q6FG74	Missense_Mutation	SNP	ENST00000243924.3	37	CCDS13344.1	36	0.016483516483516484	0	0.0	7	0.019337016574585635	0	0.0	29	0.03825857519788918	G	10.12	1.261995	0.23051	0.006809	0.040465	ENSG00000124102	ENST00000243924	T	0.23348	1.91	3.9	1.85	0.25348	.	0.708561	0.11636	N	0.544326	T	0.03220	0.0094	L	0.36672	1.1	0.09310	N	1	P	0.34826	0.471	B	0.21151	0.033	T	0.13926	-1.0491	10	0.27785	T	0.31	.	6.7736	0.23607	0.1923:0.5998:0.2079:0.0	rs41282752;rs61729432	15	P19957	ELAF_HUMAN	T	15	ENSP00000243924:A15T	ENSP00000243924:A15T	A	+	1	0	PI3	43237020	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.130000	0.10498	0.352000	0.24053	-0.311000	0.09066	GCT	G|0.973;A|0.027	0.027	strong		0.572	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638	
SENP7	57337	hgsc.bcm.edu	37	3	101066717	101066717	+	Splice_Site	SNP	T	T	A	rs2433031	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:101066717T>A	ENST00000394095.2	-	13	1889	c.1836A>T	c.(1834-1836)caA>caT	p.Q612H	SENP7_ENST00000348610.3_Splice_Site_p.Q579H|SENP7_ENST00000358203.3_Splice_Site_p.Q448H|SENP7_ENST00000394094.2_Splice_Site_p.Q547H|SENP7_ENST00000314261.7_Splice_Site_p.Q546H|SENP7_ENST00000394091.1_Splice_Site_p.Q448H	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	612			Q -> H (in dbSNP:rs2433031). {ECO:0000269|PubMed:11214970}.			intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.Q546H(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TATACTCACATTGCTGGCTTA	0.294													T|||	1508	0.301118	0.177	0.2767	5008	,	,		13620	0.3403		0.3827	False		,,,				2504	0.362				p.Q612H		Atlas-SNP	.											SENP7,NS,carcinoma,0,1	SENP7	170	1	1	Substitution - Missense(1)	prostate(1)	c.A1836T						PASS	.	T	HIS/GLN,HIS/GLN	989,3417	356.4+/-313.5	98,793,1312	66.0	67.0	67.0		1641,1836	1.1	1.0	3	dbSNP_100	67	3167,5431	468.5+/-367.3	596,1975,1728	yes	missense-near-splice,missense-near-splice	SENP7	NM_001077203.1,NM_020654.3	24,24	694,2768,3040	AA,AT,TT		36.8341,22.4467,31.9594	possibly-damaging,possibly-damaging	547/986,612/1051	101066717	4156,8848	2203	4299	6502	SO:0001630	splice_region_variant	57337	exon13			CTCACATTGCTGG		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.1837+1A>T	3.37:g.101066717T>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	87	87	1	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	678|678	0.31043956043956045|0.31043956043956045	81|81	0.16463414634146342|0.16463414634146342	103|103	0.2845303867403315|0.2845303867403315	192|192	0.3356643356643357|0.3356643356643357	302|302	0.39841688654353563|0.39841688654353563	T|T	13.81|13.81	2.347976|2.347976	0.41599|0.41599	0.224467|0.224467	0.368341|0.368341	ENSG00000138468|ENSG00000138468	ENST00000366089|ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	.|T;T;T;T;T;T	.|0.19532	.|2.14;2.16;2.16;2.16;2.16;2.14	5.69|5.69	1.12|1.12	0.20585|0.20585	.|.	.|0.239918	.|0.33938	.|N	.|0.004414	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.43271|0.43271	P|P	0.0047719999999999985|0.0047719999999999985	.|D;D;D;D	.|0.67145	.|0.995;0.996;0.991;0.993	.|P;P;D;P	.|0.63192	.|0.871;0.878;0.912;0.753	T|T	0.38243|0.38243	-0.9670|-0.9670	4|9	.|0.15066	.|T	.|0.55	-2.9468|-2.9468	5.1706|5.1706	0.15108|0.15108	0.0:0.2965:0.1434:0.5601|0.0:0.2965:0.1434:0.5601	rs2433031;rs52806065;rs2433031|rs2433031;rs52806065;rs2433031	.|448;546;579;612	.|Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.|.;.;.;SENP7_HUMAN	I|H	14|612;547;546;448;448;579	.|ENSP00000377655:Q612H;ENSP00000377654:Q547H;ENSP00000313624:Q546H;ENSP00000377651:Q448H;ENSP00000350936:Q448H;ENSP00000342159:Q579H	.|ENSP00000313624:Q546H	N|Q	-|-	2|3	0|2	SENP7|SENP7	102549407|102549407	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.862000|0.862000	0.49288|0.49288	0.454000|0.454000	0.21827|0.21827	-0.055000|-0.055000	0.13244|0.13244	-0.417000|-0.417000	0.06048|0.06048	AAT|CAA	T|0.679;A|0.321	0.321	strong		0.294	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	Missense_Mutation
OPA1	4976	hgsc.bcm.edu	37	3	193334991	193334991	+	Missense_Mutation	SNP	G	G	A	rs7624750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:193334991G>A	ENST00000392438.3	+	4	707	c.473G>A	c.(472-474)aGt>aAt	p.S158N	OPA1_ENST00000361908.3_Missense_Mutation_p.S158N|OPA1_ENST00000361150.2_Intron|OPA1-AS1_ENST00000444085.1_RNA|OPA1-AS1_ENST00000433105.1_RNA|OPA1_ENST00000361828.2_Missense_Mutation_p.S158N|OPA1_ENST00000487986.1_3'UTR|OPA1_ENST00000361510.2_Missense_Mutation_p.S158N|OPA1_ENST00000361715.2_Intron	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	158			S -> N (in dbSNP:rs7624750). {ECO:0000269|PubMed:11440988, ECO:0000269|PubMed:11440989, ECO:0000269|PubMed:12036970, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15948788, ECO:0000269|PubMed:16617242, ECO:0000269|PubMed:9628581}.		apoptotic process (GO:0006915)|axon transport of mitochondrion (GO:0019896)|cellular senescence (GO:0090398)|GTP catabolic process (GO:0006184)|inner mitochondrial membrane organization (GO:0007007)|mitochondrial fission (GO:0000266)|mitochondrial fusion (GO:0008053)|mitochondrion organization (GO:0007005)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neural tube closure (GO:0001843)|visual perception (GO:0007601)	dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial crista (GO:0030061)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)			breast(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(4)|lung(15)|upper_aerodigestive_tract(1)|urinary_tract(2)	31	all_cancers(143;9.56e-09)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;9.19e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000162)		GCCCTTCCTAGTTCAGAAGAC	0.338													A|||	2344	0.468051	0.5847	0.4683	5008	,	,		16978	0.3681		0.4573	False		,,,				2504	0.4243				p.S158N		Atlas-SNP	.											OPA1,NS,carcinoma,0,1	OPA1	79	1	0			c.G473A						PASS	.	A	ASN/SER,,,,ASN/SER,,ASN/SER,ASN/SER	2474,1930	539.4+/-375.3	696,1082,424	57.0	62.0	60.0		473,,,,473,,473,473	3.6	1.0	3	dbSNP_116	60	3988,4610	596.8+/-393.7	906,2176,1217	yes	missense,intron,intron,intron,missense,intron,missense,missense	OPA1	NM_015560.2,NM_130831.2,NM_130832.2,NM_130833.2,NM_130834.2,NM_130835.2,NM_130836.2,NM_130837.2	46,,,,46,,46,46	1602,3258,1641	AA,AG,GG		46.3829,43.8238,49.7	benign,,,,benign,,benign,benign	158/961,,,,158/979,,158/998,158/1016	193334991	6462,6540	2202	4299	6501	SO:0001583	missense	4976	exon4			TTCCTAGTTCAGA	AB011139	CCDS33917.1, CCDS43186.1	3q29	2014-09-17			ENSG00000198836	ENSG00000198836			8140	protein-coding gene	gene with protein product	"""mitochondrial dynamin-like GTPase"", ""dynamin-like guanosine triphosphatase"", ""Dynamin-like 120 kDa protein, mitochondrial"""	605290				9490303	Standard	NM_015560		Approved	NTG, KIAA0567, FLJ12460, NPG, MGM1	uc003ftg.3	O60313	OTTHUMG00000149897	ENST00000392438.3:c.473G>A	3.37:g.193334991G>A	ENSP00000376233:p.Ser158Asn	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	242	110	0.454545	NM_130836	D3DNW4	Missense_Mutation	SNP	ENST00000392438.3	37	CCDS43186.1	997|997	0.4565018315018315|0.4565018315018315	297|297	0.6036585365853658|0.6036585365853658	157|157	0.43370165745856354|0.43370165745856354	194|194	0.33916083916083917|0.33916083916083917	349|349	0.4604221635883905|0.4604221635883905	A|A	5.124|5.124	0.208417|0.208417	0.09757|0.09757	0.561762|0.561762	0.463829|0.463829	ENSG00000198836|ENSG00000198836	ENST00000361908;ENST00000392438;ENST00000361510;ENST00000361828;ENST00000419435;ENST00000392436|ENST00000434811	D;D;D;D;T;T|.	0.92965|.	-3.1;-3.14;-3.14;-3.13;1.97;-0.86|.	6.05|6.05	3.64|3.64	0.41730|0.41730	.|.	0.424265|.	0.28766|.	N|.	0.014207|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	P|P	0.999999999863361|0.999999999863361	B;B;B;B|.	0.06786|.	0.0;0.0;0.001;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.0;0.001;0.0|.	T|T	0.44907|0.44907	-0.9297|-0.9297	9|4	0.16420|.	T|.	0.52|.	-8.8622|-8.8622	6.4094|6.4094	0.21682|0.21682	0.7267:0.1327:0.1406:0.0|0.7267:0.1327:0.1406:0.0	rs7624750;rs52806158;rs58655170;rs7624750|rs7624750;rs52806158;rs58655170;rs7624750	158;158;158;158|.	O60313;E5KLJ6;E5KLJ7;E5KLJ5|.	OPA1_HUMAN;.;.;.|.	N|I	158;158;158;158;34;158|58	ENSP00000354681:S158N;ENSP00000376233:S158N;ENSP00000355324:S158N;ENSP00000354429:S158N;ENSP00000399877:S34N;ENSP00000376231:S158N|.	ENSP00000355324:S158N|.	S|V	+|+	2|1	0|0	OPA1|OPA1	194817685|194817685	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.993000|0.993000	0.82548|0.82548	3.435000|3.435000	0.52849|0.52849	0.166000|0.166000	0.19597|0.19597	-0.269000|-0.269000	0.10298|0.10298	AGT|GTT	G|0.517;A|0.483	0.483	strong		0.338	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837	
ABRA	137735	hgsc.bcm.edu	37	8	107782335	107782335	+	Silent	SNP	G	G	A	rs11996457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:107782335G>A	ENST00000311955.3	-	1	138	c.84C>T	c.(82-84)agC>agT	p.S28S		NM_139166.4	NP_631905.1			actin-binding Rho activating protein											breast(1)|kidney(4)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)	27			OV - Ovarian serous cystadenocarcinoma(57;3.83e-09)			CTCGGGCCAAGCTGATGACCA	0.647													G|||	1405	0.280551	0.5378	0.1686	5008	,	,		17334	0.1944		0.2247	False		,,,				2504	0.1585				p.S28S		Atlas-SNP	.											ABRA,NS,adenoma,0,1	ABRA	57	1	0			c.C84T						PASS	.	G		2079,2327	567.8+/-382.2	499,1081,623	61.0	65.0	64.0		84	0.7	0.5	8	dbSNP_120	64	1815,6785	324.5+/-316.5	182,1451,2667	no	coding-synonymous	ABRA	NM_139166.4		681,2532,3290	AA,AG,GG		21.1047,47.1857,29.94		28/382	107782335	3894,9112	2203	4300	6503	SO:0001819	synonymous_variant	137735	exon1			GGCCAAGCTGATG	AF503617	CCDS6305.1	8q23.1	2012-02-06			ENSG00000174429	ENSG00000174429			30655	protein-coding gene	gene with protein product	"""striated muscle activator of Rho-dependent signaling"""	609747				11983702	Standard	NM_139166		Approved	STARS	uc003ymm.4	Q8N0Z2	OTTHUMG00000164809	ENST00000311955.3:c.84C>T	8.37:g.107782335G>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	99	37	0.373737	NM_139166		Silent	SNP	ENST00000311955.3	37	CCDS6305.1																																																																																			G|0.710;A|0.290	0.290	strong		0.647	ABRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380416.1	NM_139166	
MNS1	55329	hgsc.bcm.edu	37	15	56756285	56756285	+	Missense_Mutation	SNP	T	T	G	rs1715919	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:56756285T>G	ENST00000260453.3	-	2	328	c.164A>C	c.(163-165)cAa>cCa	p.Q55P		NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	55			Q -> P (in dbSNP:rs1715919).		cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		TCTGAGAAATTGCTTGCGCTG	0.318													T|||	268	0.0535144	0.0083	0.0677	5008	,	,		19084	0.0694		0.0905	False		,,,				2504	0.0501				p.Q55P		Atlas-SNP	.											.	MNS1	39	.	0			c.A164C						PASS	.	T	PRO/GLN	130,4250	95.7+/-134.4	3,124,2063	146.0	147.0	147.0		164	3.5	0.3	15	dbSNP_89	147	922,7662	204.4+/-247.1	51,820,3421	yes	missense	MNS1	NM_018365.2	76	54,944,5484	GG,GT,TT		10.7409,2.968,8.1148	benign	55/496	56756285	1052,11912	2190	4292	6482	SO:0001583	missense	55329	exon2			AGAAATTGCTTGC	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"""spermatogenesis associated 40"""	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.164A>C	15.37:g.56756285T>G	ENSP00000260453:p.Gln55Pro	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	172	93	0.540698	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	137	0.06272893772893773	7	0.014227642276422764	22	0.06077348066298342	36	0.06293706293706294	72	0.09498680738786279	T	11.78	1.740455	0.30865	0.02968	0.107409	ENSG00000138587	ENST00000260453	T	0.14893	2.47	5.42	3.5	0.40072	.	0.111317	0.56097	D	0.000023	T	0.00210	0.0006	N	0.14661	0.345	0.80722	P	0.0	B	0.24533	0.105	B	0.19666	0.026	T	0.09975	-1.0650	9	0.66056	D	0.02	-12.8365	9.0354	0.36284	0.0:0.8152:0.0:0.1848	rs1715919;rs3736530;rs17819479;rs61224656;rs1715919	55	Q8NEH6	MNS1_HUMAN	P	55	ENSP00000260453:Q55P	ENSP00000260453:Q55P	Q	-	2	0	MNS1	54543577	0.014000	0.17966	0.258000	0.24420	0.034000	0.12701	1.225000	0.32551	1.391000	0.46566	-0.462000	0.05337	CAA	G|0.074;N|0.000	0.074	strong		0.318	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365	
CLEC4M	10332	hgsc.bcm.edu	37	19	7831047	7831047	+	Silent	SNP	G	G	A	rs868878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7831047G>A	ENST00000327325.5	+	4	856	c.738G>A	c.(736-738)aaG>aaA	p.K246K	CLEC4M_ENST00000597522.1_Intron|CLEC4M_ENST00000359059.5_Intron|CLEC4M_ENST00000357361.2_Silent_p.K246K|CLEC4M_ENST00000595496.1_Intron|CLEC4M_ENST00000596707.1_Intron|CLEC4M_ENST00000596363.1_Silent_p.K218K|CLEC4M_ENST00000248228.4_Silent_p.K224K|CLEC4M_ENST00000334806.5_Silent_p.K195K|CLEC4M_ENST00000394122.2_Silent_p.K234K	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	246	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						ACCAGTCCAAGCAGCAGCAAA	0.527													G|||	309	0.0617013	0.0076	0.0807	5008	,	,		21992	0.0506		0.1551	False		,,,				2504	0.0368				p.K246K		Atlas-SNP	.											.	CLEC4M	58	.	0			c.G738A						PASS	.	G	,,,,,,,,	130,4276	94.8+/-133.5	3,124,2076	147.0	150.0	149.0		585,666,,,,600,669,654,738	0.5	0.1	19	dbSNP_86	149	1130,7470	233.3+/-266.6	72,986,3242	no	coding-synonymous,coding-synonymous,intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLEC4M	NM_001144904.1,NM_001144905.1,NM_001144906.1,NM_001144907.1,NM_001144908.1,NM_001144909.1,NM_001144910.1,NM_001144911.1,NM_014257.4	,,,,,,,,	75,1110,5318	AA,AG,GG		13.1395,2.9505,9.6878	,,,,,,,,	195/349,222/376,,,,200/354,223/377,218/297,246/400	7831047	1260,11746	2203	4300	6503	SO:0001819	synonymous_variant	10332	exon4			GTCCAAGCAGCAG	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.738G>A	19.37:g.7831047G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	66	39	0.590909	NM_014257	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Silent	SNP	ENST00000327325.5	37	CCDS12187.1																																																																																			A|0.087;C|0.000;G|0.913	0.087	strong		0.527	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	
ITFG3	83986	hgsc.bcm.edu	37	16	304514	304514	+	Silent	SNP	C	C	T	rs3213508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:304514C>T	ENST00000399932.3	+	3	553	c.102C>T	c.(100-102)aaC>aaT	p.N34N	ITFG3_ENST00000442458.2_Silent_p.N34N|ITFG3_ENST00000301678.3_Silent_p.N34N|ITFG3_ENST00000450082.2_Silent_p.N34N|ITFG3_ENST00000301679.2_Silent_p.N34N|ITFG3_ENST00000600536.1_Silent_p.N34N	NM_001284497.1	NP_001271426.1	Q9H0X4	ITFG3_HUMAN	integrin alpha FG-GAP repeat containing 3	34						cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(3)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16		all_cancers(16;0.000129)|all_epithelial(16;0.000206)|Hepatocellular(16;0.00264)|Lung NSC(18;0.0626)|all_lung(18;0.13)				ATGAGGATAACGTGAAAAGCG	0.483											OREG0003695	type=REGULATORY REGION|Gene=C16orf9|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	992	0.198083	0.1437	0.2378	5008	,	,		16496	0.3244		0.1421	False		,,,				2504	0.1708				p.N34N		Atlas-SNP	.											.	ITFG3	42	.	0			c.C102T						PASS	.	C		507,3163		34,439,1362	122.0	134.0	131.0		102	1.5	0.0	16	dbSNP_106	131	1305,6853		103,1099,2877	no	coding-synonymous	ITFG3	NM_032039.2		137,1538,4239	TT,TC,CC		15.9966,13.8147,15.3196		34/553	304514	1812,10016	1835	4079	5914	SO:0001819	synonymous_variant	83986	exon3			GGATAACGTGAAA	AL136542	CCDS10402.1	16p13.3	2006-03-31	2006-03-31	2006-03-31	ENSG00000167930	ENSG00000167930			14163	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 9"""	C16orf9			Standard	XM_005255622		Approved	DKFZP761D0211, FLJ32603	uc002cgf.3	Q9H0X4	OTTHUMG00000060728	ENST00000399932.3:c.102C>T	16.37:g.304514C>T		Somatic	75	0	0	587	WXS	Illumina HiSeq	Phase_I	83	43	0.518072	NM_032039	D3DU45|Q7L416|Q96FR1|Q96MC7|Q96S30	Silent	SNP	ENST00000399932.3	37	CCDS10402.1																																																																																			C|0.801;T|0.199	0.199	strong		0.483	ITFG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134227.2	NM_032039	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7505146	7505146	+	Missense_Mutation	SNP	A	A	C	rs200643326		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7505146A>C	ENST00000359920.6	+	1	573	c.320A>C	c.(319-321)cAg>cCg	p.Q107P	ARHGEF18_ENST00000319670.9_Intron|CTD-2207O23.3_ENST00000593531.1_Intron	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	107					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				CTGCGGCCGCAGTCGGAGCGG	0.602													A|||	1	0.000199681	0.0	0.0	5008	,	,		13226	0.0		0.0	False		,,,				2504	0.001				p.Q107P		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.A320C						PASS	.						27.0	34.0	32.0					19																	7505146		692	1591	2283	SO:0001583	missense	23370	exon1			GGCCGCAGTCGGA	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.320A>C	19.37:g.7505146A>C	ENSP00000352995:p.Gln107Pro	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	118	53	0.449153	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999042	0.35226	.	.	ENSG00000104880	ENST00000359920	T	0.32988	1.43	5.23	1.88	0.25563	.	0.187822	0.25607	U	0.029507	T	0.17023	0.0409	N	0.24115	0.695	0.09310	N	0.999999	P	0.44521	0.837	B	0.37451	0.25	T	0.10382	-1.0632	10	0.62326	D	0.03	-7.5996	7.6096	0.28122	0.7026:0.0:0.2974:0.0	.	107	Q6ZSZ5	ARHGI_HUMAN	P	107	ENSP00000352995:Q107P	ENSP00000352995:Q107P	Q	+	2	0	ARHGEF18	7411146	0.023000	0.18921	0.031000	0.17742	0.874000	0.50279	0.774000	0.26675	0.330000	0.23485	0.459000	0.35465	CAG	A|0.999;C|0.001	0.001	weak		0.602	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
C16orf93	90835	hgsc.bcm.edu	37	16	30768895	30768895	+	Missense_Mutation	SNP	G	G	A	rs182267845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30768895G>A	ENST00000543610.1	-	9	1859	c.898C>T	c.(898-900)Cgg>Tgg	p.R300W	PHKG2_ENST00000563588.1_3'UTR|C16orf93_ENST00000541260.1_Missense_Mutation_p.R365W|PHKG2_ENST00000424889.3_Intron	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	300										breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						GCCTTGAGCCGCTCCTCCACC	0.602													G|||	2	0.000399361	0.0	0.0	5008	,	,		19044	0.002		0.0	False		,,,				2504	0.0				p.R300W		Atlas-SNP	.											.	C16orf93	33	.	0			c.C898T						PASS	.						83.0	82.0	82.0					16																	30768895		2197	4300	6497	SO:0001583	missense	90835	exon9			TGAGCCGCTCCTC	BC042548	CCDS32434.1, CCDS32434.2, CCDS55993.1	16p11.2	2012-10-10			ENSG00000196118	ENSG00000196118			28078	protein-coding gene	gene with protein product							Standard	NM_001195620		Approved	MGC104706	uc002dzm.3	A1A4V9	OTTHUMG00000167926	ENST00000543610.1:c.898C>T	16.37:g.30768895G>A	ENSP00000437532:p.Arg300Trp	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	132	77	0.583333	NM_001014979	A1A4V8|F5GX13|Q569G2	Missense_Mutation	SNP	ENST00000543610.1	37	CCDS32434.2	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	16.27	3.076069	0.55646	.	.	ENSG00000196118	ENST00000354963;ENST00000543610	.	.	.	5.97	5.01	0.66863	.	0.783976	0.11884	N	0.520267	T	0.62925	0.2468	L	0.36672	1.1	0.51767	D	0.999936	D;D;D	0.65815	0.99;0.995;0.993	P;P;P	0.56514	0.681;0.8;0.752	T	0.61227	-0.7105	9	0.87932	D	0	-7.5983	12.3168	0.54962	0.0:0.0:0.8165:0.1835	.	263;72;300	A1A4V9-2;A1A4V9-3;A1A4V9	.;.;CP093_HUMAN	W	263;300	.	ENSP00000347050:R263W	R	-	1	2	C16orf93	30676396	0.364000	0.24997	0.086000	0.20670	0.294000	0.27393	1.977000	0.40589	1.487000	0.48415	-0.274000	0.10170	CGG	A|0.001;G|0.999	0.001	strong		0.602	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979	
SMPD1	6609	hgsc.bcm.edu	37	11	6413108	6413108	+	Silent	SNP	T	T	C	rs61876771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6413108T>C	ENST00000342245.4	+	2	981	c.813T>C	c.(811-813)ccT>ccC	p.P271P	SMPD1_ENST00000527275.1_Silent_p.P270P|SMPD1_ENST00000299397.3_Silent_p.P271P|SMPD1_ENST00000356761.2_Silent_p.P271P|SMPD1_ENST00000533196.1_Intron	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	269					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	CAGCCGGCCCTTTTGATATGG	0.622													T|||	13	0.00259585	0.0008	0.0029	5008	,	,		12884	0.0		0.0099	False		,,,				2504	0.0				p.P271P		Atlas-SNP	.											.	SMPD1	108	.	0			c.T813C						PASS	.	T	,	3,4399	6.2+/-15.9	0,3,2198	85.0	102.0	96.0		813,810	-1.8	1.0	11	dbSNP_129	96	55,8537	30.1+/-81.4	0,55,4241	no	coding-synonymous,coding-synonymous	SMPD1	NM_000543.4,NM_001007593.2	,	0,58,6439	CC,CT,TT		0.6401,0.0682,0.4464	,	271/632,270/631	6413108	58,12936	2201	4296	6497	SO:0001819	synonymous_variant	6609	exon2			CGGCCCTTTTGAT	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"""acid sphingomyelinase"""	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.813T>C	11.37:g.6413108T>C		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	43	0.605634	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	37	CCDS44531.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	T	10.10	1.258006	0.22965	6.82E-4	0.006401	ENSG00000166311	ENST00000526280	.	.	.	5.02	-1.8	0.07907	.	.	.	.	.	T	0.39784	0.1091	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32561	-0.9902	4	.	.	.	-21.0652	4.6701	0.12685	0.0:0.3147:0.3048:0.3805	rs61876771	.	.	.	P	1	.	.	L	+	2	0	SMPD1	6369684	0.796000	0.28864	0.992000	0.48379	0.966000	0.64601	-0.140000	0.10342	-0.243000	0.09653	0.459000	0.35465	CTT	A|0.000;C|0.006;T|0.993	0.006	strong		0.622	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543	
KLHL35	283212	hgsc.bcm.edu	37	11	75133765	75133765	+	Silent	SNP	G	G	A	rs11539810	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:75133765G>A	ENST00000539798.1	-	6	1610	c.1611C>T	c.(1609-1611)ggC>ggT	p.G537G	KLHL35_ENST00000376292.4_Silent_p.G317G	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	537								p.G537G(1)		lung(2)|stomach(1)	3						CATCCCGCCCGCCAAGGATGT	0.592													G|||	544	0.108626	0.034	0.0432	5008	,	,		20945	0.1885		0.0656	False		,,,				2504	0.2178				p.G537G	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											KLHL35,NS,carcinoma,0,1	KLHL35	15	1	1	Substitution - coding silent(1)	stomach(1)	c.C1611T						PASS	.	G		145,3883		0,145,1869	103.0	104.0	104.0		1611	-10.7	0.6	11	dbSNP_120	104	568,7822		24,520,3651	yes	coding-synonymous	KLHL35	NM_001039548.2		24,665,5520	AA,AG,GG		6.77,3.5998,5.7417		537/584	75133765	713,11705	2014	4195	6209	SO:0001819	synonymous_variant	283212	exon6			CCGCCCGCCAAGG		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"""Kelch-like"", ""BTB/POZ domain containing"""	26597	protein-coding gene	gene with protein product			"""kelch-like 35 (Drosophila)"""				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.1611C>T	11.37:g.75133765G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	51	28	0.54902	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Silent	SNP	ENST00000539798.1	37	CCDS44685.2																																																																																			G|0.910;A|0.090	0.090	strong		0.592	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583	
DDR1	780	hgsc.bcm.edu	37	6	30860313	30860313	+	Missense_Mutation	SNP	A	A	T	rs143367160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30860313A>T	ENST00000324771.8	+	10	1641	c.1093A>T	c.(1093-1095)Atc>Ttc	p.I365F	DDR1_ENST00000454612.2_Missense_Mutation_p.I365F|DDR1_ENST00000361741.4_Missense_Mutation_p.I96F|DDR1_ENST00000376568.3_Missense_Mutation_p.I365F|DDR1_ENST00000452441.1_Missense_Mutation_p.I365F|DDR1_ENST00000446312.1_3'UTR|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000418800.2_Missense_Mutation_p.I365F|DDR1_ENST00000508312.1_Missense_Mutation_p.I383F|DDR1_ENST00000513240.1_Missense_Mutation_p.I365F|DDR1_ENST00000376569.3_Missense_Mutation_p.I365F|DDR1_ENST00000376570.4_Missense_Mutation_p.I365F|DDR1_ENST00000376567.2_Missense_Mutation_p.I365F|DDR1_ENST00000376575.3_Missense_Mutation_p.I365F			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	365	DS-like domain.				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)	AATCTCCTTCATCTCTGGTAA	0.547													A|||	13	0.00259585	0.0	0.0086	5008	,	,		16593	0.0		0.003	False		,,,				2504	0.0041				p.I383F		Atlas-SNP	.											.	DDR1	213	.	0			c.A1147T						PASS	.	A	PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE	2,4404	4.2+/-10.8	0,2,2201	63.0	69.0	67.0		1093,1093,1147,1093,1093,1093	3.1	1.0	6	dbSNP_134	67	50,8550	31.2+/-83.2	0,50,4250	yes	missense,missense,missense,missense,missense,missense	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	21,21,21,21,21,21	0,52,6451	TT,TA,AA		0.5814,0.0454,0.3998	benign,benign,benign,benign,benign,benign	365/509,365/768,383/895,365/877,365/914,365/920	30860313	52,12954	2203	4300	6503	SO:0001583	missense	780	exon8			TCCTTCATCTCTG	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.1093A>T	6.37:g.30860313A>T	ENSP00000318217:p.Ile365Phe	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	63	23	0.365079	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	13.80	2.344152	0.41498	4.54E-4	0.005814	ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240;ENST00000417521;ENST00000361741;ENST00000451954	T;T;T;T;T;T;T;T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99	4.23	3.12	0.35913	.	0.077437	0.51477	D	0.000083	T	0.08313	0.0207	L	0.43923	1.385	0.41933	D	0.990575	B;P;B;B	0.48230	0.045;0.907;0.004;0.005	B;B;B;B	0.44224	0.021;0.444;0.038;0.007	T	0.09885	-1.0654	9	.	.	.	.	4.0728	0.09891	0.5736:0.2983:0.1282:0.0	.	383;161;365;365	B7Z2K0;A2ABM8;Q08345-5;Q08345	.;.;.;DDR1_HUMAN	F	365;365;365;365;365;365;365;365;383;365;365;161;96;48	ENSP00000318217:I365F;ENSP00000407699:I365F;ENSP00000406091:I365F;ENSP00000365753:I365F;ENSP00000365759:I365F;ENSP00000365754:I365F;ENSP00000365752:I365F;ENSP00000405039:I365F;ENSP00000422442:I383F;ENSP00000365751:I365F;ENSP00000427552:I365F;ENSP00000398682:I161F;ENSP00000354844:I96F	.	I	+	1	0	DDR1	30968292	0.967000	0.33354	1.000000	0.80357	0.979000	0.70002	2.245000	0.43133	1.559000	0.49555	0.379000	0.24179	ATC	A|0.997;T|0.003	0.003	strong		0.547	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
NBPF10	100132406	hgsc.bcm.edu	37	1	145299805	145299805	+	Missense_Mutation	SNP	A	A	C	rs61814629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145299805A>C	ENST00000369338.1	+	2	231	c.41A>C	c.(40-42)gAg>gCg	p.E14A	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.E285A|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	285						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.E285A(1)|p.E14A(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)		GAGAAGGCAGAGATGAACATT	0.493													.|||	179	0.0357428	0.0015	0.0231	5008	,	,		43597	0.0635		0.0487	False		,,,				2504	0.0491				p.E285A		Atlas-SNP	.											NBPF10_ENST00000369338,extremity,malignant_melanoma,0,2	NBPF10	221	2	2	Substitution - Missense(2)	skin(2)	c.A854C						scavenged	.						9.0	8.0	8.0					1																	145299805		690	1570	2260	SO:0001583	missense	100132406	exon6			AGGCAGAGATGAA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.41A>C	1.37:g.145299805A>C	ENSP00000358344:p.Glu14Ala	Somatic	116	7	0.0603448		WXS	Illumina HiSeq	Phase_I	111	8	0.0720721	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	11.71	1.719994	0.30503	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.03663	3.85;3.85	1.05	1.05	0.20165	.	.	.	.	.	T	0.03095	0.0091	M	0.74647	2.275	0.09310	N	1	P	0.37398	0.593	P	0.45577	0.486	T	0.39941	-0.9589	9	0.66056	D	0.02	.	4.3442	0.11124	1.0:0.0:0.0:0.0	rs61814629	14	Q86T75-2	.	A	210;14;14;285	ENSP00000358344:E14A;ENSP00000345684:E285A	ENSP00000345684:E285A	E	+	2	0	NBPF10	144011162	0.002000	0.14202	0.003000	0.11579	0.032000	0.12392	-0.314000	0.08092	0.731000	0.32448	0.234000	0.17832	GAG	A|0.999;G|0.001	.	weak		0.493	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
OR52K2	119774	hgsc.bcm.edu	37	11	4471276	4471276	+	Missense_Mutation	SNP	G	G	A	rs331537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4471276G>A	ENST00000325719.4	+	1	752	c.707G>A	c.(706-708)cGc>cAc	p.R236H		NM_001005172.2	NP_001005172.2	Q8NGK3	O52K2_HUMAN	olfactory receptor, family 52, subfamily K, member 2	236			R -> H (in dbSNP:rs331537). {ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|skin(6)	25		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;1.48e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0821)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGAGGCCCGCTACAAGGCA	0.488													G|||	1116	0.222843	0.7239	0.0879	5008	,	,		22301	0.0347		0.0318	False		,,,				2504	0.0317				p.R236H		Atlas-SNP	.											.	OR52K2	61	.	0			c.G707A						PASS	.	G	HIS/ARG	2604,1798	641.6+/-397.5	782,1040,379	268.0	228.0	242.0		707	4.0	1.0	11	dbSNP_79	242	268,8328	101.6+/-162.9	4,260,4034	yes	missense	OR52K2	NM_001005172.2	29	786,1300,4413	AA,AG,GG		3.1177,40.8451,22.0957	benign	236/315	4471276	2872,10126	2201	4298	6499	SO:0001583	missense	119774	exon1			AGGCCCGCTACAA	AB065791	CCDS31351.1	11p15.4	2012-08-09			ENSG00000181963	ENSG00000181963		"""GPCR / Class A : Olfactory receptors"""	15223	protein-coding gene	gene with protein product							Standard	NM_001005172		Approved		uc001lyz.2	Q8NGK3	OTTHUMG00000165703	ENST00000325719.4:c.707G>A	11.37:g.4471276G>A	ENSP00000318956:p.Arg236His	Somatic	207	1	0.00483092		WXS	Illumina HiSeq	Phase_I	206	104	0.504854	NM_001005172	A8MUY8|B2RP35|Q6IFK4	Missense_Mutation	SNP	ENST00000325719.4	37	CCDS31351.1	439	0.20100732600732601	363	0.7378048780487805	29	0.08011049723756906	23	0.04020979020979021	24	0.0316622691292876	G	11.70	1.718104	0.30503	0.591549	0.031177	ENSG00000181963	ENST00000325719	T	0.00333	8.07	4.02	4.02	0.46733	GPCR, rhodopsin-like superfamily (1);	0.140701	0.30126	N	0.010342	T	0.00012	0.0000	M	0.86740	2.835	0.48185	P	3.990000000000382E-4	B	0.18968	0.032	B	0.19391	0.025	T	0.36962	-0.9726	9	0.87932	D	0	.	9.6637	0.39972	0.1047:0.0:0.8953:0.0	rs331537;rs59989102;rs331537	236	Q8NGK3	O52K2_HUMAN	H	236	ENSP00000318956:R236H	ENSP00000318956:R236H	R	+	2	0	OR52K2	4427852	0.001000	0.12720	0.999000	0.59377	0.879000	0.50718	0.949000	0.29109	2.082000	0.62665	0.485000	0.47835	CGC	G|0.792;A|0.208	0.208	strong		0.488	OR52K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385844.1	NM_001005172	
OR52M1	119772	hgsc.bcm.edu	37	11	4566870	4566870	+	Silent	SNP	T	T	C	rs61747520	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:4566870T>C	ENST00000360213.1	+	1	450	c.450T>C	c.(448-450)tcT>tcC	p.S150S		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	150						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGCTTGTTTCTCTCCTCCGGG	0.532													T|||	133	0.0265575	0.0303	0.0159	5008	,	,		18160	0.0337		0.0288	False		,,,				2504	0.0194				p.S150S		Atlas-SNP	.											OR52M1,right_upper_lobe,carcinoma,+1,1	OR52M1	53	1	0			c.T450C						PASS	.	T		133,4269	97.6+/-136.3	4,125,2072	102.0	101.0	101.0		450	1.1	0.3	11	dbSNP_129	101	272,8324	102.9+/-164.1	5,262,4031	no	coding-synonymous	OR52M1	NM_001004137.1		9,387,6103	CC,CT,TT		3.1643,3.0214,3.1159		150/318	4566870	405,12593	2201	4298	6499	SO:0001819	synonymous_variant	119772	exon1			TGTTTCTCTCCTC	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.450T>C	11.37:g.4566870T>C		Somatic	379	1	0.00263852		WXS	Illumina HiSeq	Phase_I	387	188	0.485788	NM_001004137		Silent	SNP	ENST00000360213.1	37	CCDS31353.1																																																																																			T|0.968;C|0.032	0.032	strong		0.532	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	rs28989168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152975715C>T	ENST00000295367.4	+	2	261	c.219C>T	c.(217-219)ggC>ggT	p.G73G	SPRR3_ENST00000331860.3_Silent_p.G73G|SPRR3_ENST00000542696.1_Silent_p.G73G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	73	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGCTGTACCAAGG	0.577													T|||	2	0.000399361	0.0015	0.0	5008	,	,		14904	0.0		0.0	False		,,,				2504	0.0				p.G73G		Atlas-SNP	.											SPRR3,colon,carcinoma,0,3	SPRR3	45	3	0			c.C219T						PASS	.						42.0	39.0	40.0					1																	152975715		2182	4268	6450	SO:0001819	synonymous_variant	6707	exon2			GCCAGGCTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.219C>T	1.37:g.152975715C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	19	0.223529	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			.	.	none		0.577	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
ANKRD18A	253650	hgsc.bcm.edu	37	9	38595886	38595886	+	Missense_Mutation	SNP	T	T	C	rs2996347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:38595886T>C	ENST00000399703.5	-	9	1825	c.1451A>G	c.(1450-1452)aAt>aGt	p.N484S		NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	484			N -> S (in dbSNP:rs2996347).					p.N484S(1)		NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						TTTTAAGGTATTGAACTTCAC	0.413													.|||	1662	0.331869	0.4826	0.317	5008	,	,		20583	0.4603		0.2187	False		,,,				2504	0.1227				p.N484S		Atlas-SNP	.											ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	1	Substitution - Missense(1)	stomach(1)	c.A1451G						PASS	.	T	SER/ASN	628,756		136,356,200	95.0	67.0	75.0		1451	1.4	0.0	9	dbSNP_101	75	651,2529		66,519,1005	no	missense	ANKRD18A	NM_147195.2	46	202,875,1205	CC,CT,TT		20.4717,45.3757,28.0237	possibly-damaging	484/993	38595886	1279,3285	692	1590	2282	SO:0001583	missense	253650	exon9			AAGGTATTGAACT	AB095935	CCDS55311.1	9p13.1	2013-01-10			ENSG00000180071	ENSG00000180071		"""Ankyrin repeat domain containing"""	23643	protein-coding gene	gene with protein product							Standard	NM_147195		Approved	KIAA2015, FLJ35740	uc004abg.4	Q8IVF6	OTTHUMG00000019950	ENST00000399703.5:c.1451A>G	9.37:g.38595886T>C	ENSP00000382610:p.Asn484Ser	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	137	56	0.408759	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	745	0.3411172161172161	249	0.5060975609756098	99	0.27348066298342544	224	0.3916083916083916	173	0.22823218997361477	T	5.964	0.361918	0.11296	0.453757	0.204717	ENSG00000180071	ENST00000399703	T	0.17370	2.28	1.35	1.35	0.21983	.	.	.	.	.	T	0.00012	0.0000	N	0.25286	0.73	0.29173	P	0.877008	B	0.12013	0.005	B	0.01281	0.0	T	0.44314	-0.9336	8	0.35671	T	0.21	.	6.8814	0.24174	0.0:0.0:0.0:1.0	rs2996347;rs7036857;rs59857660;rs2996347	484	Q8IVF6	AN18A_HUMAN	S	484	ENSP00000382610:N484S	ENSP00000382610:N484S	N	-	2	0	ANKRD18A	38585886	0.234000	0.23783	0.009000	0.14445	0.065000	0.16274	0.494000	0.22467	0.892000	0.36259	0.113000	0.15668	AAT	T|0.680;C|0.320	0.320	strong		0.413	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
ESPN	83715	hgsc.bcm.edu	37	1	6501044	6501044	+	Silent	SNP	C	C	G	rs2311045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:6501044C>G	ENST00000377828.1	+	5	1077	c.909C>G	c.(907-909)cgC>cgG	p.R303R	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	303					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		TCCGCGACCGCGACGGGTACA	0.706													.|||	912	0.182109	0.2799	0.1167	5008	,	,		12416	0.1647		0.1223	False		,,,				2504	0.1759				p.R303R		Atlas-SNP	.											.	ESPN	32	.	0			c.C909G						PASS	.	C		1033,3341		121,791,1275	14.0	14.0	14.0		909	-8.2	0.3	1	dbSNP_100	14	1018,7552		63,892,3330	no	coding-synonymous	ESPN	NM_031475.2		184,1683,4605	GG,GC,CC		11.8786,23.6168,15.8452		303/855	6501044	2051,10893	2187	4285	6472	SO:0001819	synonymous_variant	83715	exon5			CGACCGCGACGGG	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.909C>G	1.37:g.6501044C>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	93	13	0.139785	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Silent	SNP	ENST00000377828.1	37	CCDS70.1																																																																																			C|0.828;G|0.172	0.172	strong		0.706	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
TTC28	23331	hgsc.bcm.edu	37	22	28504183	28504183	+	Silent	SNP	G	G	A	rs9625408	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:28504183G>A	ENST00000397906.2	-	7	1791	c.1650C>T	c.(1648-1650)cgC>cgT	p.R550R		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	550					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						CCTGTGAGGCGCGGTCATTCA	0.582													G|||	276	0.0551118	0.0439	0.0677	5008	,	,		16746	0.003		0.0746	False		,,,				2504	0.0951				p.R550R		Atlas-SNP	.											.	TTC28	84	.	0			c.C1650T						PASS	.	G		73,1311		0,73,619	84.0	80.0	81.0		1650	-11.8	0.4	22	dbSNP_119	81	264,2918		15,234,1342	no	coding-synonymous	TTC28	NM_001145418.1		15,307,1961	AA,AG,GG		8.2967,5.2746,7.3806		550/2482	28504183	337,4229	692	1591	2283	SO:0001819	synonymous_variant	23331	exon7			TGAGGCGCGGTCA	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.1650C>T	22.37:g.28504183G>A		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	117	67	0.57265	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.949;A|0.051	0.051	strong		0.582	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
EXOC3	11336	hgsc.bcm.edu	37	5	465838	465838	+	Silent	SNP	C	C	T	rs13162508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:465838C>T	ENST00000512944.1	+	12	2133	c.1944C>T	c.(1942-1944)ttC>ttT	p.F648F	CTD-2228K2.5_ENST00000510714.1_5'Flank|EXOC3_ENST00000315013.5_Silent_p.F648F	NM_007277.4	NP_009208.2	O60645	EXOC3_HUMAN	exocyst complex component 3	659					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	exocyst (GO:0000145)|secretory granule membrane (GO:0030667)				breast(2)|cervix(1)|endometrium(4)|large_intestine(1)|lung(13)|ovary(1)|urinary_tract(1)	23		Ovarian(839;0.0563)	Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TCCAGGGTTTCGGGGAAGACG	0.627													C|||	40	0.00798722	0.0008	0.013	5008	,	,		16023	0.0		0.0298	False		,,,				2504	0.0				p.F648F		Atlas-SNP	.											.	EXOC3	54	.	0			c.C1944T						PASS	.	C		19,4237		0,19,2109	59.0	63.0	61.0		1944	-1.0	0.1	5	dbSNP_121	61	247,8203		3,241,3981	yes	coding-synonymous	EXOC3	NM_007277.4		3,260,6090	TT,TC,CC		2.9231,0.4464,2.0935		648/746	465838	266,12440	2128	4225	6353	SO:0001819	synonymous_variant	11336	exon12			GGGTTTCGGGGAA	BC034427	CCDS54830.1	5p15.33	2013-01-22	2005-11-01	2005-11-01	ENSG00000180104	ENSG00000180104			30378	protein-coding gene	gene with protein product		608186	"""SEC6-like 1 (S. cerevisiae)"""	SEC6L1		8619474	Standard	XM_005248238		Approved	Sec6p	uc003jba.3	O60645	OTTHUMG00000162205	ENST00000512944.1:c.1944C>T	5.37:g.465838C>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	95	62	0.652632	NM_007277	Q6P2E8|Q8TEN6|Q8WUW0|Q96DI4	Silent	SNP	ENST00000512944.1	37	CCDS54830.1																																																																																			C|0.986;T|0.014	0.014	strong		0.627	EXOC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367882.1	NM_007277	
NLRC3	197358	hgsc.bcm.edu	37	16	3594296	3594296	+	RNA	SNP	C	C	T	rs35402060	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3594296C>T	ENST00000301749.7	-	0	3210				NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000603507.1_RNA|LA16c-390H2.4_ENST00000573820.1_RNA|NLRC3_ENST00000359128.5_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CCACCGCACACGCTCCGTCAT	0.597													C|||	292	0.0583067	0.059	0.072	5008	,	,		17948	0.0556		0.0636	False		,,,				2504	0.045				p.A935A		Atlas-SNP	.											.	NLRC3	103	.	0			c.G2805A						PASS	.	C		259,3945		8,243,1851	72.0	78.0	76.0		2806	-10.3	0.0	16	dbSNP_126	76	558,7900		14,530,3685	yes	coding-synonymous	NLRC3	NM_178844.2		22,773,5536	TT,TC,CC		6.5973,6.1608,6.4524		935/1066	3594296	817,11845	2102	4229	6331			197358	exon17			CGCACACGCTCCG	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3594296C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				C|0.947;T|0.053	0.053	strong		0.597	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957887	152957887	+	Missense_Mutation	SNP	G	G	A	rs1611764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152957887G>A	ENST00000368762.1	+	1	181	c.181G>A	c.(181-183)Gtt>Att	p.V61I	SPRR1A_ENST00000307122.2_Missense_Mutation_p.V61I			P35321	SPR1A_HUMAN	small proline-rich protein 1A	61	6 X 8 AA approximate tandem repeats.		V -> I (in dbSNP:rs1611764). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8325635, ECO:0000269|Ref.3}.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCAGCCCAAGGTTCCAGAGCC	0.627													G|||	2810	0.561102	0.6278	0.4524	5008	,	,		15250	0.6319		0.5348	False		,,,				2504	0.502				p.V61I		Atlas-SNP	.											.	SPRR1A	17	.	0			c.G181A						PASS	.	G	ILE/VAL,ILE/VAL	2805,1601	660.2+/-400.7	897,1011,295	108.0	105.0	106.0		181,181	3.8	0.3	1	dbSNP_89	106	4674,3926	602.4+/-394.5	1279,2116,905	no	missense,missense	SPRR1A	NM_001199828.1,NM_005987.3	29,29	2176,3127,1200	AA,AG,GG		45.6512,36.3368,42.4958	benign,benign	61/90,61/90	152957887	7479,5527	2203	4300	6503	SO:0001583	missense	6698	exon2			CCCAAGGTTCCAG	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.181G>A	1.37:g.152957887G>A	ENSP00000357751:p.Val61Ile	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	104	45	0.432692	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	1269	0.5810439560439561	319	0.6483739837398373	180	0.4972375690607735	372	0.6503496503496503	398	0.525065963060686	G	12.59	1.983175	0.34942	0.636632	0.543488	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.14766	2.48;2.48	5.64	3.77	0.43336	.	0.874660	0.09328	N	0.817264	T	0.08537	0.0212	.	.	.	0.53688	P	2.5000000000052758E-5	P	0.44195	0.828	P	0.47251	0.542	T	0.21143	-1.0254	8	0.45353	T	0.12	0.414	7.7627	0.28961	0.1845:0.0:0.8155:0.0	rs1611764;rs17881890;rs58884077;rs1611764	61	P35321	SPR1A_HUMAN	I	61	ENSP00000307340:V61I;ENSP00000357751:V61I	ENSP00000307340:V61I	V	+	1	0	SPRR1A	151224511	0.044000	0.20184	0.277000	0.24703	0.039000	0.13416	1.015000	0.29963	1.389000	0.46526	-0.266000	0.10368	GTT	G|0.417;A|0.583	0.583	strong		0.627	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
WWP2	11060	hgsc.bcm.edu	37	16	69973825	69973825	+	Silent	SNP	G	G	A	rs3748389	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:69973825G>A	ENST00000359154.2	+	24	2696	c.2595G>A	c.(2593-2595)gaG>gaA	p.E865E	WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000448661.1_Silent_p.E865E|WWP2_ENST00000356003.2_Silent_p.E865E|WWP2_ENST00000568684.1_Silent_p.E426E|WWP2_ENST00000542271.1_Silent_p.E749E	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	865	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cellular protein modification process (GO:0006464)|negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transporter activity (GO:0032410)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|RNA polymerase II transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(4)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						AGGAGACCGAGGGCTTTGGAC	0.612													G|||	2646	0.528355	0.3994	0.3862	5008	,	,		17241	0.8819		0.3449	False		,,,				2504	0.6278				p.E865E		Atlas-SNP	.											WWP2,NS,carcinoma,0,1	WWP2	88	1	0			c.G2595A						PASS	.	G	,	1633,2763	497.4+/-363.8	305,1023,870	84.0	63.0	70.0		2595,1278	3.4	1.0	16	dbSNP_107	70	3045,5555	462.0+/-365.6	554,1937,1809	no	coding-synonymous,coding-synonymous	WWP2	NM_007014.3,NM_199424.1	,	859,2960,2679	AA,AG,GG		35.407,37.1474,35.9957	,	865/871,426/432	69973825	4678,8318	2198	4300	6498	SO:0001819	synonymous_variant	11060	exon24			GACCGAGGGCTTT	BC013645	CCDS10885.1, CCDS58475.1, CCDS58476.1, CCDS58477.1	16q22.1	2008-02-05			ENSG00000198373	ENSG00000198373			16804	protein-coding gene	gene with protein product		602308				9169421, 12167593	Standard	NM_007014		Approved	AIP2	uc002exv.2	O00308	OTTHUMG00000137573	ENST00000359154.2:c.2595G>A	16.37:g.69973825G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	71	37	0.521127	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Silent	SNP	ENST00000359154.2	37	CCDS10885.1																																																																																			G|0.572;A|0.428	0.428	strong		0.612	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014	
ACSBG2	81616	hgsc.bcm.edu	37	19	6156483	6156483	+	Missense_Mutation	SNP	T	T	C	rs4807840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6156483T>C	ENST00000586696.1	+	5	704	c.428T>C	c.(427-429)gTt>gCt	p.V143A	ACSBG2_ENST00000588485.1_Intron|ACSBG2_ENST00000252669.5_Missense_Mutation_p.V143A|ACSBG2_ENST00000591403.1_Missense_Mutation_p.V143A|ACSBG2_ENST00000588304.1_Missense_Mutation_p.V93A			Q5FVE4	ACBG2_HUMAN	acyl-CoA synthetase bubblegum family member 2	143			V -> A (in dbSNP:rs4807840). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15685348, ECO:0000269|PubMed:16762313}.		cell differentiation (GO:0030154)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid metabolic process (GO:0001676)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)	acyl-CoA hydrolase activity (GO:0047617)|ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(3)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTGCCGAGGTTTGTCAATAT	0.443													C|||	3566	0.712061	0.7337	0.7478	5008	,	,		20184	0.7153		0.7127	False		,,,				2504	0.6534				p.V143A		Atlas-SNP	.											ACSBG2,NS,carcinoma,+1,1	ACSBG2	83	1	0			c.T428C						scavenged	.	C	ALA/VAL	3187,1219	423.2+/-340.0	1162,863,178	168.0	159.0	162.0		428	5.9	0.1	19	dbSNP_111	162	5918,2682	431.3+/-356.8	2005,1908,387	yes	missense	ACSBG2	NM_030924.3	64	3167,2771,565	CC,CT,TT		31.186,27.6668,29.9938	benign	143/667	6156483	9105,3901	2203	4300	6503	SO:0001583	missense	81616	exon5			CCGAGGTTTGTCA		CCDS12159.1, CCDS74269.1	19p13.3	2012-10-02			ENSG00000130377	ENSG00000130377		"""Acyl-CoA synthetase family"""	24174	protein-coding gene	gene with protein product	"""bubblegum related protein"""	614363				11230166	Standard	XM_005259653		Approved	BGR, PRTD-NY3, DKFZp434K1635	uc002meh.1	Q5FVE4	OTTHUMG00000180754	ENST00000586696.1:c.428T>C	19.37:g.6156483T>C	ENSP00000465589:p.Val143Ala	Somatic	173	2	0.0115607		WXS	Illumina HiSeq	Phase_I	201	101	0.502488	NM_030924	B3KSF2|Q6UWJ3|Q7Z5A0|Q8WW03|Q96M36|Q9BYZ3|Q9H0C4	Missense_Mutation	SNP	ENST00000586696.1	37	CCDS12159.1	1605	0.7348901098901099	369	0.75	271	0.7486187845303868	420	0.7342657342657343	545	0.7189973614775725	C	4.063	0.009457	0.07912	0.723332	0.68814	ENSG00000130377	ENST00000252669	T	0.37584	1.19	5.9	5.9	0.94986	AMP-dependent synthetase/ligase (1);	0.000000	0.39146	N	0.001445	T	0.00012	0.0000	N	0.00002	-3.505	0.45806	P	0.001318999999999959	B	0.02656	0.0	B	0.01281	0.0	T	0.45190	-0.9278	9	0.02654	T	1	-29.499	13.1437	0.59448	0.0:0.9233:0.0:0.0767	rs4807840;rs17845670;rs17858608;rs52832814;rs56448071;rs59539360;rs4807840	143	Q5FVE4	ACBG2_HUMAN	A	143	ENSP00000252669:V143A	ENSP00000252669:V143A	V	+	2	0	ACSBG2	6107483	1.000000	0.71417	0.107000	0.21349	0.250000	0.25880	5.346000	0.65992	1.511000	0.48818	-0.128000	0.14901	GTT	T|0.289;C|0.711	0.711	strong		0.443	ACSBG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452898.1	NM_030924	
PROSER3	148137	hgsc.bcm.edu	37	19	36259415	36259415	+	Missense_Mutation	SNP	G	G	A	rs35178229	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36259415G>A	ENST00000396908.4	+	12	1481	c.1408G>A	c.(1408-1410)Gaa>Aaa	p.E470K	C19orf55_ENST00000536037.1_3'UTR|C19orf55_ENST00000544099.1_3'UTR|AC002398.13_ENST00000589397.1_RNA	NM_001039887.2	NP_001034976.2	Q2NL68	PRSR3_HUMAN		471										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)			GCTAAGAAGGGAAGGAGATTC	0.498													G|||	693	0.138379	0.2042	0.1628	5008	,	,		14706	0.1498		0.0895	False		,,,				2504	0.0706				p.E471K		Atlas-SNP	.											.	C19orf55	39	.	0			c.G1411A						PASS	.	G	LYS/GLU	321,1431		26,269,581	112.0	119.0	117.0		1412	4.1	0.9	19	dbSNP_126	117	413,3569		23,367,1601	yes	missense	C19orf55	NM_001039887.2	56	49,636,2182	AA,AG,GG		10.3717,18.3219,12.8008		471/481	36259415	734,5000	876	1991	2867	SO:0001583	missense	148137	exon12			AGAAGGGAAGGAG																												ENST00000396908.4:c.1408G>A	19.37:g.36259415G>A	ENSP00000380116:p.Glu470Lys	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000396908.4	37		308	0.14102564102564102	94	0.1910569105691057	62	0.1712707182320442	78	0.13636363636363635	74	0.09762532981530343	G	36	5.706541	0.96821	0.183219	0.103717	ENSG00000167595	ENST00000396908	T	0.39229	1.09	4.09	4.09	0.47781	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.37590	P	0.07984800000000003	.	.	.	.	.	.	T	0.04976	-1.0914	5	0.87932	D	0	-2.3027	12.1094	0.53830	0.0:0.0:1.0:0.0	rs35178229	.	.	.	K	470	ENSP00000380116:E470K	ENSP00000380116:E470K	E	+	1	0	C19orf55	40951255	1.000000	0.71417	0.902000	0.35471	0.735000	0.41995	1.705000	0.37867	2.567000	0.86603	0.563000	0.77884	GAA	G|0.872;A|0.128	0.128	strong		0.498	C19orf55-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
CARD11	84433	hgsc.bcm.edu	37	7	2957005	2957005	+	Silent	SNP	T	T	C	rs3735124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:2957005T>C	ENST00000396946.4	-	20	3025	c.2622A>G	c.(2620-2622)ccA>ccG	p.P874P		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	874					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GCGCTTCTTCTGGCTGCAGGG	0.567			Mis		DLBCL								C|||	2319	0.463059	0.5787	0.4207	5008	,	,		14294	0.6101		0.2087	False		,,,				2504	0.4468				p.P874P		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.A2622G						PASS	.	C		2343,2063	562.8+/-381.0	613,1117,473	37.0	49.0	45.0		2622	-10.0	0.1	7	dbSNP_107	45	1779,6819	731.4+/-406.8	165,1449,2685	no	coding-synonymous	CARD11	NM_032415.4		778,2566,3158	CC,CT,TT		20.6909,46.8225,31.6979		874/1155	2957005	4122,8882	2203	4299	6502	SO:0001819	synonymous_variant	84433	exon20			TTCTTCTGGCTGC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.2622A>G	7.37:g.2957005T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	60	30	0.5	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Silent	SNP	ENST00000396946.4	37	CCDS5336.2																																																																																			T|0.633;C|0.367	0.367	strong		0.567	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
EYS	346007	hgsc.bcm.edu	37	6	65301679	65301679	+	Missense_Mutation	SNP	T	T	C	rs17403955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301679T>C	ENST00000370621.3	-	26	4607	c.4081A>G	c.(4081-4083)Att>Gtt	p.I1361V	EYS_ENST00000370616.2_Missense_Mutation_p.I1361V|EYS_ENST00000503581.1_Missense_Mutation_p.I1361V			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1361			I -> V (in dbSNP:rs17403955). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TCCTGGACAATTTGTGCTGGG	0.428													T|||	470	0.0938498	0.0151	0.1182	5008	,	,		18415	0.1567		0.0984	False		,,,				2504	0.1135				p.I1361V		Atlas-SNP	.											.	EYS	527	.	0			c.A4081G						PASS	.	T	VAL/ILE	49,1335		1,47,644	124.0	110.0	114.0		4081	-1.2	0.0	6	dbSNP_123	114	446,2734		41,364,1185	yes	missense	EYS	NM_001142800.1	29	42,411,1829	CC,CT,TT		14.0252,3.5405,10.8457	benign	1361/3145	65301679	495,4069	692	1590	2282	SO:0001583	missense	346007	exon26			GGACAATTTGTGC		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4081A>G	6.37:g.65301679T>C	ENSP00000359655:p.Ile1361Val	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	77	77	1	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		218	0.09981684981684982	6	0.012195121951219513	44	0.12154696132596685	88	0.15384615384615385	80	0.10554089709762533	T	3.049	-0.195780	0.06259	0.035405	0.140252	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.83075	-1.68;-1.66;-1.66	5.74	-1.16	0.09678	.	.	.	.	.	T	0.36358	0.0964	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.06481	-1.0824	8	0.29301	T	0.29	.	0.8356	0.01139	0.2601:0.1429:0.1316:0.4653	rs17403955;rs52812047;rs17403955	1361;1361	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	V	1361	ENSP00000424243:I1361V;ENSP00000359655:I1361V;ENSP00000359650:I1361V	ENSP00000359650:I1361V	I	-	1	0	EYS	65358400	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	0.161000	0.16481	-0.414000	0.07495	0.482000	0.46254	ATT	T|0.900;C|0.100	0.100	strong		0.428	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
FREM2	341640	hgsc.bcm.edu	37	13	39263772	39263772	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39263772C>T	ENST00000280481.7	+	1	2507	c.2291C>T	c.(2290-2292)aCt>aTt	p.T764I		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	764					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)		TTGGTCTTGACTGACAACCCC	0.532																																					p.T764I		Atlas-SNP	.											.	FREM2	385	.	0			c.C2291T						PASS	.						84.0	89.0	87.0					13																	39263772		2203	4300	6503	SO:0001583	missense	341640	exon1			TCTTGACTGACAA	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.2291C>T	13.37:g.39263772C>T	ENSP00000280481:p.Thr764Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	99	50	0.50505	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.512067	0.44660	.	.	ENSG00000150893	ENST00000280481	T	0.42131	0.98	5.8	4.95	0.65309	.	0.222181	0.45606	D	0.000354	T	0.44767	0.1309	M	0.69523	2.12	0.53688	D	0.999972	P	0.42161	0.772	B	0.40864	0.342	T	0.48080	-0.9066	10	0.54805	T	0.06	.	11.9366	0.52876	0.1368:0.7317:0.1316:0.0	.	764	Q5SZK8	FREM2_HUMAN	I	764	ENSP00000280481:T764I	ENSP00000280481:T764I	T	+	2	0	FREM2	38161772	0.998000	0.40836	0.895000	0.35142	0.761000	0.43186	3.899000	0.56288	1.437000	0.47472	0.655000	0.94253	ACT	.	.	none		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
ABT1	29777	hgsc.bcm.edu	37	6	26598188	26598188	+	Silent	SNP	A	A	G	rs3800303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26598188A>G	ENST00000274849.1	+	2	319	c.288A>G	c.(286-288)ggA>ggG	p.G96G		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	96	RRM.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron differentiation (GO:0021522)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|urinary_tract(1)	11						CTGCCGGAGGAAAAAAGCGGT	0.587													a|||	2585	0.516174	0.4917	0.5144	5008	,	,		18490	0.6667		0.3787	False		,,,				2504	0.5368				p.G96G		Atlas-SNP	.											.	ABT1	39	.	0			c.A288G						PASS	.	G		2101,2305	554.9+/-379.1	499,1103,601	50.0	47.0	48.0		288	-10.5	0.5	6	dbSNP_107	48	3611,4989	499.0+/-374.9	794,2023,1483	no	coding-synonymous	ABT1	NM_013375.3		1293,3126,2084	GG,GA,AA		41.9884,47.685,43.9182		96/273	26598188	5712,7294	2203	4300	6503	SO:0001819	synonymous_variant	29777	exon2			CGGAGGAAAAAAG	AB027258	CCDS4616.1	6p21.31	2008-07-07			ENSG00000146109	ENSG00000146109			17369	protein-coding gene	gene with protein product						10648625	Standard	NM_013375		Approved		uc003nii.3	Q9ULW3	OTTHUMG00000016319	ENST00000274849.1:c.288A>G	6.37:g.26598188A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	131	131	1	NM_013375		Silent	SNP	ENST00000274849.1	37	CCDS4616.1																																																																																			A|0.536;G|0.464	0.464	strong		0.587	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1		
ABI3BP	25890	hgsc.bcm.edu	37	3	100473505	100473505	+	Silent	SNP	C	C	T	rs10936352	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:100473505C>T	ENST00000284322.5	-	31	2857	c.2748G>A	c.(2746-2748)ccG>ccA	p.P916P	ABI3BP_ENST00000383691.4_Silent_p.P870P|ABI3BP_ENST00000471714.1_Silent_p.P1618P	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	916	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular space (GO:0005615)|interstitial matrix (GO:0005614)	heparin binding (GO:0008201)			central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	50						CTTCACCAAGCGGGTTTTTGG	0.418													C|||	1457	0.290935	0.1157	0.4193	5008	,	,		18523	0.1181		0.3698	False		,,,				2504	0.5337				p.P916P		Atlas-SNP	.											.	ABI3BP	305	.	0			c.G2748A						PASS	.	C		554,3144		36,482,1331	85.0	76.0	79.0		2748	-9.5	0.9	3	dbSNP_120	79	3201,4987		635,1931,1528	no	coding-synonymous	ABI3BP	NM_015429.3		671,2413,2859	TT,TC,CC		39.0938,14.9811,31.5918		916/1076	100473505	3755,8131	1849	4094	5943	SO:0001819	synonymous_variant	25890	exon31			ACCAAGCGGGTTT	AB056106	CCDS46880.1	3q12.2	2013-02-11	2008-09-12		ENSG00000154175	ENSG00000154175		"""Fibronectin type III domain containing"""	17265	protein-coding gene	gene with protein product	"""target of Nesh-SH3"""	606279				11501947	Standard	NM_015429		Approved	NESHBP, DKFZP586L2024, TARSH	uc003dun.3	Q7Z7G0	OTTHUMG00000159094	ENST00000284322.5:c.2748G>A	3.37:g.100473505C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	144	67	0.465278	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Silent	SNP	ENST00000284322.5	37	CCDS46880.1	571	0.26144688644688646	69	0.1402439024390244	145	0.4005524861878453	79	0.1381118881118881	278	0.36675461741424803	C	9.300	1.052738	0.19907	0.149811	0.390938	ENSG00000154175	ENST00000495591	.	.	.	5.68	-9.53	0.00575	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999817853	.	.	.	.	.	.	T	0.38607	-0.9653	3	.	.	.	-4.6183	3.9397	0.09321	0.1613:0.4705:0.2141:0.1542	rs10936352;rs17217222;rs10936352	.	.	.	H	972	.	.	R	-	2	0	ABI3BP	101956195	0.007000	0.16637	0.897000	0.35233	0.914000	0.54420	-1.170000	0.03118	-1.214000	0.02614	-1.028000	0.02416	CGC	C|0.725;T|0.275	0.275	strong		0.418	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1		
P2RY11	5032	hgsc.bcm.edu	37	19	10224548	10224548	+	Missense_Mutation	SNP	G	G	A	rs3745601	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10224548G>A	ENST00000321826.4	+	2	443	c.259G>A	c.(259-261)Gcc>Acc	p.A87T	PPAN-P2RY11_ENST00000428358.1_3'UTR|PPAN_ENST00000556468.1_Missense_Mutation_p.A507T|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A507T	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	87			A -> T (in dbSNP:rs3745601).		activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			CCCGCTGGCCGCCTACCTCTA	0.677											OREG0025230	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	914	0.182508	0.1142	0.1585	5008	,	,		16337	0.3304		0.1083	False		,,,				2504	0.2157				p.A507T		Atlas-SNP	.											.	PPAN-P2RY11	81	.	0			c.G1519A						PASS	.	G	THR/ALA,THR/ALA,	479,3927	221.3+/-238.5	19,441,1743	31.0	29.0	30.0		1519,259,	3.5	1.0	19	dbSNP_107	30	978,7620	209.8+/-250.9	58,862,3379	yes	missense,missense,utr-3	P2RY11,PPAN-P2RY11	NM_001040664.2,NM_002566.4,NM_001198690.1	58,58,	77,1303,5122	AA,AG,GG		11.3747,10.8715,11.2042	probably-damaging,probably-damaging,	507/795,87/375,	10224548	1457,11547	2203	4299	6502	SO:0001583	missense	692312	exon13			CTGGCCGCCTACC	AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166	ENST00000321826.4:c.259G>A	19.37:g.10224548G>A	ENSP00000323872:p.Ala87Thr	Somatic	57	0	0	663	WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_001040664	B2R8X9|O43190|Q9BYU4|Q9H170	Missense_Mutation	SNP	ENST00000321826.4	37	CCDS12226.1	390	0.17857142857142858	62	0.12601626016260162	53	0.1464088397790055	193	0.3374125874125874	82	0.10817941952506596	G	16.86	3.239499	0.58995	0.108715	0.113747	ENSG00000243207;ENSG00000130810;ENSG00000244165	ENST00000393796;ENST00000556468;ENST00000321826	T;T;T	0.37915	1.17;1.17;1.17	4.62	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.824795	0.10482	U	0.669521	T	0.00012	0.0000	L	0.46670	1.46	0.43179	P	0.005009999999999959	D	0.63046	0.992	P	0.55965	0.788	T	0.36286	-0.9754	9	0.22706	T	0.39	.	11.8118	0.52188	0.0:0.0:0.7753:0.2247	rs3745601;rs59821413;rs3745601	87	Q96G91	P2Y11_HUMAN	T	507;507;87	ENSP00000377385:A507T;ENSP00000450710:A507T;ENSP00000323872:A87T	ENSP00000323872:A87T	A	+	1	0	PPAN;P2RY11;PPAN-P2RY11	10085548	0.000000	0.05858	0.997000	0.53966	0.348000	0.29142	-0.044000	0.12023	2.411000	0.81874	0.561000	0.74099	GCC	G|0.855;A|0.145	0.145	strong		0.677	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
RRP12	23223	hgsc.bcm.edu	37	10	99150237	99150237	+	Silent	SNP	G	G	A	rs41300219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99150237G>A	ENST00000370992.4	-	6	807	c.696C>T	c.(694-696)ccC>ccT	p.P232P	RRP12_ENST00000536831.1_Silent_p.P38P|RRP12_ENST00000315563.6_Intron|RRP12_ENST00000414986.1_Silent_p.P171P	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	232						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GAAGGGTCACGGGGTAGCCCC	0.612													G|||	201	0.0401358	0.0598	0.0533	5008	,	,		19526	0.0		0.0716	False		,,,				2504	0.0133				p.P232P		Atlas-SNP	.											.	RRP12	97	.	0			c.C696T						PASS	.	G	,	254,4152	148.0+/-182.4	9,236,1958	58.0	56.0	57.0		513,696	-11.0	0.0	10	dbSNP_127	57	501,8099	144.5+/-200.4	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,703,5774	AA,AG,GG		5.8256,5.7649,5.805	,	171/1237,232/1298	99150237	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon6			GGTCACGGGGTAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.696C>T	10.37:g.99150237G>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	48	19	0.395833	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.949;A|0.051	0.051	strong		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
SCFD1	23256	hgsc.bcm.edu	37	14	31164033	31164033	+	Missense_Mutation	SNP	A	A	G	rs61754285	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:31164033A>G	ENST00000458591.2	+	15	1524	c.1297A>G	c.(1297-1299)Act>Gct	p.T433A	SCFD1_ENST00000396629.2_Missense_Mutation_p.T341A|SCFD1_ENST00000544052.2_Missense_Mutation_p.T366A|SCFD1_ENST00000554486.1_3'UTR|SCFD1_ENST00000541123.1_Missense_Mutation_p.T248A|SCFD1_ENST00000421551.3_Missense_Mutation_p.T374A	NM_016106.3	NP_057190.2	Q8WVM8	SCFD1_HUMAN	sec1 family domain containing 1	433					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)		GAGCAAAACTACTCTGGATAA	0.274													A|||	31	0.0061901	0.0	0.0058	5008	,	,		16689	0.0		0.0219	False		,,,				2504	0.0051				p.T433A		Atlas-SNP	.											SCFD1,NS,carcinoma,-2,1	SCFD1	43	1	0			c.A1297G						PASS	.	A	ALA/THR,ALA/THR	15,4385	21.2+/-45.6	0,15,2185	58.0	66.0	63.0		1297,1096	4.8	1.0	14	dbSNP_129	63	175,8403	77.5+/-140.1	0,175,4114	yes	missense,missense	SCFD1	NM_016106.2,NM_182835.1	58,58	0,190,6299	GG,GA,AA		2.0401,0.3409,1.464	benign,benign	433/643,366/576	31164033	190,12788	2200	4289	6489	SO:0001583	missense	23256	exon15			AAAACTACTCTGG	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.1297A>G	14.37:g.31164033A>G	ENSP00000390783:p.Thr433Ala	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	142	54	0.380282	NM_016106	A8K2Z5|B7Z4U7|B7Z594|O60754|O94990|Q7Z529|Q9BZI3|Q9UNL3|Q9Y6A8	Missense_Mutation	SNP	ENST00000458591.2	37	CCDS9639.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	A	11.90	1.775176	0.31411	0.003409	0.020401	ENSG00000092108	ENST00000458591;ENST00000544052;ENST00000421551;ENST00000541123;ENST00000396629	T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53	5.95	4.81	0.61882	.	0.095899	0.64402	D	0.000001	T	0.08758	0.0217	N	0.11789	0.175	0.47214	D	0.999351	B;B;B;B	0.09022	0.001;0.002;0.002;0.002	B;B;B;B	0.16722	0.004;0.016;0.006;0.016	T	0.05818	-1.0862	10	0.20046	T	0.44	-10.5566	11.7324	0.51746	0.9308:0.0:0.0692:0.0	rs61754285	374;366;341;433	B7Z738;B7Z4U7;B7Z594;Q8WVM8	.;.;.;SCFD1_HUMAN	A	433;366;374;248;341	ENSP00000390783:T433A;ENSP00000443010:T366A;ENSP00000388078:T374A;ENSP00000443537:T248A;ENSP00000379870:T341A	ENSP00000309417:T441A	T	+	1	0	SCFD1	30233784	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.603000	0.67619	1.080000	0.41073	-0.256000	0.11100	ACT	A|0.987;G|0.013	0.013	strong		0.274	SCFD1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276612.3	NM_182835	
NPC1	4864	hgsc.bcm.edu	37	18	21124945	21124945	+	Missense_Mutation	SNP	C	C	G	rs1788799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:21124945C>G	ENST00000269228.5	-	12	2480	c.1926G>C	c.(1924-1926)atG>atC	p.M642I	NPC1_ENST00000412552.2_Missense_Mutation_p.M324I|NPC1_ENST00000540608.1_5'UTR	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	642	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.		M -> I (in dbSNP:rs1788799). {ECO:0000269|PubMed:11479732, ECO:0000269|PubMed:11754101, ECO:0000269|PubMed:12401890, ECO:0000269|PubMed:12408188, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15774455, ECO:0000269|PubMed:16098014, ECO:0000269|PubMed:9211849}.		adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					GACAGCTTTTCATGTGCCCCA	0.438													G|||	4165	0.831669	0.9607	0.7795	5008	,	,		13605	0.9226		0.6521	False		,,,				2504	0.7853				p.M642I		Atlas-SNP	.											.	NPC1	114	.	0			c.G1926C						PASS	.	G	ILE/MET	4008,398	200.4+/-223.7	1820,368,15	71.0	68.0	69.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1926	5.9	1.0	18	dbSNP_89	69	5547,3053	468.5+/-367.3	1805,1937,558	yes	missense	NPC1	NM_000271.4	10	3625,2305,573	GG,GC,CC		35.5,9.0331,26.5339	benign	642/1279	21124945	9555,3451	2203	4300	6503	SO:0001583	missense	4864	exon12			GCTTTTCATGTGC	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.1926G>C	18.37:g.21124945C>G	ENSP00000269228:p.Met642Ile	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	104	32	0.307692	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	1787	0.8182234432234432	472	0.959349593495935	277	0.7651933701657458	536	0.9370629370629371	502	0.662269129287599	G	6.557	0.470967	0.12461	0.909669	0.645	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.92348	-3.02;-2.93	5.91	5.91	0.95273	Sterol-sensing domain (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00389	-1.56	0.53005	P	3.399999999997849E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43861	-0.9365	9	0.02654	T	1	-28.8558	7.8687	0.29552	0.1345:0.1368:0.7287:0.0	rs1788799;rs17797480;rs17855818;rs58087863;rs1788799	653;642	Q59GR1;O15118	.;NPC1_HUMAN	I	642;324;487	ENSP00000269228:M642I;ENSP00000408606:M324I	ENSP00000269228:M642I	M	-	3	0	NPC1	19378943	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.301000	0.51842	1.514000	0.48869	-0.120000	0.15030	ATG	.	.	none		0.438	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
ACAN	176	hgsc.bcm.edu	37	15	89386652	89386652	+	Missense_Mutation	SNP	G	G	A	rs34949187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89386652G>A	ENST00000561243.1	+	5	824	c.824G>A	c.(823-825)cGg>cAg	p.R275Q	ACAN_ENST00000439576.2_Missense_Mutation_p.R275Q|ACAN_ENST00000352105.7_Missense_Mutation_p.R275Q|ACAN_ENST00000559004.1_Missense_Mutation_p.R275Q|ACAN_ENST00000558207.1_Missense_Mutation_p.R275Q			P16112	PGCA_HUMAN	aggrecan	275	G1-B'.|Link 2. {ECO:0000255|PROSITE- ProRule:PRU00323}.		R -> Q (in dbSNP:rs34949187).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|extracellular matrix structural constituent (GO:0005201)|hyaluronic acid binding (GO:0005540)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(15)|liver(2)|lung(40)|ovary(2)|prostate(5)|skin(5)|stomach(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	93	Lung NSC(78;0.0392)|all_lung(78;0.077)		BRCA - Breast invasive adenocarcinoma(143;0.146)			GAGTGCCGGCGGCTGGGTGCC	0.642													G|||	411	0.0820687	0.0076	0.0951	5008	,	,		16364	0.0764		0.165	False		,,,				2504	0.0941				p.R275Q		Atlas-SNP	.											.	ACAN	220	.	0			c.G824A						PASS	.	G	GLN/ARG,GLN/ARG	149,3725		0,149,1788	17.0	20.0	19.0		824,824	5.6	1.0	15	dbSNP_126	19	1467,6809		129,1209,2800	yes	missense,missense	ACAN	NM_001135.3,NM_013227.3	43,43	129,1358,4588	AA,AG,GG		17.726,3.8462,13.3004	possibly-damaging,possibly-damaging	275/2432,275/2531	89386652	1616,10534	1937	4138	6075	SO:0001583	missense	176	exon6			GCCGGCGGCTGGG	M55172	CCDS53970.1, CCDS53971.1	15q26.1	2013-05-07	2007-02-16	2007-02-16	ENSG00000157766	ENSG00000157766		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	319	protein-coding gene	gene with protein product	"""aggrecan proteoglycan"""	155760	"""chondroitin sulfate proteoglycan 1"", ""aggrecan 1"""	MSK16, CSPG1, AGC1		1985970	Standard	NM_013227		Approved	CSPGCP	uc010upo.1	P16112	OTTHUMG00000171989	ENST00000561243.1:c.824G>A	15.37:g.89386652G>A	ENSP00000453342:p.Arg275Gln	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	82	37	0.451219	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	205	0.09386446886446886	3	0.006097560975609756	42	0.11602209944751381	38	0.06643356643356643	122	0.16094986807387862	G	19.24	3.789786	0.70337	0.038462	0.17726	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.09255	3.0;3.0	5.56	5.56	0.83823	.	0.000000	0.30593	N	0.009286	T	0.00039	0.0001	L	0.33485	1.01	0.36564	P	0.12737600000000004	D;D;P	0.89917	1.0;1.0;0.827	D;D;B	0.66716	0.946;0.946;0.418	T	0.15150	-1.0447	9	0.36615	T	0.2	-18.6464	18.5257	0.90971	0.0:0.0:1.0:0.0	rs34949187	275;275;275	E7ENV9;E7EX88;Q6PID9	.;.;.	Q	275	ENSP00000387356:R275Q;ENSP00000341615:R275Q	ENSP00000268134:R275Q	R	+	2	0	ACAN	87187656	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	5.756000	0.68757	2.626000	0.88956	0.650000	0.86243	CGG	G|0.889;A|0.111	0.111	strong		0.642	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135	
MUC16	94025	hgsc.bcm.edu	37	19	9084299	9084299	+	Missense_Mutation	SNP	T	T	C	rs1609458	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9084299T>C	ENST00000397910.4	-	1	7719	c.7516A>G	c.(7516-7518)Acc>Gcc	p.T2506A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2506	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						CCTACACTGGTCCATGTACCT	0.498											OREG0006612	type=TRANSCRIPTION FACTOR BINDING SITE|TFbs=REST|Dataset=NRSF/REST ChIPSeq sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)	T|||	2087	0.416733	0.3411	0.5692	5008	,	,		21424	0.3264		0.4841	False		,,,				2504	0.4346				p.T2506A		Atlas-SNP	.											MUC16_ENST00000397910,colon,carcinoma,0,2	MUC16	4315	2	0			c.A7516G						scavenged	.	T	ALA/THR	1492,2872		282,928,972	72.0	74.0	74.0		7516	0.2	0.0	19	dbSNP_88	74	4373,4211		1142,2089,1061	yes	missense	MUC16	NM_024690.2	58	1424,3017,2033	CC,CT,TT		49.0564,34.1888,45.2966	possibly-damaging	2506/14508	9084299	5865,7083	2182	4292	6474	SO:0001583	missense	94025	exon1			CACTGGTCCATGT	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.7516A>G	19.37:g.9084299T>C	ENSP00000381008:p.Thr2506Ala	Somatic	134	1	0.00746269	654	WXS	Illumina HiSeq	Phase_I	133	62	0.466165	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	940	0.43040293040293043	164	0.3333333333333333	200	0.5524861878453039	207	0.3618881118881119	369	0.4868073878627968	t	1.720	-0.496774	0.04291	0.341888	0.509436	ENSG00000181143	ENST00000397910	T	0.01538	4.79	0.225	0.225	0.15325	.	.	.	.	.	T	0.00012	0.0000	.	.	.	.	.	.	P	0.49696	0.927	P	0.56563	0.801	T	0.39683	-0.9602	6	0.87932	D	0	.	.	.	.	rs1609458;rs52827802;rs1609458	2506	B5ME49	.	A	2506	ENSP00000381008:T2506A	ENSP00000381008:T2506A	T	-	1	0	MUC16	8945299	0.002000	0.14202	0.044000	0.18714	0.045000	0.14185	0.793000	0.26944	0.257000	0.21650	0.254000	0.18369	ACC	T|0.562;C|0.438	0.438	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
C2orf71	388939	hgsc.bcm.edu	37	2	29293837	29293837	+	Silent	SNP	C	C	T	rs183536545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29293837C>T	ENST00000331664.5	-	1	3290	c.3291G>A	c.(3289-3291)caG>caA	p.Q1097Q		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1097					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CCTTGTGCTCCTGAGAAGGGG	0.562													C|||	24	0.00479233	0.0008	0.0115	5008	,	,		12777	0.0		0.0119	False		,,,				2504	0.0031				p.Q1097Q		Atlas-SNP	.											.	C2orf71	146	.	0			c.G3291A						PASS	.	C		13,3861		0,13,1924	62.0	69.0	66.0		3291	2.7	0.0	2		66	114,8170		0,114,4028	no	coding-synonymous	C2orf71	NM_001029883.1		0,127,5952	TT,TC,CC		1.3761,0.3356,1.0446		1097/1289	29293837	127,12031	1937	4142	6079	SO:0001819	synonymous_variant	388939	exon1			GTGCTCCTGAGAA		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3291G>A	2.37:g.29293837C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.990;T|0.010	0.010	strong		0.562	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
ECD	11319	hgsc.bcm.edu	37	10	74899134	74899134	+	Missense_Mutation	SNP	C	C	G	rs3736518	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:74899134C>G	ENST00000372979.4	-	11	1560	c.1354G>C	c.(1354-1356)Gaa>Caa	p.E452Q	ECD_ENST00000430082.2_Missense_Mutation_p.E485Q|ECD_ENST00000454759.2_Missense_Mutation_p.E409Q	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	452			E -> Q (in dbSNP:rs3736518).		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)					TCTGAGACTTCAGTTAAGTCA	0.438													G|||	1180	0.235623	0.3676	0.1239	5008	,	,		18184	0.3145		0.0596	False		,,,				2504	0.2362				p.E485Q		Atlas-SNP	.											.	ECD	50	.	0			c.G1453C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	1434,2972	682.8+/-404.2	229,976,998	115.0	115.0	115.0		1453,1225,1354	2.2	1.0	10	dbSNP_107	115	617,7983	791.8+/-407.5	30,557,3713	yes	missense,missense,missense	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	29,29,29	259,1533,4711	GG,GC,CC		7.1744,32.5465,15.7696	benign,benign,benign	485/678,409/602,452/645	74899134	2051,10955	2203	4300	6503	SO:0001583	missense	11319	exon12			AGACTTCAGTTAA	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		ENST00000372979.4:c.1354G>C	10.37:g.74899134C>G	ENSP00000362070:p.Glu452Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	106	47	0.443396	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	460	0.21062271062271062	194	0.3943089430894309	38	0.10497237569060773	183	0.31993006993006995	45	0.059366754617414245	G	4.990	0.183852	0.09495	0.325465	0.071744	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.18810	2.19;2.19;2.19	5.4	2.23	0.28157	.	0.454089	0.24635	N	0.036854	T	0.00012	0.0000	L	0.41710	1.295	0.50813	P	1.0100000000001774E-4	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.005;0.004;0.006	T	0.46386	-0.9195	9	0.12103	T	0.63	-17.66	10.0363	0.42131	0.0:0.5212:0.3274:0.1514	rs3736518;rs52836557;rs56790976;rs3736518	409;485;452	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	Q	452;485;409	ENSP00000362070:E452Q;ENSP00000401566:E485Q;ENSP00000395786:E409Q	ENSP00000362070:E452Q	E	-	1	0	ECD	74569140	0.990000	0.36364	0.999000	0.59377	0.982000	0.71751	2.477000	0.45180	0.627000	0.30340	-0.352000	0.07741	GAA	C|0.823;G|0.177	0.177	strong		0.438	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
EBF2	64641	hgsc.bcm.edu	37	8	25708267	25708267	+	Silent	SNP	T	T	C	rs10866845	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:25708267T>C	ENST00000520164.1	-	15	2076	c.1539A>G	c.(1537-1539)tcA>tcG	p.S513S	EBF2_ENST00000408929.3_Silent_p.S365S|EBF2_ENST00000535548.1_3'UTR	NM_022659.3	NP_073150.2	Q9HAK2	COE2_HUMAN	early B-cell factor 2	513	Pro/Ser/Thr-rich.			S -> L (in Ref. 3; BAB13843). {ECO:0000305}.	adipose tissue development (GO:0060612)|brown fat cell differentiation (GO:0050873)|cell fate determination (GO:0001709)|positive regulation of chromatin binding (GO:0035563)|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)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|large_intestine(3)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(63;0.0989)|Ovarian(32;2.74e-05)|all_epithelial(46;0.0608)|Prostate(55;0.0845)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0277)|Epithelial(17;3.29e-10)|Colorectal(74;0.00383)|COAD - Colon adenocarcinoma(73;0.00738)		CGGTGGGACTTGATGACATGA	0.418													C|||	2362	0.471645	0.7005	0.4121	5008	,	,		21349	0.2341		0.4543	False		,,,				2504	0.4673				p.S513S	Esophageal Squamous(166;1018 1046 3854 8328 13429 13634 14071 26624 32918)	Atlas-SNP	.											.	EBF2	138	.	0			c.A1539G						PASS	.	C		2749,1279		944,861,209	54.0	58.0	57.0		1539	-11.3	0.0	8	dbSNP_120	57	3659,4695		818,2023,1336	no	coding-synonymous	EBF2	NM_022659.2		1762,2884,1545	CC,CT,TT		43.7994,31.7527,48.2475		513/576	25708267	6408,5974	2014	4177	6191	SO:0001819	synonymous_variant	64641	exon15			GGGACTTGATGAC	AK021562, AK001144	CCDS43726.1	8p21.1	2007-07-26			ENSG00000221818	ENSG00000221818			19090	protein-coding gene	gene with protein product		609934				9151732	Standard	NM_022659		Approved	FLJ11500, COE2	uc003xes.2	Q9HAK2	OTTHUMG00000163838	ENST00000520164.1:c.1539A>G	8.37:g.25708267T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_022659	A0PJM4|A6NMF7|F5H645|Q66VZ3|Q6DK36|Q6IS86|Q6ISA4	Silent	SNP	ENST00000520164.1	37	CCDS43726.1																																																																																			T|0.539;C|0.461	0.461	strong		0.418	EBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375886.2	NM_022659	
ZNF646	9726	hgsc.bcm.edu	37	16	31091209	31091209	+	Silent	SNP	T	T	C	rs3751855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31091209T>C	ENST00000394979.2	+	1	3987	c.3564T>C	c.(3562-3564)acT>acC	p.T1188T	ZNF646_ENST00000300850.5_Silent_p.T1188T			O15015	ZN646_HUMAN	zinc finger protein 646	1188					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						GGCTGGAGACTGCCGAGAAGG	0.612													C|||	2402	0.479633	0.652	0.4323	5008	,	,		16321	0.1121		0.3787	False		,,,				2504	0.7628				p.T1188T		Atlas-SNP	.											.	ZNF646	133	.	0			c.T3564C						PASS	.	C		2698,1696	496.5+/-363.6	844,1010,343	29.0	37.0	35.0		3564	-10.8	0.0	16	dbSNP_107	35	3119,5477	646.4+/-400.3	571,1977,1750	no	coding-synonymous	ZNF646	NM_014699.3		1415,2987,2093	CC,CT,TT		36.2843,38.5981,44.7806		1188/1833	31091209	5817,7173	2197	4298	6495	SO:0001819	synonymous_variant	9726	exon2			GGAGACTGCCGAG	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.3564T>C	16.37:g.31091209T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	129	66	0.511628	NM_014699	Q8IVD8	Silent	SNP	ENST00000394979.2	37																																																																																				A|0.000;C|0.415;T|0.584	0.415	strong		0.612	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
MAP3K15	389840	hgsc.bcm.edu	37	X	19387318	19387318	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:19387318C>A	ENST00000338883.4	-	25	3419	c.3420G>T	c.(3418-3420)gaG>gaT	p.E1140D	MAP3K15_ENST00000359173.3_Missense_Mutation_p.E575D|MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000469203.2_Missense_Mutation_p.E972D	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1140							ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					CACAGGTAGGCTCAAAGTGGG	0.602																																					p.E1140D		Atlas-SNP	.											.	MAP3K15	108	.	0			c.G3420T						PASS	.						71.0	64.0	66.0					X																	19387318		2203	4300	6503	SO:0001583	missense	389840	exon25			GGTAGGCTCAAAG	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.3420G>T	X.37:g.19387318C>A	ENSP00000345629:p.Glu1140Asp	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	37		.	.	.	.	.	.	.	.	.	.	C	11.19	1.564365	0.27915	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	T;T;T	0.73047	-0.67;-0.71;-0.67	5.34	3.51	0.40186	.	0.104397	0.64402	N	0.000005	T	0.64294	0.2585	M	0.63428	1.95	0.25693	N	0.985669	P;D	0.56521	0.68;0.976	B;P	0.45913	0.431;0.497	T	0.58544	-0.7618	10	0.37606	T	0.19	.	2.7745	0.05344	0.1497:0.5478:0.1421:0.1604	.	615;1140	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	D	1140;575;972	ENSP00000345629:E1140D;ENSP00000352093:E575D;ENSP00000428356:E972D	ENSP00000345629:E1140D	E	-	3	2	MAP3K15	19297239	0.032000	0.19561	0.063000	0.19743	0.727000	0.41649	-0.364000	0.07583	0.430000	0.26230	0.506000	0.49869	GAG	.	.	none		0.602	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388379	1388379	+	Missense_Mutation	SNP	G	G	A	rs56109734	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388379G>A	ENST00000324803.4	+	1	3040	c.80G>A	c.(79-81)tGt>tAt	p.C27Y		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	27					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			GCCTGCTCATGTGCCCATGTG	0.637													N|||	602	0.120208	0.1301	0.1124	5008	,	,		16248	0.0208		0.1899	False		,,,				2504	0.1431				p.C27Y		Atlas-SNP	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	0			c.G80A						scavenged	.						173.0	170.0	171.0					4																	1388379		2203	4300	6503	SO:0001583	missense	285464	exon1			GCTCATGTGCCCA	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.80G>A	4.37:g.1388379G>A	ENSP00000323978:p.Cys27Tyr	Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	165	22	0.133333	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	G	5.325	0.245358	0.10077	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.25579	1.79	0.824	-0.152	0.13407	.	.	.	.	.	T	0.09555	0.0235	N	0.08118	0	0.23673	N	0.997148	P	0.46912	0.886	B	0.38327	0.271	T	0.20571	-1.0271	9	0.22109	T	0.4	.	4.9218	0.13874	0.2545:0.0:0.7455:0.0	rs56109734	27	Q8N1N5	CRPAK_HUMAN	Y	27;20	ENSP00000323978:C27Y	ENSP00000323978:C27Y	C	+	2	0	CRIPAK	1378379	0.105000	0.21958	0.002000	0.10522	0.009000	0.06853	0.529000	0.23019	-0.063000	0.13065	0.420000	0.28162	TGT	G|0.996;A|0.004	0.004	strong		0.637	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
CCDC141	285025	hgsc.bcm.edu	37	2	179839833	179839833	+	Silent	SNP	A	A	G	rs10930846	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179839833A>G	ENST00000409284.1	-	4	594	c.477T>C	c.(475-477)agT>agC	p.S159S	CCDC141_ENST00000420890.2_Silent_p.S159S			Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	159										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)			AGGACTCAGCACTCTCAAACT	0.328													A|||	1625	0.324481	0.0628	0.3444	5008	,	,		19903	0.7004		0.2684	False		,,,				2504	0.3344				p.S159S		Atlas-SNP	.											.	CCDC141	362	.	0			c.T477C						PASS	.																																			SO:0001819	synonymous_variant	285025	exon4			CTCAGCACTCTCA	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.477T>C	2.37:g.179839833A>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	82	34	0.414634	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Silent	SNP	ENST00000409284.1	37																																																																																				A|0.651;G|0.348	0.348	strong		0.328	CCDC141-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000335873.1	NM_173648	
PCK1	5105	hgsc.bcm.edu	37	20	56137798	56137798	+	Silent	SNP	G	G	A	rs1062600	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:56137798G>A	ENST00000319441.4	+	4	617	c.453G>A	c.(451-453)tcG>tcA	p.S151S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.S19S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	151					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)			CGCTGGGCTCGCCTCTGTCAA	0.607													G|||	1478	0.295128	0.3101	0.3141	5008	,	,		17801	0.0308		0.4732	False		,,,				2504	0.3507				p.S151S		Atlas-SNP	.											.	PCK1	95	.	0			c.G453A						PASS	.	G		1415,2991	464.0+/-353.7	204,1007,992	65.0	53.0	57.0		453	-10.3	0.2	20	dbSNP_86	57	3953,4647	548.9+/-385.4	894,2165,1241	no	coding-synonymous	PCK1	NM_002591.3		1098,3172,2233	AA,AG,GG		45.9651,32.1153,41.2733		151/623	56137798	5368,7638	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon4			GGGCTCGCCTCTG		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.453G>A	20.37:g.56137798G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	91	91	1	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			G|0.633;A|0.367	0.367	strong		0.607	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
OR2C1	4993	hgsc.bcm.edu	37	16	3406626	3406626	+	Missense_Mutation	SNP	G	G	A	rs11648783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3406626G>A	ENST00000304936.2	+	1	738	c.686G>A	c.(685-687)cGc>cAc	p.R229H		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	229			R -> H (in dbSNP:rs11648783). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9847080}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)	cell cortex (GO:0005938)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12						CTGAAAATCCGCTCTGCAGAG	0.547													G|||	1265	0.252596	0.3389	0.2421	5008	,	,		21776	0.1429		0.2614	False		,,,				2504	0.2474				p.R229H		Atlas-SNP	.											.	OR2C1	38	.	0			c.G686A						PASS	.		HIS/ARG	1522,2872	481.7+/-359.2	249,1024,924	123.0	103.0	110.0		686	-5.3	0.3	16	dbSNP_120	110	2366,6234	395.9+/-345.2	330,1706,2264	no	missense	OR2C1	NM_012368.2	29	579,2730,3188	AA,AG,GG		27.5116,34.6381,29.9215	benign	229/313	3406626	3888,9106	2197	4300	6497	SO:0001583	missense	4993	exon1			AAATCCGCTCTGC	AF098664	CCDS10502.1	16p13.3	2012-08-09			ENSG00000168158	ENSG00000168158		"""GPCR / Class A : Olfactory receptors"""	8242	protein-coding gene	gene with protein product				OR2C2P		9847080	Standard	NM_012368		Approved	OLFmf3	uc002cuw.1	O95371	OTTHUMG00000090505	ENST00000304936.2:c.686G>A	16.37:g.3406626G>A	ENSP00000307726:p.Arg229His	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	86	39	0.453488	NM_012368	A0AVA4|Q6IF34|Q6IF55	Missense_Mutation	SNP	ENST00000304936.2	37	CCDS10502.1	563	0.25778388278388276	184	0.37398373983739835	92	0.2541436464088398	81	0.14160839160839161	206	0.2717678100263852	g	4.555	0.103149	0.08731	0.346381	0.275116	ENSG00000168158	ENST00000304936	T	0.39229	1.09	5.0	-5.29	0.02747	GPCR, rhodopsin-like superfamily (1);	0.596862	0.14073	N	0.343234	T	0.00012	0.0000	N	0.13003	0.285	0.80722	P	0.0	B	0.14012	0.009	B	0.10450	0.005	T	0.41538	-0.9503	9	0.62326	D	0.03	.	2.6261	0.04930	0.3111:0.2577:0.3384:0.0928	rs11648783;rs56545253;rs59091664;rs11648783	229	O95371	OR2C1_HUMAN	H	229	ENSP00000307726:R229H	ENSP00000307726:R229H	R	+	2	0	OR2C1	3346627	0.000000	0.05858	0.334000	0.25495	0.003000	0.03518	-0.888000	0.04148	-0.962000	0.03604	-2.321000	0.00252	CGC	G|0.723;A|0.277	0.277	strong		0.547	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3		
SEC16A	9919	hgsc.bcm.edu	37	9	139369062	139369062	+	Silent	SNP	C	C	T	rs3812595	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139369062C>T	ENST00000371706.3	-	1	2505	c.2472G>A	c.(2470-2472)ttG>ttA	p.L824L	SEC16A_ENST00000431893.2_Silent_p.L824L|SEC16A_ENST00000313050.7_Silent_p.L1002L|SEC16A_ENST00000290037.6_Silent_p.L824L			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	824					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)		CAGGATTTTCCAAAGTCCTGC	0.522													C|||	762	0.152157	0.1021	0.2608	5008	,	,		20217	0.0575		0.2535	False		,,,				2504	0.136				p.L1002L		Atlas-SNP	.											.	SEC16A	249	.	0			c.G3006A						PASS	.	C		457,3393		19,419,1487	27.0	28.0	28.0		3006	3.5	0.0	9	dbSNP_107	28	2165,6121		277,1611,2255	no	coding-synonymous	SEC16A	NM_014866.1		296,2030,3742	TT,TC,CC		26.1284,11.8701,21.6051		1002/2358	139369062	2622,9514	1925	4143	6068	SO:0001819	synonymous_variant	9919	exon3			ATTTTCCAAAGTC	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.2472G>A	9.37:g.139369062C>T		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				C|0.837;T|0.163	0.163	strong		0.522	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
CCDC62	84660	hgsc.bcm.edu	37	12	123262043	123262043	+	Silent	SNP	C	C	T	rs61956960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:123262043C>T	ENST00000253079.6	+	2	386	c.42C>T	c.(40-42)atC>atT	p.I14I	CCDC62_ENST00000537566.1_5'UTR|CCDC62_ENST00000392441.4_Silent_p.I14I	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	14					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		TTTAGAACATCGGGTCAGAAG	0.373													C|||	14	0.00279553	0.0008	0.0086	5008	,	,		21883	0.0		0.007	False		,,,				2504	0.0				p.I14I		Atlas-SNP	.											.	CCDC62	119	.	0			c.C42T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	50.0	49.0	50.0		42	-0.3	1.0	12	dbSNP_129	50	124,8476	63.9+/-126.0	1,122,4177	no	coding-synonymous	CCDC62	NM_201435.4		1,132,6370	TT,TC,CC		1.4419,0.227,1.0303		14/685	123262043	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	84660	exon2			GAACATCGGGTCA		CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"""cancer/testis antigen 109"""	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.42C>T	12.37:g.123262043C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	61	27	0.442623	NM_201435	A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Silent	SNP	ENST00000253079.6	37	CCDS9238.1																																																																																			C|0.990;T|0.010	0.010	strong		0.373	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573	
ARHGAP26	23092	hgsc.bcm.edu	37	5	142254679	142254679	+	Silent	SNP	A	A	G	rs185200	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:142254679A>G	ENST00000274498.4	+	3	633	c.255A>G	c.(253-255)agA>agG	p.R85R	ARHGAP26_ENST00000378004.3_Silent_p.R85R	NM_015071.4	NP_055886.1	Q9UNA1	RHG26_HUMAN	Rho GTPase activating protein 26	85					actin cytoskeleton organization (GO:0030036)|filopodium assembly (GO:0046847)|nervous system development (GO:0007399)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(7)|ovary(1)	25		all_hematologic(541;0.0416)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCCAGCAAGATCTTTGCAGG	0.483													G|||	3374	0.673722	0.8979	0.5058	5008	,	,		19158	0.8581		0.3091	False		,,,				2504	0.6748				p.R85R		Atlas-SNP	.											.	ARHGAP26	57	.	0			c.A255G						PASS	.	G	,	3440,966	362.4+/-316.1	1350,740,113	114.0	103.0	107.0		255,255	2.6	1.0	5	dbSNP_79	107	2569,6031	690.7+/-404.5	378,1813,2109	no	coding-synonymous,coding-synonymous	ARHGAP26	NM_001135608.1,NM_015071.4	,	1728,2553,2222	GG,GA,AA		29.8721,21.9246,46.2018	,	85/760,85/815	142254679	6009,6997	2203	4300	6503	SO:0001819	synonymous_variant	23092	exon3			AGCAAGATCTTTG	AB014521	CCDS4277.1, CCDS47297.1	5q31	2011-06-29			ENSG00000145819	ENSG00000145819		"""Rho GTPase activating proteins"""	17073	protein-coding gene	gene with protein product	"""GTPase regulator associated with the focal adhesion kinase pp125"""	605370				9858476, 8649427	Standard	NM_001135608		Approved	GRAF, KIAA0621, OPHN1L, OPHN1L1	uc011dbj.2	Q9UNA1	OTTHUMG00000059705	ENST00000274498.4:c.255A>G	5.37:g.142254679A>G		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_015071	O75117|Q5D035|Q9BYS6|Q9BYS7|Q9UJ00	Silent	SNP	ENST00000274498.4	37	CCDS4277.1																																																																																			A|0.466;G|0.534	0.534	strong		0.483	ARHGAP26-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132744.3	NM_015071	
ETV7	51513	hgsc.bcm.edu	37	6	36343721	36343721	+	Silent	SNP	G	G	A	rs2234075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36343721G>A	ENST00000340181.4	-	3	475	c.234C>T	c.(232-234)caC>caT	p.H78H	ETV7_ENST00000373738.1_Intron|ETV7_ENST00000339796.5_Silent_p.H78H|ETV7_ENST00000373737.4_Silent_p.H78H|ETV7_ENST00000538992.1_Intron	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	78	PNT. {ECO:0000255|PROSITE- ProRule:PRU00762}.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						TCTCGAACCCGTGCTCCGCGG	0.647													G|||	115	0.0229633	0.0076	0.0403	5008	,	,		19336	0.004		0.0557	False		,,,				2504	0.0174				p.R6W		Atlas-SNP	.											.	ETV7	31	.	0			c.C16T						PASS	.	G	,,TRP/ARG,,,,,	58,4348	54.9+/-90.9	0,58,2145	108.0	88.0	95.0		234,,16,234,,,,234	0.5	0.0	6	dbSNP_98	95	395,8205	126.7+/-185.1	8,379,3913	yes	coding-synonymous,intron,missense,coding-synonymous,intron,utr-5,intron,coding-synonymous	ETV7	NM_001207035.1,NM_001207036.1,NM_001207037.1,NM_001207038.1,NM_001207039.1,NM_001207040.1,NM_001207041.1,NM_016135.3	,,101,,,,,	8,437,6058	AA,AG,GG		4.593,1.3164,3.483	,,,,,,,	78/318,,6/283,78/265,,,,78/342	36343721	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	51513	exon3			GAACCCGTGCTCC	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.234C>T	6.37:g.36343721G>A		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	45	22	0.488889	NM_001207037	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	37	CCDS4819.1																																																																																			G|0.968;A|0.032	0.032	strong		0.647	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
ZNF844	284391	hgsc.bcm.edu	37	19	12187907	12187907	+	Missense_Mutation	SNP	G	G	A	rs55703333	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187907G>A	ENST00000439326.3	+	4	2147	c.1972G>A	c.(1972-1974)Gta>Ata	p.V658I	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	658			V -> I (in dbSNP:rs55703333).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GGTTCCTTTCGTAGACATAAA	0.403													.|||	76	0.0151757	0.0378	0.0086	5008	,	,		22386	0.001		0.0179	False		,,,				2504	0.001				p.V658I		Atlas-SNP	.											.	ZNF844	69	.	0			c.G1972A						PASS	.	G	ILE/VAL	71,1313		4,63,625	47.0	51.0	50.0		1972	-5.8	0.0	19	dbSNP_129	50	50,3132		2,46,1543	yes	missense	ZNF844	NM_001136501.1	29	6,109,2168	AA,AG,GG		1.5713,5.1301,2.65	benign	658/667	12187907	121,4445	692	1591	2283	SO:0001583	missense	284391	exon4			CCTTTCGTAGACA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1972G>A	19.37:g.12187907G>A	ENSP00000392024:p.Val658Ile	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	43	0.019688644688644688	23	0.046747967479674794	4	0.011049723756906077	1	0.0017482517482517483	15	0.01978891820580475	G	9.085	1.000237	0.19121	0.051301	0.015713	ENSG00000223547	ENST00000439326	T	0.05996	3.36	2.92	-5.83	0.02325	.	.	.	.	.	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	P	0.40476	0.718	B	0.21917	0.037	T	0.41233	-0.9520	9	0.87932	D	0	.	4.1975	0.10450	0.1349:0.1113:0.5622:0.1917	rs55703333	658	Q08AG5	ZN844_HUMAN	I	658	ENSP00000392024:V658I	ENSP00000392024:V658I	V	+	1	0	ZNF844	12048907	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.792000	0.00185	-1.709000	0.01399	-0.300000	0.09419	GTA	G|0.980;A|0.020	0.020	strong		0.403	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
KRT83	3889	hgsc.bcm.edu	37	12	52711549	52711549	+	Silent	SNP	G	G	A	rs2857667	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52711549G>A	ENST00000293670.3	-	4	728	c.666C>T	c.(664-666)tgC>tgT	p.C222C		NM_002282.3	NP_002273.3	P78385	KRT83_HUMAN	keratin 83	222	Coil 1B.|Rod.				aging (GO:0007568)|epidermis development (GO:0008544)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.C222C(1)		NS(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(9)|prostate(1)|skin(4)|stomach(7)|upper_aerodigestive_tract(1)	32	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		GGAGGTAGGCGCAGTCCACAT	0.622													g|||	1884	0.376198	0.5008	0.317	5008	,	,		18517	0.1885		0.4095	False		,,,				2504	0.409				p.C222C	GBM(41;747 834 12702 24089 39393)|Esophageal Squamous(97;805 1414 12559 28198 31861)	Atlas-SNP	.											KRT83,NS,carcinoma,-1,3	KRT83	64	3	1	Substitution - coding silent(1)	stomach(1)	c.C666T						PASS	.	G		2162,2244	582.0+/-385.5	554,1054,595	90.0	91.0	90.0		666	-2.6	1.0	12	dbSNP_100	90	3582,5018	511.4+/-377.7	729,2124,1447	no	coding-synonymous	KRT83	NM_002282.3		1283,3178,2042	AA,AG,GG		41.6512,49.0695,44.1642		222/494	52711549	5744,7262	2203	4300	6503	SO:0001819	synonymous_variant	3889	exon4			GTAGGCGCAGTCC	X99141	CCDS8823.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000170523	ENSG00000170523		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6460	protein-coding gene	gene with protein product	"""hard keratin type II"""	602765	"""keratin, hair, basic, 3"""	KRTHB3		9084137, 16831889	Standard	NM_002282		Approved	Hb-3	uc001saf.2	P78385	OTTHUMG00000169632	ENST00000293670.3:c.666C>T	12.37:g.52711549G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	110	41	0.372727	NM_002282	A1A4S9|B2RC21|Q6NT21|Q9NSB3	Silent	SNP	ENST00000293670.3	37	CCDS8823.1																																																																																			T|0.002;G|0.586;A|0.413	0.413	strong		0.622	KRT83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405182.1	NM_002282	
RALGDS	5900	hgsc.bcm.edu	37	9	135982493	135982493	+	Silent	SNP	C	C	T	rs45487303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135982493C>T	ENST00000372050.3	-	7	1413	c.1392G>A	c.(1390-1392)gaG>gaA	p.E464E	RALGDS_ENST00000372062.3_Silent_p.E435E|RALGDS_ENST00000393157.3_Silent_p.E463E|RALGDS_ENST00000372047.3_Silent_p.E452E|RALGDS_ENST00000393160.3_Silent_p.E409E|RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000542690.1_Silent_p.E535E	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	464	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)		CGATCCAGTGCTCCACCACCC	0.617			T	CIITA	"""PMBL, Hodgkin Lymphona, """								C|||	50	0.00998403	0.0	0.0144	5008	,	,		18802	0.0		0.0288	False		,,,				2504	0.0112				p.E464E	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.G1392A						PASS	.	C	,	20,4386	27.2+/-55.0	0,20,2183	80.0	74.0	76.0		1227,1392	0.1	1.0	9	dbSNP_127	76	158,8442	73.5+/-136.2	0,158,4142	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	0,178,6325	TT,TC,CC		1.8372,0.4539,1.3686	,	409/860,464/915	135982493	178,12828	2203	4300	6503	SO:0001819	synonymous_variant	5900	exon7			CCAGTGCTCCACC	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.1392G>A	9.37:g.135982493C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			C|0.985;T|0.015	0.015	strong		0.617	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
SEC24C	9632	hgsc.bcm.edu	37	10	75523634	75523634	+	Missense_Mutation	SNP	A	A	G	rs35528438	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75523634A>G	ENST00000339365.2	+	9	1282	c.1120A>G	c.(1120-1122)Atc>Gtc	p.I374V	SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_Missense_Mutation_p.I255V|SEC24C_ENST00000345254.4_Missense_Mutation_p.I374V|SEC24C_ENST00000546025.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	374					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TCCCCGATACATCCGATGTAC	0.542													A|||	40	0.00798722	0.0008	0.0202	5008	,	,		15779	0.0		0.0219	False		,,,				2504	0.0031				p.I374V		Atlas-SNP	.											.	SEC24C	86	.	0			c.A1120G						PASS	.	A	VAL/ILE,VAL/ILE	24,4382	29.0+/-57.7	0,24,2179	84.0	71.0	75.0		1120,1120	5.8	1.0	10	dbSNP_126	75	219,8381	91.9+/-153.9	4,211,4085	yes	missense,missense	SEC24C	NM_004922.3,NM_198597.2	29,29	4,235,6264	GG,GA,AA		2.5465,0.5447,1.8684	benign,benign	374/1095,374/1095	75523634	243,12763	2203	4300	6503	SO:0001583	missense	9632	exon8			CGATACATCCGAT	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1120A>G	10.37:g.75523634A>G	ENSP00000343405:p.Ile374Val	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	158	76	0.481013	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	37	CCDS7332.1	25	0.011446886446886446	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	17	0.022427440633245383	A	15.89	2.965859	0.53507	0.005447	0.025465	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	T;T;T	0.20200	2.09;2.09;2.09	5.77	5.77	0.91146	.	0.093915	0.64402	D	0.000001	T	0.08670	0.0215	L	0.52266	1.64	0.80722	D	1	B;B;B	0.31209	0.189;0.313;0.209	B;B;B	0.36378	0.064;0.223;0.111	T	0.03384	-1.1042	10	0.14656	T	0.56	-14.7248	16.1024	0.81184	1.0:0.0:0.0:0.0	rs35528438	255;374;374	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	V	374;374;255	ENSP00000321845:I374V;ENSP00000343405:I374V;ENSP00000402913:I255V	ENSP00000343405:I374V	I	+	1	0	SEC24C	75193640	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.393000	0.59665	2.200000	0.70718	0.459000	0.35465	ATC	A|0.983;G|0.017	0.017	strong		0.542	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
SPRR3	6707	hgsc.bcm.edu	37	1	152975739	152975739	+	Silent	SNP	T	T	A	rs17851565	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152975739T>A	ENST00000295367.4	+	2	285	c.243T>A	c.(241-243)ggT>ggA	p.G81G	SPRR3_ENST00000331860.3_Silent_p.G81G|SPRR3_ENST00000542696.1_Silent_p.G81G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	81	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)	p.G81G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGTTGTACCAAGG	0.592																																					p.G81G		Atlas-SNP	.											SPRR3,colon,carcinoma,0,4	SPRR3	45	4	1	Substitution - coding silent(1)	prostate(1)	c.T243A						scavenged	.						61.0	52.0	55.0					1																	152975739		2203	4299	6502	SO:0001819	synonymous_variant	6707	exon2			GCCAGGTTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.243T>A	1.37:g.152975739T>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	86	3	0.0348837	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			A|0.010;C|0.001;T|0.988	0.010	strong		0.592	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
PIP4K2B	8396	hgsc.bcm.edu	37	17	36926731	36926731	+	Silent	SNP	T	T	G	rs228289	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36926731T>G	ENST00000269554.3	-	9	1608	c.1128A>C	c.(1126-1128)acA>acC	p.T376T		NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	376	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						CTTTCTTCTTTGTATCGTATG	0.542													C|||	2013	0.401957	0.5068	0.3559	5008	,	,		17056	0.3591		0.2306	False		,,,				2504	0.5133				p.T376T		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.A1128C						PASS	.	C		1964,2442		433,1098,672	240.0	213.0	222.0		1128	-4.9	0.1	17	dbSNP_79	222	2018,6582		250,1518,2532	no	coding-synonymous	PIP4K2B	NM_003559.4		683,2616,3204	GG,GT,TT		23.4651,44.5756,30.6166		376/417	36926731	3982,9024	2203	4300	6503	SO:0001819	synonymous_variant	8396	exon9			CTTCTTTGTATCG	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.1128A>C	17.37:g.36926731T>G		Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	172	82	0.476744	NM_003559	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	37	CCDS11329.1																																																																																			T|0.663;G|0.337	0.337	strong		0.542	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	
CCDC137	339230	hgsc.bcm.edu	37	17	79637367	79637367	+	Missense_Mutation	SNP	C	C	G	rs7226091	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79637367C>G	ENST00000329214.8	+	3	784	c.381C>G	c.(379-381)caC>caG	p.H127Q		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	127			H -> Q (in dbSNP:rs7226091).				poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CCTATATCCACCGCATGCAGC	0.577													G|||	1198	0.239217	0.3472	0.1484	5008	,	,		17806	0.2252		0.2515	False		,,,				2504	0.1595				p.H127Q		Atlas-SNP	.											CCDC137,NS,carcinoma,0,2	CCDC137	27	2	0			c.C381G						PASS	.	G	GLN/HIS	1319,2607		239,841,883	31.0	37.0	35.0		381	0.3	0.5	17	dbSNP_116	35	1782,6530		200,1382,2574	yes	missense	CCDC137	NM_199287.2	24	439,2223,3457	GG,GC,CC		21.4389,33.5965,25.3391	benign	127/290	79637367	3101,9137	1963	4156	6119	SO:0001583	missense	339230	exon3			TATCCACCGCATG	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.381C>G	17.37:g.79637367C>G	ENSP00000329360:p.His127Gln	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	546	0.25	187	0.3800813008130081	59	0.16298342541436464	124	0.21678321678321677	176	0.23218997361477572	G	0.012	-1.648770	0.00785	0.335965	0.214389	ENSG00000185298	ENST00000329214	T	0.15952	2.38	4.88	0.343	0.16001	.	0.377525	0.26539	N	0.023820	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	0.45629	-0.9248	9	0.14656	T	0.56	-12.8019	2.9796	0.05949	0.2238:0.2606:0.4154:0.1002	rs7226091;rs60336178;rs7226091	127	Q6PK04	CC137_HUMAN	Q	127	ENSP00000329360:H127Q	ENSP00000329360:H127Q	H	+	3	2	CCDC137	77247772	0.017000	0.18338	0.502000	0.27614	0.234000	0.25298	-0.066000	0.11598	0.022000	0.15160	-0.709000	0.03644	CAC	C|0.754;G|0.245	0.245	strong		0.577	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
TRRAP	8295	hgsc.bcm.edu	37	7	98592335	98592335	+	Silent	SNP	G	G	A	rs56282945		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:98592335G>A	ENST00000359863.4	+	66	10340	c.10131G>A	c.(10129-10131)acG>acA	p.T3377T	TRRAP_ENST00000446306.3_Silent_p.T3366T|TRRAP_ENST00000355540.3_Silent_p.T3348T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3377					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)			TGGTGAGCACGTTTGGGGTGG	0.567													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18543	0.0		0.0	False		,,,				2504	0.0				p.T3377T		Atlas-SNP	.											.	TRRAP	863	.	0			c.G10131A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	187.0	180.0	182.0		10044	-9.6	0.1	7	dbSNP_129	182	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRRAP	NM_003496.3		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		3348/3831	98592335	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon66			GAGCACGTTTGGG	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.10131G>A	7.37:g.98592335G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	171	76	0.444444	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.130	0.782960	0.16189	2.27E-4	2.33E-4	ENSG00000196367	ENST00000456197	.	.	.	5.29	-9.63	0.00544	.	.	.	.	.	T	0.35248	0.0925	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42582	-0.9443	4	.	.	.	.	3.8434	0.08925	0.5236:0.2218:0.107:0.1476	rs56282945	.	.	.	H	3106	.	.	R	+	2	0	TRRAP	98430271	0.000000	0.05858	0.094000	0.20943	0.949000	0.60115	-2.691000	0.00830	-1.767000	0.01300	-0.502000	0.04539	CGT	G|1.000;A|0.000	0.000	strong		0.567	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
HELB	92797	hgsc.bcm.edu	37	12	66731864	66731864	+	Silent	SNP	C	C	A	rs1168329	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:66731864C>A	ENST00000247815.4	+	13	3305	c.3246C>A	c.(3244-3246)acC>acA	p.T1082T		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	1082					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		TCAAGCCCACCGATAATCAAG	0.343													A|||	2686	0.536342	0.5953	0.6282	5008	,	,		15529	0.5585		0.4235	False		,,,				2504	0.4847				p.T1082T		Atlas-SNP	.											.	HELB	90	.	0			c.C3246A						PASS	.	A		2477,1929	546.4+/-377.0	721,1035,447	68.0	71.0	70.0		3246	-1.6	0.0	12	dbSNP_87	70	3721,4879	617.7+/-396.7	811,2099,1390	no	coding-synonymous	HELB	NM_033647.2		1532,3134,1837	AA,AC,CC		43.2674,43.7812,47.6549		1082/1088	66731864	6198,6808	2203	4300	6503	SO:0001819	synonymous_variant	92797	exon13			GCCCACCGATAAT	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.3246C>A	12.37:g.66731864C>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	41	18	0.439024	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Silent	SNP	ENST00000247815.4	37	CCDS8976.1																																																																																			C|0.503;A|0.497	0.497	strong		0.343	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
OR5K4	403278	hgsc.bcm.edu	37	3	98073313	98073313	+	Missense_Mutation	SNP	A	A	G	rs9822460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:98073313A>G	ENST00000354924.2	+	1	616	c.616A>G	c.(616-618)Att>Gtt	p.I206V	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005517.1	NP_001005517.1	A6NMS3	OR5K4_HUMAN	olfactory receptor, family 5, subfamily K, member 4	206			I -> V (in dbSNP:rs9822460).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	21						TTCAATACCAATTCAAATCTT	0.328													A|||	1168	0.233227	0.2451	0.232	5008	,	,		18812	0.1726		0.2217	False		,,,				2504	0.2924				p.I206V		Atlas-SNP	.											.	OR5K4	75	.	0			c.A616G						PASS	.	A	VAL/ILE	1199,3207	415.0+/-337.0	180,839,1184	81.0	82.0	82.0		616	2.7	1.0	3	dbSNP_119	82	1757,6843	317.6+/-313.3	180,1397,2723	yes	missense	OR5K4	NM_001005517.1	29	360,2236,3907	GG,GA,AA		20.4302,27.2129,22.728	benign	206/322	98073313	2956,10050	2203	4300	6503	SO:0001583	missense	403278	exon1			ATACCAATTCAAA		CCDS33802.1	3q11.2	2013-09-23			ENSG00000196098	ENSG00000196098		"""GPCR / Class A : Olfactory receptors"""	31291	protein-coding gene	gene with protein product							Standard	NM_001005517		Approved		uc011bgv.2	A6NMS3	OTTHUMG00000160081	ENST00000354924.2:c.616A>G	3.37:g.98073313A>G	ENSP00000347003:p.Ile206Val	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	103	46	0.446602	NM_001005517		Missense_Mutation	SNP	ENST00000354924.2	37	CCDS33802.1	447	0.20467032967032966	116	0.23577235772357724	78	0.2154696132596685	81	0.14160839160839161	172	0.22691292875989447	A	3.044	-0.196857	0.06259	0.272129	0.204302	ENSG00000196098	ENST00000354924	T	0.00044	8.83	5.06	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33057	U	0.005331	T	0.00012	0.0000	N	0.25094	0.71	0.49687	P	1.8300000000004424E-4	B	0.16603	0.018	B	0.25405	0.06	T	0.04128	-1.0975	9	0.02654	T	1	-10.2086	7.8213	0.29290	0.827:0.0:0.173:0.0	rs9822460;rs52816954;rs9822460	206	A6NMS3	OR5K4_HUMAN	V	206	ENSP00000347003:I206V	ENSP00000347003:I206V	I	+	1	0	OR5K4	99556003	0.000000	0.05858	0.987000	0.45799	0.961000	0.63080	-0.114000	0.10757	0.493000	0.27837	0.491000	0.48974	ATT	A|0.782;G|0.218	0.218	strong		0.328	OR5K4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359114.1		
NFATC1	4772	hgsc.bcm.edu	37	18	77170505	77170505	+	Missense_Mutation	SNP	C	C	T	rs143045693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:77170505C>T	ENST00000427363.2	+	2	230	c.230C>T	c.(229-231)cCg>cTg	p.P77L	NFATC1_ENST00000587635.1_Missense_Mutation_p.P77L|NFATC1_ENST00000253506.5_Missense_Mutation_p.P77L|NFATC1_ENST00000318065.5_Missense_Mutation_p.P64L|NFATC1_ENST00000586434.1_Missense_Mutation_p.P64L|NFATC1_ENST00000329101.4_Missense_Mutation_p.P64L|NFATC1_ENST00000591814.1_Missense_Mutation_p.P77L|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000592223.1_Missense_Mutation_p.P64L|NFATC1_ENST00000542384.1_Missense_Mutation_p.P77L|NFATC1_ENST00000545796.1_Intron			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	77					calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	ACCTCCACACCGGGCATCATC	0.692													C|||	2	0.000399361	0.0	0.0	5008	,	,		13489	0.0		0.002	False		,,,				2504	0.0				p.P77L	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C230T						PASS	.	C	LEU/PRO,LEU/PRO,,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	50.0	56.0	54.0		230,191,,191,230	4.4	0.0	18	dbSNP_134	54	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,intron,missense,missense	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	98,98,,98,98	0,4,6498	TT,TC,CC		0.0349,0.0227,0.0308	benign,benign,,benign,benign	77/826,64/931,,64/813,77/717	77170505	4,13000	2203	4299	6502	SO:0001583	missense	4772	exon2			CCACACCGGGCAT	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.230C>T	18.37:g.77170505C>T	ENSP00000389377:p.Pro77Leu	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	81	44	0.54321	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	22.8	4.334065	0.81801	2.27E-4	3.49E-4	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384;ENST00000329101;ENST00000427363;ENST00000397794	T;T;T	0.39229	1.09;1.09;1.09	4.39	4.39	0.52855	.	0.400014	0.28146	N	0.016430	T	0.46386	0.1390	M	0.61703	1.905	0.80722	D	1	P;P;P;D;D;P;P	0.55605	0.904;0.904;0.946;0.972;0.972;0.773;0.946	B;B;B;B;B;B;B	0.43916	0.344;0.23;0.344;0.436;0.436;0.121;0.436	T	0.57894	-0.7732	10	0.87932	D	0	-17.9221	17.1373	0.86743	0.0:1.0:0.0:0.0	.	64;64;77;77;77;64;77	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	L	77;77;77;64;64;41	ENSP00000253506:P77L;ENSP00000442435:P77L;ENSP00000327850:P64L	ENSP00000253506:P77L	P	+	2	0	NFATC1	75271493	0.997000	0.39634	0.025000	0.17156	0.028000	0.11728	6.807000	0.75201	2.267000	0.75376	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	strong		0.692	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000436117.2_Silent_p.Q648Q|MET_ENST00000397752.3_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GGACAACACAATACAGTACAT	0.318			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93.0	92.0	92.0		1944,1944	-6.5	0.0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1944A>G	7.37:g.116397572A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	72	39	0.541667	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
ARHGAP22	58504	hgsc.bcm.edu	37	10	49658842	49658842	+	Missense_Mutation	SNP	C	C	G	rs34940331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:49658842C>G	ENST00000249601.4	-	9	1626	c.1330G>C	c.(1330-1332)Ggg>Cgg	p.G444R	ARHGAP22_ENST00000417912.2_Missense_Mutation_p.G460R|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.G277R|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.G450R|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.G335R|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.G354R|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.G285R	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	444	Ser-rich.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GAGCCGCCCCCCTTCGGGCTT	0.701													C|||	29	0.00579073	0.0	0.0115	5008	,	,		14381	0.0		0.0169	False		,,,				2504	0.0041				p.G460R		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G1378C						PASS	.	C	ARG/GLY	18,4346		0,18,2164	16.0	16.0	16.0		1330	1.9	0.1	10	dbSNP_126	16	120,8452		0,120,4166	yes	missense	ARHGAP22	NM_021226.2	125	0,138,6330	GG,GC,CC		1.3999,0.4125,1.0668	benign	444/699	49658842	138,12798	2182	4286	6468	SO:0001583	missense	58504	exon9			CGCCCCCCTTCGG	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.1330G>C	10.37:g.49658842C>G	ENSP00000249601:p.Gly444Arg	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	90	39	0.433333	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	CCDS7227.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	C	1.420	-0.573198	0.03882	0.004125	0.013999	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.25250	2.93;2.6;1.81;2.22;2.59;2.89;2.93	4.94	1.9	0.25705	.	1.698030	0.02544	N	0.094901	T	0.10852	0.0265	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B	0.17038	0.001;0.0;0.0;0.0;0.0;0.02	B;B;B;B;B;B	0.13407	0.002;0.001;0.001;0.001;0.002;0.009	T	0.16689	-1.0394	10	0.15952	T	0.53	.	7.5489	0.27783	0.2549:0.3359:0.4092:0.0	rs34940331	450;444;460;444;354;277	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	R	444;335;285;277;354;450;460	ENSP00000249601:G444R;ENSP00000363287:G335R;ENSP00000363285:G285R;ENSP00000422868:G277R;ENSP00000410054:G354R;ENSP00000416701:G450R;ENSP00000412461:G460R	ENSP00000249601:G444R	G	-	1	0	ARHGAP22	49328848	0.001000	0.12720	0.081000	0.20488	0.304000	0.27724	-0.001000	0.12947	1.074000	0.40909	-0.226000	0.12346	GGG	C|0.991;G|0.009	0.009	strong		0.701	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226	
STEAP1B	256227	hgsc.bcm.edu	37	7	22532260	22532260	+	Missense_Mutation	SNP	A	A	G	rs16881817	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:22532260A>G	ENST00000406890.2	-	4	723	c.629T>C	c.(628-630)aTa>aCa	p.I210T	STEAP1B_ENST00000404369.4_Missense_Mutation_p.I229T	NM_207342.2	NP_997225.1	Q6NZ63	STEAL_HUMAN	STEAP family member 1B	210			I -> T (in dbSNP:rs16881817).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|lung(2)	4						CAGAGCCAGTATTGCCAGTCC	0.393													a|||	1715	0.342452	0.354	0.1988	5008	,	,		16365	0.4236		0.2853	False		,,,				2504	0.4039				p.I229T		Atlas-SNP	.											STEAP1B,NS,carcinoma,0,4	STEAP1B	22	4	0			c.T686C						PASS	.	A	THR/ILE,THR/ILE	449,935		73,303,316	280.0	228.0	244.0		686,629	0.9	1.0	7	dbSNP_129	244	890,2292		135,620,836	no	missense,missense	STEAP1B	NM_001164460.1,NM_207342.2	89,89	208,923,1152	GG,GA,AA		27.9698,32.4422,29.3254	possibly-damaging,possibly-damaging	229/343,210/246	22532260	1339,3227	692	1591	2283	SO:0001583	missense	256227	exon4			GCCAGTATTGCCA		CCDS55094.1, CCDS56469.1	7p15.3	2011-05-19			ENSG00000105889	ENSG00000105889			41907	protein-coding gene	gene with protein product							Standard	NM_207342		Approved		uc010kum.2	Q6NZ63	OTTHUMG00000152529	ENST00000406890.2:c.629T>C	7.37:g.22532260A>G	ENSP00000385239:p.Ile210Thr	Somatic	234	0	0		WXS	Illumina HiSeq	Phase_I	246	110	0.447154	NM_001164460	B5MCI2	Missense_Mutation	SNP	ENST00000406890.2	37	CCDS55094.1	671	0.30723443223443225	158	0.32113821138211385	86	0.23756906077348067	206	0.36013986013986016	221	0.29155672823219	a	14.50	2.553339	0.45487	0.324422	0.279698	ENSG00000105889	ENST00000406890;ENST00000404369;ENST00000424363	D;D;D	0.91521	-2.86;-2.86;-2.86	0.893	0.893	0.19236	Flavoprotein transmembrane component (1);	0.829472	0.09645	U	0.774455	T	0.00012	0.0000	L	0.31578	0.945	0.47009	P	7.129999999999637E-4	D;P	0.54601	0.967;0.549	P;B	0.52189	0.692;0.419	T	0.00617	-1.1642	9	0.49607	T	0.09	-16.2164	6.0784	0.19928	1.0:0.0:0.0:0.0	rs62447564	229;210	B5MCI2;Q6NZ63	.;STEAL_HUMAN	T	210;229;229	ENSP00000385239:I210T;ENSP00000384370:I229T;ENSP00000416608:I229T	ENSP00000384370:I229T	I	-	2	0	STEAP1B	22498785	0.647000	0.27304	0.991000	0.47740	0.398000	0.30690	5.007000	0.63984	0.680000	0.31366	0.102000	0.15555	ATA	A|0.702;G|0.298	0.298	strong		0.393	STEAP1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326617.2		
SLC34A1	6569	hgsc.bcm.edu	37	5	176815124	176815124	+	Silent	SNP	T	T	C	rs5030873	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176815124T>C	ENST00000324417.5	+	7	865	c.774T>C	c.(772-774)caT>caC	p.H258H	SLC34A1_ENST00000512593.1_Silent_p.H258H	NM_003052.4	NP_003043.3	Q06495	NPT2A_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 1	258					arsenate ion transmembrane transport (GO:1901684)|bone remodeling (GO:0046849)|cellular response to metal ion (GO:0071248)|cellular response to parathyroid hormone stimulus (GO:0071374)|cellular response to staurosporine (GO:0072734)|dentinogenesis (GO:0097187)|gentamycin metabolic process (GO:1901128)|glycoprotein metabolic process (GO:0009100)|indole metabolic process (GO:0042431)|ion transport (GO:0006811)|kidney development (GO:0001822)|ossification (GO:0001503)|phosphate ion homeostasis (GO:0055062)|phosphate ion transport (GO:0006817)|positive regulation of membrane potential (GO:0045838)|positive regulation of phosphate transmembrane transport (GO:2000187)|positive regulation of sodium-dependent phosphate transport (GO:2000120)|protein homooligomerization (GO:0051260)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to lead ion (GO:0010288)|response to magnesium ion (GO:0032026)|response to mercury ion (GO:0046689)|response to potassium ion (GO:0035864)|response to thyroid hormone (GO:0097066)|response to vitamin A (GO:0033189)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|tricarboxylic acid metabolic process (GO:0072350)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|membrane-bounded vesicle (GO:0031988)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24	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)			TCAACATCCATGGTGGCCGTG	0.597													T|||	1066	0.212859	0.0363	0.2637	5008	,	,		16041	0.2073		0.331	False		,,,				2504	0.2996				p.H258H		Atlas-SNP	.											.	SLC34A1	73	.	0			c.T774C						PASS	.	T	,	343,4063	180.1+/-208.5	14,315,1874	76.0	65.0	69.0		774,774	-10.1	0.0	5	dbSNP_113	69	2807,5793	443.5+/-360.4	467,1873,1960	no	coding-synonymous,coding-synonymous	SLC34A1	NM_001167579.1,NM_003052.4	,	481,2188,3834	CC,CT,TT		32.6395,7.7848,24.2196	,	258/341,258/640	176815124	3150,9856	2203	4300	6503	SO:0001819	synonymous_variant	6569	exon7			CATCCATGGTGGC	L13258	CCDS4418.1, CCDS54953.1	5q35.3	2013-07-17	2013-07-17		ENSG00000131183	ENSG00000131183		"""Solute carriers"""	11019	protein-coding gene	gene with protein product	"""sodium/phosphate co-transporter"", ""solute carrier family 17 (sodium phosphate), member 2"", ""Na+-phosphate cotransporter type II"""	182309	"""solute carrier family 34 (sodium phosphate), member 1"""	NPT2, SLC17A2		8327470, 8693007	Standard	NM_003052		Approved	NAPI-3, NPTIIa, SLC11	uc003mgk.4	Q06495	OTTHUMG00000130857	ENST00000324417.5:c.774T>C	5.37:g.176815124T>C		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	57	0.491379	NM_003052	B4DPE3	Silent	SNP	ENST00000324417.5	37	CCDS4418.1																																																																																			T|0.759;C|0.241	0.241	strong		0.597	SLC34A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253431.1	NM_003052	
NACAD	23148	hgsc.bcm.edu	37	7	45124008	45124008	+	Missense_Mutation	SNP	T	T	C	rs7777835	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45124008T>C	ENST00000490531.2	-	2	1790	c.1771A>G	c.(1771-1773)Aaa>Gaa	p.K591E		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	591			K -> E (in dbSNP:rs7777835).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						AGGTCCTCTTTAGCCTGCCTG	0.587													c|||	3188	0.636581	0.8071	0.6585	5008	,	,		22932	0.378		0.6431	False		,,,				2504	0.6503				p.K591E		Atlas-SNP	.											.	NACAD	44	.	0			c.A1771G						PASS	.						65.0	62.0	63.0					7																	45124008		692	1591	2283	SO:0001583	missense	23148	exon2			CCTCTTTAGCCTG	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1771A>G	7.37:g.45124008T>C	ENSP00000420477:p.Lys591Glu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	155	154	0.993548	NM_001146334		Missense_Mutation	SNP	ENST00000490531.2	37	CCDS47582.1	1343	0.61492673992674	407	0.8272357723577236	241	0.6657458563535912	197	0.34440559440559443	498	0.6569920844327177	c	0.011	-1.724949	0.00694	.	.	ENSG00000136274	ENST00000490531	T	0.10099	2.91	1.15	1.15	0.20763	.	.	.	.	.	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	0.27905	-1.0060	8	0.02654	T	1	.	3.6638	0.08249	0.0:0.7343:0.0:0.2657	rs7777835;rs52810513;rs7777835	591	O15069	NACAD_HUMAN	E	591	ENSP00000420477:K591E	ENSP00000420477:K591E	K	-	1	0	NACAD	45090533	0.001000	0.12720	0.058000	0.19502	0.026000	0.11368	0.163000	0.16520	0.078000	0.16900	-0.724000	0.03597	AAA	T|0.384;C|0.616	0.616	strong		0.587	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
SLC22A8	9376	hgsc.bcm.edu	37	11	62763226	62763226	+	Silent	SNP	C	C	T	rs57743826	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62763226C>T	ENST00000336232.2	-	7	1086	c.951G>A	c.(949-951)ctG>ctA	p.L317L	SLC22A8_ENST00000430500.2_Silent_p.L317L|SLC22A8_ENST00000542795.1_5'Flank|SLC22A8_ENST00000535878.1_Silent_p.L194L|SLC22A8_ENST00000311438.8_Silent_p.L317L|SLC22A8_ENST00000545207.1_Silent_p.L226L	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	317					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)	GTATCCGGAACAGGTCACTTG	0.592													C|||	26	0.00519169	0.0	0.0058	5008	,	,		19074	0.0		0.0149	False		,,,				2504	0.0072				p.L317L		Atlas-SNP	.											.	SLC22A8	60	.	0			c.G951A						PASS	.	C	,,,	16,4386	22.3+/-47.3	0,16,2185	177.0	161.0	166.0		951,678,582,951	3.3	1.0	11	dbSNP_129	166	133,8463	67.3+/-129.8	1,131,4166	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC22A8	NM_001184732.1,NM_001184733.1,NM_001184736.1,NM_004254.3	,,,	1,147,6351	TT,TC,CC		1.5472,0.3635,1.1463	,,,	317/543,226/452,194/420,317/543	62763226	149,12849	2201	4298	6499	SO:0001819	synonymous_variant	9376	exon7			CCGGAACAGGTCA	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.951G>A	11.37:g.62763226C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	109	63	0.577982	NM_001184732	B4DPH7|F5GWA8|F5H5J1|O95820|Q59EW9|Q96TC1	Silent	SNP	ENST00000336232.2	37	CCDS8042.1																																																																																			C|0.989;T|0.011	0.011	strong		0.592	SLC22A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396191.1	NM_004254	
WDR25	79446	hgsc.bcm.edu	37	14	100847930	100847930	+	Silent	SNP	A	A	G	rs3742387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:100847930A>G	ENST00000335290.6	+	2	895	c.669A>G	c.(667-669)ccA>ccG	p.P223P	WDR25_ENST00000542471.2_5'Flank|WDR25_ENST00000402312.3_Silent_p.P223P|WDR25_ENST00000554175.1_Silent_p.P223P|WDR25_ENST00000554998.1_Silent_p.P223P	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	223										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				TTATTCAGCCATATTTGAATA	0.567													G|||	3236	0.646166	0.649	0.4597	5008	,	,		16083	0.4742		0.7276	False		,,,				2504	0.8681				p.P223P		Atlas-SNP	.											.	WDR25	37	.	0			c.A669G						PASS	.	G	,	2890,1516	466.8+/-354.6	944,1002,257	43.0	47.0	46.0		669,669	-11.3	0.0	14	dbSNP_107	46	6463,2137	356.5+/-330.3	2424,1615,261	no	coding-synonymous,coding-synonymous	WDR25	NM_001161476.1,NM_024515.4	,	3368,2617,518	GG,GA,AA		24.8488,34.4076,28.087	,	223/545,223/545	100847930	9353,3653	2203	4300	6503	SO:0001819	synonymous_variant	79446	exon2			TCAGCCATATTTG	BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.669A>G	14.37:g.100847930A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Silent	SNP	ENST00000335290.6	37	CCDS32157.1																																																																																			A|0.337;G|0.663	0.663	strong		0.567	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515	
CASP9	842	hgsc.bcm.edu	37	1	15850613	15850613	+	Missense_Mutation	SNP	G	G	A	rs1052571	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15850613G>A	ENST00000333868.5	-	1	177	c.83C>T	c.(82-84)gCc>gTc	p.A28V	CASP9_ENST00000375890.4_Intron|DNAJC16_ENST00000375838.1_5'Flank|DNAJC16_ENST00000375847.3_5'Flank|CASP9_ENST00000348549.5_Missense_Mutation_p.A28V|DNAJC16_ENST00000375849.1_5'Flank|CASP9_ENST00000546424.1_Missense_Mutation_p.A28V|CASP9_ENST00000469637.1_Intron	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	28	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		A -> V (in dbSNP:rs1052571). {ECO:0000269|PubMed:16780893, ECO:0000269|PubMed:8663294, ECO:0000269|PubMed:9890966, ECO:0000269|Ref.9}.		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		GCTCAGCAGGGCGTCCCAGAG	0.711													G|||	2928	0.584665	0.739	0.4986	5008	,	,		5756	0.6538		0.5149	False		,,,				2504	0.4376				p.A28V		Atlas-SNP	.											.	CASP9	40	.	0			c.C83T						PASS	.						8.0	10.0	10.0					1																	15850613		2109	4166	6275	SO:0001583	missense	842	exon1			AGCAGGGCGTCCC	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.83C>T	1.37:g.15850613G>A	ENSP00000330237:p.Ala28Val	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	30	23	0.766667	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Missense_Mutation	SNP	ENST00000333868.5	37	CCDS158.1	1291	0.5911172161172161	350	0.7113821138211383	179	0.494475138121547	358	0.6258741258741258	404	0.5329815303430079	G	15.45	2.836320	0.50951	.	.	ENSG00000132906	ENST00000546424;ENST00000333868;ENST00000348549;ENST00000440484	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	4.59	1.33	0.21861	DEATH-like (2);Caspase Recruitment (3);	0.919308	0.09391	N	0.808563	T	0.00012	0.0000	M	0.63428	1.95	0.21290	P	0.999735974	P;B;B	0.42908	0.793;0.009;0.029	B;B;B	0.39562	0.303;0.015;0.015	T	0.33394	-0.9870	9	0.22109	T	0.4	.	4.6003	0.12350	0.2169:0.0:0.6031:0.18	rs1052571;rs3192982;rs59045053;rs1052571	28;28;28	P55211-2;P55211;F8VVS7	.;CASP9_HUMAN;.	V	28	ENSP00000449584:A28V;ENSP00000330237:A28V;ENSP00000255256:A28V;ENSP00000411304:A28V	ENSP00000330237:A28V	A	-	2	0	CASP9	15723200	0.277000	0.24220	0.926000	0.36857	0.713000	0.41058	0.257000	0.18369	0.500000	0.27991	0.305000	0.20034	GCC	G|0.387;A|0.613	0.613	strong		0.711	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
ARHGAP25	9938	hgsc.bcm.edu	37	2	69040500	69040500	+	Silent	SNP	G	G	A	rs2280310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:69040500G>A	ENST00000295381.3	+	6	1172	c.753G>A	c.(751-753)caG>caA	p.Q251Q	ARHGAP25_ENST00000409202.3_Silent_p.Q252Q|ARHGAP25_ENST00000497079.1_Silent_p.Q245Q|ARHGAP25_ENST00000409220.1_Silent_p.Q245Q|ARHGAP25_ENST00000456116.2_3'UTR|ARHGAP25_ENST00000409030.3_Silent_p.Q244Q|ARHGAP25_ENST00000467265.1_Silent_p.Q212Q|ARHGAP25_ENST00000544262.1_Silent_p.Q226Q	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	251	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.Q245Q(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CCTGGAGCCAGTACGAAGGGT	0.512													G|||	1491	0.297724	0.2927	0.3213	5008	,	,		19180	0.4425		0.1839	False		,,,				2504	0.2556				p.Q252Q		Atlas-SNP	.											ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	1	Substitution - coding silent(1)	stomach(1)	c.G756A						PASS	.	G	,,,	1189,3217	416.7+/-337.7	153,883,1167	108.0	94.0	99.0		756,735,636,732	3.6	1.0	2	dbSNP_100	99	1653,6947	305.0+/-307.2	171,1311,2818	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	,,,	324,2194,3985	AA,AG,GG		19.2209,26.9859,21.8515	,,,	252/647,245/640,212/607,244/639	69040500	2842,10164	2203	4300	6503	SO:0001819	synonymous_variant	9938	exon6			GAGCCAGTACGAA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.753G>A	2.37:g.69040500G>A		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	64	62	0.96875	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Silent	SNP	ENST00000295381.3	37		616	0.28205128205128205	140	0.2845528455284553	112	0.30939226519337015	225	0.39335664335664333	139	0.18337730870712401	G	9.214	1.031745	0.19590	0.269859	0.192209	ENSG00000163219	ENST00000497259	.	.	.	5.73	3.62	0.41486	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.38351	-0.9665	3	.	.	.	.	12.3657	0.55226	0.1637:0.0:0.8363:0.0	rs2280310;rs58055279;rs2280310	.	.	.	N	111	.	.	S	+	2	0	ARHGAP25	68894004	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	0.624000	0.24462	1.432000	0.47375	0.655000	0.94253	AGT	G|0.744;A|0.256	0.256	strong		0.512	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
MUC5B	727897	hgsc.bcm.edu	37	11	1255773	1255773	+	Silent	SNP	C	C	T	rs7116614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1255773C>T	ENST00000529681.1	+	21	2551	c.2493C>T	c.(2491-2493)tgC>tgT	p.C831C	MUC5B_ENST00000447027.1_Silent_p.C834C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	831	TIL 3.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCACACACTGCGTGTCCGGCT	0.667													c|||	1700	0.339457	0.2095	0.33	5008	,	,		11037	0.5982		0.2883	False		,,,				2504	0.3078				p.C831C		Atlas-SNP	.											MUC5B,NS,carcinoma,0,2	MUC5B	473	2	0			c.C2493T						PASS	.			812,3458		79,654,1402	25.0	30.0	28.0		2493	-8.2	0.0	11	dbSNP_116	28	2440,6004		386,1668,2168	no	coding-synonymous	MUC5B	NM_002458.2		465,2322,3570	TT,TC,CC		28.8963,19.0164,25.5781		831/5763	1255773	3252,9462	2135	4222	6357	SO:0001819	synonymous_variant	727897	exon21			ACACTGCGTGTCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2493C>T	11.37:g.1255773C>T		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	144	65	0.451389	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.647;T|0.353	0.353	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
FKBP15	23307	hgsc.bcm.edu	37	9	115931703	115931703	+	Silent	SNP	G	G	A	rs3810910	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:115931703G>A	ENST00000238256.3	-	26	3403	c.3286C>T	c.(3286-3288)Ctg>Ttg	p.L1096L		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	1096					endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						GTCAGGGACAGTCTTGTGGAG	0.577													G|||	1420	0.283546	0.3351	0.2954	5008	,	,		17925	0.1617		0.3489	False		,,,				2504	0.2638				p.L1096L		Atlas-SNP	.											.	FKBP15	128	.	0			c.C3286T						PASS	.	G		1174,2710		177,820,945	96.0	98.0	98.0		3286	3.5	0.0	9	dbSNP_107	98	2704,5574		443,1818,1878	no	coding-synonymous	FKBP15	NM_015258.1		620,2638,2823	AA,AG,GG		32.6649,30.2266,31.8862		1096/1220	115931703	3878,8284	1942	4139	6081	SO:0001819	synonymous_variant	23307	exon26			GGGACAGTCTTGT	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.3286C>T	9.37:g.115931703G>A		Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	195	88	0.451282	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Silent	SNP	ENST00000238256.3	37	CCDS48007.1																																																																																			G|0.712;A|0.288	0.288	strong		0.577	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
SDC3	9672	hgsc.bcm.edu	37	1	31349647	31349647	+	Missense_Mutation	SNP	C	C	T	rs2491132	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:31349647C>T	ENST00000339394.6	-	3	796	c.622G>A	c.(622-624)Gta>Ata	p.V208I	SDC3_ENST00000336798.7_Missense_Mutation_p.V150I|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	208	Ser/Thr-rich (mucin-like).		V -> I (in dbSNP:rs2491132).		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)		AGCCTCCGTACGCCAGTGGTC	0.677													C|||	382	0.076278	0.0091	0.1009	5008	,	,		14077	0.0347		0.2107	False		,,,				2504	0.0542				p.V208I		Atlas-SNP	.											.	SDC3	45	.	0			c.G622A	GRCh37	CM066225	SDC3	M	rs2491132	PASS	.	C	ILE/VAL	184,4222	114.6+/-152.6	7,170,2026	27.0	30.0	29.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	622	-8.7	0.0	1	dbSNP_100	29	1813,6785	315.8+/-312.4	196,1421,2682	yes	missense	SDC3	NM_014654.3	29	203,1591,4708	TT,TC,CC		21.0863,4.1761,15.3568	benign	208/443	31349647	1997,11007	2203	4299	6502	SO:0001583	missense	9672	exon3			TCCGTACGCCAGT	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.622G>A	1.37:g.31349647C>T	ENSP00000344468:p.Val208Ile	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	82	9	0.109756	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Missense_Mutation	SNP	ENST00000339394.6	37	CCDS30661.1	221	0.10119047619047619	8	0.016260162601626018	46	0.1270718232044199	20	0.03496503496503497	147	0.19393139841688653	C	3.539	-0.094098	0.07053	0.041761	0.210863	ENSG00000162512	ENST00000336798;ENST00000339394	T;T	0.21932	1.99;1.98	4.99	-8.71	0.00848	.	0.851711	0.10100	N	0.716133	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.09022	0.002;0.0	B;B	0.04013	0.001;0.0	T	0.40440	-0.9563	9	0.32370	T	0.25	-0.0407	6.0353	0.19704	0.0787:0.3723:0.0849:0.4641	rs2491132;rs17263807;rs2491132	208;150	O75056;D3DPN2	SDC3_HUMAN;.	I	150;208	ENSP00000338346:V150I;ENSP00000344468:V208I	ENSP00000338346:V150I	V	-	1	0	SDC3	31122234	0.000000	0.05858	0.003000	0.11579	0.211000	0.24417	-2.237000	0.01200	-1.210000	0.02627	-0.379000	0.06801	GTA	C|0.879;G|0.000;T|0.121	0.121	strong		0.677	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
KLK4	9622	hgsc.bcm.edu	37	19	51412666	51412666	+	Silent	SNP	C	C	A	rs1654552	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51412666C>A	ENST00000324041.1	-	2	65	c.66G>T	c.(64-66)tcG>tcT	p.S22S	KLK4_ENST00000431178.2_5'Flank|KLK4_ENST00000597441.1_5'Flank	NM_004917.3	NP_004908.3	Q9Y5K2	KLK4_HUMAN	kallikrein-related peptidase 4	22			S -> A (in dbSNP:rs1654551). {ECO:0000269|PubMed:15235027}.		amelogenesis (GO:0097186)|extracellular matrix disassembly (GO:0022617)|protein catabolic process (GO:0030163)|proteolysis (GO:0006508)	extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(8)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00624)|GBM - Glioblastoma multiforme(134;0.00878)		CAGAGACGAGCGATCCTGAGG	0.637													C|||	1211	0.241813	0.0666	0.4078	5008	,	,		11864	0.1071		0.4672	False		,,,				2504	0.2679				p.S22S		Atlas-SNP	.											KLK4,colon,carcinoma,0,2	KLK4	46	2	0			c.G66T						PASS	.	C		550,3856	244.3+/-253.7	34,482,1687	89.0	99.0	95.0		66	-1.4	0.0	19	dbSNP_89	95	4082,4518	547.4+/-385.2	959,2164,1177	no	coding-synonymous	KLK4	NM_004917.3		993,2646,2864	AA,AC,CC		47.4651,12.483,35.6143		22/255	51412666	4632,8374	2203	4300	6503	SO:0001819	synonymous_variant	9622	exon2			GACGAGCGATCCT	AF113141	CCDS12809.1	19q13.41	2014-09-04	2006-10-27		ENSG00000167749	ENSG00000167749		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6365	protein-coding gene	gene with protein product		603767	"""kallikrein 4 (prostase, enamel matrix, prostate)"""	PRSS17		10077646, 10438493, 16800724, 10863090, 9465170	Standard	XM_005259441		Approved	EMSP, EMSP1, PSTS, KLK-L1	uc002pua.1	Q9Y5K2	OTTHUMG00000182964	ENST00000324041.1:c.66G>T	19.37:g.51412666C>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	108	61	0.564815	NM_004917	Q4VB16|Q96RU5|Q9GZL6|Q9UBJ6	Silent	SNP	ENST00000324041.1	37	CCDS12809.1																																																																																			C|0.685;A|0.315	0.315	strong		0.637	KLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464449.1	NM_004917	
SALL1	6299	hgsc.bcm.edu	37	16	51172786	51172786	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:51172786G>A	ENST00000251020.4	-	2	3380	c.3347C>T	c.(3346-3348)tCt>tTt	p.S1116F	SALL1_ENST00000440970.1_Missense_Mutation_p.S1019F|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1116					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GGATGTGGCAGAGGAAGACAG	0.567																																					p.S1116F	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C3347T						PASS	.						91.0	76.0	81.0					16																	51172786		2198	4300	6498	SO:0001583	missense	6299	exon2			GTGGCAGAGGAAG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3347C>T	16.37:g.51172786G>A	ENSP00000251020:p.Ser1116Phe	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.576037	0.86645	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.07800	3.16;3.17	5.42	5.42	0.78866	.	0.104526	0.64402	D	0.000003	T	0.07683	0.0193	N	0.14661	0.345	0.58432	D	0.999999	P	0.44478	0.836	B	0.40329	0.326	T	0.26430	-1.0103	10	0.59425	D	0.04	.	19.2277	0.93824	0.0:0.0:1.0:0.0	.	1116	Q9NSC2	SALL1_HUMAN	F	1116;1019;1080	ENSP00000251020:S1116F;ENSP00000407914:S1019F	ENSP00000251020:S1116F	S	-	2	0	SALL1	49730287	1.000000	0.71417	0.994000	0.49952	0.970000	0.65996	7.866000	0.87056	2.529000	0.85273	0.563000	0.77884	TCT	.	.	none		0.567	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
EPHB4	2050	hgsc.bcm.edu	37	7	100403131	100403131	+	Missense_Mutation	SNP	C	C	A	rs35638378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100403131C>A	ENST00000358173.3	-	15	3138	c.2670G>T	c.(2668-2670)gaG>gaT	p.E890D	EPHB4_ENST00000360620.3_Missense_Mutation_p.E890D	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	890	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in dbSNP:rs35638378). {ECO:0000269|PubMed:17344846}.		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)					ACCCGCCATTCTCCCGGGCCA	0.652													C|||	13	0.00259585	0.0	0.0043	5008	,	,		15943	0.0		0.006	False		,,,				2504	0.0041				p.E890D	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G2670T						PASS	.	C	ASP/GLU	7,4399	14.3+/-33.2	0,7,2196	53.0	60.0	58.0		2670	2.3	1.0	7	dbSNP_126	58	80,8520	44.9+/-103.4	1,78,4221	yes	missense	EPHB4	NM_004444.4	45	1,85,6417	AA,AC,CC		0.9302,0.1589,0.6689	benign	890/988	100403131	87,12919	2203	4300	6503	SO:0001583	missense	2050	exon15			GCCATTCTCCCGG	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.2670G>T	7.37:g.100403131C>A	ENSP00000350896:p.Glu890Asp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	100	46	0.46	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	9.167	1.020236	0.19433	0.001589	0.009302	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.76316	-1.01;-0.79	5.28	2.33	0.28932	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.120844	0.36972	N	0.002303	T	0.41488	0.1161	N	0.05031	-0.125	0.28430	N	0.917311	B;B	0.09022	0.002;0.001	B;B	0.12156	0.007;0.002	T	0.23261	-1.0193	10	0.13470	T	0.59	.	4.4028	0.11395	0.0:0.5648:0.1653:0.2699	rs35638378	890;890	Q96L35;P54760	.;EPHB4_HUMAN	D	890	ENSP00000353833:E890D;ENSP00000350896:E890D	ENSP00000350896:E890D	E	-	3	2	EPHB4	100241067	0.733000	0.28132	1.000000	0.80357	0.923000	0.55619	0.224000	0.17738	0.625000	0.30304	-0.258000	0.10820	GAG	C|0.993;A|0.007	0.007	strong		0.652	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
CHGB	1114	hgsc.bcm.edu	37	20	5903067	5903067	+	Missense_Mutation	SNP	T	T	A	rs6085324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5903067T>A	ENST00000378961.4	+	4	481	c.277T>A	c.(277-279)Tcg>Acg	p.S93T		NM_001819.2	NP_001810.2	P05060	SCG1_HUMAN	chromogranin B (secretogranin 1)	93			S -> T (in dbSNP:rs6085324). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.			extracellular region (GO:0005576)|secretory granule (GO:0030141)	hormone activity (GO:0005179)	p.S93T(1)		breast(7)|kidney(2)|large_intestine(8)|lung(19)|ovary(1)|pancreas(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	47						AGCTGATGCCTCGGAAGCCCA	0.493													T|||	1165	0.232628	0.0749	0.2392	5008	,	,		18246	0.379		0.2594	False		,,,				2504	0.2628				p.S93T		Atlas-SNP	.											CHGB,colon,carcinoma,0,2	CHGB	112	2	1	Substitution - Missense(1)	stomach(1)	c.T277A						PASS	.	T	THR/SER	530,3876	240.6+/-251.3	39,452,1712	52.0	53.0	53.0		277	0.7	0.0	20	dbSNP_114	53	2285,6315	378.2+/-338.8	307,1671,2322	yes	missense	CHGB	NM_001819.2	58	346,2123,4034	AA,AT,TT		26.5698,12.0291,21.6439	possibly-damaging	93/678	5903067	2815,10191	2203	4300	6503	SO:0001583	missense	1114	exon4			GATGCCTCGGAAG		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.277T>A	20.37:g.5903067T>A	ENSP00000368244:p.Ser93Thr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	85	41	0.482353	NM_001819	A8K021|Q59EU9|Q6IBS6|Q9BQV6|Q9UC25|Q9UJA6	Missense_Mutation	SNP	ENST00000378961.4	37	CCDS13092.1	529	0.24221611721611722	48	0.0975609756097561	78	0.2154696132596685	206	0.36013986013986016	197	0.2598944591029024	T	9.771	1.172828	0.21704	0.120291	0.265698	ENSG00000089199	ENST00000378961;ENST00000455042	T;T	0.02067	4.47;4.47	4.26	0.681	0.17986	.	0.988393	0.08223	N	0.978839	T	0.00012	0.0000	M	0.62723	1.935	0.80722	P	0.0	B	0.17268	0.021	B	0.19666	0.026	T	0.41179	-0.9523	9	0.25106	T	0.35	-4.0E-4	3.7604	0.08602	0.1617:0.1884:0.0:0.6498	rs6085324	93	P05060	SCG1_HUMAN	T	93;73	ENSP00000368244:S93T;ENSP00000416643:S73T	ENSP00000368244:S93T	S	+	1	0	CHGB	5851067	0.003000	0.15002	0.000000	0.03702	0.007000	0.05969	0.677000	0.25262	0.081000	0.16988	0.460000	0.39030	TCG	T|0.776;A|0.224	0.224	strong		0.493	CHGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077897.2	NM_001819	
PCDHAC1	56135	hgsc.bcm.edu	37	5	140306903	140306903	+	Silent	SNP	C	C	T	rs149532133	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140306903C>T	ENST00000253807.2	+	1	426	c.426C>T	c.(424-426)cgC>cgT	p.R142R	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHAC1_ENST00000409700.3_Silent_p.R142R|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	142	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGGAGCCCGCTTTACTCTCC	0.577													c|||	47	0.00938498	0.0	0.0086	5008	,	,		18763	0.001		0.007	False		,,,				2504	0.0337				p.R142R		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.C426T						PASS	.	C	,,,,,,,,,,,,,,,,,	6,4400	8.1+/-20.4	0,6,2197	67.0	68.0	68.0		426,,,,,,,,,,,,,,,,,426	0.5	1.0	5	dbSNP_134	68	103,8497	55.2+/-116.2	1,101,4198	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	1,107,6395	TT,TC,CC		1.1977,0.1362,0.8381	,,,,,,,,,,,,,,,,,	142/964,,,,,,,,,,,,,,,,,142/819	140306903	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			AGCCCGCTTTACT	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.426C>T	5.37:g.140306903C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	110	66	0.6	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			C|0.992;T|0.008	0.008	strong		0.577	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
DAXX	1616	hgsc.bcm.edu	37	6	33288271	33288271	+	Silent	SNP	A	A	G	rs1059231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33288271A>G	ENST00000374542.5	-	4	1341	c.1137T>C	c.(1135-1137)taT>taC	p.Y379Y	ZBTB22_ENST00000431845.2_5'Flank|DAXX_ENST00000477162.1_5'UTR|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000414083.2_Silent_p.Y304Y|DAXX_ENST00000266000.6_Silent_p.Y379Y	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	379	Interaction with histone H3.3.|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						GCAACATTGCATATTTGGAGA	0.552			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM								A|||	1106	0.220847	0.0182	0.3415	5008	,	,		18188	0.2619		0.2922	False		,,,				2504	0.2935				p.Y391Y		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.T1173C						PASS	.	A	,,	277,4129	154.4+/-187.8	5,267,1931	94.0	87.0	90.0		1137,1173,1137	2.1	1.0	6	dbSNP_86	90	2570,6030	417.9+/-352.6	398,1774,2128	no	coding-synonymous,coding-synonymous,coding-synonymous	DAXX	NM_001141969.1,NM_001141970.1,NM_001350.4	,,	403,2041,4059	GG,GA,AA		29.8837,6.2869,21.8899	,,	379/741,391/753,379/741	33288271	2847,10159	2203	4300	6503	SO:0001819	synonymous_variant	1616	exon4			CATTGCATATTTG	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1137T>C	6.37:g.33288271A>G		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	47	16	0.340426	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	CCDS4776.1																																																																																			A|0.778;G|0.222	0.222	strong		0.552	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
GRXCR1	389207	hgsc.bcm.edu	37	4	42895308	42895308	+	Missense_Mutation	SNP	G	G	A	rs78136490	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:42895308G>A	ENST00000399770.2	+	1	25	c.25G>A	c.(25-27)Gaa>Aaa	p.E9K	RN7SKP82_ENST00000516786.1_RNA	NM_001080476.2	NP_001073945.1	A8MXD5	GRCR1_HUMAN	glutaredoxin, cysteine rich 1	9			E -> K (in dbSNP:rs78136490). {ECO:0000269|PubMed:20137778}.		auditory receptor cell differentiation (GO:0042491)|cell redox homeostasis (GO:0045454)|inner ear receptor cell development (GO:0060119)|inner ear receptor stereocilium organization (GO:0060122)|negative regulation of phosphatase activity (GO:0010923)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of sound (GO:0007605)|vestibular receptor cell development (GO:0060118)	kinocilium (GO:0060091)|stereocilium (GO:0032420)	electron carrier activity (GO:0009055)|protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(22)|ovary(1)|prostate(2)|skin(1)	32						GATGAAGCCAGAAAGTGACAG	0.517													G|||	617	0.123203	0.2307	0.0648	5008	,	,		20255	0.1567		0.0716	False		,,,				2504	0.0378				p.E9K		Atlas-SNP	.											.	GRXCR1	78	.	0			c.G25A						PASS	.	G	LYS/GLU	732,3324		67,598,1363	91.0	99.0	96.0		25	5.0	0.9	4	dbSNP_131	96	548,7810		13,522,3644	yes	missense	GRXCR1	NM_001080476.2	56	80,1120,5007	AA,AG,GG		6.5566,18.0473,10.3109	possibly-damaging	9/291	42895308	1280,11134	2028	4179	6207	SO:0001583	missense	389207	exon1			AAGCCAGAAAGTG		CCDS43225.1	4p14	2014-06-12			ENSG00000215203	ENSG00000215203			31673	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 88"""	613283	"""deafness, autosomal recessive 25"""	DFNB25		20137778	Standard	NM_001080476		Approved	PPP1R88	uc003gwt.3	A8MXD5	OTTHUMG00000160434	ENST00000399770.2:c.25G>A	4.37:g.42895308G>A	ENSP00000382670:p.Glu9Lys	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	146	66	0.452055	NM_001080476		Missense_Mutation	SNP	ENST00000399770.2	37	CCDS43225.1	276	0.12637362637362637	117	0.23780487804878048	23	0.06353591160220995	80	0.13986013986013987	56	0.07387862796833773	G	11.87	1.769118	0.31320	0.180473	0.065566	ENSG00000215203	ENST00000399770	T	0.36878	1.23	5.83	4.99	0.66335	.	0.209202	0.40554	U	0.001072	T	0.00012	0.0000	L	0.50333	1.59	0.23376	P	0.99780957	B	0.26635	0.155	B	0.15870	0.014	T	0.14980	-1.0453	9	0.23302	T	0.38	-2.6283	16.1478	0.81583	0.0:0.1334:0.8666:0.0	.	9	A8MXD5	GRCR1_HUMAN	K	9	ENSP00000382670:E9K	ENSP00000382670:E9K	E	+	1	0	GRXCR1	42590065	0.995000	0.38212	0.896000	0.35187	0.018000	0.09664	5.087000	0.64480	1.451000	0.47736	0.650000	0.86243	GAA	G|0.906;A|0.094	0.094	strong		0.517	GRXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360576.1	NM_001080476	
LRRC16B	90668	hgsc.bcm.edu	37	14	24527220	24527220	+	Silent	SNP	C	C	T	rs4982853	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24527220C>T	ENST00000342740.5	+	16	1423	c.1269C>T	c.(1267-1269)taC>taT	p.Y423Y	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	423						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GCAGCGCCTACACACTGAGCC	0.657											OREG0022615	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	998	0.199281	0.1014	0.2032	5008	,	,		18014	0.4306		0.0616	False		,,,				2504	0.2321				p.Y423Y		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1269T						PASS	.	C		442,3964	202.8+/-225.5	21,400,1782	64.0	68.0	67.0		1269	4.2	1.0	14	dbSNP_111	67	476,8124	137.6+/-194.5	11,454,3835	no	coding-synonymous	LRRC16B	NM_138360.3		32,854,5617	TT,TC,CC		5.5349,10.0318,7.0583		423/1373	24527220	918,12088	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon16			CGCCTACACACTG	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1269C>T	14.37:g.24527220C>T		Somatic	97	0	0	772	WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.898;T|0.102	0.102	strong		0.657	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
AHSG	197	hgsc.bcm.edu	37	3	186338382	186338382	+	Missense_Mutation	SNP	G	G	C	rs4918	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:186338382G>C	ENST00000273784.5	+	7	846	c.770G>C	c.(769-771)aGc>aCc	p.S257T	AHSG_ENST00000411641.2_Missense_Mutation_p.S256T	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	256					acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		CAGCCCGTGAGCTCACAGCCC	0.597													.|||	3574	0.713658	0.7088	0.5879	5008	,	,		19708	0.745		0.6759	False		,,,				2504	0.816				p.S256T		Atlas-SNP	.											.	AHSG	40	.	0			c.G767C	GRCh37	CM052828	AHSG	M	rs4918	PASS	.	C	THR/SER	2946,1460	471.5+/-356.1	968,1010,225	115.0	115.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	767	-3.1	0.0	3	dbSNP_52	115	5604,2996	463.7+/-366.0	1822,1960,518	yes	missense	AHSG	NM_001622.2	58	2790,2970,743	CC,CG,GG		34.8372,33.1366,34.2611	benign	256/368	186338382	8550,4456	2203	4300	6503	SO:0001583	missense	197	exon7			CCGTGAGCTCACA	D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.770G>C	3.37:g.186338382G>C	ENSP00000273784:p.Ser257Thr	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	37		1507	0.690018315018315	340	0.6910569105691057	238	0.6574585635359116	434	0.7587412587412588	495	0.6530343007915568	c	1.750	-0.489521	0.04352	0.668634	0.651628	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.04917	3.53;3.53	5.32	-3.06	0.05379	.	1.592110	0.03917	N	0.282849	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	0.20773	-1.0265	8	0.15952	T	0.53	-0.5104	2.9594	0.05887	0.1293:0.4105:0.1329:0.3273	rs4918;rs1130659;rs1344306;rs2681429;rs3189769;rs17348276;rs17349454;rs17846429;rs17857414;rs17859477;rs52795137;rs4918	322;257	F5H0Q5;C9JV77	.;.	T	256;322;257	ENSP00000393887:S256T;ENSP00000273784:S257T	ENSP00000273784:S257T	S	+	2	0	AHSG	187821076	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.600000	0.05693	-1.169000	0.02772	-1.599000	0.00816	AGC	G|0.337;C|0.663	0.663	strong		0.597	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622	
NBPF15	284565	hgsc.bcm.edu	37	1	148594563	148594563	+	Missense_Mutation	SNP	G	G	T	rs146229961		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:148594563G>T	ENST00000369187.3	+	19	2425	c.1936G>T	c.(1936-1938)Gtg>Ttg	p.V646L	NBPF15_ENST00000442702.2_Missense_Mutation_p.V646L	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	646	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					CGCCCTTTACGTGGACAATAG	0.443																																					p.V646L		Atlas-SNP	.											NBPF15,brain,glioma,0,1	NBPF15	20	1	0			c.G1936T						scavenged	.						73.0	97.0	89.0					1																	148594563		2159	4285	6444	SO:0001583	missense	284565	exon19			CTTTACGTGGACA	BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"""neuroblastoma breakpoint family"""	28791	protein-coding gene	gene with protein product		610414, 614005	"""neuroblastoma breakpoint family, member 16"""	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1936G>T	1.37:g.148594563G>T	ENSP00000358188:p.Val646Leu	Somatic	457	41	0.0897155		WXS	Illumina HiSeq	Phase_I	486	36	0.0740741	NM_173638	Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	3.518	-0.098353	0.07010	.	.	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.10668	2.85;2.85	0.502	-1.0	0.10196	DUF1220 (2);	.	.	.	.	T	0.04048	0.0113	M	0.77103	2.36	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.39563	-0.9608	8	0.51188	T	0.08	.	.	.	.	.	646	Q8N660	NBPFF_HUMAN	L	646	ENSP00000416864:V646L;ENSP00000358188:V646L	ENSP00000358188:V646L	V	+	1	0	NBPF15	146861187	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.793000	0.01755	-0.873000	0.04032	-1.415000	0.01116	GTG	G|0.996;T|0.005	0.005	strong		0.443	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638	
PRRG4	79056	hgsc.bcm.edu	37	11	32852167	32852167	+	Missense_Mutation	SNP	C	C	T	rs61889489	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:32852167C>T	ENST00000257836.3	+	2	345	c.92C>T	c.(91-93)gCg>gTg	p.A31V		NM_024081.5	NP_076986.1	Q9BZD6	TMG4_HUMAN	proline rich Gla (G-carboxyglutamic acid) 4 (transmembrane)	31						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)					TCTAAGCATGCGGGAGAAGAA	0.498													C|||	213	0.0425319	0.0098	0.036	5008	,	,		14902	0.0109		0.0795	False		,,,				2504	0.0859				p.A31V		Atlas-SNP	.											.	PRRG4	15	.	0			c.C92T						PASS	.	C	VAL/ALA	80,4324	69.2+/-107.0	0,80,2122	93.0	84.0	87.0		92	1.0	0.0	11	dbSNP_129	87	720,7878	176.0+/-226.0	30,660,3609	yes	missense	PRRG4	NM_024081.5	64	30,740,5731	TT,TC,CC		8.374,1.8165,6.1529	benign	31/227	32852167	800,12202	2202	4299	6501	SO:0001583	missense	79056	exon2			AGCATGCGGGAGA	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.92C>T	11.37:g.32852167C>T	ENSP00000257836:p.Ala31Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	53	21	0.396226	NM_024081		Missense_Mutation	SNP	ENST00000257836.3	37	CCDS7881.1	95	0.043498168498168496	5	0.01016260162601626	12	0.03314917127071823	10	0.017482517482517484	68	0.08970976253298153	C	3.274	-0.148515	0.06627	0.018165	0.08374	ENSG00000135378	ENST00000257836	D	0.97831	-4.56	5.05	1.03	0.20045	.	0.370813	0.26187	N	0.025836	T	0.47002	0.1422	L	0.46157	1.445	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.68949	-0.5274	10	0.10636	T	0.68	-3.5083	4.6384	0.12536	0.1863:0.5711:0.0:0.2426	rs61889489	31	Q9BZD6	TMG4_HUMAN	V	31	ENSP00000257836:A31V	ENSP00000257836:A31V	A	+	2	0	PRRG4	32808743	0.019000	0.18553	0.019000	0.16419	0.010000	0.07245	0.040000	0.13905	-0.068000	0.12953	-0.812000	0.03155	GCG	C|0.945;T|0.055	0.055	strong		0.498	PRRG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388446.1	NM_024081	
C2orf69	205327	hgsc.bcm.edu	37	2	200776353	200776353	+	Missense_Mutation	SNP	T	T	G	rs62178345	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:200776353T>G	ENST00000319974.5	+	1	375	c.192T>G	c.(190-192)gaT>gaG	p.D64E	AC073043.1_ENST00000594069.1_RNA|C2orf69_ENST00000491721.1_3'UTR	NM_153689.5	NP_710156.3	Q8N8R5	CB069_HUMAN	chromosome 2 open reading frame 69	64						extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)|stomach(1)|urinary_tract(1)	11						CTGGAGCCGATCCGCAGCGCA	0.731													T|||	440	0.0878594	0.087	0.1167	5008	,	,		14099	0.0		0.175	False		,,,				2504	0.0695				p.D64E		Atlas-SNP	.											.	C2orf69	17	.	0			c.T192G						PASS	.						4.0	7.0	6.0					2																	200776353		642	1508	2150	SO:0001583	missense	205327	exon1			AGCCGATCCGCAG		CCDS46482.1	2q33.1	2008-08-08			ENSG00000178074	ENSG00000178074			26799	protein-coding gene	gene with protein product	"""hypothetical protein FLJ38973"""					12477932	Standard	NM_153689		Approved	FLJ38973	uc010zhb.2	Q8N8R5	OTTHUMG00000154480	ENST00000319974.5:c.192T>G	2.37:g.200776353T>G	ENSP00000312770:p.Asp64Glu	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	24	10	0.416667	NM_153689	Q8NE30	Missense_Mutation	SNP	ENST00000319974.5	37	CCDS46482.1	221	0.10119047619047619	42	0.08536585365853659	50	0.13812154696132597	8	0.013986013986013986	121	0.15963060686015831	T	12.63	1.996666	0.35226	.	.	ENSG00000178074	ENST00000319974	.	.	.	4.91	-3.14	0.05250	.	0.245514	0.38492	N	0.001678	T	0.00109	0.0003	N	0.21448	0.665	0.32198	P	0.5782510000000001	B	0.12630	0.006	B	0.17722	0.019	T	0.11867	-1.0570	8	0.22706	T	0.39	-11.8373	6.859	0.24056	0.0:0.4206:0.2233:0.3561	rs62178345	64	Q8N8R5	CB069_HUMAN	E	64	.	ENSP00000312770:D64E	D	+	3	2	C2orf69	200484598	0.976000	0.34144	0.964000	0.40570	0.447000	0.32167	-0.302000	0.08221	-0.558000	0.06118	-1.013000	0.02462	GAT	T|0.898;G|0.102	0.102	strong		0.731	C2orf69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335446.1	NM_153689	
DENND1C	79958	hgsc.bcm.edu	37	19	6468907	6468907	+	Missense_Mutation	SNP	G	G	A	rs35001260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6468907G>A	ENST00000381480.2	-	20	1577	c.1465C>T	c.(1465-1467)Cgc>Tgc	p.R489C	DENND1C_ENST00000543576.1_Missense_Mutation_p.R445C	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	489			R -> C (in dbSNP:rs35001260).		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						CGGTCTGAGCGGCTGGGGAGG	0.607													G|||	50	0.00998403	0.0015	0.0058	5008	,	,		13199	0.0		0.0229	False		,,,				2504	0.0215				p.R489C		Atlas-SNP	.											.	DENND1C	93	.	0			c.C1465T						PASS	.	G	CYS/ARG	10,3842		0,10,1916	25.0	29.0	28.0		1465	4.7	1.0	19	dbSNP_126	28	170,8058		3,164,3947	yes	missense	DENND1C	NM_024898.2	180	3,174,5863	AA,AG,GG		2.0661,0.2596,1.4901	probably-damaging	489/802	6468907	180,11900	1926	4114	6040	SO:0001583	missense	79958	exon20			CTGAGCGGCTGGG	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.1465C>T	19.37:g.6468907G>A	ENSP00000370889:p.Arg489Cys	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	60	28	0.466667	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	20	0.009157509157509158	0	0.0	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	G	16.60	3.168788	0.57584	0.002596	0.020661	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11821	2.91;2.74	4.69	4.69	0.59074	.	0.327353	0.28815	N	0.014059	T	0.09598	0.0236	L	0.53249	1.67	0.47123	D	0.999325	D	0.89917	1.0	P	0.56278	0.795	T	0.00171	-1.1959	10	0.62326	D	0.03	-15.0887	13.1025	0.59228	0.0:0.0:1.0:0.0	rs35001260;rs35001260	489	Q8IV53	DEN1C_HUMAN	C	489;445	ENSP00000370889:R489C;ENSP00000437805:R445C	ENSP00000370889:R489C	R	-	1	0	DENND1C	6419907	1.000000	0.71417	1.000000	0.80357	0.062000	0.15995	2.749000	0.47492	2.167000	0.68274	0.491000	0.48974	CGC	G|0.983;A|0.017	0.017	strong		0.607	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
FAM205A	259308	hgsc.bcm.edu	37	9	34724241	34724241	+	Missense_Mutation	SNP	C	C	A	rs3739881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:34724241C>A	ENST00000378788.3	-	4	3035	c.2996G>T	c.(2995-2997)aGt>aTt	p.S999I		NM_001141917.1	NP_001135389.1	Q6ZU69	F205A_HUMAN	family with sequence similarity 205, member A	999				S -> I (in Ref. 1; BAC86357). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)	4						CATGTCCCCACTGGGCTGTGA	0.557													C|||	2012	0.401757	0.0666	0.4006	5008	,	,		20547	0.6181		0.4851	False		,,,				2504	0.547				p.S999I		Atlas-SNP	.											.	FAM205A	45	.	0			c.G2996T						PASS	.	C	ILE/SER	171,1213		8,155,529	48.0	39.0	42.0		2996	1.0	0.0	9	dbSNP_107	42	1541,1641		364,813,414	yes	missense	FAM205A	NM_001141917.1	142	372,968,943	AA,AC,CC		48.4287,12.3555,37.4945	probably-damaging	999/1336	34724241	1712,2854	692	1591	2283	SO:0001583	missense	259308	exon4			TCCCCACTGGGCT		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.2996G>T	9.37:g.34724241C>A	ENSP00000417711:p.Ser999Ile	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	193	100	0.518135	NM_001141917	A8MVW7	Missense_Mutation	SNP	ENST00000378788.3	37	CCDS55305.1	905	0.4143772893772894	45	0.09146341463414634	148	0.4088397790055249	334	0.583916083916084	378	0.49868073878627966	C	11.43	1.635610	0.29068	0.123555	0.484287	ENSG00000205108	ENST00000378788	T	0.23147	1.92	4.13	1.05	0.20165	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P	0.38110	0.618	B	0.36845	0.234	T	0.41787	-0.9489	8	0.39692	T	0.17	.	4.0474	0.09779	0.1829:0.6091:0.0:0.208	rs3739881;rs17747021	999	Q6ZU69	F205A_HUMAN	I	999	ENSP00000417711:S999I	ENSP00000417711:S999I	S	-	2	0	RP11-195F19.10	34714241	0.000000	0.05858	0.002000	0.10522	0.398000	0.30690	-0.722000	0.04958	0.099000	0.17552	-0.143000	0.13931	AGT	C|0.579;A|0.421	0.421	strong		0.557	FAM205A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001150.2	NM_001141917	
ZNF584	201514	hgsc.bcm.edu	37	19	58928309	58928309	+	Missense_Mutation	SNP	C	C	T	rs11668789	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58928309C>T	ENST00000306910.4	+	4	947	c.424C>T	c.(424-426)Cct>Tct	p.P142S	ZNF584_ENST00000593920.1_Missense_Mutation_p.P97S|ZNF584_ENST00000599238.1_3'UTR|ZNF584_ENST00000596921.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA|ZNF584_ENST00000322834.7_3'UTR	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	142			P -> S (in dbSNP:rs11668789).		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(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		AGCTTTCCCACCTGGTTCCAG	0.522													C|||	752	0.15016	0.118	0.1772	5008	,	,		18037	0.0546		0.2485	False		,,,				2504	0.1718				p.P142S		Atlas-SNP	.											.	ZNF584	31	.	0			c.C424T						PASS	.	C	SER/PRO	511,3895	233.9+/-246.9	37,437,1729	143.0	109.0	121.0		424	-0.4	0.0	19	dbSNP_120	121	1793,6807	323.3+/-315.9	187,1419,2694	yes	missense	ZNF584	NM_173548.1	74	224,1856,4423	TT,TC,CC		20.8488,11.5978,17.7149	benign	142/422	58928309	2304,10702	2203	4300	6503	SO:0001583	missense	201514	exon4			TTCCCACCTGGTT	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"""Zinc fingers, C2H2-type"", ""-"""	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.424C>T	19.37:g.58928309C>T	ENSP00000306756:p.Pro142Ser	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	90	45	0.5	NM_173548	A8K203	Missense_Mutation	SNP	ENST00000306910.4	37	CCDS12979.1	350	0.16025641025641027	73	0.1483739837398374	67	0.1850828729281768	32	0.055944055944055944	178	0.23482849604221637	C	1.863	-0.462052	0.04508	0.115978	0.208488	ENSG00000171574	ENST00000306910;ENST00000354635	T	0.13901	2.55	2.96	-0.435	0.12279	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.14438	0.01	B	0.06405	0.002	T	0.46965	-0.9153	8	0.25106	T	0.35	.	2.5653	0.04782	0.231:0.5029:0.0:0.2661	rs11668789;rs12979849;rs11668789	142	Q8IVC4	ZN584_HUMAN	S	142;1	ENSP00000306756:P142S	ENSP00000306756:P142S	P	+	1	0	ZNF584	63620121	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-1.145000	0.03194	0.008000	0.14787	0.462000	0.41574	CCT	C|0.831;T|0.169	0.169	strong		0.522	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548	
TTC29	83894	hgsc.bcm.edu	37	4	147824864	147824864	+	Missense_Mutation	SNP	G	G	A	rs17610219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:147824864G>A	ENST00000325106.4	-	6	644	c.418C>T	c.(418-420)Cat>Tat	p.H140Y	TTC29_ENST00000513335.1_Missense_Mutation_p.H166Y|TTC29_ENST00000398886.4_Missense_Mutation_p.H166Y	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	140			H -> Y (in dbSNP:rs17610219). {ECO:0000269|Ref.1, ECO:0000269|Ref.2}.							breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					AAGTTATTATGTACATCTTCG	0.388													A|||	2745	0.548123	0.6581	0.5908	5008	,	,		17171	0.5526		0.3598	False		,,,				2504	0.5583				p.H140Y		Atlas-SNP	.											.	TTC29	63	.	0			c.C418T						PASS	.	A	TYR/HIS	2143,1549		631,881,334	51.0	49.0	50.0		418	5.6	0.9	4	dbSNP_123	50	3041,5165		543,1955,1605	yes	missense	TTC29	NM_031956.2	83	1174,2836,1939	AA,AG,GG		37.0583,41.9556,43.5703	benign	140/476	147824864	5184,6714	1846	4103	5949	SO:0001583	missense	83894	exon6			TATTATGTACATC	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"""Tetratricopeptide (TTC) repeat domain containing"""	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.418C>T	4.37:g.147824864G>A	ENSP00000316740:p.His140Tyr	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	110	108	0.981818	NM_031956	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	1071	0.49038461538461536	317	0.6443089430894309	184	0.5082872928176796	312	0.5454545454545454	258	0.3403693931398417	A	0.010	-1.746363	0.00669	0.580444	0.370583	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000398883;ENST00000504425	T;T;T;T	0.15603	2.41;2.41;2.41;2.41	5.62	5.62	0.85841	.	0.133718	0.52532	N	0.000067	T	0.00012	0.0000	N	0.00052	-2.395	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43245	-0.9403	9	0.02654	T	1	-9.3104	10.4294	0.44398	0.9266:0.0:0.0734:0.0	rs17610219;rs17856717;rs56419348;rs57564073;rs17610219	140;166;140	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	Y	166;166;140;140;140	ENSP00000423505:H166Y;ENSP00000381861:H166Y;ENSP00000316740:H140Y;ENSP00000425778:H140Y	ENSP00000316740:H140Y	H	-	1	0	TTC29	148044314	0.997000	0.39634	0.939000	0.37840	0.040000	0.13550	4.637000	0.61346	0.967000	0.38186	-0.269000	0.10298	CAT	G|0.507;A|0.493	0.493	strong		0.388	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956	
ZEB2	9839	hgsc.bcm.edu	37	2	145157593	145157593	+	Silent	SNP	T	T	C	rs146673563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:145157593T>C	ENST00000558170.2	-	8	2345	c.1161A>G	c.(1159-1161)ttA>ttG	p.L387L	ZEB2_ENST00000539609.3_Silent_p.L363L|ZEB2_ENST00000409487.3_Silent_p.L387L|ZEB2_ENST00000303660.4_Silent_p.L387L	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	387					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		TAATTTTAAGTAAGCCTGTCT	0.383													T|||	4	0.000798722	0.0	0.0029	5008	,	,		20112	0.0		0.002	False		,,,				2504	0.0				p.L387L	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											ZEB2,NS,carcinoma,0,1	ZEB2	218	1	0			c.A1161G						PASS	.	T	,	0,4406		0,0,2203	101.0	103.0	102.0		1089,1161	1.8	1.0	2	dbSNP_134	102	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous,coding-synonymous	ZEB2	NM_001171653.1,NM_014795.3	,	0,13,6490	CC,CT,TT		0.1512,0.0,0.1	,	363/1191,387/1215	145157593	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	9839	exon8			TTTAAGTAAGCCT	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	14881	protein-coding gene	gene with protein product	"""SMAD interacting protein 1"""	605802	"""zinc finger homeobox 1b"""	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.1161A>G	2.37:g.145157593T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Silent	SNP	ENST00000558170.2	37	CCDS2186.1																																																																																			T|0.999;C|0.001	0.001	strong		0.383	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795	
BSPRY	54836	hgsc.bcm.edu	37	9	116132275	116132275	+	Silent	SNP	G	G	A	rs3750529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:116132275G>A	ENST00000374183.4	+	6	1101	c.1062G>A	c.(1060-1062)ctG>ctA	p.L354L	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	354	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CAGCCCAGCTGGGTGTAGTGC	0.612													G|||	440	0.0878594	0.1293	0.0432	5008	,	,		18726	0.0317		0.0785	False		,,,				2504	0.1309				p.L354L		Atlas-SNP	.											.	BSPRY	21	.	0			c.G1062A						PASS	.	G		384,3506		17,350,1578	36.0	38.0	37.0		1062	3.6	1.0	9	dbSNP_107	37	708,7566		26,656,3455	no	coding-synonymous	BSPRY	NM_017688.2		43,1006,5033	AA,AG,GG		8.5569,9.8715,8.9773		354/403	116132275	1092,11072	1945	4137	6082	SO:0001819	synonymous_variant	54836	exon6			CCAGCTGGGTGTA	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.1062G>A	9.37:g.116132275G>A		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	60	34	0.566667	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Silent	SNP	ENST00000374183.4	37	CCDS43868.1																																																																																			G|0.919;A|0.081	0.081	strong		0.612	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
NOX3	50508	hgsc.bcm.edu	37	6	155750035	155750035	+	Silent	SNP	C	C	T	rs231954	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:155750035C>T	ENST00000159060.2	-	9	1140	c.1038G>A	c.(1036-1038)gaG>gaA	p.E346E		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	346	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)		TGAAAAAGTCCTCCTGGGGGG	0.622													T|||	3695	0.737819	0.7549	0.6297	5008	,	,		15531	0.9137		0.5666	False		,,,				2504	0.7863				p.E346E		Atlas-SNP	.											.	NOX3	93	.	0			c.G1038A						PASS	.	T		3167,1239	423.6+/-340.2	1142,883,178	59.0	62.0	61.0		1038	0.0	1.0	6	dbSNP_79	61	4760,3840	538.4+/-383.4	1334,2092,874	no	coding-synonymous	NOX3	NM_015718.2		2476,2975,1052	TT,TC,CC		44.6512,28.1207,39.0512		346/569	155750035	7927,5079	2203	4300	6503	SO:0001819	synonymous_variant	50508	exon9			AAAGTCCTCCTGG	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.1038G>A	6.37:g.155750035C>T		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	93	19	0.204301	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																			C|0.349;T|0.651	0.651	strong		0.622	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
FNDC3A	22862	hgsc.bcm.edu	37	13	49776080	49776080	+	Silent	SNP	A	A	G	rs9316430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:49776080A>G	ENST00000492622.2	+	24	3437	c.3132A>G	c.(3130-3132)aaA>aaG	p.K1044K	FNDC3A_ENST00000398316.3_Silent_p.K988K|FNDC3A_ENST00000541916.1_Silent_p.K1044K	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1044	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		CTACTCCAAAATCTGTCCCAG	0.323													A|||	358	0.0714856	0.0552	0.0288	5008	,	,		16507	0.0754		0.0487	False		,,,				2504	0.1431				p.K1044K		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3132G						PASS	.	A	,	175,4231	112.9+/-151.0	4,167,2032	73.0	75.0	75.0		3132,2964	6.2	1.0	13	dbSNP_119	75	385,8215	122.7+/-181.7	3,379,3918	no	coding-synonymous,coding-synonymous	FNDC3A	NM_001079673.1,NM_014923.3	,	7,546,5950	GG,GA,AA		4.4767,3.9719,4.3057	,	1044/1199,988/1143	49776080	560,12446	2203	4300	6503	SO:0001819	synonymous_variant	22862	exon24			TCCAAAATCTGTC	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3132A>G	13.37:g.49776080A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	152	75	0.493421	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Silent	SNP	ENST00000492622.2	37	CCDS41886.1																																																																																			A|0.949;G|0.051	0.051	strong		0.323	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
DROSHA	29102	hgsc.bcm.edu	37	5	31423007	31423007	+	Silent	SNP	T	T	C	rs2287584	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:31423007T>C	ENST00000511367.2	-	28	3550	c.3306A>G	c.(3304-3306)ccA>ccG	p.P1102P	DROSHA_ENST00000344624.3_Silent_p.P1102P|DROSHA_ENST00000442743.1_Silent_p.P1065P|DROSHA_ENST00000513349.1_Silent_p.P1065P	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	1102	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TTTGTAGAACTGGAGAAGTTT	0.333													C|||	2268	0.452875	0.5643	0.3213	5008	,	,		20165	0.6667		0.2495	False		,,,				2504	0.3845				p.P1102P		Atlas-SNP	.											.	DROSHA	130	.	0			c.A3306G						PASS	.	C	,	1805,1841		450,905,468	69.0	69.0	69.0		3195,3306	0.3	1.0	5	dbSNP_100	69	1776,6368		184,1408,2480	no	coding-synonymous,coding-synonymous	DROSHA	NM_001100412.1,NM_013235.4	,	634,2313,2948	CC,CT,TT		21.8075,49.5063,30.3732	,	1065/1338,1102/1375	31423007	3581,8209	1823	4072	5895	SO:0001819	synonymous_variant	29102	exon28			TAGAACTGGAGAA	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.3306A>G	5.37:g.31423007T>C		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	51	22	0.431373	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Silent	SNP	ENST00000511367.2	37	CCDS47195.1																																																																																			T|0.554;C|0.446	0.446	strong		0.333	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
HLA-DQA1	3117	hgsc.bcm.edu	37	6	32609207	32609207	+	Missense_Mutation	SNP	C	C	T	rs1142324		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32609207C>T	ENST00000343139.5	+	2	305	c.203C>T	c.(202-204)gCc>gTc	p.A68V	HLA-DQA1_ENST00000374949.2_Missense_Mutation_p.A68V|HLA-DQA1_ENST00000395363.1_Missense_Mutation_p.A68V	NM_002122.3	NP_002113.2	P01909	DQA1_HUMAN	major histocompatibility complex, class II, DQ alpha 1	68	Alpha-1.		V -> A (in allele DQA1*01:01, allele DQA1*01:02, allele DQA1*01:03, allele DQA1*01:04, allele DQA1*01:05, allele DQA1*01:06 and allele DQA1*01:07; dbSNP:rs1142324).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			NS(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						AAGGAGACTGCCTGGCGGTGG	0.493																																					p.A68V		Atlas-SNP	.											HLA-DQA1,colon,carcinoma,0,1	HLA-DQA1	52	1	0			c.C203T						scavenged	.						105.0	93.0	97.0					6																	32609207		2190	4222	6412	SO:0001583	missense	3117	exon2			AGACTGCCTGGCG		CCDS4752.1	6p21.3	2013-01-11			ENSG00000196735	ENSG00000196735		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4942	protein-coding gene	gene with protein product		146880		HLA-DQA			Standard	NM_002122		Approved	CELIAC1	uc003obr.3	P01909	OTTHUMG00000031106	ENST00000343139.5:c.203C>T	6.37:g.32609207C>T	ENSP00000339398:p.Ala68Val	Somatic	20	20	1		WXS	Illumina HiSeq	Phase_I	97	19	0.195876	NM_002122	O19630|O19706|P01907|P01908|P04225|P04226|P05536|P79553|Q06751|Q29876|Q29994|Q2Q6Y6|Q2Q6Y7|Q2Q6Y8|Q2WCM3|Q30064|Q30067|Q30068|Q30070|Q30071|Q30072|Q30073|Q30086|Q30101|Q5Y7D5|Q5Y7F5|Q6ICU6|Q6PR46|Q6QDB1|Q860W2|Q860W4|Q9BD37|Q9TPM3|Q9UM31	Missense_Mutation	SNP	ENST00000343139.5	37	CCDS4752.1	1044|1044	0.47802197802197804|0.47802197802197804	192|192	0.3902439024390244|0.3902439024390244	215|215	0.5939226519337016|0.5939226519337016	285|285	0.4982517482517482|0.4982517482517482	352|352	0.46437994722955145|0.46437994722955145	.|.	0.008|0.008	-1.870289|-1.870289	0.00542|0.00542	.|.	.|.	ENSG00000196735|ENSG00000196735	ENST00000343139;ENST00000395364;ENST00000395363;ENST00000496318;ENST00000374949|ENST00000486548	T;T;T;T|.	0.00478|.	7.13;7.13;7.13;7.13|.	3.97|3.97	2.8|2.8	0.32819|0.32819	.|.	0.000000|.	0.64402|.	N|.	0.000003|.	T|T	0.01320|0.01320	0.0043|0.0043	N|N	0.00041|0.00041	-2.485|-2.485	0.46499|0.46499	P|P	9.299999999999864E-4|9.299999999999864E-4	B;B|.	0.13145|.	0.007;0.0|.	B;B|.	0.09377|.	0.004;0.001|.	T|T	0.45862|0.45862	-0.9232|-0.9232	9|4	0.02654|.	T|.	1|.	.|.	9.3519|9.3519	0.38142|0.38142	0.0:0.1002:0.0:0.8998|0.0:0.1002:0.0:0.8998	rs1142324;rs3188027;rs3205986;rs9272692;rs12722056;rs17840126;rs36219698|rs1142324;rs3188027;rs3205986;rs9272692;rs12722056;rs17840126;rs36219698	74;68|.	Q59F33;G4XQK2|.	.;.|.	V|S	68|41	ENSP00000339398:A68V;ENSP00000378767:A68V;ENSP00000437302:A68V;ENSP00000364087:A68V|.	ENSP00000339398:A68V|.	A|P	+|+	2|1	0|0	HLA-DQA1|HLA-DQA1	32717185|32717185	0.000000|0.000000	0.05858|0.05858	0.951000|0.951000	0.38953|0.38953	0.036000|0.036000	0.12997|0.12997	0.579000|0.579000	0.23788|0.23788	0.215000|0.215000	0.20761|0.20761	-1.349000|-1.349000	0.01238|0.01238	GCC|CCT	C|0.523;T|0.477	0.477	strong		0.493	HLA-DQA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076176.3	NM_002122	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144852379	144852379	+	3'UTR	SNP	G	G	T	rs113954821		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144852379G>T	ENST00000369354.3	-	0	7309				PDE4DIP_ENST00000369359.4_3'UTR|PDE4DIP_ENST00000530740.1_3'UTR|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.P2355H|PDE4DIP_ENST00000313382.9_3'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						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)		CTGCACAAAAGGGGGACAGGC	0.562			T	PDGFRB	MPD																																p.P2355H		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C7064A						PASS	.						44.0	40.0	41.0					1																	144852379		1568	3582	5150	SO:0001624	3_prime_UTR_variant	9659	exon44			ACAAAAGGGGGAC	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.*79C>A	1.37:g.144852379G>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	95	30	0.315789	NM_001198834	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	.	.	.	.	.	.	.	.	.	.	.	15.40	2.822099	0.50739	.	.	ENSG00000178104	ENST00000369356	T	0.01572	4.76	4.47	-0.263	0.12954	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.48502	-0.9030	6	0.87932	D	0	.	6.2958	0.21085	0.0:0.3301:0.3332:0.3368	.	.	.	.	H	2355	ENSP00000358363:P2355H	ENSP00000358363:P2355H	P	-	2	0	PDE4DIP	143563736	0.000000	0.05858	0.004000	0.12327	0.968000	0.65278	-0.211000	0.09332	0.382000	0.24878	0.549000	0.68633	CCT	G|0.500;T|0.500	0.500	weak		0.562	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
MYH6	4624	hgsc.bcm.edu	37	14	23852443	23852443	+	Silent	SNP	G	G	A	rs200662317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23852443G>A	ENST00000356287.3	-	36	5681	c.5652C>T	c.(5650-5652)gcC>gcT	p.A1884A	MYH6_ENST00000405093.3_Silent_p.A1884A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1884					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CCGCCTCCTCGGCCTGGCGCT	0.532													G|||	2	0.000399361	0.0	0.0	5008	,	,		12269	0.002		0.0	False		,,,				2504	0.0				p.A1884A		Atlas-SNP	.											.	MYH6	274	.	0			c.C5652T						PASS	.	G		0,4406		0,0,2203	84.0	74.0	78.0		5652	-7.8	0.9	14		78	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MYH6	NM_002471.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		1884/1940	23852443	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon37			CTCCTCGGCCTGG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5652C>T	14.37:g.23852443G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	97	47	0.484536	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			G|0.997;A|0.003	0.003	strong		0.532	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
ZNF646	9726	hgsc.bcm.edu	37	16	31090407	31090407	+	Missense_Mutation	SNP	G	G	C	rs35713203	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31090407G>C	ENST00000394979.2	+	1	3185	c.2762G>C	c.(2761-2763)gGa>gCa	p.G921A	ZNF646_ENST00000300850.5_Missense_Mutation_p.G921A			O15015	ZN646_HUMAN	zinc finger protein 646	921			G -> A (in dbSNP:rs35713203).		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						GAAGAGGAAGGAGTGGCAGAG	0.647													G|||	1763	0.352037	0.2057	0.3847	5008	,	,		19833	0.1121		0.3668	False		,,,				2504	0.7587				p.G921A		Atlas-SNP	.											.	ZNF646	133	.	0			c.G2762C						PASS	.	G	ALA/GLY	1048,3340		136,776,1282	24.0	25.0	25.0		2762	2.1	1.0	16	dbSNP_126	25	3027,5559		551,1925,1817	yes	missense	ZNF646	NM_014699.3	60	687,2701,3099	CC,CG,GG		35.2551,23.8833,31.409	probably-damaging	921/1833	31090407	4075,8899	2194	4293	6487	SO:0001583	missense	9726	exon2			AGGAAGGAGTGGC	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.2762G>C	16.37:g.31090407G>C	ENSP00000378429:p.Gly921Ala	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	18	0.409091	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		544	0.2490842490842491	103	0.20934959349593496	123	0.3397790055248619	47	0.08216783216783216	271	0.3575197889182058	G	0.986	-0.695558	0.03279	0.238833	0.352551	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.09911	2.93;2.95	5.15	2.06	0.26882	.	.	.	.	.	T	0.00012	0.0000	N	0.17082	0.46	0.28081	P	0.9321985	B	0.14438	0.01	B	0.16722	0.016	T	0.48293	-0.9048	8	0.11182	T	0.66	-5.6029	4.5844	0.12275	0.2051:0.1953:0.5996:0.0	rs35713203	921	O15015-2	.	A	921	ENSP00000300850:G921A;ENSP00000378429:G921A	ENSP00000300850:G921A	G	+	2	0	ZNF646	30997908	0.992000	0.36948	0.983000	0.44433	0.715000	0.41141	2.317000	0.43770	1.138000	0.42230	0.563000	0.77884	GGA	G|0.716;C|0.284	0.284	strong		0.647	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
SGK223	157285	hgsc.bcm.edu	37	8	8176554	8176554	+	Missense_Mutation	SNP	C	C	T	rs12549973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:8176554C>T	ENST00000520004.1	-	6	3595	c.3331G>A	c.(3331-3333)Gcg>Acg	p.A1111T	SGK223_ENST00000330777.4_Missense_Mutation_p.A1111T			Q86YV5	SG223_HUMAN		1113	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TCGGGCTCCGCCTGGTGGCTG	0.682													C|||	1496	0.298722	0.0825	0.3429	5008	,	,		10743	0.5446		0.2505	False		,,,				2504	0.3558				p.A1111T	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3331A						PASS	.	C	THR/ALA	473,3653		34,405,1624	67.0	75.0	73.0		3331	3.5	0.0	8	dbSNP_120	73	2333,6071		306,1721,2175	yes	missense	SGK223	NM_001080826.1	58	340,2126,3799	TT,TC,CC		27.7606,11.4639,22.3943	probably-damaging	1111/1403	8176554	2806,9724	2063	4202	6265	SO:0001583	missense	0	exon5			GCTCCGCCTGGTG																												ENST00000520004.1:c.3331G>A	8.37:g.8176554C>T	ENSP00000428054:p.Ala1111Thr	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	690	0.3159340659340659	57	0.11585365853658537	98	0.27071823204419887	344	0.6013986013986014	191	0.2519788918205805	C	13.13	2.145121	0.37825	0.114639	0.277606	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.65732	-0.17;-0.17	5.48	3.53	0.40419	Serine/threonine-protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.791425	0.12206	N	0.489775	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.26935	0.164	B	0.28465	0.09	T	0.46707	-0.9172	9	0.18710	T	0.47	.	10.1238	0.42637	0.2011:0.6845:0.1144:0.0	rs12549973	1111	Q86YV5	SG223_HUMAN	T	1111	ENSP00000330930:A1111T;ENSP00000428054:A1111T	ENSP00000330930:A1111T	A	-	1	0	AC068353.1	8213964	0.000000	0.05858	0.001000	0.08648	0.812000	0.45895	0.043000	0.13971	0.661000	0.30985	0.467000	0.42956	GCG	C|0.701;T|0.299	0.299	strong		0.682	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
OR2T3	343173	hgsc.bcm.edu	37	1	248637543	248637543	+	Missense_Mutation	SNP	C	C	T	rs139993642	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248637543C>T	ENST00000359594.2	+	1	917	c.892C>T	c.(892-894)Cgc>Tgc	p.R298C		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTACAGTCTCCGCAACAAAGA	0.488																																					p.R298C		Atlas-SNP	.											OR2T3,NS,carcinoma,-2,1	OR2T3	79	1	0			c.C892T						scavenged	.	C	CYS/ARG	537,3867		11,515,1676	123.0	127.0	125.0		892	-0.6	0.2	1	dbSNP_134	125	673,7913		0,673,3620	no	missense	OR2T3	NM_001005495.1	180	11,1188,5296	TT,TC,CC		7.8383,12.1935,9.3149	probably-damaging	298/319	248637543	1210,11780	2202	4293	6495	SO:0001583	missense	343173	exon1			AGTCTCCGCAACA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.892C>T	1.37:g.248637543C>T	ENSP00000352604:p.Arg298Cys	Somatic	964	2	0.00207469		WXS	Illumina HiSeq	Phase_I	1103	273	0.247507	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	626	0.2866300366300366	125	0.2540650406504065	93	0.2569060773480663	233	0.40734265734265734	175	0.23087071240105542	c	13.85	2.361258	0.41801	0.121935	0.078383	ENSG00000196539	ENST00000359594	T	0.40476	1.03	2.37	-0.64	0.11493	.	.	.	.	.	T	0.00012	0.0000	M	0.77820	2.39	0.36159	P	0.15204600000000001	D	0.89917	1.0	D	0.74348	0.983	T	0.32771	-0.9894	8	0.72032	D	0.01	.	7.4986	0.27505	0.5605:0.4394:0.0:0.0	.	298	Q8NH03	OR2T3_HUMAN	C	298	ENSP00000352604:R298C	ENSP00000352604:R298C	R	+	1	0	OR2T3	246704166	0.005000	0.15991	0.198000	0.23420	0.152000	0.21847	0.085000	0.14912	-0.543000	0.06240	0.186000	0.17326	CGC	C|0.500;T|0.500	0.500	strong		0.488	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
COL25A1	84570	hgsc.bcm.edu	37	4	109841743	109841743	+	Silent	SNP	C	C	T	rs17596705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:109841743C>T	ENST00000399132.1	-	12	1256	c.726G>A	c.(724-726)ccG>ccA	p.P242P	COL25A1_ENST00000399126.1_Silent_p.P242P|COL25A1_ENST00000399127.1_Silent_p.P238P	NM_198721.2	NP_942014.1			collagen, type XXV, alpha 1											NS(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(19)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	49		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000173)		CCTTTTGTCCCGGAGGCCCTA	0.363													C|||	614	0.122604	0.1868	0.1671	5008	,	,		16387	0.003		0.2107	False		,,,				2504	0.0368				p.P242P		Atlas-SNP	.											.	COL25A1	178	.	0			c.G726A						PASS	.	C	,	643,3031		49,545,1243	157.0	140.0	145.0		726,726	-2.3	1.0	4	dbSNP_123	145	1834,6344		204,1426,2459	no	coding-synonymous,coding-synonymous	COL25A1	NM_032518.2,NM_198721.1	,	253,1971,3702	TT,TC,CC		22.426,17.5014,20.8994	,	242/643,242/655	109841743	2477,9375	1837	4089	5926	SO:0001819	synonymous_variant	84570	exon11			TTGTCCCGGAGGC	AF293340	CCDS43258.1, CCDS43259.1, CCDS58922.1	4q25	2013-01-16			ENSG00000188517	ENSG00000188517		"""Collagens"""	18603	protein-coding gene	gene with protein product		610004				11927537	Standard	NM_001256074		Approved		uc003hze.2	Q9BXS0	OTTHUMG00000150039	ENST00000399132.1:c.726G>A	4.37:g.109841743C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	70	30	0.428571	NM_198721		Silent	SNP	ENST00000399132.1	37	CCDS43258.1																																																																																			C|0.843;T|0.157	0.157	strong		0.363	COL25A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315938.2	NM_032518	
SPATA17	128153	hgsc.bcm.edu	37	1	217856626	217856626	+	Silent	SNP	G	G	A	rs12068167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:217856626G>A	ENST00000366933.4	+	5	373	c.318G>A	c.(316-318)agG>agA	p.R106R		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	106	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		GAGGCTATAGGGTTCGGAAGT	0.313													G|||	877	0.17512	0.3011	0.1268	5008	,	,		11797	0.0962		0.173	False		,,,				2504	0.1227				p.R106R		Atlas-SNP	.											.	SPATA17	59	.	0			c.G318A						PASS	.	G		1198,3200	373.4+/-320.8	166,866,1167	91.0	109.0	103.0		318	3.5	0.9	1	dbSNP_120	103	1365,7233	258.6+/-282.2	110,1145,3044	no	coding-synonymous	SPATA17	NM_138796.2		276,2011,4211	AA,AG,GG		15.8758,27.2397,19.7215		106/362	217856626	2563,10433	2199	4299	6498	SO:0001819	synonymous_variant	128153	exon5			CTATAGGGTTCGG	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.318G>A	1.37:g.217856626G>A		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	149	70	0.469799	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			G|0.826;A|0.174	0.174	strong		0.313	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
TUBA3C	7278	hgsc.bcm.edu	37	13	19753575	19753575	+	Silent	SNP	A	A	G	rs36215075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19753575A>G	ENST00000400113.3	-	2	236	c.132T>C	c.(130-132)ggT>ggC	p.G44G	RP11-408E5.4_ENST00000382988.2_5'Flank	NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	44					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		AGTCGTCCCCACCACCAATGG	0.557													G|||	151	0.0301518	0.0038	0.0461	5008	,	,		17811	0.0129		0.0596	False		,,,				2504	0.0419				p.G44G		Atlas-SNP	.											.	TUBA3C	166	.	0			c.T132C						PASS	.	G		73,4333	819.7+/-416.4	1,71,2131	226.0	183.0	198.0		132	-2.7	0.9	13	dbSNP_126	198	504,8096	796.6+/-407.5	20,464,3816	no	coding-synonymous	TUBA3C	NM_006001.2		21,535,5947	GG,GA,AA		5.8605,1.6568,4.4364		44/451	19753575	577,12429	2203	4300	6503	SO:0001819	synonymous_variant	7278	exon2			GTCCCCACCACCA	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.132T>C	13.37:g.19753575A>G		Somatic	231	0	0		WXS	Illumina HiSeq	Phase_I	268	118	0.440298	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			A|0.958;G|0.042	0.042	strong		0.557	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
CEP131	22994	hgsc.bcm.edu	37	17	79166384	79166384	+	Silent	SNP	C	C	T	rs3744150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79166384C>T	ENST00000269392.4	-	20	2695	c.2448G>A	c.(2446-2448)gcG>gcA	p.A816A	AZI1_ENST00000374782.3_Silent_p.A777A|AZI1_ENST00000575907.1_Silent_p.A780A|AZI1_ENST00000450824.2_Silent_p.A813A	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		816					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)			CTTCCAGCTCCGCCCGCTGCC	0.682													C|||	773	0.154353	0.2738	0.0403	5008	,	,		11206	0.1389		0.0755	False		,,,				2504	0.1708				p.A813A		Atlas-SNP	.											.	AZI1	145	.	0			c.G2439A						PASS	.	C	,	955,3421		102,751,1335	21.0	20.0	21.0		2331,2439	-6.6	0.0	17	dbSNP_107	21	597,7981		25,547,3717	no	coding-synonymous,coding-synonymous	AZI1	NM_001009811.2,NM_014984.2	,	127,1298,5052	TT,TC,CC		6.9597,21.8236,11.9809	,	777/1045,813/1081	79166384	1552,11402	2188	4289	6477	SO:0001819	synonymous_variant	22994	exon20			CAGCTCCGCCCGC																												ENST00000269392.4:c.2448G>A	17.37:g.79166384C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_014984	A6NHI8|B2RN11|Q96F50	Silent	SNP	ENST00000269392.4	37																																																																																				C|0.876;T|0.124	0.124	strong		0.682	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
KIAA1549L	25758	hgsc.bcm.edu	37	11	33581306	33581306	+	Silent	SNP	G	G	A	rs2281380	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:33581306G>A	ENST00000321505.4	+	6	3156	c.2976G>A	c.(2974-2976)acG>acA	p.T992T	KIAA1549L_ENST00000389726.3_Silent_p.T998T|KIAA1549L_ENST00000265654.5_Silent_p.T998T			Q6ZVL6	K154L_HUMAN	KIAA1549-like	992						integral component of membrane (GO:0016021)											TTGTGAGCACGTCCAATGCCT	0.582													G|||	1948	0.388978	0.469	0.3213	5008	,	,		22143	0.3264		0.3887	False		,,,				2504	0.3937				p.T992T		Atlas-SNP	.											.	.	.	.	0			c.G2976A						PASS	.	G		1926,2268		480,966,651	83.0	80.0	81.0		2976	-5.2	1.0	11	dbSNP_100	81	3268,5198		645,1978,1610	no	coding-synonymous	C11orf41	NM_012194.2		1125,2944,2261	AA,AG,GG		38.6015,45.9227,41.0269		992/1850	33581306	5194,7466	2097	4233	6330	SO:0001819	synonymous_variant	25758	exon6			GAGCACGTCCAAT	U10991	CCDS44565.1, CCDS44565.2	11p13	2012-08-09	2012-08-09	2012-08-09	ENSG00000110427	ENSG00000110427			24836	protein-coding gene	gene with protein product		612297	"""chromosome 11 open reading frame 69"", ""chromosome 11 open reading frame 41"""	C11orf69, C11orf41			Standard	NM_012194		Approved	G2, MGC34830	uc021qfs.1	Q6ZVL6	OTTHUMG00000150410	ENST00000321505.4:c.2976G>A	11.37:g.33581306G>A		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2	846	0.3873626373626374	227	0.4613821138211382	126	0.34806629834254144	188	0.32867132867132864	305	0.4023746701846966	G	7.557	0.663994	0.14710	0.459227	0.386015	ENSG00000110427	ENST00000526400	.	.	.	5.42	-5.21	0.02815	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999989427	.	.	.	.	.	.	T	0.44697	-0.9311	3	.	.	.	-8.4917	5.8334	0.18593	0.6112:0.1336:0.1659:0.0893	rs2281380;rs59777290;rs2281380	.	.	.	H	390	.	.	R	+	2	0	C11orf41	33537882	0.018000	0.18449	0.951000	0.38953	0.712000	0.41017	-0.872000	0.04219	-0.823000	0.04301	0.573000	0.79308	CGT	G|0.613;A|0.387	0.387	strong		0.582	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194	
GAR1	54433	hgsc.bcm.edu	37	4	110737389	110737389	+	Silent	SNP	T	T	C	rs2276326	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:110737389T>C	ENST00000226796.6	+	2	333	c.69T>C	c.(67-69)ggT>ggC	p.G23G	GAR1_ENST00000394631.3_Silent_p.G23G|RP11-602N24.3_ENST00000609440.1_lincRNA	NM_018983.3	NP_061856.1	Q9NY12	GAR1_HUMAN	GAR1 ribonucleoprotein	23	RGG-box 1.				cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|pseudouridine synthesis (GO:0001522)|rRNA processing (GO:0006364)	box H/ACA snoRNP complex (GO:0031429)|nucleolus (GO:0005730)|nucleus (GO:0005634)	cation channel activity (GO:0005261)|poly(A) RNA binding (GO:0044822)	p.G23G(1)		kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)	9						tcaaccgaggtggcagcagca	0.622													C|||	3862	0.771166	0.7292	0.585	5008	,	,		12370	0.9157		0.7505	False		,,,				2504	0.8323				p.G23G		Atlas-SNP	.											GAR1,NS,carcinoma,0,1	GAR1	16	1	1	Substitution - coding silent(1)	prostate(1)	c.T69C						PASS	.	C	,	3120,1286	425.5+/-340.8	1097,926,180	39.0	45.0	43.0		69,69	1.6	1.0	4	dbSNP_100	43	6387,2213	368.9+/-335.3	2389,1609,302	no	coding-synonymous,coding-synonymous	GAR1	NM_018983.3,NM_032993.2	,	3486,2535,482	CC,CT,TT		25.7326,29.1875,26.903	,	23/218,23/218	110737389	9507,3499	2203	4300	6503	SO:0001819	synonymous_variant	54433	exon2			CCGAGGTGGCAGC	AJ276003	CCDS34050.1	4q	2013-07-31	2013-07-31	2008-10-13	ENSG00000109534	ENSG00000109534			14264	protein-coding gene	gene with protein product		606468	"""nucleolar protein family A, member 1 (H/ACA small nucleolar RNPs)"", ""GAR1 ribonucleoprotein homolog (yeast)"""	NOLA1		10757788	Standard	XM_005263069		Approved		uc003hzu.3	Q9NY12	OTTHUMG00000161108	ENST00000226796.6:c.69T>C	4.37:g.110737389T>C		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	NM_018983	Q5MJQ2	Silent	SNP	ENST00000226796.6	37	CCDS34050.1																																																																																			T|0.264;C|0.736	0.736	strong		0.622	GAR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363810.2		
BPIFA2	140683	hgsc.bcm.edu	37	20	31760763	31760763	+	Silent	SNP	C	C	T	rs150791330		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:31760763C>T	ENST00000253362.2	+	3	329	c.183C>T	c.(181-183)gaC>gaT	p.D61D	BPIFA2_ENST00000354932.5_Silent_p.D61D			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	61						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										TGAAGGTCGACCTAGGAGTGC	0.488																																					p.D61D		Atlas-SNP	.											C20orf70,face,carcinoma,+2,1	.	.	1	0			c.C183T						scavenged	.						90.0	83.0	85.0					20																	31760763		2203	4300	6503	SO:0001819	synonymous_variant	140683	exon3			GGTCGACCTAGGA	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.183C>T	20.37:g.31760763C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	141	2	0.0141844	NM_080574	Q9BQQ0	Silent	SNP	ENST00000253362.2	37	CCDS13214.1																																																																																			C|1.000;A|0.000	.	alt		0.488	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
LILRB3	11025	hgsc.bcm.edu	37	19	54725744	54725744	+	Nonsense_Mutation	SNP	C	C	T	rs59533602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54725744C>T	ENST00000391750.1	-	5	750	c.614G>A	c.(613-615)tGg>tAg	p.W205*	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000469273.1_5'Flank|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRA6_ENST00000440558.2_Intron|LILRB3_ENST00000407860.2_Nonsense_Mutation_p.W205*|LILRB3_ENST00000424807.1_Nonsense_Mutation_p.W205*|LILRB3_ENST00000346401.6_Nonsense_Mutation_p.W205*|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Nonsense_Mutation_p.W205*|LILRA6_ENST00000270464.5_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	205	Ig-like C2-type 2.		W -> Q (requires 2 nucleotide substitutions; dbSNP:rs1063805). {ECO:0000269|PubMed:9278324}.	W -> R (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GGACCACACCCAGGGGGTGTT	0.612													.|||	437	0.0872604	0.1634	0.0865	5008	,	,		9075	0.0496		0.0736	False		,,,				2504	0.0378				p.W205X		Atlas-SNP	.											LILRB3,NS,neuroblastoma,-1,1	LILRB3	67	1	0			c.G614A						scavenged	.						26.0	48.0	42.0					19																	54725744		1198	3229	4427	SO:0001587	stop_gained	11025	exon4			CACACCCAGGGGG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.614G>A	19.37:g.54725744C>T	ENSP00000375630:p.Trp205*	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	24	16	0.666667	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Nonsense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.082149	0.36758	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860	.	.	.	2.87	2.87	0.33458	.	1.294080	0.05328	N	0.527713	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	4.9631	0.14076	0.0:0.1435:0.0:0.8565	.	.	.	.	X	205	.	ENSP00000245620:W205X	W	-	2	0	LILRB3	59417556	0.000000	0.05858	0.106000	0.21319	0.011000	0.07611	0.042000	0.13949	0.527000	0.28560	-0.359000	0.07587	TGG	C|0.500;T|0.500	0.500	strong		0.612	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14848821	14848821	+	Silent	SNP	G	G	A	rs28555630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:14848821G>A	ENST00000358984.4	+	34	3111	c.2931G>A	c.(2929-2931)acG>acA	p.T977T		NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	977				T -> M (in Ref. 3; AAK27326 and 4; BAG57852). {ECO:0000305}.						breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						TGGAACAAACGAAAAATAAGT	0.348													g|||	2352	0.469649	0.5371	0.4222	5008	,	,		15908	0.4127		0.5109	False		,,,				2504	0.4284				p.T977T		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,+1,1	ANKRD30B	237	1	0			c.G2931A						PASS	.						74.0	56.0	61.0					18																	14848821		692	1587	2279	SO:0001819	synonymous_variant	374860	exon34			ACAAACGAAAAAT	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.2931G>A	18.37:g.14848821G>A		Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	205	189	0.921951	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																			G|0.500;A|0.500	0.500	weak		0.348	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
RBL2	5934	hgsc.bcm.edu	37	16	53504721	53504721	+	Silent	SNP	T	T	C	rs10748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:53504721T>C	ENST00000262133.6	+	17	2727	c.2590T>C	c.(2590-2592)Ttg>Ctg	p.L864L	RBL2_ENST00000379935.4_3'UTR|RBL2_ENST00000544545.1_Intron	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	864	Domain B.|Pocket; binds E1A.				chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						TTCAGATGAATTGAGGAAAAA	0.378													C|||	2524	0.503994	0.8464	0.4049	5008	,	,		19554	0.1786		0.4662	False		,,,				2504	0.4857				p.L864L		Atlas-SNP	.											.	RBL2	115	.	0			c.T2590C						PASS	.	C		3377,1019	372.2+/-320.3	1309,759,130	128.0	136.0	133.0		2590	2.2	1.0	16	dbSNP_52	133	4177,4423	587.1+/-392.1	1029,2119,1152	no	coding-synonymous	RBL2	NM_005611.3		2338,2878,1282	CC,CT,TT		48.5698,23.1802,41.8744		864/1140	53504721	7554,5442	2198	4300	6498	SO:0001819	synonymous_variant	5934	exon17			GATGAATTGAGGA	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.2590T>C	16.37:g.53504721T>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	106	105	0.990566	NM_005611	B7Z913|Q15073|Q16084|Q8NE70|Q92812	Silent	SNP	ENST00000262133.6	37	CCDS10748.1																																																																																			T|0.470;C|0.530	0.530	strong		0.378	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611	
COL18A1	80781	hgsc.bcm.edu	37	21	46900410	46900410	+	Silent	SNP	C	C	T	rs2236467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46900410C>T	ENST00000359759.4	+	11	2694	c.2673C>T	c.(2671-2673)ttC>ttT	p.F891F	COL18A1_ENST00000400337.2_Silent_p.F476F|COL18A1_ENST00000355480.5_Silent_p.F656F			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	891	Nonhelical region 3 (NC3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GATCTGGCTTCGGGGGCGATC	0.637													C|||	781	0.15595	0.2821	0.0735	5008	,	,		14504	0.1081		0.0696	False		,,,				2504	0.182				p.F656F		Atlas-SNP	.											.	COL18A1	129	.	0			c.C1968T						PASS	.	C	,	1058,3020		130,798,1111	47.0	55.0	52.0		1968,1428	-2.0	0.0	21	dbSNP_98	52	549,7771		18,513,3629	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	148,1311,4740	TT,TC,CC		6.5986,25.9441,12.9618	,	656/1520,476/1340	46900410	1607,10791	2039	4160	6199	SO:0001819	synonymous_variant	80781	exon11			TGGCTTCGGGGGC		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.2673C>T	21.37:g.46900410C>T		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	160	73	0.45625	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.881;T|0.119	0.119	strong		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
BZRAP1	9256	hgsc.bcm.edu	37	17	56386289	56386289	+	Silent	SNP	C	C	T	rs145131712	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56386289C>T	ENST00000343736.4	-	22	4507	c.4344G>A	c.(4342-4344)gaG>gaA	p.E1448E	BZRAP1_ENST00000355701.3_Silent_p.E1448E|BZRAP1_ENST00000268893.6_Silent_p.E1388E			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1448						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)	p.E1448D(2)		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)					GGCCACCCCTCTCCCGTGTGG	0.706													C|||	32	0.00638978	0.0015	0.0029	5008	,	,		15411	0.0		0.0139	False		,,,				2504	0.0143				p.E1448E		Atlas-SNP	.											.	BZRAP1	287	.	2	Substitution - Missense(2)	lung(2)	c.G4344A						PASS	.	C	,	13,4315		0,13,2151	22.0	28.0	26.0		4344,4164	0.0	1.0	17	dbSNP_134	26	109,8395		0,109,4143	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	0,122,6294	TT,TC,CC		1.2817,0.3004,0.9507	,	1448/1858,1388/1798	56386289	122,12710	2164	4252	6416	SO:0001819	synonymous_variant	9256	exon22			ACCCCTCTCCCGT	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.4344G>A	17.37:g.56386289C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_004758	O75111|Q8N5W3	Silent	SNP	ENST00000343736.4	37	CCDS11605.1																																																																																			C|0.991;T|0.009	0.009	strong		0.706	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
TTC7B	145567	hgsc.bcm.edu	37	14	91252545	91252545	+	Silent	SNP	G	G	A	rs17794971	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:91252545G>A	ENST00000328459.6	-	2	370	c.249C>T	c.(247-249)acC>acT	p.T83T	TTC7B_ENST00000357056.2_Silent_p.T83T	NM_001010854.1	NP_001010854.1	Q86TV6	TTC7B_HUMAN	tetratricopeptide repeat domain 7B	83										NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	36		Melanoma(154;0.222)				CCAGGGCGGCGGTCAGATGCT	0.637													G|||	160	0.0319489	0.0038	0.1383	5008	,	,		17628	0.0		0.0368	False		,,,				2504	0.0225				p.T83T		Atlas-SNP	.											.	TTC7B	93	.	0			c.C249T						PASS	.	G		30,4376	36.0+/-67.5	0,30,2173	46.0	45.0	45.0		249	-3.1	0.6	14	dbSNP_123	45	266,8334	101.0+/-162.3	5,256,4039	no	coding-synonymous	TTC7B	NM_001010854.1		5,286,6212	AA,AG,GG		3.093,0.6809,2.2759		83/844	91252545	296,12710	2203	4300	6503	SO:0001819	synonymous_variant	145567	exon2			GGCGGCGGTCAGA	BC035865	CCDS32140.1	14q32.12	2013-01-11	2004-06-02	2004-06-04		ENSG00000165914		"""Tetratricopeptide (TTC) repeat domain containing"""	19858	protein-coding gene	gene with protein product			"""tetratricopeptide repeat domain 7 like 1"""	TTC7L1			Standard	XM_005267367		Approved		uc001xyp.3	Q86TV6		ENST00000328459.6:c.249C>T	14.37:g.91252545G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_001010854	Q86U24|Q86VT3	Silent	SNP	ENST00000328459.6	37	CCDS32140.1																																																																																			G|0.976;A|0.024	0.024	strong		0.637	TTC7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411364.2		
CSTL1	128817	hgsc.bcm.edu	37	20	23424613	23424613	+	Missense_Mutation	SNP	T	T	C	rs3746736	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:23424613T>C	ENST00000246020.2	+	2	282	c.262T>C	c.(262-264)Tgg>Cgg	p.W88R	CSTL1_ENST00000347397.1_Missense_Mutation_p.W88R			Q9H114	CST1L_HUMAN	cystatin-like 1	88			W -> R (in dbSNP:rs3746736). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(2)|endometrium(2)|large_intestine(3)|lung(4)|skin(2)|stomach(1)	14	Colorectal(13;0.0993)|Lung NSC(19;0.235)					GAAGATTGGCTGGACCAAATG	0.512													C|||	3280	0.654952	0.857	0.6023	5008	,	,		19368	0.7292		0.494	False		,,,				2504	0.5082				p.W88R		Atlas-SNP	.											.	CSTL1	30	.	0			c.T262C						PASS	.	C	ARG/TRP	3464,942	358.4+/-314.3	1363,738,102	145.0	121.0	129.0		262	-0.6	0.9	20	dbSNP_107	129	4335,4265	575.1+/-390.2	1110,2115,1075	yes	missense	CSTL1	NM_138283.1	101	2473,2853,1177	CC,CT,TT		49.593,21.3799,40.0354	benign	88/146	23424613	7799,5207	2203	4300	6503	SO:0001583	missense	128817	exon3			ATTGGCTGGACCA	AL096677	CCDS13153.1	20p11.21	2012-08-14			ENSG00000125823	ENSG00000125823			15958	protein-coding gene	gene with protein product						20565543	Standard	NM_138283		Approved	dJ322G13.4, CTES1	uc002wte.3	Q9H114	OTTHUMG00000032068	ENST00000246020.2:c.262T>C	20.37:g.23424613T>C	ENSP00000246020:p.Trp88Arg	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	85	40	0.470588	NM_138283	Q17RA8|Q64FF7	Missense_Mutation	SNP	ENST00000246020.2	37	CCDS13153.1	1444	0.6611721611721612	425	0.8638211382113821	222	0.6132596685082873	434	0.7587412587412588	363	0.4788918205804749	C	0.003	-2.488228	0.00161	0.786201	0.50407	ENSG00000125823	ENST00000347397;ENST00000246020	T;T	0.10192	2.9;2.9	4.06	-0.597	0.11653	Proteinase inhibitor I25, cystatin (2);	0.000000	0.41500	N	0.000870	T	0.00012	0.0000	N	0.00020	-2.765	0.58432	P	4.000000000004E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.20338	-1.0278	9	0.02654	T	1	-13.8332	6.2799	0.21001	0.4857:0.4075:0.0:0.1068	rs3746736;rs17683931;rs52791027;rs58676320;rs3746736	88	Q9H114	CST1L_HUMAN	R	88	ENSP00000344907:W88R;ENSP00000246020:W88R	ENSP00000246020:W88R	W	+	1	0	CSTL1	23372613	0.062000	0.20869	0.901000	0.35422	0.035000	0.12851	-0.270000	0.08584	-0.325000	0.08577	-0.929000	0.02709	TGG	C|0.629;N|0.000	0.629	strong		0.512	CSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078328.1		
OR7A5	26659	hgsc.bcm.edu	37	19	14938190	14938190	+	Silent	SNP	A	A	G	rs2240561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14938190A>G	ENST00000322301.3	-	2	951	c.864T>C	c.(862-864)ttT>ttC	p.F288F	OR7A5_ENST00000601611.1_Intron|OR7A5_ENST00000594432.1_Silent_p.F288F			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	288					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						GACTATAGATAAAGGGGTTCA	0.473																																					p.F288F		Atlas-SNP	.											.	OR7A5	43	.	0			c.T864C						PASS	.						73.0	71.0	71.0					19																	14938190		2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			ATAGATAAAGGGG	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.864T>C	19.37:g.14938190A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	115	9	0.0782609	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			A|0.999;G|0.001	0.001	strong		0.473	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227216775	227216775	+	Missense_Mutation	SNP	C	C	T	rs1929860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:227216775C>T	ENST00000366769.3	-	29	5201	c.3910G>A	c.(3910-3912)Gta>Ata	p.V1304I	CDC42BPA_ENST00000366764.2_Missense_Mutation_p.V1276I|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.V1304I|CDC42BPA_ENST00000366767.3_Missense_Mutation_p.V1223I|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.V1339I|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.V1284I|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.V1317I	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				CCAGAAGTTACGGTTTGACAC	0.473													T|||	1403	0.280152	0.1884	0.33	5008	,	,		18097	0.4028		0.332	False		,,,				2504	0.1892				p.V1304I		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.G3910A						PASS	.	T	ILE/VAL,ILE/VAL	962,3444	733.3+/-410.5	109,744,1350	69.0	56.0	60.0		3910,3667	4.2	1.0	1	dbSNP_92	60	2711,5889	681.9+/-403.8	406,1899,1995	yes	missense,missense	CDC42BPA	NM_003607.3,NM_014826.4	29,29	515,2643,3345	TT,TC,CC		31.5233,21.8339,28.2408	benign,benign	1304/1720,1223/1639	227216775	3673,9333	2203	4300	6503	SO:0001583	missense	8476	exon29			AAGTTACGGTTTG	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.3910G>A	1.37:g.227216775C>T	ENSP00000355731:p.Val1304Ile	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	54	28	0.518519	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	727|727	0.33287545787545786|0.33287545787545786	105|105	0.21341463414634146|0.21341463414634146	113|113	0.31215469613259667|0.31215469613259667	245|245	0.42832167832167833|0.42832167832167833	264|264	0.3482849604221636|0.3482849604221636	T|T	1.392|1.392	-0.580517|-0.580517	0.03854|0.03854	0.218339|0.218339	0.315233|0.315233	ENSG00000143776|ENSG00000143776	ENST00000448940;ENST00000442054;ENST00000429440;ENST00000441725|ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	.|T;T;T;T;T;T;T	.|0.04551	.|3.6;3.6;3.6;3.6;3.6;3.6;3.6	5.32|5.32	4.18|4.18	0.49190|0.49190	.|.	.|0.138886	.|0.64402	.|N	.|0.000007	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.01705|0.01705	-0.755|-0.755	0.54753|0.54753	P|P	1.799999999996249E-5|1.799999999996249E-5	.|B;B;B;B;B;B;B;B	.|0.06786	.|0.001;0.0;0.001;0.001;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B;B;B	.|0.09377	.|0.001;0.001;0.001;0.004;0.001;0.001;0.0;0.004	T|T	0.45323|0.45323	-0.9269|-0.9269	4|9	.|0.05351	.|T	.|0.99	.|.	8.5234|8.5234	0.33291|0.33291	0.0:0.0681:0.1307:0.8012|0.0:0.0681:0.1307:0.8012	rs1929860;rs3738731;rs57541261;rs1929860|rs1929860;rs3738731;rs57541261;rs1929860	.|1284;1276;619;201;1223;1304;1339;506	.|F5H5N0;Q5VT25-4;E9PEF7;Q5T7A7;Q5VT25-3;Q5VT25-5;Q5VT25-2;Q5T799	.|.;.;.;.;.;.;.;.	H|I	506;632;201;528|1304;1223;1304;1339;1276;619;1284;1317	.|ENSP00000355731:V1304I;ENSP00000355729:V1223I;ENSP00000335341:V1304I;ENSP00000355728:V1339I;ENSP00000355726:V1276I;ENSP00000443275:V1284I;ENSP00000355727:V1317I	.|ENSP00000335341:V1304I	R|V	-|-	2|1	0|0	CDC42BPA|CDC42BPA	225283398|225283398	0.269000|0.269000	0.24143|0.24143	0.994000|0.994000	0.49952|0.49952	0.965000|0.965000	0.64279|0.64279	0.457000|0.457000	0.21875|0.21875	0.411000|0.411000	0.25702|0.25702	-0.352000|-0.352000	0.07741|0.07741	CGT|GTA	T|0.301;C|0.699	0.301	strong		0.473	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
RFPL3	10738	hgsc.bcm.edu	37	22	32756407	32756407	+	Missense_Mutation	SNP	A	A	G	rs5749408	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:32756407A>G	ENST00000249007.4	+	2	747	c.542A>G	c.(541-543)tAc>tGc	p.Y181C	RFPL3_ENST00000397468.1_Missense_Mutation_p.Y152C|RFPL3_ENST00000382088.3_Missense_Mutation_p.Y152C|RFPL3S_ENST00000400234.1_3'UTR|RFPL3S_ENST00000382084.4_3'UTR|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	181	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		Y -> C (in dbSNP:rs5749408).				zinc ion binding (GO:0008270)	p.Y152C(1)|p.Y181C(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GGCCGCCACTACTGGGAGGTG	0.562													a|||	851	0.169928	0.1059	0.1124	5008	,	,		18743	0.4583		0.0467	False		,,,				2504	0.1268				p.Y181C		Atlas-SNP	.											RFPL3_ENST00000249007,NS,carcinoma,0,2	RFPL3	91	2	2	Substitution - Missense(2)	stomach(2)	c.A542G						PASS	.	A	CYS/TYR,CYS/TYR	499,3907	228.1+/-243.1	40,419,1744	85.0	86.0	85.0		542,455	0.7	0.2	22	dbSNP_114	85	479,8117	140.3+/-196.8	11,457,3830	no	missense,missense	RFPL3	NM_001098535.1,NM_006604.2	194,194	51,876,5574	GG,GA,AA		5.5724,11.3255,7.5219	benign,benign	181/318,152/289	32756407	978,12024	2203	4298	6501	SO:0001583	missense	10738	exon2			GCCACTACTGGGA	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.542A>G	22.37:g.32756407A>G	ENSP00000249007:p.Tyr181Cys	Somatic	231	1	0.004329		WXS	Illumina HiSeq	Phase_I	219	106	0.484018	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	386	0.17673992673992675	52	0.10569105691056911	46	0.1270718232044199	254	0.44405594405594406	34	0.044854881266490766	A	8.527	0.870091	0.17322	0.113255	0.055724	ENSG00000128276	ENST00000397468;ENST00000249007;ENST00000382088	T;T;T	0.74947	-0.89;-0.89;-0.89	0.704	0.704	0.18121	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.00012	0.0000	M	0.81497	2.545	0.09310	P	0.999999999404185	B	0.33413	0.411	B	0.28709	0.093	T	0.22556	-1.0213	8	0.54805	T	0.06	.	5.601	0.17353	0.9999:0.0:1.0E-4:0.0	rs5749408	181	O75679	RFPL3_HUMAN	C	152;181;152	ENSP00000380609:Y152C;ENSP00000249007:Y181C;ENSP00000371520:Y152C	ENSP00000249007:Y181C	Y	+	2	0	RFPL3	31086407	0.989000	0.36119	0.246000	0.24233	0.050000	0.14768	1.786000	0.38694	0.528000	0.28580	0.172000	0.16884	TAC	A|0.959;G|0.041	0.041	strong		0.562	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
CEP170	9859	hgsc.bcm.edu	37	1	243329049	243329049	+	Missense_Mutation	SNP	G	G	A	rs3766664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:243329049G>A	ENST00000366542.1	-	13	2264	c.2213C>T	c.(2212-2214)aCt>aTt	p.T738I	CEP170_ENST00000490813.1_5'Flank|CEP170_ENST00000366544.1_Missense_Mutation_p.T640I|RP11-261C10.4_ENST00000422938.1_RNA|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.T640I	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	738						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TACCAAAGAAGTTTCCTTATC	0.393																																					p.T738I		Atlas-SNP	.											.	CEP170	153	.	0			c.C2213T						PASS	.						211.0	204.0	206.0					1																	243329049		1864	4090	5954	SO:0001583	missense	9859	exon13			AAAGAAGTTTCCT	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2213C>T	1.37:g.243329049G>A	ENSP00000355500:p.Thr738Ile	Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	239	59	0.246862	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.512|9.512	1.106068|1.106068	0.20632|0.20632	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000336415|ENST00000366542;ENST00000366544;ENST00000366543	.|T;T;T	.|0.46819	.|0.87;0.86;0.86	5.25|5.25	3.25|3.25	0.37280|0.37280	.|.	.|1.055560	.|0.07311	.|N	.|0.875849	T|T	0.34106|0.34106	0.0886|0.0886	N|N	0.19112|0.19112	0.55|0.55	0.26599|0.26599	N|N	0.973053|0.973053	.|B;B;B;B	.|0.34200	.|0.068;0.096;0.441;0.07	.|B;B;B;B	.|0.35312	.|0.093;0.067;0.2;0.043	T|T	0.28808|0.28808	-1.0032|-1.0032	5|10	.|0.44086	.|T	.|0.13	0.1048|0.1048	7.1054|7.1054	0.25360|0.25360	0.0872:0.0:0.7427:0.1701|0.0872:0.0:0.7427:0.1701	rs3766664|rs3766664	.|701;640;640;738	.|B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.|.;.;.;CE170_HUMAN	F|I	702|738;640;640	.|ENSP00000355500:T738I;ENSP00000355502:T640I;ENSP00000355501:T640I	.|ENSP00000355500:T738I	L|T	-|-	1|2	0|0	CEP170|CEP170	241395672|241395672	0.174000|0.174000	0.23070|0.23070	0.502000|0.502000	0.27614|0.27614	0.868000|0.868000	0.49771|0.49771	1.630000|1.630000	0.37081|0.37081	1.208000|1.208000	0.43306|0.43306	0.484000|0.484000	0.47621|0.47621	CTT|ACT	G|0.167;A|0.833	0.833	weak		0.393	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
TPRX1	284355	hgsc.bcm.edu	37	19	48305550	48305550	+	Missense_Mutation	SNP	G	G	A	rs75909117	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48305550G>A	ENST00000322175.3	-	2	873	c.718C>T	c.(718-720)Cca>Tca	p.P240S	TPRX1_ENST00000543508.1_Missense_Mutation_p.P230S|TPRX1_ENST00000535759.1_Missense_Mutation_p.P337S	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	240	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		attgggcctgggatcgggcct	0.657													g|||	13	0.00259585	0.003	0.0	5008	,	,		16375	0.0		0.0089	False		,,,				2504	0.0				p.P240S	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,colon,carcinoma,0,1	TPRX1	46	1	0			c.C718T						PASS	.						10.0	8.0	9.0					19																	48305550		2124	4166	6290	SO:0001583	missense	284355	exon2			GGCCTGGGATCGG		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.718C>T	19.37:g.48305550G>A	ENSP00000323455:p.Pro240Ser	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	38	4	0.105263	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	64	0.029304029304029304	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	54	0.0712401055408971	g	1.855	-0.464017	0.04476	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D	0.93189	-1.99;-3.18	0.557	-1.11	0.09840	.	.	.	.	.	T	0.31295	0.0792	N	0.14661	0.345	0.09310	N	1	B	0.27166	0.17	B	0.17979	0.02	T	0.56013	-0.8049	8	0.26408	T	0.33	.	.	.	.	.	240	Q8N7U7	TPRX1_HUMAN	S	240;337;230	ENSP00000323455:P240S;ENSP00000438832:P337S	ENSP00000323455:P240S	P	-	1	0	TPRX1	52997362	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	1.112000	0.31172	-1.080000	0.03109	-1.403000	0.01137	CCA	G|0.971;A|0.029	0.029	strong		0.657	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
USP53	54532	hgsc.bcm.edu	37	4	120214030	120214030	+	Missense_Mutation	SNP	T	T	G	rs3749591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:120214030T>G	ENST00000274030.6	+	19	4065	c.2886T>G	c.(2884-2886)agT>agG	p.S962R	USP53_ENST00000450251.1_Missense_Mutation_p.S962R	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53									p.S961R(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						CGAAGCACAGTTTAAGTACAG	0.388													T|||	1226	0.244808	0.1195	0.2824	5008	,	,		21325	0.3859		0.3032	False		,,,				2504	0.182				p.S962R		Atlas-SNP	.											USP53,NS,carcinoma,0,1	USP53	69	1	1	Substitution - Missense(1)	stomach(1)	c.T2886G						PASS	.	T	ARG/SER	527,3265		37,453,1406	81.0	73.0	76.0		2886	-1.7	0.0	4	dbSNP_107	76	2598,5662		400,1798,1932	yes	missense	USP53	NM_019050.2	110	437,2251,3338	GG,GT,TT		31.4528,13.8977,25.9293	benign	962/1074	120214030	3125,8927	1896	4130	6026	SO:0001583	missense	54532	exon18			GCACAGTTTAAGT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.2886T>G	4.37:g.120214030T>G	ENSP00000274030:p.Ser962Arg	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_019050		Missense_Mutation	SNP	ENST00000274030.6	37	CCDS43265.1	601	0.2751831501831502	52	0.10569105691056911	87	0.24033149171270718	231	0.40384615384615385	231	0.30474934036939316	T	12.58	1.979529	0.34942	0.138977	0.314528	ENSG00000145390	ENST00000274030;ENST00000450251	T;T	0.47869	0.83;0.83	5.02	-1.66	0.08265	.	0.901431	0.09698	N	0.767375	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P	0.35433	0.501	B	0.27500	0.08	T	0.34850	-0.9812	9	0.54805	T	0.06	-6.1731	6.3273	0.21251	0.1345:0.43:0.0:0.4356	rs3749591;rs17595370;rs52832840;rs59311247;rs3749591	962	Q70EK8	UBP53_HUMAN	R	962	ENSP00000274030:S962R;ENSP00000409906:S962R	ENSP00000274030:S962R	S	+	3	2	USP53	120433478	0.000000	0.05858	0.000000	0.03702	0.977000	0.68977	-0.174000	0.09839	-0.151000	0.11176	-0.361000	0.07541	AGT	T|0.725;G|0.275	0.275	strong		0.388	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
ZNF215	7762	hgsc.bcm.edu	37	11	6977175	6977175	+	Missense_Mutation	SNP	G	G	C	rs2239730	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6977175G>C	ENST00000278319.5	+	7	1555	c.967G>C	c.(967-969)Gtg>Ctg	p.V323L	ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000529903.1_Intron|ZNF215_ENST00000414517.2_Missense_Mutation_p.V323L	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	323			V -> L (in dbSNP:rs2239730). {ECO:0000269|PubMed:10762538}.		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)		TGCTATACAAGTGGGAATTCC	0.318													C|||	979	0.195487	0.3495	0.1311	5008	,	,		20375	0.1419		0.2326	False		,,,				2504	0.0501				p.V323L		Atlas-SNP	.											ZNF215,colon,carcinoma,0,1	ZNF215	72	1	0			c.G967C						PASS	.	C	LEU/VAL	1472,2928	628.2+/-395.1	264,944,992	58.0	68.0	64.0		967	2.5	0.0	11	dbSNP_98	64	1831,6759	712.2+/-405.9	172,1487,2636	yes	missense	ZNF215	NM_013250.2	32	436,2431,3628	CC,CG,GG		21.3155,33.4545,25.4273	benign	323/518	6977175	3303,9687	2200	4295	6495	SO:0001583	missense	7762	exon7			ATACAAGTGGGAA	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.967G>C	11.37:g.6977175G>C	ENSP00000278319:p.Val323Leu	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	70	37	0.528571	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	487	0.222985347985348	162	0.32926829268292684	55	0.15193370165745856	90	0.15734265734265734	180	0.23746701846965698	C	8.824	0.938219	0.18206	0.334545	0.213155	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.05258	3.47;3.47	4.51	2.5	0.30297	.	1.157730	0.06629	N	0.758938	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	0.48547	-0.9026	9	0.62326	D	0.03	3.374	9.2561	0.37584	0.1461:0.4937:0.3602:0.0	rs2239730;rs52834188;rs60946601;rs2239730	323	Q9UL58	ZN215_HUMAN	L	323	ENSP00000278319:V323L;ENSP00000393202:V323L	ENSP00000278319:V323L	V	+	1	0	ZNF215	6933751	0.000000	0.05858	0.026000	0.17262	0.012000	0.07955	-0.162000	0.10012	0.173000	0.19788	-0.120000	0.15030	GTG	G|0.761;C|0.239	0.239	strong		0.318	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
SLC37A2	219855	hgsc.bcm.edu	37	11	124947149	124947149	+	Silent	SNP	G	G	A	rs12276567	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124947149G>A	ENST00000403796.2	+	3	466	c.165G>A	c.(163-165)tcG>tcA	p.S55S	SLC37A2_ENST00000407458.1_Silent_p.S55S|SLC37A2_ENST00000298280.5_Silent_p.S55S|SLC37A2_ENST00000308074.4_Silent_p.S55S	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	55					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	transporter activity (GO:0005215)	p.S55S(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	27	all_hematologic(175;0.215)	Breast(109;0.012)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.152)|all_lung(97;0.159)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.61e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0384)		AGAACTGCTCGGAGCAGATCA	0.542													G|||	1687	0.336861	0.5242	0.2925	5008	,	,		21821	0.1419		0.2634	False		,,,				2504	0.3916				p.S55S	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											SLC37A2_ENST00000403796,NS,adenoma,0,3	SLC37A2	105	3	1	Substitution - coding silent(1)	prostate(1)	c.G165A						PASS	.	G	,	2062,2340	569.4+/-382.6	486,1090,625	186.0	182.0	183.0		165,165	-8.6	0.0	11	dbSNP_120	183	2197,6401	374.0+/-337.2	264,1669,2366	no	coding-synonymous,coding-synonymous	SLC37A2	NM_001145290.1,NM_198277.2	,	750,2759,2991	AA,AG,GG		25.5525,46.8423,32.7615	,	55/502,55/506	124947149	4259,8741	2201	4299	6500	SO:0001819	synonymous_variant	219855	exon3			CTGCTCGGAGCAG	AK074100	CCDS31714.1, CCDS44757.1	11q24.2	2013-07-17	2013-07-17		ENSG00000134955	ENSG00000134955		"""Solute carriers"""	20644	protein-coding gene	gene with protein product			"""solute carrier family 37 (glycerol-3-phosphate transporter), member 2"""				Standard	NM_198277		Approved	FLJ00171	uc010sau.2	Q8TED4	OTTHUMG00000165879	ENST00000403796.2:c.165G>A	11.37:g.124947149G>A		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Silent	SNP	ENST00000403796.2	37	CCDS44757.1																																																																																			G|0.679;A|0.321	0.321	strong		0.542	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184	
BTN3A3	10384	hgsc.bcm.edu	37	6	26446209	26446209	+	Silent	SNP	C	C	T	rs3846848	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26446209C>T	ENST00000244519.2	+	5	954	c.711C>T	c.(709-711)atC>atT	p.I237I	BTN3A3_ENST00000339789.4_Silent_p.I195I|BTN3A3_ENST00000361232.3_Silent_p.I195I	NM_006994.4	NP_008925.1	O00478	BT3A3_HUMAN	butyrophilin, subfamily 3, member A3	237					T cell mediated immunity (GO:0002456)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(15)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30						GCATATCCATCGCAGGTCAGT	0.542													C|||	725	0.144768	0.1634	0.1772	5008	,	,		21137	0.0308		0.165	False		,,,				2504	0.1933				p.I237I		Atlas-SNP	.											.	BTN3A3	56	.	0			c.C711T						PASS	.	C	,,	787,3619	318.2+/-295.5	65,657,1481	118.0	111.0	113.0		,711,585	-6.2	0.0	6	dbSNP_108	113	1450,7150	279.0+/-293.7	125,1200,2975	no	intron,coding-synonymous,coding-synonymous	BTN3A3	NM_001242803.1,NM_006994.4,NM_197974.2	,,	190,1857,4456	TT,TC,CC		16.8605,17.862,17.1998	,,	,237/585,195/536	26446209	2237,10769	2203	4300	6503	SO:0001819	synonymous_variant	10384	exon5			ATCCATCGCAGGT	U90548	CCDS4611.1, CCDS4612.1, CCDS4612.2	6p22.1	2014-01-14			ENSG00000111801	ENSG00000111801		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1140	protein-coding gene	gene with protein product		613595				10354554, 9149941	Standard	NM_006994		Approved	BTF3, BTN3.3	uc003nhz.3	O00478	OTTHUMG00000014451	ENST00000244519.2:c.711C>T	6.37:g.26446209C>T		Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	151	78	0.516556	NM_006994	B4DWI7|E9PCP5	Silent	SNP	ENST00000244519.2	37	CCDS4611.1																																																																																			C|0.838;T|0.162	0.162	strong		0.542	BTN3A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040116.2	NM_006994	
SALL1	6299	hgsc.bcm.edu	37	16	51175658	51175658	+	Missense_Mutation	SNP	T	T	C	rs13336129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:51175658T>C	ENST00000251020.4	-	2	508	c.475A>G	c.(475-477)Agc>Ggc	p.S159G	SALL1_ENST00000440970.1_Missense_Mutation_p.S62G|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000541611.1_Intron|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	159	Poly-Ser.		S -> G (in dbSNP:rs13336129). {ECO:0000269|PubMed:9973281}.		adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S159G(1)		NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			ccgccgccgctgctgctgctg	0.632													-|||	243	0.0485224	0.0567	0.0461	5008	,	,		12570	0.0288		0.0845	False		,,,				2504	0.0225				p.S159G	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											SALL1,NS,carcinoma,0,1	SALL1	301	1	1	Substitution - Missense(1)	prostate(1)	c.A475G						scavenged	.	C	GLY/SER,GLY/SER	201,4161		4,193,1984	21.0	24.0	23.0		475,184	-0.4	0.0	16	dbSNP_121	23	540,8026		25,490,3768	no	missense,missense	SALL1	NM_002968.2,NM_001127892.1	56,56	29,683,5752	CC,CT,TT		6.304,4.608,5.7317	benign,benign	159/1325,62/1228	51175658	741,12187	2181	4283	6464	SO:0001583	missense	6299	exon2			CGCCGCTGCTGCT	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.475A>G	16.37:g.51175658T>C	ENSP00000251020:p.Ser159Gly	Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	100	95	0.95	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	125	0.05723443223443223	21	0.042682926829268296	18	0.049723756906077346	21	0.03671328671328671	65	0.08575197889182058	-	0.001	-3.561441	0.00009	0.04608	0.06304	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.06933	3.24;3.3	0.185	-0.371	0.12525	.	0.296893	0.19374	N	0.115821	T	0.00144	0.0004	N	0.08118	0	0.09310	N	1	B	0.19200	0.034	B	0.16289	0.015	T	0.43032	-0.9416	9	0.18710	T	0.47	.	.	.	.	rs13336129	159	Q9NSC2	SALL1_HUMAN	G	159;62;123	ENSP00000251020:S159G;ENSP00000407914:S62G	ENSP00000251020:S159G	S	-	1	0	SALL1	49733159	0.876000	0.30132	0.002000	0.10522	0.005000	0.04900	-0.084000	0.11268	-0.889000	0.03950	-0.925000	0.02716	AGC	T|0.933;C|0.067	0.067	strong		0.632	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
ZFP36L1	677	hgsc.bcm.edu	37	14	69259661	69259661	+	5'UTR	SNP	G	G	A	rs529200428		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:69259661G>A	ENST00000439696.2	-	0	296				ZFP36L1_ENST00000555997.1_5'Flank|ZFP36L1_ENST00000336440.3_5'UTR	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GTCATCCTGTGCGTTCGCGCG	0.597													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11745	0.0		0.0	False		,,,				2504	0.0				p.H68Y		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.C202T						PASS	.						121.0	118.0	119.0					14																	69259661		2203	4300	6503	SO:0001623	5_prime_UTR_variant	677	exon2			TCCTGTGCGTTCG	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.-6C>T	14.37:g.69259661G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	114	51	0.447368	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.485806	0.26686	.	.	ENSG00000185650	ENST00000553375	.	.	.	4.56	3.43	0.39272	.	.	.	.	.	T	0.56963	0.2021	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53933	-0.8368	4	.	.	.	.	7.8188	0.29276	0.1044:0.0:0.729:0.1666	.	.	.	.	Y	68	.	.	H	-	1	0	ZFP36L1	68329414	0.999000	0.42202	1.000000	0.80357	0.798000	0.45092	3.149000	0.50655	2.065000	0.61736	0.561000	0.74099	CAC	.	.	none		0.597	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
AGBL1	123624	hgsc.bcm.edu	37	15	86800209	86800209	+	Silent	SNP	C	C	T	rs1353578	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:86800209C>T	ENST00000441037.2	+	7	818	c.723C>T	c.(721-723)ccC>ccT	p.P241P	AGBL1_ENST00000421325.2_Silent_p.P241P	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	241					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						TCCCGGTCCCCGGGTGCATCA	0.502													T|||	2703	0.539736	0.7655	0.5346	5008	,	,		20530	0.2163		0.5765	False		,,,				2504	0.5337				p.P241P		Atlas-SNP	.											.	AGBL1	151	.	0			c.C723T						PASS	.	T		3024,1048		1123,778,135	70.0	71.0	71.0		723	2.2	0.1	15	dbSNP_88	71	5016,3370		1538,1940,715	no	coding-synonymous	AGBL1	NM_152336.2		2661,2718,850	TT,TC,CC		40.186,25.7367,35.4632		241/1067	86800209	8040,4418	2036	4193	6229	SO:0001819	synonymous_variant	123624	exon7			GGTCCCCGGGTGC	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.723C>T	15.37:g.86800209C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	107	45	0.420561	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			C|0.471;T|0.529	0.529	strong		0.502	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
OR5T2	219464	hgsc.bcm.edu	37	11	55999950	55999950	+	Missense_Mutation	SNP	G	G	C	rs12221615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55999950G>C	ENST00000313264.4	-	1	787	c.712C>G	c.(712-714)Ctc>Gtc	p.L238V		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	238			L -> V (in dbSNP:rs12221615).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L238V(1)		endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					AAGTAGAAGAGTAGAAGCTGG	0.433													g|||	507	0.101238	0.059	0.1009	5008	,	,		21064	0.125		0.1173	False		,,,				2504	0.1176				p.L238V		Atlas-SNP	.											OR5T2,right_upper_lobe,carcinoma,+2,3	OR5T2	107	3	1	Substitution - Missense(1)	stomach(1)	c.C712G						PASS	.	G	VAL/LEU	272,4130	152.5+/-186.2	9,254,1938	124.0	117.0	119.0		712	1.9	0.1	11	dbSNP_120	119	1003,7589	216.0+/-255.2	54,895,3347	yes	missense	OR5T2	NM_001004746.1	32	63,1149,5285	CC,CG,GG		11.6736,6.179,9.8122	benign	238/360	55999950	1275,11719	2201	4296	6497	SO:0001583	missense	219464	exon1			AGAAGAGTAGAAG	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.712C>G	11.37:g.55999950G>C	ENSP00000323688:p.Leu238Val	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	156	78	0.5	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	238	0.10897435897435898	34	0.06910569105691057	33	0.09116022099447514	74	0.12937062937062938	97	0.1279683377308707	G	8.300	0.819727	0.16607	0.06179	0.116736	ENSG00000181718	ENST00000313264	T	0.00164	8.64	5.07	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	0.201650	0.24403	N	0.038822	T	0.00012	0.0000	N	0.11818	0.18	0.80722	P	0.0	B	0.30068	0.267	B	0.37888	0.26	T	0.20739	-1.0266	9	0.38643	T	0.18	.	9.6981	0.40169	0.0769:0.4016:0.5216:0.0	rs12221615;rs52834703;rs12221615	238	Q8NGG2	OR5T2_HUMAN	V	238	ENSP00000323688:L238V	ENSP00000323688:L238V	L	-	1	0	OR5T2	55756526	0.000000	0.05858	0.067000	0.19924	0.132000	0.20833	-0.189000	0.09629	0.633000	0.30452	0.478000	0.44815	CTC	G|0.901;C|0.099	0.099	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
MYO18B	84700	hgsc.bcm.edu	37	22	26422980	26422980	+	Missense_Mutation	SNP	A	A	G	rs2236005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26422980A>G	ENST00000407587.2	+	43	7212	c.7043A>G	c.(7042-7044)cAa>cGa	p.Q2348R	MYO18B_ENST00000335473.7_Missense_Mutation_p.Q2347R|MYO18B_ENST00000536101.1_Missense_Mutation_p.Q2347R			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2347						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						TCGAAAACCCAATTCAGTTCC	0.567													G|||	2135	0.426318	0.9107	0.2522	5008	,	,		18809	0.244		0.174	False		,,,				2504	0.3425				p.Q2347R		Atlas-SNP	.											MYO18B,NS,carcinoma,-1,1	MYO18B	322	1	0			c.A7040G						PASS	.	G	ARG/GLN	2970,896		1156,658,119	72.0	80.0	78.0		7040	3.8	0.0	22	dbSNP_98	78	1273,6995		103,1067,2964	yes	missense	MYO18B	NM_032608.5	43	1259,1725,3083	GG,GA,AA		15.3967,23.1764,34.9679	benign	2347/2568	26422980	4243,7891	1933	4134	6067	SO:0001583	missense	84700	exon43			AAACCCAATTCAG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7043A>G	22.37:g.26422980A>G	ENSP00000386096:p.Gln2348Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		761|761	0.3484432234432234|0.3484432234432234	424|424	0.8617886178861789|0.8617886178861789	84|84	0.23204419889502761|0.23204419889502761	135|135	0.23601398601398602|0.23601398601398602	118|118	0.15567282321899736|0.15567282321899736	G|G	0.003|0.003	-2.419485|-2.419485	0.00188|0.00188	0.768236|0.768236	0.153967|0.153967	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.84589	.|-1.86;-1.86;-1.87	4.89|4.89	3.78|3.78	0.43462|0.43462	.|.	.|0.274240	.|0.23176	.|N	.|0.051064	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.00170|0.00170	-1.935|-1.935	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.01281	.|0.0;0.0;0.0;0.0;0.0	T|T	0.42699|0.42699	-0.9436|-0.9436	4|9	.|0.02654	.|T	.|1	.|.	4.7014|4.7014	0.12828|0.12828	0.2629:0.0:0.5664:0.1706|0.2629:0.0:0.5664:0.1706	rs2236005;rs56868966;rs2236005|rs2236005;rs56868966;rs2236005	.|1860;2349;2347;2348;2347	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	D|R	297|2347;2347;2348	.|ENSP00000441229:Q2347R;ENSP00000334563:Q2347R;ENSP00000386096:Q2348R	.|ENSP00000334563:Q2347R	N|Q	+|+	1|2	0|0	MYO18B|MYO18B	24752980|24752980	0.121000|0.121000	0.22262|0.22262	0.005000|0.005000	0.12908|0.12908	0.094000|0.094000	0.18550|0.18550	2.406000|2.406000	0.44557|0.44557	1.056000|1.056000	0.40484|0.40484	-0.355000|-0.355000	0.07637|0.07637	AAT|CAA	A|0.618;G|0.382	0.382	strong		0.567	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
MRPL28	10573	hgsc.bcm.edu	37	16	419092	419092	+	Silent	SNP	A	A	G	rs3830160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:419092A>G	ENST00000199706.8	-	3	452	c.417T>C	c.(415-417)taT>taC	p.Y139Y	MRPL28_ENST00000389675.2_Silent_p.Y139Y|MRPL28_ENST00000429738.1_Intron	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	139					translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				AGTCGAGCCCATAAGCCTCAT	0.577													G|||	3412	0.68131	0.8858	0.6383	5008	,	,		19336	0.5317		0.5487	False		,,,				2504	0.726				p.Y139Y		Atlas-SNP	.											.	MRPL28	15	.	0			c.T417C						PASS	.	G		3712,694	291.3+/-281.4	1568,576,59	155.0	115.0	128.0		417	-3.3	0.8	16	dbSNP_107	128	4982,3618	522.6+/-380.1	1468,2046,786	no	coding-synonymous	MRPL28	NM_006428.4		3036,2622,845	GG,GA,AA		42.0698,15.7512,33.1539		139/257	419092	8694,4312	2203	4300	6503	SO:0001819	synonymous_variant	10573	exon3			GAGCCCATAAGCC	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.417T>C	16.37:g.419092A>G		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	100	48	0.48	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Silent	SNP	ENST00000199706.8	37	CCDS32349.1																																																																																			A|0.346;G|0.654	0.654	strong		0.577	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
RBM46	166863	hgsc.bcm.edu	37	4	155720274	155720274	+	Silent	SNP	T	T	C	rs156502	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155720274T>C	ENST00000281722.3	+	4	1195	c.960T>C	c.(958-960)aaT>aaC	p.N320N	RBM46_ENST00000514866.1_Silent_p.N320N|RBM46_ENST00000510397.1_Silent_p.N320N	NM_144979.3	NP_659416.1	Q8TBY0	RBM46_HUMAN	RNA binding motif protein 46	320							nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(7)|skin(3)|urinary_tract(2)	26	all_hematologic(180;0.24)	Renal(120;0.0854)				AGCATCTTAATGGTCAGATTA	0.398													C|||	3424	0.683706	0.9213	0.6787	5008	,	,		17912	0.747		0.4155	False		,,,				2504	0.5767				p.N320N		Atlas-SNP	.											.	RBM46	76	.	0			c.T960C						PASS	.	C		3723,683	283.1+/-276.9	1594,535,74	68.0	71.0	70.0		960	3.8	1.0	4	dbSNP_79	70	3527,5073	630.4+/-398.4	710,2107,1483	no	coding-synonymous	RBM46	NM_144979.3		2304,2642,1557	CC,CT,TT		41.0116,15.5016,44.2565		320/534	155720274	7250,5756	2203	4300	6503	SO:0001819	synonymous_variant	166863	exon4			TCTTAATGGTCAG	BC028588	CCDS3790.1, CCDS64085.1, CCDS64086.1	4q32.1	2013-02-12				ENSG00000151962		"""RNA binding motif (RRM) containing"""	28401	protein-coding gene	gene with protein product	"""cancer/testis antigen 68"""					12477932	Standard	NM_144979		Approved	MGC27016, CT68	uc003ioo.4	Q8TBY0		ENST00000281722.3:c.960T>C	4.37:g.155720274T>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	158	156	0.987342	NM_144979	B3KWU8|B4DZ27	Silent	SNP	ENST00000281722.3	37	CCDS3790.1																																																																																			T|0.395;C|0.605	0.605	strong		0.398	RBM46-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365259.1	NM_144979	
SCN10A	6336	hgsc.bcm.edu	37	3	38768300	38768300	+	Missense_Mutation	SNP	T	T	C	rs57326399	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38768300T>C	ENST00000449082.2	-	16	2883	c.2884A>G	c.(2884-2886)Att>Gtt	p.I962V		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	962					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.I962V(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TTGGCAGCAATGTGGTTCTCA	0.602													C|||	1055	0.210663	0.0862	0.1153	5008	,	,		19922	0.373		0.2545	False		,,,				2504	0.2342				p.I962V		Atlas-SNP	.											SCN10A,NS,carcinoma,0,1	SCN10A	359	1	1	Substitution - Missense(1)	prostate(1)	c.A2884G						scavenged	.	C	VAL/ILE	482,3924	782.1+/-414.5	24,434,1745	60.0	62.0	61.0		2884	-4.2	0.1	3	dbSNP_129	61	2253,6347	708.4+/-405.7	296,1661,2343	yes	missense	SCN10A	NM_006514.2	29	320,2095,4088	CC,CT,TT		26.1977,10.9396,21.0288	benign	962/1957	38768300	2735,10271	2203	4300	6503	SO:0001583	missense	6336	exon16			CAGCAATGTGGTT	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.2884A>G	3.37:g.38768300T>C	ENSP00000390600:p.Ile962Val	Somatic	149	2	0.0134228		WXS	Illumina HiSeq	Phase_I	139	139	1	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	504	0.23076923076923078	35	0.07113821138211382	47	0.1298342541436464	231	0.40384615384615385	191	0.2519788918205805	C	10.05	1.245153	0.22796	0.109396	0.261977	ENSG00000185313	ENST00000449082	D	0.83837	-1.77	5.2	-4.17	0.03857	Sodium ion transport-associated (1);	6.869170	0.00447	N	0.000087	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.34103	0.437	B	0.33799	0.17	T	0.04522	-1.0945	9	0.49607	T	0.09	.	6.3619	0.21433	0.0:0.2379:0.3312:0.4309	rs57326399;rs62242441	962	Q9Y5Y9	SCNAA_HUMAN	V	962	ENSP00000390600:I962V	ENSP00000390600:I962V	I	-	1	0	SCN10A	38743304	0.000000	0.05858	0.093000	0.20910	0.059000	0.15707	0.052000	0.14163	-0.612000	0.05701	-1.337000	0.01257	ATT	T|0.779;C|0.221	0.221	strong		0.602	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
IDNK	414328	hgsc.bcm.edu	37	9	86258685	86258685	+	Missense_Mutation	SNP	A	A	C	rs1052690	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:86258685A>C	ENST00000376419.4	+	5	558	c.554A>C	c.(553-555)aAa>aCa	p.K185T	IDNK_ENST00000277124.8_Missense_Mutation_p.K139T|IDNK_ENST00000405990.3_3'UTR|IDNK_ENST00000454393.1_Missense_Mutation_p.K228T	NM_001001551.3	NP_001001551.2	Q5T6J7	GNTK_HUMAN	idnK, gluconokinase homolog (E. coli)	185			K -> T (in dbSNP:rs1052690).		D-gluconate catabolic process (GO:0046177)		ATP binding (GO:0005524)|gluconokinase activity (GO:0046316)										GAAACCCTAAAAATGAAATGA	0.403													A|||	487	0.0972444	0.0189	0.1254	5008	,	,		18949	0.0337		0.1889	False		,,,				2504	0.1544				p.K185T		Atlas-SNP	.											.	.	.	.	0			c.A554C						PASS	.	A	THR/LYS,	182,4214		8,166,2024	35.0	39.0	38.0		554,	4.0	0.0	9	dbSNP_86	38	1596,7002		141,1314,2844	yes	missense,utr-3	C9orf103	NM_001001551.2,NM_001190727.1	78,	149,1480,4868	CC,CA,AA		18.5625,4.1401,13.6832	probably-damaging,	185/188,	86258685	1778,11216	2198	4299	6497	SO:0001583	missense	414328	exon5			CCCTAAAAATGAA	BC036421	CCDS35048.1, CCDS35048.2, CCDS59134.1	9q21.32	2012-03-30	2012-03-30	2012-03-30	ENSG00000148057	ENSG00000148057			31367	protein-coding gene	gene with protein product		611343	"""chromosome 9 open reading frame 103"""	C9orf103			Standard	NM_001001551		Approved	bA522I20.2	uc004amu.3	Q5T6J7	OTTHUMG00000020105	ENST00000376419.4:c.554A>C	9.37:g.86258685A>C	ENSP00000365601:p.Lys185Thr	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	19	12	0.631579	NM_001001551	A5PLN6|Q5T6J6	Missense_Mutation	SNP	ENST00000376419.4	37	CCDS35048.2	210	0.09615384615384616	10	0.02032520325203252	58	0.16022099447513813	12	0.02097902097902098	130	0.17150395778364116	A	15.17	2.753549	0.49362	0.041401	0.185625	ENSG00000148057	ENST00000277124;ENST00000376419;ENST00000454393	T;T;T	0.29142	1.58;1.58;1.58	5.12	3.99	0.46301	.	1.305770	0.04911	N	0.453162	T	0.00039	0.0001	N	0.25245	0.725	0.80722	P	0.0	B	0.22604	0.072	B	0.32211	0.142	T	0.16041	-1.0416	9	0.49607	T	0.09	-14.0422	6.2376	0.20772	0.7759:0.0:0.0803:0.1438	rs1052690;rs3174170;rs17322759;rs58967751;rs1052690	185	Q5T6J7	GNTK_HUMAN	T	139;185;228	ENSP00000277124:K139T;ENSP00000365601:K185T;ENSP00000403290:K228T	ENSP00000277124:K139T	K	+	2	0	C9orf103	85448505	0.017000	0.18338	0.004000	0.12327	0.015000	0.08874	2.782000	0.47758	1.954000	0.56735	0.524000	0.50904	AAA	A|0.889;C|0.111	0.111	strong		0.403	IDNK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052837.2	NM_001001551	
C19orf57	79173	hgsc.bcm.edu	37	19	14003969	14003969	+	Missense_Mutation	SNP	G	G	C	rs62622787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14003969G>C	ENST00000586783.1	-	3	273	c.274C>G	c.(274-276)Ctt>Gtt	p.L92V	C19orf57_ENST00000454313.1_Missense_Mutation_p.L92V|C19orf57_ENST00000346736.2_Missense_Mutation_p.L92V|C19orf57_ENST00000591586.1_Missense_Mutation_p.L92V			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	92					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)			GAAGGAGGAAGGGGAGCTGGC	0.537													G|||	100	0.0199681	0.003	0.0331	5008	,	,		17877	0.001		0.0567	False		,,,				2504	0.0153				p.L92V		Atlas-SNP	.											.	C19orf57	34	.	0			c.C274G						PASS	.	G	VAL/LEU	65,4339		2,61,2139	45.0	43.0	44.0		274	-3.6	0.0	19	dbSNP_129	44	578,8018		22,534,3742	yes	missense	C19orf57	NM_024323.3	32	24,595,5881	CC,CG,GG		6.7241,1.4759,4.9462	possibly-damaging	92/638	14003969	643,12357	2202	4298	6500	SO:0001583	missense	79173	exon4			GAGGAAGGGGAGC	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.274C>G	19.37:g.14003969G>C	ENSP00000465822:p.Leu92Val	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		62	0.028388278388278388	1	0.0020325203252032522	15	0.04143646408839779	1	0.0017482517482517483	45	0.059366754617414245	G	14.65	2.599703	0.46318	0.014759	0.067241	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.33865	1.39;1.39	3.99	-3.6	0.04570	.	1.088120	0.07297	N	0.873518	T	0.01765	0.0056	L	0.29908	0.895	0.09310	N	1	P	0.50819	0.939	B	0.43754	0.43	T	0.09443	-1.0674	10	0.54805	T	0.06	0.0	4.4323	0.11533	0.1567:0.0:0.517:0.3264	rs62622787	92	Q0VDD7-2	.	V	92	ENSP00000404382:L92V;ENSP00000254336:L92V	ENSP00000254336:L92V	L	-	1	0	C19orf57	13864969	0.000000	0.05858	0.006000	0.13384	0.234000	0.25298	-2.428000	0.01025	-0.367000	0.08052	0.561000	0.74099	CTT	G|0.955;C|0.045	0.045	strong		0.537	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
ENPP7	339221	hgsc.bcm.edu	37	17	77709405	77709405	+	Silent	SNP	C	C	T	rs78553282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:77709405C>T	ENST00000328313.5	+	3	1184	c.963C>T	c.(961-963)taC>taT	p.Y321Y		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)			CCTTCCACTACGCCAACAACC	0.617													C|||	230	0.0459265	0.0469	0.0245	5008	,	,		16412	0.0188		0.0298	False		,,,				2504	0.1043				p.Y321Y		Atlas-SNP	.											.	ENPP7	63	.	0			c.C963T						PASS	.	C		204,4202	126.1+/-163.2	7,190,2006	73.0	68.0	70.0		963	-2.6	1.0	17	dbSNP_131	70	357,8243	119.7+/-179.0	9,339,3952	no	coding-synonymous	ENPP7	NM_178543.3		16,529,5958	TT,TC,CC		4.1512,4.63,4.3134		321/459	77709405	561,12445	2203	4300	6503	SO:0001819	synonymous_variant	339221	exon3			CCACTACGCCAAC	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.963C>T	17.37:g.77709405C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	81	33	0.407407	NM_178543		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			C|0.963;T|0.037	0.037	strong		0.617	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543	
DTX2	113878	hgsc.bcm.edu	37	7	76126737	76126737	+	Missense_Mutation	SNP	C	C	T	rs145964625		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:76126737C>T	ENST00000324432.5	+	7	1603	c.1093C>T	c.(1093-1095)Cgt>Tgt	p.R365C	DTX2_ENST00000430490.2_Missense_Mutation_p.R365C|DTX2_ENST00000446600.1_Missense_Mutation_p.R274C|DTX2_ENST00000413936.2_Missense_Mutation_p.R365C|DTX2_ENST00000307569.8_Intron|DTX2_ENST00000446820.2_Intron	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	365					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.R365C(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						TCCCGCCTCCCGTCTGGCTTC	0.557																																					p.R365C		Atlas-SNP	.											DTX2,NS,haematopoietic_neoplasm,0,3	DTX2	64	3	1	Substitution - Missense(1)	large_intestine(1)	c.C1093T						scavenged	.						34.0	34.0	34.0					7																	76126737		2199	4273	6472	SO:0001583	missense	113878	exon6			GCCTCCCGTCTGG		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1093C>T	7.37:g.76126737C>T	ENSP00000322885:p.Arg365Cys	Somatic	419	0	0		WXS	Illumina HiSeq	Phase_I	356	118	0.331461	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	37	CCDS5587.1	.	.	.	.	.	.	.	.	.	.	.	13.40	2.224425	0.39300	.	.	ENSG00000091073	ENST00000324432;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490	T;T;T;T	0.12147	2.72;2.71;2.72;2.72	5.41	-3.71	0.04424	.	1.247470	0.05079	N	0.483163	T	0.07188	0.0182	N	0.04203	-0.255	0.80722	D	1	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.22243	-1.0222	10	0.42905	T	0.14	-0.0088	12.0171	0.53319	0.1235:0.6798:0.0:0.1966	.	274;274;365	F5GX89;E7ET89;Q86UW9	.;.;DTX2_HUMAN	C	365;274;274;365;365	ENSP00000322885:R365C;ENSP00000397648:R274C;ENSP00000390218:R365C;ENSP00000411986:R365C	ENSP00000322885:R365C	R	+	1	0	AC005522.1	75964673	0.878000	0.30173	0.971000	0.41717	0.991000	0.79684	-0.087000	0.11215	-0.633000	0.05545	-0.302000	0.09304	CGT	.	.	weak		0.557	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
OR1B1	347169	hgsc.bcm.edu	37	9	125391241	125391241	+	Nonsense_Mutation	SNP	G	G	A	rs1476860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:125391241G>A	ENST00000304833.3	-	1	611	c.574C>T	c.(574-576)Cga>Tga	p.R192*	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						CAAGAGGCTCGCAGAAGTGGC	0.527													G|||	1699	0.339257	0.053	0.4683	5008	,	,		19904	0.5972		0.2763	False		,,,				2504	0.4335				p.R192X		Atlas-SNP	.											.	OR1B1	48	.	0			c.C574T	GRCh37	CM035846	OR1B1	M	rs1476860	PASS	.	G	stop/ARG	398,4008	197.7+/-221.8	14,370,1819	47.0	45.0	46.0		574	-6.1	0.1	9	dbSNP_88	46	2554,6046	415.8+/-351.9	349,1856,2095	yes	stop-gained	OR1B1	NM_001004450.1		363,2226,3914	AA,AG,GG		29.6977,9.0331,22.6972		192/319	125391241	2952,10054	2203	4300	6503	SO:0001587	stop_gained	347169	exon1			AGGCTCGCAGAAG	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.574C>T	9.37:g.125391241G>A	ENSP00000303151:p.Arg192*	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	107	37	0.345794	NM_001004450	Q6IFN3	Nonsense_Mutation	SNP	ENST00000304833.3	37	CCDS35126.1	727	0.33287545787545786	39	0.07926829268292683	149	0.4116022099447514	326	0.5699300699300699	213	0.28100263852242746	G	16.67	3.187345	0.57909	0.090331	0.296977	ENSG00000171484	ENST00000304833	.	.	.	4.63	-6.05	0.02172	.	0.503387	0.14973	N	0.287663	.	.	.	.	.	.	0.09310	P	0.999999999716479	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-0.7245	7.8675	0.29545	0.2069:0.0:0.1578:0.6353	rs1476860;rs59619152;rs1476860	.	.	.	X	192	.	ENSP00000303151:R192X	R	-	1	2	OR1B1	124431062	0.000000	0.05858	0.142000	0.22268	0.799000	0.45148	-1.276000	0.02815	-0.973000	0.03555	-1.636000	0.00776	CGA	G|0.725;A|0.275	0.275	strong		0.527	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
TULP4	56995	hgsc.bcm.edu	37	6	158870081	158870081	+	Silent	SNP	A	A	G	rs705956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:158870081A>G	ENST00000367097.3	+	4	1954	c.597A>G	c.(595-597)agA>agG	p.R199R	TULP4_ENST00000367094.2_Silent_p.R199R	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	199			R -> S (in dbSNP:rs705956).		intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		GCCACGGCAGAATGCTGGCCC	0.612													G|||	3032	0.605431	0.7844	0.5288	5008	,	,		20217	0.3968		0.5895	False		,,,				2504	0.6493				p.R199R		Atlas-SNP	.											TULP4,NS,carcinoma,+1,1	TULP4	137	1	0			c.A597G						scavenged	.	G	,	3371,1035	381.6+/-324.1	1305,761,137	166.0	121.0	136.0		597,597	3.5	1.0	6	dbSNP_86	136	5009,3591	519.7+/-379.5	1469,2071,760	no	coding-synonymous,coding-synonymous	TULP4	NM_001007466.1,NM_020245.3	,	2774,2832,897	GG,GA,AA		41.7558,23.4907,35.5682	,	199/679,199/1544	158870081	8380,4626	2203	4300	6503	SO:0001819	synonymous_variant	56995	exon4			CGGCAGAATGCTG		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.597A>G	6.37:g.158870081A>G		Somatic	57	1	0.0175439		WXS	Illumina HiSeq	Phase_I	48	48	1	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Silent	SNP	ENST00000367097.3	37	CCDS34561.1																																																																																			A|0.374;G|0.626	0.626	strong		0.612	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
RNF183	138065	hgsc.bcm.edu	37	9	116060221	116060221	+	Missense_Mutation	SNP	C	C	T	rs3750533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:116060221C>T	ENST00000478815.1	-	1	1824	c.244G>A	c.(244-246)Gcc>Acc	p.A82T	RNF183_ENST00000297894.5_Missense_Mutation_p.A82T|RNF183_ENST00000478493.1_5'Flank|RNF183_ENST00000441031.3_Missense_Mutation_p.A82T|RNF183_ENST00000416588.2_Missense_Mutation_p.A82T			Q96D59	RN183_HUMAN	ring finger protein 183	82			A -> T (in dbSNP:rs3750533). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			lung(1)|prostate(1)|skin(1)	3						CGGAGCAGGGCGAGCATGGCA	0.667													T|||	2014	0.402157	0.4478	0.196	5008	,	,		17881	0.4226		0.3032	False		,,,				2504	0.5675				p.A82T		Atlas-SNP	.											.	RNF183	11	.	0			c.G244A						PASS	.	T	THR/ALA	1881,2427		439,1003,712	33.0	41.0	38.0		244	5.2	0.8	9	dbSNP_107	38	2776,5742		468,1840,1951	yes	missense	RNF183	NM_145051.3	58	907,2843,2663	TT,TC,CC		32.5898,43.663,36.3091	benign	82/193	116060221	4657,8169	2154	4259	6413	SO:0001583	missense	138065	exon2			GCAGGGCGAGCAT		CCDS43866.1	9q32	2007-04-24			ENSG00000165188	ENSG00000165188		"""RING-type (C3HC4) zinc fingers"""	28721	protein-coding gene	gene with protein product						12477932	Standard	NM_145051		Approved	MGC4734	uc004bgz.3	Q96D59	OTTHUMG00000020520	ENST00000478815.1:c.244G>A	9.37:g.116060221C>T	ENSP00000419454:p.Ala82Thr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	170	89	0.523529	NM_145051		Missense_Mutation	SNP	ENST00000478815.1	37	CCDS43866.1	803	0.3676739926739927	238	0.483739837398374	82	0.2265193370165746	247	0.4318181818181818	236	0.3113456464379947	T	2.790	-0.251487	0.05867	0.43663	0.325898	ENSG00000165188	ENST00000441031;ENST00000416588;ENST00000478815;ENST00000297894	D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13	5.17	5.17	0.71159	.	0.643900	0.16726	N	0.202060	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.22034	-1.0228	6	0.11485	T	0.65	-20.9468	9.2761	0.37700	0.0:0.0848:0.0:0.9152	rs3750533;rs17856415;rs58380446;rs3750533	.	.	.	T	82	ENSP00000417176:A82T;ENSP00000420740:A82T;ENSP00000419454:A82T;ENSP00000417943:A82T	ENSP00000417943:A82T	A	-	1	0	RNF183	115100042	0.255000	0.24002	0.848000	0.33437	0.945000	0.59286	1.729000	0.38115	0.996000	0.38943	-0.254000	0.11334	GCC	C|0.613;T|0.386	0.386	strong		0.667	RNF183-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356360.1	NM_145051	
HRNR	388697	hgsc.bcm.edu	37	1	152191033	152191033	+	Silent	SNP	A	A	G	rs148722408	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152191033A>G	ENST00000368801.2	-	3	3147	c.3072T>C	c.(3070-3072)taT>taC	p.Y1024Y	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1024					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.Y1024Y(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)			TATATGGGCCATAGCTGGAAG	0.602													a|||	31	0.0061901	0.0023	0.0086	5008	,	,		21129	0.0		0.0219	False		,,,				2504	0.0				p.Y1024Y		Atlas-SNP	.											HRNR,NS,carcinoma,0,2	HRNR	403	2	1	Substitution - coding silent(1)	prostate(1)	c.T3072C						PASS	.	G		9,4397	16.8+/-37.8	0,9,2194	152.0	168.0	163.0		3072	-5.3	0.0	1	dbSNP_134	163	139,8461	69.4+/-131.9	2,135,4163	no	coding-synonymous	HRNR	NM_001009931.1		2,144,6357	GG,GA,AA		1.6163,0.2043,1.1379		1024/2851	152191033	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			TGGGCCATAGCTG	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.3072T>C	1.37:g.152191033A>G		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	183	96	0.52459	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			A|0.991;G|0.009	0.009	strong		0.602	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
CSTF2T	23283	hgsc.bcm.edu	37	10	53458047	53458047	+	Silent	SNP	A	A	G	rs3740228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:53458047A>G	ENST00000331173.4	-	1	1308	c.1263T>C	c.(1261-1263)cgT>cgC	p.R421R	PRKG1_ENST00000373980.4_Intron|PRKG1_ENST00000401604.2_Intron|PRKG1_ENST00000373985.1_Intron	NM_015235.2	NP_056050.1	Q9H0L4	CSTFT_HUMAN	cleavage stimulation factor, 3' pre-RNA, subunit 2, 64kDa, tau variant	421	9 X 5 AA tandem repeats of M-E-T-R-[AG].|Gly-rich.				mRNA processing (GO:0006397)	intracellular (GO:0005622)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R421R(1)		NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	30				COAD - Colon adenocarcinoma(2;0.00736)|Colorectal(2;0.00898)|all cancers(4;0.0188)|GBM - Glioblastoma multiforme(4;0.0778)|Epithelial(53;0.122)		TTTCCATGGCACGAGTCTCCA	0.527													G|||	1251	0.2498	0.4501	0.1196	5008	,	,		18282	0.2173		0.1551	False		,,,				2504	0.2025				p.R421R		Atlas-SNP	.											CSTF2T,NS,carcinoma,0,1	CSTF2T	64	1	1	Substitution - coding silent(1)	stomach(1)	c.T1263C						PASS	.	G	,,	1671,2735	656.0+/-400.0	315,1041,847	184.0	170.0	175.0		,,1263	1.4	1.0	10	dbSNP_107	175	1187,7413	764.7+/-407.6	85,1017,3198	no	intron,intron,coding-synonymous	PRKG1,CSTF2T	NM_001098512.2,NM_006258.3,NM_015235.2	,,	400,2058,4045	GG,GA,AA		13.8023,37.9256,21.9745	,,	,,421/617	53458047	2858,10148	2203	4300	6503	SO:0001819	synonymous_variant	23283	exon1			CATGGCACGAGTC	AB014589	CCDS7245.1	10q11	2013-02-12			ENSG00000177613	ENSG00000177613		"""RNA binding motif (RRM) containing"""	17086	protein-coding gene	gene with protein product		611968				12408968, 11113135	Standard	NM_015235		Approved	DKFZp434C1013, KIAA0689, CstF-64T	uc001jjp.3	Q9H0L4	OTTHUMG00000018246	ENST00000331173.4:c.1263T>C	10.37:g.53458047A>G		Somatic	204	1	0.00490196		WXS	Illumina HiSeq	Phase_I	196	102	0.520408	NM_015235	B2RAR9|O75174|Q53HK6|Q7LGE8|Q8N6T1	Silent	SNP	ENST00000331173.4	37	CCDS7245.1																																																																																			A|0.755;G|0.245	0.245	strong		0.527	CSTF2T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048097.1	NM_015235	
FBN3	84467	hgsc.bcm.edu	37	19	8191184	8191184	+	Missense_Mutation	SNP	C	C	T	rs35025963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8191184C>T	ENST00000600128.1	-	21	3016	c.2602G>A	c.(2602-2604)Gat>Aat	p.D868N	FBN3_ENST00000601739.1_Missense_Mutation_p.D868N|FBN3_ENST00000270509.2_Missense_Mutation_p.D868N			Q75N90	FBN3_HUMAN	fibrillin 3	868			D -> N (in dbSNP:rs35025963).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CAGTTACCATCGCAGGTGACA	0.647													C|||	1500	0.299521	0.0938	0.3228	5008	,	,		15630	0.379		0.2823	False		,,,				2504	0.4969				p.D868N		Atlas-SNP	.											.	FBN3	300	.	0			c.G2602A						PASS	.	C	ASN/ASP	563,3837		50,463,1687	41.0	40.0	41.0		2602	0.8	0.0	19	dbSNP_126	41	2368,6198		334,1700,2249	yes	missense	FBN3	NM_032447.3	23	384,2163,3936	TT,TC,CC		27.6442,12.7955,22.6053	benign	868/2810	8191184	2931,10035	2200	4283	6483	SO:0001583	missense	84467	exon20			TACCATCGCAGGT		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.2602G>A	19.37:g.8191184C>T	ENSP00000470498:p.Asp868Asn	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	615	0.2815934065934066	60	0.12195121951219512	118	0.3259668508287293	214	0.3741258741258741	223	0.2941952506596306	c	8.987	0.976745	0.18812	0.127955	0.276442	ENSG00000142449	ENST00000270509	D	0.90844	-2.74	3.05	0.768	0.18487	Matrix fibril-associated (2);	0.187814	0.45126	U	0.000389	T	0.00012	0.0000	N	0.20401	0.57	0.42668	P	0.006492999999999971	B	0.25048	0.117	B	0.17098	0.017	T	0.08680	-1.0710	9	0.31617	T	0.26	.	5.0229	0.14370	0.1654:0.6381:0.0:0.1965	rs35025963;rs62123265	868	Q75N90	FBN3_HUMAN	N	868	ENSP00000270509:D868N	ENSP00000270509:D868N	D	-	1	0	FBN3	8097184	1.000000	0.71417	0.028000	0.17463	0.010000	0.07245	2.090000	0.41682	0.130000	0.18549	0.555000	0.69702	GAT	C|0.760;T|0.240	0.240	strong		0.647	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
PDLIM5	10611	hgsc.bcm.edu	37	4	95496882	95496882	+	Missense_Mutation	SNP	C	C	T	rs2452600	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:95496882C>T	ENST00000317968.4	+	5	543	c.407C>T	c.(406-408)tCt>tTt	p.S136F	PDLIM5_ENST00000380180.3_Intron|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000542407.1_Missense_Mutation_p.S14F|PDLIM5_ENST00000538141.1_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	136			S -> F (in dbSNP:rs2452600). {ECO:0000269|PubMed:14702039}.		regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		GGTTCTGTGTCTTCACCAAAA	0.527													C|||	1125	0.224641	0.1051	0.2378	5008	,	,		19873	0.378		0.3121	False		,,,				2504	0.1288				p.S136F		Atlas-SNP	.											.	PDLIM5	76	.	0			c.C407T						PASS	.	C	,,,PHE/SER	594,3812	261.9+/-264.6	38,518,1647	296.0	259.0	271.0		,,,407	4.4	1.0	4	dbSNP_100	271	2668,5932	429.7+/-356.3	434,1800,2066	yes	intron,intron,intron,missense	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,155	472,2318,3713	TT,TC,CC		31.0233,13.4816,25.0807	,,,possibly-damaging	,,,136/597	95496882	3262,9744	2203	4300	6503	SO:0001583	missense	10611	exon5			CTGTGTCTTCACC	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.407C>T	4.37:g.95496882C>T	ENSP00000321746:p.Ser136Phe	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	232	126	0.543103	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	601	0.2751831501831502	43	0.08739837398373984	84	0.23204419889502761	242	0.4230769230769231	232	0.30606860158311344	C	20.8	4.042342	0.75732	0.134816	0.310233	ENSG00000163110	ENST00000317968;ENST00000542407	T;T	0.61627	0.58;0.09	5.25	4.39	0.52855	.	0.343767	0.28865	N	0.013899	T	0.00012	0.0000	L	0.44542	1.39	0.28580	P	0.9101637	P	0.49961	0.93	B	0.42214	0.38	T	0.45086	-0.9285	9	0.56958	D	0.05	.	13.5979	0.62002	0.0:0.9248:0.0:0.0752	rs2452600;rs3792659;rs52807888;rs56704997;rs2452600	136	Q96HC4	PDLI5_HUMAN	F	136;14	ENSP00000321746:S136F;ENSP00000442187:S14F	ENSP00000321746:S136F	S	+	2	0	PDLIM5	95715905	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.262000	0.43285	2.590000	0.87494	0.655000	0.94253	TCT	C|0.737;T|0.263	0.263	strong		0.527	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
FAM178B	51252	hgsc.bcm.edu	37	2	97559759	97559759	+	Silent	SNP	G	G	A	rs11677797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:97559759G>A	ENST00000417561.3	-	18	2123	c.2124C>T	c.(2122-2124)ctC>ctT	p.L708L	FAM178B_ENST00000470789.1_5'UTR|FAM178B_ENST00000490605.2_Silent_p.L560L|FAM178B_ENST00000327896.3_Silent_p.L528L|FAM178B_ENST00000393526.2_5'UTR			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	708										large_intestine(1)|ovary(1)	2						ATGGCCTCATGAGGCCCAGGA	0.622													.|||	2146	0.428514	0.236	0.4424	5008	,	,		17897	0.6766		0.1491	False		,,,				2504	0.7106				p.L560L		Atlas-SNP	.											.	FAM178B	35	.	0			c.C1680T						PASS	.	G	,,	1122,3282	394.7+/-329.4	151,820,1231	65.0	59.0	61.0		1680,57,	2.6	1.0	2	dbSNP_120	61	1572,7024	290.9+/-300.1	138,1296,2864	no	coding-synonymous,coding-synonymous,utr-5	FAM178B	NM_001122646.2,NM_001172667.1,NM_016490.4	,,	289,2116,4095	AA,AG,GG		18.2876,25.4768,20.7231	,,	560/680,19/139,	97559759	2694,10306	2202	4298	6500	SO:0001819	synonymous_variant	51252	exon14			CCTCATGAGGCCC	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.2124C>T	2.37:g.97559759G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Silent	SNP	ENST00000417561.3	37																																																																																				G|0.745;A|0.255	0.255	strong		0.622	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
TCP11L1	55346	hgsc.bcm.edu	37	11	33065394	33065394	+	Silent	SNP	C	C	T	rs1064005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:33065394C>T	ENST00000334274.4	+	2	475	c.75C>T	c.(73-75)ctC>ctT	p.L25L	TCP11L1_ENST00000432887.1_Silent_p.L25L|TCP11L1_ENST00000531632.2_Silent_p.L25L|TCP11L1_ENST00000530171.1_3'UTR	NM_018393.3	NP_060863.3	Q9NUJ3	T11L1_HUMAN	t-complex 11, testis-specific-like 1	25						microtubule (GO:0005874)				kidney(1)|liver(2)|lung(2)|skin(1)	6						AGGAAGGCCTCGAAGATGCTG	0.408													C|||	1991	0.397564	0.4576	0.4467	5008	,	,		19560	0.4226		0.3986	False		,,,				2504	0.2546				p.L25L		Atlas-SNP	.											.	TCP11L1	40	.	0			c.C75T						PASS	.	C	,	1991,2413	558.9+/-380.1	435,1121,646	199.0	205.0	203.0		75,75	-2.0	1.0	11	dbSNP_86	203	3417,5179	505.6+/-376.4	691,2035,1572	yes	coding-synonymous,coding-synonymous	TCP11L1	NM_001145541.1,NM_018393.3	,	1126,3156,2218	TT,TC,CC		39.751,45.2089,41.6	,	25/510,25/510	33065394	5408,7592	2202	4298	6500	SO:0001819	synonymous_variant	55346	exon2			AGGCCTCGAAGAT	BC041696	CCDS7882.1	11p13	2014-08-12	2012-09-20		ENSG00000176148	ENSG00000176148			25655	protein-coding gene	gene with protein product			"""t-complex 11 (mouse) like 1"""				Standard	NM_001145541		Approved	FLJ11336	uc010rei.2	Q9NUJ3	OTTHUMG00000165303	ENST00000334274.4:c.75C>T	11.37:g.33065394C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	71	31	0.43662	NM_001145541	D3DR01|Q8IVX4	Silent	SNP	ENST00000334274.4	37	CCDS7882.1																																																																																			C|0.583;T|0.417	0.417	strong		0.408	TCP11L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383377.4	NM_018393	
MUC16	94025	hgsc.bcm.edu	37	19	9083457	9083457	+	Missense_Mutation	SNP	C	C	T	rs17000886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9083457C>T	ENST00000397910.4	-	1	8561	c.8358G>A	c.(8356-8358)atG>atA	p.M2786I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	2786	Ser-rich.|Thr-rich.		M -> I (in dbSNP:rs17000886).		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						TGGTTAGTGGCATCACAGATG	0.498													C|||	953	0.190296	0.0711	0.2709	5008	,	,		21275	0.3036		0.173	False		,,,				2504	0.1953				p.M2786I		Atlas-SNP	.											.	MUC16	4315	.	0			c.G8358A						PASS	.	C	ILE/MET	288,3560		7,274,1643	63.0	61.0	61.0		8358	0.2	0.4	19	dbSNP_123	61	1491,6793		126,1239,2777	yes	missense	MUC16	NM_024690.2	10	133,1513,4420	TT,TC,CC		17.9986,7.4844,14.6637	benign	2786/14508	9083457	1779,10353	1924	4142	6066	SO:0001583	missense	94025	exon1			TAGTGGCATCACA	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.8358G>A	19.37:g.9083457C>T	ENSP00000381008:p.Met2786Ile	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	83	35	0.421687	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	c	5.769	0.326198	0.10900	0.074844	0.179986	ENSG00000181143	ENST00000397910	T	0.02085	4.46	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.33000	0.393	B	0.36030	0.216	T	0.47381	-0.9122	7	0.87932	D	0	.	.	.	.	rs17000886;rs52829317;rs17000886	2786	B5ME49	.	I	2786	ENSP00000381008:M2786I	ENSP00000381008:M2786I	M	-	3	0	MUC16	8944457	0.116000	0.22171	0.407000	0.26434	0.417000	0.31264	0.500000	0.22562	0.308000	0.22923	0.313000	0.20887	ATG	C|0.797;T|0.203	0.203	strong		0.498	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CRYZ	1429	hgsc.bcm.edu	37	1	75175886	75175886	+	Missense_Mutation	SNP	T	T	C	rs3819946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:75175886T>C	ENST00000340866.5	-	6	613	c.526A>G	c.(526-528)Att>Gtt	p.I176V	CRYZ_ENST00000370871.3_Missense_Mutation_p.I176V|CRYZ_ENST00000370872.3_Missense_Mutation_p.I39V|CRYZ_ENST00000417775.1_Missense_Mutation_p.I176V|CRYZ_ENST00000492102.1_5'Flank	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	176			I -> V (in dbSNP:rs3819946). {ECO:0000269|Ref.4}.		protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	GTGCCCAAAATCTTTAAGCCA	0.368													C|||	2307	0.460663	0.525	0.3386	5008	,	,		15728	0.7669		0.1421	False		,,,				2504	0.4724				p.I176V		Atlas-SNP	.											.	CRYZ	28	.	0			c.A526G						PASS	.	C	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	1978,2428	616.5+/-392.8	445,1088,670	75.0	76.0	75.0		526,526,115,526	5.5	1.0	1	dbSNP_107	75	1123,7477	767.3+/-407.6	74,975,3251	yes	missense,missense,missense,missense	CRYZ	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001889.3	29,29,29,29	519,2063,3921	CC,CT,TT		13.0581,44.8933,23.8428	benign,benign,benign,benign	176/330,176/296,39/193,176/330	75175886	3101,9905	2203	4300	6503	SO:0001583	missense	1429	exon6			CCAAAATCTTTAA		CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.526A>G	1.37:g.75175886T>C	ENSP00000339399:p.Ile176Val	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	214	112	0.523364	NM_001130043	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Missense_Mutation	SNP	ENST00000340866.5	37	CCDS665.1	914	0.4184981684981685	236	0.4796747967479675	111	0.30662983425414364	445	0.777972027972028	122	0.16094986807387862	C	3.968	-0.008900	0.07727	0.448933	0.130581	ENSG00000116791	ENST00000340866;ENST00000370872;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120	T;T;T;T;T;T	0.15603	2.41;2.41;2.41;2.41;4.15;4.15	5.54	5.54	0.83059	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	N	0.000000	T	0.01189	0.0039	N	0.00563	-1.375	0.53005	P	3.399999999997849E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.42344	-0.9457	9	0.02654	T	1	.	11.7379	0.51775	0.0:0.8555:0.0:0.1445	rs3819946;rs52802695;rs56521451;rs60828006;rs3819946	39;176;176	Q5HYE7;A6NN60;Q08257	.;.;QOR_HUMAN	V	176;39;176;176;176;176	ENSP00000339399:I176V;ENSP00000359909:I39V;ENSP00000399805:I176V;ENSP00000359908:I176V;ENSP00000359907:I176V;ENSP00000404289:I176V	ENSP00000339399:I176V	I	-	1	0	CRYZ	74948474	1.000000	0.71417	0.997000	0.53966	0.556000	0.35491	4.095000	0.57728	1.488000	0.48433	-0.213000	0.12676	ATT	C|0.339;N|0.000	0.339	strong		0.368	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1		
OR51B6	390058	hgsc.bcm.edu	37	11	5373251	5373251	+	Missense_Mutation	SNP	C	C	T	rs5006884	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373251C>T	ENST00000380219.1	+	1	514	c.514C>T	c.(514-516)Ctc>Ttc	p.L172F	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	172			L -> F (in dbSNP:rs5006884). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATCCCATGTACTCTCCCATGC	0.463													C|||	1170	0.233626	0.326	0.2349	5008	,	,		22587	0.0863		0.2644	False		,,,				2504	0.228				p.L172F		Atlas-SNP	.											.	OR51B6	53	.	0			c.C514T						PASS	.	C	PHE/LEU	1285,3117	439.0+/-345.5	173,939,1089	242.0	198.0	213.0		514	3.3	0.3	11	dbSNP_113	213	2270,6324	382.3+/-340.3	310,1650,2337	yes	missense	OR51B6	NM_001004750.1	22	483,2589,3426	TT,TC,CC		26.4138,29.1913,27.3546	probably-damaging	172/313	5373251	3555,9441	2201	4297	6498	SO:0001583	missense	390058	exon1			CATGTACTCTCCC		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.514C>T	11.37:g.5373251C>T	ENSP00000369568:p.Leu172Phe	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	181	80	0.441989	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	C	12.90	2.076062	0.36662	0.291913	0.264138	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.00130	8.69	5.15	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43747	D	0.000531	T	0.00012	0.0000	M	0.88310	2.945	0.46011	P	0.0011809999999999876	D	0.67145	0.996	D	0.74674	0.984	T	0.43442	-0.9391	9	0.72032	D	0.01	.	9.1576	0.37002	0.0:0.6458:0.2761:0.078	rs5006884;rs52827715;rs57078839;rs5006884	172	Q9H340	O51B6_HUMAN	F	171;172	ENSP00000369568:L172F	ENSP00000369568:L172F	L	+	1	0	OR51B6	5329827	0.006000	0.16342	0.310000	0.25168	0.529000	0.34654	0.356000	0.20181	0.748000	0.32831	0.557000	0.71058	CTC	C|0.767;T|0.233	0.233	strong		0.463	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145075775	145075775	+	Missense_Mutation	SNP	G	G	A	rs76199660	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145075775G>A	ENST00000530740.1	-	1	126	c.88C>T	c.(88-90)Cct>Tct	p.P30S	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.P30S|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.P30S|PDE4DIP_ENST00000369345.4_Missense_Mutation_p.P30S			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.P30S(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GACCGGTAAGGCGTGTAGTGA	0.716			T	PDGFRB	MPD																																p.P30S		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369348,NS,carcinoma,0,3	PDE4DIP	817	3	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C88T						PASS	.	G	SER/PRO	33,4373		0,33,2170	46.0	58.0	54.0		88	3.2	0.6	1	dbSNP_131	54	225,8371		0,225,4073	yes	missense	PDE4DIP	NM_022359.5	74	0,258,6243	AA,AG,GG		2.6175,0.749,1.9843		30/311	145075775	258,12744	2203	4298	6501	SO:0001583	missense	9659	exon1			GGTAAGGCGTGTA	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.88C>T	1.37:g.145075775G>A	ENSP00000435654:p.Pro30Ser	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	92	22	0.23913	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		.	.	.	.	.	.	.	.	.	.	G	15.58	2.874298	0.51695	0.00749	0.026175	ENSG00000178104	ENST00000530740;ENST00000369359;ENST00000369348;ENST00000369345	T;T;T	0.20069	3.21;3.17;2.1	3.25	3.25	0.37280	.	.	.	.	.	T	0.17280	0.0415	N	0.19112	0.55	0.28376	N	0.919753	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.992	T	0.05954	-1.0854	9	0.87932	D	0	.	10.1438	0.42751	0.0:0.0:1.0:0.0	.	30;30	Q5TB27;E9PJ64	.;.	S	30	ENSP00000435654:P30S;ENSP00000358366:P30S;ENSP00000358354:P30S	ENSP00000358351:P30S	P	-	1	0	PDE4DIP	143787132	0.005000	0.15991	0.570000	0.28473	0.031000	0.12232	1.155000	0.31700	1.798000	0.52647	0.511000	0.50034	CCT	A|0.016;G|0.984	0.016	strong		0.716	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
RIPK4	54101	hgsc.bcm.edu	37	21	43187167	43187167	+	Missense_Mutation	SNP	G	G	C	rs6586239	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43187167G>C	ENST00000352483.2	-	1	99	c.35C>G	c.(34-36)gCg>gGg	p.A12G	RIPK4_ENST00000544709.1_5'Flank|RIPK4_ENST00000542057.1_5'Flank|RIPK4_ENST00000332512.3_Missense_Mutation_p.A12G			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	12			A -> G (in dbSNP:rs6586239).		morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GCGCAGCAGCGCCAGGGCCCA	0.726													C|||	614	0.122604	0.2073	0.1095	5008	,	,		9853	0.0		0.1561	False		,,,				2504	0.1094				p.A12G		Atlas-SNP	.											RIPK4_ENST00000352483,colon,carcinoma,0,2	RIPK4	151	2	0			c.C35G						PASS	.	C	GLY/ALA	784,3600		74,636,1482	18.0	16.0	17.0		35	3.7	1.0	21	dbSNP_116	17	1356,7224		111,1134,3045	yes	missense	RIPK4	NM_020639.2	60	185,1770,4527	CC,CG,GG		15.8042,17.8832,16.5073	benign	12/785	43187167	2140,10824	2192	4290	6482	SO:0001583	missense	54101	exon1			AGCAGCGCCAGGG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.35C>G	21.37:g.43187167G>C	ENSP00000330161:p.Ala12Gly	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	37	25	0.675676	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37		269	0.12316849816849818	103	0.20934959349593496	43	0.11878453038674033	0	0.0	123	0.16226912928759896	C	9.236	1.037100	0.19669	0.178832	0.158042	ENSG00000183421	ENST00000332512;ENST00000352483	T;T	0.15487	2.42;2.42	3.68	3.68	0.42216	.	0.109881	0.38217	N	0.001775	T	0.00012	0.0000	N	0.00088	-2.19	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42632	-0.9440	9	0.02654	T	1	-21.985	12.1646	0.54123	0.0:0.8259:0.1741:0.0	rs6586239;rs6586239	12	P57078-2	.	G	12	ENSP00000332454:A12G;ENSP00000330161:A12G	ENSP00000332454:A12G	A	-	2	0	RIPK4	42060236	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	4.871000	0.63042	0.548000	0.28955	-0.365000	0.07479	GCG	G|0.846;C|0.154	0.154	strong		0.726	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
NCOA3	8202	hgsc.bcm.edu	37	20	46268493	46268493	+	Silent	SNP	A	A	G	rs2076546	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:46268493A>G	ENST00000371998.3	+	15	3071	c.2880A>G	c.(2878-2880)acA>acG	p.T960T	NCOA3_ENST00000371997.3_Silent_p.T955T|NCOA3_ENST00000341724.6_Silent_p.T890T|NCOA3_ENST00000372004.3_Silent_p.T960T			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	960					androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CTATTCCCACATTGCCTCTTC	0.488													G|||	673	0.134385	0.2549	0.0879	5008	,	,		20124	0.0933		0.0845	False		,,,				2504	0.0982				p.T960T		Atlas-SNP	.											.	NCOA3	156	.	0			c.A2880G						PASS	.	G	,,,	1039,3367	722.1+/-409.2	123,793,1287	91.0	93.0	92.0		2880,2865,2880,2880	-0.8	0.0	20	dbSNP_96	92	752,7848	784.0+/-407.6	43,666,3591	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	166,1459,4878	GG,GA,AA		8.7442,23.5815,13.7706	,,,	960/1424,955/1416,960/1421,960/1425	46268493	1791,11215	2203	4300	6503	SO:0001819	synonymous_variant	8202	exon15			TCCCACATTGCCT	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.2880A>G	20.37:g.46268493A>G		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			A|0.863;G|0.137	0.137	strong		0.488	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
GLYATL3	389396	hgsc.bcm.edu	37	6	49479775	49479775	+	Silent	SNP	A	A	T	rs1480615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:49479775A>T	ENST00000371197.4	+	2	185	c.72A>T	c.(70-72)tcA>tcT	p.S24S		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	24						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						TTCCTGAATCACTCAAGGTAC	0.313													A|||	2271	0.453474	0.3608	0.3631	5008	,	,		14524	0.378		0.6362	False		,,,				2504	0.5327				p.S24S		Atlas-SNP	.											GLYATL3,trunk,malignant_melanoma,+1,1	GLYATL3	19	1	0			c.A72T						PASS	.	A		562,822		112,338,242	165.0	139.0	147.0		72	1.7	1.0	6	dbSNP_88	147	2062,1120		673,716,202	no	coding-synonymous	GLYATL3	NM_001010904.1		785,1054,444	TT,TA,AA		35.198,40.6069,42.5318		24/289	49479775	2624,1942	692	1591	2283	SO:0001819	synonymous_variant	389396	exon2			TGAATCACTCAAG		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.72A>T	6.37:g.49479775A>T		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	43	43	1	NM_001010904		Silent	SNP	ENST00000371197.4	37	CCDS47440.1																																																																																			T|0.431;N|0.000	0.431	strong		0.313	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
FNDC7	163479	hgsc.bcm.edu	37	1	109273456	109273456	+	Silent	SNP	A	A	G	rs4970809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:109273456A>G	ENST00000370017.3	+	9	2062	c.1785A>G	c.(1783-1785)ggA>ggG	p.G595G	FNDC7_ENST00000271311.2_Silent_p.G596G	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	595	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		GCCTCCTAGGATGCATCACAT	0.463													A|||	2255	0.45028	0.5628	0.4352	5008	,	,		19950	0.2014		0.5388	False		,,,				2504	0.4744				p.G595G		Atlas-SNP	.											.	FNDC7	113	.	0			c.A1785G						PASS	.	A		2475,1931	624.6+/-394.4	690,1095,418	160.0	127.0	138.0		1785	2.4	1.0	1	dbSNP_111	138	4686,3914	606.1+/-395.1	1286,2114,900	no	coding-synonymous	FNDC7	NM_001144937.1		1976,3209,1318	GG,GA,AA		45.5116,43.8266,44.9408		595/734	109273456	7161,5845	2203	4300	6503	SO:0001819	synonymous_variant	163479	exon9			CCTAGGATGCATC		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.1785A>G	1.37:g.109273456A>G		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1	993	0.45467032967032966	286	0.5813008130081301	182	0.5027624309392266	117	0.20454545454545456	408	0.5382585751978892	A	10.24	1.295624	0.23564	0.561734	0.544884	ENSG00000143107	ENST00000445274	.	.	.	6.05	2.38	0.29361	.	.	.	.	.	T	0.20251	0.0487	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.11155	-1.0599	3	.	.	.	-13.482	4.9624	0.14072	0.6976:0.1224:0.0632:0.1168	rs4970809;rs17554220;rs57923010	.	.	.	V	371	.	.	M	+	1	0	FNDC7	109074979	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	0.884000	0.28214	0.146000	0.19002	0.533000	0.62120	ATG	A|0.477;G|0.523;T|0.000	0.523	strong		0.463	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
TBC1D2	55357	hgsc.bcm.edu	37	9	100995758	100995758	+	Missense_Mutation	SNP	G	G	T	rs879368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100995758G>T	ENST00000375064.1	-	4	759	c.721C>A	c.(721-723)Cca>Aca	p.P241T	TBC1D2_ENST00000342112.5_Missense_Mutation_p.P23T|TBC1D2_ENST00000375066.5_Missense_Mutation_p.P241T	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	241			P -> T (in dbSNP:rs879368). {ECO:0000269|PubMed:14702039}.		positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		CCACTCTGTGGAGAATCTTCC	0.602													G|||	1055	0.210663	0.1687	0.2507	5008	,	,		20031	0.1627		0.2744	False		,,,				2504	0.2229				p.P241T		Atlas-SNP	.											.	TBC1D2	70	.	0			c.C721A						PASS	.	G	THR/PRO	785,3621	318.0+/-295.4	79,627,1497	158.0	142.0	147.0		721	0.8	0.0	9	dbSNP_86	147	2261,6339	381.8+/-340.2	287,1687,2326	yes	missense	TBC1D2	NM_018421.3	38	366,2314,3823	TT,TG,GG		26.2907,17.8166,23.42	benign	241/918	100995758	3046,9960	2203	4300	6503	SO:0001583	missense	55357	exon4			TCTGTGGAGAATC	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.721C>A	9.37:g.100995758G>T	ENSP00000364205:p.Pro241Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	80	43	0.5375	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		494	0.2261904761904762	79	0.16056910569105692	100	0.27624309392265195	93	0.16258741258741258	222	0.2928759894459103	G	5.827	0.336876	0.11013	0.178166	0.262907	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112	T;T;T	0.15603	2.41;3.15;2.41	4.88	0.842	0.18927	.	0.473238	0.20036	N	0.100610	T	0.00012	0.0000	L	0.54323	1.7	0.80722	P	0.0	B;P	0.34724	0.335;0.465	B;B	0.31101	0.058;0.124	T	0.45425	-0.9262	9	0.18276	T	0.48	.	4.9031	0.13784	0.2703:0.1646:0.5651:0.0	rs879368;rs52794052;rs58612705;rs879368	241;241	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	T	241;241;23	ENSP00000364205:P241T;ENSP00000364207:P241T;ENSP00000341567:P23T	ENSP00000341567:P23T	P	-	1	0	TBC1D2	100035579	0.000000	0.05858	0.000000	0.03702	0.981000	0.71138	-0.811000	0.04500	-0.011000	0.14247	0.655000	0.94253	CCA	G|0.769;T|0.231	0.231	strong		0.602	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
MYEOV	26579	hgsc.bcm.edu	37	11	69063767	69063767	+	Missense_Mutation	SNP	C	C	A	rs12274095	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:69063767C>A	ENST00000308946.3	+	3	1300	c.850C>A	c.(850-852)Ccc>Acc	p.P284T	MYEOV_ENST00000441339.2_Missense_Mutation_p.P284T|MYEOV_ENST00000535407.1_Missense_Mutation_p.P226T	NM_138768.2	NP_620123.2	Q96EZ4	MYEOV_HUMAN	myeloma overexpressed	284			P -> T (in dbSNP:rs12274095).							endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(1)|lung(12)|prostate(2)|skin(1)|urinary_tract(1)	24	all_lung(4;2.21e-19)|Lung NSC(4;6.13e-19)|Melanoma(5;0.00128)		LUSC - Lung squamous cell carcinoma(11;3.33e-11)|STAD - Stomach adenocarcinoma(18;0.00654)|LUAD - Lung adenocarcinoma(13;0.0713)	Kidney(183;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(183;3.23e-08)|Lung(977;0.00361)|LUSC - Lung squamous cell carcinoma(976;0.0153)		CCAGGTGGGGCCCACTATGCA	0.642													C|||	229	0.0457268	0.0295	0.0447	5008	,	,		15154	0.0139		0.0736	False		,,,				2504	0.0726				p.P284T		Atlas-SNP	.											.	MYEOV	42	.	0			c.C850A						PASS	.	C	THR/PRO	115,4281	86.3+/-125.0	0,115,2083	54.0	52.0	52.0		850	-2.3	0.0	11	dbSNP_120	52	532,8056	143.0+/-199.1	16,500,3778	yes	missense	MYEOV	NM_138768.2	38	16,615,5861	AA,AC,CC		6.1947,2.616,4.9831	benign	284/314	69063767	647,12337	2198	4294	6492	SO:0001583	missense	26579	exon3			GTGGGGCCCACTA	AJ223366	CCDS8190.1, CCDS73340.1	11q13.2	2013-03-27	2013-03-27			ENSG00000172927			7563	protein-coding gene	gene with protein product		605625	"""myeloma overexpressed (in a subset of t(11;14) positive multiple myelomas)"""			10753852	Standard	XM_005273908		Approved	OCIM	uc001oov.3	Q96EZ4		ENST00000308946.3:c.850C>A	11.37:g.69063767C>A	ENSP00000308330:p.Pro284Thr	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	97	51	0.525773	NM_138768	Q9UGN6|Q9UGN7	Missense_Mutation	SNP	ENST00000308946.3	37	CCDS8190.1	88	0.040293040293040296	17	0.034552845528455285	20	0.055248618784530384	4	0.006993006993006993	47	0.06200527704485488	C	7.069	0.567981	0.13560	0.02616	0.061947	ENSG00000172927	ENST00000441339;ENST00000308946;ENST00000535407	T;T;T	0.26373	1.75;1.75;1.74	1.15	-2.29	0.06805	.	.	.	.	.	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.21245	-1.0251	9	0.87932	D	0	.	4.0372	0.09735	0.2057:0.4751:0.3192:0.0	rs12274095;rs60321770;rs12274095	284	Q96EZ4	MYEOV_HUMAN	T	284;284;226	ENSP00000412482:P284T;ENSP00000308330:P284T;ENSP00000438100:P226T	ENSP00000308330:P284T	P	+	1	0	MYEOV	68820343	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-0.302000	0.08221	-1.164000	0.02790	0.313000	0.20887	CCC	C|0.952;A|0.048	0.048	strong		0.642	MYEOV-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396548.1		
FAM160B2	64760	hgsc.bcm.edu	37	8	21955116	21955116	+	Silent	SNP	C	C	T	rs11352	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:21955116C>T	ENST00000289921.7	+	4	433	c.387C>T	c.(385-387)gtC>gtT	p.V129V		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	129										endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						ACCTCAGCGTCCACAGGCCTG	0.657													.|||	1855	0.370407	0.3601	0.2594	5008	,	,		16790	0.374		0.3946	False		,,,				2504	0.4346				p.V129V		Atlas-SNP	.											.	FAM160B2	35	.	0			c.C387T						PASS	.	C		1385,2707		248,889,909	24.0	29.0	27.0		387	2.3	1.0	8	dbSNP_52	27	3416,4960		701,2014,1473	no	coding-synonymous	FAM160B2	NM_022749.5		949,2903,2382	TT,TC,CC		40.7832,33.8465,38.5066		129/744	21955116	4801,7667	2046	4188	6234	SO:0001819	synonymous_variant	64760	exon4			CAGCGTCCACAGG	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"""retinoic acid induced 16"""	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.387C>T	8.37:g.21955116C>T		Somatic	202	0	0		WXS	Illumina HiSeq	Phase_I	183	78	0.42623	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Silent	SNP	ENST00000289921.7	37	CCDS6021.2																																																																																			C|0.639;T|0.361	0.361	strong		0.657	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		
CD200	4345	hgsc.bcm.edu	37	3	112063850	112063850	+	De_novo_Start_OutOfFrame	SNP	C	C	A	rs2272022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112063850C>A	ENST00000383681.3	+	0	89				CD200_ENST00000473539.1_Missense_Mutation_p.P71T|CD200_ENST00000315711.8_Missense_Mutation_p.P46T			P41217	OX2G_HUMAN	CD200 molecule						regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				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)				GCTGTACACACCTGCTTCCTT	0.413													C|||	1014	0.202476	0.1188	0.2709	5008	,	,		19654	0.1359		0.3907	False		,,,				2504	0.1421				p.P71T		Atlas-SNP	.											.	CD200	33	.	0			c.C211A						PASS	.	C	THR/PRO,THR/PRO	626,3780	268.3+/-268.4	44,538,1621	66.0	62.0	64.0		211,136	4.2	1.0	3	dbSNP_100	64	3141,5459	473.7+/-368.7	553,2035,1712	yes	missense,missense	CD200	NM_001004196.2,NM_005944.5	38,38	597,2573,3333	AA,AC,CC		36.5233,14.2079,28.9636	benign,benign	71/295,46/270	112063850	3767,9239	2203	4300	6503			4345	exon4			TACACACCTGCTT		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	ENST00000383681.3:c.-87C>A	3.37:g.112063850C>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_001004196	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Missense_Mutation	SNP	ENST00000383681.3	37		517	0.2367216117216117	60	0.12195121951219512	94	0.2596685082872928	65	0.11363636363636363	298	0.39313984168865435	C	4.367	0.067615	0.08436	0.142079	0.365233	ENSG00000091972	ENST00000315711;ENST00000473539	T;T	0.24908	1.83;1.83	6.02	4.19	0.49359	.	0.219660	0.32736	N	0.005710	T	0.00012	0.0000	N	0.16478	0.41	0.09310	P	0.9999999999999996	P;B	0.35628	0.513;0.015	B;B	0.32533	0.147;0.023	T	0.42799	-0.9430	9	0.09338	T	0.73	-4.9917	7.3101	0.26469	0.1736:0.7413:0.0:0.085	rs2272022;rs52832861;rs57361377;rs2272022	46;71	P41217-2;P41217-3	.;.	T	46;71	ENSP00000312766:P46T;ENSP00000420298:P71T	ENSP00000312766:P46T	P	+	1	0	CD200	113546540	0.599000	0.26891	0.994000	0.49952	0.260000	0.26232	0.953000	0.29162	0.831000	0.34780	0.655000	0.94253	CCT	C|0.748;A|0.252	0.252	strong		0.413	CD200-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000354080.1		
TUBAL3	79861	hgsc.bcm.edu	37	10	5436260	5436260	+	Silent	SNP	A	A	G	rs7910290	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5436260A>G	ENST00000380419.3	-	4	598	c.561T>C	c.(559-561)gcT>gcC	p.A187A	TUBAL3_ENST00000479328.1_Silent_p.A147A	NM_024803.2	NP_079079.1	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	187					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(7)|prostate(2)|skin(3)	25						GCTCTACCACAGCAGTGGAGA	0.522													G|||	3902	0.779153	0.789	0.7997	5008	,	,		19885	0.8294		0.7197	False		,,,				2504	0.7607				p.A187A		Atlas-SNP	.											.	TUBAL3	54	.	0			c.T561C						PASS	.	G	,	3393,1013	375.1+/-321.5	1300,793,110	99.0	92.0	94.0		441,561	-7.6	0.0	10	dbSNP_116	94	5978,2622	425.0+/-354.8	2091,1796,413	no	coding-synonymous,coding-synonymous	TUBAL3	NM_001171864.1,NM_024803.2	,	3391,2589,523	GG,GA,AA		30.4884,22.9914,27.9486	,	147/407,187/447	5436260	9371,3635	2203	4300	6503	SO:0001819	synonymous_variant	79861	exon4			TACCACAGCAGTG	AK025318	CCDS7066.2, CCDS53491.1	10p15.1	2007-03-15			ENSG00000178462	ENSG00000178462		"""Tubulins"""	23534	protein-coding gene	gene with protein product							Standard	NM_024803		Approved	FLJ21665	uc001ihy.3	A6NHL2	OTTHUMG00000017595	ENST00000380419.3:c.561T>C	10.37:g.5436260A>G		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_024803	B4DKL2|Q4QQJ5|Q9H6Z0	Silent	SNP	ENST00000380419.3	37	CCDS7066.2																																																																																			A|0.257;G|0.743	0.743	strong		0.522	TUBAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046548.2	NM_024803	
HGS	9146	hgsc.bcm.edu	37	17	79658569	79658569	+	Silent	SNP	C	C	T	rs148002494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79658569C>T	ENST00000329138.4	+	8	765	c.630C>T	c.(628-630)cgC>cgT	p.R210R		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	210					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			AGGAGGTGCGCGTGTGTGAGC	0.592																																					p.R210R		Atlas-SNP	.											.	HGS	54	.	0			c.C630T						PASS	.	C		0,4406		0,0,2203	141.0	120.0	127.0		630	-3.2	1.0	17	dbSNP_134	127	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	HGS	NM_004712.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		210/778	79658569	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9146	exon8			GGTGCGCGTGTGT	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.630C>T	17.37:g.79658569C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	120	58	0.483333	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	37	CCDS11784.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
KLF10	7071	hgsc.bcm.edu	37	8	103663912	103663912	+	Silent	SNP	T	T	G	rs11552577	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:103663912T>G	ENST00000285407.6	-	3	948	c.648A>C	c.(646-648)acA>acC	p.T216T	KLF10_ENST00000395884.3_Silent_p.T205T	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	216					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|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)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			CATCTGCCACTGTGTTTCTCT	0.473											OREG0018913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	678	0.135383	0.0151	0.2666	5008	,	,		24194	0.1458		0.1879	False		,,,				2504	0.1401				p.T216T	Esophageal Squamous(16;495 519 2144 16528 44005)	Atlas-SNP	.											.	KLF10	44	.	0			c.A648C						PASS	.	T	,	197,4209	124.5+/-161.8	2,193,2008	143.0	124.0	131.0		615,648	-4.3	0.0	8	dbSNP_120	131	1515,7085	287.7+/-298.4	142,1231,2927	no	coding-synonymous,coding-synonymous	KLF10	NM_001032282.2,NM_005655.2	,	144,1424,4935	GG,GT,TT		17.6163,4.4712,13.1632	,	205/470,216/481	103663912	1712,11294	2203	4300	6503	SO:0001819	synonymous_variant	7071	exon3			TGCCACTGTGTTT	U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	11810	protein-coding gene	gene with protein product		601878	"""TGFB inducible early growth response"""	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.648A>C	8.37:g.103663912T>G		Somatic	102	0	0	1375	WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_005655	A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Silent	SNP	ENST00000285407.6	37	CCDS6294.1																																																																																			T|0.865;G|0.135	0.135	strong		0.473	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1		
COL4A4	1286	hgsc.bcm.edu	37	2	227892720	227892720	+	Missense_Mutation	SNP	C	C	T	rs2229813	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227892720C>T	ENST00000396625.3	-	42	4186	c.3979G>A	c.(3979-3981)Gtg>Atg	p.V1327M	COL4A4_ENST00000329662.7_Missense_Mutation_p.V1327M	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1327	Triple-helical region.		V -> M (in dbSNP:rs2229813). {ECO:0000269|PubMed:7523402, ECO:0000269|PubMed:8365481, ECO:0000269|PubMed:9792860}.		axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GGGAATCCCACTGGTCCTTAA	0.473													T|||	2469	0.493011	0.5651	0.4784	5008	,	,		14632	0.4028		0.4384	False		,,,				2504	0.5552				p.V1327M		Atlas-SNP	.											.	COL4A4	215	.	0			c.G3979A						PASS	.	T	MET/VAL	1935,1729		497,941,394	25.0	28.0	27.0		3979	1.6	1.0	2	dbSNP_98	27	3442,4716		725,1992,1362	yes	missense	COL4A4	NM_000092.4	21	1222,2933,1756	TT,TC,CC		42.1917,47.1889,45.483	benign	1327/1691	227892720	5377,6445	1832	4079	5911	SO:0001583	missense	1286	exon42			ATCCCACTGGTCC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3979G>A	2.37:g.227892720C>T	ENSP00000379866:p.Val1327Met	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	27	16	0.592593	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	987	0.4519230769230769	257	0.5223577235772358	169	0.46685082872928174	226	0.3951048951048951	335	0.4419525065963061	T	3.225	-0.158751	0.06544	0.528111	0.421917	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93604	-3.25;-3.25	5.43	1.6	0.23607	.	.	.	.	.	T	0.00012	0.0000	N	0.01631	-0.79	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.09377	0.004	T	0.42732	-0.9434	8	0.38643	T	0.18	.	8.0333	0.30478	0.0:0.3734:0.0:0.6266	rs2229813;rs2272199;rs58880118;rs2272199	1327	P53420	CO4A4_HUMAN	M	1327	ENSP00000379866:V1327M;ENSP00000328553:V1327M	ENSP00000328553:V1327M	V	-	1	0	COL4A4	227600964	0.697000	0.27767	0.967000	0.41034	0.082000	0.17680	-0.140000	0.10342	-0.132000	0.11557	-0.982000	0.02568	GTG	C|0.549;T|0.451	0.451	strong		0.473	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
RP1L1	94137	hgsc.bcm.edu	37	8	10467160	10467160	+	Missense_Mutation	SNP	G	G	A	rs62490855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10467160G>A	ENST00000382483.3	-	4	4671	c.4448C>T	c.(4447-4449)gCc>gTc	p.A1483V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1563					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)		CATCATGGTGGCTCCGGGCGG	0.667													G|||	883	0.176318	0.0393	0.1686	5008	,	,		15524	0.1597		0.1421	False		,,,				2504	0.4192				p.A1483V		Atlas-SNP	.											.	RP1L1	453	.	0			c.C4448T						PASS	.	G	VAL/ALA	238,3682		10,218,1732	36.0	40.0	39.0		4448	-2.8	0.0	8	dbSNP_129	39	1217,7131		97,1023,3054	yes	missense	RP1L1	NM_178857.5	64	107,1241,4786	AA,AG,GG		14.5783,6.0714,11.8601	possibly-damaging	1483/2401	10467160	1455,10813	1960	4174	6134	SO:0001583	missense	94137	exon4			ATGGTGGCTCCGG	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.4448C>T	8.37:g.10467160G>A	ENSP00000371923:p.Ala1483Val	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	306	0.1401098901098901	27	0.054878048780487805	64	0.17679558011049723	100	0.17482517482517482	115	0.1517150395778364	G	12.96	2.093607	0.36952	0.060714	0.145783	ENSG00000183638	ENST00000382483	T	0.04809	3.55	4.78	-2.78	0.05859	.	1.606950	0.04389	N	0.362076	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P	0.48764	0.915	B	0.41946	0.371	T	0.40496	-0.9560	9	0.06625	T	0.88	0.1679	8.9228	0.35621	0.0:0.1989:0.2911:0.51	rs62490855	1483	A6NKC6	.	V	1483	ENSP00000371923:A1483V	ENSP00000371923:A1483V	A	-	2	0	RP1L1	10504570	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.334000	0.07883	-0.403000	0.07622	0.561000	0.74099	GCC	G|0.853;A|0.147	0.147	strong		0.667	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
KCNB2	9312	hgsc.bcm.edu	37	8	73849768	73849768	+	Silent	SNP	A	A	C	rs142525254	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:73849768A>C	ENST00000523207.1	+	3	2766	c.2178A>C	c.(2176-2178)gcA>gcC	p.A726A		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	726					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAGGCAGTGCACCACAGACCC	0.522													A|||	49	0.00978435	0.0083	0.0058	5008	,	,		17236	0.0		0.0139	False		,,,				2504	0.0204				p.A726A		Atlas-SNP	.											.	KCNB2	228	.	0			c.A2178C						PASS	.	A		43,4363	45.3+/-79.5	0,43,2160	94.0	99.0	98.0		2178	-10.1	0.2	8	dbSNP_134	98	132,8468	66.0+/-128.3	0,132,4168	no	coding-synonymous	KCNB2	NM_004770.2		0,175,6328	CC,CA,AA		1.5349,0.9759,1.3455		726/912	73849768	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			CAGTGCACCACAG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.2178A>C	8.37:g.73849768A>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	56	23	0.410714	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																			A|0.989;C|0.011	0.011	strong		0.522	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
KIAA1211	57482	hgsc.bcm.edu	37	4	57182758	57182758	+	Silent	SNP	C	C	T	rs28559894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:57182758C>T	ENST00000504228.1	+	6	3195	c.3090C>T	c.(3088-3090)gaC>gaT	p.D1030D	KIAA1211_ENST00000541073.1_Silent_p.D1023D|KIAA1211_ENST00000264229.6_Silent_p.D1030D			Q6ZU35	K1211_HUMAN	KIAA1211	1030										endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					AGAAGAGGGACGAGGAGGAAG	0.627													C|||	1128	0.22524	0.1407	0.2233	5008	,	,		12589	0.254		0.341	False		,,,				2504	0.1922				p.D1030D		Atlas-SNP	.											KIAA1211,NS,carcinoma,0,1	KIAA1211	178	1	0			c.C3090T						PASS	.	C		672,3328		52,568,1380	18.0	21.0	20.0		3090	-6.2	0.0	4	dbSNP_125	20	2858,5480		498,1862,1809	no	coding-synonymous	KIAA1211	NM_020722.1		550,2430,3189	TT,TC,CC		34.2768,16.8,28.6108		1030/1234	57182758	3530,8808	2000	4169	6169	SO:0001819	synonymous_variant	57482	exon8			GAGGGACGAGGAG	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.3090C>T	4.37:g.57182758C>T		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	30	15	0.5	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Silent	SNP	ENST00000504228.1	37	CCDS43230.1																																																																																			C|0.728;T|0.272	0.272	strong		0.627	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
PNMAL1	55228	hgsc.bcm.edu	37	19	46974077	46974077	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46974077C>T	ENST00000313683.10	-	2	521	c.216G>A	c.(214-216)gaG>gaA	p.E72E	PNMAL1_ENST00000438932.2_Silent_p.E72E|PNMAL1_ENST00000602246.1_Splice_Site_p.E72E	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	72										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		cttcaccaacctcaatgaggg	0.547																																					p.E72E		Atlas-SNP	.											.	PNMAL1	87	.	0			c.G216A						PASS	.						65.0	52.0	56.0					19																	46974077		2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			ACCAACCTCAATG	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.216G>A	19.37:g.46974077C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	77	31	0.402597	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			.	.	none		0.547	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
CPT2	1376	hgsc.bcm.edu	37	1	53676448	53676448	+	Missense_Mutation	SNP	G	G	A	rs1799821	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:53676448G>A	ENST00000371486.3	+	4	1617	c.1102G>A	c.(1102-1104)Gtc>Atc	p.V368I	RP5-1024G6.2_ENST00000452466.1_RNA	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	368			V -> I (common polymorphism associated with susceptibility to IIAE4; no effect on activity; does not affect affinity for L-carnitine; lower thermal stability compared to wild-type; dbSNP:rs1799821). {ECO:0000269|PubMed:14605500, ECO:0000269|PubMed:1528846, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18306170, ECO:0000269|PubMed:9600456, ECO:0000269|PubMed:9758712}.		carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	CTCTACTGCCGTCCACTTTGA	0.488													G|||	2069	0.413139	0.2564	0.3818	5008	,	,		20912	0.7242		0.5179	False		,,,				2504	0.2188				p.V368I		Atlas-SNP	.											.	CPT2	34	.	0			c.G1102A						PASS	.	G	ILE/VAL	1278,3128	436.1+/-344.5	212,854,1137	54.0	51.0	52.0		1102	-0.3	0.0	1	dbSNP_89	52	4658,3942	603.0+/-394.6	1246,2166,888	yes	missense	CPT2	NM_000098.2	29	1458,3020,2025	AA,AG,GG		45.8372,29.0059,45.6405	benign	368/659	53676448	5936,7070	2203	4300	6503	SO:0001583	missense	1376	exon4			ACTGCCGTCCACT	BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1102G>A	1.37:g.53676448G>A	ENSP00000360541:p.Val368Ile	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	1092	0.5	148	0.3008130081300813	140	0.3867403314917127	419	0.7325174825174825	385	0.5079155672823219	G	0.006	-2.112224	0.00353	0.290059	0.541628	ENSG00000157184	ENST00000371486	D	0.89123	-2.47	5.72	-0.261	0.12963	.	0.368277	0.33217	N	0.005156	T	0.00012	0.0000	N	0.03294	-0.36	0.46078	P	0.0011470000000000091	B	0.14805	0.011	B	0.09377	0.004	T	0.40739	-0.9547	9	0.02654	T	1	-5.8386	10.7366	0.46128	0.4954:0.0:0.5046:0.0	rs1799821;rs3737985;rs12722740;rs17369304;rs17848484;rs17849928;rs17857679;rs58369811;rs1799821	368	P23786	CPT2_HUMAN	I	368	ENSP00000360541:V368I	ENSP00000360541:V368I	V	+	1	0	CPT2	53449036	0.000000	0.05858	0.032000	0.17829	0.204000	0.24138	-0.054000	0.11826	0.038000	0.15604	-0.140000	0.14226	GTC	G|0.523;A|0.477	0.477	strong		0.488	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
BTBD11	121551	hgsc.bcm.edu	37	12	108013936	108013936	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:108013936A>G	ENST00000280758.5	+	11	3154	c.2626A>G	c.(2626-2628)Agc>Ggc	p.S876G	BTBD11_ENST00000357167.4_Missense_Mutation_p.S413G|BTBD11_ENST00000420571.2_Missense_Mutation_p.S757G|RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000490090.2_Missense_Mutation_p.S876G	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	876						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CCTGAAAGCGAGCAAGGTATG	0.507																																					p.S876G		Atlas-SNP	.											BTBD11,caecum,carcinoma,-2,1	BTBD11	122	1	0			c.A2626G						scavenged	.						113.0	110.0	111.0					12																	108013936		2203	4300	6503	SO:0001583	missense	121551	exon11			AAAGCGAGCAAGG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2626A>G	12.37:g.108013936A>G	ENSP00000280758:p.Ser876Gly	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	167	3	0.0179641	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.180979	0.38511	.	.	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000357167	T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09	5.12	5.12	0.69794	.	0.035713	0.85682	D	0.000000	T	0.76905	0.4053	M	0.73217	2.22	0.80722	D	1	P;B;P;P	0.50819	0.939;0.043;0.688;0.669	B;B;B;B	0.40940	0.344;0.027;0.182;0.264	T	0.81302	-0.0994	10	0.66056	D	0.02	.	14.9472	0.71042	1.0:0.0:0.0:0.0	.	757;413;876;876	A6QL63-2;E9PHS4;A6QL63;A6QL63-3	.;.;BTBDB_HUMAN;.	G	876;757;876;413	ENSP00000280758:S876G;ENSP00000413889:S757G;ENSP00000447319:S876G;ENSP00000349690:S413G	ENSP00000280758:S876G	S	+	1	0	BTBD11	106538066	1.000000	0.71417	0.963000	0.40424	0.321000	0.28281	6.211000	0.72182	1.920000	0.55613	0.528000	0.53228	AGC	.	.	none		0.507	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
CYP2D6	1565	hgsc.bcm.edu	37	22	42526763	42526763	+	Missense_Mutation	SNP	C	C	T	rs769258	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:42526763C>T	ENST00000360608.5	-	1	145	c.31G>A	c.(31-33)Gtg>Atg	p.V11M	NDUFA6-AS1_ENST00000608491.1_RNA|CYP2D6_ENST00000389970.3_Missense_Mutation_p.V11M|NDUFA6-AS1_ENST00000439129.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000608288.1_RNA|CYP2D6_ENST00000359033.4_Missense_Mutation_p.V11M	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	11			V -> M (in allele CYP2D6*35; dbSNP:rs769258). {ECO:0000269|PubMed:15469410}.		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)	GCCACTATCACGGCCAGGGGC	0.672													C|||	84	0.0167732	0.0023	0.0274	5008	,	,		19497	0.003		0.0527	False		,,,				2504	0.0061				p.V11M		Atlas-SNP	.											.	CYP2D6	104	.	0			c.G31A	GRCh37	CM033368	CYP2D6	M	rs769258	PASS	.	C	MET/VAL,MET/VAL	36,4352		1,34,2159	41.0	40.0	40.0		31,31	-3.0	0.0	22	dbSNP_86	40	499,8091		23,453,3819	no	missense,missense	CYP2D6	NM_000106.4,NM_001025161.1	21,21	24,487,5978	TT,TC,CC		5.8091,0.8204,4.1224	possibly-damaging,possibly-damaging	11/498,11/447	42526763	535,12443	2194	4295	6489	SO:0001583	missense	1565	exon1			CTATCACGGCCAG	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.31G>A	22.37:g.42526763C>T	ENSP00000353820:p.Val11Met	Somatic	230	0	0		WXS	Illumina HiSeq	Phase_I	259	121	0.467181	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	60	0.027472527472527472	6	0.012195121951219513	15	0.04143646408839779	3	0.005244755244755245	36	0.047493403693931395	c	3.418	-0.118739	0.06838	0.008204	0.058091	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000359033	T;T;T	0.12361	2.69;2.69;2.69	3.46	-3.03	0.05429	.	1.246930	0.05772	N	0.606947	T	0.00468	0.0015	N	0.08118	0	0.09310	N	1	P;P	0.38711	0.643;0.643	B;B	0.19148	0.024;0.024	T	0.26815	-1.0092	10	0.49607	T	0.09	.	0.9967	0.01469	0.1609:0.262:0.1584:0.4187	rs769258;rs769258	11;11	Q6NXU8;Q6NWU0	.;.	M	11	ENSP00000353820:V11M;ENSP00000374620:V11M;ENSP00000351927:V11M	ENSP00000351927:V11M	V	-	1	0	CYP2D6	40856707	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-2.219000	0.01218	-0.478000	0.06823	-0.516000	0.04426	GTG	C|0.971;T|0.029	0.029	strong		0.672	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1		
URB1	9875	hgsc.bcm.edu	37	21	33688865	33688865	+	Silent	SNP	A	A	G	rs7279896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33688865A>G	ENST00000382751.3	-	38	6661	c.6546T>C	c.(6544-6546)gcT>gcC	p.A2182A		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	2182						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						GGCCCTGGGCAGCCACCAGCT	0.627													G|||	1252	0.25	0.5779	0.1052	5008	,	,		17415	0.1369		0.1233	False		,,,				2504	0.1564				p.A2182A		Atlas-SNP	.											.	URB1	176	.	0			c.T6546C						PASS	.	G		727,657		198,331,163	21.0	27.0	25.0		6546	-1.8	0.4	21	dbSNP_116	25	408,2774		29,350,1212	no	coding-synonymous	URB1	NM_014825.2		227,681,1375	GG,GA,AA		12.8221,47.4711,24.8576		2182/2272	33688865	1135,3431	692	1591	2283	SO:0001819	synonymous_variant	9875	exon38			CTGGGCAGCCACC	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.6546T>C	21.37:g.33688865A>G		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	73	52	0.712329	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			A|0.758;G|0.242	0.242	strong		0.627	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
KLRG1	10219	hgsc.bcm.edu	37	12	9161648	9161648	+	Silent	SNP	T	T	C	rs3026251	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9161648T>C	ENST00000266551.4	+	4	450	c.435T>C	c.(433-435)gaT>gaC	p.D145D	KLRG1_ENST00000538029.1_3'UTR|KLRG1_ENST00000356986.3_Silent_p.D145D	NM_005810.3	NP_005801.3	Q96E93	KLRG1_HUMAN	killer cell lectin-like receptor subfamily G, member 1	145	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	8						GGTGGGAAGATGGATCACCTC	0.443													C|||	1269	0.253395	0.0545	0.2997	5008	,	,		-128	0.379		0.2634	False		,,,				2504	0.3497				p.D145D		Atlas-SNP	.											.	KLRG1	16	.	0			c.T435C						PASS	.	C		337,4069	795.6+/-415.3	13,311,1879	89.0	86.0	87.0		435	-0.4	1.0	12	dbSNP_102	87	2572,6028	689.7+/-404.4	382,1808,2110	no	coding-synonymous	KLRG1	NM_005810.3		395,2119,3989	CC,CT,TT		29.907,7.6487,22.3666		145/190	9161648	2909,10097	2203	4300	6503	SO:0001819	synonymous_variant	10219	exon4			GGAAGATGGATCA	AF097358	CCDS8599.1	12p13.31	2011-08-30			ENSG00000139187	ENSG00000139187		"""Killer cell lectin-like receptors"", ""C-type lectin domain containing"""	6380	protein-coding gene	gene with protein product	"""C-type lectin domain family 15, member A"""	604874				9862378, 9842918, 16461340, 16140789	Standard	NM_005810		Approved	MAFA, 2F1, MAFA-L, CLEC15A	uc001qvg.3	Q96E93		ENST00000266551.4:c.435T>C	12.37:g.9161648T>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	175	84	0.48	NM_005810	B7ZAM2|O43198|O75613	Silent	SNP	ENST00000266551.4	37																																																																																				T|0.754;C|0.246	0.246	strong		0.443	KLRG1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399145.1	NM_005810	
AMOTL1	154810	hgsc.bcm.edu	37	11	94533373	94533373	+	Silent	SNP	C	C	T	rs2303960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:94533373C>T	ENST00000433060.2	+	3	1158	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	AMOTL1_ENST00000317837.9_Silent_p.P339P|AMOTL1_ENST00000317829.8_Silent_p.P289P	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	339					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				ACCAGCACCCCGGGATGCTCC	0.587													C|||	1309	0.261382	0.0719	0.464	5008	,	,		16586	0.4444		0.1889	False		,,,				2504	0.2597				p.P339P		Atlas-SNP	.											AMOTL1,colon,carcinoma,+2,1	AMOTL1	95	1	0			c.C1017T						PASS	.	C		368,3618		18,332,1643	123.0	124.0	124.0		1017	-10.3	0.1	11	dbSNP_100	124	1729,6613		177,1375,2619	no	coding-synonymous	AMOTL1	NM_130847.2		195,1707,4262	TT,TC,CC		20.7264,9.2323,17.0101		339/957	94533373	2097,10231	1993	4171	6164	SO:0001819	synonymous_variant	154810	exon3			GCACCCCGGGATG	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.1017C>T	11.37:g.94533373C>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	74	74	1	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Silent	SNP	ENST00000433060.2	37	CCDS44712.1																																																																																			C|0.744;T|0.256	0.256	strong		0.587	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
FAM21C	253725	hgsc.bcm.edu	37	10	46254783	46254783	+	Silent	SNP	A	A	G	rs186891138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:46254783A>G	ENST00000336378.4	+	17	1687	c.1569A>G	c.(1567-1569)aaA>aaG	p.K523K	FAM21C_ENST00000537517.1_Silent_p.K499K|FAM21C_ENST00000359860.4_Silent_p.K467K|FAM21C_ENST00000540872.1_Silent_p.K523K|FAM21C_ENST00000374362.2_Silent_p.K523K	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	523					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CTTACAGCAAAAATCTCAAGC	0.403																																					p.K523K		Atlas-SNP	.											FAM21C,caecum,carcinoma,0,1	FAM21C	68	1	0			c.A1569G						scavenged	.						62.0	73.0	69.0					10																	46254783		1735	3995	5730	SO:0001819	synonymous_variant	253725	exon17			CAGCAAAAATCTC		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.1569A>G	10.37:g.46254783A>G		Somatic	436	0	0		WXS	Illumina HiSeq	Phase_I	326	27	0.0828221	NM_015262	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Silent	SNP	ENST00000336378.4	37																																																																																				A|0.375;G|0.625	0.625	strong		0.403	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
NPR1	4881	hgsc.bcm.edu	37	1	153662423	153662423	+	Missense_Mutation	SNP	G	G	A	rs35479618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153662423G>A	ENST00000368680.3	+	19	3371	c.2899G>A	c.(2899-2901)Gag>Aag	p.E967K		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	967	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.		E -> K (in dbSNP:rs35479618). {ECO:0000269|PubMed:17344846}.		body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CCGGCCCCAGGAGCAGCTGCG	0.662													G|||	17	0.00339457	0.0	0.0014	5008	,	,		14197	0.0		0.0139	False		,,,				2504	0.002				p.E967K	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.G2899A						PASS	.	G	LYS/GLU	11,4311		0,11,2150	15.0	16.0	15.0		2899	2.9	1.0	1	dbSNP_126	15	105,8313		1,103,4105	yes	missense	NPR1	NM_000906.3	56	1,114,6255	AA,AG,GG		1.2473,0.2545,0.9105	possibly-damaging	967/1062	153662423	116,12624	2161	4209	6370	SO:0001583	missense	4881	exon19			CCCCAGGAGCAGC	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2899G>A	1.37:g.153662423G>A	ENSP00000357669:p.Glu967Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	33	0.388235	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	15.02	2.709779	0.48517	0.002545	0.012473	ENSG00000169418	ENST00000368680;ENST00000428723;ENST00000368677	D	0.81739	-1.53	2.87	2.87	0.33458	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.294578	0.26324	N	0.025023	T	0.55178	0.1904	L	0.34521	1.04	0.38332	D	0.943827	B;P	0.35628	0.201;0.513	B;B	0.36922	0.236;0.134	T	0.58358	-0.7650	10	0.37606	T	0.19	.	5.8634	0.18760	0.1433:0.0:0.8567:0.0	rs35479618;rs61758573	446;967	B7Z4Y7;P16066	.;ANPRA_HUMAN	K	967;446;148	ENSP00000357669:E967K	ENSP00000357666:E148K	E	+	1	0	NPR1	151929047	0.886000	0.30341	1.000000	0.80357	0.912000	0.54170	1.368000	0.34216	1.907000	0.55213	0.462000	0.41574	GAG	G|0.993;A|0.007	0.007	strong		0.662	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
PCNT	5116	hgsc.bcm.edu	37	21	47831309	47831309	+	Silent	SNP	G	G	A	rs58559714	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47831309G>A	ENST00000359568.5	+	28	5429	c.5322G>A	c.(5320-5322)gaG>gaA	p.E1774E	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1774					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)					TGCAGAGCGAGCTGCTCTGCT	0.662													G|||	895	0.178714	0.4902	0.0937	5008	,	,		16104	0.004		0.0895	False		,,,				2504	0.09				p.E1774E		Atlas-SNP	.											.	PCNT	283	.	0			c.G5322A						PASS	.	G		1925,2481	495.8+/-363.4	423,1079,701	38.0	45.0	43.0		5322	1.7	0.9	21	dbSNP_129	43	647,7953	158.6+/-212.1	14,619,3667	no	coding-synonymous	PCNT	NM_006031.5		437,1698,4368	AA,AG,GG		7.5233,43.6904,19.7755		1774/3337	47831309	2572,10434	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon28			GAGCGAGCTGCTC	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.5322G>A	21.37:g.47831309G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			G|0.830;A|0.170	0.170	strong		0.662	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
COL6A3	1293	hgsc.bcm.edu	37	2	238244781	238244781	+	Missense_Mutation	SNP	T	T	C	rs11690358	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:238244781T>C	ENST00000295550.4	-	40	9414	c.8962A>G	c.(8962-8964)Atg>Gtg	p.M2988V	COL6A3_ENST00000353578.4_Missense_Mutation_p.M2782V|COL6A3_ENST00000346358.4_Missense_Mutation_p.M2788V|COL6A3_ENST00000347401.3_Missense_Mutation_p.M2787V|COL6A3_ENST00000409809.1_Missense_Mutation_p.M2782V|COL6A3_ENST00000472056.1_Missense_Mutation_p.M2381V	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2988	Nonhelical region.		M -> V (in dbSNP:rs11690358). {ECO:0000269|PubMed:1689238, 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)		TTCTTACCCATGGGCTTAGTG	0.572													C|||	237	0.0473243	0.0151	0.0461	5008	,	,		21536	0.0109		0.1123	False		,,,				2504	0.0624				p.M2988V		Atlas-SNP	.											.	COL6A3	608	.	0			c.A8962G						PASS	.	C	VAL/MET,VAL/MET,VAL/MET	100,3998		1,98,1950	49.0	42.0	44.0		8344,7141,8962	-4.8	0.0	2	dbSNP_120	44	749,7497		30,689,3404	yes	missense,missense,missense	COL6A3	NM_057167.3,NM_057166.4,NM_004369.3	21,21,21	31,787,5354	CC,CT,TT		9.0832,2.4402,6.8778	benign,benign,benign	2782/2972,2381/2571,2988/3178	238244781	849,11495	2049	4123	6172	SO:0001583	missense	1293	exon40			TACCCATGGGCTT	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.8962A>G	2.37:g.238244781T>C	ENSP00000295550:p.Met2988Val	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	110	0.05036630036630037	7	0.014227642276422764	16	0.04419889502762431	6	0.01048951048951049	81	0.10686015831134564	C	7.541	0.660628	0.14645	0.024402	0.090832	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.87491	-2.26;-2.24;-2.22;-2.22;-2.22;-2.21	5.56	-4.78	0.03209	Fibronectin, type III (1);	1.728000	0.03320	N	0.191771	T	0.01905	0.0060	N	0.00926	-1.1	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	0.51803	-0.8659	10	0.02654	T	1	.	2.5857	0.04829	0.1063:0.2207:0.2092:0.4637	rs11690358;rs61396974;rs11690358	2381;2782;2988	E9PFQ6;P12111-2;P12111	.;.;CO6A3_HUMAN	V	2988;2787;2782;2381;2782;2788	ENSP00000295550:M2988V;ENSP00000315609:M2787V;ENSP00000315873:M2782V;ENSP00000418285:M2381V;ENSP00000386844:M2782V;ENSP00000295546:M2788V	ENSP00000295550:M2988V	M	-	1	0	COL6A3	237909520	0.000000	0.05858	0.000000	0.03702	0.722000	0.41435	-1.242000	0.02908	-1.635000	0.01535	-0.213000	0.12676	ATG	T|0.934;C|0.066	0.066	strong		0.572	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
FCGR2A	2212	hgsc.bcm.edu	37	1	161487863	161487863	+	Silent	SNP	C	C	T	rs143182858	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161487863C>T	ENST00000271450.6	+	7	917	c.879C>T	c.(877-879)ccC>ccT	p.P293P	FCGR2A_ENST00000367972.4_Silent_p.P292P|FCGR2A_ENST00000486608.1_3'UTR|RP11-25K21.6_ENST00000537821.2_RNA	NM_001136219.1|NM_021642.3	NP_001129691.1|NP_067674.2	P12318	FCG2A_HUMAN	Fc fragment of IgG, low affinity IIa, receptor (CD32)	293					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(11)|ovary(1)	19	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTCTGAACCCCAGGGCACCTA	0.453													C|||	607	0.121206	0.0242	0.1239	5008	,	,		19315	0.2758		0.1183	False		,,,				2504	0.0941				p.P293P		Atlas-SNP	.											.	FCGR2A	38	.	0			c.C879T						PASS	.	C	,	150,4256		2,146,2055	69.0	72.0	71.0		879,876	0.6	0.0	1	dbSNP_134	71	982,7612		48,886,3363	no	coding-synonymous,coding-synonymous	FCGR2A	NM_001136219.1,NM_021642.3	,	50,1032,5418	TT,TC,CC		11.4266,3.4044,8.7077	,	293/318,292/317	161487863	1132,11868	2203	4297	6500	SO:0001819	synonymous_variant	2212	exon7			GAACCCCAGGGCA	J03619	CCDS30922.1, CCDS44264.1	1q23	2013-01-11	2005-02-02		ENSG00000143226	ENSG00000143226		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3616	protein-coding gene	gene with protein product	"""Immunoglobulin G Fc receptor II"""	146790	"""Fc fragment of IgG, low affinity IIa, receptor for (CD32)"""	FCG2, FCGR2A1, FCGR2		2139735	Standard	NM_021642		Approved	CD32, CD32A, IGFR2, CDw32	uc001gan.3	P12318	OTTHUMG00000034469	ENST00000271450.6:c.879C>T	1.37:g.161487863C>T		Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	355	279	0.785915	NM_001136219	Q8WUN1|Q8WW64	Silent	SNP	ENST00000271450.6	37	CCDS44264.1																																																																																			C|0.901;T|0.099	0.099	strong		0.453	FCGR2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083318.3	NM_021642	
COL6A1	1291	hgsc.bcm.edu	37	21	47422174	47422174	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47422174G>A	ENST00000361866.3	+	32	2223	c.2109G>A	c.(2107-2109)acG>acA	p.T703T	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	703	C-terminal globular domain.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GCACCTTCACGGGGGAGGCCC	0.697																																					p.T703T		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2109A						PASS	.						12.0	12.0	12.0					21																	47422174		2176	4278	6454	SO:0001819	synonymous_variant	1291	exon32			CTTCACGGGGGAG	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.2109G>A	21.37:g.47422174G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	40	20	0.5	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Silent	SNP	ENST00000361866.3	37	CCDS13727.1																																																																																			.	.	none		0.697	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
RASAL1	8437	hgsc.bcm.edu	37	12	113537773	113537773	+	Silent	SNP	C	C	T	rs12422659	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113537773C>T	ENST00000261729.5	-	22	2691	c.2376G>A	c.(2374-2376)caG>caA	p.Q792Q	RASAL1_ENST00000548055.1_Silent_p.Q793Q|RASAL1_ENST00000546530.1_Silent_p.Q794Q|RASAL1_ENST00000446861.3_Silent_p.Q764Q			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	792					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						TCCCTCGCTCCTGCTGCTGGA	0.677													t|||	311	0.0621006	0.031	0.0865	5008	,	,		18312	0.0		0.1521	False		,,,				2504	0.0583				p.Q794Q		Atlas-SNP	.											.	RASAL1	89	.	0			c.G2382A						PASS	.		,,	233,4173	798.1+/-415.5	7,219,1977	40.0	47.0	44.0		2382,2292,2376	3.2	0.0	12	dbSNP_120	44	1276,7324	753.5+/-407.4	94,1088,3118	no	coding-synonymous,coding-synonymous,coding-synonymous	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	,,	101,1307,5095	TT,TC,CC		14.8372,5.2882,11.6023	,,	794/807,764/777,792/805	113537773	1509,11497	2203	4300	6503	SO:0001819	synonymous_variant	8437	exon22			TCGCTCCTGCTGC	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.2376G>A	12.37:g.113537773C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	122	69	0.565574	NM_001193520	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Silent	SNP	ENST00000261729.5	37	CCDS9165.1																																																																																			C|0.897;T|0.103	0.103	strong		0.677	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
NKTR	4820	hgsc.bcm.edu	37	3	42662976	42662976	+	Silent	SNP	A	A	C	rs35419602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:42662976A>C	ENST00000232978.8	+	6	530	c.342A>C	c.(340-342)cgA>cgC	p.R114R	RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	114	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				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)		TGGCAAATCGAGGGAAACATA	0.358													A|||	35	0.00698882	0.0083	0.0072	5008	,	,		15576	0.0		0.0179	False		,,,				2504	0.001				p.R114R		Atlas-SNP	.											.	NKTR	116	.	0			c.A342C						PASS	.	A		32,4374	39.2+/-71.8	0,32,2171	76.0	73.0	74.0		342	-1.8	1.0	3	dbSNP_126	74	128,8470	65.6+/-127.9	1,126,4172	no	coding-synonymous	NKTR	NM_005385.3		1,158,6343	CC,CA,AA		1.4887,0.7263,1.2304		114/1463	42662976	160,12844	2203	4299	6502	SO:0001819	synonymous_variant	4820	exon6			AAATCGAGGGAAA		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.342A>C	3.37:g.42662976A>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	79	30	0.379747	NM_005385		Silent	SNP	ENST00000232978.8	37	CCDS2702.1																																																																																			A|0.988;C|0.012	0.012	strong		0.358	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
DPCR1	135656	hgsc.bcm.edu	37	6	30919701	30919701	+	Silent	SNP	T	T	C	rs2517449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30919701T>C	ENST00000462446.1	+	2	3488	c.3460T>C	c.(3460-3462)Ttg>Ctg	p.L1154L	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	311						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AAGGACCACATTGGCCCATGA	0.473													T|||	1177	0.235024	0.0983	0.2133	5008	,	,		21802	0.2688		0.3579	False		,,,				2504	0.274				p.L1154L		Atlas-SNP	.											.	DPCR1	99	.	0			c.T3460C						PASS	.	T		623,3783	268.9+/-268.7	42,539,1622	125.0	126.0	126.0		3460	-2.2	0.0	6	dbSNP_100	126	3225,5375	487.8+/-372.2	588,2049,1663	yes	coding-synonymous	DPCR1	NM_080870.3		630,2588,3285	CC,CT,TT		37.5,14.1398,29.5863		1154/1394	30919701	3848,9158	2203	4300	6503	SO:0001819	synonymous_variant	135656	exon2			ACCACATTGGCCC	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3460T>C	6.37:g.30919701T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	51	27	0.529412	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	37	CCDS4692.2																																																																																			T|0.723;C|0.277	0.277	strong		0.473	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
SENP5	205564	hgsc.bcm.edu	37	3	196613075	196613075	+	Silent	SNP	C	C	T	rs34533379	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196613075C>T	ENST00000323460.5	+	2	1272	c.1023C>T	c.(1021-1023)gaC>gaT	p.D341D	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Silent_p.D341D	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	341					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		TTAGTTTAGACGAAGCATTCC	0.502													C|||	1186	0.236821	0.3555	0.1239	5008	,	,		20943	0.1667		0.2346	False		,,,				2504	0.2311				p.D341D	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.C1023T						PASS	.	C		1438,2968	466.8+/-354.6	220,998,985	91.0	79.0	83.0		1023	-6.5	0.4	3	dbSNP_126	83	1844,6756	330.7+/-319.3	200,1444,2656	no	coding-synonymous	SENP5	NM_152699.4		420,2442,3641	TT,TC,CC		21.4419,32.6373,25.2345		341/756	196613075	3282,9724	2203	4300	6503	SO:0001819	synonymous_variant	205564	exon2			TTTAGACGAAGCA	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.1023C>T	3.37:g.196613075C>T		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	81	47	0.580247	NM_152699	B4DY82|Q96SA5	Silent	SNP	ENST00000323460.5	37	CCDS3322.1																																																																																			C|0.751;T|0.249	0.249	strong		0.502	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
RSPH1	89765	hgsc.bcm.edu	37	21	43896143	43896143	+	Missense_Mutation	SNP	C	C	T	rs117385282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43896143C>T	ENST00000291536.3	-	8	909	c.742G>A	c.(742-744)Ggg>Agg	p.G248R	RSPH1_ENST00000398352.3_Missense_Mutation_p.G210R	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	248					axoneme assembly (GO:0035082)|meiotic nuclear division (GO:0007126)	cytosol (GO:0005829)|motile cilium (GO:0031514)|nucleus (GO:0005634)		p.G248R(1)		large_intestine(7)|lung(2)|ovary(1)|prostate(1)|stomach(1)	12						GCCTCCTCCCCGGGTTCTCCT	0.602													C|||	420	0.0838658	0.0076	0.1254	5008	,	,		18028	0.0109		0.171	False		,,,				2504	0.1431				p.G248R	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											RSPH1,NS,carcinoma,0,1	RSPH1	36	1	1	Substitution - Missense(1)	stomach(1)	c.G742A						PASS	.	C	ARG/GLY	159,4247	108.2+/-146.6	2,155,2046	69.0	64.0	66.0		742	-0.7	0.0	21	dbSNP_132	66	1647,6953	304.1+/-306.8	179,1289,2832	yes	missense	RSPH1	NM_080860.2	125	181,1444,4878	TT,TC,CC		19.1512,3.6087,13.8859	benign	248/310	43896143	1806,11200	2203	4300	6503	SO:0001583	missense	89765	exon8			CCTCCCCGGGTTC	AB006536	CCDS13688.1, CCDS68210.1	21q22.3	2014-02-03	2007-06-25	2007-06-25	ENSG00000160188	ENSG00000160188			12371	protein-coding gene	gene with protein product	"""meichroacidin"""	609314	"""testis specific A2 homolog (mouse)"""	TSGA2		9403069, 9578619, 17451891	Standard	XM_005261208		Approved	FLJ32753, RSP44, RSPH10A, CILD24	uc002zbg.3	Q8WYR4	OTTHUMG00000086804	ENST00000291536.3:c.742G>A	21.37:g.43896143C>T	ENSP00000291536:p.Gly248Arg	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	87	46	0.528736	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Missense_Mutation	SNP	ENST00000291536.3	37	CCDS13688.1	191	0.08745421245421245	5	0.01016260162601626	50	0.13812154696132597	6	0.01048951048951049	130	0.17150395778364116	C	1.930	-0.446146	0.04604	0.036087	0.191512	ENSG00000160188	ENST00000291536;ENST00000398352	T;T	0.60171	0.29;0.21	3.39	-0.712	0.11226	.	0.549173	0.16469	N	0.213079	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.09185	-1.0686	9	0.14252	T	0.57	.	2.8184	0.05464	0.2015:0.4424:0.0:0.356	.	248	Q8WYR4	RSPH1_HUMAN	R	248;210	ENSP00000291536:G248R;ENSP00000381395:G210R	ENSP00000291536:G248R	G	-	1	0	RSPH1	42769212	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.695000	0.05109	-0.152000	0.11156	0.655000	0.94253	GGG	C|0.869;T|0.131	0.131	strong		0.602	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1		
SDHA	6389	hgsc.bcm.edu	37	5	224633	224633	+	Silent	SNP	A	A	G	rs1139424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:224633A>G	ENST00000264932.6	+	3	424	c.309A>G	c.(307-309)gcA>gcG	p.A103A	SDHA_ENST00000510361.1_Silent_p.A103A|SDHA_ENST00000504309.1_Silent_p.A103A	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	103					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)	CTGTTGCAGCACAGGTAAGAG	0.597									Familial Paragangliomas				G|||	1202	0.240016	0.5998	0.2334	5008	,	,		17131	0.0585		0.1103	False		,,,				2504	0.0787				p.A103A		Atlas-SNP	.											.	SDHA	80	.	0			c.A309G						PASS	.	G		2240,2166	562.2+/-380.9	559,1122,522	57.0	67.0	64.0		309	-6.2	0.8	5	dbSNP_86	64	1112,7482	760.9+/-407.6	57,998,3242	no	coding-synonymous	SDHA	NM_004168.2		616,2120,3764	GG,GA,AA		12.9393,49.1602,25.7846		103/665	224633	3352,9648	2203	4297	6500	SO:0001819	synonymous_variant	6389	exon3	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	TGCAGCACAGGTA	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.309A>G	5.37:g.224633A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	143	56	0.391608	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			A|0.882;G|0.118	0.118	strong		0.597	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
HLA-A	3105	hgsc.bcm.edu	37	6	29912281	29912281	+	Silent	SNP	G	G	A	rs1136917|rs35946537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29912281G>A	ENST00000396634.1	+	7	1241	c.900G>A	c.(898-900)ctG>ctA	p.L300L	HLA-A_ENST00000376809.5_Silent_p.L300L|HLA-A_ENST00000376806.5_Silent_p.L300L|HLA-A_ENST00000376802.2_Intron			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	300	Connecting peptide.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	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						TCCCAGAGCTGTCTTCCCAGC	0.592									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			g|||	780	0.155751	0.1377	0.1772	5008	,	,		18959	0.2004		0.1133	False		,,,				2504	0.1626				p.L300L		Atlas-SNP	.											.	HLA-A	89	.	0			c.G900A						PASS	.	G		345,2677		28,289,1194	81.0	76.0	78.0		900	-6.7	0.0	6	dbSNP_86	78	520,4898		36,448,2225	no	coding-synonymous	HLA-A	NM_002116.7		64,737,3419	AA,AG,GG		9.5976,11.4163,10.2488		300/366	29912281	865,7575	1511	2709	4220	SO:0001819	synonymous_variant	3105	exon5	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	AGAGCTGTCTTCC	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.900G>A	6.37:g.29912281G>A		Somatic	335	0	0		WXS	Illumina HiSeq	Phase_I	218	116	0.53211	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			G|0.872;A|0.128	0.128	strong		0.592	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
DTHD1	401124	hgsc.bcm.edu	37	4	36317970	36317970	+	Silent	SNP	T	T	C	rs9995922	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:36317970T>C	ENST00000456874.2	+	7	1885	c.1827T>C	c.(1825-1827)agT>agC	p.S609S	DTHD1_ENST00000507598.1_Silent_p.S649S|RP11-431M7.2_ENST00000504344.1_RNA|DTHD1_ENST00000357504.3_Silent_p.S444S	NM_001170700.2	NP_001164171.1	Q6ZMT9	DTHD1_HUMAN	death domain containing 1	609					signal transduction (GO:0007165)					breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|stomach(1)	8						GAAACTATAGTTGCCCTCATT	0.368													C|||	1794	0.358227	0.5287	0.3804	5008	,	,		17459	0.2153		0.3648	False		,,,				2504	0.2526				p.S609S		Atlas-SNP	.											.	DTHD1	63	.	0			c.T1827C						PASS	.	C	,	691,693		174,343,175	110.0	103.0	105.0		1332,1827	2.9	1.0	4	dbSNP_119	105	1155,2027		209,737,645	no	coding-synonymous,coding-synonymous	DTHD1	NM_001136536.3,NM_001170700.1	,	383,1080,820	CC,CT,TT		36.2979,49.9277,40.4293	,	444/617,609/782	36317970	1846,2720	692	1591	2283	SO:0001819	synonymous_variant	401124	exon7			CTATAGTTGCCCT	AK094684	CCDS54754.1	4p14	2009-10-02			ENSG00000197057	ENSG00000197057			37261	protein-coding gene	gene with protein product							Standard	NM_001170700		Approved	FLJ16686	uc021xne.2	Q6ZMT9	OTTHUMG00000160371	ENST00000456874.2:c.1827T>C	4.37:g.36317970T>C		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	92	42	0.456522	NM_001170700	B2RXK4|B4E2N7	Silent	SNP	ENST00000456874.2	37	CCDS54754.1																																																																																			T|0.642;C|0.358	0.358	strong		0.368	DTHD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001136536	
DCBLD2	131566	hgsc.bcm.edu	37	3	98519481	98519481	+	Silent	SNP	G	G	A	rs1822017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:98519481G>A	ENST00000326840.6	-	15	2162	c.1800C>T	c.(1798-1800)agC>agT	p.S600S	DCBLD2_ENST00000326857.9_Silent_p.S614S	NM_080927.3	NP_563615.3	Q96PD2	DCBD2_HUMAN	discoidin, CUB and LCCL domain containing 2	600					cell adhesion (GO:0007155)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell growth (GO:0030308)|wound healing (GO:0042060)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)				breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|prostate(1)|stomach(2)	25						GATTAACTTCGCTGCTGCTAT	0.507													g|||	797	0.159145	0.2511	0.098	5008	,	,		18050	0.0456		0.164	False		,,,				2504	0.1902				p.S600S		Atlas-SNP	.											.	DCBLD2	62	.	0			c.C1800T						PASS	.	A		971,3133		110,751,1191	211.0	207.0	208.0		1800	-3.3	0.5	3	dbSNP_92	208	1275,7117		108,1059,3029	no	coding-synonymous	DCBLD2	NM_080927.3		218,1810,4220	AA,AG,GG		15.193,23.6598,17.9738		600/776	98519481	2246,10250	2052	4196	6248	SO:0001819	synonymous_variant	131566	exon15			AACTTCGCTGCTG		CCDS46878.1	3q12.2	2006-04-12			ENSG00000057019	ENSG00000057019			24627	protein-coding gene	gene with protein product		608698				11447234	Standard	NM_080927		Approved	CLCP1, ESDN	uc003dtd.3	Q96PD2	OTTHUMG00000151985	ENST00000326840.6:c.1800C>T	3.37:g.98519481G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	151	72	0.476821	NM_080927	B7WNL1|D3DN41|Q8N6M4|Q8TDX2	Silent	SNP	ENST00000326840.6	37	CCDS46878.1																																																																																			G|0.846;A|0.154	0.154	strong		0.507	DCBLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324675.2	NM_080927	
RP1L1	94137	hgsc.bcm.edu	37	8	10467605	10467605	+	Missense_Mutation	SNP	C	C	T	rs61503212		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10467605C>T	ENST00000382483.3	-	4	4226	c.4003G>A	c.(4003-4005)Ggg>Agg	p.G1335R		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1351	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		G -> R (in allele RP1L1-2 and allele RP1L1-3; dbSNP:rs61503212).|Missing (in allele RP1L1-1).		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)		aactgcaccccctcttcttgc	0.468																																					p.G1335R		Atlas-SNP	.											RP1L1,NS,carcinoma,+1,1	RP1L1	453	1	0			c.G4003A						scavenged	.						120.0	116.0	117.0					8																	10467605		1948	4134	6082	SO:0001583	missense	94137	exon4			GCACCCCCTCTTC	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.4003G>A	8.37:g.10467605C>T	ENSP00000371923:p.Gly1335Arg	Somatic	258	14	0.0542636		WXS	Illumina HiSeq	Phase_I	177	53	0.299435	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.604607	0.28623	.	.	ENSG00000183638	ENST00000382483	T	0.05996	3.36	2.64	-0.606	0.11619	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	0.80722	P	0.0	B	0.29862	0.259	B	0.23018	0.043	T	0.36962	-0.9726	8	0.48119	T	0.1	.	7.1242	0.25463	0.0:0.3817:0.0:0.6183	rs61503212	1335	A6NKC6	.	R	1335	ENSP00000371923:G1335R	ENSP00000371923:G1335R	G	-	1	0	RP1L1	10505015	0.000000	0.05858	0.004000	0.12327	0.295000	0.27426	0.159000	0.16442	-0.082000	0.12640	0.462000	0.41574	GGG	C|0.500;T|0.500	0.500	weak		0.468	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
ZNF862	643641	hgsc.bcm.edu	37	7	149559465	149559465	+	Silent	SNP	C	C	T	rs2074701	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149559465C>T	ENST00000223210.4	+	7	3461	c.3216C>T	c.(3214-3216)ggC>ggT	p.G1072G	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	1072					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						CTGTGAACGGCGTGGCCGTCA	0.612													C|||	2193	0.437899	0.4743	0.487	5008	,	,		21205	0.3264		0.5686	False		,,,				2504	0.3344				p.G1072G		Atlas-SNP	.											ZNF862,NS,carcinoma,0,1	ZNF862	97	1	0			c.C3216T						PASS	.	C		2229,2119		580,1069,525	47.0	58.0	54.0		3216	-10.4	0.1	7	dbSNP_96	54	5033,3517		1511,2011,753	no	coding-synonymous	ZNF862	NM_001099220.1		2091,3080,1278	TT,TC,CC		41.1345,48.7351,43.6967		1072/1170	149559465	7262,5636	2174	4275	6449	SO:0001819	synonymous_variant	643641	exon7			GAACGGCGTGGCC	AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.3216C>T	7.37:g.149559465C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	69	69	1	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																			C|0.500;T|0.500	0.500	strong		0.612	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
MXRA5	25878	hgsc.bcm.edu	37	X	3240343	3240343	+	Missense_Mutation	SNP	G	G	A	rs1635246	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3240343G>A	ENST00000217939.6	-	5	3537	c.3383C>T	c.(3382-3384)gCa>gTa	p.A1128V		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1128			A -> V (in dbSNP:rs1635246). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TGTTGTTGTTGCTGTTGTGGT	0.502													G|||	1964	0.520265	0.447	0.415	3775	,	,		15049	0.2728		0.4602	False		,,,				2504	0.3548				p.A1128V		Atlas-SNP	.											.	MXRA5	815	.	0			c.C3383T						PASS	.	-	VAL/ALA	2239,1596		552,796,339,284,232	107.0	88.0	94.0		3383	-6.3	0.0	X	dbSNP_89	94	3847,2881		796,1188,1067,444,805	yes	missense	MXRA5	NM_015419.3	64	1348,1984,1406,728,1037	AA,AG,A,GG,G		42.821,41.6167,42.3838	benign	1128/2829	3240343	6086,4477	2203	4300	6503	SO:0001583	missense	25878	exon5			GTTGTTGCTGTTG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.3383C>T	X.37:g.3240343G>A	ENSP00000217939:p.Ala1128Val	Somatic	178	1	0.00561798		WXS	Illumina HiSeq	Phase_I	141	138	0.978723	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	878	0.5292344786015672	159	0.4441340782122905	93	0.33214285714285713	105	0.23863636363636365	242	0.4416058394160584	g	9.113	1.007028	0.19199	0.583833	0.57179	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.70399	-0.48	3.61	-6.31	0.02001	.	0.667190	0.12097	N	0.499817	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.39187	-0.9626	9	0.23302	T	0.38	.	3.9428	0.09334	0.1509:0.1155:0.6164:0.1172	rs1635246;rs3764755;rs56693232;rs1635246	1128	Q9NR99	MXRA5_HUMAN	V	1128	ENSP00000217939:A1128V	ENSP00000217939:A1128V	A	-	2	0	MXRA5	3250343	0.005000	0.15991	0.000000	0.03702	0.017000	0.09413	1.488000	0.35551	-1.519000	0.01775	0.519000	0.50382	GCA	G|0.441;A|0.559	0.559	strong		0.502	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
GNL3	26354	hgsc.bcm.edu	37	3	52721305	52721305	+	Missense_Mutation	SNP	G	G	A	rs11177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52721305G>A	ENST00000418458.1	+	3	289	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	PBRM1_ENST00000394830.3_5'Flank|SNORD19B_ENST00000516978.1_RNA|GNL3_ENST00000460073.1_3'UTR|SNORD19_ENST00000391191.1_RNA|GNL3_ENST00000394799.2_Missense_Mutation_p.R27Q	NM_014366.4|NM_206826.1	NP_055181.3|NP_996562.1	Q9BVP2	GNL3_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)	39	Basic. {ECO:0000250}.		R -> Q (in dbSNP:rs11177). {ECO:0000269|PubMed:11085516, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16012751}.		cell proliferation (GO:0008283)|GTP catabolic process (GO:0006184)|regulation of cell proliferation (GO:0042127)|ribosome biogenesis (GO:0042254)	extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|large_intestine(3)|lung(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.75e-05)|Kidney(197;0.000611)|KIRC - Kidney renal clear cell carcinoma(197;0.000773)|OV - Ovarian serous cystadenocarcinoma(275;0.048)		GCTAAAAAGCGGGGTCACAAG	0.398													G|||	1562	0.311901	0.1467	0.4582	5008	,	,		18389	0.4236		0.4175	False		,,,				2504	0.2076				p.R39Q		Atlas-SNP	.											.	GNL3	37	.	0			c.G116A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	761,3645	290.1+/-280.8	62,637,1504	65.0	75.0	72.0		116,80,80	1.9	1.0	3	dbSNP_52	72	3465,5135	500.9+/-375.3	720,2025,1555	yes	missense,missense,missense	GNL3	NM_014366.4,NM_206825.1,NM_206826.1	43,43,43	782,2662,3059	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	40.2907,17.2719,32.4927	benign,benign,benign	39/550,27/538,27/538	52721305	4226,8780	2203	4300	6503	SO:0001583	missense	26354	exon3			AAAAGCGGGGTCA	AK027514	CCDS2861.1, CCDS43100.1	3p21.1	2005-01-10			ENSG00000163938	ENSG00000163938			29931	protein-coding gene	gene with protein product		608011				11085516, 12464630	Standard	NM_014366		Approved	C77032, E2IG3, MGC800, NS, nucleostemin	uc003dfd.3	Q9BVP2	OTTHUMG00000158752	ENST00000418458.1:c.116G>A	3.37:g.52721305G>A	ENSP00000395772:p.Arg39Gln	Somatic	163	0	0		WXS	Illumina HiSeq	Phase_I	116	62	0.534483	NM_014366	B2RDC1|Q5PU80|Q96SV6|Q96SV7|Q9UJY0	Missense_Mutation	SNP	ENST00000418458.1	37	CCDS2861.1	848	0.3882783882783883	79	0.16056910569105692	171	0.4723756906077348	277	0.48426573426573427	321	0.4234828496042216	G	13.85	2.361061	0.41801	0.172719	0.402907	ENSG00000163938	ENST00000479230;ENST00000418458;ENST00000394799;ENST00000474423	T;T;T;T	0.41758	0.99;0.99;0.99;0.99	5.83	1.92	0.25849	GNL3L/Grn1 putative GTPase (1);	0.306688	0.37053	N	0.002263	T	0.00012	0.0000	N	0.22421	0.69	0.34398	P	0.305084	B	0.22080	0.064	B	0.16289	0.015	T	0.48768	-0.9006	9	0.15952	T	0.53	.	8.9856	0.35992	0.3608:0.0:0.6392:0.0	rs11177;rs1047396;rs3187401;rs17844878;rs17857595;rs52805757;rs60862326;rs11177	39	Q9BVP2	GNL3_HUMAN	Q	27;39;27;27	ENSP00000419734:R27Q;ENSP00000395772:R39Q;ENSP00000378278:R27Q;ENSP00000419895:R27Q	ENSP00000378278:R27Q	R	+	2	0	GNL3	52696345	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	2.766000	0.47629	0.346000	0.23899	0.655000	0.94253	CGG	G|0.658;A|0.342	0.342	strong		0.398	GNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352032.1	NM_014366	
CACNA1C	775	hgsc.bcm.edu	37	12	2721137	2721137	+	Silent	SNP	C	C	T	rs216008	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:2721137C>T	ENST00000347598.4	+	30	3846	c.3846C>T	c.(3844-3846)ttC>ttT	p.F1282F	CACNA1C_ENST00000399606.1_Silent_p.F1282F|CACNA1C_ENST00000399637.1_Silent_p.F1262F|CACNA1C_ENST00000399601.1_Silent_p.F1262F|CACNA1C_ENST00000399644.1_Silent_p.F1262F|CACNA1C_ENST00000402845.3_Silent_p.F1262F|CACNA1C_ENST00000399641.1_Silent_p.F1262F|CACNA1C_ENST00000399649.1_Silent_p.F1262F|CACNA1C_ENST00000399638.1_Silent_p.F1262F|CACNA1C_ENST00000399617.1_Silent_p.F1262F|CACNA1C_ENST00000399591.1_Silent_p.F1262F|CACNA1C_ENST00000327702.7_Silent_p.F1262F|CACNA1C_ENST00000399621.1_Silent_p.F1262F|CACNA1C_ENST00000399634.1_Silent_p.F1262F|CACNA1C_ENST00000406454.3_Silent_p.F1262F|CACNA1C_ENST00000399603.1_Silent_p.F1262F|CACNA1C_ENST00000344100.3_Silent_p.F1262F|CACNA1C_ENST00000480911.1_Silent_p.F1262F|CACNA1C_ENST00000399629.1_Silent_p.F1262F|CACNA1C_ENST00000399595.1_Silent_p.F1262F|CACNA1C_ENST00000399655.1_Silent_p.F1262F|CACNA1C_ENST00000335762.5_Silent_p.F1287F|CACNA1C_ENST00000399597.1_Silent_p.F1262F	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1282					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CTGGCCTCTTCACCGTGGAGA	0.542													C|||	1298	0.259185	0.2413	0.2262	5008	,	,		21995	0.3512		0.2087	False		,,,				2504	0.2638				p.F1282F		Atlas-SNP	.											Q6YL47_HUMAN,NS,carcinoma,+2,4	CACNA1C	1023	4	0			c.C3846T						scavenged	.						117.0	113.0	114.0					12																	2721137		2183	4296	6479	SO:0001819	synonymous_variant	775	exon30			CCTCTTCACCGTG	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.3846C>T	12.37:g.2721137C>T		Somatic	110	1	0.00909091		WXS	Illumina HiSeq	Phase_I	128	50	0.390625	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																			C|0.730;T|0.270	0.270	strong		0.542	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144880832	144880832	+	Missense_Mutation	SNP	T	T	C	rs12568796	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144880832T>C	ENST00000369354.3	-	26	3985	c.3796A>G	c.(3796-3798)Aag>Gag	p.K1266E	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.K1402E|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.K1402E|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.K1266E|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.K1222E|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1266				K -> E (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)		TGGATCTGCTTGCTGTCCTGC	0.532			T	PDGFRB	MPD																																p.K1266E		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A3796G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS	533,3873		0,533,1670	219.0	188.0	198.0		3664,3796,3796	4.9	1.0	1	dbSNP_120	198	2102,6492		0,2102,2195	no	missense,missense,missense	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	56,56,56	0,2635,3865	CC,CT,TT		24.4589,12.0971,20.2692	probably-damaging,probably-damaging,probably-damaging	1222/2241,1266/2363,1266/2347	144880832	2635,10365	2203	4297	6500	SO:0001583	missense	9659	exon26			TCTGCTTGCTGTC	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.3796A>G	1.37:g.144880832T>C	ENSP00000358360:p.Lys1266Glu	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	216	48	0.222222	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	445|445	0.20375457875457875|0.20375457875457875	49|49	0.09959349593495935|0.09959349593495935	88|88	0.2430939226519337|0.2430939226519337	115|115	0.20104895104895104|0.20104895104895104	193|193	0.2546174142480211|0.2546174142480211	T|T	32|32	5.171174|5.171174	0.94807|0.94807	0.120971|0.120971	0.244589|0.244589	ENSG00000178104|ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359|ENST00000530592	T;T;T;T;T|.	0.04083|.	3.71;3.93;3.89;3.93;3.95|.	6.07|6.07	4.95|4.95	0.65309|0.65309	.|.	.|.	.|.	.|.	.|.	T|T	0.52677|0.52677	0.1749|0.1749	M|M	0.63843|0.63843	1.955|1.955	0.80722|0.80722	D|D	1|1	D;D|.	0.71674|.	0.971;0.998|.	P;D|.	0.77004|.	0.453;0.989|.	T|T	0.54410|0.54410	-0.8298|-0.8298	9|5	0.66056|.	D|.	0.02|.	.|.	11.6787|11.6787	0.51444|0.51444	0.0:0.0:0.1583:0.8417|0.0:0.0:0.1583:0.8417	rs12568796;rs57324776|rs12568796;rs57324776	1222;1266|.	Q5VU43-3;Q5VU43|.	.;MYOME_HUMAN|.	E|R	1222;1266;1266;1402;1402|159	ENSP00000327209:K1222E;ENSP00000358360:K1266E;ENSP00000358363:K1266E;ENSP00000435654:K1402E;ENSP00000358366:K1402E|.	ENSP00000327209:K1222E|.	K|Q	-|-	1|2	0|0	PDE4DIP|PDE4DIP	143592189|143592189	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.533000|7.533000	0.81994|0.81994	1.112000|1.112000	0.41740|0.41740	0.533000|0.533000	0.62120|0.62120	AAG|CAA	T|0.794;C|0.206	0.206	strong		0.532	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PCNXL3	399909	hgsc.bcm.edu	37	11	65403651	65403651	+	Missense_Mutation	SNP	C	C	A	rs7114037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:65403651C>A	ENST00000355703.3	+	33	6005	c.5466C>A	c.(5464-5466)caC>caA	p.H1822Q	MIR4690_ENST00000578459.1_RNA|SIPA1_ENST00000534313.1_5'Flank	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1822			H -> Q (in dbSNP:rs7114037).			integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCAGGCTTCACAAGGGCTGTG	0.617													C|||	69	0.013778	0.0015	0.0187	5008	,	,		17872	0.0		0.0497	False		,,,				2504	0.0041				p.H1822Q		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C5466A						PASS	.	C	GLN/HIS	38,4042		0,38,2002	30.0	34.0	33.0		5466	-4.0	1.0	11	dbSNP_116	33	407,7943		8,391,3776	yes	missense	PCNXL3	NM_032223.2	24	8,429,5778	AA,AC,CC		4.8743,0.9314,3.58	benign	1822/2035	65403651	445,11985	2040	4175	6215	SO:0001583	missense	399909	exon33			GCTTCACAAGGGC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.5466C>A	11.37:g.65403651C>A	ENSP00000347931:p.His1822Gln	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	123	56	0.455285	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	42	0.019230769230769232	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	33	0.04353562005277045	C	12.27	1.887915	0.33348	0.009314	0.048743	ENSG00000197136	ENST00000355703	T	0.05717	3.4	4.74	-3.95	0.04118	.	0.072360	0.56097	D	0.000021	T	0.00300	0.0009	N	0.01352	-0.895	0.27955	N	0.937005	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.0	T	0.39583	-0.9607	10	0.54805	T	0.06	.	4.0192	0.09657	0.1301:0.4914:0.1474:0.231	rs7114037	709;1822	Q9H6A9-3;Q9H6A9	.;PCX3_HUMAN	Q	1822	ENSP00000347931:H1822Q	ENSP00000347931:H1822Q	H	+	3	2	PCNXL3	65160227	0.992000	0.36948	0.992000	0.48379	0.798000	0.45092	0.202000	0.17295	-0.331000	0.08501	-0.391000	0.06502	CAC	C|0.980;A|0.020	0.020	strong		0.617	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
CFAP74	85452	hgsc.bcm.edu	37	1	1888193	1888193	+	IGR	SNP	C	C	A	rs3820011	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1888193C>A								TMEM52 (37481 upstream) : C1orf222 (31369 downstream)																							ACGTAGCTGCCGAAGTCAATG	0.622													C|||	936	0.186901	0.1067	0.232	5008	,	,		19634	0.2282		0.2455	False		,,,				2504	0.1605				p.G628C		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G1882T						PASS	.	C	CYS/GLY	566,3756		44,478,1639	55.0	60.0	58.0		1882	4.8	1.0	1	dbSNP_107	58	2242,6272		294,1654,2309	yes	missense	KIAA1751	NM_001080484.1	159	338,2132,3948	AA,AC,CC		26.3331,13.0958,21.876	probably-damaging	628/763	1888193	2808,10028	2161	4257	6418	SO:0001628	intergenic_variant	85452	exon17			AGCTGCCGAAGTC																													1.37:g.1888193C>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	104	97	0.932692	NM_001080484		Missense_Mutation	SNP		37		514	0.23534798534798534	66	0.13414634146341464	89	0.24585635359116023	162	0.28321678321678323	197	0.2598944591029024	C	19.64	3.865871	0.71949	0.130958	0.263331	ENSG00000142609	ENST00000270720;ENST00000461752	.	.	.	4.75	4.75	0.60458	.	0.000000	0.64402	D	0.000001	T	0.00039	0.0001	M	0.79258	2.445	0.09310	P	1.0	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00348	-1.1799	8	0.87932	D	0	-32.4849	15.6211	0.76808	0.0:1.0:0.0:0.0	rs3820011;rs17372244;rs57075302;rs3820011	628;628	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	C	628;75	.	ENSP00000270720:G628C	G	-	1	0	C1orf222	1878053	1.000000	0.71417	0.993000	0.49108	0.683000	0.39861	5.452000	0.66638	2.352000	0.79861	0.655000	0.94253	GGC	C|0.775;A|0.225	0.225	strong	0	0.622								
RXRG	6258	hgsc.bcm.edu	37	1	165398115	165398115	+	Silent	SNP	T	T	C	rs113471	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:165398115T>C	ENST00000359842.5	-	2	440	c.138A>G	c.(136-138)acA>acG	p.T46T		NM_001256570.1|NM_006917.4	NP_001243499.1|NP_008848.1	P48443	RXRG_HUMAN	retinoid X receptor, gamma	46	Modulating. {ECO:0000250}.				gene expression (GO:0010467)|heart development (GO:0007507)|neuron differentiation (GO:0030182)|peripheral nervous system development (GO:0007422)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|response to retinoic acid (GO:0032526)|skeletal muscle tissue development (GO:0007519)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	9-cis retinoic acid receptor activity (GO:0004886)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(3)|large_intestine(6)|lung(22)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	38	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tretinoin(DB00755)	CTGGGGTATCTGTGTAGCTGG	0.602													C|||	1252	0.25	0.416	0.2896	5008	,	,		17907	0.246		0.1531	False		,,,				2504	0.1012				p.T46T		Atlas-SNP	.											RXRG,NS,carcinoma,-2,1	RXRG	91	1	0			c.A138G						scavenged	.	C		1531,2875	672.4+/-402.6	254,1023,926	64.0	59.0	61.0		138	-6.1	0.7	1	dbSNP_79	61	1321,7279	757.8+/-407.5	113,1095,3092	no	coding-synonymous	RXRG	NM_006917.4		367,2118,4018	CC,CT,TT		15.3605,34.7481,21.9283		46/464	165398115	2852,10154	2203	4300	6503	SO:0001819	synonymous_variant	6258	exon2			GGTATCTGTGTAG	U38480	CCDS1248.1, CCDS72970.1	1q22-q23	2013-01-16			ENSG00000143171	ENSG00000143171		"""Nuclear hormone receptors"""	10479	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 3"""	180247				8034312	Standard	NR_033824		Approved	NR2B3	uc001gda.3	P48443	OTTHUMG00000034626	ENST00000359842.5:c.138A>G	1.37:g.165398115T>C		Somatic	126	1	0.00793651		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_006917	A6NIP1|Q6IBU7	Silent	SNP	ENST00000359842.5	37	CCDS1248.1																																																																																			T|0.776;G|0.003	.	strong		0.602	RXRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083794.2	NM_006917	
SLC15A1	6564	hgsc.bcm.edu	37	13	99340578	99340578	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:99340578G>A	ENST00000376503.5	-	20	1662	c.1607C>T	c.(1606-1608)cCg>cTg	p.P536L		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	536					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)	ACATTGTGGCGGAATCTCTGT	0.308																																					p.P536L		Atlas-SNP	.											.	SLC15A1	92	.	0			c.C1607T						PASS	.						78.0	78.0	78.0					13																	99340578		2203	4300	6503	SO:0001583	missense	6564	exon20			TGTGGCGGAATCT	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.1607C>T	13.37:g.99340578G>A	ENSP00000365686:p.Pro536Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	97	38	0.391753	NM_005073	Q5VW82	Missense_Mutation	SNP	ENST00000376503.5	37	CCDS9489.1	.	.	.	.	.	.	.	.	.	.	G	6.435	0.448320	0.12223	.	.	ENSG00000088386	ENST00000376503	T	0.01963	4.53	5.09	1.21	0.21127	Major facilitator superfamily domain, general substrate transporter (1);	1.449500	0.03719	N	0.251497	T	0.01695	0.0054	N	0.14661	0.345	0.09310	N	1	B	0.25486	0.127	B	0.20384	0.029	T	0.44832	-0.9302	10	0.23891	T	0.37	-9.85	3.6908	0.08346	0.3572:0.1832:0.4596:0.0	.	536	P46059	S15A1_HUMAN	L	536	ENSP00000365686:P536L	ENSP00000365686:P536L	P	-	2	0	SLC15A1	98138579	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.380000	0.20602	0.674000	0.31244	-0.768000	0.03414	CCG	.	.	none		0.308	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073	
SGK223	157285	hgsc.bcm.edu	37	8	8234077	8234077	+	Silent	SNP	G	G	C	rs4840952|rs386721946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:8234077G>C	ENST00000520004.1	-	3	2106	c.1842C>G	c.(1840-1842)gcC>gcG	p.A614A	SGK223_ENST00000330777.4_Silent_p.A614A			Q86YV5	SG223_HUMAN		616							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CTGACGAGGCGGCAGGCTGGG	0.647													C|||	2132	0.425719	0.3064	0.4222	5008	,	,		17439	0.6409		0.2783	False		,,,				2504	0.5194				p.A614A	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.C1842G						PASS	.	C		1125,2761		166,793,984	37.0	42.0	41.0		1842	-3.7	0.0	8	dbSNP_111	41	2275,6009		318,1639,2185	no	coding-synonymous	SGK223	NM_001080826.1		484,2432,3169	CC,CG,GG		27.4626,28.9501,27.9376		614/1403	8234077	3400,8770	1943	4142	6085	SO:0001819	synonymous_variant	0	exon2			CGAGGCGGCAGGC																												ENST00000520004.1:c.1842C>G	8.37:g.8234077G>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			G|0.632;C|0.368	0.368	strong		0.647	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
HAUS6	54801	hgsc.bcm.edu	37	9	19058921	19058921	+	Missense_Mutation	SNP	G	G	A	rs62622380	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:19058921G>A	ENST00000380502.3	-	16	2311	c.1844C>T	c.(1843-1845)gCt>gTt	p.A615V	HAUS6_ENST00000380496.1_Missense_Mutation_p.A479V	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	615				A -> V (in Ref. 5; AAH10632/AAI14493). {ECO:0000305}.	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						TCTATGTTCAGCATCCATTTG	0.343													G|||	483	0.0964457	0.1074	0.1527	5008	,	,		20235	0.0288		0.1004	False		,,,				2504	0.1074				p.A615V		Atlas-SNP	.											.	HAUS6	66	.	0			c.C1844T						PASS	.	G	VAL/ALA	459,3947	209.5+/-230.2	22,415,1766	75.0	66.0	69.0		1844	0.1	0.0	9	dbSNP_129	69	1107,7487	222.6+/-259.6	61,985,3251	no	missense	HAUS6	NM_017645.3	64	83,1400,5017	AA,AG,GG		12.8811,10.4176,12.0462	benign	615/956	19058921	1566,11434	2203	4297	6500	SO:0001583	missense	54801	exon16			TGTTCAGCATCCA	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.1844C>T	9.37:g.19058921G>A	ENSP00000369871:p.Ala615Val	Somatic	332	1	0.00301205		WXS	Illumina HiSeq	Phase_I	391	171	0.43734	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	212	0.09706959706959707	57	0.11585365853658537	62	0.1712707182320442	12	0.02097902097902098	81	0.10686015831134564	G	0.021	-1.425946	0.01126	0.104176	0.128811	ENSG00000147874	ENST00000380502;ENST00000380496;ENST00000415524	T;T;T	0.47528	1.82;1.83;0.84	5.35	0.075	0.14397	.	1.038310	0.07557	N	0.916401	T	0.00073	0.0002	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.19583	0.007;0.037;0.015	B;B;B	0.15484	0.008;0.013;0.012	T	0.15009	-1.0452	9	0.08599	T	0.76	1.14	2.7976	0.05405	0.2119:0.124:0.5362:0.1278	rs62622380	580;479;615	Q7Z4H7-3;Q5VY60;Q7Z4H7	.;.;HAUS6_HUMAN	V	615;479;131	ENSP00000369871:A615V;ENSP00000369865:A479V;ENSP00000409615:A131V	ENSP00000369865:A479V	A	-	2	0	HAUS6	19048921	0.000000	0.05858	0.002000	0.10522	0.194000	0.23727	0.516000	0.22817	0.033000	0.15463	0.467000	0.42956	GCT	G|0.889;A|0.111	0.111	strong		0.343	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
LRRC19	64922	hgsc.bcm.edu	37	9	26998122	26998122	+	Silent	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:26998122T>G	ENST00000380055.5	-	3	309	c.199A>C	c.(199-201)Aga>Cga	p.R67R	IFT74_ENST00000443698.1_Intron|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000433700.1_Intron|LRRC19_ENST00000482770.1_5'Flank|IFT74_ENST00000380062.5_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	67						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)		TGTAGAACTCTTGTGTCTGTA	0.328																																					p.R67R		Atlas-SNP	.											.	LRRC19	24	.	0			c.A199C						PASS	.						73.0	81.0	78.0					9																	26998122		2203	4296	6499	SO:0001819	synonymous_variant	64922	exon3			GAACTCTTGTGTC	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.199A>C	9.37:g.26998122T>G		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_022901	A0AV00|B9EG91	Silent	SNP	ENST00000380055.5	37	CCDS6518.1																																																																																			.	.	none		0.328	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2	NM_022901	
PDXDC1	23042	hgsc.bcm.edu	37	16	15111218	15111218	+	Missense_Mutation	SNP	C	C	T	rs4985162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15111218C>T	ENST00000396410.4	+	11	999	c.902C>T	c.(901-903)cCg>cTg	p.P301L	PDXDC1_ENST00000455313.2_Missense_Mutation_p.P278L|PDXDC1_ENST00000447912.2_Missense_Mutation_p.P210L|PDXDC1_ENST00000535621.2_Missense_Mutation_p.P301L|PDXDC1_ENST00000450288.2_Missense_Mutation_p.P273L|PDXDC1_ENST00000569715.1_Missense_Mutation_p.P274L|PDXDC1_ENST00000325823.7_Missense_Mutation_p.P286L|PDXDC1_ENST00000563679.1_Missense_Mutation_p.P319L|RP11-680G24.5_ENST00000565178.1_RNA	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	301			P -> L (in dbSNP:rs4985162). {ECO:0000269|PubMed:14702039}.		carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						ACTCCTGGCCCGTGGCTGGGT	0.502																																					p.P301L		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C902T						PASS	.	C	LEU/PRO	639,3755		23,593,1581	86.0	91.0	89.0		902	4.5	0.5	16	dbSNP_111	89	1574,7020		29,1516,2752	no	missense	PDXDC1	NM_015027.2	98	52,2109,4333	TT,TC,CC		18.3151,14.5426,17.0388	benign	301/789	15111218	2213,10775	2197	4297	6494	SO:0001583	missense	23042	exon11			CTGGCCCGTGGCT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.902C>T	16.37:g.15111218C>T	ENSP00000379691:p.Pro301Leu	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	189	102	0.539683	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	583	0.26694139194139194	58	0.11788617886178862	127	0.35082872928176795	246	0.43006993006993005	152	0.20052770448548812	C	13.70	2.316841	0.40996	0.145426	0.183151	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19	5.45	4.49	0.54785	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.261616	0.44285	N	0.000468	T	0.00012	0.0000	N	0.19112	0.55	0.22479	P	0.999063953	B;B;B;B;B	0.15930	0.006;0.015;0.006;0.006;0.0	B;B;B;B;B	0.16722	0.006;0.016;0.01;0.01;0.001	T	0.46317	-0.9200	9	0.25106	T	0.35	-12.0274	12.4403	0.55621	0.0:0.9177:0.0:0.0823	rs4985162	273;210;301;301;278	E7EPL4;E7EMH5;Q86XE2;Q6P996;Q6P996-2	.;.;.;PDXD1_HUMAN;.	L	286;210;301;301;273;7;278	ENSP00000322807:P286L;ENSP00000400310:P210L;ENSP00000437835:P301L;ENSP00000379691:P301L;ENSP00000391147:P273L;ENSP00000406703:P278L	ENSP00000322807:P286L	P	+	2	0	PDXDC1	15018719	0.931000	0.31567	0.484000	0.27391	0.957000	0.61999	3.082000	0.50128	1.260000	0.44134	0.542000	0.68232	CCG	.	.	weak		0.502	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
COBLL1	22837	hgsc.bcm.edu	37	2	165551404	165551404	+	Missense_Mutation	SNP	G	G	A	rs17244632	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:165551404G>A	ENST00000392717.2	-	13	2730	c.2726C>T	c.(2725-2727)aCt>aTt	p.T909I	COBLL1_ENST00000194871.6_Missense_Mutation_p.T938I|COBLL1_ENST00000409184.3_Missense_Mutation_p.T871I|COBLL1_ENST00000375458.2_Missense_Mutation_p.T833I|COBLL1_ENST00000342193.4_Missense_Mutation_p.T871I			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	909						extracellular vesicular exosome (GO:0070062)		p.T871I(1)		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						AGCTGTGCCAGTGTCTCTTGT	0.448													G|||	264	0.0527157	0.0113	0.0519	5008	,	,		18589	0.0327		0.1581	False		,,,				2504	0.0215				p.T871I		Atlas-SNP	.											COBLL1,NS,carcinoma,0,1	COBLL1	122	1	1	Substitution - Missense(1)	stomach(1)	c.C2612T						PASS	.	G	ILE/THR	159,4247	107.8+/-146.2	5,149,2049	91.0	88.0	89.0		2612	0.6	0.3	2	dbSNP_123	89	1196,7404	242.9+/-272.7	80,1036,3184	yes	missense	COBLL1	NM_014900.3	89	85,1185,5233	AA,AG,GG		13.907,3.6087,10.4183	possibly-damaging	871/1167	165551404	1355,11651	2203	4300	6503	SO:0001583	missense	22837	exon12			GTGCCAGTGTCTC	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.2726C>T	2.37:g.165551404G>A	ENSP00000376478:p.Thr909Ile	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	98	38	0.387755	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		161	0.07371794871794872	7	0.014227642276422764	20	0.055248618784530384	19	0.033216783216783216	115	0.1517150395778364	G	9.264	1.043933	0.19748	0.036087	0.13907	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	.	.	.	6.17	0.63	0.17693	.	0.725118	0.13805	N	0.361548	T	0.00178	0.0005	L	0.51422	1.61	0.80722	P	0.0	P;P;P	0.50443	0.893;0.893;0.935	B;P;P	0.45610	0.383;0.486;0.487	T	0.06972	-1.0797	8	0.59425	D	0.04	-2.8783	1.7239	0.02918	0.1457:0.2523:0.3429:0.2591	rs17244632;rs52813009;rs17244632	909;938;871	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	I	833;871;871;909;938	.	ENSP00000194871:T938I	T	-	2	0	COBLL1	165259650	0.000000	0.05858	0.308000	0.25141	0.119000	0.20118	0.328000	0.19681	0.443000	0.26582	0.655000	0.94253	ACT	G|0.913;A|0.087	0.087	strong		0.448	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449434	89449434	+	Missense_Mutation	SNP	T	T	C	rs2893084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449434T>C	ENST00000321792.5	-	2	503	c.76A>G	c.(76-78)Aca>Gca	p.T26A	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.T26A	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	26	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CCAAATACTGTTTCAAGAGCT	0.413											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T26A		Atlas-SNP	.											CCBL2,NS,neuroblastoma,+1,2	.	.	2	0			c.A76G						scavenged	.						184.0	183.0	183.0					1																	89449434		2203	4300	6503	SO:0001583	missense	494115	exon3			ATACTGTTTCAAG	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.76A>G	1.37:g.89449434T>C	ENSP00000318415:p.Thr26Ala	Somatic	318	2	0.00628931	1267	WXS	Illumina HiSeq	Phase_I	486	89	0.183128	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	T	3.554	-0.091124	0.07053	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.85171	-1.95;-1.95	1.28	-2.56	0.06268	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.275039	0.28382	N	0.015553	T	0.30885	0.0779	N	0.03224	-0.385	0.20873	N	0.999835	B	0.02656	0.0	B	0.06405	0.002	T	0.49818	-0.8899	10	0.02654	T	1	7.3308	6.0529	0.19794	0.0:0.6607:0.0:0.3393	rs2893084	26	Q96E39	RBMXL_HUMAN	A	26	ENSP00000318415:T26A;ENSP00000446099:T26A	ENSP00000318415:T26A	T	-	1	0	RBMXL1	89222022	1.000000	0.71417	0.482000	0.27366	0.917000	0.54804	1.281000	0.33214	-0.855000	0.04125	-0.760000	0.03462	ACA	T|0.500;C|0.500	0.500	strong		0.413	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
ARSA	410	hgsc.bcm.edu	37	22	51064416	51064416	+	Missense_Mutation	SNP	T	T	C	rs2071421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:51064416T>C	ENST00000547307.1	-	6	1454	c.1049A>G	c.(1048-1050)aAt>aGt	p.N350S	ARSA_ENST00000453344.2_Missense_Mutation_p.N266S|ARSA_ENST00000395619.3_Missense_Mutation_p.N352S|ARSA_ENST00000547805.1_Missense_Mutation_p.N350S|ARSA_ENST00000610191.1_5'Flank|ARSA_ENST00000216124.5_Missense_Mutation_p.N352S|ARSA_ENST00000395621.3_Missense_Mutation_p.N352S|ARSA_ENST00000356098.5_Missense_Mutation_p.N352S			P15289	ARSA_HUMAN	arylsulfatase A	350			N -> S (associated with arylsulfatase A pseudodeficiency; appears to be responsible for the small size of the enzyme produced by pseudodeficiency fibroblasts because it leads to loss of an N-glycosylation site; dbSNP:rs2071421). {ECO:0000269|PubMed:10477432, ECO:0000269|PubMed:11941485, ECO:0000269|PubMed:15026521, ECO:0000269|PubMed:2574462, ECO:0000269|Ref.6}.		autophagy (GO:0006914)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to methylmercury (GO:0051597)|response to nutrient (GO:0007584)|response to pH (GO:0009268)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum lumen (GO:0005788)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|cerebroside-sulfatase activity (GO:0004098)|sulfuric ester hydrolase activity (GO:0008484)			endometrium(1)|large_intestine(1)|lung(5)|pancreas(1)|skin(1)	9		all_cancers(38;8.8e-15)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Micafungin(DB01141)|Suramin(DB04786)	CAAGGTGACATTGGGCAGTGG	0.682													T|||	1126	0.22484	0.3775	0.2522	5008	,	,		17056	0.1597		0.1392	False		,,,				2504	0.1544				p.N352S		Atlas-SNP	.											.	ARSA	19	.	0			c.A1055G	GRCh37	CM890013	ARSA	M	rs2071421	PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	1305,3057		189,927,1065	18.0	19.0	19.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1055,1055,1055,1055,797	5.5	0.9	22	dbSNP_96	19	1050,7508		60,930,3289	yes	missense,missense,missense,missense,missense	ARSA	NM_000487.5,NM_001085425.2,NM_001085426.2,NM_001085427.2,NM_001085428.2	46,46,46,46,46	249,1857,4354	CC,CT,TT		12.2692,29.9175,18.2276	benign,benign,benign,benign,benign	352/510,352/510,352/510,352/510,266/424	51064416	2355,10565	2181	4279	6460	SO:0001583	missense	410	exon7			GTGACATTGGGCA	X52150	CCDS14100.1, CCDS46736.1, CCDS14100.2	22q13.33	2013-09-19			ENSG00000100299	ENSG00000100299	3.1.6.8	"""Arylsulfatase family"""	713	protein-coding gene	gene with protein product	"""metachromatic leucodystrophy"""	607574				15772092	Standard	NM_000487		Approved		uc003bmz.5	P15289	OTTHUMG00000150180	ENST00000547307.1:c.1049A>G	22.37:g.51064416T>C	ENSP00000448440:p.Asn350Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	110	46	0.418182	NM_001085426	B2RCA6|B7XD04|F8WCC8|Q6ICI5|Q96CJ0	Missense_Mutation	SNP	ENST00000547307.1	37		457	0.20924908424908426	183	0.3719512195121951	84	0.23204419889502761	92	0.16083916083916083	98	0.12928759894459102	T	15.03	2.711093	0.48517	0.299175	0.122692	ENSG00000100299	ENST00000356098;ENST00000216124;ENST00000547307;ENST00000547805;ENST00000395621;ENST00000453344;ENST00000395619	D;D;D;D;D;D;D	0.95272	-3.66;-3.66;-3.66;-3.66;-3.66;-3.66;-3.66	5.47	5.47	0.80525	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.384707	0.32372	N	0.006190	T	0.00012	0.0000	L	0.39085	1.19	0.26949	P	0.9660681	B	0.25772	0.134	B	0.15052	0.012	T	0.00288	-1.1845	9	0.41790	T	0.15	.	13.508	0.61495	0.0:0.0:0.0:1.0	rs2071421;rs61664838;rs2071421	350	P15289	ARSA_HUMAN	S	352;352;350;350;352;266;352	ENSP00000348406:N352S;ENSP00000216124:N352S;ENSP00000448440:N350S;ENSP00000448932:N350S;ENSP00000378983:N352S;ENSP00000412542:N266S;ENSP00000378981:N352S	ENSP00000216124:N352S	N	-	2	0	ARSA	49411282	0.975000	0.34042	0.926000	0.36857	0.995000	0.86356	1.767000	0.38501	2.081000	0.62600	0.482000	0.46254	AAT	T|0.784;C|0.216	0.216	strong		0.682	ARSA-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000487	
COL4A4	1286	hgsc.bcm.edu	37	2	227892619	227892619	+	Splice_Site	SNP	C	C	T	rs2228556	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227892619C>T	ENST00000396625.3	-	42	4287	c.4080G>A	c.(4078-4080)ccG>ccA	p.P1360P	COL4A4_ENST00000329662.7_Splice_Site_p.P1360P	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1360	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GAAGCTCACCCGGAAGACCAG	0.463													T|||	2463	0.491813	0.5651	0.4769	5008	,	,		14265	0.4028		0.4384	False		,,,				2504	0.5501				p.P1360P		Atlas-SNP	.											.	COL4A4	215	.	0			c.G4080A						PASS	.	T		1957,1765		499,959,403	52.0	59.0	56.0		4080	3.4	1.0	2	dbSNP_107	56	3455,4727		729,1997,1365	no	coding-synonymous-near-splice	COL4A4	NM_000092.4		1228,2956,1768	TT,TC,CC		42.2268,47.4207,45.4637		1360/1691	227892619	5412,6492	1861	4091	5952	SO:0001630	splice_region_variant	1286	exon42			CTCACCCGGAAGA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.4081+1G>A	2.37:g.227892619C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			C|0.556;T|0.444	0.444	strong		0.463	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	Silent
SMCR8	140775	hgsc.bcm.edu	37	17	18221010	18221010	+	Missense_Mutation	SNP	A	A	G	rs12449313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:18221010A>G	ENST00000406438.3	+	1	2387	c.1907A>G	c.(1906-1908)aAc>aGc	p.N636S	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	636			N -> S (in dbSNP:rs12449313).			nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						GAAAATGCCAACCCTTCTTCC	0.587													A|||	1075	0.214657	0.1452	0.2421	5008	,	,		20342	0.3185		0.2425	False		,,,				2504	0.1534				p.N636S		Atlas-SNP	.											.	SMCR8	62	.	0			c.A1907G						PASS	.	A	SER/ASN	683,3723	288.7+/-280.0	64,555,1584	67.0	64.0	65.0		1907	-7.7	0.0	17	dbSNP_120	65	2197,6403	372.7+/-336.7	284,1629,2387	yes	missense	SMCR8	NM_144775.2	46	348,2184,3971	GG,GA,AA		25.5465,15.5016,22.1436	benign	636/938	18221010	2880,10126	2203	4300	6503	SO:0001583	missense	140775	exon1			ATGCCAACCCTTC	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1907A>G	17.37:g.18221010A>G	ENSP00000385025:p.Asn636Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	73	72	0.986301	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	527	0.2413003663003663	81	0.16463414634146342	86	0.23756906077348067	167	0.291958041958042	193	0.2546174142480211	A	0.006	-2.101022	0.00360	0.155016	0.255465	ENSG00000176994	ENST00000406438	T	0.38240	1.15	5.87	-7.65	0.01281	.	1.269400	0.05095	N	0.486016	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30650	-0.9971	9	0.13108	T	0.6	-32.4624	20.8995	0.99940	0.3953:0.0:0.6047:0.0	rs12449313;rs52833335;rs58781335;rs12449313	636	Q8TEV9	SMCR8_HUMAN	S	636	ENSP00000385025:N636S	ENSP00000385025:N636S	N	+	2	0	SMCR8	18161735	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.038000	0.03553	-2.092000	0.00857	-1.139000	0.01908	AAC	A|0.770;G|0.229	0.229	strong		0.587	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
ERCC6	2074	hgsc.bcm.edu	37	10	50678717	50678717	+	Missense_Mutation	SNP	T	T	C	rs2228526	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50678717T>C	ENST00000355832.5	-	18	3367	c.3289A>G	c.(3289-3291)Atg>Gtg	p.M1097V	ERCC6_ENST00000542458.1_Missense_Mutation_p.M467V|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1097			M -> V (in dbSNP:rs2228526). {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						TTACTACTCATGTGAGGGTCA	0.403								Direct reversal of damage;Nucleotide excision repair (NER)					T|||	914	0.182508	0.1369	0.2104	5008	,	,		21456	0.0437		0.2078	False		,,,				2504	0.3415				p.M1097V		Atlas-SNP	.											.	ERCC6	162	.	0			c.A3289G	GRCh37	CM076169	ERCC6	M	rs2228526	PASS	.	T	VAL/MET	619,3787	265.9+/-266.9	60,499,1644	172.0	164.0	167.0		3289	-6.2	0.0	10	dbSNP_98	167	1864,6736	332.1+/-320.0	196,1472,2632	yes	missense	ERCC6	NM_000124.2	21	256,1971,4276	CC,CT,TT		21.6744,14.049,19.0912	benign	1097/1494	50678717	2483,10523	2203	4300	6503	SO:0001583	missense	2074	exon18			TACTCATGTGAGG	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.3289A>G	10.37:g.50678717T>C	ENSP00000348089:p.Met1097Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	102	102	1	NM_000124	D3DX94|Q5W0L9	Missense_Mutation	SNP	ENST00000355832.5	37	CCDS7229.1	342	0.1565934065934066	62	0.12601626016260162	83	0.2292817679558011	30	0.05244755244755245	167	0.22031662269129287	T	2.555	-0.303168	0.05495	0.14049	0.216744	ENSG00000225830	ENST00000355832;ENST00000374129;ENST00000542458	D;T	0.81908	-1.55;-1.29	4.57	-6.21	0.02065	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.09377	0.004	T	0.02437	-1.1159	8	0.23891	T	0.37	0.7226	3.2523	0.06819	0.1021:0.1951:0.4168:0.286	rs2228526;rs17702442;rs52816725;rs57248630;rs2228526	1097	Q03468	ERCC6_HUMAN	V	1097;474;467	ENSP00000348089:M1097V;ENSP00000445134:M467V	ENSP00000348089:M1097V	M	-	1	0	ERCC6	50348723	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-0.211000	0.09332	-1.189000	0.02702	-0.256000	0.11100	ATG	T|0.824;C|0.176	0.176	strong		0.403	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
NUP214	8021	hgsc.bcm.edu	37	9	134020092	134020092	+	Missense_Mutation	SNP	C	C	T	rs103612	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:134020092C>T	ENST00000359428.5	+	12	1864	c.1720C>T	c.(1720-1722)Ccc>Tcc	p.P574S	RP11-544A12.4_ENST00000587408.1_RNA|RP11-544A12.4_ENST00000586290.1_RNA|NUP214_ENST00000451030.1_Missense_Mutation_p.P574S|RP11-544A12.4_ENST00000590461.1_RNA|RP11-544A12.4_ENST00000587264.1_RNA|NUP214_ENST00000411637.2_Missense_Mutation_p.P574S|RP11-544A12.4_ENST00000589667.1_RNA|RP11-544A12.4_ENST00000589540.1_RNA|RP11-544A12.4_ENST00000415391.2_RNA|RP11-544A12.4_ENST00000588378.1_RNA			P35658	NU214_HUMAN	nucleoporin 214kDa	574	11 X 5 AA approximate repeats.		P -> S (in dbSNP:rs103612). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:1549122}.		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)			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)		AGCAATGAAGCCCTCCTTCCC	0.443			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""								C|||	3215	0.641973	0.6626	0.7522	5008	,	,		17540	0.627		0.6779	False		,,,				2504	0.5143				p.P574S	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.C1720T						PASS	.	C	SER/PRO	2944,1462	679.2+/-403.7	990,964,249	63.0	57.0	59.0		1720	1.8	1.0	9	dbSNP_79	59	5753,2847	673.1+/-403.0	1927,1899,474	yes	missense	NUP214	NM_005085.2	74	2917,2863,723	TT,TC,CC		33.1047,33.182,33.1309	possibly-damaging	574/2091	134020092	8697,4309	2203	4300	6503	SO:0001583	missense	8021	exon12			ATGAAGCCCTCCT	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.1720C>T	9.37:g.134020092C>T	ENSP00000352400:p.Pro574Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	93	91	0.978495	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	1454|1454	0.6657509157509157|0.6657509157509157	312|312	0.6341463414634146|0.6341463414634146	268|268	0.7403314917127072|0.7403314917127072	359|359	0.6276223776223776|0.6276223776223776	515|515	0.679419525065963|0.679419525065963	C|C	9.078|9.078	0.998540|0.998540	0.19121|0.19121	0.66818|0.66818	0.668953|0.668953	ENSG00000126883|ENSG00000126883	ENST00000530863|ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605	.|T;T;T	.|0.31769	.|1.51;1.48;1.51	6.07|6.07	1.78|1.78	0.24846|0.24846	.|.	.|0.705821	.|0.12317	.|N	.|0.479602	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.35292|0.35292	P|P	0.21768500000000002|0.21768500000000002	.|B;B;B	.|0.15473	.|0.002;0.002;0.013	.|B;B;B	.|0.12156	.|0.007;0.005;0.007	T|T	0.30880|0.30880	-0.9963|-0.9963	4|9	.|0.14252	.|T	.|0.57	-7.3578|-7.3578	5.3463|5.3463	0.16010|0.16010	0.1512:0.5573:0.0:0.2915|0.1512:0.5573:0.0:0.2915	rs103612;rs755806;rs818061;rs17526738;rs52837203;rs60032848;rs103612|rs103612;rs755806;rs818061;rs17526738;rs52837203;rs60032848;rs103612	.|167;574;574	.|Q5JUP9;P35658-4;P35658	.|.;.;NU214_HUMAN	V|S	149|574;574;574;574;167;3	.|ENSP00000352400:P574S;ENSP00000396576:P574S;ENSP00000405014:P574S	.|ENSP00000352400:P574S	A|P	+|+	2|1	0|0	NUP214|NUP214	133009913|133009913	0.145000|0.145000	0.22656|0.22656	0.954000|0.954000	0.39281|0.39281	0.478000|0.478000	0.33099|0.33099	-0.048000|-0.048000	0.11944|0.11944	0.816000|0.816000	0.34421|0.34421	0.655000|0.655000	0.94253|0.94253	GCC|CCC	C|0.333;N|0.001	.	strong		0.443	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
FBXO32	114907	hgsc.bcm.edu	37	8	124525483	124525483	+	Silent	SNP	C	C	T	rs3739287	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124525483C>T	ENST00000517956.1	-	6	797	c.606G>A	c.(604-606)acG>acA	p.T202T	FBXO32_ENST00000443022.2_Intron	NM_058229.3|NM_148177.2	NP_478136.1|NP_680482.1	Q969P5	FBX32_HUMAN	F-box protein 32	202					cellular response to dexamethasone stimulus (GO:0071549)|protein ubiquitination (GO:0016567)|response to denervation involved in regulation of muscle adaptation (GO:0014894)	nucleolus (GO:0005730)|Z disc (GO:0030018)				autonomic_ganglia(1)|breast(3)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)|stomach(1)	21	Lung NSC(37;1.13e-13)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			AGTGGAGAATCGTCTCCATCC	0.557													C|||	1019	0.203474	0.1808	0.1772	5008	,	,		17984	0.4673		0.0895	False		,,,				2504	0.0982				p.T202T		Atlas-SNP	.											.	FBXO32	39	.	0			c.G606A						PASS	.	C	,,	784,3622	317.4+/-295.1	66,652,1485	129.0	106.0	114.0		,606,171	-9.0	0.3	8	dbSNP_107	114	802,7798	186.7+/-234.1	43,716,3541	no	intron,coding-synonymous,coding-synonymous	FBXO32	NM_001242463.1,NM_058229.3,NM_148177.2	,,	109,1368,5026	TT,TC,CC		9.3256,17.7939,12.1944	,,	,202/356,57/211	124525483	1586,11420	2203	4300	6503	SO:0001819	synonymous_variant	114907	exon6			GAGAATCGTCTCC	AJ420108	CCDS6345.1, CCDS56553.1	8q24.13	2008-01-28	2004-06-15		ENSG00000156804	ENSG00000156804		"""F-boxes /  ""other"""""	16731	protein-coding gene	gene with protein product		606604	"""F-box only protein 32"""			11679633, 11717410	Standard	NM_058229		Approved	MAFbx, ATROGIN1, Fbx32	uc003yqr.3	Q969P5	OTTHUMG00000164981	ENST00000517956.1:c.606G>A	8.37:g.124525483C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	185	67	0.362162	NM_058229	A4KYM0	Silent	SNP	ENST00000517956.1	37	CCDS6345.1																																																																																			C|0.843;T|0.157	0.157	strong		0.557	FBXO32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381281.1		
PKD1L2	114780	hgsc.bcm.edu	37	16	81211548	81211548	+	RNA	SNP	G	G	A	rs9934605	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81211548G>A	ENST00000527937.1	-	0	319				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000337114.4_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						GCACAGTGCTGATCACATAGG	0.602													G|||	1112	0.222045	0.3328	0.1772	5008	,	,		18192	0.1032		0.172	False		,,,				2504	0.2781				p.I767I		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2301T						PASS	.	G	,	1176,2894		174,828,1033	56.0	56.0	56.0		2301,2301	3.9	0.9	16	dbSNP_119	56	1410,6994		121,1168,2913	no	coding-synonymous,coding-synonymous	PKD1L2	NM_001076780.1,NM_052892.3	,	295,1996,3946	AA,AG,GG		16.7777,28.8943,20.7311	,	767/992,767/2460	81211548	2586,9888	2035	4202	6237			114780	exon14			AGTGCTGATCACA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81211548G>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	36	16	0.444444	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000527937.1	37		392	0.1794871794871795	154	0.3130081300813008	61	0.1685082872928177	53	0.09265734265734266	124	0.16358839050131926	G	3.327	-0.137495	0.06711	0.288943	0.167777	ENSG00000166473	ENST00000526632	.	.	.	4.89	3.94	0.45596	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.9999999999999992	.	.	.	.	.	.	.	.	.	.	.	.	.	-7.4679	10.5049	0.44828	0.0916:0.0:0.9084:0.0	rs9934605;rs9934605	.	.	.	X	295	.	.	Q	-	1	0	PKD1L2	79769049	1.000000	0.71417	0.921000	0.36526	0.235000	0.25334	1.823000	0.39062	1.088000	0.41272	0.549000	0.68633	CAG	G|0.813;A|0.187	0.187	strong		0.602	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
C17orf53	78995	hgsc.bcm.edu	37	17	42225547	42225547	+	Missense_Mutation	SNP	A	A	C	rs227584	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42225547A>C	ENST00000319977.4	+	3	613	c.376A>C	c.(376-378)Aca>Cca	p.T126P	C17orf53_ENST00000585683.1_Missense_Mutation_p.T126P|C17orf53_ENST00000245382.6_Missense_Mutation_p.T126P	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53	126			T -> P (in dbSNP:rs227584). {ECO:0000269|PubMed:15489334}.							NS(1)|breast(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	22		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GCTCAGAGAGACAGCAAGACC	0.522													C|||	2887	0.576478	0.9047	0.4582	5008	,	,		20956	0.7589		0.2992	False		,,,				2504	0.3139				p.T126P		Atlas-SNP	.											.	C17orf53	59	.	0			c.A376C						PASS	.	C	PRO/THR,PRO/THR	3497,909	350.8+/-311.0	1401,695,107	130.0	136.0	134.0	http://www.ncbi.nlm.nih.gov/pubmed?term	376,376	1.5	0.7	17	dbSNP_79	134	2666,5934	685.3+/-404.0	417,1832,2051	yes	missense,missense	C17orf53	NM_001171251.1,NM_024032.3	38,38	1818,2527,2158	CC,CA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	31.0,20.631,47.3858	benign,benign	126/647,126/648	42225547	6163,6843	2203	4300	6503	SO:0001583	missense	78995	exon3			AGAGAGACAGCAA	AK021656	CCDS11477.1, CCDS59293.1	17q21.31	2012-10-11			ENSG00000125319	ENSG00000125319			28460	protein-coding gene	gene with protein product							Standard	NM_001171251		Approved	MGC3130	uc002ifi.2	Q8N3J3	OTTHUMG00000181808	ENST00000319977.4:c.376A>C	17.37:g.42225547A>C	ENSP00000313500:p.Thr126Pro	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	137	70	0.510949	NM_001171251	A8K7A9|Q9BWM9|Q9HAI1	Missense_Mutation	SNP	ENST00000319977.4	37	CCDS11477.1	1253	0.5737179487179487	445	0.9044715447154471	149	0.4116022099447514	424	0.7412587412587412	235	0.3100263852242744	C	0.355	-0.942870	0.02322	0.79369	0.31	ENSG00000125319	ENST00000319977;ENST00000245382	T;T	0.42513	0.97;0.97	4.61	1.5	0.22942	.	0.782162	0.11770	N	0.531181	T	0.00012	0.0000	N	0.00308	-1.67	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.33343	-0.9872	9	0.02654	T	1	-1.4987	3.1789	0.06578	0.319:0.4178:0.0:0.2632	rs227584;rs3744431;rs17844825;rs17857536;rs57825870;rs227584	126;126;126	A8K7A9;Q8N3J3-3;Q8N3J3	.;.;CQ053_HUMAN	P	126	ENSP00000313500:T126P;ENSP00000245382:T126P	ENSP00000245382:T126P	T	+	1	0	C17orf53	39581073	0.082000	0.21442	0.737000	0.30932	0.059000	0.15707	0.105000	0.15333	0.023000	0.15187	-0.217000	0.12591	ACA	T|0.004;G|0.002	.	strong		0.522	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032	
FAM104B	90736	hgsc.bcm.edu	37	X	55172630	55172630	+	Nonsense_Mutation	SNP	G	G	A	rs113263757		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:55172630G>A	ENST00000358460.4	-	3	388	c.235C>T	c.(235-237)Cag>Tag	p.Q79*	FAM104B_ENST00000425133.2_Nonsense_Mutation_p.Q80*|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000489298.1_Nonsense_Mutation_p.Q78*|FAM104B_ENST00000332132.4_Nonsense_Mutation_p.Q80*|FAM104B_ENST00000478918.1_5'Flank|FAM104B_ENST00000477847.2_Nonsense_Mutation_p.Q76*			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	79										endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						TGCAAGAACTGGGGAAAGTTT	0.493																																					p.Q80X		Atlas-SNP	.											.	FAM104B	28	.	0			c.C238T						PASS	.						127.0	104.0	112.0					X																	55172630		2203	4300	6503	SO:0001587	stop_gained	90736	exon3			AGAACTGGGGAAA	BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518			25085	protein-coding gene	gene with protein product			"""chromosome X open reading frame 44"""	CXorf44		12477932	Standard	NM_138362		Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000358460.4:c.235C>T	X.37:g.55172630G>A	ENSP00000364101:p.Gln79*	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	46	4	0.0869565	NM_001166699	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Nonsense_Mutation	SNP	ENST00000358460.4	37	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	g	11.17	1.559418	0.27827	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298	.	.	.	1.6	1.6	0.23607	.	0.325359	0.21941	U	0.066869	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-0.2487	6.0913	0.19995	0.0:0.0:1.0:0.0	.	.	.	.	X	79;80;80;76;78	.	ENSP00000333394:Q80X	Q	-	1	0	FAM104B	55189355	0.905000	0.30787	0.015000	0.15790	0.033000	0.12548	1.600000	0.36762	1.084000	0.41184	0.436000	0.28706	CAG	.	.	weak		0.493	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056851.1	NM_138362	
COIL	8161	hgsc.bcm.edu	37	17	55028170	55028170	+	Missense_Mutation	SNP	C	C	T	rs61731978	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:55028170C>T	ENST00000240316.4	-	2	467	c.433G>A	c.(433-435)Gtc>Atc	p.V145I		NM_004645.2	NP_004636.1	P38432	COIL_HUMAN	coilin	145						Cajal body (GO:0015030)|cytoplasm (GO:0005737)|female germ cell nucleus (GO:0001674)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	disulfide oxidoreductase activity (GO:0015036)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)			NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|urinary_tract(1)	15	Breast(9;6.15e-08)					AGATCCAAGACCTTCTCATTA	0.408													C|||	445	0.0888578	0.0098	0.2176	5008	,	,		17867	0.005		0.1252	False		,,,				2504	0.1534				p.V145I		Atlas-SNP	.											.	COIL	49	.	0			c.G433A						PASS	.	C	ILE/VAL	144,4262	99.8+/-138.5	2,140,2061	155.0	147.0	150.0		433	-0.9	0.0	17	dbSNP_129	150	1036,7564	221.0+/-258.6	58,920,3322	yes	missense	COIL	NM_004645.2	29	60,1060,5383	TT,TC,CC		12.0465,3.2683,9.0727	benign	145/577	55028170	1180,11826	2203	4300	6503	SO:0001583	missense	8161	exon2			CCAAGACCTTCTC	U06632	CCDS11592.1	17q22	2012-10-02			ENSG00000121058	ENSG00000121058			2184	protein-coding gene	gene with protein product		600272				7971277	Standard	NM_004645		Approved	CLN80, p80-coilin	uc002iuu.3	P38432	OTTHUMG00000178126	ENST00000240316.4:c.433G>A	17.37:g.55028170C>T	ENSP00000240316:p.Val145Ile	Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	158	153	0.968354	NM_004645	B2R931	Missense_Mutation	SNP	ENST00000240316.4	37	CCDS11592.1	176	0.08058608058608059	4	0.008130081300813009	75	0.20718232044198895	4	0.006993006993006993	93	0.12269129287598944	C	12.68	2.010244	0.35511	0.032683	0.120465	ENSG00000121058	ENST00000240316	T	0.41758	0.99	5.62	-0.916	0.10489	.	0.786769	0.11273	N	0.581254	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.29805	0.257	B	0.24394	0.053	T	0.27191	-1.0081	9	0.38643	T	0.18	0.0682	6.4384	0.21837	0.1259:0.4771:0.0:0.3971	.	145	P38432	COIL_HUMAN	I	145	ENSP00000240316:V145I	ENSP00000240316:V145I	V	-	1	0	COIL	52383169	0.012000	0.17670	0.003000	0.11579	0.914000	0.54420	0.214000	0.17541	0.207000	0.20607	0.650000	0.86243	GTC	C|0.911;T|0.089	0.089	strong		0.408	COIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440618.1		
RTCB	51493	hgsc.bcm.edu	37	22	32795641	32795641	+	Silent	SNP	C	C	T	rs5749426	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:32795641C>T	ENST00000216038.5	-	6	701	c.603G>A	c.(601-603)caG>caA	p.Q201Q	RTCB_ENST00000451746.2_Intron|RTCB_ENST00000476619.1_5'UTR	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		TGGGGTCAGCCTGCAGCATCC	0.498													T|||	2232	0.445687	0.6392	0.3487	5008	,	,		16455	0.5179		0.3032	False		,,,				2504	0.3252				p.Q201Q		Atlas-SNP	.											.	C22orf28	43	.	0			c.G603A						PASS	.	T		2691,1715	516.5+/-369.2	800,1091,312	204.0	194.0	197.0		603	1.1	1.0	22	dbSNP_114	197	2998,5602	665.3+/-402.3	523,1952,1825	no	coding-synonymous	C22orf28	NM_014306.4		1323,3043,2137	TT,TC,CC		34.8605,38.9242,43.7414		201/506	32795641	5689,7317	2203	4300	6503	SO:0001819	synonymous_variant	51493	exon6			GTCAGCCTGCAGC	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.603G>A	22.37:g.32795641C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	111	0.982301	NM_014306		Silent	SNP	ENST00000216038.5	37	CCDS13905.1																																																																																			C|0.552;T|0.448	0.448	strong		0.498	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	
RIF1	55183	hgsc.bcm.edu	37	2	152314385	152314385	+	Silent	SNP	G	G	A	rs16830047	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:152314385G>A	ENST00000243326.5	+	23	3246	c.2763G>A	c.(2761-2763)ctG>ctA	p.L921L	RIF1_ENST00000430328.2_Silent_p.L921L|RIF1_ENST00000428287.2_Silent_p.L921L|RIF1_ENST00000444746.2_Silent_p.L921L|RIF1_ENST00000453091.2_Silent_p.L921L			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TAATATTTCTGCACAAGAATA	0.378													G|||	1244	0.248403	0.093	0.3631	5008	,	,		15359	0.3224		0.3211	False		,,,				2504	0.226				p.L921L		Atlas-SNP	.											.	RIF1	244	.	0			c.G2763A						PASS	.	G	,,,	557,3849	250.9+/-257.8	38,481,1684	91.0	90.0	90.0		2763,2763,2763,2763	0.4	1.0	2	dbSNP_123	90	2428,6172	400.3+/-346.7	337,1754,2209	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	,,,	375,2235,3893	AA,AG,GG		28.2326,12.6419,22.9509	,,,	921/2447,921/2447,921/2447,921/2473	152314385	2985,10021	2203	4300	6503	SO:0001819	synonymous_variant	55183	exon24			ATTTCTGCACAAG	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.2763G>A	2.37:g.152314385G>A		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	123	63	0.512195	NM_018151	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																			G|0.749;A|0.251	0.251	strong		0.378	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
GATA5	140628	hgsc.bcm.edu	37	20	61040951	61040951	+	Silent	SNP	C	C	T	rs6587239	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:61040951C>T	ENST00000252997.2	-	5	913	c.852G>A	c.(850-852)aaG>aaA	p.K284K		NM_080473.4	NP_536721.1	Q9BWX5	GATA5_HUMAN	GATA binding protein 5	284					blood coagulation (GO:0007596)|cellular response to BMP stimulus (GO:0071773)|intestinal epithelial cell differentiation (GO:0060575)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.K284K(1)		kidney(1)|lung(3)|ovary(1)|stomach(1)	6	Breast(26;2.05e-08)		BRCA - Breast invasive adenocarcinoma(19;3.08e-06)			GGATGCTTTCCTTCTTCATAG	0.682													C|||	2652	0.529553	0.7224	0.4769	5008	,	,		16945	0.4315		0.4622	False		,,,				2504	0.4765				p.K284K		Atlas-SNP	.											GATA5,NS,haematopoietic_neoplasm,-2,4	GATA5	22	4	1	Substitution - coding silent(1)	stomach(1)	c.G852A						PASS	.	C		2858,1536		952,954,291	93.0	86.0	88.0		852	1.9	1.0	20	dbSNP_116	88	4106,4492		985,2136,1178	no	coding-synonymous	GATA5	NM_080473.4		1937,3090,1469	TT,TC,CC		47.7553,34.9568,46.3978		284/398	61040951	6964,6028	2197	4299	6496	SO:0001819	synonymous_variant	140628	exon5			GCTTTCCTTCTTC	BC047790, BC117356	CCDS13499.1	20q13.33	2013-07-17	2001-11-28		ENSG00000130700	ENSG00000130700		"""GATA zinc finger domain containing"""	15802	protein-coding gene	gene with protein product		611496	"""GATA-binding protein 5"""			9566909	Standard	NM_080473		Approved	bB379O24.1, GATAS	uc002ycx.1	Q9BWX5	OTTHUMG00000032919	ENST00000252997.2:c.852G>A	20.37:g.61040951C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	65	28	0.430769	NM_080473	D9ZGF7|Q17RE2|Q86VU4	Silent	SNP	ENST00000252997.2	37	CCDS13499.1																																																																																			C|0.469;T|0.531	0.531	strong		0.682	GATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080038.2	NM_080473	
CCDC154	645811	hgsc.bcm.edu	37	16	1484455	1484455	+	Missense_Mutation	SNP	T	T	C	rs61743495	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1484455T>C	ENST00000389176.3	-	17	2145	c.1979A>G	c.(1978-1980)cAg>cGg	p.Q660R	CCDC154_ENST00000409671.1_Missense_Mutation_p.Q508R	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	660						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						CACCTGCTCCTGGCTGTGGGG	0.587													T|||	363	0.072484	0.149	0.0562	5008	,	,		11748	0.0119		0.0388	False		,,,				2504	0.0777				p.Q653R		Atlas-SNP	.											.	CCDC154	27	.	0			c.A1958G						PASS	.	T	ARG/GLN	172,1212		11,150,531	82.0	78.0	79.0		1958	-7.3	0.0	16	dbSNP_129	79	129,3053		2,125,1464	yes	missense	CCDC154	NM_001143980.1	43	13,275,1995	CC,CT,TT		4.0541,12.4277,6.5922	benign	653/668	1484455	301,4265	692	1591	2283	SO:0001583	missense	645811	exon17			TGCTCCTGGCTGT			16p13.3	2012-12-13			ENSG00000197599	ENSG00000197599			34454	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 29"""	C16orf29			Standard	NM_001143980		Approved	LOC645811	uc010uve.2	A6NI56	OTTHUMG00000154097	ENST00000389176.3:c.1979A>G	16.37:g.1484455T>C	ENSP00000373828:p.Gln660Arg	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	105	50	0.47619	NM_001143980	G9JV18	Missense_Mutation	SNP	ENST00000389176.3	37		124	0.056776556776556776	69	0.1402439024390244	21	0.058011049723756904	7	0.012237762237762238	27	0.03562005277044855	T	2.573	-0.299171	0.05532	0.124277	0.040541	ENSG00000197599	ENST00000409671;ENST00000389176	.	.	.	3.68	-7.35	0.01422	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14062	-1.0486	8	0.05721	T	0.95	.	3.1587	0.06512	0.1626:0.4405:0.1035:0.2933	.	660	A6NI56	CC154_HUMAN	R	508;660	.	ENSP00000373828:Q660R	Q	-	2	0	CCDC154	1424456	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-4.550000	0.00217	-1.927000	0.01060	-0.736000	0.03550	CAG	T|0.943;C|0.057	0.057	strong		0.587	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
ABCA1	19	hgsc.bcm.edu	37	9	107624029	107624029	+	Silent	SNP	C	C	T	rs2230805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107624029C>T	ENST00000374736.3	-	6	868	c.474G>A	c.(472-474)ctG>ctA	p.L158L	ABCA1_ENST00000374733.1_Silent_p.L98L|ABCA1_ENST00000423487.2_Silent_p.L158L	NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	158					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|cellular lipid metabolic process (GO:0044255)|cellular response to cholesterol (GO:0071397)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|endosomal transport (GO:0016197)|G-protein coupled receptor signaling pathway (GO:0007186)|high-density lipoprotein particle assembly (GO:0034380)|interleukin-1 beta secretion (GO:0050702)|intracellular cholesterol transport (GO:0032367)|lipoprotein metabolic process (GO:0042157)|lysosome organization (GO:0007040)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|peptide secretion (GO:0002790)|phagocytosis, engulfment (GO:0006911)|phospholipid efflux (GO:0033700)|phospholipid homeostasis (GO:0055091)|phospholipid translocation (GO:0045332)|platelet dense granule organization (GO:0060155)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cholesterol efflux (GO:0010875)|protein lipidation (GO:0006497)|regulation of Cdc42 protein signal transduction (GO:0032489)|response to drug (GO:0042493)|response to laminar fluid shear stress (GO:0034616)|response to low-density lipoprotein particle (GO:0055098)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)	endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein A-I receptor activity (GO:0034188)|apolipoprotein binding (GO:0034185)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase binding (GO:0051117)|cholesterol binding (GO:0015485)|cholesterol transporter activity (GO:0017127)|phospholipid binding (GO:0005543)|phospholipid transporter activity (GO:0005548)|receptor binding (GO:0005102)|small GTPase binding (GO:0031267)|syntaxin binding (GO:0019905)	p.L158L(1)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(31)|liver(1)|lung(40)|ovary(5)|pancreas(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	115				OV - Ovarian serous cystadenocarcinoma(323;0.023)	Adenosine triphosphate(DB00171)|Glyburide(DB01016)|Probucol(DB01599)	GGTTGTGATACAGGAACCCAG	0.413													C|||	1865	0.372404	0.4887	0.3184	5008	,	,		18535	0.4008		0.2276	False		,,,				2504	0.3732				p.L158L		Atlas-SNP	.											ABCA1,NS,carcinoma,0,1	ABCA1	244	1	1	Substitution - coding silent(1)	stomach(1)	c.G474A						PASS	.	C		1910,2496	544.9+/-376.7	422,1066,715	148.0	151.0	150.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	474	3.1	0.8	9	dbSNP_98	150	2281,6319	384.2+/-341.0	302,1677,2321	no	coding-synonymous	ABCA1	NM_005502.3		724,2743,3036	TT,TC,CC		26.5233,43.35,32.2236		158/2262	107624029	4191,8815	2203	4300	6503	SO:0001819	synonymous_variant	19	exon6			GTGATACAGGAAC	AJ012376	CCDS6762.1	9q31	2014-03-14			ENSG00000165029	ENSG00000165029		"""ATP binding cassette transporters / subfamily A"""	29	protein-coding gene	gene with protein product	"""Tangier disease"""	600046		ABC1, HDLDT1		8088782, 10431236, 10431237, 10431238	Standard	NM_005502		Approved	TGD	uc004bcl.3	O95477	OTTHUMG00000020417	ENST00000374736.3:c.474G>A	9.37:g.107624029C>T		Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	105	40	0.380952	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			C|0.656;T|0.344	0.344	strong		0.413	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
OR2T34	127068	hgsc.bcm.edu	37	1	248737595	248737595	+	Missense_Mutation	SNP	A	A	G	rs150601708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248737595A>G	ENST00000328782.2	-	1	485	c.464T>C	c.(463-465)gTt>gCt	p.V155A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V155A(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CATTCCCAAAACCCAGCAGGC	0.522																																					p.V155A		Atlas-SNP	.											OR2T34,NS,carcinoma,0,2	OR2T34	72	2	1	Substitution - Missense(1)	ovary(1)	c.T464C						scavenged	.						17.0	23.0	21.0					1																	248737595		2143	4273	6416	SO:0001583	missense	127068	exon1			CCCAAAACCCAGC	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.464T>C	1.37:g.248737595A>G	ENSP00000330904:p.Val155Ala	Somatic	512	1	0.00195312		WXS	Illumina HiSeq	Phase_I	564	119	0.210993	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	602	0.27564102564102566	196	0.3983739837398374	85	0.23480662983425415	151	0.263986013986014	170	0.22427440633245382	.	5.973	0.363525	0.11296	.	.	ENSG00000183310	ENST00000328782	T	0.38722	1.12	2.34	0.992	0.19819	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10685	0.025	0.80722	P	0.0	B	0.15930	0.015	B	0.19666	0.026	T	0.47522	-0.9111	8	0.28530	T	0.3	.	6.4829	0.22073	0.7538:0.2461:0.0:0.0	.	155	Q8NGX1	O2T34_HUMAN	A	155	ENSP00000330904:V155A	ENSP00000330904:V155A	V	-	2	0	OR2T34	246804218	0.000000	0.05858	0.011000	0.14972	0.090000	0.18270	-0.276000	0.08514	0.953000	0.37825	0.319000	0.21371	GTT	A|0.500;G|0.500	0.500	weak		0.522	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
SRFBP1	153443	hgsc.bcm.edu	37	5	121355961	121355961	+	Silent	SNP	G	G	A	rs55708726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:121355961G>A	ENST00000339397.4	+	6	603	c.531G>A	c.(529-531)gcG>gcA	p.A177A		NM_152546.2	NP_689759.2			serum response factor binding protein 1											central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|skin(1)	15		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000227)|Epithelial(69;0.000365)|all cancers(49;0.00517)		AAATATTGGCGAAGAAACCAA	0.343																																					p.A177A		Atlas-SNP	.											.	SRFBP1	47	.	0			c.G531A						PASS	.	G		328,3396		14,300,1548	112.0	103.0	106.0		531	-1.9	0.9	5	dbSNP_129	106	1111,7063		81,949,3057	no	coding-synonymous	SRFBP1	NM_152546.2		95,1249,4605	AA,AG,GG		13.5919,8.8077,12.0945		177/430	121355961	1439,10459	1862	4087	5949	SO:0001819	synonymous_variant	153443	exon6			ATTGGCGAAGAAA	AK058015	CCDS43354.1	5q23.1	2006-12-21				ENSG00000151304			26333	protein-coding gene	gene with protein product	"""BUD22 homolog (S. cerevisiae)"""	610479				15492011	Standard	NM_152546		Approved	FLJ25286, p49, STRAP, BUD22, Rlb1	uc003kst.1	Q8NEF9		ENST00000339397.4:c.531G>A	5.37:g.121355961G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_152546		Silent	SNP	ENST00000339397.4	37	CCDS43354.1																																																																																			G|0.890;A|0.110	0.110	strong		0.343	SRFBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371200.1	NM_152546	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766776	27766776	+	Silent	SNP	G	G	A	rs45553337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:27766776G>A	ENST00000451261.2	+	5	2163	c.1764G>A	c.(1762-1764)acG>acA	p.T588T		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	588								p.T555T(1)		central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						GTCACGTGACGCAGAGAGGTC	0.507													A|||	620	0.164238	0.1324	0.1167	3775	,	,		15143	0.0546		0.2078	False		,,,				2504	0.1022				p.T588T		Atlas-SNP	.											.	DCAF8L2	79	.	1	Substitution - coding silent(1)	kidney(1)	c.G1764A						PASS	.	A		250,959		19,183,29,315,146	83.0	59.0	67.0		1764	2.5	0.0	X	dbSNP_127	67	671,1720		61,306,243,433,548	no	coding-synonymous	DCAF8L2	NM_001136533.1		80,489,272,748,694	AA,AG,A,GG,G		28.0636,20.6782,25.5833		588/632	27766776	921,2679	692	1591	2283	SO:0001819	synonymous_variant	347442	exon1			CGTGACGCAGAGA		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1764G>A	X.37:g.27766776G>A		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	135	133	0.985185	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			G|0.816;A|0.184	0.184	strong		0.507	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
ADAMTS16	170690	hgsc.bcm.edu	37	5	5146335	5146335	+	Missense_Mutation	SNP	C	C	G	rs2086310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:5146335C>G	ENST00000274181.7	+	3	406	c.268C>G	c.(268-270)Ccc>Gcc	p.P90A	CTD-2297D10.1_ENST00000514848.1_RNA|ADAMTS16_ENST00000511368.1_Missense_Mutation_p.P90A	NM_139056.2	NP_620687.2	Q8TE57	ATS16_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 16	90				P -> A (in Ref. 1; CAC86015). {ECO:0000305}.	branching involved in ureteric bud morphogenesis (GO:0001658)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(72)|ovary(4)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	107						AAGAGCAGTGCCCGTGTCCGA	0.557													G|||	3483	0.695487	0.5696	0.8674	5008	,	,		17116	0.498		0.8111	False		,,,				2504	0.8282				p.P90A		Atlas-SNP	.											.	ADAMTS16	543	.	0			c.C268G						PASS	.	G	ALA/PRO	2623,1453		838,947,253	62.0	63.0	63.0	http://www.ncbi.nlm.nih.gov/omim/607510,610262|http://omim.org/entry/610262|http://omim.org/entry/607510	268	-0.9	0.0	5	dbSNP_96	63	6831,1545		2784,1263,141	yes	missense	ADAMTS16	NM_139056.2	27	3622,2210,394	GG,GC,CC		18.4456,35.6477,24.0765	benign	90/1225	5146335	9454,2998	2038	4188	6226	SO:0001583	missense	170690	exon3			GCAGTGCCCGTGT	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.268C>G	5.37:g.5146335C>G	ENSP00000274181:p.Pro90Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_139056	C6G490|Q8IVE2	Missense_Mutation	SNP	ENST00000274181.7	37	CCDS43299.1	1504	0.6886446886446886	301	0.6117886178861789	312	0.861878453038674	291	0.5087412587412588	600	0.7915567282321899	G	0	-2.590313	0.00126	0.643523	0.815544	ENSG00000145536	ENST00000274181;ENST00000511368;ENST00000536857	T;T	0.05786	3.39;3.39	5.55	-0.853	0.10709	Peptidase M12B, propeptide (1);	0.469545	0.21485	N	0.073780	T	0.00012	0.0000	N	0.00621	-1.32	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	0.11518	-1.0584	9	0.07030	T	0.85	.	2.1559	0.03811	0.2637:0.0886:0.4054:0.2424	rs2086310;rs60829908;rs2086310	90;90;90	Q8TE57;Q8TE57-2;Q2XQZ0	ATS16_HUMAN;.;.	A	90	ENSP00000274181:P90A;ENSP00000421631:P90A	ENSP00000274181:P90A	P	+	1	0	ADAMTS16	5199335	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.242000	0.08928	-0.320000	0.08640	-2.319000	0.00253	CCC	C|0.294;G|0.706	0.706	strong		0.557	ADAMTS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365657.1	NM_139056	
DHFRL1	200895	hgsc.bcm.edu	37	3	93780109	93780109	+	Missense_Mutation	SNP	G	G	C	rs61739170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:93780109G>C	ENST00000394221.2	-	2	696	c.247C>G	c.(247-249)Cct>Gct	p.P83A	DHFRL1_ENST00000481631.1_Intron|DHFRL1_ENST00000314636.2_Missense_Mutation_p.P83A|NSUN3_ENST00000314622.4_5'Flank	NM_001195643.1	NP_001182572.1	Q86XF0	DYRL1_HUMAN	dihydrofolate reductase-like 1	83	DHFR. {ECO:0000255|PROSITE- ProRule:PRU00660}.				glycine biosynthetic process (GO:0006545)|nucleotide biosynthetic process (GO:0009165)|one-carbon metabolic process (GO:0006730)|tetrahydrofolate biosynthetic process (GO:0046654)|tetrahydrofolate metabolic process (GO:0046653)|thymidine biosynthetic process (GO:0046105)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dihydrofolate reductase activity (GO:0004146)|mRNA binding (GO:0003729)|NADP binding (GO:0050661)	p.P83A(1)		kidney(1)|large_intestine(2)|lung(3)|skin(1)|stomach(1)	8						CCTTGTGGAGGTTCCTTGAGT	0.393													G|||	612	0.122204	0.0219	0.2032	5008	,	,		18489	0.1141		0.2306	False		,,,				2504	0.0971				p.P83A		Atlas-SNP	.											DHFRL1,NS,carcinoma,0,1	DHFRL1	25	1	1	Substitution - Missense(1)	stomach(1)	c.C247G						PASS	.	G	ALA/PRO,ALA/PRO	280,4126	151.4+/-185.3	11,258,1934	114.0	117.0	116.0		247,247	0.1	0.4	3	dbSNP_129	116	1978,6622	344.5+/-325.3	216,1546,2538	no	missense,missense	DHFRL1	NM_001195643.1,NM_176815.4	27,27	227,1804,4472	CC,CG,GG		23.0,6.355,17.3612	benign,benign	83/188,83/188	93780109	2258,10748	2203	4300	6503	SO:0001583	missense	200895	exon2			GTGGAGGTTCCTT	AL832912	CCDS2926.1	3q11.2	2005-08-16	2005-02-07		ENSG00000178700	ENSG00000178700			27309	protein-coding gene	gene with protein product			"""dihydrofolate reductase pseudogene 4"""	DHFRP4		12477932	Standard	NM_001195643		Approved	FLJ16119	uc003drj.3	Q86XF0	OTTHUMG00000159014	ENST00000394221.2:c.247C>G	3.37:g.93780109G>C	ENSP00000377768:p.Pro83Ala	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	227	100	0.440529	NM_001195643	D3DN30|Q6P4I9	Missense_Mutation	SNP	ENST00000394221.2	37	CCDS2926.1	329	0.15064102564102563	19	0.03861788617886179	73	0.20165745856353592	68	0.11888111888111888	169	0.22295514511873352	G	0.136	-1.107561	0.01813	0.06355	0.23	ENSG00000178700	ENST00000314636;ENST00000394221;ENST00000496983	T;T;T	0.70869	-0.52;-0.52;-0.52	1.09	0.0854	0.14441	Dihydrofolate reductase domain (2);Dihydrofolate reductase-like domain (2);	0.127127	0.53938	U	0.000053	T	0.00039	0.0001	N	0.20357	0.565	0.34752	P	0.268081	B	0.09022	0.002	B	0.09377	0.004	T	0.05241	-1.0897	9	0.09084	T	0.74	-8.8976	6.8106	0.23802	0.0:0.2956:0.7044:0.0	rs61739170	83	Q86XF0	DYRL1_HUMAN	A	83	ENSP00000319170:P83A;ENSP00000377768:P83A;ENSP00000420810:P83A	ENSP00000319170:P83A	P	-	1	0	DHFRL1	95262799	0.974000	0.33945	0.410000	0.26471	0.620000	0.37586	0.236000	0.17967	0.028000	0.15324	-0.535000	0.04281	CCT	G|0.833;C|0.167	0.167	strong		0.393	DHFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352910.1	NM_176815	
GRAMD1A	57655	hgsc.bcm.edu	37	19	35506729	35506729	+	Splice_Site	SNP	G	G	A	rs2290647|rs17851095	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35506729G>A	ENST00000317991.5	+	11	1263	c.1071G>A	c.(1069-1071)gcG>gcA	p.A357A	CTD-2527I21.14_ENST00000605640.1_RNA|GRAMD1A_ENST00000599564.1_Splice_Site_p.A444A|GRAMD1A_ENST00000411896.2_Splice_Site_p.A350A|GRAMD1A_ENST00000504615.2_Splice_Site_p.A123A	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	357						integral component of membrane (GO:0016021)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	all_lung(56;2.66e-08)|Lung NSC(56;4.13e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			TGTCTCCAGCGGACTTGGCTG	0.647													G|||	1279	0.255391	0.2723	0.3055	5008	,	,		17832	0.2183		0.3419	False		,,,				2504	0.1462				p.A357A		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.G1071A						PASS	.	G	,	1143,3127		162,819,1154	34.0	39.0	38.0		1050,1071	-8.4	0.5	19	dbSNP_100	38	2728,5728		420,1888,1920	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	GRAMD1A	NM_001136199.1,NM_020895.3	,	582,2707,3074	AA,AG,GG		32.2611,26.7681,30.418	,	350/714,357/725	35506729	3871,8855	2135	4228	6363	SO:0001630	splice_region_variant	57655	exon11			TCCAGCGGACTTG	AK074864	CCDS42546.1, CCDS46046.1	19q13.13	2008-02-05	2005-11-02	2005-11-02		ENSG00000089351			29305	protein-coding gene	gene with protein product			"""KIAA1533"""	KIAA1533		10819331	Standard	NM_020895		Approved	FLJ90346	uc010xse.1	Q96CP6		ENST00000317991.5:c.1070-1G>A	19.37:g.35506729G>A		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	61	0.559633	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Silent	SNP	ENST00000317991.5	37	CCDS42546.1	620	0.2838827838827839	128	0.2601626016260163	117	0.32320441988950277	118	0.2062937062937063	257	0.3390501319261214	G	6.190	0.403188	0.11754	0.267681	0.322611	ENSG00000089351	ENST00000453966	.	.	.	5.01	-8.37	0.00976	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.99999999470532	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.6615	0.08240	0.179:0.2012:0.463:0.1567	rs2290647;rs11555071;rs17656062;rs61450895;rs2290647	.	.	.	.	-1	.	.	.	+	.	.	GRAMD1A	40198569	0.285000	0.24296	0.526000	0.27913	0.284000	0.27059	-0.462000	0.06704	-1.894000	0.01105	-1.373000	0.01185	.	G|0.711;A|0.289	0.289	strong		0.647	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895	Silent
TMEM43	79188	hgsc.bcm.edu	37	3	14175262	14175262	+	Missense_Mutation	SNP	T	T	C	rs2340917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14175262T>C	ENST00000306077.4	+	7	790	c.536T>C	c.(535-537)aTg>aCg	p.M179T	RP11-434D12.1_ENST00000608606.1_5'Flank	NM_024334.2	NP_077310.1	Q9BTV4	TMM43_HUMAN	transmembrane protein 43	179			M -> T (in dbSNP:rs2340917). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		nuclear membrane organization (GO:0071763)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|cervix(3)|endometrium(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(2)	19						GAGTCATTCATGGCAACAGCC	0.587													C|||	2320	0.463259	0.4508	0.5058	5008	,	,		17856	0.6756		0.2624	False		,,,				2504	0.4376				p.M179T		Atlas-SNP	.											.	TMEM43	33	.	0			c.T536C						PASS	.	C	THR/MET	1787,2619	643.1+/-397.8	369,1049,785	183.0	174.0	177.0		536	5.3	0.3	3	dbSNP_100	177	2541,6059	692.5+/-404.6	389,1763,2148	yes	missense	TMEM43	NM_024334.2	81	758,2812,2933	CC,CT,TT		29.5465,40.5583,33.2769	benign	179/401	14175262	4328,8678	2203	4300	6503	SO:0001583	missense	79188	exon7			CATTCATGGCAAC	BC008054	CCDS2618.1	3p25.1	2014-09-17			ENSG00000170876	ENSG00000170876			28472	protein-coding gene	gene with protein product		612048	"""arrhythmogenic right ventricular dysplasia 5"""	ARVD5		11230166, 18313022	Standard	NM_024334		Approved	MGC3222, DKFZp586G1919, LUMA	uc003byk.2	Q9BTV4	OTTHUMG00000129802	ENST00000306077.4:c.536T>C	3.37:g.14175262T>C	ENSP00000303992:p.Met179Thr	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_024334	Q7L4N5|Q8NC30|Q96A63|Q96F19|Q96JX0|Q9H076	Missense_Mutation	SNP	ENST00000306077.4	37	CCDS2618.1	994	0.4551282051282051	243	0.49390243902439024	177	0.4889502762430939	375	0.6555944055944056	199	0.262532981530343	C	2.349	-0.349307	0.05173	0.405583	0.295465	ENSG00000170876	ENST00000306077	T	0.28666	1.6	5.32	5.32	0.75619	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00368	-1.59	0.47441	P	5.760000000000209E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	9	0.02654	T	1	-14.0095	14.2173	0.65802	0.0:0.9278:0.0:0.0722	rs2340917;rs3796313;rs17856368;rs52809893;rs58039334;rs2340917	179	Q9BTV4	TMM43_HUMAN	T	179	ENSP00000303992:M179T	ENSP00000303992:M179T	M	+	2	0	TMEM43	14150263	0.992000	0.36948	0.348000	0.25681	0.370000	0.29829	3.048000	0.49862	1.246000	0.43901	-0.186000	0.12905	ATG	T|0.607;C|0.393	0.393	strong		0.587	TMEM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252030.2	NM_024334	
C19orf80	55908	hgsc.bcm.edu	37	19	11350340	11350340	+	Silent	SNP	C	C	G	rs892066	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11350340C>G	ENST00000252453.8	+	1	46	c.27C>G	c.(25-27)ctC>ctG	p.L9L	C19orf80_ENST00000591200.1_Intron|DOCK6_ENST00000294618.7_Intron|DOCK6_ENST00000319867.7_5'Flank	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	9					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						TGTGCCTGCTCTGGGCCCTGG	0.622													G|||	1875	0.374401	0.8101	0.255	5008	,	,		18798	0.3115		0.1093	False		,,,				2504	0.2076				p.L9L		Atlas-SNP	.											.	C19orf80	8	.	0			c.C27G						PASS	.	G	,	2763,1365		932,899,233	34.0	35.0	35.0		27,	-3.2	0.2	19	dbSNP_86	35	1149,7247		92,965,3141	no	coding-synonymous,intron	C19orf80,DOCK6	NM_018687.6,NM_020812.2	,	1024,1864,3374	GG,GC,CC		13.6851,33.0669,31.236	,	9/199,	11350340	3912,8612	2064	4198	6262	SO:0001819	synonymous_variant	55908	exon1			CCTGCTCTGGGCC		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"""lipasin"", ""betatrophin"""					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.27C>G	19.37:g.11350340C>G		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	142	141	0.992958	NM_018687	Q9NQZ1	Silent	SNP	ENST00000252453.8	37	CCDS54220.1																																																																																			C|0.688;G|0.312	0.312	strong		0.622	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687	
NME4	4833	hgsc.bcm.edu	37	16	450309	450309	+	Silent	SNP	C	C	T	rs5841	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:450309C>T	ENST00000219479.2	+	5	545	c.531C>T	c.(529-531)gaC>gaT	p.D177D	DECR2_ENST00000397710.1_5'Flank|NME4_ENST00000382940.4_Silent_p.D185D|NME4_ENST00000450036.1_Silent_p.D107D|NME4_ENST00000397722.1_Silent_p.D107D|DECR2_ENST00000424398.2_5'Flank|DECR2_ENST00000219481.5_5'Flank	NM_005009.2	NP_005000.1	O00746	NDKM_HUMAN	NME/NM23 nucleoside diphosphate kinase 4	177					CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|lung(1)|stomach(1)|urinary_tract(1)	4		Hepatocellular(16;0.00015)				GCTGGGCAGACGGGGGCCAGC	0.647													C|||	2074	0.414137	0.472	0.4164	5008	,	,		18357	0.3423		0.3638	False		,,,				2504	0.4601				p.D177D		Atlas-SNP	.											.	NME4	9	.	0			c.C531T						PASS	.	C		2071,2333	554.2+/-379.0	485,1101,616	49.0	53.0	51.0		531	-6.9	0.0	16	dbSNP_52	51	3349,5245	491.7+/-373.2	633,2083,1581	no	coding-synonymous	NME4	NM_005009.2		1118,3184,2197	TT,TC,CC		38.969,47.0254,41.6987		177/188	450309	5420,7578	2202	4297	6499	SO:0001819	synonymous_variant	4833	exon5			GGCAGACGGGGGC	Y07604	CCDS10408.1, CCDS66886.1, CCDS73797.1	16p13.3	2013-04-29	2012-05-18		ENSG00000103202	ENSG00000103202			7852	protein-coding gene	gene with protein product		601818	"""non-metastatic cells 4, protein expressed in"""			9099850, 19852809	Standard	NM_005009		Approved	nm23-H4, NM23H4, NDPKD	uc002cgz.3	O00746	OTTHUMG00000047995	ENST00000219479.2:c.531C>T	16.37:g.450309C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_005009	A2IDD0|Q5U0M9	Silent	SNP	ENST00000219479.2	37	CCDS10408.1																																																																																			C|0.595;T|0.405	0.405	strong		0.647	NME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109256.2	NM_005009	
OR9K2	441639	hgsc.bcm.edu	37	12	55523685	55523685	+	Missense_Mutation	SNP	C	C	T	rs12303066	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55523685C>T	ENST00000305377.5	+	1	221	c.133C>T	c.(133-135)Cgc>Tgc	p.R45C		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	45			R -> C (in dbSNP:rs12303066).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R45S(1)		NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CTTCAGGGTACGCCCAGAGCT	0.453													-|||	1523	0.304113	0.4085	0.2421	5008	,	,		17414	0.1141		0.334	False		,,,				2504	0.3722				p.R45C		Atlas-SNP	.											OR9K2,NS,carcinoma,0,2	OR9K2	63	2	1	Substitution - Missense(1)	prostate(1)	c.C133T						PASS	.	C	CYS/ARG	1703,2703	513.6+/-368.4	308,1087,808	177.0	166.0	170.0		133	-3.9	0.0	12	dbSNP_120	170	2777,5823	441.0+/-359.7	456,1865,1979	yes	missense	OR9K2	NM_001005243.1	180	764,2952,2787	TT,TC,CC		32.2907,38.6518,34.4456	benign	45/336	55523685	4480,8526	2203	4300	6503	SO:0001583	missense	441639	exon1			AGGGTACGCCCAG	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.133C>T	12.37:g.55523685C>T	ENSP00000307598:p.Arg45Cys	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	185	76	0.410811	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	624	0.2857142857142857	200	0.4065040650406504	102	0.281767955801105	73	0.12762237762237763	249	0.32849604221635886	C	8.501	0.864300	0.17250	0.386518	0.322907	ENSG00000170605	ENST00000305377	T	0.01084	5.36	4.98	-3.9	0.04181	.	1.019550	0.07834	N	0.961843	T	0.00012	0.0000	L	0.38692	1.165	0.80722	P	0.0	B	0.15930	0.015	B	0.13407	0.009	T	0.36915	-0.9728	9	0.56958	D	0.05	6.1352	2.3085	0.04180	0.3837:0.1609:0.3173:0.1381	rs12303066;rs52808341;rs61113706;rs12303066	45	Q8NGE7	OR9K2_HUMAN	C	45	ENSP00000307598:R45C	ENSP00000307598:R45C	R	+	1	0	OR9K2	53809952	0.000000	0.05858	0.000000	0.03702	0.643000	0.38383	-1.903000	0.01594	-0.457000	0.07033	-0.766000	0.03442	CGC	C|0.679;T|0.321	0.321	strong		0.453	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
SAMD4A	23034	hgsc.bcm.edu	37	14	55227152	55227152	+	Missense_Mutation	SNP	G	G	T	rs149416017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:55227152G>T	ENST00000554335.1	+	7	2113	c.1450G>T	c.(1450-1452)Gcc>Tcc	p.A484S	SAMD4A_ENST00000357634.3_Missense_Mutation_p.A483S|SAMD4A_ENST00000251091.5_Missense_Mutation_p.A396S|SAMD4A_ENST00000392067.3_Missense_Mutation_p.A484S|SAMD4A_ENST00000555192.1_Missense_Mutation_p.A75S			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	484					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						TGGGGAGCTGGCCGTCGCCCC	0.682													G|||	40	0.00798722	0.0023	0.0159	5008	,	,		13068	0.0		0.0249	False		,,,				2504	0.001				p.A484S		Atlas-SNP	.											.	SAMD4A	68	.	0			c.G1450T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	21,3909		0,21,1944	4.0	6.0	5.0		1183,223,1447	5.2	1.0	14	dbSNP_134	5	153,7591		3,147,3722	no	missense,missense,missense	SAMD4A	NM_001161576.2,NM_001161577.1,NM_015589.5	99,99,99	3,168,5666	TT,TG,GG		1.9757,0.5344,1.4905	benign,benign,benign	395/630,75/346,483/718	55227152	174,11500	1965	3872	5837	SO:0001583	missense	23034	exon6			GAGCTGGCCGTCG	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1450G>T	14.37:g.55227152G>T	ENSP00000452535:p.Ala484Ser	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	29	0.013278388278388278	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	15.72	2.917871	0.52546	0.005344	0.019757	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.22	5.22	0.72569	.	0.112512	0.64402	D	0.000017	T	0.20251	0.0487	N	0.12182	0.205	0.34882	D	0.744671	B;B;B	0.16802	0.019;0.011;0.003	B;B;B	0.23574	0.047;0.037;0.002	T	0.34650	-0.9820	9	0.28530	T	0.3	-24.0747	18.9689	0.92707	0.0:0.0:1.0:0.0	.	75;396;484	G3V2R1;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	S	484;484;396;395;483;75	.	ENSP00000251091:A113S	A	+	1	0	SAMD4A	54296902	1.000000	0.71417	0.999000	0.59377	0.774000	0.43823	5.707000	0.68370	2.711000	0.92665	0.609000	0.83330	GCC	G|0.987;T|0.013	0.013	strong		0.682	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
ZZEF1	23140	hgsc.bcm.edu	37	17	3947644	3947644	+	Missense_Mutation	SNP	T	T	C	rs781831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3947644T>C	ENST00000381638.2	-	38	6164	c.6040A>G	c.(6040-6042)Atc>Gtc	p.I2014V		NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	2014			I -> V (in dbSNP:rs781831). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9455477}.				calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						ACAGGTCTGATTTCCTCATGA	0.343													C|||	2605	0.520168	0.8192	0.5331	5008	,	,		19967	0.3482		0.4185	False		,,,				2504	0.3885				p.I2014V		Atlas-SNP	.											.	ZZEF1	195	.	0			c.A6040G						PASS	.	C	VAL/ILE	3393,1013	375.4+/-321.6	1328,737,138	193.0	178.0	183.0		6040	-2.7	0.0	17	dbSNP_86	183	3496,5104	633.4+/-398.7	693,2110,1497	yes	missense	ZZEF1	NM_015113.3	29	2021,2847,1635	CC,CT,TT		40.6512,22.9914,47.0321	benign	2014/2962	3947644	6889,6117	2203	4300	6503	SO:0001583	missense	23140	exon38			GTCTGATTTCCTC	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.6040A>G	17.37:g.3947644T>C	ENSP00000371051:p.Ile2014Val	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	209	92	0.440191	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	1123	0.5141941391941391	404	0.8211382113821138	197	0.5441988950276243	208	0.36363636363636365	314	0.41424802110817943	C	7.263	0.605678	0.14002	0.770086	0.406512	ENSG00000074755	ENST00000381638	T	0.19105	2.17	4.43	-2.65	0.06095	.	0.703692	0.13497	N	0.383546	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17077	-1.0381	9	0.14252	T	0.57	-0.3422	10.6007	0.45365	0.0:0.344:0.0:0.656	rs781831;rs2603026;rs58109404;rs781831	2014;2014	O43149-2;O43149	.;ZZEF1_HUMAN	V	2014	ENSP00000371051:I2014V	ENSP00000371051:I2014V	I	-	1	0	ZZEF1	3894393	0.000000	0.05858	0.003000	0.11579	0.401000	0.30781	-1.644000	0.02002	-0.777000	0.04572	-0.119000	0.15052	ATC	T|0.465;G|0.001	.	strong		0.343	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
GZMH	2999	hgsc.bcm.edu	37	14	25076906	25076906	+	Missense_Mutation	SNP	C	C	G	rs20545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:25076906C>G	ENST00000216338.4	-	3	295	c.251G>C	c.(250-252)cGg>cCg	p.R84P	GZMH_ENST00000382548.4_Missense_Mutation_p.R84P|RP11-104E19.1_ENST00000557736.1_RNA|RP11-104E19.1_ENST00000555300.1_RNA|GZMH_ENST00000557220.2_Intron	NM_033423.4	NP_219491.1	P20718	GRAH_HUMAN	granzyme H (cathepsin G-like 2, protein h-CCPX)	84	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		R -> Q (in dbSNP:rs20545).		apoptotic process (GO:0006915)|cytolysis (GO:0019835)	membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)	12				GBM - Glioblastoma multiforme(265;0.0267)		CTGCTGGGTCCGCTCCTGTTC	0.532													C|||	87	0.0173722	0.0295	0.0072	5008	,	,		20942	0.0089		0.008	False		,,,				2504	0.0266				p.R84P		Atlas-SNP	.											GZMH,colon,carcinoma,-1,1	GZMH	24	1	0			c.G251C						scavenged	.						193.0	183.0	187.0					14																	25076906		2203	4300	6503	SO:0001583	missense	2999	exon3			TGGGTCCGCTCCT	M72150	CCDS9632.1, CCDS59243.1	14q11.2	2003-10-20			ENSG00000100450	ENSG00000100450			4710	protein-coding gene	gene with protein product		116831		CTSGL2		2049336	Standard	NM_033423		Approved	CGL-2, CCP-X, CTLA1, CSP-C	uc001wpr.2	P20718	OTTHUMG00000140185	ENST00000216338.4:c.251G>C	14.37:g.25076906C>G	ENSP00000216338:p.Arg84Pro	Somatic	333	3	0.00900901		WXS	Illumina HiSeq	Phase_I	460	60	0.130435	NM_033423	G3V2C5|Q6XGZ0|Q6XGZ1	Missense_Mutation	SNP	ENST00000216338.4	37	CCDS9632.1	.	.	.	.	.	.	.	.	.	.	c	9.656	1.142754	0.21205	.	.	ENSG00000100450	ENST00000216338;ENST00000382548	D;D	0.88431	-2.38;-2.38	4.7	-8.63	0.00878	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.69278	0.3093	N	0.01789	-0.72	0.09310	N	1	B;B	0.15930	0.013;0.015	B;B	0.21917	0.037;0.035	T	0.59762	-0.7393	9	0.41790	T	0.15	.	10.5759	0.45227	0.0:0.1572:0.1088:0.734	.	84;84	Q6XGZ1;P20718	.;GRAH_HUMAN	P	84	ENSP00000216338:R84P;ENSP00000371988:R84P	ENSP00000216338:R84P	R	-	2	0	GZMH	24146746	0.000000	0.05858	0.045000	0.18777	0.058000	0.15608	-5.829000	0.00096	-1.513000	0.01789	-0.367000	0.07326	CGG	.	.	alt		0.532	GZMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276538.2	NM_033423	
CPA3	1359	hgsc.bcm.edu	37	3	148614447	148614447	+	Silent	SNP	C	C	T	rs61733454	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148614447C>T	ENST00000296046.3	+	11	1259	c.1207C>T	c.(1207-1209)Cta>Tta	p.L403L	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	403					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			AGAGACCATGCTAGCTGTCAA	0.418													C|||	56	0.0111821	0.0008	0.013	5008	,	,		19860	0.0		0.0447	False		,,,				2504	0.001				p.L403L		Atlas-SNP	.											.	CPA3	75	.	0			c.C1207T						PASS	.	C		46,4360	48.9+/-83.8	0,46,2157	111.0	115.0	114.0		1207	3.2	1.0	3	dbSNP_129	114	359,8241	121.3+/-180.4	14,331,3955	no	coding-synonymous	CPA3	NM_001870.2		14,377,6112	TT,TC,CC		4.1744,1.044,3.1139		403/418	148614447	405,12601	2203	4300	6503	SO:0001819	synonymous_variant	1359	exon11			ACCATGCTAGCTG		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"""mast cell carboxypeptidase A"", ""tissue carboxypeptidase A"""	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.1207C>T	3.37:g.148614447C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	89	60	0.674157	NM_001870	Q96E94	Silent	SNP	ENST00000296046.3	37	CCDS3138.1																																																																																			C|0.971;T|0.029	0.029	strong		0.418	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870	
MEGF6	1953	hgsc.bcm.edu	37	1	3413868	3413868	+	Missense_Mutation	SNP	C	C	G	rs4648506	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:3413868C>G	ENST00000356575.4	-	27	3636	c.3410G>C	c.(3409-3411)gGc>gCc	p.G1137A	MEGF6_ENST00000294599.4_Missense_Mutation_p.G946A	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1137	EGF-like 21. {ECO:0000255|PROSITE- ProRule:PRU00076}.		G -> A (in dbSNP:rs4648506). {ECO:0000269|PubMed:9693030}.			extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GCAGGCAGCGCCAGGCGGGCA	0.716													C|||	1222	0.24401	0.146	0.3357	5008	,	,		12528	0.1865		0.3201	False		,,,				2504	0.2924				p.G1137A	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.G3410C						PASS	.	C	ALA/GLY	547,3569		48,451,1559	8.0	13.0	11.0		3410	0.1	0.0	1	dbSNP_111	11	2204,6092		339,1526,2283	no	missense	MEGF6	NM_001409.3	60	387,1977,3842	GG,GC,CC		26.567,13.2896,22.164	possibly-damaging	1137/1542	3413868	2751,9661	2058	4148	6206	SO:0001583	missense	1953	exon27			GCAGCGCCAGGCG	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3410G>C	1.37:g.3413868C>G	ENSP00000348982:p.Gly1137Ala	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	532	0.24358974358974358	83	0.16869918699186992	101	0.27900552486187846	130	0.22727272727272727	218	0.287598944591029	C	12.32	1.903437	0.33628	0.132896	0.26567	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.71934	-0.09;-0.61	4.36	0.0897	0.14460	EGF-like, laminin (2);Epidermal growth factor-like, type 3 (1);	0.182174	0.48286	N	0.000200	T	0.00012	0.0000	M	0.91663	3.23	0.40306	P	0.021338999999999997	P;P	0.51147	0.942;0.929	P;P	0.62435	0.902;0.841	T	0.05022	-1.0911	9	0.62326	D	0.03	-7.763	6.2955	0.21083	0.0:0.6314:0.1331:0.2355	rs4648506	1137;946	O75095;O75095-2	MEGF6_HUMAN;.	A	946;1137	ENSP00000294599:G946A;ENSP00000348982:G1137A	ENSP00000294599:G946A	G	-	2	0	MEGF6	3403728	0.002000	0.14202	0.000000	0.03702	0.135000	0.20990	0.253000	0.18296	-0.064000	0.13043	0.561000	0.74099	GGC	C|0.736;G|0.264	0.264	strong		0.716	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
ZNF302	55900	hgsc.bcm.edu	37	19	35175775	35175775	+	Missense_Mutation	SNP	C	C	T	rs11543232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35175775C>T	ENST00000446502.2	+	6	1173	c.965C>T	c.(964-966)aCt>aTt	p.T322I	ZNF302_ENST00000457781.2_Missense_Mutation_p.T278I|ZNF302_ENST00000505242.1_Missense_Mutation_p.T278I|ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000423823.2_Missense_Mutation_p.T278I			Q9NR11	ZN302_HUMAN	zinc finger protein 302	357					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CATCAGAGCACTCACACGGGA	0.423													C|||	1255	0.250599	0.1369	0.2075	5008	,	,		21906	0.3006		0.3767	False		,,,				2504	0.2536				p.T278I		Atlas-SNP	.											.	ZNF302	27	.	0			c.C833T						PASS	.	C	ILE/THR,ILE/THR	817,3589	324.0+/-298.4	80,657,1466	91.0	90.0	90.0		833,833	1.0	1.0	19	dbSNP_120	90	3087,5513	471.9+/-368.2	544,1999,1757	no	missense,missense	ZNF302	NM_001012320.1,NM_018443.2	89,89	624,2656,3223	TT,TC,CC		35.8953,18.5429,30.0169	benign,benign	278/400,278/400	35175775	3904,9102	2203	4300	6503	SO:0001583	missense	55900	exon5			AGAGCACTCACAC	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.965C>T	19.37:g.35175775C>T	ENSP00000396379:p.Thr322Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	87	45	0.517241	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	37		615	0.2815934065934066	74	0.15040650406504066	83	0.2292817679558011	174	0.3041958041958042	284	0.37467018469656993	C	1.640	-0.516644	0.04200	0.185429	0.358953	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000423823;ENST00000446502	T;T;T;T	0.19532	2.66;2.66;2.66;2.14	0.967	0.967	0.19674	.	.	.	.	.	T	0.00012	0.0000	N	0.12471	0.22	0.45607	P	0.0014539999999999553	D;B	0.71674	0.998;0.034	D;B	0.79784	0.993;0.017	T	0.25082	-1.0142	8	0.02654	T	1	.	3.2227	0.06721	0.0:0.7107:0.0:0.2893	rs11543232;rs12971555;rs52834410	322;278	E7EVR1;Q9NR11-2	.;.	I	278;278;278;322	ENSP00000391067:T278I;ENSP00000421028:T278I;ENSP00000405219:T278I;ENSP00000396379:T322I	ENSP00000405219:T278I	T	+	2	0	ZNF302	39867615	0.096000	0.21769	0.998000	0.56505	0.974000	0.67602	0.177000	0.16801	0.822000	0.34565	0.467000	0.42956	ACT	C|0.704;T|0.296	0.296	strong		0.423	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
EYS	346007	hgsc.bcm.edu	37	6	65301824	65301824	+	Silent	SNP	T	T	C	rs12662610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301824T>C	ENST00000370621.3	-	26	4462	c.3936A>G	c.(3934-3936)acA>acG	p.T1312T	EYS_ENST00000370616.2_Silent_p.T1312T|EYS_ENST00000503581.1_Silent_p.T1312T			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1312					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TAATTCTTAATGTTGCCAAAC	0.403													C|||	484	0.0966454	0.0257	0.1182	5008	,	,		19102	0.1567		0.0984	False		,,,				2504	0.1135				p.T1312T		Atlas-SNP	.											.	EYS	527	.	0			c.A3936G						PASS	.	C		58,1326		1,56,635	89.0	77.0	80.0		3936	0.8	0.0	6	dbSNP_120	80	446,2734		41,364,1185	no	coding-synonymous	EYS	NM_001142800.1		42,420,1820	CC,CT,TT		14.0252,4.1908,11.0429		1312/3145	65301824	504,4060	692	1590	2282	SO:0001819	synonymous_variant	346007	exon26			TCTTAATGTTGCC		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.3936A>G	6.37:g.65301824T>C		Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	35	34	0.971429	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				T|0.906;C|0.094	0.094	strong		0.403	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
SPTB	6710	hgsc.bcm.edu	37	14	65260227	65260227	+	Silent	SNP	T	T	G	rs229591	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:65260227T>G	ENST00000389721.5	-	13	2186	c.2154A>C	c.(2152-2154)atA>atC	p.I718I	SPTB_ENST00000556626.1_Silent_p.I718I|SPTB_ENST00000389720.3_Silent_p.I718I|SPTB_ENST00000542895.1_Silent_p.I718I|SPTB_ENST00000389722.3_Silent_p.I718I	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	718					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)		ACACCTCCTTTATGCGGGCCT	0.592													G|||	2255	0.45028	0.7201	0.3372	5008	,	,		19756	0.2004		0.3588	False		,,,				2504	0.5174				p.I718I		Atlas-SNP	.											.	SPTB	378	.	0			c.A2154C						PASS	.	G	,	2836,1570	489.6+/-361.5	916,1004,283	56.0	53.0	54.0		2154,2154	3.8	0.7	14	dbSNP_79	54	3147,5453	655.4+/-401.3	566,2015,1719	no	coding-synonymous,coding-synonymous	SPTB	NM_000347.5,NM_001024858.2	,	1482,3019,2002	GG,GT,TT		36.593,35.6332,46.0018	,	718/2138,718/2329	65260227	5983,7023	2203	4300	6503	SO:0001819	synonymous_variant	6710	exon13			CTCCTTTATGCGG		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.2154A>C	14.37:g.65260227T>G		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	100	100	1	NM_001024858	Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	CCDS32100.1																																																																																			T|0.558;G|0.442	0.442	strong		0.592	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1		
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634341	32634341	+	Missense_Mutation	SNP	A	A	G	rs3189152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32634341A>G	ENST00000399082.3	-	1	88	c.44T>C	c.(43-45)gTa>gCa	p.V15A	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.V15A			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	15			A -> V (in allele DQB1*03:02, allele DQB1*03:03, allele DQB1*04:01, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*06:02 and allele DQB1*06:12; dbSNP:rs3189152). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GACAGTTGCTACCCGAAGGTC	0.577									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				a|||	1916	0.382588	0.3646	0.3487	5008	,	,		10661	0.3661		0.3549	False		,,,				2504	0.4765				p.V15A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	0			c.T44C						scavenged	.	G	ALA/VAL	1086,2800		255,576,1112	53.0	51.0	52.0		44	-0.2	0.0	6	dbSNP_105	52	2480,5732		644,1192,2270	yes	missense	HLA-DQB1	NM_002123.4	64	899,1768,3382	GG,GA,AA		30.1997,27.9465,29.4759	benign	15/262	32634341	3566,8532	1943	4106	6049	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GTTGCTACCCGAA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.44T>C	6.37:g.32634341A>G	ENSP00000382032:p.Val15Ala	Somatic	4	3	0.75		WXS	Illumina HiSeq	Phase_I	26	6	0.230769	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		634	0.2902930402930403	133	0.2703252032520325	113	0.31215469613259667	187	0.3269230769230769	201	0.26517150395778366	.	0.440	-0.899235	0.02472	0.279465	0.301997	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.03496	3.91;8.45;8.45;8.45;8.45	4.07	-0.196	0.13232	.	536.546000	0.00447	N	0.000082	T	0.00906	0.0030	.	.	.	0.80722	P	0.0	B;B;B;B	0.14438	0.01;0.0;0.0;0.0	B;B;B;B	0.11329	0.006;0.0;0.0;0.0	T	0.47394	-0.9121	8	0.45353	T	0.12	.	2.9773	0.05942	0.1685:0.2496:0.4568:0.125	rs3189152;rs9274520	25;15;15;15	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	A	15	ENSP00000382032:V15A;ENSP00000382029:V15A;ENSP00000364080:V15A;ENSP00000407332:V15A;ENSP00000382034:V15A	ENSP00000364080:V15A	V	-	2	0	HLA-DQB1	32742319	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.331000	0.07914	-0.498000	0.06632	-3.953000	0.00015	GTA	A|0.710;G|0.290	0.290	strong		0.577	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
NID1	4811	hgsc.bcm.edu	37	1	236144951	236144951	+	Silent	SNP	A	A	G	rs3738525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:236144951A>G	ENST00000264187.6	-	16	3269	c.3187T>C	c.(3187-3189)Ttg>Ctg	p.L1063L	NID1_ENST00000366595.3_Silent_p.L930L	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	1063					basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)			breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	GGATTCACCAAGTCAGTCTCA	0.493													G|||	1675	0.334465	0.3555	0.2579	5008	,	,		19135	0.6151		0.1402	False		,,,				2504	0.271				p.L1063L		Atlas-SNP	.											.	NID1	196	.	0			c.T3187C						PASS	.	G		1481,2925	678.6+/-403.6	235,1011,957	92.0	91.0	91.0		3187	-3.7	0.0	1	dbSNP_107	91	1478,7122	749.6+/-407.4	118,1242,2940	no	coding-synonymous	NID1	NM_002508.2		353,2253,3897	GG,GA,AA		17.186,33.6133,22.751		1063/1248	236144951	2959,10047	2203	4300	6503	SO:0001819	synonymous_variant	4811	exon16			TCACCAAGTCAGT	BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.3187T>C	1.37:g.236144951A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																			A|0.729;G|0.271	0.271	strong		0.493	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
BTNL2	56244	hgsc.bcm.edu	37	6	32362741	32362741	+	Missense_Mutation	SNP	C	C	T	rs28362677	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32362741C>T	ENST00000374993.1	-	6	1139	c.1140G>A	c.(1138-1140)atG>atA	p.M380I	BTNL2_ENST00000414363.1_Missense_Mutation_p.M170I|BTNL2_ENST00000544175.1_Missense_Mutation_p.M103I|BTNL2_ENST00000540315.1_Missense_Mutation_p.M170I|BTNL2_ENST00000429232.2_3'UTR|HCG23_ENST00000426643.1_RNA|BTNL2_ENST00000374995.3_Missense_Mutation_p.M286I|BTNL2_ENST00000454136.3_Missense_Mutation_p.M380I	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	380			M -> I (in dbSNP:rs28362677).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CTGAAGAGCACATCGGCTGCA	0.567													c|||	821	0.163938	0.1422	0.1599	5008	,	,		19368	0.1587		0.163	False		,,,				2504	0.2025				p.M380I		Atlas-SNP	.											.	BTNL2	50	.	0			c.G1140A						PASS	.		ILE/MET	551,3855	248.1+/-256.1	28,495,1680	214.0	199.0	204.0		1140	3.3	0.6	6	dbSNP_125	204	1241,7359	248.3+/-276.0	92,1057,3151	yes	missense	BTNL2	NM_019602.1	10	120,1552,4831	TT,TC,CC		14.4302,12.5057,13.7783	benign	380/456	32362741	1792,11214	2203	4300	6503	SO:0001583	missense	56244	exon6			AGAGCACATCGGC	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.1140G>A	6.37:g.32362741C>T	ENSP00000364132:p.Met380Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	114	44	0.385965	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		346	0.15842490842490842	60	0.12195121951219512	64	0.17679558011049723	104	0.18181818181818182	118	0.15567282321899736	c	3.471	-0.107846	0.06924	0.125057	0.144302	ENSG00000204290	ENST00000468270;ENST00000374995;ENST00000414363;ENST00000374993;ENST00000540315;ENST00000544175	T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91	5.08	3.3	0.37823	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	1.021310	0.07807	N	0.957528	T	0.38799	0.1054	N	0.17082	0.46	0.09310	P	0.999999826318	B;B	0.09022	0.002;0.0	B;B	0.11329	0.003;0.006	T	0.11767	-1.0574	9	0.42905	T	0.14	.	6.9709	0.24648	0.0:0.7326:0.1751:0.0922	rs28362677	170;380	Q9UIR0-4;Q9UIR0	.;BTNL2_HUMAN	I	380;286;170;380;170;103	ENSP00000364134:M286I;ENSP00000390512:M170I;ENSP00000364132:M380I;ENSP00000444714:M170I;ENSP00000443364:M103I	ENSP00000364132:M380I	M	-	3	0	BTNL2	32470719	0.018000	0.18449	0.617000	0.29091	0.049000	0.14656	-0.068000	0.11561	0.756000	0.33013	-0.357000	0.07601	ATG	C|0.859;T|0.141	0.141	strong		0.567	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
C20orf166	128826	hgsc.bcm.edu	37	20	61167883	61167883	+	Silent	SNP	G	G	A	rs6143064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:61167883G>A	ENST00000370527.3	+	4	1132	c.353G>A	c.(352-354)tGa>tAa	p.*118*	C20orf166_ENST00000370523.1_Silent_p.*100*|C20orf166_ENST00000370524.2_Silent_p.*100*	NM_178463.3	NP_848558.1			chromosome 20 open reading frame 166											endometrium(1)|kidney(1)|lung(2)	4	Breast(26;1.04e-08)		BRCA - Breast invasive adenocarcinoma(19;7.17e-06)			AGCCACTGCTGAAGGGACTCC	0.582													G|||	1320	0.263578	0.0877	0.2968	5008	,	,		16708	0.1617		0.4016	False		,,,				2504	0.4407				p.X118X		Atlas-SNP	.											.	C20orf166	17	.	0			c.G353A						PASS	.	G		462,3564		31,400,1582	22.0	23.0	23.0		353	-0.5	0.0	20	dbSNP_114	23	3161,5151		590,1981,1585	no	coding-synonymous	C20orf166	NM_178463.3		621,2381,3167	AA,AG,GG		38.0294,11.4754,29.3646		118/118	61167883	3623,8715	2013	4156	6169	SO:0001819	synonymous_variant	128826	exon4			ACTGCTGAAGGGA	AL449263	CCDS46627.1	20q13.33	2014-01-21			ENSG00000174407	ENSG00000174407			16159	protein-coding gene	gene with protein product	"""MIR133A2 host gene"""						Standard	NM_178463		Approved	dJ353C17.1, MIR1-1HG, MIR133A2HG	uc011aaj.2	Q9H1L0	OTTHUMG00000048000	ENST00000370527.3:c.353G>A	20.37:g.61167883G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	59	59	1	NM_178463		Silent	SNP	ENST00000370527.3	37	CCDS46627.1																																																																																			G|0.722;A|0.278	0.278	strong		0.582	C20orf166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109262.1	NM_178463	
ZNF813	126017	hgsc.bcm.edu	37	19	53993670	53993670	+	Missense_Mutation	SNP	G	G	A	rs2617667	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53993670G>A	ENST00000396403.4	+	4	312	c.184G>A	c.(184-186)Gca>Aca	p.A62T	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	62	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		A -> T (in dbSNP:rs2617667).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(1)	1				GBM - Glioblastoma multiforme(134;0.00619)		CTCATCAACAGCACAAGGCAA	0.368													g|||	1495	0.298522	0.475	0.2406	5008	,	,		21430	0.2421		0.1918	False		,,,				2504	0.2689				p.A62T		Atlas-SNP	.											.	ZNF813	81	.	0			c.G184A						PASS	.	G	THR/ALA	1851,2513	489.2+/-361.4	396,1059,727	89.0	93.0	91.0		184	-1.1	0.0	19	dbSNP_100	91	1648,6938	291.6+/-300.4	158,1332,2803	no	missense	ZNF813	NM_001004301.3	58	554,2391,3530	AA,AG,GG		19.194,42.4152,27.0193	possibly-damaging	62/618	53993670	3499,9451	2182	4293	6475	SO:0001583	missense	126017	exon4			TCAACAGCACAAG	AK091460	CCDS46172.1	19q13.41	2013-01-08			ENSG00000198346	ENSG00000198346		"""Zinc fingers, C2H2-type"", ""-"""	33257	protein-coding gene	gene with protein product							Standard	NM_001004301		Approved	FLJ16542	uc002qbu.2	Q6ZN06	OTTHUMG00000158309	ENST00000396403.4:c.184G>A	19.37:g.53993670G>A	ENSP00000379684:p.Ala62Thr	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	133	61	0.458647	NM_001004301		Missense_Mutation	SNP	ENST00000396403.4	37	CCDS46172.1	578	0.26465201465201466	224	0.45528455284552843	83	0.2292817679558011	140	0.24475524475524477	131	0.17282321899736147	G	6.884	0.532613	0.13127	0.424152	0.19194	ENSG00000198346	ENST00000468450;ENST00000396403;ENST00000490956	T;T;T	0.05649	4.08;3.41;5.14	0.678	-1.13	0.09775	Krueppel-associated box (3);	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	P	0.37330	0.59	B	0.40602	0.334	T	0.37549	-0.9701	8	0.16420	T	0.52	.	4.7006	0.12825	0.0:0.0:0.3779:0.6221	rs2617667;rs52808272;rs56450222;rs59449241;rs2617667	62	Q6ZN06	ZN813_HUMAN	T	9;62;93	ENSP00000419821:A9T;ENSP00000379684:A62T;ENSP00000418289:A93T	ENSP00000379684:A62T	A	+	1	0	ZNF813	58685482	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.243000	0.08915	-0.301000	0.08882	0.205000	0.17691	GCA	G|0.745;A|0.255	0.255	strong		0.368	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
PYCRL	65263	hgsc.bcm.edu	37	8	144689146	144689146	+	Missense_Mutation	SNP	C	C	T	rs2242089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144689146C>T	ENST00000220966.6	-	3	378	c.349G>A	c.(349-351)Gtg>Atg	p.V117M	PYCRL_ENST00000495276.1_5'UTR|PYCRL_ENST00000377579.3_De_novo_Start_InFrame	NM_023078.3	NP_075566.2	Q53H96	P5CR3_HUMAN	pyrroline-5-carboxylate reductase-like	105					L-proline biosynthetic process (GO:0055129)		pyrroline-5-carboxylate reductase activity (GO:0004735)			central_nervous_system(1)|endometrium(1)|lung(2)|ovary(1)	5	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.17e-38)|Epithelial(56;7.17e-37)|all cancers(56;2.46e-32)|Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)		L-Proline(DB00172)	CTCAGAGACACCCCAGCAGCC	0.627													C|||	1231	0.245807	0.1808	0.2233	5008	,	,		19504	0.371		0.2008	False		,,,				2504	0.2669				p.V117M		Atlas-SNP	.											PYCRL,NS,carcinoma,0,1	PYCRL	14	1	0			c.G349A	GRCh37	CM067455	PYCRL	M	rs2242089	PASS	.	C	MET/VAL	821,3585	323.7+/-298.2	76,669,1458	76.0	72.0	73.0		349	2.0	0.3	8	dbSNP_98	73	1565,7035	293.2+/-301.3	156,1253,2891	yes	missense	PYCRL	NM_023078.3	21	232,1922,4349	TT,TC,CC		18.1977,18.6337,18.3454	probably-damaging	117/287	144689146	2386,10620	2203	4300	6503	SO:0001583	missense	65263	exon3			GAGACACCCCAGC	AF086378	CCDS6407.2	8q24.3	2011-09-30	2011-09-30	2011-09-30	ENSG00000104524	ENSG00000104524			25846	protein-coding gene	gene with protein product							Standard	NM_023078		Approved	FLJ13852	uc003yyy.3	Q53H96	OTTHUMG00000157010	ENST00000220966.6:c.349G>A	8.37:g.144689146C>T	ENSP00000220966:p.Val117Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	169	67	0.39645	NM_023078	B3KMB5|B4DVT6|H0Y6C3|Q8N3N9|Q96HX4|Q9H896	Missense_Mutation	SNP	ENST00000220966.6	37	CCDS6407.2	526	0.24084249084249085	89	0.18089430894308944	62	0.1712707182320442	222	0.3881118881118881	153	0.20184696569920843	C	15.51	2.855574	0.51376	0.186337	0.181977	ENSG00000104524	ENST00000220966;ENST00000433751	T;T	0.65732	-0.17;-0.17	4.82	2.0	0.26442	NAD(P)-binding domain (1);	0.273444	0.36200	N	0.002732	T	0.00012	0.0000	M	0.88906	2.99	0.09310	P	0.9999999999965832	D;D	0.67145	0.996;0.995	P;P	0.61201	0.83;0.885	T	0.12967	-1.0527	9	0.72032	D	0.01	-23.9758	7.7118	0.28682	0.0:0.7091:0.0:0.2909	rs2242089;rs11549788;rs60863986;rs2242089	117;105	D3DWK4;Q53H96	.;P5CR3_HUMAN	M	117;112	ENSP00000220966:V117M;ENSP00000404493:V112M	ENSP00000220966:V117M	V	-	1	0	PYCRL	144760289	0.313000	0.24554	0.347000	0.25668	0.682000	0.39822	0.873000	0.28052	0.101000	0.17610	0.448000	0.29417	GTG	C|0.785;T|0.215	0.215	strong		0.627	PYCRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347081.2	NM_023078	
C9orf171	389799	hgsc.bcm.edu	37	9	135374764	135374764	+	Missense_Mutation	SNP	G	G	A	rs7047726	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135374764G>A	ENST00000343036.2	+	4	457	c.409G>A	c.(409-411)Gga>Aga	p.G137R	C9orf171_ENST00000393216.2_Missense_Mutation_p.G101R|C9orf171_ENST00000393215.3_Missense_Mutation_p.G101R	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	137			G -> R (in dbSNP:rs7047726).							large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						CTCAGCCATCGGACGCTGGAA	0.642													G|||	933	0.186302	0.1021	0.1354	5008	,	,		16862	0.4792		0.0716	False		,,,				2504	0.1524				p.G137R		Atlas-SNP	.											.	C9orf171	53	.	0			c.G409A						PASS	.	G	ARG/GLY	432,3974	206.2+/-227.9	23,386,1794	49.0	50.0	49.0		409	5.3	1.0	9	dbSNP_116	49	703,7897	171.7+/-222.6	32,639,3629	yes	missense	C9orf171	NM_207417.1	125	55,1025,5423	AA,AG,GG		8.1744,9.8048,8.7267	probably-damaging	137/321	135374764	1135,11871	2203	4300	6503	SO:0001583	missense	389799	exon4			GCCATCGGACGCT	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.409G>A	9.37:g.135374764G>A	ENSP00000343290:p.Gly137Arg	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	21	8	0.380952	NM_207417	Q147X1	Missense_Mutation	SNP	ENST00000343036.2	37	CCDS6949.1	406	0.1858974358974359	53	0.10772357723577236	46	0.1270718232044199	249	0.4353146853146853	58	0.07651715039577836	G	22.2	4.260770	0.80246	0.098048	0.081744	ENSG00000188523	ENST00000393215;ENST00000343036;ENST00000393216	T;T;T	0.22134	1.97;1.97;1.97	5.26	5.26	0.73747	.	0.324081	0.29233	N	0.012760	T	0.00012	0.0000	L	0.36672	1.1	0.23834	P	0.99671562	P;D	0.54207	0.956;0.965	B;P	0.49140	0.301;0.601	T	0.54036	-0.8353	9	0.42905	T	0.14	.	18.212	0.89873	0.0:0.0:1.0:0.0	rs7047726;rs52813020;rs59419701;rs7047726	101;137	Q6ZQR2-2;Q6ZQR2	.;CI171_HUMAN	R	101;137;101	ENSP00000376908:G101R;ENSP00000343290:G137R;ENSP00000376909:G101R	ENSP00000343290:G137R	G	+	1	0	C9orf171	134364585	1.000000	0.71417	0.992000	0.48379	0.835000	0.47333	4.531000	0.60602	2.618000	0.88619	0.561000	0.74099	GGA	G|0.865;A|0.135	0.135	strong		0.642	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
C2orf16	84226	hgsc.bcm.edu	37	2	27804432	27804432	+	Missense_Mutation	SNP	T	T	C	rs28381983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27804432T>C	ENST00000408964.2	+	1	5044	c.4993T>C	c.(4993-4995)Tcc>Ccc	p.S1665P	ZNF512_ENST00000413371.2_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000355467.4_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000379717.1_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1665	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.		S -> P (in dbSNP:rs28381983). {ECO:0000269|PubMed:11230166, ECO:0000269|PubMed:17974005}.			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CCATCGCAGTTCCTCTGAGAG	0.582													C|||	3478	0.694489	0.8502	0.7147	5008	,	,		19630	0.8452		0.506	False		,,,				2504	0.5082				p.S1665P		Atlas-SNP	.											.	C2orf16	357	.	0			c.T4993C						PASS	.	C	PRO/SER	2957,853		1143,671,91	156.0	158.0	157.0		4993	-5.1	0.0	2	dbSNP_125	157	4132,4110		1057,2018,1046	no	missense	C2orf16	NM_032266.3	74	2200,2689,1137	CC,CT,TT		49.8665,22.3885,41.1799	benign	1665/1985	27804432	7089,4963	1905	4121	6026	SO:0001583	missense	84226	exon1			CGCAGTTCCTCTG	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4993T>C	2.37:g.27804432T>C	ENSP00000386190:p.Ser1665Pro	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	101	52	0.514852	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	1518	0.695054945054945	405	0.823170731707317	239	0.6602209944751382	490	0.8566433566433567	384	0.5065963060686016	C	1.081	-0.667074	0.03428	0.776115	0.501335	ENSG00000221843	ENST00000408964	T	0.04809	3.55	3.71	-5.11	0.02901	.	.	.	.	.	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38693	-0.9649	8	0.02654	T	1	.	0.1883	0.00131	0.242:0.2449:0.2388:0.2743	rs28381983	1665	Q68DN1	CB016_HUMAN	P	1665	ENSP00000386190:S1665P	ENSP00000386190:S1665P	S	+	1	0	C2orf16	27657936	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.659000	0.00852	-1.880000	0.01125	-0.642000	0.03964	TCC	T|0.364;C|0.636	0.636	strong		0.582	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
TRPV3	162514	hgsc.bcm.edu	37	17	3436080	3436080	+	Silent	SNP	C	C	T	rs395357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:3436080C>T	ENST00000576742.1	-	8	1257	c.936G>A	c.(934-936)acG>acA	p.T312T	TRPV3_ENST00000572519.1_Silent_p.T312T|TRPV3_ENST00000301365.4_Silent_p.T312T	NM_001258205.1|NM_145068.3	NP_001245134.1|NP_659505.1	Q8NET8	TRPV3_HUMAN	transient receptor potential cation channel, subfamily V, member 3	312					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)	AGTCATTCTGCGTCTTGAAGT	0.592													T|||	1783	0.35603	0.3328	0.281	5008	,	,		21646	0.254		0.4901	False		,,,				2504	0.408				p.T312T		Atlas-SNP	.											.	TRPV3	85	.	0			c.G936A						PASS	.	T		1524,2882	673.7+/-402.8	267,990,946	243.0	161.0	188.0		936	-8.1	0.3	17	dbSNP_80	188	4224,4376	583.4+/-391.6	1032,2160,1108	no	coding-synonymous	TRPV3	NM_145068.2		1299,3150,2054	TT,TC,CC		49.1163,34.5892,44.195		312/791	3436080	5748,7258	2203	4300	6503	SO:0001819	synonymous_variant	162514	exon8			ATTCTGCGTCTTG	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.936G>A	17.37:g.3436080C>T		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	239	238	0.995816	NM_001258205	Q8NDW7|Q8NET9|Q8NFH2	Silent	SNP	ENST00000576742.1	37	CCDS11029.1																																																																																			C|0.601;T|0.399	0.399	strong		0.592	TRPV3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207379.2	NM_145068	
IQCF1	132141	hgsc.bcm.edu	37	3	51930850	51930850	+	Missense_Mutation	SNP	T	T	C	rs57859638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:51930850T>C	ENST00000310914.5	-	3	231	c.169A>G	c.(169-171)Aaa>Gaa	p.K57E		NM_152397.2	NP_689610.2	Q8N6M8	IQCF1_HUMAN	IQ motif containing F1	57										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGTCATACTTTTTCTGATTTC	0.488													T|||	494	0.0986422	0.0772	0.1441	5008	,	,		15992	0.0169		0.1899	False		,,,				2504	0.0859				p.K57E		Atlas-SNP	.											IQCF1,tonsil,carcinoma,0,1	IQCF1	26	1	0			c.A169G						PASS	.	T	GLU/LYS	440,3966	211.8+/-231.9	25,390,1788	168.0	155.0	160.0		169	-5.5	0.0	3	dbSNP_129	160	1647,6953	304.8+/-307.1	158,1331,2811	yes	missense	IQCF1	NM_152397.2	56	183,1721,4599	CC,CT,TT		19.1512,9.9864,16.0464	benign	57/206	51930850	2087,10919	2203	4300	6503	SO:0001583	missense	132141	exon3			ATACTTTTTCTGA	BC029595	CCDS2836.1	3p21.31	2008-02-05			ENSG00000173389	ENSG00000173389			28607	protein-coding gene	gene with protein product						12477932	Standard	NM_152397		Approved	MGC39725	uc003dbv.3	Q8N6M8	OTTHUMG00000156908	ENST00000310914.5:c.169A>G	3.37:g.51930850T>C	ENSP00000307958:p.Lys57Glu	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	140	74	0.528571	NM_152397	Q8N711	Missense_Mutation	SNP	ENST00000310914.5	37	CCDS2836.1	258	0.11813186813186813	54	0.10975609756097561	50	0.13812154696132597	6	0.01048951048951049	148	0.19525065963060687	T	7.233	0.599696	0.13939	0.099864	0.191512	ENSG00000173389	ENST00000535733;ENST00000310914	T	0.30182	1.54	3.15	-5.5	0.02576	.	2.522450	0.01453	N	0.015570	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.18493	-1.0335	9	0.07644	T	0.81	-12.336	6.6923	0.23179	0.0:0.1824:0.1462:0.6715	rs57859638	57	Q8N6M8	IQCF1_HUMAN	E	57	ENSP00000307958:K57E	ENSP00000307958:K57E	K	-	1	0	IQCF1	51905890	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.751000	0.01821	-1.368000	0.02149	0.448000	0.29417	AAA	T|0.851;C|0.149	0.149	strong		0.488	IQCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346568.1	NM_152397	
GDPGP1	390637	hgsc.bcm.edu	37	15	90784930	90784930	+	Missense_Mutation	SNP	C	C	A	rs10152994	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:90784930C>A	ENST00000558017.1	+	4	1210	c.790C>A	c.(790-792)Cct>Act	p.P264T	GDPGP1_ENST00000329600.6_Missense_Mutation_p.P264T	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	264			P -> T (in dbSNP:rs10152994). {ECO:0000269|PubMed:14702039}.		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)										TGGGCCAGGGCCTGACTTGGA	0.587													C|||	662	0.132188	0.2436	0.1398	5008	,	,		19088	0.0		0.1789	False		,,,				2504	0.0644				p.P264T		Atlas-SNP	.											.	.	.	.	0			c.C790A						PASS	.	C	THR/PRO	872,3526	340.7+/-306.4	90,692,1417	76.0	68.0	71.0		790	4.0	0.0	15	dbSNP_119	71	1435,7161	275.6+/-291.8	131,1173,2994	yes	missense	C15orf58	NM_001013657.2	38	221,1865,4411	AA,AC,CC		16.6938,19.8272,17.7543	possibly-damaging	264/386	90784930	2307,10687	2199	4298	6497	SO:0001583	missense	390637	exon4			CCAGGGCCTGACT		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.790C>A	15.37:g.90784930C>A	ENSP00000452793:p.Pro264Thr	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	311	0.1423992673992674	114	0.23170731707317074	61	0.1685082872928177	0	0.0	136	0.17941952506596306	C	0.104	-1.147311	0.01714	0.198272	0.166938	ENSG00000183208	ENST00000329600	T	0.21031	2.03	5.95	4.0	0.46444	.	0.529862	0.20055	N	0.100211	T	0.00012	0.0000	L	0.32530	0.975	0.80722	P	0.0	P	0.41848	0.763	B	0.36608	0.229	T	0.36792	-0.9733	9	0.12103	T	0.63	-2.3515	15.5393	0.76027	0.0:0.608:0.392:0.0	rs10152994;rs60285158;rs10152994	264	Q6ZNW5	VTC2_HUMAN	T	264	ENSP00000368405:P264T	ENSP00000368405:P264T	P	+	1	0	C15orf58	88585934	0.098000	0.21812	0.009000	0.14445	0.008000	0.06430	2.045000	0.41250	0.787000	0.33731	0.655000	0.94253	CCT	C|0.833;A|0.167	0.167	strong		0.587	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
WDR18	57418	hgsc.bcm.edu	37	19	991968	991968	+	Silent	SNP	T	T	C	rs1127043	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:991968T>C	ENST00000251289.5	+	8	968	c.945T>C	c.(943-945)aaT>aaC	p.N315N	WDR18_ENST00000587001.2_Silent_p.N315N	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	315					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGTCACCAATGCCGCCATCC	0.706													N|||	1975	0.394369	0.4758	0.2738	5008	,	,		7631	0.4107		0.2962	False		,,,				2504	0.454				p.N315N		Atlas-SNP	.											.	WDR18	20	.	0			c.T945C						PASS	.	C		1912,2278		470,972,653	8.0	9.0	9.0		945	-0.6	0.9	19	dbSNP_86	9	2388,5854		417,1554,2150	no	coding-synonymous	WDR18	NM_024100.3		887,2526,2803	CC,CT,TT		28.9736,45.6325,34.5882		315/433	991968	4300,8132	2095	4121	6216	SO:0001819	synonymous_variant	57418	exon8			CACCAATGCCGCC		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.945T>C	19.37:g.991968T>C		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	9	4	0.444444	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			T|0.651;C|0.349	0.349	strong		0.706	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274319	39274319	+	Missense_Mutation	SNP	G	G	C	rs199712484		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39274319G>C	ENST00000391413.2	-	1	287	c.249C>G	c.(247-249)agC>agG	p.S83R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	83	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.S83R(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)			GCTTGCAGCAGCTGGACACAC	0.662																																					p.S83R		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,2	KRTAP4-11	94	2	1	Substitution - Missense(1)	endometrium(1)	c.C249G						scavenged	.																																			SO:0001583	missense	653240	exon1			GCAGCAGCTGGAC	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.249C>G	17.37:g.39274319G>C	ENSP00000375232:p.Ser83Arg	Somatic	48	1	0.0208333		WXS	Illumina HiSeq	Phase_I	73	8	0.109589	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	11.88	1.769671	0.31320	.	.	ENSG00000212721	ENST00000391413	T	0.00686	5.85	4.12	0.987	0.19790	.	8.728350	0.01373	U	0.012645	T	0.01835	0.0058	M	0.85710	2.77	0.20489	N	0.999895	B	0.21381	0.055	B	0.12156	0.007	T	0.50676	-0.8800	10	0.66056	D	0.02	.	3.7776	0.08667	0.3083:0.1839:0.5078:0.0	.	83	Q9BYQ6	KR411_HUMAN	R	83	ENSP00000375232:S83R	ENSP00000375232:S83R	S	-	3	2	KRTAP4-11	36527845	0.052000	0.20516	0.390000	0.26220	0.120000	0.20174	0.102000	0.15272	0.075000	0.16796	0.511000	0.50034	AGC	.	.	weak		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
CSHL1	1444	hgsc.bcm.edu	37	17	61987570	61987570	+	Missense_Mutation	SNP	G	G	T	rs2727307	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61987570G>T	ENST00000309894.5	-	4	422	c.423C>A	c.(421-423)gaC>gaA	p.D141E	CSHL1_ENST00000450719.3_Missense_Mutation_p.D47E|CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000346606.6_Missense_Mutation_p.D47E|CSHL1_ENST00000259003.10_Missense_Mutation_p.D79E|CSHL1_ENST00000438387.2_Missense_Mutation_p.D58E|CSHL1_ENST00000561003.1_Missense_Mutation_p.D58E|CSHL1_ENST00000558099.1_5'UTR	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	141			D -> E (in dbSNP:rs2727307). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						GGAGGTGATAGTCATCGCTGT	0.592													G|||	1392	0.277955	0.059	0.3256	5008	,	,		19686	0.4196		0.4185	False		,,,				2504	0.2495				p.D141E		Atlas-SNP	.											CSHL1_ENST00000561003,bladder,carcinoma,-2,4	CSHL1	42	4	0			c.C423A						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	555,3851	249.3+/-256.8	32,491,1680	90.0	78.0	82.0		141,423,174,354	3.1	0.2	17	dbSNP_100	82	3562,5038	516.7+/-378.9	747,2068,1485	no	missense,missense,missense,missense	CSHL1	NM_001318.2,NM_022579.1,NM_022580.1,NM_022581.1	45,45,45,45	779,2559,3165	TT,TG,GG		41.4186,12.5965,31.6546	benign,benign,benign,benign	47/129,141/223,58/140,118/200	61987570	4117,8889	2203	4300	6503	SO:0001583	missense	1444	exon4			GTGATAGTCATCG	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"""chorionic somatomammotropin CS-5"""	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.423C>A	17.37:g.61987570G>T	ENSP00000309524:p.Asp141Glu	Somatic	455	0	0		WXS	Illumina HiSeq	Phase_I	312	310	0.99359	NM_022579	D3DU26|D3DU27|Q0VDB2	Missense_Mutation	SNP	ENST00000309894.5	37	CCDS11652.1	708	0.3241758241758242	38	0.07723577235772358	135	0.3729281767955801	217	0.3793706293706294	318	0.41952506596306066	g	8.404	0.842563	0.16963	0.125965	0.414186	ENSG00000204414	ENST00000309894;ENST00000438387;ENST00000259003;ENST00000346606;ENST00000450719	D;D;D	0.90261	-2.64;-2.64;-2.64	3.07	3.07	0.35406	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.304551	0.31145	N	0.008174	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.99999999455923	B;B;B;B	0.32893	0.007;0.337;0.389;0.337	B;B;B;B	0.38156	0.007;0.173;0.266;0.253	T	0.08411	-1.0723	9	0.87932	D	0	.	8.2735	0.31857	0.0:0.2465:0.7534:0.0	rs2727307;rs57082825	47;58;141;118	Q14406-4;Q14406-3;Q14406;Q14406-2	.;.;CSHL_HUMAN;.	E	141;58;136;47;136	ENSP00000309524:D141E;ENSP00000402632:D58E;ENSP00000316360:D47E	ENSP00000259003:D136E	D	-	3	2	GH1	59341302	1.000000	0.71417	0.247000	0.24249	0.002000	0.02628	1.431000	0.34925	1.730000	0.51580	0.305000	0.20034	GAC	G|0.670;T|0.330	0.330	strong		0.592	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579	
PARP4	143	hgsc.bcm.edu	37	13	25016092	25016092	+	Silent	SNP	C	C	T	rs55888616	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25016092C>T	ENST00000381989.3	-	30	3663	c.3558G>A	c.(3556-3558)tcG>tcA	p.S1186S		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1186					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CAGGAAAAGGCGACTCATTCT	0.408													c|||	1926	0.384585	0.4834	0.3473	5008	,	,		24558	0.3601		0.4115	False		,,,				2504	0.2751				p.S1186S		Atlas-SNP	.											.	PARP4	142	.	0			c.G3558A						PASS	.						40.0	43.0	42.0					13																	25016092		2203	4299	6502	SO:0001819	synonymous_variant	143	exon30			AAAAGGCGACTCA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3558G>A	13.37:g.25016092C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																			C|0.673;T|0.327	0.327	strong		0.408	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
FMO2	2327	hgsc.bcm.edu	37	1	171168585	171168585	+	Silent	SNP	A	A	G	rs2020861|rs386636736	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:171168585A>G	ENST00000209929.7	+	5	743	c.585A>G	c.(583-585)tcA>tcG	p.S195S	RP1-127D3.4_ENST00000445290.1_RNA|FMO2_ENST00000529935.1_Intron|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Silent_p.S195S			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.S195S(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGGGAAACTCAGGCTCAGATA	0.488													G|||	2951	0.589257	0.7209	0.6167	5008	,	,		19431	0.6032		0.3877	False		,,,				2504	0.5849				p.S195S		Atlas-SNP	.											FMO2,NS,carcinoma,0,2	FMO2	66	2	1	Substitution - coding silent(1)	stomach(1)	c.A585G						PASS	.	G		2951,1455	468.5+/-355.1	983,985,235	135.0	140.0	139.0		585	-12.3	0.0	1	dbSNP_98	139	3589,5011	627.2+/-397.9	765,2059,1476	no	coding-synonymous	FMO2	NM_001460.2		1748,3044,1711	GG,GA,AA		41.7326,33.0232,49.7155		195/472	171168585	6540,6466	2203	4300	6503	SO:0001819	synonymous_variant	2327	exon5			AAACTCAGGCTCA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.585A>G	1.37:g.171168585A>G		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	165	164	0.993939	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	37	CCDS1293.1																																																																																			A|0.536;G|0.464	0.464	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
ALPI	248	hgsc.bcm.edu	37	2	233322958	233322958	+	Silent	SNP	T	T	C	rs41265121	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:233322958T>C	ENST00000295463.3	+	9	1100	c.1023T>C	c.(1021-1023)ggT>ggC	p.G341G		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	341					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		ATCATGAGGGTGTGGCTTACC	0.662													T|||	490	0.0978435	0.1089	0.0764	5008	,	,		16877	0.1012		0.1093	False		,,,				2504	0.0828				p.G341G		Atlas-SNP	.											.	ALPI	64	.	0			c.T1023C						PASS	.	T		471,3935	221.7+/-238.7	29,413,1761	77.0	73.0	75.0		1023	0.2	0.0	2	dbSNP_127	75	740,7860	178.9+/-228.2	31,678,3591	no	coding-synonymous	ALPI	NM_001631.3		60,1091,5352	CC,CT,TT		8.6047,10.69,9.3111		341/529	233322958	1211,11795	2203	4300	6503	SO:0001819	synonymous_variant	248	exon9			TGAGGGTGTGGCT	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.1023T>C	2.37:g.233322958T>C		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	175	89	0.508571	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			T|0.910;C|0.090	0.090	strong		0.662	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32487229	32487229	+	Silent	SNP	C	C	T	rs148633289	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32487229C>T	ENST00000374975.3	-	3	632	c.570G>A	c.(568-570)ctG>ctA	p.L190L		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						GAACTGTTTCCAGCATCACCA	0.557													C|||	1286	0.256789	0.3495	0.2305	5008	,	,		13332	0.2232		0.2425	False		,,,				2504	0.1994				p.L190L		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	0			c.G570A						scavenged	.						60.0	66.0	64.0					6																	32487229		1865	3705	5570	SO:0001819	synonymous_variant	3127	exon3			TGTTTCCAGCATC		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.570G>A	6.37:g.32487229C>T		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	129	67	0.51938	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			C|0.781;T|0.219	0.219	strong		0.557	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
ZNF502	91392	hgsc.bcm.edu	37	3	44762830	44762830	+	Missense_Mutation	SNP	A	A	G	rs56084453	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:44762830A>G	ENST00000296091.4	+	4	777	c.521A>G	c.(520-522)cAg>cGg	p.Q174R	ZNF502_ENST00000449836.1_Missense_Mutation_p.Q174R|ZNF502_ENST00000436624.2_Missense_Mutation_p.Q174R	NM_001134440.1|NM_001282880.1|NM_033210.4	NP_001127912.1|NP_001269809.1|NP_149987.2	Q8TBZ5	ZN502_HUMAN	zinc finger protein 502	174			Q -> R (in dbSNP:rs56084453).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(4)|large_intestine(8)|lung(4)|prostate(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00855)|KIRC - Kidney renal clear cell carcinoma(197;0.0471)|Kidney(197;0.0589)		ACCCAACATCAGAGAACTCAT	0.408													A|||	531	0.10603	0.0129	0.1571	5008	,	,		21464	0.0446		0.2247	False		,,,				2504	0.137				p.Q174R		Atlas-SNP	.											ZNF502,NS,carcinoma,-1,1	ZNF502	58	1	0			c.A521G						scavenged	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	190,4216	119.6+/-157.3	5,180,2018	126.0	137.0	133.0		521,521,521,521	4.7	1.0	3	dbSNP_129	133	1862,6738	329.3+/-318.7	195,1472,2633	yes	missense,missense,missense,missense	ZNF502	NM_001134440.1,NM_001134441.1,NM_001134442.1,NM_033210.4	43,43,43,43	200,1652,4651	GG,GA,AA		21.6512,4.3123,15.7773	benign,benign,benign,benign	174/545,174/545,174/545,174/545	44762830	2052,10954	2203	4300	6503	SO:0001583	missense	91392	exon4			AACATCAGAGAAC	AK022577	CCDS2719.1	3p21.32	2013-01-08			ENSG00000196653	ENSG00000196653		"""Zinc fingers, C2H2-type"""	23718	protein-coding gene	gene with protein product							Standard	NM_033210		Approved	FLJ14855, FLJ12515	uc003cnt.3	Q8TBZ5	OTTHUMG00000133086	ENST00000296091.4:c.521A>G	3.37:g.44762830A>G	ENSP00000296091:p.Gln174Arg	Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	282	0.12912087912087913	10	0.02032520325203252	73	0.20165745856353592	29	0.050699300699300696	170	0.22427440633245382	A	15.35	2.807929	0.50421	0.043123	0.216512	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624;ENST00000427783	T;T;T	0.07327	3.2;3.2;3.2	4.7	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.16098	0.37	0.37027	P	0.103526	P	0.52463	0.953	P	0.47864	0.559	T	0.52305	-0.8593	8	0.54805	T	0.06	-5.6043	13.5531	0.61745	1.0:0.0:0.0:0.0	rs56084453;rs61740962	174	Q8TBZ5	ZN502_HUMAN	R	174	ENSP00000397390:Q174R;ENSP00000296091:Q174R;ENSP00000406469:Q174R	ENSP00000296091:Q174R	Q	+	2	0	ZNF502	44737834	0.049000	0.20398	0.972000	0.41901	0.997000	0.91878	0.860000	0.27871	2.109000	0.64355	0.533000	0.62120	CAG	A|0.848;G|0.152	0.152	strong		0.408	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629764	32629764	+	Missense_Mutation	SNP	C	C	T	rs1130398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629764C>T	ENST00000399082.3	-	2	415	c.371G>A	c.(370-372)aGc>aAc	p.S124N	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.S214N|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.S214N|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.S214N|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.S214N|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	214	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GGTGATGGGGCTCTGGAGGCT	0.537									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1981	0.395567	0.3154	0.5476	5008	,	,		17107	0.4782		0.3946	False		,,,				2504	0.3119				p.S214N	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G641A						PASS	.	T	ASN/SER	1305,3089		211,883,1103	54.0	59.0	57.0		641	1.6	0.9	6	dbSNP_86	57	3090,5502		594,1902,1800	yes	missense	HLA-DQB1	NM_002123.4	46	805,2785,2903	TT,TC,CC		35.9637,29.6996,33.8441	benign	214/262	32629764	4395,8591	2197	4296	6493	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	ATGGGGCTCTGGA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.371G>A	6.37:g.32629764C>T	ENSP00000382032:p.Ser124Asn	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		930	0.4258241758241758	152	0.3089430894308943	190	0.5248618784530387	283	0.49475524475524474	305	0.4023746701846966	.	5.911	0.352128	0.11182	0.296996	0.359637	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09	4.52	1.62	0.23740	.	0.726356	0.13327	N	0.396223	T	0.00784	0.0026	.	.	.	0.52099	P	5.999999999994898E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.45977	-0.9224	8	0.59425	D	0.04	.	3.5408	0.07811	0.0:0.4996:0.1955:0.3049	rs1130398;rs3189185;rs9273924;rs12722372;rs17412846;rs28724254;rs34909169	214;179;214;214	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	N	124;214;214;214;214	ENSP00000382032:S124N;ENSP00000382029:S214N;ENSP00000364080:S214N;ENSP00000407332:S214N;ENSP00000382034:S214N	ENSP00000364080:S214N	S	-	2	0	HLA-DQB1	32737742	0.000000	0.05858	0.933000	0.37362	0.413000	0.31143	-0.126000	0.10563	0.319000	0.23209	-0.642000	0.03964	AGC	T|0.416;C|0.584	0.416	strong		0.537	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
ATR	545	hgsc.bcm.edu	37	3	142178144	142178144	+	Missense_Mutation	SNP	C	C	T	rs2229032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142178144C>T	ENST00000350721.4	-	43	7395	c.7274G>A	c.(7273-7275)cGa>cAa	p.R2425Q	ATR_ENST00000383101.3_Missense_Mutation_p.R2361Q	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2425	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		R -> Q (in dbSNP:rs2229032). {ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R2425Q(1)		NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						GAGAAATTCTCGGAATACTTT	0.403								Other conserved DNA damage response genes					C|||	512	0.102236	0.0658	0.1037	5008	,	,		17089	0.1012		0.172	False		,,,				2504	0.0798				p.R2425Q		Atlas-SNP	.											ATR,NS,carcinoma,0,1	ATR	285	1	1	Substitution - Missense(1)	stomach(1)	c.G7274A						PASS	.	C	GLN/ARG	388,4018	193.6+/-218.7	17,354,1832	67.0	66.0	67.0		7274	-9.1	0.4	3	dbSNP_98	67	1357,7243	264.2+/-285.4	118,1121,3061	yes	missense	ATR	NM_001184.3	43	135,1475,4893	TT,TC,CC		15.7791,8.8062,13.4169	benign	2425/2645	142178144	1745,11261	2203	4300	6503	SO:0001583	missense	545	exon43			AATTCTCGGAATA	U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7274G>A	3.37:g.142178144C>T	ENSP00000343741:p.Arg2425Gln	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	103	55	0.533981	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	262	0.11996336996336997	27	0.054878048780487805	39	0.10773480662983426	64	0.11188811188811189	132	0.1741424802110818	C	11.32	1.602569	0.28534	0.088062	0.157791	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.76186	-1.0;-1.0	4.58	-9.12	0.00707	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.601425	0.15707	N	0.248596	T	0.00210	0.0006	N	0.16233	0.39	0.44995	P	0.0019900000000000473	B	0.02656	0.0	B	0.04013	0.001	T	0.03278	-1.1053	9	0.16420	T	0.52	0.6971	19.1019	0.93277	0.0:0.161:0.0:0.839	rs2229032;rs17698526;rs57742124;rs2229032	2425	Q13535	ATR_HUMAN	Q	2425;2361	ENSP00000343741:R2425Q;ENSP00000372581:R2361Q	ENSP00000343741:R2425Q	R	-	2	0	ATR	143660834	0.963000	0.33076	0.437000	0.26809	0.948000	0.59901	0.044000	0.13992	-2.531000	0.00491	-1.406000	0.01132	CGA	C|0.883;T|0.117	0.117	strong		0.403	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
BCL9L	283149	hgsc.bcm.edu	37	11	118769442	118769442	+	Silent	SNP	A	A	G	rs7104819	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118769442A>G	ENST00000334801.3	-	8	5146	c.4182T>C	c.(4180-4182)ccT>ccC	p.P1394P	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1394					canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		ACATCTGTCCAGGGTGGCACA	0.662													g|||	2224	0.444089	0.6906	0.5476	5008	,	,		16915	0.2927		0.4135	False		,,,				2504	0.2249				p.P1394P		Atlas-SNP	.											.	BCL9L	254	.	0			c.T4182C						PASS	.			2760,1636		870,1020,308	20.0	20.0	20.0		4182	-6.2	0.9	11	dbSNP_116	20	3547,5037		738,2071,1483	no	coding-synonymous	BCL9L	NM_182557.2		1608,3091,1791	GG,GA,AA		41.3211,37.2157,48.5901		1394/1500	118769442	6307,6673	2198	4292	6490	SO:0001819	synonymous_variant	283149	exon8			CTGTCCAGGGTGG	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.4182T>C	11.37:g.118769442A>G		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			A|0.524;G|0.476	0.476	strong		0.662	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
SLC25A51	92014	hgsc.bcm.edu	37	9	37888101	37888101	+	Silent	SNP	C	C	T	rs2296204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37888101C>T	ENST00000377716.2	-	3	1190	c.447G>A	c.(445-447)aaG>aaA	p.K149K	RP11-613M10.9_ENST00000540557.1_Intron|SLC25A51_ENST00000380590.3_Silent_p.K149K|SLC25A51_ENST00000496760.1_Intron|SLC25A51_ENST00000242275.6_Silent_p.K149K			Q9H1U9	S2551_HUMAN	solute carrier family 25, member 51	149					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											TGTCATGATGCTTGTGGTCTT	0.468													C|||	1024	0.204473	0.0809	0.2536	5008	,	,		22501	0.3393		0.1501	False		,,,				2504	0.2536				p.K149K		Atlas-SNP	.											.	.	.	.	0			c.G447A						PASS	.	C		440,3966		21,398,1784	167.0	152.0	157.0		447	3.9	1.0	9	dbSNP_100	157	1321,7279		98,1125,3077	no	coding-synonymous	MCART1	NM_033412.3		119,1523,4861	TT,TC,CC		15.3605,9.9864,13.5399		149/298	37888101	1761,11245	2203	4300	6503	SO:0001819	synonymous_variant	92014	exon3			ATGATGCTTGTGG	BC008500	CCDS6614.1	9p13.3-p12	2013-05-22	2012-03-29	2012-03-29	ENSG00000122696	ENSG00000122696		"""Solute carriers"""	23323	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 1"""	MCART1		12477932	Standard	NM_033412		Approved	MGC14836, CG7943	uc004aav.2	Q9H1U9	OTTHUMG00000019935	ENST00000377716.2:c.447G>A	9.37:g.37888101C>T		Somatic	239	1	0.0041841		WXS	Illumina HiSeq	Phase_I	211	104	0.492891	NM_033412		Silent	SNP	ENST00000377716.2	37	CCDS6614.1																																																																																			C|0.847;T|0.153	0.153	strong		0.468	SLC25A51-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313746.1	NM_033412	
TMEM108	66000	hgsc.bcm.edu	37	3	133099245	133099245	+	Silent	SNP	G	G	A	rs1197314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:133099245G>A	ENST00000321871.6	+	4	900	c.690G>A	c.(688-690)ccG>ccA	p.P230P	TMEM108_ENST00000393130.3_Silent_p.P230P|TMEM108_ENST00000515826.1_Silent_p.P230P|TMEM108_ENST00000508711.1_Intron	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	230						integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						CTGTGGAACCGGAGCCCTCTA	0.597													A|||	1904	0.380192	0.2587	0.4856	5008	,	,		16181	0.3909		0.4473	False		,,,				2504	0.3896				p.P230P		Atlas-SNP	.											.	TMEM108	67	.	0			c.G690A						PASS	.	A	,	1318,3088	696.6+/-406.1	194,930,1079	43.0	46.0	45.0		690,690	-0.1	0.0	3	dbSNP_87	45	3718,4882	618.2+/-396.8	794,2130,1376	yes	coding-synonymous,coding-synonymous	TMEM108	NM_001136469.1,NM_023943.2	,	988,3060,2455	AA,AG,GG		43.2326,29.9138,38.7206	,	230/576,230/576	133099245	5036,7970	2203	4300	6503	SO:0001819	synonymous_variant	66000	exon4			GGAACCGGAGCCC	AL136578	CCDS33858.1, CCDS75012.1	3q22.1	2014-04-07			ENSG00000144868	ENSG00000144868			28451	protein-coding gene	gene with protein product	"""cancer/testis antigen 124"""					11214970	Standard	XM_005247726		Approved	MGC3040, CT124	uc003epi.3	Q6UXF1	OTTHUMG00000159685	ENST00000321871.6:c.690G>A	3.37:g.133099245G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	128	74	0.578125	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Silent	SNP	ENST00000321871.6	37	CCDS33858.1																																																																																			G|0.616;A|0.384	0.384	strong		0.597	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943	
PCYOX1	51449	hgsc.bcm.edu	37	2	70488470	70488470	+	Missense_Mutation	SNP	C	C	T	rs2706762	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:70488470C>T	ENST00000433351.2	+	3	474	c.446C>T	c.(445-447)tCc>tTc	p.S149F	PCYOX1_ENST00000264441.5_Missense_Mutation_p.S149F|PCYOX1_ENST00000545138.1_Missense_Mutation_p.S71F|PCYOX1_ENST00000505044.2_Missense_Mutation_p.S72F	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	149			S -> F (in dbSNP:rs2706762). {ECO:0000269|PubMed:10048485}.		prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						GGATTTCAATCCCTCCGTATG	0.373													C|||	261	0.0521166	0.0083	0.0749	5008	,	,		19929	0.0		0.1362	False		,,,				2504	0.0624				p.S149F		Atlas-SNP	.											.	PCYOX1	34	.	0			c.C446T						PASS	.	C	PHE/SER	138,4268	97.1+/-135.8	6,126,2071	189.0	173.0	178.0		446	4.6	1.0	2	dbSNP_100	178	1309,7291	259.8+/-282.9	95,1119,3086	yes	missense	PCYOX1	NM_016297.3	155	101,1245,5157	TT,TC,CC		15.2209,3.1321,11.1256	benign	149/506	70488470	1447,11559	2203	4300	6503	SO:0001583	missense	51449	exon3			TTCAATCCCTCCG	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.446C>T	2.37:g.70488470C>T	ENSP00000387654:p.Ser149Phe	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	152	84	0.552632	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Missense_Mutation	SNP	ENST00000433351.2	37	CCDS1902.1	139	0.06364468864468864	7	0.014227642276422764	29	0.08011049723756906	0	0.0	103	0.1358839050131926	C	2.209	-0.381192	0.05000	0.031321	0.152209	ENSG00000116005	ENST00000422380;ENST00000505044;ENST00000414812;ENST00000433351;ENST00000264441;ENST00000451279;ENST00000545138	T;T;T;T;T;T;T	0.14391	2.51;2.87;2.51;2.87;2.87;2.51;2.87	5.53	4.58	0.56647	Prenylcysteine lyase (1);	0.294882	0.42420	N	0.000702	T	0.00039	0.0001	N	0.02158	-0.66	0.30738	P	0.7464919999999999	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.36578	-0.9742	9	0.09338	T	0.73	-2.2309	6.6505	0.22959	0.0:0.7307:0.0:0.2693	rs2706762;rs17500206;rs52827540;rs56507972;rs57406768;rs2706762	131;149	B7Z8A2;Q9UHG3	.;PCYOX_HUMAN	F	72;72;72;149;149;72;71	ENSP00000404327:S72F;ENSP00000441566:S72F;ENSP00000413178:S72F;ENSP00000387654:S149F;ENSP00000264441:S149F;ENSP00000408751:S72F;ENSP00000439916:S71F	ENSP00000264441:S149F	S	+	2	0	PCYOX1	70341974	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	2.746000	0.47467	1.448000	0.47680	0.655000	0.94253	TCC	C|0.912;T|0.088	0.088	strong		0.373	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297	
BTN3A1	11119	hgsc.bcm.edu	37	6	26413744	26413744	+	Missense_Mutation	SNP	C	C	A	rs4712990	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26413744C>A	ENST00000289361.6	+	10	1734	c.1366C>A	c.(1366-1368)Ccc>Acc	p.P456T	BTN3A1_ENST00000414912.2_Missense_Mutation_p.P404T	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	456	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		P -> T (in dbSNP:rs4712990). {ECO:0000269|PubMed:15489334}.		activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						ACTTCCTAAGCCCCCTAAGAA	0.468													C|||	530	0.105831	0.1089	0.1455	5008	,	,		19003	0.0288		0.1163	False		,,,				2504	0.1421				p.P456T		Atlas-SNP	.											.	BTN3A1	80	.	0			c.C1366A						PASS	.	C	THR/PRO,,THR/PRO,	560,3846		31,498,1674	129.0	129.0	129.0		1210,,1366,	1.4	0.0	6	dbSNP_111	129	1048,7552		70,908,3322	yes	missense,utr-3,missense,utr-3	BTN3A1	NM_001145008.1,NM_001145009.1,NM_007048.5,NM_194441.2	38,,38,	101,1406,4996	AA,AC,CC		12.186,12.7099,12.3635	benign,,benign,	404/462,,456/514,	26413744	1608,11398	2203	4300	6503	SO:0001583	missense	11119	exon10			CCTAAGCCCCCTA	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.1366C>A	6.37:g.26413744C>A	ENSP00000289361:p.Pro456Thr	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Missense_Mutation	SNP	ENST00000289361.6	37	CCDS4608.1	220	0.10073260073260074	64	0.13008130081300814	55	0.15193370165745856	12	0.02097902097902098	89	0.11741424802110818	.	7.732	0.699391	0.15106	0.127099	0.12186	ENSG00000026950	ENST00000289361;ENST00000414912	T;T	0.68624	-0.34;-0.34	2.31	1.4	0.22301	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.57359	0.2048	M	0.81239	2.535	0.80722	P	0.0	P;P	0.48016	0.631;0.904	B;P	0.48598	0.406;0.583	T	0.54456	-0.8291	8	0.52906	T	0.07	.	6.8441	0.23979	0.0:0.7198:0.0:0.2802	rs4712990;rs17538334;rs58345406;rs4712990	404;456	E9PGB4;O00481	.;BT3A1_HUMAN	T	456;404	ENSP00000289361:P456T;ENSP00000406667:P404T	ENSP00000289361:P456T	P	+	1	0	BTN3A1	26521723	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-1.345000	0.02637	0.087000	0.17167	-0.921000	0.02739	CCC	C|0.883;A|0.117	0.117	strong		0.468	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
ATAD5	79915	hgsc.bcm.edu	37	17	29205072	29205072	+	Missense_Mutation	SNP	T	T	C	rs61745366	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:29205072T>C	ENST00000321990.4	+	17	4348	c.3970T>C	c.(3970-3972)Ttc>Ctc	p.F1324L		NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1324					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)				AATCAAAACATTCATGGCAAC	0.303													T|||	307	0.0613019	0.1974	0.0231	5008	,	,		15840	0.0		0.007	False		,,,				2504	0.0235				p.F1324L		Atlas-SNP	.											.	ATAD5	150	.	0			c.T3970C						PASS	.	T	LEU/PHE	765,3641	309.4+/-291.0	68,629,1506	121.0	134.0	130.0		3970	5.0	1.0	17	dbSNP_129	130	52,8542	32.3+/-84.9	0,52,4245	yes	missense	ATAD5	NM_024857.3	22	68,681,5751	CC,CT,TT		0.6051,17.3627,6.2846	possibly-damaging	1324/1845	29205072	817,12183	2203	4297	6500	SO:0001583	missense	79915	exon17			AAAACATTCATGG		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.3970T>C	17.37:g.29205072T>C	ENSP00000313171:p.Phe1324Leu	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	168	83	0.494048	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	111	0.050824175824175824	97	0.19715447154471544	9	0.024861878453038673	0	0.0	5	0.006596306068601583	T	21.5	4.156935	0.78114	0.173627	0.006051	ENSG00000176208	ENST00000321990	T	0.14022	2.54	5.0	5.0	0.66597	ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	N	0.16862	0.45	0.09310	P	0.99999051178	D	0.58620	0.983	P	0.59761	0.863	T	0.04153	-1.0973	9	0.02654	T	1	.	14.7379	0.69430	0.0:0.0:0.0:1.0	rs61745366	1324	Q96QE3	ATAD5_HUMAN	L	1324	ENSP00000313171:F1324L	ENSP00000313171:F1324L	F	+	1	0	ATAD5	26229198	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.272000	0.78516	1.879000	0.54435	0.397000	0.26171	TTC	T|0.943;C|0.057	0.057	strong		0.303	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
PADI4	23569	hgsc.bcm.edu	37	1	17668609	17668609	+	Missense_Mutation	SNP	C	C	T	rs1748020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17668609C>T	ENST00000375448.4	+	7	850	c.824C>T	c.(823-825)tCc>tTc	p.S275F	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	275			S -> F (in dbSNP:rs1748020). {ECO:0000269|PubMed:15087120}.		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)	CTGGACACGTCCAACCTGGTA	0.647													C|||	256	0.0511182	0.1135	0.0274	5008	,	,		16929	0.001		0.0577	False		,,,				2504	0.0286				p.S275F		Atlas-SNP	.											.	PADI4	70	.	0			c.C824T						PASS	.	C	PHE/SER	456,3950	217.1+/-235.6	26,404,1773	64.0	63.0	63.0		824	4.6	0.5	1	dbSNP_89	63	456,8144	134.9+/-192.2	16,424,3860	yes	missense	PADI4	NM_012387.2	155	42,828,5633	TT,TC,CC		5.3023,10.3495,7.0121	benign	275/664	17668609	912,12094	2203	4300	6503	SO:0001583	missense	23569	exon7			ACACGTCCAACCT	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.824C>T	1.37:g.17668609C>T	ENSP00000364597:p.Ser275Phe	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	116	105	0.905172	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	37	CCDS180.1	120	0.054945054945054944	63	0.12804878048780488	12	0.03314917127071823	0	0.0	45	0.059366754617414245	c	12.60	1.985170	0.35036	0.103495	0.053023	ENSG00000159339	ENST00000375448	T	0.14640	2.49	4.63	4.63	0.57726	Protein-arginine deiminase (PAD), central domain (1);	0.600161	0.18074	N	0.152512	T	0.00271	0.0008	M	0.73962	2.25	0.80722	P	0.0	P;P	0.48911	0.917;0.917	P;P	0.49226	0.603;0.603	T	0.04153	-1.0973	9	0.59425	D	0.04	-28.0689	13.4078	0.60924	0.0:1.0:0.0:0.0	rs1748020;rs52822621;rs61531826;rs1748020	275;275	A8K392;Q9UM07	.;PADI4_HUMAN	F	275	ENSP00000364597:S275F	ENSP00000364597:S275F	S	+	2	0	PADI4	17541196	0.000000	0.05858	0.496000	0.27539	0.137000	0.21094	0.358000	0.20216	2.290000	0.77057	0.555000	0.69702	TCC	C|0.939;T|0.061	0.061	strong		0.647	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
C19orf40	91442	hgsc.bcm.edu	37	19	33467515	33467515	+	Missense_Mutation	SNP	T	T	C	rs3816032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33467515T>C	ENST00000588258.1	+	5	685	c.575T>C	c.(574-576)aTt>aCt	p.I192T	C19orf40_ENST00000589646.1_Missense_Mutation_p.I97T|C19orf40_ENST00000590179.1_Missense_Mutation_p.I97T|C19orf40_ENST00000590281.1_Missense_Mutation_p.I192T	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	192	RuvA domain 2-like.		I -> T (in dbSNP:rs3816032).		DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					AATGCTTCCATTGGGGAACTG	0.562								Direct reversal of damage			OREG0025408	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	t|||	950	0.189696	0.0809	0.1297	5008	,	,		18717	0.3403		0.1074	False		,,,				2504	0.3088				p.I192T		Atlas-SNP	.											.	C19orf40	21	.	0			c.T575C						PASS	.	T	THR/ILE	366,4040	186.0+/-213.0	19,328,1856	127.0	114.0	118.0		575	3.2	0.0	19	dbSNP_107	118	1025,7575	218.4+/-256.8	41,943,3316	yes	missense	C19orf40	NM_152266.3	89	60,1271,5172	CC,CT,TT		11.9186,8.3069,10.6951	benign	192/216	33467515	1391,11615	2203	4300	6503	SO:0001583	missense	91442	exon5			CTTCCATTGGGGA	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 24kDa"""	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.575T>C	19.37:g.33467515T>C	ENSP00000466121:p.Ile192Thr	Somatic	101	0	0	840	WXS	Illumina HiSeq	Phase_I	132	67	0.507576	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Missense_Mutation	SNP	ENST00000588258.1	37	CCDS12426.1	352	0.16117216117216118	47	0.09552845528455285	51	0.1408839779005525	182	0.3181818181818182	72	0.09498680738786279	T	4.075	0.011771	0.07912	0.083069	0.119186	ENSG00000131944	ENST00000254262	.	.	.	5.35	3.21	0.36854	RuvA domain 2-like (1);	0.757763	0.13249	N	0.402217	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.09022	0.002	B	0.12837	0.008	T	0.28808	-1.0032	8	0.13108	T	0.6	0.3587	10.0263	0.42074	0.0:0.1423:0.0:0.8577	rs3816032;rs52824509;rs60534510;rs3816032	192	Q9BTP7	FAP24_HUMAN	T	192	.	ENSP00000254262:I192T	I	+	2	0	C19orf40	38159355	0.002000	0.14202	0.001000	0.08648	0.007000	0.05969	1.380000	0.34351	0.383000	0.24910	0.472000	0.43445	ATT	C|0.146;N|0.000	0.146	strong		0.562	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266	
MYRF	745	hgsc.bcm.edu	37	11	61539020	61539020	+	Silent	SNP	C	C	G	rs149803	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:61539020C>G	ENST00000278836.5	+	6	885	c.789C>G	c.(787-789)ccC>ccG	p.P263P	MYRF_ENST00000265460.5_Silent_p.P254P|MYRF_ENST00000327797.1_5'Flank|TMEM258_ENST00000535042.1_Intron	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	263	Pro-rich.				central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)										AATCCCCCCCCAGCACCCTCA	0.637													c|||	457	0.091254	0.0189	0.1657	5008	,	,		16030	0.002		0.2793	False		,,,				2504	0.0348				p.P263P		Atlas-SNP	.											.	.	.	.	0			c.C789G						PASS	.		,	250,4154	141.9+/-177.2	7,236,1959	80.0	90.0	86.0		789,762	4.4	1.0	11	dbSNP_79	86	2337,6261	387.9+/-342.4	333,1671,2295	no	coding-synonymous,coding-synonymous	C11orf9	NM_001127392.1,NM_013279.2	,	340,1907,4254	GG,GC,CC		27.1807,5.6767,19.8969	,	263/1152,254/1112	61539020	2587,10415	2202	4299	6501	SO:0001819	synonymous_variant	745	exon6			CCCCCCCAGCACC		CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.789C>G	11.37:g.61539020C>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	106	45	0.424528	NM_001127392	O43582|Q9P1Q6	Silent	SNP	ENST00000278836.5	37	CCDS44622.1																																																																																			C|0.825;G|0.175	0.175	strong		0.637	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
CFAP69	79846	hgsc.bcm.edu	37	7	89938680	89938680	+	Splice_Site	SNP	C	C	T	rs1134956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:89938680C>T	ENST00000389297.4	+	22	2905	c.2654C>T	c.(2653-2655)aCg>aTg	p.T885M	C7orf63_ENST00000497910.1_Splice_Site_p.T867M|C7orf63_ENST00000316089.8_Splice_Site_p.T839M	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		885			T -> M (in dbSNP:rs17865475). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CTTAACACAACGGTAAGATTC	0.323													C|||	1906	0.380591	0.2859	0.3991	5008	,	,		13101	0.2024		0.5577	False		,,,				2504	0.4969				p.T885M		Atlas-SNP	.											C7orf63_ENST00000389297,NS,carcinoma,+1,2	C7orf63	158	2	0			c.C2654T						PASS	.	C	MET/THR,MET/THR	1255,2367		217,821,773	101.0	95.0	97.0		2654,2600	5.5	1.0	7	dbSNP_86	97	4661,3489		1333,1995,747	yes	missense-near-splice,missense-near-splice	C7orf63	NM_001039706.2,NM_001160138.1	81,81	1550,2816,1520	TT,TC,CC		42.8098,34.6494,49.7452	probably-damaging,probably-damaging	885/942,867/924	89938680	5916,5856	1811	4075	5886	SO:0001630	splice_region_variant	79846	exon22			ACACAACGGTAAG																												ENST00000389297.4:c.2655+1C>T	7.37:g.89938680C>T		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	181	180	0.994475	NM_001039706	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	827	0.37866300366300365	144	0.2926829268292683	149	0.4116022099447514	104	0.18181818181818182	430	0.5672823218997362	C	21.5	4.163953	0.78226	0.346494	0.571902	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910;ENST00000449577	T;T;T;T	0.55234	1.49;0.91;1.55;0.53	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.78049	2.395	0.19945	P	0.9999490445	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.50180	-0.8858	9	0.72032	D	0.01	-10.4472	19.4207	0.94720	0.0:1.0:0.0:0.0	rs1134956;rs3178794;rs3197363;rs3208949;rs11544789;rs11563317;rs17689090;rs59337484;rs3178794	867;885	A5D8W1-5;A5D8W1	.;CG063_HUMAN	M	885;839;867;422	ENSP00000373948:T885M;ENSP00000321753:T839M;ENSP00000419549:T867M;ENSP00000391571:T422M	ENSP00000321753:T839M	T	+	2	0	C7orf63	89776616	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.335000	0.59298	2.601000	0.87937	0.585000	0.79938	ACG	C|0.596;N|0.000;T|0.404	0.404	strong		0.323	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		Missense_Mutation
OR10AD1	121275	hgsc.bcm.edu	37	12	48596484	48596484	+	Missense_Mutation	SNP	A	A	T	rs75413005	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48596484A>T	ENST00000310248.2	-	1	686	c.592T>A	c.(592-594)Tgg>Agg	p.W198R		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	198						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						AAGATTGCCCACAGACTAAAC	0.537													T|||	213	0.0425319	0.059	0.036	5008	,	,		20275	0.006		0.0924	False		,,,				2504	0.0112				p.W198R		Atlas-SNP	.											.	OR10AD1	24	.	0			c.T592A						PASS	.	T	ARG/TRP	275,4131	801.1+/-415.6	8,259,1936	61.0	50.0	54.0		592	2.3	0.0	12	dbSNP_131	54	764,7836	784.7+/-407.6	30,704,3566	yes	missense	OR10AD1	NM_001004134.1	101	38,963,5502	TT,TA,AA		8.8837,6.2415,7.9886	benign	198/318	48596484	1039,11967	2203	4300	6503	SO:0001583	missense	121275	exon1			TTGCCCACAGACT		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.592T>A	12.37:g.48596484A>T	ENSP00000308689:p.Trp198Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	99	0.04532967032967033	21	0.042682926829268296	9	0.024861878453038673	3	0.005244755244755245	66	0.0870712401055409	T	1.186	-0.636810	0.03557	0.062415	0.088837	ENSG00000172640	ENST00000310248	T	0.00058	8.79	4.77	2.31	0.28768	GPCR, rhodopsin-like superfamily (1);	1.397220	0.05124	N	0.491221	T	0.00012	0.0000	N	0.02286	-0.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	10	0.41790	T	0.15	1.3149	2.6005	0.04865	0.1486:0.0845:0.1548:0.6121	.	198	Q8NGE0	O10AD_HUMAN	R	198	ENSP00000308689:W198R	ENSP00000308689:W198R	W	-	1	0	OR10AD1	46882751	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-0.220000	0.09215	0.070000	0.16634	-0.448000	0.05591	TGG	A|0.934;T|0.066	0.066	strong		0.537	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
PDGFD	80310	hgsc.bcm.edu	37	11	103780455	103780455	+	Silent	SNP	A	A	G	rs10791649	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:103780455A>G	ENST00000393158.2	-	7	1259	c.1080T>C	c.(1078-1080)tgT>tgC	p.C360C	PDGFD_ENST00000302251.5_Silent_p.C354C			Q9GZP0	PDGFD_HUMAN	platelet derived growth factor D	360					cellular response to amino acid stimulus (GO:0071230)|multicellular organismal development (GO:0007275)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell division (GO:0051781)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				biliary_tract(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|prostate(3)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(157;0.000994)|all_hematologic(158;0.0017)|Melanoma(852;0.0563)|all_neural(303;0.165)		BRCA - Breast invasive adenocarcinoma(274;0.00136)|Epithelial(105;0.111)		AGATACAATCACATCGTTCAT	0.453													G|||	2311	0.461462	0.5106	0.3487	5008	,	,		22084	0.4603		0.4523	False		,,,				2504	0.4857				p.C360C		Atlas-SNP	.											.	PDGFD	125	.	0			c.T1080C						PASS	.	G	,	2120,2284	600.3+/-389.5	509,1102,591	324.0	263.0	284.0		1080,1062	-5.4	0.3	11	dbSNP_120	284	4117,4481	591.2+/-392.8	999,2119,1181	no	coding-synonymous,coding-synonymous	PDGFD	NM_025208.4,NM_033135.3	,	1508,3221,1772	GG,GA,AA		47.8832,48.1381,47.9695	,	360/371,354/365	103780455	6237,6765	2202	4299	6501	SO:0001819	synonymous_variant	80310	exon7			ACAATCACATCGT	AF113216	CCDS8326.1, CCDS41703.1	11q22.3	2008-02-05			ENSG00000170962	ENSG00000170962			30620	protein-coding gene	gene with protein product	"""spinal cord derived growth factor B"""	609673				11162582, 11980634	Standard	NM_033135		Approved	SCDGF-B, MSTP036, IEGF	uc001phq.3	Q9GZP0	OTTHUMG00000165953	ENST00000393158.2:c.1080T>C	11.37:g.103780455A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	117	48	0.410256	NM_025208	A8K9T6|Q9BWV5	Silent	SNP	ENST00000393158.2	37	CCDS41703.1																																																																																			A|0.527;G|0.473	0.473	strong		0.453	PDGFD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387231.2	NM_025208	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491840	110491840	+	Missense_Mutation	SNP	C	C	G	rs1783147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110491840C>G	ENST00000378402.5	+	54	9254	c.9150C>G	c.(9148-9150)caC>caG	p.H3050Q		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3050	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.		H -> Q (in dbSNP:rs1783147).		immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CTGTACCTCACCCAGGGGCAA	0.343										HNSCC(38;0.096)			C|||	2132	0.425719	0.382	0.5202	5008	,	,		20404	0.3284		0.337	False		,,,				2504	0.6094				p.H3050Q		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.C9150G						PASS	.	C	GLN/HIS	1380,2312		286,808,752	102.0	91.0	94.0		9150	-3.4	0.1	8	dbSNP_89	94	2940,5224		558,1824,1700	yes	missense	PKHD1L1	NM_177531.4	24	844,2632,2452	GG,GC,CC		36.0118,37.3781,36.4372	benign	3050/4244	110491840	4320,7536	1846	4082	5928	SO:0001583	missense	93035	exon54			ACCTCACCCAGGG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9150C>G	8.37:g.110491840C>G	ENSP00000367655:p.His3050Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	800	0.3663003663003663	171	0.3475609756097561	178	0.49171270718232046	195	0.3409090909090909	256	0.33773087071240104	C	3.578	-0.086257	0.07097	0.373781	0.360118	ENSG00000205038	ENST00000378402	D	0.87887	-2.31	5.88	-3.42	0.04825	G8 domain (2);	1.091090	0.06978	N	0.819430	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.15925	-1.0420	9	0.06625	T	0.88	.	1.9072	0.03279	0.1153:0.2046:0.2997:0.3804	rs1783147;rs17447503;rs52824856;rs58215772;rs1783147	3050	Q86WI1	PKHL1_HUMAN	Q	3050	ENSP00000367655:H3050Q	ENSP00000367655:H3050Q	H	+	3	2	PKHD1L1	110561016	0.121000	0.22262	0.067000	0.19924	0.989000	0.77384	0.097000	0.15168	-0.330000	0.08514	0.655000	0.94253	CAC	C|0.626;G|0.374	0.374	strong		0.343	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
ZNF273	10793	hgsc.bcm.edu	37	7	64389067	64389067	+	Missense_Mutation	SNP	G	G	A	rs1830080	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:64389067G>A	ENST00000476120.1	+	4	1432	c.1361G>A	c.(1360-1362)gGa>gAa	p.G454E	ZNF273_ENST00000527278.1_3'UTR|ZNF273_ENST00000319636.5_Missense_Mutation_p.G389E	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	454			G -> E (in dbSNP:rs1830080).		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)				ATTCATACTGGAGCAAAACCT	0.353													G|||	249	0.0497204	0.0212	0.0677	5008	,	,		21008	0.0962		0.0457	False		,,,				2504	0.0317				p.G454E	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.G1361A						PASS	.	G	GLU/GLY	147,4259		1,145,2057	33.0	36.0	35.0		1361	-0.1	0.8	7	dbSNP_92	35	351,8247		8,335,3956	no	missense	ZNF273	NM_021148.2	98	9,480,6013	AA,AG,GG		4.0823,3.3364,3.8296	possibly-damaging	454/570	64389067	498,12506	2203	4299	6502	SO:0001583	missense	10793	exon4			ATACTGGAGCAAA	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.1361G>A	7.37:g.64389067G>A	ENSP00000418719:p.Gly454Glu	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	20	9	0.45	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	117	0.05357142857142857	8	0.016260162601626018	26	0.0718232044198895	51	0.08916083916083917	32	0.04221635883905013	.	16.07	3.018871	0.54576	0.033364	0.040823	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.01599	4.74;4.74	1.16	-0.143	0.13444	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00144	0.0004	L	0.28556	0.865	0.37557	P	0.08106599999999997	P	0.40602	0.723	P	0.52957	0.714	T	0.49031	-0.8981	8	0.52906	T	0.07	.	4.2088	0.10502	0.5066:0.0:0.4934:0.0	rs1830080;rs1830080	454	Q14593	ZN273_HUMAN	E	454;389	ENSP00000418719:G454E;ENSP00000324518:G389E	ENSP00000324518:G389E	G	+	2	0	ZNF273	64026502	0.942000	0.31987	0.759000	0.31340	0.758000	0.43043	1.268000	0.33062	0.202000	0.20498	0.205000	0.17691	GGA	G|0.953;A|0.047	0.047	strong		0.353	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1		
ALG8	79053	hgsc.bcm.edu	37	11	77815059	77815059	+	Missense_Mutation	SNP	A	A	G	rs17825668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:77815059A>G	ENST00000299626.5	-	12	1387	c.1316T>C	c.(1315-1317)aTa>aCa	p.I439T	ALG8_ENST00000376156.3_Missense_Mutation_p.I439T|ALG8_ENST00000532552.2_5'UTR	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	439			I -> T (in dbSNP:rs17825668).		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|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)	alpha-1,3-mannosyltransferase activity (GO:0000033)			NS(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	30	all_cancers(14;3.62e-19)|all_epithelial(13;1.27e-21)|Breast(9;8.51e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;9.66e-25)			AATACTATATATGGTGAATAG	0.274													A|||	48	0.00958466	0.0008	0.0144	5008	,	,		15928	0.0		0.0348	False		,,,				2504	0.002				p.I439T		Atlas-SNP	.											.	ALG8	54	.	0			c.T1316C						PASS	.	A	THR/ILE,THR/ILE	21,4311		0,21,2145	26.0	30.0	29.0		1316,1316	3.3	1.0	11	dbSNP_123	29	311,8193		7,297,3948	yes	missense,missense	ALG8	NM_001007027.2,NM_024079.4	89,89	7,318,6093	GG,GA,AA		3.6571,0.4848,2.5865	benign,benign	439/468,439/527	77815059	332,12504	2166	4252	6418	SO:0001583	missense	79053	exon12			CTATATATGGTGA	AJ224875	CCDS8258.1, CCDS41692.1	11q14.1	2013-03-01	2013-03-01		ENSG00000159063	ENSG00000159063	2.4.1.265		23161	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Glc(1)Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	608103	"""asparagine-linked glycosylation 8 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 8, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""				Standard	XM_005274247		Approved	MGC2840	uc001oza.1	Q9BVK2	OTTHUMG00000166594	ENST00000299626.5:c.1316T>C	11.37:g.77815059A>G	ENSP00000299626:p.Ile439Thr	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	79	44	0.556962	NM_024079	A6NDW6|O60860	Missense_Mutation	SNP	ENST00000299626.5	37	CCDS8258.1	28|28	0.01282051282051282|0.01282051282051282	1|1	0.0020325203252032522|0.0020325203252032522	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	22|22	0.029023746701846966|0.029023746701846966	A|A	15.92|15.92	2.975229|2.975229	0.53720|0.53720	0.004848|0.004848	0.036571|0.036571	ENSG00000159063|ENSG00000159063	ENST00000299626;ENST00000526849;ENST00000376156|ENST00000530608;ENST00000532306	D;D;D|.	0.85773|.	-2.03;-2.03;-2.03|.	5.66|5.66	3.3|3.3	0.37823|0.37823	.|.	0.383865|.	0.29551|.	N|.	0.011838|.	T|T	0.13114|0.13114	0.0318|0.0318	L|L	0.46947|0.46947	1.48|1.48	0.23282|0.23282	N|N	0.997981|0.997981	B;B;P|.	0.34615|.	0.013;0.083;0.459|.	B;B;B|.	0.37198|.	0.043;0.219;0.243|.	T|T	0.06144|0.06144	-1.0843|-1.0843	10|5	0.33940|.	T|.	0.23|.	-2.872|-2.872	9.5721|9.5721	0.39433|0.39433	0.8521:0.0:0.1479:0.0|0.8521:0.0:0.1479:0.0	rs17825668;rs52795646;rs17825668|rs17825668;rs52795646;rs17825668	439;439;439|.	B3KQL8;Q9BVK2;A6NDW6|.	.;ALG8_HUMAN;.|.	T|H	439;110;439|141;226	ENSP00000299626:I439T;ENSP00000434388:I110T;ENSP00000365326:I439T|.	ENSP00000299626:I439T|.	I|Y	-|-	2|1	0|0	ALG8|ALG8	77492707|77492707	0.444000|0.444000	0.25649|0.25649	0.995000|0.995000	0.50966|0.50966	0.836000|0.836000	0.47400|0.47400	2.569000|2.569000	0.45973|0.45973	0.399000|0.399000	0.25367|0.25367	0.533000|0.533000	0.62120|0.62120	ATA|TAT	A|0.977;G|0.023	0.023	strong		0.274	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079	
TUBA3E	112714	hgsc.bcm.edu	37	2	130952718	130952718	+	Silent	SNP	G	G	A	rs3853852	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130952718G>A	ENST00000312988.7	-	3	409	c.309C>T	c.(307-309)taC>taT	p.Y103Y		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	103					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					GGCCCCTGGCGTAATTACTGG	0.527													.|||	2070	0.413339	0.3646	0.4827	5008	,	,		19312	0.4425		0.3698	False		,,,				2504	0.4448				p.Y103Y		Atlas-SNP	.											.	TUBA3E	73	.	0			c.C309T						PASS	.						78.0	126.0	110.0					2																	130952718		2202	4297	6499	SO:0001819	synonymous_variant	112714	exon3			CCTGGCGTAATTA	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.309C>T	2.37:g.130952718G>A		Somatic	306	0	0		WXS	Illumina HiSeq	Phase_I	267	82	0.307116	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			G|0.637;A|0.363	0.363	strong		0.527	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
RHBDL2	54933	hgsc.bcm.edu	37	1	39352271	39352271	+	Missense_Mutation	SNP	G	G	T	rs2147914	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:39352271G>T	ENST00000289248.2	-	8	1825	c.817C>A	c.(817-819)Ctg>Atg	p.L273M	RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000538156.1_Missense_Mutation_p.L340M|RHBDL2_ENST00000372985.3_Missense_Mutation_p.L353M|RHBDL2_ENST00000372990.1_Missense_Mutation_p.L273M			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	273			L -> M (in dbSNP:rs2147914).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			GGATCTTTCAGCAGTGCTTTA	0.428													G|||	1555	0.310503	0.1452	0.4798	5008	,	,		19848	0.2718		0.4513	False		,,,				2504	0.3088				p.L273M		Atlas-SNP	.											RHBDL2,bladder,carcinoma,+2,1	RHBDL2	28	1	0			c.C817A						scavenged	.	G	MET/LEU	827,3579	328.0+/-300.3	81,665,1457	126.0	118.0	121.0		817	6.0	1.0	1	dbSNP_96	121	3915,4685	546.8+/-385.0	881,2153,1266	yes	missense	RHBDL2	NM_017821.3	15	962,2818,2723	TT,TG,GG		45.5233,18.7699,36.4601	probably-damaging	273/304	39352271	4742,8264	2203	4300	6503	SO:0001583	missense	54933	exon8			CTTTCAGCAGTGC	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"""rhomboid (veinlet, Drosophila)-like 2"""				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.817C>A	1.37:g.39352271G>T	ENSP00000289248:p.Leu273Met	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	82	6	0.0731707	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Missense_Mutation	SNP	ENST00000289248.2	37	CCDS30680.1	754	0.34523809523809523	74	0.15040650406504066	170	0.4696132596685083	168	0.2937062937062937	342	0.45118733509234826	G	19.75	3.885071	0.72410	0.187699	0.455233	ENSG00000158315	ENST00000372990;ENST00000289248;ENST00000538156;ENST00000372985	T;T;T;T	0.34667	1.41;1.41;1.36;1.35	6.03	6.03	0.97812	.	0.071091	0.64402	D	0.000020	T	0.00012	0.0000	L	0.47716	1.5	0.23361	P	0.99783142	D;D	0.64830	0.994;0.988	P;P	0.59221	0.854;0.74	T	0.53201	-0.8472	9	0.33141	T	0.24	-13.991	10.462	0.44585	0.0:0.1432:0.7085:0.1483	rs2147914;rs3790440;rs17559036;rs61115096;rs2147914	353;273	B7Z1Y9;Q9NX52	.;RHBL2_HUMAN	M	273;273;340;353	ENSP00000362081:L273M;ENSP00000289248:L273M;ENSP00000439227:L340M;ENSP00000362076:L353M	ENSP00000289248:L273M	L	-	1	2	RHBDL2	39124858	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.757000	0.47557	2.861000	0.98227	0.655000	0.94253	CTG	G|0.652;T|0.348	0.348	strong		0.428	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821	
HBP1	26959	hgsc.bcm.edu	37	7	106826381	106826381	+	Silent	SNP	C	C	T	rs201145168|rs7794598	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:106826381C>T	ENST00000222574.4	+	4	720	c.534C>T	c.(532-534)caC>caT	p.H178H	HBP1_ENST00000485846.1_Silent_p.H178H|HBP1_ENST00000468410.1_Silent_p.H178H	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	178					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						CAGTAAGACACGAAAGGGTAA	0.413														792	0.158147	0.1483	0.1282	5008	,	,		18826	0.124		0.2018	False		,,,				2504	0.183				p.H188H		Atlas-SNP	.											.	HBP1	31	.	0			c.C564T						PASS	.	T		637,3769	767.1+/-413.5	61,515,1627	96.0	88.0	91.0		534	-0.4	1.0	7	dbSNP_116	91	1850,6750	730.1+/-406.7	206,1438,2656	no	coding-synonymous	HBP1	NM_012257.3		267,1953,4283	TT,TC,CC		21.5116,14.4576,19.1219		178/515	106826381	2487,10519	2203	4300	6503	SO:0001819	synonymous_variant	26959	exon4			AAGACACGAAAGG	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.534C>T	7.37:g.106826381C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Silent	SNP	ENST00000222574.4	37	CCDS5741.1																																																																																			C|0.818;T|0.182	0.182	strong		0.413	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257	
ZNF415	55786	hgsc.bcm.edu	37	19	53612311	53612311	+	Silent	SNP	T	T	C	rs4803051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53612311T>C	ENST00000500065.4	-	4	1320	c.987A>G	c.(985-987)acA>acG	p.T329T	ZNF415_ENST00000597748.1_3'UTR|ZNF415_ENST00000601493.1_Silent_p.T99T|ZNF415_ENST00000243643.4_Silent_p.T329T|ZNF415_ENST00000440291.1_Silent_p.T316T|ZNF415_ENST00000455735.2_Silent_p.T377T|ZNF415_ENST00000421033.1_Silent_p.T341T|ZNF415_ENST00000597503.1_3'UTR|ZNF415_ENST00000595193.1_3'UTR|ZNF415_ENST00000594011.1_3'UTR|ZNF415_ENST00000448501.1_Silent_p.T377T	NM_001136038.2	NP_001129510.2	Q09FC8	ZN415_HUMAN	zinc finger protein 415	377					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				GBM - Glioblastoma multiforme(134;0.0191)		ACTCTTTACATGTGTAAGGTT	0.398													C|||	2391	0.477436	0.2405	0.6254	5008	,	,		23834	0.6151		0.496	False		,,,				2504	0.5317				p.T329T		Atlas-SNP	.											.	ZNF415	68	.	0			c.A987G						PASS	.	C	,,	1235,3171	705.9+/-407.3	185,865,1153	83.0	76.0	79.0		987,987,987	-5.1	0.0	19	dbSNP_111	79	4193,4407	585.6+/-391.9	1029,2135,1136	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF415	NM_001136038.2,NM_001164309.1,NM_018355.2	,,	1214,3000,2289	CC,CT,TT		48.7558,28.03,41.7346	,,	329/556,329/556,329/556	53612311	5428,7578	2203	4300	6503	SO:0001819	synonymous_variant	55786	exon4			TTTACATGTGTAA	AK002053	CCDS12860.1, CCDS54313.1	19q13.42	2014-03-18			ENSG00000170954	ENSG00000170954		"""Zinc fingers, C2H2-type"", ""-"""	20636	protein-coding gene	gene with protein product						14702039	Standard	NM_001136038		Approved		uc002qaw.3	Q09FC8	OTTHUMG00000182865	ENST00000500065.4:c.987A>G	19.37:g.53612311T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_018355	F5H287|Q09FC7|Q09FC9|Q09FD0|Q6NSZ2|Q6P3S0|Q9NUR2	Silent	SNP	ENST00000500065.4	37	CCDS54313.1																																																																																			T|0.561;C|0.439	0.439	strong		0.398	ZNF415-025	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464043.1	NM_018355	
BRWD1	54014	hgsc.bcm.edu	37	21	40641858	40641858	+	Silent	SNP	T	T	G	rs61740760	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:40641858T>G	ENST00000333229.2	-	15	1824	c.1497A>C	c.(1495-1497)acA>acC	p.T499T	BRWD1_ENST00000380800.3_Silent_p.T499T|BRWD1_ENST00000342449.3_Silent_p.T499T	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	499					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TGGTACCTTTTGTAATATCCC	0.353													T|||	50	0.00998403	0.0023	0.0115	5008	,	,		15942	0.0		0.0368	False		,,,				2504	0.002				p.T499T	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A1497C						PASS	.	T	,	25,4381	31.7+/-61.6	0,25,2178	116.0	110.0	112.0		1497,1497	3.2	1.0	21	dbSNP_129	112	280,8320	105.4+/-166.3	5,270,4025	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	5,295,6203	GG,GT,TT		3.2558,0.5674,2.3451	,	499/2321,499/2270	40641858	305,12701	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon15			ACCTTTTGTAATA	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.1497A>C	21.37:g.40641858T>G		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	198	97	0.489899	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1	34	0.015567765567765568	0	0.0	6	0.016574585635359115	0	0.0	28	0.036939313984168866	T	9.400	1.077745	0.20227	0.005674	0.032558	ENSG00000185658	ENST00000455867	.	.	.	5.57	3.15	0.36227	.	.	.	.	.	T	0.16471	0.0396	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07986	-1.0744	4	.	.	.	-10.8021	3.5033	0.07681	0.1241:0.069:0.256:0.5509	.	.	.	.	Q	211	.	.	K	-	1	0	BRWD1	39563728	0.995000	0.38212	1.000000	0.80357	0.993000	0.82548	0.332000	0.19751	0.380000	0.24823	0.455000	0.32223	AAA	T|0.978;G|0.022	0.022	strong		0.353	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
KAZN	23254	hgsc.bcm.edu	37	1	15438990	15438990	+	Missense_Mutation	SNP	G	G	A	rs10803354	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15438990G>A	ENST00000376030.2	+	14	2410	c.2116G>A	c.(2116-2118)Gca>Aca	p.A706T		NM_201628.2	NP_963922.2	Q674X7	KAZRN_HUMAN	kazrin, periplakin interacting protein	706			A -> T (in dbSNP:rs10803354). {ECO:0000269|PubMed:14702039}.		keratinization (GO:0031424)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|desmosome (GO:0030057)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(1)|prostate(2)	25						CGTCACGCGGGCAGGAAAGGA	0.592													G|||	2214	0.442093	0.264	0.4438	5008	,	,		17210	0.6558		0.3966	False		,,,				2504	0.5082				p.A706T		Atlas-SNP	.											.	KAZN	57	.	0			c.G2116A						PASS	.	G	THR/ALA	1242,3164		170,902,1131	35.0	34.0	34.0		2116	3.6	1.0	1	dbSNP_120	34	3476,5118		700,2076,1521	yes	missense	KAZN	NM_201628.2	58	870,2978,2652	AA,AG,GG		40.4468,28.1888,36.2923	benign	706/776	15438990	4718,8282	2203	4297	6500	SO:0001583	missense	23254	exon14			ACGCGGGCAGGAA	AY505119	CCDS30604.1, CCDS41267.1, CCDS152.2, CCDS41268.1	1p36.21	2014-02-12	2011-01-31		ENSG00000189337	ENSG00000189337		"""Sterile alpha motif (SAM) domain containing"""	29173	protein-coding gene	gene with protein product						15337775, 18840647	Standard	NM_015209		Approved	KIAA1026, KAZRIN, FLJ43806	uc001avm.4	Q674X7	OTTHUMG00000002042	ENST00000376030.2:c.2116G>A	1.37:g.15438990G>A	ENSP00000365198:p.Ala706Thr	Somatic	198	0	0		WXS	Illumina HiSeq	Phase_I	228	228	1	NM_201628	B0QYQ0|B1AK78|Q5TGF1|Q674X4|Q674X6|Q6ZUD1|Q8IYN7|Q8N409|Q9UIL2|Q9UPX4	Missense_Mutation	SNP	ENST00000376030.2	37	CCDS152.2	998	0.45695970695970695	125	0.2540650406504065	159	0.43922651933701656	398	0.6958041958041958	316	0.41688654353562005	G	12.78	2.040317	0.35989	0.281888	0.404468	ENSG00000189337	ENST00000376030	T	0.18016	2.24	5.52	3.61	0.41365	.	0.444427	0.19276	N	0.118277	T	0.00012	0.0000	N	0.14661	0.345	0.09310	P	0.9999999999295361	B	0.06786	0.001	B	0.06405	0.002	T	0.21177	-1.0253	9	0.39692	T	0.17	-8.9263	6.3791	0.21523	0.1032:0.2411:0.6557:0.0	rs10803354;rs56962621;rs10803354	706	Q674X7	KAZRN_HUMAN	T	706	ENSP00000365198:A706T	ENSP00000365198:A706T	A	+	1	0	KAZN	15311577	0.998000	0.40836	0.965000	0.40720	0.662000	0.39071	1.505000	0.35736	1.333000	0.45449	0.650000	0.86243	GCA	G|0.601;A|0.399	0.399	strong		0.592	KAZN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005690.2	NM_001017999	
SLC16A4	9122	hgsc.bcm.edu	37	1	110924353	110924353	+	Silent	SNP	G	G	A	rs3738750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110924353G>A	ENST00000369779.4	-	4	534	c.285C>T	c.(283-285)ttC>ttT	p.F95F	SLC16A4_ENST00000472422.2_Intron|SLC16A4_ENST00000497687.1_Intron|SLC16A4_ENST00000437429.2_Intron|SLC16A4_ENST00000541986.1_Silent_p.F33F|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Silent_p.F95F	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	95					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)	p.F95F(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	CAGTAACAACGAAAGCCCCAA	0.418													G|||	881	0.175919	0.0318	0.1614	5008	,	,		20217	0.2609		0.1889	False		,,,				2504	0.2802				p.F95F		Atlas-SNP	.											SLC16A4,NS,carcinoma,0,2	SLC16A4	47	2	1	Substitution - coding silent(1)	stomach(1)	c.C285T						scavenged	.	G	,,,,	245,4161	145.0+/-179.8	6,233,1964	111.0	102.0	105.0		,99,,285,285	0.8	0.0	1	dbSNP_107	105	1593,7007	297.9+/-303.7	135,1323,2842	no	intron,coding-synonymous,intron,coding-synonymous,coding-synonymous	SLC16A4	NM_001201546.1,NM_001201547.1,NM_001201548.1,NM_001201549.1,NM_004696.2	,,,,	141,1556,4806	AA,AG,GG		18.5233,5.5606,14.1319	,,,,	,33/426,,95/320,95/488	110924353	1838,11168	2203	4300	6503	SO:0001819	synonymous_variant	9122	exon4			AACAACGAAAGCC	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.285C>T	1.37:g.110924353G>A		Somatic	275	2	0.00727273		WXS	Illumina HiSeq	Phase_I	253	119	0.470356	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Silent	SNP	ENST00000369779.4	37	CCDS823.1																																																																																			G|0.839;A|0.161	0.161	strong		0.418	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
ATP10D	57205	hgsc.bcm.edu	37	4	47570876	47570876	+	Missense_Mutation	SNP	G	G	A	rs17462252	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:47570876G>A	ENST00000273859.3	+	16	3145	c.2876G>A	c.(2875-2877)aGc>aAc	p.S959N		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	959			S -> N (in dbSNP:rs17462252).		cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|endometrium(5)|kidney(5)|large_intestine(14)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	66						ATGCTGATGAGCACAATTTTG	0.468													G|||	98	0.0195687	0.003	0.0216	5008	,	,		18790	0.001		0.0656	False		,,,				2504	0.0123				p.S959N		Atlas-SNP	.											.	ATP10D	168	.	0			c.G2876A						PASS	.	G	ASN/SER	41,4365	43.1+/-76.7	0,41,2162	68.0	70.0	69.0		2876	1.8	0.9	4	dbSNP_123	69	586,8014	156.0+/-209.9	20,546,3734	yes	missense	ATP10D	NM_020453.3	46	20,587,5896	AA,AG,GG		6.814,0.9305,4.8209	benign	959/1427	47570876	627,12379	2203	4300	6503	SO:0001583	missense	57205	exon16			TGATGAGCACAAT	AB040920	CCDS3476.1	4p12	2010-04-20	2007-09-19		ENSG00000145246	ENSG00000145246		"""ATPases / P-type"""	13549	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10D"""			12532265	Standard	NM_020453		Approved	ATPVD, KIAA1487	uc003gxk.1	Q9P241	OTTHUMG00000160784	ENST00000273859.3:c.2876G>A	4.37:g.47570876G>A	ENSP00000273859:p.Ser959Asn	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	67	0.030677655677655676	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	55	0.07255936675461741	G	3.395	-0.123382	0.06795	0.009305	0.06814	ENSG00000145246	ENST00000273859	D	0.82893	-1.66	6.07	1.84	0.25277	HAD-like domain (1);	0.684805	0.15746	N	0.246645	T	0.09512	0.0234	N	0.03224	-0.385	0.38349	D	0.944294	B	0.02656	0.0	B	0.06405	0.002	T	0.33803	-0.9854	10	0.02654	T	1	-2.4303	10.3286	0.43809	0.4361:0.0:0.5639:0.0	rs17462252;rs52835435;rs17462252	959	Q9P241	AT10D_HUMAN	N	959	ENSP00000273859:S959N	ENSP00000273859:S959N	S	+	2	0	ATP10D	47265633	0.729000	0.28090	0.929000	0.37066	0.951000	0.60555	0.903000	0.28475	0.421000	0.25980	0.655000	0.94253	AGC	G|0.961;A|0.039	0.039	strong		0.468	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453	
LILRB3	11025	hgsc.bcm.edu	37	19	54725913	54725913	+	Missense_Mutation	SNP	C	C	T	rs199822090	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54725913C>T	ENST00000391750.1	-	5	581	c.445G>A	c.(445-447)Gga>Aga	p.G149R	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000469273.1_5'Flank|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRA6_ENST00000440558.2_Intron|LILRB3_ENST00000407860.2_Missense_Mutation_p.G149R|LILRB3_ENST00000424807.1_Missense_Mutation_p.G149R|LILRB3_ENST00000346401.6_Missense_Mutation_p.G149R|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.G149R|LILRA6_ENST00000270464.5_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	149	Ig-like C2-type 2.			G -> R (in Ref. 2; AAB87667). {ECO:0000305}.	cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGTGATATCCCTTCTGTGAG	0.597													.|||	783	0.15635	0.3411	0.1715	5008	,	,		12077	0.002		0.1362	False		,,,				2504	0.0757				p.G149R		Atlas-SNP	.											.	LILRB3	67	.	0			c.G445A						PASS	.						23.0	15.0	18.0					19																	54725913		2079	3867	5946	SO:0001583	missense	11025	exon4			GATATCCCTTCTG	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.445G>A	19.37:g.54725913C>T	ENSP00000375630:p.Gly149Arg	Somatic	242	1	0.00413223		WXS	Illumina HiSeq	Phase_I	155	94	0.606452	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	C	6.911	0.537697	0.13188	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;5.76	2.87	-5.75	0.02384	Immunoglobulin-like fold (1);	2.192950	0.01626	N	0.023278	T	0.07683	0.0193	L	0.37800	1.135	0.80722	P	0.0	B;B;P;P;P	0.41546	0.218;0.08;0.555;0.754;0.68	B;B;B;B;B	0.39094	0.271;0.132;0.29;0.049;0.209	T	0.17258	-1.0375	9	0.41790	T	0.15	.	1.2731	0.02025	0.1365:0.1909:0.2699:0.4027	.	149;149;149;149;149	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	R	149	ENSP00000375630:G149R;ENSP00000412771:G149R;ENSP00000345184:G149R;ENSP00000245620:G149R;ENSP00000384274:G149R;ENSP00000388199:G149R	ENSP00000245620:G149R	G	-	1	0	LILRB3	59417725	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.520000	0.00951	-1.631000	0.01543	-0.510000	0.04470	GGA	C|0.931;T|0.069	0.069	strong		0.597	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
SH3RF1	57630	hgsc.bcm.edu	37	4	170037572	170037572	+	Missense_Mutation	SNP	G	G	A	rs3811813	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:170037572G>A	ENST00000284637.9	-	10	2328	c.1987C>T	c.(1987-1989)Cca>Tca	p.P663S	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	663			P -> S (in dbSNP:rs3811813).		negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|protein ubiquitination (GO:0016567)|regulation of JNK cascade (GO:0046328)	cell projection (GO:0042995)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31		Prostate(90;0.00267)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)		GAAGTCAGTGGAGCAGCTGCT	0.622													G|||	462	0.0922524	0.0083	0.062	5008	,	,		19880	0.0813		0.1362	False		,,,				2504	0.1933				p.P663S		Atlas-SNP	.											SH3RF1,NS,carcinoma,+2,1	SH3RF1	60	1	0			c.C1987T						PASS	.	G	SER/PRO	166,4240	109.1+/-147.4	3,160,2040	61.0	52.0	55.0		1987	1.4	0.0	4	dbSNP_107	55	1098,7502	228.7+/-263.7	80,938,3282	yes	missense	SH3RF1	NM_020870.3	74	83,1098,5322	AA,AG,GG		12.7674,3.7676,9.7186	benign	663/889	170037572	1264,11742	2203	4300	6503	SO:0001583	missense	57630	exon10			TCAGTGGAGCAGC	BC033203	CCDS34099.1	4q32.3	2013-01-09	2006-02-13	2006-02-13	ENSG00000154447	ENSG00000154447		"""RING-type (C3HC4) zinc fingers"""	17650	protein-coding gene	gene with protein product	"""plenty of SH3 domains"""		"""SH3 multiple domains 2"""	SH3MD2		9482736	Standard	NM_020870		Approved	POSH, RNF142, KIAA1494	uc003isa.1	Q7Z6J0	OTTHUMG00000161010	ENST00000284637.9:c.1987C>T	4.37:g.170037572G>A	ENSP00000284637:p.Pro663Ser	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	103	50	0.485437	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Missense_Mutation	SNP	ENST00000284637.9	37	CCDS34099.1	177	0.08104395604395605	5	0.01016260162601626	28	0.07734806629834254	39	0.06818181818181818	105	0.13852242744063326	G	0.259	-1.000945	0.02128	0.037676	0.127674	ENSG00000154447	ENST00000284637	T	0.10960	2.82	5.24	1.38	0.22167	.	0.261100	0.27563	N	0.018810	T	0.00039	0.0001	N	0.00926	-1.1	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43572	-0.9383	9	0.02654	T	1	-1.1484	5.8399	0.18627	0.7065:0.1407:0.1528:0.0	rs3811813;rs60713833;rs3811813	663	Q7Z6J0	SH3R1_HUMAN	S	663	ENSP00000284637:P663S	ENSP00000284637:P663S	P	-	1	0	SH3RF1	170274147	1.000000	0.71417	0.000000	0.03702	0.001000	0.01503	3.648000	0.54410	0.009000	0.14813	-0.378000	0.06908	CCA	G|0.906;A|0.094	0.094	strong		0.622	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870	
CHD2	1106	hgsc.bcm.edu	37	15	93567864	93567864	+	Silent	SNP	A	A	C	rs12906163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:93567864A>C	ENST00000394196.4	+	39	6484	c.5416A>C	c.(5416-5418)Agg>Cgg	p.R1806R		NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1806					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			CCTGGATCATAGGTCTCCTTT	0.463													A|||	934	0.186502	0.0855	0.2248	5008	,	,		21175	0.0575		0.3698	False		,,,				2504	0.2403				p.R1806R		Atlas-SNP	.											.	CHD2	280	.	0			c.A5416C						PASS	.	A		468,3276		26,416,1430	81.0	78.0	79.0		5416	3.3	0.7	15	dbSNP_121	79	3300,4930		648,2004,1463	no	coding-synonymous	CHD2	NM_001271.3		674,2420,2893	CC,CA,AA		40.0972,12.5,31.4682		1806/1829	93567864	3768,8206	1872	4115	5987	SO:0001819	synonymous_variant	1106	exon39			GATCATAGGTCTC	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.5416A>C	15.37:g.93567864A>C		Somatic	147	0	0		WXS	Illumina HiSeq	Phase_I	143	62	0.433566	NM_001271	C6G482|Q96IP5	Silent	SNP	ENST00000394196.4	37	CCDS10374.2																																																																																			A|0.767;C|0.233	0.233	strong		0.463	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
KDM2B	84678	hgsc.bcm.edu	37	12	121878659	121878659	+	Silent	SNP	C	C	T	rs1064951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121878659C>T	ENST00000377071.4	-	21	3642	c.3570G>A	c.(3568-3570)caG>caA	p.Q1190Q	KDM2B_ENST00000377069.4_Silent_p.Q1121Q|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Silent_p.Q558Q	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1190					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						GATCCCGCATCTGGGCATCCT	0.632													C|||	1675	0.334465	0.1573	0.4006	5008	,	,		16903	0.4514		0.4046	False		,,,				2504	0.3344				p.Q1190Q		Atlas-SNP	.											.	KDM2B	218	.	0			c.G3570A						PASS	.	C	,	783,3405		80,623,1391	37.0	44.0	42.0		3363,3570	4.1	1.0	12	dbSNP_86	42	3208,5234		606,1996,1619	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	686,2619,3010	TT,TC,CC		38.0005,18.6963,31.5994	,	1121/1266,1190/1337	121878659	3991,8639	2094	4221	6315	SO:0001819	synonymous_variant	84678	exon21			CCGCATCTGGGCA	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3570G>A	12.37:g.121878659C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	96	56	0.583333	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			C|0.667;T|0.333	0.333	strong		0.632	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
RAD54B	25788	hgsc.bcm.edu	37	8	95419698	95419698	+	Silent	SNP	A	A	G	rs2291439	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95419698A>G	ENST00000336148.5	-	5	874	c.750T>C	c.(748-750)aaT>aaC	p.N250N		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	250					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			GTGGTTTGCAATTTTGGAAAT	0.328								Direct reversal of damage;Homologous recombination					A|||	2094	0.418131	0.3517	0.536	5008	,	,		18131	0.4663		0.3777	False		,,,				2504	0.4162				p.N250N		Atlas-SNP	.											.	RAD54B	88	.	0			c.T750C						PASS	.	A	,	1557,2849	487.4+/-360.9	261,1035,907	76.0	74.0	75.0		198,750	2.7	0.6	8	dbSNP_100	75	3140,5460	476.8+/-369.5	549,2042,1709	yes	coding-synonymous,coding-synonymous	RAD54B	NM_001205263.1,NM_012415.3	,	810,3077,2616	GG,GA,AA		36.5116,35.3382,36.1141	,	66/727,250/911	95419698	4697,8309	2203	4300	6503	SO:0001819	synonymous_variant	25788	exon5			TTTGCAATTTTGG	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.750T>C	8.37:g.95419698A>G		Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	247	116	0.469636	NM_012415	F6WBS8	Silent	SNP	ENST00000336148.5	37	CCDS6262.1																																																																																			A|0.610;C|0.003	.	strong		0.328	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
PLG	5340	hgsc.bcm.edu	37	6	161159619	161159619	+	Silent	SNP	T	T	C	rs4252195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:161159619T>C	ENST00000308192.9	+	15	1915	c.1852T>C	c.(1852-1854)Ttg>Ctg	p.L618L		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	618	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)	AGAGTGGGTGTTGACTGCTGC	0.413													T|||	3	0.000599042	0.0	0.0014	5008	,	,		21373	0.0		0.002	False		,,,				2504	0.0				p.L618L		Atlas-SNP	.											.	PLG	150	.	0			c.T1852C						PASS	.	T		9,4397		0,9,2194	150.0	139.0	143.0		1852	-4.5	1.0	6	dbSNP_111	143	55,8545		0,55,4245	no	coding-synonymous	PLG	NM_000301.3		0,64,6439	CC,CT,TT		0.6395,0.2043,0.4921		618/811	161159619	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon15			TGGGTGTTGACTG	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.1852T>C	6.37:g.161159619T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	93	81	0.870968	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.996;C|0.004	0.004	strong		0.413	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
LEPR	3953	hgsc.bcm.edu	37	1	66075952	66075952	+	Missense_Mutation	SNP	G	G	C	rs1805094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:66075952G>C	ENST00000349533.6	+	14	2153	c.1968G>C	c.(1966-1968)aaG>aaC	p.K656N	LEPR_ENST00000371060.3_Missense_Mutation_p.K656N|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000344610.8_Missense_Mutation_p.K656N|LEPR_ENST00000371058.1_Missense_Mutation_p.K656N|LEPR_ENST00000371059.3_Missense_Mutation_p.K656N	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		CTATGAAAAAGGAGAAAAATG	0.269													G|||	713	0.142372	0.1997	0.1888	5008	,	,		18092	0.0585		0.1511	False		,,,				2504	0.1094				p.K656N		Atlas-SNP	.											.	LEPR	284	.	0			c.G1968C	GRCh37	CM025915	LEPR	M	rs8179183	PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS,ASN/LYS	828,3574	303.5+/-288.0	71,686,1444	53.0	55.0	54.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1968,1968,1968,1968,1968,1968	-2.9	0.0	1	dbSNP_117	54	1467,7121	271.3+/-289.5	134,1199,2961	yes	missense,missense,missense,missense,missense,missense	LEPR	NM_001003679.3,NM_001003680.3,NM_001198687.1,NM_001198688.1,NM_001198689.1,NM_002303.5	94,94,94,94,94,94	205,1885,4405	CC,CG,GG		17.082,18.8096,17.6674	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	656/897,656/959,656/959,656/907,656/897,656/1166	66075952	2295,10695	2201	4294	6495	SO:0001583	missense	3953	exon14			GAAAAAGGAGAAA	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.1968G>C	1.37:g.66075952G>C	ENSP00000330393:p.Lys656Asn	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	317	0.14514652014652016	87	0.17682926829268292	68	0.1878453038674033	38	0.06643356643356643	124	0.16358839050131926	G	8.525	0.869742	0.17322	0.188096	0.17082	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.57273	0.43;0.42;0.43;0.41;0.43	5.33	-2.91	0.05631	Fibronectin, type III (2);	0.254500	0.43260	D	0.000596	T	0.27313	0.0670	L	0.47190	1.495	0.25609	P	0.9865115	P;P;P	0.51351	0.696;0.798;0.944	B;B;P	0.48552	0.232;0.409;0.581	T	0.28427	-1.0044	9	0.23891	T	0.37	-8.3309	9.1333	0.36859	0.3785:0.0:0.5107:0.1108	rs8179183;rs17127774;rs52811589;rs8179183	656;656;656	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	N	656	ENSP00000340884:K656N;ENSP00000330393:K656N;ENSP00000360099:K656N;ENSP00000360098:K656N;ENSP00000360097:K656N	ENSP00000340884:K656N	K	+	3	2	LEPR	65848540	0.102000	0.21896	0.045000	0.18777	0.677000	0.39632	-0.497000	0.06428	-0.833000	0.04245	-1.000000	0.02509	AAG	G|0.841;C|0.159	0.159	strong		0.269	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
TMC1	117531	hgsc.bcm.edu	37	9	75315438	75315438	+	Missense_Mutation	SNP	G	G	A	rs1796993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:75315438G>A	ENST00000297784.5	+	8	781	c.241G>A	c.(241-243)Gaa>Aaa	p.E81K	TMC1_ENST00000396237.3_Missense_Mutation_p.E81K|TMC1_ENST00000340019.3_Missense_Mutation_p.E81K	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	81	Arg/Asp/Glu/Lys-rich (highly charged).		E -> K (in dbSNP:rs1796993). {ECO:0000269|PubMed:11850618}.		auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						TTAAAGAGAAGAAGAAGAAAT	0.323													G|||	1384	0.276358	0.2708	0.2493	5008	,	,		12579	0.381		0.163	False		,,,				2504	0.3119				p.E81K	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.G241A						PASS	.	G	LYS/GLU	1157,3249	371.0+/-319.8	156,845,1202	71.0	82.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	241	5.5	1.0	9	dbSNP_89	78	1449,7143	256.2+/-280.8	116,1217,2963	yes	missense	TMC1	NM_138691.2	56	272,2062,4165	AA,AG,GG		16.8645,26.2596,20.0492	benign	81/761	75315438	2606,10392	2203	4296	6499	SO:0001583	missense	117531	exon8			AGAGAAGAAGAAG	AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.241G>A	9.37:g.75315438G>A	ENSP00000297784:p.Glu81Lys	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	62	30	0.483871	NM_138691	A8MVZ2|B1AM91	Missense_Mutation	SNP	ENST00000297784.5	37	CCDS6643.1	603	0.2760989010989011	142	0.2886178861788618	96	0.26519337016574585	234	0.4090909090909091	131	0.17282321899736147	G	16.23	3.064900	0.55432	0.262596	0.168645	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000542143;ENST00000396237	T;T;T	0.52295	0.67;0.67;0.67	5.48	5.48	0.80851	.	0.064987	0.64402	D	0.000014	T	0.00012	0.0000	L	0.41492	1.28	0.21445	P	0.99968547	B	0.26635	0.155	B	0.18871	0.023	T	0.36359	-0.9751	9	0.09084	T	0.74	-13.9321	18.494	0.90858	0.0:0.0:1.0:0.0	rs1796993;rs17058087;rs59785599;rs1796993	81	Q8TDI8	TMC1_HUMAN	K	81;81;75;81	ENSP00000297784:E81K;ENSP00000341433:E81K;ENSP00000379538:E81K	ENSP00000297784:E81K	E	+	1	0	TMC1	74505258	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.552000	0.67281	2.730000	0.93505	0.655000	0.94253	GAA	G|0.761;A|0.239	0.239	strong		0.323	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1		
LTF	4057	hgsc.bcm.edu	37	3	46490456	46490456	+	Silent	SNP	G	G	A	rs61737000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46490456G>A	ENST00000231751.4	-	9	1405	c.1110C>T	c.(1108-1110)ggC>ggT	p.G370G	LTF_ENST00000426532.2_Silent_p.G326G|LTF_ENST00000417439.1_Silent_p.G370G	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	370	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GCTCCTGCTCGCCCACCGCAC	0.667													G|||	300	0.0599042	0.2057	0.0187	5008	,	,		15791	0.001		0.003	False		,,,				2504	0.0112				p.G370G		Atlas-SNP	.											.	LTF	98	.	0			c.C1110T						PASS	.	G	,	837,3569	321.5+/-297.2	71,695,1437	42.0	37.0	39.0		978,1110	3.0	0.6	3	dbSNP_129	39	49,8543	30.1+/-81.4	0,49,4247	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	71,744,5684	AA,AG,GG		0.5703,18.9968,6.8164	,	326/667,370/711	46490456	886,12112	2203	4296	6499	SO:0001819	synonymous_variant	4057	exon9			CTGCTCGCCCACC		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.1110C>T	3.37:g.46490456G>A		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	106	54	0.509434	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			G|0.929;A|0.071	0.071	strong		0.667	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
ABCB11	8647	hgsc.bcm.edu	37	2	169789016	169789016	+	Silent	SNP	T	T	C	rs497692	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:169789016T>C	ENST00000263817.6	-	24	3208	c.3084A>G	c.(3082-3084)gcA>gcG	p.A1028A		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	1028	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)	p.A1028A(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	CAAGAGCTGTTGCACTCAGTA	0.493													C|||	2488	0.496805	0.2254	0.5086	5008	,	,		19594	0.6409		0.5318	False		,,,				2504	0.6708				p.A1028A		Atlas-SNP	.											ABCB11,colon,carcinoma,-1,2	ABCB11	136	2	1	Substitution - coding silent(1)	stomach(1)	c.A3084G						PASS	.	C		1076,2938		160,756,1091	84.0	81.0	82.0		3084	-10.8	0.0	2	dbSNP_83	82	4552,3814		1240,2072,871	yes	coding-synonymous	ABCB11	NM_003742.2		1400,2828,1962	CC,CT,TT		45.5893,26.8062,45.4604		1028/1322	169789016	5628,6752	2007	4183	6190	SO:0001819	synonymous_variant	8647	exon24			AGCTGTTGCACTC	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.3084A>G	2.37:g.169789016T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	160	87	0.54375	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			T|0.519;C|0.481	0.481	strong		0.493	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
MUC5B	727897	hgsc.bcm.edu	37	11	1267562	1267562	+	Missense_Mutation	SNP	C	C	T	rs60268710	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1267562C>T	ENST00000529681.1	+	31	9510	c.9452C>T	c.(9451-9453)aCg>aTg	p.T3151M	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T3154M	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3151	17 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.			Missing (in Ref. 6; AAB61398). {ECO:0000305}.|TGPTA -> LPHG (in Ref. 4; CAA96577). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		ACTGGCCCCACGGCCACCCCG	0.677													c|||	1706	0.340655	0.2133	0.33	5008	,	,		17737	0.6012		0.2883	False		,,,				2504	0.3057				p.T3151M		Atlas-SNP	.											MUC5AC,NS,carcinoma,-1,1	MUC5B	473	1	0			c.C9452T						scavenged	.	C	MET/THR	782,3294		71,640,1327	53.0	69.0	63.0		9452	-3.5	0.0	11	dbSNP_129	63	2471,5819		394,1683,2068	no	missense	MUC5B	NM_002458.2	81	465,2323,3395	TT,TC,CC		29.807,19.1855,26.306	possibly-damaging	3151/5763	1267562	3253,9113	2038	4145	6183	SO:0001583	missense	727897	exon31			GCCCCACGGCCAC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.9452C>T	11.37:g.1267562C>T	ENSP00000436812:p.Thr3151Met	Somatic	316	3	0.00949367		WXS	Illumina HiSeq	Phase_I	253	123	0.486166	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	769	0.35210622710622713	111	0.22560975609756098	107	0.2955801104972376	346	0.6048951048951049	205	0.2704485488126649	c	2.006	-0.428266	0.04701	0.191855	0.29807	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20332	2.08;2.26	1.73	-3.46	0.04767	.	.	.	.	.	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P;P	0.44260	0.707;0.83	B;B	0.28139	0.029;0.086	T	0.35699	-0.9778	8	0.87932	D	0	.	5.8817	0.18858	0.0:0.1548:0.426:0.4192	rs60268710	3734;3154	A7Y9J9;E9PBJ0	.;.	M	3151;3154;3123;3111	ENSP00000436812:T3151M;ENSP00000415793:T3154M	ENSP00000343037:T3123M	T	+	2	0	MUC5B	1224138	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.828000	0.01702	-1.881000	0.01123	-0.708000	0.03648	ACG	C|0.929;T|0.071	0.071	strong		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TTC28	23331	hgsc.bcm.edu	37	22	28389453	28389453	+	Silent	SNP	T	T	C	rs470101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:28389453T>C	ENST00000397906.2	-	18	5439	c.5298A>G	c.(5296-5298)acA>acG	p.T1766T	TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000424161.1_RNA|TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000435348.1_RNA|TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000428584.1_RNA|TTC28-AS1_ENST00000433317.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000430525.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	1766					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						TCTGCTGGGATGTGTACATGG	0.637													C|||	395	0.0788738	0.0991	0.0937	5008	,	,		19292	0.0069		0.1034	False		,,,				2504	0.09				p.T1766T		Atlas-SNP	.											.	TTC28	84	.	0			c.A5298G						PASS	.	C		144,1240		7,130,555	69.0	66.0	67.0		5298	-8.9	0.5	22	dbSNP_80	67	381,2801		26,329,1236	no	coding-synonymous	TTC28	NM_001145418.1		33,459,1791	CC,CT,TT		11.9736,10.4046,11.498		1766/2482	28389453	525,4041	692	1591	2283	SO:0001819	synonymous_variant	23331	exon18			CTGGGATGTGTAC	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.5298A>G	22.37:g.28389453T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	124	61	0.491935	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			T|0.926;C|0.074	0.074	strong		0.637	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
HMCN1	83872	hgsc.bcm.edu	37	1	186031041	186031041	+	Silent	SNP	C	C	T	rs7522627	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186031041C>T	ENST00000271588.4	+	47	7600	c.7371C>T	c.(7369-7371)tgC>tgT	p.C2457C	HMCN1_ENST00000367492.2_Silent_p.C2457C	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2457	Ig-like C2-type 22.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						AATATACTTGCGTTGTAAGGA	0.378													T|||	3277	0.654353	0.8495	0.647	5008	,	,		16476	0.5903		0.5348	False		,,,				2504	0.5849				p.C2457C		Atlas-SNP	.											.	HMCN1	797	.	0			c.C7371T						PASS	.	T		3571,835	333.6+/-303.0	1454,663,86	124.0	136.0	132.0		7371	1.9	0.9	1	dbSNP_116	132	4602,3998	553.3+/-386.3	1252,2098,950	no	coding-synonymous	HMCN1	NM_031935.2		2706,2761,1036	TT,TC,CC		46.4884,18.9514,37.1598		2457/5636	186031041	8173,4833	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon47			TACTTGCGTTGTA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7371C>T	1.37:g.186031041C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	90	41	0.455556	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			C|0.372;T|0.628	0.628	strong		0.378	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
BTBD11	121551	hgsc.bcm.edu	37	12	107712880	107712880	+	Silent	SNP	C	C	T	rs10082935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:107712880C>T	ENST00000280758.5	+	1	691	c.163C>T	c.(163-165)Cta>Tta	p.L55L	BTBD11_ENST00000420571.2_Silent_p.L55L|BTBD11_ENST00000490090.2_Silent_p.L55L	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	55						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CTGGCCGCCTCTAGCTGACTC	0.647													C|||	493	0.0984425	0.0484	0.1758	5008	,	,		12283	0.0		0.1799	False		,,,				2504	0.1288				p.L55L		Atlas-SNP	.											.	BTBD11	122	.	0			c.C163T						PASS	.	C		316,4090		9,298,1896	29.0	30.0	30.0		163	4.0	1.0	12	dbSNP_119	30	1585,7009		143,1299,2855	no	coding-synonymous	BTBD11	NM_001018072.1		152,1597,4751	TT,TC,CC		18.4431,7.172,14.6231		55/1105	107712880	1901,11099	2203	4297	6500	SO:0001819	synonymous_variant	121551	exon1			CCGCCTCTAGCTG	AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.163C>T	12.37:g.107712880C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	46	17	0.369565	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			C|0.868;T|0.132	0.132	strong		0.647	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
GNB1L	54584	hgsc.bcm.edu	37	22	19808769	19808769	+	Missense_Mutation	SNP	C	C	T	rs5748449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19808769C>T	ENST00000329517.6	-	3	346	c.110G>A	c.(109-111)cGc>cAc	p.R37H	GNB1L_ENST00000460402.1_Intron|GNB1L_ENST00000405009.1_Missense_Mutation_p.R37H|GNB1L_ENST00000403325.1_Missense_Mutation_p.R37H	NM_053004.2	NP_443730.1	Q9BYB4	GNB1L_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1-like	37			R -> H (in dbSNP:rs5748449).		G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|social behavior (GO:0035176)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)				breast(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(1)	12	Colorectal(54;0.0993)					GAGGAGCGGGCGCCCCTGAGC	0.677													C|||	721	0.14397	0.0197	0.1758	5008	,	,		17191	0.0913		0.1968	False		,,,				2504	0.2894				p.R37H		Atlas-SNP	.											.	GNB1L	34	.	0			c.G110A						PASS	.	C	HIS/ARG	238,4168	134.9+/-171.1	10,218,1975	46.0	57.0	53.0		110	-4.6	0.0	22	dbSNP_114	53	1733,6867	305.6+/-307.5	180,1373,2747	yes	missense	GNB1L	NM_053004.2	29	190,1591,4722	TT,TC,CC		20.1512,5.4017,15.1545	benign	37/328	19808769	1971,11035	2203	4300	6503	SO:0001583	missense	54584	exon3			AGCGGGCGCCCCT	AF238328	CCDS13768.1	22q11.2	2013-05-21			ENSG00000185838	ENSG00000185838		"""WD repeat domain containing"""	4397	protein-coding gene	gene with protein product		610778				11072084	Standard	NM_053004		Approved	GY2, WDR14	uc002zqf.1	Q9BYB4	OTTHUMG00000150279	ENST00000329517.6:c.110G>A	22.37:g.19808769C>T	ENSP00000331313:p.Arg37His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	65	25	0.384615	NM_053004	Q9H2S2|Q9H4M4	Missense_Mutation	SNP	ENST00000329517.6	37	CCDS13768.1	280	0.1282051282051282	14	0.028455284552845527	70	0.19337016574585636	51	0.08916083916083917	145	0.19129287598944592	C	3.185	-0.167019	0.06461	0.054017	0.201512	ENSG00000185838	ENST00000329517;ENST00000403325;ENST00000405009;ENST00000453108	T;T;T;T	0.35789	2.16;2.16;5.02;1.29	4.9	-4.57	0.03421	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.391610	0.05331	N	0.528250	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	0.23190	-1.0195	9	0.16420	T	0.52	-17.5463	4.561	0.12160	0.1736:0.5063:0.1196:0.2006	rs5748449;rs5748449	37	Q9BYB4	GNB1L_HUMAN	H	37	ENSP00000331313:R37H;ENSP00000385154:R37H;ENSP00000384626:R37H;ENSP00000389412:R37H	ENSP00000331313:R37H	R	-	2	0	GNB1L	18188769	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-2.766000	0.00782	-0.600000	0.05790	-0.752000	0.03492	CGC	C|0.860;T|0.140	0.140	strong		0.677	GNB1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075202.1		
BYSL	705	hgsc.bcm.edu	37	6	41895150	41895150	+	Missense_Mutation	SNP	G	G	A	rs2296916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41895150G>A	ENST00000230340.4	+	2	682	c.307G>A	c.(307-309)Gag>Aag	p.E103K		NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	103			E -> K (in dbSNP:rs2296916).		cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGACGAGGACGAGGAGTGGCC	0.542													G|||	380	0.0758786	0.0038	0.0389	5008	,	,		19438	0.1478		0.0974	False		,,,				2504	0.1033				p.E103K		Atlas-SNP	.											.	BYSL	17	.	0			c.G307A						PASS	.	G	LYS/GLU	76,4330	66.4+/-103.9	0,76,2127	124.0	113.0	116.0		307	4.6	1.0	6	dbSNP_100	116	933,7667	206.2+/-248.4	41,851,3408	yes	missense	BYSL	NM_004053.3	56	41,927,5535	AA,AG,GG		10.8488,1.7249,7.758	possibly-damaging	103/438	41895150	1009,11997	2203	4300	6503	SO:0001583	missense	705	exon2			GAGGACGAGGAGT	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.307G>A	6.37:g.41895150G>A	ENSP00000230340:p.Glu103Lys	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	132	73	0.55303	NM_004053	Q6P5W4|Q86W44|Q96IP8	Missense_Mutation	SNP	ENST00000230340.4	37	CCDS34450.1	181	0.08287545787545787	4	0.008130081300813009	13	0.03591160220994475	84	0.14685314685314685	80	0.10554089709762533	G	34	5.361981	0.95877	0.017249	0.108488	ENSG00000112578	ENST00000230340	T	0.21932	1.98	4.62	4.62	0.57501	.	0.101901	0.64402	D	0.000003	T	0.14356	0.0347	M	0.74647	2.275	0.09310	P	0.99999999894696	P	0.45348	0.856	B	0.33295	0.161	T	0.24404	-1.0161	9	0.66056	D	0.02	-3.7104	17.0716	0.86576	0.0:0.0:1.0:0.0	rs2296916;rs52799438;rs59557183;rs2296916	103	Q13895	BYST_HUMAN	K	103	ENSP00000230340:E103K	ENSP00000230340:E103K	E	+	1	0	BYSL	42003128	1.000000	0.71417	0.975000	0.42487	0.880000	0.50808	9.177000	0.94849	2.124000	0.65301	0.643000	0.83706	GAG	G|0.919;A|0.081	0.081	strong		0.542	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2		
LRRC14	9684	hgsc.bcm.edu	37	8	145742879	145742879	+	5'Flank	SNP	T	T	C	rs2306386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145742879T>C	ENST00000292524.1	+	0	0				RECQL4_ENST00000428558.2_Silent_p.E44E|RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			GAGTGCGGTATTCCCGGTAGA	0.786													C|||	2880	0.57508	0.618	0.6282	5008	,	,		8649	0.5238		0.4891	False		,,,				2504	0.6207				p.E44E		Atlas-SNP	.											.	RECQL4	75	.	0			c.A132G						PASS	.	C		2027,1165		681,665,250	5.0	7.0	6.0		132	1.0	0.6	8	dbSNP_100	6	3861,3639		1088,1685,977	no	coding-synonymous	RECQL4	NM_004260.3		1769,2350,1227	CC,CT,TT		48.52,36.4975,44.9308		44/1209	145742879	5888,4804	1596	3750	5346	SO:0001631	upstream_gene_variant	9401	exon3			GCGGTATTCCCGG	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		8.37:g.145742879T>C	Exception_encountered	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_004260	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			T|0.468;C|0.532	0.532	strong		0.786	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
GLYATL3	389396	hgsc.bcm.edu	37	6	49489397	49489397	+	Missense_Mutation	SNP	C	C	A	rs9369905	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:49489397C>A	ENST00000371197.4	+	5	466	c.353C>A	c.(352-354)gCc>gAc	p.A118D		NM_001010904.1	NP_001010904.1	Q5SZD4	GLYL3_HUMAN	glycine-N-acyltransferase-like 3	118						mitochondrion (GO:0005739)	glycine N-acyltransferase activity (GO:0047961)	p.A118D(3)		NS(1)|endometrium(1)|kidney(3)|lung(1)|skin(3)|stomach(2)	11						AAAGCGGTTGCCAATTCAAAG	0.363													C|||	889	0.177516	0.0212	0.1931	5008	,	,		18692	0.2073		0.3439	False		,,,				2504	0.1759				p.A118D		Atlas-SNP	.											GLYATL3,NS,carcinoma,0,3	GLYATL3	19	3	3	Substitution - Missense(3)	kidney(2)|stomach(1)	c.C353A						PASS	.						209.0	173.0	184.0					6																	49489397		692	1591	2283	SO:0001583	missense	389396	exon5			CGGTTGCCAATTC		CCDS47440.1	6p12.3	2009-12-14	2009-12-14	2009-12-14	ENSG00000203972	ENSG00000203972			21349	protein-coding gene	gene with protein product		614763	"""chromosome 6 open reading frame 140"""	C6orf140			Standard	NM_001010904		Approved	bA28H17.2	uc003ozi.3	Q5SZD4	OTTHUMG00000014818	ENST00000371197.4:c.353C>A	6.37:g.49489397C>A	ENSP00000360240:p.Ala118Asp	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	88	43	0.488636	NM_001010904		Missense_Mutation	SNP	ENST00000371197.4	37	CCDS47440.1	437	0.2000915750915751	15	0.03048780487804878	75	0.20718232044198895	97	0.16958041958041958	250	0.32981530343007914	C	15.38	2.816761	0.50633	.	.	ENSG00000203972	ENST00000371197;ENST00000545705	T;T	0.20738	2.05;2.05	5.9	5.9	0.94986	Acyl-CoA N-acyltransferase (1);Glycine N-acyltransferase, N-terminal (1);	.	.	.	.	T	0.19644	0.0472	M	0.81341	2.54	0.27018	P	0.9645316	B	0.28470	0.213	B	0.32022	0.139	T	0.03335	-1.1047	8	0.36615	T	0.2	.	15.7685	0.78146	0.0:1.0:0.0:0.0	rs9369905;rs52815318;rs57040541;rs9369905	118	Q5SZD4	GLYL3_HUMAN	D	118	ENSP00000360240:A118D;ENSP00000440029:A118D	ENSP00000360240:A118D	A	+	2	0	GLYATL3	49597356	0.993000	0.37304	0.971000	0.41717	0.620000	0.37586	3.899000	0.56288	2.800000	0.96347	0.591000	0.81541	GCC	C|0.805;A|0.195	0.195	strong		0.363	GLYATL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040866.3	NM_001010904	
TPR	7175	hgsc.bcm.edu	37	1	186330768	186330768	+	Missense_Mutation	SNP	T	T	C	rs201760745		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186330768T>C	ENST00000367478.4	-	9	1240	c.944A>G	c.(943-945)aAa>aGa	p.K315R	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	315					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)		ACCAGCTTCTTTCAAAAGTTT	0.343			T	NTRK1	papillary thyroid								T|||	1	0.000199681	0.0	0.0	5008	,	,		16594	0.0		0.001	False		,,,				2504	0.0				p.K315R		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A944G						PASS	.	T	ARG/LYS	0,3662		0,0,1831	128.0	119.0	122.0		944	5.5	1.0	1		122	2,8168		0,2,4083	yes	missense	TPR	NM_003292.2	26	0,2,5914	CC,CT,TT		0.0245,0.0,0.0169	probably-damaging	315/2364	186330768	2,11830	1831	4085	5916	SO:0001583	missense	7175	exon9			GCTTCTTTCAAAA	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.944A>G	1.37:g.186330768T>C	ENSP00000356448:p.Lys315Arg	Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	202	97	0.480198	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567818	0.86439	0.0	2.45E-4	ENSG00000047410	ENST00000367478	T	0.24723	1.84	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.46658	0.1404	L	0.60455	1.87	0.42919	D	0.994283	D;D	0.69078	0.976;0.997	P;D	0.75020	0.693;0.985	T	0.39333	-0.9619	10	0.45353	T	0.12	.	14.7725	0.69691	0.0:0.0:0.0:1.0	.	315;315	Q15624;P12270	.;TPR_HUMAN	R	315	ENSP00000356448:K315R	ENSP00000356448:K315R	K	-	2	0	TPR	184597391	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.877000	0.69675	2.076000	0.62316	0.533000	0.62120	AAA	.	.	weak		0.343	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
HLA-A	3105	hgsc.bcm.edu	37	6	29910730	29910730	+	Missense_Mutation	SNP	T	T	A	rs199474436|rs281864737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910730T>A	ENST00000396634.1	+	4	611	c.270T>A	c.(268-270)aaT>aaA	p.N90K	HLA-A_ENST00000376809.5_Missense_Mutation_p.N90K|HLA-A_ENST00000376806.5_Missense_Mutation_p.N90K|HLA-A_ENST00000376802.2_Missense_Mutation_p.N90K			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	90	Alpha-1.		N -> K (in allele A*31:02).		antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						AGACACGGAATGTGAAGGCCC	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			t|||	1976	0.394569	0.3003	0.5086	5008	,	,		10700	0.4891		0.4215	False		,,,				2504	0.316				p.N90K		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.T270A						PASS	.						80.0	84.0	82.0					6																	29910730		2199	4290	6489	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ACGGAATGTGAAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.270T>A	6.37:g.29910730T>A	ENSP00000379873:p.Asn90Lys	Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	94	85	0.904255	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	837	0.38324175824175827	122	0.24796747967479674	151	0.4171270718232044	275	0.4807692307692308	289	0.3812664907651715	.	8.031	0.761803	0.15914	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00009	9.48;9.48;9.48;9.48	3.48	-6.97	0.01616	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	7739.210000	0.00166	N	0.000013	T	0.00012	0.0000	N	0.25031	0.7	0.80722	P	0.0	B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.0	B;B;B;B;B	0.17722	0.006;0.011;0.006;0.019;0.006	T	0.22243	-1.0222	9	0.02654	T	1	.	3.5967	0.08009	0.5715:0.2096:0.122:0.0969	rs1059460;rs2230995;rs3173426;rs16868229;rs41558518	90;90;90;90;90	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	K	90	ENSP00000379873:N90K;ENSP00000366002:N90K;ENSP00000366005:N90K;ENSP00000365998:N90K	ENSP00000348012:N90K	N	+	3	2	HLA-A	30018709	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.261000	0.00536	-1.477000	0.01872	-2.887000	0.00096	AAT	A|0.321;T|0.679	0.321	strong		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ABCC12	94160	hgsc.bcm.edu	37	16	48122582	48122582	+	Missense_Mutation	SNP	G	G	A	rs7193955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:48122582G>A	ENST00000311303.3	-	24	3694	c.3349C>T	c.(3349-3351)Cgt>Tgt	p.R1117C	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_3'UTR|ABCC12_ENST00000532355.1_5'Flank	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	1117			R -> C (in dbSNP:rs7193955). {ECO:0000269|PubMed:11483364}.			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)				ATCTCCCCACGGCTGGGCCAG	0.512													G|||	2961	0.591254	0.1112	0.5331	5008	,	,		18261	0.8889		0.7873	False		,,,				2504	0.773				p.R1117C		Atlas-SNP	.											ABCC12,colon,carcinoma,0,1	ABCC12	190	1	0			c.C3349T						PASS	.	G	CYS/ARG	1020,3382	375.4+/-321.6	124,772,1305	90.0	78.0	82.0		3349	2.7	0.5	16	dbSNP_116	82	6730,1870	729.2+/-406.7	2660,1410,230	yes	missense	ABCC12	NM_033226.2	180	2784,2182,1535	AA,AG,GG		21.7442,23.1713,40.3938	benign	1117/1360	48122582	7750,5252	2201	4300	6501	SO:0001583	missense	94160	exon24			CCCCACGGCTGGG	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.3349C>T	16.37:g.48122582G>A	ENSP00000311030:p.Arg1117Cys	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	105	104	0.990476	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	1384	0.6336996336996337	69	0.1402439024390244	197	0.5441988950276243	512	0.8951048951048951	606	0.7994722955145118	G	7.927	0.739832	0.15642	0.231713	0.782558	ENSG00000140798	ENST00000311303	D	0.90844	-2.74	5.87	2.67	0.31697	.	0.634955	0.17864	N	0.159431	T	0.00012	0.0000	L	0.60904	1.88	0.80722	P	0.0	B	0.11235	0.004	B	0.11329	0.006	T	0.34925	-0.9809	9	0.56958	D	0.05	.	3.9511	0.09369	0.0766:0.2455:0.4345:0.2434	rs7193955;rs52806630;rs60981757;rs7193955	1117	Q96J65	MRP9_HUMAN	C	1117	ENSP00000311030:R1117C	ENSP00000311030:R1117C	R	-	1	0	ABCC12	46680083	0.000000	0.05858	0.535000	0.28026	0.087000	0.18053	0.035000	0.13797	0.781000	0.33589	-0.150000	0.13652	CGT	G|0.395;A|0.605	0.605	strong		0.512	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
MEN1	4221	hgsc.bcm.edu	37	11	64572602	64572602	+	Silent	SNP	G	G	A	rs2071313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64572602G>A	ENST00000337652.1	-	9	1772	c.1269C>T	c.(1267-1269)gaC>gaT	p.D423D	MAP4K2_ENST00000294066.2_5'Flank|MEN1_ENST00000377321.1_Silent_p.D383D|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000377313.1_Silent_p.D423D|MEN1_ENST00000377316.2_Intron|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000394374.2_Silent_p.D423D|MEN1_ENST00000443283.1_Silent_p.D423D|MEN1_ENST00000312049.6_Silent_p.D418D|MAP4K2_ENST00000377350.3_5'Flank|MEN1_ENST00000315422.4_Silent_p.D418D|MEN1_ENST00000377326.3_Silent_p.D418D|MEN1_ENST00000394376.1_Silent_p.D423D	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	423			D -> H (in MEN1). {ECO:0000269|PubMed:15730416}.|D -> N (in MEN1). {ECO:0000269|PubMed:12050235, ECO:0000269|PubMed:12112656, ECO:0000269|PubMed:12652570, ECO:0000269|PubMed:9709921}.|Missing (in MEN1).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.L414_E425del(1)		NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						TGCAGATGCCGTCGTAGAATC	0.632			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated				G|||	1542	0.307907	0.0348	0.2997	5008	,	,		19274	0.372		0.4056	False		,,,				2504	0.5164				p.D423D	Esophageal Squamous(1;83 158 15500 18603 18803 29295)	Atlas-SNP	.	yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	MEN1,NS,adenoma,-2,1	MEN1	442	1	1	Deletion - In frame(1)	parathyroid(1)	c.C1269T	GRCh37	CD005470|CD982777|CX066452	MEN1	D|X	rs2071313	PASS	.	G	,,,,,,	399,4003	196.4+/-220.7	19,361,1821	85.0	75.0	78.0		1269,1254,1269,1269,1269,1269,1269	-1.6	1.0	11	dbSNP_96	78	3552,5042	515.8+/-378.7	751,2050,1496	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MEN1	NM_000244.3,NM_130799.2,NM_130800.2,NM_130801.2,NM_130802.2,NM_130803.2,NM_130804.2	,,,,,,	770,2411,3317	AA,AG,GG		41.3312,9.0641,30.4017	,,,,,,	423/616,418/611,423/616,423/616,423/616,423/616,423/616	64572602	3951,9045	2201	4297	6498	SO:0001819	synonymous_variant	4221	exon9	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	GATGCCGTCGTAG	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1269C>T	11.37:g.64572602G>A		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	91	45	0.494505	NM_130800	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000337652.1	37	CCDS8083.1																																																																																			G|0.698;A|0.302	0.302	strong		0.632	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
CERCAM	51148	hgsc.bcm.edu	37	9	131196695	131196695	+	Silent	SNP	C	C	T	rs7258	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131196695C>T	ENST00000372838.4	+	11	1736	c.1338C>T	c.(1336-1338)ctC>ctT	p.L446L	CERCAM_ENST00000372842.1_Silent_p.L368L|RP11-339B21.10_ENST00000610052.1_RNA	NM_016174.4	NP_057258.3	Q5T4B2	GT253_HUMAN	cerebral endothelial cell adhesion molecule	446					cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|leukocyte cell-cell adhesion (GO:0007159)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|pancreas(2)	20						ACAGCTACCTCGGACGGAAGC	0.657													C|||	1476	0.294728	0.3661	0.183	5008	,	,		16091	0.4087		0.2078	False		,,,				2504	0.2495				p.L446L		Atlas-SNP	.											.	CERCAM	104	.	0			c.C1338T						PASS	.	C		1599,2807	472.6+/-356.4	283,1033,887	39.0	44.0	43.0		1338	-10.2	0.1	9	dbSNP_52	43	1532,7068	276.4+/-292.3	127,1278,2895	no	coding-synonymous	CERCAM	NM_016174.4		410,2311,3782	TT,TC,CC		17.814,36.2914,24.0735		446/596	131196695	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	51148	exon11			CTACCTCGGACGG	AB040935	CCDS6901.2, CCDS69675.1	9q34.13	2008-02-05	2007-10-17	2007-10-17	ENSG00000167123	ENSG00000167123			23723	protein-coding gene	gene with protein product	"""glycosyltransferase 25 domain containing 3"""		"""cerebral cell adhesion molecule"""	CEECAM1		10608765	Standard	NM_016174		Approved	GLT25D3, CerCAM	uc004buz.4	Q5T4B2	OTTHUMG00000020747	ENST00000372838.4:c.1338C>T	9.37:g.131196695C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	73	73	1	NM_016174	A7MD00|C4AMA2|Q0VDF3|Q2VPJ4|Q4KMP2|Q5T4B1|Q8N107|Q96EZ5|Q9P226|Q9UMW5	Silent	SNP	ENST00000372838.4	37	CCDS6901.2																																																																																			C|0.738;T|0.262	0.262	strong		0.657	CERCAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054435.2	NM_016174	
PLEKHN1	84069	hgsc.bcm.edu	37	1	906122	906122	+	Silent	SNP	C	C	T	rs41285812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:906122C>T	ENST00000379409.2	+	5	498	c.468C>T	c.(466-468)caC>caT	p.H156H	PLEKHN1_ENST00000379407.3_Silent_p.H156H|PLEKHN1_ENST00000379410.3_Silent_p.H156H			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	156	PH 1.									central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		CCCGAGAGCACGCCTTCCAGA	0.662													C|||	9	0.00179712	0.0023	0.0	5008	,	,		15705	0.0		0.005	False		,,,				2504	0.001				p.H156H		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.C468T						PASS	.	C	,	7,4399	12.9+/-30.5	1,5,2197	50.0	59.0	56.0		468,468	-3.5	0.9	1	dbSNP_127	56	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous,coding-synonymous	PLEKHN1	NM_001160184.1,NM_032129.2	,	1,73,6429	TT,TC,CC		0.7907,0.1589,0.5767	,	156/577,156/612	906122	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	84069	exon5			AGAGCACGCCTTC	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"""Pleckstrin homology (PH) domain containing"""	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.468C>T	1.37:g.906122C>T		Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	106	99	0.933962	NM_001160184	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.662	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	
NLRP8	126205	hgsc.bcm.edu	37	19	56459458	56459458	+	Missense_Mutation	SNP	C	C	T	rs61195059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56459458C>T	ENST00000291971.3	+	1	261	c.190C>T	c.(190-192)Ctc>Ttc	p.L64F	NLRP8_ENST00000590542.1_Missense_Mutation_p.L64F	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	64	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				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)		ACTGACTGAGCTCAGTACTGG	0.562													C|||	329	0.0656949	0.1014	0.0648	5008	,	,		17703	0.005		0.0696	False		,,,				2504	0.0767				p.L64F		Atlas-SNP	.											.	NLRP8	225	.	0			c.C190T						PASS	.	C	PHE/LEU	511,3895	236.1+/-248.4	31,449,1723	112.0	88.0	96.0		190	-0.6	0.0	19	dbSNP_129	96	515,8085	145.1+/-200.9	16,483,3801	yes	missense	NLRP8	NM_176811.2	22	47,932,5524	TT,TC,CC		5.9884,11.5978,7.8887	possibly-damaging	64/1049	56459458	1026,11980	2203	4300	6503	SO:0001583	missense	126205	exon1			ACTGAGCTCAGTA	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.190C>T	19.37:g.56459458C>T	ENSP00000291971:p.Leu64Phe	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	70	43	0.614286	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	141	0.06456043956043957	57	0.11585365853658537	28	0.07734806629834254	1	0.0017482517482517483	55	0.07255936675461741	C	0.017	-1.488451	0.01018	0.115978	0.059884	ENSG00000179709	ENST00000291971	T	0.61274	0.12	1.75	-0.573	0.11742	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.00608	0.0020	L	0.38175	1.15	0.80722	P	0.0	B;B	0.13594	0.005;0.008	B;B	0.18263	0.007;0.021	T	0.08330	-1.0727	8	0.42905	T	0.14	.	2.2831	0.04119	0.299:0.5096:0.0:0.1914	rs61195059;rs61738700	64;64	Q86W28-2;Q86W28	.;NALP8_HUMAN	F	64	ENSP00000291971:L64F	ENSP00000291971:L64F	L	+	1	0	NLRP8	61151270	0.022000	0.18835	0.000000	0.03702	0.002000	0.02628	0.195000	0.17155	-0.067000	0.12976	-1.322000	0.01289	CTC	C|0.925;T|0.075	0.075	strong		0.562	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
DNAH9	1770	hgsc.bcm.edu	37	17	11833287	11833287	+	Silent	SNP	A	A	G	rs2286303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:11833287A>G	ENST00000262442.4	+	63	12050	c.11982A>G	c.(11980-11982)ccA>ccG	p.P3994P	DNAH9_ENST00000608377.1_Silent_p.P306P|DNAH9_ENST00000454412.2_Intron|DNAH9_ENST00000396001.2_3'UTR	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3994	AAA 6. {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)		GTGCAGAGCCAGCACCCTCCC	0.592													G|||	1114	0.222444	0.0787	0.2651	5008	,	,		17640	0.1815		0.341	False		,,,				2504	0.3067				p.P3994P		Atlas-SNP	.											.	DNAH9	695	.	0			c.A11982G						PASS	.	G	,	491,3915	779.8+/-414.4	32,427,1744	84.0	63.0	70.0		11982,918	-4.5	0.3	17	dbSNP_100	70	2858,5742	673.2+/-403.0	483,1892,1925	no	coding-synonymous,coding-synonymous	DNAH9	NM_001372.3,NM_004662.2	,	515,2319,3669	GG,GA,AA		33.2326,11.1439,25.7497	,	3994/4487,306/799	11833287	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon63			AGAGCCAGCACCC	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.11982A>G	17.37:g.11833287A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			A|0.755;G|0.245	0.245	strong		0.592	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
KCNJ4	3761	hgsc.bcm.edu	37	22	38823676	38823676	+	Silent	SNP	C	C	G	rs77032485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38823676C>G	ENST00000303592.3	-	2	720	c.462G>C	c.(460-462)gtG>gtC	p.V154V	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	154					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					TGGACTGGACCACCACAGCGA	0.617													C|||	6	0.00119808	0.0	0.0014	5008	,	,		17014	0.0		0.003	False		,,,				2504	0.002				p.V154V		Atlas-SNP	.											.	KCNJ4	74	.	0			c.G462C						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	78.0	69.0	72.0		462,462	2.6	1.0	22	dbSNP_131	72	57,8543	35.9+/-90.5	0,57,4243	no	coding-synonymous,coding-synonymous	KCNJ4	NM_004981.1,NM_152868.1	,	0,59,6444	GG,GC,CC		0.6628,0.0454,0.4536	,	154/446,154/446	38823676	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	3761	exon2			CTGGACCACCACA	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.462G>C	22.37:g.38823676C>G		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	89	36	0.404494	NM_004981	Q14D44	Silent	SNP	ENST00000303592.3	37	CCDS13971.1																																																																																			C|0.995;G|0.005	0.005	strong		0.617	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981	
CLCNKB	1188	hgsc.bcm.edu	37	1	16380243	16380243	+	Missense_Mutation	SNP	A	A	G	rs2275166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16380243A>G	ENST00000375679.4	+	16	1843	c.1732A>G	c.(1732-1734)Aag>Gag	p.K578E	CLCNKB_ENST00000375667.3_Missense_Mutation_p.K409E	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	578	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.		K -> E (in dbSNP:rs2275166). {ECO:0000269|PubMed:8041726, ECO:0000269|PubMed:8544406}.		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		AGACGTGGCCAAGTATCCCCT	0.607													G|||	3514	0.701677	0.82	0.5519	5008	,	,		18861	0.8056		0.6262	False		,,,				2504	0.6186				p.K578E		Atlas-SNP	.											.	CLCNKB	50	.	0			c.A1732G						PASS	.	G	GLU/LYS,GLU/LYS	3522,884		1407,708,88	92.0	73.0	79.0		1732,1225	1.4	0.2	1	dbSNP_100	79	5593,3007		1836,1921,543	yes	missense,missense	CLCNKB	NM_000085.3,NM_001165945.1	56,56	3243,2629,631	GG,GA,AA		34.9651,20.0635,29.917	benign,benign	578/688,409/519	16380243	9115,3891	2203	4300	6503	SO:0001583	missense	1188	exon16			GTGGCCAAGTATC	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1732A>G	1.37:g.16380243A>G	ENSP00000364831:p.Lys578Glu	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	187	161	0.860963	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Missense_Mutation	SNP	ENST00000375679.4	37	CCDS168.1	1534	0.7023809523809523	401	0.8150406504065041	207	0.5718232044198895	468	0.8181818181818182	458	0.604221635883905	N	0.746	-0.774522	0.02951	0.799365	0.650349	ENSG00000184908	ENST00000375668;ENST00000375679;ENST00000375667;ENST00000431772	D;D;D	0.93307	-3.2;-3.2;-2.28	4.59	1.41	0.22369	Cystathionine beta-synthase, core (3);	0.431416	0.24980	N	0.034065	T	0.00012	0.0000	N	0.00801	-1.175	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.43940	-0.9360	9	0.19147	T	0.46	.	5.3044	0.15795	0.1936:0.3277:0.4787:0.0	rs2275166;rs3978484;rs6423944;rs17356694;rs34009081;rs2275166	409;578	Q5T5Q7;P51801	.;CLCKB_HUMAN	E	76;578;409;67	ENSP00000364831:K578E;ENSP00000364819:K409E;ENSP00000389344:K67E	ENSP00000364819:K409E	K	+	1	0	CLCNKB	16252830	0.654000	0.27367	0.159000	0.22649	0.866000	0.49608	0.853000	0.27777	-0.094000	0.12374	-0.133000	0.14855	AAG	A|0.294;G|0.706	0.706	strong		0.607	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
HLCS	3141	hgsc.bcm.edu	37	21	38308911	38308911	+	Silent	SNP	G	G	A	rs1065758	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:38308911G>A	ENST00000399120.1	-	5	2064	c.834C>T	c.(832-834)agC>agT	p.S278S	HLCS_ENST00000336648.4_Silent_p.S278S	NM_001242784.1	NP_001229713.1	P50747	BPL1_HUMAN	holocarboxylase synthetase (biotin-(proprionyl-CoA-carboxylase (ATP-hydrolysing)) ligase)	278					biotin metabolic process (GO:0006768)|cell proliferation (GO:0008283)|histone biotinylation (GO:0071110)|histone modification (GO:0016570)|protein biotinylation (GO:0009305)|response to biotin (GO:0070781)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin-[acetyl-CoA-carboxylase] ligase activity (GO:0004077)|biotin-[methylcrotonoyl-CoA-carboxylase] ligase activity (GO:0004078)|biotin-[methylmalonyl-CoA-carboxytransferase] ligase activity (GO:0004079)|biotin-[propionyl-CoA-carboxylase (ATP-hydrolyzing)] ligase activity (GO:0004080)|biotin-protein ligase activity (GO:0018271)|enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(46;0.0422)			Biotin(DB00121)	GCTTCACCTCGCTCTGGTCAG	0.592													G|||	357	0.0712859	0.031	0.0821	5008	,	,		19451	0.0417		0.172	False		,,,				2504	0.045				p.S278S		Atlas-SNP	.											.	HLCS	64	.	0			c.C834T						PASS	.	G	,,	242,4164	142.3+/-177.5	7,228,1968	78.0	74.0	75.0		834,834,834	-9.0	0.0	21	dbSNP_86	75	1407,7193	271.7+/-289.7	125,1157,3018	yes	coding-synonymous,coding-synonymous,coding-synonymous	HLCS	NM_000411.6,NM_001242784.1,NM_001242785.1	,,	132,1385,4986	AA,AG,GG		16.3605,5.4925,12.6788	,,	278/727,278/727,278/727	38308911	1649,11357	2203	4300	6503	SO:0001819	synonymous_variant	3141	exon5			CACCTCGCTCTGG		CCDS13647.1	21q22.1	2012-07-13	2010-04-30		ENSG00000159267	ENSG00000159267	6.3.4.9, 6.3.4.10, 6.3.4.11, 6.3.4.15		4976	protein-coding gene	gene with protein product		609018	"""holocarboxylase synthetase (biotin-[proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)] ligase)"", ""holocarboxylase synthetase (biotin-(proprionyl-Coenzyme A-carboxylase (ATP-hydrolysing)) ligase)"""			7842009	Standard	NM_000411		Approved	HCS	uc021wjb.1	P50747	OTTHUMG00000086636	ENST00000399120.1:c.834C>T	21.37:g.38308911G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	115	50	0.434783	NM_000411	B2RAH1|D3DSG6|Q99451	Silent	SNP	ENST00000399120.1	37	CCDS13647.1																																																																																			G|0.893;A|0.107	0.107	strong		0.592	HLCS-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194687.2		
UBE2S	27338	hgsc.bcm.edu	37	19	55913038	55913038	+	Silent	SNP	C	C	T	rs7608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55913038C>T	ENST00000264552.9	-	4	622	c.435G>A	c.(433-435)gcG>gcA	p.A145A	CTD-2105E13.13_ENST00000589101.1_lincRNA|RPL28_ENST00000560055.1_Intron|UBE2S_ENST00000592570.1_5'Flank	NM_014501.2	NP_055316.2	Q16763	UBE2S_HUMAN	ubiquitin-conjugating enzyme E2S	145					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular protein modification process (GO:0006464)|exit from mitosis (GO:0010458)|free ubiquitin chain polymerization (GO:0010994)|protein K11-linked ubiquitination (GO:0070979)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)	anaphase-promoting complex (GO:0005680)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			lung(1)	1	Breast(117;0.155)		LUSC - Lung squamous cell carcinoma(43;0.13)|BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.11)		GGGCCCGAGCCGCATACTCCT	0.677													C|||	2909	0.580871	0.5726	0.5663	5008	,	,		13549	0.4831		0.6978	False		,,,				2504	0.5828				p.A145A		Atlas-SNP	.											.	UBE2S	8	.	0			c.G435A						PASS	.						10.0	13.0	12.0					19																	55913038		2150	4162	6312	SO:0001819	synonymous_variant	27338	exon4			CCGAGCCGCATAC	BC004236	CCDS33114.1	19q13.43	2008-02-05				ENSG00000108106		"""Ubiquitin-conjugating enzymes E2"""	17895	protein-coding gene	gene with protein product	"""ubiquitin carrier protein"", ""ubiquitin-conjugating enzyme E2-24 kD"", ""ubiquitin-protein ligase"""	610309				1379239	Standard	NM_014501		Approved	E2-EPF	uc002qkx.1	Q16763		ENST00000264552.9:c.435G>A	19.37:g.55913038C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	53	47	0.886792	NM_014501	Q9BTC1	Silent	SNP	ENST00000264552.9	37	CCDS33114.1																																																																																			C|0.427;T|0.573	0.573	strong		0.677	UBE2S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453088.1	NM_014501	
SLFN14	342618	hgsc.bcm.edu	37	17	33876083	33876083	+	Silent	SNP	G	G	A	rs1001441	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33876083G>A	ENST00000415846.3	-	4	1949	c.1914C>T	c.(1912-1914)acC>acT	p.T638T		NM_001129820.1	NP_001123292.1	P0C7P3	SLN14_HUMAN	schlafen family member 14	638							ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(3)	9						CTTGGCAGGTGGTTTGTTGGC	0.433													G|||	950	0.189696	0.2231	0.1902	5008	,	,		21612	0.2976		0.0954	False		,,,				2504	0.1299				p.T638T		Atlas-SNP	.											.	SLFN14	43	.	0			c.C1914T						PASS	.	G		291,1093		29,233,430	76.0	64.0	68.0		1914	-0.2	0.0	17	dbSNP_86	68	276,2906		11,254,1326	no	coding-synonymous	SLFN14	NM_001129820.1		40,487,1756	AA,AG,GG		8.6738,21.026,12.4179		638/913	33876083	567,3999	692	1591	2283	SO:0001819	synonymous_variant	342618	exon4			GCAGGTGGTTTGT		CCDS45650.1	17q12	2009-09-22				ENSG00000236320			32689	protein-coding gene	gene with protein product		614958				9846487	Standard	NM_001129820		Approved		uc010ctu.1	P0C7P3		ENST00000415846.3:c.1914C>T	17.37:g.33876083G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	111	56	0.504505	NM_001129820	B2RTW9	Silent	SNP	ENST00000415846.3	37	CCDS45650.1																																																																																			G|0.790;A|0.210	0.210	strong		0.433	SLFN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448928.1	NM_001129820	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458772	39458772	+	Missense_Mutation	SNP	G	G	A	rs117847625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39458772G>A	ENST00000391353.1	-	1	331	c.332C>T	c.(331-333)tCg>tTg	p.S111L		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	111	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											AGTAGATTCCGAGCAGGATGG	0.537													G|||	87	0.0173722	0.0015	0.0418	5008	,	,		24603	0.0		0.0537	False		,,,				2504	0.002				p.S111L		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.C332T						PASS	.																																			SO:0001583	missense	100533177	exon1			GATTCCGAGCAGG		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.332C>T	17.37:g.39458772G>A	ENSP00000375148:p.Ser111Leu	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	59	23	0.38983	NM_001257309		Missense_Mutation	SNP	ENST00000391353.1	37		53	0.024267399267399268	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	38	0.05013192612137203	G	0.058	-1.231533	0.01505	.	.	ENSG00000212658	ENST00000391353	.	.	.	5.38	-7.21	0.01490	.	.	.	.	.	T	0.06325	0.0163	.	.	.	.	.	.	.	.	.	.	.	.	T	0.40924	-0.9537	4	0.66056	D	0.02	.	5.1253	0.14880	0.6068:0.1009:0.1906:0.1018	.	.	.	.	L	111	.	ENSP00000375148:S111L	S	-	2	0	KRTAP29-1	36712298	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	-0.838000	0.04372	-1.373000	0.02134	-1.223000	0.01593	TCG	G|0.969;A|0.031	0.031	strong		0.537	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
CPAMD8	27151	hgsc.bcm.edu	37	19	17091368	17091368	+	Silent	SNP	T	T	G	rs8103646	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17091368T>G	ENST00000443236.1	-	14	1696	c.1665A>C	c.(1663-1665)cgA>cgC	p.R555R	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	508						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CCCGCTTGCTTCGCTGCTGGG	0.587													T|||	2373	0.473842	0.6475	0.3559	5008	,	,		17983	0.5506		0.3509	False		,,,				2504	0.3701				p.R555R		Atlas-SNP	.											CPAMD8,NS,carcinoma,-1,1	CPAMD8	192	1	0			c.A1665C						PASS	.	T		2244,1706		634,976,365	58.0	65.0	63.0		1665	0.6	1.0	19	dbSNP_116	63	2636,5682		401,1834,1924	no	coding-synonymous	CPAMD8	NM_015692.2		1035,2810,2289	GG,GT,TT		31.6903,43.1899,39.7783		555/1933	17091368	4880,7388	1975	4159	6134	SO:0001819	synonymous_variant	27151	exon14			CTTGCTTCGCTGC	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1665A>C	19.37:g.17091368T>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	99	48	0.484848	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	1035	0.4739010989010989	317	0.6443089430894309	133	0.3674033149171271	312	0.5454545454545454	273	0.36015831134564646	T	7.048	0.563842	0.13498	0.568101	0.316903	ENSG00000160111	ENST00000443236	.	.	.	2.9	0.633	0.17712	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999769414	.	.	.	.	.	.	T	0.43572	-0.9383	3	.	.	.	.	7.1737	0.25732	0.0:0.4272:0.0:0.5728	rs8103646	.	.	.	A	566	.	.	E	-	2	0	CPAMD8	16952368	0.968000	0.33430	0.972000	0.41901	0.565000	0.35776	-0.114000	0.10757	0.105000	0.17753	0.383000	0.25322	GAA	T|0.601;G|0.399	0.399	strong		0.587	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4451570	4451570	+	Missense_Mutation	SNP	G	G	A	rs142700966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4451570G>A	ENST00000254718.4	-	12	1898	c.1592C>T	c.(1591-1593)gCa>gTa	p.A531V	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.A531V			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	531	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						CTGGCCCGGTGCCTGCTTGAA	0.632													G|||	4	0.000798722	0.0	0.0	5008	,	,		17643	0.0		0.004	False		,,,				2504	0.0				p.A531V		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C1592T						PASS	.						66.0	65.0	65.0					17																	4451570		2203	4300	6503	SO:0001583	missense	10514	exon12			CCCGGTGCCTGCT	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.1592C>T	17.37:g.4451570G>A	ENSP00000254718:p.Ala531Val	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	3.338	-0.135261	0.06711	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.50813	0.73;0.73	5.48	-0.24	0.13047	Armadillo-type fold (1);	0.643159	0.16655	N	0.205055	T	0.21186	0.0510	L	0.35414	1.06	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.004	T	0.11155	-1.0599	10	0.22706	T	0.39	-5.7941	4.1307	0.10148	0.4189:0.1728:0.4083:0.0	.	531;531	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	V	531	ENSP00000370968:A531V;ENSP00000254718:A531V	ENSP00000254718:A531V	A	-	2	0	MYBBP1A	4398319	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.430000	0.21428	0.040000	0.15660	0.655000	0.94253	GCA	G|0.998;A|0.002	0.002	strong		0.632	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
RRP12	23223	hgsc.bcm.edu	37	10	99118716	99118716	+	Missense_Mutation	SNP	G	G	T	rs143870774	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99118716G>T	ENST00000370992.4	-	32	3803	c.3692C>A	c.(3691-3693)gCt>gAt	p.A1231D	RRP12_ENST00000536831.1_Missense_Mutation_p.A949D|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000315563.6_Missense_Mutation_p.A1131D|RRP12_ENST00000414986.1_Missense_Mutation_p.A1170D	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1231						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)		CTTGTATTCAGCCCCAGGCAT	0.612																																					p.A1231D		Atlas-SNP	.											.	RRP12	97	.	0			c.C3692A						PASS	.						91.0	65.0	74.0					10																	99118716		2203	4300	6503	SO:0001583	missense	23223	exon32			TATTCAGCCCCAG		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.3692C>A	10.37:g.99118716G>T	ENSP00000360031:p.Ala1231Asp	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	45	27	0.6	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730886	0.48939	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.58	5.58	0.84498	.	0.228748	0.45126	D	0.000387	T	0.34454	0.0898	L	0.43923	1.385	0.48762	D	0.999708	P;P;D;P	0.53745	0.937;0.935;0.962;0.937	B;P;P;B	0.51833	0.276;0.681;0.528;0.218	T	0.02498	-1.1150	10	0.12103	T	0.63	-6.7512	13.8164	0.63295	0.0733:0.0:0.9267:0.0	.	1170;1131;949;1231	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	D	1231;1131;1170;949	ENSP00000360031:A1231D;ENSP00000324315:A1131D;ENSP00000414863:A1170D;ENSP00000446184:A949D	ENSP00000324315:A1131D	A	-	2	0	RRP12	99108706	0.963000	0.33076	0.875000	0.34327	0.341000	0.28922	3.020000	0.49643	2.635000	0.89317	0.561000	0.74099	GCT	G|0.998;A|0.002	.	alt		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573754	140573754	+	Missense_Mutation	SNP	A	A	C	rs702386		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140573754A>C	ENST00000239446.4	+	1	1813	c.1629A>C	c.(1627-1629)agA>agC	p.R543S		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	543	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.			R -> S (in Ref. 2; AAK51616). {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(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)			CGCTGAGCAGAGAGGCGCTGG	0.701																																					p.R543S		Atlas-SNP	.											PCDHB10,colon,carcinoma,0,1	PCDHB10	177	1	0			c.A1629C						PASS	.						37.0	53.0	47.0					5																	140573754		2191	4291	6482	SO:0001583	missense	56126	exon1			GAGCAGAGAGGCG	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.1629A>C	5.37:g.140573754A>C	ENSP00000239446:p.Arg543Ser	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	22	22	1	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	1085	0.4967948717948718	272	0.5528455284552846	171	0.4723756906077348	330	0.5769230769230769	312	0.41160949868073876	a	3.278	-0.147626	0.06627	.	.	ENSG00000120324	ENST00000239446	T	0.46063	0.88	3.53	3.53	0.40419	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.00005	-3.295	0.50467	P	1.2299999999998423E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47636	-0.9102	8	0.02654	T	1	.	7.2252	0.26012	0.1715:0.7353:0.0:0.0932	rs702386;rs17844583	543	Q9UN67	PCDBA_HUMAN	S	543	ENSP00000239446:R543S	ENSP00000239446:R543S	R	+	3	2	PCDHB10	140553938	0.001000	0.12720	1.000000	0.80357	0.970000	0.65996	0.307000	0.19296	0.852000	0.35287	-0.233000	0.12211	AGA	.	.	weak		0.701	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
ZNF860	344787	hgsc.bcm.edu	37	3	32031962	32031962	+	Missense_Mutation	SNP	A	A	G	rs1808125	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:32031962A>G	ENST00000360311.4	+	2	1940	c.1391A>G	c.(1390-1392)cAt>cGt	p.H464R		NM_001137674.2	NP_001131146.2	A6NHJ4	ZN860_HUMAN	zinc finger protein 860	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|lung(4)|ovary(1)	8						AAGACCTTCCATCACAATTCA	0.418													a|||	3114	0.621805	0.9054	0.4813	5008	,	,		19471	0.7599		0.2773	False		,,,				2504	0.5501				p.H464R		Atlas-SNP	.											ZNF860_ENST00000360311,NS,carcinoma,0,6	ZNF860	96	6	0			c.A1391G						PASS	.						22.0	58.0	48.0					3																	32031962		627	1568	2195	SO:0001583	missense	344787	exon2			CCTTCCATCACAA	AK294003	CCDS46784.1	3p24.1	2013-01-08			ENSG00000197385	ENSG00000197385		"""Zinc fingers, C2H2-type"", ""-"""	34513	protein-coding gene	gene with protein product							Standard	NM_001137674		Approved		uc011axg.2	A6NHJ4	OTTHUMG00000155838	ENST00000360311.4:c.1391A>G	3.37:g.32031962A>G	ENSP00000373274:p.His464Arg	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	33	0.452055	NM_001137674	B4DFA4	Missense_Mutation	SNP	ENST00000360311.4	37	CCDS46784.1	991	0.45375457875457875	324	0.6585365853658537	145	0.4005524861878453	368	0.6433566433566433	154	0.20316622691292877	a	0.169	-1.073378	0.01918	.	.	ENSG00000197385	ENST00000360311	T	0.17370	2.28	0.3	-0.599	0.11645	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00399	-1.545	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.42032	-0.9475	7	.	.	.	.	4.0852	0.09943	0.2146:0.4157:0.3696:0.0	rs1808125;rs60384157	464	A6NHJ4	ZN860_HUMAN	R	464	ENSP00000373274:H464R	.	H	+	2	0	ZNF860	32006966	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.083000	0.03397	-3.961000	0.00087	-3.988000	0.00014	CAT	A|0.545;G|0.455	0.455	strong		0.418	ZNF860-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341957.1		
TDP2	51567	hgsc.bcm.edu	37	6	24667074	24667074	+	Missense_Mutation	SNP	C	C	A	rs61760186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:24667074C>A	ENST00000378198.4	-	1	187	c.17G>T	c.(16-18)tGc>tTc	p.C6F	TDP2_ENST00000341060.3_5'Flank|ACOT13_ENST00000537591.1_5'Flank|ACOT13_ENST00000230048.4_5'Flank|TDP2_ENST00000545995.1_Missense_Mutation_p.C36F			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	6					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						GCCCTCCAGGCAACTCCCCAA	0.657								Direct reversal of damage					C|||	11	0.00219649	0.003	0.0029	5008	,	,		14407	0.0		0.005	False		,,,				2504	0.0				p.C6F		Atlas-SNP	.											.	TDP2	29	.	0			c.G17T						PASS	.	C	PHE/CYS	11,4395	17.9+/-39.9	0,11,2192	92.0	107.0	102.0		17	0.6	0.0	6	dbSNP_129	102	28,8572	20.4+/-63.3	1,26,4273	yes	missense	TDP2	NM_016614.2	205	1,37,6465	AA,AC,CC		0.3256,0.2497,0.2999	probably-damaging	6/363	24667074	39,12967	2203	4300	6503	SO:0001583	missense	51567	exon1			TCCAGGCAACTCC	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"""TRAF and TNF receptor associated protein"""	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.17G>T	6.37:g.24667074C>A	ENSP00000367440:p.Cys6Phe	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	48	29	0.604167	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Missense_Mutation	SNP	ENST00000378198.4	37	CCDS4557.1	9	0.004120879120879121	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	11.65	1.701925	0.30232	0.002497	0.003256	ENSG00000111802	ENST00000378198;ENST00000545995;ENST00000545780	T;T	0.25085	1.93;1.82	4.51	0.603	0.17541	.	2.748860	0.00807	N	0.001479	T	0.05547	0.0146	N	0.22421	0.69	0.09310	N	1	B;B	0.28783	0.222;0.122	B;B	0.25759	0.063;0.025	T	0.22906	-1.0203	10	0.40728	T	0.16	-12.8014	3.1399	0.06452	0.1875:0.4951:0.0:0.3174	rs61760186	36;6	O95551-2;O95551	.;TYDP2_HUMAN	F	6;36;6	ENSP00000367440:C6F;ENSP00000437637:C36F	ENSP00000367440:C6F	C	-	2	0	TDP2	24775053	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.717000	0.04986	0.218000	0.20820	-0.127000	0.14921	TGC	C|0.997;A|0.003	0.003	strong		0.657	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1		
DHX35	60625	hgsc.bcm.edu	37	20	37601243	37601243	+	Silent	SNP	A	A	G	rs16987712	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37601243A>G	ENST00000252011.3	+	3	249	c.216A>G	c.(214-216)acA>acG	p.T72T	DHX35_ENST00000373325.2_Silent_p.T72T|DHX35_ENST00000373323.4_Intron	NM_021931.3	NP_068750.2	Q9H5Z1	DHX35_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 35	72	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	40		Myeloproliferative disorder(115;0.00878)				ATTATCAGACAGTGGTGATTG	0.358													A|||	874	0.174521	0.1558	0.1499	5008	,	,		17685	0.1319		0.2137	False		,,,				2504	0.2209				p.T72T		Atlas-SNP	.											.	DHX35	82	.	0			c.A216G						PASS	.	A	,	746,3660	306.0+/-289.3	53,640,1510	120.0	123.0	122.0		,216	-9.6	0.8	20	dbSNP_123	122	1736,6864	316.6+/-312.8	174,1388,2738	no	intron,coding-synonymous	DHX35	NM_001190809.1,NM_021931.3	,	227,2028,4248	GG,GA,AA		20.186,16.9315,19.0835	,	,72/704	37601243	2482,10524	2203	4300	6503	SO:0001819	synonymous_variant	60625	exon3			TCAGACAGTGGTG	AK026412	CCDS13310.1, CCDS54463.1	20q11.22-q12	2003-06-13	2003-06-13	2003-06-13	ENSG00000101452	ENSG00000101452		"""DEAH-boxes"""	15861	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 35"""	C20orf15, DDX35			Standard	NM_001190809		Approved	FLJ22759, KAIA0875	uc002xjh.3	Q9H5Z1	OTTHUMG00000032463	ENST00000252011.3:c.216A>G	20.37:g.37601243A>G		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_021931	A2RTX3|B4E0J0|F5GXM6|Q5THR0|Q9H4H7|Q9H6T6	Silent	SNP	ENST00000252011.3	37	CCDS13310.1																																																																																			A|0.815;G|0.185	0.185	strong		0.358	DHX35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079212.2	NM_021931	
MYT1L	23040	hgsc.bcm.edu	37	2	1842968	1842968	+	Silent	SNP	T	T	C	rs6728368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:1842968T>C	ENST00000399161.2	-	21	3780	c.3033A>G	c.(3031-3033)ggA>ggG	p.G1011G	MYT1L_ENST00000407844.1_Silent_p.G7G|MYT1L_ENST00000428368.2_Silent_p.G1009G|MYT1L_ENST00000471668.1_5'UTR	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1011					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)		AGCCGTCGCATCCTGGCGTGG	0.667													C|||	2287	0.456669	0.5575	0.3141	5008	,	,		15189	0.6558		0.3121	False		,,,				2504	0.365				p.G1009G		Atlas-SNP	.											.	MYT1L	241	.	0			c.A3027G						PASS	.	C		2557,1539		907,743,398	28.0	34.0	32.0		3027	-11.1	0.0	2	dbSNP_116	32	2826,5556		495,1836,1860	no	coding-synonymous	MYT1L	NM_015025.2		1402,2579,2258	CC,CT,TT		33.7151,37.5732,43.1399		1009/1185	1842968	5383,7095	2048	4191	6239	SO:0001819	synonymous_variant	23040	exon21			GTCGCATCCTGGC	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.3033A>G	2.37:g.1842968T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	99	36	0.363636	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				T|0.535;C|0.455;A|0.010	0.455	strong		0.667	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
PUS7L	83448	hgsc.bcm.edu	37	12	44148259	44148259	+	Missense_Mutation	SNP	T	T	C	rs1057190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:44148259T>C	ENST00000416848.2	-	2	1278	c.790A>G	c.(790-792)Aaa>Gaa	p.K264E	PUS7L_ENST00000431332.3_Intron|PUS7L_ENST00000344862.5_Missense_Mutation_p.K264E|PUS7L_ENST00000553166.1_Missense_Mutation_p.K264E|PUS7L_ENST00000551923.1_Missense_Mutation_p.K264E	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	264			K -> E (in dbSNP:rs1057190). {ECO:0000269|PubMed:17974005}.		pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		CAATTCATTTTAGAAAAAGAT	0.383													C|||	1341	0.267772	0.5908	0.1657	5008	,	,		16995	0.1905		0.1083	False		,,,				2504	0.1472				p.K264E		Atlas-SNP	.											.	PUS7L	73	.	0			c.A790G						PASS	.	C	GLU/LYS,GLU/LYS,GLU/LYS	2262,2144	579.2+/-384.9	572,1118,513	129.0	126.0	127.0		790,790,790	5.3	0.8	12	dbSNP_86	127	990,7610	772.6+/-407.7	48,894,3358	yes	missense,missense,missense	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	56,56,56	620,2012,3871	CC,CT,TT		11.5116,48.6609,25.0038	benign,benign,benign	264/702,264/702,264/702	44148259	3252,9754	2203	4300	6503	SO:0001583	missense	83448	exon2			TCATTTTAGAAAA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.790A>G	12.37:g.44148259T>C	ENSP00000415899:p.Lys264Glu	Somatic	280	0	0		WXS	Illumina HiSeq	Phase_I	256	132	0.515625	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	502	0.22985347985347984	277	0.5630081300813008	56	0.15469613259668508	92	0.16083916083916083	77	0.10158311345646438	C	0.160	-1.082297	0.01888	0.513391	0.115116	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000553166	T;T;T;T	0.21361	2.02;2.02;2.02;2.01	5.35	5.35	0.76521	Pseudouridine synthase, catalytic domain (1);	0.255452	0.44097	N	0.000491	T	0.00012	0.0000	N	0.00347	-1.61	0.27947	P	0.9373084	B	0.02656	0.0	B	0.01281	0.0	T	0.41787	-0.9489	9	0.02654	T	1	-9.231	13.0403	0.58895	0.0:0.8633:0.0:0.1367	rs1057190;rs52792291;rs60869292;rs1057190	264	Q9H0K6	PUS7L_HUMAN	E	264	ENSP00000415899:K264E;ENSP00000343081:K264E;ENSP00000447706:K264E;ENSP00000446865:K264E	ENSP00000343081:K264E	K	-	1	0	PUS7L	42434526	0.025000	0.19082	0.771000	0.31576	0.065000	0.16274	2.632000	0.46511	1.604000	0.50143	-0.119000	0.15052	AAA	T|0.749;C|0.251	0.251	strong		0.383	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
MPHOSPH8	54737	hgsc.bcm.edu	37	13	20224387	20224387	+	Silent	SNP	A	A	G	rs9578176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:20224387A>G	ENST00000361479.5	+	5	1631	c.1563A>G	c.(1561-1563)gcA>gcG	p.A521A	MPHOSPH8_ENST00000414242.2_Silent_p.A521A	NM_017520.3	NP_059990.2	Q99549	MPP8_HUMAN	M-phase phosphoprotein 8	521					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of DNA methylation (GO:0044030)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nuclear nucleosome (GO:0000788)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	methylated histone binding (GO:0035064)			breast(2)|endometrium(1)|large_intestine(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16		all_cancers(29;2.83e-16)|all_lung(29;1.16e-17)|all_epithelial(30;8.13e-16)|Lung NSC(5;6.91e-15)|Lung SC(185;0.0367)		all cancers(112;8.43e-05)|Epithelial(112;0.000426)|OV - Ovarian serous cystadenocarcinoma(117;0.00596)|Lung(94;0.015)|LUSC - Lung squamous cell carcinoma(192;0.0795)		TGTGCCAAGCAGATGAGAATT	0.408													A|||	534	0.106629	0.1974	0.0735	5008	,	,		17874	0.0754		0.0974	False		,,,				2504	0.0491				p.A521A		Atlas-SNP	.											.	MPHOSPH8	58	.	0			c.A1563G						PASS	.	A		783,3623	313.3+/-293.0	75,633,1495	144.0	123.0	130.0		1563	-9.1	0.0	13	dbSNP_119	130	646,7954	165.4+/-217.5	18,610,3672	no	coding-synonymous	MPHOSPH8	NM_017520.3		93,1243,5167	GG,GA,AA		7.5116,17.7712,10.9872		521/861	20224387	1429,11577	2203	4300	6503	SO:0001819	synonymous_variant	54737	exon5			CCAAGCAGATGAG	AK056785, AJ293409	CCDS9287.1	13q12.11	2013-01-10			ENSG00000196199	ENSG00000196199		"""Ankyrin repeat domain containing"""	29810	protein-coding gene	gene with protein product		611626				8885239	Standard	NM_017520		Approved	mpp8, HSMPP8	uc001umh.3	Q99549	OTTHUMG00000016498	ENST00000361479.5:c.1563A>G	13.37:g.20224387A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	73	30	0.410959	NM_017520	B7Z6F9|Q5JPE5|Q5JTQ0|Q86TK3|Q96MK4|Q9BTP1	Silent	SNP	ENST00000361479.5	37	CCDS9287.1																																																																																			A|0.886;G|0.114	0.114	strong		0.408	MPHOSPH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044028.2	NM_017520	
FAM83D	81610	hgsc.bcm.edu	37	20	37555116	37555116	+	Missense_Mutation	SNP	G	G	C	rs3752290	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37555116G>C	ENST00000217429.4	+	1	162	c.121G>C	c.(121-123)Gtg>Ctg	p.V41L		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	11					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(2)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)|stomach(1)	28		Myeloproliferative disorder(115;0.00878)				CCTGGACGAGGTGCCCGCCGC	0.701													C|||	2010	0.401358	0.5076	0.3847	5008	,	,		10968	0.4157		0.3429	False		,,,				2504	0.3149				p.V41L		Atlas-SNP	.											FAM83D,NS,carcinoma,0,2	FAM83D	60	2	0			c.G121C						PASS	.	C	LEU/VAL	1601,2097		394,813,642	8.0	11.0	10.0		121	3.4	0.9	20	dbSNP_107	10	2399,5669		370,1659,2005	no	missense	FAM83D	NM_030919.2	32	764,2472,2647	CC,CG,GG		29.7348,43.2937,33.9963	benign	41/616	37555116	4000,7766	1849	4034	5883	SO:0001583	missense	81610	exon1			GACGAGGTGCCCG	AL023803	CCDS42872.1	20q11.23	2014-03-13	2006-03-23	2006-03-23	ENSG00000101447	ENSG00000101447			16122	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 129"""	C20orf129		23205133	Standard	NM_030919		Approved	dJ616B8.3	uc002xjg.3	Q9H4H8	OTTHUMG00000032462	ENST00000217429.4:c.121G>C	20.37:g.37555116G>C	ENSP00000217429:p.Val41Leu	Somatic	13	0	0		WXS	Illumina HiSeq	Phase_I	15	14	0.933333	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	37	CCDS42872.1	870	0.3983516483516483	269	0.5467479674796748	136	0.3756906077348066	202	0.3531468531468531	263	0.3469656992084433	C	0.704	-0.789777	0.02884	0.432937	0.297348	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.10477	2.87	5.48	3.44	0.39384	.	0.490125	0.16258	N	0.222396	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38757	-0.9646	9	0.06891	T	0.86	.	7.0157	0.24887	0.0:0.4204:0.417:0.1626	rs3752290;rs17846649;rs17859744;rs3752290	11;11	Q9H4H8;Q9H4H8-2	FA83D_HUMAN;.	L	41;11	ENSP00000217429:V41L	ENSP00000217429:V41L	V	+	1	0	FAM83D	36988530	0.003000	0.15002	0.905000	0.35620	0.017000	0.09413	0.278000	0.18753	0.696000	0.31696	-0.120000	0.15030	GTG	G|0.618;C|0.382	0.382	strong		0.701	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1		
AAK1	22848	hgsc.bcm.edu	37	2	69709919	69709919	+	Silent	SNP	A	A	G	rs6721259	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:69709919A>G	ENST00000409085.4	-	18	2767	c.2391T>C	c.(2389-2391)tcT>tcC	p.S797S	AAK1_ENST00000406297.3_Silent_p.S797S|AAK1_ENST00000409068.1_Intron	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	797					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						AAGTGTCAGGAGATTTGAGTC	0.398													A|||	715	0.142772	0.2141	0.1023	5008	,	,		21839	0.0407		0.1938	False		,,,				2504	0.1278				p.S797S		Atlas-SNP	.											.	AAK1	121	.	0			c.T2391C						PASS	.	A		705,3121		69,567,1277	138.0	142.0	141.0		2391	4.8	1.0	2	dbSNP_116	141	1410,6856		128,1154,2851	no	coding-synonymous	AAK1	NM_014911.3		197,1721,4128	GG,GA,AA		17.0578,18.4266,17.4909		797/962	69709919	2115,9977	1913	4133	6046	SO:0001819	synonymous_variant	22848	exon18			GTCAGGAGATTTG	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.2391T>C	2.37:g.69709919A>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																			A|0.862;G|0.138	0.138	strong		0.398	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
PRDM15	63977	hgsc.bcm.edu	37	21	43258138	43258138	+	Silent	SNP	C	C	T	rs76107411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43258138C>T	ENST00000269844.3	-	15	2114	c.2004G>A	c.(2002-2004)ccG>ccA	p.P668P	PRDM15_ENST00000538201.1_Silent_p.P302P|PRDM15_ENST00000422911.1_Silent_p.P339P|PRDM15_ENST00000447207.2_Silent_p.P302P|PRDM15_ENST00000398548.1_Silent_p.P339P	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	668					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						CAGGCTCATCCGGAGGGACCT	0.547													C|||	163	0.0325479	0.0915	0.0115	5008	,	,		20003	0.001		0.0258	False		,,,				2504	0.0072				p.P668P		Atlas-SNP	.											.	PRDM15	110	.	0			c.G2004A						PASS	.	C	,	295,4111	161.8+/-193.9	13,269,1921	191.0	169.0	176.0		1017,2004	-8.4	0.0	21	dbSNP_132	176	287,8313	106.0+/-166.9	4,279,4017	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	17,548,5938	TT,TC,CC		3.3372,6.6954,4.4749	,	339/1179,668/1508	43258138	582,12424	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon15			CTCATCCGGAGGG	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.2004G>A	21.37:g.43258138C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	103	56	0.543689	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			C|0.958;T|0.042	0.042	strong		0.547	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
IFT80	57560	hgsc.bcm.edu	37	3	159997061	159997061	+	Missense_Mutation	SNP	T	T	A	rs6778728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:159997061T>A	ENST00000326448.7	-	16	2188	c.1756A>T	c.(1756-1758)Aca>Tca	p.T586S	IFT80_ENST00000483465.1_Missense_Mutation_p.T449S|IFT80_ENST00000496589.1_Missense_Mutation_p.T449S|RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.T757S	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	586			T -> S (in dbSNP:rs6778728). {ECO:0000269|PubMed:17974005}.		bone morphogenesis (GO:0060349)|chondrocyte differentiation (GO:0002062)|cilium assembly (GO:0042384)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of non-canonical Wnt signaling pathway (GO:2000051)|osteoblast differentiation (GO:0001649)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(12)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GGATATGGTGTTATGCTGATG	0.358													A|||	1309	0.261382	0.5598	0.1859	5008	,	,		17580	0.0685		0.2356	False		,,,				2504	0.137				p.T586S		Atlas-SNP	.											.	IFT80	68	.	0			c.A1756T						PASS	.	A	SER/THR,SER/THR,SER/THR	2086,2320	605.2+/-390.5	478,1130,595	96.0	96.0	96.0		1345,1345,1756	2.5	1.0	3	dbSNP_116	96	2165,6435	712.7+/-405.9	270,1625,2405	yes	missense,missense,missense	IFT80	NM_001190241.1,NM_001190242.1,NM_020800.2	58,58,58	748,2755,3000	AA,AT,TT		25.1744,47.3445,32.6849	benign,benign,benign	449/641,449/641,586/778	159997061	4251,8755	2203	4300	6503	SO:0001583	missense	57560	exon16			ATGGTGTTATGCT	AB037795	CCDS3188.1, CCDS54668.1	3q25.33	2014-07-03	2014-07-03	2005-11-02	ENSG00000068885	ENSG00000068885		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29262	protein-coding gene	gene with protein product		611177	"""WD repeat domain 56"", ""intraflagellar transport 80 homolog (Chlamydomonas)"""	WDR56		10718198	Standard	NM_020800		Approved	KIAA1374	uc021xgq.1	Q9P2H3	OTTHUMG00000158953	ENST00000326448.7:c.1756A>T	3.37:g.159997061T>A	ENSP00000312778:p.Thr586Ser	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	202	106	0.524752	NM_020800	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	37	CCDS3188.1	560	0.2564102564102564	271	0.5508130081300813	77	0.212707182320442	34	0.05944055944055944	178	0.23482849604221637	A	5.706	0.314848	0.10789	0.473445	0.251744	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	T;T;T	0.69806	0.38;-0.43;-0.43	6.16	2.54	0.30619	.	0.117523	0.36703	N	0.002458	T	0.00012	0.0000	N	0.00205	-1.85	0.53005	P	3.100000000000325E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.45571	-0.9252	9	0.02654	T	1	-25.5461	5.8425	0.18641	0.7021:0.0:0.185:0.1129	rs6778728;rs52833709;rs6778728	586	Q9P2H3	IFT80_HUMAN	S	586;449;449	ENSP00000312778:T586S;ENSP00000418196:T449S;ENSP00000420646:T449S	ENSP00000312778:T586S	T	-	1	0	IFT80	161479755	0.998000	0.40836	0.978000	0.43139	0.955000	0.61496	2.644000	0.46613	-0.015000	0.14150	-0.265000	0.10407	ACA	T|0.699;A|0.301	0.301	strong		0.358	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800	
ATP11A	23250	hgsc.bcm.edu	37	13	113508839	113508839	+	Silent	SNP	G	G	C	rs9549573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113508839G>C	ENST00000487903.1	+	19	2326	c.2238G>C	c.(2236-2238)ctG>ctC	p.L746L	ATP11A_ENST00000283558.8_Silent_p.L746L|ATP11A_ENST00000375630.2_Silent_p.L746L|ATP11A_ENST00000375645.3_Silent_p.L746L			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	746					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				GAGACAACCTGTCCGGGTAGG	0.652													C|||	3487	0.696286	0.9644	0.7262	5008	,	,		15382	0.6567		0.6044	False		,,,				2504	0.4479				p.L746L		Atlas-SNP	.											.	ATP11A	225	.	0			c.G2238C						PASS	.	C	,	4036,368		1849,338,15	38.0	39.0	38.0		2238,2238	2.8	0.8	13	dbSNP_119	38	5293,3307		1625,2043,632	no	coding-synonymous,coding-synonymous	ATP11A	NM_015205.2,NM_032189.3	,	3474,2381,647	CC,CG,GG		38.4535,8.356,28.2605	,	746/1135,746/1192	113508839	9329,3675	2202	4300	6502	SO:0001819	synonymous_variant	23250	exon19			CAACCTGTCCGGG	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.2238G>C	13.37:g.113508839G>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	38	38	1	NM_032189	Q5VXT2	Silent	SNP	ENST00000487903.1	37	CCDS32011.1	1540	0.7051282051282052	473	0.9613821138211383	258	0.712707182320442	356	0.6223776223776224	453	0.5976253298153035	C	0.639	-0.814080	0.02798	0.91644	0.615465	ENSG00000068650	ENST00000418678	.	.	.	4.66	2.84	0.33178	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999997	.	.	.	.	.	.	T	0.16897	-1.0387	3	.	.	.	.	10.7428	0.46162	0.0:0.5688:0.3611:0.0701	rs9549573;rs60929322;rs9549573	.	.	.	S	721	.	.	C	+	2	0	ATP11A	112556840	1.000000	0.71417	0.764000	0.31436	0.011000	0.07611	2.234000	0.43035	0.391000	0.25143	-0.223000	0.12442	TGT	G|0.292;C|0.708	0.708	strong		0.652	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
BOD1L1	259282	hgsc.bcm.edu	37	4	13603591	13603591	+	Missense_Mutation	SNP	C	C	T	rs17807493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:13603591C>T	ENST00000040738.5	-	10	5068	c.4933G>A	c.(4933-4935)Gtt>Att	p.V1645I		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1645			V -> I (in dbSNP:rs17807493).			nucleus (GO:0005634)	DNA binding (GO:0003677)										TCTGTCACAACGCTATTTACA	0.453													c|||	55	0.0109824	0.0008	0.0144	5008	,	,		21483	0.0		0.0348	False		,,,				2504	0.0092				p.V1645I		Atlas-SNP	.											.	.	.	.	0			c.G4933A						PASS	.	T	ILE/VAL	24,4382	31.7+/-61.6	0,24,2179	205.0	211.0	209.0		4933	2.1	0.0	4	dbSNP_123	209	285,8315	106.8+/-167.6	7,271,4022	yes	missense	BOD1L	NM_148894.2	29	7,295,6201	TT,TC,CC		3.314,0.5447,2.3758	benign	1645/3052	13603591	309,12697	2203	4300	6503	SO:0001583	missense	259282	exon10			TCACAACGCTATT	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.4933G>A	4.37:g.13603591C>T	ENSP00000040738:p.Val1645Ile	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	134	75	0.559702	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	34	0.015567765567765568	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	29	0.03825857519788918	c	3.483	-0.105443	0.06967	0.005447	0.03314	ENSG00000038219	ENST00000040738	T	0.07114	3.22	4.8	2.13	0.27403	.	0.939386	0.08806	N	0.891041	T	0.00695	0.0023	N	0.04508	-0.205	0.09310	N	1	B	0.21147	0.052	B	0.08055	0.003	T	0.43940	-0.9360	10	0.06494	T	0.89	-0.4548	4.5084	0.11899	0.1427:0.5485:0.0:0.3088	rs17807493;rs52828021;rs17807493	1645	Q8NFC6	BOD1L_HUMAN	I	1645	ENSP00000040738:V1645I	ENSP00000040738:V1645I	V	-	1	0	BOD1L	13212689	0.000000	0.05858	0.000000	0.03702	0.306000	0.27790	0.161000	0.16481	0.189000	0.20188	-0.226000	0.12346	GTT	C|0.979;T|0.021	0.021	strong		0.453	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894	
OR2T29	343563	hgsc.bcm.edu	37	1	248722777	248722777	+	Missense_Mutation	SNP	T	T	A	rs77589892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248722777T>A	ENST00000328570.3	-	1	20	c.16A>T	c.(16-18)Agg>Tgg	p.R6W	RP11-438F14.3_ENST00000438623.1_RNA	NM_001004694.2	NP_001004694.2	Q8NH02	O2T29_HUMAN	olfactory receptor, family 2, subfamily T, member 29	6						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|lung(4)	5	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TTGGCCATCCTGGTGATGTTG	0.463																																					p.R6W		Atlas-SNP	.											.	OR2T29	8	.	0			c.A16T						PASS	.	A	TRP/ARG	2570,1836		591,1388,224	78.0	65.0	69.0		16	-0.6	0.0	1	dbSNP_131	69	2027,6569		69,1889,2340	no	missense	OR2T29	NM_001004694.2	101	660,3277,2564	AA,AT,TT		23.5807,41.6704,35.3561		6/316	248722777	4597,8405	2203	4298	6501	SO:0001583	missense	343563	exon1			CCATCCTGGTGAT		CCDS55695.1	1q44	2012-08-09			ENSG00000182783	ENSG00000182783		"""GPCR / Class A : Olfactory receptors"""	31253	protein-coding gene	gene with protein product							Standard	NM_001004694		Approved		uc001ieo.2	Q8NH02	OTTHUMG00000040382	ENST00000328570.3:c.16A>T	1.37:g.248722777T>A	ENSP00000331774:p.Arg6Trp	Somatic	892	0	0		WXS	Illumina HiSeq	Phase_I	687	218	0.317322	NM_001004694		Missense_Mutation	SNP	ENST00000328570.3	37	CCDS55695.1	.	.	.	.	.	.	.	.	.	.	N	7.770	0.707330	0.15239	0.583296	0.235807	ENSG00000182783	ENST00000328570	T	0.00466	7.23	2.34	-0.604	0.11626	.	0.645074	0.13113	N	0.412838	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	.	.	.	.	.	.	T	0.00006	-1.2513	7	0.20519	T	0.43	.	7.9651	0.30094	0.4093:0.0:0.0:0.5907	.	.	.	.	W	6	ENSP00000331774:R6W	ENSP00000331774:R6W	R	-	1	2	OR2T29	246789400	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.533000	0.06157	-0.193000	0.10415	-4.084000	0.00011	AGG	T|0.770;A|0.230	0.230	strong		0.463	OR2T29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097132.1	NM_001004694	
SEMA6D	80031	hgsc.bcm.edu	37	15	48056958	48056958	+	Silent	SNP	C	C	T	rs3743281	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:48056958C>T	ENST00000316364.5	+	12	1660	c.1221C>T	c.(1219-1221)gcC>gcT	p.A407A	SEMA6D_ENST00000558014.1_Silent_p.A407A|SEMA6D_ENST00000389428.3_Silent_p.A407A|SEMA6D_ENST00000558816.1_Silent_p.A407A|SEMA6D_ENST00000389433.2_Silent_p.A407A|SEMA6D_ENST00000358066.4_Silent_p.A407A|SEMA6D_ENST00000355997.3_Silent_p.A407A|SEMA6D_ENST00000536845.2_Silent_p.A407A|SEMA6D_ENST00000537942.1_Silent_p.A407A|SEMA6D_ENST00000389425.3_Silent_p.A407A|SEMA6D_ENST00000354744.4_Silent_p.A407A|SEMA6D_ENST00000389432.2_Silent_p.A407A	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	407	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		CACCCATTGCCGATGAGCCCT	0.502													C|||	945	0.188698	0.0431	0.2075	5008	,	,		21013	0.1746		0.2724	False		,,,				2504	0.3006				p.A407A		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C1221T						PASS	.	C	,,,,,,	305,4091	165.8+/-197.2	10,285,1903	78.0	74.0	75.0		1221,1221,1221,1221,1221,1221,1221	-4.9	0.4	15	dbSNP_107	75	2174,6420	370.8+/-336.0	268,1638,2391	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA6D	NM_001198999.1,NM_020858.1,NM_024966.2,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	,,,,,,	278,1923,4294	TT,TC,CC		25.2967,6.9381,19.0839	,,,,,,	407/1012,407/1012,407/477,407/999,407/1018,407/1074,407/598	48056958	2479,10511	2198	4297	6495	SO:0001819	synonymous_variant	80031	exon12			CATTGCCGATGAG	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.1221C>T	15.37:g.48056958C>T		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	114	59	0.517544	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			C|0.814;T|0.186	0.186	strong		0.502	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
PCDHB15	56121	hgsc.bcm.edu	37	5	140626778	140626778	+	Silent	SNP	G	G	A	rs112457389	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140626778G>A	ENST00000231173.3	+	1	1632	c.1632G>A	c.(1630-1632)gaG>gaA	p.E544E		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	544	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAGCAGCGAGGCGCTGGTGC	0.697													G|||	36	0.0071885	0.0189	0.0029	5008	,	,		15462	0.0		0.005	False		,,,				2504	0.0041				p.E544E		Atlas-SNP	.											PCDHB15,NS,carcinoma,+2,1	PCDHB15	138	1	0			c.G1632A						PASS	.	G		92,4314	74.7+/-112.8	2,88,2113	38.0	47.0	44.0		1632	0.8	1.0	5	dbSNP_132	44	35,8561	24.6+/-71.5	0,35,4263	no	coding-synonymous	PCDHB15	NM_018935.2		2,123,6376	AA,AG,GG		0.4072,2.0881,0.9768		544/788	140626778	127,12875	2203	4298	6501	SO:0001819	synonymous_variant	56121	exon1			CAGCGAGGCGCTG	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1632G>A	5.37:g.140626778G>A		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	166	80	0.481928	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																			G|0.990;A|0.010	0.010	strong		0.697	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
RBM27	54439	hgsc.bcm.edu	37	5	145650597	145650597	+	Silent	SNP	A	A	G	rs17104362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145650597A>G	ENST00000265271.5	+	18	2938	c.2772A>G	c.(2770-2772)aaA>aaG	p.K924K	RBM27_ENST00000506502.1_Silent_p.K869K	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	924					mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AATTACGGAAAAAACTCAGTC	0.448													A|||	812	0.162141	0.4962	0.062	5008	,	,		18170	0.0		0.0716	False		,,,				2504	0.0419				p.K924K		Atlas-SNP	.											.	RBM27	119	.	0			c.A2772G						PASS	.	A		1272,1864		263,746,559	83.0	74.0	76.0		2772	-1.4	1.0	5	dbSNP_123	76	554,6610		32,490,3060	no	coding-synonymous	RBM27	NM_018989.1		295,1236,3619	GG,GA,AA		7.7331,40.5612,17.7282		924/1061	145650597	1826,8474	1568	3582	5150	SO:0001819	synonymous_variant	54439	exon18			ACGGAAAAAACTC	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.2772A>G	5.37:g.145650597A>G		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	180	88	0.488889	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	37	CCDS43378.1																																																																																			A|0.836;G|0.164	0.164	strong		0.448	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
SPESP1	246777	hgsc.bcm.edu	37	15	69238272	69238272	+	Missense_Mutation	SNP	G	G	T	rs3743091	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:69238272G>T	ENST00000310673.3	+	2	553	c.399G>T	c.(397-399)ttG>ttT	p.L133F	NOX5_ENST00000455873.3_Intron|NOX5_ENST00000448182.3_Intron|RP11-809H16.2_ENST00000557966.1_RNA|NOX5_ENST00000260364.5_Intron|SPESP1_ENST00000560188.1_3'UTR	NM_145658.3	NP_663633.1	Q6UW49	SPESP_HUMAN	sperm equatorial segment protein 1	133			L -> F (in dbSNP:rs3743091).		acrosome reaction (GO:0007340)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organismal development (GO:0007275)	acrosomal vesicle (GO:0001669)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	19						CCATTGTTTTGCATGCAGAGG	0.453													G|||	496	0.0990415	0.0991	0.0389	5008	,	,		18747	0.1905		0.0507	False		,,,				2504	0.0971				p.L133F		Atlas-SNP	.											SPESP1,NS,carcinoma,0,1	SPESP1	39	1	0			c.G399T						scavenged	.	G	,PHE/LEU	392,4008	194.3+/-219.2	20,352,1828	52.0	54.0	54.0		,399	2.9	0.8	15	dbSNP_107	54	441,8155	134.1+/-191.5	17,407,3874	yes	intron,missense	NOX5,SPESP1	NM_001184780.1,NM_145658.3	,22	37,759,5702	TT,TG,GG		5.1303,8.9091,6.4097	,probably-damaging	,133/351	69238272	833,12163	2200	4298	6498	SO:0001583	missense	246777	exon2			TGTTTTGCATGCA	AF275321	CCDS10230.1	15q22.31	2011-04-15				ENSG00000258484			15570	protein-coding gene	gene with protein product		609399				12773409	Standard	NM_145658		Approved	SP-ESP	uc002arn.2	Q6UW49		ENST00000310673.3:c.399G>T	15.37:g.69238272G>T	ENSP00000312284:p.Leu133Phe	Somatic	58	1	0.0172414		WXS	Illumina HiSeq	Phase_I	76	39	0.513158	NM_145658	Q8NG22|Q8WVH8	Missense_Mutation	SNP	ENST00000310673.3	37	CCDS10230.1	195	0.08928571428571429	46	0.09349593495934959	10	0.027624309392265192	101	0.17657342657342656	38	0.05013192612137203	G	12.23	1.877039	0.33162	0.089091	0.051303	ENSG00000258484	ENST00000310673	T	0.44083	0.93	5.21	2.91	0.33838	.	0.000000	0.37530	N	0.002044	T	0.00144	0.0004	L	0.36672	1.1	0.09310	P	0.999999999351199	D	0.89917	1.0	D	0.97110	1.0	T	0.08371	-1.0725	9	0.87932	D	0	-10.4237	6.8196	0.23849	0.8137:0.0:0.1863:0.0	rs3743091;rs52804089;rs59972728;rs3743091	133	Q6UW49	SPESP_HUMAN	F	133	ENSP00000312284:L133F	ENSP00000312284:L133F	L	+	3	2	SPESP1	67025326	0.203000	0.23435	0.831000	0.32960	0.009000	0.06853	0.085000	0.14912	0.410000	0.25675	-0.238000	0.12139	TTG	G|0.921;T|0.079	0.079	strong		0.453	SPESP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257125.1	NM_145658	
OR10G7	390265	hgsc.bcm.edu	37	11	123909627	123909627	+	Missense_Mutation	SNP	T	T	C	rs11219420	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:123909627T>C	ENST00000330487.5	-	1	90	c.82A>G	c.(82-84)Atc>Gtc	p.I28V		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	28			I -> V (in dbSNP:rs11219420).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I28V(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		ACCAGGAAGATTCCAAAGAGG	0.572													t|||	1598	0.319089	0.174	0.4568	5008	,	,		16316	0.3254		0.4294	False		,,,				2504	0.2975				p.I28V		Atlas-SNP	.											OR10G7,NS,carcinoma,0,1	OR10G7	103	1	1	Substitution - Missense(1)	stomach(1)	c.A82G						PASS	.						89.0	85.0	86.0					11																	123909627		2200	4298	6498	SO:0001583	missense	390265	exon1			GGAAGATTCCAAA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.82A>G	11.37:g.123909627T>C	ENSP00000329689:p.Ile28Val	Somatic	276	0	0		WXS	Illumina HiSeq	Phase_I	256	100	0.390625	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	714	0.3269230769230769	74	0.15040650406504066	161	0.4447513812154696	202	0.3531468531468531	277	0.3654353562005277	C	2.011	-0.427174	0.04701	.	.	ENSG00000182634	ENST00000330487	T	0.03035	4.07	3.38	-6.76	0.01732	.	0.824866	0.10366	N	0.683403	T	0.00012	0.0000	N	0.01473	-0.845	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.36187	-0.9758	9	0.07990	T	0.79	.	3.721	0.08456	0.0824:0.3449:0.213:0.3597	rs11219420;rs57896133	28	Q8NGN6	O10G7_HUMAN	V	28	ENSP00000329689:I28V	ENSP00000329689:I28V	I	-	1	0	OR10G7	123414837	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-6.859000	0.00051	-3.501000	0.00151	-2.770000	0.00120	ATC	T|0.681;C|0.319	0.319	strong		0.572	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
FAM83E	54854	hgsc.bcm.edu	37	19	49116359	49116359	+	Missense_Mutation	SNP	T	T	C	rs447802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49116359T>C	ENST00000263266.3	-	1	460	c.271A>G	c.(271-273)Acc>Gcc	p.T91A	FAM83E_ENST00000595110.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	91			T -> A (in dbSNP:rs447802). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TCCACATCGGTGGTGGTGGCT	0.682													C|||	2759	0.550919	0.7277	0.4986	5008	,	,		12886	0.7431		0.2614	False		,,,				2504	0.4489				p.T91A		Atlas-SNP	.											FAM83E,NS,carcinoma,0,2	FAM83E	34	2	0			c.A271G						PASS	.						12.0	21.0	18.0					19																	49116359		2090	4216	6306	SO:0001583	missense	54854	exon1			CATCGGTGGTGGT	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.271A>G	19.37:g.49116359T>C	ENSP00000263266:p.Thr91Ala	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	100	47	0.47	NM_017708	Q9NXK1	Missense_Mutation	SNP	ENST00000263266.3	37	CCDS42587.1	1077	0.49313186813186816	343	0.6971544715447154	160	0.4419889502762431	389	0.6800699300699301	185	0.24406332453825857	C	2.961	-0.214627	0.06101	.	.	ENSG00000105523	ENST00000263266	T	0.10668	2.85	3.79	-5.7	0.02421	.	1.732010	0.03225	N	0.178172	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.42565	-0.9444	9	0.02654	T	1	-0.2116	10.3255	0.43790	0.0:0.5744:0.1163:0.3093	rs447802;rs52796733;rs447802	91	Q2M2I3	FA83E_HUMAN	A	91	ENSP00000263266:T91A	ENSP00000263266:T91A	T	-	1	0	FAM83E	53808171	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.799000	0.01746	-1.443000	0.01953	-1.874000	0.00550	ACC	T|0.521;C|0.479	0.479	strong		0.682	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
TIMM10B	26515	hgsc.bcm.edu	37	11	6502780	6502780	+	Silent	SNP	C	C	A	rs11555935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6502780C>A	ENST00000254616.6	+	1	104	c.34C>A	c.(34-36)Cga>Aga	p.R12R	TIMM10B_ENST00000472836.1_Silent_p.R12R|ARFIP2_ENST00000254584.2_5'Flank|ARFIP2_ENST00000445086.2_5'Flank|ARFIP2_ENST00000396777.3_5'Flank|ARFIP2_ENST00000525235.1_5'Flank|TIMM10B_ENST00000530751.1_Silent_p.R12R|ARFIP2_ENST00000423813.2_5'Flank	NM_012192.3	NP_036324.1	Q9Y5J6	T10B_HUMAN	translocase of inner mitochondrial membrane 10 homolog B (yeast)	12					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial intermembrane space protein transporter complex (GO:0042719)	metal ion binding (GO:0046872)										acagcaACTGCGAAACGTAAG	0.607													A|||	837	0.167133	0.2118	0.1686	5008	,	,		17547	0.0327		0.1839	False		,,,				2504	0.227				p.R12R		Atlas-SNP	.											.	.	.	.	0			c.C34A						PASS	.	A		910,3492	721.9+/-409.2	93,724,1384	98.0	67.0	78.0		34	2.9	0.9	11	dbSNP_120	78	1667,6925	727.2+/-406.6	170,1327,2799	no	coding-synonymous	FXC1	NM_012192.3		263,2051,4183	AA,AC,CC		19.4018,20.6724,19.8322		12/104	6502780	2577,10417	2201	4296	6497	SO:0001819	synonymous_variant	26515	exon1			CAACTGCGAAACG	AF150105	CCDS7766.1	11p15.4	2012-12-07	2012-12-07	2012-12-07	ENSG00000132286	ENSG00000132286			4022	protein-coding gene	gene with protein product		607388	"""fracture callus 1 (rat) homolog"", ""fracture callus 1 homolog (rat)"""	FXC1		10552927	Standard	NM_012192		Approved	Tim9b, TIM10B	uc001mdn.4	Q9Y5J6	OTTHUMG00000133400	ENST00000254616.6:c.34C>A	11.37:g.6502780C>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	46	21	0.456522	NM_012192	Q96FF3	Silent	SNP	ENST00000254616.6	37	CCDS7766.1																																																																																			A|0.180;C|0.820;G|0.000;T|0.000	0.180	strong		0.607	TIMM10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257257.2	NM_012192	
TMEM8A	58986	hgsc.bcm.edu	37	16	427784	427784	+	Silent	SNP	G	G	A	rs11641742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:427784G>A	ENST00000431232.2	-	2	346	c.186C>T	c.(184-186)taC>taT	p.Y62Y	TMEM8A_ENST00000250930.3_De_novo_Start_OutOfFrame|TMEM8A_ENST00000476735.1_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	62					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						TGGCACTGCCGTACCAGCTGT	0.677													G|||	2663	0.531749	0.6188	0.4712	5008	,	,		15053	0.2996		0.5378	False		,,,				2504	0.6902				p.Y62Y		Atlas-SNP	.											.	TMEM8A	49	.	0			c.C186T						PASS	.	G		2723,1635		850,1023,306	36.0	42.0	40.0		186	-8.8	0.7	16	dbSNP_120	40	4854,3714		1426,2002,856	no	coding-synonymous	TMEM8A	NM_021259.2		2276,3025,1162	AA,AG,GG		43.3473,37.5172,41.3817		62/772	427784	7577,5349	2179	4284	6463	SO:0001819	synonymous_variant	58986	exon2			ACTGCCGTACCAG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.186C>T	16.37:g.427784G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	109	53	0.486239	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			G|0.455;A|0.545	0.545	strong		0.677	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41351321C>T	ENST00000301141.5	-	7	1059	c.1039G>A	c.(1039-1041)Gcc>Acc	p.A347T	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	347					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GGCATCTTGGCCCGGTCCTCA	0.537																																					p.A347T		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G1039A						PASS	.						115.0	104.0	108.0					19																	41351321		2203	4300	6503	SO:0001583	missense	1548	exon7			TCTTGGCCCGGTC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1039G>A	19.37:g.41351321C>T	ENSP00000301141:p.Ala347Thr	Somatic	220	0	0		WXS	Illumina HiSeq	Phase_I	306	30	0.0980392	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	4.025	0.002161	0.07819	.	.	ENSG00000255974	ENST00000301141	T	0.69306	-0.39	2.76	-2.87	0.05700	.	0.614141	0.16066	U	0.231229	T	0.43853	0.1266	L	0.31120	0.905	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.17319	-1.0373	10	0.22706	T	0.39	.	4.9051	0.13795	0.0:0.2915:0.1649:0.5436	.	347;347	Q13120;P11509	.;CP2A6_HUMAN	T	347	ENSP00000301141:A347T	ENSP00000301141:A347T	A	-	1	0	CYP2A6	46043161	0.000000	0.05858	0.011000	0.14972	0.659000	0.38960	-1.191000	0.03055	-0.603000	0.05767	-0.912000	0.02778	GCC	C|0.500;T|0.500	0.500	strong		0.537	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
POLR1E	64425	hgsc.bcm.edu	37	9	37489378	37489378	+	Missense_Mutation	SNP	C	C	T	rs11542231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37489378C>T	ENST00000442009.2	+	4	424	c.20C>T	c.(19-21)aCa>aTa	p.T7I	POLR1E_ENST00000377798.4_Silent_p.N108N|POLR1E_ENST00000377792.3_Silent_p.N170N	NM_001282766.1	NP_001269695.1	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)		AATTGTTCAACATGCAGCCAC	0.373													C|||	329	0.0656949	0.0053	0.0965	5008	,	,		14965	0.002		0.1571	False		,,,				2504	0.0971				p.N108N	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.C324T						PASS	.	C		143,4263	100.7+/-139.4	2,139,2062	97.0	93.0	94.0		324	4.4	1.0	9	dbSNP_120	94	1394,7206	269.6+/-288.5	118,1158,3024	no	coding-synonymous	POLR1E	NM_022490.1		120,1297,5086	TT,TC,CC		16.2093,3.2456,11.8176		108/420	37489378	1537,11469	2203	4300	6503	SO:0001583	missense	64425	exon4			GTTCAACATGCAG	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	ENST00000442009.2:c.20C>T	9.37:g.37489378C>T	ENSP00000399887:p.Thr7Ile	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	90	50	0.555556	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000442009.2	37		159	0.07280219780219781	4	0.008130081300813009	43	0.11878453038674033	1	0.0017482517482517483	111	0.14643799472295516	C	18.38	3.611716	0.66558	0.032456	0.162093	ENSG00000137054	ENST00000442009	T	0.22336	1.96	5.27	4.37	0.52481	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.46901	P	7.570000000000077E-4	B	0.09022	0.002	B	0.08055	0.003	T	0.16778	-1.0391	7	0.33940	T	0.23	-13.2482	6.019	0.19618	0.0:0.6758:0.1566:0.1676	rs11542231;rs16934158	7	E7EX70	.	I	7	ENSP00000399887:T7I	ENSP00000399887:T7I	T	+	2	0	POLR1E	37479378	0.999000	0.42202	1.000000	0.80357	0.980000	0.70556	0.633000	0.24598	1.236000	0.43740	0.555000	0.69702	ACA	C|0.888;T|0.112	0.112	strong		0.373	POLR1E-201	KNOWN	basic	protein_coding	protein_coding		NM_022490	
RBMX	27316	hgsc.bcm.edu	37	X	135956462	135956462	+	Missense_Mutation	SNP	G	G	C	rs74463481		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135956462G>C	ENST00000320676.7	-	9	1169	c.1015C>G	c.(1015-1017)Cgt>Ggt	p.R339G	RBMX_ENST00000562646.1_3'UTR|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Missense_Mutation_p.R211G|RBMX_ENST00000570135.1_Missense_Mutation_p.R204G|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	339	Necessary for RNA-binding.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					ACCCGATCACGACCACTTGAG	0.537																																					p.R339G		Atlas-SNP	.											.	RBMX	149	.	0			c.C1015G						PASS	.																																			SO:0001583	missense	27316	exon9			GATCACGACCACT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.1015C>G	X.37:g.135956462G>C	ENSP00000359645:p.Arg339Gly	Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	438	195	0.445205	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	12.06	1.824057	0.32237	.	.	ENSG00000147274	ENST00000320676;ENST00000449161	T	0.81247	-1.47	5.4	4.54	0.55810	.	0.000000	0.85682	U	0.000000	T	0.77350	0.4117	L	0.59436	1.845	0.19300	P	0.9999701562	P	0.47034	0.889	B	0.40101	0.319	D	0.84520	0.0627	9	0.72032	D	0.01	.	13.8398	0.63432	0.0758:0.0:0.9242:0.0	.	339	P38159	HNRPG_HUMAN	G	339;326	ENSP00000359645:R339G	ENSP00000359645:R339G	R	-	1	0	RBMX	135784128	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.693000	0.61753	1.168000	0.42723	-0.176000	0.13171	CGT	.	.	weak		0.537	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
RLF	6018	hgsc.bcm.edu	37	1	40705726	40705726	+	Missense_Mutation	SNP	A	A	T	rs10889205	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:40705726A>T	ENST00000372771.4	+	8	5379	c.5352A>T	c.(5350-5352)gaA>gaT	p.E1784D		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1784			E -> D (in dbSNP:rs10889205).		chromosome organization (GO:0051276)|DNA integration (GO:0015074)|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)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			AAGAGAAAGAAGATGATTTTG	0.358													A|||	743	0.148363	0.2542	0.1671	5008	,	,		20224	0.0625		0.1819	False		,,,				2504	0.046				p.E1784D		Atlas-SNP	.											RLF,NS,carcinoma,0,1	RLF	152	1	0			c.A5352T						PASS	.	A	ASP/GLU	1001,3405	364.6+/-317.1	110,781,1312	57.0	59.0	59.0		5352	-11.7	0.1	1	dbSNP_120	59	1718,6882	307.4+/-308.4	150,1418,2732	yes	missense	RLF	NM_012421.3	45	260,2199,4044	TT,TA,AA		19.9767,22.719,20.9057	benign	1784/1915	40705726	2719,10287	2203	4300	6503	SO:0001583	missense	6018	exon8			GAAAGAAGATGAT		CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.5352A>T	1.37:g.40705726A>T	ENSP00000361857:p.Glu1784Asp	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	122	115	0.942623	NM_012421	Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	337	0.1543040293040293	106	0.21544715447154472	47	0.1298342541436464	40	0.06993006993006994	144	0.18997361477572558	A	0.133	-1.111075	0.01813	0.22719	0.199767	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.13420	2.59	5.87	-11.7	0.00046	.	0.534594	0.21335	N	0.076226	T	0.00012	0.0000	N	0.08118	0	0.54753	P	1.799999999996249E-5	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25779	-1.0122	9	0.12103	T	0.63	-0.2135	9.5397	0.39244	0.0786:0.1215:0.1152:0.6846	rs10889205;rs52823391;rs10889205	1477;1784	F5H2M5;Q13129	.;RLF_HUMAN	D	1784;1477	ENSP00000361857:E1784D	ENSP00000361857:E1784D	E	+	3	2	RLF	40478313	0.000000	0.05858	0.059000	0.19551	0.979000	0.70002	-3.576000	0.00425	-3.937000	0.00089	-0.301000	0.09380	GAA	A|0.804;T|0.196	0.196	strong		0.358	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421	
CWF19L2	143884	hgsc.bcm.edu	37	11	107299631	107299631	+	Missense_Mutation	SNP	G	G	A	rs659040	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:107299631G>A	ENST00000282251.5	-	8	1354	c.1327C>T	c.(1327-1329)Cac>Tac	p.H443Y	CWF19L2_ENST00000433523.1_Missense_Mutation_p.H443Y	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	443			H -> Y (in dbSNP:rs659040). {ECO:0000269|PubMed:15489334}.				catalytic activity (GO:0003824)			endometrium(4)|kidney(2)|large_intestine(13)|lung(21)	40		Melanoma(852;1.75e-05)|all_epithelial(67;6.27e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0258)		Epithelial(105;7.18e-06)|BRCA - Breast invasive adenocarcinoma(274;1.65e-05)|all cancers(92;1.76e-05)		ACATGTTGGTGTTCATCAGTA	0.403													A|||	574	0.114617	0.1604	0.1369	5008	,	,		17579	0.002		0.2227	False		,,,				2504	0.0419				p.H443Y		Atlas-SNP	.											.	CWF19L2	135	.	0			c.C1327T						PASS	.	A	TYR/HIS	771,3631	752.5+/-412.3	76,619,1506	241.0	232.0	235.0		1327	-3.7	0.0	11	dbSNP_83	235	1880,6716	728.1+/-406.7	209,1462,2627	yes	missense	CWF19L2	NM_152434.2	83	285,2081,4133	AA,AG,GG		21.8706,17.5148,20.3954	benign	443/895	107299631	2651,10347	2201	4298	6499	SO:0001583	missense	143884	exon8			GTTGGTGTTCATC	AK056905	CCDS8336.2	11q23.1	2005-09-22			ENSG00000152404	ENSG00000152404			26508	protein-coding gene	gene with protein product						14702039	Standard	NM_152434		Approved	FLJ32343	uc010rvp.2	Q2TBE0	OTTHUMG00000152975	ENST00000282251.5:c.1327C>T	11.37:g.107299631G>A	ENSP00000282251:p.His443Tyr	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	164	77	0.469512	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Missense_Mutation	SNP	ENST00000282251.5	37	CCDS8336.2	287	0.13141025641025642	73	0.1483739837398374	50	0.13812154696132597	1	0.0017482517482517483	163	0.21503957783641162	A	0.052	-1.248631	0.01469	0.175148	0.218706	ENSG00000152404	ENST00000282251;ENST00000433523	T;T	0.21361	2.01;2.01	5.02	-3.67	0.04476	.	2.765330	0.00769	N	0.001196	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.33624	-0.9861	9	0.51188	T	0.08	5.6759	2.3012	0.04162	0.2483:0.3046:0.3315:0.1156	rs659040;rs52817546;rs58584040;rs659040	443	Q2TBE0	C19L2_HUMAN	Y	443	ENSP00000282251:H443Y;ENSP00000387533:H443Y	ENSP00000282251:H443Y	H	-	1	0	CWF19L2	106804841	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.808000	0.01732	-0.716000	0.04962	-1.120000	0.02017	CAC	G|0.822;A|0.178	0.178	strong		0.403	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434	
GPR1	2825	hgsc.bcm.edu	37	2	207041441	207041441	+	Silent	SNP	G	G	A	rs3732082	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:207041441G>A	ENST00000407325.2	-	3	893	c.531C>T	c.(529-531)gaC>gaT	p.D177D	GPR1_ENST00000437420.1_Silent_p.D177D	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	177					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		ACTCCACAGTGTCCCGGAAGT	0.433													G|||	1729	0.345248	0.4531	0.3112	5008	,	,		20700	0.2569		0.3738	False		,,,				2504	0.2853				p.D177D		Atlas-SNP	.											.	GPR1	38	.	0			c.C531T						PASS	.	G	,	1959,2447	546.9+/-377.1	446,1067,690	77.0	79.0	78.0		531,531	-1.2	0.6	2	dbSNP_107	78	2983,5617	460.2+/-365.1	530,1923,1847	no	coding-synonymous,coding-synonymous	GPR1	NM_001098199.1,NM_005279.3	,	976,2990,2537	AA,AG,GG		34.686,44.4621,37.9978	,	177/356,177/356	207041441	4942,8064	2203	4300	6503	SO:0001819	synonymous_variant	2825	exon3			CACAGTGTCCCGG		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.531C>T	2.37:g.207041441G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	37	0.430233	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Silent	SNP	ENST00000407325.2	37	CCDS2368.1																																																																																			G|0.626;A|0.374	0.374	strong		0.433	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
KIRREL	55243	hgsc.bcm.edu	37	1	158057633	158057633	+	Silent	SNP	C	C	G	rs36008419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158057633C>G	ENST00000359209.6	+	6	817	c.750C>G	c.(748-750)ccC>ccG	p.P250P	KIRREL_ENST00000360089.4_Silent_p.P86P|KIRREL_ENST00000368173.3_Silent_p.P250P|KIRREL_ENST00000392272.2_Silent_p.P147P|KIRREL_ENST00000368172.1_Silent_p.P48P|KIRREL_ENST00000416935.2_Silent_p.P150P			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	250	Ig-like C2-type 3.				excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)	p.P86P(1)|p.P250P(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CAGCCAACCCCGAGATCTTGG	0.597											OREG0013906	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1144	0.228435	0.2935	0.2277	5008	,	,		17136	0.2401		0.1938	False		,,,				2504	0.1646				p.P250P		Atlas-SNP	.											KIRREL_ENST00000368173,NS,carcinoma,0,2	KIRREL	346	2	2	Substitution - coding silent(2)	stomach(2)	c.C750G						PASS	.	C		1196,3210	412.8+/-336.2	162,872,1169	49.0	45.0	47.0		750	-11.2	0.0	1	dbSNP_126	47	1811,6789	319.7+/-314.3	182,1447,2671	no	coding-synonymous	KIRREL	NM_018240.5		344,2319,3840	GG,GC,CC		21.0581,27.1448,23.1201		250/758	158057633	3007,9999	2203	4300	6503	SO:0001819	synonymous_variant	55243	exon6			CAACCCCGAGATC	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.750C>G	1.37:g.158057633C>G		Somatic	77	0	0	1790	WXS	Illumina HiSeq	Phase_I	106	55	0.518868	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Silent	SNP	ENST00000359209.6	37	CCDS1172.2																																																																																			C|0.762;G|0.238	0.238	strong		0.597	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	
PCDHB2	56133	hgsc.bcm.edu	37	5	140475665	140475665	+	Missense_Mutation	SNP	C	C	A	rs116177548	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140475665C>A	ENST00000194155.4	+	1	1439	c.1291C>A	c.(1291-1293)Ccc>Acc	p.P431T		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	431	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)			CTTCGGGACACCCAGGCTGAA	0.557													C|||	48	0.00958466	0.0	0.0043	5008	,	,		19536	0.001		0.003	False		,,,				2504	0.0419				p.P431T		Atlas-SNP	.											PCDHB2,NS,carcinoma,-2,1	PCDHB2	163	1	0			c.C1291A						PASS	.	C	THR/PRO	2,4404	4.2+/-10.8	0,2,2201	138.0	127.0	131.0		1291	5.1	0.9	5	dbSNP_132	131	48,8552	31.2+/-83.2	0,48,4252	yes	missense	PCDHB2	NM_018936.2	38	0,50,6453	AA,AC,CC		0.5581,0.0454,0.3844	probably-damaging	431/799	140475665	50,12956	2203	4300	6503	SO:0001583	missense	56133	exon1			GGGACACCCAGGC	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.1291C>A	5.37:g.140475665C>A	ENSP00000194155:p.Pro431Thr	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	239	113	0.472803	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	13.48	2.249833	0.39797	4.54E-4	0.005581	ENSG00000112852	ENST00000194155	T	0.56275	0.47	5.11	5.11	0.69529	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.77631	0.4159	H	0.98133	4.155	0.45284	D	0.998288	D	0.89917	1.0	D	0.91635	0.999	D	0.86973	0.2099	9	0.87932	D	0	.	14.5945	0.68395	0.1465:0.8535:0.0:0.0	.	431	Q9Y5E7	PCDB2_HUMAN	T	431	ENSP00000194155:P431T	ENSP00000194155:P431T	P	+	1	0	PCDHB2	140455849	0.889000	0.30405	0.880000	0.34516	0.050000	0.14768	2.396000	0.44468	2.542000	0.85734	0.650000	0.86243	CCC	C|0.996;A|0.004	0.004	strong		0.557	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
GRXCR2	643226	hgsc.bcm.edu	37	5	145252239	145252239	+	Missense_Mutation	SNP	C	C	T	rs71594518	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145252239C>T	ENST00000377976.1	-	1	292	c.293G>A	c.(292-294)gGc>gAc	p.G98D		NM_001080516.1	NP_001073985.1	A6NFK2	GRCR2_HUMAN	glutaredoxin, cysteine rich 2	98						cell projection (GO:0042995)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						AGGCTGGCCGCCTGCCAAGGT	0.517													C|||	294	0.0587061	0.1233	0.0317	5008	,	,		19134	0.001		0.0378	False		,,,				2504	0.0716				p.G98D		Atlas-SNP	.											.	GRXCR2	32	.	0			c.G293A						PASS	.	C	ASP/GLY	486,3920	227.5+/-242.7	26,434,1743	80.0	71.0	74.0		293	5.9	1.0	5	dbSNP_130	74	256,8344	99.7+/-161.2	4,248,4048	yes	missense	GRXCR2	NM_001080516.1	94	30,682,5791	TT,TC,CC		2.9767,11.0304,5.7051	probably-damaging	98/249	145252239	742,12264	2203	4300	6503	SO:0001583	missense	643226	exon1			TGGCCGCCTGCCA		CCDS34263.1	5q32	2014-03-14			ENSG00000204928	ENSG00000204928			33862	protein-coding gene	gene with protein product		615762				24619944	Standard	NM_001080516		Approved	DFNB101	uc003lns.1	A6NFK2	OTTHUMG00000163417	ENST00000377976.1:c.293G>A	5.37:g.145252239C>T	ENSP00000367214:p.Gly98Asp	Somatic	174	1	0.00574713		WXS	Illumina HiSeq	Phase_I	159	157	0.987421	NM_001080516		Missense_Mutation	SNP	ENST00000377976.1	37	CCDS34263.1	103	0.04716117216117216	56	0.11382113821138211	14	0.03867403314917127	0	0.0	33	0.04353562005277045	C	21.7	4.184406	0.78677	0.110304	0.029767	ENSG00000204928	ENST00000377976	T	0.22134	1.97	5.9	5.9	0.94986	.	0.329613	0.36066	N	0.002816	T	0.00666	0.0022	M	0.62723	1.935	0.22342	P	0.999184813	D	0.55800	0.973	P	0.50192	0.634	T	0.00162	-1.1970	9	0.27785	T	0.31	-31.8609	19.0379	0.92986	0.0:1.0:0.0:0.0	.	98	A6NFK2	GRCR2_HUMAN	D	98	ENSP00000367214:G98D	ENSP00000367214:G98D	G	-	2	0	GRXCR2	145232432	0.216000	0.23585	0.958000	0.39756	0.953000	0.61014	3.847000	0.55895	2.786000	0.95864	0.561000	0.74099	GGC	C|0.949;T|0.051	0.051	strong		0.517	GRXCR2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373289.2		
FBXO24	26261	hgsc.bcm.edu	37	7	100198386	100198386	+	Missense_Mutation	SNP	C	C	T	rs11768465	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100198386C>T	ENST00000241071.6	+	10	1929	c.1607C>T	c.(1606-1608)aCg>aTg	p.T536M	FBXO24_ENST00000427939.2_Missense_Mutation_p.T574M|FBXO24_ENST00000360609.2_3'UTR|FBXO24_ENST00000468962.1_Missense_Mutation_p.T524M|PCOLCE-AS1_ENST00000442166.2_RNA|PCOLCE-AS1_ENST00000446022.1_RNA|PCOLCE-AS1_ENST00000544873.1_RNA|PCOLCE_ENST00000223061.5_5'Flank	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	536					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CAGGACCGCACGGAGAAGATG	0.642													T|||	1081	0.215855	0.379	0.2089	5008	,	,		17640	0.0188		0.2107	False		,,,				2504	0.2086				p.T574M		Atlas-SNP	.											.	FBXO24	125	.	0			c.C1721T						PASS	.	T	MET/THR,MET/THR,MET/THR	1502,2904	675.6+/-403.1	257,988,958	83.0	76.0	78.0		1571,1721,1607	3.1	1.0	7	dbSNP_120	78	2001,6599	722.8+/-406.4	244,1513,2543	yes	missense,missense,missense	FBXO24	NM_001163499.1,NM_012172.4,NM_033506.2	81,81,81	501,2501,3501	TT,TC,CC		23.2674,34.0899,26.9337	benign,benign,benign	524/569,574/619,536/581	100198386	3503,9503	2203	4300	6503	SO:0001583	missense	26261	exon10			ACCGCACGGAGAA	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"""F-boxes /  ""other"""""	13595	protein-coding gene	gene with protein product		609097	"""F-box only protein 24"""			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.1607C>T	7.37:g.100198386C>T	ENSP00000241071:p.Thr536Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	112	56	0.5	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	454	0.2078754578754579	197	0.40040650406504064	91	0.2513812154696133	4	0.006993006993006993	162	0.21372031662269128	t	11.94	1.789266	0.31685	0.340899	0.232674	ENSG00000106336	ENST00000241071;ENST00000468962;ENST00000427939	T;T;T	0.12569	2.67;2.67;2.68	4.22	3.06	0.35304	.	0.091005	0.45867	N	0.000324	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	P	0.99999999461126	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.48906	-0.8993	9	0.02654	T	1	-5.1182	7.1574	0.25645	0.0:0.1952:0.0:0.8048	rs11768465;rs56642930;rs59987023;rs11768465	524;574;536;536	B4DY42;B4DX91;A4D2D3;O75426	.;.;.;FBX24_HUMAN	M	536;524;574	ENSP00000241071:T536M;ENSP00000420239:T524M;ENSP00000416558:T574M	ENSP00000241071:T536M	T	+	2	0	FBXO24	100036322	1.000000	0.71417	0.998000	0.56505	0.790000	0.44656	3.163000	0.50763	0.190000	0.20209	-0.593000	0.04111	ACG	C|0.761;T|0.239	0.239	strong		0.642	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1		
SIRPA	140885	hgsc.bcm.edu	37	20	1895950	1895950	+	Missense_Mutation	SNP	C	C	G	rs138283486|rs386811661	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1895950C>G	ENST00000358771.4	+	2	437	c.285C>G	c.(283-285)gaC>gaG	p.D95E	SIRPA_ENST00000356025.3_Missense_Mutation_p.D95E|SIRPA_ENST00000400068.3_Missense_Mutation_p.D95E	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	95	Ig-like V-type.		D -> E. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9062191, ECO:0000269|PubMed:9070220}.		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CTGTTTCAGACCTCACAAAGA	0.527													C|||	1881	0.375599	0.2368	0.402	5008	,	,		14766	0.5883		0.2942	False		,,,				2504	0.409				p.D95E	GBM(155;1668 1920 5945 42733 48121)	Atlas-SNP	.											.	SIRPA	83	.	0			c.C285G						PASS	.						128.0	106.0	113.0					20																	1895950		2202	4287	6489	SO:0001583	missense	140885	exon3			TTCAGACCTCACA	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.285C>G	20.37:g.1895950C>G	ENSP00000351621:p.Asp95Glu	Somatic	494	0	0		WXS	Illumina HiSeq	Phase_I	262	25	0.0954198	NM_001040022	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	C	11.32	1.604197	0.28534	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.64803	-0.12;-0.12;-0.12	4.78	-2.65	0.06095	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.307559	0.27012	N	0.021368	T	0.64114	0.2569	M	0.83483	2.645	0.09310	N	0.999993	B;B;P	0.43352	0.049;0.019;0.804	B;B;P	0.46049	0.211;0.01;0.502	T	0.62296	-0.6884	10	0.54805	T	0.06	.	9.4883	0.38944	0.0:0.3689:0.0:0.6311	.	75;95;95	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	E	95	ENSP00000382941:D95E;ENSP00000348307:D95E;ENSP00000351621:D95E	ENSP00000348307:D95E	D	+	3	2	SIRPA	1843950	0.000000	0.05858	0.007000	0.13788	0.002000	0.02628	-1.635000	0.02018	-0.560000	0.06102	-0.266000	0.10368	GAC	C|0.693;G|0.307	0.307	strong		0.527	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
GZMH	2999	hgsc.bcm.edu	37	14	25076836	25076836	+	Silent	SNP	G	G	A	rs142357322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:25076836G>A	ENST00000216338.4	-	3	365	c.321C>T	c.(319-321)aaC>aaT	p.N107N	GZMH_ENST00000382548.4_Silent_p.N107N|RP11-104E19.1_ENST00000557736.1_RNA|RP11-104E19.1_ENST00000555300.1_RNA|GZMH_ENST00000557220.2_Intron	NM_033423.4	NP_219491.1	P20718	GRAH_HUMAN	granzyme H (cathepsin G-like 2, protein h-CCPX)	107	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)	membrane (GO:0016020)	serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)	12				GBM - Glioblastoma multiforme(265;0.0267)		GCATGATGTCGTTGGAGAAGT	0.542																																					p.N107N		Atlas-SNP	.											.	GZMH	24	.	0			c.C321T						PASS	.						226.0	211.0	216.0					14																	25076836		2203	4297	6500	SO:0001819	synonymous_variant	2999	exon3			GATGTCGTTGGAG	M72150	CCDS9632.1, CCDS59243.1	14q11.2	2003-10-20			ENSG00000100450	ENSG00000100450			4710	protein-coding gene	gene with protein product		116831		CTSGL2		2049336	Standard	NM_033423		Approved	CGL-2, CCP-X, CTLA1, CSP-C	uc001wpr.2	P20718	OTTHUMG00000140185	ENST00000216338.4:c.321C>T	14.37:g.25076836G>A		Somatic	308	0	0		WXS	Illumina HiSeq	Phase_I	437	63	0.144165	NM_033423	G3V2C5|Q6XGZ0|Q6XGZ1	Silent	SNP	ENST00000216338.4	37	CCDS9632.1																																																																																			G|0.721;A|0.279	0.279	strong		0.542	GZMH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276538.2	NM_033423	
C18orf8	29919	hgsc.bcm.edu	37	18	21109250	21109250	+	Silent	SNP	T	T	C	rs1788825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:21109250T>C	ENST00000269221.3	+	15	1514	c.1404T>C	c.(1402-1404)ttT>ttC	p.F468F	C18orf8_ENST00000590868.1_Silent_p.F420F	NM_013326.3	NP_037458.3	Q96DM3	MIC1_HUMAN	chromosome 18 open reading frame 8	468						lysosomal membrane (GO:0005765)				endometrium(9)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	21	all_cancers(21;0.000122)|all_epithelial(16;8.08e-07)|Lung NSC(20;0.00206)|all_lung(20;0.00659)|Colorectal(14;0.0202)|Ovarian(20;0.127)					TGTCAGCCTTTGTGGAAAAGA	0.552													C|||	4159	0.830471	0.9599	0.7781	5008	,	,		18838	0.9236		0.6531	False		,,,				2504	0.7791				p.F468F		Atlas-SNP	.											.	C18orf8	58	.	0			c.T1404C						PASS	.	C		4011,395	199.4+/-223.0	1823,365,15	64.0	59.0	61.0		1404	0.9	0.0	18	dbSNP_89	61	5565,3035	466.3+/-366.7	1812,1941,547	no	coding-synonymous	C18orf8	NM_013326.3		3635,2306,562	CC,CT,TT		35.2907,8.965,26.3724		468/658	21109250	9576,3430	2203	4300	6503	SO:0001819	synonymous_variant	29919	exon15			AGCCTTTGTGGAA	AK057192	CCDS32803.1, CCDS74199.1	18q11.2	2013-12-13			ENSG00000141452	ENSG00000141452			24326	protein-coding gene	gene with protein product	"""colon cancer associated protein Mic1"", ""macrophage inhibitory cytokine 1"""					12477932	Standard	NM_013326		Approved	MIC1, MIC-1, HsT2591	uc021uie.2	Q96DM3		ENST00000269221.3:c.1404T>C	18.37:g.21109250T>C		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	52	26	0.5	NM_013326	Q9BU17|Q9Y5M0	Silent	SNP	ENST00000269221.3	37	CCDS32803.1																																																																																			T|0.236;G|0.000;C|0.764	0.764	strong		0.552	C18orf8-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445386.1	NM_013326	
PKD1L2	114780	hgsc.bcm.edu	37	16	81219187	81219187	+	RNA	SNP	C	C	T	rs13339342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:81219187C>T	ENST00000525539.1	-	0	1906				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AACAGCCAGGCGCAGGGTGAC	0.642													c|||	762	0.152157	0.1309	0.1585	5008	,	,		16480	0.0417		0.168	False		,,,				2504	0.274				p.R636H		Atlas-SNP	.											PKD1L2_ENST00000525539,NS,carcinoma,-1,2	PKD1L2	361	2	0			c.G1907A						PASS	.	T	HIS/ARG,HIS/ARG	551,3597		37,477,1560	35.0	45.0	42.0		1907,1907	-9.7	0.0	16	dbSNP_121	42	1377,7047		113,1151,2948	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	150,1628,4508	TT,TC,CC		16.3462,13.2835,15.3357	benign,benign	636/992,636/2460	81219187	1928,10644	2074	4212	6286			114780	exon11			GCCAGGCGCAGGG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81219187C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	70	35	0.5	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		264	0.12087912087912088	62	0.12601626016260162	56	0.15469613259668508	23	0.04020979020979021	123	0.16226912928759896	c	8.903	0.956878	0.18507	0.132835	0.163462	ENSG00000166473	ENST00000337114	T	0.70749	-0.51	4.83	-9.66	0.00534	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.252640	0.05331	N	0.528415	T	0.00241	0.0007	.	.	.	0.80722	P	0.0	B;B	0.23316	0.011;0.083	B;B	0.22386	0.007;0.039	T	0.01839	-1.1263	8	0.20046	T	0.44	-3.9833	9.6762	0.40043	0.0:0.2218:0.185:0.5933	rs13339342;rs52836229;rs13339342	636;636	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	H	636	ENSP00000337397:R636H	ENSP00000337397:R636H	R	-	2	0	PKD1L2	79776688	0.000000	0.05858	0.014000	0.15608	0.622000	0.37654	-1.453000	0.02383	-1.677000	0.01455	-0.229000	0.12294	CGC	C|0.865;T|0.135	0.135	strong		0.642	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
TTN	7273	hgsc.bcm.edu	37	2	179650408	179650408	+	Missense_Mutation	SNP	G	G	A	rs35813871	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179650408G>A	ENST00000591111.1	-	15	2656	c.2432C>T	c.(2431-2433)aCa>aTa	p.T811I	TTN_ENST00000342175.6_Missense_Mutation_p.T765I|TTN_ENST00000360870.5_Missense_Mutation_p.T811I|TTN_ENST00000589042.1_Missense_Mutation_p.T811I|TTN_ENST00000342992.6_Missense_Mutation_p.T811I|TTN_ENST00000460472.2_Missense_Mutation_p.T765I|TTN_ENST00000359218.5_Missense_Mutation_p.T765I			Q8WZ42	TITIN_HUMAN	titin	33642			T -> I (in dbSNP:rs35813871). {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)			AGGGCTAGCTGTGCGGGGGCG	0.388													G|||	503	0.100439	0.0862	0.1499	5008	,	,		21394	0.001		0.2157	False		,,,				2504	0.0685				p.T811I		Atlas-SNP	.											.	TTN	18412	.	0			c.C2432T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR,ILE/THR	450,3956	216.4+/-235.1	25,400,1778	183.0	178.0	179.0		2294,2432,2432,2294,2294	5.5	1.0	2	dbSNP_126	179	2017,6583	352.4+/-328.6	240,1537,2523	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	89,89,89,89,89	265,1937,4301	AA,AG,GG		23.4535,10.2133,18.9682	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	765/26927,811/33424,811/5605,765/27052,765/27119	179650408	2467,10539	2203	4300	6503	SO:0001583	missense	7273	exon15			CTAGCTGTGCGGG	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.2432C>T	2.37:g.179650408G>A	ENSP00000465570:p.Thr811Ile	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	127	63	0.496063	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		289	0.13232600732600733	60	0.12195121951219512	62	0.1712707182320442	0	0.0	167	0.22031662269129287	G	14.19	2.460217	0.43736	0.102133	0.234535	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.64085	-0.08;0.16;0.17;0.16;0.25	5.51	5.51	0.81932	Ribonuclease H-like (1);	.	.	.	.	T	0.00073	0.0002	L	0.29908	0.895	0.37180	P	0.09653599999999996	D;D;D;D;D	0.76494	0.995;0.995;0.995;0.997;0.999	P;P;P;P;D	0.67382	0.593;0.593;0.593;0.794;0.951	T	0.02424	-1.1161	8	0.87932	D	0	.	19.7837	0.96428	0.0:0.0:1.0:0.0	rs35813871;rs62176570	765;765;765;811;811	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	I	811;765;765;765;765;811	ENSP00000343764:T811I;ENSP00000434586:T765I;ENSP00000340554:T765I;ENSP00000352154:T765I;ENSP00000354117:T811I	ENSP00000340554:T765I	T	-	2	0	TTN	179358653	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.619000	0.67729	2.738000	0.93877	0.655000	0.94253	ACA	G|0.827;A|0.173	0.173	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NMUR2	56923	hgsc.bcm.edu	37	5	151784183	151784183	+	Silent	SNP	G	G	A	rs3749787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:151784183G>A	ENST00000255262.3	-	1	657	c.492C>T	c.(490-492)ctC>ctT	p.L164L	NMUR2_ENST00000518933.1_Intron	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	164					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|arachidonic acid secretion (GO:0050482)|calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell-cell signaling (GO:0007267)|central nervous system development (GO:0007417)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|feeding behavior (GO:0007631)|grooming behavior (GO:0007625)|inositol phosphate-mediated signaling (GO:0048016)|neuropeptide signaling pathway (GO:0007218)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|reduction of food intake in response to dietary excess (GO:0002023)|regulation of smooth muscle contraction (GO:0006940)|response to pain (GO:0048265)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|GTP binding (GO:0005525)|intracellular calcium activated chloride channel activity (GO:0005229)|neuromedin U binding (GO:0042924)|neuromedin U receptor activity (GO:0001607)			breast(1)|endometrium(1)|kidney(2)|large_intestine(12)|liver(1)|lung(15)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	44		Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000106)|KIRC - Kidney renal clear cell carcinoma(527;0.000672)			CGAGGATCCTGAGGGCCCGGC	0.637													G|||	1155	0.230631	0.2466	0.2421	5008	,	,		17302	0.2956		0.1948	False		,,,				2504	0.1708				p.L164L		Atlas-SNP	.											NMUR2,NS,carcinoma,-2,1	NMUR2	111	1	0			c.C492T						PASS	.	G		1114,3292	396.0+/-329.9	131,852,1220	47.0	55.0	52.0		492	3.5	0.5	5	dbSNP_107	52	1764,6836	315.8+/-312.4	169,1426,2705	no	coding-synonymous	NMUR2	NM_020167.4		300,2278,3925	AA,AG,GG		20.5116,25.2837,22.1282		164/416	151784183	2878,10128	2203	4300	6503	SO:0001819	synonymous_variant	56923	exon1			GATCCTGAGGGCC	AF242874	CCDS4321.1	5q33.1	2012-08-08		2004-05-28	ENSG00000132911	ENSG00000132911		"""GPCR / Class A : Neuromedin U receptors"""	16454	protein-coding gene	gene with protein product		605108		NMU2R		8940772, 10894543	Standard	NM_020167		Approved		uc003luv.2	Q9GZQ4	OTTHUMG00000130131	ENST00000255262.3:c.492C>T	5.37:g.151784183G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	83	46	0.554217	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Silent	SNP	ENST00000255262.3	37	CCDS4321.1																																																																																			G|0.781;A|0.219	0.219	strong		0.637	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167	
SMYD4	114826	hgsc.bcm.edu	37	17	1690752	1690752	+	Missense_Mutation	SNP	G	G	A	rs11549830	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1690752G>A	ENST00000305513.7	-	6	1851	c.1684C>T	c.(1684-1686)Cgg>Tgg	p.R562W		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	562	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		R -> W (in dbSNP:rs11549830). {ECO:0000269|PubMed:11572484}.				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						TTTCTAATCCGCTGTGACGCC	0.572													G|||	2206	0.440495	0.4047	0.4914	5008	,	,		22833	0.5268		0.3439	False		,,,				2504	0.4632				p.R562W		Atlas-SNP	.											.	SMYD4	50	.	0			c.C1684T						PASS	.	G	TRP/ARG	1729,2671		353,1023,824	86.0	68.0	74.0		1684	2.5	0.3	17	dbSNP_120	74	2823,5767		463,1897,1935	yes	missense	SMYD4	NM_052928.2	101	816,2920,2759	AA,AG,GG		32.8638,39.2955,35.0423	probably-damaging	562/805	1690752	4552,8438	2200	4295	6495	SO:0001583	missense	114826	exon6			TAATCCGCTGTGA	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.1684C>T	17.37:g.1690752G>A	ENSP00000304360:p.Arg562Trp	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	139	67	0.482014	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	953	0.43635531135531136	224	0.45528455284552843	152	0.4198895027624309	308	0.5384615384615384	269	0.3548812664907652	G	18.51	3.640410	0.67244	0.392955	0.328638	ENSG00000186532	ENST00000305513	T	0.80393	-1.37	5.86	2.54	0.30619	SET domain (3);	1.405560	0.04087	N	0.310634	T	0.00012	0.0000	L	0.48642	1.525	0.38185	P	0.06025999999999998	D	0.69078	0.997	P	0.56916	0.809	T	0.33523	-0.9865	9	0.45353	T	0.12	4.6685	11.3134	0.49377	0.0:0.1111:0.4818:0.4072	rs11549830	562	Q8IYR2	SMYD4_HUMAN	W	562	ENSP00000304360:R562W	ENSP00000304360:R562W	R	-	1	2	SMYD4	1637502	0.456000	0.25744	0.266000	0.24541	0.743000	0.42351	0.773000	0.26661	0.244000	0.21351	0.655000	0.94253	CGG	G|0.609;A|0.391	0.391	strong		0.572	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
HHAT	55733	hgsc.bcm.edu	37	1	210577831	210577831	+	Silent	SNP	C	C	T	rs34772809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:210577831C>T	ENST00000367010.1	+	6	719	c.492C>T	c.(490-492)aaC>aaT	p.N164N	HHAT_ENST00000391905.3_Silent_p.N164N|HHAT_ENST00000541565.1_Intron|HHAT_ENST00000545154.1_Silent_p.N165N|HHAT_ENST00000308852.6_Silent_p.N119N|HHAT_ENST00000545781.1_Silent_p.N101N|HHAT_ENST00000413764.2_Silent_p.N164N|HHAT_ENST00000537898.1_Silent_p.N99N|HHAT_ENST00000261458.3_Silent_p.N164N	NM_001170580.1	NP_001164051.1	Q5VTY9	HHAT_HUMAN	hedgehog acyltransferase	164					multicellular organismal development (GO:0007275)|protein palmitoylation (GO:0018345)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|palmitoyltransferase activity (GO:0016409)			breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(81;0.0136)|all cancers(67;0.161)|KIRC - Kidney renal clear cell carcinoma(1967;0.215)		AGACAGAAAACGAGTACTACC	0.552													c|||	406	0.0810703	0.0348	0.111	5008	,	,		19835	0.002		0.1789	False		,,,				2504	0.1033				p.N165N		Atlas-SNP	.											.	HHAT	66	.	0			c.C495T						PASS	.	T	,,,,,	240,4166	140.0+/-175.5	6,228,1969	98.0	78.0	85.0		492,,492,495,297,492	-3.7	0.0	1	dbSNP_126	85	1599,7001	296.6+/-303.0	161,1277,2862	no	coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HHAT	NM_001122834.2,NM_001170564.1,NM_001170580.1,NM_001170587.1,NM_001170588.1,NM_018194.4	,,,,,	167,1505,4831	TT,TC,CC		18.593,5.4471,14.1396	,,,,,	164/494,,164/494,165/495,99/429,164/494	210577831	1839,11167	2203	4300	6503	SO:0001819	synonymous_variant	55733	exon5			AGAAAACGAGTAC	AK001586	CCDS1495.1, CCDS53471.1, CCDS53472.1, CCDS53473.1	1q32	2008-02-05			ENSG00000054392	ENSG00000054392			18270	protein-coding gene	gene with protein product		605743				11160356	Standard	NM_001170587		Approved	FLJ10724, MART-2, MART2, Skn, ski, rasp, sit, GUP2	uc009xcx.3	Q5VTY9	OTTHUMG00000036447	ENST00000367010.1:c.492C>T	1.37:g.210577831C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	71	70	0.985915	NM_001170587	B7Z4D5|B7Z5I1|B7Z868|B7ZA75|D3DT91|F5H444|Q17RZ7|Q4G0K3|Q5CZ95|Q5TGI2|Q9NVH9|Q9Y3N8	Silent	SNP	ENST00000367010.1	37	CCDS1495.1																																																																																			C|0.875;T|0.125	0.125	strong		0.552	HHAT-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088662.1	NM_018194	
HLA-A	3105	hgsc.bcm.edu	37	6	29910602	29910602	+	Missense_Mutation	SNP	G	G	T	rs41552219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910602G>T	ENST00000396634.1	+	4	483	c.142G>T	c.(142-144)Gcc>Tcc	p.A48S	HLA-A_ENST00000376809.5_Missense_Mutation_p.A48S|HLA-A_ENST00000376806.5_Missense_Mutation_p.A48S|HLA-A_ENST00000376802.2_Missense_Mutation_p.A48S			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	48	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCGCTTCATCGCCGTGGGCTA	0.697									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.A48S		Atlas-SNP	.											HLA-A,NS,carcinoma,-2,4	HLA-A	89	4	0			c.G142T						PASS	.						32.0	28.0	29.0					6																	29910602		2201	4298	6499	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	TTCATCGCCGTGG	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.142G>T	6.37:g.29910602G>T	ENSP00000379873:p.Ala48Ser	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	86	14	0.162791	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	8.545	0.874078	0.17395	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00012	9.31;9.31;9.31;9.31	3.72	-7.44	0.01379	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	3.134130	0.02442	N	0.084628	T	0.00039	0.0001	N	0.11927	0.2	0.09310	N	1	B;D;B;D;B	0.69078	0.001;0.997;0.001;0.997;0.001	B;D;B;D;B	0.91635	0.069;0.999;0.111;0.999;0.069	T	0.53989	-0.8360	10	0.44086	T	0.13	.	3.4234	0.07401	0.21:0.0831:0.5765:0.1304	rs41552219	48;48;48;48;48	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	S	48	ENSP00000379873:A48S;ENSP00000366002:A48S;ENSP00000366005:A48S;ENSP00000365998:A48S	ENSP00000348012:A48S	A	+	1	0	HLA-A	30018581	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-6.122000	0.00080	-2.883000	0.00318	-1.516000	0.00938	GCC	A|0.043;G|0.955;T|0.002	0.002	strong		0.697	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964000	88964000	+	Silent	SNP	C	C	T	rs801839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:88964000C>T	ENST00000333190.4	+	4	2313	c.1704C>T	c.(1702-1704)ttC>ttT	p.F568F		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	568							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			AATATACTTTCAGTGCAAATG	0.353										HNSCC(36;0.09)			T|||	2553	0.509784	0.7345	0.3401	5008	,	,		19433	0.7153		0.2336	False		,,,				2504	0.3988				p.F568F		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1704T						PASS	.	T		2816,1566		895,1026,270	42.0	45.0	44.0		1704	4.3	0.5	7	dbSNP_86	44	2011,6581		238,1535,2523	no	coding-synonymous	ZNF804B	NM_181646.2		1133,2561,2793	TT,TC,CC		23.4055,35.7371,37.2052		568/1350	88964000	4827,8147	2191	4296	6487	SO:0001819	synonymous_variant	219578	exon4			TACTTTCAGTGCA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1704C>T	7.37:g.88964000C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	57	29	0.508772	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	37	CCDS5613.1																																																																																			C|0.493;T|0.507	0.507	strong		0.353	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
GPR18	2841	hgsc.bcm.edu	37	13	99907341	99907341	+	Silent	SNP	G	G	A	rs3742130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:99907341G>A	ENST00000340807.3	-	3	1342	c.786C>T	c.(784-786)aaC>aaT	p.N262N	UBAC2_ENST00000403766.3_Intron|UBAC2_ENST00000376440.2_Intron|GPR18_ENST00000397470.2_Silent_p.N262N|GPR18_ENST00000397473.2_Silent_p.N262N			Q14330	GPR18_HUMAN	G protein-coupled receptor 18	262					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)	GATTGTAACTGTTCTCCCCCG	0.498													G|||	543	0.108427	0.0401	0.1499	5008	,	,		19549	0.0595		0.2217	False		,,,				2504	0.1053				p.N262N		Atlas-SNP	.											.	GPR18	23	.	0			c.C786T						PASS	.	G	,,,	362,4044	184.7+/-212.0	13,336,1854	193.0	148.0	163.0		786,,786,	0.1	0.0	13	dbSNP_107	163	1891,6709	336.9+/-322.1	223,1445,2632	no	coding-synonymous,intron,coding-synonymous,intron	GPR18,UBAC2	NM_001098200.1,NM_001144072.1,NM_005292.3,NM_177967.3	,,,	236,1781,4486	AA,AG,GG		21.9884,8.2161,17.3228	,,,	262/332,,262/332,	99907341	2253,10753	2203	4300	6503	SO:0001819	synonymous_variant	2841	exon2			GTAACTGTTCTCC	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.786C>T	13.37:g.99907341G>A		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	129	48	0.372093	NM_001098200	Q6GTM3|Q96HI6|Q9H2L2	Silent	SNP	ENST00000340807.3	37	CCDS9491.1																																																																																			G|0.849;A|0.151	0.151	strong		0.498	GPR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045585.1		
TLE2	7089	hgsc.bcm.edu	37	19	2997897	2997897	+	Silent	SNP	G	G	A	rs11150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:2997897G>A	ENST00000262953.6	-	20	2443	c.2181C>T	c.(2179-2181)atC>atT	p.I727I	TLE2_ENST00000586422.1_Intron|TLE2_ENST00000590536.1_Silent_p.I728I|TLE2_ENST00000455444.2_Silent_p.I605I|TLE2_ENST00000591529.1_3'UTR|TLE2_ENST00000443826.3_Silent_p.I605I|TLE2_ENST00000447365.2_Silent_p.I394I	NM_003260.4	NP_003251.2	Q04725	TLE2_HUMAN	transducin-like enhancer of split 2	727					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	13				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)		AGCCTGTCACGATGTATTTGT	0.542													G|||	871	0.173922	0.1218	0.2709	5008	,	,		19507	0.248		0.1561	False		,,,				2504	0.1176				p.I727I		Atlas-SNP	.											.	TLE2	35	.	0			c.C2181T						PASS	.	G	,,	493,3583		40,413,1585	82.0	82.0	82.0		,1815,2181	2.0	1.0	19	dbSNP_52	82	1189,7167		80,1029,3069	no	utr-3,coding-synonymous,coding-synonymous	TLE2	NM_001144761.1,NM_001144762.1,NM_003260.4	,,	120,1442,4654	AA,AG,GG		14.2293,12.0952,13.5296	,,	,605/622,727/744	2997897	1682,10750	2038	4178	6216	SO:0001819	synonymous_variant	7089	exon20			TGTCACGATGTAT	M99436	CCDS45911.1, CCDS45912.1, CCDS45913.1, CCDS74255.1	19p13.3	2014-03-07	2014-03-07					"""WD repeat domain containing"""	11838	protein-coding gene	gene with protein product	"""enhancer of split groucho 2"""	601041	"""transducin-like enhancer of split 2, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)"""			8808280	Standard	NM_003260		Approved	ESG2, GRG2, ESG, FLJ41188	uc002lww.3	Q04725		ENST00000262953.6:c.2181C>T	19.37:g.2997897G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	113	59	0.522124	NM_003260	B4DE03|E9PEV7|F8WCH2|Q8WVY0|Q9Y6S0	Silent	SNP	ENST00000262953.6	37	CCDS45911.1																																																																																			G|0.801;A|0.199	0.199	strong		0.542	TLE2-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452194.2	NM_003260	
HAPLN3	145864	hgsc.bcm.edu	37	15	89422353	89422353	+	Missense_Mutation	SNP	G	G	A	rs569695538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89422353G>A	ENST00000359595.3	-	4	855	c.641C>T	c.(640-642)gCg>gTg	p.A214V	HAPLN3_ENST00000562889.1_Missense_Mutation_p.A276V	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	214	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	CAGCCAGCCCGCGTTGCACCA	0.701											OREG0023445	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	,	,		15072	0.001		0.0	False		,,,				2504	0.001				p.A214V		Atlas-SNP	.											.	HAPLN3	43	.	0			c.C641T						PASS	.						29.0	33.0	32.0					15																	89422353		2199	4299	6498	SO:0001583	missense	145864	exon4			CAGCCCGCGTTGC	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.641C>T	15.37:g.89422353G>A	ENSP00000352606:p.Ala214Val	Somatic	23	0	0	1267	WXS	Illumina HiSeq	Phase_I	54	26	0.481481	NM_178232	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432313	0.43122	.	.	ENSG00000140511	ENST00000359595	T	0.13778	2.56	4.36	3.44	0.39384	C-type lectin fold (1);Link (5);C-type lectin-like (1);	0.054620	0.64402	D	0.000001	T	0.33000	0.0848	M	0.79123	2.44	0.54753	D	0.999987	D;D	0.65815	0.995;0.995	P;P	0.62184	0.899;0.899	T	0.09530	-1.0670	10	0.72032	D	0.01	-15.2009	11.1418	0.48406	0.0927:0.0:0.9073:0.0	.	214;214	A8K7T8;Q96S86	.;HPLN3_HUMAN	V	214	ENSP00000352606:A214V	ENSP00000352606:A214V	A	-	2	0	HAPLN3	87223357	1.000000	0.71417	0.066000	0.19879	0.986000	0.74619	9.207000	0.95064	0.940000	0.37473	0.655000	0.94253	GCG	.	.	none		0.701	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
RIC8A	60626	hgsc.bcm.edu	37	11	205398	205398	+	5'Flank	SNP	G	G	A	rs190584141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:205398G>A	ENST00000526104.1	+	0	0				BET1L_ENST00000486280.1_Silent_p.S57S|BET1L_ENST00000332865.6_3'UTR|BET1L_ENST00000382762.3_Silent_p.S80S|BET1L_ENST00000325147.9_3'UTR|RP11-304M2.5_ENST00000526963.1_RNA|BET1L_ENST00000410108.1_Intron|BET1L_ENST00000529614.2_Silent_p.S61S			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TGTCTTGTCCGGACCTTGCCA	0.537													G|||	4	0.000798722	0.0	0.0	5008	,	,		21271	0.0		0.004	False		,,,				2504	0.0				p.S80S		Atlas-SNP	.											.	BET1L	7	.	0			c.C240T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	84.0	88.0	87.0		240,	-4.5	1.0	11		87	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,utr-3	BET1L	NM_001098787.1,NM_016526.4	,	0,20,6483	AA,AG,GG		0.1744,0.1135,0.1538	,	80/112,	205398	20,12986	2203	4300	6503	SO:0001631	upstream_gene_variant	51272	exon4			TTGTCCGGACCTT	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069		11.37:g.205398G>A	Exception_encountered	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	161	90	0.559006	NM_001098787	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Silent	SNP	ENST00000526104.1	37																																																																																				G|0.998;A|0.002	0.002	strong		0.537	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
MROH9	80133	hgsc.bcm.edu	37	1	170934394	170934394	+	Missense_Mutation	SNP	T	T	C	rs16863872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:170934394T>C	ENST00000367758.3	+	7	577	c.478T>C	c.(478-480)Tac>Cac	p.Y160H	MROH9_ENST00000367759.4_Missense_Mutation_p.Y160H	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	160			Y -> H (in dbSNP:rs16863872).														AGTCAGAAAATACGTAAGTCA	0.398													T|||	179	0.0357428	0.0015	0.0476	5008	,	,		19974	0.0		0.0825	False		,,,				2504	0.0624				p.Y160H		Atlas-SNP	.											C1orf129_ENST00000367759,NS,carcinoma,-2,2	.	.	2	0			c.T478C						PASS	.	T	HIS/TYR,HIS/TYR	61,3761		0,61,1850	120.0	113.0	115.0		478,478	-3.0	0.0	1	dbSNP_123	115	692,7570		28,636,3467	yes	missense,missense	C1orf129	NM_001163629.1,NM_025063.2	83,83	28,697,5317	CC,CT,TT		8.3757,1.596,6.2314	benign,benign	160/862,160/574	170934394	753,11331	1911	4131	6042	SO:0001583	missense	80133	exon7			AGAAAATACGTAA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.478T>C	1.37:g.170934394T>C	ENSP00000356732:p.Tyr160His	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	83	0.038003663003663	2	0.0040650406504065045	21	0.058011049723756904	0	0.0	60	0.079155672823219	T	3.376	-0.127423	0.06753	0.01596	0.083757	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.66099	-0.19;2.54	5.6	-2.97	0.05530	.	0.627172	0.15160	N	0.277198	T	0.24699	0.0599	L	0.60455	1.87	0.80722	P	0.0	B;B	0.21071	0.051;0.023	B;B	0.21917	0.037;0.016	T	0.05068	-1.0908	9	0.17369	T	0.5	-2.7243	1.7889	0.03047	0.133:0.3193:0.1372:0.4104	rs16863872;rs52808266;rs56468374;rs16863872	160;160	F5GWX6;Q5TGP6	.;CA129_HUMAN	H	160	ENSP00000356733:Y160H;ENSP00000356732:Y160H	ENSP00000356732:Y160H	Y	+	1	0	C1orf129	169201018	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.653000	0.05360	-0.153000	0.11137	-1.162000	0.01777	TAC	T|0.955;C|0.045	0.045	strong		0.398	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
ACTN4	81	hgsc.bcm.edu	37	19	39215172	39215172	+	Silent	SNP	T	T	C	rs12986337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39215172T>C	ENST00000252699.2	+	16	2053	c.1977T>C	c.(1975-1977)aaT>aaC	p.N659N	ACTN4_ENST00000424234.2_Silent_p.N269N|ACTN4_ENST00000390009.3_Silent_p.N440N	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	659					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)			GCCAGGCCAATGTTGTGGGGC	0.637													C|||	346	0.0690895	0.0552	0.0821	5008	,	,		14639	0.0476		0.0616	False		,,,				2504	0.1084				p.N659N	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.T1977C						PASS	.	C		212,4194	779.7+/-414.4	7,198,1998	52.0	53.0	53.0		1977	0.4	0.6	19	dbSNP_121	53	541,8059	774.7+/-407.7	12,517,3771	no	coding-synonymous	ACTN4	NM_004924.4		19,715,5769	CC,CT,TT		6.2907,4.8116,5.7896		659/912	39215172	753,12253	2203	4300	6503	SO:0001819	synonymous_variant	81	exon16			GGCCAATGTTGTG	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.1977T>C	19.37:g.39215172T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	66	0.492537	NM_004924	A4K467|D6PXK4|O76048	Silent	SNP	ENST00000252699.2	37	CCDS12518.1																																																																																			T|0.942;C|0.058	0.058	strong		0.637	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
EBP	10682	hgsc.bcm.edu	37	X	48382174	48382174	+	Silent	SNP	G	G	T	rs3048	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:48382174G>T	ENST00000495186.1	+	2	838	c.15G>T	c.(13-15)gcG>gcT	p.A5A	EBP_ENST00000276096.6_Intron	NM_006579.2	NP_006570.1	Q15125	EBP_HUMAN	emopamil binding protein (sterol isomerase)	5					cholesterol biosynthetic process (GO:0006695)|cholesterol metabolic process (GO:0008203)|drug transmembrane transport (GO:0006855)|hemopoiesis (GO:0030097)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	C-8 sterol isomerase activity (GO:0000247)|cholestenol delta-isomerase activity (GO:0047750)|drug transmembrane transporter activity (GO:0015238)|steroid delta-isomerase activity (GO:0004769)|transmembrane signaling receptor activity (GO:0004888)	p.A5A(1)		NS(1)|endometrium(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|stomach(1)	11					Tamoxifen(DB00675)	CTACCAACGCGGGCCCCTTGC	0.478													g|||	1190	0.315232	0.1467	0.2305	3775	,	,		10105	0.3155		0.2724	False		,,,				2504	0.2495				p.A5A	Ovarian(41;550 1000 33077 33474 52335)	Atlas-SNP	.											.	EBP	30	.	1	Substitution - coding silent(1)	stomach(1)	c.G15T						PASS	.			786,3049		78,526,104,1028,467	58.0	42.0	47.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	15	-2.7	0.0	X	dbSNP_36	47	2306,4422		326,1040,614,1062,1258	no	coding-synonymous	EBP	NM_006579.2		404,1566,718,2090,1725	TT,TG,T,GG,G		34.2747,20.4954,29.272		5/231	48382174	3092,7471	2203	4300	6503	SO:0001819	synonymous_variant	10682	exon2			CAACGCGGGCCCC	Z37986	CCDS14300.1	Xp11.23-p11.22	2013-05-22	2001-11-28		ENSG00000147155	ENSG00000147155			3133	protein-coding gene	gene with protein product	"""3-beta-hydroxysteroid-delta-8,delta-7-isomerase"", ""Chondrodysplasia punctata-2, X-linked dominant (Happle syndrome)"", ""sterol 8-isomerase"""	300205	"""emopamil-binding protein (sterol isomerase)"""	CDPX2		7706302, 8938429	Standard	NM_006579		Approved	CPX, CPXD, CHO2	uc004djx.4	Q15125	OTTHUMG00000034482	ENST00000495186.1:c.15G>T	X.37:g.48382174G>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	41	39	0.951219	NM_006579	Q6FGL3|Q6IBI9	Silent	SNP	ENST00000495186.1	37	CCDS14300.1																																																																																			G|0.693;T|0.307	0.307	strong		0.478	EBP-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083372.1	NM_006579	
C14orf37	145407	hgsc.bcm.edu	37	14	58598357	58598357	+	Silent	SNP	C	C	T	rs45465593	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:58598357C>T	ENST00000267485.7	-	4	1898	c.1704G>A	c.(1702-1704)gtG>gtA	p.V568V	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	568						integral component of membrane (GO:0016021)				breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TGGGTTCCCCCACCATTATTC	0.493													C|||	56	0.0111821	0.003	0.0101	5008	,	,		19381	0.0		0.0408	False		,,,				2504	0.0041				p.V568V		Atlas-SNP	.											.	C14orf37	87	.	0			c.G1704A						PASS	.	C		32,4374	37.6+/-69.7	0,32,2171	114.0	108.0	110.0		1704	4.9	0.6	14	dbSNP_127	110	250,8350	99.5+/-161.0	3,244,4053	no	coding-synonymous	C14orf37	NM_001001872.2		3,276,6224	TT,TC,CC		2.907,0.7263,2.1682		568/775	58598357	282,12724	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon4			TTCCCCCACCATT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1704G>A	14.37:g.58598357C>T		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	91	44	0.483516	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			C|0.979;T|0.021	0.021	strong		0.493	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
ANKRD35	148741	hgsc.bcm.edu	37	1	145562087	145562087	+	Missense_Mutation	SNP	G	G	A	rs41315701	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145562087G>A	ENST00000355594.4	+	10	1862	c.1775G>A	c.(1774-1776)cGa>cAa	p.R592Q		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	592			R -> Q (in dbSNP:rs41315701).							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)					CCTGGGGCTCGAGGAGAGCCT	0.582													G|||	619	0.123602	0.0129	0.111	5008	,	,		17919	0.1319		0.2117	False		,,,				2504	0.183				p.R592Q	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G1775A						PASS	.	G	GLN/ARG	231,4175		11,209,1983	37.0	49.0	45.0		1775	0.9	0.0	1	dbSNP_127	45	1959,6639		230,1499,2570	yes	missense	ANKRD35	NM_144698.3	43	241,1708,4553	AA,AG,GG		22.7844,5.2429,16.841	benign	592/1002	145562087	2190,10814	2203	4299	6502	SO:0001583	missense	148741	exon10			GGGCTCGAGGAGA	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.1775G>A	1.37:g.145562087G>A	ENSP00000347802:p.Arg592Gln	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	316	0.1446886446886447	8	0.016260162601626018	44	0.12154696132596685	95	0.1660839160839161	169	0.22295514511873352	G	3.749	-0.052032	0.07362	0.052429	0.227844	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.44482	0.92	4.87	0.923	0.19413	.	0.734278	0.11613	N	0.546527	T	0.09024	0.0223	L	0.27053	0.805	0.80722	P	0.0	B	0.10296	0.003	B	0.04013	0.001	T	0.29488	-1.0010	9	0.20046	T	0.44	-1.5743	4.2906	0.10876	0.2782:0.1674:0.5544:0.0	rs41315701	592	Q8N283	ANR35_HUMAN	Q	501;592	ENSP00000347802:R592Q	ENSP00000347802:R592Q	R	+	2	0	ANKRD35	144273444	0.002000	0.14202	0.000000	0.03702	0.073000	0.16967	1.200000	0.32247	0.014000	0.14944	0.655000	0.94253	CGA	G|0.837;A|0.163	0.163	strong		0.582	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
CLDN6	9074	hgsc.bcm.edu	37	16	3065596	3065596	+	Missense_Mutation	SNP	T	T	C	rs2257295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3065596T>C	ENST00000396925.1	-	3	855	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	CLDN6_ENST00000572154.1_Intron|TNFRSF12A_ENST00000573001.1_5'Flank|CLDN6_ENST00000328796.4_Missense_Mutation_p.I143V			P56747	CLD6_HUMAN	claudin 6	143			I -> V (in dbSNP:rs2257295). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743, ECO:0000269|Ref.1, ECO:0000269|Ref.2}.		calcium-independent cell-cell adhesion (GO:0016338)|cell-cell junction organization (GO:0045216)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	10						TCCCGGATGATGGCATGCGCC	0.617													T|||	1497	0.298922	0.3548	0.3343	5008	,	,		18815	0.1925		0.3708	False		,,,				2504	0.2342				p.I143V		Atlas-SNP	.											CLDN6,rectum,carcinoma,0,3	CLDN6	31	3	0			c.A427G						PASS	.	T	VAL/ILE	1631,2761		311,1009,876	23.0	25.0	25.0		427	2.5	0.9	16	dbSNP_100	25	3379,5217		688,2003,1607	no	missense	CLDN6	NM_021195.4	29	999,3012,2483	CC,CT,TT		39.309,37.1357,38.5741	benign	143/221	3065596	5010,7978	2196	4298	6494	SO:0001583	missense	9074	exon2			GGATGATGGCATG	AJ249735	CCDS10488.1	16p13.3	2008-08-01			ENSG00000184697	ENSG00000184697		"""Claudins"""	2048	protein-coding gene	gene with protein product		615798				9892664, 18234789	Standard	NM_021195		Approved		uc002csu.4	P56747	OTTHUMG00000128999	ENST00000396925.1:c.427A>G	16.37:g.3065596T>C	ENSP00000380131:p.Ile143Val	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	108	41	0.37963	NM_021195	B3KQP9|D3DUA5	Missense_Mutation	SNP	ENST00000396925.1	37	CCDS10488.1	695	0.3182234432234432	179	0.3638211382113821	122	0.3370165745856354	124	0.21678321678321677	270	0.3562005277044855	T	6.973	0.549571	0.13374	0.371357	0.39309	ENSG00000184697	ENST00000396925;ENST00000328796	D;D	0.89270	-2.49;-2.49	4.76	2.51	0.30379	.	0.125321	0.52532	N	0.000076	T	0.00012	0.0000	L	0.33245	0.995	0.32491	P	0.540211	B	0.22276	0.067	B	0.27500	0.08	T	0.10776	-1.0615	9	0.23302	T	0.38	.	7.5467	0.27770	0.0:0.1806:0.0:0.8194	rs2257295;rs17850428;rs61137178;rs2257295	143	P56747	CLD6_HUMAN	V	143	ENSP00000380131:I143V;ENSP00000328674:I143V	ENSP00000328674:I143V	I	-	1	0	CLDN6	3005597	1.000000	0.71417	0.941000	0.38009	0.114000	0.19823	1.726000	0.38085	0.423000	0.26033	0.533000	0.62120	ATC	T|0.645;C|0.355	0.355	strong		0.617	CLDN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250988.1	NM_021195	
EGFR	1956	hgsc.bcm.edu	37	7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	rs2227983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55229255G>A	ENST00000275493.2	+	13	1739	c.1562G>A	c.(1561-1563)aGg>aAg	p.R521K	EGFR_ENST00000455089.1_Missense_Mutation_p.R476K|EGFR_ENST00000442591.1_Missense_Mutation_p.R521K|EGFR_ENST00000342916.3_Missense_Mutation_p.R521K|EGFR_ENST00000454757.2_Missense_Mutation_p.R468K|EGFR_ENST00000344576.2_Missense_Mutation_p.R521K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	521			R -> K (in dbSNP:rs2227983). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.7}.		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)	CCGGAGCCCAGGGACTGCGTC	0.617		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			G|||	1463	0.292133	0.0643	0.33	5008	,	,		17432	0.5238		0.2763	False		,,,				2504	0.3507				p.R521K		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.G1562A	GRCh37	CM942312	EGFR	M	rs2227983	PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	391,4015	196.0+/-220.5	12,367,1824	111.0	114.0	113.0		1562,1562,1562	-5.8	0.0	7	dbSNP_98	113	2245,6355	380.6+/-339.7	317,1611,2372	yes	missense,missense,missense	EGFR	NM_005228.3,NM_201282.1,NM_201284.1	26,26,26	329,1978,4196	AA,AG,GG		26.1047,8.8743,20.2676	benign,benign,benign	521/1211,521/629,521/706	55229255	2636,10370	2203	4300	6503	SO:0001583	missense	1956	exon13	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	AGCCCAGGGACTG		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.1562G>A	7.37:g.55229255G>A	ENSP00000275493:p.Arg521Lys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	65	65	1	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	652	0.29853479853479853	29	0.05894308943089431	108	0.2983425414364641	302	0.527972027972028	213	0.28100263852242746	G	1.353	-0.590998	0.03799	0.088743	0.261047	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	6.07	-5.79	0.02354	Growth factor, receptor (1);	1.067450	0.06989	N	0.821201	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.48043	-0.9069	9	0.10377	T	0.69	.	2.4933	0.04615	0.5094:0.1722:0.17:0.1484	rs2227983;rs3752650;rs11543848;rs12234746;rs17336807;rs11543848	476;521;521;521	Q504U8;P00533;P00533-3;P00533-4	.;EGFR_HUMAN;.;.	K	476;521;391;521;521;521;468;315	ENSP00000415559:R476K;ENSP00000342376:R521K;ENSP00000345973:R521K;ENSP00000275493:R521K;ENSP00000410031:R521K;ENSP00000395243:R468K	ENSP00000275493:R521K	R	+	2	0	EGFR	55196749	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-0.793000	0.04589	-1.106000	0.03008	-0.165000	0.13383	AGG	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong		0.617	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
BCAR1	9564	hgsc.bcm.edu	37	16	75263816	75263816	+	Silent	SNP	G	G	A	rs145141523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:75263816G>A	ENST00000162330.5	-	7	2332	c.2206C>T	c.(2206-2208)Ctg>Ttg	p.L736L	BCAR1_ENST00000418647.3_Silent_p.L782L|BCAR1_ENST00000393420.6_Silent_p.L754L|RP11-331F4.4_ENST00000489723.1_RNA|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000546196.1_Silent_p.L707L|BCAR1_ENST00000535626.2_Silent_p.L588L|BCAR1_ENST00000393422.2_Silent_p.L754L|BCAR1_ENST00000538440.2_Silent_p.L736L|BCAR1_ENST00000420641.3_Silent_p.L754L|BCAR1_ENST00000542031.2_Silent_p.L734L	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	736					actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GAGGGCCCCAGGCCGCCTGTT	0.657													G|||	25	0.00499201	0.0015	0.0014	5008	,	,		15958	0.0		0.0179	False		,,,				2504	0.0041				p.L782L		Atlas-SNP	.											BCAR1_ENST00000393420,NS,carcinoma,0,2	BCAR1	184	2	0			c.C2344T						PASS	.	G	,,,,,,,,	9,4377		0,9,2184	37.0	42.0	40.0		2344,2260,2260,2260,2206,2200,1762,1576,2206	2.7	1.0	16	dbSNP_134	40	169,8417		3,163,4127	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_001170721.1,NM_014567.3	,,,,,,,,	3,172,6311	AA,AG,GG		1.9683,0.2052,1.3722	,,,,,,,,	782/917,754/889,754/889,754/889,736/871,734/869,588/723,526/661,736/871	75263816	178,12794	2193	4293	6486	SO:0001819	synonymous_variant	9564	exon8			GCCCCAGGCCGCC	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.2206C>T	16.37:g.75263816G>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Silent	SNP	ENST00000162330.5	37	CCDS10915.1																																																																																			G|0.993;A|0.007	0.007	strong		0.657	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
SCAF4	57466	hgsc.bcm.edu	37	21	33074633	33074633	+	Silent	SNP	A	A	G	rs2202128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33074633A>G	ENST00000286835.7	-	5	763	c.381T>C	c.(379-381)atT>atC	p.I127I	SCAF4_ENST00000399804.1_Silent_p.I127I|SCAF4_ENST00000434667.3_Silent_p.I112I	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	127	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						GAGGTTGAATAATTTCAATTT	0.378													A|||	53	0.0105831	0.0	0.0187	5008	,	,		16978	0.001		0.0268	False		,,,				2504	0.0123				p.I127I		Atlas-SNP	.											.	SCAF4	142	.	0			c.T381C						PASS	.	A	,,	24,4382	31.7+/-61.6	0,24,2179	123.0	109.0	114.0		336,381,381	-0.9	1.0	21	dbSNP_96	114	287,8313	106.2+/-167.1	7,273,4020	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAF4	NM_001145444.1,NM_001145445.1,NM_020706.2	,,	7,297,6199	GG,GA,AA		3.3372,0.5447,2.3912	,,	112/1133,127/1126,127/1148	33074633	311,12695	2203	4300	6503	SO:0001819	synonymous_variant	57466	exon5			TTGAATAATTTCA	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.381T>C	21.37:g.33074633A>G		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	187	119	0.636364	NM_020706	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Silent	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																			A|0.977;G|0.023	0.023	strong		0.378	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
OTUD6B	51633	hgsc.bcm.edu	37	8	92083424	92083424	+	Silent	SNP	A	A	G	rs11557571	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:92083424A>G	ENST00000285420.4	+	2	330	c.231A>G	c.(229-231)caA>caG	p.Q77Q	GS1-251I9.4_ENST00000524003.1_RNA|GS1-251I9.4_ENST00000522817.1_RNA|OTUD6B_ENST00000404789.3_5'UTR	NM_016023.3	NP_057107.3	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B	47							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)			GGAGGAAGCAACTCACCGAAG	0.418													A|||	2435	0.486222	0.2262	0.4049	5008	,	,		17805	0.5833		0.5974	False		,,,				2504	0.681				p.Q77Q		Atlas-SNP	.											.	OTUD6B	28	.	0			c.A231G						PASS	.	A		1303,3103	440.0+/-345.9	207,889,1107	124.0	117.0	120.0		231	-3.8	0.7	8	dbSNP_120	120	5144,3456	635.7+/-399.0	1530,2084,686	no	coding-synonymous	OTUD6B	NM_016023.3		1737,2973,1793	GG,GA,AA		40.186,29.5733,49.5694		77/324	92083424	6447,6559	2203	4300	6503	SO:0001819	synonymous_variant	51633	exon2			GAAGCAACTCACC		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.231A>G	8.37:g.92083424A>G		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	75	39	0.52	NM_016023	A8K6I1|B4DEY0|Q9NTA4|Q9Y387	Silent	SNP	ENST00000285420.4	37	CCDS6253.2																																																																																			A|0.518;G|0.482	0.482	strong		0.418	OTUD6B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319968.1	NM_016023	
CCDC114	93233	hgsc.bcm.edu	37	19	48821757	48821757	+	Missense_Mutation	SNP	G	G	A	rs16981988	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48821757G>A	ENST00000315396.7	-	3	818	c.136C>T	c.(136-138)Cgg>Tgg	p.R46W	CCDC114_ENST00000497803.1_5'UTR	NM_144577.3	NP_653178.3	Q96M63	CC114_HUMAN	coiled-coil domain containing 114	46					outer dynein arm assembly (GO:0036158)	cilium (GO:0005929)|outer dynein arm (GO:0036157)				cervix(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)	24		all_epithelial(76;9.64e-05)|all_lung(116;0.000147)|Lung NSC(112;0.000251)|Prostate(7;0.0187)|all_neural(266;0.0228)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000162)|Epithelial(262;0.0134)|GBM - Glioblastoma multiforme(486;0.0143)		TCCCGAAGCCGCTTGACCTGG	0.662													G|||	160	0.0319489	0.0605	0.0303	5008	,	,		17279	0.0		0.0249	False		,,,				2504	0.0348				p.R46W		Atlas-SNP	.											.	CCDC114	100	.	0			c.C136T						PASS	.	G	TRP/ARG	63,1321		3,57,632	23.0	26.0	25.0		136	-0.6	1.0	19	dbSNP_123	25	91,3091		0,91,1500	yes	missense	CCDC114	NM_144577.3	101	3,148,2132	AA,AG,GG		2.8598,4.552,3.3728	probably-damaging	46/671	48821757	154,4412	692	1591	2283	SO:0001583	missense	93233	exon3			GAAGCCGCTTGAC	BC025752	CCDS12714.2	19q13.32	2013-02-22			ENSG00000105479	ENSG00000105479			26560	protein-coding gene	gene with protein product		615038				23261302, 23261303	Standard	NM_144577		Approved	FLJ32926, CILD20	uc002pir.2	Q96M63	OTTHUMG00000156161	ENST00000315396.7:c.136C>T	19.37:g.48821757G>A	ENSP00000318429:p.Arg46Trp	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_144577	Q6ZRL4|Q96M06|Q9UFG8	Missense_Mutation	SNP	ENST00000315396.7	37	CCDS12714.2	70	0.03205128205128205	36	0.07317073170731707	13	0.03591160220994475	2	0.0034965034965034965	19	0.025065963060686015	G	18.20	3.571425	0.65765	0.04552	0.028598	ENSG00000105479	ENST00000315396	T	0.25579	1.79	4.56	-0.634	0.11516	.	.	.	.	.	T	0.03220	0.0094	L	0.32530	0.975	0.32806	D	0.50074	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.30504	-0.9976	9	0.72032	D	0.01	-23.6886	11.1491	0.48447	0.0:0.0:0.3483:0.6517	rs16981988	46;46	Q96M63;Q96M63-5	CC114_HUMAN;.	W	46	ENSP00000318429:R46W	ENSP00000318429:R46W	R	-	1	2	CCDC114	53513569	1.000000	0.71417	0.996000	0.52242	0.656000	0.38851	0.342000	0.19926	0.231000	0.21079	-0.302000	0.09304	CGG	G|0.970;A|0.030	0.030	strong		0.662	CCDC114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343207.1	NM_144577	
C1orf116	79098	hgsc.bcm.edu	37	1	207195561	207195561	+	Silent	SNP	G	G	A	rs34185174	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:207195561G>A	ENST00000359470.5	-	4	1797	c.1548C>T	c.(1546-1548)gaC>gaT	p.D516D	C1orf116_ENST00000461135.2_Silent_p.D270D	NM_023938.5	NP_076427.2	Q9BW04	SARG_HUMAN	chromosome 1 open reading frame 116	516						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(4)|stomach(1)	29	Prostate(682;0.19)					GCGAGATCTTGTCCAAGAAGG	0.582													G|||	22	0.00439297	0.0015	0.0029	5008	,	,		20891	0.001		0.0139	False		,,,				2504	0.0031				p.D516D		Atlas-SNP	.											.	C1orf116	64	.	0			c.C1548T						PASS	.	G	,	15,4391	22.3+/-47.3	0,15,2188	35.0	37.0	37.0		810,1548	0.9	1.0	1	dbSNP_126	37	107,8493	57.9+/-119.4	1,105,4194	no	coding-synonymous,coding-synonymous	C1orf116	NM_001083924.1,NM_023938.5	,	1,120,6382	AA,AG,GG		1.2442,0.3404,0.938	,	270/356,516/602	207195561	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	79098	exon4			GATCTTGTCCAAG		CCDS1475.1, CCDS44306.1	1q32.1	2012-06-26			ENSG00000182795	ENSG00000182795			28667	protein-coding gene	gene with protein product	"""specifically androgen-regulated gene"""	611680				15525603, 9389513	Standard	NM_023938		Approved	SARG, FLJ36507, MGC2742, MGC4309	uc001hfd.2	Q9BW04	OTTHUMG00000036580	ENST00000359470.5:c.1548C>T	1.37:g.207195561G>A		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	57	30	0.526316	NM_023938	C9JV41|Q658X3	Silent	SNP	ENST00000359470.5	37	CCDS1475.1																																																																																			G|0.991;A|0.009	0.009	strong		0.582	C1orf116-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088973.1	NM_024115	
SAPCD1	401251	hgsc.bcm.edu	37	6	31731301	31731301	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31731301G>A	ENST00000425424.1	+	2	283	c.224G>A	c.(223-225)cGa>cAa	p.R75Q	SAPCD1_ENST00000415669.2_Missense_Mutation_p.R75Q|VWA7_ENST00000467576.1_5'Flank|MSH5_ENST00000534153.4_3'UTR|MSH5-SAPCD1_ENST00000493662.2_3'UTR|SAPCD1-AS1_ENST00000419679.1_RNA			Q5SSQ6	SAPC1_HUMAN	suppressor APC domain containing 1	75																	GAGGCACAGCGACAGCAGCTG	0.607																																					p.R75Q		Atlas-SNP	.											.	.	.	.	0			c.G224A						PASS	.						76.0	78.0	77.0					6																	31731301		1509	2708	4217	SO:0001583	missense	401251	exon2			CACAGCGACAGCA		CCDS34411.1	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000228727	ENSG00000228727			13938	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 26"""	C6orf26			Standard	NM_001039651		Approved	NG23		Q5SSQ6	OTTHUMG00000031131	ENST00000425424.1:c.224G>A	6.37:g.31731301G>A	ENSP00000413372:p.Arg75Gln	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001039651	A2ABF2|A2ABS9|Q9Y335	Missense_Mutation	SNP	ENST00000425424.1	37		.	.	.	.	.	.	.	.	.	.	G	1.914	-0.450071	0.04572	.	.	ENSG00000228727	ENST00000433778;ENST00000415669;ENST00000425424	T;T	0.79845	-1.31;-1.31	5.01	-3.43	0.04810	.	.	.	.	.	T	0.44519	0.1297	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.36480	-0.9746	8	0.18710	T	0.47	-5.3272	12.7855	0.57502	0.2885:0.0:0.7115:0.0	.	75	Q5SSQ6-2	.	Q	75	ENSP00000411948:R75Q;ENSP00000413372:R75Q	ENSP00000411948:R75Q	R	+	2	0	C6orf26	31839280	0.000000	0.05858	0.330000	0.25442	0.801000	0.45260	-0.272000	0.08560	-0.674000	0.05253	-1.004000	0.02495	CGA	.	.	none		0.607	SAPCD1-203	KNOWN	basic	protein_coding	protein_coding		NM_001039651	
WBP4	11193	hgsc.bcm.edu	37	13	41639377	41639377	+	Silent	SNP	C	C	T	rs61740513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:41639377C>T	ENST00000379487.3	+	4	616	c.216C>T	c.(214-216)gcC>gcT	p.A72A	WBP4_ENST00000542082.1_Silent_p.A51A	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	72					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AGGCAGCTGCCCTGAAAGCAT	0.368													C|||	126	0.0251597	0.0908	0.0072	5008	,	,		14418	0.0		0.001	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	WBP4	40	.	0			c.C216T						PASS	.	C		411,3995	201.5+/-224.5	14,383,1806	64.0	69.0	67.0		216	2.8	1.0	13	dbSNP_129	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WBP4	NM_007187.3		14,385,6104	TT,TC,CC		0.0233,9.3282,3.1755		72/377	41639377	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	11193	exon4			AGCTGCCCTGAAA	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.216C>T	13.37:g.41639377C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	71	39	0.549296	NM_007187	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.368	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
OBSL1	23363	hgsc.bcm.edu	37	2	220432957	220432957	+	Missense_Mutation	SNP	G	G	A	rs35009641	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220432957G>A	ENST00000404537.1	-	2	1158	c.1102C>T	c.(1102-1104)Cgc>Tgc	p.R368C	OBSL1_ENST00000491370.1_5'Flank|OBSL1_ENST00000603926.1_Missense_Mutation_p.R368C|OBSL1_ENST00000373876.1_Missense_Mutation_p.R368C|OBSL1_ENST00000373873.4_Missense_Mutation_p.R368C|OBSL1_ENST00000289656.3_5'UTR|OBSL1_ENST00000265318.4_Missense_Mutation_p.R368C	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	368	Ig-like 4.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		GTGGGGATGCGGGAGTTGGGT	0.657											OREG0003988	type=REGULATORY REGION|Gene=OBSL1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	G|||	77	0.0153754	0.0023	0.0245	5008	,	,		16539	0.0		0.0487	False		,,,				2504	0.0082				p.R368C		Atlas-SNP	.											.	OBSL1	120	.	0			c.C1102T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	33,3897		1,31,1933	29.0	34.0	32.0		1102,1102,1102	3.2	1.0	2	dbSNP_126	32	438,7844		12,414,3715	yes	missense,missense,missense	OBSL1	NM_001173408.1,NM_001173431.1,NM_015311.2	180,180,180	13,445,5648	AA,AG,GG		5.2886,0.8397,3.8569	probably-damaging,probably-damaging,probably-damaging	368/1026,368/1544,368/1897	220432957	471,11741	1965	4141	6106	SO:0001583	missense	23363	exon2			GGATGCGGGAGTT	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.1102C>T	2.37:g.220432957G>A	ENSP00000385636:p.Arg368Cys	Somatic	119	0	0	2266	WXS	Illumina HiSeq	Phase_I	134	62	0.462687	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Missense_Mutation	SNP	ENST00000404537.1	37	CCDS46520.1	59	0.027014652014652016	2	0.0040650406504065045	12	0.03314917127071823	2	0.0034965034965034965	43	0.05672823218997362	G	16.39	3.110114	0.56398	0.008397	0.052886	ENSG00000124006	ENST00000265318;ENST00000404537;ENST00000373876;ENST00000373873	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.17	3.25	0.37280	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.20901	0.0503	L	0.29908	0.895	0.37506	D	0.916948	D;D	0.89917	1.0;0.999	D;P	0.71414	0.973;0.884	T	0.56511	-0.7967	9	0.54805	T	0.06	.	7.4687	0.27336	0.0:0.1493:0.4601:0.3905	rs35009641;rs61742827	368;368	O75147;O75147-2	OBSL1_HUMAN;.	C	368	ENSP00000265318:R368C;ENSP00000385636:R368C;ENSP00000362983:R368C;ENSP00000362980:R368C	ENSP00000265318:R368C	R	-	1	0	OBSL1	220141201	0.995000	0.38212	0.996000	0.52242	1.000000	0.99986	2.518000	0.45537	1.372000	0.46190	0.650000	0.86243	CGC	G|0.968;A|0.032	0.032	strong		0.657	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
C5orf49	134121	hgsc.bcm.edu	37	5	7835555	7835555	+	Missense_Mutation	SNP	C	C	G	rs6883562	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:7835555C>G	ENST00000399810.2	-	2	672	c.204G>C	c.(202-204)caG>caC	p.Q68H	C5orf49_ENST00000509627.1_Missense_Mutation_p.Q68H	NM_001089584.2	NP_001083053.1	A4QMS7	CE049_HUMAN	chromosome 5 open reading frame 49	68			Q -> H (in dbSNP:rs6883562).							large_intestine(3)|lung(5)|skin(1)	9						GGTGCAACTTCTGATCATAAT	0.363													C|||	888	0.177316	0.1762	0.1715	5008	,	,		19617	0.0972		0.2217	False		,,,				2504	0.2198				p.Q68H		Atlas-SNP	.											.	C5orf49	27	.	0			c.G204C						PASS	.	C	HIS/GLN	739,2905		76,587,1159	128.0	123.0	124.0		204	1.7	0.7	5	dbSNP_116	124	1991,6177		224,1543,2317	yes	missense	C5orf49	NM_001089584.1	24	300,2130,3476	GG,GC,CC		24.3756,20.2799,23.1121	probably-damaging	68/148	7835555	2730,9082	1822	4084	5906	SO:0001583	missense	134121	exon2			CAACTTCTGATCA		CCDS43300.1	5p15.31	2008-07-16			ENSG00000215217	ENSG00000215217			27028	protein-coding gene	gene with protein product						12477932	Standard	NM_001089584		Approved	LOC134121	uc003jea.5	A4QMS7	OTTHUMG00000161897	ENST00000399810.2:c.204G>C	5.37:g.7835555C>G	ENSP00000382708:p.Gln68His	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_001089584		Missense_Mutation	SNP	ENST00000399810.2	37	CCDS43300.1	377	0.17261904761904762	89	0.18089430894308944	67	0.1850828729281768	51	0.08916083916083917	170	0.22427440633245382	C	16.02	3.005516	0.54254	0.202799	0.243756	ENSG00000215217	ENST00000399810;ENST00000509627	T;T	0.32023	1.47;1.47	4.95	1.68	0.24146	.	.	.	.	.	T	0.00012	0.0000	L	0.54323	1.7	0.36009	P	0.162049	D	0.54207	0.965	P	0.45138	0.471	T	0.17992	-1.0351	8	0.51188	T	0.08	-31.5049	5.3712	0.16140	0.0:0.5471:0.0:0.4529	rs6883562;rs17183443;rs6883562	68	A4QMS7	CE049_HUMAN	H	68	ENSP00000382708:Q68H;ENSP00000426019:Q68H	ENSP00000382708:Q68H	Q	-	3	2	C5orf49	7888555	0.989000	0.36119	0.714000	0.30535	0.969000	0.65631	0.512000	0.22755	0.625000	0.30304	0.561000	0.74099	CAG	C|0.808;G|0.192	0.192	strong		0.363	C5orf49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000366322.1	NM_001089584	
CDC20B	166979	hgsc.bcm.edu	37	5	54439466	54439466	+	Missense_Mutation	SNP	G	G	A	rs1021580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:54439466G>A	ENST00000381375.2	-	4	506	c.361C>T	c.(361-363)Cgc>Tgc	p.R121C	CDC20B_ENST00000331730.3_Missense_Mutation_p.R100C|CDC20B_ENST00000334206.5_Missense_Mutation_p.R121C|CDC20B_ENST00000322374.6_Missense_Mutation_p.R121C|CDC20B_ENST00000296733.1_Missense_Mutation_p.R121C			Q86Y33	CD20B_HUMAN	cell division cycle 20B	121			R -> C (in dbSNP:rs1021580). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1, ECO:0000269|Ref.4}.							kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			TGTTCTTTGCGGGATCCTACA	0.408													A|||	3728	0.744409	0.5567	0.8732	5008	,	,		19669	0.7262		0.827	False		,,,				2504	0.8405				p.R121C		Atlas-SNP	.											.	CDC20B	61	.	0			c.C361T						PASS	.	A	CYS/ARG,CYS/ARG,CYS/ARG	2642,1764	520.9+/-370.4	790,1062,351	92.0	92.0	92.0		361,361,361	-1.7	0.0	5	dbSNP_86	92	7116,1484	283.2+/-296.0	2947,1222,131	yes	missense,missense,missense	CDC20B	NM_001145734.2,NM_001170402.1,NM_152623.2	180,180,180	3737,2284,482	AA,AG,GG		17.2558,40.0363,24.9731	benign,benign,benign	121/478,121/520,121/516	54439466	9758,3248	2203	4300	6503	SO:0001583	missense	166979	exon4			CTTTGCGGGATCC	AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.361C>T	5.37:g.54439466G>A	ENSP00000370781:p.Arg121Cys	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	184	183	0.994565	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Missense_Mutation	SNP	ENST00000381375.2	37	CCDS54852.1	1622	0.7426739926739927	283	0.5752032520325203	310	0.856353591160221	417	0.7290209790209791	612	0.8073878627968337	A	1.610	-0.524320	0.04141	0.599637	0.827442	ENSG00000164287	ENST00000334206;ENST00000296733;ENST00000381375;ENST00000322374;ENST00000331730	T;T;T;T;T	0.17370	3.1;3.1;3.1;3.1;2.28	4.52	-1.69	0.08186	.	1.503420	0.04070	N	0.307886	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.27673	-1.0067	9	0.34782	T	0.22	-16.5756	0.9078	0.01288	0.2993:0.3121:0.2366:0.152	rs1021580;rs16883874;rs17846211;rs17859227;rs52822760;rs59416606;rs1021580	121;121;121;121	Q86Y33-4;Q86Y33-3;Q86Y33;Q86Y33-2	.;.;CD20B_HUMAN;.	C	121;121;121;121;100	ENSP00000335664:R121C;ENSP00000296733:R121C;ENSP00000370781:R121C;ENSP00000315720:R121C;ENSP00000330566:R100C	ENSP00000296733:R121C	R	-	1	0	CDC20B	54475223	0.000000	0.05858	0.001000	0.08648	0.076000	0.17211	-0.470000	0.06639	-0.713000	0.04981	-1.532000	0.00920	CGC	G|0.261;A|0.739	0.739	strong		0.408	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
KMT2C	58508	hgsc.bcm.edu	37	7	151873853	151873853	+	Silent	SNP	C	C	T	rs6464211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151873853C>T	ENST00000262189.6	-	38	8903	c.8685G>A	c.(8683-8685)caG>caA	p.Q2895Q	KMT2C_ENST00000355193.2_Silent_p.Q2895Q	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2895					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GAGTGGATGCCTGAATGACAT	0.398													T|||	1917	0.382788	0.7549	0.2392	5008	,	,		20363	0.3016		0.17	False		,,,				2504	0.2843				p.Q2895Q		Atlas-SNP	.											.	MLL3	1564	.	0			c.G8685A						PASS	.	T		3030,1376	455.9+/-351.1	1049,932,222	94.0	93.0	93.0		8685	-3.6	0.0	7	dbSNP_116	93	1408,7192	753.3+/-407.4	126,1156,3018	no	coding-synonymous	MLL3	NM_170606.2		1175,2088,3240	TT,TC,CC		16.3721,31.2301,34.1227		2895/4912	151873853	4438,8568	2203	4300	6503	SO:0001819	synonymous_variant	58508	exon38			GGATGCCTGAATG	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.8685G>A	7.37:g.151873853C>T		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	149	80	0.536913	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1	754	0.34523809523809523	358	0.7276422764227642	92	0.2541436464088398	170	0.2972027972027972	134	0.17678100263852242	T	0.007	-1.957464	0.00465	0.687699	0.163721	ENSG00000055609	ENST00000360104	.	.	.	5.12	-3.6	0.04570	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.46798	P	7.970000000000477E-4	.	.	.	.	.	.	T	0.38436	-0.9661	3	.	.	.	.	0.8674	0.01206	0.1496:0.2894:0.2562:0.3048	rs6464211;rs13236845;rs60172642;rs6464211	.	.	.	S	401	.	.	G	-	1	0	MLL3	151504786	0.092000	0.21681	0.000000	0.03702	0.138000	0.21146	0.169000	0.16641	-1.511000	0.01794	-1.256000	0.01477	GGC	C|0.643;T|0.357	0.357	strong		0.398	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
SH3GL1	6455	hgsc.bcm.edu	37	19	4362691	4362691	+	Silent	SNP	G	G	C	rs243261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4362691G>C	ENST00000269886.3	-	8	949	c.771C>G	c.(769-771)ccC>ccG	p.P257P	SH3GL1_ENST00000417295.2_Silent_p.P209P|AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000598564.1_Silent_p.P193P	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	257					central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		CCCGGGGCTTGGGCTTATACT	0.652			T	MLL	AL								G|||	1961	0.391573	0.3434	0.4063	5008	,	,		17905	0.6042		0.2744	False		,,,				2504	0.3476				p.P257P	NSCLC(94;1152 2133 30346 33362)	Atlas-SNP	.		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	SH3GL1	52	.	0			c.C771G						PASS	.	G	,,	1506,2900		270,966,967	58.0	56.0	57.0		627,579,771	-0.3	1.0	19	dbSNP_79	57	2423,6177		333,1757,2210	no	coding-synonymous,coding-synonymous,coding-synonymous	SH3GL1	NM_001199943.1,NM_001199944.1,NM_003025.3	,,	603,2723,3177	CC,CG,GG		28.1744,34.1807,30.2091	,,	209/321,193/305,257/369	4362691	3929,9077	2203	4300	6503	SO:0001819	synonymous_variant	6455	exon8			GGGCTTGGGCTTA		CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"""extra 11-19 leukemia fusion"", ""fusion partner of MLL"", ""SH3-containing Grb-2-like 1 protein"", ""SH3-containing protein EEN"", ""SH3 domain GRB2-like 1"""	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.771C>G	19.37:g.4362691G>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	52	29	0.557692	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Silent	SNP	ENST00000269886.3	37	CCDS32874.1																																																																																			G|0.684;C|0.316	0.316	strong		0.652	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025	
TRAP1	10131	hgsc.bcm.edu	37	16	3724352	3724352	+	Silent	SNP	G	G	A	rs11541712	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3724352G>A	ENST00000246957.5	-	9	1120	c.1032C>T	c.(1030-1032)taC>taT	p.Y344Y	TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000538171.1_Silent_p.Y291Y|TRAP1_ENST00000575671.1_Silent_p.Y135Y	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	344					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)				TGTCGGGCACGTAGAAGATGC	0.582													g|||	243	0.0485224	0.0325	0.0648	5008	,	,		20823	0.0407		0.0567	False		,,,				2504	0.0583				p.Y344Y		Atlas-SNP	.											.	TRAP1	53	.	0			c.C1032T						PASS	.	A		93,4301	76.8+/-115.0	2,89,2106	146.0	94.0	112.0		1032	-11.2	0.2	16	dbSNP_120	112	525,8075	147.7+/-203.1	16,493,3791	no	coding-synonymous	TRAP1	NM_016292.2		18,582,5897	AA,AG,GG		6.1047,2.1165,4.756		344/705	3724352	618,12376	2197	4300	6497	SO:0001819	synonymous_variant	10131	exon9			GGGCACGTAGAAG	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.1032C>T	16.37:g.3724352G>A		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Silent	SNP	ENST00000246957.5	37	CCDS10508.1																																																																																			T|0.006;G|0.845;C|0.107;A|0.041	0.041	strong		0.582	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292	
MUC6	4588	hgsc.bcm.edu	37	11	1017566	1017566	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1017566G>A	ENST00000421673.2	-	31	5285	c.5235C>T	c.(5233-5235)acC>acT	p.T1745T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1745	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGATGTAGAGGTTTTGGCCG	0.547																																					p.T1745T		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-2,2	MUC6	408	2	0			c.C5235T						scavenged	.						769.0	740.0	750.0					11																	1017566		2199	4287	6486	SO:0001819	synonymous_variant	4588	exon31			TGTAGAGGTTTTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5235C>T	11.37:g.1017566G>A		Somatic	470	11	0.0234043		WXS	Illumina HiSeq	Phase_I	612	33	0.0539216	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	none		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32917735	32917735	+	Missense_Mutation	SNP	A	A	G	rs144655116	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:32917735A>G	ENST00000361627.3	+	6	1485	c.763A>G	c.(763-765)Att>Gtt	p.I255V	ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.I255V|ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.I66V|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.I255V|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.I66V	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	255					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		CATGTTGGGTATTGATGGTCT	0.408													A|||	57	0.0113818	0.0015	0.0072	5008	,	,		19967	0.001		0.0318	False		,,,				2504	0.0174				p.I255V	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.A763G						PASS	.	A	VAL/ILE,VAL/ILE	22,4380		1,20,2180	161.0	164.0	163.0		763,763	2.3	1.0	15	dbSNP_134	163	221,8379		3,215,4082	no	missense,missense	ARHGAP11A	NM_014783.3,NM_199357.1	29,29	4,235,6262	GG,GA,AA		2.5698,0.4998,1.8689	benign,benign	255/1024,255/502	32917735	243,12759	2201	4300	6501	SO:0001583	missense	9824	exon6			TTGGGTATTGATG	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.763A>G	15.37:g.32917735A>G	ENSP00000355090:p.Ile255Val	Somatic	255	0	0		WXS	Illumina HiSeq	Phase_I	252	128	0.507937	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	30	0.013736263736263736	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	24	0.0316622691292876	.	6.545	0.468758	0.12461	0.004998	0.025698	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.08282	3.11	4.86	2.34	0.29019	.	0.908895	0.09351	N	0.814129	T	0.01092	0.0036	N	0.08118	0	0.25660	N	0.98601	B;B	0.20988	0.017;0.05	B;B	0.17722	0.003;0.019	T	0.43572	-0.9383	10	0.06099	T	0.92	.	4.967	0.14096	0.5962:0.1526:0.2512:0.0	.	255;66	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	V	255;66	ENSP00000355090:I255V	ENSP00000355090:I255V	I	+	1	0	ARHGAP11A	30705027	0.995000	0.38212	1.000000	0.80357	0.996000	0.88848	0.793000	0.26944	0.790000	0.33803	0.533000	0.62120	ATT	A|0.250;G|0.750	0.750	weak		0.408	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
ZSCAN29	146050	hgsc.bcm.edu	37	15	43653322	43653322	+	Silent	SNP	G	G	A	rs35278805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43653322G>A	ENST00000396976.2	-	5	2642	c.2508C>T	c.(2506-2508)caC>caT	p.H836H	ZSCAN29_ENST00000396972.1_Silent_p.H447H|ZSCAN29_ENST00000562072.1_3'UTR|ZSCAN29_ENST00000568898.1_Silent_p.H446H	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	836					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		GGATTTCTCCGTGCTTATTAA	0.453													G|||	685	0.136781	0.1891	0.1037	5008	,	,		21579	0.001		0.1958	False		,,,				2504	0.1687				p.H836H		Atlas-SNP	.											.	ZSCAN29	57	.	0			c.C2508T						PASS	.	G		845,3557	332.5+/-302.5	81,683,1437	89.0	90.0	90.0		2508	5.1	1.0	15	dbSNP_126	90	1622,6976	301.3+/-305.4	144,1334,2821	no	coding-synonymous	ZSCAN29	NM_152455.3		225,2017,4258	AA,AG,GG		18.8649,19.1958,18.9769		836/853	43653322	2467,10533	2201	4299	6500	SO:0001819	synonymous_variant	146050	exon5			TTCTCCGTGCTTA	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.2508C>T	15.37:g.43653322G>A		Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	147	73	0.496599	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	Silent	SNP	ENST00000396976.2	37	CCDS10095.2																																																																																			G|0.822;A|0.178	0.178	strong		0.453	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
CCDC137	339230	hgsc.bcm.edu	37	17	79639550	79639550	+	Missense_Mutation	SNP	G	G	A	rs11546630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79639550G>A	ENST00000329214.8	+	6	1089	c.686G>A	c.(685-687)cGg>cAg	p.R229Q		NM_199287.2	NP_954981.1	Q6PK04	CC137_HUMAN	coiled-coil domain containing 137	229			R -> Q (in dbSNP:rs11546630).				poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(5)|lung(2)	12	all_neural(118;0.0878)|all_lung(278;0.23)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CAGATGCTGCGGATGCTTCTG	0.647													g|||	659	0.131589	0.1997	0.0519	5008	,	,		17022	0.2232		0.0596	False		,,,				2504	0.0757				p.R229Q		Atlas-SNP	.											CCDC137,colon,carcinoma,+1,2	CCDC137	27	2	0			c.G686A						PASS	.	G	GLN/ARG	585,3565		26,533,1516	12.0	15.0	14.0		686	-3.1	0.0	17	dbSNP_120	14	392,7974		8,376,3799	yes	missense	CCDC137	NM_199287.2	43	34,909,5315	AA,AG,GG		4.6856,14.0964,7.806	benign	229/290	79639550	977,11539	2075	4183	6258	SO:0001583	missense	339230	exon6			TGCTGCGGATGCT	BC009369	CCDS42400.1	17q25.3	2008-07-04				ENSG00000185298			33451	protein-coding gene	gene with protein product		614271					Standard	NM_199287		Approved	MGC16597	uc002kbc.4	Q6PK04		ENST00000329214.8:c.686G>A	17.37:g.79639550G>A	ENSP00000329360:p.Arg229Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_199287		Missense_Mutation	SNP	ENST00000329214.8	37	CCDS42400.1	302	0.1382783882783883	114	0.23170731707317074	18	0.049723756906077346	124	0.21678321678321677	46	0.06068601583113457	G	4.032	0.003559	0.07866	0.140964	0.046856	ENSG00000185298	ENST00000329214	D	0.89939	-2.59	4.83	-3.14	0.05250	.	0.730039	0.13312	N	0.397364	T	0.00073	0.0002	L	0.29908	0.895	0.80722	P	0.0	P	0.41673	0.759	B	0.34038	0.174	T	0.17137	-1.0379	9	0.16896	T	0.51	-0.0094	7.6856	0.28538	0.6059:0.1858:0.2084:0.0	rs11546630;rs11546630	229	Q6PK04	CC137_HUMAN	Q	229	ENSP00000329360:R229Q	ENSP00000329360:R229Q	R	+	2	0	CCDC137	77249955	0.000000	0.05858	0.006000	0.13384	0.044000	0.14063	-0.589000	0.05767	-0.090000	0.12462	0.598000	0.82781	CGG	G|0.854;A|0.146	0.146	strong		0.647	CCDC137-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440387.1		
UBR3	130507	hgsc.bcm.edu	37	2	170762566	170762566	+	Silent	SNP	A	A	T	rs10194785	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:170762566A>T	ENST00000272793.5	+	10	1721	c.1671A>T	c.(1669-1671)ctA>ctT	p.L557L	UBR3_ENST00000418381.1_Silent_p.L557L			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	557					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						AGCGAGAACTAAACGAGCATG	0.408													A|||	1388	0.277157	0.2663	0.1945	5008	,	,		16538	0.376		0.1581	False		,,,				2504	0.3712				p.L557L		Atlas-SNP	.											.	UBR3	182	.	0			c.A1671T						PASS	.	A		383,1001		58,267,367	119.0	103.0	108.0		1671	1.6	1.0	2	dbSNP_119	108	545,2637		49,447,1095	no	coding-synonymous	UBR3	NM_172070.3		107,714,1462	TT,TA,AA		17.1276,27.6734,20.3241		557/1889	170762566	928,3638	692	1591	2283	SO:0001819	synonymous_variant	130507	exon10			AGAACTAAACGAG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.1671A>T	2.37:g.170762566A>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				A|0.748;T|0.252	0.252	strong		0.408	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
CPAMD8	27151	hgsc.bcm.edu	37	19	17088299	17088299	+	Missense_Mutation	SNP	T	T	C	rs1824152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17088299T>C	ENST00000443236.1	-	15	1809	c.1778A>G	c.(1777-1779)cAt>cGt	p.H593R	CPAMD8_ENST00000388925.4_Intron	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	546						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CACGGCCAGATGAAGAGAGGT	0.592													t|||	2839	0.566893	0.9213	0.3963	5008	,	,		17909	0.5625		0.3777	False		,,,				2504	0.408				p.H593R		Atlas-SNP	.											.	CPAMD8	192	.	0			c.A1778G						PASS	.	C	ARG/HIS	3115,813		1259,597,108	39.0	45.0	43.0		1778	-5.2	0.0	19	dbSNP_92	43	2825,5453		475,1875,1789	no	missense	CPAMD8	NM_015692.2	29	1734,2472,1897	CC,CT,TT		34.1266,20.6976,48.6646	benign	593/1933	17088299	5940,6266	1964	4139	6103	SO:0001583	missense	27151	exon15			GCCAGATGAAGAG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.1778A>G	19.37:g.17088299T>C	ENSP00000402505:p.His593Arg	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	35	15	0.428571	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	1126|1126	0.5155677655677655|0.5155677655677655	415|415	0.8434959349593496|0.8434959349593496	136|136	0.3756906077348066|0.3756906077348066	306|306	0.534965034965035|0.534965034965035	269|269	0.3548812664907652|0.3548812664907652	t|t	0.001|0.001	-2.964973|-2.964973	0.00049|0.00049	0.793024|0.793024	0.341266|0.341266	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	2.62|2.62	-5.24|-5.24	0.02789|0.02789	Alpha-2-macroglobulin, N-terminal 2 (1);|.	1.028330|.	0.07794|.	N|.	0.955448|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.10664|0.10664	0.02|0.02	0.21604|0.21604	P|P	0.999620117|0.999620117	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.10847|0.10847	-1.0612|-1.0612	8|4	0.15066|.	T|.	0.55|.	.|.	8.2718|8.2718	0.31849|0.31849	0.1001:0.314:0.0:0.5859|0.1001:0.314:0.0:0.5859	rs1824152;rs3745334;rs60607898;rs1824152|rs1824152;rs3745334;rs60607898;rs1824152	546|.	Q8IZJ3|.	CPMD8_HUMAN|.	R|V	593|604	.|.	ENSP00000291440:H593R|.	H|I	-|-	2|1	0|0	CPAMD8|CPAMD8	16949299|16949299	0.003000|0.003000	0.15002|0.15002	0.004000|0.004000	0.12327|0.12327	0.081000|0.081000	0.17604|0.17604	-0.493000|-0.493000	0.06459|0.06459	-3.135000|-3.135000	0.00235|0.00235	-4.516000|-4.516000	0.00005|0.00005	CAT|ATC	.	.	weak		0.592	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
FAM179A	165186	hgsc.bcm.edu	37	2	29274704	29274704	+	Silent	SNP	C	C	T	rs61749512	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29274704C>T	ENST00000379558.4	+	20	3156	c.2805C>T	c.(2803-2805)acC>acT	p.T935T	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Silent_p.T880T	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	935										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TCCTGAACACCGCCACCAGGA	0.642													C|||	1129	0.225439	0.1694	0.1859	5008	,	,		16173	0.5099		0.0915	False		,,,				2504	0.1738				p.T935T		Atlas-SNP	.											.	FAM179A	106	.	0			c.C2805T						PASS	.	C		560,3498		30,500,1499	16.0	19.0	18.0		2805	2.8	0.0	2	dbSNP_129	18	756,7610		34,688,3461	no	coding-synonymous	FAM179A	NM_199280.2		64,1188,4960	TT,TC,CC		9.0366,13.7999,10.5924		935/1020	29274704	1316,11108	2029	4183	6212	SO:0001819	synonymous_variant	165186	exon20			GAACACCGCCACC	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2805C>T	2.37:g.29274704C>T		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	153	74	0.48366	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			C|0.785;T|0.215	0.215	strong		0.642	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
WDR93	56964	hgsc.bcm.edu	37	15	90255284	90255284	+	Missense_Mutation	SNP	A	A	G	rs112224433	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:90255284A>G	ENST00000268130.7	+	5	690	c.589A>G	c.(589-591)Ata>Gta	p.I197V	WDR93_ENST00000560294.1_Missense_Mutation_p.I197V|RNU6-132P_ENST00000383863.1_RNA	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	197					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)			AACTACCTGTATAAAGATGGA	0.423													A|||	36	0.0071885	0.0	0.0144	5008	,	,		18509	0.0		0.0229	False		,,,				2504	0.0031				p.I197V		Atlas-SNP	.											.	WDR93	63	.	0			c.A589G						PASS	.	A	VAL/ILE	22,4378	28.1+/-56.4	0,22,2178	87.0	89.0	88.0		589	-10.7	0.0	15	dbSNP_132	88	251,8347	99.9+/-161.4	3,245,4051	yes	missense	WDR93	NM_020212.1	29	3,267,6229	GG,GA,AA		2.9193,0.5,2.1003	benign	197/687	90255284	273,12725	2200	4299	6499	SO:0001583	missense	56964	exon5			ACCTGTATAAAGA		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.589A>G	15.37:g.90255284A>G	ENSP00000268130:p.Ile197Val	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	19	0.358491	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	20	0.009157509157509158	0	0.0	7	0.019337016574585635	0	0.0	13	0.017150395778364115	A	0.003	-2.532775	0.00145	0.005	0.029193	ENSG00000140527	ENST00000268130	T	0.18016	2.24	5.34	-10.7	0.00240	WD40 repeat-like-containing domain (1);	1.934150	0.02465	N	0.086978	T	0.01421	0.0046	N	0.05383	-0.06	0.20563	N	0.99989	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.28522	-1.0041	10	0.02654	T	1	0.3578	1.3527	0.02176	0.3047:0.3222:0.1977:0.1754	.	197;197	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	V	197	ENSP00000268130:I197V	ENSP00000268130:I197V	I	+	1	0	WDR93	88056288	0.000000	0.05858	0.000000	0.03702	0.163000	0.22366	-3.416000	0.00478	-2.714000	0.00392	-1.556000	0.00890	ATA	A|0.981;G|0.019	0.019	strong		0.423	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
OR4C15	81309	hgsc.bcm.edu	37	11	55322211	55322211	+	Silent	SNP	A	A	G	rs9804659	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55322211A>G	ENST00000314644.2	+	1	429	c.429A>G	c.(427-429)aaA>aaG	p.K143K		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						ATGTGACAAAAACCATCTCTT	0.478										HNSCC(20;0.049)			a|||	1265	0.252596	0.1014	0.3242	5008	,	,		19759	0.3919		0.2833	False		,,,				2504	0.2311				p.K143K		Atlas-SNP	.											.	OR4C15	145	.	0			c.A429G						PASS	.	A		561,3841	252.1+/-258.6	27,507,1667	159.0	140.0	146.0		429	2.8	1.0	11	dbSNP_119	146	2288,6304	385.5+/-341.5	329,1630,2337	no	coding-synonymous	OR4C15	NM_001001920.1		356,2137,4004	GG,GA,AA		26.6294,12.7442,21.9255		143/371	55322211	2849,10145	2201	4296	6497	SO:0001819	synonymous_variant	81309	exon1			GACAAAAACCATC	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.429A>G	11.37:g.55322211A>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	80	36	0.45	NM_001001920	Q6IFE2	Silent	SNP	ENST00000314644.2	37	CCDS31501.1																																																																																			A|0.760;G|0.240	0.240	strong		0.478	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
HDAC4	9759	hgsc.bcm.edu	37	2	240003870	240003870	+	Silent	SNP	G	G	A	rs1063639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:240003870G>A	ENST00000345617.3	-	21	3356	c.2565C>T	c.(2563-2565)ccC>ccT	p.P855P	HDAC4_ENST00000543185.1_Silent_p.P439P	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	855	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		ACAGGACGCTGGGGTCGCTGT	0.592													G|||	2981	0.595248	0.59	0.6499	5008	,	,		15729	0.6885		0.4414	False		,,,				2504	0.6258				p.P855P		Atlas-SNP	.											.	HDAC4	127	.	0			c.C2565T						PASS	.	G		2499,1907	626.5+/-394.7	713,1073,417	171.0	155.0	160.0		2565	-3.0	0.0	2	dbSNP_86	160	4083,4517	561.0+/-387.7	958,2167,1175	no	coding-synonymous	HDAC4	NM_006037.3		1671,3240,1592	AA,AG,GG		47.4767,43.2819,49.3926		855/1085	240003870	6582,6424	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon21			GACGCTGGGGTCG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2565C>T	2.37:g.240003870G>A		Somatic	258	0	0		WXS	Illumina HiSeq	Phase_I	230	111	0.482609	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.456;A|0.544	0.544	strong		0.592	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
OR2T27	403239	hgsc.bcm.edu	37	1	248813785	248813785	+	Missense_Mutation	SNP	A	A	T	rs200036975	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248813785A>T	ENST00000344889.3	-	1	400	c.401T>A	c.(400-402)gTc>gAc	p.V134D		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	134						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCTCATGAGGACAGGATAGTG	0.557																																					p.V134D		Atlas-SNP	.											OR2T27,bladder,carcinoma,0,1	OR2T27	52	1	0			c.T401A						scavenged	.						88.0	56.0	67.0					1																	248813785		2200	4256	6456	SO:0001583	missense	403239	exon1			ATGAGGACAGGAT		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.401T>A	1.37:g.248813785A>T	ENSP00000342008:p.Val134Asp	Somatic	265	4	0.0150943		WXS	Illumina HiSeq	Phase_I	445	67	0.150562	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	8.174	0.792423	0.16258	.	.	ENSG00000187701	ENST00000344889	T	0.00892	5.57	2.74	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.441698	0.16541	N	0.209937	T	0.00875	0.0029	.	.	.	0.09310	N	1	B	0.22541	0.071	B	0.22601	0.04	T	0.47761	-0.9092	9	0.72032	D	0.01	.	5.1307	0.14909	0.6126:0.0:0.3874:0.0	rs1782240	134	Q8NH04	O2T27_HUMAN	D	134	ENSP00000342008:V134D	ENSP00000342008:V134D	V	-	2	0	OR2T27	246880408	0.000000	0.05858	0.003000	0.11579	0.051000	0.14879	-0.404000	0.07205	0.438000	0.26450	0.163000	0.16589	GTC	A|0.863;T|0.137	0.137	strong		0.557	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
TRIOBP	11078	hgsc.bcm.edu	37	22	38129332	38129332	+	Silent	SNP	G	G	A	rs7284476	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38129332G>A	ENST00000406386.3	+	8	4230	c.3975G>A	c.(3973-3975)caG>caA	p.Q1325Q		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1325					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)					GGGCCTTCCAGGCCCAGGACG	0.662													G|||	1689	0.33726	0.1573	0.2867	5008	,	,		14945	0.5843		0.3877	False		,,,				2504	0.3098				p.Q1325Q		Atlas-SNP	.											.	TRIOBP	262	.	0			c.G3975A						PASS	.	G		735,3103		119,497,1303	10.0	16.0	14.0		3975	5.8	1.0	22	dbSNP_116	14	3389,4547		832,1725,1411	no	coding-synonymous	TRIOBP	NM_001039141.2		951,2222,2714	AA,AG,GG		42.7041,19.1506,35.0263		1325/2366	38129332	4124,7650	1919	3968	5887	SO:0001819	synonymous_variant	11078	exon8			CTTCCAGGCCCAG	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.3975G>A	22.37:g.38129332G>A		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	189	188	0.994709	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			G|0.639;A|0.361	0.361	strong		0.662	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
HELT	391723	hgsc.bcm.edu	37	4	185940952	185940952	+	Missense_Mutation	SNP	C	C	G	rs1078461	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:185940952C>G	ENST00000515777.1	+	3	272	c.184C>G	c.(184-186)Ctg>Gtg	p.L62V	HELT_ENST00000338875.4_Missense_Mutation_p.L147V|HELT_ENST00000505610.1_Missense_Mutation_p.L62V			A6NFD8	HELT_HUMAN	helt bHLH transcription factor	62	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.		L -> V (in dbSNP:rs1078461).		central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		CGTTCAGTACCTGAGAGCACT	0.642													c|||	559	0.111621	0.0862	0.1354	5008	,	,		16083	0.1885		0.0924	False		,,,				2504	0.0695				p.L147V		Atlas-SNP	.											.	HELT	34	.	0			c.C439G						PASS	.	C	VAL/LEU	425,3981	193.3+/-218.5	21,383,1799	30.0	31.0	31.0		439	3.1	1.0	4	dbSNP_86	31	819,7781	180.6+/-229.5	39,741,3520	yes	missense	HELT	NM_001029887.1	32	60,1124,5319	GG,GC,CC		9.5233,9.6459,9.5648	probably-damaging	147/328	185940952	1244,11762	2203	4300	6503	SO:0001583	missense	391723	exon3			CAGTACCTGAGAG	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"""Basic helix-loop-helix proteins"""	33783	protein-coding gene	gene with protein product	"""megane bHLH factor"", ""HES-like"""		"""Hey-like transcription factor (zebrafish)"", ""HES/HEY-like transcription factor"""			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.184C>G	4.37:g.185940952C>G	ENSP00000426033:p.Leu62Val	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	163	83	0.509202	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Missense_Mutation	SNP	ENST00000515777.1	37		264	0.12087912087912088	41	0.08333333333333333	41	0.1132596685082873	109	0.19055944055944055	73	0.09630606860158311	C	19.49	3.837382	0.71373	0.096459	0.095233	ENSG00000187821	ENST00000505610;ENST00000515777;ENST00000338875	D;D;D	0.98060	-4.69;-4.69;-4.69	4.89	3.12	0.35913	Helix-loop-helix DNA-binding (5);	0.000000	0.64402	D	0.000010	T	0.04770	0.0129	L	0.39566	1.225	0.20975	P	0.999819995	D;P;P	0.57899	0.981;0.937;0.923	P;P;P	0.59948	0.866;0.794;0.69	T	0.05852	-1.0860	9	0.56958	D	0.05	.	9.7352	0.40384	0.0:0.7691:0.0:0.2309	rs1078461;rs4359954;rs17631598;rs1078461	147;62;62	A6NFD8;B7ZMI7;A6NFD8-2	HELT_HUMAN;.;.	V	62;62;147	ENSP00000422140:L62V;ENSP00000426033:L62V;ENSP00000343464:L147V	ENSP00000343464:L147V	L	+	1	2	HELT	186177946	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.880000	0.48530	1.288000	0.44600	0.561000	0.74099	CTG	C|0.898;G|0.102	0.102	strong		0.642	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781	
OBSCN	84033	hgsc.bcm.edu	37	1	228557755	228557755	+	Missense_Mutation	SNP	G	G	A	rs145597580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228557755G>A	ENST00000422127.1	+	91	20124	c.20080G>A	c.(20080-20082)Gcc>Acc	p.A6694T	OBSCN_ENST00000366707.4_Missense_Mutation_p.A4328T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A7651T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6694	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CAGCGAAGACGCCAAAGACTT	0.667													G|||	12	0.00239617	0.0	0.0014	5008	,	,		19459	0.0		0.004	False		,,,				2504	0.0072				p.A7651T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G22951A						PASS	.	G	THR/ALA	0,3934		0,0,1967	59.0	62.0	61.0		20080	4.7	0.8	1	dbSNP_134	61	10,8296		0,10,4143	yes	missense	OBSCN	NM_001098623.1	58	0,10,6110	AA,AG,GG		0.1204,0.0,0.0817	probably-damaging	6694/7969	228557755	10,12230	1967	4153	6120	SO:0001583	missense	84033	exon102			GAAGACGCCAAAG	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.20080G>A	1.37:g.228557755G>A	ENSP00000409493:p.Ala6694Thr	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	74	45	0.608108	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	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	G|G	16.97|16.97	3.269577|3.269577	0.59540|0.59540	0.0|0.0	0.001204|0.001204	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|.	0.68025|.	-0.3;-0.3|.	4.72|4.72	4.72|4.72	0.59763|0.59763	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	.|.	.|.	.|.	.|.	T|T	0.73281|0.73281	0.3567|0.3567	M|M	0.85710|0.85710	2.77|2.77	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.64410|.	0.925|.	T|T	0.79752|0.79752	-0.1671|-0.1671	9|5	0.87932|.	D|.	0|.	.|.	16.025|16.025	0.80536|0.80536	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6694|.	Q5VST9|.	OBSCN_HUMAN|.	T|H	6694;4328|1310	ENSP00000409493:A6694T;ENSP00000355668:A4328T|.	ENSP00000355668:A4328T|.	A|R	+|+	1|2	0|0	OBSCN|OBSCN	226624378|226624378	1.000000|1.000000	0.71417|0.71417	0.819000|0.819000	0.32651|0.32651	0.185000|0.185000	0.23345|0.23345	6.988000|6.988000	0.76212|0.76212	2.459000|2.459000	0.83118|0.83118	0.455000|0.455000	0.32223|0.32223	GCC|CGC	G|0.998;A|0.002	0.002	strong		0.667	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ARHGAP9	64333	hgsc.bcm.edu	37	12	57871437	57871437	+	Silent	SNP	C	C	T	rs34160414	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57871437C>T	ENST00000356411.2	-	4	699	c.561G>A	c.(559-561)gaG>gaA	p.E187E	ARHGAP9_ENST00000393797.2_Silent_p.E258E|ARHGAP9_ENST00000430041.2_Silent_p.E3E|ARHGAP9_ENST00000550454.1_5'UTR|ARHGAP9_ENST00000550288.1_Silent_p.E266E|ARHGAP9_ENST00000393791.3_Silent_p.E187E|ARHGAP9_ENST00000424809.2_Silent_p.E187E			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	187					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)			ACACAGGGGGCTCTGACATGA	0.647													C|||	486	0.0970447	0.289	0.0432	5008	,	,		13018	0.0		0.0288	False		,,,				2504	0.046				p.E187E		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.G561A						PASS	.	C	,,	1058,3326		138,782,1272	18.0	21.0	20.0		9,561,561	2.3	0.9	12	dbSNP_126	20	232,8348		2,228,4060	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP9	NM_001080156.1,NM_001080157.1,NM_032496.2	,,	140,1010,5332	TT,TC,CC		2.704,24.1332,9.9506	,,	3/548,187/641,187/732	57871437	1290,11674	2192	4290	6482	SO:0001819	synonymous_variant	64333	exon3			AGGGGGCTCTGAC	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.561G>A	12.37:g.57871437C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	104	40	0.384615	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Silent	SNP	ENST00000356411.2	37																																																																																				C|0.920;T|0.080	0.080	strong		0.647	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
ADORA3	140	hgsc.bcm.edu	37	1	112042732	112042732	+	Missense_Mutation	SNP	A	A	T	rs2800889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:112042732A>T	ENST00000241356.4	-	2	1202	c.797T>A	c.(796-798)aTg>aAg	p.M266K	ADORA3_ENST00000486342.1_5'Flank|ADORA3_ENST00000369716.4_Intron|ADORA3_ENST00000369717.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	266			M -> K (in dbSNP:rs2800889).		activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	CAGGATGCCCATGTACAGCAC	0.423													A|||	108	0.0215655	0.0272	0.0144	5008	,	,		23435	0.0109		0.0209	False		,,,				2504	0.0307				p.M266K		Atlas-SNP	.											.	ADORA3	104	.	0			c.T797A						PASS	.	A	LYS/MET,,	105,4301	81.9+/-120.4	1,103,2099	97.0	92.0	94.0		797,,	5.4	0.9	1	dbSNP_100	94	162,8438	77.2+/-139.8	2,158,4140	yes	missense,intron,intron	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	95,,	3,261,6239	TT,TA,AA		1.8837,2.3831,2.0529	benign,,	266/319,,	112042732	267,12739	2203	4300	6503	SO:0001583	missense	140	exon2			ATGCCCATGTACA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.797T>A	1.37:g.112042732A>T	ENSP00000241356:p.Met266Lys	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	128	47	0.367188	NM_000677	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	34	0.015567765567765568	7	0.014227642276422764	6	0.016574585635359115	7	0.012237762237762238	14	0.018469656992084433	A	13.28	2.188665	0.38609	0.023831	0.018837	ENSG00000121933	ENST00000241356	T	0.37752	1.18	5.41	5.41	0.78517	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.11580	0.0282	N	0.10874	0.06	0.26857	N	0.968033	B	0.09022	0.002	B	0.10450	0.005	T	0.30446	-0.9978	9	0.87932	D	0	.	15.1042	0.72306	1.0:0.0:0.0:0.0	rs2800889;rs52794759;rs2800889	266	P33765	AA3R_HUMAN	K	266	ENSP00000241356:M266K	ENSP00000241356:M266K	M	-	2	0	ADORA3	111844255	0.999000	0.42202	0.879000	0.34478	0.514000	0.34195	5.847000	0.69451	2.052000	0.61016	0.528000	0.53228	ATG	A|0.980;T|0.020	0.020	strong		0.423	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
SV2B	9899	hgsc.bcm.edu	37	15	91825027	91825027	+	Silent	SNP	C	C	T	rs1117388	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91825027C>T	ENST00000394232.1	+	10	1913	c.1443C>T	c.(1441-1443)gaC>gaT	p.D481D	SV2B_ENST00000330276.4_Silent_p.D481D|SV2B_ENST00000545111.2_Silent_p.D330D	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	481					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			ATTTTGAAGACGTAACATCAA	0.363													T|||	1668	0.333067	0.7617	0.1758	5008	,	,		23051	0.1419		0.2117	False		,,,				2504	0.1871				p.D481D		Atlas-SNP	.											.	SV2B	98	.	0			c.C1443T						PASS	.	T	,	2942,1454	469.8+/-355.6	1014,914,270	112.0	105.0	107.0		990,1443	0.7	1.0	15	dbSNP_86	107	1690,6906	737.8+/-407.0	174,1342,2782	no	coding-synonymous,coding-synonymous	SV2B	NM_001167580.1,NM_014848.4	,	1188,2256,3052	TT,TC,CC		19.6603,33.0755,35.6527	,	330/533,481/684	91825027	4632,8360	2198	4298	6496	SO:0001819	synonymous_variant	9899	exon11			TGAAGACGTAACA	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1443C>T	15.37:g.91825027C>T		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	102	44	0.431373	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			C|0.652;T|0.348	0.348	strong		0.363	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
RTP4	64108	hgsc.bcm.edu	37	3	187088656	187088656	+	Missense_Mutation	SNP	C	C	T	rs1047584	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:187088656C>T	ENST00000259030.2	+	2	346	c.236C>T	c.(235-237)aCa>aTa	p.T79I		NM_022147.2	NP_071430.2	Q96DX8	RTP4_HUMAN	receptor (chemosensory) transporter protein 4	79			T -> I (in dbSNP:rs1047584).		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)		GAGCACTGGACATCCCAGGGT	0.567													C|||	900	0.179712	0.1831	0.2363	5008	,	,		19987	0.0536		0.2376	False		,,,				2504	0.2055				p.T79I		Atlas-SNP	.											.	RTP4	20	.	0			c.C236T						PASS	.	C	ILE/THR	855,3551	336.5+/-304.4	92,671,1440	67.0	57.0	61.0		236	-7.8	0.0	3	dbSNP_86	61	2027,6573	353.4+/-329.1	231,1565,2504	yes	missense	RTP4	NM_022147.2	89	323,2236,3944	TT,TC,CC		23.5698,19.4054,22.159	possibly-damaging	79/247	187088656	2882,10124	2203	4300	6503	SO:0001583	missense	64108	exon2			ACTGGACATCCCA	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.236C>T	3.37:g.187088656C>T	ENSP00000259030:p.Thr79Ile	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	202	95	0.470297	NM_022147	Q9H4F3	Missense_Mutation	SNP	ENST00000259030.2	37	CCDS33910.1	396	0.1813186813186813	92	0.18699186991869918	98	0.27071823204419887	36	0.06293706293706294	170	0.22427440633245382	C	6.698	0.497523	0.12762	0.194054	0.235698	ENSG00000136514	ENST00000259030	T	0.18810	2.19	3.89	-7.78	0.01223	.	1.733720	0.02687	N	0.110196	T	0.00012	0.0000	L	0.34521	1.04	0.80722	P	0.0	P	0.48089	0.905	P	0.49047	0.599	T	0.24548	-1.0157	9	0.44086	T	0.13	-0.034	0.4251	0.00462	0.1837:0.237:0.238:0.3414	rs1047584;rs3187602;rs1047584	79	Q96DX8	RTP4_HUMAN	I	79	ENSP00000259030:T79I	ENSP00000259030:T79I	T	+	2	0	RTP4	188571350	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.121000	0.03270	-3.035000	0.00265	-0.793000	0.03317	ACA	C|0.802;T|0.198	0.198	strong		0.567	RTP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344260.1	NM_022147	
POR	5447	hgsc.bcm.edu	37	7	75615287	75615287	+	Silent	SNP	G	G	A	rs1057870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:75615287G>A	ENST00000461988.1	+	14	1821	c.1716G>A	c.(1714-1716)tcG>tcA	p.S572S	POR_ENST00000545601.1_Silent_p.S380S|POR_ENST00000394893.1_Silent_p.S572S|POR_ENST00000439269.1_Silent_p.S310S|POR_ENST00000419840.1_Intron|POR_ENST00000450476.1_Silent_p.S471S|TMEM120A_ENST00000493111.2_RNA|TMEM120A_ENST00000338761.4_RNA	NM_000941.2	NP_000932.3	P16435	NCPR_HUMAN	P450 (cytochrome) oxidoreductase	569					carnitine metabolic process (GO:0009437)|cellular organofluorine metabolic process (GO:0090346)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to peptide hormone stimulus (GO:0071375)|demethylation (GO:0070988)|fatty acid oxidation (GO:0019395)|flavonoid metabolic process (GO:0009812)|internal peptidyl-lysine acetylation (GO:0018393)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of lipase activity (GO:0060192)|nitrate catabolic process (GO:0043602)|nitric oxide catabolic process (GO:0046210)|oxidation-reduction process (GO:0055114)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|regulation of growth plate cartilage chondrocyte proliferation (GO:0003420)|response to drug (GO:0042493)|response to nutrient (GO:0007584)	endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|hydrolase activity (GO:0016787)|iron ion binding (GO:0005506)|iron-cytochrome-c reductase activity (GO:0047726)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric oxide dioxygenase activity (GO:0008941)			central_nervous_system(1)|endometrium(2)|kidney(2)|lung(3)|ovary(1)	9					Benzphetamine(DB00865)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Ethylmorphine(DB01466)|Flavin adenine dinucleotide(DB03147)|Lipoic Acid(DB00166)|Mitomycin(DB00305)|Nilutamide(DB00665)|Nitrofurantoin(DB00698)	GCCGCCGCTCGGATGAGGACT	0.697													G|||	978	0.195288	0.1256	0.2133	5008	,	,		15903	0.0377		0.341	False		,,,				2504	0.2894				p.S572S		Atlas-SNP	.											.	POR	46	.	0			c.G1716A						PASS	.	G		610,3330		41,528,1401	10.0	16.0	14.0		1716	-7.2	0.0	7	dbSNP_86	14	2849,5335		524,1801,1767	no	coding-synonymous	POR	NM_000941.2		565,2329,3168	AA,AG,GG		34.8118,15.4822,28.5302		572/681	75615287	3459,8665	1970	4092	6062	SO:0001819	synonymous_variant	5447	exon14			CCGCTCGGATGAG	AF258341	CCDS5579.1	7q11.2	2006-12-05			ENSG00000127948	ENSG00000127948			9208	protein-coding gene	gene with protein product		124015				2516426	Standard	NM_000941		Approved	CYPOR, FLJ26468	uc003udy.3	P16435	OTTHUMG00000130413	ENST00000461988.1:c.1716G>A	7.37:g.75615287G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_000941	Q16455|Q197M5|Q8N181|Q9H3M8|Q9UDT3	Silent	SNP	ENST00000461988.1	37	CCDS5579.1	402	0.18406593406593408	53	0.10772357723577236	79	0.21823204419889503	20	0.03496503496503497	250	0.32981530343007914	G	4.067	0.010290	0.07912	0.154822	0.348118	ENSG00000127948	ENST00000447222	.	.	.	3.59	-7.18	0.01505	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.54753	P	1.4999999999987246E-5	.	.	.	.	.	.	T	0.15752	-1.0426	3	.	.	.	-21.412	3.4043	0.07335	0.339:0.1397:0.4265:0.0949	rs1057870;rs2228105;rs3198404;rs10954733;rs11540676;rs17148959;rs56753821;rs1057870	.	.	.	R	623	.	.	G	+	1	0	POR	75453223	0.000000	0.05858	0.020000	0.16555	0.705000	0.40729	-2.390000	0.01057	-3.492000	0.00153	-2.868000	0.00100	GGA	G|0.826;A|0.174	0.174	strong		0.697	POR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252796.7	NM_000941	
ILK	3611	hgsc.bcm.edu	37	11	6631016	6631016	+	Silent	SNP	C	C	T	rs2292195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6631016C>T	ENST00000396751.2	+	9	1374	c.918C>T	c.(916-918)gcC>gcT	p.A306A	RP11-732A19.2_ENST00000527398.1_RNA|TAF10_ENST00000531760.1_5'Flank|ILK_ENST00000528995.1_Silent_p.A245A|ILK_ENST00000526711.1_3'UTR|ILK_ENST00000299421.4_Silent_p.A306A|ILK_ENST00000420936.2_Silent_p.A306A|ILK_ENST00000537806.1_Silent_p.A172A	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	306	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		GGGGCATGGCCTTCCTACACA	0.547													C|||	802	0.160144	0.1256	0.2219	5008	,	,		21063	0.0833		0.2575	False		,,,				2504	0.1421				p.A306A		Atlas-SNP	.											.	ILK	41	.	0			c.C918T						PASS	.	C	,,	680,3722	286.6+/-278.8	52,576,1573	136.0	120.0	126.0		918,918,918	0.7	1.0	11	dbSNP_100	126	2274,6318	384.7+/-341.2	310,1654,2332	no	coding-synonymous,coding-synonymous,coding-synonymous	ILK	NM_001014794.1,NM_001014795.1,NM_004517.2	,,	362,2230,3905	TT,TC,CC		26.4665,15.4475,22.7336	,,	306/453,306/453,306/453	6631016	2954,10040	2201	4296	6497	SO:0001819	synonymous_variant	3611	exon10			CATGGCCTTCCTA	U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"""Ankyrin repeat domain containing"""	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.918C>T	11.37:g.6631016C>T		Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	147	84	0.571429	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Silent	SNP	ENST00000396751.2	37	CCDS7768.1																																																																																			C|0.793;T|0.207	0.207	strong		0.547	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517	
SIM2	6493	hgsc.bcm.edu	37	21	38117505	38117505	+	Intron	SNP	C	C	T	rs2073602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:38117505C>T	ENST00000290399.6	+	10	2189				SIM2_ENST00000430056.3_Silent_p.G548G	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2						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						GCAGCCATGGCGGTGGGTGGC	0.602													C|||	1395	0.278554	0.3865	0.1787	5008	,	,		20123	0.2292		0.2276	False		,,,				2504	0.3067				p.G548G		Atlas-SNP	.											.	SIM2	55	.	0			c.C1644T						PASS	.	C	,	980,1668		181,618,525	46.0	55.0	52.0		,1644	-1.5	0.0	21	dbSNP_96	52	1030,3582		116,798,1392	no	intron,coding-synonymous	SIM2	NM_005069.3,NM_009586.2	,	297,1416,1917	TT,TC,CC		22.333,37.0091,27.686	,	,548/571	38117505	2010,5250	1324	2306	3630	SO:0001627	intron_variant	6493	exon10			CCATGGCGGTGGG		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.1576+68C>T	21.37:g.38117505C>T		Somatic	210	1	0.0047619		WXS	Illumina HiSeq	Phase_I	267	142	0.531835	NM_009586	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	37	CCDS13646.1																																																																																			C|0.739;T|0.261	0.261	strong		0.602	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
MDN1	23195	hgsc.bcm.edu	37	6	90402482	90402482	+	Missense_Mutation	SNP	G	G	A	rs9294445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90402482G>A	ENST00000369393.3	-	63	10382	c.10267C>T	c.(10267-10269)Cac>Tac	p.H3423Y	MDN1_ENST00000428876.1_Missense_Mutation_p.H3423Y			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3423			H -> Y (in dbSNP:rs9294445).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ATACTGCTGTGGAGTGAGGTG	0.582													G|||	3027	0.604433	0.5998	0.6988	5008	,	,		19282	0.9077		0.4602	False		,,,				2504	0.3793				p.H3423Y		Atlas-SNP	.											.	MDN1	478	.	0			c.C10267T						PASS	.	G	TYR/HIS	2654,1752	644.8+/-398.1	810,1034,359	59.0	62.0	61.0		10267	3.3	0.3	6	dbSNP_119	61	4016,4584	553.7+/-386.4	961,2094,1245	yes	missense	MDN1	NM_014611.1	83	1771,3128,1604	AA,AG,GG		46.6977,39.764,48.716	possibly-damaging	3423/5597	90402482	6670,6336	2203	4300	6503	SO:0001583	missense	23195	exon63			TGCTGTGGAGTGA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.10267C>T	6.37:g.90402482G>A	ENSP00000358400:p.His3423Tyr	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	54	53	0.981481	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	1432	0.6556776556776557	305	0.6199186991869918	242	0.6685082872928176	524	0.916083916083916	361	0.4762532981530343	G	0.053	-1.243550	0.01481	0.60236	0.466977	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.02974	4.09;4.09	5.1	3.31	0.37934	.	0.259259	0.33610	N	0.004723	T	0.01222	0.0040	M	0.62723	1.935	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.46679	-0.9174	9	0.22706	T	0.39	.	7.6737	0.28473	0.1373:0.0:0.6393:0.2234	rs9294445;rs52802793;rs60191675;rs9294445	3423	Q9NU22	MDN1_HUMAN	Y	3423	ENSP00000358400:H3423Y;ENSP00000413970:H3423Y	ENSP00000358400:H3423Y	H	-	1	0	MDN1	90459203	0.961000	0.32948	0.279000	0.24732	0.004000	0.04260	1.635000	0.37134	0.280000	0.22209	-1.579000	0.00862	CAC	G|0.429;A|0.571	0.571	strong		0.582	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
P2RX7	5027	hgsc.bcm.edu	37	12	121622563	121622563	+	Silent	SNP	G	G	A	rs1621388	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121622563G>A	ENST00000546057.1	+	13	1889	c.1746G>A	c.(1744-1746)ccG>ccA	p.P582P	P2RX7_ENST00000328963.5_Silent_p.P412P|RP11-340F14.5_ENST00000569999.1_RNA|P2RX7_ENST00000541446.1_Silent_p.P293P|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_Silent_p.P492P	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	582					apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AAGAGTTTCCGAAGAGTGAAG	0.607													C|||	1604	0.320288	0.4546	0.2003	5008	,	,		18772	0.1438		0.3837	False		,,,				2504	0.3405				p.P582P		Atlas-SNP	.											P2RX7,NS,carcinoma,0,1	P2RX7	53	1	0			c.G1746A						scavenged	.	C		1901,2449		434,1033,708	8.0	7.0	7.0		1746	1.1	0.9	12	dbSNP_89	7	3244,5208		747,1750,1729	no	coding-synonymous	P2RX7	NM_002562.5		1181,2783,2437	AA,AG,GG		38.3814,43.7011,40.189		582/596	121622563	5145,7657	2175	4226	6401	SO:0001819	synonymous_variant	5027	exon13			GTTTCCGAAGAGT	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1746G>A	12.37:g.121622563G>A		Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	106	106	1	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Silent	SNP	ENST00000546057.1	37	CCDS9213.1																																																																																			G|0.649;A|0.351	0.351	strong		0.607	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
ABCA13	154664	hgsc.bcm.edu	37	7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	rs78575608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48312084G>C	ENST00000435803.1	+	17	2845	c.2821G>C	c.(2821-2823)Gtt>Ctt	p.V941L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	941					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						AAAACAAGAAGTTGATAAAAT	0.368													G|||	126	0.0251597	0.003	0.0202	5008	,	,		17420	0.0		0.0557	False		,,,				2504	0.0532				p.V941L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G2821C						PASS	.	G	LEU/VAL	45,3611		0,45,1783	58.0	56.0	56.0		2821	-6.4	0.0	7	dbSNP_131	56	532,7648		14,504,3572	yes	missense	ABCA13	NM_152701.3	32	14,549,5355	CC,CG,GG		6.5037,1.2309,4.875	benign	941/5059	48312084	577,11259	1828	4090	5918	SO:0001583	missense	154664	exon17			CAAGAAGTTGATA	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.2821G>C	7.37:g.48312084G>C	ENSP00000411096:p.Val941Leu	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	200	85	0.425	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	47	0.02152014652014652	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	37	0.048812664907651716	G	4.662	0.123148	0.08931	0.012309	0.065037	ENSG00000179869	ENST00000435803	D	0.82984	-1.67	5.81	-6.43	0.01926	.	1.110050	0.06993	N	0.821921	T	0.09202	0.0227	N	0.16368	0.405	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.45775	-0.9238	10	0.05525	T	0.97	.	1.2609	0.02001	0.3788:0.2867:0.186:0.1485	.	941	Q86UQ4	ABCAD_HUMAN	L	941	ENSP00000411096:V941L	ENSP00000411096:V941L	V	+	1	0	ABCA13	48282630	0.000000	0.05858	0.000000	0.03702	0.986000	0.74619	-1.314000	0.02715	-0.919000	0.03803	0.655000	0.94253	GTT	G|0.974;C|0.026	0.026	strong		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
SCN10A	6336	hgsc.bcm.edu	37	3	38793989	38793989	+	Silent	SNP	G	G	A	rs7617919	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38793989G>A	ENST00000449082.2	-	11	1475	c.1476C>T	c.(1474-1476)ctC>ctT	p.L492L		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	492					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	TTCCAGAGGCGAGGCCTAGAA	0.552													G|||	1040	0.207668	0.0787	0.1052	5008	,	,		18386	0.373		0.2495	False		,,,				2504	0.2413				p.L492L		Atlas-SNP	.											.	SCN10A	359	.	0			c.C1476T						PASS	.	G		471,3935		26,419,1758	23.0	25.0	25.0		1476	-5.6	0.0	3	dbSNP_116	25	2169,6429		280,1609,2410	no	coding-synonymous	SCN10A	NM_006514.2		306,2028,4168	AA,AG,GG		25.2268,10.69,20.3014		492/1957	38793989	2640,10364	2203	4299	6502	SO:0001819	synonymous_variant	6336	exon11			AGAGGCGAGGCCT	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1476C>T	3.37:g.38793989G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	82	80	0.97561	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			G|0.780;A|0.220	0.220	strong		0.552	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
HRCT1	646962	hgsc.bcm.edu	37	9	35906583	35906583	+	Missense_Mutation	SNP	T	T	A	rs112821450|rs143611048|rs79156963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35906583T>A	ENST00000354323.2	+	1	395	c.299T>A	c.(298-300)cTc>cAc	p.L100H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	100	His-rich.					integral component of membrane (GO:0016021)		p.L100H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						cctcaccacctccaccaccac	0.667																																					p.L100H		Atlas-SNP	.											HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	1	Substitution - Missense(1)	NS(1)	c.T299A						scavenged	.						13.0	10.0	11.0					9																	35906583		1961	3863	5824	SO:0001583	missense	646962	exon1			ACCACCTCCACCA		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.299T>A	9.37:g.35906583T>A	ENSP00000346283:p.Leu100His	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	34	3	0.0882353	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	T	9.866	1.197686	0.22037	.	.	ENSG00000196196	ENST00000354323	.	.	.	3.43	-0.386	0.12466	.	.	.	.	.	T	0.09730	0.0239	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25117	-1.0141	8	0.87932	D	0	-5.7925	0.5802	0.00711	0.4571:0.1878:0.1238:0.2312	.	100	Q6UXD1	HRCT1_HUMAN	H	100	.	ENSP00000346283:L100H	L	+	2	0	HRCT1	35896583	0.000000	0.05858	0.107000	0.21349	0.466000	0.32739	-0.309000	0.08145	-0.078000	0.12730	-0.376000	0.06991	CTC	T|0.500;A|0.500	0.500	weak		0.667	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
DPP6	1804	hgsc.bcm.edu	37	7	154667628	154667628	+	Silent	SNP	A	A	G	rs2293353	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:154667628A>G	ENST00000377770.3	+	20	2037	c.1896A>G	c.(1894-1896)ccA>ccG	p.P632P	DPP6_ENST00000332007.3_Silent_p.P570P|DPP6_ENST00000404039.1_Silent_p.P568P|DPP6_ENST00000427557.1_Silent_p.P525P			P42658	DPP6_HUMAN	dipeptidyl-peptidase 6	632					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)			ATGGCACCCCAGGCAGCCAGA	0.652													G|||	2941	0.58726	0.7685	0.5937	5008	,	,		16280	0.5625		0.5219	False		,,,				2504	0.4305				p.P632P	NSCLC(125;1384 1783 2490 7422 34254)	Atlas-SNP	.											.	DPP6	383	.	0			c.A1896G						PASS	.	G	,,	3019,1113		1107,805,154	24.0	29.0	27.0		1350,1269,1269	-9.8	0.4	7	dbSNP_100	27	4329,4039		1118,2093,973	no	coding-synonymous,coding-synonymous,coding-synonymous	DPP6	NM_001039350.1,NM_001936.3,NM_130797.2	,,	2225,2898,1127	GG,GA,AA		48.2672,26.9361,41.216	,,	450/684,423/657,423/657	154667628	7348,5152	2066	4184	6250	SO:0001819	synonymous_variant	1804	exon20			CACCCCAGGCAGC	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.1896A>G	7.37:g.154667628A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	53	29	0.54717	NM_130797		Silent	SNP	ENST00000377770.3	37																																																																																				G|0.584;N|0.001	0.584	strong		0.652	DPP6-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322932.1	NM_130797	
RNF40	9810	hgsc.bcm.edu	37	16	30780861	30780861	+	Silent	SNP	C	C	T	rs142343572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30780861C>T	ENST00000324685.6	+	17	2961	c.2526C>T	c.(2524-2526)ctC>ctT	p.L842L	RNF40_ENST00000402121.3_Silent_p.L534L|RNF40_ENST00000357890.5_Silent_p.L742L|RNF40_ENST00000567365.1_3'UTR|RNF40_ENST00000563683.1_Silent_p.L802L	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	842					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			AGGGCAGCCTCGGGGGTGTGG	0.647													c|||	2	0.000399361	0.0	0.0014	5008	,	,		19891	0.0		0.001	False		,,,				2504	0.0				p.L842L		Atlas-SNP	.											.	RNF40	83	.	0			c.C2526T						PASS	.		,,	2,4392	4.2+/-10.8	0,2,2195	28.0	26.0	27.0		2526,2226,2526	-12.1	0.0	16	dbSNP_134	27	7,8591	4.3+/-15.6	0,7,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	RNF40	NM_001207033.1,NM_001207034.1,NM_014771.3	,,	0,9,6487	TT,TC,CC		0.0814,0.0455,0.0693	,,	842/1001,742/902,842/1002	30780861	9,12983	2197	4299	6496	SO:0001819	synonymous_variant	9810	exon17			CAGCCTCGGGGGT	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"""RING-type (C3HC4) zinc fingers"""	16867	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"""	607700	"""ring finger protein 40"""			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.2526C>T	16.37:g.30780861C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Silent	SNP	ENST00000324685.6	37	CCDS10691.1																																																																																			C|0.997;T|0.003	0.003	strong		0.647	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771	
OBSCN	84033	hgsc.bcm.edu	37	1	228412228	228412228	+	Missense_Mutation	SNP	G	G	A	rs386640006|rs1757153	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228412228G>A	ENST00000422127.1	+	9	2766	c.2722G>A	c.(2722-2724)Gcc>Acc	p.A908T	OBSCN_ENST00000570156.2_Missense_Mutation_p.A1000T|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A908T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	908	Ig-like 9.		A -> T (in dbSNP:rs1757153).		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)				AGGAGCCAGTGCCACACTGAG	0.617													G|||	1423	0.284145	0.3351	0.3559	5008	,	,		17550	0.1756		0.3618	False		,,,				2504	0.1963				p.A1000T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2998A						PASS	.						42.0	44.0	43.0					1																	228412228		2108	4221	6329	SO:0001583	missense	84033	exon10			GCCAGTGCCACAC	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.2722G>A	1.37:g.228412228G>A	ENSP00000409493:p.Ala908Thr	Somatic	202	1	0.00495049		WXS	Illumina HiSeq	Phase_I	202	101	0.5	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	562	0.2573260073260073	124	0.25203252032520324	120	0.3314917127071823	90	0.15734265734265734	228	0.3007915567282322	.	12.46	1.944173	0.34283	.	.	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.05996	3.36;3.36	4.42	3.5	0.40072	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.187584	0.32753	N	0.005681	T	0.00012	0.0000	M	0.83384	2.64	0.09310	P	1.0	B;D	0.56968	0.437;0.978	B;P	0.52309	0.326;0.695	T	0.50775	-0.8788	9	0.30078	T	0.28	.	12.898	0.58109	0.0795:0.0:0.9205:0.0	rs1757153;rs1757153	908;908	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	T	908	ENSP00000284548:A908T;ENSP00000409493:A908T	ENSP00000284548:A908T	A	+	1	0	OBSCN	226478851	0.998000	0.40836	0.906000	0.35671	0.036000	0.12997	2.707000	0.47143	1.211000	0.43351	0.655000	0.94253	GCC	G|0.756;A|0.244	0.244	strong		0.617	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
UVSSA	57654	hgsc.bcm.edu	37	4	1377615	1377615	+	Silent	SNP	A	A	G	rs9996817	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1377615A>G	ENST00000389851.4	+	13	2370	c.1923A>G	c.(1921-1923)tcA>tcG	p.S641S	UVSSA_ENST00000507531.1_Silent_p.S641S|UVSSA_ENST00000511563.1_Silent_p.S192S|UVSSA_ENST00000512728.1_Silent_p.S192S|UVSSA_ENST00000511216.1_Silent_p.S641S	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	641					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										ATCTCGGCTCATCCAGGTACA	0.582													G|||	3592	0.717252	0.7163	0.7939	5008	,	,		13376	0.7113		0.7058	False		,,,				2504	0.682				p.S641S		Atlas-SNP	.											KIAA1530,NS,carcinoma,0,1	.	.	1	0			c.A1923G						PASS	.	G		3172,1234	420.8+/-339.2	1164,844,195	103.0	91.0	95.0		1923	-10.1	0.0	4	dbSNP_119	95	6199,2401	396.1+/-345.3	2233,1733,334	no	coding-synonymous	KIAA1530	NM_020894.2		3397,2577,529	GG,GA,AA		27.9186,28.0073,27.9486		641/710	1377615	9371,3635	2203	4300	6503	SO:0001819	synonymous_variant	57654	exon13			CGGCTCATCCAGG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1923A>G	4.37:g.1377615A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	49	21	0.428571	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			A|0.277;G|0.723	0.723	strong		0.582	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
KIAA1429	25962	hgsc.bcm.edu	37	8	95538468	95538468	+	Silent	SNP	T	T	C	rs2890827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95538468T>C	ENST00000297591.5	-	8	2079	c.2004A>G	c.(2002-2004)ccA>ccG	p.P668P	KIAA1429_ENST00000421249.2_Silent_p.P668P|KIAA1429_ENST00000437199.1_Silent_p.P668P	NM_015496.4	NP_056311.2	Q69YN4	VIR_HUMAN	KIAA1429	668					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(16)|lung(28)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	66	Breast(36;3.29e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00185)			GAACAGGGTATGGATCATCCC	0.383													C|||	1856	0.370607	0.4637	0.3156	5008	,	,		21115	0.3194		0.2545	False		,,,				2504	0.456				p.P668P		Atlas-SNP	.											.	KIAA1429	176	.	0			c.A2004G						PASS	.	C	,	1873,2533	630.9+/-395.5	429,1015,759	87.0	76.0	80.0		2004,2004	-1.3	1.0	8	dbSNP_101	80	2625,5975	687.0+/-404.2	380,1865,2055	no	coding-synonymous,coding-synonymous	KIAA1429	NM_015496.4,NM_183009.2	,	809,2880,2814	CC,CT,TT		30.5233,42.5102,34.584	,	668/1813,668/1148	95538468	4498,8508	2203	4300	6503	SO:0001819	synonymous_variant	25962	exon8			AGGGTATGGATCA	AB037850	CCDS34923.1, CCDS47894.1	8q22.1	2008-11-25			ENSG00000164944	ENSG00000164944			24500	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 121"""					10718198	Standard	NM_015496		Approved	DKFZP434I116, fSAP121	uc003ygo.2	Q69YN4	OTTHUMG00000164426	ENST00000297591.5:c.2004A>G	8.37:g.95538468T>C		Somatic	255	1	0.00392157		WXS	Illumina HiSeq	Phase_I	195	99	0.507692	NM_015496	Q2M1N0|Q6AHX9|Q6NT78|Q7Z6C7|Q8IXH4|Q9BTH4|Q9H9C9|Q9NWR3|Q9P2B8|Q9UFW1	Silent	SNP	ENST00000297591.5	37	CCDS34923.1																																																																																			T|0.651;C|0.349	0.349	strong		0.383	KIAA1429-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378720.2	NM_015496	
AMACR	23600	hgsc.bcm.edu	37	5	34008100	34008100	+	Missense_Mutation	SNP	C	C	T	rs3195676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:34008100C>T	ENST00000335606.6	-	1	113	c.25G>A	c.(25-27)Gtg>Atg	p.V9M	AMACR_ENST00000382085.3_Missense_Mutation_p.V9M|AMACR_ENST00000382068.3_Missense_Mutation_p.V9M|AMACR_ENST00000382072.2_Missense_Mutation_p.V9M|AMACR_ENST00000441713.2_Missense_Mutation_p.V9M|RP11-1084J3.4_ENST00000382079.3_Intron|AMACR_ENST00000512079.1_Missense_Mutation_p.V9M|AMACR_ENST00000514195.1_5'UTR|AMACR_ENST00000426255.2_Missense_Mutation_p.V9M|AMACR_ENST00000502637.1_Missense_Mutation_p.V9M	NM_001167595.1|NM_014324.5	NP_001161067.1|NP_055139.4	Q9UHK6	AMACR_HUMAN	alpha-methylacyl-CoA racemase	9			V -> M (in dbSNP:rs3195676). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.5, ECO:0000269|Ref.6, ECO:0000269|Ref.9}.		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	alpha-methylacyl-CoA racemase activity (GO:0008111)|receptor binding (GO:0005102)			endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	19						GACAGCTCCACGACCGAGATG	0.692													C|||	1437	0.286941	0.1415	0.4078	5008	,	,		13433	0.3542		0.505	False		,,,				2504	0.1043				p.V9M		Atlas-SNP	.											AMACR,NS,carcinoma,0,3	AMACR	38	3	0			c.G25A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	920,3464		111,698,1383	22.0	23.0	23.0		25,25,25	-9.4	0.0	5	dbSNP_105	23	4492,4084		1195,2102,991	yes	missense,missense,missense	AMACR	NM_001167595.1,NM_014324.5,NM_203382.2	21,21,21	1306,2800,2374	TT,TC,CC		47.6213,20.9854,41.7593	benign,benign,benign	9/395,9/383,9/199	34008100	5412,7548	2192	4288	6480	SO:0001583	missense	23600	exon1			GCTCCACGACCGA	AF047020	CCDS3902.1, CCDS3903.1, CCDS54836.1	5p13.2	2012-05-16			ENSG00000242110	ENSG00000242110	5.1.99.4		451	protein-coding gene	gene with protein product		604489				9307041	Standard	NM_014324		Approved	RACE	uc003jij.3	Q9UHK6	OTTHUMG00000090734	ENST00000335606.6:c.25G>A	5.37:g.34008100C>T	ENSP00000334424:p.Val9Met	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	107	60	0.560748	NM_014324	A5YM47|B8Y916|B8Y918|F8W9N1|O43673|Q3KT79|Q96GH1|Q9Y3Q1	Missense_Mutation	SNP	ENST00000335606.6	37	CCDS3902.1	833	0.3814102564102564	75	0.1524390243902439	164	0.4530386740331492	203	0.3548951048951049	391	0.5158311345646438	C	17.23	3.337535	0.60963	0.209854	0.523787	ENSG00000242110	ENST00000335606;ENST00000382072;ENST00000382085;ENST00000502637;ENST00000441713	T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32	4.72	-9.44	0.00603	CoA-transferase family III domain (2);	0.597947	0.17508	N	0.171723	T	0.00012	0.0000	M	0.93062	3.375	0.09310	P	0.999999999608215	P;B;B;P;B	0.46987	0.888;0.24;0.155;0.858;0.155	B;B;B;P;B	0.48488	0.301;0.092;0.026;0.579;0.026	T	0.48570	-0.9024	9	0.62326	D	0.03	-4.4361	14.2962	0.66316	0.4513:0.0933:0.4554:0.0	rs3195676;rs17850511;rs3195676	9;9;9;9;9	Q6VRU4;F8W9N1;D6RB81;Q9UHK6-4;Q9UHK6	.;.;.;.;AMACR_HUMAN	M	9	ENSP00000334424:V9M;ENSP00000371504:V9M;ENSP00000371517:V9M;ENSP00000424351:V9M;ENSP00000403800:V9M	ENSP00000334424:V9M	V	-	1	0	AMACR	34043857	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.233000	0.02934	-3.351000	0.00181	-1.104000	0.02111	GTG	C|0.609;T|0.391	0.391	strong		0.692	AMACR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207467.1	NM_014324	
APOBEC3G	60489	hgsc.bcm.edu	37	22	39482557	39482557	+	Missense_Mutation	SNP	A	A	G	rs139265278		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39482557A>G	ENST00000407997.3	+	6	1366	c.1009A>G	c.(1009-1011)Ata>Gta	p.I337V	APOBEC3G_ENST00000452957.2_Missense_Mutation_p.I337V	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	337					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					CAAAATTTCAATAATGACATA	0.572																																					p.I337V		Atlas-SNP	.											.	APOBEC3G	69	.	0			c.A1009G						PASS	.		VAL/ILE	0,4406		0,0,2203	85.0	95.0	91.0		1009	1.5	0.0	22	dbSNP_134	91	2,8598		0,2,4298	no	missense	APOBEC3G	NM_021822.3	29	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	benign	337/385	39482557	2,13004	2203	4300	6503	SO:0001583	missense	60489	exon6			ATTTCAATAATGA	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"""Apolipoprotein B mRNA editing enzymes"""	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.1009A>G	22.37:g.39482557A>G	ENSP00000385057:p.Ile337Val	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	72	37	0.513889	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Missense_Mutation	SNP	ENST00000407997.3	37	CCDS13984.1	.	.	.	.	.	.	.	.	.	.	.	3.799	-0.042054	0.07452	0.0	2.33E-4	ENSG00000239713	ENST00000452957;ENST00000407997	T;T	0.64438	-0.1;-0.1	1.51	1.51	0.23008	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.43765	0.1262	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.19778	-1.0295	9	0.18276	T	0.48	.	3.2677	0.06870	0.7742:0.0:0.2258:0.0	.	337	Q9HC16	ABC3G_HUMAN	V	337	ENSP00000413376:I337V;ENSP00000385057:I337V	ENSP00000385057:I337V	I	+	1	0	APOBEC3G	37812503	0.070000	0.21116	0.024000	0.17045	0.002000	0.02628	0.249000	0.18216	0.946000	0.37632	0.373000	0.22412	ATA	A|1.000;G|0.000	0.000	weak		0.572	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204396830	204396830	+	Silent	SNP	G	G	A	rs17334387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204396830G>A	ENST00000367187.3	-	32	5089	c.4533C>T	c.(4531-4533)tcC>tcT	p.S1511S	PIK3C2B_ENST00000424712.2_Silent_p.S1483S|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1511					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGTAGGAGATGGACAGCTTCA	0.488													G|||	688	0.13738	0.2776	0.1023	5008	,	,		19457	0.0774		0.1113	False		,,,				2504	0.0613				p.S1511S		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.C4533T						PASS	.	G		1131,3275	405.1+/-333.4	142,847,1214	197.0	189.0	191.0		4533	2.2	1.0	1	dbSNP_123	191	741,7859	178.0+/-227.5	28,685,3587	no	coding-synonymous	PIK3C2B	NM_002646.3		170,1532,4801	AA,AG,GG		8.6163,25.6695,14.3934		1511/1635	204396830	1872,11134	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon32			GGAGATGGACAGC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.4533C>T	1.37:g.204396830G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	108	43	0.398148	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			G|0.857;A|0.143	0.143	strong		0.488	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
ZNF469	84627	hgsc.bcm.edu	37	16	88504204	88504204	+	Missense_Mutation	SNP	G	G	C	rs56236932	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88504204G>C	ENST00000437464.1	+	2	10242	c.10242G>C	c.(10240-10242)agG>agC	p.R3414S	ZNF469_ENST00000565624.1_Missense_Mutation_p.R3442S	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	3414					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						AGCACCTCAGGGGGGGGCGGC	0.667													G|||	20	0.00399361	0.0008	0.0058	5008	,	,		13737	0.0		0.0139	False		,,,				2504	0.001				p.R3414S		Atlas-SNP	.											ZNF469,NS,carcinoma,+1,1	ZNF469	121	1	0			c.G10242C						PASS	.	G	SER/ARG	3,1349		0,3,673	4.0	5.0	5.0		10242	-1.3	0.0	16	dbSNP_129	5	38,3064		0,38,1513	yes	missense	ZNF469	NM_001127464.1	110	0,41,2186	CC,CG,GG		1.225,0.2219,0.9205	possibly-damaging	3414/3926	88504204	41,4413	676	1551	2227	SO:0001583	missense	84627	exon2			CCTCAGGGGGGGG	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.10242G>C	16.37:g.88504204G>C	ENSP00000402343:p.Arg3414Ser	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	17	9	0.529412	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	10.54	1.378878	0.24944	0.002219	0.01225	ENSG00000225614	ENST00000437464	T	0.06218	3.33	5.14	-1.31	0.09230	Zinc finger, C2H2 (1);	.	.	.	.	T	0.01835	0.0058	N	0.24115	0.695	0.09310	N	1	B	0.30824	0.296	B	0.26202	0.067	T	0.41142	-0.9525	9	0.06365	T	0.9	.	1.7855	0.03040	0.2306:0.1127:0.4274:0.2292	rs56236932	3414	Q96JG9	ZN469_HUMAN	S	3414	ENSP00000402343:R3414S	ENSP00000402343:R3414S	R	+	3	2	ZNF469	87031705	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	-1.172000	0.03112	-0.065000	0.13021	0.561000	0.74099	AGG	G|0.994;C|0.006	0.006	strong		0.667	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
HLA-B	3106	hgsc.bcm.edu	37	6	31324711	31324711	+	Missense_Mutation	SNP	A	A	G	rs2596492	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31324711A>G	ENST00000412585.2	-	2	125	c.97T>C	c.(97-99)Tac>Cac	p.Y33H		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	33	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						ACGGAGGTGTAGAAATACCTC	0.711									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	793	0.158347	0.1241	0.1715	5008	,	,		10426	0.1647		0.169	False		,,,				2504	0.1779				p.Y33H		Atlas-SNP	.											.	HLA-B	54	.	0			c.T97C						PASS	.	A	HIS/TYR	302,3802		32,238,1782	12.0	10.0	11.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	97	-6.4	0.0	6	dbSNP_100	11	991,6975		103,785,3095	no	missense	HLA-B	NM_005514.6	83	135,1023,4877	GG,GA,AA		12.4404,7.3587,10.7125		33/363	31324711	1293,10777	2052	3983	6035	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	AGGTGTAGAAATA	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.97T>C	6.37:g.31324711A>G	ENSP00000399168:p.Tyr33His	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	356	0.163003663003663	65	0.13211382113821138	63	0.17403314917127072	110	0.19230769230769232	118	0.15567282321899736	N	0.001	-3.597536	0.00008	0.073587	0.124404	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00012	9.29;9.29	3.2	-6.41	0.01938	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	10.456400	0.00597	N	0.000371	T	0.00012	0.0000	L	0.28694	0.88	0.80722	P	0.0	B;B;B	0.09022	0.002;0.001;0.001	B;B;B	0.21151	0.017;0.007;0.033	T	0.59568	-0.7430	9	0.37606	T	0.19	.	2.3203	0.04208	0.4518:0.2122:0.201:0.135	rs2596492;rs3175989;rs3177897;rs9266188;rs9266189	33;33;8	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	H	33;44	ENSP00000399168:Y33H;ENSP00000405931:Y44H	ENSP00000399168:Y33H	Y	-	1	0	HLA-B	31432690	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-8.495000	0.00020	-7.871000	0.00000	-3.831000	0.00019	TAC	G|0.148;C|0.008;A|0.845	0.148	strong		0.711	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
PDZRN4	29951	hgsc.bcm.edu	37	12	41966306	41966306	+	Silent	SNP	G	G	A	rs12298745	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:41966306G>A	ENST00000402685.2	+	10	1733	c.1725G>A	c.(1723-1725)gaG>gaA	p.E575E	PDZRN4_ENST00000539469.2_Silent_p.E317E|PDZRN4_ENST00000298919.7_Silent_p.E315E	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	575							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ATGCAGCCGAGGACCCCAATA	0.498													G|||	892	0.178115	0.1415	0.1268	5008	,	,		20179	0.1855		0.1372	False		,,,				2504	0.2986				p.E575E		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G1725A						PASS	.	G	,	602,3804	264.1+/-265.8	47,508,1648	97.0	86.0	90.0		1725,951	3.1	1.0	12	dbSNP_120	90	1161,7439	237.9+/-269.6	73,1015,3212	no	coding-synonymous,coding-synonymous	PDZRN4	NM_001164595.1,NM_013377.3	,	120,1523,4860	AA,AG,GG		13.5,13.6632,13.5553	,	575/1037,317/779	41966306	1763,11243	2203	4300	6503	SO:0001819	synonymous_variant	29951	exon10			AGCCGAGGACCCC	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1725G>A	12.37:g.41966306G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	156	154	0.987179	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																			G|0.858;A|0.142	0.142	strong		0.498	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
DCDC2	51473	hgsc.bcm.edu	37	6	24205236	24205236	+	Silent	SNP	G	G	A	rs9467075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:24205236G>A	ENST00000378454.3	-	8	1318	c.1017C>T	c.(1015-1017)gtC>gtT	p.V339V	DCDC2_ENST00000378450.3_Silent_p.V92V	NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	339					cellular defense response (GO:0006968)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|neuron migration (GO:0001764)|visual learning (GO:0008542)					breast(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32		Ovarian(999;0.101)				TTACCTGATCGACTGGAACCT	0.398													G|||	583	0.116414	0.1218	0.1182	5008	,	,		19059	0.0417		0.1451	False		,,,				2504	0.1554				p.V339V		Atlas-SNP	.											.	DCDC2	53	.	0			c.C1017T						PASS	.	G	,	632,3774	275.2+/-272.4	41,550,1612	238.0	220.0	226.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1017,1017	-12.1	0.0	6	dbSNP_119	226	1276,7322	253.2+/-279.0	99,1078,3122	no	coding-synonymous,coding-synonymous	DCDC2	NM_001195610.1,NM_016356.3	,	140,1628,4734	AA,AG,GG		14.8407,14.3441,14.6724	,	339/477,339/477	24205236	1908,11096	2203	4299	6502	SO:0001819	synonymous_variant	51473	exon9			CTGATCGACTGGA	AB032980	CCDS4550.1	6p22.1	2008-02-05			ENSG00000146038	ENSG00000146038			18141	protein-coding gene	gene with protein product		605755				10601354, 10574461	Standard	NM_001195610		Approved	RU2, KIAA1154, DCDC2A	uc003ndx.3	Q9UHG0	OTTHUMG00000016275	ENST00000378454.3:c.1017C>T	6.37:g.24205236G>A		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	187	88	0.470588	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Silent	SNP	ENST00000378454.3	37	CCDS4550.1																																																																																			G|0.867;A|0.133	0.133	strong		0.398	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356	
GPR144	347088	hgsc.bcm.edu	37	9	127231774	127231774	+	Missense_Mutation	SNP	C	C	G	rs1570580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:127231774C>G	ENST00000334810.1	+	16	2506	c.2506C>G	c.(2506-2508)Cgc>Ggc	p.R836G				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	836					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						CCGCCGTGCCCGCATGTTGAG	0.642													C|||	2965	0.592053	0.5787	0.6326	5008	,	,		17817	0.7629		0.4245	False		,,,				2504	0.5777				p.R836G		Atlas-SNP	.											.	GPR144	33	.	0			c.C2506G						PASS	.	C	GLY/ARG	704,680		176,352,164	29.0	36.0	34.0		2506	1.2	1.0	9	dbSNP_88	34	1401,1781		311,779,501	yes	missense	GPR144	NM_001161808.1	125	487,1131,665	GG,GC,CC		44.0289,49.1329,46.1016	probably-damaging	836/964	127231774	2105,2461	692	1591	2283	SO:0001583	missense	347088	exon16			CGTGCCCGCATGT	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.2506C>G	9.37:g.127231774C>G	ENSP00000335156:p.Arg836Gly	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	134	134	1	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1273	0.5828754578754579	274	0.556910569105691	217	0.5994475138121547	453	0.791958041958042	329	0.4340369393139842	C	17.23	3.336372	0.60963	0.508671	0.440289	ENSG00000180264	ENST00000334810	T	0.52983	0.64	4.46	1.17	0.20885	GPCR, family 2-like (1);	.	.	.	.	T	0.00012	0.0000	L	0.39326	1.205	0.42109	P	0.008624999999999994	D	0.60575	0.988	P	0.61722	0.893	T	0.33137	-0.9880	8	0.56958	D	0.05	.	3.8566	0.08978	0.366:0.4211:0.0:0.2129	rs1570580;rs57102571;rs1570580	836	Q7Z7M1	GP144_HUMAN	G	836	ENSP00000335156:R836G	ENSP00000335156:R836G	R	+	1	0	GPR144	126271595	0.973000	0.33851	0.994000	0.49952	0.800000	0.45204	4.077000	0.57598	0.330000	0.23485	0.462000	0.41574	CGC	C|0.408;G|0.592	0.592	strong		0.642	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
AKAP5	9495	hgsc.bcm.edu	37	14	64935411	64935411	+	Missense_Mutation	SNP	C	C	T	rs2230491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:64935411C>T	ENST00000394718.4	+	2	677	c.299C>T	c.(298-300)cCa>cTa	p.P100L	ZBTB25_ENST00000555220.1_Intron|AKAP5_ENST00000320636.5_Missense_Mutation_p.P100L|ZBTB25_ENST00000555424.1_Intron	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	100	AKAP.|Essential to the intracellular anchoring function. {ECO:0000250}.		P -> L (in dbSNP:rs2230491).		energy reserve metabolic process (GO:0006112)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|stomach(1)	13				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		CAGCAAAAGCCATTGGAGGGT	0.473													C|||	360	0.071885	0.003	0.0821	5008	,	,		21117	0.0		0.1412	False		,,,				2504	0.1605				p.P100L		Atlas-SNP	.											.	AKAP5	23	.	0			c.C299T						PASS	.	C	LEU/PRO	143,4261	90.6+/-129.3	4,135,2063	84.0	95.0	91.0		299	-2.5	0.0	14	dbSNP_98	91	1287,7313	250.8+/-277.5	92,1103,3105	yes	missense	AKAP5	NM_004857.3	98	96,1238,5168	TT,TC,CC		14.9651,3.247,10.9966	benign	100/428	64935411	1430,11574	2202	4300	6502	SO:0001583	missense	9495	exon2			AAAAGCCATTGGA	M90359	CCDS9764.1	14q23.3	2012-05-16			ENSG00000179841	ENSG00000179841		"""A-kinase anchor proteins"""	375	protein-coding gene	gene with protein product		604688				1512224, 1618839	Standard	NM_004857		Approved	AKAP75, AKAP79	uc001xhd.4	P24588	OTTHUMG00000029634	ENST00000394718.4:c.299C>T	14.37:g.64935411C>T	ENSP00000378207:p.Pro100Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_004857	A2RRB8	Missense_Mutation	SNP	ENST00000394718.4	37	CCDS9764.1	155	0.07097069597069597	2	0.0040650406504065045	41	0.1132596685082873	0	0.0	112	0.14775725593667546	C	0.946	-0.708037	0.03230	0.03247	0.149651	ENSG00000179841	ENST00000394718;ENST00000320636	T;T	0.52754	0.65;0.65	5.38	-2.52	0.06346	Protein kinase A anchoring, WSK motif (1);	1.130530	0.06569	N	0.748123	T	0.00144	0.0004	N	0.19112	0.55	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.11108	-1.0601	9	0.29301	T	0.29	-14.732	1.5965	0.02665	0.1189:0.3807:0.2314:0.269	rs2230491;rs52806136;rs61401357;rs2230491	100	P24588	AKAP5_HUMAN	L	100	ENSP00000378207:P100L;ENSP00000315615:P100L	ENSP00000315615:P100L	P	+	2	0	AKAP5	64005164	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.552000	0.06020	-0.485000	0.06754	-0.781000	0.03364	CCA	C|0.906;T|0.094	0.094	strong		0.473	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268070.3		
EXOC3L4	91828	hgsc.bcm.edu	37	14	103566904	103566904	+	Silent	SNP	G	G	A	rs1057640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:103566904G>A	ENST00000380069.3	+	1	424	c.348G>A	c.(346-348)caG>caA	p.Q116Q	RP11-736N17.8_ENST00000559843.1_RNA	NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	116					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						GTGTCAGCCAGCAGGCATCCA	0.612													G|||	1017	0.203075	0.0787	0.3055	5008	,	,		17369	0.3433		0.1531	False		,,,				2504	0.2055				p.Q116Q		Atlas-SNP	.											.	EXOC3L4	35	.	0			c.G348A						PASS	.	G		364,4042	176.6+/-205.7	18,328,1857	23.0	23.0	23.0		348	3.1	0.0	14	dbSNP_86	23	1304,7296	237.5+/-269.3	122,1060,3118	no	coding-synonymous	EXOC3L4	NM_001077594.1		140,1388,4975	AA,AG,GG		15.1628,8.2615,12.8249		116/723	103566904	1668,11338	2203	4300	6503	SO:0001819	synonymous_variant	91828	exon1			CAGCCAGCAGGCA	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 73"""	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.348G>A	14.37:g.103566904G>A		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	178	91	0.511236	NM_001077594	Q14CR2	Silent	SNP	ENST00000380069.3	37	CCDS32163.1																																																																																			G|0.830;A|0.170	0.170	strong		0.612	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093	
CCDC154	645811	hgsc.bcm.edu	37	16	1488141	1488141	+	Silent	SNP	C	C	T	rs12925639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1488141C>T	ENST00000389176.3	-	10	1255	c.1089G>A	c.(1087-1089)ggG>ggA	p.G363G	CCDC154_ENST00000409671.1_Silent_p.G209G	NM_001143980.1	NP_001137452.1	A6NI56	CC154_HUMAN	coiled-coil domain containing 154	363						endosome (GO:0005768)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)	5						CGGCCAGCTCCCCAGCCCGGC	0.682													C|||	1214	0.242412	0.3646	0.232	5008	,	,		15426	0.1141		0.1998	False		,,,				2504	0.2607				p.G354G		Atlas-SNP	.											.	CCDC154	27	.	0			c.G1062A						PASS	.	C		480,904		85,310,297	30.0	32.0	31.0		1062	2.7	0.5	16	dbSNP_121	31	594,2584		51,492,1046	no	coding-synonymous	CCDC154	NM_001143980.1		136,802,1343	TT,TC,CC		18.691,34.6821,23.5423		354/668	1488141	1074,3488	692	1589	2281	SO:0001819	synonymous_variant	645811	exon10			CAGCTCCCCAGCC			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.1089G>A	16.37:g.1488141C>T		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_001143980	G9JV18	Silent	SNP	ENST00000389176.3	37																																																																																				C|0.791;T|0.209	0.209	strong		0.682	CCDC154-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001143980	
NUP93	9688	hgsc.bcm.edu	37	16	56873495	56873495	+	Silent	SNP	C	C	T	rs1138295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:56873495C>T	ENST00000308159.5	+	20	2320	c.2199C>T	c.(2197-2199)gcC>gcT	p.A733A	NUP93_ENST00000569842.1_Silent_p.A733A|NUP93_ENST00000542526.1_Silent_p.A610A|NUP93_ENST00000564887.1_Silent_p.A610A	NM_014669.4	NP_055484.3	Q8N1F7	NUP93_HUMAN	nucleoporin 93kDa	733					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|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 membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)			breast(2)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						GAGTGGCTGCCTTCAGAAATT	0.448													C|||	1055	0.210663	0.2126	0.2305	5008	,	,		17354	0.3075		0.1501	False		,,,				2504	0.1564				p.A733A	Colon(33;610 796 1305 1705 38917)	Atlas-SNP	.											.	NUP93	75	.	0			c.C2199T						PASS	.	C	,,	838,3558	310.0+/-291.3	85,668,1445	113.0	108.0	110.0		1830,1830,2199	5.9	1.0	16	dbSNP_86	110	1330,7270	235.6+/-268.1	107,1116,3077	no	coding-synonymous,coding-synonymous,coding-synonymous	NUP93	NM_001242795.1,NM_001242796.1,NM_014669.4	,,	192,1784,4522	TT,TC,CC		15.4651,19.0628,16.6821	,,	610/697,610/697,733/820	56873495	2168,10828	2198	4300	6498	SO:0001819	synonymous_variant	9688	exon20			GGCTGCCTTCAGA	D42085	CCDS10769.1, CCDS55996.1	16q13	2008-02-05			ENSG00000102900	ENSG00000102900			28958	protein-coding gene	gene with protein product		614351				9348540, 9531546	Standard	NM_014669		Approved	KIAA0095	uc002eka.3	Q8N1F7	OTTHUMG00000133278	ENST00000308159.5:c.2199C>T	16.37:g.56873495C>T		Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	239	129	0.539749	NM_014669	B3KPQ8|Q14705	Silent	SNP	ENST00000308159.5	37	CCDS10769.1																																																																																			C|0.811;T|0.189	0.189	strong		0.448	NUP93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257058.4	NM_014669	
OR2T4	127074	hgsc.bcm.edu	37	1	248525071	248525071	+	Silent	SNP	T	T	C	rs28499298	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248525071T>C	ENST00000366475.1	+	1	189	c.189T>C	c.(187-189)atT>atC	p.I63I		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	63						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTGTGGTCATTTTTGTGGTTT	0.483													t|||	1734	0.346246	0.3926	0.2896	5008	,	,		21339	0.4385		0.1948	False		,,,				2504	0.3845				p.I63I		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	0			c.T189C						scavenged	.						196.0	194.0	195.0					1																	248525071		2203	4300	6503	SO:0001819	synonymous_variant	127074	exon1			GGTCATTTTTGTG	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.189T>C	1.37:g.248525071T>C		Somatic	702	0	0		WXS	Illumina HiSeq	Phase_I	732	21	0.0286885	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			T|0.769;C|0.231	0.231	strong		0.483	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
ZNF717	100131827	hgsc.bcm.edu	37	3	75786753	75786753	+	Missense_Mutation	SNP	C	C	T	rs3009020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:75786753C>T	ENST00000478296.1	-	4	2147	c.1871G>A	c.(1870-1872)cGt>cAt	p.R624H	ZNF717_ENST00000400845.3_Missense_Mutation_p.R667H|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Missense_Mutation_p.R674H|MIR4273_ENST00000582824.1_RNA			Q9BY31	ZN717_HUMAN	zinc finger protein 717	664					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TACATCCATACGGTTTTTCCC	0.393													t|||	3377	0.674321	0.5204	0.7277	5008	,	,		6339	0.8254		0.7326	False		,,,				2504	0.6288				p.R674H		Atlas-SNP	.											.	ZNF717	160	.	0			c.G2021A						PASS	.						20.0	20.0	20.0					3																	75786753		627	1550	2177	SO:0001583	missense	100131827	exon5			TCCATACGGTTTT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.1871G>A	3.37:g.75786753C>T	ENSP00000419377:p.Arg624His	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	39	22	0.564103	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		.	.	.	.	.	.	.	.	.	.	.	5.123	0.208289	0.09757	.	.	ENSG00000227124	ENST00000478296;ENST00000422325;ENST00000400845	T;T;T	0.10477	2.87;2.87;2.87	1.57	-3.14	0.05250	.	.	.	.	.	T	0.04318	0.0119	N	0.04880	-0.145	0.58432	P	1.0000000000287557E-6	B	0.09022	0.002	B	0.01281	0.0	T	0.35025	-0.9805	8	0.59425	D	0.04	.	4.182	0.10380	0.4211:0.3586:0.2204:0.0	rs3009020;rs6549782;rs17028808;rs52813853;rs59232447	674	C9JSV9	.	H	624;674;667	ENSP00000419377:R624H;ENSP00000409514:R674H;ENSP00000383643:R667H	ENSP00000383643:R667H	R	-	2	0	ZNF717	75869443	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-3.497000	0.00451	-1.496000	0.01828	-1.335000	0.01260	CGT	.	.	weak		0.393	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
EYS	346007	hgsc.bcm.edu	37	6	65301408	65301408	+	Missense_Mutation	SNP	A	A	G	rs62415828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301408A>G	ENST00000370621.3	-	26	4878	c.4352T>C	c.(4351-4353)aTa>aCa	p.I1451T	EYS_ENST00000370616.2_Missense_Mutation_p.I1451T|EYS_ENST00000503581.1_Missense_Mutation_p.I1451T			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1451			I -> T (in dbSNP:rs62415828). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GGAGGCAGCTATAAGCAGGAA	0.448													G|||	471	0.0940495	0.0159	0.1182	5008	,	,		17077	0.1567		0.0984	False		,,,				2504	0.1135				p.I1451T		Atlas-SNP	.											.	EYS	527	.	0			c.T4352C						PASS	.	G	THR/ILE	49,1335		1,47,644	73.0	70.0	71.0		4352	0.5	0.0	6	dbSNP_129	71	447,2735		41,365,1185	yes	missense	EYS	NM_001142800.1	89	42,412,1829	GG,GA,AA		14.0478,3.5405,10.8629	benign	1451/3145	65301408	496,4070	692	1591	2283	SO:0001583	missense	346007	exon26			GCAGCTATAAGCA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4352T>C	6.37:g.65301408A>G	ENSP00000359655:p.Ile1451Thr	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		216	0.0989010989010989	7	0.014227642276422764	44	0.12154696132596685	86	0.15034965034965034	79	0.10422163588390501	G	0.006	-2.112469	0.00353	0.035405	0.140478	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84516	-1.86;-1.84;-1.84	5.74	0.462	0.16695	.	.	.	.	.	T	0.36771	0.0979	N	0.08118	0	0.53688	P	2.999999999997449E-5	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08659	-1.0711	8	0.02654	T	1	.	3.308	0.07007	0.1288:0.1081:0.4299:0.3332	rs62415828	1451;1451	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	T	1451	ENSP00000424243:I1451T;ENSP00000359655:I1451T;ENSP00000359650:I1451T	ENSP00000359650:I1451T	I	-	2	0	EYS	65358129	0.906000	0.30813	0.023000	0.16930	0.622000	0.37654	0.108000	0.15396	0.069000	0.16605	-0.186000	0.12905	ATA	A|0.900;G|0.100	0.100	strong		0.448	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
ABCC5	10057	hgsc.bcm.edu	37	3	183660585	183660585	+	Silent	SNP	G	G	A	rs3749442	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:183660585G>A	ENST00000334444.6	-	25	3864	c.3624C>T	c.(3622-3624)ctC>ctT	p.L1208L	ABCC5_ENST00000265586.6_Silent_p.L1165L	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1208	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	TCTTTAGGACGAGAGGGAGGT	0.507													G|||	1247	0.249002	0.1944	0.2709	5008	,	,		20136	0.4365		0.1769	False		,,,				2504	0.1881				p.L1208L		Atlas-SNP	.											.	ABCC5	142	.	0			c.C3624T						PASS	.	G		631,3227		49,533,1347	96.0	93.0	94.0		3624	3.4	1.0	3	dbSNP_107	94	1436,6808		136,1164,2822	no	coding-synonymous	ABCC5	NM_005688.2		185,1697,4169	AA,AG,GG		17.4187,16.3556,17.0798		1208/1438	183660585	2067,10035	1929	4122	6051	SO:0001819	synonymous_variant	10057	exon25			TAGGACGAGAGGG	AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.3624C>T	3.37:g.183660585G>A		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			G|0.765;A|0.235	0.235	strong		0.507	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
PCK1	5105	hgsc.bcm.edu	37	20	56137807	56137807	+	Silent	SNP	A	A	G	rs1042523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:56137807A>G	ENST00000319441.4	+	4	626	c.462A>G	c.(460-462)tcA>tcG	p.S154S	PCK1_ENST00000543666.1_Intron|PCK1_ENST00000535860.1_Silent_p.S22S	NM_002591.3	NP_002582.3	P35558	PCKGC_HUMAN	phosphoenolpyruvate carboxykinase 1 (soluble)	154					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)			CGCCTCTGTCAAAGATCGGCA	0.622													G|||	1569	0.313299	0.3222	0.3357	5008	,	,		17654	0.0308		0.5229	False		,,,				2504	0.3609				p.S154S		Atlas-SNP	.											.	PCK1	95	.	0			c.A462G						PASS	.	G		1506,2900	673.0+/-402.7	230,1046,927	67.0	55.0	59.0		462	-6.0	0.5	20	dbSNP_86	59	4342,4258	573.2+/-389.8	1084,2174,1042	no	coding-synonymous	PCK1	NM_002591.3		1314,3220,1969	GG,GA,AA		49.5116,34.1807,44.9639		154/623	56137807	5848,7158	2203	4300	6503	SO:0001819	synonymous_variant	5105	exon4			TCTGTCAAAGATC		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.462A>G	20.37:g.56137807A>G		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	92	92	1	NM_002591	A8K437|B4DT64|Q8TCA3|Q9UJD2	Silent	SNP	ENST00000319441.4	37	CCDS13460.1																																																																																			A|0.601;G|0.399	0.399	strong		0.622	PCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079851.2		
RANGAP1	5905	hgsc.bcm.edu	37	22	41652733	41652733	+	Silent	SNP	G	G	A	rs139509	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:41652733G>A	ENST00000455915.2	-	7	2339	c.870C>T	c.(868-870)ggC>ggT	p.G290G	RANGAP1_ENST00000407260.4_Silent_p.G235G|RANGAP1_ENST00000405486.1_Silent_p.G290G|RANGAP1_ENST00000356244.3_Silent_p.G290G			P46060	RAGP1_HUMAN	Ran GTPase activating protein 1	290					mitotic cell cycle (GO:0000278)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear pore (GO:0005643)|perinuclear region of cytoplasm (GO:0048471)	Ran GTPase activator activity (GO:0005098)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGGGCAGGCCGCCGCGGATGG	0.637													G|||	899	0.179513	0.2806	0.1455	5008	,	,		12396	0.004		0.2604	False		,,,				2504	0.1646				p.G290G		Atlas-SNP	.											.	RANGAP1	47	.	0			c.C870T						PASS	.	G		1108,3298	396.7+/-330.2	141,826,1236	55.0	54.0	54.0		870	-4.1	0.0	22	dbSNP_78	54	2349,6251	391.4+/-343.6	351,1647,2302	no	coding-synonymous	RANGAP1	NM_002883.2		492,2473,3538	AA,AG,GG		27.314,25.1475,26.58		290/588	41652733	3457,9549	2203	4300	6503	SO:0001819	synonymous_variant	5905	exon8			CAGGCCGCCGCGG	X82260	CCDS14012.1	22q13	2013-01-17			ENSG00000100401	ENSG00000100401			9854	protein-coding gene	gene with protein product		602362	"""segregation distorter homolog (Drosophila)"""	SD		7878053	Standard	NM_002883		Approved	Fug1, KIAA1835	uc003azu.3	P46060	OTTHUMG00000150940	ENST00000455915.2:c.870C>T	22.37:g.41652733G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_002883	Q96JJ2	Silent	SNP	ENST00000455915.2	37	CCDS14012.1	388	0.17765567765567766	127	0.258130081300813	58	0.16022099447513813	2	0.0034965034965034965	201	0.26517150395778366	G	6.216	0.408015	0.11754	0.251475	0.27314	ENSG00000100401	ENST00000446258	.	.	.	5.34	-4.13	0.03904	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999999	.	.	.	.	.	.	T	0.37454	-0.9705	3	.	.	.	-16.272	1.1057	0.01693	0.3154:0.1787:0.32:0.1859	rs139509;rs2229754;rs11557737;rs17364010;rs61130928;rs139509	.	.	.	W	186	.	.	R	-	1	2	RANGAP1	39982679	0.004000	0.15560	0.047000	0.18901	0.740000	0.42216	-1.072000	0.03434	-0.934000	0.03733	-2.646000	0.00150	CGG	G|0.769;A|0.231	0.231	strong		0.637	RANGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320606.1	NM_002883	
ACHE	43	hgsc.bcm.edu	37	7	100488658	100488658	+	Intron	SNP	G	G	C	rs1799806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100488658G>C	ENST00000412389.1	-	3	1879				ACHE_ENST00000302913.4_Missense_Mutation_p.P592R|ACHE_ENST00000411582.1_Missense_Mutation_p.P592R|UFSP1_ENST00000388761.2_5'Flank|ACHE_ENST00000241069.5_Intron|ACHE_ENST00000419336.2_Intron|ACHE_ENST00000428317.1_Intron			P22303	ACES_HUMAN	acetylcholinesterase (Yt blood group)						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)	gCCGGGCCTCGGAGCAGCCTC	0.697													G|||	1349	0.269369	0.174	0.2795	5008	,	,		13043	0.125		0.4533	False		,,,				2504	0.3507				p.P592R		Atlas-SNP	.											ACHE,NS,carcinoma,0,1	ACHE	80	1	0			c.C1775G						PASS	.	G	,ARG/PRO	771,3151		119,533,1309	6.0	5.0	5.0		,1775	1.9	1.0	7	dbSNP_89	5	3296,4702		821,1654,1524	yes	intron,missense	ACHE	NM_000665.3,NM_015831.2	,103	940,2187,2833	CC,CG,GG		41.2103,19.6583,34.1191	,benign	,592/618	100488658	4067,7853	1961	3999	5960	SO:0001627	intron_variant	43	exon5			GGCCTCGGAGCAG		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.1723+131C>G	7.37:g.100488658G>C		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	194	95	0.489691	NM_015831	A4D2E2|B7ZKZ0|D6W5X7|Q16169|Q29S23|Q2M324|Q504V3|Q53F46|Q86TM9|Q86YX9|Q9BXP7	Missense_Mutation	SNP	ENST00000412389.1	37	CCDS5709.1	613	0.2806776556776557	90	0.18292682926829268	114	0.3149171270718232	66	0.11538461538461539	343	0.4525065963060686	G	15.21	2.764618	0.49574	0.196583	0.412103	ENSG00000087085	ENST00000302913;ENST00000411582	T;T	0.64618	-0.11;-0.11	3.8	1.92	0.25849	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.42341	P	0.007662999999999975	B	0.06786	0.001	B	0.08055	0.003	T	0.43972	-0.9358	7	0.24483	T	0.36	.	5.4585	0.16604	0.115:0.2026:0.6824:0.0	rs1799806;rs17235003;rs17296925;rs17883536	592	P22303-2	.	R	592	ENSP00000303211:P592R;ENSP00000404865:P592R	ENSP00000303211:P592R	P	-	2	0	ACHE	100326594	0.995000	0.38212	0.996000	0.52242	0.965000	0.64279	0.337000	0.19841	0.367000	0.24454	0.448000	0.29417	CCG	G|0.724;C|0.276	0.276	strong		0.697	ACHE-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347201.1	NM_015831	
CNTN2	6900	hgsc.bcm.edu	37	1	205031116	205031116	+	Missense_Mutation	SNP	C	C	T	rs2229866	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:205031116C>T	ENST00000331830.4	+	9	1381	c.1097C>T	c.(1096-1098)cCt>cTt	p.P366L	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	366	Ig-like C2-type 4.		P -> L (in dbSNP:rs2229866).		adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AACGGGGAGCCTCTGGCCTCC	0.652											OREG0014144	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2760	0.551118	0.323	0.5591	5008	,	,		15503	0.876		0.339	False		,,,				2504	0.7372				p.P366L	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C1097T						PASS	.	C	LEU/PRO	1480,2924		251,978,973	16.0	18.0	17.0		1097	4.9	1.0	1	dbSNP_98	17	2953,5641		552,1849,1896	yes	missense	CNTN2	NM_005076.3	98	803,2827,2869	TT,TC,CC		34.3612,33.6058,34.1052	benign	366/1041	205031116	4433,8565	2202	4297	6499	SO:0001583	missense	6900	exon9			GGGAGCCTCTGGC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1097C>T	1.37:g.205031116C>T	ENSP00000330633:p.Pro366Leu	Somatic	47	0	0	2149	WXS	Illumina HiSeq	Phase_I	77	48	0.623377	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	1085	0.4967948717948718	153	0.31097560975609756	182	0.5027624309392266	498	0.8706293706293706	252	0.3324538258575198	C	20.8	4.055142	0.75960	0.336058	0.343612	ENSG00000184144	ENST00000331830	T	0.68025	-0.3	4.94	4.94	0.65067	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000078	T	0.00012	0.0000	M	0.66560	2.04	0.09310	P	0.999999999241044	B;B	0.18610	0.029;0.013	B;B	0.18871	0.023;0.014	T	0.40289	-0.9571	9	0.62326	D	0.03	.	17.7437	0.88414	0.0:1.0:0.0:0.0	rs2229866;rs4951164	366;366	A1L3A3;Q02246	.;CNTN2_HUMAN	L	366	ENSP00000330633:P366L	ENSP00000330633:P366L	P	+	2	0	CNTN2	203297739	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	4.643000	0.61390	2.284000	0.76573	0.557000	0.71058	CCT	C|0.586;T|0.414	0.414	strong		0.652	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
PRKCQ	5588	hgsc.bcm.edu	37	10	6472891	6472891	+	Silent	SNP	G	G	T	rs11258747	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:6472891G>T	ENST00000263125.5	-	17	1945	c.1846C>A	c.(1846-1848)Cga>Aga	p.R616R	PRKCQ_ENST00000397176.2_Silent_p.R553R|PRKCQ_ENST00000539722.1_Silent_p.R491R	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	616	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			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)	TCAGGTTCTCGCACGAAGAGC	0.587													G|||	614	0.122604	0.1271	0.1124	5008	,	,		19945	0.0308		0.2187	False		,,,				2504	0.1196				p.R616R	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.C1846A						PASS	.	G	,	624,3782	270.1+/-269.4	44,536,1623	62.0	54.0	57.0	http://www.ncbi.nlm.nih.gov/pubmed?term	1657,1846	1.6	1.0	10	dbSNP_120	57	1908,6692	337.4+/-322.3	204,1500,2596	yes	coding-synonymous,coding-synonymous	PRKCQ	NM_001242413.1,NM_006257.3	,	248,2036,4219	TT,TG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	22.186,14.1625,19.4679	,	553/644,616/707	6472891	2532,10474	2203	4300	6503	SO:0001819	synonymous_variant	5588	exon17			GTTCTCGCACGAA	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.1846C>A	10.37:g.6472891G>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	26	8	0.307692	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1	287	0.13141025641025642	56	0.11382113821138211	45	0.12430939226519337	18	0.03146853146853147	168	0.22163588390501318	G	8.847	0.943677	0.18281	0.141625	0.22186	ENSG00000065675	ENST00000397178	.	.	.	5.23	1.63	0.23807	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4448	0.27205	0.1186:0.0:0.3386:0.5427	rs11258747;rs11258747	.	.	.	X	388	.	.	C	-	3	2	PRKCQ	6512897	1.000000	0.71417	0.975000	0.42487	0.846000	0.48090	1.036000	0.30228	0.027000	0.15297	0.650000	0.86243	TGC	G|0.847;T|0.153	0.153	strong		0.587	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
ITGA3	3675	hgsc.bcm.edu	37	17	48151296	48151296	+	Silent	SNP	T	T	C	rs117783166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48151296T>C	ENST00000320031.8	+	8	1503	c.1173T>C	c.(1171-1173)gcT>gcC	p.A391A	ITGA3_ENST00000007722.7_Silent_p.A391A|ITGA3_ENST00000544892.1_Silent_p.A166A	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	391					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						CTGTGGGAGCTCCGTTTGAAG	0.557													T|||	10	0.00199681	0.0	0.0014	5008	,	,		17926	0.0		0.0089	False		,,,				2504	0.0				p.A391A		Atlas-SNP	.											.	ITGA3	128	.	0			c.T1173C						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	120.0	115.0	117.0		1173,1173	-3.8	0.9	17	dbSNP_133	117	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous,coding-synonymous	ITGA3	NM_002204.2,NM_005501.2	,	0,45,6458	CC,CT,TT		0.5116,0.0227,0.346	,	391/1052,391/1067	48151296	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	3675	exon8			GGGAGCTCCGTTT	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.1173T>C	17.37:g.48151296T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	62	20	0.322581	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	37	CCDS11558.1																																																																																			T|0.997;C|0.003	0.003	strong		0.557	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
DSC1	1823	hgsc.bcm.edu	37	18	28722133	28722133	+	Silent	SNP	T	T	C	rs36081634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:28722133T>C	ENST00000257198.5	-	9	1350	c.1089A>G	c.(1087-1089)gtA>gtG	p.V363V	DSC1_ENST00000257197.3_Silent_p.V363V|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	363	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			TGTTTTCTTCTACTTCTGTAA	0.323													T|||	94	0.01877	0.0023	0.0216	5008	,	,		17187	0.0		0.0288	False		,,,				2504	0.0481				p.V363V		Atlas-SNP	.											.	DSC1	240	.	0			c.A1089G						PASS	.	T	,	50,4356	50.2+/-85.5	1,48,2154	129.0	119.0	122.0		1089,1089	1.9	1.0	18	dbSNP_126	122	395,8205	126.8+/-185.2	5,385,3910	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	6,433,6064	CC,CT,TT		4.593,1.1348,3.4215	,	363/841,363/895	28722133	445,12561	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon9			TTCTTCTACTTCT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1089A>G	18.37:g.28722133T>C		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	136	60	0.441176	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			T|0.970;C|0.030	0.030	strong		0.323	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
RFPL3	10738	hgsc.bcm.edu	37	22	32754103	32754103	+	Missense_Mutation	SNP	A	A	C	rs58637580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:32754103A>C	ENST00000249007.4	+	1	250	c.45A>C	c.(43-45)caA>caC	p.Q15H	RFPL3_ENST00000397468.1_Intron|RFPL3_ENST00000382088.3_5'Flank|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	15							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TTTCACCTCAAGGAAATTTTC	0.463													N|||	724	0.144569	0.0265	0.0893	5008	,	,		20055	0.4583		0.0408	False		,,,				2504	0.1268				p.Q15H		Atlas-SNP	.											.	RFPL3	91	.	0			c.A45C						PASS	.	C	HIS/GLN,	138,4268	779.0+/-414.3	8,122,2073	114.0	113.0	113.0		45,	-1.3	0.0	22	dbSNP_129	113	418,8180	790.4+/-407.6	12,394,3893	no	missense,intron	RFPL3	NM_001098535.1,NM_006604.2	24,	20,516,5966	CC,CA,AA		4.8616,3.1321,4.2756	,	15/318,	32754103	556,12448	2203	4299	6502	SO:0001583	missense	10738	exon1			ACCTCAAGGAAAT	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.45A>C	22.37:g.32754103A>C	ENSP00000249007:p.Gln15His	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	237	126	0.531646	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Missense_Mutation	SNP	ENST00000249007.4	37	CCDS43011.1	296	0.13553113553113552	7	0.014227642276422764	32	0.08839779005524862	227	0.3968531468531469	30	0.0395778364116095	C	0.203	-1.042871	0.01997	0.031321	0.048616	ENSG00000128276	ENST00000249007	T	0.52526	0.66	0.784	-1.26	0.09376	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.35798	-0.9774	8	0.02654	T	1	.	1.4237	0.02318	0.3217:0.2569:0.0:0.4214	rs58637580;rs61729173	15	O75679	RFPL3_HUMAN	H	15	ENSP00000249007:Q15H	ENSP00000249007:Q15H	Q	+	3	2	RFPL3	31084103	0.002000	0.14202	0.002000	0.10522	0.029000	0.11900	-2.692000	0.00830	-1.119000	0.02958	-2.543000	0.00179	CAA	A|0.883;C|0.108;T|0.009	0.108	strong		0.463	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
STARD13	90627	hgsc.bcm.edu	37	13	33704154	33704154	+	Silent	SNP	C	C	T	rs596742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:33704154C>T	ENST00000336934.5	-	5	776	c.660G>A	c.(658-660)ccG>ccA	p.P220P	STARD13_ENST00000399365.3_Silent_p.P102P|STARD13_ENST00000255486.4_Silent_p.P212P	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	220					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		CCAGCATGACCGGGTTGTCTG	0.627													C|||	534	0.106629	0.2315	0.049	5008	,	,		16990	0.001		0.0875	False		,,,				2504	0.1074				p.P220P		Atlas-SNP	.											.	STARD13	100	.	0			c.G660A						PASS	.	C	,,	815,3591	323.4+/-298.1	71,673,1459	44.0	48.0	47.0		306,660,636	-1.1	0.0	13	dbSNP_83	47	705,7895	175.0+/-225.2	31,643,3626	no	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	102,1316,5085	TT,TC,CC		8.1977,18.4975,11.6869	,,	102/996,220/1114,212/1106	33704154	1520,11486	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			CATGACCGGGTTG	AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.660G>A	13.37:g.33704154C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	53	26	0.490566	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.894;T|0.106	0.106	strong		0.627	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
ZPR1	8882	hgsc.bcm.edu	37	11	116652892	116652892	+	Missense_Mutation	SNP	A	A	T	rs11550892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:116652892A>T	ENST00000227322.3	-	12	1220	c.1161T>A	c.(1159-1161)ttT>ttA	p.F387L		NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		387					apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		TCTTCTGGCTAAACTCCTGTA	0.478													A|||	3	0.000599042	0.0	0.0014	5008	,	,		17633	0.0		0.002	False		,,,				2504	0.0				p.F387L		Atlas-SNP	.											.	ZNF259	27	.	0			c.T1161A						PASS	.	A	LEU/PHE	4,4398	8.1+/-20.4	0,4,2197	114.0	93.0	100.0		1161	1.1	1.0	11	dbSNP_120	100	69,8523	41.7+/-99.0	0,69,4227	yes	missense	ZNF259	NM_003904.3	22	0,73,6424	TT,TA,AA		0.8031,0.0909,0.5618	probably-damaging	387/460	116652892	73,12921	2201	4296	6497	SO:0001583	missense	8882	exon12			CTGGCTAAACTCC																												ENST00000227322.3:c.1161T>A	11.37:g.116652892A>T	ENSP00000227322:p.Phe387Leu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	99	47	0.474747	NM_003904	Q2TAA0	Missense_Mutation	SNP	ENST00000227322.3	37	CCDS8375.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	A|A	24.5|24.5	4.534777|4.534777	0.85812|0.85812	9.09E-4|9.09E-4	0.008031|0.008031	ENSG00000109917|ENSG00000109917	ENST00000227322|ENST00000429220	T|.	0.45276|.	0.9|.	6.02|6.02	1.12|1.12	0.20585|0.20585	Zinc finger, ZPR1-type (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.63046|.	0.2478|.	M|M	0.79011|0.79011	2.435|2.435	0.80722|0.80722	D|D	1|1	D|.	0.56035|.	0.974|.	P|.	0.61201|.	0.885|.	T|.	0.64193|.	-0.6465|.	10|.	0.62326|.	D|.	0.03|.	-11.3214|-11.3214	10.2019|10.2019	0.43089|0.43089	0.63:0.0:0.37:0.0|0.63:0.0:0.37:0.0	rs11550892;rs35417469|rs11550892;rs35417469	387|.	O75312|.	ZPR1_HUMAN|.	L|K	387|314	ENSP00000227322:F387L|.	ENSP00000227322:F387L|.	F|X	-|-	3|1	2|0	ZNF259|ZNF259	116158102|116158102	0.888000|0.888000	0.30383|0.30383	0.998000|0.998000	0.56505|0.56505	0.935000|0.935000	0.57460|0.57460	0.349000|0.349000	0.20055|0.20055	-0.047000|-0.047000	0.13423|0.13423	0.533000|0.533000	0.62120|0.62120	TTT|TAG	A|0.996;T|0.004	0.004	strong		0.478	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106283.2		
SEC14L4	284904	hgsc.bcm.edu	37	22	30901592	30901592	+	Missense_Mutation	SNP	T	T	C	rs9608956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30901592T>C	ENST00000255858.7	-	1	90	c.7A>G	c.(7-9)Agc>Ggc	p.S3G	SEC14L4_ENST00000540456.1_5'UTR|SEC14L4_ENST00000392772.2_5'UTR|SEC14L4_ENST00000381982.3_Missense_Mutation_p.S3G	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	3			S -> G (in dbSNP:rs9608956).			integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CCGACTCGGCTGCTCATGGTG	0.736													C|||	1028	0.205272	0.2716	0.2997	5008	,	,		13779	0.0397		0.2545	False		,,,				2504	0.1687				p.S3G		Atlas-SNP	.											.	SEC14L4	43	.	0			c.A7G						PASS	.	C	GLY/SER,GLY/SER	1010,3322		147,716,1303	8.0	10.0	9.0		7,7	3.7	1.0	22	dbSNP_119	9	1922,6566		248,1426,2570	no	missense,missense	SEC14L4	NM_001161368.1,NM_174977.3	56,56	395,2142,3873	CC,CT,TT		22.6437,23.3149,22.8705	benign,benign	3/361,3/407	30901592	2932,9888	2166	4244	6410	SO:0001583	missense	284904	exon1			CTCGGCTGCTCAT	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.7A>G	22.37:g.30901592T>C	ENSP00000255858:p.Ser3Gly	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	42	15	0.357143	NM_001161368	A5D6W7|A6NCV4	Missense_Mutation	SNP	ENST00000255858.7	37	CCDS13878.1	449	0.20558608058608058	143	0.29065040650406504	90	0.24861878453038674	24	0.04195804195804196	192	0.2532981530343008	C	8.917	0.960179	0.18507	0.233149	0.226437	ENSG00000133488	ENST00000255858;ENST00000381982	T;T	0.26223	1.75;1.75	3.73	3.73	0.42828	Phosphatidylinositol transfer protein-like, N-terminal (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00006	-3.22	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37361	-0.9709	9	0.06365	T	0.9	0.1944	10.3272	0.43801	0.0:0.9033:0.0:0.0967	rs9608956;rs52821308;rs9608956	3	Q9UDX3	S14L4_HUMAN	G	3	ENSP00000255858:S3G;ENSP00000371412:S3G	ENSP00000255858:S3G	S	-	1	0	SEC14L4	29231592	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.927000	0.56499	1.167000	0.42706	-0.320000	0.08662	AGC	T|0.801;C|0.199	0.199	strong		0.736	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34827085	34827085	+	Missense_Mutation	SNP	A	A	T	rs9469913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:34827085A>T	ENST00000192788.5	+	14	3123	c.2952A>T	c.(2950-2952)caA>caT	p.Q984H	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.Q984H	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	984			Q -> H (in dbSNP:rs9469913).				histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						GCAGAACCCAAGCCTCCAGCT	0.572													A|||	952	0.190096	0.4569	0.1196	5008	,	,		22281	0.0228		0.1402	False		,,,				2504	0.1033				p.Q984H		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.A2952T						PASS	.	A	HIS/GLN	1464,2618		250,964,827	46.0	50.0	48.0		2952	-5.2	0.0	6	dbSNP_119	48	1444,6894		132,1180,2857	yes	missense	UHRF1BP1	NM_017754.3	24	382,2144,3684	TT,TA,AA		17.3183,35.8648,23.4138	possibly-damaging	984/1441	34827085	2908,9512	2041	4169	6210	SO:0001583	missense	54887	exon14			AACCCAAGCCTCC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.2952A>T	6.37:g.34827085A>T	ENSP00000192788:p.Gln984His	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	399	0.18269230769230768	234	0.47560975609756095	47	0.1298342541436464	13	0.022727272727272728	105	0.13852242744063326	A	13.88	2.368353	0.42003	0.358648	0.173183	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.09163	3.01;3.01	5.52	-5.18	0.02840	.	0.566831	0.19078	N	0.123328	T	0.02193	0.0068	N	0.19112	0.55	0.80722	P	0.0	B	0.18863	0.031	B	0.13407	0.009	T	0.35895	-0.9770	9	0.34782	T	0.22	-11.9099	15.6301	0.76899	0.316:0.0:0.684:0.0	rs9469913;rs52800736;rs9469913	984	Q6BDS2	URFB1_HUMAN	H	984	ENSP00000192788:Q984H;ENSP00000400628:Q984H	ENSP00000192788:Q984H	Q	+	3	2	UHRF1BP1	34935063	0.000000	0.05858	0.007000	0.13788	0.776000	0.43924	0.028000	0.13644	-0.862000	0.04089	0.482000	0.46254	CAA	A|0.822;T|0.178	0.178	strong		0.572	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
TPTE	7179	hgsc.bcm.edu	37	21	10920086	10920086	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:10920086G>T	ENST00000361285.4	-	19	1497	c.1168C>A	c.(1168-1170)Cag>Aag	p.Q390K	TPTE_ENST00000298232.7_Missense_Mutation_p.Q372K|TPTE_ENST00000342420.5_Missense_Mutation_p.Q352K|TPTE_ENST00000415664.2_5'UTR	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	390	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.Q390K(1)|p.Q372K(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAACTTACCTGAGAAGGAGTT	0.378																																					p.Q390K		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,0,3	TPTE	513	3	2	Substitution - Missense(2)	lung(2)	c.C1168A						PASS	.						70.0	70.0	70.0					21																	10920086		2202	4300	6502	SO:0001583	missense	7179	exon19			TTACCTGAGAAGG	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1168C>A	21.37:g.10920086G>T	ENSP00000355208:p.Gln390Lys	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	127	30	0.23622	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	12.26	1.885014	0.33255	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.99488	-6.0;-6.0;-6.0	2.32	2.32	0.28847	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99629	0.9864	H	0.97962	4.115	0.46798	D	0.999209	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.996;0.999	D	0.98186	1.0460	10	0.87932	D	0	-18.4997	8.1818	0.31315	0.0:0.0:1.0:0.0	.	352;372;390	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	K	372;390;352	ENSP00000298232:Q372K;ENSP00000355208:Q390K;ENSP00000344441:Q352K	ENSP00000298232:Q372K	Q	-	1	0	TPTE	9941957	1.000000	0.71417	0.997000	0.53966	0.311000	0.27955	5.387000	0.66243	1.313000	0.45069	0.184000	0.17185	CAG	.	.	none		0.378	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
MGAM	8972	hgsc.bcm.edu	37	7	141752154	141752154	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141752154A>T	ENST00000549489.2	+	25	2961	c.2866A>T	c.(2866-2868)Ata>Tta	p.I956L	MGAM_ENST00000475668.2_Missense_Mutation_p.I956L	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	956	P-type 2. {ECO:0000255|PROSITE- ProRule:PRU00779}.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGAATGGAGCATAAAGATAAG	0.428																																					p.I956L		Atlas-SNP	.											.	MGAM	767	.	0			c.A2866T						PASS	.						72.0	64.0	67.0					7																	141752154		1893	4125	6018	SO:0001583	missense	8972	exon25			TGGAGCATAAAGA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.2866A>T	7.37:g.141752154A>T	ENSP00000447378:p.Ile956Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	A	4.008	-0.001239	0.07819	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.88431	-2.38	4.64	-9.28	0.00656	P-type trefoil (2);	5.617280	0.00166	N	0.000008	T	0.66636	0.2809	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64676	-0.6351	10	0.11485	T	0.65	.	1.9557	0.03375	0.2744:0.3783:0.0822:0.2652	.	956	O43451	MGA_HUMAN	L	956;956;833	ENSP00000447378:I956L	ENSP00000316431:I833L	I	+	1	0	MGAM	141398623	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.999000	0.01467	-1.559000	0.01688	-0.661000	0.03856	ATA	.	.	none		0.428	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
CORO1A	11151	hgsc.bcm.edu	37	16	30198151	30198151	+	Silent	SNP	A	A	G	rs1132812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30198151A>G	ENST00000219150.5	+	4	641	c.336A>G	c.(334-336)ccA>ccG	p.P112P	RP11-455F5.5_ENST00000567153.1_RNA|RP11-455F5.5_ENST00000568506.1_RNA|RP11-455F5.5_ENST00000566144.1_RNA|CORO1A_ENST00000565497.1_Silent_p.P112P|CORO1A_ENST00000570045.1_Silent_p.P112P	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	112					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						GGGAGATCCCAGATGGGGGCC	0.657													G|||	3977	0.794129	0.9501	0.7421	5008	,	,		17961	0.9256		0.5706	False		,,,				2504	0.7147				p.P112P		Atlas-SNP	.											.	CORO1A	36	.	0			c.A336G						PASS	.	G	,	3913,479		1742,429,25	23.0	29.0	27.0		336,336	-8.4	0.1	16	dbSNP_86	27	4758,3840		1331,2096,872	no	coding-synonymous,coding-synonymous	CORO1A	NM_001193333.2,NM_007074.3	,	3073,2525,897	GG,GA,AA		44.6615,10.9062,33.2487	,	112/462,112/462	30198151	8671,4319	2196	4299	6495	SO:0001819	synonymous_variant	11151	exon4			GATCCCAGATGGG	X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"""Coronins"", ""WD repeat domain containing"""	2252	protein-coding gene	gene with protein product	"""Clabp TACO"""	605000	"""coronin, actin-binding protein, 1A"""			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.336A>G	16.37:g.30198151A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	88	45	0.511364	NM_007074	B2RBL1|Q2YD73	Silent	SNP	ENST00000219150.5	37	CCDS10673.1																																																																																			A|0.292;G|0.708	0.708	strong		0.657	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074	
ACLY	47	hgsc.bcm.edu	37	17	40065774	40065774	+	Missense_Mutation	SNP	T	T	G	rs2304497	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:40065774T>G	ENST00000352035.2	-	5	655	c.525A>C	c.(523-525)gaA>gaC	p.E175D	ACLY_ENST00000590151.1_Missense_Mutation_p.E175D|ACLY_ENST00000393896.2_Missense_Mutation_p.E175D|ACLY_ENST00000537919.1_Intron|ACLY_ENST00000353196.1_Missense_Mutation_p.E175D	NM_001096.2	NP_001087.2	P53396	ACLY_HUMAN	ATP citrate lyase	175	ATP-grasp.		E -> D (in dbSNP:rs2304497). {ECO:0000269|PubMed:1371749, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:9116495}.		ATP catabolic process (GO:0006200)|cellular carbohydrate metabolic process (GO:0044262)|cellular lipid metabolic process (GO:0044255)|citrate metabolic process (GO:0006101)|coenzyme A metabolic process (GO:0015936)|energy reserve metabolic process (GO:0006112)|lipid biosynthetic process (GO:0008610)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	citrate lyase complex (GO:0009346)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP citrate synthase activity (GO:0003878)|cofactor binding (GO:0048037)|metal ion binding (GO:0046872)|succinate-CoA ligase (ADP-forming) activity (GO:0004775)		NTN1/ACLY(2)	breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	28		Breast(137;0.000143)				CTTTCTTGTCTTCAGGGGCGT	0.562													T|||	471	0.0940495	0.1089	0.0519	5008	,	,		19799	0.0605		0.1143	False		,,,				2504	0.1176				p.E175D	Colon(64;807 1396 15971 30971)	Atlas-SNP	.											.	ACLY	85	.	0			c.A525C						PASS	.	T	ASP/GLU,ASP/GLU	423,3983	207.8+/-229.1	24,375,1804	117.0	103.0	108.0		525,525	-7.4	0.0	17	dbSNP_100	108	949,7651	208.6+/-250.0	53,843,3404	yes	missense,missense	ACLY	NM_001096.2,NM_198830.1	45,45	77,1218,5208	GG,GT,TT		11.0349,9.6005,10.549	benign,benign	175/1102,175/1092	40065774	1372,11634	2203	4300	6503	SO:0001583	missense	47	exon5			CTTGTCTTCAGGG	X64330	CCDS11412.1, CCDS11413.1	17q21.2	2010-04-27			ENSG00000131473	ENSG00000131473	2.3.3.8		115	protein-coding gene	gene with protein product	"""ATP citrate synthase"""	108728				1371749, 8088842	Standard	NM_001096		Approved	ATPCL, CLATP, ACL	uc002hyg.3	P53396	OTTHUMG00000133507	ENST00000352035.2:c.525A>C	17.37:g.40065774T>G	ENSP00000253792:p.Glu175Asp	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	173	73	0.421965	NM_001096	B4DIM0|B4E3P0|Q13037|Q9BRL0	Missense_Mutation	SNP	ENST00000352035.2	37	CCDS11412.1	201	0.09203296703296704	52	0.10569105691056911	22	0.06077348066298342	39	0.06818181818181818	88	0.11609498680738786	T	4.556	0.103286	0.08731	0.096005	0.110349	ENSG00000131473	ENST00000352035;ENST00000401700;ENST00000353196;ENST00000393896	T;T;T	0.69685	-0.42;-0.42;-0.42	5.21	-7.37	0.01412	ATP-grasp fold, subdomain 2 (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.761108	0.12996	N	0.422079	T	0.00412	0.0013	N	0.04090	-0.28	0.52099	P	5.999999999994898E-5	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.11518	-1.0584	9	0.11485	T	0.65	.	5.2134	0.15329	0.0861:0.4929:0.1735:0.2476	rs2304497;rs17584309;rs56642660;rs58904106;rs2304497	229;175;175	E7ENH9;G3XAI4;P53396	.;.;ACLY_HUMAN	D	175;229;175;175	ENSP00000253792:E175D;ENSP00000345398:E175D;ENSP00000377474:E175D	ENSP00000253792:E175D	E	-	3	2	ACLY	37319300	0.000000	0.05858	0.026000	0.17262	0.606000	0.37113	-1.122000	0.03267	-0.986000	0.03498	-0.371000	0.07208	GAA	T|0.896;G|0.104	0.104	strong		0.562	ACLY-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257465.1	NM_001096	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72513635	72513635	+	Missense_Mutation	SNP	C	C	A	rs12774070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:72513635C>A	ENST00000373207.1	+	19	2809	c.2809C>A	c.(2809-2811)Ctg>Atg	p.L937M	ADAMTS14_ENST00000373208.1_Missense_Mutation_p.L940M	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	937	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.		L -> M (in dbSNP:rs12774070).		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						ACAGTGCCTGCTGCCCCTCTC	0.682													C|||	802	0.160144	0.0159	0.2046	5008	,	,		16195	0.1637		0.2614	False		,,,				2504	0.2157				p.L940M		Atlas-SNP	.											ADAMTS14,NS,carcinoma,0,2	ADAMTS14	148	2	0			c.C2818A						PASS	.	C	MET/LEU,MET/LEU	265,4135		18,229,1953	20.0	15.0	17.0		2809,2818	3.7	1.0	10	dbSNP_121	17	2270,6322		287,1696,2313	yes	missense,missense	ADAMTS14	NM_080722.3,NM_139155.2	15,15	305,1925,4266	AA,AC,CC		26.4199,6.0227,19.512	probably-damaging,probably-damaging	937/1224,940/1227	72513635	2535,10457	2200	4296	6496	SO:0001583	missense	140766	exon19			TGCCTGCTGCCCC	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.2809C>A	10.37:g.72513635C>A	ENSP00000362303:p.Leu937Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	63	36	0.571429	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Missense_Mutation	SNP	ENST00000373207.1	37	CCDS7306.1	368	0.1684981684981685	9	0.018292682926829267	60	0.16574585635359115	103	0.18006993006993008	196	0.25857519788918204	C	20.1	3.939861	0.73557	0.060227	0.264199	ENSG00000138316	ENST00000373208;ENST00000373207	T;T	0.61392	0.11;0.11	4.58	3.68	0.42216	.	0.083179	0.49305	D	0.000150	T	0.00039	0.0001	L	0.47016	1.485	0.31497	P	0.665223	D;D	0.64830	0.99;0.994	P;D	0.63033	0.871;0.91	T	0.04165	-1.0972	9	0.72032	D	0.01	.	12.4295	0.55565	0.0:0.9178:0.0:0.0822	rs12774070;rs12774070	937;940	Q8WXS8;Q5T4G1	ATS14_HUMAN;.	M	940;937	ENSP00000362304:L940M;ENSP00000362303:L937M	ENSP00000362303:L937M	L	+	1	2	ADAMTS14	72183641	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.839000	0.62810	1.159000	0.42565	0.563000	0.77884	CTG	A|0.174;C|0.826;G|0.000	0.174	strong		0.682	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
LBP	3929	hgsc.bcm.edu	37	20	37001761	37001761	+	Missense_Mutation	SNP	T	T	C	rs2232618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37001761T>C	ENST00000217407.2	+	13	1467	c.1306T>C	c.(1306-1308)Ttc>Ctc	p.F436L		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	436			F -> L (in dbSNP:rs2232618). {ECO:0000269|PubMed:2402637, ECO:0000269|PubMed:9240454, ECO:0000269|Ref.5}.		acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				CCTTAACACCTTCTACCCCAA	0.463													C|||	629	0.125599	0.2201	0.0591	5008	,	,		19471	0.0565		0.0726	False		,,,				2504	0.1708				p.F436L		Atlas-SNP	.											.	LBP	60	.	0			c.T1306C						PASS	.	C	LEU/PHE	843,3563	746.2+/-411.7	82,679,1442	112.0	102.0	106.0		1306	-1.0	0.0	20	dbSNP_98	106	774,7826	784.1+/-407.6	25,724,3551	yes	missense	LBP	NM_004139.2	22	107,1403,4993	CC,CT,TT		9.0,19.133,12.4327	benign	436/482	37001761	1617,11389	2203	4300	6503	SO:0001583	missense	3929	exon13			AACACCTTCTACC		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.1306T>C	20.37:g.37001761T>C	ENSP00000217407:p.Phe436Leu	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	69	31	0.449275	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	188	0.08608058608058608	81	0.16463414634146342	26	0.0718232044198895	33	0.057692307692307696	48	0.0633245382585752	C	0.006	-2.060426	0.00386	0.19133	0.09	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.05925	3.37	4.82	-0.996	0.10218	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.415593	0.22646	N	0.057383	T	0.00012	0.0000	N	0.00459	-1.475	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.41360	-0.9513	9	0.18276	T	0.48	-12.5231	1.2193	0.01921	0.2711:0.3029:0.2646:0.1614	rs2232618;rs3197421;rs17422694;rs52812841;rs58745877;rs2232618	436	P18428	LBP_HUMAN	L	436	ENSP00000217407:F436L	ENSP00000217407:F436L	F	+	1	0	LBP	36435175	0.002000	0.14202	0.005000	0.12908	0.001000	0.01503	-0.516000	0.06282	-0.466000	0.06943	-1.473000	0.01005	TTC	T|0.884;C|0.116	0.116	strong		0.463	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
P2RX7	5027	hgsc.bcm.edu	37	12	121622196	121622196	+	Missense_Mutation	SNP	A	A	G	rs2230912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121622196A>G	ENST00000546057.1	+	13	1522	c.1379A>G	c.(1378-1380)cAg>cGg	p.Q460R	P2RX7_ENST00000328963.5_Missense_Mutation_p.Q290R|P2RX7_ENST00000541446.1_Missense_Mutation_p.Q171R|P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000535250.1_Missense_Mutation_p.Q370R	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	460			Q -> R (in dbSNP:rs2230912).		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)					GAGGAGATACAGCTGCTTAGA	0.572													A|||	347	0.0692891	0.0356	0.0504	5008	,	,		16092	0.001		0.1471	False		,,,				2504	0.1186				p.Q460R		Atlas-SNP	.											.	P2RX7	53	.	0			c.A1379G	GRCh37	CM063010	P2RX7	M	rs2230912	PASS	.	A	ARG/GLN	232,4174	136.5+/-172.5	5,222,1976	75.0	71.0	73.0		1379	5.2	0.8	12	dbSNP_98	73	1429,7171	274.3+/-291.2	122,1185,2993	yes	missense	P2RX7	NM_002562.5	43	127,1407,4969	GG,GA,AA		16.6163,5.2655,12.771	benign	460/596	121622196	1661,11345	2203	4300	6503	SO:0001583	missense	5027	exon13			AGATACAGCTGCT	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.1379A>G	12.37:g.121622196A>G	ENSP00000442349:p.Gln460Arg	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	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	149	0.06822344322344322	25	0.0508130081300813	16	0.04419889502762431	1	0.0017482517482517483	107	0.14116094986807387	A	11.84	1.759833	0.31137	0.052655	0.166163	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.04862	4.43;4.05;4.21;3.54	5.21	5.21	0.72293	.	1.648900	0.04098	N	0.312328	T	0.00039	0.0001	M	0.70275	2.135	0.38416	P	0.05393800000000004	B;B;B;B	0.19583	0.037;0.021;0.004;0.003	B;B;B;B	0.19148	0.024;0.016;0.004;0.006	T	0.48570	-0.9024	9	0.18276	T	0.48	.	7.8396	0.29391	0.9064:0.0:0.0936:0.0	rs2230912;rs17465760;rs52832228;rs60366484;rs2230912	290;171;370;460	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	R	460;290;370;171	ENSP00000442349:Q460R;ENSP00000330696:Q290R;ENSP00000442572:Q370R;ENSP00000437471:Q171R	ENSP00000330696:Q290R	Q	+	2	0	P2RX7	120106579	1.000000	0.71417	0.842000	0.33263	0.047000	0.14425	3.212000	0.51145	1.967000	0.57214	0.482000	0.46254	CAG	A|0.889;G|0.111	0.111	strong		0.572	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
ARNT	405	hgsc.bcm.edu	37	1	150808889	150808889	+	Silent	SNP	C	C	G	rs2228099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:150808889C>G	ENST00000358595.5	-	7	767	c.567G>C	c.(565-567)gtG>gtC	p.V189V	ARNT_ENST00000468970.1_5'UTR|ARNT_ENST00000515192.1_Silent_p.V180V|ARNT_ENST00000505755.1_Silent_p.V174V|ARNT_ENST00000354396.2_Silent_p.V189V	NM_001197325.1|NM_001668.3|NM_178427.2	NP_001184254.1|NP_001659.1|NP_848514.1	P27540	ARNT_HUMAN	aryl hydrocarbon receptor nuclear translocator	189	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|cellular response to hypoxia (GO:0071456)|embryonic placenta development (GO:0001892)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of glycolytic process (GO:0045821)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor activity (GO:0004874)|aryl hydrocarbon receptor binding (GO:0017162)|enhancer binding (GO:0035326)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.V189V(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|prostate(2)|skin(4)|stomach(1)	34	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.02)|BRCA - Breast invasive adenocarcinoma(12;0.00606)|LUSC - Lung squamous cell carcinoma(543;0.211)			CGGAGTCAGACACATACACCA	0.463			T	ETV6	AML								G|||	2359	0.471046	0.5174	0.4625	5008	,	,		16795	0.4018		0.3926	False		,,,				2504	0.5665				p.V189V		Atlas-SNP	.		Dom	yes		1	1q21	405	aryl hydrocarbon receptor nuclear translocator		L	ARNT,NS,carcinoma,0,1	ARNT	68	1	1	Substitution - coding silent(1)	stomach(1)	c.G567C						PASS	.	G	,,	2239,2167	583.2+/-385.8	564,1111,528	102.0	85.0	91.0		522,567,522	1.0	1.0	1	dbSNP_98	91	3164,5436	654.2+/-401.1	597,1970,1733	no	coding-synonymous,coding-synonymous,coding-synonymous	ARNT	NM_001197325.1,NM_001668.3,NM_178427.2	,,	1161,3081,2261	GG,GC,CC		36.7907,49.1829,41.5424	,,	174/774,189/790,174/775	150808889	5403,7603	2203	4300	6503	SO:0001819	synonymous_variant	405	exon7			GTCAGACACATAC	AF001307	CCDS970.1, CCDS971.1, CCDS65641.1, CCDS65642.1	1q21	2013-05-21			ENSG00000143437	ENSG00000143437		"""Basic helix-loop-helix proteins"""	700	protein-coding gene	gene with protein product		126110					Standard	NM_001668		Approved	HIF-1beta, bHLHe2	uc001evr.2	P27540	OTTHUMG00000035011	ENST00000358595.5:c.567G>C	1.37:g.150808889C>G		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	107	63	0.588785	NM_001668	B2R9H1|C4AMA1|F8WAP6|Q59ED4|Q5QP39|Q8NDC7	Silent	SNP	ENST00000358595.5	37	CCDS970.1																																																																																			C|0.562;G|0.438	0.438	strong		0.463	ARNT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084741.2		
ZNF180	7733	hgsc.bcm.edu	37	19	45001346	45001346	+	Missense_Mutation	SNP	G	G	A	rs2571108	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45001346G>A	ENST00000221327.4	-	2	403	c.122C>T	c.(121-123)gCc>gTc	p.A41V	ZNF180_ENST00000585514.1_5'UTR|ZNF180_ENST00000391956.4_Missense_Mutation_p.A41V|ZNF180_ENST00000592529.1_Missense_Mutation_p.A14V|ZNF180_ENST00000586637.1_Missense_Mutation_p.P10S|ZNF180_ENST00000587047.1_Missense_Mutation_p.P43S	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	41			A -> V (in dbSNP:rs2571108). {ECO:0000269|PubMed:12743021}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CTGTGCACAGGCCTTCGGGGG	0.622													G|||	1307	0.260982	0.1498	0.1844	5008	,	,		15070	0.3562		0.3857	False		,,,				2504	0.2393				p.A41V	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											ZNF180,colon,carcinoma,0,1	ZNF180	103	1	0			c.C122T						PASS	.	G	VAL/ALA	884,3522	336.5+/-304.4	97,690,1416	39.0	38.0	38.0		122	0.4	0.0	19	dbSNP_100	38	3057,5543	465.4+/-366.5	553,1951,1796	yes	missense	ZNF180	NM_013256.3	64	650,2641,3212	AA,AG,GG		35.5465,20.0635,30.3014	benign	41/693	45001346	3941,9065	2203	4300	6503	SO:0001583	missense	7733	exon2			GCACAGGCCTTCG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.122C>T	19.37:g.45001346G>A	ENSP00000221327:p.Ala41Val	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	41	17	0.414634	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	663	0.30357142857142855	67	0.13617886178861788	71	0.19613259668508287	222	0.3881118881118881	303	0.3997361477572559	G	9.934	1.215647	0.22373	0.200635	0.355465	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.08720	3.21;3.06	3.85	0.423	0.16463	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.10450	0.005;0.002;0.002	T	0.46233	-0.9206	8	0.02654	T	1	0.0079	4.3819	0.11299	0.2115:0.1858:0.6027:0.0	rs2571108;rs2571108	41;40;41	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	V	41	ENSP00000221327:A41V;ENSP00000375818:A41V	ENSP00000221327:A41V	A	-	2	0	ZNF180	49693186	0.053000	0.20554	0.005000	0.12908	0.043000	0.13939	0.391000	0.20784	0.219000	0.20840	-0.165000	0.13383	GCC	G|0.703;A|0.297	0.297	strong		0.622	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
LRRIQ4	344657	hgsc.bcm.edu	37	3	169540397	169540397	+	Silent	SNP	T	T	C	rs1920119	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:169540397T>C	ENST00000340806.6	+	1	688	c.688T>C	c.(688-690)Ttg>Ctg	p.L230L		NM_001080460.1	NP_001073929.1	A6NIV6	LRIQ4_HUMAN	leucine-rich repeats and IQ motif containing 4	230										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	30						GCCCGCGTCCTTGTGCCAGTG	0.547													C|||	2983	0.595647	0.6679	0.6066	5008	,	,		18668	0.7579		0.4036	False		,,,				2504	0.5204				p.L230L		Atlas-SNP	.											.	LRRIQ4	68	.	0			c.T688C						PASS	.	C		2393,1549		718,957,296	59.0	64.0	62.0		688	4.8	0.0	3	dbSNP_92	62	3294,5002		674,1946,1528	no	coding-synonymous	LRRIQ4	NM_001080460.1		1392,2903,1824	CC,CT,TT		39.7059,39.2948,46.47		230/561	169540397	5687,6551	1971	4148	6119	SO:0001819	synonymous_variant	344657	exon1			GCGTCCTTGTGCC		CCDS46951.1	3q26.2	2008-08-08	2008-06-12	2008-06-12	ENSG00000188306	ENSG00000188306			34298	protein-coding gene	gene with protein product	"""leucine rich repeat containing 64"""						Standard	NM_001080460		Approved	LRRC64	uc003fgb.3	A6NIV6	OTTHUMG00000164420	ENST00000340806.6:c.688T>C	3.37:g.169540397T>C		Somatic	193	1	0.00518135		WXS	Illumina HiSeq	Phase_I	215	214	0.995349	NM_001080460		Silent	SNP	ENST00000340806.6	37	CCDS46951.1																																																																																			T|0.444;C|0.556	0.556	strong		0.547	LRRIQ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378698.1	NM_001080460	
MYCBP2	23077	hgsc.bcm.edu	37	13	77632470	77632470	+	Silent	SNP	C	C	T	rs2285386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:77632470C>T	ENST00000544440.2	-	78	13115	c.13098G>A	c.(13096-13098)gaG>gaA	p.E4366E	MYCBP2_ENST00000357337.6_Silent_p.E4366E|MYCBP2_ENST00000407578.2_Silent_p.E4404E					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)		GCAGACAGTGCTCTTCGTTTT	0.483													C|||	543	0.108427	0.0772	0.1772	5008	,	,		16705	0.121		0.0865	False		,,,				2504	0.1115				p.E4404E		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.G13212A						PASS	.	C		401,4005	200.8+/-224.0	23,355,1825	165.0	132.0	143.0		13212	-1.0	1.0	13	dbSNP_100	143	826,7774	191.5+/-237.7	42,742,3516	no	coding-synonymous	MYCBP2	NM_015057.4		65,1097,5341	TT,TC,CC		9.6047,9.1012,9.4341		4404/4679	77632470	1227,11779	2203	4300	6503	SO:0001819	synonymous_variant	23077	exon78			ACAGTGCTCTTCG	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.13098G>A	13.37:g.77632470C>T		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	211	108	0.511848	NM_015057		Silent	SNP	ENST00000544440.2	37		223	0.1021062271062271	40	0.08130081300813008	55	0.15193370165745856	62	0.10839160839160839	66	0.0870712401055409	C	9.759	1.169521	0.21621	0.091012	0.096047	ENSG00000005810	ENST00000429715	.	.	.	5.42	-1.01	0.10169	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	P	0.9999999999976027	.	.	.	.	.	.	T	0.18023	-1.0350	3	.	.	.	.	6.7158	0.23302	0.0:0.4793:0.2113:0.3094	rs2285386;rs2285386	.	.	.	T	787	.	.	A	-	1	0	MYCBP2	76530471	0.189000	0.23263	0.997000	0.53966	0.991000	0.79684	-0.397000	0.07269	0.080000	0.16959	0.585000	0.79938	GCA	C|0.903;T|0.097	0.097	strong		0.483	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
ELMOD3	84173	hgsc.bcm.edu	37	2	85590286	85590286	+	Missense_Mutation	SNP	C	C	T	rs7564372	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:85590286C>T	ENST00000409890.2	+	6	863	c.196C>T	c.(196-198)Cgt>Tgt	p.R66C	ELMOD3_ENST00000428955.2_Missense_Mutation_p.R66C|ELMOD3_ENST00000409013.3_Missense_Mutation_p.R66C|ELMOD3_ENST00000490508.1_3'UTR|ELMOD3_ENST00000315658.7_Missense_Mutation_p.R66C|ELMOD3_ENST00000409344.3_Missense_Mutation_p.R66C|ELMOD3_ENST00000393852.4_Missense_Mutation_p.R66C			Q96FG2	ELMD3_HUMAN	ELMO/CED-12 domain containing 3	66			R -> C (in dbSNP:rs7564372).		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						ATGGGAGCCACGTGGTAAGGT	0.507													C|||	318	0.0634984	0.1899	0.0389	5008	,	,		17535	0.0		0.0348	False		,,,				2504	0.0051				p.R66C		Atlas-SNP	.											.	ELMOD3	53	.	0			c.C196T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	704,3702	292.4+/-282.0	53,598,1552	65.0	62.0	63.0		196,196,196,196	0.9	0.0	2	dbSNP_116	63	226,8374	93.5+/-155.5	4,218,4078	yes	missense,missense,missense,missense	ELMOD3	NM_001135021.1,NM_001135022.1,NM_001135023.1,NM_032213.4	180,180,180,180	57,816,5630	TT,TC,CC		2.6279,15.9782,7.1505	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	66/382,66/382,66/382,66/392	85590286	930,12076	2203	4300	6503	SO:0001583	missense	84173	exon6			GAGCCACGTGGTA	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.196C>T	2.37:g.85590286C>T	ENSP00000386304:p.Arg66Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	87	41	0.471264	NM_001135022	B8ZZD6|D6W5K4|Q2M1K3|Q2XSU3|Q2XSU4|Q8NAC1|Q8TCK4|Q8WV70|Q8WY75|Q9H6Q8	Missense_Mutation	SNP	ENST00000409890.2	37	CCDS46352.1	125	0.05723443223443223	82	0.16666666666666666	18	0.049723756906077346	0	0.0	25	0.032981530343007916	C	16.18	3.049921	0.55218	0.159782	0.026279	ENSG00000115459	ENST00000409331;ENST00000409013;ENST00000409890;ENST00000409344;ENST00000393852;ENST00000428955;ENST00000315658;ENST00000462891;ENST00000418268	T;T;T;T;T;T;T;T	0.33216	1.46;1.47;1.47;1.47;1.47;1.46;1.42;1.49	5.95	0.935	0.19483	.	0.581131	0.19294	N	0.117802	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	P;P	0.38922	0.651;0.519	B;B	0.33890	0.172;0.132	T	0.17961	-1.0352	9	0.59425	D	0.04	0.6767	7.3877	0.26893	0.1588:0.4767:0.3644:0.0	rs7564372;rs52800560;rs7564372	66;66	Q96FG2-6;Q96FG2	.;ELMD3_HUMAN	C	66	ENSP00000386257:R66C;ENSP00000387139:R66C;ENSP00000386304:R66C;ENSP00000386248:R66C;ENSP00000377434:R66C;ENSP00000412692:R66C;ENSP00000318264:R66C;ENSP00000393443:R66C	ENSP00000318264:R66C	R	+	1	0	ELMOD3	85443797	0.003000	0.15002	0.002000	0.10522	0.651000	0.38670	0.078000	0.14761	0.088000	0.17205	-0.211000	0.12701	CGT	C|0.935;T|0.065	0.065	strong		0.507	ELMOD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329124.1	NM_032213	
FCER2	2208	hgsc.bcm.edu	37	19	7755056	7755056	+	Silent	SNP	G	G	A	rs2228138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7755056G>A	ENST00000346664.5	-	10	929	c.717C>T	c.(715-717)caC>caT	p.H239H	FCER2_ENST00000360067.4_Silent_p.H238H|FCER2_ENST00000597921.1_Silent_p.H239H	NM_001220500.1|NM_002002.4	NP_001207429.1|NP_001993.2	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor for (CD23)	239	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				Notch signaling pathway (GO:0007219)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10						TGTAGTCCACGTGGCTCCCAT	0.592													g|||	1995	0.398363	0.6029	0.2176	5008	,	,		15752	0.3403		0.2843	False		,,,				2504	0.4274				p.H239H		Atlas-SNP	.											FCER2,colon,carcinoma,0,1	FCER2	19	1	0			c.C717T						scavenged	.		,,	2382,2024	613.1+/-392.1	638,1106,459	87.0	81.0	83.0		714,717,717	-4.9	0.0	19	dbSNP_98	83	2462,6138	406.2+/-348.7	342,1778,2180	no	coding-synonymous,coding-synonymous,coding-synonymous	FCER2	NM_001207019.2,NM_001220500.1,NM_002002.4	,,	980,2884,2639	AA,AG,GG		28.6279,45.9374,37.2443	,,	238/321,239/322,239/322	7755056	4844,8162	2203	4300	6503	SO:0001819	synonymous_variant	2208	exon10			GTCCACGTGGCTC	M15059	CCDS12184.1	19p13.3	2011-08-30	2006-03-09			ENSG00000104921		"""C-type lectin domain containing"", ""CD molecules"""	3612	protein-coding gene	gene with protein product		151445	"""Fc fragment of IgE, low affinity II, receptor for (CD23A)"""	CD23A, FCE2			Standard	NM_002002		Approved	CLEC4J, CD23	uc002mhm.2	P06734		ENST00000346664.5:c.717C>T	19.37:g.7755056G>A		Somatic	55	1	0.0181818		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_002002		Silent	SNP	ENST00000346664.5	37	CCDS12184.1																																																																																			G|0.634;A|0.366	0.366	strong		0.592	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	
MUC5B	727897	hgsc.bcm.edu	37	11	1251357	1251357	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1251357G>C	ENST00000529681.1	+	11	1401	c.1343G>C	c.(1342-1344)aGc>aCc	p.S448T	MUC5B_ENST00000447027.1_Missense_Mutation_p.S451T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	448	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGTGACTGCAGCTACGTTCTG	0.637																																					p.S448T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G1343C						PASS	.						112.0	115.0	114.0					11																	1251357		1991	4140	6131	SO:0001583	missense	727897	exon11			ACTGCAGCTACGT	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.1343G>C	11.37:g.1251357G>C	ENSP00000436812:p.Ser448Thr	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	71	34	0.478873	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	3.587	-0.084422	0.07097	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.59638	0.25;0.25	4.26	2.37	0.29283	von Willebrand factor, type D domain (3);VWC out (1);	.	.	.	.	T	0.44286	0.1286	N	0.21617	0.685	0.25405	N	0.988402	B;P;P	0.39094	0.051;0.659;0.659	B;B;B	0.42882	0.049;0.401;0.401	T	0.35375	-0.9791	9	0.87932	D	0	.	4.8917	0.13730	0.2846:0.2117:0.5037:0.0	.	448;1107;451	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	T	448;451;449;484	ENSP00000436812:S448T;ENSP00000415793:S451T	ENSP00000343037:S449T	S	+	2	0	MUC5B	1207933	0.001000	0.12720	1.000000	0.80357	0.111000	0.19643	-0.241000	0.08940	0.270000	0.21984	0.313000	0.20887	AGC	.	.	none		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
TMEM60	85025	hgsc.bcm.edu	37	7	77423574	77423574	+	Silent	SNP	G	G	A	rs7953	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:77423574G>A	ENST00000257663.3	-	2	493	c.117C>T	c.(115-117)ttC>ttT	p.F39F		NM_032936.3	NP_116325.1	Q9H2L4	TMM60_HUMAN	transmembrane protein 60	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)	4						AGACTGGAATGAATATGAGGA	0.448													A|||	2838	0.566693	0.8646	0.4424	5008	,	,		20016	0.3165		0.508	False		,,,				2504	0.5706				p.F39F		Atlas-SNP	.											.	TMEM60	24	.	0			c.C117T						PASS	.	A		3494,912	348.2+/-309.8	1386,722,95	76.0	76.0	76.0		117	3.8	1.0	7	dbSNP_52	76	4227,4373	583.0+/-391.5	1081,2065,1154	no	coding-synonymous	TMEM60	NM_032936.3		2467,2787,1249	AA,AG,GG		49.1512,20.699,40.6351		39/134	77423574	7721,5285	2203	4300	6503	SO:0001819	synonymous_variant	85025	exon2			TGGAATGAATATG	AF260336	CCDS5593.1	7q11.23	2005-07-25	2005-07-25	2005-07-25	ENSG00000135211	ENSG00000135211			21754	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 35"""	C7orf35			Standard	NM_032936		Approved	DC32	uc003ugn.3	Q9H2L4	OTTHUMG00000130689	ENST00000257663.3:c.117C>T	7.37:g.77423574G>A		Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	89	89	1	NM_032936	A4D1C3|Q86UM0	Silent	SNP	ENST00000257663.3	37	CCDS5593.1																																																																																			G|0.424;A|0.576	0.576	strong		0.448	TMEM60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253185.2	NM_032936	
DYX1C1	161582	hgsc.bcm.edu	37	15	55722872	55722872	+	Missense_Mutation	SNP	G	G	C	rs77641439	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:55722872G>C	ENST00000321149.3	-	10	1626	c.1259C>G	c.(1258-1260)tCt>tGt	p.S420C	DYX1C1_ENST00000448430.2_Intron|DYX1C1_ENST00000380679.1_Intron|DYX1C1_ENST00000348518.3_3'UTR|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000457155.2_3'UTR	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	420			S -> C. {ECO:0000269|PubMed:12954984}.		cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)	p.S420C(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		TAGTCATTAAGATTTTAGTTC	0.328													G|||	520	0.103834	0.056	0.0648	5008	,	,		13370	0.1875		0.1004	False		,,,				2504	0.1135				p.S420C		Atlas-SNP	.											DYX1C1,colon,carcinoma,0,2	DYX1C1	54	2	1	Substitution - Missense(1)	stomach(1)	c.C1259G						PASS	.	G	,,CYS/SER	322,4062	171.6+/-201.8	13,296,1883	93.0	94.0	94.0		,,1259	3.5	0.8	15	dbSNP_131	94	808,7768	187.0+/-234.4	42,724,3522	yes	utr-3,intron,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	,,112	55,1020,5405	CC,CG,GG		9.4216,7.3449,8.7191	,,probably-damaging	,,420/421	55722872	1130,11830	2192	4288	6480	SO:0001583	missense	161582	exon10			CATTAAGATTTTA		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.1259C>G	15.37:g.55722872G>C	ENSP00000323275:p.Ser420Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	82	44	0.536585	NM_130810	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	255	0.11675824175824176	21	0.042682926829268296	29	0.08011049723756906	127	0.22202797202797203	78	0.10290237467018469	G	15.68	2.905720	0.52333	0.073449	0.094216	ENSG00000256061	ENST00000321149	T	0.06768	3.26	5.6	3.52	0.40303	.	1.866580	0.02899	U	0.135200	T	0.00012	0.0000	L	0.51422	1.61	0.49687	P	1.8300000000004424E-4	D	0.89917	1.0	D	0.83275	0.996	T	0.06391	-1.0829	9	0.87932	D	0	.	11.6563	0.51320	0.0:0.1251:0.7297:0.1452	.	420	Q8WXU2	DYXC1_HUMAN	C	420	ENSP00000323275:S420C	ENSP00000323275:S420C	S	-	2	0	DYX1C1	53510164	0.998000	0.40836	0.844000	0.33320	0.937000	0.57800	3.380000	0.52448	1.355000	0.45865	0.558000	0.71614	TCT	G|0.908;C|0.092	0.092	strong		0.328	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
UBR4	23352	hgsc.bcm.edu	37	1	19499954	19499954	+	Silent	SNP	G	G	A	rs952790	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:19499954G>A	ENST00000375254.3	-	23	3171	c.3144C>T	c.(3142-3144)agC>agT	p.S1048S	UBR4_ENST00000375267.2_Silent_p.S1048S|UBR4_ENST00000375217.2_Silent_p.S1048S|UBR4_ENST00000375226.2_Silent_p.S1048S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1048					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		TGACATAGGAGCTGATCCGGA	0.428													G|||	169	0.033746	0.0061	0.0403	5008	,	,		21192	0.001		0.1054	False		,,,				2504	0.0266				p.S1048S		Atlas-SNP	.											.	UBR4	415	.	0			c.C3144T						PASS	.	G		94,4312	76.2+/-114.5	0,94,2109	63.0	61.0	62.0		3144	2.7	1.0	1	dbSNP_86	62	954,7646	209.3+/-250.5	58,838,3404	no	coding-synonymous	UBR4	NM_020765.2		58,932,5513	AA,AG,GG		11.093,2.1335,8.0578		1048/5184	19499954	1048,11958	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon23			ATAGGAGCTGATC	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.3144C>T	1.37:g.19499954G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	117	108	0.923077	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			G|0.937;A|0.063	0.063	strong		0.428	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
LCE3D	84648	hgsc.bcm.edu	37	1	152552285	152552285	+	Missense_Mutation	SNP	C	C	A	rs512208	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152552285C>A	ENST00000368787.3	-	2	184	c.128G>T	c.(127-129)gGc>gTc	p.G43V		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	43			G -> V (in dbSNP:rs512208). {ECO:0000269|PubMed:15489334}.		keratinization (GO:0031424)			p.G43V(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		AGGGCCACAGCCCCCAGAGCT	0.662													C|||	1386	0.276757	0.1384	0.2853	5008	,	,		15854	0.3264		0.3827	False		,,,				2504	0.2975				p.G43V		Atlas-SNP	.											LCE3D,NS,carcinoma,0,1	LCE3D	28	1	1	Substitution - Missense(1)	stomach(1)	c.G128T						PASS	.	C	VAL/GLY	789,3617	316.1+/-294.4	78,633,1492	57.0	66.0	63.0		128	0.3	0.6	1	dbSNP_83	63	3138,5454	473.4+/-368.6	598,1942,1756	no	missense	LCE3D	NM_032563.1	109	676,2575,3248	AA,AC,CC		36.5223,17.9074,30.2123	benign	43/93	152552285	3927,9071	2203	4296	6499	SO:0001583	missense	84648	exon2			CCACAGCCCCCAG	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"""Late cornified envelopes"""	16615	protein-coding gene	gene with protein product		612616	"""small proline rich-like (epidermal differentiation complex) 6B"""	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.128G>T	1.37:g.152552285C>A	ENSP00000357776:p.Gly43Val	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	228	219	0.960526	NM_032563	Q3MIL1	Missense_Mutation	SNP	ENST00000368787.3	37	CCDS1014.1	655	0.2999084249084249	68	0.13821138211382114	103	0.2845303867403315	188	0.32867132867132864	296	0.39050131926121373	C	0.190	-1.053864	0.01965	0.179074	0.365223	ENSG00000163202	ENST00000368787	T	0.03982	3.74	3.63	0.259	0.15583	.	.	.	.	.	T	0.01222	0.0040	.	.	.	0.48135	P	4.089999999999927E-4	B	0.34181	0.44	B	0.33750	0.169	T	0.50294	-0.8845	7	0.34782	T	0.22	.	6.4364	0.21825	0.1979:0.4157:0.3864:0.0	rs512208	43	Q9BYE3	LCE3D_HUMAN	V	43	ENSP00000357776:G43V	ENSP00000357776:G43V	G	-	2	0	LCE3D	150818909	0.111000	0.22076	0.642000	0.29436	0.005000	0.04900	0.010000	0.13242	0.318000	0.23185	-0.929000	0.02709	GGC	C|0.986;A|0.014	0.014	weak		0.662	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563	
FAM65A	79567	hgsc.bcm.edu	37	16	67578257	67578257	+	Missense_Mutation	SNP	C	C	T	rs61744916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67578257C>T	ENST00000379312.3	+	15	2789	c.2668C>T	c.(2668-2670)Cgc>Tgc	p.R890C	FAM65A_ENST00000422602.2_Missense_Mutation_p.R906C|FAM65A_ENST00000042381.4_Missense_Mutation_p.R886C|CTD-2012K14.4_ENST00000564717.1_RNA|FAM65A_ENST00000428437.2_Missense_Mutation_p.R900C|FAM65A_ENST00000540839.3_Missense_Mutation_p.R905C|CTD-2012K14.3_ENST00000563083.1_RNA	NM_001193522.1|NM_024519.3	NP_001180451.1|NP_078795.2	Q6ZS17	FA65A_HUMAN	family with sequence similarity 65, member A	890						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39		Acute lymphoblastic leukemia(13;3.76e-06)|all_hematologic(13;0.000303)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0474)|Epithelial(162;0.117)		ACCCAGTGCCCGCCCCCTCAG	0.647													C|||	316	0.063099	0.1256	0.0288	5008	,	,		17530	0.0139		0.0547	False		,,,				2504	0.0624				p.R906C		Atlas-SNP	.											.	FAM65A	104	.	0			c.C2716T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	578,3818	253.4+/-259.3	45,488,1665	87.0	82.0	84.0		2668,2716,2698,2656	3.5	0.8	16	dbSNP_129	84	476,8124	138.9+/-195.6	19,438,3843	yes	missense,missense,missense,missense	FAM65A	NM_001193522.1,NM_001193523.1,NM_001193524.1,NM_024519.3	180,180,180,180	64,926,5508	TT,TC,CC		5.5349,13.1483,8.1102	probably-damaging,probably-damaging,probably-damaging,probably-damaging	890/1224,906/1240,900/1234,886/1220	67578257	1054,11942	2198	4300	6498	SO:0001583	missense	79567	exon15			AGTGCCCGCCCCC	AK127792	CCDS10840.1, CCDS54026.1, CCDS54027.1, CCDS54028.1	16q22.1	2008-02-05			ENSG00000039523	ENSG00000039523			25836	protein-coding gene	gene with protein product						11572484	Standard	NM_001193522		Approved	FLJ13725	uc010vjp.2	Q6ZS17	OTTHUMG00000137536	ENST00000379312.3:c.2668C>T	16.37:g.67578257C>T	ENSP00000368614:p.Arg890Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_001193523	B4DEQ9|B4DIM2|E9PBS3|Q4G0A4|Q7Z5R7|Q8NDA4|Q96J39|Q96PV8|Q9H8D9	Missense_Mutation	SNP	ENST00000379312.3	37	CCDS54028.1	123|123	0.05631868131868132|0.05631868131868132	69|69	0.1402439024390244|0.1402439024390244	8|8	0.022099447513812154|0.022099447513812154	6|6	0.01048951048951049|0.01048951048951049	40|40	0.052770448548812667|0.052770448548812667	C|C	16.45|16.45	3.126241|3.126241	0.56721|0.56721	0.131483|0.131483	0.055349|0.055349	ENSG00000039523|ENSG00000039523	ENST00000428437|ENST00000379312;ENST00000042381;ENST00000422602;ENST00000540839	.|T;T;T	.|0.80123	.|-1.34;-1.34;-1.34	5.55|5.55	3.55|3.55	0.40652|0.40652	.|.	.|0.417647	.|0.24599	.|N	.|0.037154	T|T	0.01765|0.01765	0.0056|0.0056	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	.|D;D;D	.|0.71674	.|0.998;0.998;0.998	.|P;P;P	.|0.60886	.|0.88;0.88;0.88	T|T	0.52313|0.52313	-0.8592|-0.8592	4|9	.|0.54805	.|T	.|0.06	-5.4932|-5.4932	7.5821|7.5821	0.27972|0.27972	0.0:0.5971:0.3033:0.0995|0.0:0.5971:0.3033:0.0995	rs61744916|rs61744916	.|900;906;890	.|B4DIM2;E9PBS3;Q6ZS17	.|.;.;FA65A_HUMAN	L|C	879|890;886;906;900	.|ENSP00000368614:R890C;ENSP00000042381:R886C;ENSP00000400099:R906C	.|ENSP00000042381:R886C	P|R	+|+	2|1	0|0	FAM65A|FAM65A	66135758|66135758	0.001000|0.001000	0.12720|0.12720	0.818000|0.818000	0.32626|0.32626	0.983000|0.983000	0.72400|0.72400	1.033000|1.033000	0.30191|0.30191	1.360000|1.360000	0.45960|0.45960	0.655000|0.655000	0.94253|0.94253	CCG|CGC	C|0.926;T|0.074	0.074	strong		0.647	FAM65A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268866.3	NM_024519	
CORO2A	7464	hgsc.bcm.edu	37	9	100895443	100895443	+	Silent	SNP	C	C	T	rs735111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100895443C>T	ENST00000343933.5	-	5	782	c.525G>A	c.(523-525)acG>acA	p.T175T	CORO2A_ENST00000375077.4_Silent_p.T175T	NM_003389.3	NP_003380.3	Q92828	COR2A_HUMAN	coronin, actin binding protein, 2A	175					actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)	actin cytoskeleton (GO:0015629)|transcriptional repressor complex (GO:0017053)	actin filament binding (GO:0051015)			endometrium(2)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|skin(4)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				GACAGCTAATCGTACTCATGG	0.542													C|||	293	0.0585064	0.003	0.085	5008	,	,		22045	0.0347		0.0994	False		,,,				2504	0.0971				p.T175T		Atlas-SNP	.											.	CORO2A	54	.	0			c.G525A						PASS	.	C	,	110,4296	83.9+/-122.4	2,106,2095	284.0	211.0	236.0		525,525	-7.6	0.0	9	dbSNP_86	236	993,7607	215.5+/-254.8	54,885,3361	no	coding-synonymous,coding-synonymous	CORO2A	NM_003389.3,NM_052820.3	,	56,991,5456	TT,TC,CC		11.5465,2.4966,8.4807	,	175/526,175/526	100895443	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	7464	exon5			GCTAATCGTACTC	U57057	CCDS6735.1	9q22.3	2013-01-10	2001-11-28		ENSG00000106789	ENSG00000106789		"""Coronins"", ""WD repeat domain containing"""	2255	protein-coding gene	gene with protein product	"""coronin 2A"", ""coronin-like protein B"", ""WD protein IR10"", ""WD-repeat protein 2"""	602159	"""coronin, actin-binding protein, 2A"""			8985118	Standard	NM_052820		Approved	IR10, WDR2	uc004aym.3	Q92828	OTTHUMG00000020340	ENST00000343933.5:c.525G>A	9.37:g.100895443C>T		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	163	66	0.404908	NM_003389	Q5TBR5|Q92829|Q9BWS5	Silent	SNP	ENST00000343933.5	37	CCDS6735.1																																																																																			T|0.076;G|0.006	0.076	strong		0.542	CORO2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053357.1	NM_003389	
FRAS1	80144	hgsc.bcm.edu	37	4	79443850	79443850	+	Missense_Mutation	SNP	G	G	A	rs931606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:79443850G>A	ENST00000264895.6	+	69	11136	c.10696G>A	c.(10696-10698)Gta>Ata	p.V3566I		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3562					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						GAAATCTTTCGTATTGACTCC	0.428													A|||	2559	0.510982	0.5008	0.4496	5008	,	,		19846	0.4554		0.5477	False		,,,				2504	0.5879				p.V3566I		Atlas-SNP	.											.	FRAS1	779	.	0			c.G10696A						PASS	.	A	ILE/VAL	1938,1798		511,916,441	52.0	52.0	52.0		10696	4.9	1.0	4	dbSNP_86	52	4480,3738		1193,2094,822	yes	missense	FRAS1	NM_025074.6	29	1704,3010,1263	AA,AG,GG		45.4855,48.1263,46.3109	benign	3566/4013	79443850	6418,5536	1868	4109	5977	SO:0001583	missense	80144	exon69			TCTTTCGTATTGA	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.10696G>A	4.37:g.79443850G>A	ENSP00000264895:p.Val3566Ile	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	1113|1113	0.5096153846153846|0.5096153846153846	253|253	0.5142276422764228|0.5142276422764228	169|169	0.46685082872928174|0.46685082872928174	278|278	0.486013986013986|0.486013986013986	413|413	0.5448548812664907|0.5448548812664907	A|A	1.441|1.441	-0.567626|-0.567626	0.03910|0.03910	0.518737|0.518737	0.545145|0.545145	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.15718	.|2.4	6.17|6.17	4.93|4.93	0.64822|0.64822	.|.	.|0.057659	.|0.64402	.|N	.|0.000002	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.04994|0.04994	-0.135|-0.135	0.09310|0.09310	P|P	1.0|1.0	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.45338|0.45338	-0.9268|-0.9268	4|9	.|0.02654	.|T	.|1	.|.	4.8407|4.8407	0.13489|0.13489	0.698:0.1139:0.0663:0.1218|0.698:0.1139:0.0663:0.1218	rs931606;rs56516880;rs57714648;rs931606|rs931606;rs56516880;rs57714648;rs931606	.|3566	.|E9PHH6	.|.	H|I	1794|3566	.|ENSP00000264895:V3566I	.|ENSP00000264895:V3566I	R|V	+|+	2|1	0|0	FRAS1|FRAS1	79662874|79662874	1.000000|1.000000	0.71417|0.71417	0.985000|0.985000	0.45067|0.45067	0.005000|0.005000	0.04900|0.04900	2.447000|2.447000	0.44917|0.44917	1.158000|1.158000	0.42547|0.42547	-0.254000|-0.254000	0.11334|0.11334	CGT|GTA	G|0.491;A|0.509	0.509	strong		0.428	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
EYS	346007	hgsc.bcm.edu	37	6	65301734	65301734	+	Silent	SNP	G	G	A	rs12663619	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301734G>A	ENST00000370621.3	-	26	4552	c.4026C>T	c.(4024-4026)tcC>tcT	p.S1342S	EYS_ENST00000370616.2_Silent_p.S1342S|EYS_ENST00000503581.1_Silent_p.S1342S			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1342					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AAACATCTGCGGAAGAAAGAA	0.413													G|||	470	0.0938498	0.0151	0.1182	5008	,	,		18854	0.1567		0.0984	False		,,,				2504	0.1135				p.S1342S		Atlas-SNP	.											.	EYS	527	.	0			c.C4026T						PASS	.	G		49,1335		1,47,644	134.0	119.0	124.0		4026	1.8	1.0	6	dbSNP_120	124	446,2736		41,364,1186	no	coding-synonymous	EYS	NM_001142800.1		42,411,1830	AA,AG,GG		14.0163,3.5405,10.841		1342/3145	65301734	495,4071	692	1591	2283	SO:0001819	synonymous_variant	346007	exon26			ATCTGCGGAAGAA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.4026C>T	6.37:g.65301734G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				G|0.903;A|0.097	0.097	strong		0.413	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
COL2A1	1280	hgsc.bcm.edu	37	12	48376291	48376291	+	Silent	SNP	G	G	A	rs2276454	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48376291G>A	ENST00000380518.3	-	34	2459	c.2295C>T	c.(2293-2295)ggC>ggT	p.G765G	COL2A1_ENST00000337299.6_Silent_p.G696G|COL2A1_ENST00000493991.1_5'UTR	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	765	Triple-helical region.				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)	TTACCCTGTCGCCTTTGGGCC	0.617													G|||	2152	0.429712	0.3563	0.3501	5008	,	,		18562	0.5556		0.3926	False		,,,				2504	0.4939				p.G765G		Atlas-SNP	.											.	COL2A1	368	.	0			c.C2295T						PASS	.	G	,	1535,2871	483.5+/-359.7	261,1013,929	41.0	40.0	40.0		2295,2088	1.9	1.0	12	dbSNP_100	40	3496,5104	507.9+/-376.9	679,2138,1483	no	coding-synonymous,coding-synonymous	COL2A1	NM_001844.4,NM_033150.2	,	940,3151,2412	AA,AG,GG		40.6512,34.8389,38.6821	,	765/1488,696/1419	48376291	5031,7975	2203	4300	6503	SO:0001819	synonymous_variant	1280	exon34			CCTGTCGCCTTTG	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.2295C>T	12.37:g.48376291G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	120	117	0.975	NM_001844	A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	37	CCDS41778.1																																																																																			G|0.590;A|0.410	0.410	strong		0.617	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	
TDG	6996	hgsc.bcm.edu	37	12	104380734	104380734	+	Missense_Mutation	SNP	G	G	A	rs2888805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:104380734G>A	ENST00000392872.3	+	10	1333	c.1099G>A	c.(1099-1101)Gtg>Atg	p.V367M	AC078819.1_ENST00000401157.1_RNA|TDG_ENST00000542036.1_Missense_Mutation_p.V163M|TDG_ENST00000544861.1_Missense_Mutation_p.V224M|TDG_ENST00000536395.1_3'UTR|TDG_ENST00000266775.9_Missense_Mutation_p.V363M	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	367			V -> L (in dbSNP:rs2888805).|V -> M (in dbSNP:rs2888805). {ECO:0000269|Ref.2}.		base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)			large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		AGTTGAGAGCGTGGAGTTAAG	0.408								Base excision repair (BER), DNA glycosylases					G|||	563	0.11242	0.0053	0.111	5008	,	,		26412	0.2927		0.0944	False		,,,				2504	0.091				p.V367M		Atlas-SNP	.											.	TDG	43	.	0			c.G1099A						PASS	.	G	MET/VAL	97,4309	78.3+/-116.7	0,97,2106	151.0	129.0	136.0		1099	0.2	0.0	12	dbSNP_101	136	836,7764	191.8+/-238.0	26,784,3490	yes	missense	TDG	NM_003211.4	21	26,881,5596	AA,AG,GG		9.7209,2.2015,7.1736	benign	367/411	104380734	933,12073	2203	4300	6503	SO:0001583	missense	6996	exon10			GAGAGCGTGGAGT	U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.1099G>A	12.37:g.104380734G>A	ENSP00000376611:p.Val367Met	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	79	35	0.443038	NM_003211	Q8IUZ6|Q8IZM3	Missense_Mutation	SNP	ENST00000392872.3	37	CCDS9095.1	290	0.13278388278388278	4	0.008130081300813009	40	0.11049723756906077	174	0.3041958041958042	72	0.09498680738786279	G	8.454	0.853700	0.17106	0.022015	0.097209	ENSG00000139372	ENST00000392872;ENST00000266775;ENST00000544861;ENST00000542036	T;T;T;T	0.22945	2.27;2.27;2.27;1.93	4.59	0.23	0.15372	.	2.260350	0.01803	N	0.033010	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P;B;B	0.44344	0.833;0.074;0.074	B;B;B	0.31191	0.125;0.003;0.004	T	0.27806	-1.0063	9	0.46703	T	0.11	-1.0119	1.0514	0.01581	0.177:0.308:0.2758:0.2392	rs2888805;rs4135140;rs52799886;rs59502858	163;367;367	B4DI29;B2R848;Q13569	.;.;TDG_HUMAN	M	367;363;224;163	ENSP00000376611:V367M;ENSP00000266775:V363M;ENSP00000445899:V224M;ENSP00000439054:V163M	ENSP00000266775:V363M	V	+	1	0	TDG	102904864	0.026000	0.19158	0.001000	0.08648	0.002000	0.02628	0.257000	0.18369	0.022000	0.15160	-0.152000	0.13540	GTG	G|0.908;A|0.092	0.092	strong		0.408	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2		
KNDC1	85442	hgsc.bcm.edu	37	10	135012652	135012652	+	Silent	SNP	T	T	C	rs3008388	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:135012652T>C	ENST00000304613.3	+	14	2661	c.2640T>C	c.(2638-2640)gaT>gaC	p.D880D	KNDC1_ENST00000368572.2_Silent_p.D880D|KNDC1_ENST00000368571.2_Silent_p.D815D			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	880	Pro-rich.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCTGCGTGGATGCCTCGCCAC	0.687													C|||	2060	0.411342	0.1203	0.4049	5008	,	,		11469	0.6091		0.4384	False		,,,				2504	0.5777				p.D880D		Atlas-SNP	.											KNDC1,rectum,carcinoma,0,2	KNDC1	155	2	0			c.T2640C						scavenged	.						9.0	9.0	9.0					10																	135012652		2159	4223	6382	SO:0001819	synonymous_variant	85442	exon14			CGTGGATGCCTCG	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2640T>C	10.37:g.135012652T>C		Somatic	38	1	0.0263158		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	CCDS7674.1																																																																																			T|0.587;C|0.413	0.413	strong		0.687	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
PPAN	56342	hgsc.bcm.edu	37	19	10221227	10221227	+	Missense_Mutation	SNP	C	C	T	rs139737427		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10221227C>T	ENST00000253107.7	+	10	1074	c.968C>T	c.(967-969)gCg>gTg	p.A323V	SNORD105B_ENST00000458770.1_RNA|P2RY11_ENST00000321826.4_5'Flank|PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.A323V|PPAN_ENST00000556468.1_Missense_Mutation_p.A323V|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A323V|PPAN_ENST00000393793.1_Missense_Mutation_p.A270V|SNORD105_ENST00000386910.1_RNA	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	323					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)			CGGCTGAAGGCGCAGAGGCAG	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		15026	0.0		0.001	False		,,,				2504	0.0				p.A323V		Atlas-SNP	.											.	PPAN	43	.	0			c.C968T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1,4399		0,1,2199	14.0	17.0	16.0		968,968,968	3.8	0.4	19	dbSNP_134	16	18,8574		0,18,4278	yes	missense,missense,missense	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	64,64,64	0,19,6477	TT,TC,CC		0.2095,0.0227,0.1462	possibly-damaging,possibly-damaging,possibly-damaging	323/795,323/521,323/474	10221227	19,12973	2200	4296	6496	SO:0001583	missense	56342	exon10			TGAAGGCGCAGAG	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.968C>T	19.37:g.10221227C>T	ENSP00000253107:p.Ala323Val	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	82	43	0.52439	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	37	CCDS12225.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	12.64|12.64	1.999423|1.999423	0.35320|0.35320	2.27E-4|2.27E-4	0.002095|0.002095	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810|ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793|ENST00000444703	T;T;T;T;T|.	0.63255|.	1.39;-0.03;1.42;-0.03;1.44|.	4.78|4.78	3.75|3.75	0.43078|0.43078	.|.	.|.	.|.	.|.	.|.	T|T	0.49677|0.49677	0.1571|0.1571	L|L	0.61036|0.61036	1.89|1.89	0.29207|0.29207	N|N	0.874799|0.874799	P;P;P|.	0.50710|.	0.931;0.87;0.938|.	B;B;B|.	0.33960|.	0.173;0.101;0.146|.	T|T	0.47971|0.47971	-0.9075|-0.9075	9|5	0.51188|.	T|.	0.08|.	-14.6112|-14.6112	7.0518|7.0518	0.25077|0.25077	0.1706:0.7394:0.0:0.09|0.1706:0.7394:0.0:0.09	.|.	323;323;323|.	C9J3F9;C9JW41;Q9NQ55|.	.;.;SSF1_HUMAN|.	V|C	323;323;323;323;323;270|83	ENSP00000411918:A323V;ENSP00000377385:A323V;ENSP00000253107:A323V;ENSP00000450710:A323V;ENSP00000377382:A270V|.	ENSP00000253107:A323V|.	A|R	+|+	2|1	0|0	PPAN;PPAN-P2RY11|PPAN	10082227|10082227	0.950000|0.950000	0.32346|0.32346	0.433000|0.433000	0.26760|0.26760	0.029000|0.029000	0.11900|0.11900	2.089000|2.089000	0.41672|0.41672	1.008000|1.008000	0.39264|0.39264	0.561000|0.561000	0.74099|0.74099	GCG|CGC	C|0.999;T|0.001	0.001	strong		0.667	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	
PCDHGB6	56100	hgsc.bcm.edu	37	5	140789933	140789933	+	Missense_Mutation	SNP	G	G	A	rs3749767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140789933G>A	ENST00000520790.1	+	1	2164	c.2164G>A	c.(2164-2166)Gct>Act	p.A722T	PCDHGA10_ENST00000398610.2_5'Flank|PCDHGA9_ENST00000573521.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	722			A -> T (in dbSNP:rs3749767).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCAGCCCTGCTACTTGGGA	0.542													.|||	1536	0.306709	0.5265	0.2594	5008	,	,		20334	0.1935		0.1918	False		,,,				2504	0.2781				p.A722T		Atlas-SNP	.											.	PCDHGB6	120	.	0			c.G2164A						PASS	.	A	,,,,,,,,,,,,,THR/ALA,,THR/ALA	1995,2125		483,1029,548	141.0	147.0	145.0		,,,,,,,,,,,,,2164,,2164	-10.2	0.0	5	dbSNP_107	145	1821,6585		192,1437,2574	yes	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,58,,58	675,2466,3122	AA,AG,GG		21.6631,48.4223,30.4646	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,722/931,,722/821	140789933	3816,8710	2060	4203	6263	SO:0001583	missense	56100	exon1			AGCCCTGCTACTT	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"""Cadherins / Protocadherins : Clustered"""	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.2164G>A	5.37:g.140789933G>A	ENSP00000428603:p.Ala722Thr	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	229	223	0.973799	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	620	0.2838827838827839	250	0.508130081300813	94	0.2596685082872928	117	0.20454545454545456	159	0.20976253298153033	a	5.515	0.279981	0.10458	0.484223	0.216631	ENSG00000253305	ENST00000520790	T	0.14391	2.51	5.11	-10.2	0.00374	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.12837	0.003;0.008	T	0.37957	-0.9683	8	0.30854	T	0.27	.	14.1643	0.65466	0.1425:0.0:0.6368:0.2208	rs3749767;rs52817710;rs61103125;rs3749767	722;722	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	T	722	ENSP00000428603:A722T	ENSP00000428603:A722T	A	+	1	0	PCDHGB6	140770117	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.063000	0.01388	-3.157000	0.00229	-2.917000	0.00090	GCT	G|0.702;A|0.298	0.298	strong		0.542	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
MUC16	94025	hgsc.bcm.edu	37	19	9066874	9066874	+	Missense_Mutation	SNP	G	G	T	rs12609150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9066874G>T	ENST00000397910.4	-	3	20775	c.20572C>A	c.(20572-20574)Cca>Aca	p.P6858T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6860	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						CTCAAATTTGGAGGTGAACTG	0.493													g|||	1007	0.201078	0.0946	0.2824	5008	,	,		23077	0.3254		0.167	False		,,,				2504	0.1943				p.P6858T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C20572A						PASS	.	G	THR/PRO	425,3671		18,389,1641	163.0	154.0	157.0		20572	-3.0	0.0	19	dbSNP_120	157	1520,6886		138,1244,2821	yes	missense	MUC16	NM_024690.2	38	156,1633,4462	TT,TG,GG		18.0823,10.376,15.5575	probably-damaging	6858/14508	9066874	1945,10557	2048	4203	6251	SO:0001583	missense	94025	exon3			AATTTGGAGGTGA	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.20572C>A	19.37:g.9066874G>T	ENSP00000381008:p.Pro6858Thr	Somatic	327	0	0		WXS	Illumina HiSeq	Phase_I	321	148	0.461059	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	479	0.21932234432234432	56	0.11382113821138211	92	0.2541436464088398	205	0.3583916083916084	126	0.1662269129287599	g	2.557	-0.302824	0.05495	0.10376	0.180823	ENSG00000181143	ENST00000397910	T	0.26067	1.76	2.12	-2.96	0.05547	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	.	.	.	B	0.27351	0.176	B	0.19946	0.027	T	0.45381	-0.9265	8	0.87932	D	0	.	2.1735	0.03856	0.4264:0.0:0.3309:0.2427	rs12609150;rs52836809;rs12609150	6858	B5ME49	.	T	6858	ENSP00000381008:P6858T	ENSP00000381008:P6858T	P	-	1	0	MUC16	8927874	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.960000	0.03849	-0.553000	0.06158	-0.513000	0.04457	CCA	G|0.786;T|0.214	0.214	strong		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
LAG3	3902	hgsc.bcm.edu	37	12	6887020	6887020	+	Missense_Mutation	SNP	T	T	C	rs870849	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:6887020T>C	ENST00000203629.2	+	7	1697	c.1364T>C	c.(1363-1365)aTc>aCc	p.I455T		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	455			I -> T (in dbSNP:rs870849). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:1692078, ECO:0000269|Ref.5}.		cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CTGTTTCTCATCCTTGGTGTC	0.587													C|||	3352	0.669329	0.5787	0.6816	5008	,	,		18490	0.8224		0.6093	False		,,,				2504	0.6871				p.I455T		Atlas-SNP	.											.	LAG3	35	.	0			c.T1364C						PASS	.	C	THR/ILE	2446,1960	554.9+/-379.1	664,1118,421	126.0	119.0	122.0		1364	-1.6	0.5	12	dbSNP_86	122	5337,3263	490.0+/-372.8	1639,2059,602	yes	missense	LAG3	NM_002286.5	89	2303,3177,1023	CC,CT,TT		37.9419,44.4848,40.1584	probably-damaging	455/526	6887020	7783,5223	2203	4300	6503	SO:0001583	missense	3902	exon7			TTCTCATCCTTGG		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.1364T>C	12.37:g.6887020T>C	ENSP00000203629:p.Ile455Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	40	0.377358	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	1449	0.6634615384615384	284	0.5772357723577236	244	0.6740331491712708	468	0.8181818181818182	453	0.5976253298153035	C	7.987	0.752530	0.15778	0.555152	0.620581	ENSG00000089692	ENST00000203629	T	0.14022	2.54	5.32	-1.58	0.08479	.	0.572954	0.17583	N	0.169023	T	0.00012	0.0000	M	0.72118	2.19	0.37484	P	0.08388200000000001	B	0.14438	0.01	B	0.08055	0.003	T	0.11518	-1.0584	9	0.72032	D	0.01	-1.9933	6.0127	0.19584	0.0:0.4413:0.2095:0.3492	rs870849;rs1049127;rs3168603;rs59016819;rs870849	455	P18627	LAG3_HUMAN	T	455	ENSP00000203629:I455T	ENSP00000203629:I455T	I	+	2	0	LAG3	6757281	0.732000	0.28121	0.460000	0.27093	0.016000	0.09150	0.034000	0.13776	-0.208000	0.10171	-0.550000	0.04213	ATC	T|0.375;C|0.625	0.625	strong		0.587	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1		
GBP1	2633	hgsc.bcm.edu	37	1	89525966	89525966	+	Missense_Mutation	SNP	T	T	C	rs1048401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89525966T>C	ENST00000370473.4	-	3	451	c.232A>G	c.(232-234)Atc>Gtc	p.I78V		NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	78	GB1/RHD3-type G.|GTPase domain (Globular).		I -> V (in dbSNP:rs1048401).		cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		CACATCCAGATTCCTTTAGTG	0.552													.|||	222	0.0443291	0.0083	0.2075	5008	,	,		16425	0.001		0.0358	False		,,,				2504	0.0307				p.I78V		Atlas-SNP	.											.	GBP1	68	.	0			c.A232G						PASS	.	T	VAL/ILE	78,4328	69.2+/-107.0	0,78,2125	110.0	105.0	107.0		232	4.4	1.0	1	dbSNP_86	107	293,8307	107.8+/-168.5	2,289,4009	no	missense	GBP1	NM_002053.2	29	2,367,6134	CC,CT,TT		3.407,1.7703,2.8525	probably-damaging	78/593	89525966	371,12635	2203	4300	6503	SO:0001583	missense	2633	exon3			TCCAGATTCCTTT	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.232A>G	1.37:g.89525966T>C	ENSP00000359504:p.Ile78Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	135	61	0.451852	NM_002053	D3DT26|Q5T8M1	Missense_Mutation	SNP	ENST00000370473.4	37	CCDS718.1	87	0.03983516483516483	6	0.012195121951219513	51	0.1408839779005525	0	0.0	30	0.0395778364116095	T	19.50	3.839882	0.71488	0.017703	0.03407	ENSG00000117228	ENST00000370473;ENST00000542693	T	0.81078	-1.45	4.45	4.45	0.53987	Guanylate-binding protein, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.87204	0.6119	M	0.85777	2.775	0.34624	P	0.28111299999999995	D	0.89917	1.0	D	0.81914	0.995	D	0.89805	0.3978	9	0.87932	D	0	.	11.6498	0.51282	0.0:0.0:0.0:1.0	rs1048401;rs52807217;rs1048401	78	P32455	GBP1_HUMAN	V	78;41	ENSP00000359504:I78V	ENSP00000359504:I78V	I	-	1	0	GBP1	89298554	1.000000	0.71417	0.998000	0.56505	0.801000	0.45260	6.054000	0.71096	1.649000	0.50652	0.260000	0.18958	ATC	T|0.960;C|0.040	0.040	strong		0.552	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1817367	1817367	+	Silent	SNP	G	G	A	rs7003969	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:1817367G>A	ENST00000398564.1	+	7	705	c.705G>A	c.(703-705)gaG>gaA	p.E235E	ARHGEF10_ENST00000518288.1_Silent_p.E235E|ARHGEF10_ENST00000520359.1_Silent_p.E211E|ARHGEF10_ENST00000349830.3_Silent_p.E210E|ARHGEF10_ENST00000262112.6_Silent_p.E235E|ARHGEF10_ENST00000398560.1_Silent_p.E235E			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	235					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)		CAGATCCAGAGGAAGCAATTT	0.428													A|||	1181	0.235823	0.0983	0.2061	5008	,	,		18247	0.5179		0.2157	False		,,,				2504	0.1728				p.E210E		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.G630A						PASS	.	A		509,3897	778.8+/-414.3	28,453,1722	117.0	114.0	115.0		630	2.0	1.0	8	dbSNP_116	115	2033,6567	720.2+/-406.3	255,1523,2522	no	coding-synonymous	ARHGEF10	NM_014629.2		283,1976,4244	AA,AG,GG		23.6395,11.5524,19.5448		210/1345	1817367	2542,10464	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon7			TCCAGAGGAAGCA	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.705G>A	8.37:g.1817367G>A		Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	166	164	0.987952	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				G|0.777;A|0.223	0.223	strong		0.428	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
VTN	7448	hgsc.bcm.edu	37	17	26694483	26694483	+	Silent	SNP	A	A	G	rs2227728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:26694483A>G	ENST00000226218.4	-	8	1962	c.1344T>C	c.(1342-1344)aaT>aaC	p.N448N	VTN_ENST00000431468.1_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA|VTN_ENST00000536498.1_Missense_Mutation_p.I32T|TMEM199_ENST00000509083.1_Intron|VTN_ENST00000438614.1_Missense_Mutation_p.I32T|CTB-96E2.2_ENST00000555059.2_Silent_p.N106N|SARM1_ENST00000379061.4_Intron	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	448					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GTGTGCGAAGATTGACTCGGT	0.602													G|||	779	0.155551	0.1596	0.0821	5008	,	,		19913	0.245		0.0785	False		,,,				2504	0.1892				p.N448N		Atlas-SNP	.											.	VTN	45	.	0			c.T1344C						PASS	.	G		647,3759	762.5+/-413.1	50,547,1606	128.0	106.0	113.0		1344	3.3	1.0	17	dbSNP_98	113	701,7899	786.9+/-407.6	31,639,3630	no	coding-synonymous	VTN	NM_000638.3		81,1186,5236	GG,GA,AA		8.1512,14.6845,10.3644		448/479	26694483	1348,11658	2203	4300	6503	SO:0001819	synonymous_variant	7448	exon8			GCGAAGATTGACT	BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"""Endogenous ligands"""	12724	protein-coding gene	gene with protein product	"""serum spreading factor"", ""somatomedin B"", ""complement S-protein"""	193190	"""vitronectin (serum spreading factor, somatomedin B, complement S-protein)"""			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.1344T>C	17.37:g.26694483A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	127	52	0.409449	NM_000638	B2R7G0|P01141|Q9BSH7	Silent	SNP	ENST00000226218.4	37	CCDS11229.1	278	0.12728937728937728	87	0.17682926829268292	36	0.09944751381215469	100	0.17482517482517482	55	0.07255936675461741	G	9.371	1.070412	0.20147	0.146845	0.081512	ENSG00000109072;ENSG00000109072;ENSG00000258852	ENST00000536498;ENST00000438614;ENST00000555059	D;D	0.91351	-2.83;-2.83	5.27	3.28	0.37604	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	7	0.13108	T	0.6	-46.27	8.5936	0.33701	0.2913:0.0:0.7087:0.0	rs2227728;rs57255300;rs2227728	32	C9JDG5	.	T	32;32;58	ENSP00000444503:I32T;ENSP00000395142:I32T	ENSP00000395142:I32T	I	-	2	0	VTN;CTB-96E2.2	23718610	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.941000	0.40233	0.381000	0.24851	-0.186000	0.12905	ATC	A|0.881;G|0.119	0.119	strong		0.602	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638	
ANKRD35	148741	hgsc.bcm.edu	37	1	145561594	145561594	+	Missense_Mutation	SNP	C	C	T	rs6670984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145561594C>T	ENST00000355594.4	+	10	1369	c.1282C>T	c.(1282-1284)Ccc>Tcc	p.P428S		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	428			P -> S (in dbSNP:rs6670984). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					ACAGGGGCCACCCCAGAGCCC	0.547													C|||	2828	0.564696	0.5794	0.5043	5008	,	,		18882	0.7252		0.3797	False		,,,				2504	0.6125				p.P428S	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.C1282T						PASS	.	C	SER/PRO	2326,2080	586.9+/-386.6	613,1100,490	60.0	71.0	67.0		1282	-3.1	0.0	1	dbSNP_116	67	3163,5437	473.4+/-368.6	572,2019,1709	yes	missense	ANKRD35	NM_144698.3	74	1185,3119,2199	TT,TC,CC		36.7791,47.2084,42.2036	benign	428/1002	145561594	5489,7517	2203	4300	6503	SO:0001583	missense	148741	exon10			GGGCCACCCCAGA	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1282C>T	1.37:g.145561594C>T	ENSP00000347802:p.Pro428Ser	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	1154	0.5283882783882784	275	0.5589430894308943	169	0.46685082872928174	419	0.7325174825174825	291	0.3839050131926121	C	2.083	-0.410284	0.04799	0.527916	0.367791	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.64991	-0.13	5.21	-3.07	0.05363	.	1.124390	0.06867	N	0.800111	T	0.21674	0.0522	L	0.41027	1.25	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.05273	-1.0895	9	0.08837	T	0.75	0.4115	6.7985	0.23738	0.0:0.4134:0.1204:0.4661	rs6670984;rs57708309;rs6670984	428	Q8N283	ANR35_HUMAN	S	337;428	ENSP00000347802:P428S	ENSP00000347802:P428S	P	+	1	0	ANKRD35	144272951	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.280000	0.18790	-0.485000	0.06754	-0.140000	0.14226	CCC	C|0.526;T|0.474	0.474	strong		0.547	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
ATP10A	57194	hgsc.bcm.edu	37	15	25924539	25924539	+	Silent	SNP	T	T	C	rs1047700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:25924539T>C	ENST00000356865.6	-	21	4560	c.4449A>G	c.(4447-4449)caA>caG	p.Q1483Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1483					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GGTCTGGCCCTTGAAGTCCTG	0.473													C|||	1334	0.266374	0.4153	0.3386	5008	,	,		13468	0.2748		0.1382	False		,,,				2504	0.137				p.Q1483Q		Atlas-SNP	.											.	ATP10A	270	.	0			c.A4449G						PASS	.	C		1631,2775	643.7+/-397.9	298,1035,870	58.0	63.0	61.0		4449	-4.4	0.0	15	dbSNP_86	61	1339,7261	749.9+/-407.4	99,1141,3060	no	coding-synonymous	ATP10A	NM_024490.3		397,2176,3930	CC,CT,TT		15.5698,37.0177,22.8356		1483/1500	25924539	2970,10036	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon21			TGGCCCTTGAAGT	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.4449A>G	15.37:g.25924539T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			T|0.749;C|0.251	0.251	strong		0.473	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
ZHX2	22882	hgsc.bcm.edu	37	8	123964431	123964431	+	Silent	SNP	G	G	A	rs3204141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:123964431G>A	ENST00000314393.4	+	3	1516	c.681G>A	c.(679-681)tcG>tcA	p.S227S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	227	Required for homodimerization.				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)	p.S227S(1)		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)			AGATCCTCTCGAGACTCGGCG	0.597													G|||	1162	0.232029	0.0174	0.3256	5008	,	,		17175	0.1319		0.3549	False		,,,				2504	0.4325				p.S227S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											ZHX2,NS,carcinoma,0,1	ZHX2	106	1	1	Substitution - coding silent(1)	stomach(1)	c.G681A						scavenged	.	G		323,4083	170.5+/-200.9	11,301,1891	112.0	120.0	117.0		681	-6.4	0.5	8	dbSNP_105	117	2984,5616	462.5+/-365.7	510,1964,1826	no	coding-synonymous	ZHX2	NM_014943.3		521,2265,3717	AA,AG,GG		34.6977,7.3309,25.4267		227/838	123964431	3307,9699	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CCTCTCGAGACTC	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.681G>A	8.37:g.123964431G>A		Somatic	115	1	0.00869565		WXS	Illumina HiSeq	Phase_I	129	74	0.573643	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.767;A|0.233	0.233	strong		0.597	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
C9orf163	158055	hgsc.bcm.edu	37	9	139378914	139378914	+	Missense_Mutation	SNP	T	T	C	rs34376913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139378914T>C	ENST00000354376.1	+	1	968	c.14T>C	c.(13-15)cTc>cCc	p.L5P		NM_152571.2	NP_689784.1	Q8N9P6	CI163_HUMAN	chromosome 9 open reading frame 163	5			L -> P (in dbSNP:rs34376913).							kidney(1)|lung(1)	2		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.36e-06)|Epithelial(140;5.65e-06)		CCGGGCCCACTCACCTGCACA	0.682													T|||	759	0.151558	0.1021	0.2622	5008	,	,		15559	0.0536		0.2535	False		,,,				2504	0.136				p.L5P		Atlas-SNP	.											.	C9orf163	9	.	0			c.T14C						PASS	.	T	PRO/LEU	360,3524		12,336,1594	3.0	4.0	4.0		14	3.0	1.0	9	dbSNP_126	4	1520,6274		100,1320,2477	yes	missense	C9orf163	NM_152571.2	98	112,1656,4071	CC,CT,TT		19.5022,9.2688,16.0986	probably-damaging	5/204	139378914	1880,9798	1942	3897	5839	SO:0001583	missense	158055	exon1			GCCCACTCACCTG	AK055336	CCDS7001.1	9q34.3	2006-03-21			ENSG00000196366	ENSG00000196366			26718	protein-coding gene	gene with protein product							Standard	NM_152571		Approved	FLJ36779	uc004chy.3	Q8N9P6	OTTHUMG00000131725	ENST00000354376.1:c.14T>C	9.37:g.139378914T>C	ENSP00000346345:p.Leu5Pro	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	43	20	0.465116	NM_152571		Missense_Mutation	SNP	ENST00000354376.1	37	CCDS7001.1	370	0.16941391941391942	46	0.09349593495934959	86	0.23756906077348067	44	0.07692307692307693	194	0.2559366754617414	T	12.10	1.836893	0.32421	0.092688	0.195022	ENSG00000196366	ENST00000354376	T	0.57752	0.38	3.0	3.0	0.34707	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.22819	P	0.9986933	D	0.89917	1.0	D	0.79108	0.992	T	0.09640	-1.0665	8	0.87932	D	0	.	7.79	0.29114	0.0:0.0:0.0:1.0	rs34376913	5	Q8N9P6	CI163_HUMAN	P	5	ENSP00000346345:L5P	ENSP00000346345:L5P	L	+	2	0	C9orf163	138498735	0.348000	0.24861	0.981000	0.43875	0.387000	0.30353	0.664000	0.25068	1.621000	0.50320	0.459000	0.35465	CTC	T|0.830;C|0.170	0.170	strong		0.682	C9orf163-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254644.1	NM_152571	
GALNT15	117248	hgsc.bcm.edu	37	3	16268974	16268974	+	Silent	SNP	T	T	A	rs15767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:16268974T>A	ENST00000339732.5	+	10	2390	c.1887T>A	c.(1885-1887)cgT>cgA	p.R629R	GALNT15_ENST00000437509.1_Intron	NM_054110.4	NP_473451.3	Q8N3T1	GLT15_HUMAN	polypeptide N-acetylgalactosaminyltransferase 15	629	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										AGCAGTGGCGTTTTGACCAGA	0.443													A|||	1808	0.361022	0.5287	0.3876	5008	,	,		18046	0.2034		0.3887	False		,,,				2504	0.2495				p.R629R		Atlas-SNP	.											GALNTL2,colon,carcinoma,0,4	.	.	4	0			c.T1887A						PASS	.	A		2148,2258	596.7+/-388.7	516,1116,571	125.0	123.0	123.0		1887	-2.8	0.5	3	dbSNP_52	123	3240,5360	650.3+/-400.7	610,2020,1670	no	coding-synonymous	GALNTL2	NM_054110.4		1126,3136,2241	AA,AT,TT		37.6744,48.7517,41.427		629/640	16268974	5388,7618	2203	4300	6503	SO:0001819	synonymous_variant	117248	exon10			GTGGCGTTTTGAC	AY358443	CCDS33711.1	3p25.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000131386	ENSG00000131386	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	21531	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 15"""	615131	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 2"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"""	GALNTL2		12975309, 14702039, 15147861	Standard	NM_054110		Approved	GALNT7, pp-GalNAc-T15	uc003car.4	Q8N3T1	OTTHUMG00000156893	ENST00000339732.5:c.1887T>A	3.37:g.16268974T>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	75	75	1	NM_054110	A6NMN1|B2R638|F1LIP6|Q86T60|Q96C46|Q96DJ5	Silent	SNP	ENST00000339732.5	37	CCDS33711.1	850	0.3891941391941392	277	0.5630081300813008	157	0.43370165745856354	129	0.22552447552447552	287	0.3786279683377309	A	2.572	-0.299389	0.05532	0.487517	0.376744	ENSG00000131386	ENST00000543679	.	.	.	5.4	-2.78	0.05859	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.19575	P	0.9999670301	.	.	.	.	.	.	T	0.44802	-0.9304	4	0.37606	T	0.19	.	7.3671	0.26779	0.413:0.0:0.4636:0.1233	rs15767;rs712871;rs1394909;rs3188637;rs17356739;rs15767	.	.	.	D	159	.	ENSP00000445852:V159D	V	+	2	0	GALNTL2	16243978	0.001000	0.12720	0.540000	0.28089	0.098000	0.18820	-0.374000	0.07484	-0.719000	0.04942	-0.257000	0.10917	GTT	T|0.600;A|0.400	0.400	strong		0.443	GALNT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346483.2	NM_054110	
UBAP2	55833	hgsc.bcm.edu	37	9	33971740	33971740	+	Silent	SNP	A	A	G	rs3739690	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:33971740A>G	ENST00000379238.1	-	8	705	c.588T>C	c.(586-588)ccT>ccC	p.P196P	UBAP2_ENST00000379239.4_Intron|UBAP2_ENST00000449054.1_Silent_p.P196P|UBAP2_ENST00000418786.2_Intron|UBAP2_ENST00000539807.1_Intron|UBAP2_ENST00000360802.1_Silent_p.P196P					ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		AATAGTCTGCAGGATTAAATG	0.388													A|||	1427	0.284944	0.0923	0.2824	5008	,	,		19743	0.6101		0.2396	False		,,,				2504	0.2587				p.P196P		Atlas-SNP	.											.	UBAP2	82	.	0			c.T588C						PASS	.	A		509,3897	234.9+/-247.6	31,447,1725	86.0	88.0	87.0		588	4.5	1.0	9	dbSNP_107	87	1860,6740	329.7+/-318.9	212,1436,2652	no	coding-synonymous	UBAP2	NM_018449.2		243,1883,4377	GG,GA,AA		21.6279,11.5524,18.2147		196/1120	33971740	2369,10637	2203	4300	6503	SO:0001819	synonymous_variant	55833	exon8			GTCTGCAGGATTA	AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379238.1:c.588T>C	9.37:g.33971740A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_018449		Silent	SNP	ENST00000379238.1	37	CCDS6547.1																																																																																			A|0.762;G|0.238	0.238	strong		0.388	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449	
INPP5A	3632	hgsc.bcm.edu	37	10	134540400	134540400	+	Silent	SNP	C	C	T	rs945943	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134540400C>T	ENST00000368594.3	+	9	1000	c.723C>T	c.(721-723)tcC>tcT	p.S241S	INPP5A_ENST00000487614.1_3'UTR|INPP5A_ENST00000368593.3_Silent_p.S241S	NM_005539.3	NP_005530.3	Q14642	I5P1_HUMAN	inositol polyphosphate-5-phosphatase, 40kDa	241					inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	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)|PH domain binding (GO:0042731)			cervix(1)|kidney(1)|large_intestine(2)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15		all_cancers(35;8.59e-13)|all_epithelial(44;5.49e-09)|Lung NSC(174;0.000854)|all_lung(145;0.00146)|all_neural(114;0.0299)|Colorectal(31;0.0599)|Breast(234;0.0849)|Melanoma(40;0.124)|all_hematologic(284;0.196)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;0.000102)|Epithelial(32;0.00023)|all cancers(32;0.000326)		ATTCCAAGTCCGTCGTGGAGG	0.502													C|||	340	0.0678914	0.1316	0.0432	5008	,	,		19605	0.003		0.0775	False		,,,				2504	0.0562				p.S241S	Pancreas(63;823 1267 11107 20380 51626)	Atlas-SNP	.											.	INPP5A	77	.	0			c.C723T						PASS	.	C		535,3871	240.9+/-251.5	39,457,1707	121.0	113.0	116.0		723	-4.2	0.9	10	dbSNP_86	116	745,7855	179.9+/-228.9	27,691,3582	no	coding-synonymous	INPP5A	NM_005539.3		66,1148,5289	TT,TC,CC		8.6628,12.1425,9.8416		241/413	134540400	1280,11726	2203	4300	6503	SO:0001819	synonymous_variant	3632	exon9			CAAGTCCGTCGTG	X77567	CCDS7669.2	10q26.3	2008-08-07	2002-08-29		ENSG00000068383	ENSG00000068383	3.1.3.56		6076	protein-coding gene	gene with protein product	"""CTCL tumor antigen HD-CL-02"", ""43 kDa inositol polyphosphate 5-phophatase"", ""inositol polyphosphate 5-phophatase, 40kDa"", ""InsP3 5-phosphatase"", ""type I inositol-1,4,5-trisphosphate 5-phosphatase"""	600106	"""inositol polyphosphate-5-phosphatase, 40kD"""			8013665	Standard	NM_005539		Approved	5PTASE	uc001llp.3	Q14642	OTTHUMG00000019293	ENST00000368594.3:c.723C>T	10.37:g.134540400C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	79	29	0.367089	NM_005539	D3DXI3|Q14640|Q5JSF1	Silent	SNP	ENST00000368594.3	37	CCDS7669.2	124	0.056776556776556776	48	0.0975609756097561	18	0.049723756906077346	1	0.0017482517482517483	57	0.07519788918205805	C	6.915	0.538493	0.13250	0.121425	0.086628	ENSG00000068383	ENST00000342652	.	.	.	4.17	-4.22	0.03800	.	.	.	.	.	T	0.00384	0.0012	.	.	.	0.09310	P	0.9999999999999446	.	.	.	.	.	.	T	0.21827	-1.0234	3	.	.	.	-8.5713	5.8861	0.18882	0.1336:0.6069:0.0994:0.1601	rs945943;rs2230389;rs60033225;rs945943	.	.	.	C	213	.	.	R	+	1	0	INPP5A	134390390	0.844000	0.29557	0.947000	0.38551	0.718000	0.41266	-0.174000	0.09839	-0.803000	0.04415	-1.513000	0.00942	CGT	C|0.917;T|0.083	0.083	strong		0.502	INPP5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051085.1	NM_005539	
HPSE	10855	hgsc.bcm.edu	37	4	84222208	84222208	+	Silent	SNP	A	A	G	rs11031	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:84222208A>G	ENST00000405413.2	-	12	1513	c.1377T>C	c.(1375-1377)aaT>aaC	p.N459N	HPSE_ENST00000311412.5_Silent_p.N459N|HPSE_ENST00000512196.1_Silent_p.N385N|HPSE_ENST00000513463.1_Silent_p.N401N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	459					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	ACTTGGTGACATTATGGAGGT	0.353													A|||	426	0.0850639	0.3064	0.0259	5008	,	,		18825	0.0		0.003	False		,,,				2504	0.0				p.N459N		Atlas-SNP	.											.	HPSE	55	.	0			c.T1377C						PASS	.	A	,,,	1123,3283	402.2+/-332.3	156,811,1236	119.0	126.0	123.0		1377,1155,1203,1377	-3.8	1.0	4	dbSNP_52	123	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	,,,	156,829,5518	GG,GA,AA		0.2093,25.488,8.7729	,,,	459/544,385/470,401/486,459/544	84222208	1141,11865	2203	4300	6503	SO:0001819	synonymous_variant	10855	exon11			GGTGACATTATGG	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1377T>C	4.37:g.84222208A>G		Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			A|0.911;G|0.089	0.089	strong		0.353	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
RFT1	91869	hgsc.bcm.edu	37	3	53159970	53159970	+	Missense_Mutation	SNP	A	A	G	rs146354877	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:53159970A>G	ENST00000296292.3	-	2	165	c.104T>C	c.(103-105)aTt>aCt	p.I35T	RFT1_ENST00000394738.3_Missense_Mutation_p.I35T	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	35					carbohydrate transport (GO:0008643)|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)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		GAAGCGAAGAATAAATGCATT	0.413																																					p.I35T		Atlas-SNP	.											.	RFT1	34	.	0			c.T104C						PASS	.	A	THR/ILE	1,4405	2.1+/-5.4	0,1,2202	114.0	92.0	99.0		104	3.7	1.0	3	dbSNP_134	99	0,8600		0,0,4300	yes	missense	RFT1	NM_052859.3	89	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	35/542	53159970	1,13005	2203	4300	6503	SO:0001583	missense	91869	exon2			CGAAGAATAAATG	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"""congenital disorder of glycosylation 1N"""	611908	"""RFT1, requiring fifty three 1 homolog (S. cerevisiae)"""			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.104T>C	3.37:g.53159970A>G	ENSP00000296292:p.Ile35Thr	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	92	35	0.380435	NM_052859	Q96J03	Missense_Mutation	SNP	ENST00000296292.3	37	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.073820	0.36566	2.27E-4	0.0	ENSG00000163933	ENST00000296292;ENST00000394738;ENST00000467048	D;D;D	0.86497	-2.13;-2.13;-2.13	6.02	3.71	0.42584	.	0.103749	0.64402	D	0.000005	T	0.73799	0.3633	N	0.16790	0.44	0.33518	D	0.591968	B;B	0.17465	0.022;0.003	B;B	0.17433	0.018;0.01	T	0.72178	-0.4369	10	0.35671	T	0.21	.	6.0431	0.19746	0.7465:0.0:0.2535:0.0	.	35;35	B5MDE0;Q96AA3	.;RFT1_HUMAN	T	35	ENSP00000296292:I35T;ENSP00000378223:I35T;ENSP00000420325:I35T	ENSP00000296292:I35T	I	-	2	0	RFT1	53135010	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.784000	0.62411	2.304000	0.77564	0.528000	0.53228	ATT	A|0.999;G|0.001	0.001	strong		0.413	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859	
MUC16	94025	hgsc.bcm.edu	37	19	9046876	9046876	+	Missense_Mutation	SNP	G	G	T	rs4804378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9046876G>T	ENST00000397910.4	-	5	34958	c.34755C>A	c.(34753-34755)agC>agA	p.S11585R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11587	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						AAACCGTTGTGCTGGTTTCTG	0.522													G|||	927	0.185104	0.062	0.2752	5008	,	,		23096	0.3363		0.167	False		,,,				2504	0.1503				p.S11585R		Atlas-SNP	.											.	MUC16	4315	.	0			c.C34755A						PASS	.		ARG/SER	303,3659		15,273,1693	137.0	134.0	135.0		34755	-0.2	0.0	19	dbSNP_111	135	1507,6803		139,1229,2787	yes	missense	MUC16	NM_024690.2	110	154,1502,4480	TT,TG,GG		18.1348,7.6477,14.749	benign	11585/14508	9046876	1810,10462	1981	4155	6136	SO:0001583	missense	94025	exon5			CGTTGTGCTGGTT	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.34755C>A	19.37:g.9046876G>T	ENSP00000381008:p.Ser11585Arg	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	128	65	0.507812	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	464	0.21245421245421245	34	0.06910569105691057	91	0.2513812154696133	213	0.3723776223776224	126	0.1662269129287599	g	4.341	0.062787	0.08388	0.076477	0.181348	ENSG00000181143	ENST00000397910	T	0.03181	4.02	2.29	-0.244	0.13031	.	.	.	.	.	T	0.00012	0.0000	L	0.58101	1.795	.	.	.	B	0.30889	0.299	B	0.24394	0.053	T	0.45659	-0.9246	8	0.87932	D	0	.	4.6081	0.12387	0.0:0.1924:0.3015:0.506	rs4804378;rs52826356;rs57949188;rs4804378	11585	B5ME49	.	R	11585	ENSP00000381008:S11585R	ENSP00000381008:S11585R	S	-	3	2	MUC16	8907876	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.329000	0.02677	-0.010000	0.14271	0.197000	0.17608	AGC	G|0.807;T|0.193	0.193	strong		0.522	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MLNR	2862	hgsc.bcm.edu	37	13	49794650	49794650	+	Silent	SNP	C	C	A	rs9568169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:49794650C>A	ENST00000218721.1	+	1	177	c.177C>A	c.(175-177)acC>acA	p.T59T	MLNR_ENST00000398307.1_Silent_p.T59T	NM_001507.1	NP_001498.1	O43193	MTLR_HUMAN	motilin receptor	59					digestion (GO:0007586)|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)|growth hormone-releasing hormone receptor activity (GO:0016520)			endometrium(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)	14		all_lung(13;8.31e-06)|Lung NSC(96;0.000251)|Breast(56;0.0008)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;6.1e-09)		ACGTGGTGACCGTGATGCTGA	0.677													C|||	1910	0.38139	0.3162	0.3012	5008	,	,		12433	0.4702		0.2932	False		,,,				2504	0.5256				p.T59T		Atlas-SNP	.											MLNR,NS,carcinoma,0,1	MLNR	26	1	0			c.C177A						PASS	.	C		1252,3154		179,894,1130	89.0	57.0	68.0		177	-8.3	0.9	13	dbSNP_119	68	2673,5927		400,1873,2027	no	coding-synonymous	MLNR	NM_001507.1		579,2767,3157	AA,AC,CC		31.0814,28.4158,30.1784		59/413	49794650	3925,9081	2203	4300	6503	SO:0001819	synonymous_variant	2862	exon1			GGTGACCGTGATG	AF034632	CCDS9414.1	13q14-q21	2012-08-08	2004-05-27	2004-05-28	ENSG00000102539	ENSG00000102539		"""GPCR / Class A : Motilin receptors"""	4495	protein-coding gene	gene with protein product		602885	"""G protein-coupled receptor 38"""	GPR38		9441746	Standard	NM_001507		Approved		uc010tgj.2	O43193	OTTHUMG00000016909	ENST00000218721.1:c.177C>A	13.37:g.49794650C>A		Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	50	25	0.5	NM_001507		Silent	SNP	ENST00000218721.1	37	CCDS9414.1																																																																																			C|0.676;A|0.324	0.324	strong		0.677	MLNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044897.1	NM_001507	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919963	12919963	+	Missense_Mutation	SNP	T	T	G	rs72472699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12919963T>G	ENST00000240189.2	+	3	790	c.703T>G	c.(703-705)Tgc>Ggc	p.C235G		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	235					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAAGACTCTTTGCAAACTCGT	0.428													.|||	689	0.13758	0.1422	0.1614	5008	,	,		22517	0.1438		0.1302	False		,,,				2504	0.1155				p.C235G		Atlas-SNP	.											PRAMEF2,lymph_node,lymphoid_neoplasm,0,1	PRAMEF2	85	1	0			c.T703G						scavenged	.						109.0	113.0	112.0					1																	12919963		2203	4299	6502	SO:0001583	missense	65122	exon3			ACTCTTTGCAAAC		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.703T>G	1.37:g.12919963T>G	ENSP00000240189:p.Cys235Gly	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	133	11	0.0827068	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	561	0.25686813186813184	106	0.21544715447154472	76	0.20994475138121546	148	0.25874125874125875	231	0.30474934036939316	G	2.175	-0.388896	0.04932	.	.	ENSG00000120952	ENST00000240189	T	0.14516	2.5	0.842	-0.163	0.13363	.	2.817050	0.01348	N	0.011788	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44847	-0.9301	9	0.42905	T	0.14	.	2.5682	0.04788	0.0:0.4409:0.318:0.2411	.	235	O60811	PRAM2_HUMAN	G	235	ENSP00000240189:C235G	ENSP00000240189:C235G	C	+	1	0	PRAMEF2	12842550	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.855000	0.04295	-0.611000	0.05709	-3.628000	0.00027	TGC	T|0.756;G|0.244	0.244	strong		0.428	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
ZBTB1	22890	hgsc.bcm.edu	37	14	64988924	64988924	+	Silent	SNP	T	T	C	rs10133411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:64988924T>C	ENST00000554015.1	+	4	1133	c.702T>C	c.(700-702)caT>caC	p.H234H	ZBTB1_ENST00000394712.2_Silent_p.H234H|RP11-973N13.4_ENST00000554918.1_RNA|ZBTB1_ENST00000358738.3_Silent_p.H234H			Q9Y2K1	ZBTB1_HUMAN	zinc finger and BTB domain containing 1	234					B cell differentiation (GO:0030183)|innate immune response (GO:0045087)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of pro-T cell differentiation (GO:2000176)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated immunity (GO:0002711)|protein homooligomerization (GO:0051260)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(1)	13		all_lung(585;0.000567)|Myeloproliferative disorder(585;0.0255)|all_neural(303;0.0294)		UCEC - Uterine corpus endometrioid carcinoma (185;0.0182)|all cancers(60;3.78e-43)|OV - Ovarian serous cystadenocarcinoma(108;1.22e-20)|BRCA - Breast invasive adenocarcinoma(234;6.75e-06)|KIRC - Kidney renal clear cell carcinoma(182;0.00269)|STAD - Stomach adenocarcinoma(64;0.012)		TAGATGAGCATGTGCTAACCT	0.368													T|||	812	0.162141	0.0401	0.1254	5008	,	,		21323	0.2083		0.2326	False		,,,				2504	0.2331				p.H234H		Atlas-SNP	.											ZBTB1_ENST00000394712,adrenal_gland,adrenal_cortical_adenoma,0,2	ZBTB1	93	2	0			c.T702C						PASS	.	T	,	347,4059	179.7+/-208.2	16,315,1872	70.0	70.0	70.0		702,702	-1.9	1.0	14	dbSNP_119	70	1883,6717	335.4+/-321.4	212,1459,2629	yes	coding-synonymous,coding-synonymous	ZBTB1	NM_001123329.1,NM_014950.2	,	228,1774,4501	CC,CT,TT		21.8953,7.8756,17.1459	,	234/714,234/645	64988924	2230,10776	2203	4300	6503	SO:0001819	synonymous_variant	22890	exon2			TGAGCATGTGCTA	AB023214	CCDS32097.1, CCDS45126.1	14q23.3	2013-01-09			ENSG00000126804	ENSG00000126804		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	20259	protein-coding gene	gene with protein product						10231032	Standard	NM_014950		Approved	KIAA0997, ZNF909	uc010aqg.3	Q9Y2K1		ENST00000554015.1:c.702T>C	14.37:g.64988924T>C		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_014950	A8K6S8|Q86SW8	Silent	SNP	ENST00000554015.1	37	CCDS45126.1																																																																																			T|0.831;C|0.169	0.169	strong		0.368	ZBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411912.1		
CD40LG	959	hgsc.bcm.edu	37	X	135730555	135730555	+	Silent	SNP	T	T	C	rs1126535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135730555T>C	ENST00000370629.2	+	1	204	c.148T>C	c.(148-150)Ttg>Ctg	p.L50L	CD40LG_ENST00000370628.2_Silent_p.L50L	NM_000074.2	NP_000065.1	P29965	CD40L_HUMAN	CD40 ligand	50					B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|immunoglobulin secretion (GO:0048305)|inflammatory response (GO:0006954)|isotype switching (GO:0045190)|leukocyte cell-cell adhesion (GO:0007159)|negative regulation of apoptotic process (GO:0043066)|platelet activation (GO:0030168)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of interleukin-12 production (GO:0032735)|regulation of immune response (GO:0050776)|regulation of immunoglobulin secretion (GO:0051023)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	CD40 receptor binding (GO:0005174)			endometrium(1)|kidney(1)|large_intestine(8)|lung(14)|skin(1)|stomach(1)	26	Acute lymphoblastic leukemia(192;0.000127)					TCATAGAAGGTTGGACAAGGT	0.368									Immune Deficiency with Hyper-IgM				t|||	849	0.224901	0.121	0.3372	3775	,	,		16072	0.0565		0.1322	False		,,,				2504	0.271				p.L50L		Atlas-SNP	.											.	CD40LG	46	.	0			c.T148C						PASS	.			602,3233		44,414,100,1174,471	137.0	129.0	131.0		148	1.2	1.0	X	dbSNP_86	131	1221,5507		62,739,358,1627,1514	no	coding-synonymous	CD40LG	NM_000074.2		106,1153,458,2801,1985	CC,CT,C,TT,T		18.148,15.6975,17.2584		50/262	135730555	1823,8740	2203	4300	6503	SO:0001819	synonymous_variant	959	exon1	Familial Cancer Database	Hypogammaglobulinemia with Hyper-IgM, HIGM type I-V, XLHIGM	AGAAGGTTGGACA	X67878	CCDS14659.1	Xq26	2014-09-17	2008-08-01	2005-01-14	ENSG00000102245	ENSG00000102245		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"", ""Endogenous ligands"""	11935	protein-coding gene	gene with protein product	"""CD40 antigen ligand"", ""tumor necrosis factor (ligand) superfamily member 5"", ""T-B cell-activating molecule"", ""TNF-related activation protein"", ""hyper-IgM syndrome"""	300386	"""tumor necrosis factor (ligand) superfamily, member 5 (hyper-IgM syndrome)"""	HIGM1, IMD3, TNFSF5		1427881, 7678782	Standard	NM_000074		Approved	CD40L, TRAP, gp39, hCD40L, CD154	uc004faa.3	P29965	OTTHUMG00000022512	ENST00000370629.2:c.148T>C	X.37:g.135730555T>C		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	58	57	0.982759	NM_000074		Silent	SNP	ENST00000370629.2	37	CCDS14659.1																																																																																			0|0.032;C|0.165	0.165	strong		0.368	CD40LG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058501.1	NM_000074	
SLC19A1	6573	hgsc.bcm.edu	37	21	46957794	46957794	+	Missense_Mutation	SNP	T	T	C	rs1051266	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46957794T>C	ENST00000311124.4	-	2	232	c.80A>G	c.(79-81)cAc>cGc	p.H27R	SLC19A1_ENST00000380010.4_Missense_Mutation_p.H27R|SLC19A1_ENST00000567670.1_Missense_Mutation_p.H27R	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	27			H -> R (in dbSNP:rs1051266). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7615551, ECO:0000269|PubMed:7641195, ECO:0000269|PubMed:7826387, ECO:0000269|Ref.6}.		folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|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)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	GCACACGAGGTGCCGCCAGGA	0.657													C|||	2447	0.488618	0.3268	0.5821	5008	,	,		11906	0.4742		0.5487	False		,,,				2504	0.5941				p.H27R		Atlas-SNP	.											.	SLC19A1	53	.	0			c.A80G	GRCh37	CM004369	SLC19A1	M	rs1051266	PASS	.	C	ARG/HIS,ARG/HIS	1717,2669		358,1001,834	47.0	36.0	40.0		80,80	2.8	0.2	21	dbSNP_86	40	4894,3700		1416,2062,819	yes	missense,missense	SLC19A1	NM_001205206.1,NM_194255.2	29,29	1774,3063,1653	CC,CT,TT		43.0533,39.1473,49.0678	benign,benign	27/490,27/592	46957794	6611,6369	2193	4297	6490	SO:0001583	missense	6573	exon2			ACGAGGTGCCGCC	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"""Solute carriers"""	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.80A>G	21.37:g.46957794T>C	ENSP00000308895:p.His27Arg	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	19	13	0.684211	NM_001205206	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	37	CCDS13725.1	1073	0.4913003663003663	171	0.3475609756097561	205	0.5662983425414365	269	0.47027972027972026	428	0.5646437994722955	C	4.113	0.019156	0.08006	0.391473	0.569467	ENSG00000173638	ENST00000311124;ENST00000380010;ENST00000427839;ENST00000443742;ENST00000528477	T;T;T;T;D	0.85171	-1.39;-1.39;0.36;0.36;-1.95	3.85	2.77	0.32553	Major facilitator superfamily domain, general substrate transporter (1);	1.430790	0.04629	N	0.403225	T	0.00012	0.0000	N	0.00841	-1.15	0.24554	P	0.99400732	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34079	-0.9843	9	0.23891	T	0.37	-11.6327	4.7202	0.12915	0.4069:0.4723:0.0:0.1207	rs1051266;rs3171496;rs17844977;rs17857726;rs61510559;rs1051266	49;27;27	D3DSM6;E9PFY4;P41440	.;.;S19A1_HUMAN	R	27	ENSP00000308895:H27R;ENSP00000369347:H27R;ENSP00000401850:H27R;ENSP00000411345:H27R;ENSP00000435780:H27R	ENSP00000308895:H27R	H	-	2	0	SLC19A1	45782222	0.827000	0.29292	0.164000	0.22755	0.036000	0.12997	1.608000	0.36847	0.766000	0.33244	-0.197000	0.12766	CAC	T|0.518;C|0.482	0.482	strong		0.657	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
CCDC121	79635	hgsc.bcm.edu	37	2	27851918	27851918	+	5'Flank	SNP	G	G	A	rs3749147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27851918G>A	ENST00000324364.3	-	0	0				GPN1_ENST00000610189.1_5'Flank|GPN1_ENST00000424214.1_Intron|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_Intron|GPN1_ENST00000264718.3_Missense_Mutation_p.R12K|GPN1_ENST00000503738.1_Intron|GPN1_ENST00000515877.1_Intron|CCDC121_ENST00000394775.3_5'Flank|GPN1_ENST00000458167.2_Intron|GPN1_ENST00000407583.3_Intron	NM_024584.4	NP_078860.2	Q6ZUS5	CC121_HUMAN	coiled-coil domain containing 121											breast(1)|endometrium(3)|large_intestine(2)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(172;0.155)					GGTGGGGCCAGGAGGAAGATG	0.632													G|||	919	0.183506	0.0287	0.2089	5008	,	,		15900	0.3185		0.2535	False		,,,				2504	0.1636				p.R12K		Atlas-SNP	.											.	GPN1	28	.	0			c.G35A						PASS	.	G	,,,LYS/ARG	292,4114	158.1+/-190.9	5,282,1916	51.0	54.0	53.0	http://www.ncbi.nlm.nih.gov/pubmed?term	,,,35	1.9	0.0	2	dbSNP_107	53	2283,6317	382.8+/-340.5	306,1671,2323	yes	intron,intron,intron,missense	GPN1	NM_001145047.1,NM_001145048.1,NM_001145049.1,NM_007266.3	,,,26	311,1953,4239	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	26.5465,6.6273,19.7986	,,,benign	,,,12/389	27851918	2575,10431	2203	4300	6503	SO:0001631	upstream_gene_variant	11321	exon1			GGGCCAGGAGGAA	AK125354	CCDS1759.1, CCDS46247.1	2p23.2	2008-02-05			ENSG00000176714	ENSG00000176714			25833	protein-coding gene	gene with protein product							Standard	NM_024584		Approved	FLJ43364, FLJ13646	uc002rld.3	Q6ZUS5	OTTHUMG00000128427		2.37:g.27851918G>A	Exception_encountered	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_007266	B3KW66|J3KQZ8|Q9H8G6	Missense_Mutation	SNP	ENST00000324364.3	37	CCDS1759.1	501	0.22939560439560439	15	0.03048780487804878	89	0.24585635359116023	200	0.34965034965034963	197	0.2598944591029024	G	14.10	2.434824	0.43224	0.066273	0.265465	ENSG00000198522	ENST00000264718	T	0.48201	0.82	4.74	1.89	0.25635	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.53005	P	3.2999999999949736E-5	B	0.10296	0.003	B	0.08055	0.003	T	0.40136	-0.9579	8	0.07030	T	0.85	.	5.3503	0.16032	0.1889:0.1672:0.6438:0.0	rs3749147;rs3749147	12	B4DQM4	.	K	12	ENSP00000264718:R12K	ENSP00000264718:R12K	R	+	2	0	GPN1	27705422	0.000000	0.05858	0.000000	0.03702	0.518000	0.34316	0.149000	0.16243	0.285000	0.22329	0.591000	0.81541	AGG	G|0.772;A|0.228	0.228	strong		0.632	CCDC121-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250215.1	NM_024584	
SMURF2	64750	hgsc.bcm.edu	37	17	62587204	62587204	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:62587204A>G	ENST00000262435.9	-	5	585	c.398T>C	c.(397-399)gTa>gCa	p.V133A	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	133					BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			ACACTTACCTACTATCTGTCC	0.318																																					p.V133A		Atlas-SNP	.											.	SMURF2	63	.	0			c.T398C						PASS	.						130.0	116.0	121.0					17																	62587204		2203	4299	6502	SO:0001583	missense	64750	exon5			TTACCTACTATCT	AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.398T>C	17.37:g.62587204A>G	ENSP00000262435:p.Val133Ala	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	101	5	0.049505	NM_022739	Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	37	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892338	0.52121	.	.	ENSG00000108854	ENST00000262435	T	0.67171	-0.25	5.41	5.41	0.78517	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.78477	0.4289	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.74509	-0.3642	10	0.14656	T	0.56	.	15.7378	0.77859	1.0:0.0:0.0:0.0	.	133	Q9HAU4	SMUF2_HUMAN	A	133	ENSP00000262435:V133A	ENSP00000262435:V133A	V	-	2	0	SMURF2	60017666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.971000	0.93419	2.184000	0.69523	0.477000	0.44152	GTA	.	.	none		0.318	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739	
ZNF454	285676	hgsc.bcm.edu	37	5	178391860	178391860	+	Missense_Mutation	SNP	G	G	A	rs6867221	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:178391860G>A	ENST00000320129.3	+	5	758	c.455G>A	c.(454-456)tGt>tAt	p.C152Y	ZNF454_ENST00000519564.1_Missense_Mutation_p.C152Y	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	152			C -> Y (in dbSNP:rs6867221). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		TCACAGGAATGTGATGAATCC	0.498													G|||	1359	0.271366	0.1104	0.281	5008	,	,		17861	0.3403		0.3131	False		,,,				2504	0.3681				p.C152Y		Atlas-SNP	.											.	ZNF454	99	.	0			c.G455A						PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS	627,3779	272.8+/-271.0	46,535,1622	86.0	83.0	84.0		455,455,455	1.5	0.0	5	dbSNP_116	84	2728,5872	435.4+/-358.0	421,1886,1993	yes	missense,missense,missense	ZNF454	NM_001178089.1,NM_001178090.1,NM_182594.2	194,194,194	467,2421,3615	AA,AG,GG		31.7209,14.2306,25.7958	benign,benign,benign	152/523,152/523,152/523	178391860	3355,9651	2203	4300	6503	SO:0001583	missense	285676	exon5			AGGAATGTGATGA	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"""Zinc fingers, C2H2-type"", ""-"""	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.455G>A	5.37:g.178391860G>A	ENSP00000326249:p.Cys152Tyr	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	608	0.2783882783882784	63	0.12804878048780488	97	0.26795580110497236	208	0.36363636363636365	240	0.316622691292876	G	8.080	0.772256	0.16051	0.142306	0.317209	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.03951	3.75;3.75	4.61	1.45	0.22620	.	4.329230	0.00789	N	0.001329	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.18461	0.028	B	0.14023	0.01	T	0.47861	-0.9084	9	0.39692	T	0.17	7.0408	1.8445	0.03156	0.1253:0.1909:0.4704:0.2134	rs6867221;rs52835898;rs6867221	152	Q8N9F8	ZN454_HUMAN	Y	152	ENSP00000326249:C152Y;ENSP00000430354:C152Y	ENSP00000326249:C152Y	C	+	2	0	ZNF454	178324466	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.406000	0.21032	0.153000	0.19213	0.555000	0.69702	TGT	G|0.733;A|0.267	0.267	strong		0.498	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718	
SGSH	6448	hgsc.bcm.edu	37	17	78184679	78184679	+	Missense_Mutation	SNP	C	C	T	rs9894254	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:78184679C>T	ENST00000326317.6	-	8	1167	c.1081G>A	c.(1081-1083)Gtc>Atc	p.V361I	SGSH_ENST00000534910.1_Missense_Mutation_p.V158I|SGSH_ENST00000572208.1_5'Flank	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	361			V -> I (in dbSNP:rs9894254).		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)			CTGCCAAAGACGGTGGCCCAG	0.647													C|||	318	0.0634984	0.1573	0.0403	5008	,	,		17105	0.0		0.0616	False		,,,				2504	0.0204				p.V361I		Atlas-SNP	.											.	SGSH	27	.	0			c.G1081A	GRCh37	CD972443	SGSH	D	rs9894254	PASS	.	C	ILE/VAL	629,3777	272.5+/-270.8	40,549,1614	95.0	90.0	92.0		1081	4.4	0.6	17	dbSNP_119	92	437,8163	134.4+/-191.8	10,417,3873	yes	missense	SGSH	NM_000199.3	29	50,966,5487	TT,TC,CC		5.0814,14.276,8.1962	benign	361/503	78184679	1066,11940	2203	4300	6503	SO:0001583	missense	6448	exon8			CAAAGACGGTGGC	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.1081G>A	17.37:g.78184679C>T	ENSP00000314606:p.Val361Ile	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	41	20	0.487805	NM_000199	A8K5E2	Missense_Mutation	SNP	ENST00000326317.6	37	CCDS11770.1	147	0.0673076923076923	87	0.17682926829268292	13	0.03591160220994475	0	0.0	47	0.06200527704485488	C	16.94	3.260852	0.59431	0.14276	0.050814	ENSG00000181523	ENST00000326317;ENST00000534910	T;T	0.80566	-1.39;-1.39	4.45	4.45	0.53987	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.00412	0.0013	L	0.38733	1.17	0.09310	P	0.999999878388	B	0.22146	0.065	B	0.31290	0.127	T	0.25117	-1.0141	9	0.33141	T	0.24	-44.5508	16.6962	0.85336	0.0:1.0:0.0:0.0	rs9894254;rs57533899;rs9894254	361	P51688	SPHM_HUMAN	I	361;158	ENSP00000314606:V361I;ENSP00000437778:V158I	ENSP00000314606:V361I	V	-	1	0	SGSH	75799274	0.993000	0.37304	0.602000	0.28890	0.882000	0.50991	3.164000	0.50770	2.009000	0.58944	0.561000	0.74099	GTC	C|0.918;T|0.082	0.082	strong		0.647	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199	
CCDC183	84960	hgsc.bcm.edu	37	9	139693596	139693596	+	Missense_Mutation	SNP	T	T	C	rs945386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139693596T>C	ENST00000338005.6	+	2	148	c.113T>C	c.(112-114)aTg>aCg	p.M38T	RP11-216L13.18_ENST00000471502.1_RNA|RP11-216L13.17_ENST00000456614.2_Missense_Mutation_p.M94T|KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		38			M -> T (in dbSNP:rs945386).							biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		AAAGAGAATATGGACCAGAAC	0.637													C|||	1369	0.273363	0.3374	0.2968	5008	,	,		18525	0.2421		0.2147	False		,,,				2504	0.2628				p.M38T		Atlas-SNP	.											.	KIAA1984	39	.	0			c.T113C						PASS	.	C	THR/MET	1221,2859		191,839,1010	53.0	62.0	59.0		113	1.0	0.0	9	dbSNP_86	59	1821,6553		208,1405,2574	yes	missense	KIAA1984	NM_001039374.4	81	399,2244,3584	CC,CT,TT		21.7459,29.9265,24.4259	benign	38/535	139693596	3042,9412	2040	4187	6227	SO:0001583	missense	84960	exon2			AGAATATGGACCA																												ENST00000338005.6:c.113T>C	9.37:g.139693596T>C	ENSP00000338013:p.Met38Thr	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	100	43	0.43	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Missense_Mutation	SNP	ENST00000338005.6	37	CCDS43906.1	539	0.2467948717948718	160	0.3252032520325203	98	0.27071823204419887	124	0.21678321678321677	157	0.20712401055408972	C	1.102	-0.660878	0.03454	0.299265	0.217459	ENSG00000213213	ENST00000423962;ENST00000338005	T	0.10960	2.82	3.91	1.02	0.19986	.	0.979372	0.08252	N	0.974461	T	0.00012	0.0000	N	0.02142	-0.665	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.49312	-0.8953	9	0.20519	T	0.43	-3.8689	7.3765	0.26831	0.0:0.6152:0.0:0.3848	rs945386;rs945386	38	Q5T5S1	K1984_HUMAN	T	38	ENSP00000338013:M38T	ENSP00000338013:M38T	M	+	2	0	KIAA1984	138813417	0.207000	0.23482	0.025000	0.17156	0.000000	0.00434	0.284000	0.18864	-0.124000	0.11724	-0.994000	0.02522	ATG	T|0.759;C|0.241	0.241	strong		0.637	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
PBRM1	55193	hgsc.bcm.edu	37	3	52610651	52610651	+	Silent	SNP	T	T	A	rs17264436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52610651T>A	ENST00000296302.7	-	22	3598	c.3597A>T	c.(3595-3597)ccA>ccT	p.P1199P	PBRM1_ENST00000394830.3_Silent_p.P1174P|PBRM1_ENST00000410007.1_Silent_p.P1174P|PBRM1_ENST00000409114.3_Silent_p.P1214P|PBRM1_ENST00000409057.1_Silent_p.P1199P|PBRM1_ENST00000356770.4_Silent_p.P1167P|PBRM1_ENST00000337303.4_Silent_p.P1199P|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409767.1_Silent_p.P1214P			Q86U86	PB1_HUMAN	polybromo 1	1199	BAH 2. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CTGTTTCTTCTGGGTGAATGA	0.373			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	1583	0.316094	0.1483	0.4582	5008	,	,		16156	0.4276		0.4165	False		,,,				2504	0.2239				p.P1174P		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.A3522T						PASS	.	T	,,	766,3640	312.7+/-292.7	63,640,1500	118.0	115.0	116.0		3501,3522,3597	2.5	1.0	3	dbSNP_123	116	3462,5138	507.6+/-376.9	720,2022,1558	no	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	783,2662,3058	AA,AT,TT		40.2558,17.3854,32.5081	,,	1167/1603,1174/1583,1199/1583	52610651	4228,8778	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon23			TTCTTCTGGGTGA	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.3597A>T	3.37:g.52610651T>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.652;A|0.348	0.348	strong		0.373	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
MDN1	23195	hgsc.bcm.edu	37	6	90402840	90402840	+	Silent	SNP	C	C	G	rs9351212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90402840C>G	ENST00000369393.3	-	63	10024	c.9909G>C	c.(9907-9909)ctG>ctC	p.L3303L	MDN1_ENST00000428876.1_Silent_p.L3303L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3303					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TTAAATTATCCAGCCGATCCA	0.483													C|||	3833	0.765375	0.702	0.8228	5008	,	,		19711	0.9891		0.6471	False		,,,				2504	0.7014				p.L3303L		Atlas-SNP	.											.	MDN1	478	.	0			c.G9909C						PASS	.	C		3461,945		1428,605,170	40.0	40.0	40.0		9909	1.0	1.0	6	dbSNP_119	40	6886,1714		2968,950,382	no	coding-synonymous	MDN1	NM_014611.1		4396,1555,552	GG,GC,CC		19.9302,21.448,20.4444		3303/5597	90402840	10347,2659	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon63			ATTATCCAGCCGA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.9909G>C	6.37:g.90402840C>G		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	52	52	1	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			A|0.032;C|0.170;G|0.798	0.798	strong		0.483	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ARMC5	79798	hgsc.bcm.edu	37	16	31471283	31471283	+	Silent	SNP	G	G	A	rs201280100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31471283G>A	ENST00000563544.1	+	2	984	c.438G>A	c.(436-438)cgG>cgA	p.R146R	ARMC5_ENST00000538189.1_Silent_p.R178R|ARMC5_ENST00000268314.4_Silent_p.R146R|ARMC5_ENST00000457010.2_Silent_p.R146R|RP11-452L6.5_ENST00000564629.1_RNA|ARMC5_ENST00000408912.3_Silent_p.R241R|ARMC5_ENST00000412665.2_5'UTR			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	146										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GGGCGTGCCGGACCGAAGTGC	0.602													G|||	19	0.00379393	0.0	0.0043	5008	,	,		14517	0.0		0.0159	False		,,,				2504	0.0				p.R146R		Atlas-SNP	.											.	ARMC5	94	.	0			c.G438A						PASS	.	G	,	8,4040		0,8,2016	52.0	55.0	54.0		438,438	2.5	1.0	16		54	80,8282		1,78,4102	no	coding-synonymous,coding-synonymous	ARMC5	NM_001105247.1,NM_024742.2	,	1,86,6118	AA,AG,GG		0.9567,0.1976,0.7091	,	146/936,146/726	31471283	88,12322	2024	4181	6205	SO:0001819	synonymous_variant	79798	exon1			GTGCCGGACCGAA	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.438G>A	16.37:g.31471283G>A		Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	21	12	0.571429	NM_024742	Q86WM9|Q9H7P8|Q9H925	Silent	SNP	ENST00000563544.1	37	CCDS45472.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
SLC22A10	387775	hgsc.bcm.edu	37	11	63072310	63072310	+	Missense_Mutation	SNP	C	C	T	rs1201559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:63072310C>T	ENST00000332793.6	+	9	1549	c.1547C>T	c.(1546-1548)cCa>cTa	p.P516L	SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000526800.1_Intron|SLC22A10_ENST00000544661.1_3'UTR|SLC22A10_ENST00000525620.1_Intron	NM_001039752.3	NP_001034841.3	Q63ZE4	S22AA_HUMAN	solute carrier family 22, member 10	516						integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)			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)	TTCCTCCTACCAGAAACCAAG	0.433													C|||	2193	0.437899	0.2769	0.5043	5008	,	,		20979	0.4702		0.5586	False		,,,				2504	0.4509				p.P516L		Atlas-SNP	.											.	SLC22A10	79	.	0			c.C1547T						PASS	.	C	LEU/PRO	1127,2703		175,777,963	162.0	141.0	148.0		1547	2.7	0.4	11	dbSNP_87	148	4689,3563		1333,2023,770	yes	missense	SLC22A10	NM_001039752.3	98	1508,2800,1733	TT,TC,CC		43.1774,29.4256,48.1377	probably-damaging	516/542	63072310	5816,6266	1915	4126	6041	SO:0001583	missense	387775	exon9			TCCTACCAGAAAC	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.1547C>T	11.37:g.63072310C>T	ENSP00000327569:p.Pro516Leu	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	152	79	0.519737	NM_001039752	Q68CJ0	Missense_Mutation	SNP	ENST00000332793.6	37	CCDS41661.1	1041	0.4766483516483517	144	0.2926829268292683	217	0.5994475138121547	240	0.4195804195804196	440	0.5804749340369393	C	17.15	3.316435	0.60524	0.294256	0.568226	ENSG00000184999	ENST00000332793	T	0.79247	-1.25	2.73	2.73	0.32206	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	U	0.000001	T	0.00012	0.0000	H	0.96365	3.81	0.09310	P	0.9999999999999998	D	0.89917	1.0	D	0.91635	0.999	T	0.42085	-0.9472	9	0.72032	D	0.01	.	11.3654	0.49668	0.0:1.0:0.0:0.0	rs1201559;rs1209564;rs1723191;rs59020910;rs1201559	516	Q63ZE4	S22AA_HUMAN	L	516	ENSP00000327569:P516L	ENSP00000327569:P516L	P	+	2	0	SLC22A10	62828886	0.960000	0.32886	0.371000	0.25978	0.265000	0.26407	4.196000	0.58407	1.566000	0.49654	0.579000	0.79373	CCA	C|0.537;T|0.463	0.463	strong		0.433	SLC22A10-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382622.3	NM_001039752	
ALPK3	57538	hgsc.bcm.edu	37	15	85400564	85400564	+	Silent	SNP	C	C	T	rs114957070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:85400564C>T	ENST00000258888.5	+	6	3368	c.3201C>T	c.(3199-3201)ccC>ccT	p.P1067P		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1067					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGGAGGTACCCACGATGCCTT	0.647													C|||	9	0.00179712	0.0	0.0	5008	,	,		19517	0.0		0.0089	False		,,,				2504	0.0				p.P1067P		Atlas-SNP	.											.	ALPK3	289	.	0			c.C3201T						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	69.0	54.0	59.0		3201	0.4	0.0	15	dbSNP_132	59	53,8545	34.3+/-88.2	0,53,4246	no	coding-synonymous	ALPK3	NM_020778.4		0,60,6442	TT,TC,CC		0.6164,0.1589,0.4614		1067/1908	85400564	60,12944	2203	4299	6502	SO:0001819	synonymous_variant	57538	exon6			GGTACCCACGATG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.3201C>T	15.37:g.85400564C>T		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	65	42	0.646154	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
ICA1	3382	hgsc.bcm.edu	37	7	8198226	8198226	+	Silent	SNP	A	A	C	rs7798010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:8198226A>C	ENST00000402384.3	-	7	902	c.636T>G	c.(634-636)gtT>gtG	p.V212V	ICA1_ENST00000265577.7_Silent_p.V211V|ICA1_ENST00000407906.1_Silent_p.V212V|ICA1_ENST00000406470.2_Silent_p.V212V|ICA1_ENST00000401396.1_Silent_p.V200V|ICA1_ENST00000396675.3_Silent_p.V212V|ICA1_ENST00000422063.2_Silent_p.V212V			Q05084	ICA69_HUMAN	islet cell autoantigen 1, 69kDa	212	AH. {ECO:0000255|PROSITE- ProRule:PRU00294}.				neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|secretory granule membrane (GO:0030667)|synaptic vesicle membrane (GO:0030672)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|urinary_tract(1)	23		Ovarian(82;0.0612)		UCEC - Uterine corpus endometrioid carcinoma (126;0.246)		CTTTTTGACAAACATCCATCT	0.373													C|||	640	0.127796	0.4221	0.0447	5008	,	,		20615	0.0		0.0169	False		,,,				2504	0.0348				p.F212L		Atlas-SNP	.											.	ICA1	65	.	0			c.T636G						PASS	.	C	,,	1638,2768	659.2+/-400.5	304,1030,869	154.0	135.0	141.0		636,636,636	3.2	1.0	7	dbSNP_116	141	109,8491	814.3+/-407.0	0,109,4191	no	coding-synonymous,coding-synonymous,coding-synonymous	ICA1	NM_001136020.1,NM_004968.2,NM_022307.2	,,	304,1139,5060	CC,CA,AA		1.2674,37.1766,13.4323	,,	212/484,212/484,212/484	8198226	1747,11259	2203	4300	6503	SO:0001819	synonymous_variant	3382	exon7			TTGACAAACATCC		CCDS34602.1, CCDS64595.1	7p22	2006-12-13	2002-08-29		ENSG00000003147	ENSG00000003147			5343	protein-coding gene	gene with protein product		147625	"""islet cell autoantigen 1 (69kD)"""			7918678, 8777998	Standard	NM_001276478		Approved	ICAp69	uc003srm.3	Q05084	OTTHUMG00000152008	ENST00000402384.3:c.636T>G	7.37:g.8198226A>C		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	110	55	0.5	NM_001136020	A8K7U1|B3FTQ2|P78506|Q13824|Q96HG3	Missense_Mutation	SNP	ENST00000402384.3	37	CCDS34602.1																																																																																			A|0.880;C|0.120	0.120	strong		0.373	ICA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324793.1	NM_004968	
NRXN2	9379	hgsc.bcm.edu	37	11	64415767	64415767	+	Silent	SNP	G	G	A	rs3825074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64415767G>A	ENST00000377551.1	-	16	3538	c.3327C>T	c.(3325-3327)ggC>ggT	p.G1109G	AP001092.4_ENST00000433606.1_RNA|NRXN2_ENST00000409571.1_Silent_p.G1102G|NRXN2_ENST00000265459.6_Silent_p.G1109G|NRXN2_ENST00000377559.3_Silent_p.G1069G			Q9P2S2	NRX2A_HUMAN	neurexin 2	1109	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GCAAGCAGACGCCCTGGTTGG	0.627													G|||	559	0.111621	0.0076	0.0922	5008	,	,		20161	0.1935		0.1491	False		,,,				2504	0.1431				p.G1109G		Atlas-SNP	.											.	NRXN2	247	.	0			c.C3327T						PASS	.	G	,	158,4244	108.2+/-146.6	2,154,2045	105.0	91.0	95.0		3327,3207	3.4	1.0	11	dbSNP_107	95	1185,7409	241.3+/-271.7	91,1003,3203	no	coding-synonymous,coding-synonymous	NRXN2	NM_015080.3,NM_138732.2	,	93,1157,5248	AA,AG,GG		13.7887,3.5893,10.3339	,	1109/1713,1069/1643	64415767	1343,11653	2201	4297	6498	SO:0001819	synonymous_variant	9379	exon17			GCAGACGCCCTGG		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.3327C>T	11.37:g.64415767G>A		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	58	34	0.586207	NM_015080	A7E2C1|Q9Y2D6	Silent	SNP	ENST00000377551.1	37	CCDS8077.1																																																																																			G|0.897;A|0.103	0.103	strong		0.627	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276876	71276876	+	Silent	SNP	A	A	G	rs12788123		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71276876A>G	ENST00000398531.1	+	1	268	c.243A>G	c.(241-243)aaA>aaG	p.K81K	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	81	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.K81K(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GGGGCTCCAAAGGGGGCTGTG	0.682																																					p.K81K		Atlas-SNP	.											KRTAP5-10,NS,carcinoma,0,1	KRTAP5-10	37	1	1	Substitution - coding silent(1)	endometrium(1)	c.A243G						scavenged	.						51.0	72.0	65.0					11																	71276876		2140	4257	6397	SO:0001819	synonymous_variant	387273	exon1			CTCCAAAGGGGGC	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.243A>G	11.37:g.71276876A>G		Somatic	111	8	0.0720721		WXS	Illumina HiSeq	Phase_I	97	14	0.14433	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			A|0.998;G|0.002	0.002	weak		0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
ZNF80	7634	hgsc.bcm.edu	37	3	113955820	113955820	+	Silent	SNP	G	G	C	rs3732780	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113955820G>C	ENST00000482457.2	-	1	605	c.102C>G	c.(100-102)tcC>tcG	p.S34S	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	34					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				TTGGTCCCTGGGAGTCACATT	0.502													G|||	1560	0.311502	0.3593	0.2594	5008	,	,		22578	0.375		0.2734	False		,,,				2504	0.2577				p.S34S	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.C102G						PASS	.	G		1512,2894	480.8+/-358.9	252,1008,943	119.0	112.0	114.0		102	-1.5	0.0	3	dbSNP_107	114	2217,6383	375.8+/-337.9	291,1635,2374	no	coding-synonymous	ZNF80	NM_007136.3		543,2643,3317	CC,CG,GG		25.7791,34.3168,28.6714		34/274	113955820	3729,9277	2203	4300	6503	SO:0001819	synonymous_variant	7634	exon1			TCCCTGGGAGTCA	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.102C>G	3.37:g.113955820G>C		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	116	67	0.577586	NM_007136	Q6NSW4|Q6NT14	Silent	SNP	ENST00000482457.2	37	CCDS2979.1																																																																																			G|0.703;C|0.297	0.297	strong		0.502	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
MANSC4	100287284	hgsc.bcm.edu	37	12	27915718	27915718	+	Missense_Mutation	SNP	A	A	T	rs10842975	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:27915718A>T	ENST00000381273.3	-	3	975	c.976T>A	c.(976-978)Tcc>Acc	p.S326T		NM_001146221.1	NP_001139693.1	A6NHS7	MANS4_HUMAN	MANSC domain containing 4	326						integral component of membrane (GO:0016021)				kidney(1)	1						ATTTGCAAGGATCCTGATTTT	0.398													A|||	2465	0.492212	0.4939	0.572	5008	,	,		18263	0.4692		0.508	False		,,,				2504	0.4407				p.S326T		Atlas-SNP	.											.	MANSC4	9	.	0			c.T976A						PASS	.	A	THR/SER	689,695		162,365,165	200.0	150.0	165.0		976	0.2	0.0	12	dbSNP_120	165	1590,1592		403,784,404	yes	missense	MANSC4	NM_001146221.1	58	565,1149,569	TT,TA,AA		49.9686,49.7832,49.9124	benign	326/341	27915718	2279,2287	692	1591	2283	SO:0001583	missense	100287284	exon3			GCAAGGATCCTGA		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.976T>A	12.37:g.27915718A>T	ENSP00000370673:p.Ser326Thr	Somatic	236	1	0.00423729		WXS	Illumina HiSeq	Phase_I	231	103	0.445887	NM_001146221		Missense_Mutation	SNP	ENST00000381273.3	37	CCDS53770.1	1137	0.5206043956043956	259	0.5264227642276422	215	0.5939226519337016	282	0.493006993006993	381	0.5026385224274407	A	6.461	0.453164	0.12283	0.497832	0.499686	ENSG00000205693	ENST00000381273	T	0.50813	0.73	3.88	0.253	0.15551	.	1.321280	0.05157	N	0.497059	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P	0.34522	0.455	B	0.32465	0.146	T	0.44997	-0.9291	9	0.27785	T	0.31	0.1996	6.6213	0.22804	0.6726:0.0:0.3274:0.0	rs10842975;rs52835237;rs58220810;rs10842975	326	A6NHS7	MANS4_HUMAN	T	326	ENSP00000370673:S326T	ENSP00000370673:S326T	S	-	1	0	MANSC4	27806985	0.072000	0.21174	0.017000	0.16124	0.106000	0.19336	1.085000	0.30840	0.035000	0.15519	0.533000	0.62120	TCC	A|0.494;T|0.506	0.506	strong		0.398	MANSC4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000402902.1		
MESDC1	59274	hgsc.bcm.edu	37	15	81294774	81294774	+	Silent	SNP	G	G	C	rs11541231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:81294774G>C	ENST00000267984.2	+	1	1480	c.162G>C	c.(160-162)tcG>tcC	p.S54S		NM_022566.2	NP_072088.1	Q9H1K6	MESD1_HUMAN	mesoderm development candidate 1	54										endometrium(1)|lung(2)	3						TGCTGCTGTCGAGCGAGGCGC	0.701													G|||	137	0.0273562	0.003	0.0951	5008	,	,		9514	0.0		0.0457	False		,,,				2504	0.0215				p.S54S		Atlas-SNP	.											.	MESDC1	7	.	0			c.G162C						PASS	.	G		48,3752		2,44,1854	11.0	9.0	10.0		162	-8.7	0.9	15	dbSNP_120	10	281,7351		5,271,3540	no	coding-synonymous	MESDC1	NM_022566.2		7,315,5394	CC,CG,GG		3.6819,1.2632,2.8779		54/363	81294774	329,11103	1900	3816	5716	SO:0001819	synonymous_variant	59274	exon1			GCTGTCGAGCGAG	AY007810	CCDS10316.1	15q13	2008-07-18			ENSG00000140406	ENSG00000140406			13519	protein-coding gene	gene with protein product		615466				11247670	Standard	NM_022566		Approved	MGC99595	uc002bfz.3	Q9H1K6	OTTHUMG00000144185	ENST00000267984.2:c.162G>C	15.37:g.81294774G>C		Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	12	10	0.833333	NM_022566		Silent	SNP	ENST00000267984.2	37	CCDS10316.1																																																																																			G|0.972;C|0.028	0.028	strong		0.701	MESDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291390.1	NM_022566	
SMG6	23293	hgsc.bcm.edu	37	17	2202943	2202943	+	Silent	SNP	T	T	C	rs216196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:2202943T>C	ENST00000263073.6	-	2	1154	c.1104A>G	c.(1102-1104)tcA>tcG	p.S368S	SMG6_ENST00000544865.1_Silent_p.S337S	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	368	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CATCCCTGGCTGACCTCACCA	0.498													T|||	1661	0.331669	0.2171	0.1988	5008	,	,		19283	0.5913		0.2555	False		,,,				2504	0.3916				p.S368S	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A1104G						PASS	.	T	,	1096,3310	397.0+/-330.2	138,820,1245	82.0	72.0	75.0		1011,1104	-0.1	0.0	17	dbSNP_79	75	2271,6329	383.2+/-340.6	291,1689,2320	no	coding-synonymous,coding-synonymous	SMG6	NM_001170957.1,NM_017575.4	,	429,2509,3565	CC,CT,TT		26.407,24.8752,25.8881	,	337/1389,368/1420	2202943	3367,9639	2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			CCTGGCTGACCTC	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.1104A>G	17.37:g.2202943T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	225	124	0.551111	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	CCDS11016.1																																																																																			T|0.712;C|0.288	0.288	strong		0.498	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
FCGBP	8857	hgsc.bcm.edu	37	19	40392588	40392588	+	Missense_Mutation	SNP	C	C	T	rs62108885		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40392588C>T	ENST00000221347.6	-	16	7923	c.7916G>A	c.(7915-7917)aGc>aAc	p.S2639N		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2639	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			ACAGCCCTCGCTCCCCGGCGG	0.662																																					p.S2639N		Atlas-SNP	.											.	FCGBP	416	.	0			c.G7916A						PASS	.	C	ASN/SER	221,4163		1,219,1972	49.0	55.0	53.0		7916	-1.4	0.0	19	dbSNP_129	53	1712,6888		5,1702,2593	no	missense	FCGBP	NM_003890.2	46	6,1921,4565	TT,TC,CC		19.907,5.0411,14.8876	possibly-damaging	2639/5406	40392588	1933,11051	2192	4300	6492	SO:0001583	missense	8857	exon16			CCCTCGCTCCCCG	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.7916G>A	19.37:g.40392588C>T	ENSP00000221347:p.Ser2639Asn	Somatic	367	0	0		WXS	Illumina HiSeq	Phase_I	438	181	0.413242	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	228	0.1043956043956044	9	0.018292682926829267	55	0.15193370165745856	19	0.033216783216783216	145	0.19129287598944592	C	0.014	-1.577689	0.00879	0.050411	0.19907	ENSG00000090920	ENST00000221347	T	0.19105	2.17	1.4	-1.44	0.08856	von Willebrand factor, type D domain (1);	1.845400	0.03438	N	0.208802	T	0.00012	0.0000	L	0.38692	1.165	0.09310	N	1	P	0.38863	0.65	B	0.39660	0.306	T	0.15809	-1.0424	10	0.17369	T	0.5	.	5.7132	0.17946	0.0:0.5468:0.0:0.4532	rs62108885	2639	Q9Y6R7	FCGBP_HUMAN	N	2639	ENSP00000221347:S2639N	ENSP00000221347:S2639N	S	-	2	0	FCGBP	45084428	0.381000	0.25140	0.000000	0.03702	0.051000	0.14879	-0.129000	0.10515	-0.450000	0.07107	0.298000	0.19748	AGC	C|0.895;T|0.105	0.105	strong		0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CPXCR1	53336	hgsc.bcm.edu	37	X	88008807	88008807	+	Missense_Mutation	SNP	G	G	A	rs5984611	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:88008807G>A	ENST00000276127.4	+	3	651	c.392G>A	c.(391-393)cGt>cAt	p.R131H	CPXCR1_ENST00000373111.1_Missense_Mutation_p.R131H	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	131			R -> H (in dbSNP:rs5984611). {ECO:0000269|PubMed:11499681}.				metal ion binding (GO:0046872)			NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						CACAAAACTCGTTTTCGACTT	0.373													G|||	870	0.230464	0.1392	0.2017	3775	,	,		14154	0.0298		0.2684	False		,,,				2504	0.2515				p.R131H		Atlas-SNP	.											.	CPXCR1	83	.	0			c.G392A						PASS	.	G	HIS/ARG,HIS/ARG	696,3139		50,473,123,1109,448	53.0	47.0	49.0		392,392	0.1	0.0	X	dbSNP_114	49	2782,3946		410,1184,778,834,1094	yes	missense,missense	CPXCR1	NM_001184771.1,NM_033048.5	29,29	460,1657,901,1943,1542	AA,AG,A,GG,G		41.3496,18.1486,32.9263	probably-damaging,probably-damaging	131/302,131/302	88008807	3478,7085	2203	4300	6503	SO:0001583	missense	53336	exon3			AAACTCGTTTTCG	AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"""cancer/testis antigen 77"""					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.392G>A	X.37:g.88008807G>A	ENSP00000276127:p.Arg131His	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	51	51	1	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	386	0.2326702833031947	58	0.13063063063063063	52	0.16455696202531644	13	0.023297491039426525	140	0.22580645161290322	G	10.91	1.483747	0.26598	0.181486	0.413496	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.46819	0.86;0.86	3.06	0.0957	0.14486	.	1.106060	0.07158	N	0.850257	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	D	0.65815	0.995	P	0.45881	0.496	T	0.33085	-0.9882	8	.	.	.	0.0	4.5942	0.12322	0.0:0.3717:0.4741:0.1542	rs5984611;rs17253963;rs52813984;rs57073371;rs5984611	131	Q8N123	CPXCR_HUMAN	H	131	ENSP00000276127:R131H;ENSP00000362203:R131H	.	R	+	2	0	CPXCR1	87895463	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.426000	0.07008	-0.091000	0.12440	-0.223000	0.12442	CGT	0|0.003;A|0.269	0.269	strong		0.373	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048	
PPP1R16B	26051	hgsc.bcm.edu	37	20	37534665	37534665	+	Silent	SNP	C	C	T	rs4812332	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37534665C>T	ENST00000299824.1	+	7	939	c.750C>T	c.(748-750)gaC>gaT	p.D250D	PPP1R16B_ENST00000373331.2_Intron	NM_015568.2	NP_056383.1	Q96T49	PP16B_HUMAN	protein phosphatase 1, regulatory subunit 16B	250					regulation of filopodium assembly (GO:0051489)|signal transduction (GO:0007165)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(4)|kidney(3)|large_intestine(10)|lung(23)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	49		Myeloproliferative disorder(115;0.00878)				TCCTCCTGGACCATGGAGTGC	0.612													C|||	1729	0.345248	0.2995	0.3746	5008	,	,		17452	0.4167		0.336	False		,,,				2504	0.3221				p.D250D		Atlas-SNP	.											.	PPP1R16B	103	.	0			c.C750T						PASS	.	C	,	1402,3004	460.0+/-352.4	212,978,1013	106.0	95.0	98.0		,750	2.5	1.0	20	dbSNP_111	98	2770,5830	440.9+/-359.6	409,1952,1939	no	intron,coding-synonymous	PPP1R16B	NM_001172735.1,NM_015568.2	,	621,2930,2952	TT,TC,CC		32.2093,31.8202,32.0775	,	,250/568	37534665	4172,8834	2203	4300	6503	SO:0001819	synonymous_variant	26051	exon7			CCTGGACCATGGA	AB020630	CCDS13309.1, CCDS54462.1	20q11.23	2013-01-10	2011-10-04		ENSG00000101445	ENSG00000101445		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	15850	protein-coding gene	gene with protein product	"""TGF-beta-inhibited membrane-associated protein"", ""ankyrin repeat domain protein 4"""	613275	"""protein phosphatase 1, regulatory (inhibitor) subunit 16B"""			10048485, 12055102	Standard	NM_001172735		Approved	KIAA0823, TIMAP, ANKRD4	uc002xje.3	Q96T49	OTTHUMG00000032465	ENST00000299824.1:c.750C>T	20.37:g.37534665C>T		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	81	81	1	NM_015568	A2RRR6|E9PFS8|O94912|Q5W9G4|Q9NQG4	Silent	SNP	ENST00000299824.1	37	CCDS13309.1																																																																																			C|0.671;T|0.329	0.329	strong		0.612	PPP1R16B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079220.2	NM_015568	
TMEM132A	54972	hgsc.bcm.edu	37	11	60701136	60701136	+	Silent	SNP	C	C	G	rs9513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60701136C>G	ENST00000453848.2	+	8	1637	c.1479C>G	c.(1477-1479)ccC>ccG	p.P493P	TMEM132A_ENST00000005286.4_Silent_p.P494P			Q24JP5	T132A_HUMAN	transmembrane protein 132A	493						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						TGTGGGCCCCCCTGCTACCGC	0.711													G|||	2109	0.421126	0.4713	0.4452	5008	,	,		14506	0.3165		0.4225	False		,,,				2504	0.4427				p.P494P		Atlas-SNP	.											.	TMEM132A	135	.	0			c.C1482G						PASS	.	G	,	2005,2385		470,1065,660	15.0	18.0	17.0		1482,1479	-3.5	0.4	11	dbSNP_52	17	3595,4969		793,2009,1480	no	coding-synonymous,coding-synonymous	TMEM132A	NM_017870.3,NM_178031.2	,	1263,3074,2140	GG,GC,CC		41.978,45.672,43.2299	,	494/1025,493/1024	60701136	5600,7354	2195	4282	6477	SO:0001819	synonymous_variant	54972	exon8			GGCCCCCCTGCTA	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.1479C>G	11.37:g.60701136C>G		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Silent	SNP	ENST00000453848.2	37	CCDS44618.1	902	0.413003663003663	233	0.4735772357723577	164	0.4530386740331492	185	0.32342657342657344	320	0.42216358839050133	G	1.214	-0.628838	0.03610	0.45672	0.41978	ENSG00000006118	ENST00000536409	T	0.28666	1.6	4.74	-3.54	0.04653	.	0.000000	0.64402	D	0.000006	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999881	.	.	.	.	.	.	T	0.38436	-0.9661	6	0.87932	D	0	-36.0168	7.8294	0.29334	0.532:0.2072:0.2608:0.0	rs9513;rs3180958;rs58804152	.	.	.	A	85	ENSP00000439717:P85A	ENSP00000439717:P85A	P	+	1	0	TMEM132A	60457712	0.000000	0.05858	0.438000	0.26821	0.129000	0.20672	-2.894000	0.00707	-1.522000	0.01769	-2.035000	0.00420	CCT	C|0.581;G|0.419	0.419	strong		0.711	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
TMEM26	219623	hgsc.bcm.edu	37	10	63170292	63170292	+	Silent	SNP	A	A	G	rs7083475	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:63170292A>G	ENST00000399298.3	-	6	1263	c.895T>C	c.(895-897)Ttg>Ctg	p.L299L	TMEM26_ENST00000507507.1_5'UTR	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	299						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					TAGAGTTGCAACACCACCACG	0.527													A|||	1071	0.213858	0.3767	0.1671	5008	,	,		20549	0.0952		0.2386	False		,,,				2504	0.1237				p.L299L		Atlas-SNP	.											.	TMEM26	47	.	0			c.T895C						PASS	.	A		1329,2883		205,919,982	114.0	118.0	117.0		895	-0.8	0.9	10	dbSNP_116	117	1654,6806		142,1370,2718	no	coding-synonymous	TMEM26	NM_178505.6		347,2289,3700	GG,GA,AA		19.5508,31.5527,23.5401		299/369	63170292	2983,9689	2106	4230	6336	SO:0001819	synonymous_variant	219623	exon6			GTTGCAACACCAC	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.895T>C	10.37:g.63170292A>G		Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	152	73	0.480263	NM_178505	Q6ZVM0|Q8IVN9	Silent	SNP	ENST00000399298.3	37	CCDS41530.1																																																																																			A|0.802;G|0.198	0.198	strong		0.527	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505	
IVL	3713	hgsc.bcm.edu	37	1	152882979	152882979	+	Missense_Mutation	SNP	C	C	T	rs17855670		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152882979C>T	ENST00000368764.3	+	2	770	c.706C>T	c.(706-708)Cca>Tca	p.P236S	IVL_ENST00000392667.2_Missense_Mutation_p.P90S			P07476	INVO_HUMAN	involucrin	236	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].		P -> S (in dbSNP:rs17855670). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2873896}.		isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gctggagctcccacagcagca	0.677																																					p.P236S		Atlas-SNP	.											IVL,colon,carcinoma,0,2	IVL	100	2	0			c.C706T						PASS	.																																			SO:0001583	missense	3713	exon2			GAGCTCCCACAGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.706C>T	1.37:g.152882979C>T	ENSP00000357753:p.Pro236Ser	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	21	0.265823	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	126	0.057692307692307696	14	0.028455284552845527	19	0.052486187845303865	65	0.11363636363636363	28	0.036939313984168866	C	0.481	-0.879883	0.02530	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.10960	3.06;2.82	3.86	-2.86	0.05717	.	.	.	.	.	T	0.01387	0.0045	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.48198	-0.9056	9	0.09590	T	0.72	.	4.7558	0.13082	0.3537:0.2977:0.3486:0.0	rs17855670	236	P07476	INVO_HUMAN	S	236;90	ENSP00000357753:P236S;ENSP00000376435:P90S	ENSP00000357753:P236S	P	+	1	0	IVL	151149603	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.107000	0.15375	-0.341000	0.08376	-0.883000	0.02948	CCA	C|0.943;T|0.057	0.057	strong		0.677	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
MT1M	4499	hgsc.bcm.edu	37	16	56667282	56667282	+	Missense_Mutation	SNP	C	C	A	rs1827210	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:56667282C>A	ENST00000379818.3	+	2	558	c.59C>A	c.(58-60)aCg>aAg	p.T20K	AC026461.1_ENST00000600389.1_5'Flank|MT1JP_ENST00000564564.1_RNA	NM_176870.2	NP_789846.1	Q8N339	MT1M_HUMAN	metallothionein 1M	20	Beta.		T -> K (in dbSNP:rs1827210). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.		cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	5						GGCTCCTGCACGTGCAAAGAG	0.567													.|||	3559	0.710663	0.5492	0.7867	5008	,	,		19000	0.6657		0.832	False		,,,				2504	0.7965				p.T20K		Atlas-SNP	.											.	MT1M	13	.	0			c.C59A						PASS	.	A	LYS/THR	2646,1750	514.1+/-368.5	810,1026,362	90.0	90.0	90.0		59	-0.1	0.2	16	dbSNP_92	90	7317,1283	250.5+/-277.4	3113,1091,96	no	missense	MT1M	NM_176870.2	78	3923,2117,458	AA,AC,CC		14.9186,39.8089,23.338	benign	20/62	56667282	9963,3033	2198	4300	6498	SO:0001583	missense	4499	exon2			CCTGCACGTGCAA	AF136177	CCDS42166.1	16q13	2008-02-05				ENSG00000205364		"""Metallothioneins"""	14296	protein-coding gene	gene with protein product		156357	"""metallothionein 1K"""	MT1, MT1K		2286373, 8049263	Standard	NM_176870		Approved		uc002ejn.3	Q8N339		ENST00000379818.3:c.59C>A	16.37:g.56667282C>A	ENSP00000369146:p.Thr20Lys	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	171	66	0.385965	NM_176870	Q8TDN3	Missense_Mutation	SNP	ENST00000379818.3	37	CCDS42166.1	1593	0.7293956043956044	267	0.5426829268292683	291	0.8038674033149171	401	0.701048951048951	634	0.8364116094986808	A	0.004	-2.343099	0.00222	0.601911	0.850814	ENSG00000205364	ENST00000379818	T	0.07021	3.23	2.45	-0.0809	0.13704	Metallothionein domain, vertebrate (1);Metallothionein domain (1);	0.207699	0.27836	N	0.017646	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.30297	-0.9983	8	0.02654	T	1	.	4.0918	0.09973	0.3755:0.4753:0.1491:0.0	rs1827210;rs17856801;rs60427063;rs1827210	20	Q8N339	MT1M_HUMAN	K	20	ENSP00000369146:T20K	ENSP00000369146:T20K	T	+	2	0	MT1M	55224783	0.014000	0.17966	0.153000	0.22517	0.202000	0.24057	0.288000	0.18939	-0.602000	0.05775	-0.533000	0.04299	ACG	C|0.207;A|0.793	0.793	strong		0.567	MT1M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434359.1	NM_176870	
LRRC8E	80131	hgsc.bcm.edu	37	19	7964727	7964727	+	Silent	SNP	G	G	A	rs3745382	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7964727G>A	ENST00000306708.6	+	3	1421	c.1320G>A	c.(1318-1320)gaG>gaA	p.E440E	RN7SL115P_ENST00000392196.5_RNA|AC010336.1_ENST00000539278.1_Silent_p.D180D	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	440					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						GTGAGGTGGAGTCACTCAGGC	0.657													G|||	815	0.16274	0.1407	0.1671	5008	,	,		16202	0.1339		0.2445	False		,,,				2504	0.135				p.E440E		Atlas-SNP	.											.	LRRC8E	67	.	0			c.G1320A						PASS	.	G		756,3650		63,630,1510	37.0	30.0	32.0		1320	2.5	1.0	19	dbSNP_107	32	2116,6480		274,1568,2456	no	coding-synonymous	LRRC8E	NM_025061.3		337,2198,3966	AA,AG,GG		24.6161,17.1584,22.0889		440/797	7964727	2872,10130	2203	4298	6501	SO:0001819	synonymous_variant	80131	exon4			GGTGGAGTCACTC		CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1320G>A	19.37:g.7964727G>A		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	38	12	0.315789	NM_001268284	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Silent	SNP	ENST00000306708.6	37	CCDS12189.1																																																																																			G|0.802;A|0.198	0.198	strong		0.657	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
LTF	4057	hgsc.bcm.edu	37	3	46480958	46480958	+	Missense_Mutation	SNP	C	C	G	rs2073495	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46480958C>G	ENST00000231751.4	-	15	2032	c.1737G>C	c.(1735-1737)gaG>gaC	p.E579D	LTF_ENST00000493056.1_5'UTR|LTF_ENST00000426532.2_Missense_Mutation_p.E535D|LTF_ENST00000417439.1_Missense_Mutation_p.E577D	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	579	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.		E -> D (in dbSNP:rs2073495). {ECO:0000269|PubMed:11702692, ECO:0000269|PubMed:16201406, ECO:0000269|PubMed:22900286, ECO:0000269|Ref.24, ECO:0000269|Ref.9}.		antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		TAGCCCATGCCTCATTGTTAT	0.542													C|||	1388	0.277157	0.059	0.3501	5008	,	,		21415	0.3661		0.3221	False		,,,				2504	0.3824				p.E579D		Atlas-SNP	.											LTF,NS,carcinoma,0,1	LTF	98	1	0			c.G1737C	GRCh37	CM051945	LTF	M	rs2073495	PASS	.	C	ASP/GLU,ASP/GLU	441,3965	212.5+/-232.4	17,407,1779	84.0	75.0	78.0		1605,1737	-10.3	0.0	3	dbSNP_96	78	2912,5688	454.0+/-363.4	513,1886,1901	yes	missense,missense	LTF	NM_001199149.1,NM_002343.3	45,45	530,2293,3680	GG,GC,CC		33.8605,10.0091,25.7804	benign,benign	535/667,579/711	46480958	3353,9653	2203	4300	6503	SO:0001583	missense	4057	exon15			CCATGCCTCATTG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1737G>C	3.37:g.46480958C>G	ENSP00000231751:p.Glu579Asp	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	119	57	0.478992	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	37	CCDS33747.1	610	0.2793040293040293	33	0.06707317073170732	134	0.3701657458563536	206	0.36013986013986016	237	0.31266490765171506	C	6.870	0.529868	0.13127	0.100091	0.338605	ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496	T;T;T;T	0.07216	3.21;3.21;3.21;3.21	5.16	-10.3	0.00346	.	0.579288	0.18664	N	0.134621	T	0.00012	0.0000	L	0.31120	0.905	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.005;0.003;0.005	T	0.34925	-0.9809	9	0.23302	T	0.38	.	5.8011	0.18414	0.0769:0.453:0.2327:0.2375	rs55765065	577;566;579	E7ER44;E7EQB2;P02788	.;.;TRFL_HUMAN	D	579;535;577;566	ENSP00000231751:E579D;ENSP00000405719:E535D;ENSP00000405546:E577D;ENSP00000397427:E566D	ENSP00000231751:E579D	E	-	3	2	LTF	46455962	0.000000	0.05858	0.000000	0.03702	0.223000	0.24884	-4.284000	0.00260	-3.002000	0.00275	-0.984000	0.02558	GAG	C|0.739;G|0.261	0.261	strong		0.542	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
OR7A17	26333	hgsc.bcm.edu	37	19	14991643	14991643	+	Silent	SNP	G	G	A	rs10401818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14991643G>A	ENST00000327462.2	-	1	621	c.525C>T	c.(523-525)ccC>ccT	p.P175P		NM_030901.1	NP_112163.1	O14581	OR7AH_HUMAN	olfactory receptor, family 7, subfamily A, member 17	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12	Ovarian(108;0.203)					AGAAAAAGTGGGGGATTTCCA	0.483													.|||	1390	0.277556	0.438	0.2349	5008	,	,		21572	0.2867		0.2356	False		,,,				2504	0.1247				p.P175P		Atlas-SNP	.											.	OR7A17	37	.	0			c.C525T						PASS	.	G		1723,2683	516.7+/-369.2	350,1023,830	91.0	86.0	88.0		525	-2.2	0.6	19	dbSNP_119	88	1945,6655	341.3+/-324.0	215,1515,2570	no	coding-synonymous	OR7A17	NM_030901.1		565,2538,3400	AA,AG,GG		22.6163,39.1058,28.2024		175/310	14991643	3668,9338	2203	4300	6503	SO:0001819	synonymous_variant	26333	exon1			AAAGTGGGGGATT	X64993	CCDS12319.1	19p13.12	2012-08-09				ENSG00000185385		"""GPCR / Class A : Olfactory receptors"""	8363	protein-coding gene	gene with protein product						1370859	Standard	NM_030901		Approved	HTPCRX19	uc010xob.2	O14581		ENST00000327462.2:c.525C>T	19.37:g.14991643G>A		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	172	90	0.523256	NM_030901	Q6IFQ6|Q96R98	Silent	SNP	ENST00000327462.2	37	CCDS12319.1																																																																																			G|0.709;A|0.291	0.291	strong		0.483	OR7A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466523.1	NM_030901	
TAS2R30	259293	hgsc.bcm.edu	37	12	11286736	11286736	+	Silent	SNP	G	G	C	rs112605675		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:11286736G>C	ENST00000539585.1	-	1	507	c.108C>G	c.(106-108)gtC>gtG	p.V36V	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	36					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)	p.V36V(1)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						TTTGTCTCTTGACCCACTCAA	0.388																																					p.V36V		Atlas-SNP	.											TAS2R30,NS,carcinoma,0,1	TAS2R30	28	1	1	Substitution - coding silent(1)	lung(1)	c.C108G						scavenged	.						67.0	66.0	66.0					12																	11286736		2014	4225	6239	SO:0001819	synonymous_variant	259293	exon1			TCTCTTGACCCAC	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19112	protein-coding gene	gene with protein product		613963	"""taste receptor, type 2, member 47"""	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.108C>G	12.37:g.11286736G>C		Somatic	251	1	0.00398406		WXS	Illumina HiSeq	Phase_I	282	10	0.035461	NM_001097643	Q645X7	Silent	SNP	ENST00000539585.1	37	CCDS53750.1																																																																																			G|0.500;C|0.500	0.500	weak		0.388	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643	
NEK4	6787	hgsc.bcm.edu	37	3	52800284	52800284	+	Silent	SNP	T	T	C	rs2230535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:52800284T>C	ENST00000233027.5	-	3	670	c.468A>G	c.(466-468)ttA>ttG	p.L156L	NEK4_ENST00000383721.4_Silent_p.L156L|NEK4_ENST00000535191.1_Silent_p.L67L	NM_001193533.1|NM_003157.4	NP_001180462.1|NP_003148.2	P51957	NEK4_HUMAN	NIMA-related kinase 4	156	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		AGTGGTTCTCTAACACTCGGG	0.428													T|||	1664	0.332268	0.1475	0.4597	5008	,	,		18334	0.4296		0.4195	False		,,,				2504	0.3016				p.L156L		Atlas-SNP	.											.	NEK4	51	.	0			c.A468G						PASS	.	T	,	781,3625	317.2+/-295.0	69,643,1491	255.0	210.0	225.0		201,468	-8.0	0.7	3	dbSNP_98	225	3517,5083	512.6+/-378.0	738,2041,1521	no	coding-synonymous,coding-synonymous	NEK4	NM_001193533.1,NM_003157.4	,	807,2684,3012	CC,CT,TT		40.8953,17.7258,33.0463	,	67/753,156/842	52800284	4298,8708	2203	4300	6503	SO:0001819	synonymous_variant	6787	exon3			GTTCTCTAACACT	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.468A>G	3.37:g.52800284T>C		Somatic	246	1	0.00406504		WXS	Illumina HiSeq	Phase_I	299	137	0.458194	NM_003157	A5YM70|B2R633|B7Z200|Q6P576	Silent	SNP	ENST00000233027.5	37	CCDS2863.1																																																																																			T|0.652;C|0.348	0.348	strong		0.428	NEK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352386.2	NM_003157	
PKD1L1	168507	hgsc.bcm.edu	37	7	47874630	47874630	+	Missense_Mutation	SNP	G	G	A	rs66755489	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47874630G>A	ENST00000289672.2	-	39	6112	c.6062C>T	c.(6061-6063)cCg>cTg	p.P2021L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2021					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						GGCAGACCCCGGGGCTTCCTG	0.572													G|||	679	0.135583	0.2814	0.1052	5008	,	,		16637	0.0496		0.1243	False		,,,				2504	0.0603				p.P2021L		Atlas-SNP	.											PKD1L1,caecum,carcinoma,+1,1	PKD1L1	328	1	0			c.C6062T						PASS	.	G	LEU/PRO	1226,3180	422.5+/-339.8	184,858,1161	62.0	66.0	65.0		6062	-5.6	0.0	7	dbSNP_130	65	1104,7496	230.0+/-264.5	65,974,3261	yes	missense	PKD1L1	NM_138295.3	98	249,1832,4422	AA,AG,GG		12.8372,27.8257,17.9148	benign	2021/2850	47874630	2330,10676	2203	4300	6503	SO:0001583	missense	168507	exon39			GACCCCGGGGCTT	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.6062C>T	7.37:g.47874630G>A	ENSP00000289672:p.Pro2021Leu	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	87	55	0.632184	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	290	0.13278388278388278	125	0.2540650406504065	46	0.1270718232044199	26	0.045454545454545456	93	0.12269129287598944	G	4.277	0.050576	0.08243	0.278257	0.128372	ENSG00000158683	ENST00000289672	T	0.20738	2.05	3.68	-5.62	0.02481	.	.	.	.	.	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.21225	0.053	B	0.09377	0.004	T	0.45760	-0.9239	8	0.27785	T	0.31	2.6368	0.4611	0.00516	0.2946:0.3038:0.1747:0.2269	.	2021	Q8TDX9	PK1L1_HUMAN	L	2021	ENSP00000289672:P2021L	ENSP00000289672:P2021L	P	-	2	0	PKD1L1	47841155	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-1.101000	0.03336	-1.317000	0.02292	0.563000	0.77884	CCG	G|0.831;A|0.169	0.169	strong		0.572	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
DBH	1621	hgsc.bcm.edu	37	9	136509370	136509370	+	Missense_Mutation	SNP	G	G	T	rs4531	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136509370G>T	ENST00000393056.2	+	5	964	c.952G>T	c.(952-954)Gcc>Tcc	p.A318S		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	318			A -> S (in allele DBH-B; dbSNP:rs4531). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:10490716}.		behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	AGCCGGCCTTGCCTTCGGGGG	0.607													G|||	327	0.0652955	0.1316	0.0346	5008	,	,		18372	0.003		0.0716	False		,,,				2504	0.0552				p.A318S		Atlas-SNP	.											.	DBH	86	.	0			c.G952T						PASS	.	G	SER/ALA	530,3876	241.2+/-251.7	34,462,1707	99.0	94.0	96.0		952	-0.9	0.0	9	dbSNP_52	96	668,7932	167.5+/-219.3	26,616,3658	yes	missense	DBH	NM_000787.3	99	60,1078,5365	TT,TG,GG		7.7674,12.0291,9.2111	benign	318/618	136509370	1198,11808	2203	4300	6503	SO:0001583	missense	1621	exon5			GGCCTTGCCTTCG	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.952G>T	9.37:g.136509370G>T	ENSP00000376776:p.Ala318Ser	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	63	29	0.460317	NM_000787	Q5T381|Q96AG2	Missense_Mutation	SNP	ENST00000393056.2	37	CCDS6977.2	137	0.06272893772893773	66	0.13414634146341464	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	6.768	0.510628	0.12883	0.120291	0.077674	ENSG00000123454	ENST00000393056	T	0.28255	1.62	5.13	-0.852	0.10713	Copper type II, ascorbate-dependent monooxygenase, N-terminal (2);PHM/PNGase F domain (1);	0.296425	0.37012	N	0.002299	T	0.00271	0.0008	L	0.31752	0.955	0.58432	P	1.0000000000287557E-6	B	0.22276	0.067	B	0.32393	0.145	T	0.12811	-1.0533	9	0.25751	T	0.34	-27.7151	18.7539	0.91825	0.0:0.6379:0.3621:0.0	rs4531;rs4531	318	P09172	DOPO_HUMAN	S	318	ENSP00000376776:A318S	ENSP00000376776:A318S	A	+	1	0	DBH	135499191	0.697000	0.27767	0.000000	0.03702	0.003000	0.03518	0.926000	0.28804	-0.130000	0.11599	-0.311000	0.09066	GCC	G|0.913;T|0.087	0.087	strong		0.607	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
MUC16	94025	hgsc.bcm.edu	37	19	9060572	9060572	+	Silent	SNP	G	G	A	rs56405542	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9060572G>A	ENST00000397910.4	-	3	27077	c.26874C>T	c.(26872-26874)ggC>ggT	p.G8958G		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8960	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						GCTCTGGGAGGCCTGGATAAG	0.468													g|||	1012	0.202077	0.0968	0.2824	5008	,	,		22043	0.3254		0.167	False		,,,				2504	0.1963				p.G8958G		Atlas-SNP	.											.	MUC16	4315	.	0			c.C26874T						PASS	.	G		413,3555		18,377,1589	200.0	186.0	191.0		26874	-3.2	0.0	19	dbSNP_129	191	1521,6807		137,1247,2780	yes	coding-synonymous	MUC16	NM_024690.2		155,1624,4369	AA,AG,GG		18.2637,10.4083,15.7287		8958/14508	9060572	1934,10362	1984	4164	6148	SO:0001819	synonymous_variant	94025	exon3			TGGGAGGCCTGGA	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.26874C>T	19.37:g.9060572G>A		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	234	90	0.384615	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.788;A|0.212	0.212	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
TM6SF2	53345	hgsc.bcm.edu	37	19	19380996	19380996	+	Silent	SNP	G	G	T	rs2074300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19380996G>T	ENST00000389363.4	-	4	459	c.387C>A	c.(385-387)ggC>ggA	p.G129G	TM6SF2_ENST00000586107.1_5'UTR|AC138430.4_ENST00000586064.2_RNA	NM_001001524.2	NP_001001524.2	Q9BZW4	TM6S2_HUMAN	transmembrane 6 superfamily member 2	129						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	14			Epithelial(12;0.0151)			TGCAGATGGCGCCGGCCATGG	0.637													G|||	1331	0.265775	0.211	0.3141	5008	,	,		16900	0.3065		0.1501	False		,,,				2504	0.3824				p.G129G		Atlas-SNP	.											.	TM6SF2	39	.	0			c.C387A						PASS	.	G		822,3316		79,664,1326	38.0	41.0	40.0		387	-8.2	0.3	19	dbSNP_96	40	1467,6937		130,1207,2865	no	coding-synonymous	TM6SF2	NM_001001524.2		209,1871,4191	TT,TG,GG		17.456,19.8647,18.2507		129/378	19380996	2289,10253	2069	4202	6271	SO:0001819	synonymous_variant	53345	exon4			GATGGCGCCGGCC	AF255923	CCDS42528.1	19p13.3-p12	2008-02-05							11861	protein-coding gene	gene with protein product		606563				11124529	Standard	NM_001001524		Approved	Lpr4	uc002nmd.1	Q9BZW4		ENST00000389363.4:c.387C>A	19.37:g.19380996G>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	96	45	0.46875	NM_001001524	Q0IJ64	Silent	SNP	ENST00000389363.4	37	CCDS42528.1	500	0.22893772893772893	102	0.2073170731707317	100	0.27624309392265195	178	0.3111888111888112	120	0.158311345646438	G	10.72	1.430186	0.25726	0.198647	0.17456	ENSG00000213996	ENST00000431465	.	.	.	4.74	-8.25	0.01025	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49582	P	1.9700000000000273E-4	.	.	.	.	.	.	T	0.36504	-0.9745	4	0.87932	D	0	-8.7426	1.1726	0.01829	0.235:0.2013:0.3962:0.1674	rs2074300	.	.	.	E	152	.	ENSP00000391180:A152E	A	-	2	0	TM6SF2	19241996	0.000000	0.05858	0.332000	0.25469	0.729000	0.41735	-1.731000	0.01853	-1.096000	0.03046	0.505000	0.49811	GCG	G|0.794;T|0.206	0.206	strong		0.637	TM6SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460122.2	NM_203510	
FMO2	2327	hgsc.bcm.edu	37	1	171168584	171168584	+	Missense_Mutation	SNP	C	C	T	rs386636736|rs2020862	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:171168584C>T	ENST00000209929.7	+	5	742	c.584C>T	c.(583-585)tCa>tTa	p.S195L	RP1-127D3.4_ENST00000445290.1_RNA|FMO2_ENST00000529935.1_Intron|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.S195L			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	195					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.S195L(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					ATGGGAAACTCAGGCTCAGAT	0.488													C|||	2368	0.472843	0.5265	0.4827	5008	,	,		19421	0.5456		0.2962	False		,,,				2504	0.5				p.S195L		Atlas-SNP	.											FMO2,NS,carcinoma,-1,2	FMO2	66	2	1	Substitution - Missense(1)	stomach(1)	c.C584T	GRCh37	CM033900	FMO2	M	rs2020862	PASS	.	C	LEU/SER	2174,2232	585.1+/-386.2	561,1052,590	134.0	140.0	138.0		584	6.2	1.0	1	dbSNP_98	138	2753,5847	439.1+/-359.1	448,1857,1995	yes	missense	FMO2	NM_001460.2	145	1009,2909,2585	TT,TC,CC		32.0116,49.3418,37.8825	probably-damaging	195/472	171168584	4927,8079	2203	4300	6503	SO:0001583	missense	2327	exon5			GAAACTCAGGCTC	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.584C>T	1.37:g.171168584C>T	ENSP00000209929:p.Ser195Leu	Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	165	165	1	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	788	0.3608058608058608	190	0.3861788617886179	136	0.3756906077348066	272	0.4755244755244755	190	0.25065963060686014	C	22.4	4.283324	0.80803	0.493418	0.320116	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.60548	0.18;0.18	6.17	6.17	0.99709	.	0.056199	0.85682	D	0.000000	T	0.80824	0.4697	H	0.99689	4.705	0.09310	P	0.9999999445746	B	0.29232	0.238	B	0.41764	0.366	T	0.82810	-0.0273	9	0.87932	D	0	-3.8921	19.6509	0.95805	0.0:1.0:0.0:0.0	rs2020862;rs2266706;rs58871762;rs2020862	195	Q99518	FMO2_HUMAN	L	195	ENSP00000209929:S195L;ENSP00000405905:S195L	ENSP00000209929:S195L	S	+	2	0	FMO2	169435208	1.000000	0.71417	0.969000	0.41365	0.124000	0.20399	5.980000	0.70516	2.941000	0.99782	0.655000	0.94253	TCA	C|0.606;T|0.394	0.394	strong		0.488	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
FCHSD1	89848	hgsc.bcm.edu	37	5	141021294	141021294	+	Missense_Mutation	SNP	T	T	G	rs116772138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:141021294T>G	ENST00000435817.2	-	19	2032	c.1982A>C	c.(1981-1983)gAc>gCc	p.D661A	FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522126.1_3'UTR|FCHSD1_ENST00000522783.1_3'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	661	Pro-rich.								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)			TGCCATCATGTCCAGGAACCC	0.502													T|||	54	0.0107827	0.0023	0.0202	5008	,	,		19938	0.0		0.0169	False		,,,				2504	0.0204				p.D661A		Atlas-SNP	.											.	FCHSD1	51	.	0			c.A1982C						PASS	.	T	ALA/ASP	20,3806		0,20,1893	76.0	78.0	77.0		1982	5.2	1.0	5	dbSNP_132	77	206,8078		7,192,3943	yes	missense	FCHSD1	NM_033449.2	126	7,212,5836	GG,GT,TT		2.4867,0.5227,1.8662	possibly-damaging	661/691	141021294	226,11884	1913	4142	6055	SO:0001583	missense	89848	exon19			ATCATGTCCAGGA	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.1982A>C	5.37:g.141021294T>G	ENSP00000399259:p.Asp661Ala	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	61	25	0.409836	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	24	0.01098901098901099	3	0.006097560975609756	7	0.019337016574585635	0	0.0	14	0.018469656992084433	T	12.24	1.878095	0.33162	0.005227	0.024867	ENSG00000197948	ENST00000435817	T	0.26810	1.71	5.2	5.2	0.72013	.	0.198344	0.43416	D	0.000577	T	0.12561	0.0305	L	0.29908	0.895	0.80722	D	1	P;P	0.52842	0.93;0.956	P;P	0.49192	0.602;0.537	T	0.01036	-1.1473	10	0.24483	T	0.36	-9.066	11.636	0.51204	0.0:0.0:0.0:1.0	.	341;661	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	A	661	ENSP00000399259:D661A	ENSP00000399259:D661A	D	-	2	0	FCHSD1	141001478	0.791000	0.28800	1.000000	0.80357	0.706000	0.40770	2.385000	0.44371	2.308000	0.77769	0.533000	0.62120	GAC	T|0.986;G|0.014	0.014	strong		0.502	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
HLA-A	3105	hgsc.bcm.edu	37	6	29910378	29910378	+	Silent	SNP	C	C	T	rs41546314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29910378C>T	ENST00000396634.1	+	3	389	c.48C>T	c.(46-48)gcC>gcT	p.A16A	HLA-A_ENST00000376809.5_Silent_p.A16A|HLA-A_ENST00000376806.5_Silent_p.A16A|HLA-A_ENST00000376802.2_Silent_p.A16A			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	16					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						TCTCGGGGGCCCTGGCCCTGA	0.711									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	1224	0.244409	0.1755	0.3357	5008	,	,		14832	0.2917		0.3141	False		,,,				2504	0.1524				p.A16A		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.C48T						PASS	.	C		793,3603		72,649,1477	28.0	31.0	30.0		48	-3.8	0.0	6	dbSNP_131	30	2397,6193		349,1699,2247	no	coding-synonymous	HLA-A	NM_002116.7		421,2348,3724	TT,TC,CC		27.9045,18.0391,24.5649		16/366	29910378	3190,9796	2198	4295	6493	SO:0001819	synonymous_variant	3105	exon1	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGGGGCCCTGGCC	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.48C>T	6.37:g.29910378C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			C|0.769;T|0.231	0.231	strong		0.711	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
C11orf63	79864	hgsc.bcm.edu	37	11	122795688	122795688	+	Silent	SNP	T	T	C	rs11218891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:122795688T>C	ENST00000531316.1	+	3	1040	c.948T>C	c.(946-948)gaT>gaC	p.D316D	RNU4-23P_ENST00000362839.1_RNA|C11orf63_ENST00000227349.2_Silent_p.D316D			Q6NUN7	CK063_HUMAN	chromosome 11 open reading frame 63	316					axoneme assembly (GO:0035082)|brain development (GO:0007420)|cerebrospinal fluid secretion (GO:0033326)|ciliary basal body organization (GO:0032053)					breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(13)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	47		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.018)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.34e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0311)		ATCCTGAAGATAAATGGCATC	0.413													C|||	903	0.180312	0.0764	0.2104	5008	,	,		23932	0.2024		0.2903	False		,,,				2504	0.1636				p.D316D		Atlas-SNP	.											.	C11orf63	116	.	0			c.T948C						PASS	.	C		495,3909	780.0+/-414.4	36,423,1743	170.0	143.0	153.0		948	6.0	1.0	11	dbSNP_120	153	2635,5963	686.7+/-404.1	387,1861,2051	no	coding-synonymous	C11orf63	NM_024806.2		423,2284,3794	CC,CT,TT		30.6467,11.2398,24.0732		316/779	122795688	3130,9872	2202	4299	6501	SO:0001819	synonymous_variant	79864	exon4			TGAAGATAAATGG	BC068507	CCDS8438.1, CCDS8439.1	11q24.1	2012-05-25			ENSG00000109944	ENSG00000109944			26288	protein-coding gene	gene with protein product						12477932	Standard	NM_024806		Approved	FLJ23554	uc001pym.4	Q6NUN7	OTTHUMG00000166027	ENST00000531316.1:c.948T>C	11.37:g.122795688T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	107	71	0.663551	NM_024806	A8K6G0|Q96GB5|Q9H5D6	Silent	SNP	ENST00000531316.1	37	CCDS8438.1																																																																																			T|0.780;C|0.220	0.220	strong		0.413	C11orf63-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387511.1	NM_024806	
CCDC180	100499483	hgsc.bcm.edu	37	9	100122291	100122291	+	Missense_Mutation	SNP	T	T	C	rs3747495	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100122291T>C	ENST00000357054.1	+	37	4371	c.3436T>C	c.(3436-3438)Ttc>Ctc	p.F1146L	CCDC180_ENST00000529487.1_Missense_Mutation_p.F1175L|CCDC180_ENST00000375202.2_Missense_Mutation_p.F1175L|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_3'UTR			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	1146			F -> L (in dbSNP:rs3747495).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.F1146L(1)									ACTCCTCAGCTTCGTCCAAAC	0.507													T|||	1159	0.23143	0.1369	0.3444	5008	,	,		21733	0.2907		0.1879	False		,,,				2504	0.2628				p.F1175L		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.T3523C						PASS	.	T	LEU/PHE	618,3788	267.7+/-268.0	42,534,1627	166.0	166.0	166.0		3523	3.4	0.0	9	dbSNP_107	166	1588,7012	298.5+/-303.9	142,1304,2854	yes	missense	C9orf174	NM_020893.2	22	184,1838,4481	CC,CT,TT		18.4651,14.0263,16.9614	benign	1175/1702	100122291	2206,10800	2203	4300	6503	SO:0001583	missense	0	exon26			CTCAGCTTCGTCC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.3436T>C	9.37:g.100122291T>C	ENSP00000349562:p.Phe1146Leu	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	151	79	0.523179	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		508	0.2326007326007326	52	0.10569105691056911	128	0.35359116022099446	174	0.3041958041958042	154	0.20316622691292877	T	12.99	2.103262	0.37145	0.140263	0.184651	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	T;T;T	0.08102	3.13;3.15;3.15	5.71	3.39	0.38822	.	0.472963	0.25919	N	0.027445	T	0.00012	0.0000	L	0.27053	0.805	0.54753	P	1.0999999999983245E-5	B;B	0.33637	0.119;0.42	B;B	0.32090	0.097;0.14	T	0.45366	-0.9266	9	0.10377	T	0.69	-2.0155	6.8103	0.23801	0.0:0.192:0.0:0.808	rs3747495;rs13302501;rs17583370;rs52794397;rs61215609;rs3747495	1314;1146	B7ZMG3;Q9P1Z9	.;CI174_HUMAN	L	1146;1175;1175	ENSP00000349562:F1146L;ENSP00000364348:F1175L;ENSP00000434727:F1175L	ENSP00000349562:F1146L	F	+	1	0	C9orf174	99162112	0.676000	0.27567	0.002000	0.10522	0.031000	0.12232	1.588000	0.36633	0.544000	0.28883	0.459000	0.35465	TTC	T|0.807;C|0.193	0.193	strong		0.507	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
TMEM132A	54972	hgsc.bcm.edu	37	11	60703882	60703882	+	Missense_Mutation	SNP	G	G	A	rs61755079	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:60703882G>A	ENST00000453848.2	+	11	2733	c.2575G>A	c.(2575-2577)Gtg>Atg	p.V859M	TMEM132A_ENST00000005286.4_Missense_Mutation_p.V860M			Q24JP5	T132A_HUMAN	transmembrane protein 132A	859	Binds to HSPA5/GRP78. {ECO:0000250}.|Confers cellular localization similar to full-length form. {ECO:0000250}.					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						AGTCTTCTGCGTGGCCATCTT	0.607													G|||	82	0.0163738	0.0015	0.0288	5008	,	,		19848	0.0		0.0557	False		,,,				2504	0.0041				p.V860M		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G2578A						PASS	.	G	MET/VAL,MET/VAL	52,4354	51.6+/-87.1	0,52,2151	244.0	218.0	227.0		2578,2575	3.3	0.7	11	dbSNP_129	227	487,8111	141.9+/-198.1	17,453,3829	yes	missense,missense	TMEM132A	NM_017870.3,NM_178031.2	21,21	17,505,5980	AA,AG,GG		5.6641,1.1802,4.1449	benign,benign	860/1025,859/1024	60703882	539,12465	2203	4299	6502	SO:0001583	missense	54972	exon11			TTCTGCGTGGCCA	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.2575G>A	11.37:g.60703882G>A	ENSP00000405823:p.Val859Met	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	132	58	0.439394	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	52	0.023809523809523808	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	42	0.055408970976253295	G	12.95	2.090289	0.36855	0.011802	0.056641	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	T;T	0.14266	2.52;2.52	5.15	3.26	0.37387	.	0.258233	0.25657	N	0.029177	T	0.00637	0.0021	N	0.08118	0	0.35318	D	0.784534	P;P	0.35192	0.489;0.489	B;B	0.27262	0.078;0.078	T	0.40739	-0.9547	10	0.87932	D	0	-10.7859	8.8248	0.35047	0.0:0.7352:0.1742:0.0905	rs61755079	859;860	Q24JP5;Q24JP5-2	T132A_HUMAN;.	M	610;859;860	ENSP00000405823:V859M;ENSP00000005286:V860M	ENSP00000005286:V860M	V	+	1	0	TMEM132A	60460458	0.120000	0.22244	0.721000	0.30653	0.812000	0.45895	0.498000	0.22530	0.668000	0.31126	0.655000	0.94253	GTG	G|0.963;A|0.037	0.037	strong		0.607	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
NTAN1	123803	hgsc.bcm.edu	37	16	15131962	15131962	+	Missense_Mutation	SNP	A	A	G	rs1135999	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15131962A>G	ENST00000287706.3	-	10	951	c.859T>C	c.(859-861)Tct>Cct	p.S287P	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	287			S -> P (in dbSNP:rs1135999).		adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						TTATTTCCAGAAAACAGTGTG	0.393													G|||	1723	0.34405	0.1838	0.5331	5008	,	,		17634	0.37		0.3072	False		,,,				2504	0.4376				p.S287P		Atlas-SNP	.											.	NTAN1	21	.	0			c.T859C						PASS	.	G	PRO/SER	985,3409	720.3+/-409.0	118,749,1330	80.0	82.0	82.0		859	5.9	1.0	16	dbSNP_86	82	2565,6035	682.5+/-403.8	359,1847,2094	yes	missense	NTAN1	NM_173474.2	74	477,2596,3424	GG,GA,AA		29.8256,22.4169,27.3203	benign	287/311	15131962	3550,9444	2197	4300	6497	SO:0001583	missense	123803	exon10			TTCCAGAAAACAG	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.859T>C	16.37:g.15131962A>G	ENSP00000287706:p.Ser287Pro	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	134	133	0.992537	NM_173474	Q7Z4Z0	Missense_Mutation	SNP	ENST00000287706.3	37	CCDS10558.1	727	0.33287545787545786	94	0.1910569105691057	174	0.48066298342541436	216	0.3776223776223776	243	0.32058047493403696	G	7.877	0.729487	0.15507	0.224169	0.298256	ENSG00000157045	ENST00000287706	T	0.23552	1.9	5.87	5.87	0.94306	.	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00036	-2.54	0.48762	P	2.950000000000452E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.45101	-0.9284	9	0.02654	T	1	-10.699	14.696	0.69121	0.0692:0.0:0.9308:0.0	rs1135999;rs3087673;rs3199047;rs17841256;rs58432330;rs1135999	287	Q96AB6	NTAN1_HUMAN	P	287	ENSP00000287706:S287P	ENSP00000287706:S287P	S	-	1	0	NTAN1	15039463	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.104000	0.64584	1.644000	0.50603	-0.119000	0.15052	TCT	A|0.707;G|0.293	0.293	strong		0.393	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
LPCAT1	79888	hgsc.bcm.edu	37	5	1501695	1501695	+	Silent	SNP	G	G	A	rs17588991	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:1501695G>A	ENST00000283415.3	-	2	291	c.159C>T	c.(157-159)ctC>ctT	p.L53L		NM_024830.3	NP_079106.3	Q8NF37	PCAT1_HUMAN	lysophosphatidylcholine acyltransferase 1	53					cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|negative regulation of phosphatidylcholine biosynthetic process (GO:2001246)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein catabolic process (GO:0045732)|retina development in camera-type eye (GO:0060041)|small molecule metabolic process (GO:0044281)|surfactant homeostasis (GO:0043129)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)	1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkenylglycerophosphocholine O-acyltransferase activity (GO:0047159)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|1-alkylglycerophosphocholine O-acyltransferase activity (GO:0047191)|calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(12)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(19;0.0274)|all cancers(22;0.0534)	GBM - Glioblastoma multiforme(108;0.156)		GGACCGGGAAGAGCGTCAGTG	0.652													G|||	158	0.0315495	0.0227	0.0403	5008	,	,		16460	0.0		0.0577	False		,,,				2504	0.0429				p.L53L		Atlas-SNP	.											.	LPCAT1	70	.	0			c.C159T						PASS	.	G		154,4250	104.7+/-143.2	1,152,2049	42.0	50.0	47.0		159	-1.8	1.0	5	dbSNP_123	47	470,8130	138.3+/-195.1	10,450,3840	no	coding-synonymous	LPCAT1	NM_024830.3		11,602,5889	AA,AG,GG		5.4651,3.4968,4.7985		53/535	1501695	624,12380	2202	4300	6502	SO:0001819	synonymous_variant	79888	exon2			CGGGAAGAGCGTC	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.159C>T	5.37:g.1501695G>A		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	176	85	0.482955	NM_024830	Q1HAQ1|Q7Z4G6|Q8N3U7|Q8WUL8|Q9GZW6	Silent	SNP	ENST00000283415.3	37	CCDS3864.1																																																																																			G|0.956;A|0.044	0.044	strong		0.652	LPCAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304032.1	NM_024830	
KRT35	3886	hgsc.bcm.edu	37	17	39634625	39634625	+	Silent	SNP	A	A	G	rs7216017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39634625A>G	ENST00000393989.1	-	5	1029	c.987T>C	c.(985-987)gcT>gcC	p.A329A	KRT35_ENST00000246639.2_Silent_p.A299A	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	329	Coil 2.|Rod.				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)				TGCTGTGCTGAGCCTGCAGCT	0.617													G|||	2885	0.576078	0.736	0.5591	5008	,	,		18814	0.3403		0.5398	False		,,,				2504	0.6524				p.A329A		Atlas-SNP	.											.	KRT35	58	.	0			c.T987C						PASS	.	G		3100,1306	441.8+/-346.5	1078,944,181	73.0	62.0	65.0		987	4.4	1.0	17	dbSNP_116	65	4679,3921	545.7+/-384.8	1261,2157,882	no	coding-synonymous	KRT35	NM_002280.4		2339,3101,1063	GG,GA,AA		45.593,29.6414,40.1891		329/456	39634625	7779,5227	2203	4300	6503	SO:0001819	synonymous_variant	3886	exon5			GTGCTGAGCCTGC	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.987T>C	17.37:g.39634625A>G		Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_002280	O76012|Q92651	Silent	SNP	ENST00000393989.1	37	CCDS11394.2																																																																																			A|0.455;G|0.545	0.545	strong		0.617	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
AP5Z1	9907	hgsc.bcm.edu	37	7	4827330	4827330	+	Silent	SNP	C	C	T	rs17135128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4827330C>T	ENST00000348624.4	+	11	1471	c.1377C>T	c.(1375-1377)gaC>gaT	p.D459D	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000401897.1_Silent_p.D459D	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	459					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGGTGGACGCTGGCACAG	0.692													C|||	408	0.0814696	0.0401	0.036	5008	,	,		15883	0.0496		0.0736	False		,,,				2504	0.2106				p.D459D		Atlas-SNP	.											KIAA0415_ENST00000450194,rectum,carcinoma,0,2	.	.	2	0			c.C1377T						PASS	.	C		189,3981		5,179,1901	25.0	31.0	29.0		1377	-3.7	0.0	7	dbSNP_123	29	532,7742		19,494,3624	no	coding-synonymous	KIAA0415	NM_014855.2		24,673,5525	TT,TC,CC		6.4298,4.5324,5.794		459/808	4827330	721,11723	2085	4137	6222	SO:0001819	synonymous_variant	9907	exon11			GGTGGACGCTGGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1377C>T	7.37:g.4827330C>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	115	52	0.452174	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			C|0.943;T|0.057	0.057	strong		0.692	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
C10orf71	118461	hgsc.bcm.edu	37	10	50534599	50534599	+	Missense_Mutation	SNP	G	G	A	rs10857472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50534599G>A	ENST00000374144.3	+	3	4297	c.4009G>A	c.(4009-4011)Ggc>Agc	p.G1337S	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1337			G -> S (in dbSNP:rs10857472).							endometrium(1)	1						GCTGTACCCCGGCTTCCAGCC	0.711													g|||	1651	0.329673	0.2194	0.3818	5008	,	,		12951	0.1925		0.4354	False		,,,				2504	0.4744				p.G1337S		Atlas-SNP	.											.	C10orf71	179	.	0			c.G4009A						PASS	.		SER/GLY,	294,1052		47,200,426	4.0	5.0	5.0		4009,	2.6	0.0	10	dbSNP_120	5	1402,1722		371,660,531	yes	missense,intron	C10orf71	NM_001135196.1,NM_199459.3	56,	418,860,957	AA,AG,GG		44.8784,21.8425,37.9418	,	1337/1436,	50534599	1696,2774	673	1562	2235	SO:0001583	missense	118461	exon3			TACCCCGGCTTCC	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.4009G>A	10.37:g.50534599G>A	ENSP00000363259:p.Gly1337Ser	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	25	9	0.36	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	677	0.309981684981685	107	0.21747967479674796	137	0.3784530386740331	104	0.18181818181818182	329	0.4340369393139842	g	16.93	3.257811	0.59321	0.218425	0.448784	ENSG00000177354	ENST00000374144	T	0.46063	0.88	5.42	2.56	0.30785	.	0.523886	0.14240	U	0.332142	T	0.00012	0.0000	L	0.47716	1.5	0.54753	P	1.2000000000012001E-5	.	.	.	.	.	.	T	0.47471	-0.9115	7	0.30854	T	0.27	.	5.5553	0.17113	0.2869:0.1529:0.5602:0.0	rs10857472;rs10857472	.	.	.	S	1337	ENSP00000363259:G1337S	ENSP00000363259:G1337S	G	+	1	0	C10orf71	50204605	1.000000	0.71417	0.002000	0.10522	0.536000	0.34869	4.340000	0.59328	0.270000	0.21984	0.298000	0.19748	GGC	G|0.683;A|0.317	0.317	strong		0.711	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
ZNF608	57507	hgsc.bcm.edu	37	5	123983915	123983915	+	Missense_Mutation	SNP	G	G	T	rs6862252	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:123983915G>T	ENST00000306315.5	-	4	2597	c.2162C>A	c.(2161-2163)aCc>aAc	p.T721N	ZNF608_ENST00000504926.1_Missense_Mutation_p.T294N	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	721			T -> N (in dbSNP:rs6862252). {ECO:0000269|PubMed:10508479, ECO:0000269|PubMed:10574462, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.				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)		TTTGCAGTTGGTAGCTTTTTT	0.493													T|||	3155	0.629992	0.7065	0.451	5008	,	,		13373	0.753		0.5457	False		,,,				2504	0.6135				p.T721N		Atlas-SNP	.											.	ZNF608	117	.	0			c.C2162A						PASS	.	T	ASN/THR	2891,1515	473.7+/-356.8	941,1009,253	41.0	44.0	43.0		2162	-0.8	0.9	5	dbSNP_116	43	4378,4222	559.8+/-387.5	1133,2112,1055	yes	missense	ZNF608	NM_020747.2	65	2074,3121,1308	TT,TG,GG		49.093,34.3849,44.1104	benign	721/1513	123983915	7269,5737	2203	4300	6503	SO:0001583	missense	57507	exon4			CAGTTGGTAGCTT	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.2162C>A	5.37:g.123983915G>T	ENSP00000307746:p.Thr721Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	136	70	0.514706	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	1373	0.6286630036630036	359	0.7296747967479674	169	0.46685082872928174	433	0.756993006993007	412	0.5435356200527705	T	3.774	-0.046942	0.07407	0.656151	0.50907	ENSG00000168916	ENST00000504926;ENST00000306315	T;T	0.42131	0.98;0.98	5.88	-0.826	0.10805	.	0.435018	0.25283	N	0.031797	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	0.27806	-1.0063	9	0.13853	T	0.58	-13.0083	7.4732	0.27361	0.0:0.2465:0.4483:0.3052	rs6862252;rs17318183;rs45631747;rs52829176;rs59496652;rs61726319;rs6862252	721	Q9ULD9	ZN608_HUMAN	N	294;721	ENSP00000427657:T294N;ENSP00000307746:T721N	ENSP00000307746:T721N	T	-	2	0	ZNF608	124011814	0.125000	0.22332	0.870000	0.34147	0.950000	0.60333	-0.204000	0.09425	-0.377000	0.07930	-0.381000	0.06696	ACC	G|0.405;N|0.001	.	strong		0.493	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
ZCWPW1	55063	hgsc.bcm.edu	37	7	99998750	99998750	+	Silent	SNP	G	G	A	rs145308367	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99998750G>A	ENST00000398027.2	-	18	2081	c.1834C>T	c.(1834-1836)Ctg>Ttg	p.L612L	ZCWPW1_ENST00000324725.6_Silent_p.L441L|ZCWPW1_ENST00000360951.4_3'UTR|ZCWPW1_ENST00000490721.1_Silent_p.L441L	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	612							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCCAGGTCCAGGTCACTGGAG	0.637													g|||	12	0.00239617	0.0	0.0043	5008	,	,		16848	0.0		0.006	False		,,,				2504	0.0031				p.L612L		Atlas-SNP	.											.	ZCWPW1	41	.	0			c.C1834T						PASS	.	G		4,4012		0,4,2004	49.0	51.0	51.0		1834	4.1	1.0	7	dbSNP_134	51	76,8316		1,74,4121	no	coding-synonymous	ZCWPW1	NM_017984.3		1,78,6125	AA,AG,GG		0.9056,0.0996,0.6447		612/649	99998750	80,12328	2008	4196	6204	SO:0001819	synonymous_variant	55063	exon18			GGTCCAGGTCACT	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"""zinc finger, CW-type with PWWP domain 1"""			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1834C>T	7.37:g.99998750G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	111	49	0.441441	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Silent	SNP	ENST00000398027.2	37	CCDS43623.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	10.34	1.323458	0.24080	9.96E-4	0.009056	ENSG00000233389	ENST00000449355	.	.	.	5.04	4.12	0.48240	.	.	.	.	.	T	0.50274	0.1606	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52939	-0.8508	4	.	.	.	-5.4653	8.2412	0.31660	0.1153:0.0:0.8847:0.0	.	.	.	.	K	7	.	.	R	+	2	0	AC005071.3	99836686	0.998000	0.40836	1.000000	0.80357	0.228000	0.25075	0.143000	0.16115	1.416000	0.47057	0.655000	0.94253	AGG	G|0.994;A|0.006	0.006	strong		0.637	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984	
C4orf27	54969	hgsc.bcm.edu	37	4	170678993	170678993	+	Silent	SNP	T	T	C	rs11540095	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:170678993T>C	ENST00000393381.2	-	1	111	c.36A>G	c.(34-36)ggA>ggG	p.G12G		NM_017867.2	NP_060337.2	Q9NWY4	CD027_HUMAN	chromosome 4 open reading frame 27	12						nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)	12		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.018)|LUSC - Lung squamous cell carcinoma(193;0.116)		GCGGCCCCTCTCCGCCGGGCC	0.692													C|||	3893	0.777356	0.6899	0.7954	5008	,	,		12693	0.881		0.7843	False		,,,				2504	0.7689				p.G12G		Atlas-SNP	.											.	C4orf27	32	.	0			c.A36G						PASS	.	C		2972,1212		1062,848,182	5.0	6.0	6.0		36	1.7	0.7	4	dbSNP_120	6	6667,1561		2735,1197,182	no	coding-synonymous	C4orf27	NM_017867.2		3797,2045,364	CC,CT,TT		18.9718,28.9675,22.3413		12/347	170678993	9639,2773	2092	4114	6206	SO:0001819	synonymous_variant	54969	exon1			CCCCTCTCCGCCG	BC010367	CCDS3813.1	4q33	2011-01-25			ENSG00000056050	ENSG00000056050			26051	protein-coding gene	gene with protein product						11230166	Standard	NM_017867		Approved	FLJ20534	uc003isl.4	Q9NWY4	OTTHUMG00000160960	ENST00000393381.2:c.36A>G	4.37:g.170678993T>C		Somatic	10	0	0		WXS	Illumina HiSeq	Phase_I	27	9	0.333333	NM_017867		Silent	SNP	ENST00000393381.2	37	CCDS3813.1																																																																																			T|0.200;C|0.800	0.800	strong		0.692	C4orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363140.1	NM_017867	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951581	130951581	+	Silent	SNP	A	A	G	rs1052312	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130951581A>G	ENST00000312988.7	-	4	934	c.834T>C	c.(832-834)gcT>gcC	p.A278A		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	278					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					AGGCCTTCTCAGCTGAGATGA	0.597													.|||	2348	0.46885	0.587	0.5014	5008	,	,		21460	0.4365		0.3628	False		,,,				2504	0.4284				p.A278A		Atlas-SNP	.											.	TUBA3E	73	.	0			c.T834C						PASS	.						113.0	101.0	105.0					2																	130951581		2203	4300	6503	SO:0001819	synonymous_variant	112714	exon4			CTTCTCAGCTGAG	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.834T>C	2.37:g.130951581A>G		Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	373	104	0.27882	NM_207312		Silent	SNP	ENST00000312988.7	37	CCDS2158.1																																																																																			A|0.790;G|0.210	0.210	strong		0.597	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
CRIPAK	285464	hgsc.bcm.edu	37	4	1389156	1389156	+	Missense_Mutation	SNP	T	T	C	rs71614972	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1389156T>C	ENST00000324803.4	+	1	3817	c.857T>C	c.(856-858)aTg>aCg	p.M286T		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	286					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CATGTGCCGATGTGGAGTGCC	0.677													T|||	3799	0.758586	0.9349	0.7954	5008	,	,		13659	0.7014		0.6392	False		,,,				2504	0.6759				p.M286T		Atlas-SNP	.											CRIPAK,rectum,carcinoma,0,1	CRIPAK	185	1	0			c.T857C						PASS	.						131.0	131.0	131.0					4																	1389156		2202	4299	6501	SO:0001583	missense	285464	exon1			TGCCGATGTGGAG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.857T>C	4.37:g.1389156T>C	ENSP00000323978:p.Met286Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	26	0.285714	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	T	0.854	-0.737538	0.03111	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.17691	2.26	0.815	-1.63	0.08345	Post-SET domain (1);	.	.	.	.	T	0.06826	0.0174	N	0.08118	0	0.80722	P	0.0	B	0.12630	0.006	B	0.06405	0.002	T	0.38067	-0.9678	8	0.25106	T	0.35	.	5.1474	0.14993	0.0:0.3546:0.0:0.6454	.	286	Q8N1N5	CRPAK_HUMAN	T	286;228	ENSP00000323978:M286T	ENSP00000323978:M286T	M	+	2	0	CRIPAK	1379156	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.361000	0.01083	-0.674000	0.05253	-0.530000	0.04314	ATG	C|1.000;|0.000	1.000	strong		0.677	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
SH2D1B	117157	hgsc.bcm.edu	37	1	162367071	162367071	+	Silent	SNP	C	C	T	rs17852003	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:162367071C>T	ENST00000367929.2	-	4	507	c.398G>A	c.(397-399)tGa>tAa	p.*133*	SH2D1B_ENST00000359567.3_Silent_p.*78*	NM_053282.4	NP_444512.2	O14796	SH21B_HUMAN	SH2 domain containing 1B	0					leukocyte activation involved in immune response (GO:0002366)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of innate immune response (GO:0045089)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of natural killer cell activation (GO:0032814)	intracellular (GO:0005622)	protein binding, bridging (GO:0030674)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			GCCTTATCTTCAAGGCAAGAC	0.458													C|||	1539	0.307308	0.4418	0.2925	5008	,	,		19423	0.2063		0.3171	False		,,,				2504	0.2301				p.X133X		Atlas-SNP	.											.	SH2D1B	19	.	0			c.G398A						PASS	.	C		1827,2579	532.8+/-373.5	377,1073,753	93.0	85.0	88.0		398	2.9	1.0	1	dbSNP_123	88	2620,5980	423.6+/-354.4	384,1852,2064	no	coding-synonymous	SH2D1B	NM_053282.4		761,2925,2817	TT,TC,CC		30.4651,41.4662,34.1919		133/133	162367071	4447,8559	2203	4300	6503	SO:0001819	synonymous_variant	117157	exon4			TATCTTCAAGGCA	AF484964	CCDS30928.1	1q23.3	2013-02-14			ENSG00000198574	ENSG00000198574		"""SH2 domain containing"""	30416	protein-coding gene	gene with protein product		608510				9000139, 11689425	Standard	NM_053282		Approved	EAT2	uc001gbz.1	O14796	OTTHUMG00000031377	ENST00000367929.2:c.398G>A	1.37:g.162367071C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	90	37	0.411111	NM_053282	B2RBN6|Q5T0L1|Q8NI18|Q969K9	Silent	SNP	ENST00000367929.2	37	CCDS30928.1																																																																																			C|0.671;T|0.329	0.329	strong		0.458	SH2D1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076794.1	NM_053282	
NDRG4	65009	hgsc.bcm.edu	37	16	58545426	58545426	+	Silent	SNP	A	A	G	rs42945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58545426A>G	ENST00000570248.1	+	15	1111	c.1005A>G	c.(1003-1005)tcA>tcG	p.S335S	NDRG4_ENST00000394282.4_Silent_p.S374S|NDRG4_ENST00000356752.4_Silent_p.S352S|NDRG4_ENST00000562999.1_Silent_p.S310S|NDRG4_ENST00000569923.1_Silent_p.S267S|NDRG4_ENST00000258187.5_Silent_p.S354S|NDRG4_ENST00000568640.1_Silent_p.S340S|NDRG4_ENST00000563799.1_Silent_p.S340S|NDRG4_ENST00000566192.1_Silent_p.S322S|NDRG4_ENST00000394279.2_Silent_p.S354S	NM_001242835.1	NP_001229764.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	335					cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)				breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						GCACCCACTCAGAGAGCAGCG	0.682													G|||	4078	0.814297	0.9561	0.7392	5008	,	,		15744	0.9673		0.5577	False		,,,				2504	0.7822				p.S374S		Atlas-SNP	.											.	NDRG4	29	.	0			c.A1122G						PASS	.	G	,,,,,,	3883,513	222.3+/-239.2	1720,443,35	61.0	58.0	59.0		1122,1056,1020,1005,966,1062,1062	-8.2	0.1	16	dbSNP_76	59	4614,3980	526.3+/-380.9	1237,2140,920	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NDRG4	NM_001130487.1,NM_001242833.1,NM_001242834.1,NM_001242835.1,NM_001242836.1,NM_020465.3,NM_022910.3	,,,,,,	2957,2583,955	GG,GA,AA		46.3114,11.6697,34.5881	,,,,,,	374/392,352/370,340/358,335/353,322/340,354/372,354/372	58545426	8497,4493	2198	4297	6495	SO:0001819	synonymous_variant	65009	exon16			CCACTCAGAGAGC	AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000570248.1:c.1005A>G	16.37:g.58545426A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	157	75	0.477707	NM_001130487	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Silent	SNP	ENST00000570248.1	37	CCDS58466.1																																																																																			A|0.274;G|0.726	0.726	strong		0.682	NDRG4-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422671.2		
SLC9A5	6553	hgsc.bcm.edu	37	16	67286590	67286590	+	Silent	SNP	G	G	C	rs61740454	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67286590G>C	ENST00000299798.11	+	2	398	c.333G>C	c.(331-333)ctG>ctC	p.L111L	SLC9A5_ENST00000561472.2_Intron	NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	111					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		TCCTCTTCCTGCTGCCTCCTA	0.542													G|||	158	0.0315495	0.0386	0.0303	5008	,	,		20532	0.0208		0.0348	False		,,,				2504	0.0307				p.L111L		Atlas-SNP	.											.	SLC9A5	82	.	0			c.G333C						PASS	.	G		199,3991		3,193,1899	93.0	95.0	94.0		333	2.0	1.0	16	dbSNP_129	94	293,8163		8,277,3943	no	coding-synonymous	SLC9A5	NM_004594.2		11,470,5842	CC,CG,GG		3.465,4.7494,3.8906		111/897	67286590	492,12154	2095	4228	6323	SO:0001819	synonymous_variant	6553	exon2			CTTCCTGCTGCCT		CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"""Solute carriers"""	11078	protein-coding gene	gene with protein product		600477	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 5"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 5"""			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.333G>C	16.37:g.67286590G>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	129	61	0.472868	NM_004594	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																			G|0.970;C|0.030	0.030	strong		0.542	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1		
F2	2147	hgsc.bcm.edu	37	11	46745003	46745003	+	Missense_Mutation	SNP	C	C	T	rs5896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:46745003C>T	ENST00000311907.5	+	6	550	c.494C>T	c.(493-495)aCg>aTg	p.T165M	F2_ENST00000530231.1_Missense_Mutation_p.T165M	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	165	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.		T -> M (polymorphism confirmed at protein level; dbSNP:rs5896). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:22028381, ECO:0000269|Ref.5}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell surface receptor signaling pathway (GO:0007166)|cellular protein metabolic process (GO:0044267)|cytosolic calcium ion homeostasis (GO:0051480)|fibrinolysis (GO:0042730)|leukocyte migration (GO:0050900)|multicellular organismal development (GO:0007275)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|negative regulation of proteolysis (GO:0045861)|peptidyl-glutamic acid carboxylation (GO:0017187)|platelet activation (GO:0030168)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900738)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|regulation of blood coagulation (GO:0030193)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)	blood microparticle (GO:0072562)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|thrombospondin receptor activity (GO:0070053)	p.T165M(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)	27		all_lung(304;0.000414)|Lung NSC(402;0.0011)		BRCA - Breast invasive adenocarcinoma(625;0.146)	Antihemophilic Factor(DB00025)|Argatroban(DB00278)|ART-123(DB05777)|Bivalirudin(DB00006)|Coagulation Factor IX(DB00100)|Dabigatran etexilate(DB06695)|Drotrecogin alfa(DB00055)|Lepirudin(DB00001)|Menadione(DB00170)|Proflavine(DB01123)|Suramin(DB04786)|Ximelagatran(DB04898)	AGCAGCACCACGGGACCCTGG	0.612													C|||	1098	0.219249	0.0053	0.281	5008	,	,		18283	0.6002		0.1213	False		,,,				2504	0.1728				p.T165M	Esophageal Squamous(147;1147 1808 2148 38609 51144)	Atlas-SNP	.											F2,colon,carcinoma,-1,2	F2	75	2	1	Substitution - Missense(1)	stomach(1)	c.C494T	GRCh37	CM043760	F2	M	rs5896	scavenged	.	C	MET/THR	151,4251	103.0+/-141.5	3,145,2053	53.0	51.0	52.0		494	3.0	0.0	11	dbSNP_52	52	1097,7501	227.5+/-262.8	60,977,3262	yes	missense	F2	NM_000506.3	81	63,1122,5315	TT,TC,CC		12.7588,3.4303,9.6	possibly-damaging	165/623	46745003	1248,11752	2201	4299	6500	SO:0001583	missense	2147	exon6			GCACCACGGGACC	M33031	CCDS31476.1	11p11.2	2013-02-28			ENSG00000180210	ENSG00000180210	3.4.21.5	"""Endogenous ligands"""	3535	protein-coding gene	gene with protein product	"""prepro-coagulation factor II"""	176930					Standard	NM_000506		Approved		uc001ndf.4	P00734	OTTHUMG00000150344	ENST00000311907.5:c.494C>T	11.37:g.46745003C>T	ENSP00000308541:p.Thr165Met	Somatic	107	1	0.00934579		WXS	Illumina HiSeq	Phase_I	117	49	0.418803	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Missense_Mutation	SNP	ENST00000311907.5	37	CCDS31476.1	536	0.2454212454212454	6	0.012195121951219513	99	0.27348066298342544	327	0.5716783216783217	104	0.13720316622691292	C	8.604	0.887544	0.17540	0.034303	0.127588	ENSG00000180210	ENST00000311907;ENST00000530231;ENST00000442468	T;T;T	0.67171	-0.25;-0.25;-0.25	4.87	3.02	0.34903	Kringle (5);Kringle-like fold (1);Kringle, conserved site (1);	0.592033	0.19760	N	0.106682	T	0.00012	0.0000	M	0.69185	2.1	0.80722	P	0.0	B	0.29646	0.253	B	0.27500	0.08	T	0.43196	-0.9406	9	0.87932	D	0	.	6.3465	0.21353	0.1818:0.6541:0.0:0.1641	rs5896;rs3136453;rs17645388;rs60714661;rs5896	165	P00734	THRB_HUMAN	M	165;165;155	ENSP00000308541:T165M;ENSP00000433907:T165M;ENSP00000387413:T155M	ENSP00000308541:T165M	T	+	2	0	F2	46701579	0.000000	0.05858	0.004000	0.12327	0.567000	0.35839	0.245000	0.18142	0.667000	0.31107	-0.254000	0.11334	ACG	C|0.835;T|0.165	0.165	strong		0.612	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1		
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919244	51919244	+	Missense_Mutation	SNP	G	G	C	rs200798488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919244G>C	ENST00000339313.5	-	5	1048	c.932C>G	c.(931-933)cCc>cGc	p.P311R	CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.P253R|SIGLEC10_ENST00000442846.3_Intron|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.P228R|SIGLEC10_ENST00000439889.2_Missense_Mutation_p.P253R|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.P311R|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.P263R|CTD-2616J11.3_ENST00000532473.1_RNA|CTD-2616J11.2_ENST00000526996.1_RNA|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.P311R			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	311	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CTTCACCCCGGGCAGCTCCAG	0.667																																					p.P311R		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C932G						PASS	.						33.0	38.0	37.0					19																	51919244		2203	4300	6503	SO:0001583	missense	89790	exon5			ACCCCGGGCAGCT	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.932C>G	19.37:g.51919244G>C	ENSP00000345243:p.Pro311Arg	Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	108	39	0.361111	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	5.587	0.293054	0.10567	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	4.37	1.01	0.19927	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.141960	0.32868	N	0.005554	T	0.54631	0.1870	L	0.45051	1.395	0.23834	N	0.996719	B;P;P;B;B;B	0.41848	0.383;0.763;0.72;0.332;0.332;0.395	P;P;P;B;B;B	0.48571	0.464;0.582;0.447;0.333;0.333;0.208	T	0.44892	-0.9298	10	0.44086	T	0.13	.	3.6772	0.08297	0.2098:0.0:0.5964:0.1939	.	263;311;311;253;253;311	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	R	311;228;311;253;253;263;311;125	ENSP00000342389:P311R;ENSP00000396742:P228R;ENSP00000348646:P311R;ENSP00000408387:P253R;ENSP00000389132:P253R;ENSP00000414324:P263R;ENSP00000345243:P311R;ENSP00000435281:P125R	ENSP00000345243:P311R	P	-	2	0	SIGLEC10	56611056	0.544000	0.26441	0.193000	0.23327	0.071000	0.16799	0.847000	0.27696	0.130000	0.18549	0.313000	0.20887	CCC	G|0.993;C|0.007	0.007	strong		0.667	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
CRACR2B	283229	hgsc.bcm.edu	37	11	828916	828916	+	Missense_Mutation	SNP	G	G	A	rs7126805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:828916G>A	ENST00000525077.1	+	2	331	c.230G>A	c.(229-231)cGg>cAg	p.R77Q	AP006621.8_ENST00000532946.1_RNA|EFCAB4A_ENST00000450448.1_Missense_Mutation_p.R77Q|EFCAB4A_ENST00000528542.2_Missense_Mutation_p.R77Q			Q8N4Y2	EFC4A_HUMAN		77	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.		R -> Q (in dbSNP:rs7126805). {ECO:0000269|PubMed:15489334}.		cellular protein localization (GO:0034613)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(1)	3		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AGTCTGGACCGGGCTCACACT	0.657													A|||	2846	0.568291	0.4576	0.7695	5008	,	,		17747	0.6647		0.6948	False		,,,				2504	0.3456				p.R77Q		Atlas-SNP	.											.	EFCAB4A	16	.	0			c.G230A						PASS	.	A	GLN/ARG	2130,1998		567,996,501	72.0	80.0	78.0		230	2.2	1.0	11	dbSNP_116	78	5950,2446		2102,1746,350	yes	missense	EFCAB4A	NM_173584.3	43	2669,2742,851	AA,AG,GG		29.1329,48.4012,35.4839	benign	77/295	828916	8080,4444	2064	4198	6262	SO:0001583	missense	283229	exon3			TGGACCGGGCTCA																												ENST00000525077.1:c.230G>A	11.37:g.828916G>A	ENSP00000435299:p.Arg77Gln	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_173584	D5LPR2|Q8NBW8	Missense_Mutation	SNP	ENST00000525077.1	37		1457	0.6671245421245421	242	0.491869918699187	274	0.7569060773480663	412	0.7202797202797203	529	0.6978891820580475	A	10.78	1.446198	0.25987	0.515988	0.708671	ENSG00000177685	ENST00000533803;ENST00000527089;ENST00000528542;ENST00000450448;ENST00000321883;ENST00000525077	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	4.49	2.2	0.27929	EF-hand-like domain (1);	0.165886	0.39274	N	0.001412	T	0.00012	0.0000	N	0.00413	-1.525	0.46185	P	0.0010900000000000354	B;B;B	0.14805	0.011;0.001;0.0	B;B;B	0.06405	0.002;0.002;0.0	T	0.35871	-0.9771	9	0.07813	T	0.8	.	7.2868	0.26344	0.7281:0.0:0.2719:0.0	rs7126805;rs61117822;rs7126805	77;77;77	E7EWX3;Q8N4Y2-3;Q8N4Y2	.;.;EFC4A_HUMAN	Q	77	ENSP00000433602:R77Q;ENSP00000432726:R77Q;ENSP00000432334:R77Q;ENSP00000409256:R77Q;ENSP00000435299:R77Q	ENSP00000324024:R77Q	R	+	2	0	EFCAB4A	818916	0.994000	0.37717	0.997000	0.53966	0.924000	0.55760	1.510000	0.35790	0.597000	0.29811	-0.490000	0.04691	CGG	G|0.368;A|0.632	0.632	strong		0.657	EFCAB4A-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383097.1		
RBMXL1	494115	hgsc.bcm.edu	37	1	89449298	89449298	+	Missense_Mutation	SNP	C	C	G	rs111779380	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449298C>G	ENST00000321792.5	-	2	639	c.212G>C	c.(211-213)gGa>gCa	p.G71A	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.G71A	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	71	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										TAATGACTTTCCATTCATGTC	0.458											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G71A		Atlas-SNP	.											CCBL2,NS,neuroblastoma,0,1	.	.	1	0			c.G212C						PASS	.						147.0	142.0	144.0					1																	89449298		2203	4297	6500	SO:0001583	missense	494115	exon3			GACTTTCCATTCA	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.212G>C	1.37:g.89449298C>G	ENSP00000318415:p.Gly71Ala	Somatic	238	0	0	1267	WXS	Illumina HiSeq	Phase_I	352	52	0.147727	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.128562	0.77549	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.85411	-1.98;-1.98	1.59	0.441	0.16577	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.073090	0.56097	U	0.000037	D	0.83986	0.5373	M	0.61703	1.905	0.44201	D	0.997022	D	0.89917	1.0	D	0.91635	0.999	T	0.81953	-0.0697	10	0.87932	D	0	-0.977	4.6541	0.12610	0.3708:0.6292:0.0:0.0	.	71	Q96E39	RBMXL_HUMAN	A	71	ENSP00000318415:G71A;ENSP00000446099:G71A	ENSP00000318415:G71A	G	-	2	0	RBMXL1	89221886	1.000000	0.71417	0.992000	0.48379	0.978000	0.69477	4.901000	0.63259	-0.041000	0.13558	0.306000	0.20318	GGA	.	.	weak		0.458	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
LMO2	4005	hgsc.bcm.edu	37	11	33886294	33886294	+	Silent	SNP	A	A	G	rs2038602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:33886294A>G	ENST00000395833.3	-	2	540	c.111T>C	c.(109-111)atT>atC	p.I37I	LMO2_ENST00000257818.2_Silent_p.I106I	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	37	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						AGCGGTCCCCAATGTTCTGCT	0.652			T	TRD@	T-ALL								G|||	2175	0.434305	0.5847	0.2839	5008	,	,		19179	0.4067		0.4185	False		,,,				2504	0.3824				p.I106I		Atlas-SNP	.		Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	.	LMO2	21	.	0			c.T318C						PASS	.	G	,,	2446,1958	546.4+/-377.0	674,1098,430	62.0	53.0	56.0		111,111,318	-4.5	0.9	11	dbSNP_94	56	3551,5045	623.2+/-397.4	762,2027,1509	no	coding-synonymous,coding-synonymous,coding-synonymous	LMO2	NM_001142315.1,NM_001142316.1,NM_005574.3	,,	1436,3125,1939	GG,GA,AA		41.3099,44.4596,46.1308	,,	37/159,37/159,106/228	33886294	5997,7003	2202	4298	6500	SO:0001819	synonymous_variant	4005	exon5			GTCCCCAATGTTC	X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"""T-cell translocation gene 2"", ""rhombotin-like 1"""	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.111T>C	11.37:g.33886294A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	49	0.544444	NM_005574	Q9HD58	Silent	SNP	ENST00000395833.3	37	CCDS44567.1																																																																																			A|0.546;G|0.454	0.454	strong		0.652	LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574	
LRP1	4035	hgsc.bcm.edu	37	12	57571249	57571249	+	Silent	SNP	C	C	T	rs2228187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57571249C>T	ENST00000243077.3	+	26	4702	c.4236C>T	c.(4234-4236)cgC>cgT	p.R1412R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1412					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)	GCCTGCCCCGCATTGAGGCAG	0.677													C|||	18	0.00359425	0.0008	0.0101	5008	,	,		15185	0.0		0.007	False		,,,				2504	0.0031				p.R1412R		Atlas-SNP	.											.	LRP1	428	.	0			c.C4236T						PASS	.	C		1,4405		0,1,2202	36.0	39.0	38.0		4236	-7.2	0.8	12	dbSNP_98	38	73,8527	41.7+/-99.0	0,73,4227	no	coding-synonymous	LRP1	NM_002332.2		0,74,6429	TT,TC,CC		0.8488,0.0227,0.569		1412/4545	57571249	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon26			GCCCCGCATTGAG	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.4236C>T	12.37:g.57571249C>T		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	175	94	0.537143	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.994;T|0.006	0.006	strong		0.677	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
CAPN15	6650	hgsc.bcm.edu	37	16	601632	601632	+	Silent	SNP	T	T	C	rs3213574	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:601632T>C	ENST00000219611.2	+	9	2676	c.2313T>C	c.(2311-2313)ggT>ggC	p.G771G	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	771	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCAGTGAGGGTGTCTTCTGGA	0.677													c|||	3592	0.717252	0.8268	0.6758	5008	,	,		14094	0.7788		0.5199	False		,,,				2504	0.7382				p.G771G		Atlas-SNP	.											SOLH,NS,carcinoma,+1,1	SOLH	47	1	0			c.T2313C						scavenged	.			3446,952	351.3+/-311.2	1355,736,108	43.0	50.0	48.0		2313	-3.6	1.0	16	dbSNP_106	48	4476,4118	558.0+/-387.2	1149,2178,970	no	coding-synonymous	SOLH	NM_005632.2		2504,2914,1078	CC,CT,TT		47.9172,21.6462,39.024		771/1087	601632	7922,5070	2199	4297	6496	SO:0001819	synonymous_variant	6650	exon9			TGAGGGTGTCTTC	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2313T>C	16.37:g.601632T>C		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	59	58	0.983051	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																			T|0.359;C|0.641	0.641	strong		0.677	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
ZNF417	147687	hgsc.bcm.edu	37	19	58420167	58420167	+	Silent	SNP	T	T	C	rs17852300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58420167T>C	ENST00000312026.5	-	3	1643	c.1479A>G	c.(1477-1479)gaA>gaG	p.E493E	ZNF417_ENST00000536263.1_Silent_p.E294E|ZNF417_ENST00000595559.1_Silent_p.E492E|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	493					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.E493E(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|stomach(3)|upper_aerodigestive_tract(1)	18		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0151)		ATTCATTGCATTCATACGGCC	0.408													T|||	1233	0.246206	0.1543	0.219	5008	,	,		21542	0.2847		0.2972	False		,,,				2504	0.2975				p.E493E		Atlas-SNP	.											ZNF417,NS,carcinoma,0,1	ZNF417	44	1	1	Substitution - coding silent(1)	stomach(1)	c.A1479G						PASS	.	T		525,3881		63,399,1741	112.0	93.0	100.0		1479	-4.8	0.0	19	dbSNP_123	100	2020,6578		348,1324,2627	no	coding-synonymous	ZNF417	NM_152475.2		411,1723,4368	CC,CT,TT		23.4938,11.9156,19.5709		493/576	58420167	2545,10459	2203	4299	6502	SO:0001819	synonymous_variant	147687	exon3			ATTGCATTCATAC	BC025783	CCDS12965.1, CCDS74469.1	19q13.43	2013-01-08				ENSG00000173480		"""Zinc fingers, C2H2-type"", ""-"""	20646	protein-coding gene	gene with protein product							Standard	NM_152475		Approved	MGC34079	uc002qqq.3	Q8TAU3		ENST00000312026.5:c.1479A>G	19.37:g.58420167T>C		Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	141	141	1	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			T|0.773;C|0.227	0.227	strong		0.408	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475	
PCDHB4	56131	hgsc.bcm.edu	37	5	140502433	140502433	+	Missense_Mutation	SNP	G	G	C	rs149340599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140502433G>C	ENST00000194152.1	+	1	853	c.853G>C	c.(853-855)Gat>Cat	p.D285H	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	285	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCAAGCATCAGATGAAATTAA	0.348													G|||	48	0.00958466	0.0	0.0043	5008	,	,		20653	0.001		0.003	False		,,,				2504	0.0419				p.D285H		Atlas-SNP	.											.	PCDHB4	177	.	0			c.G853C						PASS	.	G	HIS/ASP	2,4398	4.2+/-10.8	0,2,2198	92.0	107.0	102.0		853	4.4	1.0	5	dbSNP_134	102	46,8554	29.6+/-80.5	0,46,4254	yes	missense	PCDHB4	NM_018938.2	81	0,48,6452	CC,CG,GG		0.5349,0.0455,0.3692	possibly-damaging	285/796	140502433	48,12952	2200	4300	6500	SO:0001583	missense	56131	exon1			GCATCAGATGAAA	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.853G>C	5.37:g.140502433G>C	ENSP00000194152:p.Asp285His	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	115	53	0.46087	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	15.05	2.718902	0.48622	4.55E-4	0.005349	ENSG00000081818	ENST00000194152	T	0.66099	-0.19	4.41	4.41	0.53225	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66257	0.2771	L	0.45285	1.41	0.43448	D	0.995638	P	0.37370	0.592	P	0.57620	0.824	T	0.72107	-0.4390	9	0.56958	D	0.05	.	17.5536	0.87884	0.0:0.0:1.0:0.0	.	285	Q9Y5E5	PCDB4_HUMAN	H	285	ENSP00000194152:D285H	ENSP00000194152:D285H	D	+	1	0	PCDHB4	140482617	0.015000	0.18098	0.996000	0.52242	0.671000	0.39405	1.433000	0.34947	2.449000	0.82847	0.650000	0.86243	GAT	G|0.996;C|0.004	0.004	strong		0.348	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
KIF5C	3800	hgsc.bcm.edu	37	2	149799216	149799216	+	Silent	SNP	T	T	C	rs61734995	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:149799216T>C	ENST00000435030.1	+	7	899	c.531T>C	c.(529-531)ccT>ccC	p.P177P	KIF5C_ENST00000414838.2_Silent_p.P82P			O60282	KIF5C_HUMAN	kinesin family member 5C	177	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		TGTCGAGCCCTGAGGAAGTCA	0.488													C|||	750	0.14976	0.3427	0.1037	5008	,	,		19701	0.0347		0.1064	False		,,,				2504	0.0849				p.P177P		Atlas-SNP	.											.	KIF5C	166	.	0			c.T531C						PASS	.	C		1115,2823		164,787,1018	74.0	73.0	73.0		242	-11.0	0.0	2	dbSNP_129	73	765,7533		44,677,3428	no	coding-synonymous	KIF5C	NM_004522.1		208,1464,4446	CC,CT,TT		9.2191,28.3139,15.3645		177/958	149799216	1880,10356	1969	4149	6118	SO:0001819	synonymous_variant	3800	exon7			GAGCCCTGAGGAA	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.531T>C	2.37:g.149799216T>C		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	135	69	0.511111	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				T|0.860;C|0.140	0.140	strong		0.488	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
TACC3	10460	hgsc.bcm.edu	37	4	1729988	1729988	+	Missense_Mutation	SNP	G	G	A	rs1063743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1729988G>A	ENST00000313288.4	+	4	965	c.859G>A	c.(859-861)Ggc>Agc	p.G287S		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	287			G -> S (in dbSNP:rs1063743). {ECO:0000269|PubMed:11298601}.		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)			GCCAGCAGATGGCACTCAGAC	0.657													G|||	851	0.169928	0.1331	0.196	5008	,	,		15628	0.1478		0.2634	False		,,,				2504	0.1278				p.G287S	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.G859A						PASS	.	G	SER/GLY	692,3714		58,576,1569	22.0	24.0	23.0		859	0.3	0.0	4	dbSNP_86	23	2117,6477		261,1595,2441	yes	missense	TACC3	NM_006342.1	56	319,2171,4010	AA,AG,GG		24.6335,15.7059,21.6077	benign	287/839	1729988	2809,10191	2203	4297	6500	SO:0001583	missense	10460	exon4			GCAGATGGCACTC	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.859G>A	4.37:g.1729988G>A	ENSP00000326550:p.Gly287Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	57	28	0.491228	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	420	0.19230769230769232	54	0.10975609756097561	68	0.1878453038674033	95	0.1660839160839161	203	0.2678100263852243	G	4.864	0.160544	0.09287	0.157059	0.246335	ENSG00000013810	ENST00000313288	T	0.17370	2.28	3.27	0.277	0.15668	.	4.968620	0.01723	N	0.028394	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.38457	-0.9660	9	0.13108	T	0.6	-0.3233	3.902	0.09166	0.2771:0.2757:0.4471:0.0	rs1063743;rs3204773;rs52801320;rs1063743	287;287	B4DYJ1;Q9Y6A5	.;TACC3_HUMAN	S	287	ENSP00000326550:G287S	ENSP00000326550:G287S	G	+	1	0	TACC3	1699786	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-1.065000	0.03458	-0.335000	0.08451	0.467000	0.42956	GGC	G|0.806;A|0.194	0.194	strong		0.657	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2		
E2F7	144455	hgsc.bcm.edu	37	12	77419341	77419341	+	Missense_Mutation	SNP	A	A	T	rs310831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:77419341A>T	ENST00000322886.7	-	12	2797	c.2562T>A	c.(2560-2562)caT>caA	p.H854Q	E2F7_ENST00000416496.2_Intron	NM_203394.2	NP_976328.2	Q96AV8	E2F7_HUMAN	E2F transcription factor 7	854			H -> Q (in dbSNP:rs310831).		chorionic trophoblast cell differentiation (GO:0060718)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|hepatocyte differentiation (GO:0070365)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokinesis (GO:0032466)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|placenta development (GO:0001890)|positive regulation of DNA endoreduplication (GO:0032877)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sprouting angiogenesis (GO:0002040)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(15)|lung(14)|ovary(3)|upper_aerodigestive_tract(2)	42						GCCTCACCTGATGTAATTTTA	0.493													A|||	211	0.0421326	0.0045	0.0677	5008	,	,		19370	0.0		0.1392	False		,,,				2504	0.0184				p.H854Q		Atlas-SNP	.											.	E2F7	201	.	0			c.T2562A						PASS	.	A	GLN/HIS	104,4302	79.9+/-118.3	2,100,2101	145.0	131.0	136.0		2562	-11.8	0.0	12	dbSNP_79	136	1050,7550	222.6+/-259.6	67,916,3317	yes	missense	E2F7	NM_203394.2	24	69,1016,5418	TT,TA,AA		12.2093,2.3604,8.8728	benign	854/912	77419341	1154,11852	2203	4300	6503	SO:0001583	missense	144455	exon12			CACCTGATGTAAT	BC016658	CCDS9016.1	12q21.1	2008-02-05				ENSG00000165891			23820	protein-coding gene	gene with protein product		612046				12893818	Standard	NM_203394		Approved		uc001sym.4	Q96AV8	OTTHUMG00000169969	ENST00000322886.7:c.2562T>A	12.37:g.77419341A>T	ENSP00000323246:p.His854Gln	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_203394	A6NC74|B2RMR7|B3KTZ5|B3KUP8|B5MED9	Missense_Mutation	SNP	ENST00000322886.7	37	CCDS9016.1	146	0.06684981684981685	3	0.006097560975609756	27	0.07458563535911603	0	0.0	116	0.15303430079155672	A	8.626	0.892520	0.17613	0.023604	0.122093	ENSG00000165891	ENST00000322886;ENST00000339887	T	0.11385	2.78	5.88	-11.8	0.00035	.	0.930262	0.09048	N	0.856273	T	0.00012	0.0000	N	0.04203	-0.255	0.26286	P	0.9782084	B	0.02656	0.0	B	0.01281	0.0	T	0.41980	-0.9478	9	0.10377	T	0.69	-2.5349	8.9135	0.35568	0.0848:0.5631:0.091:0.2612	rs310831;rs17759722;rs52796286;rs310831	854	Q96AV8	E2F7_HUMAN	Q	854;325	ENSP00000323246:H854Q	ENSP00000323246:H854Q	H	-	3	2	E2F7	75943472	0.009000	0.17119	0.012000	0.15200	0.697000	0.40408	-1.807000	0.01734	-1.729000	0.01364	-0.472000	0.04984	CAT	A|0.918;T|0.082	0.082	strong		0.493	E2F7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406716.1	XM_084871	
MYO3A	53904	hgsc.bcm.edu	37	10	26434455	26434455	+	Missense_Mutation	SNP	G	G	T	rs33947968	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:26434455G>T	ENST00000265944.5	+	22	2663	c.2497G>T	c.(2497-2499)Gca>Tca	p.A833S	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	833	Myosin motor.		A -> S (in dbSNP:rs33947968). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TCACCATTATGCAGGAAAGGT	0.318													G|||	164	0.0327476	0.0076	0.049	5008	,	,		17958	0.001		0.0964	False		,,,				2504	0.0225				p.A833S		Atlas-SNP	.											MYO3A,NS,carcinoma,0,1	MYO3A	371	1	0			c.G2497T						scavenged	.	G	SER/ALA	90,4316	74.1+/-112.3	0,90,2113	74.0	74.0	74.0		2497	5.7	1.0	10	dbSNP_126	74	802,7798	185.3+/-233.1	43,716,3541	yes	missense	MYO3A	NM_017433.4	99	43,806,5654	TT,TG,GG		9.3256,2.0427,6.8584	probably-damaging	833/1617	26434455	892,12114	2203	4300	6503	SO:0001583	missense	53904	exon22			CATTATGCAGGAA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.2497G>T	10.37:g.26434455G>T	ENSP00000265944:p.Ala833Ser	Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	142	61	0.429577	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	94	0.04304029304029304	5	0.01016260162601626	18	0.049723756906077346	0	0.0	71	0.09366754617414248	G	33	5.203455	0.95033	0.020427	0.093256	ENSG00000095777	ENST00000265944	D	0.92647	-3.08	5.72	5.72	0.89469	Myosin head, motor domain (2);	0.047262	0.85682	D	0.000000	T	0.72112	0.3420	H	0.95470	3.675	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79524	-0.1768	10	0.72032	D	0.01	.	19.88	0.96892	0.0:0.0:1.0:0.0	rs33947968	833	Q8NEV4	MYO3A_HUMAN	S	833	ENSP00000265944:A833S	ENSP00000265944:A833S	A	+	1	0	MYO3A	26474461	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.869000	0.99810	2.703000	0.92315	0.655000	0.94253	GCA	G|0.941;T|0.059	0.059	strong		0.318	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
C1orf68	100129271	hgsc.bcm.edu	37	1	152692588	152692588	+	Silent	SNP	A	A	G	rs944682	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152692588A>G	ENST00000368775.2	+	1	591	c.591A>G	c.(589-591)tcA>tcG	p.S197S		NM_001024679.2	NP_001019850.1	Q5T750	XP32_HUMAN	chromosome 1 open reading frame 68	197	Cys-rich.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)		p.S197S(1)		NS(1)|breast(1)|lung(2)|prostate(1)|stomach(3)	8						ACACAGGATCATCTGGCTGCT	0.607													G|||	1749	0.349241	0.5461	0.3804	5008	,	,		17978	0.1716		0.3608	False		,,,				2504	0.2321				p.S197S		Atlas-SNP	.											C1orf68,NS,carcinoma,+1,2	C1orf68	19	2	1	Substitution - coding silent(1)	stomach(1)	c.A591G						PASS	.	G		693,691		176,341,175	51.0	49.0	50.0		591	-8.4	0.1	1	dbSNP_86	50	1113,2069		189,735,667	no	coding-synonymous	C1orf68	NM_001024679.2		365,1076,842	GG,GA,AA		34.978,49.9277,39.5532		197/251	152692588	1806,2760	692	1591	2283	SO:0001819	synonymous_variant	100129271	exon1			AGGATCATCTGGC	AF005081	CCDS44226.1	1q21.3	2014-05-30			ENSG00000198854	ENSG00000198854			29468	protein-coding gene	gene with protein product						11698679	Standard	NM_001024679		Approved	LEP7	uc010pdu.2	Q5T750	OTTHUMG00000012401	ENST00000368775.2:c.591A>G	1.37:g.152692588A>G		Somatic	224	0	0		WXS	Illumina HiSeq	Phase_I	182	179	0.983516	NM_001024679	O14634	Silent	SNP	ENST00000368775.2	37	CCDS44226.1																																																																																			A|0.651;G|0.349	0.349	strong		0.607	C1orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034521.2	NM_001024679	
TAS2R1	50834	hgsc.bcm.edu	37	5	9629529	9629529	+	Missense_Mutation	SNP	G	G	A	rs2234233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:9629529G>A	ENST00000382492.2	-	1	934	c.616C>T	c.(616-618)Cgg>Tgg	p.R206W	CTD-2001E22.1_ENST00000504182.2_RNA	NM_019599.2	NP_062545.1	Q9NYW7	TA2R1_HUMAN	taste receptor, type 2, member 1	206			R -> W (in dbSNP:rs2234233).		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)	p.R206W(1)		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						CTCATTTGCCGGGTGTGCCTC	0.507													G|||	572	0.114217	0.028	0.1268	5008	,	,		17670	0.1071		0.1521	False		,,,				2504	0.1902				p.R206W		Atlas-SNP	.											TAS2R1,NS,carcinoma,0,1	TAS2R1	84	1	1	Substitution - Missense(1)	stomach(1)	c.C616T						PASS	.	G	TRP/ARG	216,4190	121.3+/-158.8	8,200,1995	47.0	55.0	53.0		616	-11.3	0.0	5	dbSNP_98	53	1422,7178	266.3+/-286.6	113,1196,2991	yes	missense	TAS2R1	NM_019599.2	101	121,1396,4986	AA,AG,GG		16.5349,4.9024,12.5942	benign	206/300	9629529	1638,11368	2203	4300	6503	SO:0001583	missense	50834	exon1			TTTGCCGGGTGTG	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.616C>T	5.37:g.9629529G>A	ENSP00000371932:p.Arg206Trp	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_019599	Q646G8	Missense_Mutation	SNP	ENST00000382492.2	37	CCDS3876.1	255	0.11675824175824176	15	0.03048780487804878	48	0.13259668508287292	75	0.13111888111888112	117	0.15435356200527706	G	11.62	1.692461	0.30052	0.049024	0.165349	ENSG00000169777	ENST00000382492	T	0.00986	5.47	5.65	-11.3	0.00108	.	1.250620	0.06042	N	0.655136	T	0.00012	0.0000	N	0.05574	-0.02	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.48559	-0.9025	8	.	.	.	.	2.3549	0.04293	0.2929:0.0693:0.3959:0.242	rs2234233;rs52805045;rs60592533;rs2234233	206	Q9NYW7	TA2R1_HUMAN	W	206	ENSP00000371932:R206W	.	R	-	1	2	TAS2R1	9682529	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.202000	0.09451	-2.320000	0.00642	-0.880000	0.02959	CGG	G|0.878;A|0.122	0.122	strong		0.507	TAS2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206988.2		
ANKRD65	441869	hgsc.bcm.edu	37	1	1354515	1354515	+	Missense_Mutation	SNP	C	C	G	rs534554090|rs904589	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1354515C>G	ENST00000537107.1	-	4	1302	c.1165G>C	c.(1165-1167)Gag>Cag	p.E389Q	ANKRD65_ENST00000427211.1_3'UTR|ANKRD65_ENST00000454272.1_5'UTR|RP4-758J18.7_ENST00000428932.1_RNA|ANKRD65_ENST00000520296.1_3'UTR	NM_001145210.2	NP_001138682.1	E5RJM6	ANR65_HUMAN	ankyrin repeat domain 65	389										breast(1)	1						CACTCCTTCTCCCCCCCTCCA	0.687													G|||	1617	0.322883	0.8222	0.1945	5008	,	,		16520	0.1131		0.0964	False		,,,				2504	0.1881				p.E389Q		Atlas-SNP	.											.	ANKRD65	4	.	0			c.G1165C						PASS	.						2.0	3.0	3.0					1																	1354515		507	1316	1823	SO:0001583	missense	441869	exon4			CCTTCTCCCCCCC		CCDS55558.1, CCDS57962.1, CCDS57963.1	1p36.33	2013-01-10			ENSG00000235098	ENSG00000235098		"""Ankyrin repeat domain containing"""	42950	protein-coding gene	gene with protein product							Standard	NM_001243535		Approved		uc010nyo.2	E5RJM6	OTTHUMG00000002911	ENST00000537107.1:c.1165G>C	1.37:g.1354515C>G	ENSP00000445688:p.Glu389Gln	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	172	7	0.0406977	NM_001145210	J3KR93	Missense_Mutation	SNP	ENST00000537107.1	37	CCDS55558.1	622	0.2847985347985348	404	0.8211382113821138	79	0.21823204419889503	67	0.11713286713286714	72	0.09498680738786279	G	0.243	-1.012516	0.02095	.	.	ENSG00000235098	ENST00000537107	T	0.68624	-0.34	1.28	0.254	0.15557	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.38520	-0.9657	8	0.10902	T	0.67	.	6.8436	0.23977	0.0:0.5817:0.4183:0.0	rs904589;rs3766168	389	E5RJM6	ANR65_HUMAN	Q	389	ENSP00000445688:E389Q	ENSP00000445688:E389Q	E	-	1	0	RP4-758J18.6	1344378	0.004000	0.15560	0.001000	0.08648	0.007000	0.05969	-0.137000	0.10389	-0.272000	0.09259	-0.497000	0.04613	GAG	C|0.714;G|0.286	0.286	strong		0.687	ANKRD65-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ADCYAP1	116	hgsc.bcm.edu	37	18	907675	907675	+	Silent	SNP	G	G	A	rs8192597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:907675G>A	ENST00000579794.1	+	2	404	c.126G>A	c.(124-126)gcG>gcA	p.A42A	RP11-672L10.2_ENST00000580612.1_RNA|RP11-672L10.3_ENST00000582554.1_RNA|RP11-672L10.2_ENST00000577358.1_RNA|RP11-672L10.2_ENST00000581719.2_RNA|ADCYAP1_ENST00000450565.3_Silent_p.A42A	NM_001117.3	NP_001108.2	P18509	PACA_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary)	42					activation of adenylate cyclase activity (GO:0007190)|ATP metabolic process (GO:0046034)|behavioral fear response (GO:0001662)|cAMP-mediated signaling (GO:0019933)|cell-cell signaling (GO:0007267)|cellular response to glucocorticoid stimulus (GO:0071385)|female pregnancy (GO:0007565)|histamine secretion (GO:0001821)|negative regulation of acute inflammatory response to antigenic stimulus (GO:0002865)|negative regulation of acute inflammatory response to non-antigenic stimulus (GO:0002878)|negative regulation of cell cycle (GO:0045786)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of Rho GTPase activity (GO:0034259)|neuron projection development (GO:0031175)|neuropeptide signaling pathway (GO:0007218)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|pituitary gland development (GO:0021983)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of somatostatin secretion (GO:0090274)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasodilation (GO:0045909)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)|regulation of postsynaptic membrane potential (GO:0060078)|regulation of protein localization (GO:0032880)|response to ethanol (GO:0045471)|response to starvation (GO:0042594)|sensory perception of pain (GO:0019233)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|terminal bouton (GO:0043195)	neuropeptide hormone activity (GO:0005184)|peptide hormone receptor binding (GO:0051428)|pituitary adenylate cyclase activating polypeptide activity (GO:0016521)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			endometrium(1)|large_intestine(3)|lung(7)|upper_aerodigestive_tract(1)	12						AGGAAGAGGCGTACGGCGAGG	0.726													G|||	3516	0.702077	0.5061	0.7622	5008	,	,		8604	0.8492		0.6889	False		,,,				2504	0.7863				p.A42A		Atlas-SNP	.											ADCYAP1,NS,carcinoma,0,1	ADCYAP1	24	1	0			c.G126A						scavenged	.	G	,	2350,1996		679,992,502	9.0	11.0	11.0		126,126	-3.4	1.0	18	dbSNP_117	11	6028,2476		2167,1694,391	no	coding-synonymous,coding-synonymous	ADCYAP1	NM_001099733.1,NM_001117.3	,	2846,2686,893	AA,AG,GG		29.1157,45.9273,34.8016	,	42/177,42/177	907675	8378,4472	2173	4252	6425	SO:0001819	synonymous_variant	116	exon3			AGAGGCGTACGGC	S83513	CCDS11825.1	18p11	2013-02-28			ENSG00000141433	ENSG00000141433		"""Endogenous ligands"""	241	protein-coding gene	gene with protein product	"""prepro-PACAP"""	102980				1730060	Standard	NM_001099733		Approved	PACAP	uc010dkh.4	P18509	OTTHUMG00000131479	ENST00000579794.1:c.126G>A	18.37:g.907675G>A		Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	16	12	0.75	NM_001099733	B2R7N4|Q52LQ0	Silent	SNP	ENST00000579794.1	37	CCDS11825.1																																																																																			G|0.306;A|0.694	0.694	strong		0.726	ADCYAP1-003	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440765.3	NM_001117	
BPIFA3	128861	hgsc.bcm.edu	37	20	31812923	31812923	+	Missense_Mutation	SNP	G	G	A	rs3818222	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:31812923G>A	ENST00000375454.3	+	4	616	c.406G>A	c.(406-408)Gta>Ata	p.V136I	BPIFA3_ENST00000375452.3_Missense_Mutation_p.V100I|BPIFA3_ENST00000490499.1_3'UTR	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	136			V -> I (in dbSNP:rs3818222).			extracellular region (GO:0005576)	lipid binding (GO:0008289)										TAACAACATCGTAAAGATGTG	0.507													A|||	3327	0.664337	0.789	0.428	5008	,	,		22625	0.8115		0.5229	False		,,,				2504	0.6575				p.V136I		Atlas-SNP	.											.	.	.	.	0			c.G406A						PASS	.	A	ILE/VAL,ILE/VAL	3204,1202	419.1+/-338.5	1169,866,168	165.0	157.0	160.0		298,406	-5.5	0.0	20	dbSNP_107	160	4382,4218	571.0+/-389.5	1122,2138,1040	yes	missense,missense	BPIFA3	NM_001042439.1,NM_178466.3	29,29	2291,3004,1208	AA,AG,GG		49.0465,27.281,41.6731	benign,benign	100/219,136/255	31812923	7586,5420	2203	4300	6503	SO:0001583	missense	128861	exon4			AACATCGTAAAGA		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"""BPI fold containing"""	16204	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 71"""	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.406G>A	20.37:g.31812923G>A	ENSP00000364603:p.Val136Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	134	63	0.470149	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	1412	0.6465201465201466	381	0.774390243902439	167	0.4613259668508287	465	0.8129370629370629	399	0.5263852242744064	A	0.188	-1.055829	0.01965	0.72719	0.509535	ENSG00000131059	ENST00000375454;ENST00000375452	T;T	0.04809	3.55;3.55	3.49	-5.46	0.02608	.	1.231100	0.05853	N	0.621586	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.30060	-0.9991	9	0.02654	T	1	-0.0358	4.4607	0.11665	0.2017:0.1397:0.5209:0.1376	rs3818222;rs13041676;rs61303950;rs3818222	100;136	Q9BQP9-2;Q9BQP9	.;BPIA3_HUMAN	I	136;100	ENSP00000364603:V136I;ENSP00000364601:V100I	ENSP00000364601:V100I	V	+	1	0	BPIFA3	31276584	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.653000	0.01986	-1.846000	0.01175	-0.521000	0.04368	GTA	G|0.380;A|0.620	0.620	strong		0.507	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
GALC	2581	hgsc.bcm.edu	37	14	88459448	88459448	+	Missense_Mutation	SNP	C	C	G	rs111887056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:88459448C>G	ENST00000261304.2	-	1	167	c.61G>C	c.(61-63)Gcg>Ccg	p.A21P	GALC_ENST00000393569.2_Intron|GALC_ENST00000393568.4_Missense_Mutation_p.A21P|GALC_ENST00000544807.2_5'Flank	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	21			A -> P. {ECO:0000269|PubMed:20886637}.		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						GCCGAACCCGCGGCCGCAGTC	0.721													C|||	395	0.0788738	0.0182	0.1671	5008	,	,		9993	0.005		0.1561	False		,,,				2504	0.0951				p.A21P		Atlas-SNP	.											.	GALC	48	.	0			c.G61C						PASS	.	C	PRO/ALA,PRO/ALA,	109,2871		0,109,1381	4.0	5.0	5.0		61,61,	3.2	1.0	14	dbSNP_132	5	777,5987		22,733,2627	yes	missense,missense,intron	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	27,27,	22,842,4008	GG,GC,CC		11.4873,3.6577,9.0928	possibly-damaging,possibly-damaging,	21/686,21/663,	88459448	886,8858	1490	3382	4872	SO:0001583	missense	2581	exon1			AACCCGCGGCCGC	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.61G>C	14.37:g.88459448C>G	ENSP00000261304:p.Ala21Pro	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	23	23	1	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	37	CCDS9878.2	200	0.09157509157509157	12	0.024390243902439025	56	0.15469613259668508	2	0.0034965034965034965	130	0.17150395778364116	C	21.8	4.196569	0.79015	0.036577	0.114873	ENSG00000054983	ENST00000261304;ENST00000393568;ENST00000445021	D;D	0.94966	-3.57;-3.57	3.21	3.21	0.36854	.	0.724898	0.13336	N	0.395547	T	0.07593	0.0191	L	0.60455	1.87	0.24736	P	0.99306181	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	T	0.41787	-0.9489	9	0.39692	T	0.17	-11.3759	12.6873	0.56954	0.0:1.0:0.0:0.0	.	21;21;21	E7EPA4;G3XAI6;P54803	.;.;GALC_HUMAN	P	21	ENSP00000261304:A21P;ENSP00000377198:A21P	ENSP00000261304:A21P	A	-	1	0	GALC	87529201	0.993000	0.37304	1.000000	0.80357	0.582000	0.36321	0.653000	0.24902	2.103000	0.63969	0.462000	0.41574	GCG	C|0.908;G|0.092	0.092	strong		0.721	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
BCL2	596	hgsc.bcm.edu	37	18	60985833	60985833	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:60985833G>A	ENST00000398117.1	-	1	1528	c.67C>T	c.(67-69)Ctg>Ttg	p.L23L	BCL2_ENST00000333681.4_Silent_p.L23L|BCL2_ENST00000444484.1_Silent_p.L23L|BCL2_ENST00000589955.1_Silent_p.L23L	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	23					actin filament organization (GO:0007015)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|axonogenesis (GO:0007409)|B cell homeostasis (GO:0001782)|B cell lineage commitment (GO:0002326)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|behavioral fear response (GO:0001662)|branching involved in ureteric bud morphogenesis (GO:0001658)|CD8-positive, alpha-beta T cell lineage commitment (GO:0043375)|cell aging (GO:0007569)|cell growth (GO:0016049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to organic substance (GO:0071310)|cochlear nucleus development (GO:0021747)|defense response to virus (GO:0051607)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|ear development (GO:0043583)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|female pregnancy (GO:0007565)|focal adhesion assembly (GO:0048041)|gland morphogenesis (GO:0022612)|glomerulus development (GO:0032835)|hair follicle morphogenesis (GO:0031069)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|melanin metabolic process (GO:0006582)|melanocyte differentiation (GO:0030318)|mesenchymal cell development (GO:0014031)|metanephros development (GO:0001656)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of autophagy (GO:0010507)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cellular pH reduction (GO:0032848)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of retinal cell programmed cell death (GO:0046671)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oocyte development (GO:0048599)|organ growth (GO:0035265)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pigment granule organization (GO:0048753)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell growth (GO:0030307)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron maturation (GO:0014042)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smooth muscle cell migration (GO:0014911)|post-embryonic development (GO:0009791)|protein dephosphorylation (GO:0006470)|protein polyubiquitination (GO:0000209)|reactive oxygen species metabolic process (GO:0072593)|regulation of calcium ion transport (GO:0051924)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glycoprotein biosynthetic process (GO:0010559)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|regulation of protein stability (GO:0031647)|regulation of transmembrane transporter activity (GO:0022898)|regulation of viral genome replication (GO:0045069)|release of cytochrome c from mitochondria (GO:0001836)|renal system process (GO:0003014)|response to acid chemical (GO:0001101)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to iron ion (GO:0010039)|response to ischemia (GO:0002931)|response to nicotine (GO:0035094)|response to radiation (GO:0009314)|response to toxic substance (GO:0009636)|response to UV-B (GO:0010224)|single organismal cell-cell adhesion (GO:0016337)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|channel inhibitor activity (GO:0016248)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(106)|kidney(1)|large_intestine(1)|lung(3)	113		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Ibuprofen(DB01050)|Paclitaxel(DB01229)|Rasagiline(DB01367)	CTCTGCGACAGCTTATAATGG	0.652			T	IGH@	"""NHL, CLL"""																																p.L23L		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	.	BCL2	272	.	0			c.C67T						PASS	.						68.0	76.0	73.0					18																	60985833		1972	4119	6091	SO:0001819	synonymous_variant	596	exon2			GCGACAGCTTATA	M14745	CCDS11981.1, CCDS45882.1	18q21.3	2014-03-07			ENSG00000171791	ENSG00000171791		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	990	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 50"""	151430					Standard	XM_006722523		Approved	Bcl-2, PPP1R50	uc002lit.1	P10415	OTTHUMG00000132791	ENST00000398117.1:c.67C>T	18.37:g.60985833G>A		Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	37	CCDS11981.1																																																																																			.	.	none		0.652	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657	
IL12RB1	3594	hgsc.bcm.edu	37	19	18186575	18186575	+	Silent	SNP	G	G	A	rs17852635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18186575G>A	ENST00000600835.2	-	8	982	c.684C>T	c.(682-684)ccC>ccT	p.P228P	IL12RB1_ENST00000322153.7_Silent_p.P228P|IL12RB1_ENST00000593993.2_Silent_p.P228P			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	228	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-23-mediated signaling pathway (GO:0038155)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of memory T cell differentiation (GO:0043382)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of T-helper 17 cell lineage commitment (GO:2000330)|positive regulation of T-helper 17 type immune response (GO:2000318)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|interleukin-12 receptor complex (GO:0042022)|interleukin-23 receptor complex (GO:0072536)	cytokine receptor activity (GO:0004896)			endometrium(1)|kidney(1)|lung(3)|pancreas(1)|skin(2)	8						GAACGCACACGGGGCTGCTCC	0.592													G|||	1151	0.229832	0.0998	0.1643	5008	,	,		17094	0.373		0.3111	False		,,,				2504	0.2209				p.P228P		Atlas-SNP	.											.	IL12RB1	92	.	0			c.C684T						PASS	.	G	,	589,3817	260.1+/-263.5	32,525,1646	65.0	64.0	64.0		684,684	-7.2	0.2	19	dbSNP_123	64	2715,5885	433.5+/-357.4	424,1867,2009	no	coding-synonymous,coding-synonymous	IL12RB1	NM_005535.1,NM_153701.1	,	456,2392,3655	AA,AG,GG		31.5698,13.3681,25.4037	,	228/663,228/382	18186575	3304,9702	2203	4300	6503	SO:0001819	synonymous_variant	3594	exon7			GCACACGGGGCTG	U03187	CCDS32957.1, CCDS54232.1	19p13.1	2014-09-17						"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	5971	protein-coding gene	gene with protein product		601604		IL12RB		9284929	Standard	XM_005259893		Approved	CD212	uc002nhw.1	P42701		ENST00000600835.2:c.684C>T	19.37:g.18186575G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_153701	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Silent	SNP	ENST00000600835.2	37	CCDS54232.1																																																																																			G|0.748;A|0.252	0.252	strong		0.592	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3		
TRAPPC11	60684	hgsc.bcm.edu	37	4	184615117	184615117	+	Missense_Mutation	SNP	A	A	C	rs62358032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:184615117A>C	ENST00000334690.6	+	22	2636	c.2434A>C	c.(2434-2436)Aca>Cca	p.T812P	TRAPPC11_ENST00000357207.4_Missense_Mutation_p.T812P|TRAPPC11_ENST00000512476.1_Missense_Mutation_p.T418P	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	812				T -> P (in Ref. 1; CAD91169, 4; CAG38584 and 5; CAB66686). {ECO:0000305}.	vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)											TCTTCATGGAACAGAACTGTG	0.408													A|||	220	0.0439297	0.0045	0.0375	5008	,	,		19922	0.0268		0.0944	False		,,,				2504	0.0675				p.T812P		Atlas-SNP	.											.	.	.	.	0			c.A2434C						PASS	.	A	PRO/THR,PRO/THR	100,4306	80.4+/-118.8	1,98,2104	118.0	116.0	117.0		2434,2434	-1.6	0.2	4	dbSNP_129	117	997,7603	214.5+/-254.1	66,865,3369	yes	missense,missense	C4orf41	NM_021942.4,NM_199053.1	38,38	67,963,5473	CC,CA,AA		11.593,2.2696,8.4346	benign,benign	812/1134,812/1087	184615117	1097,11909	2203	4300	6503	SO:0001583	missense	60684	exon22			CATGGAACAGAAC		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.2434A>C	4.37:g.184615117A>C	ENSP00000335371:p.Thr812Pro	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_021942	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Missense_Mutation	SNP	ENST00000334690.6	37	CCDS34112.1	124	0.056776556776556776	4	0.008130081300813009	21	0.058011049723756904	19	0.033216783216783216	80	0.10554089709762533	A	11.85	1.761997	0.31228	0.022696	0.11593	ENSG00000168538	ENST00000334690;ENST00000357207;ENST00000360109;ENST00000512476	.	.	.	5.78	-1.58	0.08479	.	0.406317	0.27185	N	0.020536	T	0.00440	0.0014	N	0.25647	0.755	0.44555	P	0.0024889999999999635	B;B;B;B	0.27316	0.175;0.055;0.0;0.045	B;B;B;B	0.35770	0.21;0.137;0.001;0.084	T	0.11842	-1.0571	8	0.28530	T	0.3	.	7.1561	0.25639	0.4422:0.0:0.438:0.1198	rs62358032	543;418;812;812	B3KR79;D6RHE5;Q7Z392;Q7Z392-3	.;.;TPC11_HUMAN;.	P	812;812;812;418	.	ENSP00000335371:T812P	T	+	1	0	C4orf41	184852111	0.004000	0.15560	0.155000	0.22561	0.802000	0.45316	0.463000	0.21972	-0.468000	0.06922	-0.336000	0.08194	ACA	A|0.924;C|0.076	0.076	strong		0.408	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
MYO3B	140469	hgsc.bcm.edu	37	2	171260797	171260797	+	Missense_Mutation	SNP	A	A	G	rs33962844	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:171260797A>G	ENST00000408978.4	+	20	2461	c.2318A>G	c.(2317-2319)gAa>gGa	p.E773G	MYO3B_ENST00000334231.6_Missense_Mutation_p.E782G|MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000409044.3_Missense_Mutation_p.E773G	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	773	Myosin motor.		E -> G (in dbSNP:rs33962844). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17344846}.		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						GTACCCGTGGAATATGAGGAC	0.507													A|||	1244	0.248403	0.0189	0.4251	5008	,	,		18184	0.2718		0.3509	False		,,,				2504	0.3037				p.E773G		Atlas-SNP	.											MYO3B,neck,malignant_melanoma,+1,1	MYO3B	320	1	0			c.A2318G						PASS	.	A	GLY/GLU,GLY/GLU,GLY/GLU	310,3512		14,282,1615	149.0	140.0	143.0		2318,2318,2318	-0.1	0.1	2	dbSNP_126	143	2876,5386		502,1872,1757	yes	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	98,98,98	516,2154,3372	GG,GA,AA		34.81,8.1109,26.3654	benign,benign,benign	773/1315,773/1276,773/1342	171260797	3186,8898	1911	4131	6042	SO:0001583	missense	140469	exon20			CCGTGGAATATGA		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.2318A>G	2.37:g.171260797A>G	ENSP00000386213:p.Glu773Gly	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	549	0.25137362637362637	12	0.024390243902439025	130	0.35911602209944754	144	0.2517482517482518	263	0.3469656992084433	A	9.337	1.061972	0.19987	0.081109	0.3481	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7	5.47	-0.0558	0.13808	Myosin head, motor domain (3);	0.464608	0.26432	N	0.024413	T	0.00012	0.0000	M	0.89287	3.02	0.35242	P	0.22210700000000005	B;B;B	0.12013	0.005;0.001;0.002	B;B;B	0.18263	0.018;0.002;0.021	T	0.13764	-1.0497	9	0.36615	T	0.2	.	3.7409	0.08530	0.5646:0.2428:0.0663:0.1263	rs33962844	773;773;773	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	G	773;773;772;782;782	ENSP00000386497:E773G;ENSP00000386213:E773G;ENSP00000446237:E782G;ENSP00000335100:E782G	ENSP00000314213:E772G	E	+	2	0	MYO3B	170969043	0.996000	0.38824	0.068000	0.19968	0.262000	0.26303	2.485000	0.45250	-0.159000	0.11021	0.533000	0.62120	GAA	A|0.726;G|0.274	0.274	strong		0.507	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
SCN3B	55800	hgsc.bcm.edu	37	11	123513161	123513161	+	Silent	SNP	G	G	A	rs1275085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:123513161G>A	ENST00000392770.2	-	3	1240	c.438C>T	c.(436-438)acC>acT	p.T146T	SCN3B_ENST00000299333.3_Silent_p.T146T|SCN3B_ENST00000530277.1_Silent_p.T146T	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	146	Ig-like C2-type.				atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	CACCCTCCTCGGTGACTCTTA	0.587													G|||	411	0.0820687	0.0953	0.0634	5008	,	,		18757	0.004		0.0984	False		,,,				2504	0.1411				p.T146T		Atlas-SNP	.											.	SCN3B	53	.	0			c.C438T						PASS	.	G	,	403,4001	200.1+/-223.5	15,373,1814	54.0	53.0	53.0		438,438	-9.2	0.8	11	dbSNP_87	53	770,7828	182.2+/-230.7	35,700,3564	no	coding-synonymous,coding-synonymous	SCN3B	NM_001040151.1,NM_018400.3	,	50,1073,5378	AA,AG,GG		8.9556,9.1508,9.0217	,	146/216,146/216	123513161	1173,11829	2202	4299	6501	SO:0001819	synonymous_variant	55800	exon3			CTCCTCGGTGACT	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"""	20665	protein-coding gene	gene with protein product		608214	"""sodium channel, voltage-gated, type III, beta"""			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.438C>T	11.37:g.123513161G>A		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Silent	SNP	ENST00000392770.2	37	CCDS8442.1																																																																																			G|0.914;A|0.086	0.086	strong		0.587	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400	
DCAF12L2	340578	hgsc.bcm.edu	37	X	125299188	125299188	+	Silent	SNP	T	T	G	rs12014937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:125299188T>G	ENST00000360028.2	-	1	746	c.720A>C	c.(718-720)ccA>ccC	p.P240P	DCAF12L2_ENST00000538699.1_Silent_p.P240P			Q5VW00	DC122_HUMAN	DDB1 and CUL4 associated factor 12-like 2	240										NS(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(36)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(3)	64						GGGCATATACTGGGAGACCCA	0.642													G|||	2050	0.543046	0.587	0.4236	3775	,	,		12575	0.3859		0.2495	False		,,,				2504	0.3476				p.P240P		Atlas-SNP	.											.	DCAF12L2	157	.	0			c.A720C						PASS	.	G		2758,1077		841,669,407,122,164	29.0	32.0	31.0		720	-7.7	0.0	X	dbSNP_120	31	1994,4730		220,988,566,1219,1304	no	coding-synonymous	DCAF12L2	NM_001013628.2		1061,1657,973,1341,1468	GG,GT,G,TT,T		29.655,28.0834,45.0043		240/464	125299188	4752,5807	2203	4297	6500	SO:0001819	synonymous_variant	340578	exon1			ATATACTGGGAGA	AL445072	CCDS43991.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198354	ENSG00000198354		"""WD repeat domain containing"""	32950	protein-coding gene	gene with protein product			"""WD repeat domain 40C"""	WDR40C			Standard	NM_001013628		Approved		uc004euk.2	Q5VW00	OTTHUMG00000022348	ENST00000360028.2:c.720A>C	X.37:g.125299188T>G		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	70	69	0.985714	NM_001013628	B2RN42	Silent	SNP	ENST00000360028.2	37	CCDS43991.1																																																																																			T|0.485;G|0.515	0.515	strong		0.642	DCAF12L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058181.1	NM_001013628	
USP6	9098	hgsc.bcm.edu	37	17	5072333	5072333	+	Missense_Mutation	SNP	T	T	G	rs3816913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5072333T>G	ENST00000574788.1	+	35	5730	c.3500T>G	c.(3499-3501)aTc>aGc	p.I1167S	USP6_ENST00000332776.4_3'UTR|USP6_ENST00000304328.5_Missense_Mutation_p.I850S|USP6_ENST00000250066.6_Missense_Mutation_p.I1167S			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	1167	USP.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						AGCGCTAACATCAGCAGCAGC	0.507			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								t|||	513	0.102436	0.1974	0.0418	5008	,	,		19709	0.0794		0.1163	False		,,,				2504	0.0266				p.I1167S		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.T3500G						PASS	.	G	SER/ILE	703,3703	278.4+/-274.2	61,581,1561	34.0	34.0	34.0		3500	1.2	0.0	17	dbSNP_107	34	945,7651	196.9+/-241.7	53,839,3406	no	missense	USP6	NM_004505.2	142	114,1420,4967	GG,GT,TT		10.9935,15.9555,12.675	benign	1167/1407	5072333	1648,11354	2203	4298	6501	SO:0001583	missense	9098	exon27			CTAACATCAGCAG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.3500T>G	17.37:g.5072333T>G	ENSP00000460380:p.Ile1167Ser	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	208	92	0.442308	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	246	0.11263736263736264	94	0.1910569105691057	16	0.04419889502762431	52	0.09090909090909091	84	0.11081794195250659	t	0.036	-1.305728	0.01353	0.159555	0.109935	ENSG00000129204	ENST00000250066;ENST00000304328	T;T	0.13778	2.98;2.56	2.35	1.22	0.21188	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.756886	0.13090	N	0.414589	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.24092	0.029;0.097	B;B	0.28011	0.03;0.085	T	0.43605	-0.9381	9	0.07813	T	0.8	.	5.438	0.16492	0.0:0.0:0.2935:0.7065	rs3816913	850;1167	P35125-2;P35125	.;UBP6_HUMAN	S	1167;850	ENSP00000250066:I1167S;ENSP00000305473:I850S	ENSP00000250066:I1167S	I	+	2	0	USP6	5013057	0.058000	0.20735	0.003000	0.11579	0.116000	0.19942	1.968000	0.40500	0.160000	0.19432	-1.396000	0.01147	ATC	T|0.884;G|0.116	0.116	strong		0.507	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
PAX2	5076	hgsc.bcm.edu	37	10	102568983	102568983	+	Silent	SNP	A	A	C	rs1800898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:102568983A>C	ENST00000428433.1	+	8	1528	c.978A>C	c.(976-978)ccA>ccC	p.P326P	PAX2_ENST00000556085.1_Silent_p.P302P|PAX2_ENST00000361791.3_Silent_p.P303P|PAX2_ENST00000355243.3_Silent_p.P303P|PAX2_ENST00000370296.2_Silent_p.P326P	NM_003987.3|NM_003990.3	NP_003978|NP_003981.2	Q02962	PAX2_HUMAN	paired box 2	326					aging (GO:0007568)|axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cell fate determination (GO:0001709)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucose stimulus (GO:0071333)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|glial cell differentiation (GO:0010001)|inner ear morphogenesis (GO:0042472)|mesenchymal to epithelial transition (GO:0060231)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate specification (GO:0007501)|mesonephric duct development (GO:0072177)|mesonephric tubule formation (GO:0072172)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric mesenchyme development (GO:0072075)|metanephric nephron tubule formation (GO:0072289)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytolysis (GO:0045918)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of programmed cell death (GO:0043069)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct formation (GO:0072179)|neural tube closure (GO:0001843)|optic chiasma development (GO:0061360)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|optic nerve development (GO:0021554)|optic nerve morphogenesis (GO:0021631)|optic nerve structural organization (GO:0021633)|pancreas development (GO:0031016)|paramesonephric duct development (GO:0061205)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of optic nerve formation (GO:2000597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|protein kinase B signaling (GO:0043491)|reactive oxygen species metabolic process (GO:0072593)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of metanephros size (GO:0035566)|response to nutrient levels (GO:0031667)|retinal pigment epithelium development (GO:0003406)|stem cell differentiation (GO:0048863)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|ureter development (GO:0072189)|ureter maturation (GO:0035799)|ureter morphogenesis (GO:0072197)|urogenital system development (GO:0001655)|vestibulocochlear nerve formation (GO:0021650)|visual perception (GO:0007601)	centriolar satellite (GO:0034451)|lysosome (GO:0005764)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|protein complex (GO:0043234)|protein-DNA complex (GO:0032993)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|superoxide-generating NADPH oxidase activity (GO:0016175)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	18		Colorectal(252;0.234)		Epithelial(162;1.32e-08)|all cancers(201;7.32e-07)		AGACATACCCAGTTGTGACTG	0.607													C|||	1882	0.375799	0.8215	0.2363	5008	,	,		18525	0.0982		0.2594	False		,,,				2504	0.2781				p.P326P		Atlas-SNP	.											.	PAX2	83	.	0			c.A978C						PASS	.	C	,,,,	3261,1145	406.2+/-333.8	1229,803,171	77.0	67.0	70.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	909,978,909,909,978	-8.4	0.0	10	dbSNP_89	70	2458,6142	695.6+/-404.8	357,1744,2199	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PAX2	NM_000278.3,NM_003987.3,NM_003988.3,NM_003989.3,NM_003990.3	,,,,	1586,2547,2370	CC,CA,AA		28.5814,25.9873,43.972	,,,,	303/395,326/418,303/397,303/410,326/433	102568983	5719,7287	2203	4300	6503	SO:0001819	synonymous_variant	5076	exon8			ATACCCAGTTGTG		CCDS7499.1, CCDS41561.1	10q24.31	2011-06-20	2007-07-12		ENSG00000075891	ENSG00000075891		"""Paired boxes"", ""Homeoboxes / PRD class"""	8616	protein-coding gene	gene with protein product		167409	"""paired box gene 2"""			8431641, 7981748	Standard	NM_003990		Approved		uc001krk.4	Q02962	OTTHUMG00000018913	ENST00000428433.1:c.978A>C	10.37:g.102568983A>C		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_003987	Q15105|Q15110|Q15837|Q5SZP2|Q5SZP3	Silent	SNP	ENST00000428433.1	37	CCDS53569.1																																																																																			A|0.594;C|0.406	0.406	strong		0.607	PAX2-202	KNOWN	basic|CCDS	protein_coding	protein_coding			
NELFB	25920	hgsc.bcm.edu	37	9	140147273	140147273	+	5'Flank	SNP	C	C	T	rs61759822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140147273C>T	ENST00000343053.4	+	0	0				C9orf173_ENST00000388931.3_Missense_Mutation_p.L218F|C9orf173_ENST00000412566.1_Missense_Mutation_p.L218F	NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B						gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											CCAGTCCCTGCTTCAGGCCTC	0.667													C|||	715	0.142772	0.0204	0.1066	5008	,	,		12190	0.3075		0.1243	False		,,,				2504	0.183				p.L218F		Atlas-SNP	.											.	C9orf173	19	.	0			c.C652T						PASS	.	C	PHE/LEU	174,3596		4,166,1715	12.0	14.0	13.0		652	1.6	0.0	9	dbSNP_129	13	866,7272		57,752,3260	yes	missense	C9orf173	NM_001004353.2	22	61,918,4975	TT,TC,CC		10.6414,4.6154,8.7336	benign	218/309	140147273	1040,10868	1885	4069	5954	SO:0001631	upstream_gene_variant	441476	exon5			TCCCTGCTTCAGG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778		9.37:g.140147273C>T	Exception_encountered	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	49	19	0.387755	NM_001004353	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Missense_Mutation	SNP	ENST00000343053.4	37	CCDS7040.1	331	0.15155677655677655	13	0.026422764227642278	37	0.10220994475138122	184	0.32167832167832167	97	0.1279683377308707	C	9.287	1.049649	0.19827	0.046154	0.106414	ENSG00000197768	ENST00000388931;ENST00000412566	T;T	0.59502	0.26;0.44	3.65	1.63	0.23807	.	1.740450	0.03652	N	0.241159	T	0.00012	0.0000	L	0.48642	1.525	0.80722	P	0.0	D;D	0.58268	0.982;0.982	P;P	0.54210	0.745;0.745	T	0.04153	-1.0973	9	0.32370	T	0.25	.	8.2084	0.31469	0.4328:0.5672:0.0:0.0	rs61759822	218;218	Q8N7X2-2;Q8N7X2-4	.;.	F	218	ENSP00000373583:L218F;ENSP00000391218:L218F	ENSP00000373583:L218F	L	+	1	0	C9orf173	139267094	0.000000	0.05858	0.003000	0.11579	0.016000	0.09150	-1.225000	0.02956	0.274000	0.22072	-0.310000	0.09108	CTT	C|0.847;T|0.153	0.153	strong		0.667	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456	
HLA-A	3105	hgsc.bcm.edu	37	6	29911951	29911951	+	Silent	SNP	C	C	T	rs1059570	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911951C>T	ENST00000396634.1	+	6	1013	c.672C>T	c.(670-672)acC>acT	p.T224T	HLA-A_ENST00000376809.5_Silent_p.T224T|HLA-A_ENST00000376806.5_Silent_p.T224T|HLA-A_ENST00000376802.2_Silent_p.T224T			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	224	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ATGAGGCCACCCTGAGGTGCT	0.597									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			c|||	793	0.158347	0.1377	0.1801	5008	,	,		19929	0.2093		0.1123	False		,,,				2504	0.1656				p.T224T		Atlas-SNP	.											.	HLA-A	89	.	0			c.C672T						PASS	.	C		447,2569		62,323,1123	79.0	103.0	94.0		672	1.7	1.0	6	dbSNP_86	94	602,4812		54,494,2159	no	coding-synonymous	HLA-A	NM_002116.7		116,817,3282	TT,TC,CC		11.1193,14.821,12.4437		224/366	29911951	1049,7381	1508	2707	4215	SO:0001819	synonymous_variant	3105	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GGCCACCCTGAGG	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.672C>T	6.37:g.29911951C>T		Somatic	417	2	0.00479616		WXS	Illumina HiSeq	Phase_I	200	116	0.58	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	weak		0.597	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
LAMA2	3908	hgsc.bcm.edu	37	6	129722425	129722425	+	Silent	SNP	G	G	A	rs3749878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:129722425G>A	ENST00000421865.2	+	38	5551	c.5502G>A	c.(5500-5502)gaG>gaA	p.E1834E		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1834	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		CTTTAAAAGAGGGCAATGACA	0.373													G|||	2721	0.543331	0.6581	0.4683	5008	,	,		20575	0.5466		0.4622	False		,,,				2504	0.5215				p.E1834E		Atlas-SNP	.											.	LAMA2	481	.	0			c.G5502A						PASS	.	G	,	2707,1699	653.4+/-399.6	833,1041,329	143.0	140.0	141.0		5502,5502	-7.6	0.5	6	dbSNP_107	141	3991,4609	553.7+/-386.3	932,2127,1241	no	coding-synonymous,coding-synonymous	LAMA2	NM_000426.3,NM_001079823.1	,	1765,3168,1570	AA,AG,GG		46.407,38.5611,48.5007	,	1834/3123,1834/3119	129722425	6698,6308	2203	4300	6503	SO:0001819	synonymous_variant	3908	exon38			AAAAGAGGGCAAT	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.5502G>A	6.37:g.129722425G>A		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	28	25	0.892857	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			G|0.461;A|0.539	0.539	strong		0.373	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
OR2T4	127074	hgsc.bcm.edu	37	1	248525290	248525290	+	Silent	SNP	C	C	T	rs202028348|rs141576206|rs386642002|rs374193555|rs57728407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248525290C>T	ENST00000366475.1	+	1	408	c.408C>T	c.(406-408)taC>taT	p.Y136Y		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y136*(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTTCTTCTACGTGACACTAG	0.522													t|||	1549	0.309305	0.2678	0.2752	5008	,	,		19688	0.4405		0.1899	False		,,,				2504	0.3773				p.Y136Y		Atlas-SNP	.											OR2T4,NS,carcinoma,0,1	OR2T4	126	1	1	Substitution - Nonsense(1)	lung(1)	c.C408T						scavenged	.																																			SO:0001819	synonymous_variant	127074	exon1			CTTCTACGTGACA	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.408C>T	1.37:g.248525290C>T		Somatic	781	0	0		WXS	Illumina HiSeq	Phase_I	877	23	0.0262258	NM_001004696	Q6IEZ8	Silent	SNP	ENST00000366475.1	37	CCDS31113.1																																																																																			C|0.840;T|0.160	0.160	strong		0.522	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081048	57081048	+	Missense_Mutation	SNP	G	G	C	rs79638626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57081048G>C	ENST00000532437.1	-	4	1425	c.1114C>G	c.(1114-1116)Cct>Gct	p.P372A	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P372A			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	372	Acidic.|Pro-rich.				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)	p.P372A(1)		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)				AAGACCTCAGGGGGTGGGCTG	0.701													G|||	108	0.0215655	0.0023	0.0418	5008	,	,		13311	0.002		0.0487	False		,,,				2504	0.0256				p.P372A		Atlas-SNP	.											TNKS1BP1,NS,haematopoietic_neoplasm,0,1	TNKS1BP1	148	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1114G						PASS	.	G	ALA/PRO	48,4254		1,46,2104	7.0	10.0	9.0		1114	-6.0	0.0	11	dbSNP_132	9	403,8029		9,385,3822	yes	missense	TNKS1BP1	NM_033396.2	27	10,431,5926	CC,CG,GG		4.7794,1.1158,3.5417	benign	372/1730	57081048	451,12283	2151	4216	6367	SO:0001583	missense	85456	exon5			CCTCAGGGGGTGG	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.1114C>G	11.37:g.57081048G>C	ENSP00000437271:p.Pro372Ala	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	44	23	0.522727	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	63	0.028846153846153848	2	0.0040650406504065045	16	0.04419889502762431	2	0.0034965034965034965	43	0.05672823218997362	G	8.473	0.857895	0.17178	0.011158	0.047794	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.29397	1.57;1.57	4.18	-6.04	0.02178	.	.	.	.	.	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.28170	-1.0052	9	0.08381	T	0.77	0.8305	1.441	0.02354	0.1918:0.3296:0.267:0.2116	.	372	Q9C0C2	TB182_HUMAN	A	372	ENSP00000350990:P372A;ENSP00000437271:P372A	ENSP00000350990:P372A	P	-	1	0	TNKS1BP1	56837624	0.001000	0.12720	0.000000	0.03702	0.644000	0.38419	-0.111000	0.10807	-1.098000	0.03038	0.462000	0.41574	CCT	G|0.970;C|0.030	0.030	strong		0.701	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	140532	140532	+	Missense_Mutation	SNP	T	T	C	rs12516846	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140532T>C	ENST00000283426.6	+	1	160	c.110T>C	c.(109-111)gTa>gCa	p.V37A	CTD-2231H16.1_ENST00000512035.1_lincRNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	37			V -> A (in dbSNP:rs12516846).				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)		ACTGGGGCAGTAGCCAGTGGG	0.677													C|||	770	0.153754	0.4009	0.0965	5008	,	,		12319	0.0129		0.1233	False		,,,				2504	0.0368				p.V37A		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.T110C						PASS	.		ALA/VAL	1476,2792		263,950,921	10.0	12.0	12.0		110	-0.9	0.0	5	dbSNP_120	12	966,7480		51,864,3308	yes	missense	PLEKHG4B	NM_052909.3	64	314,1814,4229	CC,CT,TT		11.4374,34.5829,19.2072	benign	37/1272	140532	2442,10272	2134	4223	6357	SO:0001583	missense	153478	exon1			GGGCAGTAGCCAG	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.110T>C	5.37:g.140532T>C	ENSP00000283426:p.Val37Ala	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	150	73	0.486667	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	335	0.1533882783882784	194	0.3943089430894309	35	0.09668508287292818	10	0.017482517482517484	96	0.1266490765171504	.	0.010	-1.791783	0.00623	0.345829	0.114374	ENSG00000153404	ENST00000283426	T	0.37411	1.2	2.55	-0.889	0.10580	.	.	.	.	.	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	0.40997	-0.9533	8	0.15952	T	0.53	.	0.4878	0.00559	0.1936:0.3456:0.1906:0.2702	rs12516846	37	Q96PX9	PKH4B_HUMAN	A	37	ENSP00000283426:V37A	ENSP00000283426:V37A	V	+	2	0	PLEKHG4B	193532	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.136000	0.01305	-1.995000	0.00971	-0.747000	0.03512	GTA	T|0.846;C|0.154	0.154	strong		0.677	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
UPK3A	7380	hgsc.bcm.edu	37	22	45685002	45685002	+	Silent	SNP	A	A	G	rs1135360	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:45685002A>G	ENST00000216211.4	+	4	581	c.549A>G	c.(547-549)tcA>tcG	p.S183S	UPK3A_ENST00000396082.2_Intron	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	183					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CCCTGTGGTCAGACCCCATCC	0.597													a|||	3327	0.664337	0.9032	0.5749	5008	,	,		17504	0.6954		0.4324	False		,,,				2504	0.6115				p.S183S		Atlas-SNP	.											.	UPK3A	14	.	0			c.A549G						PASS	.	G	,	3660,746	755.5+/-412.6	1512,636,55	90.0	82.0	85.0		,549	-9.6	0.2	22	dbSNP_86	85	3551,5049	516.0+/-378.7	737,2077,1486	no	intron,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	2249,2713,1541	GG,GA,AA		41.2907,16.9315,44.5564	,	,183/288	45685002	7211,5795	2203	4300	6503	SO:0001819	synonymous_variant	7380	exon4			GTGGTCAGACCCC	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.549A>G	22.37:g.45685002A>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			A|0.413;G|0.587	0.587	strong		0.597	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
CFAP61	26074	hgsc.bcm.edu	37	20	20079360	20079360	+	Missense_Mutation	SNP	A	A	G	rs6075614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:20079360A>G	ENST00000245957.5	+	8	837	c.761A>G	c.(760-762)cAt>cGt	p.H254R	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Missense_Mutation_p.H254R|C20orf26_ENST00000377306.1_Missense_Mutation_p.H254R|C20orf26_ENST00000377309.2_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		254			H -> R (in dbSNP:rs6075614).							NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		CAACTGCTGCATGAGTGCTTT	0.453													A|||	314	0.0626997	0.0053	0.0648	5008	,	,		18770	0.001		0.1302	False		,,,				2504	0.1329				p.H254R		Atlas-SNP	.											.	C20orf26	188	.	0			c.A761G						PASS	.	A	ARG/HIS,ARG/HIS	143,4263	100.3+/-138.9	5,133,2065	200.0	168.0	179.0		761,761	5.4	0.2	20	dbSNP_114	179	1256,7344	251.8+/-278.1	92,1072,3136	yes	missense,missense	C20orf26	NM_001167816.1,NM_015585.3	29,29	97,1205,5201	GG,GA,AA		14.6047,3.2456,10.7566	benign,benign	254/471,254/1238	20079360	1399,11607	2203	4300	6503	SO:0001583	missense	26074	exon8			TGCTGCATGAGTG																												ENST00000245957.5:c.761A>G	20.37:g.20079360A>G	ENSP00000245957:p.His254Arg	Somatic	228	0	0		WXS	Illumina HiSeq	Phase_I	239	101	0.422594	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	132	0.06043956043956044	3	0.006097560975609756	25	0.06906077348066299	1	0.0017482517482517483	103	0.1358839050131926	A	3.326	-0.137624	0.06711	0.032456	0.146047	ENSG00000089101	ENST00000340348;ENST00000343997;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000451767;ENST00000472660;ENST00000442372;ENST00000377297	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	5.44	5.44	0.79542	.	0.531595	0.18883	N	0.128539	T	0.00178	0.0005	N	0.21448	0.665	0.09310	P	0.9999999999999901	D;B;B;B	0.63880	0.993;0.003;0.056;0.089	P;B;B;B	0.57057	0.812;0.009;0.031;0.035	T	0.02004	-1.1231	9	0.07482	T	0.82	.	11.4723	0.50278	0.9271:0.0:0.0729:0.0	rs6075614;rs17306632;rs52815119;rs61592058;rs6075614	254;254;208;254	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	R	208;254;254;254;254;254;150;13;46	ENSP00000345553:H208R;ENSP00000245957:H254R;ENSP00000366521:H254R;ENSP00000414537:H254R;ENSP00000420498:H150R;ENSP00000397311:H13R	ENSP00000245957:H254R	H	+	2	0	C20orf26	20027360	0.994000	0.37717	0.227000	0.23927	0.124000	0.20399	5.249000	0.65427	2.066000	0.61787	0.533000	0.62120	CAT	A|0.909;G|0.091	0.091	strong		0.453	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
OR13C9	286362	hgsc.bcm.edu	37	9	107380215	107380215	+	Missense_Mutation	SNP	T	T	A	rs993658	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107380215T>A	ENST00000259362.1	-	1	270	c.271A>T	c.(271-273)Acc>Tcc	p.T91S		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	91			T -> S (in dbSNP:rs993658).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AAGGAAATGGTCTTTCTTTCT	0.502													T|||	1753	0.35004	0.351	0.2104	5008	,	,		20373	0.5645		0.1779	False		,,,				2504	0.4039				p.T91S		Atlas-SNP	.											OR13C9,colon,carcinoma,+2,1	OR13C9	42	1	0			c.A271T						PASS	.	T	SER/THR	1362,3044	451.8+/-349.8	223,916,1064	134.0	139.0	137.0		271	2.2	1.0	9	dbSNP_86	137	1654,6946	306.2+/-307.8	181,1292,2827	no	missense	OR13C9	NM_001001956.1	58	404,2208,3891	AA,AT,TT		19.2326,30.9124,23.1893	probably-damaging	91/319	107380215	3016,9990	2203	4300	6503	SO:0001583	missense	286362	exon1			AAATGGTCTTTCT		CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.271A>T	9.37:g.107380215T>A	ENSP00000259362:p.Thr91Ser	Somatic	504	1	0.00198413		WXS	Illumina HiSeq	Phase_I	453	226	0.498896	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	684	0.3131868131868132	156	0.3170731707317073	74	0.20441988950276244	322	0.5629370629370629	132	0.1741424802110818	T	11.45	1.641969	0.29157	0.309124	0.192326	ENSG00000136839	ENST00000259362	T	0.01422	4.91	4.78	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	0.282386	0.25256	N	0.031997	T	0.00012	0.0000	N	0.17764	0.52	0.54753	P	1.6000000000016E-5	B	0.06786	0.001	B	0.10450	0.005	T	0.09271	-1.0682	9	0.33141	T	0.24	.	8.3632	0.32372	0.3107:0.0:0.0:0.6893	rs993658;rs52822852;rs993658	91	Q8NGT0	O13C9_HUMAN	S	91	ENSP00000259362:T91S	ENSP00000259362:T91S	T	-	1	0	OR13C9	106420036	0.000000	0.05858	1.000000	0.80357	0.973000	0.67179	-0.033000	0.12246	0.809000	0.34255	0.519000	0.50382	ACC	T|0.743;A|0.257	0.257	strong		0.502	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
SLC26A1	10861	hgsc.bcm.edu	37	4	982852	982852	+	Silent	SNP	G	G	A	rs3796621	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:982852G>A	ENST00000361661.2	-	4	2252	c.1875C>T	c.(1873-1875)gcC>gcT	p.A625A	SLC26A1_ENST00000513138.1_5'Flank|IDUA_ENST00000453894.1_Intron|IDUA_ENST00000509744.1_Intron|IDUA_ENST00000247933.4_Intron|SLC26A1_ENST00000398520.2_Intron|SLC26A1_ENST00000398516.2_Silent_p.A625A	NM_213613.2	NP_998778.1	Q9H2B4	S26A1_HUMAN	solute carrier family 26 (anion exchanger), member 1	625	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|chloride transport (GO:0006821)|glycosaminoglycan metabolic process (GO:0030203)|ion transport (GO:0006811)|oxalate transport (GO:0019532)|small molecule metabolic process (GO:0044281)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	anion:anion antiporter activity (GO:0015301)|chloride transmembrane transporter activity (GO:0015108)|oxalate transmembrane transporter activity (GO:0019531)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(1)|endometrium(4)|pancreas(1)|prostate(1)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TGCTCACACCGGCTGCGTCTA	0.682													G|||	2194	0.438099	0.3775	0.5576	5008	,	,		15493	0.372		0.4423	False		,,,				2504	0.499				p.A625A		Atlas-SNP	.											.	SLC26A1	44	.	0			c.C1875T						PASS	.	G	,,,	1709,2639		363,983,828	14.0	15.0	15.0		,1875,,1875	-6.5	0.1	4	dbSNP_107	15	3880,4670		898,2084,1293	no	intron,coding-synonymous,intron,coding-synonymous	IDUA,SLC26A1	NM_000203.3,NM_022042.2,NM_134425.1,NM_213613.2	,,,	1261,3067,2121	AA,AG,GG		45.3801,39.3054,43.3323	,,,	,625/702,,625/702	982852	5589,7309	2174	4275	6449	SO:0001819	synonymous_variant	10861	exon3			CACACCGGCTGCG	AF297659	CCDS33933.1, CCDS33934.1	4p16.3	2013-07-18	2013-07-18		ENSG00000145217	ENSG00000145217		"""Solute carriers"""	10993	protein-coding gene	gene with protein product		610130	"""solute carrier family 26 (sulfate transporter), member 1"""				Standard	NM_213613		Approved	SAT-1, EDM4	uc003gcc.3	Q9H2B4	OTTHUMG00000160003	ENST00000361661.2:c.1875C>T	4.37:g.982852G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	82	82	1	NM_022042	A8K9N2|Q7Z5R3|Q96BK0	Silent	SNP	ENST00000361661.2	37	CCDS33934.1																																																																																			G|0.565;A|0.435	0.435	strong		0.682	SLC26A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358783.1	NM_022042, NM_134425	
MAP4	4134	hgsc.bcm.edu	37	3	47956424	47956424	+	Missense_Mutation	SNP	C	C	T	rs1137524	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:47956424C>T	ENST00000360240.6	-	8	2400	c.1882G>A	c.(1882-1884)Gtc>Atc	p.V628I	MAP4_ENST00000395734.3_Missense_Mutation_p.V628I|MAP4_ENST00000426837.2_Missense_Mutation_p.V645I|MAP4_ENST00000383737.4_Intron	NM_002375.4	NP_002366.2	P27816	MAP4_HUMAN	microtubule-associated protein 4	628			V -> I (in dbSNP:rs1137524). {ECO:0000269|PubMed:1718985, ECO:0000269|PubMed:18669648, ECO:0000269|PubMed:20068231}.		cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|microtubule sliding (GO:0051012)|mitotic spindle organization (GO:0007052)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|microtubule cytoskeleton (GO:0015630)|mitotic spindle (GO:0072686)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(2)	32				BRCA - Breast invasive adenocarcinoma(193;0.000721)|KIRC - Kidney renal clear cell carcinoma(197;0.00641)|Kidney(197;0.00736)	Docetaxel(DB01248)|Paclitaxel(DB01229)	GTTCCTGTGACGGTTTCTAAA	0.443													C|||	1947	0.388778	0.5628	0.3963	5008	,	,		18715	0.2847		0.3002	False		,,,				2504	0.3466				p.V628I		Atlas-SNP	.											.	MAP4	176	.	0			c.G1882A						PASS	.	C	ILE/VAL,ILE/VAL	2353,2053	607.5+/-391.0	627,1099,477	127.0	132.0	130.0		1882,1882	0.4	0.0	3	dbSNP_86	130	2696,5904	431.8+/-356.9	429,1838,2033	yes	missense,missense	MAP4	NM_001134364.1,NM_002375.4	29,29	1056,2937,2510	TT,TC,CC		31.3488,46.5956,38.8205	probably-damaging,probably-damaging	628/1136,628/1153	47956424	5049,7957	2203	4300	6503	SO:0001583	missense	4134	exon8			CTGTGACGGTTTC		CCDS33750.1, CCDS46818.1, CCDS46821.1	3p21	2008-07-18			ENSG00000047849	ENSG00000047849			6862	protein-coding gene	gene with protein product		157132				1905296	Standard	NM_002375		Approved		uc003csb.2	P27816	OTTHUMG00000156828	ENST00000360240.6:c.1882G>A	3.37:g.47956424C>T	ENSP00000353375:p.Val628Ile	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	104	51	0.490385	NM_001134364	Q13082|Q59FT2|Q68D74|Q6ZUW9|Q86V26|Q96A76|Q96NS9	Missense_Mutation	SNP	ENST00000360240.6	37	CCDS33750.1	736	0.336996336996337	242	0.491869918699187	129	0.356353591160221	144	0.2517482517482518	221	0.29155672823219	C	6.223	0.409250	0.11812	0.534044	0.313488	ENSG00000047849	ENST00000395734;ENST00000426837;ENST00000360240	T;T;T	0.10192	3.1;2.9;3.1	4.42	0.416	0.16416	.	.	.	.	.	T	0.00012	0.0000	M	0.72118	2.19	0.80722	P	0.0	B;B;P	0.35208	0.137;0.216;0.49	B;B;B	0.22152	0.017;0.024;0.038	T	0.40496	-0.9560	8	0.34782	T	0.22	-1.0291	1.6979	0.02866	0.1672:0.4786:0.1625:0.1917	rs1137524;rs2230170;rs3201296;rs6442089;rs11548143;rs17434449;rs52792140;rs59940954;rs6442089	605;628;628	C9JFC3;P27816-6;P27816	.;.;MAP4_HUMAN	I	628;645;628	ENSP00000379083:V628I;ENSP00000407602:V645I;ENSP00000353375:V628I	ENSP00000353375:V628I	V	-	1	0	MAP4	47931428	0.019000	0.18553	0.014000	0.15608	0.015000	0.08874	-0.083000	0.11286	-0.054000	0.13266	-1.067000	0.02272	GTC	T|0.303;G|0.116;C|0.511;N|0.000;A|0.069	0.303	strong		0.443	MAP4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346085.1	NM_002375	
ARSH	347527	hgsc.bcm.edu	37	X	2942109	2942109	+	Silent	SNP	T	T	C	rs5939407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:2942109T>C	ENST00000381130.2	+	6	949	c.949T>C	c.(949-951)Ttg>Ctg	p.L317L		NM_001011719.1	NP_001011719.1	Q5FYA8	ARSH_HUMAN	arylsulfatase family, member H	317					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)				CAACCACACCTTGGTGTACTT	0.572													T|||	2820	0.74702	0.4554	0.5706	3775	,	,		8094	0.7331		0.4911	False		,,,				2504	0.6022				p.L317L		Atlas-SNP	.											.	ARSH	72	.	0			c.T949C						PASS	.	T		2326,1509		613,768,332,251,239	51.0	47.0	48.0		949	2.0	0.1	X	dbSNP_114	48	4345,2383		998,1127,1222,303,650	no	coding-synonymous	ARSH	NM_001011719.1		1611,1895,1554,554,889	CC,CT,C,TT,T		35.4191,39.3481,36.8456		317/563	2942109	6671,3892	2203	4300	6503	SO:0001819	synonymous_variant	347527	exon6			CACACCTTGGTGT	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.949T>C	X.37:g.2942109T>C		Somatic	125	1	0.008		WXS	Illumina HiSeq	Phase_I	132	132	1	NM_001011719		Silent	SNP	ENST00000381130.2	37	CCDS35198.1																																																																																			T|0.346;C|0.654	0.654	strong		0.572	ARSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356489.1	NM_001011719	
AMPH	273	hgsc.bcm.edu	37	7	38433726	38433726	+	Missense_Mutation	SNP	T	T	G	rs35024632	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:38433726T>G	ENST00000356264.2	-	18	1702	c.1487A>C	c.(1486-1488)aAg>aCg	p.K496T	AMPH_ENST00000325590.5_Missense_Mutation_p.K454T|AMPH_ENST00000428293.2_Missense_Mutation_p.K454T|AMPH_ENST00000471913.1_5'UTR	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	496			K -> T (in dbSNP:rs35024632). {ECO:0000269|PubMed:15489334}.		endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						GACAGTGGCCTTCTCCGCCTC	0.577													T|||	351	0.0700879	0.0008	0.0519	5008	,	,		18146	0.1825		0.0726	False		,,,				2504	0.0583				p.K496T		Atlas-SNP	.											.	AMPH	157	.	0			c.A1487C						PASS	.	T	THR/LYS,THR/LYS	50,4356	52.9+/-88.7	1,48,2154	120.0	110.0	113.0		1487,1361	2.1	0.9	7	dbSNP_126	113	634,7966	164.2+/-216.6	34,566,3700	yes	missense,missense	AMPH	NM_001635.3,NM_139316.2	78,78	35,614,5854	GG,GT,TT		7.3721,1.1348,5.2591	benign,benign	496/696,454/654	38433726	684,12322	2203	4300	6503	SO:0001583	missense	273	exon18			GTGGCCTTCTCCG		CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.1487A>C	7.37:g.38433726T>G	ENSP00000348602:p.Lys496Thr	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	86	33	0.383721	NM_001635	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Missense_Mutation	SNP	ENST00000356264.2	37	CCDS5456.1	184|184	0.08424908424908426|0.08424908424908426	0|0	0.0|0.0	19|19	0.052486187845303865|0.052486187845303865	111|111	0.19405594405594406|0.19405594405594406	54|54	0.0712401055408971|0.0712401055408971	T|T	9.076|9.076	0.998033|0.998033	0.19043|0.19043	0.011348|0.011348	0.073721|0.073721	ENSG00000078053|ENSG00000078053	ENST00000441628|ENST00000325590;ENST00000356264;ENST00000428293;ENST00000353242	T|T;T;T	0.34667|0.61040	1.35|0.17;0.18;0.14	5.93|5.93	2.1|2.1	0.27182|0.27182	.|.	.|0.544311	.|0.19498	.|N	.|0.112820	T|T	0.00109|0.00109	0.0003|0.0003	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	P|P	0.0|0.0	.|D;B;B;P	.|0.67145	.|0.996;0.274;0.323;0.925	.|P;B;B;P	.|0.59948	.|0.866;0.072;0.079;0.52	T|T	0.05257|0.05257	-1.0896|-1.0896	6|9	0.13853|0.27082	T|T	0.58|0.32	-27.4888|-27.4888	3.6841|3.6841	0.08321|0.08321	0.0:0.199:0.1936:0.6074|0.0:0.199:0.1936:0.6074	rs35024632|rs35024632	.|542;454;496;384	.|Q8NFL6;P49418-2;P49418;Q8NFL4	.|.;.;AMPH_HUMAN;.	D|T	378|454;496;454;398	ENSP00000415085:E378D|ENSP00000317441:K454T;ENSP00000348602:K496T;ENSP00000390734:K454T	ENSP00000415085:E378D|ENSP00000317441:K454T	E|K	-|-	3|2	2|0	AMPH|AMPH	38400251|38400251	0.378000|0.378000	0.25114|0.25114	0.894000|0.894000	0.35097|0.35097	0.444000|0.444000	0.32077|0.32077	1.415000|1.415000	0.34748|0.34748	1.076000|1.076000	0.40961|0.40961	0.460000|0.460000	0.39030|0.39030	GAA|AAG	T|0.934;G|0.066	0.066	strong		0.577	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
DSPP	1834	hgsc.bcm.edu	37	4	88537123	88537123	+	Silent	SNP	C	C	T	rs372453629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537123C>T	ENST00000282478.7	+	4	3342	c.3309C>T	c.(3307-3309)agC>agT	p.S1103S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1103S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1103	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcgacagcagcgacagcagcg	0.547													c|||	2714	0.541933	0.5439	0.6254	5008	,	,		13665	0.5903		0.5467	False		,,,				2504	0.4254				p.S1103S		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	0			c.C3309T						scavenged	.						12.0	19.0	17.0					4																	88537123		1097	2123	3220	SO:0001819	synonymous_variant	1834	exon5			CAGCAGCGACAGC	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.3309C>T	4.37:g.88537123C>T		Somatic	17	4	0.235294		WXS	Illumina HiSeq	Phase_I	14	12	0.857143	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.547	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
ATP2A2	488	hgsc.bcm.edu	37	12	110765378	110765378	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:110765378G>A	ENST00000539276.2	+	8	760	c.651G>A	c.(649-651)ggG>ggA	p.G217G	ATP2A2_ENST00000395494.2_Silent_p.G190G|ATP2A2_ENST00000308664.6_Silent_p.G217G			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	217					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						TTGCTGCTGGGAAAGCTATGG	0.483																																					p.G217G		Atlas-SNP	.											.	ATP2A2	78	.	0			c.G651A						PASS	.						186.0	186.0	186.0					12																	110765378		2203	4300	6503	SO:0001819	synonymous_variant	488	exon8			TGCTGGGAAAGCT		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"""ATPases / P-type"""	812	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 2"", ""calcium pump 2"""	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.651G>A	12.37:g.110765378G>A		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	127	45	0.354331	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	37	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	G	9.772	1.172980	0.21704	.	.	ENSG00000174437	ENST00000548169	.	.	.	5.38	-0.366	0.12545	.	.	.	.	.	T	0.43233	0.1238	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22173	-1.0224	4	.	.	.	.	3.2414	0.06782	0.2326:0.4733:0.1189:0.1752	.	.	.	.	K	108	.	.	E	+	1	0	ATP2A2	109249761	0.385000	0.25172	0.994000	0.49952	0.998000	0.95712	-0.274000	0.08537	-0.198000	0.10333	0.585000	0.79938	GAA	.	.	none		0.483	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681	
XXYLT1	152002	hgsc.bcm.edu	37	3	194790782	194790782	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194790782G>A	ENST00000310380.6	-	4	952	c.844C>T	c.(844-846)Ccc>Tcc	p.P282S	XXYLT1_ENST00000437101.1_Missense_Mutation_p.P79S|XXYLT1_ENST00000356740.5_Missense_Mutation_p.P76S|XXYLT1_ENST00000355729.4_Missense_Mutation_p.P79S|XXYLT1_ENST00000460582.1_5'UTR|XXYLT1_ENST00000429994.1_Missense_Mutation_p.P136S	NM_152531.4	NP_689744.3	Q8NBI6	XXLT1_HUMAN	xyloside xylosyltransferase 1	282						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring pentosyl groups (GO:0016763)										AGCCCCTCGGGGGGCGGGCCC	0.672																																					p.P282S		Atlas-SNP	.											C3orf21,bladder,carcinoma,+2,1	.	.	1	0			c.C844T						scavenged	.						22.0	27.0	26.0					3																	194790782		1802	3994	5796	SO:0001583	missense	152002	exon4			CCTCGGGGGGCGG	AK075551	CCDS43188.1	3q29	2013-02-22	2011-10-19	2011-10-19	ENSG00000173950	ENSG00000173950		"""Glycosyltransferase family 8 domain containing"""	26639	protein-coding gene	gene with protein product		614552	"""chromosome 3 open reading frame 21"""	C3orf21		22117070	Standard	NM_152531		Approved	FLJ35155	uc003fum.4	Q8NBI6	OTTHUMG00000155915	ENST00000310380.6:c.844C>T	3.37:g.194790782G>A	ENSP00000309640:p.Pro282Ser	Somatic	5	0	0		WXS	Illumina HiSeq	Phase_I	14	2	0.142857	NM_152531	D3DNW5|Q8NAL3|Q8WV03|Q96ME0	Missense_Mutation	SNP	ENST00000310380.6	37	CCDS43188.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.232940	0.79688	.	.	ENSG00000173950	ENST00000310380;ENST00000437101;ENST00000355729;ENST00000429994;ENST00000356740	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.50051	0.1593	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.976;0.975	T	0.32134	-0.9918	10	0.24483	T	0.36	-21.2021	19.2443	0.93896	0.0:0.0:1.0:0.0	.	282;79;76	Q8NBI6;Q8NBI6-2;Q8NBI6-3	XXLT1_HUMAN;.;.	S	282;79;79;136;76	ENSP00000309640:P282S;ENSP00000409865:P79S;ENSP00000347967:P79S;ENSP00000399422:P136S;ENSP00000349179:P76S	ENSP00000309640:P282S	P	-	1	0	C3orf21	196272071	1.000000	0.71417	0.712000	0.30502	0.863000	0.49368	7.752000	0.85141	2.797000	0.96272	0.563000	0.77884	CCC	.	.	none		0.672	XXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342290.1	NM_152531	
SUCO	51430	hgsc.bcm.edu	37	1	172547465	172547465	+	Silent	SNP	A	A	G	rs2285664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:172547465A>G	ENST00000263688.3	+	14	1587	c.1368A>G	c.(1366-1368)gaA>gaG	p.E456E	SUCO_ENST00000610051.1_Silent_p.E419E|SUCO_ENST00000367723.4_Silent_p.E607E|SUCO_ENST00000608151.1_Silent_p.E608E	NM_014283.3	NP_055098.1	Q9UBS9	SUCO_HUMAN	SUN domain containing ossification factor	456					multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of bone remodeling (GO:0046850)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)											TGGTGGAAGAATATGAAGAAA	0.358													A|||	1273	0.254193	0.2368	0.2089	5008	,	,		17330	0.2024		0.2296	False		,,,				2504	0.3885				p.E456E		Atlas-SNP	.											.	.	.	.	0			c.A1368G						PASS	.	A	,	1025,3381	378.3+/-322.8	111,803,1289	132.0	124.0	127.0		1368,1236	5.4	1.0	1	dbSNP_100	127	2069,6531	359.0+/-331.4	229,1611,2460	no	coding-synonymous,coding-synonymous	C1orf9	NM_014283.3,NM_016227.2	,	340,2414,3749	GG,GA,AA		24.0581,23.2637,23.789	,	456/1255,412/1211	172547465	3094,9912	2203	4300	6503	SO:0001819	synonymous_variant	51430	exon14			GGAAGAATATGAA	AF097535	CCDS1303.1, CCDS65726.1, CCDS65727.1, CCDS72984.1	1q24	2012-07-10	2012-07-10	2012-07-10	ENSG00000094975	ENSG00000094975			1240	protein-coding gene	gene with protein product	"""SUN-like protein 1"", ""osteopotentia"""		"""chromosome 1 open reading frame 9"""	C1orf9		10673381, 20440000	Standard	NM_001282750		Approved	CH1, SLP1, OPT	uc001giq.4	Q9UBS9	OTTHUMG00000034839	ENST00000263688.3:c.1368A>G	1.37:g.172547465A>G		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	170	98	0.576471	NM_014283	B2RNU4|Q9BQB9|Q9BXQ2|Q9UL04	Silent	SNP	ENST00000263688.3	37	CCDS1303.1																																																																																			A|0.770;G|0.230	0.230	strong		0.358	SUCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084273.1	NM_016227	
P2RX2	22953	hgsc.bcm.edu	37	12	133196596	133196596	+	Silent	SNP	T	T	C	rs7964634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133196596T>C	ENST00000389110.3	+	5	505	c.468T>C	c.(466-468)acT>acC	p.T156T	P2RX2_ENST00000351222.4_Silent_p.T64T|P2RX2_ENST00000350048.5_Silent_p.T132T|P2RX2_ENST00000343948.4_Silent_p.T156T|P2RX2_ENST00000352418.4_Silent_p.T84T|P2RX2_ENST00000348800.5_Silent_p.T156T|P2RX2_ENST00000449132.2_Intron	NM_170682.2|NM_170683.2|NM_174873.1	NP_733782.1|NP_733783.1|NP_777362.1	Q9UBL9	P2RX2_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 2	156					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of hypoxic conditions in blood by carotid body chemoreceptor signaling (GO:0003029)|ion transmembrane transport (GO:0034220)|neuromuscular junction development (GO:0007528)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to hypoxia (GO:0001666)|sensory perception of sound (GO:0007605)|sensory perception of taste (GO:0050909)|skeletal muscle fiber development (GO:0048741)|urinary bladder smooth muscle contraction (GO:0014832)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|dendritic spine (GO:0043197)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadmium ion binding (GO:0046870)|cobalt ion binding (GO:0050897)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|identical protein binding (GO:0042802)|ligand-gated ion channel activity (GO:0015276)|mercury ion binding (GO:0045340)|nickel cation binding (GO:0016151)|phosphatidylinositol binding (GO:0035091)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(8)|ovary(1)|prostate(3)	20	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0767)		OV - Ovarian serous cystadenocarcinoma(86;2.32e-08)|Epithelial(86;8.62e-08)|all cancers(50;4.5e-06)		GCCTGAGGACTGGGCGCTGTG	0.692													C|||	3570	0.712859	0.8449	0.7522	5008	,	,		9375	0.7808		0.5616	False		,,,				2504	0.592				p.T156T		Atlas-SNP	.											P2RX2,NS,carcinoma,0,1	P2RX2	49	1	0			c.T468C						PASS	.	C	,,,,,	3486,890		1422,642,124	11.0	11.0	11.0		252,396,468,468,192,468	-6.3	0.2	12	dbSNP_116	11	4981,3583		1468,2045,769	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	P2RX2	NM_012226.3,NM_016318.2,NM_170682.2,NM_170683.2,NM_174872.1,NM_174873.1	,,,,,	2890,2687,893	CC,CT,TT		41.8379,20.3382,34.5672	,,,,,	84/400,132/448,156/472,156/498,64/380,156/405	133196596	8467,4473	2188	4282	6470	SO:0001819	synonymous_variant	22953	exon5			GAGGACTGGGCGC	AF109387	CCDS31930.1, CCDS31931.1, CCDS31932.1, CCDS31933.1, CCDS31934.1, CCDS31935.1, CCDS61286.1, CCDS73548.1	12q24.33	2013-03-22			ENSG00000187848	ENSG00000187848		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	15459	protein-coding gene	gene with protein product		600844	"""deafness, autosomal dominant 41"""	DFNA41		10570044, 7523952, 23345450	Standard	XM_005266154		Approved	P2X2	uc001ukk.1	Q9UBL9	OTTHUMG00000168018	ENST00000389110.3:c.468T>C	12.37:g.133196596T>C		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	63	25	0.396825	NM_170683	A6NGB4|A6NH93|A6NHC2|A6NHU3|A6NIG9|Q6V9R6|Q9NR37|Q9NR38|Q9UHD5|Q9UHD6|Q9UHD7|Q9Y637|Q9Y638	Silent	SNP	ENST00000389110.3	37	CCDS31931.1	1536	0.7032967032967034	399	0.8109756097560976	265	0.7320441988950276	449	0.784965034965035	423	0.558047493403694	C	1.836	-0.468560	0.04445	0.796618	0.581621	ENSG00000187848	ENST00000542301;ENST00000536121;ENST00000535910	.	.	.	4.99	-6.26	0.02033	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33701	-0.9858	3	.	.	.	-23.5422	1.2958	0.02069	0.1936:0.1398:0.2356:0.431	rs7964634;rs57252153	.	.	.	P	167;142;112	.	.	L	+	2	0	P2RX2	131706669	0.000000	0.05858	0.232000	0.24009	0.080000	0.17528	-8.920000	0.00015	-1.059000	0.03193	-1.163000	0.01768	CTG	T|0.323;C|0.677	0.677	strong		0.692	P2RX2-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397542.1		
ZNF677	342926	hgsc.bcm.edu	37	19	53741188	53741188	+	Silent	SNP	C	C	T	rs12984473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53741188C>T	ENST00000598513.1	-	5	942	c.792G>A	c.(790-792)aaG>aaA	p.K264K	CTD-2245F17.6_ENST00000596041.1_RNA|ZNF677_ENST00000333952.4_Silent_p.K264K	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	264					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)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		AGTCATTACACTTGTATGATT	0.348													T|||	2328	0.464856	0.2148	0.4294	5008	,	,		19736	0.752		0.4324	False		,,,				2504	0.5654				p.K264K		Atlas-SNP	.											.	ZNF677	94	.	0			c.G792A						PASS	.	T		1072,3334	722.8+/-409.3	106,860,1237	77.0	70.0	73.0		792	-0.4	0.0	19	dbSNP_121	73	3606,4994	624.5+/-397.6	747,2112,1441	no	coding-synonymous	ZNF677	NM_182609.2		853,2972,2678	TT,TC,CC		41.9302,24.3305,35.968		264/585	53741188	4678,8328	2203	4300	6503	SO:0001819	synonymous_variant	342926	exon5			ATTACACTTGTAT	BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.792G>A	19.37:g.53741188C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	38	20	0.526316	NM_182609		Silent	SNP	ENST00000598513.1	37	CCDS12861.1																																																																																			C|0.591;T|0.409	0.409	strong		0.348	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
CXCR5	643	hgsc.bcm.edu	37	11	118765267	118765267	+	Silent	SNP	G	G	C	rs598207	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118765267G>C	ENST00000292174.4	+	2	1190	c.1014G>C	c.(1012-1014)acG>acC	p.T338T	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	338					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		GGCTCCTGACGAAGCTGGGCT	0.627													C|||	1611	0.321685	0.4992	0.4366	5008	,	,		20978	0.2212		0.2714	False		,,,				2504	0.1554				p.T338T		Atlas-SNP	.											.	CXCR5	34	.	0			c.G1014C						PASS	.	C	,	1982,2418	615.4+/-392.6	452,1078,670	60.0	55.0	57.0		1014,879	3.2	1.0	11	dbSNP_83	57	2306,6284	704.3+/-405.4	324,1658,2313	no	coding-synonymous,coding-synonymous	CXCR5	NM_001716.4,NM_032966.2	,	776,2736,2983	CC,CG,GG		26.8452,45.0455,33.01	,	338/373,293/328	118765267	4288,8702	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGACGAAGCTG	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.1014G>C	11.37:g.118765267G>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	26	9	0.346154	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.684;C|0.316	0.316	strong		0.627	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
CRIM1	51232	hgsc.bcm.edu	37	2	36704144	36704144	+	Silent	SNP	C	C	T	rs848547	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:36704144C>T	ENST00000280527.2	+	6	1471	c.1104C>T	c.(1102-1104)acC>acT	p.T368T		NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	368	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				TCTGCTTCACCGCCCAGTGTG	0.483													T|||	3073	0.613618	0.5045	0.7378	5008	,	,		19401	0.6766		0.499	False		,,,				2504	0.726				p.T368T		Atlas-SNP	.											.	CRIM1	88	.	0			c.C1104T						PASS	.	T		2280,2126	578.9+/-384.8	567,1146,490	127.0	113.0	118.0		1104	-7.4	0.5	2	dbSNP_86	118	4428,4172	568.9+/-389.1	1152,2124,1024	no	coding-synonymous	CRIM1	NM_016441.2		1719,3270,1514	TT,TC,CC		48.5116,48.2524,48.4238		368/1037	36704144	6708,6298	2203	4300	6503	SO:0001819	synonymous_variant	51232	exon6			CTTCACCGCCCAG	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.1104C>T	2.37:g.36704144C>T		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	120	68	0.566667	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	Silent	SNP	ENST00000280527.2	37	CCDS1783.1																																																																																			C|0.450;T|0.550	0.550	strong		0.483	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
OR5D16	390144	hgsc.bcm.edu	37	11	55606818	55606818	+	Silent	SNP	C	C	T	rs11231253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:55606818C>T	ENST00000378396.1	+	1	591	c.591C>T	c.(589-591)agC>agT	p.S197S		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				CTTATCTCAGCCAGTTGCTTC	0.383													-|||	2269	0.453075	0.2746	0.4957	5008	,	,		22120	0.626		0.3638	False		,,,				2504	0.5777				p.S197S		Atlas-SNP	.											OR5D16,NS,adenoma,0,1	OR5D16	94	1	0			c.C591T						PASS	.	C		1342,3060		207,928,1066	191.0	165.0	174.0		591	-4.6	0.0	11	dbSNP_120	174	3174,5418		607,1960,1729	yes	coding-synonymous	OR5D16	NM_001005496.1		814,2888,2795	TT,TC,CC		36.9413,30.4861,34.7545		197/329	55606818	4516,8478	2201	4296	6497	SO:0001819	synonymous_variant	390144	exon1			TCTCAGCCAGTTG	AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.591C>T	11.37:g.55606818C>T		Somatic	268	0	0		WXS	Illumina HiSeq	Phase_I	218	90	0.412844	NM_001005496	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																			C|0.619;T|0.381	0.381	strong		0.383	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
ITPKC	80271	hgsc.bcm.edu	37	19	41235167	41235167	+	Missense_Mutation	SNP	G	G	A	rs112628847	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41235167G>A	ENST00000263370.2	+	3	1349	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H		NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	439					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	14			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGTGAGCAGCGCAGCCTGGAG	0.532													G|||	72	0.014377	0.0023	0.0144	5008	,	,		14148	0.0		0.0537	False		,,,				2504	0.0051				p.R439H		Atlas-SNP	.											.	ITPKC	36	.	0			c.G1316A						PASS	.	G	HIS/ARG	44,4362	47.5+/-82.1	0,44,2159	70.0	61.0	64.0		1316	2.2	1.0	19	dbSNP_132	64	505,8095	144.8+/-200.6	15,475,3810	yes	missense	ITPKC	NM_025194.2	29	15,519,5969	AA,AG,GG		5.8721,0.9986,4.2211	benign	439/684	41235167	549,12457	2203	4300	6503	SO:0001583	missense	80271	exon3			AGCAGCGCAGCCT	Y11999	CCDS12563.1	19q13.1	2011-04-28	2011-04-28		ENSG00000086544	ENSG00000086544	2.7.1.127		14897	protein-coding gene	gene with protein product		606476	"""inositol 1,4,5-trisphosphate 3-kinase C"""			11085927	Standard	NM_025194		Approved	IP3KC, IP3-3KC	uc002oot.3	Q96DU7		ENST00000263370.2:c.1316G>A	19.37:g.41235167G>A	ENSP00000263370:p.Arg439His	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_025194	Q9UE25|Q9Y475	Missense_Mutation	SNP	ENST00000263370.2	37	CCDS12563.1	46	0.021062271062271064	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	42	0.055408970976253295	G	12.47	1.948867	0.34377	0.009986	0.058721	ENSG00000086544	ENST00000263370	T	0.14266	2.52	5.49	2.23	0.28157	.	0.236396	0.44688	N	0.000430	T	0.00998	0.0033	L	0.58101	1.795	0.46131	D	0.998883	P	0.35908	0.527	B	0.21546	0.035	T	0.19095	-1.0316	10	0.51188	T	0.08	-14.7372	6.6184	0.22790	0.4071:0.0:0.5929:0.0	.	439	Q96DU7	IP3KC_HUMAN	H	439	ENSP00000263370:R439H	ENSP00000263370:R439H	R	+	2	0	ITPKC	45927007	0.003000	0.15002	1.000000	0.80357	0.998000	0.95712	0.076000	0.14712	0.819000	0.34492	0.561000	0.74099	CGC	G|0.967;A|0.033	0.033	strong		0.532	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194	
DOCK2	1794	hgsc.bcm.edu	37	5	169454941	169454941	+	Silent	SNP	C	C	G	rs9791113	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:169454941C>G	ENST00000256935.8	+	34	3536	c.3456C>G	c.(3454-3456)ctC>ctG	p.L1152L	DOCK2_ENST00000540750.1_Silent_p.L213L|DOCK2_ENST00000520908.1_Silent_p.L644L|MIR378E_ENST00000581976.1_RNA|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1152	Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACATGCAGCTCCTGGAGTCAA	0.542													G|||	2435	0.486222	0.584	0.3141	5008	,	,		19149	0.6052		0.339	False		,,,				2504	0.5051				p.L1152L		Atlas-SNP	.											.	DOCK2	389	.	0			c.C3456G						PASS	.	G		2356,2050	567.4+/-382.1	632,1092,479	104.0	95.0	98.0		3456	3.5	1.0	5	dbSNP_119	98	2923,5677	669.9+/-402.7	475,1973,1852	no	coding-synonymous	DOCK2	NM_004946.2		1107,3065,2331	GG,GC,CC		33.9884,46.5275,40.589		1152/1831	169454941	5279,7727	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon34			GCAGCTCCTGGAG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3456C>G	5.37:g.169454941C>G		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	137	75	0.547445	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			C|0.563;G|0.437	0.437	strong		0.542	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
FNDC8	54752	hgsc.bcm.edu	37	17	33454415	33454415	+	Silent	SNP	C	C	A	rs2306508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33454415C>A	ENST00000158009.5	+	2	679	c.564C>A	c.(562-564)acC>acA	p.T188T		NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	188	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	11		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.022)		TTGAGCACACCGTCAACAATT	0.542													C|||	2226	0.444489	0.1044	0.5447	5008	,	,		21013	0.7123		0.4354	False		,,,				2504	0.5665				p.T188T		Atlas-SNP	.											.	FNDC8	28	.	0			c.C564A						PASS	.	C		702,3704	283.1+/-276.9	67,568,1568	103.0	92.0	95.0		564	-7.7	1.0	17	dbSNP_100	95	3647,4953	525.0+/-380.7	779,2089,1432	no	coding-synonymous	FNDC8	NM_017559.2		846,2657,3000	AA,AC,CC		42.407,15.9328,33.4384		188/325	33454415	4349,8657	2203	4300	6503	SO:0001819	synonymous_variant	54752	exon2			GCACACCGTCAAC	BC024002	CCDS11290.1	17q12	2013-02-11			ENSG00000073598	ENSG00000073598		"""Fibronectin type III domain containing"""	25286	protein-coding gene	gene with protein product						12477932	Standard	XM_005257993		Approved	DKFZp434H2215	uc002hix.3	Q8TC99	OTTHUMG00000132932	ENST00000158009.5:c.564C>A	17.37:g.33454415C>A		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	59	57	0.966102	NM_017559	B2R9G6|Q9UFC2	Silent	SNP	ENST00000158009.5	37	CCDS11290.1																																																																																			C|0.608;A|0.392	0.392	strong		0.542	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559	
UNC13D	201294	hgsc.bcm.edu	37	17	73839137	73839137	+	Silent	SNP	G	G	A	rs3744007	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73839137G>A	ENST00000207549.4	-	4	658	c.279C>T	c.(277-279)ccC>ccT	p.P93P	UNC13D_ENST00000587504.1_5'UTR|UNC13D_ENST00000412096.2_Silent_p.P93P	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	93					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)			GGTGCTCCTCGGGCTCCACGT	0.726									Familial Hemophagocytic Lymphohistiocytosis				G|||	501	0.10004	0.087	0.036	5008	,	,		11821	0.2827		0.0239	False		,,,				2504	0.0532				p.P93P		Atlas-SNP	.											.	UNC13D	68	.	0			c.C279T						PASS	.	G		270,4132		8,254,1939	20.0	24.0	23.0		279	-8.9	0.0	17	dbSNP_107	23	193,8403		5,183,4110	no	coding-synonymous	UNC13D	NM_199242.2		13,437,6049	AA,AG,GG		2.2452,6.1336,3.5621		93/1091	73839137	463,12535	2201	4298	6499	SO:0001819	synonymous_variant	201294	exon4	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CTCCTCGGGCTCC	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.279C>T	17.37:g.73839137G>A		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	84	42	0.5	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			G|0.926;A|0.074	0.074	strong		0.726	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
RNF168	165918	hgsc.bcm.edu	37	3	196229836	196229836	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196229836G>C	ENST00000318037.3	-	1	803	c.209C>G	c.(208-210)tCt>tGt	p.S70C		NM_152617.3	NP_689830.2	Q8IYW5	RN168_HUMAN	ring finger protein 168, E3 ubiquitin protein ligase	70					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone H2A K63-linked ubiquitination (GO:0070535)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K13 ubiquitination (GO:0036351)|histone H2A-K15 ubiquitination (GO:0036352)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|negative regulation of translational elongation (GO:0045900)|positive regulation of DNA repair (GO:0045739)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|response to ionizing radiation (GO:0010212)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|K63-linked polyubiquitin binding (GO:0070530)|ligase activity (GO:0016874)|nucleosome binding (GO:0031491)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S70Y(1)		NS(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)	20	all_cancers(143;1e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;5.25e-24)|all cancers(36;5.47e-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;0.00348)		GTTGACGAGAGAATTTCTTCG	0.517																																					p.S70C		Atlas-SNP	.											RNF168,colon,carcinoma,0,1	RNF168	49	1	1	Substitution - Missense(1)	large_intestine(1)	c.C209G						PASS	.						115.0	98.0	104.0					3																	196229836		2203	4300	6503	SO:0001583	missense	165918	exon1			ACGAGAGAATTTC	AK054732	CCDS3317.1	3q29	2014-09-17	2012-02-23		ENSG00000163961	ENSG00000163961		"""RING-type (C3HC4) zinc fingers"""	26661	protein-coding gene	gene with protein product		612688	"""ring finger protein 168"""			12477932	Standard	NM_152617		Approved	FLJ35794	uc003fwq.3	Q8IYW5	OTTHUMG00000155582	ENST00000318037.3:c.209C>G	3.37:g.196229836G>C	ENSP00000320898:p.Ser70Cys	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	110	57	0.518182	NM_152617	Q8NA67|Q96NS4	Missense_Mutation	SNP	ENST00000318037.3	37	CCDS3317.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758676	0.69763	.	.	ENSG00000163961	ENST00000318037	T	0.07688	3.17	6.0	6.0	0.97389	Zinc finger, RING/FYVE/PHD-type (1);	0.323634	0.26328	N	0.025017	T	0.21881	0.0527	M	0.62723	1.935	0.41380	D	0.987549	D	0.58970	0.984	P	0.53006	0.715	T	0.00026	-1.2312	10	0.44086	T	0.13	-7.4382	20.5595	0.99322	0.0:0.0:1.0:0.0	.	70	Q8IYW5	RN168_HUMAN	C	70	ENSP00000320898:S70C	ENSP00000320898:S70C	S	-	2	0	RNF168	197714233	1.000000	0.71417	0.971000	0.41717	0.022000	0.10575	7.656000	0.83736	2.868000	0.98415	0.555000	0.69702	TCT	.	.	none		0.517	RNF168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340778.1	NM_152617	
HPSE2	60495	hgsc.bcm.edu	37	10	100219374	100219374	+	Missense_Mutation	SNP	T	T	A	rs10883100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:100219374T>A	ENST00000370552.3	-	12	1795	c.1736A>T	c.(1735-1737)tAt>tTt	p.Y579F	HPSE2_ENST00000404542.1_Missense_Mutation_p.Y467F|HPSE2_ENST00000370549.1_Missense_Mutation_p.Y521F|HPSE2_ENST00000370546.1_3'UTR	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	579			Y -> F (in dbSNP:rs10883100). {ECO:0000269|PubMed:11027606, ECO:0000269|Ref.2}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	intracellular (GO:0005622)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	heparan sulfate proteoglycan binding (GO:0043395)|heparanase activity (GO:0030305)			NS(1)|breast(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	40				Epithelial(162;1.8e-09)|all cancers(201;4.72e-07)		CTTGACCACATAAAAGCCCAT	0.597													T|||	2657	0.530551	0.6233	0.5346	5008	,	,		17494	0.5119		0.5099	False		,,,				2504	0.4427				p.Y579F		Atlas-SNP	.											HPSE2,NS,carcinoma,0,1	HPSE2	203	1	0			c.A1736T						PASS	.	T	PHE/TYR,PHE/TYR,,PHE/TYR	2738,1668	654.7+/-399.8	851,1036,316	71.0	70.0	70.0		1562,1400,,1736	5.3	1.0	10	dbSNP_120	70	4185,4415	567.2+/-388.8	1027,2131,1142	yes	missense,missense,utr-3,missense	HPSE2	NM_001166244.1,NM_001166245.1,NM_001166246.1,NM_021828.4	22,22,,22	1878,3167,1458	AA,AT,TT		48.6628,37.8575,46.7707	benign,benign,,benign	521/535,467/481,,579/593	100219374	6923,6083	2203	4300	6503	SO:0001583	missense	60495	exon12			ACCACATAAAAGC	AF282885	CCDS7477.1, CCDS53567.1, CCDS53568.1	10q23-q24	2014-05-09	2014-05-09		ENSG00000172987	ENSG00000172987			18374	protein-coding gene	gene with protein product		613469	"""urofacial syndrome"", ""heparanase 2"""	UFS		11027606, 20605132, 9199567, 20576607	Standard	NM_021828		Approved	HPA2, HPR2	uc001kpn.2	Q8WWQ2	OTTHUMG00000018880	ENST00000370552.3:c.1736A>T	10.37:g.100219374T>A	ENSP00000359583:p.Tyr579Phe	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_021828	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	1186	0.543040293040293	309	0.6280487804878049	195	0.5386740331491713	300	0.5244755244755245	382	0.503957783641161	T	13.65	2.301038	0.40694	0.621425	0.486628	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000404542	T;T;T	0.41758	0.99;1.0;1.0	5.31	5.31	0.75309	.	0.000000	0.64402	D	0.000001	T	0.00012	0.0000	N	0.17674	0.51	0.09310	P	0.9999999693858	D;D;B	0.67145	0.996;0.996;0.001	D;D;B	0.73380	0.98;0.98;0.003	T	0.04103	-1.0977	9	0.02654	T	1	-6.674	15.2788	0.73764	0.0:0.0:0.0:1.0	rs10883100;rs52819603;rs60701436;rs10883100	467;521;579	Q8WWQ2-4;Q8WWQ2-3;Q8WWQ2	.;.;HPSE2_HUMAN	F	579;521;467	ENSP00000359583:Y579F;ENSP00000359580:Y521F;ENSP00000384384:Y467F	ENSP00000359580:Y521F	Y	-	2	0	HPSE2	100209364	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.564000	0.82326	2.013000	0.59113	0.528000	0.53228	TAT	A|0.539;N|0.000	0.539	strong		0.597	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144879339	144879339	+	Missense_Mutation	SNP	C	C	T	rs145959230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144879339C>T	ENST00000369354.3	-	27	4300	c.4111G>A	c.(4111-4113)Gtc>Atc	p.V1371I	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.V1507I|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.V1507I|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.V1371I|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.V1327I|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1371					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)		TTTTGAATGACCTTGTTGGCA	0.488			T	PDGFRB	MPD																																p.V1371I		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,+2,3	PDE4DIP	817	3	0			c.G4111A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	81,4325		0,81,2122	143.0	161.0	155.0		4111,4111,3979	1.5	1.0	1	dbSNP_134	155	662,7938		0,662,3638	no	missense,missense,missense	PDE4DIP	NM_014644.4,NM_001198834.2,NM_001198832.1	29,29,29	0,743,5760	TT,TC,CC		7.6977,1.8384,5.7127	benign,benign,benign	1371/2347,1371/2363,1327/2241	144879339	743,12263	2203	4300	6503	SO:0001583	missense	9659	exon27			GAATGACCTTGTT	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.4111G>A	1.37:g.144879339C>T	ENSP00000358360:p.Val1371Ile	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	208	43	0.206731	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	155	0.07097069597069597	2	0.0040650406504065045	27	0.07458563535911603	63	0.11013986013986014	63	0.08311345646437995	C	12.34	1.909968	0.33721	0.018384	0.076977	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.02579	4.24;4.37;4.38;4.41;4.4	5.55	1.54	0.23209	.	.	.	.	.	T	0.00967	0.0032	L	0.38531	1.155	0.80722	D	1	B;B	0.15141	0.012;0.003	B;B	0.14023	0.01;0.004	T	0.48885	-0.8995	9	0.31617	T	0.26	.	8.7082	0.34367	0.0:0.6706:0.0:0.3294	.	1327;1371	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	I	1327;1371;1371;1507;1507	ENSP00000327209:V1327I;ENSP00000358360:V1371I;ENSP00000358363:V1371I;ENSP00000435654:V1507I;ENSP00000358366:V1507I	ENSP00000327209:V1327I	V	-	1	0	PDE4DIP	143590696	0.949000	0.32298	0.995000	0.50966	0.513000	0.34164	0.895000	0.28363	0.028000	0.15324	-0.216000	0.12614	GTC	C|0.940;T|0.060	0.060	strong		0.488	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
NCOA3	8202	hgsc.bcm.edu	37	20	46279860	46279860	+	Silent	SNP	G	G	A	rs151060280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:46279860G>A	ENST00000371998.3	+	20	3977	c.3786G>A	c.(3784-3786)caG>caA	p.Q1262Q	NCOA3_ENST00000371997.3_Silent_p.Q1253Q|NCOA3_ENST00000341724.6_Silent_p.Q1188Q|NCOA3_ENST00000372004.3_Silent_p.Q1258Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1262	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.Q1262Q(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						agcagcagcagcagcaacagc	0.567																																					p.Q1262Q		Atlas-SNP	.											NCOA3,bladder,carcinoma,0,6	NCOA3	156	6	1	Substitution - coding silent(1)	endometrium(1)	c.G3786A						PASS	.	G	,,,	10,4396	11.4+/-27.6	1,8,2194	53.0	58.0	56.0		3783,3759,3774,3786	-0.1	0.1	20	dbSNP_134	56	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	1,20,6482	AA,AG,GG		0.1395,0.227,0.1692	,,,	1261/1424,1253/1416,1258/1421,1262/1425	46279860	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	8202	exon20			GCAGCAGCAGCAA	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.3786G>A	20.37:g.46279860G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	80	4	0.05	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			G|0.997;A|0.003	0.003	strong		0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
TUBA3E	112714	hgsc.bcm.edu	37	2	130951949	130951949	+	Missense_Mutation	SNP	G	G	A	rs62165074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130951949G>A	ENST00000312988.7	-	4	566	c.466C>T	c.(466-468)Cgg>Tgg	p.R156W		NM_207312.2	NP_997195	Q6PEY2	TBA3E_HUMAN	tubulin, alpha 3e	156					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|kidney(7)|large_intestine(6)|lung(9)|skin(2)	28	Colorectal(110;0.1)					ACTGAGAGCCGCTCCATGAGC	0.577																																					p.R156W		Atlas-SNP	.											TUBA3E,NS,carcinoma,+2,1	TUBA3E	73	1	0			c.C466T						PASS	.	G	TRP/ARG	1567,2837	489.4+/-361.5	284,999,919	71.0	76.0	74.0		466	0.6	1.0	2	dbSNP_129	74	3350,5248	496.3+/-374.3	657,2036,1606	no	missense	TUBA3E	NM_207312.2	101	941,3035,2525	AA,AG,GG		38.9625,35.5813,37.8173	probably-damaging	156/451	130951949	4917,8085	2202	4299	6501	SO:0001583	missense	112714	exon4			AGAGCCGCTCCAT	BC057811	CCDS2158.1	2q21.1	2007-03-16			ENSG00000152086	ENSG00000152086		"""Tubulins"""	20765	protein-coding gene	gene with protein product							Standard	NM_207312		Approved		uc002tqv.3	Q6PEY2	OTTHUMG00000131626	ENST00000312988.7:c.466C>T	2.37:g.130951949G>A	ENSP00000318197:p.Arg156Trp	Somatic	370	1	0.0027027		WXS	Illumina HiSeq	Phase_I	356	159	0.446629	NM_207312		Missense_Mutation	SNP	ENST00000312988.7	37	CCDS2158.1	874	0.4001831501831502	166	0.33739837398373984	163	0.45027624309392267	269	0.47027972027972026	276	0.3641160949868074	g	12.55	1.970279	0.34754	0.355813	0.389625	ENSG00000152086	ENST00000312988	T	0.71698	-0.59	2.71	0.549	0.17213	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.49916	U	0.000125	T	0.00012	0.0000	H	0.98487	4.245	0.23700	P	0.99707653	D	0.71674	0.998	P	0.62649	0.905	T	0.18116	-1.0347	9	0.87932	D	0	.	4.7171	0.12899	0.1389:0.0:0.649:0.212	rs62165074	156	Q6PEY2	TBA3E_HUMAN	W	156	ENSP00000318197:R156W	ENSP00000318197:R156W	R	-	1	2	TUBA3E	130668419	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.313000	0.33585	0.485000	0.27652	0.449000	0.29647	CGG	G|0.500;A|0.500	0.500	weak		0.577	TUBA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254519.1	NM_207312	
OR8H1	219469	hgsc.bcm.edu	37	11	56058535	56058535	+	Missense_Mutation	SNP	C	C	T	rs11600896	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56058535C>T	ENST00000313022.2	-	1	31	c.4G>A	c.(4-6)Ggt>Agt	p.G2S		NM_001005199.1	NP_001005199.1	Q8NGG4	OR8H1_HUMAN	olfactory receptor, family 8, subfamily H, member 1	2			G -> S (in dbSNP:rs11600896).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Esophageal squamous(21;0.00448)					TTTCTTCTACCCATGATGTTC	0.353													c|||	391	0.0780751	0.0053	0.0821	5008	,	,		19107	0.0863		0.1302	False		,,,				2504	0.1115				p.G2S		Atlas-SNP	.											.	OR8H1	89	.	0			c.G4A						PASS	.	C	SER/GLY	117,4285	83.9+/-122.4	3,111,2087	78.0	73.0	75.0		4	-4.6	0.0	11	dbSNP_120	75	1199,7393	239.2+/-270.4	84,1031,3181	yes	missense	OR8H1	NM_001005199.1	56	87,1142,5268	TT,TC,CC		13.9548,2.6579,10.1278	benign	2/312	56058535	1316,11678	2201	4296	6497	SO:0001583	missense	219469	exon1			TTCTACCCATGAT	AB065836	CCDS31526.1	11q11	2012-08-09			ENSG00000181693	ENSG00000181693		"""GPCR / Class A : Olfactory receptors"""	14824	protein-coding gene	gene with protein product							Standard	NM_001005199		Approved		uc010rje.2	Q8NGG4	OTTHUMG00000162671	ENST00000313022.2:c.4G>A	11.37:g.56058535C>T	ENSP00000323595:p.Gly2Ser	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_001005199	B2RNI7|Q6IFC5	Missense_Mutation	SNP	ENST00000313022.2	37	CCDS31526.1	194	0.08882783882783883	7	0.014227642276422764	32	0.08839779005524862	60	0.1048951048951049	95	0.12532981530343007	C	7.524	0.657329	0.14580	0.026579	0.139548	ENSG00000181693	ENST00000313022	T	0.02890	4.12	3.5	-4.63	0.03359	.	1.394090	0.04559	N	0.391311	T	0.00012	0.0000	N	0.04387	-0.21	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48258	-0.9051	9	0.33940	T	0.23	.	3.4625	0.07537	0.107:0.432:0.1067:0.3543	rs11600896;rs52821264;rs11600896	2	Q8NGG4	OR8H1_HUMAN	S	2	ENSP00000323595:G2S	ENSP00000323595:G2S	G	-	1	0	OR8H1	55815111	0.003000	0.15002	0.002000	0.10522	0.002000	0.02628	-0.301000	0.08232	-0.758000	0.04690	-0.715000	0.03620	GGT	C|0.902;T|0.098	0.098	strong		0.353	OR8H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370019.1	NM_001005199	
NID2	22795	hgsc.bcm.edu	37	14	52481917	52481917	+	Silent	SNP	C	C	T	rs946615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:52481917C>T	ENST00000216286.5	-	15	3104	c.3105G>A	c.(3103-3105)cgG>cgA	p.R1035R	NID2_ENST00000541773.1_Silent_p.R934R	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1035	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					ACTGGTCATCCCGGGGGGTGC	0.627													c|||	2301	0.459465	0.5045	0.5245	5008	,	,		16732	0.7063		0.2406	False		,,,				2504	0.3231				p.R1035R		Atlas-SNP	.											NID2,NS,carcinoma,0,1	NID2	201	1	0			c.G3105A						PASS	.	C		2082,2324	542.5+/-376.0	485,1112,606	52.0	48.0	50.0		3105	2.8	0.6	14	dbSNP_86	50	2315,6285	359.1+/-331.4	338,1639,2323	no	coding-synonymous	NID2	NM_007361.3		823,2751,2929	TT,TC,CC		26.9186,47.2537,33.8075		1035/1376	52481917	4397,8609	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon15			GTCATCCCGGGGG	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3105G>A	14.37:g.52481917C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1	1004	0.4597069597069597	237	0.4817073170731707	184	0.5082872928176796	407	0.7115384615384616	176	0.23218997361477572	C	8.058	0.767452	0.15983	0.472537	0.269186	ENSG00000087303	ENST00000556572	.	.	.	5.67	2.8	0.32819	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25093	P	0.99084443	.	.	.	.	.	.	T	0.33752	-0.9856	3	.	.	.	.	4.7078	0.12858	0.3472:0.4462:0.1361:0.0705	rs946615;rs57980038;rs946615	.	.	.	R	304	.	.	G	-	1	0	NID2	51551667	0.000000	0.05858	0.556000	0.28293	0.731000	0.41821	-1.434000	0.02425	0.285000	0.22329	0.655000	0.94253	GGA	C|0.604;T|0.396	0.396	strong		0.627	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
LRRC16A	55604	hgsc.bcm.edu	37	6	25435758	25435758	+	Silent	SNP	A	A	G	rs9467515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:25435758A>G	ENST00000329474.6	+	5	665	c.297A>G	c.(295-297)tcA>tcG	p.S99S	LRRC16A_ENST00000377969.3_5'UTR|snoU13_ENST00000458807.1_RNA	NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	99					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						AGATGGCGTCACCCGAGGACG	0.517													G|||	2170	0.433307	0.525	0.4179	5008	,	,		15813	0.3175		0.4215	False		,,,				2504	0.4519				p.S99S		Atlas-SNP	.											LRRC16A_ENST00000329474,colon,carcinoma,0,2	LRRC16A	168	2	0			c.A297G						scavenged	.	G	,	1887,2177		450,987,595	63.0	67.0	66.0		297,297	-10.1	0.0	6	dbSNP_119	66	3775,4567		914,1947,1310	no	coding-synonymous,coding-synonymous	LRRC16A	NM_001173977.1,NM_017640.5	,	1364,2934,1905	GG,GA,AA		45.2529,46.4321,45.6392	,	99/1366,99/1372	25435758	5662,6744	2032	4171	6203	SO:0001819	synonymous_variant	55604	exon5			GGCGTCACCCGAG	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.297A>G	6.37:g.25435758A>G		Somatic	53	1	0.0188679		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_001173977	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Silent	SNP	ENST00000329474.6	37	CCDS54973.1																																																																																			A|0.568;G|0.432	0.432	strong		0.517	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
ENTHD2	146705	hgsc.bcm.edu	37	17	79205421	79205421	+	Missense_Mutation	SNP	G	G	A	rs61745945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79205421G>A	ENST00000300714.3	-	9	829	c.772C>T	c.(772-774)Cgc>Tgc	p.R258C	ENTHD2_ENST00000374769.2_Missense_Mutation_p.R174C|AC027601.1_ENST00000569559.1_RNA|AC027601.1_ENST00000575922.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	258						cytoplasmic vesicle (GO:0031410)											AGGAAGGCGCGTGGTCCCCGA	0.672													G|||	24	0.00479233	0.0008	0.0029	5008	,	,		19157	0.0		0.0189	False		,,,				2504	0.002				p.R258C		Atlas-SNP	.											C17orf56,NS,carcinoma,+1,1	.	.	1	0			c.C772T						PASS	.	G	CYS/ARG	20,4386	26.2+/-53.5	1,18,2184	35.0	32.0	33.0		772	2.8	0.0	17	dbSNP_129	33	144,8456	70.3+/-132.9	1,142,4157	yes	missense	C17orf56	NM_144679.2	180	2,160,6341	AA,AG,GG		1.6744,0.4539,1.261	benign	258/526	79205421	164,12842	2203	4300	6503	SO:0001583	missense	146705	exon9			AGGCGCGTGGTCC	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.772C>T	17.37:g.79205421G>A	ENSP00000300714:p.Arg258Cys	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	131	75	0.572519	NM_144679	Q6ZQU0|Q6ZSQ9	Missense_Mutation	SNP	ENST00000300714.3	37	CCDS11779.1	16	0.007326007326007326	0	0.0	0	0.0	0	0.0	16	0.021108179419525065	G	5.861	0.343069	0.11069	0.004539	0.016744	ENSG00000167302	ENST00000300714;ENST00000374769	T;T	0.24538	1.85;1.85	4.79	2.79	0.32731	.	0.526896	0.21186	N	0.078738	T	0.12518	0.0304	M	0.66939	2.045	0.09310	N	1	B;B	0.18166	0.026;0.004	B;B	0.14023	0.01;0.001	T	0.19128	-1.0315	10	0.56958	D	0.05	-2.9736	5.4861	0.16751	0.1686:0.0:0.5751:0.2563	.	258;174	Q96N21;Q96N21-2	CQ056_HUMAN;.	C	258;174	ENSP00000300714:R258C;ENSP00000363901:R174C	ENSP00000300714:R258C	R	-	1	0	C17orf56	76820016	0.379000	0.25123	0.000000	0.03702	0.006000	0.05464	3.684000	0.54671	0.569000	0.29329	-1.077000	0.02231	CGC	G|0.990;A|0.010	0.010	strong		0.672	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679	
TMC7	79905	hgsc.bcm.edu	37	16	19041595	19041595	+	Missense_Mutation	SNP	G	G	A	rs28583298	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:19041595G>A	ENST00000304381.5	+	6	891	c.761G>A	c.(760-762)gGg>gAg	p.G254E	TMC7_ENST00000569532.1_Missense_Mutation_p.G254E|TMC7_ENST00000421369.3_Missense_Mutation_p.G144E	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	254			G -> E (in dbSNP:rs28583298). {ECO:0000269|PubMed:12812529, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005}.		ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						ACCATTGATGGGGTGAAATTT	0.478													G|||	2723	0.54373	0.171	0.598	5008	,	,		20258	0.7788		0.6491	False		,,,				2504	0.6585				p.G254E		Atlas-SNP	.											.	TMC7	75	.	0			c.G761A						PASS	.	G	GLU/GLY,GLU/GLY	1084,3310	391.7+/-328.2	124,836,1237	143.0	128.0	133.0		431,761	4.5	1.0	16	dbSNP_125	133	5395,3205	653.2+/-401.0	1717,1961,622	yes	missense,missense	TMC7	NM_001160364.1,NM_024847.3	98,98	1841,2797,1859	AA,AG,GG		37.2674,24.67,49.8615	benign,benign	144/614,254/724	19041595	6479,6515	2197	4300	6497	SO:0001583	missense	79905	exon6			TTGATGGGGTGAA	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.761G>A	16.37:g.19041595G>A	ENSP00000304710:p.Gly254Glu	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	127	59	0.464567	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Missense_Mutation	SNP	ENST00000304381.5	37	CCDS10573.1	1235	0.5654761904761905	96	0.1951219512195122	213	0.5883977900552486	444	0.7762237762237763	482	0.6358839050131926	G	13.07	2.127155	0.37533	0.2467	0.627326	ENSG00000170537	ENST00000304381;ENST00000421369	T;T	0.49432	0.78;0.78	5.52	4.51	0.55191	.	0.357378	0.30076	N	0.010468	T	0.00012	0.0000	N	0.14661	0.345	0.32260	P	0.5702929999999999	B	0.02656	0.0	B	0.12156	0.007	T	0.37197	-0.9716	9	0.02654	T	1	.	13.4685	0.61270	0.0:0.3142:0.6858:0.0	rs4072393;rs5816024;rs17527436	254	Q7Z402	TMC7_HUMAN	E	254;144	ENSP00000304710:G254E;ENSP00000397081:G144E	ENSP00000304710:G254E	G	+	2	0	TMC7	18949096	0.953000	0.32496	0.997000	0.53966	0.974000	0.67602	1.028000	0.30128	2.770000	0.95276	0.655000	0.94253	GGG	G|0.443;A|0.557	0.557	strong		0.478	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	
VSTM1	284415	hgsc.bcm.edu	37	19	54545531	54545531	+	Splice_Site	SNP	T	T	C	rs2433724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54545531T>C	ENST00000338372.2	-	5	662	c.487A>G	c.(487-489)Agt>Ggt	p.S163G	VSTM1_ENST00000366170.2_Splice_Site_p.S75G|VSTM1_ENST00000376626.1_Intron|VSTM1_ENST00000425006.2_3'UTR	NM_198481.3	NP_940883.2	Q6UX27	VSTM1_HUMAN	V-set and transmembrane domain containing 1	163			S -> G (in dbSNP:rs2433724). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:22960280, ECO:0000269|Ref.3}.		immune system process (GO:0002376)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.165)		CTGAGCTCACTGTGCTGGCTG	0.493													C|||	1623	0.324081	0.388	0.4352	5008	,	,		18838	0.1597		0.4344	False		,,,				2504	0.2147				p.S163G		Atlas-SNP	.											.	VSTM1	30	.	0			c.A487G						PASS	.	C	GLY/SER	1729,2677	648.5+/-398.7	322,1085,796	98.0	89.0	92.0		487	2.5	0.6	19	dbSNP_100	92	3746,4854	616.7+/-396.6	808,2130,1362	yes	missense-near-splice	VSTM1	NM_198481.3	56	1130,3215,2158	CC,CT,TT		43.5581,39.2419,42.096	benign	163/237	54545531	5475,7531	2203	4300	6503	SO:0001630	splice_region_variant	284415	exon5			GCTCACTGTGCTG	AY358542	CCDS12872.1, CCDS74441.1, CCDS74442.1	19q13.42	2013-01-11			ENSG00000189068	ENSG00000189068		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29455	protein-coding gene	gene with protein product						12975309	Standard	NM_198481		Approved	UNQ3033	uc002qcw.4	Q6UX27	OTTHUMG00000064906	ENST00000338372.2:c.487+1A>G	19.37:g.54545531T>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	132	73	0.55303	NM_198481	B6A8C6|D2DJS3|D2DJS4|Q496B6|Q496B7	Missense_Mutation	SNP	ENST00000338372.2	37	CCDS12872.1	765	0.35027472527472525	178	0.3617886178861789	158	0.43646408839779005	95	0.1660839160839161	334	0.44063324538258575	C	0.004	-2.287139	0.00248	0.392419	0.435581	ENSG00000189068	ENST00000338372;ENST00000366170	T;T	0.40225	6.9;1.04	3.58	2.55	0.30701	.	0.810448	0.10070	N	0.719777	T	0.00012	0.0000	N	0.01352	-0.895	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.47898	-0.9081	9	0.22109	T	0.4	1.349	6.0866	0.19970	0.0:0.7659:0.0:0.2341	rs2433724;rs52834474;rs61465085;rs2433724	163	Q6UX27	VSTM1_HUMAN	G	163;75	ENSP00000343366:S163G;ENSP00000444153:S75G	ENSP00000343366:S163G	S	-	1	0	VSTM1	59237343	0.183000	0.23186	0.552000	0.28243	0.004000	0.04260	0.186000	0.16978	0.538000	0.28769	-0.136000	0.14681	AGT	T|0.619;C|0.381	0.381	strong		0.493	VSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139358.3	NM_198481	Missense_Mutation
GRM7	2917	hgsc.bcm.edu	37	3	7620382	7620382	+	Silent	SNP	C	C	T	rs7614915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:7620382C>T	ENST00000357716.4	+	8	2063	c.1789C>T	c.(1789-1791)Ctg>Ttg	p.L597L	GRM7_ENST00000458641.2_3'UTR|GRM7_ENST00000486284.1_Silent_p.L597L|GRM7_ENST00000403881.1_Silent_p.L597L|GRM7_ENST00000402647.2_Silent_p.L597L|GRM7_ENST00000389336.4_Silent_p.L597L	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	597					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TCCTGTCTTCCTGGCAATGTT	0.542													C|||	853	0.170327	0.0552	0.2565	5008	,	,		19511	0.1379		0.2932	False		,,,				2504	0.1718				p.L597L		Atlas-SNP	.											.	GRM7	223	.	0			c.C1789T						PASS	.	C	,	371,4035	187.1+/-213.8	16,339,1848	96.0	101.0	99.0		1789,1789	3.9	1.0	3	dbSNP_116	99	2397,6203	399.4+/-346.4	339,1719,2242	no	coding-synonymous,coding-synonymous	GRM7	NM_000844.3,NM_181874.2	,	355,2058,4090	TT,TC,CC		27.8721,8.4203,21.2825	,	597/916,597/923	7620382	2768,10238	2203	4300	6503	SO:0001819	synonymous_variant	2917	exon8			GTCTTCCTGGCAA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.1789C>T	3.37:g.7620382C>T		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	124	72	0.580645	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			C|0.804;T|0.196	0.196	strong		0.542	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12920067	12920067	+	Silent	SNP	C	C	G	rs17038709	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:12920067C>G	ENST00000240189.2	+	3	894	c.807C>G	c.(805-807)ctC>ctG	p.L269L		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	269					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGGAACACCTCCAGTTGCTTA	0.463													.|||	548	0.109425	0.1263	0.0994	5008	,	,		21768	0.131		0.1083	False		,,,				2504	0.0726				p.L269L		Atlas-SNP	.											PRAMEF2,NS,carcinoma,+2,1	PRAMEF2	85	1	0			c.C807G						PASS	.	C		618,3788	260.7+/-263.8	63,492,1648	91.0	91.0	91.0		807	0.8	0.0	1	dbSNP_123	91	978,7610	209.0+/-250.3	81,816,3397	no	coding-synonymous	PRAMEF2	NM_023014.1		144,1308,5045	GG,GC,CC		11.388,14.0263,12.2826		269/475	12920067	1596,11398	2203	4294	6497	SO:0001819	synonymous_variant	65122	exon3			ACACCTCCAGTTG		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.807C>G	1.37:g.12920067C>G		Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	191	15	0.078534	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			C|0.887;G|0.113	0.113	strong		0.463	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
MEGF10	84466	hgsc.bcm.edu	37	5	126746147	126746147	+	Silent	SNP	C	C	T	rs35550094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:126746147C>T	ENST00000274473.6	+	10	1251	c.984C>T	c.(982-984)aaC>aaT	p.N328N	MEGF10_ENST00000418761.2_Silent_p.N328N|MEGF10_ENST00000508365.1_Silent_p.N328N|MEGF10_ENST00000503335.2_Silent_p.N328N	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	328	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		AGTGTGTCAACGGAGGGAAGT	0.587													T|||	82	0.0163738	0.0582	0.0072	5008	,	,		20739	0.0		0.0	False		,,,				2504	0.0				p.N328N		Atlas-SNP	.											.	MEGF10	152	.	0			c.C984T						PASS	.	T		194,4212	808.7+/-415.9	4,186,2013	123.0	103.0	110.0		984	-0.9	0.9	5	dbSNP_126	110	20,8580	818.4+/-406.9	0,20,4280	no	coding-synonymous	MEGF10	NM_032446.2		4,206,6293	TT,TC,CC		0.2326,4.4031,1.6454		328/1141	126746147	214,12792	2203	4300	6503	SO:0001819	synonymous_variant	84466	exon10			TGTCAACGGAGGG	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.984C>T	5.37:g.126746147C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	145	68	0.468966	NM_032446	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																			C|0.983;T|0.017	0.017	strong		0.587	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
FSIP2	401024	hgsc.bcm.edu	37	2	186672897	186672897	+	Silent	SNP	A	A	G	rs4666690	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:186672897A>G	ENST00000424728.1	+	17	18864	c.18864A>G	c.(18862-18864)ttA>ttG	p.L6288L	FSIP2_ENST00000343098.5_Silent_p.L6377L			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	6288										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						TAGGCTTTTTAATGGTGAATG	0.323													A|||	1637	0.326877	0.2451	0.3559	5008	,	,		17961	0.4077		0.3658	False		,,,				2504	0.2935				p.L6377L		Atlas-SNP	.											FSIP2_ENST00000343098,caecum,carcinoma,+2,2	FSIP2	251	2	0			c.A19131G						PASS	.	A		874,2742		97,680,1031	46.0	43.0	44.0		19131	3.3	1.0	2	dbSNP_111	44	2881,5255		502,1877,1689	no	coding-synonymous	FSIP2	NM_173651.2		599,2557,2720	GG,GA,AA		35.4105,24.1704,31.952		6377/6997	186672897	3755,7997	1808	4068	5876	SO:0001819	synonymous_variant	401024	exon17			CTTTTTAATGGTG	AK092099	CCDS54426.1	2q32.1	2010-06-18			ENSG00000188738	ENSG00000188738			21675	protein-coding gene	gene with protein product		615796				14702039	Standard	NM_173651		Approved	FLJ34780	uc002upl.3	Q5CZC0	OTTHUMG00000153874	ENST00000424728.1:c.18864A>G	2.37:g.186672897A>G		Somatic	219	1	0.00456621		WXS	Illumina HiSeq	Phase_I	221	105	0.475113	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				A|0.658;G|0.342	0.342	strong		0.323	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651	
GFAP	2670	hgsc.bcm.edu	37	17	42987524	42987524	+	Intron	SNP	T	T	C	rs9916491|rs386797323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42987524T>C	ENST00000253408.5	-	7	1237				GFAP_ENST00000588735.1_Intron|GFAP_ENST00000435360.2_Missense_Mutation_p.T426A	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein						astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				GCCGGCGGCGTTCCATTTACA	0.542													C|||	1220	0.24361	0.2307	0.2291	5008	,	,		18243	0.251		0.2624	False		,,,				2504	0.2444				p.T426A		Atlas-SNP	.											.	GFAP	88	.	0			c.A1276G						PASS	.	C	ALA/THR,,	756,2380		88,580,900	223.0	196.0	204.0		1276,,	3.8	0.9	17	dbSNP_119	204	1965,5199		268,1429,1885	yes	missense,utr-3,intron	GFAP	NM_001131019.2,NM_001242376.1,NM_002055.4	58,,	356,2009,2785	CC,CT,TT		27.4288,24.1071,26.4175	,,	426/432,,	42987524	2721,7579	1568	3582	5150	SO:0001627	intron_variant	2670	exon8			GCGGCGTTCCATT	S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"""Intermediate filaments type III"""	4235	protein-coding gene	gene with protein product	"""intermediate filament protein"""	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.1171+458A>G	17.37:g.42987524T>C		Somatic	314	3	0.00955414		WXS	Illumina HiSeq	Phase_I	312	312	1	NM_001131019	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Missense_Mutation	SNP	ENST00000253408.5	37	CCDS11491.1	517	0.2367216117216117	86	0.17479674796747968	89	0.24585635359116023	161	0.28146853146853146	181	0.23878627968337732	C	11.02	1.517202	0.27123	0.241071	0.274288	ENSG00000131095	ENST00000435360	D	0.83837	-1.77	4.79	3.79	0.43588	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999693523	B	0.02656	0.0	B	0.01281	0.0	T	0.03807	-1.1002	8	0.35671	T	0.21	.	6.7504	0.23483	0.0:0.7291:0.1777:0.0932	rs9916491;rs9916491	426	E9PAX3	.	A	426	ENSP00000403962:T426A	ENSP00000403962:T426A	T	-	1	0	GFAP	40343050	0.983000	0.35010	0.883000	0.34634	0.200000	0.23975	0.753000	0.26376	0.924000	0.37069	-0.119000	0.15052	ACG	T|0.759;C|0.241	0.241	strong		0.542	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055	
MDN1	23195	hgsc.bcm.edu	37	6	90390443	90390443	+	Missense_Mutation	SNP	C	C	A	rs9353689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:90390443C>A	ENST00000369393.3	-	74	12245	c.12130G>T	c.(12130-12132)Gct>Tct	p.A4044S	MDN1_ENST00000428876.1_Missense_Mutation_p.A4044S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4044			A -> S (in dbSNP:rs9353689).		ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GAAGGAGCAGCGCCCTGACAC	0.542													C|||	3064	0.611821	0.612	0.7046	5008	,	,		20137	0.9077		0.4712	False		,,,				2504	0.3855				p.A4044S		Atlas-SNP	.											.	MDN1	478	.	0			c.G12130T						PASS	.	C	SER/ALA	2702,1704	651.9+/-399.3	845,1012,346	63.0	58.0	60.0		12130	-0.3	0.0	6	dbSNP_119	60	4126,4474	564.3+/-388.3	1021,2084,1195	yes	missense	MDN1	NM_014611.1	99	1866,3096,1541	AA,AC,CC		47.9767,38.6745,47.5012	benign	4044/5597	90390443	6828,6178	2203	4300	6503	SO:0001583	missense	23195	exon74			GAGCAGCGCCCTG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12130G>T	6.37:g.90390443C>A	ENSP00000358400:p.Ala4044Ser	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	29	28	0.965517	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	1449	0.6634615384615384	312	0.6341463414634146	245	0.6767955801104972	524	0.916083916083916	368	0.48548812664907653	C	7.498	0.652024	0.14580	0.613255	0.479767	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03035	4.07;4.07	3.7	-0.328	0.12690	.	1.203530	0.05725	N	0.598418	T	0.00998	0.0033	L	0.43152	1.355	0.80722	P	0.0	B	0.26258	0.145	B	0.23716	0.048	T	0.46748	-0.9169	9	0.07644	T	0.81	.	8.681	0.34209	0.0:0.6252:0.0:0.3748	rs9353689;rs52797926;rs60292364;rs9353689	4044	Q9NU22	MDN1_HUMAN	S	4044	ENSP00000358400:A4044S;ENSP00000413970:A4044S	ENSP00000358400:A4044S	A	-	1	0	MDN1	90447164	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.218000	0.09240	-0.083000	0.12618	-0.254000	0.11334	GCT	C|0.413;A|0.587	0.587	strong		0.542	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
KL	9365	hgsc.bcm.edu	37	13	33628193	33628193	+	Missense_Mutation	SNP	G	G	C	rs9527025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:33628193G>C	ENST00000380099.3	+	2	1117	c.1109G>C	c.(1108-1110)tGc>tCc	p.C370S	KL_ENST00000426690.2_Missense_Mutation_p.C63S|KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	370	Glycosyl hydrolase-1 1.		C -> S (in allele KL-VS; associated with V-352; dbSNP:rs9527025). {ECO:0000269|PubMed:11792841, ECO:0000269|PubMed:15677572}.		acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)			breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		TTTGCTCTTTGCTTTGGACCC	0.423													C|||	651	0.129992	0.2005	0.0821	5008	,	,		19195	0.0		0.1938	False		,,,				2504	0.137				p.C370S		Atlas-SNP	.											.	KL	106	.	0			c.G1109C	GRCh37	CM022034	KL	M	rs9527025	PASS	.	C	SER/CYS	816,3590	749.3+/-412.0	74,668,1461	176.0	181.0	180.0		1109	5.9	1.0	13	dbSNP_119	180	1411,7189	752.4+/-407.4	116,1179,3005	yes	missense	KL	NM_004795.3	112	190,1847,4466	CC,CG,GG		16.407,18.5202,17.1229	benign	370/1013	33628193	2227,10779	2203	4300	6503	SO:0001583	missense	9365	exon2			CTCTTTGCTTTGG	AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1109G>C	13.37:g.33628193G>C	ENSP00000369442:p.Cys370Ser	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	116	44	0.37931	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	287	0.13141025641025642	93	0.18902439024390244	41	0.1132596685082873	0	0.0	153	0.20184696569920843	C	7.622	0.677076	0.14841	0.185202	0.16407	ENSG00000133116	ENST00000426690;ENST00000380099	T;T	0.27402	1.67;1.82	5.9	5.9	0.94986	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00020	-2.78	0.43029	P	0.005404999999999993	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30534	-0.9975	9	0.23891	T	0.37	-32.9193	17.3287	0.87257	0.0:0.8748:0.1252:0.0	rs9527025;rs52797932;rs9527025	370;63	Q9UEF7;B3KUJ4	KLOT_HUMAN;.	S	63;370	ENSP00000399513:C63S;ENSP00000369442:C370S	ENSP00000369442:C370S	C	+	2	0	KL	32526193	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	5.982000	0.70532	1.527000	0.49086	-0.120000	0.15030	TGC	G|0.848;C|0.152	0.152	strong		0.423	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1		
SLC15A4	121260	hgsc.bcm.edu	37	12	129278864	129278864	+	Silent	SNP	A	A	G	rs1059312	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:129278864A>G	ENST00000266771.5	-	8	1650	c.1611T>C	c.(1609-1611)ttT>ttC	p.F537F	SLC15A4_ENST00000544112.1_Silent_p.F200F|SLC15A4_ENST00000545031.1_Silent_p.F54F	NM_145648.3	NP_663623.1	Q8N697	S15A4_HUMAN	solute carrier family 15 (oligopeptide transporter), member 4	537					ion transport (GO:0006811)|oligopeptide transport (GO:0006857)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	L-histidine transmembrane transporter activity (GO:0005290)|symporter activity (GO:0015293)			endometrium(4)|kidney(2)|large_intestine(4)|lung(11)|skin(1)	22	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.69e-06)|Epithelial(86;1.17e-05)|all cancers(50;5.07e-05)		CAGCCAGAAGAAAAAAGTAAT	0.423													A|||	2331	0.465455	0.4803	0.5389	5008	,	,		18523	0.4266		0.4195	False		,,,				2504	0.4806				p.F537F		Atlas-SNP	.											.	SLC15A4	41	.	0			c.T1611C						PASS	.	A		2103,2303	562.9+/-381.1	492,1119,592	74.0	86.0	82.0		1611	-0.8	0.7	12	dbSNP_86	82	3275,5325	484.3+/-371.4	628,2019,1653	no	coding-synonymous	SLC15A4	NM_145648.3		1120,3138,2245	GG,GA,AA		38.0814,47.7304,41.3501		537/578	129278864	5378,7628	2203	4300	6503	SO:0001819	synonymous_variant	121260	exon8			CAGAAGAAAAAAG	AY038999	CCDS9264.1	12q24.32	2013-07-18	2013-07-18		ENSG00000139370	ENSG00000139370		"""Solute carriers"""	23090	protein-coding gene	gene with protein product		615806	"""solute carrier family 15, member 4"""			11741232	Standard	NM_145648		Approved	PHT1, PTR4	uc001uhu.2	Q8N697	OTTHUMG00000168415	ENST00000266771.5:c.1611T>C	12.37:g.129278864A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	88	44	0.5	NM_145648	A6H8Y9|B3KTK1|Q71M34|Q7Z5F8|Q8TAH0	Silent	SNP	ENST00000266771.5	37	CCDS9264.1																																																																																			A|0.574;G|0.426	0.426	strong		0.423	SLC15A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399663.1	NM_145648	
SERPINB8	5271	hgsc.bcm.edu	37	18	61647069	61647069	+	Missense_Mutation	SNP	G	G	A	rs1944270	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:61647069G>A	ENST00000397985.2	+	3	459	c.203G>A	c.(202-204)cGa>cAa	p.R68Q	SERPINB8_ENST00000542677.1_5'UTR|SERPINB8_ENST00000397988.3_Missense_Mutation_p.R68Q|SERPINB8_ENST00000353706.2_Missense_Mutation_p.R68Q|HMSD_ENST00000481726.1_3'UTR	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	68			R -> Q (in dbSNP:rs1944270).		negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				GATATTCACCGAGGTTTCCAG	0.428											OREG0025042	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	1632	0.325879	0.6445	0.2262	5008	,	,		17467	0.1944		0.2863	False		,,,				2504	0.1421				p.R68Q		Atlas-SNP	.											.	SERPINB8	42	.	0			c.G203A						PASS	.	A	GLN/ARG,GLN/ARG,GLN/ARG	2526,1880	541.7+/-375.8	763,1000,440	159.0	156.0	157.0		203,203,203	-5.6	0.0	18	dbSNP_92	157	2409,6191	700.0+/-405.1	349,1711,2240	yes	missense,missense,missense	SERPINB8	NM_001031848.1,NM_002640.3,NM_198833.1	43,43,43	1112,2711,2680	AA,AG,GG		28.0116,42.6691,37.944	benign,benign,benign	68/243,68/375,68/375	61647069	4935,8071	2203	4300	6503	SO:0001583	missense	5271	exon3			TTCACCGAGGTTT	L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"""Serine (or cysteine) peptidase inhibitors"""	8952	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase 2"""	601697	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"""	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.203G>A	18.37:g.61647069G>A	ENSP00000381072:p.Arg68Gln	Somatic	73	0	0	1055	WXS	Illumina HiSeq	Phase_I	76	35	0.460526	NM_001031848	B4DTW2|Q7Z2V6|Q8N178	Missense_Mutation	SNP	ENST00000397985.2	37	CCDS11991.1	753|753	0.3447802197802198|0.3447802197802198	316|316	0.6422764227642277|0.6422764227642277	90|90	0.24861878453038674|0.24861878453038674	117|117	0.20454545454545456|0.20454545454545456	230|230	0.3034300791556728|0.3034300791556728	A|A	0.047|0.047	-1.263202|-1.263202	0.01445|0.01445	0.573309|0.573309	0.280116|0.280116	ENSG00000166401|ENSG00000166401	ENST00000295211|ENST00000397985;ENST00000353706;ENST00000397988;ENST00000448851;ENST00000441827	.|D;D;D;D;D	.|0.83837	.|-1.77;-1.77;-1.77;-1.77;-1.77	4.75|4.75	-5.63|-5.63	0.02474|0.02474	.|Serpin domain (3);	.|1.377110	.|0.03871	.|N	.|0.275640	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02379|0.02379	-0.575|-0.575	0.58432|0.58432	P|P	9.000000000036756E-6|9.000000000036756E-6	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.0;0.001	T|T	0.24693|0.24693	-1.0153|-1.0153	4|9	.|0.02654	.|T	.|1	.|.	10.5421|10.5421	0.45039|0.45039	0.2174:0.3:0.4826:0.0|0.2174:0.3:0.4826:0.0	rs1944270;rs52799646;rs1944270|rs1944270;rs52799646;rs1944270	.|68;68	.|P50452;Q8N178	.|SPB8_HUMAN;.	K|Q	10|68	.|ENSP00000381072:R68Q;ENSP00000331368:R68Q;ENSP00000381075:R68Q;ENSP00000414580:R68Q;ENSP00000393456:R68Q	.|ENSP00000331368:R68Q	E|R	+|+	1|2	0|0	SERPINB8|SERPINB8	59798049|59798049	0.000000|0.000000	0.05858|0.05858	0.049000|0.049000	0.19019|0.19019	0.030000|0.030000	0.12068|0.12068	-2.669000|-2.669000	0.00845|0.00845	-1.431000|-1.431000	0.01982|0.01982	-1.177000|-1.177000	0.01723|0.01723	GAG|CGA	G|0.632;T|0.004	.	strong		0.428	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	
WWC1	23286	hgsc.bcm.edu	37	5	167891830	167891830	+	Silent	SNP	T	T	C	rs3203960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:167891830T>C	ENST00000265293.4	+	21	3515	c.3013T>C	c.(3013-3015)Ttg>Ctg	p.L1005L	WWC1_ENST00000521089.1_Silent_p.L1011L|WWC1_ENST00000522140.1_3'UTR	NM_001161661.1|NM_001161662.1|NM_015238.2	NP_001155133.1|NP_001155134.1|NP_056053.1	Q8IX03	KIBRA_HUMAN	WW and C2 domain containing 1	1005	Interaction with histone H3.				cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|hippo signaling (GO:0035329)|negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of MAPK cascade (GO:0043410)|regulation of hippo signaling (GO:0035330)|regulation of intracellular transport (GO:0032386)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)|transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(2)|prostate(1)|skin(4)	43	Renal(175;0.000212)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0399)|all_neural(177;0.0577)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0364)|Epithelial(171;0.0765)|OV - Ovarian serous cystadenocarcinoma(192;0.0918)		GCACAGCCAATTGACCCAGGA	0.602													C|||	1698	0.339058	0.4009	0.3329	5008	,	,		17703	0.0407		0.4463	False		,,,				2504	0.4571				p.L1011L		Atlas-SNP	.											.	WWC1	98	.	0			c.T3031C						PASS	.	C	,,	1734,2672	647.5+/-398.6	333,1068,802	76.0	73.0	74.0		3031,3031,3013	5.1	1.0	5	dbSNP_105	74	3581,5019	627.1+/-397.9	764,2053,1483	no	coding-synonymous,coding-synonymous,coding-synonymous	WWC1	NM_001161661.1,NM_001161662.1,NM_015238.2	,,	1097,3121,2285	CC,CT,TT		41.6395,39.3554,40.8658	,,	1011/1120,1011/1119,1005/1114	167891830	5315,7691	2203	4300	6503	SO:0001819	synonymous_variant	23286	exon21			AGCCAATTGACCC	AF506799	CCDS4366.1, CCDS54945.1	5q34	2014-06-13	2006-11-09		ENSG00000113645	ENSG00000113645		"""WW, C2 and coiled-coil domain containing"""	29435	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 168"""	610533	"""WW, C2 and coiled-coil domain containing 1"""			10048485, 12559952	Standard	NM_001161661		Approved	KIBRA, KIAA0869, PPP1R168	uc011den.2	Q8IX03	OTTHUMG00000130408	ENST00000265293.4:c.3013T>C	5.37:g.167891830T>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	35	0.360825	NM_001161662	B4DK05|O94946|Q6MZX4|Q6Y2F8|Q7Z4G8|Q8WVM4|Q9BT29	Silent	SNP	ENST00000265293.4	37	CCDS4366.1	695	0.3182234432234432	197	0.40040650406504064	130	0.35911602209944754	17	0.02972027972027972	351	0.4630606860158311	C	6.375	0.437319	0.12104	0.393554	0.416395	ENSG00000113645	ENST00000393895;ENST00000524228	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.44050	-0.9353	3	.	.	.	.	13.9056	0.63834	0.0:0.9268:0.0:0.0732	rs3203960;rs17633483;rs17845558;rs17858456;rs60748229;rs3203960	.	.	.	T	972;781	.	.	I	+	2	0	WWC1	167824408	1.000000	0.71417	1.000000	0.80357	0.506000	0.33950	1.673000	0.37534	1.189000	0.43028	-0.227000	0.12334	ATT	T|0.625;C|0.375	0.375	strong		0.602	WWC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252791.2	NM_015238	
C4A	720	hgsc.bcm.edu	37	6	31964228	31964228	+	Missense_Mutation	SNP	A	A	G	rs577596183		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31964228A>G	ENST00000428956.2	+	28	3611	c.3527A>G	c.(3526-3528)aAc>aGc	p.N1176S	C4A_ENST00000498271.1_Missense_Mutation_p.N1176S	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1176			N -> S (in allotype C4A1; dbSNP:rs17874654). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:3696167, ECO:0000269|Ref.3, ECO:0000269|Ref.8}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of apoptotic cell clearance (GO:2000427)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	complement component C1q binding (GO:0001849)|endopeptidase inhibitor activity (GO:0004866)									Intravenous Immunoglobulin(DB00028)	TCAAAGGCAAACTCATTTTTG	0.607																																					p.S1176S		Atlas-SNP	.											.	C4A	15	.	0			c.G3527G						PASS	.						90.0	102.0	98.0					6																	31964228		1555	3540	5095	SO:0001583	missense	720	exon28			AGGCAAACTCATT	L26261, M14823, X77491, AY224378	CCDS47404.1, CCDS59005.1	6p21.3	2014-09-17	2006-01-19		ENSG00000244731	ENSG00000244731		"""Blood group antigens"", ""Complement system"""	1323	protein-coding gene	gene with protein product		120810	"""complement component 4A"""				Standard	NM_001252204		Approved	CPAMD2, C4S, CO4, C4, C4A3, C4A2, C4A4, C4A6, C4B, RG		P0C0L4	OTTHUMG00000031186	ENST00000428956.2:c.3527A>G	6.37:g.31964228A>G	ENSP00000396688:p.Asn1176Ser	Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	326	121	0.371166	NM_007293	A6H8M8|A6NHJ5|A7E2V2|B0QZR6|B0V2C8|B2RUT6|B7ZVZ6|P01028|P78445|Q13160|Q13906|Q14033|Q14835|Q4LE82|Q5JNX2|Q5JQM8|Q6P4R1|Q6U2E5|Q6U2E8|Q6U2F0|Q6U2F3|Q6U2F4|Q6U2F6|Q6U2F8|Q6U2G0|Q96EG2|Q96SA8|Q9NPK5|Q9UIP5	Silent	SNP	ENST00000428956.2	37	CCDS47404.1	.	.	.	.	.	.	.	.	.	.	a	1.772	-0.484018	0.04383	.	.	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.36340	1.26;1.26	3.47	2.24	0.28232	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.09247	0.0228	L	0.48642	1.525	0.09310	P	0.999999896602	B;B	0.11235	0.004;0.004	B;B	0.23150	0.044;0.044	T	0.30001	-0.9993	8	0.05351	T	0.99	.	6.9466	0.24522	0.7642:0.2358:0.0:0.0	rs2746414	1176;1176	A6H8M8;P0C0L4	.;CO4A_HUMAN	S	1176	ENSP00000396688:N1176S;ENSP00000420212:N1176S	ENSP00000396688:N1176S	N	+	2	0	C4A	32072207	0.016000	0.18221	0.755000	0.31263	0.803000	0.45373	1.116000	0.31221	0.338000	0.23692	0.338000	0.21704	AAC	A|0.017;G|0.983	0.983	strong		0.607	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156067	39156067	+	Silent	SNP	A	A	G	rs9890989	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39156067A>G	ENST00000391587.1	-	1	71	c.39T>C	c.(37-39)acT>acC	p.T13T		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	13	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				TGGCAGGCCCAGTGGGGACAC	0.562													.|||	1497	0.298922	0.6112	0.2075	5008	,	,		17956	0.2302		0.1223	False		,,,				2504	0.1943				p.T13T		Atlas-SNP	.											.	KRTAP3-2	11	.	0			c.T39C						PASS	.	G		1929,2475		584,761,857	62.0	79.0	73.0		39	-5.6	0.8	17	dbSNP_119	73	635,7957		41,553,3702	no	coding-synonymous	KRTAP3-2	NM_031959.2		625,1314,4559	GG,GA,AA		7.3906,43.8011,19.7291		13/99	39156067	2564,10432	2202	4296	6498	SO:0001819	synonymous_variant	83897	exon1			AGGCCCAGTGGGG	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.39T>C	17.37:g.39156067A>G		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	109	43	0.394495	NM_031959		Silent	SNP	ENST00000391587.1	37	CCDS32644.1																																																																																			A|0.750;G|0.250	0.250	strong		0.562	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1		
TCTN3	26123	hgsc.bcm.edu	37	10	97453464	97453464	+	Missense_Mutation	SNP	T	T	G	rs11553577	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:97453464T>G	ENST00000371217.5	-	1	216	c.193A>C	c.(193-195)Aca>Cca	p.T65P	TCTN3_ENST00000265993.9_Missense_Mutation_p.T83P|TCTN3_ENST00000430368.2_Missense_Mutation_p.T65P|TCTN3_ENST00000371209.5_Missense_Mutation_p.T65P			Q6NUS6	TECT3_HUMAN	tectonic family member 3	65					apoptotic process (GO:0006915)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Colorectal(252;0.0815)		Epithelial(162;1.69e-07)|all cancers(201;5.63e-06)		GGGACCACTGTAGGGAGTCCA	0.617											OREG0020392	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	513	0.102436	0.2073	0.0821	5008	,	,		18863	0.0397		0.0606	False		,,,				2504	0.0828				p.T65P		Atlas-SNP	.											.	TCTN3	66	.	0			c.A193C						PASS	.	T	PRO/THR,PRO/THR	243,1141		32,179,481	26.0	32.0	30.0		193,193	-4.3	0.0	10	dbSNP_120	30	227,2955		12,203,1376	yes	missense,missense	TCTN3	NM_001143973.1,NM_015631.5	38,38	44,382,1857	GG,GT,TT		7.1339,17.5578,10.2935	possibly-damaging,possibly-damaging	65/460,65/608	97453464	470,4096	692	1591	2283	SO:0001583	missense	26123	exon1			CCACTGTAGGGAG	AK098295	CCDS31258.2, CCDS44461.1	10q24.1	2014-01-28	2007-08-20	2007-08-20	ENSG00000119977	ENSG00000119977		"""Tectonic proteins"""	24519	protein-coding gene	gene with protein product		613847	"""chromosome 10 open reading frame 61"""	C10orf61		12975309	Standard	NM_015631		Approved	DKFZP564D116, TECT3, JBTS18	uc001klb.4	Q6NUS6	OTTHUMG00000018814	ENST00000371217.5:c.193A>C	10.37:g.97453464T>G	ENSP00000360261:p.Thr65Pro	Somatic	81	0	0	1328	WXS	Illumina HiSeq	Phase_I	95	52	0.547368	NM_015631	A6NIC8|B0QZ90|B4DR81|Q6P7P3|Q6UW27|Q6ZQQ0|Q8N7K1|Q8NBQ0|Q96GF7|Q9Y3U1	Missense_Mutation	SNP	ENST00000371217.5	37	CCDS31258.2	200	0.09157509157509157	86	0.17479674796747968	41	0.1132596685082873	31	0.05419580419580419	42	0.055408970976253295	T	18.32	3.598018	0.66332	0.175578	0.071339	ENSG00000119977	ENST00000265993;ENST00000430368;ENST00000371217;ENST00000371209	D;D	0.84660	-1.86;-1.88	4.88	-4.27	0.03744	.	1.407620	0.04281	N	0.343935	T	0.00552	0.0018	L	0.34521	1.04	0.80722	P	0.0	P;D;D	0.57571	0.838;0.98;0.966	B;P;P	0.55303	0.205;0.773;0.598	T	0.48536	-0.9027	9	0.45353	T	0.12	-15.6315	0.2657	0.00224	0.2781:0.1753:0.2846:0.262	rs11553577;rs61428494;rs11553577	65;65;65	B4DR81;Q6NUS6-2;Q6NUS6	.;.;TECT3_HUMAN	P	65;65;83;65	ENSP00000265993:T65P;ENSP00000360253:T65P	ENSP00000265993:T65P	T	-	1	0	TCTN3	97443454	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.722000	0.04958	-0.470000	0.06901	0.533000	0.62120	ACA	T|0.905;G|0.095	0.095	strong		0.617	TCTN3-009	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000471858.1	NM_015631	
SLX4	84464	hgsc.bcm.edu	37	16	3650987	3650987	+	Missense_Mutation	SNP	T	T	C	rs113490934	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3650987T>C	ENST00000294008.3	-	5	1796	c.1156A>G	c.(1156-1158)Atg>Gtg	p.M386V		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	386	Interaction with SLX4IP, ERCC4 and MSH2.		M -> V (in dbSNP:rs113490934). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						TACCTGAACATGGGTGGGCTG	0.517								Direct reversal of damage					C|||	273	0.0545128	0.0507	0.0706	5008	,	,		19560	0.0506		0.0646	False		,,,				2504	0.0419				p.M386V		Atlas-SNP	.											.	SLX4	173	.	0			c.A1156G						PASS	.	C	VAL/MET	271,4123	783.8+/-414.6	7,257,1933	39.0	40.0	40.0		1156	2.4	0.0	16	dbSNP_132	40	575,8025	774.0+/-407.7	15,545,3740	yes	missense	SLX4	NM_032444.2	21	22,802,5673	CC,CT,TT		6.686,6.1675,6.5107	benign	386/1835	3650987	846,12148	2197	4300	6497	SO:0001583	missense	84464	exon5			TGAACATGGGTGG	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.1156A>G	16.37:g.3650987T>C	ENSP00000294008:p.Met386Val	Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	174	63	0.362069	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	121	0.0554029304029304	25	0.0508130081300813	24	0.06629834254143646	24	0.04195804195804196	48	0.0633245382585752	C	3.500	-0.102080	0.06967	0.061675	0.06686	ENSG00000188827	ENST00000294008	T	0.18810	2.19	5.46	2.41	0.29592	.	2.158740	0.01671	N	0.025592	T	0.00496	0.0016	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36383	-0.9750	10	0.02654	T	1	.	5.0684	0.14594	0.145:0.6271:0.0:0.2279	.	386	Q8IY92	SLX4_HUMAN	V	386	ENSP00000294008:M386V	ENSP00000294008:M386V	M	-	1	0	SLX4	3590988	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.435000	0.21510	0.084000	0.17077	-0.128000	0.14901	ATG	T|0.945;C|0.055	0.055	strong		0.517	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
C17orf97	400566	hgsc.bcm.edu	37	17	260299	260299	+	Missense_Mutation	SNP	G	G	A	rs4581766	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:260299G>A	ENST00000571106.1	+	1	172	c.166G>A	c.(166-168)Gag>Aag	p.E56K	AC108004.3_ENST00000466740.2_RNA|AC108004.3_ENST00000599026.1_RNA|C17orf97_ENST00000360127.6_Missense_Mutation_p.E56K			Q6ZQX7	CQ097_HUMAN	chromosome 17 open reading frame 97	56	Poly-Glu.		E -> K (in dbSNP:rs4581766). {ECO:0000269|PubMed:15489334}.							breast(1)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	14						CGGCGAGGAGGAGGAGCGGGA	0.731													g|||	992	0.198083	0.2905	0.1657	5008	,	,		11861	0.2073		0.1093	False		,,,				2504	0.1779				p.E56K		Atlas-SNP	.											C17orf97_ENST00000360127,NS,carcinoma,0,4	C17orf97	76	4	0			c.G166A						scavenged	.		LYS/GLU	562,2470		32,498,986	2.0	4.0	4.0		166	3.6	0.9	17	dbSNP_111	4	498,5448		18,462,2493	yes	missense	C17orf97	NM_001013672.4	56	50,960,3479	AA,AG,GG		8.3754,18.5356,11.8066	benign	56/424	260299	1060,7918	1516	2973	4489	SO:0001583	missense	400566	exon1			GAGGAGGAGGAGC	AK128660, BC057385	CCDS32519.2	17p13.3	2008-08-15			ENSG00000187624	ENSG00000187624			33800	protein-coding gene	gene with protein product						12477932	Standard	NM_001013672		Approved	LOC400566	uc021tna.1	Q6ZQX7	OTTHUMG00000132479	ENST00000571106.1:c.166G>A	17.37:g.260299G>A	ENSP00000458320:p.Glu56Lys	Somatic	3	2	0.666667		WXS	Illumina HiSeq	Phase_I	10	8	0.8	NM_001013672	A5D8T6|Q6NSI2|Q6PFW9	Missense_Mutation	SNP	ENST00000571106.1	37		437	0.2000915750915751	157	0.31910569105691056	59	0.16298342541436464	135	0.23601398601398602	86	0.11345646437994723	g	22.1	4.246429	0.80024	0.185356	0.083754	ENSG00000187624	ENST00000360127;ENST00000491373	T;T	0.54279	0.93;0.58	3.56	3.56	0.40772	.	0.000000	0.42548	D	0.000690	T	0.00012	0.0000	L	0.27053	0.805	0.38502	P	0.05175099999999999	D	0.76494	0.999	D	0.80764	0.994	T	0.15723	-1.0427	9	0.49607	T	0.09	-0.156	10.9491	0.47319	0.0:0.0:1.0:0.0	rs4581766;rs60466803	56	Q6ZQX7-4	.	K	56;50	ENSP00000353245:E56K;ENSP00000419482:E50K	ENSP00000353245:E56K	E	+	1	0	C17orf97	260615	0.992000	0.36948	0.855000	0.33649	0.658000	0.38924	2.263000	0.43293	2.299000	0.77371	0.556000	0.70494	GAG	G|0.798;A|0.202	0.202	strong		0.731	C17orf97-003	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000436874.1	NM_001013672	
PMEL	6490	hgsc.bcm.edu	37	12	56351346	56351346	+	Silent	SNP	G	G	A	rs1052165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56351346G>A	ENST00000548747.1	-	6	1403	c.741C>T	c.(739-741)ccC>ccT	p.P247P	PMEL_ENST00000536427.1_Silent_p.P247P|PMEL_ENST00000539511.1_Silent_p.P161P|PMEL_ENST00000360714.4_Silent_p.P247P|PMEL_ENST00000550447.1_Intron|PMEL_ENST00000552882.1_Silent_p.P247P|PMEL_ENST00000550464.1_Silent_p.P161P|PMEL_ENST00000548493.1_Silent_p.P247P|PMEL_ENST00000548689.1_5'Flank|PMEL_ENST00000449260.2_Silent_p.P247P			P40967	PMEL_HUMAN	premelanosome protein	247					melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|multivesicular body membrane (GO:0032585)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GATAGCCACTGGGGTCATGGA	0.557													G|||	1067	0.213059	0.0204	0.1686	5008	,	,		21344	0.2391		0.2734	False		,,,				2504	0.4162				p.P247P		Atlas-SNP	.											.	PMEL	60	.	0			c.C741T						PASS	.	G	,,	267,4139	149.5+/-183.7	12,243,1948	113.0	117.0	116.0		483,741,741	3.8	1.0	12	dbSNP_86	116	2405,6195	397.5+/-345.8	349,1707,2244	no	coding-synonymous,coding-synonymous,coding-synonymous	PMEL	NM_001200053.1,NM_001200054.1,NM_006928.4	,,	361,1950,4192	AA,AG,GG		27.9651,6.0599,20.5444	,,	161/576,247/669,247/662	56351346	2672,10334	2203	4300	6503	SO:0001819	synonymous_variant	6490	exon6			GCCACTGGGGTCA	AK092881	CCDS8897.1, CCDS55833.1, CCDS55834.1	12q13-q14	2010-12-17	2010-12-17	2010-12-17	ENSG00000185664	ENSG00000185664			10880	protein-coding gene	gene with protein product		155550	"""silver (mouse homolog) like"", ""silver homolog (mouse)"""	SIL, SILV		8739560	Standard	NM_001200053		Approved	D12S53E, SI, Pmel17, gp100	uc001siq.3	P40967		ENST00000548747.1:c.741C>T	12.37:g.56351346G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	79	42	0.531646	NM_001200054	B3KS57|B7Z6D7|Q12763|Q14448|Q14817|Q16565	Silent	SNP	ENST00000548747.1	37	CCDS8897.1	411	0.18818681318681318	18	0.036585365853658534	63	0.17403314917127072	125	0.21853146853146854	205	0.2704485488126649	G	9.900	1.206517	0.22205	0.060599	0.279651	ENSG00000185664	ENST00000549404	.	.	.	5.6	3.75	0.43078	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.0299	12.1891	0.54257	0.1507:0.0:0.8493:0.0	rs1052165;rs3192587;rs17849477;rs58583770;rs1052165	.	.	.	X	135	.	.	Q	-	1	0	PMEL	54637613	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.096000	0.50243	1.509000	0.48786	0.655000	0.94253	CAG	G|0.799;N|0.000	.	strong		0.557	PMEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409626.1	NM_006928	
MUC16	94025	hgsc.bcm.edu	37	19	9088330	9088330	+	Missense_Mutation	SNP	G	G	A	rs17000947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9088330G>A	ENST00000397910.4	-	1	3688	c.3485C>T	c.(3484-3486)aCt>aTt	p.T1162I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1162	Thr-rich.		T -> I (in dbSNP:rs17000947).		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						GACTTTGGGAGTAGGAGAAGA	0.483													G|||	951	0.189896	0.0711	0.2709	5008	,	,		22315	0.3036		0.172	False		,,,				2504	0.1943				p.T1162I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C3485T						PASS	.	G	ILE/THR	299,3929		5,289,1820	148.0	142.0	144.0		3485	-0.7	0.0	19	dbSNP_123	144	1504,6954		128,1248,2853	yes	missense	MUC16	NM_024690.2	89	133,1537,4673	AA,AG,GG		17.782,7.0719,14.2125	benign	1162/14508	9088330	1803,10883	2114	4229	6343	SO:0001583	missense	94025	exon1			TTGGGAGTAGGAG	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.3485C>T	19.37:g.9088330G>A	ENSP00000381008:p.Thr1162Ile	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	143	68	0.475524	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.677	-0.276221	0.05679	0.070719	0.17782	ENSG00000181143	ENST00000397910	T	0.02472	4.28	1.09	-0.731	0.11151	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	B	0.19817	0.039	B	0.11329	0.006	T	0.47058	-0.9146	8	0.87932	D	0	.	3.4331	0.07436	0.4447:0.0:0.5553:0.0	rs17000947;rs17000947	1162	B5ME49	.	I	1162	ENSP00000381008:T1162I	ENSP00000381008:T1162I	T	-	2	0	MUC16	8949330	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-0.783000	0.04638	-0.176000	0.10707	0.305000	0.20034	ACT	G|0.811;A|0.189	0.189	strong		0.483	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CDCA2	157313	hgsc.bcm.edu	37	8	25364331	25364331	+	Missense_Mutation	SNP	G	G	A	rs4872318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:25364331G>A	ENST00000330560.3	+	15	2626	c.2149G>A	c.(2149-2151)Gta>Ata	p.V717I	CDCA2_ENST00000521098.2_3'UTR|CDCA2_ENST00000380665.3_Missense_Mutation_p.V702I	NM_152562.2	NP_689775.2	Q69YH5	CDCA2_HUMAN	cell division cycle associated 2	717			V -> I (in dbSNP:rs4872318). {ECO:0000269|PubMed:12188893, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:20068231, ECO:0000269|PubMed:21406692}.		mitotic nuclear division (GO:0007067)|positive regulation of protein dephosphorylation (GO:0035307)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(7)|lung(10)|ovary(1)|prostate(3)	35		all_cancers(63;0.0378)|Ovarian(32;0.000878)|all_epithelial(46;0.0162)|Breast(100;0.0164)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.022)|Epithelial(17;1.37e-11)|Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0443)		TTGTGCTTCTGTAACTGAAGA	0.393													G|||	1134	0.226438	0.031	0.3602	5008	,	,		18117	0.0982		0.3549	False		,,,				2504	0.3957				p.V717I		Atlas-SNP	.											.	CDCA2	78	.	0			c.G2149A						PASS	.	G	ILE/VAL	372,4034	176.2+/-205.4	19,334,1850	38.0	39.0	38.0		2149	0.8	0.0	8	dbSNP_111	38	2977,5623	452.4+/-362.9	502,1973,1825	yes	missense	CDCA2	NM_152562.2	29	521,2307,3675	AA,AG,GG		34.6163,8.443,25.7497	probably-damaging	717/1024	25364331	3349,9657	2203	4300	6503	SO:0001583	missense	157313	exon15			GCTTCTGTAACTG	BG354575	CCDS6049.1	8p21.2	2014-06-12			ENSG00000184661	ENSG00000184661			14623	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 81"""					12188893, 16492807	Standard	NM_152562		Approved	Repo-Man, PPP1R81	uc003xep.1	Q69YH5	OTTHUMG00000099429	ENST00000330560.3:c.2149G>A	8.37:g.25364331G>A	ENSP00000328228:p.Val717Ile	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_152562	Q3SX74|Q4G0W0|Q5RKN0|Q69YI4|Q6P464|Q8N7C1	Missense_Mutation	SNP	ENST00000330560.3	37	CCDS6049.1	469	0.21474358974358973	14	0.028455284552845527	118	0.3259668508287293	62	0.10839160839160839	275	0.3627968337730871	G	14.92	2.678756	0.47886	0.08443	0.346163	ENSG00000184661	ENST00000330560;ENST00000380665;ENST00000434814	T;T	0.47869	0.83;0.83	5.07	0.754	0.18410	.	0.967502	0.08533	N	0.931768	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	P;P	0.42908	0.793;0.793	B;B	0.40940	0.344;0.344	T	0.27706	-1.0066	9	0.36615	T	0.2	-0.7116	2.265	0.04077	0.0998:0.1708:0.3786:0.3508	rs4872318;rs17792792;rs4872318	702;717	E9PEI0;Q69YH5	.;CDCA2_HUMAN	I	717;702;116	ENSP00000328228:V717I;ENSP00000370040:V702I	ENSP00000328228:V717I	V	+	1	0	CDCA2	25420248	0.001000	0.12720	0.003000	0.11579	0.011000	0.07611	0.451000	0.21779	0.261000	0.21753	-0.188000	0.12872	GTA	G|0.761;A|0.239	0.239	strong		0.393	CDCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216891.3	NM_152562	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802331	24802331	+	Silent	SNP	C	C	T	rs72770409	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:24802331C>T	ENST00000395799.3	+	6	2497	c.2368C>T	c.(2368-2370)Ctg>Ttg	p.L790L	TNRC6A_ENST00000315183.7_Silent_p.L790L	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	790	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		CAAACCTGCTCTGAGGTGGGG	0.498													C|||	93	0.0185703	0.0015	0.0288	5008	,	,		17897	0.0		0.0547	False		,,,				2504	0.0164				p.L790L		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2368T						PASS	.	C		36,4348		0,36,2156	35.0	37.0	36.0		2368	1.1	1.0	16	dbSNP_130	36	481,8113		14,453,3830	no	coding-synonymous	TNRC6A	NM_014494.2		14,489,5986	TT,TC,CC		5.5969,0.8212,3.9837		790/1963	24802331	517,12461	2192	4297	6489	SO:0001819	synonymous_variant	27327	exon6			CCTGCTCTGAGGT	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2368C>T	16.37:g.24802331C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	35	13	0.371429	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2																																																																																			C|0.966;T|0.034	0.034	strong		0.498	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
COL4A3BP	10087	hgsc.bcm.edu	37	5	74681773	74681773	+	Silent	SNP	T	T	C	rs698912	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:74681773T>C	ENST00000405807.4	-	13	1792	c.1371A>G	c.(1369-1371)gaA>gaG	p.E457E	COL4A3BP_ENST00000261415.7_Silent_p.E431E|COL4A3BP_ENST00000508692.1_5'Flank|COL4A3BP_ENST00000380494.5_Silent_p.E585E	NM_005713.2	NP_005704.1	Q9Y5P4	C43BP_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen) binding protein	457	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|ceramide metabolic process (GO:0006672)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi ceramide transport (GO:0035621)|heart morphogenesis (GO:0003007)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|lipid homeostasis (GO:0055088)|mitochondrion morphogenesis (GO:0070584)|muscle contraction (GO:0006936)|protein phosphorylation (GO:0006468)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ceramide binding (GO:0097001)|ceramide transporter activity (GO:0035620)|phosphatidylinositol-4-phosphate binding (GO:0070273)|protein kinase activity (GO:0004672)	p.E457E(1)		breast(1)|kidney(1)|large_intestine(5)|lung(4)|skin(3)|stomach(1)|urinary_tract(1)	16		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;1e-53)		AATTGCAGACTTCATGTCCTG	0.328													t|||	1451	0.289736	0.2655	0.1715	5008	,	,		15831	0.3313		0.2197	False		,,,				2504	0.4356				p.E585E		Atlas-SNP	.											COL4A3BP,NS,carcinoma,0,1	COL4A3BP	72	1	1	Substitution - coding silent(1)	stomach(1)	c.A1755G						PASS	.	T	,,	1142,3262	398.8+/-331.0	149,844,1209	65.0	58.0	61.0		1755,1371,1293	1.4	1.0	5	dbSNP_86	61	1805,6791	318.7+/-313.8	192,1421,2685	no	coding-synonymous,coding-synonymous,coding-synonymous	COL4A3BP	NM_001130105.1,NM_005713.2,NM_031361.2	,,	341,2265,3894	CC,CT,TT		20.9981,25.931,22.6692	,,	585/753,457/625,431/599	74681773	2947,10053	2202	4298	6500	SO:0001819	synonymous_variant	10087	exon14			GCAGACTTCATGT	AF136450	CCDS4028.1, CCDS4029.1, CCDS47235.1	5q13.3	2013-01-10	2007-06-08	2007-06-08	ENSG00000113163	ENSG00000113163		"""StAR-related lipid transfer (START) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2205	protein-coding gene	gene with protein product	"""ceramide transporter"", ""StAR-related lipid transfer (START) domain containing 11"""	604677				10212244	Standard	NM_001130105		Approved	GPBP, STARD11, CERT	uc003kdt.3	Q9Y5P4	OTTHUMG00000102068	ENST00000405807.4:c.1371A>G	5.37:g.74681773T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	83	0.988095	NM_001130105	A8K7S2|B3KUB7|Q53YV1|Q53YV2|Q96Q85|Q96Q88|Q9H2S7|Q9H2S8	Silent	SNP	ENST00000405807.4	37	CCDS4028.1																																																																																			T|0.743;C|0.257	0.257	strong		0.328	COL4A3BP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219875.2	NM_005713	
CD226	10666	hgsc.bcm.edu	37	18	67534642	67534642	+	Missense_Mutation	SNP	C	C	T	rs72481820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:67534642C>T	ENST00000280200.4	-	6	1104	c.836G>A	c.(835-837)aGa>aAa	p.R279K	CD226_ENST00000582621.1_Missense_Mutation_p.R279K|CD226_ENST00000581982.1_Missense_Mutation_p.R124K|CD226_ENST00000577287.1_Missense_Mutation_p.R124K	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	279	Poly-Arg.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				CTCTCTCCTTCTCCTTCTGGA	0.353													C|||	363	0.072484	0.0847	0.1009	5008	,	,		16801	0.0288		0.0865	False		,,,				2504	0.0665				p.R279K	NSCLC(184;838 2130 8673 21498 50749)	Atlas-SNP	.											.	CD226	51	.	0			c.G836A						PASS	.	C	LYS/ARG	332,4074	173.7+/-203.5	10,312,1881	222.0	220.0	221.0		836	2.8	0.8	18	dbSNP_130	221	622,7978	159.8+/-213.0	23,576,3701	yes	missense	CD226	NM_006566.2	26	33,888,5582	TT,TC,CC		7.2326,7.5352,7.3351	benign	279/337	67534642	954,12052	2203	4300	6503	SO:0001583	missense	10666	exon6			CTCCTTCTCCTTC	U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	16961	protein-coding gene	gene with protein product		605397	"""CD226 antigen"""			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.836G>A	18.37:g.67534642C>T	ENSP00000280200:p.Arg279Lys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	69	36	0.521739	NM_006566	B2R818	Missense_Mutation	SNP	ENST00000280200.4	37	CCDS11997.1	166	0.076007326007326	45	0.09146341463414634	31	0.0856353591160221	20	0.03496503496503497	70	0.09234828496042216	C	8.882	0.951907	0.18431	0.075352	0.072326	ENSG00000150637	ENST00000280200	T	0.27104	1.69	4.61	2.84	0.33178	.	0.289768	0.31963	N	0.006790	T	0.00468	0.0015	N	0.20986	0.625	0.41481	P	0.01183500000000004	B	0.28900	0.227	B	0.17979	0.02	T	0.17992	-1.0351	9	0.25106	T	0.35	.	8.0181	0.30393	0.0:0.8455:0.0:0.1545	.	279	Q15762	CD226_HUMAN	K	279	ENSP00000280200:R279K	ENSP00000280200:R279K	R	-	2	0	CD226	65685622	0.284000	0.24287	0.818000	0.32626	0.324000	0.28378	0.468000	0.22051	0.886000	0.36113	0.655000	0.94253	AGA	C|0.926;T|0.074	0.074	strong		0.353	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566	
CDH23	64072	hgsc.bcm.edu	37	10	73434888	73434888	+	Missense_Mutation	SNP	G	G	C	rs1227049	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:73434888G>C	ENST00000224721.6	+	14	1489	c.1484G>C	c.(1483-1485)gGc>gCc	p.G495A	CDH23_ENST00000299366.7_Missense_Mutation_p.G535A	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	490	Cadherin 5. {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						AATGATGCAGGCACCTTTGGG	0.582													G|||	928	0.185304	0.0113	0.1455	5008	,	,		21889	0.2887		0.1948	False		,,,				2504	0.3323				p.G490A		Atlas-SNP	.											.	CDH23	365	.	0			c.G1469C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	149,4055		5,139,1958	93.0	97.0	95.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1469,1469,1469	5.7	1.0	10	dbSNP_87	95	1387,7083		113,1161,2961	yes	missense,missense,missense	CDH23	NM_001171930.1,NM_001171931.1,NM_022124.5	60,60,60	118,1300,4919	CC,CG,GG		16.3754,3.5442,12.1193	probably-damaging,probably-damaging,probably-damaging	490/1382,490/1062,490/3355	73434888	1536,11138	2102	4235	6337	SO:0001583	missense	64072	exon14			ATGCAGGCACCTT	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.1484G>C	10.37:g.73434888G>C	ENSP00000224721:p.Gly495Ala	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	62	38	0.612903	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		365	0.1671245421245421	7	0.014227642276422764	46	0.1270718232044199	158	0.2762237762237762	154	0.20316622691292877	G	21.9	4.222763	0.79464	0.035442	0.163754	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000398828;ENST00000299366;ENST00000224721;ENST00000442677	.	.	.	5.72	5.72	0.89469	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.88310	2.945	0.09310	P	1.0	P;D;D	0.89917	0.855;1.0;1.0	P;D;D	0.91635	0.842;0.998;0.999	T	0.00210	-1.1916	8	0.66056	D	0.02	.	19.8786	0.96886	0.0:0.0:1.0:0.0	rs1227049;rs1665702;rs52829568;rs1227049	490;493;490	Q6P152;G3XCN8;Q9H251	.;.;CAD23_HUMAN	A	495;490;490;493;493;7	.	ENSP00000224721:G495A	G	+	2	0	CDH23	73104894	1.000000	0.71417	1.000000	0.80357	0.594000	0.36715	8.658000	0.91110	2.693000	0.91896	0.655000	0.94253	GGC	G|0.821;C|0.179	0.179	strong		0.582	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
NFASC	23114	hgsc.bcm.edu	37	1	204978704	204978704	+	Silent	SNP	G	G	A	rs55678495	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204978704G>A	ENST00000401399.1	+	27	3508	c.3309G>A	c.(3307-3309)gcG>gcA	p.A1103A	NFASC_ENST00000360049.4_Silent_p.A1032A|NFASC_ENST00000338515.6_Silent_p.A1120A|NFASC_ENST00000513543.1_Silent_p.A1032A|NFASC_ENST00000539706.1_Silent_p.A1037A|NFASC_ENST00000367172.4_Silent_p.A1210A|NFASC_ENST00000367170.4_Silent_p.A1131A|NFASC_ENST00000495396.1_3'UTR|NFASC_ENST00000404076.1_Silent_p.A1020A|NFASC_ENST00000367171.4_Silent_p.A1195A|NFASC_ENST00000404907.1_Silent_p.A1037A|NFASC_ENST00000339876.6_Silent_p.A1103A|NFASC_ENST00000338586.6_Silent_p.A1087A|NFASC_ENST00000367169.4_Silent_p.A934A			O94856	NFASC_HUMAN	neurofascin	1210	Thr-rich.				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)			ACAACCAAGCGGACATCGCCA	0.582													G|||	283	0.0565096	0.0045	0.0951	5008	,	,		17780	0.0179		0.1581	False		,,,				2504	0.0348				p.A1103A		Atlas-SNP	.											.	NFASC	396	.	0			c.G3309A						PASS	.	G	,,,	147,4259	102.1+/-140.7	2,143,2058	107.0	85.0	93.0		3309,3156,3111,3096	-6.4	0.4	1	dbSNP_129	93	1369,7231	265.6+/-286.2	109,1151,3040	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001160331.1,NM_001160332.1,NM_015090.3	,,,	111,1294,5098	AA,AG,GG		15.9186,3.3364,11.6562	,,,	1103/1241,1052/1190,1037/1175,1032/1170	204978704	1516,11490	2203	4300	6503	SO:0001819	synonymous_variant	23114	exon28			CCAAGCGGACATC	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.3309G>A	1.37:g.204978704G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	48	18	0.375	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	167|167	0.07646520146520147|0.07646520146520147	4|4	0.008130081300813009|0.008130081300813009	43|43	0.11878453038674033|0.11878453038674033	7|7	0.012237762237762238|0.012237762237762238	113|113	0.14907651715039577|0.14907651715039577	G|G	9.955|9.955	1.221317|1.221317	0.22457|0.22457	0.033364|0.033364	0.159186|0.159186	ENSG00000163531|ENSG00000163531	ENST00000413225|ENST00000367173;ENST00000425360	.|.	.|.	.|.	5.26|5.26	-6.38|-6.38	0.01957|0.01957	.|.	.|.	.|.	.|.	.|.	T|T	0.00073|0.00073	0.0002|0.0002	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999991|0.9999999999999991	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.21177|0.21177	-1.0253|-1.0253	3|3	.|.	.|.	.|.	.|.	0.6603|0.6603	0.00842|0.00842	0.3737:0.1935:0.2328:0.2|0.3737:0.1935:0.2328:0.2	rs55678495|rs55678495	.|.	.|.	.|.	R|Q	150|904;161	.|.	.|.	G|R	+|+	1|2	0|0	NFASC|NFASC	203245327|203245327	0.000000|0.000000	0.05858|0.05858	0.361000|0.361000	0.25849|0.25849	0.995000|0.995000	0.86356|0.86356	-2.169000|-2.169000	0.01269|0.01269	-2.009000|-2.009000	0.00954|0.00954	-0.142000|-0.142000	0.14014|0.14014	GGA|CGG	G|0.891;A|0.109	0.109	strong		0.582	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
SERPINF1	5176	hgsc.bcm.edu	37	17	1674429	1674429	+	Silent	SNP	T	T	C	rs8074840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1674429T>C	ENST00000254722.4	+	4	553	c.390T>C	c.(388-390)acT>acC	p.T130T	SERPINF1_ENST00000571870.1_3'UTR	NM_002615.5	NP_002606.3	P36955	PEDF_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1	130					aging (GO:0007568)|cell proliferation (GO:0008283)|kidney development (GO:0001822)|multicellular organismal development (GO:0007275)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of inflammatory response (GO:0050728)|positive regulation of neurogenesis (GO:0050769)|regulation of proteolysis (GO:0030162)|response to glucocorticoid (GO:0051384)|response to retinoic acid (GO:0032526)|short-term memory (GO:0007614)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	16						ACACGGTCACTGCCCCCCAGA	0.547													T|||	1504	0.300319	0.1203	0.3631	5008	,	,		15428	0.4067		0.3101	False		,,,				2504	0.3793				p.T130T		Atlas-SNP	.											SERPINF1,NS,carcinoma,0,1	SERPINF1	31	1	0			c.T390C						PASS	.	T		695,3711	291.8+/-281.7	57,581,1565	76.0	67.0	70.0		390	-8.1	0.5	17	dbSNP_116	70	2530,6070	413.2+/-351.0	357,1816,2127	no	coding-synonymous	SERPINF1	NM_002615.5		414,2397,3692	CC,CT,TT		29.4186,15.7739,24.7962		130/419	1674429	3225,9781	2203	4300	6503	SO:0001819	synonymous_variant	5176	exon4			GGTCACTGCCCCC	M76979	CCDS11012.1	17p13.3	2014-02-18	2005-08-18		ENSG00000132386	ENSG00000132386		"""Serine (or cysteine) peptidase inhibitors"""	8824	protein-coding gene	gene with protein product	"""pigment epithelium-derived factor"", ""proliferation-inducing protein 35"""	172860	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1"""	PEDF		8434014, 24172014	Standard	NM_002615		Approved	EPC-1, PIG35	uc002ftl.3	P36955	OTTHUMG00000090571	ENST00000254722.4:c.390T>C	17.37:g.1674429T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	79	45	0.56962	NM_002615	F1T092|Q13236|Q2TU83|Q96CT1|Q96R01|Q9BWA4	Silent	SNP	ENST00000254722.4	37	CCDS11012.1																																																																																			T|0.735;C|0.265	0.265	strong		0.547	SERPINF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207109.4	NM_002615	
PLA2G2D	26279	hgsc.bcm.edu	37	1	20442054	20442054	+	Missense_Mutation	SNP	T	T	C	rs584367	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:20442054T>C	ENST00000375105.3	-	3	296	c.238A>G	c.(238-240)Agc>Ggc	p.S80G		NM_012400.2	NP_036532.1	Q9UNK4	PA2GD_HUMAN	phospholipase A2, group IID	80			S -> G (in dbSNP:rs584367). {ECO:0000269|PubMed:10455175, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.4}.		glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			endometrium(1)|lung(2)	3		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00526)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;8.01e-05)|Kidney(64;0.000175)|GBM - Glioblastoma multiforme(114;0.000798)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TTGTAGATGCTGCACCCCTGG	0.587										Multiple Myeloma(11;0.12)			C|||	3853	0.769369	0.966	0.6974	5008	,	,		19128	0.7569		0.5934	False		,,,				2504	0.7485				p.S80G	Melanoma(60;742 1548 31762 39240)	Atlas-SNP	.											.	PLA2G2D	7	.	0			c.A238G						PASS	.	C	GLY/SER	3979,427	206.8+/-228.3	1800,379,24	129.0	114.0	119.0		238	-4.4	0.0	1	dbSNP_83	119	5007,3593	520.4+/-379.7	1435,2137,728	yes	missense	PLA2G2D	NM_012400.2	56	3235,2516,752	CC,CT,TT		41.7791,9.6913,30.9088	benign	80/146	20442054	8986,4020	2203	4300	6503	SO:0001583	missense	26279	exon3			AGATGCTGCACCC	AF112982	CCDS203.1, CCDS72721.1	1p36.12	2008-09-19			ENSG00000117215	ENSG00000117215	3.1.1.4		9033	protein-coding gene	gene with protein product		605630				10455175	Standard	NM_012400		Approved	sPLA2S	uc001bcz.4	Q9UNK4	OTTHUMG00000002701	ENST00000375105.3:c.238A>G	1.37:g.20442054T>C	ENSP00000364246:p.Ser80Gly	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	114	103	0.903509	NM_012400	A8K2Z1|B1AEL9|Q9UK01	Missense_Mutation	SNP	ENST00000375105.3	37	CCDS203.1	1580	0.7234432234432234	464	0.943089430894309	242	0.6685082872928176	434	0.7587412587412588	440	0.5804749340369393	C	0.323	-0.960936	0.02249	0.903087	0.582209	ENSG00000117215	ENST00000375105	T	0.27256	1.68	5.6	-4.38	0.03622	Phospholipase A2 (3);	2.250350	0.01492	N	0.017155	T	0.00012	0.0000	N	0.17278	0.47	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36407	-0.9749	9	0.07325	T	0.83	-0.4767	1.1808	0.01844	0.1934:0.1781:0.1844:0.4441	rs584367;rs1751980;rs17354755;rs59656386;rs584367	80	Q9UNK4	PA2GD_HUMAN	G	80	ENSP00000364246:S80G	ENSP00000364246:S80G	S	-	1	0	PLA2G2D	20314641	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.253000	0.08794	-0.914000	0.03827	-2.488000	0.00195	AGC	C|0.710;N|0.000	0.710	strong		0.587	PLA2G2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007683.1		
SEC14L4	284904	hgsc.bcm.edu	37	22	30891250	30891250	+	Silent	SNP	T	T	C	rs9606738	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30891250T>C	ENST00000255858.7	-	5	497	c.414A>G	c.(412-414)caA>caG	p.Q138Q	RP4-539M6.14_ENST00000442126.1_RNA|SEC14L4_ENST00000540456.1_Silent_p.Q123Q|SEC14L4_ENST00000392772.2_Silent_p.Q84Q|SEC14L4_ENST00000381982.3_Silent_p.Q138Q|RP4-539M6.14_ENST00000610156.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	138	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CCTTCTGAGTTTGCAGCTCAC	0.617													C|||	803	0.160343	0.1505	0.2867	5008	,	,		19102	0.0397		0.2296	False		,,,				2504	0.137				p.Q138Q		Atlas-SNP	.											.	SEC14L4	43	.	0			c.A414G						PASS	.	C	,	732,3674		57,618,1528	47.0	41.0	43.0		414,414	2.8	0.3	22	dbSNP_119	43	1948,6652		219,1510,2571	no	coding-synonymous,coding-synonymous	SEC14L4	NM_001161368.1,NM_174977.3	,	276,2128,4099	CC,CT,TT		22.6512,16.6137,20.6059	,	138/361,138/407	30891250	2680,10326	2203	4300	6503	SO:0001819	synonymous_variant	284904	exon5			CTGAGTTTGCAGC	AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.414A>G	22.37:g.30891250T>C		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001161368	A5D6W7|A6NCV4	Silent	SNP	ENST00000255858.7	37	CCDS13878.1																																																																																			T|0.824;C|0.176	0.176	strong		0.617	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1	NM_174977	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103124135	103124135	+	Silent	SNP	T	T	G	rs11225634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:103124135T>G	ENST00000375735.2	+	66	10308	c.10164T>G	c.(10162-10164)acT>acG	p.T3388T	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Silent_p.T3395T	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3388	AAA 5. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCATTGTTACTGAGGTTAACT	0.348													T|||	907	0.18111	0.3752	0.1254	5008	,	,		15809	0.0933		0.1252	False		,,,				2504	0.1063				p.T3395T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10185G						PASS	.	T	,	1168,2482		189,790,846	109.0	105.0	106.0		10185,10164	0.5	1.0	11	dbSNP_120	106	955,7229		63,829,3200	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	252,1619,4046	GG,GT,TT		11.6691,32.0,17.9398	,	3395/4315,3388/4308	103124135	2123,9711	1825	4092	5917	SO:0001819	synonymous_variant	79659	exon67			TGTTACTGAGGTT	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10164T>G	11.37:g.103124135T>G		Somatic	270	1	0.0037037		WXS	Illumina HiSeq	Phase_I	199	93	0.467337	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.824;G|0.176	0.176	strong		0.348	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
URB1	9875	hgsc.bcm.edu	37	21	33719400	33719400	+	Silent	SNP	A	A	G	rs9981151	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:33719400A>G	ENST00000382751.3	-	22	3848	c.3733T>C	c.(3733-3735)Ttg>Ctg	p.L1245L		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1245						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						AACCACAGCAAGTGGGTGCAG	0.672													G|||	1118	0.223243	0.4796	0.1023	5008	,	,		17504	0.1379		0.1223	False		,,,				2504	0.1544				p.L1245L		Atlas-SNP	.											.	URB1	176	.	0			c.T3733C						PASS	.	G		587,797		132,323,237	18.0	23.0	22.0		3733	2.9	1.0	21	dbSNP_119	22	408,2774		30,348,1213	no	coding-synonymous	URB1	NM_014825.2		162,671,1450	GG,GA,AA		12.8221,42.4133,21.7915		1245/2272	33719400	995,3571	692	1591	2283	SO:0001819	synonymous_variant	9875	exon22			ACAGCAAGTGGGT	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.3733T>C	21.37:g.33719400A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	37	20	0.540541	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			A|0.788;G|0.212	0.212	strong		0.672	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
WDR11	55717	hgsc.bcm.edu	37	10	122649482	122649482	+	Silent	SNP	A	A	G	rs2289337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:122649482A>G	ENST00000263461.6	+	18	2550	c.2304A>G	c.(2302-2304)gcA>gcG	p.A768A	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.A768A(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AATTAATAGCAATGTACAATG	0.398													A|||	987	0.197085	0.2579	0.1628	5008	,	,		15097	0.0962		0.2207	False		,,,				2504	0.2188				p.A768A		Atlas-SNP	.											WDR11,NS,carcinoma,0,1	WDR11	95	1	1	Substitution - coding silent(1)	stomach(1)	c.A2304G						PASS	.	A		1230,3176	420.2+/-338.9	180,870,1153	113.0	107.0	109.0		2304	-2.9	1.0	10	dbSNP_100	109	1909,6691	338.5+/-322.8	216,1477,2607	yes	coding-synonymous	WDR11	NM_018117.11		396,2347,3760	GG,GA,AA		22.1977,27.9165,24.135		768/1225	122649482	3139,9867	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon18			AATAGCAATGTAC	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2304A>G	10.37:g.122649482A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	66	35	0.530303	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			T|0.005;G|0.229	0.229	strong		0.398	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
SLC16A2	6567	hgsc.bcm.edu	37	X	73641569	73641569	+	Missense_Mutation	SNP	T	T	C	rs6647476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:73641569T>C	ENST00000587091.1	+	1	274	c.97T>C	c.(97-99)Tct>Cct	p.S33P	SLC16A2_ENST00000276033.5_Missense_Mutation_p.S107P	NM_006517.4	NP_006508.2	P36021	MOT8_HUMAN	solute carrier family 16, member 2 (thyroid hormone transporter)	33					monocarboxylic acid transport (GO:0015718)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)|transporter activity (GO:0005215)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	21					L-Leucine(DB00149)|L-Tryptophan(DB00150)|L-Tyrosine(DB00135)|Levothyroxine(DB00451)|Liotrix(DB01583)|Pyruvic acid(DB00119)	Agagccggagtctgagccgga	0.741													C|||	2506	0.663841	0.531	0.3084	3775	,	,		5534	0.7361		0.333	False		,,,				2504	0.5245				p.S33P		Atlas-SNP	.											.	SLC16A2	54	.	0			c.T97C						PASS	.	-	PRO/SER	2247,1352		641,640,325,282,148	6.0	6.0	6.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	319		0.1	X	dbSNP_116	6	2383,4050		356,1012,659,1004,1030	yes	missense	SLC16A2	NM_006517.3	74	997,1652,984,1286,1178	CC,CT,C,TT,T		37.0434,37.566,46.1523	possibly-damaging	107/614	73641569	4630,5402	2036	4061	6097	SO:0001583	missense	6567	exon1			CCGGAGTCTGAGC		CCDS14426.1, CCDS14426.2	Xq13.2	2013-05-22	2012-03-20		ENSG00000147100	ENSG00000147100		"""Solute carriers"""	10923	protein-coding gene	gene with protein product		300095	"""solute carrier family 16 (monocarboxylic acid transporters), member 2 (putative transporter)"", ""Allan-Herndon-Dudley syndrome"", ""solute carrier family 16 (monocarboxylic acid transporters), member 2"", ""mental retardation, X-linked 22"", ""solute carrier family 16, member 2 (monocarboxylic acid transporter 8)"""	DXS128, AHDS, MRX22		7981683, 12871948, 15889350	Standard	NM_006517		Approved	XPCT, MCT8, MCT7	uc031tjy.1	P36021	OTTHUMG00000021857	ENST00000587091.1:c.97T>C	X.37:g.73641569T>C	ENSP00000465734:p.Ser33Pro	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	15	14	0.933333	NM_006517	Q7Z797	Missense_Mutation	SNP	ENST00000587091.1	37	CCDS14426.2	1048	0.6317058468957203	190	0.5828220858895705	71	0.2305194805194805	278	0.9586206896551724	182	0.3063973063973064	C	0.001	-3.547578	0.00009	0.62434	0.370434	ENSG00000147100	ENST00000276033	T	0.69306	-0.39	.	.	.	.	0.660363	0.13427	N	0.388737	T	0.00012	0.0000	N	0.00419	-1.52	0.80722	P	0.0	P	0.47604	0.898	B	0.42959	0.403	T	0.50651	-0.8803	7	0.18710	T	0.47	.	.	.	.	rs6647476	33	P36021	MOT8_HUMAN	P	107	ENSP00000276033:S107P	ENSP00000276033:S107P	S	+	1	0	SLC16A2	73558294	0.057000	0.20700	0.097000	0.21041	0.047000	0.14425	-0.390000	0.07332	-0.420000	0.07427	0.000000	0.15137	TCT	T|0.366;C|0.634	0.634	strong		0.741	SLC16A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057266.3		
IL4R	3566	hgsc.bcm.edu	37	16	27373980	27373980	+	Missense_Mutation	SNP	C	C	T	rs1805013	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:27373980C>T	ENST00000395762.2	+	11	1566	c.1307C>T	c.(1306-1308)tCg>tTg	p.S436L	IL4R_ENST00000380922.3_Missense_Mutation_p.S421L|IL4R_ENST00000543915.2_Missense_Mutation_p.S436L|IL4R_ENST00000170630.2_Missense_Mutation_p.S436L	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	436			S -> L (in dbSNP:rs1805013). {ECO:0000269|PubMed:11285129, ECO:0000269|PubMed:9070874, ECO:0000269|Ref.5}.		defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						CTTCCACCTTCGGGAAGTACG	0.622													C|||	124	0.0247604	0.0257	0.0202	5008	,	,		19671	0.0		0.0398	False		,,,				2504	0.0368				p.S436L		Atlas-SNP	.											.	IL4R	70	.	0			c.C1307T						PASS	.	C	LEU/SER	106,4288	84.4+/-122.9	1,104,2092	71.0	70.0	71.0		1307	-6.2	0.0	16	dbSNP_89	71	386,8214	124.8+/-183.5	6,374,3920	yes	missense	IL4R	NM_000418.2	145	7,478,6012	TT,TC,CC		4.4884,2.4124,3.7864	benign	436/826	27373980	492,12502	2197	4300	6497	SO:0001583	missense	3566	exon11			CACCTTCGGGAAG	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.1307C>T	16.37:g.27373980C>T	ENSP00000379111:p.Ser436Leu	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	97	41	0.42268	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	55	0.025183150183150184	15	0.03048780487804878	8	0.022099447513812154	0	0.0	32	0.04221635883905013	C	5.199	0.222231	0.09863	0.024124	0.044884	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.10005	2.92;2.92;2.92;2.92	5.31	-6.23	0.02052	.	17.929300	0.00166	N	0.000000	T	0.00967	0.0032	N	0.10874	0.06	0.09310	N	1	B;B;B	0.18968	0.032;0.014;0.014	B;B;B	0.08055	0.003;0.003;0.003	T	0.39375	-0.9617	10	0.02654	T	1	-27.3202	8.5926	0.33697	0.1059:0.29:0.0:0.6041	rs1805013;rs3883895;rs17513763;rs1805013	421;436;436	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	L	436;436;421;436	ENSP00000379111:S436L;ENSP00000441667:S436L;ENSP00000370309:S421L;ENSP00000170630:S436L	ENSP00000170630:S436L	S	+	2	0	IL4R	27281481	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.529000	0.02223	-0.982000	0.03515	-2.945000	0.00085	TCG	C|0.958;T|0.042	0.042	strong		0.622	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
ZNF138	7697	hgsc.bcm.edu	37	7	64291976	64291976	+	Missense_Mutation	SNP	G	G	A	rs10949946	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:64291976G>A	ENST00000359735.3	+	4	532	c.185G>A	c.(184-186)gGa>gAa	p.G62E	ZNF138_ENST00000440155.2_Missense_Mutation_p.G93E|ZNF138_ENST00000494380.1_3'UTR|ZNF138_ENST00000437743.1_Missense_Mutation_p.G87E|ZNF138_ENST00000307355.7_Missense_Mutation_p.G119E|ZNF138_ENST00000397136.2_Missense_Mutation_p.G62E|ZNF138_ENST00000440598.1_3'UTR|ZNF138_ENST00000430838.2_3'UTR	NM_001271637.1|NM_001271639.1	NP_001258566.1|NP_001258568.1	P52744	ZN138_HUMAN	zinc finger protein 138	62			G -> E (in dbSNP:rs10949946). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:7557990}.		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.G62E(1)		kidney(1)|large_intestine(3)|lung(2)|stomach(1)	7		Lung NSC(55;0.0795)|all_lung(88;0.18)				GAGTGTAAGGGACACCAAGGA	0.308													G|||	1638	0.327077	0.1316	0.4308	5008	,	,		17790	0.3829		0.4463	False		,,,				2504	0.3374				p.G119E		Atlas-SNP	.											ZNF138_ENST00000440155,NS,carcinoma,-1,3	ZNF138	43	3	1	Substitution - Missense(1)	stomach(1)	c.G356A						PASS	.	A	,GLU/GLY	771,3633		75,621,1506	74.0	74.0	74.0		,278	-1.7	0.0	7	dbSNP_120	74	3962,4638		930,2102,1268	no	utr-3,missense	ZNF138	NM_001160183.1,NM_006524.2	,98	1005,2723,2774	AA,AG,GG		46.0698,17.5068,36.3965	,benign	,93/294	64291976	4733,8271	2202	4300	6502	SO:0001583	missense	7697	exon4			GTAAGGGACACCA	U09847	CCDS34645.1, CCDS34645.2, CCDS55115.1, CCDS64659.1, CCDS64660.1, CCDS64661.1, CCDS75607.1	7q11.21	2013-01-08	2005-07-11		ENSG00000197008	ENSG00000197008		"""Zinc fingers, C2H2-type"", ""-"""	12922	protein-coding gene	gene with protein product		604080	"""zinc finger protein 138 (clone pHZ-32)"""				Standard	NM_006524		Approved	pHZ-32	uc031sxl.1	P52744	OTTHUMG00000156603	ENST00000359735.3:c.185G>A	7.37:g.64291976G>A	ENSP00000352770:p.Gly62Glu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	64	29	0.453125	NM_001271639	B4DFX2|B4DP87|E9PHI7|E9PHK7	Missense_Mutation	SNP	ENST00000359735.3	37		787	0.36034798534798534	67	0.13617886178861788	162	0.44751381215469616	229	0.40034965034965037	329	0.4340369393139842	.	0.355	-0.942902	0.02322	0.175068	0.460698	ENSG00000197008	ENST00000307355;ENST00000359735;ENST00000440155;ENST00000437743;ENST00000397136	T;T;T;T;T	0.05717	3.58;3.4;3.52;3.5;3.4	0.85	-1.7	0.08159	.	.	.	.	.	T	0.00012	0.0000	N	0.10837	0.055	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.10450	0.005;0.003;0.005	T	0.41945	-0.9480	8	0.38643	T	0.18	.	4.9998	0.14259	0.2573:0.0:0.7426:0.0	rs10949946;rs57546729;rs10949946	93;87;62	E9PHI7;E7EWC5;P52744	.;.;ZN138_HUMAN	E	119;62;93;87;62	ENSP00000303533:G119E;ENSP00000352770:G62E;ENSP00000407262:G93E;ENSP00000399528:G87E;ENSP00000380325:G62E	ENSP00000303533:G119E	G	+	2	0	ZNF138	63929411	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.464000	0.06688	-1.056000	0.03205	-1.051000	0.02340	GGA	G|0.629;A|0.371	0.371	strong		0.308	ZNF138-201	KNOWN	basic	protein_coding	protein_coding		NM_006524	
PLEKHA4	57664	hgsc.bcm.edu	37	19	49340661	49340661	+	Missense_Mutation	SNP	C	C	A	rs35965411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49340661C>A	ENST00000263265.6	-	20	2780	c.2225G>T	c.(2224-2226)gGa>gTa	p.G742V	HSD17B14_ENST00000599157.1_5'Flank|PLEKHA4_ENST00000355496.5_3'UTR|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	742			G -> V (in dbSNP:rs35965411).			cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGGACCTCCTCCACGCCCACT	0.706													.|||	489	0.0976438	0.2716	0.0375	5008	,	,		11132	0.001		0.0159	False		,,,				2504	0.089				p.G742V		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.G2225T						PASS	.		,VAL/GLY	832,3560		77,678,1441	24.0	28.0	26.0		,2225	4.2	0.1	19	dbSNP_126	26	92,8490		0,92,4199	yes	utr-3,missense	PLEKHA4	NM_001161354.1,NM_020904.2	,109	77,770,5640	AA,AC,CC		1.072,18.9435,7.1219	,possibly-damaging	,742/780	49340661	924,12050	2196	4291	6487	SO:0001583	missense	57664	exon20			CCTCCTCCACGCC	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.2225G>T	19.37:g.49340661C>A	ENSP00000263265:p.Gly742Val	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	79	39	0.493671	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	149	0.06822344322344322	120	0.24390243902439024	17	0.04696132596685083	0	0.0	12	0.0158311345646438	c	15.22	2.769097	0.49680	0.189435	0.01072	ENSG00000105559	ENST00000263265	T	0.10477	2.87	4.22	4.22	0.49857	.	0.000000	0.38381	N	0.001702	T	0.00012	0.0000	N	0.24115	0.695	0.19575	P	0.9999659469	P	0.41313	0.745	B	0.37346	0.247	T	0.44667	-0.9313	9	0.87932	D	0	.	12.3514	0.55151	0.0:1.0:0.0:0.0	rs35965411;rs61755450	742	Q9H4M7	PKHA4_HUMAN	V	742	ENSP00000263265:G742V	ENSP00000263265:G742V	G	-	2	0	PLEKHA4	54032473	0.000000	0.05858	0.056000	0.19401	0.173000	0.22820	-0.053000	0.11846	2.385000	0.81259	0.450000	0.29827	GGA	C|0.932;A|0.068	0.068	strong		0.706	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
SETBP1	26040	hgsc.bcm.edu	37	18	42530295	42530295	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:42530295G>A	ENST00000282030.5	+	4	1286	c.990G>A	c.(988-990)acG>acA	p.T330T		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	330						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)		AACCACCTACGGTGGGCAGCA	0.527									Schinzel-Giedion syndrome																												p.T330T		Atlas-SNP	.											.	SETBP1	577	.	0			c.G990A						PASS	.						68.0	74.0	72.0					18																	42530295		2202	4300	6502	SO:0001819	synonymous_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ACCTACGGTGGGC	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.990G>A	18.37:g.42530295G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	35	0.583333	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	37	CCDS11923.2																																																																																			.	.	none		0.527	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
COL4A4	1286	hgsc.bcm.edu	37	2	227896976	227896976	+	Silent	SNP	C	C	T	rs10203363	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227896976C>T	ENST00000396625.3	-	39	3801	c.3594G>A	c.(3592-3594)ggG>ggA	p.G1198G	COL4A4_ENST00000329662.7_Silent_p.G1198G	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	1198	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		GACCAGGTGGCCCCACATCAT	0.493													C|||	2479	0.495008	0.5613	0.4769	5008	,	,		18481	0.4028		0.4364	False		,,,				2504	0.5736				p.G1198G		Atlas-SNP	.											.	COL4A4	215	.	0			c.G3594A						PASS	.	C		1929,1773		493,943,415	35.0	36.0	36.0		3594	-3.7	1.0	2	dbSNP_119	36	3443,4761		726,1991,1385	no	coding-synonymous	COL4A4	NM_000092.4		1219,2934,1800	TT,TC,CC		41.9673,47.893,45.1201		1198/1691	227896976	5372,6534	1851	4102	5953	SO:0001819	synonymous_variant	1286	exon39			AGGTGGCCCCACA		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.3594G>A	2.37:g.227896976C>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	22	0.314286	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			C|0.544;T|0.456	0.456	strong		0.493	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
OVCH1	341350	hgsc.bcm.edu	37	12	29642573	29642573	+	Missense_Mutation	SNP	A	A	C	rs967181	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:29642573A>C	ENST00000318184.5	-	6	681	c.682T>G	c.(682-684)Tgg>Ggg	p.W228G		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	228	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		W -> G (in dbSNP:rs967181).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					TCCATTCCCCAATCAGGGAAG	0.507													C|||	2116	0.422524	0.3585	0.3012	5008	,	,		19465	0.5685		0.4692	False		,,,				2504	0.3967				p.W228G		Atlas-SNP	.											OVCH1,colon,carcinoma,0,1	OVCH1	195	1	0			c.T682G						PASS	.	C	GLY/TRP	1361,2521		229,903,809	80.0	77.0	78.0		682	0.1	0.0	12	dbSNP_86	78	3578,4670		802,1974,1348	yes	missense	OVCH1	NM_183378.2	184	1031,2877,2157	CC,CA,AA		43.3802,35.0592,40.7172	benign	228/1135	29642573	4939,7191	1941	4124	6065	SO:0001583	missense	341350	exon6			TTCCCCAATCAGG	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.682T>G	12.37:g.29642573A>C	ENSP00000326708:p.Trp228Gly	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	89	49	0.550562	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		946	0.43315018315018317	170	0.34552845528455284	101	0.27900552486187846	323	0.5646853146853147	352	0.46437994722955145	C	0	-2.714028	0.00093	0.350592	0.433802	ENSG00000187950	ENST00000318184	D	0.86230	-2.09	2.07	0.0831	0.14432	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	N	0.00014	-2.905	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.39251	-0.9623	8	0.02654	T	1	.	1.0202	0.01516	0.2314:0.3908:0.2268:0.151	rs967181;rs57245294;rs967181	228	Q7RTY7	OVCH1_HUMAN	G	228	ENSP00000326708:W228G	ENSP00000326708:W228G	W	-	1	0	OVCH1	29533840	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.817000	0.27281	-0.301000	0.08882	-0.987000	0.02553	TGG	A|0.579;C|0.421	0.421	strong		0.507	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
TAF1C	9013	hgsc.bcm.edu	37	16	84215390	84215390	+	Silent	SNP	T	T	C	rs2230127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84215390T>C	ENST00000567759.1	-	8	1178	c.996A>G	c.(994-996)gcA>gcG	p.A332A	TAF1C_ENST00000341690.6_Silent_p.A239A|TAF1C_ENST00000566732.1_Silent_p.A306A|TAF1C_ENST00000378541.4_Silent_p.A332A|TAF1C_ENST00000541676.1_Silent_p.A239A|TAF1C_ENST00000570117.1_5'UTR	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	332					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)	p.A332A(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						CCACCTGCATTGCCTGCAGAA	0.632													T|||	1663	0.332069	0.2413	0.4337	5008	,	,		17008	0.377		0.3638	False		,,,				2504	0.3037				p.A332A		Atlas-SNP	.											TAF1C,NS,carcinoma,0,1	TAF1C	60	1	1	Substitution - coding silent(1)	stomach(1)	c.A996G						PASS	.	T	,	1173,3227	411.1+/-335.6	156,861,1183	64.0	63.0	63.0		996,717	3.6	1.0	16	dbSNP_98	63	3323,5277	492.3+/-373.3	672,1979,1649	no	coding-synonymous,coding-synonymous	TAF1C	NM_005679.3,NM_139353.2	,	828,2840,2832	CC,CT,TT		38.6395,26.6591,34.5846	,	332/870,239/776	84215390	4496,8504	2200	4300	6500	SO:0001819	synonymous_variant	9013	exon8			CTGCATTGCCTGC	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.996A>G	16.37:g.84215390T>C		Somatic	191	1	0.0052356		WXS	Illumina HiSeq	Phase_I	208	208	1	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Silent	SNP	ENST00000567759.1	37	CCDS32496.1																																																																																			T|0.654;C|0.346	0.346	strong		0.632	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
OR10H2	26538	hgsc.bcm.edu	37	19	15838967	15838967	+	Silent	SNP	G	G	A	rs2285955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15838967G>A	ENST00000305899.3	+	1	134	c.114G>A	c.(112-114)acG>acA	p.T38T		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	38						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)					ACCTGTTCACGCTGCTGGGCA	0.587													G|||	1755	0.350439	0.233	0.3112	5008	,	,		22410	0.3135		0.4394	False		,,,				2504	0.4836				p.T38T		Atlas-SNP	.											OR10H2,NS,carcinoma,+1,1	OR10H2	59	1	0			c.G114A						scavenged	.	G		1225,3181		174,877,1152	237.0	198.0	211.0		114	-5.8	1.0	19	dbSNP_100	211	3845,4751		870,2105,1323	no	coding-synonymous	OR10H2	NM_013939.2		1044,2982,2475	AA,AG,GG		44.7301,27.803,38.994		38/316	15838967	5070,7932	2203	4298	6501	SO:0001819	synonymous_variant	26538	exon1			GTTCACGCTGCTG	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.114G>A	19.37:g.15838967G>A		Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	231	100	0.4329	NM_013939	Q6IFQ1|Q96R58	Silent	SNP	ENST00000305899.3	37	CCDS12333.1																																																																																			G|0.611;A|0.389	0.389	strong		0.587	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
CRTC1	23373	hgsc.bcm.edu	37	19	18876258	18876258	+	Missense_Mutation	SNP	G	G	A	rs36070283	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18876258G>A	ENST00000321949.8	+	9	957	c.931G>A	c.(931-933)Gtc>Atc	p.V311I	CRTC1_ENST00000594658.1_Missense_Mutation_p.V270I|CRTC1_ENST00000338797.6_Missense_Mutation_p.V327I|CRTC1_ENST00000601916.1_Missense_Mutation_p.V236I	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1										CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						CCCAGCTGGCGTCAGCCCCCT	0.637													G|||	150	0.0299521	0.0045	0.0447	5008	,	,		16196	0.003		0.0964	False		,,,				2504	0.0133				p.V327I		Atlas-SNP	.											.	CRTC1	88	.	0			c.G979A						PASS	.	G	ILE/VAL,ILE/VAL	68,4338	63.5+/-100.7	0,68,2135	112.0	108.0	109.0		979,931	0.9	0.2	19	dbSNP_126	109	870,7730	196.5+/-241.4	31,808,3461	yes	missense,missense	CRTC1	NM_001098482.1,NM_015321.2	29,29	31,876,5596	AA,AG,GG		10.1163,1.5433,7.2121	possibly-damaging,possibly-damaging	327/651,311/635	18876258	938,12068	2203	4300	6503	SO:0001583	missense	23373	exon10			GCTGGCGTCAGCC	AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"""transducer of regulated cAMP response element-binding protein"""	607536	"""mucoepidermoid carcinoma translocated 1"""	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.931G>A	19.37:g.18876258G>A	ENSP00000323332:p.Val311Ile	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	48	0.648649	NM_001098482		Missense_Mutation	SNP	ENST00000321949.8	37	CCDS32963.1	106	0.048534798534798536	4	0.008130081300813009	19	0.052486187845303865	1	0.0017482517482517483	82	0.10817941952506596	G	9.395	1.076611	0.20227	0.015433	0.101163	ENSG00000105662	ENST00000262813;ENST00000338797;ENST00000321949	T;T	0.11277	2.8;2.79	4.38	0.937	0.19494	.	1.378320	0.04748	N	0.424061	T	0.00210	0.0006	L	0.50333	1.59	0.27724	P	0.9450208	B;B;B	0.19583	0.037;0.018;0.01	B;B;B	0.16289	0.014;0.015;0.005	T	0.38415	-0.9662	9	0.22109	T	0.4	-21.4531	5.8943	0.18931	0.172:0.0:0.6749:0.1531	rs36070283;rs61750059	311;327;311	Q6UUV9-3;Q6UUV9-2;Q6UUV9	.;.;CRTC1_HUMAN	I	311;327;311	ENSP00000345001:V327I;ENSP00000323332:V311I	ENSP00000262813:V311I	V	+	1	0	CRTC1	18737258	0.989000	0.36119	0.223000	0.23860	0.470000	0.32858	1.967000	0.40491	0.076000	0.16826	-0.258000	0.10820	GTC	G|0.935;A|0.065	0.065	strong		0.637	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021	
SERGEF	26297	hgsc.bcm.edu	37	11	17809724	17809724	+	Missense_Mutation	SNP	T	T	C	rs1528	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:17809724T>C	ENST00000265965.5	-	11	1436	c.1285A>G	c.(1285-1287)Aaa>Gaa	p.K429E	SERGEF_ENST00000528200.1_3'UTR	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	429			K -> E (in dbSNP:rs1528).		negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						TCCATGGCTTTCTGAGATTCA	0.517													C|||	638	0.127396	0.2156	0.0663	5008	,	,		20730	0.002		0.1243	False		,,,				2504	0.184				p.K429E		Atlas-SNP	.											.	SERGEF	38	.	0			c.A1285G						PASS	.	C	GLU/LYS	769,3631	753.2+/-412.4	70,629,1501	170.0	159.0	163.0		1285	3.1	0.9	11	dbSNP_36	163	942,7644	775.4+/-407.7	48,846,3399	yes	missense	SERGEF	NM_012139.2	56	118,1475,4900	CC,CT,TT		10.9713,17.4773,13.1757	benign	429/459	17809724	1711,11275	2200	4293	6493	SO:0001583	missense	26297	exon11			TGGCTTTCTGAGA	AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.1285A>G	11.37:g.17809724T>C	ENSP00000265965:p.Lys429Glu	Somatic	329	0	0		WXS	Illumina HiSeq	Phase_I	360	164	0.455556	NM_012139	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	37	CCDS7828.1	220	0.10073260073260074	91	0.18495934959349594	26	0.0718232044198895	1	0.0017482517482517483	102	0.1345646437994723	C	8.959	0.970059	0.18659	0.174773	0.109713	ENSG00000129158	ENST00000265965	T	0.37411	1.2	4.03	3.12	0.35913	.	0.379360	0.22983	N	0.053282	T	0.00039	0.0001	N	0.01874	-0.695	0.09310	P	0.99999999140056	B	0.02656	0.0	B	0.01281	0.0	T	0.29518	-1.0009	9	0.02654	T	1	-3.1563	8.0538	0.30593	0.0:0.8044:0.0:0.1956	rs1528;rs3187843;rs17719113;rs56549460;rs61083501;rs1528	429	Q9UGK8	SRGEF_HUMAN	E	429	ENSP00000265965:K429E	ENSP00000265965:K429E	K	-	1	0	SERGEF	17766300	0.039000	0.19947	0.884000	0.34674	0.816000	0.46133	0.547000	0.23299	0.678000	0.31325	-0.215000	0.12644	AAA	T|0.878;C|0.122	0.122	strong		0.517	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139	
PLA2G15	23659	hgsc.bcm.edu	37	16	68293320	68293320	+	Silent	SNP	T	T	C	rs3743739	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68293320T>C	ENST00000219345.5	+	6	1082	c.999T>C	c.(997-999)ggT>ggC	p.G333G	RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000444212.2_Silent_p.G133G|RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000413021.2_Silent_p.G239G|PLA2G15_ENST00000566188.1_3'UTR	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	333					ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)	p.G333G(1)		kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						GCCTCTATGGTACTGGCGTCC	0.562													C|||	1090	0.217652	0.3623	0.2032	5008	,	,		22081	0.1022		0.166	False		,,,				2504	0.2045				p.G333G		Atlas-SNP	.											PLA2G15,NS,carcinoma,0,1	PLA2G15	30	1	1	Substitution - coding silent(1)	prostate(1)	c.T999C						PASS	.	C		1393,3003	687.0+/-404.8	228,937,1033	99.0	85.0	90.0		999	-1.3	0.9	16	dbSNP_107	90	1477,7123	749.3+/-407.4	162,1153,2985	no	coding-synonymous	PLA2G15	NM_012320.3		390,2090,4018	CC,CT,TT		17.1744,31.6879,22.0837		333/413	68293320	2870,10126	2198	4300	6498	SO:0001819	synonymous_variant	23659	exon6			CTATGGTACTGGC	AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066			17163	protein-coding gene	gene with protein product		609362	"""lysophospholipase 3 (lysosomal phospholipase A2)"""	LYPLA3		10092508, 16973413	Standard	XM_005255886		Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	ENST00000219345.5:c.999T>C	16.37:g.68293320T>C		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_012320	B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Silent	SNP	ENST00000219345.5	37	CCDS10864.1																																																																																			T|0.778;C|0.222	0.222	strong		0.562	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320	
ZNF33A	7581	hgsc.bcm.edu	37	10	38344700	38344700	+	Missense_Mutation	SNP	C	C	G	rs2505232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38344700C>G	ENST00000458705.2	+	5	1803	c.1645C>G	c.(1645-1647)Cag>Gag	p.Q549E	ZNF33A_ENST00000307441.9_Missense_Mutation_p.Q549E|ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Missense_Mutation_p.Q556E|ZNF33A_ENST00000374618.3_Missense_Mutation_p.Q550E			Q06730	ZN33A_HUMAN	zinc finger protein 33A	549			Q -> E (in dbSNP:rs2505232). {ECO:0000269|PubMed:14702039}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						ACACACAGGGCAGAAACCCTT	0.433													G|||	2389	0.477037	0.5272	0.5173	5008	,	,		19110	0.5754		0.493	False		,,,				2504	0.2628				p.Q550E		Atlas-SNP	.											.	ZNF33A	103	.	0			c.C1648G						PASS	.	G	GLU/GLN,GLU/GLN	2268,2138	579.8+/-385.0	553,1162,488	100.0	102.0	102.0		1648,1645	1.7	1.0	10	dbSNP_100	102	4103,4497	591.5+/-392.8	963,2177,1160	no	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	29,29	1516,3339,1648	GG,GC,CC		47.7093,48.5247,48.9851	benign,benign	550/812,549/811	38344700	6371,6635	2203	4300	6503	SO:0001583	missense	7581	exon5			ACAGGGCAGAAAC	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1645C>G	10.37:g.38344700C>G	ENSP00000387713:p.Gln549Glu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	73	70	0.958904	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	1117	0.5114468864468864	241	0.4898373983739837	181	0.5	314	0.548951048951049	381	0.5026385224274407	G	0.003	-2.414126	0.00191	0.514753	0.477093	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.11712	2.75;2.75;2.75;2.75	1.68	1.68	0.24146	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36591	N	0.002514	T	0.00012	0.0000	N	0.00783	-1.19	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	0.43572	-0.9383	9	0.02654	T	1	.	7.6052	0.28097	0.0:0.2686:0.7313:0.0	rs2505232;rs17609186;rs59756517;rs2505232	556;549;550	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	E	550;556;549;549	ENSP00000363747:Q550E;ENSP00000402467:Q556E;ENSP00000387713:Q549E;ENSP00000304268:Q549E	ENSP00000304268:Q549E	Q	+	1	0	ZNF33A	38384706	1.000000	0.71417	0.973000	0.42090	0.105000	0.19272	4.342000	0.59341	0.044000	0.15775	-0.676000	0.03789	CAG	C|0.507;G|0.493	0.493	strong		0.433	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
SOS2	6655	hgsc.bcm.edu	37	14	50585109	50585109	+	Missense_Mutation	SNP	G	G	A	rs140995728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:50585109G>A	ENST00000216373.5	-	23	4226	c.3952C>T	c.(3952-3954)Cca>Tca	p.P1318S	SOS2_ENST00000543680.1_Missense_Mutation_p.P1285S|VCPKMT_ENST00000395860.2_5'Flank|VCPKMT_ENST00000395859.2_5'Flank	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1318					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)					CTGTACAATGGGGGGTGCGAA	0.463													G|||	4	0.000798722	0.0	0.0014	5008	,	,		17130	0.0		0.003	False		,,,				2504	0.0				p.P1318S		Atlas-SNP	.											.	SOS2	195	.	0			c.C3952T						PASS	.	G	SER/PRO	2,4404	4.2+/-10.8	0,2,2201	74.0	72.0	72.0		3952	5.4	0.8	14	dbSNP_134	72	11,8589	8.4+/-32.0	0,11,4289	yes	missense	SOS2	NM_006939.2	74	0,13,6490	AA,AG,GG		0.1279,0.0454,0.1	benign	1318/1333	50585109	13,12993	2203	4300	6503	SO:0001583	missense	6655	exon23			ACAATGGGGGGTG	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.3952C>T	14.37:g.50585109G>A	ENSP00000216373:p.Pro1318Ser	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	165	73	0.442424	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	3.971	-0.008341	0.07727	4.54E-4	0.001279	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.78003	-1.14;-1.01	5.37	5.37	0.77165	.	0.056414	0.64402	D	0.000001	T	0.81293	0.4792	L	0.33485	1.01	0.58432	D	0.999999	D;D	0.63880	0.993;0.993	D;D	0.70227	0.968;0.968	T	0.75099	-0.3437	10	0.10636	T	0.68	.	19.1021	0.93277	0.0:0.0:1.0:0.0	.	1285;1318	B7ZKT6;Q07890	.;SOS2_HUMAN	S	1318;1285	ENSP00000216373:P1318S;ENSP00000445328:P1285S	ENSP00000216373:P1318S	P	-	1	0	SOS2	49654859	1.000000	0.71417	0.829000	0.32907	0.982000	0.71751	3.088000	0.50175	2.490000	0.84030	0.563000	0.77884	CCA	G|0.999;A|0.001	0.001	strong		0.463	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
LMO7	4008	hgsc.bcm.edu	37	13	76370887	76370887	+	Splice_Site	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:76370887T>C	ENST00000321797.8	+	4	484		c.e4+2		LMO7_ENST00000357063.3_Splice_Site|LMO7_ENST00000465261.2_Splice_Site|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000341547.4_Splice_Site|LMO7_ENST00000526202.1_Splice_Site|LMO7_ENST00000377534.3_Splice_Site			Q8WWI1	LMO7_HUMAN	LIM domain 7						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)		CTGACGAAGGTAAGTAAACTA	0.398																																					.		Atlas-SNP	.											.	LMO7	334	.	0			c.618+2T>C						PASS	.						112.0	99.0	103.0					13																	76370887		2203	4300	6503	SO:0001630	splice_region_variant	4008	exon7			CGAAGGTAAGTAA	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.-238+2T>C	13.37:g.76370887T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	100	26	0.26	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Splice_Site	SNP	ENST00000321797.8	37		.	.	.	.	.	.	.	.	.	.	T	9.699	1.153939	0.21371	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000526202	.	.	.	5.11	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.397	0.49847	0.1357:0.0:0.0:0.8643	.	.	.	.	.	-1	.	.	.	+	.	.	LMO7	75268888	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	7.075000	0.76798	0.844000	0.35094	0.459000	0.35465	.	.	.	none		0.398	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	Intron
SOD3	6649	hgsc.bcm.edu	37	4	24801315	24801315	+	Missense_Mutation	SNP	G	G	A	rs2536512	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:24801315G>A	ENST00000382120.3	+	2	377	c.172G>A	c.(172-174)Gcg>Acg	p.A58T		NM_003102.2	NP_003093.2	P08294	SODE_HUMAN	superoxide dismutase 3, extracellular	58			A -> T (in dbSNP:rs2536512). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:3476950, ECO:0000269|PubMed:7959763, ECO:0000269|Ref.3, ECO:0000269|Ref.4}.		removal of superoxide radicals (GO:0019430)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	copper ion binding (GO:0005507)|heparin binding (GO:0008201)|superoxide dismutase activity (GO:0004784)|zinc ion binding (GO:0008270)			prostate(1)|urinary_tract(1)	2		Breast(46;0.0503)				CGACGACGGCGCGCTCCACGC	0.726													G|||	2006	0.400559	0.1399	0.4597	5008	,	,		10919	0.3591		0.6252	False		,,,				2504	0.5225				p.A58T		Atlas-SNP	.											.	SOD3	4	.	0			c.G172A	GRCh37	CM067036	SOD3	M	rs2536512	PASS	.	G	THR/ALA	1082,3126		191,700,1213	10.0	8.0	8.0		172	-1.3	0.0	4	dbSNP_100	8	5556,2842		1919,1718,562	yes	missense	SOD3	NM_003102.2	58	2110,2418,1775	AA,AG,GG		33.8414,25.7129,47.3425	benign	58/241	24801315	6638,5968	2104	4199	6303	SO:0001583	missense	6649	exon2			GACGGCGCGCTCC		CCDS3430.1	4p15.2	2012-09-20			ENSG00000109610	ENSG00000109610	1.15.1.1		11181	protein-coding gene	gene with protein product		185490					Standard	NM_003102		Approved	EC-SOD	uc003gqz.3	P08294	OTTHUMG00000128565	ENST00000382120.3:c.172G>A	4.37:g.24801315G>A	ENSP00000371554:p.Ala58Thr	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_003102	Q5U781|Q6FHA2	Missense_Mutation	SNP	ENST00000382120.3	37	CCDS3430.1	913	0.41804029304029305	60	0.12195121951219512	179	0.494475138121547	193	0.3374125874125874	481	0.6345646437994723	G	6.521	0.464435	0.12402	0.257129	0.661586	ENSG00000109610	ENST00000382120	T	0.46819	0.86	4.66	-1.33	0.09172	Superoxide dismutase, copper/zinc binding domain (1);	0.674697	0.13107	N	0.413244	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.27765	0.188	B	0.13407	0.009	T	0.43523	-0.9386	9	0.20519	T	0.43	1.2455	2.3621	0.04309	0.2731:0.4455:0.1461:0.1353	rs2536512;rs17851148;rs2536512	58	P08294	SODE_HUMAN	T	58	ENSP00000371554:A58T	ENSP00000371554:A58T	A	+	1	0	SOD3	24410413	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.175000	0.16762	0.025000	0.15241	-0.311000	0.09066	GCG	G|0.600;A|0.400	0.400	strong		0.726	SOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250416.1		
SPP1	6696	hgsc.bcm.edu	37	4	88903853	88903853	+	Silent	SNP	C	C	T	rs397897575|rs1126616	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88903853C>T	ENST00000395080.3	+	7	877	c.750C>T	c.(748-750)gcC>gcT	p.A250A	SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000237623.7_Silent_p.A236A|SPP1_ENST00000360804.4_Silent_p.A223A	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	250					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)	p.A250A(1)		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)		AGCGGAAAGCCAATGATGAGA	0.473													C|||	1810	0.361422	0.1543	0.3775	5008	,	,		19862	0.7063		0.2813	False		,,,				2504	0.3569				p.A263A		Atlas-SNP	.											SPP1,NS,carcinoma,0,1	SPP1	35	1	1	Substitution - coding silent(1)	prostate(1)	c.C789T						PASS	.	C	,,	784,3622	315.5+/-294.2	59,666,1478	145.0	137.0	140.0		708,750,669	-1.2	0.0	4	dbSNP_86	140	2340,6260	391.7+/-343.7	348,1644,2308	no	coding-synonymous,coding-synonymous,coding-synonymous	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	,,	407,2310,3786	TT,TC,CC		27.2093,17.7939,24.0197	,,	236/301,250/315,223/288	88903853	3124,9882	2203	4300	6503	SO:0001819	synonymous_variant	6696	exon8			GAAAGCCAATGAT		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.750C>T	4.37:g.88903853C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	164	82	0.5	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Silent	SNP	ENST00000395080.3	37	CCDS43250.1																																																																																			C|0.733;G|0.000;T|0.267	0.267	strong		0.473	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643066	1643066	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1643066A>G	ENST00000399682.1	-	1	302	c.258T>C	c.(256-258)ggT>ggC	p.G86G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.G86G(1)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		CCCCCTTGGAACCCCCACAAG	0.667																																					p.G86G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,3	KRTAP5-4	78	3	1	Substitution - coding silent(1)	endometrium(1)	c.T258C						scavenged	.						9.0	15.0	13.0					11																	1643066		683	1577	2260	SO:0001819	synonymous_variant	387267	exon1			CTTGGAACCCCCA	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.258T>C	11.37:g.1643066A>G		Somatic	130	5	0.0384615		WXS	Illumina HiSeq	Phase_I	134	10	0.0746269	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.667	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
NHLRC3	387921	hgsc.bcm.edu	37	13	39613322	39613322	+	Missense_Mutation	SNP	T	T	G	rs115821169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39613322T>G	ENST00000379600.3	+	2	456	c.134T>G	c.(133-135)cTt>cGt	p.L45R	NHLRC3_ENST00000379599.2_Missense_Mutation_p.L45R|PROSER1_ENST00000350125.3_5'Flank|PROSER1_ENST00000352251.3_5'Flank|NHLRC3_ENST00000470258.1_5'UTR	NM_001012754.3	NP_001012772.1	Q5JS37	NHLC3_HUMAN	NHL repeat containing 3	45						extracellular vesicular exosome (GO:0070062)				breast(1)|kidney(1)|large_intestine(3)|lung(4)|skin(2)	11		Lung NSC(96;6.01e-07)|Breast(139;0.00394)|Prostate(109;0.00676)|Lung SC(185;0.0548)|Hepatocellular(188;0.114)		all cancers(112;2.37e-08)|Epithelial(112;3.14e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00101)|BRCA - Breast invasive adenocarcinoma(63;0.00335)|GBM - Glioblastoma multiforme(144;0.0128)		GAGAAAATTCTTTACCGGCTG	0.393													T|||	97	0.019369	0.0688	0.0029	5008	,	,		14847	0.004		0.0	False		,,,				2504	0.0				p.L45R		Atlas-SNP	.											NHLRC3,NS,carcinoma,+1,1	NHLRC3	35	1	0			c.T134G						scavenged	.	T	ARG/LEU,ARG/LEU	217,4189	130.2+/-166.9	9,199,1995	78.0	83.0	81.0		134,134	2.8	0.8	13	dbSNP_132	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	NHLRC3	NM_001012754.2,NM_001017370.1	102,102	9,200,6294	GG,GT,TT		0.0116,4.9251,1.6761	possibly-damaging,possibly-damaging	45/348,45/281	39613322	218,12788	2203	4300	6503	SO:0001583	missense	387921	exon2			AAATTCTTTACCG		CCDS31961.1, CCDS31962.1	13q13.3	2007-12-18			ENSG00000188811	ENSG00000188811			33751	protein-coding gene	gene with protein product							Standard	NM_001017370		Approved		uc001uxc.4	Q5JS37	OTTHUMG00000016765	ENST00000379600.3:c.134T>G	13.37:g.39613322T>G	ENSP00000368920:p.Leu45Arg	Somatic	82	1	0.0121951		WXS	Illumina HiSeq	Phase_I	96	51	0.53125	NM_001012754	B2RTZ2|B4DTL0|Q69YI9	Missense_Mutation	SNP	ENST00000379600.3	37	CCDS31961.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	T	13.82	2.350962	0.41599	0.049251	1.16E-4	ENSG00000188811	ENST00000379600;ENST00000379599;ENST00000537150	T;D	0.91631	0.82;-2.88	5.29	2.83	0.33086	.	0.355295	0.29676	N	0.011493	T	0.49457	0.1558	L	0.43152	1.355	0.35782	D	0.821693	B;B;B;B	0.19073	0.02;0.01;0.009;0.033	B;B;B;B	0.23018	0.012;0.013;0.006;0.043	T	0.68262	-0.5455	9	.	.	.	-6.5441	7.5159	0.27600	0.0:0.0745:0.1423:0.7833	.	45;45;45;45	B4DTL0;Q5JS37;B4DRC8;F5GZB5	.;NHLC3_HUMAN;.;.	R	45	ENSP00000368920:L45R;ENSP00000368919:L45R	.	L	+	2	0	NHLRC3	38511322	0.971000	0.33674	0.791000	0.31998	0.802000	0.45316	2.098000	0.41757	0.318000	0.23185	0.379000	0.24179	CTT	T|0.983;G|0.017	0.017	strong		0.393	NHLRC3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044616.2	NM_001012754	
KIF13B	23303	hgsc.bcm.edu	37	8	29033654	29033654	+	Silent	SNP	A	A	G	rs148531473	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:29033654A>G	ENST00000524189.1	-	10	914	c.876T>C	c.(874-876)gaT>gaC	p.D292D	KIF13B_ENST00000521515.1_Silent_p.D292D	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	292	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CAGCACTCTGATCTGCAAGAG	0.388													A|||	9	0.00179712	0.0	0.0	5008	,	,		20016	0.0		0.0089	False		,,,				2504	0.0				p.D292D		Atlas-SNP	.											.	KIF13B	192	.	0			c.T876C						PASS	.	A		7,3777		0,7,1885	74.0	70.0	71.0		876	1.7	1.0	8	dbSNP_134	71	58,8188		0,58,4065	no	coding-synonymous	KIF13B	NM_015254.3		0,65,5950	GG,GA,AA		0.7034,0.185,0.5403		292/1827	29033654	65,11965	1892	4123	6015	SO:0001819	synonymous_variant	23303	exon10			ACTCTGATCTGCA	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.876T>C	8.37:g.29033654A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	81	30	0.37037	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Silent	SNP	ENST00000524189.1	37	CCDS55217.1																																																																																			A|0.997;G|0.003	0.003	strong		0.388	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
ACTR5	79913	hgsc.bcm.edu	37	20	37396120	37396120	+	Missense_Mutation	SNP	A	A	G	rs2245231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37396120A>G	ENST00000243903.4	+	8	1484	c.1447A>G	c.(1447-1449)Att>Gtt	p.I483V		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	483			I -> V (in dbSNP:rs2245231). {ECO:0000269|PubMed:15489334}.		DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				CCCAAAGGACATTCAGGAAAT	0.433													G|||	2170	0.433307	0.4811	0.4337	5008	,	,		16712	0.4107		0.4245	False		,,,				2504	0.4008				p.I483V		Atlas-SNP	.											.	ACTR5	44	.	0			c.A1447G						PASS	.	G	VAL/ILE	2029,2377	610.8+/-391.6	468,1093,642	141.0	122.0	129.0		1447	-1.7	0.0	20	dbSNP_100	129	3714,4886	619.3+/-396.9	825,2064,1411	yes	missense	ACTR5	NM_024855.3	29	1293,3157,2053	GG,GA,AA		43.186,46.0508,44.1565	benign	483/608	37396120	5743,7263	2203	4300	6503	SO:0001583	missense	79913	exon8			AAGGACATTCAGG	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"""INO80 complex subunits"""	14671	protein-coding gene	gene with protein product	"""INO80 complex subunit M"""		"""ARP5 (actin-related protein 5, yeast) homolog"""			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.1447A>G	20.37:g.37396120A>G	ENSP00000243903:p.Ile483Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Missense_Mutation	SNP	ENST00000243903.4	37	CCDS13308.1	924	0.4230769230769231	235	0.47764227642276424	137	0.3784530386740331	232	0.40559440559440557	320	0.42216358839050133	G	0.010	-1.792507	0.00623	0.460508	0.43186	ENSG00000101442	ENST00000243903	D	0.94537	-3.45	5.81	-1.73	0.08081	.	0.919326	0.09506	N	0.792952	T	0.00012	0.0000	L	0.31476	0.935	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.10086	-1.0645	9	0.10902	T	0.67	-1.3844	9.6102	0.39659	0.4871:0.1111:0.4018:0.0	rs2245231;rs3764699;rs17759815;rs17845078;rs17857162;rs17857862;rs52808472;rs59097359;rs2245231	483	Q9H9F9	ARP5_HUMAN	V	483	ENSP00000243903:I483V	ENSP00000243903:I483V	I	+	1	0	ACTR5	36829534	0.002000	0.14202	0.001000	0.08648	0.350000	0.29205	0.095000	0.15127	-0.376000	0.07943	-0.735000	0.03563	ATT	A|0.563;G|0.437	0.437	strong		0.433	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855	
GPD1L	23171	hgsc.bcm.edu	37	3	32181761	32181761	+	Silent	SNP	C	C	T	rs9835387	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:32181761C>T	ENST00000282541.5	+	4	609	c.408C>T	c.(406-408)gaC>gaT	p.D136D		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	136					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						TCATTTCTGACATCATCCGTG	0.512													C|||	750	0.14976	0.2965	0.1182	5008	,	,		19949	0.002		0.1362	False		,,,				2504	0.1401				p.D136D		Atlas-SNP	.											.	GPD1L	25	.	0			c.C408T						PASS	.	C		1282,3124	437.6+/-345.0	178,926,1099	178.0	178.0	178.0		408	5.5	1.0	3	dbSNP_119	178	1193,7407	241.8+/-272.0	95,1003,3202	no	coding-synonymous	GPD1L	NM_015141.3		273,1929,4301	TT,TC,CC		13.8721,29.0967,19.0297		136/352	32181761	2475,10531	2203	4300	6503	SO:0001819	synonymous_variant	23171	exon4			TTCTGACATCATC	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.408C>T	3.37:g.32181761C>T		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	108	62	0.574074	NM_015141	A8K9U3|Q14702|Q9BRM5	Silent	SNP	ENST00000282541.5	37	CCDS33729.1																																																																																			C|0.828;T|0.172	0.172	strong		0.512	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141	
OR1Q1	158131	hgsc.bcm.edu	37	9	125377734	125377734	+	Missense_Mutation	SNP	A	A	G	rs727913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:125377734A>G	ENST00000297913.2	+	1	787	c.718A>G	c.(718-720)Acc>Gcc	p.T240A	RP11-64P14.7_ENST00000431442.1_RNA	NM_012364.1	NP_036496.1	Q15612	OR1Q1_HUMAN	olfactory receptor, family 1, subfamily Q, member 1	240			T -> A (in dbSNP:rs727913).		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						AACCTTTTCTACCTGCGGCTC	0.562													A|||	596	0.11901	0.0227	0.1715	5008	,	,		20215	0.3165		0.0646	False		,,,				2504	0.0644				p.T240A		Atlas-SNP	.											.	OR1Q1	46	.	0			c.A718G						PASS	.	A	ALA/THR	123,4283	90.6+/-129.3	1,121,2081	87.0	88.0	87.0		718	5.6	1.0	9	dbSNP_86	87	547,8053	150.4+/-205.3	8,531,3761	yes	missense	OR1Q1	NM_012364.1	58	9,652,5842	GG,GA,AA		6.3605,2.7916,5.1515	probably-damaging	240/315	125377734	670,12336	2203	4300	6503	SO:0001583	missense	158131	exon1			TTTTCTACCTGCG		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.718A>G	9.37:g.125377734A>G	ENSP00000297913:p.Thr240Ala	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	177	70	0.39548	NM_012364	Q6IFN4|Q8NGR7|Q96R82	Missense_Mutation	SNP	ENST00000297913.2	37	CCDS35125.1	271	0.12408424908424909	14	0.028455284552845527	52	0.143646408839779	157	0.2744755244755245	48	0.0633245382585752	A	21.8	4.196836	0.79015	0.027916	0.063605	ENSG00000165202	ENST00000297913	T	0.41065	1.01	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000100	T	0.00039	0.0001	H	0.95645	3.7	0.26992	P	0.9651202	D	0.89917	1.0	D	0.97110	1.0	T	0.04752	-1.0929	9	0.87932	D	0	-4.0098	14.8569	0.70344	1.0:0.0:0.0:0.0	rs727913;rs60075375;rs727913	240	Q15612	OR1Q1_HUMAN	A	240	ENSP00000297913:T240A	ENSP00000297913:T240A	T	+	1	0	OR1Q1	124417555	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	8.871000	0.92346	2.340000	0.79590	0.528000	0.53228	ACC	A|0.881;G|0.119	0.119	strong		0.562	OR1Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053946.1		
CSTL1	128817	hgsc.bcm.edu	37	20	23424638	23424638	+	Missense_Mutation	SNP	C	C	T	rs3746737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:23424638C>T	ENST00000246020.2	+	2	307	c.287C>T	c.(286-288)aCg>aTg	p.T96M	CSTL1_ENST00000347397.1_Missense_Mutation_p.T96M			Q9H114	CST1L_HUMAN	cystatin-like 1	96			T -> M (in dbSNP:rs3746737).			extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.T96M(1)		breast(2)|endometrium(2)|large_intestine(3)|lung(4)|skin(2)|stomach(1)	14	Colorectal(13;0.0993)|Lung NSC(19;0.235)					AGGAATGACACGAGCAATTCT	0.468													C|||	638	0.127396	0.0378	0.1542	5008	,	,		20391	0.2996		0.0795	False		,,,				2504	0.1012				p.T96M		Atlas-SNP	.											CSTL1,NS,carcinoma,0,1	CSTL1	30	1	1	Substitution - Missense(1)	stomach(1)	c.C287T						PASS	.	C	MET/THR	189,4217	118.4+/-156.1	4,181,2018	137.0	116.0	123.0		287	-7.8	0.0	20	dbSNP_107	123	695,7905	171.9+/-222.7	33,629,3638	yes	missense	CSTL1	NM_138283.1	81	37,810,5656	TT,TC,CC		8.0814,4.2896,6.7969	probably-damaging	96/146	23424638	884,12122	2203	4300	6503	SO:0001583	missense	128817	exon3			ATGACACGAGCAA	AL096677	CCDS13153.1	20p11.21	2012-08-14			ENSG00000125823	ENSG00000125823			15958	protein-coding gene	gene with protein product						20565543	Standard	NM_138283		Approved	dJ322G13.4, CTES1	uc002wte.3	Q9H114	OTTHUMG00000032068	ENST00000246020.2:c.287C>T	20.37:g.23424638C>T	ENSP00000246020:p.Thr96Met	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	98	43	0.438776	NM_138283	Q17RA8|Q64FF7	Missense_Mutation	SNP	ENST00000246020.2	37	CCDS13153.1	291	0.13324175824175824	20	0.04065040650406504	53	0.1464088397790055	160	0.27972027972027974	58	0.07651715039577836	C	7.460	0.644517	0.14451	0.042896	0.080814	ENSG00000125823	ENST00000347397;ENST00000246020	T;T	0.27104	1.69;1.69	3.92	-7.84	0.01196	Proteinase inhibitor I25, cystatin (2);	2.031310	0.02546	N	0.095146	T	0.00012	0.0000	M	0.74258	2.255	0.80722	P	0.0	P	0.42649	0.786	B	0.37833	0.259	T	0.13255	-1.0516	9	0.48119	T	0.1	-9.4384	3.2703	0.06879	0.2021:0.1623:0.4632:0.1724	rs3746737;rs17830517;rs52797059;rs58774540;rs3746737	96	Q9H114	CST1L_HUMAN	M	96	ENSP00000344907:T96M;ENSP00000246020:T96M	ENSP00000246020:T96M	T	+	2	0	CSTL1	23372638	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.916000	0.01576	-1.909000	0.01085	-1.018000	0.02450	ACG	C|0.903;T|0.097	0.097	strong		0.468	CSTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078328.1		
PLEKHA4	57664	hgsc.bcm.edu	37	19	49340746	49340746	+	Missense_Mutation	SNP	T	T	C	rs34460869	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49340746T>C	ENST00000263265.6	-	20	2695	c.2140A>G	c.(2140-2142)Acg>Gcg	p.T714A	HSD17B14_ENST00000599157.1_5'Flank|PLEKHA4_ENST00000355496.5_3'UTR|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	714			T -> A (in dbSNP:rs34460869).			cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		TCCTGGCGCGTGGGGTCCGAA	0.652													.|||	489	0.0976438	0.2716	0.0375	5008	,	,		12165	0.001		0.0159	False		,,,				2504	0.089				p.T714A		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.A2140G						PASS	.		,ALA/THR	867,3535		87,693,1421	31.0	38.0	36.0		,2140	1.5	0.0	19	dbSNP_126	36	94,8506		0,94,4206	yes	utr-3,missense	PLEKHA4	NM_001161354.1,NM_020904.2	,58	87,787,5627	CC,CT,TT		1.093,19.6956,7.3912	,benign	,714/780	49340746	961,12041	2201	4300	6501	SO:0001583	missense	57664	exon20			GGCGCGTGGGGTC	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.2140A>G	19.37:g.49340746T>C	ENSP00000263265:p.Thr714Ala	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	143	76	0.531469	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	149	0.06822344322344322	120	0.24390243902439024	17	0.04696132596685083	0	0.0	12	0.0158311345646438	t	12.76	2.033282	0.35893	0.196956	0.01093	ENSG00000105559	ENST00000263265	T	0.08634	3.07	3.76	1.51	0.23008	.	1.395420	0.04808	N	0.434704	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	4.000000000004E-6	B	0.26002	0.139	B	0.19391	0.025	T	0.47983	-0.9074	9	0.20519	T	0.43	.	8.0169	0.30387	0.0:0.0:0.4338:0.5662	rs34460869	714	Q9H4M7	PKHA4_HUMAN	A	714	ENSP00000263265:T714A	ENSP00000263265:T714A	T	-	1	0	PLEKHA4	54032558	0.001000	0.12720	0.001000	0.08648	0.315000	0.28087	0.381000	0.20619	0.142000	0.18901	0.249000	0.18162	ACG	T|0.929;C|0.071	0.071	strong		0.652	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000539801.1_Silent_p.H163H|JAK2_ENST00000544510.1_Silent_p.H14H	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	163	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATTTTGTGCACGGATGGATAA	0.343		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				T|||	1794	0.358227	0.4887	0.3905	5008	,	,		15245	0.2708		0.3002	False		,,,				2504	0.3088				p.H163H		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C489T						PASS	.	T		2047,2359	609.9+/-391.4	488,1071,644	110.0	123.0	118.0		489	-0.9	0.9	9	dbSNP_119	118	2589,6011	689.4+/-404.4	366,1857,2077	no	coding-synonymous	JAK2	NM_004972.3		854,2928,2721	TT,TC,CC		30.1047,46.4594,35.6451		163/1133	5050706	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon6	Familial Cancer Database		TGTGCACGGATGG		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.489C>T	9.37:g.5050706C>T		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	83	82	0.987952	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			C|0.647;T|0.353	0.353	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
ZBTB46	140685	hgsc.bcm.edu	37	20	62407104	62407104	+	Silent	SNP	C	C	T	rs3827026	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:62407104C>T	ENST00000245663.4	-	3	1299	c.1149G>A	c.(1147-1149)ctG>ctA	p.L383L	ZBTB46_ENST00000395104.1_Silent_p.L383L|ZBTB46_ENST00000302995.2_Silent_p.L383L	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	383					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					CGTCGGCCTTCAGCGACAGCA	0.687											OREG0026130	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	411	0.0820687	0.003	0.0634	5008	,	,		16782	0.0784		0.1272	False		,,,				2504	0.1595				p.L383L		Atlas-SNP	.											.	ZBTB46	72	.	0			c.G1149A						PASS	.	C		103,4303	81.9+/-120.4	0,103,2100	52.0	55.0	54.0		1149	-1.6	0.7	20	dbSNP_107	54	1088,7512	226.2+/-262.0	77,934,3289	no	coding-synonymous	ZBTB46	NM_025224.3		77,1037,5389	TT,TC,CC		12.6512,2.3377,9.1573		383/590	62407104	1191,11815	2203	4300	6503	SO:0001819	synonymous_variant	140685	exon3			GGCCTTCAGCGAC	AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.1149G>A	20.37:g.62407104C>T		Somatic	128	0	0	1061	WXS	Illumina HiSeq	Phase_I	128	67	0.523438	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Silent	SNP	ENST00000245663.4	37	CCDS13538.1																																																																																			C|0.909;T|0.091	0.091	strong		0.687	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
KPTN	11133	hgsc.bcm.edu	37	19	47983623	47983623	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:47983623C>A	ENST00000338134.3	-	7	748	c.641G>T	c.(640-642)cGg>cTg	p.R214L	KPTN_ENST00000595484.1_5'Flank|KPTN_ENST00000536339.1_5'UTR	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	214					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)		TGAGAGGCGCCGGGACGTGCC	0.706																																					p.R214L		Atlas-SNP	.											KPTN,NS,carcinoma,-1,1	KPTN	34	1	0			c.G641T						scavenged	.						12.0	18.0	16.0					19																	47983623		1777	3599	5376	SO:0001583	missense	11133	exon7			AGGCGCCGGGACG	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.641G>T	19.37:g.47983623C>A	ENSP00000337850:p.Arg214Leu	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	37	CCDS42583.1	.	.	.	.	.	.	.	.	.	.	C	16.30	3.083860	0.55861	.	.	ENSG00000118162	ENST00000338134	T	0.45668	0.89	4.33	1.36	0.22044	.	0.376195	0.24350	N	0.039286	T	0.30541	0.0768	L	0.55990	1.75	0.80722	D	1	P	0.35844	0.524	B	0.31946	0.138	T	0.04693	-1.0933	10	0.40728	T	0.16	-10.4754	5.4328	0.16463	0.0:0.5368:0.0:0.4632	.	214	Q9Y664	KPTN_HUMAN	L	214	ENSP00000337850:R214L	ENSP00000337850:R214L	R	-	2	0	KPTN	52675435	0.973000	0.33851	0.710000	0.30468	0.954000	0.61252	0.418000	0.21230	0.390000	0.25115	0.298000	0.19748	CGG	.	.	none		0.706	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2		
GBGT1	26301	hgsc.bcm.edu	37	9	136037742	136037742	+	Missense_Mutation	SNP	G	G	A	rs2073924	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136037742G>A	ENST00000372040.3	-	2	369	c.58C>T	c.(58-60)Ctc>Ttc	p.L20F	GBGT1_ENST00000372043.3_Missense_Mutation_p.L20F|GBGT1_ENST00000372038.3_Missense_Mutation_p.L20F|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000540636.1_Missense_Mutation_p.L20F|GBGT1_ENST00000372036.3_Missense_Mutation_p.L20F|RALGDS_ENST00000542690.1_Missense_Mutation_p.L20F	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	20			L -> F (in dbSNP:rs2073924). {ECO:0000269|PubMed:12975309, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4}.		glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		AGGACACTGAGGCTTGTGCCC	0.657													G|||	1586	0.316693	0.2579	0.2954	5008	,	,		11531	0.5288		0.1829	False		,,,				2504	0.3303				p.L20F		Atlas-SNP	.											GBGT1,NS,carcinoma,0,1	GBGT1	25	1	0			c.C58T						PASS	.	G	PHE/LEU	1215,3189		158,899,1145	36.0	33.0	34.0		58	0.9	0.0	9	dbSNP_96	34	1652,6948		167,1318,2815	yes	missense	GBGT1	NM_021996.4	22	325,2217,3960	AA,AG,GG		19.2093,27.5886,22.0471		20/348	136037742	2867,10137	2202	4300	6502	SO:0001583	missense	26301	exon2			CACTGAGGCTTGT	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.58C>T	9.37:g.136037742G>A	ENSP00000361110:p.Leu20Phe	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	69	0.507353	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Missense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	678	0.31043956043956045	139	0.28252032520325204	99	0.27348066298342544	298	0.5209790209790209	142	0.18733509234828497	G	16.05	3.014065	0.54468	0.275886	0.192093	ENSG00000160271;ENSG00000148288;ENSG00000148288;ENSG00000148288;ENSG00000148288;ENSG00000148288	ENST00000542690;ENST00000372043;ENST00000372040;ENST00000540636;ENST00000372038;ENST00000372036	T;T;T;T;T;T	0.44083	1.32;5.03;5.03;4.78;0.93;0.99	2.86	0.886	0.19194	.	1.329470	0.04963	N	0.462367	T	0.00012	0.0000	L	0.47190	1.495	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.19073	0.002;0.018;0.033;0.002	B;B;B;B	0.19946	0.014;0.018;0.027;0.014	T	0.46048	-0.9219	9	0.51188	T	0.08	0.216	3.2144	0.06694	0.146:0.0:0.5942:0.2597	rs2073924;rs17853057;rs58898475;rs2073924	20;20;20;20	B7Z8S5;F5H6M6;Q8N5D6-2;Q8N5D6	.;.;.;GBGT1_HUMAN	F	20	ENSP00000437518:L20F;ENSP00000361113:L20F;ENSP00000361110:L20F;ENSP00000437663:L20F;ENSP00000361108:L20F;ENSP00000361106:L20F	ENSP00000361106:L20F	L	-	1	0	GBGT1;RALGDS	135027563	0.202000	0.23423	0.042000	0.18584	0.580000	0.36256	0.412000	0.21131	0.218000	0.20820	0.563000	0.77884	CTC	G|0.741;A|0.259	0.259	strong		0.657	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
KCNN3	3782	hgsc.bcm.edu	37	1	154842250	154842250	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:154842250G>T	ENST00000271915.4	-	1	506	c.191C>A	c.(190-192)cCg>cAg	p.P64Q	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	64	Gln-rich.|Pro-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)	ctgaagctgcggaggctgagg	0.697																																					p.P64Q		Atlas-SNP	.											KCNN3,colon,carcinoma,0,1	KCNN3	141	1	0			c.C191A						scavenged	.						5.0	4.0	5.0					1																	154842250		1971	3893	5864	SO:0001583	missense	3782	exon1			AGCTGCGGAGGCT	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.191C>A	1.37:g.154842250G>T	ENSP00000271915:p.Pro64Gln	Somatic	31	5	0.16129		WXS	Illumina HiSeq	Phase_I	44	5	0.113636	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	0.383	-0.927562	0.02377	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56776	0.44	4.41	3.47	0.39725	.	4.657150	0.00567	N	0.000284	T	0.17916	0.0430	N	0.03608	-0.345	0.80722	D	1	.	.	.	.	.	.	T	0.04115	-1.0976	8	0.27082	T	0.32	-7.4946	9.6132	0.39676	0.0:0.0:0.7634:0.2366	.	.	.	.	Q	64;159	ENSP00000271915:P64Q	ENSP00000271915:P64Q	P	-	2	0	KCNN3	153108874	0.000000	0.05858	0.998000	0.56505	0.997000	0.91878	0.235000	0.17948	1.372000	0.46190	0.563000	0.77884	CCG	.	.	none		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
PRKCQ	5588	hgsc.bcm.edu	37	10	6498723	6498723	+	Silent	SNP	G	G	A	rs11258943	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:6498723G>A	ENST00000263125.5	-	15	1659	c.1560C>T	c.(1558-1560)atC>atT	p.I520I	PRKCQ_ENST00000397176.2_Silent_p.I520I|PRKCQ_ENST00000539722.1_Silent_p.I395I	NM_001282644.1|NM_006257.3	NP_001269573.1|NP_006248.1	Q04759	KPCT_HUMAN	protein kinase C, theta	520	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			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)	CAAAATCCGCGATCTTGATAT	0.418													G|||	708	0.141374	0.1551	0.1153	5008	,	,		20609	0.0645		0.2187	False		,,,				2504	0.1411				p.I520I	Ovarian(50;572 1126 10530 25349 30594)	Atlas-SNP	.											.	PRKCQ	113	.	0			c.C1560T						PASS	.	G	,	701,3705	291.0+/-281.2	56,589,1558	247.0	198.0	215.0		1560,1560	-9.7	0.0	10	dbSNP_120	215	1869,6731	333.1+/-320.4	186,1497,2617	no	coding-synonymous,coding-synonymous	PRKCQ	NM_001242413.1,NM_006257.3	,	242,2086,4175	AA,AG,GG		21.7326,15.9101,19.7601	,	520/644,520/707	6498723	2570,10436	2203	4300	6503	SO:0001819	synonymous_variant	5588	exon15			ATCCGCGATCTTG	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.1560C>T	10.37:g.6498723G>A		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	122	53	0.434426	NM_006257	B4DF52|Q14DH6|Q3MJF1|Q64FY5|Q9H508|Q9H549	Silent	SNP	ENST00000263125.5	37	CCDS7079.1	315	0.14423076923076922	70	0.14227642276422764	47	0.1298342541436464	29	0.050699300699300696	169	0.22295514511873352	G	0.028	-1.352505	0.01256	0.159101	0.217326	ENSG00000065675	ENST00000397178	.	.	.	5.55	-9.67	0.00531	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999999992	.	.	.	.	.	.	T	0.10706	-1.0618	3	.	.	.	.	12.5145	0.56024	0.2922:0.0:0.5408:0.167	rs11258943;rs11258943	.	.	.	L	293	.	.	S	-	2	0	PRKCQ	6538729	0.012000	0.17670	0.026000	0.17262	0.001000	0.01503	-1.264000	0.02847	-2.746000	0.00377	-2.811000	0.00111	TCG	G|0.837;A|0.163	0.163	strong		0.418	PRKCQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046665.1	NM_006257	
GAS8	2622	hgsc.bcm.edu	37	16	90102835	90102835	+	Silent	SNP	A	A	G	rs868045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:90102835A>G	ENST00000268699.4	+	6	719	c.597A>G	c.(595-597)gaA>gaG	p.E199E	GAS8_ENST00000536122.1_Silent_p.E174E|GAS8_ENST00000540721.1_3'UTR	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	199	Microtubule-binding.		E -> K (in dbSNP:rs868044).		cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		TGAGGGACGAACTCGACTTGC	0.542													G|||	1324	0.264377	0.3933	0.2493	5008	,	,		22057	0.0079		0.3907	False		,,,				2504	0.2352				p.E199E		Atlas-SNP	.											.	GAS8	29	.	0			c.A597G						PASS	.	G		1719,2677	648.6+/-398.7	337,1045,816	107.0	91.0	97.0		597	1.3	0.4	16	dbSNP_86	97	3532,5068	631.5+/-398.5	725,2082,1493	no	coding-synonymous	GAS8	NM_001481.2		1062,3127,2309	GG,GA,AA		41.0698,39.1037,40.4047		199/479	90102835	5251,7745	2198	4300	6498	SO:0001819	synonymous_variant	2622	exon6			GGACGAACTCGAC	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.597A>G	16.37:g.90102835A>G		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	121	119	0.983471	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Silent	SNP	ENST00000268699.4	37	CCDS10992.1																																																																																			A|0.644;G|0.356	0.356	strong		0.542	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
DDX60	55601	hgsc.bcm.edu	37	4	169197297	169197297	+	Missense_Mutation	SNP	C	C	T	rs550625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:169197297C>T	ENST00000393743.3	-	15	2305	c.2014G>A	c.(2014-2016)Gtg>Atg	p.V672M		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	672			V -> M (in dbSNP:rs550625).		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)		CTTTTCATCACCTGAACAGCT	0.318													T|||	668	0.133387	0.2284	0.1671	5008	,	,		17475	0.12		0.0815	False		,,,				2504	0.0481				p.V672M		Atlas-SNP	.											DDX60_ENST00000393743,NS,carcinoma,+2,2	DDX60	304	2	0			c.G2014A						scavenged	.	T	MET/VAL	838,3568	743.6+/-411.5	82,674,1447	118.0	116.0	116.0		2014	2.7	0.9	4	dbSNP_83	116	535,8065	794.2+/-407.5	19,497,3784	yes	missense	DDX60	NM_017631.5	21	101,1171,5231	TT,TC,CC		6.2209,19.0195,10.5567	benign	672/1713	169197297	1373,11633	2203	4300	6503	SO:0001583	missense	55601	exon15			TCATCACCTGAAC	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.2014G>A	4.37:g.169197297C>T	ENSP00000377344:p.Val672Met	Somatic	156	1	0.00641026		WXS	Illumina HiSeq	Phase_I	126	65	0.515873	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	312	0.14285714285714285	127	0.258130081300813	52	0.143646408839779	72	0.1258741258741259	61	0.08047493403693931	T	0.061	-1.224366	0.01530	0.190195	0.062209	ENSG00000137628	ENST00000393743	T	0.19806	2.12	5.15	2.67	0.31697	.	0.351400	0.28420	N	0.015411	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.37502	-0.9703	9	0.06365	T	0.9	.	1.8745	0.03215	0.1217:0.2224:0.1257:0.5302	rs550625;rs52803136;rs58603390;rs550625	672	Q8IY21	DDX60_HUMAN	M	672	ENSP00000377344:V672M	ENSP00000377344:V672M	V	-	1	0	DDX60	169433872	0.016000	0.18221	0.857000	0.33713	0.730000	0.41778	-0.133000	0.10451	0.353000	0.24079	-0.381000	0.06696	GTG	C|0.882;T|0.118	0.118	strong		0.318	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
SERPINA11	256394	hgsc.bcm.edu	37	14	94912799	94912799	+	Silent	SNP	G	G	A	rs12888805	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:94912799G>A	ENST00000334708.3	-	3	850	c.786C>T	c.(784-786)acC>acT	p.T262T	RP11-349I1.2_ENST00000536735.1_RNA	NM_001080451.1	NP_001073920.1	Q86U17	SPA11_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11	262					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(14)|skin(1)|upper_aerodigestive_tract(1)	24				COAD - Colon adenocarcinoma(157;0.211)		TCTGGAGGACGGTGCAAGCCA	0.532													G|||	1301	0.259784	0.0605	0.2695	5008	,	,		20967	0.1815		0.4513	False		,,,				2504	0.4059				p.T262T		Atlas-SNP	.											SERPINA11,right_lower_lobe,carcinoma,-1,1	SERPINA11	53	1	0			c.C786T						PASS	.	G		587,3819	258.6+/-262.5	46,495,1662	138.0	122.0	127.0		786	-10.8	0.1	14	dbSNP_121	127	3525,5075	515.2+/-378.5	701,2123,1476	no	coding-synonymous	SERPINA11	NM_001080451.1		747,2618,3138	AA,AG,GG		40.9884,13.3227,31.6162		262/423	94912799	4112,8894	2203	4300	6503	SO:0001819	synonymous_variant	256394	exon3			GAGGACGGTGCAA	BX248259	CCDS32149.1	14q32.13	2014-02-18	2005-08-18		ENSG00000186910	ENSG00000186910		"""Serine (or cysteine) peptidase inhibitors"""	19193	protein-coding gene	gene with protein product			"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 11"""			15014966, 24172014	Standard	NM_001080451		Approved		uc001ydd.1	Q86U17	OTTHUMG00000171348	ENST00000334708.3:c.786C>T	14.37:g.94912799G>A		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	162	160	0.987654	NM_001080451	B2RV07	Silent	SNP	ENST00000334708.3	37	CCDS32149.1																																																																																			G|0.707;A|0.293	0.293	strong		0.532	SERPINA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413091.1	NM_001080451	
DMBT1	1755	hgsc.bcm.edu	37	10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	rs75209396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124330421C>G	ENST00000338354.3	+	4	261	c.155C>G	c.(154-156)tCg>tGg	p.S52W	DMBT1_ENST00000368909.3_Missense_Mutation_p.S52W|DMBT1_ENST00000368955.3_Missense_Mutation_p.S52W|DMBT1_ENST00000359586.6_Missense_Mutation_p.S52W|DMBT1_ENST00000368956.2_Missense_Mutation_p.S52W|DMBT1_ENST00000344338.3_Missense_Mutation_p.S52W|DMBT1_ENST00000330163.4_Missense_Mutation_p.S52W			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	52			S -> W (in dbSNP:rs75209396). {ECO:0000269|PubMed:12185598, ECO:0000269|PubMed:12353266}.		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)				CCATTTCCCTCGGAGTCGACC	0.537													c|||	329	0.0656949	0.23	0.0231	5008	,	,		22102	0.001		0.007	False		,,,				2504	0.001				p.S52W	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C155G						PASS	.	C	TRP/SER,TRP/SER,TRP/SER	658,3106		51,556,1275	168.0	167.0	167.0		155,155,155	1.0	0.0	10	dbSNP_132	167	51,8185		0,51,4067	yes	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	177,177,177	51,607,5342	GG,GC,CC		0.6192,17.4814,5.9083	probably-damaging,probably-damaging,probably-damaging	52/1786,52/2414,52/2404	124330421	709,11291	1882	4118	6000	SO:0001583	missense	1755	exon4			TTCCCTCGGAGTC		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.155C>G	10.37:g.124330421C>G	ENSP00000342210:p.Ser52Trp	Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	185	81	0.437838	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		130	0.05952380952380952	118	0.23983739837398374	9	0.024861878453038673	0	0.0	3	0.00395778364116095	C	10.71	1.426167	0.25726	0.174814	0.006192	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.26223	1.85;1.84;1.78;1.85;1.84;1.78;1.75	1.9	0.968	0.19680	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P;P;D	0.76494	0.997;0.572;0.922;0.529;0.999	D;B;B;B;P	0.65443	0.935;0.152;0.206;0.202;0.902	T	0.24476	-1.0159	8	0.66056	D	0.02	.	4.3987	0.11376	0.0:0.7908:0.0:0.2092	.	52;52;52;52;52	F8WEF7;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	W	52	ENSP00000342210:S52W;ENSP00000343175:S52W;ENSP00000327747:S52W;ENSP00000357905:S52W;ENSP00000357951:S52W;ENSP00000357952:S52W;ENSP00000352593:S52W	ENSP00000331522:S52W	S	+	2	0	DMBT1	124320411	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.122000	0.15687	0.337000	0.23665	0.205000	0.17691	TCG	C|0.950;G|0.050	0.050	strong		0.537	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
BTN2A1	11120	hgsc.bcm.edu	37	6	26458871	26458871	+	Missense_Mutation	SNP	T	T	C	rs146399224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26458871T>C	ENST00000312541.5	+	2	255	c.7T>C	c.(7-9)Tca>Cca	p.S3P	BTN2A1_ENST00000541522.1_Intron|BTN2A1_ENST00000469185.1_Missense_Mutation_p.S3P|BTN2A1_ENST00000429381.1_Missense_Mutation_p.S3P	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	3					lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						GCTCATGGAATCAGCTGCTGC	0.617													T|||	2	0.000399361	0.0	0.0	5008	,	,		15890	0.0		0.002	False		,,,				2504	0.0				p.S3P		Atlas-SNP	.											.	BTN2A1	118	.	0			c.T7C						PASS	.						233.0	171.0	192.0					6																	26458871		2203	4300	6503	SO:0001583	missense	11120	exon2			ATGGAATCAGCTG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.7T>C	6.37:g.26458871T>C	ENSP00000312158:p.Ser3Pro	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	111	6	0.0540541	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.519967	0.00967	.	.	ENSG00000112763	ENST00000312541;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T	0.76448	-0.46;-1.02;-1.01	3.03	0.0692	0.14373	.	0.876207	0.09516	N	0.791659	T	0.24392	0.0591	N	0.01668	-0.77	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18053	-1.0349	10	0.42905	T	0.14	.	3.2421	0.06784	0.0:0.505:0.2251:0.2699	.	3;3	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	P	3	ENSP00000312158:S3P;ENSP00000416945:S3P;ENSP00000419043:S3P	ENSP00000265424:S3P	S	+	1	0	BTN2A1	26566850	0.150000	0.22732	0.014000	0.15608	0.022000	0.10575	0.087000	0.14958	-0.002000	0.14469	-0.354000	0.07668	TCA	T|0.999;C|0.001	0.001	weak		0.617	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
SIM1	6492	hgsc.bcm.edu	37	6	100868779	100868779	+	Missense_Mutation	SNP	G	G	T	rs3734354	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:100868779G>T	ENST00000369208.3	-	10	1836	c.1054C>A	c.(1054-1056)Cca>Aca	p.P352T	SIM1_ENST00000262901.4_Missense_Mutation_p.P352T			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	352	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.		P -> T (in dbSNP:rs3734354).		cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.P352T(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GAGAAGGCTGGTTTGGAGGCT	0.537													G|||	892	0.178115	0.0038	0.2089	5008	,	,		14363	0.4067		0.1471	False		,,,				2504	0.1881				p.P352T		Atlas-SNP	.											SIM1,NS,carcinoma,+2,2	SIM1	173	2	1	Substitution - Missense(1)	stomach(1)	c.C1054A						scavenged	.	G	THR/PRO	138,4268	95.7+/-134.4	2,134,2067	109.0	98.0	102.0		1054	5.8	1.0	6	dbSNP_107	102	1171,7429	237.9+/-269.6	62,1047,3191	yes	missense	SIM1	NM_005068.2	38	64,1181,5258	TT,TG,GG		13.6163,3.1321,10.0646	possibly-damaging	352/767	100868779	1309,11697	2203	4300	6503	SO:0001583	missense	6492	exon9			AGGCTGGTTTGGA	U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1054C>A	6.37:g.100868779G>T	ENSP00000358210:p.Pro352Thr	Somatic	127	1	0.00787402		WXS	Illumina HiSeq	Phase_I	88	17	0.193182	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	430	0.19688644688644688	5	0.01016260162601626	76	0.20994475138121546	236	0.4125874125874126	113	0.14907651715039577	G	17.17	3.320485	0.60634	0.031321	0.136163	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.03772	3.81;3.81	5.8	5.8	0.92144	Single-minded, C-terminal (1);	0.208574	0.48767	D	0.000176	T	0.03827	0.0108	L	0.50333	1.59	0.09310	P	0.99999845931	B	0.21147	0.052	B	0.17098	0.017	T	0.35525	-0.9785	9	0.42905	T	0.14	.	20.0567	0.97653	0.0:0.0:1.0:0.0	rs3734354;rs52789631;rs56928625;rs3734354	352	P81133	SIM1_HUMAN	T	352	ENSP00000358210:P352T;ENSP00000262901:P352T	ENSP00000262901:P352T	P	-	1	0	SIM1	100975500	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.059000	0.71133	2.752000	0.94435	0.650000	0.86243	CCA	T|0.145;G|0.854;A|0.000	0.145	strong		0.537	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
DCHS2	54798	hgsc.bcm.edu	37	4	155219318	155219318	+	Missense_Mutation	SNP	C	C	T	rs28561984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155219318C>T	ENST00000357232.4	-	18	4782	c.4783G>A	c.(4783-4785)Gag>Aag	p.E1595K		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1595	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs28561984).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GTAGGCGACTCGGGGGAAAGA	0.428													G|||	670	0.133786	0.0295	0.1037	5008	,	,		19868	0.1528		0.172	False		,,,				2504	0.2372				p.E1595K		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4783A						PASS	.	G	LYS/GLU	292,4114		59,174,1970	89.0	90.0	89.0		4783	0.1	0.0	4	dbSNP_125	89	1531,7069		166,1199,2935	no	missense	DCHS2	NM_017639.3	56	225,1373,4905	TT,TC,CC		17.8023,6.6273,14.0166	benign	1595/2917	155219318	1823,11183	2203	4300	6503	SO:0001583	missense	54798	exon18			GCGACTCGGGGGA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4783G>A	4.37:g.155219318C>T	ENSP00000349768:p.Glu1595Lys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	167	77	0.461078	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	G	9.333	1.060925	0.19987	0.066273	0.178023	ENSG00000197410	ENST00000357232	T	0.61158	0.13	5.66	0.139	0.14798	Cadherin (2);Cadherin-like (1);	0.917277	0.09327	N	0.817476	T	0.00073	0.0002	N	0.20986	0.625	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.04347	-1.0958	10	0.07325	T	0.83	.	3.0954	0.06308	0.1424:0.376:0.2865:0.1951	.	1595	Q6V1P9	PCD23_HUMAN	K	1595	ENSP00000349768:E1595K	ENSP00000349768:E1595K	E	-	1	0	DCHS2	155438768	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.438000	0.21559	-0.142000	0.11354	-0.127000	0.14921	GAG	C|0.867;G|0.027;T|0.106	0.106	strong		0.428	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
GLE1	2733	hgsc.bcm.edu	37	9	131285955	131285955	+	Missense_Mutation	SNP	A	A	G	rs2275260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131285955A>G	ENST00000309971.4	+	6	833	c.727A>G	c.(727-729)Atc>Gtc	p.I243V	GLE1_ENST00000372770.4_Missense_Mutation_p.I243V|GLE1_ENST00000539582.1_5'UTR|GLE1_ENST00000494417.1_3'UTR	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	243			I -> V (in dbSNP:rs2275260).		mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						AGAAGGCCAGATCCGCCTGCG	0.592													G|||	1740	0.347444	0.3767	0.2378	5008	,	,		16970	0.4782		0.2465	False		,,,				2504	0.3548				p.I243V		Atlas-SNP	.											.	GLE1	42	.	0			c.A727G						PASS	.	G	VAL/ILE,VAL/ILE	1711,2695	636.1+/-396.5	321,1069,813	48.0	53.0	51.0		727,727	-2.4	0.0	9	dbSNP_100	51	1732,6868	723.0+/-406.4	179,1374,2747	yes	missense,missense	GLE1	NM_001003722.1,NM_001499.2	29,29	500,2443,3560	GG,GA,AA		20.1395,38.8334,26.4724	benign,benign	243/699,243/660	131285955	3443,9563	2203	4300	6503	SO:0001583	missense	2733	exon6			GGCCAGATCCGCC	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"""GLE1 (yeast homolog)-like, RNA export mediator"", ""GLE1 RNA export mediator-like (yeast)"", ""GLE1 RNA export mediator (yeast)"", ""lethal congenital contracture syndrome 1"", ""GLE1 RNA export mediator homolog (yeast)"""	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.727A>G	9.37:g.131285955A>G	ENSP00000308622:p.Ile243Val	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	130	130	1	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	37	CCDS35154.1	700	0.32051282051282054	180	0.36585365853658536	78	0.2154696132596685	250	0.4370629370629371	192	0.2532981530343008	G	0.069	-1.206997	0.01568	0.388334	0.201395	ENSG00000119392	ENST00000309971;ENST00000372770	T;T	0.62105	0.05;0.47	5.62	-2.42	0.06542	.	0.828500	0.11495	N	0.558290	T	0.00012	0.0000	N	0.02011	-0.69	0.24828	P	0.99254955	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.43163	-0.9408	9	0.27785	T	0.31	-0.0864	7.9436	0.29974	0.4345:0.0992:0.4663:0.0	rs2275260;rs61109335;rs2275260	243;243	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	V	243	ENSP00000308622:I243V;ENSP00000361856:I243V	ENSP00000308622:I243V	I	+	1	0	GLE1	130325776	0.993000	0.37304	0.002000	0.10522	0.009000	0.06853	1.744000	0.38268	-1.235000	0.02545	-0.119000	0.15052	ATC	A|0.707;G|0.293	0.293	strong		0.592	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722	
MGAT5B	146664	hgsc.bcm.edu	37	17	74942478	74942478	+	Silent	SNP	C	C	T	rs8067984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74942478C>T	ENST00000569840.2	+	16	2443	c.1869C>T	c.(1867-1869)taC>taT	p.Y623Y	MGAT5B_ENST00000301618.4_Silent_p.Y621Y|MGAT5B_ENST00000428789.2_Silent_p.Y632Y	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	623					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						ACCTACCCTACGAGTACACCT	0.657													C|||	1784	0.35623	0.2451	0.2651	5008	,	,		16241	0.5357		0.4026	False		,,,				2504	0.3384				p.Y632Y		Atlas-SNP	.											.	MGAT5B	98	.	0			c.C1896T						PASS	.	C	,,	1210,3196	419.6+/-338.7	176,858,1169	88.0	62.0	70.0		1869,1863,1896	-3.6	1.0	17	dbSNP_116	70	3312,5288	493.4+/-373.6	641,2030,1629	no	coding-synonymous,coding-synonymous,coding-synonymous	MGAT5B	NM_001199172.1,NM_144677.2,NM_198955.1	,,	817,2888,2798	TT,TC,CC		38.5116,27.4626,34.7686	,,	623/793,621/791,632/802	74942478	4522,8484	2203	4300	6503	SO:0001819	synonymous_variant	146664	exon14			ACCCTACGAGTAC	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.1869C>T	17.37:g.74942478C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	57	25	0.438596	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Silent	SNP	ENST00000569840.2	37	CCDS59299.1																																																																																			C|0.639;T|0.361	0.361	strong		0.657	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720851	135720851	+	Missense_Mutation	SNP	G	G	T	rs6779903	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:135720851G>T	ENST00000264977.3	+	2	1128	c.511G>T	c.(511-513)Gcc>Tcc	p.A171S	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	171			A -> S (in dbSNP:rs6779903).		eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CGATGGGAACGCCCCATCCTT	0.423													G|||	1731	0.345647	0.5537	0.281	5008	,	,		17100	0.1964		0.2823	False		,,,				2504	0.3292				p.A171S		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.G511T						PASS	.	G	,SER/ALA	2231,2175	591.1+/-387.5	570,1091,542	74.0	79.0	77.0		,511	0.1	0.5	3	dbSNP_116	77	2364,6236	394.2+/-344.6	313,1738,2249	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,99	883,2829,2791	TT,TG,GG		27.4884,49.3645,35.3298	,benign	,171/1151	135720851	4595,8411	2203	4300	6503	SO:0001583	missense	5523	exon2			GGGAACGCCCCAT	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.511G>T	3.37:g.135720851G>T	ENSP00000264977:p.Ala171Ser	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	85	46	0.541176	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	748	0.3424908424908425	278	0.5650406504065041	111	0.30662983425414364	133	0.23251748251748253	226	0.29815303430079154	G	0.001	-2.910977	0.00056	0.506355	0.274884	ENSG00000073711	ENST00000264977	T	0.05258	3.47	5.55	0.0664	0.14361	.	0.420852	0.26000	N	0.026941	T	0.00012	0.0000	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22626	-1.0211	9	0.09590	T	0.72	.	8.5274	0.33313	0.1218:0.0:0.3925:0.4856	rs6779903;rs52800757;rs61128780;rs6779903	171	Q06190	P2R3A_HUMAN	S	171	ENSP00000264977:A171S	ENSP00000264977:A171S	A	+	1	0	PPP2R3A	137203541	0.567000	0.26626	0.471000	0.27229	0.086000	0.17979	1.057000	0.30492	0.060000	0.16281	-1.072000	0.02254	GCC	G|0.660;T|0.340	0.340	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
TYSND1	219743	hgsc.bcm.edu	37	10	71905569	71905569	+	Silent	SNP	C	C	A	rs3750774	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:71905569C>A	ENST00000287078.6	-	1	773	c.774G>T	c.(772-774)ctG>ctT	p.L258L	TYSND1_ENST00000494143.1_5'Flank|TYSND1_ENST00000335494.5_Silent_p.L258L	NM_173555.2	NP_775826.2	Q2T9J0	TYSD1_HUMAN	trypsin domain containing 1	258					protein homooligomerization (GO:0051260)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of fatty acid beta-oxidation (GO:0031998)	membrane (GO:0016020)|peroxisome (GO:0005777)	identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(2)|liver(1)|lung(3)|prostate(1)	9						CGGTGCCGGGCAGGCAGCGTG	0.721													C|||	1936	0.386581	0.1679	0.513	5008	,	,		13548	0.5327		0.4115	False		,,,				2504	0.4162				p.L258L		Atlas-SNP	.											.	TYSND1	20	.	0			c.G774T						PASS	.	C	,	604,2414		129,346,1034	2.0	3.0	3.0		774,774	1.5	1.0	10	dbSNP_107	3	2435,3707		602,1231,1238	no	coding-synonymous,coding-synonymous	TYSND1	NM_001040273.1,NM_173555.2	,	731,1577,2272	AA,AC,CC		39.6451,20.0133,33.1769	,	258/399,258/567	71905569	3039,6121	1509	3071	4580	SO:0001819	synonymous_variant	219743	exon1			GCCGGGCAGGCAG	BC016840	CCDS31213.1, CCDS31214.1	10q22.1	2009-11-06		2006-09-21	ENSG00000156521	ENSG00000156521			28531	protein-coding gene	gene with protein product		611017				17255948	Standard	NM_173555		Approved	MGC34695, NET41	uc001jqr.4	Q2T9J0	OTTHUMG00000018397	ENST00000287078.6:c.774G>T	10.37:g.71905569C>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_173555	Q5SQT4|Q5SQU1|Q8N6H2|Q96AR5	Silent	SNP	ENST00000287078.6	37	CCDS31213.1																																																																																			C|0.608;A|0.392	0.392	strong		0.721	TYSND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048483.1	NM_173555	
GGT1	2678	hgsc.bcm.edu	37	22	25023459	25023459	+	Missense_Mutation	SNP	G	G	C	rs138813205	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:25023459G>C	ENST00000400382.1	+	12	1836	c.1081G>C	c.(1081-1083)Gac>Cac	p.D361H	GGT1_ENST00000400383.1_Missense_Mutation_p.D361H|GGT1_ENST00000248923.4_Missense_Mutation_p.D361H|GGT1_ENST00000404532.1_Missense_Mutation_p.D17H|GGT1_ENST00000404920.1_Missense_Mutation_p.D17H|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000404223.1_Missense_Mutation_p.D17H|GGT1_ENST00000403838.1_Missense_Mutation_p.D17H|GGT1_ENST00000401885.1_Missense_Mutation_p.D17H|GGT1_ENST00000406383.2_Missense_Mutation_p.D361H|GGT1_ENST00000400380.1_Missense_Mutation_p.D361H			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	361				D -> H (in Ref. 10; AAI28240). {ECO:0000305}.	arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.D361H(1)		breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	GATCTCTGACGACACCACTCA	0.642																																					p.D361H		Atlas-SNP	.											GGT1,NS,carcinoma,0,1	GGT1	68	1	1	Substitution - Missense(1)	prostate(1)	c.G1081C						scavenged	.						37.0	38.0	38.0					22																	25023459		2200	4293	6493	SO:0001583	missense	2678	exon12			TCTGACGACACCA	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.1081G>C	22.37:g.25023459G>C	ENSP00000383232:p.Asp361His	Somatic	203	3	0.0147783		WXS	Illumina HiSeq	Phase_I	266	29	0.109023	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	44	0.020146520146520148	3	0.006097560975609756	3	0.008287292817679558	5	0.008741258741258742	33	0.04353562005277045	.	6.591	0.477472	0.12521	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.07021	3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23;3.23	3.4	-2.55	0.06288	.	0.371845	0.29046	N	0.013305	T	0.02119	0.0066	M	0.79614	2.46	0.29276	N	0.870324	B	0.17465	0.022	B	0.22152	0.038	T	0.14559	-1.0468	10	0.45353	T	0.12	-4.1646	8.9526	0.35799	0.6006:0.0:0.3994:0.0	.	361	P19440	GGT1_HUMAN	H	361;361;361;361;361;361;17;17;17;17;17	ENSP00000248923:D361H;ENSP00000393537:D361H;ENSP00000383232:D361H;ENSP00000383233:D361H;ENSP00000383231:D361H;ENSP00000385975:D361H;ENSP00000384381:D17H;ENSP00000385445:D17H;ENSP00000384820:D17H;ENSP00000385016:D17H;ENSP00000385001:D17H	ENSP00000248923:D361H	D	+	1	0	GGT1	23353459	0.054000	0.20591	0.000000	0.03702	0.103000	0.19146	0.359000	0.20233	-0.295000	0.08960	0.298000	0.19748	GAC	C|0.014;G|0.986	0.014	strong		0.642	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
HOXA6	3203	hgsc.bcm.edu	37	7	27185520	27185520	+	Silent	SNP	G	G	A	rs17500863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:27185520G>A	ENST00000222728.3	-	2	483	c.459C>T	c.(457-459)agC>agT	p.S153S	RP1-170O19.23_ENST00000498652.1_RNA|HOXA-AS3_ENST00000518947.2_RNA|HOXA6_ENST00000521478.1_5'UTR|HOXA-AS3_ENST00000521231.1_RNA|HOXA5_ENST00000222726.3_5'Flank|HOXA-AS3_ENST00000521197.1_RNA|RP1-170O19.22_ENST00000467897.2_RNA|HOXA-AS3_ENST00000518848.1_RNA	NM_024014.3	NP_076919.1	P31267	HXA6_HUMAN	homeobox A6	153					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(5)|lung(3)|ovary(1)	10						GGCGCCCATGGCTCCCATACA	0.662													G|||	390	0.0778754	0.2209	0.049	5008	,	,		14179	0.0		0.0278	False		,,,				2504	0.0368				p.S153S		Atlas-SNP	.											.	HOXA6	25	.	0			c.C459T						PASS	.	G		839,3567	332.0+/-302.3	72,695,1436	73.0	67.0	69.0		459	2.0	1.0	7	dbSNP_123	69	228,8372	94.0+/-155.9	3,222,4075	no	coding-synonymous	HOXA6	NM_024014.3		75,917,5511	AA,AG,GG		2.6512,19.0422,8.2039		153/234	27185520	1067,11939	2203	4300	6503	SO:0001819	synonymous_variant	3203	exon2			CCCATGGCTCCCA		CCDS5407.1	7p15.2	2011-06-20	2005-12-22		ENSG00000106006	ENSG00000106006		"""Homeoboxes / ANTP class : HOXL subclass"""	5107	protein-coding gene	gene with protein product		142951	"""homeo box A6"""	HOX1B, HOX1		1973146, 1358459	Standard	NM_024014		Approved		uc003syo.2	P31267	OTTHUMG00000023216	ENST00000222728.3:c.459C>T	7.37:g.27185520G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_024014	A4D192|Q2M3G3|Q9UPM0	Silent	SNP	ENST00000222728.3	37	CCDS5407.1																																																																																			G|0.926;A|0.074	0.074	strong		0.662	HOXA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358697.1		
GOT2	2806	hgsc.bcm.edu	37	16	58750604	58750604	+	Silent	SNP	G	G	A	rs1058192	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58750604G>A	ENST00000245206.5	-	7	944	c.816C>T	c.(814-816)tgC>tgT	p.C272C	GOT2_ENST00000434819.2_Silent_p.C229C|GOT2_ENST00000564400.1_Intron	NM_002080.2	NP_002071.2	P00505	AATM_HUMAN	glutamic-oxaloacetic transaminase 2, mitochondrial	272					2-oxoglutarate metabolic process (GO:0006103)|4-hydroxyproline catabolic process (GO:0019470)|aspartate biosynthetic process (GO:0006532)|aspartate catabolic process (GO:0006533)|aspartate metabolic process (GO:0006531)|carbohydrate metabolic process (GO:0005975)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid transport (GO:0015908)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glutamate catabolic process to 2-oxoglutarate (GO:0019551)|glutamate catabolic process to aspartate (GO:0019550)|glutamate metabolic process (GO:0006536)|oxaloacetate metabolic process (GO:0006107)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-aspartate:2-oxoglutarate aminotransferase activity (GO:0004069)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)	p.C272C(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|prostate(2)|skin(1)	22					L-Aspartic Acid(DB00128)	ATTGGCAGAGGCAAACATTAA	0.502													A|||	3607	0.720248	0.8896	0.7738	5008	,	,		20689	0.6478		0.67	False		,,,				2504	0.5798				p.C272C		Atlas-SNP	.											GOT2,NS,carcinoma,0,1	GOT2	42	1	1	Substitution - coding silent(1)	prostate(1)	c.C816T						PASS	.	A		3702,694	289.8+/-280.6	1553,596,49	73.0	60.0	65.0		816	0.8	1.0	16	dbSNP_86	65	5574,3026	466.3+/-366.7	1803,1968,529	no	coding-synonymous	GOT2	NM_002080.2		3356,2564,578	AA,AG,GG		35.186,15.7871,28.6242		272/431	58750604	9276,3720	2198	4300	6498	SO:0001819	synonymous_variant	2806	exon7			GCAGAGGCAAACA		CCDS10801.1, CCDS67045.1	16q21	2013-05-29	2013-05-29		ENSG00000125166	ENSG00000125166	2.6.1.1		4433	protein-coding gene	gene with protein product	"""kynurenine aminotransferase IV"", ""aspartate aminotransferase 2"", ""aspartate transaminase 2"""	138150	"""glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)"""			17442055	Standard	NM_002080		Approved	mitAAT, KATIV, KAT4	uc002eof.1	P00505	OTTHUMG00000133769	ENST00000245206.5:c.816C>T	16.37:g.58750604G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	43	42	0.976744	NM_002080	B4DJA6|E7ERW2|Q53FL3|Q9BWA3	Silent	SNP	ENST00000245206.5	37	CCDS10801.1																																																																																			G|0.286;A|0.714	0.714	strong		0.502	GOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258289.3		
CACNA1G	8913	hgsc.bcm.edu	37	17	48701800	48701800	+	Silent	SNP	C	C	T	rs2301835	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48701800C>T	ENST00000359106.5	+	37	6309	c.6309C>T	c.(6307-6309)ctC>ctT	p.L2103L	CACNA1G_ENST00000514717.1_Silent_p.L1953L|CACNA1G_ENST00000442258.2_Silent_p.L1969L|CACNA1G_ENST00000512389.1_Silent_p.L1999L|CACNA1G_ENST00000513964.1_Silent_p.L1965L|CACNA1G_ENST00000507609.1_Silent_p.L2003L|CACNA1G_ENST00000503485.1_Silent_p.L1976L|CACNA1G_ENST00000513689.2_Silent_p.L2013L|CACNA1G_ENST00000505165.1_Silent_p.L2010L|CACNA1G_ENST00000507336.1_Silent_p.L2092L|CACNA1G_ENST00000515765.1_Silent_p.L2047L|CACNA1G_ENST00000502264.1_Silent_p.L2032L|CACNA1G_ENST00000510115.1_Silent_p.L2024L|CACNA1G_ENST00000360761.4_Silent_p.L1987L|CACNA1G_ENST00000354983.4_Silent_p.L2069L|CACNA1G_ENST00000507896.1_Silent_p.L1999L|CACNA1G_ENST00000358244.5_Silent_p.L1976L|CTB-22K21.2_ENST00000502435.1_RNA|CACNA1G_ENST00000515165.1_Silent_p.L2010L|CACNA1G_ENST00000510366.1_Silent_p.L1958L|CACNA1G_ENST00000515411.1_Silent_p.L2040L|CACNA1G_ENST00000352832.5_Silent_p.L1976L|CACNA1G_ENST00000514181.1_Silent_p.L1985L|CACNA1G_ENST00000514079.1_Silent_p.L2017L|CACNA1G_ENST00000507510.2_Silent_p.L2058L|CACNA1G_ENST00000429973.2_Silent_p.L1992L	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	2103					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CTCATCTGCTCCAGCCCCACA	0.637													C|||	580	0.115815	0.1884	0.0533	5008	,	,		14461	0.0982		0.0885	False		,,,				2504	0.1084				p.L2103L		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C6309T						PASS	.	C	,,,,,,,,,,,,,	588,3444		33,522,1461	30.0	31.0	31.0		6309,5928,6240,5997,6072,6141,5961,6096,6030,6174,5976,5928,5907,6207	1.0	1.0	17	dbSNP_100	31	629,7751		24,581,3585	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1G	NM_018896.3,NM_198376.1,NM_198377.1,NM_198378.1,NM_198379.1,NM_198380.1,NM_198382.1,NM_198383.1,NM_198384.1,NM_198385.1,NM_198386.1,NM_198387.1,NM_198388.1,NM_198396.1	,,,,,,,,,,,,,	57,1103,5046	TT,TC,CC		7.506,14.5833,9.805	,,,,,,,,,,,,,	2103/2378,1976/2172,2080/2355,1999/2274,2024/2299,2047/2322,1987/2262,2032/2307,2010/2285,2058/2333,1992/2267,1976/2251,1969/2244,2069/2344	48701800	1217,11195	2016	4190	6206	SO:0001819	synonymous_variant	8913	exon37			TCTGCTCCAGCCC	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.6309C>T	17.37:g.48701800C>T		Somatic	267	1	0.00374532		WXS	Illumina HiSeq	Phase_I	268	132	0.492537	NM_018896	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Silent	SNP	ENST00000359106.5	37	CCDS45730.1																																																																																			C|0.878;T|0.122	0.122	strong		0.637	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
ADNP2	22850	hgsc.bcm.edu	37	18	77895192	77895192	+	Silent	SNP	G	G	A	rs3744878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:77895192G>A	ENST00000262198.4	+	4	2351	c.1896G>A	c.(1894-1896)gcG>gcA	p.A632A		NM_014913.3	NP_055728.1	Q6IQ32	ADNP2_HUMAN	ADNP homeobox 2	632					cellular response to oxidative stress (GO:0034599)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|positive regulation of cell growth (GO:0030307)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|liver(1)|lung(15)|ovary(5)|prostate(2)	42		all_cancers(4;1.06e-15)|all_epithelial(4;2.36e-10)|all_lung(4;0.000302)|Lung NSC(4;0.000518)|Esophageal squamous(42;0.0212)|Ovarian(4;0.0256)|all_hematologic(56;0.15)|Melanoma(33;0.2)		Epithelial(2;1.1e-11)|OV - Ovarian serous cystadenocarcinoma(15;7.54e-09)|BRCA - Breast invasive adenocarcinoma(31;0.00247)|STAD - Stomach adenocarcinoma(84;0.164)		GAGGCCTTGCGACTGTCGCTC	0.632													G|||	549	0.109625	0.1241	0.1254	5008	,	,		18997	0.0337		0.16	False		,,,				2504	0.1053				p.A632A		Atlas-SNP	.											.	ADNP2	102	.	0			c.G1896A						PASS	.	G		519,3887	236.5+/-248.6	33,453,1717	74.0	72.0	72.0		1896	-9.7	0.0	18	dbSNP_107	72	1405,7195	272.3+/-290.0	126,1153,3021	no	coding-synonymous	ADNP2	NM_014913.3		159,1606,4738	AA,AG,GG		16.3372,11.7794,14.7932		632/1132	77895192	1924,11082	2203	4300	6503	SO:0001819	synonymous_variant	22850	exon4			CCTTGCGACTGTC	AB020670	CCDS32853.1	18q23	2013-01-07	2007-07-17	2007-07-17	ENSG00000101544	ENSG00000101544		"""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	23803	protein-coding gene	gene with protein product			"""zinc finger protein 508"""	ZNF508			Standard	NM_014913		Approved	KIAA0863	uc002lnw.3	Q6IQ32	OTTHUMG00000172535	ENST00000262198.4:c.1896G>A	18.37:g.77895192G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	75	32	0.426667	NM_014913	A8K951|O94943|Q9H9P3	Silent	SNP	ENST00000262198.4	37	CCDS32853.1																																																																																			G|0.871;A|0.129	0.129	strong		0.632	ADNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418979.1	NM_014913	
MYO1C	4641	hgsc.bcm.edu	37	17	1370542	1370542	+	Silent	SNP	C	C	A	rs2302458	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1370542C>A	ENST00000575158.1	-	31	3230	c.3054G>T	c.(3052-3054)ctG>ctT	p.L1018L	MYO1C_ENST00000545534.2_Silent_p.L1029L|MYO1C_ENST00000359786.5_Silent_p.L1053L|MYO1C_ENST00000438665.2_Silent_p.L1034L|MYO1C_ENST00000361007.2_Silent_p.L1018L			Q12965	MYO1E_HUMAN	myosin IC	0					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	17				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		TCACCACAGCCAGGTGCCCGT	0.642													C|||	463	0.0924521	0.1112	0.0735	5008	,	,		14864	0.0903		0.0924	False		,,,				2504	0.0828				p.L1053L		Atlas-SNP	.											.	MYO1C	57	.	0			c.G3159T						PASS	.	C	,,	517,3889	223.3+/-239.8	31,455,1717	61.0	47.0	52.0		3159,3102,3054	3.3	1.0	17	dbSNP_100	52	862,7738	186.4+/-233.9	42,778,3480	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	73,1233,5197	AA,AC,CC		10.0233,11.734,10.6028	,,	1053/1064,1034/1045,1018/1029	1370542	1379,11627	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon31			CACAGCCAGGTGC	X98507	CCDS11003.1, CCDS42226.1, CCDS45562.1	17p13.3	2011-09-27			ENSG00000197879	ENSG00000197879		"""Myosins / Myosin superfamily : Class I"""	7597	protein-coding gene	gene with protein product		606538				9119401	Standard	NM_001080779		Approved	myr2	uc002fsp.3	O00159	OTTHUMG00000090323	ENST00000575158.1:c.3054G>T	17.37:g.1370542C>A		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			C|0.904;A|0.096	0.096	strong		0.642	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2		
ATP6V1C2	245973	hgsc.bcm.edu	37	2	10912719	10912719	+	Silent	SNP	G	G	A	rs72777388	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:10912719G>A	ENST00000272238.4	+	8	730	c.621G>A	c.(619-621)gtG>gtA	p.V207V	RP11-791G15.2_ENST00000606907.1_lincRNA|ATP6V1C2_ENST00000381661.3_Silent_p.V207V	NM_001039362.1	NP_001034451.1	Q8NEY4	VATC2_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C2	207					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of Wnt signaling pathway (GO:0030177)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|protein dimerization activity (GO:0046983)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.15)|OV - Ovarian serous cystadenocarcinoma(76;0.152)		CAGACATGGTGGTCCCTCGAT	0.512													G|||	622	0.124201	0.1558	0.1369	5008	,	,		21688	0.0526		0.2028	False		,,,				2504	0.0654				p.V207V	NSCLC(188;1042 2136 10807 16813 47705)	Atlas-SNP	.											.	ATP6V1C2	73	.	0			c.G621A						PASS	.	G	,	651,3755	278.4+/-274.2	45,561,1597	273.0	273.0	273.0		621,621	2.2	1.0	2	dbSNP_130	273	1774,6826	322.0+/-315.3	187,1400,2713	no	coding-synonymous,coding-synonymous	ATP6V1C2	NM_001039362.1,NM_144583.3	,	232,1961,4310	AA,AG,GG		20.6279,14.7753,18.6452	,	207/428,207/382	10912719	2425,10581	2203	4300	6503	SO:0001819	synonymous_variant	245973	exon8			CATGGTGGTCCCT	AY039759	CCDS1674.1, CCDS42653.1	2p25.1	2010-04-21	2006-01-13		ENSG00000143882	ENSG00000143882		"""ATPases / V-type"""	18264	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 42kD, V1 subunit C isoform 2"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C isoform 2"""			12384298	Standard	XR_426949		Approved	VMA5, ATP6C2	uc002ras.3	Q8NEY4	OTTHUMG00000090459	ENST00000272238.4:c.621G>A	2.37:g.10912719G>A		Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	107	41	0.383178	NM_001039362	Q96EL8	Silent	SNP	ENST00000272238.4	37	CCDS42653.1																																																																																			G|0.830;A|0.170	0.170	strong		0.512	ATP6V1C2-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000323555.1	NM_144583	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057634	46057634	+	Silent	SNP	T	T	C	rs61029972	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057634T>C	ENST00000380095.1	+	1	362	c.300T>C	c.(298-300)tgT>tgC	p.C100C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	100	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						ctgtctgctgtgtgcccgtct	0.632													C|||	539	0.107628	0.2383	0.0591	5008	,	,		18755	0.0109		0.0557	False		,,,				2504	0.1186				p.C100C		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.T300C						PASS	.						126.0	121.0	123.0					21																	46057634		2203	4298	6501	SO:0001819	synonymous_variant	353333	exon1			CTGCTGTGTGCCC	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.300T>C	21.37:g.46057634T>C		Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	145	84	0.57931	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|1.000;|0.000	1.000	weak		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
TBC1D31	93594	hgsc.bcm.edu	37	8	124138855	124138855	+	Silent	SNP	G	G	A	rs16898012	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124138855G>A	ENST00000287380.1	+	13	1902	c.1812G>A	c.(1810-1812)ctG>ctA	p.L604L	TBC1D31_ENST00000309336.3_Silent_p.L604L|TBC1D31_ENST00000522420.1_Silent_p.L499L|TBC1D31_ENST00000327098.5_Silent_p.L604L|TBC1D31_ENST00000521676.1_Silent_p.L481L|TBC1D31_ENST00000518805.1_Silent_p.L237L|TBC1D31_ENST00000378080.2_Silent_p.L499L	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	604						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										CCTTCCTTCTGATGACTGTTG	0.423													G|||	1490	0.297524	0.3858	0.3732	5008	,	,		15646	0.1815		0.2525	False		,,,				2504	0.2904				p.L604L		Atlas-SNP	.											.	WDR67	97	.	0			c.G1812A						PASS	.	G	,	1691,2715	513.1+/-368.2	325,1041,837	126.0	120.0	122.0		1812,1812	1.8	1.0	8	dbSNP_123	122	2218,6382	378.1+/-338.8	277,1664,2359	no	coding-synonymous,coding-synonymous	WDR67	NM_001145088.1,NM_145647.3	,	602,2705,3196	AA,AG,GG		25.7907,38.3795,30.0554	,	604/971,604/1067	124138855	3909,9097	2203	4300	6503	SO:0001819	synonymous_variant	93594	exon13			CCTTCTGATGACT	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.1812G>A	8.37:g.124138855G>A		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	166	89	0.536145	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	37	CCDS6338.1																																																																																			G|0.705;A|0.295	0.295	strong		0.423	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
C2CD2	25966	hgsc.bcm.edu	37	21	43338328	43338328	+	Silent	SNP	C	C	A	rs2839422	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43338328C>A	ENST00000380486.3	-	5	847	c.606G>T	c.(604-606)gtG>gtT	p.V202V	C2CD2_ENST00000329623.7_Silent_p.V47V	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	202						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						TTGTCTCAGCCACCTGGTCCT	0.507													C|||	334	0.0666933	0.112	0.0476	5008	,	,		22890	0.0		0.0298	False		,,,				2504	0.1258				p.V202V		Atlas-SNP	.											.	C2CD2	47	.	0			c.G606T						PASS	.	C	,	384,4022	192.6+/-218.0	17,350,1836	105.0	86.0	93.0		606,141	-0.6	0.0	21	dbSNP_100	93	347,8253	118.8+/-178.2	12,323,3965	no	coding-synonymous,coding-synonymous	C2CD2	NM_015500.1,NM_199050.2	,	29,673,5801	AA,AC,CC		4.0349,8.7154,5.6205	,	202/697,47/542	43338328	731,12275	2203	4300	6503	SO:0001819	synonymous_variant	25966	exon5			CTCAGCCACCTGG	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.606G>T	21.37:g.43338328C>A		Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	54	16	0.296296	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Silent	SNP	ENST00000380486.3	37	CCDS42933.1																																																																																			C|0.943;A|0.057	0.057	strong		0.507	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
FBN3	84467	hgsc.bcm.edu	37	19	8176569	8176569	+	Silent	SNP	G	G	A	rs35306870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8176569G>A	ENST00000600128.1	-	32	4461	c.4047C>T	c.(4045-4047)tgC>tgT	p.C1349C	FBN3_ENST00000601739.1_Silent_p.C1349C|FBN3_ENST00000270509.2_Silent_p.C1349C			Q75N90	FBN3_HUMAN	fibrillin 3	1349	EGF-like 20; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						AGCCCTGGCGGCAGGTGCAGC	0.632													G|||	1287	0.256989	0.1331	0.3876	5008	,	,		10551	0.4226		0.2346	False		,,,				2504	0.184				p.C1349C		Atlas-SNP	.											FBN3,colon,carcinoma,0,1	FBN3	300	1	0			c.C4047T						PASS	.	G		755,3651	297.6+/-284.8	59,637,1507	32.0	32.0	32.0		4047	1.6	0.3	19	dbSNP_126	32	2078,6522	351.7+/-328.4	242,1594,2464	no	coding-synonymous	FBN3	NM_032447.3		301,2231,3971	AA,AG,GG		24.1628,17.1357,21.7823		1349/2810	8176569	2833,10173	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon31			CTGGCGGCAGGTG		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.4047C>T	19.37:g.8176569G>A		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	149	63	0.422819	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.761;A|0.239	0.239	strong		0.632	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
DPCR1	135656	hgsc.bcm.edu	37	6	30919878	30919878	+	Missense_Mutation	SNP	G	G	C	rs11970154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30919878G>C	ENST00000462446.1	+	2	3665	c.3637G>C	c.(3637-3639)Ggg>Cgg	p.G1213R	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.G55R			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	337						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						AGAAAACCTGGGGAACACCAC	0.453													G|||	924	0.184505	0.4145	0.1614	5008	,	,		20677	0.0605		0.1491	False		,,,				2504	0.0542				p.G1213R		Atlas-SNP	.											.	DPCR1	99	.	0			c.G3637C						PASS	.	G	ARG/GLY	1532,2874	485.1+/-360.2	283,966,954	143.0	144.0	144.0		3637	-2.9	0.0	6	dbSNP_120	144	1045,7555	221.6+/-259.0	62,921,3317	yes	missense	DPCR1	NM_080870.3	125	345,1887,4271	CC,CG,GG		12.1512,34.7708,19.8139	possibly-damaging	1213/1394	30919878	2577,10429	2203	4300	6503	SO:0001583	missense	135656	exon2			AACCTGGGGAACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.3637G>C	6.37:g.30919878G>C	ENSP00000417182:p.Gly1213Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	74	37	0.5	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	385	0.1762820512820513	190	0.3861788617886179	54	0.14917127071823205	44	0.07692307692307693	97	0.1279683377308707	G	3.993	-0.003997	0.07773	0.347708	0.121512	ENSG00000168631	ENST00000462446;ENST00000450344;ENST00000304311	T;T	0.21191	2.02;2.04	3.26	-2.87	0.05700	.	.	.	.	.	T	0.02807	0.0084	N	0.19112	0.55	0.80722	P	0.0	P	0.34615	0.459	B	0.31751	0.135	T	0.38329	-0.9666	8	0.20046	T	0.44	-0.0399	6.4088	0.21680	0.3898:0.1277:0.4825:0.0	rs11970154;rs52799830;rs61397826;rs11970154	1213	E9PEI6	.	R	1213;337;55	ENSP00000417182:G1213R;ENSP00000305948:G55R	ENSP00000305948:G55R	G	+	1	0	DPCR1	31027857	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.144000	0.10280	-1.457000	0.01919	-1.183000	0.01708	GGG	G|0.816;C|0.184	0.184	strong		0.453	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000458205.2_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.I219V(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TATTCGCTCCATCTTTGGAAA	0.368		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145.0	129.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1.0	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	2203	4300	6503	SO:0001583	missense	4292	exon8	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	CGCTCCATCTTTG	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	101	44	0.435644	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
MSLN	10232	hgsc.bcm.edu	37	16	813650	813650	+	Silent	SNP	G	G	A	rs3765319	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:813650G>A	ENST00000382862.3	+	4	233	c.138G>A	c.(136-138)gcG>gcA	p.A46A	MSLN_ENST00000545450.2_Silent_p.A46A|MSLN_ENST00000566549.1_Silent_p.A46A|MSLN_ENST00000563941.1_Silent_p.A46A	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	46					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				AGGAGGCTGCGCCCCTGGACG	0.662													G|||	724	0.144569	0.0477	0.1153	5008	,	,		11642	0.3006		0.1501	False		,,,				2504	0.1299				p.A46A		Atlas-SNP	.											.	MSLN	109	.	0			c.G138A						PASS	.	G	,,	299,4089	156.6+/-189.7	11,277,1906	37.0	34.0	35.0		138,138,138	-3.2	0.0	16	dbSNP_107	35	1605,6979	289.3+/-299.2	158,1289,2845	no	coding-synonymous,coding-synonymous,coding-synonymous	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	,,	169,1566,4751	AA,AG,GG		18.6976,6.814,14.6778	,,	46/623,46/623,46/631	813650	1904,11068	2194	4292	6486	SO:0001819	synonymous_variant	10232	exon5			GGCTGCGCCCCTG	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.138G>A	16.37:g.813650G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	31	0.563636	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Silent	SNP	ENST00000382862.3	37	CCDS32356.1																																																																																			A|0.146;G|0.854;T|0.000	0.146	strong		0.662	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
SERPINB13	5275	hgsc.bcm.edu	37	18	61264468	61264468	+	Silent	SNP	C	C	T	rs1020693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:61264468C>T	ENST00000344731.5	+	8	1149	c.1047C>T	c.(1045-1047)acC>acT	p.T349T	SERPINB13_ENST00000269489.5_Silent_p.T297T	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	349					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						CAGCTGCCACCGGCATAGGCT	0.537													C|||	3944	0.78754	0.6921	0.7752	5008	,	,		18732	0.875		0.8042	False		,,,				2504	0.818				p.T349T		Atlas-SNP	.											.	SERPINB13	51	.	0			c.C1047T						PASS	.	C		3232,1174	708.8+/-407.7	1186,860,157	67.0	57.0	60.0		1047	-3.8	0.0	18	dbSNP_86	60	6790,1810	727.6+/-406.6	2685,1420,195	no	coding-synonymous	SERPINB13	NM_012397.3		3871,2280,352	TT,TC,CC		21.0465,26.6455,22.9433		349/392	61264468	10022,2984	2203	4300	6503	SO:0001819	synonymous_variant	5275	exon8			TGCCACCGGCATA	AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"""Serine (or cysteine) peptidase inhibitors"""	8944	protein-coding gene	gene with protein product		604445	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"""	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.1047C>T	18.37:g.61264468C>T		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	74	73	0.986486	NM_012397	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Silent	SNP	ENST00000344731.5	37	CCDS11985.1																																																																																			C|0.229;T|0.771	0.771	strong		0.537	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397	
PDGFRB	5159	hgsc.bcm.edu	37	5	149504348	149504348	+	Silent	SNP	C	C	T	rs56072663	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149504348C>T	ENST00000261799.4	-	13	2323	c.1854G>A	c.(1852-1854)acG>acA	p.T618T		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	618	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)			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)	GGCCATGAGCCGTGGCCTCCA	0.602			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""								C|||	92	0.0183706	0.0015	0.0173	5008	,	,		11479	0.001		0.0239	False		,,,				2504	0.0542				p.T618T		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	PDGFRB,NS,carcinoma,0,2	PDGFRB	142	2	0			c.G1854A						PASS	.	C		27,4379	33.5+/-64.1	0,27,2176	44.0	42.0	43.0		1854	-5.5	0.9	5	dbSNP_129	43	324,8276	113.5+/-173.5	9,306,3985	no	coding-synonymous	PDGFRB	NM_002609.3		9,333,6161	TT,TC,CC		3.7674,0.6128,2.6988		618/1107	149504348	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon13			ATGAGCCGTGGCC	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.1854G>A	5.37:g.149504348C>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	55	24	0.436364	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			C|0.971;T|0.029	0.029	strong		0.602	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
INHBC	3626	hgsc.bcm.edu	37	12	57843711	57843711	+	Missense_Mutation	SNP	G	G	A	rs2229357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57843711G>A	ENST00000309668.2	+	2	1092	c.965G>A	c.(964-966)cGg>cAg	p.R322Q		NM_005538.2	NP_005529.1	P55103	INHBC_HUMAN	inhibin, beta C	322			R -> Q (in dbSNP:rs2229357).		growth (GO:0040007)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	transforming growth factor beta receptor binding (GO:0005160)			breast(2)|endometrium(1)|large_intestine(6)|liver(2)|lung(4)|prostate(1)	16						CCCACGGCCCGGCGCCCCCTG	0.552													G|||	661	0.131989	0.0779	0.3098	5008	,	,		19277	0.0675		0.1948	False		,,,				2504	0.0808				p.R322Q		Atlas-SNP	.											.	INHBC	28	.	0			c.G965A						PASS	.	G	GLN/ARG	421,3985	206.2+/-227.9	15,391,1797	56.0	58.0	58.0		965	2.4	0.1	12	dbSNP_98	58	1950,6650	342.3+/-324.4	215,1520,2565	yes	missense	INHBC	NM_005538.2	43	230,1911,4362	AA,AG,GG		22.6744,9.5552,18.23	benign	322/353	57843711	2371,10635	2203	4300	6503	SO:0001583	missense	3626	exon2			CGGCCCGGCGCCC		CCDS8938.1	12q13	2008-02-05				ENSG00000175189			6068	protein-coding gene	gene with protein product		601233				7826378	Standard	NM_005538		Approved		uc001snv.1	P55103	OTTHUMG00000169994	ENST00000309668.2:c.965G>A	12.37:g.57843711G>A	ENSP00000308716:p.Arg322Gln	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	52	30	0.576923	NM_005538	A1L3Y2	Missense_Mutation	SNP	ENST00000309668.2	37	CCDS8938.1	329	0.15064102564102563	34	0.06910569105691057	103	0.2845303867403315	47	0.08216783216783216	145	0.19129287598944592	G	17.17	3.321303	0.60634	0.095552	0.226744	ENSG00000175189	ENST00000309668	D	0.83673	-1.75	4.27	2.42	0.29668	Transforming growth factor-beta, C-terminal (3);	0.183489	0.44902	N	0.000413	T	0.00012	0.0000	L	0.44542	1.39	0.58432	P	9.99999999995449E-6	B	0.30281	0.275	B	0.26094	0.066	T	0.02743	-1.1116	8	.	.	.	-5.7127	10.1755	0.42935	0.1715:0.0:0.8284:0.0	rs2229357;rs3741416	322	P55103	INHBC_HUMAN	Q	322	ENSP00000308716:R322Q	.	R	+	2	0	INHBC	56129978	0.742000	0.28228	0.101000	0.21167	0.985000	0.73830	2.087000	0.41653	0.742000	0.32697	0.655000	0.94253	CGG	G|0.838;A|0.162	0.162	strong		0.552	INHBC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406770.1	NM_005538	
TNRC18	84629	hgsc.bcm.edu	37	7	5399044	5399044	+	Silent	SNP	C	C	G	rs12531309	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5399044C>G	ENST00000430969.1	-	15	5166	c.4818G>C	c.(4816-4818)tcG>tcC	p.S1606S	TNRC18_ENST00000399537.4_Silent_p.S1606S	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1606							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)		TGATGAAGTCCGACGAGGCCT	0.547													G|||	1278	0.255192	0.2489	0.2536	5008	,	,		21101	0.2808		0.2594	False		,,,				2504	0.2342				p.S1606S		Atlas-SNP	.											.	TNRC18	311	.	0			c.G4818C						PASS	.	G		984,2968		134,716,1126	213.0	214.0	214.0		4818	-11.1	0.0	7	dbSNP_120	214	2414,5914		339,1736,2089	no	coding-synonymous	TNRC18	NM_001080495.2		473,2452,3215	GG,GC,CC		28.9866,24.8988,27.671		1606/2969	5399044	3398,8882	1976	4164	6140	SO:0001819	synonymous_variant	84629	exon15			GAAGTCCGACGAG	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.4818G>C	7.37:g.5399044C>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			C|0.729;G|0.271	0.271	strong		0.547	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PHLDB3	653583	hgsc.bcm.edu	37	19	44001345	44001345	+	Silent	SNP	C	C	T	rs7257767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44001345C>T	ENST00000292140.5	-	6	1110	c.750G>A	c.(748-750)gaG>gaA	p.E250E	PHLDB3_ENST00000599242.1_Silent_p.E250E	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	250							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				TGTCCCGATCCTCCTCCTCCT	0.632													C|||	892	0.178115	0.3321	0.1066	5008	,	,		16847	0.1131		0.1113	False		,,,				2504	0.1564				p.E250E		Atlas-SNP	.											.	PHLDB3	30	.	0			c.G750A						PASS	.	C		1146,3260	401.5+/-332.0	143,860,1200	59.0	58.0	58.0		750	1.0	1.0	19	dbSNP_116	58	891,7709	197.9+/-242.4	48,795,3457	no	coding-synonymous	PHLDB3	NM_198850.3		191,1655,4657	TT,TC,CC		10.3605,26.01,15.662		250/641	44001345	2037,10969	2203	4300	6503	SO:0001819	synonymous_variant	653583	exon6			CCGATCCTCCTCC		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.750G>A	19.37:g.44001345C>T		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	62	26	0.419355	NM_198850	Q8N7Z4	Silent	SNP	ENST00000292140.5	37	CCDS12621.2																																																																																			C|0.843;T|0.157	0.157	strong		0.632	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2		
TCTEX1D1	200132	hgsc.bcm.edu	37	1	67243024	67243024	+	Missense_Mutation	SNP	C	C	A	rs2133173	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:67243024C>A	ENST00000282670.2	+	5	555	c.427C>A	c.(427-429)Ctt>Att	p.L143I		NM_152665.2	NP_689878.2	Q8N7M0	TC1D1_HUMAN	Tctex1 domain containing 1	143			L -> I (in dbSNP:rs2133173). {ECO:0000269|PubMed:15489334}.							large_intestine(2)|lung(10)|skin(1)	13						GCAGAGCATACTTATTGGAAG	0.383													C|||	990	0.197684	0.205	0.2219	5008	,	,		17572	0.1012		0.2932	False		,,,				2504	0.1718				p.L143I		Atlas-SNP	.											.	TCTEX1D1	27	.	0			c.C427A						PASS	.	C	ILE/LEU	1034,3372	379.9+/-323.5	109,816,1278	164.0	170.0	168.0		427	1.9	0.8	1	dbSNP_96	168	2542,6058	415.5+/-351.8	397,1748,2155	yes	missense	TCTEX1D1	NM_152665.2	5	506,2564,3433	AA,AC,CC		29.5581,23.468,27.495	benign	143/180	67243024	3576,9430	2203	4300	6503	SO:0001583	missense	200132	exon5			AGCATACTTATTG	AK098192	CCDS633.1	1p31.2	2008-02-05			ENSG00000152760	ENSG00000152760			26882	protein-coding gene	gene with protein product							Standard	NM_152665		Approved	FLJ40873	uc001dcv.3	Q8N7M0	OTTHUMG00000009162	ENST00000282670.2:c.427C>A	1.37:g.67243024C>A	ENSP00000282670:p.Leu143Ile	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	142	54	0.380282	NM_152665	Q06YR9|Q5VYE1	Missense_Mutation	SNP	ENST00000282670.2	37	CCDS633.1	490	0.22435897435897437	104	0.21138211382113822	92	0.2541436464088398	60	0.1048951048951049	234	0.3087071240105541	C	5.444	0.267048	0.10294	0.23468	0.295581	ENSG00000152760	ENST00000282670	T	0.29655	1.56	5.93	1.91	0.25777	.	0.696895	0.15165	N	0.276948	T	0.11793	0.0287	L	0.59436	1.845	0.53688	P	2.8999999999945736E-5	B	0.20368	0.044	B	0.25759	0.063	T	0.15925	-1.0420	9	0.22109	T	0.4	1.5115	7.868	0.29549	0.0:0.6817:0.1202:0.1981	rs2133173;rs17495194;rs52837318;rs59922194;rs2133173	143	Q8N7M0	TC1D1_HUMAN	I	143	ENSP00000282670:L143I	ENSP00000282670:L143I	L	+	1	0	TCTEX1D1	67015612	0.160000	0.22878	0.828000	0.32881	0.190000	0.23558	1.313000	0.33585	0.105000	0.17753	0.655000	0.94253	CTT	C|0.762;N|0.000	.	strong		0.383	TCTEX1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025399.2	NM_152665	
SBF1	6305	hgsc.bcm.edu	37	22	50898026	50898026	+	Silent	SNP	G	G	A	rs58335489	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50898026G>A	ENST00000390679.3	-	27	3745	c.3561C>T	c.(3559-3561)taC>taT	p.Y1187Y	SBF1_ENST00000476293.1_5'Flank|SBF1_ENST00000380817.3_Silent_p.Y1187Y|SBF1_ENST00000348911.6_Silent_p.Y1188Y			O95248	MTMR5_HUMAN	SET binding factor 1	1187	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)		GGTTCTGGCGGTAGCAGCGGG	0.682													G|||	949	0.189497	0.0272	0.2507	5008	,	,		16077	0.4524		0.0666	False		,,,				2504	0.2209				p.Y1187Y		Atlas-SNP	.											.	SBF1	211	.	0			c.C3561T						PASS	.	G		143,4147		0,143,2002	18.0	21.0	20.0		3561	2.5	1.0	22	dbSNP_129	20	573,7889		18,537,3676	no	coding-synonymous	SBF1	NM_002972.2		18,680,5678	AA,AG,GG		6.7714,3.3333,5.6148		1187/1894	50898026	716,12036	2145	4231	6376	SO:0001819	synonymous_variant	6305	exon27			CTGGCGGTAGCAG	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.3561C>T	22.37:g.50898026G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				G|0.848;A|0.152	0.152	strong		0.682	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
TRDMT1	1787	hgsc.bcm.edu	37	10	17210881	17210881	+	Silent	SNP	A	A	G	rs7096233	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:17210881A>G	ENST00000377799.3	-	3	257	c.210T>C	c.(208-210)ttT>ttC	p.F70F	TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000488990.1_Intron|TRDMT1_ENST00000412821.3_Silent_p.F70F|TRDMT1_ENST00000351358.4_Silent_p.F70F|TRDMT1_ENST00000377766.5_Intron|TRDMT1_ENST00000457442.2_Intron|TRDMT1_ENST00000358282.7_Intron	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	70	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	AAATCATATCAAAAGATAATC	0.383													G|||	583	0.116414	0.1014	0.2205	5008	,	,		19009	0.0387		0.1521	False		,,,				2504	0.1063				p.F70F		Atlas-SNP	.											.	TRDMT1	46	.	0			c.T210C						PASS	.	G		501,3905	778.7+/-414.3	30,441,1732	72.0	71.0	71.0		210	2.1	0.4	10	dbSNP_116	71	1192,7408	761.9+/-407.6	84,1024,3192	no	coding-synonymous	TRDMT1	NM_004412.5		114,1465,4924	GG,GA,AA		13.8605,11.3709,13.0171		70/392	17210881	1693,11313	2203	4300	6503	SO:0001819	synonymous_variant	1787	exon3			CATATCAAAAGAT	AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.210T>C	10.37:g.17210881A>G		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1	253	0.11584249084249085	48	0.0975609756097561	81	0.22375690607734808	22	0.038461538461538464	102	0.1345646437994723	G	4.353	0.064939	0.08388	0.113709	0.138605	ENSG00000107614	ENST00000313936	.	.	.	5.95	2.11	0.27256	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999081761	.	.	.	.	.	.	.	.	.	.	.	.	.	-10.4036	10.9624	0.47393	0.4168:0.0:0.5832:0.0	rs7096233;rs17854513;rs58340579;rs7096233	.	.	.	R	50	.	.	X	-	1	0	TRDMT1	17250887	1.000000	0.71417	0.381000	0.26106	0.458000	0.32498	1.196000	0.32198	-0.052000	0.13311	-1.972000	0.00464	TGA	A|0.879;G|0.121	0.121	strong		0.383	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
HSPA1B	3304	hgsc.bcm.edu	37	6	31797587	31797587	+	Silent	SNP	C	C	G	rs539689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31797587C>G	ENST00000375650.3	+	1	2076	c.1860C>G	c.(1858-1860)ggC>ggG	p.G620G	HSPA1B_ENST00000545241.1_Silent_p.G529G	NM_005346.4	NP_005337.2	P08107	HSP71_HUMAN	heat shock 70kDa protein 1B	620					ATP catabolic process (GO:0006200)|cellular heat acclimation (GO:0070370)|cellular response to heat (GO:0034605)|gene expression (GO:0010467)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of inclusion body assembly (GO:0090084)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of erythrocyte differentiation (GO:0045648)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)	aggresome (GO:0016235)|blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|inclusion body (GO:0016234)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|double-stranded RNA binding (GO:0003725)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|poly(A) RNA binding (GO:0044822)|protein binding involved in protein folding (GO:0044183)|protein N-terminus binding (GO:0047485)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)|virus receptor activity (GO:0001618)			breast(1)|large_intestine(1)|prostate(1)	3						CCGGGCCTGGCGGCTTCGGGG	0.592																																					p.G620G		Atlas-SNP	.											.	HSPA1B	5	.	0			c.C1860G						PASS	.	C		1226,2110		325,576,767	56.0	67.0	64.0		1860	-8.8	0.2	6	dbSNP_83	64	2645,3863		680,1285,1289	no	coding-synonymous	HSPA1B	NM_005346.4		1005,1861,2056	GG,GC,CC		40.6423,36.7506,39.3234		620/642	31797587	3871,5973	1668	3254	4922	SO:0001819	synonymous_variant	3304	exon1			GCCTGGCGGCTTC		CCDS34415.1	6p21.3	2011-09-02	2002-08-29		ENSG00000204388	ENSG00000204388		"""Heat shock proteins / HSP70"""	5233	protein-coding gene	gene with protein product		603012	"""heat shock 70kD protein 1B"""			1700760	Standard	NM_005346		Approved	HSP70-2	uc003nxk.2	P08107	OTTHUMG00000031202	ENST00000375650.3:c.1860C>G	6.37:g.31797587C>G		Somatic	287	1	0.00348432		WXS	Illumina HiSeq	Phase_I	259	111	0.428571	NM_005346	B4E3B6|P19790|Q5JQI4|Q5SP17|Q9UQL9|Q9UQM0	Silent	SNP	ENST00000375650.3	37	CCDS34415.1																																																																																			C|0.554;G|0.446	0.446	strong		0.592	HSPA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076402.2		
HOXB1	3211	hgsc.bcm.edu	37	17	46607817	46607817	+	Silent	SNP	C	C	T	rs7207109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:46607817C>T	ENST00000239174.6	-	1	542	c.450G>A	c.(448-450)gcG>gcA	p.A150A	HOXB1_ENST00000577092.1_Silent_p.A150A	NM_002144.3	NP_002135.2	P14653	HXB1_HUMAN	homeobox B1	150					anatomical structure formation involved in morphogenesis (GO:0048646)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|multicellular organismal development (GO:0007275)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GTGCAAAGCTCGCGGTCTGCT	0.637													C|||	660	0.131789	0.1082	0.1225	5008	,	,		16178	0.0972		0.2048	False		,,,				2504	0.1309				p.A150A		Atlas-SNP	.											.	HOXB1	67	.	0			c.G450A						PASS	.	C		547,3859	248.1+/-256.1	32,483,1688	64.0	65.0	65.0		450	-4.2	0.0	17	dbSNP_116	65	1786,6814	321.2+/-315.0	184,1418,2698	no	coding-synonymous	HOXB1	NM_002144.3		216,1901,4386	TT,TC,CC		20.7674,12.4149,17.9379		150/302	46607817	2333,10673	2203	4300	6503	SO:0001819	synonymous_variant	3211	exon1			AAAGCTCGCGGTC		CCDS32675.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120094	ENSG00000120094		"""Homeoboxes / ANTP class : HOXL subclass"""	5111	protein-coding gene	gene with protein product		142968	"""homeo box B1"""	HOX2, HOX2I		1973146, 1358459	Standard	NM_002144		Approved		uc002ink.1	P14653	OTTHUMG00000159929	ENST00000239174.6:c.450G>A	17.37:g.46607817C>T		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	116	60	0.517241	NM_002144	Q4VB03	Silent	SNP	ENST00000239174.6	37	CCDS32675.1																																																																																			C|0.838;T|0.162	0.162	strong		0.637	HOXB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358383.3		
TEK	7010	hgsc.bcm.edu	37	9	27202870	27202870	+	Silent	SNP	A	A	G	rs639225	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:27202870A>G	ENST00000380036.4	+	13	2404	c.1962A>G	c.(1960-1962)tcA>tcG	p.S654S	TEK_ENST00000406359.4_Silent_p.S611S|TEK_ENST00000519097.1_Silent_p.S507S	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	654	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)	CACACTCCTCAGCTGTGATTT	0.363													G|||	2075	0.414337	0.3336	0.5086	5008	,	,		21647	0.3998		0.4811	False		,,,				2504	0.4029				p.S654S		Atlas-SNP	.											TEK_ENST00000380036,colon,carcinoma,+1,1	TEK	250	1	0			c.A1962G						PASS	.	G		1668,2738	656.9+/-400.1	300,1068,835	157.0	154.0	155.0		1962	-10.0	0.0	9	dbSNP_83	155	4136,4464	589.0+/-392.5	985,2166,1149	no	coding-synonymous	TEK	NM_000459.3		1285,3234,1984	GG,GA,AA		48.093,37.8575,44.6256		654/1125	27202870	5804,7202	2203	4300	6503	SO:0001819	synonymous_variant	7010	exon13			CTCCTCAGCTGTG	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.1962A>G	9.37:g.27202870A>G		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	199	80	0.40201	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Silent	SNP	ENST00000380036.4	37	CCDS6519.1																																																																																			A|0.569;G|0.431	0.431	strong		0.363	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
SLC22A24	283238	hgsc.bcm.edu	37	11	62848568	62848568	+	Silent	SNP	C	C	G	rs11231342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62848568C>G	ENST00000417740.1	-	9	1863	c.1422G>C	c.(1420-1422)gtG>gtC	p.V474V		NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	0					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						TCCTACCGGACACTGCATTGA	0.443													C|||	2222	0.44369	0.3442	0.4914	5008	,	,		22267	0.4196		0.5109	False		,,,				2504	0.5				p.V474V		Atlas-SNP	.											.	SLC22A24	31	.	0			c.G1422C						PASS	.	C		491,893		86,319,287	97.0	94.0	95.0		1422	-1.6	0.0	11	dbSNP_120	95	1692,1490		447,798,346	no	coding-synonymous	SLC22A24	NM_001136506.2		533,1117,633	GG,GC,CC		46.8259,35.4769,47.8099		474/553	62848568	2183,2383	692	1591	2283	SO:0001819	synonymous_variant	283238	exon9			ACCGGACACTGCA		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.1422G>C	11.37:g.62848568C>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	93	41	0.44086	NM_001136506		Silent	SNP	ENST00000417740.1	37																																																																																				C|0.539;G|0.461	0.461	strong		0.443	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
TMEM8A	58986	hgsc.bcm.edu	37	16	427479	427479	+	Missense_Mutation	SNP	T	T	C	rs11248931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:427479T>C	ENST00000431232.2	-	3	566	c.406A>G	c.(406-408)Aca>Gca	p.T136A	TMEM8A_ENST00000250930.3_5'UTR|TMEM8A_ENST00000476735.1_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	136			T -> A (in dbSNP:rs11248931). {ECO:0000269|PubMed:11006113, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						CTTCTCGGTGTGGTGCTCAGC	0.682											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2677	0.534545	0.6188	0.4755	5008	,	,		15166	0.3006		0.5408	False		,,,				2504	0.6973				p.T136A		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,1	TMEM8A	49	1	0			c.A406G						PASS	.	C	ALA/THR	2729,1649		847,1035,307	22.0	22.0	22.0		406	1.0	0.0	16	dbSNP_120	22	4876,3718		1417,2042,838	yes	missense	TMEM8A	NM_021259.2	58	2264,3077,1145	CC,CT,TT		43.2627,37.6656,41.3737	benign	136/772	427479	7605,5367	2189	4297	6486	SO:0001583	missense	58986	exon3			TCGGTGTGGTGCT	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.406A>G	16.37:g.427479T>C	ENSP00000401338:p.Thr136Ala	Somatic	124	0	0	588	WXS	Illumina HiSeq	Phase_I	109	37	0.33945	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	1089	0.49862637362637363	335	0.6808943089430894	181	0.5	163	0.28496503496503495	410	0.5408970976253298	C	0.003	-2.441316	0.00180	0.623344	0.567373	ENSG00000129925	ENST00000431232	T	0.23147	1.92	3.34	0.981	0.19756	.	3.558320	0.02310	N	0.072046	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40590	-0.9555	9	0.06099	T	0.92	-8.0545	4.5877	0.12291	0.15:0.2114:0.0:0.6386	rs11248931;rs17845652;rs17858586;rs57237473;rs11248931	136	Q9HCN3	TMM8A_HUMAN	A	136	ENSP00000401338:T136A	ENSP00000401338:T136A	T	-	1	0	TMEM8A	367480	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.411000	0.02478	-0.100000	0.12241	-1.309000	0.01313	ACA	T|0.463;C|0.537	0.537	strong		0.682	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
LAMB4	22798	hgsc.bcm.edu	37	7	107671407	107671407	+	Missense_Mutation	SNP	C	C	G	rs2528693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:107671407C>G	ENST00000388781.3	-	32	4919	c.4836G>C	c.(4834-4836)agG>agC	p.R1612S	LAMB4_ENST00000388780.3_Missense_Mutation_p.R1612S|LAMB4_ENST00000483484.1_Intron|LAMB4_ENST00000205386.4_Missense_Mutation_p.R1612S	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	1612	Domain I.		R -> S (in dbSNP:rs2528693).		cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TCTTCATTTCCCTGGTTTGAT	0.423													C|||	508	0.101438	0.2307	0.0605	5008	,	,		16353	0.0288		0.0825	False		,,,				2504	0.0501				p.R1612S		Atlas-SNP	.											.	LAMB4	253	.	0			c.G4836C						PASS	.	C	SER/ARG	935,3471	355.6+/-313.1	97,741,1365	131.0	104.0	113.0		4836	-2.7	0.0	7	dbSNP_100	113	514,8086	143.7+/-199.7	18,478,3804	yes	missense	LAMB4	NM_007356.2	110	115,1219,5169	GG,GC,CC		5.9767,21.2211,11.141	benign	1612/1762	107671407	1449,11557	2203	4300	6503	SO:0001583	missense	22798	exon32			CATTTCCCTGGTT	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.4836G>C	7.37:g.107671407C>G	ENSP00000373433:p.Arg1612Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	136	66	0.485294	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	221	0.10119047619047619	109	0.22154471544715448	28	0.07734806629834254	13	0.022727272727272728	71	0.09366754617414248	C	0.018	-1.474438	0.01044	0.212211	0.059767	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000422975;ENST00000388780	T;T;T;T	0.76968	1.56;1.56;-1.06;1.59	5.01	-2.7	0.06004	.	0.883646	0.09584	N	0.782361	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.13145	0.003;0.007	B;B	0.10450	0.005;0.003	T	0.03673	-1.1014	9	0.12766	T	0.61	.	1.1905	0.01864	0.1624:0.2599:0.1433:0.4343	rs2528693;rs52796921;rs2528693	1612;1612	A4D0S4-3;A4D0S4	.;LAMB4_HUMAN	S	1612;1612;638;1612	ENSP00000205386:R1612S;ENSP00000373433:R1612S;ENSP00000416562:R638S;ENSP00000373432:R1612S	ENSP00000205386:R1612S	R	-	3	2	LAMB4	107458643	0.000000	0.05858	0.000000	0.03702	0.170000	0.22686	-0.029000	0.12329	-0.306000	0.08818	-0.237000	0.12165	AGG	C|0.892;G|0.108	0.108	strong		0.423	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
IL18R1	8809	hgsc.bcm.edu	37	2	103001402	103001402	+	Silent	SNP	C	C	T	rs1035130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:103001402C>T	ENST00000409599.1	+	8	1109	c.753C>T	c.(751-753)ttC>ttT	p.F251F	IL18R1_ENST00000233957.1_Silent_p.F251F			Q13478	IL18R_HUMAN	interleukin 18 receptor 1	251	Ig-like C2-type 3.				immune response (GO:0006955)|natural killer cell activation (GO:0030101)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|signal transduction (GO:0007165)|T-helper 1 cell differentiation (GO:0045063)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-18 receptor activity (GO:0042008)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34						ATTGGATGTTCGGGGAAGAAA	0.328													C|||	1284	0.25639	0.1422	0.1888	5008	,	,		15374	0.4196		0.2505	False		,,,				2504	0.2965				p.F251F		Atlas-SNP	.											.	IL18R1	72	.	0			c.C753T						PASS	.	C		691,3715	286.9+/-279.0	53,585,1565	107.0	112.0	110.0		753	-0.9	0.0	2	dbSNP_86	110	2343,6257	391.3+/-343.6	333,1677,2290	no	coding-synonymous	IL18R1	NM_003855.2		386,2262,3855	TT,TC,CC		27.2442,15.6832,23.3277		251/542	103001402	3034,9972	2203	4300	6503	SO:0001819	synonymous_variant	8809	exon6			GATGTTCGGGGAA	U43672	CCDS2060.1	2q12	2013-01-29			ENSG00000115604	ENSG00000115604		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5988	protein-coding gene	gene with protein product		604494				8626725, 10191101	Standard	NM_003855		Approved	IL1RRP, IL-1Rrp, CD218a	uc010fiy.3	Q13478	OTTHUMG00000130780	ENST00000409599.1:c.753C>T	2.37:g.103001402C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	109	49	0.449541	NM_003855	B2R9Y5|Q52LC9	Silent	SNP	ENST00000409599.1	37	CCDS2060.1																																																																																			C|0.765;T|0.235	0.235	strong		0.328	IL18R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253294.2	NM_003855	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520417	72520417	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:72520417A>G	ENST00000373207.1	+	22	3480	c.3480A>G	c.(3478-3480)ccA>ccG	p.P1160P	ADAMTS14_ENST00000373208.1_Silent_p.P1163P	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1160	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						CAAGCTCCCCAGGGACCCAGC	0.632																																					p.P1163P		Atlas-SNP	.											ADAMTS14,rectum,carcinoma,+2,2	ADAMTS14	148	2	0			c.A3489G						PASS	.						61.0	60.0	60.0					10																	72520417		2203	4300	6503	SO:0001819	synonymous_variant	140766	exon22			CTCCCCAGGGACC	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.3480A>G	10.37:g.72520417A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	75	38	0.506667	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			.	.	none		0.632	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
PARP4	143	hgsc.bcm.edu	37	13	25009485	25009485	+	Missense_Mutation	SNP	C	C	G	rs1050110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25009485C>G	ENST00000381989.3	-	31	3899	c.3794G>C	c.(3793-3795)gGc>gCc	p.G1265A		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1265			G -> A (in dbSNP:rs1050110). {ECO:0000269|PubMed:10644454, ECO:0000269|PubMed:8724849}.		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TACACCTAAGCCATCCTCTTC	0.368													g|||	1935	0.386382	0.4856	0.3473	5008	,	,		20414	0.3601		0.4175	False		,,,				2504	0.2751				p.G1265A		Atlas-SNP	.											.	PARP4	142	.	0			c.G3794C						PASS	.	G	ALA/GLY	2096,2310	602.4+/-389.9	484,1128,591	81.0	87.0	85.0		3794	-2.1	0.0	13	dbSNP_86	85	3204,5396	651.7+/-400.9	595,2014,1691	no	missense	PARP4	NM_006437.3	60	1079,3142,2282	GG,GC,CC		37.2558,47.5715,40.7504	benign	1265/1725	25009485	5300,7706	2203	4300	6503	SO:0001583	missense	143	exon31			CCTAAGCCATCCT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3794G>C	13.37:g.25009485C>G	ENSP00000371419:p.Gly1265Ala	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	107	106	0.990654	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	847	0.38782051282051283	226	0.45934959349593496	121	0.3342541436464088	181	0.31643356643356646	319	0.420844327176781	g	0	-2.709352	0.00094	0.475715	0.372558	ENSG00000102699	ENST00000381989	T	0.01584	4.75	1.95	-2.08	0.07254	.	11.803900	0.01079	N	0.004944	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.44034	-0.9354	9	0.07990	T	0.79	.	4.05	0.09791	0.0:0.3716:0.2351:0.3933	rs1050110;rs3190393;rs3742173;rs1050110	1265	Q9UKK3	PARP4_HUMAN	A	1265	ENSP00000371419:G1265A	ENSP00000371419:G1265A	G	-	2	0	PARP4	23907485	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.921000	0.00693	-1.265000	0.02449	-1.962000	0.00476	GGC	.	.	weak		0.368	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
OXTR	5021	hgsc.bcm.edu	37	3	8809222	8809222	+	Missense_Mutation	SNP	C	C	T	rs4686302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:8809222C>T	ENST00000316793.3	-	3	1276	c.652G>A	c.(652-654)Gcc>Acc	p.A218T	CAV3_ENST00000472766.1_Intron	NM_000916.3	NP_000907.2	P30559	OXYR_HUMAN	oxytocin receptor	218			A -> T (in dbSNP:rs4686302). {ECO:0000269|PubMed:1313946, ECO:0000269|Ref.3}.		cell surface receptor signaling pathway (GO:0007166)|digestive tract development (GO:0048565)|eating behavior (GO:0042755)|ERK1 and ERK2 cascade (GO:0070371)|estrous cycle phase (GO:0060206)|female pregnancy (GO:0007565)|heart development (GO:0007507)|lactation (GO:0007595)|maternal behavior (GO:0042711)|maternal process involved in parturition (GO:0060137)|memory (GO:0007613)|muscle contraction (GO:0006936)|negative regulation of gastric acid secretion (GO:0060455)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of norepinephrine secretion (GO:0010701)|positive regulation of penile erection (GO:0060406)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of uterine smooth muscle contraction (GO:0070474)|response to amphetamine (GO:0001975)|response to anoxia (GO:0034059)|response to cocaine (GO:0042220)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|sleep (GO:0030431)|social behavior (GO:0035176)|sperm ejaculation (GO:0042713)|suckling behavior (GO:0001967)|telencephalon development (GO:0021537)	apical plasma membrane (GO:0016324)|cell-cell adherens junction (GO:0005913)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	oxytocin receptor activity (GO:0004990)|peptide hormone binding (GO:0017046)|vasopressin receptor activity (GO:0005000)			NS(1)|endometrium(2)|large_intestine(4)|lung(5)|urinary_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(96;0.15)	Carbetocin(DB01282)|Oxytocin(DB00107)	CCGTAGCAGGCAGCGAGCACG	0.647													C|||	714	0.142572	0.0749	0.2695	5008	,	,		15474	0.1696		0.1183	False		,,,				2504	0.1411				p.A218T		Atlas-SNP	.											.	OXTR	31	.	0			c.G652A						PASS	.	C	THR/ALA	317,4089	165.8+/-197.2	15,287,1901	36.0	35.0	35.0		652	3.5	0.9	3	dbSNP_111	35	1033,7565	217.6+/-256.2	62,909,3328	yes	missense	OXTR	NM_000916.3	58	77,1196,5229	TT,TC,CC		12.0144,7.1947,10.3814	benign	218/390	8809222	1350,11654	2203	4299	6502	SO:0001583	missense	5021	exon3			AGCAGGCAGCGAG		CCDS2570.1	3p25	2012-08-08			ENSG00000180914	ENSG00000180914		"""GPCR / Class A : Vasopressin and oxytocin receptors"""	8529	protein-coding gene	gene with protein product		167055				1313946	Standard	NM_000916		Approved		uc003brc.3	P30559	OTTHUMG00000090537	ENST00000316793.3:c.652G>A	3.37:g.8809222C>T	ENSP00000324270:p.Ala218Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_000916	Q15071	Missense_Mutation	SNP	ENST00000316793.3	37	CCDS2570.1	323	0.1478937728937729	43	0.08739837398373984	86	0.23756906077348067	95	0.1660839160839161	99	0.13060686015831136	C	7.441	0.640665	0.14386	0.071947	0.120144	ENSG00000180914	ENST00000316793	T	0.37058	1.22	5.27	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.409157	0.27245	N	0.020250	T	0.00012	0.0000	N	0.11818	0.18	0.36837	P	0.11280900000000005	B	0.09022	0.002	B	0.14023	0.01	T	0.30621	-0.9972	9	0.26408	T	0.33	-15.5806	10.46	0.44575	0.0:0.8413:0.0:0.1587	rs4686302;rs56562886;rs60516910;rs4686302	218	P30559	OXYR_HUMAN	T	218	ENSP00000324270:A218T	ENSP00000324270:A218T	A	-	1	0	OXTR	8784222	0.831000	0.29352	0.926000	0.36857	0.922000	0.55478	0.913000	0.28611	0.623000	0.30267	0.561000	0.74099	GCC	C|0.878;T|0.122	0.122	strong		0.647	OXTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207061.2		
NEU4	129807	hgsc.bcm.edu	37	2	242757820	242757820	+	Missense_Mutation	SNP	G	G	A	rs11545301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:242757820G>A	ENST00000391969.2	+	5	1612	c.901G>A	c.(901-903)Ggg>Agg	p.G301R	NEU4_ENST00000325935.6_Missense_Mutation_p.G314R|NEU4_ENST00000404257.1_Missense_Mutation_p.G313R|NEU4_ENST00000407683.1_Missense_Mutation_p.G301R|NEU4_ENST00000405370.1_Missense_Mutation_p.G301R	NM_001167602.1	NP_001161074.1	Q8WWR8	NEUR4_HUMAN	sialidase 4	301	Pro-rich.		G -> R (in dbSNP:rs11545301). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:14962670, ECO:0000269|PubMed:15498874}.		ganglioside catabolic process (GO:0006689)|glycoprotein catabolic process (GO:0006516)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|organelle inner membrane (GO:0019866)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)|exo-alpha-sialidase activity (GO:0004308)			breast(1)|lung(10)|prostate(2)|skin(2)	15		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0825)		AGTGGGCCCCGGGAGTCCCCT	0.701													G|||	1213	0.242212	0.2988	0.2176	5008	,	,		13537	0.1002		0.2783	False		,,,				2504	0.2924				p.G314R		Atlas-SNP	.											.	NEU4	39	.	0			c.G940A						PASS	.		ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	1158,3026		168,822,1102	9.0	12.0	11.0		940,901,901,901,937	-3.2	0.0	2	dbSNP_120	11	2335,5971		357,1621,2175	yes	missense,missense,missense,missense,missense	NEU4	NM_001167599.1,NM_001167600.1,NM_001167601.1,NM_001167602.1,NM_080741.2	125,125,125,125,125	525,2443,3277	AA,AG,GG		28.1122,27.6769,27.9664	benign,benign,benign,benign,benign	314/498,301/485,301/485,301/485,313/497	242757820	3493,8997	2092	4153	6245	SO:0001583	missense	129807	exon4			GGCCCCGGGAGTC	BC012899	CCDS2553.1, CCDS54441.1, CCDS54442.1	2q37.3	2008-02-05			ENSG00000204099	ENSG00000204099			21328	protein-coding gene	gene with protein product		608527					Standard	NM_001167600		Approved		uc010fzr.3	Q8WWR8	OTTHUMG00000133412	ENST00000391969.2:c.901G>A	2.37:g.242757820G>A	ENSP00000375830:p.Gly301Arg	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_001167599	A8K056|J3KNJ5|Q96D64	Missense_Mutation	SNP	ENST00000391969.2	37	CCDS54442.1	531	0.24313186813186813	153	0.31097560975609756	92	0.2541436464088398	62	0.10839160839160839	224	0.2955145118733509	G	1.760	-0.486996	0.04352	0.276769	0.281122	ENSG00000204099	ENST00000407683;ENST00000405370;ENST00000472793;ENST00000404257;ENST00000391969;ENST00000325935	T;T;T;T;T	0.75367	-0.92;-0.92;-0.93;-0.92;-0.93	3.37	-3.25	0.05079	Neuraminidase (1);	1.630680	0.03917	N	0.282864	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.03566	-1.1024	9	0.09084	T	0.74	-3.816	5.0178	0.14345	0.4482:0.0:0.4064:0.1453	rs11545301	313;313;301	A8K211;Q8WWR8-2;Q8WWR8	.;.;NEUR4_HUMAN	R	301;301;311;313;301;314	ENSP00000385402:G301R;ENSP00000384804:G301R;ENSP00000385149:G313R;ENSP00000375830:G301R;ENSP00000320318:G314R	ENSP00000320318:G314R	G	+	1	0	NEU4	242406493	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	-0.972000	0.03802	-0.372000	0.07992	-0.529000	0.04317	GGG	G|0.725;A|0.275	0.275	strong		0.701	NEU4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257270.2	NM_080741	
BSPRY	54836	hgsc.bcm.edu	37	9	116122954	116122954	+	Silent	SNP	A	A	G	rs752757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:116122954A>G	ENST00000374183.4	+	3	507	c.468A>G	c.(466-468)aaA>aaG	p.K156K	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	156					calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CGCTGCAGAAACTTGACACCA	0.617													G|||	1825	0.364417	0.5393	0.3343	5008	,	,		17996	0.3919		0.1978	False		,,,				2504	0.2924				p.K156K		Atlas-SNP	.											BSPRY,NS,carcinoma,0,2	BSPRY	21	2	0			c.A468G						PASS	.	G		1966,2332		424,1118,607	36.0	42.0	40.0		468	5.1	1.0	9	dbSNP_86	40	1813,6705		192,1429,2638	no	coding-synonymous	BSPRY	NM_017688.2		616,2547,3245	GG,GA,AA		21.2843,45.7422,29.4866		156/403	116122954	3779,9037	2149	4259	6408	SO:0001819	synonymous_variant	54836	exon3			GCAGAAACTTGAC	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.468A>G	9.37:g.116122954A>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	72	72	1	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Silent	SNP	ENST00000374183.4	37	CCDS43868.1																																																																																			G|0.353;C|0.000;N|0.000;A|0.647	0.353	strong		0.617	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
METTL21C	196541	hgsc.bcm.edu	37	13	103346806	103346806	+	Missense_Mutation	SNP	C	C	G	rs2390760	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:103346806C>G	ENST00000267273.6	-	1	48	c.43G>C	c.(43-45)Ggg>Cgg	p.G15R		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	15			G -> R (in dbSNP:rs45462291).		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						AGTCCTTCCCCCCGGCGCCCA	0.587													C|||	3708	0.740415	0.7799	0.6772	5008	,	,		11194	0.871		0.6064	False		,,,				2504	0.7352				p.G15R		Atlas-SNP	.											METTL21C,NS,adenoma,+1,1	METTL21C	23	1	0			c.G43C						PASS	.	C	ARG/GLY	3338,1066		1320,698,184	20.0	22.0	21.0		43	0.2	0.0	13	dbSNP_100	21	5257,3341		1704,1849,746	yes	missense	METTL21C	NM_001010977.1	125	3024,2547,930	GG,GC,CC		38.8579,24.2053,33.8948	benign	15/265	103346806	8595,4407	2202	4299	6501	SO:0001583	missense	196541	exon1			CTTCCCCCCGGCG		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.43G>C	13.37:g.103346806C>G	ENSP00000267273:p.Gly15Arg	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	37	CCDS32003.1	1568	0.717948717948718	374	0.7601626016260162	233	0.643646408839779	489	0.8548951048951049	472	0.6226912928759895	C	4.906	0.168310	0.09339	0.757947	0.611421	ENSG00000139780	ENST00000267273	T	0.14766	2.48	4.03	0.201	0.15186	.	1.747610	0.03239	N	0.180102	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	0.24799	-1.0150	9	0.16896	T	0.51	1.8153	7.7642	0.28970	0.0:0.3731:0.528:0.099	rs45462291	15	Q5VZV1	MT21C_HUMAN	R	15	ENSP00000267273:G15R	ENSP00000267273:G15R	G	-	1	0	METTL21C	102144807	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.239000	0.08965	-0.008000	0.14320	0.650000	0.86243	GGG	C|0.324;G|0.676	0.676	strong		0.587	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977	
MYO10	4651	hgsc.bcm.edu	37	5	16769273	16769273	+	Missense_Mutation	SNP	G	G	A	rs11750538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:16769273G>A	ENST00000513610.1	-	10	1424	c.970C>T	c.(970-972)Cgg>Tgg	p.R324W		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	324	Myosin motor.		R -> W (in dbSNP:rs11750538). {ECO:0000269|PubMed:10984435, ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GACACTTCCCGAACTTCCTCC	0.403													G|||	2410	0.48123	0.3396	0.4006	5008	,	,		17279	0.5357		0.5984	False		,,,				2504	0.5532				p.R324W		Atlas-SNP	.											.	MYO10	198	.	0			c.C970T						PASS	.	G	TRP/ARG	1489,2349		291,907,721	109.0	100.0	103.0		970	4.8	0.8	5	dbSNP_120	103	4949,3323		1492,1965,679	yes	missense	MYO10	NM_012334.2	101	1783,2872,1400	AA,AG,GG		40.1717,38.7962,46.8373	possibly-damaging	324/2059	16769273	6438,5672	1919	4136	6055	SO:0001583	missense	4651	exon10			CTTCCCGAACTTC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.970C>T	5.37:g.16769273G>A	ENSP00000421280:p.Arg324Trp	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	83	44	0.53012	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	1111	0.5086996336996337	173	0.3516260162601626	171	0.4723756906077348	314	0.548951048951049	453	0.5976253298153035	G	8.864	0.947529	0.18356	0.387962	0.598283	ENSG00000145555	ENST00000513610;ENST00000513882	D;D	0.88509	-2.39;-2.39	5.71	4.82	0.62117	Myosin head, motor domain (2);	.	.	.	.	T	0.00012	0.0000	L	0.35723	1.085	0.09310	P	0.999999999999986	D	0.61080	0.989	P	0.53185	0.72	T	0.45190	-0.9278	8	0.45353	T	0.12	.	13.5022	0.61462	0.0:0.0:0.7155:0.2845	rs11750538;rs52826195;rs60590343;rs11750538	324	Q9HD67	MYO10_HUMAN	W	324;335	ENSP00000421280:R324W;ENSP00000421309:R335W	ENSP00000421280:R324W	R	-	1	2	MYO10	16822273	0.997000	0.39634	0.769000	0.31535	0.687000	0.40016	2.849000	0.48286	1.359000	0.45940	0.585000	0.79938	CGG	G|0.492;A|0.507	0.507	strong		0.403	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
RNF19B	127544	hgsc.bcm.edu	37	1	33409693	33409693	+	Silent	SNP	G	G	A	rs194645	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:33409693G>A	ENST00000373456.7	-	6	1331	c.1332C>T	c.(1330-1332)ggC>ggT	p.G444G	RNF19B_ENST00000235150.4_Silent_p.G443G|RNF19B_ENST00000356990.5_Silent_p.G443G	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	444					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTCCACAGCCGCCTCCACGAC	0.453													G|||	944	0.188498	0.0265	0.2378	5008	,	,		20214	0.2748		0.2505	False		,,,				2504	0.2198				p.G444G		Atlas-SNP	.											.	RNF19B	43	.	0			c.C1332T						PASS	.	G	,	292,4114	158.9+/-191.5	10,272,1921	68.0	63.0	65.0		1329,1332	-2.4	1.0	1	dbSNP_79	65	1908,6692	337.6+/-322.4	206,1496,2598	no	coding-synonymous,coding-synonymous	RNF19B	NM_001127361.1,NM_153341.2	,	216,1768,4519	AA,AG,GG		22.186,6.6273,16.9153	,	443/588,444/733	33409693	2200,10806	2203	4300	6503	SO:0001819	synonymous_variant	127544	exon6			ACAGCCGCCTCCA	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"""RING-type (C3HC4) zinc fingers"""	26886	protein-coding gene	gene with protein product		610872	"""IBR domain containing 3"""	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.1332C>T	1.37:g.33409693G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	145	12	0.0827586	NM_153341	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Silent	SNP	ENST00000373456.7	37	CCDS372.2																																																																																			G|0.818;A|0.182	0.182	strong		0.453	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341	
LAMB4	22798	hgsc.bcm.edu	37	7	107720162	107720162	+	Missense_Mutation	SNP	C	C	A	rs9690688	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:107720162C>A	ENST00000388781.3	-	15	1854	c.1771G>T	c.(1771-1773)Gtt>Ttt	p.V591F	LAMB4_ENST00000388780.3_Missense_Mutation_p.V591F|LAMB4_ENST00000418464.1_Missense_Mutation_p.V591F|LAMB4_ENST00000414450.2_Missense_Mutation_p.V591F|LAMB4_ENST00000205386.4_Missense_Mutation_p.V591F	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	591	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.		V -> F (in dbSNP:rs9690688).		cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						GTCCATGTAACAGGGTTCCCA	0.507													C|||	862	0.172125	0.4841	0.0865	5008	,	,		18642	0.0099		0.0805	False		,,,				2504	0.0726				p.V591F		Atlas-SNP	.											LAMB4,NS,carcinoma,0,1	LAMB4	253	1	0			c.G1771T						PASS	.	C	PHE/VAL	1746,2660	520.7+/-370.3	354,1038,811	68.0	63.0	65.0		1771	1.5	0.0	7	dbSNP_119	65	579,8021	154.5+/-208.7	21,537,3742	yes	missense	LAMB4	NM_007356.2	50	375,1575,4553	AA,AC,CC		6.7326,39.6278,17.8764	possibly-damaging	591/1762	107720162	2325,10681	2203	4300	6503	SO:0001583	missense	22798	exon15			ATGTAACAGGGTT	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.1771G>T	7.37:g.107720162C>A	ENSP00000373433:p.Val591Phe	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	64	33	0.515625	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	358	0.16391941391941392	250	0.508130081300813	37	0.10220994475138122	6	0.01048951048951049	65	0.08575197889182058	C	16.23	3.064398	0.55432	0.396278	0.067326	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.33438	1.43;1.43;1.45;1.41;1.46	5.31	1.51	0.23008	Laminin IV (1);	0.832814	0.10185	N	0.705359	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P	0.49961	0.93	B	0.42462	0.388	T	0.43458	-0.9390	9	0.09843	T	0.71	.	5.3132	0.15841	0.0:0.4946:0.1364:0.369	rs9690688;rs10240287;rs52797611;rs60766059;rs9690688	591	A4D0S4	LAMB4_HUMAN	F	591	ENSP00000205386:V591F;ENSP00000373433:V591F;ENSP00000373432:V591F;ENSP00000402353:V591F;ENSP00000402265:V591F	ENSP00000205386:V591F	V	-	1	0	LAMB4	107507398	0.000000	0.05858	0.000000	0.03702	0.932000	0.56968	-0.202000	0.09451	0.101000	0.17610	0.655000	0.94253	GTT	C|0.819;A|0.181	0.181	strong		0.507	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
SLC25A42	284439	hgsc.bcm.edu	37	19	19212658	19212658	+	Silent	SNP	G	G	A	rs56144126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19212658G>A	ENST00000318596.7	+	3	301	c.150G>A	c.(148-150)gcG>gcA	p.A50A	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	50					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			CCAAAACAGCGGTAGCTCCCC	0.587													G|||	202	0.0403355	0.0272	0.0663	5008	,	,		15656	0.0		0.0755	False		,,,				2504	0.045				p.A50A		Atlas-SNP	.											.	SLC25A42	18	.	0			c.G150A						PASS	.	G		135,4271	95.3+/-134.0	2,131,2070	89.0	83.0	85.0		150	-10.2	0.1	19	dbSNP_129	85	683,7917	171.0+/-222.0	29,625,3646	no	coding-synonymous	SLC25A42	NM_178526.3		31,756,5716	AA,AG,GG		7.9419,3.064,6.2894		50/319	19212658	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	284439	exon3			AACAGCGGTAGCT		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"""Solute carriers"""	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.150G>A	19.37:g.19212658G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	56	35	0.625	NM_178526	D2T2J5|O14553|O43378	Silent	SNP	ENST00000318596.7	37	CCDS32966.1																																																																																			G|0.937;A|0.063	0.063	strong		0.587	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526	
SLC52A1	55065	hgsc.bcm.edu	37	17	4937575	4937575	+	Missense_Mutation	SNP	T	T	C	rs346822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4937575T>C	ENST00000424747.1	-	3	921	c.209A>G	c.(208-210)cAg>cGg	p.Q70R	SLC52A1_ENST00000512825.2_Missense_Mutation_p.Q70R|SLC52A1_ENST00000254853.5_Missense_Mutation_p.Q70R	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	70			Q -> R (riboflavin transport is unaffected; dbSNP:rs346822). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18632736, ECO:0000269|PubMed:21089064, ECO:0000269|Ref.5}.		riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										CGGGGCCAGCTGCCTCCACAG	0.652													C|||	4625	0.923522	0.9675	0.9597	5008	,	,		18049	0.8204		0.9602	False		,,,				2504	0.907				p.Q70R		Atlas-SNP	.											.	.	.	.	0			c.A209G						PASS	.	C	ARG/GLN,ARG/GLN	4232,174	113.8+/-151.8	2032,168,3	43.0	45.0	44.0		209,209	1.3	0.1	17	dbSNP_79	44	8189,411	128.2+/-186.4	3901,387,12	yes	missense,missense	GPR172B	NM_001104577.1,NM_017986.3	43,43	5933,555,15	CC,CT,TT		4.7791,3.9492,4.4979	benign,benign	70/449,70/449	4937575	12421,585	2203	4300	6503	SO:0001583	missense	55065	exon3			GCCAGCTGCCTCC	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.209A>G	17.37:g.4937575T>C	ENSP00000399979:p.Gln70Arg	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	54	54	1	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Missense_Mutation	SNP	ENST00000424747.1	37	CCDS11066.1	2023	0.9262820512820513	477	0.9695121951219512	347	0.9585635359116023	470	0.8216783216783217	729	0.9617414248021108	C	0.003	-2.496691	0.00159	0.960508	0.952209	ENSG00000132517	ENST00000254853;ENST00000512825;ENST00000424747	T;T;T	0.69806	-0.43;-0.43;-0.43	2.28	1.29	0.21616	.	0.129765	0.52532	N	0.000076	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	0.36866	-0.9730	9	0.02654	T	1	.	6.4068	0.21668	0.0:0.7159:0.0:0.2841	rs346822;rs17824474;rs17846577;rs17859658;rs346822	70;70	F5H5Y1;Q9NWF4	.;RFT_HUMAN	R	70	ENSP00000254853:Q70R;ENSP00000443026:Q70R;ENSP00000399979:Q70R	ENSP00000254853:Q70R	Q	-	2	0	GPR172B	4878299	0.987000	0.35691	0.067000	0.19924	0.022000	0.10575	0.473000	0.22132	0.087000	0.17167	-0.898000	0.02899	CAG	T|0.058;C|0.942	0.942	strong		0.652	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
NME4	4833	hgsc.bcm.edu	37	16	449659	449659	+	Silent	SNP	G	G	A	rs14293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:449659G>A	ENST00000219479.2	+	4	374	c.360G>A	c.(358-360)tcG>tcA	p.S120S	DECR2_ENST00000397710.1_5'Flank|NME4_ENST00000382940.4_Silent_p.S128S|NME4_ENST00000450036.1_Silent_p.S50S|NME4_ENST00000397722.1_Silent_p.S50S|DECR2_ENST00000424398.2_5'Flank|DECR2_ENST00000219481.5_5'Flank	NM_005009.2	NP_005000.1	O00746	NDKM_HUMAN	NME/NM23 nucleoside diphosphate kinase 4	120					CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|small molecule metabolic process (GO:0044281)|UTP biosynthetic process (GO:0006228)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside diphosphate kinase activity (GO:0004550)	p.S120S(1)		NS(1)|lung(1)|stomach(1)|urinary_tract(1)	4		Hepatocellular(16;0.00015)				TCCGCGCCTCGAGGGCCATGA	0.612													g|||	2213	0.441893	0.5598	0.4251	5008	,	,		19812	0.3671		0.3648	False		,,,				2504	0.4509				p.S120S		Atlas-SNP	.											NME4,NS,carcinoma,0,1	NME4	9	1	1	Substitution - coding silent(1)	stomach(1)	c.G360A						PASS	.	A		2418,1986	614.5+/-392.4	655,1108,439	105.0	102.0	103.0		360	-9.4	0.0	16	dbSNP_52	103	3421,5179	504.0+/-376.0	661,2099,1540	no	coding-synonymous	NME4	NM_005009.2		1316,3207,1979	AA,AG,GG		39.7791,45.0954,44.9016		120/188	449659	5839,7165	2202	4300	6502	SO:0001819	synonymous_variant	4833	exon4			CGCCTCGAGGGCC	Y07604	CCDS10408.1, CCDS66886.1, CCDS73797.1	16p13.3	2013-04-29	2012-05-18		ENSG00000103202	ENSG00000103202			7852	protein-coding gene	gene with protein product		601818	"""non-metastatic cells 4, protein expressed in"""			9099850, 19852809	Standard	NM_005009		Approved	nm23-H4, NM23H4, NDPKD	uc002cgz.3	O00746	OTTHUMG00000047995	ENST00000219479.2:c.360G>A	16.37:g.449659G>A		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	61	0.455224	NM_005009	A2IDD0|Q5U0M9	Silent	SNP	ENST00000219479.2	37	CCDS10408.1	943	0.4317765567765568	300	0.6097560975609756	144	0.39779005524861877	222	0.3881118881118881	277	0.3654353562005277	g	0.088	-1.171406	0.01660	0.549046	0.397791	ENSG00000103202	ENST00000433358	.	.	.	4.7	-9.4	0.00616	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22779	P	0.99874316	.	.	.	.	.	.	T	0.36553	-0.9743	3	.	.	.	-14.0168	3.1609	0.06520	0.3082:0.1507:0.4248:0.1162	rs14293;rs1044211;rs3169386;rs11538882;rs17356176;rs17845527;rs17858422;rs59659280	.	.	.	K	116	.	.	E	+	1	0	NME4	389660	0.000000	0.05858	0.029000	0.17559	0.006000	0.05464	-3.108000	0.00601	-2.144000	0.00802	-4.346000	0.00007	GAG	G|0.557;A|0.443	0.443	strong		0.612	NME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109256.2	NM_005009	
DYSF	8291	hgsc.bcm.edu	37	2	71780248	71780248	+	Silent	SNP	C	C	T	rs35721373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:71780248C>T	ENST00000258104.3	+	20	2137	c.1860C>T	c.(1858-1860)taC>taT	p.Y620Y	DYSF_ENST00000409651.1_Silent_p.Y652Y|DYSF_ENST00000409744.1_Silent_p.Y607Y|DYSF_ENST00000409582.3_Silent_p.Y637Y|DYSF_ENST00000410041.1_Silent_p.Y638Y|DYSF_ENST00000413539.2_Silent_p.Y651Y|DYSF_ENST00000394120.2_Silent_p.Y621Y|DYSF_ENST00000409762.1_Silent_p.Y637Y|DYSF_ENST00000409366.1_Silent_p.Y621Y|DYSF_ENST00000410020.3_Silent_p.Y638Y|DYSF_ENST00000429174.2_Silent_p.Y620Y	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	620					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						TCGGGAACTACGGGAACAAGT	0.587													c|||	179	0.0357428	0.0514	0.0202	5008	,	,		18980	0.0089		0.0258	False		,,,				2504	0.0634				p.Y652Y		Atlas-SNP	.											.	DYSF	536	.	0			c.C1956T						PASS	.	C	,,,,,,,,,,,,,	209,4197	129.0+/-165.8	5,199,1999	132.0	106.0	115.0		1863,1818,1818,1860,1953,1911,1911,1956,1863,1821,1914,1821,1914,1860	-5.2	0.8	2	dbSNP_126	115	261,8339	102.3+/-163.5	5,251,4044	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	10,450,6043	TT,TC,CC		3.0349,4.7435,3.6137	,,,,,,,,,,,,,	621/2082,606/2067,606/2088,620/2102,651/2112,637/2098,637/2119,652/2113,621/2103,607/2089,638/2099,607/2068,638/2120,620/2081	71780248	470,12536	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon21			GAACTACGGGAAC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1860C>T	2.37:g.71780248C>T		Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	144	70	0.486111	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			C|0.967;T|0.033	0.033	strong		0.587	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
CFAP46	54777	hgsc.bcm.edu	37	10	134682802	134682802	+	Missense_Mutation	SNP	C	C	T	rs7084629	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134682802C>T	ENST00000368586.5	-	33	4686	c.4586G>A	c.(4585-4587)tGc>tAc	p.C1529Y		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTCGCTGACGCACACCTGCCC	0.687													T|||	639	0.127596	0.3359	0.0432	5008	,	,		14721	0.0198		0.0249	False		,,,				2504	0.1227				p.C1529Y		Atlas-SNP	.											.	TTC40	100	.	0			c.G4586A						PASS	.																																			SO:0001583	missense	54777	exon33			CTGACGCACACCT																												ENST00000368586.5:c.4586G>A	10.37:g.134682802C>T	ENSP00000357575:p.Cys1529Tyr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	66	40	0.606061	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	210	0.09615384615384616	168	0.34146341463414637	14	0.03867403314917127	12	0.02097902097902098	16	0.021108179419525065	T	9.396	1.076860	0.20227	.	.	ENSG00000171811	ENST00000368586	T	0.08458	3.09	4.81	4.81	0.61882	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.49130	P	2.4900000000005473E-4	.	.	.	.	.	.	T	0.42699	-0.9436	5	0.02654	T	1	.	8.3416	0.32247	0.0:0.093:0.0:0.907	rs7084629;rs57852866;rs7084629	.	.	.	Y	1529	ENSP00000357575:C1529Y	ENSP00000357575:C1529Y	C	-	2	0	C10orf93	134532792	0.327000	0.24678	0.001000	0.08648	0.000000	0.00434	1.473000	0.35387	0.690000	0.31570	-0.332000	0.08345	TGC	C|0.878;T|0.122	0.122	strong		0.687	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
DCHS2	54798	hgsc.bcm.edu	37	4	155295076	155295076	+	Missense_Mutation	SNP	A	A	G	rs11721758	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155295076A>G	ENST00000357232.4	-	4	457	c.458T>C	c.(457-459)gTg>gCg	p.V153A	DCHS2_ENST00000339452.1_Intron	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	153	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		V -> A (in dbSNP:rs11721758).		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)		CCTTACCTTCACCAGGGCTAA	0.368													A|||	1747	0.348842	0.1362	0.3646	5008	,	,		17591	0.3938		0.4851	False		,,,				2504	0.4387				p.V153A		Atlas-SNP	.											.	DCHS2	594	.	0			c.T458C						PASS	.	A	,ALA/VAL	829,3577	328.0+/-300.3	84,661,1458	135.0	121.0	126.0		,458	-2.7	0.0	4	dbSNP_120	126	3884,4716	544.5+/-384.6	896,2092,1312	yes	intron,missense	DCHS2	NM_001142552.1,NM_017639.3	,64	980,2753,2770	GG,GA,AA		45.1628,18.8153,36.2371	,benign	,153/2917	155295076	4713,8293	2203	4300	6503	SO:0001583	missense	54798	exon4			ACCTTCACCAGGG	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.458T>C	4.37:g.155295076A>G	ENSP00000349768:p.Val153Ala	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	814	0.3727106227106227	69	0.1402439024390244	153	0.42265193370165743	218	0.3811188811188811	374	0.49340369393139843	A	9.034	0.987982	0.18966	0.188153	0.451628	ENSG00000197410	ENST00000357232	T	0.52526	0.66	2.74	-2.66	0.06077	Cadherin (3);Cadherin-like (1);	1.741890	0.04532	N	0.386442	T	0.00012	0.0000	N	0.12569	0.235	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.44967	-0.9293	9	0.59425	D	0.04	.	5.1587	0.15048	0.2586:0.501:0.2404:0.0	rs11721758;rs52830973;rs57135557;rs11721758	153	Q6V1P9	PCD23_HUMAN	A	153	ENSP00000349768:V153A	ENSP00000349768:V153A	V	-	2	0	DCHS2	155514526	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	0.317000	0.19487	-0.511000	0.06514	0.377000	0.23210	GTG	A|0.641;G|0.359	0.359	strong		0.368	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
SCN5A	6331	hgsc.bcm.edu	37	3	38645420	38645420	+	Missense_Mutation	SNP	T	T	C	rs1805124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:38645420T>C	ENST00000333535.4	-	12	1822	c.1673A>G	c.(1672-1674)cAc>cGc	p.H558R	SCN5A_ENST00000414099.2_Missense_Mutation_p.H558R|SCN5A_ENST00000449557.2_Missense_Mutation_p.H558R|SCN5A_ENST00000451551.2_Missense_Mutation_p.H558R|SCN5A_ENST00000413689.1_Missense_Mutation_p.H558R|SCN5A_ENST00000455624.2_Missense_Mutation_p.H558R|SCN5A_ENST00000443581.1_Missense_Mutation_p.H558R|SCN5A_ENST00000425664.1_Missense_Mutation_p.H558R|SCN5A_ENST00000450102.2_Missense_Mutation_p.H558R|SCN5A_ENST00000423572.2_Missense_Mutation_p.H558R			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	558			H -> R (channels properties are similar to wild-type; the double mutant Arg-558/ Ile-512 channel shows that Arg-558 eliminates the negative shift induced by Ile-512 but only partially restores the kinetic abnormalities; can modulate the gating defects caused by Ala-2006 and other mutations; dbSNP:rs1805124). {ECO:0000269|PubMed:11997281, ECO:0000269|PubMed:12051963, ECO:0000269|PubMed:12454206, ECO:0000269|PubMed:12569159, ECO:0000269|PubMed:14500339, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18368697, ECO:0000269|PubMed:18378609}.		AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	CAGTGATGTGTGGTGGCTCTC	0.627													C|||	1154	0.230431	0.3094	0.2277	5008	,	,		17254	0.1012		0.2167	False		,,,				2504	0.273				p.H558R		Atlas-SNP	.											SCN5A_ENST00000413689,colon,carcinoma,0,3	SCN5A	634	3	0			c.A1673G	GRCh37	CM031355	SCN5A	M	rs1805124	PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	1151,3037		156,839,1099	48.0	54.0	52.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1673,1673,1673,1673,1673,1673	2.4	1.0	3	dbSNP_89	52	1957,6475		248,1461,2507	yes	missense,missense,missense,missense,missense,missense	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	29,29,29,29,29,29	404,2300,3606	CC,CT,TT		23.2092,27.4833,24.6276	benign,benign,benign,benign,benign,benign	558/2016,558/2017,558/1999,558/1984,558/1963,558/2017	38645420	3108,9512	2094	4216	6310	SO:0001583	missense	6331	exon12			GATGTGTGGTGGC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.1673A>G	3.37:g.38645420T>C	ENSP00000328968:p.His558Arg	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	156	156	1	NM_001160160	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	450	0.20604395604395603	147	0.29878048780487804	75	0.20718232044198895	63	0.11013986013986014	165	0.21767810026385223	C	0.349	-0.945829	0.02304	0.274833	0.232092	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.94613	-3.39;-3.41;-3.41;-3.46;-3.41;-3.39;-3.42;-3.47;-3.46;-3.46	4.27	2.44	0.29823	Domain of unknown function DUF3451 (1);	0.329193	0.30602	N	0.009278	T	0.00012	0.0000	N	0.00114	-2.085	0.44771	P	0.0022280000000000078	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.45702	-0.9243	9	0.02654	T	1	.	15.5745	0.76365	0.0:0.9158:0.0:0.0842	rs1805124;rs58801095;rs1805124	558;558;558;558;558;558;558	E9PEF3;E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;.;SCN5A_HUMAN;.;.	R	558	ENSP00000398962:H558R;ENSP00000398266:H558R;ENSP00000410257:H558R;ENSP00000388797:H558R;ENSP00000397915:H558R;ENSP00000416634:H558R;ENSP00000328968:H558R;ENSP00000399524:H558R;ENSP00000403355:H558R;ENSP00000413996:H558R	ENSP00000328968:H558R	H	-	2	0	SCN5A	38620424	0.998000	0.40836	0.992000	0.48379	0.570000	0.35934	1.656000	0.37355	0.109000	0.17891	-2.400000	0.00224	CAC	T|0.790;C|0.210	0.210	strong		0.627	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346712	140346712	+	Silent	SNP	T	T	C	rs155808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140346712T>C	ENST00000289269.5	+	1	893	c.361T>C	c.(361-363)Ttg>Ctg	p.L121L	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	121	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGCTCAGCTTGGAAGTGCT	0.627													T|||	1800	0.359425	0.2239	0.402	5008	,	,		19004	0.5486		0.3419	False		,,,				2504	0.3354				p.L121L	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.T361C						PASS	.	T	,,,,,,,,,,,,,,,,,,	1108,3298	373.4+/-320.8	147,814,1242	36.0	38.0	38.0		,361,,,,,,,,,,,,,,,,,361	0.5	1.0	5	dbSNP_79	38	2917,5683	435.7+/-358.1	487,1943,1870	yes	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	634,2757,3112	CC,CT,TT		33.9186,25.1475,30.9473	,,,,,,,,,,,,,,,,,,	,121/1008,,,,,,,,,,,,,,,,,121/885	140346712	4025,8981	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			CTCAGCTTGGAAG	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.361T>C	5.37:g.140346712T>C		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	56	26	0.464286	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			T|0.675;C|0.325	0.325	strong		0.627	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
IDH3A	3419	hgsc.bcm.edu	37	15	78441769	78441769	+	Silent	SNP	T	T	C	rs11555541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78441769T>C	ENST00000299518.2	+	1	107	c.24T>C	c.(22-24)tcT>tcC	p.S8S	IDH3A_ENST00000559205.1_Silent_p.S8S|IDH3A_ENST00000441490.2_5'UTR|IDH3A_ENST00000558554.1_Silent_p.S8S	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	8					carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	12						CGTGGATCTCTAAGGTGAGCG	0.761													C|||	2672	0.533546	0.7163	0.4524	5008	,	,		9516	0.3165		0.505	False		,,,				2504	0.5971				p.S8S		Atlas-SNP	.											.	IDH3A	24	.	0			c.T24C						PASS	.	C		2890,1296		1019,852,222	7.0	8.0	8.0		24	3.2	1.0	15	dbSNP_120	8	4231,4071		1178,1875,1098	no	coding-synonymous	IDH3A	NM_005530.2		2197,2727,1320	CC,CT,TT		49.0364,30.9603,42.9773		8/367	78441769	7121,5367	2093	4151	6244	SO:0001819	synonymous_variant	3419	exon1			GATCTCTAAGGTG		CCDS10297.1	15q25.1-q25.2	2008-07-18			ENSG00000166411	ENSG00000166411	1.1.1.41		5384	protein-coding gene	gene with protein product	"""H-IDH alpha"", ""isocitric dehydrogenase"", ""isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial"", ""NAD+-specific ICDH"", ""NAD(H)-specific isocitrate dehydrogenase alpha subunit"", ""isocitrate dehydrogenase (NAD+) alpha chain"""	601149				8833160	Standard	NM_005530		Approved		uc002bdd.3	P50213	OTTHUMG00000143732	ENST00000299518.2:c.24T>C	15.37:g.78441769T>C		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	15	6	0.4	NM_005530	D3DW83|Q9H3X0	Silent	SNP	ENST00000299518.2	37	CCDS10297.1																																																																																			T|0.494;C|0.506	0.506	strong		0.761	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530	
WDR87	83889	hgsc.bcm.edu	37	19	38382328	38382328	+	Silent	SNP	C	C	T	rs953370	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38382328C>T	ENST00000303868.5	-	5	3365	c.3141G>A	c.(3139-3141)ccG>ccA	p.P1047P	WDR87_ENST00000447313.2_Silent_p.P1086P	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	1047										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						AAGAAAAAGCCGGCTTTTCAT	0.458													C|||	3236	0.646166	0.795	0.5331	5008	,	,		18527	0.8214		0.4036	False		,,,				2504	0.5941				p.P1047P		Atlas-SNP	.											.	WDR87	191	.	0			c.G3141A						PASS	.	C		1012,372		371,270,51	122.0	109.0	113.0		3141	1.1	0.1	19	dbSNP_86	113	1247,1935		254,739,598	no	coding-synonymous	WDR87	NM_031951.3		625,1009,649	TT,TC,CC		39.1892,26.8786,49.4744		1047/2874	38382328	2259,2307	692	1591	2283	SO:0001819	synonymous_variant	83889	exon5			AAAAGCCGGCTTT	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.3141G>A	19.37:g.38382328C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	94	94	1	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			C|0.366;T|0.634	0.634	strong		0.458	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
ZFHX4	79776	hgsc.bcm.edu	37	8	77765398	77765398	+	Missense_Mutation	SNP	A	A	G	rs16919452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:77765398A>G	ENST00000521891.2	+	10	6689	c.6241A>G	c.(6241-6243)Att>Gtt	p.I2081V	ZFHX4_ENST00000455469.2_Missense_Mutation_p.I2036V|ZFHX4_ENST00000050961.6_Missense_Mutation_p.I2036V|ZFHX4_ENST00000518282.1_Missense_Mutation_p.I2055V	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2036					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)			CTTTCCTTCCATTATGATGCA	0.607										HNSCC(33;0.089)			A|||	413	0.0824681	0.0091	0.1945	5008	,	,		10324	0.1825		0.0328	False		,,,				2504	0.0501				p.I2081V		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A6241G						PASS	.	A	VAL/ILE	38,3882		0,38,1922	17.0	18.0	17.0		6241	2.5	0.8	8	dbSNP_123	17	249,7885		1,247,3819	yes	missense	ZFHX4	NM_024721.4	29	1,285,5741	GG,GA,AA		3.0612,0.9694,2.381	benign	2081/3617	77765398	287,11767	1960	4067	6027	SO:0001583	missense	79776	exon10			CCTTCCATTATGA		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.6241A>G	8.37:g.77765398A>G	ENSP00000430497:p.Ile2081Val	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	146	74	0.506849	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	185	0.08470695970695971	5	0.01016260162601626	60	0.16574585635359115	95	0.1660839160839161	25	0.032981530343007916	A	15.02	2.708696	0.48517	0.009694	0.030612	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.46819	0.86;0.91;0.88;0.87	3.76	2.55	0.30701	.	0.152178	0.29853	U	0.011031	T	0.00073	0.0002	N	0.19112	0.55	0.28432	P	0.9172272	B;B;B	0.15473	0.008;0.013;0.013	B;B;B	0.14023	0.003;0.01;0.006	T	0.14035	-1.0487	9	0.15499	T	0.54	.	9.1445	0.36923	0.8362:0.0:0.0:0.1638	rs16919452;rs16919452	2036;2036;2081	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	V	2081;2065;2036;2036;2055	ENSP00000430497:I2081V;ENSP00000399605:I2036V;ENSP00000050961:I2036V;ENSP00000430848:I2055V	ENSP00000050961:I2036V	I	+	1	0	ZFHX4	77927953	1.000000	0.71417	0.818000	0.32626	0.930000	0.56654	1.529000	0.35996	0.594000	0.29761	0.374000	0.22700	ATT	A|0.927;G|0.073	0.073	strong		0.607	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629155	32629155	+	Silent	SNP	C	C	A	rs1130431	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629155C>A	ENST00000399084.1	-	5	919	c.741G>T	c.(739-741)ctG>ctT	p.L247L	HLA-DQB1_ENST00000399079.3_Intron|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Silent_p.L247L|HLA-DQB1_ENST00000374943.4_Silent_p.L247L|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	247					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)"""	TGATAAGGCCCAGCCCAAGGA	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1368	0.273163	0.2821	0.196	5008	,	,		12357	0.3254		0.2485	False		,,,				2504	0.2873				p.L247L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G741T						PASS	.	C		1110,2826		383,344,1241	34.0	30.0	31.0		741	-1.8	0.1	6	dbSNP_130	31	1989,5829		704,581,2624	no	coding-synonymous	HLA-DQB1	NM_002123.4		1087,925,3865	AA,AC,CC		25.4413,28.2012,26.3655		247/262	32629155	3099,8655	1968	3909	5877	SO:0001819	synonymous_variant	3119	exon4	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AAGGCCCAGCCCA		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.741G>T	6.37:g.32629155C>A		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	61	55	0.901639	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			C|0.805;A|0.195	0.195	strong		0.562	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
C11orf24	53838	hgsc.bcm.edu	37	11	68029738	68029738	+	Missense_Mutation	SNP	G	G	A	rs143548724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68029738G>A	ENST00000304271.6	-	4	1127	c.725C>T	c.(724-726)gCg>gTg	p.A242V	C11orf24_ENST00000530166.1_5'Flank|C11orf24_ENST00000533310.1_Intron	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	242	Pro-rich.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						AGGGCTTGCCGCGGTGTCACT	0.562													G|||	12	0.00239617	0.0	0.0043	5008	,	,		17040	0.0		0.005	False		,,,				2504	0.0041				p.A242V	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.C725T						PASS	.	G	VAL/ALA	1,4399	4.2+/-10.8	0,1,2199	110.0	108.0	108.0		725	2.7	0.0	11	dbSNP_134	108	41,8547	26.3+/-74.7	1,39,4254	yes	missense	C11orf24	NM_022338.3	64	1,40,6453	AA,AG,GG		0.4774,0.0227,0.3234	benign	242/450	68029738	42,12946	2200	4294	6494	SO:0001583	missense	53838	exon4			CTTGCCGCGGTGT	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.725C>T	11.37:g.68029738G>A	ENSP00000307264:p.Ala242Val	Somatic	452	0	0		WXS	Illumina HiSeq	Phase_I	475	238	0.501053	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	12.16	1.854439	0.32791	2.27E-4	0.004774	ENSG00000171067	ENST00000304271	T	0.30448	1.53	4.61	2.73	0.32206	.	1.566200	0.04540	N	0.387933	T	0.20251	0.0487	N	0.14661	0.345	0.21984	N	0.999436	B	0.29862	0.259	B	0.22880	0.042	T	0.26503	-1.0101	10	0.33940	T	0.23	0.7561	9.9733	0.41768	0.1699:0.0:0.8301:0.0	.	242	Q96F05	CK024_HUMAN	V	242	ENSP00000307264:A242V	ENSP00000307264:A242V	A	-	2	0	C11orf24	67786314	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.126000	0.15769	0.487000	0.27698	-0.459000	0.05422	GCG	G|0.998;A|0.002	0.002	strong		0.562	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
LILRB1	10859	hgsc.bcm.edu	37	19	55143157	55143157	+	Missense_Mutation	SNP	G	G	A	rs12460501|rs34880987|rs200526666	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55143157G>A	ENST00000396331.1	+	5	634	c.277G>A	c.(277-279)Gca>Aca	p.A93T	LILRB1_ENST00000434867.2_Missense_Mutation_p.A93T|LILRB1_ENST00000396321.2_Missense_Mutation_p.A93T|LILRB1_ENST00000396315.1_Missense_Mutation_p.A93T|LILRB1_ENST00000418536.2_Missense_Mutation_p.A93T|LILRB1_ENST00000427581.2_Missense_Mutation_p.A129T|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000396332.4_Missense_Mutation_p.A93T|LILRB1_ENST00000396317.1_Missense_Mutation_p.A93T|LILRB1_ENST00000448689.1_Missense_Mutation_p.A93T|LILRB1_ENST00000396327.3_Missense_Mutation_p.A93T|LILRB1_ENST00000324602.7_Missense_Mutation_p.A93T	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	93	Ig-like C2-type 1.		A -> T (in dbSNP:rs12460501). {ECO:0000269|PubMed:20600445}.		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)		CTGGGAACATGCAGGGCGGTA	0.552										HNSCC(37;0.09)			g|||	1071	0.213858	0.0575	0.232	5008	,	,		17924	0.505		0.1312	False		,,,				2504	0.1973				p.A93T		Atlas-SNP	.											.	LILRB1	140	.	0			c.G277A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	156,4250		8,140,2055	160.0	146.0	151.0		277,277,277,277	-0.3	0.0	19	dbSNP_120	151	644,7956		78,488,3734	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	58,58,58,58	86,628,5789	AA,AG,GG		7.4884,3.5406,6.151	benign,benign,benign,benign	93/653,93/652,93/652,93/651	55143157	800,12206	2203	4300	6503	SO:0001583	missense	10859	exon4			GAACATGCAGGGC	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.277G>A	19.37:g.55143157G>A	ENSP00000379622:p.Ala93Thr	Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	231	115	0.497835	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	376	0.17216117216117216	19	0.03861788617886179	57	0.1574585635359116	231	0.40384615384615385	69	0.09102902374670185	G	10.20	1.283574	0.23392	0.035406	0.074884	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48	2.11	-0.338	0.12651	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.246452	0.28544	N	0.014975	T	0.00012	0.0000	L	0.47190	1.495	0.80722	P	0.0	D;B;P;P;B	0.54601	0.967;0.136;0.914;0.631;0.313	P;B;P;B;B	0.56127	0.792;0.103;0.657;0.393;0.314	T	0.47005	-0.9150	9	0.45353	T	0.12	.	5.5388	0.17026	0.3128:0.0:0.6872:0.0	rs12460501;rs57567657;rs12460501	93;93;93;93;93	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	T	93;93;93;93;93;93;93;93;129;93;93	ENSP00000379614:A93T;ENSP00000391514:A93T;ENSP00000409968:A93T;ENSP00000379622:A93T;ENSP00000379618:A93T;ENSP00000315997:A93T;ENSP00000405243:A93T;ENSP00000379623:A93T;ENSP00000395004:A129T;ENSP00000379610:A93T;ENSP00000379608:A93T	ENSP00000315997:A93T	A	+	1	0	LILRB1	59834969	0.000000	0.05858	0.005000	0.12908	0.009000	0.06853	-0.346000	0.07760	-0.222000	0.09958	-1.050000	0.02344	GCA	G|0.855;A|0.145	0.145	strong		0.552	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
HAPLN3	145864	hgsc.bcm.edu	37	15	89422286	89422286	+	Silent	SNP	C	C	T	rs3809574	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89422286C>T	ENST00000359595.3	-	4	922	c.708G>A	c.(706-708)ccG>ccA	p.P236P	HAPLN3_ENST00000562889.1_Silent_p.P298P	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	236	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)	p.P236P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	GTGCCAGGCCCGGGCCACCGC	0.682											OREG0023445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1013	0.202276	0.236	0.2032	5008	,	,		14551	0.2292		0.1779	False		,,,				2504	0.1534				p.P236P		Atlas-SNP	.											HAPLN3,NS,lymphoid_neoplasm,0,1	HAPLN3	43	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G708A						PASS	.	C		1044,3336		120,804,1266	12.0	15.0	14.0		708	1.2	1.0	15	dbSNP_107	14	1460,7106		113,1234,2936	no	coding-synonymous	HAPLN3	NM_178232.2		233,2038,4202	TT,TC,CC		17.0441,23.8356,19.3419		236/361	89422286	2504,10442	2190	4283	6473	SO:0001819	synonymous_variant	145864	exon4			CAGGCCCGGGCCA	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.708G>A	15.37:g.89422286C>T		Somatic	16	0	0	1267	WXS	Illumina HiSeq	Phase_I	25	17	0.68	NM_178232	A8K7P0	Silent	SNP	ENST00000359595.3	37	CCDS10346.1																																																																																			C|0.791;T|0.209	0.209	strong		0.682	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
CHMP4A	29082	hgsc.bcm.edu	37	14	24679877	24679877	+	Missense_Mutation	SNP	C	C	T	rs2295322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24679877C>T	ENST00000609024.1	-	4	505	c.457G>A	c.(457-459)Gga>Aga	p.G153R	CHMP4A_ENST00000542700.2_5'UTR|TM9SF1_ENST00000556387.1_Missense_Mutation_p.G153R|CHMP4A_ENST00000530996.1_Missense_Mutation_p.G48R|AL136419.6_ENST00000565988.1_RNA|TM9SF1_ENST00000530611.1_Missense_Mutation_p.G153R|CHMP4A_ENST00000347519.6_Missense_Mutation_p.G196R			Q9BY43	CHM4A_HUMAN	charged multivesicular body protein 4A	153	Intramolecular interaction with N- terminus. {ECO:0000250}.		G -> R (in dbSNP:rs2295322). {ECO:0000269|PubMed:14583093, ECO:0000269|PubMed:15489334}.	FG -> LLE (in Ref. 4; AAF29098). {ECO:0000305}.	endosomal transport (GO:0016197)|membrane budding (GO:0006900)|membrane organization (GO:0061024)|membrane tubulation (GO:0097320)|negative regulation of autophagic vacuole assembly (GO:1902902)|negative regulation of neuron death (GO:1901215)|posttranslational protein targeting to membrane (GO:0006620)|protein homooligomerization (GO:0051260)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|ESCRT III complex (GO:0000815)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|nucleus (GO:0005634)	ATPase binding (GO:0051117)|identical protein binding (GO:0042802)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)			NS(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)	9				GBM - Glioblastoma multiforme(265;0.0181)		ACATCATCTCCAAAGCCCATA	0.517													C|||	1759	0.351238	0.2489	0.6196	5008	,	,		19262	0.2361		0.504	False		,,,				2504	0.2607				p.G196R		Atlas-SNP	.											.	CHMP4A	20	.	0			c.G586A						PASS	.	C	ARG/GLY	1230,3176	426.4+/-341.1	185,860,1158	214.0	170.0	185.0		586	4.3	1.0	14	dbSNP_100	185	4443,4157	587.9+/-392.3	1125,2193,982	yes	missense	CHMP4A	NM_014169.3	125	1310,3053,2140	TT,TC,CC		48.3372,27.9165,43.6183		196/266	24679877	5673,7333	2203	4300	6503	SO:0001583	missense	29082	exon4			CATCTCCAAAGCC	AF212243	CCDS9619.1	14q12	2012-10-04	2011-09-21	2005-04-04	ENSG00000254505	ENSG00000254505		"""Charged multivesicular body proteins"""	20274	protein-coding gene	gene with protein product		610051	"""chromosome 14 open reading frame 123"", ""chromatin modifying protein 4A"""	C14orf123			Standard	NM_014169		Approved	HSPC134, VPS32A		Q9BY43	OTTHUMG00000167036	ENST00000609024.1:c.457G>A	14.37:g.24679877C>T	ENSP00000476412:p.Gly153Arg	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	137	135	0.985401	NM_014169	Q14D22|Q32Q79|Q86SZ8|Q96QJ9|Q9P026	Missense_Mutation	SNP	ENST00000609024.1	37		840	0.38461538461538464	137	0.2784552845528455	223	0.6160220994475138	115	0.20104895104895104	365	0.4815303430079156	C	23.0	4.367327	0.82463	0.279165	0.516628	ENSG00000100926;ENSG00000254692;ENSG00000254505;ENSG00000254505	ENST00000556387;ENST00000530611;ENST00000347519;ENST00000533011	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	5.2	4.3	0.51218	.	0.161135	0.29868	N	0.010999	T	0.00012	0.0000	H	0.95884	3.735	0.32303	P	0.564775	P;D	0.54964	0.872;0.969	P;D	0.67103	0.675;0.949	T	0.47497	-0.9113	9	0.72032	D	0.01	-11.0912	10.6946	0.45892	0.348:0.652:0.0:0.0	rs2295322;rs11546886;rs17693554;rs52790353;rs61392271;rs2295322	153;196	Q9BY43;Q14D22	CHM4A_HUMAN;.	R	153;153;196;163	ENSP00000451949:G153R;ENSP00000433967:G153R;ENSP00000324205:G196R;ENSP00000432575:G163R	ENSP00000324205:G196R	G	-	1	0	TM9SF1;AL096870.1;RP11-468E2.1	23749717	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.529000	0.67135	1.392000	0.46585	0.561000	0.74099	GGA	C|0.594;T|0.406	0.406	strong		0.517	CHMP4A-012	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471846.1	NM_014169	
FBXO41	150726	hgsc.bcm.edu	37	2	73491514	73491514	+	Silent	SNP	C	C	T	rs61735876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73491514C>T	ENST00000521871.1	-	6	2113	c.1698G>A	c.(1696-1698)acG>acA	p.T566T	FBXO41_ENST00000520530.2_Silent_p.T566T|FBXO41_ENST00000295133.5_Silent_p.T627T			Q8TF61	FBX41_HUMAN	F-box protein 41	566										breast(2)|central_nervous_system(1)|endometrium(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)	13						GCAGTGTGCGCGTGTCCAGGT	0.627													C|||	200	0.0399361	0.0348	0.0461	5008	,	,		17773	0.001		0.0815	False		,,,				2504	0.0399				p.T566T		Atlas-SNP	.											.	FBXO41	82	.	0			c.G1698A						PASS	.	C		222,4124		10,202,1961	85.0	93.0	90.0		1698	-10.5	0.2	2	dbSNP_129	90	778,7790		27,724,3533	no	coding-synonymous	FBXO41	NM_001080410.2		37,926,5494	TT,TC,CC		9.0803,5.1081,7.7435		566/876	73491514	1000,11914	2173	4284	6457	SO:0001819	synonymous_variant	150726	exon5			TGTGCGCGTGTCC	AB075820	CCDS46337.1, CCDS46337.2	2p13.2	2004-08-24				ENSG00000163013		"""F-boxes /  ""other"""""	29409	protein-coding gene	gene with protein product		609108				11853319	Standard	NM_001080410		Approved	KIAA1940, Fbx41	uc021vjh.1	Q8TF61		ENST00000521871.1:c.1698G>A	2.37:g.73491514C>T		Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	173	76	0.439306	NM_001080410	G3V0Z7|Q2M1V8	Silent	SNP	ENST00000521871.1	37	CCDS46337.2																																																																																			C|0.950;T|0.050	0.050	strong		0.627	FBXO41-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377381.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113191533	113191533	+	Silent	SNP	C	C	T	rs75212846	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113191533C>T	ENST00000401783.2	-	35	6033	c.5697G>A	c.(5695-5697)gtG>gtA	p.V1899V	SVEP1_ENST00000374469.1_Silent_p.V1876V|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1899	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						CTGGTTCACACACAGGAGGGG	0.383													C|||	166	0.033147	0.0234	0.0259	5008	,	,		16684	0.0476		0.0457	False		,,,				2504	0.0235				p.V1899V		Atlas-SNP	.											.	SVEP1	326	.	0			c.G5697A						PASS	.	C		78,3602		1,76,1763	41.0	40.0	40.0		5697	3.3	1.0	9	dbSNP_132	40	345,7839		9,327,3756	no	coding-synonymous	SVEP1	NM_153366.3		10,403,5519	TT,TC,CC		4.2155,2.1196,3.5654		1899/3572	113191533	423,11441	1840	4092	5932	SO:0001819	synonymous_variant	79987	exon35			TTCACACACAGGA	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.5697G>A	9.37:g.113191533C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	45	24	0.533333	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			C|0.963;T|0.037	0.037	strong		0.383	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FMO2	2327	hgsc.bcm.edu	37	1	171174531	171174531	+	Missense_Mutation	SNP	A	A	G	rs2020863	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:171174531A>G	ENST00000209929.7	+	7	1099	c.941A>G	c.(940-942)gAg>gGg	p.E314G	RP1-127D3.4_ENST00000445290.1_RNA|FMO2_ENST00000529935.1_3'UTR|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.E314G			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	313					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)	p.E314G(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					GCCATCTTTGAGGATGGAACA	0.408													A|||	800	0.159744	0.0424	0.2277	5008	,	,		20245	0.2371		0.0905	False		,,,				2504	0.2618				p.E314G		Atlas-SNP	.											FMO2,NS,carcinoma,0,1	FMO2	66	1	1	Substitution - Missense(1)	stomach(1)	c.A941G						PASS	.	A	GLY/GLU	275,4131	153.3+/-186.9	9,257,1937	95.0	92.0	93.0		941	5.7	1.0	1	dbSNP_98	93	790,7810	186.3+/-233.8	35,720,3545	yes	missense	FMO2	NM_001460.2	98	44,977,5482	GG,GA,AA		9.186,6.2415,8.1885	possibly-damaging	314/472	171174531	1065,11941	2203	4300	6503	SO:0001583	missense	2327	exon7			TCTTTGAGGATGG	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.941A>G	1.37:g.171174531A>G	ENSP00000209929:p.Glu314Gly	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	296	0.13553113553113552	18	0.036585365853658534	61	0.1685082872928177	152	0.26573426573426573	65	0.08575197889182058	A	16.76	3.211991	0.58452	0.062415	0.09186	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.58940	0.3;0.3	5.67	5.67	0.87782	.	0.097167	0.64402	D	0.000002	T	0.67748	0.2926	M	0.88241	2.94	0.22591	P	0.99895097	P	0.35050	0.482	P	0.47705	0.555	T	0.75283	-0.3372	9	0.87932	D	0	-25.4404	14.8967	0.70649	1.0:0.0:0.0:0.0	rs2020863;rs2266707;rs61588049;rs2020863	314	Q99518	FMO2_HUMAN	G	314	ENSP00000209929:E314G;ENSP00000405905:E314G	ENSP00000209929:E314G	E	+	2	0	FMO2	169441155	1.000000	0.71417	0.969000	0.41365	0.738000	0.42128	4.940000	0.63533	2.154000	0.67381	0.533000	0.62120	GAG	A|0.884;G|0.116	0.116	strong		0.408	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
MT-ND5	4540	hgsc.bcm.edu	37	M	13368	13368	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:13368G>A	ENST00000361567.2	+	1	1032	c.1032G>A	c.(1030-1032)ggG>ggA	p.G344G	MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	344					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ATGTGCTCCGGGTCCATCATC	0.448																																					p.G344G		Atlas-SNP	.											.	.	.	.	0			c.G1032A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CTCCGGGTCCATC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1032G>A	M.37:g.13368G>A		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	9	9	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
ATP2C2	9914	hgsc.bcm.edu	37	16	84476200	84476200	+	Missense_Mutation	SNP	A	A	T	rs247897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84476200A>T	ENST00000262429.4	+	15	1485	c.1396A>T	c.(1396-1398)Atg>Ttg	p.M466L	ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Missense_Mutation_p.M466L	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	466			M -> L (in dbSNP:rs247897). {ECO:0000269|PubMed:14702039}.		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						GGCCCTGGCGATGAAGGTAGG	0.582													A|||	2044	0.408147	0.4713	0.3401	5008	,	,		15905	0.4226		0.3499	False		,,,				2504	0.4162				p.M466L		Atlas-SNP	.											.	ATP2C2	75	.	0			c.A1396T						PASS	.	A	LEU/MET	1590,2186		322,946,620	112.0	117.0	115.0		1396	3.8	0.9	16	dbSNP_79	115	3082,5134		589,1904,1615	yes	missense	ATP2C2	NM_014861.2	15	911,2850,2235	TT,TA,AA		37.5122,42.1081,38.9593	benign	466/947	84476200	4672,7320	1888	4108	5996	SO:0001583	missense	9914	exon15			CTGGCGATGAAGG	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.1396A>T	16.37:g.84476200A>T	ENSP00000262429:p.Met466Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	112	67	0.598214	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	37	CCDS42207.1	879	0.4024725274725275	252	0.5121951219512195	129	0.356353591160221	235	0.41083916083916083	263	0.3469656992084433	A	10.78	1.446866	0.25987	0.421081	0.375122	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	D;D	0.95342	-3.68;-3.68	4.92	3.8	0.43715	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.057448	0.64402	D	0.000001	T	0.00012	0.0000	N	0.11154	0.105	0.23010	P	0.99843986	B;B;B;B	0.27910	0.043;0.022;0.034;0.193	B;B;B;B	0.32533	0.102;0.051;0.091;0.147	T	0.29088	-1.0023	9	0.25751	T	0.34	.	11.1725	0.48579	0.8452:0.1548:0.0:0.0	rs247897;rs497275;rs56485429;rs57635635;rs247897	466;315;483;466	E7ES94;F8WAA5;O75185-2;O75185	.;.;.;AT2C2_HUMAN	L	466;466;315	ENSP00000397925:M466L;ENSP00000262429:M466L	ENSP00000262429:M466L	M	+	1	0	ATP2C2	83033701	1.000000	0.71417	0.883000	0.34634	0.277000	0.26821	6.632000	0.74281	0.794000	0.33899	0.402000	0.26972	ATG	A|0.597;T|0.403	0.403	strong		0.582	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
ZNF517	340385	hgsc.bcm.edu	37	8	146032842	146032842	+	Missense_Mutation	SNP	G	G	A	rs62531506	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:146032842G>A	ENST00000531720.1	+	4	586	c.541G>A	c.(541-543)Gtg>Atg	p.V181M	ZNF517_ENST00000525105.1_Intron|ZNF517_ENST00000526178.1_Intron|ZNF517_ENST00000359971.3_Missense_Mutation_p.V181M			Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	181					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)|large_intestine(2)|lung(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CTACAGGTGCGTGTGCGGCAA	0.667													G|||	210	0.0419329	0.0121	0.0634	5008	,	,		16100	0.0		0.1302	False		,,,				2504	0.0194				p.V181M		Atlas-SNP	.											.	ZNF517	30	.	0			c.G541A						PASS	.	G	MET/VAL	132,4252		3,126,2063	19.0	19.0	19.0		541	0.9	0.0	8	dbSNP_129	19	1148,7428		67,1014,3207	yes	missense	ZNF517	NM_213605.2	21	70,1140,5270	AA,AG,GG		13.3862,3.0109,9.8765	benign	181/493	146032842	1280,11680	2192	4288	6480	SO:0001583	missense	340385	exon5			AGGTGCGTGTGCG	AK096527	CCDS6434.1	8q24.3	2013-01-08				ENSG00000197363		"""Zinc fingers, C2H2-type"", ""-"""	27984	protein-coding gene	gene with protein product							Standard	NM_213605		Approved		uc003zed.1	Q6ZMY9		ENST00000531720.1:c.541G>A	8.37:g.146032842G>A	ENSP00000436103:p.Val181Met	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	53	18	0.339623	NM_213605		Missense_Mutation	SNP	ENST00000531720.1	37	CCDS6434.1	134	0.06135531135531135	6	0.012195121951219513	24	0.06629834254143646	0	0.0	104	0.13720316622691292	G	3.175	-0.169186	0.06461	0.030109	0.133862	ENSG00000197363	ENST00000359971;ENST00000531720	T;T	0.06528	3.29;3.29	1.82	0.917	0.19380	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.58432	P	1.999999999946489E-6	P	0.46277	0.875	B	0.29176	0.099	T	0.48352	-0.9043	8	0.59425	D	0.04	.	2.2236	0.03979	0.191:0.0:0.5022:0.3068	rs62531506	181	Q6ZMY9	ZN517_HUMAN	M	181	ENSP00000353058:V181M;ENSP00000436103:V181M	ENSP00000353058:V181M	V	+	1	0	ZNF517	146003646	0.077000	0.21312	0.014000	0.15608	0.304000	0.27724	2.167000	0.42415	0.329000	0.23460	0.462000	0.41574	GTG	G|0.922;A|0.078	0.078	strong		0.667	ZNF517-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382642.1	XM_291261	
OR2J2	26707	hgsc.bcm.edu	37	6	29141849	29141849	+	Missense_Mutation	SNP	T	T	C	rs3116856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29141849T>C	ENST00000377167.2	+	1	539	c.437T>C	c.(436-438)gTt>gCt	p.V146A		NM_030905.2	NP_112167.2	O76002	OR2J2_HUMAN	olfactory receptor, family 2, subfamily J, member 2	146			A -> V (in allele 6M1-6*02 and allele 6M1-6*03; dbSNP:rs3116856). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(17)|ovary(1)|upper_aerodigestive_tract(1)	25						CACTTGTTGGTTGCGGCTTCT	0.463													C|||	1893	0.377995	0.112	0.451	5008	,	,		21396	0.378		0.5477	False		,,,				2504	0.5112				p.V146A		Atlas-SNP	.											.	OR2J2	51	.	0			c.T437C						PASS	.	C	ALA/VAL	748,3250		75,598,1326	301.0	276.0	284.0		437	2.3	0.4	6	dbSNP_103	284	4513,3831		1237,2039,896	no	missense	OR2J2	NM_030905.2	64	1312,2637,2222	CC,CT,TT		45.9132,18.7094,42.6268	probably-damaging	146/313	29141849	5261,7081	1999	4172	6171	SO:0001583	missense	26707	exon1			TGTTGGTTGCGGC		CCDS43434.1	6p22.2-p21.31	2012-08-09			ENSG00000204700	ENSG00000204700		"""GPCR / Class A : Olfactory receptors"""	8260	protein-coding gene	gene with protein product							Standard	NM_030905		Approved	OR6-8, hs6M1-6, dJ80I19.4	uc011dlm.2	O76002	OTTHUMG00000031091	ENST00000377167.2:c.437T>C	6.37:g.29141849T>C	ENSP00000366372:p.Val146Ala	Somatic	334	1	0.00299401		WXS	Illumina HiSeq	Phase_I	367	180	0.490463	NM_030905	A6NCU9|A6NLD0|B0UY53|Q32N09|Q5ST39|Q5SUJ6|Q6IF24|Q9GZK2|Q9GZL3	Missense_Mutation	SNP	ENST00000377167.2	37	CCDS43434.1	870	0.3983516483516483	59	0.11991869918699187	166	0.4585635359116022	209	0.36538461538461536	436	0.575197889182058	C	0	-2.819406	0.00072	0.187094	0.540868	ENSG00000204700	ENST00000377167	T	0.39056	1.1	2.3	2.3	0.28687	.	.	.	.	.	T	0.05364	0.0142	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.36163	-0.9759	5	0.02654	T	1	.	7.9731	0.30138	0.0:0.8633:0.0:0.1367	rs3116856;rs17737530;rs52793747;rs3116856	.	.	.	A	146	ENSP00000366372:V146A	ENSP00000366372:V146A	V	+	2	0	OR2J2	29249828	0.000000	0.05858	0.369000	0.25952	0.019000	0.09904	-0.161000	0.10026	0.290000	0.22444	-0.971000	0.02607	GTT	T|0.566;C|0.434	0.434	strong		0.463	OR2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076131.2		
IFITM5	387733	hgsc.bcm.edu	37	11	299411	299411	+	Missense_Mutation	SNP	C	C	G	rs57285449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:299411C>G	ENST00000382614.2	-	1	115	c.80G>C	c.(79-81)gGg>gCg	p.G27A		NM_001025295.2	NP_001020466.1	A6NNB3	IFM5_HUMAN	interferon induced transmembrane protein 5	27			G -> A (in dbSNP:rs57285449).		bone mineralization (GO:0030282)|regulation of bone mineralization (GO:0030500)|response to biotic stimulus (GO:0009607)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.73e-28)|Epithelial(43;3.42e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.14e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0328)|LUSC - Lung squamous cell carcinoma(625;0.122)		GTGCGGGGCCCCCAGTGTGAG	0.682													c|||	2968	0.592652	0.7148	0.5922	5008	,	,		8718	0.6429		0.3479	False		,,,				2504	0.6278				p.G27A		Atlas-SNP	.											.	IFITM5	12	.	0			c.G80C						PASS	.	C	ALA/GLY	2610,1758		836,938,410	22.0	22.0	22.0		80	2.2	0.0	11	dbSNP_129	22	2407,6153		412,1583,2285	no	missense	IFITM5	NM_001025295.1	60	1248,2521,2695	GG,GC,CC		28.1192,40.2473,38.8072	probably-damaging	27/133	299411	5017,7911	2184	4280	6464	SO:0001583	missense	387733	exon1			GGGGCCCCCAGTG	AA463818, CR747200, DY654432	CCDS31323.1	11p15.5	2010-05-12			ENSG00000206013	ENSG00000206013			16644	protein-coding gene	gene with protein product		614757				11106657, 12659663, 18442316	Standard	NM_001025295		Approved	fragilis4, Hrmp1, BRIL	uc001low.2	A6NNB3	OTTHUMG00000165355	ENST00000382614.2:c.80G>C	11.37:g.299411C>G	ENSP00000372059:p.Gly27Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	106	50	0.471698	NM_001025295		Missense_Mutation	SNP	ENST00000382614.2	37	CCDS31323.1	1064	0.48717948717948717	325	0.6605691056910569	166	0.4585635359116022	333	0.5821678321678322	240	0.316622691292876	C	5.600	0.295412	0.10622	0.597527	0.281192	ENSG00000206013	ENST00000382614	D	0.85556	-2.0	4.23	2.25	0.28309	.	0.185737	0.35179	N	0.003399	T	0.00012	0.0000	L	0.46157	1.445	0.38741	P	0.04611500000000002	B	0.12630	0.006	B	0.15484	0.013	T	0.48328	-0.9045	9	0.13853	T	0.58	-5.224	7.931	0.29901	0.0:0.6073:0.3018:0.0908	rs57285449;rs61876233	27	A6NNB3	IFM5_HUMAN	A	27	ENSP00000372059:G27A	ENSP00000372059:G27A	G	-	2	0	IFITM5	289411	0.603000	0.26924	0.029000	0.17559	0.033000	0.12548	1.221000	0.32503	0.203000	0.20529	0.561000	0.74099	GGG	C|0.546;G|0.454	0.454	strong		0.682	IFITM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383588.1	NM_001025295	
PLXNA4	91584	hgsc.bcm.edu	37	7	131817850	131817850	+	Silent	SNP	T	T	C	rs75848889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:131817850T>C	ENST00000359827.3	-	31	6509	c.5547A>G	c.(5545-5547)gcA>gcG	p.A1849A	PLXNA4_ENST00000321063.4_Silent_p.A1849A			Q9HCM2	PLXA4_HUMAN	plexin A4	1849					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TCTCTGAGAGTGCACTCATGG	0.522													T|||	655	0.130791	0.0303	0.2853	5008	,	,		17858	0.0962		0.0984	False		,,,				2504	0.226				p.A1849A		Atlas-SNP	.											.	PLXNA4	873	.	0			c.A5547G						PASS	.	T		151,4231		2,147,2042	137.0	140.0	139.0		5547	-10.5	0.1	7	dbSNP_131	139	859,7739		48,763,3488	no	coding-synonymous	PLXNA4	NM_020911.1		50,910,5530	CC,CT,TT		9.9907,3.4459,7.7812		1849/1895	131817850	1010,11970	2191	4299	6490	SO:0001819	synonymous_variant	91584	exon31			TGAGAGTGCACTC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.5547A>G	7.37:g.131817850T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			T|0.898;C|0.102	0.102	strong		0.522	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
ANKRD18A	253650	hgsc.bcm.edu	37	9	38588602	38588602	+	Missense_Mutation	SNP	T	T	C	rs2799163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:38588602T>C	ENST00000399703.5	-	11	2437	c.2063A>G	c.(2062-2064)tAt>tGt	p.Y688C		NM_147195.2	NP_671728.2	Q8IVF6	AN18A_HUMAN	ankyrin repeat domain 18A	688			Y -> C (in dbSNP:rs2799163).							NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	16						GTCCGCAGTATAGTTCAGTAA	0.274													t|||	1964	0.392173	0.6021	0.3718	5008	,	,		16295	0.4772		0.2744	False		,,,				2504	0.1564				p.Y688C		Atlas-SNP	.											ANKRD18A,NS,carcinoma,0,1	ANKRD18A	49	1	0			c.A2063G						PASS	.						71.0	61.0	64.0					9																	38588602		692	1575	2267	SO:0001583	missense	253650	exon11			GCAGTATAGTTCA	AB095935	CCDS55311.1	9p13.1	2013-01-10			ENSG00000180071	ENSG00000180071		"""Ankyrin repeat domain containing"""	23643	protein-coding gene	gene with protein product							Standard	NM_147195		Approved	KIAA2015, FLJ35740	uc004abg.4	Q8IVF6	OTTHUMG00000019950	ENST00000399703.5:c.2063A>G	9.37:g.38588602T>C	ENSP00000382610:p.Tyr688Cys	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	201	93	0.462687	NM_147195	A7MD11|A8MVU5|Q5SY86|Q7Z468|Q8NA88	Missense_Mutation	SNP	ENST00000399703.5	37	CCDS55311.1	916	0.4194139194139194	333	0.676829268292683	125	0.3453038674033149	240	0.4195804195804196	218	0.287598944591029	T	6.894	0.534440	0.13188	.	.	ENSG00000180071	ENST00000399703	T	0.28666	1.6	1.39	0.0723	0.14386	.	.	.	.	.	T	0.00012	0.0000	L	0.37630	1.12	0.80722	P	0.0	D	0.62365	0.991	P	0.46389	0.515	T	0.37549	-0.9701	8	0.38643	T	0.18	.	2.3016	0.04163	0.2838:0.0:0.2876:0.4286	rs2799163;rs52796725;rs59755233;rs2799163	688	Q8IVF6	AN18A_HUMAN	C	688	ENSP00000382610:Y688C	ENSP00000382610:Y688C	Y	-	2	0	ANKRD18A	38578602	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.520000	0.06252	0.006000	0.14734	0.145000	0.16022	TAT	T|0.588;C|0.412	0.412	strong		0.274	ANKRD18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052506.3		
XIRP2	129446	hgsc.bcm.edu	37	2	168106246	168106246	+	Missense_Mutation	SNP	G	G	A	rs16853330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168106246G>A	ENST00000409195.1	+	9	8433	c.8344G>A	c.(8344-8346)Gta>Ata	p.V2782I	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.V2560I|XIRP2_ENST00000295237.9_Missense_Mutation_p.V2782I|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2607					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AAGAGTGACAGTACAATTGCC	0.408													A|||	1181	0.235823	0.3623	0.1686	5008	,	,		20362	0.2173		0.1282	False		,,,				2504	0.2423				p.V2782I		Atlas-SNP	.											XIRP2,NS,carcinoma,-1,1	XIRP2	914	1	0			c.G8344A						PASS	.	A	,,ILE/VAL,,ILE/VAL	1194,2546		201,792,877	62.0	59.0	60.0		,,7678,,8344	-5.0	0.0	2	dbSNP_123	60	926,7296		56,814,3241	yes	intron,intron,missense,intron,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	,,29,,29	257,1606,4118	AA,AG,GG		11.2625,31.9251,17.7228	,,possibly-damaging,,possibly-damaging	,,2560/3328,,2782/3550	168106246	2120,9842	1870	4111	5981	SO:0001583	missense	129446	exon9			GTGACAGTACAAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8344G>A	2.37:g.168106246G>A	ENSP00000386840:p.Val2782Ile	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	480	0.21978021978021978	192	0.3902439024390244	52	0.143646408839779	136	0.23776223776223776	100	0.13192612137203166	A	0.029	-1.350948	0.01256	0.319251	0.112625	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02446	4.29;4.29;4.29	6.17	-5.01	0.02991	.	1.339210	0.04273	N	0.342418	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	0.01281	0.0;0.0;0.0	T	0.47849	-0.9085	9	0.05525	T	0.97	-0.4314	12.7259	0.57170	0.2092:0.2213:0.5694:0.0	rs16853330;rs52825904;rs61575660;rs16853330	2607;2607;2560	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	I	2782;2782;2560;196	ENSP00000386840:V2782I;ENSP00000295237:V2782I;ENSP00000387255:V2560I	ENSP00000295237:V2782I	V	+	1	0	XIRP2	167814492	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-0.912000	0.04046	-1.340000	0.02227	-0.254000	0.11334	GTA	G|0.774;A|0.225	0.225	strong		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
MICB	4277	hgsc.bcm.edu	37	6	31474000	31474000	+	Missense_Mutation	SNP	G	G	A	rs1051788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31474000G>A	ENST00000252229.6	+	3	485	c.406G>A	c.(406-408)Gat>Aat	p.D136N	MICB_ENST00000399150.3_Intron|MICB_ENST00000538442.1_Missense_Mutation_p.D104N	NM_005931.3	NP_005922.2			MHC class I polypeptide-related sequence B											NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	13						TTTCTACTACGATGGGGAGCT	0.552													g|||	1415	0.282548	0.3835	0.1902	5008	,	,		17992	0.2738		0.2624	False		,,,				2504	0.2413				p.D136N		Atlas-SNP	.											.	MICB	26	.	0			c.G406A						PASS	.	T	ASN/ASP	1409,2419		251,907,756	50.0	52.0	51.0		406	-0.6	0.0	6	dbSNP_86	51	2523,5701		418,1687,2007	no	missense	MICB	NM_005931.3	23	669,2594,2763	AA,AG,GG		30.6785,36.8077,32.6253	possibly-damaging	136/384	31474000	3932,8120	1914	4112	6026	SO:0001583	missense	4277	exon3			TACTACGATGGGG		CCDS43449.1, CCDS75422.1, CCDS75423.1	6p21.3	2013-01-11			ENSG00000204516	ENSG00000204516		"""Immunoglobulin superfamily / C1-set domain containing"""	7091	protein-coding gene	gene with protein product		602436				8022771	Standard	NM_005931		Approved	PERB11.2	uc003ntn.4	Q29980	OTTHUMG00000031074	ENST00000252229.6:c.406G>A	6.37:g.31474000G>A	ENSP00000252229:p.Asp136Asn	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	188	82	0.43617	NM_005931		Missense_Mutation	SNP	ENST00000252229.6	37	CCDS43449.1	613	0.2806776556776557	199	0.40447154471544716	77	0.212707182320442	127	0.22202797202797203	210	0.2770448548812665	N	6.301	0.423715	0.11928	0.368077	0.306785	ENSG00000204516	ENST00000538442;ENST00000252229	T;T	0.02301	4.35;4.35	2.34	-0.599	0.11645	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.419890	0.17289	N	0.179739	T	0.00998	0.0033	M	0.79343	2.45	0.80722	P	0.0	B;P	0.39964	0.077;0.697	B;B	0.33521	0.019;0.165	T	0.43956	-0.9359	9	0.56958	D	0.05	.	3.6257	0.08112	0.2537:0.0:0.5513:0.1951	rs1051788;rs3176028	104;136	F5H7Q8;Q29980	.;MICB_HUMAN	N	104;136	ENSP00000442345:D104N;ENSP00000252229:D136N	ENSP00000252229:D136N	D	+	1	0	MICB	31581979	0.039000	0.19947	0.004000	0.12327	0.001000	0.01503	0.640000	0.24705	-0.172000	0.10779	-0.677000	0.03784	GAT	A|0.285;G|0.715	0.285	strong		0.552	MICB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076102.3	NM_005931	
FBN3	84467	hgsc.bcm.edu	37	19	8138054	8138054	+	Missense_Mutation	SNP	C	C	A	rs7257948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8138054C>A	ENST00000600128.1	-	62	8244	c.7830G>T	c.(7828-7830)gaG>gaT	p.E2610D	FBN3_ENST00000601739.1_Missense_Mutation_p.E2610D|FBN3_ENST00000270509.2_Missense_Mutation_p.E2610D			Q75N90	FBN3_HUMAN	fibrillin 3	2610	EGF-like 44; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		E -> D (in dbSNP:rs7257948). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:14962672, ECO:0000269|PubMed:15221638}.			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACTCATCCACCTCCTGGCAGC	0.662													A|||	2902	0.579473	0.8956	0.6441	5008	,	,		16638	0.3552		0.5586	False		,,,				2504	0.3589				p.E2610D		Atlas-SNP	.											FBN3,colon,carcinoma,0,1	FBN3	300	1	0			c.G7830T						PASS	.	A	ASP/GLU	3725,681	274.6+/-272.0	1591,543,69	41.0	46.0	44.0		7830	-3.8	0.0	19	dbSNP_116	44	4648,3952	528.8+/-381.4	1268,2112,920	yes	missense	FBN3	NM_032447.3	45	2859,2655,989	AA,AC,CC		45.9535,15.4562,35.622	benign	2610/2810	8138054	8373,4633	2203	4300	6503	SO:0001583	missense	84467	exon61			ATCCACCTCCTGG		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.7830G>T	19.37:g.8138054C>A	ENSP00000470498:p.Glu2610Asp	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	158	157	0.993671	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	1321	0.6048534798534798	428	0.8699186991869918	232	0.6408839779005525	227	0.3968531468531469	434	0.5725593667546174	A	0.032	-1.328437	0.01309	0.845438	0.540465	ENSG00000142449	ENST00000270509;ENST00000341066	T	0.22134	1.97	4.24	-3.82	0.04281	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00197	-1.87	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.31364	-0.9946	9	0.02654	T	1	.	10.1006	0.42502	0.3682:0.1137:0.5181:0.0	rs7257948;rs52831853;rs56970053;rs7257948	2610	Q75N90	FBN3_HUMAN	D	2610;673	ENSP00000270509:E2610D	ENSP00000270509:E2610D	E	-	3	2	FBN3	8044054	0.000000	0.05858	0.040000	0.18447	0.460000	0.32559	-1.163000	0.03138	-2.290000	0.00667	-1.327000	0.01280	GAG	C|0.380;A|0.620	0.620	strong		0.662	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
F13A1	2162	hgsc.bcm.edu	37	6	6174856	6174856	+	Silent	SNP	T	T	C	rs5986	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:6174856T>C	ENST00000264870.3	-	12	1969	c.1704A>G	c.(1702-1704)gaA>gaG	p.E568E		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	568					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)	p.E568E(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	CCTTCTTGAATTCTGCCTTCG	0.532													T|||	246	0.0491214	0.0386	0.0735	5008	,	,		18345	0.001		0.1133	False		,,,				2504	0.0297				p.E568E		Atlas-SNP	.											F13A1,NS,NS,0,1	F13A1	135	1	1	Substitution - coding silent(1)	pancreas(1)	c.A1704G						PASS	.	T		238,4168	140.4+/-175.9	4,230,1969	286.0	247.0	260.0		1704	-0.6	0.8	6	dbSNP_52	260	859,7741	195.2+/-240.5	36,787,3477	no	coding-synonymous	F13A1	NM_000129.3		40,1017,5446	CC,CT,TT		9.9884,5.4017,8.4346		568/733	6174856	1097,11909	2203	4300	6503	SO:0001819	synonymous_variant	2162	exon12			CTTGAATTCTGCC	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1704A>G	6.37:g.6174856T>C		Somatic	270	0	0		WXS	Illumina HiSeq	Phase_I	289	118	0.408305	NM_000129	Q59HA7|Q8N6X2|Q96P24|Q9BX29	Silent	SNP	ENST00000264870.3	37	CCDS4496.1																																																																																			T|0.924;C|0.076	0.076	strong		0.532	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
CARS2	79587	hgsc.bcm.edu	37	13	111335406	111335406	+	Missense_Mutation	SNP	C	C	T	rs146773721	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:111335406C>T	ENST00000257347.4	-	6	710	c.647G>A	c.(646-648)gGa>gAa	p.G216E	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	216				LVGVVPGPVGEPADSDK -> IGRRGPWSSPETSGLLTS (in Ref. 4; BAB93499). {ECO:0000305}.	cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	ACCTGGCTCTCCGACTGGACC	0.557													C|||	62	0.0123802	0.0	0.0403	5008	,	,		17647	0.0		0.0229	False		,,,				2504	0.0112				p.G216E		Atlas-SNP	.											.	CARS2	37	.	0			c.G647A						PASS	.	C	GLU/GLY	10,4396	16.8+/-37.8	0,10,2193	99.0	100.0	100.0		647	-4.0	0.0	13	dbSNP_134	100	168,8432	78.6+/-141.3	2,164,4134	yes	missense	CARS2	NM_024537.2	98	2,174,6327	TT,TC,CC		1.9535,0.227,1.3686	benign	216/565	111335406	178,12828	2203	4300	6503	SO:0001583	missense	79587	exon6			GGCTCTCCGACTG	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.647G>A	13.37:g.111335406C>T	ENSP00000257347:p.Gly216Glu	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	21	6	0.285714	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	31	0.014194139194139194	0	0.0	9	0.024861878453038673	0	0.0	22	0.029023746701846966	C	1.917	-0.449376	0.04572	0.00227	0.019535	ENSG00000134905	ENST00000257347	T	0.34275	1.37	5.39	-3.95	0.04118	.	0.594894	0.17421	N	0.174834	T	0.06735	0.0172	L	0.49571	1.57	0.09310	N	1	B	0.12013	0.005	B	0.16722	0.016	T	0.36383	-0.9750	10	0.02654	T	1	-22.3942	4.0182	0.09654	0.0985:0.2761:0.4232:0.2023	.	216	Q9HA77	SYCM_HUMAN	E	216	ENSP00000257347:G216E	ENSP00000257347:G216E	G	-	2	0	CARS2	110133407	0.000000	0.05858	0.019000	0.16419	0.317000	0.28152	-1.090000	0.03372	-0.357000	0.08175	0.462000	0.41574	GGA	C|0.987;T|0.013	0.013	strong		0.557	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	
MUC4	4585	hgsc.bcm.edu	37	3	195505822	195505822	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195505822G>T	ENST00000463781.3	-	2	13088	c.12629C>A	c.(12628-12630)cCt>cAt	p.P4210H	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4210H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTCGGTGACAGGAAGAGGGGT	0.592																																					p.P4210H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C12629A						scavenged	.						18.0	16.0	17.0					3																	195505822		688	1572	2260	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12629C>A	3.37:g.195505822G>T	ENSP00000417498:p.Pro4210His	Somatic	165	1	0.00606061		WXS	Illumina HiSeq	Phase_I	153	8	0.0522876	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	2.410	-0.335654	0.05278	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37058	1.22;1.26	.	.	.	.	.	.	.	.	T	0.32912	0.0845	N	0.14661	0.345	0.09310	N	0.999993	D	0.76494	0.999	D	0.72338	0.977	T	0.14117	-1.0484	7	.	.	.	.	2.6645	0.05037	0.4931:0.0:0.5069:0.0	.	4082	E7ESK3	.	H	4210	ENSP00000417498:P4210H;ENSP00000420243:P4210H	.	P	-	2	0	MUC4	196990601	.	.	0.023000	0.16930	0.027000	0.11550	.	.	0.088000	0.17205	0.089000	0.15464	CCT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TUBAL3	79861	hgsc.bcm.edu	37	10	5437365	5437365	+	Silent	SNP	A	A	G	rs11253156	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5437365A>G	ENST00000380419.3	-	3	358	c.321T>C	c.(319-321)gcT>gcC	p.A107A	TUBAL3_ENST00000479328.1_Silent_p.A67A	NM_024803.2	NP_079079.1	A6NHL2	TBAL3_HUMAN	tubulin, alpha-like 3	107					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|liver(1)|lung(7)|prostate(2)|skin(3)	25						CGTAATTGTTAGCAGCATCCT	0.617													G|||	3955	0.789736	0.8238	0.8084	5008	,	,		17992	0.8294		0.7227	False		,,,				2504	0.7587				p.A107A		Atlas-SNP	.											.	TUBAL3	54	.	0			c.T321C						PASS	.	G	,	3502,904	347.5+/-309.5	1394,714,95	145.0	138.0	140.0		201,321	-5.6	0.6	10	dbSNP_120	140	5987,2613	423.9+/-354.5	2099,1789,412	no	coding-synonymous,coding-synonymous	TUBAL3	NM_001171864.1,NM_024803.2	,	3493,2503,507	GG,GA,AA		30.3837,20.5175,27.0414	,	67/407,107/447	5437365	9489,3517	2203	4300	6503	SO:0001819	synonymous_variant	79861	exon3			ATTGTTAGCAGCA	AK025318	CCDS7066.2, CCDS53491.1	10p15.1	2007-03-15			ENSG00000178462	ENSG00000178462		"""Tubulins"""	23534	protein-coding gene	gene with protein product							Standard	NM_024803		Approved	FLJ21665	uc001ihy.3	A6NHL2	OTTHUMG00000017595	ENST00000380419.3:c.321T>C	10.37:g.5437365A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	79	36	0.455696	NM_024803	B4DKL2|Q4QQJ5|Q9H6Z0	Silent	SNP	ENST00000380419.3	37	CCDS7066.2																																																																																			A|0.247;G|0.753	0.753	strong		0.617	TUBAL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046548.2	NM_024803	
DSG3	1830	hgsc.bcm.edu	37	18	29046606	29046606	+	Missense_Mutation	SNP	G	G	A	rs16961975	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:29046606G>A	ENST00000257189.4	+	11	1608	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	509			V -> M (in dbSNP:rs16961975).		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)			TTCACCTTCCGTGGTTGTCTC	0.443													G|||	245	0.0489217	0.0469	0.0029	5008	,	,		18154	0.0486		0.0129	False		,,,				2504	0.1217				p.V509M		Atlas-SNP	.											.	DSG3	172	.	0			c.G1525A						PASS	.	G	MET/VAL	132,4274	95.7+/-134.4	3,126,2074	147.0	131.0	137.0		1525	4.9	0.3	18	dbSNP_123	137	106,8494	57.2+/-118.5	1,104,4195	yes	missense	DSG3	NM_001944.2	21	4,230,6269	AA,AG,GG		1.2326,2.9959,1.8299	probably-damaging	509/1000	29046606	238,12768	2203	4300	6503	SO:0001583	missense	1830	exon11			CCTTCCGTGGTTG	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.1525G>A	18.37:g.29046606G>A	ENSP00000257189:p.Val509Met	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	75	46	0.613333	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	69	0.03159340659340659	17	0.034552845528455285	4	0.011049723756906077	37	0.06468531468531469	11	0.014511873350923483	G	17.27	3.347887	0.61183	0.029959	0.012326	ENSG00000134757	ENST00000257189	T	0.62105	0.05	5.73	4.86	0.63082	.	0.181706	0.27181	N	0.020550	T	0.28366	0.0701	M	0.73962	2.25	0.20703	N	0.999861	D	0.89917	1.0	D	0.68353	0.957	T	0.52208	-0.8606	10	0.66056	D	0.02	.	8.3997	0.32579	0.2178:0.0:0.7822:0.0	rs16961975;rs52804074;rs16961975	509	P32926	DSG3_HUMAN	M	509	ENSP00000257189:V509M	ENSP00000257189:V509M	V	+	1	0	DSG3	27300604	0.254000	0.23992	0.297000	0.24988	0.082000	0.17680	1.686000	0.37669	2.718000	0.92993	0.585000	0.79938	GTG	G|0.975;A|0.025	0.025	strong		0.443	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
ZP2	7783	hgsc.bcm.edu	37	16	21215672	21215672	+	Silent	SNP	A	A	G	rs2075526	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:21215672A>G	ENST00000574002.1	-	9	1229	c.747T>C	c.(745-747)ccT>ccC	p.P249P	ZP2_ENST00000219593.4_Silent_p.P249P|AF001550.7_ENST00000572747.1_RNA|ZP2_ENST00000574091.1_Silent_p.P249P			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	249					binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		CCTTCTGTCCAGGAGATATAA	0.423													A|||	1593	0.318091	0.2352	0.2968	5008	,	,		22553	0.3998		0.2773	False		,,,				2504	0.4029				p.P249P		Atlas-SNP	.											.	ZP2	92	.	0			c.T747C						PASS	.	A		1023,3377	376.6+/-322.1	110,803,1287	104.0	101.0	102.0		747	2.2	0.7	16	dbSNP_96	102	2326,6274	388.4+/-342.6	330,1666,2304	no	coding-synonymous	ZP2	NM_003460.1		440,2469,3591	GG,GA,AA		27.0465,23.25,25.7615		249/746	21215672	3349,9651	2200	4300	6500	SO:0001819	synonymous_variant	7783	exon8			CTGTCCAGGAGAT	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.747T>C	16.37:g.21215672A>G		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	136	59	0.433824	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Silent	SNP	ENST00000574002.1	37	CCDS10596.1																																																																																			A|0.721;G|0.279	0.279	strong		0.423	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
SDC3	9672	hgsc.bcm.edu	37	1	31351513	31351513	+	Silent	SNP	G	G	A	rs1891419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:31351513G>A	ENST00000339394.6	-	2	387	c.213C>T	c.(211-213)ccC>ccT	p.P71P	SDC3_ENST00000336798.7_5'UTR|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	71					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)		GTTCATCATCGGGAAAGGAGT	0.617													G|||	891	0.177915	0.0295	0.2795	5008	,	,		19140	0.1111		0.3042	False		,,,				2504	0.2454				p.P71P		Atlas-SNP	.											.	SDC3	45	.	0			c.C213T						PASS	.	G		334,4072	175.5+/-204.9	16,302,1885	130.0	115.0	120.0		213	-9.2	0.7	1	dbSNP_92	120	2428,6172	402.5+/-347.5	332,1764,2204	no	coding-synonymous	SDC3	NM_014654.3		348,2066,4089	AA,AG,GG		28.2326,7.5806,21.2364		71/443	31351513	2762,10244	2203	4300	6503	SO:0001819	synonymous_variant	9672	exon2			ATCATCGGGAAAG	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.213C>T	1.37:g.31351513G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	125	1	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			G|0.818;A|0.182	0.182	strong		0.617	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144856852	144856852	+	Silent	SNP	C	C	T	rs377520030		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144856852C>T	ENST00000369354.3	-	40	6822	c.6633G>A	c.(6631-6633)gcG>gcA	p.A2211A	RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Silent_p.A2347A|PDE4DIP_ENST00000530740.1_Silent_p.A2296A|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000369356.4_Silent_p.A2211A|PDE4DIP_ENST00000313382.9_Silent_p.A2105A			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2211					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.A2211A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGAAGCTGCACGCTGATCTCA	0.502			T	PDGFRB	MPD																																p.A2211A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,-1,3	PDE4DIP	817	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G6633A						scavenged	.						39.0	31.0	34.0					1																	144856852		2199	4286	6485	SO:0001819	synonymous_variant	9659	exon40			GCTGCACGCTGAT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6633G>A	1.37:g.144856852C>T		Somatic	237	2	0.00843882		WXS	Illumina HiSeq	Phase_I	182	57	0.313187	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	5.637	0.302253	0.10678	.	.	ENSG00000178104	ENST00000530130	.	.	.	4.52	-1.01	0.10169	.	.	.	.	.	T	0.12263	0.0298	.	.	.	0.32646	N	0.519982	.	.	.	.	.	.	T	0.19745	-1.0296	4	.	.	.	.	1.5392	0.02551	0.1278:0.2204:0.3685:0.2833	.	.	.	.	H	288	.	.	R	-	2	0	PDE4DIP	143568209	0.000000	0.05858	0.052000	0.19188	0.068000	0.16541	-1.120000	0.03273	0.239000	0.21243	-0.693000	0.03709	CGT	.	.	none		0.502	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
PLRG1	5356	hgsc.bcm.edu	37	4	155461113	155461113	+	Silent	SNP	T	T	C	rs7671792	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155461113T>C	ENST00000499023.2	-	11	1158	c.1032A>G	c.(1030-1032)caA>caG	p.Q344Q	PLRG1_ENST00000302078.5_Silent_p.Q335Q|PLRG1_ENST00000393905.2_Silent_p.Q344Q	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	344					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CTGTAATAATTTGTGGTTCTG	0.338													T|||	1160	0.231629	0.1536	0.1888	5008	,	,		18870	0.1438		0.325	False		,,,				2504	0.362				p.Q344Q		Atlas-SNP	.											.	PLRG1	43	.	0			c.A1032G						PASS	.	T	,	788,3618	317.4+/-295.1	72,644,1487	201.0	178.0	186.0		1005,1032	-11.7	0.2	4	dbSNP_116	186	2829,5771	445.7+/-361.0	459,1911,1930	no	coding-synonymous,coding-synonymous	PLRG1	NM_001201564.1,NM_002669.3	,	531,2555,3417	CC,CT,TT		32.8953,17.8847,27.8102	,	335/506,344/515	155461113	3617,9389	2203	4300	6503	SO:0001819	synonymous_variant	5356	exon11			AATAATTTGTGGT	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1032A>G	4.37:g.155461113T>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	98	41	0.418367	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			T|0.738;C|0.262	0.262	strong		0.338	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
KIF13A	63971	hgsc.bcm.edu	37	6	17764731	17764731	+	Silent	SNP	G	G	C	rs6459569	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:17764731G>C	ENST00000259711.6	-	39	5133	c.5028C>G	c.(5026-5028)gcC>gcG	p.A1676A	KIF13A_ENST00000378843.2_Silent_p.A1628A|KIF13A_ENST00000378826.2_Silent_p.A1641A|KIF13A_ENST00000378816.5_Silent_p.A1641A|KIF13A_ENST00000378814.5_Silent_p.A1628A	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1676					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			GGCTCCCTTTGGCTAAGGCAC	0.468													G|||	830	0.165735	0.3979	0.098	5008	,	,		19998	0.0635		0.0696	False		,,,				2504	0.1043				p.A1676A		Atlas-SNP	.											.	KIF13A	276	.	0			c.C5028G						PASS	.	G	,,,	1359,2639		247,865,887	108.0	105.0	106.0		4923,4884,4884,5028	4.6	1.0	6	dbSNP_116	106	695,7643		31,633,3505	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	,,,	278,1498,4392	CC,CG,GG		8.3353,33.992,16.6505	,,,	1641/1771,1628/1758,1628/1750,1676/1806	17764731	2054,10282	1999	4169	6168	SO:0001819	synonymous_variant	63971	exon39			CCCTTTGGCTAAG	AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.5028C>G	6.37:g.17764731G>C		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	169	78	0.461538	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1																																																																																			G|0.857;C|0.143	0.143	strong		0.468	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
CMAS	55907	hgsc.bcm.edu	37	12	22213786	22213786	+	Silent	SNP	C	C	T	rs10841930	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:22213786C>T	ENST00000229329.2	+	5	844	c.714C>T	c.(712-714)taC>taT	p.Y238Y		NM_018686.4	NP_061156.1	Q8NFW8	NEUA_HUMAN	cytidine monophosphate N-acetylneuraminic acid synthetase	238					lipopolysaccharide biosynthetic process (GO:0009103)|N-acetylneuraminate metabolic process (GO:0006054)	membrane (GO:0016020)|nucleus (GO:0005634)	N-acylneuraminate cytidylyltransferase activity (GO:0008781)			autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	24						TGGCATACTACGAAATGCGAG	0.303													C|||	1268	0.253195	0.1452	0.1902	5008	,	,		15496	0.4524		0.0885	False		,,,				2504	0.408				p.Y238Y		Atlas-SNP	.											.	CMAS	45	.	0			c.C714T						PASS	.	C		681,3725	287.2+/-279.2	46,589,1568	118.0	123.0	121.0		714	-11.1	0.4	12	dbSNP_120	121	865,7731	197.5+/-242.1	39,787,3472	no	coding-synonymous	CMAS	NM_018686.3		85,1376,5040	TT,TC,CC		10.0628,15.4562,11.8905		238/435	22213786	1546,11456	2203	4298	6501	SO:0001819	synonymous_variant	55907	exon5			ATACTACGAAATG	AF271388	CCDS8696.1	12p12.1	2008-08-04			ENSG00000111726	ENSG00000111726			18290	protein-coding gene	gene with protein product	"""CMP-Neu5Ac synthetase"""	603316				8889549, 7566098	Standard	NM_018686		Approved		uc001rfm.4	Q8NFW8	OTTHUMG00000169097	ENST00000229329.2:c.714C>T	12.37:g.22213786C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_018686	Q96AX5|Q9NQZ0	Silent	SNP	ENST00000229329.2	37	CCDS8696.1																																																																																			C|0.831;G|0.000;T|0.169	0.169	strong		0.303	CMAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402235.1	NM_018686	
ETHE1	23474	hgsc.bcm.edu	37	19	44031324	44031324	+	Silent	SNP	C	C	T	rs3810381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44031324C>T	ENST00000292147.2	-	1	72	c.6G>A	c.(4-6)gcG>gcA	p.A2A	ETHE1_ENST00000600651.1_Silent_p.A2A|ZNF575_ENST00000458714.2_Intron	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	2					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|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)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				GTACAGCCTCCGCCATCGCGC	0.761													c|||	763	0.152356	0.177	0.085	5008	,	,		11670	0.131		0.1998	False		,,,				2504	0.1401				p.A2A		Atlas-SNP	.											.	ETHE1	7	.	0			c.G6A						PASS	.			555,3361		30,495,1433	3.0	4.0	4.0		6	-4.1	0.0	19	dbSNP_107	4	1184,6578		71,1042,2768	no	coding-synonymous	ETHE1	NM_014297.3		101,1537,4201	TT,TC,CC		15.2538,14.1726,14.8912		2/255	44031324	1739,9939	1958	3881	5839	SO:0001819	synonymous_variant	23474	exon1			AGCCTCCGCCATC		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.6G>A	19.37:g.44031324C>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_014297	Q96HR0|Q9H001	Silent	SNP	ENST00000292147.2	37	CCDS12622.1																																																																																			C|0.835;T|0.165	0.165	strong		0.761	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297	
PKP1	5317	hgsc.bcm.edu	37	1	201286771	201286771	+	Silent	SNP	C	C	T	rs1722779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201286771C>T	ENST00000352845.3	+	5	918	c.918C>T	c.(916-918)gcC>gcT	p.A306A	PKP1_ENST00000367324.3_Silent_p.A306A|PKP1_ENST00000263946.3_Silent_p.A306A|PKP1_ENST00000475988.1_3'UTR			Q13835	PKP1_HUMAN	plakophilin 1	306					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						TCCAGCAGGCCGCGGCAGGGG	0.647													C|||	844	0.16853	0.1316	0.1945	5008	,	,		17421	0.2302		0.1978	False		,,,				2504	0.1063				p.A306A		Atlas-SNP	.											.	PKP1	127	.	0			c.C918T						PASS	.	C	,	584,3818		41,502,1658	27.0	29.0	28.0		918,918	-11.1	0.0	1	dbSNP_89	28	1794,6806		192,1410,2698	no	coding-synonymous,coding-synonymous	PKP1	NM_000299.3,NM_001005337.2	,	233,1912,4356	TT,TC,CC		20.8605,13.2667,18.2895	,	306/748,306/727	201286771	2378,10624	2201	4300	6501	SO:0001819	synonymous_variant	5317	exon5			GCAGGCCGCGGCA	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.918C>T	1.37:g.201286771C>T		Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	191	102	0.534031	NM_001005337	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																			T|0.178;C|0.822;A|0.000	0.178	strong		0.647	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
MARCH4	57574	hgsc.bcm.edu	37	2	217148417	217148417	+	Silent	SNP	C	C	A	rs876771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:217148417C>A	ENST00000273067.4	-	2	2318	c.552G>T	c.(550-552)tcG>tcT	p.S184S		NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	184						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		TGCACTTGACCGAGCCATCAC	0.607													C|||	2183	0.435903	0.3147	0.4308	5008	,	,		20032	0.4345		0.493	False		,,,				2504	0.546				p.S184S		Atlas-SNP	.											.	MARCH4	50	.	0			c.G552T						PASS	.	C		1453,2953	469.0+/-355.3	243,967,993	61.0	54.0	56.0		552	-8.5	0.5	2	dbSNP_86	56	4144,4456	565.2+/-388.4	976,2192,1132	no	coding-synonymous	MARCH4	NM_020814.2		1219,3159,2125	AA,AC,CC		48.186,32.9778,43.034		184/411	217148417	5597,7409	2203	4300	6503	SO:0001819	synonymous_variant	57574	exon2			CTTGACCGAGCCA	AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	29269	protein-coding gene	gene with protein product		608208	"""membrane-associated ring finger (C3HC4) 4"""			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.552G>T	2.37:g.217148417C>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	84	40	0.47619	NM_020814	Q4KMN7|Q86WR8	Silent	SNP	ENST00000273067.4	37	CCDS33376.1																																																																																			C|0.576;A|0.424	0.424	strong		0.607	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814	
ASB18	401036	hgsc.bcm.edu	37	2	237103548	237103548	+	Silent	SNP	G	G	A	rs10177825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:237103548G>A	ENST00000409749.3	-	6	1367	c.1368C>T	c.(1366-1368)taC>taT	p.Y456Y	AC079135.1_ENST00000415226.1_RNA|ASB18_ENST00000330842.6_Silent_p.Y427Y|AC079135.1_ENST00000483218.1_RNA	NM_212556.2	NP_997721.2	Q6ZVZ8	ASB18_HUMAN	ankyrin repeat and SOCS box containing 18	456	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					large_intestine(1)|lung(3)|ovary(1)|prostate(1)	6		all_hematologic(139;0.00615)|Renal(207;0.00963)|Breast(86;0.0126)|Acute lymphoblastic leukemia(138;0.0815)		Epithelial(121;2.04e-26)|OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(100;2.88e-05)|Lung(119;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00644)|GBM - Glioblastoma multiforme(43;0.244)		CCAAAAGTAGGTAATTCTGCA	0.532													A|||	929	0.185503	0.4418	0.0951	5008	,	,		22038	0.002		0.1481	False		,,,				2504	0.1309				p.Y456Y		Atlas-SNP	.											.	ASB18	34	.	0			c.C1368T						PASS	.	A		1570,2464		306,958,753	54.0	64.0	60.0		1368	-0.9	0.1	2	dbSNP_119	60	1057,7313		69,919,3197	no	coding-synonymous	ASB18	NM_212556.2		375,1877,3950	AA,AG,GG		12.6284,38.9192,21.1787		456/467	237103548	2627,9777	2017	4185	6202	SO:0001819	synonymous_variant	401036	exon6			AAGTAGGTAATTC	AK123854	CCDS46548.1	2q37.2	2013-01-10	2011-01-25		ENSG00000182177	ENSG00000182177		"""Ankyrin repeat domain containing"""	19770	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 18"""			12076535	Standard	NM_212556		Approved		uc010znh.2	Q6ZVZ8	OTTHUMG00000153086	ENST00000409749.3:c.1368C>T	2.37:g.237103548G>A		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	122	52	0.42623	NM_212556	B6ZDL7	Silent	SNP	ENST00000409749.3	37	CCDS46548.1																																																																																			G|0.807;A|0.193	0.193	strong		0.532	ASB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329436.1	NM_212556	
MUC16	94025	hgsc.bcm.edu	37	19	9086318	9086318	+	Missense_Mutation	SNP	G	G	A	rs4520945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9086318G>A	ENST00000397910.4	-	1	5700	c.5497C>T	c.(5497-5499)Ctc>Ttc	p.L1833F		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	1833	Ser-rich.|Thr-rich.		L -> F (in dbSNP:rs4520945).		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						CTGAGAGTGAGAGAAATCCAT	0.478													G|||	952	0.190096	0.0711	0.2709	5008	,	,		22597	0.3036		0.172	False		,,,				2504	0.1953				p.L1833F		Atlas-SNP	.											.	MUC16	4315	.	0			c.C5497T						PASS	.	G	PHE/LEU	280,3662		5,270,1696	146.0	141.0	142.0		5497	0.7	0.0	19	dbSNP_111	142	1489,6845		126,1237,2804	yes	missense	MUC16	NM_024690.2	22	131,1507,4500	AA,AG,GG		17.8666,7.103,14.4102	probably-damaging	1833/14508	9086318	1769,10507	1971	4167	6138	SO:0001583	missense	94025	exon1			GAGTGAGAGAAAT	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.5497C>T	19.37:g.9086318G>A	ENSP00000381008:p.Leu1833Phe	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	146	76	0.520548	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	450	0.20604395604395603	37	0.07520325203252033	89	0.24585635359116023	193	0.3374125874125874	131	0.17282321899736147	g	2.939	-0.219341	0.06061	0.07103	0.178666	ENSG00000181143	ENST00000397910	T	0.03124	4.04	0.732	0.732	0.18283	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	.	.	.	D	0.62365	0.991	D	0.65323	0.934	T	0.55159	-0.8184	7	0.87932	D	0	.	.	.	.	rs4520945;rs52791576;rs60060127;rs4520945	1833	B5ME49	.	F	1833	ENSP00000381008:L1833F	ENSP00000381008:L1833F	L	-	1	0	MUC16	8947318	0.000000	0.05858	0.002000	0.10522	0.158000	0.22134	0.004000	0.13106	0.648000	0.30732	0.305000	0.20034	CTC	G|0.812;A|0.188	0.188	strong		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SP100	6672	hgsc.bcm.edu	37	2	231379967	231379967	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231379967C>T	ENST00000264052.5	+	25	2607	c.2252C>T	c.(2251-2253)aCc>aTc	p.T751I	SP100_ENST00000340126.4_Intron	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	751					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)		GAAATGAAAACCTATATCCCT	0.428																																					p.T751I		Atlas-SNP	.											.	SP100	167	.	0			c.C2252T						PASS	.						53.0	57.0	55.0					2																	231379967		2201	4297	6498	SO:0001583	missense	6672	exon25			TGAAAACCTATAT	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.2252C>T	2.37:g.231379967C>T	ENSP00000264052:p.Thr751Ile	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	78	36	0.461538	NM_003113	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	.	.	.	.	.	.	.	.	.	.	C	7.765	0.706193	0.15239	.	.	ENSG00000067066	ENST00000264052	T	0.17854	2.25	0.158	0.158	0.14942	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.18635	0.0447	M	0.66297	2.02	0.80722	D	1	B	0.34313	0.448	B	0.38156	0.266	T	0.05402	-1.0887	9	0.54805	T	0.06	.	6.0348	0.19702	0.0:0.9995:0.0:5.0E-4	.	751	P23497	SP100_HUMAN	I	751	ENSP00000264052:T751I	ENSP00000264052:T751I	T	+	2	0	SP100	231088211	0.593000	0.26840	0.022000	0.16811	0.022000	0.10575	-0.367000	0.07553	0.202000	0.20498	0.205000	0.17691	ACC	.	.	none		0.428	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
NCR1	9437	hgsc.bcm.edu	37	19	55420801	55420801	+	Silent	SNP	C	C	A	rs3765013	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55420801C>A	ENST00000291890.4	+	4	591	c.553C>A	c.(553-555)Cga>Aga	p.R185R	NCR1_ENST00000447255.1_Silent_p.R185R|NCR1_ENST00000350790.5_Silent_p.R90R|NCR1_ENST00000594765.1_Silent_p.R185R|NCR1_ENST00000357397.5_Silent_p.R78R|NCR1_ENST00000338835.5_Silent_p.R185R|NCR1_ENST00000598576.1_Silent_p.R173R	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	185	Ig-like 2.				cellular defense response (GO:0006968)|intracellular signal transduction (GO:0035556)|natural killer cell activation (GO:0030101)|regulation of natural killer cell mediated cytotoxicity (GO:0042269)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|SWI/SNF complex (GO:0016514)	receptor signaling protein activity (GO:0005057)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	18				GBM - Glioblastoma multiforme(193;0.0449)		CACAGCCCACCGAGGGACATA	0.567													.|||	2420	0.483227	0.7148	0.4236	5008	,	,		17754	0.5268		0.2286	False		,,,				2504	0.4294				p.R185R		Atlas-SNP	.											.	NCR1	60	.	0			c.C553A						PASS	.	A	,,,,	2787,1619	498.4+/-364.1	868,1051,284	84.0	82.0	82.0		553,553,268,268,553	-1.5	0.0	19	dbSNP_107	82	1935,6665	726.6+/-406.6	226,1483,2591	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCR1	NM_001145457.1,NM_001145458.1,NM_001242356.1,NM_001242357.1,NM_004829.5	,,,,	1094,2534,2875	AA,AC,CC		22.5,36.7453,36.3063	,,,,	185/304,185/288,90/210,90/193,185/305	55420801	4722,8284	2203	4300	6503	SO:0001819	synonymous_variant	9437	exon4			GCCCACCGAGGGA	AJ001383	CCDS12911.1, CCDS46181.1, CCDS46182.1, CCDS56103.1	19q13.42	2013-09-20	2002-11-13	2002-11-15	ENSG00000189430	ENSG00000189430		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6731	protein-coding gene	gene with protein product		604530	"""lymphocyte antigen 94 (mouse) homolog (activating NK-receptor; NK-p46)"""	LY94		9730896	Standard	NM_001145457		Approved	NK-p46, NKP46, CD335	uc002qib.2	O76036	OTTHUMG00000183212	ENST00000291890.4:c.553C>A	19.37:g.55420801C>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	32	31	0.96875	NM_001145458	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Silent	SNP	ENST00000291890.4	37	CCDS12911.1																																																																																			C|0.604;A|0.396	0.396	strong		0.567	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1		
IP6K3	117283	hgsc.bcm.edu	37	6	33703089	33703089	+	Silent	SNP	C	C	T	rs623813	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33703089C>T	ENST00000293756.4	-	2	491	c.165G>A	c.(163-165)ccG>ccA	p.P55P	IP6K3_ENST00000451316.1_Silent_p.P55P	NM_054111.4	NP_473452.2	Q96PC2	IP6K3_HUMAN	inositol hexakisphosphate kinase 3	55					inositol phosphate biosynthetic process (GO:0032958)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol metabolic process (GO:0046488)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol hexakisphosphate 1-kinase activity (GO:0052723)|inositol hexakisphosphate 3-kinase activity (GO:0052724)|inositol hexakisphosphate 5-kinase activity (GO:0000832)|inositol hexakisphosphate 6-kinase activity (GO:0000831)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			skin(1)	1						TCATGGCCAGCGGCAGGGATT	0.617													C|||	390	0.0778754	0.0734	0.098	5008	,	,		18105	0.0218		0.1551	False		,,,				2504	0.0481				p.P55P		Atlas-SNP	.											.	IP6K3	52	.	0			c.G165A						PASS	.	C	,	399,4007	186.0+/-213.0	20,359,1824	53.0	38.0	43.0		165,165	-10.9	0.3	6	dbSNP_83	43	1354,7246	251.1+/-277.7	124,1106,3070	no	coding-synonymous,coding-synonymous	IP6K3	NM_001142883.1,NM_054111.4	,	144,1465,4894	TT,TC,CC		15.7442,9.0558,13.4784	,	55/411,55/411	33703089	1753,11253	2203	4300	6503	SO:0001819	synonymous_variant	117283	exon3			GGCCAGCGGCAGG	AF393812	CCDS34435.1	6p21.31	2009-01-05	2009-01-05	2008-12-22	ENSG00000161896	ENSG00000161896			17269	protein-coding gene	gene with protein product		606993	"""inositol hexaphosphate kinase 3"""	IHPK3		11502751	Standard	NM_054111		Approved	INSP6K3	uc003ofb.2	Q96PC2	OTTHUMG00000014531	ENST00000293756.4:c.165G>A	6.37:g.33703089C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	94	27	0.287234	NM_001142883	Q96MQ9	Silent	SNP	ENST00000293756.4	37	CCDS34435.1																																																																																			C|0.889;T|0.111	0.111	strong		0.617	IP6K3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040203.1	NM_054111	
KIAA1755	85449	hgsc.bcm.edu	37	20	36841914	36841914	+	Missense_Mutation	SNP	G	G	A	rs3746471	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36841914G>A	ENST00000279024.4	-	14	3404	c.3133C>T	c.(3133-3135)Cgg>Tgg	p.R1045W		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1045			R -> W (in dbSNP:rs3746471). {ECO:0000269|PubMed:11214970}.							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)				AGGAGCATCCGGATCTCCTCA	0.672													G|||	1652	0.329872	0.1225	0.4121	5008	,	,		17757	0.4524		0.4235	False		,,,				2504	0.3292				p.R1045W		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C3133T						PASS	.	G	TRP/ARG	753,3653		83,587,1533	36.0	33.0	34.0		3133	3.3	0.9	20	dbSNP_107	34	3852,4748		872,2108,1320	yes	missense	KIAA1755	NM_001029864.1	101	955,2695,2853	AA,AG,GG		44.7907,17.0903,35.4067	probably-damaging	1045/1201	36841914	4605,8401	2203	4300	6503	SO:0001583	missense	85449	exon14			GCATCCGGATCTC	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.3133C>T	20.37:g.36841914G>A	ENSP00000279024:p.Arg1045Trp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	797	0.3649267399267399	74	0.15040650406504066	147	0.40607734806629836	241	0.42132867132867136	335	0.4419525065963061	G	8.990	0.977444	0.18812	0.170903	0.447907	ENSG00000149633	ENST00000279024	T	0.06933	3.24	5.29	3.3	0.37823	.	0.630757	0.14110	N	0.340794	T	0.00012	0.0000	L	0.29908	0.895	0.41204	P	0.013606000000000007	B	0.10296	0.003	B	0.04013	0.001	T	0.43669	-0.9377	9	0.39692	T	0.17	.	8.5627	0.33520	0.1796:0.0:0.8204:0.0	rs3746471;rs17787894;rs52829066;rs56875311;rs3746471	1045	Q5JYT7	K1755_HUMAN	W	1045	ENSP00000279024:R1045W	ENSP00000279024:R1045W	R	-	1	2	KIAA1755	36275328	0.976000	0.34144	0.866000	0.34008	0.208000	0.24298	1.844000	0.39269	1.468000	0.48064	0.561000	0.74099	CGG	G|0.644;A|0.356	0.356	strong		0.672	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
CCDC180	100499483	hgsc.bcm.edu	37	9	100087345	100087345	+	Silent	SNP	A	A	G	rs3747496	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:100087345A>G	ENST00000357054.1	+	28	2900	c.1965A>G	c.(1963-1965)tcA>tcG	p.S655S	CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000529487.1_Silent_p.S516S|CCDC180_ENST00000411667.2_Silent_p.S513S|CCDC180_ENST00000375202.2_Silent_p.S516S|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000395220.1_Missense_Mutation_p.H627R			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	655						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.S655S(1)									GGCAGAGTTCACACCTCTTCA	0.562													G|||	2995	0.598043	0.7587	0.6671	5008	,	,		18972	0.5843		0.3956	False		,,,				2504	0.5542				p.S516S		Atlas-SNP	.											KIAA1529,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.A1548G						PASS	.	G		3229,1177	412.2+/-336.0	1184,861,158	52.0	50.0	51.0		1548	-10.3	0.0	9	dbSNP_107	51	3985,4615	598.9+/-394.0	916,2153,1231	no	coding-synonymous	C9orf174	NM_020893.2		2100,3014,1389	GG,GA,AA		46.3372,26.7136,44.5333		516/1702	100087345	7214,5792	2203	4300	6503	SO:0001819	synonymous_variant	0	exon14			GAGTTCACACCTC	AK123391	CCDS35077.1, CCDS35077.2	9q22.33	2013-03-08	2013-03-08	2013-03-08		ENSG00000197816			29303	protein-coding gene	gene with protein product	"""Behcet's Disease Associated Gene 1"""		"""KIAA1529"", ""chromosome 9 open reading frame 174"""	KIAA1529, C9orf174		10819331	Standard	NM_020893		Approved	DKFZp434I2420, BDAG1	uc004axg.2	Q9P1Z9	OTTHUMG00000167001	ENST00000357054.1:c.1965A>G	9.37:g.100087345A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Silent	SNP	ENST00000357054.1	37		1225	0.5608974358974359	357	0.725609756097561	224	0.6187845303867403	341	0.5961538461538461	303	0.3997361477572559	G	2.270	-0.367181	0.05069	0.732864	0.463372	ENSG00000197816	ENST00000395220	T	0.24350	1.86	5.39	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.26155	-1.0111	5	0.16420	T	0.52	3.1745	6.5357	0.22352	0.308:0.0946:0.504:0.0934	rs3747496;rs58149924;rs3747496	.	.	.	R	627	ENSP00000378646:H627R	ENSP00000378646:H627R	H	+	2	0	C9orf174	99127166	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.804000	0.04535	-2.480000	0.00523	-2.236000	0.00289	CAC	A|0.437;G|0.563	0.563	strong		0.562	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	
TTC29	83894	hgsc.bcm.edu	37	4	147830297	147830297	+	Missense_Mutation	SNP	A	A	G	rs35123039	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:147830297A>G	ENST00000325106.4	-	5	507	c.281T>C	c.(280-282)cTg>cCg	p.L94P	TTC29_ENST00000513335.1_Missense_Mutation_p.L120P|TTC29_ENST00000398886.4_Missense_Mutation_p.L120P	NM_031956.2	NP_114162.2	Q8NA56	TTC29_HUMAN	tetratricopeptide repeat domain 29	94			L -> P (in dbSNP:rs35123039).							breast(2)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					AGCCTCCCTCAGGGCATCCCA	0.542													A|||	62	0.0123802	0.0008	0.0101	5008	,	,		17927	0.002		0.0447	False		,,,				2504	0.0072				p.L94P		Atlas-SNP	.											.	TTC29	63	.	0			c.T281C						PASS	.	A	PRO/LEU	24,3818		0,24,1897	68.0	69.0	69.0		281	5.0	0.5	4	dbSNP_126	69	340,7928		10,320,3804	yes	missense	TTC29	NM_031956.2	98	10,344,5701	GG,GA,AA		4.1122,0.6247,3.0058	possibly-damaging	94/476	147830297	364,11746	1921	4134	6055	SO:0001583	missense	83894	exon5			TCCCTCAGGGCAT	AF345910	CCDS47141.1, CCDS75200.1	4q31.23	2013-01-11				ENSG00000137473		"""Tetratricopeptide (TTC) repeat domain containing"""	29936	protein-coding gene	gene with protein product						12477932	Standard	NM_031956		Approved	NYD-SP14	uc003ikw.4	Q8NA56		ENST00000325106.4:c.281T>C	4.37:g.147830297A>G	ENSP00000316740:p.Leu94Pro	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_031956	A4GU95|Q9BXB6	Missense_Mutation	SNP	ENST00000325106.4	37	CCDS47141.1	45	0.020604395604395604	0	0.0	6	0.016574585635359115	2	0.0034965034965034965	37	0.048812664907651716	A	16.49	3.139035	0.56936	0.006247	0.041122	ENSG00000137473	ENST00000513335;ENST00000398886;ENST00000325106;ENST00000398883;ENST00000504425	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.03	5.03	0.67393	.	0.567089	0.17519	N	0.171329	T	0.07908	0.0198	M	0.65975	2.015	0.58432	D	0.999991	D;D;D	0.67145	0.991;0.996;0.991	P;D;P	0.63877	0.73;0.919;0.73	T	0.00286	-1.1847	10	0.33141	T	0.24	-1.4253	15.0811	0.72117	1.0:0.0:0.0:0.0	rs35123039	94;120;94	E7EQ14;G5E9Z5;Q8NA56	.;.;TTC29_HUMAN	P	120;120;94;94;94	ENSP00000423505:L120P;ENSP00000381861:L120P;ENSP00000316740:L94P;ENSP00000425778:L94P	ENSP00000316740:L94P	L	-	2	0	TTC29	148049747	1.000000	0.71417	0.488000	0.27440	0.773000	0.43773	4.171000	0.58236	2.016000	0.59253	0.533000	0.62120	CTG	A|0.972;G|0.028	0.028	strong		0.542	TTC29-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_031956	
RNF31	55072	hgsc.bcm.edu	37	14	24620710	24620710	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24620710C>G	ENST00000324103.6	+	10	2074	c.1754C>G	c.(1753-1755)tCt>tGt	p.S585C	RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.S60C|RNF31_ENST00000559275.1_Missense_Mutation_p.S434C|RNF31_ENST00000382687.3_Missense_Mutation_p.S434C	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	585	Interaction with RBCK1.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GAGCTCCAGTCTCTAGGCTTT	0.587																																					p.S585C		Atlas-SNP	.											RNF31,NS,carcinoma,0,1	RNF31	95	1	0			c.C1754G						PASS	.						53.0	55.0	55.0					14																	24620710		2021	4210	6231	SO:0001583	missense	55072	exon10			TCCAGTCTCTAGG	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"""RING-type (C3HC4) zinc fingers"""	16031	protein-coding gene	gene with protein product	"""HOIL-1-interacting protein"""	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1754C>G	14.37:g.24620710C>G	ENSP00000315112:p.Ser585Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	81	37	0.45679	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	9.929	1.214179	0.22289	.	.	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.47869	0.83;0.83	5.42	3.47	0.39725	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);UBA-like (1);	0.583409	0.18022	N	0.154194	T	0.37461	0.1004	N	0.19112	0.55	0.09310	N	1	D;P;D	0.54964	0.969;0.947;0.969	P;B;P	0.49683	0.619;0.36;0.563	T	0.14364	-1.0475	10	0.72032	D	0.01	-7.8769	6.4608	0.21956	0.0:0.6637:0.1566:0.1797	.	344;585;434	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	C	585;434	ENSP00000315112:S585C;ENSP00000372134:S434C	ENSP00000315112:S585C	S	+	2	0	RNF31	23690550	0.059000	0.20769	0.991000	0.47740	0.196000	0.23810	1.449000	0.35123	1.523000	0.49018	0.655000	0.94253	TCT	.	.	none		0.587	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999	
PIGK	10026	hgsc.bcm.edu	37	1	77685042	77685042	+	Missense_Mutation	SNP	T	T	C	rs12723684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:77685042T>C	ENST00000370812.3	-	1	69	c.46A>G	c.(46-48)Act>Gct	p.T16A	PIGK_ENST00000445065.1_Missense_Mutation_p.T16A|PIGK_ENST00000370813.5_Missense_Mutation_p.T16A|PIGK_ENST00000478391.1_5'UTR|PIGK_ENST00000359130.1_Missense_Mutation_p.T16A	NM_005482.2	NP_005473.1	Q92643	GPI8_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class K	16			T -> A (in dbSNP:rs12723684).		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 folding (GO:0006457)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	cysteine-type endopeptidase activity (GO:0004197)|GPI-anchor transamidase activity (GO:0003923)|protein disulfide isomerase activity (GO:0003756)			endometrium(5)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	19						AGCAACACAGTTGCCAAGACA	0.617													C|||	960	0.191693	0.4644	0.2305	5008	,	,		16366	0.0387		0.0706	False		,,,				2504	0.0777				p.T16A		Atlas-SNP	.											.	PIGK	46	.	0			c.A46G						PASS	.	C	ALA/THR	1673,2733	639.8+/-397.2	324,1025,854	34.0	35.0	34.0		46	4.6	0.0	1	dbSNP_121	34	664,7934	771.4+/-407.7	28,608,3663	yes	missense	PIGK	NM_005482.2	58	352,1633,4517	CC,CT,TT		7.7227,37.9709,17.9714	benign	16/396	77685042	2337,10667	2203	4299	6502	SO:0001583	missense	10026	exon1			ACACAGTTGCCAA	AF022913	CCDS674.1	1p31.1	2013-02-26	2006-06-28		ENSG00000142892	ENSG00000142892		"""Phosphatidylinositol glycan anchor biosynthesis"""	8965	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	605087	"""phosphatidylinositol glycan, class K"""			9356492	Standard	NM_005482		Approved	hGPI8, GPI8	uc001dhk.3	Q92643	OTTHUMG00000009686	ENST00000370812.3:c.46A>G	1.37:g.77685042T>C	ENSP00000359848:p.Thr16Ala	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	127	53	0.417323	NM_005482	B2R7K3|B4E2M3|O14822|Q5TG77	Missense_Mutation	SNP	ENST00000370812.3	37	CCDS674.1	364	0.16666666666666666	221	0.4491869918699187	70	0.19337016574585636	25	0.043706293706293704	48	0.0633245382585752	C	4.075	0.011714	0.07912	0.379709	0.077227	ENSG00000142892	ENST00000370812;ENST00000445065;ENST00000370813;ENST00000359130	T;T;T;T	0.47528	1.0;0.84;0.96;1.0	4.58	4.58	0.56647	.	0.669721	0.14612	N	0.308976	T	0.07728	0.0194	N	0.02539	-0.55	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.25257	-1.0137	9	0.12430	T	0.62	-16.2216	9.0156	0.36168	0.0:0.9013:0.0:0.0987	rs12723684;rs59888624;rs12723684	16;16;16;16	B4E2M3;B1AK81;A6NEM5;Q92643	.;.;.;GPI8_HUMAN	A	16	ENSP00000359848:T16A;ENSP00000388854:T16A;ENSP00000359849:T16A;ENSP00000352041:T16A	ENSP00000352041:T16A	T	-	1	0	PIGK	77457630	0.001000	0.12720	0.003000	0.11579	0.001000	0.01503	1.006000	0.29847	1.549000	0.49425	-0.119000	0.15052	ACT	T|0.821;C|0.179	0.179	strong		0.617	PIGK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026687.1	NM_005482	
PDE11A	50940	hgsc.bcm.edu	37	2	178682603	178682603	+	Silent	SNP	T	T	C	rs6720891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:178682603T>C	ENST00000286063.6	-	8	1943	c.1626A>G	c.(1624-1626)gcA>gcG	p.A542A	PDE11A_ENST00000389683.3_Silent_p.A98A|PDE11A_ENST00000409504.1_Silent_p.A184A|PDE11A_ENST00000497003.1_5'UTR|PDE11A_ENST00000449286.2_Silent_p.A184A|PDE11A_ENST00000358450.4_Silent_p.A292A	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	542	GAF 2.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	GTCGTTGATCTGCATCATCAA	0.383									Primary Pigmented Nodular Adrenocortical Disease, Familial				t|||	2094	0.418131	0.7315	0.2622	5008	,	,		16517	0.3056		0.3241	False		,,,				2504	0.318				p.A542A		Atlas-SNP	.											.	PDE11A	283	.	0			c.A1626G						PASS	.	C	,,,	2726,1680	648.8+/-398.8	856,1014,333	84.0	89.0	87.0		294,876,552,1626	-11.6	0.7	2	dbSNP_116	87	2778,5822	436.2+/-358.2	450,1878,1972	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	,,,	1306,2892,2305	CC,CT,TT		32.3023,38.1298,42.3189	,,,	98/490,292/684,184/576,542/934	178682603	5504,7502	2203	4300	6503	SO:0001819	synonymous_variant	50940	exon8	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	TTGATCTGCATCA	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.1626A>G	2.37:g.178682603T>C		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	64	26	0.40625	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1	900	0.41208791208791207	350	0.7113821138211383	110	0.30386740331491713	206	0.36013986013986016	234	0.3087071240105541	t	5.380	0.255377	0.10185	0.618702	0.323023	ENSG00000128655	ENST00000433879	.	.	.	5.82	-11.6	0.00059	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999999996	.	.	.	.	.	.	T	0.41645	-0.9497	3	.	.	.	.	0.7539	0.00995	0.1939:0.1937:0.2082:0.4043	rs6720891;rs58395732;rs6720891	.	.	.	R	181	.	.	Q	-	2	0	PDE11A	178390849	0.521000	0.26258	0.742000	0.31022	0.633000	0.38033	-0.365000	0.07573	-1.740000	0.01345	-4.221000	0.00009	CAG	T|0.578;C|0.422	0.422	strong		0.383	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
OTUD7B	56957	hgsc.bcm.edu	37	1	149916118	149916118	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:149916118G>C	ENST00000369135.4	-	12	2464	c.2170C>G	c.(2170-2172)Cta>Gta	p.L724V		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	724					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			TATGGTGGTAGGCCCCCGACA	0.652																																					p.L724V		Atlas-SNP	.											.	OTUD7B	76	.	0			c.C2170G						PASS	.						28.0	32.0	31.0					1																	149916118		1961	4133	6094	SO:0001583	missense	56957	exon12			GTGGTAGGCCCCC	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"""OTU domain containing"""	16683	protein-coding gene	gene with protein product		611748	"""zinc finger, A20 domain containing 1"", ""OTU domain containing 7B"""	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.2170C>G	1.37:g.149916118G>C	ENSP00000358131:p.Leu724Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	65	34	0.523077	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	37	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710511	0.30322	.	.	ENSG00000163113	ENST00000369135;ENST00000543330	T	0.35789	1.29	4.37	3.44	0.39384	.	0.146689	0.45606	D	0.000347	T	0.13756	0.0333	L	0.50333	1.59	0.41982	D	0.990803	P	0.44241	0.829	B	0.33254	0.16	T	0.03157	-1.1066	9	.	.	.	-23.4143	10.4837	0.44708	0.098:0.0:0.902:0.0	.	724	Q6GQQ9	OTU7B_HUMAN	V	724	ENSP00000358131:L724V	.	L	-	1	2	OTUD7B	148182742	0.998000	0.40836	0.903000	0.35520	0.767000	0.43475	3.982000	0.56909	1.027000	0.39758	0.455000	0.32223	CTA	.	.	none		0.652	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
OR2T34	127068	hgsc.bcm.edu	37	1	248737454	248737454	+	Missense_Mutation	SNP	A	A	G	rs79750523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248737454A>G	ENST00000328782.2	-	1	626	c.605T>C	c.(604-606)aTg>aCg	p.M202T		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	202						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GTACGTGAGCATCTTATAGAG	0.502																																					p.M202T		Atlas-SNP	.											.	OR2T34	72	.	0			c.T605C						PASS	.	G	THR/MET	336,3872		62,212,1830	189.0	206.0	200.0		605	-4.7	0.0	1	dbSNP_131	200	611,7989		5,601,3694	no	missense	OR2T34	NM_001001821.1	81	67,813,5524	GG,GA,AA		7.1047,7.9848,7.3938	benign	202/319	248737454	947,11861	2104	4300	6404	SO:0001583	missense	127068	exon1			GTGAGCATCTTAT	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.605T>C	1.37:g.248737454A>G	ENSP00000330904:p.Met202Thr	Somatic	350	0	0		WXS	Illumina HiSeq	Phase_I	460	132	0.286957	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	404	0.184981684981685	100	0.2032520325203252	48	0.13259668508287292	183	0.31993006993006995	73	0.09630606860158311	.	0	-2.867633	0.00063	0.079848	0.071047	ENSG00000183310	ENST00000328782	T	0.00054	8.8	2.37	-4.74	0.03249	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.10945	0.07	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31503	-0.9941	9	0.02654	T	1	.	5.5169	0.16912	0.3369:0.0:0.4336:0.2295	.	202	Q8NGX1	O2T34_HUMAN	T	202	ENSP00000330904:M202T	ENSP00000330904:M202T	M	-	2	0	OR2T34	246804077	0.000000	0.05858	0.001000	0.08648	0.069000	0.16628	0.183000	0.16919	-2.576000	0.00465	-1.839000	0.00587	ATG	A|0.848;G|0.152	0.152	strong		0.502	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
LIPH	200879	hgsc.bcm.edu	37	3	185236964	185236964	+	Silent	SNP	G	G	A	rs144288709	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:185236964G>A	ENST00000296252.4	-	6	993	c.852C>T	c.(850-852)tgC>tgT	p.C284C	LIPH_ENST00000424591.2_Silent_p.C250C	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	284					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)			GTGACGTGCCGCAGCTGACAC	0.478													G|||	67	0.0133786	0.0015	0.0303	5008	,	,		16887	0.0		0.0358	False		,,,				2504	0.0082				p.C284C		Atlas-SNP	.											.	LIPH	56	.	0			c.C852T						PASS	.	G		35,4371	38.4+/-70.7	1,33,2169	138.0	137.0	137.0		852	-6.1	0.0	3	dbSNP_134	137	379,8221	123.9+/-182.7	8,363,3929	no	coding-synonymous	LIPH	NM_139248.2		9,396,6098	AA,AG,GG		4.407,0.7944,3.1831		284/452	185236964	414,12592	2203	4300	6503	SO:0001819	synonymous_variant	200879	exon6			CGTGCCGCAGCTG	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.852C>T	3.37:g.185236964G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	88	38	0.431818	NM_139248	A2IBA7|Q8TEC7	Silent	SNP	ENST00000296252.4	37	CCDS3272.1	38	0.0173992673992674	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	24	0.0316622691292876	G	3.914	-0.019486	0.07634	0.007944	0.04407	ENSG00000163898	ENST00000452897	.	.	.	5.01	-6.08	0.02151	.	.	.	.	.	T	0.30166	0.0756	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60806	-0.7190	4	.	.	.	-21.7501	15.004	0.71498	0.5608:0.0:0.4392:0.0	.	.	.	.	V	75	.	.	A	-	2	0	LIPH	186719658	0.000000	0.05858	0.004000	0.12327	0.020000	0.10135	-1.077000	0.03416	-1.169000	0.02772	-0.703000	0.03666	GCG	G|0.971;A|0.029	0.029	strong		0.478	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1		
ESYT2	57488	hgsc.bcm.edu	37	7	158528254	158528254	+	Silent	SNP	G	G	A	rs34974906	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158528254G>A	ENST00000251527.5	-	20	2591	c.2526C>T	c.(2524-2526)ctC>ctT	p.L842L	ESYT2_ENST00000435514.2_Silent_p.L277L	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	870	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)	p.L842L(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						CGGCAACGTCGAGCGTTCTCC	0.458													G|||	446	0.0890575	0.1233	0.0591	5008	,	,		19168	0.0427		0.1252	False		,,,				2504	0.0746				p.L842L		Atlas-SNP	.											ESYT2,NS,malignant_melanoma,0,3	ESYT2	70	3	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C2526T						PASS	.			514,3892	236.1+/-248.4	24,466,1713	153.0	158.0	156.0		2526	1.8	0.2	7	dbSNP_126	156	1087,7513	226.8+/-262.4	62,963,3275	no	coding-synonymous	ESYT2	NM_020728.2		86,1429,4988	AA,AG,GG		12.6395,11.6659,12.3097		842/894	158528254	1601,11405	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon20			AACGTCGAGCGTT	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2526C>T	7.37:g.158528254G>A		Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	73	32	0.438356	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			G|0.884;A|0.116	0.116	strong		0.458	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
MYT1L	23040	hgsc.bcm.edu	37	2	1926617	1926617	+	Silent	SNP	G	G	A	rs2241686	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:1926617G>A	ENST00000399161.2	-	10	1671	c.924C>T	c.(922-924)aaC>aaT	p.N308N	MYT1L_ENST00000428368.2_Silent_p.N308N	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	308					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)		CCATGAGTCCGTTGTTCATGG	0.478													A|||	163	0.0325479	0.0008	0.0072	5008	,	,		22385	0.0308		0.0209	False		,,,				2504	0.1074				p.N308N		Atlas-SNP	.											.	MYT1L	241	.	0			c.C924T						PASS	.	A		13,4275		0,13,2131	150.0	155.0	153.0		924	-4.1	0.6	2	dbSNP_98	153	139,8335		3,133,4101	no	coding-synonymous	MYT1L	NM_015025.2		3,146,6232	AA,AG,GG		1.6403,0.3032,1.191		308/1185	1926617	152,12610	2144	4237	6381	SO:0001819	synonymous_variant	23040	exon10			GAGTCCGTTGTTC	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.924C>T	2.37:g.1926617G>A		Somatic	256	0	0		WXS	Illumina HiSeq	Phase_I	236	113	0.478814	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				G|0.979;A|0.021	0.021	strong		0.478	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
AKAP11	11215	hgsc.bcm.edu	37	13	42876103	42876103	+	Missense_Mutation	SNP	C	C	T	rs61756566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:42876103C>T	ENST00000025301.2	+	8	3396	c.3221C>T	c.(3220-3222)tCt>tTt	p.S1074F		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1074					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)	p.S1074F(1)		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)		ACTTTCTCATCTACAGCACTT	0.398													C|||	113	0.0225639	0.0136	0.0	5008	,	,		22265	0.0813		0.004	False		,,,				2504	0.0092				p.S1074F		Atlas-SNP	.											AKAP11,NS,carcinoma,0,1	AKAP11	146	1	1	Substitution - Missense(1)	stomach(1)	c.C3221T						PASS	.	C	PHE/SER	51,4355	51.6+/-87.1	1,49,2153	159.0	151.0	153.0		3221	5.8	0.4	13	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	AKAP11	NM_016248.3	155	1,52,6450	TT,TC,CC		0.0349,1.1575,0.4152	possibly-damaging	1074/1902	42876103	54,12952	2203	4300	6503	SO:0001583	missense	11215	exon8			TCTCATCTACAGC	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.3221C>T	13.37:g.42876103C>T	ENSP00000025301:p.Ser1074Phe	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	78	40	0.512821	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	54	0.024725274725274724	7	0.014227642276422764	0	0.0	43	0.07517482517482517	4	0.005277044854881266	C	13.10	2.136954	0.37728	0.011575	3.49E-4	ENSG00000023516	ENST00000025301	T	0.18502	2.21	5.8	5.8	0.92144	.	0.527839	0.19579	N	0.110907	T	0.02727	0.0082	M	0.67953	2.075	0.43054	D	0.994668	D	0.64830	0.994	P	0.60473	0.875	T	0.00020	-1.2350	10	0.62326	D	0.03	.	20.0706	0.97721	0.0:1.0:0.0:0.0	rs61756566	1074	Q9UKA4	AKA11_HUMAN	F	1074	ENSP00000025301:S1074F	ENSP00000025301:S1074F	S	+	2	0	AKAP11	41774103	0.269000	0.24143	0.389000	0.26208	0.087000	0.18053	3.666000	0.54540	2.744000	0.94065	0.655000	0.94253	TCT	C|0.988;T|0.012	0.012	strong		0.398	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
MRC1	4360	hgsc.bcm.edu	37	10	17875762	17875762	+	Silent	SNP	G	G	A	rs374113136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:17875762G>A	ENST00000331429.2	+	4	829	c.726G>A	c.(724-726)caG>caA	p.Q242Q	MRC1L1_ENST00000457317.1_Silent_p.Q242Q														p.Q242Q(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CGTGGCACCAGGCGAGGAAAA	0.468													g|||	178	0.0355431	0.0431	0.0346	5008	,	,		10278	0.0238		0.0497	False		,,,				2504	0.0235				p.Q242Q		Atlas-SNP	.											MRC1L1,rectum,carcinoma,0,2	MRC1	13	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G726A						scavenged	.						100.0	91.0	94.0					10																	17875762		1955	3878	5833	SO:0001819	synonymous_variant	4360	exon4			GCACCAGGCGAGG																												ENST00000331429.2:c.726G>A	10.37:g.17875762G>A		Somatic	185	1	0.00540541		WXS	Illumina HiSeq	Phase_I	80	4	0.05	NM_002438		Silent	SNP	ENST00000331429.2	37																																																																																				G|0.750;A|0.250	0.250	weak		0.468	MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1		
FGFRL1	53834	hgsc.bcm.edu	37	4	1006333	1006333	+	Silent	SNP	G	G	A	rs4647942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1006333G>A	ENST00000398484.2	+	3	640	c.60G>A	c.(58-60)ccG>ccA	p.P20P	FGFRL1_ENST00000264748.6_Silent_p.P20P|FGFRL1_ENST00000504138.1_Silent_p.P20P|FGFRL1_ENST00000510644.1_Silent_p.P20P			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	20					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)			GGGCCTTcccgccggccgccg	0.771													G|||	2551	0.509385	0.7375	0.4135	5008	,	,		8101	0.4583		0.492	False		,,,				2504	0.3395				p.P20P		Atlas-SNP	.											.	FGFRL1	77	.	0			c.G60A						PASS	.	G	,,	3010,1068		1128,754,157	7.0	9.0	8.0		60,60,60	1.5	0.9	4	dbSNP_111	8	4170,3724		1222,1726,999	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFRL1	NM_001004356.2,NM_001004358.1,NM_021923.3	,,	2350,2480,1156	AA,AG,GG		47.1751,26.1893,40.0267	,,	20/505,20/505,20/505	1006333	7180,4792	2039	3947	5986	SO:0001819	synonymous_variant	53834	exon2			CTTCCCGCCGGCC		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.60G>A	4.37:g.1006333G>A		Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Silent	SNP	ENST00000398484.2	37	CCDS3344.1																																																																																			G|0.475;A|0.525	0.525	strong		0.771	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	
CLIP2	7461	hgsc.bcm.edu	37	7	73731906	73731906	+	Silent	SNP	C	C	T	rs148561130	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:73731906C>T	ENST00000395060.1	+	1	30	c.30C>T	c.(28-30)ccC>ccT	p.P10P	CLIP2_ENST00000361545.5_Silent_p.P10P|CLIP2_ENST00000223398.6_Silent_p.P10P			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	10						cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						TGAAGCCCCCCGGCCGTGGGG	0.667													C|||	123	0.0245607	0.0	0.0432	5008	,	,		18799	0.0427		0.0298	False		,,,				2504	0.0204				p.P10P		Atlas-SNP	.											.	CLIP2	134	.	0			c.C30T						PASS	.	C	,	43,4361		0,43,2159	43.0	49.0	47.0		30,30	0.5	1.0	7	dbSNP_134	47	357,8239		6,345,3947	no	coding-synonymous,coding-synonymous	CLIP2	NM_003388.4,NM_032421.2	,	6,388,6106	TT,TC,CC		4.1531,0.9764,3.0769	,	10/1047,10/1012	73731906	400,12600	2202	4298	6500	SO:0001819	synonymous_variant	7461	exon2			GCCCCCCGGCCGT	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"""cytoplasmic linker 2"", ""Williams-Beuren syndrome chromosome region 3"""	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.30C>T	7.37:g.73731906C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	79	34	0.43038	NM_032421	O14527|O43611	Silent	SNP	ENST00000395060.1	37	CCDS5569.1																																																																																			C|0.968;T|0.032	0.032	strong		0.667	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388	
OBSCN	84033	hgsc.bcm.edu	37	1	228471379	228471379	+	Silent	SNP	G	G	C	rs56168609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228471379G>C	ENST00000422127.1	+	33	8957	c.8913G>C	c.(8911-8913)cgG>cgC	p.R2971R	OBSCN_ENST00000359599.6_Silent_p.R1818R|OBSCN_ENST00000366707.4_Silent_p.R90R|OBSCN_ENST00000366709.4_Silent_p.R90R|OBSCN_ENST00000284548.11_Silent_p.R2971R|OBSCN_ENST00000570156.2_Silent_p.R3400R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2971	Ig-like 29.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGACCCTGCGGCTCACCATCA	0.677													g|||	1153	0.230232	0.1989	0.3242	5008	,	,		17988	0.1528		0.3499	False		,,,				2504	0.1626				p.R3400R		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,+1,4	OBSCN	2142	4	0			c.G10200C						PASS	.		,	1049,3203		133,783,1210	36.0	44.0	41.0		8913,8913	0.3	0.1	1	dbSNP_129	41	3121,5357		597,1927,1715	yes	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	730,2710,2925	CC,CG,GG		36.8129,24.6707,32.7573	,	2971/7969,2971/6621	228471379	4170,8560	2126	4239	6365	SO:0001819	synonymous_variant	84033	exon38			CCTGCGGCTCACC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.8913G>C	1.37:g.228471379G>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.721;C|0.279	0.279	strong		0.677	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MUC4	4585	hgsc.bcm.edu	37	3	195509212	195509212	+	Missense_Mutation	SNP	G	G	A	rs200749420		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195509212G>A	ENST00000463781.3	-	2	9698	c.9239C>T	c.(9238-9240)tCa>tTa	p.S3080L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3080L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTGGATGCTGAGGAAGTGTC	0.597																																					p.S3080L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C9239T						PASS	.						12.0	10.0	10.0					3																	195509212		659	1537	2196	SO:0001583	missense	4585	exon2			GATGCTGAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9239C>T	3.37:g.195509212G>A	ENSP00000417498:p.Ser3080Leu	Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	137	38	0.277372	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	7.190	0.591379	0.13812	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.37;1.43	.	.	.	.	.	.	.	.	T	0.19087	0.0458	N	0.19112	0.55	0.80722	P	0.0	B	0.13145	0.007	B	0.06405	0.002	T	0.24799	-1.0150	6	.	.	.	.	5.4195	0.16392	0.0:0.0:1.0:0.0	.	2952	E7ESK3	.	L	3080	ENSP00000417498:S3080L;ENSP00000420243:S3080L	.	S	-	2	0	MUC4	196993991	0.013000	0.17824	0.004000	0.12327	0.000000	0.00434	1.082000	0.30803	0.497000	0.27926	0.000000	0.15137	TCA	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FERMT1	55612	hgsc.bcm.edu	37	20	6069723	6069723	+	Silent	SNP	G	G	A	rs35413391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:6069723G>A	ENST00000217289.4	-	10	1941	c.1153C>T	c.(1153-1155)Cta>Tta	p.L385L	FERMT1_ENST00000536936.1_Silent_p.L128L|FERMT1_ENST00000478194.1_5'UTR	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	385	FERM.|PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						GCTTTTGGTAGTAACTTCTTG	0.358													g|||	159	0.0317492	0.0038	0.0749	5008	,	,		18431	0.0		0.0825	False		,,,				2504	0.0194				p.L385L		Atlas-SNP	.											.	FERMT1	106	.	0			c.C1153T						PASS	.	G		65,4341	61.7+/-98.7	0,65,2138	113.0	121.0	118.0		1153	-4.5	0.1	20	dbSNP_126	118	658,7942	165.7+/-217.8	20,618,3662	yes	coding-synonymous	FERMT1	NM_017671.4		20,683,5800	AA,AG,GG		7.6512,1.4753,5.559		385/678	6069723	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon10			TTGGTAGTAACTT	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.1153C>T	20.37:g.6069723G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	60	20	0.333333	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			G|0.949;A|0.051	0.051	strong		0.358	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671	
MAST2	23139	hgsc.bcm.edu	37	1	46500613	46500613	+	Silent	SNP	T	T	C	rs17855317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:46500613T>C	ENST00000361297.2	+	29	4555	c.4272T>C	c.(4270-4272)acT>acC	p.T1424T	MAST2_ENST00000372009.2_Silent_p.T1234T	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)					AGCTAGCCACTTCTCGCAAGC	0.592													t|||	588	0.117412	0.0469	0.1311	5008	,	,		17772	0.0149		0.2823	False		,,,				2504	0.1391				p.T1424T		Atlas-SNP	.											MAST2_ENST00000361297,NS,carcinoma,0,1	MAST2	136	1	0			c.T4272C						scavenged	.			333,3749		18,297,1726	52.0	57.0	56.0		4272	0.8	0.2	1	dbSNP_123	56	2182,6200		293,1596,2302	no	coding-synonymous	MAST2	NM_015112.2		311,1893,4028	CC,CT,TT		26.032,8.1578,20.1781		1424/1799	46500613	2515,9949	2041	4191	6232	SO:0001819	synonymous_variant	23139	exon29			AGCCACTTCTCGC	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.4272T>C	1.37:g.46500613T>C		Somatic	139	1	0.00719424		WXS	Illumina HiSeq	Phase_I	166	82	0.493976	NM_015112		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			A|0.000;C|0.179;T|0.821	0.179	strong		0.592	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
ANKRD30B	374860	hgsc.bcm.edu	37	18	14779969	14779969	+	Missense_Mutation	SNP	C	C	G	rs9675365	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:14779969C>G	ENST00000358984.4	+	11	1611	c.1431C>G	c.(1429-1431)ttC>ttG	p.F477L	ANKRD30B_ENST00000447268.2_Missense_Mutation_p.F477L|ANKRD30B_ENST00000579292.1_Intron	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	477			F -> L (in dbSNP:rs9675365).					p.F477L(2)		breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ATCAGATGTTCCCATCAGAAT	0.279													C|||	2332	0.465655	0.4773	0.4265	5008	,	,		15526	0.4187		0.5159	False		,,,				2504	0.4744				p.F477L		Atlas-SNP	.											ANKRD30B_ENST00000358984,NS,carcinoma,0,2	ANKRD30B	237	2	2	Substitution - Missense(2)	prostate(2)	c.C1431G						PASS	.						167.0	153.0	157.0					18																	14779969		692	1591	2283	SO:0001583	missense	374860	exon11			GATGTTCCCATCA	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.1431C>G	18.37:g.14779969C>G	ENSP00000351875:p.Phe477Leu	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	107	100	0.934579	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	37	CCDS54182.1	1018	0.4661172161172161	231	0.4695121951219512	157	0.43370165745856354	240	0.4195804195804196	390	0.5145118733509235	N	12.12	1.843849	0.32606	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	T;T	0.39406	1.08;1.4	1.69	-2.4	0.06583	.	.	.	.	.	T	0.00012	0.0000	L	0.47716	1.5	0.80722	P	0.0	B	0.30584	0.286	B	0.22753	0.041	T	0.48547	-0.9026	8	0.07990	T	0.79	.	0.2761	0.00238	0.3065:0.2974:0.1877:0.2084	rs9675365;rs52827349;rs59076177;rs9675365	477	F8WAG3	.	L	477	ENSP00000351875:F477L;ENSP00000399031:F477L	ENSP00000351875:F477L	F	+	3	2	ANKRD30B	14769969	0.988000	0.35896	0.000000	0.03702	0.155000	0.21991	0.095000	0.15127	-0.611000	0.05709	0.297000	0.19635	TTC	C|0.546;G|0.454	0.454	strong		0.279	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029	
CPNE6	9362	hgsc.bcm.edu	37	14	24543808	24543808	+	Silent	SNP	G	G	C	rs2070343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24543808G>C	ENST00000397016.2	+	7	878	c.567G>C	c.(565-567)ctG>ctC	p.L189L	CPNE6_ENST00000537691.1_Silent_p.L244L|CPNE6_ENST00000216775.2_Silent_p.L189L	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	189	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		GTGATCAGCTGGTCTGGAGAA	0.517													G|||	1337	0.266973	0.0862	0.1671	5008	,	,		21595	0.5714		0.175	False		,,,				2504	0.363				p.L189L		Atlas-SNP	.											.	CPNE6	40	.	0			c.G567C						PASS	.	G		386,4020	195.0+/-219.7	18,350,1835	97.0	98.0	98.0		567	2.2	1.0	14	dbSNP_96	98	1588,7012	297.3+/-303.3	138,1312,2850	no	coding-synonymous	CPNE6	NM_006032.2		156,1662,4685	CC,CG,GG		18.4651,8.7608,15.1776		189/558	24543808	1974,11032	2203	4300	6503	SO:0001819	synonymous_variant	9362	exon6			TCAGCTGGTCTGG	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.567G>C	14.37:g.24543808G>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			G|0.789;C|0.211	0.211	strong		0.517	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
UGGT1	56886	hgsc.bcm.edu	37	2	128939817	128939817	+	Silent	SNP	G	G	A	rs1699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:128939817G>A	ENST00000259253.6	+	37	4244	c.4197G>A	c.(4195-4197)aaG>aaA	p.K1399K	UGGT1_ENST00000375990.3_Silent_p.K1375K	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	1399	Glucosyltransferase. {ECO:0000250}.				'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						GGTTCTGGAAGTCAGGGTACT	0.438													G|||	2143	0.427915	0.4198	0.3775	5008	,	,		18387	0.3224		0.4105	False		,,,				2504	0.6012				p.K1399K		Atlas-SNP	.											.	UGGT1	126	.	0			c.G4197A						PASS	.	G		1781,2625	525.2+/-371.5	373,1035,795	100.0	102.0	102.0		4197	4.5	1.0	2	dbSNP_36	102	3664,4936	526.4+/-380.9	777,2110,1413	no	coding-synonymous	UGGT1	NM_020120.3		1150,3145,2208	AA,AG,GG		42.6047,40.4222,41.8653		1399/1556	128939817	5445,7561	2203	4300	6503	SO:0001819	synonymous_variant	56886	exon37			CTGGAAGTCAGGG	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.4197G>A	2.37:g.128939817G>A		Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	151	151	1	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			G|0.589;A|0.411	0.411	strong		0.438	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
Unknown	0	hgsc.bcm.edu	37	17	17326605	17326605	+	IGR	SNP	A	A	G	rs370938128|rs7225831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:17326605A>G								NT5M (75630 upstream) : Y_RNA (37152 downstream)																							ATGATGGGGCAAATGCCAGAG	0.478													G|||	2121	0.423522	0.798	0.268	5008	,	,		23339	0.1915		0.3221	False		,,,				2504	0.3712				p.A140A		Atlas-SNP	.											.	.	.	.	0			c.A420G						PASS	.																																			SO:0001628	intergenic_variant	140776	exon3			TGGGGCAAATGCC																													17.37:g.17326605A>G		Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	NM_001243312		Silent	SNP		37																																																																																				A|0.600;G|0.400	0.400	strong	0	0.478								
MMRN1	22915	hgsc.bcm.edu	37	4	90816294	90816294	+	Missense_Mutation	SNP	A	A	G	rs1442138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:90816294A>G	ENST00000394980.1	+	2	491	c.172A>G	c.(172-174)Act>Gct	p.T58A	MMRN1_ENST00000264790.2_Missense_Mutation_p.T58A|MMRN1_ENST00000394981.1_Missense_Mutation_p.T58A			Q13201	MMRN1_HUMAN	multimerin 1	58			T -> A (in dbSNP:rs1442138).		blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		ACTGCCAACCACTCGGGTCAT	0.458													A|||	366	0.0730831	0.174	0.0461	5008	,	,		19127	0.0		0.0596	False		,,,				2504	0.045				p.T58A		Atlas-SNP	.											.	MMRN1	174	.	0			c.A172G						PASS	.	A	ALA/THR	638,3768	275.2+/-272.4	46,546,1611	64.0	69.0	67.0		172	-8.0	0.0	4	dbSNP_88	67	487,8113	141.2+/-197.6	21,445,3834	yes	missense	MMRN1	NM_007351.2	58	67,991,5445	GG,GA,AA		5.6628,14.4803,8.6499	benign	58/1229	90816294	1125,11881	2203	4300	6503	SO:0001583	missense	22915	exon1			CCAACCACTCGGG	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.172A>G	4.37:g.90816294A>G	ENSP00000378431:p.Thr58Ala	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	41	19	0.463415	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	150	0.06868131868131869	86	0.17479674796747968	18	0.049723756906077346	0	0.0	46	0.06068601583113457	A	0.191	-1.053694	0.01965	0.144803	0.056628	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000394981	T;T;T	0.80393	0.0;0.0;-1.37	4.01	-8.03	0.01114	.	1.363460	0.04858	N	0.443517	T	0.00241	0.0007	N	0.14661	0.345	0.80722	P	0.0	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.003	T	0.04178	-1.0971	9	0.19147	T	0.46	.	2.6911	0.05121	0.1636:0.4534:0.1598:0.2232	rs1442138;rs58378963;rs1442138	58;58	Q13201-2;Q13201	.;MMRN1_HUMAN	A	58	ENSP00000378431:T58A;ENSP00000264790:T58A;ENSP00000378432:T58A	ENSP00000264790:T58A	T	+	1	0	MMRN1	91035317	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.632000	0.05489	-2.072000	0.00879	0.460000	0.39030	ACT	A|0.914;G|0.086	0.086	strong		0.458	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
TCEB2	6923	hgsc.bcm.edu	37	16	2821525	2821525	+	3'UTR	SNP	G	G	A	rs4036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2821525G>A	ENST00000409906.4	-	0	880				TCEB2_ENST00000409477.1_3'UTR|TCEB2_ENST00000262306.7_Missense_Mutation_p.T145M|AC092117.2_ENST00000581119.1_RNA	NM_007108.3	NP_009039.1	Q15370	ELOB_HUMAN	transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)						cellular response to hypoxia (GO:0071456)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein complex assembly (GO:0006461)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cul2-RING ubiquitin ligase complex (GO:0031462)|Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|elongin complex (GO:0070449)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)	ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|prostate(1)	3						GGGTTCCCTCGTTGAACATGC	0.577													A|||	943	0.188299	0.466	0.1138	5008	,	,		16029	0.0754		0.1044	False		,,,				2504	0.0685				p.T145M	GBM(141;5215 5962)	Atlas-SNP	.											.	TCEB2	6	.	0			c.C434T						PASS	.	A	,MET/THR	1714,2682	650.5+/-399.1	334,1046,818	117.0	108.0	111.0		,434	0.1	0.0	16	dbSNP_36	111	788,7812	783.7+/-407.6	37,714,3549	yes	utr-3,missense	TCEB2	NM_007108.3,NM_207013.2	,81	371,1760,4367	AA,AG,GG		9.1628,38.99,19.2521	,benign	,145/162	2821525	2502,10494	2198	4300	6498	SO:0001624	3_prime_UTR_variant	6923	exon5			TCCCTCGTTGAAC	L42856	CCDS32374.1, CCDS45387.1	16p12.3	2008-02-05	2002-08-29		ENSG00000103363	ENSG00000103363			11619	protein-coding gene	gene with protein product		600787	"""transcription elongation factor B (SIII), polypeptide 2 (18kD, elongin B)"""			7638163	Standard	NM_007108		Approved	SIII	uc002crm.3	Q15370	OTTHUMG00000154125	ENST00000409906.4:c.*466C>T	16.37:g.2821525G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	151	75	0.496689	NM_207013	B7WPD3	Missense_Mutation	SNP	ENST00000409906.4	37	CCDS45387.1	384	0.17582417582417584	224	0.45528455284552843	42	0.11602209944751381	38	0.06643356643356643	80	0.10554089709762533	A	5.944	0.358230	0.11239	0.3899	0.091628	ENSG00000103363	ENST00000262306	.	.	.	2.58	0.106	0.14540	.	.	.	.	.	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	0.44143	-0.9347	7	0.02654	T	1	.	2.9225	0.05773	0.4589:0.2437:0.2974:0.0	rs4036;rs57537347;rs4036	145	B7WPD3	.	M	145	.	ENSP00000262306:T145M	T	-	2	0	TCEB2	2761526	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.772000	0.04694	-0.315000	0.08703	-0.254000	0.11334	ACG	G|0.812;A|0.188	0.188	strong		0.577	TCEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333975.2	NM_007108	
COMP	1311	hgsc.bcm.edu	37	19	18895865	18895865	+	Silent	SNP	C	C	T	rs34467947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18895865C>T	ENST00000222271.2	-	16	1799	c.1755G>A	c.(1753-1755)acG>acA	p.T585T	COMP_ENST00000542601.2_Silent_p.T552T|COMP_ENST00000425807.1_Silent_p.T532T	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	585	Mediates cell survival and induction of the IAP family of survival proteins.|TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.		T -> M (in PSACH; mild form and EDM1). {ECO:0000269|PubMed:11565064, ECO:0000269|PubMed:21922596}.|T -> R (in EDM1 and PSACH). {ECO:0000269|PubMed:21922596, ECO:0000269|PubMed:9463320}.		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						TCACATGGAACGTGCCCTCGA	0.582													C|||	98	0.0195687	0.003	0.0259	5008	,	,		16591	0.0		0.0676	False		,,,				2504	0.0082				p.T585T		Atlas-SNP	.											.	COMP	62	.	0			c.G1755A						PASS	.	C		55,4351	54.9+/-90.9	0,55,2148	166.0	137.0	147.0		1755	-5.7	1.0	19	dbSNP_126	147	636,7964	163.5+/-216.0	15,606,3679	no	coding-synonymous	COMP	NM_000095.2		15,661,5827	TT,TC,CC		7.3953,1.2483,5.3129		585/758	18895865	691,12315	2203	4300	6503	SO:0001819	synonymous_variant	1311	exon16			ATGGAACGTGCCC	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.1755G>A	19.37:g.18895865C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	116	58	0.5	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Silent	SNP	ENST00000222271.2	37	CCDS12385.1																																																																																			C|0.952;T|0.048	0.048	strong		0.582	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095	
CLUAP1	23059	hgsc.bcm.edu	37	16	3554799	3554799	+	Silent	SNP	T	T	C	rs34672214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3554799T>C	ENST00000576634.1	+	2	246	c.102T>C	c.(100-102)ctT>ctC	p.L34L	CLUAP1_ENST00000417763.2_5'UTR|LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000341633.5_Silent_p.L34L|CLUAP1_ENST00000571025.1_Silent_p.L34L	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	34					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATTTTGGACTTGTATCTGAAG	0.383													T|||	283	0.0565096	0.115	0.0331	5008	,	,		19316	0.0556		0.0159	False		,,,				2504	0.0368				p.L34L		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T102C						PASS	.	T		427,3967	207.5+/-228.8	19,389,1789	111.0	109.0	110.0		102	3.1	1.0	16	dbSNP_126	110	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	CLUAP1	NM_015041.1		19,527,5951	CC,CT,TT		1.6047,9.7178,4.3482		34/414	3554799	565,12429	2197	4300	6497	SO:0001819	synonymous_variant	23059	exon2			TGGACTTGTATCT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.102T>C	16.37:g.3554799T>C		Somatic	218	0	0		WXS	Illumina HiSeq	Phase_I	203	91	0.448276	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			T|0.955;C|0.045	0.045	strong		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
KIF25	3834	hgsc.bcm.edu	37	6	168442687	168442687	+	Missense_Mutation	SNP	A	A	C	rs12197062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:168442687A>C	ENST00000443060.2	+	8	1076	c.685A>C	c.(685-687)Aca>Cca	p.T229P	KIF25_ENST00000351261.3_Missense_Mutation_p.T229P|KIF25_ENST00000354419.2_Missense_Mutation_p.T229P			Q9UIL4	KIF25_HUMAN	kinesin family member 25	229	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.		T -> P (in dbSNP:rs12197062).		ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CAGGGAGCAAACAGAGGCAGG	0.622													A|||	561	0.112021	0.0212	0.0461	5008	,	,		17736	0.1657		0.1372	False		,,,				2504	0.2004				p.T229P		Atlas-SNP	.											.	KIF25	75	.	0			c.A685C						PASS	.	A	PRO/THR,PRO/THR	125,4135		4,117,2009	26.0	27.0	27.0		685,685	-4.6	0.0	6	dbSNP_120	27	810,7554		49,712,3421	yes	missense,missense	KIF25	NM_005355.3,NM_030615.2	38,38	53,829,5430	CC,CA,AA		9.6844,2.9343,7.4065	benign,benign	229/333,229/385	168442687	935,11689	2130	4182	6312	SO:0001583	missense	3834	exon7			GAGCAAACAGAGG	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"""Kinesins"""	6390	protein-coding gene	gene with protein product		603815	"""kinesin-like 3"""	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.685A>C	6.37:g.168442687A>C	ENSP00000388878:p.Thr229Pro	Somatic	264	0	0		WXS	Illumina HiSeq	Phase_I	149	23	0.154362	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	37	CCDS5305.1	238	0.10897435897435898	7	0.014227642276422764	20	0.055248618784530384	108	0.1888111888111888	103	0.1358839050131926	A	5.462	0.270318	0.10349	0.029343	0.096844	ENSG00000125337	ENST00000443060;ENST00000354419;ENST00000351261	T;T;T	0.74106	-0.81;-0.81;-0.0	2.63	-4.64	0.03349	Kinesin, motor domain (3);	9.148890	0.01046	N	0.004393	T	0.17023	0.0409	N	0.00666	-1.275	0.80722	P	0.0	B;B	0.14012	0.003;0.009	B;B	0.12837	0.003;0.008	T	0.24799	-1.0150	9	0.87932	D	0	.	1.5414	0.02556	0.2401:0.1959:0.408:0.156	rs12197062	229;229	Q9UIL4-2;Q9UIL4	.;KIF25_HUMAN	P	229	ENSP00000388878:T229P;ENSP00000346401:T229P;ENSP00000252688:T229P	ENSP00000252688:T229P	T	+	1	0	KIF25	168185536	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.455000	0.06762	-1.012000	0.03387	0.338000	0.21704	ACA	A|0.910;C|0.090	0.090	strong		0.622	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1		
PCDHB8	56128	hgsc.bcm.edu	37	5	140558315	140558315	+	Missense_Mutation	SNP	G	G	C	rs17844488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140558315G>C	ENST00000239444.2	+	1	945	c.700G>C	c.(700-702)Gtc>Ctc	p.V234L	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	234	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.			V -> L (in Ref. 4; AAG10031). {ECO:0000305}.	homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CATTGAAGTTGTCGATGTCAA	0.512													G|||	673	0.134385	0.0136	0.1441	5008	,	,		24549	0.3333		0.0805	False		,,,				2504	0.1411				p.V234L		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G700C						PASS	.						179.0	226.0	210.0					5																	140558315		2200	4223	6423	SO:0001583	missense	56128	exon1			GAAGTTGTCGATG	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.700G>C	5.37:g.140558315G>C	ENSP00000239444:p.Val234Leu	Somatic	977	1	0.00102354		WXS	Illumina HiSeq	Phase_I	205	48	0.234146	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-3.567528	0.00008	.	.	ENSG00000120322	ENST00000239444	T	0.17054	2.3	4.25	-1.67	0.08238	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.04137	0.0115	N	0.00811	-1.165	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40961	-0.9535	9	0.02654	T	1	.	10.755	0.46232	0.0717:0.6617:0.1685:0.0982	rs17844488	234	Q9UN66	PCDB8_HUMAN	L	234	ENSP00000239444:V234L	ENSP00000239444:V234L	V	+	1	0	PCDHB8	140538499	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.300000	0.01138	-0.925000	0.03775	-3.232000	0.00051	GTC	.	.	weak		0.512	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
APOB	338	hgsc.bcm.edu	37	2	21232195	21232195	+	Silent	SNP	G	G	A	rs693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:21232195G>A	ENST00000233242.1	-	26	7672	c.7545C>T	c.(7543-7545)acC>acT	p.T2515T		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2515					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATCTTCTAGGGTCTCTCGGA	0.438													G|||	1257	0.250998	0.2095	0.3775	5008	,	,		21485	0.0615		0.4423	False		,,,				2504	0.2157				p.T2515T		Atlas-SNP	.											.	APOB	761	.	0			c.C7545T						PASS	.	G		1082,3324	391.4+/-328.1	140,802,1261	128.0	107.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	7545	3.2	0.9	2	dbSNP_36	114	4301,4299	577.5+/-390.6	1092,2117,1091	no	coding-synonymous	APOB	NM_000384.2		1232,2919,2352	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	49.9884,24.5574,41.3886		2515/4564	21232195	5383,7623	2203	4300	6503	SO:0001819	synonymous_variant	338	exon26			TTCTAGGGTCTCT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.7545C>T	2.37:g.21232195G>A		Somatic	162	1	0.00617284		WXS	Illumina HiSeq	Phase_I	153	153	1	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			G|0.665;N|0.000	.	strong		0.438	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
SALL2	6297	hgsc.bcm.edu	37	14	21991626	21991626	+	Missense_Mutation	SNP	C	C	G	rs1263810	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21991626C>G	ENST00000327430.3	-	2	2530	c.2236G>C	c.(2236-2238)Ggg>Cgg	p.G746R	AE000658.22_ENST00000535893.1_RNA|SALL2_ENST00000538754.1_Intron|SALL2_ENST00000317492.5_Intron|SALL2_ENST00000450879.2_Missense_Mutation_p.G609R	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	746			G -> R (in dbSNP:rs1263810). {ECO:0000269|PubMed:8975705, ECO:0000269|PubMed:9205841, ECO:0000269|Ref.6}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GGGAAACTCCCTGCCCCGGAG	0.597													C|||	1223	0.244209	0.1059	0.1556	5008	,	,		18594	0.2579		0.3549	False		,,,				2504	0.3661				p.G746R		Atlas-SNP	.											.	SALL2	95	.	0			c.G2236C						PASS	.	C	ARG/GLY	650,3756	277.5+/-273.7	51,548,1604	56.0	49.0	51.0		2236	4.8	1.0	14	dbSNP_87	51	2904,5696	453.1+/-363.1	496,1912,1892	yes	missense	SALL2	NM_005407.1	125	547,2460,3496	GG,GC,CC		33.7674,14.7526,27.3258	probably-damaging	746/1008	21991626	3554,9452	2203	4300	6503	SO:0001583	missense	6297	exon2			AACTCCCTGCCCC	AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"""Zinc fingers, C2H2-type"""	10526	protein-coding gene	gene with protein product		602219	"""sal (Drosophila)-like 2"", ""sal-like 2 (Drosophila)"""			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.2236G>C	14.37:g.21991626C>G	ENSP00000333537:p.Gly746Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	89	41	0.460674	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	37	CCDS32045.1	552|552	0.25274725274725274|0.25274725274725274	52|52	0.10569105691056911|0.10569105691056911	70|70	0.19337016574585636|0.19337016574585636	157|157	0.2744755244755245|0.2744755244755245	273|273	0.36015831134564646|0.36015831134564646	C|C	15.46|15.46	2.840915|2.840915	0.51057|0.51057	0.147526|0.147526	0.337674|0.337674	ENSG00000165821|ENSG00000165821	ENST00000327430;ENST00000450879|ENST00000546363	T;T|.	0.04551|.	3.66;3.6|.	4.76|4.76	4.76|4.76	0.60689|0.60689	.|.	0.000000|.	0.39687|.	N|.	0.001296|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.27053|0.27053	0.805|0.805	0.24034|0.24034	P|P	0.99610114|0.99610114	B;B;B|.	0.17667|.	0.023;0.023;0.023|.	B;B;B|.	0.18263|.	0.021;0.021;0.021|.	T|T	0.43861|0.43861	-0.9365|-0.9365	9|4	0.38643|.	T|.	0.18|.	-27.9051|-27.9051	8.8209|8.8209	0.35025|0.35025	0.0:0.8999:0.0:0.1001|0.0:0.8999:0.0:0.1001	rs1263810;rs1754631;rs17792718;rs1263810|rs1263810;rs1754631;rs17792718;rs1263810	609;507;746|.	E7EW59;B4DFD9;Q9Y467|.	.;.;SALL2_HUMAN|.	R|H	746;609|604	ENSP00000333537:G746R;ENSP00000396773:G609R|.	ENSP00000333537:G746R|.	G|Q	-|-	1|3	0|2	SALL2|SALL2	21061466|21061466	0.008000|0.008000	0.16893|0.16893	0.964000|0.964000	0.40570|0.40570	0.128000|0.128000	0.20619|0.20619	0.893000|0.893000	0.28336|0.28336	2.468000|2.468000	0.83385|0.83385	0.563000|0.563000	0.77884|0.77884	GGG|CAG	C|0.711;G|0.289	0.289	strong		0.597	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68229051	68229051	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68229051T>C	ENST00000347230.4	-	34	6376	c.6238A>G	c.(6238-6240)Act>Gct	p.T2080A	ZFYVE26_ENST00000557306.1_5'Flank|ZFYVE26_ENST00000555452.1_Missense_Mutation_p.T2080A	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2080					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)		CGTGCAGCAGTGAGGTTCCCG	0.562																																					p.T2080A		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A6238G						PASS	.						93.0	76.0	82.0					14																	68229051		2203	4300	6503	SO:0001583	missense	23503	exon34			CAGCAGTGAGGTT	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.6238A>G	14.37:g.68229051T>C	ENSP00000251119:p.Thr2080Ala	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	105	45	0.428571	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	T	3.183	-0.167539	0.06461	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.26518	1.88;1.73	5.55	0.543	0.17179	.	0.468395	0.22794	N	0.055575	T	0.06872	0.0175	N	0.02011	-0.69	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.36335	-0.9752	10	0.11182	T	0.66	-0.8863	4.9027	0.13782	0.0:0.23:0.2765:0.4935	.	2080;2080	G3V2D8;Q68DK2	.;ZFY26_HUMAN	A	2080;2059;2080	ENSP00000251119:T2080A;ENSP00000450603:T2080A	ENSP00000251119:T2080A	T	-	1	0	ZFYVE26	67298804	0.979000	0.34478	0.895000	0.35142	0.474000	0.32979	0.238000	0.18004	0.071000	0.16664	-0.313000	0.08912	ACT	.	.	none		0.562	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
PCNT	5116	hgsc.bcm.edu	37	21	47773103	47773103	+	Silent	SNP	C	C	A	rs2249057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47773103C>A	ENST00000359568.5	+	10	1649	c.1542C>A	c.(1540-1542)tcC>tcA	p.S514S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	514	Glu-rich.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)		p.S514S(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGCATGAGTCCGAACTGGAGC	0.483													C|||	1450	0.289537	0.2141	0.1988	5008	,	,		20023	0.3839		0.3449	False		,,,				2504	0.3016				p.S514S		Atlas-SNP	.											PCNT,NS,carcinoma,0,1	PCNT	283	1	1	Substitution - coding silent(1)	prostate(1)	c.C1542A						PASS	.	C		1035,3371	379.4+/-323.3	115,805,1283	66.0	71.0	69.0		1542	-9.5	0.0	21	dbSNP_100	69	2844,5756	448.4+/-361.8	464,1916,1920	no	coding-synonymous	PCNT	NM_006031.5		579,2721,3203	AA,AC,CC		33.0698,23.4907,29.8247		514/3337	47773103	3879,9127	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon10			TGAGTCCGAACTG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.1542C>A	21.37:g.47773103C>A		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	72	34	0.472222	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.694;A|0.306	0.306	strong		0.483	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
SPAG17	200162	hgsc.bcm.edu	37	1	118629599	118629599	+	Silent	SNP	G	G	A	rs12142616	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:118629599G>A	ENST00000336338.5	-	11	1457	c.1392C>T	c.(1390-1392)ccC>ccT	p.P464P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	464						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		CCCGCAGACTGGGTGGGACGA	0.522													G|||	660	0.131789	0.0749	0.0461	5008	,	,		17193	0.2847		0.0596	False		,,,				2504	0.1861				p.P464P		Atlas-SNP	.											.	SPAG17	263	.	0			c.C1392T						PASS	.	G		339,4067	175.1+/-204.6	12,315,1876	126.0	123.0	124.0		1392	-10.1	0.0	1	dbSNP_120	124	489,8111	143.0+/-199.1	16,457,3827	no	coding-synonymous	SPAG17	NM_206996.2		28,772,5703	AA,AG,GG		5.686,7.6941,6.3663		464/2224	118629599	828,12178	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon11			CAGACTGGGTGGG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1392C>T	1.37:g.118629599G>A		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	98	46	0.469388	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			G|0.923;A|0.077	0.077	strong		0.522	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98369563	98369563	+	Silent	SNP	T	T	C	rs141067860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:98369563T>C	ENST00000339364.5	-	14	2195	c.2076A>G	c.(2074-2076)ggA>ggG	p.G692G	PIK3AP1_ENST00000371110.2_Silent_p.G514G|PIK3AP1_ENST00000371109.3_Silent_p.G291G	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	692					negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		TCTCATAGACTCCAAACTCCA	0.532													T|||	4	0.000798722	0.0	0.0029	5008	,	,		6366	0.0		0.002	False		,,,				2504	0.0				p.G692G		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.A2076G						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	236.0	242.0	240.0		2076	-2.2	1.0	10	dbSNP_134	240	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	PIK3AP1	NM_152309.2		0,15,6488	CC,CT,TT		0.1395,0.0681,0.1153		692/806	98369563	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	118788	exon14			ATAGACTCCAAAC	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.2076A>G	10.37:g.98369563T>C		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	144	59	0.409722	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Silent	SNP	ENST00000339364.5	37	CCDS31259.1																																																																																			T|0.999;C|0.001	0.001	strong		0.532	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
OR11H6	122748	hgsc.bcm.edu	37	14	20692291	20692291	+	Silent	SNP	C	C	T	rs34693535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20692291C>T	ENST00000315519.2	+	1	501	c.423C>T	c.(421-423)taC>taT	p.Y141Y		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	141						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)		ATGATCGGTACCTGGCCATCT	0.433													c|||	1958	0.390974	0.4735	0.3516	5008	,	,		22347	0.2371		0.4781	False		,,,				2504	0.3763				p.Y141Y		Atlas-SNP	.											.	OR11H6	60	.	0			c.C423T						PASS	.	C		2257,2149	595.3+/-388.4	610,1037,556	159.0	155.0	156.0		423	3.2	1.0	14	dbSNP_126	156	4156,4444	565.9+/-388.6	996,2164,1140	yes	coding-synonymous	OR11H6	NM_001004480.1		1606,3201,1696	TT,TC,CC		48.3256,48.7744,49.308		141/331	20692291	6413,6593	2203	4300	6503	SO:0001819	synonymous_variant	122748	exon1			TCGGTACCTGGCC		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.423C>T	14.37:g.20692291C>T		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	106	49	0.462264	NM_001004480	Q6IF08	Silent	SNP	ENST00000315519.2	37	CCDS32033.1																																																																																			C|0.533;T|0.467	0.467	strong		0.433	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
CRIP3	401262	hgsc.bcm.edu	37	6	43273604	43273604	+	3'UTR	SNP	A	A	G	rs2242416	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43273604A>G	ENST00000274990.4	-	0	758				CRIP3_ENST00000372569.3_Missense_Mutation_p.I188T|ZNF318_ENST00000607252.1_5'Flank			Q6Q6R5	CRIP3_HUMAN	cysteine-rich protein 3						T cell proliferation (GO:0042098)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00998)|OV - Ovarian serous cystadenocarcinoma(102;0.0305)			CACATCGCCAATGTTCACACC	0.542													A|||	2088	0.416933	0.0719	0.4035	5008	,	,		20332	0.621		0.5765	False		,,,				2504	0.5184				p.I188T		Atlas-SNP	.											.	CRIP3	30	.	0			c.T563C						PASS	.	A	THR/ILE	705,3685		55,595,1545	76.0	80.0	79.0		563	5.8	1.0	6	dbSNP_98	79	5031,3559		1445,2141,709	yes	missense	CRIP3	NM_206922.2	89	1500,2736,2254	GG,GA,AA		41.4319,16.0592,44.1911	benign	188/205	43273604	5736,7244	2195	4295	6490	SO:0001624	3_prime_UTR_variant	401262	exon8			TCGCCAATGTTCA	AY555741	CCDS4894.2	6p21	2008-02-05			ENSG00000146215	ENSG00000146215			17751	protein-coding gene	gene with protein product						15380775	Standard	NM_206922		Approved	TLP-A, bA480N24.2, TLP	uc003ouu.1	Q6Q6R5	OTTHUMG00000014727	ENST00000274990.4:c.*100T>C	6.37:g.43273604A>G		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	106	43	0.40566	NM_206922	A2A436|Q5T043|Q6Q6R4|Q6Q6R6|Q6Q6R7	Missense_Mutation	SNP	ENST00000274990.4	37		1000	0.45787545787545786	30	0.06097560975609756	157	0.43370165745856354	371	0.6486013986013986	442	0.58311345646438	A	10.18	1.279807	0.23392	0.160592	0.585681	ENSG00000146215	ENST00000372569	D	0.92397	-3.03	5.77	5.77	0.91146	.	.	.	.	.	T	0.78400	0.4277	.	.	.	0.09310	P	1.0	B	0.23891	0.093	B	0.23574	0.047	T	0.72997	-0.4121	7	0.12766	T	0.61	.	14.039	0.64663	1.0:0.0:0.0:0.0	rs2242416;rs17287893;rs56983690;rs2242416	188	Q6Q6R5-3	.	T	188	ENSP00000361650:I188T	ENSP00000361650:I188T	I	-	2	0	CRIP3	43381582	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.562000	0.60816	2.200000	0.70718	0.533000	0.62120	ATT	G|0.469;N|0.000	0.469	strong		0.542	CRIP3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000313968.1		
NPR3	4883	hgsc.bcm.edu	37	5	32786389	32786389	+	Missense_Mutation	SNP	A	A	G	rs2270915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:32786389A>G	ENST00000265074.8	+	8	1907	c.1564A>G	c.(1564-1566)Aac>Gac	p.N522D	AC026703.1_ENST00000326958.1_5'Flank|NPR3_ENST00000415167.2_Missense_Mutation_p.N521D|NPR3_ENST00000415685.2_Missense_Mutation_p.N305D|NPR3_ENST00000434067.2_Missense_Mutation_p.N306D	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	522				N -> D (in Ref. 4; BAG61896). {ECO:0000305}.	adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of smooth muscle cell proliferation (GO:0048662)|osteoclast proliferation (GO:0002158)|pancreatic juice secretion (GO:0030157)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of urine volume (GO:0035810)|regulation of blood pressure (GO:0008217)|regulation of osteoblast proliferation (GO:0033688)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	G-protein coupled peptide receptor activity (GO:0008528)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24					Nesiritide(DB04899)	AGAAGAAAGTAACCTTGGAAA	0.403													A|||	979	0.195487	0.0991	0.2147	5008	,	,		18620	0.2024		0.1879	False		,,,				2504	0.3129				p.N522D		Atlas-SNP	.											.	NPR3	65	.	0			c.A1564G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN	428,3234		33,362,1436	78.0	73.0	74.0		1561,1564,913	5.0	0.7	5	dbSNP_100	74	1649,6519		159,1331,2594	yes	missense,missense,missense	NPR3	NM_000908.3,NM_001204375.1,NM_001204376.1	23,23,23	192,1693,4030	GG,GA,AA		20.1885,11.6876,17.5571	benign,benign,benign	521/541,522/542,305/325	32786389	2077,9753	1831	4084	5915	SO:0001583	missense	4883	exon8			GAAAGTAACCTTG		CCDS47196.1, CCDS56356.1, CCDS56357.1	5p13.3	2014-03-03	2014-03-03		ENSG00000113389	ENSG00000113389			7945	protein-coding gene	gene with protein product	"""guanylate cyclase C"""	108962	"""chromosome 5 open reading frame 23"", ""atrionatriuretic peptide receptor C"", ""natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C)"", ""natriuretic peptide receptor C"""	NPRC, ANPRC, C5orf23		2162522, 1979052	Standard	NM_000908		Approved	GUCY2B, FLJ14054	uc003jhv.3	P17342	OTTHUMG00000150316	ENST00000265074.8:c.1564A>G	5.37:g.32786389A>G	ENSP00000265074:p.Asn522Asp	Somatic	174	0	0		WXS	Illumina HiSeq	Phase_I	198	100	0.50505	NM_001204375	A2RRD1|B4DT84|E7EPG9	Missense_Mutation	SNP	ENST00000265074.8	37	CCDS56357.1	388	0.17765567765567766	47	0.09552845528455285	68	0.1878453038674033	122	0.21328671328671328	151	0.19920844327176782	A	12.56	1.975892	0.34848	0.116876	0.201885	ENSG00000113389	ENST00000434067;ENST00000415685;ENST00000265074;ENST00000415167	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	6.17	5.0	0.66597	.	0.198485	0.53938	D	0.000058	T	0.00012	0.0000	N	0.08118	0	0.27179	P	0.9607229	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.003;0.002;0.003	T	0.10268	-1.0637	9	0.33940	T	0.23	-14.8784	13.7445	0.62868	0.8716:0.1283:0.0:0.0	rs2270915;rs52798471;rs59552869;rs2270915	305;522;521	E7EPG9;P17342;Q60I31	.;ANPRC_HUMAN;.	D	306;305;522;521	ENSP00000388408:N306D;ENSP00000402490:N305D;ENSP00000265074:N522D;ENSP00000398028:N521D	ENSP00000265074:N522D	N	+	1	0	NPR3	32822146	1.000000	0.71417	0.741000	0.31004	0.983000	0.72400	4.122000	0.57910	1.137000	0.42214	0.533000	0.62120	AAC	A|0.833;G|0.167	0.167	strong		0.403	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908	
HCFC1R1	54985	hgsc.bcm.edu	37	16	3073240	3073240	+	Missense_Mutation	SNP	G	G	T	rs10508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3073240G>T	ENST00000248089.3	-	3	579	c.275C>A	c.(274-276)cCa>cAa	p.P92Q	THOC6_ENST00000574549.1_5'Flank|HCFC1R1_ENST00000396916.1_Missense_Mutation_p.P92Q|HCFC1R1_ENST00000572355.1_Missense_Mutation_p.P52Q|THOC6_ENST00000326266.8_5'Flank|HCFC1R1_ENST00000574980.1_Missense_Mutation_p.P92Q|HCFC1R1_ENST00000574151.1_Missense_Mutation_p.P73Q|HCFC1R1_ENST00000354679.3_Missense_Mutation_p.P90Q|THOC6_ENST00000575576.1_5'Flank|THOC6_ENST00000253952.9_5'Flank	NM_017885.2	NP_060355.1	Q9NWW0	HPIP_HUMAN	host cell factor C1 regulator 1 (XPO1 dependent)	92			P -> Q (in dbSNP:rs10508). {ECO:0000269|PubMed:15489334}.			cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(1)|upper_aerodigestive_tract(1)	3						CTACCTGAGTGGGGGCAGGGC	0.597													G|||	947	0.189097	0.1354	0.1916	5008	,	,		15819	0.1181		0.2356	False		,,,				2504	0.2853				p.P92Q		Atlas-SNP	.											HCFC1R1_ENST00000248089,NS,carcinoma,0,2	HCFC1R1	17	2	0			c.C275A						PASS	.	G	GLN/PRO,GLN/PRO,GLN/PRO	606,3790	260.1+/-263.5	46,514,1638	38.0	43.0	41.0		218,275,275	3.1	1.0	16	dbSNP_52	41	1976,6624	342.7+/-324.6	227,1522,2551	yes	missense,missense,missense	HCFC1R1	NM_001002017.1,NM_001002018.1,NM_017885.2	76,76,76	273,2036,4189	TT,TG,GG		22.9767,13.7853,19.8677	benign,benign,benign	73/120,92/139,92/139	3073240	2582,10414	2198	4300	6498	SO:0001583	missense	54985	exon3			CTGAGTGGGGGCA	AK000575	CCDS10490.1, CCDS32375.1, CCDS73815.1	16p13.3	2008-02-05	2005-12-01			ENSG00000103145			21198	protein-coding gene	gene with protein product			"""host cell factor C1 regulator 1 (XPO1 dependant)"""			12235138	Standard	NM_001002018		Approved	HPIP, FLJ20568	uc002csy.1	Q9NWW0		ENST00000248089.3:c.275C>A	16.37:g.3073240G>T	ENSP00000248089:p.Pro92Gln	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_017885	D3DUA7|Q68EN7	Missense_Mutation	SNP	ENST00000248089.3	37	CCDS10490.1	366	0.16758241758241757	54	0.10975609756097561	75	0.20718232044198895	59	0.10314685314685315	178	0.23482849604221637	G	9.981	1.228065	0.22542	0.137853	0.229767	ENSG00000103145	ENST00000248089;ENST00000354679;ENST00000396916	T;T	0.44881	0.91;0.91	5.16	3.14	0.36123	.	1.204350	0.06110	N	0.667046	T	0.00012	0.0000	N	0.19112	0.55	0.25564	P	0.9869678	P;B	0.36837	0.571;0.037	B;B	0.34452	0.183;0.012	T	0.14364	-1.0475	9	0.49607	T	0.09	0.0011	7.4927	0.27471	0.0927:0.1666:0.7407:0.0	rs10508;rs1130914;rs1804992;rs2285974;rs3177831;rs3190341;rs11558417;rs17342478;rs17350124;rs58574567;rs10508	73;92	Q9NWW0-2;Q9NWW0	.;HPIP_HUMAN	Q	92;73;92	ENSP00000248089:P92Q;ENSP00000380123:P92Q	ENSP00000248089:P92Q	P	-	2	0	HCFC1R1	3013241	0.946000	0.32159	0.999000	0.59377	0.630000	0.37929	2.458000	0.45014	1.172000	0.42781	0.558000	0.71614	CCA	G|0.817;T|0.183	0.183	strong		0.597	HCFC1R1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436969.1	NM_017885	
OR5AP2	338675	hgsc.bcm.edu	37	11	56409010	56409010	+	Missense_Mutation	SNP	A	A	T	rs61747872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56409010A>T	ENST00000302981.1	-	1	905	c.906T>A	c.(904-906)gaT>gaA	p.D302E	OR5AP2_ENST00000544374.1_Missense_Mutation_p.D303E	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	302						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	29						CCTTTTTTACATCCTTATTTT	0.348													A|||	137	0.0273562	0.003	0.0389	5008	,	,		19574	0.0		0.0417	False		,,,				2504	0.0654				p.D302E		Atlas-SNP	.											.	OR5AP2	69	.	0			c.T906A						PASS	.	A	GLU/ASP	39,4363	40.0+/-72.8	0,39,2162	73.0	72.0	72.0		906	4.9	1.0	11	dbSNP_129	72	437,8155	132.6+/-190.3	12,413,3871	yes	missense	OR5AP2	NM_001002925.1	45	12,452,6033	TT,TA,AA		5.0861,0.886,3.6632	benign	302/317	56409010	476,12518	2201	4296	6497	SO:0001583	missense	338675	exon1			TTTTACATCCTTA	AB065854	CCDS31534.1	11q11	2012-08-09			ENSG00000172464	ENSG00000172464		"""GPCR / Class A : Olfactory receptors"""	15258	protein-coding gene	gene with protein product							Standard	NM_001002925		Approved		uc001njb.1	Q8NGF4	OTTHUMG00000166865	ENST00000302981.1:c.906T>A	11.37:g.56409010A>T	ENSP00000303111:p.Asp302Glu	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001002925	B2RNM8	Missense_Mutation	SNP	ENST00000302981.1	37	CCDS31534.1	56	0.02564102564102564	5	0.01016260162601626	18	0.049723756906077346	0	0.0	33	0.04353562005277045	A	3.227	-0.158206	0.06544	0.00886	0.050861	ENSG00000172464	ENST00000544374;ENST00000302981	T;T	0.36340	1.26;1.26	4.94	4.94	0.65067	.	0.000000	0.50627	D	0.000101	T	0.03608	0.0103	L	0.33485	1.01	0.26503	N	0.974746	B	0.06786	0.001	B	0.11329	0.006	T	0.19257	-1.0311	10	0.02654	T	1	.	10.34	0.43873	0.8352:0.1648:0.0:0.0	rs61747872	302	Q8NGF4	O5AP2_HUMAN	E	303;302	ENSP00000442701:D303E;ENSP00000303111:D302E	ENSP00000303111:D302E	D	-	3	2	OR5AP2	56165586	0.001000	0.12720	0.998000	0.56505	0.426000	0.31534	-0.351000	0.07711	2.090000	0.63153	0.519000	0.50382	GAT	A|0.960;T|0.040	0.040	strong		0.348	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925	
C18orf54	162681	hgsc.bcm.edu	37	18	51888169	51888169	+	Missense_Mutation	SNP	G	G	C	rs1657907	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:51888169G>C	ENST00000300091.5	+	3	772	c.440G>C	c.(439-441)cGa>cCa	p.R147P	C18orf54_ENST00000578138.1_Intron|C18orf54_ENST00000382911.4_Missense_Mutation_p.R147P	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	147			R -> P (in dbSNP:rs1657907).			extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	15				Colorectal(16;0.0206)|READ - Rectum adenocarcinoma(59;0.186)		CCGAGTCACCGAACGAGCAAG	0.428													G|||	304	0.0607029	0.0946	0.0432	5008	,	,		8221	0.0069		0.0646	False		,,,				2504	0.0787				p.R147P		Atlas-SNP	.											.	C18orf54	40	.	0			c.G440C						PASS	.	G	PRO/ARG	385,4021	194.0+/-219.0	17,351,1835	88.0	75.0	79.0		440	0.5	0.0	18	dbSNP_89	79	521,8079	146.5+/-202.0	15,491,3794	yes	missense	C18orf54	NM_173529.4	103	32,842,5629	CC,CG,GG		6.0581,8.7381,6.966	probably-damaging	147/373	51888169	906,12100	2203	4300	6503	SO:0001583	missense	162681	exon3			GTCACCGAACGAG	AK126503	CCDS11956.1, CCDS74223.1	18q21	2012-10-24			ENSG00000166845	ENSG00000166845			13796	protein-coding gene	gene with protein product	"""lung adenoma susceptibility protein 2"""	613258					Standard	XM_005258201		Approved	MGC33382, LAS2	uc031rij.1	Q8IYD9	OTTHUMG00000132703	ENST00000300091.5:c.440G>C	18.37:g.51888169G>C	ENSP00000300091:p.Arg147Pro	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	184	77	0.418478	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	ENST00000300091.5	37	CCDS11956.1	119	0.05448717948717949	50	0.1016260162601626	19	0.052486187845303865	4	0.006993006993006993	46	0.06068601583113457	G	9.626	1.135048	0.21123	0.087381	0.060581	ENSG00000166845	ENST00000300091;ENST00000382911	D;D	0.97529	-4.42;-4.42	5.55	0.49	0.16861	.	0.899525	0.09554	N	0.786575	T	0.52125	0.1715	M	0.62723	1.935	0.09310	N	1	D;D	0.58620	0.969;0.983	P;P	0.49683	0.619;0.619	T	0.73167	-0.4068	10	0.59425	D	0.04	-1.9999	4.7755	0.13176	0.5911:0.0:0.2429:0.1661	rs1657907;rs1657907	147;147	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	P	147	ENSP00000300091:R147P;ENSP00000372368:R147P	ENSP00000300091:R147P	R	+	2	0	C18orf54	50142167	0.002000	0.14202	0.031000	0.17742	0.053000	0.15095	-0.241000	0.08940	0.142000	0.18901	0.467000	0.42956	CGA	A|0.000;C|0.067;G|0.933	0.067	strong		0.428	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529	
UEVLD	55293	hgsc.bcm.edu	37	11	18555901	18555901	+	Silent	SNP	C	C	G	rs56151250	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18555901C>G	ENST00000396197.3	-	11	1252	c.1224G>C	c.(1222-1224)gtG>gtC	p.V408V	UEVLD_ENST00000540666.1_5'UTR|UEVLD_ENST00000535484.1_Intron|UEVLD_ENST00000379387.4_Silent_p.V386V|UEVLD_ENST00000543987.1_Intron|UEVLD_ENST00000320750.6_Intron|UEVLD_ENST00000541984.1_Intron	NM_001040697.2|NM_001261384.1	NP_001035787.1|NP_001248313.1			UEV and lactate/malate dehyrogenase domains											endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						ATACAGAATGCACTTTCTTCT	0.313													C|||	1262	0.251997	0.0469	0.2363	5008	,	,		17778	0.4415		0.1958	False		,,,				2504	0.4029				p.V408V		Atlas-SNP	.											.	UEVLD	58	.	0			c.G1224C						PASS	.	C	,	255,3441		7,241,1600	109.0	95.0	99.0		1224,	-3.6	1.0	11	dbSNP_129	99	1263,6899		116,1031,2934	no	coding-synonymous,intron	UEVLD	NM_001040697.1,NM_018314.3	,	123,1272,4534	GG,GC,CC		15.4741,6.8994,12.8015	,	408/472,	18555901	1518,10340	1848	4081	5929	SO:0001819	synonymous_variant	55293	exon11			AGAATGCACTTTC	AF503350	CCDS7843.1, CCDS41624.1, CCDS58122.1, CCDS58123.1, CCDS58124.1, CCDS58125.1, CCDS73266.1	11p15.1	2006-07-14			ENSG00000151116	ENSG00000151116			30866	protein-coding gene	gene with protein product		610985				12427560	Standard	NM_001040697		Approved	Attp, UEV3	uc001mot.4	Q8IX04	OTTHUMG00000167729	ENST00000396197.3:c.1224G>C	11.37:g.18555901C>G		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	31	12	0.387097	NM_001040697		Silent	SNP	ENST00000396197.3	37	CCDS41624.1																																																																																			C|0.794;G|0.206	0.206	strong		0.313	UEVLD-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395923.2	NM_018314	
S1PR5	53637	hgsc.bcm.edu	37	19	10624863	10624863	+	Silent	SNP	C	C	T	rs75861469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10624863C>T	ENST00000439028.3	-	2	950	c.825G>A	c.(823-825)gtG>gtA	p.V275V	S1PR5_ENST00000333430.4_Silent_p.V275V	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	275					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	CCGGGCACGCCACGTCGAGCA	0.652													C|||	96	0.0191693	0.0711	0.0029	5008	,	,		15206	0.0		0.0	False		,,,				2504	0.0				p.V275V		Atlas-SNP	.											.	S1PR5	33	.	0			c.G825A						PASS	.	C	,	236,4150	125.7+/-162.9	9,218,1966	31.0	29.0	29.0		825,825	1.2	1.0	19	dbSNP_132	29	3,8593	1.2+/-3.3	0,3,4295	no	coding-synonymous,coding-synonymous	S1PR5	NM_001166215.1,NM_030760.4	,	9,221,6261	TT,TC,CC		0.0349,5.3808,1.841	,	275/399,275/399	10624863	239,12743	2193	4298	6491	SO:0001819	synonymous_variant	53637	exon2			GCACGCCACGTCG	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	14299	protein-coding gene	gene with protein product		605146	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"""	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.825G>A	19.37:g.10624863C>T		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	56	31	0.553571	NM_030760	Q6NW11	Silent	SNP	ENST00000439028.3	37	CCDS12240.1	35	0.016025641025641024	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	9.558	1.117787	0.20877	0.053808	3.49E-4	ENSG00000180739	ENST00000359134	.	.	.	5.15	1.24	0.21308	.	.	.	.	.	T	0.05456	0.0144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09228	-1.0684	5	0.41790	T	0.15	.	1.7012	0.02873	0.1474:0.4422:0.1546:0.2558	.	.	.	.	S	244	.	ENSP00000352045:G244S	G	-	1	0	S1PR5	10485863	0.002000	0.14202	1.000000	0.80357	0.816000	0.46133	-0.292000	0.08332	0.541000	0.28827	0.491000	0.48974	GGC	C|0.981;T|0.019	0.019	strong		0.652	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760	
DAGLB	221955	hgsc.bcm.edu	37	7	6456302	6456302	+	Silent	SNP	C	C	T	rs2288152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6456302C>T	ENST00000297056.6	-	11	1552	c.1383G>A	c.(1381-1383)ccG>ccA	p.P461P	DAGLB_ENST00000421761.2_Silent_p.P205P|DAGLB_ENST00000436575.1_Silent_p.P420P|DAGLB_ENST00000425398.2_Silent_p.P332P|DAGLB_ENST00000428902.2_Silent_p.P334P	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	461					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		ACCTGACCTGCGGGTAGGCGG	0.632													C|||	895	0.178714	0.0295	0.121	5008	,	,		14766	0.4742		0.0398	False		,,,				2504	0.2597				p.P461P		Atlas-SNP	.											.	DAGLB	74	.	0			c.G1383A						PASS	.	C	,	139,4267	97.1+/-135.8	1,137,2065	43.0	51.0	49.0		996,1383	-9.3	0.0	7	dbSNP_100	49	315,8285	110.2+/-170.6	6,303,3991	no	coding-synonymous,coding-synonymous	DAGLB	NM_001142936.1,NM_139179.3	,	7,440,6056	TT,TC,CC		3.6628,3.1548,3.4907	,	332/544,461/673	6456302	454,12552	2203	4300	6503	SO:0001819	synonymous_variant	221955	exon11			GACCTGCGGGTAG	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1383G>A	7.37:g.6456302C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	88	53	0.602273	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	37	CCDS5350.1																																																																																			C|0.922;T|0.078	0.078	strong		0.632	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
ALMS1	7840	hgsc.bcm.edu	37	2	73677833	73677833	+	Silent	SNP	A	A	G	rs6546836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73677833A>G	ENST00000264448.6	+	8	4287	c.4176A>G	c.(4174-4176)caA>caG	p.Q1392Q	ALMS1_ENST00000409009.1_Silent_p.Q1350Q|ALMS1_ENST00000377715.1_Silent_p.Q1392Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1392	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TTTTCTACCAACAGTCGTTGC	0.473													A|||	1694	0.338259	0.7859	0.3847	5008	,	,		21223	0.0089		0.2256	False		,,,				2504	0.1554				p.Q1392Q		Atlas-SNP	.											ALMS1,colon,carcinoma,0,1	ALMS1	384	1	0			c.A4176G						PASS	.	A		2499,1227		847,805,211	91.0	93.0	92.0		4176	-6.8	0.0	2	dbSNP_116	92	1942,6272		217,1508,2382	no	coding-synonymous	ALMS1	NM_015120.4		1064,2313,2593	GG,GA,AA		23.6426,32.9308,37.1943		1392/4168	73677833	4441,7499	1863	4107	5970	SO:0001819	synonymous_variant	7840	exon8			CTACCAACAGTCG	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.4176A>G	2.37:g.73677833A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	135	68	0.503704	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			A|0.737;G|0.263	0.263	strong		0.473	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
IGHMBP2	3508	hgsc.bcm.edu	37	11	68703959	68703959	+	Missense_Mutation	SNP	A	A	G	rs622082	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68703959A>G	ENST00000255078.3	+	13	2122	c.2011A>G	c.(2011-2013)Acg>Gcg	p.T671A		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	671	SS DNA-binding. {ECO:0000250}.		T -> A (in dbSNP:rs622082).		ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			GGGACCTGCTACGTCCACCAG	0.622													A|||	1233	0.246206	0.0991	0.1571	5008	,	,		16529	0.2133		0.3042	False		,,,				2504	0.4826				p.T671A		Atlas-SNP	.											.	IGHMBP2	83	.	0			c.A2011G						PASS	.	A	ALA/THR	559,3841		47,465,1688	36.0	41.0	40.0		2011	-6.7	0.0	11	dbSNP_83	40	2645,5939		412,1821,2059	yes	missense	IGHMBP2	NM_002180.2	58	459,2286,3747	GG,GA,AA		30.8131,12.7045,24.6765	benign	671/994	68703959	3204,9780	2200	4292	6492	SO:0001583	missense	3508	exon13			CCTGCTACGTCCA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"""Zinc fingers, AN1-type domain containing"""	5542	protein-coding gene	gene with protein product	"""cardiac transcription factor 1"", ""zinc finger, AN1-type domain 7"""	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.2011A>G	11.37:g.68703959A>G	ENSP00000255078:p.Thr671Ala	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	61	32	0.52459	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	486	0.22252747252747251	50	0.1016260162601626	73	0.20165745856353592	130	0.22727272727272727	233	0.3073878627968338	A	0.973	-0.699547	0.03279	0.127045	0.308131	ENSG00000132740	ENST00000255078	D	0.89810	-2.57	3.86	-6.73	0.01749	.	31.798500	0.00447	N	0.000092	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	0.30995	-0.9959	9	0.07813	T	0.8	-22.2725	3.1493	0.06483	0.5684:0.1776:0.1433:0.1107	rs622082;rs57095678;rs622082	671	P38935	SMBP2_HUMAN	A	671	ENSP00000255078:T671A	ENSP00000255078:T671A	T	+	1	0	IGHMBP2	68460535	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.565000	0.05929	-1.282000	0.02396	-0.337000	0.08149	ACG	A|0.767;G|0.233	0.233	strong		0.622	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558308	140558308	+	Silent	SNP	T	T	C	rs2910316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140558308T>C	ENST00000239444.2	+	1	938	c.693T>C	c.(691-693)atT>atC	p.I231I	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	231	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGTCTACATTGAAGTTGTCG	0.507																																					p.I231I		Atlas-SNP	.											.	PCDHB8	199	.	0			c.T693C						PASS	.						168.0	210.0	195.0					5																	140558308		2202	4272	6474	SO:0001819	synonymous_variant	56128	exon1			CTACATTGAAGTT	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.693T>C	5.37:g.140558308T>C		Somatic	1000	1	0.001		WXS	Illumina HiSeq	Phase_I	214	46	0.214953	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			T|0.831;C|0.169	0.169	strong		0.507	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
IFNL2	282616	hgsc.bcm.edu	37	19	39760191	39760191	+	Missense_Mutation	SNP	A	A	G	rs8103362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39760191A>G	ENST00000331982.5	+	4	389	c.334A>G	c.(334-336)Acc>Gcc	p.T112A		NM_172138.1	NP_742150.1	Q8IZJ0	IFNL2_HUMAN	interferon, lambda 2	112			T -> A (in dbSNP:rs8103362).		defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|mucosal immune response (GO:0002385)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											TCTGGAGGCCACCGCTGACAC	0.642													G|||	1176	0.234824	0.3169	0.2262	5008	,	,		15712	0.0327		0.2256	False		,,,				2504	0.3476				p.T112A		Atlas-SNP	.											.	.	.	.	0			c.A334G						PASS	.	G	ALA/THR	1447,2959	680.2+/-403.8	237,973,993	52.0	58.0	56.0		334	-6.2	0.0	19	dbSNP_116	56	1774,6826	733.4+/-406.9	198,1378,2724	no	missense	IL28A	NM_172138.1	58	435,2351,3717	GG,GA,AA		20.6279,32.8416,24.7655	benign	112/201	39760191	3221,9785	2203	4300	6503	SO:0001583	missense	282616	exon4			GAGGCCACCGCTG	AY129148	CCDS42567.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000183709	ENSG00000183709		"""Interferons"""	18364	protein-coding gene	gene with protein product		607401	"""interleukin 28A"", ""interleukin 28A (interferon, lambda 2)"""	IL28A			Standard	NM_172138		Approved	IL-28A	uc002oku.1	Q8IZJ0		ENST00000331982.5:c.334A>G	19.37:g.39760191A>G	ENSP00000333639:p.Thr112Ala	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_172138	Q45KQ8|Q6VN55|Q8IWL7	Missense_Mutation	SNP	ENST00000331982.5	37	CCDS42567.1	422	0.19322344322344323	141	0.2865853658536585	95	0.26243093922651933	21	0.03671328671328671	165	0.21767810026385223	G	2.131	-0.399201	0.04865	0.328416	0.206279	ENSG00000183709	ENST00000331982	T	0.28069	1.63	3.09	-6.19	0.02078	.	1.433330	0.04280	N	0.343644	T	0.00012	0.0000	N	0.04203	-0.255	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31696	-0.9934	9	0.10377	T	0.69	-0.043	5.726	0.18013	0.5911:0.0:0.1584:0.2504	rs8103362;rs60021767	112	Q8IZJ0	IL28A_HUMAN	A	112	ENSP00000333639:T112A	ENSP00000333639:T112A	T	+	1	0	IL28A	44452031	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.615000	0.00414	-2.156000	0.00790	-0.528000	0.04320	ACC	A|0.795;G|0.205	0.205	strong		0.642	IFNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463833.1	NM_172138	
TAF7L	54457	hgsc.bcm.edu	37	X	100547806	100547806	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547806C>A	ENST00000372907.3	-	1	239	c.228G>T	c.(226-228)caG>caT	p.Q76H	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_De_novo_Start_OutOfFrame	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	76					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						TTTCTGGGGCCTGGGCAGCAG	0.557																																					p.Q76H	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.G228T						PASS	.						70.0	71.0	71.0					X																	100547806		2203	4300	6503	SO:0001583	missense	54457	exon1			TGGGGCCTGGGCA	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.228G>T	X.37:g.100547806C>A	ENSP00000361998:p.Gln76His	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	46	44	0.956522	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	8.598	0.886065	0.17540	.	.	ENSG00000102387	ENST00000372907	T	0.16597	2.33	3.17	-2.29	0.06805	.	5.716450	0.00953	N	0.002982	T	0.08714	0.0216	N	0.14661	0.345	0.09310	N	0.999993	P	0.39964	0.697	B	0.32465	0.146	T	0.13683	-1.0500	10	0.51188	T	0.08	6.1498	3.8568	0.08979	0.0:0.284:0.4115:0.3044	.	76	Q5H9L4	TAF7L_HUMAN	H	76	ENSP00000361998:Q76H	ENSP00000361998:Q76H	Q	-	3	2	TAF7L	100434462	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.793000	0.04589	-0.640000	0.05495	-0.340000	0.08031	CAG	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
NME8	51314	hgsc.bcm.edu	37	7	37934146	37934146	+	Missense_Mutation	SNP	T	T	C	rs56128139|rs386712272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:37934146T>C	ENST00000199447.4	+	16	1850	c.1478T>C	c.(1477-1479)aTa>aCa	p.I493T	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Missense_Mutation_p.I493T	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	493	NDK 3.		I -> T (in dbSNP:rs56128139). {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)										CCTGAGCAAATAGAGAAAATT	0.303													T|||	790	0.157748	0.0151	0.2291	5008	,	,		17475	0.1359		0.3419	False		,,,				2504	0.1329				p.I493T		Atlas-SNP	.											.	.	.	.	0			c.T1478C						PASS	.	T	THR/ILE	5,4401		2,1,2200	61.0	63.0	63.0		1478	1.1	0.0	7	dbSNP_129	63	77,8521		12,53,4234	yes	missense	TXNDC3	NM_016616.4	89	14,54,6434	CC,CT,TT		0.8956,0.1135,0.6306	benign	493/589	37934146	82,12922	2203	4299	6502	SO:0001583	missense	51314	exon16			AGCAAATAGAGAA	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.1478T>C	7.37:g.37934146T>C	ENSP00000199447:p.Ile493Thr	Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	226	226	1	NM_016616	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	343	0.15705128205128205	11	0.022357723577235773	73	0.20165745856353592	70	0.12237762237762238	189	0.24934036939313983	T	6.406	0.442939	0.12164	0.001135	0.008956	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.43688	0.94;0.94	4.05	1.11	0.20524	.	0.568879	0.14595	N	0.310022	T	0.00012	0.0000	N	0.11201	0.11	0.80722	P	0.0	B	0.14438	0.01	B	0.23275	0.045	T	0.26360	-1.0105	9	0.52906	T	0.07	-4.655	5.9615	0.19303	0.0:0.6617:0.0:0.3383	rs56128139;rs62001871	493	Q8N427	TXND3_HUMAN	T	493	ENSP00000199447:I493T;ENSP00000397063:I493T	ENSP00000199447:I493T	I	+	2	0	TXNDC3	37900671	0.012000	0.17670	0.000000	0.03702	0.002000	0.02628	0.098000	0.15189	0.265000	0.21872	-0.621000	0.04028	ATA	T|0.761;C|0.239	0.239	strong		0.303	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616	
RBMX	27316	hgsc.bcm.edu	37	X	135958696	135958696	+	Silent	SNP	T	T	C	rs112800567		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135958696T>C	ENST00000320676.7	-	5	661	c.507A>G	c.(505-507)ggA>ggG	p.G169G	RBMX_ENST00000562646.1_Silent_p.G169G|RBMX_ENST00000431446.3_Intron|RBMX_ENST00000565438.1_Silent_p.G41G|RBMX_ENST00000570135.1_Silent_p.G34G|SNORD61_ENST00000384252.1_RNA|RBMX_ENST00000496459.2_5'Flank	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	169					cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					TGCGAACTGGTCCTGAAGGTG	0.458																																					p.G169G		Atlas-SNP	.											.	RBMX	149	.	0			c.A507G						PASS	.						119.0	105.0	110.0					X																	135958696		2203	4300	6503	SO:0001819	synonymous_variant	27316	exon5			AACTGGTCCTGAA		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.507A>G	X.37:g.135958696T>C		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	340	41	0.120588	NM_002139	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Silent	SNP	ENST00000320676.7	37	CCDS14661.1																																																																																			.	.	weak		0.458	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
MEFV	4210	hgsc.bcm.edu	37	16	3297073	3297073	+	Silent	SNP	A	A	G	rs224206	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3297073A>G	ENST00000219596.1	-	5	1569	c.1530T>C	c.(1528-1530)gaT>gaC	p.D510D	MEFV_ENST00000339854.4_Silent_p.D330D|MEFV_ENST00000536379.1_Silent_p.D299D|MEFV_ENST00000541159.1_Silent_p.D299D	NM_000243.2	NP_000234.1	O15553	MEFV_HUMAN	Mediterranean fever	510	Required for homotrimerization and induction of pyroptosomes.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of macrophage inflammatory protein 1 alpha production (GO:0071641)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)	cell projection (GO:0042995)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|breast(5)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(19)|ovary(3)|prostate(1)|skin(6)	50						CAATCAGCGCATCGAGCAGGG	0.597													G|||	3321	0.663139	0.6936	0.6297	5008	,	,		20097	0.6518		0.5577	False		,,,				2504	0.7658				p.D510D		Atlas-SNP	.											.	MEFV	170	.	0			c.T1530C						PASS	.	G	,	2994,1400	460.5+/-352.6	1013,968,216	147.0	126.0	133.0		1530,897	-10.6	0.0	16	dbSNP_79	133	4597,4003	554.3+/-386.5	1255,2087,958	no	coding-synonymous,coding-synonymous	MEFV	NM_000243.2,NM_001198536.1	,	2268,3055,1174	GG,GA,AA		46.5465,31.8616,41.5807	,	510/782,299/446	3297073	7591,5403	2197	4300	6497	SO:0001819	synonymous_variant	4210	exon5			CAGCGCATCGAGC	AF018080	CCDS10498.1, CCDS55981.1	16p13.3	2014-09-17			ENSG00000103313	ENSG00000103313		"""Tripartite motif containing / Tripartite motif containing"""	6998	protein-coding gene	gene with protein product	"""pyrin"""	608107		MEF		9288094	Standard	NM_000243		Approved	FMF, TRIM20	uc002cun.1	O15553	OTTHUMG00000129324	ENST00000219596.1:c.1530T>C	16.37:g.3297073A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_000243	D3DUC0|F5H0Q3|Q3MJ84|Q96PN4|Q96PN5	Silent	SNP	ENST00000219596.1	37	CCDS10498.1																																																																																			A|0.391;G|0.609	0.609	strong		0.597	MEFV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251464.1	NM_000243	
CCDC157	550631	hgsc.bcm.edu	37	22	30765502	30765502	+	Silent	SNP	G	G	A	rs5749080	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:30765502G>A	ENST00000405659.1	+	4	1039	c.330G>A	c.(328-330)gcG>gcA	p.A110A	CCDC157_ENST00000338306.3_Silent_p.A110A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	110										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CACAGGCTGCGGGGCCCTGCA	0.652													G|||	768	0.153355	0.1324	0.1571	5008	,	,		17743	0.1458		0.2545	False		,,,				2504	0.0828				p.A110A		Atlas-SNP	.											.	CCDC157	86	.	0			c.G330A						PASS	.	G		680,3726	280.2+/-275.2	69,542,1592	41.0	40.0	41.0		330	-10.6	0.0	22	dbSNP_114	41	2211,6389	372.6+/-336.7	289,1633,2378	no	coding-synonymous	CCDC157	NM_001017437.2		358,2175,3970	AA,AG,GG		25.7093,15.4335,22.2282		110/753	30765502	2891,10115	2203	4300	6503	SO:0001819	synonymous_variant	550631	exon4			GGCTGCGGGGCCC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.330G>A	22.37:g.30765502G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			A|0.198;C|0.000;G|0.802	0.198	strong		0.652	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
PDXDC1	23042	hgsc.bcm.edu	37	16	15095675	15095675	+	Silent	SNP	C	C	A	rs9921162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15095675C>A	ENST00000396410.4	+	4	301	c.204C>A	c.(202-204)ctC>ctA	p.L68L	PDXDC1_ENST00000455313.2_Silent_p.L68L|PDXDC1_ENST00000447912.2_Intron|PDXDC1_ENST00000535621.2_Silent_p.L68L|PDXDC1_ENST00000450288.2_Intron|PDXDC1_ENST00000569715.1_Intron|PDXDC1_ENST00000325823.7_Silent_p.L53L|PDXDC1_ENST00000563679.1_Silent_p.L86L	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	68					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTCAGAATCTCATGCATGGAG	0.483																																					p.L68L		Atlas-SNP	.											PDXDC1,NS,carcinoma,0,1	PDXDC1	59	1	0			c.C204A						scavenged	.	A		909,3485		55,799,1343	60.0	58.0	58.0		204	-1.9	1.0	16	dbSNP_119	58	1467,7133		37,1393,2870	no	coding-synonymous	PDXDC1	NM_015027.2		92,2192,4213	AA,AC,CC		17.0581,20.6873,18.2854		68/789	15095675	2376,10618	2197	4300	6497	SO:0001819	synonymous_variant	23042	exon4			GAATCTCATGCAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.204C>A	16.37:g.15095675C>A		Somatic	141	1	0.0070922		WXS	Illumina HiSeq	Phase_I	177	91	0.514124	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Silent	SNP	ENST00000396410.4	37	CCDS32393.1																																																																																			C|0.773;A|0.227	0.227	strong		0.483	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
SCN1A	6323	hgsc.bcm.edu	37	2	166897864	166897864	+	Silent	SNP	A	A	G	rs6432860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:166897864A>G	ENST00000303395.4	-	13	2291	c.2292T>C	c.(2290-2292)gtT>gtC	p.V764V	SCN1A_ENST00000375405.3_Silent_p.V753V|SCN1A_ENST00000409050.1_Silent_p.V736V|AC010127.3_ENST00000595268.1_RNA|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000423058.2_Silent_p.V764V|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	764					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGTCCATCACAACCAGGTTGA	0.408													G|||	3951	0.788938	0.848	0.7594	5008	,	,		16810	0.8909		0.6909	False		,,,				2504	0.726				p.V764V		Atlas-SNP	.											SCN1A,rectum,carcinoma,-1,1	SCN1A	641	1	0			c.T2292C						PASS	.	G	,,,	3598,808	324.5+/-298.6	1462,674,67	116.0	111.0	113.0		2292,2208,2292,2259	-5.3	0.8	2	dbSNP_116	113	5810,2790	442.0+/-360.0	1950,1910,440	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	3412,2584,507	GG,GA,AA		32.4419,18.3386,27.6642	,,,	764/2010,736/1982,764/2010,753/1999	166897864	9408,3598	2203	4300	6503	SO:0001819	synonymous_variant	6323	exon13			CATCACAACCAGG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2292T>C	2.37:g.166897864A>G		Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	111	109	0.981982	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			.	.	none		0.408	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
WSB2	55884	hgsc.bcm.edu	37	12	118481134	118481134	+	Silent	SNP	C	C	T	rs199804263	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:118481134C>T	ENST00000315436.3	-	3	372	c.231G>A	c.(229-231)acG>acA	p.T77T	WSB2_ENST00000535496.1_Silent_p.T79T|WSB2_ENST00000544233.1_Intron|WSB2_ENST00000441406.2_Silent_p.T94T|WSB2_ENST00000542304.1_5'UTR|WSB2_ENST00000536738.1_5'UTR	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	77					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)			p.T77T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CCCGCCCTTTCGTCTCATTTT	0.522													C|||	2	0.000399361	0.0008	0.0	5008	,	,		19423	0.001		0.0	False		,,,				2504	0.0				p.T77T		Atlas-SNP	.											WSB2,colon,carcinoma,0,1	WSB2	32	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G231A						scavenged	.						126.0	134.0	131.0					12																	118481134		2203	4300	6503	SO:0001819	synonymous_variant	55884	exon3			CCCTTTCGTCTCA	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"""WD repeat domain containing"""	19222	protein-coding gene	gene with protein product			"""WD repeat and SOCS box-containing 2"""			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.231G>A	12.37:g.118481134C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	106	2	0.0188679	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	37	CCDS9186.1																																																																																			C|1.000;T|0.000	0.000	strong		0.522	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639	
MRPL45	84311	hgsc.bcm.edu	37	17	36453208	36453208	+	Missense_Mutation	SNP	T	T	C	rs11559007	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36453208T>C	ENST00000312513.5	+	1	220	c.59T>C	c.(58-60)tTt>tCt	p.F20S		NM_032351.4	NP_115727.4	Q9BRJ2	RM45_HUMAN	mitochondrial ribosomal protein L45	20						mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	13	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GGCTGGTGGTTTCGGCAGGTG	0.572													C|||	1310	0.261581	0.7458	0.1585	5008	,	,		18189	0.0		0.1541	False		,,,				2504	0.0603				p.F20S		Atlas-SNP	.											MRPL45,NS,carcinoma,0,1	MRPL45	27	1	0			c.T59C						scavenged	.	C	SER/PHE	641,743		287,67,338	50.0	81.0	72.0		59	3.3	1.0	17	dbSNP_134	72	225,2957		27,171,1393	no	missense	MRPL45	NM_032351.4	155	314,238,1731	CC,CT,TT		7.071,46.315,18.9663	benign	20/307	36453208	866,3700	692	1591	2283	SO:0001583	missense	84311	exon1			GGTGGTTTCGGCA	BC006235	CCDS11326.1, CCDS74047.1	17q21.2	2014-05-06			ENSG00000174100	ENSG00000278845		"""Mitochondrial ribosomal proteins / large subunits"""	16651	protein-coding gene	gene with protein product		611850				11551941, 12706105	Standard	XM_006725366		Approved	MGC11321	uc002hpy.3	Q9BRJ2	OTTHUMG00000188489	ENST00000312513.5:c.59T>C	17.37:g.36453208T>C	ENSP00000308901:p.Phe20Ser	Somatic	67	3	0.0447761		WXS	Illumina HiSeq	Phase_I	90	89	0.988889	NM_032351	A1L436|Q6ZMJ5	Missense_Mutation	SNP	ENST00000312513.5	37	CCDS11326.1	478	0.21886446886446886	267	0.5426829268292683	68	0.1878453038674033	35	0.06118881118881119	108	0.1424802110817942	C	2.695	-0.272197	0.05716	0.46315	0.07071	ENSG00000174100	ENST00000312513	T	0.25749	1.78	4.28	3.31	0.37934	.	.	.	.	.	T	0.00012	0.0000	N	0.00138	-2.015	0.48511	P	3.370000000000317E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.40664	-0.9551	8	0.29301	T	0.29	.	6.6711	0.23068	0.0:0.783:0.0:0.217	.	20	Q9BRJ2	RM45_HUMAN	S	20	ENSP00000308901:F20S	ENSP00000308901:F20S	F	+	2	0	MRPL45	.	0.996000	0.38824	0.988000	0.46212	0.947000	0.59692	0.684000	0.25364	0.565000	0.29255	-0.282000	0.10007	TTT	T|0.781;C|0.219	0.219	strong		0.572	MRPL45-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256792.3	NM_032351	
LRRN1	57633	hgsc.bcm.edu	37	3	3886721	3886721	+	Silent	SNP	C	C	A	rs3749350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:3886721C>A	ENST00000319331.3	+	2	1157	c.396C>A	c.(394-396)acC>acA	p.T132T	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	132						integral component of membrane (GO:0016021)				NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|skin(1)|urinary_tract(2)	26				Epithelial(13;0.000886)|all cancers(10;0.0032)|OV - Ovarian serous cystadenocarcinoma(96;0.00608)|STAD - Stomach adenocarcinoma(44;0.0617)		ATCAGATTACCGAGATGACTG	0.428													A|||	1458	0.291134	0.4047	0.2565	5008	,	,		20305	0.4067		0.1074	False		,,,				2504	0.2321				p.T132T		Atlas-SNP	.											.	LRRN1	82	.	0			c.C396A						PASS	.	A		1584,2822	658.8+/-400.5	301,982,920	70.0	73.0	72.0		396	-11.3	0.0	3	dbSNP_107	72	1090,7510	768.9+/-407.6	67,956,3277	no	coding-synonymous	LRRN1	NM_020873.5		368,1938,4197	AA,AC,CC		12.6744,35.951,20.5597		132/717	3886721	2674,10332	2203	4300	6503	SO:0001819	synonymous_variant	57633	exon2			GATTACCGAGATG	AB040930	CCDS33685.1	3p26.2	2013-01-11			ENSG00000175928	ENSG00000175928		"""Immunoglobulin superfamily / I-set domain containing"""	20980	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 3"""					10819331	Standard	NM_020873		Approved	FIGLER3	uc003bpt.4	Q6UXK5	OTTHUMG00000154934	ENST00000319331.3:c.396C>A	3.37:g.3886721C>A		Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	108	47	0.435185	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Silent	SNP	ENST00000319331.3	37	CCDS33685.1																																																																																			C|0.758;A|0.242	0.242	strong		0.428	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873	
TP73	7161	hgsc.bcm.edu	37	1	3645894	3645894	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:3645894C>T	ENST00000378295.4	+	10	1233	c.1078C>T	c.(1078-1080)Cga>Tga	p.R360*	TP73_ENST00000378280.1_Nonsense_Mutation_p.R311*|TP73_ENST00000378285.1_Nonsense_Mutation_p.R311*|TP73_ENST00000604074.1_Nonsense_Mutation_p.R360*|TP73_ENST00000603362.1_Nonsense_Mutation_p.R360*|TP73_ENST00000357733.3_Nonsense_Mutation_p.R360*|TP73_ENST00000604479.1_Nonsense_Mutation_p.R360*|TP73_ENST00000378290.4_Nonsense_Mutation_p.R289*|TP73_ENST00000346387.4_Nonsense_Mutation_p.R360*|TP73_ENST00000378288.4_Nonsense_Mutation_p.R311*|TP73_ENST00000354437.4_Nonsense_Mutation_p.R360*	NM_001204185.1|NM_005427.3	NP_001191114.1|NP_005418.1	O15350	P73_HUMAN	tumor protein p73	360	Interaction with HIPK2.|Oligomerization. {ECO:0000255}.				activation of MAPK activity (GO:0000187)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|cerebrospinal fluid secretion (GO:0033326)|digestive tract morphogenesis (GO:0048546)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|hippocampus development (GO:0021766)|inflammatory response (GO:0006954)|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)|kidney development (GO:0001822)|mismatch repair (GO:0006298)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell size (GO:0045793)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902167)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein tetramerization (GO:0051262)|release of cytochrome c from mitochondria (GO:0001836)|response to gamma radiation (GO:0010332)|response to organonitrogen compound (GO:0010243)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.R360*(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|lung(8)|ovary(1)|prostate(1)	20	all_cancers(77;0.0395)|Ovarian(185;0.0634)|Lung NSC(156;0.188)|all_lung(157;0.198)	all_epithelial(116;7.42e-17)|all_lung(118;1.86e-06)|Lung NSC(185;0.000163)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Lung SC(97;0.109)|Ovarian(437;0.127)		Epithelial(90;5.57e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.87e-22)|GBM - Glioblastoma multiforme(42;5.72e-16)|Colorectal(212;2.22e-05)|COAD - Colon adenocarcinoma(227;8.48e-05)|Kidney(185;0.000539)|BRCA - Breast invasive adenocarcinoma(365;0.000868)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.00751)|Lung(427;0.226)		TGCTCAGGTGCGAGGCCGGGA	0.632																																					p.R360X		Atlas-SNP	.											TP73,NS,carcinoma,0,1	TP73	54	1	1	Substitution - Nonsense(1)	lung(1)	c.C1078T						scavenged	.						76.0	72.0	73.0					1																	3645894		2203	4300	6503	SO:0001587	stop_gained	7161	exon10			CAGGTGCGAGGCC	AB055065	CCDS49.1, CCDS44049.1, CCDS44050.1, CCDS44051.1, CCDS55566.1, CCDS55567.1, CCDS55568.1, CCDS55569.1, CCDS59965.1	1p36.3	2010-06-15			ENSG00000078900	ENSG00000078900			12003	protein-coding gene	gene with protein product		601990				9296498, 9288759	Standard	NM_001204186		Approved	P73	uc001akp.3	O15350	OTTHUMG00000000610	ENST00000378295.4:c.1078C>T	1.37:g.3645894C>T	ENSP00000367545:p.Arg360*	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	111	3	0.027027	NM_005427	B7Z7J4|B7Z8Z1|B7Z9C1|C9J521|O15351|Q17RN8|Q5TBV5|Q5TBV6|Q8NHW9|Q8TDY5|Q8TDY6|Q9NTK8	Nonsense_Mutation	SNP	ENST00000378295.4	37	CCDS49.1	.	.	.	.	.	.	.	.	.	.	C	36	5.815355	0.96982	.	.	ENSG00000078900	ENST00000378295;ENST00000354437;ENST00000357733;ENST00000346387;ENST00000378288;ENST00000378285;ENST00000378280;ENST00000378290	.	.	.	4.3	4.3	0.51218	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.7696	15.7852	0.78297	0.0:1.0:0.0:0.0	.	.	.	.	X	360;360;360;360;311;311;311;289	.	ENSP00000340740:R360X	R	+	1	2	TP73	3635754	1.000000	0.71417	1.000000	0.80357	0.604000	0.37047	3.839000	0.55835	1.939000	0.56221	0.550000	0.68814	CGA	.	.	none		0.632	TP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001468.4	NM_005427	
ICK	22858	hgsc.bcm.edu	37	6	52878637	52878637	+	Silent	SNP	T	T	C	rs2297211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:52878637T>C	ENST00000350082.5	-	9	1321	c.975A>G	c.(973-975)ccA>ccG	p.P325P	ICK_ENST00000356971.3_Silent_p.P325P	NM_014920.3	NP_055735.1	Q9UPZ9	ICK_HUMAN	intestinal cell (MAK-like) kinase	325					intracellular signal transduction (GO:0035556)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.P325P(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(3)|stomach(1)	31	Lung NSC(77;0.103)					GCTTGGCTGGTGGCTGGGCAG	0.542													C|||	1243	0.248203	0.4599	0.1686	5008	,	,		15154	0.1121		0.2744	False		,,,				2504	0.1319				p.P325P		Atlas-SNP	.											ICK,NS,carcinoma,0,1	ICK	62	1	1	Substitution - coding silent(1)	stomach(1)	c.A975G						scavenged	.	C	,	1852,2554	633.7+/-396.1	381,1090,732	124.0	107.0	113.0		975,975	1.6	1.0	6	dbSNP_100	113	2244,6356	708.6+/-405.7	317,1610,2373	no	coding-synonymous,coding-synonymous	ICK	NM_014920.3,NM_016513.4	,	698,2700,3105	CC,CT,TT		26.093,42.0336,31.4932	,	325/633,325/633	52878637	4096,8910	2203	4300	6503	SO:0001819	synonymous_variant	22858	exon10			GGCTGGTGGCTGG	AB023153	CCDS4949.1	6p12.3-p11.2	2008-02-05			ENSG00000112144	ENSG00000112144			21219	protein-coding gene	gene with protein product		612325				12103360	Standard	NM_014920		Approved	MRK, LCK2, KIAA0936, MGC46090	uc003pbi.2	Q9UPZ9	OTTHUMG00000014870	ENST00000350082.5:c.975A>G	6.37:g.52878637T>C		Somatic	184	2	0.0108696		WXS	Illumina HiSeq	Phase_I	202	188	0.930693	NM_016513	A7MD41|O75985|Q5THL2|Q8IYH8|Q9BX17|Q9NYX3	Silent	SNP	ENST00000350082.5	37	CCDS4949.1																																																																																			T|0.711;C|0.289	0.289	strong		0.542	ICK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040952.1	NM_016513	
SEC16B	89866	hgsc.bcm.edu	37	1	177902388	177902388	+	Silent	SNP	G	G	A	rs3813647	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:177902388G>A	ENST00000308284.6	-	22	2873	c.2784C>T	c.(2782-2784)ccC>ccT	p.P928P	SEC16B_ENST00000495165.1_5'UTR|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	928					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CGTCTCCAGCGGGGGATGCGT	0.592													G|||	464	0.0926518	0.093	0.111	5008	,	,		17865	0.0268		0.172	False		,,,				2504	0.0654				p.P928P		Atlas-SNP	.											.	SEC16B	92	.	0			c.C2784T						PASS	.	G		434,3510		25,384,1563	29.0	36.0	34.0		2784	1.8	0.2	1	dbSNP_107	34	1498,6858		129,1240,2809	no	coding-synonymous	SEC16B	NM_033127.2		154,1624,4372	AA,AG,GG		17.9272,11.0041,15.7073		928/1061	177902388	1932,10368	1972	4178	6150	SO:0001819	synonymous_variant	89866	exon22			TCCAGCGGGGGAT	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.2784C>T	1.37:g.177902388G>A		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	103	34	0.330097	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Silent	SNP	ENST00000308284.6	37	CCDS44281.1																																																																																			G|0.878;A|0.122	0.122	strong		0.592	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
HSPB8	26353	hgsc.bcm.edu	37	12	119617350	119617350	+	Missense_Mutation	SNP	G	G	T	rs55826713		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:119617350G>T	ENST00000281938.2	+	1	904	c.233G>T	c.(232-234)aGg>aTg	p.R78M	RP11-64B16.4_ENST00000535921.1_RNA	NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	78			R -> M (in dbSNP:rs55826713). {ECO:0000269|PubMed:17344846}.		cell death (GO:0008219)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	14	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCCACCGCCAGGTTTGGGGTG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		14955	0.0		0.001	False		,,,				2504	0.0				p.R78M		Atlas-SNP	.											.	HSPB8	45	.	0			c.G233T						PASS	.	G	MET/ARG	0,4404		0,0,2202	26.0	31.0	30.0		233	4.4	0.9	12	dbSNP_129	30	8,8592	6.4+/-24.3	0,8,4292	no	missense	HSPB8	NM_014365.2	91	0,8,6494	TT,TG,GG		0.093,0.0,0.0615	benign	78/197	119617350	8,12996	2202	4300	6502	SO:0001583	missense	26353	exon1			CCGCCAGGTTTGG	AF191017	CCDS9189.1	12q24.23	2014-09-17	2004-04-23					"""Heat shock proteins / HSPB"""	30171	protein-coding gene	gene with protein product		608014	"""heat shock 27kDa protein 8"""			10833516, 11085516	Standard	NM_014365		Approved	H11, E2IG1, HSP22, HspB8	uc001txb.3	Q9UJY1		ENST00000281938.2:c.233G>T	12.37:g.119617350G>T	ENSP00000281938:p.Arg78Met	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Missense_Mutation	SNP	ENST00000281938.2	37	CCDS9189.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476262	0.44044	0.0	9.3E-4	ENSG00000152137	ENST00000281938	D	0.87650	-2.28	4.42	4.42	0.53409	HSP20-like chaperone (1);	0.414383	0.24285	N	0.039876	D	0.83968	0.5369	L	0.53249	1.67	0.47183	D	0.999349	P	0.44578	0.838	B	0.41691	0.364	D	0.83545	0.0098	9	.	.	.	.	12.7024	0.57041	0.0823:0.0:0.9177:0.0	rs55826713	78	Q9UJY1	HSPB8_HUMAN	M	78	ENSP00000281938:R78M	.	R	+	2	0	HSPB8	118101733	1.000000	0.71417	0.938000	0.37757	0.256000	0.26092	5.565000	0.67365	2.294000	0.77228	0.563000	0.77884	AGG	G|0.999;T|0.001	0.001	strong		0.672	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365	
ABCC6	368	hgsc.bcm.edu	37	16	16263662	16263662	+	Missense_Mutation	SNP	G	G	T	rs74315152|rs61340537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:16263662G>T	ENST00000205557.7	-	22	2865	c.2836C>A	c.(2836-2838)Ctc>Atc	p.L946I		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	946			L -> I (in dbSNP:rs61340537). {ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	TAGAGGCAGAGGGGGGTGCCC	0.662													G|||	54	0.0107827	0.0008	0.0202	5008	,	,		16733	0.0		0.0219	False		,,,				2504	0.0174				p.L946I		Atlas-SNP	.											.	ABCC6	110	.	0			c.C2836A	GRCh37	CM034642	ABCC6	M	rs61340537	PASS	.	G	ILE/LEU	20,4332		0,20,2156	20.0	17.0	18.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2836	-1.1	0.0	16	dbSNP_129	18	131,8445		0,131,4157	yes	missense	ABCC6	NM_001171.5	5	0,151,6313	TT,TG,GG		1.5275,0.4596,1.168	benign	946/1504	16263662	151,12777	2176	4288	6464	SO:0001583	missense	368	exon22			GGCAGAGGGGGGT	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.2836C>A	16.37:g.16263662G>T	ENSP00000205557:p.Leu946Ile	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	100	41	0.41	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	27	0.012362637362637362	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	19	0.025065963060686015	G	0.010	-1.770641	0.00645	0.004596	0.015275	ENSG00000091262	ENST00000205557	D	0.95103	-3.61	5.0	-1.06	0.10002	ABC transporter, transmembrane domain, type 1 (1);	1.097620	0.07160	N	0.850486	T	0.72946	0.3524	N	0.25957	0.775	0.31769	N	0.632287	B	0.26363	0.147	B	0.24541	0.054	T	0.74583	-0.3617	10	0.20046	T	0.44	.	3.4997	0.07668	0.0871:0.3098:0.3635:0.2396	rs61340537	946	O95255	MRP6_HUMAN	I	946	ENSP00000205557:L946I	ENSP00000205557:L946I	L	-	1	0	ABCC6	16171163	0.001000	0.12720	0.015000	0.15790	0.057000	0.15508	-0.218000	0.09240	0.121000	0.18284	-0.904000	0.02843	CTC	G|0.989;T|0.011	0.011	strong		0.662	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
UST	10090	hgsc.bcm.edu	37	6	149395197	149395197	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:149395197T>A	ENST00000367463.4	+	8	1269	c.1166T>A	c.(1165-1167)aTc>aAc	p.I389N	UST_ENST00000466695.1_3'UTR	NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	389					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		GAGGAGCCAATCGACGATGAA	0.483																																					p.I389N		Atlas-SNP	.											UST,right_upper_lobe,carcinoma,0,2	UST	42	2	0			c.T1166A						PASS	.						95.0	95.0	95.0					6																	149395197		2203	4300	6503	SO:0001583	missense	10090	exon8			AGCCAATCGACGA	AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"""Sulfotransferases, membrane-bound"""	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.1166T>A	6.37:g.149395197T>A	ENSP00000356433:p.Ile389Asn	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	86	14	0.162791	NM_005715	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	37	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.835824	0.50951	.	.	ENSG00000111962	ENST00000367463	T	0.53857	0.6	5.3	5.3	0.74995	.	0.184757	0.48767	D	0.000180	T	0.18467	0.0443	N	0.14661	0.345	0.40188	D	0.977379	P	0.35982	0.531	B	0.27796	0.083	T	0.20974	-1.0259	10	0.72032	D	0.01	-6.0612	10.7296	0.46089	0.0:0.0747:0.0:0.9252	.	389	Q9Y2C2	UST_HUMAN	N	389	ENSP00000356433:I389N	ENSP00000356433:I389N	I	+	2	0	UST	149436890	0.272000	0.24172	0.034000	0.17996	0.910000	0.53928	2.116000	0.41930	2.127000	0.65507	0.460000	0.39030	ATC	.	.	none		0.483	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715	
OR2G2	81470	hgsc.bcm.edu	37	1	247752367	247752367	+	Missense_Mutation	SNP	A	A	G	rs869111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:247752367A>G	ENST00000320065.1	+	1	706	c.706A>G	c.(706-708)Agg>Ggg	p.R236G	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	236			R -> G (in dbSNP:rs869111).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			GTCAGCTACCAGGAGACAGAA	0.483													G|||	1947	0.388778	0.3116	0.3444	5008	,	,		19344	0.4444		0.5159	False		,,,				2504	0.3364				p.R236G		Atlas-SNP	.											.	OR2G2	88	.	0			c.A706G						PASS	.	G	GLY/ARG	1377,3029	690.5+/-405.3	220,937,1046	146.0	134.0	138.0		706	4.3	0.0	1	dbSNP_86	138	4290,4310	577.6+/-390.6	1074,2142,1084	yes	missense	OR2G2	NM_001001915.1	125	1294,3079,2130	GG,GA,AA		49.8837,31.2528,43.5722	benign	236/318	247752367	5667,7339	2203	4300	6503	SO:0001583	missense	81470	exon1			GCTACCAGGAGAC	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.706A>G	1.37:g.247752367A>G	ENSP00000326349:p.Arg236Gly	Somatic	254	0	0		WXS	Illumina HiSeq	Phase_I	210	104	0.495238	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	928	0.4249084249084249	145	0.29471544715447157	143	0.39502762430939226	252	0.4405594405594406	388	0.5118733509234829	G	0.006	-2.051580	0.00394	0.312528	0.498837	ENSG00000177489	ENST00000320065	T	0.00013	9.24	4.29	4.29	0.51040	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36972	N	0.002316	T	0.00012	0.0000	N	0.00012	-2.96	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	9	0.02654	T	1	.	10.1869	0.43002	0.0989:0.0:0.9011:0.0	rs869111;rs17318855;rs52811386;rs58487812;rs869111	236	Q8NGZ5	OR2G2_HUMAN	G	236	ENSP00000326349:R236G	ENSP00000326349:R236G	R	+	1	2	OR2G2	245818990	0.290000	0.24343	0.038000	0.18304	0.008000	0.06430	0.583000	0.23849	1.023000	0.39654	-0.186000	0.12905	AGG	A|0.573;G|0.426	0.426	strong		0.483	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
LRRC18	474354	hgsc.bcm.edu	37	10	50121721	50121721	+	Silent	SNP	G	G	A	rs35986885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50121721G>A	ENST00000374160.3	-	1	556	c.480C>T	c.(478-480)ccC>ccT	p.P160P	LRRC18_ENST00000298124.3_Silent_p.P160P|RP11-523O18.7_ENST00000430438.1_RNA|WDFY4_ENST00000325239.5_Intron|WDFY4_ENST00000413659.2_Intron	NM_001006939.3	NP_001006940.3	Q8N456	LRC18_HUMAN	leucine rich repeat containing 18	160						cytoplasm (GO:0005737)				NS(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	18						AGATGCTCACGGGGATGTTGT	0.542													G|||	587	0.117212	0.1604	0.0951	5008	,	,		20476	0.002		0.1441	False		,,,				2504	0.1656				p.P160P		Atlas-SNP	.											LRRC18,scalp,malignant_melanoma,-2,1	LRRC18	52	1	0			c.C480T						PASS	.	G	,	692,3714	287.8+/-279.5	51,590,1562	98.0	93.0	95.0		480,	-2.0	0.0	10	dbSNP_126	95	1202,7398	242.2+/-272.3	105,992,3203	no	coding-synonymous,intron	WDFY4,LRRC18	NM_001006939.3,NM_020945.1	,	156,1582,4765	AA,AG,GG		13.9767,15.7059,14.5625	,	160/262,	50121721	1894,11112	2203	4300	6503	SO:0001819	synonymous_variant	474354	exon1			GCTCACGGGGATG	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.480C>T	10.37:g.50121721G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	104	54	0.519231	NM_001006939	Q6UY02	Silent	SNP	ENST00000374160.3	37	CCDS31197.1																																																																																			G|0.859;A|0.141	0.141	strong		0.542	LRRC18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047964.1	NM_001006939	
BAIAP3	8938	hgsc.bcm.edu	37	16	1389196	1389196	+	Missense_Mutation	SNP	C	C	T	rs61749061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1389196C>T	ENST00000324385.5	+	4	514	c.356C>T	c.(355-357)cCg>cTg	p.P119L	BAIAP3_ENST00000426824.3_Missense_Mutation_p.P84L|BAIAP3_ENST00000562208.1_Missense_Mutation_p.P84L|BAIAP3_ENST00000397489.1_Missense_Mutation_p.P101L|BAIAP3_ENST00000397488.2_Missense_Mutation_p.P101L|BAIAP3_ENST00000421665.2_Missense_Mutation_p.P84L|BAIAP3_ENST00000568887.1_Missense_Mutation_p.P84L	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	119					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)				CCAGCACCCCCGGAGCCTGTG	0.706													c|||	233	0.0465256	0.0825	0.0216	5008	,	,		12713	0.0317		0.0139	False		,,,				2504	0.0644				p.P119L		Atlas-SNP	.											.	BAIAP3	88	.	0			c.C356T						PASS	.	T	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	193,3991		0,193,1899	5.0	7.0	6.0		251,251,251,251,356	0.2	0.0	16	dbSNP_129	6	85,8193		0,85,4054	no	missense,missense,missense,missense,missense	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	98,98,98,98,98	0,278,5953	TT,TC,CC		1.0268,4.6128,2.2308	benign,benign,benign,benign,benign	84/1117,84/1153,84/1130,84/1125,119/1188	1389196	278,12184	2092	4139	6231	SO:0001583	missense	8938	exon4			CACCCCCGGAGCC	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.356C>T	16.37:g.1389196C>T	ENSP00000324510:p.Pro119Leu	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	42	22	0.52381	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	64	0.029304029304029304	39	0.07926829268292683	6	0.016574585635359115	13	0.022727272727272728	6	0.0079155672823219	c	9.675	1.147667	0.21288	0.046128	0.010268	ENSG00000007516	ENST00000426824;ENST00000397488;ENST00000324385;ENST00000397489;ENST00000421665	T;T;T;T;T	0.72051	-0.61;-0.55;-0.62;-0.55;-0.61	3.74	0.219	0.15274	.	1.064640	0.07299	N	0.873819	T	0.04452	0.0122	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.33494	0.103;0.002;0.103;0.414;0.226	B;B;B;B;B	0.17098	0.011;0.001;0.011;0.017;0.011	T	0.03278	-1.1053	10	0.31617	T	0.26	-0.0293	3.6148	0.08073	0.1667:0.5664:0.1634:0.1035	rs61749061	84;136;84;119;101	E7EUB9;B4DGA2;B4DIK3;O94812;A2A2B2	.;.;.;BAIP3_HUMAN;.	L	84;101;119;101;84	ENSP00000407242:P84L;ENSP00000380625:P101L;ENSP00000324510:P119L;ENSP00000380626:P101L;ENSP00000409533:P84L	ENSP00000324510:P119L	P	+	2	0	BAIAP3	1329197	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	-0.552000	0.06020	0.341000	0.23771	-0.336000	0.08194	CCG	C|0.970;T|0.030	0.030	strong		0.706	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
HCFC1	3054	hgsc.bcm.edu	37	X	153219665	153219665	+	Silent	SNP	C	C	T	rs2071133	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153219665C>T	ENST00000310441.7	-	17	5151	c.4185G>A	c.(4183-4185)gcG>gcA	p.A1395A	HCFC1_ENST00000369984.4_Silent_p.A1395A|HCFC1_ENST00000354233.3_Silent_p.A1326A	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	1395					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CGCTGGGTGCCGCCGCCACCT	0.677													C|||	1522	0.403179	0.0658	0.3573	3775	,	,		11919	0.5913		0.1441	False		,,,				2504	0.456				p.A1395A		Atlas-SNP	.											.	HCFC1	284	.	0			c.G4185A						PASS	.	C		394,3329		16,302,60,1259,509	23.0	29.0	27.0		4185	-11.6	0.0	X	dbSNP_96	27	1167,5429		69,691,338,1625,1488	no	coding-synonymous	HCFC1	NM_005334.2		85,993,398,2884,1997	TT,TC,T,CC,C		17.6925,10.5829,15.1274		1395/2036	153219665	1561,8758	2146	4211	6357	SO:0001819	synonymous_variant	3054	exon17			GGGTGCCGCCGCC		CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.4185G>A	X.37:g.153219665C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	41	41	1	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1																																																																																			C|0.603;T|0.397	0.397	strong		0.677	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334	
MUC5B	727897	hgsc.bcm.edu	37	11	1272858	1272858	+	Silent	SNP	C	C	T	rs4963059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1272858C>T	ENST00000529681.1	+	31	14806	c.14748C>T	c.(14746-14748)ttC>ttT	p.F4916F	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.F4919F	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4916	Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TGCCAACCTTCAGCGTGTCCA	0.642													C|||	1697	0.338858	0.2141	0.33	5008	,	,		19521	0.6052		0.2853	False		,,,				2504	0.2945				p.F4916F		Atlas-SNP	.											.	MUC5B	473	.	0			c.C14748T						PASS	.	C		833,3505		82,669,1418	58.0	68.0	65.0		14748	0.6	0.0	11	dbSNP_111	65	2509,6001		390,1729,2136	no	coding-synonymous	MUC5B	NM_002458.2		472,2398,3554	TT,TC,CC		29.483,19.2024,26.0118		4916/5763	1272858	3342,9506	2169	4255	6424	SO:0001819	synonymous_variant	727897	exon31			AACCTTCAGCGTG	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.14748C>T	11.37:g.1272858C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.663;T|0.337	0.337	strong		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
LMTK3	114783	hgsc.bcm.edu	37	19	49004551	49004551	+	Silent	SNP	C	C	T	rs55953841	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49004551C>T	ENST00000600059.1	-	9	1217	c.990G>A	c.(988-990)gaG>gaA	p.E330E	LMTK3_ENST00000270238.3_Silent_p.E359E			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	330	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		AGATGTTGCTCTCGCGGCTCT	0.662													c|||	37	0.00738818	0.003	0.0173	5008	,	,		1033	0.0		0.0119	False		,,,				2504	0.0092				p.E359E		Atlas-SNP	.											.	LMTK3	125	.	0			c.G1077A						PASS	.	C		12,3818		0,12,1903	49.0	56.0	54.0		1077	2.0	1.0	19	dbSNP_129	54	117,8123		0,117,4003	no	coding-synonymous	LMTK3	NM_001080434.1		0,129,5906	TT,TC,CC		1.4199,0.3133,1.0688		359/1490	49004551	129,11941	1915	4120	6035	SO:0001819	synonymous_variant	114783	exon10			GTTGCTCTCGCGG	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.990G>A	19.37:g.49004551C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	95	46	0.484211	NM_001080434	Q4G0U1	Silent	SNP	ENST00000600059.1	37																																																																																				C|0.988;T|0.012	0.012	strong		0.662	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	
GAB4	128954	hgsc.bcm.edu	37	22	17468918	17468918	+	Missense_Mutation	SNP	C	C	A	rs144427521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:17468918C>A	ENST00000400588.1	-	3	725	c.618G>T	c.(616-618)tgG>tgT	p.W206C	GAB4_ENST00000523144.1_Intron	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	206										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)				CAGGGATGGGCCAGGTGGGCG	0.647													C|||	64	0.0127796	0.0008	0.0086	5008	,	,		14101	0.0		0.0308	False		,,,				2504	0.0266				p.W206C		Atlas-SNP	.											.	GAB4	95	.	0			c.G618T						PASS	.	C	CYS/TRP	16,4090		0,16,2037	28.0	36.0	34.0		618	1.9	0.3	22	dbSNP_134	34	266,8162		6,254,3954	yes	missense	GAB4	NM_001037814.1	215	6,270,5991	AA,AC,CC		3.1561,0.3897,2.2499	probably-damaging	206/575	17468918	282,12252	2053	4214	6267	SO:0001583	missense	128954	exon3			GATGGGCCAGGTG	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.618G>T	22.37:g.17468918C>A	ENSP00000383431:p.Trp206Cys	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	110	59	0.536364	NM_001037814		Missense_Mutation	SNP	ENST00000400588.1	37	CCDS42976.1	30	0.013736263736263736	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	23	0.030343007915567283	C	6.755	0.508088	0.12883	0.003897	0.031561	ENSG00000215568	ENST00000400588	T	0.29655	1.56	1.9	1.9	0.25705	.	0.258041	0.30840	N	0.008779	T	0.05777	0.0151	N	0.22421	0.69	0.30860	N	0.73359	P	0.43094	0.799	B	0.39027	0.288	T	0.05666	-1.0871	10	0.38643	T	0.18	.	7.3004	0.26418	0.0:1.0:0.0:0.0	.	206	Q2WGN9	GAB4_HUMAN	C	206	ENSP00000383431:W206C	ENSP00000383431:W206C	W	-	3	0	GAB4	15848918	1.000000	0.71417	0.259000	0.24435	0.012000	0.07955	2.044000	0.41241	1.360000	0.45960	0.313000	0.20887	TGG	C|0.983;A|0.017	0.017	strong		0.647	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629936	32629936	+	Missense_Mutation	SNP	C	C	T	rs1049107	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629936C>T	ENST00000399082.3	-	2	243	c.199G>A	c.(199-201)Ggc>Agc	p.G67S	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.G157S|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.G157S|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.G157S|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.G157S|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	157	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TTGATCTGGCCTGGATAGAAA	0.562									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1048	0.209265	0.2216	0.1484	5008	,	,		12445	0.2431		0.1958	False		,,,				2504	0.2147				p.G157S	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G469A						PASS	.	C	SER/GLY	838,3180		119,600,1290	30.0	29.0	29.0		469	-1.2	0.1	6	dbSNP_86	29	1469,6921		227,1015,2953	no	missense	HLA-DQB1	NM_002123.4	56	346,1615,4243	TT,TC,CC		17.5089,20.8561,18.5928	benign	157/262	32629936	2307,10101	2009	4195	6204	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	TCTGGCCTGGATA		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.199G>A	6.37:g.32629936C>T	ENSP00000382032:p.Gly67Ser	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	96	71	0.739583	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		450	0.20604395604395603	119	0.241869918699187	70	0.19337016574585636	90	0.15734265734265734	171	0.22559366754617413	.	5.815	0.334684	0.11013	0.208561	0.175089	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.02737	4.18;4.18;4.18;4.18;4.18	4.52	-1.24	0.09435	.	1.197420	0.06155	N	0.674887	T	0.00666	0.0022	N	0.10664	0.02	0.80722	P	0.0	B;B;B;B	0.13145	0.006;0.003;0.003;0.007	B;B;B;B	0.27887	0.05;0.05;0.05;0.084	T	0.49643	-0.8918	9	0.72032	D	0.01	.	6.026	0.19656	0.0:0.4008:0.1358:0.4634	rs1049107;rs16870483	157;122;157;157	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	S	67;157;157;157;157;93	ENSP00000382032:G67S;ENSP00000382029:G157S;ENSP00000364080:G157S;ENSP00000407332:G157S;ENSP00000382034:G157S	ENSP00000364080:G157S	G	-	1	0	HLA-DQB1	32737914	0.000000	0.05858	0.059000	0.19551	0.264000	0.26372	-0.490000	0.06482	-0.179000	0.10654	0.313000	0.20887	GGC	C|0.812;T|0.188	0.188	strong		0.562	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
TMEM86A	144110	hgsc.bcm.edu	37	11	18723210	18723210	+	Missense_Mutation	SNP	C	C	T	rs144559255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18723210C>T	ENST00000280734.2	+	3	473	c.377C>T	c.(376-378)gCg>gTg	p.A126V	TMEM86A_ENST00000527002.1_3'UTR	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	126						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						GTGATGGCAGCGCTGTCGGGC	0.602													C|||	46	0.0091853	0.0	0.0173	5008	,	,		17494	0.0		0.0249	False		,,,				2504	0.0092				p.A126V		Atlas-SNP	.											TMEM86A,caecum,carcinoma,-1,1	TMEM86A	29	1	0			c.C377T						PASS	.	C	VAL/ALA	23,4375	29.0+/-57.7	0,23,2176	97.0	85.0	89.0		377	2.6	1.0	11	dbSNP_134	89	155,8431	75.1+/-137.7	1,153,4139	yes	missense	TMEM86A	NM_153347.1	64	1,176,6315	TT,TC,CC		1.8053,0.523,1.3709	benign	126/241	18723210	178,12806	2199	4293	6492	SO:0001583	missense	144110	exon3			TGGCAGCGCTGTC	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4		ENST00000280734.2:c.377C>T	11.37:g.18723210C>T	ENSP00000280734:p.Ala126Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	112	52	0.464286	NM_153347	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	0.322	-0.961477	0.02249	0.00523	0.018053	ENSG00000151117	ENST00000535380;ENST00000280734	T	0.20069	2.1	5.03	2.64	0.31445	.	0.537430	0.19759	N	0.106710	T	0.02848	0.0085	N	0.02403	-0.565	0.19300	N	0.999975	B	0.02656	0.0	B	0.04013	0.001	T	0.39482	-0.9612	10	0.06891	T	0.86	-2.3684	8.0781	0.30729	0.0:0.0707:0.1359:0.7934	.	126	Q8N2M4	TM86A_HUMAN	V	126	ENSP00000280734:A126V	ENSP00000280734:A126V	A	+	2	0	TMEM86A	18679786	0.054000	0.20591	0.984000	0.44739	0.608000	0.37181	2.275000	0.43399	0.477000	0.27464	-1.402000	0.01139	GCG	C|0.987;T|0.013	0.013	strong		0.602	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
IDO2	169355	hgsc.bcm.edu	37	8	39873053	39873053	+	Missense_Mutation	SNP	G	G	A	rs72632016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39873053G>A	ENST00000389060.4	+	10	1156	c.1156G>A	c.(1156-1158)Gca>Aca	p.A386T	IDO2_ENST00000502986.2_Missense_Mutation_p.A399T|IDO2_ENST00000343295.4_3'UTR			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	386					cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	heme binding (GO:0020037)|indoleamine 2,3-dioxygenase activity (GO:0033754)|metal ion binding (GO:0046872)|tryptophan 2,3-dioxygenase activity (GO:0004833)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	18						AGGTGGAACCGCAGTTATGAG	0.542													G|||	403	0.0804712	0.1884	0.0634	5008	,	,		20875	0.0119		0.0527	False		,,,				2504	0.046				p.A399T		Atlas-SNP	.											.	IDO2	78	.	0			c.G1195A						PASS	.	G	THR/ALA	714,3226		64,586,1320	115.0	113.0	114.0		1195	1.1	0.0	8	dbSNP_130	114	431,7867		11,409,3729	yes	missense	IDO2	NM_194294.2	58	75,995,5049	AA,AG,GG		5.194,18.1218,9.3561	benign	399/421	39873053	1145,11093	1970	4149	6119	SO:0001583	missense	169355	exon11			GGAACCGCAGTTA	AK128691		8p11.21	2012-04-19	2009-01-07	2009-01-07	ENSG00000188676	ENSG00000188676			27269	protein-coding gene	gene with protein product		612129	"""indoleamine-pyrrole 2,3 dioxygenase-like 1"""	INDOL1			Standard	NM_194294		Approved		uc010lwy.1	Q6ZQW0	OTTHUMG00000141271	ENST00000389060.4:c.1156G>A	8.37:g.39873053G>A	ENSP00000426447:p.Ala386Thr	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	117	53	0.452991	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		168	0.07692307692307693	94	0.1910569105691057	25	0.06906077348066299	9	0.015734265734265736	40	0.052770448548812667	G	2.319	-0.355979	0.05138	0.181218	0.05194	ENSG00000188676	ENST00000502986;ENST00000389060	T;T	0.46063	0.88;0.88	6.03	1.1	0.20463	.	0.717381	0.14006	N	0.347782	T	0.00039	0.0001	L	0.58810	1.83	0.80722	P	0.0	B;B	0.18013	0.025;0.021	B;B	0.12837	0.003;0.008	T	0.14839	-1.0458	8	.	.	.	.	1.1148	0.01712	0.1961:0.2391:0.3413:0.2235	.	399;386	F5H5G0;Q6ZQW0	.;I23O2_HUMAN	T	399;386	ENSP00000443432:A399T;ENSP00000426447:A386T	.	A	+	1	0	IDO2	39992210	0.000000	0.05858	0.000000	0.03702	0.087000	0.18053	-0.312000	0.08113	-0.080000	0.12685	0.655000	0.94253	GCA	G|0.929;A|0.071	0.071	strong		0.542	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294	
ERCC2	2068	hgsc.bcm.edu	37	19	45855524	45855524	+	Silent	SNP	G	G	A	rs1052555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45855524G>A	ENST00000391945.4	-	22	2210	c.2133C>T	c.(2131-2133)gaC>gaT	p.D711D	ERCC2_ENST00000391944.3_Silent_p.D633D	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	711					7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		GGACACCCTCGTCCACGGTCA	0.672			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	913	0.182308	0.0726	0.1527	5008	,	,		18987	0.0625		0.337	False		,,,				2504	0.316				p.D711D		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	ERCC2_ENST00000391945,trunk,malignant_melanoma,-2,1	ERCC2	78	1	0			c.C2133T	GRCh37	CM052870	ERCC2	M	rs1052555	PASS	.	G		500,3906	234.2+/-247.1	32,436,1735	96.0	72.0	80.0		2133	-10.0	0.3	19	dbSNP_86	80	2865,5735	451.6+/-362.7	512,1841,1947	no	coding-synonymous	ERCC2	NM_000400.3		544,2277,3682	AA,AG,GG		33.314,11.3482,25.8727		711/761	45855524	3365,9641	2203	4300	6503	SO:0001819	synonymous_variant	2068	exon22	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACCCTCGTCCACG		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.2133C>T	19.37:g.45855524G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	136	62	0.455882	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Silent	SNP	ENST00000391945.4	37	CCDS33049.1																																																																																			G|0.767;N|0.002	.	strong		0.672	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
C10orf10	11067	hgsc.bcm.edu	37	10	45473432	45473432	+	Missense_Mutation	SNP	C	C	T	rs149255069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45473432C>T	ENST00000298295.3	-	2	264	c.47G>A	c.(46-48)cGg>cAg	p.R16Q	RASSF4_ENST00000374417.2_Intron|RASSF4_ENST00000340258.5_Intron|C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000334940.6_Intron|RASSF4_ENST00000472561.1_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	16						mitochondrion (GO:0005739)				lung(1)	1						CGTGGTCTCCCGAATTGTGGG	0.607													C|||	5	0.000998403	0.0038	0.0	5008	,	,		16956	0.0		0.0	False		,,,				2504	0.0				p.R16Q		Atlas-SNP	.											.	C10orf10	6	.	0			c.G47A						PASS	.	C	GLN/ARG,	11,4393		0,11,2191	44.0	50.0	48.0		47,	2.7	1.0	10	dbSNP_134	48	0,8596		0,0,4298	yes	missense,intron	C10orf10,RASSF4	NM_007021.3,NM_032023.3	43,	0,11,6489	TT,TC,CC		0.0,0.2498,0.0846	benign,	16/213,	45473432	11,12989	2202	4298	6500	SO:0001583	missense	11067	exon2			GTCTCCCGAATTG	AB022718	CCDS7210.1	10q11.21	2014-07-31			ENSG00000165507	ENSG00000165507			23355	protein-coding gene	gene with protein product	"""decidual protein induced by progesterone"", ""fasting induced"", ""fat-specific expressed gene"""	611309				24530860, 19937567, 16123073	Standard	NM_007021		Approved	DEPP, FIG, Fseg	uc001jbr.4	Q9NTK1	OTTHUMG00000018063	ENST00000298295.3:c.47G>A	10.37:g.45473432C>T	ENSP00000298295:p.Arg16Gln	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	91	36	0.395604	NM_007021	B2R6A1|O94997|Q5T735|Q76MX8	Missense_Mutation	SNP	ENST00000298295.3	37	CCDS7210.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249917	0.80024	0.002498	0.0	ENSG00000165507	ENST00000298295;ENST00000432283;ENST00000448778	T;T	0.51574	0.73;0.7	5.63	2.73	0.32206	.	0.512064	0.16368	N	0.217438	T	0.22627	0.0546	N	0.12746	0.255	0.28270	N	0.924451	B	0.32800	0.385	B	0.21546	0.035	T	0.10064	-1.0646	10	0.37606	T	0.19	-18.3777	5.2281	0.15406	0.1628:0.6657:0.0:0.1715	.	16	Q9NTK1	DEPP_HUMAN	Q	16	ENSP00000298295:R16Q;ENSP00000414494:R16Q	ENSP00000298295:R16Q	R	-	2	0	C10orf10	44793438	0.989000	0.36119	0.982000	0.44146	0.994000	0.84299	0.343000	0.19944	0.302000	0.22762	0.561000	0.74099	CGG	C|0.999;T|0.001	0.001	strong		0.607	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021	
ODF3	113746	hgsc.bcm.edu	37	11	199492	199492	+	Missense_Mutation	SNP	G	G	A	rs72878024	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:199492G>A	ENST00000325113.4	+	6	975	c.658G>A	c.(658-660)Gcc>Acc	p.A220T	ODF3_ENST00000525282.1_Intron|BET1L_ENST00000410108.1_Intron	NM_053280.3	NP_444510.2	Q96PU9	ODF3A_HUMAN	outer dense fiber of sperm tails 3	220					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	outer dense fiber (GO:0001520)				biliary_tract(1)|breast(1)|kidney(1)|large_intestine(2)|ovary(1)|prostate(2)|skin(1)	9		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;3.95e-27)|Epithelial(43;2.66e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.55e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGACCAGGCGCCCACAGCCC	0.642													G|||	207	0.0413339	0.0287	0.0548	5008	,	,		15611	0.0079		0.0805	False		,,,				2504	0.0429				p.A220T		Atlas-SNP	.											.	ODF3	27	.	0			c.G658A						PASS	.	G	THR/ALA	211,4153		4,203,1975	17.0	16.0	16.0		658	5.4	1.0	11	dbSNP_130	16	613,7889		17,579,3655	yes	missense	ODF3	NM_053280.3	58	21,782,5630	AA,AG,GG		7.2101,4.835,6.4045	probably-damaging	220/255	199492	824,12042	2182	4251	6433	SO:0001583	missense	113746	exon6			CCAGGCGCCCACA	AB067774	CCDS7688.1, CCDS65981.1	11p15.5	2010-04-23			ENSG00000177947	ENSG00000177947			19905	protein-coding gene	gene with protein product	"""cancer/testis antigen 135"""	608356				11870087	Standard	NM_001286136		Approved	SHIPPO1, hSHIPPO, CT135	uc001lob.3	Q96PU9	OTTHUMG00000119073	ENST00000325113.4:c.658G>A	11.37:g.199492G>A	ENSP00000325868:p.Ala220Thr	Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	35	18	0.514286	NM_053280	B7ZLT0|Q69YX0	Missense_Mutation	SNP	ENST00000325113.4	37	CCDS7688.1	105	0.04807692307692308	13	0.026422764227642278	19	0.052486187845303865	5	0.008741258741258742	68	0.08970976253298153	G	21.7	4.188959	0.78789	0.04835	0.072101	ENSG00000177947	ENST00000325113	T	0.37235	1.21	5.41	5.41	0.78517	.	0.000000	0.48767	D	0.000164	T	0.03178	0.0093	L	0.48218	1.51	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.00294	-1.1840	10	0.34782	T	0.22	-41.0965	14.6916	0.69091	0.0:0.0:1.0:0.0	.	220	Q96PU9	ODF3A_HUMAN	T	220	ENSP00000325868:A220T	ENSP00000325868:A220T	A	+	1	0	ODF3	189492	0.991000	0.36638	1.000000	0.80357	0.941000	0.58515	4.443000	0.59994	2.519000	0.84933	0.561000	0.74099	GCC	G|0.940;A|0.060	0.060	strong		0.642	ODF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239287.1		
OR5T1	390155	hgsc.bcm.edu	37	11	56043604	56043604	+	Missense_Mutation	SNP	A	A	G	rs12360890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56043604A>G	ENST00000313033.2	+	1	576	c.490A>G	c.(490-492)Agc>Ggc	p.S164G		NM_001004745.1	NP_001004745.1	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T, member 1	164			S -> G (in dbSNP:rs12360890).			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(5)|kidney(1)|large_intestine(2)|lung(27)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	43	Esophageal squamous(21;0.00448)					CTATGTTGCTAGCATTTTACA	0.438													N|||	2210	0.441294	0.1649	0.5821	5008	,	,		22277	0.6478		0.3708	False		,,,				2504	0.5746				p.S164G		Atlas-SNP	.											.	OR5T1	95	.	0			c.A490G						PASS	.	G	GLY/SER	887,3515	740.4+/-411.2	94,699,1408	270.0	230.0	243.0		490	0.4	0.0	11	dbSNP_120	243	3190,5402	651.3+/-400.8	610,1970,1716	no	missense	OR5T1	NM_001004745.1	56	704,2669,3124	GG,GA,AA		37.1276,20.1499,31.376	benign	164/327	56043604	4077,8917	2201	4296	6497	SO:0001583	missense	390155	exon1			GTTGCTAGCATTT	AB065962	CCDS31525.1	11q11	2012-08-09		2004-03-10	ENSG00000181698	ENSG00000181698		"""GPCR / Class A : Olfactory receptors"""	14821	protein-coding gene	gene with protein product				OR5T1P			Standard	NM_001004745		Approved		uc001nio.1	Q8NG75	OTTHUMG00000166853	ENST00000313033.2:c.490A>G	11.37:g.56043604A>G	ENSP00000323612:p.Ser164Gly	Somatic	317	0	0		WXS	Illumina HiSeq	Phase_I	348	189	0.543103	NM_001004745	B2RNM9	Missense_Mutation	SNP	ENST00000313033.2	37	CCDS31525.1	873	0.39972527472527475	62	0.12601626016260162	201	0.5552486187845304	350	0.6118881118881119	260	0.34300791556728233	G	0.011	-1.717357	0.00706	0.201499	0.371276	ENSG00000181698	ENST00000313033	T	0.40476	1.03	3.44	0.435	0.16544	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	N	0.000089	T	0.00012	0.0000	N	0.00178	-1.915	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40850	-0.9541	9	0.02654	T	1	.	3.9789	0.09486	0.3848:0.0:0.4522:0.163	rs12360890;rs52827403;rs58144141;rs12360890	164	Q8NG75	OR5T1_HUMAN	G	164	ENSP00000323612:S164G	ENSP00000323612:S164G	S	+	1	0	OR5T1	55800180	0.064000	0.20934	0.001000	0.08648	0.019000	0.09904	1.817000	0.39002	-0.007000	0.14345	-0.405000	0.06341	AGC	A|0.653;G|0.347	0.347	strong		0.438	OR5T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391600.1	NM_001004745	
IL9R	3581	hgsc.bcm.edu	37	X	155239827	155239827	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:155239827A>G	ENST00000244174.5	+	9	1498	c.1319A>G	c.(1318-1320)aAc>aGc	p.N440S	IL9R_ENST00000424344.3_Missense_Mutation_p.N419S|IL9R_ENST00000369423.2_3'UTR|IL9R_ENST00000540897.1_3'UTR	NM_002186.2	NP_002177.2	Q01113	IL9R_HUMAN	interleukin 9 receptor	440	Poly-Asn.				cell proliferation (GO:0008283)|positive regulation of cell growth (GO:0030307)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	interleukin-9 receptor activity (GO:0004919)	p.N440S(1)		NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(12)|upper_aerodigestive_tract(1)	23	all_cancers(53;1.86e-17)|all_epithelial(53;2.71e-11)|all_lung(58;1.84e-07)|Lung NSC(58;5.62e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					agcagcaacaacaacaACTAC	0.642													a|||	523	0.104433	0.0136	0.0605	5008	,	,		13185	0.0298		0.1471	False		,,,				2504	0.2914				p.N440S		Atlas-SNP	.											.	IL9R	73	.	1	Substitution - Missense(1)	kidney(1)	c.A1319G						PASS	.						7.0	13.0	11.0					X																	155239827		2072	4217	6289	SO:0001583	missense	3581	exon9			GCAACAACAACAA	M84747	CCDS14771.4, CCDS59180.1	Xq28 and Yq12	2008-02-05			ENSG00000124334	ENSG00000124334		"""Pseudoautosomal regions / PAR2"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6030	protein-coding gene	gene with protein product		300007				1376929, 8666384	Standard	NM_002186		Approved	CD129	uc004fnv.1	Q01113	OTTHUMG00000022720	ENST00000244174.5:c.1319A>G	X.37:g.155239827A>G	ENSP00000244174:p.Asn440Ser	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	140	124	0.885714	NM_002186	B9ZVT0|Q14634|Q8WWU1|Q96TF0	Missense_Mutation	SNP	ENST00000244174.5	37	CCDS14771.4	.	.	.	.	.	.	.	.	.	.	a	0	-2.858724	0.00065	.	.	ENSG00000124334	ENST00000244174;ENST00000424344	T;T	0.07908	3.16;3.15	.	.	.	.	12.144800	0.00166	N	0.000006	T	0.03827	0.0108	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.33317	-0.9873	5	0.10636	T	0.68	.	.	.	.	.	440	Q01113	IL9R_HUMAN	S	440;419	ENSP00000244174:N440S;ENSP00000388918:N419S	ENSP00000244174:N440S	N	+	2	0	IL9R	154893021	0.004000	0.15560	0.007000	0.13788	0.007000	0.05969	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	AAC	.	.	weak		0.642	IL9R-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058981.1	NM_002186	
PDE3A	5139	hgsc.bcm.edu	37	12	20522252	20522252	+	Missense_Mutation	SNP	G	G	A	rs12305038	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:20522252G>A	ENST00000359062.3	+	1	74	c.34G>A	c.(34-36)Gac>Aac	p.D12N	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	12			D -> N (in dbSNP:rs12305038). {ECO:0000269|PubMed:8695850}.		blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	ACGAGTCAGGGACAAGCCCGT	0.726													G|||	1671	0.333666	0.5061	0.219	5008	,	,		10216	0.3056		0.3091	False		,,,				2504	0.2362				p.D12N		Atlas-SNP	.											PDE3A,NS,carcinoma,0,1	PDE3A	184	1	0			c.G34A						PASS	.	G	ASN/ASP	1554,2186		396,762,712	4.0	7.0	6.0		34	3.9	0.0	12	dbSNP_120	6	1943,5269		352,1239,2015	yes	missense	PDE3A	NM_000921.4	23	748,2001,2727	AA,AG,GG		26.9412,41.5508,31.9302	possibly-damaging	12/1142	20522252	3497,7455	1870	3606	5476	SO:0001583	missense	5139	exon1			GTCAGGGACAAGC		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.34G>A	12.37:g.20522252G>A	ENSP00000351957:p.Asp12Asn	Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	13	13	1	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	726	0.3324175824175824	269	0.5467479674796748	81	0.22375690607734808	140	0.24475524475524477	236	0.3113456464379947	G	9.693	1.152350	0.21371	0.415508	0.269412	ENSG00000172572	ENST00000359062	T	0.62232	0.04	3.9	3.9	0.45041	.	4.361550	0.00166	N	0.000016	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.23058	0.079	B	0.20955	0.032	T	0.33059	-0.9883	9	0.33940	T	0.23	.	11.4979	0.50419	0.0:0.1835:0.8165:0.0	rs12305038;rs12305038	12	Q14432	PDE3A_HUMAN	N	12	ENSP00000351957:D12N	ENSP00000351957:D12N	D	+	1	0	PDE3A	20413519	0.164000	0.22935	0.032000	0.17829	0.460000	0.32559	3.310000	0.51911	1.999000	0.58509	0.484000	0.47621	GAC	G|0.663;A|0.337	0.337	strong		0.726	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
IBA57	200205	hgsc.bcm.edu	37	1	228362682	228362682	+	Missense_Mutation	SNP	G	G	A	rs2298014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228362682G>A	ENST00000366711.3	+	2	633	c.631G>A	c.(631-633)Ggc>Agc	p.G211S	IBA57_ENST00000484749.1_3'UTR|IBA57_ENST00000546123.1_Missense_Mutation_p.G18S	NM_001010867.2	NP_001010867.1	Q5T440	CAF17_HUMAN	IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)	211			G -> S (in dbSNP:rs2298014).		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						GGTGCCCGGGGGCCGGCTCGG	0.687													G|||	786	0.156949	0.0371	0.2666	5008	,	,		15317	0.0546		0.329	False		,,,				2504	0.1697				p.G211S		Atlas-SNP	.											.	IBA57	22	.	0			c.G631A						PASS	.	G	SER/GLY	373,4015		17,339,1838	16.0	21.0	20.0		631	1.7	0.0	1	dbSNP_100	20	2959,5621		527,1905,1858	yes	missense	IBA57	NM_001010867.2	56	544,2244,3696	AA,AG,GG		34.4872,8.5005,25.694	benign	211/357	228362682	3332,9636	2194	4290	6484	SO:0001583	missense	200205	exon2			CCCGGGGGCCGGC	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.631G>A	1.37:g.228362682G>A	ENSP00000355672:p.Gly211Ser	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	29	18	0.62069	NM_001010867		Missense_Mutation	SNP	ENST00000366711.3	37	CCDS31046.1	402	0.18406593406593408	16	0.032520325203252036	105	0.2900552486187845	32	0.055944055944055944	249	0.32849604221635886	G	9.295	1.051708	0.19827	0.085005	0.344872	ENSG00000181873	ENST00000366711;ENST00000546123	T;T	0.74632	-0.86;0.99	4.89	1.69	0.24217	Glycine cleavage T-protein, N-terminal (1);	0.415911	0.28119	N	0.016538	T	0.00012	0.0000	L	0.41824	1.3	0.80722	P	0.0	B	0.10296	0.003	B	0.12156	0.007	T	0.12863	-1.0531	9	0.07325	T	0.83	-8.7236	3.9045	0.09176	0.2665:0.0:0.5435:0.19	rs2298014	211	Q5T440	CAF17_HUMAN	S	211;18	ENSP00000355672:G211S;ENSP00000437347:G18S	ENSP00000355672:G211S	G	+	1	0	IBA57	226429305	0.003000	0.15002	0.000000	0.03702	0.010000	0.07245	0.534000	0.23098	0.622000	0.30249	0.655000	0.94253	GGC	G|0.783;A|0.217	0.217	strong		0.687	IBA57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095980.1	NM_001010867	
SLC12A5	57468	hgsc.bcm.edu	37	20	44680424	44680424	+	Silent	SNP	G	G	T	rs79522550	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:44680424G>T	ENST00000454036.2	+	18	2410	c.2361G>T	c.(2359-2361)ggG>ggT	p.G787G	SLC12A5_ENST00000243964.3_Silent_p.G764G	NM_001134771.1	NP_001128243.1	Q9H2X9	S12A5_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 5	787					cellular ion homeostasis (GO:0006873)|chloride transmembrane transport (GO:1902476)|ion transport (GO:0006811)|learning (GO:0007612)|multicellular organism growth (GO:0035264)|potassium ion transport (GO:0006813)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|thermosensory behavior (GO:0040040)|transmembrane transport (GO:0055085)|transport (GO:0006810)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(1)|lung(38)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	80		Myeloproliferative disorder(115;0.0122)			Bumetanide(DB00887)|Potassium Chloride(DB00761)	GGGGCCTCGGGGGGCTGCAGC	0.597													G|||	24	0.00479233	0.0	0.0029	5008	,	,		13704	0.0		0.0169	False		,,,				2504	0.0051				p.G787G		Atlas-SNP	.											.	SLC12A5	181	.	0			c.G2361T						PASS	.	G	,	13,4393	21.2+/-45.6	0,13,2190	76.0	76.0	76.0		2361,2292	0.9	1.0	20	dbSNP_132	76	124,8476	64.2+/-126.4	0,124,4176	no	coding-synonymous,coding-synonymous	SLC12A5	NM_001134771.1,NM_020708.4	,	0,137,6366	TT,TG,GG		1.4419,0.2951,1.0534	,	787/1140,764/1117	44680424	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	57468	exon18			CCTCGGGGGGCTG	AB033002	CCDS13391.1, CCDS46610.1	20q13.12	2013-05-22	2010-04-20		ENSG00000124140	ENSG00000124140		"""Solute carriers"""	13818	protein-coding gene	gene with protein product		606726					Standard	NM_020708		Approved	KIAA1176, KCC2	uc010zxl.1	Q9H2X9	OTTHUMG00000032638	ENST00000454036.2:c.2361G>T	20.37:g.44680424G>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	72	36	0.5	NM_001134771	A2RTX2|Q5VZ41|Q9H4Z0|Q9ULP4	Silent	SNP	ENST00000454036.2	37	CCDS46610.1																																																																																			G|0.989;T|0.011	0.011	strong		0.597	SLC12A5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471538.1		
WDR18	57418	hgsc.bcm.edu	37	19	991129	991129	+	Missense_Mutation	SNP	G	G	A	rs11538683	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:991129G>A	ENST00000251289.5	+	6	813	c.790G>A	c.(790-792)Gtc>Atc	p.V264I	WDR18_ENST00000587001.2_Missense_Mutation_p.V264I	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	264			V -> I (in dbSNP:rs11538683).		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)		CGCCGGGAAGGTCTTCAAAGG	0.682													.|||	772	0.154153	0.0514	0.1081	5008	,	,		11617	0.1964		0.1252	False		,,,				2504	0.3119				p.V264I		Atlas-SNP	.											.	WDR18	20	.	0			c.G790A						PASS	.	G	ILE/VAL	346,4014		14,318,1848	47.0	38.0	41.0		790	1.3	1.0	19	dbSNP_120	41	973,7579		62,849,3365	yes	missense	WDR18	NM_024100.3	29	76,1167,5213	AA,AG,GG		11.3775,7.9358,10.2153	benign	264/433	991129	1319,11593	2180	4276	6456	SO:0001583	missense	57418	exon6			GGGAAGGTCTTCA		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.790G>A	19.37:g.991129G>A	ENSP00000251289:p.Val264Ile	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	38	18	0.473684	NM_024100	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	37	CCDS12051.1	275	0.1259157509157509	28	0.056910569105691054	40	0.11049723756906077	108	0.1888111888111888	99	0.13060686015831136	G	9.743	1.165481	0.21538	0.079358	0.113775	ENSG00000065268	ENST00000251289	T	0.61040	0.14	3.62	1.26	0.21427	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.310461	0.28612	N	0.014740	T	0.00039	0.0001	N	0.17082	0.46	0.24767	P	0.99289647	B	0.21606	0.058	B	0.24269	0.052	T	0.08827	-1.0703	9	0.21540	T	0.41	.	7.2122	0.25939	0.1982:0.1575:0.6442:0.0	rs11538683	264	Q9BV38	WDR18_HUMAN	I	264	ENSP00000251289:V264I	ENSP00000251289:V264I	V	+	1	0	WDR18	942129	1.000000	0.71417	0.998000	0.56505	0.883000	0.51084	1.639000	0.37176	0.734000	0.32515	0.591000	0.81541	GTC	G|0.891;A|0.109	0.109	strong		0.682	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
SEC23A	10484	hgsc.bcm.edu	37	14	39545199	39545199	+	Silent	SNP	A	A	G	rs17108797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:39545199A>G	ENST00000307712.6	-	8	1444	c.927T>C	c.(925-927)ccT>ccC	p.P309P	SEC23A_ENST00000536508.1_Silent_p.P183P|SEC23A_ENST00000537403.1_Silent_p.P107P|SEC23A_ENST00000545328.2_Silent_p.P280P	NM_006364.2	NP_006355.2	Q15436	SC23A_HUMAN	Sec23 homolog A (S. cerevisiae)	309					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			kidney(2)|large_intestine(3)|liver(1)|lung(11)|ovary(4)|pancreas(1)|upper_aerodigestive_tract(1)	23	Hepatocellular(127;0.213)		Lung(238;0.00047)|LUAD - Lung adenocarcinoma(48;0.000565)	GBM - Glioblastoma multiforme(112;0.0151)		ACGATCTTATAGGTGTCTTCA	0.398													A|||	108	0.0215655	0.0	0.0303	5008	,	,		15386	0.0		0.0656	False		,,,				2504	0.0215				p.P309P		Atlas-SNP	.											.	SEC23A	73	.	0			c.T927C						PASS	.	A		59,4347	54.9+/-90.9	0,59,2144	96.0	85.0	89.0		927	-1.0	1.0	14	dbSNP_123	89	557,8043	152.1+/-206.7	9,539,3752	no	coding-synonymous	SEC23A	NM_006364.2		9,598,5896	GG,GA,AA		6.4767,1.3391,4.7363		309/766	39545199	616,12390	2203	4300	6503	SO:0001819	synonymous_variant	10484	exon8			TCTTATAGGTGTC	X97064	CCDS9668.1	14q21.1	2008-05-14	2001-11-28		ENSG00000100934	ENSG00000100934			10701	protein-coding gene	gene with protein product		610511	"""Sec23 (S. cerevisiae) homolog A"""			8898360, 10329445	Standard	NM_006364		Approved		uc001wup.1	Q15436	OTTHUMG00000028812	ENST00000307712.6:c.927T>C	14.37:g.39545199A>G		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	149	78	0.52349	NM_006364	B2R5P4|B3KXI2|Q8NE16	Silent	SNP	ENST00000307712.6	37	CCDS9668.1																																																																																			A|0.959;G|0.041	0.041	strong		0.398	SEC23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276728.2		
FOXK1	221937	hgsc.bcm.edu	37	7	4800907	4800907	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4800907G>A	ENST00000328914.4	+	8	1909	c.1909G>A	c.(1909-1911)Ggc>Agc	p.G637S	FOXK1_ENST00000446823.1_Missense_Mutation_p.G474S	NM_001037165.1	NP_001032242.1			forkhead box K1											breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CAGTTTAGCCGGCAACGCTTA	0.622																																					p.G637S		Atlas-SNP	.											.	FOXK1	64	.	0			c.G1909A						PASS	.						38.0	36.0	36.0					7																	4800907		2203	4300	6503	SO:0001583	missense	221937	exon8			TTAGCCGGCAACG	BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1909G>A	7.37:g.4800907G>A	ENSP00000328720:p.Gly637Ser	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	34	22	0.647059	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	37	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	G	8.542	0.873550	0.17322	.	.	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.95622	-3.47;-3.76	5.46	1.56	0.23342	.	0.476626	0.23481	N	0.047714	D	0.88418	0.6431	L	0.36672	1.1	0.33097	D	0.538647	B;B	0.29037	0.231;0.135	B;B	0.21151	0.022;0.033	T	0.80924	-0.1165	10	0.06891	T	0.86	.	7.8657	0.29535	0.3396:0.0:0.6604:0.0	.	637;474	P85037;P85037-2	FOXK1_HUMAN;.	S	474;393;637;520	ENSP00000394442:G474S;ENSP00000328720:G637S	ENSP00000328720:G637S	G	+	1	0	FOXK1	4767433	0.665000	0.27466	0.071000	0.20095	0.015000	0.08874	1.058000	0.30504	0.008000	0.14787	0.655000	0.94253	GGC	.	.	none		0.622	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
PXDNL	137902	hgsc.bcm.edu	37	8	52321966	52321966	+	Missense_Mutation	SNP	G	G	A	rs201280324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:52321966G>A	ENST00000356297.4	-	17	2318	c.2218C>T	c.(2218-2220)Ccc>Tcc	p.P740S	PXDNL_ENST00000543296.1_Missense_Mutation_p.P740S	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	740					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)				CCCCACGTGGGCTGCTGCAGG	0.701													G|||	7	0.00139776	0.0	0.0014	5008	,	,		8293	0.0		0.005	False		,,,				2504	0.001				p.P740S		Atlas-SNP	.											PXDNL_ENST00000356297,NS,carcinoma,+2,1	PXDNL	414	1	0			c.C2218T						scavenged	.	G	SER/PRO	8,4010		0,8,2001	17.0	19.0	18.0		2218	1.8	0.0	8		18	58,8254		0,58,4098	yes	missense	PXDNL	NM_144651.4	74	0,66,6099	AA,AG,GG		0.6978,0.1991,0.5353	probably-damaging	740/1464	52321966	66,12264	2009	4156	6165	SO:0001583	missense	137902	exon17			ACGTGGGCTGCTG		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.2218C>T	8.37:g.52321966G>A	ENSP00000348645:p.Pro740Ser	Somatic	28	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	16.46	3.130556	0.56828	0.001991	0.006978	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.78246	-1.16;-1.16	3.71	1.79	0.24919	.	.	.	.	.	T	0.79736	0.4497	M	0.76727	2.345	0.36838	D	0.887265	D	0.65815	0.995	D	0.70016	0.967	T	0.81002	-0.1130	9	0.72032	D	0.01	.	5.8018	0.18417	0.1109:0.0:0.6977:0.1914	.	740	A1KZ92	PXDNL_HUMAN	S	740	ENSP00000348645:P740S;ENSP00000444865:P740S	ENSP00000348645:P740S	P	-	1	0	PXDNL	52484519	1.000000	0.71417	0.042000	0.18584	0.667000	0.39255	8.437000	0.90302	0.153000	0.19213	0.555000	0.69702	CCC	G|0.998;A|0.002	0.002	strong		0.701	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
KRT26	353288	hgsc.bcm.edu	37	17	38928014	38928014	+	Missense_Mutation	SNP	A	A	G	rs9898164	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38928014A>G	ENST00000335552.4	-	1	400	c.352T>C	c.(352-354)Tgg>Cgg	p.W118R		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				TTCTCGTACCAGCCCTTGATC	0.507													A|||	780	0.155751	0.1626	0.2853	5008	,	,		17988	0.1667		0.1173	False		,,,				2504	0.0828				p.W118R		Atlas-SNP	.											.	KRT26	49	.	0			c.T352C						PASS	.	A	ARG/TRP	661,3745	281.4+/-275.9	57,547,1599	119.0	117.0	118.0		352	5.7	0.8	17	dbSNP_119	118	1028,7572	219.5+/-257.5	58,912,3330	yes	missense	KRT26	NM_181539.4	101	115,1459,4929	GG,GA,AA		11.9535,15.0023,12.9863	probably-damaging	118/469	38928014	1689,11317	2203	4300	6503	SO:0001583	missense	353288	exon1			CGTACCAGCCCTT	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30840	protein-coding gene	gene with protein product			"""keratin 25B"""	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.352T>C	17.37:g.38928014A>G	ENSP00000334798:p.Trp118Arg	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	174	78	0.448276	NM_181539		Missense_Mutation	SNP	ENST00000335552.4	37	CCDS11374.1	351	0.16071428571428573	83	0.16869918699186992	85	0.23480662983425415	103	0.18006993006993008	80	0.10554089709762533	A	18.75	3.690448	0.68271	0.150023	0.119535	ENSG00000186393	ENST00000335552	D	0.88431	-2.38	5.72	5.72	0.89469	Filament (1);	0.000000	0.56097	D	0.000031	T	0.00608	0.0020	M	0.89904	3.07	0.22446	P	0.999093195	D	0.69078	0.997	D	0.72075	0.976	T	0.00000	-1.3292	9	0.48119	T	0.1	.	15.4767	0.75485	1.0:0.0:0.0:0.0	rs9898164;rs52817174;rs59378032;rs9898164	118	Q7Z3Y9	K1C26_HUMAN	R	118	ENSP00000334798:W118R	ENSP00000334798:W118R	W	-	1	0	KRT26	36181540	1.000000	0.71417	0.842000	0.33263	0.776000	0.43924	8.525000	0.90583	2.304000	0.77564	0.528000	0.53228	TGG	A|0.854;G|0.146	0.146	strong		0.507	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539	
TRIP11	9321	hgsc.bcm.edu	37	14	92460176	92460176	+	Missense_Mutation	SNP	C	C	G	rs137974620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92460176C>G	ENST00000267622.4	-	15	5510	c.5137G>C	c.(5137-5139)Gaa>Caa	p.E1713Q		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1713					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		ACTTTTCCTTCCAGATTTTCT	0.328			T	PDGFRB	AML								C|||	4	0.000798722	0.0	0.0	5008	,	,		18129	0.0		0.004	False		,,,				2504	0.0				p.E1713Q	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G5137C						PASS	.	C	GLN/GLU	3,4401	6.2+/-15.9	0,3,2199	141.0	128.0	133.0		5137	4.5	1.0	14	dbSNP_134	133	29,8567	21.0+/-64.5	0,29,4269	yes	missense	TRIP11	NM_004239.3	29	0,32,6468	GG,GC,CC		0.3374,0.0681,0.2462	probably-damaging	1713/1980	92460176	32,12968	2202	4298	6500	SO:0001583	missense	9321	exon15			TTCCTTCCAGATT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.5137G>C	14.37:g.92460176C>G	ENSP00000267622:p.Glu1713Gln	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	158	86	0.544304	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	4|4	0.0018315018315018315|0.0018315018315018315	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	C|C	17.47|17.47	3.397608|3.397608	0.62177|0.62177	6.81E-4|6.81E-4	0.003374|0.003374	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.04862|.	3.54|.	5.41|5.41	4.51|4.51	0.55191|0.55191	.|.	0.050641|.	0.85682|.	N|.	0.000000|.	T|T	0.66228|0.66228	0.2768|0.2768	M|M	0.70275|0.70275	2.135|2.135	0.44899|0.44899	D|D	0.99791|0.99791	D;D|.	0.58970|.	0.976;0.984|.	P;P|.	0.62435|.	0.799;0.902|.	T|T	0.70749|0.70749	-0.4787|-0.4787	10|5	0.42905|.	T|.	0.14|.	.|.	15.1012|15.1012	0.72279|0.72279	0.0:0.8575:0.1425:0.0|0.0:0.8575:0.1425:0.0	.|.	1449;1713|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	Q|A	1713;1449|1428	ENSP00000267622:E1713Q|.	ENSP00000267622:E1713Q|.	E|G	-|-	1|2	0|0	TRIP11|TRIP11	91529929|91529929	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	3.187000|3.187000	0.50950|0.50950	1.363000|1.363000	0.46019|0.46019	0.655000|0.655000	0.94253|0.94253	GAA|GGA	C|0.998;G|0.002	0.002	strong		0.328	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
TMEM245	23731	hgsc.bcm.edu	37	9	111881856	111881856	+	Missense_Mutation	SNP	T	T	C	rs1051474	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:111881856T>C	ENST00000374586.3	-	1	369	c.338A>G	c.(337-339)cAc>cGc	p.H113R		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	113						integral component of membrane (GO:0016021)											GTGCGCGCGGTGCAGGCGCTG	0.726													T|||	986	0.196885	0.0174	0.3256	5008	,	,		10110	0.2937		0.2793	False		,,,				2504	0.1636				p.H113R		Atlas-SNP	.											.	.	.	.	0			c.A338G						PASS	.	T	ARG/HIS	133,3651		2,129,1761	4.0	8.0	7.0		338	2.6	1.0	9	dbSNP_86	7	1618,6032		132,1354,2339	no	missense	C9orf5	NM_032012.3	29	134,1483,4100	CC,CT,TT		21.1503,3.5148,15.314	benign	113/880	111881856	1751,9683	1892	3825	5717	SO:0001583	missense	23731	exon1			GCGCGGTGCAGGC	AF153415	CCDS43858.1	9q31	2012-03-06	2012-03-06	2012-03-06	ENSG00000106771	ENSG00000106771			1363	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 5"""	C9orf5		10564813	Standard	NM_032012		Approved	CG-2	uc004bdt.4	Q9H330	OTTHUMG00000020469	ENST00000374586.3:c.338A>G	9.37:g.111881856T>C	ENSP00000363714:p.His113Arg	Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	5	5	1	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Missense_Mutation	SNP	ENST00000374586.3	37	CCDS43858.1	502	0.22985347985347984	16	0.032520325203252036	101	0.27900552486187846	175	0.30594405594405594	210	0.2770448548812665	T	3.632	-0.075434	0.07184	0.035148	0.211503	ENSG00000106771	ENST00000374587;ENST00000374586;ENST00000223608	T	0.20881	2.04	4.9	2.58	0.30949	.	0.127703	0.53938	N	0.000041	T	0.00012	0.0000	N	0.04508	-0.205	0.28353	P	0.9208218	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.46247	-0.9205	9	0.33141	T	0.24	-7.6069	7.8579	0.29493	0.0:0.2415:0.0:0.7585	rs1051474;rs3174326;rs1051474	113;113	Q9H330-2;Q9H330	.;CI005_HUMAN	R	113	ENSP00000363714:H113R	ENSP00000223608:H113R	H	-	2	0	C9orf5	110921677	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	1.881000	0.39638	0.724000	0.32296	0.533000	0.62120	CAC	T|0.646;C|0.354	0.354	strong		0.726	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012	
DSPP	1834	hgsc.bcm.edu	37	4	88535832	88535832	+	Missense_Mutation	SNP	A	A	G	rs201553143|rs142316753		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88535832A>G	ENST00000282478.7	+	4	2051	c.2018A>G	c.(2017-2019)gAt>gGt	p.D673G	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D673G			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	673	Asp/Ser-rich.			D -> DSSDSSS (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gacagcagtgatagcagtgac	0.488																																					p.D673G		Atlas-SNP	.											.	DSPP	174	.	0			c.A2018G						PASS	.						122.0	139.0	133.0					4																	88535832		1702	3108	4810	SO:0001583	missense	1834	exon5			GCAGTGATAGCAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2018A>G	4.37:g.88535832A>G	ENSP00000282478:p.Asp673Gly	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	188	38	0.202128	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	-	0.506	-0.868666	0.02570	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87650	-2.28;-2.28	2.58	1.3	0.21679	.	.	.	.	.	T	0.78972	0.4368	L	0.43923	1.385	0.09310	N	0.999992	B	0.13145	0.007	B	0.09377	0.004	T	0.62492	-0.6843	9	0.29301	T	0.29	-9.092	4.9808	0.14164	0.6876:0.0:0.3124:0.0	.	673	Q9NZW4	DSPP_HUMAN	G	673	ENSP00000382213:D673G;ENSP00000282478:D673G	ENSP00000282478:D673G	D	+	2	0	DSPP	88754856	0.507000	0.26146	0.889000	0.34880	0.021000	0.10359	1.818000	0.39012	0.190000	0.20209	0.139000	0.15985	GAT	.	.	weak		0.488	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31084170	31084170	+	Intron	SNP	A	A	C	rs1042127	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31084170A>C	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Missense_Mutation_p.S408A|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						GGTAAACCGGAGCTGCTGGAA	0.642													A|||	981	0.195887	0.0893	0.2104	5008	,	,		16545	0.2054		0.1968	False		,,,				2504	0.319				p.S408A		Atlas-SNP	.											.	CDSN	48	.	0			c.T1222G						PASS	.	A	ALA/SER,	505,3901		22,461,1720	39.0	45.0	43.0		1222,	2.8	0.3	6	dbSNP_86	43	1566,7034		146,1274,2880	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	99,	168,1735,4600	CC,CA,AA		18.2093,11.4616,15.9234	possibly-damaging,	408/530,	31084170	2071,10935	2203	4300	6503	SO:0001627	intron_variant	1041	exon2			AACCGGAGCTGCT	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+1502A>C	6.37:g.31084170A>C		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	46	46	1	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	349	0.15979853479853479	44	0.08943089430894309	79	0.21823204419889503	90	0.15734265734265734	136	0.17941952506596306	A	14.96	2.692342	0.48202	0.114616	0.182093	ENSG00000204539	ENST00000376288	T	0.07444	3.19	3.92	2.75	0.32379	.	0.370638	0.19960	N	0.102238	T	0.03564	0.0102	L	0.34521	1.04	0.80722	P	0.0	P	0.49783	0.928	P	0.50049	0.629	T	0.43245	-0.9403	9	0.33940	T	0.23	.	5.8931	0.18925	0.8765:0.0:0.1235:0.0	rs1042127;rs3181593;rs9263655;rs17840015;rs60353924;rs1042127	408	Q15517	CDSN_HUMAN	A	408	ENSP00000365465:S408A	ENSP00000365465:S408A	S	-	1	0	CDSN	31192149	0.090000	0.21635	0.258000	0.24420	0.822000	0.46500	1.327000	0.33746	0.667000	0.31107	0.386000	0.25728	TCC	A|0.846;C|0.154	0.154	strong		0.642	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
L3MBTL2	83746	hgsc.bcm.edu	37	22	41613188	41613188	+	Silent	SNP	C	C	T	rs9611519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:41613188C>T	ENST00000216237.5	+	5	740	c.582C>T	c.(580-582)ccC>ccT	p.P194P	RP4-756G23.5_ENST00000451176.1_RNA|RP4-756G23.5_ENST00000441316.1_RNA	NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	194					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.P194P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AGGCTGCTCCCGTCAGCTGTT	0.632													C|||	1205	0.240615	0.1112	0.4625	5008	,	,		17448	0.0526		0.3072	False		,,,				2504	0.3834				p.P194P		Atlas-SNP	.											L3MBTL2,NS,carcinoma,0,1	L3MBTL2	61	1	1	Substitution - coding silent(1)	stomach(1)	c.C582T						PASS	.	C		562,3844	250.9+/-257.8	39,484,1680	75.0	65.0	69.0		582	0.3	1.0	22	dbSNP_119	69	2398,6202	398.5+/-346.1	338,1722,2240	no	coding-synonymous	L3MBTL2	NM_031488.4		377,2206,3920	TT,TC,CC		27.8837,12.7553,22.7587		194/706	41613188	2960,10046	2203	4300	6503	SO:0001819	synonymous_variant	83746	exon5			TGCTCCCGTCAGC	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.582C>T	22.37:g.41613188C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	31	11	0.354839	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Silent	SNP	ENST00000216237.5	37	CCDS14011.1	492	0.22527472527472528	53	0.10772357723577236	172	0.47513812154696133	32	0.055944055944055944	235	0.3100263852242744	C	13.71	2.319041	0.41096	0.127553	0.278837	ENSG00000100395	ENST00000449635	.	.	.	5.15	0.282	0.15692	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.47661	-0.9100	3	.	.	.	.	3.7648	0.08619	0.1031:0.1411:0.106:0.6499	rs9611519;rs9611519	.	.	.	C	142	.	.	R	+	1	0	L3MBTL2	39943134	0.007000	0.16637	1.000000	0.80357	0.977000	0.68977	-1.167000	0.03126	0.149000	0.19098	-1.044000	0.02363	CGT	C|0.775;T|0.225	0.225	strong		0.632	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488	
FREM2	341640	hgsc.bcm.edu	37	13	39452993	39452993	+	Missense_Mutation	SNP	C	C	T	rs7996253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39452993C>T	ENST00000280481.7	+	23	9101	c.8885C>T	c.(8884-8886)gCg>gTg	p.A2962V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2962			A -> V (in dbSNP:rs7996253).		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)		GAGACACAAGCGACCAGTTTT	0.438													C|||	113	0.0225639	0.0817	0.0058	5008	,	,		18911	0.0		0.001	False		,,,				2504	0.0				p.A2962V		Atlas-SNP	.											.	FREM2	385	.	0			c.C8885T						PASS	.	C	VAL/ALA	291,4115	158.5+/-191.2	6,279,1918	152.0	139.0	144.0		8885	2.8	1.0	13	dbSNP_116	144	0,8600		0,0,4300	yes	missense	FREM2	NM_207361.4	64	6,279,6218	TT,TC,CC		0.0,6.6046,2.2374	benign	2962/3170	39452993	291,12715	2203	4300	6503	SO:0001583	missense	341640	exon23			CACAAGCGACCAG	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.8885C>T	13.37:g.39452993C>T	ENSP00000280481:p.Ala2962Val	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	155	66	0.425806	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	39	0.017857142857142856	35	0.07113821138211382	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	15.76	2.927535	0.52759	0.066046	0.0	ENSG00000150893	ENST00000280481	T	0.63580	-0.05	5.71	2.83	0.33086	.	0.227351	0.44902	N	0.000401	T	0.07954	0.0199	M	0.69823	2.125	0.58432	D	0.999992	P	0.43750	0.816	B	0.37198	0.243	T	0.04333	-1.0959	10	0.26408	T	0.33	.	9.1802	0.37136	0.2607:0.6709:0.0:0.0683	rs7996253;rs52813429;rs7996253	2962	Q5SZK8	FREM2_HUMAN	V	2962	ENSP00000280481:A2962V	ENSP00000280481:A2962V	A	+	2	0	FREM2	38350993	0.994000	0.37717	0.999000	0.59377	0.713000	0.41058	3.132000	0.50523	0.723000	0.32274	0.563000	0.77884	GCG	C|0.978;T|0.022	0.022	strong		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
NKAIN4	128414	hgsc.bcm.edu	37	20	61879074	61879074	+	Silent	SNP	C	C	T	rs11906010	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:61879074C>T	ENST00000370316.3	-	4	416	c.327G>A	c.(325-327)gaG>gaA	p.E109E	NKAIN4_ENST00000466885.1_5'UTR|NKAIN4_ENST00000370313.1_Silent_p.E47E|NKAIN4_ENST00000370307.2_Silent_p.E47E	NM_152864.3	NP_690603.3	Q8IVV8	NKAI4_HUMAN	Na+/K+ transporting ATPase interacting 4	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|lung(1)|ovary(1)	4	all_cancers(38;2.72e-09)					CTGGCCAGCGCTCACGCCACC	0.692													C|||	323	0.0644968	0.205	0.0403	5008	,	,		15594	0.0		0.0189	False		,,,				2504	0.0051				p.E109E		Atlas-SNP	.											.	NKAIN4	23	.	0			c.G327A						PASS	.	C		622,3288		41,540,1374	20.0	19.0	19.0		327	0.3	0.0	20	dbSNP_120	19	126,7270		0,126,3572	no	coding-synonymous	NKAIN4	NM_152864.3		41,666,4946	TT,TC,CC		1.7036,15.9079,6.616		109/209	61879074	748,10558	1955	3698	5653	SO:0001819	synonymous_variant	128414	exon4			CCAGCGCTCACGC	BC041812	CCDS13514.1	20q13.33	2007-10-04	2007-10-04	2007-10-04	ENSG00000101198	ENSG00000101198		"""Na+/K+ transporting ATPase interacting"""	16191	protein-coding gene	gene with protein product		612873	"""chromosome 20 open reading frame 58"""	C20orf58		17606467	Standard	NM_152864		Approved	bA261N11.2, FAM77A	uc002yek.3	Q8IVV8	OTTHUMG00000032959	ENST00000370316.3:c.327G>A	20.37:g.61879074C>T		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	218	122	0.559633	NM_152864	Q4VXQ6|Q9BQU8|Q9BQU9	Silent	SNP	ENST00000370316.3	37	CCDS13514.1																																																																																			C|0.922;T|0.078	0.078	strong		0.692	NKAIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080117.3	NM_152864	
NPAS2	4862	hgsc.bcm.edu	37	2	101594191	101594191	+	Missense_Mutation	SNP	C	C	T	rs11541353	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:101594191C>T	ENST00000335681.5	+	15	1697	c.1412C>T	c.(1411-1413)tCg>tTg	p.S471L	AC016738.3_ENST00000433012.1_RNA|AC016738.3_ENST00000439150.1_RNA|NPAS2_ENST00000542504.1_Missense_Mutation_p.S536L|AC016738.3_ENST00000446644.1_RNA	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	471			S -> L (susceptibility to seasonal affective disorder (SAD) and diurnal preference; dbSNP:rs11541353). {ECO:0000269|PubMed:9012850}.		cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCTTCCCCATCGTCCTGCGAC	0.627													C|||	414	0.0826677	0.0696	0.0922	5008	,	,		17197	0.001		0.17	False		,,,				2504	0.0879				p.S471L		Atlas-SNP	.											.	NPAS2	88	.	0			c.C1412T	GRCh37	CM035892	NPAS2	M	rs11541353	PASS	.	C	LEU/SER	382,4024	193.0+/-218.2	14,354,1835	101.0	103.0	102.0		1412	5.7	0.0	2	dbSNP_120	102	1565,7035	293.9+/-301.6	166,1233,2901	yes	missense	NPAS2	NM_002518.3	145	180,1587,4736	TT,TC,CC		18.1977,8.67,14.97	benign	471/825	101594191	1947,11059	2203	4300	6503	SO:0001583	missense	4862	exon15			CCCCATCGTCCTG	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.1412C>T	2.37:g.101594191C>T	ENSP00000338283:p.Ser471Leu	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	203	0.09294871794871795	46	0.09349593495934959	37	0.10220994475138122	0	0.0	120	0.158311345646438	C	8.842	0.942506	0.18281	0.0867	0.181977	ENSG00000170485	ENST00000335681;ENST00000542504;ENST00000450763	T;T;T	0.32023	3.47;3.45;1.47	5.69	5.69	0.88448	.	1.520810	0.03482	N	0.215274	T	0.00039	0.0001	N	0.22421	0.69	0.80722	P	0.0	B;B;B	0.19817	0.039;0.002;0.007	B;B;B	0.12837	0.008;0.0;0.004	T	0.03773	-1.1005	9	0.23891	T	0.37	.	12.2995	0.54866	0.0:0.92:0.0:0.08	rs11541353	536;471;471	F5H027;A0PJF9;Q99743	.;.;NPAS2_HUMAN	L	471;536;70	ENSP00000338283:S471L;ENSP00000438428:S536L;ENSP00000392125:S70L	ENSP00000338283:S471L	S	+	2	0	NPAS2	100960623	0.006000	0.16342	0.007000	0.13788	0.307000	0.27823	2.026000	0.41069	2.677000	0.91161	0.655000	0.94253	TCG	C|0.870;T|0.130	0.130	strong		0.627	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
TMEM132E	124842	hgsc.bcm.edu	37	17	32962004	32962004	+	Silent	SNP	C	C	T	rs73988752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:32962004C>T	ENST00000321639.5	+	8	1933	c.1605C>T	c.(1603-1605)acC>acT	p.T535T		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	535						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		TGGAGGTCACCGACCTAGTCA	0.622													C|||	435	0.086861	0.1929	0.0303	5008	,	,		15370	0.005		0.0358	False		,,,				2504	0.1207				p.T535T		Atlas-SNP	.											.	TMEM132E	122	.	0			c.C1605T						PASS	.	C		745,3661	300.4+/-286.3	61,623,1519	90.0	69.0	76.0		1605	-8.0	1.0	17	dbSNP_130	76	276,8324	104.6+/-165.6	4,268,4028	no	coding-synonymous	TMEM132E	NM_207313.1		65,891,5547	TT,TC,CC		3.2093,16.9088,7.8502		535/985	32962004	1021,11985	2203	4300	6503	SO:0001819	synonymous_variant	124842	exon8			GGTCACCGACCTA	BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.1605C>T	17.37:g.32962004C>T		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	63	26	0.412698	NM_207313	Q8WUF4|Q8WVA5	Silent	SNP	ENST00000321639.5	37	CCDS11283.1																																																																																			C|0.929;T|0.071	0.071	strong		0.622	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
MANEA	79694	hgsc.bcm.edu	37	6	96053922	96053922	+	Missense_Mutation	SNP	T	T	A	rs35772543	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:96053922T>A	ENST00000358812.4	+	5	1164	c.1030T>A	c.(1030-1032)Ttt>Att	p.F344I		NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	344	Catalytic. {ECO:0000305}.			F -> I (in Ref. 2; AAQ75077, 3; BAB14298 and 4; CAE45927). {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)		CCTAAAATTATTTTGTGATAA	0.378													T|||	226	0.0451278	0.0038	0.0605	5008	,	,		18638	0.0595		0.0765	False		,,,				2504	0.0429				p.F344I		Atlas-SNP	.											.	MANEA	58	.	0			c.T1030A						PASS	.	T	ILE/PHE	84,4322	68.1+/-105.8	2,80,2121	59.0	64.0	62.0		1030	6.2	0.9	6	dbSNP_126	62	740,7858	177.2+/-226.9	39,662,3598	yes	missense	MANEA	NM_024641.3	21	41,742,5719	AA,AT,TT		8.6067,1.9065,6.3365	probably-damaging	344/463	96053922	824,12180	2203	4299	6502	SO:0001583	missense	79694	exon5			AAATTATTTTGTG	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.1030T>A	6.37:g.96053922T>A	ENSP00000351669:p.Phe344Ile	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	33	5	0.151515	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Missense_Mutation	SNP	ENST00000358812.4	37	CCDS5032.1	136	0.06227106227106227	2	0.0040650406504065045	29	0.08011049723756906	37	0.06468531468531469	68	0.08970976253298153	T	29.1	4.981294	0.93044	0.019065	0.086067	ENSG00000172469	ENST00000358812	D	0.92647	-3.08	6.17	6.17	0.99709	.	0.086298	0.85682	N	0.000000	D	0.95990	0.8694	M	0.86740	2.835	0.09310	P	0.9999999800898	D	0.89917	1.0	D	0.87578	0.998	D	0.95687	0.8737	9	0.46703	T	0.11	-24.0744	16.0034	0.80327	0.0:0.0:0.0:1.0	rs35772543	344	Q5SRI9	MANEA_HUMAN	I	344	ENSP00000351669:F344I	ENSP00000351669:F344I	F	+	1	0	MANEA	96160643	1.000000	0.71417	0.915000	0.36163	0.910000	0.53928	7.603000	0.82811	2.371000	0.80710	0.533000	0.62120	TTT	T|0.936;A|0.064	0.064	strong		0.378	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
OXER1	165140	hgsc.bcm.edu	37	2	42991200	42991200	+	Missense_Mutation	SNP	C	C	G	rs34142793	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:42991200C>G	ENST00000378661.2	-	1	201	c.120G>C	c.(118-120)atG>atC	p.M40I		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	40					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						TATGAAGTTCCATGGGCTGCT	0.572													.|||	63	0.0125799	0.0	0.013	5008	,	,		19145	0.002		0.0229	False		,,,				2504	0.0297				p.M40I		Atlas-SNP	.											.	OXER1	33	.	0			c.G120C						PASS	.	C	ILE/MET	21,4385	28.1+/-56.4	0,21,2182	85.0	72.0	76.0		120	2.9	0.6	2	dbSNP_126	76	250,8350	98.8+/-160.4	5,240,4055	yes	missense	OXER1	NM_148962.4	10	5,261,6237	GG,GC,CC		2.907,0.4766,2.0837	benign	40/424	42991200	271,12735	2203	4300	6503	SO:0001583	missense	165140	exon1			AAGTTCCATGGGC	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.120G>C	2.37:g.42991200C>G	ENSP00000367930:p.Met40Ile	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	113	110	0.973451	NM_148962	Q86WP7|Q8NGW4	Missense_Mutation	SNP	ENST00000378661.2	37	CCDS1810.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	C	16.20	3.055731	0.55325	0.004766	0.02907	ENSG00000162881	ENST00000378661	T	0.59224	0.28	2.89	2.89	0.33648	.	.	.	.	.	T	0.15219	0.0367	N	0.19112	0.55	0.26801	N	0.969202	P	0.39551	0.678	B	0.30646	0.118	T	0.05178	-1.0901	9	0.45353	T	0.12	.	9.4891	0.38948	0.0:1.0:0.0:0.0	rs34142793	40	Q8TDS5	OXER1_HUMAN	I	40	ENSP00000367930:M40I	ENSP00000367930:M40I	M	-	3	0	OXER1	42844704	0.986000	0.35501	0.635000	0.29338	0.553000	0.35397	2.424000	0.44714	1.934000	0.56057	0.555000	0.69702	ATG	C|0.981;G|0.019	0.019	strong		0.572	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962	
CUBN	8029	hgsc.bcm.edu	37	10	17147521	17147521	+	Missense_Mutation	SNP	G	G	T	rs1801224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:17147521G>T	ENST00000377833.4	-	11	1230	c.1165C>A	c.(1165-1167)Cca>Aca	p.P389T		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	389			P -> T (in dbSNP:rs1801224). {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)	CATCCATTTGGCCCATAACCA	0.448													G|||	2676	0.534345	0.3676	0.6009	5008	,	,		18892	0.6558		0.5875	False		,,,				2504	0.5327				p.P389T		Atlas-SNP	.											.	CUBN	515	.	0			c.C1165A						PASS	.	G	THR/PRO	1819,2587	533.3+/-373.7	371,1077,755	146.0	126.0	133.0		1165	1.4	0.5	10	dbSNP_89	133	5823,2777	678.5+/-403.5	1983,1857,460	yes	missense	CUBN	NM_001081.3	38	2354,2934,1215	TT,TG,GG		32.2907,41.2846,41.2425	possibly-damaging	389/3624	17147521	7642,5364	2203	4300	6503	SO:0001583	missense	8029	exon11			CATTTGGCCCATA	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.1165C>A	10.37:g.17147521G>T	ENSP00000367064:p.Pro389Thr	Somatic	173	0	0		WXS	Illumina HiSeq	Phase_I	178	81	0.455056	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	1225	0.5608974358974359	205	0.4166666666666667	220	0.6077348066298343	365	0.6381118881118881	435	0.5738786279683378	G	14.04	2.415303	0.42817	0.412846	0.677093	ENSG00000107611	ENST00000377833	T	0.40756	1.02	5.65	1.37	0.22104	Growth factor, receptor (1);Epidermal growth factor-like (1);	0.670270	0.13115	N	0.412718	T	0.00012	0.0000	L	0.53249	1.67	0.09310	P	0.999999999795783	P	0.39282	0.666	B	0.35859	0.212	T	0.37384	-0.9708	9	0.66056	D	0.02	.	5.4646	0.16635	0.0693:0.1251:0.5467:0.2588	rs1801224;rs2228052;rs10795446;rs41538725;rs41538899;rs41539425;rs52807320;rs61727981;rs10795446	389	O60494	CUBN_HUMAN	T	389	ENSP00000367064:P389T	ENSP00000367064:P389T	P	-	1	0	CUBN	17187527	0.991000	0.36638	0.490000	0.27465	0.703000	0.40648	3.034000	0.49751	0.296000	0.22592	-0.282000	0.10007	CCA	T|0.469;G|0.343;C|0.092;A|0.097	0.469	strong		0.448	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
OR5H6	79295	hgsc.bcm.edu	37	3	97983265	97983265	+	Missense_Mutation	SNP	C	C	A	rs4241472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:97983265C>A	ENST00000383696.2	+	1	178	c.137C>A	c.(136-138)gCa>gAa	p.A46E	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005479.1	NP_001005479.1	Q8NGV6	OR5H6_HUMAN	olfactory receptor, family 5, subfamily H, member 6 (gene/pseudogene)	46			A -> E (in dbSNP:rs4241472).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(2)|endometrium(1)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CTCTTCCTGGCATTCTTGGTA	0.408													C|||	888	0.177316	0.0234	0.2161	5008	,	,		20782	0.4653		0.0835	False		,,,				2504	0.1575				p.A46E		Atlas-SNP	.											.	OR5H6	89	.	0			c.C137A						PASS	.	C	GLU/ALA	138,4268		0,138,2065	204.0	213.0	210.0		137	-3.3	0.0	3	dbSNP_111	210	746,7852		27,692,3580	yes	missense	OR5H6	NM_001005479.1	107	27,830,5645	AA,AC,CC		8.6764,3.1321,6.7979	benign	46/326	97983265	884,12120	2203	4299	6502	SO:0001583	missense	79295	exon1			TCCTGGCATTCTT	BK004374	CCDS33800.1	3q12.1	2013-10-10	2013-10-10		ENSG00000230301	ENSG00000230301		"""GPCR / Class A : Olfactory receptors"""	14767	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily H, member 6"""				Standard	NM_001005479		Approved		uc003dsi.1	Q8NGV6	OTTHUMG00000160078	ENST00000383696.2:c.137C>A	3.37:g.97983265C>A	ENSP00000373196:p.Ala46Glu	Somatic	302	0	0		WXS	Illumina HiSeq	Phase_I	312	158	0.50641	NM_001005479	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	37	CCDS33800.1	457	0.20924908424908426	16	0.032520325203252036	60	0.16574585635359115	312	0.5454545454545454	69	0.09102902374670185	-	12.31	1.898753	0.33535	0.031321	0.086764	ENSG00000230301	ENST00000383696	T	0.03004	4.08	2.19	-3.27	0.05048	.	0.920339	0.08881	N	0.880049	T	0.00012	0.0000	L	0.52573	1.65	0.80722	P	0.0	P	0.40794	0.729	B	0.42555	0.391	T	0.32851	-0.9891	9	0.87932	D	0	.	3.6066	0.08045	0.0:0.2504:0.1996:0.5499	rs4241472;rs4241472	46	Q8NGV6	OR5H6_HUMAN	E	46	ENSP00000373196:A46E	ENSP00000373196:A46E	A	+	2	0	OR5H6	99465955	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	0.713000	0.25794	-0.808000	0.04387	0.194000	0.17425	GCA	C|0.873;A|0.127	0.127	strong		0.408	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2		
MUC6	4588	hgsc.bcm.edu	37	11	1017773	1017773	+	Silent	SNP	G	G	A	rs57384288	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1017773G>A	ENST00000421673.2	-	31	5078	c.5028C>T	c.(5026-5028)agC>agT	p.S1676S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1676	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.S1676S(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGCTGGTCCCGCTGGTGGTCA	0.557													A|||	1486	0.296725	0.3298	0.1542	5008	,	,		31162	0.3165		0.2505	False		,,,				2504	0.3804				p.S1676S		Atlas-SNP	.											MUC6,NS,carcinoma,0,1	MUC6	408	1	1	Substitution - coding silent(1)	ovary(1)	c.C5028T						scavenged	.						688.0	686.0	687.0					11																	1017773		2198	4294	6492	SO:0001819	synonymous_variant	4588	exon31			GGTCCCGCTGGTG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5028C>T	11.37:g.1017773G>A		Somatic	776	38	0.0489691		WXS	Illumina HiSeq	Phase_I	878	65	0.0740319	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			G|0.500;A|0.500	0.500	strong		0.557	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ULK4	54986	hgsc.bcm.edu	37	3	41877410	41877410	+	Missense_Mutation	SNP	T	T	G	rs192218045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:41877410T>G	ENST00000301831.4	-	18	2172	c.1710A>C	c.(1708-1710)ttA>ttC	p.L570F		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	570				AIVLLTELIRENFRNSKLKQCLLPTLGE -> TTSSIGIGI LNCLVQHSTPVPRQCLVYV (in Ref. 3; AAH14794). {ECO:0000305}.	cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GGCACTGTTTTAATTTGCTGT	0.363													T|||	5	0.000998403	0.0008	0.0014	5008	,	,		14639	0.0		0.003	False		,,,				2504	0.0				p.L570F		Atlas-SNP	.											.	ULK4	150	.	0			c.A1710C						PASS	.	T	PHE/LEU	2,3672		0,2,1835	136.0	136.0	136.0		1710	1.3	1.0	3		136	29,8139		0,29,4055	yes	missense	ULK4	NM_017886.2	22	0,31,5890	GG,GT,TT		0.355,0.0544,0.2618	probably-damaging	570/1276	41877410	31,11811	1837	4084	5921	SO:0001583	missense	54986	exon18			CTGTTTTAATTTG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1710A>C	3.37:g.41877410T>G	ENSP00000301831:p.Leu570Phe	Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	255	118	0.462745	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	19.99	3.928909	0.73327	5.44E-4	0.00355	ENSG00000168038	ENST00000301831	T	0.67171	-0.25	5.37	1.28	0.21552	Armadillo-like helical (1);Armadillo-type fold (2);	0.091392	0.45361	U	0.000380	T	0.71762	0.3378	L	0.57536	1.79	0.80722	D	1	D;D	0.65815	0.991;0.995	P;P	0.61800	0.894;0.894	T	0.70063	-0.4975	10	0.62326	D	0.03	.	8.263	0.31797	0.0:0.4472:0.0:0.5528	.	570;570	B4E2M4;Q96C45	.;ULK4_HUMAN	F	570	ENSP00000301831:L570F	ENSP00000301831:L570F	L	-	3	2	ULK4	41852414	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.467000	0.22035	0.316000	0.23135	0.528000	0.53228	TTA	T|0.997;G|0.003	0.003	strong		0.363	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
IL2	3558	hgsc.bcm.edu	37	4	123377482	123377482	+	Silent	SNP	C	C	A	rs2069763	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:123377482C>A	ENST00000226730.4	-	1	398	c.114G>T	c.(112-114)ctG>ctT	p.L38L		NM_000586.3	NP_000577.2	P60568	IL2_HUMAN	interleukin 2	38					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|immune response (GO:0006955)|natural killer cell activation (GO:0030101)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of heart contraction (GO:0045822)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic spine development (GO:0060999)|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-17 production (GO:0032740)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of T cell homeostatic proliferation (GO:0046013)|T cell differentiation (GO:0030217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|cytokine activity (GO:0005125)|glycosphingolipid binding (GO:0043208)|growth factor activity (GO:0008083)|interleukin-2 receptor binding (GO:0005134)|kinase activator activity (GO:0019209)			endometrium(2)|large_intestine(4)|lung(6)|skin(1)	13				LUSC - Lung squamous cell carcinoma(721;0.185)	Pseudoephedrine(DB00852)	GTAAATCCAGCAGTAAATGCT	0.333			T	TNFRSF17	intestinal T-cell lymphoma								C|||	1496	0.298722	0.0772	0.4366	5008	,	,		18545	0.4613		0.3449	False		,,,				2504	0.2853				p.L38L		Atlas-SNP	.		Dom	yes		4	4q26-q27	3558	interleukin 2		L	.	IL2	23	.	0			c.G114T	GRCh37	CS060537	IL2	S	rs2069763	PASS	.	C		558,3848	247.8+/-255.9	37,484,1682	115.0	107.0	110.0		114	1.4	0.0	4	dbSNP_96	110	2791,5809	439.8+/-359.3	452,1887,1961	no	coding-synonymous	IL2	NM_000586.3		489,2371,3643	AA,AC,CC		32.4535,12.6645,25.7497		38/154	123377482	3349,9657	2203	4300	6503	SO:0001819	synonymous_variant	3558	exon1			ATCCAGCAGTAAA	U25676	CCDS3726.1	4q26-q27	2011-07-14			ENSG00000109471	ENSG00000109471		"""Interleukins and interleukin receptors"""	6001	protein-coding gene	gene with protein product	"""T cell growth factor"""	147680				3260003	Standard	NM_000586		Approved	IL-2, TCGF	uc003ier.3	P60568	OTTHUMG00000133075	ENST00000226730.4:c.114G>T	4.37:g.123377482C>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	146	71	0.486301	NM_000586	P01585	Silent	SNP	ENST00000226730.4	37	CCDS3726.1																																																																																			C|0.718;A|0.282	0.282	strong		0.333	IL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256715.2		
NBN	4683	hgsc.bcm.edu	37	8	90958422	90958422	+	Silent	SNP	T	T	C	rs1061302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:90958422T>C	ENST00000265433.3	-	13	2170	c.2016A>G	c.(2014-2016)ccA>ccG	p.P672P	NBN_ENST00000409330.1_Silent_p.P590P	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	672					blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			TTATGCCAGATGGATTTCTGG	0.323								Homologous recombination					T|||	1767	0.352835	0.2156	0.3761	5008	,	,		16654	0.4673		0.3062	False		,,,				2504	0.4519				p.P672P		Atlas-SNP	.											.	NBN	86	.	0			c.A2016G						PASS	.	T		1003,3403	371.2+/-319.9	121,761,1321	107.0	108.0	108.0		2016	-7.3	0.0	8	dbSNP_86	108	2692,5904	430.6+/-356.6	410,1872,2016	no	coding-synonymous	NBN	NM_002485.4		531,2633,3337	CC,CT,TT		31.3169,22.7644,28.4187		672/755	90958422	3695,9307	2203	4298	6501	SO:0001819	synonymous_variant	4683	exon13			GCCAGATGGATTT	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.2016A>G	8.37:g.90958422T>C		Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	130	48	0.369231	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Silent	SNP	ENST00000265433.3	37	CCDS6249.1																																																																																			T|0.690;C|0.310	0.310	strong		0.323	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
DUSP23	54935	hgsc.bcm.edu	37	1	159752066	159752066	+	Missense_Mutation	SNP	G	G	A	rs1129923	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:159752066G>A	ENST00000368107.1	+	2	489	c.391G>A	c.(391-393)Ggc>Agc	p.G131S	DUSP23_ENST00000368108.3_Missense_Mutation_p.G131S|DUSP23_ENST00000368109.1_Missense_Mutation_p.G131S			Q9BVJ7	DUS23_HUMAN	dual specificity phosphatase 23	131	Tyrosine-protein phosphatase.		G -> S (in dbSNP:rs1129923).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			lung(1)	1	all_hematologic(112;0.0537)					ACTACGACCCGGCTCCATCGA	0.582													G|||	323	0.0644968	0.003	0.0663	5008	,	,		19688	0.0099		0.1183	False		,,,				2504	0.1472				p.G131S		Atlas-SNP	.											.	DUSP23	9	.	0			c.G391A	GRCh37	CM067373	DUSP23	M	rs1129923	PASS	.	G	SER/GLY	73,4333	63.5+/-100.7	0,73,2130	106.0	97.0	100.0		391	4.3	1.0	1	dbSNP_86	100	792,7808	186.3+/-233.8	41,710,3549	yes	missense	DUSP23	NM_017823.3	56	41,783,5679	AA,AG,GG		9.2093,1.6568,6.6508	probably-damaging	131/151	159752066	865,12141	2203	4300	6503	SO:0001583	missense	54935	exon3			CGACCCGGCTCCA		CCDS1187.1	1q23.1	2011-06-09			ENSG00000158716	ENSG00000158716		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	21480	protein-coding gene	gene with protein product						15147733	Standard	XM_005245289		Approved	FLJ20442, DUSP25	uc001ftz.1	Q9BVJ7	OTTHUMG00000022795	ENST00000368107.1:c.391G>A	1.37:g.159752066G>A	ENSP00000357087:p.Gly131Ser	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	139	74	0.532374	NM_017823	Q9NX48	Missense_Mutation	SNP	ENST00000368107.1	37	CCDS1187.1	127	0.05815018315018315	3	0.006097560975609756	28	0.07734806629834254	3	0.005244755244755245	93	0.12269129287598944	G	34	5.344228	0.95807	0.016568	0.092093	ENSG00000158716	ENST00000368109;ENST00000368108;ENST00000368107	T;T;T	0.25579	1.79;1.79;1.79	4.32	4.32	0.51571	Dual specificity phosphatase, catalytic domain (1);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.42245	0.1194	M	0.73598	2.24	0.09310	P	0.99999999446355	D	0.89917	1.0	D	0.87578	0.998	T	0.48364	-0.9042	9	0.72032	D	0.01	-19.8429	14.363	0.66785	0.0:0.0:1.0:0.0	rs1129923;rs3188245;rs52830627;rs60777461;rs1129923	131	Q9BVJ7	DUS23_HUMAN	S	131	ENSP00000357089:G131S;ENSP00000357088:G131S;ENSP00000357087:G131S	ENSP00000357087:G131S	G	+	1	0	DUSP23	158018690	1.000000	0.71417	0.999000	0.59377	0.943000	0.58893	9.307000	0.96226	2.222000	0.72286	0.561000	0.74099	GGC	G|0.938;A|0.062	0.062	strong		0.582	DUSP23-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085552.1	NM_017823	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629891	32629891	+	Missense_Mutation	SNP	C	C	T	rs386699585|rs1063323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629891C>T	ENST00000399082.3	-	2	288	c.244G>A	c.(244-246)Gcc>Acc	p.A82T	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.A172T|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.A172T|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.A172T|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.A172T|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	172	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	ACAACGCCGGCTGTCTCCTCC	0.547									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	1979	0.395168	0.3154	0.5447	5008	,	,		15401	0.4782		0.3946	False		,,,				2504	0.3119				p.A172T	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,colon,carcinoma,+1,1	HLA-DQB1	15	1	0			c.G514A						PASS	.	T	THR/ALA	1264,3120		198,868,1126	45.0	47.0	47.0		514	1.8	0.0	6	dbSNP_86	47	3012,5578		578,1856,1861	no	missense	HLA-DQB1	NM_002123.4	58	776,2724,2987	TT,TC,CC		35.064,28.8321,32.9582	benign	172/262	32629891	4276,8698	2192	4295	6487	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	CGCCGGCTGTCTC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.244G>A	6.37:g.32629891C>T	ENSP00000382032:p.Ala82Thr	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	103	44	0.427184	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		927	0.42445054945054944	152	0.3089430894308943	189	0.5220994475138122	281	0.49125874125874125	305	0.4023746701846966	.	0.892	-0.725235	0.03158	0.288321	0.35064	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.02812	4.15;4.15;4.15;4.15;4.15	4.52	1.78	0.24846	.	0.459394	0.20863	N	0.084310	T	0.00815	0.0027	.	.	.	0.80722	P	0.0	B;B;B;B	0.13594	0.002;0.001;0.008;0.0	B;B;B;B	0.12837	0.003;0.003;0.008;0.003	T	0.48969	-0.8987	8	0.31617	T	0.26	.	8.6058	0.33773	0.0:0.7426:0.0:0.2574	rs1063323;rs3204390;rs9280014;rs17840143;rs28724256;rs34109183	172;137;172;172	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	T	82;172;172;172;172;108	ENSP00000382032:A82T;ENSP00000382029:A172T;ENSP00000364080:A172T;ENSP00000407332:A172T;ENSP00000382034:A172T	ENSP00000364080:A172T	A	-	1	0	HLA-DQB1	32737869	0.000000	0.05858	0.034000	0.17996	0.001000	0.01503	0.431000	0.21444	0.057000	0.16193	-1.922000	0.00515	GCC	C|0.587;T|0.413	0.413	strong		0.547	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
IFIT5	24138	hgsc.bcm.edu	37	10	91178000	91178000	+	Silent	SNP	C	C	T	rs304448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:91178000C>T	ENST00000371795.4	+	2	1257	c.1044C>T	c.(1042-1044)taC>taT	p.Y348Y	IFIT5_ENST00000416601.1_Silent_p.Y300Y	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	348					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						CCAACATGTACGCTGAAGGAG	0.443													T|||	3259	0.650759	0.7201	0.5029	5008	,	,		21282	0.8571		0.5358	False		,,,				2504	0.5675				p.Y348Y		Atlas-SNP	.											.	IFIT5	32	.	0			c.C1044T						PASS	.	T		3035,1371	454.7+/-350.8	1052,931,220	110.0	102.0	105.0		1044	-2.0	0.0	10	dbSNP_79	105	4349,4251	573.8+/-389.9	1105,2139,1056	no	coding-synonymous	IFIT5	NM_012420.2		2157,3070,1276	TT,TC,CC		49.4302,31.1167,43.2262		348/483	91178000	7384,5622	2203	4300	6503	SO:0001819	synonymous_variant	24138	exon2			CATGTACGCTGAA	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"""Tetratricopeptide (TTC) repeat domain containing"""	13328	protein-coding gene	gene with protein product	"""retinoic acid- and interferon-inducible protein (58kD)"""					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.1044C>T	10.37:g.91178000C>T		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	136	68	0.5	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Silent	SNP	ENST00000371795.4	37	CCDS7403.1																																																																																			C|0.376;T|0.624	0.624	strong		0.443	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420	
SAAL1	113174	hgsc.bcm.edu	37	11	18127464	18127464	+	Missense_Mutation	SNP	C	C	T	rs77233279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18127464C>T	ENST00000524803.1	-	1	174	c.125G>A	c.(124-126)gGa>gAa	p.G42E	SAAL1_ENST00000533851.1_5'UTR|SAAL1_ENST00000300013.4_Missense_Mutation_p.G42E|SAAL1_ENST00000529318.1_Missense_Mutation_p.G42E			Q96ER3	SAAL1_HUMAN	serum amyloid A-like 1	42										breast(2)|large_intestine(5)|lung(8)	15						CTGGATGAGTCCGCTGAGGAC	0.682											OREG0020819	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	50	0.00998403	0.0015	0.0086	5008	,	,		14972	0.001		0.0408	False		,,,				2504	0.0				p.G42E		Atlas-SNP	.											SAAL1,NS,carcinoma,0,1	SAAL1	34	1	0			c.G125A						PASS	.	C	GLU/GLY	27,4371		0,27,2172	61.0	43.0	49.0		125	4.5	1.0	11	dbSNP_131	49	248,8334		3,242,4046	yes	missense	SAAL1	NM_138421.2	98	3,269,6218	TT,TC,CC		2.8898,0.6139,2.1186	benign	42/475	18127464	275,12705	2199	4291	6490	SO:0001583	missense	113174	exon1			ATGAGTCCGCTGA	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.125G>A	11.37:g.18127464C>T	ENSP00000432487:p.Gly42Glu	Somatic	22	0	0	723	WXS	Illumina HiSeq	Phase_I	39	20	0.512821	NM_138421	A6NH05	Missense_Mutation	SNP	ENST00000524803.1	37	CCDS31439.1	33|33	0.01510989010989011|0.01510989010989011	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	30|30	0.0395778364116095|0.0395778364116095	C|C	9.842|9.842	1.191290|1.191290	0.21954|0.21954	0.006139|0.006139	0.028898|0.028898	ENSG00000166788|ENSG00000166788	ENST00000532452|ENST00000524803;ENST00000300013;ENST00000529318;ENST00000530180	.|T;T;T;T	.|0.33865	.|1.39;1.39;1.39;1.39	5.46|5.46	4.48|4.48	0.54585|0.54585	.|.	.|0.168649	.|0.52532	.|D	.|0.000068	T|T	0.04048|0.04048	0.0113|0.0113	N|N	0.14661|0.14661	0.345|0.345	0.30455|0.30455	N|N	0.774862|0.774862	.|B;B;B	.|0.26845	.|0.161;0.161;0.161	.|B;B;B	.|0.24394	.|0.053;0.033;0.033	T|T	0.06881|0.06881	-1.0802|-1.0802	5|10	.|0.14656	.|T	.|0.56	-5.7028|-5.7028	7.9343|7.9343	0.29920|0.29920	0.1614:0.7563:0.0:0.0823|0.1614:0.7563:0.0:0.0823	.|.	.|42;42;42	.|E9PRZ1;G1UCX3;Q96ER3	.|.;.;SAAL1_HUMAN	N|E	35|42	.|ENSP00000432487:G42E;ENSP00000300013:G42E;ENSP00000432216:G42E;ENSP00000431489:G42E	.|ENSP00000300013:G42E	D|G	-|-	1|2	0|0	SAAL1|SAAL1	18084040|18084040	0.556000|0.556000	0.26538|0.26538	1.000000|1.000000	0.80357|0.80357	0.909000|0.909000	0.53808|0.53808	0.892000|0.892000	0.28322|0.28322	2.720000|2.720000	0.93068|0.93068	0.655000|0.655000	0.94253|0.94253	GAC|GGA	C|0.981;T|0.019	0.019	strong		0.682	SAAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389728.1	NM_138421	
LIPG	9388	hgsc.bcm.edu	37	18	47093864	47093864	+	Missense_Mutation	SNP	C	C	T	rs2000813	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:47093864C>T	ENST00000261292.4	+	3	610	c.332C>T	c.(331-333)aCa>aTa	p.T111I	LIPG_ENST00000427224.2_Missense_Mutation_p.T111I|LIPG_ENST00000577628.1_Missense_Mutation_p.T147I|LIPG_ENST00000580036.1_Missense_Mutation_p.T111I	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	111			T -> I (in dbSNP:rs2000813). {ECO:0000269|PubMed:12966036}.		cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						GCCCTGCACACAAGAGAGAAA	0.493													C|||	1205	0.240615	0.0673	0.2277	5008	,	,		16337	0.3274		0.3022	False		,,,				2504	0.3313				p.T111I	Pancreas(126;280 1778 12814 26243 34948)	Atlas-SNP	.											.	LIPG	47	.	0			c.C332T	GRCh37	CM077882	LIPG	M	rs2000813	PASS	.	C	ILE/THR	473,3933	225.2+/-241.2	20,433,1750	88.0	75.0	79.0		332	-3.7	0.2	18	dbSNP_92	79	2506,6094	410.5+/-350.2	364,1778,2158	yes	missense	LIPG	NM_006033.2	89	384,2211,3908	TT,TC,CC		29.1395,10.7354,22.9048	benign	111/501	47093864	2979,10027	2203	4300	6503	SO:0001583	missense	9388	exon3			TGCACACAAGAGA	AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.332C>T	18.37:g.47093864C>T	ENSP00000261292:p.Thr111Ile	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	49	0.583333	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Missense_Mutation	SNP	ENST00000261292.4	37	CCDS11938.1	532	0.24358974358974358	29	0.05894308943089431	101	0.27900552486187846	182	0.3181818181818182	220	0.29023746701846964	C	10.03	1.238711	0.22711	0.107354	0.291395	ENSG00000101670	ENST00000261292;ENST00000427224	D;D	0.90444	-2.67;-2.67	5.13	-3.65	0.04502	Lipase, N-terminal (1);	0.762883	0.13306	N	0.397833	T	0.00012	0.0000	N	0.12853	0.265	0.80722	P	0.0	B;B;B	0.12013	0.005;0.003;0.002	B;B;B	0.11329	0.006;0.006;0.004	T	0.07539	-1.0767	9	0.49607	T	0.09	-23.8984	5.0178	0.14345	0.372:0.2221:0.0:0.4059	rs2000813;rs3786250;rs52802490;rs56604138;rs58046713;rs2000813	111;111;111	B4DTR8;Q9Y5X9;Q9Y5X9-2	.;LIPE_HUMAN;.	I	111	ENSP00000261292:T111I;ENSP00000387978:T111I	ENSP00000261292:T111I	T	+	2	0	LIPG	45347862	0.013000	0.17824	0.170000	0.22879	0.332000	0.28634	0.406000	0.21032	-0.342000	0.08363	0.561000	0.74099	ACA	C|0.760;T|0.240	0.240	strong		0.493	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033	
FBN2	2201	hgsc.bcm.edu	37	5	127595153	127595153	+	Silent	SNP	G	G	C	rs34383505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:127595153G>C	ENST00000508053.1	-	71	9707	c.8733C>G	c.(8731-8733)ctC>ctG	p.L2911L	FBN2_ENST00000262464.4_Silent_p.L2911L			P35556	FBN2_HUMAN	fibrillin 2	2911					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)		AGGGTTAATAGAGCTGAATCT	0.458													G|||	138	0.0275559	0.0998	0.0086	5008	,	,		15857	0.0		0.0	False		,,,				2504	0.0				p.L2911L		Atlas-SNP	.											.	FBN2	858	.	0			c.C8733G						PASS	.	G		323,4083	171.9+/-202.1	11,301,1891	96.0	95.0	95.0		8733	3.7	1.0	5	dbSNP_126	95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FBN2	NM_001999.3		11,303,6189	CC,CG,GG		0.0233,7.3309,2.4988		2911/2913	127595153	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon65			TTAATAGAGCTGA	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.8733C>G	5.37:g.127595153G>C		Somatic	197	0	0		WXS	Illumina HiSeq	Phase_I	220	111	0.504545	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			G|0.973;C|0.027	0.027	strong		0.458	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
MLN	4295	hgsc.bcm.edu	37	6	33768897	33768897	+	Missense_Mutation	SNP	A	A	G	rs2281820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33768897A>G	ENST00000430124.2	-	2	109	c.44T>C	c.(43-45)gTa>gCa	p.V15A	MLN_ENST00000266003.5_Missense_Mutation_p.V15A|MLN_ENST00000507738.1_Missense_Mutation_p.V15A	NM_001040109.1|NM_001184698.1|NM_002418.2	NP_001035198.1|NP_001171627.1|NP_002409.1	P12872	MOTI_HUMAN	motilin	15			V -> A (in dbSNP:rs2281820). {ECO:0000269|PubMed:15489334}.		cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)	receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)	6						CATGGCAGCTACATGCACCAC	0.577													G|||	3163	0.631589	0.4932	0.5216	5008	,	,		20036	0.8562		0.5368	False		,,,				2504	0.7628				p.V15A		Atlas-SNP	.											.	MLN	16	.	0			c.T44C						PASS	.	G	ALA/VAL,ALA/VAL,ALA/VAL	2229,2177	585.3+/-386.2	560,1109,534	98.0	86.0	90.0		44,44,44	-1.1	0.0	6	dbSNP_100	90	4994,3606	520.8+/-379.8	1460,2074,766	yes	missense,missense,missense	MLN	NM_001040109.1,NM_001184698.1,NM_002418.2	64,64,64	2020,3183,1300	GG,GA,AA		41.9302,49.4099,44.4641	benign,benign,benign	15/115,15/109,15/116	33768897	7223,5783	2203	4300	6503	SO:0001583	missense	4295	exon2			GCAGCTACATGCA		CCDS4786.1, CCDS47412.1, CCDS54993.1	6p21.31	2014-01-30			ENSG00000096395	ENSG00000096395		"""Endogenous ligands"""	7141	protein-coding gene	gene with protein product	"""prepromotilin"""	158270					Standard	NM_001184698		Approved		uc003off.1	P12872	OTTHUMG00000014536	ENST00000430124.2:c.44T>C	6.37:g.33768897A>G	ENSP00000388825:p.Val15Ala	Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	154	69	0.448052	NM_002418	B7ZLR7|E9PDN2|J3KN51|Q2M1L2|Q5T975|Q6NSY7	Missense_Mutation	SNP	ENST00000430124.2	37	CCDS4786.1	1328	0.608058608058608	256	0.5203252032520326	185	0.511049723756906	475	0.8304195804195804	412	0.5435356200527705	G	0.628	-0.818365	0.02776	0.505901	0.580698	ENSG00000096395	ENST00000430124;ENST00000266003;ENST00000507738	T;T;T	0.51325	0.71;0.71;0.71	5.43	-1.12	0.09808	.	1.272520	0.05417	N	0.543508	T	0.11067	0.0270	L	0.28115	0.83	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12682	-1.0538	9	0.10636	T	0.68	0.251	7.2176	0.25969	0.4771:0.12:0.4029:0.0	rs2281820;rs52813189;rs61381966;rs2281820	15;15	E9PDN2;P12872	.;MOTI_HUMAN	A	15	ENSP00000388825:V15A;ENSP00000266003:V15A;ENSP00000425467:V15A	ENSP00000266003:V15A	V	-	2	0	MLN	33876875	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.753000	0.04792	-0.651000	0.05415	-0.812000	0.03155	GTA	A|0.403;G|0.597	0.597	strong		0.577	MLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040211.4		
TMEM63B	55362	hgsc.bcm.edu	37	6	44121579	44121579	+	Splice_Site	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:44121579G>A	ENST00000259746.9	+	21	2292	c.2109G>A	c.(2107-2109)acG>acA	p.T703T	TMEM63B_ENST00000323267.6_Splice_Site_p.T703T			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	703					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CCATGCGCACGGGTGAGGGAT	0.642																																					p.T703T		Atlas-SNP	.											TMEM63B,NS,carcinoma,+1,1	TMEM63B	77	1	0			c.G2109A						scavenged	.						47.0	46.0	46.0					6																	44121579		2203	4300	6503	SO:0001630	splice_region_variant	55362	exon21			GCGCACGGGTGAG	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.2110+1G>A	6.37:g.44121579G>A		Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	128	2	0.015625	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	.	.	.	.	.	.	.	.	.	.	G	9.268	1.044939	0.19748	.	.	ENSG00000137216	ENST00000371893	.	.	.	5.16	-3.32	0.04973	.	.	.	.	.	T	0.21509	0.0518	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37979	-0.9682	4	.	.	.	.	1.3761	0.02221	0.3043:0.2937:0.2617:0.1403	.	.	.	.	Q	632	.	.	R	+	2	0	TMEM63B	44229557	0.004000	0.15560	0.993000	0.49108	0.977000	0.68977	-0.954000	0.03873	-0.289000	0.09038	0.561000	0.74099	CGG	.	.	none		0.642	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	Silent
IQSEC3	440073	hgsc.bcm.edu	37	12	274647	274647	+	Silent	SNP	T	T	C	rs4980859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:274647T>C	ENST00000538872.1	+	10	2875	c.2757T>C	c.(2755-2757)ttT>ttC	p.F919F	IQSEC3_ENST00000326261.4_Silent_p.F919F|IQSEC3_ENST00000382841.2_Silent_p.F616F|RP11-598F7.6_ENST00000537295.1_lincRNA|RP11-598F7.5_ENST00000540136.1_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	919	PH.				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)			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)		CGTACACCTTTTGCAAGTCAG	0.488													C|||	1306	0.260783	0.087	0.3199	5008	,	,		23066	0.3393		0.326	False		,,,				2504	0.3057				p.F919F		Atlas-SNP	.											.	IQSEC3	154	.	0			c.T2757C						PASS	.	C	,	593,3813	771.3+/-413.8	37,519,1647	189.0	176.0	180.0		2757,1848	4.9	1.0	12	dbSNP_111	180	2729,5871	680.5+/-403.6	434,1861,2005	yes	coding-synonymous,coding-synonymous	IQSEC3	NM_001170738.1,NM_015232.1	,	471,2380,3652	CC,CT,TT		31.7326,13.4589,25.5421	,	919/1183,616/760	274647	3322,9684	2203	4300	6503	SO:0001819	synonymous_variant	440073	exon10			CACCTTTTGCAAG	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.2757T>C	12.37:g.274647T>C		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	117	117	1	NM_001170738	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	37	CCDS53728.1																																																																																			T|0.740;C|0.260	0.260	strong		0.488	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
FCGBP	8857	hgsc.bcm.edu	37	19	40368619	40368619	+	Silent	SNP	G	G	A	rs150027077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40368619G>A	ENST00000221347.6	-	28	12736	c.12729C>T	c.(12727-12729)ggC>ggT	p.G4243G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4243	VWFD 10. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCAGCTGCCGCCCCAGATGG	0.647																																					p.G4243G		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.C12729T						scavenged	.						12.0	15.0	14.0					19																	40368619		2182	4225	6407	SO:0001819	synonymous_variant	8857	exon28			GCTGCCGCCCCAG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.12729C>T	19.37:g.40368619G>A		Somatic	335	1	0.00298507		WXS	Illumina HiSeq	Phase_I	436	45	0.103211	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.932;A|0.068	0.068	strong		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
RBM19	9904	hgsc.bcm.edu	37	12	114377885	114377885	+	Silent	SNP	G	G	C	rs2290790	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:114377885G>C	ENST00000545145.2	-	15	1896	c.1818C>G	c.(1816-1818)acC>acG	p.T606T	RBM19_ENST00000392561.3_Silent_p.T606T|RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Silent_p.T606T	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	606	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AATGGCCGAAGGTCTCCTGCA	0.632													G|||	1099	0.219449	0.0688	0.2565	5008	,	,		17610	0.1756		0.3191	False		,,,				2504	0.3395				p.T606T		Atlas-SNP	.											.	RBM19	117	.	0			c.C1818G						PASS	.	G	,,	469,3937	221.0+/-238.3	31,407,1765	67.0	72.0	70.0		1818,1818,1818	0.1	0.2	12	dbSNP_100	70	2825,5775	441.5+/-359.8	470,1885,1945	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	501,2292,3710	CC,CG,GG		32.8488,10.6446,25.3268	,,	606/961,606/961,606/961	114377885	3294,9712	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon15			GCCGAAGGTCTCC	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.1818C>G	12.37:g.114377885G>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	36	0.473684	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.761;C|0.239	0.239	strong		0.632	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
APOBEC4	403314	hgsc.bcm.edu	37	1	183617266	183617266	+	Silent	SNP	C	C	G	rs17436878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:183617266C>G	ENST00000308641.4	-	2	922	c.651G>C	c.(649-651)ggG>ggC	p.G217G	APOBEC4_ENST00000481562.1_Intron|RGL1_ENST00000304685.4_Intron|RGL1_ENST00000536277.1_Intron	NM_203454.2	NP_982279.1	Q8WW27	ABEC4_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 4 (putative)	217					mRNA processing (GO:0006397)		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(6)|skin(1)	21						CCAGTGCTCTCCCAGTTAAAA	0.428													C|||	700	0.139776	0.0113	0.1527	5008	,	,		22584	0.0288		0.2853	False		,,,				2504	0.2689				p.G217G		Atlas-SNP	.											.	APOBEC4	45	.	0			c.G651C						PASS	.	C	,	262,4144	147.6+/-182.1	11,240,1952	83.0	83.0	83.0		,651	0.4	0.2	1	dbSNP_123	83	2463,6137	407.1+/-349.0	373,1717,2210	no	intron,coding-synonymous	RGL1,APOBEC4	NM_015149.3,NM_203454.2	,	384,1957,4162	GG,GC,CC		28.6395,5.9464,20.9519	,	,217/368	183617266	2725,10281	2203	4300	6503	SO:0001819	synonymous_variant	403314	exon2			TGCTCTCCCAGTT	BC021711	CCDS1358.1	1q25.3	2008-02-05	2005-10-27	2005-10-27	ENSG00000173627	ENSG00000173627		"""Apolipoprotein B mRNA editing enzymes"""	32152	protein-coding gene	gene with protein product		609908	"""chromosome 1 open reading frame 169"""	C1orf169		16082223	Standard	NM_203454		Approved	MGC26594, FLJ25691, RP1-127C7.4	uc001gqn.3	Q8WW27	OTTHUMG00000035459	ENST00000308641.4:c.651G>C	1.37:g.183617266C>G		Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	140	140	1	NM_203454	Q8N7F6	Silent	SNP	ENST00000308641.4	37	CCDS1358.1																																																																																			C|0.811;G|0.189	0.189	strong		0.428	APOBEC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086126.1	NM_203454	
SMG1	23049	hgsc.bcm.edu	37	16	18882775	18882775	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:18882775G>A	ENST00000446231.2	-	16	2625	c.2213C>T	c.(2212-2214)gCa>gTa	p.A738V	snoU13_ENST00000459248.1_RNA|SMG1_ENST00000389467.3_Missense_Mutation_p.A738V			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	738	Interaction with SMG8 and SMG9.				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						TAAAACAGCTGCTTCCAAAGC	0.348																																					p.A738V		Atlas-SNP	.											.	SMG1	401	.	0			c.C2213T						PASS	.						59.0	54.0	55.0					16																	18882775		1816	4081	5897	SO:0001583	missense	23049	exon16			ACAGCTGCTTCCA	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.2213C>T	16.37:g.18882775G>A	ENSP00000402515:p.Ala738Val	Somatic	282	0	0		WXS	Illumina HiSeq	Phase_I	295	118	0.4	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.295768	0.23564	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.64803	-0.12;-0.12	5.21	5.21	0.72293	Armadillo-type fold (1);	0.096968	0.41823	N	0.000802	T	0.27663	0.0680	N	0.00926	-1.1	0.24424	N	0.99461	B	0.02656	0.0	B	0.01281	0.0	T	0.23261	-1.0193	10	0.05436	T	0.98	.	11.34	0.49527	0.9281:0.0:0.0719:0.0	.	738	Q96Q15	SMG1_HUMAN	V	738	ENSP00000402515:A738V;ENSP00000374118:A738V	ENSP00000374118:A738V	A	-	2	0	SMG1	18790276	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.236000	0.78154	0.925000	0.37094	-0.381000	0.06696	GCA	.	.	none		0.348	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
DCAF6	55827	hgsc.bcm.edu	37	1	168013850	168013850	+	Missense_Mutation	SNP	T	T	C	rs11558511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:168013850T>C	ENST00000312263.6	+	13	1844	c.1640T>C	c.(1639-1641)gTg>gCg	p.V547A	DCAF6_ENST00000367840.3_Missense_Mutation_p.V624A|DCAF6_ENST00000367843.3_Missense_Mutation_p.V567A|DCAF6_ENST00000432587.2_Missense_Mutation_p.V593A	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	547			V -> A (in dbSNP:rs11558511). {ECO:0000269|PubMed:15489334}.		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	36						TCAGAGGATGTGACAAAATAT	0.373													T|||	924	0.184505	0.0545	0.1383	5008	,	,		18636	0.2044		0.2823	False		,,,				2504	0.272				p.V624A		Atlas-SNP	.											.	DCAF6	99	.	0			c.T1871C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL,ALA/VAL	383,4023	192.6+/-218.0	13,357,1833	104.0	105.0	105.0		1640,1871,1778,1700	2.5	0.9	1	dbSNP_120	105	2364,6236	394.6+/-344.7	324,1716,2260	yes	missense,missense,missense,missense	DCAF6	NM_001017977.2,NM_001198956.1,NM_001198957.1,NM_018442.3	64,64,64,64	337,2073,4093	CC,CT,TT		27.4884,8.6927,21.121	benign,benign,benign,benign	547/861,624/952,593/921,567/881	168013850	2747,10259	2203	4300	6503	SO:0001583	missense	55827	exon15			AGGATGTGACAAA	AL136738	CCDS1267.2, CCDS30933.1, CCDS55657.1, CCDS55658.1	1q23.3	2013-01-09	2009-07-17	2009-07-17	ENSG00000143164	ENSG00000143164		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30002	protein-coding gene	gene with protein product		610494	"""IQ motif and WD repeats 1"""	IQWD1		12032826	Standard	NM_018442		Approved	PC326	uc001gex.3	Q58WW2	OTTHUMG00000034572	ENST00000312263.6:c.1640T>C	1.37:g.168013850T>C	ENSP00000311949:p.Val547Ala	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	414	0.18956043956043955	24	0.04878048780487805	62	0.1712707182320442	117	0.20454545454545456	211	0.2783641160949868	T	3.734	-0.054977	0.07362	0.086927	0.274884	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	4.91	2.53	0.30540	WD40 repeat-like-containing domain (1);	1.234980	0.05717	N	0.597043	T	0.02807	0.0084	N	0.03608	-0.345	0.09310	P	1.0	B;B;B;B	0.12013	0.001;0.001;0.005;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.35624	-0.9781	9	0.07175	T	0.84	.	2.2628	0.04071	0.2191:0.2799:0.0:0.501	rs11558511;rs17855508;rs56482202;rs11558511	593;624;547;567	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	A	567;593;547;624	ENSP00000356817:V567A;ENSP00000396238:V593A;ENSP00000311949:V547A;ENSP00000356814:V624A	ENSP00000311949:V547A	V	+	2	0	DCAF6	166280474	0.002000	0.14202	0.895000	0.35142	0.932000	0.56968	-0.106000	0.10890	0.704000	0.31869	0.533000	0.62120	GTG	C|0.196;N|0.000	0.196	strong		0.373	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442	
SERPINI2	5276	hgsc.bcm.edu	37	3	167189607	167189607	+	Missense_Mutation	SNP	A	A	C	rs17246389	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:167189607A>C	ENST00000476257.1	-	3	314	c.16T>G	c.(16-18)Ttg>Gtg	p.L6V	SERPINI2_ENST00000471111.1_Missense_Mutation_p.L6V|SERPINI2_ENST00000465031.1_5'UTR|SERPINI2_ENST00000264677.4_Missense_Mutation_p.L6V|SERPINI2_ENST00000461846.1_Missense_Mutation_p.L6V			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	6			L -> V (in dbSNP:rs17246389).		cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						AGACTCCACAAGAAGATTGTG	0.338													A|||	840	0.167732	0.056	0.134	5008	,	,		16707	0.0972		0.2624	False		,,,				2504	0.318				p.L16V		Atlas-SNP	.											.	SERPINI2	85	.	0			c.T46G	GRCh37	CM067714	SERPINI2	M	rs17246389	PASS	.	A	VAL/LEU	391,4015	191.2+/-216.9	14,363,1826	108.0	120.0	116.0		16	-1.4	0.0	3	dbSNP_123	116	2220,6378	375.5+/-337.8	304,1612,2383	yes	missense	SERPINI2	NM_006217.3	32	318,1975,4209	CC,CA,AA		25.82,8.8743,20.0784	possibly-damaging	6/406	167189607	2611,10393	2203	4299	6502	SO:0001583	missense	5276	exon3			TCCACAAGAAGAT	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"""Serine (or cysteine) peptidase inhibitors"""	8945	protein-coding gene	gene with protein product		605587	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2"", ""serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"""	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.16T>G	3.37:g.167189607A>C	ENSP00000420621:p.Leu6Val	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	79	41	0.518987	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	338	0.15476190476190477	31	0.06300813008130081	56	0.15469613259668508	52	0.09090909090909091	199	0.262532981530343	A	10.34	1.322455	0.23994	0.088743	0.2582	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111;ENST00000466903;ENST00000467583	T;T;T;T;T;T	0.81247	-0.94;-0.94;-0.94;-0.94;-0.94;-1.47	5.41	-1.41	0.08941	Serpin domain (1);	0.649667	0.14912	N	0.291166	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	P;P	0.37781	0.608;0.608	B;B	0.32090	0.14;0.14	T	0.01972	-1.1237	9	0.72032	D	0.01	.	9.7473	0.40455	0.5821:0.0:0.4179:0.0	rs17246389;rs52822774;rs59746421;rs17246389	6;6	B4DDY9;O75830	.;SPI2_HUMAN	V	6	ENSP00000420621:L6V;ENSP00000417692:L6V;ENSP00000264677:L6V;ENSP00000419407:L6V;ENSP00000417752:L6V;ENSP00000419255:L6V	ENSP00000264677:L6V	L	-	1	2	SERPINI2	168672301	0.030000	0.19436	0.010000	0.14722	0.015000	0.08874	0.115000	0.15540	-0.484000	0.06763	-0.417000	0.06048	TTG	A|0.830;C|0.170	0.170	strong		0.338	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
TMEM72	643236	hgsc.bcm.edu	37	10	45430153	45430153	+	Silent	SNP	G	G	A	rs17157262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45430153G>A	ENST00000544540.1	+	4	529	c.45G>A	c.(43-45)cgG>cgA	p.R15R	TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.9_ENST00000425541.2_lincRNA			A0PK05	TMM72_HUMAN	transmembrane protein 72	133						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						TGAGCAAGCGGAAGAAGAGGA	0.602													G|||	57	0.0113818	0.0386	0.0086	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.R133R		Atlas-SNP	.											.	TMEM72	25	.	0			c.G399A						PASS	.	G		91,3045		1,89,1478	77.0	81.0	80.0		399	-3.8	0.9	10	dbSNP_123	80	2,7162		0,2,3580	no	coding-synonymous	TMEM72	NM_001123376.1		1,91,5058	AA,AG,GG		0.0279,2.9018,0.9029		133/276	45430153	93,10207	1568	3582	5150	SO:0001819	synonymous_variant	643236	exon5			CAAGCGGAAGAAG	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 127"""	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.45G>A	10.37:g.45430153G>A		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_001123376	A1L181|Q5T740	Silent	SNP	ENST00000544540.1	37																																																																																				G|0.990;A|0.010	0.010	strong		0.602	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	
DCHS2	54798	hgsc.bcm.edu	37	4	155411065	155411065	+	Silent	SNP	T	T	C	rs7656522	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155411065T>C	ENST00000339452.1	-	1	1803	c.1443A>G	c.(1441-1443)ctA>ctG	p.L481L	DCHS2_ENST00000456341.2_Silent_p.L474L|DCHS2_ENST00000443500.1_Silent_p.L481L	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1641	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(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)		GGCCGCCGGGTAGCAACGCGA	0.622													C|||	3889	0.776558	0.6036	0.8141	5008	,	,		14779	0.9891		0.7505	False		,,,				2504	0.7914				p.L481L		Atlas-SNP	.											.	DCHS2	594	.	0			c.A1443G						PASS	.	C	,	803,581		232,339,121	17.0	22.0	20.0		1443,1443	-7.4	0.0	4	dbSNP_116	20	2313,869		843,627,121	no	coding-synonymous,coding-synonymous	DCHS2	NM_001142552.1,NM_001142553.1	,	1075,966,242	CC,CT,TT		27.3099,41.9798,31.7565	,	481/1370,481/710	155411065	3116,1450	692	1591	2283	SO:0001819	synonymous_variant	54798	exon1			GCCGGGTAGCAAC	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		ENST00000339452.1:c.1443A>G	4.37:g.155411065T>C		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000339452.1	37	CCDS47150.1																																																																																			T|0.235;C|0.765	0.765	strong		0.622	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
EYS	346007	hgsc.bcm.edu	37	6	65301854	65301854	+	Silent	SNP	G	G	A	rs12663916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65301854G>A	ENST00000370621.3	-	26	4432	c.3906C>T	c.(3904-3906)caC>caT	p.H1302H	EYS_ENST00000370616.2_Silent_p.H1302H|EYS_ENST00000503581.1_Silent_p.H1302H			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1302					detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						GGAGAATGTCGTGCTTGACAA	0.408													A|||	470	0.0938498	0.0151	0.1182	5008	,	,		18956	0.1567		0.0984	False		,,,				2504	0.1135				p.H1302H		Atlas-SNP	.											.	EYS	527	.	0			c.C3906T						PASS	.	A		49,1335		1,47,644	72.0	61.0	65.0		3906	1.6	0.0	6	dbSNP_120	65	446,2734		41,364,1185	no	coding-synonymous	EYS	NM_001142800.1		42,411,1829	AA,AG,GG		14.0252,3.5405,10.8457		1302/3145	65301854	495,4069	692	1590	2282	SO:0001819	synonymous_variant	346007	exon26			AATGTCGTGCTTG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.3906C>T	6.37:g.65301854G>A		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	24	23	0.958333	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				G|0.904;A|0.096	0.096	strong		0.408	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
MICAL2	9645	hgsc.bcm.edu	37	11	12281414	12281414	+	Missense_Mutation	SNP	G	G	A	rs148517207		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12281414G>A	ENST00000256194.4	+	26	3592	c.3304G>A	c.(3304-3306)Gcc>Acc	p.A1102T	MICAL2_ENST00000379612.3_Missense_Mutation_p.A876T|MICAL2_ENST00000342902.5_Missense_Mutation_p.A1081T|MICAL2_ENST00000537344.1_Missense_Mutation_p.A912T|RP11-265D17.2_ENST00000527288.1_RNA|MICAL2_ENST00000527546.1_Missense_Mutation_p.A912T	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	1102					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)		CGCAGTGGCCGCCATTGGCAC	0.597																																					p.A1102T		Atlas-SNP	.											.	MICAL2	114	.	0			c.G3304A						PASS	.	G	THR/ALA	1,4401	2.1+/-5.4	0,1,2200	43.0	43.0	43.0		3304	3.7	0.4	11	dbSNP_134	43	0,8588		0,0,4294	no	missense	MICAL2	NM_014632.2	58	0,1,6494	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	1102/1125	12281414	1,12989	2201	4294	6495	SO:0001583	missense	9645	exon26			GTGGCCGCCATTG	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.3304G>A	11.37:g.12281414G>A	ENSP00000256194:p.Ala1102Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	141	53	0.375887	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	G	6.866	0.529211	0.13127	2.27E-4	0.0	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.61040	0.14;0.15;0.14;0.15;0.15	5.56	3.68	0.42216	.	0.230508	0.30940	N	0.008579	T	0.40570	0.1122	N	0.24115	0.695	0.09310	N	1	B;D;B;B;B;D	0.67145	0.224;0.972;0.007;0.209;0.007;0.996	B;B;B;B;B;P	0.44518	0.016;0.367;0.003;0.015;0.003;0.452	T	0.22208	-1.0223	10	0.15499	T	0.54	.	9.8179	0.40865	0.2194:0.0:0.7806:0.0	.	445;1081;912;855;876;1102	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	T	912;445;1102;912;1081;876	ENSP00000441689:A912T;ENSP00000256194:A1102T;ENSP00000433965:A912T;ENSP00000344894:A1081T;ENSP00000368932:A876T	ENSP00000256194:A1102T	A	+	1	0	MICAL2	12237990	0.987000	0.35691	0.433000	0.26760	0.023000	0.10783	2.954000	0.49113	1.333000	0.45449	0.591000	0.81541	GCC	G|1.000;A|0.000	0.000	weak		0.597	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33665969	33665969	+	Silent	SNP	C	C	T	rs139800499	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:33665969C>T	ENST00000252015.2	-	2	266	c.177G>A	c.(175-177)gaG>gaA	p.E59E	TRPC4AP_ENST00000451813.2_Silent_p.E59E|TRPC4AP_ENST00000432634.2_Silent_p.E59E			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	59	Interaction with TNFRSF1A. {ECO:0000250}.				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)			TCAAAAAAGTCTCAGTGAACT	0.458													C|||	6	0.00119808	0.0008	0.0014	5008	,	,		17571	0.0		0.004	False		,,,				2504	0.0				p.E59E		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.G177A						PASS	.	C	,	12,4394	19.1+/-41.9	0,12,2191	99.0	90.0	93.0		177,177	0.4	1.0	20	dbSNP_134	93	65,8535	39.3+/-95.6	0,65,4235	no	coding-synonymous,coding-synonymous	TRPC4AP	NM_015638.2,NM_199368.1	,	0,77,6426	TT,TC,CC		0.7558,0.2724,0.592	,	59/798,59/790	33665969	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	26133	exon2			AAAAGTCTCAGTG	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	ENST00000252015.2:c.177G>A	20.37:g.33665969C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	77	32	0.415584	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			C|0.995;T|0.005	0.005	strong		0.458	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
ZNF154	7710	hgsc.bcm.edu	37	19	58213952	58213952	+	Missense_Mutation	SNP	C	C	A	rs2074078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58213952C>A	ENST00000512439.2	-	3	561	c.365G>T	c.(364-366)gGt>gTt	p.G122V	ZNF154_ENST00000426889.1_Missense_Mutation_p.G122V|ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	122			G -> V (in dbSNP:rs2074078).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GATGGCCCCACCGTCGCTTTT	0.498													C|||	836	0.166933	0.084	0.2435	5008	,	,		19657	0.3671		0.1173	False		,,,				2504	0.0695				p.G122V		Atlas-SNP	.											.	ZNF154	34	.	0			c.G365T						PASS	.	C	VAL/GLY	284,3662		14,256,1703	177.0	172.0	174.0		365	-1.5	0.0	19	dbSNP_96	174	1024,7288		64,896,3196	yes	missense	ZNF154	NM_001085384.1	109	78,1152,4899	AA,AC,CC		12.3195,7.1972,10.6706	benign	122/438	58213952	1308,10950	1973	4156	6129	SO:0001583	missense	7710	exon3			GCCCCACCGTCGC	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.365G>T	19.37:g.58213952C>A	ENSP00000421258:p.Gly122Val	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	179	96	0.536313	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Missense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	449	0.20558608058608058	52	0.10569105691056911	84	0.23204419889502761	228	0.3986013986013986	85	0.11213720316622691	C	2.938	-0.219437	0.06061	0.071972	0.123195	ENSG00000179909	ENST00000512439;ENST00000426889	T;T	0.06608	3.28;3.28	2.49	-1.45	0.08828	.	.	.	.	.	T	0.00012	0.0000	L	0.60957	1.885	0.80722	P	0.0	B	0.17465	0.022	B	0.15052	0.012	T	0.45818	-0.9235	8	0.87932	D	0	.	2.2067	0.03937	0.2421:0.414:0.0:0.3439	rs2074078;rs52838251;rs58249782;rs2074078	122	Q13106	ZN154_HUMAN	V	122	ENSP00000421258:G122V;ENSP00000442370:G122V	ENSP00000442370:G122V	G	-	2	0	ZNF154	62905764	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.223000	0.17719	-0.205000	0.10219	-0.377000	0.06932	GGT	C|0.818;A|0.182	0.182	strong		0.498	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
SLC2A2	6514	hgsc.bcm.edu	37	3	170715830	170715830	+	Silent	SNP	G	G	A	rs5398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:170715830G>A	ENST00000314251.3	-	11	1516	c.1437C>T	c.(1435-1437)ttC>ttT	p.F479F	SLC2A2_ENST00000382808.4_Silent_p.F360F	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	479					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)			central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	TAAAAAATGTGAACAGGGTAA	0.438													A|||	1866	0.372604	0.6354	0.3084	5008	,	,		17963	0.2411		0.2903	False		,,,				2504	0.2832				p.F479F		Atlas-SNP	.											.	SLC2A2	71	.	0			c.C1437T						PASS	.	A		2589,1817	496.7+/-363.6	767,1055,381	43.0	47.0	46.0		1437	-3.7	0.1	3	dbSNP_52	46	2567,6033	674.3+/-403.1	354,1859,2087	no	coding-synonymous	SLC2A2	NM_000340.1		1121,2914,2468	AA,AG,GG		29.8488,41.2392,39.6432		479/525	170715830	5156,7850	2203	4300	6503	SO:0001819	synonymous_variant	6514	exon11			AAATGTGAACAGG	J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.1437C>T	3.37:g.170715830G>A		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	86	35	0.406977	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																			G|0.622;A|0.378	0.378	strong		0.438	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
SPAG17	200162	hgsc.bcm.edu	37	1	118624123	118624123	+	Silent	SNP	C	C	T	rs2298176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:118624123C>T	ENST00000336338.5	-	14	1970	c.1905G>A	c.(1903-1905)ccG>ccA	p.P635P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	635						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GGTTGTCCCACGGTATGTTGA	0.438													T|||	633	0.126398	0.053	0.0447	5008	,	,		21696	0.2877		0.0596	False		,,,				2504	0.1861				p.P635P		Atlas-SNP	.											.	SPAG17	263	.	0			c.G1905A						PASS	.	T		258,4148	803.5+/-415.7	6,246,1951	189.0	177.0	181.0		1905	-5.0	0.9	1	dbSNP_100	181	489,8111	797.1+/-407.5	16,457,3827	no	coding-synonymous	SPAG17	NM_206996.2		22,703,5778	TT,TC,CC		5.686,5.8557,5.7435		635/2224	118624123	747,12259	2203	4300	6503	SO:0001819	synonymous_variant	200162	exon14			GTCCCACGGTATG		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1905G>A	1.37:g.118624123C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	120	67	0.558333	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	37	CCDS899.1																																																																																			C|0.922;T|0.078	0.078	strong		0.438	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
DENND5B	160518	hgsc.bcm.edu	37	12	31600503	31600503	+	Missense_Mutation	SNP	T	T	C	rs34129725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:31600503T>C	ENST00000389082.5	-	6	2094	c.1830A>G	c.(1828-1830)atA>atG	p.I610M	DENND5B_ENST00000306833.6_Missense_Mutation_p.I645M|DENND5B_ENST00000354285.4_Missense_Mutation_p.I632M|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000536562.1_Missense_Mutation_p.I645M	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	610					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						ATTTCTGATATATAGATGTCC	0.398													T|||	8	0.00159744	0.0	0.0	5008	,	,		18530	0.0		0.005	False		,,,				2504	0.0031				p.I610M		Atlas-SNP	.											.	DENND5B	114	.	0			c.A1830G						PASS	.	T	MET/ILE	13,3669		0,13,1828	60.0	57.0	58.0		1830	-4.4	1.0	12	dbSNP_126	58	86,8100		1,84,4008	yes	missense	DENND5B	NM_144973.3	10	1,97,5836	CC,CT,TT		1.0506,0.3531,0.8342	benign	610/1275	31600503	99,11769	1841	4093	5934	SO:0001583	missense	160518	exon6			CTGATATATAGAT	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1830A>G	12.37:g.31600503T>C	ENSP00000373734:p.Ile610Met	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	152	69	0.453947	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	T	8.110	0.778637	0.16120	0.003531	0.010506	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.05	-4.42	0.03579	.	0.231333	0.35903	N	0.002910	T	0.09379	0.0231	N	0.03115	-0.41	0.24313	N	0.99507	B;B;B	0.13145	0.007;0.001;0.003	B;B;B	0.16289	0.015;0.004;0.009	T	0.06303	-1.0834	10	0.40728	T	0.16	-11.2663	3.3897	0.07285	0.3423:0.0629:0.3752:0.2196	rs34129725	632;610;645	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	M	610;645;645;632	ENSP00000373734:I610M;ENSP00000306482:I645M;ENSP00000444889:I645M;ENSP00000346238:I632M	ENSP00000306482:I645M	I	-	3	3	DENND5B	31491770	0.000000	0.05858	0.988000	0.46212	0.994000	0.84299	-2.825000	0.00747	-0.495000	0.06659	0.460000	0.39030	ATA	T|0.995;C|0.005	0.005	strong		0.398	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
KIAA0141	9812	hgsc.bcm.edu	37	5	141309824	141309824	+	Missense_Mutation	SNP	G	G	A	rs351260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:141309824G>A	ENST00000432126.2	+	7	873	c.739G>A	c.(739-741)Gct>Act	p.A247T	KIAA0141_ENST00000194118.4_Missense_Mutation_p.A247T	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	247			A -> T (in dbSNP:rs351260). {ECO:0000269|PubMed:15489334}.		extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGTTTCCATCGCTTTCAACTT	0.463													G|||	817	0.163139	0.0234	0.2161	5008	,	,		20734	0.1329		0.3062	False		,,,				2504	0.1984				p.A247T		Atlas-SNP	.											.	KIAA0141	44	.	0			c.G739A						PASS	.	G	THR/ALA,THR/ALA	320,4086	168.0+/-198.9	14,292,1897	63.0	62.0	62.0		739,739	4.0	1.0	5	dbSNP_79	62	2900,5700	453.4+/-363.2	481,1938,1881	yes	missense,missense	KIAA0141	NM_001142603.1,NM_014773.3	58,58	495,2230,3778	AA,AG,GG		33.7209,7.2628,24.7578	benign,benign	247/516,247/516	141309824	3220,9786	2203	4300	6503	SO:0001583	missense	9812	exon7			TCCATCGCTTTCA	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.739G>A	5.37:g.141309824G>A	ENSP00000396225:p.Ala247Thr	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	68	0.544	NM_001142603	Q969R4|Q96EU9	Missense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	411	0.18818681318681318	21	0.042682926829268296	90	0.24861878453038674	75	0.13111888111888112	225	0.29683377308707126	G	13.51	2.258234	0.39896	0.072628	0.337209	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	T;T;T	0.62232	0.53;0.53;0.04	4.86	3.97	0.46021	Tetratricopeptide-like helical (1);	0.219160	0.39544	N	0.001326	T	0.00012	0.0000	M	0.91972	3.26	0.40341	P	0.020966999999999958	P	0.41214	0.742	B	0.36534	0.227	T	0.09509	-1.0671	9	0.44086	T	0.13	-3.5127	9.3661	0.38226	0.0989:0.0:0.9011:0.0	rs351260;rs17850264;rs17850666;rs17850731;rs52801955;rs56492989;rs61460168;rs351260	247	Q14154	DELE_HUMAN	T	247	ENSP00000396225:A247T;ENSP00000194118:A247T;ENSP00000422686:A247T	ENSP00000194118:A247T	A	+	1	0	KIAA0141	141290008	0.998000	0.40836	0.999000	0.59377	0.991000	0.79684	2.644000	0.46613	1.243000	0.43853	0.455000	0.32223	GCT	G|0.771;T|0.005	.	strong		0.463	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
IFIT3	3437	hgsc.bcm.edu	37	10	91098877	91098877	+	Silent	SNP	G	G	A	rs34847428	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:91098877G>A	ENST00000371818.4	+	2	645	c.465G>A	c.(463-465)gcG>gcA	p.A155A	IFIT3_ENST00000371811.4_Silent_p.A155A|LIPA_ENST00000371837.1_Intron|LIPA_ENST00000487618.1_Intron	NM_001549.4	NP_001540.2	O14879	IFIT3_HUMAN	interferon-induced protein with tetratricopeptide repeats 3	155					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)|urinary_tract(1)	15						ATGAAAGGGCGAAGGTGTGTT	0.438													G|||	51	0.0101837	0.0	0.0101	5008	,	,		20691	0.001		0.0189	False		,,,				2504	0.0245				p.A155A		Atlas-SNP	.											IFIT3,colon,carcinoma,0,2	IFIT3	36	2	0			c.G465A						PASS	.	G	,	15,4391	21.2+/-45.6	0,15,2188	75.0	84.0	81.0		465,465	-9.0	0.0	10	dbSNP_126	81	153,8447	73.5+/-136.2	1,151,4148	no	coding-synonymous,coding-synonymous	IFIT3	NM_001031683.2,NM_001549.4	,	1,166,6336	AA,AG,GG		1.7791,0.3404,1.2917	,	155/491,155/491	91098877	168,12838	2203	4300	6503	SO:0001819	synonymous_variant	3437	exon2			AAGGGCGAAGGTG	U52513	CCDS7402.1, CCDS31241.1	10q23.31	2014-05-22	2004-07-16	2004-07-16	ENSG00000119917	ENSG00000119917		"""Tetratricopeptide (TTC) repeat domain containing"""	5411	protein-coding gene	gene with protein product		604650	"""interferon-induced protein with tetratricopeptide repeats 4"""	IFIT4		9828129, 9391139	Standard	NM_001031683		Approved	ISG60, RIG-G, CIG-49, IFI60, GARG-49, IRG2	uc001kgg.3	O14879	OTTHUMG00000018708	ENST00000371818.4:c.465G>A	10.37:g.91098877G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	37	17	0.459459	NM_001549	Q99634|Q9BSK7	Silent	SNP	ENST00000371818.4	37	CCDS7402.1																																																																																			G|0.987;A|0.013	0.013	strong		0.438	IFIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049294.1	NM_001549	
SH3TC1	54436	hgsc.bcm.edu	37	4	8228943	8228943	+	Missense_Mutation	SNP	G	G	A	rs34994651	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:8228943G>A	ENST00000245105.3	+	12	1589	c.1522G>A	c.(1522-1524)Gcc>Acc	p.A508T	SH3TC1_ENST00000514274.1_3'UTR|SH3TC1_ENST00000539824.1_Missense_Mutation_p.A432T	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	508										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GTTCCTGAACGCCCCTGGGTA	0.647													G|||	151	0.0301518	0.0053	0.0677	5008	,	,		16753	0.002		0.0805	False		,,,				2504	0.0143				p.A508T	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G1522A						PASS	.	G	THR/ALA	59,4333		1,57,2138	18.0	15.0	16.0		1522	-0.4	0.0	4	dbSNP_126	16	765,7825		32,701,3562	yes	missense	SH3TC1	NM_018986.3	58	33,758,5700	AA,AG,GG		8.9057,1.3434,6.3473	benign	508/1337	8228943	824,12158	2196	4295	6491	SO:0001583	missense	54436	exon12			CTGAACGCCCCTG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.1522G>A	4.37:g.8228943G>A	ENSP00000245105:p.Ala508Thr	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	108	49	0.453704	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	81	0.03708791208791209	0	0.0	27	0.07458563535911603	2	0.0034965034965034965	52	0.06860158311345646	G	0.560	-0.845788	0.02671	0.013434	0.089057	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.75704	-0.96;-0.94	4.66	-0.429	0.12303	.	0.738581	0.13317	N	0.396990	T	0.03095	0.0091	N	0.21448	0.665	0.09310	N	1	B	0.23854	0.092	B	0.15484	0.013	T	0.01570	-1.1322	10	0.14252	T	0.57	-3.8094	5.7455	0.18118	0.5505:0.1486:0.301:0.0	rs34994651	508	Q8TE82	S3TC1_HUMAN	T	246;508;432;337	ENSP00000245105:A508T;ENSP00000441045:A432T	ENSP00000245105:A508T	A	+	1	0	SH3TC1	8279843	0.000000	0.05858	0.001000	0.08648	0.028000	0.11728	0.110000	0.15437	-0.142000	0.11354	0.561000	0.74099	GCC	G|0.948;A|0.052	0.052	strong		0.647	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
GPR144	347088	hgsc.bcm.edu	37	9	127230891	127230891	+	Missense_Mutation	SNP	G	G	A	rs10760365	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:127230891G>A	ENST00000334810.1	+	14	2248	c.2248G>A	c.(2248-2250)Gtg>Atg	p.V750M				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	750					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						GTGGAGGAAGGTGGTAGCTGT	0.622													G|||	2605	0.520168	0.5371	0.5274	5008	,	,		16910	0.6171		0.4195	False		,,,				2504	0.4959				p.V750M		Atlas-SNP	.											.	GPR144	33	.	0			c.G2248A						PASS	.	G	MET/VAL	661,723		154,353,185	98.0	84.0	88.0		2248	4.9	1.0	9	dbSNP_120	88	1390,1792		305,780,506	yes	missense	GPR144	NM_001161808.1	21	459,1133,691	AA,AG,GG		43.6832,47.7601,44.919	probably-damaging	750/964	127230891	2051,2515	692	1591	2283	SO:0001583	missense	347088	exon14			AGGAAGGTGGTAG	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.2248G>A	9.37:g.127230891G>A	ENSP00000335156:p.Val750Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	108	105	0.972222	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	1132|1132	0.5183150183150184|0.5183150183150184	242|242	0.491869918699187|0.491869918699187	185|185	0.511049723756906|0.511049723756906	381|381	0.666083916083916|0.666083916083916	324|324	0.42744063324538256|0.42744063324538256	G|G	17.72|17.72	3.459464|3.459464	0.63401|0.63401	0.477601|0.477601	0.436832|0.436832	ENSG00000180264|ENSG00000180264	ENST00000446588|ENST00000334810	.|T	.|0.49432	.|0.78	4.94|4.94	4.94|4.94	0.65067|0.65067	.|GPCR, family 2-like (1);	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.72894|0.72894	2.215|2.215	0.22610|0.22610	P|P	0.99893717|0.99893717	D|D	0.63046|0.76494	0.992|0.999	P|D	0.56865|0.87578	0.808|0.998	T|T	0.50311|0.50311	-0.8843|-0.8843	7|8	0.44086|0.72032	T|D	0.13|0.01	.|.	16.7766|16.7766	0.85552|0.85552	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs10760365;rs57939835;rs10760365|rs10760365;rs57939835;rs10760365	18|750	A1E4E8|Q7Z7M1	.|GP144_HUMAN	D|M	18|750	.|ENSP00000335156:V750M	ENSP00000414478:G18D|ENSP00000335156:V750M	G|V	+|+	2|1	0|0	GPR144|GPR144	126270712|126270712	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.233000|0.233000	0.25261|0.25261	8.590000|8.590000	0.90821|0.90821	2.278000|2.278000	0.76064|0.76064	0.561000|0.561000	0.74099|0.74099	GGT|GTG	G|0.465;A|0.535	0.535	strong		0.622	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
GRXCR2	643226	hgsc.bcm.edu	37	5	145252377	145252377	+	Missense_Mutation	SNP	C	C	T	rs34892428	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145252377C>T	ENST00000377976.1	-	1	154	c.155G>A	c.(154-156)aGt>aAt	p.S52N		NM_001080516.1	NP_001073985.1	A6NFK2	GRCR2_HUMAN	glutaredoxin, cysteine rich 2	52						cell projection (GO:0042995)				breast(1)|endometrium(1)|large_intestine(2)|lung(1)|urinary_tract(2)	7						TTGCAGAAAACTGTGAGGGTA	0.498													C|||	295	0.0589058	0.1241	0.0317	5008	,	,		19176	0.001		0.0378	False		,,,				2504	0.0716				p.S52N		Atlas-SNP	.											.	GRXCR2	32	.	0			c.G155A						PASS	.	C	ASN/SER	486,3920	227.5+/-242.7	26,434,1743	121.0	119.0	120.0		155	5.1	1.0	5	dbSNP_126	120	256,8344	99.7+/-161.2	4,248,4048	yes	missense	GRXCR2	NM_001080516.1	46	30,682,5791	TT,TC,CC		2.9767,11.0304,5.7051	probably-damaging	52/249	145252377	742,12264	2203	4300	6503	SO:0001583	missense	643226	exon1			AGAAAACTGTGAG		CCDS34263.1	5q32	2014-03-14			ENSG00000204928	ENSG00000204928			33862	protein-coding gene	gene with protein product		615762				24619944	Standard	NM_001080516		Approved	DFNB101	uc003lns.1	A6NFK2	OTTHUMG00000163417	ENST00000377976.1:c.155G>A	5.37:g.145252377C>T	ENSP00000367214:p.Ser52Asn	Somatic	197	1	0.00507614		WXS	Illumina HiSeq	Phase_I	172	171	0.994186	NM_001080516		Missense_Mutation	SNP	ENST00000377976.1	37	CCDS34263.1	103	0.04716117216117216	56	0.11382113821138211	14	0.03867403314917127	0	0.0	33	0.04353562005277045	C	16.71	3.198429	0.58126	0.110304	0.029767	ENSG00000204928	ENST00000377976	T	0.61980	0.06	5.07	5.07	0.68467	.	0.080590	0.85682	D	0.000000	T	0.05731	0.0150	M	0.63843	1.955	0.09310	P	0.99999246546	D	0.89917	1.0	D	0.85130	0.997	T	0.27123	-1.0083	9	0.31617	T	0.26	-27.4265	17.7365	0.88395	0.0:1.0:0.0:0.0	rs34892428;rs60839603	52	A6NFK2	GRCR2_HUMAN	N	52	ENSP00000367214:S52N	ENSP00000367214:S52N	S	-	2	0	GRXCR2	145232570	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	4.943000	0.63554	2.786000	0.95864	0.561000	0.74099	AGT	C|0.949;T|0.051	0.051	strong		0.498	GRXCR2-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373289.2		
HSD17B7	51478	hgsc.bcm.edu	37	1	162775267	162775267	+	Silent	SNP	C	C	T	rs12563263	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:162775267C>T	ENST00000254521.3	+	8	943	c.888C>T	c.(886-888)taC>taT	p.Y296Y	HSD17B7_ENST00000367917.3_Silent_p.Y261Y|HSD17B7_ENST00000485405.1_3'UTR	NM_016371.2	NP_057455.1	P56937	DHB7_HUMAN	hydroxysteroid (17-beta) dehydrogenase 7	296					cholesterol biosynthetic process (GO:0006695)|estrogen biosynthetic process (GO:0006703)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	3-keto sterol reductase activity (GO:0000253)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_hematologic(112;0.115)					GAAGAAATTACATTATGACCC	0.458													C|||	916	0.182907	0.1467	0.2536	5008	,	,		21225	0.1369		0.3211	False		,,,				2504	0.0869				p.Y296Y		Atlas-SNP	.											.	HSD17B7	25	.	0			c.C888T						PASS	.	C		758,3648	303.8+/-288.1	69,620,1514	55.0	50.0	52.0		888	-9.4	0.0	1	dbSNP_120	52	2812,5782	438.1+/-358.8	470,1872,1955	no	coding-synonymous	HSD17B7	NM_016371.2		539,2492,3469	TT,TC,CC		32.7205,17.2038,27.4615		296/342	162775267	3570,9430	2203	4297	6500	SO:0001819	synonymous_variant	51478	exon8			AAATTACATTATG	AF098786	CCDS1242.1	1q23	2011-09-14			ENSG00000132196	ENSG00000132196	1.1.1.270	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5215	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 37C, member 1"""	606756				10544267, 10419022, 19027726	Standard	NM_016371		Approved	PRAP, SDR37C1	uc001gci.3	P56937	OTTHUMG00000034420	ENST00000254521.3:c.888C>T	1.37:g.162775267C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	182	90	0.494505	NM_016371	Q5T246|Q7Z4V9|Q8WWS2|Q9UF00	Silent	SNP	ENST00000254521.3	37	CCDS1242.1																																																																																			T|1.000;|0.000	1.000	weak		0.458	HSD17B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083207.1	NM_016371	
TRPC1	7220	hgsc.bcm.edu	37	3	142443441	142443441	+	Missense_Mutation	SNP	G	G	A	rs78975236	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:142443441G>A	ENST00000476941.1	+	1	526	c.40G>A	c.(40-42)Gcc>Acc	p.A14T	TRPC1_ENST00000273482.6_Missense_Mutation_p.A14T	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	14					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						CCTCTCGGGCGcctcctcctc	0.692													G|||	65	0.0129792	0.0015	0.013	5008	,	,		10311	0.0		0.0487	False		,,,				2504	0.0051				p.A14T		Atlas-SNP	.											.	TRPC1	82	.	0			c.G40A						PASS	.	G	THR/ALA	30,4374	33.5+/-64.1	0,30,2172	56.0	51.0	53.0		40	3.3	1.0	3	dbSNP_131	53	387,8211	120.6+/-179.8	9,369,3921	no	missense	TRPC1	NM_003304.4	58	9,399,6093	AA,AG,GG		4.501,0.6812,3.2072	benign	14/760	142443441	417,12585	2202	4299	6501	SO:0001583	missense	7220	exon1			TCGGGCGCCTCCT	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.40G>A	3.37:g.142443441G>A	ENSP00000419313:p.Ala14Thr	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	32	17	0.53125	NM_001251845	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	37	CCDS58856.1	41	0.018772893772893772	0	0.0	5	0.013812154696132596	0	0.0	36	0.047493403693931395	G	20.3	3.969631	0.74246	0.006812	0.04501	ENSG00000144935	ENST00000476941;ENST00000273482	T;T	0.79749	-0.95;-1.3	4.3	3.26	0.37387	.	6.841970	0.00682	N	0.000686	T	0.24547	0.0595	N	0.08118	0	0.23266	N	0.998015	B;B	0.16166	0.009;0.016	B;B	0.08055	0.001;0.003	T	0.48559	-0.9025	10	0.13853	T	0.58	-0.3623	8.2108	0.31481	0.0:0.0:0.6985:0.3015	.	14;14	P48995;P48995-2	TRPC1_HUMAN;.	T	14	ENSP00000419313:A14T;ENSP00000273482:A14T	ENSP00000273482:A14T	A	+	1	0	TRPC1	143926131	.	.	1.000000	0.80357	0.945000	0.59286	.	.	2.111000	0.64477	0.536000	0.68110	GCC	G|0.977;A|0.023	0.023	strong		0.692	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53671754	53671754	+	Missense_Mutation	SNP	C	C	T	rs2111119	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:53671754C>T	ENST00000379925.3	-	21	3123	c.3073G>A	c.(3073-3075)Ggc>Agc	p.G1025S	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.G991S|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.G1025S|RPGRIP1L_ENST00000568009.1_5'UTR|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.G991S	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1025			G -> S (in dbSNP:rs2111119). {ECO:0000269|PubMed:19430481}.		camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)	p.G1025S(1)		endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				TCTACACTGCCTTCTTGTGAA	0.358													T|||	832	0.166134	0.171	0.0778	5008	,	,		18350	0.3204		0.0855	False		,,,				2504	0.1462				p.G1025S		Atlas-SNP	.											RPGRIP1L,NS,carcinoma,0,1	RPGRIP1L	118	1	1	Substitution - Missense(1)	stomach(1)	c.G3073A						PASS	.	T	SER/GLY,SER/GLY	688,3708	758.8+/-412.8	46,596,1556	115.0	110.0	111.0		2971,3073	3.0	0.5	16	dbSNP_96	111	744,7856	784.1+/-407.6	27,690,3583	yes	missense,missense	RPGRIP1L	NM_001127897.1,NM_015272.2	56,56	73,1286,5139	TT,TC,CC		8.6512,15.6506,11.0188	benign,benign	991/1236,1025/1316	53671754	1432,11564	2198	4300	6498	SO:0001583	missense	23322	exon21			CACTGCCTTCTTG		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"""fantom homolog"", ""Meckel syndrome, type 5"", ""protein phosphatase 1, regulatory subunit 134"""	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3073G>A	16.37:g.53671754C>T	ENSP00000369257:p.Gly1025Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	94	47	0.5	NM_015272	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	332	0.152014652014652	83	0.16869918699186992	24	0.06629834254143646	161	0.28146853146853146	64	0.08443271767810026	T	0.361	-0.939658	0.02322	0.156506	0.086512	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.74632	-0.64;-0.86	5.23	2.95	0.34219	.	0.323250	0.30781	N	0.008887	T	0.00012	0.0000	N	0.08118	0	0.22489	P	0.999050911	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.08269	-1.0730	9	0.02654	T	1	-0.0432	8.5044	0.33179	0.0:0.289:0.0:0.711	rs2111119;rs52836388;rs57405487;rs2111119	1025;991	Q68CZ1;Q68CZ1-2	FTM_HUMAN;.	S	1025;991	ENSP00000369257:G1025S;ENSP00000262135:G991S	ENSP00000262135:G991S	G	-	1	0	RPGRIP1L	52229255	0.984000	0.35163	0.546000	0.28166	0.630000	0.37929	1.723000	0.38053	0.024000	0.15214	-0.361000	0.07541	GGC	C|0.869;T|0.131	0.131	strong		0.358	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
NUP50	10762	hgsc.bcm.edu	37	22	45574145	45574145	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:45574145A>G	ENST00000347635.4	+	5	833	c.367A>G	c.(367-369)Acc>Gcc	p.T123A	NUP50_ENST00000396096.2_Missense_Mutation_p.T95A|NUP50_ENST00000407019.2_Missense_Mutation_p.T95A|CTA-268H5.12_ENST00000610217.1_RNA|NUP50_ENST00000486184.1_3'UTR|NUP50_ENST00000425733.2_5'UTR	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	123	5 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.T123A(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGGCCCTACCACCTTGGTTGA	0.403																																					p.T123A		Atlas-SNP	.											NUP50,hand,carcinoma,0,2	NUP50	24	2	1	Substitution - Missense(1)	skin(1)	c.A367G						scavenged	.						70.0	69.0	69.0					22																	45574145		2203	4300	6503	SO:0001583	missense	10762	exon5			CCTACCACCTTGG	AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"""nucleoporin 50kD"""	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.367A>G	22.37:g.45574145A>G	ENSP00000345895:p.Thr123Ala	Somatic	243	13	0.0534979		WXS	Illumina HiSeq	Phase_I	254	24	0.0944882	NM_007172	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Missense_Mutation	SNP	ENST00000347635.4	37	CCDS14062.1	.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042164	0.01997	.	.	ENSG00000093000	ENST00000347635;ENST00000407019;ENST00000396096	.	.	.	5.46	-6.61	0.01818	Nuclear pore complex, NUP2/50/61 (1);	1.214170	0.05550	N	0.567335	T	0.23572	0.0570	L	0.36672	1.1	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.24657	-1.0154	9	0.09338	T	0.73	-0.2565	3.9641	0.09423	0.2425:0.1011:0.4317:0.2247	.	123	Q9UKX7	NUP50_HUMAN	A	123;95;95	.	ENSP00000345895:T123A	T	+	1	0	NUP50	43952809	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.532000	0.06164	-1.798000	0.01250	-5.607000	0.00000	ACC	.	.	none		0.403	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2		
CFAP61	26074	hgsc.bcm.edu	37	20	20150027	20150027	+	Silent	SNP	C	C	T	rs6075630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:20150027C>T	ENST00000245957.5	+	13	1384	c.1308C>T	c.(1306-1308)aaC>aaT	p.N436N	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000451767.2_Silent_p.N436N|C20orf26_ENST00000377306.1_Silent_p.N436N|C20orf26_ENST00000377309.2_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		436										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TCATCCAGAACTTCGTGAAAA	0.478													C|||	700	0.139776	0.0371	0.1254	5008	,	,		13679	0.0407		0.2664	False		,,,				2504	0.2607				p.N436N		Atlas-SNP	.											.	C20orf26	188	.	0			c.C1308T						PASS	.	C	,	277,4129	154.0+/-187.5	14,249,1940	124.0	110.0	115.0		1308,1308	3.6	1.0	20	dbSNP_114	115	2287,6313	386.3+/-341.8	306,1675,2319	no	coding-synonymous,coding-synonymous	C20orf26	NM_001167816.1,NM_015585.3	,	320,1924,4259	TT,TC,CC		26.593,6.2869,19.714	,	436/471,436/1238	20150027	2564,10442	2203	4300	6503	SO:0001819	synonymous_variant	26074	exon13			CCAGAACTTCGTG																												ENST00000245957.5:c.1308C>T	20.37:g.20150027C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	115	61	0.530435	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	37	CCDS33447.1	296	0.13553113553113552	21	0.042682926829268296	43	0.11878453038674033	25	0.043706293706293704	207	0.27308707124010556	C	7.575	0.667501	0.14710	0.062869	0.26593	ENSG00000089101	ENST00000431753	.	.	.	5.87	3.59	0.41128	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999026	.	.	.	.	.	.	T	0.16808	-1.0390	3	.	.	.	.	8.8967	0.35470	0.0:0.7867:0.0:0.2133	rs6075630;rs17399316;rs6075630	.	.	.	I	2	.	.	T	+	2	0	C20orf26	20098027	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	0.958000	0.29227	1.625000	0.50366	0.655000	0.94253	ACT	C|0.834;T|0.166	0.166	strong		0.478	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
ATE1	11101	hgsc.bcm.edu	37	10	123549691	123549691	+	Silent	SNP	T	T	G	rs35350755	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123549691T>G	ENST00000224652.6	-	11	1456	c.1371A>C	c.(1369-1371)ccA>ccC	p.P457P	ATE1_ENST00000543447.1_Silent_p.P342P|ATE1_ENST00000540606.1_Silent_p.P450P|ATE1_ENST00000535655.1_Silent_p.P158P|ATE1_ENST00000369043.3_Silent_p.P457P|ATE1_ENST00000369040.3_Silent_p.P361P	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	457					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)				TACCTGCTTCTGGGTCCTGGT	0.483													T|||	2512	0.501597	0.4879	0.4813	5008	,	,		20044	0.5387		0.4284	False		,,,				2504	0.5716				p.P457P		Atlas-SNP	.											.	ATE1	67	.	0			c.A1371C						PASS	.	T	,	2112,2294	576.7+/-384.3	511,1090,602	110.0	110.0	110.0		1371,1371	-8.7	0.8	10	dbSNP_126	110	3825,4775	539.9+/-383.7	856,2113,1331	no	coding-synonymous,coding-synonymous	ATE1	NM_001001976.1,NM_007041.2	,	1367,3203,1933	GG,GT,TT		44.4767,47.9346,45.6482	,	457/519,457/519	123549691	5937,7069	2203	4300	6503	SO:0001819	synonymous_variant	11101	exon11			TGCTTCTGGGTCC	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.1371A>C	10.37:g.123549691T>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	98	50	0.510204	NM_001001976	O95261|Q5SQQ3|Q8WW04	Silent	SNP	ENST00000224652.6	37	CCDS31300.1																																																																																			T|0.544;G|0.456	0.456	strong		0.483	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	
KRT6A	3853	hgsc.bcm.edu	37	12	52886478	52886478	+	Silent	SNP	T	T	C	rs376545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52886478T>C	ENST00000330722.6	-	1	563	c.495A>G	c.(493-495)gaA>gaG	p.E165E		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	165	Coil 1A.|Rod.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCTTGATCTGTTCACGCTCCT	0.587													T|||	1808	0.361022	0.3238	0.3458	5008	,	,		19063	0.5397		0.3748	False		,,,				2504	0.2239				p.E165E		Atlas-SNP	.											.	KRT6A	89	.	0			c.A495G						PASS	.	T		1353,3053	449.6+/-349.1	213,927,1063	178.0	164.0	169.0		495	2.4	1.0	12	dbSNP_80	169	3145,5453	473.5+/-368.6	610,1925,1764	no	coding-synonymous	KRT6A	NM_005554.3		823,2852,2827	CC,CT,TT		36.5783,30.7081,34.5894		165/565	52886478	4498,8506	2203	4299	6502	SO:0001819	synonymous_variant	3853	exon1			GATCTGTTCACGC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.495A>G	12.37:g.52886478T>C		Somatic	343	0	0		WXS	Illumina HiSeq	Phase_I	303	134	0.442244	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																			T|0.615;C|0.385	0.385	strong		0.587	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
NUP133	55746	hgsc.bcm.edu	37	1	229623338	229623338	+	Missense_Mutation	SNP	T	T	C	rs1065674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:229623338T>C	ENST00000261396.3	-	10	1308	c.1217A>G	c.(1216-1218)cAg>cGg	p.Q406R	NUP133_ENST00000537506.1_Missense_Mutation_p.Q390R	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	406			Q -> R (in dbSNP:rs1065674).		carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				GACCGTCAACTGACACAAAAT	0.338													C|||	1519	0.303315	0.5802	0.3271	5008	,	,		16738	0.1607		0.2097	False		,,,				2504	0.1554				p.Q406R		Atlas-SNP	.											.	NUP133	111	.	0			c.A1217G						PASS	.	C	ARG/GLN	2321,2085	571.2+/-383.0	600,1121,482	83.0	85.0	84.0		1217	2.2	0.4	1	dbSNP_86	84	1863,6737	729.6+/-406.7	201,1461,2638	yes	missense	NUP133	NM_018230.2	43	801,2582,3120	CC,CT,TT		21.6628,47.3218,32.1698	benign	406/1157	229623338	4184,8822	2203	4300	6503	SO:0001583	missense	55746	exon10			GTCAACTGACACA		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1217A>G	1.37:g.229623338T>C	ENSP00000261396:p.Gln406Arg	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	44	44	1	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	612	0.2802197802197802	275	0.5589430894308943	100	0.27624309392265195	80	0.13986013986013987	157	0.20712401055408972	C	0.017	-1.505721	0.00992	0.526782	0.216628	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.35605	1.3;1.3;1.3	5.07	2.2	0.27929	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.167226	0.56097	N	0.000039	T	0.00012	0.0000	N	0.01015	-1.05	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48525	-0.9028	9	0.02654	T	1	-5.5753	9.3235	0.37980	0.0:0.583:0.0:0.417	rs1065674;rs17355666;rs60689296;rs1065674	406	Q8WUM0	NU133_HUMAN	R	406;406;406;390	ENSP00000261396:Q406R;ENSP00000355640:Q406R;ENSP00000443496:Q390R	ENSP00000261396:Q406R	Q	-	2	0	NUP133	227689961	0.910000	0.30920	0.355000	0.25773	0.580000	0.36256	1.748000	0.38308	0.029000	0.15352	-1.952000	0.00485	CAG	T|0.691;C|0.309	0.309	strong		0.338	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
PRDM15	63977	hgsc.bcm.edu	37	21	43221826	43221826	+	Silent	SNP	T	T	C	rs2236696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43221826T>C	ENST00000269844.3	-	31	4208	c.4098A>G	c.(4096-4098)ttA>ttG	p.L1366L	PRDM15_ENST00000538201.1_Silent_p.L1020L|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000422911.1_Silent_p.L1057L|PRDM15_ENST00000447207.2_Silent_p.L1000L|PRDM15_ENST00000398548.1_Silent_p.L1037L	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1366					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						TGATGTTGGTTAAGCCGACTG	0.547													c|||	3948	0.788339	0.9569	0.6182	5008	,	,		17439	0.7718		0.6978	False		,,,				2504	0.7914				p.L1366L		Atlas-SNP	.											.	PRDM15	110	.	0			c.A4098G						PASS	.		,	4029,377	189.9+/-215.9	1842,345,16	66.0	66.0	66.0		3111,4098	2.6	0.9	21	dbSNP_98	66	6243,2357	392.8+/-344.1	2261,1721,318	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	4103,2066,334	CC,CT,TT		27.407,8.5565,21.0211	,	1037/1179,1366/1508	43221826	10272,2734	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon31			GTTGGTTAAGCCG	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4098A>G	21.37:g.43221826T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	122	122	1	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			T|0.226;C|0.774	0.774	strong		0.547	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
XDH	7498	hgsc.bcm.edu	37	2	31571786	31571786	+	Silent	SNP	A	A	G	rs1884725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:31571786A>G	ENST00000379416.3	-	27	3078	c.3030T>C	c.(3028-3030)ttT>ttC	p.F1010F		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	1010					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	AAGGAACTGTAAAGCTTATTC	0.393													G|||	4006	0.79992	0.7655	0.7565	5008	,	,		21625	0.8482		0.7903	False		,,,				2504	0.8374				p.F1010F	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T3030C						PASS	.	G		3517,889	344.4+/-308.1	1404,709,90	100.0	100.0	100.0		3030	4.1	0.9	2	dbSNP_92	100	6536,2064	357.1+/-330.6	2464,1608,228	no	coding-synonymous	XDH	NM_000379.3		3868,2317,318	GG,GA,AA		24.0,20.177,22.7049		1010/1334	31571786	10053,2953	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon27			AACTGTAAAGCTT	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.3030T>C	2.37:g.31571786A>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	144	69	0.479167	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			A|0.214;G|0.786	0.786	strong		0.393	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
CROCC	9696	hgsc.bcm.edu	37	1	17272037	17272037	+	Missense_Mutation	SNP	G	G	A	rs142404824	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17272037G>A	ENST00000375541.5	+	15	2141	c.2072G>A	c.(2071-2073)cGc>cAc	p.R691H	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCGCTGAGCCGCGCCACACTG	0.637																																					p.R691H		Atlas-SNP	.											CROCC,colon,carcinoma,-1,1	CROCC	185	1	0			c.G2072A						PASS	.						18.0	15.0	16.0					1																	17272037		2196	4279	6475	SO:0001583	missense	9696	exon15			TGAGCCGCGCCAC	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.2072G>A	1.37:g.17272037G>A	ENSP00000364691:p.Arg691His	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	326	18	0.0552147	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	52	0.023809523809523808	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	35	0.04617414248021108	G	9.043	0.990268	0.18966	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.11063	2.81	5.01	0.883	0.19177	.	.	.	.	.	T	0.00784	0.0026	N	0.14661	0.345	0.09310	N	1	P;B	0.43578	0.811;0.002	B;B	0.36504	0.226;0.001	T	0.37079	-0.9721	9	0.62326	D	0.03	.	4.9211	0.13871	0.3313:0.1887:0.48:0.0	.	554;691	A1L0S8;Q5TZA2	.;CROCC_HUMAN	H	691;572	ENSP00000364691:R691H	ENSP00000364691:R691H	R	+	2	0	CROCC	17144624	0.000000	0.05858	0.061000	0.19648	0.207000	0.24258	-0.033000	0.12246	0.298000	0.22638	-0.224000	0.12420	CGC	G|0.972;A|0.028	0.028	strong		0.637	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
TTN	7273	hgsc.bcm.edu	37	2	179605725	179605725	+	Missense_Mutation	SNP	T	T	C	rs34070843	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179605725T>C	ENST00000591111.1	-	46	11508	c.11284A>G	c.(11284-11286)Att>Gtt	p.I3762V	TTN_ENST00000342175.6_Missense_Mutation_p.I3908V|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.I4079V|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I3716V|TTN_ENST00000359218.5_Missense_Mutation_p.I3841V			Q8WZ42	TITIN_HUMAN	titin	33926			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)			GCTTTCAAAATGGTGTCTTTT	0.433													T|||	81	0.0161741	0.0	0.0202	5008	,	,		21621	0.0		0.0268	False		,,,				2504	0.0409				p.I4079V		Atlas-SNP	.											.	TTN	18412	.	0			c.A12235G						PASS	.	T	VAL/ILE,,VAL/ILE,VAL/ILE	20,3700		0,20,1840	125.0	121.0	122.0		11146,,11521,11722	-1.7	0.0	2	dbSNP_126	122	152,8056		1,150,3953	yes	missense,intron,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	29,,29,29	1,170,5793	CC,CT,TT		1.8519,0.5376,1.442	,,,	3716/26927,,3841/27052,3908/27119	179605725	172,11756	1860	4104	5964	SO:0001583	missense	7273	exon48			TCAAAATGGTGTC	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.11284A>G	2.37:g.179605725T>C	ENSP00000465570:p.Ile3762Val	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	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		20	0.009157509157509158	0	0.0	7	0.019337016574585635	0	0.0	13	0.017150395778364115	T	4.390	0.072015	0.08436	0.005376	0.018519	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.60920	0.23;0.15;0.16	5.37	-1.66	0.08265	.	.	.	.	.	T	0.23572	0.0570	L	0.27053	0.805	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	0.22243	-1.0222	9	0.87932	D	0	.	5.8073	0.18448	0.0:0.2752:0.2348:0.49	rs34070843	3716;3841;3908	D3DPF9;E7EQE6;E7ET18	.;.;.	V	3716;3908;3841;3716	ENSP00000434586:I3716V;ENSP00000340554:I3908V;ENSP00000352154:I3841V	ENSP00000340554:I3908V	I	-	1	0	TTN	179313970	0.018000	0.18449	0.023000	0.16930	0.061000	0.15899	0.033000	0.13754	-0.441000	0.07201	-0.290000	0.09829	ATT	T|0.989;C|0.011	0.011	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TMPRSS11BNL	401136	hgsc.bcm.edu	37	4	69056974	69056974	+	Silent	SNP	T	T	G	rs114552880	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:69056974T>G	ENST00000432593.3	-	4	469	c.303A>C	c.(301-303)tcA>tcC	p.S101S	FTLP10_ENST00000503647.1_RNA|RP11-646E20.6_ENST00000510782.1_RNA					TMPRSS11B N-terminal like, pseudogene											autonomic_ganglia(1)	1						TACACCAGTGTGATGACTTGA	0.318													T|||	107	0.0213658	0.0015	0.0504	5008	,	,		18643	0.001		0.0507	False		,,,				2504	0.0184				p.S101S		Atlas-SNP	.											TMPRSS11BNL,caecum,carcinoma,0,1	TMPRSS11BNL	4	1	0			c.A303C						PASS	.	T		12,1372		0,12,680	340.0	279.0	298.0		303	3.4	1.0	4	dbSNP_132	298	138,3040		7,124,1458	no	coding-synonymous	TMPRSS11BNL	NM_001129907.2		7,136,2138	GG,GT,TT		4.3424,0.8671,3.288		101/106	69056974	150,4412	692	1589	2281	SO:0001819	synonymous_variant	401136	exon4			CCAGTGTGATGAC			4q13.2	2014-05-09	2014-05-08		ENSG00000226894	ENSG00000250026			37262	pseudogene	pseudogene			"""TMPRSS11B N terminal-like"", ""TMPRSS11B N-terminal like"""				Standard	NR_104048		Approved	FLJ41562	uc003hdv.1		OTTHUMG00000160802	ENST00000432593.3:c.303A>C	4.37:g.69056974T>G		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	97	46	0.474227	NM_001129907		Silent	SNP	ENST00000432593.3	37	CCDS47066.1																																																																																			T|0.973;G|0.027	0.027	strong		0.318	TMPRSS11BNL-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001129907	
FAM21C	253725	hgsc.bcm.edu	37	10	46254776	46254776	+	Missense_Mutation	SNP	A	A	C	rs199848673		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:46254776A>C	ENST00000336378.4	+	17	1680	c.1562A>C	c.(1561-1563)tAc>tCc	p.Y521S	FAM21C_ENST00000537517.1_Missense_Mutation_p.Y497S|FAM21C_ENST00000359860.4_Missense_Mutation_p.Y465S|FAM21C_ENST00000540872.1_Missense_Mutation_p.Y521S|FAM21C_ENST00000374362.2_Missense_Mutation_p.Y521S	NM_015262.2	NP_056077.2	Q9Y4E1	FA21C_HUMAN	family with sequence similarity 21, member C	521				Y -> S (in Ref. 1; BAA25518 and 2; BAG64168). {ECO:0000305}.	retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|endosome (GO:0005768)|plasma membrane (GO:0005886)|WASH complex (GO:0071203)		p.Y520S(3)|p.Y521S(2)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						ACCTTATCTTACAGCAAAAAT	0.413																																					p.Y521S		Atlas-SNP	.											FAM21C,NS,carcinoma,0,6	FAM21C	68	6	5	Substitution - Missense(5)	prostate(4)|skin(1)	c.A1562C						scavenged	.	C	SER/TYR,SER/TYR,SER/TYR	254,3222		29,196,1513	61.0	73.0	69.0		1562,1490,1562	3.3	0.7	10	dbSNP_134	69	410,7550		58,294,3628	yes	missense,missense,missense	FAM21C	NM_001169106.1,NM_001169107.1,NM_015262.2	144,144,144	87,490,5141	CC,CA,AA		5.1508,7.3072,5.8062	benign,benign,benign	521/1280,497/1246,521/1321	46254776	664,10772	1738	3980	5718	SO:0001583	missense	253725	exon17			TATCTTACAGCAA		CCDS44374.1, CCDS44374.2, CCDS53528.1, CCDS53529.1	10q11.22	2014-05-09			ENSG00000172661	ENSG00000172661			23414	protein-coding gene	gene with protein product		613631				20498093	Standard	NM_015262		Approved	Em:AC012044.3, KIAA0592	uc001jcu.3	Q9Y4E1	OTTHUMG00000018089	ENST00000336378.4:c.1562A>C	10.37:g.46254776A>C	ENSP00000337541:p.Tyr521Ser	Somatic	398	1	0.00251256		WXS	Illumina HiSeq	Phase_I	285	41	0.14386	NM_015262	B4DZQ6|B9EK53|F5H0J6|F5H871|Q5SQU4|Q5SQU5|Q7L521|Q9UG79	Missense_Mutation	SNP	ENST00000336378.4	37		.	.	.	.	.	.	.	.	.	.	C	0.006	-2.057382	0.00390	0.073072	0.051508	ENSG00000172661	ENST00000336378;ENST00000540872;ENST00000537517;ENST00000374362;ENST00000399588;ENST00000359860;ENST00000436993	.	.	.	3.26	3.26	0.37387	.	0.662706	0.15995	N	0.234623	T	0.00496	0.0016	N	0.00099	-2.14	0.54753	P	1.4999999999987246E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.25950	-1.0117	8	0.02654	T	1	0.2567	9.8043	0.40783	0.2076:0.7924:0.0:0.0	.	497;521;521;466	F5H871;Q9Y4E1-4;Q9Y4E1;Q9Y4E1-3	.;.;FA21C_HUMAN;.	S	521;521;497;521;521;465;433	.	ENSP00000337541:Y521S	Y	+	2	0	FAM21C	45574782	0.554000	0.26522	0.660000	0.29694	0.197000	0.23852	2.157000	0.42320	0.721000	0.32231	-0.488000	0.04728	TAC	A|0.300;C|0.700	0.700	strong		0.413	FAM21C-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276888	71276888	+	Silent	SNP	T	T	C	rs12793134		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71276888T>C	ENST00000398531.1	+	1	280	c.255T>C	c.(253-255)ggT>ggC	p.G85G	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	85	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GGGGCTGTGGTTCCTGTGGGG	0.682																																					p.G85G		Atlas-SNP	.											KRTAP5-10,NS,neuroblastoma,0,1	KRTAP5-10	37	1	0			c.T255C						scavenged	.						44.0	64.0	57.0					11																	71276888		2125	4249	6374	SO:0001819	synonymous_variant	387273	exon1			CTGTGGTTCCTGT	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.255T>C	11.37:g.71276888T>C		Somatic	109	1	0.00917431		WXS	Illumina HiSeq	Phase_I	93	6	0.0645161	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			T|0.998;C|0.002	0.002	weak		0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
CDON	50937	hgsc.bcm.edu	37	11	125830906	125830906	+	Silent	SNP	T	T	G	rs139588649		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:125830906T>G	ENST00000392693.3	-	20	3922	c.3795A>C	c.(3793-3795)acA>acC	p.T1265T	CDON_ENST00000531738.1_Silent_p.T619T|RP11-680F20.12_ENST00000582823.1_RNA|CDON_ENST00000263577.7_Silent_p.T1242T	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	1265					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)		GAGACCACATTGTCTTCTCAG	0.507													T|||	1	0.000199681	0.0	0.0	5008	,	,		16578	0.0		0.0	False		,,,				2504	0.001				p.T1265T		Atlas-SNP	.											.	CDON	137	.	0			c.A3795C						PASS	.	T		1,4401	2.1+/-5.4	0,1,2200	129.0	127.0	128.0		3726	-1.1	0.0	11	dbSNP_134	128	6,8592	5.0+/-18.6	0,6,4293	no	coding-synonymous	CDON	NM_016952.4		0,7,6493	GG,GT,TT		0.0698,0.0227,0.0538		1242/1265	125830906	7,12993	2201	4299	6500	SO:0001819	synonymous_variant	50937	exon20			CCACATTGTCTTC	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.3795A>C	11.37:g.125830906T>G		Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	198	96	0.484848	NM_001243597	O14631	Silent	SNP	ENST00000392693.3	37	CCDS58192.1																																																																																			T|1.000;G|0.000	0.000	weak		0.507	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	
MOG	4340	hgsc.bcm.edu	37	6	29627313	29627313	+	Silent	SNP	A	A	G	rs34758289	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29627313A>G	ENST00000376917.3	+	2	535	c.306A>G	c.(304-306)aaA>aaG	p.K102K	MOG_ENST00000490427.1_Intron|MOG_ENST00000483013.1_Intron|MOG_ENST00000494692.1_Silent_p.K102K|MOG_ENST00000376894.4_Silent_p.K102K|MOG_ENST00000396701.2_Silent_p.K102K|MOG_ENST00000469603.1_3'UTR|MOG_ENST00000376888.2_Intron|MOG_ENST00000431798.2_Silent_p.K102K|MOG_ENST00000376898.3_Silent_p.K102K|MOG_ENST00000376902.3_Silent_p.K102K|MOG_ENST00000396704.3_Silent_p.K102K|MOG_ENST00000416766.2_Silent_p.K102K|MOG_ENST00000533330.2_Silent_p.K102K|MOG_ENST00000376891.4_Silent_p.K102K	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein	102	Ig-like V-type.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						AGCTGCTGAAAGATGCTATTG	0.517													A|||	22	0.00439297	0.0	0.0101	5008	,	,		20536	0.0		0.0149	False		,,,				2504	0.0				p.K102K		Atlas-SNP	.											.	MOG	47	.	0			c.A306G						PASS	.	A	,,,,,,,,	6,3016		0,6,1505	95.0	94.0	95.0		306,306,,306,306,306,306,306,	0.7	1.0	6	dbSNP_126	95	77,5341		1,75,2633	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	MOG	NM_001008228.2,NM_001008229.2,NM_001170418.1,NM_002433.4,NM_206809.3,NM_206810.3,NM_206811.3,NM_206812.3,NM_206814.5	,,,,,,,,	1,81,4138	GG,GA,AA		1.4212,0.1985,0.9834	,,,,,,,,	102/225,102/207,,102/253,102/248,102/214,102/230,102/209,	29627313	83,8357	1511	2709	4220	SO:0001819	synonymous_variant	4340	exon2			GCTGAAAGATGCT		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099	ENST00000376917.3:c.306A>G	6.37:g.29627313A>G		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	150	69	0.46	NM_001008229	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Silent	SNP	ENST00000376917.3	37	CCDS34370.1																																																																																			A|0.992;G|0.008	0.008	strong		0.517	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433	
PYGB	5834	hgsc.bcm.edu	37	20	25259006	25259006	+	Missense_Mutation	SNP	G	G	T	rs2228976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25259006G>T	ENST00000216962.4	+	8	1017	c.907G>T	c.(907-909)Gcc>Tcc	p.A303S		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	303			A -> S (in dbSNP:rs2228976).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)	p.A303S(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						CGTGGTGGCCGCCACGCTCCA	0.607													g|||	813	0.16234	0.053	0.1297	5008	,	,		17613	0.3512		0.1849	False		,,,				2504	0.1155				p.A303S		Atlas-SNP	.											PYGB,NS,carcinoma,0,2	PYGB	84	2	1	Substitution - Missense(1)	stomach(1)	c.G907T						PASS	.	G	SER/ALA	352,4054	181.2+/-209.3	10,332,1861	80.0	73.0	75.0		907	3.6	1.0	20	dbSNP_98	75	1597,7003	296.5+/-302.9	154,1289,2857	yes	missense	PYGB	NM_002862.3	99	164,1621,4718	TT,TG,GG		18.5698,7.9891,14.9854	probably-damaging	303/844	25259006	1949,11057	2203	4300	6503	SO:0001583	missense	5834	exon8			GTGGCCGCCACGC		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.907G>T	20.37:g.25259006G>T	ENSP00000216962:p.Ala303Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	101	46	0.455446	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	427	0.1955128205128205	29	0.05894308943089431	58	0.16022099447513813	198	0.34615384615384615	142	0.18733509234828497	G	29.8	5.036398	0.93630	0.079891	0.185698	ENSG00000100994	ENST00000216962	D	0.96459	-4.02	3.61	3.61	0.41365	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.89095	3.005	0.09310	P	0.9999999999226815	D	0.55385	0.971	D	0.66084	0.941	T	0.00000	-1.8628	9	0.54805	T	0.06	-33.8764	15.4242	0.75038	0.0:0.0:1.0:0.0	rs2228976;rs3818199;rs2228976	303	P11216	PYGB_HUMAN	S	303	ENSP00000216962:A303S	ENSP00000216962:A303S	A	+	1	0	PYGB	25207006	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.378000	0.97191	2.027000	0.59764	0.462000	0.41574	GCC	G|0.833;T|0.167	0.167	strong		0.607	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
ZNF596	169270	hgsc.bcm.edu	37	8	194695	194695	+	Missense_Mutation	SNP	C	C	A	rs148383942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:194695C>A	ENST00000398612.1	+	5	683	c.300C>A	c.(298-300)agC>agA	p.S100R	ZNF596_ENST00000308811.4_Missense_Mutation_p.S100R|ZNF596_ENST00000320552.2_Intron	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(5)	14		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)		CCACCATCAGCACAATGGTAA	0.358													.|||	10	0.00199681	0.0008	0.0014	5008	,	,		19470	0.0		0.002	False		,,,				2504	0.0061				p.S100R		Atlas-SNP	.											.	ZNF596	34	.	0			c.C300A						PASS	.	C	ARG/SER,ARG/SER,ARG/SER	0,4406		0,0,2203	120.0	101.0	108.0		300,300,300	-3.2	0.0	8	dbSNP_134	108	20,8580		0,20,4280	yes	missense,missense,missense	ZNF596	NM_001042415.1,NM_001042416.1,NM_173539.2	110,110,110	0,20,6483	AA,AC,CC		0.2326,0.0,0.1538	benign,benign,benign	100/505,100/505,100/505	194695	20,12986	2203	4300	6503	SO:0001583	missense	169270	exon5			CATCAGCACAATG	BC026190	CCDS5951.2	8p23.3	2013-01-08			ENSG00000172748	ENSG00000172748		"""Zinc fingers, C2H2-type"", ""-"""	27268	protein-coding gene	gene with protein product						12477932	Standard	NM_001287256		Approved		uc003wot.3	Q8TC21	OTTHUMG00000086931	ENST00000398612.1:c.300C>A	8.37:g.194695C>A	ENSP00000381613:p.Ser100Arg	Somatic	212	1	0.00471698		WXS	Illumina HiSeq	Phase_I	219	117	0.534247	NM_173539	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	.	6.943	0.543844	0.13312	0.0	0.002326	ENSG00000172748	ENST00000521145;ENST00000308811;ENST00000522866;ENST00000398612	T;T;T	0.13778	2.56;3.47;3.47	2.91	-3.16	0.05217	.	.	.	.	.	T	0.02342	0.0072	N	0.03194	-0.395	0.09310	N	1	B	0.21381	0.055	B	0.12837	0.008	T	0.40757	-0.9546	9	0.10111	T	0.7	.	1.2469	0.01974	0.2252:0.2777:0.3413:0.1559	.	100	Q8TC21	ZN596_HUMAN	R	100	ENSP00000429671:S100R;ENSP00000310033:S100R;ENSP00000381613:S100R	ENSP00000310033:S100R	S	+	3	2	ZNF596	184695	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.119000	0.03276	-0.755000	0.04709	0.591000	0.81541	AGC	C|0.997;A|0.003	0.003	strong		0.358	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539	
ZNF664	144348	hgsc.bcm.edu	37	12	124496864	124496864	+	Missense_Mutation	SNP	T	T	G	rs80197353	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124496864T>G	ENST00000539644.1	+	6	2003	c.173T>G	c.(172-174)gTc>gGc	p.V58G	ZNF664_ENST00000538932.2_Missense_Mutation_p.V58G|ZNF664_ENST00000337815.4_Missense_Mutation_p.V58G|FAM101A_ENST00000545615.1_Intron|ZNF664_ENST00000392404.3_Missense_Mutation_p.V58G			Q8N3J9	ZN664_HUMAN	zinc finger protein 664	58					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(5)|lung(6)|skin(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.000239)|OV - Ovarian serous cystadenocarcinoma(86;0.000247)|all cancers(50;0.00155)|BRCA - Breast invasive adenocarcinoma(302;0.249)		GGAGAGAAGGTCTATAAATGT	0.373													T|||	255	0.0509185	0.0333	0.0447	5008	,	,		21967	0.0		0.0984	False		,,,				2504	0.0828				p.V58G		Atlas-SNP	.											.	ZNF664	27	.	0			c.T173G						PASS	.	T	GLY/VAL,,GLY/VAL	212,4194		0,212,1991	92.0	101.0	98.0		173,,173	3.2	1.0	12	dbSNP_131	98	827,7773		0,827,3473	yes	missense,intron,missense	ZNF664,ZNF664-FAM101A	NM_001204298.1,NM_001204299.1,NM_152437.2	109,,109	0,1039,5464	GG,GT,TT		9.6163,4.8116,7.9886	benign,,benign	58/262,,58/262	124496864	1039,11967	2203	4300	6503	SO:0001583	missense	144348	exon5			AGAAGGTCTATAA		CCDS9257.1	12q24.31	2013-05-10			ENSG00000179195	ENSG00000179195		"""Zinc fingers, C2H2-type"""	25406	protein-coding gene	gene with protein product			"""zinc finger protein 176"""	ZNF176		12477932	Standard	NM_001204298		Approved	ZFOC1, DKFZp761B128	uc001uga.3	Q8N3J9	OTTHUMG00000168596	ENST00000539644.1:c.173T>G	12.37:g.124496864T>G	ENSP00000441405:p.Val58Gly	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	174	48	0.275862	NM_152437	B3KP97|Q15914|Q3ZCQ7	Missense_Mutation	SNP	ENST00000539644.1	37	CCDS9257.1	107	0.04899267399267399	14	0.028455284552845527	18	0.049723756906077346	0	0.0	75	0.09894459102902374	T	15.37	2.814650	0.50527	0.048116	0.096163	ENSG00000179195	ENST00000539644;ENST00000392404;ENST00000538932;ENST00000337815	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	4.4	3.25	0.37280	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36628	N	0.002500	T	0.00384	0.0012	L	0.33668	1.02	0.54753	D	0.999987	P	0.40083	0.702	P	0.44623	0.455	T	0.28299	-1.0048	9	.	.	.	-24.1678	6.119	0.20142	0.0:0.1965:0.0:0.8035	.	58	Q8N3J9	ZN664_HUMAN	G	58	ENSP00000441405:V58G;ENSP00000376205:V58G;ENSP00000440645:V58G;ENSP00000337320:V58G	.	V	+	2	0	ZNF664	123062817	0.989000	0.36119	0.994000	0.49952	0.992000	0.81027	2.596000	0.46205	1.007000	0.39238	0.533000	0.62120	GTC	T|0.928;G|0.072	0.072	strong		0.373	ZNF664-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400365.1	NM_152437	
TMEM230	29058	hgsc.bcm.edu	37	20	5086918	5086918	+	Silent	SNP	G	G	A	rs147693982	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5086918G>A	ENST00000379286.2	-	4	558	c.138C>T	c.(136-138)atC>atT	p.I46I	TMEM230_ENST00000342308.5_Silent_p.I109I|TMEM230_ENST00000379283.2_Silent_p.I46I|TMEM230_ENST00000379277.2_Silent_p.I46I|TMEM230_ENST00000202834.7_Silent_p.I46I|TMEM230_ENST00000379279.2_Silent_p.I46I|TMEM230_ENST00000492419.1_5'UTR	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	46						integral component of membrane (GO:0016021)											TGGCAAGTGCGATGGCCTTAT	0.443													G|||	21	0.00419329	0.0	0.0058	5008	,	,		15312	0.0		0.0169	False		,,,				2504	0.0				p.I109I		Atlas-SNP	.											.	.	.	.	0			c.C327T						PASS	.	G	,,,	26,4380	32.6+/-62.9	0,26,2177	63.0	62.0	62.0		327,138,138,138	-5.4	0.7	20	dbSNP_134	62	156,8444	74.5+/-137.1	2,152,4146	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C20orf30	NM_001009923.1,NM_001009924.1,NM_001009925.1,NM_014145.4	,,,	2,178,6323	AA,AG,GG		1.814,0.5901,1.3994	,,,	109/184,46/121,46/121,46/121	5086918	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	29058	exon4			AAGTGCGATGGCC	AF161392	CCDS13086.1, CCDS33438.1	20p13	2012-03-16	2012-03-16	2012-03-16	ENSG00000089063	ENSG00000089063			15876	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 30"""	C20orf30			Standard	XM_005260713		Approved	HSPC274	uc002wlk.3	Q96A57	OTTHUMG00000031796	ENST00000379286.2:c.138C>T	20.37:g.5086918G>A		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	94	53	0.56383	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Silent	SNP	ENST00000379286.2	37	CCDS13086.1																																																																																			G|0.990;A|0.010	0.010	strong		0.443	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26422651	26422651	+	Silent	SNP	G	G	A	rs199593757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26422651G>A	ENST00000407587.2	+	43	6883	c.6714G>A	c.(6712-6714)ccG>ccA	p.P2238P	MYO18B_ENST00000335473.7_Silent_p.P2237P|MYO18B_ENST00000536101.1_Silent_p.P2237P			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2237						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						ATACATCCCCGCTGTCGAGGG	0.597													G|||	13	0.00259585	0.0	0.0014	5008	,	,		18385	0.0		0.001	False		,,,				2504	0.0112				p.P2237P		Atlas-SNP	.											.	MYO18B	322	.	0			c.G6711A						PASS	.	G		2,3830		0,2,1914	25.0	27.0	26.0		6711	-4.2	0.0	22		26	25,8189		0,25,4082	no	coding-synonymous	MYO18B	NM_032608.5		0,27,5996	AA,AG,GG		0.3044,0.0522,0.2241		2237/2568	26422651	27,12019	1916	4107	6023	SO:0001819	synonymous_variant	84700	exon43			ATCCCCGCTGTCG	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.6714G>A	22.37:g.26422651G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	86	48	0.55814	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	11.64	1.698433	0.30142	5.22E-4	0.003044	ENSG00000133454	ENST00000543971	.	.	.	4.94	-4.2	0.03823	.	.	.	.	.	T	0.32793	0.0841	.	.	.	0.31759	N	0.633626	.	.	.	.	.	.	T	0.42032	-0.9475	4	.	.	.	.	5.7129	0.17945	0.2701:0.3964:0.3335:0.0	.	.	.	.	H	187	.	.	R	+	2	0	MYO18B	24752651	0.000000	0.05858	0.003000	0.11579	0.699000	0.40488	-2.672000	0.00843	-1.013000	0.03383	0.491000	0.48974	CGC	G|0.993;A|0.007	0.007	strong		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
ZNF652	22834	hgsc.bcm.edu	37	17	47394516	47394516	+	Missense_Mutation	SNP	C	C	T	rs368716483		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:47394516C>T	ENST00000362063.2	-	2	890	c.572G>A	c.(571-573)aGa>aAa	p.R191K	ZNF652_ENST00000430262.2_Missense_Mutation_p.R191K	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			TCTCCTGGTTCTCCTTTGTGT	0.483																																					p.R191K		Atlas-SNP	.											.	ZNF652	54	.	0			c.G572A						PASS	.	C	LYS/ARG,LYS/ARG	0,4406		0,0,2203	91.0	95.0	93.0		572,572	5.2	1.0	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF652	NM_001145365.1,NM_014897.2	26,26	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	191/607,191/607	47394516	1,13005	2203	4300	6503	SO:0001583	missense	22834	exon2			CTGGTTCTCCTTT	AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"""Zinc fingers, C2H2-type"""	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.572G>A	17.37:g.47394516C>T	ENSP00000354686:p.Arg191Lys	Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	188	93	0.494681	NM_001145365	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	37	CCDS32677.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616802	0.46736	0.0	1.16E-4	ENSG00000198740	ENST00000362063;ENST00000430262	T;T	0.07444	3.19;3.19	5.22	5.22	0.72569	.	0.213072	0.50627	D	0.000118	T	0.05777	0.0151	N	0.14661	0.345	0.42015	D	0.990951	B	0.20261	0.043	B	0.22601	0.04	T	0.13872	-1.0493	10	0.02654	T	1	-12.121	18.5632	0.91108	0.0:1.0:0.0:0.0	.	191	Q9Y2D9	ZN652_HUMAN	K	191	ENSP00000354686:R191K;ENSP00000416305:R191K	ENSP00000354686:R191K	R	-	2	0	ZNF652	44749515	1.000000	0.71417	0.969000	0.41365	0.980000	0.70556	3.567000	0.53813	2.715000	0.92844	0.655000	0.94253	AGA	.	.	weak		0.483	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897	
STK36	27148	hgsc.bcm.edu	37	2	219562675	219562675	+	Missense_Mutation	SNP	G	G	A	rs1863704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219562675G>A	ENST00000295709.3	+	25	3287	c.3008G>A	c.(3007-3009)gGt>gAt	p.G1003D	STK36_ENST00000392105.3_Missense_Mutation_p.G982D|STK36_ENST00000392106.2_Missense_Mutation_p.G982D|STK36_ENST00000440309.1_Missense_Mutation_p.G1003D	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CTCCTTATAGGTGTCTTGGCC	0.557													G|||	950	0.189696	0.0212	0.3285	5008	,	,		21184	0.0556		0.3757	False		,,,				2504	0.2658				p.G1003D		Atlas-SNP	.											STK36,rectum,carcinoma,0,1	STK36	111	1	0			c.G3008A						PASS	.	G	ASP/GLY	336,4070	178.7+/-207.4	11,314,1878	149.0	131.0	137.0		3008	2.0	0.0	2	dbSNP_92	137	3284,5316	492.8+/-373.4	656,1972,1672	yes	missense	STK36	NM_015690.4	94	667,2286,3550	AA,AG,GG		38.186,7.626,27.8333	possibly-damaging	1003/1316	219562675	3620,9386	2203	4300	6503	SO:0001583	missense	27148	exon25			TTATAGGTGTCTT	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.3008G>A	2.37:g.219562675G>A	ENSP00000295709:p.Gly1003Asp	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	192	83	0.432292	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	454|454	0.2078754578754579|0.2078754578754579	23|23	0.046747967479674794|0.046747967479674794	112|112	0.30939226519337015|0.30939226519337015	36|36	0.06293706293706294|0.06293706293706294	283|283	0.3733509234828496|0.3733509234828496	G|G	0.208|0.208	-1.039006|-1.039006	0.02013|0.02013	0.07626|0.07626	0.38186|0.38186	ENSG00000163482|ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309|ENST00000431040	T;T;T;T|.	0.69561|.	-0.4;-0.4;-0.41;-0.4|.	5.82|5.82	2.01|2.01	0.26516|0.26516	.|.	0.790460|.	0.11084|.	N|.	0.601535|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	P|P	0.0|0.0	B;P;B|.	0.39424|.	0.001;0.673;0.179|.	B;B;B|.	0.36464|.	0.001;0.225;0.077|.	T|T	0.47699|0.47699	-0.9097|-0.9097	9|4	0.32370|.	T|.	0.25|.	-0.0347|-0.0347	6.8511|6.8511	0.24014|0.24014	0.3342:0.0:0.5491:0.1167|0.3342:0.0:0.5491:0.1167	rs1863704;rs56519430;rs57906514;rs1863704|rs1863704;rs56519430;rs57906514;rs1863704	982;982;1003|.	A8MU99;Q9NRP7-2;Q9NRP7|.	.;.;STK36_HUMAN|.	D|M	1003;982;982;1003|196	ENSP00000295709:G1003D;ENSP00000375955:G982D;ENSP00000375954:G982D;ENSP00000394095:G1003D|.	ENSP00000295709:G1003D|.	G|V	+|+	2|1	0|0	STK36|STK36	219270919|219270919	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.823000|0.823000	0.27366|0.27366	0.122000|0.122000	0.18314|0.18314	-0.797000|-0.797000	0.03246|0.03246	GGT|GTG	G|0.767;A|0.233	0.233	strong		0.557	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
PDXDC1	23042	hgsc.bcm.edu	37	16	15098047	15098047	+	Missense_Mutation	SNP	C	C	G	rs11549900	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15098047C>G	ENST00000396410.4	+	5	343	c.246C>G	c.(244-246)atC>atG	p.I82M	PDXDC1_ENST00000455313.2_Missense_Mutation_p.I82M|PDXDC1_ENST00000447912.2_Intron|PDXDC1_ENST00000535621.2_Missense_Mutation_p.I82M|PDXDC1_ENST00000450288.2_Missense_Mutation_p.I54M|PDXDC1_ENST00000569715.1_Missense_Mutation_p.I55M|PDXDC1_ENST00000325823.7_Missense_Mutation_p.I67M|PDXDC1_ENST00000563679.1_Missense_Mutation_p.I100M	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	82				I -> M (in Ref. 2; BAG61167 and 5; AAZ14099). {ECO:0000305}.	carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TTAACAGAATCCAAAATATTG	0.348																																					p.I82M		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C246G						PASS	.						107.0	119.0	115.0					16																	15098047		2197	4300	6497	SO:0001583	missense	23042	exon5			CAGAATCCAAAAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.246C>G	16.37:g.15098047C>G	ENSP00000379691:p.Ile82Met	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	254	118	0.464567	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	653	0.298992673992674	66	0.13414634146341464	138	0.3812154696132597	251	0.4388111888111888	198	0.2612137203166227	C	6.258	0.415784	0.11870	.	.	ENSG00000179889	ENST00000325823;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000455313	T;T;T;T;T	0.37915	1.17;1.17;1.17;2.07;1.17	5.72	2.76	0.32466	Pyridoxal phosphate-dependent transferase, major domain (1);	0.318283	0.36555	N	0.002527	T	0.00012	0.0000	N	0.08118	0	0.09310	P	1.0	B;B;B;B	0.20780	0.048;0.005;0.048;0.005	B;B;B;B	0.19391	0.02;0.005;0.012;0.025	T	0.47142	-0.9140	9	0.40728	T	0.16	.	9.1032	0.36681	0.0:0.6898:0.0:0.3102	rs11549900	54;82;82;82	E7EPL4;Q86XE2;Q6P996;Q6P996-2	.;.;PDXD1_HUMAN;.	M	67;82;82;54;82	ENSP00000322807:I67M;ENSP00000437835:I82M;ENSP00000379691:I82M;ENSP00000391147:I54M;ENSP00000406703:I82M	ENSP00000322807:I67M	I	+	3	3	PDXDC1	15005548	1.000000	0.71417	1.000000	0.80357	0.351000	0.29236	1.821000	0.39041	0.455000	0.26910	-0.142000	0.14014	ATC	C|0.742;G|0.258	0.258	strong		0.348	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
HIGD1C	613227	hgsc.bcm.edu	37	12	51354803	51354803	+	Silent	SNP	C	C	T	rs12306808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51354803C>T	ENST00000398455.3	+	2	224	c.147C>T	c.(145-147)taC>taT	p.Y49Y		NM_001109619.1	NP_001103089.1	A8MV81	HIG1C_HUMAN	HIG1 hypoxia inducible domain family, member 1C	49	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.					integral component of membrane (GO:0016021)				lung(1)	1						AGCTAAAGTACAGAAGAGATC	0.418													C|||	1318	0.263179	0.1793	0.1585	5008	,	,		19096	0.494		0.163	False		,,,				2504	0.316				p.Y49Y		Atlas-SNP	.											.	HIGD1C	4	.	0			c.C147T						PASS	.	C		621,3197		54,513,1342	94.0	94.0	94.0		147	3.6	1.0	12	dbSNP_120	94	1276,6968		105,1066,2951	no	coding-synonymous	HIGD1C	NM_001109619.1		159,1579,4293	TT,TC,CC		15.4779,16.2651,15.7271		49/98	51354803	1897,10165	1909	4122	6031	SO:0001819	synonymous_variant	613227	exon2			AAAGTACAGAAGA	DQ029494	CCDS44882.1	12q13.12	2011-09-16	2009-03-17		ENSG00000214511	ENSG00000214511			28044	protein-coding gene	gene with protein product			"""HIG1 domain family, member 1C"""				Standard	NM_001109619		Approved	Gm921	uc010smw.2	A8MV81	OTTHUMG00000169488	ENST00000398455.3:c.147C>T	12.37:g.51354803C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	175	82	0.468571	NM_001109619		Silent	SNP	ENST00000398455.3	37	CCDS44882.1																																																																																			C|0.758;T|0.242	0.242	strong		0.418	HIGD1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404340.2	NM_001109619	
CLEC18A	348174	hgsc.bcm.edu	37	16	69985383	69985383	+	Silent	SNP	G	G	A	rs4985466		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:69985383G>A	ENST00000288040.6	+	1	301	c.114G>A	c.(112-114)ccG>ccA	p.P38P	CLEC18A_ENST00000449317.2_Silent_p.P38P|CLEC18A_ENST00000393701.2_Silent_p.P38P|CLEC18A_ENST00000568461.1_Silent_p.P38P	NM_001136214.2	NP_001129686.1	A5D8T8	CL18A_HUMAN	C-type lectin domain family 18, member A	38						extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(2)|lung(1)|skin(1)	5						AGCAGGCTCCGATGGCCGGAG	0.667																																					p.P38P		Atlas-SNP	.											CLEC18A,NS,carcinoma,0,1	CLEC18A	9	1	0			c.G114A						scavenged	.						49.0	50.0	50.0					16																	69985383		1509	3170	4679	SO:0001819	synonymous_variant	348174	exon2			GGCTCCGATGGCC	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.114G>A	16.37:g.69985383G>A		Somatic	269	0	0		WXS	Illumina HiSeq	Phase_I	414	84	0.202899	NM_001271197	A8K1G9|Q6DCB3|Q7Z5K9|Q96HH2	Silent	SNP	ENST00000288040.6	37	CCDS10886.1																																																																																			G|0.500;A|0.500	0.500	weak		0.667	CLEC18A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000268955.2	NM_182619	
OR13C2	392376	hgsc.bcm.edu	37	9	107367841	107367841	+	Missense_Mutation	SNP	A	A	T	rs10991326	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107367841A>T	ENST00000542196.1	-	1	110	c.68T>A	c.(67-69)cTt>cAt	p.L23H		NM_001004481.1	NP_001004481.1	Q8NGS9	O13C2_HUMAN	olfactory receptor, family 13, subfamily C, member 2	23						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						GAGTAACTCAAGTCTTGGGTG	0.408													A|||	1868	0.373003	0.4342	0.2161	5008	,	,		20515	0.5645		0.1789	False		,,,				2504	0.4039				p.L23H		Atlas-SNP	.											OR13C2,NS,carcinoma,-1,1	OR13C2	46	1	0			c.T68A						PASS	.						31.0	35.0	33.0					9																	107367841		2181	4289	6470	SO:0001583	missense	392376	exon1			AACTCAAGTCTTG		CCDS35092.1	9q31.1	2012-10-03			ENSG00000257019	ENSG00000276119		"""GPCR / Class A : Olfactory receptors"""	14701	protein-coding gene	gene with protein product							Standard	NM_001004481		Approved		uc011lvq.2	Q8NGS9	OTTHUMG00000020415	ENST00000542196.1:c.68T>A	9.37:g.107367841A>T	ENSP00000438815:p.Leu23His	Somatic	428	0	0		WXS	Illumina HiSeq	Phase_I	413	137	0.331719	NM_001004481	B9EGV8|Q6IF54	Missense_Mutation	SNP	ENST00000542196.1	37	CCDS35092.1	708	0.3241758241758242	184	0.37398373983739835	74	0.20441988950276244	319	0.5576923076923077	131	0.17282321899736147	A	10.73	1.431549	0.25813	.	.	ENSG00000257019	ENST00000542196	T	0.03413	3.94	3.39	3.39	0.38822	.	0.000000	0.33477	U	0.004878	T	0.00012	0.0000	M	0.78456	2.415	0.80722	P	0.0	D	0.76494	0.999	D	0.63033	0.91	T	0.36866	-0.9730	9	0.87932	D	0	.	9.8158	0.40851	1.0:0.0:0.0:0.0	rs10991326;rs60657466	23	Q8NGS9	O13C2_HUMAN	H	23	ENSP00000438815:L23H	ENSP00000438815:L23H	L	-	2	0	OR13C2	106407662	0.001000	0.12720	0.022000	0.16811	0.190000	0.23558	1.352000	0.34033	1.409000	0.46915	0.379000	0.24179	CTT	A|0.026;T|0.974	0.974	strong		0.408	OR13C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053489.2	NM_001004481	
HLA-A	3105	hgsc.bcm.edu	37	6	29911198	29911198	+	Missense_Mutation	SNP	T	T	C	rs1059516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911198T>C	ENST00000396634.1	+	5	838	c.497T>C	c.(496-498)aTc>aCc	p.I166T	HLA-A_ENST00000376809.5_Missense_Mutation_p.I166T|HLA-A_ENST00000376806.5_Missense_Mutation_p.I166T|HLA-A_ENST00000376802.2_Missense_Mutation_p.I166T			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	166	Alpha-2.		I -> T (in dbSNP:rs1059516).		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						GCGGCTCAGATCACCAAGCGC	0.652									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.I166T		Atlas-SNP	.											.	HLA-A	89	.	0			c.T497C						PASS	.						35.0	26.0	29.0					6																	29911198		1505	2704	4209	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CTCAGATCACCAA	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.497T>C	6.37:g.29911198T>C	ENSP00000379873:p.Ile166Thr	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	173	80	0.462428	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	2.214|2.214	-0.380071|-0.380071	0.05000|0.05000	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	T;T;T;T|.	0.01059|.	5.39;5.39;5.39;5.39|.	3.78|3.78	-2.67|-2.67	0.06059|0.06059	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);|.	0.798396|.	0.09977|.	U|.	0.731481|.	T|T	0.25005|0.25005	0.0607|0.0607	.|.	.|.	.|.	0.52501|0.52501	P|P	4.300000000001525E-5|4.300000000001525E-5	P;B;D;B;D;B;B|.	0.57899|.	0.659;0.001;0.981;0.001;0.981;0.001;0.001|.	P;B;D;B;D;B;B|.	0.80764|.	0.865;0.009;0.994;0.018;0.994;0.018;0.009|.	T|T	0.33854|0.33854	-0.9852|-0.9852	8|4	0.21540|0.87932	T|D	0.41|0	.|.	5.1484|5.1484	0.14996|0.14996	0.4238:0.0:0.1441:0.432|0.4238:0.0:0.1441:0.432	rs1059516;rs2975062;rs3179199;rs3200216;rs41549614|rs1059516;rs2975062;rs3179199;rs3200216;rs41549614	45;166;166;166;166;166;166|.	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439|.	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN|.	T|P	166|141	ENSP00000379873:I166T;ENSP00000366002:I166T;ENSP00000366005:I166T;ENSP00000365998:I166T|.	ENSP00000365998:I166T|ENSP00000348012:S141P	I|S	+|+	2|1	0|0	HLA-A|HLA-A	30019177|30019177	0.078000|0.078000	0.21339|0.21339	0.103000|0.103000	0.21229|0.21229	0.007000|0.007000	0.05969|0.05969	0.159000|0.159000	0.16442|0.16442	-0.176000|-0.176000	0.10707|0.10707	-1.108000|-1.108000	0.02087|0.02087	ATC|TCA	T|0.717;C|0.283	0.283	strong		0.652	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
PDZRN3	23024	hgsc.bcm.edu	37	3	73433494	73433494	+	Silent	SNP	T	T	C	rs13091636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:73433494T>C	ENST00000263666.4	-	10	2337	c.2223A>G	c.(2221-2223)tcA>tcG	p.S741S	PDZRN3_ENST00000466780.1_Silent_p.S398S|PDZRN3_ENST00000479530.1_Silent_p.S458S|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Silent_p.S398S|PDZRN3_ENST00000535920.1_Silent_p.S463S	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	741					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		CGGTGATATCTGAGAGCTCGT	0.612													T|||	1794	0.358227	0.1331	0.428	5008	,	,		17770	0.5357		0.4702	False		,,,				2504	0.3149				p.S741S		Atlas-SNP	.											.	PDZRN3	196	.	0			c.A2223G						PASS	.	T		796,3610	319.3+/-296.1	79,638,1486	50.0	45.0	47.0		2223	-4.7	0.9	3	dbSNP_121	47	3931,4669	547.3+/-385.1	898,2135,1267	no	coding-synonymous	PDZRN3	NM_015009.1		977,2773,2753	CC,CT,TT		45.7093,18.0663,36.3448		741/1067	73433494	4727,8279	2203	4300	6503	SO:0001819	synonymous_variant	23024	exon10			GATATCTGAGAGC	AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2223A>G	3.37:g.73433494T>C		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	52	27	0.519231	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																			A|0.000;C|0.372;T|0.627	0.372	strong		0.612	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
EPS8L1	54869	hgsc.bcm.edu	37	19	55587822	55587822	+	Missense_Mutation	SNP	G	G	A	rs12609976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55587822G>A	ENST00000201647.6	+	2	66	c.10G>A	c.(10-12)Gcc>Acc	p.A4T	EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000540810.1_5'UTR	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	4			A -> T (in dbSNP:rs12609976). {ECO:0000269|PubMed:12620401, 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)		CATGAGCACCGCCACAGGGTA	0.672													N|||	489	0.0976438	0.0408	0.1455	5008	,	,		12199	0.1002		0.162	False		,,,				2504	0.0716				p.A4T	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											EPS8L1,NS,carcinoma,0,1	EPS8L1	122	1	0			c.G10A						PASS	.		THR/ALA	237,4167		12,213,1977	35.0	40.0	39.0		10	2.5	0.6	19	dbSNP_120	39	1436,7162		141,1154,3004	yes	missense	EPS8L1	NM_133180.2	58	153,1367,4981	AA,AG,GG		16.7016,5.3815,12.8673	benign	4/724	55587822	1673,11329	2202	4299	6501	SO:0001583	missense	54869	exon2			AGCACCGCCACAG	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.10G>A	19.37:g.55587822G>A	ENSP00000201647:p.Ala4Thr	Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	160	87	0.54375	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	267	0.12225274725274725	17	0.034552845528455285	56	0.15469613259668508	62	0.10839160839160839	132	0.1741424802110818	N	4.224	0.040468	0.08148	0.053815	0.167016	ENSG00000131037	ENST00000201647	T	0.04275	3.66	2.54	2.54	0.30619	.	1.601540	0.05427	N	0.545204	T	0.00012	0.0000	N	0.08118	0	0.35532	P	0.197631	B	0.02656	0.0	B	0.01281	0.0	T	0.40887	-0.9539	9	0.02654	T	1	-1.0811	4.8871	0.13708	0.8496:0.0:0.1504:0.0	rs12609976;rs57914190;rs12609976	4	Q8TE68	ES8L1_HUMAN	T	4	ENSP00000201647:A4T	ENSP00000201647:A4T	A	+	1	0	EPS8L1	60279634	0.000000	0.05858	0.570000	0.28473	0.481000	0.33189	-0.017000	0.12590	0.409000	0.25649	-1.729000	0.00701	GCC	G|0.878;A|0.122	0.122	strong		0.672	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
INPP4B	8821	hgsc.bcm.edu	37	4	143324094	143324094	+	Silent	SNP	G	G	A	rs1982966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:143324094G>A	ENST00000513000.1	-	8	802	c.369C>T	c.(367-369)gaC>gaT	p.D123D	INPP4B_ENST00000509777.1_Silent_p.D123D|INPP4B_ENST00000508116.1_Silent_p.D123D|INPP4B_ENST00000308502.4_Silent_p.D123D|INPP4B_ENST00000506217.1_Silent_p.D123D|INPP4B_ENST00000262992.4_Silent_p.D123D	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	123	C2.				cellular calcium ion homeostasis (GO:0006874)|inositol phosphate metabolic process (GO:0043647)|negative regulation of osteoclast differentiation (GO:0045671)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of bone remodeling (GO:0046850)|regulation of nucleocytoplasmic transport (GO:0046822)|regulation of protein kinase B signaling (GO:0051896)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	lipid binding (GO:0008289)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity (GO:0016316)|phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity (GO:0034597)	p.D123D(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(29)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58	all_hematologic(180;0.158)					TACTTACGGTGTCATGAGACT	0.363													G|||	1265	0.252596	0.0318	0.2378	5008	,	,		20821	0.2907		0.3489	False		,,,				2504	0.4233				p.D123D		Atlas-SNP	.											INPP4B,NS,carcinoma,0,1	INPP4B	132	1	1	Substitution - coding silent(1)	stomach(1)	c.C369T						PASS	.	G	,	374,4032	188.1+/-214.6	16,342,1845	164.0	129.0	141.0		369,369	2.8	1.0	4	dbSNP_92	141	2980,5620	462.6+/-365.7	489,2002,1809	no	coding-synonymous,coding-synonymous	INPP4B	NM_001101669.1,NM_003866.2	,	505,2344,3654	AA,AG,GG		34.6512,8.4884,25.7881	,	123/925,123/925	143324094	3354,9652	2203	4300	6503	SO:0001819	synonymous_variant	8821	exon8			TACGGTGTCATGA	U96922	CCDS3757.1	4q31.1	2008-02-05	2002-08-29			ENSG00000109452			6075	protein-coding gene	gene with protein product		607494	"""inositol polyphosphate-4-phosphatase, type II, 105kD"""			9295334	Standard	NM_003866		Approved		uc003iiw.4	O15327		ENST00000513000.1:c.369C>T	4.37:g.143324094G>A		Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	59	22	0.372881	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			G|0.743;A|0.257	0.257	strong		0.363	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	
ESPNL	339768	hgsc.bcm.edu	37	2	239039057	239039057	+	Missense_Mutation	SNP	A	A	G	rs13033248	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:239039057A>G	ENST00000343063.3	+	9	1965	c.1702A>G	c.(1702-1704)Atc>Gtc	p.I568V	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.I200V|ESPNL_ENST00000409169.1_Missense_Mutation_p.I524V	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	568			I -> V (in dbSNP:rs13033248). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(1)|lung(8)|pancreas(2)|skin(2)	13		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGAGGCCTCAATCCCAGCGGC	0.711													A|||	1976	0.394569	0.3411	0.3876	5008	,	,		14221	0.4444		0.3847	False		,,,				2504	0.4305				p.I568V		Atlas-SNP	.											.	ESPNL	63	.	0			c.A1702G						PASS	.	A	VAL/ILE	1561,2787		305,951,918	9.0	12.0	11.0		1702	-2.8	0.0	2	dbSNP_121	11	3366,5156		703,1960,1598	no	missense	ESPNL	NM_194312.2	29	1008,2911,2516	GG,GA,AA		39.4978,35.9016,38.2828	benign	568/1006	239039057	4927,7943	2174	4261	6435	SO:0001583	missense	339768	exon9			GCCTCAATCCCAG	AK124559	CCDS2525.1	2q37.3	2013-01-10			ENSG00000144488	ENSG00000144488		"""Ankyrin repeat domain containing"""	27937	protein-coding gene	gene with protein product						12975309	Standard	NM_194312		Approved	FLJ42568	uc002vxq.4	Q6ZVH7	OTTHUMG00000133335	ENST00000343063.3:c.1702A>G	2.37:g.239039057A>G	ENSP00000339115:p.Ile568Val	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	48	25	0.520833	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	856	0.39194139194139194	179	0.3638211382113821	150	0.4143646408839779	240	0.4195804195804196	287	0.3786279683377309	A	0	-2.766231	0.00082	0.359016	0.394978	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.61274	0.12;1.23;0.81	3.37	-2.79	0.05841	.	.	.	.	.	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	0.36286	-0.9754	8	0.02654	T	1	0.231	0.1428	0.00085	0.2568:0.1676:0.237:0.3387	rs13033248	524;568	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	V	568;524;200	ENSP00000339115:I568V;ENSP00000386577:I524V;ENSP00000386579:I200V	ENSP00000339115:I568V	I	+	1	0	ESPNL	238703796	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-0.058000	0.11750	-0.164000	0.10927	-0.548000	0.04221	ATC	A|0.615;G|0.385	0.385	strong		0.711	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312	
TMPRSS12	283471	hgsc.bcm.edu	37	12	51236802	51236802	+	Missense_Mutation	SNP	T	T	C	rs10876100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51236802T>C	ENST00000398458.3	+	1	87	c.55T>C	c.(55-57)Tac>Cac	p.Y19H	RN7SL519P_ENST00000497925.2_RNA|TMPRSS12_ENST00000551456.1_Missense_Mutation_p.Y19H	NM_182559.2	NP_872365	Q86WS5	TMPSC_HUMAN	transmembrane (C-terminal) protease, serine 12	19			Y -> H (in dbSNP:rs10876100).			integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	18						CTCTCACTTATACTCAGACCA	0.652													T|||	1497	0.298922	0.3328	0.2709	5008	,	,		14242	0.4038		0.2207	False		,,,				2504	0.2454				p.Y19H		Atlas-SNP	.											.	TMPRSS12	33	.	0			c.T55C						PASS	.	T	HIS/TYR	1296,2708		208,880,914	29.0	30.0	30.0		55	1.1	0.0	12	dbSNP_120	30	1798,6492		209,1380,2556	yes	missense	TMPRSS12	NM_182559.2	83	417,2260,3470	CC,CT,TT		21.6888,32.3676,25.1667	benign	19/349	51236802	3094,9200	2002	4145	6147	SO:0001583	missense	283471	exon1			CACTTATACTCAG	BC048112	CCDS44881.1	12q13.12	2014-08-12	2010-04-21		ENSG00000186452	ENSG00000186452		"""Serine peptidases / Transmembrane"""	28779	protein-coding gene	gene with protein product			"""transmembrane protease, serine 12"""				Standard	NM_182559		Approved	MGC57341, CT151	uc001rwx.4	Q86WS5	OTTHUMG00000169483	ENST00000398458.3:c.55T>C	12.37:g.51236802T>C	ENSP00000381476:p.Tyr19His	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	48	0.521739	NM_182559	B9ZVX2	Missense_Mutation	SNP	ENST00000398458.3	37	CCDS44881.1	625	0.28617216117216115	163	0.3313008130081301	100	0.27624309392265195	212	0.3706293706293706	150	0.19788918205804748	T	4.132	0.022751	0.08006	0.323676	0.216888	ENSG00000186452	ENST00000551456;ENST00000398458	D;D	0.90133	-2.62;-2.53	3.44	1.08	0.20341	.	1.518320	0.04643	N	0.405589	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04128	-1.0975	9	0.16896	T	0.51	0.5913	6.9674	0.24631	0.0:0.2249:0.0:0.7751	rs10876100;rs52803962;rs10876100	19;19	F8WBX2;Q86WS5	.;TMPSC_HUMAN	H	19	ENSP00000447259:Y19H;ENSP00000381476:Y19H	ENSP00000381476:Y19H	Y	+	1	0	TMPRSS12	49523069	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.077000	0.11394	-0.057000	0.13199	-1.777000	0.00654	TAC	T|0.715;C|0.285	0.285	strong		0.652	TMPRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404289.1	NM_182559	
HYKK	123688	hgsc.bcm.edu	37	15	78807407	78807407	+	Nonsense_Mutation	SNP	T	T	A	rs183603441	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78807407T>A	ENST00000569878.1	+	2	435	c.435T>A	c.(433-435)taT>taA	p.Y145*	HYKK_ENST00000566332.1_Nonsense_Mutation_p.Y145*|HYKK_ENST00000563233.1_Nonsense_Mutation_p.Y145*|HYKK_ENST00000388988.4_Nonsense_Mutation_p.Y145*|HYKK_ENST00000408962.2_Nonsense_Mutation_p.Y145*|HYKK_ENST00000360519.3_Nonsense_Mutation_p.Y145*			A2RU49	HYKK_HUMAN	hydroxylysine kinase	145						cytoplasm (GO:0005737)	hydroxylysine kinase activity (GO:0047992)										AGCTATTGTATGAAATTGGAA	0.423													T|||	17	0.00339457	0.0	0.0072	5008	,	,		10848	0.0		0.0119	False		,,,				2504	0.0				p.Y145X		Atlas-SNP	.											.	AGPHD1	22	.	0			c.T435A						PASS	.	T	stop/TYR,stop/TYR	16,3672		0,16,1828	56.0	55.0	55.0		435,435	-0.5	0.0	15		55	111,8049		2,107,3971	yes	stop-gained,stop-gained	AGPHD1	NM_001013619.2,NM_001083612.1	,	2,123,5799	AA,AT,TT		1.3603,0.4338,1.0719	,	145/374,145/221	78807407	127,11721	1844	4080	5924	SO:0001587	stop_gained	123688	exon3			ATTGTATGAAATT	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.435T>A	15.37:g.78807407T>A	ENSP00000455459:p.Tyr145*	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	63	34	0.539683	NM_001013619	B7ZMA5|F8W6X5|Q6ZTN0	Nonsense_Mutation	SNP	ENST00000569878.1	37	CCDS42063.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	T	17.20	3.329975	0.60743	0.004338	0.013603	ENSG00000188266	ENST00000408962;ENST00000388988;ENST00000360519	.	.	.	5.82	-0.508	0.11980	.	0.062767	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.785	10.0692	0.42322	0.0:0.3516:0.0:0.6484	.	.	.	.	X	145	.	ENSP00000353710:Y145X	Y	+	3	2	AGPHD1	76594462	0.325000	0.24660	0.004000	0.12327	0.136000	0.21042	-0.494000	0.06451	-0.074000	0.12820	0.533000	0.62120	TAT	T|0.993;A|0.007	0.007	strong		0.423	HYKK-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435834.1	NM_001013619	
ASCC3	10973	hgsc.bcm.edu	37	6	100964147	100964147	+	Missense_Mutation	SNP	G	G	C	rs240780	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:100964147G>C	ENST00000369162.2	-	39	6328	c.5984C>G	c.(5983-5985)tCc>tGc	p.S1995C		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1995	SEC63 2.		S -> C (in dbSNP:rs240780). {ECO:0000269|PubMed:12077347, ECO:0000269|Ref.7}.		cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.S1995C(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		TTCAGGAAGGGACTCGATGGA	0.458													C|||	3845	0.767772	0.9486	0.611	5008	,	,		17929	0.7857		0.5795	False		,,,				2504	0.8098				p.S1995C		Atlas-SNP	.											ASCC3,NS,carcinoma,0,1	ASCC3	205	1	1	Substitution - Missense(1)	prostate(1)	c.C5984G	GRCh37	CM064987	ASCC3	M	rs240780	scavenged	.	C	CYS/SER	3843,563	250.6+/-257.6	1677,489,37	133.0	128.0	130.0		5984	5.0	1.0	6	dbSNP_79	130	5027,3573	518.9+/-379.4	1469,2089,742	yes	missense	ASCC3	NM_006828.2	112	3146,2578,779	CC,CG,GG		41.5465,12.778,31.8007	benign	1995/2203	100964147	8870,4136	2203	4300	6503	SO:0001583	missense	10973	exon39			GGAAGGGACTCGA	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.5984C>G	6.37:g.100964147G>C	ENSP00000358159:p.Ser1995Cys	Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	59	53	0.898305	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	1556	0.7124542124542125	469	0.9532520325203252	232	0.6408839779005525	433	0.756993006993007	422	0.5567282321899736	C	10.40	1.340708	0.24339	0.87222	0.584535	ENSG00000112249	ENST00000369162	T	0.66099	-0.19	4.96	4.96	0.65561	Sec63 domain (3);	0.060161	0.64402	N	0.000002	T	0.25232	0.0613	N	0.08118	0	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03829	-1.1000	9	0.33141	T	0.24	.	14.8991	0.70664	0.0:0.8558:0.1442:0.0	rs240780;rs17303636;rs52801369;rs57462599;rs240780	1995	Q8N3C0	HELC1_HUMAN	C	1995	ENSP00000358159:S1995C	ENSP00000358159:S1995C	S	-	2	0	ASCC3	101070868	1.000000	0.71417	1.000000	0.80357	0.503000	0.33858	3.029000	0.49712	1.244000	0.43870	-0.352000	0.07741	TCC	G|0.308;C|0.692	0.692	strong		0.458	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
OR5B12	390191	hgsc.bcm.edu	37	11	58207203	58207203	+	Missense_Mutation	SNP	C	C	T	rs11229457|rs386753911	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58207203C>T	ENST00000302572.2	-	1	443	c.422G>A	c.(421-423)tGc>tAc	p.C141Y		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	141			C -> R (in dbSNP:rs4938895). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.|C -> Y (in dbSNP:rs11229457).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TATGGCCAGGCAAGCACATAC	0.473													C|||	1119	0.223442	0.2708	0.2032	5008	,	,		20166	0.1438		0.2097	False		,,,				2504	0.2699				p.C141Y		Atlas-SNP	.											.	OR5B12	80	.	0			c.G422A						PASS	.	C	TYR/CYS	1033,3369	375.1+/-321.5	104,825,1272	135.0	128.0	131.0		422	2.5	0.0	11	dbSNP_120	131	1846,6744	321.6+/-315.2	199,1448,2648	yes	missense	OR5B12	NM_001004733.2	194	303,2273,3920	TT,TC,CC		21.4901,23.4666,22.1598	benign	141/315	58207203	2879,10113	2201	4295	6496	SO:0001583	missense	390191	exon1			GCCAGGCAAGCAC	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.422G>A	11.37:g.58207203C>T	ENSP00000306657:p.Cys141Tyr	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	91	41	0.450549	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	407	0.18635531135531136	127	0.258130081300813	57	0.1574585635359116	81	0.14160839160839161	142	0.18733509234828497	C	0.001	-3.150305	0.00029	0.234666	0.214901	ENSG00000172362	ENST00000302572	T	0.00084	8.75	4.44	2.46	0.29980	GPCR, rhodopsin-like superfamily (1);	0.766506	0.11955	N	0.513292	T	0.00012	0.0000	N	0.21097	0.63	0.80722	P	0.0	B	0.09022	0.002	B	0.10450	0.005	T	0.13361	-1.0512	9	0.02654	T	1	-16.6186	4.2654	0.10761	0.259:0.5239:0.1357:0.0815	rs11229457;rs60468483;rs11229457	141	Q96R08	OR5BC_HUMAN	Y	141	ENSP00000306657:C141Y	ENSP00000306657:C141Y	C	-	2	0	OR5B12	57963779	0.000000	0.05858	0.021000	0.16686	0.072000	0.16883	-1.307000	0.02733	0.560000	0.29169	0.462000	0.41574	TGC	C|0.782;T|0.218	0.218	strong		0.473	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
TARBP1	6894	hgsc.bcm.edu	37	1	234541801	234541801	+	Silent	SNP	A	A	G	rs12073170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:234541801A>G	ENST00000040877.1	-	24	3836	c.3837T>C	c.(3835-3837)tgT>tgC	p.C1279C	TARBP1_ENST00000483404.1_5'UTR	NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	1279					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)			TGTGATTGAAACACCACTGCA	0.373													A|||	569	0.113618	0.146	0.1744	5008	,	,		21750	0.0853		0.0885	False		,,,				2504	0.0818				p.C1279C		Atlas-SNP	.											.	TARBP1	111	.	0			c.T3837C						PASS	.	A		579,3827	259.2+/-262.9	48,483,1672	117.0	113.0	114.0		3837	-4.3	0.1	1	dbSNP_120	114	773,7827	183.0+/-231.3	39,695,3566	no	coding-synonymous	TARBP1	NM_005646.3		87,1178,5238	GG,GA,AA		8.9884,13.1412,10.3952		1279/1622	234541801	1352,11654	2203	4300	6503	SO:0001819	synonymous_variant	6894	exon24			ATTGAAACACCAC		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.3837T>C	1.37:g.234541801A>G		Somatic	176	0	0		WXS	Illumina HiSeq	Phase_I	189	79	0.417989	NM_005646	Q9H581	Silent	SNP	ENST00000040877.1	37	CCDS1601.1																																																																																			A|0.897;G|0.103	0.103	strong		0.373	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
OR2D2	120776	hgsc.bcm.edu	37	11	6913243	6913243	+	Missense_Mutation	SNP	T	T	C	rs1965207|rs386750330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6913243T>C	ENST00000299459.2	-	1	587	c.489A>G	c.(487-489)atA>atG	p.I163M		NM_003700.1	NP_003691.1	Q9H210	OR2D2_HUMAN	olfactory receptor, family 2, subfamily D, member 2	163			I -> M (in dbSNP:rs1965207).|I -> T (in dbSNP:rs1965208). {ECO:0000269|PubMed:11416212, ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9787077, ECO:0000269|Ref.3}.		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(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|skin(2)	18		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GTAGCCTCAGTATGAAGGTGG	0.502													T|||	668	0.133387	0.1293	0.0937	5008	,	,		20670	0.0764		0.162	False		,,,				2504	0.1963				p.I163M		Atlas-SNP	.											.	OR2D2	52	.	0			c.A489G						PASS	.		MET/ILE	603,3799		33,537,1631	113.0	86.0	95.0		489	-10.2	0.0	11	dbSNP_92	95	1190,7402		99,992,3205	yes	missense	OR2D2	NM_003700.1	10	132,1529,4836	CC,CT,TT		13.8501,13.6983,13.7987	benign	163/309	6913243	1793,11201	2201	4296	6497	SO:0001583	missense	120776	exon1			CCTCAGTATGAAG	AB065824	CCDS31416.1	11p15.4	2012-08-09			ENSG00000166368	ENSG00000166368		"""GPCR / Class A : Olfactory receptors"""	8244	protein-coding gene	gene with protein product		608494		OR2D1		9787077	Standard	NM_003700		Approved	OR11-610, hg27	uc010rau.2	Q9H210	OTTHUMG00000165741	ENST00000299459.2:c.489A>G	11.37:g.6913243T>C	ENSP00000299459:p.Ile163Met	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_003700	B9EIL5|O95224|Q6IF28|Q8NGH4|Q96R52	Missense_Mutation	SNP	ENST00000299459.2	37	CCDS31416.1	236	0.10805860805860806	61	0.12398373983739837	35	0.09668508287292818	39	0.06818181818181818	101	0.13324538258575197	t	12.79	2.042140	0.35989	0.136983	0.138501	ENSG00000166368	ENST00000299459	T	0.00107	8.72	5.12	-10.2	0.00374	GPCR, rhodopsin-like superfamily (1);	0.126744	0.36034	N	0.002839	T	0.00012	0.0000	L	0.41124	1.26	0.80722	P	0.0	B	0.33044	0.395	P	0.47162	0.54	T	0.46261	-0.9204	9	0.59425	D	0.04	-13.1389	4.3554	0.11176	0.3217:0.0604:0.4446:0.1732	rs1965207;rs1965207	163	Q9H210	OR2D2_HUMAN	M	163	ENSP00000299459:I163M	ENSP00000299459:I163M	I	-	3	3	OR2D2	6869819	0.000000	0.05858	0.003000	0.11579	0.790000	0.44656	-2.769000	0.00780	-2.599000	0.00452	-1.564000	0.00881	ATA	T|0.866;C|0.134	0.134	strong		0.502	OR2D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385986.1	NM_003700	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204403659	204403659	+	Silent	SNP	A	A	G	rs3747636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204403659A>G	ENST00000367187.3	-	25	4150	c.3594T>C	c.(3592-3594)aaT>aaC	p.N1198N	PIK3C2B_ENST00000424712.2_Silent_p.N1170N|RP11-739N20.2_ENST00000443515.1_RNA	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	1198	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			TGATGTTGTCATTATGTCGGT	0.537													G|||	2028	0.404952	0.525	0.2666	5008	,	,		23776	0.5089		0.2594	False		,,,				2504	0.3834				p.N1198N		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.T3594C						PASS	.	G		2104,2302	601.4+/-389.7	495,1114,594	92.0	71.0	78.0		3594	-7.8	0.4	1	dbSNP_107	78	1876,6724	728.1+/-406.7	189,1498,2613	no	coding-synonymous	PIK3C2B	NM_002646.3		684,2612,3207	GG,GA,AA		21.814,47.7531,30.6013		1198/1635	204403659	3980,9026	2203	4300	6503	SO:0001819	synonymous_variant	5287	exon25			GTTGTCATTATGT	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.3594T>C	1.37:g.204403659A>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	187	82	0.438503	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			A|0.650;G|0.350	0.350	strong		0.537	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
XIRP2	129446	hgsc.bcm.edu	37	2	168103925	168103925	+	Missense_Mutation	SNP	A	A	G	rs7607246	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168103925A>G	ENST00000409195.1	+	9	6112	c.6023A>G	c.(6022-6024)aAt>aGt	p.N2008S	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.N1786S|XIRP2_ENST00000295237.9_Missense_Mutation_p.N2008S|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1833					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TGCCATGGCAATTTAGTAGAA	0.453													A|||	865	0.172724	0.2882	0.1196	5008	,	,		18614	0.12		0.1123	False		,,,				2504	0.1708				p.N2008S		Atlas-SNP	.											.	XIRP2	914	.	0			c.A6023G						PASS	.	A	,,,SER/ASN,SER/ASN	965,2753		134,697,1028	49.0	46.0	47.0		,,,6023,5357	0.6	0.0	2	dbSNP_116	47	799,7383		42,715,3334	yes	intron,intron,intron,missense,missense	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199145.1,NM_152381.5,NM_001199144.1	,,,46,46	176,1412,4362	GG,GA,AA		9.7653,25.9548,14.8235	,,,benign,benign	,,,2008/3550,1786/3328	168103925	1764,10136	1859	4091	5950	SO:0001583	missense	129446	exon9			ATGGCAATTTAGT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6023A>G	2.37:g.168103925A>G	ENSP00000386840:p.Asn2008Ser	Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	155	74	0.477419	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	353	0.16163003663003664	151	0.30691056910569103	42	0.11602209944751381	72	0.1258741258741259	88	0.11609498680738786	A	0.005	-2.172963	0.00312	0.259548	0.097653	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.02280	4.36;4.36;4.37	5.31	0.559	0.17272	.	1.282890	0.04902	N	0.451569	T	0.00012	0.0000	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.001	T	0.42982	-0.9419	9	0.06365	T	0.9	-0.0303	1.6411	0.02753	0.3781:0.3315:0.1676:0.1227	rs7607246;rs57219008;rs7607246	1833;1833;1786	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	2008;2008;1786	ENSP00000386840:N2008S;ENSP00000295237:N2008S;ENSP00000387255:N1786S	ENSP00000295237:N2008S	N	+	2	0	XIRP2	167812171	0.003000	0.15002	0.000000	0.03702	0.029000	0.11900	0.881000	0.28173	0.080000	0.16959	0.528000	0.53228	AAT	A|0.837;G|0.163	0.163	strong		0.453	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
PKD1	5310	hgsc.bcm.edu	37	16	2140010	2140010	+	Silent	SNP	A	A	G	rs7203729	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2140010A>G	ENST00000262304.4	-	46	12838	c.12630T>C	c.(12628-12630)ccT>ccC	p.P4210P	MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA|PKD1_ENST00000423118.1_Silent_p.P4209P	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4210					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						GGGAGGGCTCAGGCTCACACC	0.677													G|||	1392	0.277955	0.7247	0.2104	5008	,	,		12411	0.0		0.2028	False		,,,				2504	0.0859				p.P4210P		Atlas-SNP	.											.	PKD1	184	.	0			c.T12630C						PASS	.	G	,	2652,1718		818,1016,351	23.0	24.0	24.0		12627,12630	-9.8	0.0	16	dbSNP_116	24	1629,6961		158,1313,2824	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	976,2329,3175	GG,GA,AA		18.9639,39.3135,33.0324	,	4209/4303,4210/4304	2140010	4281,8679	2185	4295	6480	SO:0001819	synonymous_variant	5310	exon46			GGGCTCAGGCTCA	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.12630T>C	16.37:g.2140010A>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	88	42	0.477273	NM_001009944	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			A|0.688;G|0.312	0.312	strong		0.677	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
TP53BP1	7158	hgsc.bcm.edu	37	15	43707808	43707808	+	Silent	SNP	A	A	T	rs2230451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43707808A>T	ENST00000263801.3	-	23	5310	c.5058T>A	c.(5056-5058)tcT>tcA	p.S1686S	TP53BP1_ENST00000450115.2_Silent_p.S1691S|TP53BP1_ENST00000382039.3_Silent_p.S1641S|TP53BP1_ENST00000382044.4_Silent_p.S1691S	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1686					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)		TTACTGTGGCAGACTTGCGAC	0.488								Other conserved DNA damage response genes					A|||	644	0.128594	0.1664	0.1052	5008	,	,		20467	0.001		0.1938	False		,,,				2504	0.1585				p.S1691S		Atlas-SNP	.											.	TP53BP1	157	.	0			c.T5073A						PASS	.	A	,,	744,3658	307.2+/-289.9	69,606,1526	120.0	102.0	108.0		5073,5073,5058	2.9	1.0	15	dbSNP_98	108	1633,6963	303.6+/-306.5	146,1341,2811	no	coding-synonymous,coding-synonymous,coding-synonymous	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	,,	215,1947,4337	TT,TA,AA		18.9972,16.9014,18.2874	,,	1691/1976,1691/1978,1686/1973	43707808	2377,10621	2201	4298	6499	SO:0001819	synonymous_variant	7158	exon23			TGTGGCAGACTTG	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.5058T>A	15.37:g.43707808A>T		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	112	55	0.491071	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																			A|0.828;T|0.172	0.172	strong		0.488	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
OR51Q1	390061	hgsc.bcm.edu	37	11	5444150	5444150	+	Silent	SNP	C	C	T	rs118011081	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5444150C>T	ENST00000300778.4	+	1	810	c.720C>T	c.(718-720)ctC>ctT	p.L240L	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron	NM_001004757.2	NP_001004757.1	Q8NH59	O51Q1_HUMAN	olfactory receptor, family 51, subfamily Q, member 1 (gene/pseudogene)	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(3)|liver(2)|lung(21)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	37		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.18e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCGTGCCCTCAATAACTGCC	0.488													C|||	45	0.00898562	0.0	0.0187	5008	,	,		20993	0.0		0.0278	False		,,,				2504	0.0041				p.L240L		Atlas-SNP	.											.	OR51Q1	79	.	0			c.C720T						PASS	.	C		21,4381	28.1+/-56.4	0,21,2180	137.0	114.0	122.0		720	3.1	0.9	11	dbSNP_132	122	170,8424	79.5+/-142.1	0,170,4127	no	coding-synonymous	OR51Q1	NM_001004757.2		0,191,6307	TT,TC,CC		1.9781,0.4771,1.4697		240/318	5444150	191,12805	2201	4297	6498	SO:0001819	synonymous_variant	390061	exon1			TGCCCTCAATAAC	AB065531	CCDS31381.1	11p15.4	2013-10-10	2013-10-10		ENSG00000167360	ENSG00000167360		"""GPCR / Class A : Olfactory receptors"""	14851	protein-coding gene	gene with protein product			"""olfactory receptor, family 51, subfamily Q, member 1"""				Standard	NM_001004757		Approved		uc010qzd.2	Q8NH59	OTTHUMG00000066896	ENST00000300778.4:c.720C>T	11.37:g.5444150C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	146	66	0.452055	NM_001004757	B2RNN1	Silent	SNP	ENST00000300778.4	37	CCDS31381.1																																																																																			C|0.985;T|0.015	0.015	strong		0.488	OR51Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143373.1	NM_001004757	
SAMD9L	219285	hgsc.bcm.edu	37	7	92762681	92762681	+	Silent	SNP	A	A	G	rs1029357	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92762681A>G	ENST00000318238.4	-	5	3820	c.2604T>C	c.(2602-2604)gcT>gcC	p.A868A	SAMD9L_ENST00000411955.1_Silent_p.A868A|SAMD9L_ENST00000437805.1_Silent_p.A868A	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	868					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)		p.A868A(1)		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)			TGGCACCAAAAGCTCTTTGTT	0.353													A|||	1456	0.290735	0.5174	0.3285	5008	,	,		21598	0.3482		0.0716	False		,,,				2504	0.1237				p.A868A		Atlas-SNP	.											SAMD9L,NS,carcinoma,0,1	SAMD9L	227	1	1	Substitution - coding silent(1)	stomach(1)	c.T2604C						PASS	.	A		1856,2548	517.3+/-369.4	407,1042,753	83.0	92.0	89.0		2604	-0.6	1.0	7	dbSNP_86	89	705,7893	172.3+/-223.0	29,647,3623	no	coding-synonymous	SAMD9L	NM_152703.2		436,1689,4376	GG,GA,AA		8.1996,42.1435,19.697		868/1585	92762681	2561,10441	2202	4299	6501	SO:0001819	synonymous_variant	219285	exon5			ACCAAAAGCTCTT	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.2604T>C	7.37:g.92762681A>G		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	129	51	0.395349	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Silent	SNP	ENST00000318238.4	37	CCDS34681.1																																																																																			A|0.774;G|0.226	0.226	strong		0.353	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
ZNF761	388561	hgsc.bcm.edu	37	19	53959343	53959343	+	RNA	SNP	G	G	A	rs2708742	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:53959343G>A	ENST00000454407.1	+	0	2035							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)			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)		TAATGAGTGCGGCAAGACCTT	0.443													g|||	1820	0.363419	0.3306	0.5303	5008	,	,		22273	0.2401		0.3956	False		,,,				2504	0.3834				p.G528S		Atlas-SNP	.											.	ZNF761	104	.	0			c.G1582A						PASS	.	G	SER/GLY	1498,2908	477.0+/-357.8	254,990,959	104.0	101.0	102.0		1583	1.1	0.0	19	dbSNP_100	102	3492,5108	509.5+/-377.3	704,2084,1512	no	missense	ZNF761	NM_001008401.3	56	958,3074,2471	AA,AG,GG		40.6047,33.9991,38.3669	benign	528/747	53959343	4990,8016	2203	4300	6503			388561	exon7			GAGTGCGGCAAGA	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.53959343G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	63	31	0.492063	NM_001008401	Q6ZNB9	Missense_Mutation	SNP	ENST00000454407.1	37																																																																																				G|0.635;A|0.365	0.365	strong		0.443	ZNF761-203	KNOWN	basic	processed_transcript	processed_transcript		NM_001008401	
ASPHD2	57168	hgsc.bcm.edu	37	22	26830316	26830316	+	Silent	SNP	G	G	A	rs11705277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26830316G>A	ENST00000215906.5	+	2	1173	c.735G>A	c.(733-735)agG>agA	p.R245R		NM_020437.4	NP_065170.2	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	245					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	16						GGAACTGTAGGAAGTGCCCAC	0.562													G|||	311	0.0621006	0.0401	0.0576	5008	,	,		20689	0.0169		0.1372	False		,,,				2504	0.0644				p.R245R		Atlas-SNP	.											.	ASPHD2	42	.	0			c.G735A						PASS	.	G		312,4094	167.3+/-198.3	10,292,1901	134.0	126.0	129.0		735	2.7	1.0	22	dbSNP_120	129	1439,7161	276.8+/-292.5	125,1189,2986	no	coding-synonymous	ASPHD2	NM_020437.4		135,1481,4887	AA,AG,GG		16.7326,7.0813,13.463		245/370	26830316	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	57168	exon2			CTGTAGGAAGTGC	AK097157	CCDS13834.2	22q12.1	2006-02-02			ENSG00000128203	ENSG00000128203			30437	protein-coding gene	gene with protein product							Standard	NM_020437		Approved	FLJ39838	uc003acg.2	Q6ICH7	OTTHUMG00000150884	ENST00000215906.5:c.735G>A	22.37:g.26830316G>A		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_020437	B2RCH3|Q7L0W3|Q9NSN3	Silent	SNP	ENST00000215906.5	37	CCDS13834.2																																																																																			G|0.880;A|0.120	0.120	strong		0.562	ASPHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320422.1	NM_020437	
NDST1	3340	hgsc.bcm.edu	37	5	149907602	149907602	+	Silent	SNP	A	A	G	rs2273234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149907602A>G	ENST00000261797.6	+	3	1252	c.750A>G	c.(748-750)ccA>ccG	p.P250P	NDST1_ENST00000523767.1_Silent_p.P250P	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	250	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)			AGTCCATCCCACACCTGGGCG	0.637													G|||	1500	0.299521	0.1157	0.4885	5008	,	,		20451	0.1458		0.4592	False		,,,				2504	0.408				p.P250P		Atlas-SNP	.											.	NDST1	79	.	0			c.A750G						PASS	.	G		774,3630	743.9+/-411.5	78,618,1506	42.0	35.0	38.0		750	-5.6	0.9	5	dbSNP_100	38	4005,4595	591.4+/-392.8	956,2093,1251	yes	coding-synonymous	NDST1	NM_001543.4		1034,2711,2757	GG,GA,AA		46.5698,17.5749,36.7502		250/883	149907602	4779,8225	2202	4300	6502	SO:0001819	synonymous_variant	3340	exon3			CATCCCACACCTG	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.750A>G	5.37:g.149907602A>G		Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	46	20	0.434783	NM_001543	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																			A|0.687;G|0.313	0.313	strong		0.637	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
DNASE1	1773	hgsc.bcm.edu	37	16	3707747	3707747	+	Missense_Mutation	SNP	G	G	A	rs1053874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3707747G>A	ENST00000246949.5	+	8	3940	c.731G>A	c.(730-732)cGa>cAa	p.R244Q	DNASE1_ENST00000414110.2_Missense_Mutation_p.R127Q|DNASE1_ENST00000407479.1_Missense_Mutation_p.R244Q	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I	244			R -> Q (in allele DNASE1*1; dbSNP:rs1053874). {ECO:0000269|PubMed:7762978}.		apoptotic process (GO:0006915)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	deoxyribonuclease I activity (GO:0004530)			lung(1)	1		Ovarian(90;0.0261)		Kidney(780;0.0556)		ATGCTGCTCCGAGGCGCCGTT	0.567													A|||	2475	0.494209	0.8177	0.3473	5008	,	,		20043	0.4286		0.3032	False		,,,				2504	0.4254				p.R244Q		Atlas-SNP	.											.	DNASE1	16	.	0			c.G731A	GRCh37	CM042698	DNASE1	M	rs1053874	PASS	.	A	GLN/ARG	3251,1143	405.3+/-333.4	1206,839,152	79.0	67.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	731	4.5	0.3	16	dbSNP_86	71	2606,5994	688.3+/-404.3	405,1796,2099	yes	missense	DNASE1	NM_005223.3	43	1611,2635,2251	AA,AG,GG		30.3023,26.0127,45.0746	benign	244/283	3707747	5857,7137	2197	4300	6497	SO:0001583	missense	1773	exon8			TGCTCCGAGGCGC		CCDS10507.1	16p13.3	2008-02-05			ENSG00000213918	ENSG00000213918	3.1.21.1		2956	protein-coding gene	gene with protein product		125505		DNL1		2349940	Standard	XM_005255148		Approved		uc002cvr.3	P24855	OTTHUMG00000129426	ENST00000246949.5:c.731G>A	16.37:g.3707747G>A	ENSP00000246949:p.Arg244Gln	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	99	51	0.515152	NM_005223	B4DV35|Q14UU9|Q14UV0	Missense_Mutation	SNP	ENST00000246949.5	37	CCDS10507.1	1062	0.48626373626373626	414	0.8414634146341463	141	0.38950276243093923	273	0.4772727272727273	234	0.3087071240105541	A	5.843	0.339737	0.11069	0.739873	0.303023	ENSG00000213918	ENST00000407479;ENST00000246949;ENST00000414110	T;T;T	0.32272	1.46;1.46;1.46	4.5	4.5	0.54988	Endonuclease/exonuclease/phosphatase (2);	0.225509	0.42172	N	0.000756	T	0.00012	0.0000	N	0.01424	-0.875	0.28650	P	0.9067025	B	0.12630	0.006	B	0.04013	0.001	T	0.32613	-0.9900	9	0.07813	T	0.8	-9.4549	5.216	0.15342	0.7586:0.0:0.0848:0.1566	rs1053874;rs1801110;rs3169473;rs17255932;rs17418314;rs59499103;rs1053874	244	P24855	DNAS1_HUMAN	Q	244;244;127	ENSP00000385905:R244Q;ENSP00000246949:R244Q;ENSP00000416699:R127Q	ENSP00000246949:R244Q	R	+	2	0	DNASE1	3647748	0.000000	0.05858	0.315000	0.25238	0.004000	0.04260	0.033000	0.13754	0.875000	0.35847	-0.361000	0.07541	CGA	G|0.520;A|0.480	0.480	strong		0.567	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2		
HERC2	8924	hgsc.bcm.edu	37	15	28459095	28459095	+	Silent	SNP	G	G	A	rs191942261		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459095G>A	ENST00000261609.7	-	42	6687	c.6579C>T	c.(6577-6579)ccC>ccT	p.P2193P		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)		TCTCGGAGTCGGGGAAGTAGT	0.587																																					p.P2193P		Atlas-SNP	.											.	HERC2	501	.	0			c.C6579T						PASS	.						34.0	31.0	32.0					15																	28459095		2203	4297	6500	SO:0001819	synonymous_variant	8924	exon42			GGAGTCGGGGAAG	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.6579C>T	15.37:g.28459095G>A		Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	191	15	0.078534	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.993;A|0.007	0.007	strong		0.587	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
CLSTN1	22883	hgsc.bcm.edu	37	1	9811541	9811541	+	Silent	SNP	A	A	G	rs11674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:9811541A>G	ENST00000377298.4	-	5	1431	c.639T>C	c.(637-639)gtT>gtC	p.V213V	CLSTN1_ENST00000377288.3_Silent_p.V213V|CLSTN1_ENST00000361311.4_Silent_p.V203V	NM_001009566.1	NP_001009566.1	O94985	CSTN1_HUMAN	calsyntenin 1	213	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)|calcium ion binding (GO:0005509)|kinesin binding (GO:0019894)|X11-like protein binding (GO:0042988)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(9)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	36	all_lung(157;0.222)	all_lung(284;4.03e-05)|Lung NSC(185;6.93e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;8.36e-08)|COAD - Colon adenocarcinoma(227;1.93e-05)|Kidney(185;0.000342)|BRCA - Breast invasive adenocarcinoma(304;0.000949)|KIRC - Kidney renal clear cell carcinoma(229;0.00122)|STAD - Stomach adenocarcinoma(132;0.00644)|READ - Rectum adenocarcinoma(331;0.0419)		CATCTTTGTCAACAGTAAAGG	0.522													G|||	1550	0.309505	0.6089	0.2219	5008	,	,		19507	0.1855		0.0775	False		,,,				2504	0.3333				p.V213V		Atlas-SNP	.											.	CLSTN1	88	.	0			c.T639C						PASS	.	G	,	2304,2102	573.6+/-383.6	595,1114,494	84.0	81.0	82.0		639,609	-11.2	0.0	1	dbSNP_52	82	725,7875	786.9+/-407.6	41,643,3616	no	coding-synonymous,coding-synonymous	CLSTN1	NM_001009566.1,NM_014944.3	,	636,1757,4110	GG,GA,AA		8.4302,47.7077,23.2893	,	213/982,203/972	9811541	3029,9977	2203	4300	6503	SO:0001819	synonymous_variant	22883	exon5			TTTGTCAACAGTA	AB020718	CCDS105.1, CCDS30580.1	1p36.22	2011-07-01			ENSG00000171603	ENSG00000171603		"""Cadherins / Cadherin-related"""	17447	protein-coding gene	gene with protein product	"""cadherin-related family member 12"""	611321				10048485	Standard	XM_005263432		Approved	CSTN1, KIAA0911, CDHR12	uc001aqh.3	O94985	OTTHUMG00000001451	ENST00000377298.4:c.639T>C	1.37:g.9811541A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	150	13	0.0866667	NM_001009566	A8K183|Q5SR52|Q5UE58|Q71MN0|Q8N4K9	Silent	SNP	ENST00000377298.4	37	CCDS30580.1																																																																																			A|0.749;G|0.251	0.251	strong		0.522	CLSTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004239.1		
BRCA1	672	hgsc.bcm.edu	37	17	41244429	41244429	+	Missense_Mutation	SNP	C	C	T	rs4986852	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:41244429C>T	ENST00000357654.3	-	10	3237	c.3119G>A	c.(3118-3120)aGc>aAc	p.S1040N	BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.S1040N|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.S1040N|BRCA1_ENST00000493795.1_Missense_Mutation_p.S993N|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.S1040N|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000309486.4_Missense_Mutation_p.S744N	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1040			S -> N (rare polymorphism; dbSNP:rs4986852). {ECO:0000269|PubMed:15026808, ECO:0000269|PubMed:7894491, ECO:0000269|PubMed:7894493, ECO:0000269|PubMed:9482581, ECO:0000269|Ref.6}.		androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ATTGCTTGAGCTGGCTTCTTT	0.363			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)			C|||	49	0.00978435	0.0023	0.0202	5008	,	,		19992	0.0		0.0288	False		,,,				2504	0.0031				p.S1040N		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,0,1	BRCA1	304	1	0			c.G3119A	GRCh37	CM940175	BRCA1	M	rs4986852	scavenged	.	C	ASN/SER,ASN/SER,,,ASN/SER	27,4379	34.3+/-65.2	0,27,2176	129.0	122.0	124.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3119,2978,,,3119	2.0	0.6	17	dbSNP_111	124	188,8412	83.7+/-146.2	2,184,4114	yes	missense,missense,intron,intron,missense	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	46,46,,,46	2,211,6290	TT,TC,CC		2.186,0.6128,1.6531	benign,benign,,,benign	1040/1864,993/1817,,,1040/1885	41244429	215,12791	2203	4300	6503	SO:0001583	missense	672	exon10	Familial Cancer Database		CTTGAGCTGGCTT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.3119G>A	17.37:g.41244429C>T	ENSP00000350283:p.Ser1040Asn	Somatic	203	1	0.00492611		WXS	Illumina HiSeq	Phase_I	214	99	0.462617	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	26	0.011904761904761904	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	16	0.021108179419525065	C	12.49	1.952634	0.34471	0.006128	0.02186	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	5.23	2.01	0.26516	.	0.625158	0.15975	N	0.235595	T	0.73321	0.3572	M	0.85945	2.785	0.09310	N	1	B;B;B;P;D;B	0.56035	0.011;0.011;0.32;0.795;0.974;0.433	B;B;B;B;P;B	0.58013	0.006;0.012;0.225;0.222;0.831;0.272	T	0.68281	-0.5450	10	0.59425	D	0.04	.	4.0226	0.09672	0.0:0.534:0.1748:0.2912	rs4986852;rs52807709;rs4986852	1040;999;1040;1040;1040;1040	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	N	1040;1040;1040;1040;744;1040;993	ENSP00000350283:S1040N;ENSP00000326002:S1040N;ENSP00000246907:S1040N;ENSP00000310938:S744N;ENSP00000418960:S1040N;ENSP00000418775:S993N	ENSP00000310938:S744N	S	-	2	0	BRCA1	38497955	0.001000	0.12720	0.572000	0.28498	0.816000	0.46133	-0.426000	0.07008	0.796000	0.33947	0.557000	0.71058	AGC	C|0.982;T|0.018	0.018	strong		0.363	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222316	140222316	+	Silent	SNP	G	G	A	rs202126810		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140222316G>A	ENST00000531613.1	+	1	1410	c.1410G>A	c.(1408-1410)ccG>ccA	p.P470P	PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000378123.3_Silent_p.P470P|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	470	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAACCCGCCGGGCTGCCACA	0.672																																					p.P470P		Atlas-SNP	.											PCDHA8_ENST00000531613,rectum,carcinoma,0,2	PCDHA8	366	2	0			c.G1410A						PASS	.						38.0	43.0	41.0					5																	140222316		2193	4252	6445	SO:0001819	synonymous_variant	56140	exon1			CCCGCCGGGCTGC	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1410G>A	5.37:g.140222316G>A		Somatic	242	0	0		WXS	Illumina HiSeq	Phase_I	304	152	0.5	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																			G|0.999;T|0.001	.	alt		0.672	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
OR51B6	390058	hgsc.bcm.edu	37	11	5373170	5373170	+	Missense_Mutation	SNP	C	C	G	rs5006886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5373170C>G	ENST00000380219.1	+	1	433	c.433C>G	c.(433-435)Cgg>Ggg	p.R145G	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	145			R -> G (in dbSNP:rs5006886). {ECO:0000269|PubMed:11121057}.		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	21		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GATTGGTGTGCGGGTATTGAC	0.478													G|||	1170	0.233626	0.326	0.2349	5008	,	,		23785	0.0863		0.2644	False		,,,				2504	0.228				p.R145G		Atlas-SNP	.											OR51B6,caecum,carcinoma,-1,1	OR51B6	53	1	0			c.C433G						PASS	.	G	GLY/ARG	1267,3135	694.8+/-405.9	173,921,1107	162.0	133.0	142.0		433	5.0	0.0	11	dbSNP_113	142	2260,6334	704.9+/-405.4	310,1640,2347	yes	missense	OR51B6	NM_001004750.1	125	483,2561,3454	GG,GC,CC		26.2974,28.7824,27.1391	benign	145/313	5373170	3527,9469	2201	4297	6498	SO:0001583	missense	390058	exon1			GGTGTGCGGGTAT		CCDS31379.1	11p15.4	2012-08-09			ENSG00000176239	ENSG00000176239		"""GPCR / Class A : Olfactory receptors"""	19600	protein-coding gene	gene with protein product							Standard	NM_001004750		Approved		uc010qzb.2	Q9H340	OTTHUMG00000066669	ENST00000380219.1:c.433C>G	11.37:g.5373170C>G	ENSP00000369568:p.Arg145Gly	Somatic	247	0	0		WXS	Illumina HiSeq	Phase_I	197	64	0.324873	NM_001004750		Missense_Mutation	SNP	ENST00000380219.1	37	CCDS31379.1	472	0.21611721611721613	159	0.3231707317073171	91	0.2513812154696133	30	0.05244755244755245	192	0.2532981530343008	G	0.009	-1.810739	0.00600	0.287824	0.262974	ENSG00000176239	ENST00000537299;ENST00000380219	T	0.33865	1.39	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.415428	0.20723	N	0.086862	T	0.00012	0.0000	N	0.00015	-2.885	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31194	-0.9952	9	0.12103	T	0.63	.	14.4601	0.67442	0.0:0.1483:0.8517:0.0	rs5006886;rs52816653;rs5006886	145	Q9H340	O51B6_HUMAN	G	144;145	ENSP00000369568:R145G	ENSP00000369568:R145G	R	+	1	2	OR51B6	5329746	0.000000	0.05858	0.033000	0.17914	0.234000	0.25298	0.344000	0.19962	1.353000	0.45828	-0.371000	0.07208	CGG	C|0.755;G|0.245	0.245	strong		0.478	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750	
GALC	2581	hgsc.bcm.edu	37	14	88442712	88442712	+	Missense_Mutation	SNP	C	C	T	rs34362748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:88442712C>T	ENST00000261304.2	-	7	848	c.742G>A	c.(742-744)Gat>Aat	p.D248N	GALC_ENST00000393569.2_Missense_Mutation_p.D222N|GALC_ENST00000554916.1_5'UTR|GALC_ENST00000393568.4_Missense_Mutation_p.D225N|GALC_ENST00000544807.2_Missense_Mutation_p.D192N	NM_000153.3|NM_001201401.1	NP_000144.2|NP_001188330.1	P54803	GALC_HUMAN	galactosylceramidase	248			D -> N (in dbSNP:rs34362748). {ECO:0000269|PubMed:20886637}.		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						CCTATAACATCAACCACCTTG	0.418													C|||	398	0.0794728	0.0174	0.1657	5008	,	,		17654	0.005		0.159	False		,,,				2504	0.0971				p.D248N		Atlas-SNP	.											.	GALC	48	.	0			c.G742A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	171,3681		0,171,1755	114.0	106.0	108.0		742,673,664	5.3	1.0	14	dbSNP_126	108	1259,7021		87,1085,2968	yes	missense,missense,missense	GALC	NM_000153.3,NM_001201401.1,NM_001201402.1	23,23,23	87,1256,4723	TT,TC,CC		15.2053,4.4393,11.787	probably-damaging,probably-damaging,probably-damaging	248/686,225/663,222/660	88442712	1430,10702	1926	4140	6066	SO:0001583	missense	2581	exon7			TAACATCAACCAC	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.742G>A	14.37:g.88442712C>T	ENSP00000261304:p.Asp248Asn	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	47	46	0.978723	NM_000153	B4DKE8|B4DYN1|B4DZJ8|B7Z7Z2|J3KN25|J3KPP8|Q8J030	Missense_Mutation	SNP	ENST00000261304.2	37	CCDS9878.2	200	0.09157509157509157	12	0.024390243902439025	56	0.15469613259668508	2	0.0034965034965034965	130	0.17150395778364116	C	16.73	3.202800	0.58234	0.044393	0.152053	ENSG00000054983	ENST00000261304;ENST00000544807;ENST00000393569;ENST00000539620;ENST00000393568;ENST00000445021	D;D;D;D	0.99769	-6.7;-6.7;-6.7;-6.7	5.32	5.32	0.75619	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.147324	0.64402	D	0.000011	T	0.47395	0.1443	M	0.89095	3.005	0.09310	P	0.999999411641	P;P;P;B;P	0.44260	0.707;0.83;0.575;0.432;0.629	B;P;B;B;B	0.46940	0.102;0.532;0.166;0.117;0.255	T	0.00000	-1.3817	9	0.46703	T	0.11	-25.1535	11.9665	0.53038	0.0:0.9156:0.0:0.0844	rs34362748	192;225;222;248;248	P54803-5;E7EPA4;P54803-4;G3XAI6;P54803	.;.;.;.;GALC_HUMAN	N	248;192;222;37;225;248	ENSP00000261304:D248N;ENSP00000437513:D192N;ENSP00000377199:D222N;ENSP00000377198:D225N	ENSP00000261304:D248N	D	-	1	0	GALC	87512465	1.000000	0.71417	1.000000	0.80357	0.525000	0.34531	5.296000	0.65698	2.467000	0.83353	0.591000	0.81541	GAT	C|0.895;T|0.105	0.105	strong		0.418	GALC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071559.2		
CARD8	22900	hgsc.bcm.edu	37	19	48737764	48737764	+	5'UTR	SNP	A	A	G	rs2288876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48737764A>G	ENST00000359009.4	-	0	284				CARD8_ENST00000520015.1_Silent_p.L82L|CARD8_ENST00000519940.1_Silent_p.L82L|ZNF114_ENST00000597695.1_Intron|CARD8_ENST00000391898.3_Silent_p.L82L|CARD8_ENST00000520753.1_Silent_p.L82L|CARD8_ENST00000357778.5_5'UTR|CARD8_ENST00000520153.1_Silent_p.L32L|CARD8_ENST00000447740.2_Silent_p.L32L|CARD8_ENST00000521613.1_Silent_p.L32L			Q9Y2G2	CARD8_HUMAN	caspase recruitment domain family, member 8						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)|NLRP3 inflammasome complex (GO:0072559)|nucleus (GO:0005634)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|NACHT domain binding (GO:0032089)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	15		all_lung(116;0.000112)|Lung NSC(112;0.000192)|all_epithelial(76;0.000349)|all_neural(266;0.0228)|Ovarian(192;0.113)|Prostate(7;0.184)		OV - Ovarian serous cystadenocarcinoma(262;0.000112)|all cancers(93;0.000293)|Epithelial(262;0.0129)|GBM - Glioblastoma multiforme(486;0.0336)		AGATGTCACAAAGGGTCTCAG	0.438													A|||	1349	0.269369	0.1959	0.3674	5008	,	,		19111	0.1944		0.2932	False		,,,				2504	0.3517				p.L82L		Atlas-SNP	.											.	CARD8	53	.	0			c.T246C						PASS	.	A	,,,,	953,3453	357.1+/-313.8	98,757,1348	99.0	83.0	88.0		246,96,246,246,96	-0.1	0.0	19	dbSNP_100	88	2819,5781	442.7+/-360.2	486,1847,1967	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CARD8	NM_001184900.1,NM_001184901.1,NM_001184902.1,NM_001184903.1,NM_014959.3	,,,,	584,2604,3315	GG,GA,AA		32.7791,21.6296,29.002	,,,,	82/538,32/488,82/393,82/393,32/488	48737764	3772,9234	2203	4300	6503	SO:0001623	5_prime_UTR_variant	22900	exon3			GTCACAAAGGGTC	AB023172	CCDS12712.1, CCDS12712.2, CCDS54287.1, CCDS54288.1, CCDS54289.1	19q13.33	2011-05-24			ENSG00000105483	ENSG00000105483			17057	protein-coding gene	gene with protein product		609051				10231032, 11408476	Standard	NM_001184900		Approved	TUCAN, KIAA0955, CARDINAL, NDPP, Dakar	uc010xzj.2	Q9Y2G2	OTTHUMG00000165047	ENST00000359009.4:c.-29T>C	19.37:g.48737764A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	68	68	1	NM_001184900	B5KVR6|B7Z496|B7Z4A2|E9PEM7|G3XAM9|Q6PGP8|Q96P82	Silent	SNP	ENST00000359009.4	37																																																																																				A|0.758;G|0.242	0.242	strong		0.438	CARD8-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014959	
MFRP	83552	hgsc.bcm.edu	37	11	119216279	119216279	+	Silent	SNP	G	G	A	rs36015759	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:119216279G>A	ENST00000530681.1	-	5	636	c.492C>T	c.(490-492)taC>taT	p.Y164Y	MFRP_ENST00000449574.2_Silent_p.Y164Y|MFRP_ENST00000555262.1_Silent_p.Y164Y|MFRP_ENST00000360167.4_Silent_p.Y164Y|MFRP_ENST00000529147.1_5'UTR|C1QTNF5_ENST00000445041.2_5'UTR	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	164	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		TGTTGGGGGGGTAAGGGTCTG	0.572													G|||	1009	0.201478	0.2489	0.1657	5008	,	,		18533	0.2024		0.2028	False		,,,				2504	0.1605				p.Y164Y		Atlas-SNP	.											.	MFRP	63	.	0			c.C492T						PASS	.	G	,	1038,3360	379.7+/-323.4	135,768,1296	50.0	49.0	49.0		,492	2.1	1.0	11	dbSNP_126	49	1885,6705	332.8+/-320.3	210,1465,2620	no	utr-5,coding-synonymous	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,	345,2233,3916	AA,AG,GG		21.9441,23.6016,22.5054	,	,164/580	119216279	2923,10065	2199	4295	6494	SO:0001819	synonymous_variant	83552	exon5			GGGGGGGTAAGGG	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"""membrane-type frizzled-related protein"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 1"""	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.492C>T	11.37:g.119216279G>A		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	50	27	0.54	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Silent	SNP	ENST00000530681.1	37	CCDS8421.1																																																																																			G|0.781;A|0.219	0.219	strong		0.572	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433	
LIPJ	142910	hgsc.bcm.edu	37	10	90356598	90356598	+	Missense_Mutation	SNP	A	A	G	rs1409136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:90356598A>G	ENST00000371939.3	+	8	942	c.628A>G	c.(628-630)Att>Gtt	p.I210V		NM_001010939.2	NP_001010939.2	Q5W064	LIPJ_HUMAN	lipase, family member J	210			I -> V (in dbSNP:rs1409136). {ECO:0000269|PubMed:15489334}.		lipid catabolic process (GO:0016042)		hydrolase activity, acting on ester bonds (GO:0016788)			large_intestine(4)|lung(4)|ovary(1)	9		all_cancers(4;2.79e-10)|Prostate(4;1.68e-15)|all_epithelial(4;1.43e-09)|Colorectal(252;0.0381)|Breast(4;0.141)|Melanoma(5;0.2)|all_hematologic(4;0.222)		Colorectal(12;1.02e-05)|COAD - Colon adenocarcinoma(12;1.54e-05)		TAAAAAATTCATTGGTTCAAA	0.313													A|||	4470	0.892572	0.9788	0.8487	5008	,	,		15818	0.994		0.7505	False		,,,				2504	0.8487				p.I210V		Atlas-SNP	.											.	LIPJ	32	.	0			c.A628G						PASS	.	A	VAL/ILE	4081,323	780.3+/-414.4	1890,301,11	74.0	87.0	83.0		628	-8.2	0.0	10	dbSNP_88	83	6179,2411	693.4+/-404.7	2217,1745,333	yes	missense	LIPJ	NM_001010939.2	29	4107,2046,344	GG,GA,AA		28.0675,7.3342,21.0405	benign	210/367	90356598	10260,2734	2202	4295	6497	SO:0001583	missense	142910	exon8			AAATTCATTGGTT	BC031219	CCDS31240.1	10q23.31	2008-02-04	2008-02-04	2007-02-27	ENSG00000204022	ENSG00000204022			21773	protein-coding gene	gene with protein product		613921	"""lipase-like, ab-hydrolase domain containing 1"", ""lipase, family member J"""	LIPL1			Standard	NM_001010939		Approved	bA425M17.2	uc001kff.3	Q5W064	OTTHUMG00000018691	ENST00000371939.3:c.628A>G	10.37:g.90356598A>G	ENSP00000361007:p.Ile210Val	Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	38	17	0.447368	NM_001010939	A8MT98|Q0P671	Missense_Mutation	SNP	ENST00000371939.3	37	CCDS31240.1	1914	0.8763736263736264	477	0.9695121951219512	303	0.8370165745856354	568	0.993006993006993	566	0.7467018469656992	A	1.239	-0.622008	0.03636	0.926658	0.719325	ENSG00000204022	ENST00000371939	T	0.62232	0.04	4.12	-8.23	0.01033	Alpha/beta hydrolase fold-1 (1);	1.812040	0.03101	N	0.161129	T	0.00012	0.0000	N	0.02129	-0.67	0.80722	P	0.0	B	0.02656	0.0	B	0.12837	0.008	T	0.31558	-0.9939	9	0.30854	T	0.27	-16.8714	4.417	0.11461	0.4656:0.2874:0.1665:0.0805	rs1409136;rs17345596;rs56428728;rs1409136	210	Q5W064	LIPJ_HUMAN	V	210	ENSP00000361007:I210V	ENSP00000361007:I210V	I	+	1	0	LIPJ	90346578	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-6.308000	0.00071	-2.506000	0.00507	-1.990000	0.00449	ATT	A|0.165;G|0.835	0.835	strong		0.313	LIPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049248.2	XM_084377	
GPR1	2825	hgsc.bcm.edu	37	2	207041053	207041053	+	Missense_Mutation	SNP	T	T	C	rs3732083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:207041053T>C	ENST00000407325.2	-	3	1281	c.919A>G	c.(919-921)Att>Gtt	p.I307V	GPR1_ENST00000437420.1_Missense_Mutation_p.I307V	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	307			I -> V (in dbSNP:rs3732083). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:16303743}.		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TTCTTACTAATTAGGACATAA	0.488													T|||	2316	0.46246	0.6483	0.5735	5008	,	,		20495	0.2579		0.4831	False		,,,				2504	0.3221				p.I307V		Atlas-SNP	.											.	GPR1	38	.	0			c.A919G						PASS	.	T	VAL/ILE,VAL/ILE	2780,1626	662.2+/-401.0	882,1016,305	101.0	100.0	100.0		919,919	5.7	1.0	2	dbSNP_107	100	3870,4730	542.9+/-384.3	881,2108,1311	yes	missense,missense	GPR1	NM_001098199.1,NM_005279.3	29,29	1763,3124,1616	CC,CT,TT		45.0,36.9042,48.8698	benign,benign	307/356,307/356	207041053	6650,6356	2203	4300	6503	SO:0001583	missense	2825	exon3			TACTAATTAGGAC		CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.919A>G	2.37:g.207041053T>C	ENSP00000384345:p.Ile307Val	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	101	99	0.980198	NM_001098199	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Missense_Mutation	SNP	ENST00000407325.2	37	CCDS2368.1	1029	0.47115384615384615	308	0.6260162601626016	209	0.5773480662983426	144	0.2517482517482518	368	0.48548812664907653	T	10.35	1.325180	0.24080	0.630958	0.45	ENSG00000183671	ENST00000407325;ENST00000437420	T;T	0.36699	1.24;1.24	5.7	5.7	0.88788	.	0.127093	0.53938	D	0.000051	T	0.00012	0.0000	N	0.08118	0	0.25801	P	0.9845058	B	0.23128	0.08	B	0.14578	0.011	T	0.35351	-0.9792	9	0.35671	T	0.21	.	12.4853	0.55868	0.0:0.0:0.1394:0.8606	rs3732083;rs52828782;rs61202419;rs3732083	307	P46091	GPR1_HUMAN	V	307	ENSP00000384345:I307V;ENSP00000397535:I307V	ENSP00000384345:I307V	I	-	1	0	GPR1	206749298	1.000000	0.71417	0.995000	0.50966	0.599000	0.36880	3.455000	0.52993	2.177000	0.69029	0.533000	0.62120	ATT	T|0.502;C|0.498	0.498	strong		0.488	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2	NM_001098199	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33541216	33541216	+	Missense_Mutation	SNP	G	G	C	rs111814125		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:33541216G>C	ENST00000290943.6	+	7	976	c.880G>C	c.(880-882)Ggt>Cgt	p.G294R		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	294								p.G294R(1)		NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						aagaaaagaaGGTGCAAAAGG	0.343																																					p.G294R		Atlas-SNP	.											ANKRD18B,NS,carcinoma,0,1	ANKRD18B	46	1	1	Substitution - Missense(1)	prostate(1)	c.G880C						scavenged	.																																			SO:0001583	missense	441459	exon7			AAAGAAGGTGCAA			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.880G>C	9.37:g.33541216G>C	ENSP00000290943:p.Gly294Arg	Somatic	276	1	0.00362319		WXS	Illumina HiSeq	Phase_I	343	56	0.163265	NM_001244752		Missense_Mutation	SNP	ENST00000290943.6	37		.	.	.	.	.	.	.	.	.	.	g	0.030	-1.339649	0.01277	.	.	ENSG00000230453	ENST00000290943	T	0.26660	1.72	0.225	0.225	0.15325	.	.	.	.	.	T	0.18087	0.0434	.	.	.	0.23076	N	0.998333	.	.	.	.	.	.	T	0.34625	-0.9821	4	0.19147	T	0.46	.	.	.	.	.	.	.	.	R	294	ENSP00000290943:G294R	ENSP00000290943:G294R	G	+	1	0	ANKRD18B	33531216	0.013000	0.17824	0.008000	0.14137	0.008000	0.06430	0.337000	0.19841	0.300000	0.22699	0.305000	0.20034	GGT	G|0.500;C|0.500	0.500	weak		0.343	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
ZNF584	201514	hgsc.bcm.edu	37	19	58928302	58928302	+	Silent	SNP	T	T	C	rs10423138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58928302T>C	ENST00000306910.4	+	4	940	c.417T>C	c.(415-417)gcT>gcC	p.A139A	ZNF584_ENST00000593920.1_Silent_p.A94A|ZNF584_ENST00000599238.1_3'UTR|ZNF584_ENST00000596921.1_3'UTR|CTD-2619J13.16_ENST00000596296.1_lincRNA|ZNF584_ENST00000322834.7_3'UTR	NM_173548.1	NP_775819.1	Q8IVC4	ZN584_HUMAN	zinc finger protein 584	139					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(3)|large_intestine(3)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14		all_cancers(17;5.3e-17)|all_epithelial(17;3.71e-12)|Lung NSC(17;8.3e-05)|Colorectal(82;0.000147)|all_lung(17;0.000386)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0271)		ATGGGGCAGCTTTCCCACCTG	0.517													C|||	2507	0.500599	0.7882	0.379	5008	,	,		17868	0.3254		0.497	False		,,,				2504	0.3824				p.A139A		Atlas-SNP	.											.	ZNF584	31	.	0			c.T417C						PASS	.	C		3379,1027	378.0+/-322.7	1306,767,130	147.0	112.0	124.0		417	1.0	0.0	19	dbSNP_119	124	4150,4450	587.3+/-392.2	1008,2134,1158	no	coding-synonymous	ZNF584	NM_173548.1		2314,2901,1288	CC,CT,TT		48.2558,23.3091,42.1113		139/422	58928302	7529,5477	2203	4300	6503	SO:0001819	synonymous_variant	201514	exon4			GGCAGCTTTCCCA	AK097218	CCDS12979.1	19q13.43	2013-01-08			ENSG00000171574	ENSG00000171574		"""Zinc fingers, C2H2-type"", ""-"""	27318	protein-coding gene	gene with protein product							Standard	NM_173548		Approved	FLJ39899	uc002qsp.3	Q8IVC4		ENST00000306910.4:c.417T>C	19.37:g.58928302T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	94	48	0.510638	NM_173548	A8K203	Silent	SNP	ENST00000306910.4	37	CCDS12979.1																																																																																			T|0.459;C|0.541	0.541	strong		0.517	ZNF584-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467022.1	NM_173548	
RHOBTB3	22836	hgsc.bcm.edu	37	5	95091194	95091194	+	Silent	SNP	C	C	T	rs34898	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:95091194C>T	ENST00000379982.3	+	6	1285	c.777C>T	c.(775-777)taC>taT	p.Y259Y	GLRX_ENST00000508780.1_Intron	NM_014899.3	NP_055714.3	O94955	RHBT3_HUMAN	Rho-related BTB domain containing 3	259	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.				ATP catabolic process (GO:0006200)|retrograde transport, endosome to Golgi (GO:0042147)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|GTP binding (GO:0005525)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|skin(1)	16		all_cancers(142;2.58e-06)|all_epithelial(76;4.19e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0164)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.79e-16)		TGGTATTTTACAACCCCAATT	0.418													C|||	2272	0.453674	0.2806	0.3329	5008	,	,		16305	0.6895		0.4324	False		,,,				2504	0.5521				p.Y259Y		Atlas-SNP	.											.	RHOBTB3	43	.	0			c.C777T						PASS	.	C		1359,3047	451.2+/-349.6	206,947,1050	173.0	167.0	169.0		777	4.0	0.9	5	dbSNP_76	169	3572,5028	518.5+/-379.3	729,2114,1457	no	coding-synonymous	RHOBTB3	NM_014899.3		935,3061,2507	TT,TC,CC		41.5349,30.8443,37.9133		259/612	95091194	4931,8075	2203	4300	6503	SO:0001819	synonymous_variant	22836	exon6			ATTTTACAACCCC	AB020685	CCDS4077.1	5q15	2014-05-09			ENSG00000164292	ENSG00000164292		"""BTB/POZ domain containing"""	18757	protein-coding gene	gene with protein product		607353				11222756, 17035353	Standard	NM_014899		Approved	KIAA0878	uc003klm.3	O94955	OTTHUMG00000121171	ENST00000379982.3:c.777C>T	5.37:g.95091194C>T		Somatic	217	0	0		WXS	Illumina HiSeq	Phase_I	210	208	0.990476	NM_014899	A0PJA4|A8K1W9|Q8IW06	Silent	SNP	ENST00000379982.3	37	CCDS4077.1																																																																																			C|0.586;T|0.414	0.414	strong		0.418	RHOBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241658.1	NM_014899	
USP6	9098	hgsc.bcm.edu	37	17	5042837	5042837	+	Missense_Mutation	SNP	C	C	T	rs61745111	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5042837C>T	ENST00000574788.1	+	22	3596	c.1366C>T	c.(1366-1368)Cgg>Tgg	p.R456W	USP6_ENST00000332776.4_Missense_Mutation_p.R456W|USP6_ENST00000304328.5_Missense_Mutation_p.R139W|USP6_ENST00000250066.6_Missense_Mutation_p.R456W			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	456					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.R456W(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GTCAATGCCCCGGCTCCCAAC	0.612			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	509	0.101637	0.1982	0.0375	5008	,	,		18531	0.0784		0.1153	False		,,,				2504	0.0266				p.R456W		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	USP6,NS,carcinoma,0,1	USP6	213	1	1	Substitution - Missense(1)	lung(1)	c.C1366T						PASS	.	C	TRP/ARG	710,3696	291.3+/-281.4	62,586,1555	51.0	59.0	56.0		1366	-0.5	0.0	17	dbSNP_129	56	951,7649	208.3+/-249.8	52,847,3401	yes	missense	USP6	NM_004505.2	101	114,1433,4956	TT,TC,CC		11.0581,16.1144,12.771	benign	456/1407	5042837	1661,11345	2203	4300	6503	SO:0001583	missense	9098	exon14			ATGCCCCGGCTCC	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.1366C>T	17.37:g.5042837C>T	ENSP00000460380:p.Arg456Trp	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	250	0.11446886446886446	97	0.19715447154471544	16	0.04419889502762431	52	0.09090909090909091	85	0.11213720316622691	C	1.018	-0.685710	0.03328	0.161144	0.110581	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.25749	2.19;2.68;1.78	0.266	-0.532	0.11890	.	0.290613	0.37012	N	0.002286	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38373	-0.9664	8	0.87932	D	0	.	.	.	.	rs61745111	139;456	P35125-2;P35125	.;UBP6_HUMAN	W	456;456;139	ENSP00000328010:R456W;ENSP00000250066:R456W;ENSP00000305473:R139W	ENSP00000250066:R456W	R	+	1	2	USP6	4983561	0.025000	0.19082	0.000000	0.03702	0.000000	0.00434	-1.254000	0.02874	-2.211000	0.00737	-2.287000	0.00268	CGG	C|0.881;T|0.119	0.119	strong		0.612	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
PRKX	5613	hgsc.bcm.edu	37	X	3592725	3592725	+	Silent	SNP	G	G	A	rs10871864	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3592725G>A	ENST00000262848.5	-	2	603	c.249C>T	c.(247-249)ccC>ccT	p.P83P		NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	83	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				GGATGACGTCGGGAATGCTCA	0.557													G|||	1719	0.455364	0.261	0.4885	3775	,	,		14631	0.2788		0.4334	False		,,,				2504	0.3252				p.P83P		Atlas-SNP	.											.	PRKX	29	.	0			c.C249T						PASS	.	G		1469,2366		242,764,221,626,350	255.0	165.0	196.0		249	-5.2	0.9	X	dbSNP_120	196	3862,2866		809,1151,1093,468,779	no	coding-synonymous	PRKX	NM_005044.4		1051,1915,1314,1094,1129	AA,AG,A,GG,G		42.5981,38.3051,49.5314		83/359	3592725	5331,5232	2203	4300	6503	SO:0001819	synonymous_variant	5613	exon2			GACGTCGGGAATG		CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.249C>T	X.37:g.3592725G>A		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	128	126	0.984375	NM_005044		Silent	SNP	ENST00000262848.5	37	CCDS14125.1																																																																																			G|0.502;A|0.498	0.498	strong		0.557	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044	
LRRC52	440699	hgsc.bcm.edu	37	1	165532746	165532746	+	Missense_Mutation	SNP	T	T	A	rs17407838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:165532746T>A	ENST00000294818.1	+	2	917	c.627T>A	c.(625-627)gaT>gaA	p.D209E	RP11-280O1.2_ENST00000416424.1_RNA|RP11-280O1.2_ENST00000438275.1_RNA|RP11-280O1.2_ENST00000421273.1_RNA	NM_001005214.3	NP_001005214.2	Q8N7C0	LRC52_HUMAN	leucine rich repeat containing 52	209	LRRCT.		D -> E (in dbSNP:rs17407838).		ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)	18	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TCTTAGATGATCTAAATGCCA	0.572													T|||	293	0.0585064	0.1006	0.062	5008	,	,		20087	0.0		0.1034	False		,,,				2504	0.0133				p.D209E		Atlas-SNP	.											.	LRRC52	50	.	0			c.T627A						PASS	.	T	GLU/ASP	411,3995	198.1+/-222.0	14,383,1806	45.0	37.0	40.0		627	-8.6	0.0	1	dbSNP_123	40	905,7695	195.9+/-241.0	54,797,3449	yes	missense	LRRC52	NM_001005214.3	45	68,1180,5255	AA,AT,TT		10.5233,9.3282,10.1184	benign	209/314	165532746	1316,11690	2203	4300	6503	SO:0001583	missense	440699	exon2			AGATGATCTAAAT	AK098677	CCDS30930.1	1q23.3	2008-02-05			ENSG00000162763	ENSG00000162763			32156	protein-coding gene	gene with protein product		615218					Standard	NM_001005214		Approved	FLJ25811	uc001gde.2	Q8N7C0	OTTHUMG00000034625	ENST00000294818.1:c.627T>A	1.37:g.165532746T>A	ENSP00000294818:p.Asp209Glu	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_001005214	A2RUN7|Q5T9K5	Missense_Mutation	SNP	ENST00000294818.1	37	CCDS30930.1	144	0.06593406593406594	49	0.09959349593495935	21	0.058011049723756904	0	0.0	74	0.09762532981530343	T	0.006	-2.043824	0.00398	0.093282	0.105233	ENSG00000162763	ENST00000294818	T	0.64803	-0.12	4.28	-8.56	0.00904	.	0.544586	0.19975	N	0.101883	T	0.07188	0.0182	N	0.08118	0	0.24481	P	0.994347	B	0.02656	0.0	B	0.01281	0.0	T	0.14924	-1.0455	9	0.02654	T	1	.	4.7372	0.12993	0.1777:0.3642:0.3582:0.0998	rs17407838;rs52823561;rs17407838	209	Q8N7C0	LRC52_HUMAN	E	209	ENSP00000294818:D209E	ENSP00000294818:D209E	D	+	3	2	LRRC52	163799370	0.000000	0.05858	0.000000	0.03702	0.400000	0.30750	-4.590000	0.00211	-3.350000	0.00181	-1.123000	0.02005	GAT	T|0.917;A|0.083	0.083	strong		0.572	LRRC52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083793.1	NM_001005214	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035301	110035301	+	Silent	SNP	A	A	G	rs1026607	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:110035301A>G	ENST00000278590.3	+	6	1542	c.1491A>G	c.(1489-1491)acA>acG	p.T497T	ZC3H12C_ENST00000528673.1_Silent_p.T498T|ZC3H12C_ENST00000453089.2_Silent_p.T466T	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	497							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		GCATAAGGACACAAGTCTACC	0.448													G|||	1222	0.24401	0.3041	0.2248	5008	,	,		23059	0.2004		0.2724	False		,,,				2504	0.1922				p.T497T		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1491G						PASS	.	G		1098,2738		170,758,990	108.0	105.0	106.0		1491	-1.1	0.9	11	dbSNP_86	106	2086,6162		248,1590,2286	no	coding-synonymous	ZC3H12C	NM_033390.1		418,2348,3276	GG,GA,AA		25.291,28.6236,26.3489		497/884	110035301	3184,8900	1918	4124	6042	SO:0001819	synonymous_variant	85463	exon6			AAGGACACAAGTC		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1491A>G	11.37:g.110035301A>G		Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	33	0.471429	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			A|0.729;G|0.271	0.271	strong		0.448	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
SIRPB1	10326	hgsc.bcm.edu	37	20	1592193	1592193	+	Intron	SNP	C	C	T	rs371465078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:1592193C>T	ENST00000381605.4	-	1	141				SIRPB1_ENST00000568365.1_Silent_p.Q81Q|SIRPB1_ENST00000381596.1_5'UTR|SIRPB1_ENST00000381603.3_Intron|SIRPB1_ENST00000279477.7_Silent_p.Q81Q|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1						cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						GGCCTTCTTTCTGATTGTAGA	0.522													t|||	2823	0.563698	0.68	0.3876	5008	,	,		6072	0.631		0.3748	False		,,,				2504	0.6564				p.Q81Q		Atlas-SNP	.											SIRPB1_ENST00000279477,NS,malignant_melanoma,0,1	SIRPB1	83	1	0			c.G243A						PASS	.						94.0	111.0	106.0					20																	1592193		447	1317	1764	SO:0001627	intron_variant	10326	exon2			TTCTTTCTGATTG	Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.76+8321G>A	20.37:g.1592193C>T		Somatic	463	1	0.00215983		WXS	Illumina HiSeq	Phase_I	22	19	0.863636	NM_001135844	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			.	.	weak		0.522	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
ATXN1	6310	hgsc.bcm.edu	37	6	16327897	16327897	+	Missense_Mutation	SNP	C	C	A	rs184327938		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:16327897C>A	ENST00000244769.4	-	8	1581	c.645G>T	c.(643-645)caG>caT	p.Q215H	ATXN1_ENST00000436367.1_Missense_Mutation_p.Q215H	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	215	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.Q215H(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)				gctgctgctgctgctgctgct	0.667																																					p.Q215H		Atlas-SNP	.											ATXN1,NS,carcinoma,0,3	ATXN1	117	3	1	Substitution - Missense(1)	central_nervous_system(1)	c.G645T						PASS	.						4.0	8.0	7.0					6																	16327897		1730	3633	5363	SO:0001583	missense	6310	exon7			CTGCTGCTGCTGC	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.645G>T	6.37:g.16327897C>A	ENSP00000244769:p.Gln215His	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	54	21	0.388889	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	161	0.07371794871794872	7	0.014227642276422764	16	0.04419889502762431	116	0.20279720279720279	22	0.029023746701846966	-	1.752	-0.489019	0.04352	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.56611	0.45;0.45	.	.	.	.	.	.	.	.	T	0.13713	0.0332	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.21245	-1.0251	5	0.59425	D	0.04	.	.	.	.	.	215	P54253	ATX1_HUMAN	H	215	ENSP00000244769:Q215H;ENSP00000416360:Q215H	ENSP00000244769:Q215H	Q	-	3	2	ATXN1	16435876	0.000000	0.05858	0.011000	0.14972	0.097000	0.18754	-0.615000	0.05597	0.107000	0.17824	0.109000	0.15622	CAG	C|0.926;A|0.074	0.074	strong		0.667	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
C1orf86	199990	hgsc.bcm.edu	37	1	2125258	2125258	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2125258G>T	ENST00000378546.4	-	3	314	c.290C>A	c.(289-291)cCg>cAg	p.P97Q	C1orf86_ENST00000400919.3_5'UTR|C1orf86_ENST00000378545.3_Missense_Mutation_p.P200Q|C1orf86_ENST00000487186.1_5'UTR	NM_182533.2	NP_872339	Q6NZ36	FAP20_HUMAN	chromosome 1 open reading frame 86	97					cellular response to DNA damage stimulus (GO:0006974)|interstrand cross-link repair (GO:0036297)|translesion synthesis (GO:0019985)	cell junction (GO:0030054)|chromosome (GO:0005694)|Fanconi anaemia nuclear complex (GO:0043240)|nucleus (GO:0005634)	K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|polyubiquitin binding (GO:0031593)|ubiquitin binding (GO:0043130)			central_nervous_system(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	4	all_cancers(77;0.000134)|all_epithelial(69;4.45e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.09e-37)|OV - Ovarian serous cystadenocarcinoma(86;1.5e-23)|GBM - Glioblastoma multiforme(42;1.61e-08)|Colorectal(212;3.98e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00437)|STAD - Stomach adenocarcinoma(132;0.0134)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.199)		GGAACGGCCCGGGCCCCACAG	0.701																																					p.P97Q		Atlas-SNP	.											C1orf86,NS,carcinoma,0,1	C1orf86	20	1	0			c.C290A						scavenged	.						26.0	34.0	31.0					1																	2125258		2198	4297	6495	SO:0001583	missense	199990	exon3			CGGCCCGGGCCCC	AK126870	CCDS38.2, CCDS57965.1, CCDS72686.1, CCDS72687.1	1p36.33	2013-05-22			ENSG00000162585	ENSG00000162585			26428	protein-coding gene	gene with protein product		615183				14702039	Standard	NM_182533		Approved	FLJ31031, FAAP20	uc031pkt.1	Q6NZ36	OTTHUMG00000001404	ENST00000378546.4:c.290C>A	1.37:g.2125258G>T	ENSP00000367808:p.Pro97Gln	Somatic	83	1	0.0120482		WXS	Illumina HiSeq	Phase_I	89	2	0.0224719	NM_001256946	A6PW39|A6PW40|A6PW41|A8MQT6|F2Z2L4|Q6ZT64|Q71M24|Q96ND7	Missense_Mutation	SNP	ENST00000378546.4	37	CCDS38.2	.	.	.	.	.	.	.	.	.	.	G	12.02	1.812718	0.32053	.	.	ENSG00000162585	ENST00000400918;ENST00000378546;ENST00000378545	T;T;T	0.46063	0.95;0.98;0.88	3.62	-2.37	0.06643	.	2.059420	0.02904	N	0.135770	T	0.27594	0.0678	.	.	.	0.09310	N	1	B	0.25850	0.136	B	0.20767	0.031	T	0.21280	-1.0250	9	0.72032	D	0.01	-0.8643	1.4492	0.02371	0.1332:0.2453:0.3685:0.253	.	97	Q6NZ36	CA086_HUMAN	Q	97;97;200	ENSP00000383709:P97Q;ENSP00000367808:P97Q;ENSP00000367807:P200Q	ENSP00000367807:P200Q	P	-	2	0	C1orf86	2115118	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.500000	0.06405	-0.327000	0.08551	0.462000	0.41574	CCG	.	.	none		0.701	C1orf86-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316541.1	NM_182533	
CTSS	1520	hgsc.bcm.edu	37	1	150727539	150727539	+	Missense_Mutation	SNP	G	G	A	rs2230061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:150727539G>A	ENST00000368985.3	-	4	597	c.337C>T	c.(337-339)Cgg>Tgg	p.R113W	CTSS_ENST00000480760.1_5'UTR|CTSS_ENST00000448301.2_Intron	NM_001199739.1|NM_004079.4	NP_001186668.1|NP_004070.3	P25774	CATS_HUMAN	cathepsin S	113			R -> W (in dbSNP:rs2230061). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.5}.		adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|basement membrane disassembly (GO:0034769)|cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of inflammatory response (GO:0050729)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.R113W(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|urinary_tract(1)	15	all_cancers(9;6.17e-52)|all_epithelial(9;9.7e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.00146)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0485)|Epithelial(6;5.02e-21)|all cancers(9;1.28e-20)|OV - Ovarian serous cystadenocarcinoma(6;1.09e-14)|BRCA - Breast invasive adenocarcinoma(12;0.00501)|LUSC - Lung squamous cell carcinoma(543;0.171)			GGCAATATCCGATTAGGGTTT	0.433													G|||	1915	0.382388	0.261	0.4366	5008	,	,		20296	0.3532		0.3698	False		,,,				2504	0.5511				p.R113W		Atlas-SNP	.											CTSS,NS,carcinoma,0,1	CTSS	31	1	1	Substitution - Missense(1)	stomach(1)	c.C337T						PASS	.	G	,TRP/ARG	1229,3177	426.4+/-341.1	167,895,1141	214.0	206.0	209.0		,337	1.2	0.0	1	dbSNP_98	209	3052,5548	470.0+/-367.7	551,1950,1799	yes	intron,missense	CTSS	NM_001199739.1,NM_004079.4	,101	718,2845,2940	AA,AG,GG		35.4884,27.8938,32.9156	,possibly-damaging	,113/332	150727539	4281,8725	2203	4300	6503	SO:0001583	missense	1520	exon4			ATATCCGATTAGG	M90696	CCDS968.1, CCDS55634.1	1q21	2008-02-05			ENSG00000163131	ENSG00000163131	3.4.22.27	"""Cathepsins"""	2545	protein-coding gene	gene with protein product		116845				1373132	Standard	NM_001199739		Approved		uc001evn.3	P25774	OTTHUMG00000035010	ENST00000368985.3:c.337C>T	1.37:g.150727539G>A	ENSP00000357981:p.Arg113Trp	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	134	64	0.477612	NM_004079	B4DWC9|D3DV05|Q5T5I0|Q6FHS5|Q9BUG3	Missense_Mutation	SNP	ENST00000368985.3	37	CCDS968.1	768	0.3516483516483517	133	0.2703252032520325	156	0.430939226519337	202	0.3531468531468531	277	0.3654353562005277	G	9.045	0.990707	0.18966	0.278938	0.354884	ENSG00000163131	ENST00000368985	T	0.22539	1.95	5.47	1.23	0.21249	.	3.731250	0.00357	N	0.000022	T	0.05868	0.0153	L	0.37697	1.125	0.80722	P	0.0	P	0.48016	0.904	B	0.38655	0.278	T	0.14448	-1.0472	9	0.40728	T	0.16	.	4.546	0.12081	0.0765:0.1336:0.5144:0.2756	rs2230061;rs10888390;rs17357778;rs17607024;rs17849640;rs52835690;rs60119206;rs10888390	113	P25774	CATS_HUMAN	W	113	ENSP00000357981:R113W	ENSP00000357981:R113W	R	-	1	2	CTSS	148994163	0.004000	0.15560	0.009000	0.14445	0.359000	0.29487	0.427000	0.21379	-0.025000	0.13918	0.591000	0.81541	CGG	T|0.068;G|0.534;C|0.117;N|0.000;A|0.281	0.281	strong		0.433	CTSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084737.1	NM_004079	
F7	2155	hgsc.bcm.edu	37	13	113770068	113770068	+	Silent	SNP	C	C	T	rs6042	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113770068C>T	ENST00000375581.3	+	6	560	c.525C>T	c.(523-525)caC>caT	p.H175H	F7_ENST00000541084.1_Silent_p.H106H|F7_ENST00000346342.3_Silent_p.H153H	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	175	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	GTCGGTGCCACGAGGGGTACT	0.617													C|||	729	0.145567	0.1346	0.1282	5008	,	,		19696	0.0446		0.1213	False		,,,				2504	0.3016				p.H175H		Atlas-SNP	.											F7,NS,carcinoma,0,1	F7	49	1	0			c.C525T						PASS	.	C	,	590,3816	257.0+/-261.6	43,504,1656	64.0	54.0	57.0		525,459	-3.2	0.4	13	dbSNP_52	57	1008,7592	215.7+/-255.0	62,884,3354	no	coding-synonymous,coding-synonymous	F7	NM_000131.3,NM_019616.2	,	105,1388,5010	TT,TC,CC		11.7209,13.3908,12.2866	,	175/467,153/445	113770068	1598,11408	2203	4300	6503	SO:0001819	synonymous_variant	2155	exon6			GTGCCACGAGGGG		CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"""eptacog alfa"", ""FVII coagulation protein"", ""factor VII"""	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.525C>T	13.37:g.113770068C>T		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	69	26	0.376812	NM_000131	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Silent	SNP	ENST00000375581.3	37	CCDS9528.1																																																																																			C|0.876;T|0.124	0.124	strong		0.617	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045838.4	NM_000131	
ITGA11	22801	hgsc.bcm.edu	37	15	68643659	68643659	+	Silent	SNP	G	G	A	rs61729770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:68643659G>A	ENST00000315757.7	-	8	917	c.831C>T	c.(829-831)agC>agT	p.S277S	ITGA11_ENST00000562826.1_5'UTR|ITGA11_ENST00000423218.2_Silent_p.S277S	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	277	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			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						CCAGGTCTGGGCTGTCGTGGG	0.567													G|||	13	0.00259585	0.0	0.0043	5008	,	,		20370	0.0		0.0099	False		,,,				2504	0.0				p.S277S		Atlas-SNP	.											.	ITGA11	110	.	0			c.C831T						PASS	.	G		9,4145		0,9,2068	122.0	130.0	127.0		831	4.5	1.0	15	dbSNP_129	127	78,8372		0,78,4147	no	coding-synonymous	ITGA11	NM_001004439.1		0,87,6215	AA,AG,GG		0.9231,0.2167,0.6903		277/1189	68643659	87,12517	2077	4225	6302	SO:0001819	synonymous_variant	22801	exon8			GTCTGGGCTGTCG	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.831C>T	15.37:g.68643659G>A		Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	152	72	0.473684	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.995;A|0.005	0.005	strong		0.567	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
TRIM3	10612	hgsc.bcm.edu	37	11	6478619	6478619	+	Silent	SNP	G	G	A	rs16913748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6478619G>A	ENST00000525074.1	-	5	997	c.603C>T	c.(601-603)atC>atT	p.I201I	TRIM3_ENST00000529058.1_5'UTR|TRIM3_ENST00000359518.3_Silent_p.I201I|TRIM3_ENST00000536344.1_Silent_p.I82I|TRIM3_ENST00000345851.3_Silent_p.I201I|TRIM3_ENST00000537602.1_Silent_p.I201I	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	201					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACGCTGCACTGATCTGGGCCA	0.617													G|||	938	0.1873	0.2973	0.1772	5008	,	,		20774	0.0188		0.1849	False		,,,				2504	0.2219				p.I201I	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.C603T						PASS	.	G	,	1271,3131	434.1+/-343.8	178,915,1108	95.0	87.0	90.0		603,603	2.1	1.0	11	dbSNP_123	90	1764,6828	318.4+/-313.7	189,1386,2721	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	367,2301,3829	AA,AG,GG		20.5307,28.8732,23.3569	,	201/745,201/745	6478619	3035,9959	2201	4296	6497	SO:0001819	synonymous_variant	10612	exon5			TGCACTGATCTGG	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.603C>T	11.37:g.6478619G>A		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	68	31	0.455882	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			G|0.791;A|0.209	0.209	strong		0.617	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
UEVLD	55293	hgsc.bcm.edu	37	11	18600322	18600322	+	Silent	SNP	T	T	G	rs10500835	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18600322T>G	ENST00000541984.1	-	2	138	c.76A>C	c.(76-78)Agg>Cgg	p.R26R	UEVLD_ENST00000540666.1_Intron|UEVLD_ENST00000535484.1_5'UTR|UEVLD_ENST00000300038.7_Silent_p.R26R|UEVLD_ENST00000379387.4_Silent_p.R26R|UEVLD_ENST00000396197.3_Silent_p.R26R|UEVLD_ENST00000543987.1_Silent_p.R26R|UEVLD_ENST00000320750.6_Silent_p.R26R	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						TTTACATTCCTTAGTTCTTCC	0.328													T|||	822	0.164137	0.0121	0.1787	5008	,	,		19656	0.2579		0.1402	False		,,,				2504	0.2873				p.R26R		Atlas-SNP	.											.	UEVLD	58	.	0			c.A76C						PASS	.	T	,	156,4242	104.3+/-142.8	4,148,2047	109.0	103.0	105.0		76,76	5.8	1.0	11	dbSNP_119	105	1025,7561	218.5+/-256.9	73,879,3341	no	coding-synonymous,coding-synonymous	UEVLD	NM_001040697.1,NM_018314.3	,	77,1027,5388	GG,GT,TT		11.938,3.5471,9.0958	,	26/472,26/380	18600322	1181,11803	2199	4293	6492	SO:0001819	synonymous_variant	55293	exon2			CATTCCTTAGTTC	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.76A>C	11.37:g.18600322T>G		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	55	26	0.472727	NM_001040697		Silent	SNP	ENST00000541984.1	37	CCDS58125.1																																																																																			T|0.879;G|0.121	0.121	strong		0.328	UEVLD-015	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000395928.1	NM_018314	
DDX41	51428	hgsc.bcm.edu	37	5	176943352	176943352	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176943352G>C	ENST00000507955.1	-	3	758	c.235C>G	c.(235-237)Cta>Gta	p.L79V	DDX41_ENST00000506965.1_5'UTR	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	79					apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			TGAGGGCCTAGCGGGATGTCG	0.607																																					p.L79V		Atlas-SNP	.											.	DDX41	49	.	0			c.C235G						PASS	.						133.0	126.0	128.0					5																	176943352		2203	4300	6503	SO:0001583	missense	51428	exon3			GGCCTAGCGGGAT	AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"""DEAD-boxes"""	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.235C>G	5.37:g.176943352G>C	ENSP00000422753:p.Leu79Val	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	126	59	0.468254	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	37	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	G	9.895	1.205196	0.22205	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.26810	1.71;1.72	5.38	2.1	0.27182	.	0.377447	0.23291	N	0.049795	T	0.17408	0.0418	L	0.34521	1.04	0.31726	N	0.637673	B	0.14805	0.011	B	0.11329	0.006	T	0.12656	-1.0539	10	0.30078	T	0.28	-7.6704	9.3594	0.38186	0.3981:0.0:0.6019:0.0	.	79	Q9UJV9	DDX41_HUMAN	V	97;79	ENSP00000330349:L97V;ENSP00000422753:L79V	ENSP00000330349:L97V	L	-	1	2	DDX41	176875958	0.121000	0.22262	0.561000	0.28357	0.816000	0.46133	0.337000	0.19841	0.620000	0.30215	0.491000	0.48974	CTA	.	.	none		0.607	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222	
MOV10L1	54456	hgsc.bcm.edu	37	22	50589196	50589196	+	Silent	SNP	C	C	A	rs2294396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50589196C>A	ENST00000262794.5	+	21	2843	c.2760C>A	c.(2758-2760)ggC>ggA	p.G920G	MOV10L1_ENST00000540615.1_Silent_p.G900G|MOV10L1_ENST00000354853.2_Intron|MOV10L1_ENST00000545383.1_Silent_p.G920G|MOV10L1_ENST00000395843.1_Intron|MOV10L1_ENST00000395858.3_Silent_p.G920G|MOV10L1_ENST00000395852.1_Silent_p.G47G	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	920					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)		TGCAGCTCGGCCCAGTCATTA	0.607													C|||	723	0.144369	0.0219	0.1081	5008	,	,		18749	0.2431		0.172	False		,,,				2504	0.2055				p.G920G		Atlas-SNP	.											.	MOV10L1	238	.	0			c.C2760A						PASS	.	C	,,,	170,4236		2,166,2035	139.0	100.0	113.0		2760,2700,141,2760	-6.0	0.3	22	dbSNP_100	113	1290,7310		96,1098,3106	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MOV10L1	NM_001164104.1,NM_001164105.1,NM_001164106.1,NM_018995.2	,,,	98,1264,5141	AA,AC,CC		15.0,3.8584,11.2256	,,,	920/1166,900/1166,47/339,920/1212	50589196	1460,11546	2203	4300	6503	SO:0001819	synonymous_variant	54456	exon21			GCTCGGCCCAGTC	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.2760C>A	22.37:g.50589196C>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	114	63	0.552632	NM_018995	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Silent	SNP	ENST00000262794.5	37	CCDS14084.1																																																																																			C|0.878;A|0.122	0.122	strong		0.607	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
ARC	23237	hgsc.bcm.edu	37	8	143694520	143694520	+	Silent	SNP	C	C	T	rs371075422		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143694520C>T	ENST00000356613.2	-	1	2313	c.1113G>A	c.(1111-1113)ccG>ccA	p.P371P	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	122					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				CATCCTCCACCGGGAGGTGGG	0.726																																					p.P371P		Atlas-SNP	.											ARC,colon,carcinoma,-2,1	ARC	34	1	0			c.G1113A						PASS	.	C		0,4302		0,0,2151	8.0	11.0	10.0		1113	-2.4	0.0	8		10	1,8483		0,1,4241	no	coding-synonymous	ARC	NM_015193.3		0,1,6392	TT,TC,CC		0.0118,0.0,0.0078		371/397	143694520	1,12785	2151	4242	6393	SO:0001819	synonymous_variant	23237	exon1			CTCCACCGGGAGG	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.1113G>A	8.37:g.143694520C>T		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	53	23	0.433962	NM_015193	B4DFL0|O60937	Silent	SNP	ENST00000356613.2	37	CCDS34950.1																																																																																			.	.	weak		0.726	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2		
COL6A5	256076	hgsc.bcm.edu	37	3	130124491	130124491	+	Silent	SNP	G	G	A	rs10934940	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130124491G>A	ENST00000432398.2	+	14	4835	c.4341G>A	c.(4339-4341)gcG>gcA	p.A1447A	COL6A5_ENST00000265379.6_Silent_p.A1447A	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1447	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						GTCCAGGGGCGTGGGGTCAGA	0.478													G|||	2245	0.448283	0.3343	0.4885	5008	,	,		18453	0.1736		0.7654	False		,,,				2504	0.5307				p.A1447A		Atlas-SNP	.											COL6A5,colon,carcinoma,0,1	COL6A5	205	1	0			c.G4341A						PASS	.	G		583,801		123,337,232	128.0	124.0	125.0		4341	-3.6	0.0	3	dbSNP_120	125	2403,779		924,555,112	no	coding-synonymous	COL6A5	NM_153264.5		1047,892,344	AA,AG,GG		24.4815,42.1243,34.6036		1447/2527	130124491	2986,1580	692	1591	2283	SO:0001819	synonymous_variant	256076	exon14			AGGGGCGTGGGGT	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.4341G>A	3.37:g.130124491G>A		Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				G|0.508;A|0.492	0.492	strong		0.478	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
OR6C74	254783	hgsc.bcm.edu	37	12	55641328	55641328	+	Missense_Mutation	SNP	G	G	A	rs6581025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:55641328G>A	ENST00000343870.4	+	1	347	c.257G>A	c.(256-258)gGt>gAt	p.G86D		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	86			G -> D (in dbSNP:rs6581025).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|large_intestine(3)|lung(7)|prostate(1)	12						ATGGCAACAGGTGATAAGACC	0.398													G|||	1140	0.227636	0.1248	0.2291	5008	,	,		20270	0.1141		0.333	False		,,,				2504	0.3742				p.G86D		Atlas-SNP	.											.	OR6C74	52	.	0			c.G257A						PASS	.	G	ASP/GLY	692,3714	288.7+/-280.0	48,596,1559	198.0	200.0	199.0		257	4.5	0.2	12	dbSNP_116	199	2717,5883	433.8+/-357.5	426,1865,2009	yes	missense	OR6C74	NM_001005490.1	94	474,2461,3568	AA,AG,GG		31.593,15.7059,26.211	probably-damaging	86/313	55641328	3409,9597	2203	4300	6503	SO:0001583	missense	254783	exon1			CAACAGGTGATAA		CCDS31816.1	12q13.13	2012-08-09			ENSG00000197706	ENSG00000197706		"""GPCR / Class A : Olfactory receptors"""	31303	protein-coding gene	gene with protein product							Standard	NM_001005490		Approved		uc010spg.2	A6NCV1	OTTHUMG00000165162	ENST00000343870.4:c.257G>A	12.37:g.55641328G>A	ENSP00000342836:p.Gly86Asp	Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	166	74	0.445783	NM_001005490		Missense_Mutation	SNP	ENST00000343870.4	37	CCDS31816.1	478	0.21886446886446886	66	0.13414634146341464	95	0.26243093922651933	70	0.12237762237762238	247	0.3258575197889182	g	13.46	2.244713	0.39697	0.157059	0.31593	ENSG00000197706	ENST00000343870	T	0.02787	4.16	5.36	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000062	T	0.00012	0.0000	L	0.47016	1.485	0.80722	P	0.0	P	0.36465	0.554	B	0.38458	0.274	T	0.50783	-0.8787	9	0.87932	D	0	.	9.0034	0.36097	0.2317:0.0:0.7683:0.0	rs6581025;rs17442303;rs6581025	86	A6NCV1	O6C74_HUMAN	D	86	ENSP00000342836:G86D	ENSP00000342836:G86D	G	+	2	0	OR6C74	53927595	0.000000	0.05858	0.204000	0.23530	0.953000	0.61014	0.584000	0.23864	1.371000	0.46172	0.551000	0.68910	GGT	G|0.760;A|0.240	0.240	strong		0.398	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1		
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000417302.1_Silent_p.H27H|HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000397596.2_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"""E, L, M"""	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135.0	123.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1.0	1.0	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	87	40	0.45977	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795	
APBB2	323	hgsc.bcm.edu	37	4	41015823	41015823	+	Silent	SNP	G	G	A	rs2292234	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:41015823G>A	ENST00000295974.8	-	6	1241	c.612C>T	c.(610-612)ggC>ggT	p.G204G	APBB2_ENST00000513140.1_Silent_p.G204G|APBB2_ENST00000506352.1_Silent_p.G204G|APBB2_ENST00000508593.1_Silent_p.G204G	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	204					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						GCAGCAAATCGCCATTCCCAA	0.562													G|||	1539	0.307308	0.0484	0.2882	5008	,	,		17107	0.5387		0.3131	False		,,,				2504	0.4264				p.G204G	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.C612T						PASS	.	G	,,	276,3724		21,234,1745	285.0	273.0	277.0		612,612,612	-11.6	0.0	4	dbSNP_100	277	2020,6314		393,1234,2540	no	coding-synonymous,coding-synonymous,coding-synonymous	APBB2	NM_001166050.1,NM_004307.1,NM_173075.4	,,	414,1468,4285	AA,AG,GG		24.2381,6.9,18.6152	,,	204/759,204/760,204/737	41015823	2296,10038	2000	4167	6167	SO:0001819	synonymous_variant	323	exon6			CAAATCGCCATTC	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.612C>T	4.37:g.41015823G>A		Somatic	188	0	0		WXS	Illumina HiSeq	Phase_I	222	115	0.518018	NM_173075	B4DSL4|E9PG87|Q8IUI6	Silent	SNP	ENST00000295974.8	37	CCDS54761.1	802	0.36721611721611724	34	0.06910569105691057	120	0.3314917127071823	358	0.6258741258741258	290	0.38258575197889183	G	0.025	-1.383928	0.01194	0.069	0.242381	ENSG00000163697	ENST00000513611	.	.	.	5.8	-11.6	0.00059	.	.	.	.	.	.	.	.	.	.	.	0.22001	P	0.999423172	.	.	.	.	.	.	.	.	.	.	.	.	.	-22.7855	5.8279	0.18564	0.555:0.1079:0.2288:0.1084	rs2292234	.	.	.	X	194	.	.	R	-	1	2	APBB2	40710580	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.509000	0.00960	-4.040000	0.00079	-1.598000	0.00824	CGA	A|0.342;G|0.575;T|0.083	0.342	strong		0.562	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
CLEC10A	10462	hgsc.bcm.edu	37	17	6980273	6980273	+	Missense_Mutation	SNP	C	C	T	rs16956478	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6980273C>T	ENST00000254868.4	-	4	546	c.218G>A	c.(217-219)aGa>aAa	p.R73K	CLEC10A_ENST00000416562.2_Missense_Mutation_p.R73K|CLEC10A_ENST00000571664.1_Missense_Mutation_p.R73K|CLEC10A_ENST00000576617.1_Missense_Mutation_p.R73K	NM_182906.2	NP_878910.1	Q8IUN9	CLC10_HUMAN	C-type lectin domain family 10, member A	73			R -> K (in dbSNP:rs16956478).		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						AAAATCTGTTCTCAGGGTCAC	0.552													c|||	225	0.0449281	0.1097	0.0245	5008	,	,		17787	0.0218		0.0278	False		,,,				2504	0.0133				p.R73K		Atlas-SNP	.											.	CLEC10A	40	.	0			c.G218A						PASS	.	C	LYS/ARG,LYS/ARG	462,3944	220.4+/-237.8	30,402,1771	104.0	102.0	103.0		218,218	1.7	0.1	17	dbSNP_123	103	230,8370	93.1+/-155.1	2,226,4072	yes	missense,missense	CLEC10A	NM_006344.2,NM_182906.2	26,26	32,628,5843	TT,TC,CC		2.6744,10.4857,5.3206	benign,benign	73/293,73/317	6980273	692,12314	2203	4300	6503	SO:0001583	missense	10462	exon4			TCTGTTCTCAGGG	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.218G>A	17.37:g.6980273C>T	ENSP00000254868:p.Arg73Lys	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	116	53	0.456897	NM_182906	A8K8J8|Q14538|Q6PIW3	Missense_Mutation	SNP	ENST00000254868.4	37	CCDS11087.1	97	0.044413919413919416	61	0.12398373983739837	8	0.022099447513812154	9	0.015734265734265736	19	0.025065963060686015	C	10.32	1.316773	0.23908	0.104857	0.026744	ENSG00000132514	ENST00000254868;ENST00000416562	T;T	0.17691	2.26;2.26	4.86	1.74	0.24563	Hepatic lectin, N-terminal (1);	0.226724	0.31461	N	0.007602	T	0.00178	0.0005	L	0.32530	0.975	0.09310	N	0.999999	P;P;P;B	0.48407	0.48;0.536;0.91;0.077	B;B;P;B	0.50082	0.12;0.286;0.63;0.023	T	0.13388	-1.0511	10	0.17369	T	0.5	.	3.0702	0.06227	0.1967:0.5313:0.0:0.2719	rs16956478;rs52812287;rs16956478	73;73;73;73	Q8IUN9-3;A8K7G0;Q8IUN9;Q8IUN9-2	.;.;CLC10_HUMAN;.	K	73	ENSP00000254868:R73K;ENSP00000414938:R73K	ENSP00000254868:R73K	R	-	2	0	CLEC10A	6920997	0.009000	0.17119	0.103000	0.21229	0.109000	0.19521	0.078000	0.14761	0.729000	0.32403	0.650000	0.86243	AGA	C|0.948;T|0.052	0.052	strong		0.552	CLEC10A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439837.2	NM_006344	
DCHS2	54798	hgsc.bcm.edu	37	4	155410731	155410731	+	Missense_Mutation	SNP	G	G	C	rs72731016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155410731G>C	ENST00000339452.1	-	1	2137	c.1777C>G	c.(1777-1779)Caa>Gaa	p.Q593E	DCHS2_ENST00000456341.2_Missense_Mutation_p.Q586E|DCHS2_ENST00000443500.1_Missense_Mutation_p.Q593E	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1715	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(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)		ATCTTTGATTGCAGGGAGCCG	0.587													G|||	857	0.171126	0.0333	0.3084	5008	,	,		17861	0.1548		0.2117	False		,,,				2504	0.2352				p.Q593E		Atlas-SNP	.											.	DCHS2	594	.	0			c.C1777G						PASS	.						25.0	27.0	26.0					4																	155410731		692	1591	2283	SO:0001583	missense	54798	exon1			TTGATTGCAGGGA	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		ENST00000339452.1:c.1777C>G	4.37:g.155410731G>C	ENSP00000345062:p.Gln593Glu	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	79	46	0.582278	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	359	0.16437728937728938	17	0.034552845528455285	96	0.26519337016574585	81	0.14160839160839161	165	0.21767810026385223	G	0	-2.682450	0.00101	.	.	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.57273	0.45;0.41;0.42	5.17	-4.3	0.03710	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B;B	0.12630	0.0;0.006	B;B	0.13407	0.002;0.009	T	0.15378	-1.0439	7	0.02654	T	1	.	0.525	0.00618	0.3191:0.1286:0.165:0.3873	.	593;593	E9PG03;E9PC11	.;.	E	593;593;586;593	ENSP00000345062:Q593E;ENSP00000408543:Q586E;ENSP00000395539:Q593E	ENSP00000345062:Q593E	Q	-	1	0	DCHS2	155630181	.	.	0.000000	0.03702	0.006000	0.05464	.	.	-0.635000	0.05531	0.557000	0.71058	CAA	G|0.836;C|0.164	0.164	strong		0.587	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
DDX55	57696	hgsc.bcm.edu	37	12	124104686	124104686	+	Silent	SNP	G	G	A	rs3204541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124104686G>A	ENST00000238146.4	+	14	1852	c.1802G>A	c.(1801-1803)tGa>tAa	p.*601*	DDX55_ENST00000538744.1_Silent_p.*570*|DDX55_ENST00000421670.3_Silent_p.*208*	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	0						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)		GATGACTGCTGATTCCAGTGC	0.418													G|||	1263	0.252196	0.4463	0.2205	5008	,	,		19827	0.0159		0.2654	False		,,,				2504	0.2423				p.X601X		Atlas-SNP	.											.	DDX55	51	.	0			c.G1802A						PASS	.	G		1828,2578	531.5+/-373.2	384,1060,759	75.0	75.0	75.0		1802	5.5	1.0	12	dbSNP_105	75	2376,6224	393.5+/-344.4	341,1694,2265	no	coding-synonymous	DDX55	NM_020936.1		725,2754,3024	AA,AG,GG		27.6279,41.4889,32.3235		601/601	124104686	4204,8802	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon14			ACTGCTGATTCCA	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.1802G>A	12.37:g.124104686G>A		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	113	57	0.504425	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			G|0.707;A|0.293	0.293	strong		0.418	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
USP10	9100	hgsc.bcm.edu	37	16	84778690	84778690	+	Silent	SNP	C	C	T	rs1812062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84778690C>T	ENST00000219473.7	+	4	716	c.603C>T	c.(601-603)ccC>ccT	p.P201P	USP10_ENST00000570191.1_Silent_p.P205P|USP10_ENST00000562743.1_3'UTR	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	201					autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						GTGACATGCCCCCGTCAGTTA	0.542													C|||	1406	0.280751	0.2337	0.121	5008	,	,		17581	0.4107		0.1531	False		,,,				2504	0.455				p.P205P		Atlas-SNP	.											.	USP10	51	.	0			c.C615T						PASS	.	C		800,3184		77,646,1269	31.0	30.0	30.0		603	-5.5	0.0	16	dbSNP_92	30	1136,7192		76,984,3104	no	coding-synonymous	USP10	NM_005153.2		153,1630,4373	TT,TC,CC		13.6407,20.0803,15.7245		201/799	84778690	1936,10376	1992	4164	6156	SO:0001819	synonymous_variant	9100	exon5			CATGCCCCCGTCA	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.603C>T	16.37:g.84778690C>T		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	144	55	0.381944	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1																																																																																			C|0.773;T|0.227	0.227	strong		0.542	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
AGGF1	55109	hgsc.bcm.edu	37	5	76343999	76343999	+	Silent	SNP	T	T	C	rs13155212	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:76343999T>C	ENST00000312916.7	+	7	1597	c.1215T>C	c.(1213-1215)atT>atC	p.I405I		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	405					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)		AAGACAAAATTTGGCCCCCAT	0.353													T|||	1112	0.222045	0.2352	0.2334	5008	,	,		15147	0.1587		0.2386	False		,,,				2504	0.2444				p.I405I		Atlas-SNP	.											.	AGGF1	71	.	0			c.T1215C						PASS	.	T		970,3436	364.9+/-317.2	107,756,1340	104.0	99.0	101.0		1215	2.2	1.0	5	dbSNP_121	101	2243,6355	378.3+/-338.9	290,1663,2346	no	coding-synonymous	AGGF1	NM_018046.4		397,2419,3686	CC,CT,TT		26.0875,22.0154,24.7078		405/715	76343999	3213,9791	2203	4299	6502	SO:0001819	synonymous_variant	55109	exon7			CAAAATTTGGCCC	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.1215T>C	5.37:g.76343999T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	88	46	0.522727	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	37	CCDS4035.1																																																																																			C|0.234;N|0.001	0.234	strong		0.353	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046	
OR5B2	390190	hgsc.bcm.edu	37	11	58190136	58190136	+	Missense_Mutation	SNP	A	A	G	rs4298923	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58190136A>G	ENST00000302581.2	-	1	650	c.599T>C	c.(598-600)aTg>aCg	p.M200T		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	200			M -> T (in dbSNP:rs4298923). {ECO:0000269|PubMed:12213199, 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(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AAAGCTTGACATAAAAACCAG	0.368													A|||	2461	0.491414	0.7413	0.4481	5008	,	,		23375	0.2738		0.4394	False		,,,				2504	0.4622				p.M200T		Atlas-SNP	.											.	OR5B2	75	.	0			c.T599C						PASS	.	A	THR/MET	2907,1495	675.0+/-403.0	960,987,254	58.0	56.0	57.0		599	3.7	0.0	11	dbSNP_111	57	3593,4997	518.5+/-379.3	776,2041,1478	yes	missense	OR5B2	NM_001005566.2	81	1736,3028,1732	GG,GA,AA		41.8277,33.9618,49.9692	benign	200/310	58190136	6500,6492	2201	4295	6496	SO:0001583	missense	390190	exon1			CTTGACATAAAAA	AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"""GPCR / Class A : Olfactory receptors"""	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.599T>C	11.37:g.58190136A>G	ENSP00000303076:p.Met200Thr	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	37	CCDS31550.1	1035	0.4739010989010989	364	0.7398373983739838	155	0.4281767955801105	181	0.31643356643356646	335	0.4419525065963061	A	4.201	0.035935	0.08148	0.660382	0.418277	ENSG00000172365	ENST00000302581	T	0.00063	8.78	3.73	3.73	0.42828	GPCR, rhodopsin-like superfamily (1);	1.026440	0.07826	U	0.960623	T	0.00012	0.0000	N	0.02802	-0.49	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.44877	-0.9299	9	0.59425	D	0.04	-0.1418	11.6478	0.51271	1.0:0.0:0.0:0.0	rs4298923;rs12808878;rs17565506;rs52811139;rs61660780;rs4298923	200	Q96R09	OR5B2_HUMAN	T	200	ENSP00000303076:M200T	ENSP00000303076:M200T	M	-	2	0	OR5B2	57946712	0.000000	0.05858	0.004000	0.12327	0.004000	0.04260	0.514000	0.22786	1.703000	0.51240	0.477000	0.44152	ATG	A|0.507;G|0.493	0.493	strong		0.368	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566	
DPAGT1	1798	hgsc.bcm.edu	37	11	118967758	118967758	+	Missense_Mutation	SNP	T	T	C	rs643788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118967758T>C	ENST00000409993.2	-	11	2728	c.1177A>G	c.(1177-1179)Atc>Gtc	p.I393V	DPAGT1_ENST00000354202.4_Missense_Mutation_p.I393V|H2AFX_ENST00000530167.1_5'Flank|DPAGT1_ENST00000432443.2_Missense_Mutation_p.I312V			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	393			I -> V (in dbSNP:rs643788). {ECO:0000269|PubMed:15489334}.		cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		GAGAAGGTGATGGCACTGCCC	0.488													T|||	2170	0.433307	0.2844	0.2983	5008	,	,		23742	0.631		0.4563	False		,,,				2504	0.5031				p.I393V		Atlas-SNP	.											.	DPAGT1	43	.	0			c.A1177G						PASS	.	T	VAL/ILE	1307,3093	441.0+/-346.2	199,909,1092	146.0	131.0	136.0		1177	-4.2	0.0	11	dbSNP_83	136	3723,4867	530.4+/-381.8	811,2101,1383	yes	missense	DPAGT1	NM_001382.3	29	1010,3010,2475	CC,CT,TT		43.3411,29.7045,38.7221	benign	393/409	118967758	5030,7960	2200	4295	6495	SO:0001583	missense	1798	exon9			AGGTGATGGCACT	Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.1177A>G	11.37:g.118967758T>C	ENSP00000386597:p.Ile393Val	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	159	66	0.415094	NM_001382	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	37	CCDS8411.1	938	0.42948717948717946	120	0.24390243902439024	127	0.35082872928176795	357	0.6241258741258742	334	0.44063324538258575	T	0.012	-1.647350	0.00792	0.297045	0.433411	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	D;D;D	0.91068	-2.78;-2.78;-2.63	5.38	-4.23	0.03789	.	0.950055	0.08878	N	0.880464	T	0.00012	0.0000	N	0.16478	0.41	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.36016	-0.9765	9	0.12766	T	0.61	-29.2396	2.1096	0.03699	0.2219:0.1524:0.1217:0.504	rs643788;rs3186349;rs17259019;rs17854515;rs58852432;rs643788	312;393	E7EW40;Q9H3H5	.;GPT_HUMAN	V	393;393;312	ENSP00000386597:I393V;ENSP00000346142:I393V;ENSP00000404036:I312V	ENSP00000346142:I393V	I	-	1	0	DPAGT1	118472968	0.000000	0.05858	0.037000	0.18230	0.231000	0.25187	-0.320000	0.08028	-0.993000	0.03467	-3.207000	0.00054	ATC	A|0.003;C|0.413	0.413	strong		0.488	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2	NM_001382	
A2ML1	144568	hgsc.bcm.edu	37	12	9016456	9016456	+	Missense_Mutation	SNP	C	C	T	rs73040625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9016456C>T	ENST00000299698.7	+	29	3749	c.3569C>T	c.(3568-3570)gCg>gTg	p.A1190V	A2ML1_ENST00000539547.1_Missense_Mutation_p.A699V	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						TCTGAGCCTGCGGCTGTAGAT	0.493													C|||	113	0.0225639	0.0015	0.0375	5008	,	,		-128	0.0		0.0736	False		,,,				2504	0.0112				p.A1190V		Atlas-SNP	.											.	A2ML1	199	.	0			c.C3569T						PASS	.	C	VAL/ALA	58,3810		1,56,1877	76.0	75.0	75.0		3569	-1.4	0.0	12	dbSNP_130	75	684,7620		30,624,3498	yes	missense	A2ML1	NM_144670.3	64	31,680,5375	TT,TC,CC		8.237,1.4995,6.096	benign	1190/1455	9016456	742,11430	1934	4152	6086	SO:0001583	missense	144568	exon29			AGCCTGCGGCTGT	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.3569C>T	12.37:g.9016456C>T	ENSP00000299698:p.Ala1190Val	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	85	39	0.458824	NM_144670		Missense_Mutation	SNP	ENST00000299698.7	37	CCDS8596.2	76	0.0347985347985348	2	0.0040650406504065045	17	0.04696132596685083	0	0.0	57	0.07519788918205805	C	10.21	1.286592	0.23478	0.014995	0.08237	ENSG00000166535	ENST00000299698;ENST00000539161;ENST00000541459;ENST00000539547	T;T;T	0.37411	1.2;1.2;1.2	4.39	-1.35	0.09114	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	2.157560	0.02058	N	0.050561	T	0.01222	0.0040	N	0.13272	0.32	0.09310	N	1	B	0.26363	0.147	B	0.26094	0.066	T	0.17018	-1.0383	10	0.44086	T	0.13	.	8.9867	0.35999	0.2037:0.5711:0.0:0.2252	.	1190	A8K2U0	A2ML1_HUMAN	V	1190;1190;740;699	ENSP00000299698:A1190V;ENSP00000443174:A740V;ENSP00000438292:A699V	ENSP00000299698:A1190V	A	+	2	0	A2ML1	8907723	0.000000	0.05858	0.001000	0.08648	0.457000	0.32468	-0.559000	0.05971	-0.242000	0.09667	-2.756000	0.00123	GCG	C|0.949;T|0.051	0.051	strong		0.493	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670	
SEZ6L	23544	hgsc.bcm.edu	37	22	26688388	26688388	+	Silent	SNP	A	A	C	rs35377445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26688388A>C	ENST00000248933.6	+	2	206	c.111A>C	c.(109-111)ggA>ggC	p.G37G	SEZ6L_ENST00000360929.3_Silent_p.G37G|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000403121.1_5'UTR|SEZ6L_ENST00000404234.3_Silent_p.G37G|SEZ6L_ENST00000343706.4_Silent_p.G37G|SEZ6L_ENST00000529632.2_Silent_p.G37G			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	37					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TTCCCGAGGGAGATGCTAGCC	0.572													A|||	217	0.0433307	0.0129	0.0793	5008	,	,		18827	0.001		0.1233	False		,,,				2504	0.0204				p.G37G		Atlas-SNP	.											SEZ6L,NS,carcinoma,+2,1	SEZ6L	174	1	0			c.A111C						PASS	.	A	,,,,,	127,4279	92.0+/-130.7	2,123,2078	46.0	37.0	40.0		111,111,111,111,111,111	2.4	0.9	22	dbSNP_126	40	1029,7571	213.8+/-253.6	61,907,3332	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	63,1030,5410	CC,CA,AA		11.9651,2.8824,8.8882	,,,,,	37/1024,37/1014,37/1012,37/950,37/949,37/1025	26688388	1156,11850	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon2			CGAGGGAGATGCT	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.111A>C	22.37:g.26688388A>C		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	63	28	0.444444	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			A|0.919;C|0.081	0.081	strong		0.572	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
FAM160A2	84067	hgsc.bcm.edu	37	11	6239139	6239139	+	Silent	SNP	A	A	G	rs11040809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6239139A>G	ENST00000449352.2	-	9	1940	c.1677T>C	c.(1675-1677)cgT>cgC	p.R559R	FAM160A2_ENST00000265978.4_Silent_p.R573R|FAM160A2_ENST00000524416.1_Silent_p.R559R|FAM160A2_ENST00000529360.1_5'Flank			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	559					early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	FHF complex (GO:0070695)				NS(1)|endometrium(3)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCACACCACGACGTGCCTCAC	0.642													A|||	547	0.109225	0.0106	0.1167	5008	,	,		11293	0.0456		0.2336	False		,,,				2504	0.1748				p.R573R		Atlas-SNP	.											.	FAM160A2	100	.	0			c.T1719C						PASS	.	A	,	207,4195	127.0+/-164.0	7,193,2001	65.0	61.0	62.0		1677,1719	1.6	1.0	11	dbSNP_120	62	2176,6416	366.5+/-334.3	280,1616,2400	no	coding-synonymous,coding-synonymous	FAM160A2	NM_001098794.1,NM_032127.3	,	287,1809,4401	GG,GA,AA		25.3259,4.7024,18.3392	,	559/973,573/987	6239139	2383,10611	2201	4296	6497	SO:0001819	synonymous_variant	84067	exon9			ACCACGACGTGCC		CCDS7760.1, CCDS44530.1	11p15.4	2008-06-05	2008-06-05	2008-06-05	ENSG00000051009	ENSG00000051009			25378	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 56"""	C11orf56		11230166, 11214970	Standard	NM_001098794		Approved	FLJ22665, KIAA1759, DKFZP566M1046	uc001mck.4	Q8N612	OTTHUMG00000133379	ENST00000449352.2:c.1677T>C	11.37:g.6239139A>G		Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Silent	SNP	ENST00000449352.2	37	CCDS44530.1																																																																																			A|0.841;G|0.159;N|0.000;T|0.000	0.159	strong		0.642	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127	
SAMD12	401474	hgsc.bcm.edu	37	8	119391791	119391791	+	Silent	SNP	T	T	C	rs5020517	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:119391791T>C	ENST00000314727.4	-	4	607	c.471A>G	c.(469-471)ctA>ctG	p.L157L	SAMD12_ENST00000409003.4_Intron|SAMD12_ENST00000527515.1_Intron|AC023590.1_ENST00000430457.1_Intron	NM_207506.2	NP_997389.2	Q8N8I0	SAM12_HUMAN	sterile alpha motif domain containing 12	157										endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)	9	all_cancers(13;3.91e-25)|Lung NSC(37;1.13e-07)|Ovarian(258;0.0249)		STAD - Stomach adenocarcinoma(47;0.00391)			CAGGAAGCAATAGGGTACCTT	0.468													C|||	3008	0.600639	0.8654	0.5259	5008	,	,		18611	0.3244		0.6938	False		,,,				2504	0.4847				p.L157L		Atlas-SNP	.											.	SAMD12	24	.	0			c.A471G						PASS	.	C	,	3727,679	287.2+/-279.2	1574,579,50	149.0	135.0	140.0		,471	3.0	0.0	8	dbSNP_113	140	5913,2687	430.6+/-356.6	2006,1901,393	no	intron,coding-synonymous	SAMD12	NM_001101676.1,NM_207506.2	,	3580,2480,443	CC,CT,TT		31.2442,15.4108,25.8804	,	,157/202	119391791	9640,3366	2203	4300	6503	SO:0001819	synonymous_variant	401474	exon4			AAGCAATAGGGTA	AK096777	CCDS6325.1, CCDS47913.1	8q24.12	2013-01-10			ENSG00000177570	ENSG00000177570		"""Sterile alpha motif (SAM) domain containing"""	31750	protein-coding gene	gene with protein product							Standard	NM_207506		Approved	FLJ39458	uc003yom.2	Q8N8I0	OTTHUMG00000059817	ENST00000314727.4:c.471A>G	8.37:g.119391791T>C		Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	288	139	0.482639	NM_207506	Q0P502	Silent	SNP	ENST00000314727.4	37	CCDS6325.1																																																																																			T|0.303;C|0.697	0.697	strong		0.468	SAMD12-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132989.3	NM_207506	
NLRC4	58484	hgsc.bcm.edu	37	2	32463365	32463365	+	Missense_Mutation	SNP	C	C	A	rs149451729	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:32463365C>A	ENST00000404025.2	-	7	2845	c.2357G>T	c.(2356-2358)gGc>gTc	p.G786V	NLRC4_ENST00000360906.5_Missense_Mutation_p.G786V|NLRC4_ENST00000402280.1_Missense_Mutation_p.G786V|NLRC4_ENST00000342905.6_Missense_Mutation_p.G121V			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	786					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GTTTTTCAGGCCTTCAGCTGA	0.358													C|||	3	0.000599042	0.0	0.0043	5008	,	,		19325	0.0		0.0	False		,,,				2504	0.0				p.G786V		Atlas-SNP	.											.	NLRC4	165	.	0			c.G2357T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY	4,4402	8.1+/-20.4	0,4,2199	94.0	93.0	94.0		2357,2357,2357	2.8	0.0	2	dbSNP_134	94	39,8561	25.7+/-73.6	0,39,4261	yes	missense,missense,missense	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	109,109,109	0,43,6460	AA,AC,CC		0.4535,0.0908,0.3306	probably-damaging,probably-damaging,probably-damaging	786/1025,786/1025,786/1025	32463365	43,12963	2203	4300	6503	SO:0001583	missense	58484	exon6			TTCAGGCCTTCAG	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2357G>T	2.37:g.32463365C>A	ENSP00000385090:p.Gly786Val	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	83	37	0.445783	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	7.093	0.572525	0.13623	9.08E-4	0.004535	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	4.63	2.78	0.32641	.	0.000000	0.41294	D	0.000913	T	0.42787	0.1218	L	0.56769	1.78	0.36099	D	0.843987	D;D	0.62365	0.98;0.991	P;P	0.58013	0.693;0.831	T	0.56080	-0.8038	9	0.16420	T	0.52	-8.9282	6.4653	0.21977	0.0:0.7173:0.1834:0.0993	.	121;786	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	V	786;786;121;786	ENSP00000354159:G786V;ENSP00000385428:G786V;ENSP00000339666:G121V;ENSP00000385090:G786V	ENSP00000339666:G121V	G	-	2	0	NLRC4	32316869	0.035000	0.19736	0.016000	0.15963	0.041000	0.13682	0.929000	0.28844	0.663000	0.31027	-0.150000	0.13652	GGC	C|0.997;A|0.003	0.003	strong		0.358	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
GINS2	51659	hgsc.bcm.edu	37	16	85711860	85711860	+	Silent	SNP	C	C	T	rs1053328	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85711860C>T	ENST00000253462.3	-	5	616	c.516G>A	c.(514-516)acG>acA	p.T172T		NM_016095.2	NP_057179.1	Q9Y248	PSF2_HUMAN	GINS complex subunit 2 (Psf2 homolog)	172					DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)	nucleoplasm (GO:0005654)				endometrium(2)|large_intestine(2)|lung(2)	6						GCTGGAGGTTCGTGCGGAGTT	0.537													C|||	1877	0.3748	0.2859	0.3156	5008	,	,		16030	0.494		0.3429	False		,,,				2504	0.4468				p.T172T		Atlas-SNP	.											GINS2,colon,carcinoma,-1,1	GINS2	15	1	0			c.G516A						PASS	.	C		1339,3057	447.5+/-348.4	199,941,1058	98.0	94.0	95.0		516	-6.7	0.9	16	dbSNP_86	95	3099,5501	474.0+/-368.7	563,1973,1764	no	coding-synonymous	GINS2	NM_016095.2		762,2914,2822	TT,TC,CC		36.0349,30.4595,34.149		172/186	85711860	4438,8558	2198	4300	6498	SO:0001819	synonymous_variant	51659	exon5			GAGGTTCGTGCGG	BC003186	CCDS10953.1	16q24.1	2008-02-05			ENSG00000131153	ENSG00000131153			24575	protein-coding gene	gene with protein product		610609				11042152, 10810093	Standard	NM_016095		Approved	PSF2, Pfs2	uc002fja.3	Q9Y248	OTTHUMG00000137646	ENST00000253462.3:c.516G>A	16.37:g.85711860C>T		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	204	86	0.421569	NM_016095	D3DUM5|Q6IAG9	Silent	SNP	ENST00000253462.3	37	CCDS10953.1																																																																																			C|0.657;T|0.343	0.343	strong		0.537	GINS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269098.1	NM_016095	
RP1L1	94137	hgsc.bcm.edu	37	8	10467604	10467604	+	Missense_Mutation	SNP	C	C	A	rs74366179		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:10467604C>A	ENST00000382483.3	-	4	4227	c.4004G>T	c.(4003-4005)gGg>gTg	p.G1335V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1351	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		G -> R (in allele RP1L1-2 and allele RP1L1-3; dbSNP:rs61503212).|Missing (in allele RP1L1-1).		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)		taactgcaccccctcttcttg	0.463																																					p.G1335V		Atlas-SNP	.											RP1L1,NS,carcinoma,0,1	RP1L1	453	1	0			c.G4004T						PASS	.	C	VAL/GLY	516,3388		31,454,1467	118.0	115.0	116.0		4004	-0.4	0.0	8	dbSNP_131	116	1257,7009		110,1037,2986	yes	missense	RP1L1	NM_178857.5	109	141,1491,4453	AA,AC,CC		15.2069,13.2172,14.5686	probably-damaging	1335/2401	10467604	1773,10397	1952	4133	6085	SO:0001583	missense	94137	exon4			TGCACCCCCTCTT	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.4004G>T	8.37:g.10467604C>A	ENSP00000371923:p.Gly1335Val	Somatic	257	1	0.00389105		WXS	Illumina HiSeq	Phase_I	177	103	0.581921	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	383	0.17536630036630035	73	0.1483739837398374	68	0.1878453038674033	127	0.22202797202797203	115	0.1517150395778364	c	10.70	1.422679	0.25639	0.132172	0.152069	ENSG00000183638	ENST00000382483	T	0.05855	3.38	2.91	-0.449	0.12226	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.999999999950489E-6	D	0.65815	0.995	P	0.53185	0.72	T	0.51060	-0.8753	8	0.72032	D	0.01	.	6.5765	0.22569	0.0:0.4875:0.0:0.5125	.	1335	A6NKC6	.	V	1335	ENSP00000371923:G1335V	ENSP00000371923:G1335V	G	-	2	0	RP1L1	10505014	0.000000	0.05858	0.004000	0.12327	0.297000	0.27493	-0.865000	0.04250	0.008000	0.14787	0.462000	0.41574	GGG	C|0.824;A|0.176	0.176	strong		0.463	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
NALCN	259232	hgsc.bcm.edu	37	13	101828654	101828654	+	Silent	SNP	T	T	C	rs17582557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:101828654T>C	ENST00000251127.6	-	15	1917	c.1836A>G	c.(1834-1836)aaA>aaG	p.K612K		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	612					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)	p.K612K(1)		NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					TACTTACTTGTTTAAGCTTCT	0.318													T|||	116	0.0231629	0.0	0.0346	5008	,	,		14020	0.0		0.0716	False		,,,				2504	0.0204				p.K612K		Atlas-SNP	.											NALCN,NS,carcinoma,0,1	NALCN	431	1	1	Substitution - coding silent(1)	stomach(1)	c.A1836G						PASS	.	T		37,4369	40.0+/-72.8	0,37,2166	85.0	81.0	83.0		1836	5.9	1.0	13	dbSNP_123	83	458,8138	137.1+/-194.1	12,434,3852	no	coding-synonymous	NALCN	NM_052867.2		12,471,6018	CC,CT,TT		5.3281,0.8398,3.8071		612/1739	101828654	495,12507	2203	4298	6501	SO:0001819	synonymous_variant	259232	exon15			TACTTGTTTAAGC	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.1836A>G	13.37:g.101828654T>C		Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_052867	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Silent	SNP	ENST00000251127.6	37	CCDS9498.1																																																																																			T|0.965;C|0.035	0.035	strong		0.318	NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329892	55329892	+	Missense_Mutation	SNP	A	A	G	rs149123986	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55329892A>G	ENST00000391728.4	+	3	226	c.193A>G	c.(193-195)Aga>Gga	p.R65G	KIR3DL1_ENST00000541392.1_Missense_Mutation_p.R65G|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.R65G|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.R65G|KIR3DL1_ENST00000358178.4_Intron|KIR3DL1_ENST00000538269.1_Missense_Mutation_p.R65G	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	65	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CAAAGAAGACAGAATCCACAT	0.507													a|||	512	0.102236	0.0893	0.1398	5008	,	,		13666	0.001		0.2435	False		,,,				2504	0.0521				p.R65G		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A193G						PASS	.	A	GLY/ARG	602,3742		197,208,1767	65.0	92.0	83.0		193	-2.5	0.0	19	dbSNP_134	83	1898,6330		595,708,2811	yes	missense	KIR3DL1	NM_013289.2	125	792,916,4578	GG,GA,AA		23.0676,13.8582,19.8855		65/445	55329892	2500,10072	2172	4114	6286	SO:0001583	missense	3811	exon3			GAAGACAGAATCC	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.193A>G	19.37:g.55329892A>G	ENSP00000375608:p.Arg65Gly	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	42	25	0.595238	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	306	0.1401098901098901	46	0.09349593495934959	52	0.143646408839779	2	0.0034965034965034965	206	0.2717678100263852	A	0.005	-2.154994	0.00325	0.138582	0.230676	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.00730	5.77;5.77;5.77;5.77;5.77	1.25	-2.51	0.06365	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	179.731000	0.00166	U	0.000000	T	0.00012	0.0000	N	0.03983	-0.305	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.42882	-0.9425	9	0.23302	T	0.38	.	4.707	0.12855	0.5341:0.0:0.4659:0.0	.	65;65;65	Q15702;F6QF33;P43629	.;.;KI3L1_HUMAN	G	65;65;65;43;65;65	ENSP00000384528:R65G;ENSP00000443350:R65G;ENSP00000442355:R65G;ENSP00000375608:R65G;ENSP00000326868:R65G	ENSP00000326868:R65G	R	+	1	2	KIR3DL1	60021704	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.579000	0.05834	-0.706000	0.05028	-1.194000	0.01681	AGA	A|0.860;G|0.140	0.140	strong		0.507	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
HERC2	8924	hgsc.bcm.edu	37	15	28459325	28459325	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459325C>T	ENST00000261609.7	-	41	6560	c.6452G>A	c.(6451-6453)cGc>cAc	p.R2151H		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.R2151H(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)		GTGCAGCGTGCGCAGCAGTGC	0.637																																					p.R2151H		Atlas-SNP	.											HERC2,NS,carcinoma,0,2	HERC2	501	2	2	Substitution - Missense(2)	prostate(2)	c.G6452A						scavenged	.						60.0	56.0	57.0					15																	28459325		2203	4300	6503	SO:0001583	missense	8924	exon41			AGCGTGCGCAGCA	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.6452G>A	15.37:g.28459325C>T	ENSP00000261609:p.Arg2151His	Somatic	90	1	0.0111111		WXS	Illumina HiSeq	Phase_I	104	5	0.0480769	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544886	0.65198	.	.	ENSG00000128731	ENST00000261609	T	0.61392	0.11	4.75	4.75	0.60458	.	0.057517	0.64402	D	0.000004	T	0.77485	0.4137	M	0.81942	2.565	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.81212	-0.1035	10	0.72032	D	0.01	.	17.9388	0.89021	0.0:1.0:0.0:0.0	.	2151	O95714	HERC2_HUMAN	H	2151	ENSP00000261609:R2151H	ENSP00000261609:R2151H	R	-	2	0	HERC2	26132920	1.000000	0.71417	0.415000	0.26534	0.134000	0.20937	7.305000	0.78891	2.461000	0.83175	0.484000	0.47621	CGC	.	.	none		0.637	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
PASD1	139135	hgsc.bcm.edu	37	X	150817094	150817094	+	Missense_Mutation	SNP	C	C	G	rs5924658	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:150817094C>G	ENST00000370357.4	+	9	882	c.637C>G	c.(637-639)Caa>Gaa	p.Q213E		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	213			Q -> E (in dbSNP:rs5924658).			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)					TAGTAGCTCTCAAGGTCAAAG	0.393													C|||	511	0.135364	0.0083	0.1571	3775	,	,		13523	0.0188		0.2306	False		,,,				2504	0.1431				p.Q213E		Atlas-SNP	.											.	PASD1	286	.	0			c.C637G						PASS	.	C	GLU/GLN	159,3676		4,130,21,1498,550	140.0	133.0	135.0		637	1.1	0.0	X	dbSNP_114	135	1861,4867		184,964,529,1280,1343	yes	missense	PASD1	NM_173493.2	29	188,1094,550,2778,1893	GG,GC,G,CC,C		27.6605,4.146,19.1234	possibly-damaging	213/774	150817094	2020,8543	2203	4300	6503	SO:0001583	missense	139135	exon9			AGCTCTCAAGGTC	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.637C>G	X.37:g.150817094C>G	ENSP00000359382:p.Gln213Glu	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	125	124	0.992	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	242	0.1458710066305003	5	0.01020408163265306	28	0.0875	11	0.01929824561403509	110	0.1751592356687898	C	10.24	1.296431	0.23650	0.04146	0.276605	ENSG00000166049	ENST00000370357	T	0.70749	-0.51	4.0	1.12	0.20585	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	P	0.41041	0.736	B	0.35607	0.206	T	0.04825	-1.0924	8	0.37606	T	0.19	.	4.0817	0.09929	0.0:0.5643:0.1934:0.2423	rs5924658;rs5924658	213	Q8IV76	PASD1_HUMAN	E	213	ENSP00000359382:Q213E	ENSP00000359382:Q213E	Q	+	1	0	PASD1	150567750	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.766000	0.04725	-0.009000	0.14296	0.422000	0.28245	CAA	0|0.024;C|0.826;G|0.150	0.150	strong		0.393	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
OR10G3	26533	hgsc.bcm.edu	37	14	22038450	22038450	+	Silent	SNP	G	G	A	rs11626669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:22038450G>A	ENST00000303532.1	-	1	425	c.426C>T	c.(424-426)agC>agT	p.S142S		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	142						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)		CAAGCAAGGCGCTCAGCTTAG	0.597													A|||	2364	0.472045	0.4402	0.6643	5008	,	,		20195	0.498		0.4125	False		,,,				2504	0.4131				p.S142S		Atlas-SNP	.											.	OR10G3	40	.	0			c.C426T						PASS	.	A		1949,2457	622.0+/-393.9	435,1079,689	60.0	59.0	59.0		426	-4.1	0.0	14	dbSNP_120	59	3769,4831	615.0+/-396.3	817,2135,1348	no	coding-synonymous	OR10G3	NM_001005465.1		1252,3214,2037	AA,AG,GG		43.8256,44.2351,43.9643		142/314	22038450	5718,7288	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			CAAGGCGCTCAGC		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.426C>T	14.37:g.22038450G>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	101	55	0.544554	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			G|0.547;A|0.453	0.453	strong		0.597	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
LRRC16B	90668	hgsc.bcm.edu	37	14	24529209	24529209	+	Silent	SNP	C	C	T	rs61564890	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24529209C>T	ENST00000342740.5	+	23	2053	c.1899C>T	c.(1897-1899)ccC>ccT	p.P633P	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	633						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TGTCCTTCCCCGTGAGCGACA	0.642													C|||	959	0.191494	0.0416	0.2104	5008	,	,		20833	0.4643		0.0616	False		,,,				2504	0.2331				p.P633P		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C1899T						PASS	.	C		199,4207	122.1+/-159.5	6,187,2010	154.0	131.0	139.0		1899	-9.1	0.2	14	dbSNP_129	139	474,8126	139.5+/-196.2	11,452,3837	no	coding-synonymous	LRRC16B	NM_138360.3		17,639,5847	TT,TC,CC		5.5116,4.5166,5.1745		633/1373	24529209	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	90668	exon23			CTTCCCCGTGAGC	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1899C>T	14.37:g.24529209C>T		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	125	57	0.456	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																			C|0.908;T|0.092	0.092	strong		0.642	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
MAPK6	5597	hgsc.bcm.edu	37	15	52353498	52353498	+	Missense_Mutation	SNP	C	C	G	rs17853426|rs35697691	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:52353498C>G	ENST00000261845.5	+	5	1675	c.868C>G	c.(868-870)Ctg>Gtg	p.L290V	CTD-2184D3.5_ENST00000558607.1_RNA	NM_002748.3	NP_002739.1	Q16659	MK06_HUMAN	mitogen-activated protein kinase 6	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> V (in dbSNP:rs35697691). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		cell cycle (GO:0007049)|MAPK cascade (GO:0000165)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)	p.L290V(2)		breast(3)|endometrium(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	20				all cancers(107;0.0028)		CTCTGCAGCACTGGATTTCCT	0.358													C|||	164	0.0327476	0.0061	0.0735	5008	,	,		18672	0.0		0.0875	False		,,,				2504	0.0174				p.L290V		Atlas-SNP	.											MAPK6,face,carcinoma,0,5	MAPK6	70	5	2	Substitution - Missense(2)	lung(1)|skin(1)	c.C868G						PASS	.	C	VAL/LEU	100,4290	77.8+/-116.1	4,92,2099	93.0	89.0	91.0		868	5.1	1.0	15	dbSNP_126	91	794,7792	182.5+/-230.9	35,724,3534	yes	missense	MAPK6	NM_002748.3	32	39,816,5633	GG,GC,CC		9.2476,2.2779,6.8896	probably-damaging	290/722	52353498	894,12082	2195	4293	6488	SO:0001583	missense	5597	exon5			GCAGCACTGGATT	L77964	CCDS10147.1	15q21	2011-06-10			ENSG00000069956	ENSG00000069956		"""Mitogen-activated protein kinase cascade / Kinases"""	6879	protein-coding gene	gene with protein product		602904		PRKM6		8875998	Standard	NM_002748		Approved	ERK3, p97MAPK, HsT17250	uc002abp.3	Q16659	OTTHUMG00000131891	ENST00000261845.5:c.868C>G	15.37:g.52353498C>G	ENSP00000261845:p.Leu290Val	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	209	100	0.478469	NM_002748	B2R945|B5BU65|Q68DH4|Q8IYN8	Missense_Mutation	SNP	ENST00000261845.5	37	CCDS10147.1	93	0.042582417582417584	4	0.008130081300813009	25	0.06906077348066299	0	0.0	64	0.08443271767810026	C	16.84	3.233417	0.58886	0.022779	0.092476	ENSG00000069956	ENST00000261845	T	0.66099	-0.19	5.13	5.13	0.70059	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	0.07007	0.0178	N	0.17379	0.485	0.09310	P	0.999999574787	D	0.69078	0.997	D	0.79108	0.992	T	0.47341	-0.9125	9	0.37606	T	0.19	-0.3463	18.5662	0.91118	0.0:1.0:0.0:0.0	rs35697691	290	Q16659	MK06_HUMAN	V	290	ENSP00000261845:L290V	ENSP00000261845:L290V	L	+	1	2	MAPK6	50140790	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.015000	0.40961	2.399000	0.81585	0.585000	0.79938	CTG	C|0.939;G|0.061	0.061	strong		0.358	MAPK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254841.2	NM_002748	
PLD2	5338	hgsc.bcm.edu	37	17	4722876	4722876	+	Splice_Site	SNP	G	G	A	rs3764897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4722876G>A	ENST00000263088.6	+	23	2592	c.2461G>A	c.(2461-2463)Ggt>Agt	p.G821S	PLD2_ENST00000572940.1_Intron	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	821			G -> R (in dbSNP:rs3764897).|G -> S (in dbSNP:rs3764897). {ECO:0000269|Ref.3}.		cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			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)	GCACTGCTTCGGGTAGAGCTG	0.617													A|||	918	0.183307	0.3033	0.1671	5008	,	,		16910	0.1071		0.168	False		,,,				2504	0.1268				p.G821S		Atlas-SNP	.											.	PLD2	138	.	0			c.G2461A						PASS	.	A	SER/GLY	1198,3208	707.7+/-407.5	167,864,1172	68.0	51.0	57.0		2461	3.8	1.0	17	dbSNP_107	57	1363,7237	754.6+/-407.5	111,1141,3048	yes	missense-near-splice	PLD2	NM_002663.4	56	278,2005,4220	AA,AG,GG		15.8488,27.1902,19.6909	benign	821/934	4722876	2561,10445	2203	4300	6503	SO:0001630	splice_region_variant	5338	exon23			TGCTTCGGGTAGA	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.2462+1G>A	17.37:g.4722876G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	38	21	0.552632	NM_002663	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	384	0.17582417582417584	162	0.32926829268292684	53	0.1464088397790055	55	0.09615384615384616	114	0.1503957783641161	A	11.54	1.668938	0.29604	0.271902	0.158488	ENSG00000129219	ENST00000263088	T	0.06142	3.34	3.82	3.82	0.43975	.	0.048535	0.85682	N	0.000000	T	0.00012	0.0000	N	0.00128	-2.045	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40664	-0.9551	9	0.21540	T	0.41	-2.6275	7.5853	0.27989	0.893:0.0:0.107:0.0	rs3764897;rs3764897	821	O14939	PLD2_HUMAN	S	821	ENSP00000263088:G821S	ENSP00000263088:G821S	G	+	1	0	PLD2	4669842	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	3.580000	0.53907	0.645000	0.30675	-0.521000	0.04368	GGT	G|0.804;A|0.196	0.196	strong		0.617	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	Missense_Mutation
HLA-DQA2	3118	hgsc.bcm.edu	37	6	32713018	32713018	+	Silent	SNP	C	C	T	rs17213281	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32713018C>T	ENST00000374940.3	+	2	267	c.165C>T	c.(163-165)gaC>gaT	p.D55D		NM_020056.4	NP_064440.1	P01906	DQA2_HUMAN	major histocompatibility complex, class II, DQ alpha 2	55	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)			endometrium(2)|large_intestine(3)|lung(7)|skin(1)	13					"""""""Insulin(DB00071)"""	TTGATGGAGACGAGGAGTTCT	0.483													C|||	872	0.174121	0.27	0.2089	5008	,	,		22829	0.0734		0.1571	False		,,,				2504	0.1411				p.D55D		Atlas-SNP	.											.	HLA-DQA2	27	.	0			c.C165T						PASS	.	C		669,2353		76,517,918	190.0	184.0	186.0		165	-6.4	0.4	6	dbSNP_123	186	870,4548		64,742,1903	no	coding-synonymous	HLA-DQA2	NM_020056.4		140,1259,2821	TT,TC,CC		16.0576,22.1377,18.2346		55/256	32713018	1539,6901	1511	2709	4220	SO:0001819	synonymous_variant	3118	exon2			TGGAGACGAGGAG		CCDS4753.1	6p21.3	2013-01-11			ENSG00000237541	ENSG00000237541		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4943	protein-coding gene	gene with protein product		613503		HLA-DXA			Standard	NM_020056		Approved		uc003obx.3	P01906	OTTHUMG00000031108	ENST00000374940.3:c.165C>T	6.37:g.32713018C>T		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	194	98	0.505155	NM_020056	A2BF37|B0V0E7|O19789|Q5SQ94|Q5SR04	Silent	SNP	ENST00000374940.3	37	CCDS4753.1																																																																																			C|0.824;T|0.176	0.176	strong		0.483	HLA-DQA2-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076179.2	NM_020056	
LAMA1	284217	hgsc.bcm.edu	37	18	7049171	7049171	+	Missense_Mutation	SNP	C	C	T	rs140718292	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:7049171C>T	ENST00000389658.3	-	5	767	c.674G>A	c.(673-675)cGc>cAc	p.R225H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	225	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				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)				CAAGCGAAGGCGAATATATCG	0.468													C|||	11	0.00219649	0.0	0.0058	5008	,	,		16222	0.0		0.006	False		,,,				2504	0.001				p.R225H		Atlas-SNP	.											LAMA1,scalp,carcinoma,-1,1	LAMA1	458	1	0			c.G674A						PASS	.	C	HIS/ARG	7,4399	12.9+/-30.5	0,7,2196	149.0	123.0	132.0		674	5.0	1.0	18	dbSNP_134	132	87,8513	50.6+/-110.7	0,87,4213	yes	missense	LAMA1	NM_005559.3	29	0,94,6409	TT,TC,CC		1.0116,0.1589,0.7227	probably-damaging	225/3076	7049171	94,12912	2203	4300	6503	SO:0001583	missense	284217	exon5			CGAAGGCGAATAT	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.674G>A	18.37:g.7049171C>T	ENSP00000374309:p.Arg225His	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	104	46	0.442308	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	33	5.214689	0.95104	0.001589	0.010116	ENSG00000101680	ENST00000389658	D	0.84800	-1.9	5.85	4.97	0.65823	Laminin, N-terminal (3);	0.064020	0.64402	D	0.000007	D	0.93520	0.7932	H	0.96861	3.895	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.95070	0.8203	10	0.87932	D	0	.	16.9089	0.86135	0.0:0.872:0.128:0.0	.	225	P25391	LAMA1_HUMAN	H	225	ENSP00000374309:R225H	ENSP00000374309:R225H	R	-	2	0	LAMA1	7039171	1.000000	0.71417	0.992000	0.48379	0.944000	0.59088	7.818000	0.86416	1.436000	0.47453	0.557000	0.71058	CGC	C|0.993;T|0.007	0.007	strong		0.468	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
MUC4	4585	hgsc.bcm.edu	37	3	195506693	195506693	+	Missense_Mutation	SNP	G	G	A	rs146525749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506693G>A	ENST00000463781.3	-	2	12217	c.11758C>T	c.(11758-11760)Cgt>Tgt	p.R3920C	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.R3920C	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGACGGGTGGTGTCA	0.592													.|||	15	0.00299521	0.0015	0.0029	5008	,	,		10708	0.0		0.0089	False		,,,				2504	0.002				p.R3920C		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	0			c.C11758T						PASS	.						28.0	27.0	27.0					3																	195506693		542	1109	1651	SO:0001583	missense	4585	exon2			GAAGACGGGTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11758C>T	3.37:g.195506693G>A	ENSP00000417498:p.Arg3920Cys	Somatic	1	0	0		WXS	Illumina HiSeq	Phase_I	130	129	0.992308	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	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	g	7.530	0.658436	0.14645	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.4;1.39	.	.	.	.	.	.	.	.	T	0.17789	0.0427	N	0.14661	0.345	0.25472	N	0.987813	D	0.60160	0.987	P	0.49799	0.622	T	0.12066	-1.0562	7	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3792	E7ESK3	.	C	3920	ENSP00000417498:R3920C;ENSP00000420243:R3920C	.	R	-	1	0	MUC4	196991472	.	.	0.011000	0.14972	0.010000	0.07245	.	.	0.064000	0.16427	0.064000	0.15345	CGT	G|0.995;A|0.005	0.005	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
HLA-B	3106	hgsc.bcm.edu	37	6	31322303	31322303	+	Splice_Site	SNP	C	C	G	rs3210072|rs2308655	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31322303C>G	ENST00000412585.2	-	7	1074	c.1046G>C	c.(1045-1047)tGc>tCc	p.C349S		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	349			C -> S (in dbSNP:rs2308655).|C -> Y (in dbSNP:rs2308655).		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						ACTGTCGCTGCCTGGAGTAGA	0.607									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				G|||	2966	0.592252	0.6853	0.6167	5008	,	,		13086	0.626		0.4503	False		,,,				2504	0.5603				p.C349S		Atlas-SNP	.											.	HLA-B	54	.	0			c.G1046C						PASS	.	G	SER/CYS	2731,1675		847,1037,319	58.0	60.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1046	0.3	0.0	6	dbSNP_118	59	3714,4886		849,2016,1435	yes	missense-near-splice	HLA-B	NM_005514.6	112	1696,3053,1754	GG,GC,CC		43.186,38.0163,49.5541		349/363	31322303	6445,6561	2203	4300	6503	SO:0001630	splice_region_variant	3106	exon7	Familial Cancer Database	;Lichen Sclerosis, Familial	TCGCTGCCTGGAG	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.1046-1G>C	6.37:g.31322303C>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	129	127	0.984496	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	1235	0.5654761904761905	323	0.6565040650406504	237	0.6546961325966851	343	0.5996503496503497	332	0.43799472295514513	N	1.559	-0.537263	0.04082	0.619837	0.43186	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596	T	0.01145	5.27	3.2	0.307	0.15811	MHC class I, alpha chain, C-terminal (1);	62.229500	0.00481	N	0.000138	T	0.00178	0.0005	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.36163	-0.9759	8	0.02654	T	1	.	5.6555	0.17640	0.0:0.616:0.1698:0.2142	rs2308655;rs2394962;rs3819300;rs3926874;rs6457399;rs9266109;rs17199307;rs52794465	349	P01889	1B07_HUMAN	S	349;228;189	ENSP00000399168:C349S	ENSP00000399168:C349S	C	-	2	0	HLA-B	31430282	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.321000	0.01119	-0.358000	0.08162	-1.622000	0.00790	TGC	.	.	weak		0.607	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	Missense_Mutation
SEC24C	9632	hgsc.bcm.edu	37	10	75506674	75506674	+	Silent	SNP	T	T	C	rs2306325	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75506674T>C	ENST00000339365.2	+	3	246	c.84T>C	c.(82-84)taT>taC	p.Y28Y	SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_5'UTR|SEC24C_ENST00000345254.4_Silent_p.Y28Y|SEC24C_ENST00000546025.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	28					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.Y28Y(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					AGTCCAGCTATGGTGGGCAAT	0.542													c|||	765	0.152756	0.1528	0.1182	5008	,	,		15519	0.1587		0.1332	False		,,,				2504	0.1912				p.Y28Y		Atlas-SNP	.											SEC24C,NS,carcinoma,0,1	SEC24C	86	1	1	Substitution - coding silent(1)	stomach(1)	c.T84C						scavenged	.	C	,	653,3753	765.4+/-413.4	55,543,1605	97.0	84.0	88.0		84,84	1.1	1.0	10	dbSNP_100	88	1233,7367	762.0+/-407.6	85,1063,3152	no	coding-synonymous,coding-synonymous	SEC24C	NM_004922.3,NM_198597.2	,	140,1606,4757	CC,CT,TT		14.3372,14.8207,14.501	,	28/1095,28/1095	75506674	1886,11120	2203	4300	6503	SO:0001819	synonymous_variant	9632	exon2			CAGCTATGGTGGG	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.84T>C	10.37:g.75506674T>C		Somatic	114	1	0.00877193		WXS	Illumina HiSeq	Phase_I	139	61	0.438849	NM_198597	B4DZT4|Q8WV25	Silent	SNP	ENST00000339365.2	37	CCDS7332.1																																																																																			T|0.851;C|0.149	0.149	strong		0.542	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643255	1643255	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1643255G>A	ENST00000399682.1	-	1	113	c.69C>T	c.(67-69)ggC>ggT	p.G23G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)		p.G23G(1)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		cagagccacagcccccacagc	0.687																																					p.G23G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	1	Substitution - coding silent(1)	kidney(1)	c.C69T						scavenged	.						4.0	8.0	7.0					11																	1643255		646	1526	2172	SO:0001819	synonymous_variant	387267	exon1			GCCACAGCCCCCA	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.69C>T	11.37:g.1643255G>A		Somatic	89	1	0.011236		WXS	Illumina HiSeq	Phase_I	154	8	0.0519481	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
STRA8	346673	hgsc.bcm.edu	37	7	134925411	134925411	+	Silent	SNP	G	G	A	rs7805859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:134925411G>A	ENST00000275764.3	+	2	201	c.201G>A	c.(199-201)gcG>gcA	p.A67A		NM_182489.1	NP_872295.1			stimulated by retinoic acid 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(1)	16						CCCTGGCAGCGCTCTTCAACA	0.617													G|||	1957	0.390775	0.3487	0.4063	5008	,	,		15246	0.2133		0.4553	False		,,,				2504	0.5532				p.A67A		Atlas-SNP	.											.	STRA8	39	.	0			c.G201A						PASS	.	G		1629,2777	497.1+/-363.7	302,1025,876	58.0	60.0	59.0		201	-2.2	0.2	7	dbSNP_116	59	3858,4742	537.5+/-383.2	890,2078,1332	no	coding-synonymous	STRA8	NM_182489.1		1192,3103,2208	AA,AG,GG		44.8605,36.9723,42.1882		67/331	134925411	5487,7519	2203	4300	6503	SO:0001819	synonymous_variant	346673	exon2			GGCAGCGCTCTTC	AF513502	CCDS5839.1	7q33	2012-12-07	2012-12-07		ENSG00000146857	ENSG00000146857			30653	protein-coding gene	gene with protein product		609987	"""stimulated by retinoic acid gene 8 homolog (mouse)"", ""stimulated by retinoic acid 8 homolog (mouse)"""			12489526	Standard	NM_182489		Approved		uc011kpx.2	Q7Z7C7	OTTHUMG00000155415	ENST00000275764.3:c.201G>A	7.37:g.134925411G>A		Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	224	117	0.522321	NM_182489		Silent	SNP	ENST00000275764.3	37	CCDS5839.1																																																																																			G|0.591;A|0.409	0.409	strong		0.617	STRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340028.1	NM_182489	
SPECC1	92521	hgsc.bcm.edu	37	17	20109189	20109189	+	Silent	SNP	C	C	T	rs2703807	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:20109189C>T	ENST00000261503.5	+	4	1878	c.1827C>T	c.(1825-1827)aaC>aaT	p.N609N	AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395529.3_Silent_p.N609N|SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000395525.3_Silent_p.N528N|SPECC1_ENST00000395522.2_Silent_p.N528N|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395530.2_Silent_p.N528N|SPECC1_ENST00000584527.1_Silent_p.N27N|SPECC1_ENST00000395527.4_Silent_p.N609N	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1	609					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)		TAAAGGCAAACGGTGAAATTA	0.433													C|||	2618	0.522764	0.348	0.4669	5008	,	,		21165	0.7927		0.3986	False		,,,				2504	0.6483				p.N609N		Atlas-SNP	.											.	SPECC1	100	.	0			c.C1827T						PASS	.	C	,,,	1554,2832		282,990,921	88.0	88.0	88.0		1827,1584,1584,1827	-3.0	0.3	17	dbSNP_100	88	3381,5203		688,2005,1599	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPECC1	NM_001033553.2,NM_001033554.2,NM_001033555.2,NM_152904.4	,,,	970,2995,2520	TT,TC,CC		39.3872,35.4309,38.0493	,,,	609/1069,528/710,528/988,609/791	20109189	4935,8035	2193	4292	6485	SO:0001819	synonymous_variant	92521	exon4			GGCAAACGGTGAA	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.1827C>T	17.37:g.20109189C>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_001033553	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Silent	SNP	ENST00000261503.5	37	CCDS32590.1																																																																																			C|0.553;T|0.447	0.447	strong		0.433	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	
LAMP2	3920	hgsc.bcm.edu	37	X	119590533	119590533	+	Silent	SNP	T	T	A	rs12097	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:119590533T>A	ENST00000200639.4	-	2	292	c.156A>T	c.(154-156)gtA>gtT	p.V52V	LAMP2_ENST00000538785.1_Intron|LAMP2_ENST00000371335.4_Silent_p.V52V|LAMP2_ENST00000434600.2_Silent_p.V52V|LAMP2_ENST00000540603.1_Silent_p.V5V			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	52	First lumenal domain.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						TTTCATAGCGTACTGTGAAAT	0.313													t|||	1438	0.380927	0.2466	0.2622	3775	,	,		10113	0.2817		0.3519	False		,,,				2504	0.2986				p.V52V		Atlas-SNP	.											.	LAMP2	101	.	0			c.A156T						PASS	.		,,	1343,2492		204,749,186,679,385	51.0	42.0	45.0		156,156,156	2.1	0.0	X	dbSNP_52	45	2867,3861		431,1205,800,792,1072	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMP2	NM_001122606.1,NM_002294.2,NM_013995.2	,,	635,1954,986,1471,1457	AA,AT,A,TT,T		42.613,35.0196,39.8561	,,	52/412,52/411,52/411	119590533	4210,6353	2203	4300	6503	SO:0001819	synonymous_variant	3920	exon2			ATAGCGTACTGTG	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"""CD molecules"""	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.156A>T	X.37:g.119590533T>A		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	106	104	0.981132	NM_013995	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Silent	SNP	ENST00000200639.4	37	CCDS14599.1																																																																																			T|0.602;0|0.012	.	strong		0.313	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1		
TLN2	83660	hgsc.bcm.edu	37	15	63131117	63131117	+	Silent	SNP	T	T	A	rs937418	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:63131117T>A	ENST00000561311.1	+	57	7667	c.7437T>A	c.(7435-7437)gcT>gcA	p.A2479A	RP11-1069G10.1_ENST00000558404.1_RNA|TLN2_ENST00000306829.6_Silent_p.A2479A			Q9Y4G6	TLN2_HUMAN	talin 2	2479	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AGAAGGCAGCTTTTGGCAAAG	0.428													A|||	2121	0.423522	0.6967	0.3732	5008	,	,		21619	0.2907		0.2336	False		,,,				2504	0.4223				p.A2479A		Atlas-SNP	.											.	TLN2	253	.	0			c.T7437A						PASS	.	A		2612,1794	527.1+/-372.1	773,1066,364	115.0	108.0	111.0		7437	-4.3	1.0	15	dbSNP_86	111	1915,6685	726.7+/-406.6	209,1497,2594	no	coding-synonymous	TLN2	NM_015059.2		982,2563,2958	AA,AT,TT		22.2674,40.7172,34.807		2479/2543	63131117	4527,8479	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon55			GGCAGCTTTTGGC	AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.7437T>A	15.37:g.63131117T>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	84	45	0.535714	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			T|0.656;A|0.344	0.344	strong		0.428	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
MUC4	4585	hgsc.bcm.edu	37	3	195512235	195512235	+	Silent	SNP	T	T	C	rs62282484	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195512235T>C	ENST00000463781.3	-	2	6675	c.6216A>G	c.(6214-6216)tcA>tcG	p.S2072S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.S2072S	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)		CTGTGGATGCTGAGGAAGGGT	0.562																																					p.S2072S		Atlas-SNP	.											.	MUC4	1505	.	0			c.A6216G						PASS	.						23.0	22.0	22.0					3																	195512235		688	1568	2256	SO:0001819	synonymous_variant	4585	exon2			GGATGCTGAGGAA	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.6216A>G	3.37:g.195512235T>C		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	192	39	0.203125	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			T|0.500;C|0.500	0.500	weak		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
STK31	56164	hgsc.bcm.edu	37	7	23775477	23775477	+	Missense_Mutation	SNP	G	G	T	rs10264967	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:23775477G>T	ENST00000355870.3	+	7	923	c.804G>T	c.(802-804)aaG>aaT	p.K268N	STK31_ENST00000405627.3_3'UTR|STK31_ENST00000354639.3_Missense_Mutation_p.K245N|STK31_ENST00000428484.1_Missense_Mutation_p.K245N|STK31_ENST00000433467.2_Missense_Mutation_p.K268N	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	268			K -> N (in dbSNP:rs10264967). {ECO:0000269|PubMed:17344846}.			acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						TTGACTTGAAGGATGAAAATG	0.408													g|||	449	0.0896565	0.0772	0.1196	5008	,	,		18423	0.0308		0.173	False		,,,				2504	0.0603				p.K268N		Atlas-SNP	.											.	STK31	175	.	0			c.G804T						PASS	.	G	ASN/LYS,ASN/LYS,ASN/LYS	404,4002	197.4+/-221.5	18,368,1817	68.0	71.0	70.0		735,804,735	4.7	1.0	7	dbSNP_119	70	1622,6978	299.5+/-304.5	133,1356,2811	yes	missense,missense,missense	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	94,94,94	151,1724,4628	TT,TG,GG		18.8605,9.1693,15.5774	probably-damaging,probably-damaging,probably-damaging	245/997,268/1020,245/997	23775477	2026,10980	2203	4300	6503	SO:0001583	missense	56164	exon7			CTTGAAGGATGAA	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.804G>T	7.37:g.23775477G>T	ENSP00000348132:p.Lys268Asn	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	38	36	0.947368	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Missense_Mutation	SNP	ENST00000355870.3	37	CCDS5386.1	243	0.11126373626373626	43	0.08739837398373984	55	0.15193370165745856	15	0.026223776223776224	130	0.17150395778364116	g	12.88	2.070656	0.36566	0.091693	0.188605	ENSG00000196335	ENST00000355870;ENST00000433467;ENST00000354639;ENST00000428484	T;T;T;T	0.20598	2.06;2.06;2.06;2.06	4.71	4.71	0.59529	.	0.135740	0.47455	D	0.000236	T	0.00039	0.0001	M	0.62723	1.935	0.35467	P	0.20294199999999996	D;D	0.60575	0.988;0.988	P;P	0.53912	0.737;0.737	T	0.04900	-1.0919	9	0.54805	T	0.06	-6.4717	11.1853	0.48653	0.0908:0.0:0.9092:0.0	rs10264967;rs10264967	268;268	B4DZ06;Q9BXU1	.;STK31_HUMAN	N	268;268;245;245	ENSP00000348132:K268N;ENSP00000411852:K268N;ENSP00000346660:K245N;ENSP00000406146:K245N	ENSP00000346660:K245N	K	+	3	2	STK31	23742002	1.000000	0.71417	0.994000	0.49952	0.023000	0.10783	3.548000	0.53670	2.332000	0.79248	0.467000	0.42956	AAG	G|0.862;T|0.138	0.138	strong		0.408	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1808256	1808256	+	Silent	SNP	A	A	G	rs749822	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:1808256A>G	ENST00000398564.1	+	4	459	c.459A>G	c.(457-459)gtA>gtG	p.V153V	ARHGEF10_ENST00000518288.1_Silent_p.V153V|ARHGEF10_ENST00000520359.1_Silent_p.V129V|ARHGEF10_ENST00000349830.3_Silent_p.V129V|ARHGEF10_ENST00000262112.6_Silent_p.V153V|ARHGEF10_ENST00000398560.1_Silent_p.V153V			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	153					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)		TGGTGCCTGTACCCTGCGGCT	0.657													A|||	286	0.0571086	0.0242	0.0706	5008	,	,		16794	0.1002		0.0736	False		,,,				2504	0.0307				p.V129V		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.A387G						PASS	.	A		102,4304	80.9+/-119.3	0,102,2101	141.0	116.0	124.0		387	3.6	1.0	8	dbSNP_86	124	660,7940	167.4+/-219.2	20,620,3660	no	coding-synonymous	ARHGEF10	NM_014629.2		20,722,5761	GG,GA,AA		7.6744,2.315,5.8588		129/1345	1808256	762,12244	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon4			GCCTGTACCCTGC	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.459A>G	8.37:g.1808256A>G		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	146	74	0.506849	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				A|0.940;G|0.060	0.060	strong		0.657	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
DNAH5	1767	hgsc.bcm.edu	37	5	13829799	13829799	+	Silent	SNP	G	G	A	rs1348689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13829799G>A	ENST00000265104.4	-	38	6368	c.6264C>T	c.(6262-6264)gcC>gcT	p.A2088A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2088	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					CCTGCCGTCCGGCATAGCCAG	0.423									Kartagener syndrome				G|||	2220	0.443291	0.4705	0.4207	5008	,	,		21016	0.626		0.3698	False		,,,				2504	0.3098				p.A2088A		Atlas-SNP	.											.	DNAH5	868	.	0			c.C6264T						PASS	.	G		2011,2395	561.5+/-380.7	451,1109,643	69.0	66.0	67.0		6264	-9.1	0.7	5	dbSNP_88	67	3135,5465	478.5+/-369.9	576,1983,1741	no	coding-synonymous	DNAH5	NM_001369.2		1027,3092,2384	AA,AG,GG		36.4535,45.6423,39.5664		2088/4625	13829799	5146,7860	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon38	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCGTCCGGCATAG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6264C>T	5.37:g.13829799G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	88	88	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.574;A|0.426	0.426	strong		0.423	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
CUL4A	8451	hgsc.bcm.edu	37	13	113882307	113882307	+	Missense_Mutation	SNP	T	T	C	rs113697945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113882307T>C	ENST00000375440.4	+	4	470	c.386T>C	c.(385-387)gTt>gCt	p.V129A	CUL4A_ENST00000451881.1_Missense_Mutation_p.V29A|CUL4A_ENST00000463426.1_3'UTR|CUL4A_ENST00000375441.3_Missense_Mutation_p.V29A|CUL4A_ENST00000326335.4_Missense_Mutation_p.V29A	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	129					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CTAGATAGTGTTTTATTTTTA	0.363													T|||	10	0.00199681	0.0	0.0014	5008	,	,		20658	0.0		0.008	False		,,,				2504	0.001				p.V129A		Atlas-SNP	.											.	CUL4A	50	.	0			c.T386C						PASS	.	T	ALA/VAL,ALA/VAL	9,4397	16.8+/-37.8	0,9,2194	73.0	73.0	73.0		386,86	5.1	0.7	13	dbSNP_132	73	78,8522	45.4+/-104.0	1,76,4223	yes	missense,missense	CUL4A	NM_001008895.1,NM_003589.2	64,64	1,85,6417	CC,CT,TT		0.907,0.2043,0.6689	benign,benign	129/760,29/660	113882307	87,12919	2203	4300	6503	SO:0001583	missense	8451	exon4			ATAGTGTTTTATT	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.386T>C	13.37:g.113882307T>C	ENSP00000364589:p.Val129Ala	Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	50	37	0.74	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	T	11.40	1.626934	0.28978	0.002043	0.00907	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.12	5.12	0.69794	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.413435	0.24245	N	0.040226	T	0.70430	0.3223	M	0.71581	2.175	0.47862	D	0.999532	B	0.09022	0.002	B	0.25506	0.061	T	0.69881	-0.5025	10	0.16420	T	0.52	-22.1362	15.2361	0.73432	0.0:0.0:0.0:1.0	.	129	Q13619	CUL4A_HUMAN	A	29;29;29;129	ENSP00000364590:V29A;ENSP00000389118:V29A;ENSP00000322132:V29A;ENSP00000364589:V129A	ENSP00000322132:V29A	V	+	2	0	CUL4A	112930308	1.000000	0.71417	0.667000	0.29798	0.042000	0.13812	7.791000	0.85805	2.058000	0.61347	0.528000	0.53228	GTT	T|0.995;C|0.005	0.005	strong		0.363	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	
PLCH1	23007	hgsc.bcm.edu	37	3	155301264	155301264	+	Silent	SNP	T	T	C	rs9289957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:155301264T>C	ENST00000340059.7	-	5	731	c.732A>G	c.(730-732)caA>caG	p.Q244Q	PLCH1_ENST00000494598.1_Silent_p.Q244Q|PLCH1_ENST00000447496.2_Silent_p.Q244Q|PLCH1_ENST00000414191.1_Silent_p.Q226Q|PLCH1_ENST00000460012.1_Silent_p.Q226Q|PLCH1_ENST00000334686.6_Silent_p.Q226Q	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	244					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			ATGATACCTTTTGCTCCACCT	0.338													T|||	108	0.0215655	0.0008	0.0346	5008	,	,		15835	0.0		0.0726	False		,,,				2504	0.0102				p.Q244Q		Atlas-SNP	.											.	PLCH1	406	.	0			c.A732G						PASS	.	T	,,	54,4352	52.3+/-87.9	0,54,2149	99.0	104.0	103.0		732,732,678	2.8	1.0	3	dbSNP_119	103	576,8024	152.7+/-207.2	18,540,3742	no	coding-synonymous,coding-synonymous,coding-synonymous	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	,,	18,594,5891	CC,CT,TT		6.6977,1.2256,4.8439	,,	244/1694,244/1003,226/1656	155301264	630,12376	2203	4300	6503	SO:0001819	synonymous_variant	23007	exon5			TACCTTTTGCTCC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.732A>G	3.37:g.155301264T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	55	0.474138	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Silent	SNP	ENST00000340059.7	37	CCDS46939.1																																																																																			T|0.957;C|0.043	0.043	strong		0.338	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
GLIS1	148979	hgsc.bcm.edu	37	1	54060016	54060016	+	Missense_Mutation	SNP	G	G	C	rs35227000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:54060016G>C	ENST00000312233.2	-	3	1126	c.560C>G	c.(559-561)gCa>gGa	p.A187G		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						CACCCTGCCTGCCAGGCCCAG	0.697													G|||	1070	0.213658	0.1104	0.1643	5008	,	,		13194	0.1885		0.2962	False		,,,				2504	0.3292				p.A187G		Atlas-SNP	.											.	GLIS1	52	.	0			c.C560G						PASS	.	G	GLY/ALA	547,3825		59,429,1698	14.0	14.0	14.0		560	-1.2	0.2	1	dbSNP_126	14	2796,5746		502,1792,1977	no	missense	GLIS1	NM_147193.2	60	561,2221,3675	CC,CG,GG		32.7324,12.5114,25.8866	benign	187/621	54060016	3343,9571	2186	4271	6457	SO:0001583	missense	148979	exon3			CTGCCTGCCAGGC	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"""Zinc fingers, C2H2-type"""	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.560C>G	1.37:g.54060016G>C	ENSP00000309653:p.Ala187Gly	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	29	15	0.517241	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	477	0.2184065934065934	66	0.13414634146341464	67	0.1850828729281768	114	0.1993006993006993	230	0.3034300791556728	G	8.908	0.958011	0.18507	0.125114	0.327324	ENSG00000174332	ENST00000312233	T	0.10860	2.83	4.67	-1.17	0.09648	.	0.628717	0.14183	N	0.335887	T	0.00012	0.0000	L	0.29908	0.895	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.48352	-0.9043	9	0.24483	T	0.36	.	5.9742	0.19369	0.3294:0.1274:0.5432:0.0	rs35227000	187	Q8NBF1	GLIS1_HUMAN	G	187	ENSP00000309653:A187G	ENSP00000309653:A187G	A	-	2	0	GLIS1	53832604	0.000000	0.05858	0.203000	0.23512	0.475000	0.33008	0.042000	0.13949	-0.010000	0.14271	0.462000	0.41574	GCA	G|0.757;C|0.243	0.243	strong		0.697	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
C12orf43	64897	hgsc.bcm.edu	37	12	121442883	121442883	+	Silent	SNP	G	G	A	rs11537856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121442883G>A	ENST00000288757.3	-	5	397	c.375C>T	c.(373-375)ttC>ttT	p.F125F	C12orf43_ENST00000539736.1_Intron|C12orf43_ENST00000445832.3_Silent_p.F95F|C12orf43_ENST00000366211.2_Silent_p.F83F|C12orf43_ENST00000537817.1_Silent_p.F126F|C12orf43_ENST00000536407.2_Intron	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	125										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAGAtgtgaagaaaaggcgga	0.433													.|||	170	0.0339457	0.0045	0.0461	5008	,	,		14389	0.006		0.0616	False		,,,				2504	0.0654				p.F125F		Atlas-SNP	.											.	C12orf43	30	.	0			c.C375T						PASS	.	G		43,4337		1,41,2148	43.0	44.0	44.0		375	4.1	1.0	12	dbSNP_120	44	429,8133		10,409,3862	no	coding-synonymous	C12orf43	NM_022895.1		11,450,6010	AA,AG,GG		5.0105,0.9817,3.647		125/263	121442883	472,12470	2190	4281	6471	SO:0001819	synonymous_variant	64897	exon5			TGTGAAGAAAAGG	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.375C>T	12.37:g.121442883G>A		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	51	31	0.607843	NM_022895	Q53HF0|Q9H9Z7	Silent	SNP	ENST00000288757.3	37	CCDS9210.1	75	0.034340659340659344	5	0.01016260162601626	19	0.052486187845303865	2	0.0034965034965034965	49	0.06464379947229551	G	9.371	1.070519	0.20147	0.009817	0.050105	ENSG00000157895	ENST00000546272	.	.	.	5.86	4.05	0.47172	.	.	.	.	.	T	0.15478	0.0373	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18209	-1.0344	4	.	.	.	-21.0836	10.3316	0.43827	0.1534:0.0:0.8466:0.0	rs11537856	.	.	.	F	78	.	.	S	-	2	0	C12orf43	119927266	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	3.648000	0.54410	0.944000	0.37579	0.650000	0.86243	TCT	G|0.965;A|0.035	0.035	strong		0.433	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36622482	36622482	+	Silent	SNP	G	G	C	rs8075324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:36622482G>C	ENST00000431231.2	+	7	626	c.558G>C	c.(556-558)ccG>ccC	p.P186P	ARHGAP23_ENST00000443378.1_Silent_p.P92P|ARHGAP23_ENST00000437668.3_Silent_p.P186P	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	186	Pro-rich.				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						CAGAGCCACCGCCGATCTGCT	0.652													C|||	1496	0.298722	0.646	0.2421	5008	,	,		12774	0.0298		0.3509	False		,,,				2504	0.093				p.P186P		Atlas-SNP	.											.	ARHGAP23	48	.	0			c.G558C						PASS	.						32.0	40.0	37.0					17																	36622482		692	1591	2283	SO:0001819	synonymous_variant	57636	exon7			GCCACCGCCGATC	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.558G>C	17.37:g.36622482G>C		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	42	42	1	NM_001199417		Silent	SNP	ENST00000431231.2	37	CCDS56027.1																																																																																			G|0.680;C|0.320	0.320	strong		0.652	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
APCDD1	147495	hgsc.bcm.edu	37	18	10487918	10487918	+	Silent	SNP	C	C	T	rs3185480	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:10487918C>T	ENST00000355285.5	+	5	1782	c.1428C>T	c.(1426-1428)ctC>ctT	p.L476L		NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CAGAGGACCTCGCAGAAGACA	0.647													C|||	2053	0.409944	0.205	0.4769	5008	,	,		14532	0.6181		0.4304	False		,,,				2504	0.4039				p.L476L		Atlas-SNP	.											.	APCDD1	57	.	0			c.C1428T						PASS	.	C		1073,3333	373.7+/-320.9	132,809,1262	62.0	63.0	63.0		1428	-3.8	0.0	18	dbSNP_105	63	3515,5085	490.0+/-372.7	713,2089,1498	no	coding-synonymous	APCDD1	NM_153000.4		845,2898,2760	TT,TC,CC		40.8721,24.3532,35.276		476/515	10487918	4588,8418	2203	4300	6503	SO:0001819	synonymous_variant	147495	exon5			GGACCTCGCAGAA	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1428C>T	18.37:g.10487918C>T		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	79	37	0.468354	NM_153000		Silent	SNP	ENST00000355285.5	37	CCDS11849.1																																																																																			C|0.613;T|0.387	0.387	strong		0.647	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
MUC6	4588	hgsc.bcm.edu	37	11	1016889	1016889	+	Missense_Mutation	SNP	G	G	A	rs373231068		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1016889G>A	ENST00000421673.2	-	31	5962	c.5912C>T	c.(5911-5913)cCa>cTa	p.P1971L		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1971	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)		CCCTGTAGGTGGGGAGTGTGT	0.587																																					p.P1971L		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,-1,2	MUC6	408	2	0			c.C5912T						scavenged	.						1041.0	1055.0	1050.0					11																	1016889		2203	4298	6501	SO:0001583	missense	4588	exon31			GTAGGTGGGGAGT	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.5912C>T	11.37:g.1016889G>A	ENSP00000406861:p.Pro1971Leu	Somatic	703	1	0.00142248		WXS	Illumina HiSeq	Phase_I	724	40	0.0552486	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.862334	0.32884	.	.	ENSG00000184956	ENST00000421673	T	0.18016	2.24	3.08	0.802	0.18686	.	.	.	.	.	T	0.12220	0.0297	L	0.47716	1.5	0.09310	N	1	B	0.23650	0.089	B	0.16722	0.016	T	0.36744	-0.9735	9	0.13108	T	0.6	.	6.4541	0.21920	0.0:0.2122:0.5938:0.194	.	1971	Q6W4X9	MUC6_HUMAN	L	1971	ENSP00000406861:P1971L	ENSP00000406861:P1971L	P	-	2	0	MUC6	1006889	0.003000	0.15002	0.002000	0.10522	0.377000	0.30045	1.212000	0.32394	0.602000	0.29896	0.306000	0.20318	CCA	.	.	weak		0.587	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
SVEP1	79987	hgsc.bcm.edu	37	9	113191597	113191597	+	Missense_Mutation	SNP	G	G	A	rs76469101	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113191597G>A	ENST00000401783.2	-	35	5969	c.5633C>T	c.(5632-5634)aCt>aTt	p.T1878I	SVEP1_ENST00000374469.1_Missense_Mutation_p.T1855I|SVEP1_ENST00000297826.5_5'Flank	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1878	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ACCGGCCAGAGTATATCCTTT	0.373													G|||	51	0.0101837	0.0	0.0144	5008	,	,		16574	0.0		0.0368	False		,,,				2504	0.0041				p.T1878I		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.C5633T						PASS	.	G	ILE/THR	15,3637		0,15,1811	31.0	29.0	30.0		5633	0.5	0.2	9	dbSNP_132	30	249,7915		6,237,3839	no	missense	SVEP1	NM_153366.3	89	6,252,5650	AA,AG,GG		3.05,0.4107,2.2343	possibly-damaging	1878/3572	113191597	264,11552	1826	4082	5908	SO:0001583	missense	79987	exon35			GCCAGAGTATATC	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.5633C>T	9.37:g.113191597G>A	ENSP00000384917:p.Thr1878Ile	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	29	13	0.448276	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	39	0.017857142857142856	0	0.0	8	0.022099447513812154	0	0.0	31	0.040897097625329816	G	8.910	0.958458	0.18507	0.004107	0.0305	ENSG00000165124	ENST00000401783;ENST00000374469	T;T	0.65549	-0.16;-0.16	5.17	0.493	0.16878	Complement control module (2);Sushi/SCR/CCP (3);	0.564203	0.19954	N	0.102353	T	0.13243	0.0321	L	0.33293	1	0.09310	N	0.99999	B	0.17667	0.023	B	0.15052	0.012	T	0.06092	-1.0846	10	0.37606	T	0.19	.	1.835	0.03138	0.1462:0.1919:0.3544:0.3075	.	1878	Q4LDE5	SVEP1_HUMAN	I	1878;1855	ENSP00000384917:T1878I;ENSP00000363593:T1855I	ENSP00000363593:T1855I	T	-	2	0	SVEP1	112231418	0.001000	0.12720	0.220000	0.23810	0.893000	0.52053	-0.099000	0.11007	0.282000	0.22254	0.650000	0.86243	ACT	G|0.980;A|0.020	0.020	strong		0.373	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MYO5C	55930	hgsc.bcm.edu	37	15	52527951	52527951	+	Missense_Mutation	SNP	T	T	C	rs55753304	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:52527951T>C	ENST00000261839.7	-	23	3039	c.2878A>G	c.(2878-2880)Aag>Gag	p.K960E	MYO5C_ENST00000443683.2_3'UTR	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	960						extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TTCTGAAGCTTTGCCAATTTC	0.388													T|||	60	0.0119808	0.0	0.013	5008	,	,		20400	0.0169		0.0298	False		,,,				2504	0.0041				p.K960E		Atlas-SNP	.											.	MYO5C	162	.	0			c.A2878G						PASS	.	T	GLU/LYS	17,3607		0,17,1795	114.0	101.0	105.0		2878	4.1	1.0	15	dbSNP_129	105	171,7975		3,165,3905	yes	missense	MYO5C	NM_018728.3	56	3,182,5700	CC,CT,TT		2.0992,0.4691,1.5973	benign	960/1743	52527951	188,11582	1812	4073	5885	SO:0001583	missense	55930	exon23			GAAGCTTTGCCAA	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.2878A>G	15.37:g.52527951T>C	ENSP00000261839:p.Lys960Glu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	120	60	0.5	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	35	0.016025641025641024	0	0.0	6	0.016574585635359115	5	0.008741258741258742	24	0.0316622691292876	T	3.899	-0.022431	0.07634	0.004691	0.020992	ENSG00000128833	ENST00000261839	T	0.18657	2.2	5.26	4.14	0.48551	.	0.129153	0.50627	D	0.000106	T	0.03564	0.0102	N	0.24115	0.695	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.08889	-1.0700	10	0.02654	T	1	.	10.7384	0.46139	0.0:0.0754:0.0:0.9246	rs55753304	960	Q9NQX4	MYO5C_HUMAN	E	960	ENSP00000261839:K960E	ENSP00000261839:K960E	K	-	1	0	MYO5C	50315243	0.434000	0.25570	1.000000	0.80357	0.983000	0.72400	2.269000	0.43346	0.959000	0.37980	0.533000	0.62120	AAG	T|0.980;C|0.020	0.020	strong		0.388	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
DOCK8	81704	hgsc.bcm.edu	37	9	449874	449874	+	Missense_Mutation	SNP	G	G	C	rs34908836	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:449874G>C	ENST00000453981.1	+	45	6020	c.5908G>C	c.(5908-5910)Gca>Cca	p.A1970P	DOCK8_ENST00000432829.2_Missense_Mutation_p.A1902P|DOCK8_ENST00000382329.1_Missense_Mutation_p.A1437P|DOCK8_ENST00000469391.1_Missense_Mutation_p.A1870P			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1970	DHR-2.		A -> P (in dbSNP:rs34908836). {ECO:0000269|PubMed:10729223}.		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)		GCCGCCTGATGCAAAGATGCT	0.463													C|||	513	0.102436	0.1543	0.0519	5008	,	,		19958	0.0099		0.0696	False		,,,				2504	0.1973				p.A1970P		Atlas-SNP	.											.	DOCK8	401	.	0			c.G5908C						PASS	.	C	PRO/ALA,PRO/ALA,PRO/ALA	584,3822	771.3+/-413.8	28,528,1647	112.0	106.0	108.0		5608,5704,5908	3.7	1.0	9	dbSNP_126	108	392,8208	801.7+/-407.4	12,368,3920	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	27,27,27	40,896,5567	CC,CG,GG		4.5581,13.2547,7.5042	benign,benign,benign	1870/2000,1902/2032,1970/2100	449874	976,12030	2203	4300	6503	SO:0001583	missense	81704	exon45			CCTGATGCAAAGA	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.5908G>C	9.37:g.449874G>C	ENSP00000408464:p.Ala1970Pro	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	41	0.493976	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	149	0.06822344322344322	77	0.1565040650406504	17	0.04696132596685083	7	0.012237762237762238	48	0.0633245382585752	C	10.71	1.427945	0.25726	0.132547	0.045581	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382329	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.53	3.68	0.42216	.	0.049968	0.85682	N	0.000000	T	0.00073	0.0002	N	0.16201	0.385	0.23975	P	0.99629877	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12837	0.001;0.008;0.002	T	0.10337	-1.0634	9	0.40728	T	0.16	.	18.6541	0.91441	0.0:0.2288:0.7712:0.0	rs34908836	1870;1437;1970	E9PH09;A2A369;Q8NF50	.;.;DOCK8_HUMAN	P	1970;1938;1902;1870;1437	ENSP00000408464:A1970P;ENSP00000394888:A1902P;ENSP00000419438:A1870P;ENSP00000371766:A1437P	ENSP00000287364:A1938P	A	+	1	0	DOCK8	439874	1.000000	0.71417	0.995000	0.50966	0.985000	0.73830	2.937000	0.48979	0.452000	0.26830	-0.824000	0.03097	GCA	G|0.927;C|0.073	0.073	strong		0.463	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
PTPRN2	5799	hgsc.bcm.edu	37	7	157931144	157931144	+	Missense_Mutation	SNP	C	C	T	rs1130499	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:157931144C>T	ENST00000389418.4	-	7	983	c.974G>A	c.(973-975)aGt>aAt	p.S325N	PTPRN2_ENST00000404321.2_Missense_Mutation_p.S348N|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S325N|PTPRN2_ENST00000409483.1_Missense_Mutation_p.S287N|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S308N	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	325			S -> N (in dbSNP:rs1130499). {ECO:0000269|PubMed:8954911, ECO:0000269|Ref.4}.		negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CTCCAGGCCACTCAGGCCCCT	0.637													C|||	1879	0.3752	0.4387	0.4395	5008	,	,		19314	0.4663		0.2903	False		,,,				2504	0.2372				p.S325N		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G974A						PASS	.		ASN/SER,ASN/SER,ASN/SER	1935,2471	546.4+/-377.0	421,1093,689	65.0	67.0	66.0		974,923,974	2.2	0.0	7	dbSNP_86	66	2540,6060	411.0+/-350.3	362,1816,2122	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	46,46,46	783,2909,2811	TT,TC,CC		29.5349,43.9174,34.4072	possibly-damaging,possibly-damaging,possibly-damaging	325/1016,308/999,325/987	157931144	4475,8531	2203	4300	6503	SO:0001583	missense	5799	exon7			AGGCCACTCAGGC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.974G>A	7.37:g.157931144C>T	ENSP00000374069:p.Ser325Asn	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	80	38	0.475	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	897	0.4107142857142857	237	0.4817073170731707	134	0.3701657458563536	302	0.527972027972028	224	0.2955145118733509	C	9.887	1.203049	0.22121	0.439174	0.295349	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03330	3.98;3.98;3.98;3.98;3.97	4.11	2.21	0.28008	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B	0.16396	0.017;0.01;0.017;0.01;0.01	B;B;B;B;B	0.18561	0.022;0.01;0.022;0.01;0.01	T	0.30707	-0.9969	8	0.41790	T	0.15	.	4.3887	0.11330	0.0:0.5974:0.19:0.2126	rs1130499;rs3189416;rs3752370;rs10434937;rs52826743;rs1130499	348;287;325;308;325	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	N	287;325;308;325;348	ENSP00000387114:S287N;ENSP00000374064:S325N;ENSP00000374067:S308N;ENSP00000374069:S325N;ENSP00000385464:S348N	ENSP00000374064:S325N	S	-	2	0	PTPRN2	157623905	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.503000	0.22610	0.274000	0.22072	0.650000	0.86243	AGT	C|0.623;T|0.377	0.377	strong		0.637	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
OR56B1	387748	hgsc.bcm.edu	37	11	5758646	5758646	+	Silent	SNP	T	T	C	rs4486660	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5758646T>C	ENST00000317121.3	+	1	966	c.900T>C	c.(898-900)taT>taC	p.Y300Y	TRIM5_ENST00000380027.1_Intron	NM_001005180.2	NP_001005180.1	Q8NGI3	O56B1_HUMAN	olfactory receptor, family 56, subfamily B, member 1	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|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)		CTACAGTTTATGCACTTCAGA	0.423													T|||	473	0.0944489	0.0575	0.0922	5008	,	,		19244	0.1696		0.0557	False		,,,				2504	0.1084				p.Y300Y		Atlas-SNP	.											.	OR56B1	38	.	0			c.T900C						PASS	.	T		186,4216	119.6+/-157.3	8,170,2023	237.0	224.0	228.0		900	2.2	1.0	11	dbSNP_111	228	409,8185	129.2+/-187.3	10,389,3898	no	coding-synonymous	OR56B1	NM_001005180.2		18,559,5921	CC,CT,TT		4.7591,4.2254,4.5783		300/325	5758646	595,12401	2201	4297	6498	SO:0001819	synonymous_variant	387748	exon1			AGTTTATGCACTT	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.900T>C	11.37:g.5758646T>C		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	101	41	0.405941	NM_001005180	B2RNY6|B3KV42|Q6IF76	Silent	SNP	ENST00000317121.3	37	CCDS31395.1																																																																																			T|0.941;C|0.059	0.059	strong		0.423	OR56B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143354.1	NM_001005180	
SLC27A5	10998	hgsc.bcm.edu	37	19	59023174	59023174	+	Missense_Mutation	SNP	A	A	G	rs35350976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:59023174A>G	ENST00000263093.2	-	1	258	c.149T>C	c.(148-150)aTg>aCg	p.M50T	SLC27A5_ENST00000601355.1_Missense_Mutation_p.M50T	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	50			M -> T (in dbSNP:rs35350976).		bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		CCGTGCTAACATGGCCAGCCC	0.701													A|||	809	0.161542	0.1823	0.1715	5008	,	,		17235	0.0556		0.2187	False		,,,				2504	0.1769				p.M50T		Atlas-SNP	.											.	SLC27A5	58	.	0			c.T149C						PASS	.	A	THR/MET	749,3597		75,599,1499	9.0	11.0	10.0		149	-0.9	0.0	19	dbSNP_126	10	1449,7049		128,1193,2928	yes	missense	SLC27A5	NM_012254.2	81	203,1792,4427	GG,GA,AA		17.0511,17.2342,17.113	benign	50/691	59023174	2198,10646	2173	4249	6422	SO:0001583	missense	10998	exon1			GCTAACATGGCCA	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.149T>C	19.37:g.59023174A>G	ENSP00000263093:p.Met50Thr	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	75	41	0.546667	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	349	0.15979853479853479	100	0.2032520325203252	62	0.1712707182320442	34	0.05944055944055944	153	0.20184696569920843	a	8.140	0.784999	0.16189	0.172342	0.170511	ENSG00000083807	ENST00000263093	T	0.51574	0.7	4.31	-0.944	0.10392	.	2.348050	0.01898	N	0.038985	T	0.00039	0.0001	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.09818	-1.0657	9	0.34782	T	0.22	-0.0265	0.6905	0.00890	0.3719:0.1775:0.1056:0.345	rs35350976	50	Q9Y2P5	S27A5_HUMAN	T	50	ENSP00000263093:M50T	ENSP00000263093:M50T	M	-	2	0	SLC27A5	63714986	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.040000	0.13905	-0.051000	0.13334	0.374000	0.22700	ATG	A|0.840;G|0.160	0.160	strong		0.701	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
TMPRSS3	64699	hgsc.bcm.edu	37	21	43803167	43803167	+	Missense_Mutation	SNP	T	T	C	rs2839500	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43803167T>C	ENST00000291532.3	-	8	1712	c.757A>G	c.(757-759)Atc>Gtc	p.I253V	TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.I253V|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.I251V|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.I337V|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.I253V	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	253	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		I -> V (in dbSNP:rs2839500). {ECO:0000269|PubMed:11424922}.		cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						GCAGCAGTGATGATCCACAGG	0.592													C|||	1208	0.241214	0.3041	0.134	5008	,	,		20674	0.3323		0.1113	False		,,,				2504	0.272				p.I253V		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.A757G						PASS	.	C	VAL/ILE,VAL/ILE	1196,3210	708.6+/-407.6	161,874,1168	75.0	64.0	68.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	757,757	4.6	0.5	21	dbSNP_100	68	887,7713	778.9+/-407.7	37,813,3450	yes	missense,missense	TMPRSS3	NM_024022.2,NM_032405.1	29,29	198,1687,4618	CC,CT,TT		10.314,27.1448,16.0157	benign,benign	253/455,253/345	43803167	2083,10923	2203	4300	6503	SO:0001583	missense	64699	exon8			CAGTGATGATCCA	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.757A>G	21.37:g.43803167T>C	ENSP00000291532:p.Ile253Val	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	60	59	0.983333	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	494	0.2261904761904762	154	0.3130081300813008	54	0.14917127071823205	203	0.3548951048951049	83	0.10949868073878628	C	0.696	-0.792701	0.02884	0.271448	0.10314	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;T;T;T;T	0.80994	0.25;-1.44;-1.44;0.25;-1.44	5.5	4.59	0.56863	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.159777	0.42053	N	0.000763	T	0.00012	0.0000	N	0.11698	0.16	0.58432	P	1.999999999946489E-6	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.14980	-1.0453	8	.	.	.	.	8.2005	0.31421	0.0:0.5343:0.3254:0.1403	rs2839500;rs52817606;rs60045807;rs2839500	253;253;253	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	V	253;253;251;337;253	ENSP00000291532:I253V;ENSP00000411013:I253V;ENSP00000381442:I251V;ENSP00000369762:I337V;ENSP00000381434:I253V	.	I	-	1	0	TMPRSS3	42676236	0.025000	0.19082	0.465000	0.27155	0.794000	0.44872	0.113000	0.15499	0.658000	0.30925	-0.186000	0.12905	ATC	A|0.006;C|0.194	0.194	strong		0.592	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
SERGEF	26297	hgsc.bcm.edu	37	11	17809639	17809639	+	Missense_Mutation	SNP	C	C	T	rs10788	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:17809639C>T	ENST00000265965.5	-	11	1521	c.1370G>A	c.(1369-1371)gGa>gAa	p.G457E	SERGEF_ENST00000528200.1_3'UTR	NM_012139.2	NP_036271.1	Q9UGK8	SRGEF_HUMAN	secretion regulating guanine nucleotide exchange factor	457			G -> E (in dbSNP:rs10788).		negative regulation of protein secretion (GO:0050709)|positive regulation of Ran GTPase activity (GO:0032853)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)	Ran guanyl-nucleotide exchange factor activity (GO:0005087)			autonomic_ganglia(1)|central_nervous_system(1)|large_intestine(5)|lung(5)	12						CTATCACAGTCCCCCATTTCT	0.463													C|||	637	0.127196	0.2156	0.0663	5008	,	,		21229	0.002		0.1233	False		,,,				2504	0.184				p.G457E		Atlas-SNP	.											.	SERGEF	38	.	0			c.G1370A						PASS	.	C	GLU/GLY	767,3633	308.6+/-290.6	69,629,1502	175.0	172.0	173.0		1370	-0.8	0.0	11	dbSNP_52	173	937,7649	205.4+/-247.8	48,841,3404	yes	missense	SERGEF	NM_012139.2	98	117,1470,4906	TT,TC,CC		10.9131,17.4318,13.1218	probably-damaging	457/459	17809639	1704,11282	2200	4293	6493	SO:0001583	missense	26297	exon11			CACAGTCCCCCAT	AJ243950	CCDS7828.1	11p14.3	2006-03-09			ENSG00000129158	ENSG00000129158			17499	protein-coding gene	gene with protein product		606051				10571079, 12459492	Standard	NM_012139		Approved	DelGEF, Gnefr	uc001mnm.3	Q9UGK8	OTTHUMG00000166420	ENST00000265965.5:c.1370G>A	11.37:g.17809639C>T	ENSP00000265965:p.Gly457Glu	Somatic	296	1	0.00337838		WXS	Illumina HiSeq	Phase_I	269	120	0.446097	NM_012139	Q9UGK9	Missense_Mutation	SNP	ENST00000265965.5	37	CCDS7828.1	219	0.10027472527472528	91	0.18495934959349594	26	0.0718232044198895	1	0.0017482517482517483	101	0.13324538258575197	C	16.93	3.259426	0.59321	0.174318	0.109131	ENSG00000129158	ENST00000265965	T	0.49720	0.77	4.77	-0.839	0.10759	.	0.861858	0.09852	N	0.747502	T	0.00073	0.0002	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.12604	-1.0541	9	0.59425	D	0.04	-0.6271	5.124	0.14875	0.0:0.3847:0.1506:0.4648	rs10788;rs17792293;rs52814345;rs57745125;rs10788	457	Q9UGK8	SRGEF_HUMAN	E	457	ENSP00000265965:G457E	ENSP00000265965:G457E	G	-	2	0	SERGEF	17766215	0.000000	0.05858	0.000000	0.03702	0.494000	0.33585	-0.662000	0.05305	-0.059000	0.13154	-0.258000	0.10820	GGA	C|0.875;T|0.125	0.125	strong		0.463	SERGEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389538.1	NM_012139	
AIPL1	23746	hgsc.bcm.edu	37	17	6337247	6337247	+	Missense_Mutation	SNP	C	C	G	rs12449580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:6337247C>G	ENST00000381129.3	-	2	348	c.268G>C	c.(268-270)Gac>Cac	p.D90H	AIPL1_ENST00000575265.1_Missense_Mutation_p.D90H|AIPL1_ENST00000570466.1_Missense_Mutation_p.D68H|AIPL1_ENST00000576776.1_Missense_Mutation_p.D90H|AIPL1_ENST00000576307.1_Intron|AIPL1_ENST00000574506.1_Missense_Mutation_p.D78H|AIPL1_ENST00000571740.1_Missense_Mutation_p.D90H|AIPL1_ENST00000250087.5_Missense_Mutation_p.D90H	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	90	PPIase FKBP-type.		D -> H (in dbSNP:rs12449580). {ECO:0000269|PubMed:10615133, ECO:0000269|PubMed:21602930}.		negative regulation of apoptotic process (GO:0043066)|phototransduction, visible light (GO:0007603)|protein farnesylation (GO:0018343)|protein folding (GO:0006457)|regulation of cGMP metabolic process (GO:0030823)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)	farnesylated protein binding (GO:0001918)|unfolded protein binding (GO:0051082)			NS(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	12				COAD - Colon adenocarcinoma(228;0.141)		ACGATGGTGTCGCACCAGAAC	0.597													C|||	901	0.179912	0.0673	0.196	5008	,	,		17150	0.3462		0.2316	False		,,,				2504	0.0961				p.D90H		Atlas-SNP	.											.	AIPL1	34	.	0			c.G268C						PASS	.	C	HIS/ASP,,HIS/ASP	383,4023	191.2+/-216.9	23,337,1843	101.0	75.0	84.0		268,,268	4.0	1.0	17	dbSNP_120	84	1768,6832	315.7+/-312.4	192,1384,2724	yes	missense,intron,missense	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	81,,81	215,1721,4567	GG,GC,CC		20.5581,8.6927,16.5385	benign,,benign	90/322,,90/385	6337247	2151,10855	2203	4300	6503	SO:0001583	missense	23746	exon2			TGGTGTCGCACCA	AF148864	CCDS11075.1, CCDS32539.1, CCDS32540.1, CCDS67130.1, CCDS67131.1, CCDS67132.1, CCDS67133.1	17p13.1	2013-01-08	2001-11-29		ENSG00000129221	ENSG00000129221			359	protein-coding gene	gene with protein product		604392	"""aryl hydrocarbon receptor-interacting protein-like 1"""	LCA4		10615133, 14555765, 15365173	Standard	NM_001285402		Approved		uc002gcp.3	Q9NZN9	OTTHUMG00000102043	ENST00000381129.3:c.268G>C	17.37:g.6337247C>G	ENSP00000370521:p.Asp90His	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Missense_Mutation	SNP	ENST00000381129.3	37	CCDS11075.1	491	0.22481684981684982	36	0.07317073170731707	65	0.17955801104972377	218	0.3811188811188811	172	0.22691292875989447	C	15.06	2.721236	0.48728	0.086927	0.205581	ENSG00000129221	ENST00000381129;ENST00000250087;ENST00000444243	D;D	0.91792	-2.91;-2.91	5.05	4.03	0.46877	.	0.098333	0.64402	D	0.000002	T	0.00012	0.0000	L	0.55213	1.73	0.09310	P	0.99999897138	B;B;B;D;P	0.89917	0.069;0.173;0.069;1.0;0.715	B;B;B;D;P	0.91635	0.071;0.124;0.071;0.999;0.583	T	0.00345	-1.1801	9	0.19590	T	0.45	-50.3039	12.6104	0.56547	0.166:0.834:0.0:0.0	rs12449580;rs17202007;rs52790044;rs56554925;rs12449580	90;68;90;90;90	Q659W3;Q659W4;F1T0C4;Q9NZN9-3;Q9NZN9	.;.;.;.;AIPL1_HUMAN	H	90	ENSP00000370521:D90H;ENSP00000250087:D90H	ENSP00000250087:D90H	D	-	1	0	AIPL1	6277971	1.000000	0.71417	0.983000	0.44433	0.756000	0.42949	4.644000	0.61397	2.323000	0.78572	0.650000	0.86243	GAC	C|0.803;G|0.197	0.197	strong		0.597	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336	
MUC2	4583	hgsc.bcm.edu	37	11	1092890	1092890	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1092890C>T	ENST00000441003.2	+	30	4736	c.4709C>T	c.(4708-4710)aCc>aTc	p.T1570I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1571I|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ACCACGGTGaccccaacccca	0.637																																					p.T1570I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-1,2	MUC2	614	2	0			c.C4709T						PASS	.						119.0	156.0	143.0					11																	1092890		1961	3652	5613	SO:0001583	missense	4583	exon30			CGGTGACCCCAAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4709C>T	11.37:g.1092890C>T	ENSP00000415183:p.Thr1570Ile	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	86	12	0.139535	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	1.561	-0.536608	0.04082	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15487	2.42;3.24	1.3	-2.33	0.06724	.	0.589600	0.12692	U	0.447130	T	0.07548	0.0190	.	.	.	0.09310	N	1	P	0.34699	0.464	B	0.21546	0.035	T	0.24799	-1.0150	9	0.38643	T	0.18	.	4.395	0.11358	0.3284:0.4793:0.1923:0.0	.	1570	E7EUV1	.	I	1570;1571	ENSP00000415183:T1570I;ENSP00000351956:T1571I	ENSP00000351956:T1571I	T	+	2	0	MUC2	1082890	0.002000	0.14202	0.000000	0.03702	0.033000	0.12548	0.404000	0.20999	-0.107000	0.12088	0.064000	0.15345	ACC	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
GAS2L3	283431	hgsc.bcm.edu	37	12	101018161	101018161	+	Silent	SNP	C	C	T	rs1045603	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101018161C>T	ENST00000539410.1	+	9	1964	c.1578C>T	c.(1576-1578)tcC>tcT	p.S526S	GAS2L3_ENST00000266754.5_Silent_p.S526S|GAS2L3_ENST00000547754.1_Silent_p.S526S|GAS2L3_ENST00000537247.1_Silent_p.S422S			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	526					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						AAACCAGTTCCAAAACCATAG	0.448													C|||	504	0.100639	0.093	0.1427	5008	,	,		18489	0.0962		0.1123	False		,,,				2504	0.0736				p.S526S		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1578T						PASS	.	C		350,4056	181.2+/-209.3	12,326,1865	55.0	56.0	56.0		1578	-2.7	0.4	12	dbSNP_86	56	881,7719	199.0+/-243.2	49,783,3468	no	coding-synonymous	GAS2L3	NM_174942.1		61,1109,5333	TT,TC,CC		10.2442,7.9437,9.4649		526/695	101018161	1231,11775	2203	4300	6503	SO:0001819	synonymous_variant	283431	exon10			CAGTTCCAAAACC	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1578C>T	12.37:g.101018161C>T		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	31	0.584906	NM_174942	B2RCN2	Silent	SNP	ENST00000539410.1	37	CCDS9079.1																																																																																			C|0.901;T|0.099	0.099	strong		0.448	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
LGR6	59352	hgsc.bcm.edu	37	1	202287754	202287754	+	Missense_Mutation	SNP	G	G	A	rs75658797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:202287754G>A	ENST00000367278.3	+	18	2412	c.2323G>A	c.(2323-2325)Gtg>Atg	p.V775M	LGR6_ENST00000439764.2_Missense_Mutation_p.V636M|LGR6_ENST00000255432.7_Missense_Mutation_p.V723M	NM_001017403.1	NP_001017403.1	Q9HBX8	LGR6_HUMAN	leucine-rich repeat containing G protein-coupled receptor 6	775					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of Wnt signaling pathway (GO:0030177)|Wnt signaling pathway (GO:0016055)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)|vesicle (GO:0031982)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	36						GGTGAGGCACGTGGCCTGGCT	0.637													G|||	411	0.0820687	0.059	0.1037	5008	,	,		17778	0.0526		0.1113	False		,,,				2504	0.0982				p.V775M		Atlas-SNP	.											.	LGR6	102	.	0			c.G2323A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	235,4171	138.4+/-174.2	8,219,1976	100.0	79.0	86.0		2323,1906,2167	2.6	1.0	1	dbSNP_131	86	1129,7471	234.6+/-267.5	79,971,3250	yes	missense,missense,missense	LGR6	NM_001017403.1,NM_001017404.1,NM_021636.2	21,21,21	87,1190,5226	AA,AG,GG		13.1279,5.3336,10.4875	benign,benign,benign	775/968,636/829,723/916	202287754	1364,11642	2203	4300	6503	SO:0001583	missense	59352	exon18			AGGCACGTGGCCT	AF190501	CCDS1424.1, CCDS30971.1, CCDS30972.1	1q32.1	2012-08-21	2011-01-25		ENSG00000133067	ENSG00000133067		"""GPCR / Class A : Orphans"""	19719	protein-coding gene	gene with protein product		606653	"""leucine-rich repeat-containing G protein-coupled receptor 6"""			10935549	Standard	XM_005245404		Approved	FLJ14471	uc001gxu.3	Q9HBX8	OTTHUMG00000041383	ENST00000367278.3:c.2323G>A	1.37:g.202287754G>A	ENSP00000356247:p.Val775Met	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	144	62	0.430556	NM_001017403	Q5T509|Q5T512|Q6UY15|Q86VU0|Q96K69|Q9BYD7	Missense_Mutation	SNP	ENST00000367278.3	37	CCDS30971.1	190	0.08699633699633699	38	0.07723577235772358	42	0.11602209944751381	32	0.055944055944055944	78	0.10290237467018469	G	13.00	2.107063	0.37145	0.053336	0.131279	ENSG00000133067	ENST00000367278;ENST00000255432;ENST00000439764	T;T;T	0.40225	1.04;1.04;1.04	4.49	2.58	0.30949	.	0.137493	0.48767	N	0.000170	T	0.00271	0.0008	N	0.20530	0.585	0.25761	P	0.9849419	D;P;P	0.54047	0.964;0.941;0.793	B;P;B	0.45881	0.244;0.496;0.409	T	0.06481	-1.0824	9	0.11794	T	0.64	.	6.5745	0.22557	0.1589:0.1488:0.6924:0.0	.	636;723;775	Q9HBX8-1;Q9HBX8-2;Q9HBX8	.;.;LGR6_HUMAN	M	775;723;636	ENSP00000356247:V775M;ENSP00000255432:V723M;ENSP00000387869:V636M	ENSP00000255432:V723M	V	+	1	0	LGR6	200554377	1.000000	0.71417	0.986000	0.45419	0.985000	0.73830	3.339000	0.52135	0.626000	0.30322	0.485000	0.47835	GTG	G|0.899;A|0.101	0.101	strong		0.637	LGR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099143.1	NM_021636	
C11orf1	64776	hgsc.bcm.edu	37	11	111754574	111754574	+	Silent	SNP	A	A	C	rs1045282	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:111754574A>C	ENST00000260276.3	+	4	760	c.423A>C	c.(421-423)tcA>tcC	p.S141S	C11orf1_ENST00000528125.1_Silent_p.S95S|C11orf1_ENST00000529270.1_Silent_p.S181S|C11orf1_ENST00000530214.1_Missense_Mutation_p.Q119P	NM_022761.2	NP_073598.1	Q9H5F2	CK001_HUMAN	chromosome 11 open reading frame 1	141						nucleus (GO:0005634)				kidney(2)|lung(3)	5		all_cancers(61;1.26e-15)|all_epithelial(67;9.52e-10)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|Medulloblastoma(222;0.0228)|all_neural(223;0.0281)		all cancers(92;6.28e-09)|Epithelial(105;4.11e-08)|OV - Ovarian serous cystadenocarcinoma(223;1.52e-07)|BRCA - Breast invasive adenocarcinoma(274;1.1e-06)		CAGAAAAGTCAACTTACATGA	0.398													A|||	1200	0.239617	0.1952	0.3069	5008	,	,		18184	0.1905		0.3231	False		,,,				2504	0.2168				p.S141S		Atlas-SNP	.											.	C11orf1	15	.	0			c.A423C						PASS	.	A		963,3439	363.1+/-316.4	106,751,1344	114.0	108.0	110.0		423	4.2	1.0	11	dbSNP_86	110	2579,6015	419.8+/-353.2	394,1791,2112	no	coding-synonymous	C11orf1	NM_022761.2		500,2542,3456	CC,CA,AA		30.0093,21.8764,27.2545		141/151	111754574	3542,9454	2201	4297	6498	SO:0001819	synonymous_variant	64776	exon4			AAAGTCAACTTAC	AJ250229	CCDS8350.1	11q23.1	2012-05-30			ENSG00000137720	ENSG00000137720			1163	protein-coding gene	gene with protein product						10873569	Standard	NM_022761		Approved	FLJ23499	uc001pmd.3	Q9H5F2	OTTHUMG00000166884	ENST00000260276.3:c.423A>C	11.37:g.111754574A>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	66	30	0.454545	NM_022761	Q6I9X7|Q9NQC6	Silent	SNP	ENST00000260276.3	37	CCDS8350.1	583	0.26694139194139194	114	0.23170731707317074	126	0.34806629834254144	101	0.17657342657342656	242	0.31926121372031663	A	10.58	1.389114	0.25118	0.218764	0.300093	ENSG00000137720	ENST00000530214	T	0.25085	1.82	5.37	4.22	0.49857	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999999994803	.	.	.	.	.	.	T	0.43196	-0.9406	5	0.62326	D	0.03	-22.8715	5.7886	0.18347	0.5843:0.3324:0.0833:0.0	rs1045282;rs3168261;rs17489575;rs59543330;rs1045282	.	.	.	P	119	ENSP00000435864:Q119P	ENSP00000435864:Q119P	Q	+	2	0	C11orf1	111259784	0.960000	0.32886	0.982000	0.44146	0.994000	0.84299	1.708000	0.37899	1.017000	0.39495	0.528000	0.53228	CAA	A|0.734;C|0.266	0.266	strong		0.398	C11orf1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391650.1	NM_022761	
PLCH2	9651	hgsc.bcm.edu	37	1	2436256	2436256	+	Silent	SNP	G	G	A	rs138038983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2436256G>A	ENST00000419816.2	+	22	4129	c.3855G>A	c.(3853-3855)ggG>ggA	p.G1285G	PLCH2_ENST00000449969.1_3'UTR|PLCH2_ENST00000378488.3_Silent_p.G1249G|PLCH2_ENST00000378486.3_Silent_p.G1285G			O75038	PLCH2_HUMAN	phospholipase C, eta 2	1285					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		TCCCGGGAGGGACACGGCGGG	0.662													G|||	53	0.0105831	0.0008	0.0245	5008	,	,		15355	0.0		0.0298	False		,,,				2504	0.0051				p.G1285G		Atlas-SNP	.											.	PLCH2	131	.	0			c.G3855A						PASS	.	G		21,3963		0,21,1971	13.0	16.0	15.0		3855	-0.4	0.0	1	dbSNP_134	15	235,8037		3,229,3904	no	coding-synonymous	PLCH2	NM_014638.2		3,250,5875	AA,AG,GG		2.8409,0.5271,2.0888		1285/1417	2436256	256,12000	1992	4136	6128	SO:0001819	synonymous_variant	9651	exon22			GGGAGGGACACGG	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"""EF-hand domain containing"""	29037	protein-coding gene	gene with protein product		612836	"""phospholipase C-like 4"""	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.3855G>A	1.37:g.2436256G>A		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	110	6	0.0545455	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	37		30	0.013736263736263736	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	0.060	-1.225743	0.01530	0.005271	0.028409	ENSG00000149527	ENST00000419816	.	.	.	4.32	-0.385	0.12470	.	2.338380	0.02026	N	0.048201	T	0.09468	0.0233	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23904	-1.0175	6	0.42905	T	0.14	.	1.6475	0.02764	0.1628:0.1426:0.4036:0.291	.	.	.	.	E	580	.	ENSP00000389803:G580E	G	+	2	0	PLCH2	2426116	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.414000	0.07114	0.781000	0.33589	0.491000	0.48974	GGA	G|0.983;A|0.017	0.017	strong		0.662	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638	
OR52E2	119678	hgsc.bcm.edu	37	11	5080234	5080234	+	Silent	SNP	T	T	C	rs2445333	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5080234T>C	ENST00000321522.2	-	1	623	c.624A>G	c.(622-624)ctA>ctG	p.L208L		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	208						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)		TGTCAAACACTAGATTACAAA	0.413													T|||	1525	0.304513	0.4054	0.1599	5008	,	,		23141	0.1746		0.2853	False		,,,				2504	0.4243				p.L208L		Atlas-SNP	.											.	OR52E2	63	.	0			c.A624G						PASS	.	T		1605,2797	497.4+/-363.8	294,1017,890	90.0	79.0	83.0		624	-7.5	0.0	11	dbSNP_100	83	2538,6058	414.1+/-351.3	379,1780,2139	no	coding-synonymous	OR52E2	NM_001005164.2		673,2797,3029	CC,CT,TT		29.5254,36.4607,31.8741		208/326	5080234	4143,8855	2201	4298	6499	SO:0001819	synonymous_variant	119678	exon1			AAACACTAGATTA	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.624A>G	11.37:g.5080234T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	104	55	0.528846	NM_001005164		Silent	SNP	ENST00000321522.2	37	CCDS31371.1																																																																																			T|0.698;C|0.302	0.302	strong		0.413	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20131116	20131116	+	Missense_Mutation	SNP	G	G	A	rs80226867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20131116G>A	ENST00000334554.7	+	10	2104	c.1963G>A	c.(1963-1965)Gcc>Acc	p.A655T	ZDHHC8_ENST00000320602.7_Missense_Mutation_p.A563T|ZDHHC8_ENST00000405930.3_Missense_Mutation_p.A655T	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	655					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					CAGCAGCAACGCCCCGGGGCC	0.726													G|||	252	0.0503195	0.0045	0.0101	5008	,	,		14224	0.0823		0.0527	False		,,,				2504	0.1053				p.A655T		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.G1963A						PASS	.	G	THR/ALA,THR/ALA	51,4313		0,51,2131	17.0	18.0	18.0		1963,1963	2.4	0.9	22	dbSNP_131	18	453,8131		15,423,3854	no	missense,missense	ZDHHC8	NM_001185024.1,NM_013373.3	58,58	15,474,5985	AA,AG,GG		5.2773,1.1687,3.8925	benign,benign	655/779,655/766	20131116	504,12444	2182	4292	6474	SO:0001583	missense	29801	exon10			AGCAACGCCCCGG	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1963G>A	22.37:g.20131116G>A	ENSP00000334490:p.Ala655Thr	Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	34	14	0.411765	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Missense_Mutation	SNP	ENST00000334554.7	37	CCDS13776.1	93	0.042582417582417584	2	0.0040650406504065045	4	0.011049723756906077	42	0.07342657342657342	45	0.059366754617414245	.	10.53	1.376581	0.24857	0.011687	0.052773	ENSG00000099904	ENST00000334554;ENST00000320602;ENST00000405930	T;T;T	0.71934	1.4;-0.61;1.31	4.57	2.4	0.29515	.	0.643418	0.15734	N	0.247275	T	0.14485	0.0350	L	0.51422	1.61	0.33178	D	0.549168	P;B;B	0.44044	0.825;0.133;0.103	P;B;B	0.49502	0.613;0.026;0.017	T	0.53114	-0.8484	10	0.23302	T	0.38	.	6.5739	0.22553	0.1598:0.1473:0.6929:0.0	.	563;655;655	Q9ULC8-2;Q9ULC8-3;Q9ULC8	.;.;ZDHC8_HUMAN	T	655;563;655	ENSP00000334490:A655T;ENSP00000317804:A563T;ENSP00000384716:A655T	ENSP00000317804:A563T	A	+	1	0	ZDHHC8	18511116	0.999000	0.42202	0.882000	0.34594	0.104000	0.19210	4.203000	0.58453	0.893000	0.36288	0.313000	0.20887	GCC	G|0.962;A|0.038	0.038	strong		0.726	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
PARP4	143	hgsc.bcm.edu	37	13	25009441	25009441	+	Missense_Mutation	SNP	C	C	G	rs13428	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:25009441C>G	ENST00000381989.3	-	31	3943	c.3838G>C	c.(3838-3840)Ggt>Cgt	p.G1280R		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1280			G -> R (in dbSNP:rs13428). {ECO:0000269|PubMed:10644454, ECO:0000269|PubMed:8724849}.		cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.G1280R(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TTTTCCACACCTCCACGTTCC	0.388													c|||	1929	0.385184	0.4849	0.3473	5008	,	,		20026	0.3601		0.4125	False		,,,				2504	0.2751				p.G1280R		Atlas-SNP	.											PARP4,NS,carcinoma,0,1	PARP4	142	1	1	Substitution - Missense(1)	stomach(1)	c.G3838C						PASS	.	C	ARG/GLY	2076,2330	570.7+/-382.9	472,1132,599	92.0	98.0	96.0		3838	-1.3	0.0	13	dbSNP_52	96	3204,5396	483.7+/-371.2	594,2016,1690	no	missense	PARP4	NM_006437.3	125	1066,3148,2289	GG,GC,CC		37.2558,47.1176,40.5966	benign	1280/1725	25009441	5280,7726	2203	4300	6503	SO:0001583	missense	143	exon31			CCACACCTCCACG	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3838G>C	13.37:g.25009441C>G	ENSP00000371419:p.Gly1280Arg	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	169	168	0.994083	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	843	0.385989010989011	226	0.45934959349593496	121	0.3342541436464088	181	0.31643356643356646	315	0.4155672823218997	c	3.922	-0.017936	0.07681	0.471176	0.372558	ENSG00000102699	ENST00000381989	T	0.01665	4.7	1.95	-1.34	0.09143	.	1.603710	0.04481	U	0.377866	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.28324	0.207	B	0.21917	0.037	T	0.33033	-0.9884	9	0.34782	T	0.22	0.2916	5.0283	0.14396	0.2244:0.3332:0.4424:0.0	rs13428;rs3190395;rs3742174;rs11557034;rs52831662;rs13428	1280	Q9UKK3	PARP4_HUMAN	R	1280	ENSP00000371419:G1280R	ENSP00000371419:G1280R	G	-	1	0	PARP4	23907441	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.178000	0.03093	-0.420000	0.07427	-0.802000	0.03209	GGT	G|0.405;C|0.595;A|0.000	0.405	strong		0.388	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458598	4458598	+	Missense_Mutation	SNP	G	G	C	rs3809849	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4458598G>C	ENST00000254718.4	-	1	328	c.22C>G	c.(22-24)Cag>Gag	p.Q8E	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.Q8E			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	8	Interaction with MYB. {ECO:0000250}.		Q -> E (in dbSNP:rs3809849).		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						GACATCGGCTGGGCGGGATCC	0.652													C|||	1061	0.211861	0.2496	0.1772	5008	,	,		14645	0.1488		0.2078	False		,,,				2504	0.2546				p.Q8E		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C22G						PASS	.	C	GLU/GLN,GLU/GLN	1012,3384		139,734,1325	13.0	15.0	14.0		22,22	4.1	0.0	17	dbSNP_107	14	1775,6811		198,1379,2716	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	29,29	337,2113,4041	CC,CG,GG		20.6732,23.0209,21.4682	benign,benign	8/1333,8/1329	4458598	2787,10195	2198	4293	6491	SO:0001583	missense	10514	exon1			TCGGCTGGGCGGG	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.22C>G	17.37:g.4458598G>C	ENSP00000254718:p.Gln8Glu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	86	46	0.534884	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	468	0.21428571428571427	118	0.23983739837398374	73	0.20165745856353592	110	0.19230769230769232	167	0.22031662269129287	C	5.998	0.368018	0.11352	0.230209	0.206732	ENSG00000132382	ENST00000381556;ENST00000254718;ENST00000426435	T;T	0.15718	2.4;2.41	4.08	4.08	0.47627	.	0.340848	0.26927	N	0.021789	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	0.37641	-0.9697	9	0.02654	T	1	-25.8904	13.5965	0.61994	0.0:0.842:0.158:0.0	rs3809849;rs3809849	8;8	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	E	8	ENSP00000370968:Q8E;ENSP00000254718:Q8E	ENSP00000254718:Q8E	Q	-	1	0	MYBBP1A	4405347	0.001000	0.12720	0.003000	0.11579	0.001000	0.01503	0.812000	0.27211	1.325000	0.45301	-0.187000	0.12897	CAG	G|0.795;C|0.205	0.205	strong		0.652	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
JRK	8629	hgsc.bcm.edu	37	8	143746416	143746416	+	RNA	SNP	A	A	G	rs754957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143746416A>G	ENST00000507178.2	-	0	1394							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				tgtagcgggcatgggggccct	0.612													G|||	2671	0.533347	0.7209	0.3213	5008	,	,		18399	0.5188		0.3917	False		,,,				2504	0.591				p.H354H		Atlas-SNP	.											.	.	.	.	0			c.T1062C						PASS	.	G	,	2462,1536		789,884,326	8.0	9.0	9.0		1062,1062	-0.7	0.0	8	dbSNP_86	9	3105,5209		657,1791,1709	yes	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	1446,2675,2035	GG,GA,AA		37.3466,38.4192,45.216	,	354/557,354/569	143746416	5567,6745	1999	4157	6156			8629	exon2			GCGGGCATGGGGG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746416A>G		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	93	40	0.430108	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				A|0.478;G|0.522	0.522	strong		0.612	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
CASP9	842	hgsc.bcm.edu	37	1	15844615	15844615	+	Silent	SNP	A	A	G	rs1132312	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15844615A>G	ENST00000333868.5	-	2	502	c.408T>C	c.(406-408)ttT>ttC	p.F136F	CASP9_ENST00000375890.4_Silent_p.F53F|CASP9_ENST00000348549.5_Silent_p.F136F|CASP9_ENST00000546424.1_Silent_p.F136F|CASP9_ENST00000469637.1_5'Flank	NM_001229.3	NP_001220.2	P55211	CASP9_HUMAN	caspase 9, apoptosis-related cysteine peptidase	136			F -> L (in dbSNP:rs1820204).		activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell apoptotic process (GO:0034349)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of apoptotic process (GO:0042981)|regulation of response to DNA damage stimulus (GO:2001020)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|signal transduction in response to DNA damage (GO:0042770)	apoptosome (GO:0043293)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|enzyme activator activity (GO:0008047)|peptidase activity (GO:0008233)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)	p.F136F(1)		central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|stomach(1)	18		Breast(348;0.000207)|all_lung(284;0.000211)|Colorectal(325;0.000259)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;8.49e-07)|COAD - Colon adenocarcinoma(227;4.36e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00013)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00763)|READ - Rectum adenocarcinoma(331;0.0655)		CGACATCACCAAATCCTCCAG	0.507													G|||	2929	0.584864	0.739	0.4986	5008	,	,		18823	0.6538		0.5149	False		,,,				2504	0.4387				p.F136F		Atlas-SNP	.											CASP9,NS,carcinoma,0,1	CASP9	40	1	1	Substitution - coding silent(1)	stomach(1)	c.T408C						PASS	.	G	,	3099,1307	441.8+/-346.5	1100,899,204	113.0	101.0	105.0		408,159	-3.0	0.0	1	dbSNP_92	105	4542,4058	559.4+/-387.4	1215,2112,973	no	coding-synonymous,coding-synonymous	CASP9	NM_001229.3,NM_032996.2	,	2315,3011,1177	GG,GA,AA		47.186,29.6641,41.2502	,	136/417,53/334	15844615	7641,5365	2203	4300	6503	SO:0001819	synonymous_variant	842	exon2			ATCACCAAATCCT	U60521	CCDS158.1, CCDS159.1, CCDS159.2, CCDS59995.1	1p36.21	2012-04-17	2005-08-17		ENSG00000132906	ENSG00000132906		"""Caspases"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 56"""	602234	"""caspase 9, apoptosis-related cysteine protease"""			8663294, 9390557	Standard	NM_001229		Approved	MCH6, ICE-LAP6, APAF-3, PPP1R56	uc001awn.4	P55211	OTTHUMG00000002256	ENST00000333868.5:c.408T>C	1.37:g.15844615A>G		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	130	121	0.930769	NM_001229	B4E1A3|O95348|Q53Y70|Q5JRU9|Q5UGI1|Q92852|Q9BQ62|Q9UEQ3|Q9UIJ8	Silent	SNP	ENST00000333868.5	37	CCDS158.1																																																																																			G|0.589;A|0.411	0.589	strong		0.507	CASP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006438.1	NM_032996	
EDARADD	128178	hgsc.bcm.edu	37	1	236645670	236645670	+	Silent	SNP	C	C	T	rs604070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:236645670C>T	ENST00000334232.4	+	6	536	c.369C>T	c.(367-369)gaC>gaT	p.D123D	EDARADD_ENST00000359362.5_Silent_p.D113D	NM_145861.2	NP_665860.2	Q8WWZ3	EDAD_HUMAN	EDAR-associated death domain	123	Death.				cell differentiation (GO:0030154)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)|trachea gland development (GO:0061153)	cytoplasm (GO:0005737)				endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|stomach(1)	12	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.0232)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ACTTACTAGACGTGATCAGGA	0.488													C|||	667	0.133187	0.0545	0.1095	5008	,	,		17837	0.1062		0.2753	False		,,,				2504	0.138				p.D123D		Atlas-SNP	.											.	EDARADD	31	.	0			c.C369T						PASS	.	C	,	354,4052	182.9+/-210.6	13,328,1862	99.0	94.0	95.0		339,369	-5.2	0.3	1	dbSNP_83	95	2113,6487	363.5+/-333.2	275,1563,2462	no	coding-synonymous,coding-synonymous	EDARADD	NM_080738.3,NM_145861.2	,	288,1891,4324	TT,TC,CC		24.5698,8.0345,18.9682	,	113/206,123/216	236645670	2467,10539	2203	4300	6503	SO:0001819	synonymous_variant	128178	exon6			ACTAGACGTGATC	AY028914	CCDS1610.1, CCDS31065.1	1q42.3	2013-05-22			ENSG00000186197	ENSG00000186197			14341	protein-coding gene	gene with protein product		606603				11780064	Standard	NM_145861		Approved		uc001hxu.1	Q8WWZ3	OTTHUMG00000039954	ENST00000334232.4:c.369C>T	1.37:g.236645670C>T		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	111	68	0.612613	NM_145861	A2VCK5|A8K7B5|B1AL54|B9ZVW5|Q5VYJ7	Silent	SNP	ENST00000334232.4	37	CCDS1610.1																																																																																			C|0.824;T|0.176	0.176	strong		0.488	EDARADD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096368.1	NM_145861	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32632744	32632744	+	Silent	SNP	C	C	T	rs1049082	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32632744C>T	ENST00000399084.1	-	3	388	c.210G>A	c.(208-210)gcG>gcA	p.A70A	HLA-DQB1_ENST00000399079.3_Silent_p.A70A|HLA-DQB1_ENST00000399082.3_Intron|HLA-DQB1_ENST00000434651.2_Silent_p.A70A|HLA-DQB1_ENST00000374943.4_Silent_p.A70A|XXbac-BPG254F23.6_ENST00000443574.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	70	Beta-1.		A -> T (in allele DQB1*03:20; dbSNP:rs45519640).|A -> V (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*06:01, allele DQB1*06:28 and allele DQB1*06:35; dbSNP:rs1063318).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TGTCGAAGCGCGCGTACTCCT	0.607									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1874	0.374201	0.2806	0.4827	5008	,	,		6825	0.4365		0.3897	False		,,,				2504	0.3436				p.A70A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G210A						PASS	.	C		1037,3243		221,595,1324	37.0	37.0	37.0		210	3.1	0.9	6	dbSNP_86	37	3122,5344		846,1430,1957	no	coding-synonymous	HLA-DQB1	NM_002123.4		1067,2025,3281	TT,TC,CC		36.8769,24.229,32.6298		70/262	32632744	4159,8587	2140	4233	6373	SO:0001819	synonymous_variant	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GAAGCGCGCGTAC		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.210G>A	6.37:g.32632744C>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	36	14	0.388889	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1																																																																																			C|0.668;T|0.332	0.332	strong		0.607	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123	
DTX1	1840	hgsc.bcm.edu	37	12	113532617	113532617	+	Silent	SNP	A	A	G	rs12427377	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113532617A>G	ENST00000257600.3	+	6	1754	c.1251A>G	c.(1249-1251)cgA>cgG	p.R417R	DTX1_ENST00000547974.1_3'UTR	NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	417					cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						GCATGGAGCGACTGGTCACAG	0.672													G|||	324	0.0646965	0.0401	0.0879	5008	,	,		14354	0.0		0.1521	False		,,,				2504	0.0583				p.R417R		Atlas-SNP	.											DTX1,NS,carcinoma,0,1	DTX1	83	1	0			c.A1251G						scavenged	.	G		271,4135	780.3+/-414.4	8,255,1940	40.0	37.0	38.0		1251	-4.8	0.9	12	dbSNP_120	38	1261,7339	739.1+/-407.1	94,1073,3133	no	coding-synonymous	DTX1	NM_004416.2		102,1328,5073	GG,GA,AA		14.6628,6.1507,11.7792		417/621	113532617	1532,11474	2203	4300	6503	SO:0001819	synonymous_variant	1840	exon6			GGAGCGACTGGTC	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"""deltex homolog 1 (Drosophila)"""			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.1251A>G	12.37:g.113532617A>G		Somatic	153	2	0.0130719		WXS	Illumina HiSeq	Phase_I	129	70	0.542636	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			A|0.898;G|0.102	0.102	strong		0.672	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2		
ANO1	55107	hgsc.bcm.edu	37	11	70034065	70034065	+	Silent	SNP	C	C	T	rs61731870	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:70034065C>T	ENST00000355303.5	+	26	3221	c.2916C>T	c.(2914-2916)ctC>ctT	p.L972L	ANO1_ENST00000530676.1_Silent_p.L826L|ANO1_ENST00000531349.1_Silent_p.L681L|ANO1_ENST00000398543.2_Silent_p.L826L|ANO1_ENST00000538023.1_Silent_p.L972L|ANO1_ENST00000525494.1_3'UTR|ANO1-AS1_ENST00000524987.1_RNA	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	972					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of membrane potential (GO:0042391)|trachea development (GO:0060438)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(12)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)	29					Crofelemer(DB04941)	CAGACAGCCTCGGCAGCCCAG	0.667													C|||	8	0.00159744	0.0008	0.0043	5008	,	,		14629	0.0		0.004	False		,,,				2504	0.0				p.L972L		Atlas-SNP	.											.	ANO1	156	.	0			c.C2916T						PASS	.	C		0,3988		0,0,1994	10.0	22.0	18.0		2916	-2.4	0.0	11	dbSNP_129	18	38,8242		0,38,4102	no	coding-synonymous	ANO1	NM_018043.5		0,38,6096	TT,TC,CC		0.4589,0.0,0.3097		972/987	70034065	38,12230	1994	4140	6134	SO:0001819	synonymous_variant	55107	exon26			CAGCCTCGGCAGC	BC033036	CCDS44663.1	11q13.2	2014-04-09	2008-08-28	2008-08-28	ENSG00000131620	ENSG00000131620		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	21625	protein-coding gene	gene with protein product		610108	"""oral cancer overexpressed 2"", ""transmembrane protein 16A"""	ORAOV2, TMEM16A		15067359, 18724360, 24692353	Standard	NM_018043		Approved	TAOS2, FLJ10261, DOG1	uc001opj.3	Q5XXA6	OTTHUMG00000167204	ENST00000355303.5:c.2916C>T	11.37:g.70034065C>T		Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Silent	SNP	ENST00000355303.5	37	CCDS44663.1																																																																																			C|0.998;T|0.002	0.002	strong		0.667	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043	
RRP12	23223	hgsc.bcm.edu	37	10	99126513	99126513	+	Silent	SNP	C	C	T	rs45527941	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99126513C>T	ENST00000370992.4	-	27	3312	c.3201G>A	c.(3199-3201)caG>caA	p.Q1067Q	RRP12_ENST00000536831.1_Silent_p.Q785Q|RRP12_ENST00000479481.1_5'UTR|RRP12_ENST00000315563.6_Silent_p.Q967Q|RRP12_ENST00000414986.1_Silent_p.Q1006Q	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1067	Glu-rich.					integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CACCTTTGCCCTGGGCGGGct	0.672													C|||	128	0.0255591	0.0038	0.0548	5008	,	,		15272	0.0		0.0716	False		,,,				2504	0.0133				p.Q1067Q		Atlas-SNP	.											.	RRP12	97	.	0			c.G3201A						PASS	.	C	,	58,4348	56.2+/-92.4	0,58,2145	70.0	82.0	78.0		3018,3201	4.8	1.0	10	dbSNP_127	78	501,8099	143.6+/-199.6	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	17,525,5961	TT,TC,CC		5.8256,1.3164,4.298	,	1006/1237,1067/1298	99126513	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon27			TTTGCCCTGGGCG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3201G>A	10.37:g.99126513C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	62	36	0.580645	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			C|0.962;T|0.038	0.038	strong		0.672	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
LIN9	286826	hgsc.bcm.edu	37	1	226474132	226474132	+	Silent	SNP	G	G	A	rs10799347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:226474132G>A	ENST00000328205.5	-	6	1019	c.474C>T	c.(472-474)ttC>ttT	p.F158F	LIN9_ENST00000481685.1_Silent_p.F123F|LIN9_ENST00000366801.1_Silent_p.F107F	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	142	Sufficient for interaction with RB1.				DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|transcriptional repressor complex (GO:0017053)				breast(3)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.158)			GBM - Glioblastoma multiforme(131;0.131)		GACATACACAGAAGTCATTAT	0.323													G|||	3543	0.707468	0.7542	0.6657	5008	,	,		17002	0.745		0.6799	False		,,,				2504	0.6636				p.F158F	Ovarian(197;1696 2974 11248 14117)	Atlas-SNP	.											.	LIN9	57	.	0			c.C474T						PASS	.	G		3263,1141	706.0+/-407.3	1196,871,135	58.0	63.0	62.0		474	-1.2	1.0	1	dbSNP_120	62	5897,2699	678.4+/-403.5	2018,1861,419	no	coding-synonymous	LIN9	NM_173083.2		3214,2732,554	AA,AG,GG		31.3983,25.9083,29.5385		158/559	226474132	9160,3840	2202	4298	6500	SO:0001819	synonymous_variant	286826	exon6			TACACAGAAGTCA	AY166858	CCDS1553.1	1q42	2014-07-17	2014-07-17		ENSG00000183814	ENSG00000183814			30830	protein-coding gene	gene with protein product	"""TUDOR gene similar"", ""rb related pathway actor"""	609375	"""lin-9 homolog (C. elegans)"""			15538385, 23667535	Standard	NM_173083		Approved	TGS	uc001hqa.3	Q5TKA1	OTTHUMG00000037557	ENST00000328205.5:c.474C>T	1.37:g.226474132G>A		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	53	27	0.509434	NM_173083	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Silent	SNP	ENST00000328205.5	37	CCDS1553.1																																																																																			G|0.296;A|0.704	0.704	strong		0.323	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083	
SLC2A10	81031	hgsc.bcm.edu	37	20	45354291	45354291	+	Missense_Mutation	SNP	G	G	A	rs2235491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:45354291G>A	ENST00000359271.2	+	2	866	c.616G>A	c.(616-618)Gcc>Acc	p.A206T		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	206			A -> T (associated with lower insulin level; dbSNP:rs2235491).		glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				GGGAGGTGAGGCCCCCAAGCT	0.632													G|||	875	0.17472	0.3109	0.1916	5008	,	,		20843	0.1161		0.0497	False		,,,				2504	0.1677				p.A206T		Atlas-SNP	.											.	SLC2A10	75	.	0			c.G616A	GRCh37	CM032381	SLC2A10	M	rs2235491	PASS	.	G	THR/ALA	1151,3255	399.7+/-331.3	156,839,1208	58.0	50.0	53.0		616	-0.6	0.0	20	dbSNP_98	53	379,8221	122.2+/-181.2	7,365,3928	yes	missense	SLC2A10	NM_030777.3	58	163,1204,5136	AA,AG,GG		4.407,26.1235,11.7638	benign	206/542	45354291	1530,11476	2203	4300	6503	SO:0001583	missense	81031	exon2			GGTGAGGCCCCCA	AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"""Solute carriers"""	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.616G>A	20.37:g.45354291G>A	ENSP00000352216:p.Ala206Thr	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	58	30	0.517241	NM_030777	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	37	CCDS13402.1	312	0.14285714285714285	165	0.3353658536585366	51	0.1408839779005525	57	0.09965034965034965	39	0.051451187335092345	G	7.293	0.611374	0.14066	0.261235	0.04407	ENSG00000197496	ENST00000359271	T	0.74421	-0.84	6.0	-0.597	0.11653	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	7.689020	0.00357	N	0.000036	T	0.00012	0.0000	L	0.28054	0.825	0.80722	P	0.0	B	0.06786	0.001	B	0.12156	0.007	T	0.06881	-1.0802	9	0.13853	T	0.58	-0.0159	3.0227	0.06080	0.2397:0.1119:0.533:0.1154	rs2235491	206	O95528	GTR10_HUMAN	T	206	ENSP00000352216:A206T	ENSP00000352216:A206T	A	+	1	0	SLC2A10	44787698	0.013000	0.17824	0.033000	0.17914	0.656000	0.38851	0.261000	0.18442	-0.303000	0.08856	0.609000	0.83330	GCC	G|0.878;A|0.122	0.122	strong		0.632	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2		
OR5M1	390168	hgsc.bcm.edu	37	11	56380134	56380134	+	Missense_Mutation	SNP	C	C	G	rs4939078	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56380134C>G	ENST00000526538.1	-	1	844	c.845G>C	c.(844-846)aGc>aCc	p.S282T		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, member 1	282			S -> T (in dbSNP:rs4939078).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						CAGCATTGGGCTCAAAAAAGT	0.398													C|||	2095	0.418331	0.1815	0.5605	5008	,	,		17293	0.622		0.3141	False		,,,				2504	0.5348				p.S282T		Atlas-SNP	.											.	OR5M1	92	.	0			c.G845C						PASS	.	C	THR/SER	726,2938		76,574,1182	181.0	175.0	177.0		845	2.8	0.9	11	dbSNP_111	177	2452,5744		372,1708,2018	no	missense	OR5M1	NM_001004740.1	58	448,2282,3200	GG,GC,CC		29.917,19.8144,26.796	probably-damaging	282/316	56380134	3178,8682	1832	4098	5930	SO:0001583	missense	390168	exon1			ATTGGGCTCAAAA	AB065742	CCDS53631.1	11q11	2012-08-09				ENSG00000255012		"""GPCR / Class A : Olfactory receptors"""	8352	protein-coding gene	gene with protein product							Standard	NM_001004740		Approved	OST050	uc001nja.1	Q8NGP8		ENST00000526538.1:c.845G>C	11.37:g.56380134C>G	ENSP00000435416:p.Ser282Thr	Somatic	385	0	0		WXS	Illumina HiSeq	Phase_I	356	158	0.44382	NM_001004740	Q6IF60|Q96RB6	Missense_Mutation	SNP	ENST00000526538.1	37	CCDS53631.1	867	0.39697802197802196	77	0.1565040650406504	198	0.5469613259668509	354	0.6188811188811189	238	0.31398416886543534	C	12.26	1.884258	0.33255	0.198144	0.29917	ENSG00000255012	ENST00000526538	T	0.38240	1.15	3.71	2.77	0.32553	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00205	-1.85	0.41029	P	0.014854000000000034	D	0.67145	0.996	D	0.68039	0.955	T	0.15065	-1.0450	8	0.72032	D	0.01	.	6.8855	0.24197	0.1801:0.4941:0.3259:0.0	rs4939078	282	Q8NGP8	OR5M1_HUMAN	T	282	ENSP00000435416:S282T	ENSP00000435416:S282T	S	-	2	0	OR5M1	56136710	0.001000	0.12720	0.879000	0.34478	0.505000	0.33919	0.674000	0.25218	0.775000	0.33450	0.280000	0.19369	AGC	C|0.621;G|0.379	0.379	strong		0.398	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740	
LRRC23	10233	hgsc.bcm.edu	37	12	7022085	7022085	+	Missense_Mutation	SNP	T	T	A	rs1057077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7022085T>A	ENST00000007969.8	+	7	1170	c.950T>A	c.(949-951)gTg>gAg	p.V317E	ENO2_ENST00000535366.1_5'Flank|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000541477.1_5'Flank|ENO2_ENST00000538763.1_5'Flank|ENO2_ENST00000229277.1_5'Flank|ENO2_ENST00000544774.1_5'Flank|LRRC23_ENST00000429740.1_Intron|LRRC23_ENST00000436789.1_Intron|LRRC23_ENST00000443597.2_Missense_Mutation_p.V317E|LRRC23_ENST00000323702.5_Intron	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	317	LRRCT.		V -> E (in dbSNP:rs1057077).							NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						GAGGCTGATGTGATTCGACAG	0.557													A|||	2010	0.401358	0.7141	0.2752	5008	,	,		-128	0.2579		0.2952	False		,,,				2504	0.3252				p.V317E		Atlas-SNP	.											.	LRRC23	46	.	0			c.T950A						PASS	.	A	GLU/VAL,,GLU/VAL	2718,1688	510.6+/-367.6	851,1016,336	157.0	157.0	157.0		950,,950	5.3	1.0	12	dbSNP_86	157	2410,6190	699.6+/-405.1	350,1710,2240	yes	missense,intron,missense	LRRC23	NM_001135217.1,NM_006992.3,NM_201650.2	121,,121	1201,2726,2576	AA,AT,TT		28.0233,38.3114,39.428	benign,,benign	317/344,,317/344	7022085	5128,7878	2203	4300	6503	SO:0001583	missense	10233	exon7			CTGATGTGATTCG	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.950T>A	12.37:g.7022085T>A	ENSP00000007969:p.Val317Glu	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	45	25	0.555556	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	830	0.38003663003663	340	0.6910569105691057	125	0.3453038674033149	142	0.24825174825174826	223	0.2941952506596306	A	0.372	-0.933309	0.02359	0.616886	0.280233	ENSG00000010626	ENST00000007969;ENST00000443597	T;T	0.52526	0.66;0.66	5.27	5.27	0.74061	.	.	.	.	.	T	0.00012	0.0000	N	0.00082	-2.215	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45279	-0.9272	8	0.02654	T	1	-19.078	11.9037	0.52699	0.8693:0.0:0.0:0.1307	rs1057077;rs3759354;rs52834149;rs1057077	317	Q53EV4	LRC23_HUMAN	E	317	ENSP00000007969:V317E;ENSP00000390932:V317E	ENSP00000007969:V317E	V	+	2	0	LRRC23	6892346	1.000000	0.71417	0.979000	0.43373	0.029000	0.11900	4.721000	0.61951	0.931000	0.37242	-0.376000	0.06991	GTG	T|0.598;A|0.402	0.402	strong		0.557	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
NOTCH2	4853	hgsc.bcm.edu	37	1	120458161	120458161	+	Nonsense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:120458161G>C	ENST00000256646.2	-	34	7403	c.7184C>G	c.(7183-7185)tCa>tGa	p.S2395*		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2395					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)		AGCAGCATTTGAGGAAGCATA	0.567			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.S2395X		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C7184G						PASS	.						123.0	108.0	113.0					1																	120458161		2203	4300	6503	SO:0001587	stop_gained	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GCATTTGAGGAAG	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.7184C>G	1.37:g.120458161G>C	ENSP00000256646:p.Ser2395*	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	125	51	0.408	NM_024408	Q5T3X7|Q99734|Q9H240	Nonsense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	48	14.309534	0.99789	.	.	ENSG00000134250	ENST00000256646	.	.	.	5.35	5.35	0.76521	.	0.000000	0.30879	U	0.008688	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.2129	0.82178	0.0:0.0:1.0:0.0	.	.	.	.	X	2395	.	ENSP00000256646:S2395X	S	-	2	0	NOTCH2	120259684	1.000000	0.71417	0.953000	0.39169	0.975000	0.68041	9.145000	0.94634	2.506000	0.84524	0.591000	0.81541	TCA	.	.	none		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
PLCE1	51196	hgsc.bcm.edu	37	10	95931011	95931011	+	Missense_Mutation	SNP	A	A	G	rs61751494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:95931011A>G	ENST00000371380.3	+	3	1802	c.1567A>G	c.(1567-1569)Atc>Gtc	p.I523V	PLCE1_ENST00000371385.3_Missense_Mutation_p.I215V|PLCE1_ENST00000260766.3_Missense_Mutation_p.I523V|PLCE1_ENST00000371375.1_Missense_Mutation_p.I215V			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	523					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)				CAAGGAGCTGATCGATCTGCA	0.547													A|||	4	0.000798722	0.0	0.0014	5008	,	,		19426	0.0		0.003	False		,,,				2504	0.0				p.I523V		Atlas-SNP	.											.	PLCE1	543	.	0			c.A1567G						PASS	.	A	VAL/ILE,VAL/ILE	1,4009		0,1,2004	131.0	130.0	130.0		643,1567	5.7	1.0	10	dbSNP_129	130	29,8301		0,29,4136	yes	missense,missense	PLCE1	NM_001165979.1,NM_016341.3	29,29	0,30,6140	GG,GA,AA		0.3481,0.0249,0.2431	benign,benign	215/1995,523/2303	95931011	30,12310	2005	4165	6170	SO:0001583	missense	51196	exon4			GAGCTGATCGATC		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.1567A>G	10.37:g.95931011A>G	ENSP00000360431:p.Ile523Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	147	84	0.571429	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	A	6.986	0.551950	0.13374	2.49E-4	0.003481	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.32515	1.45;1.45;1.45;1.45	5.71	5.71	0.89125	Guanine-nucleotide dissociation stimulator CDC25 (1);Ras guanine nucleotide exchange factor, domain (1);	0.202476	0.42964	D	0.000633	T	0.15998	0.0385	N	0.17082	0.46	0.28138	N	0.929892	B;B;B	0.12630	0.006;0.002;0.006	B;B;B	0.09377	0.003;0.004;0.002	T	0.14531	-1.0469	10	0.20046	T	0.44	.	5.7292	0.18030	0.7122:0.1472:0.1406:0.0	rs61751494	523;215;523	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	V	523;523;215;215	ENSP00000260766:I523V;ENSP00000360431:I523V;ENSP00000360438:I215V;ENSP00000360426:I215V	ENSP00000260766:I523V	I	+	1	0	PLCE1	95921001	0.998000	0.40836	0.998000	0.56505	0.263000	0.26337	0.905000	0.28504	2.172000	0.68678	0.460000	0.39030	ATC	A|0.996;G|0.004	0.004	strong		0.547	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341	
ITPR2	3709	hgsc.bcm.edu	37	12	26784850	26784850	+	Silent	SNP	G	G	A	rs2230372	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:26784850G>A	ENST00000381340.3	-	22	3299	c.2883C>T	c.(2881-2883)caC>caT	p.H961H	RP11-666F17.1_ENST00000414098.2_RNA|ITPR2_ENST00000545902.1_5'Flank	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	961					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)	TCACATCCTCGTGCTCGGTGG	0.517													G|||	2468	0.492812	0.5393	0.3285	5008	,	,		18215	0.3839		0.497	False		,,,				2504	0.6544				p.H961H		Atlas-SNP	.											.	ITPR2	270	.	0			c.C2883T						PASS	.	G		2377,1783		685,1007,388	123.0	131.0	128.0		2883	-10.1	0.0	12	dbSNP_98	128	4188,4244		1077,2034,1105	no	coding-synonymous	ITPR2	NM_002223.2		1762,3041,1493	AA,AG,GG		49.6679,42.8606,47.8637		961/2702	26784850	6565,6027	2080	4216	6296	SO:0001819	synonymous_variant	3709	exon22			ATCCTCGTGCTCG	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.2883C>T	12.37:g.26784850G>A		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	105	41	0.390476	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.527;A|0.473	0.473	strong		0.517	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
PPP2R3A	5523	hgsc.bcm.edu	37	3	135720673	135720673	+	Silent	SNP	T	T	C	rs9872542	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:135720673T>C	ENST00000264977.3	+	2	950	c.333T>C	c.(331-333)gaT>gaC	p.D111D	PPP2R3A_ENST00000490467.1_Intron	NM_001190447.1|NM_002718.4	NP_001177376.1|NP_002709.2	Q06190	P2R3A_HUMAN	protein phosphatase 2, regulatory subunit B'', alpha	111					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein catabolic process (GO:0045732)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|somite development (GO:0061053)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	protein phosphatase type 2A complex (GO:0000159)	calcium ion binding (GO:0005509)|protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|cervix(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ACTTAAAGGATATTGCAGGAG	0.423													C|||	936	0.186901	0.202	0.1455	5008	,	,		21751	0.0288		0.2783	False		,,,				2504	0.2648				p.D111D		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.T333C						PASS	.	C	,	954,3452	727.3+/-409.8	99,756,1348	42.0	43.0	43.0		,333	5.8	1.0	3	dbSNP_119	43	2713,5885	678.3+/-403.4	417,1879,2003	no	intron,coding-synonymous	PPP2R3A	NM_001190447.1,NM_002718.4	,	516,2635,3351	CC,CT,TT		31.5538,21.6523,28.199	,	,111/1151	135720673	3667,9337	2203	4299	6502	SO:0001819	synonymous_variant	5523	exon2			AAAGGATATTGCA	L12146	CCDS3087.1, CCDS3088.1, CCDS54642.1	3q22.2-q22.3	2013-01-10	2010-06-18	2002-04-26	ENSG00000073711	ENSG00000073711	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""EF-hand domain containing"""	9307	protein-coding gene	gene with protein product		604944	"""protein phosphatase 2 (formerly 2A), regulatory subunit B'' (PR 72), alpha isoform and (PR 130), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', alpha"""	PPP2R3		8392071	Standard	NM_002718		Approved		uc003eqv.2	Q06190	OTTHUMG00000159766	ENST00000264977.3:c.333T>C	3.37:g.135720673T>C		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	31	0.430556	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Silent	SNP	ENST00000264977.3	37	CCDS3087.1																																																																																			T|0.802;C|0.198	0.198	strong		0.423	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718	
DENND6B	414918	hgsc.bcm.edu	37	22	50751529	50751529	+	Silent	SNP	G	G	C	rs67248662	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50751529G>C	ENST00000413817.3	-	17	1427	c.1356C>G	c.(1354-1356)ccC>ccG	p.P452P	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	452					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										GCTGGATCTGGGGGGGAGTCT	0.632													g|||	1535	0.30651	0.236	0.3242	5008	,	,		13163	0.2669		0.2962	False		,,,				2504	0.4407				p.P452P		Atlas-SNP	.											FAM116B,caecum,carcinoma,0,1	.	.	1	0			c.C1356G						PASS	.			921,3213		97,727,1243	18.0	23.0	21.0		1356	0.6	1.0	22	dbSNP_130	21	2300,6000		340,1620,2190	no	coding-synonymous	FAM116B	NM_001001794.3		437,2347,3433	CC,CG,GG		27.7108,22.2787,25.9048		452/586	50751529	3221,9213	2067	4150	6217	SO:0001819	synonymous_variant	414918	exon17			GATCTGGGGGGGA	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.1356C>G	22.37:g.50751529G>C		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	114	65	0.570175	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1																																																																																			G|0.713;C|0.287	0.287	strong		0.632	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
C10orf71	118461	hgsc.bcm.edu	37	10	50534350	50534350	+	Missense_Mutation	SNP	G	G	A	rs11101095	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50534350G>A	ENST00000374144.3	+	3	4048	c.3760G>A	c.(3760-3762)Gtc>Atc	p.V1254I	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1254			V -> I (in dbSNP:rs11101095).							endometrium(1)	1						CTCGGAGCCTGTCGGGAGGCG	0.711													g|||	516	0.103035	0.0779	0.0735	5008	,	,		12166	0.122		0.1193	False		,,,				2504	0.1217				p.V1254I		Atlas-SNP	.											C10orf71_ENST00000374144,NS,carcinoma,0,1	C10orf71	179	1	0			c.G3760A						PASS	.						2.0	4.0	4.0					10																	50534350		476	1307	1783	SO:0001583	missense	118461	exon3			GAGCCTGTCGGGA	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.3760G>A	10.37:g.50534350G>A	ENSP00000363259:p.Val1254Ile	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	42	19	0.452381	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	233	0.10668498168498168	53	0.10772357723577236	31	0.0856353591160221	60	0.1048951048951049	89	0.11741424802110818	g	4.860	0.159868	0.09287	.	.	ENSG00000177354	ENST00000374144	T	0.04119	3.7	5.81	-10.0	0.00425	.	2.286840	0.02567	N	0.097430	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.23297	-1.0192	7	0.17369	T	0.5	.	12.0882	0.53710	0.7132:0.1795:0.1073:0.0	rs11101095;rs58564182;rs11101095	.	.	.	I	1254	ENSP00000363259:V1254I	ENSP00000363259:V1254I	V	+	1	0	C10orf71	50204356	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.235000	0.17948	-1.922000	0.01067	0.479000	0.44913	GTC	G|0.909;A|0.091	0.091	strong		0.711	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
FCAR	2204	hgsc.bcm.edu	37	19	55401170	55401170	+	Missense_Mutation	SNP	A	A	G	rs16986050	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55401170A>G	ENST00000355524.3	+	5	815	c.805A>G	c.(805-807)Agc>Ggc	p.S269G	FCAR_ENST00000391726.3_Missense_Mutation_p.S161G|FCAR_ENST00000391723.3_3'UTR|FCAR_ENST00000359272.4_Missense_Mutation_p.S257G|CTB-61M7.2_ENST00000594721.1_lincRNA|FCAR_ENST00000391724.3_Missense_Mutation_p.S235G|FCAR_ENST00000391725.3_Missense_Mutation_p.S247G|FCAR_ENST00000345937.4_Missense_Mutation_p.S173G|FCAR_ENST00000482092.2_3'UTR|FCAR_ENST00000353758.4_Missense_Mutation_p.S160G	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for	269			S -> G (in dbSNP:rs16986050). {ECO:0000269|PubMed:17548632}.		immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		ACCGAGCTGGAGCCAACAGAT	0.547													.|||	778	0.155351	0.3434	0.1081	5008	,	,		18910	0.0198		0.1839	False		,,,				2504	0.045				p.S269G		Atlas-SNP	.											FCAR,NS,carcinoma,-2,1	FCAR	110	1	0			c.A805G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,,GLY/SER,GLY/SER	1384,3022	454.9+/-350.8	206,972,1025	154.0	155.0	155.0		805,739,517,769,481,,478,703	0.9	0.0	19	dbSNP_123	155	1522,7078	287.7+/-298.4	135,1252,2913	yes	missense,missense,missense,missense,missense,utr-3,missense,missense	FCAR	NM_002000.2,NM_133269.2,NM_133271.2,NM_133272.2,NM_133273.2,NM_133274.2,NM_133277.2,NM_133278.2	56,56,56,56,56,,56,56	341,2224,3938	GG,GA,AA		17.6977,31.4117,22.3435	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	269/288,247/266,173/192,257/276,161/180,,160/179,235/254	55401170	2906,10100	2203	4300	6503	SO:0001583	missense	2204	exon5			AGCTGGAGCCAAC	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936	ENST00000355524.3:c.805A>G	19.37:g.55401170A>G	ENSP00000347714:p.Ser269Gly	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	29	16	0.551724	NM_002000	Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Missense_Mutation	SNP	ENST00000355524.3	37	CCDS12907.1	363	0.1662087912087912	170	0.34552845528455284	48	0.13259668508287292	10	0.017482517482517484	135	0.17810026385224276	A	9.725	1.160659	0.21538	0.314117	0.176977	ENSG00000186431	ENST00000391726;ENST00000355524;ENST00000391725;ENST00000345937;ENST00000353758;ENST00000359272;ENST00000391724	T;T;T;T;T;T;T	0.04406	3.63;6.77;6.35;4.65;6.45;6.61;6.22	2.95	0.854	0.19007	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B;B;B;B;B	0.34372	0.451;0.307;0.101;0.0;0.199;0.053;0.311	B;B;B;B;B;B;B	0.30179	0.112;0.097;0.039;0.003;0.097;0.021;0.103	T	0.49062	-0.8978	8	0.34782	T	0.22	.	4.7474	0.13043	0.7178:0.0:0.2822:0.0	rs16986050;rs52827522;rs60168829;rs16986050	160;235;161;257;247;173;269	Q92592;Q92593;Q92587;Q9UEK0;Q53X39;P24071-3;P24071	.;.;.;.;.;.;FCAR_HUMAN	G	161;269;247;173;160;257;235	ENSP00000375606:S161G;ENSP00000347714:S269G;ENSP00000375605:S247G;ENSP00000338257:S173G;ENSP00000338058:S160G;ENSP00000352218:S257G;ENSP00000375604:S235G	ENSP00000338257:S173G	S	+	1	0	FCAR	60092982	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	1.154000	0.31688	0.108000	0.17862	-0.379000	0.06801	AGC	A|0.795;G|0.205	0.205	strong		0.547	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000	
RGPD3	653489	hgsc.bcm.edu	37	2	107049604	107049604	+	Silent	SNP	T	T	C	rs200768799	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:107049604T>C	ENST00000409886.3	-	16	2430	c.2343A>G	c.(2341-2343)ccA>ccG	p.P781P	RGPD3_ENST00000304514.7_Silent_p.P781P	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	781					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TGGTAGGAGATGGTGTAGAAT	0.343																																					p.P781P		Atlas-SNP	.											RGPD3_ENST00000304514,NS,carcinoma,-1,2	RGPD3	316	2	0			c.A2343G						scavenged	.						6.0	11.0	10.0					2																	107049604		633	1454	2087	SO:0001819	synonymous_variant	653489	exon16			AGGAGATGGTGTA		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.2343A>G	2.37:g.107049604T>C		Somatic	381	0	0		WXS	Illumina HiSeq	Phase_I	477	116	0.243187	NM_001144013	B8ZZM4	Silent	SNP	ENST00000409886.3	37	CCDS46379.1																																																																																			.	.	weak		0.343	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
ZNF70	7621	hgsc.bcm.edu	37	22	24086026	24086026	+	Silent	SNP	C	C	T	rs41277301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:24086026C>T	ENST00000341976.3	-	2	1762	c.1302G>A	c.(1300-1302)ctG>ctA	p.L434L		NM_021916.2	NP_068735.1	Q9UC06	ZNF70_HUMAN	zinc finger protein 70	434					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	21						GATGGCGAATCAGGTGCGAGC	0.542													c|||	68	0.0135783	0.003	0.0288	5008	,	,		18914	0.0		0.0348	False		,,,				2504	0.0092				p.L434L		Atlas-SNP	.											.	ZNF70	49	.	0			c.G1302A						PASS	.	C		27,4379	33.5+/-64.1	0,27,2176	102.0	106.0	105.0		1302	-0.1	0.7	22	dbSNP_127	105	306,8294	111.2+/-171.5	3,300,3997	no	coding-synonymous	ZNF70	NM_021916.2		3,327,6173	TT,TC,CC		3.5581,0.6128,2.5604		434/447	24086026	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	7621	exon2			GCGAATCAGGTGC	X60077	CCDS13812.1	22q11.23	2013-01-08	2006-05-12		ENSG00000187792	ENSG00000187792		"""Zinc fingers, C2H2-type"""	13140	protein-coding gene	gene with protein product		194544	"""zinc finger protein 70 (Cos17)"""			1639391	Standard	NM_021916		Approved	Cos17, MGC48959	uc002zxs.3	Q9UC06	OTTHUMG00000150739	ENST00000341976.3:c.1302G>A	22.37:g.24086026C>T		Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	149	76	0.510067	NM_021916		Silent	SNP	ENST00000341976.3	37	CCDS13812.1																																																																																			C|0.974;T|0.026	0.026	strong		0.542	ZNF70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319881.1	NM_021916	
DMBT1	1755	hgsc.bcm.edu	37	10	124339378	124339378	+	Missense_Mutation	SNP	A	A	G	rs1969620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124339378A>G	ENST00000338354.3	+	10	1070	c.964A>G	c.(964-966)Aac>Gac	p.N322D	DMBT1_ENST00000368909.3_Missense_Mutation_p.N322D|DMBT1_ENST00000368955.3_Missense_Mutation_p.N322D|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368956.2_Missense_Mutation_p.N322D|DMBT1_ENST00000344338.3_Missense_Mutation_p.N322D|DMBT1_ENST00000330163.4_Missense_Mutation_p.N322D			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	322	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.		N -> D (in dbSNP:rs1969620). {ECO:0000269|PubMed:12353266}.		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)				GCTCACCCACAACTGTGGCCA	0.567													A|||	507	0.101238	0.1339	0.0951	5008	,	,		19316	0.1994		0.006	False		,,,				2504	0.0583				p.N322D	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A964G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN	385,3441		18,349,1546	84.0	83.0	84.0		964,964,964	3.9	0.7	10	dbSNP_92	84	71,8213		0,71,4071	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	23,23,23	18,420,5617	GG,GA,AA		0.8571,10.0627,3.7655	benign,benign,benign	322/1786,322/2414,322/2404	124339378	456,11654	1913	4142	6055	SO:0001583	missense	1755	exon10			ACCCACAACTGTG		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.964A>G	10.37:g.124339378A>G	ENSP00000342210:p.Asn322Asp	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	141	64	0.453901	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		222	0.10164835164835165	62	0.12601626016260162	30	0.08287292817679558	128	0.22377622377622378	2	0.002638522427440633	A	17.31	3.357713	0.61403	0.100627	0.008571	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.45276	0.9;0.9;0.9;0.9;0.9;0.9	3.94	3.94	0.45596	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.00039	0.0001	L	0.52011	1.625	0.09310	P	1.0	B;D;B;D;B	0.62365	0.31;0.989;0.211;0.991;0.231	P;D;B;D;P	0.80764	0.617;0.987;0.165;0.994;0.65	T	0.02646	-1.1129	8	0.38643	T	0.18	.	13.1512	0.59490	1.0:0.0:0.0:0.0	rs1969620;rs3980989;rs52823791;rs1969620	322;322;322;322;322	Q9UGM3-4;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	D	322	ENSP00000342210:N322D;ENSP00000343175:N322D;ENSP00000327747:N322D;ENSP00000357905:N322D;ENSP00000357951:N322D;ENSP00000357952:N322D	ENSP00000331522:N322D	N	+	1	0	DMBT1	124329368	0.999000	0.42202	0.730000	0.30809	0.034000	0.12701	4.137000	0.58010	1.580000	0.49851	0.414000	0.27820	AAC	A|0.909;G|0.091	0.091	strong		0.567	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
SLC9A3	6550	hgsc.bcm.edu	37	5	483564	483564	+	Silent	SNP	A	A	G	rs56098739	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:483564A>G	ENST00000264938.3	-	6	975	c.966T>C	c.(964-966)taT>taC	p.Y322Y	SLC9A3_ENST00000514375.1_Silent_p.Y322Y|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	322					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TGGCCTTCACATACTTCTGAC	0.632													a|||	512	0.102236	0.0068	0.2061	5008	,	,		17448	0.001		0.2793	False		,,,				2504	0.0798				p.Y322Y		Atlas-SNP	.											SLC9A3,NS,carcinoma,0,1	SLC9A3	89	1	0			c.T966C						PASS	.	A		215,4179		4,207,1986	45.0	32.0	37.0		966	-2.6	1.0	5	dbSNP_129	37	2096,6494		276,1544,2475	no	coding-synonymous	SLC9A3	NM_004174.2		280,1751,4461	GG,GA,AA		24.4005,4.893,17.7988		322/835	483564	2311,10673	2197	4295	6492	SO:0001819	synonymous_variant	6550	exon6			CTTCACATACTTC		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.966T>C	5.37:g.483564A>G		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	170	73	0.429412	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			A|0.839;G|0.161	0.161	strong		0.632	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
CIB2	10518	hgsc.bcm.edu	37	15	78398139	78398139	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78398139C>T	ENST00000258930.3	-	5	812	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	CIB2_ENST00000539011.1_Missense_Mutation_p.G119S|CIB2_ENST00000557846.1_Missense_Mutation_p.G113S|CIB2_ENST00000560618.1_Missense_Mutation_p.G119S	NM_006383.2	NP_006374.1	O75838	CIB2_HUMAN	calcium and integrin binding family member 2	162	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						CCCAGCTTGCCGTCACCGTCC	0.617																																					p.G162S		Atlas-SNP	.											.	CIB2	24	.	0			c.G484A						PASS	.						183.0	150.0	161.0					15																	78398139		2196	4293	6489	SO:0001583	missense	10518	exon5			GCTTGCCGTCACC	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.484G>A	15.37:g.78398139C>T	ENSP00000258930:p.Gly162Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	63	27	0.428571	NM_006383	B4DDF0|H0YM71|Q05BT6	Missense_Mutation	SNP	ENST00000258930.3	37	CCDS10296.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457318	0.63401	.	.	ENSG00000136425	ENST00000258930;ENST00000539011	D;D	0.83591	-1.74;-1.74	5.59	5.59	0.84812	EF-hand-like domain (1);	0.239373	0.43110	D	0.000604	D	0.90556	0.7040	M	0.90977	3.165	0.53688	D	0.999973	D;P	0.65815	0.995;0.657	P;B	0.51516	0.672;0.147	D	0.92297	0.5846	10	0.62326	D	0.03	-22.6145	18.5768	0.91158	0.0:1.0:0.0:0.0	.	162;162	B4DDF0;O75838	.;CIB2_HUMAN	S	162;119	ENSP00000258930:G162S;ENSP00000442459:G119S	ENSP00000258930:G162S	G	-	1	0	CIB2	76185194	0.992000	0.36948	0.956000	0.39512	0.792000	0.44763	2.522000	0.45572	2.641000	0.89580	0.591000	0.81541	GGC	.	.	none		0.617	CIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289798.1	NM_006383	
DPF1	8193	hgsc.bcm.edu	37	19	38702950	38702950	+	Silent	SNP	G	G	A	rs11547760	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38702950G>A	ENST00000420980.2	-	10	1068	c.1042C>T	c.(1042-1044)Ctg>Ttg	p.L348L	DPF1_ENST00000355526.4_Silent_p.L382L|DPF1_ENST00000416611.1_Silent_p.L366L|DPF1_ENST00000456296.1_Silent_p.L356L|DPF1_ENST00000414789.1_Silent_p.L300L|DPF1_ENST00000412732.1_Silent_p.L300L	NM_004647.2	NP_004638.2	Q92782	DPF1_HUMAN	D4, zinc and double PHD fingers family 1	348					apoptotic process (GO:0006915)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(1)|skin(1)	7	all_cancers(60;1.24e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			GGGGGACTCAGGCAGTACATG	0.657													N|||	338	0.067492	0.0023	0.0994	5008	,	,		3690	0.0437		0.1103	False		,,,				2504	0.1135				p.L382L		Atlas-SNP	.											.	DPF1	54	.	0			c.C1144T						PASS	.	G	,,	73,4223		2,69,2077	11.0	12.0	12.0		1144,898,1042	3.7	1.0	19	dbSNP_120	12	691,7681		17,657,3512	no	coding-synonymous,coding-synonymous,coding-synonymous	DPF1	NM_001135155.1,NM_001135156.1,NM_004647.2	,,	19,726,5589	AA,AG,GG		8.2537,1.6993,6.0309	,,	382/415,300/333,348/381	38702950	764,11904	2148	4186	6334	SO:0001819	synonymous_variant	8193	exon11			GACTCAGGCAGTA	U43843	CCDS33008.2, CCDS46064.1, CCDS46065.1	19q13.12	2013-01-28			ENSG00000011332	ENSG00000011332		"""Zinc fingers, PHD-type"""	20225	protein-coding gene	gene with protein product		601670				8812431	Standard	XM_005259288		Approved	neuro-d4, NEUD4, BAF45b	uc002ohm.3	Q92782	OTTHUMG00000157164	ENST00000420980.2:c.1042C>T	19.37:g.38702950G>A		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	38	0.5	NM_001135155	B3KSY8|Q08AJ0	Silent	SNP	ENST00000420980.2	37	CCDS33008.2	143	0.06547619047619048	2	0.0040650406504065045	39	0.10773480662983426	24	0.04195804195804196	78	0.10290237467018469	G	9.165	1.019756	0.19355	0.016993	0.082537	ENSG00000011332	ENST00000355526	.	.	.	3.71	3.71	0.42584	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.21930	-1.0231	3	.	.	.	-8.7884	8.48	0.33036	0.1108:0.0:0.8892:0.0	rs11547760	.	.	.	L	374	.	.	P	-	2	0	DPF1	43394790	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.718000	0.54919	1.896000	0.54893	0.579000	0.79373	CCT	G|0.929;A|0.071	0.071	strong		0.657	DPF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347721.1		
C17orf47	284083	hgsc.bcm.edu	37	17	56620501	56620501	+	Silent	SNP	A	A	G	rs17222523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56620501A>G	ENST00000321691.3	-	1	1228	c.1047T>C	c.(1045-1047)caT>caC	p.H349H	RP11-112H10.4_ENST00000580769.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000412945.3_5'Flank|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_5'Flank	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	349										NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					GAACTGTCACATGGTGAGTTG	0.527													A|||	810	0.161741	0.1362	0.1513	5008	,	,		18876	0.1766		0.1809	False		,,,				2504	0.1687				p.H349H		Atlas-SNP	.											.	C17orf47	59	.	0			c.T1047C						PASS	.	A		604,3802	266.2+/-267.1	43,518,1642	139.0	124.0	129.0		1047	-0.7	0.0	17	dbSNP_123	129	1713,6887	312.9+/-311.0	181,1351,2768	no	coding-synonymous	C17orf47	NM_001038704.2		224,1869,4410	GG,GA,AA		19.9186,13.7086,17.8149		349/571	56620501	2317,10689	2203	4300	6503	SO:0001819	synonymous_variant	284083	exon1			TGTCACATGGTGA		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.1047T>C	17.37:g.56620501A>G		Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	170	95	0.558824	NM_001038704	Q8N821	Silent	SNP	ENST00000321691.3	37	CCDS32691.1																																																																																			A|0.825;G|0.175	0.175	strong		0.527	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110035262	110035262	+	Silent	SNP	A	A	G	rs1026608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:110035262A>G	ENST00000278590.3	+	6	1503	c.1452A>G	c.(1450-1452)cgA>cgG	p.R484R	ZC3H12C_ENST00000528673.1_Silent_p.R485R|ZC3H12C_ENST00000453089.2_Silent_p.R453R	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	484							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		ATGTCAAACGAGGTGCTCCAA	0.458													A|||	1103	0.220248	0.2186	0.2161	5008	,	,		23480	0.2004		0.2724	False		,,,				2504	0.1922				p.R484R		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.A1452G						PASS	.	A		807,3057		89,629,1214	106.0	104.0	105.0		1452	-2.8	1.0	11	dbSNP_86	105	2087,6189		246,1595,2297	no	coding-synonymous	ZC3H12C	NM_033390.1		335,2224,3511	GG,GA,AA		25.2175,20.8851,23.8386		484/884	110035262	2894,9246	1932	4138	6070	SO:0001819	synonymous_variant	85463	exon6			CAAACGAGGTGCT		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.1452A>G	11.37:g.110035262A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	77	42	0.545455	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			A|0.746;G|0.254	0.254	strong		0.458	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
ZNF598	90850	hgsc.bcm.edu	37	16	2049640	2049640	+	Missense_Mutation	SNP	A	A	G	rs2286469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2049640A>G	ENST00000563630.1	-	9	1987	c.1745T>C	c.(1744-1746)aTg>aCg	p.M582T	ZNF598_ENST00000562103.1_Missense_Mutation_p.M582T|AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000431526.1_Missense_Mutation_p.M637T			Q86UK7	ZN598_HUMAN	zinc finger protein 598	637							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						CGGGCCCTCCATGTGTCCATT	0.711													G|||	2883	0.575679	0.8533	0.5202	5008	,	,		14090	0.371		0.5616	False		,,,				2504	0.4652				p.M637T		Atlas-SNP	.											ZNF598,NS,carcinoma,0,4	ZNF598	55	4	0			c.T1910C						PASS	.	G	THR/MET	2978,674		1239,500,87	15.0	19.0	18.0		1912	2.7	0.0	16	dbSNP_100	18	4537,3493		1304,1929,782	yes	missense	ZNF598	NM_178167.2	81	2543,2429,869	GG,GA,AA		43.4994,18.4556,35.6703	possibly-damaging	637/905	2049640	7515,4167	1826	4015	5841	SO:0001583	missense	90850	exon11			CCCTCCATGTGTC	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.1745T>C	16.37:g.2049640A>G	ENSP00000455882:p.Met582Thr	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	47	21	0.446809	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		1206	0.5521978021978022	406	0.8252032520325203	177	0.4889502762430939	213	0.3723776223776224	410	0.5408970976253298	.	0.003	-2.398634	0.00198	0.815444	0.565006	ENSG00000167962	ENST00000431526	T	0.15256	2.44	4.67	2.72	0.32119	.	1.291550	0.04967	N	0.463147	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	.	.	.	.	.	.	T	0.31998	-0.9923	6	0.02654	T	1	-0.1002	9.0277	0.36241	0.2363:0.0:0.7637:0.0	rs2286469;rs17857385;rs58709811;rs2286469	.	.	.	T	637	ENSP00000411409:M637T	ENSP00000411409:M637T	M	-	2	0	ZNF598	1989641	0.004000	0.15560	0.018000	0.16275	0.024000	0.10985	1.411000	0.34702	0.234000	0.21139	-0.124000	0.14976	ATG	A|0.429;G|0.571	0.571	strong		0.711	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110534512	110534512	+	Silent	SNP	G	G	A	rs1563578	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110534512G>A	ENST00000378402.5	+	74	12233	c.12129G>A	c.(12127-12129)tcG>tcA	p.S4043S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4043					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTAACATTTCGTCCATGTCTA	0.388										HNSCC(38;0.096)			G|||	1429	0.285343	0.3464	0.3991	5008	,	,		17113	0.3244		0.1412	False		,,,				2504	0.2301				p.S4043S		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+1,1	PKHD1L1	522	1	0			c.G12129A						PASS	.	G		1209,2491		198,813,839	84.0	81.0	82.0		12129	0.8	1.0	8	dbSNP_88	82	1326,6866		117,1092,2887	no	coding-synonymous	PKHD1L1	NM_177531.4		315,1905,3726	AA,AG,GG		16.1865,32.6757,21.3169		4043/4244	110534512	2535,9357	1850	4096	5946	SO:0001819	synonymous_variant	93035	exon74			CATTTCGTCCATG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.12129G>A	8.37:g.110534512G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	65	29	0.446154	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|0.740;A|0.260	0.260	strong		0.388	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
TAF3	83860	hgsc.bcm.edu	37	10	8007260	8007260	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:8007260A>C	ENST00000344293.5	+	3	1993	c.1787A>C	c.(1786-1788)gAa>gCa	p.E596A		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	596	Lys-rich.				maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						AAAGAATTTGAAGATGTTGAT	0.373																																					p.E596A		Atlas-SNP	.											.	TAF3	93	.	0			c.A1787C						PASS	.						78.0	77.0	77.0					10																	8007260		1819	4076	5895	SO:0001583	missense	83860	exon3			AATTTGAAGATGT	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1787A>C	10.37:g.8007260A>C	ENSP00000340271:p.Glu596Ala	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	74	41	0.554054	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	37	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	A	7.734	0.699927	0.15106	.	.	ENSG00000165632	ENST00000344293	T	0.20332	2.08	5.82	5.82	0.92795	.	0.540850	0.18799	N	0.130845	T	0.29158	0.0725	M	0.73962	2.25	0.38863	D	0.956539	B	0.17038	0.02	B	0.15870	0.014	T	0.05903	-1.0857	10	0.39692	T	0.17	-14.8166	15.8582	0.79000	1.0:0.0:0.0:0.0	.	596	Q5VWG9	TAF3_HUMAN	A	596	ENSP00000340271:E596A	ENSP00000340271:E596A	E	+	2	0	TAF3	8047266	0.999000	0.42202	0.941000	0.38009	0.097000	0.18754	3.650000	0.54424	2.232000	0.73038	0.528000	0.53228	GAA	.	.	none		0.373	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923	
ANKS1A	23294	hgsc.bcm.edu	37	6	35048899	35048899	+	Silent	SNP	T	T	C	rs35455943	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35048899T>C	ENST00000360359.3	+	17	2811	c.2673T>C	c.(2671-2673)ccT>ccC	p.P891P	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	891					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						TCCATGACCCTGCGGCACCCT	0.657													C|||	109	0.0217652	0.0507	0.0144	5008	,	,		17797	0.0089		0.0209	False		,,,				2504	0.002				p.P891P		Atlas-SNP	.											.	ANKS1A	123	.	0			c.T2673C						PASS	.	C		207,4199	806.9+/-415.9	3,201,1999	62.0	56.0	58.0		2673	-2.3	0.0	6	dbSNP_126	58	182,8418	810.9+/-407.1	2,178,4120	no	coding-synonymous	ANKS1A	NM_015245.2		5,379,6119	CC,CT,TT		2.1163,4.6981,2.9909		891/1135	35048899	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	23294	exon17			TGACCCTGCGGCA	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2673T>C	6.37:g.35048899T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	49	18	0.367347	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Silent	SNP	ENST00000360359.3	37	CCDS4798.1																																																																																			T|0.970;C|0.030	0.030	strong		0.657	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	
OR5B21	219968	hgsc.bcm.edu	37	11	58275303	58275303	+	Silent	SNP	G	G	A	rs146345059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58275303G>A	ENST00000360374.2	-	1	275	c.276C>T	c.(274-276)taC>taT	p.Y92Y		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	92						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)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CACATCCATCGTAGGAGATGG	0.532													G|||	4	0.000798722	0.0	0.0058	5008	,	,		21630	0.0		0.0	False		,,,				2504	0.0				p.Y92Y		Atlas-SNP	.											OR5B21,rectum,NS,0,1	OR5B21	59	1	0			c.C276T						scavenged	.	G		0,4402		0,0,2201	122.0	96.0	105.0		276	2.2	0.5	11	dbSNP_134	105	8,8582	6.4+/-24.3	0,8,4287	no	coding-synonymous	OR5B21	NM_001005218.1		0,8,6488	AA,AG,GG		0.0931,0.0,0.0616		92/310	58275303	8,12984	2201	4295	6496	SO:0001819	synonymous_variant	219968	exon1			TCCATCGTAGGAG		CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"""GPCR / Class A : Olfactory receptors"""	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.276C>T	11.37:g.58275303G>A		Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	118	54	0.457627	NM_001005218		Silent	SNP	ENST00000360374.2	37	CCDS31552.1																																																																																			G|0.999;A|0.001	0.001	strong		0.532	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218	
WWC3	55841	hgsc.bcm.edu	37	X	10085674	10085674	+	Silent	SNP	T	T	C	rs6530368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:10085674T>C	ENST00000380861.4	+	11	1966	c.1575T>C	c.(1573-1575)gaT>gaC	p.D525D	WWC3_ENST00000454666.1_Silent_p.D525D	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	525					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TCCCCGGGGATGGGGAAGGGC	0.701													C|||	3621	0.959205	0.7572	0.7089	3775	,	,		10616	0.7579		0.663	False		,,,				2504	0.7127				p.D525D		Atlas-SNP	.											.	WWC3	142	.	0			c.T1575C						PASS	.	C		3391,72		1436,59,460,0,13	6.0	6.0	6.0		1575	-8.5	0.0	X	dbSNP_116	6	5349,820		1737,497,1378,39,245	no	coding-synonymous	WWC3	NM_015691.3		3173,556,1838,39,258	CC,CT,C,TT,T		13.2923,2.0791,9.2608		525/1093	10085674	8740,892	1968	3896	5864	SO:0001819	synonymous_variant	55841	exon11			CGGGGATGGGGAA	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1575T>C	X.37:g.10085674T>C		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	17	17	1	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			T|0.061;C|0.939	0.939	strong		0.701	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
KIF1C	10749	hgsc.bcm.edu	37	17	4926882	4926882	+	Silent	SNP	A	A	G	rs346828	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4926882A>G	ENST00000320785.5	+	23	3105	c.2748A>G	c.(2746-2748)ccA>ccG	p.P916P		NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	916					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						CCCCCTCGCCACCACTGTCAA	0.677													A|||	3381	0.67512	0.5204	0.7392	5008	,	,		12936	0.6627		0.7107	False		,,,				2504	0.8149				p.P916P	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											KIF1C,NS,carcinoma,0,1	KIF1C	70	1	0			c.A2748G						PASS	.	A		2475,1923		723,1029,447	30.0	29.0	29.0		2748	-9.8	0.2	17	dbSNP_79	29	6147,2433		2260,1627,403	no	coding-synonymous	KIF1C	NM_006612.5		2983,2656,850	GG,GA,AA		28.3566,43.7244,33.5645		916/1104	4926882	8622,4356	2199	4290	6489	SO:0001819	synonymous_variant	10749	exon23			CTCGCCACCACTG	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.2748A>G	17.37:g.4926882A>G		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	149	58	0.389262	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			A|0.339;G|0.661	0.661	strong		0.677	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
ZNF717	100131827	hgsc.bcm.edu	37	3	75786440	75786440	+	Silent	SNP	C	C	T	rs145944373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:75786440C>T	ENST00000478296.1	-	4	2460	c.2184G>A	c.(2182-2184)ggG>ggA	p.G728G	ZNF717_ENST00000400845.3_Silent_p.G771G|ZNF717_ENST00000491507.1_Intron|ZNF717_ENST00000477374.1_Intron|ZNF717_ENST00000422325.1_Silent_p.G778G|MIR4273_ENST00000582824.1_RNA			Q9BY31	ZN717_HUMAN	zinc finger protein 717	768					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						CTGAGTGAGTCCCCTGATGCG	0.413													c|||	3116	0.622204	0.3684	0.7133	5008	,	,		10213	0.8204		0.7167	False		,,,				2504	0.5992				p.G778G		Atlas-SNP	.											ZNF717,NS,carcinoma,0,1	ZNF717	160	1	0			c.G2334A						scavenged	.						7.0	7.0	7.0					3																	75786440		648	1313	1961	SO:0001819	synonymous_variant	100131827	exon5			GTGAGTCCCCTGA	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965	ENST00000478296.1:c.2184G>A	3.37:g.75786440C>T		Somatic	42	1	0.0238095		WXS	Illumina HiSeq	Phase_I	31	30	0.967742	NM_001128223		Silent	SNP	ENST00000478296.1	37																																																																																				C|0.603;T|0.397	0.397	strong		0.413	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
LRRC37B	114659	hgsc.bcm.edu	37	17	30376271	30376271	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:30376271G>A	ENST00000341671.7	+	10	2539	c.2534G>A	c.(2533-2535)cGa>cAa	p.R845Q	LRRC37B_ENST00000394713.3_Missense_Mutation_p.R794Q|LRRC37B_ENST00000327564.7_Missense_Mutation_p.R872Q|LRRC37B_ENST00000543378.2_Missense_Mutation_p.R763Q|LRRC37B_ENST00000584368.1_Missense_Mutation_p.R806Q	NM_052888.2	NP_443120.2	Q96QE4	LR37B_HUMAN	leucine rich repeat containing 37B	845						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	29		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.111)|Ovarian(249;0.182)|Breast(31;0.244)				CTCATGTTGCGAACAGGCCTC	0.438																																					p.R845Q		Atlas-SNP	.											LRRC37B,colon,carcinoma,+1,1	LRRC37B	67	1	0			c.G2534A						scavenged	.						77.0	68.0	71.0					17																	30376271		2203	4298	6501	SO:0001583	missense	114659	exon10			TGTTGCGAACAGG	AJ314647	CCDS32609.1	17q11.2	2006-11-29		2005-08-09	ENSG00000185158	ENSG00000185158			29070	protein-coding gene	gene with protein product	"""KIAA0563-related"""					11468690, 10843809	Standard	NM_052888		Approved		uc002hgu.3	Q96QE4	OTTHUMG00000132785	ENST00000341671.7:c.2534G>A	17.37:g.30376271G>A	ENSP00000340519:p.Arg845Gln	Somatic	307	0	0		WXS	Illumina HiSeq	Phase_I	331	5	0.0151057	NM_052888	Q17RC9|Q5YKG6	Missense_Mutation	SNP	ENST00000341671.7	37	CCDS32609.1	.	.	.	.	.	.	.	.	.	.	N	4.826	0.153648	0.09185	.	.	ENSG00000185158	ENST00000543378;ENST00000327564;ENST00000394713;ENST00000341671	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	1.78	-1.64	0.08318	.	.	.	.	.	T	0.38825	0.1055	M	0.80183	2.485	0.09310	N	1	P;P	0.47034	0.889;0.889	B;B	0.27076	0.076;0.076	T	0.35773	-0.9775	9	0.22109	T	0.4	.	5.0015	0.14266	0.5756:0.0:0.4244:0.0	.	794;845	Q17RC9;Q96QE4	.;LR37B_HUMAN	Q	763;872;794;845	ENSP00000443345:R763Q;ENSP00000332536:R872Q;ENSP00000378202:R794Q;ENSP00000340519:R845Q	ENSP00000332536:R872Q	R	+	2	0	LRRC37B	27400384	0.007000	0.16637	0.013000	0.15412	0.001000	0.01503	0.282000	0.18829	-0.414000	0.07495	-0.706000	0.03657	CGA	.	.	none		0.438	LRRC37B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446508.1	NM_052888	
KRT40	125115	hgsc.bcm.edu	37	17	39140272	39140272	+	Missense_Mutation	SNP	A	A	G	rs17843015	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39140272A>G	ENST00000398486.2	-	3	414	c.254T>C	c.(253-255)tTc>tCc	p.F85S	KRT40_ENST00000377755.4_Missense_Mutation_p.F85S	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	85	Head.		F -> S (in dbSNP:rs17843015). {ECO:0000269|PubMed:15617563}.			intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				ATTGCTAGTGAACACCCCATC	0.557													A|||	809	0.161542	0.1566	0.1715	5008	,	,		20527	0.1548		0.1302	False		,,,				2504	0.2004				p.F85S		Atlas-SNP	.											.	KRT40	27	.	0			c.T254C						PASS	.	A	SER/PHE	662,3736	251.5+/-258.2	51,560,1588	176.0	176.0	176.0		254	5.1	1.0	17	dbSNP_123	176	928,7644	198.6+/-242.9	52,824,3410	yes	missense	KRT40	NM_182497.3	155	103,1384,4998	GG,GA,AA		10.8259,15.0523,12.2591	benign	85/432	39140272	1590,11380	2199	4286	6485	SO:0001583	missense	125115	exon3			CTAGTGAACACCC	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.254T>C	17.37:g.39140272A>G	ENSP00000381500:p.Phe85Ser	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	162	78	0.481481	NM_182497	Q6IFU5	Missense_Mutation	SNP	ENST00000398486.2	37	CCDS42320.1	334	0.15293040293040294	82	0.16666666666666666	53	0.1464088397790055	95	0.1660839160839161	104	0.13720316622691292	A	15.87	2.959361	0.53400	0.150523	0.108259	ENSG00000204889	ENST00000377755;ENST00000398486	D;D	0.82711	-1.64;-1.64	5.06	5.06	0.68205	.	0.000000	0.35235	N	0.003359	T	0.02012	0.0063	M	0.79258	2.445	0.34665	P	0.276888	P	0.45986	0.87	P	0.59948	0.866	T	0.31251	-0.9950	9	0.72032	D	0.01	.	14.2835	0.66228	1.0:0.0:0.0:0.0	rs17843015	85	Q6A162	K1C40_HUMAN	S	85	ENSP00000366984:F85S;ENSP00000381500:F85S	ENSP00000366984:F85S	F	-	2	0	KRT40	36393798	0.977000	0.34250	0.979000	0.43373	0.589000	0.36550	5.337000	0.65941	2.037000	0.60232	0.482000	0.46254	TTC	A|0.851;G|0.148	0.148	strong		0.557	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32629963	32629963	+	Missense_Mutation	SNP	C	C	T	rs1049100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32629963C>T	ENST00000399082.3	-	2	216	c.172G>A	c.(172-174)Gtc>Atc	p.V58I	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.V148I|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.V148I|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.V148I|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.V148I|HLA-DQB1_ENST00000460185.1_5'Flank|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1-AS1_ENST00000419852.1_RNA			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	148	Beta-1.		Y -> G (in allele DQB1*03:05, allele DQB1*03:17, allele DQB1*04:01, allele DQB1*04:02, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*05:04, allele DQB1*05:05 and allele DQB1*06:23; requires 2 nucleotide substitutions).|Y -> L (in allele DQB1*02:01, allele DQB1*02:02, allele DQB1*02:03, allele DQB1*02:04, allele DQB1*02:05, allele DQB1*03:02, allele DQB1*03:03, allele DQB1*03:06, allele DQB1*03:07, allele DQB1*03:08, allele DQB1*03:11, allele DQB1*03:12, allele DQB1*03:15, allele DQB1*03:18, allele DQB1*03:20, allele DQB1*03:23, allele DQB1*03:25, allele DQB1*03:26, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:05, allele DQB1*06:06, allele DQB1*06:07, allele DQB1*06:08, allele DQB1*06:09, allele DQB1*06:10, allele DQB1*06:11, allele DQB1*06:12, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:17, allele DQB1*06:18, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:21, allele DQB1*06:22, allele DQB1*06:24, allele DQB1*06:25, allele DQB1*06:27, allele DQB1*06:28, allele DQB1*06:29, allele DQB1*06:30, allele DQB1*06:31, allele DQB1*06:32, allele DQB1*06:33, allele DQB1*06:34, allele DQB1*06:36, allele DQB1*06:37, allele DQB1*06:38 and allele DQB1*06:39; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	ACCGAGCAGACCAGCAGGTTG	0.552									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				C|||	1067	0.213059	0.2284	0.1527	5008	,	,		12092	0.244		0.2008	False		,,,				2504	0.2157				p.V148I	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.G442A						PASS	.	C	ILE/VAL	766,3122		97,572,1275	26.0	24.0	25.0		442	3.6	1.0	6	dbSNP_86	25	1351,6891		155,1041,2925	no	missense	HLA-DQB1	NM_002123.4	29	252,1613,4200	TT,TC,CC		16.3917,19.7016,17.4526	benign	148/262	32629963	2117,10013	1944	4121	6065	SO:0001583	missense	3119	exon3	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AGCAGACCAGCAG		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.172G>A	6.37:g.32629963C>T	ENSP00000382032:p.Val58Ile	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	93	71	0.763441	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		444	0.2032967032967033	119	0.241869918699187	69	0.19060773480662985	90	0.15734265734265734	166	0.21899736147757257	.	13.20	2.166325	0.38217	0.197016	0.163917	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.02974	4.09;4.09;4.09;4.09;4.09	4.52	3.64	0.41730	.	0.322278	0.29653	N	0.011558	T	0.01421	0.0046	L	0.49256	1.55	0.37850	P	0.07064300000000001	B;B;B;B	0.18310	0.006;0.003;0.002;0.027	B;B;B;B	0.24701	0.02;0.02;0.02;0.055	T	0.29243	-1.0018	9	0.87932	D	0	.	6.057	0.19816	0.0:0.7833:0.0:0.2166	rs1049100;rs3189191;rs16870489	148;113;148;148	A2AAZ0;A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.;.	I	58;148;148;148;148;84	ENSP00000382032:V58I;ENSP00000382029:V148I;ENSP00000364080:V148I;ENSP00000407332:V148I;ENSP00000382034:V148I	ENSP00000364080:V148I	V	-	1	0	HLA-DQB1	32737941	0.967000	0.33354	1.000000	0.80357	0.683000	0.39861	0.196000	0.17176	2.065000	0.61736	0.313000	0.20887	GTC	C|0.816;T|0.184	0.184	strong		0.552	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
WDR78	79819	hgsc.bcm.edu	37	1	67313249	67313249	+	Silent	SNP	G	G	A	rs57010209	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:67313249G>A	ENST00000371026.3	-	8	1264	c.1209C>T	c.(1207-1209)gaC>gaT	p.D403D	WDR78_ENST00000371023.3_Silent_p.D403D|WDR78_ENST00000431318.1_Silent_p.D149D	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78	403					hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						TAAAAAATAAGTCCTGATGAA	0.323													G|||	1108	0.221246	0.0613	0.1787	5008	,	,		17566	0.5466		0.0338	False		,,,				2504	0.3252				p.D403D		Atlas-SNP	.											.	WDR78	102	.	0			c.C1209T						PASS	.	G	,	285,4121	154.8+/-188.1	9,267,1927	73.0	75.0	75.0		1209,1209	-0.9	1.0	1	dbSNP_129	75	298,8302	107.8+/-168.5	8,282,4010	no	coding-synonymous,coding-synonymous	WDR78	NM_024763.4,NM_207014.2	,	17,549,5937	AA,AG,GG		3.4651,6.4685,4.4825	,	403/849,403/546	67313249	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	79819	exon8			AAATAAGTCCTGA	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.1209C>T	1.37:g.67313249G>A		Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	234	109	0.465812	NM_207014	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Silent	SNP	ENST00000371026.3	37	CCDS635.1																																																																																			G|0.910;A|0.090	0.090	strong		0.323	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	
HAUS6	54801	hgsc.bcm.edu	37	9	19093287	19093287	+	Silent	SNP	A	A	G	rs41269011	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:19093287A>G	ENST00000380502.3	-	4	785	c.318T>C	c.(316-318)agT>agC	p.S106S	HAUS6_ENST00000380496.1_5'Flank	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	106					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)		p.S106S(1)		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						GAGGAAAGCTACTTCCACATT	0.323													A|||	585	0.116813	0.0976	0.2046	5008	,	,		18063	0.0744		0.1034	False		,,,				2504	0.138				p.S106S		Atlas-SNP	.											HAUS6,NS,carcinoma,0,1	HAUS6	66	1	1	Substitution - coding silent(1)	stomach(1)	c.T318C						PASS	.	A		448,3958	212.8+/-232.6	23,402,1778	60.0	55.0	57.0		318	0.6	1.0	9	dbSNP_127	57	1177,7415	238.3+/-269.8	63,1051,3182	no	coding-synonymous	HAUS6	NM_017645.3		86,1453,4960	GG,GA,AA		13.6988,10.168,12.5019		106/956	19093287	1625,11373	2203	4296	6499	SO:0001819	synonymous_variant	54801	exon4			AAAGCTACTTCCA	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.318T>C	9.37:g.19093287A>G		Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	250	132	0.528	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			A|0.878;G|0.122	0.122	strong		0.323	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
TOPBP1	11073	hgsc.bcm.edu	37	3	133341988	133341988	+	Missense_Mutation	SNP	T	T	C	rs10935070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:133341988T>C	ENST00000260810.5	-	19	3256	c.3125A>G	c.(3124-3126)aAt>aGt	p.N1042S		NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	1042			N -> S (in dbSNP:rs10935070).		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						CTCTTTATTATTGGTGGCCAT	0.289								Other conserved DNA damage response genes					T|||	941	0.187899	0.0106	0.2997	5008	,	,		17163	0.0258		0.3588	False		,,,				2504	0.3395				p.N1042S	Ovarian(21;193 658 4424 15423 17362)	Atlas-SNP	.											.	TOPBP1	218	.	0			c.A3125G						PASS	.	T	SER/ASN	212,3394		4,204,1595	40.0	37.0	38.0		3125	-9.4	0.0	3	dbSNP_120	38	2657,5461		434,1789,1836	yes	missense	TOPBP1	NM_007027.3	46	438,1993,3431	CC,CT,TT		32.7297,5.8791,24.4712	benign	1042/1523	133341988	2869,8855	1803	4059	5862	SO:0001583	missense	11073	exon19			TTATTATTGGTGG	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.3125A>G	3.37:g.133341988T>C	ENSP00000260810:p.Asn1042Ser	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	108	58	0.537037	NM_007027	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	389	0.17811355311355312	6	0.012195121951219513	94	0.2596685082872928	18	0.03146853146853147	271	0.3575197889182058	T	2.223	-0.377961	0.05000	0.058791	0.327297	ENSG00000163781	ENST00000260810	T	0.11385	2.78	5.82	-9.36	0.00629	.	1.012260	0.07897	N	0.972048	T	0.00012	0.0000	N	0.12182	0.205	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46652	-0.9176	9	0.07813	T	0.8	.	20.6666	0.99681	0.0:0.0977:0.0:0.9023	rs10935070;rs17301444;rs52791815;rs61344352;rs10935070	955;1042	A0AV47;Q92547	.;TOPB1_HUMAN	S	1042	ENSP00000260810:N1042S	ENSP00000260810:N1042S	N	-	2	0	TOPBP1	134824678	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.948000	0.00679	-2.029000	0.00930	-0.250000	0.11733	AAT	T|0.819;C|0.181	0.181	strong		0.289	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1	NM_007027	
STAB2	55576	hgsc.bcm.edu	37	12	104123911	104123911	+	Silent	SNP	C	C	T	rs10778281	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:104123911C>T	ENST00000388887.2	+	49	5304	c.5100C>T	c.(5098-5100)aaC>aaT	p.N1700N		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TGTATATAAACAATAAGGCTA	0.338													T|||	1424	0.284345	0.6702	0.2522	5008	,	,		17391	0.0367		0.1511	False		,,,				2504	0.1779				p.N1700N		Atlas-SNP	.											.	STAB2	370	.	0			c.C5100T						PASS	.	T		2627,1779	525.4+/-371.6	785,1057,361	120.0	140.0	134.0		5100	3.4	1.0	12	dbSNP_120	134	1197,7403	763.6+/-407.6	76,1045,3179	no	coding-synonymous	STAB2	NM_017564.9		861,2102,3540	TT,TC,CC		13.9186,40.3768,29.4018		1700/2552	104123911	3824,9182	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon49			TATAAACAATAAG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.5100C>T	12.37:g.104123911C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	47	17	0.361702	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.717;T|0.283	0.283	strong		0.338	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
TECTA	7007	hgsc.bcm.edu	37	11	120989335	120989335	+	Missense_Mutation	SNP	A	A	G	rs612969	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:120989335A>G	ENST00000392793.1	+	7	1382	c.1111A>G	c.(1111-1113)Aga>Gga	p.R371G	TECTA_ENST00000264037.2_Missense_Mutation_p.R371G			O75443	TECTA_HUMAN	tectorin alpha	371	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.		R -> G (in dbSNP:rs612969). {ECO:0000269|PubMed:10987647, ECO:0000269|PubMed:9590290}.		cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGAACACCGCAGAGGTTCAGC	0.547													G|||	2220	0.443291	0.7428	0.3818	5008	,	,		19359	0.246		0.4314	False		,,,				2504	0.2975				p.R371G		Atlas-SNP	.											.	TECTA	329	.	0			c.A1111G						PASS	.	G	GLY/ARG	2922,1484	474.6+/-357.0	963,996,244	93.0	93.0	93.0		1111	3.9	0.0	11	dbSNP_83	93	3545,5053	629.9+/-398.3	740,2065,1494	yes	missense	TECTA	NM_005422.2	125	1703,3061,1738	GG,GA,AA		41.2305,33.6813,49.7309	benign	371/2156	120989335	6467,6537	2203	4299	6502	SO:0001583	missense	7007	exon6			CACCGCAGAGGTT	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.1111A>G	11.37:g.120989335A>G	ENSP00000376543:p.Arg371Gly	Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	118	50	0.423729	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	1008	0.46153846153846156	356	0.7235772357723578	147	0.40607734806629836	170	0.2972027972027972	335	0.4419525065963061	G	3.893	-0.023615	0.07634	0.663187	0.412305	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.58060	0.36;0.36	5.72	3.86	0.44501	von Willebrand factor, type D domain (3);	0.115400	0.64402	N	0.000018	T	0.00012	0.0000	N	0.00223	-1.815	0.50632	P	1.1899999999998023E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.47799	-0.9089	9	0.02654	T	1	.	11.7181	0.51666	0.1898:0.0:0.8102:0.0	rs612969;rs58667510;rs612969	371	O75443	TECTA_HUMAN	G	371	ENSP00000376543:R371G;ENSP00000264037:R371G	ENSP00000264037:R371G	R	+	1	2	TECTA	120494545	1.000000	0.71417	0.003000	0.11579	0.877000	0.50540	4.856000	0.62932	0.364000	0.24374	-0.213000	0.12676	AGA	A|0.525;G|0.475	0.475	strong		0.547	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
MCTP2	55784	hgsc.bcm.edu	37	15	94884108	94884108	+	Silent	SNP	G	G	C	rs8025851	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:94884108G>C	ENST00000357742.4	+	6	924	c.924G>C	c.(922-924)gtG>gtC	p.V308V	MCTP2_ENST00000451018.3_Silent_p.V308V|MCTP2_ENST00000543482.1_Silent_p.V308V|MCTP2_ENST00000331706.4_5'UTR	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	308					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.V308V(1)		autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			GAGTGATCGTGTTAAATTTGA	0.363													C|||	2410	0.48123	0.587	0.5418	5008	,	,		18919	0.3383		0.5099	False		,,,				2504	0.4131				p.V308V		Atlas-SNP	.											MCTP2,NS,carcinoma,0,2	MCTP2	122	2	1	Substitution - coding silent(1)	stomach(1)	c.G924C						PASS	.	C	,	2483,1911	544.8+/-376.6	705,1073,419	93.0	91.0	92.0		924,924	-6.0	0.6	15	dbSNP_116	92	3895,4701	605.3+/-394.9	902,2091,1305	no	coding-synonymous,coding-synonymous	MCTP2	NM_001159643.1,NM_018349.3	,	1607,3164,1724	CC,CG,GG		45.3118,43.4911,49.0993	,	308/824,308/879	94884108	6378,6612	2197	4298	6495	SO:0001819	synonymous_variant	55784	exon6			GATCGTGTTAAAT	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.924G>C	15.37:g.94884108G>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	79	77	0.974684	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			G|0.505;C|0.495	0.495	strong		0.363	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825662	34825662	+	Silent	SNP	T	T	C	rs16894959	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:34825662T>C	ENST00000192788.5	+	13	1906	c.1735T>C	c.(1735-1737)Ttg>Ctg	p.L579L	UHRF1BP1_ENST00000452449.2_Silent_p.L579L	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	579							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						AGATGAACACTTGGACATCCG	0.443													T|||	693	0.138379	0.3071	0.0994	5008	,	,		20564	0.0119		0.1262	False		,,,				2504	0.0808				p.L579L		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.T1735C						PASS	.	T		878,2966		98,682,1142	117.0	109.0	112.0		1735	-10.2	0.3	6	dbSNP_123	112	1244,7018		101,1042,2988	no	coding-synonymous	UHRF1BP1	NM_017754.3		199,1724,4130	CC,CT,TT		15.0569,22.8408,17.5285		579/1441	34825662	2122,9984	1922	4131	6053	SO:0001819	synonymous_variant	54887	exon13			GAACACTTGGACA	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1735T>C	6.37:g.34825662T>C		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	106	44	0.415094	NM_017754	Q9NXE0	Silent	SNP	ENST00000192788.5	37	CCDS43455.1																																																																																			T|0.852;C|0.148	0.148	strong		0.443	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
PNPLA1	285848	hgsc.bcm.edu	37	6	36270130	36270130	+	Missense_Mutation	SNP	C	C	A	rs12199580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36270130C>A	ENST00000394571.2	+	6	1268	c.1268C>A	c.(1267-1269)cCc>cAc	p.P423H	PNPLA1_ENST00000388715.3_Missense_Mutation_p.P328H|PNPLA1_ENST00000312917.5_Missense_Mutation_p.P337H	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	423	Pro-rich.		P -> H (in dbSNP:rs12199580). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						CCCACTTCACCCAGGCCATCC	0.607											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1414	0.282348	0.1679	0.5231	5008	,	,		20276	0.1756		0.4036	False		,,,				2504	0.2515				p.P423H		Atlas-SNP	.											PNPLA1,back,malignant_melanoma,-1,1	PNPLA1	92	1	0			c.C1268A						scavenged	.	C	HIS/PRO,HIS/PRO,HIS/PRO	913,3493	351.3+/-311.2	103,707,1393	131.0	118.0	122.0		1010,1268,983	1.7	0.0	6	dbSNP_120	122	3723,4877	530.7+/-381.8	819,2085,1396	yes	missense,missense,missense	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	77,77,77	922,2792,2789	AA,AC,CC		43.2907,20.7217,35.6451	benign,benign,benign	337/447,423/533,328/438	36270130	4636,8370	2203	4300	6503	SO:0001583	missense	285848	exon6			CTTCACCCAGGCC		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1268C>A	6.37:g.36270130C>A	ENSP00000378072:p.Pro423His	Somatic	102	2	0.0196078	861	WXS	Illumina HiSeq	Phase_I	89	46	0.516854	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	736	0.336996336996337	81	0.16463414634146342	193	0.5331491712707183	138	0.24125874125874125	324	0.42744063324538256	C	10.48	1.363188	0.24684	0.207217	0.432907	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.35605	1.32;1.31;1.3;1.3	4.64	1.74	0.24563	.	0.692649	0.12534	N	0.460552	T	0.08447	0.0210	N	0.19112	0.55	0.80722	P	0.0	B;B	0.20261	0.005;0.043	B;B	0.21546	0.005;0.035	T	0.22208	-1.0223	9	0.42905	T	0.14	-1.6793	5.3121	0.15835	0.3599:0.5418:0.0:0.0983	rs12199580;rs58373772;rs12199580	423;337	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	H	328;337;424;423	ENSP00000373367:P328H;ENSP00000321116:P337H;ENSP00000391868:P424H;ENSP00000378072:P423H	ENSP00000321116:P337H	P	+	2	0	PNPLA1	36378108	0.004000	0.15560	0.002000	0.10522	0.121000	0.20230	0.074000	0.14662	0.112000	0.17975	0.650000	0.86243	CCC	C|0.661;A|0.339	0.339	strong		0.607	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
SERTAD4	56256	hgsc.bcm.edu	37	1	210415626	210415626	+	Missense_Mutation	SNP	A	A	C	rs559261349		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:210415626A>C	ENST00000367012.3	+	4	1245	c.1015A>C	c.(1015-1017)Aag>Cag	p.K339Q		NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	339						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		CTTACGGAAAAAGGAGGCTTC	0.388													A|||	1	0.000199681	0.0	0.0	5008	,	,		20269	0.0		0.001	False		,,,				2504	0.0				p.K339Q		Atlas-SNP	.											.	SERTAD4	53	.	0			c.A1015C						PASS	.						54.0	55.0	54.0					1																	210415626		2202	4300	6502	SO:0001583	missense	56256	exon4			CGGAAAAAGGAGG	BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.1015A>C	1.37:g.210415626A>C	ENSP00000355979:p.Lys339Gln	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	90	34	0.377778	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	37	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.427383	0.62733	.	.	ENSG00000082497	ENST00000367012	.	.	.	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000001	T	0.56077	0.1961	L	0.29908	0.895	0.34642	D	0.720729	D	0.60160	0.987	P	0.54544	0.755	T	0.69094	-0.5236	9	0.72032	D	0.01	-2.7444	16.2108	0.82158	1.0:0.0:0.0:0.0	.	339	Q9NUC0	SRTD4_HUMAN	Q	339	.	ENSP00000355979:K339Q	K	+	1	0	SERTAD4	208482249	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.336000	0.72954	2.232000	0.73038	0.533000	0.62120	AAG	.	.	none		0.388	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605	
SMYD4	114826	hgsc.bcm.edu	37	17	1686410	1686410	+	Missense_Mutation	SNP	T	T	C	rs9902398	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1686410T>C	ENST00000305513.7	-	10	2347	c.2180A>G	c.(2179-2181)tAc>tGc	p.Y727C		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	727			Y -> C (in dbSNP:rs9902398). {ECO:0000269|PubMed:11572484, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						CTCCACCACGTAGAGACTCCT	0.498													C|||	3890	0.776757	0.9198	0.7565	5008	,	,		16446	0.7758		0.7386	False		,,,				2504	0.638				p.Y727C		Atlas-SNP	.											.	SMYD4	50	.	0			c.A2180G						PASS	.	C	CYS/TYR	3925,481	226.2+/-241.8	1743,439,21	68.0	75.0	73.0		2180	-11.7	0.0	17	dbSNP_119	73	6085,2515	411.6+/-350.5	2159,1767,374	yes	missense	SMYD4	NM_052928.2	194	3902,2206,395	CC,CT,TT		29.2442,10.9169,23.0355	benign	727/805	1686410	10010,2996	2203	4300	6503	SO:0001583	missense	114826	exon10			ACCACGTAGAGAC	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.2180A>G	17.37:g.1686410T>C	ENSP00000304360:p.Tyr727Cys	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	96	94	0.979167	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	1735	0.7944139194139194	455	0.9247967479674797	256	0.7071823204419889	447	0.7814685314685315	577	0.7612137203166227	C	5.222	0.226433	0.09916	0.890831	0.707558	ENSG00000186532	ENST00000305513	T	0.62941	-0.01	5.84	-11.7	0.00046	Tetratricopeptide-like helical (1);	1.753970	0.02292	N	0.070408	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.19583	0.037	B	0.09377	0.004	T	0.47611	-0.9104	9	0.41790	T	0.15	10.414	12.5806	0.56388	0.0647:0.1443:0.069:0.722	rs9902398;rs17857050;rs57727381;rs9902398	727	Q8IYR2	SMYD4_HUMAN	C	727	ENSP00000304360:Y727C	ENSP00000304360:Y727C	Y	-	2	0	SMYD4	1633160	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-3.368000	0.00495	-2.928000	0.00302	-1.212000	0.01626	TAC	T|0.220;C|0.780	0.780	strong		0.498	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
ZNF592	9640	hgsc.bcm.edu	37	15	85341859	85341859	+	Missense_Mutation	SNP	G	G	A	rs8182086	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:85341859G>A	ENST00000560079.2	+	8	3065	c.2777G>A	c.(2776-2778)aGc>aAc	p.S926N	ZNF592_ENST00000299927.3_Missense_Mutation_p.S926N	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	926			S -> N (in dbSNP:rs8182086). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9039502}.		cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GAGCTGTCAAGCCTCCAGTCT	0.612													G|||	1895	0.378395	0.3775	0.3602	5008	,	,		19325	0.4782		0.2326	False		,,,				2504	0.4397				p.S926N		Atlas-SNP	.											ZNF592,colon,carcinoma,0,1	ZNF592	95	1	0			c.G2777A						PASS	.	G	ASN/SER	1446,2960	465.3+/-354.1	231,984,988	47.0	49.0	48.0		2777	4.8	1.0	15	dbSNP_117	48	1887,6711	332.4+/-320.1	202,1483,2614	yes	missense	ZNF592	NM_014630.2	46	433,2467,3602	AA,AG,GG		21.947,32.8189,25.6306	benign	926/1268	85341859	3333,9671	2203	4299	6502	SO:0001583	missense	9640	exon8			TGTCAAGCCTCCA	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2777G>A	15.37:g.85341859G>A	ENSP00000452877:p.Ser926Asn	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	58	26	0.448276	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	746	0.3415750915750916	189	0.38414634146341464	122	0.3370165745856354	256	0.44755244755244755	179	0.23614775725593667	G	15.12	2.740064	0.49045	0.328189	0.21947	ENSG00000166716	ENST00000299927	T	0.00606	6.26	4.75	4.75	0.60458	.	0.433085	0.28252	N	0.016036	T	0.00012	0.0000	N	0.14661	0.345	0.36165	P	0.15164100000000003	B	0.28350	0.208	B	0.22152	0.038	T	0.36792	-0.9733	9	0.15066	T	0.55	-18.739	15.2915	0.73870	0.0:0.0:1.0:0.0	rs8182086;rs52828108;rs61533520;rs8182086	926	Q92610	ZN592_HUMAN	N	926	ENSP00000299927:S926N	ENSP00000299927:S926N	S	+	2	0	ZNF592	83142863	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.816000	0.38992	2.439000	0.82584	0.655000	0.94253	AGC	G|0.705;A|0.295	0.295	strong		0.612	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
BRINP1	1620	hgsc.bcm.edu	37	9	121929932	121929932	+	Silent	SNP	C	C	T	rs147029533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:121929932C>T	ENST00000265922.3	-	8	2177	c.1716G>A	c.(1714-1716)tcG>tcA	p.S572S	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	572					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)											TCCAGCCCTCCGAATGGCTCC	0.557													C|||	10	0.00199681	0.0	0.0043	5008	,	,		19432	0.0		0.007	False		,,,				2504	0.0				p.S572S		Atlas-SNP	.											DBC1,NS,carcinoma,-2,1	DBC1	194	1	0			c.G1716A						PASS	.	C		5,4401		0,5,2198	43.0	44.0	44.0		1716	-11.3	0.3	9	dbSNP_134	44	70,8524		1,68,4228	no	coding-synonymous	DBC1	NM_014618.2		1,73,6426	TT,TC,CC		0.8145,0.1135,0.5769		572/762	121929932	75,12925	2203	4297	6500	SO:0001819	synonymous_variant	1620	exon8			GCCCTCCGAATGG	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.1716G>A	9.37:g.121929932C>T		Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	86	41	0.476744	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			C|0.994;T|0.006	0.006	strong		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
TP53BP1	7158	hgsc.bcm.edu	37	15	43748304	43748304	+	Silent	SNP	A	A	G	rs690367	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43748304A>G	ENST00000263801.3	-	12	2739	c.2487T>C	c.(2485-2487)gaT>gaC	p.D829D	TP53BP1_ENST00000605155.1_5'UTR|TP53BP1_ENST00000450115.2_Silent_p.D834D|TP53BP1_ENST00000382039.3_Silent_p.D834D|TP53BP1_ENST00000382044.4_Silent_p.D834D	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	829					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)		GCTGTGAAGAATCTTGCTCTA	0.423								Other conserved DNA damage response genes					G|||	2635	0.526158	0.9735	0.33	5008	,	,		22112	0.3879		0.3032	False		,,,				2504	0.4325				p.D834D		Atlas-SNP	.											.	TP53BP1	157	.	0			c.T2502C						PASS	.	G	,,	3740,662	282.5+/-276.6	1594,552,55	169.0	164.0	166.0		2502,2502,2487	3.4	0.2	15	dbSNP_83	166	2606,5990	687.7+/-404.2	386,1834,2078	no	coding-synonymous,coding-synonymous,coding-synonymous	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	,,	1980,2386,2133	GG,GA,AA		30.3164,15.0386,48.8229	,,	834/1976,834/1978,829/1973	43748304	6346,6652	2201	4298	6499	SO:0001819	synonymous_variant	7158	exon12			TGAAGAATCTTGC	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.2487T>C	15.37:g.43748304A>G		Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	114	46	0.403509	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Silent	SNP	ENST00000263801.3	37	CCDS10096.1																																																																																			A|0.491;G|0.509	0.509	strong		0.423	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3		
IL16	3603	hgsc.bcm.edu	37	15	81598416	81598416	+	Silent	SNP	G	G	A	rs1803275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:81598416G>A	ENST00000302987.4	+	16	3588	c.3588G>A	c.(3586-3588)agG>agA	p.R1196R	IL16_ENST00000394652.2_Silent_p.R495R|IL16_ENST00000394660.2_Silent_p.R1196R|RP11-761I4.4_ENST00000607019.1_RNA			Q14005	IL16_HUMAN	interleukin 16	1196	Interaction with PPP1R12A, PPP1R12B and PPP1R12C.|PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						TTGTCACAAGGAAGCTGACTC	0.552													G|||	732	0.146166	0.2398	0.1614	5008	,	,		20807	0.1637		0.0746	False		,,,				2504	0.0644				p.R1196R		Atlas-SNP	.											.	IL16	254	.	0			c.G3588A						PASS	.	G	,,	882,3524	342.8+/-307.3	102,678,1423	113.0	114.0	113.0		3588,1485,3588	4.6	0.1	15	dbSNP_89	113	718,7882	175.8+/-225.7	26,666,3608	no	coding-synonymous,coding-synonymous,coding-synonymous	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	,,	128,1344,5031	AA,AG,GG		8.3488,20.0182,12.302	,,	1196/1332,495/632,1196/1333	81598416	1600,11406	2203	4300	6503	SO:0001819	synonymous_variant	3603	exon17			CACAAGGAAGCTG	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3588G>A	15.37:g.81598416G>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	52	25	0.480769	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			G|0.855;A|0.145	0.145	strong		0.552	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
CACNA1A	773	hgsc.bcm.edu	37	19	13397560	13397560	+	Missense_Mutation	SNP	C	C	T	rs16027	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:13397560C>T	ENST00000360228.5	-	20	3309	c.3310G>A	c.(3310-3312)Ggc>Agc	p.G1104S	CACNA1A_ENST00000573710.2_Missense_Mutation_p.G1105S	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1105					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	AGCATGGGGCCGGGGTCGGTG	0.726													C|||	503	0.100439	0.0234	0.0807	5008	,	,		10414	0.0714		0.0974	False		,,,				2504	0.2515				p.G1105S		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G3313A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	128,3734		3,122,1806	15.0	20.0	19.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3322,3313,3310,3313,3322	-0.3	0.3	19	dbSNP_54	19	765,7457		27,711,3373	yes	missense,missense,missense,missense,missense	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	56,56,56,56,56	30,833,5179	TT,TC,CC		9.3043,3.3143,7.3899	benign,benign,benign,benign,benign	1108/2267,1105/2262,1104/2507,1105/2264,1108/2513	13397560	893,11191	1931	4111	6042	SO:0001583	missense	773	exon20			TGGGGCCGGGGTC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.3310G>A	19.37:g.13397560C>T	ENSP00000353362:p.Gly1104Ser	Somatic	24	0	0		WXS	Illumina HiSeq	Phase_I	57	35	0.614035	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	149	0.06822344322344322	11	0.022357723577235773	30	0.08287292817679558	40	0.06993006993006994	68	0.08970976253298153	C	3.833	-0.035285	0.07497	0.033143	0.093043	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.95588	-3.75	4.85	-0.306	0.12780	.	1.520630	0.04301	N	0.347306	T	0.30823	0.0777	L	0.29908	0.895	0.80722	P	0.0	B;B	0.26975	0.001;0.165	B;B	0.22152	0.001;0.038	T	0.69939	-0.5009	9	0.08837	T	0.75	.	2.091	0.03656	0.1377:0.4694:0.1532:0.2397	rs16027;rs17846901;rs52804691;rs61602983;rs16027	1105;1108	O00555;E9PD31	CAC1A_HUMAN;.	S	1104;1108;1105;1105	ENSP00000353362:G1104S	ENSP00000317661:G1105S	G	-	1	0	CACNA1A	13258560	0.023000	0.18921	0.277000	0.24703	0.073000	0.16967	0.202000	0.17295	0.440000	0.26502	0.542000	0.68232	GGC	C|0.927;T|0.073	0.073	strong		0.726	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978090	45978090	+	Missense_Mutation	SNP	C	C	T	rs233252	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45978090C>T	ENST00000391620.1	-	1	553	c.509G>A	c.(508-510)tGc>tAc	p.C170Y	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	170	18 X 5 AA repeats of C-C-X(3).		C -> Y (in dbSNP:rs233252). {ECO:0000269|PubMed:14962103, ECO:0000269|PubMed:15028290}.	Missing (in Ref. 3; AAI33678). {ECO:0000305}.		keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGGCACACAGCAGGTGGACCT	0.716													T|||	4352	0.86901	0.8964	0.8473	5008	,	,		15593	0.7649		0.9563	False		,,,				2504	0.865				p.C170Y		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.G509A						PASS	.	T	,TYR/CYS	3904,502	230.7+/-244.8	1727,450,26	64.0	71.0	69.0		,509	0.2	0.6	21	dbSNP_79	69	8194,406	127.2+/-185.5	3907,380,13	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,194	5634,830,39	TT,TC,CC		4.7209,11.3936,6.9814	,probably-damaging	,170/222	45978090	12098,908	2203	4300	6503	SO:0001583	missense	386682	exon1			ACACAGCAGGTGG	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.509G>A	21.37:g.45978090C>T	ENSP00000375478:p.Cys170Tyr	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	100	98	0.98	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	1908	0.8736263736263736	436	0.8861788617886179	323	0.8922651933701657	420	0.7342657342657343	729	0.9617414248021108	t	9.110	1.006368	0.19199	0.886064	0.952791	ENSG00000212935	ENST00000391620	T	0.02812	4.15	3.36	0.176	0.15049	.	.	.	.	.	T	0.00012	0.0000	M	0.89214	3.015	0.39095	P	0.03882399999999997	B	0.02656	0.0	B	0.11329	0.006	T	0.28170	-1.0052	8	0.33141	T	0.24	.	7.1537	0.25624	0.0:0.6493:0.1469:0.2037	rs233252;rs52803444;rs57691947;rs233252	170	P60369	KR103_HUMAN	Y	170	ENSP00000375478:C170Y	ENSP00000375478:C170Y	C	-	2	0	KRTAP10-3	44802518	0.968000	0.33430	0.559000	0.28332	0.001000	0.01503	0.052000	0.14163	-0.021000	0.14009	-0.940000	0.02684	TGC	C|0.106;T|0.894	0.894	strong		0.716	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
UTP14C	9724	hgsc.bcm.edu	37	13	52603241	52603241	+	Missense_Mutation	SNP	A	A	G	rs3742290	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:52603241A>G	ENST00000521776.2	+	2	1034	c.301A>G	c.(301-303)Act>Gct	p.T101A	ALG11_ENST00000521508.1_3'UTR|ALG11_ENST00000523764.1_3'UTR	NM_021645.5	NP_067677.4	Q5TAP6	UT14C_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog C (yeast)	101			T -> A (in dbSNP:rs3742290).		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)		p.T101A(1)		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)		TTCTTTGGCCACTGTAAAAAA	0.413													A|||	401	0.0800719	0.0431	0.1239	5008	,	,		20314	0.0546		0.1203	False		,,,				2504	0.0838				p.T101A		Atlas-SNP	.											UTP14C,NS,carcinoma,0,1	UTP14C	67	1	1	Substitution - Missense(1)	stomach(1)	c.A301G						PASS	.	A	,ALA/THR	278,4128	154.8+/-188.1	10,258,1935	106.0	111.0	109.0		,301	0.2	0.1	13	dbSNP_107	109	1023,7577	218.8+/-257.1	63,897,3340	yes	utr-3,missense	UTP14C,ALG11	NM_001004127.2,NM_021645.5	,58	73,1155,5275	GG,GA,AA		11.8953,6.3096,10.0031	,benign	,101/767	52603241	1301,11705	2203	4300	6503	SO:0001583	missense	9724	exon2			TTGGCCACTGTAA	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.301A>G	13.37:g.52603241A>G	ENSP00000428619:p.Thr101Ala	Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	210	112	0.533333	NM_021645	Q5FWG3|Q92555	Missense_Mutation	SNP	ENST00000521776.2	37	CCDS31978.1	202	0.0924908424908425	24	0.04878048780487805	50	0.13812154696132597	34	0.05944055944055944	94	0.12401055408970976	A	0.898	-0.723189	0.03158	0.063096	0.118953	ENSG00000253797	ENST00000521776	T	0.15952	2.38	2.74	0.149	0.14863	.	0.962373	0.08680	N	0.909561	T	0.00039	0.0001	N	0.04090	-0.28	0.80722	P	0.0	B	0.11235	0.004	B	0.16289	0.015	T	0.43015	-0.9417	9	0.06891	T	0.86	1.0892	5.6359	0.17536	0.7254:0.0:0.2746:0.0	rs3742290;rs17401964;rs52823735;rs56602905;rs58559624;rs3742290	101	Q5TAP6	UT14C_HUMAN	A	101	ENSP00000428619:T101A	ENSP00000428619:T101A	T	+	1	0	UTP14C	51501242	0.000000	0.05858	0.077000	0.20336	0.680000	0.39746	0.029000	0.13666	-0.059000	0.13154	0.368000	0.22195	ACT	A|0.911;G|0.089	0.089	strong		0.413	UTP14C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045049.2	NM_021645	
ALDH3B2	222	hgsc.bcm.edu	37	11	67432799	67432799	+	Silent	SNP	G	G	A	rs80147122		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:67432799G>A	ENST00000349015.3	-	7	1101	c.663C>T	c.(661-663)cgC>cgT	p.R221R	ALDH3B2_ENST00000530069.1_Silent_p.R221R|ALDH3B2_ENST00000531881.1_5'Flank	NM_000695.3	NP_000686	P48448	AL3B2_HUMAN	aldehyde dehydrogenase 3 family, member B2	221					alcohol metabolic process (GO:0006066)|ethanol catabolic process (GO:0006068)|lipid metabolic process (GO:0006629)		3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	18						CAATGGCCACGCGGCTGCAGC	0.632																																					p.R221R		Atlas-SNP	.											ALDH3B2,NS,haematopoietic_neoplasm,0,2	ALDH3B2	46	2	0			c.C663T						scavenged	.						52.0	59.0	57.0					11																	67432799		2200	4293	6493	SO:0001819	synonymous_variant	222	exon7			GGCCACGCGGCTG	U37519	CCDS31622.1	11q13.2	2014-09-04			ENSG00000132746	ENSG00000132746	1.2.1.5	"""Aldehyde dehydrogenases"""	411	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase 8"", ""acetaldehyde dehydrogenase 8"""	601917		ALDH8		8890755, 9161417	Standard	NM_000695		Approved		uc001oms.3	P48448	OTTHUMG00000167284	ENST00000349015.3:c.663C>T	11.37:g.67432799G>A		Somatic	230	1	0.00434783		WXS	Illumina HiSeq	Phase_I	233	6	0.0257511	NM_001031615	Q53Y98|Q8NAL5|Q96IB2	Silent	SNP	ENST00000349015.3	37	CCDS31622.1																																																																																			.	.	strong		0.632	ALDH3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394004.1	NM_000695	
RPL13A	23521	hgsc.bcm.edu	37	19	49993535	49993535	+	Silent	SNP	C	C	G	rs1064257	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49993535C>G	ENST00000391857.4	+	3	211	c.135C>G	c.(133-135)ggC>ggG	p.G45G	SNORD34_ENST00000365633.1_RNA|RPL13A_ENST00000477613.2_3'UTR|CTD-3148I10.15_ENST00000595815.1_RNA|SNORD33_ENST00000362761.1_RNA|SNORD32A_ENST00000364805.1_RNA|SNORD35A_ENST00000363389.1_RNA	NM_001270491.1|NM_012423.3	NP_001257420.1|NP_036555.1	P40429	RL13A_HUMAN	ribosomal protein L13a	45					cellular protein metabolic process (GO:0044267)|cellular response to interferon-gamma (GO:0071346)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|negative regulation of formation of translation preinitiation complex (GO:1901194)|negative regulation of translation (GO:0017148)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|GAIT complex (GO:0097452)|large ribosomal subunit (GO:0015934)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)	2		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		ACATTTCTGGCAATTTCTACA	0.567													C|||	80	0.0159744	0.0023	0.0331	5008	,	,		18852	0.0		0.0477	False		,,,				2504	0.0061				p.G45G		Atlas-SNP	.											.	RPL13A	13	.	0			c.C135G						PASS	.	C		46,4360	50.2+/-85.5	0,46,2157	52.0	49.0	50.0		135	-0.3	1.0	19	dbSNP_86	50	443,8157	133.9+/-191.4	11,421,3868	no	coding-synonymous	RPL13A	NM_012423.2		11,467,6025	GG,GC,CC		5.1512,1.044,3.7598		45/204	49993535	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	23521	exon3			TTCTGGCAATTTC	X56932	CCDS12768.1, CCDS74421.1	19q13.3	2011-04-06			ENSG00000142541	ENSG00000142541		"""L ribosomal proteins"""	10304	protein-coding gene	gene with protein product			"""tissue specific transplantation antigen 1"""	TSTA1			Standard	NM_012423		Approved	L13A	uc031rlt.1	P40429	OTTHUMG00000134289	ENST00000391857.4:c.135C>G	19.37:g.49993535C>G		Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	46	18	0.391304	NM_012423	A8K505	Silent	SNP	ENST00000391857.4	37	CCDS12768.1																																																																																			C|0.964;G|0.036	0.036	strong		0.567	RPL13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258989.1		
SESTD1	91404	hgsc.bcm.edu	37	2	179979930	179979930	+	Silent	SNP	T	T	C	rs2289993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179979930T>C	ENST00000428443.3	-	16	2017	c.1701A>G	c.(1699-1701)caA>caG	p.Q567Q		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	567							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			AGCGCAAAGATTGGCATAACA	0.388													T|||	972	0.194089	0.2882	0.1081	5008	,	,		17715	0.0645		0.166	False		,,,				2504	0.2904				p.Q567Q		Atlas-SNP	.											.	SESTD1	66	.	0			c.A1701G						PASS	.	T		1082,3324	391.7+/-328.2	128,826,1249	71.0	63.0	66.0		1701	0.9	1.0	2	dbSNP_100	66	1358,7242	265.8+/-286.4	112,1134,3054	no	coding-synonymous	SESTD1	NM_178123.4		240,1960,4303	CC,CT,TT		15.7907,24.5574,18.7606		567/697	179979930	2440,10566	2203	4300	6503	SO:0001819	synonymous_variant	91404	exon16			CAAAGATTGGCAT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1701A>G	2.37:g.179979930T>C		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	99	41	0.414141	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																			T|0.810;C|0.190	0.190	strong		0.388	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
TMEM222	84065	hgsc.bcm.edu	37	1	27660731	27660731	+	Silent	SNP	G	G	C	rs6663062	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:27660731G>C	ENST00000374076.4	+	5	536	c.498G>C	c.(496-498)gtG>gtC	p.V166V	TMEM222_ENST00000608611.1_Silent_p.V133V	NM_032125.2	NP_115501.2	Q9H0R3	TM222_HUMAN	transmembrane protein 222	166						integral component of membrane (GO:0016021)				biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						GGAATATGGTGACGCTCTGCT	0.582													G|||	162	0.0323482	0.0386	0.0259	5008	,	,		23077	0.001		0.0507	False		,,,				2504	0.0419				p.V166V		Atlas-SNP	.											.	TMEM222	16	.	0			c.G498C						PASS	.	G		165,4241	109.5+/-147.8	1,163,2039	224.0	189.0	201.0		498	3.2	1.0	1	dbSNP_116	201	288,8312	107.8+/-168.5	5,278,4017	no	coding-synonymous	TMEM222	NM_032125.2		6,441,6056	CC,CG,GG		3.3488,3.7449,3.483		166/209	27660731	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	84065	exon5			TATGGTGACGCTC	AL136683	CCDS297.2	1p36.11	2008-07-07	2008-07-07	2008-07-07	ENSG00000186501	ENSG00000186501			25363	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 160"""	C1orf160		11230166	Standard	NM_032125		Approved	DKFZP564D0478	uc001bnr.4	Q9H0R3	OTTHUMG00000004410	ENST00000374076.4:c.498G>C	1.37:g.27660731G>C		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	129	114	0.883721	NM_032125	D3DPL6|Q53HD8|Q5FVE9	Silent	SNP	ENST00000374076.4	37	CCDS297.2	63	0.028846153846153848	18	0.036585365853658534	9	0.024861878453038673	1	0.0017482517482517483	35	0.04617414248021108	G	9.718	1.158967	0.21454	0.037449	0.033488	ENSG00000186501	ENST00000464813	.	.	.	5.09	3.23	0.37069	.	.	.	.	.	T	0.16642	0.0400	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11767	-1.0574	4	.	.	.	-30.776	6.0198	0.19623	0.2303:0.2043:0.5653:0.0	rs6663062;rs6663062	.	.	.	H	139	.	.	D	+	1	0	TMEM222	27533318	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	1.287000	0.33284	0.739000	0.32628	0.655000	0.94253	GAC	G|0.969;C|0.031	0.031	strong		0.582	TMEM222-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000012809.2	NM_032125	
XIRP2	129446	hgsc.bcm.edu	37	2	168115797	168115797	+	Missense_Mutation	SNP	G	G	C	rs75758327	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168115797G>C	ENST00000409728.1	+	11	2929	c.2840G>C	c.(2839-2841)aGa>aCa	p.R947T	XIRP2_ENST00000409043.1_Missense_Mutation_p.R914T|XIRP2_ENST00000409605.1_Missense_Mutation_p.R692T|XIRP2_ENST00000420519.1_Missense_Mutation_p.R947T|XIRP2_ENST00000409195.1_3'UTR|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.R914T	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGTTTCCCAGAGTGGAGGTG	0.448													G|||	466	0.0930511	0.1838	0.049	5008	,	,		18315	0.0129		0.0845	False		,,,				2504	0.093				p.R947T		Atlas-SNP	.											.	XIRP2	914	.	0			c.G2840C						PASS	.	G	THR/ARG,THR/ARG,,THR/ARG,	646,3228		53,540,1344	79.0	73.0	75.0		2741,2840,,2075,	-1.6	0.0	2	dbSNP_131	75	606,7688		26,554,3567	yes	missense,missense,utr-3,missense,utr-3	XIRP2	NM_001079810.3,NM_001199143.1,NM_001199144.1,NM_001199145.1,NM_152381.5	71,71,,71,	79,1094,4911	CC,CG,GG		7.3065,16.6753,10.2893	,,,,	914/939,947/972,,692/717,	168115797	1252,10916	1937	4147	6084	SO:0001583	missense	129446	exon11			TTCCCAGAGTGGA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2840G>C	2.37:g.168115797G>C	ENSP00000386619:p.Arg947Thr	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	191	0.08745421245421245	88	0.17886178861788618	21	0.058011049723756904	14	0.024475524475524476	68	0.08970976253298153	G	13.02	2.113098	0.37339	0.166753	0.073065	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.77877	-1.13;-1.13;-1.13;-1.13;-1.13	5.7	-1.62	0.08372	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.80722	P	0.0	B;B	0.16802	0.004;0.019	B;B	0.15052	0.008;0.012	T	0.06023	-1.0850	7	0.54805	T	0.06	.	1.9647	0.03393	0.2847:0.2083:0.4003:0.1066	.	914;947	A4UGR9-4;A4UGR9-6	.;.	T	914;947;914;947;692	ENSP00000386454:R914T;ENSP00000386619:R947T;ENSP00000386724:R914T;ENSP00000415541:R947T;ENSP00000386981:R692T	ENSP00000386454:R914T	R	+	2	0	XIRP2	167824043	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.318000	0.19504	-0.318000	0.08665	0.650000	0.86243	AGA	G|0.922;C|0.078	0.078	strong		0.448	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
DNTTIP2	30836	hgsc.bcm.edu	37	1	94341267	94341267	+	Silent	SNP	A	A	G	rs2273165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:94341267A>G	ENST00000436063.2	-	3	1797	c.1740T>C	c.(1738-1740)ttT>ttC	p.F580F	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	580	TdBR region; mediates interaction with DNTT.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TATCTGCATTAAAATTAATAT	0.363													G|||	2673	0.533746	0.5378	0.4337	5008	,	,		15809	0.621		0.4225	False		,,,				2504	0.6237				p.F580F		Atlas-SNP	.											.	DNTTIP2	59	.	0			c.T1740C						PASS	.	G		1895,1789		462,971,409	202.0	173.0	182.0		1740	-0.2	1.0	1	dbSNP_100	182	3509,4671		723,2063,1304	no	coding-synonymous	DNTTIP2	NM_014597.4		1185,3034,1713	GG,GA,AA		42.8973,48.5613,45.5496		580/757	94341267	5404,6460	1842	4090	5932	SO:0001819	synonymous_variant	30836	exon3			TGCATTAAAATTA	AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.1740T>C	1.37:g.94341267A>G		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	76	1	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Silent	SNP	ENST00000436063.2	37	CCDS44174.1																																																																																			A|0.510;G|0.490	0.490	strong		0.363	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597	
MUC4	4585	hgsc.bcm.edu	37	3	195506747	195506747	+	Missense_Mutation	SNP	C	C	T	rs62282470	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506747C>T	ENST00000463781.3	-	2	12163	c.11704G>A	c.(11704-11706)Gcc>Acc	p.A3902T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3902T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3902T(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACGTGTG	0.592													.|||	553	0.110423	0.0287	0.1095	5008	,	,		8458	0.0536		0.2256	False		,,,				2504	0.1616				p.A3902T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	1	Substitution - Missense(1)	endometrium(1)	c.G11704A						PASS	.						10.0	9.0	9.0					3																	195506747		528	1045	1573	SO:0001583	missense	4585	exon2			GGGTGGCGTGACG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11704G>A	3.37:g.195506747C>T	ENSP00000417498:p.Ala3902Thr	Somatic	21	0	0		WXS	Illumina HiSeq	Phase_I	76	58	0.763158	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	205	0.09386446886446886	39	0.07926829268292683	27	0.07458563535911603	37	0.06468531468531469	102	0.1345646437994723	c	7.588	0.670216	0.14776	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.54;1.44	.	.	.	.	.	.	.	.	T	0.00144	0.0004	N	0.19112	0.55	0.09310	N	1	B	0.26975	0.165	B	0.06405	0.002	T	0.18272	-1.0342	7	.	.	.	.	2.1866	0.03888	0.0:0.3341:0.3337:0.3322	rs62282470	3774	E7ESK3	.	T	3902	ENSP00000417498:A3902T;ENSP00000420243:A3902T	.	A	-	1	0	MUC4	196991526	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-2.501000	0.00966	-2.037000	0.00920	-2.088000	0.00374	GCC	C|0.920;T|0.080	0.080	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NDUFB1	4707	hgsc.bcm.edu	37	14	92588002	92588002	+	5'UTR	SNP	T	T	G	rs3818263	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92588002T>G	ENST00000553514.1	-	0	66				NDUFB1_ENST00000555441.1_5'Flank|NDUFB1_ENST00000605997.1_5'UTR|NDUFB1_ENST00000329559.3_Silent_p.V40V|CPSF2_ENST00000298875.4_5'Flank|NDUFB1_ENST00000556555.1_5'UTR			O75438	NDUB1_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1, 7kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|lung(1)	2		all_cancers(154;0.0766)		COAD - Colon adenocarcinoma(157;0.205)		CCTCAGCGCCTACAGCGACCC	0.711													G|||	2703	0.539736	0.5514	0.379	5008	,	,		10980	0.8552		0.334	False		,,,				2504	0.5245				p.V40V		Atlas-SNP	.											NDUFB1,rectum,carcinoma,0,1	NDUFB1	5	1	0			c.A120C						PASS	.	G		2232,2174		573,1086,544	33.0	39.0	37.0		120	-7.0	0.0	14	dbSNP_107	37	2915,5681		489,1937,1872	no	coding-synonymous	NDUFB1	NM_004545.3		1062,3023,2416	GG,GT,TT		33.9111,49.3418,39.5862		40/106	92588002	5147,7855	2203	4298	6501	SO:0001623	5_prime_UTR_variant	4707	exon1			AGCGCCTACAGCG	BC104672	CCDS9901.1	14q31.3	2011-07-04	2002-08-29		ENSG00000183648	ENSG00000183648		"""Mitochondrial respiratory chain complex / Complex I"""	7695	protein-coding gene	gene with protein product	"""complex I MNLL subunit"""	603837	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 1 (7kD, MNLL)"""			9763677	Standard	NM_004545		Approved	MNLL, CI-MNLL	uc001yaf.3	O75438		ENST00000553514.1:c.-140A>C	14.37:g.92588002T>G		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	93	39	0.419355	NM_004545	A0AV68	Silent	SNP	ENST00000553514.1	37																																																																																				T|0.520;G|0.480	0.480	strong		0.711	NDUFB1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000412116.2	NM_004545	
GDPGP1	390637	hgsc.bcm.edu	37	15	90785060	90785060	+	Missense_Mutation	SNP	C	C	T	rs10153004	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:90785060C>T	ENST00000558017.1	+	4	1340	c.920C>T	c.(919-921)aCa>aTa	p.T307I	GDPGP1_ENST00000329600.6_Missense_Mutation_p.T307I	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	307			T -> I (in dbSNP:rs10153004). {ECO:0000269|PubMed:14702039}.		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)										TCAGCCCTCACAGGGGTCCGA	0.557													C|||	658	0.13139	0.2405	0.1398	5008	,	,		19012	0.0		0.1789	False		,,,				2504	0.0644				p.T307I		Atlas-SNP	.											.	.	.	.	0			c.C920T						PASS	.	C	ILE/THR	869,3529	339.9+/-306.0	88,693,1418	92.0	90.0	91.0		920	3.7	0.0	15	dbSNP_119	91	1433,7163	275.0+/-291.5	131,1171,2996	yes	missense	C15orf58	NM_001013657.2	89	219,1864,4414	TT,TC,CC		16.6705,19.759,17.7159	benign	307/386	90785060	2302,10692	2199	4298	6497	SO:0001583	missense	390637	exon4			CCCTCACAGGGGT		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.920C>T	15.37:g.90785060C>T	ENSP00000452793:p.Thr307Ile	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	311	0.1423992673992674	114	0.23170731707317074	61	0.1685082872928177	0	0.0	136	0.17941952506596306	C	10.97	1.501071	0.26861	0.19759	0.166705	ENSG00000183208	ENST00000329600	T	0.23147	1.92	5.62	3.71	0.42584	.	0.493880	0.19174	N	0.120863	T	0.00012	0.0000	L	0.38175	1.15	0.80722	P	0.0	B	0.27656	0.184	B	0.21151	0.033	T	0.28299	-1.0048	9	0.38643	T	0.18	-0.9139	8.6185	0.33847	0.0:0.7589:0.1583:0.0829	rs10153004;rs52820774;rs10153004	307	Q6ZNW5	VTC2_HUMAN	I	307	ENSP00000368405:T307I	ENSP00000368405:T307I	T	+	2	0	C15orf58	88586064	0.000000	0.05858	0.025000	0.17156	0.889000	0.51656	0.164000	0.16542	0.709000	0.31976	0.655000	0.94253	ACA	C|0.835;T|0.165	0.165	strong		0.557	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
DNHD1	144132	hgsc.bcm.edu	37	11	6580495	6580495	+	Silent	SNP	G	G	A	rs72901756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6580495G>A	ENST00000527990.2	+	26	9501	c.9501G>A	c.(9499-9501)caG>caA	p.Q3167Q	DNHD1_ENST00000254579.6_Silent_p.Q3167Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	3167					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TGGAACAGCAGCTGAAAGACT	0.483													G|||	364	0.0726837	0.0204	0.1037	5008	,	,		21689	0.0159		0.0736	False		,,,				2504	0.1789				p.Q3167Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.G9501A						PASS	.	G		45,1339		1,43,648	106.0	90.0	95.0		9501	2.5	0.9	11	dbSNP_130	95	339,2843		20,299,1272	no	coding-synonymous	DNHD1	NM_144666.2		21,342,1920	AA,AG,GG		10.6537,3.2514,8.41		3167/4754	6580495	384,4182	692	1591	2283	SO:0001819	synonymous_variant	144132	exon28			ACAGCAGCTGAAA	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.9501G>A	11.37:g.6580495G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	117	57	0.487179	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.957;A|0.043	0.043	strong		0.483	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
FGD3	89846	hgsc.bcm.edu	37	9	95782667	95782667	+	Silent	SNP	C	C	T	rs11790517	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:95782667C>T	ENST00000375482.3	+	13	1951	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F	FGD3_ENST00000416701.2_Silent_p.F485F|FGD3_ENST00000538555.1_Silent_p.F88F|FGD3_ENST00000337352.6_Silent_p.F485F	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	485					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						GTGGCGCCTTCAGCCAGGATG	0.577													C|||	1414	0.282348	0.3812	0.3876	5008	,	,		16496	0.2411		0.2903	False		,,,				2504	0.1084				p.F485F		Atlas-SNP	.											.	FGD3	116	.	0			c.C1455T						PASS	.	C	,	1536,2680		298,940,870	60.0	66.0	64.0		1455,1455	0.2	0.0	9	dbSNP_120	64	2352,6102		331,1690,2206	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	629,2630,3076	TT,TC,CC		27.8211,36.4326,30.6867	,	485/726,485/726	95782667	3888,8782	2108	4227	6335	SO:0001819	synonymous_variant	89846	exon13			CGCCTTCAGCCAG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1455C>T	9.37:g.95782667C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	102	47	0.460784	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|0.684;T|0.316	0.316	strong		0.577	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
C16orf70	80262	hgsc.bcm.edu	37	16	67166731	67166731	+	Missense_Mutation	SNP	G	G	A	rs34017457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67166731G>A	ENST00000219139.3	+	6	555	c.367G>A	c.(367-369)Gct>Act	p.A123T	C16orf70_ENST00000569600.1_Missense_Mutation_p.A123T|C16orf70_ENST00000569683.1_3'UTR	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	123										cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		GTACAACTCCGCTGAGCAGCT	0.483													G|||	14	0.00279553	0.0	0.0014	5008	,	,		23042	0.0		0.0119	False		,,,				2504	0.001				p.A123T		Atlas-SNP	.											.	C16orf70	38	.	0			c.G367A						PASS	.	G	THR/ALA	12,4388	17.9+/-39.9	0,12,2188	129.0	119.0	122.0		367	4.1	1.0	16	dbSNP_126	122	81,8519	47.6+/-106.9	1,79,4220	yes	missense	C16orf70	NM_025187.3	58	1,91,6408	AA,AG,GG		0.9419,0.2727,0.7154	possibly-damaging	123/423	67166731	93,12907	2200	4300	6500	SO:0001583	missense	80262	exon6			AACTCCGCTGAGC	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 6"""	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510	ENST00000219139.3:c.367G>A	16.37:g.67166731G>A	ENSP00000219139:p.Ala123Thr	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	134	60	0.447761	NM_025187	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	37	CCDS10828.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	15.47	2.842233	0.51057	0.002727	0.009419	ENSG00000125149	ENST00000219139	.	.	.	6.05	4.08	0.47627	.	0.051952	0.85682	N	0.000000	T	0.42877	0.1222	L	0.52759	1.655	0.58432	D	0.999998	B;D	0.56521	0.295;0.976	B;P	0.49451	0.089;0.611	T	0.35201	-0.9798	9	0.17832	T	0.49	-11.1355	11.3429	0.49543	0.1492:0.0:0.8508:0.0	rs34017457	198;123	Q9BSU1-2;Q9BSU1	.;CP070_HUMAN	T	123	.	ENSP00000219139:A123T	A	+	1	0	C16orf70	65724232	1.000000	0.71417	0.963000	0.40424	0.990000	0.78478	6.526000	0.73799	0.871000	0.35750	-0.142000	0.14014	GCT	G|0.994;A|0.006	0.006	strong		0.483	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187	
MRPL4	51073	hgsc.bcm.edu	37	19	10370310	10370310	+	Missense_Mutation	SNP	A	A	G	rs77884668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10370310A>G	ENST00000253099.6	+	9	1044	c.757A>G	c.(757-759)Atg>Gtg	p.M253V	CTD-2369P2.4_ENST00000587088.1_RNA|MRPL4_ENST00000393733.2_3'UTR|MRPL4_ENST00000307422.5_Missense_Mutation_p.M253V|CTD-2369P2.5_ENST00000592893.1_RNA	NM_015956.2|NM_146388.1	NP_057040.2|NP_666500.1	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	253					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		TGTGCACAGCATGCTCAAGCA	0.677													A|||	73	0.0145767	0.0537	0.0029	5008	,	,		6135	0.0		0.0	False		,,,				2504	0.0				p.M253V		Atlas-SNP	.											.	MRPL4	22	.	0			c.A757G						PASS	.	A	VAL/MET,VAL/MET,	184,4222	109.5+/-147.8	2,180,2021	38.0	29.0	32.0		757,757,	2.9	1.0	19	dbSNP_131	32	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,utr-3	MRPL4	NM_015956.2,NM_146387.1,NM_146388.1	21,21,	2,181,6320	GG,GA,AA		0.0116,4.1761,1.4224	possibly-damaging,possibly-damaging,	253/312,253/312,	10370310	185,12821	2203	4300	6503	SO:0001583	missense	51073	exon10			CACAGCATGCTCA	AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364		"""Mitochondrial ribosomal proteins / large subunits"""	14276	protein-coding gene	gene with protein product		611823					Standard	NM_015956		Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.757A>G	19.37:g.10370310A>G	ENSP00000253099:p.Met253Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	74	40	0.540541	NM_146387	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	Missense_Mutation	SNP	ENST00000253099.6	37	CCDS12230.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	a	14.63	2.592614	0.46214	0.041761	1.16E-4	ENSG00000105364	ENST00000253099;ENST00000307422	.	.	.	5.1	2.89	0.33648	Ribosomal protein L4 domain (2);	0.224207	0.50627	D	0.000113	T	0.12860	0.0312	L	0.32530	0.975	0.39810	D	0.972685	P	0.37955	0.612	P	0.51055	0.657	T	0.20338	-1.0278	9	0.44086	T	0.13	-21.9678	10.159	0.42840	0.678:0.322:0.0:0.0	.	253	Q9BYD3	RM04_HUMAN	V	253	.	ENSP00000253099:M253V	M	+	1	0	MRPL4	10231310	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	1.695000	0.37763	0.232000	0.21100	0.449000	0.29647	ATG	A|0.984;G|0.016	0.016	strong		0.677	MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1		
MMP17	4326	hgsc.bcm.edu	37	12	132335592	132335592	+	Missense_Mutation	SNP	G	G	A	rs11835665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:132335592G>A	ENST00000360564.1	+	10	1687	c.1585G>A	c.(1585-1587)Gat>Aat	p.D529N	MMP17_ENST00000535291.1_Missense_Mutation_p.D445N|MMP17_ENST00000535004.1_Missense_Mutation_p.D69N	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	529					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	CTCACAGGCCGATGGATCTGT	0.677													G|||	706	0.140974	0.1785	0.2061	5008	,	,		12118	0.0		0.2167	False		,,,				2504	0.1115				p.D529N		Atlas-SNP	.											.	MMP17	77	.	0			c.G1585A						PASS	.	G	ASN/ASP	791,3611		76,639,1486	28.0	27.0	27.0		1585	1.5	0.0	12	dbSNP_120	27	1858,6736		210,1438,2649	yes	missense	MMP17	NM_016155.4	23	286,2077,4135	AA,AG,GG		21.6197,17.9691,20.3832	benign	529/604	132335592	2649,10347	2201	4297	6498	SO:0001583	missense	4326	exon10			CAGGCCGATGGAT	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.1585G>A	12.37:g.132335592G>A	ENSP00000353767:p.Asp529Asn	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	177	94	0.531073	NM_016155	Q14850	Missense_Mutation	SNP	ENST00000360564.1	37	CCDS31927.1	337	0.1543040293040293	88	0.17886178861788618	86	0.23756906077348067	0	0.0	163	0.21503957783641162	G	9.426	1.084275	0.20309	0.179691	0.216197	ENSG00000198598	ENST00000360564;ENST00000535291;ENST00000535004	T;T;T	0.18502	2.21;2.21;2.28	4.49	1.51	0.23008	.	26.769500	0.05589	U	0.574407	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.19935	0.04	B	0.09377	0.004	T	0.41698	-0.9494	9	0.54805	T	0.06	.	7.369	0.26790	0.1576:0.1381:0.7043:0.0	rs11835665;rs59290415;rs11835665	529	Q9ULZ9	MMP17_HUMAN	N	529;445;69	ENSP00000353767:D529N;ENSP00000441106:D445N;ENSP00000445620:D69N	ENSP00000353767:D529N	D	+	1	0	MMP17	130901545	0.910000	0.30920	0.000000	0.03702	0.009000	0.06853	3.377000	0.52425	0.008000	0.14787	0.491000	0.48974	GAT	G|0.816;A|0.184	0.184	strong		0.677	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
SLC25A10	1468	hgsc.bcm.edu	37	17	79682558	79682558	+	Silent	SNP	T	T	C	rs2072700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79682558T>C	ENST00000350690.5	+	3	350	c.264T>C	c.(262-264)cgT>cgC	p.R88R	SLC25A10_ENST00000571730.1_Silent_p.R243R|SLC25A10_ENST00000541223.1_Silent_p.R243R|SLC25A10_ENST00000545862.1_Silent_p.R45R|SLC25A10_ENST00000331531.5_Silent_p.R88R	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	88					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)			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)	TGCGGGACCGTGTGGCCAAGG	0.701													C|||	2135	0.426318	0.4985	0.4582	5008	,	,		14533	0.3859		0.4384	False		,,,				2504	0.3354				p.R88R		Atlas-SNP	.											SLC25A10,NS,carcinoma,0,1	SLC25A10	24	1	0			c.T264C						PASS	.	C		2153,2253	590.6+/-387.4	533,1087,583	131.0	136.0	134.0		264	-7.8	0.0	17	dbSNP_96	134	3457,5143	631.6+/-398.5	717,2023,1560	no	coding-synonymous	SLC25A10	NM_012140.3		1250,3110,2143	CC,CT,TT		40.1977,48.8652,43.1339		88/288	79682558	5610,7396	2203	4300	6503	SO:0001819	synonymous_variant	1468	exon3			GGACCGTGTGGCC		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.264T>C	17.37:g.79682558T>C		Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	72	70	0.972222	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Silent	SNP	ENST00000350690.5	37	CCDS11786.1																																																																																			T|0.579;C|0.421	0.421	strong		0.701	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1		
ANKRD50	57182	hgsc.bcm.edu	37	4	125592065	125592065	+	Silent	SNP	C	C	A	rs10018651	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:125592065C>A	ENST00000504087.1	-	4	3404	c.2367G>T	c.(2365-2367)gcG>gcT	p.A789A	ANKRD50_ENST00000515641.1_Silent_p.A610A	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	789										NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|kidney(4)|large_intestine(14)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	55						GACCCATAGACGCTGCTGCTA	0.458													A|||	1436	0.286741	0.3918	0.2233	5008	,	,		24284	0.2619		0.2107	False		,,,				2504	0.2935				p.A789A		Atlas-SNP	.											.	ANKRD50	136	.	0			c.G2367T						PASS	.	A	,	1568,2838	668.5+/-402.0	259,1050,894	141.0	131.0	134.0		1830,2367	-0.4	0.9	4	dbSNP_119	134	1800,6800	732.8+/-406.9	201,1398,2701	no	coding-synonymous,coding-synonymous	ANKRD50	NM_001167882.1,NM_020337.2	,	460,2448,3595	AA,AC,CC		20.9302,35.5878,25.8957	,	610/1251,789/1430	125592065	3368,9638	2203	4300	6503	SO:0001819	synonymous_variant	57182	exon4			CATAGACGCTGCT	AB033049	CCDS34060.1, CCDS54802.1	4q28.1	2013-01-10			ENSG00000151458	ENSG00000151458		"""Ankyrin repeat domain containing"""	29223	protein-coding gene	gene with protein product							Standard	NM_020337		Approved	KIAA1223	uc010inw.3	Q9ULJ7	OTTHUMG00000161398	ENST00000504087.1:c.2367G>T	4.37:g.125592065C>A		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	161	88	0.546584	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Silent	SNP	ENST00000504087.1	37	CCDS34060.1																																																																																			C|0.743;A|0.257	0.257	strong		0.458	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337	
PIK3R1	5295	hgsc.bcm.edu	37	5	67522722	67522722	+	Silent	SNP	C	C	T	rs706713	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:67522722C>T	ENST00000521381.1	+	2	835	c.219C>T	c.(217-219)taC>taT	p.Y73Y	PIK3R1_ENST00000521657.1_Silent_p.Y73Y|PIK3R1_ENST00000396611.1_Silent_p.Y73Y|PIK3R1_ENST00000274335.5_Silent_p.Y73Y	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	73	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CGGGAACTTACGTAGAATATA	0.498			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)			T|||	2100	0.419329	0.4425	0.3602	5008	,	,		16257	0.6746		0.2455	False		,,,				2504	0.3456				p.Y73Y		Atlas-SNP	.		Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	.	PIK3R1	869	.	1	Whole gene deletion(1)	large_intestine(1)	c.C219T						PASS	.	T		1803,2603	606.6+/-390.8	360,1083,760	45.0	56.0	53.0		219	-9.6	0.2	5	dbSNP_86	53	2012,6588	713.3+/-405.9	256,1500,2544	no	coding-synonymous	PIK3R1	NM_181523.2		616,2583,3304	TT,TC,CC		23.3953,40.9215,29.3326		73/725	67522722	3815,9191	2203	4300	6503	SO:0001819	synonymous_variant	5295	exon2			AACTTACGTAGAA	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.219C>T	5.37:g.67522722C>T		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	138	71	0.514493	NM_181523	B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Silent	SNP	ENST00000521381.1	37	CCDS3993.1																																																																																			C|0.633;T|0.367	0.367	strong		0.498	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	
FER	2241	hgsc.bcm.edu	37	5	108133967	108133967	+	Silent	SNP	A	A	G	rs2229085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:108133967A>G	ENST00000281092.4	+	3	468	c.84A>G	c.(82-84)gtA>gtG	p.V28V	FER_ENST00000536402.1_Silent_p.V28V|FER_ENST00000502752.1_3'UTR|FER_ENST00000438717.2_5'UTR	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	28	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.|Important for interaction with membranes containing phosphoinositides.				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)		TGGAAACAGTAAAGAAATTTA	0.363													A|||	891	0.177915	0.2988	0.17	5008	,	,		17170	0.0575		0.167	False		,,,				2504	0.1554				p.V28V	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.A84G						PASS	.	A		1242,3162	427.0+/-341.4	179,884,1139	87.0	90.0	89.0		84	1.1	1.0	5	dbSNP_98	89	1534,7066	288.9+/-299.0	135,1264,2901	no	coding-synonymous	FER	NM_005246.2		314,2148,4040	GG,GA,AA		17.8372,28.2016,21.3473		28/823	108133967	2776,10228	2202	4300	6502	SO:0001819	synonymous_variant	2241	exon3			AACAGTAAAGAAA	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.84A>G	5.37:g.108133967A>G		Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	219	101	0.461187	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			A|0.801;G|0.199	0.199	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
RUFY4	285180	hgsc.bcm.edu	37	2	218940259	218940259	+	Silent	SNP	C	C	T	rs7423696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:218940259C>T	ENST00000344321.7	+	9	1562	c.1044C>T	c.(1042-1044)ccC>ccT	p.P348P	RUFY4_ENST00000441828.2_3'UTR|RUFY4_ENST00000463872.1_3'UTR|RUFY4_ENST00000374155.3_Silent_p.P368P	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	348							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TGCTGATGCCCAGCCCCAGAG	0.617													C|||	1161	0.231829	0.034	0.3444	5008	,	,		16738	0.2312		0.3052	False		,,,				2504	0.3446				p.P348P		Atlas-SNP	.											.	RUFY4	59	.	0			c.C1044T						PASS	.	C		292,3696		15,262,1717	31.0	36.0	34.0		1044	2.8	0.1	2	dbSNP_116	34	2412,5996		348,1716,2140	no	coding-synonymous	RUFY4	NM_198483.3		363,1978,3857	TT,TC,CC		28.687,7.322,21.8135		348/572	218940259	2704,9692	1994	4204	6198	SO:0001819	synonymous_variant	285180	exon9			GATGCCCAGCCCC	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"""Zinc fingers, FYVE domain containing"""	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1044C>T	2.37:g.218940259C>T		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	117	64	0.547009	NM_198483	Q6ZR96	Silent	SNP	ENST00000344321.7	37																																																																																				C|0.769;T|0.231	0.231	strong		0.617	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
TBC1D1	23216	hgsc.bcm.edu	37	4	37962133	37962133	+	Intron	SNP	G	G	A	rs2290740	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:37962133G>A	ENST00000261439.4	+	3	772				TBC1D1_ENST00000508802.1_Intron|PTTG2_ENST00000504686.1_Silent_p.L26L	NM_001253914.1|NM_001253915.1|NM_015173.3	NP_001240843.1|NP_001240844.1|NP_055988.2	Q86TI0	TBCD1_HUMAN	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1						membrane organization (GO:0061024)|regulation of protein localization (GO:0032880)	cytosol (GO:0005829)|nucleus (GO:0005634)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(3)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	36						TGCTGAAGCTGGAGTCTAGAC	0.453													G|||	1176	0.234824	0.3048	0.1066	5008	,	,		20340	0.3125		0.1322	False		,,,				2504	0.2566				p.L26L		Atlas-SNP	.											.	PTTG2	15	.	0			c.G78A						PASS	.	G	,	1293,3109	417.2+/-337.8	190,913,1098	66.0	72.0	70.0		78,	-0.8	0.0	4	dbSNP_100	70	1238,7362	245.7+/-274.4	107,1024,3169	no	coding-synonymous,intron	PTTG2,TBC1D1	NM_006607.2,NM_015173.2	,	297,1937,4267	AA,AG,GG		14.3953,29.373,19.4662	,	26/192,	37962133	2531,10471	2201	4300	6501	SO:0001627	intron_variant	10744	exon1			GAAGCTGGAGTCT	AB029031	CCDS33972.1, CCDS58897.1	4p14	2013-07-09			ENSG00000065882	ENSG00000065882			11578	protein-coding gene	gene with protein product		609850				10965142, 18258599	Standard	NM_015173		Approved	TBC, TBC1, KIAA1108	uc003gtb.3	Q86TI0	OTTHUMG00000150302	ENST00000261439.4:c.418-53997G>A	4.37:g.37962133G>A		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	186	106	0.569892	NM_006607	B7Z3D9|E9PGH8|Q96K82|Q9UPP4	Silent	SNP	ENST00000261439.4	37	CCDS33972.1																																																																																			G|0.784;A|0.216	0.216	strong		0.453	TBC1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317443.2	NM_015173	
CAD	790	hgsc.bcm.edu	37	2	27447310	27447310	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27447310G>A	ENST00000403525.1	+	9	1350	c.1206G>A	c.(1204-1206)ggG>ggA	p.G402G	CAD_ENST00000264705.4_Silent_p.G402G			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGGCTCAGGGGGCCTCTCCA	0.597																																					p.G402G		Atlas-SNP	.											CAD,NS,carcinoma,+2,1	CAD	199	1	0			c.G1206A						PASS	.						67.0	72.0	70.0					2																	27447310		2203	4300	6503	SO:0001819	synonymous_variant	790	exon9			CTCAGGGGGCCTC	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.1206G>A	2.37:g.27447310G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	90	40	0.444444	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37																																																																																				.	.	none		0.597	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
AGPS	8540	hgsc.bcm.edu	37	2	178364363	178364363	+	Silent	SNP	A	A	C	rs148418568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:178364363A>C	ENST00000264167.4	+	14	1526	c.1380A>C	c.(1378-1380)ccA>ccC	p.P460P	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	460					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			GATTTGACCCAAATCAGCTAA	0.308													A|||	2	0.000399361	0.0	0.0029	5008	,	,		14276	0.0		0.0	False		,,,				2504	0.0				p.P460P		Atlas-SNP	.											.	AGPS	56	.	0			c.A1380C						PASS	.	A		0,4406		0,0,2203	94.0	90.0	91.0		1380	1.5	1.0	2	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AGPS	NM_003659.3		0,1,6502	CC,CA,AA		0.0116,0.0,0.0077		460/659	178364363	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8540	exon14			TGACCCAAATCAG	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.1380A>C	2.37:g.178364363A>C		Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	23	6	0.26087	NM_003659	A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	CCDS2275.1																																																																																			A|1.000;C|0.000	0.000	strong		0.308	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2		
MIB2	142678	hgsc.bcm.edu	37	1	1562536	1562536	+	Silent	SNP	G	G	A	rs11544452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1562536G>A	ENST00000357210.4	+	11	1713	c.1497G>A	c.(1495-1497)gcG>gcA	p.A499A	MIB2_ENST00000518681.1_Silent_p.A491A|MIB2_ENST00000378708.1_Silent_p.A405A|MIB2_ENST00000360522.4_Silent_p.A464A|MIB2_ENST00000504599.1_Silent_p.A455A|MIB2_ENST00000378712.1_Silent_p.A376A|MIB2_ENST00000378710.3_Silent_p.A463A|MIB2_ENST00000355826.5_Silent_p.A542A|MIB2_ENST00000520777.1_Silent_p.A552A|MIB2_ENST00000505820.2_Silent_p.A556A	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	499					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGGAGGTGGCGCTGGGTAACG	0.687													.|||	707	0.141174	0.0061	0.2896	5008	,	,		13564	0.1746		0.1362	False		,,,				2504	0.1892				p.A556A		Atlas-SNP	.											.	MIB2	62	.	0			c.G1668A						PASS	.	G	,,,,	105,3907		3,99,1904	13.0	18.0	16.0		1656,1626,1473,1128,1668	-9.1	0.3	1	dbSNP_120	16	1011,7311		45,921,3195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MIB2	NM_001170686.1,NM_001170687.1,NM_001170688.1,NM_001170689.1,NM_080875.2	,,,,	48,1020,5099	AA,AG,GG		12.1485,2.6171,9.0482	,,,,	552/1067,542/1057,491/1006,376/754,556/1071	1562536	1116,11218	2006	4161	6167	SO:0001819	synonymous_variant	142678	exon11			GGTGGCGCTGGGT	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	30577	protein-coding gene	gene with protein product		611141	"""zinc finger, ZZ type with ankyrin repeat domain 1"", ""mindbomb homolog 2 (Drosophila)"""	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.1497G>A	1.37:g.1562536G>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	99	90	0.909091	NM_080875	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Silent	SNP	ENST00000357210.4	37		305	0.13965201465201466	4	0.008130081300813009	75	0.20718232044198895	114	0.1993006993006993	112	0.14775725593667546	G	3.666	-0.068494	0.07228	0.026171	0.121485	ENSG00000197530	ENST00000514234	T	0.53640	0.61	4.59	-9.07	0.00724	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	.	.	.	0.09310	P	0.9999999999995995	.	.	.	.	.	.	T	0.06110	-1.0845	6	0.87932	D	0	-18.8304	2.0692	0.03609	0.2581:0.3798:0.0945:0.2676	rs11544452	.	.	.	T	315	ENSP00000427680:A315T	ENSP00000427680:A315T	A	+	1	0	MIB2	1552399	0.000000	0.05858	0.254000	0.24359	0.884000	0.51177	-2.937000	0.00685	-1.519000	0.01775	0.455000	0.32223	GCT	G|0.860;A|0.140	0.140	strong		0.687	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144931087	144931087	+	Intron	SNP	T	T	C	rs41315684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144931087T>C	ENST00000369354.3	-	6	826				PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.T208A|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.T208A|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000479408.2_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000313382.9_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						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)		GGTTCTTCAGTGCAAATGCTG	0.537			T	PDGFRB	MPD																																p.T208A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A622G						PASS	.	T	ALA/THR,,,,	372,4034		0,372,1831	86.0	88.0	87.0		622,,,,	4.9	1.0	1	dbSNP_127	87	2213,6387		0,2213,2087	yes	missense,intron,intron,intron,intron	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	58,,,,	0,2585,3918	CC,CT,TT		25.7326,8.443,19.8754	,,,,	208/1133,,,,	144931087	2585,10421	2203	4300	6503	SO:0001627	intron_variant	9659	exon1			CTTCAGTGCAAAT	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.637-7266A>G	1.37:g.144931087T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	156	46	0.294872	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	345	0.15796703296703296	12	0.024390243902439025	83	0.2292817679558011	68	0.11888111888111888	182	0.24010554089709762	T	11.16	1.557414	0.27827	0.08443	0.257326	ENSG00000178104	ENST00000369353;ENST00000313431;ENST00000529945	T;T	0.11930	2.73;2.73	4.95	4.95	0.65309	.	.	.	.	.	T	0.12518	0.0304	L	0.47716	1.5	0.80722	D	1	D	0.53151	0.958	P	0.57776	0.827	T	0.11348	-1.0591	9	0.15499	T	0.54	.	12.5595	0.56273	0.0:0.0:0.0:1.0	rs41315684	208	Q5VU43-2	.	A	208	ENSP00000316434:T208A;ENSP00000433392:T208A	ENSP00000316434:T208A	T	-	1	0	PDE4DIP	143642444	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	2.884000	0.48562	1.856000	0.53863	0.379000	0.24179	ACT	T|0.845;C|0.155	0.155	strong		0.537	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
C2orf16	84226	hgsc.bcm.edu	37	2	27801418	27801418	+	Missense_Mutation	SNP	C	C	A	rs1919126	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27801418C>A	ENST00000408964.2	+	1	2030	c.1979C>A	c.(1978-1980)gCa>gAa	p.A660E		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	660			A -> E (in dbSNP:rs1919126).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GTGAAGTCTGCAGAATTAACC	0.393													A|||	3303	0.659545	0.7368	0.6888	5008	,	,		21677	0.8462		0.498	False		,,,				2504	0.5082				p.A660E		Atlas-SNP	.											.	C2orf16	357	.	0			c.C1979A						PASS	.	A	GLU/ALA	2621,1157		901,819,169	97.0	94.0	95.0		1979	-3.1	0.6	2	dbSNP_92	95	4093,4147		1033,2027,1060	yes	missense	C2orf16	NM_032266.3	107	1934,2846,1229	AA,AC,CC		49.6723,30.6247,44.1338	benign	660/1985	27801418	6714,5304	1889	4120	6009	SO:0001583	missense	84226	exon1			AGTCTGCAGAATT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.1979C>A	2.37:g.27801418C>A	ENSP00000386190:p.Ala660Glu	Somatic	286	0	0		WXS	Illumina HiSeq	Phase_I	242	102	0.421488	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	1446	0.6620879120879121	359	0.7296747967479674	228	0.6298342541436464	490	0.8566433566433567	369	0.4868073878627968	A	3.617	-0.078286	0.07184	0.693753	0.496723	ENSG00000221843	ENST00000408964	T	0.08807	3.05	4.83	-3.09	0.05331	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.10064	-1.0646	8	0.33141	T	0.24	.	1.8543	0.03175	0.3285:0.3785:0.1261:0.1669	rs1919126;rs17705292;rs56730508;rs1919126	660	Q68DN1	CB016_HUMAN	E	660	ENSP00000386190:A660E	ENSP00000386190:A660E	A	+	2	0	C2orf16	27654922	0.755000	0.28372	0.604000	0.28916	0.421000	0.31385	-1.056000	0.03489	-1.023000	0.03342	-0.363000	0.07495	GCA	C|0.365;A|0.635	0.635	strong		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
ADAT3	113179	hgsc.bcm.edu	37	19	1912934	1912934	+	Silent	SNP	T	T	C	rs12984675	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1912934T>C	ENST00000602400.1	+	2	1068	c.840T>C	c.(838-840)acT>acC	p.T280T	ADAT3_ENST00000329478.2_Silent_p.T296T|SCAMP4_ENST00000414057.2_Intron|SCAMP4_ENST00000409472.1_Intron|SCAMP4_ENST00000316097.8_Intron			Q96EY9	ADAT3_HUMAN	adenosine deaminase, tRNA-specific 3	280					tRNA processing (GO:0008033)		hydrolase activity (GO:0016787)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|pancreas(1)|skin(2)	7		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACCTGTGCACTGGCTACGACC	0.726													C|||	1819	0.363219	0.4803	0.4193	5008	,	,		11860	0.4038		0.2048	False		,,,				2504	0.2863				p.T296T		Atlas-SNP	.											.	ADAT3	15	.	0			c.T888C						PASS	.	C	,	1904,2498	591.8+/-387.6	426,1052,723	57.0	52.0	54.0		,840	-6.8	0.5	19	dbSNP_121	54	1294,7292	728.8+/-406.7	102,1090,3101	no	intron,coding-synonymous	SCAMP4,ADAT3	NM_079834.2,NM_138422.1	,	528,2142,3824	CC,CT,TT		15.071,43.2531,24.6227	,	,280/352	1912934	3198,9790	2201	4293	6494	SO:0001819	synonymous_variant	113179	exon2			GTGCACTGGCTAC	BC011824	CCDS12076.1, CCDS12076.2	19p13.3	2011-05-19	2011-05-19		ENSG00000213638	ENSG00000213638			25151	protein-coding gene	gene with protein product	"""tRNA-specific adenosine deaminase 3 homolog (S. cerevisiae)"""	615302	"""adenosine deaminase, tRNA-specific 3, TAD3 homolog (S. cerevisiae)"""			12457566	Standard	NM_138422		Approved	TAD3	uc002luh.4	Q96EY9	OTTHUMG00000154591	ENST00000602400.1:c.840T>C	19.37:g.1912934T>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	15	15	1	NM_138422		Silent	SNP	ENST00000602400.1	37																																																																																				T|0.727;C|0.273	0.273	strong		0.726	ADAT3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_138422	
COL13A1	1305	hgsc.bcm.edu	37	10	71562437	71562437	+	Silent	SNP	G	G	A	rs10998973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:71562437G>A	ENST00000398978.3	+	1	750	c.258G>A	c.(256-258)acG>acA	p.T86T	COL13A1_ENST00000398972.3_Silent_p.T86T|COL13A1_ENST00000520267.1_Silent_p.T86T|COL13A1_ENST00000398971.3_Silent_p.T86T|COL13A1_ENST00000522165.1_Silent_p.T86T|COL13A1_ENST00000357811.3_Silent_p.T86T|COL13A1_ENST00000398974.3_Silent_p.T86T|COL13A1_ENST00000398966.3_Silent_p.T86T|COL13A1_ENST00000398969.3_Silent_p.T86T|COL13A1_ENST00000398964.3_Silent_p.T86T|COL13A1_ENST00000398968.3_Silent_p.T86T|COL13A1_ENST00000354547.3_Silent_p.T86T|COL13A1_ENST00000356340.3_Silent_p.T86T|COL13A1_ENST00000520133.1_Silent_p.T86T|COL13A1_ENST00000517713.1_Silent_p.T86T|COL13A1_ENST00000398973.3_Silent_p.T86T	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1											endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						AAATGGAGACGGCTATTTTGG	0.657													G|||	2640	0.527157	0.3139	0.6571	5008	,	,		13707	0.7073		0.5686	False		,,,				2504	0.4949				p.T86T		Atlas-SNP	.											COL13A1_ENST00000398978,NS,carcinoma,0,2	COL13A1	133	2	0			c.G258A						PASS	.	G	,,,,,	1204,2784		193,818,983	154.0	162.0	159.0		258,258,258,258,258,258	4.4	1.0	10	dbSNP_120	159	4509,3829		1236,2037,896	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL13A1	NM_001130103.1,NM_080798.3,NM_080800.3,NM_080801.3,NM_080802.3,NM_080805.3	,,,,,	1429,2855,1879	AA,AG,GG		45.9223,30.1906,46.3492	,,,,,	86/718,86/646,86/687,86/696,86/669,86/611	71562437	5713,6613	1994	4169	6163	SO:0001819	synonymous_variant	1305	exon1			GGAGACGGCTATT	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.258G>A	10.37:g.71562437G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	148	58	0.391892	NM_080802		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			G|0.444;A|0.556	0.556	strong		0.657	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203	
MON2	23041	hgsc.bcm.edu	37	12	62979216	62979216	+	Silent	SNP	G	G	A	rs11174557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:62979216G>A	ENST00000393632.2	+	33	5233	c.4842G>A	c.(4840-4842)agG>agA	p.R1614R	MON2_ENST00000546600.1_Silent_p.R1614R|MON2_ENST00000552738.1_Silent_p.R1585R|MON2_ENST00000280379.6_Silent_p.R1615R|MON2_ENST00000551397.1_5'Flank|MON2_ENST00000393629.2_Silent_p.R1608R|MON2_ENST00000393630.3_Silent_p.R1615R	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1614					actin cytoskeleton organization (GO:0030036)|Golgi to endosome transport (GO:0006895)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	extracellular vesicular exosome (GO:0070062)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(15)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	57			BRCA - Breast invasive adenocarcinoma(9;0.218)	GBM - Glioblastoma multiforme(28;0.128)		TTTTAAAGAGGTCCCAAGATG	0.348													G|||	390	0.0778754	0.0129	0.1095	5008	,	,		17108	0.0169		0.1859	False		,,,				2504	0.0951				p.R1614R		Atlas-SNP	.											.	MON2	160	.	0			c.G4842A						PASS	.	G		167,4239	109.5+/-147.8	8,151,2044	74.0	71.0	72.0		4842	0.9	1.0	12	dbSNP_120	72	1564,7036	293.4+/-301.3	130,1304,2866	no	coding-synonymous	MON2	NM_015026.2		138,1455,4910	AA,AG,GG		18.186,3.7903,13.3092		1614/1718	62979216	1731,11275	2203	4300	6503	SO:0001819	synonymous_variant	23041	exon33			AAAGAGGTCCCAA		CCDS31849.1, CCDS61175.1, CCDS61177.1, CCDS61178.1	12q14.1	2014-08-12	2006-04-04		ENSG00000061987	ENSG00000061987			29177	protein-coding gene	gene with protein product			"""MON2 homolog (yeast)"""			16301316, 24285343	Standard	NM_015026		Approved	KIAA1040	uc001sre.3	Q7Z3U7	OTTHUMG00000169992	ENST00000393632.2:c.4842G>A	12.37:g.62979216G>A		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	119	69	0.579832	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Silent	SNP	ENST00000393632.2	37	CCDS31849.1																																																																																			G|0.884;A|0.116	0.116	strong		0.348	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026	
FN1	2335	hgsc.bcm.edu	37	2	216298084	216298084	+	Silent	SNP	G	G	A	rs2289202	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:216298084G>A	ENST00000359671.1	-	3	643	c.378C>T	c.(376-378)atC>atT	p.I126I	FN1_ENST00000421182.1_Silent_p.I126I|AC012462.1_ENST00000412951.1_RNA|FN1_ENST00000426059.1_Silent_p.I126I|FN1_ENST00000354785.4_Silent_p.I126I|FN1_ENST00000432072.2_Silent_p.I126I|FN1_ENST00000345488.5_Silent_p.I126I|FN1_ENST00000357009.2_Silent_p.I126I|FN1_ENST00000443816.1_Silent_p.I126I|FN1_ENST00000357867.4_Silent_p.I126I|FN1_ENST00000323926.6_Silent_p.I126I|FN1_ENST00000446046.1_Silent_p.I126I|FN1_ENST00000336916.4_Silent_p.I126I|FN1_ENST00000346544.3_Silent_p.I126I|FN1_ENST00000356005.4_Silent_p.I126I			P02751	FINC_HUMAN	fibronectin 1	126	Fibrin- and heparin-binding 1.|Fibronectin type-I 2. {ECO:0000255|PROSITE-ProRule:PRU00478}.			I -> V (in Ref. 5; CAH18136). {ECO:0000305}.	acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	GCCCAGCCCCGATGCAGGTAC	0.448													G|||	722	0.144169	0.2549	0.1427	5008	,	,		21425	0.001		0.2445	False		,,,				2504	0.0399				p.I126I		Atlas-SNP	.											FN1,NS,carcinoma,-2,1	FN1	521	1	0			c.C378T						PASS	.	G	,,,,,	1058,3348	387.0+/-326.3	123,812,1268	159.0	144.0	149.0		378,378,378,378,378,378	-5.8	0.8	2	dbSNP_100	149	2099,6501	363.0+/-333.0	266,1567,2467	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FN1	NM_002026.2,NM_054034.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	,,,,,	389,2379,3735	AA,AG,GG		24.407,24.0127,24.2734	,,,,,	126/2356,126/658,126/2177,126/2297,126/2331,126/2478	216298084	3157,9849	2203	4300	6503	SO:0001819	synonymous_variant	2335	exon3			AGCCCCGATGCAG		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.378C>T	2.37:g.216298084G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	112	57	0.508929	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	37																																																																																				G|0.783;A|0.217	0.217	strong		0.448	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
PLA2G5	5322	hgsc.bcm.edu	37	1	20411332	20411332	+	Silent	SNP	C	C	T	rs2020887	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:20411332C>T	ENST00000375108.3	+	2	277	c.9C>T	c.(7-9)ggC>ggT	p.G3G	PLA2G5_ENST00000486277.1_3'UTR	NM_000929.2	NP_000920.1	P39877	PA2G5_HUMAN	phospholipase A2, group V	3					arachidonic acid secretion (GO:0050482)|glycerophospholipid biosynthetic process (GO:0046474)|leukotriene biosynthetic process (GO:0019370)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|heparin binding (GO:0008201)	p.G3G(1)		NS(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		AGATGAAAGGCCTCCTCCCAC	0.537													C|||	1259	0.251398	0.0953	0.2608	5008	,	,		18264	0.3065		0.338	False		,,,				2504	0.3098				p.G3G		Atlas-SNP	.											PLA2G5,NS,carcinoma,+2,2	PLA2G5	21	2	1	Substitution - coding silent(1)	stomach(1)	c.C9T						PASS	.	C		558,3848	251.8+/-258.4	29,500,1674	161.0	152.0	155.0		9	-1.6	0.0	1	dbSNP_98	155	3009,5591	464.4+/-366.2	510,1989,1801	no	coding-synonymous	PLA2G5	NM_000929.2		539,2489,3475	TT,TC,CC		34.9884,12.6645,27.4258		3/139	20411332	3567,9439	2203	4300	6503	SO:0001819	synonymous_variant	5322	exon2			GAAAGGCCTCCTC	U03090	CCDS202.1	1p36-p34	2008-09-19			ENSG00000127472	ENSG00000127472	3.1.1.4		9038	protein-coding gene	gene with protein product		601192				8838795, 8300559	Standard	NM_000929		Approved		uc001bcy.3	P39877	OTTHUMG00000002698	ENST00000375108.3:c.9C>T	1.37:g.20411332C>T		Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	189	186	0.984127	NM_000929	Q8N435	Silent	SNP	ENST00000375108.3	37	CCDS202.1																																																																																			C|0.724;T|0.276	0.276	strong		0.537	PLA2G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007668.1	NM_000929	
NCF2	4688	hgsc.bcm.edu	37	1	183542387	183542387	+	Missense_Mutation	SNP	T	T	C	rs2274064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:183542387T>C	ENST00000367535.3	-	5	793	c.542A>G	c.(541-543)aAg>aGg	p.K181R	NCF2_ENST00000418089.1_Intron|NCF2_ENST00000367536.1_Missense_Mutation_p.K181R|NCF2_ENST00000413720.1_Missense_Mutation_p.K136R	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	181			K -> R (in dbSNP:rs2274064). {ECO:0000269|PubMed:10498624, ECO:0000269|PubMed:10598813, ECO:0000269|PubMed:12207919, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.4, ECO:0000269|Ref.8}.		aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	TCGAAACAGCTTGCCCACAGG	0.512													C|||	2462	0.491613	0.3306	0.598	5008	,	,		21080	0.621		0.4672	False		,,,				2504	0.5256				p.K181R		Atlas-SNP	.											.	NCF2	69	.	0			c.A542G						PASS	.	C	ARG/LYS,ARG/LYS,,ARG/LYS	1581,2825	667.0+/-401.8	294,993,916	203.0	185.0	191.0		542,542,,407	1.3	1.0	1	dbSNP_100	191	4012,4588	597.2+/-393.7	952,2108,1240	yes	missense,missense,intron,missense	NCF2	NM_000433.3,NM_001127651.2,NM_001190789.1,NM_001190794.1	26,26,,26	1246,3101,2156	CC,CT,TT		46.6512,35.8829,43.0032	benign,benign,,benign	181/527,181/527,,136/482	183542387	5593,7413	2203	4300	6503	SO:0001583	missense	4688	exon6			AACAGCTTGCCCA	BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	7661	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.542A>G	1.37:g.183542387T>C	ENSP00000356505:p.Lys181Arg	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	120	63	0.525	NM_001127651	B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Missense_Mutation	SNP	ENST00000367535.3	37	CCDS1356.1	1097	0.5022893772893773	176	0.35772357723577236	198	0.5469613259668509	369	0.6451048951048951	354	0.46701846965699206	C	5.163	0.215651	0.09810	0.358829	0.466512	ENSG00000116701	ENST00000367536;ENST00000392014;ENST00000413720;ENST00000367535	T;T;T	0.65732	-0.17;-0.1;-0.17	5.08	1.27	0.21489	.	0.555420	0.21403	N	0.075117	T	0.00012	0.0000	N	0.04043	-0.29	0.09310	P	0.999999999854424	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.44467	-0.9326	9	0.06891	T	0.86	-10.3885	9.9264	0.41494	0.0:0.53:0.0:0.47	rs2274064;rs12691462;rs17434977;rs17844914;rs17857636;rs34730753;rs58356110;rs2274064	136;181	E9PHX3;P19878	.;NCF2_HUMAN	R	181;209;136;181	ENSP00000356506:K181R;ENSP00000399294:K136R;ENSP00000356505:K181R	ENSP00000356505:K181R	K	-	2	0	NCF2	181809010	0.992000	0.36948	0.998000	0.56505	0.968000	0.65278	0.583000	0.23849	0.100000	0.17581	-0.962000	0.02626	AAG	T|0.538;C|0.462	0.462	strong		0.512	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433	
PRR22	163154	hgsc.bcm.edu	37	19	5783905	5783905	+	Missense_Mutation	SNP	G	G	A	rs3745640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5783905G>A	ENST00000419421.2	-	3	457	c.353C>T	c.(352-354)cCt>cTt	p.P118L		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	118	Pro-rich.		P -> L (in dbSNP:rs3745640).							endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GTAGGGCTGAGGCTCCAGGAG	0.706													G|||	1540	0.307508	0.3147	0.1859	5008	,	,		10380	0.5437		0.165	False		,,,				2504	0.2873				p.P118L		Atlas-SNP	.											.	PRR22	25	.	0			c.C353T						PASS	.	G	LEU/PRO	990,3048		90,810,1119	4.0	6.0	5.0		353	4.5	0.4	19	dbSNP_107	5	1119,7019		66,987,3016	yes	missense	PRR22	NM_001134316.1	98	156,1797,4135	AA,AG,GG		13.7503,24.5171,17.321	possibly-damaging	118/423	5783905	2109,10067	2019	4069	6088	SO:0001583	missense	163154	exon3			GGCTGAGGCTCCA	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.353C>T	19.37:g.5783905G>A	ENSP00000407653:p.Pro118Leu	Somatic	30	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	638	0.29212454212454214	154	0.3130081300813008	75	0.20718232044198895	282	0.493006993006993	127	0.16754617414248021	G	19.20	3.782414	0.70222	0.245171	0.137503	ENSG00000212123	ENST00000419421	T	0.45668	0.89	4.51	4.51	0.55191	.	.	.	.	.	T	0.00012	0.0000	L	0.27053	0.805	0.28455	P	0.9161476	P;D	0.57571	0.944;0.98	P;P	0.51806	0.548;0.68	T	0.48790	-0.9004	8	0.72032	D	0.01	-9.3203	14.7247	0.69336	0.0:0.0:1.0:0.0	rs3745640;rs3745640	118;116	E9PB31;Q8IZ63	.;PRR22_HUMAN	L	118	ENSP00000407653:P118L	ENSP00000407653:P118L	P	-	2	0	PRR22	5734905	0.736000	0.28164	0.388000	0.26195	0.756000	0.42949	5.938000	0.70170	2.338000	0.79540	0.436000	0.28706	CCT	G|0.702;A|0.298	0.298	strong		0.706	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
PCSK1N	27344	hgsc.bcm.edu	37	X	48690749	48690749	+	Silent	SNP	C	C	T	rs11538178		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:48690749C>T	ENST00000218230.5	-	2	217	c.117G>A	c.(115-117)gaG>gaA	p.E39E	PCSK1N_ENST00000478242.1_5'UTR	NM_013271.2	NP_037403.1	Q9UHG2	PCSK1_HUMAN	proprotein convertase subtilisin/kexin type 1 inhibitor	39	ProSAAS(1-180). {ECO:0000250}.				neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|response to cold (GO:0009409)|response to dietary excess (GO:0002021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)	endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)										GGCCGCGGGGCTCCTGCGGGA	0.682													c|||	1198	0.317351	0.5234	0.0807	3775	,	,		6872	0.1151		0.0666	False		,,,				2504	0.273				p.E39E		Atlas-SNP	.											.	PCSK1N	6	.	0			c.G117A						PASS	.			1039,1413		118,601,202,343,126	2.0	2.0	2.0		117	0.3	0.9	X	dbSNP_120	2	346,4094		11,224,100,1486,898	yes	coding-synonymous	PCSK1N	NM_013271.2		129,825,302,1829,1024	TT,TC,T,CC,C		7.7928,42.3736,20.0958		39/261	48690749	1385,5507	1390	2719	4109	SO:0001819	synonymous_variant	27344	exon2			GCGGGGCTCCTGC	AF181562	CCDS14307.1	Xp11.23	2008-07-28			ENSG00000102109	ENSG00000102109			17301	protein-coding gene	gene with protein product		300399				10632593	Standard	NM_013271		Approved	SAAS	uc004dkz.4	Q9UHG2	OTTHUMG00000034502	ENST00000218230.5:c.117G>A	X.37:g.48690749C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	10	9	0.9	NM_013271	Q4VC04	Silent	SNP	ENST00000218230.5	37	CCDS14307.1																																																																																			C|0.763;T|0.237	0.237	strong		0.682	PCSK1N-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083444.1	NM_013271	
SLITRK2	84631	hgsc.bcm.edu	37	X	144904252	144904252	+	Silent	SNP	G	G	A	rs3810704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:144904252G>A	ENST00000370490.1	+	1	4564	c.309G>A	c.(307-309)acG>acA	p.T103T	SLITRK2_ENST00000428560.2_Silent_p.T103T|SLITRK2_ENST00000434188.2_Silent_p.T103T|SLITRK2_ENST00000413937.2_Silent_p.T103T|SLITRK2_ENST00000447897.2_Silent_p.T103T			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	103					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					AGATCCGAACGGGGGCATTCA	0.483													G|||	592	0.156821	0.1407	0.0591	3775	,	,		14738	0.0407		0.1412	False		,,,				2504	0.1861				p.T103T		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G309A						PASS	.	G	,,,,,,,	719,3116		63,494,99,1075,472	72.0	63.0	66.0		309,309,309,309,309,309,309,309	-9.8	0.0	X	dbSNP_107	66	1124,5604		56,670,342,1702,1530	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLITRK2	NM_001144003.2,NM_001144004.2,NM_001144005.2,NM_001144006.2,NM_001144008.2,NM_001144009.2,NM_001144010.2,NM_032539.4	,,,,,,,	119,1164,441,2777,2002	AA,AG,A,GG,G		16.7063,18.7484,17.4477	,,,,,,,	103/846,103/846,103/846,103/846,103/846,103/846,103/846,103/846	144904252	1843,8720	2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			CCGAACGGGGGCA	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.309G>A	X.37:g.144904252G>A		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	84	82	0.97619	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																			G|0.836;A|0.164	0.164	strong		0.483	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
DSCAML1	57453	hgsc.bcm.edu	37	11	117391966	117391966	+	Silent	SNP	G	G	A	rs2276340	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:117391966G>A	ENST00000321322.6	-	6	1273	c.1272C>T	c.(1270-1272)cgC>cgT	p.R424R	DSCAML1_ENST00000527706.1_Silent_p.R154R	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	364	Ig-like C2-type 5.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		TGCTGAGCCCGCGGATGGAGA	0.652													G|||	1000	0.199681	0.0938	0.1888	5008	,	,		15433	0.253		0.1581	False		,,,				2504	0.3384				p.R424R		Atlas-SNP	.											DSCAML1,colon,carcinoma,-1,1	DSCAML1	286	1	0			c.C1272T						PASS	.	G		458,3944	216.8+/-235.3	25,408,1768	121.0	102.0	108.0		1272	0.5	1.0	11	dbSNP_100	108	1391,7201	268.5+/-287.9	102,1187,3007	no	coding-synonymous	DSCAML1	NM_020693.2		127,1595,4775	AA,AG,GG		16.1895,10.4044,14.2296		424/2114	117391966	1849,11145	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon6			GAGCCCGCGGATG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.1272C>T	11.37:g.117391966G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	92	44	0.478261	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			G|0.848;A|0.152	0.152	strong		0.652	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20126741	20126741	+	Silent	SNP	G	G	T	rs61737216	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:20126741G>T	ENST00000334554.7	+	2	270	c.129G>T	c.(127-129)gtG>gtT	p.V43V	ZDHHC8_ENST00000468112.1_Intron|ZDHHC8_ENST00000320602.7_Silent_p.V43V|ZDHHC8_ENST00000405930.3_Silent_p.V43V	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	43					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					CACGAGCTGTGTCCCCAGCTG	0.592													G|||	251	0.0501198	0.0045	0.0101	5008	,	,		16726	0.0813		0.0527	False		,,,				2504	0.1053				p.V43V		Atlas-SNP	.											.	ZDHHC8	77	.	0			c.G129T						PASS	.	G	,	52,4354	52.3+/-87.9	0,52,2151	172.0	146.0	155.0		129,129	1.0	1.0	22	dbSNP_129	155	466,8134	138.7+/-195.5	18,430,3852	no	coding-synonymous,coding-synonymous	ZDHHC8	NM_001185024.1,NM_013373.3	,	18,482,6003	TT,TG,GG		5.4186,1.1802,3.9828	,	43/779,43/766	20126741	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	29801	exon2			AGCTGTGTCCCCA	AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.129G>T	22.37:g.20126741G>T		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	112	58	0.517857	NM_001185024	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Silent	SNP	ENST00000334554.7	37	CCDS13776.1																																																																																			G|0.959;T|0.041	0.041	strong		0.592	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1	NM_013373	
CHL1	10752	hgsc.bcm.edu	37	3	361508	361508	+	Missense_Mutation	SNP	C	C	T	rs2272522	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:361508C>T	ENST00000256509.2	+	3	691	c.49C>T	c.(49-51)Ctc>Ttc	p.L17F	CHL1_ENST00000397491.2_Missense_Mutation_p.L17F	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.L17F(1)		NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		TCTAATGTTCCTCCTGTTAAA	0.338													T|||	1763	0.352037	0.5643	0.2378	5008	,	,		16826	0.3085		0.2048	False		,,,				2504	0.3425				p.L17F		Atlas-SNP	.											CHL1,caecum,carcinoma,0,2	CHL1	242	2	1	Substitution - Missense(1)	stomach(1)	c.C49T	GRCh37	CM023348	CHL1	M	rs2272522	PASS	.	T	PHE/LEU	2278,2126	572.4+/-383.3	567,1144,491	63.0	66.0	65.0		49	-2.0	0.0	3	dbSNP_100	65	1740,6860	732.3+/-406.8	185,1370,2745	yes	missense	CHL1	NM_006614.2	22	752,2514,3236	TT,TC,CC		20.2326,48.2743,30.8982	benign	17/1225	361508	4018,8986	2202	4300	6502	SO:0001583	missense	10752	exon1			ATGTTCCTCCTGT	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.49C>T	3.37:g.361508C>T	ENSP00000256509:p.Leu17Phe	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	46	23	0.5	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	678	0.31043956043956045	272	0.5528455284552846	84	0.23204419889502761	176	0.3076923076923077	146	0.19261213720316622	T	0.103	-1.149599	0.01714	0.517257	0.202326	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;T;T;T	0.65732	0.16;0.19;1.01;0.21;0.13;-0.17	4.78	-2.03	0.07365	.	0.510152	0.20101	N	0.099240	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.36286	-0.9754	9	0.02654	T	1	.	10.7653	0.46291	0.0:0.4333:0.0:0.5667	rs2272522;rs57759025;rs2272522	17;17;17	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	F	17	ENSP00000256509:L17F;ENSP00000380628:L17F;ENSP00000403311:L17F;ENSP00000413628:L17F;ENSP00000397445:L17F;ENSP00000390440:L17F	ENSP00000256509:L17F	L	+	1	0	CHL1	336508	0.756000	0.28383	0.003000	0.11579	0.135000	0.20990	-0.166000	0.09954	-0.954000	0.03640	-1.197000	0.01672	CTC	C|0.678;T|0.322	0.322	strong		0.338	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
ESYT2	57488	hgsc.bcm.edu	37	7	158528233	158528233	+	Silent	SNP	A	A	G	rs3816462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:158528233A>G	ENST00000251527.5	-	20	2612	c.2547T>C	c.(2545-2547)agT>agC	p.S849S	ESYT2_ENST00000435514.2_Silent_p.S284S	NM_020728.2	NP_065779.1	A0FGR8	ESYT2_HUMAN	extended synaptotagmin-like protein 2	877	C2 3. {ECO:0000255|PROSITE- ProRule:PRU00041}.				endocytosis (GO:0006897)|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)|membrane (GO:0016020)|organelle membrane contact site (GO:0044232)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|identical protein binding (GO:0042802)|phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(16)|prostate(2)	32						GGAAGCCGCCACTGTTCTTCA	0.458													G|||	1770	0.353435	0.4387	0.183	5008	,	,		18629	0.6022		0.173	False		,,,				2504	0.2883				p.S849S		Atlas-SNP	.											.	ESYT2	70	.	0			c.T2547C						PASS	.			1645,2761	504.6+/-365.9	321,1003,879	160.0	168.0	165.0		2547	-9.9	0.3	7	dbSNP_107	165	1486,7114	281.2+/-294.9	126,1234,2940	no	coding-synonymous	ESYT2	NM_020728.2		447,2237,3819	GG,GA,AA		17.2791,37.3355,24.0735		849/894	158528233	3131,9875	2203	4300	6503	SO:0001819	synonymous_variant	57488	exon20			GCCGCCACTGTTC	AB033054	CCDS34791.1	7q36.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000117868	ENSG00000117868		"""Synaptotagmins"""	22211	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member B"""	FAM62B		17672888	Standard	NM_020728		Approved	KIAA1228, CHR2SYT	uc003wob.1	A0FGR8	OTTHUMG00000151436	ENST00000251527.5:c.2547T>C	7.37:g.158528233A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	75	34	0.453333	NM_020728	A4D229|Q69YJ2|Q6UKI4|Q6ZTU0|Q6ZVU1|Q9BQS0|Q9NW47|Q9ULJ2	Silent	SNP	ENST00000251527.5	37	CCDS34791.1																																																																																			A|0.703;G|0.297	0.297	strong		0.458	ESYT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322647.1	NM_020728	
LRP4	4038	hgsc.bcm.edu	37	11	46897446	46897446	+	Missense_Mutation	SNP	G	G	A	rs2306033	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:46897446G>A	ENST00000378623.1	-	26	3850	c.3608C>T	c.(3607-3609)gCg>gTg	p.A1203V	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1203			A -> V (in dbSNP:rs2306033).		dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GATGAGCACCGCGCGGTCTGA	0.542													G|||	1098	0.219249	0.0045	0.2781	5008	,	,		20112	0.6101		0.1193	False		,,,				2504	0.1677				p.A1203V		Atlas-SNP	.											.	LRP4	160	.	0			c.C3608T						PASS	.	G	VAL/ALA	148,4254	101.6+/-140.2	3,142,2056	131.0	99.0	110.0		3608	5.7	0.0	11	dbSNP_100	110	1051,7547	222.0+/-259.2	55,941,3303	yes	missense	LRP4	NM_002334.3	64	58,1083,5359	AA,AG,GG		12.2238,3.3621,9.2231	benign	1203/1906	46897446	1199,11801	2201	4299	6500	SO:0001583	missense	4038	exon26			AGCACCGCGCGGT	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.3608C>T	11.37:g.46897446G>A	ENSP00000367888:p.Ala1203Val	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	204	112	0.54902	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	537	0.24587912087912087	4	0.008130081300813009	98	0.27071823204419887	332	0.5804195804195804	103	0.1358839050131926	G	0.720	-0.783875	0.02907	0.033621	0.122238	ENSG00000134569	ENST00000378623	D	0.93811	-3.29	5.71	5.71	0.89125	Six-bladed beta-propeller, TolB-like (1);	0.497398	0.23189	N	0.050940	T	0.00012	0.0000	N	0.02202	-0.64	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.36187	-0.9758	9	0.20046	T	0.44	.	7.4774	0.27385	0.1975:0.0:0.8025:0.0	rs2306033;rs17197332;rs52799813;rs56867112;rs2306033	1203	O75096	LRP4_HUMAN	V	1203	ENSP00000367888:A1203V	ENSP00000367888:A1203V	A	-	2	0	LRP4	46854022	0.599000	0.26891	0.021000	0.16686	0.212000	0.24457	3.696000	0.54757	2.704000	0.92352	0.555000	0.69702	GCG	G|0.848;A|0.152	0.152	strong		0.542	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24381387	24381387	+	IGR	SNP	G	G	C	rs1207577	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:24381387G>C								AC004552.1 (14364 upstream) : PDK3 (101950 downstream)																							TACGTCCAACGATGCAGACTT	0.468													G|||	2036	0.539338	0.5756	0.3141	3775	,	,		16356	0.3423		0.1998	False		,,,				2504	0.5225				p.T170T		Atlas-SNP	.											.	.	.	.	0			c.G510C						PASS	.	G		1856,771		543,413,357,103,152	222.0	214.0	217.0		510	-6.8	0.0	X	dbSNP_87	217	1472,4026		145,737,445,1034,1221	no	coding-synonymous	FAM48B1	NM_001136234.1		688,1150,802,1137,1373	CC,CG,C,GG,G		26.7734,29.3491,40.96		170/888	24381387	3328,4797	1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			TCCAACGATGCAG																													X.37:g.24381387G>C		Somatic	406	1	0.00246305		WXS	Illumina HiSeq	Phase_I	467	466	0.997859	NM_001136234		Silent	SNP		37																																																																																				G|0.535;C|0.465	0.465	strong	0	0.468								
FAM83E	54854	hgsc.bcm.edu	37	19	49106995	49106995	+	Missense_Mutation	SNP	G	G	A	rs3745728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49106995G>A	ENST00000263266.3	-	4	1121	c.932C>T	c.(931-933)cCg>cTg	p.P311L		NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	311			P -> L (in dbSNP:rs3745728). {ECO:0000269|PubMed:14702039}.					p.P311L(1)		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)		CACGCGGTGCGGGCTGCGGCC	0.776													G|||	914	0.182508	0.1316	0.1484	5008	,	,		6380	0.3333		0.1233	False		,,,				2504	0.181				p.P311L		Atlas-SNP	.											FAM83E,NS,NS,0,1	FAM83E	34	1	1	Substitution - Missense(1)	NS(1)	c.C932T						scavenged	.	G	LEU/PRO	319,3115		18,283,1416	4.0	4.0	4.0		932	2.7	0.5	19	dbSNP_107	4	790,6694		40,710,2992	no	missense	FAM83E	NM_017708.3	98	58,993,4408	AA,AG,GG		10.5559,9.2895,10.1575	probably-damaging	311/479	49106995	1109,9809	1717	3742	5459	SO:0001583	missense	54854	exon4			CGGTGCGGGCTGC	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.932C>T	19.37:g.49106995G>A	ENSP00000263266:p.Pro311Leu	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_017708	Q9NXK1	Missense_Mutation	SNP	ENST00000263266.3	37	CCDS42587.1	405	0.18543956043956045	68	0.13821138211382114	52	0.143646408839779	194	0.33916083916083917	91	0.12005277044854881	G	18.13	3.555078	0.65425	0.092895	0.105559	ENSG00000105523	ENST00000263266	T	0.11277	2.79	3.79	2.65	0.31530	.	11.390300	0.00166	N	0.000000	T	0.00012	0.0000	L	0.32530	0.975	0.29073	P	0.883177	D	0.69078	0.997	P	0.53035	0.716	T	0.36939	-0.9727	9	0.35671	T	0.21	-5.1491	9.7456	0.40444	0.0:0.2122:0.7878:0.0	rs3745728	311	Q2M2I3	FA83E_HUMAN	L	311	ENSP00000263266:P311L	ENSP00000263266:P311L	P	-	2	0	FAM83E	53798807	1.000000	0.71417	0.455000	0.27031	0.142000	0.21351	4.236000	0.58675	1.845000	0.53610	0.549000	0.68633	CCG	G|0.814;A|0.186	0.186	strong		0.776	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
KIF5C	3800	hgsc.bcm.edu	37	2	149806388	149806388	+	Silent	SNP	C	C	T	rs60169973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:149806388C>T	ENST00000435030.1	+	9	1118	c.750C>T	c.(748-750)gaC>gaT	p.D250D	KIF5C_ENST00000414838.2_Silent_p.D155D|KIF5C_ENST00000464066.1_3'UTR|KIF5C_ENST00000397413.1_Silent_p.D18D			O60282	KIF5C_HUMAN	kinesin family member 5C	250	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.|Microtubule-binding.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		CTGTTCTTGACGAAGCTAAAA	0.443													C|||	654	0.130591	0.3086	0.0965	5008	,	,		18947	0.0159		0.0924	False		,,,				2504	0.0716				p.D250D		Atlas-SNP	.											.	KIF5C	166	.	0			c.C750T						PASS	.	C		997,2855		141,715,1070	105.0	102.0	103.0		461	-7.3	0.3	2	dbSNP_129	103	701,7595		36,629,3483	no	coding-synonymous	KIF5C	NM_004522.1		177,1344,4553	TT,TC,CC		8.4499,25.8827,13.9776		250/958	149806388	1698,10450	1926	4148	6074	SO:0001819	synonymous_variant	3800	exon9			TCTTGACGAAGCT	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.750C>T	2.37:g.149806388C>T		Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	108	54	0.5	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				C|0.884;T|0.116	0.116	strong		0.443	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
RNASE9	390443	hgsc.bcm.edu	37	14	21026773	21026773	+	5'UTR	SNP	C	C	T	rs891297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:21026773C>T	ENST00000557068.1	-	0	181				RNASE9_ENST00000404716.3_5'UTR|RNASE9_ENST00000557209.1_Splice_Site|RNASE9_ENST00000338904.3_Intron|RNASE9_ENST00000555230.1_5'UTR|RNASE9_ENST00000553541.1_Intron|RNASE9_ENST00000429244.2_Intron|RNASE9_ENST00000553706.1_Splice_Site|RNASE9_ENST00000554964.1_Intron|RNASE9_ENST00000556208.1_5'UTR			P60153	RNAS9_HUMAN	ribonuclease, RNase A family, 9 (non-active)							extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|ovary(2)|urinary_tract(1)	8	all_cancers(95;0.00238)		Epithelial(56;3.32e-06)|all cancers(55;2.46e-05)	GBM - Glioblastoma multiforme(265;0.0141)		TCGGAACATACTCTCACAAGA	0.507													T|||	1571	0.313698	0.6868	0.2536	5008	,	,		18354	0.1171		0.1849	False		,,,				2504	0.1871				.		Atlas-SNP	.											.	RNASE9	30	.	0			c.1+1G>A						PASS	.						92.0	86.0	88.0					14																	21026773		692	1591	2283	SO:0001623	5_prime_UTR_variant	390443	exon5			AACATACTCTCAC	AY665804	CCDS32036.1, CCDS53883.1, CCDS55904.1	14q11.2	2006-10-31				ENSG00000188655		"""Ribonucleases, RNase A"""	20673	protein-coding gene	gene with protein product		614014				15676279, 12920233	Standard	NM_001001673		Approved	h461	uc010ahu.3	P60153		ENST00000557068.1:c.-1545G>A	14.37:g.21026773C>T		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	104	56	0.538462	NM_001110361	A2RQR8|A8QJS1|Q5GAN7|Q6KG53	Splice_Site	SNP	ENST00000557068.1	37	CCDS32036.1	612	0.2802197802197802	324	0.6585365853658537	91	0.2513812154696133	59	0.10314685314685315	138	0.1820580474934037	T	0.163	-1.079531	0.01903	.	.	ENSG00000188655	ENST00000553706;ENST00000557209	.	.	.	2.14	-4.27	0.03744	.	.	.	.	.	.	.	.	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.911	0.05737	0.1585:0.4886:0.1496:0.2034	rs891297;rs1756412;rs891297	.	.	.	.	-1	.	.	.	-	.	.	RNASE9	20096613	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.794000	0.04584	-2.392000	0.00585	-1.341000	0.01249	.	C|0.689;T|0.311	0.311	strong		0.507	RNASE9-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411094.1	NM_001001673	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45258333	45258333	+	Missense_Mutation	SNP	C	C	G	rs9614957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:45258333C>G	ENST00000389774.2	+	13	1394	c.1253C>G	c.(1252-1254)cCt>cGt	p.P418R	ARHGAP8_ENST00000336963.4_3'UTR|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.P518R|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.P509R|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.P597R|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.P387R|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.P597R	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	418			P -> R (in dbSNP:rs9614957).		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)		CCGGAGGCACCTGGGGAGCAC	0.622													C|||	196	0.0391374	0.0061	0.049	5008	,	,		17837	0.0		0.1362	False		,,,				2504	0.0174				p.P509R		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C1526G						PASS	.	C	ARG/PRO,,ARG/PRO,ARG/PRO	111,4295	84.8+/-123.5	3,105,2095	48.0	48.0	48.0		1253,,1526,1160	1.1	0.0	22	dbSNP_119	48	1110,7490	229.7+/-264.3	73,964,3263	yes	missense,utr-3,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	103,,103,103	76,1069,5358	GG,GC,CC		12.907,2.5193,9.388	benign,,benign,benign	418/465,,509/556,387/434	45258333	1221,11785	2203	4300	6503	SO:0001583	missense	553158	exon15			AGGCACCTGGGGA	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.1253C>G	22.37:g.45258333C>G	ENSP00000374424:p.Pro418Arg	Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	85	85	1	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	132|132	0.06043956043956044|0.06043956043956044	4|4	0.008130081300813009|0.008130081300813009	21|21	0.058011049723756904|0.058011049723756904	0|0	0.0|0.0	107|107	0.14116094986807387|0.14116094986807387	C|C	2.648|2.648	-0.282562|-0.282562	0.05642|0.05642	0.025193|0.025193	0.12907|0.12907	ENSG00000248405|ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000515632|ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000356099	.|T;T;T;T;T;T	.|0.19669	.|2.21;2.19;2.19;2.21;2.13;2.13	3.32|3.32	1.13|1.13	0.20643|0.20643	.|Rho GTPase-activating protein domain (1);	.|1.642920	.|0.04238	.|N	.|0.336372	T|T	0.00073|0.00073	0.0002|0.0002	N|N	0.11064|0.11064	0.09|0.09	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.10296	.|0.001;0.003;0.002;0.0;0.002	.|B;B;B;B;B	.|0.13407	.|0.002;0.002;0.009;0.0;0.004	T|T	0.31530|0.31530	-0.9940|-0.9940	4|9	.|0.23302	.|T	.|0.38	.|.	7.0174|7.0174	0.24895|0.24895	0.0:0.6846:0.2075:0.1079|0.0:0.6846:0.2075:0.1079	rs9614957|rs9614957	.|440;423;418;597;518	.|B7ZMA4;A2RU51;P85298;B1AHC4;B1AHC3	.|.;.;RHG08_HUMAN;.;.	V|R	458|518;597;597;509;418;387	.|ENSP00000354732:P518R;ENSP00000262731:P597R;ENSP00000429240:P597R;ENSP00000374423:P509R;ENSP00000374424:P418R;ENSP00000348407:P387R	.|ENSP00000348407:P387R	L|P	+|+	1|2	2|0	PRR5-ARHGAP8|PRR5-ARHGAP8;ARHGAP8	43636997|43636997	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	0.333000|0.333000	0.19768|0.19768	0.377000|0.377000	0.24735|0.24735	0.655000|0.655000	0.94253|0.94253	CTG|CCT	C|0.911;G|0.089	0.089	strong		0.622	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
MICA	100507436	hgsc.bcm.edu	37	6	31379773	31379773	+	Silent	SNP	C	C	T	rs1051796	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31379773C>T	ENST00000449934.2	+	4	717	c.663C>T	c.(661-663)atC>atT	p.I221I	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				AGGGCAACATCACCGTGACAT	0.602													c|||	1821	0.363618	0.4766	0.4049	5008	,	,		20346	0.3006		0.3141	False		,,,				2504	0.2975				p.I221I		Atlas-SNP	.											.	MICA	21	.	0			c.C663T						PASS	.	C		579,805		132,315,245	31.0	34.0	33.0		663	1.6	0.0	6	dbSNP_86	33	913,2269		126,661,804	no	coding-synonymous	MICA	NM_001177519.1		258,976,1049	TT,TC,CC		28.6926,41.8353,32.6763		221/333	31379773	1492,3074	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon4			CAACATCACCGTG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.663C>T	6.37:g.31379773C>T		Somatic	138	1	0.00724638		WXS	Illumina HiSeq	Phase_I	65	64	0.984615	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			.	.	weak		0.602	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32557489	32557489	+	Missense_Mutation	SNP	A	A	T	rs199514452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32557489A>T	ENST00000360004.5	-	1	136	c.31T>A	c.(31-33)Tgc>Agc	p.C11S		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	11					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GCTGTCATGCAGGAGCCTCCA	0.582										Multiple Myeloma(14;0.17)			A|||	371	0.0740815	0.1225	0.0389	5008	,	,		25825	0.0585		0.0417	False		,,,				2504	0.0828				p.C11S		Atlas-SNP	.											HLA-DRB1,colon,carcinoma,0,1	HLA-DRB1	41	1	0			c.T31A						scavenged	.						86.0	103.0	97.0					6																	32557489		1511	2709	4220	SO:0001583	missense	3123	exon1			TCATGCAGGAGCC	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.31T>A	6.37:g.32557489A>T	ENSP00000353099:p.Cys11Ser	Somatic	275	2	0.00727273		WXS	Illumina HiSeq	Phase_I	246	22	0.0894309	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.88	1.772049	0.31320	.	.	ENSG00000196126	ENST00000360004	T	0.00241	8.46	4.68	2.29	0.28610	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.48362	1.52	0.09310	N	1	B	0.20887	0.049	B	0.23419	0.046	T	0.38308	-0.9667	9	0.45353	T	0.12	.	3.8919	0.09122	0.7162:0.0:0.0991:0.1848	.	11	P01911	2B1F_HUMAN	S	11	ENSP00000353099:C11S	ENSP00000353099:C11S	C	-	1	0	HLA-DRB1	32665467	0.021000	0.18746	0.048000	0.18961	0.007000	0.05969	0.788000	0.26872	0.321000	0.23259	-0.530000	0.04314	TGC	A|0.864;T|0.136	0.136	strong		0.582	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ATG9A	79065	hgsc.bcm.edu	37	2	220087088	220087088	+	Silent	SNP	T	T	G	rs146429396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220087088T>G	ENST00000409618.1	-	12	2372	c.1933A>C	c.(1933-1935)Agg>Cgg	p.R645R	ATG9A_ENST00000361242.4_Silent_p.R645R|AC068946.1_ENST00000408417.1_RNA|ATG9A_ENST00000396761.2_Silent_p.R645R|ATG9A_ENST00000409422.1_Silent_p.R584R			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	645					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)		ACTTCAGCCCTGTGCCTGGAG	0.662													t|||	25	0.00499201	0.0008	0.0043	5008	,	,		17208	0.0		0.0209	False		,,,				2504	0.0				p.R645R		Atlas-SNP	.											ATG9A,NS,carcinoma,+1,1	ATG9A	50	1	0			c.A1933C						PASS	.	T	,	12,3924		0,12,1956	43.0	50.0	48.0		1933,1933	3.0	1.0	2	dbSNP_134	48	165,8109		1,163,3973	no	coding-synonymous,coding-synonymous	ATG9A	NM_001077198.1,NM_024085.3	,	1,175,5929	GG,GT,TT		1.9942,0.3049,1.4496	,	645/840,645/840	220087088	177,12033	1968	4137	6105	SO:0001819	synonymous_variant	79065	exon12			CAGCCCTGTGCCT	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.1933A>C	2.37:g.220087088T>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	94	41	0.43617	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Silent	SNP	ENST00000409618.1	37	CCDS42820.1																																																																																			T|0.990;G|0.010	0.010	strong		0.662	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085	
OR2T34	127068	hgsc.bcm.edu	37	1	248737348	248737348	+	Silent	SNP	G	G	A	rs61833442	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:248737348G>A	ENST00000328782.2	-	1	732	c.711C>T	c.(709-711)gcC>gcT	p.A237A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTGCGGCCGGCGGCAGAAT	0.567													g|||	1625	0.324481	0.5098	0.2349	5008	,	,		20077	0.251		0.2107	False		,,,				2504	0.3303				p.A237A		Atlas-SNP	.											OR2T34,NS,carcinoma,-2,1	OR2T34	72	1	0			c.C711T						scavenged	.						110.0	124.0	119.0					1																	248737348		2176	4300	6476	SO:0001819	synonymous_variant	127068	exon1			GCGGCCGGCGGCA	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.711C>T	1.37:g.248737348G>A		Somatic	353	0	0		WXS	Illumina HiSeq	Phase_I	365	48	0.131507	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Silent	SNP	ENST00000328782.2	37	CCDS31120.1																																																																																			G|0.787;A|0.213	0.213	strong		0.567	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
PEG3	5178	hgsc.bcm.edu	37	19	57327503	57327503	+	Silent	SNP	A	A	G	rs33931963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57327503A>G	ENST00000326441.9	-	10	2670	c.2307T>C	c.(2305-2307)taT>taC	p.Y769Y	PEG3_ENST00000598410.1_Silent_p.Y645Y|PEG3_ENST00000423103.2_Silent_p.Y769Y|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000593695.1_Silent_p.Y643Y|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000601070.1_Intron	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	769					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		ATTTTGCCTCATAGACATTTT	0.423													A|||	1006	0.200879	0.1876	0.2075	5008	,	,		20993	0.1062		0.2565	False		,,,				2504	0.2546				p.Y769Y		Atlas-SNP	.											ZIM2_ENST00000326441,NS,carcinoma,-1,2	PEG3	414	2	0			c.T2307C						PASS	.	A	,,,,,,,	985,3421	363.9+/-316.7	103,779,1321	166.0	165.0	165.0		2307,1929,2307,1935,,,2307,	-1.3	0.0	19	dbSNP_126	165	2248,6352	378.4+/-338.9	279,1690,2331	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron	PEG3,ZIM2	NM_001146184.1,NM_001146185.1,NM_001146186.1,NM_001146187.1,NM_001146326.1,NM_001146327.1,NM_006210.2,NM_015363.4	,,,,,,,	382,2469,3652	GG,GA,AA		26.1395,22.3559,24.8578	,,,,,,,	769/1589,643/1463,769/1589,645/1465,,,769/1589,	57327503	3233,9773	2203	4300	6503	SO:0001819	synonymous_variant	5178	exon9			TGCCTCATAGACA	AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.2307T>C	19.37:g.57327503A>G		Somatic	260	0	0		WXS	Illumina HiSeq	Phase_I	255	116	0.454902	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Silent	SNP	ENST00000326441.9	37	CCDS12948.1																																																																																			A|0.767;G|0.233	0.233	strong		0.423	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
COL22A1	169044	hgsc.bcm.edu	37	8	139824057	139824057	+	Silent	SNP	G	G	A	rs10101430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:139824057G>A	ENST00000303045.6	-	9	1880	c.1434C>T	c.(1432-1434)tgC>tgT	p.C478C	COL22A1_ENST00000435777.1_Silent_p.C478C	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	478	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)			CTCCAGCTGGGCAGGAGCAGT	0.592										HNSCC(7;0.00092)			G|||	2407	0.480631	0.4062	0.4438	5008	,	,		12375	0.5694		0.5527	False		,,,				2504	0.4417				p.C478C		Atlas-SNP	.											.	COL22A1	390	.	0			c.C1434T						PASS	.	G		1849,2557	534.8+/-374.1	387,1075,741	76.0	65.0	69.0		1434	1.2	1.0	8	dbSNP_119	69	4608,3992	598.7+/-394.0	1275,2058,967	no	coding-synonymous	COL22A1	NM_152888.1		1662,3133,1708	AA,AG,GG		46.4186,41.9655,49.6463		478/1627	139824057	6457,6549	2203	4300	6503	SO:0001819	synonymous_variant	169044	exon9			AGCTGGGCAGGAG	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.1434C>T	8.37:g.139824057G>A		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	192	87	0.453125	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			G|0.507;A|0.493	0.493	strong		0.592	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
CASQ2	845	hgsc.bcm.edu	37	1	116310967	116310967	+	Missense_Mutation	SNP	T	T	C	rs4074536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:116310967T>C	ENST00000261448.5	-	1	435	c.196A>G	c.(196-198)Acg>Gcg	p.T66A	CASQ2_ENST00000456138.2_Missense_Mutation_p.T66A	NM_001232.3	NP_001223.2	O14958	CASQ2_HUMAN	calsequestrin 2 (cardiac muscle)	66			T -> A (no effect on calcium-binding and calcium-dependent dimerization; dbSNP:rs4074536). {ECO:0000269|PubMed:14571276, ECO:0000269|PubMed:17881003}.		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)		TGTTTTTGCGTGACCTTATCT	0.473													C|||	2009	0.401158	0.4856	0.3674	5008	,	,		19899	0.5159		0.2922	False		,,,				2504	0.3047				p.T66A		Atlas-SNP	.											CASQ2,colon,carcinoma,0,1	CASQ2	54	1	0			c.A196G						PASS	.	C	ALA/THR	1928,2478	622.1+/-393.9	416,1096,691	175.0	166.0	169.0	http://www.ncbi.nlm.nih.gov/pubmed?term	196	3.4	0.0	1	dbSNP_108	169	2486,6114	695.2+/-404.8	347,1792,2161	yes	missense	CASQ2	NM_001232.3	58	763,2888,2852	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	28.907,43.7585,33.9382	benign	66/400	116310967	4414,8592	2203	4300	6503	SO:0001583	missense	845	exon1			TTTGCGTGACCTT	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.196A>G	1.37:g.116310967T>C	ENSP00000261448:p.Thr66Ala	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	135	62	0.459259	NM_001232	B2R7M6|B4DIB0|Q5T1D2|Q8TBW8	Missense_Mutation	SNP	ENST00000261448.5	37	CCDS884.1	902	0.413003663003663	253	0.5142276422764228	133	0.3674033149171271	285	0.4982517482517482	231	0.30474934036939316	C	0.005	-2.171649	0.00315	0.437585	0.28907	ENSG00000118729	ENST00000261448;ENST00000456138;ENST00000446755	T;T	0.37752	1.18;1.18	5.49	3.44	0.39384	Thioredoxin-like fold (2);	0.442334	0.26300	N	0.025162	T	0.02047	0.0064	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43410	-0.9393	9	0.05959	T	0.93	-3.1292	8.6205	0.33857	0.3705:0.5482:0.0:0.0813	rs4074536;rs52800545;rs59883665;rs4074536	66;66	B4DIB0;O14958	.;CASQ2_HUMAN	A	66	ENSP00000261448:T66A;ENSP00000403858:T66A	ENSP00000261448:T66A	T	-	1	0	CASQ2	116112490	0.257000	0.24022	0.001000	0.08648	0.019000	0.09904	1.594000	0.36697	0.685000	0.31468	-0.186000	0.12905	ACG	T|0.631;C|0.369	0.369	strong		0.473	CASQ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033091.1	NM_001232	
ATP4A	495	hgsc.bcm.edu	37	19	36051333	36051333	+	Missense_Mutation	SNP	G	G	T	rs139075511	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36051333G>T	ENST00000262623.3	-	6	747	c.719C>A	c.(718-720)cCc>cAc	p.P240H		NM_000704.2	NP_000695.2	P20648	ATP4A_HUMAN	ATPase, H+/K+ exchanging, alpha polypeptide	240					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|ion transmembrane transport (GO:0034220)|pH reduction (GO:0045851)|regulation of proton transport (GO:0010155)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|magnesium ion binding (GO:0000287)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(26)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	53	all_lung(56;1.05e-07)|Lung NSC(56;1.63e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)		Esomeprazole(DB00736)|Lansoprazole(DB00448)|Omeprazole(DB00338)|Pantoprazole(DB00213)|Rabeprazole(DB01129)	CGTGCACTCGGGTGAGCGGGT	0.657													g|||	21	0.00419329	0.0008	0.0072	5008	,	,		15173	0.0		0.005	False		,,,				2504	0.0102				p.P240H		Atlas-SNP	.											.	ATP4A	123	.	0			c.C719A						PASS	.		HIS/PRO	12,4394	19.1+/-41.9	0,12,2191	82.0	81.0	81.0		719	4.2	0.9	19	dbSNP_134	81	108,8490	57.9+/-119.4	1,106,4192	yes	missense	ATP4A	NM_000704.2	77	1,118,6383	TT,TG,GG		1.2561,0.2724,0.9228	possibly-damaging	240/1036	36051333	120,12884	2203	4299	6502	SO:0001583	missense	495	exon6			CACTCGGGTGAGC		CCDS12467.1	19q13.1	2010-04-20			ENSG00000105675	ENSG00000105675	3.6.3.10	"""ATPases / P-type"""	819	protein-coding gene	gene with protein product	"""gastric H,K-ATPase alpha subunit"", ""H(+)-K(+)-ATPase alpha subunit"", ""proton pump"""	137216				1330887	Standard	NM_000704		Approved	ATP6A	uc002oal.1	P20648	OTTHUMG00000048106	ENST00000262623.3:c.719C>A	19.37:g.36051333G>T	ENSP00000262623:p.Pro240His	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	61	31	0.508197	NM_000704	O00738	Missense_Mutation	SNP	ENST00000262623.3	37	CCDS12467.1	10	0.004578754578754579	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	6	0.0079155672823219	g	16.25	3.069950	0.55539	0.002724	0.012561	ENSG00000105675	ENST00000262623	D	0.90955	-2.76	4.16	4.16	0.48862	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.64402	D	0.000004	D	0.90752	0.7097	L	0.53561	1.675	0.58432	D	0.999998	D	0.58970	0.984	D	0.62955	0.909	D	0.91917	0.5544	10	0.87932	D	0	.	14.3183	0.66468	0.0:0.0:1.0:0.0	.	240	P20648	ATP4A_HUMAN	H	240	ENSP00000262623:P240H	ENSP00000262623:P240H	P	-	2	0	ATP4A	40743173	1.000000	0.71417	0.920000	0.36463	0.179000	0.23085	4.380000	0.59581	2.314000	0.78098	0.486000	0.48141	CCC	G|0.993;T|0.007	0.007	strong		0.657	ATP4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109470.2	NM_000704	
HERC2	8924	hgsc.bcm.edu	37	15	28474686	28474686	+	Missense_Mutation	SNP	G	G	C	rs118112076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28474686G>C	ENST00000261609.7	-	33	5148	c.5040C>G	c.(5038-5040)agC>agG	p.S1680R		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)		AGAAATTCTTGCTCGCCAGTT	0.383													G|||	36	0.0071885	0.0	0.013	5008	,	,		20078	0.0		0.0209	False		,,,				2504	0.0061				p.S1680R		Atlas-SNP	.											.	HERC2	501	.	0			c.C5040G						PASS	.	G	ARG/SER	7,4399	14.3+/-33.2	0,7,2196	114.0	120.0	118.0		5040	1.2	1.0	15	dbSNP_132	118	104,8496	55.2+/-116.2	1,102,4197	yes	missense	HERC2	NM_004667.4	110	1,109,6393	CC,CG,GG		1.2093,0.1589,0.8535	benign	1680/4835	28474686	111,12895	2203	4300	6503	SO:0001583	missense	8924	exon33			ATTCTTGCTCGCC	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.5040C>G	15.37:g.28474686G>C	ENSP00000261609:p.Ser1680Arg	Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	348	151	0.433908	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	G	5.734	0.319824	0.10845	0.001589	0.012093	ENSG00000128731	ENST00000261609	T	0.38401	1.14	4.41	1.17	0.20885	.	1.006310	0.07993	N	0.987509	T	0.12944	0.0314	L	0.36672	1.1	0.37675	D	0.923287	B	0.19583	0.037	B	0.23150	0.044	T	0.21552	-1.0242	10	0.16420	T	0.52	.	4.4623	0.11671	0.0742:0.3516:0.3391:0.235	.	1680	O95714	HERC2_HUMAN	R	1680	ENSP00000261609:S1680R	ENSP00000261609:S1680R	S	-	3	2	HERC2	26148281	0.942000	0.31987	0.987000	0.45799	0.977000	0.68977	0.009000	0.13219	0.444000	0.26612	0.555000	0.69702	AGC	G|0.990;C|0.010	0.010	strong		0.383	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
NCOR2	9612	hgsc.bcm.edu	37	12	124826462	124826462	+	Missense_Mutation	SNP	C	C	T	rs2229840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124826462C>T	ENST00000405201.1	-	34	5095	c.5095G>A	c.(5095-5097)Gcg>Acg	p.A1699T	NCOR2_ENST00000404121.2_Missense_Mutation_p.A1260T|NCOR2_ENST00000397355.1_Missense_Mutation_p.A1690T|NCOR2_ENST00000429285.2_Missense_Mutation_p.A1689T|NCOR2_ENST00000404621.1_Missense_Mutation_p.A1689T|NCOR2_ENST00000356219.3_Missense_Mutation_p.A1706T			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1707					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)		GCGGTGGCCGCGTTGTGGTGC	0.662													C|||	806	0.160942	0.112	0.2637	5008	,	,		16539	0.1071		0.1551	False		,,,				2504	0.2157				p.A1699T		Atlas-SNP	.											.	NCOR2	475	.	0			c.G5095A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	505,3851		23,459,1696	68.0	87.0	81.0		5065,5065,5095	4.4	0.8	12	dbSNP_98	81	1392,7176		116,1160,3008	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	58,58,58	139,1619,4704	TT,TC,CC		16.2465,11.5932,14.6781	possibly-damaging,possibly-damaging,possibly-damaging	1689/2459,1689/2505,1699/2515	124826462	1897,11027	2178	4284	6462	SO:0001583	missense	9612	exon36			TGGCCGCGTTGTG	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.5095G>A	12.37:g.124826462C>T	ENSP00000384018:p.Ala1699Thr	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	321|321	0.14697802197802198|0.14697802197802198	48|48	0.0975609756097561|0.0975609756097561	84|84	0.23204419889502761|0.23204419889502761	65|65	0.11363636363636363|0.11363636363636363	124|124	0.16358839050131926|0.16358839050131926	C|C	15.92|15.92	2.976007|2.976007	0.53720|0.53720	0.115932|0.115932	0.162465|0.162465	ENSG00000196498|ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285|ENST00000453428	T;T;T;T;T;T|.	0.20069|.	2.1;2.37;2.1;2.37;2.11;2.37|.	4.37|4.37	4.37|4.37	0.52481|0.52481	.|.	0.069881|.	0.56097|.	D|.	0.000027|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.21448|0.21448	0.665|0.665	0.20307|0.20307	P|P	0.9999163375|0.9999163375	P;D;P|.	0.89917|.	0.92;1.0;0.939|.	B;D;B|.	0.77557|.	0.218;0.99;0.315|.	T|T	0.21143|0.21143	-1.0254|-1.0254	9|4	0.25751|.	T|.	0.34|.	-26.8749|-26.8749	10.5892|10.5892	0.45300|0.45300	0.0:0.9103:0.0:0.0897|0.0:0.9103:0.0:0.0897	rs2229840;rs59703581;rs2229840|rs2229840;rs59703581;rs2229840	1689;1690;1699|.	C9J0Q5;C9J239;C9JFD3|.	.;.;.|.	T|H	1699;1689;1706;1690;1698;1260;1689|47	ENSP00000384018:A1699T;ENSP00000384202:A1689T;ENSP00000348551:A1706T;ENSP00000380513:A1690T;ENSP00000385618:A1260T;ENSP00000400281:A1689T|.	ENSP00000348551:A1706T|.	A|R	-|-	1|2	0|0	NCOR2|NCOR2	123392415|123392415	1.000000|1.000000	0.71417|0.71417	0.755000|0.755000	0.31263|0.31263	0.859000|0.859000	0.49053|0.49053	4.646000|4.646000	0.61411|0.61411	1.985000|1.985000	0.57927|0.57927	0.491000|0.491000	0.48974|0.48974	GCG|CGC	C|0.859;T|0.141	0.141	strong		0.662	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
ZNF850	342892	hgsc.bcm.edu	37	19	37239278	37239278	+	Silent	SNP	C	C	A	rs11672680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37239278C>A	ENST00000591344.1	-	5	2822	c.2664G>T	c.(2662-2664)cgG>cgT	p.R888R	ZNF850_ENST00000589390.1_Intron	NM_001193552.1|NM_001267779.1	NP_001180481.1|NP_001254708.1	A8MQ14	ZN850_HUMAN	zinc finger protein 850	888					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										TGTGAATTCGCCGATGTTGGA	0.413													C|||	1237	0.247005	0.2027	0.1888	5008	,	,		23678	0.1776		0.2922	False		,,,				2504	0.3732				p.R888R		Atlas-SNP	.											.	ZNF850	14	.	0			c.G2664T						PASS	.																																			SO:0001819	synonymous_variant	342892	exon5			AATTCGCCGATGT	BC052603	CCDS59379.1, CCDS74350.1	19q13.12	2013-01-08	2010-08-02	2010-08-02		ENSG00000267041		"""Zinc fingers, C2H2-type"", ""-"""	27994	protein-coding gene	gene with protein product			"""zinc finger protein 850 pseudogene"", ""zinc finger protein 850 (pseudogene)"""	ZNF850P		12477932	Standard	NM_001193552		Approved		uc010efc.3	A8MQ14		ENST00000591344.1:c.2664G>T	19.37:g.37239278C>A		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_001193552		Silent	SNP	ENST00000591344.1	37	CCDS59379.1																																																																																			C|0.777;A|0.223	0.223	strong		0.413	ZNF850-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453557.1	XM_001720258	
OR10G9	219870	hgsc.bcm.edu	37	11	123893801	123893801	+	Missense_Mutation	SNP	A	A	G	rs74791330	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:123893801A>G	ENST00000375024.1	+	1	82	c.82A>G	c.(82-84)Atc>Gtc	p.I28V		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	28						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I28V(3)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		ACTCTTTGGAATCTTCCTGGT	0.572																																					p.I28V		Atlas-SNP	.											OR10G9,NS,haematopoietic_neoplasm,0,3	OR10G9	80	3	3	Substitution - Missense(3)	lung(1)|stomach(1)|skin(1)	c.A82G						scavenged	.						200.0	185.0	190.0					11																	123893801		2201	4299	6500	SO:0001583	missense	219870	exon1			TTTGGAATCTTCC	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.82A>G	11.37:g.123893801A>G	ENSP00000364164:p.Ile28Val	Somatic	402	1	0.00248756		WXS	Illumina HiSeq	Phase_I	309	46	0.148867	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	G	0.717	-0.785033	0.02907	.	.	ENSG00000236981	ENST00000375024	T	0.03035	4.07	3.33	-6.67	0.01783	.	0.824866	0.10366	N	0.683403	T	0.01189	0.0039	N	0.04655	-0.195	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39035	-0.9633	10	0.02654	T	1	.	4.5432	0.12067	0.1864:0.3395:0.3804:0.0938	.	28	Q8NGN4	O10G9_HUMAN	V	28	ENSP00000364164:I28V	ENSP00000364164:I28V	I	+	1	0	OR10G9	123399011	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.504000	0.00224	-2.845000	0.00333	-2.883000	0.00097	ATC	A|0.814;G|0.186	0.186	strong		0.572	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
ATAD5	79915	hgsc.bcm.edu	37	17	29159404	29159404	+	Silent	SNP	G	G	C	rs999796|rs372459410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:29159404G>C	ENST00000321990.4	+	1	417	c.39G>C	c.(37-39)ccG>ccC	p.P13P	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	13					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CAGCTGCTCCGCCTCCCGTGA	0.627													C|||	1441	0.28774	0.5681	0.2305	5008	,	,		16614	0.1349		0.1173	False		,,,				2504	0.2822				p.P13P		Atlas-SNP	.											ATAD5,NS,carcinoma,0,1	ATAD5	150	1	0			c.G39C						scavenged	.	C		2118,2288	595.7+/-388.5	507,1104,592	67.0	73.0	71.0		39	2.8	1.0	17	dbSNP_86	71	961,7639	773.6+/-407.7	45,871,3384	yes	coding-synonymous	ATAD5	NM_024857.3		552,1975,3976	CC,CG,GG		11.1744,48.0708,23.6737		13/1845	29159404	3079,9927	2203	4300	6503	SO:0001819	synonymous_variant	79915	exon1			TGCTCCGCCTCCC		CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.39G>C	17.37:g.29159404G>C		Somatic	72	1	0.0138889		WXS	Illumina HiSeq	Phase_I	66	29	0.439394	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Silent	SNP	ENST00000321990.4	37	CCDS11260.1																																																																																			G|0.765;C|0.235	0.235	strong		0.627	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
AHRR	57491	hgsc.bcm.edu	37	5	434722	434722	+	Missense_Mutation	SNP	G	G	C	rs34453673	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:434722G>C	ENST00000505113.1	+	11	1923	c.1879G>C	c.(1879-1881)Gac>Cac	p.D627H	AHRR_ENST00000506456.1_Missense_Mutation_p.D483H|AHRR_ENST00000512529.1_Missense_Mutation_p.D473H|AHRR_ENST00000316418.5_Missense_Mutation_p.D645H	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	627	Needed for transcriptional repression. {ECO:0000250}.		D -> H (in dbSNP:rs34453673).		negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			GGAGCCCACAGACGGCCTTCC	0.701													C|||	776	0.154952	0.0113	0.2363	5008	,	,		18582	0.004		0.4036	False		,,,				2504	0.1912				p.D645H		Atlas-SNP	.											AHRR,colon,carcinoma,0,1	AHRR	67	1	0			c.G1933C						PASS	.	C	HIS/ASP,HIS/ASP	288,3746		12,264,1741	11.0	15.0	13.0		1879,1933	3.3	0.0	5	dbSNP_126	13	3041,5303		580,1881,1711	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	81,81	592,2145,3452	CC,CG,GG		36.4453,7.1393,26.8945	benign,benign	627/702,645/720	434722	3329,9049	2017	4172	6189	SO:0001583	missense	57491	exon12			CCCACAGACGGCC	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.1879G>C	5.37:g.434722G>C	ENSP00000424601:p.Asp627His	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	109	58	0.53211	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	413	0.1891025641025641	7	0.014227642276422764	97	0.26795580110497236	0	0.0	309	0.4076517150395778	C	0.012	-1.666056	0.00765	0.071393	0.364453	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.21734	2.33;2.31;1.99;1.99	3.32	3.32	0.38043	.	0.872680	0.09850	N	0.747721	T	0.00012	0.0000	N	0.01168	-0.975	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	0.48559	-0.9025	9	0.13470	T	0.59	.	5.0538	0.14522	0.0:0.6575:0.2193:0.1232	rs34453673	483;627;645	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	H	627;645;473;483	ENSP00000424601:D627H;ENSP00000323816:D645H;ENSP00000424880:D473H;ENSP00000426932:D483H	ENSP00000323816:D645H	D	+	1	0	AHRR	487722	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.329000	0.19698	0.508000	0.28173	-0.216000	0.12614	GAC	G|0.808;C|0.192	0.192	strong		0.701	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
DOCK8	81704	hgsc.bcm.edu	37	9	377111	377111	+	Silent	SNP	G	G	C	rs10814431	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:377111G>C	ENST00000453981.1	+	20	2452	c.2340G>C	c.(2338-2340)ctG>ctC	p.L780L	DOCK8_ENST00000432829.2_Silent_p.L712L|DOCK8_ENST00000382329.1_Silent_p.L247L|DOCK8_ENST00000469391.1_Silent_p.L712L|DOCK8_ENST00000382331.1_Silent_p.L82L			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	780					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TCATCTGCCTGAACTCCTCCC	0.612													G|||	1145	0.228634	0.3094	0.2262	5008	,	,		18085	0.0794		0.2505	False		,,,				2504	0.2526				p.L780L		Atlas-SNP	.											.	DOCK8	401	.	0			c.G2340C						PASS	.	G	,,	1271,3135	430.1+/-342.5	177,917,1109	59.0	42.0	48.0		2136,2136,2340	-11.2	0.7	9	dbSNP_120	48	2196,6404	371.0+/-336.1	275,1646,2379	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	452,2563,3488	CC,CG,GG		25.5349,28.847,26.6569	,,	712/2000,712/2032,780/2100	377111	3467,9539	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon20			CTGCCTGAACTCC	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.2340G>C	9.37:g.377111G>C		Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	23	13	0.565217	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			G|0.749;C|0.251	0.251	strong		0.612	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
OR5V1	81696	hgsc.bcm.edu	37	6	29323905	29323905	+	Missense_Mutation	SNP	A	A	C	rs6930033	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29323905A>C	ENST00000377154.1	-	4	367	c.68T>G	c.(67-69)tTg>tGg	p.L23W	OR5V1_ENST00000543825.1_Missense_Mutation_p.L23W			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	23			L -> W (in dbSNP:rs6930033). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TAAAAACTGCAATTCATTTAG	0.373													A|||	1258	0.251198	0.1672	0.2478	5008	,	,		18385	0.4038		0.17	False		,,,				2504	0.2935				p.L23W	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											.	OR5V1	63	.	0			c.T68G						PASS	.	A	TRP/LEU	651,3745		51,549,1598	73.0	76.0	75.0		68	4.4	0.0	6	dbSNP_116	75	1376,7208		125,1126,3041	yes	missense	OR5V1	NM_030876.5	61	176,1675,4639	CC,CA,AA		16.0298,14.8089,15.6163	probably-damaging	23/322	29323905	2027,10953	2198	4292	6490	SO:0001583	missense	81696	exon1			AACTGCAATTCAT		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"""GPCR / Class A : Olfactory receptors"""	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.68T>G	6.37:g.29323905A>C	ENSP00000366359:p.Leu23Trp	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	105	47	0.447619	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	37	CCDS4657.1	516	0.23626373626373626	76	0.15447154471544716	93	0.2569060773480663	231	0.40384615384615385	116	0.15303430079155672	A	15.56	2.868850	0.51588	0.148089	0.160298	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.05580	3.42;3.42	4.37	4.37	0.52481	.	0.341744	0.16651	N	0.205208	T	0.11879	0.0289	M	0.76170	2.325	0.80722	P	0.0	D	0.69078	0.997	P	0.57283	0.817	T	0.01951	-1.1241	9	0.56958	D	0.05	-14.7225	13.6641	0.62384	1.0:0.0:0.0:0.0	rs6930033;rs52796609;rs60291414;rs6930033	23	Q9UGF6	OR5V1_HUMAN	W	23	ENSP00000366359:L23W;ENSP00000443309:L23W	ENSP00000366356:L23W	L	-	2	0	OR5V1	29431884	0.000000	0.05858	0.004000	0.12327	0.852000	0.48524	1.174000	0.31932	1.953000	0.56701	0.438000	0.28831	TTG	A|0.805;C|0.195	0.195	strong		0.373	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3		
LILRB3	11025	hgsc.bcm.edu	37	19	54724443	54724443	+	Missense_Mutation	SNP	G	G	A	rs201735825	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:54724443G>A	ENST00000391750.1	-	7	1349	c.1213C>T	c.(1213-1215)Cac>Tac	p.H405Y	LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000469273.1_5'UTR|LILRA6_ENST00000440558.2_Missense_Mutation_p.H405Y|LILRB3_ENST00000407860.2_Missense_Mutation_p.H405Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H405Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H405Y|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000245620.9_Missense_Mutation_p.H405Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H405Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	405	Ig-like C2-type 4.		H -> Y (in dbSNP:rs1132604). {ECO:0000269|PubMed:9548455}.		cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GACAGCAGGTGGGGGTTGGAG	0.627													.|||	941	0.187899	0.4085	0.1772	5008	,	,		7731	0.005		0.1481	False		,,,				2504	0.1268				p.H405Y		Atlas-SNP	.											.	LILRB3	67	.	0			c.C1213T						PASS	.						16.0	9.0	11.0					19																	54724443		2160	3980	6140	SO:0001583	missense	11025	exon6			GCAGGTGGGGGTT	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.1213C>T	19.37:g.54724443G>A	ENSP00000375630:p.His405Tyr	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	62	38	0.612903	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	g	0.003	-2.389985	0.00200	.	.	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464	T;T;T;T;T;T;T	0.00669	5.9;5.9;5.9;5.9;5.9;5.9;5.9	2.87	-5.11	0.02901	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.167250	0.06702	N	0.771663	T	0.00271	0.0008	N	0.00329	-1.635	0.58432	P	1.0000000000287557E-6	B;B;B;B;B;B	0.09022	0.0;0.0;0.0;0.002;0.0;0.0	B;B;B;B;B;B	0.08055	0.001;0.001;0.001;0.003;0.0;0.0	T	0.45977	-0.9224	9	0.02654	T	1	.	10.4418	0.44471	0.4586:0.0:0.5414:0.0	.	405;405;405;405;405;405	B5MCX0;F8WCY4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;LIRB3_HUMAN;.	Y	405	ENSP00000375630:H405Y;ENSP00000412771:H405Y;ENSP00000345184:H405Y;ENSP00000245620:H405Y;ENSP00000384274:H405Y;ENSP00000390120:H405Y;ENSP00000270464:H405Y	ENSP00000270464:H405Y	H	-	1	0	LILRB3;LILRA6	59416255	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.211000	0.02997	-1.561000	0.01684	-1.799000	0.00621	CAC	G|0.860;A|0.140	0.140	strong		0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
CFAP46	54777	hgsc.bcm.edu	37	10	134682833	134682833	+	Missense_Mutation	SNP	C	C	T	rs149742494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134682833C>T	ENST00000368586.5	-	33	4655	c.4555G>A	c.(4555-4557)Gcg>Acg	p.A1519T		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCATGGCGCGCGGCTGCTTCT	0.677													C|||	52	0.0103834	0.0045	0.0072	5008	,	,		15122	0.002		0.0129	False		,,,				2504	0.0266				p.A1519T		Atlas-SNP	.											.	TTC40	100	.	0			c.G4555A						PASS	.																																			SO:0001583	missense	54777	exon33			GGCGCGCGGCTGC																												ENST00000368586.5:c.4555G>A	10.37:g.134682833C>T	ENSP00000357575:p.Ala1519Thr	Somatic	34	0	0		WXS	Illumina HiSeq	Phase_I	57	34	0.596491	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	12	0.005494505494505495	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	10.60	1.395276	0.25205	.	.	ENSG00000171811	ENST00000368586	T	0.09817	2.94	4.81	-5.4	0.02656	.	.	.	.	.	T	0.03095	0.0091	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.43228	-0.9404	6	0.15952	T	0.53	.	5.1632	0.15071	0.3408:0.1599:0.0:0.4993	.	.	.	.	T	1519	ENSP00000357575:A1519T	ENSP00000357575:A1519T	A	-	1	0	C10orf93	134532823	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.298000	0.01140	-1.398000	0.02066	-0.218000	0.12543	GCG	C|0.994;T|0.006	0.006	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
LGALS14	56891	hgsc.bcm.edu	37	19	40196627	40196627	+	Intron	SNP	G	G	A	rs72480733	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40196627G>A	ENST00000392052.3	+	2	238				LGALS14_ENST00000360675.3_Missense_Mutation_p.R27H	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14						apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			TGGGAAGGACGTCCATTGCCC	0.483													G|||	756	0.150958	0.0234	0.2723	5008	,	,		19793	0.3968		0.0457	False		,,,				2504	0.092				p.R27H		Atlas-SNP	.											LGALS14,colon,carcinoma,+1,1	LGALS14	38	1	0			c.G80A						PASS	.	G	,HIS/ARG	148,4258		0,148,2055	197.0	146.0	163.0		,80	-0.4	0.0	19	dbSNP_130	163	453,8147		8,437,3855	yes	intron,missense	LGALS14	NM_020129.2,NM_203471.1	,29	8,585,5910	AA,AG,GG		5.2674,3.3591,4.6209	,	,27/169	40196627	601,12405	2203	4300	6503	SO:0001627	intron_variant	56891	exon2			AAGGACGTCCATT	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.16-610G>A	19.37:g.40196627G>A		Somatic	166	1	0.0060241		WXS	Illumina HiSeq	Phase_I	187	186	0.994652	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	370	0.16941391941391942	13	0.026422764227642278	88	0.2430939226519337	233	0.40734265734265734	36	0.047493403693931395	.	7.582	0.668879	0.14776	0.033591	0.052674	ENSG00000006659	ENST00000360675	T	0.07908	3.15	0.896	-0.44	0.12261	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.56287	0.975	B	0.29663	0.105	T	0.48536	-0.9027	8	0.51188	T	0.08	.	2.9713	0.05924	0.6042:0.0:0.3958:0.0	.	27	A8MPV8	.	H	27	ENSP00000353893:R27H	ENSP00000353893:R27H	R	+	2	0	LGALS14	44888467	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-0.186000	0.09670	-0.200000	0.10300	0.305000	0.20034	CGT	G|0.919;A|0.081	0.081	strong		0.483	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	
FAH	2184	hgsc.bcm.edu	37	15	80472561	80472561	+	Silent	SNP	C	C	T	rs1801374	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:80472561C>T	ENST00000407106.1	+	13	1211	c.1056C>T	c.(1054-1056)agC>agT	p.S352S	FAH_ENST00000261755.5_Silent_p.S352S|FAH_ENST00000561421.1_Silent_p.S352S|FAH_ENST00000539156.1_Silent_p.S282S			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	352					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGACCATCAGCGGGCCGGTGA	0.632									Tyrosinemia, type 1				c|||	300	0.0599042	0.034	0.062	5008	,	,		17302	0.0833		0.0626	False		,,,				2504	0.0665				p.S352S		Atlas-SNP	.											.	FAH	36	.	0			c.C1056T						PASS	.	T		147,4259	101.2+/-139.8	2,143,2058	35.0	34.0	35.0		1056	-6.6	0.6	15	dbSNP_89	35	394,8206	125.8+/-184.4	7,380,3913	no	coding-synonymous	FAH	NM_000137.2		9,523,5971	TT,TC,CC		4.5814,3.3364,4.1596		352/420	80472561	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	2184	exon12	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	CATCAGCGGGCCG	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.1056C>T	15.37:g.80472561C>T		Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	27	10	0.37037	NM_000137	B2R9X1|D3DW95|Q53XA7	Silent	SNP	ENST00000407106.1	37	CCDS10314.1																																																																																			C|0.952;T|0.048	0.048	strong		0.632	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2		
GAK	2580	hgsc.bcm.edu	37	4	844781	844781	+	Silent	SNP	G	G	A	rs75072999	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:844781G>A	ENST00000314167.4	-	26	3710	c.3600C>T	c.(3598-3600)acC>acT	p.T1200T	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Silent_p.T1121T	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1200					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)	p.T1200T(1)		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)		TCTCTGCAATGGTCTTTGGCC	0.522													G|||	134	0.0267572	0.0015	0.036	5008	,	,		16676	0.0		0.0835	False		,,,				2504	0.0235				p.T1200T		Atlas-SNP	.											GAK,rectum,carcinoma,0,1	GAK	104	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C3600T						PASS	.	G		92,4314	74.1+/-112.3	2,88,2113	213.0	192.0	199.0		3600	2.3	1.0	4	dbSNP_132	199	802,7798	187.4+/-234.7	48,706,3546	no	coding-synonymous	GAK	NM_005255.2		50,794,5659	AA,AG,GG		9.3256,2.0881,6.8738		1200/1312	844781	894,12112	2203	4300	6503	SO:0001819	synonymous_variant	2580	exon26			TGCAATGGTCTTT	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.3600C>T	4.37:g.844781G>A		Somatic	239	0	0		WXS	Illumina HiSeq	Phase_I	198	78	0.393939	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	70	0.03205128205128205	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	55	0.07255936675461741	G	12.15	1.852878	0.32699	0.020881	0.093256	ENSG00000178950	ENST00000511980	.	.	.	5.41	2.33	0.28932	.	.	.	.	.	T	0.08447	0.0210	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41627	-0.9498	5	0.87932	D	0	-52.9883	11.0372	0.47808	0.0:0.2378:0.6265:0.1357	.	.	.	.	L	356	.	ENSP00000424553:P66L	P	-	2	0	GAK	834781	1.000000	0.71417	0.998000	0.56505	0.856000	0.48823	0.666000	0.25097	0.625000	0.30304	0.655000	0.94253	CCA	G|0.939;A|0.061	0.061	strong		0.522	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
SPATC1L	84221	hgsc.bcm.edu	37	21	47588465	47588465	+	Missense_Mutation	SNP	C	C	T	rs77889636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47588465C>T	ENST00000291672.5	-	3	1362	c.301G>A	c.(301-303)Gac>Aac	p.D101N	SPATC1L_ENST00000330205.6_5'UTR	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	101																	GGGGAGGTGTCGTCCTCGCTG	0.647													C|||	277	0.0553115	0.1974	0.0202	5008	,	,		17137	0.0		0.002	False		,,,				2504	0.0				p.D101N		Atlas-SNP	.											.	.	.	.	0			c.G301A						PASS	.	C	ASN/ASP,	231,1153		19,193,480	41.0	42.0	42.0		301,	5.5	0.1	21	dbSNP_131	42	6,3176		0,6,1585	yes	missense,utr-5	C21orf56	NM_001142854.1,NM_032261.4	23,	19,199,2065	TT,TC,CC		0.1886,16.6908,5.1905	possibly-damaging,	101/341,	47588465	237,4329	692	1591	2283	SO:0001583	missense	84221	exon3			AGGTGTCGTCCTC	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.301G>A	21.37:g.47588465C>T	ENSP00000291672:p.Asp101Asn	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	65	31	0.476923	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	87	0.03983516483516483	80	0.16260162601626016	7	0.019337016574585635	0	0.0	0	0.0	C	15.13	2.741313	0.49151	0.166908	0.001886	ENSG00000160284	ENST00000291672	T	0.43688	0.94	5.46	5.46	0.80206	.	0.120313	0.36482	N	0.002564	T	0.00109	0.0003	L	0.27053	0.805	0.09310	N	1	P	0.47106	0.89	B	0.44224	0.444	T	0.00630	-1.1636	10	0.25751	T	0.34	-12.5296	14.8041	0.69938	0.0:1.0:0.0:0.0	.	101	Q9H0A9	CU056_HUMAN	N	101	ENSP00000291672:D101N	ENSP00000291672:D101N	D	-	1	0	C21orf56	46412893	0.091000	0.21658	0.095000	0.20976	0.085000	0.17905	1.459000	0.35234	2.568000	0.86640	0.467000	0.42956	GAC	C|0.967;T|0.033	0.033	strong		0.647	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
ABCA13	154664	hgsc.bcm.edu	37	7	48311563	48311563	+	Missense_Mutation	SNP	T	T	G	rs17712293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48311563T>G	ENST00000435803.1	+	17	2324	c.2300T>G	c.(2299-2301)aTt>aGt	p.I767S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	767			I -> S (in dbSNP:rs17712293).		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						ACAGAGGATATTCTGAATATA	0.378													T|||	974	0.194489	0.1543	0.2709	5008	,	,		12995	0.2153		0.1322	False		,,,				2504	0.2372				p.I767S		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T2300G						PASS	.	T	SER/ILE	588,3046		47,494,1276	52.0	49.0	50.0		2300	3.4	0.0	7	dbSNP_123	50	1161,6985		91,979,3003	yes	missense	ABCA13	NM_152701.3	142	138,1473,4279	GG,GT,TT		14.2524,16.1805,14.8472	benign	767/5059	48311563	1749,10031	1817	4073	5890	SO:0001583	missense	154664	exon17			AGGATATTCTGAA	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.2300T>G	7.37:g.48311563T>G	ENSP00000411096:p.Ile767Ser	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	121	59	0.487603	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	401	0.18360805860805862	84	0.17073170731707318	89	0.24585635359116023	129	0.22552447552447552	99	0.13060686015831136	T	7.752	0.703480	0.15172	0.161805	0.142524	ENSG00000179869	ENST00000435803	D	0.86694	-2.16	5.81	3.42	0.39159	.	1.087280	0.07167	N	0.851812	T	0.00073	0.0002	L	0.40543	1.245	0.80722	P	0.0	B	0.30763	0.294	B	0.24974	0.057	T	0.06092	-1.0846	9	0.72032	D	0.01	.	7.4921	0.27469	0.0:0.2457:0.0:0.7543	rs17712293;rs52795922;rs17712293	767	Q86UQ4	ABCAD_HUMAN	S	767	ENSP00000411096:I767S	ENSP00000411096:I767S	I	+	2	0	ABCA13	48282109	0.000000	0.05858	0.005000	0.12908	0.231000	0.25187	0.606000	0.24194	1.029000	0.39812	0.477000	0.44152	ATT	T|0.817;G|0.183	0.183	strong		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
TYRO3	7301	hgsc.bcm.edu	37	15	41865525	41865525	+	Missense_Mutation	SNP	G	G	T	rs62001448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:41865525G>T	ENST00000263798.3	+	17	2229	c.2005G>T	c.(2005-2007)Gtg>Ttg	p.V669L	TYRO3_ENST00000559066.1_Missense_Mutation_p.V624L	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	669	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GGACATGACAGTGTGTGTGGC	0.562																																					p.V669L		Atlas-SNP	.											.	TYRO3	169	.	0			c.G2005T						PASS	.						209.0	211.0	211.0					15																	41865525		2203	4300	6503	SO:0001583	missense	7301	exon17			ATGACAGTGTGTG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.2005G>T	15.37:g.41865525G>T	ENSP00000263798:p.Val669Leu	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	98	14	0.142857	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	177	0.08104395604395605	12	0.024390243902439025	34	0.09392265193370165	11	0.019230769230769232	120	0.158311345646438	G	28.2	4.901936	0.92035	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	D	0.85861	-2.04	5.55	5.55	0.83447	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.436224	0.16821	N	0.198144	T	0.03136	0.0092	L	0.41027	1.25	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.54715	-0.8252	10	0.87932	D	0	-8.3883	19.5084	0.95130	0.0:0.0:1.0:0.0	rs62001448	669	Q06418	TYRO3_HUMAN	L	601;669	ENSP00000263798:V669L	ENSP00000263798:V669L	V	+	1	0	TYRO3	39652817	1.000000	0.71417	0.964000	0.40570	0.975000	0.68041	9.869000	0.99810	2.612000	0.88384	0.655000	0.94253	GTG	G|0.915;T|0.085	0.085	strong		0.562	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
KRT27	342574	hgsc.bcm.edu	37	17	38938316	38938316	+	Missense_Mutation	SNP	C	C	T	rs12453124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38938316C>T	ENST00000301656.3	-	1	470	c.430G>A	c.(430-432)Gaa>Aaa	p.E144K		NM_181537.3	NP_853515.2			keratin 27											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(3)|skin(1)|stomach(1)	21		Breast(137;0.000812)				TTCTTAAGTTCGTCAATAATT	0.433													C|||	744	0.148562	0.143	0.2795	5008	,	,		17138	0.1617		0.1183	False		,,,				2504	0.0808				p.E144K		Atlas-SNP	.											.	KRT27	41	.	0			c.G430A						PASS	.	C	LYS/GLU	591,3815	259.5+/-263.1	46,499,1658	93.0	82.0	86.0		430	5.7	1.0	17	dbSNP_120	86	1024,7576	218.7+/-257.0	58,908,3334	yes	missense	KRT27	NM_181537.3	56	104,1407,4992	TT,TC,CC		11.907,13.4135,12.4173	benign	144/460	38938316	1615,11391	2203	4300	6503	SO:0001583	missense	342574	exon1			TAAGTTCGTCAAT	AJ564206	CCDS11375.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000171446	ENSG00000171446		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30841	protein-coding gene	gene with protein product			"""keratin 25C"""	KRT25C		16831889	Standard	NM_181537		Approved		uc002hvg.3	Q7Z3Y8	OTTHUMG00000133371	ENST00000301656.3:c.430G>A	17.37:g.38938316C>T	ENSP00000301656:p.Glu144Lys	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	30	16	0.533333	NM_181537		Missense_Mutation	SNP	ENST00000301656.3	37	CCDS11375.1	337	0.1543040293040293	71	0.1443089430894309	83	0.2292817679558011	102	0.17832167832167833	81	0.10686015831134564	C	22.7	4.320464	0.81469	0.134135	0.11907	ENSG00000171446	ENST00000301656	D	0.85861	-2.04	5.66	5.66	0.87406	Filament (1);	0.080948	0.53938	D	0.000058	T	0.00210	0.0006	M	0.78916	2.43	0.23994	P	0.99623872	P	0.36125	0.538	B	0.36567	0.228	T	0.03795	-1.1003	9	0.72032	D	0.01	.	19.093	0.93235	0.0:1.0:0.0:0.0	rs12453124;rs56415029;rs59320269;rs12453124	144	Q7Z3Y8	K1C27_HUMAN	K	144	ENSP00000301656:E144K	ENSP00000301656:E144K	E	-	1	0	KRT27	36191842	0.997000	0.39634	0.976000	0.42696	0.791000	0.44710	3.663000	0.54518	2.815000	0.96918	0.650000	0.86243	GAA	C|0.859;T|0.141	0.141	strong		0.433	KRT27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257216.1	NM_181537	
SVEP1	79987	hgsc.bcm.edu	37	9	113208250	113208250	+	Missense_Mutation	SNP	T	T	G	rs7863519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:113208250T>G	ENST00000401783.2	-	26	4666	c.4330A>C	c.(4330-4332)Atg>Ctg	p.M1444L	SVEP1_ENST00000374469.1_Missense_Mutation_p.M1421L|SVEP1_ENST00000302728.8_Missense_Mutation_p.M1444L|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	1444	Pentaxin.		M -> L (in dbSNP:rs7863519).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.M1444L(2)		NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						GATGGGAGCATGCCATCTAGC	0.438													C|||	1701	0.339657	0.4569	0.2205	5008	,	,		20843	0.4504		0.1918	False		,,,				2504	0.3037				p.M1444L		Atlas-SNP	.											SVEP1,NS,carcinoma,0,2	SVEP1	326	2	2	Substitution - Missense(2)	prostate(2)	c.A4330C						scavenged	.	C	LEU/MET	1478,2424		275,928,748	119.0	114.0	116.0		4330	3.6	0.0	9	dbSNP_116	116	1600,6712		164,1272,2720	yes	missense	SVEP1	NM_153366.3	15	439,2200,3468	GG,GT,TT		19.2493,37.878,25.2006	benign	1444/3572	113208250	3078,9136	1951	4156	6107	SO:0001583	missense	79987	exon26			GGAGCATGCCATC	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.4330A>C	9.37:g.113208250T>G	ENSP00000384917:p.Met1444Leu	Somatic	118	1	0.00847458		WXS	Illumina HiSeq	Phase_I	126	58	0.460317	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	699	0.32005494505494503	228	0.4634146341463415	80	0.22099447513812154	241	0.42132867132867136	150	0.19788918205804748	C	0.025	-1.378392	0.01204	0.37878	0.192493	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728	T;T;T	0.71817	3.35;3.35;-0.6	5.5	3.62	0.41486	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.301359	0.35466	N	0.003189	T	0.00012	0.0000	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.09022	0.001;0.002	B;B	0.08055	0.0;0.003	T	0.41197	-0.9522	9	0.10377	T	0.69	.	8.2245	0.31560	0.0:0.6915:0.1135:0.195	rs7863519;rs52830057;rs60340468;rs7863519	1444;1444	E9PBN8;Q4LDE5	.;SVEP1_HUMAN	L	1444;1421;1444	ENSP00000384917:M1444L;ENSP00000363593:M1421L;ENSP00000304118:M1444L	ENSP00000304118:M1444L	M	-	1	0	SVEP1	112248071	0.004000	0.15560	0.023000	0.16930	0.138000	0.21146	0.095000	0.15127	0.361000	0.24292	-0.119000	0.15052	ATG	T|0.684;G|0.316	0.316	strong		0.438	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CDT1	81620	hgsc.bcm.edu	37	16	88870967	88870967	+	Silent	SNP	T	T	C	rs475667	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88870967T>C	ENST00000301019.4	+	2	862	c.243T>C	c.(241-243)agT>agC	p.S81S		NM_030928.3	NP_112190.2			chromatin licensing and DNA replication factor 1											central_nervous_system(1)|endometrium(2)|kidney(1)|lung(3)	7				BRCA - Breast invasive adenocarcinoma(80;0.0476)		CCAGCCCCAGTACCCCCGAGG	0.642													T|||	656	0.13099	0.1846	0.1268	5008	,	,		12894	0.1419		0.0805	False		,,,				2504	0.1022				p.S81S	Melanoma(159;511 3380 30971)	Atlas-SNP	.											.	CDT1	30	.	0			c.T243C						PASS	.	T		733,3663	290.1+/-280.8	52,629,1517	35.0	40.0	38.0		243	-5.8	0.0	16	dbSNP_83	38	679,7917	167.7+/-219.4	25,629,3644	no	coding-synonymous	CDT1	NM_030928.3		77,1258,5161	CC,CT,TT		7.899,16.6742,10.8682		81/547	88870967	1412,11580	2198	4298	6496	SO:0001819	synonymous_variant	81620	exon2			CCCCAGTACCCCC	AF070552	CCDS32510.1	16q24.3	2014-08-12			ENSG00000167513	ENSG00000167513			24576	protein-coding gene	gene with protein product		605525				11896191, 11555648	Standard	NM_030928		Approved	DUP, RIS2	uc002flu.3	Q9H211	OTTHUMG00000173467	ENST00000301019.4:c.243T>C	16.37:g.88870967T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	116	36	0.310345	NM_030928		Silent	SNP	ENST00000301019.4	37	CCDS32510.1																																																																																			T|0.874;C|0.126	0.126	strong		0.642	CDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423215.1	NM_030928	
PHC1	1911	hgsc.bcm.edu	37	12	9070366	9070366	+	Silent	SNP	T	T	A	rs4883198	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9070366T>A	ENST00000543824.1	+	3	425	c.93T>A	c.(91-93)ctT>ctA	p.L31L	PHC1_ENST00000536844.1_5'UTR|PHC1_ENST00000544916.1_Silent_p.L31L|PHC1_ENST00000433847.2_3'UTR|PHC1_ENST00000433083.2_Silent_p.L31L			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	31					cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						AAATGTCACTTTATGAACGAC	0.517													A|||	3444	0.6877	0.5469	0.5908	5008	,	,		-128	0.749		0.7167	False		,,,				2504	0.8538				p.L31L		Atlas-SNP	.											.	PHC1	67	.	0			c.T93A						PASS	.	A		2632,1774	521.7+/-370.6	772,1088,343	40.0	37.0	38.0		93	2.0	1.0	12	dbSNP_111	38	6238,2362	391.8+/-343.8	2240,1758,302	no	coding-synonymous	PHC1	NM_004426.2		3012,2846,645	AA,AT,TT		27.4651,40.2633,31.8007		31/1005	9070366	8870,4136	2203	4300	6503	SO:0001819	synonymous_variant	1911	exon2			GTCACTTTATGAA	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.93T>A	12.37:g.9070366T>A		Somatic	211	0	0		WXS	Illumina HiSeq	Phase_I	199	197	0.98995	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Silent	SNP	ENST00000543824.1	37	CCDS8597.1																																																																																			T|0.310;A|0.690	0.690	strong		0.517	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
DBNL	28988	hgsc.bcm.edu	37	7	44099664	44099664	+	Silent	SNP	T	T	C	rs11552797	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:44099664T>C	ENST00000448521.1	+	12	1163	c.1065T>C	c.(1063-1065)gcT>gcC	p.A355A	DBNL_ENST00000456905.1_Silent_p.A307A|DBNL_ENST00000490734.2_Silent_p.A261A|DBNL_ENST00000468694.1_Silent_p.A364A|DBNL_ENST00000452943.1_Silent_p.A331A|DBNL_ENST00000494774.1_Silent_p.A356A|DBNL_ENST00000440166.1_Silent_p.A252A|DBNL_ENST00000497184.1_3'UTR	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	355					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)	p.A356A(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						AGCAAGGTGCTGGCTCTGAGC	0.607													C|||	1337	0.266973	0.4387	0.2882	5008	,	,		20099	0.1141		0.2406	False		,,,				2504	0.2045				p.A364A	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											DBNL,NS,carcinoma,0,1	DBNL	26	1	1	Substitution - coding silent(1)	stomach(1)	c.T1092C						PASS	.	C	,,	1849,2557	629.4+/-395.3	390,1069,744	54.0	46.0	48.0		1065,1092,1068	-7.6	0.0	7	dbSNP_120	48	1992,6608	721.0+/-406.3	239,1514,2547	no	coding-synonymous,coding-synonymous,coding-synonymous	DBNL	NM_001014436.2,NM_001122956.1,NM_014063.6	,,	629,2583,3291	CC,CT,TT		23.1628,41.9655,29.5325	,,	355/431,364/440,356/432	44099664	3841,9165	2203	4300	6503	SO:0001819	synonymous_variant	28988	exon12			AGGTGCTGGCTCT	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.1065T>C	7.37:g.44099664T>C		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	192	97	0.505208	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Silent	SNP	ENST00000448521.1	37	CCDS34623.1	558|558	0.2554945054945055|0.2554945054945055	194|194	0.3943089430894309|0.3943089430894309	106|106	0.292817679558011|0.292817679558011	68|68	0.11888111888111888|0.11888111888111888	190|190	0.25065963060686014|0.25065963060686014	C|C	11.21|11.21	1.572572|1.572572	0.28092|0.28092	0.419655|0.419655	0.231628|0.231628	ENSG00000136279|ENSG00000136279	ENST00000452661|ENST00000432854	.|.	.|.	.|.	5.53|5.53	-7.58|-7.58	0.01313|0.01313	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.03296|0.03296	-1.1051|-1.1051	3|3	.|.	.|.	.|.	-2.7619|-2.7619	18.0703|18.0703	0.89404|0.89404	0.0:0.6938:0.0:0.3062|0.0:0.6938:0.0:0.3062	rs11552797;rs11764534;rs17358190;rs59746704;rs11552797|rs11552797;rs11764534;rs17358190;rs59746704;rs11552797	.|.	.|.	.|.	P|R	63|284	.|.	.|.	L|W	+|+	2|1	0|0	DBNL|DBNL	44066189|44066189	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.541000|0.541000	0.35023|0.35023	-0.487000|-0.487000	0.06505|0.06505	-1.961000|-1.961000	0.01016|0.01016	-1.095000|-1.095000	0.02154|0.02154	CTG|TGG	T|0.715;C|0.285	0.285	strong		0.607	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
DOCK8	81704	hgsc.bcm.edu	37	9	390512	390512	+	Silent	SNP	C	C	T	rs2297075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:390512C>T	ENST00000453981.1	+	24	3028	c.2916C>T	c.(2914-2916)acC>acT	p.T972T	DOCK8_ENST00000432829.2_Silent_p.T904T|DOCK8_ENST00000382329.1_Silent_p.T439T|DOCK8_ENST00000469391.1_Silent_p.T872T|DOCK8_ENST00000382331.1_Silent_p.T274T			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	972					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TGGTCAGCACCGGAATGGTGA	0.433													T|||	1277	0.254992	0.3964	0.245	5008	,	,		21549	0.0972		0.2495	False		,,,				2504	0.2393				p.T972T		Atlas-SNP	.											DOCK8_ENST00000453981,NS,adenoma,0,2	DOCK8	401	2	0			c.C2916T						PASS	.	T	,,	1592,2814	664.8+/-401.4	290,1012,901	256.0	215.0	229.0		2616,2712,2916	0.1	1.0	9	dbSNP_100	229	2115,6485	716.0+/-406.1	261,1593,2446	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	551,2605,3347	TT,TC,CC		24.593,36.1325,28.5022	,,	872/2000,904/2032,972/2100	390512	3707,9299	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon24			CAGCACCGGAATG	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.2916C>T	9.37:g.390512C>T		Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	264	138	0.522727	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			C|0.729;T|0.271	0.271	strong		0.433	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
NUCB2	4925	hgsc.bcm.edu	37	11	17351683	17351683	+	Missense_Mutation	SNP	C	C	G	rs757081	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:17351683C>G	ENST00000529010.1	+	12	1231	c.1012C>G	c.(1012-1014)Cag>Gag	p.Q338E	NUCB2_ENST00000458064.2_Missense_Mutation_p.Q308E|NUCB2_ENST00000323688.6_Missense_Mutation_p.Q338E	NM_005013.2	NP_005004	P80303	NUCB2_HUMAN	nucleobindin 2	338	Binds to necdin. {ECO:0000250}.		Q -> E (in dbSNP:rs757081).			cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nuclear outer membrane (GO:0005640)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14						GACATTAGATCAGCAACAGTT	0.284													C|||	1191	0.237819	0.0182	0.2795	5008	,	,		16337	0.3552		0.3111	False		,,,				2504	0.3088				p.Q338E		Atlas-SNP	.											.	NUCB2	31	.	0			c.C1012G						PASS	.	C	GLU/GLN	210,3390		5,200,1595	20.0	18.0	18.0		1012	5.7	1.0	11	dbSNP_86	18	2604,5522		412,1780,1871	yes	missense	NUCB2	NM_005013.2	29	417,1980,3466	GG,GC,CC		32.0453,5.8333,23.998	benign	338/421	17351683	2814,8912	1800	4063	5863	SO:0001583	missense	4925	exon12			TTAGATCAGCAAC	AF052642	CCDS41623.1	11p15.1	2013-01-10						"""EF-hand domain containing"""	8044	protein-coding gene	gene with protein product		608020				7811391	Standard	NM_005013		Approved	NEFA	uc001mmw.3	P80303		ENST00000529010.1:c.1012C>G	11.37:g.17351683C>G	ENSP00000436455:p.Gln338Glu	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	57	34	0.596491	NM_005013	A8K642|D3DQX5|Q8NFT5	Missense_Mutation	SNP	ENST00000529010.1	37	CCDS41623.1	560|560	0.2564102564102564|0.2564102564102564	14|14	0.028455284552845527|0.028455284552845527	101|101	0.27900552486187846|0.27900552486187846	220|220	0.38461538461538464|0.38461538461538464	225|225	0.29683377308707126|0.29683377308707126	C|C	11.12|11.12	1.546059|1.546059	0.27652|0.27652	0.058333|0.058333	0.320453|0.320453	ENSG00000070081|ENSG00000070081	ENST00000323688;ENST00000529010;ENST00000458064|ENST00000527580	T;T;T|.	0.17370|.	2.38;2.38;2.28|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.209202|.	0.51477|.	D|.	0.000092|.	T|.	0.00012|.	0.0000|.	L|L	0.39566|0.39566	1.225|1.225	0.19300|0.19300	P|P	0.9999784196|0.9999784196	B;B|.	0.21309|.	0.004;0.054|.	B;B|.	0.24006|.	0.007;0.05|.	T|.	0.35871|.	-0.9771|.	9|.	0.11794|.	T|.	0.64|.	-4.6078|-4.6078	15.3316|15.3316	0.74215|0.74215	0.0:0.8608:0.1392:0.0|0.0:0.8608:0.1392:0.0	rs757081;rs52826791;rs757081|rs757081;rs52826791;rs757081	308;338|.	E7EV42;P80303|.	.;NUCB2_HUMAN|.	E|X	338;338;308|115	ENSP00000320168:Q338E;ENSP00000436455:Q338E;ENSP00000408702:Q308E|.	ENSP00000320168:Q338E|.	Q|S	+|+	1|2	0|0	NUCB2|NUCB2	17308259|17308259	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	3.992000|3.992000	0.56980|0.56980	2.692000|2.692000	0.91855|0.91855	0.655000|0.655000	0.94253|0.94253	CAG|TCA	C|0.738;G|0.262	0.262	strong		0.284	NUCB2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387614.2	NM_005013	
SAMD9	54809	hgsc.bcm.edu	37	7	92730687	92730687	+	Missense_Mutation	SNP	C	C	T	rs148724199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92730687C>T	ENST00000379958.2	-	3	4993	c.4724G>A	c.(4723-4725)gGa>gAa	p.G1575E		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1575						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)			AATGGAAAATCCCAGGTAAAA	0.368																																					p.G1575E		Atlas-SNP	.											.	SAMD9	239	.	0			c.G4724A						PASS	.	C	GLU/GLY,GLU/GLY	1,4405	2.1+/-5.4	0,1,2202	126.0	133.0	131.0		4724,4724	4.4	1.0	7	dbSNP_134	131	7,8591	5.7+/-21.5	0,7,4292	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	98,98	0,8,6494	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging,probably-damaging	1575/1590,1575/1590	92730687	8,12996	2203	4299	6502	SO:0001583	missense	54809	exon2			GAAAATCCCAGGT	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.4724G>A	7.37:g.92730687C>T	ENSP00000369292:p.Gly1575Glu	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	64	28	0.4375	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106178	0.77096	2.27E-4	8.14E-4	ENSG00000205413	ENST00000379958	T	0.77750	-1.12	4.44	4.44	0.53790	.	0.000000	0.64402	U	0.000003	D	0.86176	0.5870	M	0.62723	1.935	0.51482	D	0.999924	D	0.89917	1.0	D	0.91635	0.999	D	0.87750	0.2591	10	0.87932	D	0	.	16.1321	0.81446	0.0:1.0:0.0:0.0	.	1575	Q5K651	SAMD9_HUMAN	E	1575	ENSP00000369292:G1575E	ENSP00000369292:G1575E	G	-	2	0	SAMD9	92568623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.170000	0.77587	2.478000	0.83669	0.609000	0.83330	GGA	C|0.999;T|0.001	0.001	strong		0.368	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
KRT14	3861	hgsc.bcm.edu	37	17	39742856	39742856	+	Silent	SNP	G	G	A	rs6503639	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39742856G>A	ENST00000167586.6	-	1	317	c.231C>T	c.(229-231)agC>agT	p.S77S		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	77	Head.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				caaagcTGCTGCTGCTGCTGC	0.652													g|||	763	0.152356	0.1528	0.2003	5008	,	,		14066	0.0		0.3012	False		,,,				2504	0.1217				p.S77S		Atlas-SNP	.											.	KRT14	65	.	0			c.C231T						PASS	.	G		731,3673		54,623,1525	61.0	65.0	64.0		231	3.1	1.0	17	dbSNP_116	64	2884,5716		486,1912,1902	no	coding-synonymous	KRT14	NM_000526.4		540,2535,3427	AA,AG,GG		33.5349,16.5985,27.7991		77/473	39742856	3615,9389	2202	4300	6502	SO:0001819	synonymous_variant	3861	exon1			GCTGCTGCTGCTG	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.231C>T	17.37:g.39742856G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	42	23	0.547619	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			G|0.774;A|0.226	0.226	strong		0.652	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
SPHK2	56848	hgsc.bcm.edu	37	19	49132634	49132634	+	Silent	SNP	G	G	A	rs3745733	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49132634G>A	ENST00000245222.4	+	7	1935	c.1569G>A	c.(1567-1569)ctG>ctA	p.L523L	SPHK2_ENST00000600537.1_Silent_p.L464L|SPHK2_ENST00000443164.1_Silent_p.L585L|SPHK2_ENST00000599029.1_Silent_p.L487L|SPHK2_ENST00000598088.1_Silent_p.L523L|SPHK2_ENST00000340932.3_Silent_p.L485L|SPHK2_ENST00000599748.1_Silent_p.L487L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	523					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TGCCTCCGCTGGGCACCCCGC	0.701													G|||	379	0.0756789	0.0272	0.0994	5008	,	,		12711	0.0714		0.1203	False		,,,				2504	0.0828				p.L523L		Atlas-SNP	.											SPHK2,NS,carcinoma,0,1	SPHK2	62	1	0			c.G1569A						PASS	.	G	,,,	176,4224		3,170,2027	20.0	23.0	22.0		1392,1569,1461,1569	-0.4	0.3	19	dbSNP_107	22	1188,7404		79,1030,3187	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	82,1200,5214	AA,AG,GG		13.8268,4.0,10.4988	,,,	464/596,523/655,487/619,523/655	49132634	1364,11628	2200	4296	6496	SO:0001819	synonymous_variant	56848	exon7			TCCGCTGGGCACC	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1569G>A	19.37:g.49132634G>A		Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	52	34	0.653846	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.907;A|0.093	0.093	strong		0.701	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
IDI2	91734	hgsc.bcm.edu	37	10	1068639	1068639	+	Silent	SNP	C	C	T	rs13377037	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:1068639C>T	ENST00000277517.1	-	3	283	c.219G>A	c.(217-219)acG>acA	p.T73T	IDI2-AS1_ENST00000536039.1_RNA|IDI2-AS1_ENST00000428780.2_RNA|IDI2-AS1_ENST00000420381.1_RNA|IDI2-AS1_ENST00000434470.1_RNA|IDI2-AS1_ENST00000437374.1_RNA	NM_033261.2	NP_150286.1	Q9BXS1	IDI2_HUMAN	isopentenyl-diphosphate delta isomerase 2	73	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				cholesterol biosynthetic process (GO:0006695)|dimethylallyl diphosphate biosynthetic process (GO:0050992)|isopentenyl diphosphate metabolic process (GO:0046490)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|isopentenyl-diphosphate delta-isomerase activity (GO:0004452)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(49;0.235)	OV - Ovarian serous cystadenocarcinoma(33;0.143)	Epithelial(11;0.067)|OV - Ovarian serous cystadenocarcinoma(14;0.169)|all cancers(11;0.192)		ACGTGACTTTCGTGTCCGACC	0.522													C|||	501	0.10004	0.1483	0.1182	5008	,	,		18980	0.1081		0.0815	False		,,,				2504	0.0327				p.T73T		Atlas-SNP	.											.	IDI2	20	.	0			c.G219A						PASS	.	C		590,3816	259.2+/-262.9	34,522,1647	127.0	100.0	109.0		219	-5.2	0.0	10	dbSNP_121	109	670,7930	168.6+/-220.1	29,612,3659	no	coding-synonymous	IDI2	NM_033261.2		63,1134,5306	TT,TC,CC		7.7907,13.3908,9.6878		73/228	1068639	1260,11746	2203	4300	6503	SO:0001819	synonymous_variant	91734	exon3			GACTTTCGTGTCC	AF271725	CCDS7055.1	10p15.3	2003-11-19			ENSG00000148377	ENSG00000148377			23487	protein-coding gene	gene with protein product		615389				12477932	Standard	NM_033261		Approved	IPPI2	uc001ifv.1	Q9BXS1	OTTHUMG00000017537	ENST00000277517.1:c.219G>A	10.37:g.1068639C>T		Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	48	22	0.458333	NM_033261		Silent	SNP	ENST00000277517.1	37	CCDS7055.1																																																																																			C|0.900;N|0.000	.	strong		0.522	IDI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046411.1	NM_033261	
SLC52A1	55065	hgsc.bcm.edu	37	17	4936336	4936336	+	Silent	SNP	A	A	T	rs72822610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4936336A>T	ENST00000424747.1	-	5	1975	c.1263T>A	c.(1261-1263)ctT>ctA	p.L421L	SLC52A1_ENST00000512825.2_3'UTR|SLC52A1_ENST00000254853.5_Silent_p.L421L	NM_001104577.1	NP_001098047.1	Q9NWF4	S52A1_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	421					riboflavin transport (GO:0032218)	integral component of plasma membrane (GO:0005887)	riboflavin transporter activity (GO:0032217)|virus receptor activity (GO:0001618)										CACCGGCACCAAGCAGGGAGC	0.617													A|||	501	0.10004	0.1445	0.1066	5008	,	,		19163	0.0605		0.1441	False		,,,				2504	0.0307				p.L421L		Atlas-SNP	.											.	.	.	.	0			c.T1263A						PASS	.	A	,	598,3808	263.1+/-265.3	43,512,1648	83.0	79.0	81.0		1263,1263	-1.7	0.1	17	dbSNP_130	81	1231,7369	246.8+/-275.1	83,1065,3152	no	coding-synonymous,coding-synonymous	GPR172B	NM_001104577.1,NM_017986.3	,	126,1577,4800	TT,TA,AA		14.314,13.5724,14.0627	,	421/449,421/449	4936336	1829,11177	2203	4300	6503	SO:0001819	synonymous_variant	55065	exon5			GGCACCAAGCAGG	AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517		"""Solute carriers"""	30225	protein-coding gene	gene with protein product	"""riboflavin transporter 1"""	607883	"""G protein-coupled receptor 172B"""	GPR172B		12740431, 18632736	Standard	NM_001104577		Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000424747.1:c.1263T>A	17.37:g.4936336A>T		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	59	31	0.525424	NM_017986	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	Silent	SNP	ENST00000424747.1	37	CCDS11066.1																																																																																			A|0.868;T|0.132	0.132	strong		0.617	SLC52A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216913.1	NM_017986	
OR4D2	124538	hgsc.bcm.edu	37	17	56247101	56247101	+	Missense_Mutation	SNP	C	C	A	rs60994383	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56247101C>A	ENST00000545221.1	+	1	85	c.85C>A	c.(85-87)Cta>Ata	p.L29I		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	29			L -> I (in dbSNP:rs60994383).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						TTTCCTGTTTCTAATGTTCCT	0.483													C|||	1178	0.235224	0.3775	0.1599	5008	,	,		20152	0.1657		0.2147	False		,,,				2504	0.1892				p.L29I		Atlas-SNP	.											.	OR4D2	48	.	0			c.C85A						PASS	.	C	ILE/LEU	1567,2839	490.4+/-361.8	275,1017,911	159.0	141.0	147.0		85	-5.0	0.9	17	dbSNP_129	147	1963,6637	346.7+/-326.3	234,1495,2571	yes	missense	OR4D2	NM_001004707.3	5	509,2512,3482	AA,AC,CC		22.8256,35.5651,27.1413	benign	29/308	56247101	3530,9476	2203	4300	6503	SO:0001583	missense	124538	exon1			CTGTTTCTAATGT		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"""GPCR / Class A : Olfactory receptors"""	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.85C>A	17.37:g.56247101C>A	ENSP00000441354:p.Leu29Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	135	60	0.444444	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	CCDS32688.1	498	0.22802197802197802	178	0.3617886178861789	66	0.18232044198895028	90	0.15734265734265734	164	0.21635883905013192	C	4.031	0.003271	0.07866	0.355651	0.228256	ENSG00000255713	ENST00000545221	T	0.00272	8.36	5.4	-5.02	0.02982	.	0.596543	0.13642	N	0.372932	T	0.00012	0.0000	L	0.28014	0.82	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.31475	-0.9942	9	0.42905	T	0.14	-0.2109	2.2874	0.04130	0.2069:0.334:0.3064:0.1527	rs60994383;rs62083702	29	P58180	OR4D2_HUMAN	I	29	ENSP00000441354:L29I	ENSP00000441354:L29I	L	+	1	2	OR4D2	53602100	0.000000	0.05858	0.947000	0.38551	0.016000	0.09150	-2.547000	0.00931	-0.561000	0.06094	-1.610000	0.00802	CTA	C|0.745;A|0.255	0.255	strong		0.483	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
TRMU	55687	hgsc.bcm.edu	37	22	46733831	46733831	+	Missense_Mutation	SNP	G	G	A	rs55952751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:46733831G>A	ENST00000290846.4	+	2	578	c.238G>A	c.(238-240)Gat>Aat	p.D80N	TRMU_ENST00000381019.3_Missense_Mutation_p.D80N|TRMU_ENST00000424260.2_Missense_Mutation_p.D45N	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	80					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|sulfurtransferase activity (GO:0016783)|tRNA binding (GO:0000049)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)	10		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)		GTATTGGAATGATGTGTTCAG	0.502													G|||	5	0.000998403	0.0	0.0	5008	,	,		23073	0.0		0.005	False		,,,				2504	0.0				p.D80N		Atlas-SNP	.											.	TRMU	23	.	0			c.G238A						PASS	.	G	ASN/ASP	0,4406	2.1+/-5.4	0,0,2203	188.0	159.0	169.0		238	2.5	0.1	22	dbSNP_129	169	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TRMU	NM_018006.4	23	0,9,6494	AA,AG,GG		0.1047,0.0,0.0692	possibly-damaging	80/422	46733831	9,12997	2203	4300	6503	SO:0001583	missense	55687	exon2			TGGAATGATGTGT	AY062123	CCDS14075.1, CCDS63510.1	22q13	2005-08-11	2005-08-11	2005-08-11	ENSG00000100416	ENSG00000100416	2.1.1.61		25481	protein-coding gene	gene with protein product		610230	"""tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase """	TRMT		14746906	Standard	XM_005261678		Approved	FLJ10140, MTO2	uc003bhp.3	O75648	OTTHUMG00000150424	ENST00000290846.4:c.238G>A	22.37:g.46733831G>A	ENSP00000290846:p.Asp80Asn	Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	92	32	0.347826	NM_018006	A8K3U7|Q05C99|Q5W9C8|Q66K31|Q6ICC3|Q9NWC1	Missense_Mutation	SNP	ENST00000290846.4	37	CCDS14075.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.359	1.067422	0.20067	0.0	0.001047	ENSG00000100416	ENST00000290846;ENST00000381019;ENST00000424260	T;T;T	0.72282	-0.64;-0.64;-0.64	4.8	2.45	0.29901	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.550552	0.19343	N	0.116585	T	0.36276	0.0961	N	0.12527	0.23	0.33732	D	0.618343	P;B;B	0.39920	0.695;0.435;0.005	B;B;B	0.34452	0.183;0.085;0.019	T	0.55366	-0.8152	10	0.02654	T	1	-12.8828	14.316	0.66452	0.0:0.2562:0.7438:0.0	rs55952751	80;80;80	B4DHM1;O75648-2;O75648	.;.;MTU1_HUMAN	N	80;80;45	ENSP00000290846:D80N;ENSP00000370407:D80N;ENSP00000406038:D45N	ENSP00000290846:D80N	D	+	1	0	TRMU	45112495	1.000000	0.71417	0.071000	0.20095	0.176000	0.22953	3.992000	0.56980	2.197000	0.70478	0.557000	0.71058	GAT	G|0.999;A|0.001	0.001	strong		0.502	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	NM_018006	
PRSS53	339105	hgsc.bcm.edu	37	16	31096164	31096164	+	Missense_Mutation	SNP	G	G	C	rs7199949	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31096164G>C	ENST00000280606.6	-	8	1369	c.1216C>G	c.(1216-1218)Cct>Gct	p.P406A		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	406	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						TGGTGGTCAGGATAGGGCAGG	0.692													C|||	2399	0.479034	0.652	0.4323	5008	,	,		17467	0.1121		0.3767	False		,,,				2504	0.7618				p.P406A		Atlas-SNP	.											PRSS53,NS,carcinoma,0,2	PRSS53	29	2	0			c.C1216G						PASS	.	C	ALA/PRO	2270,1688		698,874,407	7.0	9.0	8.0		1216	-3.0	0.0	16	dbSNP_116	8	2881,5337		574,1733,1802	yes	missense	PRSS53	NM_001039503.2	27	1272,2607,2209	CC,CG,GG		35.0572,42.6478,42.3045	benign	406/554	31096164	5151,7025	1979	4109	6088	SO:0001583	missense	339105	exon8			GGTCAGGATAGGG		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.1216C>G	16.37:g.31096164G>C	ENSP00000280606:p.Pro406Ala	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	242	121	0.5	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	771	0.35302197802197804	305	0.6199186991869918	140	0.3867403314917127	47	0.08216783216783216	279	0.36807387862796836	C	0.011	-1.734285	0.00687	0.573522	0.350572	ENSG00000151006	ENST00000280606	D	0.87334	-2.24	5.28	-3.03	0.05429	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.466390	0.15290	N	0.270185	T	0.00012	0.0000	N	0.02736	-0.51	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31336	-0.9947	9	0.02654	T	1	.	0.6908	0.00891	0.2112:0.3345:0.2057:0.2487	rs7199949;rs57732931;rs7199949	406	Q2L4Q9	PRS53_HUMAN	A	406	ENSP00000280606:P406A	ENSP00000280606:P406A	P	-	1	0	PRSS53	31003665	0.000000	0.05858	0.000000	0.03702	0.365000	0.29674	-0.533000	0.06157	-1.322000	0.02278	-0.225000	0.12378	CCT	G|0.648;C|0.352	0.352	strong		0.692	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
PLRG1	5356	hgsc.bcm.edu	37	4	155459194	155459194	+	Silent	SNP	A	A	T	rs7668818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155459194A>T	ENST00000499023.2	-	13	1344	c.1218T>A	c.(1216-1218)atT>atA	p.I406I	PLRG1_ENST00000302078.5_Silent_p.I397I|PLRG1_ENST00000393905.2_Silent_p.I406I	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	406					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				AAAGATTTTGAATGAAACTTC	0.303													A|||	1155	0.230631	0.1498	0.1888	5008	,	,		15715	0.1438		0.325	False		,,,				2504	0.362				p.I406I		Atlas-SNP	.											.	PLRG1	43	.	0			c.T1218A						PASS	.	A	,	776,3624	294.7+/-283.3	70,636,1494	42.0	43.0	43.0		1191,1218	4.5	1.0	4	dbSNP_116	43	2813,5757	430.5+/-356.5	456,1901,1928	no	coding-synonymous,coding-synonymous	PLRG1	NM_001201564.1,NM_002669.3	,	526,2537,3422	TT,TA,AA		32.8238,17.6364,27.6715	,	397/506,406/515	155459194	3589,9381	2200	4285	6485	SO:0001819	synonymous_variant	5356	exon13			ATTTTGAATGAAA	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1218T>A	4.37:g.155459194A>T		Somatic	209	0	0		WXS	Illumina HiSeq	Phase_I	212	112	0.528302	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	37	CCDS34083.1																																																																																			A|0.748;T|0.252	0.252	strong		0.303	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
STRN3	29966	hgsc.bcm.edu	37	14	31425437	31425437	+	Silent	SNP	T	T	C	rs12886419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:31425437T>C	ENST00000357479.5	-	2	490	c.294A>G	c.(292-294)gcA>gcG	p.A98A	STRN3_ENST00000355683.5_Silent_p.A98A	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	98					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		CTTGTAGAAATGCAATCCGGG	0.328													T|||	859	0.171526	0.2526	0.17	5008	,	,		19408	0.003		0.2704	False		,,,				2504	0.135				p.A98A		Atlas-SNP	.											.	STRN3	117	.	0			c.A294G						PASS	.	T	,	1093,3313	395.4+/-329.6	135,823,1245	125.0	113.0	117.0		294,294	2.8	1.0	14	dbSNP_121	117	2247,6351	379.4+/-339.3	260,1727,2312	no	coding-synonymous,coding-synonymous	STRN3	NM_001083893.1,NM_014574.3	,	395,2550,3557	CC,CT,TT		26.134,24.8071,25.6844	,	98/798,98/714	31425437	3340,9664	2203	4299	6502	SO:0001819	synonymous_variant	29966	exon2			TAGAAATGCAATC		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.294A>G	14.37:g.31425437T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	48	0.489796	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Silent	SNP	ENST00000357479.5	37	CCDS41938.1																																																																																			T|0.773;C|0.227	0.227	strong		0.328	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
UNC93A	54346	hgsc.bcm.edu	37	6	167719436	167719436	+	Missense_Mutation	SNP	G	G	A	rs2072767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167719436G>A	ENST00000230256.3	+	6	1049	c.874G>A	c.(874-876)Gtc>Atc	p.V292I	UNC93A_ENST00000366829.2_Missense_Mutation_p.V250I	NM_018974.3	NP_061847.2	Q86WB7	UN93A_HUMAN	unc-93 homolog A (C. elegans)	292			V -> I (in dbSNP:rs2072767). {ECO:0000269|PubMed:12381271}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	40		Breast(66;7.62e-05)|Ovarian(120;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CATCCAGTTCGTCGGCTACGT	0.612													G|||	1404	0.280351	0.2587	0.2349	5008	,	,		20543	0.2629		0.2753	False		,,,				2504	0.365				p.V292I		Atlas-SNP	.											.	UNC93A	66	.	0			c.G874A						PASS	.	G	ILE/VAL,ILE/VAL	1158,3248	409.7+/-335.1	153,852,1198	285.0	237.0	253.0		748,874	3.9	0.0	6	dbSNP_96	253	2187,6413	373.3+/-337.0	263,1661,2376	yes	missense,missense	UNC93A	NM_001143947.1,NM_018974.3	29,29	416,2513,3574	AA,AG,GG		25.4302,26.2823,25.7189	benign,benign	250/416,292/458	167719436	3345,9661	2203	4300	6503	SO:0001583	missense	54346	exon6			CAGTTCGTCGGCT	AJ508812	CCDS5300.1, CCDS47515.1	6q27	2014-05-16	2001-11-28		ENSG00000112494	ENSG00000112494			12570	protein-coding gene	gene with protein product		607995	"""unc93 (C.elegans) homolog A"""			12381271	Standard	NM_001143947		Approved	dJ366N23.2, dJ366N23.1	uc003qvq.3	Q86WB7	OTTHUMG00000016021	ENST00000230256.3:c.874G>A	6.37:g.167719436G>A	ENSP00000230256:p.Val292Ile	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	67	66	0.985075	NM_018974	B3KRP5|Q4QQJ4|Q5JZD6	Missense_Mutation	SNP	ENST00000230256.3	37	CCDS5300.1	590	0.27014652014652013	141	0.2865853658536585	88	0.2430939226519337	157	0.2744755244755245	204	0.2691292875989446	G	10.35	1.326484	0.24080	0.262823	0.254302	ENSG00000112494	ENST00000230256;ENST00000366829	T;T	0.16457	2.34;2.62	4.73	3.87	0.44632	Major facilitator superfamily domain, general substrate transporter (1);	0.131212	0.50627	N	0.000115	T	0.04588	0.0125	L	0.49256	1.55	0.19945	P	0.9999408312	P;P	0.51351	0.944;0.506	B;B	0.35073	0.195;0.078	T	0.19160	-1.0314	9	0.09084	T	0.74	-39.111	12.2369	0.54520	0.083:0.0:0.917:0.0	rs2072767;rs56604367;rs58276443;rs2072767	250;292	Q4QQJ4;Q86WB7	.;UN93A_HUMAN	I	292;250	ENSP00000230256:V292I;ENSP00000355794:V250I	ENSP00000230256:V292I	V	+	1	0	UNC93A	167639426	1.000000	0.71417	0.021000	0.16686	0.154000	0.21943	5.362000	0.66098	1.003000	0.39130	-0.222000	0.12452	GTC	G|0.732;A|0.268	0.268	strong		0.612	UNC93A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043125.2	NM_018974	
CDH7	1005	hgsc.bcm.edu	37	18	63530016	63530016	+	Missense_Mutation	SNP	A	A	G	rs2291343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:63530016A>G	ENST00000397968.2	+	11	2153	c.1727A>G	c.(1726-1728)aAc>aGc	p.N576S	CDH7_ENST00000323011.3_Missense_Mutation_p.N576S|RP11-389J22.1_ENST00000581987.1_RNA|CDH7_ENST00000536984.2_Missense_Mutation_p.N576S	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	576	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		N -> S (in dbSNP:rs2291343). {ECO:0000269|PubMed:10861224, ECO:0000269|PubMed:10995570}.		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)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				AGCAGCACCAACACCCTCACC	0.537													A|||	3153	0.629593	0.2814	0.7421	5008	,	,		18957	0.9196		0.7087	False		,,,				2504	0.6401				p.N576S		Atlas-SNP	.											.	CDH7	362	.	0			c.A1727G						PASS	.	A	SER/ASN,SER/ASN	1561,2845	489.9+/-361.6	274,1013,916	137.0	102.0	114.0		1727,1727	5.4	1.0	18	dbSNP_100	114	6106,2494	695.4+/-404.8	2172,1762,366	yes	missense,missense	CDH7	NM_004361.2,NM_033646.1	46,46	2446,2775,1282	GG,GA,AA		29.0,35.429,41.0503	benign,benign	576/786,576/786	63530016	7667,5339	2203	4300	6503	SO:0001583	missense	1005	exon11			GCACCAACACCCT	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.1727A>G	18.37:g.63530016A>G	ENSP00000381058:p.Asn576Ser	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	189	94	0.497355	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	37	CCDS11993.1	1482	0.6785714285714286	137	0.2784552845528455	274	0.7569060773480663	536	0.9370629370629371	535	0.7058047493403694	A	11.44	1.639132	0.29157	0.35429	0.71	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.49720	0.77;0.77;0.77	5.37	5.37	0.77165	Cadherin (4);Cadherin-like (1);	0.049542	0.85682	D	0.000000	T	0.00012	0.0000	N	0.11201	0.11	0.20975	P	0.999818259	B;B	0.17465	0.002;0.022	B;B	0.19946	0.016;0.027	T	0.41215	-0.9521	9	0.02654	T	1	.	15.3548	0.74418	1.0:0.0:0.0:0.0	rs2291343;rs17853704;rs52834695;rs61438627;rs2291343	576;576	F5H5X9;Q9ULB5	.;CADH7_HUMAN	S	576	ENSP00000319166:N576S;ENSP00000443030:N576S;ENSP00000381058:N576S	ENSP00000319166:N576S	N	+	2	0	CDH7	61680996	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.177000	0.50871	2.044000	0.60594	0.482000	0.46254	AAC	A|0.380;G|0.620	0.620	strong		0.537	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
SEC16A	9919	hgsc.bcm.edu	37	9	139369212	139369212	+	Silent	SNP	G	G	A	rs17567909	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139369212G>A	ENST00000371706.3	-	1	2355	c.2322C>T	c.(2320-2322)ccC>ccT	p.P774P	SEC16A_ENST00000431893.2_Silent_p.P774P|SEC16A_ENST00000313050.7_Silent_p.P952P|SEC16A_ENST00000290037.6_Silent_p.P774P			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	774					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)		TAGCAAATCCGGGAAGAGCAC	0.507													G|||	464	0.0926518	0.0045	0.0648	5008	,	,		21202	0.004		0.1213	False		,,,				2504	0.2935				p.P952P		Atlas-SNP	.											.	SEC16A	249	.	0			c.C2856T						PASS	.	G		99,3753		5,89,1832	74.0	73.0	73.0		2856	-10.3	0.0	9	dbSNP_123	73	1043,7215		66,911,3152	no	coding-synonymous	SEC16A	NM_014866.1		71,1000,4984	AA,AG,GG		12.6302,2.5701,9.4302		952/2358	139369212	1142,10968	1926	4129	6055	SO:0001819	synonymous_variant	9919	exon3			AAATCCGGGAAGA	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.2322C>T	9.37:g.139369212G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	50	24	0.48	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.926;A|0.074	0.074	strong		0.507	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
KCTD2	23510	hgsc.bcm.edu	37	17	73058249	73058249	+	Missense_Mutation	SNP	A	A	G	rs61750318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73058249A>G	ENST00000322444.6	+	5	677	c.671A>G	c.(670-672)aAt>aGt	p.N224S	KCTD2_ENST00000581589.1_Missense_Mutation_p.N25S	NM_015353.1	NP_056168.1	Q14681	KCTD2_HUMAN	potassium channel tetramerization domain containing 2	224					protein homooligomerization (GO:0051260)		protein complex binding (GO:0032403)			kidney(1)|lung(2)	3	all_lung(278;0.226)					AACTACGGCAATGAGGATCAG	0.438													A|||	4	0.000798722	0.0	0.0014	5008	,	,		20398	0.001		0.002	False		,,,				2504	0.0				p.N224S		Atlas-SNP	.											.	KCTD2	15	.	0			c.A671G						PASS	.	A	SER/ASN	1,4405	2.1+/-5.4	0,1,2202	147.0	130.0	135.0		671	4.5	1.0	17	dbSNP_129	135	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KCTD2	NM_015353.1	46	0,4,6499	GG,GA,AA		0.0349,0.0227,0.0308	benign	224/264	73058249	4,13002	2203	4300	6503	SO:0001583	missense	23510	exon5			ACGGCAATGAGGA	BC033329	CCDS32728.1	17q25.2	2013-06-20	2013-06-20			ENSG00000180901			21294	protein-coding gene	gene with protein product		613422	"""potassium channel tetramerisation domain containing 2"""			12620391	Standard	XR_248405		Approved	KIAA0176	uc002jmp.3	Q14681		ENST00000322444.6:c.671A>G	17.37:g.73058249A>G	ENSP00000312814:p.Asn224Ser	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	239	95	0.39749	NM_015353		Missense_Mutation	SNP	ENST00000322444.6	37	CCDS32728.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	12.24	1.879309	0.33162	2.27E-4	3.49E-4	ENSG00000180901	ENST00000322444;ENST00000375286	T	0.75821	-0.97	5.55	4.48	0.54585	.	0.045672	0.85682	D	0.000000	T	0.55130	0.1901	N	0.16743	0.435	0.52501	D	0.999952	B	0.10296	0.003	B	0.06405	0.002	T	0.50311	-0.8843	10	0.14656	T	0.56	-8.6415	10.8859	0.46965	0.9267:0.0:0.0733:0.0	rs61750318	224	Q14681	KCTD2_HUMAN	S	224;206	ENSP00000312814:N224S	ENSP00000312814:N224S	N	+	2	0	KCTD2	70569844	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	6.366000	0.73095	2.110000	0.64415	0.460000	0.39030	AAT	A|0.999;G|0.001	0.001	strong		0.438	KCTD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445538.1		
ADPRH	141	hgsc.bcm.edu	37	3	119301139	119301139	+	Silent	SNP	C	C	T	rs20568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:119301139C>T	ENST00000478399.1	+	2	1528	c.123C>T	c.(121-123)ggC>ggT	p.G41G	ADPRH_ENST00000471850.1_Intron|ADPRH_ENST00000465513.1_Silent_p.G41G|RP11-190C22.9_ENST00000609385.1_RNA|ADPRH_ENST00000478927.1_Silent_p.G41G|ADPRH_ENST00000357003.3_Silent_p.G41G			P54922	ADPRH_HUMAN	ADP-ribosylarginine hydrolase	41					cellular protein modification process (GO:0006464)|protein de-ADP-ribosylation (GO:0051725)		ADP-ribosylarginine hydrolase activity (GO:0003875)|magnesium ion binding (GO:0000287)			breast(1)|kidney(1)|lung(10)|ovary(1)	13		Lung NSC(201;0.0977)		GBM - Glioblastoma multiforme(114;0.23)		CCCAGCTGGGCGGCTTGGATG	0.582													C|||	733	0.146366	0.1271	0.0476	5008	,	,		18431	0.2579		0.0577	False		,,,				2504	0.2188				p.G41G	GBM(133;579 1804 5989 9967 40052)	Atlas-SNP	.											.	ADPRH	33	.	0			c.C123T						PASS	.	C		411,3995	203.5+/-225.9	15,381,1807	81.0	79.0	80.0		123	-11.8	0.0	3	dbSNP_67	80	538,8062	149.4+/-204.5	13,512,3775	no	coding-synonymous	ADPRH	NM_001125.2		28,893,5582	TT,TC,CC		6.2558,9.3282,7.2966		41/358	119301139	949,12057	2203	4300	6503	SO:0001819	synonymous_variant	141	exon3			GCTGGGCGGCTTG	L13291	CCDS2990.1	3q13.31-q13.33	2004-02-27			ENSG00000144843	ENSG00000144843			269	protein-coding gene	gene with protein product		603081				8349667, 12070318	Standard	NM_001125		Approved	ARH1	uc003ecs.3	P54922	OTTHUMG00000159420	ENST00000478399.1:c.123C>T	3.37:g.119301139C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	166	84	0.506024	NM_001125	B2R8H1|D3DN83	Silent	SNP	ENST00000478399.1	37	CCDS2990.1																																																																																			C|0.915;T|0.085	0.085	strong		0.582	ADPRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355199.1	NM_001125	
KBTBD2	25948	hgsc.bcm.edu	37	7	32909182	32909182	+	Silent	SNP	G	G	A	rs752730	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:32909182G>A	ENST00000304056.4	-	4	2346	c.1647C>T	c.(1645-1647)taC>taT	p.Y549Y	KBTBD2_ENST00000485611.1_5'Flank|AVL9_ENST00000404479.1_Intron	NM_015483.2	NP_056298.2	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	549										endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1)	17			GBM - Glioblastoma multiforme(11;0.0499)			GGTAGGTGACGTATTTAGCTC	0.468													G|||	965	0.192692	0.0756	0.4207	5008	,	,		20479	0.2242		0.2018	False		,,,				2504	0.1472				p.Y549Y		Atlas-SNP	.											.	KBTBD2	37	.	0			c.C1647T						PASS	.	G		400,4006	198.4+/-222.2	15,370,1818	165.0	150.0	155.0		1647	-3.8	0.9	7	dbSNP_86	155	1865,6735	332.8+/-320.3	204,1457,2639	no	coding-synonymous	KBTBD2	NM_015483.2		219,1827,4457	AA,AG,GG		21.686,9.0785,17.415		549/624	32909182	2265,10741	2203	4300	6503	SO:0001819	synonymous_variant	25948	exon4			GGTGACGTATTTA	AB040922	CCDS34614.1	7p14.3	2013-01-08	2003-12-12	2003-12-12	ENSG00000170852	ENSG00000170852		"""BTB/POZ domain containing"""	21751	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 1"""	BKLHD1		10819331	Standard	NM_015483		Approved	DKFZP566C134	uc003tdb.2	Q8IY47	OTTHUMG00000152984	ENST00000304056.4:c.1647C>T	7.37:g.32909182G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	112	47	0.419643	NM_015483	A8K9T7|Q86Y62|Q9P239|Q9UFM7|Q9Y382	Silent	SNP	ENST00000304056.4	37	CCDS34614.1																																																																																			G|0.819;A|0.181	0.181	strong		0.468	KBTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328890.1	XM_291224	
KDM4C	23081	hgsc.bcm.edu	37	9	7103816	7103816	+	Silent	SNP	C	C	T	rs3763651	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:7103816C>T	ENST00000381309.3	+	18	3121	c.2556C>T	c.(2554-2556)gaC>gaT	p.D852D	KDM4C_ENST00000381306.3_Silent_p.D852D|KDM4C_ENST00000428870.2_Silent_p.D539D|KDM4C_ENST00000536108.1_3'UTR|KDM4C_ENST00000442236.2_Silent_p.D597D	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	852					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						AGCCTGATGACTGGCCTTATG	0.552													T|||	2865	0.572085	0.621	0.634	5008	,	,		21359	0.7143		0.4225	False		,,,				2504	0.4693				p.D852D		Atlas-SNP	.											.	KDM4C	186	.	0			c.C2556T						PASS	.	T	,	2659,1747	521.1+/-370.4	816,1027,360	162.0	126.0	138.0		2556,2556	-5.4	0.3	9	dbSNP_107	138	3732,4868	617.6+/-396.7	792,2148,1360	no	coding-synonymous,coding-synonymous	KDM4C	NM_001146694.1,NM_015061.3	,	1608,3175,1720	TT,TC,CC		43.3953,39.6505,49.1389	,	852/1048,852/1057	7103816	6391,6615	2203	4300	6503	SO:0001819	synonymous_variant	23081	exon18			TGATGACTGGCCT	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.2556C>T	9.37:g.7103816C>T		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	164	164	1	NM_001146694	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Silent	SNP	ENST00000381309.3	37	CCDS6471.1																																																																																			C|0.456;T|0.544	0.544	strong		0.552	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
MUC5B	727897	hgsc.bcm.edu	37	11	1264581	1264581	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1264581C>T	ENST00000529681.1	+	31	6529	c.6471C>T	c.(6469-6471)ccC>ccT	p.P2157P	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.P2160P	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2157	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)		ggacaactcccatccccccag	0.647																																					p.P2157P		Atlas-SNP	.											MUC5B,NS,carcinoma,+1,2	MUC5B	473	2	0			c.C6471T						scavenged	.						105.0	136.0	126.0					11																	1264581		2094	4146	6240	SO:0001819	synonymous_variant	727897	exon31			AACTCCCATCCCC	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.6471C>T	11.37:g.1264581C>T		Somatic	579	2	0.00345423		WXS	Illumina HiSeq	Phase_I	505	5	0.00990099	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	none		0.647	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PKD1	5310	hgsc.bcm.edu	37	16	2161793	2161793	+	Silent	SNP	G	G	A	rs74331768	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2161793G>A	ENST00000262304.4	-	15	3583	c.3375C>T	c.(3373-3375)tcC>tcT	p.S1125S	PKD1_ENST00000423118.1_Silent_p.S1125S|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1125	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CGGAGGGCAGGGAGGCGCGCA	0.677													g|||	569	0.113618	0.2897	0.111	5008	,	,		15925	0.0		0.0944	False		,,,				2504	0.0143				p.S1125S		Atlas-SNP	.											.	PKD1	184	.	0			c.C3375T						PASS	.	G	,	1046,3330		140,766,1282	20.0	21.0	21.0		3375,3375	-6.9	0.0	16	dbSNP_131	21	826,7752		53,720,3516	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	193,1486,4798	AA,AG,GG		9.6293,23.9031,14.4511	,	1125/4303,1125/4304	2161793	1872,11082	2188	4289	6477	SO:0001819	synonymous_variant	5310	exon15			GGGCAGGGAGGCG	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.3375C>T	16.37:g.2161793G>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	60	33	0.55	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			G|0.856;A|0.144	0.144	strong		0.677	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
TTLL4	9654	hgsc.bcm.edu	37	2	219617523	219617523	+	Missense_Mutation	SNP	A	A	G	rs116116034	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219617523A>G	ENST00000392102.1	+	17	3354	c.3014A>G	c.(3013-3015)gAt>gGt	p.D1005G	TTLL4_ENST00000442769.1_Missense_Mutation_p.D941G|TTLL4_ENST00000457313.1_Missense_Mutation_p.D840G|TTLL4_ENST00000258398.4_Missense_Mutation_p.D1005G	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	1005					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)		CTGACACCAGATGATGTTCGG	0.483													A|||	5	0.000998403	0.0	0.0	5008	,	,		21764	0.0		0.005	False		,,,				2504	0.0				p.D1005G	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.A3014G						PASS	.	A	GLY/ASP	5,4401	9.9+/-24.2	0,5,2198	209.0	190.0	196.0		3014	5.4	1.0	2	dbSNP_132	196	39,8561	25.7+/-73.6	0,39,4261	yes	missense	TTLL4	NM_014640.4	94	0,44,6459	GG,GA,AA		0.4535,0.1135,0.3383	possibly-damaging	1005/1200	219617523	44,12962	2203	4300	6503	SO:0001583	missense	9654	exon17			CACCAGATGATGT		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.3014A>G	2.37:g.219617523A>G	ENSP00000375951:p.Asp1005Gly	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	262	140	0.534351	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	A|A	26.6|26.6	4.754504|4.754504	0.89843|0.89843	0.001135|0.001135	0.004535|0.004535	ENSG00000135912|ENSG00000135912	ENST00000457313;ENST00000392102;ENST00000442769;ENST00000258398|ENST00000417855	T;T;T;T|.	0.04317|.	3.79;4.02;3.65;4.02|.	5.38|5.38	5.38|5.38	0.77491|0.77491	.|.	0.234860|.	0.42821|.	D|.	0.000658|.	T|T	0.67970|0.67970	0.2950|0.2950	M|M	0.75615|0.75615	2.305|2.305	0.80722|0.80722	D|D	1|1	B;D;D;B|.	0.67145|.	0.044;0.996;0.995;0.402|.	B;P;P;B|.	0.62649|.	0.048;0.905;0.791;0.119|.	T|T	0.72763|0.72763	-0.4195|-0.4195	10|5	0.56958|.	D|.	0.05|.	.|.	14.7359|14.7359	0.69414|0.69414	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	208;840;941;1005|.	B4DJF5;E9PH58;E7EX20;Q14679|.	.;.;.;TTLL4_HUMAN|.	G|V	840;1005;941;1005|31	ENSP00000393332:D840G;ENSP00000375951:D1005G;ENSP00000396555:D941G;ENSP00000258398:D1005G|.	ENSP00000258398:D1005G|.	D|M	+|+	2|1	0|0	TTLL4|TTLL4	219325767|219325767	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.809000|6.809000	0.75211|0.75211	2.254000|2.254000	0.74563|0.74563	0.533000|0.533000	0.62120|0.62120	GAT|ATG	A|0.996;G|0.004	0.004	strong		0.483	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640	
STEAP2	261729	hgsc.bcm.edu	37	7	89856608	89856608	+	Silent	SNP	C	C	T	rs110360	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:89856608C>T	ENST00000287908.3	+	3	1209	c.816C>T	c.(814-816)ctC>ctT	p.L272L	STEAP2_ENST00000394621.2_Silent_p.L272L|STEAP2_ENST00000394626.1_Silent_p.L272L|STEAP2_ENST00000394622.2_Silent_p.L272L|STEAP2_ENST00000394632.1_Silent_p.L272L|STEAP2_ENST00000394629.2_Silent_p.L272L|STEAP2_ENST00000402625.2_Silent_p.L272L	NM_001244944.1|NM_152999.3	NP_001231873.1|NP_694544.2	Q8NFT2	STEA2_HUMAN	STEAP family member 2, metalloreductase	272	Ferric oxidoreductase.				copper ion import (GO:0015677)|endocytosis (GO:0006897)|ferric iron import into cell (GO:0097461)|Golgi to plasma membrane transport (GO:0006893)|iron ion homeostasis (GO:0055072)|regulated secretory pathway (GO:0045055)|response to hormone (GO:0009725)	cytosol (GO:0005829)|early endosome (GO:0005769)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|trans-Golgi network transport vesicle (GO:0030140)	cupric reductase activity (GO:0008823)|ferric-chelate reductase (NADPH) activity (GO:0052851)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)	15	all_hematologic(106;0.112)					TAGTATACCTCGCAGGTCTTC	0.403													c|||	2194	0.438099	0.475	0.4467	5008	,	,		18568	0.2609		0.5119	False		,,,				2504	0.4888				p.L272L		Atlas-SNP	.											STEAP2_ENST00000394626,NS,carcinoma,0,2	STEAP2	78	2	0			c.C816T						PASS	.	C	,,	2178,2228	585.0+/-386.2	531,1116,556	88.0	84.0	85.0		816,816,816	-7.3	0.8	7	dbSNP_79	85	4556,4042	594.3+/-393.3	1225,2106,968	no	coding-synonymous,coding-synonymous,coding-synonymous	STEAP2	NM_001040665.1,NM_001040666.1,NM_152999.3	,,	1756,3222,1524	TT,TC,CC		47.0109,49.4326,48.2159	,,	272/491,272/455,272/491	89856608	6734,6270	2203	4299	6502	SO:0001819	synonymous_variant	261729	exon4			ATACCTCGCAGGT	AF455138	CCDS5615.1, CCDS43612.1, CCDS59064.1	7q21.13	2011-09-30	2011-09-30		ENSG00000157214	ENSG00000157214			17885	protein-coding gene	gene with protein product		605094	"""prostate cancer associated protein 1"", ""six transmembrane epithelial antigen of the prostate 2"""	PCANAP1		10613842, 12095985	Standard	NM_001040665		Approved	IPCA-1, STAMP1, STMP	uc003ujz.3	Q8NFT2	OTTHUMG00000023341	ENST00000287908.3:c.816C>T	7.37:g.89856608C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	177	176	0.99435	NM_001244946	A4D1F1|G5E9C6|Q6UXN6|Q6YPB1|Q8IUE7	Silent	SNP	ENST00000287908.3	37	CCDS5615.1																																																																																			C|0.523;T|0.477	0.477	strong		0.403	STEAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059662.4	NM_152999	
SIL1	64374	hgsc.bcm.edu	37	5	138456815	138456815	+	Silent	SNP	T	T	C	rs3088052	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:138456815T>C	ENST00000394817.2	-	3	292	c.153A>G	c.(151-153)acA>acG	p.T51T	SIL1_ENST00000265195.5_Silent_p.T51T|SIL1_ENST00000509534.1_Silent_p.T58T	NM_022464.4	NP_071909.1	Q9H173	SIL1_HUMAN	SIL1 nucleotide exchange factor	51	Interaction with HSPA5 and localization to the endoplasmic reticulum. {ECO:0000250}.				intracellular protein transport (GO:0006886)|protein folding (GO:0006457)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	unfolded protein binding (GO:0051082)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTTTTCTCTCTGTTTCTTTGG	0.552									Marinesco-Sjgren syndrome				C|||	2138	0.426917	0.6861	0.4366	5008	,	,		19994	0.1815		0.4076	False		,,,				2504	0.3425				p.T51T		Atlas-SNP	.											.	SIL1	31	.	0			c.A153G						PASS	.	C	,	2983,1423	463.0+/-353.4	1006,971,226	140.0	147.0	145.0		153,153	-2.0	0.5	5	dbSNP_102	145	3705,4895	619.8+/-397.0	810,2085,1405	no	coding-synonymous,coding-synonymous	SIL1	NM_001037633.1,NM_022464.4	,	1816,3056,1631	CC,CT,TT		43.0814,32.2969,48.5776	,	51/462,51/462	138456815	6688,6318	2203	4300	6503	SO:0001819	synonymous_variant	64374	exon4	Familial Cancer Database	Marinesco-Sjogren syndrome	TCTCTCTGTTTCT	AK075177	CCDS4209.1	5q31	2013-08-21	2013-08-21		ENSG00000120725	ENSG00000120725			24624	protein-coding gene	gene with protein product		608005	"""Marinesco-Sjogren syndrome"", ""SIL1 homolog, endoplasmic reticulum chaperone (S. cerevisiae)"""	MSS		11101517, 12356756, 16282977	Standard	XM_006714671		Approved	BAP, ULG5	uc003ldp.3	Q9H173	OTTHUMG00000129226	ENST00000394817.2:c.153A>G	5.37:g.138456815T>C		Somatic	111	1	0.00900901		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_001037633	D3DQC2|Q8N2L3	Silent	SNP	ENST00000394817.2	37	CCDS4209.1																																																																																			T|0.513;C|0.487	0.487	strong		0.552	SIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251319.1	NM_022464	
SLC12A8	84561	hgsc.bcm.edu	37	3	124829057	124829057	+	Silent	SNP	A	A	G	rs11714448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124829057A>G	ENST00000393469.4	-	8	1084	c.1035T>C	c.(1033-1035)ccT>ccC	p.P345P	SLC12A8_ENST00000423114.2_Silent_p.P374P|SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000469902.1_Silent_p.P345P|SLC12A8_ENST00000430155.2_Silent_p.P146P|SLC12A8_ENST00000314584.7_Silent_p.P98P	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	345					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						AGGCAAGTGCAGGGATCACTT	0.493													A|||	56	0.0111821	0.0015	0.0173	5008	,	,		19172	0.0		0.0219	False		,,,				2504	0.0204				p.P345P		Atlas-SNP	.											.	SLC12A8	81	.	0			c.T1035C						PASS	.	A	,	20,3788		0,20,1884	89.0	90.0	89.0		1035,1035	-6.4	0.9	3	dbSNP_120	89	255,7991		3,249,3871	no	coding-synonymous,coding-synonymous	SLC12A8	NM_001195483.1,NM_024628.5	,	3,269,5755	GG,GA,AA		3.0924,0.5252,2.2814	,	345/715,345/715	124829057	275,11779	1904	4123	6027	SO:0001819	synonymous_variant	84561	exon9			AAGTGCAGGGATC		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1035T>C	3.37:g.124829057A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	72	24	0.333333	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Silent	SNP	ENST00000393469.4	37	CCDS43143.1																																																																																			A|0.986;G|0.013	0.013	strong		0.493	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
DHX34	9704	hgsc.bcm.edu	37	19	47879279	47879279	+	Silent	SNP	G	G	A	rs2694558	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:47879279G>A	ENST00000328771.4	+	11	2755	c.2406G>A	c.(2404-2406)ctG>ctA	p.L802L		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	802					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		TGCTGAAGCTGGTGCTGGGCC	0.657													G|||	609	0.121605	0.2481	0.121	5008	,	,		15865	0.0942		0.0577	False		,,,				2504	0.045				p.L802L		Atlas-SNP	.											.	DHX34	98	.	0			c.G2406A						PASS	.	G		929,3451		109,711,1370	33.0	34.0	34.0		2406	3.0	1.0	19	dbSNP_100	34	434,8100		9,416,3842	no	coding-synonymous	DHX34	NM_014681.5		118,1127,5212	AA,AG,GG		5.0855,21.21,10.5544		802/1144	47879279	1363,11551	2190	4267	6457	SO:0001819	synonymous_variant	9704	exon11			GAAGCTGGTGCTG	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.2406G>A	19.37:g.47879279G>A		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	70	36	0.514286	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	37	CCDS12700.1																																																																																			G|0.887;A|0.113	0.113	strong		0.657	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
SOCS6	9306	hgsc.bcm.edu	37	18	67992684	67992684	+	Silent	SNP	C	C	T	rs1047657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:67992684C>T	ENST00000397942.3	+	2	1096	c.780C>T	c.(778-780)cgC>cgT	p.R260R	SOCS6_ENST00000582322.1_Silent_p.R260R	NM_004232.3	NP_004223.2	O14544	SOCS6_HUMAN	suppressor of cytokine signaling 6	260					defense response (GO:0006952)|JAK-STAT cascade (GO:0007259)|negative regulation of signal transduction (GO:0009968)|negative regulation of T cell activation (GO:0050868)|proteasomal protein catabolic process (GO:0010498)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|immunological synapse (GO:0001772)				NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	22		Esophageal squamous(42;0.129)|Colorectal(73;0.152)				TGGGAGGGCGCGCTTTCCCCG	0.552													C|||	384	0.0766773	0.0825	0.1455	5008	,	,		19163	0.0238		0.1044	False		,,,				2504	0.046				p.R260R	Melanoma(84;1024 1361 24382 36583 42651)	Atlas-SNP	.											SOCS6,NS,carcinoma,+2,2	SOCS6	54	2	0			c.C780T						PASS	.	C		462,3944	219.1+/-236.9	24,414,1765	111.0	92.0	98.0		780	2.3	0.0	18	dbSNP_86	98	905,7695	201.8+/-245.2	53,799,3448	no	coding-synonymous	SOCS6	NM_004232.3		77,1213,5213	TT,TC,CC		10.5233,10.4857,10.5105		260/536	67992684	1367,11639	2203	4300	6503	SO:0001819	synonymous_variant	9306	exon2			AGGGCGCGCTTTC	AB006968	CCDS11998.1	18q22	2013-02-14	2004-02-25	2004-02-27	ENSG00000170677	ENSG00000170677		"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	16833	protein-coding gene	gene with protein product		605118	"""suppressor of cytokine signaling 4"""	SOCS4		9344848, 11042152	Standard	NM_004232		Approved	CIS4, SSI4, HSPC060, STATI4, STAI4, Cish4	uc002lkr.1	O14544	OTTHUMG00000132816	ENST00000397942.3:c.780C>T	18.37:g.67992684C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	234	101	0.431624	NM_004232	Q8WUM3	Silent	SNP	ENST00000397942.3	37	CCDS11998.1																																																																																			C|0.900;T|0.100	0.100	strong		0.552	SOCS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256270.2		
HSPA6	3310	hgsc.bcm.edu	37	1	161495040	161495040	+	Missense_Mutation	SNP	C	C	T	rs63749092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161495040C>T	ENST00000309758.4	+	1	1005	c.592C>T	c.(592-594)Ctc>Ttc	p.L198F	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	198			L -> F (in dbSNP:rs1079109). {ECO:0000269|Ref.2}.		ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCGCAACGTGCTCATTTTTGA	0.622													c|||	622	0.124201	0.0272	0.1268	5008	,	,		15815	0.2837		0.1183	False		,,,				2504	0.0951				p.L198F		Atlas-SNP	.											.	HSPA6	53	.	0			c.C592T						PASS	.	C	PHE/LEU	175,4231		3,169,2031	39.0	45.0	43.0		592	2.3	0.8	1	dbSNP_129	43	990,7610		57,876,3367	no	missense	HSPA6	NM_002155.3	22	60,1045,5398	TT,TC,CC		11.5116,3.9719,8.9574	probably-damaging	198/644	161495040	1165,11841	2203	4300	6503	SO:0001583	missense	3310	exon1			AACGTGCTCATTT		CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.592C>T	1.37:g.161495040C>T	ENSP00000310219:p.Leu198Phe	Somatic	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	281	264	0.939502	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	307	0.14056776556776557	19	0.03861788617886179	39	0.10773480662983426	154	0.2692307692307692	95	0.12532981530343007	.	15.86	2.957350	0.53400	0.039719	0.115116	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.13538	2.58	3.19	2.27	0.28462	.	0.000000	0.34291	U	0.004084	T	0.34658	0.0905	H	0.97158	3.95	0.21984	P	0.999432756	D	0.89917	1.0	D	0.97110	1.0	T	0.43212	-0.9405	9	0.72032	D	0.01	-29.3593	7.5914	0.28023	0.0:0.8669:0.0:0.1331	rs63749092	198	P17066	HSP76_HUMAN	F	198;174	ENSP00000310219:L198F	ENSP00000310219:L198F	L	+	1	0	HSPA6	159761664	0.999000	0.42202	0.751000	0.31187	0.707000	0.40811	3.892000	0.56235	0.519000	0.28406	0.486000	0.48141	CTC	C|0.897;T|0.103	0.103	strong		0.622	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
ANAPC16	119504	hgsc.bcm.edu	37	10	73992862	73992862	+	Silent	SNP	C	C	G	rs9275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:73992862C>G	ENST00000299381.4	+	4	439	c.321C>G	c.(319-321)ccC>ccG	p.P107P	ANAPC16_ENST00000470481.2_3'UTR	NM_001242546.1|NM_001242547.1|NM_001242548.1|NM_173473.3	NP_001229475.1|NP_001229476.1|NP_001229477.1|NP_775744.1	Q96DE5	APC16_HUMAN	anaphase promoting complex subunit 16	107					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	anaphase-promoting complex (GO:0005680)|cytoplasm (GO:0005737)				large_intestine(1)|ovary(1)	2						GATTCACCCCCTCTTCAGGTT	0.542													C|||	364	0.0726837	0.2595	0.0274	5008	,	,		14954	0.0		0.002	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	ANAPC16	10	.	0			c.C321G						PASS	.	C	,,,	919,3487	344.1+/-307.9	90,739,1374	66.0	64.0	65.0		321,321,246,321	-0.3	1.0	10	dbSNP_52	65	13,8587	9.1+/-34.3	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANAPC16	NM_001242546.1,NM_001242547.1,NM_001242548.1,NM_173473.3	,,,	90,752,5661	GG,GC,CC		0.1512,20.8579,7.1659	,,,	107/111,107/111,82/86,107/111	73992862	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	119504	exon5			CACCCCCTCTTCA	BC009530	CCDS7314.1, CCDS73147.1	10q22.2	2011-08-12	2010-04-06	2010-04-06	ENSG00000166295	ENSG00000166295		"""Anaphase promoting complex subunits"""	26976	protein-coding gene	gene with protein product	"""centromere protein 27"""	613427	"""chromosome 10 open reading frame 104"""	C10orf104		14702039, 20360068	Standard	NM_001242546		Approved	bA570G20.3, FLJ33728, APC16, CENP-27	uc021psp.1	Q96DE5	OTTHUMG00000018433	ENST00000299381.4:c.321C>G	10.37:g.73992862C>G		Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	40	24	0.6	NM_001242546		Silent	SNP	ENST00000299381.4	37	CCDS7314.1																																																																																			G|0.064;C|0.936	0.064	strong		0.542	ANAPC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048565.2	NM_173473	
OR5B2	390190	hgsc.bcm.edu	37	11	58190112	58190112	+	Missense_Mutation	SNP	A	A	G	rs10466659	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58190112A>G	ENST00000302581.2	-	1	674	c.623T>C	c.(622-624)gTt>gCt	p.V208A		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	208			V -> A (in dbSNP:rs10466659).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V208A(1)		NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AACTAGAAGAACAAAAAAGAT	0.383													G|||	1120	0.223642	0.2708	0.2032	5008	,	,		22875	0.1448		0.2097	False		,,,				2504	0.2699				p.V208A		Atlas-SNP	.											OR5B2,NS,carcinoma,0,1	OR5B2	75	1	1	Substitution - Missense(1)	stomach(1)	c.T623C						PASS	.	G	ALA/VAL	1033,3369	726.5+/-409.7	104,825,1272	61.0	60.0	61.0		623	3.7	0.8	11	dbSNP_119	61	1854,6736	729.5+/-406.7	200,1454,2641	yes	missense	OR5B2	NM_001005566.2	64	304,2279,3913	GG,GA,AA		21.5832,23.4666,22.2214	benign	208/310	58190112	2887,10105	2201	4295	6496	SO:0001583	missense	390190	exon1			AGAAGAACAAAAA	AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"""GPCR / Class A : Olfactory receptors"""	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.623T>C	11.37:g.58190112A>G	ENSP00000303076:p.Val208Ala	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	107	47	0.439252	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Missense_Mutation	SNP	ENST00000302581.2	37	CCDS31550.1	476	0.21794871794871795	159	0.3231707317073171	60	0.16574585635359115	95	0.1660839160839161	162	0.21372031662269128	G	0.003	-2.458902	0.00173	0.234666	0.215832	ENSG00000172365	ENST00000302581	T	0.37235	1.21	3.73	3.73	0.42828	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35291	N	0.003307	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39313	-0.9620	9	0.07813	T	0.8	-5.0223	7.397	0.26942	0.1004:0.1696:0.73:0.0	rs10466659;rs17565464;rs10466659	208	Q96R09	OR5B2_HUMAN	A	208	ENSP00000303076:V208A	ENSP00000303076:V208A	V	-	2	0	OR5B2	57946688	0.013000	0.17824	0.831000	0.32960	0.037000	0.13140	1.975000	0.40569	0.932000	0.37266	-0.197000	0.12766	GTT	A|0.781;G|0.219	0.219	strong		0.383	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566	
MAML2	84441	hgsc.bcm.edu	37	11	95825404	95825404	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:95825404C>T	ENST00000524717.1	-	2	3075	c.1791G>A	c.(1789-1791)caG>caA	p.Q597Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	597					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgct	0.532			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q597Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,caecum,carcinoma,0,1	MAML2	94	1	0			c.G1791A						scavenged	.						25.0	32.0	29.0					11																	95825404		2096	4109	6205	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1791G>A	11.37:g.95825404C>T		Somatic	108	2	0.0185185		WXS	Illumina HiSeq	Phase_I	135	4	0.0296296	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.	.	none		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
MPDZ	8777	hgsc.bcm.edu	37	9	13190162	13190162	+	Missense_Mutation	SNP	T	T	A	rs4740548	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:13190162T>A	ENST00000319217.7	-	16	2352	c.2105A>T	c.(2104-2106)gAg>gTg	p.E702V	MPDZ_ENST00000381015.4_Missense_Mutation_p.E702V|MPDZ_ENST00000541718.1_Missense_Mutation_p.E702V|MPDZ_ENST00000536827.1_Missense_Mutation_p.E702V|MPDZ_ENST00000381022.2_Missense_Mutation_p.E702V|MPDZ_ENST00000546205.1_Missense_Mutation_p.E702V|MPDZ_ENST00000447879.1_Missense_Mutation_p.E702V	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	702	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.		E -> K (in dbSNP:rs4741289).|E -> V (in dbSNP:rs4740548).		cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		TTTCTCCAGCTCTATGTGCTG	0.438													T|||	156	0.0311502	0.0348	0.0173	5008	,	,		17041	0.004		0.002	False		,,,				2504	0.0941				p.E702V		Atlas-SNP	.											.	MPDZ	324	.	0			c.A2105T						PASS	.						72.0	69.0	70.0					9																	13190162		2002	4182	6184	SO:0001583	missense	8777	exon16			TCCAGCTCTATGT	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2105A>T	9.37:g.13190162T>A	ENSP00000320006:p.Glu702Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	80	39	0.4875	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		21	0.009615384615384616	12	0.024390243902439025	7	0.019337016574585635	2	0.0034965034965034965	0	0.0	T	21.2	4.109642	0.77096	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205	T;T;T;T;T;T;T	0.27104	1.69;1.69;1.69;1.69;1.69;1.69;1.69	5.83	4.68	0.58851	.	0.000000	0.44285	D	0.000475	T	0.22044	0.0531	L	0.55103	1.725	0.80722	D	1	D;D;D	0.64830	0.972;0.965;0.994	P;P;P	0.58172	0.834;0.744;0.804	T	0.04153	-1.0973	10	0.87932	D	0	.	8.1209	0.30971	0.1341:0.0:0.1404:0.7255	rs4740548;rs4740548	702;702;702	B7ZMI4;O75970-3;O75970-2	.;.;.	V	702;702;702;702;702;702;652;702	ENSP00000320006:E702V;ENSP00000439807:E702V;ENSP00000370410:E702V;ENSP00000444151:E702V;ENSP00000415208:E702V;ENSP00000370403:E702V;ENSP00000446358:E702V	ENSP00000320006:E702V	E	-	2	0	MPDZ	13180162	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	5.808000	0.69165	1.016000	0.39470	0.533000	0.62120	GAG	T|0.988;A|0.012	0.012	strong		0.438	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
OBSCN	84033	hgsc.bcm.edu	37	1	228412308	228412308	+	Silent	SNP	G	G	A	rs1757152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228412308G>A	ENST00000422127.1	+	9	2846	c.2802G>A	c.(2800-2802)tcG>tcA	p.S934S	OBSCN_ENST00000570156.2_Silent_p.S1026S|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.S934S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	934	Ig-like 9.|Poly-Ser.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GCTCCAGCTCGAAAGTGTGCA	0.662													G|||	2066	0.41254	0.5885	0.402	5008	,	,		19773	0.3839		0.3678	False		,,,				2504	0.2577				p.S1026S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G3078A						PASS	.	G	,	2342,1864		643,1056,404	58.0	59.0	59.0		2802,2802	-9.0	0.0	1	dbSNP_89	59	3317,5133		663,1991,1571	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1306,3047,1975	AA,AG,GG		39.2544,44.3176,44.714	,	934/7969,934/6621	228412308	5659,6997	2103	4225	6328	SO:0001819	synonymous_variant	84033	exon10			CAGCTCGAAAGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2802G>A	1.37:g.228412308G>A		Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	255	143	0.560784	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.567;A|0.433	0.433	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
EYS	346007	hgsc.bcm.edu	37	6	65612302	65612302	+	Silent	SNP	A	A	G	rs75634595	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65612302A>G	ENST00000370621.3	-	17	3259	c.2733T>C	c.(2731-2733)aaT>aaC	p.N911N	EYS_ENST00000370616.2_Silent_p.N911N|EYS_ENST00000503581.1_Silent_p.N911N			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	911	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						TGTACCTGAAATTGTTGACCA	0.323													A|||	81	0.0161741	0.0045	0.0115	5008	,	,		16940	0.0		0.0298	False		,,,				2504	0.0378				p.N911N		Atlas-SNP	.											.	EYS	527	.	0			c.T2733C						PASS	.	A		10,1374		0,10,682	151.0	124.0	132.0		2733	1.9	1.0	6	dbSNP_132	132	88,3094		2,84,1505	no	coding-synonymous	EYS	NM_001142800.1		2,94,2187	GG,GA,AA		2.7656,0.7225,2.1463		911/3145	65612302	98,4468	692	1591	2283	SO:0001819	synonymous_variant	346007	exon17			CCTGAAATTGTTG		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2733T>C	6.37:g.65612302A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	70	59	0.842857	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				A|0.981;G|0.019	0.019	strong		0.323	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
SCN8A	6334	hgsc.bcm.edu	37	12	52200499	52200499	+	Silent	SNP	C	C	A	rs370268493		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52200499C>A	ENST00000354534.6	+	27	5407	c.5229C>A	c.(5227-5229)atC>atA	p.I1743I	RP11-923I11.3_ENST00000565518.1_lincRNA|SCN8A_ENST00000545061.1_Silent_p.I1702I	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1743					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)	CAGTGGGCATCTTCTTCTTTG	0.498																																					p.I1743I		Atlas-SNP	.											.	SCN8A	331	.	0			c.C5229A						PASS	.	C	,	1,4343		0,1,2171	81.0	89.0	87.0		5106,5229	5.3	1.0	12		87	3,8567		0,3,4282	no	coding-synonymous,coding-synonymous	SCN8A	NM_001177984.1,NM_014191.2	,	0,4,6453	AA,AC,CC		0.035,0.023,0.031	,	1702/1940,1743/1981	52200499	4,12910	2172	4285	6457	SO:0001819	synonymous_variant	6334	exon27			GGGCATCTTCTTC	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.5229C>A	12.37:g.52200499C>A		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	163	96	0.588957	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																			.	.	weak		0.498	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
ECD	11319	hgsc.bcm.edu	37	10	74894375	74894375	+	Missense_Mutation	SNP	T	T	C	rs2271904	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:74894375T>C	ENST00000372979.4	-	14	2107	c.1901A>G	c.(1900-1902)gAt>gGt	p.D634G	ECD_ENST00000430082.2_Missense_Mutation_p.D667G|ECD_ENST00000454759.2_Missense_Mutation_p.D591G	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	634			D -> G (in dbSNP:rs2271904).		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)	p.D634G(1)		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)					TGGTCTGTGATCGGTGTTGTC	0.378													T|||	890	0.177716	0.1664	0.0994	5008	,	,		17335	0.3145		0.0537	False		,,,				2504	0.2352				p.D667G		Atlas-SNP	.											ECD,NS,carcinoma,-1,2	ECD	50	2	1	Substitution - Missense(1)	stomach(1)	c.A2000G						PASS	.	T	GLY/ASP,GLY/ASP,GLY/ASP	665,3741	283.1+/-276.9	57,551,1595	80.0	76.0	77.0		2000,1772,1901	5.7	0.8	10	dbSNP_100	77	571,8029	153.7+/-208.1	26,519,3755	yes	missense,missense,missense	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	94,94,94	83,1070,5350	CC,CT,TT		6.6395,15.0931,9.5033	possibly-damaging,possibly-damaging,possibly-damaging	667/678,591/602,634/645	74894375	1236,11770	2203	4300	6503	SO:0001583	missense	11319	exon15			CTGTGATCGGTGT	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		ENST00000372979.4:c.1901A>G	10.37:g.74894375T>C	ENSP00000362070:p.Asp634Gly	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	163	63	0.386503	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	354	0.1620879120879121	99	0.20121951219512196	31	0.0856353591160221	183	0.31993006993006995	41	0.05408970976253298	T	35	5.550067	0.96501	0.150931	0.066395	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.26223	2.14;1.99;1.75	5.66	5.66	0.87406	.	0.042742	0.85682	D	0.000000	T	0.00012	0.0000	L	0.51853	1.615	0.09310	P	0.999999813439	D;D;D	0.89917	1.0;1.0;0.987	D;D;P	0.74348	0.983;0.983;0.729	T	0.27123	-1.0083	9	0.41790	T	0.15	0.4873	14.7124	0.69244	0.0:0.0:0.0:1.0	rs2271904;rs56533217;rs58236811;rs2271904	591;667;634	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	G	634;667;591	ENSP00000362070:D634G;ENSP00000401566:D667G;ENSP00000395786:D591G	ENSP00000362070:D634G	D	-	2	0	ECD	74564381	1.000000	0.71417	0.803000	0.32268	0.756000	0.42949	6.527000	0.73803	2.144000	0.66660	0.460000	0.39030	GAT	T|0.869;C|0.131	0.131	strong		0.378	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
RASAL1	8437	hgsc.bcm.edu	37	12	113573237	113573237	+	Missense_Mutation	SNP	C	C	G	rs7960087	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113573237C>G	ENST00000261729.5	-	2	346	c.31G>C	c.(31-33)Gtg>Ctg	p.V11L	RASAL1_ENST00000548055.1_Missense_Mutation_p.V11L|RASAL1_ENST00000418411.2_5'UTR|RASAL1_ENST00000546530.1_Missense_Mutation_p.V11L|RASAL1_ENST00000446861.3_Missense_Mutation_p.V11L			O95294	RASL1_HUMAN	RAS protein activator like 1 (GAP1 like)	11	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.		V -> L (in dbSNP:rs7960087). {ECO:0000269|PubMed:15489334}.		intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|phospholipid binding (GO:0005543)|Ras GTPase activator activity (GO:0005099)	p.V11L(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(19)|ovary(3)|prostate(2)|skin(2)	43						CCCTCCACCACGCGAACATTC	0.677													C|||	97	0.019369	0.0144	0.0317	5008	,	,		11792	0.0		0.0457	False		,,,				2504	0.0102				p.V11L		Atlas-SNP	.											RASAL1,NS,carcinoma,0,2	RASAL1	89	2	2	Substitution - Missense(2)	prostate(2)	c.G31C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	90,4306		2,86,2110	34.0	30.0	31.0		31,31,31	3.4	1.0	12	dbSNP_116	31	309,8285		5,299,3993	yes	missense,missense,missense	RASAL1	NM_001193520.1,NM_001193521.1,NM_004658.2	32,32,32	7,385,6103	GG,GC,CC		3.5955,2.0473,3.0716	benign,benign,benign	11/807,11/777,11/805	113573237	399,12591	2198	4297	6495	SO:0001583	missense	8437	exon2			CCACCACGCGAAC	AF086713	CCDS9165.1, CCDS55888.1, CCDS55889.1, CCDS73529.1	12q23-q24	2013-01-10			ENSG00000111344	ENSG00000111344		"""Pleckstrin homology (PH) domain containing"""	9873	protein-coding gene	gene with protein product		604118				9751798	Standard	NM_001193520		Approved	RASAL	uc001tul.3	O95294	OTTHUMG00000169705	ENST00000261729.5:c.31G>C	12.37:g.113573237C>G	ENSP00000261729:p.Val11Leu	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	164	86	0.52439	NM_004658	B7ZKM4|C9JFK5|F8VQX1|Q52M03|Q59H24|Q96CC7	Missense_Mutation	SNP	ENST00000261729.5	37	CCDS9165.1	45	0.020604395604395604	5	0.01016260162601626	7	0.019337016574585635	0	0.0	33	0.04353562005277045	C	9.955	1.221292	0.22457	0.020473	0.035955	ENSG00000111344	ENST00000546530;ENST00000261729;ENST00000446861;ENST00000548055	T;T;T;T	0.12465	2.68;2.68;2.68;2.68	3.44	3.44	0.39384	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.301944	0.26362	N	0.024816	T	0.01454	0.0047	N	0.10760	0.04	0.26908	N	0.966964	B;B;B;B;B;B	0.14805	0.011;0.009;0.011;0.005;0.003;0.009	B;B;B;B;B;B	0.14578	0.011;0.006;0.011;0.009;0.01;0.006	T	0.22765	-1.0207	10	0.49607	T	0.09	.	10.5931	0.45321	0.0:1.0:0.0:0.0	rs7960087;rs7960087	11;11;23;11;11;11	B4DG06;F8VRH9;Q59H24;F8VQX1;O95294;O95294-2	.;.;.;.;RASL1_HUMAN;.	L	11	ENSP00000450244:V11L;ENSP00000261729:V11L;ENSP00000395920:V11L;ENSP00000448510:V11L	ENSP00000261729:V11L	V	-	1	0	RASAL1	112057620	1.000000	0.71417	1.000000	0.80357	0.053000	0.15095	1.663000	0.37429	1.946000	0.56461	0.484000	0.47621	GTG	C|0.974;G|0.026	0.026	strong		0.677	RASAL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405522.2	NM_004658	
FAM21A	387680	hgsc.bcm.edu	37	10	47915898	47915898	+	Silent	SNP	A	A	G	rs183064568		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:47915898A>G	ENST00000358474.5	+	15	1305	c.1305A>G	c.(1303-1305)aaA>aaG	p.K435K		NM_018232.1	NP_060702.1	Q5SNT6	FA21B_HUMAN		435					retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|WASH complex (GO:0071203)		p.K435K(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10						CTTCCAGCAAAAATCTCAAGC	0.408																																					p.K435K		Atlas-SNP	.											FAM21B_ENST00000358474,NS,carcinoma,0,1	FAM21B	31	1	1	Substitution - coding silent(1)	stomach(1)	c.A1305G						scavenged	.						20.0	29.0	26.0					10																	47915898		1759	4018	5777	SO:0001819	synonymous_variant	55747	exon15			CAGCAAAAATCTC																												ENST00000358474.5:c.1305A>G	10.37:g.47915898A>G		Somatic	443	0	0		WXS	Illumina HiSeq	Phase_I	321	92	0.286604	NM_018232		Silent	SNP	ENST00000358474.5	37	CCDS44379.1																																																																																			A|0.375;G|0.625	0.625	strong		0.408	FAM21B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047871.2		
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978591	45978591	+	Missense_Mutation	SNP	G	G	A	rs79221051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45978591G>A	ENST00000391620.1	-	1	52	c.8C>T	c.(7-9)aCg>aTg	p.T3M	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	3			T -> A (in dbSNP:rs452472). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						CATGGTAGACGTGGCCATGCT	0.647													.|||	646	0.128994	0.171	0.1282	5008	,	,		17637	0.005		0.175	False		,,,				2504	0.1534				p.T3M		Atlas-SNP	.											KRTAP10-3,rectum,carcinoma,-1,1	KRTAP10-3	17	1	0			c.C8T						scavenged	.	G	,MET/THR	711,3695	281.1+/-275.7	54,603,1546	59.0	59.0	59.0		,8	1.5	0.0	21	dbSNP_131	59	1608,6992	289.6+/-299.4	151,1306,2843	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,81	205,1909,4389	AA,AG,GG		18.6977,16.1371,17.8302	,benign	,3/222	45978591	2319,10687	2203	4300	6503	SO:0001583	missense	386682	exon1			GTAGACGTGGCCA	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.8C>T	21.37:g.45978591G>A	ENSP00000375478:p.Thr3Met	Somatic	95	1	0.0105263		WXS	Illumina HiSeq	Phase_I	126	64	0.507937	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	290	0.13278388278388278	112	0.22764227642276422	50	0.13812154696132597	1	0.0017482517482517483	127	0.16754617414248021	g	2.833	-0.242255	0.05906	0.161371	0.186977	ENSG00000212935	ENST00000391620	T	0.06449	3.3	3.32	1.47	0.22746	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.43556	-0.9384	8	0.87932	D	0	.	7.1646	0.25683	0.2335:0.0:0.7665:0.0	.	3	P60369	KR103_HUMAN	M	3	ENSP00000375478:T3M	ENSP00000375478:T3M	T	-	2	0	KRTAP10-3	44803019	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.141000	0.16076	0.245000	0.21373	-0.265000	0.10407	ACG	G|0.850;A|0.150	0.150	strong		0.647	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
GALNT4	8693	hgsc.bcm.edu	37	12	89917349	89917349	+	Silent	SNP	C	C	T	rs200228838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:89917349C>T	ENST00000529983.2	-	1	1234	c.978G>A	c.(976-978)acG>acA	p.T326T	RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000548729.1_Silent_p.T323T|POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000549035.1_Intron|POC1B_ENST00000393179.4_Intron|GALNT4_ENST00000413530.1_Silent_p.T154T|POC1B_ENST00000549504.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	326	Catalytic subdomain B.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						CTGTGTCATACGTTCCAAGGT	0.493													C|||	2	0.000399361	0.0	0.0	5008	,	,		19273	0.0		0.002	False		,,,				2504	0.0				p.T326T		Atlas-SNP	.											.	GALNT4	38	.	0			c.G978A						PASS	.	C	,,,,	0,4026		0,0,2013	182.0	183.0	182.0		,969,462,978,	-11.7	0.0	12		182	15,8367		0,15,4176	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,,,,	0,15,6189	TT,TC,CC		0.179,0.0,0.1209	,,,,	,323/576,154/407,326/579,	89917349	15,12393	2013	4191	6204	SO:0001819	synonymous_variant	8693	exon1			GTCATACGTTCCA	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.978G>A	12.37:g.89917349C>T		Somatic	275	0	0		WXS	Illumina HiSeq	Phase_I	290	141	0.486207	NM_003774	B2R775|B4DMX6|O00208	Silent	SNP	ENST00000529983.2	37	CCDS53817.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
PCDHB10	56126	hgsc.bcm.edu	37	5	140572668	140572668	+	Silent	SNP	C	C	T	rs597064	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140572668C>T	ENST00000239446.4	+	1	727	c.543C>T	c.(541-543)aaC>aaT	p.N181N		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	181	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCATATTAACATTAGTGGCG	0.478													t|||	2440	0.48722	0.5083	0.5432	5008	,	,		18344	0.5685		0.4076	False		,,,				2504	0.4172				p.N181N		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C543T						PASS	.	A		2071,2335	578.4+/-384.7	491,1089,623	129.0	151.0	144.0		543	-2.5	0.0	5	dbSNP_83	144	3527,5073	626.0+/-397.8	760,2007,1533	no	coding-synonymous	PCDHB10	NM_018930.3		1251,3096,2156	TT,TC,CC		41.0116,47.0041,43.0417		181/801	140572668	5598,7408	2203	4300	6503	SO:0001819	synonymous_variant	56126	exon1			TATTAACATTAGT	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.543C>T	5.37:g.140572668C>T		Somatic	199	1	0.00502513		WXS	Illumina HiSeq	Phase_I	144	144	1	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.561;T|0.439	0.439	strong		0.478	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
PCNT	5116	hgsc.bcm.edu	37	21	47836426	47836426	+	Silent	SNP	T	T	C	rs57108405	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47836426T>C	ENST00000359568.5	+	30	6701	c.6594T>C	c.(6592-6594)ggT>ggC	p.G2198G	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2198					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)					GCGTACTTGGTGGCTCCCGCC	0.557													C|||	778	0.155351	0.4713	0.0634	5008	,	,		17022	0.003		0.0239	False		,,,				2504	0.0859				p.G2198G		Atlas-SNP	.											.	PCNT	283	.	0			c.T6594C						PASS	.	C		1769,2637	623.2+/-394.1	355,1059,789	53.0	66.0	62.0		6594	-10.4	0.0	21	dbSNP_129	62	117,8483	803.0+/-407.3	0,117,4183	no	coding-synonymous	PCNT	NM_006031.5		355,1176,4972	CC,CT,TT		1.3605,40.1498,14.501		2198/3337	47836426	1886,11120	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon30			ACTTGGTGGCTCC	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.6594T>C	21.37:g.47836426T>C		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	45	0.473684	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			T|0.876;C|0.124	0.124	strong		0.557	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MUC4	4585	hgsc.bcm.edu	37	3	195506364	195506364	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506364G>C	ENST00000463781.3	-	2	12546	c.12087C>G	c.(12085-12087)caC>caG	p.H4029Q	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H4029Q	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)		CAGGGGTGGCGTGACCTGTGG	0.582																																					p.H4029Q		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C12087G						scavenged	.						22.0	14.0	17.0					3																	195506364		662	1415	2077	SO:0001583	missense	4585	exon2			GGTGGCGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12087C>G	3.37:g.195506364G>C	ENSP00000417498:p.His4029Gln	Somatic	23	0	0		WXS	Illumina HiSeq	Phase_I	70	4	0.0571429	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.368	0.435983	0.12104	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30182	1.56;1.54	.	.	.	.	0.528491	0.09936	U	0.736553	T	0.16896	0.0406	N	0.19112	0.55	0.09310	N	1	B	0.18610	0.029	B	0.04013	0.001	T	0.28522	-1.0041	8	.	.	.	.	6.7067	0.23254	2.0E-4:0.0:0.9998:0.0	.	3901	E7ESK3	.	Q	4029	ENSP00000417498:H4029Q;ENSP00000420243:H4029Q	.	H	-	3	2	MUC4	196991143	0.038000	0.19896	0.002000	0.10522	0.012000	0.07955	2.703000	0.47110	0.488000	0.27723	0.064000	0.15345	CAC	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR2W1	26692	hgsc.bcm.edu	37	6	29012067	29012067	+	Missense_Mutation	SNP	C	C	T	rs35771565	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29012067C>T	ENST00000377175.1	-	1	950	c.886G>A	c.(886-888)Gac>Aac	p.D296N		NM_030903.3	NP_112165.1	Q9Y3N9	OR2W1_HUMAN	olfactory receptor, family 2, subfamily W, member 1	296			D -> N (in allele 6M1-15*02; dbSNP:rs35771565). {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(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|skin(1)	23						TCCTTCATGTCCTTATTTCTT	0.418													C|||	1249	0.249401	0.236	0.2522	5008	,	,		18451	0.3929		0.172	False		,,,				2504	0.1973				p.D296N		Atlas-SNP	.											.	OR2W1	36	.	0			c.G886A						PASS	.	C	,ASN/ASP	656,2366		58,540,913	57.0	50.0	53.0		,886	3.9	1.0	6	dbSNP_126	53	813,4605		69,675,1965	yes	utr-5,missense	OR2W1,LOC100129636	NM_001195202.1,NM_030903.3	,23	127,1215,2878	TT,TC,CC		15.0055,21.7075,17.4052	,benign	,296/321	29012067	1469,6971	1511	2709	4220	SO:0001583	missense	26692	exon1			TCATGTCCTTATT	AL035402	CCDS4656.1	6p22.1	2012-08-09			ENSG00000204704	ENSG00000204704		"""GPCR / Class A : Olfactory receptors"""	8281	protein-coding gene	gene with protein product							Standard	NM_030903		Approved	hs6M1-15	uc003nlw.2	Q9Y3N9	OTTHUMG00000031048	ENST00000377175.1:c.886G>A	6.37:g.29012067C>T	ENSP00000366380:p.Asp296Asn	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	187	90	0.481283	NM_030903	B0S7Y5|Q5JNZ1|Q6IEU0|Q96R17|Q9GZL0|Q9GZL1	Missense_Mutation	SNP	ENST00000377175.1	37	CCDS4656.1	545	0.24954212454212454	102	0.2073170731707317	94	0.2596685082872928	237	0.4143356643356643	112	0.14775725593667546	C	21.8	4.195218	0.78902	0.217075	0.150055	ENSG00000204704	ENST00000377175	T	0.38077	1.16	4.79	3.92	0.45320	.	0.117279	0.38381	N	0.001706	T	0.17534	0.0421	N	0.25144	0.715	0.23845	P	0.99668764	P	0.45348	0.856	P	0.46275	0.51	T	0.04708	-1.0932	9	0.72032	D	0.01	.	11.7323	0.51744	0.0:0.9122:0.0:0.0878	rs35771565;rs62407609	296	Q9Y3N9	OR2W1_HUMAN	N	296	ENSP00000366380:D296N	ENSP00000366380:D296N	D	-	1	0	OR2W1	29120046	0.949000	0.32298	1.000000	0.80357	0.991000	0.79684	2.309000	0.43699	0.982000	0.38575	0.591000	0.81541	GAC	C|0.806;T|0.194	0.194	strong		0.418	OR2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076053.2		
FBXO5	26271	hgsc.bcm.edu	37	6	153296370	153296370	+	Missense_Mutation	SNP	G	G	A	rs7763565	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:153296370G>A	ENST00000229758.3	-	2	548	c.490C>T	c.(490-492)Ctc>Ttc	p.L164F	FBXO5_ENST00000477822.1_5'Flank|FBXO5_ENST00000367241.3_Missense_Mutation_p.L118F	NM_012177.3	NP_036309.1	Q9UKT4	FBX5_HUMAN	F-box protein 5	164	Interaction with EVI5.		L -> F (in dbSNP:rs7763565).		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibition of mitotic anaphase-promoting complex activity (GO:0060565)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|negative regulation of meiosis (GO:0045835)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|oocyte maturation (GO:0001556)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|spindle assembly involved in female meiosis I (GO:0007057)|vesicle organization (GO:0016050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)	15		Ovarian(120;0.125)		OV - Ovarian serous cystadenocarcinoma(155;4.38e-10)|BRCA - Breast invasive adenocarcinoma(81;0.0893)		TCCTCCAGGAGGCTACCTTCT	0.423													G|||	478	0.0954473	0.1551	0.1988	5008	,	,		17886	0.0198		0.0517	False		,,,				2504	0.0644				p.L164F	NSCLC(121;372 1757 17721 17977 29669)	Atlas-SNP	.											.	FBXO5	40	.	0			c.C490T						PASS	.	G	PHE/LEU,PHE/LEU	611,3795	265.9+/-266.9	40,531,1632	123.0	126.0	125.0		352,490	0.9	0.1	6	dbSNP_116	125	549,8051	150.4+/-205.3	18,513,3769	yes	missense,missense	FBXO5	NM_001142522.1,NM_012177.3	22,22	58,1044,5401	AA,AG,GG		6.3837,13.8675,8.919	probably-damaging,probably-damaging	118/402,164/448	153296370	1160,11846	2203	4300	6503	SO:0001583	missense	26271	exon2			CCAGGAGGCTACC	AF129535	CCDS5242.1, CCDS47501.1	6q25-q26	2008-02-05	2004-06-15		ENSG00000112029	ENSG00000112029		"""F-boxes /  ""other"""""	13584	protein-coding gene	gene with protein product		606013	"""F-box only protein 5"""			10531035, 10531037	Standard	NM_012177		Approved	FBX5, Fbxo31, EMI1	uc003qpg.3	Q9UKT4	OTTHUMG00000015854	ENST00000229758.3:c.490C>T	6.37:g.153296370G>A	ENSP00000229758:p.Leu164Phe	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	101	11	0.108911	NM_012177	B3KNX5|Q5TF47|Q8WV29|Q9UGC8	Missense_Mutation	SNP	ENST00000229758.3	37	CCDS5242.1	187	0.08562271062271062	67	0.13617886178861788	62	0.1712707182320442	16	0.027972027972027972	42	0.055408970976253295	G	14.99	2.700064	0.48307	0.138675	0.063837	ENSG00000112029	ENST00000229758;ENST00000367241	T;T	0.47528	0.84;0.84	5.92	0.943	0.19531	.	0.649006	0.15030	N	0.284489	T	0.33381	0.0861	M	0.61703	1.905	0.80722	P	0.0	D	0.56521	0.976	P	0.52267	0.694	T	0.10520	-1.0626	9	0.48119	T	0.1	-5.5095	4.4233	0.11492	0.3194:0.0:0.3789:0.3017	rs7763565;rs52802786;rs60639869;rs7763565	164	Q9UKT4	FBX5_HUMAN	F	164;118	ENSP00000229758:L164F;ENSP00000356210:L118F	ENSP00000229758:L164F	L	-	1	0	FBXO5	153338063	0.000000	0.05858	0.097000	0.21041	0.992000	0.81027	0.319000	0.19522	0.417000	0.25871	0.655000	0.94253	CTC	G|0.911;A|0.089	0.089	strong		0.423	FBXO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042757.1		
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73969541	73969541	+	Missense_Mutation	SNP	A	A	G	rs2301895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:73969541A>G	ENST00000265755.3	+	18	2347	c.1954A>G	c.(1954-1956)Atg>Gtg	p.M652V	GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.M684V|GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.M652V|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.M652V	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	652			M -> V (in dbSNP:rs2301895). {ECO:0000269|PubMed:10575229, ECO:0000269|PubMed:10642537, ECO:0000269|PubMed:15489334}.		multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGAGCCCATCATGGATAGTCA	0.642													G|||	2076	0.414537	0.6354	0.3386	5008	,	,		16237	0.5129		0.2465	False		,,,				2504	0.2413				p.M684V		Atlas-SNP	.											.	GTF2IRD1	91	.	0			c.A2050G						PASS	.	G	VAL/MET,VAL/MET,VAL/MET	2589,1817	637.7+/-396.8	743,1103,357	71.0	76.0	74.0		2050,1954,1954	-3.7	0.0	7	dbSNP_100	74	2261,6339	381.8+/-340.2	285,1691,2324	no	missense,missense,missense	GTF2IRD1	NM_001199207.1,NM_005685.3,NM_016328.2	21,21,21	1028,2794,2681	GG,GA,AA		26.2907,41.2392,37.2905	benign,benign,benign	684/977,652/945,652/960	73969541	4850,8156	2203	4300	6503	SO:0001583	missense	9569	exon18			CCCATCATGGATA	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1954A>G	7.37:g.73969541A>G	ENSP00000265755:p.Met652Val	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	59	30	0.508475	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	37	CCDS5571.1	912|912	0.4175824175824176|0.4175824175824176	307|307	0.6239837398373984|0.6239837398373984	118|118	0.3259668508287293|0.3259668508287293	306|306	0.534965034965035|0.534965034965035	181|181	0.23878627968337732|0.23878627968337732	a|a	0.003|0.003	-2.436450|-2.436450	0.00182|0.00182	0.587608|0.587608	0.262907|0.262907	ENSG00000006704|ENSG00000006704	ENST00000470715|ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	.|T;T;T;T	.|0.26957	.|1.7;1.7;1.7;1.7	3.58|3.58	-3.69|-3.69	0.04450|0.04450	.|.	.|1.276180	.|0.05184	.|N	.|0.501930	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0	.|B;B;B;B	.|0.04013	.|0.0;0.001;0.0;0.0	T|T	0.43718|0.43718	-0.9374|-0.9374	4|9	.|0.15499	.|T	.|0.54	-0.1391|-0.1391	1.4402|1.4402	0.02353|0.02353	0.5017:0.1192:0.1189:0.2602|0.5017:0.1192:0.1189:0.2602	rs2301895;rs10394322;rs17856562;rs58275858|rs2301895;rs10394322;rs17856562;rs58275858	.|684;652;652;652	.|Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.|.;.;GT2D1_HUMAN;.	R|V	29|652;684;652;652	.|ENSP00000265755:M652V;ENSP00000397566:M684V;ENSP00000408477:M652V;ENSP00000418383:M652V	.|ENSP00000265755:M652V	H|M	+|+	2|1	0|0	GTF2IRD1|GTF2IRD1	73607477|73607477	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.209000|0.209000	0.24338|0.24338	-0.981000|-0.981000	0.03766|0.03766	-1.273000|-1.273000	0.02424|0.02424	-0.755000|-0.755000	0.03482|0.03482	CAT|ATG	A|0.616;G|0.384	0.384	strong		0.642	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
BRAF	673	hgsc.bcm.edu	37	7	140477811	140477811	+	Missense_Mutation	SNP	T	T	A	rs397507476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:140477811T>A	ENST00000288602.6	-	12	1557	c.1497A>T	c.(1495-1497)aaA>aaT	p.K499N		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	499	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262}.|K -> N (in CFC1). {ECO:0000269|PubMed:18042262, ECO:0000269|PubMed:19206169}.		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)	CTACTTCATTTTTGAAGGCTT	0.393		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.K499N	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.A1497T	GRCh37	CM080110	BRAF	M		PASS	.						108.0	97.0	101.0					7																	140477811		2203	4300	6503	SO:0001583	missense	673	exon12	Familial Cancer Database	CFC, CFCS	TTCATTTTTGAAG	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.1497A>T	7.37:g.140477811T>A	ENSP00000288602:p.Lys499Asn	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	70	26	0.371429	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.427562|4.427562	0.83667|0.83667	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	D|D	0.81739|0.82619	-1.53|-1.63	4.96|4.96	4.96|4.96	0.65561|0.65561	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.82742|0.82742	0.5103|0.5103	L|L	0.35793|0.35793	1.09|1.09	0.80722|0.80722	D|D	1|1	.|P	.|0.51653	.|0.947	.|P	.|0.52031	.|0.688	D|D	0.85140|0.85140	0.0980|0.0980	8|10	0.87932|0.87932	D|D	0|0	.|.	14.3436|14.3436	0.66643|0.66643	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|499	.|P15056	.|BRAF_HUMAN	I|N	107|499	ENSP00000419060:K107I|ENSP00000288602:K499N	ENSP00000419060:K107I|ENSP00000288602:K499N	K|K	-|-	2|3	0|2	BRAF|BRAF	140124280|140124280	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.114000|3.114000	0.50383|0.50383	1.853000|1.853000	0.53794|0.53794	0.472000|0.472000	0.43445|0.43445	AAA|AAA	.	.	none		0.393	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
FAM126B	285172	hgsc.bcm.edu	37	2	201846180	201846180	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:201846180A>G	ENST00000418596.3	-	12	1593	c.1406T>C	c.(1405-1407)aTt>aCt	p.I469T	AC005037.3_ENST00000332935.6_RNA|AC005037.3_ENST00000413848.1_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	469						intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GCCAACCCCAATGCTGGTACT	0.463																																					p.I469T		Atlas-SNP	.											FAM126B,NS,carcinoma,-1,1	FAM126B	34	1	0			c.T1406C						PASS	.						107.0	83.0	91.0					2																	201846180		2203	4300	6503	SO:0001583	missense	285172	exon12			ACCCCAATGCTGG	BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744			28593	protein-coding gene	gene with protein product						12477932	Standard	NM_173822		Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.1406T>C	2.37:g.201846180A>G	ENSP00000393667:p.Ile469Thr	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	132	63	0.477273	NM_173822	B2RCG7|Q4ZG87|Q53TX6	Missense_Mutation	SNP	ENST00000418596.3	37	CCDS2335.1	.	.	.	.	.	.	.	.	.	.	A	1.870	-0.460559	0.04508	.	.	ENSG00000155744	ENST00000418596	T	0.76578	-1.03	5.72	5.72	0.89469	.	0.413650	0.27773	N	0.017905	T	0.63331	0.2502	N	0.22421	0.69	0.29765	N	0.835254	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.54662	-0.8260	10	0.16896	T	0.51	-6.7283	11.9287	0.52835	0.8549:0.1451:0.0:0.0	.	275;469	B3KUG1;Q8IXS8	.;F126B_HUMAN	T	469	ENSP00000393667:I469T	ENSP00000393667:I469T	I	-	2	0	FAM126B	201554425	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.848000	0.48278	2.177000	0.69029	0.533000	0.62120	ATT	.	.	none		0.463	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256285.3	NM_173822	
FREM1	158326	hgsc.bcm.edu	37	9	14801710	14801710	+	Missense_Mutation	SNP	C	C	A	rs35870000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:14801710C>A	ENST00000380880.3	-	20	4417	c.3634G>T	c.(3634-3636)Gcc>Tcc	p.A1212S	FREM1_ENST00000422223.2_Missense_Mutation_p.A1212S|FREM1_ENST00000380881.4_Missense_Mutation_p.A1213S			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1212					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TGAGGGTTGGCTGGCTGCTTA	0.488													C|||	1302	0.259984	0.0681	0.3991	5008	,	,		18978	0.2321		0.3579	False		,,,				2504	0.3487				p.A1212S		Atlas-SNP	.											.	FREM1	261	.	0			c.G3634T						PASS	.	C	SER/ALA	472,3482		41,390,1546	146.0	143.0	144.0		3634	1.8	0.0	9	dbSNP_126	144	2824,5528		465,1894,1817	yes	missense	FREM1	NM_144966.5	99	506,2284,3363	AA,AC,CC		33.8123,11.9373,26.7837	benign	1212/2180	14801710	3296,9010	1977	4176	6153	SO:0001583	missense	158326	exon21			GGTTGGCTGGCTG	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.3634G>T	9.37:g.14801710C>A	ENSP00000370262:p.Ala1212Ser	Somatic	244	0	0		WXS	Illumina HiSeq	Phase_I	250	245	0.98	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	591	0.2706043956043956	43	0.08739837398373984	158	0.43646408839779005	127	0.22202797202797203	263	0.3469656992084433	C	9.841	1.191048	0.21954	0.119373	0.338123	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.10860	2.83;2.83;2.83	5.12	1.79	0.24919	.	1.028690	0.07657	N	0.932920	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.10296	0.003	B	0.14578	0.011	T	0.47086	-0.9144	9	0.09338	T	0.73	-0.03	2.6233	0.04922	0.0:0.376:0.2601:0.3638	rs35870000;rs61737620	1212	Q5H8C1	FREM1_HUMAN	S	1213;1212;1212	ENSP00000370263:A1213S;ENSP00000412940:A1212S;ENSP00000370262:A1212S	ENSP00000370257:A1215S	A	-	1	0	FREM1	14791710	0.003000	0.15002	0.001000	0.08648	0.084000	0.17831	0.988000	0.29616	0.542000	0.28846	0.591000	0.81541	GCC	C|0.719;A|0.281	0.281	strong		0.488	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
NTAN1	123803	hgsc.bcm.edu	37	16	15133889	15133889	+	Silent	SNP	T	T	G	rs14347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:15133889T>G	ENST00000287706.3	-	8	668	c.576A>C	c.(574-576)gcA>gcC	p.A192A	PDXDC1_ENST00000535621.2_Intron	NM_001270766.1|NM_173474.3	NP_001257695.1|NP_775745.1	Q96AB6	NTAN1_HUMAN	N-terminal asparagine amidase	192					adult locomotory behavior (GO:0008344)|memory (GO:0007613)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-N-terminal asparagine amidohydrolase activity (GO:0008418)			endometrium(1)|large_intestine(4)|lung(3)	8						CTTGAAAGGATGCTCTGTAAA	0.458													G|||	1726	0.344649	0.1846	0.5331	5008	,	,		20562	0.372		0.3072	False		,,,				2504	0.4376				p.A192A		Atlas-SNP	.											.	NTAN1	21	.	0			c.A576C						PASS	.	G		1000,3394	729.0+/-410.0	121,758,1318	115.0	121.0	119.0		576	-1.8	0.9	16	dbSNP_52	119	2588,6012	689.3+/-404.4	360,1868,2072	no	coding-synonymous	NTAN1	NM_173474.2		481,2626,3390	GG,GT,TT		30.093,22.7583,27.6127		192/311	15133889	3588,9406	2197	4300	6497	SO:0001819	synonymous_variant	123803	exon8			AAAGGATGCTCTG	AF092440	CCDS10558.1, CCDS73832.1	16p13	2008-02-05			ENSG00000157045	ENSG00000157045			29909	protein-coding gene	gene with protein product		615367				8910481	Standard	NM_173474		Approved		uc002ddd.4	Q96AB6	OTTHUMG00000129849	ENST00000287706.3:c.576A>C	16.37:g.15133889T>G		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	57	55	0.964912	NM_173474	Q7Z4Z0	Silent	SNP	ENST00000287706.3	37	CCDS10558.1																																																																																			T|0.710;G|0.290	0.290	strong		0.458	NTAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252089.1	NM_173474	
PITPNM2	57605	hgsc.bcm.edu	37	12	123471094	123471094	+	Silent	SNP	G	G	A	rs12811109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:123471094G>A	ENST00000542749.1	-	23	3678	c.3615C>T	c.(3613-3615)caC>caT	p.H1205H	PITPNM2_ENST00000392428.1_Silent_p.H926H|PITPNM2_ENST00000280562.5_Silent_p.H1199H|PITPNM2_ENST00000320201.4_Silent_p.H1205H			Q9BZ72	PITM2_HUMAN	phosphatidylinositol transfer protein, membrane-associated 2	1205					metabolic process (GO:0008152)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)			NS(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	39	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.55e-05)|Epithelial(86;8.43e-05)|BRCA - Breast invasive adenocarcinoma(302;0.123)		CATAGGCCGCGTGCACGCGCA	0.682													G|||	613	0.122404	0.0431	0.1873	5008	,	,		15693	0.002		0.2157	False		,,,				2504	0.2117				p.H1205H		Atlas-SNP	.											PITPNM2,colon,carcinoma,0,1	PITPNM2	105	1	0			c.C3615T						PASS	.	G		308,4096		7,294,1901	25.0	22.0	23.0		3615	0.1	1.0	12	dbSNP_121	23	1667,6931		136,1395,2768	no	coding-synonymous	PITPNM2	NM_020845.2		143,1689,4669	AA,AG,GG		19.3882,6.9936,15.19		1205/1350	123471094	1975,11027	2202	4299	6501	SO:0001819	synonymous_variant	57605	exon24			GGCCGCGTGCACG	AF334585	CCDS9242.1, CCDS73543.1	12q24.31	2008-02-05				ENSG00000090975			21044	protein-coding gene	gene with protein product		608920				10022914	Standard	XM_005253582		Approved	RDGBA2, RDGB2, NIR3	uc001uej.1	Q9BZ72		ENST00000542749.1:c.3615C>T	12.37:g.123471094G>A		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	116	70	0.603448	NM_020845	Q9P271	Silent	SNP	ENST00000542749.1	37	CCDS9242.1																																																																																			G|0.860;A|0.140	0.140	strong		0.682	PITPNM2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401342.1	NM_020845	
ZMYM5	9205	hgsc.bcm.edu	37	13	20425948	20425948	+	Missense_Mutation	SNP	T	T	C	rs9579718	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:20425948T>C	ENST00000337963.4	-	3	637	c.373A>G	c.(373-375)Ata>Gta	p.I125V	ZMYM5_ENST00000382907.4_Missense_Mutation_p.I125V|ZMYM5_ENST00000382905.4_Missense_Mutation_p.I125V	NM_001142684.1	NP_001136156.1	Q9UJ78	ZMYM5_HUMAN	zinc finger, MYM-type 5	125			I -> V (in dbSNP:rs9579718). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.2}.			nucleus (GO:0005634)	zinc ion binding (GO:0008270)			kidney(1)|large_intestine(5)|lung(9)	15		all_cancers(29;2.96e-22)|all_epithelial(30;3.76e-20)|all_lung(29;4.38e-20)|Lung NSC(5;5.8e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.61e-05)|Epithelial(112;4.89e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00171)|Lung(94;0.00942)|LUSC - Lung squamous cell carcinoma(192;0.0431)		TTTGTTTCTATGTCCTCTTCA	0.373													T|||	491	0.0980431	0.1717	0.0735	5008	,	,		19623	0.0813		0.0924	False		,,,				2504	0.0389				p.I125V		Atlas-SNP	.											.	ZMYM5	73	.	0			c.A373G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	709,3697	287.8+/-279.5	63,583,1557	68.0	72.0	71.0		373,373,373	0.1	1.0	13	dbSNP_119	71	590,8010	156.0+/-209.9	15,560,3725	yes	missense,missense,missense	ZMYM5	NM_001039649.2,NM_001039650.2,NM_001142684.1	29,29,29	78,1143,5282	CC,CT,TT		6.8605,16.0917,9.9877	benign,benign,benign	125/209,125/383,125/670	20425948	1299,11707	2203	4300	6503	SO:0001583	missense	9205	exon3			TTTCTATGTCCTC	AF161535	CCDS31942.1, CCDS31943.1	13q12	2013-01-08	2005-09-12	2005-09-12	ENSG00000132950	ENSG00000132950		"""Zinc fingers, MYM type"""	13029	protein-coding gene	gene with protein product			"""zinc finger protein 237"""	ZNF237			Standard	NM_001039650		Approved	ZNF198L1, MYM	uc010tcn.1	Q9UJ78	OTTHUMG00000016504	ENST00000337963.4:c.373A>G	13.37:g.20425948T>C	ENSP00000337034:p.Ile125Val	Somatic	146	0	0		WXS	Illumina HiSeq	Phase_I	131	55	0.419847	NM_001039650	B2R6V1|Q5T6E1|Q5T6E2|Q5T6E4|Q96IY6|Q9NZY5|Q9UBW0|Q9UJ77	Missense_Mutation	SNP	ENST00000337963.4	37		193	0.08836996336996338	71	0.1443089430894309	26	0.0718232044198895	35	0.06118881118881119	61	0.08047493403693931	T	5.678	0.309723	0.10733	0.160917	0.068605	ENSG00000132950	ENST00000337963;ENST00000502168;ENST00000382907;ENST00000382905	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	4.41	0.0975	0.14494	.	.	.	.	.	T	0.00073	0.0002	L	0.39898	1.24	0.50313	P	1.3799999999997148E-4	B;B;B	0.20671	0.005;0.047;0.017	B;B;B	0.17979	0.004;0.02;0.013	T	0.16188	-1.0411	8	0.41790	T	0.15	-0.003	4.8086	0.13331	0.4309:0.0784:0.0:0.4907	rs9579718;rs17850147;rs52817925;rs9579718	125;125;125	Q9UJ78;Q9UJ78-2;Q9UJ78-1	ZMYM5_HUMAN;.;.	V	125;115;125;125	ENSP00000337034:I125V;ENSP00000445779:I115V;ENSP00000372364:I125V;ENSP00000372361:I125V	ENSP00000337034:I125V	I	-	1	0	ZMYM5	19323948	0.858000	0.29795	0.982000	0.44146	0.538000	0.34931	-0.078000	0.11375	-0.036000	0.13669	0.402000	0.26972	ATA	T|0.901;C|0.099	0.099	strong		0.373	ZMYM5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014242	
MUC4	4585	hgsc.bcm.edu	37	3	195509941	195509941	+	Missense_Mutation	SNP	A	A	C	rs199849290	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195509941A>C	ENST00000463781.3	-	2	8969	c.8510T>G	c.(8509-8511)aTc>aGc	p.I2837S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.I2837S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.I2837S(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGAGGAAGGGATGGTGACAGG	0.592													.|||	318	0.0634984	0.0045	0.0432	5008	,	,		7808	0.0417		0.1521	False		,,,				2504	0.089				p.I2837S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	kidney(1)	c.T8510G						scavenged	.	T	,,SER/ILE	2,1378		0,2,688	109.0	67.0	80.0		,,8510		0.0	3		80	27,3107		0,27,1540	no	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,142	0,29,2228	CC,CA,AA		0.8615,0.1449,0.6424	,,benign	,,2837/5413	195509941	29,4485	690	1567	2257	SO:0001583	missense	4585	exon2			GAAGGGATGGTGA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.8510T>G	3.37:g.195509941A>C	ENSP00000417498:p.Ile2837Ser	Somatic	253	3	0.0118577		WXS	Illumina HiSeq	Phase_I	164	13	0.0792683	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	7.247	0.602483	0.13939	0.001449	0.008615	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.6	.	.	.	.	.	.	.	.	T	0.08133	0.0203	N	0.08118	0	0.21290	N	0.99974	B	0.30727	0.292	B	0.21708	0.036	T	0.26503	-1.0101	7	.	.	.	.	5.3345	0.15949	0.9999:0.0:1.0E-4:0.0	.	2709	E7ESK3	.	S	2837	ENSP00000417498:I2837S;ENSP00000420243:I2837S	.	I	-	2	0	MUC4	196994720	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.560000	0.00113	-0.000000	0.14550	0.000000	0.15137	ATC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CHFR	55743	hgsc.bcm.edu	37	12	133423695	133423695	+	Silent	SNP	A	A	G	rs2306537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:133423695A>G	ENST00000432561.2	-	15	1778	c.1705T>C	c.(1705-1707)Ttg>Ctg	p.L569L	CHFR_ENST00000541837.2_5'UTR|CHFR_ENST00000450056.2_Silent_p.L557L|CHFR_ENST00000537522.1_Silent_p.L191L|CHFR_ENST00000443047.2_Silent_p.L477L|CHFR_ENST00000315585.7_Silent_p.L528L|CHFR_ENST00000541341.1_5'UTR|CHFR_ENST00000266880.7_Silent_p.L568L			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	569					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		TTCCATGTCAAACCTCTGGTT	0.458													A|||	713	0.142372	0.0106	0.1571	5008	,	,		19964	0.1736		0.2803	False		,,,				2504	0.136				p.L569L		Atlas-SNP	.											.	CHFR	83	.	0			c.T1705C						PASS	.	A	,,,,	223,4183	136.5+/-172.5	9,205,1989	102.0	104.0	103.0		1705,1702,1669,1429,1582	2.2	1.0	12	dbSNP_100	103	2569,6031	416.9+/-352.3	384,1801,2115	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CHFR	NM_001161344.1,NM_001161345.1,NM_001161346.1,NM_001161347.1,NM_018223.2	,,,,	393,2006,4104	GG,GA,AA		29.8721,5.0613,21.467	,,,,	569/665,568/664,557/653,477/573,528/624	133423695	2792,10214	2203	4300	6503	SO:0001819	synonymous_variant	55743	exon15			ATGTCAAACCTCT	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.1705T>C	12.37:g.133423695A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	40	14	0.35	NM_001161344	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Silent	SNP	ENST00000432561.2	37	CCDS53849.1																																																																																			A|0.803;G|0.197	0.197	strong		0.458	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397130.2		
IL37	27178	hgsc.bcm.edu	37	2	113676219	113676219	+	Missense_Mutation	SNP	T	T	C	rs2708947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113676219T>C	ENST00000263326.3	+	5	532	c.490T>C	c.(490-492)Tgg>Cgg	p.W164R	IL37_ENST00000353225.3_Missense_Mutation_p.W124R|IL37_ENST00000352179.3_Missense_Mutation_p.W143R|IL37_ENST00000311328.2_Missense_Mutation_p.W138R|IL37_ENST00000349806.3_Missense_Mutation_p.W103R	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	164			W -> R (in dbSNP:rs2708947). {ECO:0000269|Ref.6}.		immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						GGTGGGCTCCTGGAACATGCT	0.517													c|||	384	0.0766773	0.174	0.0591	5008	,	,		17070	0.003		0.0815	False		,,,				2504	0.0286				p.W164R		Atlas-SNP	.											.	IL37	56	.	0			c.T490C						PASS	.		ARG/TRP,ARG/TRP,ARG/TRP,ARG/TRP,ARG/TRP	734,3672	756.4+/-412.6	53,628,1522	50.0	57.0	55.0		490,427,307,370,412	-7.6	0.0	2	dbSNP_100	55	690,7910	788.2+/-407.6	37,616,3647	yes	missense,missense,missense,missense,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1,NM_173205.1	101,101,101,101,101	90,1244,5169	CC,CT,TT		8.0233,16.6591,10.9488	benign,benign,benign,benign,benign	164/219,143/198,103/158,124/179,138/193	113676219	1424,11582	2203	4300	6503	SO:0001583	missense	27178	exon5			GGCTCCTGGAACA	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.490T>C	2.37:g.113676219T>C	ENSP00000263326:p.Trp164Arg	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	137	65	0.474453	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	164	0.07509157509157509	81	0.16463414634146342	26	0.0718232044198895	1	0.0017482517482517483	56	0.07387862796833773	c	2.666	-0.278613	0.05679	0.166591	0.080233	ENSG00000125571	ENST00000263326;ENST00000352179;ENST00000349806;ENST00000353225;ENST00000311328	T;T;T;T;T	0.15603	2.41;2.41;3.01;3.01;2.41	3.81	-7.62	0.01294	.	2.692820	0.01879	N	0.037776	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.29119	-1.0022	9	0.25106	T	0.35	0.1931	1.1973	0.01877	0.424:0.1454:0.1054:0.3252	rs2708947;rs52818665;rs59798096;rs2708947	138;103;124;143;164	Q9NZH6-2;Q9NZH6-5;Q9NZH6-3;Q9NZH6-4;Q9NZH6	.;.;.;.;IL37_HUMAN	R	164;143;103;124;138	ENSP00000263326:W164R;ENSP00000263327:W143R;ENSP00000263328:W103R;ENSP00000309208:W124R;ENSP00000309883:W138R	ENSP00000263326:W164R	W	+	1	0	IL37	113392690	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.273000	0.00135	-2.171000	0.00775	-1.079000	0.02226	TGG	T|0.902;C|0.098	0.098	strong		0.517	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
FGL1	2267	hgsc.bcm.edu	37	8	17739639	17739639	+	Missense_Mutation	SNP	C	C	A	rs78484373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17739639C>A	ENST00000398056.2	-	5	928	c.113G>T	c.(112-114)cGc>cTc	p.R38L	FGL1_ENST00000381840.2_Missense_Mutation_p.R38L|RP11-156K13.2_ENST00000519368.1_RNA|FGL1_ENST00000522444.1_Missense_Mutation_p.R38L|FGL1_ENST00000381841.2_Missense_Mutation_p.R38L|FGL1_ENST00000518650.1_Missense_Mutation_p.R38L|FGL1_ENST00000427924.1_Missense_Mutation_p.R38L|FGL1_ENST00000398054.1_Missense_Mutation_p.R38L			Q08830	FGL1_HUMAN	fibrinogen-like 1	38					adipose tissue development (GO:0060612)|cholesterol metabolic process (GO:0008203)|regulation of glucose metabolic process (GO:0010906)|response to stilbenoid (GO:0035634)	extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)	13				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		CTCAAGCAGGCGCACCTGGGC	0.512													c|||	106	0.0211661	0.0076	0.0173	5008	,	,		16069	0.0		0.0378	False		,,,				2504	0.047				p.R38L		Atlas-SNP	.											FGL1,colon,carcinoma,-1,3	FGL1	31	3	0			c.G113T						scavenged	.	T	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	26,4380	35.2+/-66.4	0,26,2177	87.0	81.0	83.0		113,113,113,113	-8.5	0.0	8	dbSNP_131	83	194,8406	86.1+/-148.5	3,188,4109	yes	missense,missense,missense,missense	FGL1	NM_004467.3,NM_147203.2,NM_201552.1,NM_201553.1	102,102,102,102	3,214,6286	AA,AC,CC		2.2558,0.5901,1.6915	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	38/313,38/313,38/313,38/313	17739639	220,12786	2203	4300	6503	SO:0001583	missense	2267	exon4			AGCAGGCGCACCT	D14446	CCDS6004.1	8p22	2013-02-06			ENSG00000104760	ENSG00000104760		"""Fibrinogen C domain containing"""	3695	protein-coding gene	gene with protein product		605776				8390249	Standard	NM_004467		Approved	HFREP-1	uc003wyb.3	Q08830	OTTHUMG00000096989	ENST00000398056.2:c.113G>T	8.37:g.17739639C>A	ENSP00000381133:p.Arg38Leu	Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	101	43	0.425743	NM_201553	A6NKU4|Q4PJH9|Q53YF1|Q8NG32|Q96KW6|Q96QM6	Missense_Mutation	SNP	ENST00000398056.2	37	CCDS6004.1	43	0.019688644688644688	3	0.006097560975609756	10	0.027624309392265192	0	0.0	30	0.0395778364116095	c	16.12	3.034336	0.54896	0.005901	0.022558	ENSG00000104760	ENST00000221204;ENST00000398056;ENST00000521427;ENST00000522444;ENST00000381841;ENST00000427924;ENST00000398054;ENST00000381840;ENST00000518650	T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.84	-8.5	0.00927	.	1.142930	0.06304	N	0.701514	T	0.11965	0.0291	L	0.27053	0.805	0.09310	N	1	B;B;B	0.33583	0.418;0.049;0.22	B;B;B	0.32624	0.149;0.029;0.096	T	0.11966	-1.0566	10	0.33940	T	0.23	.	18.9966	0.92815	0.0:0.7383:0.0:0.2617	.	8;38;38	E7ERS0;Q8NG32;Q08830	.;.;FGL1_HUMAN	L	38;38;8;38;38;38;38;38;38	ENSP00000381133:R38L;ENSP00000429757:R38L;ENSP00000371263:R38L;ENSP00000401952:R38L;ENSP00000381131:R38L;ENSP00000371262:R38L;ENSP00000428430:R38L	ENSP00000221204:R38L	R	-	2	0	FGL1	17783919	0.042000	0.20092	0.039000	0.18376	0.960000	0.62799	-0.795000	0.04580	-1.571000	0.01663	-0.788000	0.03338	CGC	C|0.981;A|0.019	0.019	strong		0.512	FGL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375254.1	NM_004467	
TENM2	57451	hgsc.bcm.edu	37	5	167553880	167553880	+	Silent	SNP	C	C	T	rs10055910	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:167553880C>T	ENST00000518659.1	+	12	2370	c.2331C>T	c.(2329-2331)caC>caT	p.H777H	TENM2_ENST00000545108.1_Silent_p.H777H|CTB-178M22.1_ENST00000517408.1_RNA|TENM2_ENST00000520394.1_Silent_p.H545H|TENM2_ENST00000519204.1_Silent_p.H656H|TENM2_ENST00000403607.2_Silent_p.H610H	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	777	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)										GCATTGAGCACGGGACCTGTA	0.607													C|||	778	0.155351	0.2572	0.1758	5008	,	,		16535	0.003		0.2336	False		,,,				2504	0.0798				p.H777H		Atlas-SNP	.											.	.	.	.	0			c.C2331T						PASS	.	C		897,3189		97,703,1243	44.0	51.0	49.0		2331	4.8	1.0	5	dbSNP_119	49	1952,6406		229,1494,2456	no	coding-synonymous	ODZ2	NM_001122679.1		326,2197,3699	TT,TC,CC		23.3549,21.953,22.8946		777/2766	167553880	2849,9595	2043	4179	6222	SO:0001819	synonymous_variant	57451	exon12			TGAGCACGGGACC	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.2331C>T	5.37:g.167553880C>T		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	171	78	0.45614	NM_001122679	Q9ULU2	Silent	SNP	ENST00000518659.1	37																																																																																				C|0.828;T|0.172	0.172	strong		0.607	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
ATPAF2	91647	hgsc.bcm.edu	37	17	17921995	17921995	+	Silent	SNP	C	C	T	rs33997182	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:17921995C>T	ENST00000474627.3	-	8	892	c.738G>A	c.(736-738)caG>caA	p.Q246Q	ATPAF2_ENST00000585101.1_Intron|ATPAF2_ENST00000469327.1_5'UTR	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	246					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					TGCCCCACTTCTGGATCTGAG	0.607													C|||	82	0.0163738	0.003	0.0159	5008	,	,		19791	0.0		0.0427	False		,,,				2504	0.0245				p.Q246Q		Atlas-SNP	.											.	ATPAF2	15	.	0			c.G738A						PASS	.	C		33,4373	37.6+/-69.7	0,33,2170	85.0	86.0	86.0		738	2.1	1.0	17	dbSNP_126	86	279,8321	106.0+/-166.9	5,269,4026	no	coding-synonymous	ATPAF2	NM_145691.3		5,302,6196	TT,TC,CC		3.2442,0.749,2.3989		246/290	17921995	312,12694	2203	4300	6503	SO:0001819	synonymous_variant	91647	exon8			CCACTTCTGGATC	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"""Mitochondrial respiratory chain complex assembly factors"""	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.738G>A	17.37:g.17921995C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	29	0.391892	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Silent	SNP	ENST00000474627.3	37	CCDS32585.1																																																																																			C|0.978;T|0.022	0.022	strong		0.607	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691	
ALMS1	7840	hgsc.bcm.edu	37	2	73717567	73717567	+	Missense_Mutation	SNP	G	G	T	rs2056486	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73717567G>T	ENST00000264448.6	+	10	8589	c.8478G>T	c.(8476-8478)agG>agT	p.R2826S	AC096546.1_ENST00000408160.1_RNA|ALMS1_ENST00000409009.1_Missense_Mutation_p.R2784S	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2826					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						CCAGTACCAGGGCAAATTGTA	0.393													T|||	1794	0.358227	0.8578	0.3905	5008	,	,		19374	0.0089		0.2266	False		,,,				2504	0.1554				p.R2826S		Atlas-SNP	.											.	ALMS1	384	.	0			c.G8478T						PASS	.	T	SER/ARG	2699,1011		994,711,150	60.0	57.0	58.0		8478	0.3	0.0	2	dbSNP_94	58	1935,6237		218,1499,2369	yes	missense	ALMS1	NM_015120.4	110	1212,2210,2519	TT,TG,GG		23.6784,27.2507,39.0002	benign	2826/4168	73717567	4634,7248	1855	4086	5941	SO:0001583	missense	7840	exon10			TACCAGGGCAAAT	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.8478G>T	2.37:g.73717567G>T	ENSP00000264448:p.Arg2826Ser	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	75	35	0.466667	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	730	0.3342490842490842	418	0.8495934959349594	126	0.34806629834254144	8	0.013986013986013986	178	0.23482849604221637	T	0.011	-1.709383	0.00712	0.727493	0.236784	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.04654	3.58;3.58	4.33	0.258	0.15578	.	0.517985	0.18103	N	0.151608	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	0.16070	-1.0415	9	0.02654	T	1	.	6.6891	0.23161	0.1571:0.0:0.4864:0.3565	rs2056486;rs17349629;rs17848863;rs52800268;rs60591669;rs2056486	2826;2784;2826	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	S	2784;2826	ENSP00000386627:R2784S;ENSP00000264448:R2826S	ENSP00000264448:R2826S	R	+	3	2	ALMS1	73571075	0.000000	0.05858	0.000000	0.03702	0.746000	0.42486	-0.037000	0.12164	-0.189000	0.10482	-0.264000	0.10439	AGG	G|0.663;T|0.337	0.337	strong		0.393	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
RTCB	51493	hgsc.bcm.edu	37	22	32784051	32784051	+	Silent	SNP	T	T	C	rs11635	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:32784051T>C	ENST00000216038.5	-	12	1544	c.1446A>G	c.(1444-1446)gtA>gtG	p.V482V	RTCB_ENST00000451746.2_3'UTR|RP1-149A16.17_ENST00000444848.1_lincRNA	NM_014306.4	NP_055121.1			RNA 2',3'-cyclic phosphate and 5'-OH ligase																		GGCAGGTATTTACCACATCTG	0.443													T|||	817	0.163139	0.0915	0.0893	5008	,	,		19332	0.4593		0.0467	False		,,,				2504	0.1268				p.V482V		Atlas-SNP	.											.	C22orf28	43	.	0			c.A1446G						PASS	.	T		451,3955	212.5+/-232.4	26,399,1778	156.0	130.0	139.0		1446	1.5	1.0	22	dbSNP_52	139	486,8114	140.9+/-197.4	11,464,3825	no	coding-synonymous	C22orf28	NM_014306.4		37,863,5603	CC,CT,TT		5.6512,10.236,7.2044		482/506	32784051	937,12069	2203	4300	6503	SO:0001819	synonymous_variant	51493	exon12			GGTATTTACCACA	BC016707	CCDS13905.1	22q12.3	2013-05-22	2013-05-22	2013-05-22	ENSG00000100220	ENSG00000100220	6.5.1.3		26935	protein-coding gene	gene with protein product	"""focal adhesion-associated protein"""	613901	"""chromosome 22 open reading frame 28"""	C22orf28		11042152, 21209330, 21311021	Standard	NM_014306		Approved	HSPC117, FAAP		Q9Y3I0	OTTHUMG00000030300	ENST00000216038.5:c.1446A>G	22.37:g.32784051T>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	147	76	0.517007	NM_014306		Silent	SNP	ENST00000216038.5	37	CCDS13905.1																																																																																			T|0.883;C|0.117	0.117	strong		0.443	RTCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075188.3	NM_014306	
NSUN2	54888	hgsc.bcm.edu	37	5	6600150	6600150	+	Silent	SNP	G	G	A	rs3822434	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:6600150G>A	ENST00000264670.6	-	19	2504	c.2193C>T	c.(2191-2193)gaC>gaT	p.D731D	NSUN2_ENST00000506139.1_Silent_p.D696D|NSUN2_ENST00000539938.1_Silent_p.D495D	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	731					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CCTCAGTCACGTCATTGTCTG	0.572													C|||	869	0.173522	0.0825	0.2507	5008	,	,		18174	0.2321		0.1402	False		,,,				2504	0.2157				p.D731D		Atlas-SNP	.											NSUN2,colon,carcinoma,0,1	NSUN2	82	1	0			c.C2193T						scavenged	.	C	,	411,3995		17,377,1809	182.0	144.0	157.0		2088,2193	-0.6	0.0	5	dbSNP_107	157	1279,7321		105,1069,3126	no	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	122,1446,4935	AA,AG,GG		14.8721,9.3282,12.994	,	696/733,731/768	6600150	1690,11316	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon19			AGTCACGTCATTG	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.2193C>T	5.37:g.6600150G>A		Somatic	105	1	0.00952381		WXS	Illumina HiSeq	Phase_I	125	67	0.536	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			G|0.862;C|0.000;A|0.138	0.138	strong		0.572	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
PDE8B	8622	hgsc.bcm.edu	37	5	76708987	76708987	+	Silent	SNP	A	A	G	rs335614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:76708987A>G	ENST00000264917.5	+	17	1809	c.1764A>G	c.(1762-1764)gaA>gaG	p.E588E	PDE8B_ENST00000505283.1_Silent_p.E53E|PDE8B_ENST00000340978.3_Silent_p.E541E|PDE8B_ENST00000333194.4_Silent_p.E533E|PDE8B_ENST00000342343.4_Silent_p.E568E|PDE8B_ENST00000346042.3_Silent_p.E491E	NM_003719.3	NP_003710.1	O95263	PDE8B_HUMAN	phosphodiesterase 8B	588					cAMP catabolic process (GO:0006198)|cyclic nucleotide metabolic process (GO:0009187)|negative regulation of insulin secretion (GO:0046676)|negative regulation of steroid hormone biosynthetic process (GO:0090032)|phosphorelay signal transduction system (GO:0000160)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)		GMDS/PDE8B(2)	NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(15)|ovary(1)|prostate(2)|skin(3)	40		all_lung(232;0.00043)|Lung NSC(167;0.00114)|Ovarian(174;0.0107)|Prostate(461;0.0605)		OV - Ovarian serous cystadenocarcinoma(54;2.21e-49)|Epithelial(54;5.82e-43)|all cancers(79;4.06e-38)	Caffeine(DB00201)|Ketotifen(DB00920)	GAGTATGTGAATTTTTAAACT	0.478													A|||	3832	0.765176	0.8154	0.7305	5008	,	,		16882	0.8175		0.672	False		,,,				2504	0.7638				p.E588E		Atlas-SNP	.											.	PDE8B	103	.	0			c.A1764G						PASS	.	A	,,,,	3478,928	738.1+/-410.9	1380,718,105	207.0	198.0	201.0		1473,1599,1704,1623,1764	2.1	1.0	5	dbSNP_79	201	5563,3037	662.5+/-402.0	1845,1873,582	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE8B	NM_001029851.2,NM_001029852.2,NM_001029853.2,NM_001029854.2,NM_003719.3	,,,,	3225,2591,687	GG,GA,AA		35.314,21.0622,30.4859	,,,,	491/789,533/831,568/866,541/839,588/886	76708987	9041,3965	2203	4300	6503	SO:0001819	synonymous_variant	8622	exon17			ATGTGAATTTTTA	AF079529	CCDS4037.1, CCDS34190.1, CCDS34191.1, CCDS34192.1, CCDS34193.1	5q14.1	2008-05-15			ENSG00000113231	ENSG00000113231	3.1.4.17	"""Phosphodiesterases"""	8794	protein-coding gene	gene with protein product		603390				9784418	Standard	NM_003719		Approved		uc003kfa.3	O95263	OTTHUMG00000102170	ENST00000264917.5:c.1764A>G	5.37:g.76708987A>G		Somatic	194	0	0		WXS	Illumina HiSeq	Phase_I	207	94	0.454106	NM_003719	Q5J7V7|Q86XK8|Q8IUJ7|Q8IUJ8|Q8IUJ9|Q8IUK0|Q8N3T2	Silent	SNP	ENST00000264917.5	37	CCDS4037.1																																																																																			A|0.284;G|0.716	0.716	strong		0.478	PDE8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000220015.3	NM_003719	
OR5K3	403277	hgsc.bcm.edu	37	3	98109640	98109640	+	Missense_Mutation	SNP	G	G	A	rs13068323	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:98109640G>A	ENST00000383695.1	+	1	131	c.131G>A	c.(130-132)gGt>gAt	p.G44D	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	44			G -> D (in dbSNP:rs13068323).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						GGGAACATTGGTTTGGTGGCA	0.413													G|||	825	0.164736	0.1271	0.1153	5008	,	,		21130	0.2222		0.162	False		,,,				2504	0.1943				p.G44D		Atlas-SNP	.											OR5K3,rectum,carcinoma,-1,1	OR5K3	60	1	0			c.G131A						PASS	.	G	ASP/GLY	594,3812	260.1+/-263.5	41,512,1650	277.0	258.0	264.0		131	5.3	0.9	3	dbSNP_121	264	1263,7337	252.8+/-278.7	96,1071,3133	yes	missense	OR5K3	NM_001005516.1	94	137,1583,4783	AA,AG,GG		14.686,13.4816,14.278	probably-damaging	44/322	98109640	1857,11149	2203	4300	6503	SO:0001583	missense	403277	exon1			ACATTGGTTTGGT		CCDS33803.1	3q11.2	2013-09-23			ENSG00000206536	ENSG00000206536		"""GPCR / Class A : Olfactory receptors"""	31290	protein-coding gene	gene with protein product							Standard	NM_001005516		Approved		uc011bgw.2	A6NET4	OTTHUMG00000160077	ENST00000383695.1:c.131G>A	3.37:g.98109640G>A	ENSP00000373194:p.Gly44Asp	Somatic	327	1	0.0030581		WXS	Illumina HiSeq	Phase_I	369	173	0.468835	NM_001005516		Missense_Mutation	SNP	ENST00000383695.1	37	CCDS33803.1	362	0.16575091575091574	69	0.1402439024390244	50	0.13812154696132597	114	0.1993006993006993	129	0.17018469656992086	G	12.49	1.955038	0.34471	0.134816	0.14686	ENSG00000206536	ENST00000383695	T	0.01981	4.52	5.35	5.35	0.76521	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000846	T	0.00012	0.0000	M	0.93462	3.42	0.58432	P	8.000000000008E-6	D	0.58268	0.982	D	0.65010	0.931	T	0.01972	-1.1237	9	0.87932	D	0	-25.2713	11.9377	0.52882	0.0:0.0:0.8262:0.1737	rs13068323;rs13068323	44	A6NET4	OR5K3_HUMAN	D	44	ENSP00000373194:G44D	ENSP00000373194:G44D	G	+	2	0	OR5K3	99592330	0.000000	0.05858	0.936000	0.37596	0.090000	0.18270	-0.556000	0.05992	2.633000	0.89246	0.603000	0.83216	GGT	G|0.846;A|0.154	0.154	strong		0.413	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1		
INCA1	388324	hgsc.bcm.edu	37	17	4892176	4892176	+	Missense_Mutation	SNP	C	C	G	rs74744272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4892176C>G	ENST00000574617.1	-	7	814	c.459G>C	c.(457-459)gaG>gaC	p.E153D	CAMTA2_ENST00000414043.3_5'Flank|INCA1_ENST00000355025.3_Missense_Mutation_p.E138D|CAMTA2_ENST00000381311.5_5'Flank|INCA1_ENST00000576820.1_Missense_Mutation_p.E153D|CAMTA2_ENST00000348066.3_5'Flank|CAMTA2_ENST00000572543.1_5'Flank|INCA1_ENST00000575780.1_Missense_Mutation_p.E138D|CAMTA2_ENST00000358183.4_5'Flank|RP5-1050D4.5_ENST00000574260.1_RNA|RP5-1050D4.4_ENST00000575985.1_RNA|INCA1_ENST00000396829.2_Missense_Mutation_p.E153D|CAMTA2_ENST00000361571.5_5'Flank			Q0VD86	INCA1_HUMAN	inhibitor of CDK, cyclin A1 interacting protein 1	153				E -> D (in Ref. 1; AAT09152/AAT09153). {ECO:0000305}.	negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|positive regulation of apoptotic signaling pathway (GO:2001235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			upper_aerodigestive_tract(1)	1						ATCCACAGCCCTCTTCGCCAA	0.577													C|||	280	0.0559105	0.0287	0.0605	5008	,	,		18952	0.0486		0.1262	False		,,,				2504	0.0245				p.E153D		Atlas-SNP	.											.	INCA1	17	.	0			c.G459C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	173,4233	112.9+/-151.0	3,167,2033	99.0	80.0	87.0		414,459,459,414	-3.5	0.0	17	dbSNP_131	87	1019,7581	218.3+/-256.7	61,897,3342	yes	missense,missense,missense,missense	INCA1	NM_001167985.1,NM_001167986.1,NM_001167987.1,NM_213726.2	45,45,45,45	64,1064,5375	GG,GC,CC		11.8488,3.9265,9.165	benign,benign,benign,benign	138/222,153/237,153/237,138/222	4892176	1192,11814	2203	4300	6503	SO:0001583	missense	388324	exon8			ACAGCCCTCTTCG	AY601906, AAT09152	CCDS11064.1, CCDS54074.1	17p13.2	2010-03-19	2009-04-20		ENSG00000196388	ENSG00000196388			32224	protein-coding gene	gene with protein product						15159402, 18756329	Standard	NM_213726		Approved		uc002gak.3	Q0VD86		ENST00000574617.1:c.459G>C	17.37:g.4892176C>G	ENSP00000458316:p.Glu153Asp	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	87	37	0.425287	NM_001167986	Q6J273|Q6PKN9	Missense_Mutation	SNP	ENST00000574617.1	37	CCDS54074.1	166	0.076007326007326	11	0.022357723577235773	24	0.06629834254143646	32	0.055944055944055944	99	0.13060686015831136	C	13.12	2.142853	0.37825	0.039265	0.118488	ENSG00000196388	ENST00000396829;ENST00000355025	.	.	.	4.45	-3.55	0.04639	.	0.551536	0.16685	N	0.203770	T	0.00109	0.0003	N	0.11201	0.11	0.80722	P	0.0	B;B	0.13594	0.008;0.008	B;B	0.13407	0.009;0.009	T	0.20107	-1.0285	8	0.13853	T	0.58	-1.016	0.8359	0.01140	0.3451:0.2294:0.2534:0.172	.	138;153	Q0VD86-2;Q0VD86	.;INCA1_HUMAN	D	153;138	.	ENSP00000347129:E138D	E	-	3	2	INCA1	4832900	0.000000	0.05858	0.002000	0.10522	0.661000	0.39034	-0.928000	0.03980	-0.572000	0.06006	0.655000	0.94253	GAG	C|0.915;G|0.085	0.085	strong		0.577	INCA1-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438886.1	NM_213726	
ETV1	2115	hgsc.bcm.edu	37	7	14025766	14025766	+	Intron	SNP	T	T	A	rs10215655	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:14025766T>A	ENST00000430479.1	-	5	849				ETV1_ENST00000420159.2_Silent_p.P12P|ETV1_ENST00000343495.5_Intron|ETV1_ENST00000403685.1_Intron|ETV1_ENST00000399357.3_Silent_p.P12P|ETV1_ENST00000476720.2_5'Flank|ETV1_ENST00000405358.4_Intron|ETV1_ENST00000405192.2_Intron|ETV1_ENST00000405218.2_Intron|ETV1_ENST00000403527.1_Silent_p.P12P|ETV1_ENST00000242066.5_Intron	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1						axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						GTGAACAAGGTGGAAAGAAGA	0.383			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""								T|||	2825	0.564097	0.6672	0.6282	5008	,	,		16364	0.5813		0.5437	False		,,,				2504	0.3824				p.P12P		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"""M, E"""	.	ETV1	138	.	0			c.A36T						PASS	.	T	,,,,,,	1960,1176		642,676,250	93.0	79.0	83.0		,,,36,36,36,	2.0	1.0	7	dbSNP_119	83	3748,3412		972,1804,804	no	intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,intron	ETV1	NM_001163147.1,NM_001163148.1,NM_001163149.1,NM_001163150.1,NM_001163151.1,NM_001163152.1,NM_004956.4	,,,,,,	1614,2480,1054	AA,AT,TT		47.6536,37.5,44.561	,,,,,,	,,,12/438,12/420,12/375,	14025766	5708,4588	1568	3580	5148	SO:0001627	intron_variant	2115	exon1			ACAAGGTGGAAAG		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.181+496A>T	7.37:g.14025766T>A		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	27	27	1	NM_001163152	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Silent	SNP	ENST00000430479.1	37	CCDS55088.1																																																																																			T|0.412;A|0.588	0.588	strong		0.383	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956	
PYGB	5834	hgsc.bcm.edu	37	20	25262769	25262769	+	Missense_Mutation	SNP	G	G	A	rs2227891	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25262769G>A	ENST00000216962.4	+	12	1614	c.1504G>A	c.(1504-1506)Gat>Aat	p.D502N		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	502			D -> N (in dbSNP:rs2227891).		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glycogen phosphorylase activity (GO:0008184)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	31						GGGGCTGGCCGATACCATCGT	0.612													G|||	812	0.162141	0.0514	0.1297	5008	,	,		16098	0.3502		0.1849	False		,,,				2504	0.1176				p.D502N		Atlas-SNP	.											.	PYGB	84	.	0			c.G1504A						PASS	.	G	ASN/ASP	349,4051	176.6+/-205.7	10,329,1861	33.0	40.0	38.0		1504	3.9	0.1	20	dbSNP_98	38	1593,7005	290.5+/-299.9	155,1283,2861	yes	missense	PYGB	NM_002862.3	23	165,1612,4722	AA,AG,GG		18.5276,7.9318,14.9408	benign	502/844	25262769	1942,11056	2200	4299	6499	SO:0001583	missense	5834	exon12			CTGGCCGATACCA		CCDS13171.1	20p11.21	2013-03-01			ENSG00000100994	ENSG00000100994	2.4.1.1	"""Glycogen phosphorylases"""	9723	protein-coding gene	gene with protein product	"""glycogen phosphorylase, brain form"""	138550					Standard	NM_002862		Approved		uc002wup.3	P11216	OTTHUMG00000032117	ENST00000216962.4:c.1504G>A	20.37:g.25262769G>A	ENSP00000216962:p.Asp502Asn	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	53	30	0.566038	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	424	0.19413919413919414	27	0.054878048780487805	58	0.16022099447513813	197	0.34440559440559443	142	0.18733509234828497	G	14.15	2.448638	0.43531	0.079318	0.185276	ENSG00000100994	ENST00000216962	D	0.93189	-3.18	3.93	3.93	0.45458	.	0.197780	0.51477	D	0.000095	T	0.00012	0.0000	L	0.39245	1.2	0.09310	P	0.99999999854778	B	0.14012	0.009	B	0.15052	0.012	T	0.01977	-1.1236	9	0.36615	T	0.2	-19.3115	16.1009	0.81169	0.0:0.0:1.0:0.0	rs2227891;rs2261789;rs13044002;rs16987631;rs2227891	502	P11216	PYGB_HUMAN	N	502	ENSP00000216962:D502N	ENSP00000216962:D502N	D	+	1	0	PYGB	25210769	1.000000	0.71417	0.069000	0.20011	0.430000	0.31655	7.572000	0.82409	2.182000	0.69389	0.462000	0.41574	GAT	G|0.839;A|0.161	0.161	strong		0.612	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39149904	39149904	+	Silent	SNP	G	G	A	rs200999166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:39149904G>A	ENST00000297668.6	-	10	1621	c.1548C>T	c.(1546-1548)ctC>ctT	p.L516L	CNTNAP3_ENST00000377656.2_Silent_p.L516L|CNTNAP3_ENST00000358144.2_Silent_p.L428L|CNTNAP3_ENST00000323947.7_Intron|CNTNAP3_ENST00000377659.1_Silent_p.L516L	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	516	Laminin G-like 2. {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)		CAATGGTGATGAGCCTTAGGC	0.532													.|||	3	0.000599042	0.0	0.0014	5008	,	,		14869	0.0		0.002	False		,,,				2504	0.0				p.L516L		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.C1548T						PASS	.	G		0,4292		0,0,2146	10.0	11.0	11.0		1548	1.2	1.0	9		11	6,8376		0,6,4185	no	coding-synonymous	CNTNAP3	NM_033655.3		0,6,6331	AA,AG,GG		0.0716,0.0,0.0473		516/1289	39149904	6,12668	2146	4191	6337	SO:0001819	synonymous_variant	79937	exon10			GGTGATGAGCCTT	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.1548C>T	9.37:g.39149904G>A		Somatic	816	0	0		WXS	Illumina HiSeq	Phase_I	1008	254	0.251984	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			G|0.999;A|0.001	0.001	weak		0.532	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
PIGZ	80235	hgsc.bcm.edu	37	3	196674259	196674259	+	Silent	SNP	G	G	A	rs61179255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196674259G>A	ENST00000412723.1	-	3	1655	c.1509C>T	c.(1507-1509)acC>acT	p.T503T		NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	503					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)		CTGGTTGTCTGGTGAAGCTTT	0.647													G|||	528	0.105431	0.0151	0.0879	5008	,	,		16353	0.0694		0.1491	False		,,,				2504	0.2321				p.T503T		Atlas-SNP	.											.	PIGZ	34	.	0			c.C1509T						PASS	.	G		183,4223	117.1+/-155.0	1,181,2021	57.0	55.0	55.0		1509	4.2	0.9	3	dbSNP_129	55	1337,7263	259.2+/-282.6	108,1121,3071	yes	coding-synonymous	PIGZ	NM_025163.2		109,1302,5092	AA,AG,GG		15.5465,4.1534,11.6869		503/580	196674259	1520,11486	2203	4300	6503	SO:0001819	synonymous_variant	80235	exon3			TTGTCTGGTGAAG	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.1509C>T	3.37:g.196674259G>A		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	34	21	0.617647	NM_025163	Q9H9G6	Silent	SNP	ENST00000412723.1	37	CCDS3324.1																																																																																			G|0.889;A|0.111	0.111	strong		0.647	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
FCGR1B	2210	hgsc.bcm.edu	37	1	120934573	120934573	+	Missense_Mutation	SNP	C	C	T	rs201922049	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:120934573C>T	ENST00000369384.4	-	3	157	c.115G>A	c.(115-117)Gta>Ata	p.V39I	FCGR1B_ENST00000472543.1_5'UTR|FCGR1B_ENST00000369383.4_Intron|RP11-439A17.9_ENST00000457996.1_RNA|RP11-439A17.10_ENST00000426275.1_RNA	NM_001017986.3	NP_001017986.1	Q92637	FCGRB_HUMAN	Fc fragment of IgG, high affinity Ib, receptor (CD64)	39	Ig-like C2-type 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 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)	TGCAAGGTTACGGTTTCCTCT	0.502													C|||	712	0.142173	0.0068	0.1441	5008	,	,		18366	0.1567		0.1302	False		,,,				2504	0.3211				p.V39I		Atlas-SNP	.											FCGR1B,NS,carcinoma,0,1	FCGR1B	14	1	0			c.G115A						scavenged	.						1.0	1.0	1.0					1																	120934573		890	1911	2801	SO:0001583	missense	2210	exon3			AGGTTACGGTTTC		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.115G>A	1.37:g.120934573C>T	ENSP00000358391:p.Val39Ile	Somatic	605	0	0		WXS	Illumina HiSeq	Phase_I	576	115	0.199653	NM_001017986	Q7KZ13|Q92638	Missense_Mutation	SNP	ENST00000369384.4	37	CCDS30821.1	202|202	0.0924908424908425|0.0924908424908425	9|9	0.018292682926829267|0.018292682926829267	38|38	0.10497237569060773|0.10497237569060773	80|80	0.13986013986013987|0.13986013986013987	75|75	0.09894459102902374|0.09894459102902374	C|C	10.20|10.20	1.283913|1.283913	0.23392|0.23392	.|.	.|.	ENSG00000198019|ENSG00000198019	ENST00000369178|ENST00000369384	.|T	.|0.15256	.|2.44	2.44|2.44	2.44|2.44	0.29823|0.29823	.|Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.|0.000000	.|0.47093	.|D	.|0.000242	T|T	0.34600|0.34600	0.0903|0.0903	M|M	0.90870|0.90870	3.155|3.155	0.38349|0.38349	P|P	0.055703999999999976|0.055703999999999976	.|D;D;D	.|0.76494	.|0.994;0.999;0.995	.|D;D;D	.|0.81914	.|0.987;0.995;0.992	T|T	0.36648|0.36648	-0.9739|-0.9739	4|9	.|0.87932	.|D	.|0	.|.	8.522|8.522	0.33282|0.33282	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|39;39;39	.|P12314-2;Q92637-2;Q92637	.|.;.;FCGRB_HUMAN	H|I	23|39	.|ENSP00000358391:V39I	.|ENSP00000358391:V39I	R|V	-|-	2|1	0|0	FCGR1B|FCGR1B	120736096|120736096	0.033000|0.033000	0.19621|0.19621	0.069000|0.069000	0.20011|0.20011	0.050000|0.050000	0.14768|0.14768	0.924000|0.924000	0.28777|0.28777	1.692000|1.692000	0.51112|0.51112	0.184000|0.184000	0.17185|0.17185	CGT|GTA	.	.	weak		0.502	FCGR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098241.1		
DEPDC7	91614	hgsc.bcm.edu	37	11	33053107	33053107	+	Silent	SNP	C	C	T	rs966191	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:33053107C>T	ENST00000241051.3	+	5	1058	c.966C>T	c.(964-966)gaC>gaT	p.D322D	DEPDC7_ENST00000311388.3_Silent_p.D313D	NM_001077242.1	NP_001070710.1	Q96QD5	DEPD7_HUMAN	DEP domain containing 7	322					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)				endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17						ACTTATCTGACGTTCATAATG	0.373													C|||	1987	0.396765	0.4402	0.4553	5008	,	,		21448	0.4236		0.4105	False		,,,				2504	0.2546				p.D322D		Atlas-SNP	.											.	DEPDC7	94	.	0			c.C966T						PASS	.	C	,	1578,2102		331,916,593	88.0	83.0	85.0		966,939	-4.4	0.9	11	dbSNP_86	85	3291,4905		676,1939,1483	no	coding-synonymous,coding-synonymous	DEPDC7	NM_001077242.1,NM_139160.2	,	1007,2855,2076	TT,TC,CC		40.1537,42.8804,40.9987	,	322/512,313/503	33053107	4869,7007	1840	4098	5938	SO:0001819	synonymous_variant	91614	exon5			ATCTGACGTTCAT		CCDS41632.1, CCDS41633.1	11p13	2006-03-24			ENSG00000121690	ENSG00000121690			29899	protein-coding gene	gene with protein product		612294				10568747	Standard	NM_001077242		Approved		uc001mub.3	Q96QD5	OTTHUMG00000166242	ENST00000241051.3:c.966C>T	11.37:g.33053107C>T		Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	85	42	0.494118	NM_001077242	G5E941|Q8N602|Q8NCU9|Q9UGK5	Silent	SNP	ENST00000241051.3	37	CCDS41632.1																																																																																			C|0.588;T|0.412	0.412	strong		0.373	DEPDC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388655.1	NM_139160	
HIGD2A	192286	hgsc.bcm.edu	37	5	175815874	175815874	+	Silent	SNP	T	T	C	rs1060588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:175815874T>C	ENST00000274787.2	+	1	127	c.54T>C	c.(52-54)ccT>ccC	p.P18P	NOP16_ENST00000509257.1_5'Flank|NOP16_ENST00000507413.1_5'Flank|NOP16_ENST00000510123.1_5'Flank|NOP16_ENST00000389158.5_5'UTR	NM_138820.2	NP_620175.1	Q9BW72	HIG2A_HUMAN	HIG1 hypoxia inducible domain family, member 2A	18					negative regulation of apoptotic process (GO:0043066)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)				large_intestine(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	Kidney(146;0.0965)		CATCGAAGCCTCCAGTCATTG	0.582													T|||	398	0.0794728	0.1846	0.0648	5008	,	,		16148	0.0		0.0905	False		,,,				2504	0.0184				p.P18P		Atlas-SNP	.											.	HIGD2A	7	.	0			c.T54C						PASS	.	T		704,3702	270.7+/-269.8	46,612,1545	81.0	89.0	86.0		54	2.5	0.9	5	dbSNP_86	86	826,7774	179.5+/-228.6	41,744,3515	no	coding-synonymous	HIGD2A	NM_138820.2		87,1356,5060	CC,CT,TT		9.6047,15.9782,11.7638		18/107	175815874	1530,11476	2203	4300	6503	SO:0001819	synonymous_variant	192286	exon1			GAAGCCTCCAGTC	BC007502	CCDS4401.1	5q35.2	2009-03-17	2009-03-17		ENSG00000146066	ENSG00000146066			28311	protein-coding gene	gene with protein product			"""HIG1 domain family, member 2A"""			12477932	Standard	NM_138820		Approved	MGC2198	uc003meg.3	Q9BW72	OTTHUMG00000130657	ENST00000274787.2:c.54T>C	5.37:g.175815874T>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_138820		Silent	SNP	ENST00000274787.2	37	CCDS4401.1																																																																																			T|0.893;C|0.107	0.107	strong		0.582	HIGD2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253147.1	NM_138820	
ZNF256	10172	hgsc.bcm.edu	37	19	58453342	58453342	+	Silent	SNP	T	T	C	rs959231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58453342T>C	ENST00000282308.3	-	3	1030	c.834A>G	c.(832-834)caA>caG	p.Q278Q	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	278					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		GGCTAGAGCTTTGCCTATAGG	0.393													T|||	1336	0.266773	0.1596	0.3112	5008	,	,		24363	0.3145		0.3002	False		,,,				2504	0.2965				p.Q278Q	NSCLC(55;1313 1552 8040 11996)	Atlas-SNP	.											.	ZNF256	117	.	0			c.A834G						PASS	.	T		767,3639		72,623,1508	114.0	108.0	110.0		834	0.9	0.0	19	dbSNP_86	110	2549,6051		369,1811,2120	no	coding-synonymous	ZNF256	NM_005773.2		441,2434,3628	CC,CT,TT		29.6395,17.4081,25.4959		278/628	58453342	3316,9690	2203	4300	6503	SO:0001819	synonymous_variant	10172	exon3			AGAGCTTTGCCTA	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"""Zinc fingers, C2H2-type"", ""-"""	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.834A>G	19.37:g.58453342T>C		Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	127	127	1	NM_005773	B2RA92|Q53Y85|Q9BV71	Silent	SNP	ENST00000282308.3	37	CCDS12966.1																																																																																			T|0.741;C|0.259	0.259	strong		0.393	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1		
VAV3	10451	hgsc.bcm.edu	37	1	108319891	108319891	+	Silent	SNP	A	A	G	rs17020006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:108319891A>G	ENST00000370056.4	-	4	682	c.408T>C	c.(406-408)aaT>aaC	p.N136N	VAV3_ENST00000527011.1_Silent_p.N136N|VAV3_ENST00000343258.4_5'UTR|AL591042.1_ENST00000579317.1_RNA|VAV3_ENST00000371846.4_Silent_p.N71N	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	136					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TGTCTTCATCATTAATGCTTT	0.383													A|||	37	0.00738818	0.0061	0.0043	5008	,	,		19347	0.0198		0.005	False		,,,				2504	0.001				p.N136N		Atlas-SNP	.											.	VAV3	176	.	0			c.T408C						PASS	.	A		20,4386	27.2+/-55.0	0,20,2183	130.0	128.0	129.0		408	-1.2	0.0	1	dbSNP_123	129	55,8545	35.9+/-90.5	1,53,4246	no	coding-synonymous	VAV3	NM_006113.4		1,73,6429	GG,GA,AA		0.6395,0.4539,0.5767		136/848	108319891	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	10451	exon4			TTCATCATTAATG	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.408T>C	1.37:g.108319891A>G		Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	113	54	0.477876	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Silent	SNP	ENST00000370056.4	37	CCDS785.1	24	0.01098901098901099	1	0.0020325203252032522	3	0.008287292817679558	16	0.027972027972027972	4	0.005277044854881266	A	3.803	-0.041247	0.07452	0.004539	0.006395	ENSG00000134215	ENST00000490388	.	.	.	5.64	-1.21	0.09524	.	.	.	.	.	T	0.38480	0.1042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35624	-0.9781	4	.	.	.	.	8.2294	0.31589	0.5499:0.103:0.3471:0.0	rs17020006;rs17020006	.	.	.	T	131	.	.	M	-	2	0	VAV3	108121414	0.025000	0.19082	0.033000	0.17914	0.676000	0.39594	-0.143000	0.10296	-0.464000	0.06963	-1.139000	0.01908	ATG	A|0.992;G|0.008	0.008	strong		0.383	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
TYRO3	7301	hgsc.bcm.edu	37	15	41862356	41862356	+	Splice_Site	SNP	T	T	C	rs149022093		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:41862356T>C	ENST00000263798.3	+	10	1606		c.e10+2		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GCGGTTTGGGTAAGGGGATGG	0.567																																					.		Atlas-SNP	.											TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	0			c.1382+2T>C						PASS	.						76.0	75.0	75.0					15																	41862356		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon10			TTTGGGTAAGGGG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1382+2T>C	15.37:g.41862356T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	119	8	0.0672269	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.181954	0.78677	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3401	0.74290	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39649648	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.789000	0.75110	2.208000	0.71279	0.533000	0.62120	.	.	.	weak		0.567	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron
ZNF782	158431	hgsc.bcm.edu	37	9	99581882	99581882	+	Silent	SNP	C	C	T	rs35658789	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:99581882C>T	ENST00000481138.1	-	6	1084	c.423G>A	c.(421-423)gcG>gcA	p.A141A	ZNF782_ENST00000535338.1_Silent_p.A9A|ZNF782_ENST00000466833.1_5'UTR	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	141					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				AAGCAGACCCCGCAATGTCAC	0.418													C|||	51	0.0101837	0.0129	0.0144	5008	,	,		18056	0.0		0.0149	False		,,,				2504	0.0092				p.A141A		Atlas-SNP	.											.	ZNF782	64	.	0			c.G423A						PASS	.	C		53,4353	54.2+/-90.2	0,53,2150	104.0	106.0	105.0		423	-1.9	0.0	9	dbSNP_126	105	163,8437	76.6+/-139.3	1,161,4138	no	coding-synonymous	ZNF782	NM_001001662.1		1,214,6288	TT,TC,CC		1.8953,1.2029,1.6608		141/700	99581882	216,12790	2203	4300	6503	SO:0001819	synonymous_variant	158431	exon6			AGACCCCGCAATG	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.423G>A	9.37:g.99581882C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	174	84	0.482759	NM_001001662	B2RNR0	Silent	SNP	ENST00000481138.1	37	CCDS35075.1	25	0.011446886446886446	5	0.01016260162601626	5	0.013812154696132596	0	0.0	15	0.01978891820580475	C	3.083	-0.188585	0.06299	0.012029	0.018953	ENSG00000196597	ENST00000289032	.	.	.	3.4	-1.91	0.07641	.	.	.	.	.	T	0.10551	0.0258	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23084	-1.0198	4	.	.	.	.	3.0802	0.06260	0.3047:0.2032:0.0:0.4921	rs35658789	.	.	.	R	130	.	.	G	-	1	0	ZNF782	98621703	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.289000	0.02780	-0.376000	0.07943	-1.188000	0.01700	GGG	C|0.984;T|0.016	0.016	strong		0.418	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
DHRS9	10170	hgsc.bcm.edu	37	2	169952233	169952233	+	Silent	SNP	T	T	C	rs1059261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:169952233T>C	ENST00000327239.4	+	8	2420	c.916T>C	c.(916-918)Ttg>Ctg	p.L306L	DHRS9_ENST00000357546.2_Silent_p.L306L|DHRS9_ENST00000436483.2_Silent_p.L306L|DHRS9_ENST00000602501.1_Silent_p.L306L|DHRS9_ENST00000412271.1_Silent_p.L306L|DHRS9_ENST00000432060.2_Silent_p.L366L|DHRS9_ENST00000421653.1_Silent_p.L159L|DHRS9_ENST00000428522.1_Silent_p.L306L	NM_005771.4	NP_005762.2	Q9BPW9	DHRS9_HUMAN	dehydrogenase/reductase (SDR family) member 9	306					9-cis-retinoic acid biosynthetic process (GO:0042904)|androgen metabolic process (GO:0008209)|epithelial cell differentiation (GO:0030855)|progesterone metabolic process (GO:0042448)|retinol metabolic process (GO:0042572)	integral component of endoplasmic reticulum membrane (GO:0030176)	alcohol dehydrogenase (NAD) activity (GO:0004022)|racemase and epimerase activity (GO:0016854)|retinol dehydrogenase activity (GO:0004745)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			breast(1)|endometrium(3)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	13						AGACTTTTTATTGTTGAAACA	0.438													T|||	1376	0.27476	0.4221	0.2522	5008	,	,		20683	0.3214		0.1799	False		,,,				2504	0.1411				p.L306L		Atlas-SNP	.											.	DHRS9	29	.	0			c.T916C						PASS	.	T	,,,	1618,2788	501.5+/-365.0	296,1026,881	81.0	80.0	80.0		916,916,916,916	0.8	1.0	2	dbSNP_86	80	1728,6872	315.3+/-312.2	178,1372,2750	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DHRS9	NM_001142270.1,NM_001142271.1,NM_005771.4,NM_199204.1	,,,	474,2398,3631	CC,CT,TT		20.093,36.7227,25.7266	,,,	306/320,306/320,306/320,306/320	169952233	3346,9660	2203	4300	6503	SO:0001819	synonymous_variant	10170	exon8			TTTTTATTGTTGA	AF067174	CCDS2231.1, CCDS74600.1	2q31.1	2011-09-14			ENSG00000073737	ENSG00000073737		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	16888	protein-coding gene	gene with protein product	"""NADP-dependent retinol dehydrogenase/reductase"", ""3-alpha hydroxysteroid dehydrogenase"", ""retinol dehydrogenase homolog"", ""short chain dehydrogenase/reductase family 9C, member 4"""	612131				11304534, 11294878, 19027726	Standard	NM_001142270		Approved	RDHL, 3alpha-HSD, RETSDR8, RDH15, SDR9C4	uc010zde.2	Q9BPW9	OTTHUMG00000132180	ENST00000327239.4:c.916T>C	2.37:g.169952233T>C		Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	168	85	0.505952	NM_005771	B7Z416|D3DPC1|Q5RKX1|Q9NRA9|Q9NRB0	Silent	SNP	ENST00000327239.4	37	CCDS2231.1																																																																																			T|0.732;C|0.268	0.268	strong		0.438	DHRS9-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333612.3	NM_005771	
FAM177A1	283635	hgsc.bcm.edu	37	14	35546373	35546373	+	Silent	SNP	T	T	C	rs3211139	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:35546373T>C	ENST00000382406.3	+	4	345	c.288T>C	c.(286-288)ggT>ggC	p.G96G	FAM177A1_ENST00000396472.1_Silent_p.G96G|FAM177A1_ENST00000280987.4_Silent_p.G119G			Q8N128	F177A_HUMAN	family with sequence similarity 177, member A1	96										breast(1)|large_intestine(1)|lung(2)|urinary_tract(1)	5						TTACCTGGGGTCCCTACTTAT	0.373													C|||	707	0.141174	0.2292	0.1066	5008	,	,		18771	0.0327		0.1272	False		,,,				2504	0.1728				p.G119G		Atlas-SNP	.											.	FAM177A1	9	.	0			c.T357C						PASS	.	C	,	953,3453	734.7+/-410.6	111,731,1361	265.0	247.0	253.0		288,357	0.1	1.0	14	dbSNP_116	253	1312,7288	757.8+/-407.5	103,1106,3091	no	coding-synonymous,coding-synonymous	FAM177A1	NM_001079519.1,NM_173607.3	,	214,1837,4452	CC,CT,TT		15.2558,21.6296,17.415	,	96/214,119/237	35546373	2265,10741	2203	4300	6503	SO:0001819	synonymous_variant	283635	exon3			CTGGGGTCCCTAC	BG722411	CCDS9653.2, CCDS41944.1	14q13.2	2008-07-09	2008-07-09	2008-07-09	ENSG00000151327	ENSG00000151327			19829	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 24"""	C14orf24			Standard	NM_001079519		Approved		uc001wsq.3	Q8N128	OTTHUMG00000140217	ENST00000382406.3:c.288T>C	14.37:g.35546373T>C		Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	179	68	0.379888	NM_173607	Q68CT2	Silent	SNP	ENST00000382406.3	37	CCDS41944.1																																																																																			T|0.844;C|0.156	0.156	strong		0.373	FAM177A1-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410816.1	NM_173607	
TRIM26	7726	hgsc.bcm.edu	37	6	30154049	30154049	+	Silent	SNP	G	G	A	rs16897204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30154049G>A	ENST00000454678.2	-	10	1660	c.1224C>T	c.(1222-1224)gaC>gaT	p.D408D	TRIM26_ENST00000453195.1_Silent_p.D408D|TRIM26_ENST00000437089.1_Silent_p.D408D	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	408	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			lung(1)|ovary(2)	3						TTTCCCAGTCGTCATATCCAT	0.567													G|||	95	0.0189696	0.003	0.0216	5008	,	,		19480	0.002		0.0656	False		,,,				2504	0.0082				p.D408D		Atlas-SNP	.											.	TRIM26	74	.	0			c.C1224T						PASS	.	G	,	24,2996		0,24,1486	138.0	76.0	98.0		1224,1224	-10.1	0.0	6	dbSNP_123	98	278,5140		7,264,2438	yes	coding-synonymous,coding-synonymous	TRIM26	NM_001242783.1,NM_003449.4	,	7,288,3924	AA,AG,GG		5.131,0.7947,3.579	,	408/540,408/540	30154049	302,8136	1510	2709	4219	SO:0001819	synonymous_variant	7726	exon9			CCAGTCGTCATAT	AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.1224C>T	6.37:g.30154049G>A		Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	122	57	0.467213	NM_001242783	A6NG96|Q5SRL2	Silent	SNP	ENST00000454678.2	37	CCDS4678.1																																																																																			G|0.968;A|0.032	0.032	strong		0.567	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
XRCC2	7516	hgsc.bcm.edu	37	7	152346007	152346007	+	Missense_Mutation	SNP	C	C	T	rs3218536	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:152346007C>T	ENST00000359321.1	-	3	648	c.563G>A	c.(562-564)cGc>cAc	p.R188H	XRCC2_ENST00000495707.1_5'UTR	NM_005431.1	NP_005422.1	O43543	XRCC2_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 2	188			R -> H (in dbSNP:rs3218536). {ECO:0000269|Ref.4}.		centrosome organization (GO:0051297)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of neurogenesis (GO:0050769)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|strand invasion (GO:0042148)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|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)			NS(1)|breast(1)|large_intestine(5)|liver(1)|lung(1)|prostate(2)	11		all_hematologic(28;0.0592)|Prostate(32;0.081)	OV - Ovarian serous cystadenocarcinoma(82;0.0423)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0429)		AAGAACCAGGCGATAGTCATT	0.448								Homologous recombination					C|||	263	0.052516	0.0076	0.0461	5008	,	,		18392	0.002		0.1004	False		,,,				2504	0.1207				p.R188H		Atlas-SNP	.											.	XRCC2	30	.	0			c.G563A	GRCh37	CM021368	XRCC2	M	rs3218536	PASS	.	C	HIS/ARG	61,4345	58.1+/-94.6	0,61,2142	129.0	132.0	131.0		563	1.9	1.0	7	dbSNP_106	131	665,7935	168.0+/-219.6	24,617,3659	yes	missense	XRCC2	NM_005431.1	29	24,678,5801	TT,TC,CC		7.7326,1.3845,5.582	benign	188/281	152346007	726,12280	2203	4300	6503	SO:0001583	missense	7516	exon3			ACCAGGCGATAGT	Y08837	CCDS5933.1	7q36	2006-05-04			ENSG00000196584	ENSG00000196584			12829	protein-coding gene	gene with protein product	"""RAD51-like"""	600375				7607692, 10422536	Standard	NM_005431		Approved		uc003wld.3	O43543	OTTHUMG00000151470	ENST00000359321.1:c.563G>A	7.37:g.152346007C>T	ENSP00000352271:p.Arg188His	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	84	33	0.392857	NM_005431	B2R925	Missense_Mutation	SNP	ENST00000359321.1	37	CCDS5933.1	93	0.042582417582417584	6	0.012195121951219513	19	0.052486187845303865	0	0.0	68	0.08970976253298153	C	5.732	0.319507	0.10845	0.013845	0.077326	ENSG00000196584	ENST00000359321	T	0.65916	-0.18	5.06	1.85	0.25348	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.374735	0.30269	N	0.010002	T	0.01489	0.0048	N	0.11927	0.2	0.28617	P	0.908374	B	0.20671	0.047	B	0.14578	0.011	T	0.04090	-1.0978	9	0.31617	T	0.26	-14.1329	5.3045	0.15795	0.0:0.4388:0.0:0.5612	rs3218536;rs61094667;rs3218536	188	O43543	XRCC2_HUMAN	H	188	ENSP00000352271:R188H	ENSP00000352271:R188H	R	-	2	0	XRCC2	151976940	0.998000	0.40836	0.987000	0.45799	0.327000	0.28475	1.550000	0.36223	0.556000	0.29098	-0.363000	0.07495	CGC	C|0.949;T|0.051	0.051	strong		0.448	XRCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322783.1	NM_005431	
CNTN3	5067	hgsc.bcm.edu	37	3	74344356	74344356	+	Silent	SNP	T	T	G	rs10490832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:74344356T>G	ENST00000263665.6	-	18	2460	c.2433A>C	c.(2431-2433)gcA>gcC	p.A811A		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	811	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ATAGGCTATTTGCAGAGACTT	0.388													T|||	445	0.0888578	0.0068	0.0706	5008	,	,		18103	0.0288		0.1421	False		,,,				2504	0.2198				p.A811A		Atlas-SNP	.											.	CNTN3	174	.	0			c.A2433C						PASS	.	T		139,4267	98.0+/-136.7	4,131,2068	100.0	93.0	95.0		2433	-2.5	0.2	3	dbSNP_119	95	1410,7190	270.5+/-289.0	131,1148,3021	yes	coding-synonymous	CNTN3	NM_020872.1		135,1279,5089	GG,GT,TT		16.3953,3.1548,11.9099		811/1029	74344356	1549,11457	2203	4300	6503	SO:0001819	synonymous_variant	5067	exon18			GCTATTTGCAGAG	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2433A>C	3.37:g.74344356T>G		Somatic	105	0	0		WXS	Illumina HiSeq	Phase_I	113	56	0.495575	NM_020872	B9EK50|Q9H039	Silent	SNP	ENST00000263665.6	37	CCDS33790.1																																																																																			T|0.912;G|0.088	0.088	strong		0.388	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
HSPA2	3306	hgsc.bcm.edu	37	14	65008251	65008251	+	Silent	SNP	C	C	T	rs1063391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:65008251C>T	ENST00000394709.1	+	2	760	c.684C>T	c.(682-684)gaC>gaT	p.D228D	HSPA2_ENST00000554883.1_3'UTR|HSPA2_ENST00000247207.6_Silent_p.D228D|RP11-973N13.4_ENST00000554918.1_RNA			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	228					male meiosis (GO:0007140)|male meiosis I (GO:0007141)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G2/M transition of mitotic cell cycle (GO:0031662)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)|spermatid development (GO:0007286)|synaptonemal complex disassembly (GO:0070194)	blood microparticle (GO:0072562)|CatSper complex (GO:0036128)|cell surface (GO:0009986)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycolipid binding (GO:0051861)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	22				all cancers(60;0.00515)|OV - Ovarian serous cystadenocarcinoma(108;0.00584)|BRCA - Breast invasive adenocarcinoma(234;0.045)		CGGCCGGCGACACCCACCTGG	0.602													C|||	3268	0.652556	0.3956	0.696	5008	,	,		18230	0.8601		0.6819	False		,,,				2504	0.7249				p.D228D	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											HSPA2,right_upper_lobe,carcinoma,+1,1	HSPA2	83	1	0			c.C684T						PASS	.	C		1935,2471	548.2+/-377.5	446,1043,714	62.0	66.0	65.0		684	3.4	1.0	14	dbSNP_86	65	5877,2723	679.6+/-403.6	2002,1873,425	no	coding-synonymous	HSPA2	NM_021979.3		2448,2916,1139	TT,TC,CC		31.6628,43.9174,39.9354		228/640	65008251	7812,5194	2203	4300	6503	SO:0001819	synonymous_variant	3306	exon1			CGGCGACACCCAC	L26336, BC001752	CCDS9766.1	14q23	2012-10-02	2002-08-29		ENSG00000126803	ENSG00000126803		"""Heat shock proteins / HSP70"""	5235	protein-coding gene	gene with protein product		140560	"""heat shock 70kD protein 2"""				Standard	NM_021979		Approved		uc001xhk.4	P54652	OTTHUMG00000141311	ENST00000394709.1:c.684C>T	14.37:g.65008251C>T		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	69	35	0.507246	NM_021979	Q15508|Q53XM3|Q9UE78	Silent	SNP	ENST00000394709.1	37	CCDS9766.1																																																																																			C|0.368;T|0.632	0.632	strong		0.602	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1		
PIK3CD	5293	hgsc.bcm.edu	37	1	9784423	9784423	+	Silent	SNP	C	C	T	rs11121484	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:9784423C>T	ENST00000377346.4	+	22	3003	c.2808C>T	c.(2806-2808)taC>taT	p.Y936Y	PIK3CD_ENST00000361110.2_Silent_p.Y960Y|PIK3CD_ENST00000536656.1_Silent_p.Y960Y	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	936	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				adaptive immune response (GO:0002250)|B cell activation (GO:0042113)|B cell chemotaxis (GO:0035754)|B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|cytokine production (GO:0001816)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell chemotaxis (GO:0002551)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|natural killer cell activation (GO:0030101)|natural killer cell chemotaxis (GO:0035747)|natural killer cell differentiation (GO:0001779)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein phosphorylation (GO:0006468)|respiratory burst involved in defense response (GO:0002679)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|mast cell granule (GO:0042629)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31	all_lung(157;0.222)	all_lung(118;2.44e-05)|Lung NSC(185;4.08e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00314)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0231)|Colorectal(212;7.52e-08)|COAD - Colon adenocarcinoma(227;1.78e-05)|Kidney(185;0.000322)|KIRC - Kidney renal clear cell carcinoma(229;0.00114)|BRCA - Breast invasive adenocarcinoma(304;0.0021)|STAD - Stomach adenocarcinoma(132;0.00395)|READ - Rectum adenocarcinoma(331;0.0419)	Caffeine(DB00201)	TCCTCACCTACGACTTTGTCC	0.517													T|||	1532	0.305911	0.5983	0.219	5008	,	,		21084	0.131		0.0755	False		,,,				2504	0.3896				p.Y936Y		Atlas-SNP	.											.	PIK3CD	86	.	0			c.C2808T						PASS	.	T		2271,2135	578.2+/-384.6	588,1095,520	104.0	117.0	113.0		2808	-3.2	1.0	1	dbSNP_120	113	727,7873	786.7+/-407.6	33,661,3606	no	coding-synonymous	PIK3CD	NM_005026.3		621,1756,4126	TT,TC,CC		8.4535,48.4567,23.0509		936/1045	9784423	2998,10008	2203	4300	6503	SO:0001819	synonymous_variant	5293	exon22			CACCTACGACTTT		CCDS104.1	1p36.2	2014-09-17	2012-07-13		ENSG00000171608	ENSG00000171608	2.7.1.153		8977	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase, catalytic, delta polypeptide"", ""phosphoinositide-3-kinase C"""	602839	"""phosphoinositide-3-kinase, catalytic, delta polypeptide"""			9113989, 9455486	Standard	NM_005026		Approved	p110D	uc001aqb.4	O00329	OTTHUMG00000001450	ENST00000377346.4:c.2808C>T	1.37:g.9784423C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	136	11	0.0808824	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Silent	SNP	ENST00000377346.4	37	CCDS104.1																																																																																			C|0.800;T|0.200	0.200	strong		0.517	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026	
PKP1	5317	hgsc.bcm.edu	37	1	201288955	201288955	+	Missense_Mutation	SNP	G	G	A	rs1626370	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201288955G>A	ENST00000352845.3	+	7	1244	c.1244G>A	c.(1243-1245)gGc>gAc	p.G415D	PKP1_ENST00000367324.3_Intron|PKP1_ENST00000263946.3_Missense_Mutation_p.G415D|PKP1_ENST00000475988.1_3'UTR			Q13835	PKP1_HUMAN	plakophilin 1	415			G -> D (in dbSNP:rs1626370).		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						AAGAGACTGGGCATGCGGGAG	0.612													G|||	788	0.157348	0.0923	0.1859	5008	,	,		18069	0.2302		0.1988	False		,,,				2504	0.1074				p.G415D		Atlas-SNP	.											.	PKP1	127	.	0			c.G1244A						PASS	.	G	ASP/GLY,	432,3974	209.2+/-230.0	20,392,1791	72.0	73.0	73.0		1244,	1.9	0.0	1	dbSNP_89	73	1821,6779	328.4+/-318.3	192,1437,2671	yes	missense,intron	PKP1	NM_000299.3,NM_001005337.2	94,	212,1829,4462	AA,AG,GG		21.1744,9.8048,17.3228	,	415/748,	201288955	2253,10753	2203	4300	6503	SO:0001583	missense	5317	exon7			GACTGGGCATGCG	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.1244G>A	1.37:g.201288955G>A	ENSP00000295597:p.Gly415Asp	Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	25	9	0.36	NM_000299	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	389	0.17811355311355312	59	0.11991869918699187	60	0.16574585635359115	125	0.21853146853146854	145	0.19129287598944592	G	0.383	-0.927896	0.02377	0.098048	0.211744	ENSG00000081277	ENST00000263946;ENST00000352845	T;T	0.75154	-0.91;-0.91	2.9	1.92	0.25849	Armadillo-like helical (1);Armadillo-type fold (1);	8.226640	0.01544	U	0.019377	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.31893	0.345	B	0.22601	0.04	T	0.07347	-1.0777	9	0.54805	T	0.06	-23.9375	7.3593	0.26737	0.0:0.2733:0.7267:0.0	rs1626370;rs52796338;rs58820226;rs1626370	415	Q13835	PKP1_HUMAN	D	415	ENSP00000263946:G415D;ENSP00000295597:G415D	ENSP00000263946:G415D	G	+	2	0	PKP1	199555578	0.000000	0.05858	0.004000	0.12327	0.056000	0.15407	0.116000	0.15561	0.391000	0.25143	0.491000	0.48974	GGC	G|0.825;A|0.175	0.175	strong		0.612	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
CFAP46	54777	hgsc.bcm.edu	37	10	134680995	134680995	+	Missense_Mutation	SNP	C	C	T	rs150661681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134680995C>T	ENST00000368586.5	-	34	4727	c.4627G>A	c.(4627-4629)Gcg>Acg	p.A1543T		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TTTTTCAACGCGATCTCTTTT	0.458													C|||	46	0.0091853	0.0	0.0072	5008	,	,		16700	0.002		0.0129	False		,,,				2504	0.0266				p.A1543T		Atlas-SNP	.											.	TTC40	100	.	0			c.G4627A						PASS	.																																			SO:0001583	missense	54777	exon34			TCAACGCGATCTC																												ENST00000368586.5:c.4627G>A	10.37:g.134680995C>T	ENSP00000357575:p.Ala1543Thr	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	2.465	-0.323251	0.05350	.	.	ENSG00000171811	ENST00000368586	T	0.10960	2.82	4.08	2.18	0.27775	.	.	.	.	.	T	0.07863	0.0197	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.24297	-1.0164	6	0.54805	T	0.06	.	5.1014	0.14762	0.0:0.6678:0.216:0.1161	.	.	.	.	T	1543	ENSP00000357575:A1543T	ENSP00000357575:A1543T	A	-	1	0	C10orf93	134530985	0.010000	0.17322	0.186000	0.23195	0.034000	0.12701	0.119000	0.15626	1.044000	0.40200	0.585000	0.79938	GCG	C|0.993;T|0.007	0.007	strong		0.458	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
ACACB	32	hgsc.bcm.edu	37	12	109693982	109693982	+	Silent	SNP	C	C	T	rs3742023	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109693982C>T	ENST00000338432.7	+	45	6323	c.6204C>T	c.(6202-6204)caC>caT	p.H2068H	ACACB_ENST00000543201.1_Silent_p.H734H|ACACB_ENST00000377848.3_Silent_p.H2068H|ACACB_ENST00000377854.5_Silent_p.H1998H			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	2068	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TCTTTGACCACGGCAGTTTCA	0.607													C|||	1278	0.255192	0.1241	0.2709	5008	,	,		17499	0.2817		0.3777	False		,,,				2504	0.2679				p.H2068H		Atlas-SNP	.											.	ACACB	330	.	0			c.C6204T						PASS	.	C		675,3731	284.9+/-277.9	58,559,1586	72.0	66.0	68.0		6204	-3.5	0.9	12	dbSNP_107	68	3088,5512	473.1+/-368.5	550,1988,1762	no	coding-synonymous	ACACB	NM_001093.3		608,2547,3348	TT,TC,CC		35.907,15.32,28.9328		2068/2459	109693982	3763,9243	2203	4300	6503	SO:0001819	synonymous_variant	32	exon44			TGACCACGGCAGT	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.6204C>T	12.37:g.109693982C>T		Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	145	69	0.475862	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.719;T|0.281	0.281	strong		0.607	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
UVSSA	57654	hgsc.bcm.edu	37	4	1374695	1374695	+	Silent	SNP	C	C	A	rs28614045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1374695C>A	ENST00000389851.4	+	12	2227	c.1780C>A	c.(1780-1782)Cgg>Agg	p.R594R	UVSSA_ENST00000507531.1_Silent_p.R594R|UVSSA_ENST00000511563.1_Silent_p.R145R|UVSSA_ENST00000512728.1_Silent_p.R145R|UVSSA_ENST00000511216.1_Silent_p.R594R	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	594					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										GATTGTTCCACGGGACGACGA	0.682													A|||	3507	0.70028	0.702	0.7781	5008	,	,		18903	0.7004		0.665	False		,,,				2504	0.6789				p.R594R		Atlas-SNP	.											KIAA1530,NS,carcinoma,0,1	.	.	1	0			c.C1780A						PASS	.	A		3125,1279	431.8+/-343.0	1126,873,203	67.0	64.0	65.0		1780	3.5	0.1	4	dbSNP_125	65	5861,2739	433.6+/-357.5	2001,1859,440	no	coding-synonymous	KIAA1530	NM_020894.2		3127,2732,643	AA,AC,CC		31.8488,29.0418,30.8982		594/710	1374695	8986,4018	2202	4300	6502	SO:0001819	synonymous_variant	57654	exon12			GTTCCACGGGACG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1780C>A	4.37:g.1374695C>A		Somatic	305	1	0.00327869		WXS	Illumina HiSeq	Phase_I	321	151	0.470405	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			C|0.306;A|0.694	0.694	strong		0.682	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
NPR2	4882	hgsc.bcm.edu	37	9	35792423	35792423	+	Silent	SNP	T	T	C	rs2228580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35792423T>C	ENST00000342694.2	+	1	273	c.18T>C	c.(16-18)ctT>ctC	p.L6L		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	6					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	TGCCATCACTTCTGCTGTTGG	0.677													C|||	1570	0.313498	0.4985	0.2334	5008	,	,		12482	0.3819		0.2028	False		,,,				2504	0.1636				p.L6L		Atlas-SNP	.											.	NPR2	162	.	0			c.T18C						PASS	.	C		2004,2400		469,1066,667	21.0	23.0	22.0		18	2.2	1.0	9	dbSNP_98	22	1743,6853		170,1403,2725	no	coding-synonymous	NPR2	NM_003995.3		639,2469,3392	CC,CT,TT		20.2769,45.5041,28.8231		6/1048	35792423	3747,9253	2202	4298	6500	SO:0001819	synonymous_variant	4882	exon1			ATCACTTCTGCTG	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.18T>C	9.37:g.35792423T>C		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	38	0.4	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1																																																																																			T|0.691;C|0.309	0.309	strong		0.677	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
FCHSD1	89848	hgsc.bcm.edu	37	5	141021108	141021108	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:141021108G>A	ENST00000435817.2	-	20	2080	c.2030C>T	c.(2029-2031)cCg>cTg	p.P677L	FCHSD1_ENST00000523856.1_5'UTR|FCHSD1_ENST00000522126.1_3'UTR|FCHSD1_ENST00000522783.1_3'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	677	Pro-rich.								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)			GGCTTTAGCCGGCGGGGGAGG	0.587																																					p.P677L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C2030T						PASS	.						37.0	45.0	42.0					5																	141021108		1941	4133	6074	SO:0001583	missense	89848	exon20			TTAGCCGGCGGGG	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.2030C>T	5.37:g.141021108G>A	ENSP00000399259:p.Pro677Leu	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	112	62	0.553571	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.401255	0.62288	.	.	ENSG00000197948	ENST00000435817	T	0.28454	1.61	5.25	5.25	0.73442	.	0.143676	0.48286	D	0.000182	T	0.44787	0.1310	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.31475	-0.9942	10	0.72032	D	0.01	-9.0948	14.5305	0.67923	0.0:0.0:1.0:0.0	.	357;677	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	L	677	ENSP00000399259:P677L	ENSP00000399259:P677L	P	-	2	0	FCHSD1	141001292	0.998000	0.40836	0.831000	0.32960	0.910000	0.53928	4.883000	0.63128	2.885000	0.99019	0.655000	0.94253	CCG	.	.	none		0.587	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
KALRN	8997	hgsc.bcm.edu	37	3	124181454	124181454	+	Silent	SNP	C	C	T	rs2289839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124181454C>T	ENST00000240874.3	+	25	4156	c.3999C>T	c.(3997-3999)atC>atT	p.I1333I	KALRN_ENST00000460856.1_Silent_p.I1324I|KALRN_ENST00000360013.3_Silent_p.I1333I	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1333	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						TTGGCAACATCCAAGAGATCT	0.478													C|||	278	0.0555112	0.0113	0.0418	5008	,	,		18784	0.131		0.0517	False		,,,				2504	0.0511				p.I1333I		Atlas-SNP	.											.	KALRN	556	.	0			c.C3999T						PASS	.	C	,	85,4321	72.0+/-110.0	1,83,2119	86.0	78.0	81.0		3999,3999	5.4	1.0	3	dbSNP_100	81	478,8122	139.5+/-196.2	14,450,3836	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	15,533,5955	TT,TC,CC		5.5581,1.9292,4.3288	,	1333/2987,1333/1664	124181454	563,12443	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon25			CAACATCCAAGAG	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.3999C>T	3.37:g.124181454C>T		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	82	46	0.560976	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	124	0.056776556776556776	7	0.014227642276422764	15	0.04143646408839779	71	0.12412587412587413	31	0.040897097625329816	C	10.31	1.315409	0.23908	0.019292	0.055581	ENSG00000160145	ENST00000354186	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22591	-1.0212	3	.	.	.	.	9.4037	0.38449	0.0:0.8424:0.0:0.1576	rs2289839;rs61373308;rs2289839	.	.	.	F	1302	.	.	S	+	2	0	KALRN	125664144	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.153000	0.31676	2.826000	0.97356	0.655000	0.94253	TCC	C|0.950;T|0.050	0.050	strong		0.478	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
TSC1	7248	hgsc.bcm.edu	37	9	135786904	135786904	+	Missense_Mutation	SNP	A	A	G	rs1073123	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135786904A>G	ENST00000298552.3	-	10	1186	c.965T>C	c.(964-966)aTg>aCg	p.M322T	TSC1_ENST00000403810.1_Missense_Mutation_p.M322T|TSC1_ENST00000545250.1_Missense_Mutation_p.M271T|TSC1_ENST00000440111.2_Missense_Mutation_p.M322T	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	322			M -> T (in dbSNP:rs1073123). {ECO:0000269|PubMed:10533067, ECO:0000269|PubMed:10570911, ECO:0000269|PubMed:10607950, ECO:0000269|PubMed:9328481, 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)		CTGCCCTGGCATATTTAACAA	0.493			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				G|||	677	0.135184	0.2337	0.0937	5008	,	,		15968	0.0744		0.1312	False		,,,				2504	0.0982				p.M322T		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.T965C						PASS	.	G	THR/MET,THR/MET,THR/MET	967,3439	734.0+/-410.5	117,733,1353	166.0	145.0	152.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	965,965,812	3.0	0.0	9	dbSNP_86	152	1185,7415	764.1+/-407.6	93,999,3208	yes	missense,missense,missense	TSC1	NM_000368.4,NM_001162426.1,NM_001162427.1	81,81,81	210,1732,4561	GG,GA,AA		13.7791,21.9473,16.5462	benign,benign,benign	322/1165,322/1164,271/1114	135786904	2152,10854	2203	4300	6503	SO:0001583	missense	7248	exon10	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CCTGGCATATTTA	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.965T>C	9.37:g.135786904A>G	ENSP00000298552:p.Met322Thr	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	110	109	0.990909	NM_000368	B7Z897|Q5VVN5	Missense_Mutation	SNP	ENST00000298552.3	37	CCDS6956.1	299	0.13690476190476192	116	0.23577235772357724	39	0.10773480662983426	37	0.06468531468531469	107	0.14116094986807387	G	0.299	-0.975294	0.02215	0.219473	0.137791	ENSG00000165699	ENST00000298552;ENST00000440111;ENST00000545250;ENST00000537172;ENST00000424271;ENST00000403810	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-1.91;-2.04	5.79	2.95	0.34219	.	0.355274	0.36134	N	0.002766	T	0.00039	0.0001	N	0.01267	-0.92	0.80722	P	0.0	B;B;B;B;B;B	0.12630	0.006;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.002;0.0;0.001;0.002;0.001;0.0	T	0.09271	-1.0682	9	0.02654	T	1	-1.4519	7.1757	0.25742	0.3837:0.0:0.6163:0.0	rs1073123;rs4621943;rs56594598;rs59426674;rs1073123	201;271;322;322;322;322	B7Z604;B7Z897;Q86WV8;Q59IT9;Q32NF0;Q92574	.;.;.;.;.;TSC1_HUMAN	T	322;322;271;201;201;322	ENSP00000298552:M322T;ENSP00000394524:M322T;ENSP00000444017:M271T;ENSP00000438099:M201T;ENSP00000386093:M322T	ENSP00000298552:M322T	M	-	2	0	TSC1	134776725	0.406000	0.25344	0.009000	0.14445	0.955000	0.61496	1.378000	0.34328	0.818000	0.34468	-0.726000	0.03593	ATG	A|0.859;C|0.001	.	strong		0.493	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
GALNT3	2591	hgsc.bcm.edu	37	2	166621413	166621413	+	Silent	SNP	C	C	T	rs13423840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:166621413C>T	ENST00000392701.3	-	3	1444	c.669G>A	c.(667-669)gtG>gtA	p.V223V	GALNT3_ENST00000409882.1_5'Flank	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	223	Catalytic subdomain A.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						TAGCATCATCCACCAAAATGA	0.393													t|||	50	0.00998403	0.034	0.0072	5008	,	,		17855	0.0		0.0	False		,,,				2504	0.0				p.V223V		Atlas-SNP	.											.	GALNT3	65	.	0			c.G669A						PASS	.	T		126,4280	92.0+/-130.7	1,124,2078	177.0	165.0	169.0		669	2.8	1.0	2	dbSNP_121	169	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GALNT3	NM_004482.3		1,125,6377	TT,TC,CC		0.0116,2.8597,0.9765		223/634	166621413	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	2591	exon3			ATCATCCACCAAA		CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4125	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 3"""	601756	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"""			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.669G>A	2.37:g.166621413C>T		Somatic	232	1	0.00431034		WXS	Illumina HiSeq	Phase_I	269	117	0.434944	NM_004482	Q53TG9|Q7Z476	Silent	SNP	ENST00000392701.3	37	CCDS2226.1																																																																																			C|0.987;T|0.013	0.013	strong		0.393	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482	
CHDH	55349	hgsc.bcm.edu	37	3	53856653	53856653	+	Silent	SNP	C	C	T	rs2241808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:53856653C>T	ENST00000315251.6	-	4	1157	c.720G>A	c.(718-720)gcG>gcA	p.A240A		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	240					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)	AGGCACAGGCCGCGCTCCACC	0.647													C|||	2217	0.442692	0.1581	0.4438	5008	,	,		19438	0.5655		0.5268	False		,,,				2504	0.6135				p.A240A		Atlas-SNP	.											CHDH,colon,carcinoma,-2,1	CHDH	34	1	0			c.G720A						PASS	.	C		986,3420	368.8+/-318.8	111,764,1328	74.0	62.0	66.0		720	-11.3	0.0	3	dbSNP_98	66	4716,3884	606.1+/-395.1	1280,2156,864	no	coding-synonymous	CHDH	NM_018397.4		1391,2920,2192	TT,TC,CC		45.1628,22.3786,43.8413		240/595	53856653	5702,7304	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon4			ACAGGCCGCGCTC	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.720G>A	3.37:g.53856653C>T		Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	64	39	0.609375	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			C|0.555;T|0.444	0.444	strong		0.647	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
PVR	5817	hgsc.bcm.edu	37	19	45162189	45162189	+	Intron	SNP	C	C	A	rs35385129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:45162189C>A	ENST00000425690.3	+	6	1449				PVR_ENST00000344956.4_Intron|PVR_ENST00000406449.4_Missense_Mutation_p.R391S|PVR_ENST00000403059.4_Intron|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor						adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		CCagagctgccgtaattgagc	0.532													C|||	827	0.165136	0.0651	0.0749	5008	,	,		18119	0.3393		0.1481	False		,,,				2504	0.2025				p.R391S		Atlas-SNP	.											.	PVR	23	.	0			c.C1171A						PASS	.	C	,,SER/ARG,	367,4039	186.0+/-213.0	18,331,1854	73.0	74.0	73.0		,,1171,	1.0	0.0	19	dbSNP_126	73	1382,7218	268.0+/-287.6	118,1146,3036	yes	intron,intron,missense,intron	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	,,110,	136,1477,4890	AA,AC,CC		16.0698,8.3296,13.4476	,,,	,,391/393,	45162189	1749,11257	2203	4300	6503	SO:0001627	intron_variant	5817	exon6			AGCTGCCGTAATT	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.1150+21C>A	19.37:g.45162189C>A		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	151	65	0.430464	NM_001135770	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	358	0.16391941391941392	32	0.06504065040650407	25	0.06906077348066299	188	0.32867132867132864	113	0.14907651715039577	C	3.809	-0.040136	0.07497	0.083296	0.160698	ENSG00000073008	ENST00000406449	D	0.87412	-2.25	2.11	0.956	0.19608	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.22146	0.065	B	0.17722	0.019	T	0.03630	-1.1018	6	.	.	.	.	6.1885	0.20510	0.0:0.6791:0.3209:0.0	rs35385129	391	P15151-4	.	S	391	ENSP00000383907:R391S	.	R	+	1	0	PVR	49854029	0.001000	0.12720	0.000000	0.03702	0.205000	0.24178	0.662000	0.25038	0.397000	0.25310	0.555000	0.69702	CGT	C|0.834;A|0.166	0.166	strong		0.532	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
GPR112	139378	hgsc.bcm.edu	37	X	135426968	135426968	+	Missense_Mutation	SNP	C	C	A	rs5930931	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135426968C>A	ENST00000394143.1	+	6	1394	c.1103C>A	c.(1102-1104)cCt>cAt	p.P368H	GPR112_ENST00000370652.1_Missense_Mutation_p.P368H|GPR112_ENST00000412101.1_Missense_Mutation_p.P163H|GPR112_ENST00000287534.4_Missense_Mutation_p.P305H|GPR112_ENST00000394141.1_Missense_Mutation_p.P163H	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	368			P -> H (in dbSNP:rs5930931). {ECO:0000269|Ref.2}.		G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P368L(1)		NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					TTTCAACCACCTACACCTTCT	0.368													c|||	1700	0.450331	0.4213	0.3545	3775	,	,		16744	0.2024		0.3738	False		,,,				2504	0.3241				p.P368H		Atlas-SNP	.											.	GPR112	459	.	1	Substitution - Missense(1)	prostate(1)	c.C1103A						PASS	.		HIS/PRO	2081,1754		479,816,307,337,264	84.0	78.0	80.0		1103	2.1	0.0	X	dbSNP_114	80	3200,3528		554,1184,908,690,964	yes	missense	GPR112	NM_153834.3	77	1033,2000,1215,1027,1228	AA,AC,A,CC,C		47.5624,45.7366,49.9953	possibly-damaging	368/3081	135426968	5281,5282	2203	4300	6503	SO:0001583	missense	139378	exon6			AACCACCTACACC	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1103C>A	X.37:g.135426968C>A	ENSP00000377699:p.Pro368His	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	53	52	0.981132	NM_153834	A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Missense_Mutation	SNP	ENST00000394143.1	37	CCDS35409.1	706	0.4255575647980711	138	0.3689839572192513	80	0.27972027972027974	76	0.15702479338842976	186	0.3174061433447099	c	2.747	-0.260836	0.05791	0.542634	0.475624	ENSG00000156920	ENST00000394143;ENST00000370652;ENST00000412101;ENST00000287534;ENST00000394141	T;T;T;T;T	0.29397	1.61;1.61;1.57;1.71;1.57	3.95	2.08	0.27032	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P	0.55605	0.972;0.924;0.875	P;P;B	0.49047	0.599;0.46;0.271	T	0.44544	-0.9321	8	0.66056	D	0.02	.	8.6564	0.34066	0.3924:0.6076:0.0:0.0	rs5930931;rs58573078;rs5930931	305;163;368	Q8IZF6-2;Q8IZF6-3;Q8IZF6	.;.;GP112_HUMAN	H	368;368;163;305;163	ENSP00000377699:P368H;ENSP00000359686:P368H;ENSP00000416526:P163H;ENSP00000287534:P305H;ENSP00000377697:P163H	ENSP00000287534:P305H	P	+	2	0	GPR112	135254634	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.303000	0.19210	0.238000	0.21222	-0.519000	0.04390	CCT	0|0.025;A|0.455	0.455	strong		0.368	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1		
PCNT	5116	hgsc.bcm.edu	37	21	47841941	47841941	+	Missense_Mutation	SNP	A	A	G	rs7277175	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47841941A>G	ENST00000359568.5	+	32	7189	c.7082A>G	c.(7081-7083)cAa>cGa	p.Q2361R	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2361			Q -> R (in dbSNP:rs7277175).		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)					CCTGAGGCTCAAACTGCTGGT	0.597													G|||	894	0.178514	0.4871	0.0937	5008	,	,		15445	0.004		0.0924	False		,,,				2504	0.09				p.Q2361R		Atlas-SNP	.											.	PCNT	283	.	0			c.A7082G						PASS	.	G	ARG/GLN	1914,2492	625.4+/-394.5	417,1080,706	74.0	78.0	76.0		7082	1.3	0.0	21	dbSNP_116	76	652,7948	789.7+/-407.6	15,622,3663	yes	missense	PCNT	NM_006031.5	43	432,1702,4369	GG,GA,AA		7.5814,43.4408,19.7294	benign	2361/3337	47841941	2566,10440	2203	4300	6503	SO:0001583	missense	5116	exon32			AGGCTCAAACTGC	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.7082A>G	21.37:g.47841941A>G	ENSP00000352572:p.Gln2361Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	68	36	0.529412	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	345	0.15796703296703296	233	0.4735772357723577	37	0.10220994475138122	2	0.0034965034965034965	73	0.09630606860158311	G	0.115	-1.132788	0.01756	0.434408	0.075814	ENSG00000160299	ENST00000359568	T	0.01430	4.9	4.19	1.33	0.21861	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.06373	-1.0830	8	0.15952	T	0.53	.	7.8418	0.29403	0.4414:0.3959:0.1627:0.0	rs7277175;rs60677505;rs7277175	2243;2361	O95613-2;O95613	.;PCNT_HUMAN	R	2361	ENSP00000352572:Q2361R	ENSP00000352572:Q2361R	Q	+	2	0	PCNT	46666369	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.075000	0.11431	-0.074000	0.12820	-3.852000	0.00018	CAA	A|0.802;G|0.198	0.198	strong		0.597	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
ITPRIPL1	150771	hgsc.bcm.edu	37	2	96993757	96993757	+	Missense_Mutation	SNP	C	C	T	rs2279105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:96993757C>T	ENST00000439118.2	+	3	1639	c.1388C>T	c.(1387-1389)aCg>aTg	p.T463M	ITPRIPL1_ENST00000361124.4_Missense_Mutation_p.T471M|ITPRIPL1_ENST00000536814.1_Missense_Mutation_p.T455M|ITPRIPL1_ENST00000542887.1_Missense_Mutation_p.T455M	NM_001008949.2	NP_001008949.1	Q6GPH6	IPIL1_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 1	463			T -> M (in dbSNP:rs2279105).			integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTGCCCCTCACGGACTGGGCC	0.567													C|||	1806	0.360623	0.2421	0.3141	5008	,	,		19389	0.2312		0.3191	False		,,,				2504	0.7301				p.T471M		Atlas-SNP	.											.	ITPRIPL1	58	.	0			c.C1412T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR	1099,3307	395.4+/-329.6	133,833,1237	90.0	90.0	90.0		1388,1364,1364,1412	5.5	0.4	2	dbSNP_100	90	2883,5717	451.4+/-362.6	507,1869,1924	yes	missense,missense,missense,missense	ITPRIPL1	NM_001008949.2,NM_001163523.1,NM_001163524.1,NM_178495.5	81,81,81,81	640,2702,3161	TT,TC,CC		33.5233,24.9433,30.6166	probably-damaging,probably-damaging,probably-damaging,probably-damaging	463/556,455/548,455/548,471/564	96993757	3982,9024	2203	4300	6503	SO:0001583	missense	150771	exon1			CCCTCACGGACTG		CCDS33250.1, CCDS46360.1, CCDS54378.1	2q11.2	2011-04-28	2011-04-28	2008-08-11	ENSG00000198885	ENSG00000198885			29371	protein-coding gene	gene with protein product			"""KIAA1754-like"", ""inositol 1,4,5-triphosphate receptor interacting protein-like 1"""	KIAA1754L		12477932	Standard	NM_178495		Approved		uc010yul.2	Q6GPH6	OTTHUMG00000155230	ENST00000439118.2:c.1388C>T	2.37:g.96993757C>T	ENSP00000389308:p.Thr463Met	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	123	58	0.471545	NM_178495	F5H1L8|Q8NE61	Missense_Mutation	SNP	ENST00000439118.2	37	CCDS46360.1	582|582	0.2664835164835165|0.2664835164835165	107|107	0.21747967479674796|0.21747967479674796	112|112	0.30939226519337015|0.30939226519337015	121|121	0.21153846153846154|0.21153846153846154	242|242	0.31926121372031663|0.31926121372031663	C|C	13.57|13.57	2.275854|2.275854	0.40294|0.40294	0.249433|0.249433	0.335233|0.335233	ENSG00000198885|ENSG00000198885	ENST00000420728|ENST00000536814;ENST00000439118;ENST00000361124;ENST00000542887	.|T;T;T;T	.|0.08282	.|3.11;3.11;3.11;3.11	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.299368	.|0.23750	.|N	.|0.044930	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	.|D;D	.|0.71674	.|0.998;0.998	.|P;P	.|0.51266	.|0.534;0.664	T|T	0.60409|0.60409	-0.7269|-0.7269	4|9	.|0.45353	.|T	.|0.12	-6.5149|-6.5149	18.332|18.332	0.90272|0.90272	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs2279105;rs52800255;rs58471167;rs2279105|rs2279105;rs52800255;rs58471167;rs2279105	.|471;463	.|Q6GPH6-2;Q6GPH6	.|.;IPIL1_HUMAN	W|M	495|455;463;471;455	.|ENSP00000439566:T455M;ENSP00000389308:T463M;ENSP00000355121:T471M;ENSP00000438212:T455M	.|ENSP00000355121:T471M	R|T	+|+	1|2	2|0	ITPRIPL1|ITPRIPL1	96357484|96357484	0.143000|0.143000	0.22626|0.22626	0.363000|0.363000	0.25875|0.25875	0.875000|0.875000	0.50365|0.50365	2.765000|2.765000	0.47621|0.47621	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	CGG|ACG	C|0.705;T|0.295	0.295	strong		0.567	ITPRIPL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338896.1	NM_178495	
KCNQ4	9132	hgsc.bcm.edu	37	1	41289831	41289831	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41289831A>G	ENST00000347132.5	+	9	1275	c.1193A>G	c.(1192-1194)gAg>gGg	p.E398G	KCNQ4_ENST00000509682.2_Intron|KCNQ4_ENST00000506017.1_3'UTR	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	398					inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	CGGCCCCTGGAGGTGCGGCGG	0.706																																					p.E398G		Atlas-SNP	.											.	KCNQ4	58	.	0			c.A1193G						PASS	.						6.0	7.0	7.0					1																	41289831		2093	4057	6150	SO:0001583	missense	9132	exon9			CCCTGGAGGTGCG	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.1193A>G	1.37:g.41289831A>G	ENSP00000262916:p.Glu398Gly	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	44	39	0.886364	NM_004700	O96025	Missense_Mutation	SNP	ENST00000347132.5	37	CCDS456.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.669119	0.47677	.	.	ENSG00000117013	ENST00000347132	D	0.98947	-5.26	5.74	5.74	0.90152	.	0.381642	0.26255	N	0.025436	D	0.96281	0.8787	N	0.08118	0	0.80722	D	1	D	0.58268	0.982	P	0.53006	0.715	D	0.95540	0.8611	10	0.30078	T	0.28	-19.2463	12.4719	0.55792	1.0:0.0:0.0:0.0	.	398	P56696	KCNQ4_HUMAN	G	398	ENSP00000262916:E398G	ENSP00000262916:E398G	E	+	2	0	KCNQ4	41062418	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.349000	0.59385	2.201000	0.70794	0.477000	0.44152	GAG	.	.	none		0.706	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
GBGT1	26301	hgsc.bcm.edu	37	9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	rs35898523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136029645G>T	ENST00000372040.3	-	7	674	c.363C>A	c.(361-363)taC>taA	p.Y121*	GBGT1_ENST00000372043.3_Intron|GBGT1_ENST00000372038.3_Missense_Mutation_p.H134N|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000540636.1_Nonsense_Mutation_p.Y104*|RALGDS_ENST00000542690.1_Intron	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	121					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		TGAAATGAGTGTACCTAGTGA	0.587													G|||	215	0.0429313	0.034	0.0418	5008	,	,		18455	0.002		0.0815	False		,,,				2504	0.0583				p.Y121X		Atlas-SNP	.											GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	0			c.C363A						PASS	.	G	stop/TYR	199,4207	121.7+/-159.2	8,183,2012	39.0	40.0	39.0		363	1.5	0.9	9	dbSNP_126	39	629,7971	155.7+/-209.7	18,593,3689	yes	stop-gained	GBGT1	NM_021996.4		26,776,5701	TT,TG,GG		7.314,4.5166,6.3663		121/348	136029645	828,12178	2203	4300	6503	SO:0001587	stop_gained	26301	exon7			ATGAGTGTACCTA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.363C>A	9.37:g.136029645G>T	ENSP00000361110:p.Tyr121*	Somatic	20	0	0		WXS	Illumina HiSeq	Phase_I	28	13	0.464286	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Nonsense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	108|108	0.04945054945054945|0.04945054945054945	23|23	0.046747967479674794|0.046747967479674794	16|16	0.04419889502762431|0.04419889502762431	2|2	0.0034965034965034965|0.0034965034965034965	67|67	0.08839050131926121|0.08839050131926121	G|G	17.35|17.35	3.367115|3.367115	0.61513|0.61513	0.045166|0.045166	0.07314|0.07314	ENSG00000148288|ENSG00000148288	ENST00000372038|ENST00000372040;ENST00000540636	T|.	0.36157|.	1.27|.	5.38|5.38	1.47|1.47	0.22746|0.22746	.|.	.|0.137701	.|0.50627	.|D	.|0.000106	T|.	0.01156|.	0.0038|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.02358|.	-1.1171|.	6|.	0.05833|0.07813	T|T	0.94|0.8	-15.2709|-15.2709	6.0904|6.0904	0.19991|0.19991	0.2143:0.0:0.6535:0.1322|0.2143:0.0:0.6535:0.1322	rs35898523;rs62638704|rs35898523;rs62638704	.|.	.|.	.|.	N|X	134|121;104	ENSP00000361108:H134N|.	ENSP00000361108:H134N|ENSP00000361110:Y121X	H|Y	-|-	1|3	0|2	GBGT1|GBGT1	135019466|135019466	0.883000|0.883000	0.30277|0.30277	0.900000|0.900000	0.35374|0.35374	0.243000|0.243000	0.25628|0.25628	0.687000|0.687000	0.25407|0.25407	0.008000|0.008000	0.14787|0.14787	0.491000|0.491000	0.48974|0.48974	CAC|TAC	G|0.941;T|0.059	0.059	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978592	45978592	+	Missense_Mutation	SNP	T	T	C	rs452472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45978592T>C	ENST00000391620.1	-	1	51	c.7A>G	c.(7-9)Acg>Gcg	p.T3A	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	3			T -> A (in dbSNP:rs452472). {ECO:0000269|PubMed:15489334}.			keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						ATGGTAGACGTGGCCATGCTG	0.642													.|||	1067	0.213059	0.1483	0.2594	5008	,	,		17698	0.1964		0.337	False		,,,				2504	0.1575				p.T3A		Atlas-SNP	.											KRTAP10-3,rectum,carcinoma,0,1	KRTAP10-3	17	1	0			c.A7G						PASS	.	T	,ALA/THR	730,3676	732.5+/-410.4	60,610,1533	59.0	59.0	59.0		,7	-3.7	0.0	21	dbSNP_80	59	2840,5760	661.1+/-401.8	475,1890,1935	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,58	535,2500,3468	CC,CT,TT		33.0233,16.5683,27.4489	,benign	,3/222	45978592	3570,9436	2203	4300	6503	SO:0001583	missense	386682	exon1			TAGACGTGGCCAT	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.7A>G	21.37:g.45978592T>C	ENSP00000375478:p.Thr3Ala	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	127	62	0.488189	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	482	0.2206959706959707	65	0.13211382113821138	91	0.2513812154696133	102	0.17832167832167833	224	0.2955145118733509	c	0.001	-2.986087	0.00046	0.165683	0.330233	ENSG00000212935	ENST00000391620	T	0.02863	4.13	3.32	-3.69	0.04450	.	.	.	.	.	T	0.00012	0.0000	N	0.00128	-2.045	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36720	-0.9736	8	0.02654	T	1	.	3.4126	0.07364	0.1224:0.5648:0.1215:0.1914	rs452472	3	P60369	KR103_HUMAN	A	3	ENSP00000375478:T3A	ENSP00000375478:T3A	T	-	1	0	KRTAP10-3	44803020	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.871000	0.04223	-1.132000	0.02907	-2.541000	0.00179	ACG	T|0.735;C|0.265	0.265	strong		0.642	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
ARSE	415	hgsc.bcm.edu	37	X	2852957	2852957	+	Silent	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:2852957C>G	ENST00000381134.3	-	11	1752	c.1686G>C	c.(1684-1686)ctG>ctC	p.L562L	ARSE_ENST00000545496.1_Silent_p.L587L|ARSE_ENST00000540563.1_Silent_p.L517L	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	562					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGATGTTGCCCAGCCTGTCCA	0.592																																					p.L562L		Atlas-SNP	.											.	ARSE	43	.	0			c.G1686C						PASS	.						43.0	32.0	36.0					X																	2852957		2203	4296	6499	SO:0001819	synonymous_variant	415	exon11			GTTGCCCAGCCTG	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1686G>C	X.37:g.2852957C>G		Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	144	143	0.993056	NM_000047	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																			.	.	none		0.592	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
TMEM187	8269	hgsc.bcm.edu	37	X	153247745	153247745	+	Missense_Mutation	SNP	A	A	G	rs7350355	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153247745A>G	ENST00000369982.4	+	2	979	c.232A>G	c.(232-234)Atg>Gtg	p.M78V	MIR3202-1_ENST00000580198.1_RNA	NM_003492.2	NP_003483.1	Q14656	TM187_HUMAN	transmembrane protein 187	78			M -> V (in dbSNP:rs7350355).			integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				breast(1)|large_intestine(1)|lung(1)|prostate(2)	5	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GGGCGGCGCGATGGGGCTGGG	0.692													G|||	2039	0.540132	0.4644	0.3991	3775	,	,		12161	0.5546		0.1461	False		,,,				2504	0.4519				p.M78V		Atlas-SNP	.											.	TMEM187	21	.	0			c.A232G						PASS	.	G	VAL/MET	2148,1682		503,806,336,322,232	33.0	29.0	30.0		232	2.7	0.0	X	dbSNP_116	30	1229,5494		76,721,356,1630,1513	yes	missense	TMEM187	NM_003492.2	21	579,1527,692,1952,1745	GG,GA,G,AA,A		18.2805,43.9164,32.0004	benign	78/262	153247745	3377,7176	2199	4296	6495	SO:0001583	missense	8269	exon2			GGCGCGATGGGGC	X92475	CCDS14739.1	Xq28	2007-03-14	2007-03-14	2007-03-14	ENSG00000177854	ENSG00000177854			13705	protein-coding gene	gene with protein product		300059	"""chromosome X open reading frame 12"""	CXorf12		8661027	Standard	NM_003492		Approved	ITBA1, DXS9878E	uc004fjq.2	Q14656	OTTHUMG00000024220	ENST00000369982.4:c.232A>G	X.37:g.153247745A>G	ENSP00000358999:p.Met78Val	Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	76	75	0.986842	NM_003492	B2RC47|Q6IAV7	Missense_Mutation	SNP	ENST00000369982.4	37	CCDS14739.1	761	0.458710066305003	156	0.4126984126984127	91	0.30743243243243246	208	0.5683060109289617	80	0.11594202898550725	G	6.827	0.521765	0.13005	0.560836	0.182805	ENSG00000177854	ENST00000369982	T	0.20881	2.04	3.6	2.71	0.32032	.	3.362720	0.01821	N	0.034052	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45948	-0.9226	9	0.12430	T	0.62	.	4.6881	0.12767	0.2141:0.1773:0.6086:0.0	rs7350355;rs57609307;rs7350355	78	Q14656	TM187_HUMAN	V	78	ENSP00000358999:M78V	ENSP00000358999:M78V	M	+	1	0	TMEM187	152900939	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.132000	0.15891	0.012000	0.14892	-0.396000	0.06452	ATG	A|0.587;0|0.003	.	strong		0.692	TMEM187-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061093.1	NM_003492	
SLC2A6	11182	hgsc.bcm.edu	37	9	136341407	136341407	+	Missense_Mutation	SNP	T	T	C	rs147872568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136341407T>C	ENST00000371899.4	-	4	591	c.514A>G	c.(514-516)Aca>Gca	p.T172A	SLC2A6_ENST00000371897.4_Missense_Mutation_p.T172A|SLC2A6_ENST00000485978.1_5'UTR	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	172					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		AGCTGGGGTGTGGCCCCCAGA	0.627													T|||	2	0.000399361	0.0	0.0	5008	,	,		16727	0.0		0.0	False		,,,				2504	0.002				p.T172A		Atlas-SNP	.											.	SLC2A6	31	.	0			c.A514G						PASS	.	T	ALA/THR,ALA/THR	0,4404		0,0,2202	85.0	66.0	72.0		514,514	5.0	1.0	9	dbSNP_134	72	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	SLC2A6	NM_001145099.1,NM_017585.3	58,58	0,3,6499	CC,CT,TT		0.0349,0.0,0.0231	benign,benign	172/446,172/508	136341407	3,13001	2202	4300	6502	SO:0001583	missense	11182	exon4			GGGGTGTGGCCCC	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"""Solute carriers"""	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.514A>G	9.37:g.136341407T>C	ENSP00000360966:p.Thr172Ala	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	69	30	0.434783	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	37	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.820748	0.32145	0.0	3.49E-4	ENSG00000160326	ENST00000371897;ENST00000371899;ENST00000432868;ENST00000414172	T;T;T	0.58506	0.33;0.33;0.33	4.98	4.98	0.66077	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.098719	0.64402	D	0.000002	T	0.39489	0.1080	N	0.17723	0.515	0.32320	N	0.562593	B;B;P;P	0.42556	0.012;0.024;0.783;0.679	B;B;B;B	0.40636	0.05;0.089;0.287;0.335	T	0.48703	-0.9012	10	0.22706	T	0.39	.	8.2846	0.31922	0.2861:0.0:0.0:0.7139	.	172;172;172;172	B4DH85;F2Z2F6;Q9UGQ3-2;Q9UGQ3	.;.;.;GTR6_HUMAN	A	172;172;172;99	ENSP00000360964:T172A;ENSP00000360966:T172A;ENSP00000405124:T172A	ENSP00000360964:T172A	T	-	1	0	SLC2A6	135331228	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	6.118000	0.71583	1.853000	0.53794	0.533000	0.62120	ACA	T|1.000;C|0.000	0.000	strong		0.627	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585	
EPB41	2035	hgsc.bcm.edu	37	1	29320013	29320013	+	Missense_Mutation	SNP	G	G	A	rs111642750	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:29320013G>A	ENST00000343067.4	+	3	767	c.640G>A	c.(640-642)Gtt>Att	p.V214I	EPB41_ENST00000356093.2_Missense_Mutation_p.V214I|EPB41_ENST00000347529.3_Missense_Mutation_p.V214I|EPB41_ENST00000373798.1_Missense_Mutation_p.V214I|EPB41_ENST00000373797.1_Missense_Mutation_p.V214I|EPB41_ENST00000373800.3_Missense_Mutation_p.V5I|EPB41_ENST00000398863.2_Missense_Mutation_p.V214I|EPB41_ENST00000349460.4_Missense_Mutation_p.V5I	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	214	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		V -> I (in dbSNP:rs111642750). {ECO:0000269|Ref.9}.		actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		GCACTGCAAGGTTTCTTTGTT	0.368													G|||	78	0.0155751	0.0023	0.0346	5008	,	,		15817	0.0		0.0408	False		,,,				2504	0.0102				p.V214I		Atlas-SNP	.											.	EPB41	118	.	0			c.G640A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	50,4356	50.9+/-86.3	1,48,2154	146.0	132.0	137.0		640,640,13,13,13,640	4.3	1.0	1	dbSNP_132	137	442,8158	134.7+/-192.1	11,420,3869	yes	missense,missense,missense,missense,missense,missense	EPB41	NM_001166005.1,NM_001166006.1,NM_001166007.1,NM_004437.3,NM_203342.2,NM_203343.2	29,29,29,29,29,29	12,468,6023	AA,AG,GG		5.1395,1.1348,3.7829	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	214/865,214/721,5/602,5/589,5/642,214/776	29320013	492,12514	2203	4300	6503	SO:0001583	missense	2035	exon3			TGCAAGGTTTCTT	BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"""elliptocytosis 1, RH-linked"""	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.640G>A	1.37:g.29320013G>A	ENSP00000345259:p.Val214Ile	Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	136	122	0.897059	NM_203343	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Missense_Mutation	SNP	ENST00000343067.4	37	CCDS53288.1	40	0.018315018315018316	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	26	0.03430079155672823	G	17.06	3.293288	0.60086	0.011348	0.051395	ENSG00000159023	ENST00000358989;ENST00000343067;ENST00000356093;ENST00000398863;ENST00000398865;ENST00000349460;ENST00000373800;ENST00000347529;ENST00000373798;ENST00000373797	D;D;D;D;D;T;D;D	0.84223	-1.82;-1.82;-1.82;-1.82;-1.82;-1.0;-1.82;-1.82	5.22	4.31	0.51392	FERM, N-terminal (1);Band 4.1 domain (1);FERM domain (1);	0.335198	0.31031	N	0.008382	T	0.62696	0.2449	L	0.55481	1.735	0.58432	D	0.999999	B;B;B;B;B;B;B;P;B	0.47484	0.005;0.061;0.151;0.027;0.05;0.034;0.041;0.896;0.009	B;B;B;B;B;B;B;P;B	0.60173	0.025;0.067;0.127;0.028;0.04;0.047;0.046;0.87;0.015	T	0.75975	-0.3128	9	.	.	.	.	12.4262	0.55548	0.0807:0.0:0.9193:0.0	.	214;214;214;214;214;231;214;5;5	E9PEW9;C9JTS2;P11171;P11171-2;P11171-7;Q59F12;P11171-5;P11171-4;P11171-3	.;.;41_HUMAN;.;.;.;.;.;.	I	231;214;214;214;214;5;5;214;214;214	ENSP00000345259:V214I;ENSP00000348397:V214I;ENSP00000381839:V214I;ENSP00000317597:V5I;ENSP00000362906:V5I;ENSP00000290100:V214I;ENSP00000362904:V214I;ENSP00000362903:V214I	.	V	+	1	0	EPB41	29192600	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.671000	0.61590	1.189000	0.43028	0.557000	0.71058	GTT	G|0.968;A|0.032	0.032	strong		0.368	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	NM_203342	
UBE2I	7329	hgsc.bcm.edu	37	16	1364365	1364365	+	Silent	SNP	A	A	G	rs4610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1364365A>G	ENST00000355803.4	+	3	689	c.138A>G	c.(136-138)ccA>ccG	p.P46P	UBE2I_ENST00000566587.1_Silent_p.P46P|UBE2I_ENST00000406620.1_Silent_p.P46P|UBE2I_ENST00000397514.3_Silent_p.P46P|UBE2I_ENST00000402301.1_Silent_p.P46P|UBE2I_ENST00000403747.2_Silent_p.P46P|UBE2I_ENST00000397515.2_Silent_p.P46P|UBE2I_ENST00000325437.5_Silent_p.P46P	NM_194260.2	NP_919236.1	P63279	UBC9_HUMAN	ubiquitin-conjugating enzyme E2I	46					cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chromosome segregation (GO:0007059)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intracellular steroid hormone receptor signaling pathway (GO:0033145)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|post-translational protein modification (GO:0043687)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein sumoylation (GO:0016925)|regulation of receptor activity (GO:0010469)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|fibrillar center (GO:0001650)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|synapse (GO:0045202)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RING-like zinc finger domain binding (GO:0071535)|SUMO ligase activity (GO:0019789)|transcription factor binding (GO:0008134)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(1)	5		Hepatocellular(780;0.00369)				GCGCCATTCCAGGAAAGAAAG	0.577													A|||	696	0.138978	0.1634	0.2262	5008	,	,		17411	0.0456		0.1382	False		,,,				2504	0.1411				p.P46P		Atlas-SNP	.											.	UBE2I	15	.	0			c.A138G						PASS	.	A	,,,	691,3707	286.3+/-278.7	58,575,1566	67.0	65.0	66.0		138,138,138,138	-4.0	0.7	16	dbSNP_52	66	1228,7372	246.2+/-274.8	87,1054,3159	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UBE2I	NM_003345.4,NM_194259.2,NM_194260.2,NM_194261.2	,,,	145,1629,4725	GG,GA,AA		14.2791,15.7117,14.7638	,,,	46/159,46/159,46/159,46/159	1364365	1919,11079	2199	4300	6499	SO:0001819	synonymous_variant	7329	exon3			CATTCCAGGAAAG	D45050	CCDS10433.1	16p13.3	2011-05-19	2011-05-19		ENSG00000103275	ENSG00000103275	6.3.2.19	"""Ubiquitin-conjugating enzymes E2"""	12485	protein-coding gene	gene with protein product		601661	"""ubiquitin-conjugating enzyme E2I (homologous to yeast UBC9)"", ""ubiquitin-conjugating enzyme E2I (UBC9 homolog, yeast)"""			8565643	Standard	NM_003345		Approved	UBC9	uc002cld.2	P63279	OTTHUMG00000047845	ENST00000355803.4:c.138A>G	16.37:g.1364365A>G		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	83	38	0.457831	NM_003345	D3DU69|P50550|Q15698|Q59GX1|Q86VB3	Silent	SNP	ENST00000355803.4	37	CCDS10433.1																																																																																			A|0.870;G|0.130	0.130	strong		0.577	UBE2I-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250317.2	NM_003345	
PGC	5225	hgsc.bcm.edu	37	6	41704716	41704716	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41704716G>T	ENST00000373025.3	-	9	1103	c.1041C>A	c.(1039-1041)gtC>gtA	p.V347V	TFEB_ENST00000403298.4_5'Flank|TFEB_ENST00000373033.1_5'Flank|RP11-298J23.5_ENST00000438967.1_RNA|TFEB_ENST00000230323.4_5'Flank|TFEB_ENST00000358871.2_5'Flank|TFEB_ENST00000420312.1_5'Flank	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	347					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)			AGGTGGGCTCGACTCCCACGG	0.572																																					p.V347V		Atlas-SNP	.											.	PGC	56	.	0			c.C1041A						PASS	.						69.0	64.0	66.0					6																	41704716		2203	4300	6503	SO:0001819	synonymous_variant	5225	exon9			GGGCTCGACTCCC		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.1041C>A	6.37:g.41704716G>T		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	104	53	0.509615	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Silent	SNP	ENST00000373025.3	37	CCDS4859.1																																																																																			.	.	none		0.572	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2		
ERCC6	2074	hgsc.bcm.edu	37	10	50678544	50678544	+	Silent	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50678544A>C	ENST00000355832.5	-	18	3540	c.3462T>G	c.(3460-3462)tcT>tcG	p.S1154S	ERCC6_ENST00000542458.1_Silent_p.S524S|ERCC6_ENST00000465653.1_5'Flank|RP11-123B3.2_ENST00000423283.1_RNA	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1154					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						CTCTTTTGTAAGAAAGACCTA	0.358								Direct reversal of damage;Nucleotide excision repair (NER)																													p.A1154A		Atlas-SNP	.											ERCC6,NS,haematopoietic_neoplasm,-1,1	ERCC6	162	1	0			c.C3462G						scavenged	.						75.0	74.0	74.0					10																	50678544		2203	4300	6503	SO:0001819	synonymous_variant	2074	exon18			TTTGTAAGAAAGA	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.3462T>G	10.37:g.50678544A>C		Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	156	58	0.371795	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			.	.	none		0.358	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
SLC25A32	81034	hgsc.bcm.edu	37	8	104427541	104427541	+	5'Flank	SNP	C	C	T	rs3134296	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:104427541C>T	ENST00000297578.4	-	0	0				DCAF13_ENST00000521716.1_5'Flank|DCAF13_ENST00000521971.1_5'Flank|SLC25A32_ENST00000543107.1_5'Flank|DCAF13_ENST00000519682.1_5'Flank|DCAF13_ENST00000297579.5_Missense_Mutation_p.P108L	NM_030780.3	NP_110407.2	Q9H2D1	MFTC_HUMAN	solute carrier family 25 (mitochondrial folate carrier), member 32						folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|mitochondrial transport (GO:0006839)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	folic acid transporter activity (GO:0008517)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	9			OV - Ovarian serous cystadenocarcinoma(57;2.79e-06)|STAD - Stomach adenocarcinoma(118;0.197)		Folic Acid(DB00158)	CCAGTTGAGCCAGCAGGCCGC	0.642													C|||	1112	0.222045	0.1626	0.2262	5008	,	,		16959	0.3323		0.168	False		,,,				2504	0.2413				p.P108L		Atlas-SNP	.											DCAF13,NS,carcinoma,-1,1	DCAF13	66	1	0			c.C323T						PASS	.	C	LEU/PRO	734,3668		49,636,1516	31.0	40.0	37.0		323	0.6	0.0	8	dbSNP_103	37	1117,7477		83,951,3263	yes	missense	DCAF13	NM_015420.6	98	132,1587,4779	TT,TC,CC		12.9974,16.6742,14.2428	benign	108/598	104427541	1851,11145	2201	4297	6498	SO:0001631	upstream_gene_variant	25879	exon1			TTGAGCCAGCAGG	AF283645	CCDS6300.1	8q22.3	2013-05-22	2013-03-15		ENSG00000164933	ENSG00000164933		"""Solute carriers"""	29683	protein-coding gene	gene with protein product		610815	"""solute carrier family 25, member 32"""			10978331	Standard	NM_030780		Approved	MFTC	uc003yll.4	Q9H2D1	OTTHUMG00000164790		8.37:g.104427541C>T	Exception_encountered	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	75	40	0.533333	NM_015420	Q96JZ6|Q96SU7	Missense_Mutation	SNP	ENST00000297578.4	37	CCDS6300.1	489	0.2239010989010989	86	0.17479674796747968	76	0.20994475138121546	196	0.34265734265734266	131	0.17282321899736147	C	12.25	1.882032	0.33255	0.166742	0.129974	ENSG00000164934	ENST00000297579	T	0.78126	-1.15	4.55	0.585	0.17428	.	1.567910	0.04564	U	0.392106	T	0.00012	0.0000	.	.	.	0.58432	P	4.000000000004E-6	.	.	.	.	.	.	T	0.04178	-1.0971	6	0.25106	T	0.35	.	2.547	0.04739	0.1381:0.4278:0.2698:0.1642	rs3134296;rs3736048;rs28364768;rs3134296	.	.	.	L	108	ENSP00000297579:P108L	ENSP00000297579:P108L	P	+	2	0	DCAF13	104496717	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.198000	0.09505	0.226000	0.20979	-0.253000	0.11424	CCA	C|0.817;T|0.183	0.183	strong		0.642	SLC25A32-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380290.2	NM_030780	
PLA2G1B	5319	hgsc.bcm.edu	37	12	120762837	120762837	+	Silent	SNP	A	A	G	rs5634	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:120762837A>G	ENST00000308366.4	-	3	257	c.222T>C	c.(220-222)taT>taC	p.Y74Y	PLA2G1B_ENST00000423423.3_Intron|PLA2G1B_ENST00000549767.1_Silent_p.Y45Y	NM_000928.2	NP_000919.1	P04054	PA21B_HUMAN	phospholipase A2, group IB (pancreas)	74					actin filament organization (GO:0007015)|activation of MAPK activity (GO:0000187)|activation of phospholipase A2 activity (GO:0032431)|antibacterial humoral response (GO:0019731)|arachidonic acid secretion (GO:0050482)|cellular response to insulin stimulus (GO:0032869)|defense response to Gram-positive bacterium (GO:0050830)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response in mucosa (GO:0002227)|interleukin-8 production (GO:0032637)|intracellular signal transduction (GO:0035556)|leukotriene biosynthetic process (GO:0019370)|multicellular organismal lipid catabolic process (GO:0044240)|neutrophil chemotaxis (GO:0030593)|neutrophil mediated immunity (GO:0002446)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine metabolic process (GO:0046470)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of immune response (GO:0050778)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule (GO:0030141)	bile acid binding (GO:0032052)|calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|phospholipase A2 activity (GO:0004623)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(3)|skin(2)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)				Niflumic Acid(DB04552)|Sulfasalazine(DB00795)	TGGCCTGGTCATAGCAGTTGT	0.537											OREG0022189	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	456	0.0910543	0.0522	0.1945	5008	,	,		17074	0.1151		0.0537	False		,,,				2504	0.0838				p.Y74Y	NSCLC(64;1781 1795 22266 42732)|Esophageal Squamous(30;459 829 25326 35148)	Atlas-SNP	.											.	PLA2G1B	8	.	0			c.T222C						PASS	.	G		271,4135	801.8+/-415.6	8,255,1940	179.0	131.0	147.0		222	0.5	0.1	12	dbSNP_52	147	392,8208	801.8+/-407.4	7,378,3915	no	coding-synonymous	PLA2G1B	NM_000928.2		15,633,5855	GG,GA,AA		4.5581,6.1507,5.0976		74/149	120762837	663,12343	2203	4300	6503	SO:0001819	synonymous_variant	5319	exon3			CTGGTCATAGCAG		CCDS9195.1	12q24.31	2013-09-19			ENSG00000170890	ENSG00000170890	3.1.1.4		9030	protein-coding gene	gene with protein product		172410		PLA2, PPLA2, PLA2A		8175726	Standard	NM_000928		Approved		uc001tyd.3	P04054	OTTHUMG00000169343	ENST00000308366.4:c.222T>C	12.37:g.120762837A>G		Somatic	194	0	0	1506	WXS	Illumina HiSeq	Phase_I	189	103	0.544974	NM_000928	B2R4H5|Q3KPI1	Silent	SNP	ENST00000308366.4	37	CCDS9195.1																																																																																			A|0.934;G|0.066	0.066	strong		0.537	PLA2G1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403626.1		
MT-CYB	4519	hgsc.bcm.edu	37	M	14905	14905	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:14905G>A	ENST00000361789.2	+	1	159	c.159G>A	c.(157-159)atG>atA	p.M53I	MT-TH_ENST00000387441.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND6_ENST00000361681.2_5'Flank			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	53					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						TTCCTAGCCATACACTACTCA	0.532																																					p.M53M		Atlas-SNP	.											.	.	.	.	0			c.G159A						PASS	.																																			SO:0001583	missense	0	exon1			AGCCATGCACTAC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.159G>A	M.37:g.14905G>A	ENSP00000354554:p.Met53Ile	Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	21	21	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.532	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246163	47246163	+	Missense_Mutation	SNP	T	T	C	rs7224888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:47246163T>C	ENST00000300404.2	+	10	1455	c.1396T>C	c.(1396-1398)Tgc>Cgc	p.C466R	B4GALNT2_ENST00000504681.1_Missense_Mutation_p.C380R|B4GALNT2_ENST00000393354.2_Missense_Mutation_p.C406R	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	466			C -> R (in dbSNP:rs7224888).		lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			CTTCCCCAGCTGCGTGGTGAC	0.552													T|||	661	0.131989	0.202	0.0793	5008	,	,		18553	0.0218		0.1203	False		,,,				2504	0.2004				p.C466R	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.T1396C						PASS	.	T	ARG/CYS,ARG/CYS,ARG/CYS	790,3616	317.4+/-295.1	60,670,1473	85.0	62.0	70.0		1216,1138,1396	4.4	0.1	17	dbSNP_116	70	905,7695	201.4+/-244.9	49,807,3444	yes	missense,missense,missense	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	180,180,180	109,1477,4917	CC,CT,TT		10.5233,17.9301,13.0324	probably-damaging,probably-damaging,probably-damaging	406/507,380/481,466/567	47246163	1695,11311	2203	4300	6503	SO:0001583	missense	124872	exon10			CCCAGCTGCGTGG	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1396T>C	17.37:g.47246163T>C	ENSP00000300404:p.Cys466Arg	Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	97	44	0.453608	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	255	0.11675824175824176	116	0.23577235772357724	29	0.08011049723756906	17	0.02972027972027972	93	0.12269129287598944	T	18.24	3.579392	0.65878	0.179301	0.105233	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.27720	1.65;1.65;1.65	5.55	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.00039	0.0001	M	0.87097	2.86	0.09310	P	0.999999999186281	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	T	0.04693	-1.0933	9	0.87932	D	0	-21.2945	10.8219	0.46610	0.142:0.0:0.0:0.858	rs7224888;rs59743746;rs7224888	406;466	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	R	380;406;466	ENSP00000425510:C380R;ENSP00000377022:C406R;ENSP00000300404:C466R	ENSP00000300404:C466R	C	+	1	0	B4GALNT2	44601162	1.000000	0.71417	0.121000	0.21740	0.816000	0.46133	7.132000	0.77251	0.875000	0.35847	0.459000	0.35465	TGC	T|0.874;C|0.126	0.126	strong		0.552	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446	
ZNF91	7644	hgsc.bcm.edu	37	19	23543834	23543834	+	Silent	SNP	C	C	T	rs7255296	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:23543834C>T	ENST00000300619.7	-	4	2152	c.1947G>A	c.(1945-1947)aaG>aaA	p.K649K	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Silent_p.K617K|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	649					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TATGAATTCTCTTATGTTTAG	0.388													C|||	696	0.138978	0.2171	0.1153	5008	,	,		5248	0.0218		0.1849	False		,,,				2504	0.1237				p.K649K		Atlas-SNP	.											.	ZNF91	349	.	0			c.G1947A						PASS	.	C		853,3345		93,667,1339	58.0	61.0	60.0		1947	-2.2	0.0	19	dbSNP_116	60	1769,6713		175,1419,2647	no	coding-synonymous	ZNF91	NM_003430.2		268,2086,3986	TT,TC,CC		20.8559,20.3192,20.6782		649/1192	23543834	2622,10058	2099	4241	6340	SO:0001819	synonymous_variant	7644	exon4			AATTCTCTTATGT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.1947G>A	19.37:g.23543834C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	73	26	0.356164	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			C|0.854;T|0.146	0.146	strong		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
COL18A1	80781	hgsc.bcm.edu	37	21	46899842	46899842	+	Silent	SNP	C	C	T	rs1131100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46899842C>T	ENST00000359759.4	+	9	2541	c.2520C>T	c.(2518-2520)ccC>ccT	p.P840P	COL18A1_ENST00000400337.2_Silent_p.P425P|COL18A1_ENST00000355480.5_Silent_p.P605P			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	840	Triple-helical region 2 (COL2).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		AAGGCTTCCCCGGGACTCCAG	0.677													C|||	817	0.163139	0.2965	0.0922	5008	,	,		16956	0.1101		0.0696	False		,,,				2504	0.184				p.P605P		Atlas-SNP	.											COL18A1_ENST00000359759,NS,carcinoma,0,2	COL18A1	129	2	0			c.C1815T						PASS	.	C	,	1059,2899		144,771,1064	52.0	63.0	59.0		1815,1275	-8.0	0.2	21	dbSNP_86	59	546,7746		18,510,3618	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	162,1281,4682	TT,TC,CC		6.5847,26.7559,13.102	,	605/1520,425/1340	46899842	1605,10645	1979	4146	6125	SO:0001819	synonymous_variant	80781	exon9			CTTCCCCGGGACT		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2520C>T	21.37:g.46899842C>T		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	44	26	0.590909	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.882;T|0.118	0.118	strong		0.677	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
ZNF804B	219578	hgsc.bcm.edu	37	7	88965021	88965021	+	Missense_Mutation	SNP	G	G	A	rs10487075	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:88965021G>A	ENST00000333190.4	+	4	3334	c.2725G>A	c.(2725-2727)Gaa>Aaa	p.E909K		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	909			E -> K (in dbSNP:rs10487075).				metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TGGCCCTTCAGAAACCACAGA	0.458										HNSCC(36;0.09)			G|||	269	0.0537141	0.003	0.0576	5008	,	,		17988	0.0843		0.0994	False		,,,				2504	0.0409				p.E909K		Atlas-SNP	.											.	ZNF804B	322	.	0			c.G2725A						PASS	.	G	LYS/GLU	105,4301	80.9+/-119.3	1,103,2099	85.0	90.0	88.0		2725	2.0	0.1	7	dbSNP_119	88	917,7683	203.2+/-246.3	43,831,3426	yes	missense	ZNF804B	NM_181646.2	56	44,934,5525	AA,AG,GG		10.6628,2.3831,7.8579	benign	909/1350	88965021	1022,11984	2203	4300	6503	SO:0001583	missense	219578	exon4			CCTTCAGAAACCA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2725G>A	7.37:g.88965021G>A	ENSP00000329638:p.Glu909Lys	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	125	61	0.488	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	148	0.06776556776556776	1	0.0020325203252032522	29	0.08011049723756906	39	0.06818181818181818	79	0.10422163588390501	G	12.56	1.975107	0.34848	0.023831	0.106628	ENSG00000182348	ENST00000333190	T	0.04970	3.52	5.1	2.02	0.26589	.	1.409490	0.03949	N	0.288266	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.37033	-0.9723	10	0.66056	D	0.02	-2.7179	6.8002	0.23746	0.2428:0.1476:0.6096:0.0	rs10487075;rs17679226;rs56460583;rs60463003;rs10487075	909	A4D1E1	Z804B_HUMAN	K	909	ENSP00000329638:E909K	ENSP00000329638:E909K	E	+	1	0	ZNF804B	88802957	0.003000	0.15002	0.089000	0.20774	0.044000	0.14063	0.532000	0.23067	0.710000	0.31997	0.655000	0.94253	GAA	G|0.916;A|0.084	0.084	strong		0.458	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs41307110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:22102293C>T	ENST00000542433.1	-	1	803	c.706G>A	c.(706-708)Gct>Act	p.A236T		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CTCCCATCAGCGGTGCGTATC	0.542																																					p.A236T		Atlas-SNP	.											OR10G2,NS,carcinoma,0,1	OR10G2	35	1	0			c.G706A						scavenged	.						39.0	41.0	40.0					14																	22102293		2179	4246	6425	SO:0001583	missense	26534	exon1			CATCAGCGGTGCG		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.706G>A	14.37:g.22102293C>T	ENSP00000445383:p.Ala236Thr	Somatic	293	0	0		WXS	Illumina HiSeq	Phase_I	29	27	0.931035	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	37	CCDS32047.1	347	0.15888278388278387	55	0.11178861788617886	40	0.11049723756906077	137	0.2395104895104895	115	0.1517150395778364	c	2.861	-0.236170	0.05944	.	.	ENSG00000255582	ENST00000542433	T	0.00174	8.62	3.92	2.07	0.26955	GPCR, rhodopsin-like superfamily (1);	0.146443	0.31134	N	0.008190	T	0.00012	0.0000	L	0.41236	1.265	0.80722	P	0.0	B	0.29378	0.243	B	0.25506	0.061	T	0.41305	-0.9516	9	0.41790	T	0.15	-5.7356	13.1106	0.59270	0.0:0.9007:0.0:0.0993	rs41307110;rs41428047;rs61753936;rs41307110	236	Q8NGC3	O10G2_HUMAN	T	236	ENSP00000445383:A236T	ENSP00000445383:A236T	A	-	1	0	OR10G2	21172133	0.000000	0.05858	0.819000	0.32651	0.005000	0.04900	-0.178000	0.09782	0.045000	0.15804	-2.571000	0.00171	GCT	C|0.750;T|0.250	0.250	weak		0.542	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84611805	84611805	+	Missense_Mutation	SNP	C	C	T	rs61752778	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:84611805C>T	ENST00000286744.5	+	19	2685	c.2461C>T	c.(2461-2463)Cca>Tca	p.P821S	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.P821S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	821	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)			AGACTGTCCTCCACATTTAGC	0.493													C|||	66	0.0131789	0.0008	0.0101	5008	,	,		21353	0.0		0.0288	False		,,,				2504	0.0297				p.P821S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C2461T						PASS	.	C	SER/PRO	11,4395	17.9+/-39.9	0,11,2192	66.0	58.0	60.0		2461	5.1	0.5	15	dbSNP_129	60	160,8440	75.7+/-138.4	1,158,4141	yes	missense	ADAMTSL3	NM_207517.2	74	1,169,6333	TT,TC,CC		1.8605,0.2497,1.3148	probably-damaging	821/1692	84611805	171,12835	2203	4300	6503	SO:0001583	missense	57188	exon19			TGTCCTCCACATT	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.2461C>T	15.37:g.84611805C>T	ENSP00000286744:p.Pro821Ser	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	65	33	0.507692	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	28	0.01282051282051282	0	0.0	4	0.011049723756906077	0	0.0	24	0.0316622691292876	C	14.08	2.428426	0.43122	0.002497	0.018605	ENSG00000156218	ENST00000286744	T	0.60797	0.16	5.08	5.08	0.68730	.	0.450530	0.16546	N	0.209689	T	0.47857	0.1468	L	0.53671	1.685	0.54753	D	0.999986	P;D	0.89917	0.754;1.0	P;D	0.85130	0.45;0.997	T	0.57242	-0.7845	10	0.11794	T	0.64	.	18.0594	0.89372	0.0:1.0:0.0:0.0	rs61752778	821;821	P82987-2;P82987	.;ATL3_HUMAN	S	821	ENSP00000286744:P821S	ENSP00000286744:P821S	P	+	1	0	ADAMTSL3	82402809	0.994000	0.37717	0.490000	0.27465	0.988000	0.76386	4.535000	0.60629	2.358000	0.79984	0.655000	0.94253	CCA	C|0.988;T|0.012	0.012	strong		0.493	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
USP21	27005	hgsc.bcm.edu	37	1	161132777	161132777	+	Missense_Mutation	SNP	G	G	A	rs17356051	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161132777G>A	ENST00000289865.8	+	6	1183	c.962G>A	c.(961-963)gGc>gAc	p.G321D	USP21_ENST00000368001.1_Missense_Mutation_p.G321D|USP21_ENST00000368002.3_Missense_Mutation_p.G321D	NM_012475.4	NP_036607.3	Q9UK80	UBP21_HUMAN	ubiquitin specific peptidase 21	321	USP.		G -> D (in dbSNP:rs17356051).		histone deubiquitination (GO:0016578)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	cysteine-type peptidase activity (GO:0008234)|metal ion binding (GO:0046872)|NEDD8-specific protease activity (GO:0019784)|transcription coactivator activity (GO:0003713)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|ovary(3)|prostate(3)	29	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AACCGCCGAGGCCGCCGGGCT	0.582													G|||	107	0.0213658	0.0008	0.0231	5008	,	,		16906	0.0		0.0746	False		,,,				2504	0.0153				p.G321D		Atlas-SNP	.											.	USP21	63	.	0			c.G962A						PASS	.	G	ASP/GLY,ASP/GLY	46,4360	46.7+/-81.2	0,46,2157	56.0	64.0	61.0		962,962	3.8	1.0	1	dbSNP_123	61	504,8096	143.9+/-199.8	11,482,3807	yes	missense,missense	USP21	NM_001014443.2,NM_012475.4	94,94	11,528,5964	AA,AG,GG		5.8605,1.044,4.2288	possibly-damaging,possibly-damaging	321/566,321/566	161132777	550,12456	2203	4300	6503	SO:0001583	missense	27005	exon6			GCCGAGGCCGCCG	AF177758	CCDS30920.1	1q22	2008-04-11	2005-08-08		ENSG00000143258	ENSG00000143258		"""Ubiquitin-specific peptidases"""	12620	protein-coding gene	gene with protein product		604729	"""ubiquitin specific protease 21"""	USP23		12838346, 10799498	Standard	XM_006711273		Approved	USP16	uc010pkd.2	Q9UK80	OTTHUMG00000033154	ENST00000289865.8:c.962G>A	1.37:g.161132777G>A	ENSP00000289865:p.Gly321Asp	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	132	64	0.484848	NM_012475	Q59H60|Q5BKT5|Q5VTW9|Q5VTX0|Q9BTV1|Q9HBS2|Q9NYN4	Missense_Mutation	SNP	ENST00000289865.8	37	CCDS30920.1	66	0.03021978021978022	0	0.0	11	0.03038674033149171	0	0.0	55	0.07255936675461741	G	15.82	2.945230	0.53079	0.01044	0.058605	ENSG00000143258	ENST00000368002;ENST00000289865;ENST00000368001	T;T;T	0.29917	1.55;1.55;1.55	4.72	3.8	0.43715	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	2.377030	0.03429	U	0.207571	T	0.29355	0.0731	L	0.41079	1.255	0.41560	D	0.988622	D	0.76494	0.999	D	0.67231	0.95	T	0.47071	-0.9145	10	0.10111	T	0.7	.	12.152	0.54055	0.0853:0.0:0.9147:0.0	rs17356051	321	Q9UK80	UBP21_HUMAN	D	321	ENSP00000356981:G321D;ENSP00000289865:G321D;ENSP00000356980:G321D	ENSP00000289865:G321D	G	+	2	0	USP21	159399401	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.474000	0.53129	1.202000	0.43218	0.455000	0.32223	GGC	G|0.960;A|0.040	0.040	strong		0.582	USP21-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080801.1		
ADRA2C	152	hgsc.bcm.edu	37	4	3769573	3769573	+	Missense_Mutation	SNP	G	G	C	rs370580020		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3769573G>C	ENST00000330055.5	+	1	1449	c.1240G>C	c.(1240-1242)Gtg>Ctg	p.V414L	ADRA2C_ENST00000509482.1_Intron	NM_000683.3	NP_000674.2	P18825	ADA2C_HUMAN	adrenoceptor alpha 2C	414					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|platelet activation (GO:0030168)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of vasoconstriction (GO:0045907)|regulation of insulin secretion (GO:0050796)|regulation of sensory perception of pain (GO:0051930)|small molecule metabolic process (GO:0044281)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Fenoldopam(DB00800)|Iloperidone(DB04946)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GGCCTGCCAGGTGCCCGGCCC	0.592																																					p.V414L	Esophageal Squamous(12;454 628 4517 14479)	Atlas-SNP	.											.	ADRA2C	24	.	0			c.G1240C						PASS	.						34.0	40.0	38.0					4																	3769573		2195	4299	6494	SO:0001583	missense	152	exon1			TGCCAGGTGCCCG	AY455666	CCDS47004.1	4p16.3	2013-10-22	2012-05-09		ENSG00000184160	ENSG00000184160		"""GPCR / Class A : Adrenoceptors : alpha"""	283	protein-coding gene	gene with protein product		104250	"""adrenergic, alpha-2C-, receptor"""	ADRA2L2, ADRA2RL2		1849485	Standard	NM_000683		Approved	ADRARL2	uc003ghm.3	P18825	OTTHUMG00000159830	ENST00000330055.5:c.1240G>C	4.37:g.3769573G>C	ENSP00000386069:p.Val414Leu	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	35	0.454545	NM_000683	P35369|Q9HB49	Missense_Mutation	SNP	ENST00000330055.5	37	CCDS47004.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960398	0.53400	.	.	ENSG00000184160	ENST00000330055	T	0.72394	-0.65	3.66	1.85	0.25348	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.60830	0.2299	L	0.39692	1.235	0.24721	N	0.993141	P	0.38551	0.636	B	0.40602	0.334	T	0.47548	-0.9109	9	0.33940	T	0.23	.	8.0626	0.30642	0.0:0.2357:0.6079:0.1563	.	414	P18825	ADA2C_HUMAN	L	414	ENSP00000386069:V414L	ENSP00000386069:V414L	V	+	1	0	ADRA2C	3739371	0.246000	0.23909	0.999000	0.59377	0.985000	0.73830	0.541000	0.23207	0.202000	0.20498	0.603000	0.83216	GTG	.	.	alt		0.592	ADRA2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357607.1	NM_000683	
THBS3	7059	hgsc.bcm.edu	37	1	155172725	155172725	+	Missense_Mutation	SNP	T	T	C	rs35154152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155172725T>C	ENST00000368378.3	-	8	855	c.835A>G	c.(835-837)Agc>Ggc	p.S279G	RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000422665.1_RNA|THBS3_ENST00000541990.1_5'UTR|RP11-263K19.4_ENST00000454348.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|THBS3_ENST00000457183.2_Missense_Mutation_p.S159G|THBS3_ENST00000486260.1_5'UTR|RP11-263K19.4_ENST00000436772.1_RNA|THBS3_ENST00000541576.1_5'Flank|RP11-263K19.4_ENST00000453136.1_RNA	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	279			S -> G (in dbSNP:rs35154152).		bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGATTGGGGCTGCAGTGGGAA	0.612													T|||	634	0.126597	0.2595	0.0706	5008	,	,		19705	0.0218		0.1272	False		,,,				2504	0.0941				p.S279G		Atlas-SNP	.											.	THBS3	70	.	0			c.A835G						PASS	.	T	GLY/SER	1068,3338	387.7+/-326.6	131,806,1266	43.0	47.0	46.0		835	5.2	1.0	1	dbSNP_126	46	946,7654	207.5+/-249.2	47,852,3401	yes	missense	THBS3	NM_007112.3	56	178,1658,4667	CC,CT,TT		11.0,24.2397,15.4852	benign	279/957	155172725	2014,10992	2203	4300	6503	SO:0001583	missense	7059	exon8			TGGGGCTGCAGTG	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.835A>G	1.37:g.155172725T>C	ENSP00000357362:p.Ser279Gly	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	110	62	0.563636	NM_007112	B1AVR8|B4DQ20|Q8WV34	Missense_Mutation	SNP	ENST00000368378.3	37	CCDS1099.1	265	0.12133699633699634	137	0.2784552845528455	22	0.06077348066298342	14	0.024475524475524476	92	0.12137203166226913	T	13.41	2.228504	0.39399	0.242397	0.11	ENSG00000169231	ENST00000368378;ENST00000457183;ENST00000428962	D;D;T	0.82255	-1.54;-1.59;1.58	5.24	5.24	0.73138	Epidermal growth factor-like (1);	0.234814	0.48286	D	0.000198	T	0.62208	0.2409	L	0.31476	0.935	0.29923	P	0.822577	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.08055	0.003;0.001;0.002;0.001	T	0.59899	-0.7367	9	0.31617	T	0.26	-35.8628	13.4093	0.60933	0.0:0.0:0.0:1.0	rs35154152;rs35154152	159;279;279;279	B4DQ20;Q53FK6;Q2HIZ0;P49746	.;.;.;TSP3_HUMAN	G	279;159;129	ENSP00000357362:S279G;ENSP00000392207:S159G;ENSP00000404040:S129G	ENSP00000357362:S279G	S	-	1	0	THBS3	153439349	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.777000	0.47717	2.326000	0.78906	0.533000	0.62120	AGC	T|0.857;C|0.143	0.143	strong		0.612	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112	
ASTN1	460	hgsc.bcm.edu	37	1	176992676	176992676	+	Silent	SNP	C	C	T	rs10798496	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:176992676C>T	ENST00000367654.3	-	7	1513	c.1302G>A	c.(1300-1302)caG>caA	p.Q434Q	ASTN1_ENST00000367657.3_Silent_p.Q434Q|ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Silent_p.Q434Q|ASTN1_ENST00000361833.2_Silent_p.Q434Q	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	434					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						TGGCATCCAGCTGGCTCCCCT	0.607													C|||	1187	0.237021	0.264	0.2248	5008	,	,		18455	0.003		0.4364	False		,,,				2504	0.2454				p.Q434Q		Atlas-SNP	.											.	ASTN1	314	.	0			c.G1302A						PASS	.	C	,	1212,3194	414.6+/-336.9	177,858,1168	41.0	38.0	39.0		1302,1302	2.7	1.0	1	dbSNP_120	39	3682,4918	520.5+/-379.7	777,2128,1395	no	coding-synonymous,coding-synonymous	ASTN1	NM_004319.1,NM_207108.1	,	954,2986,2563	TT,TC,CC		42.814,27.5079,37.6288	,	434/1295,434/1217	176992676	4894,8112	2203	4300	6503	SO:0001819	synonymous_variant	460	exon7			ATCCAGCTGGCTC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.1302G>A	1.37:g.176992676C>T		Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	123	53	0.430894	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Silent	SNP	ENST00000367654.3	37																																																																																				C|0.677;T|0.323	0.323	strong		0.607	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
OR4N4	283694	hgsc.bcm.edu	37	15	22383064	22383064	+	Missense_Mutation	SNP	C	C	A	rs12441468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:22383064C>A	ENST00000328795.4	+	1	683	c.592C>A	c.(592-594)Cta>Ata	p.L198I	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	198						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)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		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)		GGTGGAGCTTCTAATGGTCTT	0.527													c|||	2105	0.420327	0.4297	0.3862	5008	,	,		26389	0.4127		0.4642	False		,,,				2504	0.3947				p.L198I		Atlas-SNP	.											OR4N4,colon,carcinoma,0,1	OR4N4	108	1	0			c.C592A						scavenged	.						118.0	95.0	103.0					15																	22383064		2190	4259	6449	SO:0001583	missense	283694	exon1			GAGCTTCTAATGG	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"""GPCR / Class A : Olfactory receptors"""	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.592C>A	15.37:g.22383064C>A	ENSP00000332500:p.Leu198Ile	Somatic	411	2	0.00486618		WXS	Illumina HiSeq	Phase_I	409	125	0.305623	NM_001005241	Q6IEY3|Q6IF56	Missense_Mutation	SNP	ENST00000328795.4	37	CCDS32173.1	506	0.2316849816849817	135	0.27439024390243905	79	0.21823204419889503	111	0.19405594405594406	181	0.23878627968337732	.	10.53	1.375419	0.24857	.	.	ENSG00000183706	ENST00000328795	T	0.38240	1.15	3.37	2.44	0.29823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38897	N	0.001523	T	0.00012	0.0000	L	0.61218	1.895	0.80722	P	0.0	P	0.50156	0.932	P	0.59546	0.859	T	0.08046	-1.0741	9	0.49607	T	0.09	-7.7168	5.5233	0.16945	0.0:0.7375:0.0:0.2625	rs12441468	198	Q8N0Y3	OR4N4_HUMAN	I	198	ENSP00000332500:L198I	ENSP00000332500:L198I	L	+	1	2	OR4N4	19884428	0.000000	0.05858	0.064000	0.19789	0.288000	0.27193	-1.473000	0.02339	0.731000	0.32448	0.404000	0.27445	CTA	C|0.770;A|0.230	0.230	strong		0.527	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1		
KDM2B	84678	hgsc.bcm.edu	37	12	121881848	121881848	+	Silent	SNP	G	G	A	rs10849885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121881848G>A	ENST00000377071.4	-	16	2490	c.2418C>T	c.(2416-2418)taC>taT	p.Y806Y	KDM2B_ENST00000377069.4_Silent_p.Y775Y|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Silent_p.Y174Y	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	806					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						GGGGCTTCTCGTATTTCCGCT	0.657											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1617	0.322883	0.1543	0.3919	5008	,	,		14673	0.4435		0.3956	False		,,,				2504	0.3027				p.Y806Y		Atlas-SNP	.											KDM2B_ENST00000377071,NS,carcinoma,0,2	KDM2B	218	2	0			c.C2418T						PASS	.	G	,	724,3338		72,580,1379	68.0	75.0	73.0		2325,2418	-9.6	0.3	12	dbSNP_120	73	3095,5229		576,1943,1643	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	648,2523,3022	AA,AG,GG		37.1816,17.8237,30.8332	,	775/1266,806/1337	121881848	3819,8567	2031	4162	6193	SO:0001819	synonymous_variant	84678	exon16			CTTCTCGTATTTC	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.2418C>T	12.37:g.121881848G>A		Somatic	79	0	0	1514	WXS	Illumina HiSeq	Phase_I	93	54	0.580645	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.666;A|0.334	0.334	strong		0.657	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
DPPA4	55211	hgsc.bcm.edu	37	3	109049384	109049384	+	Silent	SNP	T	T	C	rs13059848	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:109049384T>C	ENST00000335658.6	-	5	720	c.666A>G	c.(664-666)ccA>ccG	p.P222P	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	222					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						AGGCCTCTTGTGGAGATTCCA	0.478													T|||	339	0.0676917	0.0106	0.0836	5008	,	,		16038	0.003		0.1481	False		,,,				2504	0.1176				p.P222P		Atlas-SNP	.											.	DPPA4	56	.	0			c.A666G						PASS	.	T		191,4215	118.4+/-156.1	2,187,2014	48.0	51.0	50.0		666	-5.4	0.0	3	dbSNP_121	50	1574,7026	283.3+/-296.1	142,1290,2868	no	coding-synonymous	DPPA4	NM_018189.3		144,1477,4882	CC,CT,TT		18.3023,4.335,13.5707		222/305	109049384	1765,11241	2203	4300	6503	SO:0001819	synonymous_variant	55211	exon5			CTCTTGTGGAGAT	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.666A>G	3.37:g.109049384T>C		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	61	0.469231	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Silent	SNP	ENST00000335658.6	37	CCDS33814.1																																																																																			T|0.879;C|0.121	0.121	strong		0.478	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
DLC1	10395	hgsc.bcm.edu	37	8	12957475	12957475	+	Missense_Mutation	SNP	C	C	T	rs532841	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:12957475C>T	ENST00000276297.4	-	9	2780	c.2371G>A	c.(2371-2373)Gtg>Atg	p.V791M	DLC1_ENST00000520226.1_Missense_Mutation_p.V280M|DLC1_ENST00000358919.2_Missense_Mutation_p.V354M|DLC1_ENST00000512044.2_Missense_Mutation_p.V388M	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	791	Focal adhesion-targeting (FAT).		V -> M (in dbSNP:rs532841). {ECO:0000269|PubMed:10649492, ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		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)	p.V791M(1)		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						TTCTGCTCCACCACGTTGTTA	0.527													T|||	2487	0.496605	0.6089	0.3847	5008	,	,		20867	0.3363		0.495	False		,,,				2504	0.591				p.V791M		Atlas-SNP	.											DLC1,NS,carcinoma,0,1	DLC1	411	1	1	Substitution - Missense(1)	stomach(1)	c.G2371A						PASS	.	T	MET/VAL,MET/VAL,MET/VAL	2595,1811	530.8+/-373.0	768,1059,376	96.0	90.0	92.0		838,1060,2371	-6.1	0.0	8	dbSNP_83	92	4236,4364	581.8+/-391.3	1035,2166,1099	yes	missense,missense,missense	DLC1	NM_001164271.1,NM_006094.4,NM_182643.2	21,21,21	1803,3225,1475	TT,TC,CC		49.2558,41.103,47.4781	benign,benign,benign	280/1018,354/1092,791/1529	12957475	6831,6175	2203	4300	6503	SO:0001583	missense	10395	exon9			GCTCCACCACGTT	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.2371G>A	8.37:g.12957475C>T	ENSP00000276297:p.Val791Met	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	31	19	0.612903	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	1035	0.4739010989010989	299	0.6077235772357723	157	0.43370165745856354	210	0.36713286713286714	369	0.4868073878627968	T	5.482	0.273981	0.10403	0.58897	0.492558	ENSG00000164741	ENST00000276297;ENST00000358919;ENST00000512044;ENST00000520226	T;T;T;T	0.05649	3.64;3.41;3.41;3.41	4.23	-6.1	0.02138	.	0.850997	0.11061	N	0.604004	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.39078	-0.9631	9	0.38643	T	0.18	.	11.1358	0.48373	0.0:0.5335:0.1626:0.3039	rs532841;rs3183774;rs3739299;rs61158109;rs532841	791;388;354	Q96QB1;E9PDZ8;Q96QB1-1	RHG07_HUMAN;.;.	M	791;354;388;280	ENSP00000276297:V791M;ENSP00000351797:V354M;ENSP00000422595:V388M;ENSP00000428028:V280M	ENSP00000276297:V791M	V	-	1	0	DLC1	13001846	0.000000	0.05858	0.001000	0.08648	0.716000	0.41182	-0.575000	0.05861	-1.397000	0.02068	-1.197000	0.01672	GTG	C|0.490;T|0.510	0.510	strong		0.527	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
CYP11B2	1585	hgsc.bcm.edu	37	8	143994041	143994041	+	Missense_Mutation	SNP	C	C	T	rs4545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143994041C>T	ENST00000323110.2	-	8	1305	c.1303G>A	c.(1303-1305)Ggc>Agc	p.G435S		NM_000498.3	NP_000489.3	P19099	C11B2_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 2	435			G -> S (in dbSNP:rs4545). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210}.		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)	AAGTTCCTGCCGGAGCCCCTG	0.622									Familial Hyperaldosteronism type I				.|||	814	0.16254	0.0295	0.1009	5008	,	,		13703	0.496		0.0229	False		,,,				2504	0.1861				p.G435S		Atlas-SNP	.											CYP11B2,NS,carcinoma,+2,1	CYP11B2	107	1	0			c.G1303A	GRCh37	CM033362	CYP11B2	M	rs4545	PASS	.	C	SER/GLY	113,4293		3,107,2093	72.0	82.0	79.0		1303	-5.9	0.0	8	dbSNP_52	79	178,8422		6,166,4128	no	missense	CYP11B2	NM_000498.3	56	9,273,6221	TT,TC,CC		2.0698,2.5647,2.2374	benign	435/504	143994041	291,12715	2203	4300	6503	SO:0001583	missense	1585	exon8	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	TCCTGCCGGAGCC	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.1303G>A	8.37:g.143994041C>T	ENSP00000325822:p.Gly435Ser	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	119	51	0.428571	NM_000498	B0ZBE4|Q16726	Missense_Mutation	SNP	ENST00000323110.2	37	CCDS6393.1	335	0.1533882783882784	14	0.028455284552845527	30	0.08287292817679558	276	0.4825174825174825	15	0.01978891820580475	.	8.410	0.843957	0.16963	0.025647	0.020698	ENSG00000179142	ENST00000323110	T	0.68331	-0.32	2.96	-5.92	0.02261	.	1.825320	0.02980	N	0.145573	T	0.00012	0.0000	L	0.42008	1.315	0.80722	P	0.0	B	0.24483	0.104	B	0.21708	0.036	T	0.24476	-1.0159	9	0.08837	T	0.75	.	7.4483	0.27223	0.0:0.2907:0.1428:0.5665	rs4545;rs57715984;rs4545	435	P19099	C11B2_HUMAN	S	435	ENSP00000325822:G435S	ENSP00000325822:G435S	G	-	1	0	CYP11B2	143991043	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.484000	0.06528	-2.274000	0.00680	-0.471000	0.05019	GGC	C|0.914;T|0.086	0.086	strong		0.622	CYP11B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359904.1		
LBP	3929	hgsc.bcm.edu	37	20	36989381	36989381	+	Silent	SNP	G	G	A	rs2232596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36989381G>A	ENST00000217407.2	+	6	773	c.612G>A	c.(610-612)tcG>tcA	p.S204S		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	204					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)				TCCAGAAATCGGTGTCCTCCG	0.473													A|||	3252	0.649361	0.6498	0.5375	5008	,	,		15930	0.8819		0.4901	False		,,,				2504	0.6524				p.S204S		Atlas-SNP	.											.	LBP	60	.	0			c.G612A						PASS	.	A		2716,1690	511.7+/-367.9	830,1056,317	179.0	177.0	178.0		612	-8.4	0.0	20	dbSNP_98	178	4410,4190	568.8+/-389.1	1124,2162,1014	no	coding-synonymous	LBP	NM_004139.2		1954,3218,1331	AA,AG,GG		48.7209,38.3568,45.2099		204/482	36989381	7126,5880	2203	4300	6503	SO:0001819	synonymous_variant	3929	exon6			GAAATCGGTGTCC		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.612G>A	20.37:g.36989381G>A		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	99	44	0.444444	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Silent	SNP	ENST00000217407.2	37	CCDS13304.1																																																																																			G|0.400;A|0.599	0.599	strong		0.473	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
WBSCR28	135886	hgsc.bcm.edu	37	7	73279361	73279361	+	Silent	SNP	C	C	T	rs61742124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:73279361C>T	ENST00000320531.2	+	2	147	c.111C>T	c.(109-111)ctC>ctT	p.L37L		NM_182504.3	NP_872310.2	Q6UE05	WBS28_HUMAN	Williams-Beuren syndrome chromosome region 28	37						integral component of membrane (GO:0016021)				breast(2)|kidney(2)|lung(6)|skin(1)	11		Lung NSC(55;0.159)				ATTTCCTGCTCCTCAAGATCA	0.582													C|||	1049	0.209465	0.3268	0.219	5008	,	,		16536	0.0784		0.2028	False		,,,				2504	0.1861				p.L37L		Atlas-SNP	.											.	WBSCR28	24	.	0			c.C111T						PASS	.	C		1004,2802		144,716,1043	263.0	271.0	269.0		111	-6.3	0.8	7	dbSNP_129	269	1622,6604		168,1286,2659	no	coding-synonymous	WBSCR28	NM_182504.3		312,2002,3702	TT,TC,CC		19.718,26.3794,21.8251		37/266	73279361	2626,9406	1903	4113	6016	SO:0001819	synonymous_variant	135886	exon2			CCTGCTCCTCAAG	BC030643	CCDS43597.1	7q11.23	2006-07-04			ENSG00000175877	ENSG00000175877			23018	protein-coding gene	gene with protein product		612547				8812460	Standard	NM_182504		Approved	MGC26719	uc003tzk.2	Q6UE05	OTTHUMG00000157243	ENST00000320531.2:c.111C>T	7.37:g.73279361C>T		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	169	78	0.461538	NM_182504	Q6UE04|Q8NHP4	Silent	SNP	ENST00000320531.2	37	CCDS43597.1																																																																																			C|0.789;T|0.211	0.211	strong		0.582	WBSCR28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348130.1	NM_182504	
NFASC	23114	hgsc.bcm.edu	37	1	204970302	204970302	+	Silent	SNP	T	T	C	rs4951151	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:204970302T>C	ENST00000401399.1	+	25	3223	c.3024T>C	c.(3022-3024)ccT>ccC	p.P1008P	NFASC_ENST00000360049.4_Intron|NFASC_ENST00000338515.6_Intron|NFASC_ENST00000513543.1_Intron|NFASC_ENST00000539706.1_Intron|NFASC_ENST00000367172.4_Silent_p.P1115P|NFASC_ENST00000367170.4_Silent_p.P1036P|NFASC_ENST00000495396.1_Intron|NFASC_ENST00000404076.1_Intron|NFASC_ENST00000367171.4_Silent_p.P1100P|NFASC_ENST00000404907.1_Intron|NFASC_ENST00000339876.6_Silent_p.P1008P|NFASC_ENST00000338586.6_Intron|NFASC_ENST00000367169.4_Intron			O94856	NFASC_HUMAN	neurofascin	1115	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)			CACCAGCCCCTGATGAGCAGT	0.537													t|||	1155	0.230631	0.1573	0.1787	5008	,	,		19216	0.2401		0.2575	False		,,,				2504	0.3292				p.P1008P		Atlas-SNP	.											NFASC_ENST00000339876,NS,carcinoma,0,1	NFASC	396	1	0			c.T3024C						PASS	.	T	,,,	570,2562		54,462,1050	64.0	57.0	59.0		3024,,,	-0.9	1.0	1	dbSNP_111	59	1759,5405		206,1347,2029	no	coding-synonymous,intron,intron,intron	NFASC	NM_001005388.2,NM_001160331.1,NM_001160332.1,NM_015090.3	,,,	260,1809,3079	CC,CT,TT		24.5533,18.1992,22.6204	,,,	1008/1241,,,	204970302	2329,7967	1566	3582	5148	SO:0001819	synonymous_variant	23114	exon26			AGCCCCTGATGAG	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.3024T>C	1.37:g.204970302T>C		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	118	60	0.508475	NM_001005388	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	462	0.21153846153846154	64	0.13008130081300814	80	0.22099447513812154	124	0.21678321678321677	194	0.2559366754617414	t	9.682	1.149614	0.21288	0.181992	0.245533	ENSG00000163531	ENST00000413225	.	.	.	5.39	-0.904	0.10530	.	.	.	.	.	.	.	.	.	.	.	0.25184	P	0.99018937	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.876	0.24147	0.0:0.4903:0.1123:0.3974	rs4951151;rs4951151	.	.	.	R	55	.	.	X	+	1	0	NFASC	203236925	0.016000	0.18221	0.984000	0.44739	0.994000	0.84299	-1.014000	0.03641	-0.204000	0.10235	-0.140000	0.14226	TGA	T|0.790;C|0.210	0.210	strong		0.537	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
DRC7	84229	hgsc.bcm.edu	37	16	57738810	57738810	+	Missense_Mutation	SNP	T	T	A	rs58373934	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:57738810T>A	ENST00000360716.3	+	7	943	c.722T>A	c.(721-723)gTg>gAg	p.V241E	CCDC135_ENST00000394337.4_Missense_Mutation_p.V241E|CCDC135_ENST00000336825.8_Missense_Mutation_p.V176E			Q8IY82	CC135_HUMAN		241			V -> E (in dbSNP:rs58373934).		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						GAGGAAAAGGTGCTGCCTAAG	0.547													t|||	334	0.0666933	0.0696	0.0692	5008	,	,		20096	0.001		0.1402	False		,,,				2504	0.0532				p.V241E		Atlas-SNP	.											.	CCDC135	97	.	0			c.T722A						PASS	.	T	GLU/VAL	309,4087	166.9+/-198.0	11,287,1900	94.0	85.0	88.0		722	-2.1	0.0	16	dbSNP_129	88	1164,7436	238.2+/-269.8	72,1020,3208	yes	missense	CCDC135	NM_032269.5	121	83,1307,5108	AA,AT,TT		13.5349,7.0291,11.3343	benign	241/875	57738810	1473,11523	2198	4300	6498	SO:0001583	missense	84229	exon6			AAAAGGTGCTGCC																												ENST00000360716.3:c.722T>A	16.37:g.57738810T>A	ENSP00000353942:p.Val241Glu	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	60	31	0.516667	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	178	0.0815018315018315	41	0.08333333333333333	26	0.0718232044198895	1	0.0017482517482517483	110	0.14511873350923482	T	6.791	0.514952	0.12944	0.070291	0.135349	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.74002	-0.8;-0.8;-0.8	5.04	-2.11	0.07187	.	1.383340	0.04493	N	0.379924	T	0.00384	0.0012	N	0.19112	0.55	0.80722	P	0.0	B;B	0.15141	0.012;0.011	B;B	0.10450	0.005;0.005	T	0.04454	-1.0950	9	0.06099	T	0.92	1.3473	4.9736	0.14129	0.1411:0.4079:0.0:0.451	rs58373934	176;241	Q8IY82-2;Q8IY82	.;CC135_HUMAN	E	241;176;241	ENSP00000377869:V241E;ENSP00000338938:V176E;ENSP00000353942:V241E	ENSP00000338938:V176E	V	+	2	0	CCDC135	56296311	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-1.069000	0.03444	-0.145000	0.11294	-0.656000	0.03901	GTG	T|0.897;A|0.103	0.103	strong		0.547	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2		
PRPF18	8559	hgsc.bcm.edu	37	10	13642257	13642257	+	Missense_Mutation	SNP	A	A	G	rs142307573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13642257A>G	ENST00000378572.3	+	3	318	c.158A>G	c.(157-159)gAg>gGg	p.E53G		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	53					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						CAGCCAAAAGAGGAGGACCAG	0.333													A|||	11	0.00219649	0.0	0.0043	5008	,	,		18338	0.0		0.008	False		,,,				2504	0.0				p.E53G		Atlas-SNP	.											.	PRPF18	32	.	0			c.A158G						PASS	.	A	GLY/GLU	0,4406		0,0,2203	93.0	93.0	93.0		158	5.8	1.0	10	dbSNP_134	93	26,8574	15.3+/-51.7	0,26,4274	yes	missense	PRPF18	NM_003675.3	98	0,26,6477	GG,GA,AA		0.3023,0.0,0.1999	benign	53/343	13642257	26,12980	2203	4300	6503	SO:0001583	missense	8559	exon3			CAAAAGAGGAGGA	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"""PRP18 pre-mRNA processing factor 18 homolog (yeast)"", ""PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"""			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.158A>G	10.37:g.13642257A>G	ENSP00000367835:p.Glu53Gly	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	53	22	0.415094	NM_003675	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	37	CCDS7100.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	15.59	2.878789	0.51801	0.0	0.003023	ENSG00000165630	ENST00000378572;ENST00000417658;ENST00000320054;ENST00000378544	.	.	.	5.76	5.76	0.90799	.	0.242726	0.48286	D	0.000184	T	0.42245	0.1194	L	0.31207	0.915	0.52501	D	0.999951	B	0.02656	0.0	B	0.04013	0.001	T	0.37709	-0.9694	9	0.23302	T	0.38	-18.2333	14.9492	0.71057	1.0:0.0:0.0:0.0	.	53	Q99633	PRP18_HUMAN	G	53;47;38;47	.	ENSP00000367824:E38G	E	+	2	0	PRPF18	13682263	1.000000	0.71417	0.995000	0.50966	0.978000	0.69477	5.371000	0.66150	2.323000	0.78572	0.528000	0.53228	GAG	A|0.998;G|0.002	0.002	strong		0.333	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
HERC4	26091	hgsc.bcm.edu	37	10	69773841	69773841	+	Silent	SNP	G	G	A	rs866255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:69773841G>A	ENST00000395198.3	-	9	1258	c.1011C>T	c.(1009-1011)agC>agT	p.S337S	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000373700.4_Silent_p.S337S|HERC4_ENST00000412272.2_Silent_p.S337S|HERC4_ENST00000277817.6_Silent_p.S227S	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	337					cell differentiation (GO:0030154)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	27						CAGTAAAGGGGCTTTTCCTGT	0.418													A|||	2601	0.519369	0.4039	0.4741	5008	,	,		16334	0.8413		0.331	False		,,,				2504	0.5695				p.S337S		Atlas-SNP	.											.	HERC4	78	.	0			c.C1011T						PASS	.	A	,	1694,2712	652.8+/-399.5	332,1030,841	104.0	99.0	101.0		1011,1011	2.1	1.0	10	dbSNP_86	101	2830,5770	675.1+/-403.2	460,1910,1930	no	coding-synonymous,coding-synonymous	HERC4	NM_015601.3,NM_022079.2	,	792,2940,2771	AA,AG,GG		32.907,38.4476,34.7839	,	337/1050,337/1058	69773841	4524,8482	2203	4300	6503	SO:0001819	synonymous_variant	26091	exon9			AAAGGGGCTTTTC	AY221963	CCDS7274.1, CCDS41533.1, CCDS60541.1, CCDS60542.1	10q21.3	2013-09-20	2012-02-23		ENSG00000148634	ENSG00000148634			24521	protein-coding gene	gene with protein product		609248	"""hect domain and RLD 4"""			10997877	Standard	NM_022079		Approved	DKFZP564G092, KIAA1593	uc001jng.4	Q5GLZ8	OTTHUMG00000018343	ENST00000395198.3:c.1011C>T	10.37:g.69773841G>A		Somatic	151	0	0		WXS	Illumina HiSeq	Phase_I	151	56	0.370861	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Silent	SNP	ENST00000395198.3	37	CCDS41533.1																																																																																			G|0.595;A|0.405	0.405	strong		0.418	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601	
PHC2	1912	hgsc.bcm.edu	37	1	33820515	33820515	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:33820515C>G	ENST00000257118.5	-	7	1369	c.1316G>C	c.(1315-1317)gGc>gCc	p.G439A	PHC2_ENST00000431992.1_Missense_Mutation_p.G410A|PHC2_ENST00000373416.1_5'UTR|RP11-415J8.5_ENST00000432703.1_RNA|PHC2_ENST00000373422.3_Missense_Mutation_p.G44A|PHC2_ENST00000419414.2_Missense_Mutation_p.G439A	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	439					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GTGGGGCACGCCCTCGGGATG	0.607																																					p.G439A		Atlas-SNP	.											.	PHC2	78	.	0			c.G1316C						PASS	.						75.0	70.0	72.0					1																	33820515		2203	4300	6503	SO:0001583	missense	1912	exon7			GGCACGCCCTCGG	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1316G>C	1.37:g.33820515C>G	ENSP00000257118:p.Gly439Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	98	93	0.94898	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	C	0.732	-0.779508	0.02929	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000373422;ENST00000419414	T;T;T;T	0.39997	2.06;1.68;1.05;2.1	5.86	2.88	0.33553	.	0.800952	0.11105	N	0.599163	T	0.29684	0.0741	L	0.56769	1.78	0.54753	D	0.999989	P;P;P	0.40050	0.7;0.7;0.7	B;B;B	0.36092	0.217;0.217;0.217	T	0.36335	-0.9752	10	0.02654	T	1	-2.4586	4.4467	0.11600	0.1605:0.6014:0.1549:0.0832	.	439;410;439	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	A	410;439;44;439	ENSP00000389436:G410A;ENSP00000257118:G439A;ENSP00000362521:G44A;ENSP00000391440:G439A	ENSP00000257118:G439A	G	-	2	0	PHC2	33593102	0.989000	0.36119	0.212000	0.23672	0.034000	0.12701	1.042000	0.30303	0.339000	0.23719	0.591000	0.81541	GGC	.	.	none		0.607	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
TBC1D31	93594	hgsc.bcm.edu	37	8	124142489	124142489	+	Silent	SNP	T	T	C	rs2272724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:124142489T>C	ENST00000287380.1	+	16	2412	c.2322T>C	c.(2320-2322)gaT>gaC	p.D774D	TBC1D31_ENST00000309336.3_Silent_p.D774D|TBC1D31_ENST00000522420.1_Silent_p.D669D|TBC1D31_ENST00000327098.5_Silent_p.D774D|TBC1D31_ENST00000521676.1_Silent_p.D651D|TBC1D31_ENST00000518805.1_Silent_p.D328D|TBC1D31_ENST00000378080.2_3'UTR	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	774						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										ACTTACAAGATGCTGCAAGAA	0.363													T|||	1679	0.335264	0.4244	0.4337	5008	,	,		19856	0.1825		0.337	False		,,,				2504	0.3006				p.D774D		Atlas-SNP	.											.	WDR67	97	.	0			c.T2322C						PASS	.	T	,	1880,2526	543.3+/-376.2	409,1062,732	132.0	128.0	129.0		2322,2322	-0.5	0.9	8	dbSNP_100	129	2976,5624	462.6+/-365.7	508,1960,1832	no	coding-synonymous,coding-synonymous	WDR67	NM_001145088.1,NM_145647.3	,	917,3022,2564	CC,CT,TT		34.6047,42.6691,37.3366	,	774/971,774/1067	124142489	4856,8150	2203	4300	6503	SO:0001819	synonymous_variant	93594	exon16			ACAAGATGCTGCA	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.2322T>C	8.37:g.124142489T>C		Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	209	108	0.516746	NM_001145088	B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Silent	SNP	ENST00000287380.1	37	CCDS6338.1																																																																																			T|0.650;C|0.350	0.350	strong		0.363	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
USP10	9100	hgsc.bcm.edu	37	16	84778697	84778697	+	Missense_Mutation	SNP	G	G	C	rs1812061	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84778697G>C	ENST00000219473.7	+	4	723	c.610G>C	c.(610-612)Gtt>Ctt	p.V204L	USP10_ENST00000570191.1_Missense_Mutation_p.V208L|USP10_ENST00000562743.1_3'UTR	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	204			V -> L (in dbSNP:rs1812061). {ECO:0000269|PubMed:15489334}.		autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						GCCCCCGTCAGTTACGCCCAG	0.552													G|||	1406	0.280751	0.2337	0.121	5008	,	,		17449	0.4107		0.1531	False		,,,				2504	0.455				p.V208L		Atlas-SNP	.											.	USP10	51	.	0			c.G622C						PASS	.	G	LEU/VAL	831,3131		80,671,1230	29.0	29.0	29.0		610	5.2	0.0	16	dbSNP_92	29	1174,7140		85,1004,3068	no	missense	USP10	NM_005153.2	32	165,1675,4298	CC,CG,GG		14.1208,20.9743,16.3327	benign	204/799	84778697	2005,10271	1981	4157	6138	SO:0001583	missense	9100	exon5			CCGTCAGTTACGC	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.610G>C	16.37:g.84778697G>C	ENSP00000219473:p.Val204Leu	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	146	53	0.363014	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Missense_Mutation	SNP	ENST00000219473.7	37	CCDS45537.1	528	0.24175824175824176	114	0.23170731707317074	48	0.13259668508287292	256	0.44755244755244755	110	0.14511873350923482	G	9.251	1.040870	0.19669	0.209743	0.141208	ENSG00000103194	ENST00000219473	T	0.06687	3.27	5.17	5.17	0.71159	.	1.756670	0.03339	N	0.194567	T	0.00012	0.0000	N	0.22421	0.69	0.52099	P	5.999999999994898E-5	B;B	0.20261	0.043;0.025	B;B	0.24541	0.054;0.024	T	0.47636	-0.9102	9	0.31617	T	0.26	-8.596	15.8288	0.78736	0.0:0.0:1.0:0.0	rs1812061;rs17849289;rs1812061	208;204	Q14694-3;Q14694	.;UBP10_HUMAN	L	204	ENSP00000219473:V204L	ENSP00000219473:V204L	V	+	1	0	USP10	83336198	0.426000	0.25506	0.007000	0.13788	0.173000	0.22820	2.140000	0.42159	2.403000	0.81681	0.491000	0.48974	GTT	G|0.896;C|0.104	0.104	strong		0.552	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
ZSCAN5B	342933	hgsc.bcm.edu	37	19	56704260	56704260	+	Silent	SNP	C	C	T	rs61742908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:56704260C>T	ENST00000586855.2	-	2	475	c.162G>A	c.(160-162)gaG>gaA	p.E54E	ZSCAN5B_ENST00000358992.3_Silent_p.E54E			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	54	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.E54E(1)		breast(1)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GGTCCGACTCCTCTGGGCAGC	0.562													C|||	422	0.0842652	0.0068	0.1614	5008	,	,		18013	0.253		0.0358	False		,,,				2504	0.0102				p.E54E		Atlas-SNP	.											ZSCAN5B_ENST00000358992,NS,carcinoma,0,1	ZSCAN5B	160	1	1	Substitution - coding silent(1)	stomach(1)	c.G162A						PASS	.	C		38,4368	40.0+/-72.8	0,38,2165	42.0	41.0	42.0		162	0.1	0.0	19	dbSNP_129	42	225,8375	91.9+/-153.9	4,217,4079	no	coding-synonymous	ZSCAN5B	NM_001080456.2		4,255,6244	TT,TC,CC		2.6163,0.8625,2.0221		54/496	56704260	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	342933	exon1			CGACTCCTCTGGG		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"""-"", ""Zinc fingers, C2H2-type"""	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.162G>A	19.37:g.56704260C>T		Somatic	361	0	0		WXS	Illumina HiSeq	Phase_I	428	198	0.462617	NM_001080456		Silent	SNP	ENST00000586855.2	37	CCDS46203.1																																																																																			C|0.913;T|0.087	0.087	strong		0.562	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456	
POLR3D	661	hgsc.bcm.edu	37	8	22105502	22105502	+	Silent	SNP	T	T	C	rs1126677	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22105502T>C	ENST00000397802.4	+	3	557	c.342T>C	c.(340-342)gcT>gcC	p.A114A	POLR3D_ENST00000306433.4_Silent_p.A114A|MIR320A_ENST00000385302.1_RNA			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	114					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	13				Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		AGGGCCCAGCTGAAATGATGA	0.517													C|||	3545	0.707867	0.4501	0.7565	5008	,	,		21834	0.8264		0.7237	False		,,,				2504	0.8834				p.A114A		Atlas-SNP	.											.	POLR3D	26	.	0			c.T342C						PASS	.	C		2121,2285	599.5+/-389.3	513,1095,595	109.0	101.0	104.0		342	-11.5	0.3	8	dbSNP_86	104	5971,2629	424.5+/-354.7	2055,1861,384	no	coding-synonymous	POLR3D	NM_001722.2		2568,2956,979	CC,CT,TT		30.5698,48.1389,37.7826		114/399	22105502	8092,4914	2203	4300	6503	SO:0001819	synonymous_variant	661	exon4			CCCAGCTGAAATG	M17754	CCDS34858.1	8q21	2013-01-21	2003-04-01	2003-04-04	ENSG00000168495	ENSG00000168495		"""RNA polymerase subunits"""	1080	protein-coding gene	gene with protein product		187280	"""BN51 (BHK21) temperature sensitivity complementing"""	BN51T		12391170, 11279001	Standard	NM_001722		Approved	TSBN51, RPC4	uc003xbl.3	P05423	OTTHUMG00000163778	ENST00000397802.4:c.342T>C	8.37:g.22105502T>C		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	37	CCDS34858.1																																																																																			A|0.000;C|0.657;G|0.000;T|0.342	0.657	strong		0.517	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722	
OR10R2	343406	hgsc.bcm.edu	37	1	158450314	158450314	+	Missense_Mutation	SNP	A	A	G	rs6679056	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158450314A>G	ENST00000368152.1	+	1	647	c.647A>G	c.(646-648)gAa>gGa	p.E216G	RP11-144L1.4_ENST00000419738.1_RNA|RP11-144L1.4_ENST00000426251.1_RNA	NM_001004472.1	NP_001004472.1	Q8NGX6	O10R2_HUMAN	olfactory receptor, family 10, subfamily R, member 2	216			E -> G (in dbSNP:rs6679056).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(26)|pancreas(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	41	all_hematologic(112;0.0378)					GATGTTAACGAATTTGTGATA	0.403													A|||	2486	0.496406	0.4781	0.4424	5008	,	,		23048	0.5675		0.5577	False		,,,				2504	0.4233				p.E216G		Atlas-SNP	.											OR10R2,colon,carcinoma,+1,1	OR10R2	81	1	0			c.A647G						PASS	.	A	GLY/GLU	2124,2282	577.1+/-384.4	498,1128,577	158.0	147.0	151.0		647	4.4	0.1	1	dbSNP_116	151	4582,4018	596.6+/-393.6	1248,2086,966	yes	missense	OR10R2	NM_001004472.1	98	1746,3214,1543	GG,GA,AA		46.7209,48.207,48.4392	probably-damaging	216/336	158450314	6706,6300	2203	4300	6503	SO:0001583	missense	343406	exon1			TTAACGAATTTGT	AB065640	CCDS30898.1	1q23.1	2012-08-09			ENSG00000198965	ENSG00000198965		"""GPCR / Class A : Olfactory receptors"""	14820	protein-coding gene	gene with protein product							Standard	NM_001004472		Approved	OR10R2Q	uc010pik.2	Q8NGX6	OTTHUMG00000019632	ENST00000368152.1:c.647A>G	1.37:g.158450314A>G	ENSP00000357134:p.Glu216Gly	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	223	101	0.452915	NM_001004472	Q5VWM8|Q6IFS1|Q96R61	Missense_Mutation	SNP	ENST00000368152.1	37	CCDS30898.1	1191	0.5453296703296703	246	0.5	162	0.44751381215469616	349	0.6101398601398601	434	0.5725593667546174	a	10.57	1.387362	0.25031	0.48207	0.532791	ENSG00000198965	ENST00000368152	T	0.00258	8.41	4.37	4.37	0.52481	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00109	0.0003	M	0.73962	2.25	0.58432	P	4.000000000004E-6	B	0.20052	0.041	B	0.25405	0.06	T	0.23261	-1.0193	8	0.56958	D	0.05	.	8.3167	0.32104	0.8235:0.0:0.0:0.1765	rs6679056;rs17629469;rs61345997;rs6679056	216	Q8NGX6	O10R2_HUMAN	G	216	ENSP00000357134:E216G	ENSP00000357134:E216G	E	+	2	0	OR10R2	156716938	0.008000	0.16893	0.124000	0.21820	0.888000	0.51559	1.838000	0.39211	1.801000	0.52704	0.533000	0.62120	GAA	A|0.467;G|0.533	0.533	strong		0.403	OR10R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051847.2	NM_001004472	
UBASH3B	84959	hgsc.bcm.edu	37	11	122646967	122646967	+	Missense_Mutation	SNP	G	G	A	rs12790613	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:122646967G>A	ENST00000284273.5	+	2	577	c.202G>A	c.(202-204)Gca>Aca	p.A68T		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	68	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.		A -> T (in dbSNP:rs12790613). {ECO:0000269|Ref.3}.		negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.A68T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		AAGTGTTCAGGCAGCATGTGA	0.403													G|||	980	0.195687	0.0325	0.3069	5008	,	,		21037	0.1726		0.3111	False		,,,				2504	0.2423				p.A68T		Atlas-SNP	.											UBASH3B,NS,carcinoma,0,1	UBASH3B	73	1	1	Substitution - Missense(1)	stomach(1)	c.G202A						PASS	.	G	THR/ALA	376,4028	191.9+/-217.4	17,342,1843	100.0	99.0	100.0		202	4.2	1.0	11	dbSNP_121	100	2756,5842	439.0+/-359.1	445,1866,1988	yes	missense	UBASH3B	NM_032873.4	58	462,2208,3831	AA,AG,GG		32.054,8.5377,24.0886	possibly-damaging	68/650	122646967	3132,9870	2202	4299	6501	SO:0001583	missense	84959	exon2			GTTCAGGCAGCAT	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.202G>A	11.37:g.122646967G>A	ENSP00000284273:p.Ala68Thr	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	43	17	0.395349	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	465	0.2129120879120879	20	0.04065040650406504	114	0.3149171270718232	109	0.19055944055944055	222	0.2928759894459103	G	17.81	3.480055	0.63849	0.085377	0.32054	ENSG00000154127	ENST00000284273	T	0.22743	1.94	5.14	4.23	0.50019	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (2);Ubiquitin-associated/translation elongation factor EF1B, N-terminal (1);UBA-like (1);	0.100500	0.64402	D	0.000002	T	0.00012	0.0000	L	0.59967	1.855	0.09310	P	0.9999973605	P	0.46277	0.875	P	0.51297	0.665	T	0.45071	-0.9286	9	0.20046	T	0.44	-8.9395	13.6404	0.62246	0.0746:0.0:0.9254:0.0	rs12790613;rs52802139;rs59822329;rs12790613	68	Q8TF42	UBS3B_HUMAN	T	68	ENSP00000284273:A68T	ENSP00000284273:A68T	A	+	1	0	UBASH3B	122152177	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.092000	0.71414	1.176000	0.42840	-0.140000	0.14226	GCA	G|0.779;A|0.221	0.221	strong		0.403	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	
CNN2	1265	hgsc.bcm.edu	37	19	1036444	1036444	+	Silent	SNP	G	G	A	rs930231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1036444G>A	ENST00000263097.4	+	6	900	c.537G>A	c.(535-537)tcG>tcA	p.S179S	AC011558.5_ENST00000585757.1_RNA|CNN2_ENST00000562958.2_Silent_p.S200S|CNN2_ENST00000348419.3_Silent_p.S140S|CNN2_ENST00000565096.2_Silent_p.S168S|CNN2_ENST00000606983.1_3'UTR	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	179					actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAGCCAGTCGGGCATGACTG	0.592													G|||	851	0.169928	0.0439	0.3646	5008	,	,		17922	0.0496		0.3002	False		,,,				2504	0.1922				p.S179S		Atlas-SNP	.											.	CNN2	26	.	0			c.G537A						PASS	.	G	,	401,4005	196.4+/-220.7	19,363,1821	65.0	61.0	62.0		537,420	-8.4	0.8	19	dbSNP_86	62	2734,5866	433.9+/-357.6	444,1846,2010	no	coding-synonymous,coding-synonymous	CNN2	NM_004368.2,NM_201277.1	,	463,2209,3831	AA,AG,GG		31.7907,9.1012,24.1043	,	179/310,140/271	1036444	3135,9871	2203	4300	6503	SO:0001819	synonymous_variant	1265	exon6			CCAGTCGGGCATG	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.537G>A	19.37:g.1036444G>A		Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	143	140	0.979021	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			G|0.770;C|0.000;A|0.230	0.230	strong		0.592	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368	
MDM1	56890	hgsc.bcm.edu	37	12	68707287	68707287	+	Missense_Mutation	SNP	G	G	A	rs2306392	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:68707287G>A	ENST00000303145.7	-	11	1741	c.1655C>T	c.(1654-1656)cCa>cTa	p.P552L	MDM1_ENST00000411698.2_Missense_Mutation_p.P517L|MDM1_ENST00000540418.1_Missense_Mutation_p.P272L	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	552			P -> L (in dbSNP:rs2306392). {ECO:0000269|PubMed:15489334}.		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)		CCTCTGTTCTGGGGCTGGAGG	0.363													G|||	1059	0.211462	0.0726	0.2161	5008	,	,		19059	0.1736		0.3052	False		,,,				2504	0.3384				p.P552L		Atlas-SNP	.											.	MDM1	74	.	0			c.C1655T						PASS	.	G	LEU/PRO,LEU/PRO	557,3849	249.0+/-256.6	33,491,1679	84.0	89.0	88.0		1550,1655	2.2	0.0	12	dbSNP_100	88	2693,5907	432.3+/-357.1	398,1897,2005	yes	missense,missense	MDM1	NM_001205028.1,NM_017440.4	98,98	431,2388,3684	AA,AG,GG		31.314,12.6419,24.9885	benign,benign	517/680,552/715	68707287	3250,9756	2203	4300	6503	SO:0001583	missense	56890	exon11			TGTTCTGGGGCTG	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.1655C>T	12.37:g.68707287G>A	ENSP00000302537:p.Pro552Leu	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	100	40	0.4	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Missense_Mutation	SNP	ENST00000303145.7	37	CCDS8983.1	475	0.2174908424908425	51	0.10365853658536585	95	0.26243093922651933	95	0.1660839160839161	234	0.3087071240105541	G	1.012	-0.687468	0.03328	0.126419	0.31314	ENSG00000111554	ENST00000540418;ENST00000303145;ENST00000411698	T;T;T	0.22945	1.93;2.25;2.25	5.08	2.23	0.28157	.	0.415012	0.27986	N	0.017058	T	0.00012	0.0000	N	0.14661	0.345	0.49483	P	2.0399999999998197E-4	B;B	0.10296	0.001;0.003	B;B	0.09377	0.002;0.004	T	0.47548	-0.9109	8	.	.	.	1.4607	9.8312	0.40944	0.2266:0.0:0.7734:0.0	rs2306392;rs17350216;rs17845852;rs17858825;rs52796173;rs60355924;rs2306392	517;552	E7EPQ3;Q8TC05	.;MDM1_HUMAN	L	272;552;517	ENSP00000443815:P272L;ENSP00000302537:P552L;ENSP00000391006:P517L	.	P	-	2	0	MDM1	66993554	0.925000	0.31364	0.010000	0.14722	0.973000	0.67179	3.017000	0.49615	0.258000	0.21686	0.555000	0.69702	CCA	G|0.764;A|0.236	0.236	strong		0.363	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
DSG1	1828	hgsc.bcm.edu	37	18	28898294	28898294	+	Missense_Mutation	SNP	A	A	G	rs1426310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:28898294A>G	ENST00000257192.4	+	1	243	c.31A>G	c.(31-33)Atg>Gtg	p.M11V		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	11			M -> V (in dbSNP:rs1426310). {ECO:0000269|PubMed:1711210, ECO:0000269|PubMed:1770008}.		apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			AGTAGTTGCAATGCTGTTCAT	0.383													G|||	1816	0.36262	0.4349	0.2997	5008	,	,		19378	0.0694		0.4911	False		,,,				2504	0.4796				p.M11V		Atlas-SNP	.											.	DSG1	176	.	0			c.A31G						PASS	.	G	VAL/MET	2051,2355	608.7+/-391.2	475,1101,627	190.0	169.0	176.0		31	4.3	0.1	18	dbSNP_88	176	4191,4409	585.3+/-391.9	1010,2171,1119	yes	missense	DSG1	NM_001942.2	21	1485,3272,1746	GG,GA,AA		48.7326,46.5502,47.9932	benign	11/1050	28898294	6242,6764	2203	4300	6503	SO:0001583	missense	1828	exon1			GTTGCAATGCTGT	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.31A>G	18.37:g.28898294A>G	ENSP00000257192:p.Met11Val	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	55	29	0.527273	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	755	0.3456959706959707	214	0.4349593495934959	125	0.3453038674033149	37	0.06468531468531469	379	0.5	G	2.884	-0.231213	0.05983	0.465502	0.487326	ENSG00000134760	ENST00000257192	T	0.54071	0.59	6.16	4.32	0.51571	.	0.683152	0.13353	N	0.394257	T	0.00012	0.0000	N	0.00538	-1.39	0.29189	P	0.876017	B	0.02656	0.0	B	0.01281	0.0	T	0.46442	-0.9191	9	0.06891	T	0.86	.	6.0664	0.19866	0.0691:0.2287:0.5715:0.1307	rs1426310;rs58912989;rs1426310	11	Q02413	DSG1_HUMAN	V	11	ENSP00000257192:M11V	ENSP00000257192:M11V	M	+	1	0	DSG1	27152292	0.767000	0.28508	0.081000	0.20488	0.895000	0.52256	1.404000	0.34623	0.446000	0.26666	-0.128000	0.14901	ATG	A|0.579;G|0.421	0.421	strong		0.383	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
EPS8L1	54869	hgsc.bcm.edu	37	19	55594996	55594996	+	Missense_Mutation	SNP	C	C	G	rs1628576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55594996C>G	ENST00000201647.6	+	14	1425	c.1369C>G	c.(1369-1371)Cag>Gag	p.Q457E	EPS8L1_ENST00000586329.1_Missense_Mutation_p.Q471E|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000245618.5_Missense_Mutation_p.Q330E|EPS8L1_ENST00000540810.1_Missense_Mutation_p.Q393E|EPS8L1_ENST00000588359.1_Missense_Mutation_p.Q143E	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	457			Q -> E (in dbSNP:rs1628576). {ECO:0000269|PubMed:12620401, 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)		AAGCGCCCCCCAGGTCGCTGT	0.701													C|||	659	0.131589	0.0847	0.1801	5008	,	,		10389	0.1012		0.2237	False		,,,				2504	0.0971				p.Q457E	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.C1369G						PASS	.	C	GLU/GLN,GLU/GLN	364,3978		30,304,1837	7.0	8.0	8.0		988,1369	2.8	1.0	19	dbSNP_89	8	1622,6896		171,1280,2808	yes	missense,missense	EPS8L1	NM_017729.3,NM_133180.2	29,29	201,1584,4645	GG,GC,CC		19.042,8.3832,15.4432	benign,benign	330/597,457/724	55594996	1986,10874	2171	4259	6430	SO:0001583	missense	54869	exon14			GCCCCCCAGGTCG	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.1369C>G	19.37:g.55594996C>G	ENSP00000201647:p.Gln457Glu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	65	37	0.569231	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	336	0.15384615384615385	37	0.07520325203252033	68	0.1878453038674033	64	0.11188811188811189	167	0.22031662269129287	C	10.53	1.376645	0.24857	0.083832	0.19042	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.05786	3.65;3.4;3.39	2.83	2.83	0.33086	.	8.307050	0.00166	N	0.000000	T	0.00012	0.0000	M	0.67953	2.075	0.32092	P	0.591758	P;B;P;B;P	0.52842	0.956;0.341;0.726;0.021;0.924	P;B;B;B;P	0.62184	0.899;0.217;0.231;0.029;0.857	T	0.39057	-0.9632	9	0.07175	T	0.84	-22.3553	9.2533	0.37568	0.0:1.0:0.0:0.0	rs1628576;rs1628576	393;471;236;330;457	B4DKV7;Q8TE68-3;Q8TE68-4;Q8TE68-2;Q8TE68	.;.;.;.;ES8L1_HUMAN	E	471;457;393;330;143	ENSP00000201647:Q457E;ENSP00000437541:Q393E;ENSP00000245618:Q330E	ENSP00000201647:Q457E	Q	+	1	0	EPS8L1	60286808	0.794000	0.28838	1.000000	0.80357	0.993000	0.82548	1.444000	0.35068	1.615000	0.50252	0.561000	0.74099	CAG	C|0.859;G|0.141	0.141	strong		0.701	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
COL19A1	1310	hgsc.bcm.edu	37	6	70733547	70733547	+	Missense_Mutation	SNP	C	C	G	rs2273426	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:70733547C>G	ENST00000322773.4	+	12	1157	c.1055C>G	c.(1054-1056)gCt>gGt	p.A352G		NM_001858.4	NP_001849.2	Q14993	COJA1_HUMAN	collagen, type XIX, alpha 1	352	Collagen-like 2.		A -> G (in dbSNP:rs2273426).		cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)|skeletal muscle tissue development (GO:0007519)|skeletal system development (GO:0001501)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(8)|lung(54)|ovary(3)|prostate(2)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	109						GGAGATCCAGCTCTGGCTGGC	0.308													G|||	1416	0.282748	0.5522	0.1744	5008	,	,		18317	0.2986		0.1123	False		,,,				2504	0.1544				p.A352G		Atlas-SNP	.											.	COL19A1	232	.	0			c.C1055G						PASS	.	G	GLY/ALA	2030,2376	610.5+/-391.6	482,1066,655	90.0	88.0	89.0		1055	5.5	1.0	6	dbSNP_100	89	922,7678	777.1+/-407.7	50,822,3428	yes	missense	COL19A1	NM_001858.4	60	532,1888,4083	GG,GC,CC		10.7209,46.0735,22.6972	benign	352/1143	70733547	2952,10054	2203	4300	6503	SO:0001583	missense	1310	exon12			ATCCAGCTCTGGC		CCDS4970.1	6q12-q13	2013-01-16			ENSG00000082293	ENSG00000082293		"""Collagens"""	2196	protein-coding gene	gene with protein product		120165				7916703, 9143499	Standard	NM_001858		Approved		uc003pfc.1	Q14993	OTTHUMG00000014987	ENST00000322773.4:c.1055C>G	6.37:g.70733547C>G	ENSP00000316030:p.Ala352Gly	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	52	9	0.173077	NM_001858	Q00559|Q05850|Q12885|Q13676|Q14DH1|Q5JUF0|Q5T424|Q9H572|Q9NPZ2|Q9NQP2	Missense_Mutation	SNP	ENST00000322773.4	37	CCDS4970.1	565	0.2586996336996337	241	0.4898373983739837	62	0.1712707182320442	175	0.30594405594405594	87	0.11477572559366754	G	14.10	2.434956	0.43224	0.460735	0.107209	ENSG00000082293	ENST00000322773	T	0.71934	-0.61	5.5	5.5	0.81552	.	0.068567	0.64402	N	0.000018	T	0.08133	0.0203	N	0.00012	-2.965	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30679	-0.9970	9	0.02654	T	1	.	15.6391	0.76981	0.0:0.1376:0.8624:0.0	rs2273426;rs61647969;rs2273426	352	Q14993	COJA1_HUMAN	G	352	ENSP00000316030:A352G	ENSP00000316030:A352G	A	+	2	0	COL19A1	70790268	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	4.235000	0.58666	1.342000	0.45619	-0.120000	0.15030	GCT	C|0.761;G|0.239	0.239	strong		0.308	COL19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041127.1		
SLC22A24	283238	hgsc.bcm.edu	37	11	62886800	62886800	+	Missense_Mutation	SNP	G	G	C	rs4963245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62886800G>C	ENST00000417740.1	-	3	955	c.514C>G	c.(514-516)Cgg>Ggg	p.R172G	SLC22A24_ENST00000326192.5_Missense_Mutation_p.R172G	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	172					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						ATGATCTTCCGTCCAACCCTA	0.418													G|||	820	0.163738	0.0522	0.3415	5008	,	,		20519	0.0317		0.3002	False		,,,				2504	0.184				p.R172G		Atlas-SNP	.											.	SLC22A24	31	.	0			c.C514G						PASS	.	G	GLY/ARG	145,1239		10,125,557	132.0	116.0	121.0		514	-3.7	0.0	11	dbSNP_111	121	1023,2159		172,679,740	yes	missense	SLC22A24	NM_001136506.2	125	182,804,1297	CC,CG,GG		32.1496,10.4769,25.5804	probably-damaging	172/553	62886800	1168,3398	692	1591	2283	SO:0001583	missense	283238	exon3			TCTTCCGTCCAAC		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.514C>G	11.37:g.62886800G>C	ENSP00000396586:p.Arg172Gly	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	67	34	0.507463	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		369	0.16895604395604397	28	0.056910569105691054	102	0.281767955801105	23	0.04020979020979021	216	0.2849604221635884	G	13.83	2.352998	0.41700	0.104769	0.321496	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.84370	-1.84;-0.25	3.86	-3.71	0.04424	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	T	0.00039	0.0001	H	0.98446	4.235	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.48559	-0.9025	9	0.87932	D	0	.	5.6254	0.17480	0.1821:0.0:0.2292:0.5887	rs4963245;rs52815620;rs4963245	172;172	Q8N4F4;C9JC66	S22AO_HUMAN;.	G	172	ENSP00000396586:R172G;ENSP00000321549:R172G	ENSP00000321549:R172G	R	-	1	2	SLC22A24	62643376	0.000000	0.05858	0.000000	0.03702	0.083000	0.17756	-3.203000	0.00559	-0.444000	0.07170	-0.403000	0.06358	CGG	G|0.827;C|0.173	0.173	strong		0.418	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
CXorf21	80231	hgsc.bcm.edu	37	X	30577846	30577846	+	Silent	SNP	A	A	C	rs887369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:30577846A>C	ENST00000378962.3	-	3	949	c.627T>G	c.(625-627)gtT>gtG	p.V209V		NM_025159.2	NP_079435.1	Q9HAI6	CX021_HUMAN	chromosome X open reading frame 21	209										kidney(1)|large_intestine(3)|lung(13)|ovary(1)|stomach(1)|urinary_tract(1)	20						ACTCATTCAGAACTGCATTAG	0.423													C|||	3387	0.897219	0.7012	0.6916	3775	,	,		15942	0.7103		0.5815	False		,,,				2504	0.6943				p.V209V		Atlas-SNP	.											.	CXorf21	42	.	0			c.T627G						PASS	.	C		3451,382		1318,298,517,15,54	156.0	139.0	145.0		627	2.2	0.9	X	dbSNP_86	145	5043,1685		1352,929,1410,147,462	no	coding-synonymous	CXorf21	NM_025159.2		2670,1227,1927,162,516	CC,CA,C,AA,A		25.0446,9.9661,19.572		209/302	30577846	8494,2067	2202	4300	6502	SO:0001819	synonymous_variant	80231	exon3			ATTCAGAACTGCA	BC020611	CCDS14224.1	Xp21.3	2006-04-12			ENSG00000120280	ENSG00000120280			25667	protein-coding gene	gene with protein product						12477932	Standard	NM_025159		Approved	FLJ11577	uc004dcg.2	Q9HAI6	OTTHUMG00000021325	ENST00000378962.3:c.627T>G	X.37:g.30577846A>C		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	92	91	0.98913	NM_025159		Silent	SNP	ENST00000378962.3	37	CCDS14224.1																																																																																			A|0.160;0|0.002	.	strong		0.423	CXorf21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056164.1	NM_025159	
KMT2C	58508	hgsc.bcm.edu	37	7	151882672	151882672	+	Missense_Mutation	SNP	C	C	A	rs145848316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151882672C>A	ENST00000262189.6	-	34	5271	c.5053G>T	c.(5053-5055)Gca>Tca	p.A1685S	KMT2C_ENST00000355193.2_Missense_Mutation_p.A1685S	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1685					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A1685S(2)									TGTGAGCTTGCTTTTCTCCAC	0.343																																					p.A1685S		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,0,2	MLL3	1564	2	2	Substitution - Missense(2)	kidney(2)	c.G5053T						PASS	.	C	SER/ALA	43,4361	34.3+/-65.2	0,43,2159	146.0	126.0	132.0		5053	5.0	1.0	7	dbSNP_134	132	136,8464	55.6+/-116.7	0,136,4164	yes	missense	MLL3	NM_170606.2	99	0,179,6323	AA,AC,CC		1.5814,0.9764,1.3765	probably-damaging	1685/4912	151882672	179,12825	2202	4300	6502	SO:0001583	missense	58508	exon34			AGCTTGCTTTTCT	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.5053G>T	7.37:g.151882672C>A	ENSP00000262189:p.Ala1685Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	178	35	0.196629	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	55	0.025183150183150184	3	0.006097560975609756	6	0.016574585635359115	36	0.06293706293706294	10	0.013192612137203167	C	21.2	4.107153	0.77096	0.009764	0.015814	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.93712	-3.27;-3.27	5.03	5.03	0.67393	High mobility group, HMG1/HMG2 (1);	0.000000	0.45867	D	0.000330	T	0.78136	0.4236	L	0.46157	1.445	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.994;0.997	D	0.84697	0.0726	10	0.52906	T	0.07	.	18.3905	0.90481	0.0:1.0:0.0:0.0	.	1685;746	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	S	1685	ENSP00000262189:A1685S;ENSP00000347325:A1685S	ENSP00000262189:A1685S	A	-	1	0	MLL3	151513605	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.670000	0.83925	2.330000	0.79161	0.643000	0.83706	GCA	C|0.983;A|0.017	0.017	strong		0.343	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
DCHS2	54798	hgsc.bcm.edu	37	4	155156412	155156412	+	Missense_Mutation	SNP	G	G	A	rs61746132	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:155156412G>A	ENST00000357232.4	-	25	8026	c.8027C>T	c.(8026-8028)cCa>cTa	p.P2676L		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2676					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P2676L(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ACCCGAGTCTGGCACCCTGGA	0.517													G|||	464	0.0926518	0.1415	0.0418	5008	,	,		19875	0.1409		0.005	False		,,,				2504	0.1033				p.P2676L		Atlas-SNP	.											DCHS2,NS,carcinoma,0,1	DCHS2	594	1	1	Substitution - Missense(1)	stomach(1)	c.C8027T						PASS	.	G	LEU/PRO	520,3886	238.7+/-250.0	40,440,1723	82.0	76.0	78.0		8027	4.7	1.0	4	dbSNP_129	78	86,8514	48.1+/-107.5	1,84,4215	yes	missense	DCHS2	NM_017639.3	98	41,524,5938	AA,AG,GG		1.0,11.8021,4.6594	possibly-damaging	2676/2917	155156412	606,12400	2203	4300	6503	SO:0001583	missense	54798	exon25			GAGTCTGGCACCC	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.8027C>T	4.37:g.155156412G>A	ENSP00000349768:p.Pro2676Leu	Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	152	64	0.421053	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	188	0.08608058608058608	76	0.15447154471544716	21	0.058011049723756904	88	0.15384615384615385	3	0.00395778364116095	G	19.08	3.757140	0.69648	0.118021	0.01	ENSG00000197410	ENST00000357232	T	0.59906	0.23	5.54	4.7	0.59300	.	0.000000	0.64402	D	0.000002	T	0.00524	0.0017	M	0.80422	2.495	0.09310	P	1.0	B	0.29627	0.252	B	0.26614	0.071	T	0.30592	-0.9973	9	0.72032	D	0.01	.	14.5734	0.68229	0.0705:0.0:0.9295:0.0	.	2676	Q6V1P9	PCD23_HUMAN	L	2676	ENSP00000349768:P2676L	ENSP00000349768:P2676L	P	-	2	0	DCHS2	155375862	1.000000	0.71417	0.976000	0.42696	0.901000	0.52897	7.928000	0.87587	1.335000	0.45486	0.460000	0.39030	CCA	G|0.943;A|0.057	0.057	strong		0.517	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
DENND6B	414918	hgsc.bcm.edu	37	22	50754648	50754648	+	Silent	SNP	T	T	C	rs11553141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50754648T>C	ENST00000413817.3	-	7	665	c.594A>G	c.(592-594)gcA>gcG	p.A198A	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	198					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										TCTGCCCAGGTGCAGGCGCCG	0.647																																					p.A198A		Atlas-SNP	.											FAM116B,NS,carcinoma,0,2	.	.	2	0			c.A594G						PASS	.	C		2248,1766		631,986,390	24.0	28.0	27.0		594	1.4	0.0	22	dbSNP_120	27	3462,4856		742,1978,1439	no	coding-synonymous	FAM116B	NM_001001794.3		1373,2964,1829	CC,CT,TT		41.6206,43.996,46.3023		198/586	50754648	5710,6622	2007	4159	6166	SO:0001819	synonymous_variant	414918	exon7			CCCAGGTGCAGGC	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.594A>G	22.37:g.50754648T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	37	13	0.351351	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	987	0.4519230769230769	283	0.5752032520325203	142	0.39226519337016574	241	0.42132867132867136	321	0.4234828496042216	C	0.639	-0.814211	0.02798	0.56004	0.416206	ENSG00000205593	ENST00000433760	.	.	.	4.97	1.42	0.22433	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999719988	.	.	.	.	.	.	T	0.47446	-0.9117	3	.	.	.	0.0609	7.78	0.29060	0.2608:0.6011:0.0:0.1381	rs11553141	.	.	.	R	219	.	.	H	-	2	0	FAM116B	49097220	0.002000	0.14202	0.008000	0.14137	0.092000	0.18411	-0.015000	0.12634	-0.303000	0.08856	-2.888000	0.00096	CAC	T|0.547;C|0.453	0.453	strong		0.647	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
KRT6A	3853	hgsc.bcm.edu	37	12	52886490	52886490	+	Silent	SNP	A	A	G	rs711317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52886490A>G	ENST00000330722.6	-	1	551	c.483T>C	c.(481-483)gcT>gcC	p.A161A		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	161	Head.				cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.A161A(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		CACGCTCCTCAGCCCGCACCC	0.597													A|||	2249	0.449081	0.1331	0.6023	5008	,	,		18611	0.6319		0.6044	False		,,,				2504	0.4192				p.A161A		Atlas-SNP	.											KRT6A,NS,carcinoma,0,1	KRT6A	89	1	1	Substitution - coding silent(1)	prostate(1)	c.T483C						PASS	.	A		868,3538	339.9+/-306.0	77,714,1412	169.0	155.0	160.0		483	-10.6	0.3	12	dbSNP_86	160	5019,3581	627.2+/-397.9	1467,2085,748	no	coding-synonymous	KRT6A	NM_005554.3		1544,2799,2160	GG,GA,AA		41.6395,19.7004,45.2637		161/565	52886490	5887,7119	2203	4300	6503	SO:0001819	synonymous_variant	3853	exon1			CTCCTCAGCCCGC	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.483T>C	12.37:g.52886490A>G		Somatic	358	1	0.0027933		WXS	Illumina HiSeq	Phase_I	317	130	0.410095	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Silent	SNP	ENST00000330722.6	37	CCDS41786.1																																																																																			A|0.452;G|0.547	0.547	strong		0.597	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
MIOX	55586	hgsc.bcm.edu	37	22	50926768	50926768	+	Silent	SNP	C	C	T	rs2232883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50926768C>T	ENST00000216075.6	+	5	479	c.405C>T	c.(403-405)ccC>ccT	p.P135P	MIOX_ENST00000395732.3_Silent_p.P135P|MIOX_ENST00000395733.3_Missense_Mutation_p.P146L	NM_017584.5	NP_060054.4	Q9UGB7	MIOX_HUMAN	myo-inositol oxygenase	135					inositol catabolic process (GO:0019310)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)	aldo-keto reductase (NADP) activity (GO:0004033)|ferric iron binding (GO:0008199)|inositol oxygenase activity (GO:0050113)|NADP binding (GO:0050661)|oxidoreductase activity, acting on NAD(P)H (GO:0016651)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	13		all_cancers(38;4.58e-14)|all_epithelial(38;1.12e-12)|all_lung(38;3.07e-05)|Breast(42;6.27e-05)|Lung NSC(38;0.000813)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TCGGGGAGCCCCAGGTAAGAG	0.647													c|||	427	0.0852636	0.093	0.0908	5008	,	,		14186	0.0278		0.1392	False		,,,				2504	0.0746				p.P135P		Atlas-SNP	.											.	MIOX	21	.	0			c.C405T						PASS	.	C		450,3956	211.5+/-231.7	30,390,1783	55.0	57.0	56.0		405	-2.2	1.0	22	dbSNP_98	56	1244,7356	245.7+/-274.4	101,1042,3157	no	coding-synonymous	MIOX	NM_017584.5		131,1432,4940	TT,TC,CC		14.4651,10.2133,13.0248		135/286	50926768	1694,11312	2203	4300	6503	SO:0001819	synonymous_variant	55586	exon5			GGAGCCCCAGGTA	AF197129	CCDS14092.1	22q13.3	2008-06-11	2005-06-15	2005-06-15	ENSG00000100253	ENSG00000100253			14522	protein-coding gene	gene with protein product	"""kidney-specific protein 32"""	606774	"""aldehyde reductase (aldose reductase) like 6"""	ALDRL6		10944187, 11716759	Standard	NM_017584		Approved		uc003bll.1	Q9UGB7	OTTHUMG00000150207	ENST00000216075.6:c.405C>T	22.37:g.50926768C>T		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	93	56	0.602151	NM_017584	Q05DJ6|Q5S8C9|Q9BZZ1|Q9UHB8	Silent	SNP	ENST00000216075.6	37	CCDS14092.1	212	0.09706959706959707	48	0.0975609756097561	38	0.10497237569060773	16	0.027972027972027972	110	0.14511873350923482	C	10.08	1.251662	0.22880	0.102133	0.144651	ENSG00000100253	ENST00000395733	.	.	.	4.29	-2.17	0.07059	.	0.057262	0.64402	D	0.000001	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	B	0.09022	0.002	B	0.09377	0.004	T	0.07366	-1.0776	7	0.72032	D	0.01	-9.7685	0.8144	0.01099	0.163:0.2381:0.3211:0.2778	rs2232883	146	Q9UGB7-2	.	L	146	.	ENSP00000379082:P146L	P	+	2	0	MIOX	49273634	0.009000	0.17119	1.000000	0.80357	0.751000	0.42716	-0.849000	0.04322	0.058000	0.16222	0.436000	0.28706	CCC	C|0.878;T|0.122	0.122	strong		0.647	MIOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316835.1	NM_017584	
HLA-A	3105	hgsc.bcm.edu	37	6	29911296	29911296	+	Missense_Mutation	SNP	G	G	A	rs41559916	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29911296G>A	ENST00000396634.1	+	5	936	c.595G>A	c.(595-597)Ggg>Agg	p.G199R	HLA-A_ENST00000376809.5_Missense_Mutation_p.G199R|HLA-A_ENST00000376806.5_Missense_Mutation_p.G199R|HLA-A_ENST00000376802.2_Missense_Mutation_p.G199R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	199	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						CCTGGAGAACGGGAAGGAGAC	0.662									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.G199R		Atlas-SNP	.											HLA-A,NS,carcinoma,0,1	HLA-A	89	1	0			c.G595A						PASS	.						48.0	43.0	45.0					6																	29911296		1510	2704	4214	SO:0001583	missense	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGAACGGGAAGG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.595G>A	6.37:g.29911296G>A	ENSP00000379873:p.Gly199Arg	Somatic	189	0	0		WXS	Illumina HiSeq	Phase_I	138	23	0.166667	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	310	0.14194139194139194	89	0.18089430894308944	51	0.1408839779005525	52	0.09090909090909091	118	0.15567282321899736	.	13.19	2.162852	0.38217	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	T;T;T;T	0.01068	5.38;5.38;5.38;5.38	3.54	3.54	0.40534	MHC class I, alpha chain, alpha1/alpha2 (8);MHC classes I/II-like antigen recognition protein (4);MHC class I-like antigen recognition (4);	0.000000	0.38605	U	0.001626	T	0.06325	0.0163	H	0.95328	3.655	0.34266	P	0.31949700000000003	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;0.998;1.0;1.0;1.0	T	0.01805	-1.1270	9	0.72032	D	0.01	.	13.0189	0.58775	0.0:0.0:1.0:0.0	rs41559916	78;199;199;199;199;199;199	B4DVB9;P13746;Q5SRN7;P16188;Q5SRN5;P30455;P04439	.;1A11_HUMAN;.;1A30_HUMAN;.;1A36_HUMAN;1A03_HUMAN	R	199	ENSP00000379873:G199R;ENSP00000366002:G199R;ENSP00000366005:G199R;ENSP00000365998:G199R	ENSP00000365998:G199R	G	+	1	0	HLA-A	30019275	1.000000	0.71417	0.505000	0.27651	0.339000	0.28857	4.611000	0.61162	1.987000	0.57996	0.485000	0.47835	GGG	A|0.146;G|0.854	0.146	strong		0.662	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1017974C>G	ENST00000421673.2	-	31	4877	c.4827G>C	c.(4825-4827)caG>caC	p.Q1609H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1609	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.Q1609H(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAAGTGTGGTCTGAGGGTGTG	0.547																																					p.Q1609H		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	large_intestine(2)	c.G4827C						scavenged	.						473.0	441.0	452.0					11																	1017974		2186	4282	6468	SO:0001583	missense	4588	exon31			TGTGGTCTGAGGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4827G>C	11.37:g.1017974C>G	ENSP00000406861:p.Gln1609His	Somatic	404	7	0.0173267		WXS	Illumina HiSeq	Phase_I	497	18	0.0362173	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	5.277	0.236564	0.10023	.	.	ENSG00000184956	ENST00000421673	T	0.35421	1.31	2.39	0.333	0.15943	.	.	.	.	.	T	0.26702	0.0653	L	0.52011	1.625	0.09310	N	1	B	0.25486	0.127	B	0.27715	0.082	T	0.28681	-1.0036	9	0.22109	T	0.4	.	3.4702	0.07565	0.0:0.5042:0.2173:0.2785	.	1609	Q6W4X9	MUC6_HUMAN	H	1609	ENSP00000406861:Q1609H	ENSP00000406861:Q1609H	Q	-	3	2	MUC6	1007974	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-2.394000	0.01054	-0.057000	0.13199	-0.710000	0.03640	CAG	.	.	weak		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
OR10AD1	121275	hgsc.bcm.edu	37	12	48596579	48596579	+	Missense_Mutation	SNP	C	C	T	rs17224674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48596579C>T	ENST00000310248.2	-	1	591	c.497G>A	c.(496-498)cGa>cAa	p.R166Q		NM_001004134.1	NP_001004134.1	Q8NGE0	O10AD_HUMAN	olfactory receptor, family 10, subfamily AD, member 1	166			R -> Q (in dbSNP:rs17224674).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|stomach(1)|urinary_tract(1)	9						GAAGGGCTCTCGGAATGAAAT	0.507													C|||	123	0.0245607	0.0076	0.0317	5008	,	,		21550	0.0		0.0815	False		,,,				2504	0.0092				p.R166Q		Atlas-SNP	.											.	OR10AD1	24	.	0			c.G497A						PASS	.	C	GLN/ARG	90,4316	76.2+/-114.5	0,90,2113	53.0	46.0	48.0		497	0.7	0.0	12	dbSNP_123	48	713,7887	173.9+/-224.3	27,659,3614	yes	missense	OR10AD1	NM_001004134.1	43	27,749,5727	TT,TC,CC		8.2907,2.0427,6.1741	probably-damaging	166/318	48596579	803,12203	2203	4300	6503	SO:0001583	missense	121275	exon1			GGCTCTCGGAATG		CCDS31787.1	12q13.11	2013-09-24	2002-11-13	2002-11-15	ENSG00000172640	ENSG00000172640		"""GPCR / Class A : Olfactory receptors"""	14819	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily AD, member 1 pseudogene"""	OR10AD1P			Standard	NM_001004134		Approved		uc001rrl.1	Q8NGE0	OTTHUMG00000168027	ENST00000310248.2:c.497G>A	12.37:g.48596579C>T	ENSP00000308689:p.Arg166Gln	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	143	65	0.454545	NM_001004134	B9EGT9|Q6IFA8	Missense_Mutation	SNP	ENST00000310248.2	37	CCDS31787.1	70	0.03205128205128205	4	0.008130081300813009	8	0.022099447513812154	0	0.0	58	0.07651715039577836	C	3.399	-0.122722	0.06795	0.020427	0.082907	ENSG00000172640	ENST00000310248	T	0.00145	8.67	4.83	0.729	0.18266	GPCR, rhodopsin-like superfamily (1);	0.538596	0.14094	N	0.341831	T	0.00012	0.0000	N	0.05199	-0.095	0.09310	N	1	B	0.22346	0.068	B	0.13407	0.009	T	0.01316	-1.1387	10	0.15499	T	0.54	-0.4284	3.3589	0.07179	0.1804:0.5273:0.0:0.2923	rs17224674;rs56500145;rs17224674	166	Q8NGE0	O10AD_HUMAN	Q	166	ENSP00000308689:R166Q	ENSP00000308689:R166Q	R	-	2	0	OR10AD1	46882846	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.917000	0.00695	0.348000	0.23949	0.561000	0.74099	CGA	C|0.954;T|0.046	0.046	strong		0.507	OR10AD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397577.1		
TMEM99	147184	hgsc.bcm.edu	37	17	38991003	38991003	+	Missense_Mutation	SNP	T	T	C	rs10558	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38991003T>C	ENST00000301665.3	+	3	539	c.235T>C	c.(235-237)Tat>Cat	p.Y79H		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	79			Y -> H (in dbSNP:rs10558).			integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				CTTTCTTCGCTATCTTGGGAC	0.468													T|||	1690	0.33746	0.4758	0.1499	5008	,	,		20764	0.4077		0.1839	False		,,,				2504	0.3691				p.Y79H		Atlas-SNP	.											.	TMEM99	21	.	0			c.T235C						PASS	.	T	HIS/TYR,HIS/TYR,HIS/TYR	1614,2202		360,894,654	229.0	228.0	228.0		235,235,235	-0.5	0.0	17	dbSNP_52	228	1357,6897		120,1117,2890	yes	missense,missense,missense	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	83,83,83	480,2011,3544	CC,CT,TT		16.4405,42.2956,24.6147	benign,benign,benign	79/259,79/259,79/259	38991003	2971,9099	1908	4127	6035	SO:0001583	missense	147184	exon3			CTTCGCTATCTTG	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.235T>C	17.37:g.38991003T>C	ENSP00000301665:p.Tyr79His	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	227	117	0.515419	NM_001195386	B4DQ34|Q96BP9	Missense_Mutation	SNP	ENST00000301665.3	37	CCDS42319.1	651	0.2980769230769231	221	0.4491869918699187	63	0.17403314917127072	231	0.40384615384615385	136	0.17941952506596306	T	1.938	-0.444291	0.04604	0.422956	0.164405	ENSG00000167920	ENST00000436612;ENST00000301665	T;T	0.31247	1.5;1.5	0.235	-0.47	0.12131	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.25955	0.138	B	0.20577	0.03	T	0.45440	-0.9261	7	0.87932	D	0	.	.	.	.	rs10558;rs3169918;rs52809908;rs58229259;rs10558	79	Q8N816	TMM99_HUMAN	H	79	ENSP00000390036:Y79H;ENSP00000301665:Y79H	ENSP00000301665:Y79H	Y	+	1	0	TMEM99	36244529	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	-1.878000	0.01630	-0.905000	0.03871	-0.946000	0.02672	TAT	T|0.704;C|0.296	0.296	strong		0.468	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48142636	48142636	+	Missense_Mutation	SNP	C	C	T	rs12422983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:48142636C>T	ENST00000449771.2	-	11	1208	c.1120G>A	c.(1120-1122)Ggc>Agc	p.G374S	RAPGEF3_ENST00000171000.4_Missense_Mutation_p.G332S|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.G332S|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.G374S|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.G332S|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.G332S|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.G374S			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	374			G -> S (in dbSNP:rs12422983).		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		CGGGAAGGGCCGGCGCCCTGA	0.592													C|||	452	0.0902556	0.0998	0.1354	5008	,	,		16760	0.0298		0.1451	False		,,,				2504	0.0511				p.G374S		Atlas-SNP	.											RAPGEF3,colon,carcinoma,+1,1	RAPGEF3	98	1	0			c.G1120A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	488,3918	227.8+/-242.9	27,434,1742	165.0	152.0	156.0		1120,994,994	3.3	0.0	12	dbSNP_120	156	1253,7347	251.5+/-278.0	78,1097,3125	yes	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	56,56,56	105,1531,4867	TT,TC,CC		14.5698,11.0758,13.3861	possibly-damaging,possibly-damaging,possibly-damaging	374/924,332/882,332/882	48142636	1741,11265	2203	4300	6503	SO:0001583	missense	10411	exon11			AAGGGCCGGCGCC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1120G>A	12.37:g.48142636C>T	ENSP00000395708:p.Gly374Ser	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	152	77	0.506579	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	221	0.10119047619047619	52	0.10569105691056911	56	0.15469613259668508	16	0.027972027972027972	97	0.1279683377308707	C	9.169	1.020728	0.19433	0.110758	0.145698	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358	T;T;T;T;T;T;T	0.69806	-0.26;-0.26;-0.26;-0.26;-0.26;-0.43;-0.32	4.19	3.3	0.37823	Ras guanine nucleotide exchange factor, domain (1);	1.144270	0.06284	N	0.698024	T	0.00524	0.0017	N	0.19112	0.55	0.58432	P	1.999999999946489E-6	P;D	0.63880	0.627;0.993	B;P	0.52793	0.034;0.709	T	0.10870	-1.0611	9	0.37606	T	0.19	.	5.7708	0.18251	0.0:0.7053:0.0:0.2947	rs12422983;rs52812325;rs12422983	386;374	B7Z5J6;O95398	.;RPGF3_HUMAN	S	332;374;21;332;332;332;374;386;332;374	ENSP00000384521:G332S;ENSP00000395708:G374S;ENSP00000448619:G332S;ENSP00000171000:G332S;ENSP00000373864:G374S;ENSP00000448480:G332S;ENSP00000378764:G374S	ENSP00000171000:G332S	G	-	1	0	RAPGEF3	46428903	0.000000	0.05858	0.023000	0.16930	0.065000	0.16274	0.404000	0.20999	1.349000	0.45751	0.650000	0.86243	GGC	C|0.880;T|0.120	0.120	strong		0.592	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
DNHD1	144132	hgsc.bcm.edu	37	11	6549779	6549779	+	Missense_Mutation	SNP	A	A	C	rs4633449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6549779A>C	ENST00000527990.2	+	9	1865	c.1865A>C	c.(1864-1866)gAc>gCc	p.D622A	DNHD1_ENST00000254579.6_Missense_Mutation_p.D622A			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	622					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GACTCAAAAGACGAATTTCTG	0.532													C|||	3656	0.730032	0.6944	0.6585	5008	,	,		19003	0.874		0.6302	False		,,,				2504	0.7832				p.D622A		Atlas-SNP	.											.	DNHD1	198	.	0			c.A1865C						PASS	.	C	ALA/ASP	954,430		326,302,64	94.0	85.0	88.0		1865	-2.8	0.0	11	dbSNP_111	88	2138,1044		723,692,176	yes	missense	DNHD1	NM_144666.2	126	1049,994,240	CC,CA,AA		32.8096,31.0694,32.2821	benign	622/4754	6549779	3092,1474	692	1591	2283	SO:0001583	missense	144132	exon11			CAAAAGACGAATT	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.1865A>C	11.37:g.6549779A>C	ENSP00000436180:p.Asp622Ala	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	93	93	1	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	1562	0.7152014652014652	353	0.717479674796748	236	0.6519337016574586	487	0.8513986013986014	486	0.6411609498680739	C	4.359	0.066121	0.08388	0.689306	0.671904	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.24151	1.87;1.87	4.47	-2.8	0.05823	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25257	-1.0137	8	0.07175	T	0.84	.	3.7229	0.08463	0.408:0.2437:0.0:0.3484	rs4633449;rs61259590;rs4633449	622	Q96M86	DNHD1_HUMAN	A	622	ENSP00000254579:D622A;ENSP00000436180:D622A	ENSP00000254579:D622A	D	+	2	0	DNHD1	6506355	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-1.220000	0.02971	-1.046000	0.03246	-0.217000	0.12591	GAC	A|0.272;C|0.728	0.728	strong		0.532	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
C6orf57	135154	hgsc.bcm.edu	37	6	71289189	71289189	+	Missense_Mutation	SNP	A	A	G	rs1048886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:71289189A>G	ENST00000370474.3	+	2	161	c.137A>G	c.(136-138)cAg>cGg	p.Q46R		NM_145267.2	NP_660310.2	Q5VUM1	SDHF4_HUMAN	chromosome 6 open reading frame 57	46			Q -> R (in dbSNP:rs1048886).		innate immune response (GO:0045087)	extracellular region (GO:0005576)|mitochondrion (GO:0005739)				kidney(1)|lung(1)|skin(1)	3						CTTGTCAAACAGTCCCTTAAG	0.403													A|||	992	0.198083	0.3192	0.2161	5008	,	,		14511	0.0833		0.175	False		,,,				2504	0.1636				p.Q46R		Atlas-SNP	.											.	C6orf57	13	.	0			c.A137G						PASS	.	A	ARG/GLN	1319,3087	444.5+/-347.4	207,905,1091	112.0	111.0	111.0	http://www.ncbi.nlm.nih.gov/pubmed?term	137	4.6	0.1	6	dbSNP_86	111	1468,7132	281.2+/-294.9	141,1186,2973	yes	missense	C6orf57	NM_145267.2	43	348,2091,4064	GG,GA,AA	http://www.ncbi.nlm.nih.gov/pubmed?term	17.0698,29.9365,21.4286	probably-damaging	46/109	71289189	2787,10219	2203	4300	6503	SO:0001583	missense	135154	exon2			TCAAACAGTCCCT	BC018085	CCDS4972.1	6q12	2011-12-13			ENSG00000154079	ENSG00000154079			20957	protein-coding gene	gene with protein product							Standard	NM_145267		Approved		uc003pfq.1	Q5VUM1	OTTHUMG00000014992	ENST00000370474.3:c.137A>G	6.37:g.71289189A>G	ENSP00000359505:p.Gln46Arg	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	35	7	0.2	NM_145267	E1P532	Missense_Mutation	SNP	ENST00000370474.3	37	CCDS4972.1	447	0.20467032967032966	165	0.3353658536585366	78	0.2154696132596685	63	0.11013986013986014	141	0.18601583113456466	A	10.53	1.375636	0.24857	0.299365	0.170698	ENSG00000154079	ENST00000370474	T	0.31247	1.5	5.82	4.64	0.57946	.	0.101718	0.64402	D	0.000002	T	0.21307	0.0513	M	0.72894	2.215	0.47511	P	5.519999999999969E-4	B	0.27910	0.193	B	0.34536	0.185	T	0.08229	-1.0732	9	0.54805	T	0.06	-6.9699	10.8459	0.46743	0.8415:0.1584:0.0:0.0	rs1048886;rs3188927;rs56527910;rs61433581;rs1048886	46	Q5VUM1	CF057_HUMAN	R	46	ENSP00000359505:Q46R	ENSP00000359505:Q46R	Q	+	2	0	C6orf57	71345910	0.926000	0.31397	0.062000	0.19696	0.196000	0.23810	4.409000	0.59768	0.989000	0.38761	0.472000	0.43445	CAG	A|0.787;G|0.213	0.213	strong		0.403	C6orf57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041140.1	NM_145267	
SPINK5	11005	hgsc.bcm.edu	37	5	147480112	147480112	+	Silent	SNP	T	T	C	rs2303065	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:147480112T>C	ENST00000256084.7	+	13	1230	c.1188T>C	c.(1186-1188)caT>caC	p.H396H	SPINK5_ENST00000398454.1_Silent_p.H396H|SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Silent_p.H396H	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	396	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.H396H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGAAAGTGCATGGCAACACCT	0.478													t|||	2168	0.432907	0.1989	0.6167	5008	,	,		17745	0.4851		0.4861	False		,,,				2504	0.5102				p.H396H		Atlas-SNP	.											SPINK5,NS,carcinoma,0,1	SPINK5	245	1	1	Substitution - coding silent(1)	stomach(1)	c.T1188C						scavenged	.	C	,,	994,2980		127,740,1120	155.0	154.0	155.0		1188,1188,1188	-0.5	0.6	5	dbSNP_100	155	4264,4084		1079,2106,989	no	coding-synonymous,coding-synonymous,coding-synonymous	SPINK5	NM_001127698.1,NM_001127699.1,NM_006846.3	,,	1206,2846,2109	CC,CT,TT		48.9219,25.0126,42.6716	,,	396/1095,396/917,396/1065	147480112	5258,7064	1987	4174	6161	SO:0001819	synonymous_variant	11005	exon13			AGTGCATGGCAAC	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1188T>C	5.37:g.147480112T>C		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	60	60	1	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Silent	SNP	ENST00000256084.7	37	CCDS43382.1																																																																																			T|0.546;C|0.454	0.454	strong		0.478	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
FSCB	84075	hgsc.bcm.edu	37	14	44975511	44975511	+	Missense_Mutation	SNP	G	G	A	rs372153461|rs45478391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:44975511G>A	ENST00000340446.4	-	1	971	c.680C>T	c.(679-681)cCg>cTg	p.P227L	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)		TAAAAGTACCGGGGGACCTTT	0.408													G|||	541	0.108027	0.0053	0.1009	5008	,	,		18318	0.0833		0.2296	False		,,,				2504	0.1524				p.P227L		Atlas-SNP	.											.	FSCB	173	.	0			c.C680T						PASS	.	G	LEU/PRO	169,4237	111.2+/-149.4	2,165,2036	97.0	99.0	98.0		680	-6.0	0.0	14	dbSNP_127	98	1818,6782	326.4+/-317.4	186,1446,2668	yes	missense	FSCB	NM_032135.3	98	188,1611,4704	AA,AG,GG		21.1395,3.8357,15.2776	benign	227/826	44975511	1987,11019	2203	4300	6503	SO:0001583	missense	84075	exon1			AGTACCGGGGGAC	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.680C>T	14.37:g.44975511G>A	ENSP00000344579:p.Pro227Leu	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	154	71	0.461039	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	287	0.13141025641025642	4	0.008130081300813009	49	0.13535911602209943	49	0.08566433566433566	185	0.24406332453825857	G	5.123	0.208391	0.09757	0.038357	0.211395	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.23754	1.89	4.24	-5.98	0.02220	.	.	.	.	.	T	0.00012	0.0000	L	0.40543	1.245	0.80722	P	0.0	B	0.23891	0.093	B	0.16722	0.016	T	0.39121	-0.9629	8	0.30078	T	0.28	7.679	2.1036	0.03686	0.4745:0.1129:0.2656:0.147	rs45478391;rs61739486	227	Q5H9T9	FSCB_HUMAN	L	227	ENSP00000344579:P227L	ENSP00000344579:P227L	P	-	2	0	FSCB	44045261	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.326000	0.07965	-1.143000	0.02866	-0.140000	0.14226	CCG	G|0.852;A|0.148	0.148	strong		0.408	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135	
L3MBTL2	83746	hgsc.bcm.edu	37	22	41610024	41610024	+	Silent	SNP	G	G	A	rs139451	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:41610024G>A	ENST00000216237.5	+	3	548	c.390G>A	c.(388-390)agG>agA	p.R130R	RP4-756G23.5_ENST00000451176.1_RNA|RP4-756G23.5_ENST00000441316.1_RNA|L3MBTL2_ENST00000489136.1_3'UTR	NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	130					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TCTTGGCTAGGTTACAGGTGA	0.527													A|||	1823	0.364018	0.5749	0.3357	5008	,	,		18957	0.1885		0.3638	False		,,,				2504	0.2802				p.R130R		Atlas-SNP	.											.	L3MBTL2	61	.	0			c.G390A						PASS	.	A		2451,1955	552.3+/-378.5	691,1069,443	96.0	92.0	93.0		390	0.9	0.6	22	dbSNP_78	93	3277,5323	647.6+/-400.4	659,1959,1682	no	coding-synonymous	L3MBTL2	NM_031488.4		1350,3028,2125	AA,AG,GG		38.1047,44.3713,44.0412		130/706	41610024	5728,7278	2203	4300	6503	SO:0001819	synonymous_variant	83746	exon3			GGCTAGGTTACAG	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.390G>A	22.37:g.41610024G>A		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	96	47	0.489583	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Silent	SNP	ENST00000216237.5	37	CCDS14011.1																																																																																			G|0.598;A|0.402	0.402	strong		0.527	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488	
OR13D1	286365	hgsc.bcm.edu	37	9	107457725	107457725	+	Silent	SNP	G	G	A	rs12338899	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:107457725G>A	ENST00000318763.5	+	1	1066	c.1023G>A	c.(1021-1023)ctG>ctA	p.L341L		NM_001004484.1	NP_001004484.1	Q8NGV5	O13D1_HUMAN	olfactory receptor, family 13, subfamily D, member 1	341						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						GCAGACATCTGCATTTATTGA	0.408													G|||	1353	0.270168	0.1657	0.183	5008	,	,		19813	0.4821		0.1909	False		,,,				2504	0.3364				p.L341L		Atlas-SNP	.											.	OR13D1	42	.	0			c.G1023A						PASS	.	G		789,3617	314.4+/-293.6	75,639,1489	58.0	59.0	59.0		1023	-6.9	0.0	9	dbSNP_120	59	1824,6776	323.0+/-315.8	224,1376,2700	yes	coding-synonymous	OR13D1	NM_001004484.1		299,2015,4189	AA,AG,GG		21.2093,17.9074,20.0907		341/347	107457725	2613,10393	2203	4300	6503	SO:0001819	synonymous_variant	286365	exon1			ACATCTGCATTTA		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.1023G>A	9.37:g.107457725G>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	92	39	0.423913	NM_001004484	B9EIS1|Q6IFL1	Silent	SNP	ENST00000318763.5	37	CCDS35094.1																																																																																			G|0.786;A|0.214	0.214	strong		0.408	OR13D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053483.1		
SIGLEC1	6614	hgsc.bcm.edu	37	20	3682126	3682126	+	Missense_Mutation	SNP	C	C	T	rs34924243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3682126C>T	ENST00000344754.4	-	6	1390	c.1391G>A	c.(1390-1392)cGc>cAc	p.R464H	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.R464H	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	464	Ig-like C2-type 4.		R -> H (in dbSNP:rs34924243).		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						ACCACTGAAGCGTGGGCTGTG	0.602													C|||	137	0.0273562	0.0015	0.0375	5008	,	,		21082	0.0129		0.0567	False		,,,				2504	0.0399				p.R464H		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G1391A						PASS	.	C	HIS/ARG	70,4336	63.5+/-100.7	0,70,2133	104.0	79.0	87.0		1391	5.7	1.0	20	dbSNP_126	87	605,7995	158.5+/-212.0	20,565,3715	yes	missense	SIGLEC1	NM_023068.3	29	20,635,5848	TT,TC,CC		7.0349,1.5887,5.1899	probably-damaging	464/1710	3682126	675,12331	2203	4300	6503	SO:0001583	missense	6614	exon6			CTGAAGCGTGGGC	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.1391G>A	20.37:g.3682126C>T	ENSP00000341141:p.Arg464His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	151	76	0.503311	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	37	CCDS13060.1	72	0.03296703296703297	1	0.0020325203252032522	21	0.058011049723756904	4	0.006993006993006993	46	0.06068601583113457	C	21.0	4.075425	0.76415	0.015887	0.070349	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.79653	-1.29;-1.29	5.69	5.69	0.88448	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.41294	D	0.000902	T	0.46814	0.1412	M	0.63843	1.955	0.41958	D	0.990691	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.993	T	0.74303	-0.3709	10	0.59425	D	0.04	.	17.2983	0.87175	0.0:1.0:0.0:0.0	rs34924243	464;464	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	H	464	ENSP00000341141:R464H;ENSP00000202578:R464H	ENSP00000202578:R464H	R	-	2	0	SIGLEC1	3630126	1.000000	0.71417	0.996000	0.52242	0.533000	0.34776	3.228000	0.51270	2.676000	0.91093	0.655000	0.94253	CGC	C|0.952;T|0.048	0.048	strong		0.602	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
ATP13A5	344905	hgsc.bcm.edu	37	3	193036794	193036794	+	Silent	SNP	G	G	C	rs6788770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:193036794G>C	ENST00000342358.4	-	17	2136	c.2019C>G	c.(2017-2019)gtC>gtG	p.V673V		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	673						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)		CTAAGTGCTCGACTTCTGAAA	0.478													C|||	4487	0.895966	0.9334	0.8415	5008	,	,		21399	0.9821		0.8171	False		,,,				2504	0.8763				p.V673V		Atlas-SNP	.											.	ATP13A5	171	.	0			c.C2019G						PASS	.	C		4026,380	191.2+/-216.9	1841,344,18	113.0	114.0	114.0		2019	0.4	0.0	3	dbSNP_116	114	7013,1587	297.0+/-303.2	2852,1309,139	no	coding-synonymous	ATP13A5	NM_198505.2		4693,1653,157	CC,CG,GG		18.4535,8.6246,15.1238		673/1219	193036794	11039,1967	2203	4300	6503	SO:0001819	synonymous_variant	344905	exon17			GTGCTCGACTTCT	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.2019C>G	3.37:g.193036794G>C		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	50	50	1	NM_198505	Q6UWS4|Q6ZWL0	Silent	SNP	ENST00000342358.4	37	CCDS33914.1																																																																																			G|0.140;C|0.860	0.860	strong		0.478	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505	
TAS2R4	50832	hgsc.bcm.edu	37	7	141478574	141478574	+	Missense_Mutation	SNP	G	G	C	rs2234001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141478574G>C	ENST00000247881.2	+	1	333	c.286G>C	c.(286-288)Gtc>Ctc	p.V96L	SSBP1_ENST00000465582.1_Intron	NM_016944.1	NP_058640.1	Q9NYW5	TA2R4_HUMAN	taste receptor, type 2, member 4	96			V -> L (in dbSNP:rs2234001).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|respiratory gaseous exchange (GO:0007585)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|large_intestine(4)|lung(2)	7	Melanoma(164;0.0171)			BRCA - Breast invasive adenocarcinoma(188;0.196)		CTCGAGCAGTGTCTGGTTTGT	0.423													C|||	2637	0.526558	0.3192	0.5793	5008	,	,		21049	0.745		0.4722	False		,,,				2504	0.6002				p.V96L		Atlas-SNP	.											.	TAS2R4	25	.	0			c.G286C						PASS	.	C	LEU/VAL	1575,2831	493.1+/-362.6	314,947,942	218.0	192.0	201.0		286	2.7	0.9	7	dbSNP_98	201	4274,4326	575.0+/-390.2	1055,2164,1081	yes	missense	TAS2R4	NM_016944.1	32	1369,3111,2023	CC,CG,GG		49.6977,35.7467,44.9716	benign	96/300	141478574	5849,7157	2203	4300	6503	SO:0001583	missense	50832	exon1			AGCAGTGTCTGGT	AF227131	CCDS5868.1	7q31.3-q32	2012-08-22			ENSG00000127364	ENSG00000127364		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14911	protein-coding gene	gene with protein product		604869				10761934, 10761935	Standard	NM_016944		Approved	T2R4	uc003vwq.1	Q9NYW5	OTTHUMG00000157634	ENST00000247881.2:c.286G>C	7.37:g.141478574G>C	ENSP00000247881:p.Val96Leu	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	213	104	0.488263	NM_016944	Q645W5|Q75MV8	Missense_Mutation	SNP	ENST00000247881.2	37	CCDS5868.1	1150	0.5265567765567766	166	0.33739837398373984	204	0.56353591160221	427	0.7465034965034965	353	0.4656992084432718	g	0.015	-1.567101	0.00895	0.357467	0.496977	ENSG00000127364	ENST00000247881	T	0.00631	6.09	5.52	2.73	0.32206	.	0.169609	0.35805	N	0.002963	T	0.00012	0.0000	N	0.00347	-1.61	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.10451	-1.0629	9	0.02654	T	1	.	10.3055	0.43678	0.0:0.5464:0.382:0.0716	rs2234001;rs3735278;rs17523539;rs52815299;rs2234001	96	Q9NYW5	TA2R4_HUMAN	L	96	ENSP00000247881:V96L	ENSP00000247881:V96L	V	+	1	0	TAS2R4	141125043	0.000000	0.05858	0.918000	0.36340	0.152000	0.21847	0.138000	0.16016	0.147000	0.19030	-0.876000	0.02978	GTC	G|0.508;C|0.492	0.492	strong		0.423	TAS2R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349285.1		
PHC1	1911	hgsc.bcm.edu	37	12	9086898	9086898	+	Missense_Mutation	SNP	A	A	G	rs1049925	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:9086898A>G	ENST00000543824.1	+	11	2409	c.2077A>G	c.(2077-2079)Act>Gct	p.T693A	PHC1_ENST00000536844.1_Missense_Mutation_p.T299A|PHC1_ENST00000544916.1_Missense_Mutation_p.T693A|PHC1_ENST00000433083.2_Missense_Mutation_p.T648A			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	693			T -> A (in dbSNP:rs1049925). {ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cellular response to retinoic acid (GO:0071300)|histone ubiquitination (GO:0016574)|multicellular organismal development (GO:0007275)	nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|large_intestine(8)|liver(2)|lung(3)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	27						GAATGCTAATACTCCAAGCAG	0.448													A|||	1770	0.353435	0.1551	0.3818	5008	,	,		-128	0.4107		0.4274	False		,,,				2504	0.4663				p.T693A		Atlas-SNP	.											.	PHC1	67	.	0			c.A2077G						PASS	.	A	ALA/THR	868,3538	335.2+/-303.8	82,704,1417	102.0	96.0	98.0		2077	0.9	0.1	12	dbSNP_86	98	3806,4794	524.3+/-380.5	784,2238,1278	yes	missense	PHC1	NM_004426.2	58	866,2942,2695	GG,GA,AA		44.2558,19.7004,35.9373	benign	693/1005	9086898	4674,8332	2203	4300	6503	SO:0001583	missense	1911	exon10			GCTAATACTCCAA	U89277	CCDS8597.1	12p13	2013-01-10	2006-09-12	2002-11-15	ENSG00000111752	ENSG00000111752		"""Sterile alpha motif (SAM) domain containing"""	3182	protein-coding gene	gene with protein product		602978	"""early development regulator 1 (homolog of polyhomeotic 1)"", ""polyhomeotic-like 1 (Drosophila)"""	EDR1		9121482	Standard	XM_005253334		Approved	HPH1, RAE28	uc001qvd.3	P78364	OTTHUMG00000168275	ENST00000543824.1:c.2077A>G	12.37:g.9086898A>G	ENSP00000440674:p.Thr693Ala	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	83	74	0.891566	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	37	CCDS8597.1	803	0.3676739926739927	71	0.1443089430894309	135	0.3729281767955801	268	0.46853146853146854	329	0.4340369393139842	A	8.336	0.827685	0.16749	0.197004	0.442558	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;T	0.36340	1.99;1.99;1.99;1.99;1.26	5.32	0.937	0.19494	.	0.365346	0.27008	N	0.021396	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.47861	-0.9084	9	0.25106	T	0.35	-4.416	3.3522	0.07156	0.425:0.3732:0.0766:0.1252	rs1049925;rs12818486;rs16915798;rs17294227;rs17729971;rs52819214;rs59173968;rs1049925	693	P78364	PHC1_HUMAN	A	693;693;648;693;299	ENSP00000440674:T693A;ENSP00000251757:T693A;ENSP00000399194:T648A;ENSP00000437659:T693A;ENSP00000440488:T299A	ENSP00000251757:T693A	T	+	1	0	PHC1	8978165	0.000000	0.05858	0.105000	0.21289	0.907000	0.53573	-0.529000	0.06186	-0.009000	0.14296	0.533000	0.62120	ACT	A|0.630;G|0.370	0.370	strong		0.448	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426	
UTP20	27340	hgsc.bcm.edu	37	12	101693534	101693534	+	Missense_Mutation	SNP	C	C	G	rs4764643	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101693534C>G	ENST00000261637.4	+	13	1679	c.1505C>G	c.(1504-1506)tCt>tGt	p.S502C		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	502			S -> C (in dbSNP:rs4764643).		endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CATCTTTTATCTATAATTAAG	0.338													C|||	529	0.105631	0.0439	0.1254	5008	,	,		19257	0.0288		0.1849	False		,,,				2504	0.1728				p.S502C		Atlas-SNP	.											.	UTP20	222	.	0			c.C1505G						PASS	.	C	CYS/SER	249,4157	140.8+/-176.2	7,235,1961	63.0	66.0	65.0		1505	5.8	0.0	12	dbSNP_111	65	1627,6971	300.4+/-304.9	169,1289,2841	yes	missense	UTP20	NM_014503.2	112	176,1524,4802	GG,GC,CC		18.923,5.6514,14.4263	probably-damaging	502/2786	101693534	1876,11128	2203	4299	6502	SO:0001583	missense	27340	exon13			TTTTATCTATAAT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.1505C>G	12.37:g.101693534C>G	ENSP00000261637:p.Ser502Cys	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	239	0.10943223443223443	27	0.054878048780487805	50	0.13812154696132597	17	0.02972027972027972	145	0.19129287598944592	C	13.57	2.277826	0.40294	0.056514	0.18923	ENSG00000120800	ENST00000261637	T	0.67698	-0.28	5.75	5.75	0.90469	Armadillo-type fold (1);	0.055091	0.85682	D	0.000000	T	0.00210	0.0006	L	0.36672	1.1	0.39688	P	0.028996000000000022	D	0.56521	0.976	P	0.49192	0.602	T	0.00885	-1.1527	9	0.51188	T	0.08	-11.3363	18.1211	0.89572	0.0:1.0:0.0:0.0	rs4764643;rs56577815;rs4764643	502	O75691	UTP20_HUMAN	C	502	ENSP00000261637:S502C	ENSP00000261637:S502C	S	+	2	0	UTP20	100217665	0.661000	0.27430	0.019000	0.16419	0.014000	0.08584	2.834000	0.48167	2.716000	0.92895	0.650000	0.86243	TCT	C|0.865;G|0.135	0.135	strong		0.338	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
MUC4	4585	hgsc.bcm.edu	37	3	195511102	195511102	+	Missense_Mutation	SNP	G	G	A	rs200212097		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195511102G>A	ENST00000463781.3	-	2	7808	c.7349C>T	c.(7348-7350)cCt>cTt	p.P2450L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2450L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGGTGACAGGAAGAGGGGT	0.582																																					p.P2450L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C7349T						PASS	.						40.0	38.0	38.0					3																	195511102		675	1586	2261	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7349C>T	3.37:g.195511102G>A	ENSP00000417498:p.Pro2450Leu	Somatic	425	0	0		WXS	Illumina HiSeq	Phase_I	395	37	0.0936709	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	6.334	0.429752	0.11987	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35236	1.42;1.32	1.04	-2.07	0.07276	.	.	.	.	.	T	0.17109	0.0411	N	0.19112	0.55	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.23511	-1.0186	8	.	.	.	.	2.913	0.05743	0.2179:0.0:0.5196:0.2625	.	2450	E7ESK3	.	L	2450	ENSP00000417498:P2450L;ENSP00000420243:P2450L	.	P	-	2	0	MUC4	196995497	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-0.435000	0.07264	0.000000	0.15137	CCT	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC12A6	9990	hgsc.bcm.edu	37	15	34551082	34551082	+	Silent	SNP	G	G	A	rs7164902	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:34551082G>A	ENST00000354181.3	-	5	967	c.475C>T	c.(475-477)Ctg>Ttg	p.L159L	RP11-1084A12.2_ENST00000559867.1_RNA|SLC12A6_ENST00000560164.1_Silent_p.L20L|SLC12A6_ENST00000451844.2_Silent_p.L20L|SLC12A6_ENST00000397702.2_Silent_p.L100L|SLC12A6_ENST00000558589.1_Silent_p.L150L|SLC12A6_ENST00000558667.1_Silent_p.L159L|SLC12A6_ENST00000397707.2_Silent_p.L144L|SLC12A6_ENST00000290209.5_Silent_p.L108L|SLC12A6_ENST00000458406.2_Silent_p.L100L|SLC12A6_ENST00000560611.1_Silent_p.L159L			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	159					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	CCTTGAGTCAGATTAGTGTAA	0.448													G|||	1386	0.276757	0.1982	0.2161	5008	,	,		18454	0.3542		0.2406	False		,,,				2504	0.3834				p.L159L		Atlas-SNP	.											.	SLC12A6	205	.	0			c.C475T						PASS	.	G	,,,,,	951,3451	361.4+/-315.7	105,741,1355	231.0	217.0	222.0		298,298,448,430,322,475	2.8	1.0	15	dbSNP_116	222	2092,6504	361.6+/-332.4	259,1574,2465	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC12A6	NM_001042494.1,NM_001042495.1,NM_001042496.1,NM_001042497.1,NM_005135.2,NM_133647.1	,,,,,	364,2315,3820	AA,AG,GG		24.3369,21.6038,23.4113	,,,,,	100/1092,100/1092,150/1142,144/1136,108/1100,159/1151	34551082	3043,9955	2201	4298	6499	SO:0001819	synonymous_variant	9990	exon4			GAGTCAGATTAGT	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"""Solute carriers"""	10914	protein-coding gene	gene with protein product		604878	"""agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"""	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.475C>T	15.37:g.34551082G>A		Somatic	371	0	0		WXS	Illumina HiSeq	Phase_I	348	125	0.359195	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Silent	SNP	ENST00000354181.3	37	CCDS58352.1																																																																																			G|0.751;A|0.249	0.249	strong		0.448	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45696037	45696037	+	Missense_Mutation	SNP	T	T	G	rs34101857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:45696037T>G	ENST00000310806.4	-	10	2207	c.1749A>C	c.(1747-1749)gaA>gaC	p.E583D		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	583			E -> D (in dbSNP:rs34101857).		CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						TTCCAATTAATTCCTTCAAAA	0.259													T|||	536	0.107029	0.0333	0.1081	5008	,	,		15326	0.128		0.1103	False		,,,				2504	0.181				p.E583D		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.A1749C						PASS	.	T	ASP/GLU	159,4103		3,153,1975	30.0	30.0	30.0		1749	-1.5	0.7	14	dbSNP_126	30	703,7653		29,645,3504	yes	missense	MIS18BP1	NM_018353.4	45	32,798,5479	GG,GT,TT		8.4131,3.7306,6.8315	possibly-damaging	583/1133	45696037	862,11756	2131	4178	6309	SO:0001583	missense	55320	exon10			AATTAATTCCTTC	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"""kinetochore null 2 homolog (C. elegans)"""		"""chromosome 14 open reading frame 106"""	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.1749A>C	14.37:g.45696037T>G	ENSP00000309790:p.Glu583Asp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Missense_Mutation	SNP	ENST00000310806.4	37	CCDS9684.1	214	0.09798534798534798	19	0.03861788617886179	32	0.08839779005524862	71	0.12412587412587413	92	0.12137203166226913	T	14.46	2.543022	0.45280	0.037306	0.084131	ENSG00000129534	ENST00000310806	T	0.20463	2.07	4.23	-1.47	0.08772	.	0.102176	0.38720	N	0.001582	T	0.00178	0.0005	L	0.47716	1.5	0.53688	P	2.8000000000028002E-5	B	0.14012	0.009	B	0.12837	0.008	T	0.16897	-1.0387	9	0.26408	T	0.33	-1.3897	0.4801	0.00546	0.1762:0.2104:0.1818:0.4316	rs34101857	583	Q6P0N0	M18BP_HUMAN	D	583	ENSP00000309790:E583D	ENSP00000309790:E583D	E	-	3	2	MIS18BP1	44765787	0.995000	0.38212	0.747000	0.31113	0.436000	0.31835	1.019000	0.30014	-0.185000	0.10550	0.454000	0.30748	GAA	T|0.910;G|0.090	0.090	strong		0.259	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
GZF1	64412	hgsc.bcm.edu	37	20	23345844	23345844	+	Missense_Mutation	SNP	A	A	C	rs6048760	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:23345844A>C	ENST00000338121.5	+	2	901	c.824A>C	c.(823-825)cAg>cCg	p.Q275P	GZF1_ENST00000542987.1_Intron|GZF1_ENST00000377051.2_Missense_Mutation_p.Q275P|GZF1_ENST00000544236.1_Intron			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	275			Q -> L (in dbSNP:rs6048760).|Q -> P (in dbSNP:rs6048760). {ECO:0000269|PubMed:14702039}.|Q -> R (in dbSNP:rs6048760).		branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					GAGATGGAGCAGGTTTCCAAA	0.577													C|||	3347	0.668331	0.829	0.5807	5008	,	,		17615	0.8879		0.4602	False		,,,				2504	0.501				p.Q275P		Atlas-SNP	.											.	GZF1	61	.	0			c.A824C						PASS	.	C	PRO/GLN	3404,1002	371.0+/-319.8	1316,772,115	59.0	69.0	66.0		824	2.0	0.0	20	dbSNP_114	66	3963,4637	602.3+/-394.5	926,2111,1263	yes	missense	GZF1	NM_022482.3	76	2242,2883,1378	CC,CA,AA		46.0814,22.7417,43.3569	benign	275/712	23345844	7367,5639	2203	4300	6503	SO:0001583	missense	64412	exon1			TGGAGCAGGTTTC	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.824A>C	20.37:g.23345844A>C	ENSP00000338290:p.Gln275Pro	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	89	44	0.494382	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	CCDS13151.1	1480	0.6776556776556777	409	0.8313008130081301	218	0.6022099447513812	518	0.9055944055944056	335	0.4419525065963061	C	0.001	-3.390654	0.00014	0.772583	0.460814	ENSG00000125812	ENST00000338121;ENST00000377051	T;T	0.09630	2.96;2.96	4.0	2.02	0.26589	.	0.516003	0.17790	N	0.161934	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	0.07986	-1.0744	9	0.25106	T	0.35	.	3.5377	0.07799	0.3515:0.4578:0.0:0.1907	rs6048760;rs17750716;rs52801271;rs59283284;rs6048760	275	Q9H116	GZF1_HUMAN	P	275	ENSP00000338290:Q275P;ENSP00000366250:Q275P	ENSP00000338290:Q275P	Q	+	2	0	GZF1	23293844	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.133000	0.15912	0.130000	0.18549	-2.594000	0.00164	CAG	A|0.371;C|0.627;G|0.002;T|0.000	0.627	strong		0.577	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
ZNF260	339324	hgsc.bcm.edu	37	19	37004938	37004938	+	Silent	SNP	T	T	C	rs2967505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37004938T>C	ENST00000523638.1	-	3	2324	c.1203A>G	c.(1201-1203)tcA>tcG	p.S401S	ZNF260_ENST00000588993.1_Silent_p.S401S|ZNF260_ENST00000592282.1_Silent_p.S401S|ZNF260_ENST00000593142.1_Silent_p.S401S	NM_001166036.1|NM_001166037.1|NM_001166038.1	NP_001159508.1|NP_001159509.1|NP_001159510.1	Q3ZCT1	ZN260_HUMAN	zinc finger protein 260	401					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)	15	Esophageal squamous(110;0.162)					TAATGTGATGTGACTTTTGGC	0.378													T|||	1728	0.345048	0.4153	0.2478	5008	,	,		20286	0.245		0.3479	False		,,,				2504	0.4192				p.S401S		Atlas-SNP	.											.	ZNF260	34	.	0			c.A1203G						PASS	.	T	,,,	1831,2575	532.8+/-373.5	364,1103,736	85.0	82.0	83.0		1203,1203,1203,1203	1.7	1.0	19	dbSNP_101	83	2926,5674	456.4+/-364.1	518,1890,1892	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF260	NM_001012756.2,NM_001166036.1,NM_001166037.1,NM_001166038.1	,,,	882,2993,2628	CC,CT,TT		34.0233,41.557,36.5754	,,,	401/413,401/413,401/413,401/413	37004938	4757,8249	2203	4300	6503	SO:0001819	synonymous_variant	339324	exon3			GTGATGTGACTTT	AK122854	CCDS33003.1	19q13.12	2013-01-08				ENSG00000254004		"""Zinc fingers, C2H2-type"""	13499	protein-coding gene	gene with protein product		613749					Standard	NM_001166036		Approved	ozrf1, Zfp260	uc002oed.2	Q3ZCT1		ENST00000523638.1:c.1203A>G	19.37:g.37004938T>C		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	99	35	0.353535	NM_001166038	Q0VF43	Silent	SNP	ENST00000523638.1	37	CCDS33003.1																																																																																			T|0.648;C|0.352	0.352	strong		0.378	ZNF260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109564.2	NM_001012756	
BAZ2B	29994	hgsc.bcm.edu	37	2	160289863	160289863	+	Silent	SNP	T	T	C	rs61733380	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:160289863T>C	ENST00000392783.2	-	9	1800	c.1305A>G	c.(1303-1305)aaA>aaG	p.K435K	BAZ2B_ENST00000392782.1_Silent_p.K433K|BAZ2B_ENST00000355831.2_Silent_p.K435K|BAZ2B_ENST00000343439.5_Silent_p.K433K	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	435					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						GGAATGCCTGTTTATATTGTT	0.333													T|||	185	0.0369409	0.028	0.0375	5008	,	,		17794	0.002		0.0527	False		,,,				2504	0.0685				p.K435K		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A1305G						PASS	.	T		103,3595		2,99,1748	100.0	93.0	95.0		1305	1.6	1.0	2	dbSNP_129	95	431,7731		16,399,3666	no	coding-synonymous	BAZ2B	NM_013450.2		18,498,5414	CC,CT,TT		5.2806,2.7853,4.5025		435/2169	160289863	534,11326	1849	4081	5930	SO:0001819	synonymous_variant	29994	exon9			TGCCTGTTTATAT	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.1305A>G	2.37:g.160289863T>C		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	103	45	0.436893	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Silent	SNP	ENST00000392783.2	37	CCDS2209.2																																																																																			T|0.956;C|0.044	0.044	strong		0.333	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
MCM10	55388	hgsc.bcm.edu	37	10	13239651	13239651	+	Missense_Mutation	SNP	A	A	G	rs2274110	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13239651A>G	ENST00000484800.2	+	15	2109	c.2006A>G	c.(2005-2007)aAa>aGa	p.K669R	MCM10_ENST00000378714.3_Missense_Mutation_p.K668R|MCM10_ENST00000378694.1_Missense_Mutation_p.K668R			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	669			K -> R (in dbSNP:rs2274110). {ECO:0000269|PubMed:15489334}.		cell proliferation (GO:0008283)|DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.K669R(1)		central_nervous_system(1)|large_intestine(4)|ovary(2)|skin(1)|stomach(1)	9						TTAAGGGCAAAAGGCCAGGTT	0.418													A|||	547	0.109225	0.0129	0.134	5008	,	,		16861	0.1002		0.1948	False		,,,				2504	0.1431				p.K669R		Atlas-SNP	.											MCM10,NS,carcinoma,0,1	MCM10	76	1	1	Substitution - Missense(1)	stomach(1)	c.A2006G						PASS	.	A	ARG/LYS,ARG/LYS	171,4235	112.1+/-150.2	4,163,2036	85.0	81.0	83.0		2003,2006	5.3	1.0	10	dbSNP_100	83	1605,6995	297.1+/-303.3	163,1279,2858	yes	missense,missense	MCM10	NM_018518.4,NM_182751.2	26,26	167,1442,4894	GG,GA,AA		18.6628,3.8811,13.6552	probably-damaging,probably-damaging	668/875,669/876	13239651	1776,11230	2203	4300	6503	SO:0001583	missense	55388	exon15			GGGCAAAAGGCCA	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.2006A>G	10.37:g.13239651A>G	ENSP00000418268:p.Lys669Arg	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	89	43	0.483146	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	260	0.11904761904761904	8	0.016260162601626018	56	0.15469613259668508	52	0.09090909090909091	144	0.18997361477572558	A	26.1	4.704765	0.88924	0.038811	0.186628	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.18810	2.2;2.2;2.19	5.33	5.33	0.75918	Replication factor Mcm10 (1);	0.042443	0.85682	D	0.000000	T	0.00073	0.0002	L	0.58969	1.84	0.09310	P	0.9999999831145	D;P;D	0.57571	0.98;0.947;0.957	P;P;P	0.59012	0.824;0.766;0.85	T	0.01252	-1.1405	9	0.40728	T	0.16	-4.2679	15.6241	0.76840	1.0:0.0:0.0:0.0	rs2274110;rs52802669;rs59009311;rs2274110	668;668;669	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	R	668;669;669;668	ENSP00000367986:K668R;ENSP00000418268:K669R;ENSP00000367966:K668R	ENSP00000354945:K669R	K	+	2	0	MCM10	13279657	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.021000	0.76425	2.145000	0.66743	0.533000	0.62120	AAA	A|0.880;G|0.120	0.120	strong		0.418	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751	
PLEKHM3	389072	hgsc.bcm.edu	37	2	208841407	208841407	+	Missense_Mutation	SNP	C	C	T	rs192125155	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:208841407C>T	ENST00000427836.2	-	3	2003	c.1514G>A	c.(1513-1515)cGa>cAa	p.R505Q	PLEKHM3_ENST00000457206.1_Missense_Mutation_p.R505Q|PLEKHM3_ENST00000389247.4_Missense_Mutation_p.R505Q	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	505					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGTGAGTCCTCGTTCCAAAGA	0.438													C|||	4	0.000798722	0.0	0.0014	5008	,	,		20227	0.0		0.001	False		,,,				2504	0.002				p.R505Q		Atlas-SNP	.											PLEKHM3_ENST00000427836,NS,carcinoma,-1,4	PLEKHM3	101	4	0			c.G1514A						scavenged	.	C	GLN/ARG	2,3844		0,2,1921	67.0	66.0	66.0		1514	5.5	1.0	2		66	9,8255		0,9,4123	yes	missense	PLEKHM3	NM_001080475.2	43	0,11,6044	TT,TC,CC		0.1089,0.052,0.0908	benign	505/762	208841407	11,12099	1923	4132	6055	SO:0001583	missense	389072	exon3			AGTCCTCGTTCCA	AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"""Pleckstrin homology (PH) domain containing"""	34006	protein-coding gene	gene with protein product	"""differentiation associated protein"""		"""pleckstrin homology domain containing, family M, member 1-like"""	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.1514G>A	2.37:g.208841407C>T	ENSP00000417003:p.Arg505Gln	Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	139	2	0.0143885	NM_001080475	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	37	CCDS42808.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.05	3.536471	0.65085	5.2E-4	0.001089	ENSG00000178385	ENST00000427836;ENST00000389247;ENST00000457206	D;D;D	0.82893	-1.63;-1.64;-1.66	5.52	5.52	0.82312	.	0.047958	0.85682	D	0.000000	T	0.73289	0.3568	L	0.29908	0.895	0.49483	D	0.99979	P;P	0.49635	0.926;0.711	B;B	0.34093	0.174;0.175	T	0.76310	-0.3006	10	0.41790	T	0.15	.	19.8024	0.96513	0.0:1.0:0.0:0.0	.	505;505	C9J119;Q6ZWE6	.;PKHM3_HUMAN	Q	505	ENSP00000417003:R505Q;ENSP00000373899:R505Q;ENSP00000400150:R505Q	ENSP00000373899:R505Q	R	-	2	0	PLEKHM3	208549652	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.164000	0.64954	2.752000	0.94435	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	strong		0.438	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475	
NPR2	4882	hgsc.bcm.edu	37	9	35806500	35806500	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35806500C>T	ENST00000342694.2	+	16	2739	c.2484C>T	c.(2482-2484)cgC>cgT	p.R828R		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	828					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	AGGAAAAACGCAAGGCTGAAG	0.512																																					p.R828R		Atlas-SNP	.											.	NPR2	162	.	0			c.C2484T						PASS	.						119.0	106.0	110.0					9																	35806500		2203	4300	6503	SO:0001819	synonymous_variant	4882	exon16			AAAACGCAAGGCT	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.2484C>T	9.37:g.35806500C>T		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	102	54	0.529412	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	6.453	0.451797	0.12283	.	.	ENSG00000159899	ENST00000421267	.	.	.	6.17	5.26	0.73747	.	.	.	.	.	T	0.72787	0.3504	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72561	-0.4256	4	.	.	.	.	16.1789	0.81887	0.0:0.8665:0.1335:0.0	.	.	.	.	V	175	.	.	A	+	2	0	NPR2	35796500	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.000000	0.29770	1.587000	0.49959	0.655000	0.94253	GCA	.	.	none		0.512	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
SEC16A	9919	hgsc.bcm.edu	37	9	139368953	139368953	+	Missense_Mutation	SNP	G	G	A	rs3812594	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139368953G>A	ENST00000371706.3	-	1	2614	c.2581C>T	c.(2581-2583)Cgt>Tgt	p.R861C	SEC16A_ENST00000431893.2_Missense_Mutation_p.R861C|SEC16A_ENST00000313050.7_Missense_Mutation_p.R1039C|SEC16A_ENST00000290037.6_Missense_Mutation_p.R861C			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	861			R -> C (in dbSNP:rs3812594).		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)		TGATAAAAACGGTCAAGGTTA	0.582													G|||	672	0.134185	0.0401	0.255	5008	,	,		19516	0.0536		0.2535	False		,,,				2504	0.136				p.R1039C		Atlas-SNP	.											.	SEC16A	249	.	0			c.C3115T						PASS	.	G	CYS/ARG	279,3541		9,261,1640	24.0	25.0	24.0		3115	0.6	0.0	9	dbSNP_107	24	2154,6088		280,1594,2247	yes	missense	SEC16A	NM_014866.1	180	289,1855,3887	AA,AG,GG		26.1344,7.3037,20.1708	benign	1039/2358	139368953	2433,9629	1910	4121	6031	SO:0001583	missense	9919	exon3			AAAAACGGTCAAG	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.2581C>T	9.37:g.139368953G>A	ENSP00000360771:p.Arg861Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		341	0.15613553113553114	23	0.046747967479674794	83	0.2292817679558011	41	0.07167832167832168	194	0.2559366754617414	G	11.24	1.581289	0.28180	0.073037	0.261344	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893	T;T;T;T	0.23950	1.88;1.88;1.88;1.89	5.54	0.615	0.17608	.	0.748857	0.13402	N	0.390529	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B;B;B	0.11235	0.003;0.004;0.004	B;B;B	0.04013	0.0;0.001;0.001	T	0.40459	-0.9562	9	0.45353	T	0.12	-0.4352	5.7952	0.18383	0.3436:0.1238:0.5327:0.0	rs3812594;rs17489354;rs52817374;rs60457368;rs3812594	1039;861;861	F1T0I1;O15027-5;O15027-4	.;.;.	C	1039;861;861;861	ENSP00000325827:R1039C;ENSP00000360771:R861C;ENSP00000290037:R861C;ENSP00000387583:R861C	ENSP00000290037:R861C	R	-	1	0	SEC16A	138488774	0.722000	0.28017	0.001000	0.08648	0.013000	0.08279	0.335000	0.19806	-0.076000	0.12775	-0.794000	0.03295	CGT	G|0.852;A|0.148	0.148	strong		0.582	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
VENTX	27287	hgsc.bcm.edu	37	10	135051562	135051562	+	Silent	SNP	A	A	G	rs2998143	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:135051562A>G	ENST00000325980.9	+	1	655	c.144A>G	c.(142-144)ccA>ccG	p.P48P		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	48					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(1)	14		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		TCCCTGGCCCAGGCCAGACAT	0.706													G|||	3991	0.796925	0.8268	0.6643	5008	,	,		12276	0.994		0.6054	False		,,,				2504	0.8446				p.P48P		Atlas-SNP	.											VENTX,NS,carcinoma,0,1	VENTX	24	1	0			c.A144G						PASS	.	G		3080,772		1299,482,145	4.0	6.0	6.0		144	-3.6	0.0	10	dbSNP_101	6	4807,3287		1548,1711,788	no	coding-synonymous	VENTX	NM_014468.2		2847,2193,933	GG,GA,AA		40.6103,20.0415,33.9779		48/259	135051562	7887,4059	1926	4047	5973	SO:0001819	synonymous_variant	27287	exon1			TGGCCCAGGCCAG	AF068006	CCDS7675.1	10q26.3	2011-06-20	2011-06-01	2005-09-27	ENSG00000151650	ENSG00000151650		"""Homeoboxes / ANTP class : NKL subclass"""	13639	protein-coding gene	gene with protein product		607158	"""VENT-like homeobox 2"", ""VENT homeobox homolog (Xenopus laevis)"""	VENTX2		10790436	Standard	NM_014468		Approved	HPX42B	uc010quy.1	O95231	OTTHUMG00000019307	ENST00000325980.9:c.144A>G	10.37:g.135051562A>G		Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_014468	Q32MZ3	Silent	SNP	ENST00000325980.9	37	CCDS7675.1																																																																																			A|0.248;G|0.752	0.752	strong		0.706	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
DNAH5	1767	hgsc.bcm.edu	37	5	13845045	13845045	+	Silent	SNP	G	G	A	rs10041113	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:13845045G>A	ENST00000265104.4	-	32	5276	c.5172C>T	c.(5170-5172)gcC>gcT	p.A1724A		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1724	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCTCTAGAAGGGCAGGATCTG	0.443									Kartagener syndrome				A|||	2277	0.454673	0.5174	0.4092	5008	,	,		18672	0.622		0.3598	False		,,,				2504	0.3272				p.A1724A		Atlas-SNP	.											.	DNAH5	868	.	0			c.C5172T						PASS	.	A		2201,2205	588.0+/-386.8	546,1109,548	84.0	88.0	87.0		5172	-1.3	0.4	5	dbSNP_119	87	2993,5607	664.8+/-402.2	512,1969,1819	no	coding-synonymous	DNAH5	NM_001369.2		1058,3078,2367	AA,AG,GG		34.8023,49.9546,39.9354		1724/4625	13845045	5194,7812	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon32	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TAGAAGGGCAGGA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5172C>T	5.37:g.13845045G>A		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	104	104	1	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.574;A|0.426	0.426	strong		0.443	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
SLC24A3	57419	hgsc.bcm.edu	37	20	19565671	19565671	+	Silent	SNP	G	G	A	rs17293432	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:19565671G>A	ENST00000328041.6	+	5	677	c.480G>A	c.(478-480)tcG>tcA	p.S160S		NM_020689.3	NP_065740.2	Q9HC58	NCKX3_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 3	160					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CGGGAAGTTCGGCCCCAGAGC	0.552													G|||	185	0.0369409	0.0454	0.0504	5008	,	,		16242	0.0		0.0716	False		,,,				2504	0.0184				p.S160S		Atlas-SNP	.											.	SLC24A3	92	.	0			c.G480A						PASS	.	G		249,4157	144.2+/-179.2	8,233,1962	97.0	83.0	88.0		480	-8.7	0.9	20	dbSNP_123	88	792,7808	185.7+/-233.4	46,700,3554	no	coding-synonymous	SLC24A3	NM_020689.3		54,933,5516	AA,AG,GG		9.2093,5.6514,8.004		160/645	19565671	1041,11965	2203	4300	6503	SO:0001819	synonymous_variant	57419	exon5			AAGTTCGGCCCCA	AF169257	CCDS13140.1	20p13	2013-05-22			ENSG00000185052	ENSG00000185052		"""Solute carriers"""	10977	protein-coding gene	gene with protein product		609839					Standard	NM_020689		Approved		uc002wrl.3	Q9HC58	OTTHUMG00000031993	ENST00000328041.6:c.480G>A	20.37:g.19565671G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	76	54	0.710526	NM_020689	B1AKV7|Q9BQJ9|Q9BQL7|Q9BQY3|Q9H519	Silent	SNP	ENST00000328041.6	37	CCDS13140.1																																																																																			G|0.931;A|0.069	0.069	strong		0.552	SLC24A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078207.4	NM_020689	
ABHD12	26090	hgsc.bcm.edu	37	20	25282944	25282944	+	Silent	SNP	A	A	G	rs10966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:25282944A>G	ENST00000339157.5	-	12	1340	c.1068T>C	c.(1066-1068)gaT>gaC	p.D356D	ABHD12_ENST00000376542.3_Silent_p.D356D	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	356					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						GAACTTTGAAATCTCGGAAGC	0.547													G|||	2712	0.541534	0.4629	0.3516	5008	,	,		19604	0.9107		0.4374	False		,,,				2504	0.5092				p.D356D		Atlas-SNP	.											.	ABHD12	46	.	0			c.T1068C						PASS	.	G	,	1987,2419	617.9+/-393.1	434,1119,650	126.0	112.0	117.0		1068,1068	5.0	1.0	20	dbSNP_52	117	3754,4846	616.2+/-396.5	809,2136,1355	no	coding-synonymous,coding-synonymous	ABHD12	NM_001042472.2,NM_015600.4	,	1243,3255,2005	GG,GA,AA		43.6512,45.0976,44.1412	,	356/399,356/405	25282944	5741,7265	2203	4300	6503	SO:0001819	synonymous_variant	26090	exon12			TTTGAAATCTCGG	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"""Abhydrolase domain containing"""	15868	protein-coding gene	gene with protein product		613599	"""chromosome 20 open reading frame 22"""	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.1068T>C	20.37:g.25282944A>G		Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	50	19	0.38	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Silent	SNP	ENST00000339157.5	37	CCDS42857.1																																																																																			A|0.530;G|0.470	0.470	strong		0.547	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600	
SERPINF2	5345	hgsc.bcm.edu	37	17	1648294	1648294	+	Missense_Mutation	SNP	C	C	T	rs2070862	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1648294C>T	ENST00000324015.3	+	2	82	c.5C>T	c.(4-6)gCg>gTg	p.A2V	SERPINF2_ENST00000382061.4_Missense_Mutation_p.A2V|SERPINF2_ENST00000450523.2_Missense_Mutation_p.A2V	NM_000934.3	NP_000925.2	P08697	A2AP_HUMAN	serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2	2			A -> V (in dbSNP:rs2070862). {ECO:0000269|PubMed:15489334}.		acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|collagen fibril organization (GO:0030199)|fibrinolysis (GO:0042730)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of plasminogen activation (GO:0010757)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of proteolysis (GO:0030162)|response to organic substance (GO:0010033)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	endopeptidase inhibitor activity (GO:0004866)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(1)|kidney(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)	Ocriplasmin(DB08888)	AGGAACATGGCGCTGCTCTGG	0.642													C|||	991	0.197883	0.236	0.245	5008	,	,		13572	0.1716		0.2237	False		,,,				2504	0.1135				p.A2V		Atlas-SNP	.											SERPINF2,NS,carcinoma,-1,1	SERPINF2	33	1	0			c.C5T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1065,3341	386.3+/-326.1	140,785,1278	50.0	47.0	48.0		5,5,5	-0.9	0.8	17	dbSNP_96	48	1902,6698	335.9+/-321.6	222,1458,2620	yes	missense,missense,missense	SERPINF2	NM_000934.3,NM_001165920.1,NM_001165921.1	64,64,64	362,2243,3898	TT,TC,CC		22.1163,24.1716,22.8125	possibly-damaging,possibly-damaging,possibly-damaging	2/492,2/492,2/428	1648294	2967,10039	2203	4300	6503	SO:0001583	missense	5345	exon2			ACATGGCGCTGCT	D00174	CCDS11011.1, CCDS54064.1	17p13.3	2014-02-18	2005-08-18		ENSG00000167711	ENSG00000167711		"""Serine (or cysteine) peptidase inhibitors"""	9075	protein-coding gene	gene with protein product	"""alpha-2-plasmin inhibitor"", ""alpha-2-antiplasmin"""	613168	"""serine (or cysteine) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2"""	PLI		3416655, 24172014	Standard	NM_000934		Approved	API, ALPHA-2-PI, A2AP, AAP	uc002ftk.1	P08697	OTTHUMG00000090552	ENST00000324015.3:c.5C>T	17.37:g.1648294C>T	ENSP00000321853:p.Ala2Val	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	84	41	0.488095	NM_000934	B4E1B7|Q8N5U7|Q9UCG2|Q9UCG3	Missense_Mutation	SNP	ENST00000324015.3	37	CCDS11011.1	475	0.2174908424908425	109	0.22154471544715448	84	0.23204419889502761	102	0.17832167832167833	180	0.23746701846965698	C	12.20	1.866016	0.32977	0.241716	0.221163	ENSG00000167711	ENST00000453066;ENST00000324015;ENST00000450523;ENST00000423861;ENST00000453723;ENST00000382061	D;D;D;D;D	0.86230	-1.78;-1.91;-2.09;-1.6;-1.91	4.85	-0.868	0.10652	.	1.218600	0.05399	N	0.540414	T	0.00073	0.0002	N	0.14661	0.345	0.45528	P	0.0015140000000000153	B;B	0.10296	0.003;0.003	B;B	0.06405	0.002;0.002	T	0.02126	-1.1209	9	0.32370	T	0.25	.	8.9521	0.35796	0.0:0.4852:0.0:0.5148	rs2070862;rs57053177;rs2070862	2;2	B4E1B7;P08697	.;A2AP_HUMAN	V	2	ENSP00000402286:A2V;ENSP00000321853:A2V;ENSP00000403877:A2V;ENSP00000402056:A2V;ENSP00000371493:A2V	ENSP00000321853:A2V	A	+	2	0	SERPINF2	1595044	0.401000	0.25303	0.840000	0.33206	0.798000	0.45092	-0.536000	0.06135	-0.288000	0.09051	-0.263000	0.10527	GCG	C|0.780;T|0.220	0.220	strong		0.642	SERPINF2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207078.3	NM_000934	
KRT35	3886	hgsc.bcm.edu	37	17	39633349	39633349	+	Missense_Mutation	SNP	G	G	C	rs2071601	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39633349G>C	ENST00000393989.1	-	7	1369	c.1327C>G	c.(1327-1329)Ccc>Gcc	p.P443A	KRT35_ENST00000246639.2_Missense_Mutation_p.P413A	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	443	Tail.		P -> A (in dbSNP:rs2071601). {ECO:0000269|PubMed:8823373}.		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)				ATGGGGCGGGGGCTGCAGTTT	0.617													G|||	2746	0.548323	0.6354	0.5432	5008	,	,		14894	0.3462		0.5388	False		,,,				2504	0.6524				p.P443A		Atlas-SNP	.											.	KRT35	58	.	0			c.C1327G						PASS	.	G	ALA/PRO	2362,1462		720,922,270	44.0	51.0	48.0		1327	5.4	1.0	17	dbSNP_96	48	4492,3756		1203,2086,835	yes	missense	KRT35	NM_002280.4	27	1923,3008,1105	CC,CG,GG		45.5383,38.2322,43.224	benign	443/456	39633349	6854,5218	1912	4124	6036	SO:0001583	missense	3886	exon7			GGCGGGGGCTGCA	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.1327C>G	17.37:g.39633349G>C	ENSP00000377558:p.Pro443Ala	Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	82	38	0.463415	NM_002280	O76012|Q92651	Missense_Mutation	SNP	ENST00000393989.1	37	CCDS11394.2	1130	0.5173992673992674	327	0.6646341463414634	218	0.6022099447513812	177	0.3094405594405594	408	0.5382585751978892	G	15.68	2.905373	0.52333	0.617678	0.544617	ENSG00000197079	ENST00000246639;ENST00000393989	T;T	0.81078	-1.45;-1.38	5.41	5.41	0.78517	.	0.105088	0.42964	D	0.000624	T	0.00012	0.0000	L	0.58101	1.795	0.26219	P	0.9791864	B	0.19706	0.038	B	0.18561	0.022	T	0.49093	-0.8975	9	0.51188	T	0.08	.	14.573	0.68224	0.0:0.0:1.0:0.0	rs2071601;rs60687291;rs2071601	443	Q92764	KRT35_HUMAN	A	413;443	ENSP00000246639:P413A;ENSP00000377558:P443A	ENSP00000246639:P413A	P	-	1	0	KRT35	36886875	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	4.118000	0.57884	2.816000	0.96949	0.563000	0.77884	CCC	G|0.489;C|0.511	0.511	strong		0.617	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
TACC2	10579	hgsc.bcm.edu	37	10	123970569	123970569	+	Missense_Mutation	SNP	C	C	T	rs2295874	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123970569C>T	ENST00000369005.1	+	9	6969	c.6629C>T	c.(6628-6630)gCa>gTa	p.A2210V	TACC2_ENST00000513429.1_Missense_Mutation_p.A356V|TACC2_ENST00000368999.1_Missense_Mutation_p.A288V|TACC2_ENST00000360561.3_Missense_Mutation_p.A288V|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000369004.3_Missense_Mutation_p.A288V|TACC2_ENST00000453444.2_Missense_Mutation_p.A2214V|TACC2_ENST00000358010.1_Missense_Mutation_p.A356V|TACC2_ENST00000334433.3_Missense_Mutation_p.A2210V|TACC2_ENST00000260733.3_Missense_Mutation_p.A288V|TACC2_ENST00000515273.1_Missense_Mutation_p.A2214V|TACC2_ENST00000515603.1_Missense_Mutation_p.A2165V	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2210			A -> V (in dbSNP:rs2295874).		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)				TCAGAGAGTGCAGAAGGGGTT	0.647													C|||	519	0.103634	0.0613	0.1354	5008	,	,		15166	0.1161		0.0765	False		,,,				2504	0.1534				p.A2210V		Atlas-SNP	.											.	TACC2	271	.	0			c.C6629T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	311,4085		12,287,1899	31.0	39.0	36.0		863,863,1067,6629	2.7	0.0	10	dbSNP_100	36	976,7624		52,872,3376	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	64,64,64,64	64,1159,5275	TT,TC,CC		11.3488,7.0746,9.903	benign,benign,benign,benign	288/1027,288/997,356/1095,2210/2949	123970569	1287,11709	2198	4300	6498	SO:0001583	missense	10579	exon9			AGAGTGCAGAAGG	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.6629C>T	10.37:g.123970569C>T	ENSP00000358001:p.Ala2210Val	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	52	20	0.384615	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	219	0.10027472527472528	39	0.07926829268292683	44	0.12154696132596685	74	0.12937062937062938	62	0.08179419525065963	C	0.307	-0.969967	0.02232	0.070746	0.113488	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539;ENST00000505639	T;T;T;T;T;T;T;T;T;T;T;T;T	0.18016	4.08;3.66;4.11;4.16;4.08;3.66;4.11;3.55;3.63;3.63;3.55;3.15;2.24	5.54	2.66	0.31614	.	0.725325	0.11376	N	0.570283	T	0.00109	0.0003	L	0.35288	1.05	0.80722	P	0.0	B;B;B;B;B;B;B;B;B	0.29481	0.003;0.151;0.001;0.058;0.151;0.001;0.001;0.001;0.245	B;B;B;B;B;B;B;B;B	0.27170	0.006;0.052;0.002;0.077;0.052;0.004;0.004;0.006;0.077	T	0.29579	-1.0007	9	0.29301	T	0.29	-0.7571	6.2216	0.20685	0.0:0.5418:0.0:0.4582	rs2295874;rs52789604;rs61447396;rs2295874	305;2214;288;2165;2214;288;288;356;2210	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	V	2210;356;2214;2165;2210;356;2214;2200;288;288;288;288;305;51	ENSP00000358001:A2210V;ENSP00000425062:A356V;ENSP00000424467:A2214V;ENSP00000427618:A2165V;ENSP00000334280:A2210V;ENSP00000350701:A356V;ENSP00000395048:A2214V;ENSP00000353763:A288V;ENSP00000357995:A288V;ENSP00000422815:A288V;ENSP00000260733:A288V;ENSP00000420967:A305V;ENSP00000426303:A51V	ENSP00000260733:A288V	A	+	2	0	TACC2	123960559	0.025000	0.19082	0.001000	0.08648	0.051000	0.14879	1.792000	0.38754	0.686000	0.31488	0.655000	0.94253	GCA	C|0.900;T|0.100	0.100	strong		0.647	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
SFXN5	94097	hgsc.bcm.edu	37	2	73226090	73226090	+	Silent	SNP	G	G	A	rs12233055	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:73226090G>A	ENST00000272433.2	-	9	652	c.522C>T	c.(520-522)gcC>gcT	p.A174A	SFXN5_ENST00000410065.1_Silent_p.A174A|SFXN5_ENST00000474528.1_5'UTR	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5	174					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)|citrate transmembrane transporter activity (GO:0015137)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)	9						CAATGGAGACGGCGCTGATGA	0.592													g|||	1689	0.33726	0.4259	0.2795	5008	,	,		20111	0.4931		0.2197	False		,,,				2504	0.2188				p.A174A		Atlas-SNP	.											SFXN5,NS,carcinoma,-2,1	SFXN5	31	1	0			c.C522T						PASS	.	A		1841,2565	532.6+/-373.5	402,1037,764	112.0	101.0	105.0		522	-12.1	0.3	2	dbSNP_120	105	1897,6703	334.0+/-320.8	200,1497,2603	no	coding-synonymous	SFXN5	NM_144579.2		602,2534,3367	AA,AG,GG		22.0581,41.7839,28.7406		174/341	73226090	3738,9268	2203	4300	6503	SO:0001819	synonymous_variant	94097	exon9			GGAGACGGCGCTG	AY044437	CCDS1922.1	2p13	2008-05-21			ENSG00000144040	ENSG00000144040		"""Sideroflexins"""	16073	protein-coding gene	gene with protein product		615572				12039050, 12150972	Standard	XM_005264648		Approved	BBG-TCC	uc002siq.3	Q8TD22	OTTHUMG00000129775	ENST00000272433.2:c.522C>T	2.37:g.73226090G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	86	36	0.418605	NM_144579	A8K116|Q494Y3|Q53T29	Silent	SNP	ENST00000272433.2	37	CCDS1922.1	772	0.3534798534798535	219	0.4451219512195122	100	0.27624309392265195	280	0.48951048951048953	173	0.22823218997361477	g	8.569	0.879549	0.17467	0.417839	0.220581	ENSG00000144040	ENST00000411783	.	.	.	6.07	-12.1	0.00011	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999129714	.	.	.	.	.	.	T	0.10776	-1.0615	3	.	.	.	-7.2324	12.5892	0.56434	0.7043:0.1036:0.1921:0.0	rs12233055;rs12233055	.	.	.	C	164	.	.	R	-	1	0	SFXN5	73079598	0.011000	0.17503	0.287000	0.24848	0.837000	0.47467	-1.585000	0.02112	-2.225000	0.00724	-2.203000	0.00303	CGT	G|0.682;A|0.318	0.318	strong		0.592	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579	
JMJD1C	221037	hgsc.bcm.edu	37	10	64945364	64945364	+	Silent	SNP	G	G	A	rs3211105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:64945364G>A	ENST00000399262.2	-	20	7007	c.6789C>T	c.(6787-6789)gaC>gaT	p.D2263D	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000402544.1_Silent_p.D2026D|JMJD1C_ENST00000542921.1_Silent_p.D2081D	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2263					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					CTGAAGGCCAGTCTTTCAATT	0.373													A|||	2910	0.58107	0.3139	0.5389	5008	,	,		17630	0.6369		0.7962	False		,,,				2504	0.6933				p.D2263D		Atlas-SNP	.											.	JMJD1C	347	.	0			c.C6789T						PASS	.	A	,	1533,2119		320,893,613	154.0	136.0	142.0		6078,6789	-7.7	0.7	10	dbSNP_105	142	6564,1606		2641,1282,162	no	coding-synonymous,coding-synonymous	JMJD1C	NM_004241.2,NM_032776.1	,	2961,2175,775	AA,AG,GG		19.6573,41.977,31.5091	,	2026/2304,2263/2541	64945364	8097,3725	1826	4085	5911	SO:0001819	synonymous_variant	221037	exon20			AGGCCAGTCTTTC	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.6789C>T	10.37:g.64945364G>A		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	61	60	0.983607	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Silent	SNP	ENST00000399262.2	37	CCDS41532.1	1331	0.6094322344322345	152	0.3089430894308943	221	0.6104972375690608	351	0.6136363636363636	607	0.8007915567282322	A	7.822	0.718083	0.15372	0.41977	0.803427	ENSG00000171988	ENST00000327520	.	.	.	5.71	-7.74	0.01241	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999995888	.	.	.	.	.	.	T	0.09509	-1.0671	3	.	.	.	-18.0578	21.7453	0.99960	0.3105:0.0:0.6895:0.0	rs3211105;rs17414931;rs17655093;rs59282382;rs3211105	.	.	.	I	810	.	.	T	-	2	0	JMJD1C	64615370	0.117000	0.22190	0.722000	0.30670	0.947000	0.59692	-0.379000	0.07437	-1.694000	0.01425	-1.022000	0.02435	ACT	G|0.356;A|0.644	0.644	strong		0.373	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552029	32552029	+	Missense_Mutation	SNP	A	A	T	rs17884945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32552029A>T	ENST00000360004.5	-	2	332	c.227T>A	c.(226-228)tTc>tAc	p.F76Y		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	76	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CACCGCCCGGAACTCCCCCAC	0.627										Multiple Myeloma(14;0.17)			a|||	2200	0.439297	0.4433	0.5115	5008	,	,		9910	0.4802		0.4453	False		,,,				2504	0.3344				p.F76Y		Atlas-SNP	.											HLA-DRB1,NS,carcinoma,0,1	HLA-DRB1	41	1	0			c.T227A	GRCh37	CM033913	HLA-DRB1	M	rs17884945	PASS	.	T	TYR/PHE	1656,2738		217,1222,758	37.0	39.0	38.0		227	-7.0	0.2	6	dbSNP_124	38	3323,5263		307,2709,1277	yes	missense	HLA-DRB1	NM_002124.3	22	524,3931,2035	TT,TA,AA		38.7025,37.6878,38.359		76/267	32552029	4979,8001	2197	4293	6490	SO:0001583	missense	3123	exon2			GCCCGGAACTCCC	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.227T>A	6.37:g.32552029A>T	ENSP00000353099:p.Phe76Tyr	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	46	16	0.347826	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	1042	0.47710622710622713	219	0.4451219512195122	201	0.5552486187845304	270	0.47202797202797203	352	0.46437994722955145	.	0.007	-2.014756	0.00422	0.376878	0.387025	ENSG00000196126	ENST00000360004	T	0.00265	8.39	3.52	-7.04	0.01578	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	0.630386	0.16708	N	0.202822	T	0.00012	0.0000	N	0.04043	-0.29	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37731	-0.9693	9	0.02654	T	1	.	14.4073	0.67090	0.8814:0.0:0.0:0.1186	rs17884945;rs28724095	76	P01911	2B1F_HUMAN	Y	76	ENSP00000353099:F76Y	ENSP00000353099:F76Y	F	-	2	0	HLA-DRB1	32660007	0.000000	0.05858	0.196000	0.23383	0.021000	0.10359	-7.135000	0.00043	-2.726000	0.00386	-2.365000	0.00237	TTC	A|0.523;T|0.477	0.477	strong		0.627	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
CEP85	64793	hgsc.bcm.edu	37	1	26596080	26596080	+	Missense_Mutation	SNP	G	G	A	rs7550997	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26596080G>A	ENST00000252992.4	+	9	1755	c.1624G>A	c.(1624-1626)Gca>Aca	p.A542T	CEP85_ENST00000469609.1_3'UTR|CEP85_ENST00000451429.2_Missense_Mutation_p.A491T	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	542			A -> T (in dbSNP:rs7550997).			centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						GCAGAGAGAAGCAGAATTCTC	0.502													G|||	648	0.129393	0.2027	0.1052	5008	,	,		16924	0.0228		0.1889	False		,,,				2504	0.0961				p.A542T		Atlas-SNP	.											.	CEP85	61	.	0			c.G1624A						PASS	.	G	THR/ALA	701,3705	292.4+/-282.0	60,581,1562	59.0	57.0	58.0		1624	3.1	1.0	1	dbSNP_116	58	1432,7168	273.7+/-290.8	110,1212,2978	yes	missense	CEP85	NM_022778.2	58	170,1793,4540	AA,AG,GG		16.6512,15.9101,16.4001	benign	542/763	26596080	2133,10873	2203	4300	6503	SO:0001583	missense	64793	exon9			AGAGAAGCAGAAT	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.1624G>A	1.37:g.26596080G>A	ENSP00000252992:p.Ala542Thr	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	59	53	0.898305	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	287	0.13141025641025642	80	0.16260162601626016	41	0.1132596685082873	12	0.02097902097902098	154	0.20316622691292877	G	8.915	0.959619	0.18507	0.159101	0.166512	ENSG00000130695	ENST00000451429;ENST00000252992	T;T	0.10960	2.82;2.82	5.06	3.11	0.35812	.	0.570233	0.20173	N	0.097692	T	0.00012	0.0000	L	0.36672	1.1	0.44946	P	0.0020320000000000338	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.002;0.002	T	0.36261	-0.9755	9	0.27785	T	0.31	-2.0585	5.216	0.15342	0.193:0.2319:0.5751:0.0	rs7550997;rs17257183;rs35972494;rs59910526;rs7550997	491;542;542	F8W7K4;Q6P2H3;Q6P2H3-2	.;CEP85_HUMAN;.	T	491;542	ENSP00000417002:A491T;ENSP00000252992:A542T	ENSP00000252992:A542T	A	+	1	0	CEP85	26468667	0.981000	0.34729	1.000000	0.80357	0.126000	0.20510	0.154000	0.16343	1.365000	0.46057	0.561000	0.74099	GCA	G|0.849;A|0.151	0.151	strong		0.502	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
OR4K15	81127	hgsc.bcm.edu	37	14	20444441	20444441	+	Missense_Mutation	SNP	C	C	A	rs10135246	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:20444441C>A	ENST00000305051.5	+	1	839	c.764C>A	c.(763-765)gCa>gAa	p.A255E		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	255			A -> E (in dbSNP:rs10135246). {ECO:0000269|PubMed:15489334}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CGCTCCTCTGCAAGCATGGCG	0.458													C|||	1080	0.215655	0.2042	0.1715	5008	,	,		21839	0.123		0.2227	False		,,,				2504	0.3507				p.A255E		Atlas-SNP	.											.	OR4K15	82	.	0			c.C764A						PASS	.	C	GLU/ALA	1008,3398		108,792,1303	127.0	112.0	117.0		764	2.1	0.0	14	dbSNP_119	117	2283,6317		290,1703,2307	no	missense	OR4K15	NM_001005486.1	107	398,2495,3610	AA,AC,CC		26.5465,22.8779,25.3037	probably-damaging	255/349	20444441	3291,9715	2203	4300	6503	SO:0001583	missense	81127	exon1			CCTCTGCAAGCAT		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.764C>A	14.37:g.20444441C>A	ENSP00000304077:p.Ala255Glu	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	148	67	0.452703	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	393	0.17994505494505494	89	0.18089430894308944	65	0.17955801104972377	65	0.11363636363636363	174	0.22955145118733508	.	1.804	-0.476388	0.04414	0.228779	0.265465	ENSG00000169488	ENST00000305051	T	0.00030	8.9	4.08	2.06	0.26882	GPCR, rhodopsin-like superfamily (1);	0.129719	0.35013	N	0.003519	T	0.00012	0.0000	N	0.03930	-0.32	0.80722	P	0.0	B	0.28055	0.199	B	0.28709	0.093	T	0.00000	-1.2884	9	0.08837	T	0.75	.	7.3359	0.26609	0.1774:0.4762:0.3463:0.0	rs10135246;rs17210955;rs58507224;rs10135246	255	Q8NH41	OR4KF_HUMAN	E	255	ENSP00000304077:A255E	ENSP00000304077:A255E	A	+	2	0	OR4K15	19514281	0.000000	0.05858	0.032000	0.17829	0.016000	0.09150	0.606000	0.24194	0.886000	0.36113	0.585000	0.79938	GCA	C|0.776;A|0.224	0.224	strong		0.458	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
ELFN2	114794	hgsc.bcm.edu	37	22	37770357	37770357	+	Silent	SNP	A	A	G	rs7292751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:37770357A>G	ENST00000402918.2	-	3	2003	c.1218T>C	c.(1216-1218)ttT>ttC	p.F406F	RP1-63G5.5_ENST00000430883.1_RNA|RP1-63G5.8_ENST00000609322.1_RNA|ELFN2_ENST00000435824.1_5'Flank	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	406					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					TAACCATGCCAAAGAGGCAGC	0.617													G|||	2234	0.446086	0.6135	0.6225	5008	,	,		20561	0.3492		0.3698	False		,,,				2504	0.273				p.F406F		Atlas-SNP	.											.	ELFN2	89	.	0			c.T1218C						PASS	.	G		2713,1693	511.4+/-367.8	834,1045,324	99.0	92.0	95.0		1218	-0.1	1.0	22	dbSNP_116	95	3273,5327	647.7+/-400.4	629,2015,1656	no	coding-synonymous	ELFN2	NM_052906.3		1463,3060,1980	GG,GA,AA		38.0581,38.4249,46.0249		406/821	37770357	5986,7020	2203	4300	6503	SO:0001819	synonymous_variant	114794	exon3			CATGCCAAAGAGG	BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.1218T>C	22.37:g.37770357A>G		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	83	34	0.409639	NM_052906	Q96PY3	Silent	SNP	ENST00000402918.2	37	CCDS33642.1																																																																																			A|0.542;G|0.458	0.458	strong		0.617	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2	NM_052906	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449390	89449390	+	Missense_Mutation	SNP	T	T	C	rs112636230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449390T>C	ENST00000321792.5	-	2	547	c.120A>G	c.(118-120)atA>atG	p.I40M	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.I40M	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	40	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CACGGTCTTTTATCAAGAGTA	0.413											OREG0013593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I40M		Atlas-SNP	.											.	.	.	.	0			c.A120G						PASS	.						210.0	199.0	203.0					1																	89449390		2203	4300	6503	SO:0001583	missense	494115	exon3			GTCTTTTATCAAG	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.120A>G	1.37:g.89449390T>C	ENSP00000318415:p.Ile40Met	Somatic	255	0	0	1267	WXS	Illumina HiSeq	Phase_I	386	67	0.173575	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	T	3.243	-0.154977	0.06544	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	D;D	0.81908	-1.55;-1.55	1.59	0.297	0.15762	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.052815	0.64402	N	0.000001	T	0.34542	0.0901	N	0.13168	0.305	0.29511	N	0.85423	B	0.02656	0.0	B	0.14023	0.01	T	0.29366	-1.0014	10	0.02654	T	1	-6.6339	4.2012	0.10467	0.0:0.7491:0.0:0.2509	.	40	Q96E39	RBMXL_HUMAN	M	40	ENSP00000318415:I40M;ENSP00000446099:I40M	ENSP00000318415:I40M	I	-	3	3	RBMXL1	89221978	1.000000	0.71417	0.975000	0.42487	0.841000	0.47740	3.335000	0.52105	-0.006000	0.14370	-0.760000	0.03462	ATA	.	.	weak		0.413	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
IL37	27178	hgsc.bcm.edu	37	2	113675269	113675269	+	Missense_Mutation	SNP	C	C	T	rs2723187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113675269C>T	ENST00000263326.3	+	4	365	c.323C>T	c.(322-324)cCg>cTg	p.P108L	IL37_ENST00000353225.3_Missense_Mutation_p.P68L|IL37_ENST00000352179.3_Missense_Mutation_p.P87L|IL37_ENST00000311328.2_Missense_Mutation_p.P82L|IL37_ENST00000349806.3_Missense_Mutation_p.P47L	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	108			P -> L (in dbSNP:rs2723187). {ECO:0000269|Ref.6}.		immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						AAAGGAAGTCCGATTCTCCTG	0.483													c|||	380	0.0758786	0.174	0.0591	5008	,	,		20339	0.001		0.0795	False		,,,				2504	0.0286				p.P108L		Atlas-SNP	.											.	IL37	56	.	0			c.C323T						PASS	.		LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	730,3676	303.5+/-288.0	51,628,1524	168.0	177.0	174.0		323,260,140,203,245	0.2	0.0	2	dbSNP_100	174	690,7910	171.6+/-222.5	37,616,3647	yes	missense,missense,missense,missense,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1,NM_173205.1	98,98,98,98,98	88,1244,5171	TT,TC,CC		8.0233,16.5683,10.918	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	108/219,87/198,47/158,68/179,82/193	113675269	1420,11586	2203	4300	6503	SO:0001583	missense	27178	exon4			GAAGTCCGATTCT	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.323C>T	2.37:g.113675269C>T	ENSP00000263326:p.Pro108Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	60	32	0.533333	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	164	0.07509157509157509	81	0.16463414634146342	26	0.0718232044198895	1	0.0017482517482517483	56	0.07387862796833773	c	12.74	2.028918	0.35797	0.165683	0.080233	ENSG00000125571	ENST00000263326;ENST00000352179;ENST00000349806;ENST00000353225;ENST00000311328	T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66	3.19	0.218	0.15270	.	0.468291	0.16426	N	0.214927	T	0.00144	0.0004	M	0.68952	2.095	0.80722	P	0.0	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;0.999	D;D;D;D;D	0.68943	0.961;0.947;0.947;0.923;0.954	T	0.04565	-1.0942	9	0.33940	T	0.23	-3.2686	2.7929	0.05393	0.2203:0.5236:0.0:0.2561	rs2723187;rs52826923;rs60103356;rs2723187	82;47;68;87;108	Q9NZH6-2;Q9NZH6-5;Q9NZH6-3;Q9NZH6-4;Q9NZH6	.;.;.;.;IL37_HUMAN	L	108;87;47;68;82	ENSP00000263326:P108L;ENSP00000263327:P87L;ENSP00000263328:P47L;ENSP00000309208:P68L;ENSP00000309883:P82L	ENSP00000263326:P108L	P	+	2	0	IL37	113391740	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.287000	0.08388	0.031000	0.15407	0.558000	0.71614	CCG	C|0.903;T|0.097	0.097	strong		0.483	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
MXRA5	25878	hgsc.bcm.edu	37	X	3239545	3239545	+	Missense_Mutation	SNP	C	C	T	rs1726199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:3239545C>T	ENST00000217939.6	-	5	4335	c.4181G>A	c.(4180-4182)gGc>gAc	p.G1394D		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1394			G -> D (in dbSNP:rs1726199). {ECO:0000269|Ref.1}.			extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				AACAGGTATGCCTGTCTGTAG	0.488													T|||	2723	0.721325	0.6104	0.5115	3775	,	,		14108	0.5595		0.5268	False		,,,				2504	0.4775				p.G1394D		Atlas-SNP	.											.	MXRA5	815	.	0			c.G4181A						PASS	.	T	ASP/GLY	2945,890		969,569,438,94,133	34.0	33.0	33.0		4181	1.7	0.1	X	dbSNP_89	33	4340,2388		1020,1107,1193,301,679	yes	missense	MXRA5	NM_015419.3	94	1989,1676,1631,395,812	TT,TC,T,CC,C		35.4935,23.2073,31.0329	benign	1394/2829	3239545	7285,3278	2203	4300	6503	SO:0001583	missense	25878	exon5			GGTATGCCTGTCT	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.4181G>A	X.37:g.3239545C>T	ENSP00000217939:p.Gly1394Asp	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	61	61	1	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	1198	0.7221217600964437	214	0.6993464052287581	129	0.49615384615384617	206	0.5885714285714285	272	0.5291828793774319	t	0.001	-3.030648	0.00041	0.767927	0.645065	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.61158	0.13	2.92	1.69	0.24217	.	0.413025	0.17741	N	0.163572	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	0.42849	-0.9427	9	0.02654	T	1	.	7.3365	0.26613	0.0:0.7527:0.0:0.2473	rs1726199;rs60762451;rs1726199	1394	Q9NR99	MXRA5_HUMAN	D	1394	ENSP00000217939:G1394D	ENSP00000217939:G1394D	G	-	2	0	MXRA5	3249545	0.001000	0.12720	0.127000	0.21898	0.068000	0.16541	-0.017000	0.12590	-0.241000	0.09681	-0.573000	0.04149	GGC	0|0.013;T|0.704	0.704	strong		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
ANKRD20A2	441430	hgsc.bcm.edu	37	9	42368549	42368549	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:42368549C>T	ENST00000377601.2	+	1	247	c.135C>T	c.(133-135)gaC>gaT	p.D45D	RP11-216M21.7_ENST00000450520.1_RNA	NM_001012421.1	NP_001012421.1	Q5SQ80	A20A2_HUMAN	ankyrin repeat domain 20 family, member A2	45										large_intestine(1)|lung(1)|ovary(1)|urinary_tract(1)	4						TCAAAGGCGACGCCGCGGAGG	0.677																																					p.D45D		Atlas-SNP	.											ANKRD20A2,bladder,carcinoma,+2,2	ANKRD20A2	9	2	0			c.C135T						scavenged	.						8.0	7.0	8.0					9																	42368549		2144	4122	6266	SO:0001819	synonymous_variant	441430	exon1			AGGCGACGCCGCG		CCDS35028.1	9p12	2013-01-10			ENSG00000183148	ENSG00000183148		"""Ankyrin repeat domain containing"""	31979	protein-coding gene	gene with protein product							Standard	XM_005272519		Approved			Q5SQ80	OTTHUMG00000058641	ENST00000377601.2:c.135C>T	9.37:g.42368549C>T		Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	228	65	0.285088	NM_001012421		Silent	SNP	ENST00000377601.2	37	CCDS35028.1																																																																																			.	.	weak		0.677	ANKRD20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129794.1	NM_001012421	
RAB11B	9230	hgsc.bcm.edu	37	19	8468337	8468337	+	Silent	SNP	C	C	T	rs2230876	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:8468337C>T	ENST00000328024.6	+	5	770	c.552C>T	c.(550-552)cgC>cgT	p.R184R		NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	184				R -> C (in Ref. 6; CAG46492). {ECO:0000305}.	cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						TCGCAGACCGCGCTGCCCACG	0.652													C|||	1653	0.330072	0.2632	0.219	5008	,	,		15294	0.5188		0.2873	False		,,,				2504	0.3487				p.R184R		Atlas-SNP	.											.	RAB11B	15	.	0			c.C552T						PASS	.	C		1104,3302	397.2+/-330.3	144,816,1243	137.0	110.0	119.0		552	-5.4	0.0	19	dbSNP_98	119	2468,6132	407.7+/-349.2	355,1758,2187	no	coding-synonymous	RAB11B	NM_004218.3		499,2574,3430	TT,TC,CC		28.6977,25.0567,27.4642		184/219	8468337	3572,9434	2203	4300	6503	SO:0001819	synonymous_variant	9230	exon5			AGACCGCGCTGCC	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"""RAB, member RAS oncogene"""	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.552C>T	19.37:g.8468337C>T		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	115	48	0.417391	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Silent	SNP	ENST00000328024.6	37	CCDS12201.1																																																																																			C|0.701;A|0.004	.	strong		0.652	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218	
VEPH1	79674	hgsc.bcm.edu	37	3	156983414	156983414	+	Silent	SNP	T	T	C	rs7652298	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:156983414T>C	ENST00000362010.2	-	13	2473	c.2166A>G	c.(2164-2166)aaA>aaG	p.K722K	VEPH1_ENST00000392832.2_Silent_p.K722K|RP11-550I24.2_ENST00000488040.1_RNA|RP11-550I24.2_ENST00000487238.1_RNA|VEPH1_ENST00000392833.2_Silent_p.K677K|RP11-550I24.2_ENST00000475102.1_RNA|VEPH1_ENST00000543418.1_Silent_p.K677K	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	722	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					plasma membrane (GO:0005886)		p.K722K(1)		autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			TCTCTTTAAGTTTTCCTTCTA	0.373													T|||	1170	0.233626	0.0522	0.4712	5008	,	,		21410	0.3323		0.2575	False		,,,				2504	0.184				p.K722K		Atlas-SNP	.											VEPH1,NS,carcinoma,0,1	VEPH1	129	1	1	Substitution - coding silent(1)	stomach(1)	c.A2166G						PASS	.	T	,,	395,4011	196.4+/-220.7	23,349,1831	147.0	137.0	140.0		2031,2166,2166	1.8	1.0	3	dbSNP_116	140	2089,6511	360.1+/-331.8	241,1607,2452	no	coding-synonymous,coding-synonymous,coding-synonymous	VEPH1	NM_001167911.1,NM_001167912.1,NM_024621.2	,,	264,1956,4283	CC,CT,TT		24.2907,8.965,19.0989	,,	677/789,722/834,722/834	156983414	2484,10522	2203	4300	6503	SO:0001819	synonymous_variant	79674	exon13			TTTAAGTTTTCCT	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.2166A>G	3.37:g.156983414T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	124	52	0.419355	NM_001167912	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Silent	SNP	ENST00000362010.2	37	CCDS3179.1																																																																																			T|0.781;C|0.219	0.219	strong		0.373	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
ZHX2	22882	hgsc.bcm.edu	37	8	123964819	123964819	+	Missense_Mutation	SNP	G	G	A	rs9649951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:123964819G>A	ENST00000314393.4	+	3	1904	c.1069G>A	c.(1069-1071)Gtg>Atg	p.V357M		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	357	Required for homodimerization.|Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.		V -> M (in dbSNP:rs9649951).		mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCCCACAAAGGTGACGCAGCC	0.617													G|||	50	0.00998403	0.0015	0.0144	5008	,	,		17314	0.001		0.0258	False		,,,				2504	0.0112				p.V357M	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G1069A						PASS	.	G	MET/VAL	41,4365	45.3+/-79.5	0,41,2162	77.0	64.0	69.0		1069	1.4	0.4	8	dbSNP_119	69	373,8227	123.1+/-182.0	6,361,3933	yes	missense	ZHX2	NM_014943.3	21	6,402,6095	AA,AG,GG		4.3372,0.9305,3.1831	benign	357/838	123964819	414,12592	2203	4300	6503	SO:0001583	missense	22882	exon3			ACAAAGGTGACGC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1069G>A	8.37:g.123964819G>A	ENSP00000314709:p.Val357Met	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	130	56	0.430769	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	17	0.022427440633245383	G	6.657	0.489767	0.12702	0.009305	0.043372	ENSG00000178764	ENST00000314393	T	0.17370	2.28	5.62	1.42	0.22433	.	0.551628	0.20995	N	0.081968	T	0.02119	0.0066	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.24404	-1.0161	10	0.40728	T	0.16	-6.6533	8.5687	0.33556	0.636:0.0:0.364:0.0	rs9649951;rs9649951	357	Q9Y6X8	ZHX2_HUMAN	M	357	ENSP00000314709:V357M	ENSP00000314709:V357M	V	+	1	0	ZHX2	124034000	1.000000	0.71417	0.392000	0.26245	0.782000	0.44232	1.466000	0.35310	0.008000	0.14787	-0.361000	0.07541	GTG	G|0.974;A|0.026	0.026	strong		0.617	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
NLN	57486	hgsc.bcm.edu	37	5	65118738	65118738	+	Missense_Mutation	SNP	C	C	T	rs6860508	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:65118738C>T	ENST00000380985.5	+	13	2288	c.2110C>T	c.(2110-2112)Ccg>Tcg	p.P704S	NLN_ENST00000515595.1_3'UTR|NLN_ENST00000502464.1_Missense_Mutation_p.P600S	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	704			P -> S (in dbSNP:rs6860508).			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)		CCTGCATGCTCCGTGAACTGG	0.502													T|||	401	0.0800719	0.2073	0.0504	5008	,	,		15703	0.0		0.0308	False		,,,				2504	0.0624				p.P704S		Atlas-SNP	.											.	NLN	51	.	0			c.C2110T						PASS	.	T	SER/PRO	745,3661	755.6+/-412.6	51,643,1509	147.0	135.0	139.0		2110	-0.8	0.1	5	dbSNP_116	139	360,8240	803.6+/-407.3	6,348,3946	yes	missense	NLN	NM_020726.4	74	57,991,5455	TT,TC,CC		4.186,16.9088,8.4961	probably-damaging	704/705	65118738	1105,11901	2203	4300	6503	SO:0001583	missense	57486	exon13			CATGCTCCGTGAA	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.2110C>T	5.37:g.65118738C>T	ENSP00000370372:p.Pro704Ser	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	47	0.534091	NM_020726	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	152	0.0695970695970696	103	0.20934959349593496	26	0.0718232044198895	0	0.0	23	0.030343007915567283	T	12.48	1.950087	0.34377	0.169088	0.04186	ENSG00000123213	ENST00000380985;ENST00000502464;ENST00000511299	T;T;T	0.09911	3.07;2.94;2.93	6.02	-0.749	0.11084	.	0.567629	0.20664	N	0.087970	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38908	-0.9639	9	0.87932	D	0	.	6.4829	0.22073	0.0:0.4223:0.2142:0.3636	rs6860508;rs59551514;rs6860508	381;704	Q96K48;Q9BYT8	.;NEUL_HUMAN	S	704;600;414	ENSP00000370372:P704S;ENSP00000423214:P600S;ENSP00000427417:P414S	ENSP00000370372:P704S	P	+	1	0	NLN	65154494	0.000000	0.05858	0.050000	0.19076	0.080000	0.17528	-0.039000	0.12124	-0.372000	0.07992	-0.254000	0.11334	CCG	C|0.918;T|0.082	0.082	strong		0.502	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1		
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504794	227504794	+	Silent	SNP	T	T	C	rs11804613	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:227504794T>C	ENST00000366769.3	-	1	1381	c.90A>G	c.(88-90)acA>acG	p.T30T	CDC42BPA_ENST00000366764.2_Silent_p.T30T|CDC42BPA_ENST00000334218.5_Silent_p.T30T|CDC42BPA_ENST00000366767.3_Silent_p.T30T|CDC42BPA_ENST00000366766.2_Silent_p.T30T|CDC42BPA_ENST00000535525.1_Silent_p.T30T|CDC42BPA_ENST00000366765.3_Silent_p.T30T	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TATCCAGTAATGTCTCCACAC	0.438													N|||	1358	0.271166	0.3411	0.2954	5008	,	,		16521	0.3363		0.1521	False		,,,				2504	0.2147				p.T30T		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.A90G						PASS	.	C	,	1318,3088	696.9+/-406.1	191,936,1076	135.0	121.0	126.0		90,90	-9.6	0.0	1	dbSNP_120	126	1229,7371	762.3+/-407.6	80,1069,3151	no	coding-synonymous,coding-synonymous	CDC42BPA	NM_003607.3,NM_014826.4	,	271,2005,4227	CC,CT,TT		14.2907,29.9138,19.5833	,	30/1720,30/1639	227504794	2547,10459	2203	4300	6503	SO:0001819	synonymous_variant	8476	exon1			CAGTAATGTCTCC	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.90A>G	1.37:g.227504794T>C		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	217	103	0.474654	NM_003607		Silent	SNP	ENST00000366769.3	37	CCDS1558.1																																																																																			T|0.768;C|0.232	0.232	strong		0.438	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
BOC	91653	hgsc.bcm.edu	37	3	112998265	112998265	+	Silent	SNP	A	A	G	rs2649878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112998265A>G	ENST00000495514.1	+	12	2687	c.1983A>G	c.(1981-1983)ccA>ccG	p.P661P	BOC_ENST00000273395.4_Silent_p.P662P|BOC_ENST00000355385.3_Silent_p.P661P			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	661	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CCATCCCCCCATCGCGGCTGT	0.627													A|||	2798	0.558706	0.8359	0.4741	5008	,	,		17802	0.6101		0.336	False		,,,				2504	0.4202				p.P661P		Atlas-SNP	.											.	BOC	139	.	0			c.A1983G						PASS	.	A		3419,987	727.6+/-409.9	1346,727,130	43.0	52.0	49.0		1983	0.3	1.0	3	dbSNP_100	49	2586,6014	419.8+/-353.2	382,1822,2096	no	coding-synonymous	BOC	NM_033254.2		1728,2549,2226	GG,GA,AA		30.0698,22.4013,46.171		661/1115	112998265	6005,7001	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon12			CCCCCCATCGCGG	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1983A>G	3.37:g.112998265A>G		Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	55	55	1	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			A|0.504;G|0.496	0.496	strong		0.627	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
ZNF512	84450	hgsc.bcm.edu	37	2	27838058	27838058	+	Silent	SNP	C	C	A	rs11127071	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27838058C>A	ENST00000355467.4	+	11	1238	c.1155C>A	c.(1153-1155)ctC>ctA	p.L385L	ZNF512_ENST00000413371.2_Silent_p.L308L|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000416005.2_Silent_p.L356L|ZNF512_ENST00000556601.1_Silent_p.L254L|ZNF512_ENST00000379717.1_Silent_p.L384L	NM_001271287.1|NM_001271288.1|NM_001271289.1|NM_001271318.1|NM_032434.3	NP_001258216.1|NP_001258217.1|NP_001258218.1|NP_001258247.1|NP_115810.2	Q96ME7	ZN512_HUMAN	zinc finger protein 512	385					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)					GTCCAGGGCTCCCTACCTTCA	0.378													A|||	3269	0.652756	0.7148	0.6873	5008	,	,		17541	0.8452		0.497	False		,,,				2504	0.5061				p.L385L		Atlas-SNP	.											.	ZNF512	54	.	0			c.C1155A						PASS	.	A		2965,1441	466.0+/-354.4	979,1007,217	176.0	168.0	170.0		1155	-6.0	0.4	2	dbSNP_120	170	4252,4348	581.1+/-391.2	1064,2124,1112	no	coding-synonymous	ZNF512	NM_032434.2		2043,3131,1329	AA,AC,CC		49.4419,32.7054,44.5102		385/568	27838058	7217,5789	2203	4300	6503	SO:0001819	synonymous_variant	84450	exon11			AGGGCTCCCTACC	AL833748	CCDS1758.1, CCDS59428.1, CCDS59429.1	2p23	2008-02-05			ENSG00000243943	ENSG00000243943		"""Zinc fingers, C2H2-type"""	29380	protein-coding gene	gene with protein product						11347906	Standard	NM_032434		Approved	KIAA1805	uc002rla.4	Q96ME7	OTTHUMG00000097786	ENST00000355467.4:c.1155C>A	2.37:g.27838058C>A		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	135	63	0.466667	NM_032434	B4DSM5|Q53RZ7|Q86XK6|Q96JM0	Silent	SNP	ENST00000355467.4	37	CCDS1758.1																																																																																			C|0.399;A|0.601	0.601	strong		0.378	ZNF512-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215029.2	NM_032434	
ZNF169	169841	hgsc.bcm.edu	37	9	97062981	97062981	+	Missense_Mutation	SNP	C	C	T	rs12236219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:97062981C>T	ENST00000395395.2	+	5	1231	c.1141C>T	c.(1141-1143)Cgt>Tgt	p.R381C	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	381			R -> C (in dbSNP:rs12236219).		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(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				TGAGTGTGGGCGTAGCTTCAG	0.567													C|||	873	0.174321	0.0938	0.2565	5008	,	,		21660	0.3542		0.0517	False		,,,				2504	0.1656				p.R381C		Atlas-SNP	.											ZNF169,NS,carcinoma,-1,1	ZNF169	60	1	0			c.C1141T						PASS	.	C	CYS/ARG	347,4059	179.0+/-207.6	14,319,1870	64.0	56.0	59.0		1141	0.9	0.9	9	dbSNP_120	59	380,8220	123.4+/-182.3	10,360,3930	yes	missense	ZNF169	NM_194320.2	180	24,679,5800	TT,TC,CC		4.4186,7.8756,5.5897	probably-damaging	381/604	97062981	727,12279	2203	4300	6503	SO:0001583	missense	169841	exon5			TGTGGGCGTAGCT	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"""Zinc fingers, C2H2-type"", ""-"""	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1141C>T	9.37:g.97062981C>T	ENSP00000378792:p.Arg381Cys	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	74	38	0.513514	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	362	0.16575091575091574	43	0.08739837398373984	81	0.22375690607734808	192	0.3356643356643357	46	0.06068601583113457	C	9.160	1.018407	0.19355	0.078756	0.044186	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.19806	2.12	2.71	0.852	0.18995	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.65677	2.01	0.43703	P	0.003834000000000004	D	0.89917	1.0	D	0.79784	0.993	T	0.31861	-0.9928	8	0.87932	D	0	.	2.4738	0.04571	0.2347:0.4919:0.0:0.2734	rs12236219;rs52793080;rs59355579;rs12236219	381	Q14929	ZN169_HUMAN	C	381;190	ENSP00000378792:R381C	ENSP00000340711:R190C	R	+	1	0	ZNF169	96102802	0.417000	0.25432	0.911000	0.35937	0.002000	0.02628	0.802000	0.27069	0.230000	0.21059	-0.199000	0.12753	CGT	C|0.894;T|0.106	0.106	strong		0.567	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3392021	3392021	+	Silent	SNP	C	C	T	rs140551015	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:3392021C>T	ENST00000324266.5	+	2	822	c.627C>T	c.(625-627)ttC>ttT	p.F209F	TRAPPC12_ENST00000382110.2_Silent_p.F209F	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	209					vesicle-mediated transport (GO:0016192)												TCAGCACGTTCTTCGGAGACA	0.672													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		7296	0.0		0.0099	False		,,,				2504	0.0				p.F209F		Atlas-SNP	.											.	.	.	.	0			c.C627T						PASS	.	C		16,4390	19.1+/-41.9	0,16,2187	32.0	39.0	37.0		627	-2.8	0.6	2	dbSNP_134	37	122,8478	57.2+/-118.5	0,122,4178	no	coding-synonymous	TTC15	NM_016030.5		0,138,6365	TT,TC,CC		1.4186,0.3631,1.061		209/736	3392021	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	51112	exon2			CACGTTCTTCGGA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.627C>T	2.37:g.3392021C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	58	24	0.413793	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1																																																																																			C|0.991;T|0.009	0.009	strong		0.672	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
TPRX1	284355	hgsc.bcm.edu	37	19	48305555	48305555	+	Missense_Mutation	SNP	G	G	A	rs147380237		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48305555G>A	ENST00000322175.3	-	2	868	c.713C>T	c.(712-714)cCg>cTg	p.P238L	TPRX1_ENST00000543508.1_Missense_Mutation_p.P228L|TPRX1_ENST00000535759.1_Missense_Mutation_p.P335L	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	238	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		gcctgggatcgggcctgggtt	0.662																																					p.P238L	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											TPRX1,colon,carcinoma,+1,1	TPRX1	46	1	0			c.C713T						PASS	.						10.0	8.0	9.0					19																	48305555		2095	4129	6224	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.713C>T	19.37:g.48305555G>A	ENSP00000323455:p.Pro238Leu	Somatic	29	0	0		WXS	Illumina HiSeq	Phase_I	38	7	0.184211	NM_198479	A5D8Y3|B2RPL5	Missense_Mutation	SNP	ENST00000322175.3	37	CCDS33066.1	24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	g	8.014	0.758252	0.15846	.	.	ENSG00000178928	ENST00000322175;ENST00000535759;ENST00000543508	D;D	0.93659	-2.01;-3.26	0.495	0.495	0.16890	.	.	.	.	.	T	0.79936	0.4532	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	P	0.60286	0.872	T	0.76977	-0.2759	8	0.45353	T	0.12	.	.	.	.	.	238	Q8N7U7	TPRX1_HUMAN	L	238;335;228	ENSP00000323455:P238L;ENSP00000438832:P335L	ENSP00000323455:P238L	P	-	2	0	TPRX1	52997367	0.000000	0.05858	0.020000	0.16555	0.015000	0.08874	-2.180000	0.01258	0.561000	0.29186	0.420000	0.28162	CCG	G|0.989;A|0.011	0.011	strong		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
JMJD4	65094	hgsc.bcm.edu	37	1	227920665	227920665	+	Missense_Mutation	SNP	A	A	G	rs41270159	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:227920665A>G	ENST00000366758.3	-	5	1023	c.1024T>C	c.(1024-1026)Ttc>Ctc	p.F342L	JMJD4_ENST00000485807.1_5'UTR|SNAP47_ENST00000315781.5_5'Flank|SNAP47_ENST00000366759.4_5'Flank|JMJD4_ENST00000438896.2_Missense_Mutation_p.F342L|SNAP47_ENST00000366760.1_Intron|SNAP47_ENST00000480897.1_3'UTR	NM_023007.2	NP_075383.2	Q9H9V9	JMJD4_HUMAN	jumonji domain containing 4	342	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.									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)				TGCTGCAAGAAGCGCCACATG	0.617													A|||	99	0.0197684	0.003	0.036	5008	,	,		21632	0.001		0.0636	False		,,,				2504	0.0051				p.F342L		Atlas-SNP	.											.	JMJD4	28	.	0			c.T1024C						PASS	.	A	LEU/PHE,LEU/PHE	36,4370		0,36,2167	78.0	68.0	71.0		1024,1024	3.8	1.0	1	dbSNP_127	71	332,8268		7,318,3975	yes	missense,missense	JMJD4	NM_001161465.1,NM_023007.2	22,22	7,354,6142	GG,GA,AA		3.8605,0.8171,2.8295	benign,benign	342/448,342/464	227920665	368,12638	2203	4300	6503	SO:0001583	missense	65094	exon5			GCAAGAAGCGCCA	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.1024T>C	1.37:g.227920665A>G	ENSP00000355720:p.Phe342Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	64	32	0.5	NM_023007	Q5TBZ1|Q5TBZ6|Q9H970	Missense_Mutation	SNP	ENST00000366758.3	37	CCDS1561.1	72	0.03296703296703297	2	0.0040650406504065045	17	0.04696132596685083	1	0.0017482517482517483	52	0.06860158311345646	.	12.73	2.025098	0.35701	0.008171	0.038605	ENSG00000081692	ENST00000366758	T	0.69685	-0.42	4.96	3.82	0.43975	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.09949	0.0244	L	0.58354	1.805	0.54753	D	0.999987	B;B	0.24882	0.113;0.112	B;B	0.20955	0.032;0.014	T	0.15492	-1.0435	10	0.30854	T	0.27	-35.462	10.0615	0.42277	0.8305:0.1695:0.0:0.0	rs41270159	342;342	Q9H9V9-2;Q9H9V9	.;JMJD4_HUMAN	L	342	ENSP00000355720:F342L	ENSP00000355720:F342L	F	-	1	0	JMJD4	225987288	1.000000	0.71417	0.997000	0.53966	0.818000	0.46254	8.104000	0.89551	0.887000	0.36136	0.533000	0.62120	TTC	A|0.967;G|0.033	0.033	strong		0.617	JMJD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091970.1	NM_023007	
ABCA7	10347	hgsc.bcm.edu	37	19	1054267	1054267	+	Missense_Mutation	SNP	G	G	A	rs534172941		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1054267G>A	ENST00000263094.6	+	27	3884	c.3653G>A	c.(3652-3654)cGc>cAc	p.R1218H	ABCA7_ENST00000433129.1_Missense_Mutation_p.R1218H|ABCA7_ENST00000435683.2_Missense_Mutation_p.R1080H	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1218					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCACTGACCCGCCAGCAGCTC	0.697													G|||	1	0.000199681	0.0	0.0	5008	,	,		14782	0.0		0.0	False		,,,				2504	0.001				p.R1218H		Atlas-SNP	.											.	ABCA7	174	.	0			c.G3653A						PASS	.						12.0	16.0	15.0					19																	1054267		2185	4270	6455	SO:0001583	missense	10347	exon27			TGACCCGCCAGCA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3653G>A	19.37:g.1054267G>A	ENSP00000263094:p.Arg1218His	Somatic	26	0	0		WXS	Illumina HiSeq	Phase_I	25	13	0.52	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	g	11.52	1.664688	0.29604	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86865	-2.18;-2.18	3.54	-5.43	0.02632	.	.	.	.	.	T	0.74068	0.3668	L	0.42529	1.33	0.09310	N	1	B;B	0.24426	0.103;0.007	B;B	0.23852	0.049;0.004	T	0.59958	-0.7356	9	0.17369	T	0.5	.	0.5118	0.00597	0.3927:0.134:0.2029:0.2704	.	1080;1218	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	H	1218	ENSP00000263094:R1218H;ENSP00000414062:R1218H	ENSP00000263094:R1218H	R	+	2	0	ABCA7	1005267	0.000000	0.05858	0.002000	0.10522	0.778000	0.44026	-1.209000	0.03002	-1.417000	0.02017	-0.649000	0.03915	CGC	.	.	none		0.697	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
RPS6KL1	83694	hgsc.bcm.edu	37	14	75386576	75386576	+	Missense_Mutation	SNP	G	G	A	rs2286913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:75386576G>A	ENST00000555647.1	-	4	649	c.362C>T	c.(361-363)cCg>cTg	p.P121L	RPS6KL1_ENST00000354625.2_Missense_Mutation_p.P121L|RPS6KL1_ENST00000557413.1_Missense_Mutation_p.P121L|RPS6KL1_ENST00000358328.4_Missense_Mutation_p.P121L|RPS6KL1_ENST00000554900.1_5'UTR			Q9Y6S9	RPKL1_HUMAN	ribosomal protein S6 kinase-like 1	121			P -> L (in dbSNP:rs2286913). {ECO:0000269|PubMed:17344846}.			ribosome (GO:0005840)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(234;0.00658)		ACTGCTCAGCGGCCGCTGCAG	0.647													G|||	1492	0.297923	0.0174	0.3876	5008	,	,		14334	0.5853		0.3738	False		,,,				2504	0.2393				p.P121L		Atlas-SNP	.											RPS6KL1,colon,carcinoma,0,1	RPS6KL1	35	1	0			c.C362T						PASS	.	G	LEU/PRO	368,4038	178.7+/-207.4	22,324,1857	26.0	27.0	27.0		362	4.1	0.3	14	dbSNP_100	27	3149,5449	456.4+/-364.1	574,2001,1724	yes	missense	RPS6KL1	NM_031464.4	98	596,2325,3581	AA,AG,GG		36.6248,8.3522,27.0455	benign	121/550	75386576	3517,9487	2203	4299	6502	SO:0001583	missense	83694	exon3			CTCAGCGGCCGCT	BC004540	CCDS9834.1, CCDS9834.2	14q24.2	2011-04-05				ENSG00000198208			20222	protein-coding gene	gene with protein product							Standard	NM_031464		Approved	MGC11287	uc010tux.2	Q9Y6S9		ENST00000555647.1:c.362C>T	14.37:g.75386576G>A	ENSP00000452027:p.Pro121Leu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	119	65	0.546219	NM_031464	A6NGM9|Q69YT9|Q6ZMQ6|Q96NR9|Q9BSU9	Missense_Mutation	SNP	ENST00000555647.1	37	CCDS9834.2	754	0.34523809523809523	12	0.024390243902439025	136	0.3756906077348066	318	0.5559440559440559	288	0.37994722955145116	G	7.553	0.663135	0.14710	0.083522	0.366248	ENSG00000198208	ENST00000555647;ENST00000354625;ENST00000557413;ENST00000358328	T;T;T;T	0.22539	1.95;3.3;1.95;1.95	4.99	4.07	0.47477	MIT (1);	0.411157	0.26812	N	0.022368	T	0.00012	0.0000	L	0.29908	0.895	0.32626	P	0.522599	B;P;B	0.36027	0.106;0.533;0.186	B;B;B	0.28553	0.03;0.091;0.024	T	0.36529	-0.9744	9	0.35671	T	0.21	-4.1088	13.2998	0.60317	0.0:0.1589:0.8411:0.0	rs2286913;rs2286913	121;121;121	Q9Y6S9;Q9Y6S9-4;Q9Y6S9-2	RPKL1_HUMAN;.;.	L	121	ENSP00000452027:P121L;ENSP00000346644:P121L;ENSP00000450567:P121L;ENSP00000351086:P121L	ENSP00000346644:P121L	P	-	2	0	RPS6KL1	74456329	0.998000	0.40836	0.306000	0.25113	0.017000	0.09413	3.053000	0.49901	1.297000	0.44761	0.655000	0.94253	CCG	G|0.708;A|0.292	0.292	strong		0.647	RPS6KL1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413732.1		
LETM1	3954	hgsc.bcm.edu	37	4	1824020	1824020	+	Missense_Mutation	SNP	C	C	T	rs28681468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1824020C>T	ENST00000302787.2	-	10	1792	c.1496G>A	c.(1495-1497)cGt>cAt	p.R499H		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	499					cristae formation (GO:0042407)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(2)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	13			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			AGCTACCACACGTTCGGGCTC	0.592													c|||	59	0.0117812	0.0091	0.0173	5008	,	,		18177	0.0		0.0268	False		,,,				2504	0.0082				p.R499H		Atlas-SNP	.											.	LETM1	48	.	0			c.G1496A						PASS	.	C	HIS/ARG	52,4354	50.9+/-86.3	0,52,2151	59.0	53.0	55.0		1496	-0.7	0.0	4	dbSNP_125	55	266,8334	102.3+/-163.5	3,260,4037	yes	missense	LETM1	NM_012318.2	29	3,312,6188	TT,TC,CC		3.093,1.1802,2.445	benign	499/740	1824020	318,12688	2203	4300	6503	SO:0001583	missense	3954	exon10			ACCACACGTTCGG	AF061025	CCDS3355.1	4p16.3	2013-01-10			ENSG00000168924	ENSG00000168924		"""EF-hand domain containing"""	6556	protein-coding gene	gene with protein product	"""Mdm38 homolog (yeast)"""	604407				10486213	Standard	NM_012318		Approved		uc003gdv.3	O95202	OTTHUMG00000121149	ENST00000302787.2:c.1496G>A	4.37:g.1824020C>T	ENSP00000305653:p.Arg499His	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	110	53	0.481818	NM_012318	B4DED2|Q9UF65	Missense_Mutation	SNP	ENST00000302787.2	37	CCDS3355.1	24	0.01098901098901099	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	11.17	1.560042	0.27827	0.011802	0.03093	ENSG00000168924	ENST00000302787	.	.	.	4.65	-0.707	0.11245	.	0.970810	0.08436	N	0.946208	T	0.05456	0.0144	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	9	0.45353	T	0.12	-2.8575	3.2806	0.06913	0.6202:0.1675:0.0962:0.1161	rs28681468;rs28681468	499	O95202	LETM1_HUMAN	H	499	.	ENSP00000305653:R499H	R	-	2	0	LETM1	1793818	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.573000	0.23699	-0.059000	0.13154	0.456000	0.33151	CGT	C|0.980;T|0.020	0.020	strong		0.592	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1		
PLIN4	729359	hgsc.bcm.edu	37	19	4510530	4510530	+	Missense_Mutation	SNP	G	G	A	rs7250947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4510530G>A	ENST00000301286.3	-	3	3399	c.3400C>T	c.(3400-3402)Cgc>Tgc	p.R1134C		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	1134			R -> C (in dbSNP:rs7250947).			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						ATTGCCAAGCGTGGGGCTTCT	0.657													G|||	332	0.0662939	0.1339	0.0821	5008	,	,		16074	0.001		0.0835	False		,,,				2504	0.0133				p.R1134C		Atlas-SNP	.											.	PLIN4	191	.	0			c.C3400T						PASS	.	G	CYS/ARG	485,3683		21,443,1620	46.0	51.0	50.0		3400	-7.8	0.0	19	dbSNP_116	50	692,7724		26,640,3542	yes	missense	PLIN4	NM_001080400.1	180	47,1083,5162	AA,AG,GG		8.2224,11.6363,9.3531	possibly-damaging	1134/1358	4510530	1177,11407	2084	4208	6292	SO:0001583	missense	729359	exon3			CCAAGCGTGGGGC	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.3400C>T	19.37:g.4510530G>A	ENSP00000301286:p.Arg1134Cys	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	103	54	0.524272	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	183	0.08379120879120878	77	0.1565040650406504	35	0.09668508287292818	1	0.0017482517482517483	70	0.09234828496042216	G	11.86	1.764994	0.31228	0.116363	0.082224	ENSG00000167676	ENST00000301286	T	0.03496	3.91	3.93	-7.85	0.01192	.	1.273050	0.05905	N	0.630730	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.53151	0.958	B	0.38296	0.27	T	0.43782	-0.9370	9	0.49607	T	0.09	.	1.3532	0.02177	0.1302:0.2043:0.2664:0.399	rs7250947;rs60853748;rs7250947	1134	Q96Q06	PLIN4_HUMAN	C	1134	ENSP00000301286:R1134C	ENSP00000301286:R1134C	R	-	1	0	PLIN4	4461530	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.071000	0.03437	-0.976000	0.03542	-0.416000	0.06073	CGC	G|0.909;A|0.091	0.091	strong		0.657	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
TUBA3C	7278	hgsc.bcm.edu	37	13	19753554	19753554	+	Silent	SNP	C	C	T	rs36215076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19753554C>T	ENST00000400113.3	-	2	257	c.153G>A	c.(151-153)acG>acA	p.T51T	RP11-408E5.4_ENST00000382988.2_5'Flank	NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	51					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		CACTGAAGAACGTGTTGAAGG	0.567													C|||	150	0.0299521	0.0038	0.0461	5008	,	,		18374	0.0129		0.0586	False		,,,				2504	0.0419				p.T51T		Atlas-SNP	.											.	TUBA3C	166	.	0			c.G153A						PASS	.	C		73,4333	65.8+/-103.3	1,71,2131	199.0	163.0	175.0		153	-0.7	1.0	13	dbSNP_126	175	505,8095	144.7+/-200.5	20,465,3815	no	coding-synonymous	TUBA3C	NM_006001.2		21,536,5946	TT,TC,CC		5.8721,1.6568,4.4441		51/451	19753554	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	7278	exon2			GAAGAACGTGTTG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.153G>A	13.37:g.19753554C>T		Somatic	240	0	0		WXS	Illumina HiSeq	Phase_I	265	113	0.426415	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			C|0.958;T|0.042	0.042	strong		0.567	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
MPV17L2	84769	hgsc.bcm.edu	37	19	18305824	18305824	+	Silent	SNP	C	C	T	rs2271881	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:18305824C>T	ENST00000599612.2	+	4	592	c.492C>T	c.(490-492)ccC>ccT	p.P164P		NM_032683.2	NP_116072.2	Q567V2	M17L2_HUMAN	MPV17 mitochondrial membrane protein-like 2	164						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				large_intestine(1)|lung(2)|urinary_tract(1)	4						TCGTGCCCCCCCAATTTCGAG	0.647													C|||	1226	0.244808	0.2708	0.3184	5008	,	,		12401	0.0685		0.3539	False		,,,				2504	0.227				p.P164P		Atlas-SNP	.											.	MPV17L2	12	.	0			c.C492T						PASS	.	C		1120,3036		141,838,1099	112.0	112.0	112.0		492	3.2	1.0	19	dbSNP_100	112	2952,5470		515,1922,1774	no	coding-synonymous	MPV17L2	NM_032683.2		656,2760,2873	TT,TC,CC		35.0511,26.949,32.374		164/207	18305824	4072,8506	2078	4211	6289	SO:0001819	synonymous_variant	84769	exon4			GCCCCCCCAATTT	AK094091	CCDS42522.1	19p13.11	2011-05-26			ENSG00000254858	ENSG00000254858			28177	protein-coding gene	gene with protein product						12477932	Standard	NM_032683		Approved	FKSG24, MGC12972	uc002nid.3	Q567V2	OTTHUMG00000165628	ENST00000599612.2:c.492C>T	19.37:g.18305824C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	86	86	1	NM_032683	Q96P34|Q96QA0|Q9BSG4	Silent	SNP	ENST00000599612.2	37	CCDS42522.1																																																																																			C|0.706;T|0.294	0.294	strong		0.647	MPV17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466294.2	NM_032683	
ITPR3	3710	hgsc.bcm.edu	37	6	33654857	33654857	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:33654857C>A	ENST00000374316.5	+	45	7111	c.6051C>A	c.(6049-6051)ctC>ctA	p.L2017L	ITPR3_ENST00000605930.1_Silent_p.L2017L			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2017					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)	AGCGAATCCTCATCAGCCTGC	0.667																																					p.L2017L		Atlas-SNP	.											ITPR3_ENST00000374316,right_lower_lobe,carcinoma,0,2	ITPR3	409	2	0			c.C6051A						scavenged	.						53.0	51.0	52.0					6																	33654857		2203	4296	6499	SO:0001819	synonymous_variant	3710	exon44			AATCCTCATCAGC	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.6051C>A	6.37:g.33654857C>A		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	96	2	0.0208333	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			.	.	none		0.667	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
JPH3	57338	hgsc.bcm.edu	37	16	87723838	87723838	+	Silent	SNP	T	T	C	rs34767155	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:87723838T>C	ENST00000284262.2	+	4	2114	c.1872T>C	c.(1870-1872)caT>caC	p.H624H	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	624					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		TGGAGACGCATCCCCAGAAAA	0.662													C|||	2214	0.442093	0.7148	0.428	5008	,	,		12875	0.2659		0.3161	False		,,,				2504	0.3947				p.H624H		Atlas-SNP	.											JPH3,NS,carcinoma,0,1	JPH3	95	1	0			c.T1872C						PASS	.	C		2697,1651		852,993,329	15.0	16.0	16.0		1872	3.9	1.0	16	dbSNP_126	16	2527,6049		404,1719,2165	no	coding-synonymous	JPH3	NM_020655.2		1256,2712,2494	CC,CT,TT		29.466,37.9715,40.4209		624/749	87723838	5224,7700	2174	4288	6462	SO:0001819	synonymous_variant	57338	exon4			GACGCATCCCCAG	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1872T>C	16.37:g.87723838T>C		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	93	48	0.516129	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Silent	SNP	ENST00000284262.2	37	CCDS10962.1																																																																																			T|0.583;C|0.417	0.417	strong		0.662	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
TBCK	93627	hgsc.bcm.edu	37	4	107157623	107157623	+	Missense_Mutation	SNP	G	G	A	rs34307452	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:107157623G>A	ENST00000273980.5	-	15	1721	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	TBCK_ENST00000432496.2_Missense_Mutation_p.T425M|TBCK_ENST00000394706.3_Missense_Mutation_p.T386M|TBCK_ENST00000394708.2_Missense_Mutation_p.T425M|TBCK_ENST00000361687.4_Missense_Mutation_p.T362M					TBC1 domain containing kinase											NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	25						TAAAGGGAGCGTGGCAGCTGC	0.358													G|||	82	0.0163738	0.0008	0.0202	5008	,	,		12577	0.001		0.0378	False		,,,				2504	0.0286				p.T425M		Atlas-SNP	.											TBCK,NS,carcinoma,+1,1	TBCK	89	1	0			c.C1274T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	38,4368	41.6+/-74.8	0,38,2165	62.0	64.0	63.0		1274,1274,1157,1085	5.0	1.0	4	dbSNP_126	63	373,8227	121.5+/-180.6	10,353,3937	yes	missense,missense,missense,missense	TBCK	NM_001163435.1,NM_001163436.1,NM_001163437.1,NM_033115.3	81,81,81,81	10,391,6102	AA,AG,GG		4.3372,0.8625,3.1601	benign,benign,benign,benign	425/894,425/894,386/855,362/831	107157623	411,12595	2203	4300	6503	SO:0001583	missense	93627	exon14			GGGAGCGTGGCAG		CCDS3673.1, CCDS54788.1, CCDS54789.1	4q24	2014-09-17			ENSG00000145348	ENSG00000145348			28261	protein-coding gene	gene with protein product						12471243	Standard	XR_427553		Approved	MGC16169, HSPC302	uc010ilv.2	Q8TEA7	OTTHUMG00000131214	ENST00000273980.5:c.1274C>T	4.37:g.107157623G>A	ENSP00000273980:p.Thr425Met	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_001163436		Missense_Mutation	SNP	ENST00000273980.5	37	CCDS54788.1	35	0.016025641025641024	0	0.0	8	0.022099447513812154	0	0.0	27	0.03562005277044855	G	16.71	3.199261	0.58126	0.008625	0.043372	ENSG00000145348	ENST00000273980;ENST00000432496;ENST00000361687;ENST00000394706;ENST00000394708	T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03	5.87	5.03	0.67393	.	0.131721	0.64402	D	0.000002	T	0.03095	0.0091	L	0.44542	1.39	0.38864	D	0.956556	P;D;P	0.58620	0.857;0.983;0.912	B;P;P	0.52856	0.302;0.711;0.498	T	0.02053	-1.1222	10	0.51188	T	0.08	.	12.284	0.54781	0.0:0.1117:0.6914:0.1969	rs34307452	425;386;362	Q8TEA7;Q8TEA7-2;Q8TEA7-3	TBCK_HUMAN;.;.	M	425;425;362;386;425	ENSP00000273980:T425M;ENSP00000405847:T425M;ENSP00000355338:T362M;ENSP00000378196:T386M;ENSP00000378198:T425M	ENSP00000273980:T425M	T	-	2	0	TBCK	107377072	1.000000	0.71417	0.978000	0.43139	0.979000	0.70002	2.884000	0.48562	1.473000	0.48159	-0.179000	0.13096	ACG	G|0.974;A|0.026	0.026	strong		0.358	TBCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253953.4	NM_033115	
CER1	9350	hgsc.bcm.edu	37	9	14720193	14720193	+	Silent	SNP	C	C	T	rs61759465	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:14720193C>T	ENST00000380911.3	-	2	743	c.699G>A	c.(697-699)gtG>gtA	p.V233V		NM_005454.2	NP_005445.1	O95813	CER1_HUMAN	cerberus 1, DAN family BMP antagonist	233	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				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)		CCACCAGCATCACCACCTTGA	0.532													C|||	22	0.00439297	0.0008	0.0043	5008	,	,		18707	0.0		0.0149	False		,,,				2504	0.0031				p.V233V		Atlas-SNP	.											.	CER1	41	.	0			c.G699A						PASS	.	C		17,4389	24.3+/-50.5	0,17,2186	132.0	108.0	116.0		699	3.6	1.0	9	dbSNP_129	116	153,8447	74.8+/-137.4	2,149,4149	no	coding-synonymous	CER1	NM_005454.2		2,166,6335	TT,TC,CC		1.7791,0.3858,1.3071		233/268	14720193	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	9350	exon2			CAGCATCACCACC	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.699G>A	9.37:g.14720193C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	134	70	0.522388	NM_005454	Q6ISJ1|Q6ISJ6|Q6ISQ2|Q6ISS1	Silent	SNP	ENST00000380911.3	37	CCDS6476.1																																																																																			C|0.989;T|0.011	0.011	strong		0.532	CER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055453.1	NM_005454	
COL5A1	1289	hgsc.bcm.edu	37	9	137686951	137686951	+	Silent	SNP	G	G	A	rs41310207	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:137686951G>A	ENST00000371817.3	+	33	3138	c.2724G>A	c.(2722-2724)ccG>ccA	p.P908P		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	908	Triple-helical region.		P -> L (found in a renal cell carcinoma case; somatic mutation). {ECO:0000269|PubMed:21248752}.		axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AGCCAGGACCGCGGGGGCAGC	0.622													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		15385	0.001		0.0408	False		,,,				2504	0.0061				p.P908P		Atlas-SNP	.											COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	0			c.G2724A						PASS	.	G		23,4383	29.9+/-59.1	0,23,2180	51.0	59.0	56.0		2724	-8.9	1.0	9	dbSNP_127	56	325,8275	114.4+/-174.4	9,307,3984	no	coding-synonymous	COL5A1	NM_000093.3		9,330,6164	AA,AG,GG		3.7791,0.522,2.6757		908/1839	137686951	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	1289	exon33			AGGACCGCGGGGG	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.2724G>A	9.37:g.137686951G>A		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	61	29	0.47541	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			G|0.975;A|0.025	0.025	strong		0.622	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
UFL1	23376	hgsc.bcm.edu	37	6	96997651	96997651	+	Silent	SNP	C	C	T	rs149844923	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:96997651C>T	ENST00000369278.4	+	15	1860	c.1794C>T	c.(1792-1794)gaC>gaT	p.D598D		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	598					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)										TGGCAGTAGACGATCCTGCAG	0.378													T|||	43	0.00858626	0.0303	0.0043	5008	,	,		15664	0.0		0.0	False		,,,				2504	0.0				p.D598D		Atlas-SNP	.											.	.	.	.	0			c.C1794T						PASS	.	T		105,4301	814.7+/-416.2	0,105,2098	133.0	118.0	123.0		1794	-11.3	0.1	6	dbSNP_134	123	5,8595	817.9+/-406.9	0,5,4295	no	coding-synonymous	UFL1	NM_015323.4		0,110,6393	TT,TC,CC		0.0581,2.3831,0.8458		598/795	96997651	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	23376	exon15			AGTAGACGATCCT	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.1794C>T	6.37:g.96997651C>T		Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	61	4	0.0655738	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																			C|0.991;T|0.009	0.009	strong		0.378	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323	
VCAN	1462	hgsc.bcm.edu	37	5	82833391	82833391	+	Silent	SNP	A	A	G	rs16900528	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:82833391A>G	ENST00000265077.3	+	8	5134	c.4569A>G	c.(4567-4569)acA>acG	p.T1523T	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Silent_p.T536T|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1523	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AATCAGTCACAGAGAGAGATA	0.443													A|||	288	0.057508	0.0098	0.036	5008	,	,		21611	0.0685		0.0825	False		,,,				2504	0.1002				p.T1523T		Atlas-SNP	.											.	VCAN	498	.	0			c.A4569G						PASS	.	A	,,,	109,4297	84.8+/-123.5	0,109,2094	77.0	75.0	75.0		,1608,,4569	-3.3	0.0	5	dbSNP_123	75	697,7903	171.4+/-222.4	26,645,3629	no	intron,coding-synonymous,intron,coding-synonymous	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,,	26,754,5723	GG,GA,AA		8.1047,2.4739,6.1971	,,,	,536/2410,,1523/3397	82833391	806,12200	2203	4300	6503	SO:0001819	synonymous_variant	1462	exon8			AGTCACAGAGAGA	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.4569A>G	5.37:g.82833391A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	70	42	0.6	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Silent	SNP	ENST00000265077.3	37	CCDS4060.1																																																																																			A|0.942;G|0.058	0.058	strong		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
ASPHD2	57168	hgsc.bcm.edu	37	22	26829914	26829914	+	Silent	SNP	T	T	C	rs3747128	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26829914T>C	ENST00000215906.5	+	2	771	c.333T>C	c.(331-333)ccT>ccC	p.P111P		NM_020437.4	NP_065170.2	Q6ICH7	ASPH2_HUMAN	aspartate beta-hydroxylase domain containing 2	111					peptidyl-amino acid modification (GO:0018193)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	16						GCCAGTCCCCTGAGTGCGTGC	0.647													C|||	324	0.0646965	0.0439	0.0591	5008	,	,		19562	0.0169		0.1382	False		,,,				2504	0.0706				p.P111P		Atlas-SNP	.											.	ASPHD2	42	.	0			c.T333C						PASS	.	C		309,4097	793.6+/-415.2	8,293,1902	59.0	49.0	52.0		333	-4.1	1.0	22	dbSNP_107	52	1442,7158	747.7+/-407.3	129,1184,2987	no	coding-synonymous	ASPHD2	NM_020437.4		137,1477,4889	CC,CT,TT		16.7674,7.0132,13.463		111/370	26829914	1751,11255	2203	4300	6503	SO:0001819	synonymous_variant	57168	exon2			GTCCCCTGAGTGC	AK097157	CCDS13834.2	22q12.1	2006-02-02			ENSG00000128203	ENSG00000128203			30437	protein-coding gene	gene with protein product							Standard	NM_020437		Approved	FLJ39838	uc003acg.2	Q6ICH7	OTTHUMG00000150884	ENST00000215906.5:c.333T>C	22.37:g.26829914T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	39	21	0.538462	NM_020437	B2RCH3|Q7L0W3|Q9NSN3	Silent	SNP	ENST00000215906.5	37	CCDS13834.2																																																																																			T|0.890;C|0.110	0.110	strong		0.647	ASPHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320422.1	NM_020437	
SLC23A2	9962	hgsc.bcm.edu	37	20	4854682	4854682	+	Silent	SNP	A	A	G	rs1110277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4854682A>G	ENST00000379333.1	-	11	1394	c.1002T>C	c.(1000-1002)gaT>gaC	p.D334D	SLC23A2_ENST00000338244.1_Silent_p.D334D|SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000424750.2_Silent_p.D220D	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	334					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)	p.D334D(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						GAGGGAAGACATCTGTCACCG	0.562													G|||	2144	0.428115	0.7163	0.3458	5008	,	,		20174	0.249		0.341	False		,,,				2504	0.3712				p.D334D		Atlas-SNP	.											SLC23A2,NS,carcinoma,0,2	SLC23A2	62	2	1	Substitution - coding silent(1)	prostate(1)	c.T1002C						PASS	.	G	,	2903,1503	477.0+/-357.8	964,975,264	147.0	123.0	131.0		1002,1002	-9.8	0.0	20	dbSNP_86	131	2870,5730	673.0+/-403.0	462,1946,1892	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1426,2921,2156	GG,GA,AA		33.3721,34.1126,44.3872	,	334/651,334/651	4854682	5773,7233	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon11			GAAGACATCTGTC	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.1002T>C	20.37:g.4854682A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	95	53	0.557895	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1	879	0.4024725274725275	366	0.7439024390243902	122	0.3370165745856354	136	0.23776223776223776	255	0.33641160949868076	G	0.232	-1.020330	0.02061	0.658874	0.333721	ENSG00000089057	ENST00000423430	.	.	.	5.72	-9.75	0.00506	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999887	.	.	.	.	.	.	T	0.01630	-1.1308	3	.	.	.	-23.4039	19.8078	0.96537	0.7996:0.0:0.2004:0.0	rs1110277;rs17339239;rs17845367;rs17858220;rs58558129;rs1110277	.	.	.	R	91	.	.	C	-	1	0	SLC23A2	4802682	0.008000	0.16893	0.032000	0.17829	0.001000	0.01503	-0.850000	0.04317	-2.523000	0.00496	-1.767000	0.00664	TGT	A|0.562;C|0.001	.	strong		0.562	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
OBSL1	23363	hgsc.bcm.edu	37	2	220427395	220427395	+	Splice_Site	SNP	G	G	A	rs3183099	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220427395G>A	ENST00000404537.1	-	8	2738	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	OBSL1_ENST00000603926.1_Splice_Site_p.D894D|OBSL1_ENST00000373876.1_Splice_Site_p.D894D|OBSL1_ENST00000373873.4_Splice_Site_p.D894D|OBSL1_ENST00000289656.3_Splice_Site_p.D481D|OBSL1_ENST00000265318.4_Splice_Site_p.D894D	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	894					cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACGAGGAGACGTCTGGAGGAC	0.647													G|||	822	0.164137	0.0772	0.2608	5008	,	,		17765	0.2123		0.2386	False		,,,				2504	0.0869				p.D894D		Atlas-SNP	.											.	OBSL1	120	.	0			c.C2682T						PASS	.	G	,,	461,3787		40,381,1703	18.0	22.0	21.0		2682,2682,2682	-7.6	0.4	2	dbSNP_105	21	1962,6404		251,1460,2472	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	OBSL1	NM_001173408.1,NM_001173431.1,NM_015311.2	,,	291,1841,4175	AA,AG,GG		23.4521,10.8522,19.2088	,,	894/1026,894/1544,894/1897	220427395	2423,10191	2124	4183	6307	SO:0001630	splice_region_variant	23363	exon8			GGAGACGTCTGGA	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.2681-1C>T	2.37:g.220427395G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	66	31	0.469697	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			G|0.802;A|0.198	0.198	strong		0.647	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		Silent
GAS2L3	283431	hgsc.bcm.edu	37	12	101018014	101018014	+	Silent	SNP	T	T	C	rs1045602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101018014T>C	ENST00000539410.1	+	9	1817	c.1431T>C	c.(1429-1431)aaT>aaC	p.N477N	GAS2L3_ENST00000266754.5_Silent_p.N477N|GAS2L3_ENST00000547754.1_Silent_p.N477N|GAS2L3_ENST00000537247.1_Silent_p.N373N			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	477					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)	p.N477N(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						TGAAACATAATCATATTTCTT	0.393													T|||	1691	0.33766	0.2685	0.3818	5008	,	,		19486	0.2748		0.5338	False		,,,				2504	0.2628				p.N477N		Atlas-SNP	.											GAS2L3,NS,carcinoma,0,1	GAS2L3	76	1	1	Substitution - coding silent(1)	stomach(1)	c.T1431C						PASS	.	T		1297,3109	416.3+/-337.5	202,893,1108	61.0	66.0	64.0		1431	2.0	0.0	12	dbSNP_86	64	4599,3999	592.0+/-392.9	1228,2143,928	no	coding-synonymous	GAS2L3	NM_174942.1		1430,3036,2036	CC,CT,TT		46.5108,29.4371,45.3399		477/695	101018014	5896,7108	2203	4299	6502	SO:0001819	synonymous_variant	283431	exon10			ACATAATCATATT	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1431T>C	12.37:g.101018014T>C		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	73	40	0.547945	NM_174942	B2RCN2	Silent	SNP	ENST00000539410.1	37	CCDS9079.1																																																																																			T|0.585;C|0.415	0.415	strong		0.393	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
IL34	146433	hgsc.bcm.edu	37	16	70690989	70690989	+	Missense_Mutation	SNP	G	G	C	rs8046424	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:70690989G>C	ENST00000288098.2	+	4	750	c.367G>C	c.(367-369)Gag>Cag	p.E123Q	IL34_ENST00000429149.2_Missense_Mutation_p.E123Q|IL34_ENST00000566361.1_Missense_Mutation_p.E98Q	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	123			E -> Q (in dbSNP:rs8046424). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:18467591}.		inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						GCAGGAGGTGGAGACGCTGCT	0.607													C|||	3581	0.715056	0.9826	0.5994	5008	,	,		20344	0.6687		0.4742	False		,,,				2504	0.7311				p.E123Q		Atlas-SNP	.											.	IL34	26	.	0			c.G367C						PASS	.	C	GLN/GLU,GLN/GLU,GLN/GLU	3958,438	209.8+/-230.5	1790,378,30	115.0	84.0	94.0		364,367,367	3.0	0.1	16	dbSNP_116	94	4199,4401	583.6+/-391.6	1032,2135,1133	yes	missense,missense,missense	IL34	NM_001172771.1,NM_001172772.1,NM_152456.2	29,29,29	2822,2513,1163	CC,CG,GG		48.8256,9.9636,37.2345	benign,benign,benign	122/242,123/243,123/243	70690989	8157,4839	2198	4300	6498	SO:0001583	missense	146433	exon5			GAGGTGGAGACGC	BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368		"""Interleukins and interleukin receptors"""	28529	protein-coding gene	gene with protein product		612081	"""chromosome 16 open reading frame 77"""	C16orf77		18467591	Standard	NM_152456		Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.367G>C	16.37:g.70690989G>C	ENSP00000288098:p.Glu123Gln	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	108	60	0.555556	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Missense_Mutation	SNP	ENST00000288098.2	37	CCDS10895.1	1429	0.6543040293040293	478	0.9715447154471545	203	0.5607734806629834	397	0.6940559440559441	351	0.4630606860158311	C	10.33	1.319045	0.23994	0.900364	0.488256	ENSG00000157368	ENST00000429149;ENST00000288098	T;T	0.44083	0.93;0.93	5.18	3.04	0.35103	.	0.691102	0.13631	N	0.373759	T	0.00012	0.0000	N	0.01048	-1.04	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36040	-0.9764	9	0.06365	T	0.9	-10.8047	2.4406	0.04493	0.1665:0.5233:0.1616:0.1486	rs8046424;rs17856848;rs57318770;rs8046424	122;123	Q6ZMJ4-2;Q6ZMJ4	.;IL34_HUMAN	Q	123	ENSP00000397863:E123Q;ENSP00000288098:E123Q	ENSP00000288098:E123Q	E	+	1	0	IL34	69248490	0.020000	0.18652	0.115000	0.21578	0.440000	0.31957	1.221000	0.32503	1.197000	0.43143	-0.322000	0.08575	GAG	G|0.354;C|0.646	0.646	strong		0.607	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456	
CRIPAK	285464	hgsc.bcm.edu	37	4	1388378	1388378	+	Missense_Mutation	SNP	T	T	C	rs55884223	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1388378T>C	ENST00000324803.4	+	1	3039	c.79T>C	c.(79-81)Tgt>Cgt	p.C27R		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	27					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CGCCTGCTCATGTGCCCATGT	0.637													N|||	782	0.15615	0.1952	0.1412	5008	,	,		16132	0.0278		0.2286	False		,,,				2504	0.1718				p.C27R		Atlas-SNP	.											CRIPAK,NS,carcinoma,-1,1	CRIPAK	185	1	0			c.T79C						scavenged	.						172.0	171.0	171.0					4																	1388378		2203	4300	6503	SO:0001583	missense	285464	exon1			TGCTCATGTGCCC	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"""cysteine-rich PAK1inhibitor"""			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.79T>C	4.37:g.1388378T>C	ENSP00000323978:p.Cys27Arg	Somatic	149	4	0.0268456		WXS	Illumina HiSeq	Phase_I	167	27	0.161677	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	T	2.439	-0.329099	0.05314	.	.	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.25414	1.8	0.824	-1.65	0.08291	.	.	.	.	.	T	0.08223	0.0205	N	0.08118	0	0.34679	D	0.724554	B	0.20052	0.041	B	0.11329	0.006	T	0.40850	-0.9541	9	0.09338	T	0.73	.	2.0645	0.03600	0.2577:0.2174:0.0:0.5249	rs55884223	27	Q8N1N5	CRPAK_HUMAN	R	27;20	ENSP00000323978:C27R	ENSP00000323978:C27R	C	+	1	0	CRIPAK	1378378	0.017000	0.18338	0.001000	0.08648	0.007000	0.05969	-0.458000	0.06737	-0.973000	0.03555	0.344000	0.21773	TGT	T|0.993;C|0.007	0.007	strong		0.637	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918	
C2CD2	25966	hgsc.bcm.edu	37	21	43338302	43338302	+	Missense_Mutation	SNP	A	A	G	rs2839421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:43338302A>G	ENST00000380486.3	-	5	873	c.632T>C	c.(631-633)gTt>gCt	p.V211A	C2CD2_ENST00000329623.7_Missense_Mutation_p.V56A	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	211			V -> A (in dbSNP:rs2839421).			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						GTCCTTGAGAACGTCAGACAT	0.502													G|||	401	0.0800719	0.1566	0.0548	5008	,	,		23094	0.0		0.0308	False		,,,				2504	0.1278				p.V211A		Atlas-SNP	.											.	C2CD2	47	.	0			c.T632C						PASS	.	G	ALA/VAL,ALA/VAL	593,3813	771.6+/-413.8	31,531,1641	134.0	106.0	115.0		632,167	-0.2	0.0	21	dbSNP_100	115	351,8249	803.6+/-407.3	12,327,3961	yes	missense,missense	C2CD2	NM_015500.1,NM_199050.2	64,64	43,858,5602	GG,GA,AA		4.0814,13.4589,7.2582	benign,benign	211/697,56/542	43338302	944,12062	2203	4300	6503	SO:0001583	missense	25966	exon5			TTGAGAACGTCAG	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.632T>C	21.37:g.43338302A>G	ENSP00000369853:p.Val211Ala	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	66	21	0.318182	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	122	0.055860805860805864	79	0.16056910569105692	21	0.058011049723756904	0	0.0	22	0.029023746701846966	G	6.013	0.370763	0.11409	0.134589	0.040814	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.21543	2.0;2.0	4.87	-0.165	0.13355	.	1.141250	0.06328	N	0.705647	T	0.00039	0.0001	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	0.36915	-0.9728	9	0.29301	T	0.29	1.2767	4.9411	0.13965	0.3411:0.2954:0.3635:0.0	rs2839421;rs2839421	56;211	Q6P6D1;Q9Y426	.;CU025_HUMAN	A	56;211	ENSP00000329302:V56A;ENSP00000369853:V211A	ENSP00000329302:V56A	V	-	2	0	C2CD2	42211371	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.260000	0.18424	-0.542000	0.06249	-0.119000	0.15052	GTT	A|0.929;G|0.071	0.071	strong		0.502	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
SGK223	157285	hgsc.bcm.edu	37	8	8176221	8176221	+	Missense_Mutation	SNP	C	C	T	rs13269488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:8176221C>T	ENST00000520004.1	-	6	3928	c.3664G>A	c.(3664-3666)Ggc>Agc	p.G1222S	SGK223_ENST00000330777.4_Missense_Mutation_p.G1222S			Q86YV5	SG223_HUMAN		1226	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TTTGGGGTGCCGCCCGGCTTC	0.657													C|||	2413	0.481829	0.4085	0.5058	5008	,	,		9810	0.5665		0.5229	False		,,,				2504	0.4346				p.G1222S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3664A						PASS	.	C	SER/GLY	1665,2079		378,909,585	26.0	29.0	28.0		3664	0.7	0.1	8	dbSNP_121	28	4397,3789		1188,2021,884	yes	missense	SGK223	NM_001080826.1	56	1566,2930,1469	TT,TC,CC		46.2863,44.4712,49.1869	probably-damaging	1222/1403	8176221	6062,5868	1872	4093	5965	SO:0001583	missense	0	exon5			GGGTGCCGCCCGG																												ENST00000520004.1:c.3664G>A	8.37:g.8176221C>T	ENSP00000428054:p.Gly1222Ser	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	54	18	0.333333	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	1130	0.5173992673992674	210	0.4268292682926829	167	0.4613259668508287	356	0.6223776223776224	397	0.5237467018469657	C	6.482	0.457070	0.12283	0.444712	0.537137	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.64085	-0.08;-0.08	4.95	0.737	0.18314	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.515636	0.22128	N	0.064233	T	0.00012	0.0000	L	0.37697	1.125	0.58432	P	6.999999999979245E-6	D	0.71674	0.998	P	0.62740	0.906	T	0.46789	-0.9166	9	0.36615	T	0.2	.	3.5532	0.07854	0.1775:0.3829:0.0:0.4396	rs13269488	1222	Q86YV5	SG223_HUMAN	S	1222	ENSP00000330930:G1222S;ENSP00000428054:G1222S	ENSP00000330930:G1222S	G	-	1	0	AC068353.1	8213631	0.000000	0.05858	0.137000	0.22149	0.060000	0.15804	-0.622000	0.05553	0.252000	0.21531	0.467000	0.42956	GGC	C|0.478;T|0.522	0.522	strong		0.657	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
LETMD1	25875	hgsc.bcm.edu	37	12	51442944	51442944	+	Missense_Mutation	SNP	G	G	A	rs12379	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51442944G>A	ENST00000262055.4	+	2	289	c.250G>A	c.(250-252)Gtc>Atc	p.V84I	LETMD1_ENST00000547008.1_Missense_Mutation_p.V84I|LETMD1_ENST00000548516.1_3'UTR|LETMD1_ENST00000552739.1_Intron|LETMD1_ENST00000550929.1_Missense_Mutation_p.V28I|LETMD1_ENST00000418425.2_Missense_Mutation_p.V84I|LETMD1_ENST00000380123.2_Missense_Mutation_p.V84I	NM_015416.4	NP_056231.3	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1	84	LETM1.|Required and sufficient for mitochondrial import.		V -> I (in dbSNP:rs12379). {ECO:0000269|PubMed:12879013, ECO:0000269|PubMed:17974005, ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						CCGCTTCTATGTCCTGTACAC	0.403													G|||	2876	0.574281	0.4887	0.5029	5008	,	,		20532	0.8938		0.3787	False		,,,				2504	0.6125				p.V84I		Atlas-SNP	.											.	LETMD1	33	.	0			c.G250A						PASS	.	G	ILE/VAL,ILE/VAL	2100,2306	573.3+/-383.5	494,1112,597	99.0	90.0	93.0		82,250	0.6	1.0	12	dbSNP_52	93	3186,5414	482.7+/-370.9	589,2008,1703	yes	missense,missense	LETMD1	NM_001024668.1,NM_015416.4	29,29	1083,3120,2300	AA,AG,GG		37.0465,47.6623,40.6428	benign,benign	28/305,84/361	51442944	5286,7720	2203	4300	6503	SO:0001583	missense	25875	exon2			TTCTATGTCCTGT	AF195651	CCDS8806.1, CCDS58231.1, CCDS73469.1	12q13.13	2006-04-12				ENSG00000050426			24241	protein-coding gene	gene with protein product	"""cervical cancer 1 protooncogene"""					12879013, 12061725	Standard	NM_015416		Approved	HCCR1	uc009zlw.3	Q6P1Q0	OTTHUMG00000169538	ENST00000262055.4:c.250G>A	12.37:g.51442944G>A	ENSP00000262055:p.Val84Ile	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	158	62	0.392405	NM_001243689	A6NER7|B3KXK7|Q6X2E4|Q6X2E5|Q7L2G9|Q7L690|Q8WXW6|Q96PK7|Q9BY59|Q9Y3X3	Missense_Mutation	SNP	ENST00000262055.4	37	CCDS8806.1	1209|1209	0.5535714285714286|0.5535714285714286	234|234	0.47560975609756095|0.47560975609756095	177|177	0.4889502762430939|0.4889502762430939	512|512	0.8951048951048951|0.8951048951048951	286|286	0.37730870712401055|0.37730870712401055	G|G	11.15|11.15	1.555445|1.555445	0.27739|0.27739	0.476623|0.476623	0.370465|0.370465	ENSG00000050426|ENSG00000050426	ENST00000547256|ENST00000551477;ENST00000550929;ENST00000262055;ENST00000550442;ENST00000549340;ENST00000548209;ENST00000548251;ENST00000380123;ENST00000548401;ENST00000418425;ENST00000448283;ENST00000547008	.|T;T;T;T;T;T;T;T;T;T;T	.|0.46819	.|0.99;0.99;0.99;0.89;0.87;0.86;0.89;0.9;0.89;0.99;0.9	4.78|4.78	0.617|0.617	0.17619|0.17619	.|LETM1-like (1);	.|0.949792	.|0.08768	.|N	.|0.896721	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.38175|0.38175	1.15|1.15	0.42819|0.42819	P|P	0.006017999999999968|0.006017999999999968	.|B;B;B;B;B;B	.|0.11235	.|0.004;0.0;0.002;0.002;0.0;0.002	.|B;B;B;B;B;B	.|0.17098	.|0.006;0.002;0.012;0.004;0.002;0.017	T|T	0.24012|0.24012	-1.0172|-1.0172	4|9	.|0.37606	.|T	.|0.19	0.0|0.0	4.4438|4.4438	0.11588|0.11588	0.281:0.3092:0.4098:0.0|0.281:0.3092:0.4098:0.0	rs12379;rs1130801;rs3190075;rs3190103;rs11542236;rs17525439;rs56494382;rs56789645;rs12379|rs12379;rs1130801;rs3190075;rs3190103;rs11542236;rs17525439;rs56494382;rs56789645;rs12379	.|84;84;84;84;84;84	.|B7Z9A7;F8VVQ3;B3KXK7;F8W6J0;F8W1Z2;Q6P1Q0	.|.;.;.;.;.;LTMD1_HUMAN	I|I	28|51;28;84;84;84;84;84;84;91;84;84;84	.|ENSP00000446862:V51I;ENSP00000450163:V28I;ENSP00000262055:V84I;ENSP00000448110:V84I;ENSP00000449896:V84I;ENSP00000450275:V84I;ENSP00000447166:V84I;ENSP00000369466:V84I;ENSP00000450082:V91I;ENSP00000389903:V84I;ENSP00000447419:V84I	.|ENSP00000262055:V84I	M|V	+|+	3|1	0|0	LETMD1|LETMD1	49729211|49729211	0.111000|0.111000	0.22076|0.22076	0.974000|0.974000	0.42286|0.42286	0.989000|0.989000	0.77384|0.77384	-0.421000|-0.421000	0.07053|0.07053	0.004000|0.004000	0.14682|0.14682	0.655000|0.655000	0.94253|0.94253	ATG|GTC	G|0.509;A|0.491	0.491	strong		0.403	LETMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404710.1	NM_015416	
AK5	26289	hgsc.bcm.edu	37	1	77759578	77759578	+	Silent	SNP	A	A	G	rs2815311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:77759578A>G	ENST00000354567.2	+	3	611	c.348A>G	c.(346-348)gcA>gcG	p.A116A	AK5_ENST00000344720.5_Silent_p.A90A|AK5_ENST00000317704.4_3'UTR	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	116					ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						CTGAGACTGCAGAGTTGATTG	0.428													A|||	576	0.115016	0.0613	0.1023	5008	,	,		14067	0.1359		0.2038	False		,,,				2504	0.0838				p.A116A		Atlas-SNP	.											.	AK5	86	.	0			c.A348G						PASS	.	A	,	333,4073	173.7+/-203.5	12,309,1882	69.0	70.0	69.0		270,348	-7.4	1.0	1	dbSNP_100	69	1806,6794	325.1+/-316.8	178,1450,2672	no	coding-synonymous,coding-synonymous	AK5	NM_012093.3,NM_174858.2	,	190,1759,4554	GG,GA,AA		21.0,7.5579,16.4463	,	90/537,116/563	77759578	2139,10867	2203	4300	6503	SO:0001819	synonymous_variant	26289	exon3			GACTGCAGAGTTG	AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"""Adenylate kinases"""	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.348A>G	1.37:g.77759578A>G		Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	172	70	0.406977	NM_174858	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Silent	SNP	ENST00000354567.2	37	CCDS675.1																																																																																			A|0.843;G|0.157	0.157	strong		0.428	AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858	
UVSSA	57654	hgsc.bcm.edu	37	4	1343405	1343405	+	Silent	SNP	T	T	C	rs2276903	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1343405T>C	ENST00000389851.4	+	3	639	c.192T>C	c.(190-192)atT>atC	p.I64I	UVSSA_ENST00000507531.1_Silent_p.I64I|UVSSA_ENST00000511216.1_Silent_p.I64I	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	64	VHS-like.				protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										CCTTCCAGATTGTGGAGGAAC	0.607													C|||	3170	0.632987	0.8495	0.7032	5008	,	,		18832	0.5317		0.5447	False		,,,				2504	0.4857				p.I64I		Atlas-SNP	.											.	.	.	.	0			c.T192C						PASS	.	C		3502,904	349.8+/-310.5	1401,700,102	90.0	78.0	82.0		192	-10.0	0.0	4	dbSNP_100	82	4800,3800	534.9+/-382.7	1323,2154,823	no	coding-synonymous	KIAA1530	NM_020894.2		2724,2854,925	CC,CT,TT		44.186,20.5175,36.1679		64/710	1343405	8302,4704	2203	4300	6503	SO:0001819	synonymous_variant	57654	exon3			CCAGATTGTGGAG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.192T>C	4.37:g.1343405T>C		Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	149	75	0.503356	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			T|0.371;C|0.629	0.629	strong		0.607	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
SLC45A1	50651	hgsc.bcm.edu	37	1	8390384	8390384	+	Silent	SNP	G	G	C	rs56125713	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:8390384G>C	ENST00000471889.1	+	5	1216	c.831G>C	c.(829-831)ctG>ctC	p.L277L	SLC45A1_ENST00000377479.2_Silent_p.L311L|SLC45A1_ENST00000289877.8_Silent_p.L277L|Y_RNA_ENST00000516445.1_RNA			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	277					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(2)	33	Ovarian(185;0.0661)|all_lung(157;0.127)	all_epithelial(116;1.22e-15)|all_lung(118;0.000147)|Lung NSC(185;0.000251)|Renal(390;0.000469)|Colorectal(325;0.00578)|Breast(348;0.00686)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;3.95e-66)|GBM - Glioblastoma multiforme(8;5.93e-33)|Colorectal(212;2.86e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000513)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00199)|READ - Rectum adenocarcinoma(331;0.0649)		CGGTCACCCTGAGCGTCACCA	0.652													G|||	683	0.136382	0.0416	0.1225	5008	,	,		13280	0.0575		0.1759	False		,,,				2504	0.3149				p.L277L		Atlas-SNP	.											.	SLC45A1	85	.	0			c.G831C						PASS	.	G		279,4127	154.4+/-187.8	5,269,1929	61.0	62.0	62.0		831	3.5	1.0	1	dbSNP_129	62	1507,7093	284.0+/-296.4	136,1235,2929	no	coding-synonymous	SLC45A1	NM_001080397.1		141,1504,4858	CC,CG,GG		17.5233,6.3323,13.7321		277/749	8390384	1786,11220	2203	4300	6503	SO:0001819	synonymous_variant	50651	exon4			CACCCTGAGCGTC	AF118274	CCDS30577.1	1p36.23	2014-01-28	2005-10-04	2005-10-04	ENSG00000162426	ENSG00000162426		"""Solute carriers"""	17939	protein-coding gene	gene with protein product	"""H+/sugar symporter"""	605763	"""deleted in neuroblastoma 5"""	DNB5		10729226	Standard	XM_005263467		Approved		uc001apb.3	Q9Y2W3	OTTHUMG00000000503	ENST00000471889.1:c.831G>C	1.37:g.8390384G>C		Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	88	10	0.113636	NM_001080397	Q5VY46|Q5VY49	Silent	SNP	ENST00000471889.1	37	CCDS30577.1																																																																																			G|0.867;C|0.133	0.133	strong		0.652	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5		
LAMB3	3914	hgsc.bcm.edu	37	1	209788703	209788703	+	Silent	SNP	T	T	C	rs1049607	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:209788703T>C	ENST00000356082.4	-	23	3566	c.3432A>G	c.(3430-3432)tcA>tcG	p.S1144S	LAMB3_ENST00000367030.3_Silent_p.S1144S|LAMB3_ENST00000391911.1_Silent_p.S1144S	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	1144	Domain I.				brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		TCAGGTCCGCTGAGCGCAGCA	0.592													t|||	2320	0.463259	0.6694	0.3689	5008	,	,		19698	0.381		0.3648	False		,,,				2504	0.4376				p.S1144S		Atlas-SNP	.											.	LAMB3	136	.	0			c.A3432G						PASS	.	T	,,	2646,1760	646.2+/-398.3	791,1064,348	114.0	93.0	100.0		3432,3432,3432	-10.8	0.1	1	dbSNP_86	100	3088,5512	471.9+/-368.2	555,1978,1767	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	,,	1346,3042,2115	CC,CT,TT		35.907,39.9455,44.0873	,,	1144/1173,1144/1173,1144/1173	209788703	5734,7272	2203	4300	6503	SO:0001819	synonymous_variant	3914	exon23			GTCCGCTGAGCGC	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.3432A>G	1.37:g.209788703T>C		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	47	24	0.510638	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Silent	SNP	ENST00000356082.4	37	CCDS1487.1																																																																																			T|0.560;C|0.440	0.440	strong		0.592	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31107648	31107648	+	Missense_Mutation	SNP	C	C	T	rs1063646	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31107648C>T	ENST00000259881.9	+	6	687	c.398C>T	c.(397-399)cCa>cTa	p.P133L	PSORS1C1_ENST00000547221.1_Missense_Mutation_p.P85L|PSORS1C2_ENST00000259845.4_5'Flank|PSORS1C1_ENST00000481450.2_Missense_Mutation_p.P70L	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	133			P -> L (in dbSNP:rs1063646). {ECO:0000269|PubMed:12930300}.							kidney(1)|ovary(2)|prostate(1)|skin(1)	5						ACCTTGGCTCCAACTCTATTG	0.567													C|||	708	0.141374	0.1566	0.1354	5008	,	,		17740	0.0952		0.172	False		,,,				2504	0.1411				p.P133L		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.C398T						PASS	.	C	LEU/PRO	519,2503		36,447,1028	252.0	223.0	233.0		398	-0.1	0.0	6	dbSNP_86	233	899,4519		78,743,1888	yes	missense	PSORS1C1	NM_014068.2	98	114,1190,2916	TT,TC,CC		16.5928,17.1741,16.8009	probably-damaging	133/153	31107648	1418,7022	1511	2709	4220	SO:0001583	missense	170679	exon6			TGGCTCCAACTCT	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.398C>T	6.37:g.31107648C>T	ENSP00000259881:p.Pro133Leu	Somatic	253	1	0.00395257		WXS	Illumina HiSeq	Phase_I	270	269	0.996296	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	301	0.13782051282051283	77	0.1565040650406504	53	0.1464088397790055	58	0.10139860139860139	113	0.14907651715039577	C	7.648	0.682212	0.14907	0.171741	0.165928	ENSG00000204540	ENST00000259881;ENST00000547221;ENST00000481450	T;T;T	0.16457	2.34;2.34;2.34	1.84	-0.116	0.13555	.	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	0.80722	P	0.0	B;B	0.28850	0.225;0.225	B;B	0.17979	0.02;0.02	T	0.45175	-0.9279	8	0.08381	T	0.77	.	3.1931	0.06624	0.0:0.4996:0.3096:0.1909	rs1063646;rs3173368;rs1063646	82;133	Q9UIG5-2;Q9UIG5	.;PS1C1_HUMAN	L	133;85;70	ENSP00000259881:P133L;ENSP00000449471:P85L;ENSP00000447158:P70L	ENSP00000259881:P133L	P	+	2	0	PSORS1C1	31215627	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.033000	0.13754	-0.045000	0.13468	0.478000	0.44815	CCA	C|0.847;N|0.000	.	strong		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
OR1B1	347169	hgsc.bcm.edu	37	9	125391677	125391677	+	Silent	SNP	T	T	C	rs12347681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:125391677T>C	ENST00000304833.3	-	1	175	c.138A>G	c.(136-138)acA>acG	p.T46T	RP11-64P14.7_ENST00000419604.1_RNA|RP11-64P14.7_ENST00000431442.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	46						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						GCAGCACCAGTGTCACATTCC	0.498													T|||	1330	0.265575	0.112	0.3674	5008	,	,		21251	0.3175		0.2256	False		,,,				2504	0.3885				p.T46T		Atlas-SNP	.											OR1B1,NS,carcinoma,0,1	OR1B1	48	1	0			c.A138G						PASS	.	T		539,3867	243.7+/-253.3	30,479,1694	101.0	90.0	94.0		138	-4.3	0.0	9	dbSNP_120	94	2082,6518	361.3+/-332.3	247,1588,2465	no	coding-synonymous	OR1B1	NM_001004450.1		277,2067,4159	CC,CT,TT		24.2093,12.2333,20.1522		46/319	125391677	2621,10385	2203	4300	6503	SO:0001819	synonymous_variant	347169	exon1			CACCAGTGTCACA	AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.138A>G	9.37:g.125391677T>C		Somatic	148	0	0		WXS	Illumina HiSeq	Phase_I	167	87	0.520958	NM_001004450	Q6IFN3	Silent	SNP	ENST00000304833.3	37	CCDS35126.1																																																																																			T|0.778;C|0.222	0.222	strong		0.498	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254530	30254530	+	Silent	SNP	A	A	G	rs2071310	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:30254530A>G	ENST00000361644.2	+	5	1226	c.489A>G	c.(487-489)gtA>gtG	p.V163V		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	163	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.V163V(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						TGGAGGTGGTATTTGGTGTTG	0.408													A|||	1761	0.46649	0.2474	0.3746	3775	,	,		15794	0.4008		0.3648	False		,,,				2504	0.4121				p.V163V		Atlas-SNP	.											.	MAGEB3	54	.	1	Substitution - coding silent(1)	prostate(1)	c.A489G						PASS	.	A		1297,2536		173,753,198,705,373	92.0	85.0	88.0		489	-7.2	0.1	X	dbSNP_96	88	3010,3718		470,1217,853,741,1019	no	coding-synonymous	MAGEB3	NM_002365.4		643,1970,1051,1446,1392	GG,GA,G,AA,A		44.7384,33.8377,40.7821		163/347	30254530	4307,6254	2202	4300	6502	SO:0001819	synonymous_variant	4114	exon5			GGTGGTATTTGGT	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.489A>G	X.37:g.30254530A>G		Somatic	158	1	0.00632911		WXS	Illumina HiSeq	Phase_I	162	161	0.993827	NM_002365	A0AVE4|B3KQ52|O75861	Silent	SNP	ENST00000361644.2	37	CCDS14220.1																																																																																			A|0.567;0|0.003	.	strong		0.408	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
ESR1	2099	hgsc.bcm.edu	37	6	152420095	152420095	+	Silent	SNP	G	G	A	rs2228480	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:152420095G>A	ENST00000206249.3	+	8	2144	c.1782G>A	c.(1780-1782)acG>acA	p.T594T	ESR1_ENST00000338799.5_Silent_p.T594T|ESR1_ENST00000427531.2_Intron|ESR1_ENST00000456483.2_Silent_p.T482T|ESR1_ENST00000440973.1_Silent_p.T594T|ESR1_ENST00000406599.1_Silent_p.T333T|ESR1_ENST00000443427.1_Silent_p.T594T	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	594	Interaction with AKAP13.|Self-association.|Transactivation AF-2.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	TCCCTGCCACGGTCTGAGAGC	0.532													A|||	945	0.188698	0.1452	0.2378	5008	,	,		20228	0.2014		0.175	False		,,,				2504	0.2137				p.T594T		Atlas-SNP	.											.	ESR1	94	.	0			c.G1782A	GRCh37	CM056948	ESR1	M	rs2228480	PASS	.	A	,,,	691,3715	760.6+/-413.0	45,601,1557	47.0	44.0	45.0		1782,1782,1782,1782	-10.3	0.0	6	dbSNP_98	45	1546,7054	745.0+/-407.3	129,1288,2883	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESR1	NM_000125.3,NM_001122740.1,NM_001122741.1,NM_001122742.1	,,,	174,1889,4440	AA,AG,GG		17.9767,15.6832,17.1998	,,,	594/596,594/596,594/596,594/596	152420095	2237,10769	2203	4300	6503	SO:0001819	synonymous_variant	2099	exon8			TGCCACGGTCTGA	X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.1782G>A	6.37:g.152420095G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	36	36	1	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1																																																																																			G|0.822;A|0.178	0.178	strong		0.532	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
FAM200B	285550	hgsc.bcm.edu	37	4	15689928	15689928	+	Missense_Mutation	SNP	G	G	A	rs4235380	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:15689928G>A	ENST00000422728.2	+	2	2166	c.1328G>A	c.(1327-1329)aGt>aAt	p.S443N	FAM200B_ENST00000504137.1_Intron	NM_001145191.1	NP_001138663.1	P0CF97	F200B_HUMAN	family with sequence similarity 200, member B	443							nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						aatgaactgagtttaaaacta	0.303													G|||	1574	0.314297	0.2201	0.3602	5008	,	,		18299	0.4683		0.2763	False		,,,				2504	0.2894				p.S443N		Atlas-SNP	.											.	FAM200B	56	.	0			c.G1328A						PASS	.	G	ASN/SER	319,1065		34,251,407	52.0	41.0	44.0		1328	2.5	1.0	4	dbSNP_111	44	961,2215		150,661,777	yes	missense	FAM200B	NM_001145191.1	46	184,912,1184	AA,AG,GG		30.2582,23.0491,28.0702	benign	443/658	15689928	1280,3280	692	1588	2280	SO:0001583	missense	285550	exon2			AACTGAGTTTAAA	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.1328G>A	4.37:g.15689928G>A	ENSP00000393017:p.Ser443Asn	Somatic	181	0	0		WXS	Illumina HiSeq	Phase_I	165	77	0.466667	NM_001145191		Missense_Mutation	SNP	ENST00000422728.2	37	CCDS47028.1	712	0.326007326007326	116	0.23577235772357724	126	0.34806629834254144	260	0.45454545454545453	210	0.2770448548812665	G	0.141	-1.101788	0.01828	0.230491	0.302582	ENSG00000237765	ENST00000422728	T	0.80214	-1.35	2.48	2.48	0.30137	Ribonuclease H-like (1);	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.49798	P	1.7699999999998273E-4	B	0.09022	0.002	B	0.08055	0.003	T	0.35773	-0.9775	7	.	.	.	.	8.5475	0.33430	0.0:0.0:1.0:0.0	rs4235380;rs16898467;rs52818507;rs57685138;rs4235380	443	P0CF97	F200B_HUMAN	N	443	ENSP00000393017:S443N	.	S	+	2	0	FAM200B	15299026	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	2.988000	0.49386	1.712000	0.51347	0.484000	0.47621	AGT	G|0.679;A|0.321	0.321	strong		0.303	FAM200B-005	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360100.1	NM_001145191	
SRRM5	100170229	hgsc.bcm.edu	37	19	44116956	44116956	+	Missense_Mutation	SNP	A	A	G	rs13343696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:44116956A>G	ENST00000607544.1	+	3	1005	c.683A>G	c.(682-684)aAg>aGg	p.K228R	SRRM5_ENST00000417606.1_Missense_Mutation_p.K228R|ZNF428_ENST00000300811.3_Intron|SRRM5_ENST00000526798.1_Missense_Mutation_p.K243R			B3KS81	SRRM5_HUMAN	serine/arginine repetitive matrix 5	228	Ser-rich.									endometrium(11)|kidney(2)|skin(1)|stomach(1)	15						ATTCCCTCCAAGGAGAAGAGT	0.532													A|||	1182	0.236022	0.2708	0.1628	5008	,	,		18481	0.1508		0.2565	False		,,,				2504	0.3078				p.K228R		Atlas-SNP	.											.	SRRM5	38	.	0			c.A683G						PASS	.	A	ARG/LYS,	317,1067		33,251,408	105.0	109.0	108.0		683,	0.1	0.0	19	dbSNP_121	108	856,2326		116,624,851	yes	missense,intron	ZNF428,SRRM5	NM_001145641.1,NM_182498.3	26,	149,875,1259	GG,GA,AA		26.9013,22.9046,25.6899	benign,	228/716,	44116956	1173,3393	692	1591	2283	SO:0001583	missense	100170229	exon1			CCTCCAAGGAGAA	AK297891	CCDS46095.1	19q13.31	2013-09-20			ENSG00000226763	ENSG00000226763			37248	protein-coding gene	gene with protein product							Standard	NM_001145641		Approved		uc010xwr.2	B3KS81	OTTHUMG00000165480	ENST00000607544.1:c.683A>G	19.37:g.44116956A>G	ENSP00000476253:p.Lys228Arg	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	58	58	1	NM_001145641	B4DNF0	Missense_Mutation	SNP	ENST00000607544.1	37	CCDS46095.1	470	0.21520146520146521	129	0.2621951219512195	60	0.16574585635359115	86	0.15034965034965034	195	0.25725593667546176	A	8.857	0.946048	0.18356	0.229046	0.269013	ENSG00000226763	ENST00000526798;ENST00000417606	.	.	.	4.85	0.142	0.14816	.	.	.	.	.	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.20550	0.046	B	0.19666	0.026	T	0.33701	-0.9858	7	0.07175	T	0.84	.	4.3778	0.11279	0.5267:0.1684:0.3049:0.0	rs13343696	228	B3KS81	SRRM5_HUMAN	R	243;228	.	ENSP00000414512:K228R	K	+	2	0	SRRM5	48808796	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.028000	0.13644	-0.155000	0.11098	0.533000	0.62120	AAG	A|0.784;G|0.216	0.216	strong		0.532	SRRM5-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000384398.2	NM_001145641	
LOXHD1	125336	hgsc.bcm.edu	37	18	44157764	44157764	+	Missense_Mutation	SNP	C	C	A	rs34589386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:44157764C>A	ENST00000398722.4	-	7	1041	c.1042G>T	c.(1042-1044)Ggc>Tgc	p.G348C	LOXHD1_ENST00000441551.2_Missense_Mutation_p.G626C|LOXHD1_ENST00000536736.1_Missense_Mutation_p.G626C			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	348	PLAT 3. {ECO:0000255|PROSITE- ProRule:PRU00152}.		G -> C (in dbSNP:rs34589386).		calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						GAGCCTTTGCCATCGTGTCTG	0.582													C|||	64	0.0127796	0.0121	0.0144	5008	,	,		19545	0.0		0.0129	False		,,,				2504	0.0256				p.G626C		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G1876T						PASS	.	C	CYS/GLY	21,1363		0,21,671	51.0	61.0	58.0		1876	5.7	1.0	18	dbSNP_126	58	45,3137		0,45,1546	yes	missense	LOXHD1	NM_144612.6	159	0,66,2217	AA,AC,CC		1.4142,1.5173,1.4455	probably-damaging	626/2212	44157764	66,4500	692	1591	2283	SO:0001583	missense	125336	exon14			CTTTGCCATCGTG	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1042G>T	18.37:g.44157764C>A	ENSP00000381707:p.Gly348Cys	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	73	39	0.534247	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		29|29	0.013278388278388278|0.013278388278388278	13|13	0.026422764227642278|0.026422764227642278	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	16.20|16.20	3.055236|3.055236	0.55325|0.55325	0.015173|0.015173	0.014142|0.014142	ENSG00000167210|ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000335730|ENST00000441551	T;T|.	0.25414|.	1.8;1.8|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.162693|.	0.53938|.	D|.	0.000050|.	T|T	0.70518|0.70518	0.3233|0.3233	M|M	0.89840|0.89840	3.065|3.065	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.82157|0.82157	-0.0596|-0.0596	10|5	0.66056|.	D|.	0.02|.	.|.	19.7398|19.7398	0.96223|0.96223	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34589386|rs34589386	626;348|.	F5GZB4;Q8IVV2-2|.	.;.|.	C|L	348;626;348|606	ENSP00000381707:G348C;ENSP00000444586:G626C|.	ENSP00000338222:G348C|.	G|W	-|-	1|2	0|0	LOXHD1|LOXHD1	42411762|42411762	1.000000|1.000000	0.71417|0.71417	0.964000|0.964000	0.40570|0.40570	0.900000|0.900000	0.52787|0.52787	7.701000|7.701000	0.84566|0.84566	2.665000|2.665000	0.90641|0.90641	0.561000|0.561000	0.74099|0.74099	GGC|TGG	C|0.983;A|0.017	0.017	strong		0.582	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
CCHCR1	54535	hgsc.bcm.edu	37	6	31116220	31116220	+	Silent	SNP	G	G	A	rs130070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31116220G>A	ENST00000376266.5	-	10	1397	c.1275C>T	c.(1273-1275)gcC>gcT	p.A425A	CCHCR1_ENST00000451521.2_Silent_p.A478A|CCHCR1_ENST00000396263.2_Silent_p.A425A|CCHCR1_ENST00000480060.1_5'Flank|CCHCR1_ENST00000396268.3_Silent_p.A514A	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	425					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GCTGCTCCTCGGCTGAGGCTG	0.627													G|||	572	0.114217	0.1528	0.1254	5008	,	,		17316	0.0625		0.167	False		,,,				2504	0.0532				p.A514A		Atlas-SNP	.											.	CCHCR1	68	.	0			c.C1542T						PASS	.		,,	449,2571		33,383,1094	105.0	105.0	105.0		1434,1542,1275	-10.5	0.0	6	dbSNP_78	105	807,4609		68,671,1969	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	101,1054,3063	AA,AG,GG		14.9003,14.8675,14.8886	,,	478/836,514/872,425/783	31116220	1256,7180	1510	2708	4218	SO:0001819	synonymous_variant	54535	exon10			CTCCTCGGCTGAG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1275C>T	6.37:g.31116220G>A		Somatic	133	1	0.0075188		WXS	Illumina HiSeq	Phase_I	130	128	0.984615	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			G|0.871;A|0.129	0.129	strong		0.627	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
C17orf47	284083	hgsc.bcm.edu	37	17	56620167	56620167	+	Missense_Mutation	SNP	C	C	T	rs17822735	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:56620167C>T	ENST00000321691.3	-	1	1562	c.1381G>A	c.(1381-1383)Ggt>Agt	p.G461S	RP11-112H10.4_ENST00000580769.1_RNA|RP11-112H10.4_ENST00000578022.1_RNA|SEPT4_ENST00000412945.3_5'Flank|RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000457347.2_5'Flank	NM_001038704.2	NP_001033793	Q8NEP4	CQ047_HUMAN	chromosome 17 open reading frame 47	461			G -> S (in dbSNP:rs17822735).							NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	24	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ATTTTAAAACCGGACAATAAA	0.473													C|||	810	0.161741	0.1362	0.1513	5008	,	,		19840	0.1766		0.1809	False		,,,				2504	0.1687				p.G461S		Atlas-SNP	.											.	C17orf47	59	.	0			c.G1381A						PASS	.	C	SER/GLY	602,3804	263.8+/-265.7	43,516,1644	152.0	167.0	162.0		1381	-6.0	0.0	17	dbSNP_123	162	1713,6887	311.2+/-310.2	181,1351,2768	yes	missense	C17orf47	NM_001038704.2	56	224,1867,4412	TT,TC,CC		19.9186,13.6632,17.7995	benign	461/571	56620167	2315,10691	2203	4300	6503	SO:0001583	missense	284083	exon1			TAAAACCGGACAA		CCDS32691.1	17q23.2	2012-10-11			ENSG00000181013	ENSG00000181013			26844	protein-coding gene	gene with protein product							Standard	NM_001038704		Approved	FLJ40121	uc002iwq.2	Q8NEP4	OTTHUMG00000179244	ENST00000321691.3:c.1381G>A	17.37:g.56620167C>T	ENSP00000354874:p.Gly461Ser	Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	97	39	0.402062	NM_001038704	Q8N821	Missense_Mutation	SNP	ENST00000321691.3	37	CCDS32691.1	401	0.18360805860805862	80	0.16260162601626016	50	0.13812154696132597	119	0.20804195804195805	152	0.20052770448548812	C	1.826	-0.470969	0.04445	0.136632	0.199186	ENSG00000181013	ENST00000321691	T	0.28255	1.62	5.61	-6.01	0.02199	.	1.519990	0.03633	N	0.238298	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.22909	0.077	B	0.18871	0.023	T	0.20907	-1.0261	9	0.19590	T	0.45	0.4427	4.2276	0.10587	0.2238:0.1304:0.5221:0.1237	rs17822735;rs52817228;rs17822735	461	Q8NEP4	CQ047_HUMAN	S	461	ENSP00000354874:G461S	ENSP00000354874:G461S	G	-	1	0	C17orf47	53975166	0.000000	0.05858	0.005000	0.12908	0.002000	0.02628	-0.175000	0.09825	-0.727000	0.04888	-1.526000	0.00926	GGT	C|0.828;N|0.000	.	strong		0.473	C17orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445443.1	NM_001038704	
GPR114	221188	hgsc.bcm.edu	37	16	57601792	57601792	+	Silent	SNP	C	C	T	rs9937918	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:57601792C>T	ENST00000340339.4	+	9	1369	c.846C>T	c.(844-846)cgC>cgT	p.R282R	GPR114_ENST00000394361.4_3'UTR|GPR114_ENST00000349457.3_Silent_p.R282R	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	282					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CCTTAACACGCATCCACATGA	0.597													c|||	2275	0.454273	0.3759	0.5029	5008	,	,		23261	0.7123		0.2783	False		,,,				2504	0.4407				p.R282R		Atlas-SNP	.											.	GPR114	52	.	0			c.C846T						PASS	.			1618,2778	499.8+/-364.5	299,1020,879	94.0	76.0	82.0		846	-4.1	0.1	16	dbSNP_119	82	2432,6168	398.2+/-346.0	342,1748,2210	no	coding-synonymous	GPR114	NM_153837.1		641,2768,3089	TT,TC,CC		28.2791,36.8062,31.1634		282/529	57601792	4050,8946	2198	4300	6498	SO:0001819	synonymous_variant	221188	exon9			AACACGCATCCAC	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"""-"", ""GPCR / Class B : Orphans"""	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.846C>T	16.37:g.57601792C>T		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	47	47	1	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Silent	SNP	ENST00000340339.4	37	CCDS10785.1																																																																																			C|0.625;T|0.375	0.375	strong		0.597	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837	
SLIT2	9353	hgsc.bcm.edu	37	4	20544184	20544184	+	Silent	SNP	C	C	T	rs7690492	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:20544184C>T	ENST00000504154.1	+	21	2463	c.2211C>T	c.(2209-2211)gtC>gtT	p.V737V	SLIT2_ENST00000503823.1_Silent_p.V729V|SLIT2_ENST00000503837.1_Silent_p.V733V|SLIT2_ENST00000273739.5_Silent_p.V741V|SLIT2_ENST00000509394.2_3'UTR	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	737	LRRNT 4.				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						TGGATACAGTCGTCCGATGTA	0.413													T|||	1762	0.351837	0.4947	0.1758	5008	,	,		17424	0.373		0.2336	False		,,,				2504	0.3834				p.V737V		Atlas-SNP	.											.	SLIT2	290	.	0			c.C2211T						PASS	.	T		2018,2388	613.2+/-392.1	474,1070,659	314.0	293.0	300.0		2211	-11.3	0.0	4	dbSNP_116	300	1691,6909	738.3+/-407.1	153,1385,2762	no	coding-synonymous	SLIT2	NM_004787.1		627,2455,3421	TT,TC,CC		19.6628,45.8012,28.5176		737/1530	20544184	3709,9297	2203	4300	6503	SO:0001819	synonymous_variant	9353	exon21			TACAGTCGTCCGA	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.2211C>T	4.37:g.20544184C>T		Somatic	222	1	0.0045045		WXS	Illumina HiSeq	Phase_I	167	85	0.508982	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			C|0.682;T|0.318	0.318	strong		0.413	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835055	27835055	+	Silent	SNP	G	G	A	rs116008322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:27835055G>A	ENST00000331442.3	-	1	304	c.253C>T	c.(253-255)Ctg>Ttg	p.L85L		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	85	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						TTGAGGCCCAGCTTAATGCGG	0.577													G|||	45	0.00898562	0.0038	0.0101	5008	,	,		16701	0.004		0.0278	False		,,,				2504	0.001				p.L85L		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C253T						PASS	.	G		40,4366	43.8+/-77.6	0,40,2163	124.0	135.0	131.0		253	3.7	1.0	6	dbSNP_132	131	238,8362	96.6+/-158.3	4,230,4066	no	coding-synonymous	HIST1H1B	NM_005322.2		4,270,6229	AA,AG,GG		2.7674,0.9079,2.1375		85/227	27835055	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3009	exon1			GGCCCAGCTTAAT	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.253C>T	6.37:g.27835055G>A		Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	157	82	0.522293	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			G|0.982;A|0.018	0.018	strong		0.577	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
CFAP46	54777	hgsc.bcm.edu	37	10	134671148	134671148	+	Missense_Mutation	SNP	C	C	T	rs144154094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134671148C>T	ENST00000368586.5	-	39	5620	c.5520G>A	c.(5518-5520)atG>atA	p.M1840I	TTC40_ENST00000263170.5_Start_Codon_SNP_p.M1I	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTTCCTCAGCCATGGCGCCCT	0.592													C|||	46	0.0091853	0.0	0.0072	5008	,	,		16347	0.002		0.0129	False		,,,				2504	0.0266				p.M1840I		Atlas-SNP	.											.	TTC40	100	.	0			c.G5520A						PASS	.	C	ILE/MET	5,4401	6.2+/-15.9	0,5,2198	140.0	92.0	108.0		456	-0.1	0.0	10	dbSNP_134	108	58,8542	21.0+/-64.5	0,58,4242	yes	missense	C10orf92	NM_001200049.1	10	0,63,6440	TT,TC,CC		0.6744,0.1135,0.4844	benign	152/1028	134671148	63,12943	2203	4300	6503	SO:0001583	missense	54777	exon39			CTCAGCCATGGCG																												ENST00000368586.5:c.5520G>A	10.37:g.134671148C>T	ENSP00000357575:p.Met1840Ile	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	123	55	0.447154	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	38	0.0173992673992674	8	0.016260162601626018	6	0.016574585635359115	7	0.012237762237762238	17	0.022427440633245383	C	4.658	0.122270	0.08931	0.001135	0.006744	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.12465	3.01;2.68	0.924	-0.142	0.13448	.	.	.	.	.	T	0.02342	0.0072	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42103	-0.9471	9	0.23302	T	0.38	.	3.2464	0.06798	0.0:0.6673:0.0:0.3327	.	1	Q8IYW2	CJ092_HUMAN	I	1840;1	ENSP00000357575:M1840I;ENSP00000263170:M1I	ENSP00000263170:M1I	M	-	3	0	C10orf93	134521138	0.031000	0.19500	0.005000	0.12908	0.041000	0.13682	-0.661000	0.05311	-0.024000	0.13941	0.064000	0.15345	ATG	C|0.988;T|0.012	0.012	strong		0.592	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
MSX2	4488	hgsc.bcm.edu	37	5	174156168	174156168	+	Missense_Mutation	SNP	T	T	C	rs4242182	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:174156168T>C	ENST00000239243.6	+	2	513	c.386T>C	c.(385-387)aTg>aCg	p.M129T	MSX2_ENST00000507785.1_3'UTR	NM_002449.4	NP_002440.2	P35548	MSX2_HUMAN	msh homeobox 2	129			M -> T (in dbSNP:rs4242182). {ECO:0000269|PubMed:10742103, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7687426, ECO:0000269|PubMed:7897272, ECO:0000269|PubMed:8101453, ECO:0000269|PubMed:8106171, ECO:0000269|Ref.5, ECO:0000269|Ref.7}.		activation of meiosis (GO:0090427)|anagen (GO:0042640)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone trabecula formation (GO:0060346)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte development (GO:0002063)|cranial suture morphogenesis (GO:0060363)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|enamel mineralization (GO:0070166)|endochondral bone growth (GO:0003416)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|frontal suture morphogenesis (GO:0060364)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of keratinocyte differentiation (GO:0045617)|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)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of catagen (GO:0051795)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|positive regulation of osteoblast differentiation (GO:0045669)|signal transduction involved in regulation of gene expression (GO:0023019)|wound healing, spreading of epidermal cells (GO:0035313)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|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)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10	Renal(175;0.000159)|Lung NSC(126;0.0196)|all_lung(126;0.0303)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CTAGGACATATGAGCCCTACC	0.493													T|||	3835	0.765775	0.3578	0.8516	5008	,	,		16431	0.9821		0.8797	False		,,,				2504	0.9162				p.M129T		Atlas-SNP	.											MSX2,NS,carcinoma,-1,1	MSX2	24	1	0			c.T386C						PASS	.	T	THR/MET	2071,2335	569.4+/-382.6	464,1143,596	45.0	42.0	43.0		386	5.3	0.9	5	dbSNP_111	43	7752,848	780.0+/-407.7	3490,772,38	yes	missense	MSX2	NM_002449.4	81	3954,1915,634	CC,CT,TT		9.8605,47.0041,24.4733	benign	129/268	174156168	9823,3183	2203	4300	6503	SO:0001583	missense	4488	exon2			GACATATGAGCCC	D26145	CCDS4392.1	5q35.2	2011-06-20	2006-11-21		ENSG00000120149	ENSG00000120149		"""Homeoboxes / ANTP class : NKL subclass"""	7392	protein-coding gene	gene with protein product	"""craniosynostosis, type 2"""	123101	"""msh (Drosophila) homeo box homolog 2"", ""parietal foramina 1"", ""msh homeobox homolog 2 (Drosophila)"""	PFM1		8668339, 8786091	Standard	XM_006714868		Approved	CRS2, FPP, HOX8, MSH, PFM	uc003mcy.3	P35548	OTTHUMG00000130556	ENST00000239243.6:c.386T>C	5.37:g.174156168T>C	ENSP00000239243:p.Met129Thr	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	76	31	0.407895	NM_002449	D3DQN1|Q53XM4|Q9UD60	Missense_Mutation	SNP	ENST00000239243.6	37	CCDS4392.1	1718	0.7866300366300366	181	0.3678861788617886	303	0.8370165745856354	563	0.9842657342657343	671	0.8852242744063324	T	11.64	1.698414	0.30142	0.470041	0.901395	ENSG00000120149	ENST00000239243	D	0.95447	-3.71	5.28	5.28	0.74379	Homeodomain-related (1);	0.379291	0.33382	N	0.004979	T	0.00012	0.0000	L	0.27053	0.805	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.48068	-0.9067	9	0.36615	T	0.2	-5.198	15.3678	0.74538	0.0:0.0:0.0:1.0	rs4242182;rs17851300;rs52789643;rs57699937;rs4242182	129	P35548	MSX2_HUMAN	T	129	ENSP00000239243:M129T	ENSP00000239243:M129T	M	+	2	0	MSX2	174088774	1.000000	0.71417	0.929000	0.37066	0.792000	0.44763	4.549000	0.60726	2.219000	0.72066	0.533000	0.62120	ATG	T|0.240;C|0.760	0.760	strong		0.493	MSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252981.3		
GRIN3A	116443	hgsc.bcm.edu	37	9	104433235	104433235	+	Missense_Mutation	SNP	C	C	T	rs10989589	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104433235C>T	ENST00000361820.3	-	3	2059	c.1459G>A	c.(1459-1461)Gga>Aga	p.G487R		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	487			G -> R (in dbSNP:rs10989589). {ECO:0000269|PubMed:11735224, 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)	ACAATCTTTCCCCCCTGCCAG	0.498													C|||	1329	0.265375	0.1097	0.3617	5008	,	,		18574	0.2262		0.4076	False		,,,				2504	0.3016				p.G487R		Atlas-SNP	.											GRIN3A,caecum,carcinoma,+1,1	GRIN3A	186	1	0			c.G1459A						PASS	.	C	ARG/GLY	741,3665	303.0+/-287.7	64,613,1526	166.0	161.0	163.0		1459	5.8	0.3	9	dbSNP_120	163	3549,5051	515.9+/-378.7	726,2097,1477	yes	missense	GRIN3A	NM_133445.2	125	790,2710,3003	TT,TC,CC		41.2674,16.818,32.9848	possibly-damaging	487/1116	104433235	4290,8716	2203	4300	6503	SO:0001583	missense	116443	exon3			TCTTTCCCCCCTG		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.1459G>A	9.37:g.104433235C>T	ENSP00000355155:p.Gly487Arg	Somatic	253	0	0		WXS	Illumina HiSeq	Phase_I	245	241	0.983673	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	618	0.28296703296703296	54	0.10975609756097561	147	0.40607734806629836	115	0.20104895104895104	302	0.39841688654353563	C	14.17	2.454432	0.43634	0.16818	0.412674	ENSG00000198785	ENST00000361820	T	0.11277	2.79	5.76	5.76	0.90799	.	0.135566	0.49305	D	0.000160	T	0.00012	0.0000	L	0.56396	1.775	0.09310	P	0.99999884003	P	0.52842	0.956	P	0.56474	0.799	T	0.52697	-0.8541	9	0.48119	T	0.1	.	13.5255	0.61593	0.0:0.9287:0.0:0.0713	rs10989589;rs52814301;rs10989589	487	Q8TCU5	NMD3A_HUMAN	R	487	ENSP00000355155:G487R	ENSP00000355155:G487R	G	-	1	0	GRIN3A	103473056	1.000000	0.71417	0.252000	0.24328	0.990000	0.78478	5.989000	0.70587	2.882000	0.98803	0.655000	0.94253	GGA	C|0.670;T|0.330	0.330	strong		0.498	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
SNX25	83891	hgsc.bcm.edu	37	4	186283092	186283092	+	Missense_Mutation	SNP	C	C	T	rs34120554	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:186283092C>T	ENST00000504273.1	+	17	2468	c.2174C>T	c.(2173-2175)aCa>aTa	p.T725I	SNX25_ENST00000264694.8_Missense_Mutation_p.T725I|SNX25_ENST00000512853.1_3'UTR			Q9H3E2	SNX25_HUMAN	sorting nexin 25	725			T -> I (in dbSNP:rs34120554).		negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		ATCCGGGACACAGTCAGCTGG	0.383													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		15815	0.0		0.0099	False		,,,				2504	0.002				p.T725I		Atlas-SNP	.											.	SNX25	100	.	0			c.C2174T						PASS	.	C	ILE/THR	9,4397	16.8+/-37.8	0,9,2194	83.0	86.0	85.0		2174	4.3	1.0	4	dbSNP_126	85	105,8495	57.2+/-118.5	0,105,4195	yes	missense	SNX25	NM_031953.2	89	0,114,6389	TT,TC,CC		1.2209,0.2043,0.8765	probably-damaging	725/841	186283092	114,12892	2203	4300	6503	SO:0001583	missense	83891	exon17			GGGACACAGTCAG	AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"""Sorting nexins"""	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.2174C>T	4.37:g.186283092C>T	ENSP00000426255:p.Thr725Ile	Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	30	13	0.433333	NM_031953	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	37	CCDS34116.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	21.1	4.091462	0.76756	0.002043	0.012209	ENSG00000109762	ENST00000504273;ENST00000264694;ENST00000264693	T;T	0.30714	1.52;1.52	5.15	4.3	0.51218	Sorting nexin, C-terminal (1);	0.053228	0.85682	D	0.000000	T	0.35335	0.0928	L	0.41573	1.285	0.50313	D	0.99986	D;P;D	0.89917	0.999;0.728;1.0	D;B;D	0.91635	0.995;0.299;0.999	T	0.09818	-1.0657	10	0.21540	T	0.41	-3.1783	13.6912	0.62547	0.0:0.9249:0.0:0.0751	rs34120554	441;258;725	Q8N6K3;Q9H5Q8;Q9H3E2	.;.;SNX25_HUMAN	I	725;725;258	ENSP00000426255:T725I;ENSP00000264694:T725I	ENSP00000264693:T258I	T	+	2	0	SNX25	186520086	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.732000	0.68563	1.300000	0.44818	0.542000	0.68232	ACA	C|0.993;T|0.007	0.007	strong		0.383	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953	
ACAD11	84129	hgsc.bcm.edu	37	3	132337477	132337477	+	Splice_Site	SNP	C	C	A	rs41272317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132337477C>A	ENST00000264990.6	-	11	2386		c.e11+1		ACAD11_ENST00000481970.2_Missense_Mutation_p.G472V|ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000355458.3_Splice_Site	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11						fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)	p.?(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						AATGTAGTAACCTGGTGCTTG	0.338													C|||	212	0.0423323	0.0333	0.0029	5008	,	,		15862	0.0704		0.0159	False		,,,				2504	0.0808				.		Atlas-SNP	.											ACAD11,NS,carcinoma,0,1	ACAD11	78	1	1	Unknown(1)	stomach(1)	c.1414+1G>T						scavenged	.	C		114,4292	76.2+/-114.5	1,112,2090	65.0	66.0	66.0			5.5	1.0	3	dbSNP_127	66	133,8465	63.9+/-126.0	1,131,4167	yes	splice-5	ACAD11	NM_032169.4		2,243,6257	AA,AC,CC		1.5469,2.5874,1.8994			132337477	247,12757	2203	4299	6502	SO:0001630	splice_region_variant	84129	exon12			TAGTAACCTGGTG	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"""acyl-Coenzyme A dehydrogenase family, member 11"""				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1414+1G>T	3.37:g.132337477C>A		Somatic	136	2	0.0147059		WXS	Illumina HiSeq	Phase_I	153	66	0.431373	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Splice_Site	SNP	ENST00000264990.6	37	CCDS3074.1	78|78	0.03571428571428571|0.03571428571428571	22|22	0.044715447154471545|0.044715447154471545	2|2	0.0055248618784530384|0.0055248618784530384	42|42	0.07342657342657342|0.07342657342657342	12|12	0.0158311345646438|0.0158311345646438	C|C	18.10|18.10	3.548345|3.548345	0.65311|0.65311	0.025874|0.025874	0.015469|0.015469	ENSG00000240303|ENSG00000240303	ENST00000355458;ENST00000264990|ENST00000481970	.|T	.|0.22134	.|1.97	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|.	.|.	.|.	.|.	.|T	.|0.06872	.|0.0175	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	.|T	.|0.03473	.|-1.1033	.|8	.|0.87932	.|D	.|0	.|.	19.3995|19.3995	0.94621|0.94621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs41272317|rs41272317	.|472	.|D6RDI8	.|.	.|V	-1|472	.|ENSP00000420907:G472V	.|ENSP00000420907:G472V	.|G	-|-	.|2	.|0	ACAD11|ACAD11	133820167|133820167	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.712000|0.712000	0.41017|0.41017	7.426000|7.426000	0.80270|0.80270	2.754000|2.754000	0.94517|0.94517	0.650000|0.650000	0.86243|0.86243	.|GGT	A|0.027;C|0.973;T|0.000	0.027	strong		0.338	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169	Intron
CCDC79	283847	hgsc.bcm.edu	37	16	66812797	66812797	+	Silent	SNP	C	C	T	rs363162	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:66812797C>T	ENST00000558713.2	-	9	894	c.822G>A	c.(820-822)acG>acA	p.T274T	CCDC79_ENST00000433574.1_Silent_p.T274T|CCDC79_ENST00000415744.1_Silent_p.T274T|CCDC79_ENST00000561333.1_5'UTR|CCDC79_ENST00000432602.1_Silent_p.T274T|CCDC79_ENST00000433154.1_Silent_p.T274T			Q8NA31	TERB1_HUMAN	coiled-coil domain containing 79	274					meiotic telomere clustering (GO:0045141)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|skin(2)	7						CCACAGTCTTCGTCACAACCA	0.403													T|||	2896	0.578275	0.677	0.4928	5008	,	,		19836	0.6498		0.4384	False		,,,				2504	0.5757				p.T274T		Atlas-SNP	.											.	CCDC79	32	.	0			c.G822A						PASS	.	T		867,517		271,325,96	165.0	127.0	139.0		822	3.6	1.0	16	dbSNP_79	139	1387,1795		308,771,512	no	coding-synonymous	CCDC79	NM_001136505.1		579,1096,608	TT,TC,CC		43.5889,37.3555,49.3649		274/728	66812797	2254,2312	692	1591	2283	SO:0001819	synonymous_variant	283847	exon10			AGTCTTCGTCACA	AK093213		16q22.1	2012-10-03			ENSG00000249961	ENSG00000249961			26675	protein-coding gene	gene with protein product							Standard	NM_001136505		Approved	FLJ35894	uc010viv.2	Q8NA31	OTTHUMG00000133562	ENST00000558713.2:c.822G>A	16.37:g.66812797C>T		Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	97	95	0.979381	NM_001136505	A0AUW1	Silent	SNP	ENST00000558713.2	37																																																																																				C|0.441;T|0.559	0.559	strong		0.403	CCDC79-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000418864.2		
KCNJ11	3767	hgsc.bcm.edu	37	11	17409069	17409069	+	Silent	SNP	G	G	A	rs5218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:17409069G>A	ENST00000339994.4	-	1	1137	c.570C>T	c.(568-570)gcC>gcT	p.A190A	KCNJ11_ENST00000528731.1_Silent_p.A103A|KCNJ11_ENST00000526747.1_5'Flank	NM_000525.3	NP_000516.3	Q14654	KCJ11_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 11	190					cellular response to glucose stimulus (GO:0071333)|cellular response to nicotine (GO:0071316)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|negative regulation of insulin secretion (GO:0046676)|neurological system process (GO:0050877)|positive regulation of cation channel activity (GO:2001259)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ischemia (GO:0002931)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	ATP-sensitive potassium channel complex (GO:0008282)|axolemma (GO:0030673)|cell body fiber (GO:0070852)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|ATP-activated inward rectifier potassium channel activity (GO:0015272)|ion channel binding (GO:0044325)|potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(3)|skin(2)	16				READ - Rectum adenocarcinoma(2;0.0276)|Colorectal(2;0.0633)	Diazoxide(DB01119)|Glimepiride(DB00222)|Glyburide(DB01016)|Ibutilide(DB00308)|Levosimendan(DB00922)|Thiamylal(DB01154)|Verapamil(DB00661)|Yohimbine(DB01392)	CGTGGCGCAGGGCGATCACCG	0.587											OREG0020810	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1139	0.227436	0.0257	0.1816	5008	,	,		21810	0.5129		0.3221	False		,,,				2504	0.1411				p.A190A		Atlas-SNP	.											.	KCNJ11	39	.	0			c.C570T	GRCh37	CM035697	KCNJ11	M	rs5218	PASS	.	G	,	331,4069	170.1+/-200.6	16,299,1885	61.0	43.0	49.0		570,309	-0.1	0.7	11	dbSNP_52	49	2563,6023	408.6+/-349.5	388,1787,2118	no	coding-synonymous,coding-synonymous	KCNJ11	NM_000525.3,NM_001166290.1	,	404,2086,4003	AA,AG,GG		29.8509,7.5227,22.2855	,	190/391,103/304	17409069	2894,10092	2200	4293	6493	SO:0001819	synonymous_variant	3767	exon1			GCGCAGGGCGATC	D50582	CCDS31436.1, CCDS53606.1	11p15.1	2011-07-05						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6257	protein-coding gene	gene with protein product		600937				7502040, 16382105	Standard	NM_001166290		Approved	Kir6.2, BIR	uc001mna.3	Q14654		ENST00000339994.4:c.570C>T	11.37:g.17409069G>A		Somatic	65	0	0	717	WXS	Illumina HiSeq	Phase_I	60	26	0.433333	NM_000525	B4DWI4|E9PNK0|Q2M1H7|Q58EX3|Q8IW96	Silent	SNP	ENST00000339994.4	37	CCDS31436.1																																																																																			G|0.773;A|0.227	0.227	strong		0.587	KCNJ11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387037.1	NM_000525	
ERAP1	51752	hgsc.bcm.edu	37	5	96130836	96130836	+	Missense_Mutation	SNP	T	T	C	rs26618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96130836T>C	ENST00000443439.2	-	5	894	c.828A>G	c.(826-828)atA>atG	p.I276M	ERAP1_ENST00000296754.3_Missense_Mutation_p.I276M	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	276			I -> M (in dbSNP:rs26618).		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)		CTGCTTGATTTATCTTGTCTG	0.403													T|||	1135	0.226637	0.1959	0.1441	5008	,	,		20699	0.2857		0.2187	False		,,,				2504	0.274				p.I276M		Atlas-SNP	.											.	ERAP1	59	.	0			c.A828G	GRCh37	CM020527	ERAP1	M	rs26618	PASS	.	T	MET/ILE,MET/ILE,MET/ILE	889,3517	342.8+/-307.3	73,743,1387	72.0	66.0	68.0		828,828,828	-0.2	1.0	5	dbSNP_76	68	1965,6635	344.4+/-325.3	230,1505,2565	yes	missense,missense,missense	ERAP1	NM_001040458.1,NM_001198541.1,NM_016442.3	10,10,10	303,2248,3952	CC,CT,TT		22.8488,20.177,21.9437	possibly-damaging,possibly-damaging,possibly-damaging	276/942,276/942,276/949	96130836	2854,10152	2203	4300	6503	SO:0001583	missense	51752	exon5			TTGATTTATCTTG	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.828A>G	5.37:g.96130836T>C	ENSP00000406304:p.Ile276Met	Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	70	70	1	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Missense_Mutation	SNP	ENST00000443439.2	37	CCDS47250.1	456	0.2087912087912088	100	0.2032520325203252	55	0.15193370165745856	135	0.23601398601398602	166	0.21899736147757257	T	17.12	3.308085	0.60305	0.20177	0.228488	ENSG00000164307	ENST00000296754;ENST00000443439;ENST00000414384	T;T	0.02916	4.11;4.11	5.71	-0.178	0.13303	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.85462	2.755	0.22896	P	0.99859659	P;P;P	0.47106	0.89;0.774;0.732	P;P;P	0.52031	0.593;0.688;0.561	T	0.30736	-0.9968	9	0.51188	T	0.08	.	10.711	0.45984	0.1063:0.0:0.5215:0.3722	rs26618;rs52799291;rs59427621;rs26618	276;276;276	A8K6H1;Q9NZ08;Q9NZ08-2	.;ERAP1_HUMAN;.	M	276	ENSP00000296754:I276M;ENSP00000406304:I276M	ENSP00000296754:I276M	I	-	3	3	ERAP1	96156592	0.074000	0.21230	0.984000	0.44739	0.976000	0.68499	-0.670000	0.05256	0.044000	0.15775	0.528000	0.53228	ATA	T|0.783;C|0.217	0.217	strong		0.403	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442	
NDUFV3	4731	hgsc.bcm.edu	37	21	44323720	44323720	+	Intron	SNP	C	C	T	rs4148974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:44323720C>T	ENST00000340344.4	+	3	235				NDUFV3_ENST00000354250.2_Nonsense_Mutation_p.R200*|NDUFV3_ENST00000460259.1_3'UTR	NM_001001503.1	NP_001001503.1	P56181	NDUV3_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)|skin(1)	10				STAD - Stomach adenocarcinoma(101;0.0606)		CAGAGCCCCCCGAGTTACAGT	0.532													C|||	262	0.0523163	0.0038	0.0591	5008	,	,		14752	0.0804		0.0755	False		,,,				2504	0.0603				p.R200X		Atlas-SNP	.											NDUFV3,caecum,carcinoma,-1,1	NDUFV3	23	1	0			c.C598T						PASS	.	C	,stop/ARG	41,4363		0,41,2161	55.0	64.0	61.0		,598	-5.0	0.0	21	dbSNP_110	61	485,8115		20,445,3835	yes	intron,stop-gained	NDUFV3	NM_001001503.1,NM_021075.3	,	20,486,5996	TT,TC,CC		5.6395,0.931,4.0449	,	,200/474	44323720	526,12478	2202	4300	6502	SO:0001627	intron_variant	4731	exon3			GCCCCCCGAGTTA		CCDS33572.1, CCDS33573.1	21q22.3	2011-07-04	2002-08-29		ENSG00000160194	ENSG00000160194	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7719	protein-coding gene	gene with protein product	"""complex I 10kDa subunit"""	602184	"""NADH dehydrogenase (ubiquinone) flavoprotein 3 (10kD)"""			9344673	Standard	NM_021075		Approved	CI-10k	uc002zcm.3	P56181	OTTHUMG00000086823	ENST00000340344.4:c.170-5254C>T	21.37:g.44323720C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	32	14	0.4375	NM_021075	A8K0M1|J3KNX7|Q6FGD3|Q8WU60|Q9HCR5	Nonsense_Mutation	SNP	ENST00000340344.4	37	CCDS33573.1	132	0.06043956043956044	2	0.0040650406504065045	26	0.0718232044198895	47	0.08216783216783216	57	0.07519788918205805	C	15.30	2.793667	0.50102	0.00931	0.056395	ENSG00000160194	ENST00000354250	.	.	.	5.01	-4.99	0.03010	.	1.040030	0.07531	N	0.912177	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.08179	T	0.78	-0.4734	9.7331	0.40372	0.3071:0.5546:0.1383:0.0	rs4148974;rs52794594;rs58448131;rs4148974	.	.	.	X	200	.	ENSP00000346196:R200X	R	+	1	2	NDUFV3	43196789	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.397000	0.07269	-0.810000	0.04375	0.655000	0.94253	CGA	C|0.950;T|0.050	0.050	strong		0.532	NDUFV3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195448.2		
ACACB	32	hgsc.bcm.edu	37	12	109605730	109605730	+	Silent	SNP	C	C	T	rs4766516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:109605730C>T	ENST00000338432.7	+	4	935	c.816C>T	c.(814-816)gcC>gcT	p.A272A	ACACB_ENST00000377848.3_Silent_p.A272A|ACACB_ENST00000377854.5_Silent_p.A272A			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	272	Biotin carboxylation.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GGATTGCCGCCGTGAAGTGCA	0.597													C|||	1160	0.231629	0.0424	0.2089	5008	,	,		14485	0.5099		0.1769	False		,,,				2504	0.273				p.A272A		Atlas-SNP	.											.	ACACB	330	.	0			c.C816T						PASS	.	C		332,4074	172.7+/-202.6	13,306,1884	138.0	96.0	110.0		816	-8.6	0.3	12	dbSNP_111	110	1711,6889	312.7+/-311.0	179,1353,2768	no	coding-synonymous	ACACB	NM_001093.3		192,1659,4652	TT,TC,CC		19.8953,7.5352,15.7081		272/2459	109605730	2043,10963	2203	4300	6503	SO:0001819	synonymous_variant	32	exon3			TGCCGCCGTGAAG	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.816C>T	12.37:g.109605730C>T		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	127	48	0.377953	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			C|0.805;T|0.195	0.195	strong		0.597	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
WIPI2	26100	hgsc.bcm.edu	37	7	5257639	5257639	+	Silent	SNP	G	G	A	rs147063855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5257639G>A	ENST00000288828.4	+	7	895	c.663G>A	c.(661-663)tcG>tcA	p.S221S	WIPI2_ENST00000404704.3_Silent_p.S221S|WIPI2_ENST00000382384.2_Silent_p.S203S|WIPI2_ENST00000401525.3_Silent_p.S203S|WIPI2_ENST00000484262.1_Silent_p.S162S	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	221					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)		CCACGGCTTCGGAGAAGGTGA	0.537																																					p.S221S		Atlas-SNP	.											WIPI2,NS,carcinoma,+1,1	WIPI2	41	1	0			c.G663A						PASS	.	G	,,,,	0,4406		0,0,2203	125.0	116.0	119.0		663,609,486,663,609	-11.6	0.1	7	dbSNP_134	119	15,8585	11.2+/-40.8	0,15,4285	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	,,,,	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	,,,,	221/444,203/426,162/385,221/455,203/437	5257639	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	26100	exon7			GGCTTCGGAGAAG		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.663G>A	7.37:g.5257639G>A		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	171	84	0.491228	NM_015610	B3KNC2|Q5MNZ8|Q6FI96|Q75L50|Q96IE4|Q9Y364	Silent	SNP	ENST00000288828.4	37	CCDS5339.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	WIPI2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241669.2	NM_015610	
MICA	100507436	hgsc.bcm.edu	37	6	31378425	31378425	+	Missense_Mutation	SNP	A	A	G	rs1051786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31378425A>G	ENST00000449934.2	+	2	230	c.176A>G	c.(175-177)tAt>tGt	p.Y59C	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TTCCTGCGCTATGACAGGCAG	0.542													g|||	1827	0.364816	0.4788	0.4078	5008	,	,		19566	0.3006		0.3141	False		,,,				2504	0.2986				p.Y59C		Atlas-SNP	.											.	MICA	21	.	0			c.A176G						PASS	.	G	CYS/TYR	579,805		132,315,245	40.0	44.0	43.0		176	-5.5	0.0	6	dbSNP_86	43	919,2263		126,667,798	no	missense	MICA	NM_001177519.1	194	258,982,1043	GG,GA,AA		28.8812,41.8353,32.8077	benign	59/333	31378425	1498,3068	692	1591	2283	SO:0001583	missense	100507436	exon2			TGCGCTATGACAG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.176A>G	6.37:g.31378425A>G	ENSP00000413079:p.Tyr59Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	195	191	0.979487	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	799	0.3658424908424908	227	0.4613821138211382	169	0.46685082872928174	160	0.27972027972027974	243	0.32058047493403696	N	4.126	0.021662	0.08006	0.418353	0.288812	ENSG00000204520	ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.03635	3.86;3.86	2.89	-5.5	0.02576	.	0.906056	0.08949	N	0.870393	T	0.00695	0.0023	.	.	.	0.80722	P	0.0	B	0.22983	0.078	B	0.24541	0.054	T	0.44922	-0.9296	8	0.34782	T	0.22	.	3.6542	0.08214	0.5494:0.0:0.1662:0.2844	rs1051786;rs3192167;rs16899591;rs17200165;rs17845517;rs17858407;rs17879747;rs58269144	59	Q96QC4	.	C	59;59;59;46	ENSP00000413079:Y59C;ENSP00000402410:Y46C	ENSP00000365394:Y59C	Y	+	2	0	MICA	31486404	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.180000	0.00569	-2.184000	0.00762	-2.615000	0.00158	TAT	A|0.641;G|0.359	0.359	strong		0.542	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
CGB2	114336	hgsc.bcm.edu	37	19	49536390	49536390	+	Missense_Mutation	SNP	C	C	A	rs62126039	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49536390C>A	ENST00000359342.6	+	3	522	c.404C>A	c.(403-405)gCc>gAc	p.A135D	CTB-60B18.6_ENST00000591656.1_Intron	NM_033378.1	NP_203696.2	Q6NT52	CGB2_HUMAN	chorionic gonadotropin, beta polypeptide 2	167						extracellular region (GO:0005576)		p.A135D(1)		large_intestine(1)|lung(1)|stomach(1)	3		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		CGCTTCCAGGCCTCCTCTTCC	0.637													c|||	1481	0.295727	0.3381	0.3718	5008	,	,		12440	0.1567		0.336	False		,,,				2504	0.2863				p.A135D		Atlas-SNP	.											CGB2,NS,carcinoma,0,1	CGB2	6	1	1	Substitution - Missense(1)	stomach(1)	c.C404A						scavenged	.						19.0	27.0	24.0					19																	49536390		2161	4265	6426	SO:0001583	missense	114336	exon3			TCCAGGCCTCCTC	K03184	CCDS12750.2	19q13.32	2008-02-05			ENSG00000104818	ENSG00000104818			16722	protein-coding gene	gene with protein product		608824				6194155	Standard	NM_033378		Approved		uc002plw.3	Q6NT52	OTTHUMG00000150185	ENST00000359342.6:c.404C>A	19.37:g.49536390C>A	ENSP00000352295:p.Ala135Asp	Somatic	209	1	0.00478469		WXS	Illumina HiSeq	Phase_I	237	5	0.021097	NM_033378	B9ZVM5	Missense_Mutation	SNP	ENST00000359342.6	37	CCDS12750.2	.	.	.	.	.	.	.	.	.	.	c	0.395	-0.921146	0.02396	.	.	ENSG00000104818	ENST00000359342	T	0.36520	1.25	1.79	0.719	0.18208	.	.	.	.	.	T	0.11707	0.0285	N	0.02916	-0.46	0.47905	P	4.6000000000001595E-4	.	.	.	.	.	.	T	0.34254	-0.9836	6	0.11182	T	0.66	.	5.5188	0.16921	0.3275:0.6725:0.0:0.0	.	.	.	.	D	135	ENSP00000352295:A135D	ENSP00000352295:A135D	A	+	2	0	CGB2	54228202	0.010000	0.17322	0.167000	0.22817	0.014000	0.08584	0.011000	0.13264	0.323000	0.23307	-1.276000	0.01395	GCC	A|1.000;|0.000	1.000	weak		0.637	CGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316745.1	NM_033378	
ZNF175	7728	hgsc.bcm.edu	37	19	52090100	52090100	+	Silent	SNP	T	T	C	rs45541134	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:52090100T>C	ENST00000262259.2	+	5	874	c.516T>C	c.(514-516)aaT>aaC	p.N172N	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	172					defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		CAGAAAGCAATTGTGAATATA	0.413													T|||	727	0.145168	0.0991	0.1686	5008	,	,		20625	0.0238		0.2684	False		,,,				2504	0.1892				p.N172N		Atlas-SNP	.											.	ZNF175	65	.	0			c.T516C						PASS	.	T		464,3942	218.4+/-236.5	26,412,1765	96.0	92.0	93.0		516	-0.4	0.0	19	dbSNP_127	93	2339,6261	388.9+/-342.7	333,1673,2294	no	coding-synonymous	ZNF175	NM_007147.2		359,2085,4059	CC,CT,TT		27.1977,10.5311,21.5516		172/712	52090100	2803,10203	2203	4300	6503	SO:0001819	synonymous_variant	7728	exon5			AAGCAATTGTGAA	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.516T>C	19.37:g.52090100T>C		Somatic	124	0	0		WXS	Illumina HiSeq	Phase_I	117	52	0.444444	NM_007147	A8K9H2	Silent	SNP	ENST00000262259.2	37	CCDS12837.1																																																																																			T|0.795;C|0.205	0.205	strong		0.413	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
PLCB3	5331	hgsc.bcm.edu	37	11	64026685	64026685	+	Silent	SNP	C	C	T	rs28395882	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64026685C>T	ENST00000540288.1	+	13	1597	c.1494C>T	c.(1492-1494)tcC>tcT	p.S498S	PLCB3_ENST00000325234.5_Silent_p.S431S|PLCB3_ENST00000279230.6_Silent_p.S498S	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	498					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						GCGAGAGCTCCGCGGCCACCG	0.706													C|||	865	0.172724	0.0234	0.147	5008	,	,		12937	0.1339		0.3012	False		,,,				2504	0.3006				p.S498S		Atlas-SNP	.											PLCB3,NS,carcinoma,0,1	PLCB3	103	1	0			c.C1494T						scavenged	.	C	,	242,4066		8,226,1920	9.0	11.0	11.0		1494,1293	-9.8	0.0	11	dbSNP_126	11	2553,5907		423,1707,2100	no	coding-synonymous,coding-synonymous	PLCB3	NM_000932.2,NM_001184883.1	,	431,1933,4020	TT,TC,CC		30.1773,5.6175,21.8907	,	498/1235,431/1168	64026685	2795,9973	2154	4230	6384	SO:0001819	synonymous_variant	5331	exon13			GAGCTCCGCGGCC	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.1494C>T	11.37:g.64026685C>T		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	5	3	0.6	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	37	CCDS8064.1																																																																																			C|0.817;T|0.183	0.183	strong		0.706	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605971	84605971	+	Missense_Mutation	SNP	C	C	A	rs111857392	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:84605971C>A	ENST00000344803.2	+	4	633	c.586C>A	c.(586-588)Ccc>Acc	p.P196T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	196	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTCTCCACCACCCCCCTTAAT	0.562													C|||	22	0.00439297	0.0	0.0072	5008	,	,		18895	0.0		0.0139	False		,,,				2504	0.0031				p.P196T		Atlas-SNP	.											.	.	.	.	0			c.C586A						PASS	.	C	THR/PRO	17,3775		0,17,1879	110.0	109.0	109.0		586	2.2	0.0	9	dbSNP_132	109	160,8096		1,158,3969	yes	missense	FAM75D1	NM_001001670.2	38	1,175,5848	AA,AC,CC		1.938,0.4483,1.4691	probably-damaging	196/1577	84605971	177,11871	1896	4128	6024	SO:0001583	missense	389763	exon4			CCACCACCCCCCT		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.586C>A	9.37:g.84605971C>A	ENSP00000341988:p.Pro196Thr	Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	202	88	0.435644	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	C	11.73	1.724802	0.30593	0.004483	0.01938	ENSG00000214929	ENST00000344803	T	0.06218	3.33	3.1	2.18	0.27775	.	0.787804	0.10809	N	0.631791	T	0.05318	0.0141	L	0.40543	1.245	0.09310	N	1	D	0.67145	0.996	P	0.62014	0.897	T	0.31558	-0.9939	10	0.17832	T	0.49	-1.7487	6.3149	0.21184	0.0:0.8593:0.0:0.1407	.	196	Q6ZQQ2	F75D1_HUMAN	T	196	ENSP00000341988:P196T	ENSP00000341988:P196T	P	+	1	0	FAM75D1	83795791	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.464000	0.21988	0.895000	0.36342	0.644000	0.83932	CCC	C|0.989;A|0.011	0.011	strong		0.562	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
UBC	7316	hgsc.bcm.edu	37	12	125397435	125397435	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:125397435G>A	ENST00000536769.1	-	1	2459	c.883C>T	c.(883-885)Ctg>Ttg	p.L295L	UBC_ENST00000339647.5_Silent_p.L295L|UBC_ENST00000536661.1_5'Flank|UBC_ENST00000546120.1_Silent_p.L219L|MIR5188_ENST00000583467.1_RNA|UBC_ENST00000538617.1_Intron			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	281	2	0.00711744		WXS	Illumina HiSeq	Phase_I	262	4	0.0152672	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	
BANP	54971	hgsc.bcm.edu	37	16	88066717	88066717	+	Missense_Mutation	SNP	C	C	T	rs74992447	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88066717C>T	ENST00000393207.1	+	9	1263	c.1042C>T	c.(1042-1044)Ccg>Tcg	p.P348S	BANP_ENST00000393208.2_Missense_Mutation_p.P317S|BANP_ENST00000355163.5_Missense_Mutation_p.P323S|BANP_ENST00000479780.2_Missense_Mutation_p.P317S|BANP_ENST00000286122.7_Missense_Mutation_p.P348S|BANP_ENST00000538234.1_Missense_Mutation_p.P356S|BANP_ENST00000355022.4_Missense_Mutation_p.P317S	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	348	DNA-binding. {ECO:0000250}.|Necessary and sufficient for TP53 activation. {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)		CCCCACAGAGCCGATGATGAG	0.647													c|||	923	0.184305	0.1672	0.0735	5008	,	,		15135	0.1349		0.1243	False		,,,				2504	0.3988				p.P356S		Atlas-SNP	.											BANP,rectum,carcinoma,-1,1	BANP	67	1	0			c.C1066T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO	698,3698	284.9+/-277.9	49,600,1549	28.0	25.0	26.0		1066,967,949,1066,1042,949,949	2.7	1.0	16	dbSNP_131	26	889,7711	194.4+/-239.8	59,771,3470	no	missense,missense,missense,missense,missense,missense,missense	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	74,74,74,74,74,74,74	108,1371,5019	TT,TC,CC		10.3372,15.8781,12.2114	benign,benign,benign,benign,benign,benign,benign	356/506,323/498,317/467,356/509,348/520,317/470,317/492	88066717	1587,11409	2198	4300	6498	SO:0001583	missense	54971	exon9			ACAGAGCCGATGA	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.1042C>T	16.37:g.88066717C>T	ENSP00000376902:p.Pro348Ser	Somatic	243	0	0		WXS	Illumina HiSeq	Phase_I	279	136	0.487455	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Missense_Mutation	SNP	ENST00000393207.1	37	CCDS54054.1	283	0.1295787545787546	84	0.17073170731707318	37	0.10220994475138122	58	0.10139860139860139	104	0.13720316622691292	C	0.012	-1.671606	0.00758	0.158781	0.103372	ENSG00000172530	ENST00000286122;ENST00000355163;ENST00000289484;ENST00000479780;ENST00000393208;ENST00000540932;ENST00000355022;ENST00000538234;ENST00000393207	.	.	.	3.75	2.65	0.31530	.	0.536094	0.20729	N	0.086754	T	0.00039	0.0001	N	0.03608	-0.345	0.45554	P	0.0014979999999999993	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.04013	0.0;0.0;0.0;0.0;0.0;0.001	T	0.22452	-1.0216	8	0.09338	T	0.73	.	7.0763	0.25207	0.7505:0.2495:0.0:0.0	.	356;323;317;348;317;317	B4DE54;B4DNJ9;B2RCF7;Q8N9N5;Q8N9N5-2;Q8N9N5-4	.;.;.;BANP_HUMAN;.;.	S	348;323;313;317;317;317;317;356;348	.	ENSP00000286122:P348S	P	+	1	0	BANP	86624218	1.000000	0.71417	0.998000	0.56505	0.171000	0.22731	1.255000	0.32909	0.625000	0.30304	0.305000	0.20034	CCG	C|0.875;T|0.125	0.125	strong		0.647	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
NCOA3	8202	hgsc.bcm.edu	37	20	46279836	46279836	+	Silent	SNP	A	A	G	rs2664522|rs147879509|rs397778717|rs3830809		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:46279836A>G	ENST00000371998.3	+	20	3953	c.3762A>G	c.(3760-3762)caA>caG	p.Q1254Q	NCOA3_ENST00000371997.3_Silent_p.Q1245Q|NCOA3_ENST00000341724.6_Silent_p.Q1180Q|NCOA3_ENST00000372004.3_Silent_p.Q1250Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1254	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcagcaacagcagcagc	0.552																																					p.Q1254Q		Atlas-SNP	.											NCOA3,NS,carcinoma,0,1	NCOA3	156	1	0			c.A3762G						PASS	.						45.0	52.0	50.0					20																	46279836		2201	4299	6500	SO:0001819	synonymous_variant	8202	exon20			GCAGCAACAGCAG	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.3762A>G	20.37:g.46279836A>G		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	72	9	0.125	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	weak		0.552	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
SMYD4	114826	hgsc.bcm.edu	37	17	1704296	1704296	+	Missense_Mutation	SNP	C	C	A	rs7224496	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1704296C>A	ENST00000305513.7	-	5	559	c.392G>T	c.(391-393)aGa>aTa	p.R131I		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	131			R -> I (in dbSNP:rs7224496). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						TGTCTGTGCTCTGTTAATGTC	0.433													C|||	1439	0.28734	0.2073	0.2594	5008	,	,		19093	0.2688		0.4851	False		,,,				2504	0.2311				p.R131I		Atlas-SNP	.											.	SMYD4	50	.	0			c.G392T						PASS	.	C	ILE/ARG	1001,3405	359.9+/-315.0	106,789,1308	132.0	134.0	133.0		392	4.0	0.9	17	dbSNP_116	133	4198,4402	558.9+/-387.3	1007,2184,1109	yes	missense	SMYD4	NM_052928.2	97	1113,2973,2417	AA,AC,CC		48.814,22.719,39.9739	possibly-damaging	131/805	1704296	5199,7807	2203	4300	6503	SO:0001583	missense	114826	exon5			TGTGCTCTGTTAA	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.392G>T	17.37:g.1704296C>A	ENSP00000304360:p.Arg131Ile	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	94	45	0.478723	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	741	0.3392857142857143	91	0.18495934959349594	109	0.3011049723756906	157	0.2744755244755245	384	0.5065963060686016	C	13.14	2.148721	0.37923	0.22719	0.48814	ENSG00000186532	ENST00000305513	T	0.18810	2.19	5.98	3.97	0.46021	Tetratricopeptide-like helical (1);	0.518027	0.24193	N	0.040700	T	0.00012	0.0000	M	0.86028	2.79	0.20403	P	0.9999024143	D	0.63880	0.993	D	0.68943	0.961	T	0.47302	-0.9128	9	0.35671	T	0.21	-5.7323	9.7875	0.40686	0.0:0.7882:0.0:0.2118	rs7224496;rs11549831;rs17846126;rs17859131;rs60531171;rs7224496	131	Q8IYR2	SMYD4_HUMAN	I	131	ENSP00000304360:R131I	ENSP00000304360:R131I	R	-	2	0	SMYD4	1651046	1.000000	0.71417	0.942000	0.38095	0.069000	0.16628	3.005000	0.49521	0.844000	0.35094	-0.157000	0.13467	AGA	C|0.642;A|0.358	0.358	strong		0.433	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
SEMA5A	9037	hgsc.bcm.edu	37	5	9136646	9136646	+	Silent	SNP	C	C	G	rs17238609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:9136646C>G	ENST00000382496.5	-	13	2234	c.1569G>C	c.(1567-1569)acG>acC	p.T523T		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	523					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						GTTCCCACTGCGTCATGCTCA	0.577													C|||	378	0.0754792	0.0492	0.0476	5008	,	,		18462	0.0129		0.0905	False		,,,				2504	0.18				p.T523T		Atlas-SNP	.											SEMA5A,NS,carcinoma,0,1	SEMA5A	236	1	0			c.G1569C						PASS	.	C		210,4196	128.2+/-165.1	6,198,1999	116.0	92.0	100.0		1569	-8.2	0.7	5	dbSNP_123	100	743,7857	179.6+/-228.7	27,689,3584	no	coding-synonymous	SEMA5A	NM_003966.2		33,887,5583	GG,GC,CC		8.6395,4.7662,7.3274		523/1075	9136646	953,12053	2203	4300	6503	SO:0001819	synonymous_variant	9037	exon13			CCACTGCGTCATG	U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1569G>C	5.37:g.9136646C>G		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	57	26	0.45614	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			C|0.930;G|0.070	0.070	strong		0.577	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2		
ADCY7	113	hgsc.bcm.edu	37	16	50342658	50342658	+	Silent	SNP	C	C	T	rs17289102	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:50342658C>T	ENST00000394697.2	+	17	2356	c.2016C>T	c.(2014-2016)gcC>gcT	p.A672A	ADCY7_ENST00000538642.1_Silent_p.A672A|ADCY7_ENST00000254235.3_Silent_p.A672A|ADCY7_ENST00000537579.1_3'UTR|ADCY7_ENST00000566433.2_Silent_p.A672A			P51828	ADCY7_HUMAN	adenylate cyclase 7	672					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		TGACCCTGGCCGTCCTGACCA	0.642													C|||	490	0.0978435	0.025	0.1009	5008	,	,		17502	0.0119		0.2515	False		,,,				2504	0.1247				p.A672A		Atlas-SNP	.											ADCY7,NS,carcinoma,0,1	ADCY7	90	1	0			c.C2016T						PASS	.	C		271,4125	152.5+/-186.2	14,243,1941	52.0	49.0	50.0		2016	-5.0	0.0	16	dbSNP_123	50	2215,6385	374.0+/-337.2	276,1663,2361	yes	coding-synonymous	ADCY7	NM_001114.3		290,1906,4302	TT,TC,CC		25.7558,6.1647,19.129		672/1081	50342658	2486,10510	2198	4300	6498	SO:0001819	synonymous_variant	113	exon16			CCTGGCCGTCCTG	D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"""Adenylate cyclases"""	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.2016C>T	16.37:g.50342658C>T		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_001114	A0AVA6	Silent	SNP	ENST00000394697.2	37	CCDS10741.1																																																																																			C|0.842;T|0.158	0.158	strong		0.642	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3		
PODXL	5420	hgsc.bcm.edu	37	7	131195959	131195959	+	Missense_Mutation	SNP	C	C	T	rs3735035	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:131195959C>T	ENST00000378555.3	-	2	581	c.334G>A	c.(334-336)Ggc>Agc	p.G112S	PODXL_ENST00000322985.9_Missense_Mutation_p.G112S|PODXL_ENST00000537928.1_Missense_Mutation_p.G112S|PODXL_ENST00000465001.1_5'UTR|PODXL_ENST00000541194.1_Missense_Mutation_p.G114S			O00592	PODXL_HUMAN	podocalyxin-like	112	Thr-rich.		G -> S (in dbSNP:rs3735035).		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)					TTGCCTGAGCCGCCTCCTCTA	0.567													C|||	1822	0.363818	0.0363	0.3948	5008	,	,		19092	0.6518		0.4354	False		,,,				2504	0.4141				p.G112S		Atlas-SNP	.											.	PODXL	53	.	0			c.G334A						PASS	.	C	SER/GLY,SER/GLY	470,3936	219.7+/-237.4	26,418,1759	161.0	163.0	163.0		334,334	-5.6	0.0	7	dbSNP_107	163	4070,4530	559.7+/-387.5	966,2138,1196	yes	missense,missense	PODXL	NM_001018111.2,NM_005397.3	56,56	992,2556,2955	TT,TC,CC		47.3256,10.6673,34.907	benign,benign	112/559,112/527	131195959	4540,8466	2203	4300	6503	SO:0001583	missense	5420	exon2			CTGAGCCGCCTCC		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.334G>A	7.37:g.131195959C>T	ENSP00000367817:p.Gly112Ser	Somatic	259	1	0.003861		WXS	Illumina HiSeq	Phase_I	258	138	0.534884	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	37	CCDS34755.1	856	0.39194139194139194	30	0.06097560975609756	130	0.35911602209944754	351	0.6136363636363636	345	0.4551451187335092	C	3.668	-0.068070	0.07228	0.106673	0.473256	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000544955;ENST00000378555;ENST00000322985	T;T;T;T	0.10573	3.06;2.86;3.06;3.02	2.82	-5.63	0.02474	.	16.508200	0.00166	N	0.000000	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.18610	0.029;0.017	B;B	0.06405	0.002;0.001	T	0.41305	-0.9516	9	0.09084	T	0.74	1.8737	1.2318	0.01945	0.3764:0.2453:0.2502:0.1281	rs3735035;rs17744768;rs52837657;rs60330344;rs3735035	112;112	O00592-2;O00592	.;PODXL_HUMAN	S	114;112;102;112;112	ENSP00000440518:G114S;ENSP00000442655:G112S;ENSP00000367817:G112S;ENSP00000319782:G112S	ENSP00000319782:G112S	G	-	1	0	PODXL	130846499	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.188000	0.03064	-2.759000	0.00371	-1.890000	0.00535	GGC	C|0.627;T|0.373	0.373	strong		0.567	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
CD97	976	hgsc.bcm.edu	37	19	14512489	14512489	+	Missense_Mutation	SNP	G	G	A	rs2230748	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14512489G>A	ENST00000242786.5	+	11	1180	c.1100G>A	c.(1099-1101)cGg>cAg	p.R367Q	CTC-548K16.5_ENST00000590626.1_RNA|CD97_ENST00000358600.3_Missense_Mutation_p.R274Q|CD97_ENST00000357355.3_Missense_Mutation_p.R318Q	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	367			R -> Q (in dbSNP:rs2230748).		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						ATCCAGGAGCGGGGGGACAAG	0.637													g|||	1084	0.216454	0.0764	0.1499	5008	,	,		18239	0.4593		0.1054	False		,,,				2504	0.317				p.R367Q		Atlas-SNP	.											.	CD97	86	.	0			c.G1100A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	375,4031	189.9+/-215.9	15,345,1843	63.0	52.0	55.0		953,821,1100	-2.5	0.0	19	dbSNP_98	55	1132,7468	232.5+/-266.1	84,964,3252	no	missense,missense,missense	CD97	NM_001025160.2,NM_001784.4,NM_078481.3	43,43,43	99,1309,5095	AA,AG,GG		13.1628,8.5111,11.587	benign,benign,benign	318/787,274/743,367/836	14512489	1507,11499	2203	4300	6503	SO:0001583	missense	976	exon11			AGGAGCGGGGGGA		CCDS32929.1, CCDS32930.1, CCDS32931.1	19p13	2014-08-08	2006-03-28			ENSG00000123146		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	1711	protein-coding gene	gene with protein product	"""leukocyte antigen CD97"", ""seven-span transmembrane protein"", ""seven-transmembrane, heterodimeric receptor associated with inflammation"", ""seven transmembrane helix receptor"""	601211	"""CD97 antigen"""			7636245, 8786105	Standard	NM_078481		Approved	TM7LN1	uc002myl.3	P48960		ENST00000242786.5:c.1100G>A	19.37:g.14512489G>A	ENSP00000242786:p.Arg367Gln	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	93	44	0.473118	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Missense_Mutation	SNP	ENST00000242786.5	37	CCDS32929.1	429	0.19642857142857142	43	0.08739837398373984	62	0.1712707182320442	244	0.42657342657342656	80	0.10554089709762533	G	1.460	-0.562593	0.03939	0.085111	0.131628	ENSG00000123146	ENST00000242786;ENST00000357355;ENST00000358600;ENST00000393059	T;T;T	0.70045	-0.45;-0.37;0.01	5.29	-2.53	0.06326	.	.	.	.	.	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	0.04013	0.001;0.001;0.001	T	0.27536	-1.0071	8	0.02654	T	1	.	7.4003	0.26960	0.2883:0.5487:0.163:0.0	rs2230748;rs2252171;rs52805742;rs60220444;rs2230748	274;318;367	P48960-2;P48960-3;P48960	.;.;CD97_HUMAN	Q	367;318;274;317	ENSP00000242786:R367Q;ENSP00000349918:R318Q;ENSP00000351413:R274Q	ENSP00000242786:R367Q	R	+	2	0	CD97	14373489	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	-2.727000	0.00807	-0.574000	0.05990	-1.786000	0.00637	CGG	G|0.848;A|0.152	0.152	strong		0.637	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481	
COL4A1	1282	hgsc.bcm.edu	37	13	110864225	110864225	+	Silent	SNP	A	A	T	rs532625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:110864225A>T	ENST00000375820.4	-	7	553	c.432T>A	c.(430-432)gcT>gcA	p.A144A	COL4A1_ENST00000543140.1_Silent_p.A144A	NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	144					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)			CGGGATTTCCAGCGAAACCAG	0.488													A|||	2368	0.472843	0.3631	0.3804	5008	,	,		14518	0.5407		0.4493	False		,,,				2504	0.6411				p.A144A		Atlas-SNP	.											.	COL4A1	372	.	0			c.T432A						PASS	.	A		1655,2751	504.9+/-366.0	322,1011,870	132.0	153.0	146.0		432	-3.6	0.0	13	dbSNP_83	146	4062,4538	555.0+/-386.6	954,2154,1192	no	coding-synonymous	COL4A1	NM_001845.4		1276,3165,2062	TT,TA,AA		47.2326,37.5624,43.9566		144/1670	110864225	5717,7289	2203	4300	6503	SO:0001819	synonymous_variant	1282	exon7			ATTTCCAGCGAAA	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.432T>A	13.37:g.110864225A>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	113	70	0.619469	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Silent	SNP	ENST00000375820.4	37	CCDS9511.1																																																																																			A|0.550;N|0.000	.	strong		0.488	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3		
THSD7A	221981	hgsc.bcm.edu	37	7	11509561	11509561	+	Missense_Mutation	SNP	G	G	C	rs2285744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:11509561G>C	ENST00000423059.4	-	9	2564	c.2313C>G	c.(2311-2313)gaC>gaG	p.D771E	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	771	TSP type-1 8. {ECO:0000255|PROSITE- ProRule:PRU00210}.		D -> E (in dbSNP:rs2285744).		angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TCACAATACAGTCCTTCTTAC	0.448										HNSCC(18;0.044)			G|||	1396	0.278754	0.1195	0.2435	5008	,	,		17089	0.2252		0.4125	False		,,,				2504	0.4366				p.D771E		Atlas-SNP	.											.	THSD7A	219	.	0			c.C2313G						PASS	.	G	GLU/ASP	604,3212		60,484,1364	64.0	56.0	59.0		2313	3.7	1.0	7	dbSNP_100	59	3576,4686		762,2052,1317	yes	missense	THSD7A	NM_015204.2	45	822,2536,2681	CC,CG,GG		43.2825,15.8281,34.6084	probably-damaging	771/1658	11509561	4180,7898	1908	4131	6039	SO:0001583	missense	221981	exon9			AATACAGTCCTTC		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2313C>G	7.37:g.11509561G>C	ENSP00000406482:p.Asp771Glu	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	100	50	0.5	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	600	0.27472527472527475	71	0.1443089430894309	102	0.281767955801105	123	0.21503496503496503	304	0.40105540897097625	G	21.5	4.156823	0.78114	0.158281	0.432825	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.20332	2.08	5.56	3.74	0.42951	.	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.90595	3.13	0.19775	P	0.9999597667	D	0.89917	1.0	D	0.91635	0.999	T	0.45234	-0.9275	9	0.23302	T	0.38	.	8.8978	0.35476	0.2856:0.0:0.7144:0.0	rs2285744;rs17631276;rs52802345;rs2285744	771	Q9UPZ6	THS7A_HUMAN	E	771	ENSP00000406482:D771E	ENSP00000262042:D771E	D	-	3	2	THSD7A	11476086	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.051000	0.41307	0.801000	0.34066	0.650000	0.86243	GAC	G|0.719;C|0.281	0.281	strong		0.448	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
CSMD3	114788	hgsc.bcm.edu	37	8	113237045	113237045	+	Silent	SNP	C	C	T	rs4876458	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:113237045C>T	ENST00000297405.5	-	71	11323	c.11079G>A	c.(11077-11079)gcG>gcA	p.A3693A	CSMD3_ENST00000343508.3_Silent_p.A3653A|CSMD3_ENST00000352409.3_Silent_p.A3623A|CSMD3_ENST00000455883.2_Silent_p.A3524A	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3693						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						CAAATCGTACCGCCTTCCCTT	0.438										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			c|||	267	0.0533147	0.003	0.0865	5008	,	,		17999	0.004		0.1312	False		,,,				2504	0.0685				p.A3693A		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,-1,6	CSMD3	2325	6	0			c.G11079A						PASS	.	T	,,	106,4300	82.9+/-121.4	0,106,2097	408.0	345.0	366.0		10572,11079,10959	-6.7	0.3	8	dbSNP_111	366	1047,7553	221.2+/-258.7	74,899,3327	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	74,1005,5424	TT,TC,CC		12.1744,2.4058,8.8651	,,	3524/3539,3693/3708,3653/3668	113237045	1153,11853	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon71			TCGTACCGCCTTC	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.11079G>A	8.37:g.113237045C>T		Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	271	140	0.516605	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			C|0.918;T|0.082	0.082	strong		0.438	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
DHX37	57647	hgsc.bcm.edu	37	12	125448960	125448960	+	Silent	SNP	C	C	T	rs4076777	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:125448960C>T	ENST00000308736.2	-	15	2123	c.2025G>A	c.(2023-2025)acG>acA	p.T675T	DHX37_ENST00000544745.1_Silent_p.T462T	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	675	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						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)		GGCCGGGCTCCGTCCGTCCTG	0.632													T|||	1829	0.365216	0.2088	0.3386	5008	,	,		17000	0.6448		0.33	False		,,,				2504	0.3436				p.T675T		Atlas-SNP	.											.	DHX37	114	.	0			c.G2025A						PASS	.	T		946,3460	735.6+/-410.7	90,766,1347	69.0	68.0	68.0		2025	-3.7	0.8	12	dbSNP_108	68	2828,5772	675.3+/-403.2	461,1906,1933	no	coding-synonymous	DHX37	NM_032656.3		551,2672,3280	TT,TC,CC		32.8837,21.4707,29.0174		675/1158	125448960	3774,9232	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon15			GGGCTCCGTCCGT	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.2025G>A	12.37:g.125448960C>T		Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	53	32	0.603774	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1	888	0.4065934065934066	111	0.22560975609756098	134	0.3701657458563536	391	0.6835664335664335	252	0.3324538258575198	T	11.92	1.782963	0.31502	0.214707	0.328837	ENSG00000150990	ENST00000543962	.	.	.	5.17	-3.66	0.04489	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999813	.	.	.	.	.	.	T	0.37820	-0.9689	4	0.87932	D	0	-36.7754	2.5483	0.04742	0.1757:0.3673:0.0949:0.3621	rs4076777;rs4316603;rs11558557	.	.	.	Q	127	.	ENSP00000443661:R127Q	R	-	2	0	DHX37	124014913	0.000000	0.05858	0.809000	0.32408	0.837000	0.47467	-2.742000	0.00798	-1.499000	0.01821	-0.521000	0.04368	CGG	C|0.671;T|0.329	0.329	strong		0.632	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
TTN	7273	hgsc.bcm.edu	37	2	179447755	179447755	+	Silent	SNP	G	G	A	rs72646867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179447755G>A	ENST00000591111.1	-	263	61076	c.60852C>T	c.(60850-60852)agC>agT	p.S20284S	RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN_ENST00000342175.6_Silent_p.S13052S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Silent_p.S21925S|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342992.6_Silent_p.S19357S|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000460472.2_Silent_p.S12860S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN_ENST00000359218.5_Silent_p.S12985S|TTN-AS1_ENST00000591332.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20284	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)			TCCGGTTCACGCTGAATAGCT	0.428													G|||	8	0.00159744	0.0	0.0014	5008	,	,		18214	0.0		0.003	False		,,,				2504	0.0041				p.S21925S		Atlas-SNP	.											.	TTN	18412	.	0			c.C65775T						PASS	.	G	,,,	1,3963		0,1,1981	89.0	87.0	87.0		38580,58071,38955,39156	-10.5	0.7	2	dbSNP_130	87	14,8306		0,14,4146	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,15,6127	AA,AG,GG		0.1683,0.0252,0.1221	,,,	12860/26927,19357/33424,12985/27052,13052/27119	179447755	15,12269	1982	4160	6142	SO:0001819	synonymous_variant	7273	exon313			GTTCACGCTGAAT	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.60852C>T	2.37:g.179447755G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	187	84	0.449198	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|0.999;A|0.001	0.001	weak		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ATAD3C	219293	hgsc.bcm.edu	37	1	1390875	1390875	+	Silent	SNP	C	C	T	rs1781147	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1390875C>T	ENST00000378785.2	+	5	1409	c.414C>T	c.(412-414)gaC>gaT	p.D138D		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	138							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GACCCCAGGACGTGCTGGAGG	0.677													c|||	2129	0.42512	0.528	0.4323	5008	,	,		12946	0.499		0.1879	False		,,,				2504	0.4489				p.D138D		Atlas-SNP	.											ATAD3C,NS,carcinoma,+2,1	ATAD3C	23	1	0			c.C414T						PASS	.	C		656,728		164,328,200	61.0	62.0	62.0		414	-1.4	0.2	1	dbSNP_89	62	617,2565		72,473,1046	no	coding-synonymous	ATAD3C	NM_001039211.2		236,801,1246	TT,TC,CC		19.3903,47.3988,27.88		138/412	1390875	1273,3293	692	1591	2283	SO:0001819	synonymous_variant	219293	exon5			CCAGGACGTGCTG	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.414C>T	1.37:g.1390875C>T		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	159	158	0.993711	NM_001039211	Q8N1Z5	Silent	SNP	ENST00000378785.2	37	CCDS44039.1																																																																																			C|0.608;T|0.392	0.392	strong		0.677	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
SERPINA6	866	hgsc.bcm.edu	37	14	94776221	94776221	+	Missense_Mutation	SNP	A	A	C	rs2228541	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:94776221A>C	ENST00000341584.3	-	3	882	c.736T>G	c.(736-738)Tcg>Gcg	p.S246A		NM_001756.3	NP_001747	P08185	CBG_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6	246			S -> A (in dbSNP:rs2228541). {ECO:0000269|PubMed:15489334}.		glucocorticoid metabolic process (GO:0008211)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|transport (GO:0006810)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)|steroid binding (GO:0005496)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	26		all_cancers(154;0.0482)|all_epithelial(191;0.166)		COAD - Colon adenocarcinoma(157;0.211)	Alclometasone(DB00240)|Beclomethasone(DB00394)|Ciclesonide(DB01410)|Flumethasone Pivalate(DB00663)|Flunisolide(DB00180)|Fluocinolone Acetonide(DB00591)|Fluocinonide(DB01047)|Fluorometholone(DB00324)|Flurandrenolide(DB00846)|Fluticasone Propionate(DB00588)|Halobetasol Propionate(DB00596)|Medrysone(DB00253)|Mitotane(DB00648)|Paramethasone(DB01384)|Prednisolone(DB00860)|Rimexolone(DB00896)|Triamcinolone(DB00620)	GGGAGCTCCGAGTCATGAAGG	0.547													A|||	2995	0.598043	0.407	0.6816	5008	,	,		21548	0.9325		0.4364	False		,,,				2504	0.6186				p.S246A		Atlas-SNP	.											SERPINA6_ENST00000341584,NS,adenoma,+2,1	SERPINA6	102	1	0			c.T736G	GRCh37	CM045664	SERPINA6	M	rs2228541	PASS	.	A	ALA/SER	1690,2716	511.4+/-367.8	331,1028,844	137.0	112.0	120.0		736	-10.7	0.0	14	dbSNP_98	120	3910,4690	546.9+/-385.1	918,2074,1308	yes	missense	SERPINA6	NM_001756.3	99	1249,3102,2152	CC,CA,AA		45.4651,38.3568,43.0571	benign	246/406	94776221	5600,7406	2203	4300	6503	SO:0001583	missense	866	exon3			GCTCCGAGTCATG	J02943	CCDS9924.1	14q32.13	2014-02-18	2005-08-18		ENSG00000170099	ENSG00000170099		"""Serine (or cysteine) peptidase inhibitors"""	1540	protein-coding gene	gene with protein product	"""corticosteroid binding globulin"", ""transcortin"""	122500	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6"""	CBG		3299377, 7912884, 24172014	Standard	NM_001756		Approved		uc001ycv.3	P08185	OTTHUMG00000171346	ENST00000341584.3:c.736T>G	14.37:g.94776221A>C	ENSP00000342850:p.Ser246Ala	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	104	102	0.980769	NM_001756	A8K456|Q7Z2Q9	Missense_Mutation	SNP	ENST00000341584.3	37	CCDS9924.1	1271	0.581959706959707	194	0.3943089430894309	236	0.6519337016574586	522	0.9125874125874126	319	0.420844327176781	A	12.58	1.979713	0.34942	0.383568	0.454651	ENSG00000170099	ENST00000341584	D	0.87966	-2.32	5.33	-10.7	0.00240	Serpin domain (3);	1.223890	0.05905	N	0.630684	T	0.00012	0.0000	L	0.39326	1.205	0.80722	P	0.0	B	0.06786	0.001	B	0.14023	0.01	T	0.48581	-0.9023	9	0.52906	T	0.07	.	0.3477	0.00343	0.3765:0.2023:0.1678:0.2534	rs2228541;rs17846540;rs17859614;rs17859637;rs58567943;rs2228541	246	P08185	CBG_HUMAN	A	246	ENSP00000342850:S246A	ENSP00000342850:S246A	S	-	1	0	SERPINA6	93845974	0.000000	0.05858	0.001000	0.08648	0.172000	0.22775	-4.329000	0.00252	-1.670000	0.01468	-0.313000	0.08912	TCG	T|0.003;G|0.002	.	strong		0.547	SERPINA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413065.1	NM_001756	
DOCK6	57572	hgsc.bcm.edu	37	19	11348911	11348911	+	Silent	SNP	A	A	G	rs7252937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11348911A>G	ENST00000294618.7	-	15	1724	c.1713T>C	c.(1711-1713)gcT>gcC	p.A571A	C19orf80_ENST00000591200.1_Intron|C19orf80_ENST00000252453.8_5'Flank|DOCK6_ENST00000319867.7_5'Flank	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	571	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(11)|large_intestine(8)|liver(2)|lung(9)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	39						GCACTCGCACAGCAAGGTTGC	0.667													a|||	888	0.177316	0.4811	0.0793	5008	,	,		17025	0.0804		0.0557	False		,,,				2504	0.0613				p.A571A		Atlas-SNP	.											.	DOCK6	104	.	0			c.T1713C						PASS	.	A		1647,2473		309,1029,722	38.0	44.0	42.0		1713	-2.9	0.8	19	dbSNP_116	42	660,7740		36,588,3576	no	coding-synonymous	DOCK6	NM_020812.2		345,1617,4298	GG,GA,AA		7.8571,39.9757,18.4265		571/2048	11348911	2307,10213	2060	4200	6260	SO:0001819	synonymous_variant	57572	exon15			TCGCACAGCAAGG		CCDS45975.1	19p13.2	2011-08-04			ENSG00000130158	ENSG00000130158			19189	protein-coding gene	gene with protein product		614194				12432077	Standard	NM_020812		Approved	KIAA1395, ZIR1	uc002mqs.5	Q96HP0		ENST00000294618.7:c.1713T>C	19.37:g.11348911A>G		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	82	36	0.439024	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			A|0.830;G|0.170	0.170	strong		0.667	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812	
KLK3	354	hgsc.bcm.edu	37	19	51362803	51362803	+	Intron	SNP	C	C	T	rs35192866	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51362803C>T	ENST00000326003.2	+	5	671				KLK3_ENST00000360617.3_Silent_p.T216T|KLK3_ENST00000597483.1_Silent_p.T173T|KLK3_ENST00000595952.1_Intron	NM_001030047.1|NM_001030048.1|NM_001648.2	NP_001025218.1|NP_001025219.1|NP_001639.1	P07288	KLK3_HUMAN	kallikrein-related peptidase 3						cellular protein metabolic process (GO:0044267)|negative regulation of angiogenesis (GO:0016525)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|cervix(2)|kidney(2)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00763)|GBM - Glioblastoma multiforme(134;0.0144)		TTCTGATCACCGAACTGACCA	0.612													c|||	359	0.0716853	0.0893	0.0807	5008	,	,		17561	0.0665		0.0944	False		,,,				2504	0.0235				p.T216T	Colon(185;1767 2023 13025 30120 37630)	Atlas-SNP	.											.	KLK3	76	.	0			c.C648T						PASS	.	T	,,	379,4027	191.6+/-217.2	19,341,1843	117.0	94.0	102.0		648,,	-3.3	0.0	19	dbSNP_126	102	743,7857	178.5+/-227.8	28,687,3585	no	coding-synonymous,intron,intron	KLK3	NM_001030047.1,NM_001030048.1,NM_001648.2	,,	47,1028,5428	TT,TC,CC		8.6395,8.6019,8.6268	,,	216/239,,	51362803	1122,11884	2203	4300	6503	SO:0001627	intron_variant	354	exon5			GATCACCGAACTG	X14810	CCDS12807.1, CCDS33083.1, CCDS46155.1	19q13.41	2012-10-02	2006-10-27			ENSG00000142515		"""Kallikreins"""	6364	protein-coding gene	gene with protein product		176820	"""kallikrein 3, (prostate specific antigen)"""	APS		2456523, 2436946, 16800724, 16800723	Standard	NM_001648		Approved	PSA	uc021uyi.1	P07288		ENST00000326003.2:c.631-425C>T	19.37:g.51362803C>T		Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	91	48	0.527473	NM_001030047	C9JXH3|G3V0H4|G3XAE3|Q15096|Q16272|Q86TG8|Q8IXI4	Silent	SNP	ENST00000326003.2	37	CCDS12807.1																																																																																			C|0.912;T|0.088	0.088	strong		0.612	KLK3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464067.1	NM_145864	
SPATA19	219938	hgsc.bcm.edu	37	11	133714522	133714522	+	Missense_Mutation	SNP	G	G	A	rs2282602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:133714522G>A	ENST00000299140.3	-	3	203	c.149C>T	c.(148-150)gCt>gTt	p.A50V	SPATA19_ENST00000532889.1_Missense_Mutation_p.A50V	NM_174927.1	NP_777587.1	Q7Z5L4	SPT19_HUMAN	spermatogenesis associated 19	50			A -> V (in dbSNP:rs2282602). {ECO:0000269|PubMed:12688595}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	mitochondrial outer membrane (GO:0005741)				cervix(1)|endometrium(2)|large_intestine(2)|lung(5)|prostate(1)	11	all_hematologic(175;0.127)	all_cancers(12;5.59e-17)|all_epithelial(12;2.65e-12)|all_lung(97;0.00045)|Lung NSC(97;0.000861)|Breast(109;0.000873)|Medulloblastoma(222;0.0425)|Esophageal squamous(93;0.0844)|all_neural(223;0.117)		Epithelial(10;4.36e-10)|all cancers(11;7.1e-09)|BRCA - Breast invasive adenocarcinoma(10;8.45e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00286)|Lung(977;0.207)		GCCCCGAGAAGCCTCTTCTTC	0.498													G|||	1700	0.339457	0.1044	0.317	5008	,	,		20435	0.6022		0.3926	False		,,,				2504	0.3476				p.A50V		Atlas-SNP	.											.	SPATA19	36	.	0			c.C149T						PASS	.	G	VAL/ALA	741,3661	305.5+/-289.0	65,611,1525	100.0	102.0	101.0		149	5.0	1.0	11	dbSNP_100	101	3216,5378	485.9+/-371.8	616,1984,1697	yes	missense	SPATA19	NM_174927.1	64	681,2595,3222	AA,AG,GG		37.4215,16.8333,30.4478	possibly-damaging	50/168	133714522	3957,9039	2201	4297	6498	SO:0001583	missense	219938	exon3			CGAGAAGCCTCTT	AK098717	CCDS8493.1	11q25	2010-04-23				ENSG00000166118			30614	protein-coding gene	gene with protein product	"""spergen 1"", ""cancer/testis antigen 132"""	609805				12477932	Standard	XM_005271448		Approved	FLJ25851, spergen1, SPAS1, CT132	uc001qgv.1	Q7Z5L4		ENST00000299140.3:c.149C>T	11.37:g.133714522G>A	ENSP00000299140:p.Ala50Val	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	99	42	0.424242	NM_174927	Q8N7A9	Missense_Mutation	SNP	ENST00000299140.3	37	CCDS8493.1	796	0.36446886446886445	48	0.0975609756097561	120	0.3314917127071823	329	0.5751748251748252	299	0.3944591029023747	G	20.4	3.990884	0.74703	0.168333	0.374215	ENSG00000166118	ENST00000299140;ENST00000532889	T;T	0.56611	0.45;0.45	5.02	5.02	0.67125	.	0.000000	0.56097	D	0.000029	T	0.00012	0.0000	L	0.34521	1.04	0.26466	P	0.9753572	D	0.76494	0.999	D	0.80764	0.994	T	0.50734	-0.8793	9	0.52906	T	0.07	-6.9761	14.1925	0.65646	0.0:0.0:1.0:0.0	rs2282602;rs61530072;rs2282602	50	Q7Z5L4	SPT19_HUMAN	V	50	ENSP00000299140:A50V;ENSP00000435248:A50V	ENSP00000299140:A50V	A	-	2	0	SPATA19	133219732	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	3.306000	0.51881	2.493000	0.84123	0.655000	0.94253	GCT	G|0.673;A|0.327	0.327	strong		0.498	SPATA19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393281.1	NM_174927	
SPATC1	375686	hgsc.bcm.edu	37	8	145095328	145095328	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145095328T>A	ENST00000377470.3	+	2	832	c.730T>A	c.(730-732)Tcc>Acc	p.S244T	SPATC1_ENST00000447830.2_Missense_Mutation_p.S244T	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	244						centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGGGCCCCAGTCCCCAGCTTG	0.677																																					p.S244T		Atlas-SNP	.											.	SPATC1	77	.	0			c.T730A						PASS	.						14.0	16.0	16.0					8																	145095328		2198	4293	6491	SO:0001583	missense	375686	exon2			CCCCAGTCCCCAG	BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.730T>A	8.37:g.145095328T>A	ENSP00000366690:p.Ser244Thr	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	90	53	0.588889	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Missense_Mutation	SNP	ENST00000377470.3	37	CCDS6413.2	.	.	.	.	.	.	.	.	.	.	T	5.096	0.203364	0.09704	.	.	ENSG00000186583	ENST00000377470;ENST00000447830	T	0.44083	0.93	3.69	-3.7	0.04437	.	1.671390	0.03864	N	0.274514	T	0.23094	0.0558	L	0.36672	1.1	0.09310	N	1	B;B	0.14012	0.009;0.003	B;B	0.16289	0.015;0.006	T	0.16541	-1.0399	10	0.02654	T	1	-2.9873	0.8322	0.01132	0.172:0.1768:0.344:0.3072	.	244;244	B4DWW9;Q76KD6	.;SPERI_HUMAN	T	244	ENSP00000366690:S244T	ENSP00000366690:S244T	S	+	1	0	SPATC1	145167316	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.964000	0.01512	-0.526000	0.06383	0.260000	0.18958	TCC	.	.	none		0.677	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572	
ANKRD61	100310846	hgsc.bcm.edu	37	7	6071115	6071115	+	Missense_Mutation	SNP	A	A	G	rs12334093	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:6071115A>G	ENST00000409061.1	+	1	109	c.109A>G	c.(109-111)Atg>Gtg	p.M37V	EIF2AK1_ENST00000199389.6_Intron|EIF2AK1_ENST00000536084.1_Intron	NM_001271700.1	NP_001258629.1	A6NGH8	ANR61_HUMAN	ankyrin repeat domain 61	37																	TGAAGCCATCATGAGAGAAGA	0.507													A|||	574	0.114617	0.2413	0.1138	5008	,	,		18893	0.0268		0.0984	False		,,,				2504	0.0511				p.M37V		Atlas-SNP	.											.	.	.	.	0			c.A109G						PASS	.																																			SO:0001583	missense	100310846	exon1			GCCATCATGAGAG		CCDS64590.1	7p22	2013-01-10			ENSG00000157999	ENSG00000157999		"""Ankyrin repeat domain containing"""	22467	protein-coding gene	gene with protein product							Standard	NM_001271700		Approved		uc031swn.1	A6NGH8	OTTHUMG00000154561	ENST00000409061.1:c.109A>G	7.37:g.6071115A>G	ENSP00000386502:p.Met37Val	Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	155	83	0.535484	NM_001271700		Missense_Mutation	SNP	ENST00000409061.1	37		223	0.1021062271062271	107	0.21747967479674796	37	0.10220994475138122	10	0.017482517482517484	69	0.09102902374670185	A	5.583	0.292429	0.10567	.	.	ENSG00000157999	ENST00000409061	T	0.53423	0.62	5.69	0.268	0.15626	.	0.298325	0.29119	N	0.013091	T	0.00039	0.0001	.	.	.	0.29275	P	0.870392	.	.	.	.	.	.	T	0.18524	-1.0334	6	0.22109	T	0.4	-13.9545	6.9436	0.24506	0.4099:0.4344:0.0:0.1558	rs12334093;rs52791415;rs58280047;rs12334093	.	.	.	V	37	ENSP00000386502:M37V	ENSP00000386502:M37V	M	+	1	0	ANKRD61	6037641	0.884000	0.30299	0.150000	0.22450	0.058000	0.15608	0.142000	0.16096	-0.174000	0.10743	0.533000	0.62120	ATG	A|0.885;G|0.115	0.115	strong		0.507	ANKRD61-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000335991.1		
TMEM255B	348013	hgsc.bcm.edu	37	13	114498154	114498154	+	Missense_Mutation	SNP	G	G	C	rs150323609	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:114498154G>C	ENST00000375353.3	+	4	313	c.286G>C	c.(286-288)Gtg>Ctg	p.V96L		NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	96						integral component of membrane (GO:0016021)											CAGTTTTGGCGTGGTGGCCGC	0.542													G|||	45	0.00898562	0.0	0.0014	5008	,	,		17083	0.0		0.007	False		,,,				2504	0.0378				p.V96L		Atlas-SNP	.											.	.	.	.	0			c.G286C						PASS	.		LEU/VAL	3,4403	6.2+/-15.9	0,3,2200	117.0	94.0	101.0		286	4.1	1.0	13	dbSNP_134	101	45,8555	30.1+/-81.4	0,45,4255	yes	missense	FAM70B	NM_182614.2	32	0,48,6455	CC,CG,GG		0.5233,0.0681,0.3691	possibly-damaging	96/327	114498154	48,12958	2203	4300	6503	SO:0001583	missense	348013	exon4			TTTGGCGTGGTGG	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.286G>C	13.37:g.114498154G>C	ENSP00000364502:p.Val96Leu	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	47	18	0.382979	NM_182614		Missense_Mutation	SNP	ENST00000375353.3	37	CCDS45071.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	17.18	3.322841	0.60634	6.81E-4	0.005233	ENSG00000184497	ENST00000375353;ENST00000375348	T;T	0.56941	0.43;0.43	4.06	4.06	0.47325	.	.	.	.	.	T	0.53786	0.1818	M	0.76838	2.35	0.58432	D	0.999994	D	0.56287	0.975	P	0.48627	0.584	T	0.68565	-0.5375	9	0.72032	D	0.01	-18.814	15.0297	0.71696	0.0:0.0:1.0:0.0	.	96	Q8WV15	FA70B_HUMAN	L	96;104	ENSP00000364502:V96L;ENSP00000364497:V104L	ENSP00000364497:V104L	V	+	1	0	FAM70B	113615789	1.000000	0.71417	0.968000	0.41197	0.190000	0.23558	5.129000	0.64739	1.806000	0.52798	0.394000	0.25966	GTG	G|0.996;C|0.004	0.004	strong		0.542	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614	
HSD17B14	51171	hgsc.bcm.edu	37	19	49339098	49339098	+	Missense_Mutation	SNP	T	T	C	rs8110220	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49339098T>C	ENST00000263278.4	-	2	357	c.91A>G	c.(91-93)Aac>Gac	p.N31D	HSD17B14_ENST00000599157.1_Missense_Mutation_p.N31D	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	31			N -> D (in dbSNP:rs8110220).		steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		GCCCCGCTGTTCACTGAGAAT	0.607											OREG0025610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	1722	0.34385	0.6165	0.2867	5008	,	,		16704	0.0893		0.2674	False		,,,				2504	0.3569				p.N31D		Atlas-SNP	.											.	HSD17B14	25	.	0			c.A91G						PASS	.		ASP/ASN	2378,2028		645,1088,470	87.0	73.0	78.0		91	-1.8	0.1	19	dbSNP_116	78	2126,6472		258,1610,2431	yes	missense	HSD17B14	NM_016246.2	23	903,2698,2901	CC,CT,TT		24.7267,46.0281,34.6355	benign	31/271	49339098	4504,8500	2203	4299	6502	SO:0001583	missense	51171	exon2			CGCTGTTCACTGA	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.91A>G	19.37:g.49339098T>C	ENSP00000263278:p.Asn31Asp	Somatic	42	0	0	961	WXS	Illumina HiSeq	Phase_I	33	17	0.515152	NM_016246	Q9UKU3	Missense_Mutation	SNP	ENST00000263278.4	37	CCDS12736.1	665	0.30448717948717946	285	0.5792682926829268	115	0.31767955801104975	67	0.11713286713286714	198	0.2612137203166227	-	0.019	-1.451578	0.01080	0.539719	0.247267	ENSG00000087076	ENST00000263278	T	0.21031	2.03	3.1	-1.77	0.07982	NAD(P)-binding domain (1);	0.876083	0.09791	N	0.755389	T	0.00012	0.0000	N	0.03891	-0.335	0.52099	P	5.500000000002725E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	9	0.21540	T	0.41	.	4.0567	0.09819	0.0:0.3503:0.3462:0.3035	rs8110220;rs52799828;rs61231150;rs8110220	31	Q9BPX1	DHB14_HUMAN	D	31	ENSP00000263278:N31D	ENSP00000263278:N31D	N	-	1	0	HSD17B14	54030910	0.109000	0.22037	0.063000	0.19743	0.073000	0.16967	-0.043000	0.12043	-0.518000	0.06452	-0.382000	0.06688	AAC	C|0.335;N|0.001	0.335	strong		0.607	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
POU4F3	5459	hgsc.bcm.edu	37	5	145719368	145719368	+	Silent	SNP	G	G	A	rs113137300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145719368G>A	ENST00000230732.4	+	2	467	c.378G>A	c.(376-378)acG>acA	p.T126T	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	126					auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCGCCCACGCTGAGTGTGA	0.687													G|||	14	0.00279553	0.0091	0.0029	5008	,	,		13001	0.0		0.0	False		,,,				2504	0.0				p.T126T		Atlas-SNP	.											.	POU4F3	47	.	0			c.G378A						PASS	.	G		34,4372	39.2+/-71.8	0,34,2169	76.0	71.0	73.0		378	1.8	1.0	5	dbSNP_132	73	0,8598		0,0,4299	no	coding-synonymous	POU4F3	NM_002700.2		0,34,6468	AA,AG,GG		0.0,0.7717,0.2615		126/339	145719368	34,12970	2203	4299	6502	SO:0001819	synonymous_variant	5459	exon2			GCCCACGCTGAGT	U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"""Homeoboxes / POU class"""	9220	protein-coding gene	gene with protein product		602460	"""POU domain class 4, transcription factor 3"""	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.378G>A	5.37:g.145719368G>A		Somatic	44	0	0		WXS	Illumina HiSeq	Phase_I	59	29	0.491525	NM_002700	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	37	CCDS4281.1																																																																																			G|0.997;A|0.003	0.003	strong		0.687	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700	
FCN1	2219	hgsc.bcm.edu	37	9	137801800	137801800	+	Silent	SNP	T	T	C	rs1071583	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:137801800T>C	ENST00000371806.3	-	9	916	c.825A>G	c.(823-825)caA>caG	p.Q275Q		NM_002003.3	NP_001994.2	O00602	FCN1_HUMAN	ficolin (collagen/fibrinogen domain containing) 1	275	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell surface pattern recognition receptor signaling pathway (GO:0002752)|complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|opsonization (GO:0008228)|positive regulation of interleukin-8 secretion (GO:2000484)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extrinsic component of external side of plasma membrane (GO:0031232)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|G-protein coupled receptor binding (GO:0001664)|signaling pattern recognition receptor activity (GO:0008329)			endometrium(3)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	37		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.46e-08)|Epithelial(140;6.01e-08)|all cancers(34;3.69e-07)		ACCAGGCTCCTTGGAACTTCT	0.493													C|||	3424	0.683706	0.9523	0.4784	5008	,	,		20225	0.4712		0.6302	False		,,,				2504	0.7403				p.Q275Q		Atlas-SNP	.											.	FCN1	62	.	0			c.A825G						PASS	.	C		3989,417	202.8+/-225.5	1818,353,32	189.0	185.0	186.0		825	-2.9	0.0	9	dbSNP_86	186	5463,3137	477.3+/-369.6	1710,2043,547	no	coding-synonymous	FCN1	NM_002003.3		3528,2396,579	CC,CT,TT		36.4767,9.4644,27.3258		275/327	137801800	9452,3554	2203	4300	6503	SO:0001819	synonymous_variant	2219	exon9			GGCTCCTTGGAAC	D83920	CCDS6985.1	9q34	2013-02-06	2002-01-14		ENSG00000085265	ENSG00000085265		"""Fibrinogen C domain containing"""	3623	protein-coding gene	gene with protein product		601252	"""ficolin (collagen/fibrinogen domain-containing) 1"""			8573080, 8884275	Standard	NM_002003		Approved	FCNM	uc004cfi.3	O00602	OTTHUMG00000020895	ENST00000371806.3:c.825A>G	9.37:g.137801800T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	177	173	0.977401	NM_002003	Q5VYV5|Q92596	Silent	SNP	ENST00000371806.3	37	CCDS6985.1																																																																																			T|0.300;C|0.700	0.700	strong		0.493	FCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054963.1	NM_002003	
MDC1	9656	hgsc.bcm.edu	37	6	30680916	30680916	+	Missense_Mutation	SNP	C	C	T	rs9262152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30680916C>T	ENST00000376406.3	-	5	1450	c.803G>A	c.(802-804)aGg>aAg	p.R268K	MDC1_ENST00000376405.2_Missense_Mutation_p.R268K|MDC1_ENST00000494654.1_5'Flank|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	268	Required for nuclear localization (NLS1).		R -> K (in dbSNP:rs9262152). {ECO:0000269|PubMed:14574404, ECO:0000269|PubMed:17974005}.		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						ATCATTGTCCCTCTCCTTCAC	0.512								Other conserved DNA damage response genes					C|||	534	0.106629	0.0091	0.1412	5008	,	,		20215	0.0556		0.1789	False		,,,				2504	0.1922				p.R268K		Atlas-SNP	.											.	MDC1	218	.	0			c.G803A						PASS	.	C	LYS/ARG	96,2926		4,88,1419	136.0	124.0	128.0		803	-2.1	0.0	6	dbSNP_118	128	857,4561		72,713,1924	yes	missense	MDC1	NM_014641.2	26	76,801,3343	TT,TC,CC		15.8176,3.1767,11.2915	benign	268/2090	30680916	953,7487	1511	2709	4220	SO:0001583	missense	9656	exon5			TTGTCCCTCTCCT	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.803G>A	6.37:g.30680916C>T	ENSP00000365588:p.Arg268Lys	Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	218	99	0.454128	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	234	0.10714285714285714	9	0.018292682926829267	46	0.1270718232044199	41	0.07167832167832168	138	0.1820580474934037	C	1.495	-0.553583	0.03996	0.031767	0.158176	ENSG00000137337	ENST00000376406;ENST00000376405;ENST00000429610;ENST00000422104	T;T	0.02280	4.36;4.37	4.59	-2.14	0.07123	.	0.689133	0.12094	N	0.500150	T	0.00328	0.0010	N	0.20401	0.57	0.80722	P	0.0	B;B;B	0.20550	0.046;0.017;0.001	B;B;B	0.17722	0.019;0.011;0.001	T	0.44112	-0.9349	9	0.06891	T	0.86	1.8205	1.2461	0.01973	0.1313:0.3147:0.183:0.3711	rs9262152;rs59033148;rs9262152	268;140;268	Q14676-2;B4DYH4;Q14676	.;.;MDC1_HUMAN	K	268;268;268;140	ENSP00000365588:R268K;ENSP00000365587:R268K	ENSP00000365587:R268K	R	-	2	0	MDC1	30788895	0.000000	0.05858	0.000000	0.03702	0.112000	0.19704	-0.735000	0.04888	-0.391000	0.07763	0.655000	0.94253	AGG	C|0.897;T|0.103	0.103	strong		0.512	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
IRX4	50805	hgsc.bcm.edu	37	5	1878325	1878325	+	Missense_Mutation	SNP	C	C	T	rs201914951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:1878325C>T	ENST00000505790.1	-	6	1774	c.1318G>A	c.(1318-1320)Gac>Aac	p.D440N	IRX4_ENST00000231357.2_Missense_Mutation_p.D440N|IRX4_ENST00000505938.1_5'Flank|IRX4_ENST00000513692.1_Missense_Mutation_p.D440N	NM_001278634.1	NP_001265563.1	P78413	IRX4_HUMAN	iroquois homeobox 4	440					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)		AAGACCCCGTCCACCCAGTTT	0.697													c|||	8	0.00159744	0.0	0.0029	5008	,	,		12438	0.0		0.006	False		,,,				2504	0.0				p.D440N		Atlas-SNP	.											.	IRX4	45	.	0			c.G1318A						PASS	.		ASN/ASP	2,4350		0,2,2174	8.0	11.0	10.0		1318	3.4	1.0	5		10	45,8507		0,45,4231	yes	missense	IRX4	NM_016358.2	23	0,47,6405	TT,TC,CC		0.5262,0.046,0.3642	probably-damaging	440/520	1878325	47,12857	2176	4276	6452	SO:0001583	missense	50805	exon5			CCCCGTCCACCCA	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.1318G>A	5.37:g.1878325C>T	ENSP00000423161:p.Asp440Asn	Somatic	25	0	0		WXS	Illumina HiSeq	Phase_I	37	18	0.486486	NM_016358	B2RMW5|D3DTC5|H1AFL0|H1AFL1|Q2NL64|Q9UHR2	Missense_Mutation	SNP	ENST00000505790.1	37	CCDS3867.1	.	.	.	.	.	.	.	.	.	.	c	16.51	3.142339	0.57044	4.6E-4	0.005262	ENSG00000113430	ENST00000231357;ENST00000505790;ENST00000513692	T;T;T	0.74842	-0.88;-0.88;-0.88	3.42	3.42	0.39159	.	0.177118	0.47093	D	0.000247	T	0.77705	0.4170	M	0.66939	2.045	0.58432	D	0.999997	D	0.89917	1.0	D	0.80764	0.994	T	0.77590	-0.2531	10	0.14656	T	0.56	-33.678	15.442	0.75190	0.0:1.0:0.0:0.0	.	440	P78413	IRX4_HUMAN	N	440	ENSP00000231357:D440N;ENSP00000423161:D440N;ENSP00000424235:D440N	ENSP00000231357:D440N	D	-	1	0	IRX4	1931325	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	6.829000	0.75314	1.927000	0.55829	0.552000	0.68991	GAC	C|0.993;T|0.007	0.007	weak		0.697	IRX4-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365500.1	NM_016358	
CCDC74A	90557	hgsc.bcm.edu	37	2	132290912	132290912	+	Missense_Mutation	SNP	G	G	A	rs140033985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:132290912G>A	ENST00000295171.6	+	8	1216	c.1078G>A	c.(1078-1080)Gag>Aag	p.E360K	CCDC74A_ENST00000467992.2_3'UTR|CCDC74A_ENST00000409856.3_Missense_Mutation_p.E294K	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	360										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CAACTTTGCCGAGAGGCAGAA	0.632													g|||	28	0.00559105	0.0	0.0058	5008	,	,		18487	0.0		0.0179	False		,,,				2504	0.0061				p.E360K		Atlas-SNP	.											.	CCDC74A	44	.	0			c.G1078A						PASS	.	G	LYS/GLU	11,4395		0,11,2192	44.0	42.0	43.0		1078	3.1	0.8	2	dbSNP_134	43	139,8455		2,135,4160	no	missense	CCDC74A	NM_138770.1	56	2,146,6352	AA,AG,GG		1.6174,0.2497,1.1538	probably-damaging	360/379	132290912	150,12850	2203	4297	6500	SO:0001583	missense	90557	exon8			TTTGCCGAGAGGC		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.1078G>A	2.37:g.132290912G>A	ENSP00000295171:p.Glu360Lys	Somatic	272	1	0.00367647		WXS	Illumina HiSeq	Phase_I	255	118	0.462745	NM_138770	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	.	15.00	2.701859	0.48307	0.002497	0.016174	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.36878	1.23;1.23	3.07	3.07	0.35406	.	0.000000	0.33235	U	0.005125	T	0.36248	0.0960	M	0.69823	2.125	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.925	T	0.46775	-0.9167	10	0.72032	D	0.01	.	6.44	0.21845	0.1445:0.0:0.8555:0.0	.	294;360	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	K	360;294	ENSP00000295171:E360K;ENSP00000387009:E294K	ENSP00000295171:E360K	E	+	1	0	CCDC74A	132007382	1.000000	0.71417	0.764000	0.31436	0.199000	0.23934	4.182000	0.58310	1.436000	0.47453	0.430000	0.28490	GAG	G|0.991;A|0.009	0.009	strong		0.632	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
FMN1	342184	hgsc.bcm.edu	37	15	33261185	33261185	+	Missense_Mutation	SNP	G	G	A	rs117804335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:33261185G>A	ENST00000559047.1	-	5	2716	c.2717C>T	c.(2716-2718)cCg>cTg	p.P906L	SNORD77_ENST00000391113.1_RNA|FMN1_ENST00000334528.9_Missense_Mutation_p.P683L|FMN1_ENST00000561249.1_Missense_Mutation_p.P808L			Q68DA7	FMN1_HUMAN	formin 1	906	FH1.|Pro-rich.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		tggaggaggcggaggtggtag	0.662													G|||	162	0.0323482	0.0008	0.0418	5008	,	,		6346	0.0238		0.0596	False		,,,				2504	0.0491				p.P683L		Atlas-SNP	.											.	FMN1	174	.	0			c.C2048T						PASS	.	G	LEU/PRO	41,3881		1,39,1921	10.0	10.0	10.0		2048	-0.4	0.5	15	dbSNP_132	10	433,7805		8,417,3694	yes	missense	FMN1	NM_001103184.2	98	9,456,5615	AA,AG,GG		5.2561,1.0454,3.898	benign	683/1197	33261185	474,11686	1961	4119	6080	SO:0001583	missense	342184	exon4			GGAGGCGGAGGTG	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.2717C>T	15.37:g.33261185G>A	ENSP00000454047:p.Pro906Leu	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	46	22	0.478261	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		70	0.03205128205128205	1	0.0020325203252032522	16	0.04419889502762431	13	0.022727272727272728	40	0.052770448548812667	G	0.005	-2.175145	0.00312	0.010454	0.052561	ENSG00000248905	ENST00000334528	T	0.56941	0.43	0.225	-0.451	0.12214	.	0.121036	0.30771	U	0.008906	T	0.04407	0.0121	N	0.12182	0.205	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.03364	-1.1044	8	0.32370	T	0.25	.	.	.	.	.	683	Q68DA7-5	.	L	683	ENSP00000333950:P683L	ENSP00000333950:P683L	P	-	2	0	FMN1	31048477	0.026000	0.19158	0.515000	0.27774	0.017000	0.09413	0.162000	0.16501	-0.709000	0.05008	-0.704000	0.03662	CCG	G|0.966;A|0.034	0.034	strong		0.662	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
PFKP	5214	hgsc.bcm.edu	37	10	3155353	3155353	+	Silent	SNP	C	C	T	rs3816699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:3155353C>T	ENST00000381125.4	+	12	1273	c.1197C>T	c.(1195-1197)atC>atT	p.I399I	PFKP_ENST00000381075.2_Silent_p.I391I	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	399	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GACTTGCCATCAAGCTGCCGG	0.597													C|||	616	0.123003	0.152	0.1888	5008	,	,		18819	0.0536		0.162	False		,,,				2504	0.0685				p.I399I		Atlas-SNP	.											.	PFKP	182	.	0			c.C1197T						PASS	.	C	,	675,3731	279.3+/-274.7	62,551,1590	87.0	74.0	78.0		1173,1197	-0.7	0.9	10	dbSNP_107	78	1427,7173	269.8+/-288.6	109,1209,2982	no	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	171,1760,4572	TT,TC,CC		16.593,15.32,16.1618	,	391/777,399/785	3155353	2102,10904	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon12			TGCCATCAAGCTG	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.1197C>T	10.37:g.3155353C>T		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	51	20	0.392157	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																			C|0.848;T|0.152	0.152	strong		0.597	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
MKI67	4288	hgsc.bcm.edu	37	10	129902368	129902368	+	Missense_Mutation	SNP	T	T	A	rs79661992	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:129902368T>A	ENST00000368654.3	-	13	8111	c.7736A>T	c.(7735-7737)gAc>gTc	p.D2579V	MKI67_ENST00000368653.3_Missense_Mutation_p.D2219V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2579	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.D2579V(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				TGTGTTTTTGTCAATAGTCAT	0.478													T|||	204	0.0407348	0.0643	0.0375	5008	,	,		19458	0.0188		0.0586	False		,,,				2504	0.0153				p.D2579V		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	1	Substitution - Missense(1)	pancreas(1)	c.A7736T						PASS	.	T	VAL/ASP,VAL/ASP	208,4198	127.4+/-164.3	6,196,2001	91.0	92.0	92.0		6656,7736	-2.9	0.0	10	dbSNP_131	92	480,8120	140.0+/-196.6	14,452,3834	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	152,152	20,648,5835	AA,AT,TT		5.5814,4.7208,5.2899	probably-damaging,probably-damaging	2219/2897,2579/3257	129902368	688,12318	2203	4300	6503	SO:0001583	missense	4288	exon13			TTTTTGTCAATAG	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.7736A>T	10.37:g.129902368T>A	ENSP00000357643:p.Asp2579Val	Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	81	80	0.987654	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	106	0.048534798534798536	31	0.06300813008130081	18	0.049723756906077346	9	0.015734265734265736	48	0.0633245382585752	T	10.98	1.504090	0.26949	0.047208	0.055814	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.01745	4.79;4.66	2.62	-2.94	0.05581	.	.	.	.	.	T	0.00178	0.0005	L	0.40543	1.245	0.09310	N	1	P;B;B	0.37101	0.582;0.22;0.296	B;B;B	0.31614	0.133;0.042;0.041	T	0.44711	-0.9310	9	0.26408	T	0.33	.	3.244	0.06791	0.2094:0.4109:0.0:0.3796	.	2578;2219;2579	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	2579;2219;2578	ENSP00000357643:D2579V;ENSP00000357642:D2219V	ENSP00000357642:D2219V	D	-	2	0	MKI67	129792358	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.003000	0.01463	-0.713000	0.04981	-0.371000	0.07208	GAC	T|0.949;A|0.051	0.051	strong		0.478	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
FBXW8	26259	hgsc.bcm.edu	37	12	117383320	117383320	+	Missense_Mutation	SNP	G	G	A	rs4076700	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117383320G>A	ENST00000309909.5	+	3	657	c.575G>A	c.(574-576)cGa>cAa	p.R192Q	FBXW8_ENST00000455858.2_Missense_Mutation_p.R126Q			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	192			R -> Q (in dbSNP:rs4076700). {ECO:0000269|PubMed:10531037, ECO:0000269|PubMed:15489334}.		cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		CACATGTTACGAACCAACTGG	0.493													G|||	3214	0.641773	0.2315	0.8429	5008	,	,		22283	0.7302		0.8201	False		,,,				2504	0.7791				p.R192Q		Atlas-SNP	.											.	FBXW8	53	.	0			c.G575A						PASS	.	G	GLN/ARG,GLN/ARG	1381,3025	456.7+/-351.4	213,955,1035	110.0	88.0	95.0		377,575	5.2	1.0	12	dbSNP_108	95	7289,1311	758.0+/-407.5	3102,1085,113	yes	missense,missense	FBXW8	NM_012174.1,NM_153348.2	43,43	3315,2040,1148	AA,AG,GG		15.2442,31.3436,33.3385	possibly-damaging,possibly-damaging	126/533,192/599	117383320	8670,4336	2203	4300	6503	SO:0001583	missense	26259	exon3			TGTTACGAACCAA	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13597	protein-coding gene	gene with protein product		609073	"""F-box only protein 29"", ""F-box and WD-40 domain protein 8"""	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.575G>A	12.37:g.117383320G>A	ENSP00000310686:p.Arg192Gln	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	79	38	0.481013	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	1494	0.6840659340659341	132	0.2682926829268293	301	0.8314917127071824	431	0.7534965034965035	630	0.8311345646437994	G	20.7	4.031213	0.75504	0.313436	0.847558	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.25085	1.82;1.82	6.08	5.19	0.71726	F-box domain, Skp2-like (1);	0.121454	0.52532	D	0.000080	T	0.00012	0.0000	M	0.62723	1.935	0.24394	P	0.99473928	D;D	0.89917	0.971;1.0	P;D	0.72338	0.457;0.977	T	0.02457	-1.1156	9	0.39692	T	0.17	-11.4729	13.0064	0.58707	0.1328:0.0:0.8672:0.0	rs4076700;rs17583026;rs17846206;rs17859222;rs52794996;rs60076551;rs4076700	192;126	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	Q	192;126;126	ENSP00000310686:R192Q;ENSP00000389144:R126Q	ENSP00000310686:R192Q	R	+	2	0	FBXW8	115867703	1.000000	0.71417	0.990000	0.47175	0.984000	0.73092	4.602000	0.61098	1.585000	0.49928	0.655000	0.94253	CGA	G|0.340;A|0.660	0.660	strong		0.493	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174	
EPHA1	2041	hgsc.bcm.edu	37	7	143093538	143093538	+	Silent	SNP	G	G	A	rs10952549	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:143093538G>A	ENST00000275815.3	-	11	1923	c.1837C>T	c.(1837-1839)Ctg>Ttg	p.L613L		NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	613					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)				GTAAAGTCCAGGGCTCCCTGT	0.592													A|||	4306	0.859824	0.7542	0.8876	5008	,	,		17225	0.996		0.7922	False		,,,				2504	0.9121				p.L613L		Atlas-SNP	.											.	EPHA1	193	.	0			c.C1837T						PASS	.	A		3347,1059	385.8+/-325.9	1274,799,130	84.0	67.0	73.0		1837	1.7	1.0	7	dbSNP_120	73	6833,1767	319.6+/-314.2	2705,1423,172	no	coding-synonymous	EPHA1	NM_005232.4		3979,2222,302	AA,AG,GG		20.5465,24.0354,21.7284		613/977	143093538	10180,2826	2203	4300	6503	SO:0001819	synonymous_variant	2041	exon11			AGTCCAGGGCTCC	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.1837C>T	7.37:g.143093538G>A		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	78	42	0.538462	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Silent	SNP	ENST00000275815.3	37	CCDS5884.1																																																																																			G|0.193;A|0.807	0.807	strong		0.592	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
RANBP3	8498	hgsc.bcm.edu	37	19	5914470	5914470	+	IGR	SNP	G	G	A	rs143117009	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5914470G>A	ENST00000340578.6	-	0	3233				CAPS_ENST00000222125.5_Missense_Mutation_p.R18H|CAPS_ENST00000588776.1_Missense_Mutation_p.R104H|CAPS_ENST00000452990.2_Missense_Mutation_p.R18H|AC104532.4_ENST00000591109.1_RNA|AC104532.2_ENST00000588891.1_3'UTR	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3						intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						TGCCTGTCCCGCGGGGCCTCG	0.672													G|||	17	0.00339457	0.0	0.0029	5008	,	,		15870	0.0		0.0129	False		,,,				2504	0.002				p.R18H		Atlas-SNP	.											.	CAPS	14	.	0			c.G53A						PASS	.	G	HIS/ARG,HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	43.0	47.0	45.0		53,53	5.0	1.0	19	dbSNP_134	45	130,8470	64.6+/-126.8	1,128,4171	yes	missense,missense	CAPS	NM_004058.3,NM_080590.2	29,29	1,140,6362	AA,AG,GG		1.5116,0.2724,1.0918	probably-damaging,probably-damaging	18/190,18/163	5914470	142,12864	2203	4300	6503	SO:0001628	intergenic_variant	828	exon2			TGTCCCGCGGGGC	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4			19.37:g.5914470G>A		Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	104	52	0.5	NM_080590	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	25.1	4.602108	0.87055	0.002724	0.015116	ENSG00000105519	ENST00000394521;ENST00000222125;ENST00000452990	T;T	0.57273	0.41;0.79	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000017	T	0.46288	0.1385	M	0.80332	2.49	0.20403	N	0.999902	D;P	0.65815	0.995;0.877	P;B	0.47402	0.546;0.097	T	0.58578	-0.7612	10	0.59425	D	0.04	-10.7081	15.7308	0.77804	0.0:0.0:1.0:0.0	.	151;18	Q8NF12;Q13938	.;CAYP1_HUMAN	H	151;18;18	ENSP00000222125:R18H;ENSP00000403263:R18H	ENSP00000222125:R18H	R	+	2	0	CAPS	5865470	0.867000	0.29959	0.990000	0.47175	0.760000	0.43138	5.362000	0.66098	2.307000	0.77673	0.561000	0.74099	CGC	G|0.988;A|0.012	0.012	strong		0.672	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322	
CCDC127	133957	hgsc.bcm.edu	37	5	205565	205565	+	Silent	SNP	G	G	A	rs10060089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:205565G>A	ENST00000296824.3	-	3	762	c.630C>T	c.(628-630)acC>acT	p.T210T		NM_145265.2	NP_660308.1	Q96BQ5	CC127_HUMAN	coiled-coil domain containing 127	210										breast(1)|endometrium(4)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12			all cancers(22;0.0236)|Lung(60;0.113)			GAAATATGTCGGTGAGACCGG	0.537													G|||	595	0.11881	0.1619	0.2017	5008	,	,		18964	0.0585		0.1064	False		,,,				2504	0.0767				p.T210T		Atlas-SNP	.											.	CCDC127	27	.	0			c.C630T						PASS	.	G		682,3724	287.8+/-279.5	41,600,1562	90.0	85.0	86.0		630	-9.2	0.0	5	dbSNP_119	86	1131,7469	232.5+/-266.1	70,991,3239	no	coding-synonymous	CCDC127	NM_145265.2		111,1591,4801	AA,AG,GG		13.1512,15.4789,13.9397		210/261	205565	1813,11193	2203	4300	6503	SO:0001819	synonymous_variant	133957	exon3			TATGTCGGTGAGA	AK098567	CCDS3852.1	5p15.33	2008-02-05			ENSG00000164366	ENSG00000164366			30520	protein-coding gene	gene with protein product						12477932	Standard	NM_145265		Approved	FLJ25701	uc003jam.1	Q96BQ5	OTTHUMG00000161586	ENST00000296824.3:c.630C>T	5.37:g.205565G>A		Somatic	120	0	0		WXS	Illumina HiSeq	Phase_I	107	49	0.457944	NM_145265		Silent	SNP	ENST00000296824.3	37	CCDS3852.1																																																																																			G|0.869;A|0.131	0.131	strong		0.537	CCDC127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365459.2	NM_145265	
ATP10A	57194	hgsc.bcm.edu	37	15	25926179	25926179	+	Missense_Mutation	SNP	C	C	T	rs2076744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:25926179C>T	ENST00000356865.6	-	18	3646	c.3535G>A	c.(3535-3537)Gcc>Acc	p.A1179T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1179			A -> T (in dbSNP:rs2076744).		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CTCTGGAAGGCGGCGTCGGCC	0.517													c|||	1413	0.282149	0.4735	0.3516	5008	,	,		19333	0.2599		0.1441	False		,,,				2504	0.1391				p.A1179T		Atlas-SNP	.											ATP10A,colon,carcinoma,0,1	ATP10A	270	1	0			c.G3535A						PASS	.	C	THR/ALA	1839,2567	535.6+/-374.3	379,1081,743	90.0	86.0	87.0		3535	0.3	0.2	15	dbSNP_96	87	1378,7222	268.2+/-287.7	103,1172,3025	yes	missense	ATP10A	NM_024490.3	58	482,2253,3768	TT,TC,CC		16.0233,41.7385,24.7347	benign	1179/1500	25926179	3217,9789	2203	4300	6503	SO:0001583	missense	57194	exon18			GGAAGGCGGCGTC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3535G>A	15.37:g.25926179C>T	ENSP00000349325:p.Ala1179Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	109	55	0.504587	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	637	0.2916666666666667	239	0.48577235772357724	118	0.3259668508287293	172	0.3006993006993007	108	0.1424802110817942	c	8.127	0.782181	0.16189	0.417385	0.160233	ENSG00000206190	ENST00000356865	T	0.43688	0.94	4.84	0.298	0.15766	.	0.495561	0.22824	N	0.055187	T	0.00012	0.0000	N	0.11255	0.115	0.53005	P	3.399999999997849E-5	P	0.38729	0.644	B	0.28849	0.095	T	0.47355	-0.9124	9	0.48119	T	0.1	-16.3478	1.5902	0.02653	0.2175:0.4237:0.1137:0.2452	rs2076744;rs2076744	1179	O60312	AT10A_HUMAN	T	1179	ENSP00000349325:A1179T	ENSP00000349325:A1179T	A	-	1	0	ATP10A	23477272	0.152000	0.22762	0.210000	0.23637	0.050000	0.14768	0.681000	0.25320	0.111000	0.17947	-1.349000	0.01238	GCC	C|0.734;T|0.266	0.266	strong		0.517	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
ZC3HC1	51530	hgsc.bcm.edu	37	7	129663533	129663533	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129663533G>A	ENST00000358303.4	-	8	1135	c.1051C>T	c.(1051-1053)Cga>Tga	p.R351*	RP11-306G20.1_ENST00000587038.1_RNA|RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000311873.5_Nonsense_Mutation_p.R330*|ZC3HC1_ENST00000360708.5_Intron|ZC3HC1_ENST00000481503.1_Nonsense_Mutation_p.R308*	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	351					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					CTCCGAGTTCGAGAGACAATG	0.512																																					p.R351X	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											ZC3HC1,NS,carcinoma,0,1	ZC3HC1	45	1	0			c.C1051T						PASS	.						67.0	62.0	64.0					7																	129663533		2203	4300	6503	SO:0001587	stop_gained	51530	exon8			GAGTTCGAGAGAC	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1051C>T	7.37:g.129663533G>A	ENSP00000351052:p.Arg351*	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	74	27	0.364865	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Nonsense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305782	0.81247	.	.	ENSG00000091732	ENST00000358303;ENST00000311873;ENST00000481503	.	.	.	5.49	3.59	0.41128	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.802	12.559	0.56271	0.0:0.0:0.5483:0.4517	.	.	.	.	X	351;330;308	.	ENSP00000309301:R330X	R	-	1	2	ZC3HC1	129450769	0.997000	0.39634	0.999000	0.59377	0.984000	0.73092	2.978000	0.49305	1.297000	0.44761	0.563000	0.77884	CGA	.	.	none		0.512	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
NPAS2	4862	hgsc.bcm.edu	37	2	101580575	101580575	+	Silent	SNP	G	G	A	rs41280595	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:101580575G>A	ENST00000335681.5	+	8	939	c.654G>A	c.(652-654)gtG>gtA	p.V218V	NPAS2_ENST00000542504.1_Silent_p.V283V|NPAS2_ENST00000486017.1_3'UTR	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	218					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						CTTGCCGGGTGCCACTAGGAA	0.527													G|||	434	0.0866613	0.0825	0.0951	5008	,	,		18708	0.001		0.169	False		,,,				2504	0.09				p.V218V		Atlas-SNP	.											.	NPAS2	88	.	0			c.G654A						PASS	.	G		411,3995	202.1+/-225.0	15,381,1807	123.0	113.0	116.0		654	0.9	0.6	2	dbSNP_127	116	1588,7012	297.4+/-303.4	175,1238,2887	no	coding-synonymous	NPAS2	NM_002518.3		190,1619,4694	AA,AG,GG		18.4651,9.3282,15.3698		218/825	101580575	1999,11007	2203	4300	6503	SO:0001819	synonymous_variant	4862	exon8			CCGGGTGCCACTA	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.654G>A	2.37:g.101580575G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	119	62	0.521008	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	37	CCDS2048.1																																																																																			G|0.866;A|0.134	0.134	strong		0.527	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
TMEM260	54916	hgsc.bcm.edu	37	14	57072338	57072338	+	Silent	SNP	C	C	T	rs3737170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:57072338C>T	ENST00000261556.6	+	5	695	c.573C>T	c.(571-573)caC>caT	p.H191H	TMEM260_ENST00000538838.1_Silent_p.H191H|TMEM260_ENST00000536419.1_5'UTR	NM_017799.3	NP_060269.3	Q9NX78	TM260_HUMAN	transmembrane protein 260	191						integral component of membrane (GO:0016021)											GTAACCAGCACACAATAATAC	0.269													C|||	643	0.128395	0.2466	0.0591	5008	,	,		13874	0.1825		0.0398	False		,,,				2504	0.0532				p.H191H		Atlas-SNP	.											.	.	.	.	0			c.C573T						PASS	.	C		1018,3386	377.5+/-322.5	124,770,1308	130.0	144.0	139.0		573	2.7	1.0	14	dbSNP_107	139	417,8177	129.5+/-187.6	8,401,3888	no	coding-synonymous	C14orf101	NM_017799.3		132,1171,5196	TT,TC,CC		4.8522,23.1153,11.0402		191/708	57072338	1435,11563	2202	4297	6499	SO:0001819	synonymous_variant	0	exon5			CCAGCACACAATA	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.573C>T	14.37:g.57072338C>T		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	102	49	0.480392	NM_017799	A8KAN4|B3KPF5|Q86XE1	Silent	SNP	ENST00000261556.6	37	CCDS9727.2																																																																																			C|0.874;T|0.126	0.126	strong		0.269	TMEM260-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276924.1	NM_017799	
SH2D3A	10045	hgsc.bcm.edu	37	19	6755007	6755007	+	Silent	SNP	T	T	C	rs2305806	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6755007T>C	ENST00000245908.6	-	5	1085	c.816A>G	c.(814-816)acA>acG	p.T272T	SH2D3A_ENST00000599563.1_5'UTR|SH2D3A_ENST00000437152.3_Silent_p.T150T	NM_005490.2	NP_005481.2	Q9BRG2	SH23A_HUMAN	SH2 domain containing 3A	272					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						CCTGTGGTCTTGTAAAACATC	0.612													C|||	1690	0.33746	0.4939	0.3213	5008	,	,		16849	0.37		0.2783	False		,,,				2504	0.1646				p.T272T		Atlas-SNP	.											.	SH2D3A	53	.	0			c.A816G						PASS	.	C		1998,2406	590.6+/-387.4	455,1088,659	155.0	180.0	172.0		816	-0.3	0.0	19	dbSNP_100	172	2419,6181	685.1+/-404.0	361,1697,2242	no	coding-synonymous	SH2D3A	NM_005490.2		816,2785,2901	CC,CT,TT		28.1279,45.3678,33.9665		272/577	6755007	4417,8587	2202	4300	6502	SO:0001819	synonymous_variant	10045	exon5			TGGTCTTGTAAAA	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.816A>G	19.37:g.6755007T>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	66	33	0.5	NM_005490	A8K9R6|B4DRS7|Q9Y2X4	Silent	SNP	ENST00000245908.6	37	CCDS12173.1																																																																																			T|0.656;C|0.344	0.344	strong		0.612	SH2D3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458016.1	NM_005490	
PKD1	5310	hgsc.bcm.edu	37	16	2140680	2140680	+	Missense_Mutation	SNP	T	T	C	rs10960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2140680T>C	ENST00000262304.4	-	44	12341	c.12133A>G	c.(12133-12135)Atc>Gtc	p.I4045V	MIR1225_ENST00000408729.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.I4044V	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	4045			I -> V (in dbSNP:rs10960). {ECO:0000269|PubMed:10647901, ECO:0000269|PubMed:11058904, ECO:0000269|PubMed:11773467, ECO:0000269|PubMed:11967008, ECO:0000269|PubMed:12070253, ECO:0000269|PubMed:15772804, ECO:0000269|PubMed:18837007, ECO:0000269|PubMed:9521593}.		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						CCTACCAGGATGGCCAGCTGG	0.652													c|||	1262	0.251997	0.6346	0.2046	5008	,	,		15937	0.0		0.1968	False		,,,				2504	0.0849				p.I4045V		Atlas-SNP	.											.	PKD1	184	.	0			c.A12133G						PASS	.		VAL/ILE,VAL/ILE	2428,1940	521.7+/-370.6	675,1078,431	31.0	35.0	33.0		12130,12133	-1.5	0.1	16	dbSNP_52	33	1605,6993	722.4+/-406.4	145,1315,2839	yes	missense,missense	PKD1	NM_000296.3,NM_001009944.2	29,29	820,2393,3270	CC,CT,TT		18.6671,44.4139,31.1044	benign,benign	4044/4303,4045/4304	2140680	4033,8933	2184	4299	6483	SO:0001583	missense	5310	exon44			CCAGGATGGCCAG	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.12133A>G	16.37:g.2140680T>C	ENSP00000262304:p.Ile4045Val	Somatic	43	0	0		WXS	Illumina HiSeq	Phase_I	51	24	0.470588	NM_001009944	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	522	0.23901098901098902	295	0.5995934959349594	81	0.22375690607734808	0	0.0	146	0.19261213720316622	c	0.012	-1.659587	0.00772	0.555861	0.186671	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.69040	-0.37;-0.37	3.49	-1.55	0.08558	Polycystin cation channel, PKD1/PKD2 (1);	0.414816	0.23431	N	0.048256	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	0.003;0.004	T	0.43940	-0.9360	9	0.17369	T	0.5	.	0.9634	0.01400	0.2747:0.2029:0.1051:0.4173	rs10960;rs3209985;rs11544588;rs17134793	4044;4045	P98161-3;P98161	.;PKD1_HUMAN	V	4045;4044;3379	ENSP00000262304:I4045V;ENSP00000399501:I4044V	ENSP00000262304:I4045V	I	-	1	0	PKD1	2080681	0.001000	0.12720	0.083000	0.20561	0.108000	0.19459	-0.085000	0.11250	-0.387000	0.07809	-0.674000	0.03794	ATC	T|0.709;C|0.291	0.291	strong		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
PCDHB7	56129	hgsc.bcm.edu	37	5	140554481	140554481	+	Missense_Mutation	SNP	G	G	T	rs1811237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140554481G>T	ENST00000231137.3	+	1	2239	c.2065G>T	c.(2065-2067)Gtg>Ttg	p.V689L	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	689					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGTCTACCTGGTGGTGGCGTT	0.711													G|||	1672	0.333866	0.2504	0.3516	5008	,	,		22188	0.5278		0.2465	False		,,,				2504	0.3241				p.V689L		Atlas-SNP	.											PCDHB7,NS,carcinoma,0,1	PCDHB7	231	1	0			c.G2065T						PASS	.	G	LEU/VAL	958,3440		139,680,1380	63.0	100.0	87.0		2065	2.9	0.5	5	dbSNP_92	87	1772,6820		228,1316,2752	no	missense	PCDHB7	NM_018940.2	32	367,1996,4132	TT,TG,GG		20.6238,21.7826,21.0162	probably-damaging	689/794	140554481	2730,10260	2199	4296	6495	SO:0001583	missense	56129	exon1			TACCTGGTGGTGG	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.2065G>T	5.37:g.140554481G>T	ENSP00000231137:p.Val689Leu	Somatic	220	1	0.00454545		WXS	Illumina HiSeq	Phase_I	112	111	0.991071	NM_018940	A1L3Y8	Missense_Mutation	SNP	ENST00000231137.3	37	CCDS4249.1	704	0.32234432234432236	117	0.23780487804878048	106	0.292817679558011	301	0.5262237762237763	180	0.23746701846965698	G	21.8	4.203707	0.79127	0.217826	0.206238	ENSG00000113212	ENST00000231137	T	0.46819	0.86	3.77	2.86	0.33363	.	.	.	.	.	T	0.00012	0.0000	H	0.97682	4.055	0.32646	P	0.520018	D	0.76494	0.999	D	0.85130	0.997	T	0.45702	-0.9243	8	0.87932	D	0	.	7.7855	0.29089	0.2703:0.0:0.7297:0.0	rs62378900	689	Q9Y5E2	PCDB7_HUMAN	L	689	ENSP00000231137:V689L	ENSP00000231137:V689L	V	+	1	0	PCDHB7	140534665	1.000000	0.71417	0.546000	0.28166	0.957000	0.61999	1.707000	0.37888	1.808000	0.52836	0.449000	0.29647	GTG	G|0.758;T|0.242	0.242	strong		0.711	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940	
NOX4	50507	hgsc.bcm.edu	37	11	89088168	89088168	+	Silent	SNP	G	G	A	rs75735530	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:89088168G>A	ENST00000263317.4	-	13	1417	c.1179C>T	c.(1177-1179)tcC>tcT	p.S393S	NOX4_ENST00000424319.1_Silent_p.S369S|NOX4_ENST00000534731.1_Silent_p.S393S|NOX4_ENST00000531342.1_Silent_p.S86S|NOX4_ENST00000532825.1_Silent_p.S369S|NOX4_ENST00000343727.5_Silent_p.S369S|NOX4_ENST00000413594.2_Silent_p.S414S|NOX4_ENST00000525196.1_Intron|NOX4_ENST00000535633.1_Silent_p.S369S|NOX4_ENST00000527626.1_Silent_p.S227S|NOX4_ENST00000542487.1_Silent_p.S369S|NOX4_ENST00000528341.1_Silent_p.S368S|NOX4_ENST00000375979.3_Silent_p.S86S|NOX4_ENST00000527956.1_Silent_p.S369S			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	393	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.|Mediates interaction with TLR4.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				GCAGAATTTCGGAGTCTTGAC	0.373													G|||	433	0.0864617	0.0023	0.1686	5008	,	,		15054	0.0883		0.0815	False		,,,				2504	0.1452				p.S393S		Atlas-SNP	.											NOX4,right_upper_lobe,carcinoma,-1,1	NOX4	101	1	0			c.C1179T						PASS	.	G	,,	70,4332	61.1+/-98.1	1,68,2132	52.0	52.0	52.0		1179,1107,1179	-4.4	1.0	11	dbSNP_131	52	637,7953	159.7+/-212.9	25,587,3683	no	coding-synonymous,coding-synonymous,coding-synonymous	NOX4	NM_001143836.1,NM_001143837.1,NM_016931.3	,,	26,655,5815	AA,AG,GG		7.4156,1.5902,5.4418	,,	393/539,369/555,393/579	89088168	707,12285	2201	4295	6496	SO:0001819	synonymous_variant	50507	exon13			AATTTCGGAGTCT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.1179C>T	11.37:g.89088168G>A		Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	166	59	0.355422	NM_001143836	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Silent	SNP	ENST00000263317.4	37	CCDS8285.1																																																																																			G|0.942;A|0.058	0.058	strong		0.373	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
LCLAT1	253558	hgsc.bcm.edu	37	2	30863108	30863108	+	Missense_Mutation	SNP	A	A	G	rs12471868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:30863108A>G	ENST00000309052.4	+	7	1077	c.868A>G	c.(868-870)Ata>Gta	p.I290V	LCLAT1_ENST00000540623.1_Missense_Mutation_p.I252V|LCLAT1_ENST00000379509.3_Missense_Mutation_p.I252V|LCLAT1_ENST00000491680.2_3'UTR	NM_182551.3	NP_872357.2	Q6UWP7	LCLT1_HUMAN	lysocardiolipin acyltransferase 1	290			I -> V (in dbSNP:rs12471868).		cardiolipin acyl-chain remodeling (GO:0035965)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|multicellular organismal development (GO:0007275)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)	19						CCGGTATCCAATAGACACCCT	0.512													A|||	844	0.16853	0.0923	0.2205	5008	,	,		19969	0.2232		0.1183	False		,,,				2504	0.2301				p.I290V		Atlas-SNP	.											.	LCLAT1	51	.	0			c.A868G						PASS	.	A	VAL/ILE,VAL/ILE	375,4031	190.9+/-216.7	20,335,1848	93.0	88.0	89.0		754,868	-7.0	0.0	2	dbSNP_120	89	1150,7450	236.8+/-268.9	94,962,3244	yes	missense,missense	LCLAT1	NM_001002257.1,NM_182551.3	29,29	114,1297,5092	GG,GA,AA		13.3721,8.5111,11.7254	benign,benign	252/377,290/415	30863108	1525,11481	2203	4300	6503	SO:0001583	missense	253558	exon7			TATCCAATAGACA	AK095284	CCDS1772.1, CCDS42670.1	2p23.1	2008-12-15	2008-12-15	2008-12-15	ENSG00000172954	ENSG00000172954			26756	protein-coding gene	gene with protein product		614241	"""lysocardiolipin acyltransferase"""	LYCAT		18931347, 15152008, 16620771, 17675553	Standard	NM_001002257		Approved	FLJ37965, ALCAT1, AGPAT8	uc002rnl.3	Q6UWP7	OTTHUMG00000099349	ENST00000309052.4:c.868A>G	2.37:g.30863108A>G	ENSP00000310551:p.Ile290Val	Somatic	151	1	0.00662252		WXS	Illumina HiSeq	Phase_I	146	145	0.993151	NM_182551	A6H8Z7|Q8N1Q7	Missense_Mutation	SNP	ENST00000309052.4	37	CCDS1772.1	331	0.15155677655677655	41	0.08333333333333333	74	0.20441988950276244	119	0.20804195804195805	97	0.1279683377308707	A	0.008	-1.886745	0.00527	0.085111	0.133721	ENSG00000172954	ENST00000379509;ENST00000444270;ENST00000309052;ENST00000540623	T;T;T	0.53640	0.61;0.61;0.61	5.77	-6.96	0.01622	.	0.419198	0.27126	N	0.020818	T	0.00012	0.0000	N	0.10664	0.02	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.21861	-1.0233	9	0.13108	T	0.6	-1.6084	12.2763	0.54737	0.2097:0.0:0.7143:0.076	rs12471868;rs52802369;rs61598697;rs12471868	290	Q6UWP7	LCLT1_HUMAN	V	252;252;290;252	ENSP00000368823:I252V;ENSP00000310551:I290V;ENSP00000442857:I252V	ENSP00000310551:I290V	I	+	1	0	LCLAT1	30716612	0.023000	0.18921	0.000000	0.03702	0.048000	0.14542	0.249000	0.18216	-1.202000	0.02655	-0.379000	0.06801	ATA	A|0.870;G|0.130	0.130	strong		0.512	LCLAT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216780.1	NM_182551	
ATF6B	1388	hgsc.bcm.edu	37	6	32088854	32088854	+	Silent	SNP	G	G	C	rs2228628	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:32088854G>C	ENST00000375203.3	-	7	644	c.612C>G	c.(610-612)tcC>tcG	p.S204S	ATF6B_ENST00000375201.4_Silent_p.S201S	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	204					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						ATCCTGAAGGGGACAGGGACT	0.547													G|||	877	0.17512	0.0197	0.2968	5008	,	,		18996	0.1776		0.2982	False		,,,				2504	0.1697				p.S204S		Atlas-SNP	.											.	ATF6B	40	.	0			c.C612G						PASS	.	G	,	300,4106	162.5+/-194.5	17,266,1920	47.0	46.0	46.0		603,612	-0.2	0.3	6	dbSNP_98	46	2458,6142	403.9+/-348.0	361,1736,2203	yes	coding-synonymous,coding-synonymous	ATF6B	NM_001136153.1,NM_004381.4	,	378,2002,4123	CC,CG,GG		28.5814,6.8089,21.2056	,	201/701,204/704	32088854	2758,10248	2203	4300	6503	SO:0001819	synonymous_variant	1388	exon7			TGAAGGGGACAGG		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.612C>G	6.37:g.32088854G>C		Somatic	129	0	0		WXS	Illumina HiSeq	Phase_I	134	72	0.537313	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Silent	SNP	ENST00000375203.3	37	CCDS4737.1																																																																																			G|0.784;C|0.216	0.216	strong		0.547	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2		
